Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2485
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: 359192
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 4
Found at i:88566 original size:12 final size:12
Alignment explanation
Indices: 88551--88648 Score: 55
Period size: 11 Copynumber: 8.2 Consensus size: 12
88541 TAATATTTAT
88551 ATTTAATATAAA
1 ATTTAATATAAA
88563 ATTT-A-ATAAA
1 ATTTAATATAAA
*
88573 A-TTAATTTTATAA
1 ATTTAA-TATA-AA
* *
88586 ATTAAATAATATTA
1 ATTTAAT-ATA-AA
88600 ATTTAAT-TAAAA
1 ATTTAATAT-AAA
* *
88612 ATTTTATTTAAAA
1 ATTTAATAT-AAA
88625 ATTTAA-ATAAA
1 ATTTAATATAAA
88636 ATTTAA-ATAAA
1 ATTTAATATAAA
88647 AT
1 AT
88649 AAAAATAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
9 2 0.03
10 7 0.10
11 17 0.25
12 15 0.22
13 15 0.22
14 13 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTAATATAAA
Found at i:88622 original size:17 final size:18
Alignment explanation
Indices: 88563--88622 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
88553 TTAATATAAA
*
88563 ATTTAATAAAATTAATTTT
1 ATTTAATTAAA-TAATTTT
* *
88582 A-TAAATTAAATAATATTA
1 ATTTAATTAAATAAT-TTT
88600 ATTTAATTAAA-AATTTT
1 ATTTAATTAAATAATTTT
88617 ATTTAA
1 ATTTAA
88623 AAATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 12 0.35
18 13 0.38
19 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAATTAAATAATTTT
Found at i:88638 original size:11 final size:11
Alignment explanation
Indices: 88622--88658 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
88612 ATTTTATTTA
88622 AAAATTTAAAT
1 AAAATTTAAAT
88633 AAAATTTAAAT
1 AAAATTTAAAT
**
88644 AAAATAAAAAT
1 AAAATTTAAAT
88655 AAAA
1 AAAA
88659 ATGATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATTTAAAT
Found at i:89718 original size:83 final size:84
Alignment explanation
Indices: 89624--89789 Score: 255
Period size: 84 Copynumber: 2.0 Consensus size: 84
89614 AAATAAGATC
* * *
89624 ATATTAATTTTTTCTTTTTATATTATT-GATTAAAAATTATTATATTGATAAATTA-CAAACAAA
1 ATATTAATTTTTTATTTTTATATTATTAAATAAAAAATTATTATATTGATAAATTATC-AACAAA
89687 AATTAAAATATTAAATAATT
65 AATTAAAATATTAAATAATT
* *
89707 ATATTCATTTTTTATTTTTATATTATTAAATAAAAAATTATTATATTGATAAATTATCAATAAAA
1 ATATTAATTTTTTATTTTTATATTATTAAATAAAAAATTATTATATTGATAAATTATCAACAAAA
*
89772 ATTAAAATATTGAATAAT
66 ATTAAAATATTAAATAAT
89790 AATACAAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
83 25 0.33
84 49 0.65
85 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (84 bp):
ATATTAATTTTTTATTTTTATATTATTAAATAAAAAATTATTATATTGATAAATTATCAACAAAA
ATTAAAATATTAAATAATT
Found at i:89780 original size:42 final size:42
Alignment explanation
Indices: 89655--89780 Score: 103
Period size: 42 Copynumber: 3.0 Consensus size: 42
89645 ATTATTGATT
*
89655 AAAAATTATTATATTGATAAATTA-CAAACAAAAATTAAAATA
1 AAAAATTATTATATTGATAAATTATC-AATAAAAATTAAAATA
** * * *** *** **
89697 TTAAATAATTATATTCATTTTTTATTTTTATATTATT-AAATA
1 AAAAATTATTATATTGATAAATTATCAATA-AAAATTAAAATA
89739 AAAAATTATTATATTGATAAATTATCAATAAAAATTAAAATA
1 AAAAATTATTATATTGATAAATTATCAATAAAAATTAAAATA
89781 TTGAATAATA
Statistics
Matches: 56, Mismatches: 25, Indels: 6
0.64 0.29 0.07
Matches are distributed among these distances:
41 4 0.07
42 48 0.86
43 4 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (42 bp):
AAAAATTATTATATTGATAAATTATCAATAAAAATTAAAATA
Found at i:91188 original size:13 final size:13
Alignment explanation
Indices: 91170--91194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
91160 AAATTTAAAA
91170 ATTATTTTATATT
1 ATTATTTTATATT
91183 ATTATTTTATAT
1 ATTATTTTATAT
91195 ATTTTATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTTTATATT
Found at i:91249 original size:13 final size:14
Alignment explanation
Indices: 91233--91265 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
91223 TTTTTAATTA
91233 TTAAAAT-ATTAAT
1 TTAAAATAATTAAT
91246 TTAAAATAAATTAAT
1 TTAAAAT-AATTAAT
91261 TTAAA
1 TTAAA
91266 TTAACAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATAATTAAT
Found at i:91275 original size:36 final size:36
Alignment explanation
Indices: 91207--91276 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
91197 TTTATATTTA
* * **
91207 AATTTAAATACAATTATTTTTAATTATTAAAATATT
1 AATTTAAATACAATTAATTTAAATTAACAAAATATT
91243 AATTTAAAATA-AATTAATTTAAATTAACAAAATA
1 AATTT-AAATACAATTAATTTAAATTAACAAAATA
91277 CCTATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 24 0.83
37 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (36 bp):
AATTTAAATACAATTAATTTAAATTAACAAAATATT
Found at i:94233 original size:16 final size:16
Alignment explanation
Indices: 94212--94270 Score: 84
Period size: 17 Copynumber: 3.7 Consensus size: 16
94202 AATCTAATTT
94212 TAATTTAAAATTAAAA
1 TAATTTAAAATTAAAA
*
94228 TAATTTAAATTTAAAAA
1 TAATTTAAAATT-AAAA
*
94245 TAATTTAAAATTTAAA
1 TAATTTAAAATTAAAA
94261 -AATTTAAAAT
1 TAATTTAAAAT
94271 AATTAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
15 10 0.26
16 14 0.36
17 15 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTTAAAATTAAAA
Found at i:94236 original size:33 final size:32
Alignment explanation
Indices: 94175--94268 Score: 98
Period size: 33 Copynumber: 2.9 Consensus size: 32
94165 ATCAAAAATT
* * *
94175 AAAATAATTTAAATTCTAAACAACTTAAATCTA
1 AAAATAATTTAAAAT-TAAAAAATTTAAATCTA
*** *
94208 ATTTTAATTTAAAATTAAAATAATTTAAATTTA
1 AAAATAATTTAAAATTAAAA-AATTTAAATCTA
*
94241 AAAATAATTTAAAATTTAAAAATTTAAA
1 AAAATAATTTAAAATTAAAAAATTTAAA
94269 ATAATTAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
32 12 0.24
33 37 0.76
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (32 bp):
AAAATAATTTAAAATTAAAAAATTTAAATCTA
Found at i:94246 original size:17 final size:17
Alignment explanation
Indices: 94212--94263 Score: 79
Period size: 18 Copynumber: 3.1 Consensus size: 17
94202 AATCTAATTT
*
94212 TAATTTAAAATT-AAAA
1 TAATTTAAATTTAAAAA
94228 TAATTTAAATTTAAAAA
1 TAATTTAAATTTAAAAA
94245 TAATTTAAAATTTAAAAA
1 TAATTT-AAATTTAAAAA
94263 T
1 T
94264 TTAAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
16 11 0.33
17 10 0.30
18 12 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATTTAAATTTAAAAA
Found at i:94276 original size:17 final size:17
Alignment explanation
Indices: 94212--94285 Score: 84
Period size: 15 Copynumber: 4.4 Consensus size: 17
94202 AATCTAATTT
94212 TAATTTAAAA-TTAAAA
1 TAATTTAAAATTTAAAA
94228 TAATTT-AAATTTAAAAA
1 TAATTTAAAATTT-AAAA
94245 TAATTTAAAATTT-AAA
1 TAATTTAAAATTTAAAA
94261 -AATTTAAAATAATTAAAA
1 TAATTTAAAAT--TTAAAA
94279 TTAATTT
1 -TAATTT
94286 GATGTGAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.26
16 11 0.22
17 12 0.24
18 9 0.18
20 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTTAAAATTTAAAA
Found at i:94280 original size:16 final size:16
Alignment explanation
Indices: 94154--94284 Score: 63
Period size: 17 Copynumber: 7.9 Consensus size: 16
94144 AATTGATACG
* *
94154 AATTTAAAATTATCAA
1 AATTTAAAATAATTAA
* *
94170 AAATTAAAATAATTTA
1 AATTTAAAATAATTAA
*
94186 AATTCTAAACA-ACTT-A
1 AATT-TAAA-ATAATTAA
* **
94202 AATCTAATTTTAATTTAA
1 AATTTAA-AATAA-TTAA
*
94220 AA-TTAAAATAATTTA
1 AATTTAAAATAATTAA
94235 AATTTAAAAATAATTTAA
1 AATTT-AAAATAA-TTAA
*
94253 AATTTAAAA-ATTTAA
1 AATTTAAAATAATTAA
94268 AATAATTAAAATTAATT
1 AAT--TTAAAA-TAATT
94285 TGATGTGAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
15 15 0.18
16 26 0.31
17 29 0.34
18 12 0.14
19 3 0.04
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAAATAATTAA
Found at i:96617 original size:97 final size:96
Alignment explanation
Indices: 96367--96606 Score: 376
Period size: 97 Copynumber: 2.5 Consensus size: 96
96357 AGTGAAAAAT
* *
96367 GAGGTTGGAGTATCCC-TCGGAGGAATGGGATTGGAATGTCCTCGATGATGACAATTTAAGCGAG
1 GAGGTTGGAGTATCCCTTCGGAGGAATGGG-TTGGAATATCCCCGATGATGACAATTTAAGCGAG
*
96431 AATAATATTTAAACTTTGATGAGTTTAAAAGC
65 AATAAGATTTAAACTTTGATGAGTTTAAAAGC
*
96463 GGGGTTGGAGTAT-CCTCTCGGAGGAATGAGGTTGGAATATCCCCGATGATGACAATTTAAGCGA
1 GAGGTTGGAGTATCCCT-TCGGAGGAATG-GGTTGGAATATCCCCGATGATGACAATTTAAGCGA
96527 GAATAAGATTTAAACTTTGATGAGTTTAAAAGC
64 GAATAAGATTTAAACTTTGATGAGTTTAAAAGC
* *
96560 GAGGTTGGAGTATCCCTTCGGAGGAATAGGGTTAGAGTATCCCCGAT
1 GAGGTTGGAGTATCCCTTCGGAGGAAT-GGGTTGGAATATCCCCGAT
96607 AAATAAAATT
Statistics
Matches: 132, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
95 2 0.02
96 12 0.09
97 112 0.85
98 6 0.05
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (96 bp):
GAGGTTGGAGTATCCCTTCGGAGGAATGGGTTGGAATATCCCCGATGATGACAATTTAAGCGAGA
ATAAGATTTAAACTTTGATGAGTTTAAAAGC
Found at i:98161 original size:114 final size:115
Alignment explanation
Indices: 97992--98209 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 115
97982 TCCAATTTTA
97992 CAATCATTTACGAAAATAATAGCTTAAAAGAATTGTTTTGATATTTTATATCAAAACAATAATTG
1 CAATCATTTACGAAAATAATAGCTTAAAAGAATTGTTTTGATATTTTATATCAAAACAATAATTG
* * *
98057 ATGTCCAATGGTTGGAGATTTTTTCTTCATGGGTGGCCTAAGTTCAAATG
66 AGGTCCAATGATTGAAGATTTTTTCTTCATGGGTGGCCTAAGTTCAAATG
*
98107 CAATCATTTACGGAAATAAT-GACTTAAAA-AATTGTTTTGATATTTTATATCAAAACAATAATT
1 CAATCATTTACGAAAATAATAG-CTTAAAAGAATTGTTTTGATATTTTATATCAAAACAATAATT
* *
98170 GAGGTCCAATGATTGAAGCTTTTTTCTTCGTGGGTGGCCT
65 GAGGTCCAATGATTGAAGATTTTTTCTTCATGGGTGGCCT
98210 GGGTTTAAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 70 0.73
115 26 0.27
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (115 bp):
CAATCATTTACGAAAATAATAGCTTAAAAGAATTGTTTTGATATTTTATATCAAAACAATAATTG
AGGTCCAATGATTGAAGATTTTTTCTTCATGGGTGGCCTAAGTTCAAATG
Found at i:99129 original size:336 final size:336
Alignment explanation
Indices: 98516--99149 Score: 1268
Period size: 336 Copynumber: 1.9 Consensus size: 336
98506 GGATCGCTCT
98516 AAAAATCTAATATGCTCTCACACTCAATGGAAATTTCTTTTTCACCGTTCAGATTTTTCAAATAA
1 AAAAATCTAATATGCTCTCACACTCAATGGAAATTTCTTTTTCACCGTTCAGATTTTTCAAATAA
98581 TCACTGGAACCTCTTCAATCGGAAATCTCACTTTGTTTTTTTTGGGAAAGCTTTCTCTCTCTCTC
66 TCACTGGAACCTCTTCAATCGGAAATCTCACTTTGTTTTTTTTGGGAAAGCTTTCTCTCTCTCTC
98646 TTTTTTTTTCTTTACTCGACCCCTCCCATTTTATCAAATATTTTTATCTTTTTTTTTCTTTTTTT
131 TTTTTTTTTCTTTACTCGACCCCTCCCATTTTATCAAATATTTTTATCTTTTTTTTTCTTTTTTT
98711 CATTTTCGATCAATTTGTTAGCCACCAACTTTATCCATCGAAAGTTAATTTGTTTTTATTATTTT
196 CATTTTCGATCAATTTGTTAGCCACCAACTTTATCCATCGAAAGTTAATTTGTTTTTATTATTTT
98776 TTTCGATTTTTCGATTTTTTCATAACTTTTTCTTTTATAAAGTTAATTTGTTTTTATTATTTTTT
261 TTTCGATTTTTCGATTTTTTCATAACTTTTTCTTTTATAAAGTTAATTTGTTTTTATTATTTTTT
98841 TAGATTTTTTC
326 TAGATTTTTTC
98852 AAAAATCTAATATGCTCTCACACTCAATGGAAATTTCTTTTTCACCGTTCAGATTTTTCAAATAA
1 AAAAATCTAATATGCTCTCACACTCAATGGAAATTTCTTTTTCACCGTTCAGATTTTTCAAATAA
98917 TCACTGGAACCTCTTCAATCGGAAATCTCACTTTGTTTTTTTTGGGAAAGCTTTCTCTCTCTCTC
66 TCACTGGAACCTCTTCAATCGGAAATCTCACTTTGTTTTTTTTGGGAAAGCTTTCTCTCTCTCTC
98982 TTTTTTTTTCTTTACTCGACCCCTCCCATTTTATCAAATATTTTTATCTTTTTTTTTCTTTTTTT
131 TTTTTTTTTCTTTACTCGACCCCTCCCATTTTATCAAATATTTTTATCTTTTTTTTTCTTTTTTT
99047 CATTTTCGATCAATTTGTTAGCCACCAACTTTATCCATCGAAAGTTAATTTGTTTTTATTATTTT
196 CATTTTCGATCAATTTGTTAGCCACCAACTTTATCCATCGAAAGTTAATTTGTTTTTATTATTTT
99112 TTTCGATTTTTCGATTTTTTCATAACTTTTTCTTTTAT
261 TTTCGATTTTTCGATTTTTTCATAACTTTTTCTTTTAT
99150 TTCTGTCATT
Statistics
Matches: 298, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
336 298 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.51
Consensus pattern (336 bp):
AAAAATCTAATATGCTCTCACACTCAATGGAAATTTCTTTTTCACCGTTCAGATTTTTCAAATAA
TCACTGGAACCTCTTCAATCGGAAATCTCACTTTGTTTTTTTTGGGAAAGCTTTCTCTCTCTCTC
TTTTTTTTTCTTTACTCGACCCCTCCCATTTTATCAAATATTTTTATCTTTTTTTTTCTTTTTTT
CATTTTCGATCAATTTGTTAGCCACCAACTTTATCCATCGAAAGTTAATTTGTTTTTATTATTTT
TTTCGATTTTTCGATTTTTTCATAACTTTTTCTTTTATAAAGTTAATTTGTTTTTATTATTTTTT
TAGATTTTTTC
Found at i:99268 original size:17 final size:19
Alignment explanation
Indices: 99246--99281 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
99236 TTCTAAGCCA
99246 CTCATTTTC-TTT-TTTTT
1 CTCATTTTCGTTTCTTTTT
99263 CTCATTTTCGTTTCTTTTT
1 CTCATTTTCGTTTCTTTTT
99282 TAATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (19 bp):
CTCATTTTCGTTTCTTTTT
Found at i:101762 original size:20 final size:20
Alignment explanation
Indices: 101726--101795 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
101716 AATCAATTAA
* *
101726 ATAAATAATTT-ATATTTTT
1 ATAAATTATTTAATATTTAT
101745 ATAAATTATTTAATATTTAT
1 ATAAATTATTTAATATTTAT
101765 A-AAATTAATTTAA-ATTATAAT
1 ATAAATT-ATTTAATATT-T-AT
*
101786 ATAAAATATT
1 ATAAATTATT
101796 AATTATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
19 18 0.42
20 15 0.35
21 6 0.14
22 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATTATTTAATATTTAT
Found at i:101784 original size:18 final size:19
Alignment explanation
Indices: 101728--101777 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
101718 TCAATTAAAT
* *
101728 AAATAATTT-ATATTTTTA
1 AAATTATTTAATATTTATA
101746 TAAATTATTTAATATTTATA
1 -AAATTATTTAATATTTATA
101766 AAATTAATTTAA
1 AAATT-ATTTAA
101778 ATTATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTATTTAATATTTATA
Found at i:103783 original size:2 final size:2
Alignment explanation
Indices: 103776--103814 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
103766 ATCCCTCCGC
103776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
103815 GAAGTTGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:107938 original size:14 final size:14
Alignment explanation
Indices: 107919--107947 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
107909 GGCTTGGGTA
107919 GTGGCTAACAGGTG
1 GTGGCTAACAGGTG
107933 GTGGCTAACAGGTG
1 GTGGCTAACAGGTG
107947 G
1 G
107948 CCGTTCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.45, T:0.21
Consensus pattern (14 bp):
GTGGCTAACAGGTG
Found at i:122363 original size:2 final size:2
Alignment explanation
Indices: 122356--122381 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
122346 ATACTTCCAC
122356 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
122382 GTTTATATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:122416 original size:15 final size:16
Alignment explanation
Indices: 122392--122440 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
122382 GTTTATATGC
122392 AAAT-ATAAAT-TTTA
1 AAATAATAAATATTTA
122406 AAATAATAAATATTTA
1 AAATAATAAATATTTA
122422 ATATATAA-AAATATTTA
1 A-A-ATAATAAATATTTA
122439 AA
1 AA
122441 CATCAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.13
15 6 0.19
16 6 0.19
17 11 0.35
18 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAATAAATATTTA
Found at i:122553 original size:21 final size:21
Alignment explanation
Indices: 122529--122587 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
122519 TTTATTTTGT
122529 AAATATAATTATAAAAAATTA
1 AAATATAATTATAAAAAATTA
** *
122550 AAATACCATAATAAAAAAATTA
1 AAATATAATTAT-AAAAAATTA
122572 AAAT-TAATT-TAAAAAA
1 AAATATAATTATAAAAAA
122588 AATCAAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 11 0.35
22 13 0.42
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATATAATTATAAAAAATTA
Found at i:123505 original size:16 final size:16
Alignment explanation
Indices: 123484--123525 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
123474 AATATAAAAT
123484 TAAATTAATTTTTTAA
1 TAAATTAATTTTTTAA
*
123500 -ATAATTAATATTTTAA
1 TA-AATTAATTTTTTAA
123516 TAAATTAATT
1 TAAATTAATT
123526 ATTAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTAATTTTTTAA
Found at i:123759 original size:12 final size:11
Alignment explanation
Indices: 123742--123775 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
123732 AAATAAATAT
123742 AAATTATATAAA
1 AAATTATA-AAA
123754 AAATTATAAAA
1 AAATTATAAAA
123765 AAA-TATAAAA
1 AAATTATAAAA
123775 A
1 A
123776 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 6 0.27
12 8 0.36
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:129121 original size:13 final size:15
Alignment explanation
Indices: 129088--129127 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 15
129078 CAATTCAGTG
129088 TGTATCGATACCAACA
1 TGTATCGATA-CAACA
129104 TGTATCGATAC-A-A
1 TGTATCGATACAACA
129117 TGTATCGATAC
1 TGTATCGATAC
129128 TAAGCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
15 1 0.04
16 10 0.42
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (15 bp):
TGTATCGATACAACA
Found at i:131607 original size:13 final size:13
Alignment explanation
Indices: 131589--131649 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
131579 AGTGCCCATG
*
131589 TATCGATACAGTA
1 TATCGATACAATA
*
131602 TATCGATACAATG
1 TATCGATACAATA
* *
131615 TATCGATATAGTA
1 TATCGATACAATA
*
131628 TATCGATACAATG
1 TATCGATACAATA
131641 TATCGATAC
1 TATCGATAC
131650 TAAGAACACA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:131615 original size:26 final size:26
Alignment explanation
Indices: 131586--131649 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
131576 AATAGTGCCC
131586 ATGTATCGATACAGTATATCGATACA
1 ATGTATCGATACAGTATATCGATACA
*
131612 ATGTATCGATATAGTATATCGATACA
1 ATGTATCGATACAGTATATCGATACA
131638 ATGTATCGATAC
1 ATGTATCGATAC
131650 TAAGAACACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (26 bp):
ATGTATCGATACAGTATATCGATACA
Found at i:136131 original size:3 final size:3
Alignment explanation
Indices: 136123--136168 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
136113 TGAGTCAACT
** **
136123 TCA TCA TCA TCA TCA TCA TCA TTT TCA TCA TCA TTT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
136169 TGATGGTTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.43
Consensus pattern (3 bp):
TCA
Found at i:136140 original size:12 final size:12
Alignment explanation
Indices: 136122--136169 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
136112 CTGAGTCAAC
*
136122 TTCATCATCATC
1 TTCATCATCATT
*
136134 ATCATCATCATT
1 TTCATCATCATT
136146 TTCATCATCATT
1 TTCATCATCATT
136158 TTCATCATCATT
1 TTCATCATCATT
136170 GATGGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (12 bp):
TTCATCATCATT
Found at i:139795 original size:28 final size:28
Alignment explanation
Indices: 139755--139826 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
139745 GGAATAAAGC
** *
139755 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
139783 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
139811 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
139827 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:139884 original size:52 final size:50
Alignment explanation
Indices: 139815--139984 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
139805 AAATAACGAG
* * *
139815 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
139867 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
139920 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
139971 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
139985 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:140003 original size:28 final size:28
Alignment explanation
Indices: 139958--140039 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
139948 AGTGTTTTAA
* *
139958 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
139985 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
140012 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
140040 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:142476 original size:13 final size:13
Alignment explanation
Indices: 142458--142483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
142448 ACAAAGATCC
142458 ATGTATCGATACA
1 ATGTATCGATACA
142471 ATGTATCGATACA
1 ATGTATCGATACA
142484 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142479 original size:33 final size:33
Alignment explanation
Indices: 142437--142503 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
142427 AAAATTTCCA
***
142437 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
142470 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
142503 A
1 A
142504 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:142547 original size:19 final size:18
Alignment explanation
Indices: 142523--142590 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
142513 CAGTAGCTAA
142523 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
142542 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
142557 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
142574 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
142591 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:142563 original size:13 final size:13
Alignment explanation
Indices: 142545--142569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142535 ACAATACTTA
142545 TGTATCGATACAT
1 TGTATCGATACAT
142558 TGTATCGATACA
1 TGTATCGATACA
142570 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:142567 original size:32 final size:32
Alignment explanation
Indices: 142526--142588 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
142516 TAGCTAATTA
*
142526 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
142558 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
142589 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:142670 original size:21 final size:21
Alignment explanation
Indices: 142646--142702 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
142636 CATTTGTAGG
142646 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
142667 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
142688 ATGTATCGATACATT
1 ATGTATCGATACATT
142703 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:142712 original size:1 final size:1
Alignment explanation
Indices: 142706--142758 Score: 79
Period size: 1 Copynumber: 53.0 Consensus size: 1
142696 ATACATTTAA
***
142706 TTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
142759 CAAACACTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:142744 original size:28 final size:28
Alignment explanation
Indices: 142704--142761 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
142694 CGATACATTT
142704 AATTTTTTTTTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTTTTTTTTC
142732 AATTTTTTTTTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTTTTTTTTC
142760 AA
1 AA
142762 ACACTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.86
Consensus pattern (28 bp):
AATTTTTTTTTTTTTTTTTTTTTTTTTC
Found at i:143433 original size:55 final size:55
Alignment explanation
Indices: 143349--143974 Score: 951
Period size: 55 Copynumber: 11.4 Consensus size: 55
143339 ATAAATTGTA
* * * * * *
143349 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
143404 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
143459 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
143514 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
143569 TCCTGTTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
143624 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
143679 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
143734 TCCTGTTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
143789 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
143844 TCCTGCTCGTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
143899 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
143954 TCCTGCTCTTTGGGGACTGAA
1 TCCTGCTCTTTGAGGACTGAA
143975 GCGGAAGGAG
Statistics
Matches: 525, Mismatches: 35, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
54 16 0.03
55 495 0.94
56 14 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:143556 original size:165 final size:165
Alignment explanation
Indices: 143349--143974 Score: 1103
Period size: 165 Copynumber: 3.8 Consensus size: 165
143339 ATAAATTGTA
* * * *
143349 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* * *
143413 TTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAA-AAGTGTCCTGCTCTTTGGGGAAT
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGACT
143477 GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
129 GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
143514 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
143579 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
143644 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
131 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
143679 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
143744 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
143809 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
131 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
143844 TCCTGCTCGTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
143909 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
143974 A
131 A
143975 GCGGAAGGAG
Statistics
Matches: 446, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
164 2 0.00
165 440 0.99
166 4 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (165 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGA
AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:144975 original size:13 final size:13
Alignment explanation
Indices: 144952--144999 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
144942 TTTTCTCTCT
144952 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
144966 TTTTTTTGTTTTG
1 TTTTTTTGTTTTG
* *
144979 TTTTTTTTTTTTC
1 TTTTTTTGTTTTG
144992 TTTTTTTG
1 TTTTTTTG
145000 AAGAGAAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
13 27 0.87
14 4 0.13
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:144978 original size:18 final size:18
Alignment explanation
Indices: 144951--144995 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
144941 CTTTTCTCTC
144951 TTTTTC-TTTGTTTTGTT
1 TTTTTCTTTTGTTTTGTT
* *
144968 TTTTTGTTTTGTTTTTTT
1 TTTTTCTTTTGTTTTGTT
144986 TTTTTCTTTT
1 TTTTTCTTTT
144996 TTTGAAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (18 bp):
TTTTTCTTTTGTTTTGTT
Found at i:157565 original size:28 final size:28
Alignment explanation
Indices: 157525--157596 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
157515 GGAATAAAGC
** *
157525 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
157553 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
157581 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
157597 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:157654 original size:52 final size:50
Alignment explanation
Indices: 157585--157754 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
157575 AAATAACGAG
* * *
157585 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
157637 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
157690 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
157741 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
157755 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:157773 original size:28 final size:28
Alignment explanation
Indices: 157728--157809 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
157718 AGTGTTTTAA
* *
157728 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
157755 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
157782 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
157810 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:160246 original size:13 final size:13
Alignment explanation
Indices: 160228--160253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160218 ACAAAGATCC
160228 ATGTATCGATACA
1 ATGTATCGATACA
160241 ATGTATCGATACA
1 ATGTATCGATACA
160254 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:160249 original size:33 final size:33
Alignment explanation
Indices: 160207--160273 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
160197 AAAATTTCCA
***
160207 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
160240 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
160273 A
1 A
160274 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:160317 original size:19 final size:18
Alignment explanation
Indices: 160293--160360 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
160283 CAGTAGCTAA
160293 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
160312 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
160327 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
160344 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
160361 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:160333 original size:13 final size:13
Alignment explanation
Indices: 160315--160339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160305 ACAATACTTA
160315 TGTATCGATACAT
1 TGTATCGATACAT
160328 TGTATCGATACA
1 TGTATCGATACA
160340 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:160337 original size:32 final size:32
Alignment explanation
Indices: 160296--160358 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
160286 TAGCTAATTA
*
160296 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
160328 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
160359 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:160440 original size:21 final size:21
Alignment explanation
Indices: 160416--160472 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
160406 CATTTGTAGG
160416 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
160437 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
160458 ATGTATCGATACATT
1 ATGTATCGATACATT
160473 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:160482 original size:1 final size:1
Alignment explanation
Indices: 160476--160500 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
160466 ATACATTTAA
160476 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
160501 CAAACACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:161238 original size:17 final size:17
Alignment explanation
Indices: 161216--161251 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
161206 GAAGGTAAGG
161216 TGGCTGGAGTTAATGTT
1 TGGCTGGAGTTAATGTT
161233 TGGCTGGAGTTAATGTT
1 TGGCTGGAGTTAATGTT
161250 TG
1 TG
161252 ACAGCCTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.36, T:0.42
Consensus pattern (17 bp):
TGGCTGGAGTTAATGTT
Found at i:163782 original size:21 final size:21
Alignment explanation
Indices: 163758--163865 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 21
163748 TCATGATTTA
163758 TATGTGAAAGCAAGACTGTTG
1 TATGTGAAAGCAAGACTGTTG
**** * *
163779 TATGTGTTTCTCATGA-T-TTA
1 TATGTG-AAAGCAAGACTGTTG
163799 TATGTGAAAGCAAGACTGTTG
1 TATGTGAAAGCAAGACTGTTG
**** * *
163820 TATGTGTTTCTCATGA-T-TTA
1 TATGTG-AAAGCAAGACTGTTG
163840 TATGTGAAAGCAAGACTGTTG
1 TATGTGAAAGCAAGACTGTTG
163861 TATGT
1 TATGT
163866 ATTTCAGTAA
Statistics
Matches: 57, Mismatches: 24, Indels: 12
0.61 0.26 0.13
Matches are distributed among these distances:
19 8 0.14
20 18 0.32
21 23 0.40
22 8 0.14
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (21 bp):
TATGTGAAAGCAAGACTGTTG
Found at i:163797 original size:41 final size:41
Alignment explanation
Indices: 163740--163870 Score: 253
Period size: 41 Copynumber: 3.2 Consensus size: 41
163730 TTCTCATACT
163740 TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
1 TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
163781 TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
1 TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
163822 TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
1 TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
*
163863 TGTATTTC
1 TGTGTTTC
163871 AGTAAAAGCA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (41 bp):
TGTGTTTCTCATGATTTATATGTGAAAGCAAGACTGTTGTA
Found at i:163804 original size:20 final size:20
Alignment explanation
Indices: 163779--163845 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
163769 AAGACTGTTG
163779 TATGTGTTTCTCATGATTTA
1 TATGTGTTTCTCATGATTTA
**** * *
163799 TATGTG-AAAGCAAGACTGTTG
1 TATGTGTTTCTCATGA-T-TTA
163820 TATGTGTTTCTCATGATTTA
1 TATGTGTTTCTCATGATTTA
163840 TATGTG
1 TATGTG
163846 AAAGCAAGAC
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
19 4 0.12
20 15 0.47
21 9 0.28
22 4 0.12
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (20 bp):
TATGTGTTTCTCATGATTTA
Found at i:164898 original size:26 final size:26
Alignment explanation
Indices: 164869--164924 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
164859 TATAGAGATA
164869 AGATTGATAAAGTTTAACTTTATTTG
1 AGATTGATAAAGTTTAACTTTATTTG
164895 AGATTGATAAAGTTTAACTTTATTTG
1 AGATTGATAAAGTTTAACTTTATTTG
164921 -GATT
1 AGATT
164925 CTAGATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (26 bp):
AGATTGATAAAGTTTAACTTTATTTG
Found at i:165390 original size:52 final size:53
Alignment explanation
Indices: 165329--165430 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 53
165319 TGATATTTAA
* *
165329 TAATTAAAAATTATTTTTTA-TTTAAATTAAT-TATAAAAAATATAAAAATAT
1 TAATTAAAAATAATTTTTAATTTTAAATTAATATATAAAAAATATAAAAATAT
** * *
165380 TAATATAAAAATAATTTTTAATTTTTTATTGATATATAAATAATATAAAAA
1 TAAT-TAAAAATAATTTTTAATTTTAAATTAATATATAAAAAATATAAAAA
165431 AACTGAACGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 4 0.10
52 14 0.33
53 8 0.19
54 16 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (53 bp):
TAATTAAAAATAATTTTTAATTTTAAATTAATATATAAAAAATATAAAAATAT
Found at i:166008 original size:14 final size:14
Alignment explanation
Indices: 165979--166012 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
165969 TAAATATATA
*
165979 AATATT-TTATATT
1 AATATTATTAAATT
165992 AATATTATTAAATT
1 AATATTATTAAATT
166006 AATATTA
1 AATATTA
166013 ATATCATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATTATTAAATT
Found at i:166271 original size:22 final size:20
Alignment explanation
Indices: 166241--166333 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 20
166231 AAAATTTTAT
*
166241 TATTATATAATTTAATTTAAAA
1 TATTATAT-ATTT-ATATAAAA
*
166263 TATTTTATATTTATATAAAA
1 TATTATATATTTATATAAAA
166283 T-TT-TATA-TTA-ATAATTAA
1 TATTATATATTTATATAA--AA
166301 TATTATATAATTT-TA-AAAA
1 TATTATAT-ATTTATATAAAA
*
166320 TA-TATATTTTTATA
1 TATTATATATTTATA
166334 ATATTATATT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
16 4 0.07
17 6 0.10
18 14 0.23
19 8 0.13
20 11 0.18
21 7 0.12
22 10 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATATATTTATATAAAA
Found at i:166341 original size:18 final size:18
Alignment explanation
Indices: 166256--166342 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 18
166246 TATAATTTAA
* *
166256 TTTAAAATATTTTATATT
1 TTTATAATATTATATATT
* * *
166274 TATATAAAATTTTATATT
1 TTTATAATATTATATATT
* * *
166292 AATAATTAATATTATATAAT
1 -TTTA-TAATATTATATATT
*
166312 TTTA-AA-AATATATATT
1 TTTATAATATTATATATT
166328 TTTATAATATTATAT
1 TTTATAATATTATAT
166343 TTTAATTATT
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
16 12 0.24
17 4 0.08
18 21 0.41
19 3 0.06
20 11 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATAATATTATATATT
Found at i:166348 original size:13 final size:13
Alignment explanation
Indices: 166318--166377 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
166308 TAATTTTAAA
*
166318 AATATATATTTTTAT
1 AATAT-TATATTT-T
166333 AATATTATATTTT
1 AATATTATATTTT
* *
166346 AATTATTTTATTTA
1 AA-TATTATATTTT
166360 AATAATTATA-TTT
1 AAT-ATTATATTTT
166373 AATAT
1 AATAT
166378 GATCTAACCA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 2 0.05
13 9 0.24
14 22 0.58
15 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATATTATATTTT
Found at i:166356 original size:16 final size:16
Alignment explanation
Indices: 166297--166376 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 16
166287 ATATTAATAA
*
166297 TTAATATTA-TATAATT
1 TTAATAATATTAT-ATT
*
166313 TTAAAAATA-TATATT
1 TTAATAATATTATATT
*
166328 TTTATAATATTATATT
1 TTAATAATATTATATT
*
166344 TTAAT--TATTTTATT
1 TTAATAATATTATATT
*
166358 TAAAT-A-ATTATA-T
1 TTAATAATATTATATT
166371 TTAATA
1 TTAATA
166377 TGATCTAACC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
13 5 0.10
14 17 0.33
15 10 0.19
16 20 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATAATATTATATT
Found at i:166357 original size:14 final size:14
Alignment explanation
Indices: 166335--166374 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
166325 ATTTTTATAA
*
166335 TATTATATTTTAAT
1 TATTATATTTAAAT
*
166349 TATTTTATTTAAAT
1 TATTATATTTAAAT
*
166363 AATTATATTTAA
1 TATTATATTTAA
166375 TATGATCTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATATTTAAAT
Found at i:174401 original size:2 final size:2
Alignment explanation
Indices: 174390--174429 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
174380 AAGTGTTGTT
* *
174390 TA TA TA -A TA TA TA CA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
174430 TTTATCCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:174458 original size:2 final size:2
Alignment explanation
Indices: 174451--174482 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
174441 GTGGTTTACA
174451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
174483 TTTATTGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175114 original size:16 final size:16
Alignment explanation
Indices: 175093--175123 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
175083 GTTAAAAAAT
175093 CCAAACTCGAAAGAAA
1 CCAAACTCGAAAGAAA
*
175109 CCAAACTTGAAAGAA
1 CCAAACTCGAAAGAA
175124 CCTGAACTCC
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:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (16 bp):
CCAAACTCGAAAGAAA
Found at i:175370 original size:22 final size:22
Alignment explanation
Indices: 175345--175388 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
175335 AAATAGTAAT
175345 TTATCAAAAAA-TAAATTATATC
1 TTAT-AAAAAAGTAAATTATATC
*
175367 TTATAAAAAAGTAGATTATATC
1 TTATAAAAAAGTAAATTATATC
175389 ATGAGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATAAAAAAGTAAATTATATC
Found at i:178408 original size:22 final size:23
Alignment explanation
Indices: 178364--178405 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
178354 TCACATCTCA
178364 TTAATAAATAAATAAATAAAATT
1 TTAATAAATAAATAAATAAAATT
*
178387 TTAA-AAAT-AATTAATAAAA
1 TTAATAAATAAATAAATAAAA
178406 ATTATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAATAAATAAATAAATAAAATT
Found at i:179607 original size:16 final size:16
Alignment explanation
Indices: 179588--179637 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
179578 GCCCAAACTC
**
179588 GAATAAACTTGAACCT
1 GAATAAACCCGAACCT
*
179604 GAATAGACCCGAACCT
1 GAATAAACCCGAACCT
*
179620 GAATAAGCCCGAACCT
1 GAATAAACCCGAACCT
179636 GA
1 GA
179638 GAGAATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (16 bp):
GAATAAACCCGAACCT
Found at i:180195 original size:187 final size:191
Alignment explanation
Indices: 179879--180245 Score: 550
Period size: 187 Copynumber: 1.9 Consensus size: 191
179869 TATGTTAAAG
* * *
179879 AAATAATTTTACTTAAAATTGTGAACACTTTTTTTAAAAAATATATAAATATATCAATTACTAAA
1 AAATAATTTTACTTAAAATTATGAACAATTTTTTTAAAAAATATATAAATATATCAATAACTAAA
* *
179944 TAATACATTTTTCATCAAAACAACAAAAATCTTTTATTAAAATAATAAATTTAAAAGTTTGAGTT
66 CAATACATTTTTCATCAAAACAACAAAAATCTTTTATTAAAATAATAAAGTTAAAAGTTTGAGTT
* *
180009 TAGAA-TT-TATT-TTTTTATAATATTTTA-TTTCTATCTAACTTTTATGTCAACGTAAAAT
131 TAGAAGTTGGATTATTTTTATAATATTTTATTTTC-ATCTAACTCTTATGTCAACGTAAAAT
*
180067 AAATAATTTTACTTAAAATTAT-ATATAATTTTTTTAAAAAATA-ATAAATATATCAATAACTAA
1 AAATAATTTTACTTAAAATTATGA-ACAATTTTTTTAAAAAATATATAAATATATCAATAACTAA
* *
180130 ACAATATATTTTTCATCAAAAACAAGAAAAAT-TTTTATTAAAATAATAAAGTTAAAAGTTTGAG
65 ACAATACATTTTTCATC-AAAACAACAAAAATCTTTTATTAAAATAATAAAGTTAAAAGTTTGAG
* *
180194 TTTAGAAGTTGGGTTATTTTTATAATCTTTTATTTTCATCTAACTCTTATGT
129 TTTAGAAGTTGGATTATTTTTATAATATTTTATTTTCATCTAACTCTTATGT
180246 TAATAAAAAG
Statistics
Matches: 161, Mismatches: 12, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
187 73 0.45
188 53 0.33
189 2 0.01
190 29 0.18
191 4 0.02
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (191 bp):
AAATAATTTTACTTAAAATTATGAACAATTTTTTTAAAAAATATATAAATATATCAATAACTAAA
CAATACATTTTTCATCAAAACAACAAAAATCTTTTATTAAAATAATAAAGTTAAAAGTTTGAGTT
TAGAAGTTGGATTATTTTTATAATATTTTATTTTCATCTAACTCTTATGTCAACGTAAAAT
Found at i:180577 original size:2 final size:2
Alignment explanation
Indices: 180570--180607 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
180560 AATTTATTTA
180570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
180608 TAGGGATCAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180805 original size:14 final size:16
Alignment explanation
Indices: 180781--180812 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
180771 TATAAATTAC
180781 ATTTAATT-AAAAATA
1 ATTTAATTAAAAAATA
180796 ATTT-ATTAAAAAATA
1 ATTTAATTAAAAAATA
180811 AT
1 AT
180813 AATTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAATTAAAAAATA
Found at i:180836 original size:38 final size:40
Alignment explanation
Indices: 180794--180880 Score: 90
Period size: 43 Copynumber: 2.1 Consensus size: 40
180784 TAATTAAAAA
180794 TAATTTATT-AAAAAATAATA-ATTTAAA-TAATATTATTT
1 TAATTTATTAAAAAAATAATATATTTAAATTAA-ATTATTT
* * *
180832 TAATTAAAATTAAAAAAATATTATATTTAAATTTAACTTATTT
1 TAATT--TATTAAAAAAATAATATATTTAAA-TTAAATTATTT
180875 TAATTT
1 TAATTT
180881 GAATCTATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
38 5 0.13
40 3 0.08
41 10 0.26
42 7 0.18
43 11 0.28
44 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (40 bp):
TAATTTATTAAAAAAATAATATATTTAAATTAAATTATTT
Found at i:181163 original size:16 final size:15
Alignment explanation
Indices: 181140--181182 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
181130 TAAAAAAATT
181140 AAAATATAATATAAA
1 AAAATATAATATAAA
181155 AATAATATAA-ATAAA
1 AA-AATATAATATAAA
* *
181170 TAAATATATTATA
1 AAAATATAATATA
181183 TAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATATAATATAAA
Found at i:181171 original size:26 final size:26
Alignment explanation
Indices: 181141--181192 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
181131 AAAAAAATTA
181141 AAATATAATATA-AAAATAATATAAAT
1 AAATA-AATATATAAAATAATATAAAT
* *
181167 AAATAAATATATTATATAATATAAAT
1 AAATAAATATATAAAATAATATAAAT
181193 TACTGATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATAAATATATAAAATAATATAAAT
Found at i:181257 original size:15 final size:16
Alignment explanation
Indices: 181229--181262 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
181219 ATATAAATTT
*
181229 TAAATAAATTATAATA
1 TAAATAAATAATAATA
181245 TAAA-AAATAATAATA
1 TAAATAAATAATAATA
181260 TAA
1 TAA
181263 TATGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAATAAATAATAATA
Found at i:181531 original size:5 final size:5
Alignment explanation
Indices: 181523--181553 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
181513 GGATAGAATT
181523 ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
181554 AAATAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:181592 original size:17 final size:17
Alignment explanation
Indices: 181569--181607 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
181559 ATTAAATTTT
181569 TATATAAAATAAGATATAA
1 TATA-AAAATAAGATA-AA
*
181588 TATAAAAATAATATAAA
1 TATAAAAATAAGATAAA
181605 TAT
1 TAT
181608 TTTATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TATAAAAATAAGATAAA
Found at i:181643 original size:19 final size:20
Alignment explanation
Indices: 181593--181687 Score: 60
Period size: 19 Copynumber: 4.9 Consensus size: 20
181583 TATAATATAA
181593 AAATA-ATATAAATATTTTAT
1 AAATATATAT-AATATTTTAT
*
181613 GAATATAT-TAATATTTTA-
1 AAATATATATAATATTTTAT
* *
181631 AAATTTATATAATATAAATTAT
1 AAATATATATAATAT--TTTAT
*
181653 TAATATAT-TAAT-TTTATAT
1 AAATATATATAATATTT-TAT
*
181672 AAAT-T-TAAAATATTTT
1 AAATATATATAATATTTT
181688 GAATATAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
17 1 0.02
18 12 0.21
19 24 0.41
20 6 0.10
21 9 0.16
22 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
AAATATATATAATATTTTAT
Found at i:181862 original size:16 final size:19
Alignment explanation
Indices: 181822--181863 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
181812 TAAAATTATA
*
181822 ATAATATATTATATCAAAT
1 ATAATATATTATATCAAAG
181841 ATAATA-ATTAT-T-AAAG
1 ATAATATATTATATCAAAG
181857 ATAATAT
1 ATAATAT
181864 TTCACCTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 5 0.24
19 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAATATATTATATCAAAG
Found at i:182410 original size:28 final size:28
Alignment explanation
Indices: 182358--182412 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
182348 AAACACAAAT
*
182358 AATATTATTATTAATTATATTATAATTA
1 AATATTATTATTAATTATATAATAATTA
*
182386 AATATTATTAATTAATTTTA-AATAATT
1 AATATTATT-ATTAATTATATAATAATT
182413 TATTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AATATTATTATTAATTATATAATAATTA
Found at i:182416 original size:25 final size:25
Alignment explanation
Indices: 182354--182441 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 25
182344 AATAAAACAC
*
182354 AAATAATATTATTATTAATTATATTAT
1 AAATAAT-TTATTATTAATTA-ATTTT
* *
182381 AATTAA-ATATTATTAATTAATTTT
1 AAATAATTTATTATTAATTAATTTT
*
182405 AAATAATTTATTA--AATAAATTTT
1 AAATAATTTATTATTAATTAATTTT
*
182428 AAAAAAATTTATTA
1 -AAATAATTTATTA
182442 ACGAGCTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
23 9 0.17
24 21 0.40
25 17 0.33
27 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATAATTTATTATTAATTAATTTT
Found at i:182804 original size:16 final size:16
Alignment explanation
Indices: 182785--182904 Score: 69
Period size: 16 Copynumber: 7.8 Consensus size: 16
182775 TATGATGTAA
182785 TTATATTTATAATATT
1 TTATATTTATAATATT
*
182801 TTATATTTATATAAATT
1 TTATATTTATA-ATATT
* *
182818 TTA-ATATATAAATAAT
1 TTATATTTAT-AATATT
182834 TTATA-TTAT-ATA--
1 TTATATTTATAATATT
*
182846 -TAT-TTTAAAATATT
1 TTATATTTATAATATT
182860 TATATATTTATATCATATT
1 T-TATATTTATA--ATATT
** *
182879 TTA-ATTT-TTTTATA
1 TTATATTTATAATATT
182893 TTATATTTATAA
1 TTATATTTATAA
182905 AATTATGTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
11 6 0.08
12 3 0.04
14 9 0.12
15 4 0.05
16 30 0.38
17 18 0.23
18 2 0.03
19 6 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTTATAATATT
Found at i:182820 original size:27 final size:26
Alignment explanation
Indices: 182786--182898 Score: 86
Period size: 28 Copynumber: 4.0 Consensus size: 26
182776 ATGATGTAAT
182786 TATA-TTTATAATATTTTATATTTATA
1 TATATTTTATAATATTTTATA-TTATA
*
182812 TAAATTTTAATATATAAATAATTTATATTATA
1 TATATTTT-ATA-AT--AT--TTTATATTATA
*
182844 TATATTTTAAAATATTTATATATTTATA
1 TATATTTTATAATATTT-TATA-TTATA
* *
182872 TCATATTTTA-ATTTTTTTATATTATA
1 T-ATATTTTATAATATTTTATATTATA
182898 T
1 T
182899 TTATAAAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
26 11 0.15
27 11 0.15
28 16 0.22
29 10 0.14
30 2 0.03
31 4 0.06
32 12 0.17
33 6 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATTTTATAATATTTTATATTATA
Found at i:182828 original size:32 final size:32
Alignment explanation
Indices: 182792--182908 Score: 95
Period size: 32 Copynumber: 3.8 Consensus size: 32
182782 TAATTATATT
182792 TATAATATTTTATATTTATATAAATTTTAATA
1 TATAATATTTTATATTTATATAAATTTTAATA
* *
182824 TATAAATAATTTATA-TTATATATATTTTAA-A
1 TAT-AATATTTTATATTTATATAAATTTTAATA
* *
182855 -AT-AT-TTATATATTTATATCATATTTTAAT-
1 TATAATATTTTATATTTATAT-AAATTTTAATA
* ** *
182884 TTTTTTATATTATATTTATA-AAATT
1 TATAATATTTTATATTTATATAAATT
182909 ATGTTTATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
27 5 0.07
28 8 0.12
29 9 0.13
30 7 0.10
31 2 0.03
32 28 0.41
33 10 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
TATAATATTTTATATTTATATAAATTTTAATA
Found at i:182877 original size:19 final size:19
Alignment explanation
Indices: 182792--182903 Score: 68
Period size: 21 Copynumber: 5.7 Consensus size: 19
182782 TAATTATATT
182792 TATAATATTT-TATATTTA
1 TATAATATTTATATATTTA
*
182810 TATAA-ATTT-TAATATATA
1 TATAATATTTAT-ATATTTA
* *
182828 AATAATTTATATTATATATATTT
1 TATAA--TAT-TTATATAT-TTA
*
182851 TAAAATATTTATATATTTA
1 TATAATATTTATATATTTA
* * *
182870 TATCATATTTTAATTTTTTTA
1 TATAATA-TTT-ATATATTTA
*
182891 TATTATATTTATA
1 TATAATATTTATA
182904 AAATTATGTT
Statistics
Matches: 72, Mismatches: 13, Indels: 17
0.71 0.13 0.17
Matches are distributed among these distances:
17 5 0.07
18 15 0.21
19 9 0.12
20 14 0.19
21 18 0.25
22 6 0.08
23 5 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TATAATATTTATATATTTA
Found at i:182890 original size:29 final size:27
Alignment explanation
Indices: 182827--182898 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
182817 TTTAATATAT
*
182827 AAATAATT-TATATTATATATATTTTA
1 AAATATTTATATATTATATATATTTTA
182853 AAATATTTATATATTTATATCATATTTT-
1 AAATATTTATATA-TTATAT-ATATTTTA
* *
182881 -AATTTTTTTATATTATAT
1 AAATATTTATATATTATAT
182899 TTATAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.32
27 14 0.35
28 6 0.15
29 7 0.17
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
AAATATTTATATATTATATATATTTTA
Found at i:183030 original size:16 final size:16
Alignment explanation
Indices: 183011--183099 Score: 69
Period size: 16 Copynumber: 5.4 Consensus size: 16
183001 TACGATATAA
183011 TTATATTTATAATATT
1 TTATATTTATAATATT
*
183027 TTATATTTATATAAATT
1 TTATATTTATA-ATATT
* *
183044 TTA-ATATATAAATAAT
1 TTATATTTAT-AATATT
183060 TTATATTATATAA-ATT
1 TTATATT-TATAATATT
183076 TTAAAATATTTAT-ATA-T
1 TT---ATATTTATAATATT
183093 TTATATT
1 TTATATT
183100 ATATTGTATC
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
14 5 0.08
16 26 0.44
17 16 0.27
18 7 0.12
19 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATAATATT
Found at i:183050 original size:18 final size:17
Alignment explanation
Indices: 183011--183078 Score: 74
Period size: 16 Copynumber: 4.2 Consensus size: 17
183001 TACGATATAA
*
183011 TTATATTTATA-ATATT
1 TTATATTTATATAAATT
183027 TTATATTTATATAAATT
1 TTATATTTATATAAATT
183044 TTA-A--TATATAAATAAT
1 TTATATTTATATAAAT--T
183060 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
183076 TTA
1 TTA
183079 AAATATTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
14 9 0.20
16 20 0.43
17 8 0.17
18 9 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:183053 original size:14 final size:14
Alignment explanation
Indices: 183034--183084 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
183024 ATTTTATATT
183034 TATATAAATTTTAA
1 TATATAAATTTTAA
183048 TATATAAATAATTTATA
1 TATATAAAT--TTTA-A
183065 TTATATAAATTTTAA
1 -TATATAAATTTTAA
*
183080 AATAT
1 TATAT
183085 TTATATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 13 0.41
15 1 0.03
16 8 0.25
17 1 0.03
18 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:183069 original size:32 final size:32
Alignment explanation
Indices: 183021--183103 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
183011 TTATATTTAT
* *
183021 AATATTTTATATTTATATAAATTTTAATATATA
1 AATAATTTATA-TTATATAAATTTTAAAATATA
*
183054 AATAATTTATATTATATAAATTTTAAAATATT
1 AATAATTTATATTATATAAATTTTAAAATATA
*
183086 TATATATTTATATTATAT
1 AATA-ATTTATATTATAT
183104 TGTATCATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 22 0.49
33 23 0.51
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTAAAATATA
Found at i:183095 original size:33 final size:33
Alignment explanation
Indices: 183013--183103 Score: 121
Period size: 32 Copynumber: 2.7 Consensus size: 33
183003 CGATATAATT
*
183013 ATATTTATAATATTTTATATTTATATAAATTTTAAT
1 ATATTTAT-ATA-TTTATA-TTATATAAATTTTAAA
**
183049 ATATAAATA-ATTTATATTATATAAATTTTAAA
1 ATATTTATATATTTATATTATATAAATTTTAAA
183081 ATATTTATATATTTATATTATAT
1 ATATTTATATATTTATATTATAT
183104 TGTATCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
32 22 0.45
33 19 0.39
34 1 0.02
35 1 0.02
36 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTTATATATTTATATTATATAAATTTTAAA
Found at i:183102 original size:38 final size:37
Alignment explanation
Indices: 183013--183136 Score: 102
Period size: 38 Copynumber: 3.5 Consensus size: 37
183003 CGATATAATT
*
183013 ATATTTATA-A-TATTTTATATTTATAT-AAATTTT-A
1 ATATTTATATATTATATTATA-TTATATCAAATTTTAA
* *
183047 ATA--TATAAATAAT-TTATATTATAT-AAATTTTAAA
1 ATATTTATATATTATATTATATTATATCAAATTTT-AA
* *
183081 ATATTTATATATTTATATTATATTGTATCATATTTTAA
1 ATATTTATATA-TTATATTATATTATATCAAATTTTAA
* *
183119 TTATTTTTATATTATATT
1 ATATTTATATATTATATT
183137 TATAGAATTG
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
32 17 0.23
33 6 0.08
34 9 0.12
36 5 0.07
37 10 0.14
38 21 0.28
39 6 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (37 bp):
ATATTTATATATTATATTATATTATATCAAATTTTAA
Found at i:183104 original size:11 final size:11
Alignment explanation
Indices: 183088--183140 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
183078 AAAATATTTA
183088 TATATTTATAT
1 TATATTTATAT
183099 TATATTGTATCA-
1 TATATT-TAT-AT
183111 TAT-TTTA-AT
1 TATATTTATAT
*
183120 TATTTTTATAT
1 TATATTTATAT
183131 TATATTTATA
1 TATATTTATA
183141 GAATTGTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
8 1 0.03
9 3 0.08
10 6 0.17
11 19 0.53
12 6 0.17
13 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:184362 original size:6 final size:6
Alignment explanation
Indices: 184353--184424 Score: 51
Period size: 6 Copynumber: 11.7 Consensus size: 6
184343 AGCTTTTATA
* * *
184353 ATATTT ATATTT ATA-TT ATATTG ATA--T ATTTTT ATATTTT ATAATT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATA-TTT ATATTT
184399 ATATTT AAAATATTAT ATATTT ATAT
1 ATATTT ---ATATT-T ATATTT ATAT
184425 AAATTTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
4 2 0.04
5 5 0.10
6 28 0.54
7 11 0.21
9 5 0.10
10 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:184401 original size:21 final size:21
Alignment explanation
Indices: 184346--184404 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
184336 CAAAAACAGC
* *
184346 TTTTATAATATTTATATTTATA
1 TTTTATAAT-TATATTTTTATA
* *
184368 TTATATTGA-TATATTTTTATA
1 TTTTA-TAATTATATTTTTATA
184389 TTTTATAATTATATTT
1 TTTTATAATTATATTT
184405 AAAATATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.07
21 21 0.72
22 4 0.14
23 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATAATTATATTTTTATA
Found at i:184424 original size:8 final size:8
Alignment explanation
Indices: 184347--184425 Score: 58
Period size: 8 Copynumber: 10.0 Consensus size: 8
184337 AAAAACAGCT
184347 TTTATAATA
1 TTTAT-ATA
184356 TTTATAT-
1 TTTATATA
184363 TTATATTATA
1 TT-TA-TATA
*
184373 TTGATATA
1 TTTATATA
*
184381 TTTTTATA
1 TTTATATA
184389 TTT-TATA
1 TTTATATA
*
184396 ATTATAT-
1 TTTATATA
* *
184403 TTAAAATA
1 TTTATATA
184411 -TTATATA
1 TTTATATA
184418 TTTATATA
1 TTTATATA
184426 AATTTTAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
7 17 0.31
8 27 0.49
9 9 0.16
10 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:184435 original size:37 final size:38
Alignment explanation
Indices: 184357--184483 Score: 115
Period size: 37 Copynumber: 3.4 Consensus size: 38
184347 TTTATAATAT
* * *
184357 TTATATTTATATTATATTGATATATTTTTAT-ATTTTATAA
1 TTATATTTA-ATAATATT-ATATATTTATATAAATTT-TAA
184397 TTATATTTAA-AATATTATATATTTATATAAATTTTAA
1 TTATATTTAATAATATTATATATTTATATAAATTTTAA
*
184434 TT-TA-TTAATAATAATTAT-TATATA-ATTAAATTTTAA
1 TTATATTTAATAAT-ATTATATATTTATA-TAAATTTTAA
184470 -TATATTTATATAAT
1 TTATATTTA-ATAAT
184484 TATGTCTTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
35 6 0.08
36 22 0.29
37 24 0.32
38 14 0.18
39 1 0.01
40 9 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.57
Consensus pattern (38 bp):
TTATATTTAATAATATTATATATTTATATAAATTTTAA
Found at i:186258 original size:16 final size:16
Alignment explanation
Indices: 186235--186272 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
186225 TAGTGTGTTA
186235 AATA-TTATTATAATT
1 AATATTTATTATAATT
186250 AATATTTATTATAATT
1 AATATTTATTATAATT
186266 AAT-TTTA
1 AATATTTA
186273 CTAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTTATTATAATT
Found at i:186367 original size:20 final size:21
Alignment explanation
Indices: 186342--186389 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
186332 TTATATATAT
186342 AAATAATAA-AAAATTT-TAAA
1 AAATAATAATAAAATTTGT-AA
*
186362 AAATAA-AATAATATTTGTAA
1 AAATAATAATAAAATTTGTAA
186382 AAATAATA
1 AAATAATA
186390 TTTTGATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATAATAATAAAATTTGTAA
Found at i:186552 original size:23 final size:22
Alignment explanation
Indices: 186526--186571 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
186516 ATATGTATTA
*
186526 TATTTATATTATCATATAAAAAT
1 TATTTA-ATTATCAAATAAAAAT
* *
186549 TATTTAATTTTTAAATAAAAAT
1 TATTTAATTATCAAATAAAAAT
186571 T
1 T
186572 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTAATTATCAAATAAAAAT
Found at i:188808 original size:20 final size:20
Alignment explanation
Indices: 188777--188831 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
188767 AATATAGGAG
188777 AAAAATAA-TTAAATATTAT
1 AAAAATAATTTAAATATTAT
188796 AAAAATAATTTAAA-ATTTAT
1 AAAAATAATTTAAATA-TTAT
* *
188816 ATAAAT-ATATAAATAT
1 AAAAATAATTTAAATAT
188832 AATTTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATAATTTAAATATTAT
Found at i:188826 original size:8 final size:8
Alignment explanation
Indices: 188813--188879 Score: 53
Period size: 8 Copynumber: 7.4 Consensus size: 8
188803 ATTTAAAATT
188813 TATATAAA
1 TATATAAA
188821 TATATAAA
1 TATATAAA
*
188829 TATAATTTTAA
1 TAT-A--TAAA
188840 TATAATAAAA
1 TAT-AT-AAA
188850 TATATAAA
1 TATATAAA
188858 TATAATATTAA
1 TAT-ATA--AA
188869 TATATAAA
1 TATATAAA
188877 TAT
1 TAT
188880 GACATTAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
8 22 0.44
9 7 0.14
10 8 0.16
11 13 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:188869 original size:29 final size:28
Alignment explanation
Indices: 188781--188876 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 28
188771 TAGGAGAAAA
* * *
188781 ATAATTAAATATTATAAAAATAATTTAAA
1 ATAATAAAATA-TATAAATATAATTTAAT
*
188810 ATTTATATAAATATATAAATATAATTTTAAT
1 A-TAATA-AAATATATAAATATAA-TTTAAT
188841 ATAATAAAATATATAAATATAATATTAAT
1 ATAATAAAATATATAAATATAAT-TTAAT
188870 AT-ATAAA
1 ATAATAAA
188877 TATGACATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
28 6 0.10
29 24 0.41
30 17 0.29
31 11 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAATAAAATATATAAATATAATTTAAT
Found at i:188872 original size:19 final size:19
Alignment explanation
Indices: 188838--188890 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
188828 ATATAATTTT
*
188838 AATATAATA-AAATATATA
1 AATATAATATTAATATATA
188856 AATATAATATTAATATATA
1 AATATAATATTAATATATA
* *
188875 AATATGACATTAATAT
1 AATATAATATTAATAT
188891 TGCAACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATAATATTAATATATA
Found at i:191314 original size:2 final size:2
Alignment explanation
Indices: 191307--191351 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
191297 CAATATTATG
191307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191349 TA T
1 TA T
191352 TTCCCATGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:191588 original size:31 final size:32
Alignment explanation
Indices: 191548--191611 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
191538 TATAAATTTG
** *
191548 AAATCTAATTTTATTAAATATTTTAA-TTAATT
1 AAATCTAATTAAATTAAA-ATTTGAATTTAATT
191580 AAAT-TAATTAAATTAAAATTTGAATTTAATT
1 AAATCTAATTAAATTAAAATTTGAATTTAATT
191611 A
1 A
191612 GACGTAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 6 0.21
31 18 0.64
32 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
AAATCTAATTAAATTAAAATTTGAATTTAATT
Found at i:191812 original size:2 final size:2
Alignment explanation
Indices: 191807--191846 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
191797 AAGTATGAAC
191807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
191847 GCTTTACCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:192246 original size:15 final size:16
Alignment explanation
Indices: 192206--192246 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
192196 TCAATTTGTA
*
192206 TTTAA-TTGTTTATTT
1 TTTAATTTGTTTATTG
192221 TTTAGATTTGTTTA-TG
1 TTTA-ATTTGTTTATTG
192237 TTTAATTTGT
1 TTTAATTTGT
192247 GTTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 6 0.26
17 7 0.30
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTAATTTGTTTATTG
Found at i:193327 original size:14 final size:14
Alignment explanation
Indices: 193308--193337 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
193298 TTTTAACTTA
*
193308 AAAAATAATAAATT
1 AAAAATAAAAAATT
193322 AAAAATAAAAAATT
1 AAAAATAAAAAATT
193336 AA
1 AA
193338 TTTAATTATA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAAAAAATT
Found at i:193359 original size:22 final size:21
Alignment explanation
Indices: 193326--193366 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
193316 TAAATTAAAA
193326 ATAAAAAATTAATTTAATTAT
1 ATAAAAAATTAATTTAATTAT
*
193347 ATAAAATATTTAATTTAATT
1 ATAAAA-AATTAATTTAATT
193367 GTAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAAAAATTAATTTAATTAT
Found at i:196484 original size:20 final size:20
Alignment explanation
Indices: 196445--196484 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
196435 TATATCATTA
*
196445 TTTAATTAATAAAAATATTT
1 TTTAATTAATAAAAAAATTT
196465 TTTAA-TAATAAAATAAATTT
1 TTTAATTAATAAAA-AAATTT
196485 ATCAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATTAATAAAAAAATTT
Found at i:204514 original size:13 final size:13
Alignment explanation
Indices: 204496--204523 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
204486 ATACAAAGAT
204496 CAATGTATCGATA
1 CAATGTATCGATA
204509 CAATGTATCGATA
1 CAATGTATCGATA
204522 CA
1 CA
204524 TTGAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:204538 original size:33 final size:33
Alignment explanation
Indices: 204478--204543 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
204468 AAATTCCCAG
*
204478 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATATATCGATACA
**
204511 ATGTATCGATACATTGAAT-AATATATCGATACA
1 ATGTATCGATACAAAG-ATCAATATATCGATACA
204544 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATATATCGATACA
Found at i:204639 original size:21 final size:19
Alignment explanation
Indices: 204575--204646 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
204565 AGTGATACAT
*
204575 TGTATCGATACAACACTTA
1 TGTATCGATACAATACTTA
204594 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
* *
204613 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-ATACT-TA
204634 TGTATCGATACAA
1 TGTATCGATACAA
204647 ATTATTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 30 0.64
20 4 0.09
21 13 0.28
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Done.