Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 117 of 313
Found at i:37945043 original size:20 final size:20
Alignment explanation
Indices: 37945018--37945057 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
37945008 TGCAACTTTG
37945018 AAAATT-TTTAATGTTTCCAA
1 AAAATTCTTTAA-GTTTCCAA
*
37945038 AAAATTCTTTGAGTTTCCAA
1 AAAATTCTTTAAGTTTCCAA
37945058 TTTAGTCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (20 bp):
AAAATTCTTTAAGTTTCCAA
Found at i:37945594 original size:21 final size:20
Alignment explanation
Indices: 37945566--37945633 Score: 50
Period size: 23 Copynumber: 3.2 Consensus size: 20
37945556 CACAACTTTT
37945566 TTAA-CTAATAATTCT-AAA
1 TTAATCTAATAATTCTAAAA
* *
37945584 TTAAATTCTAAATATTTTTAAAA
1 TT-AA-TCT-AATAATTCTAAAA
37945607 TTAATCTAATAATATACTAAAAA
1 TTAATCTAATAAT-T-CT-AAAA
37945630 TTAA
1 TTAA
37945634 AGGGCATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 5 0.13
21 6 0.16
22 10 0.26
23 13 0.34
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATCTAATAATTCTAAAA
Found at i:37951431 original size:20 final size:21
Alignment explanation
Indices: 37951389--37951430 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
37951379 CAATATTTGT
37951389 ATTTGTAGACTCGCTTAAAAA
1 ATTTGTAGACTCGCTTAAAAA
*
37951410 ATTTGTAGACTTGCTTAAAAA
1 ATTTGTAGACTCGCTTAAAAA
37951431 TACCGATGTT
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:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
ATTTGTAGACTCGCTTAAAAA
Found at i:37953631 original size:27 final size:27
Alignment explanation
Indices: 37953590--37953664 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
37953580 AGTATTGACA
* * *
37953590 CCTATTTGGAAGGCGTCAATGGTGGTG
1 CCTATCTGGGAGGCGCCAATGGTGGTG
37953617 CCTATCTAGGG-GGCGCCAATGGTGGTG
1 CCTATCT-GGGAGGCGCCAATGGTGGTG
*
37953644 CTTATCTGGGAGGCGCCAATG
1 CCTATCTGGGAGGCGCCAATG
37953665 CTTTGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.88
28 2 0.05
ACGTcount: A:0.17, C:0.20, G:0.37, T:0.25
Consensus pattern (27 bp):
CCTATCTGGGAGGCGCCAATGGTGGTG
Found at i:37953705 original size:19 final size:19
Alignment explanation
Indices: 37953681--37953721 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
37953671 TTTTTTCGGG
*
37953681 TTTAGGGTTATGTTATAAA
1 TTTAGGATTATGTTATAAA
*
37953700 TTTAGGATTATGTTATAGA
1 TTTAGGATTATGTTATAAA
37953719 TTT
1 TTT
37953722 TTGTGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTAGGATTATGTTATAAA
Found at i:37953964 original size:19 final size:19
Alignment explanation
Indices: 37953932--37953983 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
37953922 ATTCATACAA
37953932 ATTAT-TTA-AAATTTAGG
1 ATTATGTTATAAATTTAGG
37953949 ATTATGTTATAAATTTAGG
1 ATTATGTTATAAATTTAGG
37953968 ATTATGTTATAAATTT
1 ATTATGTTATAAATTT
37953984 TTGTGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 25 0.76
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
ATTATGTTATAAATTTAGG
Found at i:37954151 original size:260 final size:262
Alignment explanation
Indices: 37953681--37954188 Score: 948
Period size: 260 Copynumber: 1.9 Consensus size: 262
37953671 TTTTTTCGGG
* *
37953681 TTTAGGGTTATGTTATAAATTTAGGATTATGTTATAGATTTTTGTGTTTGTAATTATTTAAAATT
1 TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATT
37953746 CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
66 CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
37953811 TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
131 TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
*
37953876 TATATCCCGACATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAATTATTTAA
196 TATATCCCGACATTACAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAA
37953941 AA
261 AA
*
37953943 TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAATTT
1 TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATT
*
37954008 TAATTTATTAGTAATAAATTACAAAATTACTAATAAG-T-TACTAATAAATTTATAACATAATCC
66 CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
*
37954071 TAAATTACTAACAAATTAATTATAAAATAATTTCAATATTCATACAAAAAATTACAATATTACAA
131 TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
37954136 TATATCCCGACATTACAATATTCACACAAAATTACAATATTACAATATTCATA
196 TATATCCCGACATTACAATATTCACACAAAATTACAATATTACAATATTCATA
37954189 TAAAATTGCA
Statistics
Matches: 240, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
260 141 0.59
261 1 0.00
262 98 0.41
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (262 bp):
TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATT
CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
TATATCCCGACATTACAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAA
AA
Found at i:37954183 original size:27 final size:27
Alignment explanation
Indices: 37954147--37954203 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
37954137 ATATCCCGAC
37954147 ATTACAATATTCACACAAAATTACAAT
1 ATTACAATATTCACACAAAATTACAAT
* * *
37954174 ATTACAATATTCATATAAAATTGCAAT
1 ATTACAATATTCACACAAAATTACAAT
37954201 ATT
1 ATT
37954204 TTTTTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCACACAAAATTACAAT
Found at i:37954269 original size:22 final size:22
Alignment explanation
Indices: 37954244--37954330 Score: 120
Period size: 22 Copynumber: 3.7 Consensus size: 22
37954234 TCTATATTTA
37954244 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
37954266 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
*
37954293 GTATGAATATTGCAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
37954315 GTATGAATATTGTAAT
1 GTATGAATATTGTAAT
37954331 ATTGTAATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
22 32 0.55
23 1 0.02
24 4 0.07
25 4 0.07
26 1 0.02
27 16 0.28
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (22 bp):
GTATGAATATTGTAATTTTTTT
Found at i:37954298 original size:49 final size:49
Alignment explanation
Indices: 37954239--37954338 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
37954229 GATTATCTAT
*
37954239 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTAGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
* *
37954288 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA
1 ATTTAGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
37954337 AT
1 AT
37954339 ATTATAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
ATTTAGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:37954333 original size:8 final size:8
Alignment explanation
Indices: 37954320--37954391 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
37954310 TTTTTGTATG
37954320 AATATTGT
1 AATATTGT
37954328 AATATTGT
1 AATATTGT
*
37954336 AATATTAT
1 AATATTGT
*
37954344 AATTTTGTAT
1 AATATTG--T
37954354 GAATATTGT
1 -AATATTGT
* * *
37954363 AATGTCGGG
1 AATAT-TGT
37954372 ATATATTGT
1 A-ATATTGT
37954381 AATATTGT
1 AATATTGT
37954389 AAT
1 AAT
37954392 TTTTTGTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
8 34 0.69
9 5 0.10
10 4 0.08
11 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.47
Consensus pattern (8 bp):
AATATTGT
Found at i:37954577 original size:27 final size:27
Alignment explanation
Indices: 37954546--37954612 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
37954536 TAACATAAAT
*
37954546 TTCATTGGCGCCTCTCTATAAGGCACC
1 TTCATTGGCGCCTCTCTATAAGACACC
*
37954573 TTCATTGGCGCCTCTCTATGAGACACC
1 TTCATTGGCGCCTCTCTATAAGACACC
* *
37954600 TTTATTAGCGCCT
1 TTCATTGGCGCCT
37954613 ACCTGATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATAAGACACC
Found at i:37962307 original size:40 final size:40
Alignment explanation
Indices: 37962259--37962397 Score: 144
Period size: 40 Copynumber: 3.5 Consensus size: 40
37962249 AACACACCAG
*
37962259 TTTGCACCCAGTGCCTCATCGGATAATTC-GAAATAATAA
1 TTTGCACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
* * *
37962298 TTTGACACCCAGTGTCTCATCGGCTAA-ACTGAAGT-A-AA
1 TTTG-CACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
* **
37962336 TTAGCACCCAGTGCCTCATCAAAT-ATATCTGAAGTAATAA
1 TTTGCACCCAGTGCCTCATCGGATAAT-TCTGAAGTAATAA
*
37962376 TTTGACACCCAGTGTCTCATCG
1 TTTG-CACCCAGTGCCTCATCG
37962398 ACTCGAAGTC
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
36 1 0.01
37 16 0.20
38 12 0.15
39 7 0.09
40 29 0.36
41 15 0.19
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGCACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
Found at i:37963554 original size:16 final size:16
Alignment explanation
Indices: 37963533--37963565 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
37963523 TAATTTCTCC
*
37963533 TTTCTTTCTTTCTCTT
1 TTTCTTTCTTTCCCTT
37963549 TTTCTTTCTTTCCCTT
1 TTTCTTTCTTTCCCTT
37963565 T
1 T
37963566 CTGTTTTCGT
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTTTCCCTT
Found at i:37978455 original size:29 final size:29
Alignment explanation
Indices: 37978422--37978517 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 29
37978412 CAATTACAAA
37978422 TAAAATTATTTTATATTAATTATTGCAAT
1 TAAAATTATTTTATATTAATTATTGCAAT
* * *
37978451 TAAAATATAATATT-TA-CAATTATTTACAAT
1 TAAAAT-T-ATTTTATATTAATTA-TTGCAAT
37978481 ATAAAAATTATTTTATATTAATTATTGCAAT
1 -T-AAAATTATTTTATATTAATTATTGCAAT
37978512 TAAAAT
1 TAAAAT
37978518 ATAATATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
29 16 0.30
30 14 0.26
31 14 0.26
32 10 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAAATTATTTTATATTAATTATTGCAAT
Found at i:37978502 original size:61 final size:59
Alignment explanation
Indices: 37978415--37978527 Score: 208
Period size: 61 Copynumber: 1.9 Consensus size: 59
37978405 TTACTTACAA
37978415 TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
1 TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
37978474 TTACAATATAAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTA
1 TTACAA-AT-AAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTA
37978528 AAAAATTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
59 6 0.12
60 2 0.04
61 44 0.85
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (59 bp):
TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
Found at i:37979501 original size:4 final size:4
Alignment explanation
Indices: 37979494--37979519 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
37979484 TAAATTGATG
37979494 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
37979520 AATGTGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:37986741 original size:16 final size:16
Alignment explanation
Indices: 37986717--37986769 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
37986707 TAGCCAAAAT
*
37986717 ATTATTTATTTAATCA
1 ATTAATTATTTAATCA
*
37986733 ATTAATTATTTAATTA
1 ATTAATTATTTAATCA
* *
37986749 AATAATTTTTTCAATCCA
1 ATTAATTATTT-AAT-CA
37986767 ATT
1 ATT
37986770 CTAATTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 23 0.79
17 3 0.10
18 3 0.10
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATTATTTAATCA
Found at i:37987140 original size:15 final size:15
Alignment explanation
Indices: 37987122--37987152 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37987112 AGGGCTTAAA
37987122 TAATTATAATATTAT
1 TAATTATAATATTAT
37987137 TAATTATAATATTAT
1 TAATTATAATATTAT
37987152 T
1 T
37987153 TAGTCATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATAATATTAT
Found at i:37990425 original size:90 final size:89
Alignment explanation
Indices: 37990244--37990468 Score: 337
Period size: 90 Copynumber: 2.5 Consensus size: 89
37990234 TATGTAGCAT
* * * * *
37990244 CACCAAGGTGGTCATGCTAAAGAGAATGGTTCCACCAAAAT-AAAAT-AAAAATCATTTTTATGG
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATAATTTTTATGG
37990307 TGGTCACACCATTCTCAATGGCAC
66 TGGTCACACCATTCTCAATGGCAC
37990331 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATTAATTTTTATG
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAA-TAATTTTTATG
*
37990396 GTGGTCACGCCATTCTCAATGGCAC
65 GTGGTCACACCATTCTCAATGGCAC
* * * *
37990421 CACCAAAGTGGTCACGTCAAAGTGAATGACTCCACTAAAATAAAAATA
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATA
37990469 TTTTATTATT
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
87 37 0.30
88 5 0.04
89 5 0.04
90 78 0.62
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (89 bp):
CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATAATTTTTATGG
TGGTCACACCATTCTCAATGGCAC
Found at i:37992763 original size:22 final size:22
Alignment explanation
Indices: 37992705--37992763 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
37992695 TTTTTGCATG
* * *
37992705 TTATTTTCTTGTTATTTTGCTA
1 TTATTTTATTGTTATGTTACTA
* * * *
37992727 CTGTTTTACTATTATGTTACTA
1 TTATTTTATTGTTATGTTACTA
37992749 TTATTTTATTGTTAT
1 TTATTTTATTGTTAT
37992764 TGTTTGTATA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (22 bp):
TTATTTTATTGTTATGTTACTA
Found at i:37992830 original size:30 final size:30
Alignment explanation
Indices: 37992796--37992855 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
37992786 TATTTTATTA
37992796 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
37992826 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
37992856 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:37992991 original size:11 final size:11
Alignment explanation
Indices: 37992977--37993002 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
37992967 TATATATGTT
37992977 TAAAAATAATA
1 TAAAAATAATA
37992988 TAAAAATAATA
1 TAAAAATAATA
37992999 TAAA
1 TAAA
37993003 TAATTAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:37993289 original size:13 final size:14
Alignment explanation
Indices: 37993268--37993301 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
37993258 AACATACAAA
37993268 AATAATT-AAAAAT
1 AATAATTAAAAAAT
*
37993281 AATATTTAAAAAAT
1 AATAATTAAAAAAT
37993295 AATAATT
1 AATAATT
37993302 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATTAAAAAAT
Found at i:37994963 original size:30 final size:31
Alignment explanation
Indices: 37994903--37994963 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
37994893 TTGTTATTTT
* *
37994903 ATATATTTTTATAATTAAATTTTAATTTAAA
1 ATATATTTTTATAATTAAATTTGAAATTAAA
*
37994934 ATAT-TTTTTATTATTGAAA-TTGAAATTAAA
1 ATATATTTTTATAATT-AAATTTGAAATTAAA
37994964 CCGACATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
ATATATTTTTATAATTAAATTTGAAATTAAA
Found at i:38000646 original size:16 final size:16
Alignment explanation
Indices: 38000622--38000657 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38000612 CAGATTATGG
* *
38000622 ATTTTAAAATGTTAGT
1 ATTTCAAAATATTAGT
38000638 ATTTCAAAATATTAGT
1 ATTTCAAAATATTAGT
38000654 ATTT
1 ATTT
38000658 GTGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
ATTTCAAAATATTAGT
Found at i:38001984 original size:8 final size:9
Alignment explanation
Indices: 38001955--38001982 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
38001945 TAATCGATTC
38001955 AATTAAAAA
1 AATTAAAAA
38001964 AATTAAAAA
1 AATTAAAAA
38001973 AATTAAAAA
1 AATTAAAAA
38001982 A
1 A
38001983 TTTCGGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTAAAAA
Found at i:38006120 original size:8 final size:8
Alignment explanation
Indices: 38006107--38006132 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
38006097 TTATTGATTA
38006107 ATAAAATT
1 ATAAAATT
38006115 ATAAAATT
1 ATAAAATT
38006123 ATAAAATT
1 ATAAAATT
38006131 AT
1 AT
38006133 TATCTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAAAATT
Found at i:38006414 original size:17 final size:16
Alignment explanation
Indices: 38006394--38006436 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
38006384 AATATAAAAA
*
38006394 ATTATATATATTAAATT
1 ATTATAAAT-TTAAATT
38006411 ATTATAAATTTAAATT
1 ATTATAAATTTAAATT
38006427 -TTATACAATT
1 ATTATA-AATT
38006437 AACAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATAAATTTAAATT
Found at i:38006438 original size:15 final size:15
Alignment explanation
Indices: 38006392--38006438 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
38006382 TAAATATAAA
*
38006392 AAATTA-TATATATT
1 AAATTATTATAAATT
38006406 AAATTATTATAAATTT
1 AAATTATTATAAA-TT
38006422 AAATT-TTATACAATT
1 AAATTATTATA-AATT
38006437 AA
1 AA
38006439 CAAAATCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.21
15 14 0.48
16 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTATTATAAATT
Found at i:38010335 original size:13 final size:13
Alignment explanation
Indices: 38010317--38010367 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
38010307 AGTTGTTTAT
*
38010317 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
38010330 TGCTTTTCAGAAG
1 TGCTTTTCAGAAG
*
38010343 TACTTTTCAGAAG
1 TGCTTTTCAGAAG
*
38010356 TGCTTTTGAGAA
1 TGCTTTTCAGAA
38010368 ATTTGAGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTCAGAAG
Found at i:38010976 original size:22 final size:21
Alignment explanation
Indices: 38010951--38010994 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
38010941 AAGCATATGA
*
38010951 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
38010973 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
38010994 A
1 A
38010995 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:38017794 original size:20 final size:20
Alignment explanation
Indices: 38017743--38017794 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
38017733 ATCTATATTG
**
38017743 AAGTATCGATACTTTTCCTA
1 AAGTATCGATACTTTGACTA
* *
38017763 TAGTATCAATACTTTGACTA
1 AAGTATCGATACTTTGACTA
*
38017783 AAGTATTGATAC
1 AAGTATCGATAC
38017795 CTTCCTTAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
AAGTATCGATACTTTGACTA
Found at i:38025414 original size:20 final size:20
Alignment explanation
Indices: 38025370--38025415 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
38025360 ATCTATATTG
*
38025370 AAGTATCAATACCTTTCCTA
1 AAGTATCAATACCTTTACTA
*
38025390 TAGTATCAATA-CTTTGACTA
1 AAGTATCAATACCTTT-ACTA
38025410 AAGTAT
1 AAGTAT
38025416 TGATACCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
AAGTATCAATACCTTTACTA
Found at i:38030207 original size:12 final size:13
Alignment explanation
Indices: 38030187--38030225 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
38030177 TATTTTCTGA
38030187 AATTAAATATAAT
1 AATTAAATATAAT
38030200 AATT-AATATAA-
1 AATTAAATATAAT
38030211 AATTAAATATAAT
1 AATTAAATATAAT
38030224 AA
1 AA
38030226 ATTGGACCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 14 0.58
13 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:38039347 original size:229 final size:229
Alignment explanation
Indices: 38038941--38039403 Score: 908
Period size: 229 Copynumber: 2.0 Consensus size: 229
38038931 TAGGCTCTTA
*
38038941 ACATATTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
1 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
38039006 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
66 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
*
38039071 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTATCGTTAATA
131 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
38039136 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
196 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
38039170 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
1 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
38039235 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
66 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
38039300 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
131 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
38039365 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
196 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
38039399 ACATT
1 ACATT
38039404 GATCTTTTAA
Statistics
Matches: 232, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 232 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (229 bp):
ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
Found at i:38052688 original size:41 final size:41
Alignment explanation
Indices: 38052631--38052828 Score: 297
Period size: 41 Copynumber: 4.8 Consensus size: 41
38052621 TTATATAAAA
* * * *
38052631 CACCGGCATAAAGCCTGCTAGGCACAAAGTCCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
38052672 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGTTACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
38052713 CACCGGCACAGAGCTTGCTAGGCATAAAGCCCAATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
*
38052754 CACTGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
38052795 CACCGGTACAGAGCCTGCTAGGCATAAAACCCGA
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGA
38052829 ACTTACAAAG
Statistics
Matches: 141, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 141 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (41 bp):
CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
Found at i:38053032 original size:47 final size:47
Alignment explanation
Indices: 38052976--38053242 Score: 284
Period size: 47 Copynumber: 5.6 Consensus size: 47
38052966 ACATTCGGTC
* *
38052976 ATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAACT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * * * *
38053023 ATAGATTAATTCATTTCAATGTATAACAAAAATATATATATACATTCGACC
1 ATAGATTAATTCATTTCTATGCATAAC---AAT-TACATATACATTCAACT
* * * *
38053074 ATAGTTTAATTTATTTCTTTGCATAACAATTACATATACATTCAGCT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * * * *
38053121 ATAGATTAATTCATTTCAATGTATAACAAATATATATATACATTCGACC
1 ATAGATTAATTCATTTCTATGCATAAC-AAT-TACATATACATTCAACT
* * * *
38053170 ATAGTTTAATTTATTTCTTTGCATAACAATTACATATACATTCAGCT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
38053217 ATAGATTAATTCATTT-TCATGCATAA
1 ATAGATTAATTCATTTCT-ATGCATAA
38053243 AAAATATATT
Statistics
Matches: 176, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
46 1 0.01
47 92 0.52
48 9 0.05
49 35 0.20
50 3 0.02
51 36 0.20
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (47 bp):
ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
Found at i:38053213 original size:96 final size:96
Alignment explanation
Indices: 38052933--38053256 Score: 515
Period size: 96 Copynumber: 3.4 Consensus size: 96
38052923 TAACTTCAAA
* * ** * *
38052933 TAATTTATTTCAATACATAACAAATATATATATACATTCGGTCATAGTTTAATTCATTTCTCTGC
1 TAATTCATTTCAATGCATAACAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTTGC
*
38052998 ATAACAATTACATATACATTCAACTATAGAT
66 ATAACAATTACATATACATTCAGCTATAGAT
*
38053029 TAATTCATTTCAATGTATAACAAAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTT
1 TAATTCATTTCAATGCATAAC--AAATATATATATACATTCGACCATAGTTTAATTTATTTCTTT
38053094 GCATAACAATTACATATACATTCAGCTATAGAT
64 GCATAACAATTACATATACATTCAGCTATAGAT
*
38053127 TAATTCATTTCAATGTATAACAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTTGC
1 TAATTCATTTCAATGCATAACAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTTGC
38053192 ATAACAATTACATATACATTCAGCTATAGAT
66 ATAACAATTACATATACATTCAGCTATAGAT
* *
38053223 TAATTCATTTTC-ATGCATAAAAAATATATTTATA
1 TAATTCA-TTTCAATGCATAACAAATATATATATA
38053257 TATATACATA
Statistics
Matches: 214, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
96 119 0.56
97 4 0.02
98 91 0.43
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (96 bp):
TAATTCATTTCAATGCATAACAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTTGC
ATAACAATTACATATACATTCAGCTATAGAT
Found at i:38064009 original size:45 final size:46
Alignment explanation
Indices: 38063942--38064065 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
38063932 CATATGACCT
*
38063942 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
38063985 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
38064031 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
38064066 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:38064048 original size:46 final size:45
Alignment explanation
Indices: 38063942--38064176 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
38063932 CATATGACCT
*
38063942 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
38063985 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
38064031 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
38064068 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
38064105 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
38064142 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
38064177 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:38064069 original size:37 final size:37
Alignment explanation
Indices: 38064027--38064203 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
38064017 AGCTGAAGCT
* **
38064027 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
38064064 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
38064101 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
38064138 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
38064175 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
38064204 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:38071704 original size:45 final size:46
Alignment explanation
Indices: 38071637--38071760 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
38071627 CATATGACCT
*
38071637 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
38071680 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
38071726 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
38071761 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:38071743 original size:46 final size:45
Alignment explanation
Indices: 38071637--38071871 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
38071627 CATATGACCT
*
38071637 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
38071680 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
38071726 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
38071763 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
38071800 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
38071837 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
38071872 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:38071764 original size:37 final size:37
Alignment explanation
Indices: 38071722--38071898 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
38071712 AGCTGAAGCT
* **
38071722 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
38071759 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
38071796 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
38071833 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
38071870 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
38071899 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:38077577 original size:17 final size:17
Alignment explanation
Indices: 38077557--38077593 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
38077547 ACTTATACAC
*
38077557 ATTTAGTACAATTTCTA
1 ATTTAGCACAATTTCTA
*
38077574 ATTTAGCATAATTTCTA
1 ATTTAGCACAATTTCTA
38077591 ATT
1 ATT
38077594 AGCCCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTTAGCACAATTTCTA
Found at i:38083921 original size:88 final size:83
Alignment explanation
Indices: 38083796--38084014 Score: 278
Period size: 84 Copynumber: 2.6 Consensus size: 83
38083786 AAGTCACTGT
* * *
38083796 TTTTTTTTTACACTCAATTGGGTACTTGAACTT-TCAAAATGCATAAAAAGGCCCTCAAACTTTT
1 TTTTTTTTTGCACTCAATTGGATACTTGAA-TTGTCAAAATACATAAAAAGGCCCTCAAACTTTT
*
38083860 TCAAATAAAGCAATTAAGCCCC
65 TCAAA-AAA--AATTAAGCCAC
* *
38083882 TACTTTTTTTTGCACTTAATTGGATAATTGAATTGTCAAAATACATCAAAAAGGCCCTCAAACTT
1 T--TTTTTTTTGCACTCAATTGGATACTTGAATTGTCAAAATACAT-AAAAAGGCCCTCAAACTT
**
38083947 TTTCAAAAAAAATTAATTCAC
63 TTTCAAAAAAAATTAAGCCAC
* *
38083968 TTTTTTTTTGCACTCAATTGGATACTTGAACTGCCAAAATACATAAA
1 TTTTTTTTTGCACTCAATTGGATACTTGAATTGTCAAAATACATAAA
38084015 TTTATAAAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
83 3 0.03
84 39 0.33
86 10 0.09
87 2 0.02
88 38 0.32
89 25 0.21
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (83 bp):
TTTTTTTTTGCACTCAATTGGATACTTGAATTGTCAAAATACATAAAAAGGCCCTCAAACTTTTT
CAAAAAAAATTAAGCCAC
Found at i:38084425 original size:9 final size:10
Alignment explanation
Indices: 38084390--38084485 Score: 78
Period size: 9 Copynumber: 9.9 Consensus size: 10
38084380 TTCTTTTTCT
38084390 ATATTTCTAT-
1 ATATTT-TATA
38084400 ATATTTTATA
1 ATATTTTATA
*
38084410 ATATTTTATG
1 ATATTTTATA
38084420 AT-TTTTATA
1 ATATTTTATA
*
38084429 AAATTTTA-A
1 ATATTTTATA
38084438 ATATTTT-TA
1 ATATTTTATA
*
38084447 TATTTTTTATTA
1 -ATATTTTA-TA
* *
38084459 AAATTTAATA
1 ATATTTTATA
38084469 AT-TTTTATA
1 ATATTTTATA
38084478 AT-TTTTAT
1 ATATTTTAT
38084486 TGATTTTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
9 32 0.46
10 31 0.44
11 5 0.07
12 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
ATATTTTATA
Found at i:38084425 original size:19 final size:19
Alignment explanation
Indices: 38084390--38084452 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
38084380 TTCTTTTTCT
38084390 ATATTTCTATATATTTTATA
1 ATATTT-TATATATTTTATA
38084410 ATATTTTATGAT-TTTTATA
1 ATATTTTAT-ATATTTTATA
* *
38084429 AAATTTTAAATATTTT-T-
1 ATATTTTATATATTTTATA
38084446 ATATTTT
1 ATATTTT
38084453 TTATTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 21 0.55
20 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATATTTTATATATTTTATA
Found at i:38084475 original size:10 final size:10
Alignment explanation
Indices: 38084403--38084494 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
38084393 TTTCTATATA
38084403 TTTT-ATAAT
1 TTTTAATAAT
*
38084412 ATTTT-ATGAT
1 -TTTTAATAAT
*
38084422 TTTTATAAAAT
1 TTTTA-ATAAT
*
38084433 TTTAAAT-AT
1 TTTTAATAAT
*
38084442 TTTT-ATATT
1 TTTTAATAAT
* *
38084451 TTTTATTAAA
1 TTTTAATAAT
*
38084461 ATTTAATAAT
1 TTTTAATAAT
38084471 TTTT-ATAAT
1 TTTTAATAAT
* *
38084480 TTTTATTGAT
1 TTTTAATAAT
38084490 TTTTA
1 TTTTA
38084495 TTTTTTATCA
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
8 2 0.03
9 23 0.38
10 29 0.48
11 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:38084484 original size:19 final size:18
Alignment explanation
Indices: 38084403--38084509 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 18
38084393 TTTCTATATA
*
38084403 TTTTATAATATTTTATGAT
1 TTTTATAAT-TTTTATAAT
* *
38084422 TTTTATAAAATTTTAAATAT
1 TTTTAT-AATTTTTATA-AT
* *
38084442 TTTTATATTTTTTATTAAAA
1 TTTTATAATTTTTA-T-AAT
*
38084462 TTTAATAATTTTTATAAT
1 TTTTATAATTTTTATAAT
*
38084480 TTTTATTGATTTTTAT--T
1 TTTTA-TAATTTTTATAAT
*
38084497 TTTTATCATTTTT
1 TTTTATAATTTTT
38084510 TGCCACATGT
Statistics
Matches: 70, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
16 7 0.10
17 6 0.09
18 6 0.09
19 27 0.39
20 23 0.33
21 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATAATTTTTATAAT
Found at i:38084484 original size:48 final size:47
Alignment explanation
Indices: 38084390--38084500 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 47
38084380 TTCTTTTTCT
* * * * *
38084390 ATATTTCTATATATTTTATAATATTTTATGATTTTTATAAAATTTTAA
1 ATATTTTTATATTTTTTATAAAATTTAATAATTTTTATAAAATTTT-A
*
38084438 ATATTTTTATATTTTTTATTAAAATTTAATAATTTTTAT-AATTTTTA
1 ATATTTTTATATTTTTTA-TAAAATTTAATAATTTTTATAAAATTTTA
*
38084485 TTGATTTTTAT-TTTTT
1 AT-ATTTTTATATTTTT
38084501 ATCATTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
47 7 0.13
48 30 0.56
49 17 0.31
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (47 bp):
ATATTTTTATATTTTTTATAAAATTTAATAATTTTTATAAAATTTTA
Found at i:38084494 original size:29 final size:28
Alignment explanation
Indices: 38084402--38084509 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 28
38084392 ATTTCTATAT
* *
38084402 ATTTTATAATATTTTATGATTTTTATAAA
1 ATTTTATAAT-TTTTATAATTTTTATTAA
* *
38084431 ATTTTAAATATTTTTATATTTTTTATTAAA
1 ATTTTATA-ATTTTTATAATTTTTATT-AA
* *
38084461 ATTTAATAATTTTTATAATTTTTATT-G
1 ATTTTATAATTTTTATAATTTTTATTAA
* *
38084488 ATTTT-TATTTTTTATCATTTTT
1 ATTTTATAATTTTTATAATTTTT
38084510 TGCCACATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 15 0.23
27 4 0.06
29 37 0.56
30 10 0.15
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (28 bp):
ATTTTATAATTTTTATAATTTTTATTAA
Found at i:38084495 original size:10 final size:10
Alignment explanation
Indices: 38084440--38084496 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
38084430 AATTTTAAAT
38084440 ATTTTTA-TA
1 ATTTTTATTA
*
38084449 TTTTTTATTA
1 ATTTTTATTA
** *
38084459 AAATTTAATA
1 ATTTTTATTA
38084469 ATTTTTA-TA
1 ATTTTTATTA
*
38084478 ATTTTTATTG
1 ATTTTTATTA
38084488 ATTTTTATT
1 ATTTTTATT
38084497 TTTTATCATT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
9 15 0.39
10 23 0.61
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:38086396 original size:90 final size:93
Alignment explanation
Indices: 38086234--38086465 Score: 244
Period size: 93 Copynumber: 2.5 Consensus size: 93
38086224 CGCCCCTAGC
* * * * *
38086234 CTTTTTGATGCATTTTTG-CAGTTCAAGTGCCCAATT-AGTACTAAAAAAGAGCAGATGCTTAAT
1 CTTTTTGATGCA-TTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGATGATTAAT
*
38086297 TGCT-TTTTTTGGAAAAAGTTTAAGG-GA
65 TGCTGTTTTTTGGAAAAAGTTTAAGGTCA
*
38086324 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAGAAAAAAAAG-AGGTGATTAAT
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCA-AAAAAAAAGCAGATGATTAAT
**** * *
38086388 TG-TGTTTTTTTTTTTAAATTTTGAGGTCA
65 TGCTG-TTTTTTGGAAAAAGTTTAAGGTCA
* * *
38086417 TTTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAA
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAA
38086466 CAAGACTTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
89 5 0.04
90 30 0.25
91 22 0.18
92 24 0.20
93 39 0.32
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (93 bp):
CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGATGATTAATT
GCTGTTTTTTGGAAAAAGTTTAAGGTCA
Found at i:38087062 original size:39 final size:38
Alignment explanation
Indices: 38086989--38087095 Score: 119
Period size: 39 Copynumber: 2.8 Consensus size: 38
38086979 ATGTGATGCC
* * **
38086989 AAAATCTTTAACGGATGTCAAAATCTCTAACAAATA-T
1 AAAATCTCTAACTGATACCAAAATCTCTAACAAATACT
38087026 AAAAAAT-TCTAACTGATACCAAAATCTCTAACCAAATACT
1 --AAAATCTCTAACTGATACCAAAATCTCTAA-CAAATACT
* *
38087066 AAAGTCTCTAATTGATACCAAAATCTCTAA
1 AAAATCTCTAACTGATACCAAAATCTCTAA
38087096 TGGATACCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
38 24 0.41
39 34 0.58
40 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.28
Consensus pattern (38 bp):
AAAATCTCTAACTGATACCAAAATCTCTAACAAATACT
Found at i:38087092 original size:19 final size:19
Alignment explanation
Indices: 38086982--38087108 Score: 87
Period size: 19 Copynumber: 6.6 Consensus size: 19
38086972 AAGCCTAATG
* *
38086982 TGATGCCAAAATCTTTAAC
1 TGATACCAAAATCTCTAAC
* **
38087001 GGATGTCAAAATCTCTAAC
1 TGATACCAAAATCTCTAAC
** **
38087020 AAATATAAAAAAT-TCTAAC
1 TGATA-CCAAAATCTCTAAC
38087039 TGATACCAAAATCTCTAACC
1 TGATACCAAAATCTCTAA-C
** * * *
38087059 AAATACTAAAGTCTCTAAT
1 TGATACCAAAATCTCTAAC
38087078 TGATACCAAAATCTCTAA-
1 TGATACCAAAATCTCTAAC
38087096 TGGATACCAAAAT
1 T-GATACCAAAAT
38087109 TTGTAACCAA
Statistics
Matches: 83, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
18 6 0.07
19 57 0.69
20 20 0.24
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.28
Consensus pattern (19 bp):
TGATACCAAAATCTCTAAC
Found at i:38087144 original size:13 final size:13
Alignment explanation
Indices: 38087126--38087151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38087116 CAAATACCAC
38087126 AATCTCTAACAAA
1 AATCTCTAACAAA
38087139 AATCTCTAACAAA
1 AATCTCTAACAAA
38087152 TACCAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
AATCTCTAACAAA
Found at i:38087165 original size:19 final size:19
Alignment explanation
Indices: 38087007--38087167 Score: 102
Period size: 19 Copynumber: 8.7 Consensus size: 19
38086997 TAACGGATGT
*
38087007 CAAAATCTCTAACAAATATA
1 CAAAATCTCTAACAAATA-C
* **
38087027 AAAAAT-TCTAACTGATAC
1 CAAAATCTCTAACAAATAC
38087045 CAAAATCTCTAACCAAATAC
1 CAAAATCTCTAA-CAAATAC
* * ***
38087065 TAAAGTCTCTAATTGATAC
1 CAAAATCTCTAACAAATAC
***
38087084 CAAAATCTCTAATGGATAC
1 CAAAATCTCTAACAAATAC
* *
38087103 CAAAATTTGTAACCAAATAC
1 CAAAATCTCTAA-CAAATAC
*
38087123 CACAATCTCTAAC----A-
1 CAAAATCTCTAACAAATAC
38087137 -AAAATCTCTAACAAATAC
1 CAAAATCTCTAACAAATAC
*
38087155 CAAAATTTCTAAC
1 CAAAATCTCTAAC
38087168 CATATATAGA
Statistics
Matches: 107, Mismatches: 25, Indels: 19
0.71 0.17 0.13
Matches are distributed among these distances:
13 11 0.10
15 1 0.01
17 1 0.01
18 5 0.05
19 56 0.52
20 33 0.31
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (19 bp):
CAAAATCTCTAACAAATAC
Found at i:38094232 original size:35 final size:33
Alignment explanation
Indices: 38094151--38094235 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
38094141 AAAACACGAG
* * *
38094151 AATTTTTGAAAACACGAGAATTTGTAAACACGAA
1 AATTTTT-AAAACACGAAAATTTGTAAAAAAGAA
*
38094185 AA-TTTTAGAAACACGAAAATTTTTAGAAAAAAGAA
1 AATTTTTA-AAACACGAAAATTTGT--AAAAAAGAA
38094220 AATTTTTAAAACACGA
1 AATTTTTAAAACACGA
38094236 CATTTTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 1 0.02
33 18 0.42
34 2 0.05
35 17 0.40
36 5 0.12
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (33 bp):
AATTTTTAAAACACGAAAATTTGTAAAAAAGAA
Found at i:38094343 original size:52 final size:52
Alignment explanation
Indices: 38094286--38094498 Score: 150
Period size: 52 Copynumber: 4.1 Consensus size: 52
38094276 GCGAGAATAT
* *
38094286 TTTGAAACACAAATTTTTTTTTAAACACGAGAATTTTTGAAAACATGAAAAC
1 TTTGAAACACGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
* * ** * *
38094338 TTTGAAACACCGGA-GTTTTTGAAAACACGAGAATTTGTG-AAACACGAAAAT
1 TTTGAAACA-CGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
* * * * **
38094389 TTGTGAAAACACGTATTTTTTTTTAAAAACACGAAAATTTTTG-AAACGCCAGAATT
1 TT-TG-AAACACGAATTTTTTTTT--AAACACGAGAATTTTTGAAAACACGA-AAAC
** ** *
38094445 TTTGAAAACACGAA-GATTTTCAAAACACGAAAATTTTTGAAAACAC-AAAA-
1 TTTG-AAACACGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
38094495 TTTG
1 TTTG
38094499 TTGAACAGGG
Statistics
Matches: 129, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
50 4 0.03
51 14 0.11
52 53 0.41
53 17 0.13
54 4 0.03
55 32 0.25
56 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (52 bp):
TTTGAAACACGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
Found at i:38094396 original size:35 final size:35
Alignment explanation
Indices: 38094302--38094503 Score: 144
Period size: 35 Copynumber: 5.7 Consensus size: 35
38094292 ACACAAATTT
* * *
38094302 TTTTTTAAACACGAGAATTTTTGAAAACATGAAAA
1 TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
* * * *
38094337 -CTTTGAAACACCG-GAGTTTTTGAAAACACGAGAA
1 TTTTTGAAACA-CGAAAATTTTTGAAAACACGAAAA
* * ***
38094371 TTTGTGAAACACGAAAATTTGTGAAAACACGTATTTT
1 TTTTTGAAACACGAAAATTTTTGAAAACACG-A-AAA
* * * *
38094408 TTTTTAAAAACACGAAAATTTTTG-AAACGCCAGAA
1 TTTTT-GAAACACGAAAATTTTTGAAAACACGAAAA
* *
38094443 TTTTTGAAAACACGAAGA-TTTTCAAAACACGAAAA
1 TTTTTG-AAACACGAAAATTTTTGAAAACACGAAAA
38094478 TTTTTGAAAACAC-AAAATTTGTTGAA
1 TTTTTG-AAACACGAAAATTT-TTGAA
38094504 CAGGGAATTT
Statistics
Matches: 128, Mismatches: 29, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
34 35 0.27
35 62 0.48
36 6 0.05
37 9 0.07
38 16 0.12
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (35 bp):
TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:38094456 original size:90 final size:89
Alignment explanation
Indices: 38094319--38094490 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 89
38094309 AACACGAGAA
* * * * *
38094319 TTTTTGAAAACATGAAAACTTTGAAACACCGGAGTTTTTGAAAACACG-AGAATTTGT-GAAACA
1 TTTTTAAAAACACGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAG-ATTT-TCAAAACA
38094382 CGAAAATTTGTGAAAACACGTATTTT
64 CGAAAATTTGTGAAAACACGTATTTT
* *
38094408 TTTTTAAAAACACGAAAATTTTTGAAACGCCAGAATTTTTGAAAACACGAAGATTTTCAAAACAC
1 TTTTTAAAAACACGAAAA-CTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTTCAAAACAC
*
38094473 GAAAATTTTTGAAAACAC
65 GAAAATTTGTGAAAACAC
38094491 AAAATTTGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 17 0.24
90 53 0.74
91 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (89 bp):
TTTTTAAAAACACGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTTCAAAACACG
AAAATTTGTGAAAACACGTATTTT
Found at i:38094502 original size:18 final size:18
Alignment explanation
Indices: 38094135--38094503 Score: 194
Period size: 18 Copynumber: 21.4 Consensus size: 18
38094125 ACGAAAGTTT
* *
38094135 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
38094153 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
38094171 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
38094187 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
38094204 TTTTTAGAAAA-AAGAAAA
1 TTTTT-GAAAACACGAAAA
**
38094222 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
38094240 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
38094254 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
* ** *
38094268 --ATTG-AAATGCGAGAA
1 TTTTTGAAAACACGAAAA
*
38094283 TATTTTG-AAACAC-AAATT
1 T-TTTTGAAAACACGAAA-A
** *
38094301 TTTTTTTAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
38094319 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
38094337 -CTTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
38094353 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
38094371 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* ***
38094388 TTTGTGAAAACACGTATTTT
1 TTTTTGAAAACACG-A-AAA
*
38094408 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
38094426 TTTTTG-AAACGCCAGAA
1 TTTTTGAAAACACGAAAA
*
38094443 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
*
38094461 -TTTTCAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
38094478 TTTTTGAAAACAC-AAAA
1 TTTTTGAAAACACGAAAA
38094495 TTTGTTGAA
1 TTT-TTGAA
38094504 CAGGGAATTT
Statistics
Matches: 268, Mismatches: 54, Indels: 58
0.71 0.14 0.15
Matches are distributed among these distances:
12 8 0.03
14 7 0.03
15 3 0.01
16 24 0.09
17 87 0.32
18 120 0.45
19 7 0.03
20 12 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:38094571 original size:18 final size:16
Alignment explanation
Indices: 38094543--38094604 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
38094533 AATTGATCAT
38094543 CGAAATTTTTGAGAACA
1 CGAAATTTTTGA-AACA
38094560 CGAAATTTTTTGAAACA
1 CGAAA-TTTTTGAAACA
* *
38094577 CCAGGATTTTTGAAAACA
1 CGA-AATTTTTG-AAACA
38094595 CGAAATTTTT
1 CGAAATTTTT
38094605 TTAAATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (16 bp):
CGAAATTTTTGAAACA
Found at i:38094605 original size:18 final size:17
Alignment explanation
Indices: 38094135--38094604 Score: 153
Period size: 18 Copynumber: 27.3 Consensus size: 17
38094125 ACGAAAGTTT
*
38094135 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
38094153 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
*
38094171 --TTTGTAAACACGAAA
1 TTTTTGAAAACACGAAA
*
38094186 ATTTT-AGAAACACGAAAA
1 TTTTTGA-AAACACG-AAA
*
38094204 TTTTTAGAAAA-AAGAAAA
1 TTTTT-GAAAACACG-AAA
*
38094222 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-A-A
38094240 TTTTTG-AAACACG--A
1 TTTTTGAAAACACGAAA
*
38094254 --TTT-AAAAAAC-AAA
1 TTTTTGAAAACACGAAA
** **
38094267 -AATTG-AAATGCGAGAA
1 TTTTTGAAAACACGA-AA
38094283 TATTTTG-AAACAC-AAA
1 T-TTTTGAAAACACGAAA
**
38094299 TTTTTTTTTAAACACGAGAA
1 --TTTTTGAAAACACGA-AA
*
38094319 TTTTTGAAAACATGAAA
1 TTTTTGAAAACACGAAA
** * *
38094336 ACTTTG-AAACACCGGAG
1 TTTTTGAAAACA-CGAAA
38094353 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
*
38094371 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACG-AAA
* **
38094388 TTTGTGAAAACACGTATTTT
1 TTTTTGAAAACACG-A--AA
*
38094408 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
* *
38094426 TTTTTG-AAACGCCAGAA
1 TTTTTGAAAACACGA-AA
38094443 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
*
38094461 -TTTTCAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
38094478 TTTTTGAAAACACAAAA
1 TTTTTGAAAACACGAAA
* *
38094495 TTTGTTG--AACAGGGAATT
1 TTT-TTGAAAACA-CGAA-A
**
38094513 TTTTTGAAAACGAAAAAAA
1 TTTTTGAAAAC--ACGAAA
*** *
38094532 AAATTG--ATCATCGAAA
1 TTTTTGAAAACA-CGAAA
*
38094548 TTTTTGAGAACACGAAA
1 TTTTTGAAAACACGAAA
* *
38094565 TTTTTTG-AAACACCAGGA
1 -TTTTTGAAAACACGA-AA
38094583 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
38094600 TTTTT
1 TTTTT
38094605 TTAAATATTT
Statistics
Matches: 336, Mismatches: 67, Indels: 99
0.67 0.13 0.20
Matches are distributed among these distances:
12 8 0.02
13 1 0.00
14 6 0.02
15 4 0.01
16 37 0.11
17 110 0.33
18 141 0.42
19 10 0.03
20 18 0.05
21 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:38094934 original size:10 final size:9
Alignment explanation
Indices: 38094916--38094973 Score: 62
Period size: 10 Copynumber: 6.0 Consensus size: 9
38094906 ATTAAACCCC
38094916 TTTTTTTCT
1 TTTTTTTCT
38094925 TTTTTCTTCT
1 TTTTT-TTCT
*
38094935 TTTATCTTCT
1 TTT-TTTTCT
*
38094945 TTTTTCCTCT
1 TTTTT-TTCT
38094955 CTTTTTTTCT
1 -TTTTTTTCT
38094965 TTTTTTTCT
1 TTTTTTTCT
38094974 GGACTGGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 15 0.37
10 20 0.49
11 6 0.15
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:38094946 original size:20 final size:18
Alignment explanation
Indices: 38094915--38094973 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 18
38094905 AATTAAACCC
38094915 CTTTTTTTCTTTTTTCTT
1 CTTTTTTTCTTTTTTCTT
38094933 CTTTTATCTTCTTTTTTCCTCT
1 CTTTT-T-TTCTTTTTT-CT-T
38094955 CTTTTTTTCTTTTTT-TT
1 CTTTTTTTCTTTTTTCTT
38094972 CT
1 CT
38094974 GGACTGGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.08
18 6 0.16
19 1 0.03
20 18 0.49
21 3 0.08
22 6 0.16
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTTTTCTTTTTTCTT
Found at i:38095022 original size:22 final size:23
Alignment explanation
Indices: 38094994--38095043 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
38094984 GGCCTGTTGG
*
38094994 GCTGCTG-CTAGGCCTGGGGGCT
1 GCTGCTGACTAGGCCTGGGGCCT
38095016 GCTGCTGCACTAGGCCTGGGGCCT
1 GCTGCTG-ACTAGGCCTGGGGCCT
38095040 GCTG
1 GCTG
38095044 GGCCTGCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.06, C:0.30, G:0.42, T:0.22
Consensus pattern (23 bp):
GCTGCTGACTAGGCCTGGGGCCT
Found at i:38095258 original size:104 final size:103
Alignment explanation
Indices: 38095135--38095348 Score: 401
Period size: 104 Copynumber: 2.1 Consensus size: 103
38095125 TCTGTTTTGG
38095135 TTTTTTTTTGGGCTGGCCTGCTACTGCTGTTGGGTTGTTGGGTGCTGTGGGTCGGGTCAATTTTG
1 TTTTTTTTTGGGCTGGCCTGCTACTGCTGTTGGGTTGTTGGGTGCTGTGGGTCGGGTCAATTTTG
*
38095200 CGGGTCGGGTCGGGTTGACCCGACTGTGATATTTTTCT
66 CGGGTCGGGTCGGGTTGACCCGACTGTGATATATTTCT
38095238 TTTTTTTTTCGGGCTGGCCTGCTACTGCTGTTGGGTTGTTGGGTGCTGTGGGTCGGGTCAATTTT
1 TTTTTTTTT-GGGCTGGCCTGCTACTGCTGTTGGGTTGTTGGGTGCTGTGGGTCGGGTCAATTTT
*
38095303 GCGGGTCGGGTCGGTTTGACCCGACTGTGATATATTTCT
65 GCGGGTCGGGTCGGGTTGACCCGACTGTGATATATTTCT
38095342 TTTTTTT
1 TTTTTTT
38095349 CTTTTTTCTT
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
103 9 0.08
104 99 0.92
ACGTcount: A:0.07, C:0.16, G:0.34, T:0.43
Consensus pattern (103 bp):
TTTTTTTTTGGGCTGGCCTGCTACTGCTGTTGGGTTGTTGGGTGCTGTGGGTCGGGTCAATTTTG
CGGGTCGGGTCGGGTTGACCCGACTGTGATATATTTCT
Found at i:38095360 original size:6 final size:6
Alignment explanation
Indices: 38095337--38095417 Score: 67
Period size: 6 Copynumber: 13.0 Consensus size: 6
38095327 CTGTGATATA
* * *
38095337 TTTCTT TTT-TT TCTT-TT TTCTTTT TTTCTT TCTCTT TTTCTT CTCTCTT
1 TTTCTT TTTCTT T-TTCTT TT-TCTT TTTCTT TTTCTT TTTCTT -TTTCTT
*
38095386 TTTCCTT CTTTCTT TTTCTT TTTCTT CTTCTT
1 TTT-CTT -TTTCTT TTTCTT TTTCTT TTTCTT
38095418 CTTCGGGCCG
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 4 0.06
6 41 0.65
7 15 0.24
8 3 0.05
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:38095362 original size:14 final size:14
Alignment explanation
Indices: 38095337--38095420 Score: 77
Period size: 15 Copynumber: 6.1 Consensus size: 14
38095327 CTGTGATATA
38095337 TTTCTTTTTT-TTC
1 TTTCTTTTTTCTTC
* *
38095350 TTTTTTCTTTTTTTC
1 TTTCTT-TTTTCTTC
38095365 TTTCTCTTTTTCTTC
1 TTTCT-TTTTTCTTC
* *
38095380 TCTCTTTTTCCTTC
1 TTTCTTTTTTCTTC
38095394 TTTC-TTTTTCTT-
1 TTTCTTTTTTCTTC
*
38095406 TTTC-TTCTTCTTC
1 TTTCTTTTTTCTTC
38095419 TT
1 TT
38095421 CGGGCCGTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
12 11 0.19
13 14 0.24
14 15 0.25
15 18 0.31
16 1 0.02
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTTCTTC
Found at i:38095385 original size:27 final size:27
Alignment explanation
Indices: 38095343--38095420 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
38095333 TATATTTCTT
* *
38095343 TTTTTTCTTTTTTCTTTTT-TTCTTTC
1 TTTTTTCTTCTCTCTTTTTCTTCTTTC
38095369 TCTTTTTCTTCTCTCTTTTTCCTTCTTTC
1 T-TTTTTCTTCTCTCTTTTT-CTTCTTTC
* *
38095398 -TTTTTCTT-TTTCTTCTTCTTCTT
1 TTTTTTCTTCTCTCTTTTTCTTCTT
38095421 CGGGCCGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
25 6 0.13
26 8 0.18
27 24 0.53
29 7 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTTCTTCTCTCTTTTTCTTCTTTC
Found at i:38095984 original size:30 final size:29
Alignment explanation
Indices: 38095950--38096108 Score: 133
Period size: 29 Copynumber: 5.4 Consensus size: 29
38095940 TATGGGGCTA
* * *
38095950 AAATGTAATTTATAGAAAGTTTAGGGGCCC
1 AAATGTAATTTAGA-AAAGTTTAGGGGTCG
* * **
38095980 AAATGAAATTTAGAAAATTTTAGGGGTAT
1 AAATGTAATTTAGAAAAGTTTAGGGGTCG
* * *
38096009 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTG
1 AAATGT-AATTTAGA-AAAGTTTAGGGGTCG
*
38096039 AAATGTAATTTCA-AAAAGTTTAGGGGTTG
1 AAATGTAATTT-AGAAAAGTTTAGGGGTCG
** * *
38096068 AAATGTAATTTAGAAAAGTACAGGGGCCA
1 AAATGTAATTTAGAAAAGTTTAGGGGTCG
38096097 AAATGTAATTTA
1 AAATGTAATTTA
38096109 TATTTTTTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.01
29 70 0.67
30 34 0.32
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTTAGGGGTCG
Found at i:38096016 original size:59 final size:58
Alignment explanation
Indices: 38095950--38096108 Score: 162
Period size: 59 Copynumber: 2.7 Consensus size: 58
38095940 TATGGGGCTA
* * * *
38095950 AAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGAAATTTAGAAAATTTTAGGGGTAT-
1 AAATGTAATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTTA-AAAAGTTTAGGGGT-TG
* * ***
38096009 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTGAAATGTAATTTCAAAAAGTTTAGGGGTTG
1 AAATGT-AATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTT-AAAAAGTTTAGGGGTTG
**
38096068 AAATGTAATTTAGA-AAAGTACAGGGGCCAAAATGTAATTTA
1 AAATGTAATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTTA
38096109 TATTTTTTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
57 1 0.01
58 26 0.32
59 48 0.59
60 6 0.07
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
AAATGTAATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTTAAAAAGTTTAGGGGTTG
Found at i:38096058 original size:29 final size:29
Alignment explanation
Indices: 38095950--38096086 Score: 136
Period size: 29 Copynumber: 4.7 Consensus size: 29
38095940 TATGGGGCTA
* ***
38095950 AAATGTAATTTATAGAAAGTTTAGGGGCCC
1 AAATGTAATTTAGA-AAAGTTTAGGGGTTG
* *
38095980 AAATGAAATTTAGAAAATTTTAGGGGTAT-
1 AAATGTAATTTAGAAAAGTTTAGGGGT-TG
* *
38096009 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTG
1 AAATGT-AATTTAGA-AAAGTTTAGGGGTTG
38096039 AAATGTAATTTCA-AAAAGTTTAGGGGTTG
1 AAATGTAATTT-AGAAAAGTTTAGGGGTTG
38096068 AAATGTAATTTAGAAAAGT
1 AAATGTAATTTAGAAAAGT
38096087 ACAGGGGCCA
Statistics
Matches: 89, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.01
29 54 0.61
30 34 0.38
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTTAGGGGTTG
Found at i:38096639 original size:163 final size:164
Alignment explanation
Indices: 38096462--38098127 Score: 2071
Period size: 163 Copynumber: 10.5 Consensus size: 164
38096452 AAAAATAGAT
* *
38096462 ATTGAAAATACCTCAGCGTAACCCGAGGCTCAAAC-CATCTCTCGCATTATGAGTTGATTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTC-AACTCACCTCTCGCATTATGAGTTGATTTTTTT
* *
38096526 TGAAAA-AGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAAGCTCAACTCACTTCTCGGAAT
65 TGAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAT
38096590 ATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
130 ATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
**
38096625 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTTACATTATGAGTTGA-TTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
* * * *
38096689 GAAAAAAGAAATTTAAAAGAAATTCATCAGCGTGCGACTCGAGGCTCAACTCACTTCTCGCAATA
66 GAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATA
*
38096754 TGAGTTAATTTTTTTGAAAAACAGAGAAACATAA
131 TGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
*
38096788 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
* *
38096853 -AAAAGAGAAATTTAAAAGAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATA
66 GAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATA
*
38096917 TGAGTTGATTTTTTTGAAAAACAGAGGAACATAA
131 TGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
*
38096951 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
* *
38097016 -AAAAGAGAAATTTAAAAGAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATA
66 GAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATA
*
38097080 TGAGTTGATTTTTTTGAAAAACAGAGGAACATAA
131 TGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
*
38097114 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
* *
38097179 -AAAAGAGAAATTTAAAAGAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATA
66 GAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATA
38097243 TGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
131 TGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
38097277 ATTGAAAATACCTCAGCGTGACCTGAGGTTCAACTCACCTCTCGCATTATGA----ATTTATTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT-TTTT
* * * * *
38097338 TGAAAA-ACGAAAATTTGAAAGAAATACCTCGGCAT--GACCCGAGGCTCAACTCACATCT-GTA
65 TGAAAACA-G-AAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCA
* **
38097399 TTATGAGTTGA--TTTTTGAAAAAC-GA-AAATTTGAA
128 ATATGAGTTGATTTTTTTGAAAAACAGAGAAACAT-AA
* * **
38097433 A--G-AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTGTTATGAGTTGA---TTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
* * *
38097491 GAAAA-ACGAAAATTTAAAAGAAATACCTC-GACAT--GACCCGAGGCTCAACTCACCTCT-GTA
66 GAAAACA-G-AAATTTAAAAGAAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACTTCTCGCA
* **
38097551 TTATGAGTTGA--TTTTTGAAAAAC-GA-AAATTTGAA
128 ATATGAGTTGATTTTTTTGAAAAACAGAGAAACAT-AA
* * * * *
38097585 A--G-AAATACCTCGGCATGACCCGAGGCTCAACTCACTTCTGGCAATATGAGTTGATTTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
* * *
38097647 GAAAAACAGAAATTTAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAAT
66 G-AAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAT
*
38097712 ATGAGTTGA--TTTTTGAAAAA-ACAG-AA-AT--
130 ATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
38097740 -TT-AAAATACCTCAGCGTGCGACCCGAGGCTCAACCCACTTCTCGCATTATGAGTTGA---TTT
1 ATTGAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
* *
38097800 TTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGTA
64 TTG-AAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCA
*
38097863 ATATGAGTTGA--TTTTTGAAAAA-ACAG-AA-AT--
128 ATATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
38097893 -TT-AAAATACCTCAGCGTGCAATCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGA---TTT
1 ATTGAAAATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
*
38097953 TTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCTGAGGCTCAACTCAGC-TCTCGC
64 TTG-AAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCA-CTTCTCGC
*
38098015 AATATGAGTTGATTTTTTTGAAAAA-ACAG-AA-AT--
127 AATATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
*
38098048 -TT-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTT
1 ATTGAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
*
38098108 TTGAAAACAGAAATTGAAAA
64 TTGAAAACAGAAATTTAAAA
38098128 ATATTTTTTA
Statistics
Matches: 1401, Mismatches: 65, Indels: 83
0.90 0.04 0.05
Matches are distributed among these distances:
151 2 0.00
152 140 0.10
153 224 0.16
154 18 0.01
155 118 0.08
156 45 0.03
157 19 0.01
158 60 0.04
159 42 0.03
160 27 0.02
161 5 0.00
162 37 0.03
163 657 0.47
164 7 0.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (164 bp):
ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTT
GAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATA
TGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
Found at i:38097424 original size:76 final size:77
Alignment explanation
Indices: 38096467--38098127 Score: 1743
Period size: 76 Copynumber: 21.0 Consensus size: 77
38096457 TAGATATTGA
* *
38096467 AAATACCTCAGCGTAACCCGAGGCTCAAAC-CATCTCTCGCATTATGAGTTGATTTTTTTTG-AA
1 AAATACCTCAGCGTGACCCGAGGCTC-AACTCACCTCTCGCATTATGAGTTGA---TTTTTGAAA
38096530 AA-AGAAATTTAAAAG
62 AACAGAAATTTAAAAG
* * * *
38096545 AAATACCTCAGCGTGCGACCCGAAGCTCAACTCACTTCTCGGAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAA
** *
38096610 AACAGAGAAACATAAATTG
62 AAC--AGAAATTTAAA-AG
**
38096629 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTTACATTATGAGTTGATTTTTTTGAAAA
1 -AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAAA
38096694 A-AGAAATTTAAAAG
63 ACAGAAATTTAAAAG
* * * * * *
38096708 AAATTCATCAGCGTGCGACTCGAGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTGAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAA
** *
38096773 AACAGAGAAACATAAATTG
62 AAC--AGAAATTTAAA-AG
* **
38096792 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTTAAAA
1 -AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAA
*
38096857 GAGAAATTTAAAAG
64 CAGAAATTTAAAAG
* * *
38096871 AAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAA
** *
38096936 AACAGAGGAACATAAATTG
62 AACAGA--AATTTAAA-AG
* **
38096955 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTTAAAA
1 -AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAA
*
38097020 GAGAAATTTAAAAG
64 CAGAAATTTAAAAG
* * *
38097034 AAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAA
** *
38097099 AACAGAGGAACATAAATTG
62 AACAGA--AATTTAAA-AG
* **
38097118 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTTAAAA
1 -AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAA
*
38097183 GAGAAATTTAAAAG
64 CAGAAATTTAAAAG
* * *
38097197 AAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAA
** *
38097262 AACAGAGAAACATAAATTG
62 AAC--AGAAATTTAAA-AG
* * * *
38097281 AAAATACCTCAGCGTGACCTGAGGTTCAACTCACCTCTCGCATTATGAATTTATTTTTGAAAAAC
1 -AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
*
38097346 -GAAAATTTGAAAG
65 AG-AAATTTAAAAG
* * * *
38097359 AAATACCTCGGCATGACCCGAGGCTCAACTCACATCT-GTATTATGAGTTGATTTTTGAAAAAC-
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACA
*
38097422 GAAAATTTGAAAG
66 G-AAATTTAAAAG
* * **
38097435 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTGTTATGAGTTGATTTTTGAAAAAC-
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACA
38097498 GAAAATTTAAAAG
66 G-AAATTTAAAAG
* *
38097511 AAATACCTC-GACATGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAAC
1 AAATACCTCAG-CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
*
38097574 -GAAAATTTGAAAG
65 AG-AAATTTAAAAG
* * * * *
38097587 AAATACCTCGGCATGACCCGAGGCTCAACTCACTTCTGGCAATATGAGTTGATTTTTTTTGAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA---TTTTTGAAAA
*
38097652 ACAGAAATTTAAAAA
63 ACAGAAATTTAAAAG
* *
38097667 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAA
38097732 ACAGAAATTT---A-
63 ACAGAAATTTAAAAG
* *
38097743 AAATACCTCAGCGTGCGACCCGAGGCTCAACCCACTTCTCGCATTATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA
38097808 CAGAAATTTAAAAG
64 CAGAAATTTAAAAG
* *
38097822 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAAAC
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAAC
38097887 AGAAATTT---A-
65 AGAAATTTAAAAG
* *
38097896 AAATACCTCAGCGTGCAATCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA
38097961 CAGAAATTTAAAAG
64 CAGAAATTTAAAAG
* * *
38097975 AAATACCTCAGCGTGACCTGAGGCTCAACTCAGCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTG-AAAA
38098040 ACAGAAATTT---A-
63 ACAGAAATTTAAAAG
*
38098051 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA
*
38098115 CAGAAATTGAAAA
64 CAGAAATTTAAAA
38098128 ATATTTTTTA
Statistics
Matches: 1373, Mismatches: 143, Indels: 135
0.83 0.09 0.08
Matches are distributed among these distances:
74 27 0.02
75 30 0.02
76 330 0.24
77 120 0.09
78 122 0.09
79 62 0.05
80 270 0.20
81 49 0.04
82 72 0.05
83 218 0.16
84 5 0.00
85 68 0.05
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (77 bp):
AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACA
GAAATTTAAAAG
Found at i:38099039 original size:17 final size:18
Alignment explanation
Indices: 38099013--38099046 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38099003 TTTTGTCTGT
38099013 TTTTTCTGTTCTTTTTTC
1 TTTTTCTGTTCTTTTTTC
*
38099031 TTTTT-TGTTGTTTTTT
1 TTTTTCTGTTCTTTTTT
38099047 TAAGCATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (18 bp):
TTTTTCTGTTCTTTTTTC
Found at i:38104445 original size:35 final size:35
Alignment explanation
Indices: 38104349--38104777 Score: 225
Period size: 35 Copynumber: 12.5 Consensus size: 35
38104339 ACGAAAGTTT
* *
38104349 TTTTTA-AAACACGAGAATTTTTGAAAACACGAGAA
1 TTTTTAGAAACACGAAAATTTTT-AAAACACGAAAA
*
38104384 TTTGT--AAACACGAAAA-TTTTAGAAACACGAAAA
1 TTTTTAGAAACACGAAAATTTTTA-AAACACGAAAA
* * * *
38104417 TTTTTAGAAAAACAAAAATTTTTAAAACACGACAT
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* ** * *
38104452 TTTTTTGAAACACGGGAATTTTTAAAACAGGGAAA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* *
38104487 -TTTTAGAAACACGAAAATTTTTAAAACACGACAT
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* *
38104521 TTTTTTGAAACACG---A--TTTAAAAAAC-AAAA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* * * * *
38104550 --ATT-GAAATACGAGAATATTTTGAAACAC-AAATT
1 TTTTTAGAAACACGAAAAT-TTTTAAAACACGAAA-A
** * * *
38104583 TTTTTTTAAACGCGAGAATTTTTGAAAACATGAAAA
1 TTTTTAGAAACACGAAAATTTTT-AAAACACGAAAA
* * * *
38104619 -ATTT-GAAACACCG-GAGTTTTTGAAAACACGAGAA
1 TTTTTAGAAACA-CGAAAATTTTT-AAAACACGAAAA
* * * **
38104653 TTTGT-GAAACATGAAAATTTGTGAAAACACGTAATTT
1 TTTTTAGAAACACGAAAATTT-TTAAAACACG-AA-AA
* * ** * *
38104690 TTTTTAAAAACACGAAAATTTTTGAAATGCTAGAA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
*
38104725 TTTTT-GAAAACACGAAGATTTTTAAAACACGAAAA
1 TTTTTAG-AAACACGAAAATTTTTAAAACACGAAAA
38104760 TTTTT-GAAAACACGAAAA
1 TTTTTAG-AAACACGAAAA
38104778 CACAAAATTT
Statistics
Matches: 295, Mismatches: 74, Indels: 50
0.70 0.18 0.12
Matches are distributed among these distances:
26 7 0.02
27 2 0.01
29 3 0.01
30 9 0.03
32 13 0.04
33 18 0.06
34 60 0.20
35 135 0.46
36 23 0.08
37 12 0.04
38 13 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
Found at i:38104507 original size:69 final size:71
Alignment explanation
Indices: 38104349--38104534 Score: 231
Period size: 69 Copynumber: 2.7 Consensus size: 71
38104339 ACGAAAGTTT
* * * *
38104349 TTTTTA-AAACACGAGAATTTTTGAAAACACGAGA-ATTTGT-AAACAC-GAAAATTTTAGAAAC
1 TTTTTAGAAACACGAAAATTTTT-AAAACACGACATTTTTTTGAAACACGGAAAATTTTAGAAAC
38104410 ACGAAAA
65 ACGAAAA
* * * *
38104417 TTTTTAGAAAAACAAAAATTTTTAAAACACGACATTTTTTTGAAACACGGGAATTTTTA-AAACA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACGGAAAATTTTAGAAACA
* *
38104481 GGGAAA
66 CGAAAA
38104487 -TTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACG
1 TTTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACG
38104535 ATTTAAAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
68 16 0.16
69 63 0.62
70 15 0.15
71 8 0.08
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (71 bp):
TTTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACGGAAAATTTTAGAAACA
CGAAAA
Found at i:38104775 original size:18 final size:18
Alignment explanation
Indices: 38104348--38104777 Score: 232
Period size: 18 Copynumber: 25.0 Consensus size: 18
38104338 AACGAAAGTT
* *
38104348 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
38104366 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
38104384 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
38104400 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
38104417 TTTTTAGAAAA-ACAAAAA
1 TTTTT-GAAAACACGAAAA
**
38104435 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
**
38104453 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
38104470 TTTTT-AAAACAGGGAAA
1 TTTTTGAAAACACGAAAA
*
38104487 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
38104504 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
38104522 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
38104536 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
* * *
38104550 --ATTG-AAATACGAGAA
1 TTTTTGAAAACACGAAAA
*
38104565 TATTTTG-AAACAC-AAATT
1 T-TTTTGAAAACACGAAA-A
** * *
38104583 TTTTTTTAAACGCGAGAA
1 TTTTTGAAAACACGAAAA
*
38104601 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
38104619 -ATTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
38104635 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
38104653 TTTGTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
* **
38104670 TTTGTGAAAACACGTAATTT
1 TTTTTGAAAACACG-AA-AA
*
38104690 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
** * *
38104708 TTTTTG-AAATGCTAGAA
1 TTTTTGAAAACACGAAAA
*
38104725 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
38104743 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
38104760 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
38104778 CACAAAATTT
Statistics
Matches: 313, Mismatches: 66, Indels: 66
0.70 0.15 0.15
Matches are distributed among these distances:
12 8 0.03
14 8 0.03
15 3 0.01
16 24 0.08
17 118 0.38
18 131 0.42
19 9 0.03
20 12 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:38104862 original size:17 final size:16
Alignment explanation
Indices: 38104840--38104898 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
38104830 TGATCATCGG
38104840 AATTTTTGAGAACACAA
1 AATTTTTGA-AACACAA
*
38104857 AATTTTTTGAAACACCAG
1 AA-TTTTTGAAACA-CAA
* *
38104875 GATTTTTGAAAACACGA
1 AATTTTTG-AAACACAA
38104892 AATTTTT
1 AATTTTT
38104899 TGAATATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
AATTTTTGAAACACAA
Found at i:38104865 original size:18 final size:17
Alignment explanation
Indices: 38104842--38104902 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
38104832 ATCATCGGAA
38104842 TTTTTGAGAACACAAAAT
1 TTTTTGA-AACACAAAAT
**
38104860 TTTTTGAAACACCAGGA-
1 TTTTTGAAACA-CAAAAT
*
38104877 TTTTTGAAAACACGAAAT
1 TTTTTG-AAACACAAAAT
38104895 TTTTTGAA
1 TTTTTGAA
38104903 TATTTACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
TTTTTGAAACACAAAAT
Found at i:38105277 original size:10 final size:10
Alignment explanation
Indices: 38105259--38105317 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
38105249 ATTAAAACCC
38105259 TTTTT-TTCT
1 TTTTTCTTCT
38105268 TTTTTCTTCT
1 TTTTTCTTCT
*
38105278 TTTATCTTCT
1 TTTTTCTTCT
38105288 TTTTTCCTCTCT
1 TTTTT-CT-TCT
38105300 TTTTT-TT-T
1 TTTTTCTTCT
*
38105308 TTTTTTTTCT
1 TTTTTCTTCT
38105318 GGACTGGGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 6 0.14
9 8 0.19
10 19 0.44
11 2 0.05
12 8 0.19
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:38105437 original size:13 final size:13
Alignment explanation
Indices: 38105419--38105475 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
38105409 TGCATTTGGG
38105419 CTGCTTCTTTCTT
1 CTGCTTCTTTCTT
38105432 CTGCTTCTTTCTTT
1 CTGCTTCTTTC-TT
* * *
38105446 CTTTCTTTTTTCTG
1 C-TGCTTCTTTCTT
*
38105460 CTGCTTCTTTTTT
1 CTGCTTCTTTCTT
38105473 CTG
1 CTG
38105476 TTTTGGTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
13 22 0.63
14 5 0.14
15 8 0.23
ACGTcount: A:0.00, C:0.26, G:0.09, T:0.65
Consensus pattern (13 bp):
CTGCTTCTTTCTT
Found at i:38105451 original size:25 final size:23
Alignment explanation
Indices: 38105423--38105474 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
38105413 TTTGGGCTGC
*
38105423 TTCTTTCTTCTGCTTCTTTCTTTCT
1 TTCTTTCTTCTGCTGC-TTCTTT-T
*
38105448 TTCTTTTTTCTGCTGCTTCTTTT
1 TTCTTTCTTCTGCTGCTTCTTTT
38105471 TTCT
1 TTCT
38105475 GTTTTGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (23 bp):
TTCTTTCTTCTGCTGCTTCTTTT
Found at i:38105607 original size:14 final size:14
Alignment explanation
Indices: 38105588--38105644 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
38105578 GTGATATATT
38105588 TCTTTTTTTCTTTC
1 TCTTTTTTTCTTTC
38105602 TC--TTTTTC-TTC
1 TCTTTTTTTCTTTC
* *
38105613 TCTCTTTTTCCTTC
1 TCTTTTTTTCTTTC
*
38105627 T-TTCTTTTTCTTTT
1 TCTT-TTTTTCTTTC
38105641 TCTT
1 TCTT
38105645 CTTCTTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
11 5 0.14
12 6 0.17
13 7 0.20
14 15 0.43
15 2 0.06
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTTTCTTTC
Found at i:38105611 original size:6 final size:6
Alignment explanation
Indices: 38105592--38105650 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
38105582 TATATTTCTT
* *
38105592 TTTTTC TTTCTC TTTTTC TTCTCTC TTTTTCC TTCTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC TTTTTC TTTTTC
*
38105643 TTCTTC TT
1 TTTTTC TT
38105651 CTTCGGGCCG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 31 0.69
7 11 0.24
8 3 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:38106283 original size:29 final size:29
Alignment explanation
Indices: 38106205--38106317 Score: 106
Period size: 29 Copynumber: 3.9 Consensus size: 29
38106195 TTAGGAGCCC
* * *
38106205 AAATGAAATTTAGAAAATTTTAGGGGTAT-
1 AAATGTAATTTAGAAAAGTTCAGGGGT-TG
* * *
38106234 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTG
1 AAATGT-AATTTAGA-AAAGTTCAGGGGTTG
38106264 AAATGTAATTTCA-AAAAGTTCAGGGGTTG
1 AAATGTAATTT-AGAAAAGTTCAGGGGTTG
*
38106293 AAATGTAATTTAGAAAAGTACAGGG
1 AAATGTAATTTAGAAAAGTTCAGGG
38106318 CCAAAATGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.01
29 47 0.67
30 22 0.31
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.31
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTCAGGGGTTG
Found at i:38115020 original size:71 final size:71
Alignment explanation
Indices: 38114937--38115078 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
38114927 AGCCAAGAGT
*
38114937 TAGTTGCTCTTACTCTCGAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
1 TAGTTGCTCTTACTCTCCAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
38115002 AGTAAA
66 AGTAAA
38115008 TAGTTGCTCTTACTCTCCAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
1 TAGTTGCTCTTACTCTCCAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
38115073 AGTAAA
66 AGTAAA
38115079 GAAATTGCGT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (71 bp):
TAGTTGCTCTTACTCTCCAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
AGTAAA
Found at i:38121237 original size:21 final size:19
Alignment explanation
Indices: 38121198--38121240 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
38121188 GTATGTAATT
38121198 TATATGAAATTAAATTAAA
1 TATATGAAATTAAATTAAA
38121217 TATAT-AATATTATAATGTAAA
1 TATATGAA-ATTA-AAT-TAAA
38121238 TAT
1 TAT
38121241 TAAAGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.10
19 9 0.43
20 3 0.14
21 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TATATGAAATTAAATTAAA
Found at i:38124147 original size:22 final size:22
Alignment explanation
Indices: 38124119--38124161 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
38124109 GCACTAACGA
*
38124119 ACAGAGAGCACTAAGGTGCTAT
1 ACAGAGAGCACGAAGGTGCTAT
*
38124141 ACAGAGAGCACGAATGTGCTA
1 ACAGAGAGCACGAAGGTGCTA
38124162 AATGGATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (22 bp):
ACAGAGAGCACGAAGGTGCTAT
Found at i:38126917 original size:27 final size:27
Alignment explanation
Indices: 38126879--38126934 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
38126869 GCTTCATGGA
*
38126879 TATCAATAGGTACAGTAGCAGATAAAC
1 TATCAATAGGTACAATAGCAGATAAAC
* * *
38126906 TATCAGTAGGTACAATATCAGATGAAC
1 TATCAATAGGTACAATAGCAGATAAAC
38126933 TA
1 TA
38126935 GTTACCCTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (27 bp):
TATCAATAGGTACAATAGCAGATAAAC
Found at i:38135800 original size:31 final size:31
Alignment explanation
Indices: 38135762--38135822 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
38135752 CCTTCCATCA
* *
38135762 TTGCGATAGCTGCCTTGTACTCTAGTGATCC
1 TTGCGATAGCTGCCTCGTACTCCAGTGATCC
38135793 TTGCGATAGCTGCCTCGTACTCCAGTGATC
1 TTGCGATAGCTGCCTCGTACTCCAGTGATC
38135823 AATTTGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (31 bp):
TTGCGATAGCTGCCTCGTACTCCAGTGATCC
Found at i:38144758 original size:58 final size:56
Alignment explanation
Indices: 38144687--38144862 Score: 211
Period size: 58 Copynumber: 3.2 Consensus size: 56
38144677 GCTAAGCTAC
* *
38144687 CACTTATCACTTGTCGCTTGTCACTGATTAGATAAGTGTAGCTAATGCTACCAATTAT
1 CACTTATCACTTGTC-CTTGTCACTGATCAGATAAGTGTAGCTAA-GCTACCACTTAT
* *
38144745 GACTTATCA------CTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CACTTATCACTTGTCCTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTAT
* *
38144796 CACTTGTCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTATCACTTGTC-CTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTAT
38144854 CACTTATCA
1 CACTTATCA
38144863 GAAGTACTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
51 43 0.43
52 2 0.02
58 55 0.55
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (56 bp):
CACTTATCACTTGTCCTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTAT
Found at i:38144761 original size:51 final size:51
Alignment explanation
Indices: 38144642--38144862 Score: 277
Period size: 51 Copynumber: 4.2 Consensus size: 51
38144632 CTTACGTATG
38144642 ATCACTTATCACTTGTC-CTTGATCAGATAAGTGTAGCTAAGCTACCACTT
1 ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTT
* * * *
38144692 ATCACTTGTCGCTTGTCAC-TGATTAGATAAGTGTAGCTAATGCTACCAATT
1 ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAA-GCTACCACTT
* *
38144743 ATGACTTATCACTTGTCAC-TGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTT
*
38144794 ATCACTTGTCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTATCACTTGTCACTTG------ATCAGATAAGTGTAGCT-AAGCTACCACTT
38144852 ATCACTTATCA
1 ATCACTTATCA
38144863 GAAGTACTTA
Statistics
Matches: 146, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
50 35 0.24
51 69 0.47
52 4 0.03
58 38 0.26
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTT
Found at i:38144807 original size:14 final size:14
Alignment explanation
Indices: 38144788--38144825 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
38144778 GCTGAAGCTA
38144788 TCACTTATCACTTG
1 TCACTTATCACTTG
*
38144802 TCACTTGTCACTTG
1 TCACTTATCACTTG
*
38144816 TCACTAATCA
1 TCACTTATCA
38144826 GATAAGTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (14 bp):
TCACTTATCACTTG
Found at i:38150477 original size:44 final size:44
Alignment explanation
Indices: 38150414--38150722 Score: 300
Period size: 44 Copynumber: 6.6 Consensus size: 44
38150404 TTTGAGTACT
*
38150414 TCTGATCAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
38150458 TCTGATCAGTGACACGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTG--AC-----AAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
38150509 TCTGATCAGTGACAAGTGATAAGTGATAAATGGTAGC-TTAGCTACTCTTA
1 TCTGATCAGTGACAAGTGATAA--G-----TGGTAGCTTTAGCTACACTTA
* *
38150559 TCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAGTG---A----CAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
38150610 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
** * *
38150654 TCTGATCAGTGACAAGTGGCAAGTGATAAG-TGGTAGC-ACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGT-AGCT-TTAGCTACACTTA
*
38150698 TCTGATCAGGGACAAGTGATAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
38150723 ATCATACGTA
Statistics
Matches: 225, Mismatches: 16, Indels: 48
0.78 0.06 0.17
Matches are distributed among these distances:
44 103 0.46
45 5 0.02
46 2 0.01
48 1 0.00
49 2 0.01
50 29 0.13
51 71 0.32
53 1 0.00
55 1 0.00
57 10 0.04
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:38150498 original size:51 final size:51
Alignment explanation
Indices: 38150421--38150724 Score: 404
Period size: 51 Copynumber: 6.3 Consensus size: 51
38150411 ACTTCTGATC
38150421 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
38150472 CGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
38150523 AGTGATAAGTGATAAATGGTAGC-TTAGCTACTCTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** * *
38150573 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGAC-
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
38150623 ------AAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** *
38150668 AGTGGCAAGTGATAAGT-G--G---TAGC-ACACTTATCTGATCAGGGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
38150712 AGTGATAAGTGAT
1 AGTGATAAGTGAT
38150725 CATACGTAAG
Statistics
Matches: 228, Mismatches: 17, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
44 72 0.32
45 3 0.01
48 1 0.00
50 46 0.20
51 106 0.46
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:38151164 original size:29 final size:30
Alignment explanation
Indices: 38151141--38151229 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
38151131 ATTTTTATTT
*
38151141 TTGCATTTTGACCCCTAAAATTTTCTAAAA
1 TTGCATTTTAACCCCTAAAATTTTCTAAAA
*
38151171 TTGCATTTTAACCCCT-AAACTTTCTCAAAA
1 TTGCATTTTAACCCCTAAAATTTTCT-AAAA
* *
38151201 TTACATTTCT-ACCCCTAAAATTTTTTAAA
1 TTGCATTT-TAACCCCTAAAATTTTCTAAA
38151230 TTACATTCGG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.16
30 35 0.69
31 8 0.16
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (30 bp):
TTGCATTTTAACCCCTAAAATTTTCTAAAA
Found at i:38151175 original size:30 final size:30
Alignment explanation
Indices: 38151144--38151301 Score: 114
Period size: 29 Copynumber: 5.4 Consensus size: 30
38151134 TTTATTTTTG
*
38151144 CATTTTGACCCCTAAAATTTTCTAAAATTG
1 CATTTTGACCCCTAAAATTTTCTAAAATTA
* *
38151174 CATTTTAACCCCT-AAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAAATTTTCT-AAAATTA
*
38151204 CATTTCT-ACCCCTAAAATTTT-TTAAATTA
1 CATTT-TGACCCCTAAAATTTTCTAAAATTA
** * * *
38151233 CATTCGGGCCCTTAAAA-TATCTATAAATTA
1 CATTTTGACCCCTAAAATTTTCTA-AAATTA
* * *
38151263 CA-TTTGGCCCC--ATATTTTCCTAAAATTG
1 CATTTTGACCCCTAAAATTTT-CTAAAATTA
*
38151291 CATTTTTACCC
1 CATTTTGACCC
38151302 TAGAAACTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
27 2 0.02
28 11 0.11
29 42 0.42
30 38 0.38
31 7 0.07
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAAATTTTCTAAAATTA
Found at i:38151667 original size:35 final size:35
Alignment explanation
Indices: 38151622--38151688 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
38151612 CAACTAGCAA
38151622 AACAACCAAAA-AGCAAAAAAAAAAAAGAAAGAAAC
1 AACAACCAAAAGAG-AAAAAAAAAAAAGAAAGAAAC
* *
38151657 AACAAGCAAAAGAGAAAAAAAAAAGAGAAAGA
1 AACAACCAAAAGAGAAAAAAAAAAAAGAAAGA
38151689 GAAAAGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.76, C:0.10, G:0.13, T:0.00
Consensus pattern (35 bp):
AACAACCAAAAGAGAAAAAAAAAAAAGAAAGAAAC
Found at i:38151811 original size:4 final size:4
Alignment explanation
Indices: 38151802--38151866 Score: 62
Period size: 4 Copynumber: 15.8 Consensus size: 4
38151792 GGCTGATCGG
*
38151802 GAAA GAAA GAAA AAATA GAAA GAAAA GAGAA GAAA GAAA GAAA GAAA -AAGA
1 GAAA GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAA-A
*
38151853 GAAA -ACA GAAA GAA
1 GAAA GAAA GAAA GAA
38151867 GGAAGGAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 4 0.08
4 34 0.67
5 13 0.25
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:38151837 original size:31 final size:30
Alignment explanation
Indices: 38151802--38151880 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
38151792 GGCTGATCGG
*
38151802 GAAAGAAAGAAAAAATAGAAAGAAAAGAG-AA
1 GAAAGAAAGAAAAAA-A-AAAGAAAACAGAAA
*
38151833 GAAAGAAAGAAAGAAAAAGAGAAAACAGAAA
1 GAAAGAAAGAAA-AAAAAAAGAAAACAGAAA
* *
38151864 GAAGGAAGGAAAAAAAA
1 GAAAGAAAGAAAAAAAA
38151881 GGGAGATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.33
31 25 0.60
32 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (30 bp):
GAAAGAAAGAAAAAAAAAAGAAAACAGAAA
Found at i:38151862 original size:23 final size:22
Alignment explanation
Indices: 38151803--38151866 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
38151793 GCTGATCGGG
*
38151803 AAAGA-AAGAAAAAATAGAAAGA
1 AAAGAGAAGAAAGAA-AGAAAGA
38151825 AAAGAGAAGAAAGAAAGAAAGAA
1 AAAGAGAAGAAAGAAAGAAAG-A
38151848 AAAGAGAA-AACAGAAAGAA
1 AAAGAGAAGAA-AGAAAGAA
38151867 GGAAGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
22 13 0.34
23 25 0.66
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAGAGAAGAAAGAAAGAAAGA
Found at i:38151876 original size:19 final size:19
Alignment explanation
Indices: 38151807--38151866 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
38151797 ATCGGGAAAG
* *
38151807 AAAGAAAAAATAGAAAGAA
1 AAAGAGAAAACAGAAAGAA
*
38151826 AAGAGAAGAAAGAAAGAAAGAA
1 AA-AG-AGAAA-ACAGAAAGAA
38151848 AAAGAGAAAACAGAAAGAA
1 AAAGAGAAAACAGAAAGAA
38151867 GGAAGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 11 0.31
20 7 0.20
21 6 0.17
22 11 0.31
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAGAGAAAACAGAAAGAA
Found at i:38152663 original size:21 final size:20
Alignment explanation
Indices: 38152630--38152672 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
38152620 ATCGTGTTTC
*
38152630 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTCCGTGTTTTCAA
38152650 AAAAATTTCCCGTGTTTTCAA
1 AAAAATTT-CCGTGTTTTCAA
38152671 AA
1 AA
38152673 TTCTCGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAAATTTCCGTGTTTTCAA
Found at i:38152753 original size:75 final size:74
Alignment explanation
Indices: 38152669--38152833 Score: 208
Period size: 75 Copynumber: 2.2 Consensus size: 74
38152659 CCGTGTTTTC
* * * *
38152669 AAAATTCTCGTATTT-TAAAATTTTCTTGTTTTCAAAAAATGATT-TCTGTGTTTCATAAATTTT
1 AAAATTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAA--ATTGACCGTGTTTCATAAATTTT
**
38152732 TTTGTTTTAAAA
64 CGTG-TTTAAAA
*
38152744 AAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTTCG
1 AAAATTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTTCG
*
38152809 TGTTTCAAA
66 TGTTTAAAA
*
38152818 AAAATTCTCGTGTTTC
1 AAAATTCTCGTATTTC
38152834 GTTTTTATCA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
74 24 0.30
75 33 0.42
76 22 0.28
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (74 bp):
AAAATTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTTCG
TGTTTAAAA
Found at i:38152782 original size:38 final size:37
Alignment explanation
Indices: 38152630--38152833 Score: 179
Period size: 37 Copynumber: 5.5 Consensus size: 37
38152620 ATCGTGTTTC
* *
38152630 AAAAATTTTCGTGTTTTCAAAAAAATTTCCCGTGTTTTC--
1 AAAAATTCTCGTG-TTTC--AAAAATTT-TCGTGTTTTCAA
* * *
38152669 -AAAATTCTCGTATTT-TAAAATTTTCTTGTTTTCAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAA
* ** *
38152704 AAAATGATT-TCTGTGTTTCATAAATTTTTTTGTTTTAAA
1 AAAA--ATTCTC-GTGTTTCAAAAATTTTCGTGTTTTCAA
*
38152743 AAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAA
*
38152780 AAAAATTGAC-CGTGTTTCATAAATTTTCGTG-TTTCAA
1 AAAAATT--CTCGTGTTTCAAAAATTTTCGTGTTTTCAA
38152817 AAAAATTCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
38152834 GTTTTTATCA
Statistics
Matches: 137, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
33 8 0.06
34 7 0.05
35 1 0.01
36 11 0.08
37 50 0.36
38 39 0.28
39 21 0.15
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (37 bp):
AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAA
Found at i:38152887 original size:16 final size:17
Alignment explanation
Indices: 38152866--38152978 Score: 59
Period size: 20 Copynumber: 6.3 Consensus size: 17
38152856 TTTCAAAAAC
*
38152866 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
38152882 AAATTTTCGTGTTTCAAAA
1 AAATTTTCGTGTTTC--AA
** *
38152901 AGAAAATTCGTGTTTTAAAA
1 A-AATTTTCGTG-TTT-CAA
* *
38152921 AAAATCTCGTGTTTC-A
1 AAATTTTCGTGTTTCAA
*
38152937 AAATTTTCGTGTTTTTAAAA
1 AAATTTTCGTG--TTT-CAA
* *
38152957 AAAATTTCGTGTTTCTA
1 AAATTTTCGTGTTTCAA
38152974 AAATT
1 AAATT
38152979 CTTGTATTTA
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
16 17 0.23
17 11 0.15
18 9 0.12
19 11 0.15
20 22 0.30
21 3 0.04
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:38152888 original size:38 final size:37
Alignment explanation
Indices: 38152843--38152921 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
38152833 CGTTTTTATC
* * *
38152843 AAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTA
1 AAAATTTTCATG-TTTCAAAAACAAAATTCGTGTTTTA
* *
38152881 AAAATTTTCGTGTTTCAAAAAGAAAATTCGTGTTTTA
1 AAAATTTTCATGTTTCAAAAACAAAATTCGTGTTTTA
38152918 AAAA
1 AAAA
38152922 AAATCTCGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 26 0.72
38 10 0.28
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (37 bp):
AAAATTTTCATGTTTCAAAAACAAAATTCGTGTTTTA
Found at i:38152914 original size:37 final size:38
Alignment explanation
Indices: 38152856--38152939 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 38
38152846 ATTTTTATGT
* * * *
38152856 TTTCAAAAACAAATTTTGTGTTTT-AAAAATTTTCGTG
1 TTTCAAAAACAAAATTCGTGTTTTAAAAAAATCTCGTG
*
38152893 TTTCAAAAAGAAAATTCGTGTTTTAAAAAAAATCTCGTG
1 TTTCAAAAACAAAATTCGTGTTTT-AAAAAAATCTCGTG
38152932 TTTCAAAA
1 TTTCAAAA
38152940 TTTTCGTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 21 0.52
39 19 0.47
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (38 bp):
TTTCAAAAACAAAATTCGTGTTTTAAAAAAATCTCGTG
Found at i:38152947 original size:55 final size:57
Alignment explanation
Indices: 38152853--38152976 Score: 155
Period size: 55 Copynumber: 2.2 Consensus size: 57
38152843 AAAATTTTTA
* *
38152853 TGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTG-TTTCAAAAAGAAAATTCG
1 TGTTTT-AAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAA-AAAATTCG
* * *
38152911 TGTTTTAAAAA-AAATCTCGTG-TTTCAAAATTTTCGTGTTTTTAAAAAAAATTTCG
1 TGTTTTAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAAAAATTCG
38152966 TGTTTCTAAAA
1 TGTTT-TAAAA
38152977 TTCTTGTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 27 0.46
56 21 0.36
57 5 0.08
58 6 0.10
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (57 bp):
TGTTTTAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAAAAATTCG
Found at i:38152960 original size:36 final size:35
Alignment explanation
Indices: 38152907--38153011 Score: 133
Period size: 36 Copynumber: 2.9 Consensus size: 35
38152897 AAAAAGAAAA
38152907 TTCGTGTTTTAAAAAAAATCTCGTGTTTCAAAATT-
1 TTCGTGTTTTAAAAAAAAT-TCGTGTTTCAAAATTC
38152942 TTCGTGTTTTTAAAAAAAATTTCGTGTTTCTAAAATTC
1 TTCGTG-TTTTAAAAAAAA-TTCGTGTTTC-AAAATTC
* *
38152980 TT-GTATTTAAAAAAAAATTCGTGTTTTCAAAA
1 TTCGTGTTTTAAAAAAAATTCGTG-TTTCAAAA
38153012 AAAAAAGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
35 16 0.25
36 36 0.57
37 9 0.14
38 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (35 bp):
TTCGTGTTTTAAAAAAAATTCGTGTTTCAAAATTC
Found at i:38158383 original size:1 final size:1
Alignment explanation
Indices: 38158377--38158444 Score: 64
Period size: 1 Copynumber: 68.0 Consensus size: 1
38158367 TATTATGCCT
* * * * * * * *
38158377 AAAAAAACAAAAAAAAAACAAACAAAAAAAACAAAAAAACAAAAAAAAACAAAAAAGAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38158442 AAA
1 AAA
38158445 TCAAGATGAA
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:38158392 original size:10 final size:10
Alignment explanation
Indices: 38158377--38158432 Score: 78
Period size: 10 Copynumber: 5.4 Consensus size: 10
38158367 TATTATGCCT
38158377 AAAAAAACAAA
1 AAAAAAAC-AA
38158388 AAAAAAACAA
1 AAAAAAACAA
38158398 ACAAAAAA-AA
1 A-AAAAAACAA
38158408 CAAAAAAACAA
1 -AAAAAAACAA
38158419 AAAAAAACAA
1 AAAAAAACAA
38158429 AAAA
1 AAAA
38158433 GAAAAAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
10 25 0.60
11 17 0.40
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:38158407 original size:17 final size:16
Alignment explanation
Indices: 38158377--38158444 Score: 84
Period size: 17 Copynumber: 4.1 Consensus size: 16
38158367 TATTATGCCT
38158377 AAAAAAAC-AAAAAAA
1 AAAAAAACAAAAAAAA
*
38158392 AAACAAACAAAAAAAA
1 AAAAAAACAAAAAAAA
38158408 CAAAAAAACAAAAAAAA
1 -AAAAAAACAAAAAAAA
*
38158425 ACAAAAAAGAAAAAGAAA
1 A-AAAAAACAAAAA-AAA
38158443 AA
1 AA
38158445 TCAAGATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 7 0.15
16 8 0.17
17 27 0.59
18 4 0.09
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAAAA
Found at i:38158408 original size:24 final size:23
Alignment explanation
Indices: 38158377--38158444 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
38158367 TATTATGCCT
*
38158377 AAAAAAACAAAAAAAAAACAAACA
1 AAAAAAACAAAAAAAAAA-AAAAA
38158401 AAAAAAACAAAAAAACAAAAAAAA
1 AAAAAAACAAAAAAA-AAAAAAAA
* *
38158425 ACAAAAAAGAAAAAGAAAAA
1 A-AAAAAACAAAAAAAAAAA
38158445 TCAAGATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
24 24 0.62
25 15 0.38
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (23 bp):
AAAAAAACAAAAAAAAAAAAAAA
Found at i:38158412 original size:18 final size:18
Alignment explanation
Indices: 38158377--38158432 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
38158367 TATTATGCCT
38158377 AAAAAAAC--AAAAAAA-
1 AAAAAAACAAAAAAAAAC
*
38158392 AAACAAAC-AAAAAAAAC
1 AAAAAAACAAAAAAAAAC
38158409 AAAAAAACAAAAAAAAAC
1 AAAAAAACAAAAAAAAAC
38158427 AAAAAA
1 AAAAAA
38158433 GAAAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 7 0.19
16 7 0.19
17 7 0.19
18 15 0.42
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAC
Done.