Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009233.1 Hibiscus syriacus cultivar Beakdansim tig00112852_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: 663203
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:341166 original size:29 final size:30
Alignment explanation
Indices: 341085--341232 Score: 117
Period size: 29 Copynumber: 5.0 Consensus size: 30
341075 TATCTTTGAA
* * *
341085 TTTAGATTTTTTACTCCTTAGTCTCTATAC
1 TTTAGATTTTTTACACCTTAGTCCCTAAAC
* **
341115 TTTAG-GTTTTTACATGTTAGTCCCTAAAC
1 TTTAGATTTTTTACACCTTAGTCCCTAAAC
*
341144 TTTAG-TTTTTTAC-CCTTAGGTCCCTAGAC
1 TTTAGATTTTTTACACCTTA-GTCCCTAAAC
* * *
341173 TTTAGATTTTTTACA-CTTAGGTCCTTAGTAT
1 TTTAGATTTTTTACACCTTA-GTCCCTA-AAC
* *
341204 TTTATA-TTTTTACCACCTTAGTCCTTAAA
1 TTTAGATTTTTTA-CACCTTAGTCCCTAAA
341233 TTAAAGGATA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.03
29 44 0.45
30 31 0.32
31 15 0.15
32 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTAGATTTTTTACACCTTAGTCCCTAAAC
Found at i:342446 original size:23 final size:23
Alignment explanation
Indices: 342401--342447 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
342391 TATACTTCTT
* *
342401 ATCTCTTATTTCTTATTCATATA
1 ATCTCTTAATTCATATTCATATA
342424 ATCTCTTAAATTCATATTC-TATA
1 ATCTCTT-AATTCATATTCATATA
342447 A
1 A
342448 CTTATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (23 bp):
ATCTCTTAATTCATATTCATATA
Found at i:342750 original size:18 final size:18
Alignment explanation
Indices: 342727--342778 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
342717 ATATAACACA
* *
342727 TATGTCTCGAAGGACCAT
1 TATGTCCCGAAGGACCAC
* *
342745 TATGTCCCAAAAGACCAC
1 TATGTCCCGAAGGACCAC
342763 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
342779 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:344917 original size:23 final size:23
Alignment explanation
Indices: 344872--344918 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
344862 TATACTTCTT
* *
344872 ATCTCTTATTTCTTATTCATATA
1 ATCTCTTAATTCATATTCATATA
344895 ATCTCTTACATTCATATTC-TATA
1 ATCTCTTA-ATTCATATTCATATA
344918 A
1 A
344919 CTTATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (23 bp):
ATCTCTTAATTCATATTCATATA
Found at i:345221 original size:18 final size:18
Alignment explanation
Indices: 345198--345249 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
345188 ATATAACACA
* *
345198 TATGTCTCGAAGGACCAT
1 TATGTCCCGAAGGACCAC
* *
345216 TATGTCCCAAAAGACCAC
1 TATGTCCCGAAGGACCAC
345234 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
345250 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:346853 original size:8 final size:8
Alignment explanation
Indices: 346842--346868 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
346832 TTTTATCCCC
346842 AAATTCTA
1 AAATTCTA
346850 AAATTCTA
1 AAATTCTA
346858 AAATTCTA
1 AAATTCTA
346866 AAA
1 AAA
346869 CTCTTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATTCTA
Found at i:347164 original size:17 final size:17
Alignment explanation
Indices: 347144--347179 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
347134 TTATTGGTGC
347144 TCAAGGTGCCTTGGTCA
1 TCAAGGTGCCTTGGTCA
347161 TCAAGGTGCCTTGGTCA
1 TCAAGGTGCCTTGGTCA
347178 TC
1 TC
347180 TATCTCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.31
Consensus pattern (17 bp):
TCAAGGTGCCTTGGTCA
Found at i:349942 original size:16 final size:16
Alignment explanation
Indices: 349921--349953 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
349911 TTGATTTTCT
*
349921 TAGCTAGCATTAGGGA
1 TAGCTAGCATTACGGA
349937 TAGCTAGCATTACGGA
1 TAGCTAGCATTACGGA
349953 T
1 T
349954 GGGCATGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (16 bp):
TAGCTAGCATTACGGA
Found at i:352545 original size:22 final size:21
Alignment explanation
Indices: 352503--352545 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
352493 ATTGGGAGTT
* *
352503 TTCTACAACAAAATTTATATA
1 TTCTACAACAAAACTAATATA
*
352524 TTCTACAACCAAACTAAGTATA
1 TTCTACAACAAAACTAA-TATA
352546 CTATGTAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (21 bp):
TTCTACAACAAAACTAATATA
Found at i:352813 original size:14 final size:14
Alignment explanation
Indices: 352794--352820 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
352784 GAGGAATTTG
352794 AAATTAAATTTATT
1 AAATTAAATTTATT
352808 AAATTAAATTTAT
1 AAATTAAATTTAT
352821 GACCAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTAAATTTATT
Found at i:354575 original size:4 final size:4
Alignment explanation
Indices: 354566--354859 Score: 570
Period size: 4 Copynumber: 73.5 Consensus size: 4
354556 TCCCAAATTT
* *
354566 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
354614 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
354662 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
354710 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
354758 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
354806 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
354854 ATAC AT
1 ATAC AT
354860 TTTTTTTGAA
Statistics
Matches: 288, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 288 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:365387 original size:3 final size:3
Alignment explanation
Indices: 365364--365410 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
365354 GAAGAAAAAG
* * *
365364 GAT G-T GAT CAT GAT CAT GAT GAT GAT GAT GAT GGT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
365411 CATCATCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:371990 original size:2 final size:2
Alignment explanation
Indices: 371985--372019 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
371975 GGAAGGGGGG
371985 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
372020 GTTAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:372426 original size:2 final size:2
Alignment explanation
Indices: 372383--372408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
372373 TTGAGAAATA
372383 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
372409 TTAAAATATT
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:376663 original size:24 final size:23
Alignment explanation
Indices: 376613--376663 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
376603 AAAATGTTCG
* *
376613 TTTAATGTTCGCGAACGTATTTG
1 TTTAATGTTCACGAACGTATTTA
376636 TTTATATGTTCACGAACGT-TTTCA
1 TTTA-ATGTTCACGAACGTATTT-A
376660 TTTA
1 TTTA
376664 GCGTTGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.47
Consensus pattern (23 bp):
TTTAATGTTCACGAACGTATTTA
Found at i:376739 original size:23 final size:21
Alignment explanation
Indices: 376690--376731 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
376680 CGTTTAGTGC
376690 TCATTTAATATTCGTTTATAT
1 TCATTTAATATTCGTTTATAT
* *
376711 TCATTTAGTGTTCGTTTATAT
1 TCATTTAATATTCGTTTATAT
376732 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TCATTTAATATTCGTTTATAT
Found at i:381529 original size:180 final size:181
Alignment explanation
Indices: 381200--381551 Score: 444
Period size: 180 Copynumber: 2.0 Consensus size: 181
381190 ACATTCTCCT
* * * * *
381200 CTGTTCCCACCAATTCACTCTTCTCCTGGGCATTTTGATAAACATCTGGCCTGCCAGACGACGAT
1 CTGTTCCCACCAATTCACTCCTCTCCTGGGCATTTTGAGAAACACCCGGCCTGCCAGACAACGAT
* * *
381265 TGTTTTATAAACTCAGACTCCCTGGCATTGGTTCGTGGGGTAACTGAAAACCCAGATGGGATTTC
66 TGTTCTATAAACTCAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTC
* * * *
381330 ACCTGAGGTTACTTTAACAGCTCCAAAAATTTCAGTTATTTCATTTCGCTC
131 ACCTGAGGTAACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTC
* * *
381381 CTGTT-CCACCAATTCACTCCTCTGCTGGGCATTTTGAGAAACACCCGGCCTTCTAGACAACGAT
1 CTGTTCCCACCAATTCACTCCTCTCCTGGGCATTTTGAGAAACACCCGGCCTGCCAGACAACGAT
* * * *
381445 TGTTCTATAAACTCA-AGCTCACTGGC-TGTGTTTCGTGGAGTTATTGAAAACCCAGATTTGG-T
66 TGTTCTATAAACTCAGA-CTCACTGGCAT-TGGTTCGTGGAGTAACTGAAAACCCAGA-TGGGAT
* *
381507 TTCATCTG-GAGTAACATTAACAGATCCTAAAATATCAGTTATTTC
128 TTCACCTGAG-GTAACATTAACAGATCCAAAAATATCAGTTATTTC
381552 CTGGAAGAGT
Statistics
Matches: 146, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
179 3 0.02
180 135 0.92
181 8 0.05
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (181 bp):
CTGTTCCCACCAATTCACTCCTCTCCTGGGCATTTTGAGAAACACCCGGCCTGCCAGACAACGAT
TGTTCTATAAACTCAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTC
ACCTGAGGTAACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTC
Found at i:382398 original size:13 final size:13
Alignment explanation
Indices: 382380--382408 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
382370 TTATACTTTC
382380 ATGAAATTACATT
1 ATGAAATTACATT
382393 ATGAAATTACATT
1 ATGAAATTACATT
382406 ATG
1 ATG
382409 GTGTTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (13 bp):
ATGAAATTACATT
Found at i:389389 original size:21 final size:21
Alignment explanation
Indices: 389363--389402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
389353 CCCCCTTTGA
*
389363 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
389384 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
389403 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:391355 original size:17 final size:17
Alignment explanation
Indices: 391333--391380 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
391323 TTTCAACATT
391333 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
391350 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
391367 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
391381 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:391663 original size:30 final size:31
Alignment explanation
Indices: 391614--391686 Score: 112
Period size: 30 Copynumber: 2.3 Consensus size: 31
391604 GGAGAAGAAT
391614 AGGTGTTAAATGTTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTTACATAATAAATTGA
*
391645 AGGTGTTCAATG-TTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTTACATAATAAATTGA
391675 AGAAGTGTTAAA
1 AG--GTGTTAAA
391687 GTAAGGGGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 20 0.53
31 11 0.29
32 7 0.18
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (31 bp):
AGGTGTTAAATGTTTTTACATAATAAATTGA
Found at i:392131 original size:76 final size:75
Alignment explanation
Indices: 391995--392201 Score: 299
Period size: 75 Copynumber: 2.7 Consensus size: 75
391985 CAAAGCCAAA
* * **
391995 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
392060 TTTGGCCCCGAG
65 TTT-GCCCCGAG
*
392072 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
392137 TTGCTCCGAG
66 TTGCCCCGAG
* * * *
392147 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
392202 CTTGTACAAC
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
74 17 0.14
75 40 0.34
76 36 0.30
77 26 0.22
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGCCCCGAG
Found at i:392278 original size:21 final size:21
Alignment explanation
Indices: 392239--392278 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
392229 TTTACACTTA
**
392239 GGAACCGATTCCCTTCAAGGG
1 GGAACCGATTCCCCCCAAGGG
392260 GGAACCGATTCCCCCCAAG
1 GGAACCGATTCCCCCCAAG
392279 CTCCAAGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (21 bp):
GGAACCGATTCCCCCCAAGGG
Found at i:393507 original size:19 final size:19
Alignment explanation
Indices: 393483--393520 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
393473 GATCAGATGT
393483 TCTTCGCTGAATTGATGAG
1 TCTTCGCTGAATTGATGAG
393502 TCTTCGCTGAATTGATGAG
1 TCTTCGCTGAATTGATGAG
393521 GGAAGCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
TCTTCGCTGAATTGATGAG
Found at i:398387 original size:5 final size:5
Alignment explanation
Indices: 398374--398419 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
398364 CTTGCAAGAG
* *
398374 GAAAT GAGAT GAGAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT G
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT G
398420 CAGGTGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:400911 original size:180 final size:180
Alignment explanation
Indices: 400588--400930 Score: 415
Period size: 180 Copynumber: 1.9 Consensus size: 180
400578 TCCTCTGTTC
* * * * * *
400588 CCACCAATTCACTCTTCTCCTGGGCATTTTGATAAACATCTGGCCTGCCAGACGACGATTGTTTT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* *
400653 ATAAACTCAGACTCCCTGGCATTGGTTCGTGGGGTAACTGAAAACCCAGATGGGATATCACCTGA
66 ATAAACTCAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATATCACCTGA
* * * * *
400718 GGTTACTTTAACAGCTCCAAAAATTTCATTTATCTCATTTCGCTCCTTTT
131 GGTAACATTAACAGATCCAAAAATATCAGTTATCTCATTTCGCTCCTTTT
* * *
400768 CCACCAATTCACTCCTCTGCTGGGCATTTTGACAAACACCCGGCCTTCTAGACAACGATTGTTCT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * * * * *
400833 ATAAACTCA-AGCTCACTGGC-TGTGTTTCGTGGAGTTATTGAAAACCCAGATTTGG-TTTCATC
66 ATAAACTCAGA-CTCACTGGCAT-TGGTTCGTGGAGTAACTGAAAACCCAGA-TGGGATATCACC
*
400895 TG-GAGTAACATTAACAGATCCTAAAATATCAGTTAT
128 TGAG-GTAACATTAACAGATCCAAAAATATCAGTTAT
400931 TTCCTGGAAG
Statistics
Matches: 136, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
179 3 0.02
180 130 0.96
181 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (180 bp):
CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
ATAAACTCAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATATCACCTGA
GGTAACATTAACAGATCCAAAAATATCAGTTATCTCATTTCGCTCCTTTT
Found at i:408172 original size:21 final size:23
Alignment explanation
Indices: 408148--408191 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
408138 CATACATAGC
408148 ATCTTTCA-GCTTT-GCTAGCCA
1 ATCTTTCACGCTTTCGCTAGCCA
*
408169 ATCTTTGACGCTTTCGCTAGCCA
1 ATCTTTCACGCTTTCGCTAGCCA
408192 CGGACTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (23 bp):
ATCTTTCACGCTTTCGCTAGCCA
Found at i:408851 original size:35 final size:35
Alignment explanation
Indices: 408812--408889 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
408802 GATGATATAT
* * * *
408812 CAAAATGATGTCATTTTAGATACTTGAAAAATCAC
1 CAAAACGATGTCATTCTAGATAATTGAAAAACCAC
408847 CAAAACGATGTCATTCTAGATAATTGAAAAACCAC
1 CAAAACGATGTCATTCTAGATAATTGAAAAACCAC
408882 CAAAACGA
1 CAAAACGA
408890 CGTCGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (35 bp):
CAAAACGATGTCATTCTAGATAATTGAAAAACCAC
Found at i:411206 original size:47 final size:46
Alignment explanation
Indices: 411098--411207 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 46
411088 GAAATATGTG
* *
411098 AAACAAATTTTTCGATTCGGTTCGATTCTGTAATACTATTTTTGAT
1 AAACAAATTTTTCGATTCGGTTCGATTCGGTAATACGATTTTTGAT
** * * *
411144 AAACTGA-TTTT---TTCGGTTCGGTTCGGTAATGCGGTTTTTGAT
1 AAACAAATTTTTCGATTCGGTTCGATTCGGTAATACGATTTTTGAT
411186 AAACCAAATTTTTCGATTCGGT
1 AAA-CAAATTTTTCGATTCGGT
411208 AATGAGTTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
42 29 0.58
43 2 0.04
44 4 0.08
45 4 0.08
46 5 0.10
47 6 0.12
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.44
Consensus pattern (46 bp):
AAACAAATTTTTCGATTCGGTTCGATTCGGTAATACGATTTTTGAT
Found at i:413571 original size:15 final size:15
Alignment explanation
Indices: 413547--413578 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
413537 TGGTAGATCC
*
413547 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
413562 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
413577 AA
1 AA
413579 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:415823 original size:21 final size:22
Alignment explanation
Indices: 415782--415824 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
415772 CATTATTTTA
* *
415782 TTGTTGCATGTTGATGACATGC
1 TTGTTGCAGGTTCATGACATGC
415804 TTGTTGCAGGTTCA-GACATGC
1 TTGTTGCAGGTTCATGACATGC
415825 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (22 bp):
TTGTTGCAGGTTCATGACATGC
Found at i:417500 original size:15 final size:15
Alignment explanation
Indices: 417480--417509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
417470 ATATCAACAC
417480 CATTTTGCATACATT
1 CATTTTGCATACATT
*
417495 CATTTTTCATACATT
1 CATTTTGCATACATT
417510 ACTCATAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (15 bp):
CATTTTGCATACATT
Found at i:425188 original size:18 final size:18
Alignment explanation
Indices: 425165--425201 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
425155 TCCAAGTTTA
425165 TCTTTTCAAAATTCAATT
1 TCTTTTCAAAATTCAATT
**
425183 TCTTTTTGAAATTCAATT
1 TCTTTTCAAAATTCAATT
425201 T
1 T
425202 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.54
Consensus pattern (18 bp):
TCTTTTCAAAATTCAATT
Found at i:425929 original size:122 final size:121
Alignment explanation
Indices: 425723--426158 Score: 678
Period size: 122 Copynumber: 3.6 Consensus size: 121
425713 TTCCAGAGAA
* * *
425723 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAAAAGAAGTTCATAATGAGAAGAACTTATTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
425788 ACCTTTGCATGACTCTATCACAGAAGGAAATAGATCATCATCAACTTTTCCAGAGAA-
66 ACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCC-G-GAAG
* *
425845 AGTTCATAATGAGAAGAACTTATCTTAAGAGGAATAAGAAGTTCATAATGAGAA-AAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAA-CTTGTTC
*
425909 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACGTTGCCGGAAGG
65 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCCGGAA-G
* *
425967 AGTTCATAATGAAAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
426032 ACCTTTGTATGACTCTCTCACAGAAGGAGATAGATCAACATCAACATTGCCGGAAGG
66 ACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCCGGAA-G
*
426089 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
426154 ACCTT
66 ACCTT
426159 AGCTTGATTC
Statistics
Matches: 293, Mismatches: 17, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
120 3 0.01
121 3 0.01
122 286 0.98
123 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (121 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCCGGAAG
Found at i:426510 original size:16 final size:16
Alignment explanation
Indices: 426461--426502 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
426451 GTTCATAATG
*
426461 AGAAGAACTCAACTGA
1 AGAAGAACTCATCTGA
*
426477 AGAAGAATTCATCTGA
1 AGAAGAACTCATCTGA
426493 AGAAGAACTC
1 AGAAGAACTC
426503 GTCCGAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (16 bp):
AGAAGAACTCATCTGA
Found at i:427060 original size:17 final size:16
Alignment explanation
Indices: 427037--427075 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
427027 ATTTTCCAAA
* *
427037 AAAATAAGTTAAATAG
1 AAAATAAATAAAATAG
427053 ATAAATAAATAAAATAG
1 A-AAATAAATAAAATAG
427070 AAAATA
1 AAAATA
427076 TGATAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (16 bp):
AAAATAAATAAAATAG
Found at i:427507 original size:2 final size:2
Alignment explanation
Indices: 427500--427609 Score: 213
Period size: 2 Copynumber: 55.5 Consensus size: 2
427490 ATTTTTATTT
427500 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
427542 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
427583 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
427610 TATATATAAT
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 106 0.99
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:435426 original size:33 final size:33
Alignment explanation
Indices: 435384--435446 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
435374 GGCGACATCG
*
435384 AAGGTCTGCTGCAACAGACGTGGTGGATGCTCC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
* *
435417 AAGGTCTGCTGCATCAGATGCGGTGGATGC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGC
435447 ATCCTCTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (33 bp):
AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
Found at i:440971 original size:5 final size:5
Alignment explanation
Indices: 440957--440992 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
440947 GCAAGAGGAG
* *
440957 ATGAG ATGAA ATGAA ATCAA ATGAA ATGAA ATGAA A
1 ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA A
440993 ATGCAGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.58, C:0.03, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGAA
Found at i:445018 original size:173 final size:173
Alignment explanation
Indices: 444725--445065 Score: 594
Period size: 173 Copynumber: 2.0 Consensus size: 173
444715 CAAAGCTGGA
*
444725 TTAGTGGGCATGACTTTGGGCATTAAGCATCTGACATGTCGATGACGTCAACACCTTATAGAAGG
1 TTAGTGGGCATGACTTTGGGCATTAAGCATCTAACATGTCGATGACGTCAACACCTTATAGAAGG
* * *
444790 TTCAATCACCGCTTCTAGAAGAACGAATGGACCAGTCGCACGTTTCTATAATTCGGATTTAAATT
66 TCCAATCACCGCTTCTAGAAGAACGAATGGACCAGCCGCACGTTTCTACAATTCGGATTTAAATT
444855 AAACTCATGTTTTAGGATATTATTTTAAATATTATATTTTATC
131 AAACTCATGTTTTAGGATATTATTTTAAATATTATATTTTATC
*
444898 TTAGTGGGCATGACTTTGGGCATTAAGCATCTAACATGGT-GATGACGTCAGCACCTTATAGAAG
1 TTAGTGGGCATGACTTTGGGCATTAAGCATCTAACAT-GTCGATGACGTCAACACCTTATAGAAG
* * *
444962 GTCCAATCATCGCTTTTAGAAGAACGAATGGATCAGCCGCACGTTTCTACAATTCGGATTTAAAT
65 GTCCAATCACCGCTTCTAGAAGAACGAATGGACCAGCCGCACGTTTCTACAATTCGGATTTAAAT
445027 TAAACTCATGTTTTAGGATATTATTTTAAATATTATATT
130 TAAACTCATGTTTTAGGATATTATTTTAAATATTATATT
445066 ATATTTTATC
Statistics
Matches: 159, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
173 157 0.99
174 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (173 bp):
TTAGTGGGCATGACTTTGGGCATTAAGCATCTAACATGTCGATGACGTCAACACCTTATAGAAGG
TCCAATCACCGCTTCTAGAAGAACGAATGGACCAGCCGCACGTTTCTACAATTCGGATTTAAATT
AAACTCATGTTTTAGGATATTATTTTAAATATTATATTTTATC
Found at i:445153 original size:19 final size:18
Alignment explanation
Indices: 445119--445159 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
445109 TTTTAAGTAT
445119 TTTAATTAGGATTTTATTC
1 TTTAATTAGGATTTTA-TC
445138 TTTAATATAGGA-TTTATC
1 TTTAAT-TAGGATTTTATC
445156 TTTA
1 TTTA
445160 CCTTGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTAATTAGGATTTTATC
Found at i:452396 original size:20 final size:20
Alignment explanation
Indices: 452371--452408 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
452361 CACATGTTAA
*
452371 AGAATGTATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
452391 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
452409 TCAAGAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:453249 original size:29 final size:30
Alignment explanation
Indices: 453154--453255 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
453144 GGTTCTTAGG
* *
453154 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
453184 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* * *
453214 GACCTCTGGATAGTTACTG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
453243 GACCTCTGGATAG
1 GACCTCTGGATAG
453256 GTCCTTCGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 21 0.31
30 46 0.69
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:455276 original size:23 final size:23
Alignment explanation
Indices: 455250--455304 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
455240 AATCCTTAGA
*
455250 CCTTATATTACACATTTAGCATC
1 CCTTATATTACACATTTACCATC
*
455273 CCTTCTATTACACATTTACCATC
1 CCTTATATTACACATTTACCATC
*
455296 CCTTGTATT
1 CCTTATATT
455305 TTCATTGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.42
Consensus pattern (23 bp):
CCTTATATTACACATTTACCATC
Found at i:457041 original size:34 final size:32
Alignment explanation
Indices: 456988--457058 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 32
456978 CCTTACAAAC
*
456988 TCCCTAGTTTTTCCGGGCTAAACTAGAACCAT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCAT
* *
457020 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCAT
457054 TCCCT
1 TCCCT
457059 TTTACAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCAT
Found at i:457297 original size:20 final size:22
Alignment explanation
Indices: 457272--457311 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
457262 AGTCGTATAT
457272 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
457292 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
457312 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:457491 original size:21 final size:22
Alignment explanation
Indices: 457458--457502 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
457448 GGAATTTGAG
457458 CCTTCAGGGGGGTA-TGGATACC
1 CCTTCAGGGGGGTATTGG-TACC
457480 CCTTCA-GGGGGTATTGGTACC
1 CCTTCAGGGGGGTATTGGTACC
457501 CC
1 CC
457503 ATAACATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (22 bp):
CCTTCAGGGGGGTATTGGTACC
Found at i:457789 original size:19 final size:18
Alignment explanation
Indices: 457734--457791 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
457724 TTGTTTAATG
*
457734 AAAAAGATATCAATTGTT
1 AAAAAGATACCAATTGTT
* *
457752 ACAAAAGGATACTAGTTGTT
1 A-AAAA-GATACCAATTGTT
457772 AAAAAGATAACCAATTGTT
1 AAAAAGAT-ACCAATTGTT
457791 A
1 A
457792 CCAATTGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.12
19 17 0.53
20 11 0.34
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:458849 original size:19 final size:20
Alignment explanation
Indices: 458806--458853 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
458796 TCTAAATCTT
*
458806 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
458826 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
458845 TTTTCAAAA
1 TTTTCAAAA
458854 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:459601 original size:32 final size:34
Alignment explanation
Indices: 459565--459634 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
459555 CCTTACAAAC
* *
459565 TCCCTAG-TTTTTC-CGGGCTAAACTAAAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAAAACATT
* *
459597 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGCTAAACTAAAACATT
459631 TCCC
1 TCCC
459635 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAAAACATT
Found at i:459945 original size:21 final size:21
Alignment explanation
Indices: 459919--459960 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
459909 TCACGATAGG
459919 GGGTATCGATACCCCTTCATA
1 GGGTATCGATACCCCTTCATA
*
459940 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACCCCTTCATA
459961 AAATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCCCTTCATA
Found at i:460013 original size:17 final size:17
Alignment explanation
Indices: 459991--460041 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
459981 GTTGCAGCCA
*
459991 GGGGGTATAGATACCCT
1 GGGGGTATAGATACCAT
*
460008 GGGGGTATTGATACCAT
1 GGGGGTATAGATACCAT
460025 GGGGGTATAGATACCAT
1 GGGGGTATAGATACCAT
460042 CCGAGCAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (17 bp):
GGGGGTATAGATACCAT
Found at i:460091 original size:21 final size:21
Alignment explanation
Indices: 460067--460106 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
460057 TTTGAGCCTT
460067 TAGGGGGTAT-GGATACCCCTG
1 TAGGGGGTATCGG-TACCCCTG
460088 TAGGGGGTATCGGTACCCC
1 TAGGGGGTATCGGTACCCC
460107 ATAACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (21 bp):
TAGGGGGTATCGGTACCCCTG
Found at i:460192 original size:30 final size:29
Alignment explanation
Indices: 460156--460226 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
460146 AATTATTTTT
* *
460156 AAAACATTTTAAAACTTAAATTTAAGTCTA
1 AAAACATTTTAAAA-TTAAATTCAAGTCCA
* *
460186 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTTT-AAAATTAAATTCAAGTCCA
460216 AAAACATTTTA
1 AAAACATTTTA
460227 CCTTAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAACATTTTAAAATTAAATTCAAGTCCA
Found at i:461711 original size:21 final size:22
Alignment explanation
Indices: 461656--461714 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
461646 ATAAGTTTTC
*
461656 TTTATCTCAATTTATTTTATTTA
1 TTTATCTCAATTTA-TTTATATA
**
461679 TTTAT-T-TGTTTATTTA-ATA
1 TTTATCTCAATTTATTTATATA
461698 TTTATCTCAATTTATTT
1 TTTATCTCAATTTATTT
461715 CTTTAAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.24
20 5 0.17
21 11 0.38
22 1 0.03
23 5 0.17
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTATCTCAATTTATTTATATA
Found at i:463562 original size:146 final size:148
Alignment explanation
Indices: 463297--463590 Score: 556
Period size: 146 Copynumber: 2.0 Consensus size: 148
463287 CGCAATGAAG
463297 ATAATGTGTTAGATAATGTAAAATAAAAATAAAAAAGGGAAAACAAAATAACTTAAAGCACTAAT
1 ATAATGTGTTAGATAATGTAAAATAAAAATAAAAAAGGGAAAACAAAATAACTTAAAGCACTAAT
463362 GTCAGAAAAAATAACAAAATCATAAATCTGGAAAACGTTGGGTCAACTTGAGAAAC-GTTTTTAG
66 GTCAGAAAAAATAACAAAATCATAAATCTGGAAAACGTTGGGTCAACTTGAGAAACAGTTTTTAG
463426 GGGGTTACCAGTGTCAAT
131 GGGGTTACCAGTGTCAAT
463444 ATAATGTGTTAGATAATGTAAAATAAAAAT-AAAAAGGGAAAACAAAATAACTTAAAGCACTAAT
1 ATAATGTGTTAGATAATGTAAAATAAAAATAAAAAAGGGAAAACAAAATAACTTAAAGCACTAAT
*
463508 GTCAGAAAAAATAACAAAATCATAAATCTGGAAAACGTTGGGTCAACTTGAGAAACATTTTTTTA
66 GTCAGAAAAAATAACAAAATCATAAATCTGGAAAACGTTGGGTCAACTTGAGAAACA-GTTTTTA
463573 GGGGGTTACCAGTGTCAA
130 GGGGGTTACCAGTGTCAA
463591 AATATTTTGG
Statistics
Matches: 144, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
146 90 0.62
147 30 0.21
148 24 0.17
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (148 bp):
ATAATGTGTTAGATAATGTAAAATAAAAATAAAAAAGGGAAAACAAAATAACTTAAAGCACTAAT
GTCAGAAAAAATAACAAAATCATAAATCTGGAAAACGTTGGGTCAACTTGAGAAACAGTTTTTAG
GGGGTTACCAGTGTCAAT
Found at i:467391 original size:15 final size:15
Alignment explanation
Indices: 467371--467403 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
467361 AGCAAGGCTC
467371 TTCGAGTGAAGCTTG
1 TTCGAGTGAAGCTTG
*
467386 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
467401 TTC
1 TTC
467404 AAATGGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.30, T:0.39
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:470242 original size:180 final size:180
Alignment explanation
Indices: 469919--470264 Score: 405
Period size: 180 Copynumber: 1.9 Consensus size: 180
469909 TCCTCTGTTC
* * * * *
469919 CCACCAATTCACTCTGCTCCTGGGCATTTTGATAAACATCTGGCCTGCCAGACGACGATTGTTTT
1 CCACCAATTCACTCTGCTCCTGGGCATTTTGAGAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * *
469984 ATAAACTCAGACTCCCATGCATTGGTTCGTGGGGTAACTGAAAACCCAGATGGGATTTCACCTGA
66 ATAAACTCAGACTCACATGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTCACATGA
* * *
470049 TGTTACTTTAACAGCTCCAAAAATTTCAGTTATTTCATTTCGCTCCTTTT
131 TGTTACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTCCTTTT
* * * *
470099 CCACCAATTCACTCTTCTGCTGGGCATTTTGAGAAACACCCGGCCTTCTAGACAACGATTGTTCT
1 CCACCAATTCACTCTGCTCCTGGGCATTTTGAGAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * * * ** *
470164 ATAAACTCCAG-CTCAC-TGGC-TGTGTTTCGTGGATTTATTGAAAACCCAGATTTTG-TTTCAT
66 ATAAACT-CAGACTCACAT-GCAT-TGGTTCGTGGAGTAACTGAAAACCCAGA-TGGGATTTCAC
*
470225 ATGGA-GTTACATTAACAGATCCTAAAATATCAGTTATTTC
127 AT-GATGTTACATTAACAGATCCAAAAATATCAGTTATTTC
470265 CTGTAAGAGT
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
179 2 0.01
180 129 0.93
181 7 0.05
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (180 bp):
CCACCAATTCACTCTGCTCCTGGGCATTTTGAGAAACACCCGGCCTGCCAGACAACGATTGTTCT
ATAAACTCAGACTCACATGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTCACATGA
TGTTACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTCCTTTT
Found at i:473522 original size:27 final size:28
Alignment explanation
Indices: 473429--473522 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
473419 ATTTACCCTT
473429 AAATTCAATATAGCCATTAGCCTACATC
1 AAATTCAATATAGCCATTAGCCTACATC
* * * *
473457 AAATT-AATAGTCGACTCAAATAGCAT-GAT-
1 AAATTCAATA-TAG-C-C-ATTAGCCTACATC
*
473486 TAATTCAATATAGCCATTAGCCTACATC
1 AAATTCAATATAGCCATTAGCCTACATC
473514 AAATT-AATA
1 AAATTCAATA
473523 GTCGACTCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 15
0.66 0.14 0.20
Matches are distributed among these distances:
26 6 0.12
27 11 0.22
28 12 0.24
29 7 0.14
30 7 0.14
31 6 0.12
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (28 bp):
AAATTCAATATAGCCATTAGCCTACATC
Found at i:474656 original size:225 final size:225
Alignment explanation
Indices: 474253--474676 Score: 667
Period size: 225 Copynumber: 1.9 Consensus size: 225
474243 CAGATTTGTT
* *
474253 AGATGTTGAAGCCACTCCGGAAGGTGCCGACACTTTGGAATATTTTTGAGATGGAGATACCGTAG
1 AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTCGAGATGGAGATACCGTAG
*
474318 GCTCGTATAATCTTGGAATATTTGGATGCCATCTGCAGATAGCTCAAGCTCCGTGCAGTCGATTA
66 GCTCGTATAATCTTGGAATATTTGGATGCCATCTGCAGATAGCTCAAGCTCCGTGCAGTCGACTA
* * *
474383 TTCGAAGCATTTCAAGGGAAGTGAGATGTTGGAATCCAGGAGAGAGTGACCTCAATCCACTGCAA
131 ATAGAAGCATTTCAAGGGAAGTGAGATGTTGGAATCCAGGAAAGAGTGACCTCAATCCACTGCAA
474448 TTCTCTATATGCAACGATTTCAAGTGAACA
196 TTCTCTATATGCAACGATTTCAAGTGAACA
* *
474478 AGATGTTGAAGCCACTCCGGAAGATGCCGACATTTTGGAATATTTTCGAG-TAGTAGATACCGTA
1 AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTCGAGAT-GGAGATACCGTA
* * * *
474542 GGCTCGTATAATCTTGGAATATTTGGATGCCCTCTTCAGATAGCTCGAGCTCCTTGCAGT-GACT
65 GGCTCGTATAATCTTGGAATATTTGGATGCCATCTGCAGATAGCTCAAGCTCCGTGCAGTCGACT
*
474606 AATAGAAAG-ACTTTCAAGGGAAGTTAGATGTTGGAA-CACAGGAAAGAGTGACCTCAATCCACT
130 AATAG-AAGCA-TTTCAAGGGAAGTGAGATGTTGGAATC-CAGGAAAGAGTGACCTCAATCCACT
474669 GCAATTCT
192 GCAATTCT
474677 TGATTTCTAG
Statistics
Matches: 182, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
224 9 0.05
225 173 0.95
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (225 bp):
AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTCGAGATGGAGATACCGTAG
GCTCGTATAATCTTGGAATATTTGGATGCCATCTGCAGATAGCTCAAGCTCCGTGCAGTCGACTA
ATAGAAGCATTTCAAGGGAAGTGAGATGTTGGAATCCAGGAAAGAGTGACCTCAATCCACTGCAA
TTCTCTATATGCAACGATTTCAAGTGAACA
Found at i:483614 original size:5 final size:5
Alignment explanation
Indices: 483604--483628 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
483594 CTTGCAAGAG
483604 GAAAT GAAAT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT
483629 TTAACAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:486913 original size:22 final size:23
Alignment explanation
Indices: 486872--486919 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
486862 AAAAGAAATG
486872 TAAATATAATATAATTTATAATA
1 TAAATATAATATAATTTATAATA
486895 TAAATAT-ATAT-ATTGTATAATA
1 TAAATATAATATAATT-TATAATA
486917 TAA
1 TAA
486920 GGACGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 14 0.58
23 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATATAATATAATTTATAATA
Found at i:487160 original size:20 final size:20
Alignment explanation
Indices: 487137--487175 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
487127 ATCCTTCGTC
*
487137 GTGAAATTGAAATCAAACTT
1 GTGAAACTGAAATCAAACTT
* *
487157 GTGAAGCTGAAATCGAACT
1 GTGAAACTGAAATCAAACT
487176 CAGAGTTCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
GTGAAACTGAAATCAAACTT
Found at i:487788 original size:211 final size:208
Alignment explanation
Indices: 487234--488070 Score: 1443
Period size: 211 Copynumber: 4.0 Consensus size: 208
487224 CGTTGTGGAG
* * * *
487234 CTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCATGAAGTTGAACTTGCGTTG
1 CTGAAATTGAGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
*
487299 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGA
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
*
487364 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCGGAGTCCAATATCCTTC-----
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCCGGAGTCCAATATCCTTCGTTGA
487424 -GTTGAAATTGGCT
195 AGTTGAAATTGGCT
*
487437 CTTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
1 C-TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
*
487502 TCTGGAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
* *
487567 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATACCCTTCGTTGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCCGGAGTCCAATATCCTTCG-T-T
487632 GAAGTTGAAATTGGCT
193 GAAGTTGAAATTGGCT
*
487648 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
487713 CTGGAGTCCAATATCCTTCGTTGTGAAGTTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
*
487778 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCCGGAGTCCAATATCCTTCG-T-T
487843 GAAGTTGAAATTGGCT
193 GAAGTTGAAATTGGCT
487859 CTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
487924 CTGGAGTCCAATATCCTTCGTTGTGAAGTTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
*
487989 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCGGAGTCCAATATCCTTCGTTGA
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCCGGAGTCCAATATCCTTCGTTGA
488054 AGTTGAAATTGGCT
195 AGTTGAAATTGGCT
488068 CTG
1 CTG
488071 GGTAAAACCT
Statistics
Matches: 609, Mismatches: 15, Indels: 14
0.95 0.02 0.02
Matches are distributed among these distances:
203 167 0.27
204 12 0.02
209 20 0.03
210 92 0.15
211 318 0.52
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (208 bp):
CTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAC
AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCCGGAGTCCAATATCCTTCGTTGAA
GTTGAAATTGGCT
Found at i:487821 original size:106 final size:105
Alignment explanation
Indices: 487424--488070 Score: 1208
Period size: 105 Copynumber: 6.2 Consensus size: 105
487414 AATATCCTTC
487424 GTTGAAATTGGCTCTTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 GTTGAAATTGGCTC-TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
487489 TGAACTTACGTTGTCTGGAATCCAATATCCTTCGTTGTGAA
65 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
487530 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
487595 GAACTTACGTTGTCTGGAGTCCAATACCCTTCGTTGTGAA
66 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
487635 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
487700 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
487740 GTTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 G-TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
487805 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
65 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
487846 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
487911 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
487951 GTTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 G-TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
488016 TGAACTTGCGTTGTCCGGAGTCCAATATCCTTCG-T-TGAA
65 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
488055 GTTGAAATTGGCTCTG
1 GTTGAAATTGGCTCTG
488071 GGTAAAACCT
Statistics
Matches: 532, Mismatches: 7, Indels: 7
0.97 0.01 0.01
Matches are distributed among these distances:
103 15 0.03
104 5 0.01
105 299 0.56
106 213 0.40
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
Found at i:501113 original size:22 final size:23
Alignment explanation
Indices: 501072--501119 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
501062 AAAAGAAATG
501072 TAAATATAATATAATTTATAATA
1 TAAATATAATATAATTTATAATA
501095 TAAATAT-ATAT-ATTGTATAATA
1 TAAATATAATATAATT-TATAATA
501117 TAA
1 TAA
501120 GGACGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 14 0.58
23 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATATAATATAATTTATAATA
Found at i:505960 original size:16 final size:17
Alignment explanation
Indices: 505939--505970 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
505929 ATTTGATATA
505939 ATTTTGGTTTA-ATAAT
1 ATTTTGGTTTATATAAT
505955 ATTTTGGTTTATATAA
1 ATTTTGGTTTATATAA
505971 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
ATTTTGGTTTATATAAT
Found at i:511098 original size:21 final size:20
Alignment explanation
Indices: 511012--511169 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
511002 AAATGACCAA
**
511012 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
511031 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
511051 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
511071 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
511092 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
511113 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
511133 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
511154 CAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
511170 ACACATAAAT
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 47 0.45
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:511159 original size:20 final size:20
Alignment explanation
Indices: 511012--511186 Score: 90
Period size: 20 Copynumber: 8.7 Consensus size: 20
511002 AAATGACCAA
511012 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
511031 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
511051 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
511070 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
511092 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
511112 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
511133 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
*
511154 CAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
511173 CATAAATCGCAACG
1 CA-AAATCGCAACG
511187 TGTATCCGTA
Statistics
Matches: 116, Mismatches: 30, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
18 1 0.01
19 16 0.14
20 53 0.46
21 43 0.37
22 3 0.03
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.18
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:511198 original size:20 final size:20
Alignment explanation
Indices: 511175--511445 Score: 332
Period size: 20 Copynumber: 13.6 Consensus size: 20
511165 CGCGAACACA
511175 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
511195 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
511215 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
* *
511235 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
511255 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
* *
511275 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
*
511295 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
*
511315 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
511335 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
511355 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
511375 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
511395 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
511415 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
511435 TAAATCACAAC
1 TAAATCGCAAC
511446 ACTGAAATTT
Statistics
Matches: 225, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
20 225 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGTGTATCCG
Found at i:512166 original size:24 final size:24
Alignment explanation
Indices: 512127--512173 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
512117 AAATTTGGTC
512127 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
512151 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
512174 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:514705 original size:33 final size:34
Alignment explanation
Indices: 514654--514798 Score: 161
Period size: 33 Copynumber: 4.2 Consensus size: 34
514644 CGGAAATTAC
* *
514654 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* *
514687 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAG
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
514721 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* * *
514759 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
514792 AATCGCA
1 AATCGCA
514799 TTGCGATTCT
Statistics
Matches: 97, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
32 1 0.01
33 48 0.49
34 15 0.15
36 2 0.02
38 15 0.15
39 16 0.16
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:514737 original size:19 final size:19
Alignment explanation
Indices: 514668--514804 Score: 150
Period size: 19 Copynumber: 7.7 Consensus size: 19
514658 GCAACGAGAG
514668 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
514687 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
514701 AATCGCAATGCGGAAATGAG
1 AATCGCAATGC-GAAATGAA
514721 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
514740 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
514759 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
514773 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
514792 AATCGCATTGCGA
1 AATCGCAATGCGA
514805 TTCTCCCGTT
Statistics
Matches: 99, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.22
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 54 0.55
20 15 0.15
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:514761 original size:72 final size:71
Alignment explanation
Indices: 514668--514804 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 71
514658 GCAACGAGAG
*
514668 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAGAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAAAATCGCAATGC
514732 GAAATGAA
64 GAAATGAA
* * * *
514740 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
514805 TTCTCCCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
71 18 0.31
72 40 0.68
73 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:514853 original size:19 final size:19
Alignment explanation
Indices: 514813--514910 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
514803 GATTCTCCCG
*
514813 TTGCGATTTTAATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
514833 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
514852 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
514866 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
514885 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
514904 TTGCGAT
1 TTGCGAT
514911 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 36 0.51
20 14 0.20
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:514907 original size:52 final size:53
Alignment explanation
Indices: 514794--514910 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
514784 GAAATTAAAA
514794 TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
* *
514847 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
514899 TCGCATTGCGAT
1 TCGCATTGCGAT
514911 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
Found at i:515043 original size:13 final size:14
Alignment explanation
Indices: 515016--515051 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
515006 CATCAATTAC
515016 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
515030 ACAAATCATC-TTT
1 ACAAATCAACTTTT
515043 ACAAATCAA
1 ACAAATCAA
515052 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:517049 original size:14 final size:14
Alignment explanation
Indices: 517030--517086 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
517020 GCGAAATGAA
*
517030 AATCGCAACGACAG
1 AATCGCAACGAAAG
517044 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
517061 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
517077 AATCGCAACG
1 AATCGCAACG
517087 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:517062 original size:33 final size:33
Alignment explanation
Indices: 517011--517103 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
517001 GCGAAACCAA
* *
517011 AATCACAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
517044 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
517077 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
517104 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:517068 original size:19 final size:19
Alignment explanation
Indices: 516974--517108 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
516964 TAGTTTACTT
* *
516974 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
516994 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
517013 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
517032 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
517046 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
517065 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
517079 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
517098 TCGCAATGCGA
1 TCGCAACGCGA
517109 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 45 0.47
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:517126 original size:19 final size:19
Alignment explanation
Indices: 517104--517232 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
517094 AAAATCGCAA
517104 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
517123 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
517137 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
517156 TGCGA--TT-CTAT--CGT
1 TGCGATTTTGGTTTCGCGT
**
517170 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
517189 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
517208 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
517228 TGCGA
1 TGCGA
517233 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 1 0.01
16 5 0.06
17 5 0.06
18 1 0.01
19 45 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:517146 original size:33 final size:33
Alignment explanation
Indices: 517104--517195 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
517094 AAAATCGCAA
*
517104 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TATCGT
517137 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
**
517170 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
517196 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
Found at i:517411 original size:93 final size:93
Alignment explanation
Indices: 517280--517746 Score: 886
Period size: 93 Copynumber: 5.1 Consensus size: 93
517270 ATGGATTGCA
517280 TTAC-TTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
517343 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
517371 TTACTTTCAATCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACATAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
517436 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
517464 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
517529 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
517557 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
517621 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
517649 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
517714 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
517742 TTACT
1 TTACT
517747 AAGCAATCTA
Statistics
Matches: 368, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 4 0.01
92 105 0.29
93 259 0.70
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:517610 original size:185 final size:186
Alignment explanation
Indices: 517280--517746 Score: 886
Period size: 185 Copynumber: 2.5 Consensus size: 186
517270 ATGGATTGCA
517280 TTAC-TTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
517343 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAATCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
517408 ATTTCACAGTGTTAAAGAATACATAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
517464 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
517529 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
517593 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
517649 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
517714 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
517747 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
184 4 0.01
185 183 0.66
186 91 0.33
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:519492 original size:32 final size:33
Alignment explanation
Indices: 519445--519558 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
519435 TCTTTTGGTT
*
519445 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
519478 GAAATG-AAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
519510 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
519543 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
519559 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 30 0.39
33 47 0.61
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:519523 original size:19 final size:19
Alignment explanation
Indices: 519499--519563 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
519489 GCAACTAGAG
519499 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
519518 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
519532 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
519551 AATCGCAATGCGA
1 AATCGCAACGCGA
519564 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:519537 original size:14 final size:14
Alignment explanation
Indices: 519453--519541 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 14
519443 TTGAAATGAA
519453 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
519467 AATCGTAACGCGAAATG
1 AATCGCAA--CGAGA-G
*
519484 AAATCGCAACTAGAG
1 -AATCGCAACGAGAG
*
519499 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
519518 AATCGCAACGAGAG
1 AATCGCAACGAGAG
519532 AATCGCAACG
1 AATCGCAACG
519542 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
14 27 0.47
15 2 0.03
16 8 0.14
17 3 0.05
18 8 0.14
19 10 0.17
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:519594 original size:14 final size:14
Alignment explanation
Indices: 519575--519631 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
519565 TTTGGTTTCG
519575 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
519589 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
519608 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
519622 CGTTGCGATT
1 CGTTGCGATT
519632 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:519609 original size:33 final size:33
Alignment explanation
Indices: 519572--519636 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
519562 GATTTTGGTT
519572 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
519605 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
519637 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:519672 original size:41 final size:41
Alignment explanation
Indices: 519615--519692 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
519605 TCGCGTTGCG
*
519615 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
519656 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
519693 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:519677 original size:20 final size:21
Alignment explanation
Indices: 519616--519691 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
519606 CGCGTTGCGA
519616 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
519637 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
519657 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
519678 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
519692 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:519813 original size:33 final size:33
Alignment explanation
Indices: 519771--519841 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
519761 AATACTAACT
*
519771 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
519804 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
519837 TGAAA
1 TGAAA
519842 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:520075 original size:22 final size:22
Alignment explanation
Indices: 520023--520077 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
520013 TGGTTGTGAG
**
520023 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
520045 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
520067 GGATTTCTTCG
1 GGATTTCTTCG
520078 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:520249 original size:20 final size:20
Alignment explanation
Indices: 520224--520316 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
520214 CTTTAAATAT
520224 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
520244 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
520264 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
520284 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
520304 CGCGTTGCGATTT
1 CGCGTTGCGATTT
520317 TGATATTCGC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.98
21 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:520325 original size:20 final size:20
Alignment explanation
Indices: 520284--520460 Score: 94
Period size: 20 Copynumber: 8.8 Consensus size: 20
520274 TTTACGGATA
*
520284 CGCGTTGCGATTTATG-TGTT
1 CGCGTTGCGATTT-TGATATT
520304 CGCGTTGCGATTTTGATATT
1 CGCGTTGCGATTTTGATATT
* *
520324 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT-GATATT
** *
520345 CGCAATGCGAATTTG-TACTAT
1 CGCGTTGCGATTTTGATA-T-T
* * * *
520366 CGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTT-GATATT
* *
520387 CGCGTTGCGATTTTGGAAACT
1 CGCGTTGCGATTTT-GATATT
** * **
520408 -GATTTGCGATTCTGGGGA-T
1 CGCGTTGCGATT-TTGATATT
*
520427 CGCGTTGCGATTTTTAT-TT
1 CGCGTTGCGATTTTGATATT
520446 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
520461 TTGGTCATTT
Statistics
Matches: 118, Mismatches: 30, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
19 20 0.17
20 51 0.43
21 46 0.39
23 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTTGATATT
Found at i:520353 original size:21 final size:21
Alignment explanation
Indices: 520303--520405 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
520293 ATTTATGTGT
* * *
520303 TCGCGTTGCGATTTT-GATAT
1 TCGCATTGCGATTTTGGAAAA
*
520323 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
520344 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
520365 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
520386 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
520406 CTGATTTGCG
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.25
21 47 0.72
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:520396 original size:42 final size:41
Alignment explanation
Indices: 520303--520460 Score: 112
Period size: 42 Copynumber: 3.9 Consensus size: 41
520293 ATTTATGTGT
* *
520303 TCGCGTTGCGATTTTGATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
520344 TCGCAATGCGAATTTG-TACTATCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGATA-T-TCGCATTGCGATTTTGCAA-AA
* * * ***
520386 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
520426 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
520461 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 20
0.70 0.15 0.16
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 26 0.29
42 29 0.33
43 1 0.01
44 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:526250 original size:21 final size:20
Alignment explanation
Indices: 526164--526321 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
526154 AAATGACCAA
**
526164 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
526183 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
526203 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
526223 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
526244 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
526265 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
526285 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
526306 CAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
526322 ACACATAAAT
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 47 0.45
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:526311 original size:20 final size:20
Alignment explanation
Indices: 526164--526338 Score: 90
Period size: 20 Copynumber: 8.7 Consensus size: 20
526154 AAATGACCAA
526164 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
526183 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
526203 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
526222 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
526244 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
526264 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
526285 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
*
526306 CAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
526325 CATAAATCGCAACG
1 CA-AAATCGCAACG
526339 TGTATCCGTA
Statistics
Matches: 116, Mismatches: 30, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
18 1 0.01
19 16 0.14
20 53 0.46
21 43 0.37
22 3 0.03
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.18
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:526350 original size:20 final size:20
Alignment explanation
Indices: 526327--526597 Score: 332
Period size: 20 Copynumber: 13.6 Consensus size: 20
526317 CGCGAACACA
526327 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
526347 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
526367 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
* *
526387 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
526407 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
* *
526427 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
*
526447 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
*
526467 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
526487 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
526507 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
526527 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
526547 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
526567 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
526587 TAAATCACAAC
1 TAAATCGCAAC
526598 ACTGAAATTT
Statistics
Matches: 225, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
20 225 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGTGTATCCG
Found at i:527318 original size:24 final size:24
Alignment explanation
Indices: 527279--527325 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
527269 AAATTTGGTC
527279 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
527303 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
527326 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:529857 original size:33 final size:34
Alignment explanation
Indices: 529806--529950 Score: 161
Period size: 33 Copynumber: 4.2 Consensus size: 34
529796 CGGAAATTAC
* *
529806 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* *
529839 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAG
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
529873 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* * *
529911 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
529944 AATCGCA
1 AATCGCA
529951 TTGCGATTCT
Statistics
Matches: 97, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
32 1 0.01
33 48 0.49
34 15 0.15
36 2 0.02
38 15 0.15
39 16 0.16
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:529889 original size:19 final size:19
Alignment explanation
Indices: 529820--529956 Score: 150
Period size: 19 Copynumber: 7.7 Consensus size: 19
529810 GCAACGAGAG
529820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
529839 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
529853 AATCGCAATGCGGAAATGAG
1 AATCGCAATGC-GAAATGAA
529873 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
529892 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
529911 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
529925 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
529944 AATCGCATTGCGA
1 AATCGCAATGCGA
529957 TTCTCCCGTT
Statistics
Matches: 99, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.22
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 54 0.55
20 15 0.15
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:529913 original size:72 final size:71
Alignment explanation
Indices: 529820--529956 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 71
529810 GCAACGAGAG
*
529820 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAGAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAAAATCGCAATGC
529884 GAAATGAA
64 GAAATGAA
* * * *
529892 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
529957 TTCTCCCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
71 18 0.31
72 40 0.68
73 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:530005 original size:19 final size:19
Alignment explanation
Indices: 529965--530062 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
529955 GATTCTCCCG
*
529965 TTGCGATTTTAATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
529985 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
530004 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
530018 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
530037 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
530056 TTGCGAT
1 TTGCGAT
530063 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 36 0.51
20 14 0.20
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:530059 original size:52 final size:53
Alignment explanation
Indices: 529946--530062 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
529936 GAAATTAAAA
529946 TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
* *
529999 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
530051 TCGCATTGCGAT
1 TCGCATTGCGAT
530063 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTAATTTCCGCATTGCGATTTTCATT
Found at i:530188 original size:14 final size:14
Alignment explanation
Indices: 530169--530205 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
530159 CATCAATTAC
530169 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
530183 ACAAATCATCTTTT
1 ACAAATCAACTTTT
530197 ACAAATCAA
1 ACAAATCAA
530206 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:532204 original size:14 final size:14
Alignment explanation
Indices: 532185--532241 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
532175 GCGAAATGAA
*
532185 AATCGCAACGACAG
1 AATCGCAACGAAAG
532199 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
532216 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
532232 AATCGCAACG
1 AATCGCAACG
532242 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:532217 original size:33 final size:33
Alignment explanation
Indices: 532166--532258 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
532156 GCGAAACCAA
* *
532166 AATCACAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
532199 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
532232 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
532259 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:532223 original size:19 final size:19
Alignment explanation
Indices: 532129--532263 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
532119 TAGTTTACTT
* *
532129 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
532149 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
532168 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
532187 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
532201 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
532220 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
532234 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
532253 TCGCAATGCGA
1 TCGCAACGCGA
532264 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 45 0.47
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:532281 original size:19 final size:19
Alignment explanation
Indices: 532259--532387 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
532249 AAAATCGCAA
532259 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
532278 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
532292 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
532311 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
532325 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
532344 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
532363 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
532383 TGCGA
1 TGCGA
532388 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:532301 original size:33 final size:33
Alignment explanation
Indices: 532259--532350 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
532249 AAAATCGCAA
532259 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
532292 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
532325 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
532351 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:532551 original size:93 final size:93
Alignment explanation
Indices: 532435--532903 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
532425 ATGGATTGCA
532435 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
532499 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
532527 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
532592 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
532620 TTACTTTCAACCAAAAGACAAAACAAAAACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
532685 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
532713 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
532778 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
532806 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
532871 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
532899 TTACT
1 TTACT
532904 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:534629 original size:14 final size:14
Alignment explanation
Indices: 534610--534699 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
534600 TTGAAATGAA
534610 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
534624 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
534643 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
534657 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
534676 AATCGCAACGAGAG
1 AATCGCAACGAGAG
534690 AATCGCAACG
1 AATCGCAACG
534700 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:534642 original size:33 final size:33
Alignment explanation
Indices: 534602--534716 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
534592 TCTTTTGGTT
534602 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
534635 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
534668 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
534701 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
534717 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:534648 original size:19 final size:19
Alignment explanation
Indices: 534624--534721 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
534614 GCAACGAGAG
534624 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
534643 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
534657 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
534676 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
534690 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
534709 AATCGCAATGCGA
1 AATCGCAACGCGA
534722 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:534752 original size:14 final size:14
Alignment explanation
Indices: 534733--534789 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
534723 TTTGGTTTCG
534733 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
534747 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
534766 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
534780 CGTTGCGATT
1 CGTTGCGATT
534790 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:534767 original size:33 final size:33
Alignment explanation
Indices: 534730--534794 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
534720 GATTTTGGTT
534730 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
534763 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
534795 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:534830 original size:41 final size:41
Alignment explanation
Indices: 534773--534850 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
534763 TCGCGTTGCG
*
534773 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
534814 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
534851 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:534835 original size:20 final size:21
Alignment explanation
Indices: 534774--534849 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
534764 CGCGTTGCGA
534774 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
534795 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
534815 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
534836 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
534850 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Done.