Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 98 of 125
Found at i:29496229 original size:40 final size:42
Alignment explanation
Indices: 29496165--29496242 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 42
29496155 CAGCAAATGA
29496165 TTTTAAAATTATTAAAATTATTAAAATTAATTTAAAATTAAT
1 TTTTAAAATTATTAAAATTATTAAAATTAATTTAAAATTAAT
* *
29496207 TTTTAAAA-TA-TAAAATTGTTAAAATTATTTTAAAAT
1 TTTTAAAATTATTAAAATTATTAAAATTAATTTAAAAT
29496243 ATAGTCATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 24 0.71
41 2 0.06
42 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (42 bp):
TTTTAAAATTATTAAAATTATTAAAATTAATTTAAAATTAAT
Found at i:29509483 original size:115 final size:115
Alignment explanation
Indices: 29509281--29509499 Score: 343
Period size: 115 Copynumber: 1.9 Consensus size: 115
29509271 AAACCATTGA
*
29509281 TTTCTGATTTCTATTTAAGTTTTATTTCTATTTCTAATTAGATTTATGAACAGTTTTATTCCTGG
1 TTTCTGATTTCCATTTAAGTTTTATTTCTATTTCTAATTAGATTTATGAACAGTTTTATTCCTGG
*
29509346 ACCATCTTTTCTTTCTGTTGATGCTCAAAGAAACTCATTTTCTTCGACGG
66 ACCATCTTATCTTTCTGTTGATGCTCAAAGAAACTCATTTTCTTCGACGG
*
29509396 TTTCTGATTTCCATTTTAGTTTTATTAT-TACTTT-TAATTAGATTTATGAACAGTTTTATTCCT
1 TTTCTGATTTCCATTTAAGTTTTATT-TCTA-TTTCTAATTAGATTTATGAACAGTTTTATTCCT
* ***
29509459 GGACTATCTTATCTTTCTGTTGATGCTTGTAGAAACTCATT
64 GGACCATCTTATCTTTCTGTTGATGCTCAAAGAAACTCATT
29509500 CGCAGGAGTA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
115 91 0.96
116 4 0.04
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (115 bp):
TTTCTGATTTCCATTTAAGTTTTATTTCTATTTCTAATTAGATTTATGAACAGTTTTATTCCTGG
ACCATCTTATCTTTCTGTTGATGCTCAAAGAAACTCATTTTCTTCGACGG
Found at i:29512873 original size:33 final size:32
Alignment explanation
Indices: 29512826--29512891 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
29512816 CCTTTTGTAA
*
29512826 ATATATATACATGTGTATGTATACATAGTATAC
1 ATATATATACATGTGTATATATACAT-GTATAC
** * *
29512859 ATATATATGTATGTGTGTATATGCATGTATAC
1 ATATATATACATGTGTATATATACATGTATAC
29512891 A
1 A
29512892 CCAATAGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (32 bp):
ATATATATACATGTGTATATATACATGTATAC
Found at i:29516044 original size:78 final size:78
Alignment explanation
Indices: 29515938--29516089 Score: 295
Period size: 78 Copynumber: 1.9 Consensus size: 78
29515928 CTCAATTTTA
*
29515938 TTTTTTTTATTTAAAATTTCACATTTATTAATTCCCTATTCTCGCAAGTACATCAAAATCACACT
1 TTTTTTTTATTTAAAATTTCACAGTTATTAATTCCCTATTCTCGCAAGTACATCAAAATCACACT
29516003 CACAAAGTAAATT
66 CACAAAGTAAATT
29516016 TTTTTTTTATTTAAAATTTCACAGTTATTAATTCCCTATTCTCGCAAGTACATCAAAATCACACT
1 TTTTTTTTATTTAAAATTTCACAGTTATTAATTCCCTATTCTCGCAAGTACATCAAAATCACACT
29516081 CACAAAGTA
66 CACAAAGTA
29516090 GATTATTACT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.40
Consensus pattern (78 bp):
TTTTTTTTATTTAAAATTTCACAGTTATTAATTCCCTATTCTCGCAAGTACATCAAAATCACACT
CACAAAGTAAATT
Found at i:29522933 original size:30 final size:29
Alignment explanation
Indices: 29522897--29522960 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
29522887 AGTTTGTGAG
29522897 AATTAAATC-AAATCAAAATTTCATATATAA
1 AATTAAA-CAAAATCAAAA-TTCATATATAA
* *
29522927 AATTAAACAAAAATCAAAATTCTTATGTAA
1 AATTAAAC-AAAATCAAAATTCATATATAA
29522957 AATT
1 AATT
29522961 GCACATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 20 0.67
31 9 0.30
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (29 bp):
AATTAAACAAAATCAAAATTCATATATAA
Found at i:29524264 original size:24 final size:24
Alignment explanation
Indices: 29524231--29524277 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
29524221 AGAAATAATC
*
29524231 TTTCAGTTAAACTCTGTTTATTTA
1 TTTCAATTAAACTCTGTTTATTTA
29524255 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
29524278 GTTTGAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTA
Found at i:29524290 original size:24 final size:24
Alignment explanation
Indices: 29524239--29524293 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
29524229 TCTTTCAGTT
*
29524239 AAACTCTGTTTATTTATTTCAATT
1 AAACTCTGTTTATTTATTTCAATC
* * *
29524263 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTATTTCAATC
29524287 AAACTCT
1 AAACTCT
29524294 TATTACTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:29525387 original size:162 final size:162
Alignment explanation
Indices: 29525120--29525441 Score: 572
Period size: 162 Copynumber: 2.0 Consensus size: 162
29525110 AGATTGACGA
*
29525120 TGAGGATCAAGCTATTCTATTATTGTGCTCTTTACCCCCTTCATACAAGTCTTTTAGGGAGACCT
1 TGAGGATCAAGCTATGCTATTATTGTGCTCTTTACCCCCTTCATACAAGTCTTTTAGGGAGACCT
* *
29525185 TGATTTATGATAGAGATAAACTCCCGTTTGAGGATGTGAAGGGTTATTTGTTGAGCAAAGACAAA
66 TGATTTATGATAGAGATAAACTCCCGTTTGAGGATGTGAAGAGTCATTTGTTGAGCAAAGACAAA
29525250 CTCGATAATGAGTTTGGTTCAGATAGTAAGAC
131 CTCGATAATGAGTTTGGTTCAGATAGTAAGAC
* * * *
29525282 TGAGGATCAGGTTATGCTATTGTTGTGCTCTTTACCCCCTTTATACAAGTCTTTTAGGGAGACCT
1 TGAGGATCAAGCTATGCTATTATTGTGCTCTTTACCCCCTTCATACAAGTCTTTTAGGGAGACCT
*
29525347 TGATTTATGGTAGAGATAAACTCCCGTTTGAGGATGTGAAGAGTCATTTGTTGAGCAAAGACAAA
66 TGATTTATGATAGAGATAAACTCCCGTTTGAGGATGTGAAGAGTCATTTGTTGAGCAAAGACAAA
29525412 CTCGATAATGAGTTTGGTTCAGATAGTAAG
131 CTCGATAATGAGTTTGGTTCAGATAGTAAG
29525442 GTAGATAAGC
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 152 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (162 bp):
TGAGGATCAAGCTATGCTATTATTGTGCTCTTTACCCCCTTCATACAAGTCTTTTAGGGAGACCT
TGATTTATGATAGAGATAAACTCCCGTTTGAGGATGTGAAGAGTCATTTGTTGAGCAAAGACAAA
CTCGATAATGAGTTTGGTTCAGATAGTAAGAC
Found at i:29530664 original size:237 final size:239
Alignment explanation
Indices: 29530241--29530709 Score: 730
Period size: 238 Copynumber: 2.0 Consensus size: 239
29530231 AATAGAGAAT
*
29530241 ATTCTTTTGTATTCTTTAGGGTACCTTTTGTAGGTATAAATGACATATTGTTCATAATTATATGT
1 ATTCTTTTGTATTCTTTAGGGTACCTTTTGTAGGTATAAATGACATATTGTTCATAATTACATGT
*
29530306 ACTTCTCTAGCAAATACAATATCCTGGGTATTTATGAAAATATTTAGCTCTGGTGTAACATGGAC
66 ACTTCTATAGCAAATACAATATCCTGGGTATTTATGAAAATATTTAGCTCTGGTGTAACATGGAC
* *
29530371 CTAATTACTGTGCTGTGAACAATTATTGTTTCTTTGTATTTTTAACCATTATGTGTATA-ACTTC
131 CTAATTACTGTGCTGTGAACAATTATTGTTTCTTTGTATTTTGAACCATCATGTGTATAGACTTC
29530435 CTTAAGATAGGCTAGATTGATATTCATTATTTGTATTAGAGCAG
196 CTTAAGATAGGCTAGATTGATATTCATTATTTGTATTAGAGCAG
* *
29530479 ATTCTTTTGTATTCTTTAGGGTTCCTTTTGTAGGTATAAATGACATATTGTTCATTATTACATGT
1 ATTCTTTTGTATTCTTTAGGGTACCTTTTGTAGGTATAAATGACATATTGTTCATAATTACATGT
** *
29530544 ACTTCTATAGCAAATA-TGTATCCTGGGTATTTA-GCAAAATATTTAGCTTTGGTGTAACATGGA
66 ACTTCTATAGCAAATACAATATCCTGGGTATTTATG-AAAATATTTAGCTCTGGTGTAACATGGA
* * * *
29530607 CCTAATTACTGTGCTGTGCACAATTATTGTTTGTTTTTA-TTTGAAGCCATCATGTGTATAGCCT
130 CCTAATTACTGTGCTGTGAACAATTATTGTTTCTTTGTATTTTGAA-CCATCATGTGTATAGACT
* * * * *
29530671 TCCTTGAGATGGGCTAGATTGATTTTTATTTTTTGTATT
194 TCCTTAAGATAGGCTAGATTGATATTCATTATTTGTATT
29530710 TTTAACAATT
Statistics
Matches: 210, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
236 6 0.03
237 91 0.43
238 113 0.54
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (239 bp):
ATTCTTTTGTATTCTTTAGGGTACCTTTTGTAGGTATAAATGACATATTGTTCATAATTACATGT
ACTTCTATAGCAAATACAATATCCTGGGTATTTATGAAAATATTTAGCTCTGGTGTAACATGGAC
CTAATTACTGTGCTGTGAACAATTATTGTTTCTTTGTATTTTGAACCATCATGTGTATAGACTTC
CTTAAGATAGGCTAGATTGATATTCATTATTTGTATTAGAGCAG
Found at i:29557568 original size:16 final size:16
Alignment explanation
Indices: 29557547--29557577 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29557537 ATAAATCCAA
*
29557547 TTAGTTCGATTCTGAT
1 TTAGTTCAATTCTGAT
29557563 TTAGTTCAATTCTGA
1 TTAGTTCAATTCTGA
29557578 CAACATTGAT
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:0.13, G:0.16, T:0.48
Consensus pattern (16 bp):
TTAGTTCAATTCTGAT
Found at i:29566638 original size:27 final size:28
Alignment explanation
Indices: 29566608--29566661 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
29566598 AACTTAGTTA
29566608 CAACTGAC-ATTAACAAAC-TAACTGCTG
1 CAACT-ACTATTAACAAACTTAACTGCTG
* *
29566635 CAACTACTTTTAACAACCTTAACTGCT
1 CAACTACTATTAACAAACTTAACTGCT
29566662 ATACTAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 13 0.57
28 8 0.35
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.28
Consensus pattern (28 bp):
CAACTACTATTAACAAACTTAACTGCTG
Found at i:29569025 original size:28 final size:29
Alignment explanation
Indices: 29568961--29569026 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
29568951 TATTAGAATT
29568961 TTTTAAATTTTTTTAAAAAATATATAAAA
1 TTTTAAATTTTTTTAAAAAATATATAAAA
* * *
29568990 -TTTGAATTTTTTGT-AAATAT-TTTAAAA
1 TTTTAAATTTTTT-TAAAAAATATATAAAA
29569017 TTTTAAATTT
1 TTTTAAATTT
29569027 ATTTCGACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 6 0.19
28 24 0.77
29 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTAAATTTTTTTAAAAAATATATAAAA
Found at i:29571835 original size:31 final size:31
Alignment explanation
Indices: 29571753--29571842 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
29571743 TGGTTATTTA
* *
29571753 ATTAAAAAAATTATAATTTAA-TTATTAAATT
1 ATTAAAAAAATT-TAATTTAAGTTATTGAACT
* * * *
29571784 ATTTAAAAATTTTGAGTTAAGTTATTGAACT
1 ATTAAAAAAATTTAATTTAAGTTATTGAACT
*
29571815 ATTCAAAAAAATTT-ATTTAAGTTGTTGA
1 ATT-AAAAAAATTTAATTTAAGTTATTGA
29571843 GATGTTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 6 0.13
31 33 0.70
32 8 0.17
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (31 bp):
ATTAAAAAAATTTAATTTAAGTTATTGAACT
Found at i:29579666 original size:166 final size:164
Alignment explanation
Indices: 29579394--29579724 Score: 590
Period size: 166 Copynumber: 2.0 Consensus size: 164
29579384 AAAAGCTTTT
* ***
29579394 TTGGACTGAAGTAAAGCACCTTGCTTGTTAGGTCTAAAAACTCTTTTGGCATTTTTATGGTCCAT
1 TTGGACTGAAGTAAAGCACCTTGCTTGTAAGGTCTAAAAACTCCACTGGCATTTTTATGGTCCAT
29579459 TGGTCAAATATTGAAAGGTATAGAGTTTCATATTGTTCTTTTTCTTACTAGGAAAAGGACATCTA
66 TGGTCAAATATTGAAAGGTATAGAGTTTCATATTGTTCTTTTTCTTACTAGGAAAAGGACATCTA
29579524 ATGAAAAAGTTTAGCCAAGACACATTAACATGCC
131 ATGAAAAAGTTTAGCCAAGACACATTAACATGCC
*
29579558 TTGGACTGAAGTAAAGCACCTTGCTTTTGTAAGGTTTAAAAACTCCACTGGCATTTTTATGGTCC
1 TTGGACTGAAGTAAAGCACCTTGC--TTGTAAGGTCTAAAAACTCCACTGGCATTTTTATGGTCC
*
29579623 ATTGGTCAAATATTGAAAGGTATAGAGTTTCATATTGTTCTTTTTCTTGCTAGGAAAAGGACATC
64 ATTGGTCAAATATTGAAAGGTATAGAGTTTCATATTGTTCTTTTTCTTACTAGGAAAAGGACATC
29579688 TAATGAAAAAGTTTAGCCAAGACACATTAACATGCC
129 TAATGAAAAAGTTTAGCCAAGACACATTAACATGCC
29579724 T
1 T
29579725 CTGATCAAAT
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
164 24 0.15
166 135 0.85
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (164 bp):
TTGGACTGAAGTAAAGCACCTTGCTTGTAAGGTCTAAAAACTCCACTGGCATTTTTATGGTCCAT
TGGTCAAATATTGAAAGGTATAGAGTTTCATATTGTTCTTTTTCTTACTAGGAAAAGGACATCTA
ATGAAAAAGTTTAGCCAAGACACATTAACATGCC
Found at i:29581104 original size:31 final size:32
Alignment explanation
Indices: 29581053--29581112 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
29581043 TATAAGGTAA
*
29581053 AAAAAATTGTTAGTTTTTTACTAAAATAATAT
1 AAAAAATTGTTAGTTTTTTACCAAAATAATAT
29581085 AAAAAATT-TTA-TTTATTTACCAAAATAA
1 AAAAAATTGTTAGTTT-TTTACCAAAATAA
29581113 ATTAAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.12
31 15 0.58
32 8 0.31
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
AAAAAATTGTTAGTTTTTTACCAAAATAATAT
Found at i:29581546 original size:14 final size:15
Alignment explanation
Indices: 29581527--29581561 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
29581517 TAGTAGATTA
29581527 TATTTTA-AAATTTT
1 TATTTTATAAATTTT
29581541 TATTTTATTAAATTTT
1 TATTTTA-TAAATTTT
29581557 TATTT
1 TATTT
29581562 ATTTTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
16 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATAAATTTT
Found at i:29581956 original size:24 final size:24
Alignment explanation
Indices: 29581929--29581974 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29581919 ATGTGGAACT
* * *
29581929 AGTAGAAAATGAATATTTAACTCC
1 AGTAAAAAATGAAGATCTAACTCC
29581953 AGTAAAAAATGAAGATCTAACT
1 AGTAAAAAATGAAGATCTAACT
29581975 TCGTGTATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (24 bp):
AGTAAAAAATGAAGATCTAACTCC
Found at i:29584364 original size:26 final size:26
Alignment explanation
Indices: 29584324--29584375 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
29584314 ATGAATTTGG
*
29584324 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
29584350 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
29584376 TGATTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:29584567 original size:9 final size:8
Alignment explanation
Indices: 29584546--29584587 Score: 52
Period size: 7 Copynumber: 5.4 Consensus size: 8
29584536 TTTATAATTA
29584546 TTTAAGG-
1 TTTAAGGT
29584553 TTTAAGGTT
1 TTTAAGG-T
29584562 TTTAAGG-
1 TTTAAGGT
*
29584569 TTTAATGT
1 TTTAAGGT
29584577 TTTAAGGT
1 TTTAAGGT
29584585 TTT
1 TTT
29584588 GGATTTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 13 0.43
8 10 0.33
9 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (8 bp):
TTTAAGGT
Found at i:29584567 original size:16 final size:15
Alignment explanation
Indices: 29584514--29584697 Score: 69
Period size: 14 Copynumber: 12.2 Consensus size: 15
29584504 TTTCGTGGAT
*
29584514 TTTTATGGTTTAAGG
1 TTTTAAGGTTTAAGG
* **
29584529 -TTTATGGTTTATAAT
1 TTTTAAGGTTTA-AGG
29584544 TATTTAAGGTTTAAGG
1 T-TTTAAGGTTTAAGG
*
29584560 TTTTTAAGGTTTAATG
1 -TTTTAAGGTTTAAGG
*
29584576 TTTTAAGGTTT-TGG
1 TTTTAAGGTTTAAGG
*
29584590 ATTTT-AGGATTTTA-G
1 -TTTTAAGG-TTTAAGG
**
29584605 AATT-AGAGTTT-AGG
1 TTTTAAG-GTTTAAGG
* *
29584619 ATTTTCAAAGTTTAATG
1 -TTTT-AAGGTTTAAGG
* *
29584636 TTTTAAGGTATTGAGT
1 TTTTAAGGT-TTAAGG
29584652 TTTTAAGGTTT-AGG
1 TTTTAAGGTTTAAGG
* * *
29584666 ATTTAGGGTTTAAAG
1 TTTTAAGGTTTAAGG
* *
29584681 TTTTGA-GTTTAGGG
1 TTTTAAGGTTTAAGG
29584695 TTT
1 TTT
29584698 AATTTATGCA
Statistics
Matches: 126, Mismatches: 28, Indels: 31
0.68 0.15 0.17
Matches are distributed among these distances:
13 1 0.01
14 43 0.34
15 34 0.27
16 34 0.27
17 14 0.11
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.51
Consensus pattern (15 bp):
TTTTAAGGTTTAAGG
Found at i:29584581 original size:15 final size:16
Alignment explanation
Indices: 29584546--29584586 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
29584536 TTTATAATTA
29584546 TTTAAGGTTTAAGGTT
1 TTTAAGGTTTAAGGTT
*
29584562 TTTAAGGTTTAATG-T
1 TTTAAGGTTTAAGGTT
29584577 TTTAAGGTTT
1 TTTAAGGTTT
29584587 TGGATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (16 bp):
TTTAAGGTTTAAGGTT
Found at i:29584594 original size:15 final size:15
Alignment explanation
Indices: 29584546--29584595 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
29584536 TTTATAATTA
*
29584546 TTTAAGGTTTAAGGTT
1 TTTAAGGTTTATGG-T
29584562 TTTAAGGTTTAAT-GT
1 TTTAAGGTTT-ATGGT
29584577 TTTAAGGTTT-TGGAT
1 TTTAAGGTTTATGG-T
29584592 TTTA
1 TTTA
29584596 GGATTTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.03
14 1 0.03
15 16 0.53
16 11 0.37
17 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTAAGGTTTATGGT
Found at i:29584683 original size:21 final size:21
Alignment explanation
Indices: 29584653--29584699 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
29584643 GTATTGAGTT
*
29584653 TTTAAGGTTTAGGA-TTTAGGG
1 TTTAAAGTTT-GGAGTTTAGGG
*
29584674 TTTAAAGTTTTGAGTTTAGGG
1 TTTAAAGTTTGGAGTTTAGGG
29584695 TTTAA
1 TTTAA
29584700 TTTATGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (21 bp):
TTTAAAGTTTGGAGTTTAGGG
Found at i:29587242 original size:3 final size:3
Alignment explanation
Indices: 29587234--29587274 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29587224 TAGATATTTG
29587234 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
29587275 ACTTTTTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:29587760 original size:30 final size:30
Alignment explanation
Indices: 29587728--29587785 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
29587718 ATATAATACA
29587728 AAAAT-AATAATTACATACCAAAATGGTAC
1 AAAATAAATAATTACATACCAAAATGGTAC
* *
29587757 AAAATAAATATTTATATACCAAAATGGTA
1 AAAATAAATAATTACATACCAAAATGGTA
29587786 TCCGCACCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (30 bp):
AAAATAAATAATTACATACCAAAATGGTAC
Found at i:29587941 original size:27 final size:26
Alignment explanation
Indices: 29587911--29587964 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
29587901 TATTACTTAC
29587911 TTACTTACT-ACTAATAACAAAATAAAA
1 TTACTTACTAAC-AA-AACAAAATAAAA
*
29587938 TTACTTACTAACAAAATAAAATAAAA
1 TTACTTACTAACAAAACAAAATAAAA
29587964 T
1 T
29587965 AAAACTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 12 0.48
27 11 0.44
28 2 0.08
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (26 bp):
TTACTTACTAACAAAACAAAATAAAA
Found at i:29590227 original size:3 final size:3
Alignment explanation
Indices: 29590219--29590279 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
29590209 TTAAAAGTAA
* * * *
29590219 AAT AAT AAT AAT AAT AAT AAT CAT CAT CAT CAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29590267 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
29590280 GTTGAAACAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29590529 original size:23 final size:24
Alignment explanation
Indices: 29590488--29590534 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29590478 TTTTTTCAAA
* *
29590488 TTTCGAGTTCGAATCAATTTGAAT
1 TTTCGAATTCGAATCAATTCGAAT
29590512 TTTCGAATTCGAAT-AATTCGAAT
1 TTTCGAATTCGAATCAATTCGAAT
29590535 AAATCGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (24 bp):
TTTCGAATTCGAATCAATTCGAAT
Found at i:29591279 original size:84 final size:83
Alignment explanation
Indices: 29591135--29591407 Score: 323
Period size: 84 Copynumber: 3.2 Consensus size: 83
29591125 AATCACACTG
* * *
29591135 GCACATAAGTGCATCATTGGATGTATCCGAAGAAAATATACTGGTAAGTAAGTACATCATTGGAT
1 GCACATAAGTGCATCATCGGATGTAT-CGAAGAAAATATACTAGTAA-TAAGTGCATCATTGGAT
*
29591200 ATACCGAAGCAATTATACTG
64 ATACCGAAGCAATTATACTA
* * *
29591220 GTACGTAAGTGCATCATCGGATGTATCGAAGAAAATATACTAGTACATAAGTGCATCATTGAATA
1 GCACATAAGTGCATCATCGGATGTATCGAAGAAAATATACTAGTA-ATAAGTGCATCATTGGATA
*
29591285 TACCGATGCAATTATACTA
65 TACCGAAGCAATTATACTA
* * * * * * ** * *
29591304 GCACGTTAGTGCATCATCAGATGTACCGAA-ATAAATATACTAGCATGTAAACGCAACATCGGAT
1 GCACATAAGTGCATCATCGGATGTATCGAAGA-AAATATACTAGTA-ATAAGTGCATCATTGGAT
*
29591368 ATGCCGAAGCAATTATACTA
64 ATACCGAAGCAATTATACTA
29591388 GCACATAAGTGCATCATCGG
1 GCACATAAGTGCATCATCGG
29591408 CTAAACCGAA
Statistics
Matches: 161, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
83 1 0.01
84 136 0.84
85 24 0.15
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (83 bp):
GCACATAAGTGCATCATCGGATGTATCGAAGAAAATATACTAGTAATAAGTGCATCATTGGATAT
ACCGAAGCAATTATACTA
Found at i:29591417 original size:42 final size:42
Alignment explanation
Indices: 29591135--29591418 Score: 237
Period size: 42 Copynumber: 6.7 Consensus size: 42
29591125 AATCACACTG
* * * * *
29591135 GCACATAAGTGCATCATTGGATGTATCCGAAGAAAATATACTG
1 GCACATAAGTGCATCATCGGATATA-CCGAAGCAATTATACTA
* * * *
29591178 GTA-AGTAAGTACATCATTGGATATACCGAAGCAATTATACTG
1 GCACA-TAAGTGCATCATCGGATATACCGAAGCAATTATACTA
* * * * * *
29591220 GTACGTAAGTGCATCATCGGATGTATCGAAGAAAATATACTA
1 GCACATAAGTGCATCATCGGATATACCGAAGCAATTATACTA
* * * *
29591262 GTACATAAGTGCATCATTGAATATACCGATGCAATTATACTA
1 GCACATAAGTGCATCATCGGATATACCGAAGCAATTATACTA
* * * * ** *
29591304 GCACGTTAGTGCATCATCAGATGTACCGAAATAAATATACTA
1 GCACATAAGTGCATCATCGGATATACCGAAGCAATTATACTA
** ** * *
29591346 GCATGTAAACGCAACATCGGATATGCCGAAGCAATTATACTA
1 GCACATAAGTGCATCATCGGATATACCGAAGCAATTATACTA
* *
29591388 GCACATAAGTGCATCATCGGCTAAACCGAAG
1 GCACATAAGTGCATCATCGGATATACCGAAG
29591419 TATATGCATG
Statistics
Matches: 188, Mismatches: 51, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
42 168 0.89
43 20 0.11
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (42 bp):
GCACATAAGTGCATCATCGGATATACCGAAGCAATTATACTA
Found at i:29591846 original size:3 final size:3
Alignment explanation
Indices: 29591838--29591895 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
29591828 TTGATTGGCA
*
29591838 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29591886 AAT AAT AAT A
1 AAT AAT AAT A
29591896 GACATGTAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29592454 original size:20 final size:19
Alignment explanation
Indices: 29592428--29592480 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
29592418 ACAACACTAG
29592428 AGTATCGATACTTAATCCCA
1 AGTATCGATACTTAAT-CCA
* * *
29592448 TGTATCGATACATTAGTGCA
1 AGTATCGATAC-TTAATCCA
29592468 AGTATCGATACTT
1 AGTATCGATACTT
29592481 TAGGTCATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.79
21 4 0.14
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (19 bp):
AGTATCGATACTTAATCCA
Found at i:29594693 original size:2 final size:2
Alignment explanation
Indices: 29594686--29594741 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
29594676 ATGGAGGAGG
29594686 GA GA GA GA GA GA GA 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 GA GA GA GA
29594728 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
29594742 TTTAAGGAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29608468 original size:34 final size:34
Alignment explanation
Indices: 29608430--29608499 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
29608420 GGGAAAAATG
**
29608430 AGAGGAAGGCCAAGAGCAATGGTTTGAGAGTGGA
1 AGAGGAAGGCCAAGAGCAACAGTTTGAGAGTGGA
* **
29608464 AGAGGAAGGCTAAGAGCGGCAGTTTGAGAGTGGA
1 AGAGGAAGGCCAAGAGCAACAGTTTGAGAGTGGA
29608498 AG
1 AG
29608500 GATAGGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.43, T:0.14
Consensus pattern (34 bp):
AGAGGAAGGCCAAGAGCAACAGTTTGAGAGTGGA
Found at i:29611299 original size:88 final size:85
Alignment explanation
Indices: 29611172--29611414 Score: 326
Period size: 88 Copynumber: 2.8 Consensus size: 85
29611162 AGACTTTTAA
* *
29611172 AAAAAAACAATTAAACCCTTTTTTTTTTACACTCAATTGGATACTTGAACTTTTAAAATGTATCA
1 AAAAAAACAATTAAGCCCTGTTTTTTTT-CACTCAATTGGATACTTGAACTTTTAAAATGTATCA
* *
29611237 AAAAGACCCTTAAACTTTTTC
65 AAAAGACCCTCAAAATTTTTC
* * *
29611258 AAAAAAACAATTAAGCCCATGCTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT
1 AAAAAAACAATTAAGCCC-TG-TTTTTTTT-CACTCAATTGGATACTTGAACTTTTAAAATGTAT
*
29611323 CAAAAAGGCCCTCAAAATTTTTC
63 CAAAAAGACCCTCAAAATTTTTC
* * *
29611346 AAAAAAAGCAATTAAGCCTCTGTTTTTTTTCATTCAATTGGATACTTGAACTGTT-AAATATATC
1 AAAAAAA-CAATTAAGCC-CTGTTTTTTTTCACTCAATTGGATACTTGAACTTTTAAAATGTATC
29611410 AAAAA
64 AAAAA
29611415 AACCTTCTGG
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
86 29 0.21
87 22 0.16
88 74 0.54
89 12 0.09
90 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (85 bp):
AAAAAAACAATTAAGCCCTGTTTTTTTTCACTCAATTGGATACTTGAACTTTTAAAATGTATCAA
AAAGACCCTCAAAATTTTTC
Found at i:29611542 original size:14 final size:13
Alignment explanation
Indices: 29611520--29611558 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
29611510 ACATGTGACA
29611520 AAAAAATATAAAT
1 AAAAAATATAAAT
29611533 AAATAAATATAAAT
1 AAA-AAATATAAAT
*
29611547 AAAATATATAAA
1 AAAAAATATAAA
29611559 AGTTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATATAAAT
Found at i:29611568 original size:10 final size:9
Alignment explanation
Indices: 29611547--29611638 Score: 67
Period size: 10 Copynumber: 9.4 Consensus size: 9
29611537 AAATATAAAT
29611547 AAAATATATA
1 AAAAT-TATA
*
29611557 AAAGTTATTA
1 AAAATTA-TA
**
29611567 AATTTTAATA
1 AAAATTA-TA
29611577 AAAATTATA
1 AAAATTATA
*
29611586 AAATTTATTA
1 AAAATTA-TA
29611596 AAAATTATAA
1 AAAATTAT-A
*
29611606 AAAATCATA
1 AAAATTATA
*
29611615 AAAATCATAAA
1 AAAAT--TATA
29611626 AAAATTATA
1 AAAATTATA
29611635 AAAA
1 AAAA
29611639 ATTGTAAACT
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
9 24 0.37
10 34 0.52
11 7 0.11
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:29611568 original size:19 final size:19
Alignment explanation
Indices: 29611545--29611626 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
29611535 ATAAATATAA
*
29611545 ATAAAATAT-ATAAAAGTT
1 ATAAAATATAATAAAAATT
* *
29611563 ATTAAATTTTAATAAAAATT
1 A-TAAAATATAATAAAAATT
* *
29611583 ATAAAATTTATTAAAAATT
1 ATAAAATATAATAAAAATT
* * *
29611602 ATAAAAAATCATAAAAATC
1 ATAAAATATAATAAAAATT
29611621 ATAAAA
1 ATAAAA
29611627 AAATTATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 1 0.02
19 42 0.81
20 9 0.17
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (19 bp):
ATAAAATATAATAAAAATT
Found at i:29611588 original size:9 final size:9
Alignment explanation
Indices: 29611574--29611638 Score: 67
Period size: 9 Copynumber: 6.8 Consensus size: 9
29611564 TTAAATTTTA
29611574 ATAAAAATT
1 ATAAAAATT
*
29611583 ATAAAATTT
1 ATAAAAATT
29611592 ATTAAAAATT
1 A-TAAAAATT
*
29611602 ATAAAAAATC
1 AT-AAAAATT
29611612 ATAAAAATCAT
1 ATAAAAAT--T
*
29611623 AAAAAAATT
1 ATAAAAATT
29611632 ATAAAAA
1 ATAAAAA
29611639 ATTGTAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 23 0.50
10 16 0.35
11 7 0.15
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:29611608 original size:29 final size:30
Alignment explanation
Indices: 29611576--29611668 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 30
29611566 AAATTTTAAT
29611576 AAAAATTATAAAATTTAT-TAAAAATTATA
1 AAAAATTATAAAATTTATATAAAAATTATA
* * * *
29611605 AAAAATCATAAAAATCATAAAAAAATTATA
1 AAAAATTATAAAATTTATATAAAAATTATA
* * **
29611635 AAAAATTGTAAACTTT-TATAAAAAGCATA
1 AAAAATTATAAAATTTATATAAAAATTATA
29611664 AAAAA
1 AAAAA
29611669 ACCCCTTTAA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
29 30 0.59
30 21 0.41
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATTATAAAATTTATATAAAAATTATA
Found at i:29611639 original size:10 final size:10
Alignment explanation
Indices: 29611576--29611646 Score: 74
Period size: 10 Copynumber: 7.2 Consensus size: 10
29611566 AAATTTTAAT
29611576 AAAAATTAT-
1 AAAAATTATA
* *
29611585 AAAATTTATT
1 AAAAATTATA
29611595 AAAAATTATA
1 AAAAATTATA
*
29611605 AAAAATCAT-
1 AAAAATTATA
*
29611614 AAAAATCATAA
1 AAAAATTAT-A
29611625 AAAAATTATA
1 AAAAATTATA
*
29611635 AAAAATTGTA
1 AAAAATTATA
29611645 AA
1 AA
29611647 CTTTTATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
9 17 0.32
10 28 0.53
11 8 0.15
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:29611883 original size:18 final size:20
Alignment explanation
Indices: 29611842--29611901 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
29611832 AGTACGACAA
* *
29611842 TTTTATAATTTT-TTAAGAA
1 TTTTATAATTTTCTTACGAT
* *
29611861 GTTTAT-ATTTTTTTAC-AT
1 TTTTATAATTTTCTTACGAT
29611879 TTTTATAATTTTCTTACGAT
1 TTTTATAATTTTCTTACGAT
29611899 TTT
1 TTT
29611902 CTTACGATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 11 0.33
19 17 0.52
20 5 0.15
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTCTTACGAT
Found at i:29611889 original size:19 final size:19
Alignment explanation
Indices: 29611842--29611901 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
29611832 AGTACGACAA
* * *
29611842 TTTTATAATTTTTTAAGAA
1 TTTTATAATTTTTTTACAT
*
29611861 GTTTAT-ATTTTTTTACAT
1 TTTTATAATTTTTTTACAT
*
29611879 TTTTATAATTTTCTTACGAT
1 TTTTATAATTTTTTTAC-AT
29611899 TTT
1 TTT
29611902 CTTACGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.42
19 14 0.42
20 5 0.15
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTTACAT
Found at i:29611900 original size:11 final size:11
Alignment explanation
Indices: 29611886--29611912 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29611876 CATTTTTATA
29611886 ATTTTCTTACG
1 ATTTTCTTACG
29611897 ATTTTCTTACG
1 ATTTTCTTACG
29611908 ATTTT
1 ATTTT
29611913 ATAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (11 bp):
ATTTTCTTACG
Found at i:29612226 original size:90 final size:88
Alignment explanation
Indices: 29612071--29612235 Score: 219
Period size: 91 Copynumber: 1.9 Consensus size: 88
29612061 TGGTTCAAAT
*
29612071 ACCCAATTGAGTGCAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAGTTTGAAGGCT-TTTT
1 ACCCAATTCAGTGCAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAGTTTGAAGGCTCTTTT
* *
29612135 TTATGTATTTCAAAAGTTTAAGC
66 TGATGCATTTCAAAAGTTTAAGC
* *
29612158 ACCCAATTCAGTGCAAAAAAAGTGTAGGGGCTTAATTGTCTTTTTTTGAAAAAGTTT-AAGAG-T
1 ACCCAATTCAGTGC-AAAAAA--GCAGGGGCTTAATTG-CTATTTTTGAAAAAGTTTGAAG-GCT
29612221 CTTTTTGATGCATTT
61 CTTTTTGATGCATTT
29612236 TGATAGTTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
87 13 0.19
88 6 0.09
90 18 0.27
91 30 0.45
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (88 bp):
ACCCAATTCAGTGCAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAGTTTGAAGGCTCTTTT
TGATGCATTTCAAAAGTTTAAGC
Found at i:29612256 original size:91 final size:87
Alignment explanation
Indices: 29612063--29612317 Score: 217
Period size: 91 Copynumber: 2.8 Consensus size: 87
29612053 ATTAGGGATG
*
29612063 GTTCAAATACCCAATTGAGTGCAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAGTTTGAAG
1 GTTCAAATACCCAATTCAGTGCAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAGTTTGAAG
* *
29612128 GCTTTTTTTATGTATTTCAAAA
66 GCTTTTTTGATGCATTTCAAAA
* ** * *
29612150 GTTTAAGCACCCAATTCAGTGCAAAAAAAGTGTAGGGGCTTAATTGTCTTTTTTTGAAAAAGTTT
1 GTTCAAATACCCAATTCAGTGC-AAAAAA--GCAGGGGCTTAATTG-CTATTTTTGAAAAAGTTT
** *
29612215 -AAGAG-TCTTTTTGATGCATTTTGATA
62 GAAG-GCT-TTTTTGATGCATTTCAAAA
* * * * * * * *
29612241 GTTCAAATACACAATTGAGTTTGAAAAGAAAGTAAGGGCTTAATTACTTTTTTTTTGAAAAATTT
1 GTTCAAATACCCAATTCAG--TGCAAA-AAAGCAGGGGCTTAATTGC--TATTTTTGAAAAAGTT
*
29612306 TGAGGGCTTTTT
61 TGAAGGCTTTTT
29612318 ACATTCTTAA
Statistics
Matches: 134, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
87 18 0.13
88 6 0.04
90 19 0.14
91 59 0.44
92 24 0.18
93 8 0.06
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (87 bp):
GTTCAAATACCCAATTCAGTGCAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAGTTTGAAG
GCTTTTTTGATGCATTTCAAAA
Found at i:29617390 original size:14 final size:14
Alignment explanation
Indices: 29617373--29617407 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29617363 TATTTGGTAA
*
29617373 ATATTTTTAAAATT
1 ATATTTTAAAAATT
29617387 ATATTTTAAAAATT
1 ATATTTTAAAAATT
29617401 AT-TTTTA
1 ATATTTTA
29617408 GTGACACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTTTAAAAATT
Found at i:29617395 original size:13 final size:12
Alignment explanation
Indices: 29617374--29617407 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
29617364 ATTTGGTAAA
29617374 TATTTTTAAAAT
1 TATTTTTAAAAT
29617386 TATATTTTAAAAAT
1 TAT-TTTT-AAAAT
29617400 TATTTTTA
1 TATTTTTA
29617408 GTGACACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTTAAAAT
Found at i:29617912 original size:12 final size:12
Alignment explanation
Indices: 29617895--29617919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29617885 ATATCACATC
29617895 AAAAAATTAACA
1 AAAAAATTAACA
29617907 AAAAAATTAACA
1 AAAAAATTAACA
29617919 A
1 A
29617920 TATTAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATTAACA
Found at i:29618706 original size:9 final size:8
Alignment explanation
Indices: 29618684--29618708 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29618674 ATAAATATTT
29618684 TTAAAAAA
1 TTAAAAAA
29618692 TTAAAAAA
1 TTAAAAAA
29618700 TTAAAAAA
1 TTAAAAAA
29618708 T
1 T
29618709 AATATGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:29619275 original size:8 final size:9
Alignment explanation
Indices: 29619225--29619288 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 9
29619215 ATGTAAACAT
29619225 TAAAATAATA
1 TAAAAT-ATA
29619235 TTAAAATGACTA
1 -TAAAAT-A-TA
*
29619247 TTAAAAAATA
1 -TAAAATATA
*
29619257 AAAAATATA
1 TAAAATATA
29619266 TAAAAT-TA
1 TAAAATATA
29619274 TAAAATAT-
1 TAAAATATA
29619282 TAAAATA
1 TAAAATA
29619289 AAATAATATG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
8 15 0.33
9 13 0.28
10 2 0.04
11 8 0.17
12 8 0.17
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAATATA
Found at i:29624140 original size:15 final size:15
Alignment explanation
Indices: 29624120--29624155 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
29624110 AAGTATTAGA
29624120 TTTTTTTTTAG-AAT
1 TTTTTTTTTAGTAAT
*
29624134 TTTTTTTTTGGTAAT
1 TTTTTTTTTAGTAAT
29624149 TTTTTTT
1 TTTTTTT
29624156 GAACCATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTAGTAAT
Found at i:29631281 original size:16 final size:16
Alignment explanation
Indices: 29631260--29631291 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29631250 GAAGATAAAA
29631260 ACTGTTTAGTGCACTG
1 ACTGTTTAGTGCACTG
29631276 ACTGTTTAGTGCACTG
1 ACTGTTTAGTGCACTG
29631292 GCATCAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
ACTGTTTAGTGCACTG
Found at i:29634553 original size:6 final size:6
Alignment explanation
Indices: 29634542--29634600 Score: 66
Period size: 6 Copynumber: 9.8 Consensus size: 6
29634532 GAGCCAATGC
* * *
29634542 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGT TGTTGCA -GATGA TGATGA
1 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTTG-A TGTTGA TGTTGA
*
29634590 TGTTGC TGTTG
1 TGTTGA TGTTG
29634601 TTGAAAATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 1 0.02
6 45 0.98
ACGTcount: A:0.15, C:0.03, G:0.34, T:0.47
Consensus pattern (6 bp):
TGTTGA
Found at i:29636642 original size:26 final size:25
Alignment explanation
Indices: 29636574--29636643 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 25
29636564 TGAGTAAATT
** *
29636574 AAAAAAAATTCATAATTGGGTGACC
1 AAAAAAAATGGATAGTTGGGTGACC
29636599 AAAAAAAATGGCCCATAGTTGGGTGACC
1 AAAAAAAATGG---ATAGTTGGGTGACC
29636627 AAAAAAAAATGGATAGT
1 -AAAAAAAATGGATAGT
29636644 CATATCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 9 0.24
26 5 0.13
28 13 0.34
29 11 0.29
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (25 bp):
AAAAAAAATGGATAGTTGGGTGACC
Found at i:29637755 original size:7 final size:7
Alignment explanation
Indices: 29637738--29637768 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
29637728 CAAACCATAC
29637738 ATTTCATT
1 ATTT-ATT
29637746 ATTTATT
1 ATTTATT
29637753 ATTTATT
1 ATTTATT
29637760 ATTTATT
1 ATTTATT
29637767 AT
1 AT
29637769 ATGTTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTATT
Found at i:29637775 original size:14 final size:14
Alignment explanation
Indices: 29637743--29637776 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29637733 CATACATTTC
*
29637743 ATTATTTATTATTT
1 ATTATTTATTATAT
29637757 ATTATTTATTATAT
1 ATTATTTATTATAT
*
29637771 GTTATT
1 ATTATT
29637777 GGTAAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
ATTATTTATTATAT
Found at i:29641710 original size:38 final size:37
Alignment explanation
Indices: 29641659--29641730 Score: 126
Period size: 38 Copynumber: 1.9 Consensus size: 37
29641649 TAATTCATAT
*
29641659 TTTAATAATAATTATATTAAAACTATTATTAAATTGTA
1 TTTAATAATAATTATATTAAAA-TATAATTAAATTGTA
29641697 TTTAATAATAATTATATTAAAATATAATTAAATT
1 TTTAATAATAATTATATTAAAATATAATTAAATT
29641731 ATTTATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTAATAATAATTATATTAAAATATAATTAAATTGTA
Found at i:29641959 original size:16 final size:17
Alignment explanation
Indices: 29641938--29641975 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
29641928 TAAATTACTG
29641938 ATTACAACCT-TATTCC
1 ATTACAACCTCTATTCC
*
29641954 ATTAC-AGCTCTATTCC
1 ATTACAACCTCTATTCC
29641970 ATTACA
1 ATTACA
29641976 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.37
Consensus pattern (17 bp):
ATTACAACCTCTATTCC
Found at i:29643820 original size:23 final size:23
Alignment explanation
Indices: 29643778--29643821 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29643768 CAAAAGTAAA
29643778 TAAAAAATAAAAAAACAGAACTC
1 TAAAAAATAAAAAAACAGAACTC
*
29643801 TAAAATAATAATAAAA-AGAAC
1 TAAAA-AATAAAAAAACAGAAC
29643822 AATGTCGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (23 bp):
TAAAAAATAAAAAAACAGAACTC
Found at i:29647421 original size:19 final size:20
Alignment explanation
Indices: 29647399--29647440 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
29647389 GTTAAATACC
29647399 TTTTTCAATTTT-TAT-ATA
1 TTTTTCAATTTTGTATAATA
29647417 TTTTTCAATTTTGTATAATA
1 TTTTTCAATTTTGTATAATA
29647437 TTTT
1 TTTT
29647441 GATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.55
19 3 0.14
20 7 0.32
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTCAATTTTGTATAATA
Found at i:29647457 original size:20 final size:20
Alignment explanation
Indices: 29647435--29647502 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 20
29647425 TTTTGTATAA
29647435 TATTTTGATTT-TTAA-ATTT
1 TATTTT-ATTTATTAATATTT
29647454 ATATTTATATATTTATTAATATTT
1 -TATTT-TA--TTTATTAATATTT
29647478 TATTTTATTTATTAATATTT
1 TATTTTATTTATTAATATTT
29647498 TATTT
1 TATTT
29647503 ATTAATGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
20 24 0.56
21 1 0.02
22 5 0.12
23 9 0.21
24 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (20 bp):
TATTTTATTTATTAATATTT
Found at i:29647478 original size:58 final size:60
Alignment explanation
Indices: 29647406--29647526 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 60
29647396 ACCTTTTTCA
29647406 ATTTTTATATATTTTTCAATTT-TGTA-TAATATTTTGATTT-TTAA-ATTTATAT-TTATAT
1 ATTTTTATATA-TTTT-AATTTATGTATTAATATTTT-ATTTATTAAGATTTATATATTATAT
* *
29647464 ATTTATTA-ATATTTTATTTTATTTATTAATATTTTATTTATTAATGATTTATATATTATAT
1 ATTT-TTATATATTTTAATTTATGTATTAATATTTTATTTATTAA-GATTTATATATTATAT
29647525 AT
1 AT
29647527 GATTTTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
56 4 0.07
57 11 0.20
58 20 0.37
59 3 0.06
60 8 0.15
61 8 0.15
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (60 bp):
ATTTTTATATATTTTAATTTATGTATTAATATTTTATTTATTAAGATTTATATATTATAT
Found at i:29647496 original size:15 final size:15
Alignment explanation
Indices: 29647432--29647526 Score: 69
Period size: 15 Copynumber: 6.4 Consensus size: 15
29647422 CAATTTTGTA
29647432 TAATATTTTGATTT-T
1 TAATATTTT-ATTTAT
29647447 TAA-ATTTATATTTA-
1 TAATATTT-TATTTAT
29647461 T-ATA-TTTATTAATAT
1 TAATATTTTATT--TAT
*
29647476 T-TTATTTTATTTAT
1 TAATATTTTATTTAT
29647490 TAATATTTTATTTAT
1 TAATATTTTATTTAT
*
29647505 TAATGA-TTTATATAT
1 TAAT-ATTTTATTTAT
29647520 TATATAT
1 TA-ATAT
29647527 GATTTTTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
12 4 0.06
13 3 0.05
14 16 0.24
15 34 0.52
16 9 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TAATATTTTATTTAT
Found at i:29647539 original size:58 final size:57
Alignment explanation
Indices: 29647432--29647541 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 57
29647422 CAATTTTGTA
*
29647432 TAATATTTTGATTTTTAAATTTATATTTATATATTTATTAATATTTTATTTTATTTAT
1 TAATATTTTGATTTTTAAATTTATATTTATATATTGATT-ATATTTTATTTTATTTAT
*
29647490 TAATATTTT-ATTTATTAATGATTTATATATTATATA-TGATT-TTTTTTATTTT
1 TAATATTTTGATTT-TTAA--ATTTATAT-TTATATATTGATTATATTTTATTTT
29647542 TATACAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
57 4 0.09
58 23 0.50
60 12 0.26
61 7 0.15
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (57 bp):
TAATATTTTGATTTTTAAATTTATATTTATATATTGATTATATTTTATTTTATTTAT
Found at i:29647645 original size:21 final size:22
Alignment explanation
Indices: 29647619--29647659 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29647609 GGTCAACGGT
*
29647619 GGTTAATG-TTGGTCAACATCC
1 GGTTAATGATGGGTCAACATCC
29647640 GGTTAATGATGGGTCAACAT
1 GGTTAATGATGGGTCAACAT
29647660 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (22 bp):
GGTTAATGATGGGTCAACATCC
Found at i:29666387 original size:3 final size:3
Alignment explanation
Indices: 29666381--29666409 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29666371 ATCAAAATGA
29666381 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29666410 ACAACAGAGC
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29667705 original size:57 final size:59
Alignment explanation
Indices: 29667601--29667744 Score: 147
Period size: 57 Copynumber: 2.5 Consensus size: 59
29667591 ATTAGAAAAA
* * * * *
29667601 ATATAAAAATC--ACAAAAATTATAAAAAATAATAATTAATTTATAAAAATTGTAATTTT
1 ATATAAAAATCGTA-AAAAATTATAAAAAATAATAAGTAATATAGAAAAAATATAATTTT
* *
29667659 ATATAAAAATCGTAAAAAATTATAAAATAT-AT-AGTAATATAGAAAAAATATATTTTT
1 ATATAAAAATCGTAAAAAATTATAAAAAATAATAAGTAATATAGAAAAAATATAATTTT
*
29667716 A-AT-AAAATTGTAAAAAATATTATAAAAAA
1 ATATAAAAATCGT-AAAAA-ATTATAAAAAA
29667745 ATCATAAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
55 7 0.10
56 7 0.10
57 30 0.41
58 13 0.18
59 15 0.21
60 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (59 bp):
ATATAAAAATCGTAAAAAATTATAAAAAATAATAAGTAATATAGAAAAAATATAATTTT
Found at i:29674486 original size:7 final size:7
Alignment explanation
Indices: 29674474--29674505 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
29674464 AACATGTAGA
29674474 AGAGAAG
1 AGAGAAG
29674481 AGAGAAG
1 AGAGAAG
29674488 AGAG-A-
1 AGAGAAG
29674493 AGAGAAG
1 AGAGAAG
29674500 AGAGAA
1 AGAGAA
29674506 AATCCGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.17
6 2 0.09
7 17 0.74
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
AGAGAAG
Found at i:29674488 original size:12 final size:12
Alignment explanation
Indices: 29674471--29674505 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
29674461 GGAAACATGT
29674471 AGAAGAGA-AGAG
1 AGAAGAGAGA-AG
29674483 AGAAGAGAGAAG
1 AGAAGAGAGAAG
29674495 AGAAGAGAGAA
1 AGAAGAGAGAA
29674506 AATCCGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 21 0.95
13 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAAGAGAGAAG
Found at i:29677622 original size:20 final size:20
Alignment explanation
Indices: 29677599--29677645 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29677589 AGAACTTCTC
29677599 TTCTACTAATACAACTATAA
1 TTCTACTAATACAACTATAA
** * *
29677619 TTCTACCGATACAAGTATGA
1 TTCTACTAATACAACTATAA
29677639 TTCTACT
1 TTCTACT
29677646 GGAACAACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (20 bp):
TTCTACTAATACAACTATAA
Found at i:29682053 original size:12 final size:12
Alignment explanation
Indices: 29682036--29682077 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
29682026 TTAACTTAAT
29682036 CGAACATGTTCA
1 CGAACATGTTCA
**
29682048 CGAACAT-TAAA
1 CGAACATGTTCA
29682059 CGAACATGTTCA
1 CGAACATGTTCA
*
29682071 TGAACAT
1 CGAACAT
29682078 ATAATTGAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:29682057 original size:23 final size:23
Alignment explanation
Indices: 29682031--29682100 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
29682021 TTTATTTAAC
29682031 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* *
29682054 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
29682077 TATAATTGAACATGTTCACTAACA
1 T-TAATCGAACATGTTCACGAACA
29682101 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:29682956 original size:29 final size:29
Alignment explanation
Indices: 29682899--29682956 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
29682889 AAATTAGATC
*
29682899 AAATCAAATTTCATGTATAAAATTGCACA
1 AAATCAAATTTCATGTATAAAATTACACA
* *
29682928 AAATCAAAGTTT-ATGTATATAGTTACACA
1 AAATCAAA-TTTCATGTATAAAATTACACA
29682957 TTAAACCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (29 bp):
AAATCAAATTTCATGTATAAAATTACACA
Found at i:29692664 original size:17 final size:17
Alignment explanation
Indices: 29692639--29692672 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29692629 TAATTTACAT
*
29692639 AATTTATATATAATAAA
1 AATTAATATATAATAAA
*
29692656 AATTAATATATTATAAA
1 AATTAATATATAATAAA
29692673 TTTGAAAACG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAATATATAATAAA
Found at i:29698796 original size:20 final size:20
Alignment explanation
Indices: 29698773--29698812 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29698763 TTTTTAGAAA
29698773 TTAAAAAACATTAAAATTAT
1 TTAAAAAACATTAAAATTAT
*
29698793 TTAAAAAGCATTAAAATTAT
1 TTAAAAAACATTAAAATTAT
29698813 AAAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
TTAAAAAACATTAAAATTAT
Found at i:29711067 original size:16 final size:17
Alignment explanation
Indices: 29711036--29711068 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29711026 TAAAAATTAT
*
29711036 TATTTATTTGATTTTAA
1 TATTTACTTGATTTTAA
29711053 TATTTACTT-ATTTTAA
1 TATTTACTTGATTTTAA
29711069 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTACTTGATTTTAA
Found at i:29712849 original size:14 final size:15
Alignment explanation
Indices: 29712827--29712860 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29712817 ACTCTAAAAA
*
29712827 TTAAAAAAATTATTT
1 TTAAAAAAATCATTT
29712842 TTAAAAAAATCATTT
1 TTAAAAAAATCATTT
29712857 TTAA
1 TTAA
29712861 CCCTCATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAAAAATCATTT
Found at i:29714293 original size:14 final size:14
Alignment explanation
Indices: 29714276--29714308 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29714266 GGTTAAAAAT
29714276 AATTTTTTTTTAAA
1 AATTTTTTTTTAAA
*
29714290 AA-TTATTTTTAAA
1 AATTTTTTTTTAAA
29714303 AATTTT
1 AATTTT
29714309 AGAGTTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 2
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTTTTTTAAA
Found at i:29714567 original size:20 final size:20
Alignment explanation
Indices: 29714530--29714568 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29714520 TTAACTCCGG
* *
29714530 AAAAATTTAATCACTAAATA
1 AAAAAATTAATAACTAAATA
*
29714550 AAAAAATTAATAATTAAAT
1 AAAAAATTAATAACTAAAT
29714569 GATGAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTAATAACTAAATA
Found at i:29719011 original size:21 final size:22
Alignment explanation
Indices: 29718985--29719032 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
29718975 CTTGGACAAG
* *
29718985 GAAGAGAAGAAAATAGAGT-AA
1 GAAGAGAAGAAAACAGAATGAA
29719006 GAAGAGAAGAAAACAGAATGAA
1 GAAGAGAAGAAAACAGAATGAA
29719028 GAAGA
1 GAAGA
29719033 AGACGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.29, T:0.06
Consensus pattern (22 bp):
GAAGAGAAGAAAACAGAATGAA
Found at i:29724839 original size:17 final size:16
Alignment explanation
Indices: 29724808--29724863 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 16
29724798 CAAAATTTTA
29724808 AAAAATATAACAAAAACT
1 AAAAATA-AA-AAAAACT
29724826 AAAAATCATAAAAAAA-T
1 AAAAAT-A-AAAAAAACT
29724843 AAAAATAAAAAAAACT
1 AAAAATAAAAAAAACT
29724859 CAAAA
1 -AAAA
29724864 CTCAAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 11 0.31
18 11 0.31
19 4 0.11
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAATAAAAAAAACT
Found at i:29724870 original size:17 final size:16
Alignment explanation
Indices: 29724819--29724871 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
29724809 AAAATATAAC
29724819 AAAAACTAAAAATCATA
1 AAAAACTAAAAATCA-A
* *
29724836 AAAAAATAAAAATAAA
1 AAAAACTAAAAATCAA
*
29724852 AAAAACTCAAAACTCAA
1 AAAAACT-AAAAATCAA
29724869 AAA
1 AAA
29724872 CTTATTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAACTAAAAATCAA
Found at i:29725478 original size:17 final size:16
Alignment explanation
Indices: 29725458--29725505 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
29725448 TTTTTAGTTT
29725458 TTTTATAATTTTTTAA
1 TTTTATAATTTTTTAA
29725474 GTTTTA-ATATTTTTTAA
1 -TTTTATA-ATTTTTTAA
29725491 TTTTATAATATTTTT
1 TTTTATAAT-TTTTT
29725506 TGGATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTATAATTTTTTAA
Found at i:29725513 original size:19 final size:18
Alignment explanation
Indices: 29725465--29725506 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
29725455 TTTTTTTATA
*
29725465 ATTTTTTAAGTTT-TAAT
1 ATTTTTTAATTTTATAAT
29725482 ATTTTTTAATTTTATAAT
1 ATTTTTTAATTTTATAAT
29725500 ATTTTTT
1 ATTTTTT
29725507 GGATTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTTAATTTTATAAT
Found at i:29727202 original size:2 final size:2
Alignment explanation
Indices: 29727195--29727219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29727185 TCTGAGACTT
29727195 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
29727220 TTTGTAAATT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29731588 original size:20 final size:21
Alignment explanation
Indices: 29731565--29731615 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
29731555 ATTAATTATT
*
29731565 TATAAAATT-TAATTTGAATA
1 TATAAAATTATAATTTAAATA
*
29731585 TAT-AAATTATATTTTAAATA
1 TATAAAATTATAATTTAAATA
29731605 T-TAAAA-TATAA
1 TATAAAATTATAA
29731616 CCAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAAATTATAATTTAAATA
Found at i:29747389 original size:17 final size:17
Alignment explanation
Indices: 29747363--29747399 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29747353 CCACCTTGAT
* *
29747363 AAGAATTCTCTACGAAC
1 AAGAACTCTCAACGAAC
29747380 AAGAACTCTCAACGAAC
1 AAGAACTCTCAACGAAC
29747397 AAG
1 AAG
29747400 TTCTCCACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (17 bp):
AAGAACTCTCAACGAAC
Found at i:29759261 original size:11 final size:11
Alignment explanation
Indices: 29759245--29759271 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29759235 TGAAAAAAAA
29759245 TATAAATTAAT
1 TATAAATTAAT
29759256 TATAAATTAAT
1 TATAAATTAAT
29759267 TATAA
1 TATAA
29759272 GTGCTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:29760420 original size:14 final size:14
Alignment explanation
Indices: 29760403--29760463 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
29760393 CCCATTGACT
*
29760403 TTTTATATTATTTG
1 TTTTATATTATTTA
*
29760417 TTTTTTATTATTTA
1 TTTTATATTATTTA
* *
29760431 TTATATAATATTTAA
1 TTTTATATTATTT-A
* *
29760446 ATTTATATT-TTCA
1 TTTTATATTATTTA
29760459 TTTTA
1 TTTTA
29760464 ACTAATATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
13 5 0.14
14 24 0.67
15 7 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTATATTATTTA
Found at i:29760754 original size:18 final size:18
Alignment explanation
Indices: 29760723--29760773 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
29760713 AAAATAGAAT
* *
29760723 ATATTAATTAAAATAAAA
1 ATATAAATTTAAATAAAA
* *
29760741 ATATACATTTAAATTAAA
1 ATATAAATTTAAATAAAA
*
29760759 TTATAAATTTAAATA
1 ATATAAATTTAAATA
29760774 TTATATAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATTTAAATAAAA
Found at i:29760755 original size:24 final size:22
Alignment explanation
Indices: 29760679--29760758 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 22
29760669 TACAGAAAAA
* *
29760679 AAATTTAAATAAAAATAAGTTTT
1 AAATTAAAATAAAAATAA-ATTT
29760702 AAAATT-AAATAAAAATAGAATATAT
1 -AAATTAAAATAAAAATA-AAT-T-T
*
29760727 TAATTAAAATAAAAATATACATTT
1 AAATTAAAATAAAAATA-A-ATTT
29760751 AAATTAAA
1 AAATTAAA
29760759 TTATAAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
23 12 0.26
24 19 0.40
25 14 0.30
26 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (22 bp):
AAATTAAAATAAAAATAAATTT
Found at i:29760759 original size:23 final size:21
Alignment explanation
Indices: 29760683--29760759 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 21
29760673 GAAAAAAAAT
*
29760683 TTAAATAAAAATAAGTTTTAAAA
1 TTAAATAAAAATAA-ATTT-AAA
*
29760706 TTAAATAAAAATAGAATATATTAA
1 TTAAATAAAAATA-AAT-T-TAAA
29760730 TTAAAATAAAAATATACATTTAAA
1 TT-AAATAAAAATA-A-ATTTAAA
29760754 TTAAAT
1 TTAAAT
29760760 TATAAATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 18 0.40
24 11 0.24
25 14 0.31
26 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (21 bp):
TTAAATAAAAATAAATTTAAA
Found at i:29761650 original size:92 final size:92
Alignment explanation
Indices: 29761484--29761651 Score: 225
Period size: 92 Copynumber: 1.8 Consensus size: 92
29761474 CAAGCCTTAC
* * *
29761484 TTTTCATGATTTATTATTTATTTTTTTAAATTTAAATTTTTTTTGTGATATCATATTAAATGATA
1 TTTTAATGATTTATTATTTATTTTTTAAAATTTAAATTTTTTTGGTGATATCATATTAAATGATA
*
29761549 CAACTACTTTTTTAAATCAGCTTCTTT
66 CAACCACTTTTTTAAATCAGCTTCTTT
29761576 TTTTAATGATTTATTATTTATTTTTTAAAAAATTTAAATTTTTTGTGGTG-T-T-ATATTAAATG
1 TTTTAATGATTTATTATTTATTTTTT--AAAATTTAAATTTTTT-TGGTGATATCATATTAAATG
* * *
29761638 GTGCCACCACTTTT
63 ATACAACCACTTTT
29761652 CCTAAATCTC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
92 45 0.68
93 1 0.02
94 16 0.24
95 4 0.06
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (92 bp):
TTTTAATGATTTATTATTTATTTTTTAAAATTTAAATTTTTTTGGTGATATCATATTAAATGATA
CAACCACTTTTTTAAATCAGCTTCTTT
Found at i:29761887 original size:20 final size:19
Alignment explanation
Indices: 29761862--29761904 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
29761852 ATTATTTATT
29761862 ATTTAATATTTAAATATATA
1 ATTTAA-ATTTAAATATATA
29761882 ATTT-AATTTAAATATATA
1 ATTTAAATTTAAATATATA
*
29761900 TTTTA
1 ATTTA
29761905 TTTTTGGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 16 0.76
19 1 0.05
20 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAAATTTAAATATATA
Found at i:29761892 original size:18 final size:18
Alignment explanation
Indices: 29761869--29761904 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29761859 ATTATTTAAT
29761869 ATTTAAATATATAATTTA
1 ATTTAAATATATAATTTA
*
29761887 ATTTAAATATATATTTTA
1 ATTTAAATATATAATTTA
29761905 TTTTTGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAATTTA
Found at i:29763373 original size:24 final size:25
Alignment explanation
Indices: 29763328--29763374 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29763318 GAAATTATGG
* *
29763328 AAAACTCTAATTAATATGAGAAACA
1 AAAACTCTAATAAAAATGAGAAACA
*
29763353 AAAACTCTAA-AAAAATTAGAAA
1 AAAACTCTAATAAAAATGAGAAA
29763375 AGGGAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAACTCTAATAAAAATGAGAAACA
Found at i:29765778 original size:5 final size:5
Alignment explanation
Indices: 29765770--29765796 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29765760 AAAAAAATCC
29765770 AACCA AACCA AACCA AACCA AACCA AA
1 AACCA AACCA AACCA AACCA AACCA AA
29765797 ATCACCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCA
Found at i:29771095 original size:33 final size:35
Alignment explanation
Indices: 29771055--29771125 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
29771045 ATGTCAATAA
* *
29771055 AATTATCACA-AGTTATTTTAATA-A-AATTATCGT
1 AATTATCACATAGTT-CTTTAATAGATAATTATCAT
29771088 AATTATCACATAGTTCTTTAATAGATAATTATCAT
1 AATTATCACATAGTTCTTTAATAGATAATTATCAT
29771123 AAT
1 AAT
29771126 CCGTAATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 17 0.52
34 5 0.15
35 11 0.33
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (35 bp):
AATTATCACATAGTTCTTTAATAGATAATTATCAT
Found at i:29771710 original size:17 final size:18
Alignment explanation
Indices: 29771672--29771707 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29771662 TTTAATAGGT
29771672 ATAAAATGTTATTTAAAA
1 ATAAAATGTTATTTAAAA
*
29771690 ATAAAATTTTATTTAAAA
1 ATAAAATGTTATTTAAAA
29771708 TAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAAAATGTTATTTAAAA
Found at i:29773631 original size:20 final size:20
Alignment explanation
Indices: 29773608--29773662 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 20
29773598 TAAAGTTTAT
29773608 TAAAAATTAGAAAAAAATTA
1 TAAAAATTAGAAAAAAATTA
29773628 TAAAAATT-GTAAAAAAATTA
1 TAAAAATTAG-AAAAAAATTA
29773648 TAAAATATATAGAAA
1 TAAAA-AT-TAGAAA
29773663 TATAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.03
20 23 0.74
21 2 0.06
22 4 0.13
23 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAAATTAGAAAAAAATTA
Found at i:29773652 original size:29 final size:29
Alignment explanation
Indices: 29773620--29773710 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 29
29773610 AAAATTAGAA
29773620 AAAAATTATAAAAATTGTAAAAAAATTAT
1 AAAAATTATAAAAATTGTAAAAAAATTAT
* *
29773649 -AAAATATATAGAAA-TATAGAAAAAATTAT
1 AAAAAT-TATAAAAATTGTA-AAAAAATTAT
** * * *
29773678 AAATTTTAT-AAACTCGTAATAAAATTAT
1 AAAAATTATAAAAATTGTAAAAAAATTAT
29773706 AAAAA
1 AAAAA
29773711 ATGTAAAGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
28 22 0.47
29 22 0.47
30 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATTATAAAAATTGTAAAAAAATTAT
Found at i:29773716 original size:20 final size:20
Alignment explanation
Indices: 29773621--29773728 Score: 61
Period size: 20 Copynumber: 5.6 Consensus size: 20
29773611 AAATTAGAAA
* *
29773621 AAAATTATAAAAATTGTAAA
1 AAAATTATAAAAAATGTAAT
*
29773641 AAAATTAT--AAAATAT-AT
1 AAAATTATAAAAAATGTAAT
*
29773658 AGAAATATAGAAAAAAT-T-AT
1 A-AAAT-TATAAAAAATGTAAT
* * *
29773678 -AAATTTTATAAACTCGTAAT
1 AAAATTATAAAAAAT-GTAAT
29773698 AAAATTATAAAAAATGTAA-
1 AAAATTATAAAAAATGTAAT
29773717 AGAAA-TATAAAA
1 A-AAATTATAAAA
29773729 TTCATAAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
17 8 0.12
18 13 0.19
19 11 0.16
20 20 0.29
21 16 0.24
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAAATGTAAT
Found at i:29773949 original size:9 final size:9
Alignment explanation
Indices: 29773937--29774029 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 9
29773927 ATTTTATATT
*
29773937 TTTTTATGA
1 TTTTTATAA
29773946 TTTTTATAAA
1 TTTTTAT-AA
* *
29773956 ATTTTACAA
1 TTTTTATAA
*
29773965 TTTTCTATAT
1 TTTT-TATAA
*
29773975 TTTTTATGA
1 TTTTTATAA
29773984 TTTTTATAAAA
1 TTTTTAT--AA
*
29773995 TTTTAATAA
1 TTTTTATAA
*
29774004 ATTTTA-AA
1 TTTTTATAA
*
29774012 TATTTTGTATA
1 T-TTTTATA-A
29774023 TTTTTAT
1 TTTTTAT
29774030 TAAAATTTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
8 2 0.03
9 32 0.52
10 19 0.31
11 9 0.15
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29773950 original size:19 final size:19
Alignment explanation
Indices: 29773915--29773991 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
29773905 TTGCTAAATG
*
29773915 ATTTTTTGATGCA-TTTTAT
1 ATTTTTTTATG-ATTTTTAT
29773934 ATTTTTTTATGATTTTTAT
1 ATTTTTTTATGATTTTTAT
*** **
29773953 AAAATTTTACAATTTTCTAT
1 ATTTTTTTATGATTTT-TAT
29773973 A-TTTTTTATGATTTTTAT
1 ATTTTTTTATGATTTTTAT
29773991 A
1 A
29773992 AAATTTTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
18 5 0.11
19 37 0.80
20 4 0.09
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTTTTTATGATTTTTAT
Found at i:29773983 original size:38 final size:40
Alignment explanation
Indices: 29773927--29774058 Score: 154
Period size: 38 Copynumber: 3.5 Consensus size: 40
29773917 TTTTTGATGC
*
29773927 ATTTTATAT-TTTTTTATGATTTTTATAAAATTTT-A-CA
1 ATTTTATATATTTTTTATGATTTTTATAAAATTTTAATAA
*
29773964 ATTTTCTATATTTTTTATGATTTTTATAAAATTTTAATAA
1 ATTTTATATATTTTTTATGATTTTTATAAAATTTTAATAA
* *
29774004 ATTTTAAATATTTTGTAT-ATTTTTATTAAAA-TTTAAT-A
1 ATTTTATATATTTTTTATGATTTTTA-TAAAATTTTAATAA
29774042 ATGTTTAT-T-TTTTTTAT
1 AT-TTTATATATTTTTTAT
29774059 TTTTTCCACG
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
37 15 0.18
38 29 0.35
39 18 0.22
40 21 0.25
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (40 bp):
ATTTTATATATTTTTTATGATTTTTATAAAATTTTAATAA
Found at i:29773998 original size:19 final size:19
Alignment explanation
Indices: 29773938--29773999 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
29773928 TTTTATATTT
29773938 TTTTATGATTTTTATAAAA
1 TTTTATGATTTTTATAAAA
** **
29773957 TTTTACAATTTTCTAT-ATT
1 TTTTATGATTTT-TATAAAA
29773976 TTTTATGATTTTTATAAAA
1 TTTTATGATTTTTATAAAA
29773995 TTTTA
1 TTTTA
29774000 ATAAATTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 3 0.09
19 27 0.82
20 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTATGATTTTTATAAAA
Found at i:29774357 original size:87 final size:87
Alignment explanation
Indices: 29774162--29774414 Score: 226
Period size: 88 Copynumber: 3.0 Consensus size: 87
29774152 GGTTAAATAG
* * *
29774162 CTTTTTGATGCATTTTAACAGTTTAAGTACCCAATT-AA-ATAAAAAAAAAGAGACTTAATTG--
1 CTTTTTGATGCATTTTAA-AATTTAAGTA-CCAATTGAATGTAAAAAATAAGAGACTTAA-TGAA
** * *
29774223 TTTTTTTTGAAAAAGTTT-AAGGAT
63 TTTTTTTAAAAAAAATTTGAAAGAT
*
29774247 CTTTTTGATGCGTTTTGAAAATTTAAGTACTCAATTGAATGTAAAAAAGTAAGAG-CTTAATGAA
1 CTTTTTGATGCATTTT-AAAATTTAAGTAC-CAATTGAATGTAAAAAA-TAAGAGACTTAATGAA
29774311 TTTTTTTAAAAAAAATTTGAAAG-T
63 TTTTTTTAAAAAAAATTTGAAAGAT
* * * *
29774335 CTTTTTGATACATTTTAAAATTT---CACCAATTGAGTG-AAAAAAAATAGAGACTTAA--ATAT
1 CTTTTTGATGCATTTTAAAATTTAAGTACCAATTGAATGTAAAAAATA-AGAGACTTAATGA-AT
*
29774394 ATTTTTAAAAAAAATTTGAAA
64 TTTTTTAAAAAAAATTTGAAA
29774415 TTTTTTTACA
Statistics
Matches: 143, Mismatches: 14, Indels: 25
0.79 0.08 0.14
Matches are distributed among these distances:
81 2 0.01
82 32 0.22
83 14 0.10
84 3 0.02
85 29 0.20
86 6 0.04
87 19 0.13
88 35 0.24
89 3 0.02
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (87 bp):
CTTTTTGATGCATTTTAAAATTTAAGTACCAATTGAATGTAAAAAATAAGAGACTTAATGAATTT
TTTTAAAAAAAATTTGAAAGAT
Found at i:29774686 original size:5 final size:5
Alignment explanation
Indices: 29774678--29774709 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
29774668 ACAAACAGCA
29774678 AAAAG -AAA- AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
29774710 AGCCCAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:29775226 original size:2 final size:2
Alignment explanation
Indices: 29775221--29775256 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29775211 ATCTGGTATG
*
29775221 CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29775257 TTATTTCCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29781055 original size:2 final size:2
Alignment explanation
Indices: 29781048--29781085 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29781038 CGCCATCCTT
29781048 TC TC TC TC TC TC TC 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
29781086 GTCTTTCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:29803158 original size:17 final size:17
Alignment explanation
Indices: 29803134--29803173 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
29803124 TCAATATCAC
*
29803134 CAAAAAAAAGTAAAATTA
1 CAAAAAAAACT-AAATTA
29803152 CAAAAAAAACTAAATTA
1 CAAAAAAAACTAAATTA
29803169 CAAAA
1 CAAAA
29803174 TATGTAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (17 bp):
CAAAAAAAACTAAATTA
Found at i:29805451 original size:15 final size:15
Alignment explanation
Indices: 29805431--29805464 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
29805421 GTTTAGGCAA
29805431 AGCAAAACACTGCAT
1 AGCAAAACACTGCAT
29805446 AGCAAAACACTGCAT
1 AGCAAAACACTGCAT
29805461 AGCA
1 AGCA
29805465 TAAATTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.12
Consensus pattern (15 bp):
AGCAAAACACTGCAT
Found at i:29813955 original size:15 final size:15
Alignment explanation
Indices: 29813931--29813961 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29813921 ACACATAAAT
29813931 ATATTATTGATGCAC
1 ATATTATTGATGCAC
*
29813946 ATATTGTTGATGCAC
1 ATATTATTGATGCAC
29813961 A
1 A
29813962 ATCCCCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (15 bp):
ATATTATTGATGCAC
Found at i:29816214 original size:12 final size:12
Alignment explanation
Indices: 29816197--29816221 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29816187 ATTAAAAATT
29816197 TTTAAAAATAAA
1 TTTAAAAATAAA
29816209 TTTAAAAATAAA
1 TTTAAAAATAAA
29816221 T
1 T
29816222 ACATTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTAAAAATAAA
Found at i:29816275 original size:21 final size:24
Alignment explanation
Indices: 29816251--29816294 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 24
29816241 CTCATTCTCA
29816251 TTCTCCTT-CTT-TTT-TTTCTTC
1 TTCTCCTTCCTTGTTTCTTTCTTC
*
29816272 TTCTTCTTCCTTGTTTCTTTCTT
1 TTCTCCTTCCTTGTTTCTTTCTT
29816295 TCTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 3 0.16
24 6 0.32
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.70
Consensus pattern (24 bp):
TTCTCCTTCCTTGTTTCTTTCTTC
Found at i:29819607 original size:14 final size:14
Alignment explanation
Indices: 29819588--29819617 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29819578 TAATTATACC
29819588 ATATCAAAATTCAT
1 ATATCAAAATTCAT
*
29819602 ATATCAAATTTCAT
1 ATATCAAAATTCAT
29819616 AT
1 AT
29819618 TAAATTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATCAAAATTCAT
Found at i:29828727 original size:39 final size:42
Alignment explanation
Indices: 29828638--29828731 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 42
29828628 ATAGAATAGG
*
29828638 GCTGTAATCAGTAATTCAGTTATTTGGTTGAATGGAATGGAATAAA
1 GCTGTAAT-AGTAATTCAGTTATTTGATTGAATGGAATGG-AT--A
29828684 GCTGTAATAGT-ATTCA-TGTATTTGATTGAATGGAATGG-T-
1 GCTGTAATAGTAATTCAGT-TATTTGATTGAATGGAATGGATA
29828723 GCTGTAATA
1 GCTGTAATA
29828732 ACATAAGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
39 9 0.20
42 1 0.02
43 1 0.02
44 24 0.52
45 3 0.07
46 8 0.17
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (42 bp):
GCTGTAATAGTAATTCAGTTATTTGATTGAATGGAATGGATA
Found at i:29828876 original size:55 final size:57
Alignment explanation
Indices: 29828817--29828950 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 57
29828807 TTTTAATAAG
*
29828817 ATTATTATTAAATATAATTTAAT-AATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAATAATAAATAATTTAATAATATTTTTAACATA
* *
29828872 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAATAATAAATAATTTAATAATATTTTTAACATA
29828930 ATTATTATTAAAATATGAATT
1 ATTATTATT-AAATAT-AATT
29828951 AGTAAAAATC
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
55 23 0.32
57 20 0.28
58 18 0.25
59 6 0.08
60 4 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (57 bp):
ATTATTATTAAATATAATTTAATAAATAATAAATAATTTAATAATATTTTTAACATA
Found at i:29838194 original size:17 final size:18
Alignment explanation
Indices: 29838169--29838220 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
29838159 CGAATAAAAA
29838169 TATTATTTAAATATAAT-T
1 TATT-TTTAAATATAATAT
* *
29838187 TATTTTTATATATTATGAT
1 TATTTTTAAATATAAT-AT
29838206 TATTTTTAAAATATA
1 TATTTTT-AAATATA
29838221 TATAGAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 10 0.37
18 4 0.15
19 8 0.30
20 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTTTAAATATAATAT
Done.