Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 35 of 240
Found at i:12358936 original size:61 final size:58
Alignment explanation
Indices: 12358825--12359007 Score: 163
Period size: 61 Copynumber: 2.9 Consensus size: 58
12358815 ATTACTTTAA
* *
12358825 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
*
12358883 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATT-AATTCTAATATTAAGATAAT
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATT-TAATATT---A-AAT
12358947 CAC
58 --C
* *
12358950 TTTAATATTAAATTAATAAAATAC-TATCAAGATAAGTATTAAATTAAATTTAAGTATT
1 -----TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAA-TATT
12359008 TTATTAATTT
Statistics
Matches: 102, Mismatches: 6, Indels: 23
0.78 0.05 0.18
Matches are distributed among these distances:
58 20 0.20
60 5 0.05
61 24 0.24
64 1 0.01
65 3 0.03
67 1 0.01
68 20 0.20
69 9 0.09
71 2 0.02
72 17 0.17
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:12359005 original size:18 final size:17
Alignment explanation
Indices: 12358982--12359025 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
12358972 ACTATCAAGA
12358982 TAAGTATTAAATTAAATT
1 TAAGTATTAAATT-AATT
**
12359000 TAAGTATTTTATTAATT
1 TAAGTATTAAATTAATT
12359017 TAA-TATTAA
1 TAAGTATTAA
12359026 GTCTTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TAAGTATTAAATTAATT
Found at i:12360719 original size:4 final size:4
Alignment explanation
Indices: 12360710--12360743 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
12360700 TGAAATTAAC
*
12360710 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TCTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
12360744 CATCATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:12365236 original size:11 final size:11
Alignment explanation
Indices: 12365204--12365258 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
12365194 TAACTATAAG
12365204 TTAAT-TAATA
1 TTAATATAATA
* *
12365214 GT-ATATTATA
1 TTAATATAATA
12365224 TTAAT-TAATTA
1 TTAATATAA-TA
12365235 TTAATATAATA
1 TTAATATAATA
*
12365246 TTAATATATTA
1 TTAATATAATA
12365257 TT
1 TT
12365259 TTTAAGCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
9 2 0.06
10 8 0.22
11 23 0.64
12 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TTAATATAATA
Found at i:12365241 original size:22 final size:21
Alignment explanation
Indices: 12365204--12365258 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
12365194 TAACTATAAG
* *
12365204 TTAATTAA-TAGTATATTATA
1 TTAATTAATTATTATATAATA
12365224 TTAATTAATTATTAATATAATA
1 TTAATTAATTATT-ATATAATA
12365246 TTAA-TATATTATT
1 TTAATTA-ATTATT
12365259 TTTAAGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 8 0.27
21 5 0.17
22 17 0.57
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATTAATTATTATATAATA
Found at i:12372257 original size:18 final size:18
Alignment explanation
Indices: 12372231--12372277 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
12372221 GTAGTGATTC
* *
12372231 AATTGGGTTAATTTGGGT
1 AATTCGGTTAATTCGGGT
12372249 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
12372267 AATCCGGTTAA
1 AATTCGGTTAA
12372278 CCGACCGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.38
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:12379204 original size:22 final size:22
Alignment explanation
Indices: 12379179--12379225 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
12379169 AACAGCGCAA
12379179 AAGTTGTAATGCCTTCAAATCT
1 AAGTTGTAATGCCTTCAAATCT
12379201 AAGTTGTAATGCCTTCAAATCT
1 AAGTTGTAATGCCTTCAAATCT
12379223 AAG
1 AAG
12379226 CATGTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (22 bp):
AAGTTGTAATGCCTTCAAATCT
Found at i:12400743 original size:11 final size:11
Alignment explanation
Indices: 12400729--12400755 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12400719 ATTTTAAGGA
12400729 ATTTTTTATAT
1 ATTTTTTATAT
12400740 ATTTTTTATAT
1 ATTTTTTATAT
12400751 ATTTT
1 ATTTT
12400756 ATAAAATTTA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:12405607 original size:3 final size:3
Alignment explanation
Indices: 12405588--12405641 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
12405578 AATTTATTTC
* * * *
12405588 ATA AT- ATA ATA ACA ATA ATA TTA ATA ATG ACA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12405634 ATA A-A ATA
1 ATA ATA ATA
12405642 TCATTTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12408534 original size:19 final size:21
Alignment explanation
Indices: 12408496--12408536 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
12408486 ATTGGGTGGA
*
12408496 TCAGCTTTTACGAGCTTCTGT
1 TCAGCTTTTACGACCTTCTGT
12408517 TCAGC-TTT-CGACCTTCTGT
1 TCAGCTTTTACGACCTTCTGT
12408536 T
1 T
12408537 GGCGTATCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.44
Consensus pattern (21 bp):
TCAGCTTTTACGACCTTCTGT
Found at i:12409166 original size:18 final size:17
Alignment explanation
Indices: 12409135--12409168 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12409125 AGTTGATGAA
*
12409135 TTGAATTAATTTGTATT
1 TTGAATTAAATTGTATT
12409152 TTGAGATTAAATTGTAT
1 TTGA-ATTAAATTGTAT
12409169 ATAATTGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (17 bp):
TTGAATTAAATTGTATT
Found at i:12409552 original size:121 final size:123
Alignment explanation
Indices: 12409418--12409643 Score: 323
Period size: 123 Copynumber: 1.9 Consensus size: 123
12409408 GTGGGCTCTT
* * * *
12409418 CTCTTGAATAAAAAATGGAGACATT-AA-AGAGAAAT-GAACATGTTAAAAGTATTTGTGAATCC
1 CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAA-ATGTTAAAAATATTTGCGAAGCC
* ** * *
12409480 ATGAGAGGCTTCATTGGTGCAATATGAACATGATCCACTAACTATACAGGATGCCTCCC
65 AGGAGACACTTCATTGGTCCAATATGAAAATGATCCACTAACTATACAGGATGCCTCCC
*
12409539 CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAAATGTTAAAAATATTTGCGAAGCTA
1 CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAAATGTTAAAAATATTTGCGAAGCCA
*
12409604 GGAGACACTTTATTGGTCCAATATGAAAATGATCCACTAA
66 GGAGACACTTCATTGGTCCAATATGAAAATGATCCACTAA
12409644 TTGTATTGGT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
121 24 0.26
122 2 0.02
123 62 0.68
124 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (123 bp):
CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAAATGTTAAAAATATTTGCGAAGCCA
GGAGACACTTCATTGGTCCAATATGAAAATGATCCACTAACTATACAGGATGCCTCCC
Found at i:12411351 original size:3 final size:3
Alignment explanation
Indices: 12411337--12411392 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
12411327 AAATTGTTAT
* *
12411337 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
12411383 TTA TTT TTA T
1 TTA TTA TTA T
12411393 ATTCATGCGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:12411667 original size:28 final size:27
Alignment explanation
Indices: 12411613--12411673 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 27
12411603 TATATATTTT
* *
12411613 TATATTTTTTTTATGTTCATAAGTGTA
1 TATATTTTTTTTATATTCATAAATGTA
12411640 T-TATTTTTTTTATATTCATATTAATGTA
1 TATATTTTTTTTATATTCATA--AATGTA
12411668 TATATT
1 TATATT
12411674 ATGTGCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 18 0.62
27 1 0.03
28 6 0.21
29 4 0.14
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (27 bp):
TATATTTTTTTTATATTCATAAATGTA
Found at i:12411869 original size:15 final size:15
Alignment explanation
Indices: 12411846--12411878 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12411836 GTGATATGTC
12411846 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
12411861 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
12411876 ATT
1 ATT
12411879 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:12412267 original size:98 final size:98
Alignment explanation
Indices: 12412152--12412348 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
12412142 TTAAAAATAA
*
12412152 TAAAGGAAATATTCCGAGTTTGAGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
12412217 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
12412250 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
12412315 TTAAATTTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
12412348 T
1 T
12412349 TCTATTATAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:12413226 original size:22 final size:22
Alignment explanation
Indices: 12413201--12413246 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
12413191 TAGAACAGGT
*
12413201 CCGAGCCCGAGATAGATCTGAC
1 CCGAGCCCGAGATAAATCTGAC
** *
12413223 CCGAGCTTGAGATAAATTTGAC
1 CCGAGCCCGAGATAAATCTGAC
12413245 CC
1 CC
12413247 AAAGCCTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (22 bp):
CCGAGCCCGAGATAAATCTGAC
Found at i:12414381 original size:127 final size:126
Alignment explanation
Indices: 12414179--12414538 Score: 492
Period size: 126 Copynumber: 2.9 Consensus size: 126
12414169 AAAAACTTTT
* * * *
12414179 TTTTTCTACAGTAGTTTTTG-AAAAATAATTTTGAAAAAACGGTTCTA-AA-AGATAATGTAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTC-AGAACAAATAGTGTAAAA
* * * *
12414241 AGCGCTTAAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAATAGCTCCCATGTGGATGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAA-AGCTCCCACGTGGATGCTC
* *
12414304 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCAGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTCAGAACAAATAGTGTAAAAA
* *
12414369 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGATGCTC
* * * *
12414430 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTCAGAACAAATAGTGTAAAAA
* * * * *
12414495 ACTCTTCAAGCAAGATGTACTGTCAGCAAAATTATTGAAAAAAG
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAG
12414539 TTACATAAGT
Statistics
Matches: 211, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
125 20 0.09
126 141 0.67
127 50 0.24
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACGGTTCAGAACAAATAGTGTAAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGATGCTC
Found at i:12416043 original size:227 final size:227
Alignment explanation
Indices: 12415648--12416106 Score: 909
Period size: 227 Copynumber: 2.0 Consensus size: 227
12415638 AAAAAGTACA
12415648 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
1 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
12415713 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
66 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
12415778 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
131 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
12415843 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
196 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
12415875 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
1 AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
12415940 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
66 TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
*
12416005 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAATGCGGATCCAAGAACTTCAGTG
131 TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
12416070 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
196 TCGGTCTTAATTGCCAATATTTGTAGCCAATT
12416102 AAGGT
1 AAGGT
12416107 ACACGCATTC
Statistics
Matches: 231, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 231 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (227 bp):
AAGGTCCACATACATGTGTTGCTGGTACAGTATCACTGGTGTTTAGGGTTTTTGAATAATACTGT
TATTACGTAATGTTGCATTATTTAACGTGCTTCGTTGACAAGTGTTTCACAAGATCATCCCAAGA
TGGATTCAGATATGTTAGCTAGCTTAATACTACCGACGGTAAAGGCGGATCCAAGAACTTCAGTG
TCGGTCTTAATTGCCAATATTTGTAGCCAATT
Found at i:12417737 original size:24 final size:24
Alignment explanation
Indices: 12417681--12417737 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
12417671 AAGAACTTCT
*
12417681 ATTTTATTAAAAATATAAAAATAA
1 ATTTTATTAAAAATATAAAAACAA
*
12417705 ATTACTATT-AAAATATTAAAAACAA
1 ATT-TTATTAAAAATA-TAAAAACAA
*
12417730 CTTTTATT
1 ATTTTATT
12417738 TTATAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTTTATTAAAAATATAAAAACAA
Found at i:12417879 original size:93 final size:92
Alignment explanation
Indices: 12417685--12417876 Score: 318
Period size: 93 Copynumber: 2.1 Consensus size: 92
12417675 ACTTCTATTT
*
12417685 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
1 TATTAAAAATATAAAAATAAATTACTAATAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
*
12417750 ACAATATAAAAATAGTTTGTACAAATA
66 ACAATATAAAAATAGATTGTACAAATA
*
12417777 TATTAAAAATATAAAAAATAAATTACTAATAAAATATTAAAAGCAACTTTTATTTTATTAAA-TG
1 TATTAAAAATAT-AAAAATAAATTACTAATAAAATATTAAAAACAACTTTTATTTTA-TAAATTG
12417841 AAACAATATAAAAA-A-ATTGTACAAATA
64 AAACAATATAAAAATAGATTGTACAAATA
12417868 TATTAAAAA
1 TATTAAAAA
12417877 AATCAATGTT
Statistics
Matches: 95, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
91 20 0.21
92 13 0.14
93 58 0.61
94 4 0.04
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (92 bp):
TATTAAAAATATAAAAATAAATTACTAATAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
ACAATATAAAAATAGATTGTACAAATA
Found at i:12419851 original size:18 final size:20
Alignment explanation
Indices: 12419828--12419867 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
12419818 AAAATTAATT
*
12419828 AAAATTACATAA-A-TGAAA
1 AAAATTAAATAATATTGAAA
12419846 AAAATTAAATAATATTGAAA
1 AAAATTAAATAATATTGAAA
12419866 AA
1 AA
12419868 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAATTAAATAATATTGAAA
Found at i:12421820 original size:10 final size:10
Alignment explanation
Indices: 12421807--12421840 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12421797 CACACCCCCT
*
12421807 CTCTCTCTCT
1 CTCTCTCTCA
12421817 CTCTCTCTCA
1 CTCTCTCTCA
*
12421827 CTCTTTCTCA
1 CTCTCTCTCA
12421837 CTCT
1 CTCT
12421841 GGTTTAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.47, G:0.00, T:0.47
Consensus pattern (10 bp):
CTCTCTCTCA
Found at i:12433314 original size:190 final size:180
Alignment explanation
Indices: 12432961--12433322 Score: 458
Period size: 190 Copynumber: 2.0 Consensus size: 180
12432951 AAAATAAAAA
12432961 GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAATAGGTAAAATTTTGGAAGGAAAATATTAAAA
1 GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAATAGGTAAAATTTTGGAAGGAAAATATTAAAA
* ** *
12433026 AAAAATTGGGGGGATGGGTTTGGGGTAGATGAGGGTGGGAAAGGAGGGGAGTAAAAGTTTTAGGG
66 AAAAATTGGGGGAATGAATTTGGGGTAGATGAGGGTGGGAAAGGAGGGAAGTAAAAGTTTTAGGG
*
12433091 GGAAAGTGGGAGGGAGTAAAAATTTTGGGGAAAAATAAAAAGTTTTAAGG
131 GGAAAGTGGGAAGGAGTAAAAATTTTGGGGAAAAATAAAAAGTTTTAAGG
* ** *
12433141 GTTTTT-GGGAGTAAAATTTTGAGGGAAAGTAAATGGGAGAGTAAAATTTTTTAGGGAAAATATT
1 GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAAT---AG-GTAAAATTTTGGAAGGAAAATATT
* **
12433205 AAAAAAATATATTTGGTGGGAAATGAATTTTGGGTAGATGAGGGATTGGGATGGGAGGGAAGTAA
62 AAAAAAA-A-A-TTGG-GGG-AATGAATTTGGGGTAGATGAGGG--TGGGAAAGGAGGGAAGTAA
* * * *
12433270 AAGTTTT-GGGGGGAAGTGGGAAGGAGTTAAAGTTTTGGGGGAAAAGTAAAAAG
120 AAGTTTTAGGGGGAAAGTGGGAAGGAGTAAAAATTTT-GGGGAAAAATAAAAAG
12433323 GTCTGGGGTT
Statistics
Matches: 154, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
179 27 0.18
180 6 0.04
182 2 0.01
183 28 0.18
184 1 0.01
185 1 0.01
186 4 0.03
187 3 0.02
188 19 0.12
189 25 0.16
190 38 0.25
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.27
Consensus pattern (180 bp):
GTTTTTGGGGAATAAAATTTTGAGGGAAAGTAAATAGGTAAAATTTTGGAAGGAAAATATTAAAA
AAAAATTGGGGGAATGAATTTGGGGTAGATGAGGGTGGGAAAGGAGGGAAGTAAAAGTTTTAGGG
GGAAAGTGGGAAGGAGTAAAAATTTTGGGGAAAAATAAAAAGTTTTAAGG
Found at i:12446411 original size:40 final size:40
Alignment explanation
Indices: 12446309--12446478 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
12446299 TCCTCGTTCA
* * * *
12446309 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
12446348 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* *
12446388 AATGCCTTCGGGACTTAATCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
12446428 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
12446468 AAGGCCTTCGG
1 AATGCCTTCGG
12446479 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 34 0.29
40 83 0.71
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:12446451 original size:80 final size:79
Alignment explanation
Indices: 12446307--12446531 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 79
12446297 GCTCCTCGTT
* * * * * *
12446307 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAGTCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
12446372 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* *
12446386 CGAATGCCTTCGGGACTTAATCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGTCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
** *
12446451 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
* * * * * * * *
12446466 CAAAGGCCTTC-GGATCTTAGTCCAGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGTCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG
12446530 GA
64 GA
12446532 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 37 0.30
80 80 0.66
81 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGTCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:12454323 original size:40 final size:40
Alignment explanation
Indices: 12454141--12454363 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
12454131 TCCTCGTTCA
* * * * *
12454141 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
12454180 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
12454220 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
12454260 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
12454300 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
12454340 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
12454364 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:12454372 original size:41 final size:41
Alignment explanation
Indices: 12454295--12454372 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
12454285 TTAGTATCTC
* * *
12454295 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
12454336 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
12454373 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:12459009 original size:16 final size:16
Alignment explanation
Indices: 12458975--12459026 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
12458965 TAGTTCGCTA
* **
12458975 TAATGGAATAAAGATG
1 TAATGGAATAGAGGCG
*
12458991 TAATGGAATAGATGCG
1 TAATGGAATAGAGGCG
12459007 TAATGGAATAGAGGCG
1 TAATGGAATAGAGGCG
12459023 TAAT
1 TAAT
12459027 AGGTAATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.42, C:0.04, G:0.29, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGCG
Found at i:12459095 original size:44 final size:46
Alignment explanation
Indices: 12459012--12459103 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 46
12459002 ATGCGTAATG
* *
12459012 GAATAGAGGCGTAATAGGTAATTCTTTTATTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGGTAATTCTTGTATTTGGATGAATGGAATA
*
12459058 GAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGATGAATGGAATA
1 GAATAGAGGCGTAATAGGTAATTCTTGTATTTGGATGAATGGAATA
12459102 GA
1 GA
12459104 GGTGTAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 25 0.58
45 3 0.07
46 15 0.35
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTCTTGTATTTGGATGAATGGAATA
Found at i:12459436 original size:49 final size:49
Alignment explanation
Indices: 12459360--12459457 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
12459350 AATTATTATT
* * * *
12459360 AAATATAATTTAATATCATGAATCAAAAGGTGAACACTTTATAAAATTA
1 AAATATAATTTAATATCATGAACCAAAAGCTCAACACTGTATAAAATTA
12459409 AAAT-TAATTTCAATATCATGAACCAAAAGCTCAACACTGTATAAAATTA
1 AAATATAATTT-AATATCATGAACCAAAAGCTCAACACTGTATAAAATTA
12459458 TAACACATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 6 0.14
49 38 0.86
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (49 bp):
AAATATAATTTAATATCATGAACCAAAAGCTCAACACTGTATAAAATTA
Found at i:12473907 original size:3 final size:3
Alignment explanation
Indices: 12473899--12473938 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12473889 AGACGACAAT
12473899 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
12473939 GACCTGAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12483828 original size:13 final size:13
Alignment explanation
Indices: 12483812--12483866 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
12483802 AATAAATATA
*
12483812 TATTTTTTATTTT
1 TATTTTTAATTTT
12483825 TATTTTTAATTTT
1 TATTTTTAATTTT
*
12483838 TAATTTTAAATTTT
1 T-ATTTTTAATTTT
* * *
12483852 AAATTTTAAATTT
1 TATTTTTAATTTT
12483865 TA
1 TA
12483867 AAATACTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTTTAATTTT
Found at i:12483846 original size:6 final size:6
Alignment explanation
Indices: 12483816--12483867 Score: 50
Period size: 7 Copynumber: 8.0 Consensus size: 6
12483806 AATATATATT
* *
12483816 TTTTAT TTTTAT TTTTAA TTTTTAA TTTTAAA TTTTAAA TTTTAAA TTTTAA
1 TTTTAA TTTTAA TTTTAA -TTTTAA TTTT-AA TTTT-AA TTTT-AA TTTTAA
12483868 AATACTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 17 0.40
7 26 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:12483849 original size:7 final size:7
Alignment explanation
Indices: 12483826--12483868 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
12483816 TTTTATTTTT
*
12483826 ATTTTTA
1 ATTTTAA
*
12483833 ATTTTTA
1 ATTTTAA
12483840 ATTTTAA
1 ATTTTAA
12483847 ATTTTAA
1 ATTTTAA
12483854 ATTTTAA
1 ATTTTAA
12483861 ATTTTAA
1 ATTTTAA
12483868 A
1 A
12483869 ATACTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:12488420 original size:20 final size:20
Alignment explanation
Indices: 12488395--12488434 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12488385 TTTCAAATTA
*
12488395 ATTTTACCAAATATAATATT
1 ATTTTAACAAATATAATATT
**
12488415 ATTTTAATGAATATAATATT
1 ATTTTAACAAATATAATATT
12488435 TATCTAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTTAACAAATATAATATT
Found at i:12492953 original size:54 final size:54
Alignment explanation
Indices: 12492846--12492991 Score: 168
Period size: 54 Copynumber: 2.7 Consensus size: 54
12492836 CTAACAGAAC
* * * * * * * *
12492846 ACGCCATACAGGCAAT-CATATAGAGTATGCCACCAAGTCGATCCATTCTGAGT
1 ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
* * *
12492899 ATGCCACAAAGGCAATCCATTTAAAGTGTGCCACAAAGGCGAGCCAGTCAGAGT
1 ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
* *
12492953 ACGCCACAAAGGCAATCCAATTAGAGTACGCCACAAAGG
1 ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGG
12492992 AAATCCAGTT
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
53 13 0.17
54 63 0.83
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (54 bp):
ACGCCACAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
Found at i:12493012 original size:27 final size:27
Alignment explanation
Indices: 12492866--12493012 Score: 143
Period size: 27 Copynumber: 5.4 Consensus size: 27
12492856 GGCAATCATA
* * *
12492866 TAGAGTATGCCACCAAGTCGATCCA-T
1 TAGAGTATGCCACAAAGGCAATCCAGT
* *
12492892 TCTGAGTATGCCACAAAGGCAATCCATT
1 T-AGAGTATGCCACAAAGGCAATCCAGT
* * * *
12492920 TAAAGTGTGCCACAAAGGCGAGCCAGT
1 TAGAGTATGCCACAAAGGCAATCCAGT
* * *
12492947 CAGAGTACGCCACAAAGGCAATCCAAT
1 TAGAGTATGCCACAAAGGCAATCCAGT
* *
12492974 TAGAGTACGCCACAAAGGAAATCCAGT
1 TAGAGTATGCCACAAAGGCAATCCAGT
*
12493001 TAGAGTTTGCCA
1 TAGAGTATGCCA
12493013 TGGTCATGGA
Statistics
Matches: 97, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 94 0.97
28 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (27 bp):
TAGAGTATGCCACAAAGGCAATCCAGT
Found at i:12497355 original size:26 final size:26
Alignment explanation
Indices: 12497307--12497356 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
12497297 ATGAAAAAGG
**
12497307 GGTTGCTAAGTACAGATTTCCCGAGA
1 GGTTGCTAAGTACAGATGCCCCGAGA
* *
12497333 GGTTGCTAAGTGCTGATGCCCCGA
1 GGTTGCTAAGTACAGATGCCCCGA
12497357 ATTATTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (26 bp):
GGTTGCTAAGTACAGATGCCCCGAGA
Found at i:12533930 original size:17 final size:17
Alignment explanation
Indices: 12533893--12533930 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12533883 TTTTATACCG
**
12533893 TAAAGTTCCTCTATTTT
1 TAAAGTTCCTCTATTGA
12533910 TAAAGTTCCTCTATTGA
1 TAAAGTTCCTCTATTGA
12533927 TAAA
1 TAAA
12533931 TTCAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (17 bp):
TAAAGTTCCTCTATTGA
Found at i:12534318 original size:27 final size:28
Alignment explanation
Indices: 12534288--12534352 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
12534278 CTTATCAGGT
12534288 AGGCGCCAATGAAA-GTGCCTCATAGAG
1 AGGCGCCAATGAAATGTGCCTCATAGAG
* * *
12534315 AGGCACCAA-GAAATGTGCCTCTTAGGG
1 AGGCGCCAATGAAATGTGCCTCATAGAG
12534342 AGGCGCCAATG
1 AGGCGCCAATG
12534353 GTGGCCTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 27 0.84
28 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (28 bp):
AGGCGCCAATGAAATGTGCCTCATAGAG
Found at i:12534498 original size:17 final size:17
Alignment explanation
Indices: 12534473--12534529 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
12534463 GTAGGAAAAA
*
12534473 AAAAAGAGAGAAAGGAG
1 AAAAAGAGAGAAAGAAG
*
12534490 AAGAAGAGA-AGAAGAAG
1 AAAAAGAGAGA-AAGAAG
* *
12534507 AAAAAGAAAGAAAGAAA
1 AAAAAGAGAGAAAGAAG
12534524 AAAAAG
1 AAAAAG
12534530 GTAATGTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAGAAAGAAG
Found at i:12534685 original size:19 final size:19
Alignment explanation
Indices: 12534657--12534845 Score: 114
Period size: 19 Copynumber: 9.2 Consensus size: 19
12534647 TTGGATTAGT
*
12534657 ATTTTATATGAATATTGTA
1 ATTTTGTATGAATATTGTA
12534676 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
* *
12534695 ATTATTTTAT-AATTAAATTAATA
1 ATT-TTGTATGAA-T--ATT-GTA
* * * *
12534718 TTTTTAGTTTTGGAT-TAGT-
1 ATTTT-G-TATGAATATTGTA
12534737 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
12534756 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
12534775 ATTTTTTGTATGAATGTTGTA
1 A--TTTTGTATGAATATTGTA
*
12534796 ATTTCGGGATATATTGTAATATTGTAA
1 ATTT-----TGTA-TG-AATATTGT-A
12534823 ATTTTTGTATGAATATTGTA
1 A-TTTTGTATGAATATTGTA
12534843 ATT
1 ATT
12534846 ATTTTATAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
17 5 0.04
18 4 0.03
19 52 0.39
20 9 0.07
21 27 0.20
22 7 0.05
23 7 0.05
24 6 0.05
25 3 0.02
26 7 0.05
27 2 0.02
28 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:12534723 original size:61 final size:58
Alignment explanation
Indices: 12534658--12534863 Score: 139
Period size: 61 Copynumber: 3.3 Consensus size: 58
12534648 TGGATTAGTA
*
12534658 TTTTATATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTAT-AATTAAAT-TAATAT
1 TTTTATATGAAT-TTGTAATTTTGTATGAATATTGTAATT-TTGTATGAA-T-AATGTAAT-T
* * * *
12534719 TTTTAGTTTTGGATTAGT-ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATT
1 TTTTA--TATGAATTTGTAATTTTGTATGAATATTGTAATTTTGTATGAATAATGTAATT
* * *
12534778 TTTTGTATGAATGTTGTAATTTCGGGATATATTGTAATATTGTAAATTTTTGTATGAATATTGTA
1 TTTTATATGAAT-TTGTAATTT-----TGTA-TG-AATATTGT-AA-TTTTGTATGAATAATGTA
12534843 ATT
56 ATT
*
12534846 ATTTTATAATTAATTTGT
1 -TTTTAT-ATGAATTTGT
12534864 TAGTAATTTA
Statistics
Matches: 116, Mismatches: 12, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
57 5 0.04
58 3 0.03
59 11 0.09
60 10 0.09
61 29 0.25
62 3 0.03
63 5 0.04
64 3 0.03
65 2 0.02
66 8 0.07
67 2 0.02
68 21 0.18
69 9 0.08
70 5 0.04
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (58 bp):
TTTTATATGAATTTGTAATTTTGTATGAATATTGTAATTTTGTATGAATAATGTAATT
Found at i:12534783 original size:21 final size:21
Alignment explanation
Indices: 12534738--12534799 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
12534728 TGGATTAGTA
12534738 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
12534757 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
12534778 TTTTGTATGAATGTTGTAATT
1 TTTTGTATGAATATTGTAATT
12534799 T
1 T
12534800 CGGGATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:12534908 original size:60 final size:60
Alignment explanation
Indices: 12534838--12534959 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
12534828 TGTATGAATA
* * * * *
12534838 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
12534898 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
12534958 TT
1 TT
12534960 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:12535098 original size:16 final size:15
Alignment explanation
Indices: 12535077--12535113 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
12535067 CTCATTTAAT
12535077 TTTTATATAATGTAA
1 TTTTATATAATGTAA
*
12535092 CTTTTATATAATTTAA
1 -TTTTATATAATGTAA
12535108 TTTTAT
1 TTTTAT
12535114 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:12540241 original size:24 final size:24
Alignment explanation
Indices: 12540189--12540241 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12540179 ATACCTTATC
* *
12540189 CTTCTTCTTCTTTACCTTTCTTTT
1 CTTCTTCTGCCTTACCTTTCTTTT
*
12540213 TTTCTTCTGCCTT-CCTTTCTATTT
1 CTTCTTCTGCCTTACCTTTCT-TTT
12540237 CTTCT
1 CTTCT
12540242 GTTTCTCTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (24 bp):
CTTCTTCTGCCTTACCTTTCTTTT
Found at i:12540370 original size:27 final size:27
Alignment explanation
Indices: 12540297--12540374 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
12540287 GAAAAATCAG
*
12540297 ACCATTGGCGCCTCTTAACAT-GGCACC
1 ACCATTGGCGCCT-TTAAGATAGGCACC
* * *
12540324 ACTATTGGCGCCTCTCAGATAGGCACC
1 ACCATTGGCGCCTTTAAGATAGGCACC
*
12540351 ACCATTGGCGCCTTTGAGATAGGC
1 ACCATTGGCGCCTTTAAGATAGGC
12540375 GCCAATACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.09
27 39 0.91
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (27 bp):
ACCATTGGCGCCTTTAAGATAGGCACC
Found at i:12540606 original size:30 final size:29
Alignment explanation
Indices: 12540553--12540630 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 29
12540543 TGAAAAAAGT
* *
12540553 ACCCCATTTTGGTAAATAATTTTTCTGAC
1 ACCCCATTTTAGTAAAAAATTTTTCTGAC
* * *
12540582 ACCCCATTTTAGTACAAAAATTTTTTTTAT
1 ACCCCATTTTAGTA-AAAAATTTTTCTGAC
12540612 ACCCCATTTTAGTAAAAAA
1 ACCCCATTTTAGTAAAAAA
12540631 ACCCCTATAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (29 bp):
ACCCCATTTTAGTAAAAAATTTTTCTGAC
Found at i:12543410 original size:3 final size:3
Alignment explanation
Indices: 12543389--12543433 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
12543379 TTAAAATACT
* *
12543389 TAA TAA TCA TAA -AA AAA TAA TAA TAA -AA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12543434 GATCTGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:12543416 original size:11 final size:11
Alignment explanation
Indices: 12543397--12543433 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
12543387 CTTAATAATC
*
12543397 ATAAAAAAATA
1 ATAATAAAATA
12543408 ATAATAAAATA
1 ATAATAAAATA
12543419 ATAATAAAATA
1 ATAATAAAATA
12543430 ATAA
1 ATAA
12543434 GATCTGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:12543418 original size:8 final size:9
Alignment explanation
Indices: 12543389--12543433 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
12543379 TTAAAATACT
*
12543389 TAATAATCA
1 TAATAATAA
*
12543398 TAA-AAAAA
1 TAATAATAA
12543406 TAATAATAA
1 TAATAATAA
12543415 -AATAATAA
1 TAATAATAA
12543423 TAA-AATAA
1 TAATAATAA
12543431 TAA
1 TAA
12543434 GATCTGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
8 22 0.71
9 9 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
TAATAATAA
Found at i:12543433 original size:14 final size:14
Alignment explanation
Indices: 12543389--12543425 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12543379 TTAAAATACT
*
12543389 TAATAATCATAAAA
1 TAATAATAATAAAA
*
12543403 AAATAATAATAAAA
1 TAATAATAATAAAA
12543417 TAATAATAA
1 TAATAATAA
12543426 AATAATAAGA
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:12545642 original size:17 final size:16
Alignment explanation
Indices: 12545620--12545680 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
12545610 ATAATGATTC
*
12545620 TTTAATTTTATATATTT
1 TTTAATTTT-TATAATT
12545637 TTTAATTTTTATAATT
1 TTTAATTTTTATAATT
* * *
12545653 TATAATTTATACTTATT
1 TTTAATTTTTA-TAATT
*
12545670 TTTATTTTTTA
1 TTTAATTTTTA
12545681 ATGATTATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATTTTTATAATT
Found at i:12545658 original size:16 final size:17
Alignment explanation
Indices: 12545622--12545660 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
12545612 AATGATTCTT
* *
12545622 TAATTTTATATATTTTT
1 TAATTTTATATAATTTA
12545639 TAATTTT-TATAATTTA
1 TAATTTTATATAATTTA
12545655 TAATTT
1 TAATTT
12545661 ATACTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTATATAATTTA
Found at i:12547236 original size:49 final size:49
Alignment explanation
Indices: 12547142--12547234 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
12547132 TTGATTTTAT
12547142 AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAATTGA
1 AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAATTGA
* * *
12547191 AAATAATATATTTATTAATTAAAAA-ATTAATTAAGAATAAAAAA
1 AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAA
12547235 ATGTTTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 17 0.41
49 24 0.59
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (49 bp):
AAATAAAATATTTATTAATTAAAAATATGAATTAAAAATAAAAAATTGA
Found at i:12549570 original size:23 final size:23
Alignment explanation
Indices: 12549544--12549625 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
12549534 CACAACCTAT
*
12549544 CGGGACGCTCCGAAGAGCTATAA
1 CGGGATGCTCCGAAGAGCTATAA
* *
12549567 CGGGAAGCT-CGCAAGAACCATATAA
1 CGGGATGCTCCG-AAG-AGC-TATAA
*
12549592 CGGGATGCTCATG-AGAGCTAATAA
1 CGGGATGCTC-CGAAGAGCT-ATAA
12549616 CGGGATGCTC
1 CGGGATGCTC
12549626 TTTCAAGCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 2 0.04
23 12 0.25
24 18 0.38
25 15 0.31
27 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (23 bp):
CGGGATGCTCCGAAGAGCTATAA
Found at i:12555673 original size:56 final size:50
Alignment explanation
Indices: 12555605--12555797 Score: 226
Period size: 50 Copynumber: 3.7 Consensus size: 50
12555595 AGGAATGAGA
* *
12555605 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTAAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAGG
* * *
12555661 TCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* **
12555711 TCCTC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* *
12555761 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12555798 GTACAGAAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.01
50 82 0.68
51 3 0.02
55 1 0.01
56 34 0.28
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
Found at i:12555768 original size:100 final size:103
Alignment explanation
Indices: 12555610--12555797 Score: 265
Period size: 100 Copynumber: 1.8 Consensus size: 103
12555600 TGAGATCCCA
* **
12555610 TGTAAGACCATGTCTAGGACATGGCATTGGCATCATTAAGATTATGAGAGGTCCCATGTAAGACC
1 TGTAAGACCATGTCTAGGACATGGCATGGGCATC---AAGATTATGAGAACTCCCATGTAAGACC
* *
12555675 ATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGGTCCTC
63 ATATCTGGGATATGGCATTGGCACCGAGATGAGAGGTCCTC
* *
12555716 TGTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATA
1 TGTAAGACCATGTCTAGGACATGGCATGGGCATCAAGATTATGAGAACTCCCATGTAAGACCATA
12555778 TCTGGGATATGGCATTGGCA
66 TCTGGGATATGGCATTGGCA
12555798 GTACAGAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 42 0.56
101 2 0.03
105 1 0.01
106 30 0.40
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (103 bp):
TGTAAGACCATGTCTAGGACATGGCATGGGCATCAAGATTATGAGAACTCCCATGTAAGACCATA
TCTGGGATATGGCATTGGCACCGAGATGAGAGGTCCTC
Found at i:12556063 original size:12 final size:12
Alignment explanation
Indices: 12556046--12556084 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12556036 ATGAGTTATT
12556046 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
12556058 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
12556070 TAAGTGAGTAAG
1 TAAGTAAGCAAG
12556082 TAA
1 TAA
12556085 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:12557080 original size:20 final size:19
Alignment explanation
Indices: 12557043--12557081 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12557033 AATTTTAAAA
*
12557043 TATTTTTAAAATACTTTTT
1 TATTTTTAAAATAATTTTT
12557062 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
12557082 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:12558489 original size:31 final size:31
Alignment explanation
Indices: 12558451--12558513 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
12558441 TTATTCGGGA
**
12558451 TACGCAATGTCACTGTTAAGGAAGAAGTTAT
1 TACGCAATGTCACCATTAAGGAAGAAGTTAT
12558482 TACGCAATGTCACCATTAAGGAAGAAGTTAT
1 TACGCAATGTCACCATTAAGGAAGAAGTTAT
12558513 T
1 T
12558514 CACGAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (31 bp):
TACGCAATGTCACCATTAAGGAAGAAGTTAT
Found at i:12561085 original size:22 final size:18
Alignment explanation
Indices: 12561062--12561100 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12561052 AGAAATAGAG
12561062 AAAGAAACAGAGAAGCAA
1 AAAGAAACAGAGAAGCAA
12561080 AAAGAAACAGAGAAGCAA
1 AAAGAAACAGAGAAGCAA
12561098 AAA
1 AAA
12561101 CAAAGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAACAGAGAAGCAA
Found at i:12562046 original size:41 final size:39
Alignment explanation
Indices: 12561989--12562124 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
12561979 TGACTTCGAG
12561989 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATATAT
1 TCGATGAGACACTGGGTGTCAA-TTATTACTTCGGAT-TAT
* * * *
12562030 TCGATGAGGCACTGGGTGCCAA-T-TCACTTCGGTTTA-
1 TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
* * *
12562066 GCTGATGAGACACTAGGTGTCAAATTATTACTTCGAATTAT
1 TC-GATGAGACACTGGGTGTC-AATTATTACTTCGGATTAT
* * *
12562107 CCGATGGGGCACTGGGTG
1 TCGATGAGACACTGGGTG
12562125 CCAAACTGGT
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.01
37 17 0.23
38 11 0.15
39 2 0.03
40 23 0.31
41 21 0.28
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
Found at i:12569088 original size:13 final size:13
Alignment explanation
Indices: 12569070--12569118 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
12569060 CATTCTCATT
12569070 CCCTTTCCCCTAC
1 CCCTTTCCCCTAC
12569083 CCCTTTCCCCTTATCC
1 CCCTTTCCCC-TA--C
12569099 TTCCCTTTCCCCTAC
1 --CCCTTTCCCCTAC
12569114 CCCTT
1 CCCTT
12569119 CCCTTTCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 15 0.48
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 10 0.32
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.37
Consensus pattern (13 bp):
CCCTTTCCCCTAC
Found at i:12569106 original size:18 final size:18
Alignment explanation
Indices: 12569083--12569126 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
12569073 TTTCCCCTAC
*
12569083 CCCTTTCCCCTTA-TCCTT
1 CCCTTTCCCC-TACCCCTT
12569101 CCCTTTCCCCTACCCCTT
1 CCCTTTCCCCTACCCCTT
12569119 CCCTTTCC
1 CCCTTTCC
12569127 TGTTTCGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.05, C:0.57, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCTTTCCCCTACCCCTT
Found at i:12569109 original size:37 final size:36
Alignment explanation
Indices: 12569043--12569126 Score: 87
Period size: 37 Copynumber: 2.3 Consensus size: 36
12569033 ACCCATTCTT
* * * * *
12569043 CTCCCCTTTCTCCTTCTCATTCTCATTCCCTTTCCC
1 CTCCCCTTTCCCCTTATCATTCCCATTCCCCTACCC
* *
12569079 CTACCCCTTTCCCCTTATCCTTCCCTTTCCCCTACCC
1 CT-CCCCTTTCCCCTTATCATTCCCATTCCCCTACCC
*
12569116 CTTCCCTTTCC
1 CTCCCCTTTCC
12569127 TGTTTCGAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 10 0.26
37 29 0.74
ACGTcount: A:0.06, C:0.54, G:0.00, T:0.40
Consensus pattern (36 bp):
CTCCCCTTTCCCCTTATCATTCCCATTCCCCTACCC
Found at i:12570461 original size:30 final size:30
Alignment explanation
Indices: 12570425--12570482 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12570415 GCATTTGTAC
* *
12570425 AAGACCATAAGTTCCAATTTACTATGACAT
1 AAGACCATAAGTACCAACTTACTATGACAT
*
12570455 AAGACCATAAGTACCAACTTGCTATGAC
1 AAGACCATAAGTACCAACTTACTATGAC
12570483 TGGAATGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (30 bp):
AAGACCATAAGTACCAACTTACTATGACAT
Found at i:12571653 original size:34 final size:35
Alignment explanation
Indices: 12571598--12571664 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12571588 CAAACACCAG
*
12571598 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
12571633 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12571665 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12572006 original size:29 final size:30
Alignment explanation
Indices: 12571960--12572018 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
12571950 GAATTAGATC
12571960 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
12571990 AAATCAAAATTT-ATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
12572019 TTAAACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:12574240 original size:21 final size:19
Alignment explanation
Indices: 12574175--12574241 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 19
12574165 ATAATTAAAA
*
12574175 TAATAATTTTGTACAATTTT
1 TAATAATTTT-TATAATTTT
* *
12574195 T-ATAATTCTTAATCATTTT
1 TAATAATT-TTTATAATTTT
12574214 TAAATAATTTTCTATAATTATT
1 T-AATAATTTT-TATAATT-TT
12574236 TAATAA
1 TAATAA
12574242 GCTAATCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
19 13 0.35
20 5 0.14
21 16 0.43
22 3 0.08
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (19 bp):
TAATAATTTTTATAATTTT
Found at i:12574354 original size:21 final size:20
Alignment explanation
Indices: 12574329--12574374 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
12574319 TAGATGTTGA
*
12574329 TTTTAATAATTTAAAAATATT
1 TTTTAACAATTTAAAAAT-TT
* *
12574350 TTTTAACATTTTAAATATTT
1 TTTTAACAATTTAAAAATTT
12574370 TTTTA
1 TTTTA
12574375 TAAATTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAACAATTTAAAAATTT
Found at i:12583634 original size:46 final size:46
Alignment explanation
Indices: 12583564--12583652 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
12583554 ACAATGTTAT
12583564 AACTCAATATGGATTTCTTCACTGAAATACCATACCTACGTTCCAC
1 AACTCAATATGGATTTCTTCACTGAAATACCATACCTACGTTCCAC
* * *
12583610 AACTCAGTAT-GATTTTCTTTACTGAATTACCATACCTACGTTC
1 AACTCAATATGGA-TTTCTTCACTGAAATACCATACCTACGTTC
12583653 AACACTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 2 0.05
46 37 0.95
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAATATGGATTTCTTCACTGAAATACCATACCTACGTTCCAC
Found at i:12593287 original size:16 final size:16
Alignment explanation
Indices: 12593268--12593306 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12593258 TTTTAATAAA
12593268 ATTAAAACTAATTGTT
1 ATTAAAACTAATTGTT
**
12593284 ATTAAATTTAATTGTT
1 ATTAAAACTAATTGTT
*
12593300 AGTAAAA
1 ATTAAAA
12593307 TTATCAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:12593289 original size:22 final size:22
Alignment explanation
Indices: 12593240--12593294 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
12593230 CCCGTTTTTA
* * *
12593240 ATTAAAATTAAAATTATTTTTT
1 ATTAAAATTAAAACTAATTGTT
*
12593262 AATAAAATTAAAACTAATTGTT
1 ATTAAAATTAAAACTAATTGTT
*
12593284 ATTAAATTTAA
1 ATTAAAATTAA
12593295 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAAATTAAAACTAATTGTT
Found at i:12593389 original size:59 final size:59
Alignment explanation
Indices: 12593320--12593489 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
12593310 TCAAATTATT
*
12593320 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
12593379 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
12593438 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
12593490 ACAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:12593599 original size:23 final size:23
Alignment explanation
Indices: 12593559--12593602 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12593549 AAATAAACTT
** *
12593559 AAAATAAAAACTATTATATTTTA
1 AAAATAAAAAAAAATATATTTTA
12593582 AAAATAAAAAAAAATATATTT
1 AAAATAAAAAAAAATATATTT
12593603 AATATTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATAAAAAAAAATATATTTTA
Found at i:12594641 original size:21 final size:22
Alignment explanation
Indices: 12594603--12594672 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 22
12594593 AACAAACAAT
*
12594603 AAATAACCATATATATAAATATA
1 AAATAATCATA-ATATAAATATA
12594626 AAATAATCA-AATATAAATAT-
1 AAATAATCATAATATAAATATA
* * *
12594646 TAATAATTATATTATAAATA-A
1 AAATAATCATAATATAAATATA
12594667 AAATAA
1 AAATAA
12594673 ACATCCAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.17
21 24 0.60
22 1 0.03
23 8 0.20
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAATCATAATATAAATATA
Found at i:12595539 original size:20 final size:21
Alignment explanation
Indices: 12595495--12595547 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
12595485 AAAGACATGG
12595495 ATTATGTTTTACTTGAGATTT
1 ATTATGTTTTACTTGAGATTT
*
12595516 -TTATTTTTTACCTT-AG-TTT
1 ATTATGTTTTA-CTTGAGATTT
*
12595535 ATTAT-ATTTACTT
1 ATTATGTTTTACTT
12595548 TAAAGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.11
19 7 0.25
20 15 0.54
21 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (21 bp):
ATTATGTTTTACTTGAGATTT
Found at i:12598089 original size:30 final size:30
Alignment explanation
Indices: 12598055--12598116 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12598045 CTTAACTAAA
*
12598055 TTACAAAATGGTCATTAAATTATTCAAAAG
1 TTACAAAATAGTCATTAAATTATTCAAAAG
* *
12598085 TTACAAAATAGTTATTAAATTATTCTAAAG
1 TTACAAAATAGTCATTAAATTATTCAAAAG
12598115 TT
1 TT
12598117 TTTATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (30 bp):
TTACAAAATAGTCATTAAATTATTCAAAAG
Found at i:12602281 original size:19 final size:20
Alignment explanation
Indices: 12602247--12602284 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12602237 AAGCAGTCTG
*
12602247 TAAAAAATGTAGTATATAAA
1 TAAAAAATATAGTATATAAA
12602267 TAAAAAATATA-TATATAA
1 TAAAAAATATAGTATATAA
12602285 TATGATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAAAATATAGTATATAAA
Found at i:12603434 original size:20 final size:21
Alignment explanation
Indices: 12603396--12603435 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12603386 AAATCAAATG
*
12603396 AAAATAAAAATCTTGAAATTC
1 AAAATAAAAATATTGAAATTC
*
12603417 AAAATAAAATTATT-AAATT
1 AAAATAAAAATATTGAAATT
12603436 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATAAAAATATTGAAATTC
Found at i:12607294 original size:30 final size:31
Alignment explanation
Indices: 12607242--12607342 Score: 109
Period size: 30 Copynumber: 3.3 Consensus size: 31
12607232 ATATTTTATG
* *
12607242 TATCATTATATTAAATTATTTAAATATGATT
1 TATCATTATATTAAAATATTTAAATATAATT
12607273 TATCATTATA-TAAAATATTTAAATATAATT
1 TATCATTATATTAAAATATTTAAATATAATT
* * * *
12607303 TCTTATTGTATTTAAAAT-TTTAAA-ATATTT
1 TATCATTATA-TTAAAATATTTAAATATAATT
12607333 TATCTATTAT
1 TATC-ATTAT
12607343 TAAATTTACA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
30 32 0.55
31 20 0.34
32 6 0.10
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (31 bp):
TATCATTATATTAAAATATTTAAATATAATT
Found at i:12613424 original size:21 final size:21
Alignment explanation
Indices: 12613400--12613464 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
12613390 TATTGGTTTA
*
12613400 TTGCGGATCAAGTCAAGTTAC
1 TTGCGGAACAAGTCAAGTTAC
12613421 TTGCGGAACAAGTCAAGTTAC
1 TTGCGGAACAAGTCAAGTTAC
*
12613442 TTGCGGAACAAGTCAAGTCAC
1 TTGCGGAACAAGTCAAGTTAC
12613463 TT
1 TT
12613465 TCTATAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (21 bp):
TTGCGGAACAAGTCAAGTTAC
Found at i:12620775 original size:24 final size:24
Alignment explanation
Indices: 12620743--12620791 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12620733 GTCTTTTACC
*
12620743 ACCCTTAAAGGGCTTTCATATACT
1 ACCCGTAAAGGGCTTTCATATACT
*
12620767 ACCCGTAAAGGTCTTTCATATACT
1 ACCCGTAAAGGGCTTTCATATACT
12620791 A
1 A
12620792 GTGTGCAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (24 bp):
ACCCGTAAAGGGCTTTCATATACT
Found at i:12630232 original size:8 final size:7
Alignment explanation
Indices: 12630197--12630238 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
12630187 TTTTTAACGC
12630197 ATATTTT
1 ATATTTT
12630204 ATATTTT
1 ATATTTT
*
12630211 ATAATTT
1 ATATTTT
*
12630218 ATA-TAT
1 ATATTTT
12630224 ATATTTAT
1 ATATTT-T
12630232 ATATTTT
1 ATATTTT
12630239 TCTTTATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
7 18 0.60
8 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:12635242 original size:21 final size:24
Alignment explanation
Indices: 12635217--12635267 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
12635207 AAAAATATTT
*
12635217 AAAAATATAAAAA-AA-AAGAAAG
1 AAAAATAAAAAAAGAAGAAGAAAG
12635239 AAAAAGTAAAAAAAGAAGAAGAAAG
1 AAAAA-TAAAAAAAGAAGAAGAAAG
12635264 AAAA
1 AAAA
12635268 TAGAAAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 2 0.08
25 11 0.44
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (24 bp):
AAAAATAAAAAAAGAAGAAGAAAG
Found at i:12635249 original size:19 final size:18
Alignment explanation
Indices: 12635227--12635267 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
12635217 AAAAATATAA
12635227 AAAAAAAGAAAGAA-AAAG
1 AAAAAAAG-AAGAAGAAAG
12635245 TAAAAAAAGAAGAAGAAAG
1 -AAAAAAAGAAGAAGAAAG
12635264 AAAA
1 AAAA
12635268 TAGAAAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAGAAGAAAG
Found at i:12635251 original size:18 final size:18
Alignment explanation
Indices: 12635228--12635274 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
12635218 AAAATATAAA
12635228 AAAAAAGAAAGAA-AAAG
1 AAAAAAGAAAGAAGAAAG
12635245 TAAAAAA-AGAAGAAGAAAG
1 -AAAAAAGA-AAGAAGAAAG
*
12635264 AAAATAGAAAG
1 AAAAAAGAAAG
12635275 GCCAAGGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 19 0.76
19 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAAAAGAAAGAAGAAAG
Found at i:12636617 original size:88 final size:88
Alignment explanation
Indices: 12636464--12637019 Score: 767
Period size: 88 Copynumber: 6.3 Consensus size: 88
12636454 GTGAAGATAA
* * * *
12636464 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACCCGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
12636529 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
12636552 CAGATCTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
12636617 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* ** *
12636640 CAGATCTTGCCTTCTTGCACTGACAGTAAAGCAGATCGAAGACACCAGCCTTGCCTCCTTAGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
* *
12636705 GTAGCGGAGCAAGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
12636728 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
*
12636793 GCAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
12636816 CAGATCTTGCCTT-CTAGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
1 CAGATCTTGCCTTCCT-GCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGT
* *
12636880 TGCAGCGGAGCAGATTGAAAATAG
65 TGCAGCGGAGCAGGTTAAAAATAG
* ** * ** * * *
12636904 CAGATATTGCCTTTATGTACTGACAATGAAGTAGATCGAA-AGCACAAAGCCTTGCCTCCTTAGG
1 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGA-CAC-CAGCCTTGCCTCCCTAGG
* * *
12636968 TTGCAGCGGAGCAGGTTGAAAACAC
64 TTGCAGCGGAGCAGGTTAAAAATAG
**
12636993 CAG-TCTTGCCTTCCTATACTGACAGCG
1 CAGATCTTGCCTTCCTGCACTGACAGCG
12637020 GAGTAGACTT
Statistics
Matches: 421, Mismatches: 43, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
87 3 0.01
88 377 0.90
89 41 0.10
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:12636942 original size:264 final size:265
Alignment explanation
Indices: 12636464--12637007 Score: 846
Period size: 264 Copynumber: 2.1 Consensus size: 265
12636454 GTGAAGATAA
* * *
12636464 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACCCGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
12636529 GCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGA
66 GCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGA
* *
12636594 CACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCTTGCA
131 CACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGATTAAAAATAGCAGATATTGCCTTCTTGCA
* * *
12636659 CTGACAGTAAAGCAGATCG-AAG-ACACCAGCCTTGCCTCCTTAGGTTGTAGCGGAGCAAGTTAA
196 CTGACAATAAAGCAGATCGAAAGCACA-AAGCCTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTAA
* *
12636722 AAATAG
260 AAACAC
12636728 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
12636793 GCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT-CTAGCACCGACAGCGAAGCAGATCGAAG
66 GCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCT-GCACCGACAGCGAAGCAGATCGAAG
* *
12636857 ACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGATTGAAAATAGCAGATATTGCCTT-TATG
130 ACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGATTAAAAATAGCAGATATTGCCTTCT-TG
* * * * *
12636921 TACTGACAATGAAGTAGATCGAAAGCACAAAGCCTTGCCTCCTTAGGTTGCAGCGGAGCAGGTTG
194 CACTGACAATAAAGCAGATCGAAAGCACAAAGCCTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTA
12636986 AAAACAC
259 AAAACAC
12636993 CAG-TCTTGCCTTCCT
1 CAGATCTTGCCTTCCT
12637008 ATACTGACAG
Statistics
Matches: 256, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
263 3 0.01
264 207 0.81
265 43 0.17
266 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (265 bp):
CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGA
CACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGATTAAAAATAGCAGATATTGCCTTCTTGCA
CTGACAATAAAGCAGATCGAAAGCACAAAGCCTTGCCTCCTTAGGTTGCAGCGGAGCAAGTTAAA
AACAC
Found at i:12637137 original size:44 final size:44
Alignment explanation
Indices: 12637087--12637417 Score: 242
Period size: 44 Copynumber: 7.6 Consensus size: 44
12637077 GAGACCAGCC
* *
12637087 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGGAAATTACAAATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCGAAATTACAAATCT
* * * * * ** * *
12637131 TATCTCCCTAAGAAGTAGTGGAGCA-GATCGAAGTCCCCAACCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCGAAATTACAAATCT
* * ** *
12637174 TATCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCGAAATTACAAATCT
* * * * ** * **
12637218 TATCTCCCTAAGCAGGAGTGGAGCA-GATCGAAGTCCCCAGCCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCGAAATTACAAATCT
* * *
12637261 TATCTCACTGAGCAGCAGTGGAGTAGGTT-GAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCG-AAATTACAAATCT
* * * * ** * *
12637305 TATCTCCCTAAGCAGTAGTAGAGCA-GATCGAAGA-CCCCAACCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCGAA-ATTACAAATCT
*
12637348 TACCTCCCTAAGCAGCAGTGGAGTAGGTT-GAAAATTACAAATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTCG-AAATTACAAATCT
* *
12637392 TATCTCCCTAAACAGTAGTGGAGTAG
1 TATCTCCCTAAGCAGCAGTGGAGTAG
12637418 ATCGAAGATA
Statistics
Matches: 205, Mismatches: 74, Indels: 16
0.69 0.25 0.05
Matches are distributed among these distances:
43 92 0.45
44 113 0.55
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (44 bp):
TATCTCCCTAAGCAGCAGTGGAGTAGGTTCGAAATTACAAATCT
Found at i:12637180 original size:87 final size:87
Alignment explanation
Indices: 12637087--12637424 Score: 525
Period size: 87 Copynumber: 3.9 Consensus size: 87
12637077 GAGACCAGCC
*
12637087 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGGAAATTACAAATCTTATCTCCCTAAGAAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAAATCTTATCTCCCTAAGAAGTAGTGG
12637152 AGCAGATCGAAGTCCCCAACCT
66 AGCAGATCGAAGTCCCCAACCT
* * * * *
12637174 TATCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGGAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAAATCTTATCTCCCTAAGAAGTAGTGG
*
12637239 AGCAGATCGAAGTCCCCAGCCT
66 AGCAGATCGAAGTCCCCAACCT
* * * *
12637261 TATCTCACTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTAG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAAATCTTATCTCCCTAAGAAGTAGTGG
*
12637326 AGCAGATCGAAGACCCCAACCT
66 AGCAGATCGAAGTCCCCAACCT
* *
12637348 TACCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAAATCTTATCTCCCTAA-ACAGTAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAAATCTTATCTCCCTAAGA-AGTAGTG
*
12637412 GAGTAGATCGAAG
65 GAGCAGATCGAAG
12637425 ATAGCAAATC
Statistics
Matches: 229, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
87 229 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (87 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAAATCTTATCTCCCTAAGAAGTAGTGG
AGCAGATCGAAGTCCCCAACCT
Found at i:12637275 original size:43 final size:43
Alignment explanation
Indices: 12637129--12637370 Score: 182
Period size: 43 Copynumber: 5.6 Consensus size: 43
12637119 AATTACAAAT
* * *
12637129 CTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGTCCCCAAC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGC
* * * * ** * ** *
12637172 CTTATCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCA-GATCGAAGTCCCCAG-C
*
12637216 CTTATCTCCCTAAGCAGGAGTGGAGCAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGC
* * * * * * ** *
12637259 CTTATCTCACTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCG-AAGTCCCCAG-C
* * * *
12637303 CTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACCCCAAC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGC
*
12637346 CTTACCTCCCTAAGCAGCAGTGGAG
1 CTTATCTCCCTAAGCAGCAGTGGAG
12637371 TAGGTTGAAA
Statistics
Matches: 143, Mismatches: 50, Indels: 12
0.70 0.24 0.06
Matches are distributed among these distances:
43 82 0.57
44 61 0.43
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGC
Found at i:12639111 original size:8 final size:7
Alignment explanation
Indices: 12639076--12639117 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
12639066 TTTTTAACGC
12639076 ATATTTT
1 ATATTTT
12639083 ATATTTT
1 ATATTTT
*
12639090 ATAATTT
1 ATATTTT
*
12639097 ATA-TAT
1 ATATTTT
12639103 ATATTTAT
1 ATATTT-T
12639111 ATATTTT
1 ATATTTT
12639118 CTTTATTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
7 18 0.60
8 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:12647860 original size:2 final size:2
Alignment explanation
Indices: 12647853--12647887 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12647843 GTAAACAAAT
12647853 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
12647888 GATACTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12648951 original size:19 final size:19
Alignment explanation
Indices: 12648927--12648964 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12648917 ATCTTTATAG
*
12648927 TTTTTAAAGGATTAAATAA
1 TTTTTAAAGAATTAAATAA
12648946 TTTTTAAAGAATTAAATAA
1 TTTTTAAAGAATTAAATAA
12648965 AATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
TTTTTAAAGAATTAAATAA
Found at i:12649190 original size:68 final size:68
Alignment explanation
Indices: 12649081--12649216 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
12649071 GCACTGCCAG
* *
12649081 CTGCCAGATATGCCACTACCTGTGTGTTGAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
1 CTGCCAGATACGCCACTACCTGTGTGTTAAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
12649146 TTA
66 TTA
*
12649149 CTGCCAGATACGCCACTACCTGTGTGTTAAGCTTATAAGTTATATAATATTTTCTGATGCTGAAA
1 CTGCCAGATACGCCACTACCTGTGTGTTAAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
12649214 TTA
66 TTA
12649217 ATAGAGTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (68 bp):
CTGCCAGATACGCCACTACCTGTGTGTTAAGCTTATAAGTTATATAATATTTTCCGATGCTGAAA
TTA
Found at i:12664642 original size:7 final size:7
Alignment explanation
Indices: 12664630--12664661 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12664620 TAACATTTTA
12664630 ATCACTC
1 ATCACTC
12664637 ATCACTC
1 ATCACTC
12664644 ATCACTC
1 ATCACTC
12664651 ATCACTC
1 ATCACTC
12664658 ATCA
1 ATCA
12664662 GCCACGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (7 bp):
ATCACTC
Found at i:12669363 original size:19 final size:17
Alignment explanation
Indices: 12669329--12669363 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
12669319 AAAAAATAGT
12669329 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
12669346 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
12669364 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:12678871 original size:15 final size:15
Alignment explanation
Indices: 12678851--12678928 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
12678841 TTTATGGAAA
12678851 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
12678866 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
12678880 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
12678896 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
12678910 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
12678926 ATC
1 ATC
12678929 GAGATATTTG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:12678888 original size:30 final size:30
Alignment explanation
Indices: 12678847--12678928 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
12678837 CATATTTATG
*
12678847 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
12678877 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
12678907 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
12678929 GAGATATTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:12683536 original size:15 final size:15
Alignment explanation
Indices: 12683516--12683623 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
12683506 TTTATGGAAA
12683516 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
12683531 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
12683545 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
12683561 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
12683575 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
12683591 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
12683605 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
12683621 ATC
1 ATC
12683624 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:12683553 original size:30 final size:30
Alignment explanation
Indices: 12683510--12683633 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
12683500 TCCATATTTA
* *
12683510 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
12683540 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
12683570 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
12683600 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
12683631 TGG
1 TGG
12683634 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:12689209 original size:2 final size:2
Alignment explanation
Indices: 12689202--12689229 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12689192 AAAGATAAAG
12689202 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12689230 GATGTTTGGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12696184 original size:79 final size:79
Alignment explanation
Indices: 12696094--12696253 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
12696084 ACTAGTAGTA
12696094 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
1 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
12696159 GATAAGATTCTAGC
66 GATAAGATTCTAGC
12696173 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
1 AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
12696238 GATAAGATTCTAGC
66 GATAAGATTCTAGC
12696252 AG
1 AG
12696254 AGATTATGGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (79 bp):
AGGAGAGGAGGAATCGACTTGTGTTAGAAGATAGATTATCTAGCCTTTATAATCAAAACCCTTCT
GATAAGATTCTAGC
Found at i:12703601 original size:12 final size:12
Alignment explanation
Indices: 12703586--12703618 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12703576 AATTAAAACC
12703586 AAAAAAAAG-AA
1 AAAAAAAAGAAA
12703597 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
12703609 AAAGAAAAGA
1 AAAAAAAAGA
12703619 GAGAAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:12703602 original size:11 final size:11
Alignment explanation
Indices: 12703586--12703618 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
12703576 AATTAAAACC
12703586 AAAAAAAAGAA
1 AAAAAAAAGAA
12703597 AAAAAAAAGAA
1 AAAAAAAAGAA
12703608 AAAAGAAAAGA
1 AAAA-AAAAGA
12703619 GAGAAGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:12707957 original size:5 final size:5
Alignment explanation
Indices: 12707947--12707974 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12707937 CTAACTGCTA
12707947 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
12707975 GAAGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:12720482 original size:125 final size:125
Alignment explanation
Indices: 12720300--12720541 Score: 421
Period size: 125 Copynumber: 1.9 Consensus size: 125
12720290 GCCTCCAGTA
* *
12720300 GGATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
1 GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
* *
12720365 ATGTAGGAAATAATTATTTTTTGACGTTTTTAAGCAAATAGTATAAAATCGCTGATACCG
66 ATGTAGGAAATAATTATTTTTTAACGTTTCTAAGCAAATAGTATAAAATCGCTGATACCG
*
12720425 GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTC
1 GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
* *
12720490 ATGTAGGAAATAATTATTTTTTAACGTTTCTGAGCAAATAGTATCAAATCGC
66 ATGTAGGAAATAATTATTTTTTAACGTTTCTAAGCAAATAGTATAAAATCGC
12720542 GCCCTCGTGG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (125 bp):
GGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTAGACGCGATTTCGCTACAGTTGGTC
ATGTAGGAAATAATTATTTTTTAACGTTTCTAAGCAAATAGTATAAAATCGCTGATACCG
Found at i:12723790 original size:56 final size:57
Alignment explanation
Indices: 12723700--12723809 Score: 170
Period size: 56 Copynumber: 1.9 Consensus size: 57
12723690 GTAAAACTAG
* * *
12723700 GTAAAATTATTACATCCCAAAAAATTTTGTTAATGGTTAGTAA-ACTTATCAAATTAT
1 GTAAAATTATTACAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGA-TTATCAAATTAT
12723757 GTAAAATTATTA-AGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 GTAAAATTATTACAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
12723810 CCGATGAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 36 0.73
57 13 0.27
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (57 bp):
GTAAAATTATTACAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAATTAT
Found at i:12723863 original size:23 final size:23
Alignment explanation
Indices: 12723837--12724087 Score: 322
Period size: 23 Copynumber: 10.3 Consensus size: 23
12723827 GGTTTTTACA
12723837 TTAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
12723860 TTAATTAAATTAGGTTAGGGTTTTT
1 TTAATTAAATTAGGTTAGGG--TTT
12723885 AATTAAATTAAATTAGGTTAGGGTTT
1 --TT-AATTAAATTAGGTTAGGGTTT
*
12723911 TAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
* *
12723934 TAAATTAAATTAGGTTAGGATTTTT
1 TTAATTAAATTAGGTTAGG--GTTT
12723959 AATTAAATTAAATTAGGTTAGGGTTT
1 --TT-AATTAAATTAGGTTAGGGTTT
12723985 TTAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
*
12724008 TAAATTAAATTAGGTTAGGGTTTTT
1 TTAATTAAATTAGGTTAGGG--TTT
12724033 AATTAAATTAAATTAGGTTAGGGTTT
1 --TT-AATTAAATTAGGTTAGGGTTT
*
12724059 TTAATTAAATTACGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTT
12724082 TTAATT
1 TTAATT
12724088 TTAATCAAAT
Statistics
Matches: 206, Mismatches: 7, Indels: 30
0.85 0.03 0.12
Matches are distributed among these distances:
23 126 0.61
24 5 0.02
25 9 0.04
26 9 0.04
27 4 0.02
28 53 0.26
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (23 bp):
TTAATTAAATTAGGTTAGGGTTT
Found at i:12723882 original size:51 final size:50
Alignment explanation
Indices: 12723822--12724087 Score: 368
Period size: 51 Copynumber: 5.3 Consensus size: 50
12723812 GATGAGTTAT
12723822 GTTAGGGTTTTTACATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTA-ATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
*
12723873 GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTAAATTAAATTAG
1 GTTAGGGTTTTTAATT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
*
12723924 GTTAGGG-TTTT-A--AATTAAATTAGGTTAGGATTTTTAATTAAATTAAATTAG
1 GTTAGGGTTTTTAATTAATTAAATTAGGTTAGG--GTTT--TT-AATTAAATTAG
*
12723975 GTTAGGG--TTT--TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAG
1 GTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
*
12724021 GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAC
1 GTTAGGGTTTTTAATT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
12724072 GTTAGGGTTTTTAATT
1 GTTAGGGTTTTTAATT
12724088 TTAATCAAAT
Statistics
Matches: 195, Mismatches: 7, Indels: 26
0.86 0.03 0.11
Matches are distributed among these distances:
46 35 0.18
47 1 0.01
48 6 0.03
49 4 0.02
50 13 0.07
51 136 0.70
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.47
Consensus pattern (50 bp):
GTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAG
Found at i:12723918 original size:74 final size:74
Alignment explanation
Indices: 12723837--12724087 Score: 457
Period size: 74 Copynumber: 3.4 Consensus size: 74
12723827 GGTTTTTACA
*
12723837 TTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
12723902 TTAGGGTTT
66 TTAGGGTTT
* *
12723911 TAAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGATTTTTAATTAAATTAAATTAGG
1 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
12723976 TTAGGGTTT
66 TTAGGGTTT
12723985 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
12724050 TTAGGGTTT
66 TTAGGGTTT
* *
12724059 TTAATTAAATTACGTTAGGGTTTTTAATT
1 TTAATTAAATTAGGTTAGGGTTTTAAATT
12724088 TTAATCAAAT
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 170 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (74 bp):
TTAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
TTAGGGTTT
Found at i:12726530 original size:30 final size:29
Alignment explanation
Indices: 12726485--12726542 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
12726475 TTGAAGGAAA
* *
12726485 TTGAGAGGATTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTGGAAGGAAATTGAGAGT
12726514 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAA-TTTGGAAGGAAATTGAGAG
12726543 AATTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.29
Consensus pattern (29 bp):
TTGAGAGAATTTGGAAGGAAATTGAGAGT
Found at i:12726539 original size:22 final size:22
Alignment explanation
Indices: 12726514--12726576 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
12726504 ATTTGAGAGT
*
12726514 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
*
12726536 TTGAGAGAATTTTTGAAGTAAA
1 TTGAGAGAATTTTTGAAGGAAA
12726558 TTGAGAGAATTTTTGAAGG
1 TTGAGAGAATTTTTGAAGG
12726577 GTATGAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:12727632 original size:23 final size:24
Alignment explanation
Indices: 12727597--12727642 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12727587 TTAATCTTTA
12727597 TATTTTTATTTTTAAAAATTTAAT
1 TATTTTTATTTTTAAAAATTTAAT
*
12727621 TATTTTTATTTTT-TAAATTTAA
1 TATTTTTATTTTTAAAAATTTAA
12727643 AAATTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTTTATTTTTAAAAATTTAAT
Found at i:12727660 original size:31 final size:31
Alignment explanation
Indices: 12727593--12727661 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
12727583 TAATTTAATC
** *
12727593 TTTATATTTTTATTTTTAAAAATTTAATTATT
1 TTTAT-TTTTTAAATTTAAAAATTTAATTATA
12727625 TTTATTTTTTAAATTTAAAAATTTAAGTT-TA
1 TTTATTTTTTAAATTTAAAAATTTAA-TTATA
12727656 TTTATT
1 TTTATT
12727662 AACGTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTATTTTTTAAATTTAAAAATTTAATTATA
Found at i:12753210 original size:24 final size:24
Alignment explanation
Indices: 12753183--12753234 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12753173 TTAGTAAGTC
*
12753183 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12753207 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12753231 AAAT
1 AAAT
12753235 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.