Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 122 of 199
Found at i:34870738 original size:112 final size:109
Alignment explanation
Indices: 34870551--34870882 Score: 463
Period size: 112 Copynumber: 3.0 Consensus size: 109
34870541 TCAAATAATT
* *
34870551 AAAAAAAATTTTACATTCATAAAAAAATCACAATAAACATTAAACTAAATACAAACAATTTATAA
1 AAAAAAAA-TTTACATTCAT--AAAAATCACAA-AAA-ACTAAACTAAACACAAACAATTTATAA
* * * *
34870616 CCTAACCATAAATTACTAACAAAATGACTTTCAAATAATTTAAAAAATAC
61 CCTAATCATAAATTACTAACAAAATAACTATAAAATAATTTAAAAAA-AC
* *
34870666 AAAAAGAAATTTACGTTCATGAAAAATCACAAAAAACTAAACTAAACACAAACAATTTATAACCA
1 AAAAA-AAATTTACATTCAT-AAAAATCACAAAAAACTAAACTAAACACAAACAATTTATAACCT
34870731 AATCATAAATTACTAACAAAATAACTATAAAATAA-TTAAAAAAAC
64 AATCATAAATTACTAACAAAATAACTATAAAATAATTTAAAAAAAC
*
34870776 AAAAAAAA-TTACATTCATAAAAATCACAAAATACTAAACTAAACACAAACAATTTATAACCTAA
1 AAAAAAAATTTACATTCATAAAAATCACAAAAAACTAAACTAAACACAAACAATTTATAACCTAA
* *
34870840 TCATAAATTATTAA-AAAGTAACTATAAAATAATTTTAAAAAAA
66 TCATAAATTACTAACAAAATAACTATAAAATAA-TTTAAAAAAA
34870883 TTTACATTAA
Statistics
Matches: 200, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
106 17 0.09
107 57 0.28
108 18 0.09
109 3 0.01
110 7 0.04
111 8 0.04
112 58 0.29
113 3 0.01
114 11 0.05
115 15 0.08
116 3 0.01
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (109 bp):
AAAAAAAATTTACATTCATAAAAATCACAAAAAACTAAACTAAACACAAACAATTTATAACCTAA
TCATAAATTACTAACAAAATAACTATAAAATAATTTAAAAAAAC
Found at i:34871025 original size:98 final size:98
Alignment explanation
Indices: 34870777--34871025 Score: 333
Period size: 101 Copynumber: 2.5 Consensus size: 98
34870767 TAAAAAAACA
* *
34870777 AAAAAAATTACATTCAT-AAAAATCACAAAATACTAAACTAAACACAAACAATTTATAACCTAAT
1 AAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAAAACAAACAATTTATAACCTAAT
* *
34870841 CATAAATTATTAAAAAGTAACTATAAAATAATTTT
66 CATAAATTACTAAAAAATAACTATAAAATAA--TT
* * *
34870876 AAAAAAATTTACATTAATAAAAATTCACAAAACACTAAACTAAATACAAACAATTTATAACCTAA
1 AAAAAAA-TTACATTCATAAAAAATCACAAAACACTAAACTAAAAACAAACAATTTATAACCTAA
* *
34870941 TCATAAATTACTAACAAAATAACTTTCAAATAA-T
65 TCATAAATTACTAA-AAAATAACTATAAAATAATT
* *
34870975 AAAAAAATAACATTCATAAAAAATCACAAAACA-TAAAACTAAAAATAAACA
1 AAAAAAATTACATTCATAAAAAATCACAAAACACT-AAACTAAAAACAAACA
34871026 CAAACACAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
97 1 0.01
98 37 0.28
99 15 0.11
100 9 0.07
101 56 0.42
102 15 0.11
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.25
Consensus pattern (98 bp):
AAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAAAACAAACAATTTATAACCTAAT
CATAAATTACTAAAAAATAACTATAAAATAATT
Found at i:34871079 original size:208 final size:207
Alignment explanation
Indices: 34870451--34871075 Score: 526
Period size: 208 Copynumber: 3.0 Consensus size: 207
34870441 AATAAATAAC
*
34870451 AAAATTTGCATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
1 AAAATTTACATTCAT-AAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCTAA
* *
34870516 TCAAAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAATTTTACATTCATAAAAAAATCA
63 TCATAAATTACTAACAAAATAACTTTCAAATAA-T-AAAAAAA--TAACATTCAT-AAAAAATCA
* * * *** * * ** *
34870581 CAATAAACATTAAACTAAATACAAACA-ATTTATAACCTAA-CCAT-A-AATTACTAACAAAATG
123 C-A-AAACATAAAACTAAAAATAAACACAAACACAAAC-AATTTATAATAATTAATAACAAAA--
**
34870642 ACTTTCAA-ATAATTTAAAA-AATACAAAA
183 A--AACAATATAA---AAAATAATACAAAA
* * * *
34870670 AGAAATTTACGTTCATGAAAAATCACAAAAAACTAAACTAAACACAAACAATTTATAACCAAATC
1 A-AAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATC
* * * * **
34870735 ATAAATTACTAACAAAATAACTATAAAATAAT-TAAAAA-AACA---A-AAAAAATTAC-ATTCA
65 ATAAATTACTAACAAAATAACTTTCAAATAATAAAAAAATAACATTCATAAAAAATCACAAAACA
* * **
34870793 TAAAAATCACAAAATACTAA-ACTAAACACAAACAATTTATAACCTAATCATAAATTATTAAAAA
130 TAAAACT-A-AAAATA--AACAC-AAACACAAACAATTTATAA--TAAT--T-AATAACAAAAAA
** ***
34870857 GTAACTAT--AAAATAATTTTAAA
185 ACAA-TATAAAAAATAATACAAAA
* * *
34870879 AAAATTTACATTAATAAAAATTCACAAAACACTAAACTAAATACAAACAATTTATAACCTAATCA
1 AAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCA
34870944 TAAATTACTAACAAAATAACTTTCAAATAATAAAAAAATAACATTCATAAAAAATCACAAAACAT
66 TAAATTACTAACAAAATAACTTTCAAATAATAAAAAAATAACATTCATAAAAAATCACAAAACAT
34871009 AAAACTAAAAATAAACACAAACACAAACAATTTATAATAATTAATAACAAAAAAACAATATAAAA
131 AAAACTAAAAATAAACACAAACACAAACAATTTATAATAATTAATAACAAAAAAACAATATAAAA
34871074 AA
196 AA
34871076 ATAACTAATC
Statistics
Matches: 325, Mismatches: 53, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
203 8 0.02
204 1 0.00
205 7 0.02
206 21 0.06
207 9 0.03
208 98 0.30
209 17 0.05
210 4 0.01
211 26 0.08
212 5 0.02
213 10 0.03
214 16 0.05
215 15 0.05
216 1 0.00
217 64 0.20
218 1 0.00
219 10 0.03
220 12 0.04
ACGTcount: A:0.60, C:0.15, G:0.01, T:0.25
Consensus pattern (207 bp):
AAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCA
TAAATTACTAACAAAATAACTTTCAAATAATAAAAAAATAACATTCATAAAAAATCACAAAACAT
AAAACTAAAAATAAACACAAACACAAACAATTTATAATAATTAATAACAAAAAAACAATATAAAA
AATAATACAAAA
Found at i:34871514 original size:23 final size:24
Alignment explanation
Indices: 34871471--34871520 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
34871461 CGACACTACT
* *
34871471 AAATAAAATAATATTTCTTAA-AA
1 AAATAAAATAATAATTATTAACAA
34871494 AAATAAAAATAA-AATTATTAACAA
1 AAAT-AAAATAATAATTATTAACAA
34871518 AAA
1 AAA
34871521 GGTGATGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAAATAATAATTATTAACAA
Found at i:34875393 original size:27 final size:22
Alignment explanation
Indices: 34875322--34875387 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 22
34875312 GTCAAGGGTT
34875322 AGGG-TTAGGGTTTTTAAGTTA
1 AGGGTTTAGGGTTTTTAAGTTA
34875343 AGGGTTTAGGGTTTTTAAGTTA
1 AGGGTTTAGGGTTTTTAAGTTA
34875365 AGGGTTTAGGGTTTGTTAA-TTA
1 AGGGTTTAGGGTTT-TTAAGTTA
34875387 A
1 A
34875388 ATTAAGCATT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.09
22 35 0.81
23 4 0.09
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (22 bp):
AGGGTTTAGGGTTTTTAAGTTA
Found at i:34875951 original size:18 final size:17
Alignment explanation
Indices: 34875920--34875959 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
34875910 ACTCGGAAAG
* *
34875920 AGGAACATATAAGGGTT
1 AGGAACATAAAAGGGCT
34875937 AGGATACATAAAAGGGCT
1 AGGA-ACATAAAAGGGCT
34875955 AGGAA
1 AGGAA
34875960 ACGCACCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.45, C:0.07, G:0.30, T:0.17
Consensus pattern (17 bp):
AGGAACATAAAAGGGCT
Found at i:34879740 original size:122 final size:122
Alignment explanation
Indices: 34879573--34879817 Score: 445
Period size: 122 Copynumber: 2.0 Consensus size: 122
34879563 ATAGATACTC
34879573 TATAAGATTAAAGTTATCTTCTTGGAATTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGT
1 TATAAGATTAAAGTTATCTTCTTGGAATTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGT
* *
34879638 TTCAATCCGGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTTTTTTTA
66 TTCAATCCAGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTATTTTTA
* *
34879695 TATAAGATTGAAGTTGTCTTCTTGGAATTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGT
1 TATAAGATTAAAGTTATCTTCTTGGAATTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGT
*
34879760 TTCAATCCAGGTAAAACCTTGGAGAAAGAGTGAACTAACCTTCCATATCTATTTTTA
66 TTCAATCCAGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTATTTTTA
34879817 T
1 T
34879818 TGTATCATTC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (122 bp):
TATAAGATTAAAGTTATCTTCTTGGAATTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGT
TTCAATCCAGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTATTTTTA
Found at i:34904623 original size:68 final size:68
Alignment explanation
Indices: 34904500--34904662 Score: 177
Period size: 68 Copynumber: 2.4 Consensus size: 68
34904490 CATAGCCTAA
* * * ** * * **
34904500 CTATGGTCTTACACTATATGATGTCACGTTTACTTTCCTGGTGGATTTCATATGTTGTTATAACT
1 CTATGGTCTTACACAATATGGTGTCATGTTTACTTTCCTGGCAGACTTCACATGTTGCCAT-ACT
*
34904565 -CTG
65 GCAG
*
34904568 CTATGGTCTTACACAATATGGTGTCATGTTTA-TTGTCCTGGCAGACTTCACATGTTGCCATAGT
1 CTATGGTCTTACACAATATGGTGTCATGTTTACTT-TCCTGGCAGACTTCACATGTTGCCATACT
34904632 GCAG
65 GCAG
* *
34904636 CTATGGTCTTACACAACATGGTTTCAT
1 CTATGGTCTTACACAATATGGTGTCAT
34904663 ATTTTCCCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
67 4 0.05
68 76 0.95
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (68 bp):
CTATGGTCTTACACAATATGGTGTCATGTTTACTTTCCTGGCAGACTTCACATGTTGCCATACTG
CAG
Found at i:34910395 original size:27 final size:27
Alignment explanation
Indices: 34910364--34910540 Score: 203
Period size: 27 Copynumber: 6.5 Consensus size: 27
34910354 TAAATTGTAC
34910364 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
34910391 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34910417 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
34910445 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
34910473 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34910500 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
34910527 AGCACTGAGTGTGC
1 AGCACTAAGTGTGC
34910541 AGACTCAATA
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:34910478 original size:82 final size:81
Alignment explanation
Indices: 34910365--34910520 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34910355 AAATTGTACA
* *
34910365 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34910429 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
34910446 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34910511 TGCGAGTTGA
65 TGCGAATTGA
34910521 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34910532 original size:82 final size:81
Alignment explanation
Indices: 34910361--34910540 Score: 227
Period size: 82 Copynumber: 2.2 Consensus size: 81
34910351 GATTAAATTG
* *
34910361 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
34910426 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
34910442 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
34910506 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
34910524 TATAGCACTGAGTGTGC
1 TACAGCACTAAGTGTGC
34910541 AGACTCAATA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:34912469 original size:16 final size:16
Alignment explanation
Indices: 34912448--34912478 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34912438 TTCACTATTA
*
34912448 TGTCTTTTTTATTTTT
1 TGTCTTTTATATTTTT
34912464 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
34912479 GCATGCATAG
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:0.10, C:0.06, G:0.06, T:0.77
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:34914196 original size:21 final size:20
Alignment explanation
Indices: 34914161--34914223 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
34914151 TATCTTGTAG
* * *
34914161 ATAAGTATTCTATTATTTTA
1 ATAAATATTATATTAATTTA
34914181 ATAAGAT-TTAATATTAAATTTA
1 ATAA-ATATT-ATATT-AATTTA
34914203 ATAAATATTATATTAATTTA
1 ATAAATATTATATTAATTTA
34914223 A
1 A
34914224 AATTAAAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 13 0.36
21 12 0.33
22 11 0.31
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (20 bp):
ATAAATATTATATTAATTTA
Found at i:34914812 original size:38 final size:38
Alignment explanation
Indices: 34914754--34914905 Score: 187
Period size: 38 Copynumber: 4.0 Consensus size: 38
34914744 TAGACTATTT
**
34914754 TCATGGTGTCGCTCCGTAGAGCCAATAGATAATAATTC
1 TCATGGTGTCGCTCCGTAGAGCCAATAGATAACCATTC
* * * * *
34914792 TCATAGTGTCACTCCATAGAGCCAGTAGTTAACCATTC
1 TCATGGTGTCGCTCCGTAGAGCCAATAGATAACCATTC
*
34914830 TCATGGTGTCGCTTCGTAGAGCCAATAGATAACCATTC
1 TCATGGTGTCGCTCCGTAGAGCCAATAGATAACCATTC
* * * * *
34914868 TCACGGTGTCGCTCTGTAGAACTAGTAGATAACCATTC
1 TCATGGTGTCGCTCCGTAGAGCCAATAGATAACCATTC
34914906 CACGATGCCG
Statistics
Matches: 95, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 95 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (38 bp):
TCATGGTGTCGCTCCGTAGAGCCAATAGATAACCATTC
Found at i:34914877 original size:76 final size:75
Alignment explanation
Indices: 34914723--34914905 Score: 217
Period size: 76 Copynumber: 2.4 Consensus size: 75
34914713 CCTCTTTCAA
* * *
34914723 GGTGTCACTCCATAGAACCTGTAG--ACTATTTTCATGGTGTCGCTCCGTAGAGCCAATAGATAA
1 GGTGTCACTCCATAGAACCAGTAGTAACCATTCTCATGGTGTCGCTCCGTAGAGCCAATAGATAA
* *
34914786 TAATTCTCAT
66 CAATTCTCAC
* * *
34914796 AGTGTCACTCCATAGAGCCAGTAGTTAACCATTCTCATGGTGTCGCTTCGTAGAGCCAATAGATA
1 GGTGTCACTCCATAGAACCAGTAG-TAACCATTCTCATGGTGTCGCTCCGTAGAGCCAATAGATA
*
34914861 ACCATTCTCAC
65 ACAATTCTCAC
* ** *
34914872 GGTGTCGCTCTGTAGAACTAGTAGATAACCATTC
1 GGTGTCACTCCATAGAACCAGTAG-TAACCATTC
34914906 CACGATGCCG
Statistics
Matches: 91, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
73 21 0.23
76 70 0.77
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (75 bp):
GGTGTCACTCCATAGAACCAGTAGTAACCATTCTCATGGTGTCGCTCCGTAGAGCCAATAGATAA
CAATTCTCAC
Found at i:34915991 original size:18 final size:17
Alignment explanation
Indices: 34915968--34916024 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 17
34915958 TTTGAAATTT
34915968 ATTTAATATTTTTATAAA
1 ATTTAATATTTTT-TAAA
34915986 ATTTAATAATTTTTTTAAA
1 ATTTAAT-A-TTTTTTAAA
**
34916005 AAAT-ATATTTTTTAAA
1 ATTTAATATTTTTTAAA
34916021 ATTT
1 ATTT
34916025 TTAAAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 11 0.33
17 1 0.03
18 9 0.27
19 7 0.21
20 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATATTTTTTAAA
Found at i:34916000 original size:21 final size:22
Alignment explanation
Indices: 34915962--34916036 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
34915952 GAAAATTTTG
* *
34915962 AAATTTATTTAATATTTTTATA
1 AAATTTATATAATATTTTTAAA
*
34915984 AAATTTA-ATAATTTTTTTAAAA
1 AAATTTATATAATATTTTT-AAA
* * *
34916006 AATATATTTTTTAAAATTTTTAAA
1 AA-AT-TTATATAATATTTTTAAA
34916030 AAATTTA
1 AAATTTA
34916037 AGCTTTGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
21 9 0.22
22 13 0.32
23 4 0.10
24 7 0.17
25 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATTTATATAATATTTTTAAA
Found at i:34916014 original size:25 final size:25
Alignment explanation
Indices: 34915986--34916033 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
34915976 TTTTTATAAA
**
34915986 ATTTAATAATTTTTTTAAAAAATAT
1 ATTTAATAAAATTTTTAAAAAATAT
**
34916011 ATTTTTTAAAATTTTTAAAAAAT
1 ATTTAATAAAATTTTTAAAAAAT
34916034 TTAAGCTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAATAAAATTTTTAAAAAATAT
Found at i:34922530 original size:15 final size:15
Alignment explanation
Indices: 34922512--34922546 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34922502 AAATTTCATG
34922512 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
* *
34922527 ATAAAAAATTATAAA
1 ATAAAAAATAAAAAA
34922542 ATAAA
1 ATAAA
34922547 TAACATGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAAAATAAAAAA
Found at i:34923306 original size:21 final size:21
Alignment explanation
Indices: 34923282--34923327 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
34923272 AAAAAACAAG
*
34923282 AAAATAGCGACAAAACAGTAA
1 AAAATAGCAACAAAACAGTAA
** *
34923303 AAAATATTAAGAAAACAGTAA
1 AAAATAGCAACAAAACAGTAA
34923324 AAAA
1 AAAA
34923328 ATAACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (21 bp):
AAAATAGCAACAAAACAGTAA
Found at i:34931398 original size:12 final size:13
Alignment explanation
Indices: 34931374--34931402 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34931364 AGGCTATAAC
34931374 TATTGCATTTATT
1 TATTGCATTTATT
34931387 TATTGC-TTTATT
1 TATTGCATTTATT
34931399 TATT
1 TATT
34931403 CGTGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:34936755 original size:379 final size:379
Alignment explanation
Indices: 34936050--34936808 Score: 1329
Period size: 379 Copynumber: 2.0 Consensus size: 379
34936040 AGTGGGAGAT
* * * *
34936050 TGTTAGAGTTTGCCTAAAGATCAATCATGAGATGGTTGTAATAACATACTTGATTTATCATGTTT
1 TGTTAGAATATGCCCAAAGATCAATCATGAAATGGTTGTAATAACATACTTGATTTATCATGTTT
*
34936115 ATTAATATAAGGCGTTACCATTATTATTTCAGTTTCTTTTTTGTGTGTATAAATAAACTATTTTA
66 ATTAATATAAGGCGTTACCATTATTATTTCAGTTTCTTTTCTGTGTGTATAAATAAACTATTTTA
* * * *
34936180 CAATAATGTCCTGAGAATAATATGATTATTCTTAAAAGGTCCTTAGTCAAGTATTATTGTTGGCT
131 CAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTTAGTAAAGTATTATTGTTGGAT
*
34936245 AGGACAACAATAATGCATTAAGACTAACATGTAGTTGATTGATGATAAAGAGTTGTCATTGATAT
196 AGGACAACAATAATGCATTAAGACTAACATGTAGTTGATTGATGATAAAGAGTTGCCATTGATAT
*
34936310 GGAATGTCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGACCCGTTATG
261 GGAATGTCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGACCCATTATG
34936375 AGTATGTTTCTTGGATTATCATGTAATTGTCACAACATTACTCATAGTAATTAA
326 AGTATGTTTCTTGGATTATCATGTAATTGTCACAACATTACTCATAGTAATTAA
34936429 TGTTAGAATATGCCCAAAGATCAATCATGAAATGGTTGTAATAACATACTTGATTTATCATGTTT
1 TGTTAGAATATGCCCAAAGATCAATCATGAAATGGTTGTAATAACATACTTGATTTATCATGTTT
* * *
34936494 ATTAATATAAGGTGTTACCATTATTATTTCAGTTTCTTTTCTGTGTTTGTAAATAAACTATTTTA
66 ATTAATATAAGGCGTTACCATTATTATTTCAGTTTCTTTTCTGTGTGTATAAATAAACTATTTTA
*
34936559 TAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTTAGTAAAGTATTATTGTTGGAT
131 CAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTTAGTAAAGTATTATTGTTGGAT
*
34936624 AGGACAACGATAATGCATTAAGACTAACATGTAGTTGATTGATGATAAAGAGTTGCCATTGATAT
196 AGGACAACAATAATGCATTAAGACTAACATGTAGTTGATTGATGATAAAGAGTTGCCATTGATAT
* *
34936689 GGAATGTCAGAATCGATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGACCCATTATG
261 GGAATGTCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGACCCATTATG
* * *
34936754 AGTATGTTTCTTGGATTATTATGTAATTGTCACGACATTACTCATAGTGATTAA
326 AGTATGTTTCTTGGATTATCATGTAATTGTCACAACATTACTCATAGTAATTAA
34936808 T
1 T
34936809 ATGTATATGA
Statistics
Matches: 359, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
379 359 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (379 bp):
TGTTAGAATATGCCCAAAGATCAATCATGAAATGGTTGTAATAACATACTTGATTTATCATGTTT
ATTAATATAAGGCGTTACCATTATTATTTCAGTTTCTTTTCTGTGTGTATAAATAAACTATTTTA
CAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTTAGTAAAGTATTATTGTTGGAT
AGGACAACAATAATGCATTAAGACTAACATGTAGTTGATTGATGATAAAGAGTTGCCATTGATAT
GGAATGTCAAAATCAATGCATGAATATGTGTGTTAGAGAACAACATATTGGACTGACCCATTATG
AGTATGTTTCTTGGATTATCATGTAATTGTCACAACATTACTCATAGTAATTAA
Found at i:34937426 original size:17 final size:17
Alignment explanation
Indices: 34937390--34937432 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
34937380 GTGTCGCTTG
*
34937390 AATTAAATTAATTCTAT
1 AATTAAATTAATTCGAT
* *
34937407 AATTAATTTAATTCGGT
1 AATTAAATTAATTCGAT
*
34937424 AATCAAATT
1 AATTAAATT
34937433 TCCAACACAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (17 bp):
AATTAAATTAATTCGAT
Found at i:34939367 original size:12 final size:12
Alignment explanation
Indices: 34939350--34939376 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34939340 ATTCCGAAGT
34939350 ATATATATATAC
1 ATATATATATAC
34939362 ATATATATATAC
1 ATATATATATAC
34939374 ATA
1 ATA
34939377 AGTATGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:34939886 original size:27 final size:27
Alignment explanation
Indices: 34939855--34940030 Score: 192
Period size: 27 Copynumber: 6.5 Consensus size: 27
34939845 TAAATTGTAC
34939855 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
34939882 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34939908 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
34939936 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
34939964 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
34939991 AGCACTAAGTGTGCGAGTTGATTTTAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
34940018 AGCACTGAGTGTG
1 AGCACTAAGTGTG
34940031 GNNNNNNNNN
Statistics
Matches: 126, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 103 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:34939969 original size:82 final size:81
Alignment explanation
Indices: 34939856--34940011 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34939846 AAATTGTACA
* *
34939856 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34939920 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
34939937 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34940002 TGCGAGTTGA
65 TGCGAATTGA
34940012 TTTTATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34939996 original size:55 final size:54
Alignment explanation
Indices: 34939855--34940009 Score: 195
Period size: 55 Copynumber: 2.9 Consensus size: 54
34939845 TAAATTGTAC
* **
34939855 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATG
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTTGAATATG
* * ** *
34939908 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTTGAATATG
* *
34939963 TAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTT
1 -AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTT
34940010 GATTTTATAG
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 38 0.44
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTTGAATATG
Found at i:34961105 original size:33 final size:33
Alignment explanation
Indices: 34961054--34961407 Score: 152
Period size: 33 Copynumber: 10.4 Consensus size: 33
34961044 CATATAAAGG
**
34961054 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
34961087 GGTCGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T----GGT
* *
34961130 GGCTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
**
34961157 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
34961190 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T----GGT
34961233 GGTTGCTAAGTGCTGATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTC-ATTGGT
*
34961260 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
34961293 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATATGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AT-T--CAT-T---GGT
*
34961335 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
**
34961362 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
34961395 GGTTGCTAAGTGC
1 GGTTGCTAAGTGC
34961408 GGAATCCATC
Statistics
Matches: 244, Mismatches: 28, Indels: 98
0.66 0.08 0.26
Matches are distributed among these distances:
27 61 0.25
28 6 0.02
30 1 0.00
31 5 0.02
32 6 0.02
33 67 0.27
34 9 0.04
35 5 0.02
36 1 0.00
37 4 0.02
38 6 0.02
39 3 0.01
41 2 0.01
42 26 0.11
43 42 0.17
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:34961379 original size:102 final size:103
Alignment explanation
Indices: 34961050--34961407 Score: 619
Period size: 103 Copynumber: 3.5 Consensus size: 103
34961040 ATTGCATATA
*
34961050 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTCGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
34961115 TTAAATGTGAAAGGGGGCTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
34961153 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
34961218 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * *
34961256 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
* *
34961321 TGAAATATG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
34961358 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGC
34961408 GGAATCCATC
Statistics
Matches: 241, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
102 74 0.31
103 167 0.69
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:34963086 original size:42 final size:42
Alignment explanation
Indices: 34962954--34963309 Score: 366
Period size: 42 Copynumber: 8.4 Consensus size: 42
34962944 ACGTCGCTAA
* *
34962954 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-TGAAAAAAA-GCCGCTAAAGATCATGTT
* * *
34962998 CTTTAGCGGCGCTAAGGAAATAAAAGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAA-AAAAGCCGCTAAAGATCATGTT
*
34963041 CTTTAGCGGCGCTTATGAAAAAATA-CTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAA-AGCCGCTAAAGATCATGTT
* * *
34963083 CTTTAACGGCGCTTAGGAAAAAAAGCCGCTAAAGATCGTGTT
1 CTTTAGCGGCGCTTATGAAAAAAAGCCGCTAAAGATCATGTT
* * *
34963125 CTTTAGCGGCGCTT-TGAAAAAAATGCCGCTAAAGTTCGTGTA
1 CTTTAGCGGCGCTTATGAAAAAAA-GCCGCTAAAGATCATGTT
*
34963167 CTTTAGCGGCGCTT-TGAAAAAAACGCCGCTAAAGATCGTGTT
1 CTTTAGCGGCGCTTATGAAAAAAA-GCCGCTAAAGATCATGTT
* * *
34963209 CTTTAGCGGCGCTT-TGGAGGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT-GA-AAAAAAGCCGCTAAAGA-TCATGTT
* * * ** *
34963252 CTATAGTGGCGCTTGTTCAAAAACGCCGCTAATAG-T-AGTGTT
1 CTTTAGCGGCGCTTATGAAAAAAAGCCGCTAA-AGATCA-TGTT
34963294 CTTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
34963310 TTCACAAACG
Statistics
Matches: 270, Mismatches: 31, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
41 10 0.04
42 169 0.63
43 69 0.26
44 22 0.08
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAAAGCCGCTAAAGATCATGTT
Found at i:34963771 original size:12 final size:12
Alignment explanation
Indices: 34963748--34963783 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
34963738 TGAACCTCTA
*
34963748 CTTCTATCGCTG
1 CTTCTCTCGCTG
*
34963760 CTTCTCTTGCTG
1 CTTCTCTCGCTG
34963772 CTTCTCTCGCTG
1 CTTCTCTCGCTG
34963784 TAGCATCTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.36, G:0.17, T:0.44
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:34975239 original size:11 final size:11
Alignment explanation
Indices: 34975223--34975266 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
34975213 GAGAGCAGAA
34975223 TTTTCTTTGAG
1 TTTTCTTTGAG
*
34975234 TTTTCTTTAAG
1 TTTTCTTTGAG
34975245 ATTTCTCTCTTGAG
1 -TTT-TCT-TTGAG
34975259 TTTTCTTT
1 TTTTCTTT
34975267 AGAAGTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 12 0.43
12 6 0.21
13 6 0.21
14 4 0.14
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.64
Consensus pattern (11 bp):
TTTTCTTTGAG
Found at i:34975258 original size:25 final size:23
Alignment explanation
Indices: 34975222--34975267 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
34975212 TGAGAGCAGA
34975222 ATTTTCTTTGAGTTTTCTTTAAG
1 ATTTTCTTTGAGTTTTCTTTAAG
34975245 ATTTCTCTCTTGAGTTTTCTTTA
1 ATTT-TCT-TTGAGTTTTCTTTA
34975268 GAAGTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 14 0.67
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.61
Consensus pattern (23 bp):
ATTTTCTTTGAGTTTTCTTTAAG
Found at i:34981910 original size:40 final size:40
Alignment explanation
Indices: 34981858--34982051 Score: 228
Period size: 40 Copynumber: 4.8 Consensus size: 40
34981848 TCAATGGAAT
* ** *
34981858 CGAAGTGCAAACAGGGGCACAAATGTGCATTCAAGGACAC
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGCAC
* * * *
34981898 CAAAGTAAAAACAGGGGTA-GATATGTGCATTCAGGGGCAC
1 CGAAGTACAAACAGGGGCACG-TATGTGCATTCAAGGGCAC
* * *
34981938 CGAAGTGCAAACAGGGGCACGTATGTGCATTCAGGGGTAC
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGCAC
* * * *
34981978 TGAAGTGCAAACAGGGGCATGTATGTGCATTCAAGGGTAC
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGCAC
*
34982018 CGAAGTATAAACAGGGGCACGTATGTGCATTCAA
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAA
34982052 TAGTAGTTTC
Statistics
Matches: 132, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
40 131 0.99
41 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (40 bp):
CGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGCAC
Found at i:34981945 original size:20 final size:20
Alignment explanation
Indices: 34981922--34982023 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 20
34981912 GGGTAGATAT
34981922 GTGCATTCAGGGGCACCGAA
1 GTGCATTCAGGGGCACCGAA
** *
34981942 GTGCAAACAGGGGCA-CGTAT
1 GTGCATTCAGGGGCACCG-AA
* *
34981962 GTGCATTCAGGGGTACTGAA
1 GTGCATTCAGGGGCACCGAA
** * *
34981982 GTGCAAACAGGGGCA-TGTAT
1 GTGCATTCAGGGGCACCG-AA
* *
34982002 GTGCATTCAAGGGTACCGAA
1 GTGCATTCAGGGGCACCGAA
34982022 GT
1 GT
34982024 ATAAACAGGG
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
19 4 0.07
20 54 0.90
21 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (20 bp):
GTGCATTCAGGGGCACCGAA
Found at i:34982437 original size:17 final size:18
Alignment explanation
Indices: 34982399--34982437 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
34982389 AATATAATTT
*
34982399 ATTTCATTTATTAGCTTAA
1 ATTTCATATATTAGC-TAA
34982418 ATTTCATATATTAG-TAA
1 ATTTCATATATTAGCTAA
34982435 ATT
1 ATT
34982438 CTAAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTCATATATTAGCTAA
Found at i:34985696 original size:477 final size:475
Alignment explanation
Indices: 34984799--34985758 Score: 1740
Period size: 477 Copynumber: 2.0 Consensus size: 475
34984789 GATATTTTTT
*
34984799 TTACATTGGGAGGAGGAGTTGTGTCATGGAAATCCTCAAAACAAACGATTATAACCAGATCTACA
1 TTAC-TTGGGAGGAGGAGTTATGTCATGGAAATCCTCAAAACAAACGATTATAACCAGATCTACA
34984864 ATAGAATCTGAGTTTGTAGCTCTAGACAAATCTAAAGAAGAGGCTAAAAAGATTCGAAACTTCTT
65 ATAGAATCTGAGTTTGTAGCTCTAGACAAATCTAAAGAAGAGGCTAAAAAGATTCGAAACTTCTT
*
34984929 GGACTATTCCTAACTGGCCAAAGCCTATGCCCACAATATGCATATATTGTGATAACTAAGAAACA
130 GGAATATTCCTAACTGGCCAAAGCCTATGCCCACAATATGCATATATTGTGATAACTAAGAAACA
34984994 ATTGATAGAGCACAGAATGTAATGTATAATGGTAAGTTGAGACATATGCATCATCGACACAGTAC
195 ATTGATAGAGCACAGAATGTAATGTATAATGGTAAGTTGAGACATATGCATCATCGACACAGTAC
*
34985059 CGTTAGACAACTGATCTCAAATGGAGTTATCTCTATTTATTTTGTAAAATAAAAAGATAACATTA
260 CGTTAGACAACTGACCTCAAATGGAGTTATCTCTATTTATTTTGTAAAATAAAAAGATAACATTA
*
34985124 CGAATCTGCTAACTAAAGGATTAAATTGAGATTAGGTTGATTAAACATCAAAAGGAATGAGACTA
325 CGAATCTGCTAACTAAAGGATTAAATTGAGATTAGGTTGATAAAACATCAAAAGGAATGAGACTA
*
34985189 AAGCCCATGAAAATTAAAGGTTCTATGTGAAGGAAAACCCAACCTAGTTGACTGGAGATCCTAAG
390 AAGCCCATGAAAATTAAAGGTTCTATGTGAAGGAAAACCCAACCTAGTTGACTGGAGATCCCAAG
34985254 ATCTAGGTTTAAAGGGACAAC
455 ATCTAGGTTTAAAGGGACAAC
* *
34985275 TTACTTGGGAGGAGGAGTTATGTCATGGAAATCCTTAAAACAAATGATTATAACCAGATCTACAA
1 TTACTTGGGAGGAGGAGTTATGTCATGGAAATCCTCAAAACAAACGATTATAACCAGATCTACAA
* **
34985340 TAGAATCTGAGTTTGTAGCTCTAGACAAATCTAGAGAAGAGGCTAAATGGATTCGAAACTTCTTG
66 TAGAATCTGAGTTTGTAGCTCTAGACAAATCTAAAGAAGAGGCTAAAAAGATTCGAAACTTCTTG
* *
34985405 GAGGATATTCCTAACTGGCCAAAGCCTGTGCCCACAATATGCCTATATTGTGATAACTAAGAAAC
131 GA--ATATTCCTAACTGGCCAAAGCCTATGCCCACAATATGCATATATTGTGATAACTAAGAAAC
* *
34985470 AATTGGTAGAGCACAGAATGTAATGTATAATGGTAAGTTGAGACATATGCGTCATCGACACAGTA
194 AATTGATAGAGCACAGAATGTAATGTATAATGGTAAGTTGAGACATATGCATCATCGACACAGTA
34985535 CCGTTAGACAACTGACCTCAAATGGAGTTATCTCTATTTATTTTGTAAAATAAAAAGATAACATT
259 CCGTTAGACAACTGACCTCAAATGGAGTTATCTCTATTTATTTTGTAAAATAAAAAGATAACATT
*
34985600 ACGAATCTGCTAACTAAAGGATTAAATTGAGATTAGGTTGATAAAACATCAAAAGGAATGGGACT
324 ACGAATCTGCTAACTAAAGGATTAAATTGAGATTAGGTTGATAAAACATCAAAAGGAATGAGACT
* *
34985665 AAAGTCCATGAAAATTAAAGGTTCTATGTGAAGGAAAACCCAGCCTAGTTGACTGGAGATCCCAA
389 AAAGCCCATGAAAATTAAAGGTTCTATGTGAAGGAAAACCCAACCTAGTTGACTGGAGATCCCAA
34985730 GATCTAGGTTTAAAGGGACAAC
454 GATCTAGGTTTAAAGGGACAAC
34985752 TTACTTG
1 TTACTTG
34985759 CATAGACCTT
Statistics
Matches: 465, Mismatches: 17, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
475 122 0.26
476 4 0.01
477 339 0.73
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (475 bp):
TTACTTGGGAGGAGGAGTTATGTCATGGAAATCCTCAAAACAAACGATTATAACCAGATCTACAA
TAGAATCTGAGTTTGTAGCTCTAGACAAATCTAAAGAAGAGGCTAAAAAGATTCGAAACTTCTTG
GAATATTCCTAACTGGCCAAAGCCTATGCCCACAATATGCATATATTGTGATAACTAAGAAACAA
TTGATAGAGCACAGAATGTAATGTATAATGGTAAGTTGAGACATATGCATCATCGACACAGTACC
GTTAGACAACTGACCTCAAATGGAGTTATCTCTATTTATTTTGTAAAATAAAAAGATAACATTAC
GAATCTGCTAACTAAAGGATTAAATTGAGATTAGGTTGATAAAACATCAAAAGGAATGAGACTAA
AGCCCATGAAAATTAAAGGTTCTATGTGAAGGAAAACCCAACCTAGTTGACTGGAGATCCCAAGA
TCTAGGTTTAAAGGGACAAC
Found at i:34988967 original size:30 final size:30
Alignment explanation
Indices: 34988933--34988990 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
34988923 CATGTTTATG
*
34988933 TTATGGAGGTGAGTGATTCTTTCAAGTTGT
1 TTATGGAGGTGAGTAATTCTTTCAAGTTGT
*
34988963 TTATGGTGGTGAGTAATTCTTTCAAGTT
1 TTATGGAGGTGAGTAATTCTTTCAAGTT
34988991 AGCCAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (30 bp):
TTATGGAGGTGAGTAATTCTTTCAAGTTGT
Found at i:35002727 original size:25 final size:25
Alignment explanation
Indices: 35002699--35002752 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
35002689 CTCATCTGCA
* *
35002699 CTGAATAACAGTAAGCTCCTTCGAG
1 CTGAATAACAGTAAGCTCATACGAG
*
35002724 CTGAATAATAGTAAGCTCATACGAG
1 CTGAATAACAGTAAGCTCATACGAG
35002749 CTGA
1 CTGA
35002753 GTATCGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (25 bp):
CTGAATAACAGTAAGCTCATACGAG
Found at i:35002762 original size:25 final size:24
Alignment explanation
Indices: 35002734--35002788 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
35002724 CTGAATAATA
* * *
35002734 GTAAGCTCATACGAGCTGAGTATCG
1 GTAACCTCATACAAGCTGA-AATCG
*
35002759 GTAACCTCATATAAGCTGAAATCG
1 GTAACCTCATACAAGCTGAAATCG
35002783 GTAACC
1 GTAACC
35002789 CTAATGACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
GTAACCTCATACAAGCTGAAATCG
Found at i:35010332 original size:25 final size:25
Alignment explanation
Indices: 35010283--35010345 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
35010273 TACTAGTTAT
* *
35010283 AAACAGTAAGCTCCTTTAAGTTGAA
1 AAACAGTAAGCTCCTCTAAGCTGAA
*
35010308 TAACAGTAAGCTCCTCCT-AGCTGAA
1 AAACAGTAAGCTCCT-CTAAGCTGAA
*
35010333 AAACGGTAAGCTC
1 AAACAGTAAGCTC
35010346 ATGCGAGCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (25 bp):
AAACAGTAAGCTCCTCTAAGCTGAA
Found at i:35010354 original size:25 final size:25
Alignment explanation
Indices: 35010326--35010383 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
35010316 AGCTCCTCCT
* *
35010326 AGCTGAAAAACGGTAAGCTCATGCG
1 AGCTGAAAAACGGTAAGCTCATACA
** *
35010351 AGCTGAGTATCGGTAAGCTCATACA
1 AGCTGAAAAACGGTAAGCTCATACA
35010376 AGCTGAAA
1 AGCTGAAA
35010384 TCGGTAACCC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCTGAAAAACGGTAAGCTCATACA
Found at i:35016552 original size:29 final size:29
Alignment explanation
Indices: 35016480--35016558 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
35016470 ACTATGTGTT
*
35016480 GGTGATTATATTTATTAGATACTATGTACC
1 GGTGATCATA-TTATTAGATACTATGTACC
* * * *
35016510 GAT-AACTATTTTATTAGGTACTATGTACC
1 GGTGATC-ATATTATTAGATACTATGTACC
*
35016539 GGTGATCATATTATCAGATA
1 GGTGATCATATTATTAGATA
35016559 TTTTGTATTG
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
29 31 0.84
30 6 0.16
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (29 bp):
GGTGATCATATTATTAGATACTATGTACC
Found at i:35046407 original size:15 final size:16
Alignment explanation
Indices: 35046378--35046407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35046368 CAAACATGCT
35046378 TTAACACATTATCAAA
1 TTAACACATTATCAAA
35046394 TTAACACA-TATCAA
1 TTAACACATTATCAA
35046408 CAACGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:35052627 original size:15 final size:16
Alignment explanation
Indices: 35052598--35052627 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35052588 CAAACATGCT
35052598 TTAACACATTATCAAA
1 TTAACACATTATCAAA
35052614 TTAACACA-TATCAA
1 TTAACACATTATCAA
35052628 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:35053836 original size:27 final size:25
Alignment explanation
Indices: 35053770--35053840 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
35053760 CATGTACATA
*
35053770 TATGCTCACACGAGCTATGAATAAG
1 TATGCTCACACGAGCTGTGAATAAG
*
35053795 TATGCTCACATGAGCTGTGAA-AATGGG
1 TATGCTCACACGAGCTGTGAATAA---G
*
35053822 TCTGCTCACACGAGCTGTG
1 TATGCTCACACGAGCTGTG
35053841 GGTCAGAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 19 0.49
27 18 0.46
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (25 bp):
TATGCTCACACGAGCTGTGAATAAG
Found at i:35061479 original size:5 final size:5
Alignment explanation
Indices: 35061469--35061521 Score: 90
Period size: 5 Copynumber: 10.8 Consensus size: 5
35061459 CAACTCTTTT
*
35061469 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT- TCCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC
35061518 TTCT
1 TTCT
35061522 TCTACTTCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 3 0.07
5 42 0.93
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTC
Found at i:35061529 original size:9 final size:8
Alignment explanation
Indices: 35061472--35061529 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
35061462 CTCTTTTTTC
35061472 TCTTCTCT
1 TCTTCTCT
35061480 TC-TCT-T
1 TCTTCTCT
35061486 CTCTTCTCT
1 -TCTTCTCT
35061495 TC-TCT-T
1 TCTTCTCT
35061501 CTCTTCTCT
1 -TCTTCTCT
35061510 TCTTCCTCT
1 TCTT-CTCT
35061519 TCTTCTACT
1 TCTTCT-CT
35061528 TC
1 TC
35061530 AATATTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
6 2 0.05
7 10 0.24
8 16 0.38
9 14 0.33
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.59
Consensus pattern (8 bp):
TCTTCTCT
Found at i:35062006 original size:14 final size:15
Alignment explanation
Indices: 35061989--35062018 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35061979 CATAATTCAA
35061989 AAAATAT-ATTTTAC
1 AAAATATAATTTTAC
35062003 AAAATATAATTTTAC
1 AAAATATAATTTTAC
35062018 A
1 A
35062019 TTTCAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATAATTTTAC
Found at i:35064725 original size:25 final size:24
Alignment explanation
Indices: 35064697--35064746 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
35064687 CTTTTTTTTT
*
35064697 GAAAAAAAATTATTCAAAAAAAAAA
1 GAAAAAAAA-GATTCAAAAAAAAAA
*
35064722 GAAAACAAAGATTCAAAAAAAAAA
1 GAAAAAAAAGATTCAAAAAAAAAA
35064746 G
1 G
35064747 CAAGCAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (24 bp):
GAAAAAAAAGATTCAAAAAAAAAA
Found at i:35065775 original size:9 final size:9
Alignment explanation
Indices: 35065761--35065809 Score: 75
Period size: 9 Copynumber: 5.7 Consensus size: 9
35065751 CATACATACT
35065761 TATATATTC
1 TATATATTC
35065770 TATATATTC
1 TATATATTC
35065779 TATATATTC
1 TATATATTC
*
35065788 TATATATTT
1 TATATATTC
35065797 TATA-ATT-
1 TATATATTC
35065804 TATATA
1 TATATA
35065810 CATATCTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
7 4 0.11
8 4 0.11
9 30 0.79
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATATTC
Found at i:35066227 original size:20 final size:20
Alignment explanation
Indices: 35066192--35066229 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35066182 TTACTCAAAT
35066192 TATTTTTATTCACATTATCA
1 TATTTTTATTCACATTATCA
35066212 TATTTATTATTC-CATTAT
1 TATTT-TTATTCACATTAT
35066230 GCATGTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTTATTCACATTATCA
Found at i:35066503 original size:108 final size:109
Alignment explanation
Indices: 35066263--35066575 Score: 399
Period size: 106 Copynumber: 2.9 Consensus size: 109
35066253 AAGGAAAATT
* * **
35066263 TTTCTAAA-TAAGTCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGTTCTAATGTGCTGGGTT
1 TTTC-AAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
*
35066327 TCGATTTTT-T-GTTCGACCAAATAGCTAAATAT-CTTTTTAAAA
65 TCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAA
* *
35066369 TTTCAAAGTAAGGCGATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGATTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
35066434 CGATTTTTCTCGTTCGACCAAATAACCAAATATCCTTTTT-TAA
66 CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAA
** * * *
35066477 TTTTGAAGTAAGGTAATATTTTGCGTTTGGAAATTC-AAATAAACGTGCCCTAATGTGCCGGGTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGA-AAACGTGCCCTAATGTGCTGGGTT
* * *
35066541 TCGA--TTTCCCGTTTGACCAAATAGTCAAATATCCT
65 TCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCT
35066576 CTTAAATCTC
Statistics
Matches: 182, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
105 3 0.02
106 90 0.49
107 3 0.02
108 80 0.44
109 6 0.03
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (109 bp):
TTTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAA
Found at i:35066810 original size:22 final size:22
Alignment explanation
Indices: 35066767--35066811 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
35066757 TCGTGGACCA
* *
35066767 AAATCGTTTTTTTAATAAAATC
1 AAATCGTTTTATTAAAAAAATC
35066789 AAATCG-TTTATTAAAAACAATC
1 AAATCGTTTTATTAAAAA-AATC
35066811 A
1 A
35066812 CTTTTTAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATCGTTTTATTAAAAAAATC
Found at i:35067148 original size:20 final size:20
Alignment explanation
Indices: 35067125--35067162 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35067115 CAATTTAATC
35067125 AAATCAACTTGAATTTTTTT
1 AAATCAACTTGAATTTTTTT
* *
35067145 AAATCGAGTTGAATTTTT
1 AAATCAACTTGAATTTTT
35067163 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (20 bp):
AAATCAACTTGAATTTTTTT
Found at i:35083362 original size:3 final size:3
Alignment explanation
Indices: 35083354--35083378 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35083344 GAGAACCAGT
35083354 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
35083379 CTTGAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:35088223 original size:56 final size:55
Alignment explanation
Indices: 35088137--35088244 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 55
35088127 GTATCCATTG
*
35088137 GATGATAAATCATCACTTTTAATTTGAATAGTGCTTACGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACGAATAATT-AATTTGTAA
*
35088193 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACGAATAATTAATTTG
35088245 CAATCTACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 6 0.12
56 44 0.88
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACGAATAATTAATTTGTAA
Found at i:35093240 original size:25 final size:26
Alignment explanation
Indices: 35093212--35093285 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 26
35093202 TATGCCCATA
* *
35093212 CGAG-CATGTAATCAGGAAGCTC-TTT
1 CGAGCCATGTAAT-GGGAAGCTCATGT
*
35093237 CGAGCCATATAATGGGAAGCTCATGT
1 CGAGCCATGTAATGGGAAGCTCATGT
35093263 -GAGCCATGTAATGGGAAGCTCAT
1 CGAGCCATGTAATGGGAAGCTCAT
35093286 AAGAGTCGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 34 0.79
26 9 0.21
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (26 bp):
CGAGCCATGTAATGGGAAGCTCATGT
Found at i:35093354 original size:25 final size:25
Alignment explanation
Indices: 35093326--35093465 Score: 116
Period size: 25 Copynumber: 5.6 Consensus size: 25
35093316 CAATATCGGA
35093326 AAGCTCTGGAGAGCCATTAATCGAG
1 AAGCTCTGGAGAGCCATTAATCGAG
35093351 AAGCTC-GTGAGAGCCAATT-ATC-ATG
1 AAGCTCTG-GAGAGCC-ATTAATCGA-G
* *
35093376 AAGCTCAT--ACGAGCCATAAAT-GGG
1 AAGCTC-TGGA-GAGCCATTAATCGAG
* * *
35093400 AAGCTCTGAAGAGCTATTAATCGGG
1 AAGCTCTGGAGAGCCATTAATCGAG
35093425 AAGCTCAT-GAGAGCCAATT-ATCGAG
1 AAGCTC-TGGAGAGCC-ATTAATCGAG
35093450 AAGCTCTGGAGAGCCA
1 AAGCTCTGGAGAGCCA
35093466 AATAACGGGA
Statistics
Matches: 94, Mismatches: 7, Indels: 29
0.72 0.05 0.22
Matches are distributed among these distances:
23 1 0.01
24 23 0.24
25 63 0.67
26 7 0.07
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
AAGCTCTGGAGAGCCATTAATCGAG
Found at i:35093380 original size:74 final size:74
Alignment explanation
Indices: 35093227--35093455 Score: 234
Period size: 74 Copynumber: 3.1 Consensus size: 74
35093217 ATGTAATCAG
* * * * * *
35093227 GAAGCTCTTTCGAGCCATATAATGGGAAGCTCATG-TGAGCCATGTAAT-GGGAAGCTCATAAGA
1 GAAGCTCATACGAGCCATA-AATGGAAAGCTC-TGAAGAGCCAT-TAATCGAGAAGCTCATGAGA
* * * *
35093290 GTC-GTAATTGA
63 GCCAATTATCGA
* * *
35093301 GAAGCTCATACGAGCCA-ATATCGGAAAGCTCTGGAGAGCCATTAATCGAGAAGCTCGTGAGAGC
1 GAAGCTCATACGAGCCATAAAT-GGAAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGC
35093365 CAATTATC-A
65 CAATTATCGA
* * *
35093374 TGAAGCTCATACGAGCCATAAATGGGAAGCTCTGAAGAGCTATTAATCGGGAAGCTCATGAGAGC
1 -GAAGCTCATACGAGCCATAAATGGAAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGC
35093439 CAATTATCGA
65 CAATTATCGA
35093449 GAAGCTC
1 GAAGCTC
35093456 TGGAGAGCCA
Statistics
Matches: 130, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
72 8 0.06
73 31 0.24
74 87 0.67
75 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (74 bp):
GAAGCTCATACGAGCCATAAATGGAAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGCC
AATTATCGA
Found at i:35093464 original size:74 final size:75
Alignment explanation
Indices: 35093301--35093491 Score: 232
Period size: 74 Copynumber: 2.6 Consensus size: 75
35093291 TCGTAATTGA
* * * * *
35093301 GAAGCTCATACGAGCC-AATATCGGAAAGCTCTGGAGAGCCATTAATCGAGAAGCTCGTGAGAGC
1 GAAGCTCATACGAGCCAAATAACGGGAAGCTCTGAAGAGCTATTAATCGAGAAGCTCATGAGAGC
35093365 CAATTATCAT
66 CAATTATCAT
* * *
35093375 GAAGCTCATACGAGCCATA-AATGGGAAGCTCTGAAGAGCTATTAATCGGGAAGCTCATGAGAGC
1 GAAGCTCATACGAGCCAAATAACGGGAAGCTCTGAAGAGCTATTAATCGAGAAGCTCATGAGAGC
35093439 CAATTATCGA-
66 CAATTATC-AT
35093449 GAAGCTC-TGGA-GAGCCAAATAACGGGAAGCTCAT-AAGAGCTAT
1 GAAGCTCAT--ACGAGCCAAATAACGGGAAGCTC-TGAAGAGCTAT
35093492 GGTGTGTCTT
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
73 1 0.01
74 76 0.75
75 23 0.23
76 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (75 bp):
GAAGCTCATACGAGCCAAATAACGGGAAGCTCTGAAGAGCTATTAATCGAGAAGCTCATGAGAGC
CAATTATCAT
Found at i:35093466 original size:25 final size:25
Alignment explanation
Indices: 35093312--35093480 Score: 108
Period size: 25 Copynumber: 6.8 Consensus size: 25
35093302 AAGCTCATAC
35093312 GAGCCAA-TATCG-GAAAGCTCTGGA
1 GAGCCAATTATCGAG-AAGCTCTGGA
35093336 GAGCC-ATTAATCGAGAAGCTC-GTGA
1 GAGCCAATT-ATCGAGAAGCTCTG-GA
35093361 GAGCCAATTATC-ATGAAGCTCAT--A
1 GAGCCAATTATCGA-GAAGCTC-TGGA
* * *
35093385 CGAGCC-ATAAAT-GGGAAGCTCTGAA
1 -GAGCCAAT-TATCGAGAAGCTCTGGA
* *
35093410 GAG-CTATTAATCGGGAAGCTCAT-GA
1 GAGCCAATT-ATCGAGAAGCTC-TGGA
35093435 GAGCCAATTATCGAGAAGCTCTGGA
1 GAGCCAATTATCGAGAAGCTCTGGA
* * *
35093460 GAGCCAAATAACGGGAAGCTC
1 GAGCCAATTATCGAGAAGCTC
35093481 ATAAGAGCTA
Statistics
Matches: 117, Mismatches: 9, Indels: 37
0.72 0.06 0.23
Matches are distributed among these distances:
23 3 0.03
24 26 0.22
25 79 0.68
26 9 0.08
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (25 bp):
GAGCCAATTATCGAGAAGCTCTGGA
Found at i:35093487 original size:25 final size:25
Alignment explanation
Indices: 35093238--35093488 Score: 88
Period size: 25 Copynumber: 10.2 Consensus size: 25
35093228 AAGCTCTTTC
* * **
35093238 GAGCCATATAATGGGAAGCTCATGT
1 GAGCCAAATAACGGGAAGCTCATAA
** *
35093263 GAGCCATGTAATGGGAAGCTCATAA
1 GAGCCAAATAACGGGAAGCTCATAA
* * * * *
35093288 GAGTC--GTAATTGAGAAGCTCATAC
1 GAGCCAAATAA-CGGGAAGCTCATAA
* * *
35093312 GAGCC-AATATCGGAAAGCTC-TGGA
1 GAGCCAAATAACGGGAAGCTCAT-AA
* * * *
35093336 GAGCC-ATTAATCGAGAAGCTCGTGA
1 GAGCCAAATAA-CGGGAAGCTCATAA
* * ** *
35093361 GAGCCAATTATCATGAAGCTCATAC
1 GAGCCAAATAACGGGAAGCTCATAA
* *
35093386 GAGCCATA-AATGGGAAGCTC-TGAA
1 GAGCCAAATAACGGGAAGCTCAT-AA
* * *
35093410 GAG-CTATTAATCGGGAAGCTCATGA
1 GAGCCAAATAA-CGGGAAGCTCATAA
* * * *
35093435 GAGCCAATTATCGAGAAGCTC-TGGA
1 GAGCCAAATAACGGGAAGCTCAT-AA
35093460 GAGCCAAATAACGGGAAGCTCATAA
1 GAGCCAAATAACGGGAAGCTCATAA
35093485 GAGC
1 GAGC
35093489 TATGGTGTGT
Statistics
Matches: 170, Mismatches: 43, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
23 7 0.04
24 46 0.27
25 105 0.62
26 12 0.07
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGCCAAATAACGGGAAGCTCATAA
Found at i:35093625 original size:8 final size:8
Alignment explanation
Indices: 35093612--35093636 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35093602 ATACTTTCGG
35093612 ATATGTTT
1 ATATGTTT
35093620 ATATGTTT
1 ATATGTTT
35093628 ATATGTTT
1 ATATGTTT
35093636 A
1 A
35093637 AGTAATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
ATATGTTT
Found at i:35096126 original size:55 final size:55
Alignment explanation
Indices: 35096028--35096134 Score: 189
Period size: 55 Copynumber: 1.9 Consensus size: 55
35096018 GTATCCATTG
35096028 GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATT-AATTTGTAA
*
35096084 GATGATAAATCATCACTTTTA-TTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATTAATTTG
35096135 CAATCTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 6 0.12
55 23 0.46
56 21 0.42
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.40
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATTAATTTGTAA
Found at i:35109937 original size:1 final size:1
Alignment explanation
Indices: 35109892--35109917 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35109882 TTCGAGATAG
35109892 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
35109918 AACCACTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35111468 original size:56 final size:55
Alignment explanation
Indices: 35111382--35111489 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 55
35111372 GTATCCATTG
*
35111382 GATGATAAATCATCACTTTTAATTTGAATAGTGCTTACGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACGAATAATT-AATTTGTAA
*
35111438 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACGAATAATTAATTTG
35111490 CAATCTACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 6 0.12
56 44 0.88
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACGAATAATTAATTTGTAA
Found at i:35116491 original size:25 final size:26
Alignment explanation
Indices: 35116463--35116536 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 26
35116453 TATGCCCATA
* *
35116463 CGAG-CATGTAATCAGGAAGCTC-TTT
1 CGAGCCATGTAAT-GGGAAGCTCATGT
*
35116488 CGAGCCATATAATGGGAAGCTCATGT
1 CGAGCCATGTAATGGGAAGCTCATGT
35116514 -GAGCCATGTAATGGGAAGCTCAT
1 CGAGCCATGTAATGGGAAGCTCAT
35116537 AAGAGTCGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 34 0.79
26 9 0.21
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (26 bp):
CGAGCCATGTAATGGGAAGCTCATGT
Found at i:35116605 original size:25 final size:25
Alignment explanation
Indices: 35116577--35116716 Score: 116
Period size: 25 Copynumber: 5.6 Consensus size: 25
35116567 CAATATCGGA
35116577 AAGCTCTGGAGAGCCATTAATCGAG
1 AAGCTCTGGAGAGCCATTAATCGAG
35116602 AAGCTC-GTGAGAGCCAATT-ATC-ATG
1 AAGCTCTG-GAGAGCC-ATTAATCGA-G
* *
35116627 AAGCTCAT--ACGAGCCATAAAT-GGG
1 AAGCTC-TGGA-GAGCCATTAATCGAG
* * *
35116651 AAGCTCTGAAGAGCTATTAATCGGG
1 AAGCTCTGGAGAGCCATTAATCGAG
35116676 AAGCTCAT-GAGAGCCAATT-ATCGAG
1 AAGCTC-TGGAGAGCC-ATTAATCGAG
35116701 AAGCTCTGGAGAGCCA
1 AAGCTCTGGAGAGCCA
35116717 AATAACGGGA
Statistics
Matches: 94, Mismatches: 7, Indels: 29
0.72 0.05 0.22
Matches are distributed among these distances:
23 1 0.01
24 23 0.24
25 63 0.67
26 7 0.07
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
AAGCTCTGGAGAGCCATTAATCGAG
Found at i:35116631 original size:74 final size:74
Alignment explanation
Indices: 35116478--35116706 Score: 234
Period size: 74 Copynumber: 3.1 Consensus size: 74
35116468 ATGTAATCAG
* * * * * *
35116478 GAAGCTCTTTCGAGCCATATAATGGGAAGCTCATG-TGAGCCATGTAAT-GGGAAGCTCATAAGA
1 GAAGCTCATACGAGCCATA-AATGGAAAGCTC-TGAAGAGCCAT-TAATCGAGAAGCTCATGAGA
* * * *
35116541 GTC-GTAATTGA
63 GCCAATTATCGA
* * *
35116552 GAAGCTCATACGAGCCA-ATATCGGAAAGCTCTGGAGAGCCATTAATCGAGAAGCTCGTGAGAGC
1 GAAGCTCATACGAGCCATAAAT-GGAAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGC
35116616 CAATTATC-A
65 CAATTATCGA
* * *
35116625 TGAAGCTCATACGAGCCATAAATGGGAAGCTCTGAAGAGCTATTAATCGGGAAGCTCATGAGAGC
1 -GAAGCTCATACGAGCCATAAATGGAAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGC
35116690 CAATTATCGA
65 CAATTATCGA
35116700 GAAGCTC
1 GAAGCTC
35116707 TGGAGAGCCA
Statistics
Matches: 130, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
72 8 0.06
73 31 0.24
74 87 0.67
75 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (74 bp):
GAAGCTCATACGAGCCATAAATGGAAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGCC
AATTATCGA
Found at i:35116715 original size:74 final size:75
Alignment explanation
Indices: 35116552--35116742 Score: 232
Period size: 74 Copynumber: 2.6 Consensus size: 75
35116542 TCGTAATTGA
* * * * *
35116552 GAAGCTCATACGAGCC-AATATCGGAAAGCTCTGGAGAGCCATTAATCGAGAAGCTCGTGAGAGC
1 GAAGCTCATACGAGCCAAATAACGGGAAGCTCTGAAGAGCTATTAATCGAGAAGCTCATGAGAGC
35116616 CAATTATCAT
66 CAATTATCAT
* * *
35116626 GAAGCTCATACGAGCCATA-AATGGGAAGCTCTGAAGAGCTATTAATCGGGAAGCTCATGAGAGC
1 GAAGCTCATACGAGCCAAATAACGGGAAGCTCTGAAGAGCTATTAATCGAGAAGCTCATGAGAGC
35116690 CAATTATCGA-
66 CAATTATC-AT
35116700 GAAGCTC-TGGA-GAGCCAAATAACGGGAAGCTCAT-AAGAGCTAT
1 GAAGCTCAT--ACGAGCCAAATAACGGGAAGCTC-TGAAGAGCTAT
35116743 GGTGTGTCTT
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
73 1 0.01
74 76 0.75
75 23 0.23
76 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (75 bp):
GAAGCTCATACGAGCCAAATAACGGGAAGCTCTGAAGAGCTATTAATCGAGAAGCTCATGAGAGC
CAATTATCAT
Found at i:35116717 original size:25 final size:25
Alignment explanation
Indices: 35116563--35116731 Score: 108
Period size: 25 Copynumber: 6.8 Consensus size: 25
35116553 AAGCTCATAC
35116563 GAGCCAA-TATCG-GAAAGCTCTGGA
1 GAGCCAATTATCGAG-AAGCTCTGGA
35116587 GAGCC-ATTAATCGAGAAGCTC-GTGA
1 GAGCCAATT-ATCGAGAAGCTCTG-GA
35116612 GAGCCAATTATC-ATGAAGCTCAT--A
1 GAGCCAATTATCGA-GAAGCTC-TGGA
* * *
35116636 CGAGCC-ATAAAT-GGGAAGCTCTGAA
1 -GAGCCAAT-TATCGAGAAGCTCTGGA
* *
35116661 GAG-CTATTAATCGGGAAGCTCAT-GA
1 GAGCCAATT-ATCGAGAAGCTC-TGGA
35116686 GAGCCAATTATCGAGAAGCTCTGGA
1 GAGCCAATTATCGAGAAGCTCTGGA
* * *
35116711 GAGCCAAATAACGGGAAGCTC
1 GAGCCAATTATCGAGAAGCTC
35116732 ATAAGAGCTA
Statistics
Matches: 117, Mismatches: 9, Indels: 37
0.72 0.06 0.23
Matches are distributed among these distances:
23 3 0.03
24 26 0.22
25 79 0.68
26 9 0.08
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (25 bp):
GAGCCAATTATCGAGAAGCTCTGGA
Found at i:35116738 original size:25 final size:25
Alignment explanation
Indices: 35116489--35116739 Score: 88
Period size: 25 Copynumber: 10.2 Consensus size: 25
35116479 AAGCTCTTTC
* * **
35116489 GAGCCATATAATGGGAAGCTCATGT
1 GAGCCAAATAACGGGAAGCTCATAA
** *
35116514 GAGCCATGTAATGGGAAGCTCATAA
1 GAGCCAAATAACGGGAAGCTCATAA
* * * * *
35116539 GAGTC--GTAATTGAGAAGCTCATAC
1 GAGCCAAATAA-CGGGAAGCTCATAA
* * *
35116563 GAGCC-AATATCGGAAAGCTC-TGGA
1 GAGCCAAATAACGGGAAGCTCAT-AA
* * * *
35116587 GAGCC-ATTAATCGAGAAGCTCGTGA
1 GAGCCAAATAA-CGGGAAGCTCATAA
* * ** *
35116612 GAGCCAATTATCATGAAGCTCATAC
1 GAGCCAAATAACGGGAAGCTCATAA
* *
35116637 GAGCCATA-AATGGGAAGCTC-TGAA
1 GAGCCAAATAACGGGAAGCTCAT-AA
* * *
35116661 GAG-CTATTAATCGGGAAGCTCATGA
1 GAGCCAAATAA-CGGGAAGCTCATAA
* * * *
35116686 GAGCCAATTATCGAGAAGCTC-TGGA
1 GAGCCAAATAACGGGAAGCTCAT-AA
35116711 GAGCCAAATAACGGGAAGCTCATAA
1 GAGCCAAATAACGGGAAGCTCATAA
35116736 GAGC
1 GAGC
35116740 TATGGTGTGT
Statistics
Matches: 170, Mismatches: 43, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
23 7 0.04
24 46 0.27
25 105 0.62
26 12 0.07
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGCCAAATAACGGGAAGCTCATAA
Found at i:35116876 original size:8 final size:8
Alignment explanation
Indices: 35116863--35116887 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35116853 ATACTTTCGG
35116863 ATATGTTT
1 ATATGTTT
35116871 ATATGTTT
1 ATATGTTT
35116879 ATATGTTT
1 ATATGTTT
35116887 A
1 A
35116888 AGTAATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
ATATGTTT
Found at i:35119395 original size:55 final size:55
Alignment explanation
Indices: 35119297--35119403 Score: 189
Period size: 55 Copynumber: 1.9 Consensus size: 55
35119287 GTATCCATTG
35119297 GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATT-AATTTGTAA
*
35119353 GATGATAAATCATCACTTTTA-TTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATTAATTTG
35119404 CAATCTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 6 0.12
55 23 0.46
56 21 0.42
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.40
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTACTTTGAATAGTGCTAATGAATAATTAATTTGTAA
Found at i:35125797 original size:2 final size:2
Alignment explanation
Indices: 35125790--35125848 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
35125780 GAAGGACAAA
35125790 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35125832 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
35125849 AGTACCTCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35130035 original size:48 final size:50
Alignment explanation
Indices: 35129977--35130158 Score: 206
Period size: 50 Copynumber: 3.7 Consensus size: 50
35129967 GGGATGAGAC
* * **
35129977 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCA-TTA-ATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
*
35130025 CCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * * * **
35130075 CCCCCGTAAGATCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * * * *
35130125 CCCATGCAAGACCATATCTGGGATATGACATTGG
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGG
35130159 AAGTACAGGA
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
48 33 0.29
49 1 0.01
50 78 0.70
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
Found at i:35130450 original size:20 final size:20
Alignment explanation
Indices: 35130425--35130473 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
35130415 TGAGTTATTT
35130425 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
35130445 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
35130465 AAG-AAGCAA
1 AAGTAAGCAA
35130474 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:35134326 original size:20 final size:20
Alignment explanation
Indices: 35134287--35134391 Score: 72
Period size: 20 Copynumber: 5.2 Consensus size: 20
35134277 ACACCAGGGA
*
35134287 GCACCGTAGTGC-TATCAGAG
1 GCACCGTAGTGCAAAT-AGAG
35134307 GCACCGTAGTGCAAATAGAG
1 GCACCGTAGTGCAAATAGAG
* *
35134327 GTA-CGATTGTGC-AATCAGAG
1 GCACCG-TAGTGCAAAT-AGAG
* *
35134347 GCACTGGAGTGCAAATAGAG
1 GCACCGTAGTGCAAATAGAG
* ** * *
35134367 ACACCAAAGTGTAAACAGAG
1 GCACCGTAGTGCAAATAGAG
35134387 GCACC
1 GCACC
35134392 AAAGTCCAAG
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
19 5 0.08
20 55 0.83
21 6 0.09
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (20 bp):
GCACCGTAGTGCAAATAGAG
Found at i:35141943 original size:20 final size:20
Alignment explanation
Indices: 35141917--35141964 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
35141907 TTCCATATTT
35141917 CAGAGGCACCATAGTGCTTA
1 CAGAGGCACCATAGTGCTTA
*
35141937 TAGAGGCACCATAGTGCTTA
1 CAGAGGCACCATAGTGCTTA
35141957 CAGAGGCA
1 CAGAGGCA
35141965 TGAATGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (20 bp):
CAGAGGCACCATAGTGCTTA
Found at i:35142072 original size:60 final size:60
Alignment explanation
Indices: 35141973--35142086 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
35141963 CATGAATGTG
* * * *
35141973 CAAACAAGGGTACCGAAGTACAAACAGGGGAACTAAAGTAAAAAAAGGAGTACCAAAGTA
1 CAAACAAGGGTACCAAAGTACAAACAGGAGAACCAAAGTAAAAAAAGAAGTACCAAAGTA
* * * * * *
35142033 CAAACAGGGGTACCAAAGTACAAGCAGGAGTACCGAAGTACAAACAGAAGTACC
1 CAAACAAGGGTACCAAAGTACAAACAGGAGAACCAAAGTAAAAAAAGAAGTACC
35142087 TGTAACAACC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (60 bp):
CAAACAAGGGTACCAAAGTACAAACAGGAGAACCAAAGTAAAAAAAGAAGTACCAAAGTA
Found at i:35142084 original size:20 final size:20
Alignment explanation
Indices: 35141973--35142086 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
35141963 CATGAATGTG
*
35141973 CAAACAAGG-GTACCGAAGTA
1 CAAAC-AGGAGTACCAAAGTA
* * *
35141993 CAAACAGGGGAACTAAAGTA
1 CAAACAGGAGTACCAAAGTA
* *
35142013 AAAAAAGGAGTACCAAAGTA
1 CAAACAGGAGTACCAAAGTA
*
35142033 CAAACAGGGGTACCAAAGTA
1 CAAACAGGAGTACCAAAGTA
* *
35142053 CAAGCAGGAGTACCGAAGTA
1 CAAACAGGAGTACCAAAGTA
*
35142073 CAAACAGAAGTACC
1 CAAACAGGAGTACC
35142087 TGTAACAACC
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
19 3 0.04
20 74 0.96
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (20 bp):
CAAACAGGAGTACCAAAGTA
Found at i:35142086 original size:40 final size:40
Alignment explanation
Indices: 35141978--35142079 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 40
35141968 ATGTGCAAAC
* *
35141978 AAGG-GTACCGAAGTACAAACAGGGGAACTAAAGTAAAAA
1 AAGGAGTACCGAAGTACAAACAGGGGTACCAAAGTAAAAA
* * *
35142017 AAGGAGTACCAAAGTACAAACAGGGGTACCAAAGTACAAG
1 AAGGAGTACCGAAGTACAAACAGGGGTACCAAAGTAAAAA
*
35142057 CAGGAGTACCGAAGTACAAACAG
1 AAGGAGTACCGAAGTACAAACAG
35142080 AAGTACCTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 4 0.07
40 51 0.93
ACGTcount: A:0.48, C:0.17, G:0.25, T:0.10
Consensus pattern (40 bp):
AAGGAGTACCGAAGTACAAACAGGGGTACCAAAGTAAAAA
Found at i:35143789 original size:39 final size:40
Alignment explanation
Indices: 35143672--35143895 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
35143662 GCTCCTCGTT
* * *
35143672 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
35143712 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
35143752 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
35143791 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
35143830 CAAATGCCTTC-GGATCTTAGTCCGGATATT-TTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
35143871 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35143896 CATCATTCAA
Statistics
Matches: 164, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 71 0.43
40 76 0.46
41 15 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:35143855 original size:118 final size:120
Alignment explanation
Indices: 35143672--35143895 Score: 298
Period size: 118 Copynumber: 1.9 Consensus size: 120
35143662 GCTCCTCGTT
*
35143672 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
*
35143737 AT-TTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATATT-GTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * **
35143791 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCC
* *
35143853 GGATATTTTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATTGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
35143896 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
117 4 0.04
118 53 0.58
119 35 0.38
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
ATATTGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:35144485 original size:22 final size:21
Alignment explanation
Indices: 35144460--35144503 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
35144450 GTACCACATA
*
35144460 TAATGACA-TACATTTTACTAAC
1 TAATG-CATTACATATTA-TAAC
35144482 TAATGCATTACATATTATAAC
1 TAATGCATTACATATTATAAC
35144503 T
1 T
35144504 CAATATGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.39
Consensus pattern (21 bp):
TAATGCATTACATATTATAAC
Found at i:35146220 original size:23 final size:24
Alignment explanation
Indices: 35146189--35146236 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
35146179 GTTAAGGGAC
*
35146189 TTTTCATGATGTTT-ATAAATTAT
1 TTTTCATGATATTTGATAAATTAT
* *
35146212 TTTTGATGATATTTGATAGATTAT
1 TTTTCATGATATTTGATAAATTAT
35146236 T
1 T
35146237 AATCTTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (24 bp):
TTTTCATGATATTTGATAAATTAT
Found at i:35147659 original size:12 final size:12
Alignment explanation
Indices: 35147642--35147671 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35147632 TCAATGAGTT
*
35147642 ACACGGCCTAGC
1 ACACGGCCTAAC
35147654 ACACGGCCTAAC
1 ACACGGCCTAAC
35147666 ACACGG
1 ACACGG
35147672 GCGTGTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:35152479 original size:27 final size:26
Alignment explanation
Indices: 35152448--35152506 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
35152438 AAGGTTGTTT
*
35152448 AATGACCGAAATACCCCTATAAGGTA
1 AATGACCGAAATACCCCTAGAAGGTA
* * *
35152474 GAATGACCGTAATGCCCCTAGAGGGTA
1 -AATGACCGAAATACCCCTAGAAGGTA
35152501 AATGAC
1 AATGAC
35152507 TATTTTGCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AATGACCGAAATACCCCTAGAAGGTA
Found at i:35154029 original size:20 final size:20
Alignment explanation
Indices: 35153999--35154050 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
35153989 GGCGTGTTAC
*
35153999 AGTACCGAAGTCCAAACAGG
1 AGTACCGAAGTACAAACAGG
* *
35154019 GGTACCAAAGTACAAACAGG
1 AGTACCGAAGTACAAACAGG
35154039 AGTACCGAAGTA
1 AGTACCGAAGTA
35154051 AATTCCTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (20 bp):
AGTACCGAAGTACAAACAGG
Found at i:35158241 original size:16 final size:17
Alignment explanation
Indices: 35158211--35158243 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35158201 TGCCAAAATG
*
35158211 AGATCAAAATCATCAAA
1 AGATAAAAATCATCAAA
35158228 AGATAAAAAT-ATCAAA
1 AGATAAAAATCATCAAA
35158244 CTAGCAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
AGATAAAAATCATCAAA
Found at i:35161264 original size:20 final size:20
Alignment explanation
Indices: 35161236--35161389 Score: 159
Period size: 20 Copynumber: 7.8 Consensus size: 20
35161226 TACAGAGGCA
35161236 CAAATGTACAAATAGGGGTAC
1 CAAA-GTACAAATAGGGGTAC
*
35161257 AAAAGTACAAATAGGGGTAC
1 CAAAGTACAAATAGGGGTAC
** * *
35161277 TGAAGTACTAGTA-GGGTAC
1 CAAAGTACAAATAGGGGTAC
**
35161296 CAAAGTACAAACGGGGGTAC
1 CAAAGTACAAATAGGGGTAC
** *
35161316 TGAAGTACAAATAGTGGTAC
1 CAAAGTACAAATAGGGGTAC
*
35161336 CGAAGTACAAATA-GGGTAC
1 CAAAGTACAAATAGGGGTAC
* *
35161355 GAAAGTACAAACAGGGGTAC
1 CAAAGTACAAATAGGGGTAC
*
35161375 CAGAGTACAAATAGG
1 CAAAGTACAAATAGG
35161390 AATACCGAAG
Statistics
Matches: 107, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
19 28 0.26
20 76 0.71
21 3 0.03
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17
Consensus pattern (20 bp):
CAAAGTACAAATAGGGGTAC
Found at i:35161303 original size:39 final size:39
Alignment explanation
Indices: 35161241--35161389 Score: 176
Period size: 39 Copynumber: 3.8 Consensus size: 39
35161231 AGGCACAAAT
*
35161241 GTACAAATAGGGGTACAAAAGTACAAATAGGGGTACTGAA
1 GTACAAATA-GGGTACCAAAGTACAAATAGGGGTACTGAA
* * **
35161281 GTACTAGTAGGGTACCAAAGTACAAACGGGGGTACTGAA
1 GTACAAATAGGGTACCAAAGTACAAATAGGGGTACTGAA
*
35161320 GTACAAATAGTGGTACCGAAGTACAAATA-GGGTAC-GAAA
1 GTACAAATAG-GGTACCAAAGTACAAATAGGGGTACTG-AA
* *
35161359 GTACAAACAGGGGTACCAGAGTACAAATAGG
1 GTACAAATA-GGGTACCAAAGTACAAATAGG
35161390 AATACCGAAG
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 67 0.73
40 24 0.26
ACGTcount: A:0.42, C:0.13, G:0.28, T:0.17
Consensus pattern (39 bp):
GTACAAATAGGGTACCAAAGTACAAATAGGGGTACTGAA
Found at i:35161335 original size:59 final size:58
Alignment explanation
Indices: 35161236--35161401 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 58
35161226 TACAGAGGCA
* * * *
35161236 CAAATGTACAAATAGGGGTACAAAAGTACAAATAGGGGTACTGAAGTACTAGTAGGGTAC
1 CAAA-GTACAAACAGGGGTAC-AAAGTACAAATAGGGGTACCGAAGTACAAATAGGGTAC
* * *
35161296 CAAAGTACAAACGGGGGTACTGAAGTACAAATAGTGGTACCGAAGTACAAATAGGGTAC
1 CAAAGTACAAACAGGGGTAC-AAAGTACAAATAGGGGTACCGAAGTACAAATAGGGTAC
* * **
35161355 GAAAGTACAAACAGGGGTACCAGAGTACAAATAGGAATACCGAAGTA
1 CAAAGTACAAACAGGGGTA-CAAAGTACAAATAGGGGTACCGAAGTA
35161402 AATTCCCATA
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 85 0.94
60 5 0.06
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.17
Consensus pattern (58 bp):
CAAAGTACAAACAGGGGTACAAAGTACAAATAGGGGTACCGAAGTACAAATAGGGTAC
Found at i:35162767 original size:6 final size:6
Alignment explanation
Indices: 35162758--35162791 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35162748 AATAAAATAA
* *
35162758 AAATCT AAATCT AAATCC AAATCC AAATCC AAAT
1 AAATCC AAATCC AAATCC AAATCC AAATCC AAAT
35162792 GAGCCCTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (6 bp):
AAATCC
Found at i:35173680 original size:27 final size:27
Alignment explanation
Indices: 35173641--35174081 Score: 597
Period size: 27 Copynumber: 16.4 Consensus size: 27
35173631 GATTCGTGGG
35173641 AAAATGACTGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
35173668 AAAATGACCGAAATACCCCCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
35173695 AAAATGACTGAAATACCCTCAAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
35173722 AAAATGACCGAAATACCCTCAAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
35173749 AAAATGATTGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
35173776 AAAATGAAC-GAAATACCCTCGAAGGGT
1 AAAATG-ACTGAAATACCCTCGAAGGGT
*
35173803 AAAATGACTGAAATACCCTCGAAAGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
35173830 AAAATGACTGAAATACCCCCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* * *
35173857 AAAATGA-TCAAAATACCCTCAAAAGGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
* *
35173884 AAAATGACAGAAATACCC-CGAAAGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
35173910 AAAATGACTAAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
35173937 AAAATGACTAAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
35173964 AAAATGA-TCGAAATACCCTCGAAGGGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
* *
35173991 AAAATAACCGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
35174018 AAAAT-AATCGAAATACCCCCGAAGGGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
* * *
35174045 AAAATGATTGAAATACCC-CCATAGAGT
1 AAAATGACTGAAATACCCTCGA-AGGGT
35174072 AAAATGACTG
1 AAAATGACTG
35174082 TTATACTCTT
Statistics
Matches: 371, Mismatches: 33, Indels: 20
0.88 0.08 0.05
Matches are distributed among these distances:
26 30 0.08
27 338 0.91
28 3 0.01
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTCGAAGGGT
Found at i:35174507 original size:33 final size:34
Alignment explanation
Indices: 35174456--35174526 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
35174446 TAAGGCCCGC
* *
35174456 ACTGTTACTATTTTGGGCTAAAGCCCACACTG-T
1 ACTGTTACTATATAGGGCTAAAGCCCACACTGAT
* * * *
35174489 ACTGTTACTGTATAGGGCTCAGGCCCAGACTGAT
1 ACTGTTACTATATAGGGCTAAAGCCCACACTGAT
35174523 ACTG
1 ACTG
35174527 CATGATTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTACTATATAGGGCTAAAGCCCACACTGAT
Found at i:35178377 original size:27 final size:27
Alignment explanation
Indices: 35178325--35178383 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
35178315 ATATGCACTC
* *
35178325 CATGCATTCCATACGAATCATGCATTT
1 CATGCATTCCATACGAACCATACATTT
*
35178352 CATGCATTCCATGC-AACCCATACATTT
1 CATGCATTCCATACGAA-CCATACATTT
35178379 CATGC
1 CATGC
35178384 GGATCATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (27 bp):
CATGCATTCCATACGAACCATACATTT
Found at i:35190453 original size:5 final size:5
Alignment explanation
Indices: 35190445--35190469 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35190435 TAAAAAAAAA
35190445 AAACT AAACT AAACT AAACT AAACT
1 AAACT AAACT AAACT AAACT AAACT
35190470 CACCGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AAACT
Found at i:35196855 original size:24 final size:24
Alignment explanation
Indices: 35196810--35196872 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
35196800 TGGATCTCTT
*
35196810 GAGCTTCCTGATATATGGCTCTCAC
1 GAGCTTCCCGAT-TATGGCTCTCAC
* *
35196835 GAGCTTCCCGATTATGGCTCTTAT
1 GAGCTTCCCGATTATGGCTCTCAC
35196859 GAGCTTCCCG-TTAT
1 GAGCTTCCCGATTAT
35196873 ATAGCTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 4 0.11
24 20 0.57
25 11 0.31
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGATTATGGCTCTCAC
Found at i:35196885 original size:25 final size:24
Alignment explanation
Indices: 35196835--35196905 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 24
35196825 TGGCTCTCAC
* * **
35196835 GAGCTTCCCGATTATGGCTCTTAT
1 GAGCTTCCCGTTTATAGCTCAAAT
35196859 GAGCTTCCCGTTATATAGCTCAAAT
1 GAGCTTCCCGTT-TATAGCTCAAAT
35196884 GAGCTTCCCGTTTATATGCTCA
1 GAGCTTCCCGTTTATA-GCTCA
35196906 CACGAGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 15 0.37
25 26 0.63
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTTATAGCTCAAAT
Found at i:35196912 original size:25 final size:25
Alignment explanation
Indices: 35196810--35196912 Score: 84
Period size: 25 Copynumber: 4.2 Consensus size: 25
35196800 TGGATCTCTT
* * * *
35196810 GAGCTTCCTGATATATGGCTCTCAC
1 GAGCTTCCCGTTATATAGCTCACAC
* * ** *
35196835 GAGCTTCCCGAT-TATGGCTCTTAT
1 GAGCTTCCCGTTATATAGCTCACAC
* *
35196859 GAGCTTCCCGTTATATAGCTCAAAT
1 GAGCTTCCCGTTATATAGCTCACAC
35196884 GAGCTTCCCGTT-TATATGCTCACAC
1 GAGCTTCCCGTTATATA-GCTCACAC
35196909 GAGC
1 GAGC
35196913 ATTCTCGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
24 25 0.37
25 42 0.63
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCACAC
Found at i:35201577 original size:29 final size:26
Alignment explanation
Indices: 35201522--35201587 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 26
35201512 ACTCTTAGTG
35201522 ATTTTAAAATTTATTCTTTTACTTTT
1 ATTTTAAAATTTATTCTTTTACTTTT
*
35201548 ATTTTAAGGAATTTAATTTTTTTACTTTT
1 ATTTTAA--AATTT-ATTCTTTTACTTTT
35201577 ATGATTTAAAA
1 AT--TTTAAAA
35201588 ATGTAAGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 7 0.21
28 5 0.15
29 17 0.50
31 5 0.15
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (26 bp):
ATTTTAAAATTTATTCTTTTACTTTT
Found at i:35201910 original size:3 final size:3
Alignment explanation
Indices: 35201902--35201935 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
35201892 GGTTTATCAA
*
35201902 AAG AAG AAG AAA AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
35201936 AAAAAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35201917 original size:12 final size:12
Alignment explanation
Indices: 35201900--35201943 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
35201890 AGGGTTTATC
35201900 AAAAGAAGAAGA
1 AAAAGAAGAAGA
35201912 AAAAGAAGAAGA
1 AAAAGAAGAAGA
*
35201924 AGAAGAA-AAGA
1 AAAAGAAGAAGA
35201935 AAAA-AAGAA
1 AAAAGAAGAA
35201944 TTTGGGATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 2 0.07
11 9 0.31
12 18 0.62
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAGA
Found at i:35201919 original size:9 final size:9
Alignment explanation
Indices: 35201905--35201943 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
35201895 TTATCAAAAG
35201905 AAGAAGAAA
1 AAGAAGAAA
*
35201914 AAGAAGAAG
1 AAGAAGAAA
35201923 AAGAAG-AA
1 AAGAAGAAA
35201931 AAGAA-AAA
1 AAGAAGAAA
35201939 AAGAA
1 AAGAA
35201944 TTTGGGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 13 0.48
9 14 0.52
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:35202714 original size:3 final size:3
Alignment explanation
Indices: 35202708--35202741 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35202698 TTTTACAATC
35202708 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
35202742 AATCTTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:35202925 original size:31 final size:30
Alignment explanation
Indices: 35202888--35202956 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
35202878 ATGTTAGTGC
*
35202888 GTGACTGATTTGTCACTTTTTGATAACGTT-A
1 GTGACTGATTTGTCA-TTTTT-ATAAAGTTGA
* * *
35202919 GTGACTGTTTTGTTATTTTTCTAAAGTTGA
1 GTGACTGATTTGTCATTTTTATAAAGTTGA
35202949 GTGACTGA
1 GTGACTGA
35202957 AATGAAACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 6 0.19
30 13 0.41
31 13 0.41
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (30 bp):
GTGACTGATTTGTCATTTTTATAAAGTTGA
Found at i:35205982 original size:3 final size:3
Alignment explanation
Indices: 35205974--35206015 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
35205964 ATCTTCATCT
35205974 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35206016 TTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35206020 original size:3 final size:3
Alignment explanation
Indices: 35206014--35206044 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35206004 ATAATAATAA
35206014 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35206045 TTGTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35234588 original size:43 final size:43
Alignment explanation
Indices: 35234541--35234633 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
35234531 ATCTCCTATT
*
35234541 GATGCCAACAGCCC-AGCCATGGCCTTACACGAAATAACATATC
1 GATGCCAA-AGCCCTAGACATGGCCTTACACGAAATAACATATC
* * * **
35234584 GATGCCAATGCCCTATACATGGCCTTACACGAAGTCTCATATC
1 GATGCCAAAGCCCTAGACATGGCCTTACACGAAATAACATATC
35234627 GATGCCA
1 GATGCCA
35234634 TATCCGAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (43 bp):
GATGCCAAAGCCCTAGACATGGCCTTACACGAAATAACATATC
Found at i:35241354 original size:43 final size:42
Alignment explanation
Indices: 35241307--35241409 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 42
35241297 TAGCTCAGCT
* *
35241307 ATGGTCTTACACGAAATCACATATCAATGCCAATGTCCCATAC
1 ATGGTCTTACACGAAATCACATATCAATGCC-ATATCCCAAAC
* * * * *
35241350 ATGGTCTTACACGAAGTCTCATATCGATGCCATATCCTAAAT
1 ATGGTCTTACACGAAATCACATATCAATGCCATATCCCAAAC
*
35241392 ATGGTCTTACACGTAATC
1 ATGGTCTTACACGAAATC
35241410 TCGGAAACCC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
42 23 0.45
43 28 0.55
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGAAATCACATATCAATGCCATATCCCAAAC
Found at i:35243145 original size:40 final size:39
Alignment explanation
Indices: 35243081--35243371 Score: 307
Period size: 40 Copynumber: 7.3 Consensus size: 39
35243071 TCTTCGGAAT
* *
35243081 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
*
35243120 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
35243160 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * * *
35243200 TTAACTCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
35243240 TTAGCCCAGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * * *
35243280 TTAACCCGGGTATAGCAACTCGTACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
35243320 TTAGCCCGGATAAAATCACTAGCATAATTGCCTTCGGG-C
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
*
35243359 TTAGCCCAGATAT
1 TTAGCCCGGATAT
35243372 CATTCAAATG
Statistics
Matches: 206, Mismatches: 39, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.00
39 23 0.11
40 172 0.83
41 10 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:35243219 original size:80 final size:80
Alignment explanation
Indices: 35243081--35243361 Score: 449
Period size: 80 Copynumber: 3.5 Consensus size: 80
35243071 TCTTCGGAAT
* * * * * * *
35243081 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
35243145 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
35243160 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACTCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
35243225 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
35243240 TTAGCCCAGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGTAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
35243305 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
35243320 TTAGCCCGGATAAAATCACTAGCATAATTGCCTTCGGG-CTTA
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTA
35243362 GCCCAGATAT
Statistics
Matches: 188, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
79 8 0.04
80 180 0.96
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:35251298 original size:40 final size:39
Alignment explanation
Indices: 35251234--35251525 Score: 343
Period size: 40 Copynumber: 7.3 Consensus size: 39
35251224 TCTTCGGAAT
* *
35251234 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
* *
35251273 TTAGCCCGGATATATCAACTCGCACAAATACCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
35251313 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
35251353 TTAACCCGGGTATAGCAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
35251393 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
35251433 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
35251473 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGGC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
35251513 TTAGCCCGGATAT
1 TTAGCCCGGATAT
35251526 CATTCAAATG
Statistics
Matches: 212, Mismatches: 34, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
39 13 0.06
40 189 0.89
41 10 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:35251361 original size:80 final size:80
Alignment explanation
Indices: 35251234--35251525 Score: 469
Period size: 80 Copynumber: 3.7 Consensus size: 80
35251224 TCTTCGGAAT
* * * * * *
35251234 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
*
35251298 AAATACCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
35251313 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTTGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
35251378 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
35251393 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
35251458 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
35251473 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGGCTTAGCCCGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATAT
35251526 CATTCAAATG
Statistics
Matches: 199, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
79 4 0.02
80 195 0.98
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:35253954 original size:79 final size:82
Alignment explanation
Indices: 35253837--35254021 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 82
35253827 GCTACTCGTT
* * *
35253837 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTCA-CC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTT-AGCC
* *
35253899 CGGATTTAGTAAC-TCGCA
64 CGGATATAGTAACTTAGCA
* *
35253917 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAGCCCG
* *
35253980 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
35253997 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35254022 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 4 0.04
79 53 0.58
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAGCCCG
GATATAGTAACTTAGCA
Found at i:35254021 original size:40 final size:40
Alignment explanation
Indices: 35253818--35254021 Score: 222
Period size: 40 Copynumber: 5.1 Consensus size: 40
35253808 CGGAATTTAA
** *
35253818 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
35253858 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTCA-C
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTT-AGC
*
35253898 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
35253937 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
35253977 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
35254017 CCGGA
1 CCGGA
35254022 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
38 3 0.02
39 32 0.23
40 91 0.65
41 13 0.09
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:35256420 original size:30 final size:29
Alignment explanation
Indices: 35256380--35256627 Score: 169
Period size: 30 Copynumber: 8.3 Consensus size: 29
35256370 TACCGATCAA
*
35256380 GAAAGGGGATGGTGACGACCATCAAACTAT
1 GAAAAGGGATGGT-ACGACCATCAAACTAT
35256410 GAAAAGGGATGGTGACGACCATCAAACTAT
1 GAAAAGGGATGGT-ACGACCATCAAACTAT
* * * *
35256440 GAAAAGGGATGGCTTC-AGCTATCGATCTAT
1 GAAAAGGGATGG-TACGA-CCATCAAACTAT
* ** *** *
35256470 G-AAAGGGATGCTTTGGGTATCAATCTAT
1 GAAAAGGGATGGTACGACCATCAAACTAT
* * * *
35256498 GAAAAGGGATGGCTTCGACTATCGATCTAT
1 GAAAAGGGATGG-TACGACCATCAAACTAT
* * * *
35256528 GAAAAGGGATGGCTTCGGCCTTCAAATTAT
1 GAAAAGGGATGG-TACGACCATCAAACTAT
* *
35256558 GAAAAGGGATGGTGATGACCATCGAA-TCAT
1 GAAAAGGGATGGT-ACGACCATCAAACT-AT
* *
35256588 GAAAAGGGATGGTGATGACCATCAAATTAT
1 GAAAAGGGATGGT-ACGACCATCAAACTAT
*
35256618 GAAAAAGGAT
1 GAAAAGGGAT
35256628 AGCTTTGGCT
Statistics
Matches: 182, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
28 13 0.07
29 21 0.12
30 146 0.80
31 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (29 bp):
GAAAAGGGATGGTACGACCATCAAACTAT
Found at i:35256472 original size:60 final size:60
Alignment explanation
Indices: 35256406--35256658 Score: 216
Period size: 60 Copynumber: 4.2 Consensus size: 60
35256396 GACCATCAAA
35256406 CTATGAAAAGGGATGGTGACGACCATCAAACTATGAAAAGGGATGGCTTCAG-CTATCGAT
1 CTATGAAAAGGGATGGT-ACGACCATCAAACTATGAAAAGGGATGGCTTCAGACTATCGAT
* ** *** *
35256466 CTATG-AAAGGGATGCTTTGGGTATCAATCTATGAAAAGGGATGGCTTC-GACTATCGAT
1 CTATGAAAAGGGATGGTACGACCATCAAACTATGAAAAGGGATGGCTTCAGACTATCGAT
* * * * * *
35256524 CTATGAAAAGGGATGGCTTCGGCCTTCAAATTATGAAAAGGGATGG--TGATGACCATCGAAT
1 CTATGAAAAGGGATGG-TACGACCATCAAACTATGAAAAGGGATGGCTTCA-GACTATCG-AT
* * * * * * *
35256585 C-ATGAAAAGGGATGGTGATGACCATCAAATTATGAAAAAGGATAGCTT-TGGCTATCAAAT
1 CTATGAAAAGGGATGGT-ACGACCATCAAACTATGAAAAGGGATGGCTTCAGACTATC-GAT
35256645 -TATGAAAAGGGATG
1 CTATGAAAAGGGATG
35256659 TGCCAATCAT
Statistics
Matches: 156, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
57 1 0.01
58 40 0.26
59 20 0.13
60 91 0.58
61 3 0.02
62 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (60 bp):
CTATGAAAAGGGATGGTACGACCATCAAACTATGAAAAGGGATGGCTTCAGACTATCGAT
Done.