Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019399.1 Corchorus olitorius cultivar O-4 contig19432, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 18993
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:1587 original size:323 final size:318
Alignment explanation
Indices: 464--1669 Score: 1053
Period size: 323 Copynumber: 3.7 Consensus size: 318
454 GACGAATTTT
* * * * *
464 TTTTTTCTCAATTTTTTGCGACAATAGTCATAAAAAATATATAATTTAACGGCAAAAAAATTGAA
1 TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTG-A
* * ** *
529 GGATTTTTCACACTTCTAATATTGTTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAAACGAA
65 TGATATTTCACACTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
** * * * *
593 ACAAGATTCAGATGTTCGTAAAAATAAATCGTTAAATCAAATTTGGCTG-GATTTGGTTCGATGA
130 ACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGACATTTGGTTCGATGA
*
657 ATATAGATATTTCAAGGAGTCTTTACGCC-AAAATCATTCAAAACTGAGCCGGGGTCTC-GGAAC
195 ATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGG-CTCGGGAAC
* * * * * *
720 GTG-GTTTTAGCAAAAAACCGTGATAGTTAGTATA-ATATTTCAGCGAAAGTTTTGCAACAACTG
259 GCGTG-TTTAGCAAAAAACCATGATGGTTAGTACACA-ATTT---CG---G--CT--AAAAACTG
783 ACCCGAAAAA
312 A--CG-AAAA
* * * * *
793 TTTTTCCTCAATTTTTTTTTGCCACAATAGTCAGAAAAAATACACAATTCAACGCAAAAAAAAAT
1 TTTTTTCTCAA---TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC-CAAAAAAAT
* * * * ** * * *
858 TGA-AATATTTTCTCGCTTCAAATATCATTTTTTAATTTTTTTTTCGAATCT-ATATCTTATTAA
62 TGATGATA-TTTCACACTTCTAATATCATTTTTCCA-TTTTTTTCCGAAT-TAATTTCTAATTAA
* * *
921 ATCGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAAGAGCCTGAG
124 ATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATGTGGCT--GA--C--A-
* * * *
986 ATTGGTTAGATGAATATAAATATTTC---GAGT-TTTTCTGCCAAAAATCATGCAAAACTGAGCC
182 TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAACTGAGCC
* * * * *
1047 GGGGCCCGCGAAACGCGTTTTTAGTCAAAAAACCATGATGGTCAGTACACGATTTTCGGCTAAAA
246 GGGGCTCG-GGAACGCGTGTTTAG-CAAAAAACCATGATGGTTAGTACAC-AATTTCGGCTAAAA
1112 ACTGAC-----
308 ACTGACGAAAA
* * * *
1118 ------C-CGAATTTTTTGCCACAATACT-AAAAAAAAAATATAATTCAACACCAAAAAGATTGA
1 TTTTTTCTC-AATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGA
* * * * * * *
1175 TGGTCTTTTCACACTTTTAATATAATTTTTCCAATTTGTTCCGAAATAATTTCTAATTAAATCGA
65 TGAT-ATTTCACACTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * *
1240 AACAAGATTCAGATACTCGTAAAAACAGATCCTTATATCCAATGTGGCTGACATTTGGTTTGATG
129 AACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGACATTTGGTTCGATG
* * * * *
1305 AATATAGATATTTAAAAGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAAC
194 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCTCGGGAAC
* *
1370 GCGTGTTTAGCCAAAAATCATGATGGTTAGTACACAATTTCGGCCT-AAAACTGATCGGAAAA
259 GCGTGTTTAGCAAAAAACCATGATGGTTAGTACACAATTTCGG-CTAAAAACTGA-C-GAAAA
*
1432 GTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA
1 -TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGA
* * * * *
1497 TGGGTATTTCACAATTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTTTAATTAAATTG
65 T-GATATTTCACACTTCTAATATCATTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCG
* * * ** * *
1562 AAACAAGATTCAGATACTCGTAAAAACAAAT-ATATAAATCGAACGTGGCTGGGATTTTGTTCAA
128 AAACAAGATTCAGATACTCGTAAAAACAAATCCT-TAAATCAAATGTGGCTGACATTTGGTTCGA
* *
1626 TGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCA
192 TGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCA
1670 CAAAAAAAAT
Statistics
Matches: 710, Mismatches: 115, Indels: 110
0.76 0.12 0.12
Matches are distributed among these distances:
307 37 0.05
308 26 0.04
309 13 0.02
310 35 0.05
311 4 0.01
312 2 0.00
313 1 0.00
314 78 0.11
315 39 0.05
316 16 0.02
318 1 0.00
319 3 0.00
321 20 0.03
322 58 0.08
323 120 0.17
329 10 0.01
331 3 0.00
332 56 0.08
333 18 0.03
334 68 0.10
335 2 0.00
336 1 0.00
337 1 0.00
338 4 0.01
339 9 0.01
340 26 0.04
341 12 0.02
342 43 0.06
343 3 0.00
344 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (318 bp):
TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAT
GATATTTCACACTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
CAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGACATTTGGTTCGATGAA
TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCTCGGGAACGC
GTGTTTAGCAAAAAACCATGATGGTTAGTACACAATTTCGGCTAAAAACTGACGAAAA
Found at i:3025 original size:548 final size:545
Alignment explanation
Indices: 2025--3066 Score: 1359
Period size: 548 Copynumber: 1.9 Consensus size: 545
2015 GATTGATGGT
*
2025 TTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
1 TTTTTCACGCTTTAAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * *
2090 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATA
66 AGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGACAATTGGTTAGATGAATA
* * * *
2155 TAGATATTTCAAGGAGTCTTTGCGACAAAAATCATGCAAAATTGAGTCGGGGCTTGGGAACGCGT
131 TAGATAGTTCAAGGAGTCTTTGCGACAAAAATCATGCAAAACTGAGTC---GCTAGGGAACACGT
* * * * * * *
2220 TTTTAGCCAAAAACCGTGATTGTTAGTACATGATTTCGGCTAAAAACTTATCGGAAAAGTTTTTT
193 TTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCG-AAAGTTTTTT
* *
2285 CTCAATTTTTTGGCCTCAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATAGGCT
257 CTCAATTTTTTGGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATAGGCT
* * * *
2350 TTTCACGTCTTCTAATATCTATTTTCCTTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAG
322 TTCCACGTCTTCTAATATCTATTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
** **
2415 ATTCAGATGCTCGTAAAAACAAATACTTAAATTGAACGTGGCTGGGATTTTGTTCGATGAATATA
387 ATTCAGATGCTCGTAAAAACAAATACTTAAATCCAACGTGGCTGACATTTTGTTCGATGAATATA
* * *
2480 GATATTTCTAGGAGTATTTATGTCAAAAATCAGGCAAAAACAAAAAAAAAAATCGGCAAAAAATA
452 GATATTTCAAGGAGTATTTACGCCAAAAATCAGGCAAAAACAAAAAAAAAAATCGGCAAAAAATA
2545 CACAATTCAACGCAAAAAAAAATGAAATA
517 CACAATTCAACGCAAAAAAAAATGAAATA
* * * *
2574 TTTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCTGAATCT-ATTTCTAATTAAATCGAAAC
1 TTTTTCACGCTTTAAATATCATTTTTCCAATTTTTTCCGAAT-TAATTTCTAATTAAATCGAAAC
* * * *
2638 AATATTCAAATGCTCGTAACAACAAATCCTTAAATCTAATGTGGTTGAGAGCCTGAGATTGGTTA
65 AAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT--GA--C--A-ATTGGTTA
*
2703 GATGAATATAGATAGTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAG-C-C-AGGG-
123 GATGAATATAGATAGTTCAAGGAGTCTTTGC-GACAAAAATCATGCAAAACTGAGTCGCTAGGGA
* *
2763 CCACGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGTTTTTCAGCTAAAAACTGACCCG-AA
187 ACACGTTTTTAG-CCAAAAACCATGATGGTTAGTACACG-ATTTCAGCTAAAAACTGACCCGAAA
* * * *
2827 TTTTTTTTTGAATTTTTT-GCCACAGTACTCAGAAAAAATATATAATTCAACACCAAAAAGATTG
250 GTTTTTTCTCAATTTTTTGGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTG
*
2891 AT-GGTCTTTCCACG-CTTTTAATATC-ATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAA
315 ATAGG-CTTTCCACGTCTTCTAATATCTA-TTTTCC-ATTTTTTCCGAATTAATTTCTAATTAAA
* * * * * *
2953 TCGAAGCAATATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTTGTTT
377 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAACGTGGCTGACATTTTGTTC
* * *
3018 GATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAA
442 GATGAATATAGATATTTCAAGGAGTATTTACGCCAAAAATCAGGCAAAA
3067 TTGAGTCGGG
Statistics
Matches: 425, Mismatches: 54, Indels: 29
0.84 0.11 0.06
Matches are distributed among these distances:
546 1 0.00
547 18 0.04
548 176 0.41
549 124 0.29
550 27 0.06
551 20 0.05
553 1 0.00
555 3 0.01
556 55 0.13
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (545 bp):
TTTTTCACGCTTTAAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
AGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGACAATTGGTTAGATGAATA
TAGATAGTTCAAGGAGTCTTTGCGACAAAAATCATGCAAAACTGAGTCGCTAGGGAACACGTTTT
TAGCCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAGTTTTTTCTCA
ATTTTTTGGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATAGGCTTTCC
ACGTCTTCTAATATCTATTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTC
AGATGCTCGTAAAAACAAATACTTAAATCCAACGTGGCTGACATTTTGTTCGATGAATATAGATA
TTTCAAGGAGTATTTACGCCAAAAATCAGGCAAAAACAAAAAAAAAAATCGGCAAAAAATACACA
ATTCAACGCAAAAAAAAATGAAATA
Found at i:5129 original size:323 final size:322
Alignment explanation
Indices: 4326--5138 Score: 888
Period size: 323 Copynumber: 2.5 Consensus size: 322
4316 CCTCGTTTTA
*
4326 AATATCA-TTTTCC-TATTTTTTCCGAATCT-ATTTCTAATTAAATCT-AAACAAAATTCAGATG
1 AATATCATTTTTCCAT-TTTTTTCCGAAT-TAATTTCTAATTAAAT-TGAAACAAGATTCAGATG
* *
4387 CTCGTAAAAACAAATCCTTAAATCTAATGTAGCTGAGAGCCTGAGATTGGTTAGATGAATATAGA
63 CTCGTAAAAACAAATCCTTAAATCCAATGTAGCT--G-G---GA-TTTGGTTAGATGAATATAGA
* * * * *
4452 TATTTCAAAGAGTCTTTCTGCCAAAAATCATGAAAAACTGAGTCGGGGCCCGAAACACGTTTTTA
121 TATTTCAAAGAGTCTTTC-GTCAAAAATCATGCAAAACTGAGTCAGGGCCAGAAACACATTTTTA
* * * * *
4517 ACCCAAAAGCCATGATGGTTAGTATACGATATTTAGCTAAAAATTGACCCGAATTTTTTTTTTCT
185 ACCCAAAAGCCAGGATGGTTAGTACACGATATTAAGCTAAAAACTGACCCGAATGTTTTTTTTCT
* * * * *
4582 GAATTTTTTGACACAATACTTAGAAAAAATATATAATTGATCACAAAAAAGATTGATGGTCTTTT
250 CAATTTTTTGACACAATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGAAGGTCTTTT
*
4647 CATGCTTT
315 CACGCTTT
* * *
4655 AATATCATTTTTTTTTCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGAT
1 AATATCA----TTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAGAT
* * * ** * *
4720 GCTTGCAAAAACAAATCCTTATATCCAATGTAGCTGATATTTGGTTTGATGAATATAAATATTTC
62 GCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTGGGATTTGGTTAGATGAATATAGATATTTC
* * * * * *
4785 AAAGAGTCTTT-GTACCAAAAATCATGCGAAATTGAGTCAGGGCTCAGGAGCGCATTTTT-AGCC
127 AAAGAGTCTTTCGT--CAAAAATCATGCAAAACTGAGTCAGGGC-CAGAAACACATTTTTAACCC
*** * *
4848 AAAA-TTGGGATGGTTAGTACACGAT-TTAAGCTAAAAACTGATCGGAATAGTTTTTTTTCTCAA
189 AAAAGCCAGGATGGTTAGTACACGATATTAAGCTAAAAACTGACCCGAAT-GTTTTTTTTCTCAA
* * *
4911 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGACAGG-CTTTTCA
253 TTTTTTGACACAATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGA-AGGTCTTTTCA
4975 CGCTTCT
317 CGCTT-T
* *
4982 AATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTC
1 AATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTC
* * * * * * *
5047 GTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGG
66 GTAAAAACAAATCCTTAAATCCAATGTAGCTGGGATTTGGTTAGATGAATATAGATATTTCAAAG
*
5112 AGTATTTACGTCAAAAATCATGCAAAA
131 AGTCTTT-CGTCAAAAATCATGCAAAA
5139 ACAAAAAAAA
Statistics
Matches: 405, Mismatches: 63, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
323 126 0.31
325 22 0.05
326 86 0.21
327 75 0.19
328 11 0.03
329 7 0.02
332 1 0.00
333 1 0.00
334 75 0.19
335 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (322 bp):
AATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTC
GTAAAAACAAATCCTTAAATCCAATGTAGCTGGGATTTGGTTAGATGAATATAGATATTTCAAAG
AGTCTTTCGTCAAAAATCATGCAAAACTGAGTCAGGGCCAGAAACACATTTTTAACCCAAAAGCC
AGGATGGTTAGTACACGATATTAAGCTAAAAACTGACCCGAATGTTTTTTTTCTCAATTTTTTGA
CACAATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGAAGGTCTTTTCACGCTTT
Found at i:5969 original size:561 final size:559
Alignment explanation
Indices: 4856--6248 Score: 2215
Period size: 561 Copynumber: 2.5 Consensus size: 559
4846 CCAAAATTGG
** * * *
4856 GATGGTTAGTACACGA-TTTAAGCTAAAAACTGATCGGAATAGTTTTTTTTCTCAATTTTTTGCC
1 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCG-AT--TTTTTTTTCTGAA-TTTTTGCC
*
4920 ACAATACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGACAGGCTTTTCACGCTTCTAAT
62 ACAGTACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGACAGGCTTTTCACGCTTCTAAT
4985 ATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCGTA
127 ATCATTTTTCCA-TTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCGTA
*
5050 AAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGT
191 AAAACAAATACTTAAATCAAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGT
*
5115 ATTTACGTCAAAAATCATGCAAAAACAAAAAAAAATATTTTCGGCCAAAAATACACAATTCAACG
256 ATTTACGTCAAAAATCATGCAAAAACAAAAAAAAAAATTTTCGGCCAAAAATACACAATTCAACG
5180 CAAAAAAAAAATTGAAATATTTTCCCGCTTTAAATATCATTTTTCAATTTTTTTTCCGAATCTAT
321 C-AAAAAAAAATTGAAATATTTTCCCGCTTTAAATATCATTTTTCAATTTTTTTTCCGAATCTAT
*
5245 TTCTAATTAAATCGAAACAATATTCAAATGCTCGTAACAACAAATTCTTAAATCTAATGTGACTG
385 TTATAATTAAATCGAAACAATATTCAAATGCTCGTAACAACAAATTCTTAAATCTAATGTGACTG
*
5310 AGGTCCTAAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAG
450 AGGTCCTAAGATTGGTTAGATGAATACAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAG
5375 AACTGAGCCGGGGCCCCCAAAACGCGTTTTTAGGCCAAAAACCAT
515 AACTGAGCCGGGGCCCCCAAAACGCGTTTTTAGGCCAAAAACCAT
5420 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGATTTTTTTTTTTCTGAATTTTTGCCAC
1 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGA--TTTTTTTTTCTGAATTTTTGCCAC
5485 AGTACTCAGAAAAAATATATAATAT-AACGCGAAAAAGATTGACAGGCTTTTCACGCTTCTAATA
64 AGTACTCAGAAAAAATATATAAT-TCAACGCGAAAAAGATTGACAGGCTTTTCACGCTTCTAATA
*
5549 TCATTTTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTTAAATGCTCGTAAA
128 TCATTTTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCGTAAA
5614 AACAAATACTTAAATCAAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGTAT
193 AACAAATACTTAAATCAAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGTAT
*
5679 TTACGTCAAAAATCATGCAAACACAAAAAAAAAAATTTTCGGCCAAAAATACACAATTCAACGC-
258 TTACGTCAAAAATCATGCAAAAACAAAAAAAAAAATTTTCGGCCAAAAATACACAATTCAACGCA
*
5743 AAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTTTCAATTTTTTTTTCCGAATCTATTT
323 AAAAAAAATTGAAATATTTTCCCGCTTTAAATATCATTTTTCAA-TTTTTTTTCCGAATCTATTT
*
5808 ATAATTAAATCGAAACAATATTCAAATGCTCGTAACAACAAATTCTTAAATCTAATGTGGCTGAG
387 ATAATTAAATCGAAACAATATTCAAATGCTCGTAACAACAAATTCTTAAATCTAATGTGACTGAG
5873 GTCCTAAGATTGGTTAGATGAATACAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAGAA
452 GTCCTAAGATTGGTTAGATGAATACAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAGAA
*
5938 CTGAGCCGGGGCCCCTAAAACGCGTTTTTAGGCCAAAAACCAT
517 CTGAGCCGGGGCCCCCAAAACGCGTTTTTAGGCCAAAAACCAT
*
5981 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGA---------ATG--TTTTTGCCACAG
1 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGATTTTTTTTTCTGAATTTTTGCCACAG
* * * * *
6035 TACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGA-TGATCTTGTT-ACGCTTTTAATAT
66 TACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGACAG-GCTT-TTCACGCTTCTAATAT
* * * * *
6098 CATTTTTCCAATTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAA
129 CATTTTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCGTAAAA
* * * * * ** * * * *
6163 ACAAATCCTTATATCCAATGTGGTTGACATTTGGTTTGATGAATATAGAAATTTCAAGGAGTCTT
194 ACAAATACTTAAATCAAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGTATT
* *
6228 TGCGCCAAAAATCATGCAAAA
259 TACGTCAAAAATCATGCAAAA
6249 TTGAATCGGG
Statistics
Matches: 780, Mismatches: 41, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
547 2 0.00
548 194 0.25
549 2 0.00
550 2 0.00
560 43 0.06
561 228 0.29
562 179 0.23
563 82 0.11
564 30 0.04
565 17 0.02
566 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (559 bp):
GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGATTTTTTTTTCTGAATTTTTGCCACAG
TACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCA
TTTTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCGTAAAAAC
AAATACTTAAATCAAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTA
CGTCAAAAATCATGCAAAAACAAAAAAAAAAATTTTCGGCCAAAAATACACAATTCAACGCAAAA
AAAAATTGAAATATTTTCCCGCTTTAAATATCATTTTTCAATTTTTTTTCCGAATCTATTTATAA
TTAAATCGAAACAATATTCAAATGCTCGTAACAACAAATTCTTAAATCTAATGTGACTGAGGTCC
TAAGATTGGTTAGATGAATACAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAGAACTGA
GCCGGGGCCCCCAAAACGCGTTTTTAGGCCAAAAACCAT
Found at i:9187 original size:192 final size:192
Alignment explanation
Indices: 8860--9238 Score: 584
Period size: 192 Copynumber: 2.0 Consensus size: 192
8850 ATATAGATGG
* * *
8860 TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGGGCCGGGGCCCCCGAAACGCGTTTTTAG
1 TTCAAGGAGTCTTTCTGCCAAAAATCATGAAAAACTGAGACGGGG-CCCCGAAACGCGTTTTTAG
* * *
8925 CCCAAAAACTATGATGGTTACTACACGATTTTCGGCTAAAAACTTACCCGAATTTTTTTTTCTGA
65 CCCAAAAACCATGATGGTTACTACACGATTTTCGGCTAAAAAATGACCCGAATTTTTTTTTCTGA
* * *
8990 ATTTTTCA-CCACATTACTTAG-AAAAAATATATAATTCAACACCAAAAAGATTGATGAGATAT
130 ATTTTT-AGACACAATACTCAGAAAAAAATATATAATTCAACACCAAAAAGATTGATGAGATAT
* * *
9052 TTCAAGGAGTCTTTCTGTCAAAAATCATGAAAAACTGAGACGGGG-TCCGAAAGGCGTTTTTAGC
1 TTCAAGGAGTCTTTCTGCCAAAAATCATGAAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGC
*
9116 CCAAAAACCATGATGGTTAAGTACACGATTTTCGGCTAAAAAATGACCCGAATTTTTTTTTTCTG
66 CCAAAAACCATGATGGTT-ACTACACGATTTTCGGCTAAAAAATGACCCGAA-TTTTTTTTTCTG
9181 AATTTTTAGACACAATACTCAGAAAAAAATATATAATTCAACACCAAAAAGATTGATG
129 AATTTTTAGACACAATACTCAGAAAAAAATATATAATTCAACACCAAAAAGATTGATG
9239 GTCTTTTCAC
Statistics
Matches: 170, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
190 34 0.20
191 31 0.18
192 70 0.41
193 35 0.21
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (192 bp):
TTCAAGGAGTCTTTCTGCCAAAAATCATGAAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGC
CCAAAAACCATGATGGTTACTACACGATTTTCGGCTAAAAAATGACCCGAATTTTTTTTTCTGAA
TTTTTAGACACAATACTCAGAAAAAAATATATAATTCAACACCAAAAAGATTGATGAGATAT
Found at i:9805 original size:7 final size:7
Alignment explanation
Indices: 9793--10016 Score: 298
Period size: 7 Copynumber: 32.3 Consensus size: 7
9783 TTTTCCTATT
9793 TTTAGGG
1 TTTAGGG
9800 TTTAGGG
1 TTTAGGG
*
9807 TTTATGG
1 TTTAGGG
*
9814 TTTATGG
1 TTTAGGG
9821 -TTAGGG
1 TTTAGGG
9827 TTTAGGG
1 TTTAGGG
9834 -TTAGGG
1 TTTAGGG
9840 TTTAGGG
1 TTTAGGG
*
9847 GTTAGGG
1 TTTAGGG
9854 TTTTAGGG
1 -TTTAGGG
9862 TTTAGGG
1 TTTAGGG
9869 -TTAGGGG
1 TTTA-GGG
9876 TTTAGGG
1 TTTAGGG
9883 TTTAGGG
1 TTTAGGG
*
9890 TTTATGGT
1 TTTA-GGG
9898 TTTAGGG
1 TTTAGGG
9905 TTTAGGG
1 TTTAGGG
9912 TTTAGGG
1 TTTAGGG
9919 TTTATGGG
1 TTTA-GGG
9927 TTTAGGG
1 TTTAGGG
9934 TTTAGGG
1 TTTAGGG
*
9941 TTTATGG
1 TTTAGGG
9948 TTTAGGG
1 TTTAGGG
9955 -TTAGGG
1 TTTAGGG
*
9961 TTTTGGG
1 TTTAGGG
9968 TTTAGGG
1 TTTAGGG
9975 TTTAGGG
1 TTTAGGG
* *
9982 -ATATGG
1 TTTAGGG
9988 TTTAGGG
1 TTTAGGG
9995 TTTAGGG
1 TTTAGGG
10002 TTTAGGG
1 TTTAGGG
10009 -TTAGGG
1 TTTAGGG
10015 TT
1 TT
10017 CAGAGCCTGA
Statistics
Matches: 193, Mismatches: 14, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
6 30 0.16
7 141 0.73
8 22 0.11
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:9822 original size:21 final size:21
Alignment explanation
Indices: 9793--10016 Score: 298
Period size: 20 Copynumber: 10.8 Consensus size: 21
9783 TTTTCCTATT
*
9793 TTTAGGGTTTAGGGTTTATGG
1 TTTAGGGTTTAGGGTTTAGGG
*
9814 TTTATGG-TTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
*
9834 -TTAGGGTTTAGGGGTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
9854 TTTTAGGGTTTAGGG-TTAGGGG
1 -TTTAGGGTTTAGGGTTTA-GGG
*
9876 TTTAGGGTTTAGGGTTTATGGT
1 TTTAGGGTTTAGGGTTTA-GGG
9898 TTTAGGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
9919 TTTATGGGTTTAGGGTTTAGGG
1 TTTA-GGGTTTAGGGTTTAGGG
*
9941 TTTATGGTTTAGGG-TTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
*
9961 TTTTGGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
* *
9982 -ATATGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
10002 TTTAGGG-TTAGGGTT
1 TTTAGGGTTTAGGGTT
10017 CAGAGCCTGA
Statistics
Matches: 180, Mismatches: 15, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
19 5 0.03
20 67 0.37
21 48 0.27
22 60 0.33
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAGGG
Found at i:10664 original size:319 final size:321
Alignment explanation
Indices: 10039--10727 Score: 809
Period size: 319 Copynumber: 2.1 Consensus size: 321
10029 TTGGTTAGAT
* * *
10039 GAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAAC
1 GAATATAGATA-TTCAAGGAGTCTTTATGACAAAAATCATGCAAAACTGAGCCGGGACCCGAAAC
* * * ***
10104 GTGTTTTTAGACCAGAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATTT
65 GCGTTTTTAGACCAAAAACCATGATGGTTAGTACACGATTTTCAGCTAAAAACTGACCCGAAAAG
*
10169 TTTTTTCTGAATCTTTTTGACACAATACTCATAAAAAATTTAGAATTCAACACCAAAAAGATTGA
130 TTTTTTCTCAATCTTTTTGACACAATACTCATAAAAAA-TTAGAATTCAACACCAAAAAGATTGA
* * * *
10234 TGGTCTTTTCACGCTTTTAAAATCATTTTTCAATTTTTTCTGAATTAATTTCTAATCAAATCAAA
194 CGGGCTTTTCACGCTTCTAAAATCATTTTTCAATTTTTTCCGAATTAATTTCTAATCAAATCAAA
** * *
10299 ACAAGATTCAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCT-GACATTTTGTTTGAG
259 ACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTGGA-ATTTTGTTCGAG
* * * * ** * *
10362 GAATATAAATATTCCAAGGAGTCTTTGTGACAAAAATCATGAAAAATTGATTCGGGACTCGGGAA
1 GAATATAGATATT-CAAGGAGTCTTTATGACAAAAATCATGCAAAACTGAGCCGGGAC-CCGAAA
* * * *
10427 CGCGTTTTTAG-CCAAAAATCGTGATGGTTAGTACACGA-TTTCAGCTAAAAACTGATCGGAAAA
64 CGCGTTTTTAGACCAAAAACCATGATGGTTAGTACACGATTTTCAGCTAAAAACTGACCCGAAAA
** * * *
10490 GTTTTTTCTCAAT-TTTTTTCCACAATACTCATAAAAAA-TA-TA-TCAACGCGAAAAAGATTGA
129 GTTTTTTCTCAATCTTTTTGACACAATACTCATAAAAAATTAGAATTCAACACCAAAAAGATTGA
* * * * *
10551 CGGGCTTTTCACGCTTCTAATAA-CGTTTTTCCATTTTTTTTCCGAATTAATTTTTAATTAAATT
194 CGGGCTTTTCACGCTTCTAA-AATCATTTTT-CA-ATTTTTTCCGAATTAATTTCTAATCAAATC
* ** *
10615 GAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGTATGTGGCTGGAGTTTTGTTCGA
256 AAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTGGAATTTTGTTCGA
*
10680 T
321 G
* * *
10681 GAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAC
1 GAATATAGATA-TTCAAGGAGTCTTTATGACAAAAATCATGCAAAAC
10728 CAAAAAAAAT
Statistics
Matches: 308, Mismatches: 51, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
317 40 0.13
318 5 0.02
319 118 0.38
320 4 0.01
321 23 0.07
322 33 0.11
323 71 0.23
324 14 0.05
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (321 bp):
GAATATAGATATTCAAGGAGTCTTTATGACAAAAATCATGCAAAACTGAGCCGGGACCCGAAACG
CGTTTTTAGACCAAAAACCATGATGGTTAGTACACGATTTTCAGCTAAAAACTGACCCGAAAAGT
TTTTTCTCAATCTTTTTGACACAATACTCATAAAAAATTAGAATTCAACACCAAAAAGATTGACG
GGCTTTTCACGCTTCTAAAATCATTTTTCAATTTTTTCCGAATTAATTTCTAATCAAATCAAAAC
AAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTGGAATTTTGTTCGAG
Found at i:11487 original size:317 final size:319
Alignment explanation
Indices: 10798--11601 Score: 838
Period size: 317 Copynumber: 2.5 Consensus size: 319
10788 TTTCTCGTTT
*
10798 TAAATATCA-TTTTCCTATTTTTTTCCGAATCT-ATTTCTAGTTAAATCGAAACAAA-ATTCAGA
1 TAAA-ATCATTTTTCC-ATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAA-AAAGATTCAGA
* *
10860 TGCTCGTAAAAACAAATCCTTAAAAT-AAATGTGGCTGAGACCCTGAGATTGGTAAGATGAATAT
62 TGCTCGTAAAAACAAATCCTT-AAATCAAATGTGGCT--GA--C--A-TTTGGTTAGATGAATAT
* *
10924 AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGAAAAACTGAGCCGGGGTCCGAAACGCGTTT
119 AGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGTCCGAAACGCGTTT
** ** * * *
10989 TTAGCCCAAAAACCATGATGGTTAGCACACGATTTTCGGCTAAAAACTTACCCTAATTTTTTTTT
184 TTAG-CCAAAAACCATGAACGTTA--ACACGATTTTCGGCTAAAAACTTACCAAAAGTCTTTTTC
** * * **
11054 TGAATTTTTTGACACAATACTCAGAAAAAATCTATAATTCAACACAAAAAAGATTGATGGTCTTT
246 CCAATTTTTTGACACAATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGACGGGATTT
* *
11119 TCACGCTTT
311 TCACACTTC
* * *
11128 TAAAATCATTTTTCAATTTTTTTCCAAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGTT
1 TAAAATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGCT
* * * *
11193 CATAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAG
66 CGTAAAAACAAATCCTTAAATCAAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAG
* * * * * *
11258 GAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAG-TAAACA
131 GAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGG-TCCGAAACGCGTTTTTAGCCAAA-A
* *
11322 ACTAT-AACG-T-ACACGA-TTTCGGCTAAAAACTTATCGGAAAAGTCTTTTTCCCAATTTTTTG
194 ACCATGAACGTTAACACGATTTTCGGCTAAAAACTTA-C-CAAAAGTCTTTTTCCCAATTTTTTG
* * *
11383 CCATAATACTCAG-AAAAATATATAATTCAACACCAAAAAGATTGACGGGATTTTCACACTTC
257 ACACAATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGACGGGATTTTCACACTTC
* * * * * * * *
11445 TAATATCGTTTTTCCATTTTTTTTCGAATTAATTTTTAATTAATTTGAAACAAGATTCAGATACT
1 TAAAATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGCT
* * * * ** * *
11510 CGTAAAAACAAATACTTAAATCGAACGTGGTTGGGATTTTGTTCGATGAATA-AGATATTTCAAG
66 CGTAAAAACAAATCCTTAAATCAAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAG
* * * *
11574 GACTATTTACGTCAAAAATCATGCAAAA
131 GAGTCTTTATGCCAAAAATCATGCAAAA
11602 ACAAAAAAAA
Statistics
Matches: 403, Mismatches: 63, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
316 52 0.13
317 145 0.36
318 28 0.07
320 1 0.00
321 5 0.01
322 66 0.16
323 17 0.04
325 1 0.00
327 2 0.00
328 7 0.02
329 70 0.17
330 9 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (319 bp):
TAAAATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGCT
CGTAAAAACAAATCCTTAAATCAAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAG
GAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGTCCGAAACGCGTTTTTAGCCAAAAAC
CATGAACGTTAACACGATTTTCGGCTAAAAACTTACCAAAAGTCTTTTTCCCAATTTTTTGACAC
AATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGACGGGATTTTCACACTTC
Found at i:12362 original size:876 final size:876
Alignment explanation
Indices: 10018--13924 Score: 5032
Period size: 870 Copynumber: 4.5 Consensus size: 876
10008 GTTAGGGTTC
10018 AGAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
1 AGAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
* *
10083 AACTGAGCCGGGGCCCGAAACGTGTTTTTAGACCAGAAACCATGATGGTTAGTACACGATTTTCG
66 AACTGAGCCGGGGCCCGAAACGCGTTTTTAGACCAAAAACCATGA--GTTAGTACACGATTTTCG
* *
10148 GCTAAAAACTGACCCGAATTTTTTTTTCTGAATCTTTTTGACACAATACTCATAAAAAATTTAGA
129 GCTAAAAACTGACCCGAA-TTTTTTTTCTGAAT-TTTTTGACACAATACTCATAAAAAATATATA
*
10213 ATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAAAATCATTTTTCAATTTTTTCTGAA
192 ATTCAACACCAAAAAGATTGATAGTCTTTTCACGCTTTTAAAATCATTTTTCAATTTTTTCTGAA
* * **
10278 TTAATTTCTAATCAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATTTTTATATCCAATGT
257 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGT
* * * * * *
10343 GGCTGACATTTTGTTTGAGGAATATAAATATTCCAAGGAGTCTTTGTGACAAAAATCATGAAAAA
322 GGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAA
* * *
10408 TTGATTCGGGACTCGGGAACGCGTTTTTAGCCAAAAA-TCGTGATGGTTA-GTACACGATTTCAG
387 TTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAACT-GTGAT-G-TACGTACACGATTTCGG
* * *
10471 CTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTTCCACAATACTCATAAAAA-ATAT-A-T
449 CTAAAAACTGATCGAAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATT
* *
10533 CAACG-CGAAAAAGATTGACGGGCTTTTCACGCTTCTAATAACGTTTTTCCATTTTTTTTCCGAA
514 CAACGAC-AAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCA-TTTTTTTCCGAA
* *
10597 TTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGTATGT
577 TTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGT
10662 GGCT-GGAGTTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGC-AA
642 GGCTGGGAGTTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAA
*
10725 AACCAAAAAAAATATTTTCGGCAAAAAATACACAATTCAACGCAATAAAAAAATTGAAATATTTT
707 AACAAAAAAAAATATTTTCGGCAAAAAATACACAATTCAACGC-A-AAAAAAATTGAAATATTTT
* * *
10790 TCTCGTTTTAAATATCATTTTCCTATTTTTTTCCGAATCTATTTCTAGTTAAATCGAAACAAAAT
770 TCTCGCTTTAAATATCATTTTCCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATAT
* *
10855 TCAGATGCTCGTAA-AAACAAATCCTTAAAAT-AAATGTGGCTG
835 TCAAATGCTCGTAACAAA-AAATCCTT-AAATCTAATGTGGCTG
* * * *
10897 AGACCCTGAGATTGGTAAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGAAA
1 AGAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
* * *
10962 AACTGAGCCGGGGTCCGAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGCACACGATTTTCG
66 AACTGAGCCGGGGCCCGAAACGCGTTTTTAGACCAAAAACCATGA--GTTAGTACACGATTTTCG
* * * * *
11027 GCTAAAAACTTACCCTAATTTTTTTTTTGAATTTTTTGACACAATACTCAGAAAAAATCTATAAT
129 GCTAAAAACTGACCCGAATTTTTTTTCTGAATTTTTTGACACAATACTCATAAAAAATATATAAT
* * **
11092 TCAACACAAAAAAGATTGATGGTCTTTTCACGCTTTTAAAATCATTTTTCAATTTTTTTCCAAAT
194 TCAACACCAAAAAGATTGATAGTCTTTTCACGCTTTTAAAATCATTTTTCAA-TTTTTTCTGAAT
* * *
11157 TAATTTCTAATTAAATCGAAAAAAGATTCAGATGTTCATAAAAACAAATCCTTATATCCAATGTG
258 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
11222 GCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAAT
323 GCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAAT
* *
11287 TGAGTCGGGGCTCGGGAACGCGTTTTTAG-TAAACAAC--T-AT-AACGTACACGATTTCGGCTA
388 TGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAA-AACTGTGATGTACGTACACGATTTCGGCTA
* * * *
11347 AAAACTTATCGGAAAAGTCTTTTTCCCAATTTTTTGCCATAATACTCAGAAAAATATATAATTCA
452 AAAACTGATCGAAAAAGT-TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATTCA
* *
11412 AC-ACCAAAAAGATTGACGGGATTTTCACACTTCTAATATCGTTTTTCCATTTTTTTTCGAATTA
516 ACGA-CAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTA
* * *
11476 ATTTTTAATTAATTTGAAACAAGATTCAGATACTCGTAAAAACAAATACTTAAATCGAACGTGGT
580 ATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGC
*
11541 TGGGA-TTTTGTTCGATGAATA-AGATATTTCAAGGACTATTTACGTCAAAAATCATGCAAAAAC
645 TGGGAGTTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAAC
**
11604 AAAAAAAAATATTTTCGGCAAAAAATACACAATTCAACGCAAAAAGTATTGAAATATTTTTCTCG
710 AAAAAAAAATATTTTCGGCAAAAAATACACAATTCAACGCAAAAAAAATTGAAATATTTTTCTCG
* *
11669 CTTTAAATATCATTTTCCTATTTTTTTCCAAATCTATTTCTAATTAAATCGAAACAATATTTAAA
775 CTTTAAATATCATTTTCCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAAA
11734 TGCTCGTAACAAAAAATCCTTAAATCTAATGTGGCTG
840 TGCTCGTAACAAAAAATCCTTAAATCTAATGTGGCTG
* *
11771 AAAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCGAAAAATCATGCAA
1 AGAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
*
11836 AACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGACCAAAAACCATGA-TAACGTACACGATTTTC
66 AACTGAGCCGGGG--CCCGAAACGCGTTTTTAGACCAAAAACCATGAGTTA-GTACACGATTTTC
*
11900 GGCTAAAAACTTACCCGAA-TTTTTTTCTGAATTTTTTGACACAATACTCATAAAAAATATATAA
128 GGCTAAAAACTGACCCGAATTTTTTTTCTGAATTTTTTGACACAATACTCATAAAAAATATATAA
* *
11964 TTCAACACCAAAAAGATTGATAGTTTTTTCACGCTTTTAATATCATTTTTCAATTTTTTCTGAAT
193 TTCAACACCAAAAAGATTGATAGTCTTTTCACGCTTTTAAAATCATTTTTCAATTTTTTCTGAAT
*
12029 TGATTTCTAATTAAATCGAAACAAGAATT-AGATGCTCGTAAAAACAAATCCTTATATCCAATGT
258 TAATTTCTAATTAAATCGAAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGT
* * *
12093 GGCTGACATTTAGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAA
322 GGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAA
* * **
12158 TTGAGTCGGGGCTCAGGAACGCTTTTTTAGCCAAAAACTGTGATGGTTTGTACACGATTTCGGCT
387 TTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAACTGTGAT-GTACGTACACGATTTCGGCT
* * * *
12223 AAAAACTTATCGAAAAAG-TTTTTCTCAA-TTTTTGTTCATAATACTCATAAAAAATATATAATT
451 AAAAACTGATCGAAAAAGTTTTTTCTCAATTTTTTG-CCACAATACTCA-GAAAAATATATAATT
* * *
12286 CAACGACAAAAAGATTGAAGAGCTTTTCACACTTCTAATATCATTTTTTCCA-TTTTTTCCGAAT
514 CAACGACAAAAAGATTGACGGGCTTTTCACACTTCTAATATC-GTTTTTCCATTTTTTTCCGAAT
12350 TAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTG
578 TAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTG
* * * * *
12415 GTTGGGATTTTTTTTCGATGATTATAGATATTTCATGGAGTATTTACGTCAAAAATCATGCAAAA
643 GCTGGGAGTTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAA
* *
12480 ACAAAAAATATATATTTTCGGCAAATAATACACAATTCAACGCAAAAAAAATTGAAATATTTTTC
708 ACAAAAAA-AAATATTTTCGGCAAAAAATACACAATTCAACGCAAAAAAAATTGAAATATTTTTC
* *
12545 TCGCTTTAAATATCATTTTTCTATTTTTTTTCCCGAATCTATTTCTAATCAAATCGAAACAATAT
772 TCGCTTTAAATATCATTTTCCTA-TTTTTTT-CCGAATCTATTTCTAATTAAATCGAAACAATAT
*
12610 TCAAATGCTCGTAACAACAAATCCTTAAATCTAATGTGGCTG
835 TCAAATGCTCGTAACAAAAAATCCTTAAATCTAATGTGGCTG
*
12652 AGAGCCTGAGATTGATTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCC-AAAATCATGCAA
1 AGAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
* *
12716 AACTGAGCCGGGGACCCCGAAACGCGTTTTTAGCCCAAAAACCATGTTGGTTAGTACACGATTTT
66 AACTGAGCCGGGG--CCCGAAACGCGTTTTTAGACCAAAAACCATG--AGTTAGTACACGATTTT
* * * *
12781 CGTCTAAAAACTGACCC--A----------G-ATTTTTTGCCACAGTACTCA-GAAAAATATATA
127 CGGCTAAAAACTGACCCGAATTTTTTTTCTGAATTTTTTGACACAATACTCATAAAAAATATATA
* * *
12832 ATTCAACACCAAAAAGATTGATAGTCTTTTCACGCCTTTAATATCATTTTACCAATTTTTTCTGA
192 ATTCAACACCAAAAAGATTGATAGTCTTTTCACGCTTTTAAAATCATTTT-TCAATTTTTTCTGA
12897 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATG
256 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATG
12962 TGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAA
321 TGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAA
*
13027 ATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGTAACGTACACGATTTCGGC
386 ATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAACTGTGATGT-ACGTACACGATTTCGGC
13092 TAAAAACTGATCGAAAAAGTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATT
450 TAAAAACTGATCGAAAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATT
* *
13157 CAACGCCAAAAAAATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCC-TTTTTTTCCGAATT
514 CAACGACAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATT
* * *
13221 AGTTTTTAATTAAATTGAAACAAGATTTAGATGCCTCATAAAAACAAATACTTAAATCGAACGTG
579 AATTTTTAATTAAATTGAAACAAGATTCAGATG-CTCGTAAAAACAAATACTTAAATCGAACGTG
** * *
13286 GCTAAGA-TTTTGTTCGATTAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGTAAAA
643 GCTGGGAGTTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAA
* * * * ** ** *
13350 A-AATAAAATATATATT---C-----AT----AATTTAACGCAAAAAGGATTGAAGGACTTTTCA
708 ACAAAAAAAAATATTTTCGGCAAAAAATACACAATTCAACGCAAAAAAAATTGAAATATTTTTC-
* ** * * * * *
13402 T-GATTTTAAA-ATTGTTTTTC-ATATTTTTCTGAAT-TAATTTATAATTAAATCGAAACAAAAT
772 TCG-CTTTAAATATCATTTTCCTATTTTTTTCCGAATCT-ATTTCTAATTAAATCGAAACAATAT
* * * *
13463 TCAGATGCTCGTAA-AAAAAATTCTTAAATCTGATGTAGCTG
835 TCAAATGCTCGTAACAAAAAATCCTTAAATCTAATGTGGCTG
* * *
13504 AGA---T----TTGATTAGATGAATATGGATA-TCTCAAAGAGT-TTTGGC-GCCAAAAATCATG
1 AGAGCCTGAGATTGGTTAGATGAATATAGATAGT-TCAAGGAGTCTTT--CTGCCAAAAATCATG
* * * * * *
13559 CAAAACTTAGCCGGGGCCCCGGAATGCGTTGTTAG-CCAAAAACCGTGATGATTATTACACGATT
63 CAAAACTGAGCCGGGG-CCCGAAACGCGTTTTTAGACCAAAAACCATGA-G-TTAGTACACGATT
* * ** * * * * * *
13623 TT-GGCTAGAATTTTGCAAAAATTGACTCGAAAGTTATTTCTTCAATTTTTAGCCGCAATAGTCA
125 TTCGGC--------T--AAAAACTGACCCGAATTTTTTTTC-TGAATTTTTTGACACAATACTCA
** * * * * **
13687 GT--AAAATCATATAATTCAACGTCAAAAAGATTGA-AGGGCTTTTCATGCATCTAGTATCATTT
179 -TAAAAAAT-ATATAATTCAACACCAAAAAGATTGATA-GTCTTTTCACGCTTTTAAAATCATTT
* ** * * ***
13749 TTCCTATTATTTTCAAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACA
241 TT-CAATT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * * * *
13813 AATCCTTAAATCCATTGTGGATGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTTGC
304 AATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGT
* * * ** * *
13878 GCAAAAAATCATGCAACACTGAACCGGGGC-CCGGAACGTGTTTTTAG
369 GCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAG
13925 GAAAAAAAAC
Statistics
Matches: 2715, Mismatches: 230, Indels: 178
0.87 0.07 0.06
Matches are distributed among these distances:
843 3 0.00
844 29 0.01
845 47 0.02
846 25 0.01
849 1 0.00
851 1 0.00
852 27 0.01
853 50 0.02
854 6 0.00
855 2 0.00
856 35 0.01
857 7 0.00
860 2 0.00
865 1 0.00
867 37 0.01
868 144 0.05
869 114 0.04
870 332 0.12
871 87 0.03
872 180 0.07
873 142 0.05
874 248 0.09
875 67 0.02
876 299 0.11
877 189 0.07
878 216 0.08
879 211 0.08
880 64 0.02
881 120 0.04
882 27 0.01
883 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (876 bp):
AGAGCCTGAGATTGGTTAGATGAATATAGATAGTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
AACTGAGCCGGGGCCCGAAACGCGTTTTTAGACCAAAAACCATGAGTTAGTACACGATTTTCGGC
TAAAAACTGACCCGAATTTTTTTTCTGAATTTTTTGACACAATACTCATAAAAAATATATAATTC
AACACCAAAAAGATTGATAGTCTTTTCACGCTTTTAAAATCATTTTTCAATTTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCT
GACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGA
GTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAACTGTGATGTACGTACACGATTTCGGCTAAAAA
CTGATCGAAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATTCAACGAC
AAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTTT
AATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGAG
TTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAACAAAAAA
AAATATTTTCGGCAAAAAATACACAATTCAACGCAAAAAAAATTGAAATATTTTTCTCGCTTTAA
ATATCATTTTCCTATTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAAATGCTCG
TAACAAAAAATCCTTAAATCTAATGTGGCTG
Found at i:14884 original size:332 final size:331
Alignment explanation
Indices: 13352--16486 Score: 2635
Period size: 332 Copynumber: 9.5 Consensus size: 331
13342 ATGTAAAAAA
* * * * * *
13352 ATAAAATATATATTCATAATTTAACG-CAAAAAGGATTGAAGGACTTTTCATGATTTTAAAATTG
1 ATAAAAAATATA-T-ATAATTCAACGCCAAAAA-GATTGAAGGACTTTTCACGCTTTTAATATCG
* *
13416 TTTTTCATATTTTTCTGAATTAATTTATAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA-
63 TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* ** * * * * *
13480 AAATTCTTAAATCTGATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGAGTTTTGG
128 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGG
* * * *
13545 CGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAATGCGTTGTTAGCCAAAAACCGTGATGA
193 CGCCAAAAATCATGCAAAACTGAACCGGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGA
* * * * *
13610 TTATTACACGATTTTGGCTAGAATTTTGCAAAAATTGA-CTCGAAAGTTATTTCTTCAATTTTTA
257 TTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCT-GAAA-TTATTTCCTCAATTTTTA
*** *
13674 GCCGCAATAGTC
320 GCTAAAATACTC
* * * * * * * *
13686 AGT--AAAAT-CATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCATGCATCTAGTATCATT
1 A-TAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTT
* ** * * ***
13748 TTTCCTATTATTTTCAAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTAC
65 TTTCATA-T-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * * *
13812 AAATCCTTAAATCCATTGTGGATGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTTTG
128 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGG
* * * ** *
13877 CGCAAAAAATCATGCAACACTGAACCGGGGCCCGGAACGTGTTTTTAGGAAAAAAAACAGTGATT
193 CGCCAAAAATCATGCAAAACTGAACCGGGGCCCGGAACGCGTTTTTA-G-CCAAAAACCGTGA--
* * * * ***
13942 TCGACTAACGTACACAATTTCGGCTAATATTTTGCAAAAATTGAGAAGAAA-TAGTTTTCCTCAA
254 T-GA-TTA-TTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAAATTA--TTTCCTCAA
14006 TTTTT-GTCTAAAATAC-C
314 TTTTTAG-CTAAAATACTC
* * * * *
14023 -CAAAGAATATATATAATTCAACTCCAAGAATATT-AGAGGACTTTTCACGCTTTTAATATCGTT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGA-AGGACTTTTCACGCTTTTAATATCGTT
** * *
14086 TTTCATATTTTTCTGAATTAAAATCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAATAA
65 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
** * * * * * **
14151 ATTTTTAAATGCAATGTGGCTGAGAATTGATTAGATGAATATATATATTTCAAGGAGCCTCGATG
130 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
* * * * *
14216 CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAACCAAAAAAAACGTGATGG
195 CCAAAAATCATGCAAAACTGAACCGGGG-CCCGGAACGCGTTTTTAGCC--AAAAACCGTGATGA
* * * *
14281 TTAGTACACAATTTCGCCTAAAATTTTACAAAAAA-GACCTGAAGATT-TTTCCTCAATTTTTGG
257 TTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAA-ATTATTTCCTCAATTTTTAG
14344 CTAAAATACT-
321 CTAAAATACTC
** * * * *
14354 -TATGAAATATATATAATTTAACGCCAAAAAGATTGAAGGA-TCTTTCACGATTTTCATATTGTT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACT-TTTCACGCTTTTAATATCGTT
* * * *
14417 TTTCATAATTTTTTCTGAATTAATTTCTAATTTAATCGAAATAAGATTTAGATGGTCGTAAAAAC
65 TTTCAT-A-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* ** * * * * *
14482 AAATCCTTAAATGCAATGTCTCTGAGATTTGATTCGATGAATATGGATATCTCAAGTAGTCTTAG
128 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGG
* * *
14547 CGCCAAAAATCATGCAAAACT-AACCAAGGGCCCTGGAACGCATTTTTAGCCAAAAACCATGATG
193 CGCCAAAAATCATGCAAAACTGAACC-GGGGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * * *
14611 ATTATTACACGATTTCGGCTAAAATTTTACAAAAAATGACCGGAAAGTTATTTCCTCGATTTTTT
256 ATTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAAA-TTATTTCCTCAATTTTTA
*
14676 GCTAAATTA-TC
320 GCTAAAATACTC
* * * * * *
14687 ATAAAAAATA-ATATAATTCTATGCCAAAAATATTGAAGGATTTTTTACGCTTCTAATATCGTTT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTT
* * * *
14751 TTCCTACTATTTTC-GAATTAATTTCTCATTAAATCGAAACAAGATTTAGATGCTCGTAAAAATA
66 TTCATA-T-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * *
14815 AATCCTTAAATCCAATGTAGCTGAGATTTGATTAGTTTAATATAGATAGTTCAAGGAGTCTTGGC
129 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGC
* * * ****
14880 GCCAAAAA-CATGCAATAC--AACTCGGGGTCCTGGAACGCGTTTTTA-ACAAAAA-AAAAATCG
194 GCCAAAAATCATGCAAAACTGAAC-CGGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G
* * * * *
14940 -TTATGTTGCACGATTTCGGCTAATATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTT
256 ATTA--TTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAAAT-TATTTCCTCAATTTT
*
15004 TAG-TCACAATACTC
318 TAGCT-AAAATACTC
* * * *
15018 AT--AAAA-ATATATAATTCAATGCCAAAAAGATTGAAGGACTTTTAACGCTTCTAATATTGTTT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTT
* * * * * *
15080 TTCCTATTCTTTTCCGAATTAATTTCTAATTAAAAAC-AAACACGATTTAGATGCTTGT------
66 TTCATA-T-TTTTCTGAATTAATTTCTAATT-AAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * *
15138 -AA-----AAA--CAA--TGGCT-AGGATTTGGTTAAATGAATATAGATATTTCAAGGAGTCTCG
128 AAATCCTTAAATCCAATGTGGCTGA-GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG
* ** ** * * * *
15192 GCACCAAAAATCATTTAAAACTGAAATGGGTCTCGGAACGTGATTTTAGCCAAAAACCGTGATGA
192 GCGCCAAAAATCATGCAAAACTGAACCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGA
* * * * *
15257 TTATAACACAATTTCGGCTAAAATTTTACAAAAATTGACCTGAAAGATAATTCCTCAATTTTTAG
257 TTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAAA-TTATTTCCTCAATTTTTAG
* * *
15322 CCATAATATTC
321 CTAAAATACTC
* * * *
15333 ATAAAAAA-ATATATAATTCAACGCCAAAAA-ATTGAAAGACTTTTGACACTTTTAATATCATTT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTT
*
15396 TTCATATTTTTCT-ACATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTTAAAAACA
66 TTCATATTTTTCTGA-ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-TAAAAAC-
**** * * * * * * *
15460 AAAAAAAATAAATGCAATGTGGCTAAGATTTTACTAGATGAATATAGTTATTTCAAGGAGTGTCG
128 -AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG
* ** *
15525 GTGCCAAAAATCATGCAAAACTGAATTGGTGGCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG
192 GCGCCAAAAATCATGCAAAACTGAACCGG-GGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * * * *
15590 GTTAGTACACAA--------AAAAATTTGCAAAATATAACCCGGAAAATT-TTTCCTCAATTTTT
256 ATTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGA-CCTG-AAATTATTTCCTCAATTTTT
* * *
15646 TGATAAAATAATC
319 AGCTAAAATACTC
* * * * *
15659 CTAAAATATATATATATATAATTTAACGGCAAAACGATTGGAGGACTTTTCACGCTTTTAATATC
1 AT-AAA-A-A-ATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC
* * * * *
15724 GTTTTTCATATTTTTCTGTATTAATTTATAATTAAATCGAAACAAGATTTAAATGCTTGTAAAAA
62 GTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
** * * * *
15789 CAAATTTTTAAATCCAATGTGGTTGAGATTTGATTAGATGAGTATAGATATCTCAAAGAGTCTTG
127 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG
** * * ** * * *
15854 ATGCCAAAAATCATGCAAAACTGAGCCGGGACCACAAAACGCTTTTTTATCCAAAAACTGTGATG
192 GCGCCAAAAATCATGCAAAACTGAACCGGGGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * * * * * *
15919 GTTTTTACACGATTTCGGCTAAAATTTT---ATAACT-A-TTG--A-TATTTTCTCAATTTTTGG
256 ATTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAAATTATTTCCTCAATTTTTAG
15976 CTAAAATACTC
321 CTAAAATACTC
* * * *
15987 AT-AAAAA-ATATATAACTCAACGCC-AAAA-ATTGAAGGGCTTTTGACG-TTTCTTATATCGTT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAATATCGTT
** * * * *
16047 TTTCATATTTTTTCCAAATTAATTTCTAATTAAATTGAAACAAAATTCAAATGCTCGTAAAGACA
65 TTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * *
16112 AATCCTTAAATCTAATGTGGGTGAGATTTGATTAGATGAATATAGATATTTCAAGCAGTCTCGGA
129 AATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGC
* * * ** * * *
16177 GCCAGAAATCATGCGAAATTGAGTCGGGTCCCCGGAACGTGTTTTTAGCCAAAAACCATGATGGT
194 GCCAAAAATCATGCAAAACTGAACCGGG-GCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G-
* * * *
16242 TTGTTAGTACACAATTTCGGCTAAAATTTTGTAAAAATTGACAC-GAAA-TATTTCTTCTCAATT
256 --ATTATTACACAATTTCGGCTAAAATTTTGCAAAAAATGAC-CTGAAATTATTTC--CTCAATT
*
16305 TTTGGCTAAAATACTC
316 TTTAGCTAAAATACTC
* * * * *
16321 AT-AAAAATATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTTACGCTTTTAATATCGTAT
1 ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTT
* * * * *
16385 TTCTTTTTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAATAAA
66 TTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * *
16450 TTCTTAAATCCAATGTTGTTGAGATTTGGTTAGATGA
131 TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
16487 TGTAAAATAT
Statistics
Matches: 2255, Mismatches: 420, Indels: 250
0.77 0.14 0.09
Matches are distributed among these distances:
313 6 0.00
314 82 0.04
315 82 0.04
316 45 0.02
317 32 0.01
318 3 0.00
319 3 0.00
320 31 0.01
321 152 0.07
322 17 0.01
323 3 0.00
324 3 0.00
325 26 0.01
326 38 0.02
327 8 0.00
328 43 0.02
329 189 0.08
330 154 0.07
331 194 0.09
332 338 0.15
333 317 0.14
334 85 0.04
335 18 0.01
336 135 0.06
337 125 0.06
338 126 0.06
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (331 bp):
ATAAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTT
TTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
TCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGC
CAAAAATCATGCAAAACTGAACCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAT
TACACAATTTCGGCTAAAATTTTGCAAAAAATGACCTGAAATTATTTCCTCAATTTTTAGCTAAA
ATACTC
Found at i:16838 original size:13 final size:13
Alignment explanation
Indices: 16798--16839 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
16788 TTGTATTTAC
16798 AATATCTTTACAT
1 AATATCTTTACAT
* *
16811 AAT-TTTTTGATAT
1 AATATCTTT-ACAT
16824 AATATCTTTACAT
1 AATATCTTTACAT
16837 AAT
1 AAT
16840 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (13 bp):
AATATCTTTACAT
Found at i:18404 original size:16 final size:16
Alignment explanation
Indices: 18383--18414 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18373 TATGGGATTG
18383 AAAATTCAATATTTCA
1 AAAATTCAATATTTCA
18399 AAAATTCAATATTTCA
1 AAAATTCAATATTTCA
18415 TGATTGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTCAATATTTCA
Found at i:18818 original size:22 final size:22
Alignment explanation
Indices: 18772--18818 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
18762 CACCTTTGCA
* *
18772 TTAAGTGTCCATTTGGCCTAAC
1 TTAAGGGTCCATTTGGCCCAAC
* *
18794 TTAAGGGTCCGTTTGGCCCAGC
1 TTAAGGGTCCATTTGGCCCAAC
18816 TTA
1 TTA
18819 TTTAACAGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
TTAAGGGTCCATTTGGCCCAAC
Found at i:18887 original size:13 final size:13
Alignment explanation
Indices: 18869--18893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18859 AACGGAAAAT
18869 CAGAAGTGCTTTC
1 CAGAAGTGCTTTC
18882 CAGAAGTGCTTT
1 CAGAAGTGCTTT
18894 TCAGTTGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
CAGAAGTGCTTTC
Done.