Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007863.1 Hibiscus syriacus cultivar Beakdansim tig00110234_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1653362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:443649 original size:105 final size:105
Alignment explanation
Indices: 443438--443657 Score: 253
Period size: 105 Copynumber: 2.1 Consensus size: 105
443428 ATTTGATATA
* * * * **
443438 ATTATTAATATAAATTGTAATGAACTTGTTTGACATTAAGATTATATTTTGTGACCATTGATATT
1 ATTATTAATAGAAATTGTAATAAACTTGTTTGACATTAACAATATATTTTGTGACCATCAATATT
* * *
443503 ATCACACTAAGTAGTTTTTAGTGACAAAATGTTCGATACT
66 ATCACACTAAGTAGTTTTTAATGACAAAATGTTCAACACT
* * * * *
443543 ATTATCAATAGAAATTGTGATAAATTTGTTTTGACATTGACAATATATTTTGTGACCATCAATGT
1 ATTATTAATAGAAATTGTAATAAACTTG-TTTGACATTAACAATATATTTTGTGACCATCAATAT
* * * * *
443608 TATC-GATTAAGTATTTTTTAATGACCAAATGTTTAACACT
65 TATCACACTAAGTAGTTTTTAATGACAAAATGTTCAACACT
443648 ATTATTAATA
1 ATTATTAATA
443658 ATTTTGTCAC
Statistics
Matches: 94, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
105 60 0.64
106 34 0.36
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (105 bp):
ATTATTAATAGAAATTGTAATAAACTTGTTTGACATTAACAATATATTTTGTGACCATCAATATT
ATCACACTAAGTAGTTTTTAATGACAAAATGTTCAACACT
Found at i:444293 original size:20 final size:23
Alignment explanation
Indices: 444251--444296 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
444241 GGAATTAATT
444251 TTATTATATATATATAATATTAA
1 TTATTATATATATATAATATTAA
444274 TTATTATA-ATA-ATAAT-TTAA
1 TTATTATATATATATAATATTAA
444294 TTA
1 TTA
444297 AATTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 3 0.13
23 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTATATATATATAATATTAA
Found at i:445073 original size:3 final size:3
Alignment explanation
Indices: 445065--445093 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
445055 GTCTGAGTCT
445065 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
445094 TATGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:446685 original size:5 final size:5
Alignment explanation
Indices: 446666--446710 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
446656 TTTTCACTTC
* * *
446666 TTTTCA TTTCA TTTTA TTTTG TTTTA TTTTA GTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
446711 TGTGGAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
5 30 0.91
6 3 0.09
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:448571 original size:19 final size:20
Alignment explanation
Indices: 448549--448587 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
448539 CGTTATGAGA
448549 TGGGGGTATCGGTAC-CTCC
1 TGGGGGTATCGGTACACTCC
448568 TGGGGGTATCGGTACACTCC
1 TGGGGGTATCGGTACACTCC
448588 GAGCAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.13, C:0.26, G:0.36, T:0.26
Consensus pattern (20 bp):
TGGGGGTATCGGTACACTCC
Found at i:449007 original size:19 final size:19
Alignment explanation
Indices: 448983--449023 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
448973 ATTTTAAGAT
448983 TTTCTAATTGAAAATCAAG
1 TTTCTAATTGAAAATCAAG
449002 TTTCTAATTGAAAATCAAG
1 TTTCTAATTGAAAATCAAG
449021 TTT
1 TTT
449024 TGAAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
TTTCTAATTGAAAATCAAG
Found at i:450849 original size:13 final size:14
Alignment explanation
Indices: 450831--450868 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
450821 ATGGGCAATT
*
450831 TTTGAAAATCGA-G
1 TTTGAAAATCAAGG
450844 TTTGAAAA-CAAGG
1 TTTGAAAATCAAGG
450857 TTTGAAAATCAA
1 TTTGAAAATCAA
450869 TATATGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 17 0.77
14 3 0.14
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (14 bp):
TTTGAAAATCAAGG
Found at i:451380 original size:22 final size:20
Alignment explanation
Indices: 451336--451391 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 20
451326 ACCCCATGGA
*
451336 GGGTATCGGTACCCTCAAGG
1 GGGTATCGGTACCCTCAAAG
451356 GGGTATCGGTACCTACTCAAAG
1 GGGTATCGGTACC--CTCAAAG
451378 GGGTATCGGTACCC
1 GGGTATCGGTACCC
451392 ATGCAAGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
22 19 0.58
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.21
Consensus pattern (20 bp):
GGGTATCGGTACCCTCAAAG
Found at i:451404 original size:22 final size:20
Alignment explanation
Indices: 451336--451412 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 20
451326 ACCCCATGGA
451336 GGGTATCGGTACCC-TCAAGG
1 GGGTATCGGTACCCATCAA-G
*
451356 GGGTATCGGTACCTACTCAAAG
1 GGGTATCGGTACCCA-TC-AAG
451378 GGGTATCGGTACCCATGCAAG
1 GGGTATCGGTACCCAT-CAAG
*
451399 GAGGTATCGATACC
1 G-GGTATCGGTACC
451413 TAGCCCAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
20 13 0.27
21 5 0.10
22 29 0.59
23 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (20 bp):
GGGTATCGGTACCCATCAAG
Found at i:455253 original size:21 final size:22
Alignment explanation
Indices: 455218--455258 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
455208 AAGACTATTT
*
455218 TCATTTTTTTAATTTTGAAACA
1 TCATTTTTGTAATTTTGAAACA
455240 TCATTTTTGT-ATTTTGAAA
1 TCATTTTTGTAATTTTGAAA
455259 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (22 bp):
TCATTTTTGTAATTTTGAAACA
Found at i:459601 original size:12 final size:12
Alignment explanation
Indices: 459575--459618 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
459565 TGAACTCGTT
*
459575 TATTTGTCTTTAA
1 TATTT-TCTTAAA
459588 TATTTTCTTAAA
1 TATTTTCTTAAA
*
459600 TATTTTTTTAAAA
1 TATTTTCTT-AAA
459613 TATTTT
1 TATTTT
459619 AATGATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 14 0.50
13 14 0.50
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTTTCTTAAA
Found at i:460529 original size:27 final size:28
Alignment explanation
Indices: 460482--460534 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
460472 GGCGAGGATA
*
460482 AAAGCAAAGAAAAAAGTAAAA-AAAATT
1 AAAGCAAAGAAAAAAGAAAAAGAAAATT
*
460509 AAAGGAAA-AAAAGAAGAAAAAGAAAA
1 AAAGCAAAGAAAA-AAGAAAAAGAAAA
460535 CAAAAGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
27 14 0.64
28 4 0.18
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (28 bp):
AAAGCAAAGAAAAAAGAAAAAGAAAATT
Found at i:463058 original size:66 final size:67
Alignment explanation
Indices: 462972--463105 Score: 216
Period size: 66 Copynumber: 2.0 Consensus size: 67
462962 AACAAAATTG
* * *
462972 ATAAAACCTTTGAGATTGTTTCTCTTGAAAGAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
1 ATAAAACCATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
463037 AC
66 AC
* *
463039 ATAAAA-CATTGATATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAA
1 ATAAAACCATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
463103 AC
66 AC
463105 A
1 A
463106 AATGATCCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
66 56 0.90
67 6 0.10
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (67 bp):
ATAAAACCATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
AC
Found at i:463361 original size:137 final size:135
Alignment explanation
Indices: 463136--463590 Score: 470
Period size: 137 Copynumber: 3.3 Consensus size: 135
463126 AGTCATTCTC
* ** *
463136 ATCACGTAGGAACCGTGTCATCCACCGAAAAAAATCTCCTCATCACTTAAGAGCCGCGTCACCCT
1 ATCACGTAGGAACTGTGTCATCCACCG-ACCAAATCTCCTCATCA-TTAGGAGCCGCGTCACCCT
*
463201 TAGATAGCCAGACTTCTTCATCACGTAGGAATCGTGTTATCTTCATTATCCCTAAAGATGGCCAA
64 TAGATAGCCAGACTTCTT-ATCACGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATGGCCAA
463266 CCGTCCTT
128 CCGTCCTT
* **
463274 ATCGCGTAGGAACTGTGTCATCCACCGACCAAATCTCCTCATCATATAGGAGCCATGTCACCCTT
1 ATCACGTAGGAACTGTGTCATCCACCGACCAAATCTCCTCATCAT-TAGGAGCCGCGTCACCCTT
* * * * *** *
463339 AGATAACCAGACTTCCTTATCACGTAGGAACCATGTTATCTTTATTACCCCTAAAGATTATCAAT
65 AGATAGCCAGACTT-CTTATCACGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATGGCCAAC
*
463404 CGTCCTC
129 CGTCCTT
* * ** * * * * *
463411 ATCATGTAGGAAATGTGTCATTAACCAACCAGATCTCTTTATCATGTAGGAGCCGCATCA-CCTT
1 ATCACGTAGGAACTGTGTCATCCACCGACCAAATCTCCTCATCAT-TAGGAGCCGCGTCACCCTT
* * ** * *
463475 ATATAGCCAGACTTTCTCATCTTGTAGGAACCGTGTGATC-TCTATTATCCCTAAAGATGGCCAG
65 AGATAGCCAGAC-TTCTTATCACGTAGGAACCGTGTTATCTTC-ATTATCCCTAAAGATGGCCAA
463539 CCGTCCTCT
128 CCGTCCT-T
**
463548 A-CATATAGGAA-TCGTGTCATCCACCGA-CAAGATCTCCTCATCA
1 ATCACGTAGGAACT-GTGTCATCCACCGACCAA-ATCTCCTCATCA
463591 CGTATGAGTC
Statistics
Matches: 258, Mismatches: 52, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
135 4 0.02
136 87 0.34
137 139 0.54
138 28 0.11
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (135 bp):
ATCACGTAGGAACTGTGTCATCCACCGACCAAATCTCCTCATCATTAGGAGCCGCGTCACCCTTA
GATAGCCAGACTTCTTATCACGTAGGAACCGTGTTATCTTCATTATCCCTAAAGATGGCCAACCG
TCCTT
Found at i:476576 original size:16 final size:17
Alignment explanation
Indices: 476548--476589 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
476538 TTTTACCGAA
476548 TTTTAACACTTTATAGT
1 TTTTAACACTTTATAGT
476565 TTTTAACA-TTTATAGT
1 TTTTAACACTTTATAGT
476581 TTTTAACAC
1 TTTTAACAC
476590 CAATTCCGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTTAACACTTTATAGT
Found at i:481497 original size:27 final size:27
Alignment explanation
Indices: 481467--481518 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
481457 TATAACATCT
*
481467 ATAACCCGCATATGTATACTGACACCC
1 ATAACCCGCATATGTATACTAACACCC
* *
481494 ATAACCCGTATATGTGTACTAACAC
1 ATAACCCGCATATGTATACTAACAC
481519 GAGTTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (27 bp):
ATAACCCGCATATGTATACTAACACCC
Found at i:485190 original size:95 final size:95
Alignment explanation
Indices: 485025--485216 Score: 366
Period size: 95 Copynumber: 2.0 Consensus size: 95
485015 TCTTTTACAA
*
485025 TTTATATCTTCTTATTTTTGAAAAGATTTGTATCAAGTATGCTCTACTTCCTCACTAAAGATATA
1 TTTATATCTTCTTATTTTTGAAAAGATTTGTATCAAGTAGGCTCTACTTCCTCACTAAAGATATA
485090 CGATGTTTATATTATTCCGAGCAAAATTAC
66 CGATGTTTATATTATTCCGAGCAAAATTAC
485120 TTTATATCTTCTTATTTTTGAAAAGATTTGTATCAAGTAGGCTCTACTTCCTCACTAAAGATATA
1 TTTATATCTTCTTATTTTTGAAAAGATTTGTATCAAGTAGGCTCTACTTCCTCACTAAAGATATA
*
485185 TGATGTTTATATTATTCCGAGCAAAATTAC
66 CGATGTTTATATTATTCCGAGCAAAATTAC
485215 TT
1 TT
485217 CTAAGGTAGT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (95 bp):
TTTATATCTTCTTATTTTTGAAAAGATTTGTATCAAGTAGGCTCTACTTCCTCACTAAAGATATA
CGATGTTTATATTATTCCGAGCAAAATTAC
Found at i:485706 original size:25 final size:25
Alignment explanation
Indices: 485672--485732 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
485662 CTTGTATAAA
485672 AAGGTAGTTGTCAATGGGAGGCTGC
1 AAGGTAGTTGTCAATGGGAGGCTGC
485697 AAGGTAGTTGTCAATGGGAGGCTGC
1 AAGGTAGTTGTCAATGGGAGGCTGC
485722 AAGGTAGTTGT
1 AAGGTAGTTGT
485733 ATAAAAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.26
Consensus pattern (25 bp):
AAGGTAGTTGTCAATGGGAGGCTGC
Found at i:488226 original size:24 final size:25
Alignment explanation
Indices: 488194--488241 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
488184 GATCCAATCC
488194 GATCCAAAAA-AATAACCGAAAATA
1 GATCCAAAAACAATAACCGAAAATA
*
488218 GATCCAAAAACCGATAACCGAAAA
1 GATCCAAAAA-CAATAACCGAAAA
488242 AAACCGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
26 11 0.52
ACGTcount: A:0.58, C:0.21, G:0.10, T:0.10
Consensus pattern (25 bp):
GATCCAAAAACAATAACCGAAAATA
Found at i:488252 original size:16 final size:17
Alignment explanation
Indices: 488223--488254 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
488213 AAATAGATCC
488223 AAAAACCGATAACCGAA
1 AAAAACCGATAACCGAA
488240 AAAAACCGA-AACCGA
1 AAAAACCGATAACCGA
488255 TTTAATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.25, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAACCGATAACCGAA
Found at i:492495 original size:18 final size:19
Alignment explanation
Indices: 492472--492513 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
492462 AAACGGGGAT
492472 GTCAACAGTT-AGGTCAAA
1 GTCAACAGTTCAGGTCAAA
* *
492490 GTCAACGGTTCAGGTCAAG
1 GTCAACAGTTCAGGTCAAA
492509 GTCAA
1 GTCAA
492514 TAGGTCATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (19 bp):
GTCAACAGTTCAGGTCAAA
Found at i:494718 original size:12 final size:12
Alignment explanation
Indices: 494701--494734 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
494691 CACCCCCACA
494701 CCAGATTGGCTT
1 CCAGATTGGCTT
*
494713 CCAGATTGGTTT
1 CCAGATTGGCTT
494725 CCAGATTGGC
1 CCAGATTGGC
494735 CTTCAGTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (12 bp):
CCAGATTGGCTT
Found at i:495994 original size:33 final size:32
Alignment explanation
Indices: 495951--496012 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
495941 GGTATAAAAC
495951 TTTTTCACAAATAGCAGAGCATAAGTATCAAT
1 TTTTTCACAAATAGCAGAGCATAAGTATCAAT
* *
495983 TTTTTCCACAAATATCATAGCATAAGTATC
1 TTTTT-CACAAATAGCAGAGCATAAGTATC
496013 GATATAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
TTTTTCACAAATAGCAGAGCATAAGTATCAAT
Found at i:497008 original size:181 final size:176
Alignment explanation
Indices: 496697--497089 Score: 388
Period size: 181 Copynumber: 2.2 Consensus size: 176
496687 CTAAAGCTCT
* * * *
496697 ATCAGCTTAAATTCTGGTAACATTTTAGGCTCAACCCACTTTATTGTAAAATATTAATGTTCTAG
1 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACCCACTTTATTATAAAATATTAATGTTCCAG
* * * * * * **
496762 ATCACAACTTACTTTTTTAGTGAATCATGATATTCTGGGCGCAATTTTATTTATTATAGATATTC
66 ATAACAACCTAATTTCTTAGTGAAACATGATATTCTGGACGCAATCGTATTTATTATA-ATATTC
* * **
496827 ATAATATTTTTAACTTTTA-C-TATTTTGTTATCTTGAGAAATTTAAGGTTCC
130 -----ATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAA-ATAAGGCACC
* * *
496878 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACTCATTTTATTAATAAAAATTTTAACT-TTC
1 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACCCACTTTATT-AT-AAAATATTAA-TGTTC
*
496942 CATATAACAACCTAATTTCTTAGTGAACCACATGATATTCTTGGACGCAATCGTA-TTA-T-T-A
63 CAGATAACAACCTAATTTCTTAGTGAA--ACATGATATTC-TGGACGCAATCGTATTTATTATAA
* *
497003 TATTCATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAATCAGGCAGC
125 TATTCATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAATAAGGCACC
* **
497055 ATCAGCTTAAAATCTAATAATA-TTTAGGCGCAACC
1 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACC
497090 TAAAATTTTA
Statistics
Matches: 178, Mismatches: 26, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
176 26 0.15
177 25 0.14
178 19 0.11
181 47 0.26
182 1 0.01
183 34 0.19
184 2 0.01
185 13 0.07
186 11 0.06
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (176 bp):
ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACCCACTTTATTATAAAATATTAATGTTCCAG
ATAACAACCTAATTTCTTAGTGAAACATGATATTCTGGACGCAATCGTATTTATTATAATATTCA
TTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAATAAGGCACC
Found at i:497496 original size:10 final size:10
Alignment explanation
Indices: 497481--497510 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
497471 ATGTTAAGCT
*
497481 GTCTGTTGGA
1 GTCTGTTAGA
497491 GTCTGTTAGA
1 GTCTGTTAGA
497501 GTCTGTTAGA
1 GTCTGTTAGA
497511 TTGCAGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (10 bp):
GTCTGTTAGA
Found at i:499737 original size:183 final size:182
Alignment explanation
Indices: 499430--499797 Score: 718
Period size: 183 Copynumber: 2.0 Consensus size: 182
499420 TCCGATTTAT
499430 GGGGGCCTACTCACGTTGTATCCAATGAGTTTCATTACTATATTTCTTTGTTGATGCATGTACAC
1 GGGGGCCTACTCACGTTGTATCCAATGAGTTTCATTACTATATTTCTTTGTTGATGCATGTACAC
*
499495 GTTATACATGATTTATCTCCTCAAAAATAAAGCACAAGCTTTTACAACATTTCAAATGTTTCAAA
66 GTTATACATGATTTATCTCCTCAAAAATAAAGCACAAGCTTGTACAACATTTCAAATGTTTCAAA
499560 AGCTTGTAGATAATCAGTTTGGAATGTCAATCAAGGCAGTTCAGTCAAATTG
131 AGCTTGTAGATAATCAGTTTGGAATGTCAATCAAGGCAGTTCAGTCAAATTG
499612 GGGGGCCTACTCACGTTGTATCCAATGAGTTTCATTACTATATTTCCTTTGTTGATGCATGTACA
1 GGGGGCCTACTCACGTTGTATCCAATGAGTTTCATTACTATATTT-CTTTGTTGATGCATGTACA
499677 CGTTATACATGATTTATCTCCTCAAAAATAAAGCACAAGCTTGTACAACATTTCAAATGTTTCAA
65 CGTTATACATGATTTATCTCCTCAAAAATAAAGCACAAGCTTGTACAACATTTCAAATGTTTCAA
499742 AAGCTTGTAGATAATCAGTTTGGAATGTCAATCAAGGCAGTTCAGTCAAATTG
130 AAGCTTGTAGATAATCAGTTTGGAATGTCAATCAAGGCAGTTCAGTCAAATTG
499795 GGG
1 GGG
499798 TAGTGAATAT
Statistics
Matches: 184, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
182 45 0.24
183 139 0.76
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (182 bp):
GGGGGCCTACTCACGTTGTATCCAATGAGTTTCATTACTATATTTCTTTGTTGATGCATGTACAC
GTTATACATGATTTATCTCCTCAAAAATAAAGCACAAGCTTGTACAACATTTCAAATGTTTCAAA
AGCTTGTAGATAATCAGTTTGGAATGTCAATCAAGGCAGTTCAGTCAAATTG
Found at i:503822 original size:14 final size:14
Alignment explanation
Indices: 503799--503837 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
503789 AAACCCAAAT
*
503799 CACTAAACCTAATC
1 CACTAAACCTAACC
503813 CACTAAACCT-ACC
1 CACTAAACCTAACC
503826 CACTAAACCTAA
1 CACTAAACCTAA
503838 AAAACATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (14 bp):
CACTAAACCTAACC
Found at i:504717 original size:30 final size:30
Alignment explanation
Indices: 504683--504795 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
504673 TAAAACTTAA
504683 AAATTTCTGTTTTTGCCATTTTAGTCTTTT
1 AAATTTCTGTTTTTGCCATTTTAGTCTTTT
* ** * *
504713 AAATTTC--ATTTTGTAATATTTGGTC-TTC
1 AAATTTCTGTTTTTGCCAT-TTTAGTCTTTT
* * * *
504741 AAATTTTATATTTTTACTATTTTAGTCTTTT
1 AAA-TTTCTGTTTTTGCCATTTTAGTCTTTT
*
504772 AAATTTCTGTTTGTGCCATTTTAG
1 AAATTTCTGTTTTTGCCATTTTAG
504796 CCCTTTTATT
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
28 12 0.20
29 9 0.15
30 29 0.48
31 11 0.18
ACGTcount: A:0.22, C:0.11, G:0.10, T:0.58
Consensus pattern (30 bp):
AAATTTCTGTTTTTGCCATTTTAGTCTTTT
Found at i:504738 original size:29 final size:31
Alignment explanation
Indices: 504700--504778 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
504690 TGTTTTTGCC
504700 ATTTTAGTCTTTTAAATTTCAT-TTTGTAAT
1 ATTTTAGTCTTTTAAATTTCATATTTGTAAT
* * * * *
504730 A-TTTGGTC-TTCAAATTTTATATTTTTACT
1 ATTTTAGTCTTTTAAATTTCATATTTGTAAT
504759 ATTTTAGTCTTTTAAATTTC
1 ATTTTAGTCTTTTAAATTTC
504779 TGTTTGTGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 10 0.26
29 13 0.34
30 7 0.18
31 8 0.21
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.59
Consensus pattern (31 bp):
ATTTTAGTCTTTTAAATTTCATATTTGTAAT
Found at i:517394 original size:2 final size:2
Alignment explanation
Indices: 517387--517487 Score: 188
Period size: 2 Copynumber: 51.5 Consensus size: 2
517377 GCTATGATTT
517387 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
517429 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA -A 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
517469 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
517488 GAATCTATGT
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 95 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:523543 original size:10 final size:10
Alignment explanation
Indices: 523528--523552 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
523518 ATTTGTCGTA
523528 AAATAATTAT
1 AAATAATTAT
523538 AAATAATTAT
1 AAATAATTAT
523548 AAATA
1 AAATA
523553 TATTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATAATTAT
Found at i:524362 original size:15 final size:15
Alignment explanation
Indices: 524342--524371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
524332 AAACTGTTTA
524342 TAATACTGATATAAC
1 TAATACTGATATAAC
524357 TAATACTGATATAAC
1 TAATACTGATATAAC
524372 AAAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
TAATACTGATATAAC
Found at i:540794 original size:187 final size:187
Alignment explanation
Indices: 540477--540826 Score: 440
Period size: 187 Copynumber: 1.9 Consensus size: 187
540467 AACAAATTTT
* * * *
540477 TGGTAACATTTTAGGTGTAACCCATTTTATTAATAAAAATATTAACATTCCATATTACAACATAC
1 TGGTAACATTTTAGCTGCAACCCATTTTAGTAATAAAAATATTAACATTCCATATAACAACATAC
* * * * *
540542 TTTCTATGTGAATCATGACATTCTTGGGTGCAATTGTATTTGTTATAGATATTTATAACATTTTC
66 TTTCTATGTGAATCATGACATTATTAGGTGCAATTGTATTTATTATAGATATTCATAAAATTTTC
*
540607 -AGTTTGAACTTATTTTGTT-TACTTGGGAAAATTTAAGGTTTTATCACCTTAAACTC
131 AAGTTTGAACTTATTTTGTTAT-CGTGGGAAAATTTAAGGTTTTATCACCTTAAACTC
* ** *
540663 TGGTAACATTTTAGACT-CAACCTATTTTAGTAATAAAAATTATTAATGTTCCATA-AAGCAACT
1 TGGTAACATTTTAG-CTGCAACCCATTTTAGTAATAAAAA-TATTAACATTCCATATAA-CAACA
* * *
540726 TATTTTCT-TAGTGAATCATGATATTATTAGGTGTAATTGTATTTATTATAGATATTCATAAAAT
63 TACTTTCTAT-GTGAATCATGACATTATTAGGTGCAATTGTATTTATTATAGATATTCATAAAAT
* * *
540790 TTTCAATTTTTATCTTATTTTGTTATCGTGGGAAAAT
127 TTTCAAGTTTGAACTTATTTTGTTATCGTGGGAAAAT
540827 CTATGGTTCC
Statistics
Matches: 138, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
186 35 0.25
187 76 0.55
188 26 0.19
189 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (187 bp):
TGGTAACATTTTAGCTGCAACCCATTTTAGTAATAAAAATATTAACATTCCATATAACAACATAC
TTTCTATGTGAATCATGACATTATTAGGTGCAATTGTATTTATTATAGATATTCATAAAATTTTC
AAGTTTGAACTTATTTTGTTATCGTGGGAAAATTTAAGGTTTTATCACCTTAAACTC
Found at i:545474 original size:21 final size:21
Alignment explanation
Indices: 545450--545490 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
545440 GGCCGTAATG
545450 GCGCCCGCGACAACCGCAATA
1 GCGCCCGCGACAACCGCAATA
**
545471 GCGCCCGCGACGGCCGCAAT
1 GCGCCCGCGACAACCGCAAT
545491 CACGGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.44, G:0.29, T:0.05
Consensus pattern (21 bp):
GCGCCCGCGACAACCGCAATA
Found at i:554610 original size:35 final size:35
Alignment explanation
Indices: 554545--554614 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
554535 AACATCTACC
554545 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
*
554580 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
554615 TTGGTTGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:559124 original size:36 final size:35
Alignment explanation
Indices: 559065--559144 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 35
559055 ACCCATTCCT
*
559065 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* * *
559099 ATTTTTCAAAGAAACATTTATCAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
559135 ATTTTCAAAG
1 ATTTTCAAAG
559145 TTGGTTGCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 14 0.35
36 25 0.62
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (35 bp):
ATTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:561005 original size:20 final size:19
Alignment explanation
Indices: 560980--561033 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
560970 GCGAAATAAA
560980 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
561000 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
561020 AATCGCAACGCGAT
1 AATCGCAACGCGAT
561034 AGTACAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:561087 original size:20 final size:20
Alignment explanation
Indices: 561062--561114 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
561052 GATTTTCCAG
*
561062 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
561082 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
*
561102 AATTGCAACGCGA
1 AATCGCAACGCGA
561115 TTTTGACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:561163 original size:16 final size:17
Alignment explanation
Indices: 561134--561165 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
561124 TCGCAACGAG
561134 TATCCGTAAAATCGCAT
1 TATCCGTAAAATCGCAT
561151 TATCCGT-AAATCGCA
1 TATCCGTAAAATCGCA
561166 ACGACAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (17 bp):
TATCCGTAAAATCGCAT
Found at i:561168 original size:37 final size:40
Alignment explanation
Indices: 561124--561330 Score: 192
Period size: 40 Copynumber: 5.2 Consensus size: 40
561114 ATTTTGACTT
* *
561124 TCGCAACGAGTATCCGTAAAATCGC-A-T-TATCCGTAAA
1 TCGCAACGAGAATACGTAAAATCGCAACTGTATCCGTAAA
* *
561161 TCGCAACGACAATACATAAAATCGCAACGTGTATCCGTAAA
1 TCGCAACGAGAATACGTAAAATCGCAAC-TGTATCCGTAAA
* * *
561202 TCGCAACGAGAATACGT-AAATCACAACGCGTATCTGTAAA
1 TCGCAACGAGAATACGTAAAATCGCAAC-TGTATCCGTAAA
* *
561242 TAGTAACGAGAATACGT-AAATCGCAA-TGCGTATCCGTAAA
1 TCGCAACGAGAATACGTAAAATCGCAACT--GTATCCGTAAA
* * * * * *
561282 TTGTAATGACAATACGTAAAATCGCAACGCGTATCTGTAAA
1 TCGCAACGAGAATACGTAAAATCGCAAC-TGTATCCGTAAA
561323 TCGCAACG
1 TCGCAACG
561331 CGATCGATAA
Statistics
Matches: 139, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
37 21 0.15
38 1 0.01
40 68 0.49
41 49 0.35
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (40 bp):
TCGCAACGAGAATACGTAAAATCGCAACTGTATCCGTAAA
Found at i:561204 original size:20 final size:20
Alignment explanation
Indices: 561124--561330 Score: 134
Period size: 20 Copynumber: 10.4 Consensus size: 20
561114 ATTTTGACTT
561124 TCGCAACGAGTATCCGTAAAA
1 TCGCAACGAGTATCCGT-AAA
*
561145 TCG---C-ATTATCCGTAAA
1 TCGCAACGAGTATCCGTAAA
** * *
561161 TCGCAACGACAATACATAAAA
1 TCGCAACGAGTATCCGT-AAA
*
561182 TCGCAACGTGTATCCGTAAA
1 TCGCAACGAGTATCCGTAAA
* *
561202 TCGCAACGAGAATACGTAAA
1 TCGCAACGAGTATCCGTAAA
* * *
561222 TCACAACGCGTATCTGTAAA
1 TCGCAACGAGTATCCGTAAA
* * * *
561242 TAGTAACGAGAATACGTAAA
1 TCGCAACGAGTATCCGTAAA
* *
561262 TCGCAATGCGTATCCGTAAA
1 TCGCAACGAGTATCCGTAAA
* * * ** *
561282 TTGTAATGACAATACGTAAAA
1 TCGCAACGAGTATCCGT-AAA
* *
561303 TCGCAACGCGTATCTGTAAA
1 TCGCAACGAGTATCCGTAAA
561323 TCGCAACG
1 TCGCAACG
561331 CGATCGATAA
Statistics
Matches: 135, Mismatches: 45, Indels: 13
0.70 0.23 0.07
Matches are distributed among these distances:
16 6 0.04
17 8 0.06
18 1 0.01
19 1 0.01
20 89 0.66
21 30 0.22
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
TCGCAACGAGTATCCGTAAA
Found at i:561235 original size:40 final size:41
Alignment explanation
Indices: 561151--561330 Score: 229
Period size: 40 Copynumber: 4.4 Consensus size: 41
561141 AAAATCGCAT
* *
561151 TATCCGTAAATCGCAACGACAATACATAAAATCGCAACGTG
1 TATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCG
* *
561192 TATCCGTAAATCGCAACGAGAATACGT-AAATCACAACGCG
1 TATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCG
* * * * *
561232 TATCTGTAAATAGTAACGAGAATACGT-AAATCGCAATGCG
1 TATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCG
* * *
561272 TATCCGTAAATTGTAATGACAATACGTAAAATCGCAACGCG
1 TATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCG
*
561313 TATCTGTAAATCGCAACG
1 TATCCGTAAATCGCAACG
561331 CGATCGATAA
Statistics
Matches: 120, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 69 0.57
41 51 0.43
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.22
Consensus pattern (41 bp):
TATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCG
Found at i:561331 original size:20 final size:19
Alignment explanation
Indices: 561179--561351 Score: 116
Period size: 20 Copynumber: 8.7 Consensus size: 19
561169 ACAATACATA
*
561179 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAT-CGT
* *
561199 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGTAT-CGT
*
561219 AAATCACAACGCGTATCTGT
1 AAATCGCAACGCGTATC-GT
* * * *
561239 AAATAGTAACGAGAATACGT
1 AAATCGCAACGCGTAT-CGT
*
561259 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAT-CGT
* * * *
561279 AAATTGTAATGAC-AATACGT
1 AAATCGCAACG-CGTAT-CGT
561299 AAAATCGCAACGCGTATCTGT
1 -AAATCGCAACGCGTATC-GT
561320 AAATCGCAACGCG-ATCGAT
1 AAATCGCAACGCGTATCG-T
*
561339 AATTCGCAACGCG
1 AAATCGCAACGCG
561352 ATCTCCGGTA
Statistics
Matches: 120, Mismatches: 26, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
18 1 0.01
19 17 0.14
20 88 0.73
21 14 0.12
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGTATCGT
Found at i:561452 original size:19 final size:20
Alignment explanation
Indices: 561428--561466 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
561418 CAAATTGCGT
561428 TGCGAATCTGTAAAT-GCAA
1 TGCGAATCTGTAAATCGCAA
561447 TGCGAATCTGTAAATCGCAA
1 TGCGAATCTGTAAATCGCAA
561467 CGAGATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCGAATCTGTAAATCGCAA
Found at i:561476 original size:20 final size:19
Alignment explanation
Indices: 561431--561476 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
561421 ATTGCGTTGC
* *
561431 GAATCTGTAAATGCAATGC
1 GAATCTGTAAATGCAACGA
561450 GAATCTGTAAATCGCAACGA
1 GAATCTGTAAAT-GCAACGA
*
561470 GATTCTG
1 GAATCTG
561477 ACTATCCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (19 bp):
GAATCTGTAAATGCAACGA
Found at i:562352 original size:24 final size:24
Alignment explanation
Indices: 562325--562380 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
562315 CAGTATTCGA
*
562325 AATTTGATTTTGGTCAATACCCGG
1 AATTTGATCTTGGTCAATACCCGG
*
562349 AATTTGATCTTGGTCAATACTCGG
1 AATTTGATCTTGGTCAATACCCGG
*
562373 ATTTTGAT
1 AATTTGAT
562381 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
AATTTGATCTTGGTCAATACCCGG
Found at i:564814 original size:20 final size:19
Alignment explanation
Indices: 564789--564978 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
564779 GACATTCATT
*
564789 TGACTATCGCAACGCGAATA
1 TGACTATCGCAATGCGAA-A
**
564809 TGACTATCGCAACACGGAAA
1 TGACTATCGCAATGC-GAAA
*
564829 TGACTATCGCAATGCAGAAT
1 TGACTATCGCAATGC-GAAA
* *
564849 TGACTATCGTAACGCGGAAA
1 TGACTATCGCAATGC-GAAA
* *
564869 TGACTATCGTAA--CGAGA
1 TGACTATCGCAATGCGAAA
564886 -GA--ATCGCAATGCGAAA
1 TGACTATCGCAATGCGAAA
**
564902 TGAGAATCGCAATGCGAAA
1 TGACTATCGCAATGCGAAA
**
564921 TGAGAATCGCAATGCGAAA
1 TGACTATCGCAATGCGAAA
**
564940 TGAAAATCGCAATGCGAAA
1 TGACTATCGCAATGCGAAA
** *
564959 TGAAAATCGCAACGCGAAA
1 TGACTATCGCAATGCGAAA
564978 T
1 T
564979 TAGTTTCGTG
Statistics
Matches: 150, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
14 6 0.04
16 6 0.04
17 5 0.03
18 1 0.01
19 70 0.47
20 59 0.39
21 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (19 bp):
TGACTATCGCAATGCGAAA
Found at i:564853 original size:40 final size:40
Alignment explanation
Indices: 564789--564882 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
564779 GACATTCATT
564789 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
* * *
564829 TGACTATCGCAATGCAGAAT-TGACTATCGTAACGCGGAAA
1 TGACTATCGCAACGC-GAATATGACTATCGCAACACGGAAA
*
564869 TGACTATCGTAACG
1 TGACTATCGCAACG
564883 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
Found at i:564908 original size:19 final size:19
Alignment explanation
Indices: 564884--564978 Score: 163
Period size: 19 Copynumber: 5.0 Consensus size: 19
564874 ATCGTAACGA
564884 GAGAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
564903 GAGAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
564922 GAGAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
*
564941 GAAAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
* *
564960 GAAAATCGCAACGCGAAAT
1 GAGAATCGCAATGCGAAAT
564979 TAGTTTCGTG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 74 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (19 bp):
GAGAATCGCAATGCGAAAT
Found at i:565044 original size:33 final size:33
Alignment explanation
Indices: 564988--565071 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
564978 TTAGTTTCGT
564988 GTTGCGATTTTCATTTTCGCATTGCGATTCACTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCACTC
*
565022 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCACTC
**
565055 GTTGCGATAGTCATTTC
1 GTTGCGATTTTCATTTC
565072 CACGTTGCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCACTC
Found at i:565079 original size:20 final size:20
Alignment explanation
Indices: 565054--565097 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
565044 GCGATTCTCT
565054 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCA
565074 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCA
565094 CGTT
1 CGTT
565098 TCAATAGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCA
Found at i:565104 original size:20 final size:20
Alignment explanation
Indices: 565054--565106 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
565044 GCGATTCTCT
*
565054 CGTTGCGATAGTCATTTCCA
1 CGTTGCAATAGTCATTTCCA
*
565074 CGTTGCGATAGTCATTTCCA
1 CGTTGCAATAGTCATTTCCA
*
565094 CGTTTCAATAGTC
1 CGTTGCAATAGTC
565107 TGTTTTGCAT
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:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (20 bp):
CGTTGCAATAGTCATTTCCA
Found at i:565223 original size:14 final size:14
Alignment explanation
Indices: 565204--565240 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
565194 CATCAATTAA
565204 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
565218 ACAAATCATCTTTT
1 ACAAATCAACATTT
565232 ACAAATCAA
1 ACAAATCAA
565241 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:566693 original size:42 final size:42
Alignment explanation
Indices: 566614--566706 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
566604 CCTCTTCAAC
* * *
566614 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
566656 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
566698 GATGACAGG
1 GATGACAGG
566707 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:567212 original size:20 final size:20
Alignment explanation
Indices: 567189--567273 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
567179 CTTAAAATCG
*
567189 CAATGCGAAAATTACTATCA
1 CAATGCGAAAATGACTATCA
*
567209 CAATGCGAAAATGACTATCG
1 CAATGCGAAAATGACTATCA
*
567229 CAATGAGAAAATGACTATCA
1 CAATGCGAAAATGACTATCA
** *
567249 CAATGCGAATTTGACTATCG
1 CAATGCGAAAATGACTATCA
567269 CAATG
1 CAATG
567274 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (20 bp):
CAATGCGAAAATGACTATCA
Found at i:567240 original size:40 final size:40
Alignment explanation
Indices: 567185--567276 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
567175 GAAACTTAAA
* *
567185 ATCGCAATGCGAAAATTACTATCACAATGCGAAAATGACT
1 ATCGCAATGAGAAAATGACTATCACAATGCGAAAATGACT
**
567225 ATCGCAATGAGAAAATGACTATCACAATGCGAATTTGACT
1 ATCGCAATGAGAAAATGACTATCACAATGCGAAAATGACT
567265 ATCGCAATGAGA
1 ATCGCAATGAGA
567277 GAATCGCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (40 bp):
ATCGCAATGAGAAAATGACTATCACAATGCGAAAATGACT
Found at i:567328 original size:19 final size:19
Alignment explanation
Indices: 567306--567349 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
567296 AAATCACAAC
567306 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
567325 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
567344 GCGATT
1 GCGATT
567350 TTGTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:567350 original size:19 final size:19
Alignment explanation
Indices: 567315--567382 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
567305 CGCGATTATA
567315 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
567334 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
567352 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
567367 GTTTCACGTTGCGATT
1 GTTTCGCGTTGCGATT
567383 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 28 0.64
ACGTcount: A:0.07, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:567359 original size:14 final size:14
Alignment explanation
Indices: 567340--567398 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
567330 TTTGGTTTCG
567340 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
567354 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
* *
567371 CACGTTGCGATTCTCT
1 --CGTTGCGATTTTGT
567387 CGTTGCGATTTT
1 CGTTGCGATTTT
567399 CATTTCTCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 23 0.62
15 1 0.03
16 1 0.03
17 1 0.03
19 11 0.30
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:567363 original size:33 final size:33
Alignment explanation
Indices: 567321--567445 Score: 164
Period size: 33 Copynumber: 3.8 Consensus size: 33
567311 TATAGTTTCG
** * *
567321 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
** *
567354 CGTTGCGATTTTGGTTTCACGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
567387 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
567420 CGTTGCGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
567446 AGTCATTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
31 17 0.20
33 68 0.80
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:567408 original size:19 final size:17
Alignment explanation
Indices: 567368--567445 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 17
567358 GCGATTTTGG
*
567368 TTTCACGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
567384 --TCTCGTTGCGATTTTCA
1 TTTCTCGTTGCGA--TTCA
567401 TTTCTCGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
567417 --TCTCGTTGCGATTCA
1 TTTCTCGTTGCGATTCA
*
567432 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
567446 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
14 24 0.46
16 3 0.06
17 14 0.27
19 11 0.21
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (17 bp):
TTTCTCGTTGCGATTCA
Found at i:567679 original size:94 final size:94
Alignment explanation
Indices: 567533--567912 Score: 566
Period size: 94 Copynumber: 4.1 Consensus size: 94
567523 ATGGATTGCA
* * * *
567533 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
567597 TTAGCAGAATTGGCAACAACCTAACAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
567626 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
567691 TTAGTAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
* *
567720 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * * ** *
567785 TTAGGAGAAATGACAGTAACCGAATAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
*
567814 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAA-AAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
567878 TTTAGCAGTATTGGCAACAACCAAATAAAT
65 TTTAGCAGAATTGGCAACAACCGAACAAAT
567908 TTACT
1 TTACT
567913 AAGCAATCTA
Statistics
Matches: 260, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
93 21 0.08
94 239 0.92
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAACAACCGAACAAAT
Found at i:569665 original size:19 final size:19
Alignment explanation
Indices: 569610--569680 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
569600 TGAAATGAAA
*
569610 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
* *
569630 TTCGCAATGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
**
569650 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
569669 ATCGCAATGCGA
1 ATCGCAACGCGA
569681 TTTTAGTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 18 0.43
20 22 0.52
21 2 0.05
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:569726 original size:21 final size:21
Alignment explanation
Indices: 569700--569778 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
569690 CGCGTTGCGA
*
569700 TTCTCTCGTTGCCATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
569721 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
569742 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
569762 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
569779 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.11, C:0.20, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:570358 original size:20 final size:20
Alignment explanation
Indices: 570333--570547 Score: 184
Period size: 20 Copynumber: 10.6 Consensus size: 20
570323 CTTTAAAAAT
570333 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
570353 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
570373 TGTCGTTGCGATTTACGAATA
1 CG-CGTTGCGATTTACGGATA
*
570394 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
570414 TGTCGTTGCGATTTACGAATA
1 CG-CGTTGCGATTTACGGATA
* * * *
570435 CGCATTGTGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
570455 CTCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
570475 TGCGTTGCGATTTTATGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
570495 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
570516 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
**
570537 CTTGTTGCGAT
1 CGCGTTGCGAT
570548 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 26, Indels: 20
0.78 0.13 0.10
Matches are distributed among these distances:
20 91 0.57
21 68 0.43
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:570480 original size:81 final size:81
Alignment explanation
Indices: 570335--570547 Score: 309
Period size: 81 Copynumber: 2.6 Consensus size: 81
570325 TTAAAAATCG
*
570335 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGAATACGCGTT
570400 GCGATTTTACGTATTGT
65 GCGATTTTACGTATTGT
* * * * * *
570417 CGTTGCGATTTACGAATACGCATTGTGATTTACGTATTCTCGTTGTGATTTACGGATATGCGTTG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACGCGTTG
*
570482 CGATTTTATGTATTGT
66 CGATTTTACGTATTGT
* * *
570498 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTTGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGAT
570548 AGTCAGAATC
Statistics
Matches: 115, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 73 0.63
82 42 0.37
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (81 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACGCGTTG
CGATTTTACGTATTGT
Found at i:570547 original size:41 final size:41
Alignment explanation
Indices: 570335--570532 Score: 317
Period size: 41 Copynumber: 4.9 Consensus size: 41
570325 TTAAAAATCG
570335 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
*
570376 CGTTGCGATTTACGAATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * * *
570417 CGTTGCGATTTACGAATACGCATTGTGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * *
570457 CGTTGTGATTTACGGATATGCGTTGCGATTTTATGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
570498 CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
570533 GATACTTGTT
Statistics
Matches: 142, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 34 0.24
41 108 0.76
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
Found at i:570570 original size:122 final size:122
Alignment explanation
Indices: 570335--570608 Score: 336
Period size: 122 Copynumber: 2.2 Consensus size: 122
570325 TTAAAAATCG
570335 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCGTT
* ** * **
570400 GCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCATTGTGATTTACGTATTCT
66 GCGATTTTACGGATACTCGTTGCGATTCACGAATACGCATTGCAATTTACGTATTCT
* * * *
570457 CGTTGTGATTTACGGATATGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCGTT
* * ** * *
570522 GCGATTTTACGGATACTTGTTGCGATAGTCA-GAAT-CGCGTTGCAATTTATATGTTCG
66 GCGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCATTGCAATTTACGTATTCT
* ** *
570579 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
570609 CTGGAAAATC
Statistics
Matches: 128, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
122 122 0.95
123 4 0.03
124 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (122 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCGTT
GCGATTTTACGGATACTCGTTGCGATTCACGAATACGCATTGCAATTTACGTATTCT
Found at i:570605 original size:20 final size:20
Alignment explanation
Indices: 570332--570608 Score: 86
Period size: 20 Copynumber: 13.7 Consensus size: 20
570322 GCTTTAAAAA
* **
570332 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
* *
570352 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CATAT
*
570373 T-GTCGTTGCGATTTACGA-AT
1 TCG-CGTTGCGATTTTC-ATAT
* *
570393 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CATAT
*
570414 T-GTCGTTGCGATTTACGA-AT
1 TCG-CGTTGCGATTTTC-ATAT
* * * * *
570434 ACGCATTGTGATTTACGTAT
1 TCGCGTTGCGATTTTCATAT
* * *
570454 TCTCGTTGTGATTTACGGATA-
1 TCGCGTTGCGATTTTC--ATAT
570475 T-GCGTTGCGATTTT-ATGTAT
1 TCGCGTTGCGATTTTCA--TAT
* **
570495 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTTCATAT
* **
570515 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGATTTT-CATAT
* ** ** * *
570536 ACTTGTTGCGATAGTCAGAA
1 TCGCGTTGCGATTTTCATAT
* *
570556 TCGCGTTGCAATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
570576 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
570596 TCGCGTTGCGATT
1 TCGCGTTGCGATT
570609 CTGGAAAATC
Statistics
Matches: 191, Mismatches: 45, Indels: 42
0.69 0.16 0.15
Matches are distributed among these distances:
17 1 0.01
19 3 0.02
20 124 0.65
21 61 0.32
22 2 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:570669 original size:42 final size:42
Alignment explanation
Indices: 570576--570669 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
570566 ATTTATATGT
* *
570576 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
570617 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
570659 TCGCGTTGCGA
1 TCGCGTTGCGA
570670 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:570707 original size:20 final size:19
Alignment explanation
Indices: 570658--570711 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
570648 ATTCTTCATA
570658 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
570677 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
570698 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
570712 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:571362 original size:30 final size:30
Alignment explanation
Indices: 571289--571380 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
571279 GGATTCAGGT
* * *
571289 GTTAAATTAATATTTTATATAAAGTCT-AG
1 GTTAAATTAGTATTTTATATAAAATTTAAG
* *
571318 GAATTAACTTAGTATTTTATGTAAAATTTAAG
1 G--TTAAATTAGTATTTTATATAAAATTTAAG
* *
571350 GTTAAATTAGTATTTTGTCTAAAATTTAAG
1 GTTAAATTAGTATTTTATATAAAATTTAAG
571380 G
1 G
571381 ATAATGATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 27 0.52
31 21 0.40
32 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (30 bp):
GTTAAATTAGTATTTTATATAAAATTTAAG
Found at i:573009 original size:20 final size:21
Alignment explanation
Indices: 572967--573010 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
572957 AAGTAATTAC
*
572967 CTATCTGCAACTAACTACTAA
1 CTATCTGCAACTAACTACAAA
572988 CTAT-TGCAACTAA-TCACAAA
1 CTATCTGCAACTAACT-ACAAA
573008 CTA
1 CTA
573011 ATTAGCAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.76
21 4 0.19
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (21 bp):
CTATCTGCAACTAACTACAAA
Found at i:573181 original size:30 final size:31
Alignment explanation
Indices: 573124--573191 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
573114 GATAATATTT
* *
573124 AATTTGATATCTAAATTTTAGATAAAATATC
1 AATTTGATATCTAAACTTTAAATAAAATATC
*
573155 ATTTTGATAT-TAAACTTTAAATAAAATATC
1 AATTTGATATCTAAACTTTAAATAAAATATC
573185 AATTTGA
1 AATTTGA
573192 CCTTTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (31 bp):
AATTTGATATCTAAACTTTAAATAAAATATC
Found at i:574706 original size:36 final size:36
Alignment explanation
Indices: 574666--574768 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
574656 ACGATGGTGG
574666 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
574702 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
574738 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
574769 ATGGATAAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:575563 original size:22 final size:23
Alignment explanation
Indices: 575538--575587 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
575528 TTTTCAACCA
575538 TCAAACTCAA-TAAATTTGTAAT
1 TCAAACTCAACTAAATTTGTAAT
* * *
575560 TCAATCTCAACTCAATTTTTAAT
1 TCAAACTCAACTAAATTTGTAAT
575583 TCAAA
1 TCAAA
575588 TTTCAGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (23 bp):
TCAAACTCAACTAAATTTGTAAT
Found at i:582492 original size:36 final size:36
Alignment explanation
Indices: 582447--582548 Score: 152
Period size: 36 Copynumber: 2.8 Consensus size: 36
582437 TGATGCTGGA
*
582447 CATTGATACACGAATGTATCAAAGCTGATATGATAAC
1 CATTAATACACGAATGTATCAAAGCTGATATGAT-AC
*
582484 C-TTAATACACGAATGTACCAAAGCTGATATGATAC
1 CATTAATACACGAATGTATCAAAGCTGATATGATAC
* *
582519 CATTGATACATGAATGTATCAAAGCTGATA
1 CATTAATACACGAATGTATCAAAGCTGATA
582549 ATGGATAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
35 3 0.05
36 55 0.93
37 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (36 bp):
CATTAATACACGAATGTATCAAAGCTGATATGATAC
Found at i:584446 original size:10 final size:10
Alignment explanation
Indices: 584431--584456 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
584421 TGACATCATC
584431 AAAATTTCGT
1 AAAATTTCGT
584441 AAAATTTCGT
1 AAAATTTCGT
584451 AAAATT
1 AAAATT
584457 CCAATTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (10 bp):
AAAATTTCGT
Found at i:588270 original size:29 final size:30
Alignment explanation
Indices: 588225--588281 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
588215 TAAATTCTAG
*
588225 AAATTACACTTTTGGTCCCCAAACTTTTAA
1 AAATTACACCTTTGGTCCCCAAACTTTTAA
**
588255 AAATTAC-CCTTTGGTCCTTAAACTTTT
1 AAATTACACCTTTGGTCCCCAAACTTTT
588282 CCAAACTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AAATTACACCTTTGGTCCCCAAACTTTTAA
Found at i:588922 original size:2 final size:2
Alignment explanation
Indices: 588915--588942 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
588905 TTTGAAATTA
588915 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
588943 GATGTACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:591939 original size:13 final size:13
Alignment explanation
Indices: 591921--591959 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
591911 GTCATAAATC
591921 TATGACACGCATT
1 TATGACACGCATT
*
591934 TATGACACACATT
1 TATGACACGCATT
*
591947 TATGACGCGCATT
1 TATGACACGCATT
591960 GAGCGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:598386 original size:16 final size:16
Alignment explanation
Indices: 598361--598391 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
598351 GACCCAGATC
598361 GTTGAATTTGACCAAT
1 GTTGAATTTGACCAAT
*
598377 GTTGACTTTGACCAA
1 GTTGAATTTGACCAA
598392 AAGTTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (16 bp):
GTTGAATTTGACCAAT
Found at i:600511 original size:16 final size:16
Alignment explanation
Indices: 600490--600520 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
600480 AGGGAGACGC
*
600490 TTGAGTTCTTATAGGG
1 TTGAGTTCTAATAGGG
600506 TTGAGTTCTAATAGG
1 TTGAGTTCTAATAGG
600521 TTTTAAACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (16 bp):
TTGAGTTCTAATAGGG
Found at i:606704 original size:22 final size:22
Alignment explanation
Indices: 606676--606725 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
606666 TTATTTTCCC
606676 AATGTATGCCAAATGAGAACGA
1 AATGTATGCCAAATGAGAACGA
* *
606698 AATGTATGCCAAATGAGAATGT
1 AATGTATGCCAAATGAGAACGA
606720 AATGTA
1 AATGTA
606726 CATGCATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (22 bp):
AATGTATGCCAAATGAGAACGA
Found at i:607007 original size:135 final size:137
Alignment explanation
Indices: 606746--607007 Score: 372
Period size: 138 Copynumber: 1.9 Consensus size: 137
606736 ACCGAAGTGC
*
606746 CAAAATGGAAATTCACAAACACATTATGAATTCCATGGATGCACTCATAGTGCTAATAGTACACA
1 CAAAATGGAAATTCACAAACACATTATGAATACCATGGATGCACTCATAGTGCTAATAGTACACA
* *
606811 TAGTACTAATACGAAAATGAACCGTTATGCATTAAACAAAATCGATCGATAACTTTTATACATAA
66 TAG-ACTAATACGAAAATGAACCGTTATGCATTAAACAAAATCGATCGATAACTATCATACATAA
606876 TTGTATAT
130 TTGTATAT
* * * *
606884 CAAAATGGTAATTCATAAACTCATTATGAATACCAT-GATTGCACATC-TAGTGTTGAA-AGTAC
1 CAAAATGGAAATTCACAAACACATTATGAATACCATGGA-TGCAC-TCATAGTGCT-AATAGTAC
* *
606946 ACATA-A-TAATACGAAAATGAATCGTTATGCATTAATCAAAATCGATCGATAACTATCATACA
63 ACATAGACTAATACGAAAATGAACCGTTATGCATTAAACAAAATCGATCGATAACTATCATACA
607008 CAAAGTATGT
Statistics
Matches: 112, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
135 52 0.46
136 1 0.01
137 2 0.02
138 53 0.47
139 4 0.04
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.29
Consensus pattern (137 bp):
CAAAATGGAAATTCACAAACACATTATGAATACCATGGATGCACTCATAGTGCTAATAGTACACA
TAGACTAATACGAAAATGAACCGTTATGCATTAAACAAAATCGATCGATAACTATCATACATAAT
TGTATAT
Found at i:616890 original size:10 final size:9
Alignment explanation
Indices: 616863--616900 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
616853 TAAATAAAAT
616863 AATAATAGA
1 AATAATAGA
616872 AA-AATAGA
1 AATAATAGA
616880 AATATATAGA
1 AATA-ATAGA
616890 AATATATAGA
1 AATA-ATAGA
616900 A
1 A
616901 CAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.30
9 3 0.11
10 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (9 bp):
AATAATAGA
Found at i:616890 original size:18 final size:19
Alignment explanation
Indices: 616854--616891 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
616844 ACATAGTATT
616854 AAATAAAATAATAATAGAA
1 AAATAAAATAATAATAGAA
616873 AAATAGAAAT-AT-ATAGAA
1 AAATA-AAATAATAATAGAA
616891 A
1 A
616892 TATATAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAAAATAATAATAGAA
Found at i:617077 original size:2 final size:2
Alignment explanation
Indices: 617070--617100 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
617060 GTATACTTAA
617070 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
617101 TAATAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:618557 original size:106 final size:107
Alignment explanation
Indices: 618374--618605 Score: 331
Period size: 106 Copynumber: 2.2 Consensus size: 107
618364 ATCTTCTGTC
* * * * **
618374 GTGAAGTTGAAGTTGGTTCTGGAACTGGGAAATTGTTTTGTTGACAGTCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
* *
618439 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATGCCCTTCAAT
66 TGAAGTTGAACTTGTACTGTCTCGAGTCCAATACCCTTCAAT
*
618481 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTG-TTTGTTGACAACCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
* * * **
618545 TGAAGTTGAACTTGTATTGTCTTGAGTCCAATATCCTTTGAT
66 TGAAGTTGAACTTGTACTGTCTCGAGTCCAATACCCTTCAAT
618587 GTGAAGTTGAAATTGGCTC
1 GTGAAGTTGAAATTGGCTC
618606 TAGCTAAAAC
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 81 0.73
107 30 0.27
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (107 bp):
GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
TGAAGTTGAACTTGTACTGTCTCGAGTCCAATACCCTTCAAT
Found at i:619051 original size:31 final size:31
Alignment explanation
Indices: 619016--619142 Score: 89
Period size: 31 Copynumber: 3.9 Consensus size: 31
619006 GGGAAATAAA
619016 CTCAAA-GATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAACGATTTTGTGTTTCAAGAGAAACT-T
** * *
619047 CTCAAGGGAGACGAAATT-TGTTTCAAGGGAAACAAT
1 CTC-A---A-ACGATTTTGTGTTTCAAGAGAAAC-TT
*
619083 CTCAAA-GGTTTTGTGTTTCAAGAGAAACATT
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC-TT
* * *
619114 TTCAAAGGTTTTTGTGTTTCAAGAGAAAC
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC
619143 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
30 3 0.04
31 25 0.33
32 23 0.30
35 2 0.03
36 19 0.25
37 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (31 bp):
CTCAAACGATTTTGTGTTTCAAGAGAAACTT
Found at i:619051 original size:67 final size:67
Alignment explanation
Indices: 618919--619110 Score: 251
Period size: 67 Copynumber: 2.8 Consensus size: 67
618909 TGTCTTAAAA
* * * * *
618919 AGACAGAATTCGTTTCAAGGGAAACAATCTTAAAGATATATGTTGTTTCATGAGAAACGACCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGACCTCA
618984 AGGG
64 AGGG
* * * *
618988 AGACAAAATTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTG-TCTCAA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC-GACCTCAA
619052 GGG
65 GGG
* *
619055 AGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
619111 ATTTTCAAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
67 73 0.68
68 4 0.04
69 31 0.29
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGACCTCAAG
GG
Found at i:619169 original size:36 final size:32
Alignment explanation
Indices: 619065--619178 Score: 158
Period size: 32 Copynumber: 3.5 Consensus size: 32
619055 AGACGAAATT
* *
619065 TGTTTCAAGGGAAACAATCTCAAAGG-TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTG
*
619096 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTG
619128 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG----TTTTTG
619164 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
619179 TGTATCAAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
32 30 0.41
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTG
Found at i:619319 original size:36 final size:36
Alignment explanation
Indices: 619219--619573 Score: 183
Period size: 36 Copynumber: 10.4 Consensus size: 36
619209 CAAGGATTGA
*
619219 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
619256 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
619293 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
619329 T-TTT-AATG-TAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-GAGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
619356 TGTTTCAAGGGAAACTGTTTTC-A-A-AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
619385 ATGTTTCAATAGAAACTGTCTCAA-AGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATT
* *
619422 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
619458 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
619486 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
619524 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
619560 CATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
619574 TGTTTTCAAT
Statistics
Matches: 250, Mismatches: 38, Indels: 61
0.72 0.11 0.17
Matches are distributed among these distances:
27 4 0.02
28 7 0.03
29 27 0.11
30 26 0.10
31 2 0.01
32 4 0.02
33 2 0.01
34 9 0.04
35 8 0.03
36 80 0.32
37 62 0.25
38 19 0.08
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:619379 original size:30 final size:30
Alignment explanation
Indices: 619345--619403 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
619335 TGTAAACATA
*
619345 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
619375 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
619404 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:619549 original size:102 final size:102
Alignment explanation
Indices: 619358--619662 Score: 504
Period size: 102 Copynumber: 3.0 Consensus size: 102
619348 AAAGATTTTG
* * *
619358 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
619422 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
619460 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
619525 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
619562 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
619627 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
65 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
619663 CTTGTTTTAA
Statistics
Matches: 192, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
101 46 0.24
102 111 0.58
103 3 0.02
104 32 0.17
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:621168 original size:183 final size:183
Alignment explanation
Indices: 620860--621209 Score: 655
Period size: 183 Copynumber: 1.9 Consensus size: 183
620850 GGTTTAACTA
620860 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
620925 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
620990 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
*
621043 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
*
621108 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
621173 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
621210 CGGATTTAAT
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 162 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:625188 original size:21 final size:21
Alignment explanation
Indices: 625150--625200 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
625140 ACATAGTATT
625150 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
625170 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
625191 ATATATAGAA
1 AAATA-AGAA
625201 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:625378 original size:2 final size:2
Alignment explanation
Indices: 625371--625395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
625361 AGTATACTTA
625371 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 A
625396 CTAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:628730 original size:28 final size:30
Alignment explanation
Indices: 628666--628730 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 30
628656 TGTAGTTAGA
*
628666 TAATTTAATCTCTAAAATTATTATATTTAC
1 TAATTTAATCTCTAAAATTAATATATTTAC
* *
628696 TATTTTAATCT-T-ATATTAATATATTTA-
1 TAATTTAATCTCTAAAATTAATATATTTAC
628723 TAAATTTA
1 T-AATTTA
628731 TTTTATTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 18 0.60
29 1 0.03
30 10 0.33
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (30 bp):
TAATTTAATCTCTAAAATTAATATATTTAC
Found at i:629674 original size:14 final size:14
Alignment explanation
Indices: 629655--629690 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
629645 TTTTTATTTA
*
629655 TTTAATTTCATTCC
1 TTTAATTTCATTAC
629669 TTTAATTTCATTAC
1 TTTAATTTCATTAC
629683 TTTAATTT
1 TTTAATTT
629691 ACTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTCATTAC
Found at i:632014 original size:21 final size:21
Alignment explanation
Indices: 631990--632033 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
631980 CATGTGCATC
*
631990 TATACTTTAACAT-ATATACAT
1 TATACATT-ACATGATATACAT
*
632011 TATACATTACATGGTATACAT
1 TATACATTACATGATATACAT
632032 TA
1 TA
632034 CATCTCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (21 bp):
TATACATTACATGATATACAT
Found at i:633371 original size:23 final size:23
Alignment explanation
Indices: 633317--633413 Score: 101
Period size: 24 Copynumber: 4.2 Consensus size: 23
633307 AGATATATCA
* *
633317 AAAAGA-AGACAAAGAAAATAACAA
1 AAAAGAGAGA-AAAGAAAAGAA-AG
633341 AAAAGAGAGAAAAGAAAAGAAAG
1 AAAAGAGAGAAAAGAAAAGAAAG
*
633364 AAAAGAGAGAAAA-AAGAGAAAG
1 AAAAGAGAGAAAAGAAAAGAAAG
*
633386 CAAAAGAAAAGAAAAGAAAA-AAAG
1 -AAAAG-AGAGAAAAGAAAAGAAAG
633410 AAAA
1 AAAA
633414 CATGTCAAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.12
23 23 0.36
24 27 0.42
25 6 0.09
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (23 bp):
AAAAGAGAGAAAAGAAAAGAAAG
Found at i:633391 original size:6 final size:5
Alignment explanation
Indices: 633322--633413 Score: 70
Period size: 5 Copynumber: 18.4 Consensus size: 5
633312 TATCAAAAAG
* *
633322 AAGACA AAGAA AATAA CAA-AA AAG-A GAGAA AAGAA AAG-A AAGAA AAGAGA
1 AAGA-A AAGAA AAGAA -AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGA-A
633372 GAA-AA AAGAGA AAGCAA AAGAA AAGAA AAG-A AA-AA AAGAA AA
1 -AAGAA AAGA-A AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA AA
633414 CATGTCAAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 23
0.73 0.03 0.23
Matches are distributed among these distances:
4 17 0.24
5 36 0.50
6 16 0.22
7 3 0.04
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAGAA
Found at i:633391 original size:32 final size:34
Alignment explanation
Indices: 633340--633410 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
633330 GAAAATAACA
633340 AAAAAGAGAGAAAAGAAAAG-AAAGAAAAGAGAG
1 AAAAAGAGAGAAAAGAAAAGAAAAGAAAAGAGAG
633373 AAAAA-AGAG-AAAGCAAAAGAAAAGAAAAGA-A-
1 AAAAAGAGAGAAAAG-AAAAGAAAAGAAAAGAGAG
633404 AAAAAGA
1 AAAAAGA
633411 AAACATGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
31 9 0.26
32 11 0.31
33 15 0.43
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (34 bp):
AAAAAGAGAGAAAAGAAAAGAAAAGAAAAGAGAG
Found at i:633393 original size:10 final size:9
Alignment explanation
Indices: 633351--633413 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
633341 AAAAGAGAGA
633351 AAAGAAAAG
1 AAAGAAAAG
633360 AAAGAAAAG
1 AAAGAAAAG
*
633369 AGAG-AAA-
1 AAAGAAAAG
633376 AAAGAGAAAG
1 AAAGA-AAAG
633386 CAAAAGAAAAG
1 --AAAGAAAAG
633397 AAAAGAAAA-
1 -AAAGAAAAG
633406 AAAGAAAA
1 AAAGAAAA
633414 CATGTCAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
7 3 0.06
8 11 0.23
9 15 0.32
10 9 0.19
11 4 0.09
12 5 0.11
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:635475 original size:53 final size:54
Alignment explanation
Indices: 635381--635495 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 54
635371 CCCAATTGAT
* * *
635381 ATGAA-TTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTTAA
1 ATGAATTTTGAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAA
*
635434 ATGAATTTTGAAAGAAACTAAGCCT-ATTTTTTAGGGG-TTCTTGATATTTTCAA
1 ATGAATTTTGAAAGAAACTAAGCCTGA-TTTTCAGGGGTTTCTTGATATTTTCAA
*
635487 ATGAGTTTT
1 ATGAATTTT
635496 TTATAAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 28 0.51
54 27 0.49
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (54 bp):
ATGAATTTTGAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAA
Found at i:635575 original size:33 final size:33
Alignment explanation
Indices: 635534--635599 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
635524 TATCGAAAAG
* * *
635534 AAGAATTTTTAAAGAAGTTAAGCATGATTTTCA
1 AAGAATTTTCAAAGAAGCTAAGCATAATTTTCA
*
635567 AAGAATTTTCAAAGAAGCTAAGCCTAATTTTCA
1 AAGAATTTTCAAAGAAGCTAAGCATAATTTTCA
635600 GGGGTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (33 bp):
AAGAATTTTCAAAGAAGCTAAGCATAATTTTCA
Found at i:637038 original size:59 final size:59
Alignment explanation
Indices: 636657--637037 Score: 465
Period size: 59 Copynumber: 6.5 Consensus size: 59
636647 GTTCGACCTA
* * ** * *
636657 TTGCTCGATTCATGTCATTTCGAATCAACAATGCCTCACTTGAAAGATTAGCATTTCAT
1 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
* * *
636716 TTTCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAATATTTCTT
1 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
*
636775 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCTT
1 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
*** * * *
636834 TTGCTCGATTCATAATATTTCGAATCAACAACGCCTCGCTTGAGGGATTAACATTTCCT
1 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
** ** ** * * *
636893 TTGCTCGATTCACAGCATTTTGAATCAGTAACACCTCGCTTGAGGGATTAACCTTACCT
1 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
* * * * *
636952 TTTCTCGATTCATGACATTTTGAATCAGCGATGCCTCACTTGAGGGATTAACATTACCT
1 TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
* * *
637011 TTGCTCAATTCAAGGCATTTCGAATCA
1 TTGCTCGATTCATGGCATTTTGAATCA
637038 GTGACTTCTC
Statistics
Matches: 281, Mismatches: 41, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 281 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (59 bp):
TTGCTCGATTCATGGCATTTTGAATCAACAATGCCTCACTTGAGGGATTAACATTTCCT
Found at i:637175 original size:93 final size:93
Alignment explanation
Indices: 637007--637180 Score: 215
Period size: 93 Copynumber: 1.9 Consensus size: 93
636997 GATTAACATT
*** * * * *
637007 ACCTTTGCTCAATTCAAGGCATTTCGAATCAGTGACTTCTCACTCGAGGGACCAACATTTCCAGT
1 ACCTTTGCTCAATTCAAGGCATTTCGAATCAACAACGTCTCACTCAAGGAACCAACATTTCCAAT
637072 AGAGAATTCATAATGAATAACTTGTTCA
66 AGAGAATTCATAATGAATAACTTGTTCA
** * * * *
637100 ACCTTTGCTTGATTCATGGCATTTCGAATCAACAACGTCTCGCTCAAGGAATCAAGATTTCCAAT
1 ACCTTTGCTCAATTCAAGGCATTTCGAATCAACAACGTCTCACTCAAGGAACCAACATTTCCAAT
637165 AGA-AAGTTCATAATGA
66 AGAGAA-TTCATAATGA
637181 GAATAACCTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
92 2 0.03
93 65 0.97
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (93 bp):
ACCTTTGCTCAATTCAAGGCATTTCGAATCAACAACGTCTCACTCAAGGAACCAACATTTCCAAT
AGAGAATTCATAATGAATAACTTGTTCA
Found at i:641335 original size:26 final size:27
Alignment explanation
Indices: 641305--641365 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
641295 TATACATAGA
641305 TTTTCTCTTGAGGCGCACGAT-ACAGG
1 TTTTCTCTTGAGGCGCACGATAACAGG
641331 TTTTCTCTTGAGGCGCACGATAACAGG
1 TTTTCTCTTGAGGCGCACGATAACAGG
*
641358 GTTTCTCT
1 TTTTCTCT
641366 GGGCGTACGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (27 bp):
TTTTCTCTTGAGGCGCACGATAACAGG
Found at i:646520 original size:18 final size:18
Alignment explanation
Indices: 646487--646521 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
646477 CTAGTGGATT
*
646487 TAAAATCAGTTAAAAAGG
1 TAAAATCAGCTAAAAAGG
*
646505 TAAAATCAGCTGAAAAG
1 TAAAATCAGCTAAAAAG
646522 ATCAACAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (18 bp):
TAAAATCAGCTAAAAAGG
Found at i:649429 original size:14 final size:14
Alignment explanation
Indices: 649410--649444 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
649400 CTCATACCGA
649410 TTTGACCCGTTAAC
1 TTTGACCCGTTAAC
649424 TTTGACCCGTTAAC
1 TTTGACCCGTTAAC
649438 TTTGACC
1 TTTGACC
649445 AAACTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (14 bp):
TTTGACCCGTTAAC
Found at i:649460 original size:18 final size:18
Alignment explanation
Indices: 649433--649470 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
649423 CTTTGACCCG
*
649433 TTAACTTTGA-CCAAACTA
1 TTAACCTTGATCC-AACTA
649451 TTAACCTTGATCCAACTA
1 TTAACCTTGATCCAACTA
649469 TT
1 TT
649471 GAATTTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (18 bp):
TTAACCTTGATCCAACTA
Found at i:651631 original size:21 final size:19
Alignment explanation
Indices: 651584--651633 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
651574 TTTTATGTCT
651584 CAAAGGATCGATCGCTTAC
1 CAAAGGATCGATCGCTTAC
*
651603 CAAAAGGATCGATCTCTTTAAC
1 C-AAAGGATCGATCGC-TT-AC
651625 CAAAGGATC
1 CAAAGGATC
651634 AATCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 13 0.48
21 10 0.37
22 3 0.11
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (19 bp):
CAAAGGATCGATCGCTTAC
Found at i:652756 original size:44 final size:44
Alignment explanation
Indices: 652706--652792 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
652696 GGCTATGCAC
652706 ATGTTGTTTTGTGCATTTGGTCCTAATATCTATGAAGGAGCTTT
1 ATGTTGTTTTGTGCATTTGGTCCTAATATCTATGAAGGAGCTTT
652750 ATGTTGTTTTGTGCATTTGGTCCTAATATCTATGAAGGAGCTT
1 ATGTTGTTTTGTGCATTTGGTCCTAATATCTATGAAGGAGCTT
652793 CTTCTTGTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.45
Consensus pattern (44 bp):
ATGTTGTTTTGTGCATTTGGTCCTAATATCTATGAAGGAGCTTT
Found at i:654529 original size:20 final size:20
Alignment explanation
Indices: 654501--654556 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
654491 TTCTCTGGCT
* *
654501 AAAATGATCAATCCCTT-AGC
1 AAAAGGATCGATCCCTTGA-C
654521 AAAAGGATCGATCCCTTGAC
1 AAAAGGATCGATCCCTTGAC
654541 AAAAGGATCGATCCCT
1 AAAAGGATCGATCCCT
654557 CGAGGAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTGAC
Found at i:655894 original size:18 final size:18
Alignment explanation
Indices: 655873--655911 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
655863 TTTTCAATAG
655873 AAAATACATAAAAAATTT
1 AAAATACATAAAAAATTT
* * *
655891 AAAATATATAATAATTTT
1 AAAATACATAAAAAATTT
655909 AAA
1 AAA
655912 TTTTTAGGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATACATAAAAAATTT
Found at i:660767 original size:11 final size:11
Alignment explanation
Indices: 660744--660781 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
660734 GAGATTTGCA
660744 TGTTGATTT-GT
1 TGTTG-TTTCGT
660755 TGTTGTTTCGT
1 TGTTGTTTCGT
660766 TGTTGTTTCGT
1 TGTTGTTTCGT
660777 TGTTG
1 TGTTG
660782 AGTGTTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 3 0.12
11 23 0.88
ACGTcount: A:0.03, C:0.05, G:0.29, T:0.63
Consensus pattern (11 bp):
TGTTGTTTCGT
Found at i:662440 original size:26 final size:26
Alignment explanation
Indices: 662385--662444 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
662375 CACACACATC
*
662385 TTACAGTAGAAACATTAACTCCTAAA
1 TTACATTAGAAACATTAACTCCTAAA
**
662411 TTACATTAGAAACATTAACTCCTACG
1 TTACATTAGAAACATTAACTCCTAAA
662437 TTACATTA
1 TTACATTA
662445 CAATACAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (26 bp):
TTACATTAGAAACATTAACTCCTAAA
Found at i:662795 original size:43 final size:41
Alignment explanation
Indices: 662651--662795 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 41
662641 TCCACTAAAG
* * * * *
662651 TTTTGGAACAAACGCCACAAAATGTCAGATTATAACGGCGT
1 TTTTGGAACAAACGCCGCAAAAGGTCAAATTATAGCGGCTT
* *
662692 TTTTGGAACAAACGCCGTAAAAGATCAAGATTAATAGCGG-TGT
1 TTTTGGAACAAACGCCGCAAAAGGTCAA-ATT-ATAGCGGCT-T
** *
662735 TTGTTCCAA-AAATGCCGCAAAAGGTCAAATCTATAGCGGCTT
1 TT-TTGGAACAAACGCCGCAAAAGGTCAAAT-TATAGCGGCTT
662777 TTTTGGATACAAACGCCGC
1 TTTTGGA-ACAAACGCCGC
662796 TAATTACCTT
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
41 26 0.32
42 16 0.20
43 35 0.43
44 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (41 bp):
TTTTGGAACAAACGCCGCAAAAGGTCAAATTATAGCGGCTT
Done.