Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 7 of 18
Found at i:3485617 original size:38 final size:38
Alignment explanation
Indices: 3485549--3485632 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
3485539 CCTGGTGTGA
3485549 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGGT
1 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGT-GGT
*
3485588 CTGGACTGGGCTGGCA-CCTCTTGGGCCTCCTGGTGGT
1 CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGT
3485625 CTGGACTG
1 CTGGACTG
3485633 TGGCCACGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 11 0.25
38 17 0.39
39 16 0.36
ACGTcount: A:0.07, C:0.30, G:0.38, T:0.25
Consensus pattern (38 bp):
CTGGACTGGGCTGGCACCCTCTTGGGCCTCCAGGTGGT
Found at i:3489558 original size:23 final size:23
Alignment explanation
Indices: 3489497--3489550 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
3489487 CAAGGTATTC
*
3489497 ATGTAAATATAATATGTCATTTA
1 ATGTAAATATAACATGTCATTTA
3489520 ATGTAAATATAACATGTCATTTA
1 ATGTAAATATAACATGTCATTTA
3489543 ATGTAAAT
1 ATGTAAAT
3489551 CACCCATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (23 bp):
ATGTAAATATAACATGTCATTTA
Found at i:3493151 original size:20 final size:22
Alignment explanation
Indices: 3493126--3493166 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3493116 AGATATGGAG
3493126 AAAATAA-AAA-TATATTATTT
1 AAAATAATAAATTATATTATTT
3493146 AAAATAATTAAATTATATTAT
1 AAAATAA-TAAATTATATTAT
3493167 AGTAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATAATAAATTATATTATTT
Found at i:3493455 original size:27 final size:26
Alignment explanation
Indices: 3493413--3493479 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
3493403 TCATCATTTA
* *
3493413 AAAAAATTAAAATAAAATATATAATAT
1 AAAAAATTAAAATAAAAAATA-AAAAT
* *
3493440 AAAAAATTATATTAAAAAATAAAAAT
1 AAAAAATTAAAATAAAAAATAAAAAT
*
3493466 AAAATATATAAAAT
1 AAAAAAT-TAAAAT
3493480 TATGACAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAAATTAAAATAAAAAATAAAAAT
Found at i:3493468 original size:13 final size:13
Alignment explanation
Indices: 3493413--3493479 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
3493403 TCATCATTTA
*
3493413 AAAAAATTAAAAT
1 AAAAAATAAAAAT
* *
3493426 AAAATATATAATAT
1 AAAAAATA-AAAAT
* * *
3493440 AAAAAATTATATT
1 AAAAAATAAAAAT
3493453 AAAAAATAAAAAT
1 AAAAAATAAAAAT
*
3493466 AAAATATATAAAAT
1 AAAAAATA-AAAAT
3493480 TATGACAAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
13 25 0.62
14 15 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:3493748 original size:15 final size:15
Alignment explanation
Indices: 3493726--3493784 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
3493716 ACTTACGATC
3493726 ATATTATTTATAATT
1 ATATTATTTATAATT
* *
3493741 ACATTATTTACAATT
1 ATATTATTTATAATT
* *
3493756 ATATTACTTATAATC
1 ATATTATTTATAATT
3493771 ATATTATATTATAA
1 ATATTAT-TTATAA
3493785 AATATCAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
15 30 0.83
16 6 0.17
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTATTTATAATT
Found at i:3493976 original size:2 final size:2
Alignment explanation
Indices: 3493969--3493994 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3493959 GTTGTGTTTG
3493969 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3493995 TTGTCTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3494414 original size:122 final size:122
Alignment explanation
Indices: 3494203--3494427 Score: 337
Period size: 122 Copynumber: 1.8 Consensus size: 122
3494193 CAATCAAACC
**
3494203 TAAATTAATTTAAACTCGAACTTAATCAAAAATCCATTTGTTAAAAAATTATAATGAAGTGGGCT
1 TAAATTAATTTAAACTCGAACTTAATCAAAAATCCATCCGTTAAAAAATTATAATGAAGTGGGCT
* *
3494268 TTTCTTGATAAAAACTATTTGAGATCCAATTCACTTTTCGAAAGTTTATATCAAATT
66 TTTATTGATAAAAACTATTCGAGATCCAATTCACTTTTCGAAAGTTTATATCAAATT
* *
3494325 TAAATTAATTTAAACTCGAACTTATTCAAAAA-CTCATCCGTTAAAAAATTCTAAT-AAGATGGG
1 TAAATTAATTTAAACTCGAACTTAATCAAAAATC-CATCCGTTAAAAAATTATAATGAAG-TGGG
* * *
3494388 CTTTTATTGATAAGAACTATTCGAGATCCAGTTCGCTTTT
64 CTTTTATTGATAAAAACTATTCGAGATCCAATTCACTTTT
3494428 TGAAGGCATA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
121 4 0.04
122 88 0.96
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (122 bp):
TAAATTAATTTAAACTCGAACTTAATCAAAAATCCATCCGTTAAAAAATTATAATGAAGTGGGCT
TTTATTGATAAAAACTATTCGAGATCCAATTCACTTTTCGAAAGTTTATATCAAATT
Found at i:3499324 original size:114 final size:114
Alignment explanation
Indices: 3499192--3499425 Score: 344
Period size: 114 Copynumber: 2.1 Consensus size: 114
3499182 GATTTTCTCA
* * *
3499192 CTTCTCAAAGGATTGTTGATAGTCAAGAAAAG-AGAGAAAGAAAAGACCTTGCCAATTTTTAAGG
1 CTTCTCAAAGGATTGTTGATAGTCAAGAAAAGAAAAAAAAGAAAAGACCTTGCCAATTTCTAAGG
* * *
3499256 TTTAAAAAGGTAGGTTGATATCCAGGGTTTAAGGTATTGTGCTGATTCCT
66 TTTAAAAA-GTAAGCTAATATCCAGGGTTTAAGGTATTGTGCTGATTCCT
* * * *
3499306 CTTCTCAAAGGATTGTTGATAGTTAAGAAAAGAAAAAAAAGAAAAGGCCTTGTCAATTTCTAGGG
1 CTTCTCAAAGGATTGTTGATAGTCAAGAAAAGAAAAAAAAGAAAAGACCTTGCCAATTTCTAAGG
*
3499371 TTTTAAAAGTAAGCTAATATCCAGGGTTTAAGGTATTGTGCTGATTCCT
66 TTTAAAAAGTAAGCTAATATCCAGGGTTTAAGGTATTGTGCTGATTCCT
*
3499420 TTTCTC
1 CTTCTC
3499426 TCACTTTTCT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
114 74 0.69
115 33 0.31
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (114 bp):
CTTCTCAAAGGATTGTTGATAGTCAAGAAAAGAAAAAAAAGAAAAGACCTTGCCAATTTCTAAGG
TTTAAAAAGTAAGCTAATATCCAGGGTTTAAGGTATTGTGCTGATTCCT
Found at i:3500771 original size:16 final size:16
Alignment explanation
Indices: 3500728--3500762 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3500718 ATGACTTAAT
3500728 TAATA-ATAAAAATAA
1 TAATATATAAAAATAA
*
3500743 TAATATATAAAAATAT
1 TAATATATAAAAATAA
3500759 TAAT
1 TAAT
3500763 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATATATAAAAATAA
Found at i:3502727 original size:21 final size:20
Alignment explanation
Indices: 3502700--3502746 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
3502690 ATGGCTTCAA
*
3502700 TTAAAAAA-ATGGTAATTAAT
1 TTAAAAAAGA-GGTAATGAAT
3502720 TATAAAAAAGAGGTAATGAAT
1 T-TAAAAAAGAGGTAATGAAT
3502741 TTAAAA
1 TTAAAA
3502747 CAATTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 17 0.71
22 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (20 bp):
TTAAAAAAGAGGTAATGAAT
Found at i:3503312 original size:54 final size:53
Alignment explanation
Indices: 3503220--3503321 Score: 159
Period size: 54 Copynumber: 1.9 Consensus size: 53
3503210 AAAATCAAGG
* * *
3503220 AAATATCTAGAATCTTTATAACTGTAACAATTATAAATAAAAGACGAACCAATA
1 AAATATCTAGAATCATTATAACTGTAACAACTACAAATAAAA-ACGAACCAATA
*
3503274 AAATATCTAGAATCATTATAACTGTAATAACTACAAATAAAAACGAAC
1 AAATATCTAGAATCATTATAACTGTAACAACTACAAATAAAAACGAAC
3503322 ATTCAAACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 6 0.14
54 38 0.86
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (53 bp):
AAATATCTAGAATCATTATAACTGTAACAACTACAAATAAAAACGAACCAATA
Found at i:3507570 original size:2 final size:2
Alignment explanation
Indices: 3507565--3507610 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
3507555 TGTGTGTGGT
3507565 GA GA GA GA GA GCA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA G-A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3507608 GA G
1 GA G
3507611 TCTTAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3511372 original size:21 final size:21
Alignment explanation
Indices: 3511348--3511392 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3511338 AGACAAATGA
*
3511348 TGTCCTCTCATCTCAAAATTC
1 TGTCCTCTCATCTCAAAACTC
* * *
3511369 TGTCGTTTCATCTGAAAACTC
1 TGTCCTCTCATCTCAAAACTC
3511390 TGT
1 TGT
3511393 GGATCTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (21 bp):
TGTCCTCTCATCTCAAAACTC
Found at i:3524691 original size:31 final size:31
Alignment explanation
Indices: 3524656--3524719 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
3524646 TACCATATTC
* *
3524656 AATATAACTATTTAAATAGTTATATTATGAA
1 AATATAACCATTTAAATAATTATATTATGAA
* *
3524687 AATATAACCCTTTGAATAATTATATTATGAA
1 AATATAACCATTTAAATAATTATATTATGAA
3524718 AA
1 AA
3524720 GAAATAGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (31 bp):
AATATAACCATTTAAATAATTATATTATGAA
Found at i:3525259 original size:27 final size:27
Alignment explanation
Indices: 3525198--3525279 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
3525188 AACATTACTG
*
3525198 CAACAACAATTGTTGCTGCAACCACAA
1 CAACTACAATTGTTGCTGCAACCACAA
* *
3525225 CAATTACAATTGTTGCTGCATCCACAA
1 CAACTACAATTGTTGCTGCAACCACAA
** * * * *
3525252 TTACTACAACTATTACTGCTACCACAA
1 CAACTACAATTGTTGCTGCAACCACAA
3525279 C
1 C
3525280 CATTGTTGAA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (27 bp):
CAACTACAATTGTTGCTGCAACCACAA
Found at i:3531570 original size:31 final size:30
Alignment explanation
Indices: 3531515--3531594 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 30
3531505 TGAAGAATTA
* *
3531515 TGAATAG-TATTTTATTAAA-TATAACTGTT
1 TGAATAGTTATATTA-TAAAGTATAACTCTT
*
3531544 TGAATATTTATATTATGAAAGTATAACTCTT
1 TGAATAGTTATATTAT-AAAGTATAACTCTT
3531575 TGAATAGTTATATTATAAAG
1 TGAATAGTTATATTATAAAG
3531595 GGAAACAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 7 0.16
30 13 0.30
31 24 0.55
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (30 bp):
TGAATAGTTATATTATAAAGTATAACTCTT
Found at i:3533107 original size:15 final size:17
Alignment explanation
Indices: 3533087--3533119 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3533077 ATTACAATTA
3533087 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAACGTT
3533102 ATAATTTTTATAACGTT
1 ATAATTTTTATAACGTT
3533119 A
1 A
3533120 ATACAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
ATAATTTTTATAACGTT
Found at i:3534068 original size:21 final size:20
Alignment explanation
Indices: 3534042--3534080 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3534032 TATAAAAATA
3534042 TGTTACACGCTATGGTTAAGT
1 TGTTACACGCTAT-GTTAAGT
3534063 TGTTACACGCTATGTTAA
1 TGTTACACGCTATGTTAA
3534081 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
TGTTACACGCTATGTTAAGT
Found at i:3534084 original size:45 final size:46
Alignment explanation
Indices: 3533942--3534085 Score: 143
Period size: 45 Copynumber: 3.2 Consensus size: 46
3533932 ACACACCATA
* *
3533942 TACAGAAATATGTTACACGTCATGGTTAGGTTGTTATACGCTATG-
1 TACAAAAATATGTTACACGTCATGGTTAGGTTGTTACACGCTATGT
** * * * *
3533987 TACAAAAACGTGTGATACGTCATAGTTAGGTTGTTACATG-TCAT-T
1 TACAAAAATATGTTACACGTCATGGTTAGGTTGTTACACGCT-ATGT
* *
3534032 TATAAAAATATGTTACACG-CTATGGTTAAGTTGTTACACGCTATGT
1 TACAAAAATATGTTACACGTC-ATGGTTAGGTTGTTACACGCTATGT
*
3534078 TAAAAAAA
1 TACAAAAA
3534086 AATTACTGTT
Statistics
Matches: 77, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
44 2 0.03
45 66 0.86
46 9 0.12
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (46 bp):
TACAAAAATATGTTACACGTCATGGTTAGGTTGTTACACGCTATGT
Found at i:3534221 original size:29 final size:29
Alignment explanation
Indices: 3534166--3534228 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
3534156 ATGTTGAAAA
*
3534166 AAAAAATACTGTTATTACACGCCATATTG
1 AAAAAATACTGTTATTACACGCCATATTC
* * **
3534195 AAAAAATATTGTTGTTACACGTTATATTC
1 AAAAAATACTGTTATTACACGCCATATTC
3534224 AAAAA
1 AAAAA
3534229 CATTTTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAAAATACTGTTATTACACGCCATATTC
Found at i:3534239 original size:27 final size:29
Alignment explanation
Indices: 3534166--3534240 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 29
3534156 ATGTTGAAAA
* *
3534166 AAAAAATACTGTTATTACACGCCATATTG
1 AAAAAACATTGTTATTACACGCCATATTG
* * **
3534195 AAAAAATATTGTTGTTACACGTTATATT-
1 AAAAAACATTGTTATTACACGCCATATTG
*
3534223 CAAAAACATT-TTATTACA
1 AAAAAACATTGTTATTACA
3534241 TTTTAATGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.18
28 8 0.21
29 24 0.62
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (29 bp):
AAAAAACATTGTTATTACACGCCATATTG
Found at i:3544632 original size:23 final size:22
Alignment explanation
Indices: 3544593--3544639 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3544583 AAAGATAATT
*
3544593 TTACTTTTAATTAATTTTTATTA
1 TTACTATTAATTAA-TTTTATTA
3544616 TTACTATTATATT-ATTTTATTA
1 TTACTATTA-ATTAATTTTATTA
3544638 TT
1 TT
3544640 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 9 0.41
24 3 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTACTATTAATTAATTTTATTA
Found at i:3546973 original size:15 final size:15
Alignment explanation
Indices: 3546951--3546996 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
3546941 ACATTACAAT
3546951 GCAATGTGATTACAG
1 GCAATGTGATTACAG
* * *
3546966 GTAATGTGATTGCAA
1 GCAATGTGATTACAG
3546981 GCAATGTGATTACAG
1 GCAATGTGATTACAG
3546996 G
1 G
3546997 GAAAATAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (15 bp):
GCAATGTGATTACAG
Found at i:3547226 original size:6 final size:6
Alignment explanation
Indices: 3547215--3547289 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
3547205 ATATCATATA
* * * *
3547215 TTTTAT TTTTAT TTATTAT TATAAT ATTTTAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* *
3547265 TTATAT TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
3547290 ATAATATCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 3 0.05
6 31 0.56
7 21 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:3547252 original size:23 final size:23
Alignment explanation
Indices: 3547218--3547281 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
3547208 TCATATATTT
3547218 TATTTT-TA-TTTATTATTATAA
1 TATTTTATATTTTATTATTATAA
3547239 TATTTTATATTTTATT-TT-TAA
1 TATTTTATATTTTATTATTATAA
3547260 TATATTTATATTTTTATTATTA
1 TAT-TTTATA-TTTTATTATTA
3547282 ATTTTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
21 12 0.32
22 10 0.27
23 13 0.35
24 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTATATTTTATTATTATAA
Found at i:3547292 original size:23 final size:22
Alignment explanation
Indices: 3547220--3547292 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
3547210 ATATATTTTA
*
3547220 TTTTTAT-TTATTATTA-TAAT
1 TTTTTATATTTTTATTATTAAT
* *
3547240 ATTTTATA-TTTTATTTTTAAT
1 TTTTTATATTTTTATTATTAAT
*
3547261 ATATTTATATTTTTATTATTAAT
1 -TTTTTATATTTTTATTATTAAT
3547284 TTTTATATA
1 TTTT-TATA
3547293 ATATCATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
20 12 0.29
21 4 0.10
22 9 0.22
23 16 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATATTTTTATTATTAAT
Found at i:3547340 original size:113 final size:114
Alignment explanation
Indices: 3547141--3547369 Score: 401
Period size: 113 Copynumber: 2.0 Consensus size: 114
3547131 AAAATATAAA
3547141 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTGTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTGTAA
3547206 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
66 TATCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATT
*
3547255 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTGTA
*
3547318 ATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
65 ATATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
3547368 TT
1 TT
3547370 CATTTCTTTA
Statistics
Matches: 111, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
112 3 0.03
113 91 0.82
114 17 0.15
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTGTAA
TATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
Found at i:3547360 original size:10 final size:9
Alignment explanation
Indices: 3547210--3547366 Score: 58
Period size: 8 Copynumber: 18.2 Consensus size: 9
3547200 TTGTAATATC
3547210 ATATA-TTT
1 ATATATTTT
3547218 -TAT-TTTT
1 ATATATTTT
*
3547225 ATTTATTATT
1 ATATATT-TT
3547235 ATA-ATATTT
1 ATATAT-TTT
3547244 -TATATTTT
1 ATATATTTT
*
3547252 AT-T-TTTA
1 ATATATTTT
3547259 ATATA-TTT
1 ATATATTTT
3547267 ATAT-TTTT
1 ATATATTTT
3547275 ATTATTAATTTT
1 A-TA-T-ATTTT
**
3547287 -TATATAAT
1 ATATATTTT
3547295 ATCATATTTT
1 AT-ATATTTT
3547305 AAATATATTTT
1 --ATATATTTT
* *
3547316 -TA-ATGTC
1 ATATATTTT
3547323 ATATA-TTT
1 ATATATTTT
3547331 -TAT-TTTT
1 ATATATTTT
*
3547338 ATTTATTATT
1 ATATATT-TT
3547348 ATA-ATTTT
1 ATATATTTT
3547356 ATATATTTT
1 ATATATTTT
3547365 AT
1 AT
3547367 TTTCATTTCT
Statistics
Matches: 110, Mismatches: 14, Indels: 49
0.64 0.08 0.28
Matches are distributed among these distances:
7 20 0.18
8 34 0.31
9 26 0.24
10 17 0.15
11 7 0.06
12 6 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
ATATATTTT
Found at i:3547360 original size:33 final size:33
Alignment explanation
Indices: 3547323--3547408 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
3547313 TTTTAATGTC
*
3547323 ATATATTTTATTTTTATTTA-TTATTATAATTTT
1 ATATATTTTATTTTTATTTATTTAATAT-ATTTT
* *
3547356 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTTAATATATTTT
* *
3547389 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
3547409 TAATTTGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTTAATATATTTT
Found at i:3547481 original size:24 final size:25
Alignment explanation
Indices: 3547386--3547494 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 25
3547376 TTTAATATAT
*
3547386 TTTTTATATTATATATTTTATTTTAA
1 TTTTTATA-TCTATATTTTATTTTAA
* *
3547412 TTTGTTTTATCTATATTATATAAATATTAA
1 TTT-TTATATCTATATT-T-T--ATTTTAA
*
3547442 TTTTTTATAT-TTTATTTTATTTTAA
1 -TTTTTATATCTATATTTTATTTTAA
*
3547467 TTTTTAT-TCTATATTATATATTT-A
1 TTTTTATATCTATATTTTAT-TTTAA
3547491 TTTT
1 TTTT
3547495 AATTATAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
23 1 0.01
24 20 0.30
25 9 0.13
26 10 0.15
27 6 0.09
28 2 0.03
29 5 0.07
30 11 0.16
31 3 0.04
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (25 bp):
TTTTTATATCTATATTTTATTTTAA
Found at i:3561241 original size:9 final size:9
Alignment explanation
Indices: 3561227--3561252 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3561217 AGTGCCACAT
3561227 CAGCAGCAA
1 CAGCAGCAA
3561236 CAGCAGCAA
1 CAGCAGCAA
3561245 CAGCAGCA
1 CAGCAGCA
3561253 GCACCAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.35, G:0.23, T:0.00
Consensus pattern (9 bp):
CAGCAGCAA
Found at i:3566007 original size:39 final size:36
Alignment explanation
Indices: 3565944--3566015 Score: 108
Period size: 39 Copynumber: 1.9 Consensus size: 36
3565934 ATCAGATGCC
3565944 TACTCAAATGCAGGAGAGCATGGGAATGGAGAGGCA
1 TACTCAAATGCAGGAGAGCATGGGAATGGAGAGGCA
*
3565980 TACTCAAATGCGGAAGGAGAGCCTGGGAATGGAGAG
1 TACTCAAATGC---AGGAGAGCATGGGAATGGAGAG
3566016 ACCGACTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 11 0.34
39 21 0.66
ACGTcount: A:0.35, C:0.14, G:0.38, T:0.14
Consensus pattern (36 bp):
TACTCAAATGCAGGAGAGCATGGGAATGGAGAGGCA
Found at i:3568765 original size:2 final size:2
Alignment explanation
Indices: 3568744--3568782 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3568734 AAATCAGCCC
* * *
3568744 AT AT AT AA AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3568783 AGAAGAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:3575811 original size:17 final size:18
Alignment explanation
Indices: 3575770--3575811 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3575760 GTCACATGAC
* *
3575770 ATGTCACGTCATCATATTG
1 ATGTCACGTCA-CATACTA
3575789 ATGTCACGTCA-ATACTA
1 ATGTCACGTCACATACTA
3575806 ATGTCA
1 ATGTCA
3575812 TTCCTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
19 11 0.52
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (18 bp):
ATGTCACGTCACATACTA
Found at i:3577477 original size:144 final size:145
Alignment explanation
Indices: 3577216--3577639 Score: 707
Period size: 141 Copynumber: 3.0 Consensus size: 145
3577206 TATTTTAACC
* * * *
3577216 ATAAAAATATAACACTTAAAAAAATTCTTAAATTATTTAAAAAATTCATATAAATCTTTTTTTCT
1 ATAAAAGTATAATACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTCT
* *
3577281 CATTTTTTTAACAAAAGTCTATACCTTTTTTGAAGAAATATGCTCCTAAATTATTCAAAAAATTC
66 CATTTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAAATTC
3577346 AAATAAATCCAAAAG
131 AAATAAATCCAAAAG
3577361 ATAAAAGTATAATACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTCT
1 ATAAAAGTATAATACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTCT
3577426 CA-TTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTC--AAAATTC
66 CATTTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAAATTC
*
3577488 AAATAAATCTAAAAG
131 AAATAAATCCAAAAG
*
3577503 ATAAAAGTACAATACTT-AAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTGC--TTTTTC
1 ATAAAAGTATAATACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGT-CTTTTTTTC
* *
3577565 TCATTTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAGTTATACAAAAAATT
65 TCATTTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAAATT
3577630 CAAATAAATC
130 CAAATAAATC
3577640 ATTTTCTTGT
Statistics
Matches: 265, Mismatches: 10, Indels: 10
0.93 0.04 0.04
Matches are distributed among these distances:
140 9 0.03
141 88 0.33
142 38 0.14
143 16 0.06
144 51 0.19
145 63 0.24
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.38
Consensus pattern (145 bp):
ATAAAAGTATAATACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTCT
CATTTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAAAATTC
AAATAAATCCAAAAG
Found at i:3577715 original size:141 final size:138
Alignment explanation
Indices: 3577235--3577778 Score: 576
Period size: 142 Copynumber: 3.8 Consensus size: 138
3577225 TAACACTTAA
* * * *
3577235 AAAAATTCTTAAATTATTTAAAAAATTCATATAAATCTTTTTTTCTCATTTTTTTAACAAAAGTC
1 AAAAACTCCTAAATTATTTAAAAAATTCAAATAAGTC--TTTTTCTCA-TTTTTTAACAAAAGTC
* * *
3577300 TATACCTTTTTTGAAGAAATATGCTCCTAAATTATTCAAAAAATTCAAATAAATCCAAAAGATAA
63 TATAGCTTTTATGAAGAAATATGCTCCT-AATTATTCAAAAAATTCAAATAAATCTAAAAGATAA
* *
3577365 AAGTATAATACTT
127 AAG-ACAAGACTT
* *
3577378 AAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTCTTTTTTTCTCATTTTTTAACAAAAGT
1 --AAAAACTCCTAAATTATTTAAAAAATTCAAATAAGTC--TTTTTCTCATTTTTTAACAAAAGT
3577443 CTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTC--AAAATTCAAATAAATCTAAAAGATA
62 CTATAGCTTTTATGAAGAAATATGCTCCT-AATTATTCAAAAAATTCAAATAAATCTAAAAGATA
*
3577506 AAAGTACAATACTT
126 AAAG-ACAAGACTT
* *
3577520 AAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTGCTTTTTCTCATTTTTTTAACAAAAGTC
1 -AAAAACTCCTAAATTATTTAAAAAATTCAAATAAGT-CTTTTTCTCA-TTTTTTAACAAAAGTC
* ****
3577585 TATAGCTTTTATGAAGAAATATGCTCCTAAGTTATACAAAAAATTCAAATAAATCATTTTCTTGT
63 TATAGCTTTTATGAAGAAATATGCTCCTAA-TTATTCAAAAAATTCAAATAAATC---TAAAAG-
* *** *
3577650 TTTTCA-ACAAGAGTCT
123 ATAAAAGACAAGACT-T
* * *
3577666 -ACAGCTCCTAAA-TATTTAGAAAATTCAAATAAGTCATTTTTCTCATTTTTTAACAAAAGTCTA
1 AAAAACTCCTAAATTATTTAAAAAATTCAAATAAGTC-TTTTTCTCATTTTTTAACAAAAGTCTA
* * * *
3577729 TAGCTTTTGTGAAGACATATGCTACTGAACTATTCAAAAAATTCAAATAA
65 TAGCTTTTATGAAGAAATATGCTCCT-AATTATTCAAAAAATTCAAATAA
3577779 GACTTTTGTT
Statistics
Matches: 360, Mismatches: 27, Indels: 27
0.87 0.07 0.07
Matches are distributed among these distances:
140 11 0.03
141 86 0.24
142 99 0.28
143 48 0.13
144 59 0.16
145 52 0.14
146 3 0.01
147 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (138 bp):
AAAAACTCCTAAATTATTTAAAAAATTCAAATAAGTCTTTTTCTCATTTTTTAACAAAAGTCTAT
AGCTTTTATGAAGAAATATGCTCCTAATTATTCAAAAAATTCAAATAAATCTAAAAGATAAAAGA
CAAGACTT
Found at i:3577772 original size:285 final size:285
Alignment explanation
Indices: 3577229--3577778 Score: 702
Period size: 285 Copynumber: 1.9 Consensus size: 285
3577219 AAAATATAAC
*
3577229 ACTTAAAAAAATTCTTAAATTATTTAAAAAATTCATATAAATCTTTTTTTCTCATTTTTTTAACA
1 ACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAATC-TTTTTTCTCATTTTTTTAACA
* *
3577294 AAAGTCTATACCTTTTTTGAAGAAATATGCTCCTAAATTATTCAAAAAATTCAAATAAATCCAAA
65 AAAGTCTATACCTTTTATGAAGAAATATGCTCCTAAATTATACAAAAAATTCAAATAAATCCAAA
* * *
3577359 AGATAAAAGTATAATACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTCTTTTTTT
130 AGATAAAAGTATAATAC-TAAAAAAACTCCTAAATTATTTAAAAAATTCAAATAAGTCTATTTTT
* *
3577424 CTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAATTATTCAAAATTCA
194 CTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTACTAAACTATTCAAAATTCA
3577489 AATAAATCTAAAAGATAAAAGTACAAT
259 AATAAATCTAAAAGATAAAAGTACAAT
*
3577516 ACTT-AAAAAATTCTTAAATTATTTAAAAAATTCAAATAAGTGC-TTTTTCTCATTTTTTTAACA
1 ACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAAT-CTTTTTTCTCATTTTTTTAACA
* * **
3577579 AAAGTCTATAGCTTTTATGAAGAAATATGCTCCTAAGTTATACAAAAAATTCAAATAAAT-CATT
65 AAAGTCTATACCTTTTATGAAGAAATATGCTCCTAAATTATACAAAAAATTCAAATAAATCCAAA
*** **** * * * * *
3577643 TTCT-TGTTTTTCA-AC-AAGAGTCTACAGCTCCTAAA-TATTTAGAAAATTCAAATAAGTC-AT
130 AGATAAAAGTATAATACTAA-A----AAAACTCCTAAATTATTTAAAAAATTCAAATAAGTCTAT
* * *
3577703 TTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTGTGAAGACATATGCTACTGAACTATTCAAAA
190 TTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTACTAAACTATTC--AA
3577768 AATTCAAATAA
253 AATTCAAATAA
3577779 GACTTTTGTT
Statistics
Matches: 227, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
280 2 0.01
281 1 0.00
282 2 0.01
283 60 0.26
284 25 0.11
285 97 0.43
286 35 0.15
287 5 0.02
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (285 bp):
ACTTAAAAAAATTCTTAAATTATTTAAAAAATTCAAATAAATCTTTTTTCTCATTTTTTTAACAA
AAGTCTATACCTTTTATGAAGAAATATGCTCCTAAATTATACAAAAAATTCAAATAAATCCAAAA
GATAAAAGTATAATACTAAAAAAACTCCTAAATTATTTAAAAAATTCAAATAAGTCTATTTTTCT
CATTTTTTAACAAAAGTCTATAGCTTTTATGAAGAAATATGCTACTAAACTATTCAAAATTCAAA
TAAATCTAAAAGATAAAAGTACAAT
Found at i:3577829 original size:82 final size:80
Alignment explanation
Indices: 3577678--3577964 Score: 364
Period size: 82 Copynumber: 3.5 Consensus size: 80
3577668 AGCTCCTAAA
* * * *
3577678 TATTTAGAAAATTCAAATAAGTCATTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTGTGAAG
1 TATTCAGAAAATTCAAATAAG-CTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAA
3577743 ACATATGCTACTGAAC
65 ACATATGCTACTGAAC
*
3577759 TATTCAAAAAATTCAAATAAGACTTTTGTTCTCATTTTTTAACAAAAGTCTAT-GACTTTTATGA
1 TATTCAGAAAATTCAAATAAG-CTTTT-TTCTCATTTTTTAACAAAAGTCTATAG-CTTTTATGA
3577823 AAACATATGCTACTGAAC
63 AAACATATGCTACTGAAC
* * *
3577841 TACTCAGAAAATTCAAATAAG-TTATTTTCTCGTTTTTTAACAAAAGTCTACAGCTTTTATGAAG
1 TATTCAGAAAATTCAAATAAGCTT-TTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAA-
* *
3577905 AA-ATATGCTCCTAAAC
64 AACATATGCTACTGAAC
* * **
3577921 TATTCAGAAAATTCAAATATGTTTTTTTTCTTGTTTTTTAACAA
1 TATTCAGAAAATTCAAATAAG-CTTTTTTCTCATTTTTTAACAA
3577965 CAGTGTACAA
Statistics
Matches: 184, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
80 66 0.36
81 47 0.26
82 71 0.39
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (80 bp):
TATTCAGAAAATTCAAATAAGCTTTTTTCTCATTTTTTAACAAAAGTCTATAGCTTTTATGAAAA
CATATGCTACTGAAC
Found at i:3581130 original size:17 final size:17
Alignment explanation
Indices: 3581111--3581146 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
3581101 GTTAATTGTT
3581111 TATAAATAATAGATAATTA
1 TATAAA-AATA-ATAATTA
3581130 TATAAAAATAATAATTA
1 TATAAAAATAATAATTA
3581147 ATGTTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATAAAAATAATAATTA
Found at i:3586042 original size:2 final size:2
Alignment explanation
Indices: 3586035--3586076 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3586025 ATCCATCAAG
3586035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3586077 GTATCTTCGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3598758 original size:23 final size:21
Alignment explanation
Indices: 3598727--3598768 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3598717 TTTCCCTCTT
3598727 TCTTCTTCCTTCCTCTCCTCTGC
1 TCTTCTTCCTT--TCTCCTCTGC
*
3598750 TCTTTTTCCTTTCTCCTCT
1 TCTTCTTCCTTTCTCCTCT
3598769 TTCTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.00, C:0.43, G:0.02, T:0.55
Consensus pattern (21 bp):
TCTTCTTCCTTTCTCCTCTGC
Found at i:3600929 original size:23 final size:23
Alignment explanation
Indices: 3600898--3600941 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3600888 ATATTTATAT
* *
3600898 AAAATTATTACTTAAAATAAATA
1 AAAAATATTAATTAAAATAAATA
*
3600921 AAAAATATTAATTATAATAAA
1 AAAAATATTAATTAAAATAAA
3600942 AATTTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAAATATTAATTAAAATAAATA
Found at i:3602132 original size:20 final size:20
Alignment explanation
Indices: 3602104--3602148 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3602094 TATTTCTATG
*
3602104 TAAATTTATAATAT-TAAATA
1 TAAAATTATAATATATAAA-A
3602124 TAAAATTATAATATATAAAA
1 TAAAATTATAATATATAAAA
3602144 TAAAA
1 TAAAA
3602149 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATTATAATATATAAAA
Found at i:3604460 original size:13 final size:14
Alignment explanation
Indices: 3604433--3604462 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3604423 TGTTCTTCAA
3604433 TAAAAGTCAAAACT
1 TAAAAGTCAAAACT
3604447 TAAAAGTC-AAACT
1 TAAAAGTCAAAACT
3604460 TAA
1 TAA
3604463 TTTATCGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (14 bp):
TAAAAGTCAAAACT
Found at i:3604768 original size:20 final size:20
Alignment explanation
Indices: 3604717--3604769 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3604707 ACAAAAGGCA
* *
3604717 ATGTATTGATAAATTAACAT
1 ATGTATCGATACATTAACAT
3604737 ATGTATCGATACATTAACAT
1 ATGTATCGATACATTAACAT
3604757 ATGTATCGATACA
1 ATGTATCGATACA
3604770 ATATGACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTAACAT
Found at i:3614894 original size:31 final size:31
Alignment explanation
Indices: 3614858--3614932 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
3614848 CATGAGAATC
*
3614858 AAATTACATAAAATTATAAAGTATACAAATT
1 AAATTACACAAAATTATAAAGTATACAAATT
* * * *
3614889 AAATTAAACAAAATTTTATAGTATAGAAATT
1 AAATTACACAAAATTATAAAGTATACAAATT
3614920 AAATTACACAAAA
1 AAATTACACAAAA
3614933 CTCTATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.31
Consensus pattern (31 bp):
AAATTACACAAAATTATAAAGTATACAAATT
Found at i:3617261 original size:3 final size:3
Alignment explanation
Indices: 3617253--3617277 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3617243 TAAGATAAGG
3617253 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
3617278 AAAAGGCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3619071 original size:2 final size:2
Alignment explanation
Indices: 3619064--3619095 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3619054 GACAACAATG
3619064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3619096 TTCTTGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3623014 original size:2 final size:2
Alignment explanation
Indices: 3623007--3623048 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
3622997 TAAAGGTTCA
* *
3623007 AG AG AG AG AG AA AG AG AG AG A- AA AG AG ACG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG
3623049 GTGAAGCGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3623401 original size:2 final size:2
Alignment explanation
Indices: 3623390--3623422 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3623380 ATGGCAGCAG
3623390 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3623423 CGGGTATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3626824 original size:7 final size:7
Alignment explanation
Indices: 3626812--3626855 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
3626802 TAATCTTATT
3626812 TTAAAGG
1 TTAAAGG
3626819 TTAAAGG
1 TTAAAGG
3626826 TTAAAGG
1 TTAAAGG
*
3626833 TTAAATG
1 TTAAAGG
3626840 -TAAAGG
1 TTAAAGG
3626846 TTTAAAGG
1 -TTAAAGG
3626854 TT
1 TT
3626856 GCACTTGAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.15
7 22 0.67
8 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (7 bp):
TTAAAGG
Found at i:3628878 original size:23 final size:26
Alignment explanation
Indices: 3628849--3628902 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 26
3628839 CACTATCAAA
*
3628849 TCATTTTTCTAG-ACTA-TTTCTTT-
1 TCATTTTTCTAGAACCATTTTCTTTG
3628872 TCATTTTTCTAGAACCATTTTCTTTG
1 TCATTTTTCTAGAACCATTTTCTTTG
3628898 TCATT
1 TCATT
3628903 GACGAGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 12 0.44
24 3 0.11
25 7 0.26
26 5 0.19
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.57
Consensus pattern (26 bp):
TCATTTTTCTAGAACCATTTTCTTTG
Found at i:3629905 original size:33 final size:33
Alignment explanation
Indices: 3629845--3629921 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
3629835 TCTTTCAATG
* *
3629845 TAAAGAGTTGTTTCTTATCATATTATAACTATT
1 TAAAGAGTTATTTCTTATCATAATATAACTATT
* *
3629878 TAAATAGTTATTTTTTATCATAATATAACTATT
1 TAAAGAGTTATTTCTTATCATAATATAACTATT
*
3629911 CAAAGAGTTAT
1 TAAAGAGTTAT
3629922 ATTTAATAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (33 bp):
TAAAGAGTTATTTCTTATCATAATATAACTATT
Found at i:3640791 original size:3 final size:3
Alignment explanation
Indices: 3640783--3640810 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3640773 ATAGTAACTT
3640783 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3640811 CTTCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3641791 original size:2 final size:2
Alignment explanation
Indices: 3641784--3641810 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3641774 CATTTGAAGC
3641784 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3641811 TCAAAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3642902 original size:2 final size:2
Alignment explanation
Indices: 3642895--3642927 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3642885 TCAATAGTAG
3642895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3642928 AACCATAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3653260 original size:14 final size:15
Alignment explanation
Indices: 3653232--3653261 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3653222 CTCCATAAGC
3653232 TTGCATTTCATCATA
1 TTGCATTTCATCATA
3653247 TTGCATTT-ATCATA
1 TTGCATTTCATCATA
3653261 T
1 T
3653262 ACATATGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (15 bp):
TTGCATTTCATCATA
Found at i:3664763 original size:203 final size:201
Alignment explanation
Indices: 3664405--3664896 Score: 615
Period size: 203 Copynumber: 2.4 Consensus size: 201
3664395 AAATGCCTAA
** * * *
3664405 AAACTAGTGAACAAAAGCATCAAAACAGGAGATGAATTGCATAAGTCATGCACCGCCAGTCTCAT
1 AAACTAGTGAACAAAAGCATCAAAACAAAAGATGAATTGCACAAGTCACGCACCGCCAG-C-CTT
* * * * * *
3664470 AATACCTCATAATAAGTTACTTAATGCGTAATATCTACTCACATTATGCCAACGTAACTAATCAT
64 AATACCTAATAATAAGTCACTTAATGCGTAATATCCACTAACATTATGCCAACATAACTAATCAC
* * * * * * *
3664535 GTAACGGCCCAATGTCATGCAAAACATAACAACAAGTCACGCAATACATAAAAATCAGTAATGCA
129 ATAACAGCCCAATATAATGCAAAACATAACAACAAGTCACGCAATACATAAAAACCAATAACGCA
3664600 ATATCTAC
194 ATATCTAC
* * * * *
3664608 AAACTAATGAACAAAAGCCTCAAAAGAAAAGATGAATTGCACAAGTCACGCATCGTCAGCCTTGC
1 AAACTAGTGAACAAAAGCATCAAAACAAAAGATGAATTGCACAAGTCACGCACCGCCAGCCTT--
* * *
3664673 AATACCTAATAATAAGTCACTTAATGCGTAATATCCACTAACATTATGCCACCATAACTAGTTAC
64 AATACCTAATAATAAGTCACTTAATGCGTAATATCCACTAACATTATGCCAACATAACTAATCAC
* * *
3664738 ATAACAGCCCAATATAATTCAAAACATAACAACAAGTCACGCAATACGTAAAAACCAATCACGCA
129 ATAACAGCCCAATATAATGCAAAACATAACAACAAGTCACGCAATACATAAAAACCAATAACGCA
*
3664803 ATGTCTAC
194 ATATCTAC
* * * * *
3664811 AAACTAGTGAACAAAAGCTTCAAAATAAAAGATAAATTGCACAAGTCACGTACCCCCAGTCTCTT
1 AAACTAGTGAACAAAAGCATCAAAACAAAAGATGAATTGCACAAGTCACGCACCGCCAG-C-CTT
3664876 AATACCTAATAATAAGTCACT
64 AATACCTAATAATAAGTCACT
3664897 CAAAGCATAA
Statistics
Matches: 247, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
201 2 0.01
202 1 0.00
203 240 0.97
204 1 0.00
205 3 0.01
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (201 bp):
AAACTAGTGAACAAAAGCATCAAAACAAAAGATGAATTGCACAAGTCACGCACCGCCAGCCTTAA
TACCTAATAATAAGTCACTTAATGCGTAATATCCACTAACATTATGCCAACATAACTAATCACAT
AACAGCCCAATATAATGCAAAACATAACAACAAGTCACGCAATACATAAAAACCAATAACGCAAT
ATCTAC
Found at i:3665900 original size:28 final size:28
Alignment explanation
Indices: 3665862--3665918 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3665852 AATGTTGATA
*
3665862 TAAGTGTAATTAAGGAGCTTGAATTAGT
1 TAAGTGCAATTAAGGAGCTTGAATTAGT
* *
3665890 TAAGTGCAATTAAGGGGGTTGAATTAGT
1 TAAGTGCAATTAAGGAGCTTGAATTAGT
3665918 T
1 T
3665919 GTTAAGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (28 bp):
TAAGTGCAATTAAGGAGCTTGAATTAGT
Found at i:3665971 original size:63 final size:63
Alignment explanation
Indices: 3665898--3666285 Score: 499
Period size: 63 Copynumber: 6.1 Consensus size: 63
3665888 GTTAAGTGCA
* * * * * *
3665898 ATTAAGGGGGTTGAATTAGTTGTTAAGCATTTCC-AATTCTCTTATAATTTTACAGAATTTATT
1 ATTAAAGGGGTTGAATTAGTTATTAAGTA-TTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
* * * *
3665961 ATTAAAGGGGTCGAATTAGTTATTAAGTATTCTTAATTCTCTTCTAATTTTATAGAATTTGTT
1 ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
* * *
3666024 ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTTTAATTTTACAGAATTTATT
1 ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
* * * * *
3666087 ATTAAGGGGGCTGAATTGGTTATTAAGTATTCCTCATTCTCTTCTAATTTTATAAAATTTGTT
1 ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
** * *
3666150 ATTAAAATGGTTGAATTGGTTATTAAGTATTCCTAATTCTCTTCTAATTTTATAAAATTTGTT
1 ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
** * * * *
3666213 ATTAAAATGGTTGAATTGGTCATTAAGTATTCCTAATTCTCTTTTAAATTTACAAAATTTGTT
1 ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
3666276 ATTAAGAGGG
1 ATTAA-AGGG
3666286 CTAAATTAGT
Statistics
Matches: 291, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
62 3 0.01
63 286 0.98
64 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (63 bp):
ATTAAAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTACAAAATTTGTT
Found at i:3666218 original size:189 final size:189
Alignment explanation
Indices: 3665898--3666295 Score: 564
Period size: 189 Copynumber: 2.1 Consensus size: 189
3665888 GTTAAGTGCA
* * *
3665898 ATTAAGGGGGTTGAATTAGTTGTTAAGCATTTCCAATTCTCTTATAATTTTACAGAATTTATTAT
1 ATTAAGGGGGCTGAATTAGTTATTAAGCATTTCCAATTCTCTTATAATTTTACAAAATTTATTAT
* * *
3665963 TAAAGGGGTCGAATTAGTTATTAAGTATTCTTAATTCTCTTCTAATTTTATAGAATTTGTTATTA
66 TAAAAGGGTCGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTATAAAATTTGTTATTA
* * * *
3666028 AAGGGGTTGAATTAGTTATTAAGTATTCCTAATTCTCTTTTAATTTTACAGAATTTATT
131 AAAGGGTTGAATTAGTCATTAAGTATTCCTAATTCTCTTTTAAATTTACAAAATTTATT
* * * * * *
3666087 ATTAAGGGGGCTGAATTGGTTATTAAGTA-TTCCTCATTCTCTTCTAATTTTATAAAATTTGTTA
1 ATTAAGGGGGCTGAATTAGTTATTAAGCATTTCC-AATTCTCTTATAATTTTACAAAATTTATTA
* * *
3666151 TTAAAATGGTTGAATTGGTTATTAAGTATTCCTAATTCTCTTCTAATTTTATAAAATTTGTTATT
65 TTAAAAGGGTCGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTATAAAATTTGTTATT
* * *
3666216 AAAATGGTTGAATTGGTCATTAAGTATTCCTAATTCTCTTTTAAATTTACAAAATTTGTT
130 AAAAGGGTTGAATTAGTCATTAAGTATTCCTAATTCTCTTTTAAATTTACAAAATTTATT
* *
3666276 ATTAAGAGGGCTAAATTAGT
1 ATTAAGGGGGCTGAATTAGT
3666296 AGATAATCAC
Statistics
Matches: 183, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
188 4 0.02
189 179 0.98
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (189 bp):
ATTAAGGGGGCTGAATTAGTTATTAAGCATTTCCAATTCTCTTATAATTTTACAAAATTTATTAT
TAAAAGGGTCGAATTAGTTATTAAGTATTCCTAATTCTCTTCTAATTTTATAAAATTTGTTATTA
AAAGGGTTGAATTAGTCATTAAGTATTCCTAATTCTCTTTTAAATTTACAAAATTTATT
Found at i:3668668 original size:26 final size:25
Alignment explanation
Indices: 3668626--3668692 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
3668616 TCTTTTTTGT
*
3668626 TAAATGATCCAAAAAAGAAAAATATG
1 TAAATGATACAAAAAAG-AAAATATG
* *
3668652 TAAATGATACAACAAAGAATATATG
1 TAAATGATACAAAAAAGAAAATATG
* *
3668677 GACATGATACAAAAAA
1 TAAATGATACAAAAAA
3668693 ATGTTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (25 bp):
TAAATGATACAAAAAAGAAAATATG
Found at i:3678914 original size:37 final size:34
Alignment explanation
Indices: 3678873--3678978 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
3678863 TTTAAAGGTT
3678873 GTATACAATTGACTTCATAAATTACAAAAGAATCAAA
1 GTATACAATTGACTTC---AATTACAAAAGAATCAAA
*** **
3678910 GTATATGTTTTCCTTCAATTACAAAAGAATCAAA
1 GTATACAATTGACTTCAATTACAAAAGAATCAAA
*** **
3678944 GTATATGTTTTCCTTCAATTACAAAAGAATCAAA
1 GTATACAATTGACTTCAATTACAAAAGAATCAAA
3678978 G
1 G
3678979 AATATTAACA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 53 0.83
37 11 0.17
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.32
Consensus pattern (34 bp):
GTATACAATTGACTTCAATTACAAAAGAATCAAA
Found at i:3678935 original size:34 final size:34
Alignment explanation
Indices: 3678892--3678983 Score: 175
Period size: 34 Copynumber: 2.7 Consensus size: 34
3678882 TGACTTCATA
3678892 AATTACAAAAGAATCAAAGTATATGTTTTCCTTC
1 AATTACAAAAGAATCAAAGTATATGTTTTCCTTC
3678926 AATTACAAAAGAATCAAAGTATATGTTTTCCTTC
1 AATTACAAAAGAATCAAAGTATATGTTTTCCTTC
*
3678960 AATTACAAAAGAATCAAAGAATAT
1 AATTACAAAAGAATCAAAGTATAT
3678984 TAACAAATGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.32
Consensus pattern (34 bp):
AATTACAAAAGAATCAAAGTATATGTTTTCCTTC
Found at i:3684027 original size:65 final size:64
Alignment explanation
Indices: 3683923--3684067 Score: 254
Period size: 65 Copynumber: 2.2 Consensus size: 64
3683913 TTCAATGCCA
*
3683923 TCAAGATATGTAGCTTTTTCCAAGATACCCAGTCACTTACATTGCTACTTTTTTAAAAAAATATT
1 TCAAGATATGTAGCTTTTTCCAAGATACCCAATCACTTACATTGCTAC-TTTTTAAAAAAATATT
*
3683988 TCAAGATATGTAGCTTTTTCCAAGATACCCAATTACTTACATTGCTACTTTTTAAAAAAATATT
1 TCAAGATATGTAGCTTTTTCCAAGATACCCAATCACTTACATTGCTACTTTTTAAAAAAATATT
*
3684052 TCATGATATGTAGCTT
1 TCAAGATATGTAGCTT
3684068 AAGTCAGAGT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
64 31 0.40
65 46 0.60
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (64 bp):
TCAAGATATGTAGCTTTTTCCAAGATACCCAATCACTTACATTGCTACTTTTTAAAAAAATATT
Found at i:3694842 original size:42 final size:41
Alignment explanation
Indices: 3694796--3694905 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 41
3694786 TAAATTTGAA
*
3694796 AAATTGAT-TAAAATTATTAATATTTGAATCATAATAAT-ATTT
1 AAATT-ATATAAAA-TATTAATATTTGAA-AATAATAATGATTT
* *
3694838 AAATTATAAATAAAATATTAATATTTTAAAATATTAATGATTT
1 AAATTAT--ATAAAATATTAATATTTGAAAATAATAATGATTT
*
3694881 AATTATATATAAAATATTAATATTT
1 AAAT-TATATAAAATATTAATATTT
3694906 AAATTATCGA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
41 2 0.03
42 29 0.49
43 20 0.34
44 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (41 bp):
AAATTATATAAAATATTAATATTTGAAAATAATAATGATTT
Found at i:3694869 original size:16 final size:17
Alignment explanation
Indices: 3694848--3694880 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3694838 AAATTATAAA
3694848 TAAAATATTAAT-ATTT
1 TAAAATATTAATGATTT
3694864 TAAAATATTAATGATTT
1 TAAAATATTAATGATTT
3694881 AATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TAAAATATTAATGATTT
Found at i:3694928 original size:42 final size:42
Alignment explanation
Indices: 3694836--3694935 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
3694826 ATAATAATAT
* *
3694836 TTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGA
1 TTAAATTATATATAAAATATTAATATTTTAAAATATCAATGA
* * * *
3694878 TTTAATTATATATAAAATATTAATA-TTTAAATTATCGATTA
1 TTAAATTATATATAAAATATTAATATTTTAAAATATCAATGA
3694919 TTAATATTAT-TATAAAA
1 TTAA-ATTATATATAAAA
3694936 AAGTTTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 22 0.44
42 28 0.56
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (42 bp):
TTAAATTATATATAAAATATTAATATTTTAAAATATCAATGA
Found at i:3695339 original size:15 final size:16
Alignment explanation
Indices: 3695316--3695348 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3695306 TATTTAAATT
3695316 ATATATT-AAATATTA
1 ATATATTAAAATATTA
*
3695331 ATATTTTAAAATATTA
1 ATATATTAAAATATTA
3695347 AT
1 AT
3695349 TCTTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTAAAATATTA
Found at i:3695354 original size:15 final size:16
Alignment explanation
Indices: 3695323--3695355 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3695313 ATTATATATT
*
3695323 AAATATTAATATTTTA
1 AAATATTAATATCTTA
3695339 AAATATTAAT-TCTTA
1 AAATATTAATATCTTA
3695354 AA
1 AA
3695356 TTATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTAATATCTTA
Found at i:3695372 original size:26 final size:26
Alignment explanation
Indices: 3695336--3695387 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3695326 TATTAATATT
*
3695336 TTAAAATATTAAT-TCTTAAATTATAA
1 TTAAAAGATTAATATC-TAAATTATAA
3695362 TTAAAAGATTAATATCTAAATTATAA
1 TTAAAAGATTAATATCTAAATTATAA
3695388 ATTATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAAAGATTAATATCTAAATTATAA
Found at i:3695408 original size:27 final size:26
Alignment explanation
Indices: 3695378--3695448 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
3695368 GATTAATATC
3695378 TAAATTATAAATTATAAATATTTTAAA
1 TAAATTATAAA-TATAAATATTTTAAA
* *
3695405 TAAAGTATAAAAAT-AATATTTTAAAAA
1 TAAATTATAAATATAAATATTTT--AAA
3695432 TAAA--ATAAATATAAATA
1 TAAATTATAAATATAAATA
3695449 ATCATAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 15 0.39
26 6 0.16
27 17 0.45
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (26 bp):
TAAATTATAAATATAAATATTTTAAA
Found at i:3695445 original size:25 final size:24
Alignment explanation
Indices: 3695384--3695445 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 24
3695374 TATCTAAATT
3695384 ATAAATTATAAATATTTTAAATAAAG
1 ATAAA-TAT-AATATTTTAAATAAAG
*
3695410 TATAAAAATAATATTTTAAAAATAAA-
1 -ATAAATATAATATTTT--AAATAAAG
3695436 ATAAATATAA
1 ATAAATATAA
3695446 ATAATCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 17 0.55
26 2 0.06
27 12 0.39
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAAATATAATATTTTAAATAAAG
Found at i:3695467 original size:27 final size:26
Alignment explanation
Indices: 3695437--3695509 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
3695427 AAAAATAAAA
*
3695437 TAAATATAAATAATCATAATAATATTT
1 TAAATATAAATAA-AATAATAATATTT
*
3695464 TAAATTATAAATAAAATATTAATATTT
1 TAAA-TATAAATAAAATAATAATATTT
* *
3695491 AAAAAATAATATAAAATAA
1 TAAATATAA-ATAAAATAA
3695510 AAAATAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 26 0.67
28 9 0.23
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAATATAAATAAAATAATAATATTT
Found at i:3695595 original size:22 final size:21
Alignment explanation
Indices: 3695569--3695617 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
3695559 AATAATAATA
3695569 ATATAAAAATAAATTATTTTTATT
1 ATAT-AAAAT-AATTA-TTTTATT
*
3695593 ATATATAATAATTATTTTATT
1 ATATAAAATAATTATTTTATT
3695614 ATAT
1 ATAT
3695618 TCTCATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 5 0.21
23 4 0.17
24 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAAAATAATTATTTTATT
Found at i:3695630 original size:5 final size:5
Alignment explanation
Indices: 3695604--3695666 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
3695594 TATATAATAA
* * * *
3695604 TTATT TTATT ATATT CTCATT TTATT TTATT TTCATA TTATAG TTATT
1 TTATT TTATT TTATT -TTATT TTATT TTATT TT-ATT TTAT-T TTATT
3695652 TTATT TTATT CTTAT
1 TTATT TTATT -TTAT
3695667 CTATTCTGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
5 32 0.68
6 15 0.32
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (5 bp):
TTATT
Found at i:3695666 original size:16 final size:15
Alignment explanation
Indices: 3695604--3695666 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
3695594 TATATAATAA
*
3695604 TTATTTTATTATATT
1 TTATTTTATTTTATT
*
3695619 CTCATTTTATTTTATT
1 -TTATTTTATTTTATT
* *
3695635 TTCATATTATAGTTATT
1 TT-ATTTTAT-TTTATT
3695652 TTATTTTATTCTTAT
1 TTATTTTATT-TTAT
3695667 CTATTCTGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 1 0.03
16 29 0.78
17 7 0.19
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (15 bp):
TTATTTTATTTTATT
Found at i:3698764 original size:2 final size:2
Alignment explanation
Indices: 3698757--3698788 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3698747 ACCCAATACT
3698757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3698789 CACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3727549 original size:83 final size:86
Alignment explanation
Indices: 3727406--3727573 Score: 202
Period size: 83 Copynumber: 2.0 Consensus size: 86
3727396 GAATTAAGAA
* * * *
3727406 AAATACTTTTTGATGAAAGTCATTCAATACAATTACAATTCTTATTTATAAATTGAATAAATTTT
1 AAATACTTTTTAATGAAAATCATTCAATACAAGTACAATTCTTACTTATAAATTGAATAAATTTT
3727471 AATAACT-TTTATAAT-AAAAG
66 AATAA-TATTTATAATCAAAAG
* * * *
3727491 AAATA-TTTTTAATGAAAATCA-TCCATGCAAGTAGAATTTTTACTTATAAATT-ATATAAATTT
1 AAATACTTTTTAATGAAAATCATTCAATACAAGTACAATTCTTACTTATAAATTGA-ATAAATTT
*
3727553 TATTAATATTTATAATCAAAA
65 TAATAATATTTATAATCAAAA
3727574 TGTTTAAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
82 2 0.03
83 46 0.65
84 18 0.25
85 5 0.07
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (86 bp):
AAATACTTTTTAATGAAAATCATTCAATACAAGTACAATTCTTACTTATAAATTGAATAAATTTT
AATAATATTTATAATCAAAAG
Found at i:3729795 original size:7 final size:7
Alignment explanation
Indices: 3729783--3729813 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3729773 TAGGGGTAAT
3729783 TCTGAAA
1 TCTGAAA
3729790 TCTGAAA
1 TCTGAAA
3729797 TCTGAAA
1 TCTGAAA
3729804 TCTGAAA
1 TCTGAAA
3729811 TCT
1 TCT
3729814 ACTCTTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (7 bp):
TCTGAAA
Found at i:3731957 original size:3 final size:3
Alignment explanation
Indices: 3731949--3731974 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3731939 ACCATCATTC
3731949 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
3731975 CACGTGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:3740577 original size:4 final size:4
Alignment explanation
Indices: 3740570--3740598 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3740560 CATCATCTTT
3740570 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
3740599 ATATAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:3745287 original size:27 final size:26
Alignment explanation
Indices: 3745257--3745350 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 26
3745247 TATAACAATC
* *
3745257 TTTTCATTATGTCATGTAATAATTAATT
1 TTTTCAATATG-CATATAATAATTAA-T
* * *
3745285 TTTTTAATATGACGTATAATAATTAAA
1 TTTTCAATATG-CATATAATAATTAAT
*
3745312 TCTTCAATATGCTATATAATAATTACAT
1 TTTTCAATATGC-ATATAATAATTA-AT
3745340 TTTTCAATATG
1 TTTTCAATATG
3745351 ACGTGTAACA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.02
27 20 0.38
28 32 0.60
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTCAATATGCATATAATAATTAAT
Found at i:3745304 original size:28 final size:27
Alignment explanation
Indices: 3745273--3745413 Score: 104
Period size: 28 Copynumber: 5.1 Consensus size: 27
3745263 TTATGTCATG
3745273 TAATAATTAATTTTTTTAATATGACGTA
1 TAATAATTAA-TTTTTTAATATGACGTA
* * * *
3745301 TAATAATTAAATCTTCAATATG-CTATA
1 TAATAATTAATTTTTTAATATGAC-GTA
* *
3745328 TAATAATTACATTTTTCAATATGACGTG
1 TAATAATTA-ATTTTTTAATATGACGTA
* * * * *
3745356 TAACAACTAAATTTTTAATATAACATA
1 TAATAATTAATTTTTTAATATGACGTA
** * *
3745383 TAACGATTACATTTTTTAACATGATGTA
1 TAATAATTA-ATTTTTTAATATGACGTA
3745411 TAA
1 TAA
3745414 CAACTAAATT
Statistics
Matches: 87, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
26 1 0.01
27 40 0.46
28 45 0.52
29 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (27 bp):
TAATAATTAATTTTTTAATATGACGTA
Found at i:3745349 original size:55 final size:55
Alignment explanation
Indices: 3745273--3745428 Score: 181
Period size: 55 Copynumber: 2.8 Consensus size: 55
3745263 TTATGTCATG
* * * *
3745273 TAATAATTA-ATTTTTTTAATATGACGTATAATAATTAAATCTTCAATAT-GCTATA
1 TAATAATTACA-TTTTTTAATATGACGTATAACAACTAAATTTTCAATATAAC-ATA
* * *
3745328 TAATAATTACATTTTTCAATATGACGTGTAACAACTAAATTTTTAATATAACATA
1 TAATAATTACATTTTTTAATATGACGTATAACAACTAAATTTTCAATATAACATA
** * *
3745383 TAACGATTACATTTTTTAACATGATGTATAACAACTAAATTTTCAA
1 TAATAATTACATTTTTTAATATGACGTATAACAACTAAATTTTCAA
3745429 CATTGAGTGT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
55 83 0.98
56 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (55 bp):
TAATAATTACATTTTTTAATATGACGTATAACAACTAAATTTTCAATATAACATA
Found at i:3745386 original size:27 final size:27
Alignment explanation
Indices: 3745285--3745425 Score: 113
Period size: 27 Copynumber: 5.1 Consensus size: 27
3745275 ATAATTAATT
*
3745285 TTTTTAATATGACGTATAATAATTAAA
1 TTTTTAATATGACGTATAACAATTAAA
* * * * *
3745312 TCTTCAATATG-CTATATAATAATTACA
1 TTTTTAATATGAC-GTATAACAATTAAA
* *
3745339 TTTTTCAATATGACGTGTAACAACTAAA
1 TTTTT-AATATGACGTATAACAATTAAA
* * * *
3745367 TTTTTAATATAACATATAACGATTACAT
1 TTTTTAATATGACGTATAACAATTA-AA
* * *
3745395 TTTTTAACATGATGTATAACAACTAAA
1 TTTTTAATATGACGTATAACAATTAAA
3745422 TTTT
1 TTTT
3745426 CAACATTGAG
Statistics
Matches: 86, Mismatches: 24, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
26 1 0.01
27 44 0.51
28 40 0.47
29 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTTTAATATGACGTATAACAATTAAA
Found at i:3751616 original size:32 final size:32
Alignment explanation
Indices: 3751570--3751702 Score: 110
Period size: 32 Copynumber: 4.1 Consensus size: 32
3751560 AAAAGAAATT
* *
3751570 AAAATATAATATATAATATAAAAATTATATTA
1 AAAATAAAAAATATAATATAAAAATTATATTA
* * *
3751602 AAAATAAAAAATATAATATGTAAGATTATAATAA
1 AAAATAAAAAATATAATAT-AAAAATTAT-ATTA
* *
3751636 AAAATAAAATATATGATAATAAAAA-TATATT-
1 AAAATAAAAAATATAAT-ATAAAAATTATATTA
* * * *
3751667 TAAA-AAATAATATTATATAAAAATTAATAATA
1 AAAATAAAAAATATAATATAAAAATT-ATATTA
3751699 AAAA
1 AAAA
3751703 ATACAAGTAA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
29 7 0.09
30 10 0.13
31 7 0.09
32 22 0.28
33 10 0.13
34 21 0.27
35 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (32 bp):
AAAATAAAAAATATAATATAAAAATTATATTA
Found at i:3751657 original size:25 final size:27
Alignment explanation
Indices: 3751604--3751657 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
3751594 TTATATTAAA
* *
3751604 AATAAAAAATATAATATGTAAGATTAT
1 AATAAAAAATATAATATATAAGATAAT
*
3751631 AATAAAAAATA-AA-ATATATGATAAT
1 AATAAAAAATATAATATATAAGATAAT
3751656 AA
1 AA
3751658 AAATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (27 bp):
AATAAAAAATATAATATATAAGATAAT
Found at i:3751671 original size:34 final size:34
Alignment explanation
Indices: 3751570--3751686 Score: 107
Period size: 34 Copynumber: 3.5 Consensus size: 34
3751560 AAAAGAAATT
*
3751570 AAAATATAATATATAAT-ATAAAAAT-TATATT-A
1 AAAATAAAATATATAATAATAAAAATATAT-TTAA
* * * * *
3751602 AAAATAAAAAATATAATATGTAAGATTATA-ATAA
1 AAAATAAAATATATAATA-ATAAAAATATATTTAA
*
3751636 AAAATAAAATATATGATAATAAAAATATATTTAA
1 AAAATAAAATATATAATAATAAAAATATATTTAA
*
3751670 AAAATAATATTATATAA
1 AAAATAA-AATATATAA
3751687 AAATTAATAA
Statistics
Matches: 65, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
32 15 0.23
33 9 0.14
34 32 0.49
35 9 0.14
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (34 bp):
AAAATAAAATATATAATAATAAAAATATATTTAA
Found at i:3751674 original size:13 final size:16
Alignment explanation
Indices: 3751641--3751695 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
3751631 AATAAAAAAT
*
3751641 AAAAT-ATATGATAATA
1 AAAATAATATTAT-ATA
3751657 AAAAT-ATATT-TA-A
1 AAAATAATATTATATA
3751670 AAAATAATATTATATA
1 AAAATAATATTATATA
3751686 AAAATTAATA
1 AAAA-TAATA
3751696 ATAAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 6 0.18
14 6 0.18
15 3 0.09
16 14 0.41
17 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATAATATTATATA
Found at i:3751678 original size:16 final size:17
Alignment explanation
Indices: 3751626--3751695 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
3751616 AATATGTAAG
*
3751626 ATTATAATAAAAAATAAA
1 ATTAT-ATAAAAAATAAT
*
3751644 ATATATGATAATAAA-AAT
1 AT-TAT-ATAAAAAATAAT
*
3751662 A-TATTTAAAAAATAAT
1 ATTATATAAAAAATAAT
*
3751678 ATTATATAAAAATTAAT
1 ATTATATAAAAAATAAT
3751695 A
1 A
3751696 ATAAAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
15 6 0.14
16 7 0.17
17 14 0.33
18 5 0.12
19 10 0.24
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (17 bp):
ATTATATAAAAAATAAT
Found at i:3751679 original size:14 final size:14
Alignment explanation
Indices: 3751656--3751705 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
3751646 ATATGATAAT
3751656 AAAAAT-ATATTTA
1 AAAAATAATATTTA
3751669 AAAAATAATATTATA
1 AAAAATAATATT-TA
*
3751684 TAAAAATTAATA-ATA
1 -AAAAA-TAATATTTA
3751699 AAAAATA
1 AAAAATA
3751706 CAAGTAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.25
14 10 0.31
15 4 0.12
16 5 0.16
17 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAATAATATTTA
Found at i:3751697 original size:64 final size:66
Alignment explanation
Indices: 3751570--3751705 Score: 163
Period size: 64 Copynumber: 2.1 Consensus size: 66
3751560 AAAAGAAATT
* * *
3751570 AAAATATAATATATAATATAAAAATTATATTAAAAATAAAAAATATAATATGTAAGATTATAATA
1 AAAATAAAATATATAATATAAAAATTATATTAAAAATAAAAAATATAATATGAAAAATTATAATA
3751635 A
66 A
* * * *
3751636 AAAATAAAATATATGATAATAAAAA-TATATT-TAAA-AAATAATATTATAT-AAAAATTAATAA
1 AAAATAAAATATATAAT-ATAAAAATTATATTAAAAATAAAAAATATAATATGAAAAATT-ATAA
3751697 TAA
64 TAA
3751700 AAAATA
1 AAAATA
3751706 CAAGTAATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
63 5 0.08
64 25 0.41
65 3 0.05
66 21 0.34
67 7 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (66 bp):
AAAATAAAATATATAATATAAAAATTATATTAAAAATAAAAAATATAATATGAAAAATTATAATA
A
Found at i:3755579 original size:57 final size:57
Alignment explanation
Indices: 3755486--3755594 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
3755476 TGTGAGAAAG
* *
3755486 TATTCCGGATACTAGTTACTGATTACAACCATTTTAACGATTCCTTCTCAATGCCAT
1 TATTACGGATACTAGTTACTAATTACAACCATTTTAACGATTCCTTCTCAATGCCAT
*
3755543 TATTACGGATACTAGTTACTAATTACAACCATTTTAACTATTCCTTCTCAAT
1 TATTACGGATACTAGTTACTAATTACAACCATTTTAACGATTCCTTCTCAAT
3755595 ACTATTACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (57 bp):
TATTACGGATACTAGTTACTAATTACAACCATTTTAACGATTCCTTCTCAATGCCAT
Found at i:3756476 original size:90 final size:90
Alignment explanation
Indices: 3756315--3756499 Score: 234
Period size: 90 Copynumber: 2.1 Consensus size: 90
3756305 TCCAATCTCT
* *
3756315 TAAGTTTGGTTATTGTTTAGTTTTCATCATCTTCAAGCTTCTAAAAGATTTCAATGATTGGGTTT
1 TAAGTTTGGTTATTATTTAGTTTTCATCATCTCCAAGCTTCTAAAAGATTTCAATGATTGGGTTT
* * *
3756380 TGATTTCTAGTTTTAGCAAATCAGG
66 TAATTTCTAGCTTTAACAAATCAGG
* *
3756405 TAAGTATTGG-TATTATTTTGTTTTCATTATCTCCAAGCTT-TAAAAGGATTTCAATTG-TT-GG
1 TAAGT-TTGGTTATTATTTAGTTTTCATCATCTCCAAGCTTCTAAAA-GATTTCAA-TGATTGGG
*
3756466 TCTTTAATTTCTAGCTTTAACAAATCATG
63 T-TTTAATTTCTAGCTTTAACAAATCAGG
3756495 TAAGT
1 TAAGT
3756500 GACTTAATAT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
89 8 0.10
90 69 0.83
91 6 0.07
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (90 bp):
TAAGTTTGGTTATTATTTAGTTTTCATCATCTCCAAGCTTCTAAAAGATTTCAATGATTGGGTTT
TAATTTCTAGCTTTAACAAATCAGG
Found at i:3756946 original size:26 final size:26
Alignment explanation
Indices: 3756866--3756937 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
3756856 AATTTGAAGA
*
3756866 ATAATTTTATCACCAAAAGTAGATAG
1 ATAATTTTATCACTAAAAGTAGATAG
*
3756892 ATAATTTTA-CTA-TAAAAAATAGATAG
1 ATAATTTTATC-ACT-AAAAGTAGATAG
3756918 ATAATTTTATCACTAAAAGT
1 ATAATTTTATCACTAAAAGT
3756938 GAATGGATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 1 0.03
26 36 0.92
27 2 0.05
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (26 bp):
ATAATTTTATCACTAAAAGTAGATAG
Found at i:3770023 original size:18 final size:19
Alignment explanation
Indices: 3770002--3770037 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3769992 AATCCAAAAA
*
3770002 TAAAAATG-GAAAAGAAAG
1 TAAAAATGTAAAAAGAAAG
3770020 TAAAAATGTAAAAAGAAA
1 TAAAAATGTAAAAAGAAA
3770038 ATAATTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (19 bp):
TAAAAATGTAAAAAGAAAG
Found at i:3770654 original size:18 final size:18
Alignment explanation
Indices: 3770611--3770676 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
3770601 TTTGTTTTCC
* *
3770611 AACATAACTATTTGAACA
1 AACATAATTGTTTGAACA
**
3770629 AATTTAATTGTTTGAACA
1 AACATAATTGTTTGAACA
*
3770647 AACATAATT-CTTGAACA
1 AACATAATTGTTTGAACA
*
3770664 ATCATAATTGTTT
1 AACATAATTGTTT
3770677 AAAAGACTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 15 0.39
18 23 0.61
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (18 bp):
AACATAATTGTTTGAACA
Found at i:3770662 original size:17 final size:17
Alignment explanation
Indices: 3770640--3770672 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3770630 ATTTAATTGT
3770640 TTGAACAAACATAATTC
1 TTGAACAAACATAATTC
*
3770657 TTGAACAATCATAATT
1 TTGAACAAACATAATT
3770673 GTTTAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (17 bp):
TTGAACAAACATAATTC
Found at i:3772629 original size:35 final size:35
Alignment explanation
Indices: 3772574--3772661 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
3772564 TTTTCAACTG
* * *
3772574 GATCATGCGTAACCT-TACAACATGCCTTTTACAA
1 GATCAGGCATAACCTCTACAACATGCCATTTACAA
* * **
3772608 GATTAGGCATAACTTCTACAACATGCCATTTGTAA
1 GATCAGGCATAACCTCTACAACATGCCATTTACAA
3772643 GATCAGGCATAACCTCTAC
1 GATCAGGCATAACCTCTAC
3772662 CAAGATGCTA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 11 0.25
35 33 0.75
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (35 bp):
GATCAGGCATAACCTCTACAACATGCCATTTACAA
Found at i:3774525 original size:24 final size:24
Alignment explanation
Indices: 3774489--3774557 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
3774479 ACAACTATTT
* *
3774489 ATTTCCAATAAACACAATTGTCTA
1 ATTTTCAACAAACACAATTGTCTA
3774513 ATTTTCAACAAACACAATTGTCTA
1 ATTTTCAACAAACACAATTGTCTA
* *
3774537 ATTTTCAACAAATATAATTGT
1 ATTTTCAACAAACACAATTGT
3774558 TTGTTTTCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTTTCAACAAACACAATTGTCTA
Found at i:3776942 original size:2 final size:2
Alignment explanation
Indices: 3776920--3776959 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3776910 CTACCACAAA
*
3776920 TC TC T- TC TC -C TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3776960 CATGGACTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:3803725 original size:21 final size:23
Alignment explanation
Indices: 3803701--3803742 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
3803691 CTTTGAGCTA
3803701 ATTTTTATTT-T-TATTTTTAAT
1 ATTTTTATTTATATATTTTTAAT
3803722 ATTTTTATTTATATATTTTTA
1 ATTTTTATTTATATATTTTTA
3803743 GATCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
ATTTTTATTTATATATTTTTAAT
Found at i:3803737 original size:14 final size:15
Alignment explanation
Indices: 3803706--3803742 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3803696 AGCTAATTTT
*
3803706 TATTTTTATTTTTAA
1 TATTTTTATTTATAA
3803721 TATTTTTATTTAT-A
1 TATTTTTATTTATAA
3803735 TATTTTTA
1 TATTTTTA
3803743 GATCATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTATTTATAA
Found at i:3804080 original size:16 final size:17
Alignment explanation
Indices: 3804049--3804085 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3804039 AGAGTTTAGA
3804049 GATTTTGAAAAATTTTT
1 GATTTTGAAAAATTTTT
*
3804066 GATTTT-AAGAATTTTT
1 GATTTTGAAAAATTTTT
3804082 -ATTT
1 GATTT
3804086 ATTTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (17 bp):
GATTTTGAAAAATTTTT
Found at i:3814896 original size:27 final size:27
Alignment explanation
Indices: 3814866--3814942 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
3814856 CTTTCTATGG
* *
3814866 TTGGAACTATCTTGGGCGCTTCTGCAC
1 TTGGAACGACCTTGGGCGCTTCTGCAC
* * *
3814893 TTGGAACGCCCTTGGGTGCTTCTGTAC
1 TTGGAACGACCTTGGGCGCTTCTGCAC
* * *
3814920 TTGGAACGCCCATGGGTGCTTCT
1 TTGGAACGACCTTGGGCGCTTCT
3814943 ATGGCCCTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.13, C:0.26, G:0.29, T:0.32
Consensus pattern (27 bp):
TTGGAACGACCTTGGGCGCTTCTGCAC
Found at i:3815004 original size:27 final size:26
Alignment explanation
Indices: 3814974--3815236 Score: 151
Period size: 27 Copynumber: 9.9 Consensus size: 26
3814964 CTTGGAATGC
*
3814974 CCCTAGCTGCTTCTGCGCTTGGAACA
1 CCCTAGCTGCTTCTGTGCTTGGAACA
* *
3815000 TCCCTAGAC-GCTTCTATACTTGGAACA
1 -CCCTAG-CTGCTTCTGTGCTTGGAACA
* * * *
3815027 CCCTAGGTGTTTCTGTGTTTAGAACA
1 CCCTAGCTGCTTCTGTGCTTGGAACA
* * *
3815053 CCCCTAGGTGCTTCTGTACTTGAAACA
1 -CCCTAGCTGCTTCTGTGCTTGGAACA
3815080 CCCTAAGCAT--TTCTGTGCTTGGAACA
1 CCCT-AGC-TGCTTCTGTGCTTGGAACA
* *
3815106 CCCTTAGGTGCTTCTGTGCTTGGAACGC
1 CCC-TAGCTGCTTCTGTGCTTGGAAC-A
* * ** *
3815134 CCCTTGGTGCTTCTACGCTTGGAACT
1 CCCTAGCTGCTTCTGTGCTTGGAACA
* * *
3815160 CCCTGGGC-GCTTCTGTACTTGGAACGC
1 CCCT-AGCTGCTTCTGTGCTTGGAAC-A
* * **
3815187 CCCTGGGC-GTTTCTCCGCTTGGAACA
1 CCCT-AGCTGCTTCTGTGCTTGGAACA
**
3815213 CCCTGAGCT-CTTCTGCACTTGGAA
1 CCCT-AGCTGCTTCTGTGCTTGGAA
3815237 TGCCCTTGGG
Statistics
Matches: 186, Mismatches: 38, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
25 1 0.01
26 79 0.42
27 101 0.54
28 5 0.03
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (26 bp):
CCCTAGCTGCTTCTGTGCTTGGAACA
Found at i:3815172 original size:53 final size:53
Alignment explanation
Indices: 3814964--3815344 Score: 203
Period size: 53 Copynumber: 7.2 Consensus size: 53
3814954 TGCTTTTATT
* * * * * * *
3814964 CTTGGAATGCCCCTAGCTGCTTCTGCGCTTGGAACATCCCTAGACGCTTCTATA
1 CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACA-CCCTGGGCGCTTCTGTA
* * * ** * * * *
3815018 CTTGGAAC-ACCCTAGGTGTTTCTGTGTTTAGAACACCCCTAGGTGCTTCTGTA
1 CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACA-CCCTGGGCGCTTCTGTA
* * ** *** ** * * *
3815071 CTTGAAAC-ACCCTAAGCATTTCTGTGCTTGGAACACCCTTAGGTGCTTCTGTG
1 CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACACCC-TGGGCGCTTCTGTA
*
3815124 CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACTCCCTGGGCGCTTCTGTA
1 CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACACCCTGGGCGCTTCTGTA
* * * * * * *
3815177 CTTGGAACGCCCCTGGGCGTTTCTCCGCTTGGAACACCCTGAGCTCTTCTGCA
1 CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACACCCTGGGCGCTTCTGTA
* * *** * * * ** *
3815230 CTTGGAATG-CCCTTGGGTGCTTTTGTACTTGAAATACCTTGGGCATTTTTGTA
1 CTTGGAACGCCCCTT-GGTGCTTCTACGCTTGGAACACCCTGGGCGCTTCTGTA
* * * ** *
3815283 CTTGGAATG-CCCTTAGGTGCTTCTGCACTTGGAATGCCCTTGGGCGCTTCTATA
1 CTTGGAACGCCCCTT-GGTGCTTCTACGCTTGGAACACCC-TGGGCGCTTCTGTA
3815337 CTTGGAAC
1 CTTGGAAC
3815345 ACCTTGGGCG
Statistics
Matches: 257, Mismatches: 66, Indels: 8
0.78 0.20 0.02
Matches are distributed among these distances:
52 7 0.03
53 205 0.80
54 45 0.18
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.32
Consensus pattern (53 bp):
CTTGGAACGCCCCTTGGTGCTTCTACGCTTGGAACACCCTGGGCGCTTCTGTA
Found at i:3815226 original size:26 final size:26
Alignment explanation
Indices: 3815151--3815373 Score: 87
Period size: 27 Copynumber: 8.4 Consensus size: 26
3815141 TGCTTCTACG
* * *
3815151 CTTGGAACTCCCTGGGCGCTTCTGTA
1 CTTGGAACACCCTGGGCTCTTCTGCA
* * *
3815177 CTTGGAACGCCCCTGGGCGT-TTCTCCG
1 CTTGGAAC-ACCCTGGGC-TCTTCTGCA
*
3815204 CTTGGAACACCCTGAGCTCTTCTGCA
1 CTTGGAACACCCTGGGCTCTTCTGCA
** * *
3815230 CTTGGAATGCCCTTGGG-TGCTTTTGTA
1 CTTGGAACACCC-TGGGCT-CTTCTGCA
* * * * *
3815257 CTTGAAATACCTTGGGCAT-TTTTGTA
1 CTTGGAACACCCTGGGC-TCTTCTGCA
** *
3815283 CTTGGAATGCCCTTAGG-TGCTTCTGCA
1 CTTGGAACACCC-TGGGCT-CTTCTGCA
** * **
3815310 CTTGGAATGCCCTTGGGCGCTTCTATA
1 CTTGGAACACCC-TGGGCTCTTCTGCA
* * *
3815337 CTTGGAACACCTTGGGCGT-TTCAGCT
1 CTTGGAACACCCTGGGC-TCTTCTGCA
3815363 CTTGGAACACC
1 CTTGGAACACC
3815374 GCAAGGAACG
Statistics
Matches: 150, Mismatches: 35, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
25 2 0.01
26 70 0.47
27 77 0.51
28 1 0.01
ACGTcount: A:0.15, C:0.27, G:0.25, T:0.32
Consensus pattern (26 bp):
CTTGGAACACCCTGGGCTCTTCTGCA
Found at i:3815312 original size:27 final size:27
Alignment explanation
Indices: 3815090--3815343 Score: 151
Period size: 27 Copynumber: 9.5 Consensus size: 27
3815080 CCCTAAGCAT
* ** *
3815090 TTCTGTGCTTGGAACACCCTTAGGTGC
1 TTCTGTACTTGGAATGCCCTTGGGTGC
* *
3815117 TTCTGTGCTTGGAACGCCCCTT-GGTGC
1 TTCTGTACTTGGAATG-CCCTTGGGTGC
*** *
3815144 TTCTACGCTTGGAACT-CCC-TGGGCGC
1 TTCTGTACTTGGAA-TGCCCTTGGGTGC
* * * *
3815170 TTCTGTACTTGGAACGCCCCTGGGCGT
1 TTCTGTACTTGGAATGCCCTTGGGTGC
*** ** *
3815197 TTCTCCGCTTGGAACACCC-TGAGCT-C
1 TTCTGTACTTGGAATGCCCTTG-GGTGC
*
3815223 TTCTGCACTTGGAATGCCCTTGGGTGC
1 TTCTGTACTTGGAATGCCCTTGGGTGC
* * * ***
3815250 TTTTGTACTTGAAAT-ACCTTGGGCAT
1 TTCTGTACTTGGAATGCCCTTGGGTGC
* *
3815276 TTTTGTACTTGGAATGCCCTTAGGTGC
1 TTCTGTACTTGGAATGCCCTTGGGTGC
* *
3815303 TTCTGCACTTGGAATGCCCTTGGGCGC
1 TTCTGTACTTGGAATGCCCTTGGGTGC
*
3815330 TTCTATACTTGGAA
1 TTCTGTACTTGGAA
3815344 CACCTTGGGC
Statistics
Matches: 177, Mismatches: 41, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.01
26 61 0.34
27 110 0.62
28 5 0.03
ACGTcount: A:0.14, C:0.27, G:0.26, T:0.33
Consensus pattern (27 bp):
TTCTGTACTTGGAATGCCCTTGGGTGC
Found at i:3815367 original size:80 final size:80
Alignment explanation
Indices: 3814963--3815370 Score: 269
Period size: 80 Copynumber: 5.1 Consensus size: 80
3814953 CTGCTTTTAT
* * * * * * *
3814963 TCTTGGAATGCCCCTAGCTGCTTCTGCGCTTGGAACAT-CCC-TAGACGCTTCTATACTTGGAAC
1 TCTTGGAACGCCCTTAGGTGCTTCTGCACTTGG-A-ATGCCCTTGGGCGCTTCTGTACTTGGAAC
* * *
3815026 ACCCTAGGTGTTTCTG-
64 ACCTTGGGCGTTTCTGC
* * * * * * ** ** ** *
3815042 TGTTTAGAACACCCCTAGGTGCTTCTGTACTTGAAACACCC-TAAGCATTTCTGTGCTTGGAACA
1 T-CTTGGAACGCCCTTAGGTGCTTCTGCACTTGGAATGCCCTTGGGCGCTTCTGTACTTGGAACA
* * *
3815106 CCCTTAGGTGCTTCTG-
65 -CCTTGGGCGTTTCTGC
* *
3815122 TGCTTGGAACGCCCCTT-GGTGCTTCTACGCTTGGAACT-CCC-TGGGCGCTTCTGTACTTGGAA
1 T-CTTGGAACG-CCCTTAGGTGCTTCTGCACTTGGAA-TGCCCTTGGGCGCTTCTGTACTTGGAA
* * *
3815184 CGCCCCTGGGCGTTTCTCC
63 C-ACCTTGGGCGTTTCTGC
* * * * * * * *
3815203 GCTTGGAACACCCTGAGCT-CTTCTGCACTTGGAATGCCCTTGGGTGCTTTTGTACTTGAAATAC
1 TCTTGGAACGCCCTTAGGTGCTTCTGCACTTGGAATGCCCTTGGGCGCTTCTGTACTTGGAACAC
* *
3815267 CTTGGGCATTTTTG-
66 CTTGGGCGTTTCTGC
* *
3815281 TACTTGGAATGCCCTTAGGTGCTTCTGCACTTGGAATGCCCTTGGGCGCTTCTATACTTGGAACA
1 T-CTTGGAACGCCCTTAGGTGCTTCTGCACTTGGAATGCCCTTGGGCGCTTCTGTACTTGGAACA
*
3815346 CCTTGGGCGTTTCAGC
65 CCTTGGGCGTTTCTGC
3815362 TCTTGGAAC
1 TCTTGGAAC
3815371 ACCGCAAGGA
Statistics
Matches: 250, Mismatches: 66, Indels: 25
0.73 0.19 0.07
Matches are distributed among these distances:
78 2 0.01
79 67 0.27
80 176 0.70
81 5 0.02
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.32
Consensus pattern (80 bp):
TCTTGGAACGCCCTTAGGTGCTTCTGCACTTGGAATGCCCTTGGGCGCTTCTGTACTTGGAACAC
CTTGGGCGTTTCTGC
Found at i:3819996 original size:18 final size:20
Alignment explanation
Indices: 3819973--3820011 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3819963 TGATGTTTTC
*
3819973 TTAAT-CTTTGTT-TATTAG
1 TTAATCCTTTATTATATTAG
3819991 TTAATCCTTTATTATATTAG
1 TTAATCCTTTATTATATTAG
3820011 T
1 T
3820012 AGATTAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (20 bp):
TTAATCCTTTATTATATTAG
Found at i:3822681 original size:26 final size:26
Alignment explanation
Indices: 3822651--3822701 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3822641 TCTAACCATG
* *
3822651 CCATCTCATATACTCTCACTATGCTA
1 CCATCTCACATACTCTCACCATGCTA
*
3822677 CCATCTCACATATTCTCACCATGCT
1 CCATCTCACATACTCTCACCATGCT
3822702 GCGTCACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.37, G:0.04, T:0.33
Consensus pattern (26 bp):
CCATCTCACATACTCTCACCATGCTA
Found at i:3822855 original size:24 final size:24
Alignment explanation
Indices: 3822794--3822883 Score: 128
Period size: 24 Copynumber: 3.8 Consensus size: 24
3822784 CCTTTCATGG
* *
3822794 CATGTCACATATTCTCA-TCATGT
1 CATGTCACATATTCTCACCCTTGT
** *
3822817 TGTGTTACATATTCTCACCCTTGT
1 CATGTCACATATTCTCACCCTTGT
3822841 CATGTCACATATTCTCACCCTTGT
1 CATGTCACATATTCTCACCCTTGT
3822865 CATGTCACATATTCTCACC
1 CATGTCACATATTCTCACC
3822884 ATGTCGTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 14 0.24
24 44 0.76
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39
Consensus pattern (24 bp):
CATGTCACATATTCTCACCCTTGT
Found at i:3823198 original size:141 final size:141
Alignment explanation
Indices: 3822936--3823200 Score: 316
Period size: 141 Copynumber: 1.9 Consensus size: 141
3822926 CATCATGCTA
* * * * *
3822936 TGTCACATATTCTTACCATGTCATGTCACATATTCCCTCTATGTCGTATCACATATTCTCACTAT
1 TGTCACATATTCTCACCATGTCATATCACATATTCCATCTATGTCGTATCACATATTCCCACCAT
** * * * * *
3823001 GTTGTGTTACATATTACTTTCATGGCATGTCACATATTCCCTCTAAAGCGTGTCACATAAACCCT
66 GTTGTGTTACATATTACTCACACGCCATGTCACATATTCCCACCAAAGCGTATCACATAAACCCT
3823066 AAACCTTATTG
131 AAACCTTATTG
* * * * * * *
3823077 TGTCACATATTCTCACCATGTCGTATTACATATTCCATTTATGTGGTCTCACATTTTCCCTCCAT
1 TGTCACATATTCTCACCATGTCATATCACATATTCCATCTATGTCGTATCACATATTCCCACCAT
* **
3823142 GTTGTGTTACATATT-CTCACACCGCCATGTCACATATTCTCACCATGGCGTATCACATA
66 GTTGTGTTACATATTACTCACA-CGCCATGTCACATATTCCCACCAAAGCGTATCACATA
3823201 TTCTTAATAT
Statistics
Matches: 101, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
140 4 0.04
141 97 0.96
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (141 bp):
TGTCACATATTCTCACCATGTCATATCACATATTCCATCTATGTCGTATCACATATTCCCACCAT
GTTGTGTTACATATTACTCACACGCCATGTCACATATTCCCACCAAAGCGTATCACATAAACCCT
AAACCTTATTG
Found at i:3823200 original size:92 final size:91
Alignment explanation
Indices: 3823077--3823253 Score: 248
Period size: 92 Copynumber: 1.9 Consensus size: 91
3823067 AACCTTATTG
* * **
3823077 TGTCACATATTCTCACCATGTCGTATTACATATTCCATT-TATGTGGTCTCACATTTTCCCTCCA
1 TGTCACATATTCTCACCATGGCGTATCACATATT-C-TTATATGTCATCTCACATTTTCCCTCCA
* * *
3823141 TGTTGTGTTACATATTCTCACACCGCCA
64 TATTGTCTCACATATTCTCACACCGCCA
*
3823169 TGTCACATATTCTCACCATGGCGTATCACATATTCTTAATATGTCATGTCACATTTTCCCTCCAT
1 TGTCACATATTCTCACCATGGCGTATCACATATTCTT-ATATGTCATCTCACATTTTCCCTCCAT
3823234 ATTGTCTCACATATTCTCAC
65 ATTGTCTCACATATTCTCAC
3823254 CATGTTGTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 2 0.03
91 1 0.01
92 72 0.96
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.39
Consensus pattern (91 bp):
TGTCACATATTCTCACCATGGCGTATCACATATTCTTATATGTCATCTCACATTTTCCCTCCATA
TTGTCTCACATATTCTCACACCGCCA
Found at i:3823261 original size:23 final size:23
Alignment explanation
Indices: 3822753--3823270 Score: 222
Period size: 23 Copynumber: 22.3 Consensus size: 23
3822743 TTTTCCATGT
* * *
3822753 CACATATTCTTACCATGCCGTTT
1 CACATATTCTCACCATGTCGTGT
** * *
3822776 CACATATTC-CTTTCATGGCATGT
1 CACATATTCTC-ACCATGTCGTGT
* *
3822799 CACATATTCTCATCATGTTGTGT
1 CACATATTCTCACCATGTCGTGT
* * *
3822822 TACATATTCTCACCCTTGTCATGT
1 CACATATTCTCA-CCATGTCGTGT
* *
3822846 CACATATTCTCACCCTTGTCATGT
1 CACATATTCTCA-CCATGTCGTGT
*
3822870 CACATATTCTCACCATGTCGTCT
1 CACATATTCTCACCATGTCGTGT
* * * *
3822893 CGCATACTCTTACCATGTCGTCT
1 CACATATTCTCACCATGTCGTGT
* * *
3822916 CATATACTT-TCATCATG-CTATGT
1 CACATA-TTCTCACCATGTC-GTGT
* *
3822939 CACATATTCTTACCATGTCATGT
1 CACATATTCTCACCATGTCGTGT
* * * *
3822962 CACATATTCCCTCTATGTCGTAT
1 CACATATTCTCACCATGTCGTGT
* *
3822985 CACATATTCTCACTATGTTGTGT
1 CACATATTCTCACCATGTCGTGT
* ** * *
3823008 TACATATTACT-TTCATGGCATGT
1 CACATATT-CTCACCATGTCGTGT
* * * *
3823031 CACATATTCCCTCTAAAG-CGTGT
1 CACATATTCTCAC-CATGTCGTGT
** * * * *
3823054 CACATAAACCCTAAACCTTATTGTGT
1 CACAT--ATTCT-CACCATGTCGTGT
*
3823080 CACATATTCTCACCATGTCGTAT
1 CACATATTCTCACCATGTCGTGT
* ** * *
3823103 TACATATTC-CATTTATGTGGTCT
1 CACATATTCTCA-CCATGTCGTGT
* * * *
3823126 CACATTTTCCCTCCATGTTGTGT
1 CACATATTCTCACCATGTCGTGT
* * * *
3823149 TACATATTCTCA-CACCGCCATGT
1 CACATATTCTCACCA-TGTCGTGT
* *
3823172 CACATATTCTCACCATGGCGTAT
1 CACATATTCTCACCATGTCGTGT
* ** *
3823195 CACATATTCTTAATATGTCATGT
1 CACATATTCTCACCATGTCGTGT
* * * * * *
3823218 CACATTTTCCCTCCATATTGTCT
1 CACATATTCTCACCATGTCGTGT
*
3823241 CACATATTCTCACCATGTTGTGT
1 CACATATTCTCACCATGTCGTGT
*
3823264 CAGATAT
1 CACATAT
3823271 ATTTCTTACA
Statistics
Matches: 358, Mismatches: 119, Indels: 36
0.70 0.23 0.07
Matches are distributed among these distances:
22 8 0.02
23 283 0.79
24 55 0.15
25 2 0.01
26 10 0.03
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (23 bp):
CACATATTCTCACCATGTCGTGT
Found at i:3833396 original size:51 final size:51
Alignment explanation
Indices: 3833336--3833443 Score: 148
Period size: 51 Copynumber: 2.1 Consensus size: 51
3833326 AGAAATTTAG
3833336 TTCATCTTGTCATTAAT-GTTATTAATAAC-CCTATACAGAAAATTAACTAAT
1 TTCATCTTGTCATTAATCG-TATTAATAACTCC-ATACAGAAAATTAACTAAT
* * * *
3833387 TTCATCTTGTCATTAATCGTATTACTAACTCCATACGGATAATTAATTAAT
1 TTCATCTTGTCATTAATCGTATTAATAACTCCATACAGAAAATTAACTAAT
3833438 TTCATC
1 TTCATC
3833444 AATTGGTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
51 48 0.94
52 3 0.06
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (51 bp):
TTCATCTTGTCATTAATCGTATTAATAACTCCATACAGAAAATTAACTAAT
Found at i:3833523 original size:17 final size:18
Alignment explanation
Indices: 3833492--3833529 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3833482 TAATACTCAA
3833492 TAAATTAATAATTTTGAT
1 TAAATTAATAATTTTGAT
* *
3833510 TAAA-TAATATTTTTGGT
1 TAAATTAATAATTTTGAT
3833527 TAA
1 TAA
3833530 TCTCAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
TAAATTAATAATTTTGAT
Done.