Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_pilon, 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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:603029 original size:20 final size:19
Alignment explanation
Indices: 602994--603060 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
602984 GAAACTTAAA
602994 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
603013 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
603033 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
603052 ATCGCAACG
1 ATCGCAACG
603061 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:603068 original size:14 final size:14
Alignment explanation
Indices: 603049--603106 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
603039 ATGCGAAATG
603049 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
603063 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
603079 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
603095 AAAATCGCAACG
1 AAAATCGCAACG
603107 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:603091 original size:32 final size:33
Alignment explanation
Indices: 603033--603111 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
603023 GGAAATGGCT
603033 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
603066 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
603098 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
603112 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:603159 original size:14 final size:14
Alignment explanation
Indices: 603140--603197 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
603130 TTTCATTTCG
603140 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
603154 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
603170 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
603186 CGTTGCGATTTT
1 CGTTGCGATTTT
603198 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:603204 original size:33 final size:33
Alignment explanation
Indices: 603123--603213 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
603113 ACAAATCGCA
*
603123 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
603156 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
603188 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
603214 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:603232 original size:20 final size:19
Alignment explanation
Indices: 603198--603252 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
603188 TTGCGATTTT
*
603198 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
603217 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
603237 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
603253 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:603773 original size:18 final size:18
Alignment explanation
Indices: 603731--603778 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
603721 CGGGTCGATC
*
603731 AGATGATGGCTCTGGGTA
1 AGATGATGGCTCTGGGCA
* * *
603749 AGGTGATAGCTCTGGGCG
1 AGATGATGGCTCTGGGCA
603767 AGATGATGGCTC
1 AGATGATGGCTC
603779 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.25
Consensus pattern (18 bp):
AGATGATGGCTCTGGGCA
Found at i:605426 original size:22 final size:22
Alignment explanation
Indices: 605401--605444 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
605391 GATTTAGATA
605401 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
605423 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
605445 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:605657 original size:20 final size:20
Alignment explanation
Indices: 605632--605725 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
605622 GATTATGTAT
605632 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
605652 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
605672 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
605693 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
605713 TATCGCATTGCGA
1 TATCGCGTTGCGA
605726 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:605726 original size:20 final size:20
Alignment explanation
Indices: 605612--605726 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
605602 CGCTTTGAAA
*
605612 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
605633 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
605653 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
605673 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
605694 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
605714 ATCGCATTGCGAT
1 ATCGCATTGCGAT
605727 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:605744 original size:21 final size:21
Alignment explanation
Indices: 605715--605807 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
605705 ATAGTCAGTA
*
605715 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
605736 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
* *
605756 TCTCATTGCGATTTTTCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
605777 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
605797 TCGCATTGCGA
1 TCGCATTGCGA
605808 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:605745 original size:41 final size:40
Alignment explanation
Indices: 605654--605788 Score: 128
Period size: 41 Copynumber: 3.3 Consensus size: 40
605644 AAAGTCAGTA
* * ** *
605654 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTATT
1 TCGCGTTGCGATAGTAAGTATCTCATTGCGATTTTCCAAT
* * *
605694 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCTCATTGCGATTTT-CCAAT
* **
605736 TCGCGTTGCGAT-TTACTTATTCTCATTGCGATTTTTCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCTCATTGCGA-TTTTCCAAT
605777 TCGCGTTGCGAT
1 TCGCGTTGCGAT
605789 TTACTTATTC
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
40 3 0.04
41 68 0.88
42 6 0.08
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (40 bp):
TCGCGTTGCGATAGTAAGTATCTCATTGCGATTTTCCAAT
Found at i:605789 original size:41 final size:41
Alignment explanation
Indices: 605715--605807 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
605705 ATAGTCAGTA
605715 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
* *
605756 TCTCATTGCGATTTTTCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
605797 TCGCATTGCGA
1 TCGCATTGCGA
605808 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:608918 original size:2 final size:2
Alignment explanation
Indices: 608907--608938 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
608897 ATTTTATAAC
608907 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
608939 TTTTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:609531 original size:21 final size:21
Alignment explanation
Indices: 609414--609550 Score: 75
Period size: 21 Copynumber: 6.7 Consensus size: 21
609404 ACGCGAAATA
**
609414 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
609434 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
609454 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
609475 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
609496 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
609517 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
609537 AAAATCGCAACGCG
1 AAAATCGCAACGCG
609551 TATCCGTAAA
Statistics
Matches: 86, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 37 0.43
21 46 0.53
22 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:609566 original size:20 final size:20
Alignment explanation
Indices: 609519--609727 Score: 208
Period size: 20 Copynumber: 10.4 Consensus size: 20
609509 GATTTTCCAG
* ** *
609519 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
609539 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
609559 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
*
609579 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
609599 AATCACAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
609619 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
609639 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
609659 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
609679 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
609699 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
609719 AATCACAAC
1 AATCGCAAC
609728 ACTGAAATTT
Statistics
Matches: 158, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 156 0.99
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:610407 original size:24 final size:24
Alignment explanation
Indices: 610375--610429 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
610365 GTGAGTACTA
* *
610375 GTCAGTATTCGAAATTTGATCTTG
1 GTCAATATTCGAAATTTGATATTG
* *
610399 GTCAATATTCGGACTTTGATATTG
1 GTCAATATTCGAAATTTGATATTG
610423 GTCAATA
1 GTCAATA
610430 CACGGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
GTCAATATTCGAAATTTGATATTG
Found at i:610435 original size:24 final size:24
Alignment explanation
Indices: 610389--610442 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
610379 GTATTCGAAA
* **
610389 TTTGATCTTGGTCAATATTCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
610413 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
610437 TTTGAT
1 TTTGAT
610443 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:610634 original size:12 final size:12
Alignment explanation
Indices: 610617--610641 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
610607 ATATAATCCT
610617 GAAGAAGAAAAA
1 GAAGAAGAAAAA
610629 GAAGAAGAAAAA
1 GAAGAAGAAAAA
610641 G
1 G
610642 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:612199 original size:19 final size:19
Alignment explanation
Indices: 612157--612293 Score: 122
Period size: 19 Copynumber: 7.4 Consensus size: 19
612147 TAGTTTACTT
* *
612157 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
612177 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* *
612196 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
* *
612215 TCGCAACGTGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
612234 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
612253 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
* *
612267 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
612286 TCGCAACG
1 TCGCAACG
612294 AGAGAATCGC
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 69 0.72
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:612278 original size:33 final size:33
Alignment explanation
Indices: 612232--612310 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
612222 GTGAAACCAA
*
612232 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGACAG
*
612265 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGACAG
612298 AATCGCAATGCGA
1 AATCGCAATGCGA
612311 TTTTGGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGACAG
Found at i:612328 original size:19 final size:19
Alignment explanation
Indices: 612306--612383 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
612296 AGAATCGCAA
612306 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
612325 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
612344 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
612358 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
612377 TGCGATT
1 TGCGATT
612384 CTCTCGTTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 11 0.22
16 1 0.02
17 1 0.02
18 1 0.02
19 37 0.73
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:612360 original size:14 final size:14
Alignment explanation
Indices: 612341--612397 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
612331 TTTGGTTTCG
*
612341 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
612355 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
612374 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
612388 CGTTGCGATT
1 CGTTGCGATT
612398 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:612364 original size:33 final size:33
Alignment explanation
Indices: 612322--612413 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
612312 TTTGGTTTCG
* *
612322 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGT
1 CGTTGCGATTTTAGTTTCGCGTTGCGATTCTCT
612355 CGTTGCGATTTTCA-TTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTT-AGTTTCGCGTTGCGATTCTCT
*
612388 CGTTGCGATTTTAAGTTTCGTGTTGC
1 CGTTGCGATTTT-AGTTTCGCGTTGC
612414 AAAAGTAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
33 43 0.81
34 10 0.19
ACGTcount: A:0.09, C:0.20, G:0.26, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTAGTTTCGCGTTGCGATTCTCT
Found at i:614360 original size:20 final size:20
Alignment explanation
Indices: 614329--614392 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
614319 TTTTGGTTGA
614329 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
614349 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
614369 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
614390 AAT
1 AAT
614393 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:614381 original size:21 final size:21
Alignment explanation
Indices: 614327--614391 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
614317 TCTTTTGGTT
614327 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
614348 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
614368 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
614389 GAA
1 GAA
614392 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:614395 original size:14 final size:14
Alignment explanation
Indices: 614376--614432 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
614366 GAGAAATGAA
614376 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
614390 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
614409 AATCGTAACGAGAG
1 AATCGCAACGAGAG
614423 AATCGCAACG
1 AATCGCAACG
614433 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:614408 original size:33 final size:33
Alignment explanation
Indices: 614327--614449 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
614317 TCTTTTGGTT
*
614327 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
614368 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
614401 GAAATGAAAATCGTAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
614434 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
614450 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
33 48 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:614418 original size:19 final size:19
Alignment explanation
Indices: 614327--614454 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
614317 TCTTTTGGTT
*
614327 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
614346 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
614368 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
614385 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
614401 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
614418 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
614434 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
614453 GA
1 GA
614455 TTTTGGTTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
14 19 0.23
15 2 0.02
16 4 0.05
17 3 0.04
18 2 0.02
19 25 0.30
20 12 0.15
21 11 0.13
22 4 0.05
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:614523 original size:21 final size:20
Alignment explanation
Indices: 614477--614569 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
614467 GTTGCGATTC
614477 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
614496 TCGCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCA-TTT
**
614517 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
614538 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
614558 CTCTCGTTGCGA
1 -TCTCGTTGCGA
614570 CTCTTCTGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
19 16 0.26
20 9 0.15
21 31 0.50
22 6 0.10
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:614545 original size:42 final size:40
Alignment explanation
Indices: 614474--614569 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 40
614464 CGCGTTGCGA
** *
614474 TTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCAT
*
614514 TTTTCTCGTTGCAGATAGTCATTTTCACGTTGCGATTTTCAT
1 TTCTCTCGTTGC-GATAGTCA-TTTCACGTTGCGATTTTCAT
614556 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
614570 CTCTTCTGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 11 0.22
41 8 0.16
42 30 0.61
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (40 bp):
TTCTCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCAT
Found at i:614691 original size:33 final size:33
Alignment explanation
Indices: 614649--614719 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
614639 CATACTAACT
614649 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
614682 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
614715 TGAAA
1 TGAAA
614720 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:615124 original size:20 final size:20
Alignment explanation
Indices: 615099--615291 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
615089 CTTTAAAAAT
615099 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
615119 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
615139 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
615160 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
615180 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
615200 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
615220 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
615240 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
615260 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
615280 CGCGTTGCGATT
1 CGCGTTGCGATT
615292 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:616427 original size:63 final size:62
Alignment explanation
Indices: 616344--616465 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 62
616334 AACAGATAAT
* * *
616344 AATATTTTTTAATTTGAAATATTCAAAAGATATATACTCAT-TTTACTATTCAAACTTAATCA
1 AATATTTTTTAATTTAAAATATTCAAAAG-TATATAATCATCTTTAATATTCAAACTTAATCA
* *
616406 AATATTATTTTAATTTAAAATATTCAAAAGTATATAATTATCTTTAATATTCAAAGTTAA
1 AATATT-TTTTAATTTAAAATATTCAAAAGTATATAATCATCTTTAATATTCAAACTTAA
616466 AAAAATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 15 0.28
63 38 0.72
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (62 bp):
AATATTTTTTAATTTAAAATATTCAAAAGTATATAATCATCTTTAATATTCAAACTTAATCA
Found at i:619919 original size:62 final size:63
Alignment explanation
Indices: 619787--619940 Score: 170
Period size: 62 Copynumber: 2.5 Consensus size: 63
619777 CAGTGTGTAT
* * * ** * *
619787 CGATGCACAGGGAGTGCATCGATGCACCCATTAAAATGGAAACATCGAATGCGATTGGTGCAT
1 CGATGCATAAGGAGTGCATCGATGCACCCACTAAAATACAAACATCGAATGCGATTGATGCAC
* *
619850 CGATGCATAAGGAGTGCATCGATGCATCCC-CT-AAATACAAACATCGAATGGGATTTATGCAC
1 CGATGCATAAGGAGTGCATCGATGCA-CCCACTAAAATACAAACATCGAATGCGATTGATGCAC
* *
619912 CGATGCAT-AGATAGTACATCGATGCACCC
1 CGATGCATAAG-GAGTGCATCGATGCACCC
619941 GTCTAGGGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
61 5 0.06
62 45 0.58
63 25 0.32
64 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (63 bp):
CGATGCATAAGGAGTGCATCGATGCACCCACTAAAATACAAACATCGAATGCGATTGATGCAC
Found at i:622978 original size:2 final size:2
Alignment explanation
Indices: 622971--623021 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
622961 CATGATATGA
622971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
623013 AT AT AT AT A
1 AT AT AT AT A
623022 AAGGAAAAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:624095 original size:62 final size:63
Alignment explanation
Indices: 623961--624096 Score: 159
Period size: 62 Copynumber: 2.2 Consensus size: 63
623951 TTCAGTGTGT
* * * ** * *
623961 ATCGATGCACAGGGAGTGCATCGATGCACCCATTAAAATGGAAACATCTAATGCGATTGGTGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCACTAAAATAAAAACATCAAATGCGATTGATGC
* *
624024 ATCGATGCATAAGGAGTGCATCGATGCATCCC-CT-AAATAAAAACATCAAATGGGATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCA-CCCACTAAAATAAAAACATCAAATGCGATTGATGC
*
624086 ATTGATGCATA
1 ATCGATGCATA
624097 GATAGTACAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 32 0.52
63 27 0.44
64 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCACTAAAATAAAAACATCAAATGCGATTGATGC
Found at i:626125 original size:6 final size:6
Alignment explanation
Indices: 626093--626124 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
626083 AACGTCTCAA
*
626093 GCTAAG GCTAAG GCTAAG GCTAAG GCCAAG GC
1 GCTAAG GCTAAG GCTAAG GCTAAG GCTAAG GC
626125 CGTAAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.34, T:0.12
Consensus pattern (6 bp):
GCTAAG
Found at i:628373 original size:3 final size:3
Alignment explanation
Indices: 628365--628398 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
628355 GTTCAGACAT
*
628365 ATA ATA ATA ATC ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
628399 AACTACCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:633567 original size:13 final size:13
Alignment explanation
Indices: 633528--633566 Score: 62
Period size: 12 Copynumber: 3.0 Consensus size: 13
633518 AAATAATAAT
633528 TTAAACATATAAAA
1 TTAAA-ATATAAAA
633542 TTAAAATATAAAA
1 TTAAAATATAAAA
633555 TT-AAATATAAAA
1 TTAAAATATAAAA
633567 AGTAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAATATAAAA
Found at i:634818 original size:3 final size:3
Alignment explanation
Indices: 634810--634897 Score: 110
Period size: 3 Copynumber: 30.0 Consensus size: 3
634800 GGCCTGTTTG
* *
634810 TAA TAA TAA -AT TAA TAA TAA T-A TAA T-A TAA TAA TAA TATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
**
634853 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
634898 AATGGAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
2 5 0.07
3 66 0.90
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:635559 original size:76 final size:76
Alignment explanation
Indices: 635047--635532 Score: 945
Period size: 76 Copynumber: 6.4 Consensus size: 76
635037 GAGGTCTTAA
635047 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
635112 AGGCTTTTTGG
66 AGGCTTTTTGG
635123 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
635188 AGGCTTTTTGG
66 AGGCTTTTTGG
635199 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
635264 AGGCTTTTTGG
66 AGGCTTTTTGG
*
635275 AAACATCATACACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
635340 AGGCTTTTTGG
66 AGGCTTTTTGG
*
635351 AAACATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
635416 AGGCTTTTTGG
66 AGGCTTTTTGG
*
635427 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
635492 AGGCTTTTTGG
66 AGGCTTTTTGG
635503 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
635533 TAGGAAATAG
Statistics
Matches: 405, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 405 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:635787 original size:185 final size:184
Alignment explanation
Indices: 635473--635832 Score: 616
Period size: 185 Copynumber: 2.0 Consensus size: 184
635463 AGGCTTTAAA
635473 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
** *
635538 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGA
66 AATAGTTTAATAAGTAAAAAAACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAGA
*
635603 AAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAGATAAAATGAGAAACTAGGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
635657 AACATCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGT-GG
1 AACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGG
*
635721 AAAATAGTTTACTAAGT-AAAAAACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATTTTT
65 -AAATAGTTTAATAAGTAAAAAAACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCA-TTTT
**
635785 AGAAAAGATTGAATGAGAAACTAGGGAAATCGTTTTCTCATTATTTTT
128 AGAAAAGATAAAATGAGAAACTAGGGAAATCGTTTTCTCATTATTTTT
635833 TTTTCAAAAT
Statistics
Matches: 166, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
184 47 0.28
185 119 0.72
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (184 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
AATAGTTTAATAAGTAAAAAAACTAAAAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAGA
AAAGATAAAATGAGAAACTAGGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
Found at i:636421 original size:22 final size:22
Alignment explanation
Indices: 636396--636472 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
636386 CATAAAGCTT
636396 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
636418 TCATCTTTAAAAAGAGAATCTT
1 TCATCTTTGAAAAGAGAATCTA
636440 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
636462 TCATATTTGAA
1 TCATCTTTGAA
636473 GAATGTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:637759 original size:17 final size:19
Alignment explanation
Indices: 637727--637762 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
637717 CATATATCTC
637727 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
637746 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
637763 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:638356 original size:63 final size:65
Alignment explanation
Indices: 638246--638393 Score: 187
Period size: 63 Copynumber: 2.3 Consensus size: 65
638236 TCTTTCAATG
* * * *
638246 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTAT-TTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTT-TCTTTA
638309 A
65 A
* * *
638310 AAGG-ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCACTA-CTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCTTTA
638373 A
65 A
638374 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
638394 TATGAATGTG
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
63 44 0.60
64 15 0.21
65 14 0.19
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (65 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCTTTAA
Found at i:641574 original size:114 final size:114
Alignment explanation
Indices: 641374--641713 Score: 599
Period size: 114 Copynumber: 3.0 Consensus size: 114
641364 GATCATGCAG
* * * ** *
641374 TTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
641439 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
641488 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
*
641553 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
641602 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
* *
641667 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTATACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
641714 CATGGAACTT
Statistics
Matches: 216, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 216 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:643907 original size:22 final size:21
Alignment explanation
Indices: 643872--643913 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
643862 TTTTTCCCTT
* *
643872 TTTTTTATTTATTTATTTTTCC
1 TTTTTCATTCATTT-TTTTTCC
643894 TTTTTCATTCATTTTTTTTC
1 TTTTTCATTCATTTTTTTTC
643914 TTTCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCATTCATTTTTTTTCC
Found at i:643950 original size:22 final size:23
Alignment explanation
Indices: 643918--643963 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
643908 TTTTTCTTTC
643918 TTTTTTCTTCTTTCTTTGCTGGA
1 TTTTTTCTTCTTTCTTTGCTGGA
*
643941 TTTTTT-TTCTTTCTTTGTTGGA
1 TTTTTTCTTCTTTCTTTGCTGGA
643963 T
1 T
643964 GAGTATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (23 bp):
TTTTTTCTTCTTTCTTTGCTGGA
Found at i:649049 original size:20 final size:20
Alignment explanation
Indices: 649011--649049 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
649001 ATAAATAATG
*
649011 AAAATAAAATACTTGAAAAT
1 AAAATAAAATACTTAAAAAT
649031 AAAATAAAAATA-TTAAAAA
1 AAAAT-AAAATACTTAAAAA
649050 ATAATATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATAAAATACTTAAAAAT
Found at i:649088 original size:28 final size:26
Alignment explanation
Indices: 649038--649104 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 26
649028 AATAAAATAA
*
649038 AAATATTA-AAAAATAATATACATAT
1 AAATATTATGAAAATAATATACATAT
649063 AAATATTATGAAAATAATAAGTACATAT
1 AAATATTATGAAAATAAT-A-TACATAT
* *
649091 AAAAATTTTGAAAA
1 AAATATTATGAAAA
649105 GAAAGAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.22
26 8 0.22
27 1 0.03
28 19 0.53
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (26 bp):
AAATATTATGAAAATAATATACATAT
Found at i:649945 original size:12 final size:13
Alignment explanation
Indices: 649903--649949 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 13
649893 AATTATGAAA
649903 ATAATAATTCAAACAT
1 ATAA-AATT-AAA-AT
649919 ATAAAATTAAAAT
1 ATAAAATTAAAAT
649932 ATAAAATT-AAAT
1 ATAAAATTAAAAT
649944 ATAAAA
1 ATAAAA
649950 AGTAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.32
13 10 0.32
14 3 0.10
15 4 0.13
16 4 0.13
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:651134 original size:113 final size:113
Alignment explanation
Indices: 650943--651621 Score: 783
Period size: 113 Copynumber: 5.9 Consensus size: 113
650933 AATTTAAATC
* * * *
650943 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
651008 AGAGGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACTTAAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * *
651056 CATCACTCGGTGGATCAGCATTACTAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTCGATGGATCAACATTACCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
651120 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTCGCTTGAATT
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* *
651169 CATCATTCGATGGATCAGCATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
651234 AGAA-AAAGTTCATAATAAGAAGAACTTGTTCAAC-TTTTGTTTGAATT
66 AGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * * *
651281 CATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGGAATG
1 CATCACTCGATGGATCAACATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAA-GAAGG
* * * * *
651346 AAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCATGACTCTAT
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGA--AT-T
* *** * * *
651398 CATAGAAGGAGATAGATCAACATCAACTTTTCCAGAG-GAAGTTCATAATGAGAATAACTCATCT
1 CAT--CACTCGATGGATC-A-A-C-A--TTACCAGAGAG-AGTTCATAATGAGAAGAACTCATCT
* * *
651462 GAAG-AGGAAGCAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
57 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * * *
651518 CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
651583 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAA-CTTTT
651622 GCATGATTCT
Statistics
Matches: 483, Mismatches: 62, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
112 104 0.22
113 250 0.52
114 16 0.03
115 1 0.00
116 2 0.00
117 5 0.01
118 8 0.02
119 8 0.02
120 5 0.01
121 2 0.00
122 1 0.00
123 45 0.09
124 1 0.00
125 35 0.07
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCACTCGATGGATCAACATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:651351 original size:226 final size:224
Alignment explanation
Indices: 650943--651627 Score: 869
Period size: 226 Copynumber: 3.0 Consensus size: 224
650933 AATTTAAATC
* *
650943 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
651008 AGAGGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT-TACTTAAATTCATCACTCGGTGGATC
66 AGAGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGT--TTGAATTCATCACTCGATGGATC
* * * * ** *
651072 AGCATTACTAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
129 AACTTTTCCAGAG-AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
* *
651136 TGAGAAGAATTTGTTCAA-CTTTTCGCTTGAATT
193 TGAGAAGAATTTGTTCAACCTTTT-GCATG-ACT
* *
651169 CATCATTCGATGGATCAGCATTACCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
651234 AGAAAAAGTTCATAATAAGAAGAACTTGTTCAACTTTTGTTTGAATTCATCACTCGATGGATCAA
66 AGAGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTGAATTCATCACTCGATGGATCAA
*
651299 CTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGGAATGAAGAAGAAATTCATAATG
131 CTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA-GAAGGAAGAAGAAATTCATAATG
*
651364 AGAAGAATTTGTTTAACCTTTTGCATGACT
195 AGAAGAATTTGTTCAACCTTTTGCATGACT
** * *
651394 CTATCATAGAAGGAGATAGATCAACATCAACTTTTCCAGAG-GAAGTTCATAATGAGAATAACTC
1 C-ATCAT-----TCGATGGATC-A-A-C-A--TTTCCAGAGAG-AGTTCATAATGAGAAGAACTC
* *
651458 ATCTGAAG-AGGAAGCAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCAT
53 ATCTGAAGAAGGAAG-AGAAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGTTTGAATTCAT
*
651521 CACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
116 CACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
* * *
651586 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGA
181 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATGA
651628 TTCTATCACA
Statistics
Matches: 404, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
225 58 0.14
226 143 0.35
227 6 0.01
231 7 0.02
232 1 0.00
234 1 0.00
235 1 0.00
236 76 0.19
237 111 0.27
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (224 bp):
CATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTGAATTCATCACTCGATGGATCAA
CTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTGCATGACT
Found at i:651459 original size:125 final size:123
Alignment explanation
Indices: 651294--651669 Score: 477
Period size: 123 Copynumber: 3.1 Consensus size: 123
651284 CACTCGATGG
*
651294 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGGAATGAAGAAGAAATTCA
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA-GAAGGAAGAAGAAATTCA
* * *
651359 TAATGAGAAGAATTTGTTTAACCTTTTGCATGACTCTATCATAGAAGGAGATAGATCAAC
65 TAATGAGAAGAATTTGTTCAACCTTTTGCATGA-TCTATCATAGAAGAAGATAGATCAGC
* * * *
651419 ATCAACTTTTCCAGAGGAAGTTCATAATGAGAATAACTCATCTGAAG-AGGAAGCAGAAATTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* * * * * *
651483 AATGAGAAGAATTTGTTCAACCTTTTGCTTGA-AT-TCAT-----CA-CTTGAT--GG
66 AATGAGAAGAATTTGTTCAACCTTTTGCATGATCTATCATAGAAGAAGATAGATCAGC
*
651531 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* * *
651596 AATGAGAAGAACTTGTTCAATCTTTTGCATGATTCTATCACAGAAGAAGATAGATCAGC
66 AATGAGAAGAATTTGTTCAACCTTTTGCATGA-TCTATCATAGAAGAAGATAGATCAGC
*
651655 ATCAACATTTCCAGA
1 ATCAACTTTTCCAGA
651670 TTACATCACA
Statistics
Matches: 211, Mismatches: 28, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
112 44 0.21
113 44 0.21
114 4 0.02
115 2 0.01
116 3 0.01
120 4 0.02
121 2 0.01
122 4 0.02
123 45 0.21
124 16 0.08
125 43 0.20
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
AATGAGAAGAATTTGTTCAACCTTTTGCATGATCTATCATAGAAGAAGATAGATCAGC
Found at i:651636 original size:113 final size:112
Alignment explanation
Indices: 651419--651636 Score: 314
Period size: 112 Copynumber: 1.9 Consensus size: 112
651409 ATAGATCAAC
* * * *
651419 ATCAACTTTTCCAGAGGAAGTTCATAATGAGAATAACTCATCTGAAG-AGGAAGCAGAAATTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
*
651483 AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGG
66 AATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGG
* * *
651531 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
*
651596 AATGAGAAGAACTTGTTCAATCTTTTGCATG-ATTCTATCAC
66 AATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATTC-ATCAC
651637 AGAAGAAGAT
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
112 48 0.50
113 48 0.50
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (112 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
AATGAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCACTTGATGG
Found at i:651891 original size:3 final size:3
Alignment explanation
Indices: 651885--651938 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
651875 TTCATTTGAA
651885 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
651931 TAT TAT TA
1 TAT TAT TA
651939 AAAAATAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:653209 original size:3 final size:3
Alignment explanation
Indices: 653196--653255 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
653186 TTATTTGCAA
* * * *
653196 TAT TAT T-T TAT TAT TAT TGT TGT TTT TAAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
*
653240 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
653256 TATATAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 3 0.06
3 42 0.89
4 2 0.04
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:653258 original size:27 final size:27
Alignment explanation
Indices: 653196--653260 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
653186 TTATTTGCAA
* *
653196 TATTATTT-TATTATTATTGTTGTTTT
1 TATTATTTATATTATTATTATTATTTT
653222 TAATTA-TTAT-TTCATTATTATTATTTT
1 T-ATTATTTATATT-ATTATTATTATTTT
653249 TATTATTTATAT
1 TATTATTTATAT
653261 AAATAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
26 9 0.28
27 22 0.69
28 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (27 bp):
TATTATTTATATTATTATTATTATTTT
Found at i:653281 original size:20 final size:18
Alignment explanation
Indices: 653256--653296 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
653246 TTTTATTATT
653256 TATATAAATAAATAAATATA
1 TATATAAAT-AATAAATA-A
*
653276 TATATATATAATAAATAA
1 TATATAAATAATAAATAA
653294 TAT
1 TAT
653297 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATATAAATAATAAATAA
Found at i:658893 original size:2 final size:2
Alignment explanation
Indices: 658888--658928 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
658878 TCATTTTTTT
*
658888 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
658929 GTTTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:659062 original size:15 final size:15
Alignment explanation
Indices: 659042--659098 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
659032 TATTATACGG
659042 TTTTAAAAAAAACAT
1 TTTTAAAAAAAACAT
*
659057 TTTTAAAATAAATATAAT
1 TTTTAAAA-AAA-A-CAT
659075 TTTTAAAAAGAAACAT
1 TTTTAAAAA-AAACAT
*
659091 TTTGAAAA
1 TTTTAAAA
659099 CATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 8 0.23
16 12 0.34
17 3 0.09
18 12 0.34
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (15 bp):
TTTTAAAAAAAACAT
Found at i:659106 original size:34 final size:33
Alignment explanation
Indices: 659042--659106 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
659032 TATTATACGG
* *
659042 TTTTAAAAAAAACATTTTTAAAATAAATATAAT
1 TTTTAAAAAAAACATTTTGAAAACAAATATAAT
*
659075 TTTTAAAAAGAAACATTTTGAAAACATATATA
1 TTTTAAAAA-AAACATTTTGAAAACAAATATA
659107 TATTATATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (33 bp):
TTTTAAAAAAAACATTTTGAAAACAAATATAAT
Found at i:659153 original size:34 final size:36
Alignment explanation
Indices: 658914--659180 Score: 115
Period size: 36 Copynumber: 7.2 Consensus size: 36
658904 TATATATATA
* **
658914 TATATATATAATATAGTTTTAAAAACATATTTGAAATATT
1 TATATA-AT-ATATAGTTTTAAAAACAT-TTTTAAA-AAC
* * * *
658954 TATATATTATATATAGTTTTTAAAATACTTTGAAAATA-
1 TATATA--ATATATAGTTTTAAAAACATTTTTAAAA-AC
* * * *
658992 AATATAATATATAATTTTTAAAACGTTTTTTAAAAA-
1 TATATAATATATAGTTTTAAAAAC-ATTTTTAAAAAC
* * **
659028 AATATATTATACGGTTTTAAAAAAAACATTTTT--AAA-
1 TATATAATATATAGTTTT---AAAAACATTTTTAAAAAC
* *
659064 -ATA-AATATA-ATTTTTAAAAAGAAACA-TTTTGAAAAC
1 TATATAATATATAGTTTT---AA-AAACATTTTTAAAAAC
* *
659100 ATATATATATTATATAGTTTTGAAATCA-TTTTAAAAAC
1 -TATATA-A-TATATAGTTTTAAAAACATTTTTAAAAAC
*
659138 T-TATAATATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTAAAAACATTTTTAAAAAC
659173 TATATAAT
1 TATATAAT
659181 TTTGAAAGCG
Statistics
Matches: 183, Mismatches: 26, Indels: 40
0.73 0.10 0.16
Matches are distributed among these distances:
33 13 0.07
34 26 0.14
35 17 0.09
36 44 0.24
37 8 0.04
38 27 0.15
39 14 0.08
40 22 0.12
41 7 0.04
42 5 0.03
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAAACATTTTTAAAAAC
Found at i:659194 original size:29 final size:29
Alignment explanation
Indices: 659142--659209 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
659132 AAAAACTTAT
* *
659142 AATATATAGTTTTAAAAACATTTTTGAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
* * * *
659171 ACTATATAATTTTGAAAGCGTTTTTAAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
*
659200 AAAATATAAT
1 AATATATAAT
659210 ATATAATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (29 bp):
AATATATAATTTTAAAAACATTTTTAAAA
Found at i:659307 original size:14 final size:14
Alignment explanation
Indices: 659288--659332 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
659278 ATTATCGTTG
659288 TTATTTATTTTTAT
1 TTATTTATTTTTAT
659302 TTATTTATTTTTAT
1 TTATTTATTTTTAT
* *
659316 TAATTTTATTTTCAT
1 TTA-TTTATTTTTAT
659331 TT
1 TT
659333 TAATTGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:660742 original size:13 final size:14
Alignment explanation
Indices: 660726--660755 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
660716 TTTTCATTTC
660726 TTTTATTATT-TTA
1 TTTTATTATTATTA
660739 TTTTATTATTATTA
1 TTTTATTATTATTA
660753 TTT
1 TTT
660756 CTTTCTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:662023 original size:16 final size:16
Alignment explanation
Indices: 662002--662045 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
661992 GGAAGTAAAG
662002 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
662018 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
662034 CATGTGGGGTAG
1 CATGTGGGGTAG
662046 GATTTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.41, T:0.30
Consensus pattern (16 bp):
CATGTGGGGTAGATAT
Found at i:662821 original size:19 final size:19
Alignment explanation
Indices: 662797--662842 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
662787 ATTTAGACAT
*
662797 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTATTATTTTC
662816 TTTGCATTTTATTATTTTC
1 TTTGCATTTTATTATTTTC
662835 TTTGCATT
1 TTTGCATT
662843 CACATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTATTATTTTC
Found at i:666404 original size:165 final size:165
Alignment explanation
Indices: 666139--666718 Score: 609
Period size: 165 Copynumber: 3.5 Consensus size: 165
666129 CTACCTGCCA
* * ** * *
666139 CAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGTACATCATTCACAGCATAACTCAACG-C
1 CAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAA-GTC
* * * * * *
666203 TAGAAGAGTTATCTGTCAA-CAAAAACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
65 GAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
* * *
666267 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C
130 TTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGAC
* * * * * * * *
666302 CAAAGACAC-TTAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATACCTGAAGT
1 CAAAGAC-CTTTGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCATAGCTTAAGT
* * * *
666366 CGAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA
64 CGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCA
* * *
666431 TTTGCATCACAACTTAAGTCTAGAAGGGTTGTCTGGAAAC
129 TTTGCAGCATAACTTAAGTCTAGAAGGGTTATCT-G--AC
* * * *
666471 AAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCTGTATAGCTTAAGTCG
1 CAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCG
** * * * *
666536 AGAAGGGCTATCTG----CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCAT
66 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCAT
* * *
666597 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
130 TTGCAGCATAACTTAAGTCTAGAAGGGTTATC--TGAC
* *
666635 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTC
1 C-AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTC
666700 GAGAAGGGCTATCTGCCAA
65 GAGAAGGGCTATCTGCCAA
666719 AGACTCCCGA
Statistics
Matches: 342, Mismatches: 58, Indels: 28
0.80 0.14 0.07
Matches are distributed among these distances:
163 25 0.07
164 69 0.20
165 179 0.52
166 2 0.01
167 1 0.00
168 42 0.12
169 24 0.07
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
CAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCG
AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCTAGAAGGGTTATCTGAC
Found at i:666456 original size:84 final size:83
Alignment explanation
Indices: 666122--666715 Score: 555
Period size: 84 Copynumber: 7.2 Consensus size: 83
666112 GCTCAAGGCC
* * * *
666122 AGAAGGGCTACCTGCCA-CAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGTACATCATT
1 AGAAGGGTTATCTGCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
** * *
666185 CACAGCATAACTCAACG-CT
65 TGCAGCATAACTTAA-GTCG
* * *
666204 AGAAGAGTTATCTGTCAA-CAAAAACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-CAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
666268 TGCAGCATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* * * * * * *
666287 AGAAGGGCTATCTG---CCAAAGACAC-TTAAGTTCAATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCAACCAAAGAC-CTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* *
666348 TTGCAGCATACCTGAAGTCG
64 TTGCAGCATAACTTAAGTCG
* * *
666368 AGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTG-CAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
666433 TGCATCACAACTTAAGTCT
65 TGCAGCATAACTTAAGTCG
* * *
666452 AGAAGGGTTGTCTGGAAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCT-GCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * *
666516 TTGCTGTATAGCTTAAGTCG
64 TTGCAGCATAACTTAAGTCG
* *** * * * * *
666536 AGAAGGGCTATCTG---CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGGTTATCTGCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
* * * *
666598 TACAGCATAACTCAAGGCT
65 TGCAGCATAACTTAAGTCG
** *
666617 AGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATA
1 AGAAGGGTTATCTGCAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
666682 TGCAGCATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
*
666701 AGAAGGGCTATCTGC
1 AGAAGGGTTATCTGC
666716 CAAAGACTCC
Statistics
Matches: 411, Mismatches: 82, Indels: 36
0.78 0.16 0.07
Matches are distributed among these distances:
80 48 0.12
81 81 0.20
82 13 0.03
83 69 0.17
84 152 0.37
85 48 0.12
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
AGAAGGGTTATCTGCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCG
Found at i:666576 original size:249 final size:247
Alignment explanation
Indices: 666113--666714 Score: 789
Period size: 249 Copynumber: 2.4 Consensus size: 247
666103 TCAGGCTTAG
* * * *
666113 CTCAAGGCCAGAAGGGCTACCTGCCA-CAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGG
1 CTCAAGGCGAGAAGGGTTATCTGCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GG
* ** * * **
666176 TACATCATTCACAGCATAACTCAACG-CTAGAAGAGTTATCTGTCAACAAAAACCTTTGAGTTCG
65 CACATCATTTGCAGCATAACTTAA-GTCTAGAAGGGTTATCTGGAAACAAAAACCTTTGAGTTCG
666240 ACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
129 ACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
** * *
666305 AGACACTTAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAC
194 AGACACCCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * *
666359 CTGAAGTCGAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCGAGAAGGGTTATCTG-CAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * * *
666424 CATATCATTTGCATCACAACTTAAGTCTAGAAGGGTTGTCTGGAAACAAAAGACCTTTGAGTTCG
65 CACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGGAAACAAAA-ACCTTTGAGTTCG
* * *
666489 ACTACGCTCAGCT-CAACGGCACATCATTTGCTGTATAGCTTAAGTCGAGAAGGGCTATCTGCCA
129 ACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * **
666553 AAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
193 AAGACACCCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* **
666608 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCGAGAAGGGTTATCTGCAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * * *
666673 CACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
65 CACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG
666715 CCAAAGACTC
Statistics
Matches: 304, Mismatches: 45, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
246 17 0.06
247 3 0.01
248 76 0.25
249 208 0.68
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (247 bp):
CTCAAGGCGAGAAGGGTTATCTGCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGGAAACAAAAACCTTTGAGTTCGAC
TACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
ACACCCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:666719 original size:165 final size:165
Alignment explanation
Indices: 666140--666788 Score: 607
Period size: 165 Copynumber: 3.9 Consensus size: 165
666130 TACCTGCCAC
* ** * * *
666140 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGTACATCATTCACAGCATAACTCAACG-CT
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAA-GTCG
* * * * ***
666204 AGAAGAGTTATCTGTCAACAAAAACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
65 AGAAGGGCTATCTG--ACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
* * * * * *
666269 GCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-
128 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
* * * * * * * *
666303 AAAGACAC-TTAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATACCTGAAGTC
1 AAAGAC-CTTTGAGTTCGACTACGCTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTC
* * ** * *
666367 GAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCAT
64 GAGAAGGGCTATCTG---ACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCAT
* * * * * * *
666432 TTGCATCACAACTTAAGTCTAGAAGGGTTGTCTG-GAAACA
126 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTG-ACCA
* *
666472 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCTGTATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * *
666537 GAAGGGCTATCTG-CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAC
66 GAAGGGCTATCTGACCAAAGACCCCCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTAC
666601 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
130 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
*
666637 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATATGCAGCATAGCTTAAGTCG
1 AAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCG
* * * * * *
666701 AGAAGGGCTATCTG-CCAAAGACTCCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTA
65 AGAAGGGCTATCTGACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGG-CACATCATTTA
* * * *
666765 CAACATAGCTCATGGCAAGAAGGG
129 CAGCATAACTCAAGGCTAGAAGGG
666789 CTATTTGTCA
Statistics
Matches: 402, Mismatches: 70, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
163 24 0.06
164 67 0.17
165 240 0.60
166 5 0.01
168 43 0.11
169 23 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (165 bp):
AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
GAAGGGCTATCTGACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACA
GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
Found at i:667357 original size:2 final size:2
Alignment explanation
Indices: 667350--667379 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
667340 TCGTCTCATT
667350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
667380 AAATATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:667517 original size:15 final size:15
Alignment explanation
Indices: 667497--667552 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
667487 TATTATACGG
667497 TTTAAAAAAAACATT
1 TTTAAAAAAAACATT
*
667512 TTTAAAATAAATATAATT
1 TTTAAAA-AAA-A-CATT
667530 TTTAAAAAGAAACATT
1 TTTAAAAA-AAACATT
*
667546 TTGAAAA
1 TTTAAAA
667553 CATATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 7 0.21
16 12 0.35
17 3 0.09
18 12 0.35
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (15 bp):
TTTAAAAAAAACATT
Found at i:667560 original size:34 final size:33
Alignment explanation
Indices: 667497--667560 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
667487 TATTATACGG
* *
667497 TTTAAAAAAAACATTTTTAAAATAAATATAATT
1 TTTAAAAAAAACATTTTGAAAACAAATATAATT
*
667530 TTTAAAAAGAAACATTTTGAAAACATATATA
1 TTTAAAAA-AAACATTTTGAAAACAAATATA
667561 TATTATATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 8 0.30
34 19 0.70
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (33 bp):
TTTAAAAAAAACATTTTGAAAACAAATATAATT
Found at i:667607 original size:34 final size:36
Alignment explanation
Indices: 667374--667634 Score: 132
Period size: 36 Copynumber: 7.2 Consensus size: 36
667364 TATATATATA
* * * **
667374 TATATAAAATATAGTTTTGAAAACATATTTGAAACATT
1 TATATAATATATAGTTTTAAAAACAT-TTTTAAA-AAC
* * * *
667412 TATATATTATATAGTTTTTAAAACACTTTGAAAATA-
1 TATATAATATATAGTTTTAAAAACATTTTTAAAA-AC
* * *
667448 AATATAATATATAGTTTTTAAAACGTTTTTATAAAA-
1 TATATAATATATAGTTTTAAAAACATTTTTA-AAAAC
* ** *
667484 -ATATATTATACGGTTTAAAAAAAACATTTTT--AAA-
1 TATATAATATATAGTTT--TAAAAACATTTTTAAAAAC
* *
667518 -ATA-AATATA-ATTTTTAAAAAGAAACA-TTTTGAAAAC
1 TATATAATATATAGTTTT---AA-AAACATTTTTAAAAAC
* *
667554 ATATATATATTATATAGTTTTGAAATCA-TTTTAAAAAC
1 -TATATA-A-TATATAGTTTTAAAAACATTTTTAAAAAC
*
667592 T-TATAATATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTAAAAACATTTTTAAAAAC
667627 TATATAAT
1 TATATAAT
667635 TTTGAAAGCG
Statistics
Matches: 177, Mismatches: 27, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
32 3 0.02
33 11 0.06
34 27 0.15
35 27 0.15
36 38 0.21
37 21 0.12
38 38 0.21
39 2 0.01
40 1 0.01
41 4 0.02
42 5 0.03
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAAACATTTTTAAAAAC
Found at i:667648 original size:29 final size:29
Alignment explanation
Indices: 667596--667663 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
667586 AAAAACTTAT
* *
667596 AATATATAGTTTTAAAAACATTTTTGAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
* * * *
667625 ACTATATAATTTTGAAAGCGTTTTTAAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
*
667654 AAAATATAAT
1 AATATATAAT
667664 ATATAATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (29 bp):
AATATATAATTTTAAAAACATTTTTAAAA
Found at i:667761 original size:14 final size:14
Alignment explanation
Indices: 667742--667786 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
667732 ATTATCGTTG
667742 TTATTTATTTTTAT
1 TTATTTATTTTTAT
667756 TTATTTATTTTTAT
1 TTATTTATTTTTAT
* *
667770 TAATTTTATTTTCAT
1 TTA-TTTATTTTTAT
667785 TT
1 TT
667787 TAATTGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:669208 original size:13 final size:14
Alignment explanation
Indices: 669190--669219 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
669180 TTTTCATCTC
669190 TTTTATTATT-TTA
1 TTTTATTATTATTA
669203 TTTTATTATTATTA
1 TTTTATTATTATTA
669217 TTT
1 TTT
669220 CTTTCTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:682904 original size:21 final size:20
Alignment explanation
Indices: 682875--682931 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
682865 TTTATAAAAA
*
682875 AAATTAAAATTTTAATATTAT
1 AAATAAAAATTTTAATATT-T
682896 AAATAAAAA-TTTAATATTT
1 AAATAAAAATTTTAATATTT
*
682915 AAA-AAATATTTATAATA
1 AAATAAAAATTT-TAATA
682932 AACTTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.12
19 6 0.19
20 14 0.44
21 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATAAAAATTTTAATATTT
Found at i:682915 original size:27 final size:26
Alignment explanation
Indices: 682848--682916 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
682838 GTAATTTAGT
* * *
682848 AAAATATAATATTAAATTTTATAAAA
1 AAAATTTAATATTTAATATTATAAAA
*
682874 AAAA-TTAAAATTTTAATATTATAAATA
1 AAAATTTAATA-TTTAATATTATAAA-A
682901 AAAATTTAATATTTAA
1 AAAATTTAATATTTAA
682917 AAAATATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 4 0.11
26 16 0.46
27 10 0.29
28 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAATTTAATATTTAATATTATAAAA
Found at i:684159 original size:26 final size:27
Alignment explanation
Indices: 684110--684164 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
684100 TTTATTTTTA
*
684110 TTTTAAATTATTAAATATATTTTATTT
1 TTTTAAATTATTAAATATAATTTATTT
*
684137 TTTTAACTTATTAAATA-AATTTATTT
1 TTTTAAATTATTAAATATAATTTATTT
684163 TT
1 TT
684165 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTAAATTATTAAATATAATTTATTT
Found at i:684291 original size:19 final size:19
Alignment explanation
Indices: 684264--684306 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
684254 TGAAAATTAA
* *
684264 ATATATTTTTATTTTATCT
1 ATATATTTTGATTGTATCT
* *
684283 ATATCTTTTGATTGTATTT
1 ATATATTTTGATTGTATCT
684302 ATATA
1 ATATA
684307 CGTAATCATT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
ATATATTTTGATTGTATCT
Found at i:685633 original size:21 final size:21
Alignment explanation
Indices: 685604--685662 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
685594 TGACCGGGTT
*
685604 TTAT-ATTTATATATTTTTTA
1 TTATAATTTATTTATTTTTTA
*
685624 TTATAATTTATTTA-TTATTA
1 TTATAATTTATTTATTTTTTA
*
685644 TTAATAATTTCTTTATTTT
1 TT-ATAATTTATTTATTTT
685663 ATTTTTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.34
21 19 0.59
22 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATAATTTATTTATTTTTTA
Found at i:687186 original size:23 final size:23
Alignment explanation
Indices: 687160--687219 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
687150 TAATTCATTA
* *
687160 TCTTATTTTATTTTATTTATTT-T
1 TCTT-TTTTATATGATTTATTTAT
*
687183 TCTTTTTTTCTATGATTTATTTAT
1 TC-TTTTTTATATGATTTATTTAT
687207 TCATTTTTTATAT
1 TC-TTTTTTATAT
687220 AACATTTTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (23 bp):
TCTTTTTTATATGATTTATTTAT
Found at i:687298 original size:12 final size:12
Alignment explanation
Indices: 687281--687307 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
687271 GAATCGAGTT
687281 TTTAAATTTCAA
1 TTTAAATTTCAA
687293 TTTAAATTTCAA
1 TTTAAATTTCAA
687305 TTT
1 TTT
687308 TTCGCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:691867 original size:106 final size:106
Alignment explanation
Indices: 690972--691863 Score: 1386
Period size: 106 Copynumber: 8.5 Consensus size: 106
690962 TTCAATTTCA
* * *
690972 TTCAGAGTCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
* * *
691037 CGACGAAGGGACCACTGGTTGTCAATAAATAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* *
691078 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
*
691143 CGACGAAGGGACCGCTGGTTGTCAAC-AAC---TTCCCAAA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
691180 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
* **
691245 CGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCGTAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* *
691285 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTGAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
*
691350 CGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
691390 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
*
691455 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
691496 TTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCGAGACAATGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
* * *
691561 CAACGATGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* *
691602 TTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
* * *
691667 CAACGAAGGGA-CGATTGGTTGTCAACAAATAATTTCCCAAT
66 CGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAAT
* *
691708 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
* *
691773 CAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
691814 TTC-GAAGCCAATTTTAACTTCACAACGAAGGATATTAGACTCGAGACAAC
1 TTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
691864 ACAACTTTCA
Statistics
Matches: 737, Mismatches: 42, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
102 100 0.14
105 199 0.27
106 437 0.59
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
Found at i:692097 original size:124 final size:124
Alignment explanation
Indices: 691873--692097 Score: 353
Period size: 124 Copynumber: 1.8 Consensus size: 124
691863 CACAACTTTC
* * * * *
691873 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTCCACGACGGAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTCCACAACGAAGGGACCA
* *
691938 TCCACGGTTTCAACTTCACGATGAATGGAAACGTACACACAAGCAGCATTCATCTTTAG
66 TCCACGGTTTCAACCTCACGACGAATGGAAACGTACACACAAGCAGCATTCATCTTTAG
* *
691997 ATTGGATTTCAACTTCATGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCA
1 ATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTCCACAACGAAGGGACCA
692062 TCCACGGTTTCAACCTCACGACGAA-GGAAATCGTAC
66 TCCACGGTTTCAACCTCACGACGAATGGAAA-CGTAC
692098 CCACCAACAA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 5 0.05
124 86 0.95
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (124 bp):
ATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTCCACAACGAAGGGACCA
TCCACGGTTTCAACCTCACGACGAATGGAAACGTACACACAAGCAGCATTCATCTTTAG
Found at i:692267 original size:36 final size:36
Alignment explanation
Indices: 692208--692313 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
692198 CAAAACTAAG
* * * *
692208 TTTTATCTTTCTTGAGACGGTTTCTCTTGAAATAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
692244 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
692280 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACA
692314 CCAATCTTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:692766 original size:20 final size:20
Alignment explanation
Indices: 692737--692785 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
692727 TGATCGGGTT
*
692737 TTAT-ATTTATATATTTTTA
1 TTATAATTTATATATTATTA
*
692756 TTATAATTTATTTATTATTA
1 TTATAATTTATATATTATTA
692776 TTAATAATTT
1 TT-ATAATTT
692786 CTTTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATAATTTATATATTATTA
Found at i:694443 original size:12 final size:12
Alignment explanation
Indices: 694426--694452 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
694416 GAATCGAGTT
694426 TTTAAATTTCAA
1 TTTAAATTTCAA
694438 TTTAAATTTCAA
1 TTTAAATTTCAA
694450 TTT
1 TTT
694453 TTCGCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:695154 original size:27 final size:27
Alignment explanation
Indices: 695121--695174 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
695111 AATTAATAAC
695121 GTTGATAATATTAAACACATCAATTAA
1 GTTGATAATATTAAACACATCAATTAA
695148 GTTGATAATATTAAACACATCAATTAA
1 GTTGATAATATTAAACACATCAATTAA
695175 TCGAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (27 bp):
GTTGATAATATTAAACACATCAATTAA
Found at i:695188 original size:27 final size:27
Alignment explanation
Indices: 695130--695191 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
695120 CGTTGATAAT
* * *
695130 ATTAAACACATCAATTAAGTTGATAAT
1 ATTAAACACATCAATTAAGTCGAAAAA
695157 ATTAAACACATCAATTAA-TCGAAAAA
1 ATTAAACACATCAATTAAGTCGAAAAA
695183 ATTTAAACA
1 A-TTAAACA
695192 TCTAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 6 0.19
27 25 0.81
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (27 bp):
ATTAAACACATCAATTAAGTCGAAAAA
Found at i:695370 original size:81 final size:80
Alignment explanation
Indices: 695206--695449 Score: 425
Period size: 81 Copynumber: 3.0 Consensus size: 80
695196 AAAAAAGAAA
* *
695206 ATGATATAATTTAAGAATTTATTGTTATATTAAGCCTAAGAAAAACATAATATTCTTACATGTAA
1 ATGATATAATTTTAGAATTTATTGTTATATTAAGCCTAAG--AAACATAATATTCTTACATGCAA
695271 ATGCAGCACATTTAGTT
64 ATGCAGCACATTTAGTT
695288 ATGATATAATTTTAGAATTTATTGTTATATTAAGCCTAAGACAACATAATATTCTTACATGCAAA
1 ATGATATAATTTTAGAATTTATTGTTATATTAAGCCTAAGA-AACATAATATTCTTACATGCAAA
695353 TGCAGCACATTTAGTT
65 TGCAGCACATTTAGTT
*
695369 ATGATATAATTTTAGAATTTGTTGTTATATTAAGCCTAATGAAACATAATATTCTTACATGCAAA
1 ATGATATAATTTTAGAATTTATTGTTATATTAAGCCTAA-GAAACATAATATTCTTACATGCAAA
695434 TGCAGCACATTTAGTT
65 TGCAGCACATTTAGTT
695450 GAAGATCTCT
Statistics
Matches: 157, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
80 1 0.01
81 115 0.73
82 41 0.26
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (80 bp):
ATGATATAATTTTAGAATTTATTGTTATATTAAGCCTAAGAAACATAATATTCTTACATGCAAAT
GCAGCACATTTAGTT
Found at i:697228 original size:12 final size:12
Alignment explanation
Indices: 697211--697250 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
697201 ATTTGTTGTG
697211 TATACATACATA
1 TATACATACATA
*
697223 TATACATTCATA
1 TATACATACATA
* *
697235 TATATATATATA
1 TATACATACATA
697247 TATA
1 TATA
697251 TATATATGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (12 bp):
TATACATACATA
Found at i:697237 original size:2 final size:2
Alignment explanation
Indices: 697232--697257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
697222 ATATACATTC
697232 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
697258 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:700480 original size:4 final size:4
Alignment explanation
Indices: 700473--700519 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
700463 CATTTTCATT
*
700473 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC AATC CAT
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CAT
700520 TCTCTTGGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (4 bp):
CATC
Found at i:703194 original size:16 final size:16
Alignment explanation
Indices: 703166--703208 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
703156 AAGTTATATG
*
703166 ATATGATATATGTGATT
1 ATATGCTATATGTGA-T
703183 ATATGC-ATATGTGAT
1 ATATGCTATATGTGAT
703198 ATATGCTATAT
1 ATATGCTATAT
703209 AATATGACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 12 0.50
17 5 0.21
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (16 bp):
ATATGCTATATGTGAT
Found at i:703449 original size:23 final size:23
Alignment explanation
Indices: 703396--703494 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
703386 GTTCTATGCA
* *
703396 GTCCTTCAGGACA-ATTCTACGAG
1 GTCCTTCGGGACATA-TCTACGTG
703419 GTCCTTCGGGACATATCTACGTG
1 GTCCTTCGGGACATATCTACGTG
* *
703442 GTCCTTCGGAACAT-T-TATGTG
1 GTCCTTCGGGACATATCTACGTG
* * *
703463 GTCCTTCGAGACATTTCTATGTG
1 GTCCTTCGGGACATATCTACGTG
703486 G-CACTTCGG
1 GTC-CTTCGG
703495 TGTAATTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
21 17 0.26
22 3 0.05
23 44 0.68
24 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (23 bp):
GTCCTTCGGGACATATCTACGTG
Found at i:707040 original size:3 final size:3
Alignment explanation
Indices: 707032--707066 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
707022 GAATTGGGTT
*
707032 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG GTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
707067 TAATGATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:713201 original size:44 final size:43
Alignment explanation
Indices: 713130--713212 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
713120 TATGCACATG
* *
713130 TGATATATGCTATGAGATATGACCTATGTGCCTACATGTGAAA
1 TGATATAAGCTATGAGATATGACCTATGTGACTACATGTGAAA
* *
713173 TGATATAAGCTAT-ATGATTATGAGCTATGTGAGTACATGT
1 TGATATAAGCTATGA-GA-TATGACCTATGTGACTACATGT
713213 ATATTTGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.03
43 14 0.41
44 19 0.56
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.35
Consensus pattern (43 bp):
TGATATAAGCTATGAGATATGACCTATGTGACTACATGTGAAA
Found at i:713430 original size:23 final size:23
Alignment explanation
Indices: 713323--713419 Score: 158
Period size: 23 Copynumber: 4.2 Consensus size: 23
713313 GAGTCGAGGG
* *
713323 TTCTACACGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAT
*
713346 TTCTACGAGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
713369 TTCTACGCGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
*
713392 TTCTACGCGGTCCTTCGGGATAT
1 TTCTACGCGGTCCTTCGGGACAT
713415 TTCTA
1 TTCTA
713420 TGTGGCACTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:714047 original size:15 final size:16
Alignment explanation
Indices: 714027--714061 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
714017 AATTTTTACT
*
714027 ATGTTTTA-AAAGCAC
1 ATGTTTTAGAAAGCAA
714042 ATGTTTTAGAAAGCAA
1 ATGTTTTAGAAAGCAA
714058 ATGT
1 ATGT
714062 AACACCTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (16 bp):
ATGTTTTAGAAAGCAA
Found at i:715208 original size:14 final size:16
Alignment explanation
Indices: 715178--715211 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
715168 TTAGGGTTCC
715178 TATATAATATGACATA
1 TATATAATATGACATA
715194 TATATAATAT-A-ATA
1 TATATAATATGACATA
715208 TATA
1 TATA
715212 GTTCTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
TATATAATATGACATA
Found at i:715244 original size:17 final size:17
Alignment explanation
Indices: 715222--715277 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
715212 GTTCTTTTTG
715222 AAAATATATAGTTTATA
1 AAAATATATAGTTTATA
715239 AAAATATATA---TATA
1 AAAATATATAGTTTATA
* *
715253 ATATATATGTAGTTT-TA
1 A-AAATATATAGTTTATA
715270 AAAATATA
1 AAAATATA
715278 AAATATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 5 0.16
17 13 0.42
18 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAATATATAGTTTATA
Found at i:715284 original size:32 final size:32
Alignment explanation
Indices: 715225--715289 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
715215 CTTTTTGAAA
*
715225 ATATATAGTTTATAAAAATATATATATAATAT
1 ATATATAGTTTATAAAAATATAAATATAATAT
*
715257 ATATGTAGTTT-TAAAAATATAAAATATAATAT
1 ATATATAGTTTATAAAAATAT-AAATATAATAT
715289 A
1 A
715290 GTTTTGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (32 bp):
ATATATAGTTTATAAAAATATAAATATAATAT
Found at i:715304 original size:21 final size:20
Alignment explanation
Indices: 715277--715330 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
715267 TTAAAAATAT
715277 AAAATATAATATAG-TTTTG
1 AAAATATAATATAGTTTTTG
*
715296 AAAGTATATTATATAGTTTTTG
1 AAA--ATATAATATAGTTTTTG
715318 AAAATATAATATA
1 AAAATATAATATA
715331 TATTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.10
20 9 0.30
21 10 0.33
22 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (20 bp):
AAAATATAATATAGTTTTTG
Found at i:715309 original size:26 final size:27
Alignment explanation
Indices: 715225--715310 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 27
715215 CTTTTTGAAA
715225 ATATATAGTTTATAAAAATATATATATAAT
1 ATATATAGTTT-TAAAAATATATA-AT-AT
*
715255 ATATATGTAGTTTTAAAAATATAAAATAT
1 ATATA--TAGTTTTAAAAATATATAATAT
* * *
715284 A-ATATAGTTTTGAAAGTATATTATAT
1 ATATATAGTTTTAAAAATATATAATAT
715310 A
1 A
715311 GTTTTTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 19 0.39
28 3 0.06
29 3 0.06
30 7 0.14
31 11 0.22
32 6 0.12
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (27 bp):
ATATATAGTTTTAAAAATATATAATAT
Found at i:715319 original size:22 final size:21
Alignment explanation
Indices: 715277--715332 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
715267 TTAAAAATAT
715277 AAAATATA--ATATAGTTTTG
1 AAAATATATTATATAGTTTTG
*
715296 AAAGTATATTATATAGTTTTTG
1 AAAATATATTATATAG-TTTTG
*
715318 AAAATATAATATATA
1 AAAATATATTATATA
715333 TTATATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
21 6 0.19
22 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
AAAATATATTATATAGTTTTG
Found at i:715452 original size:15 final size:15
Alignment explanation
Indices: 715428--715464 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
715418 TATATTTATC
*
715428 ATTATCATTATCATT
1 ATTATTATTATCATT
715443 ATTATTATTATCATT
1 ATTATTATTATCATT
715458 ATTATTA
1 ATTATTA
715465 CCTATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATCATT
Found at i:715464 original size:12 final size:12
Alignment explanation
Indices: 715423--715462 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
715413 ATGTATATAT
*
715423 TTATCATTATCA
1 TTATCATTATTA
715435 TTATCATTATTA
1 TTATCATTATTA
* *
715447 TTATTATCATTA
1 TTATCATTATTA
715459 TTAT
1 TTAT
715463 TACCTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:717482 original size:23 final size:23
Alignment explanation
Indices: 717456--717536 Score: 135
Period size: 23 Copynumber: 3.5 Consensus size: 23
717446 TTCCTTTACG
717456 TGTCCCATAATACTTCTCAAACT
1 TGTCCCATAATACTTCTCAAACT
717479 TGTCCCATAATACTTCTCAAACT
1 TGTCCCATAATACTTCTCAAACT
* *
717502 TGTCCCATAATACTTCTTAAACA
1 TGTCCCATAATACTTCTCAAACT
*
717525 TGTCCCAAAATA
1 TGTCCCATAATA
717537 ATCTATATGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (23 bp):
TGTCCCATAATACTTCTCAAACT
Found at i:717980 original size:19 final size:19
Alignment explanation
Indices: 717956--718026 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
717946 AATTACCAAT
717956 AAATTCGCAACGTGATCTC
1 AAATTCGCAACGTGATCTC
* *
717975 AAATTCGCAACGCGAACTCC
1 AAATTCGCAACGTGATCT-C
* *
717995 AAATTCGCAACACTGAATTTC
1 AAATTCGCAAC-GTG-ATCTC
718016 AAATTCGCAAC
1 AAATTCGCAAC
718027 TCGATTTCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.37
20 12 0.28
21 13 0.30
22 2 0.05
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.23
Consensus pattern (19 bp):
AAATTCGCAACGTGATCTC
Found at i:718020 original size:21 final size:20
Alignment explanation
Indices: 717956--718026 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
717946 AATTACCAAT
* *
717956 AAATTCGCAACGTG-ATCTC
1 AAATTCGCAACCTGAATTTC
* *
717975 AAATTCGCAACGC-GAACTCC
1 AAATTCGCAAC-CTGAATTTC
717995 AAATTCGCAACACTGAATTTC
1 AAATTCGCAAC-CTGAATTTC
718016 AAATTCGCAAC
1 AAATTCGCAAC
718027 TCGATTTCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.29
20 14 0.33
21 16 0.38
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACCTGAATTTC
Found at i:718042 original size:20 final size:19
Alignment explanation
Indices: 718017--718086 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
718007 CTGAATTTCA
718017 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTT-TG
* *
718037 AATTCGTAACGCGAATTTTG
1 AATTCGCAACTCG-ATTTTG
** *
718057 TTTTCGCAAGTCGATTTTCG
1 AATTCGCAACTCGATTTT-G
718077 AATTCGCAAC
1 AATTCGCAAC
718087 ACAAATTTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 5 0.13
20 29 0.76
21 4 0.11
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (19 bp):
AATTCGCAACTCGATTTTG
Found at i:718064 original size:40 final size:40
Alignment explanation
Indices: 717996--718106 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 40
717986 GCGAACTCCA
* * *
717996 AATTCGCAACACTGAATTTCAAATTCGCAACTCGA-TTTCTG
1 AATTCGCAACAC-AAATTTTAATTTCGCAACTCGATTTTC-G
* * * ** *
718037 AATTCGTAACGCGAATTTTGTTTTCGCAAGTCGATTTTCG
1 AATTCGCAACACAAATTTTAATTTCGCAACTCGATTTTCG
718077 AATTCGCAACACAAATTTTAATTTCGCAAC
1 AATTCGCAACACAAATTTTAATTTCGCAAC
718107 ACAAATGTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
40 42 0.75
41 14 0.25
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (40 bp):
AATTCGCAACACAAATTTTAATTTCGCAACTCGATTTTCG
Found at i:718902 original size:12 final size:12
Alignment explanation
Indices: 718881--718914 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
718871 ACCACATTTC
*
718881 CAATACCAAACA
1 CAATATCAAACA
718893 CAATATCAAACA
1 CAATATCAAACA
*
718905 CAATCTCAAA
1 CAATATCAAA
718915 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:719052 original size:24 final size:24
Alignment explanation
Indices: 719025--719078 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
719015 GTATTCAAAA
719025 TTTGATCTTGGTCAATACTCAGAC
1 TTTGATCTTGGTCAATACTCAGAC
*
719049 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
719073 TTTGAT
1 TTTGAT
719079 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:722218 original size:194 final size:194
Alignment explanation
Indices: 721873--722240 Score: 634
Period size: 194 Copynumber: 1.9 Consensus size: 194
721863 TCCAAATACA
*
721873 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
1 TTCACGCAGCTCACTTCAAGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
721938 ACATCTAAAACCAACAAACATCAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACATCAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
*
722003 AACAAGTATATAACAGTTAACAACACTTGCACAAACTTCCCAATTTATGGATAAATACATCAAT
131 AACAAGTATATAACAGTTAACAACACTTGCACAAACTTACCAATTTATGGATAAATACATCAAT
*
722067 TTCACGCAGCTCACTTCAAGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACATTTTCTAC
1 TTCACGCAGCTCACTTCAAGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
*
722132 ACATTTAAAACCAACAAACATCAAATTATTGAATTCTAGGTACTT-AACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACATCAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
* *
722196 AACAAAG-AGTATATA-TGTTAACAACACTTGCTCAAACTTACCAAT
131 AAC-AAGTA-TATA-ACAGTTAACAACACTTGCACAAACTTACCAAT
722241 AACAAATGGT
Statistics
Matches: 165, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
193 23 0.14
194 141 0.85
195 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (194 bp):
TTCACGCAGCTCACTTCAAGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
ACATCTAAAACCAACAAACATCAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
AACAAGTATATAACAGTTAACAACACTTGCACAAACTTACCAATTTATGGATAAATACATCAAT
Done.