Quick and dirty parser

input

chr10_0    CTCTGCCCTGGGGTTTGAGATCCGCGGGTGCTTACTGACCCTTTTGGGTTGGAGTTAGCTCAAGCGGTTACCTCCTCAGGCTGGACTTTCTATCTGTCCAAAGCCAACtg
           ---------------------CCGCGGGTGCTTACTGACCCTTTT-----------------------------------------------------------------    1    teste

chr10_0    CTCTGCCCTGGGGTTTGAGATCCGCGGGTGCTTACTGACCCTTTTGGGTTGGAGTTAGCTCAAGCGGTTACCTCCTCAGGCTGGACTTTCTATCTGTCCAAAGCCAACtg
           ----------------------CGCGGGTGCTTACTGACC----------------------------------------------------------------------    129    teste

chr10_0    CTCTGCCCTGGGGTTTGAGATCCGCGGGTGCTTACTGACCCTTTTGGGTTGGAGTTAGCTCAAGCGGTTACCTCCTCAGGCTGGACTTTCTATCTGTCCAAAGCCAACtg
           ----------------------CGCGGGTGCTTACTGACCC---------------------------------------------------------------------    56    teste

chr10_10   CCTTGCCCGTCACGCAATGGAAGTTCGTGGGGAACCTGGCGCTAAACCATTCGTAGACTATCTGCTTCTGGGTCGGGGTT
           ---------------------------------ACCTGGCGCTAAACCATTCGTAGAC----------------------    1    teste

chr10_10   CCTTGCCCGTCACGCAATGGAAGTTCGTGGGGAACCTGGCGCTAAACCATTCGTAGACTATCTGCTTCTGGGTCGGGGTT
           ---------------------------------------CGCTAAACCATTCGTAGA-----------------------    1    teste

output

chr10_0    CTCTGCCCTGGGGTTTGAGATCCGCGGGTGCTTACTGACCCTTTTGGGTTGGAGTTAGCTCAAGCGGTTACCTCCTCAGGCTGGACTTTCTATCTGTCCAAAGCCAACtg
           ---------------------CCGCGGGTGCTTACTGACCCTTTT-----------------------------------------------------------------    1    teste
           ----------------------CGCGGGTGCTTACTGACC----------------------------------------------------------------------    129    teste
           ----------------------CGCGGGTGCTTACTGACCC---------------------------------------------------------------------    56    teste

chr10_10   CCTTGCCCGTCACGCAATGGAAGTTCGTGGGGAACCTGGCGCTAAACCATTCGTAGACTATCTGCTTCTGGGTCGGGGTT
           ---------------------------------ACCTGGCGCTAAACCATTCGTAGAC----------------------    1    teste
           ---------------------------------------CGCTAAACCATTCGTAGA-----------------------    1    teste

parse.py

from __future__ import print_function

from collections import OrderedDict


parsed = OrderedDict()
with open('input', 'r') as dataset:
    header = True
    while header:
        header = dataset.readline().rstrip()
        match = dataset.readline().rstrip()
        _ = dataset.readline()

        if header:
            key, seq = header.split()
            if key not in parsed:
                parsed[key] = {'seq': header, 'alignments': []}
            parsed[key]['alignments'].append(match)

for k in parsed:
    print(parsed[k]['seq'])
    print(*(parsed[k]['alignments']), sep='\n')
    print()