Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold325
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: 982141
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 57799 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:279580 original size:32 final size:32
Alignment explanation
Indices: 279538--279733 Score: 250
Period size: 32 Copynumber: 6.1 Consensus size: 32
279528 TTGATAGCTT
*
279538 TGTGTCGATCATATTACCATTACTGATGGTTG
1 TGTGCCGATCATATTACCATTACTGATGGTTG
*
279570 TGTGCCGATCATATTACCATTACTGATAGTTG
1 TGTGCCGATCATATTACCATTACTGATGGTTG
*
279602 TGTGCCGATCATATTACCATTATTGATGGTTG
1 TGTGCCGATCATATTACCATTACTGATGGTTG
* *
279634 TGTGTCGATCATATTACTATTACTGATGGCTT-
1 TGTGCCGATCATATTACCATTACTGATGG-TTG
* * * *
279666 TGTACCGATCATACTACTATTATTGATGGTTG
1 TGTGCCGATCATATTACCATTACTGATGGTTG
* *** *
279698 TGTGCCAATCATATTACTGCTACTGATGGCTG
1 TGTGCCGATCATATTACCATTACTGATGGTTG
279730 TGTG
1 TGTG
279734 TTGGGTTGGT
Statistics
Matches: 144, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
31 2 0.01
32 140 0.97
33 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (32 bp):
TGTGCCGATCATATTACCATTACTGATGGTTG
Found at i:279715 original size:64 final size:64
Alignment explanation
Indices: 279529--279733 Score: 277
Period size: 64 Copynumber: 3.2 Consensus size: 64
279519 GCAATGCAAT
* * *
279529 TGATAGCTTTGTGTCGATCATATTACCATTACTGATGGTTGTGTGCCGATCATATTACCATTAC
1 TGATAGCTTTGTGCCGATCATATTACCATTATTGATGGTTGTGTGCCGATCATATTACTATTAC
*
279593 TGATAG-TTGTGTGCCGATCATATTACCATTATTGATGGTTGTGTGTCGATCATATTACTATTAC
1 TGATAGCTT-TGTGCCGATCATATTACCATTATTGATGGTTGTGTGCCGATCATATTACTATTAC
* * * * * **
279657 TGATGGCTTTGTACCGATCATACTACTATTATTGATGGTTGTGTGCCAATCATATTACTGCTAC
1 TGATAGCTTTGTGCCGATCATATTACCATTATTGATGGTTGTGTGCCGATCATATTACTATTAC
* *
279721 TGATGGCTGTGTG
1 TGATAGCTTTGTG
279734 TTGGGTTGGT
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
63 2 0.02
64 121 0.97
65 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (64 bp):
TGATAGCTTTGTGCCGATCATATTACCATTATTGATGGTTGTGTGCCGATCATATTACTATTAC
Found at i:279917 original size:28 final size:28
Alignment explanation
Indices: 279886--279963 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
279876 ATTGTTACTA
*
279886 TATTGGGCTAAGGTCCACACTGATTCTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
279914 TATTGGGCTAAGGCCCACACTGATTCTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
*
279942 TGTTGGGCTAAGGCCCACACTG
1 TATTGGGCTAAGGCCCACACTG
279964 TACTGTTACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACACTGATTCTG
Found at i:282296 original size:40 final size:40
Alignment explanation
Indices: 282241--282326 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
282231 AATCATAAGT
*
282241 ATACACGACCTAATGAATGAATGCTTTTAAGCTAACTTAA
1 ATACACGACCTAATGAATGAATGCTTTTAAGCTAACTCAA
282281 ATACACGACCTAATGAATGAATGCTTTTAAGCTAACTCAA
1 ATACACGACCTAATGAATGAATGCTTTTAAGCTAACTCAA
282321 AGTACA
1 A-TACA
282327 ACTACAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (40 bp):
ATACACGACCTAATGAATGAATGCTTTTAAGCTAACTCAA
Found at i:286340 original size:45 final size:45
Alignment explanation
Indices: 286276--286362 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
286266 TGTGAACCGA
* *
286276 ACATCATTAATTAGTAAGGTGGTTGCTATGTGCTGATTCCACTAG
1 ACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCACTAG
*
286321 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
1 ACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
286363 CTAGGATCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (45 bp):
ACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCACTAG
Found at i:295264 original size:27 final size:28
Alignment explanation
Indices: 295233--295624 Score: 309
Period size: 27 Copynumber: 14.5 Consensus size: 28
295223 CCCCAAAATA
** *
295233 GGTAAAATGACAAAAATACCCCTGA-AG
1 GGTAAAATGACTGAAATACCCCTCATAG
** *
295260 GGTAAAATGACT-ATTTTACCCCTAATA-
1 GGTAAAATGACTGA-AATACCCCTCATAG
* * * *
295287 GATGAAAATGACAGAAATA-ACCTCAGAG
1 GGT-AAAATGACTGAAATACCCCTCATAG
*
295315 GGTAAAATGA-TCGAAATA-TCCTCATAG
1 GGTAAAATGACT-GAAATACCCCTCATAG
*
295342 GGTAAAAT-AATCGAAATACCCC-CATAG
1 GGTAAAATGACT-GAAATACCCCTCATAG
*
295369 GGTAAAATGAGTGAAATACCCC-CATAG
1 GGTAAAATGACTGAAATACCCCTCATAG
*
295396 GGTAAAATGACTGAAATA-CCCTCATAA
1 GGTAAAATGACTGAAATACCCCTCATAG
* *
295423 GGTAAAATAACTGAAATACCCC-AATAG
1 GGTAAAATGACTGAAATACCCCTCATAG
* * **
295450 GATAAAAGGACCAAAATACCCC-CATAG
1 GGTAAAATGACTGAAATACCCCTCATAG
* * **
295477 GGTAAAAAGACCGAAATA-CCCAGATAG
1 GGTAAAATGACTGAAATACCCCTCATAG
* *
295504 GGTAAAATAATTGAAATACCCC-CATAG
1 GGTAAAATGACTGAAATACCCCTCATAG
* *
295531 GGTAAAATGA-TCGAAATACCCC-AAAAG
1 GGTAAAATGACT-GAAATACCCCTCATAG
* * * *
295558 GGTAAAATGACAGAAGTTCCCCT-ATAA
1 GGTAAAATGACTGAAATACCCCTCATAG
295585 GGTAAAATGA-TCGAAATACCCCT-ATAG
1 GGTAAAATGACT-GAAATACCCCTCATAG
295612 GGTAAAATGACTG
1 GGTAAAATGACTG
295625 TTATACCCAT
Statistics
Matches: 298, Mismatches: 49, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
26 9 0.03
27 264 0.89
28 24 0.08
29 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.19
Consensus pattern (28 bp):
GGTAAAATGACTGAAATACCCCTCATAG
Found at i:295632 original size:27 final size:27
Alignment explanation
Indices: 295291--295624 Score: 334
Period size: 27 Copynumber: 12.4 Consensus size: 27
295281 CTAATAGATG
* * * *
295291 AAAATGACAGAAATAACCTCAGAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
295318 AAAATGA-TCGAAATATCCTCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
*
295345 AAAAT-AATCGAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
*
295372 AAAATGAGTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
295399 AAAATGACTGAAATACCCTCATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * *
295426 AAAATAACTGAAATACCCCAATAGGAT
1 AAAATGACTGAAATACCCCCATAGGGT
* **
295453 AAAAGGACCAAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * **
295480 AAAAAGACCGAAATACCCAGATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
295507 AAAATAATTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
295534 AAAATGA-TCGAAATACCCCAAAAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* * * * *
295561 AAAATGACAGAAGTTCCCCTATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
295588 AAAATGA-TCGAAATACCCCTATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
295615 AAAATGACTG
1 AAAATGACTG
295625 TTATACCCAT
Statistics
Matches: 257, Mismatches: 43, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 252 0.98
28 3 0.01
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.19
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:295934 original size:26 final size:26
Alignment explanation
Indices: 295855--295935 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
295845 TTTGCCACAT
*
295855 ATACTATTACTGGCAGCTTTGTTGCA
1 ATACTATTACTGGCAGCTTTGTTGCG
* *
295881 ATACTGA-TACTGGCAGCTCTGCTGCG
1 ATACT-ATTACTGGCAGCTTTGTTGCG
* * *
295907 ATTCTATTACTGGTAGCTTTGTTACG
1 ATACTATTACTGGCAGCTTTGTTGCG
295933 ATA
1 ATA
295936 TTGGTGTGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
25 1 0.02
26 42 0.95
27 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGTTGCG
Found at i:296135 original size:56 final size:55
Alignment explanation
Indices: 296075--296187 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 55
296065 CATAGATTTG
* * *
296075 GTATTGAGCTAAGGTCCACACTGATT-CTATATTGGGCTAAGGCCCACACTGTTACT
1 GTATTGAGCTAAGGCCCACACTG-TTACTATATTGGGCGAAGGACCACACTG-TACT
296131 GTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACT
1 GTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACT
296186 GT
1 GT
296188 CACTAAATAG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
55 8 0.15
56 45 0.85
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (55 bp):
GTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACT
Found at i:296182 original size:28 final size:28
Alignment explanation
Indices: 296076--296182 Score: 144
Period size: 28 Copynumber: 3.8 Consensus size: 28
296066 ATAGATTTGG
*
296076 TATTGAGCTAAGGTCCACACTGATT-CTA
1 TATTGAGCTAAGGCCCACACTG-TTACTA
* *
296104 TATTGGGCTAAGGCCCACACTGTTACTG
1 TATTGAGCTAAGGCCCACACTGTTACTA
296132 TATTGAGCTAAGGCCCACACTGTTACTA
1 TATTGAGCTAAGGCCCACACTGTTACTA
* * *
296160 TATTGGGCGAAGGACCACACTGT
1 TATTGAGCTAAGGCCCACACTGT
296183 ACTGTCACTA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
27 2 0.03
28 68 0.97
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (28 bp):
TATTGAGCTAAGGCCCACACTGTTACTA
Found at i:296215 original size:33 final size:33
Alignment explanation
Indices: 296150--296215 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
296140 TAAGGCCCAC
* * *
296150 ACTGTTACTATATTGGGCGAAGGACCACACTGT
1 ACTGTCACTAAATAGGGCGAAGGACCACACTGT
* * *
296183 ACTGTCACTAAATAGGGCTAAGGCCCAGACTGT
1 ACTGTCACTAAATAGGGCGAAGGACCACACTGT
296216 TGCTGCATGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (33 bp):
ACTGTCACTAAATAGGGCGAAGGACCACACTGT
Found at i:296392 original size:227 final size:227
Alignment explanation
Indices: 295997--296451 Score: 759
Period size: 227 Copynumber: 2.0 Consensus size: 227
295987 GTACGGAGTG
*
295997 GTGTGTGGGTTGGATTGGGATGGGTTACATTATTGCACTGCACGGTTACTGTATTGGGCTACAAC
1 GTGTGTGGGCTGGATTGGGATGGGTTACATTATTGCACTGCACGGTTACTGTATTGGGCTACAAC
* * *
296062 CAACATAGATTTGGTATTGAGCTAAGGTCCACACTGATTCTATATTGGGCTAAGGCCCACACTGT
66 CAACACAGATTTGGTATTGAGCTAAGGCCCACACTGATTCTATATTGGGCTAAGGCCCACACTAT
296127 TACTGTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACTG-TCAC
131 TACTGTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACTGTTC-C
*
296191 TAAATAGGGCTAAGGCCCAGACTGTTGCTGCAT
195 TAAATAGGGCTAAGGCCCAGACTGTTGATGCAT
* *
296224 GTGTGTGGGCTGGATTGGGATGGGTTACATTCTTGCACTGCACGGTTACTGTATTGGGCTACGAC
1 GTGTGTGGGCTGGATTGGGATGGGTTACATTATTGCACTGCACGGTTACTGTATTGGGCTACAAC
* * * *
296289 CCACACAGATTTTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGGCTAAGGCCCACACTAT
66 CAACACAGATTTGGTATTGAGCTAAGGCCCACACTGATTCTATATTGGGCTAAGGCCCACACTAT
* * *
296354 TATTGTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCTAAGGACTACACTGTACTGTTCCT
131 TACTGTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACTGTTCCT
*
296419 GAATAGGGCTAAGGCCCAGACTGTTGATGCAT
196 AAATAGGGCTAAGGCCCAGACTGTTGATGCAT
296451 G
1 G
296452 CTGTTTACTG
Statistics
Matches: 212, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
227 210 0.99
228 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (227 bp):
GTGTGTGGGCTGGATTGGGATGGGTTACATTATTGCACTGCACGGTTACTGTATTGGGCTACAAC
CAACACAGATTTGGTATTGAGCTAAGGCCCACACTGATTCTATATTGGGCTAAGGCCCACACTAT
TACTGTATTGAGCTAAGGCCCACACTGTTACTATATTGGGCGAAGGACCACACTGTACTGTTCCT
AAATAGGGCTAAGGCCCAGACTGTTGATGCAT
Found at i:296399 original size:56 final size:56
Alignment explanation
Indices: 296268--296399 Score: 187
Period size: 56 Copynumber: 2.4 Consensus size: 56
296258 GCACTGCACG
* * *
296268 GTTACTGTATTGGGCTACGACCCACACAGATTTTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACAGATTTTGTATTGAGCTAAGGCCCACACT
*
296324 GATT-CTGTATTGGGCTAAGGCCCACAC-TATTATTGTATTGAGCTAAGGCCCACACT
1 G-TTACTGTATTGGGCTAAGGCCCACACAGATT-TTGTATTGAGCTAAGGCCCACACT
*
296380 GTTACTATATTGGGCTAAGG
1 GTTACTGTATTGGGCTAAGG
296400 ACTACACTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
55 5 0.07
56 61 0.90
57 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (56 bp):
GTTACTGTATTGGGCTAAGGCCCACACAGATTTTGTATTGAGCTAAGGCCCACACT
Found at i:296406 original size:28 final size:28
Alignment explanation
Indices: 296268--296414 Score: 165
Period size: 28 Copynumber: 5.3 Consensus size: 28
296258 GCACTGCACG
* * *
296268 GTTACTGTATTGGGCTACGACCCACACA
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
296296 GATT-TTGTATTGGGCTAAGGCCCACACT
1 G-TTACTGTATTGGGCTAAGGCCCACACT
296324 GATT-CTGTATTGGGCTAAGGCCCACACT
1 G-TTACTGTATTGGGCTAAGGCCCACACT
* * *
296352 ATTATTGTATTGAGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * *
296380 GTTACTATATTGGGCTAAGGACTACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
296408 G-TACTGT
1 GTTACTGT
296415 TCCTGAATAG
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
27 7 0.07
28 93 0.91
29 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:299340 original size:33 final size:33
Alignment explanation
Indices: 299298--299364 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
299288 GGTTTTGAGC
299298 AAGGGAACAGTTAGGAACTGGACATAAATACTT
1 AAGGGAACAGTTAGGAACTGGACATAAATACTT
299331 AAGGGAACAGTTAGGAACTGGACATAAATACTT
1 AAGGGAACAGTTAGGAACTGGACATAAATACTT
299364 A
1 A
299365 GTTGTACAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (33 bp):
AAGGGAACAGTTAGGAACTGGACATAAATACTT
Found at i:300853 original size:27 final size:27
Alignment explanation
Indices: 300822--300894 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
300812 CTAATAGATG
*
300822 AAAATGACTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGAGT
* *
300849 AAAATTACTGAAATACCCCTATAGAGT
1 AAAATGACTGAAATACCCCCATAGAGT
*
300876 AAAATGACTAAAATACCCC
1 AAAATGACTGAAATACCCC
300895 AAAACTGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGAGT
Found at i:301989 original size:19 final size:18
Alignment explanation
Indices: 301947--302006 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 18
301937 CATGGGCTTA
301947 GGCCGAAATGGGCCATGT-TG
1 GGCC-AAATGGG-C-TGTGTG
301967 GGCCAAAATGGGCTGTGTG
1 GGCC-AAATGGGCTGTGTG
* *
301986 GGCCCAATGGG-TTTGTG
1 GGCCAAATGGGCTGTGTG
302003 GGCC
1 GGCC
302007 CCACACGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.25
18 9 0.25
19 7 0.19
20 11 0.31
ACGTcount: A:0.17, C:0.20, G:0.42, T:0.22
Consensus pattern (18 bp):
GGCCAAATGGGCTGTGTG
Found at i:301996 original size:18 final size:17
Alignment explanation
Indices: 301973--302007 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
301963 GTTGGGCCAA
301973 AATGGGCTGTGTGGGCCC
1 AATGGG-TGTGTGGGCCC
*
301991 AATGGGTTTGTGGGCCC
1 AATGGGTGTGTGGGCCC
302008 CACACGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.20, G:0.43, T:0.26
Consensus pattern (17 bp):
AATGGGTGTGTGGGCCC
Found at i:302326 original size:27 final size:27
Alignment explanation
Indices: 302295--302546 Score: 249
Period size: 27 Copynumber: 9.3 Consensus size: 27
302285 TTAATAGATG
*
302295 AAAATGACTGAAATACCCCCATAGGGT
1 AAAATGACTAAAATACCCCCATAGGGT
* *
302322 AAAATTACTAAAATACCCTCATAGGGT
1 AAAATGACTAAAATACCCCCATAGGGT
* *
302349 AAGATGACTAAAATACCCCCATAGGAT
1 AAAATGACTAAAATACCCCCATAGGGT
* * * *
302376 AAAATG-GTCGAAATACCCTCATAGGAT
1 AAAATGACT-AAAATACCCCCATAGGGT
* *
302403 AAAATGACCAAAATTCCCCCATAGGGT
1 AAAATGACTAAAATACCCCCATAGGGT
* *
302430 AAAATTACTAAAATACCTCCATAAGGG-
1 AAAATGACTAAAATACCCCCAT-AGGGT
** *
302457 AAAATGACCGAAATACCCCCGTAAGGG-
1 AAAATGACTAAAATACCCCCAT-AGGGT
* * * **
302484 AAAATGACCAAAATACCGCTATAAAGT
1 AAAATGACTAAAATACCCCCATAGGGT
* *
302511 AAAATGAGTGAAATACCCCCATAGGGT
1 AAAATGACTAAAATACCCCCATAGGGT
302538 AAAATGACT
1 AAAATGACT
302547 GTTATACCCA
Statistics
Matches: 181, Mismatches: 40, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
26 3 0.02
27 174 0.96
28 4 0.02
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (27 bp):
AAAATGACTAAAATACCCCCATAGGGT
Found at i:302822 original size:26 final size:26
Alignment explanation
Indices: 302785--302859 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
302775 ACATACACTG
*
302785 TTACTAGCAGCTTTGCTGCGATACTGA
1 TTACTAGTAGCTTTGCTGCGATACT-A
* * *
302812 -TACTGGTAGCTTTGCTGTGATGCTA
1 TTACTAGTAGCTTTGCTGCGATACTA
302837 TTACTAGTAGCTTTGCTGCGATA
1 TTACTAGTAGCTTTGCTGCGATA
302860 TTGGTGTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (26 bp):
TTACTAGTAGCTTTGCTGCGATACTA
Found at i:303013 original size:28 final size:28
Alignment explanation
Indices: 302973--303105 Score: 169
Period size: 28 Copynumber: 4.8 Consensus size: 28
302963 CTGTTACTGA
* * * *
302973 ATTGGGCTAAGGCCTAAACTCATTTTGT
1 ATTGGGCTAAGGCCCACACTGATTCTGT
*
303001 ATTGGACTAAGGCCCACACTGATTCTGT
1 ATTGGGCTAAGGCCCACACTGATTCTGT
* *
303029 ATTGGACTAAGGCCCACACTGATTTTGT
1 ATTGGGCTAAGGCCCACACTGATTCTGT
*
303057 ATTGGGCTAAGGCCTACACTG-TTACTGT
1 ATTGGGCTAAGGCCCACACTGATT-CTGT
*
303085 ATTGGGCTAAGGCCAACACTG
1 ATTGGGCTAAGGCCCACACTG
303106 TACTGTCAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 2 0.02
28 92 0.98
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (28 bp):
ATTGGGCTAAGGCCCACACTGATTCTGT
Found at i:303054 original size:56 final size:56
Alignment explanation
Indices: 302961--303105 Score: 204
Period size: 56 Copynumber: 2.6 Consensus size: 56
302951 TGTTGCACTG
* *
302961 CACTGTTACTGAATTGGGCTAAGGCCTAA-ACTCATTTTGTATTGGACTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCC-AACACTGATTTTGTATTGGACTAAGGCCCA
* * * *
303017 CACTGATT-CTGTATTGGACTAAGGCCCACACTGATTTTGTATTGGGCTAAGGCCTA
1 CACTG-TTACTGTATTGGGCTAAGGCCAACACTGATTTTGTATTGGACTAAGGCCCA
303073 CACTGTTACTGTATTGGGCTAAGGCCAACACTG
1 CACTGTTACTGTATTGGGCTAAGGCCAACACTG
303106 TACTGTCAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
55 3 0.04
56 73 0.94
57 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (56 bp):
CACTGTTACTGTATTGGGCTAAGGCCAACACTGATTTTGTATTGGACTAAGGCCCA
Found at i:303106 original size:28 final size:27
Alignment explanation
Indices: 302961--303111 Score: 151
Period size: 28 Copynumber: 5.4 Consensus size: 27
302951 TGTTGCACTG
*
302961 CACTGTTACTGAATTGGGCTAAGGCCTAA
1 CACTGTT-CTGTATTGGGCTAAGGCC-AA
* * * *
302990 -ACTCATTTTGTATTGGACTAAGGCCCA
1 CACT-GTTCTGTATTGGGCTAAGGCCAA
* *
303017 CACTGATTCTGTATTGGACTAAGGCCCA
1 CACTG-TTCTGTATTGGGCTAAGGCCAA
* *
303045 CACTGATTTTGTATTGGGCTAAGGCCTA
1 CACTG-TTCTGTATTGGGCTAAGGCCAA
303073 CACTGTTACTGTATTGGGCTAAGGCCAA
1 CACTGTT-CTGTATTGGGCTAAGGCCAA
*
303101 CACTGTACTGT
1 CACTGTTCTGT
303112 CAATGAATAG
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.07
28 96 0.91
29 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (27 bp):
CACTGTTCTGTATTGGGCTAAGGCCAA
Found at i:304516 original size:12 final size:12
Alignment explanation
Indices: 304499--304537 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
304489 AACATAAACA
*
304499 TGTTCTTGTTCT
1 TGTTCTTATTCT
304511 TGTTCTTATTCT
1 TGTTCTTATTCT
* *
304523 TATTCTTATACT
1 TGTTCTTATTCT
304535 TGT
1 TGT
304538 ACTGTTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.10, C:0.15, G:0.10, T:0.64
Consensus pattern (12 bp):
TGTTCTTATTCT
Found at i:306378 original size:31 final size:31
Alignment explanation
Indices: 306340--306407 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
306330 TTGAAGTTTC
306340 TCGAATCGAGTCGAGTGAGATGGAATTCGAA
1 TCGAATCGAGTCGAGTGAGATGGAATTCGAA
306371 TCGAATCGAGTCGAGTGAGATGGAATTCGAA
1 TCGAATCGAGTCGAGTGAGATGGAATTCGAA
306402 TCGAAT
1 TCGAAT
306408 ATATCTGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (31 bp):
TCGAATCGAGTCGAGTGAGATGGAATTCGAA
Found at i:307308 original size:9 final size:9
Alignment explanation
Indices: 307291--307321 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
307281 TCGAGTTGAT
307291 TCGAATAAC
1 TCGAATAAC
*
307300 TCGATTAAC
1 TCGAATAAC
307309 TCGAATAAC
1 TCGAATAAC
307318 TCGA
1 TCGA
307322 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:333219 original size:20 final size:20
Alignment explanation
Indices: 333154--333219 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
333144 ACATACGTGT
*
333154 CCCC-GTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTCGGTA
* * * *
333173 CCCCTGAATTGCACATAC-GTG
1 CCCCTG-TTTGTAC-TTCGGTA
333194 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
333214 CCCCTG
1 CCCCTG
333220 AATTACACAT
Statistics
Matches: 34, Mismatches: 9, Indels: 7
0.68 0.18 0.14
Matches are distributed among these distances:
19 6 0.18
20 14 0.41
21 13 0.38
22 1 0.03
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:333287 original size:42 final size:41
Alignment explanation
Indices: 333136--333302 Score: 219
Period size: 41 Copynumber: 4.0 Consensus size: 41
333126 ATATTATTGT
* *
333136 TGAATTGCACATACGTGTCCCC-GTTTGTACTTTGGTACCCC
1 TGAATTACACATACGTG-CCCCTGTTTGTACTTCGGTACCCC
*
333177 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATTACACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
333218 TGAATTACACATGCGTACCCCTCTTTGTACTTTGGTACCCCC
1 TGAATTACACATACGTGCCCCTGTTTGTACTTCGGTA-CCCC
* * *
333260 TAAATTACACATATGTGTCCCTGTTTGTACTTCGGTACCCC
1 TGAATTACACATACGTGCCCCTGTTTGTACTTCGGTACCCC
333301 TG
1 TG
333303 GATGCACTTT
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 4 0.04
41 72 0.65
42 34 0.31
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (41 bp):
TGAATTACACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:340809 original size:20 final size:22
Alignment explanation
Indices: 340768--340809 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
340758 GAAAATTCAA
340768 TCAAGGGTCTCGAGACATATGGG
1 TCAAGGGTCTCGAGA-ATATGGG
340791 TCAA-GGTCTCGAG-ATATGG
1 TCAAGGGTCTCGAGAATATGG
340810 TCCCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (22 bp):
TCAAGGGTCTCGAGAATATGGG
Found at i:351955 original size:27 final size:27
Alignment explanation
Indices: 351916--352203 Score: 297
Period size: 27 Copynumber: 10.6 Consensus size: 27
351906 AAAAGTTGTT
* * *
351916 AAATGATCATAATACCCCTGTATGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * * *
351943 AAATCACCGTAATATCCCTATAGGTTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
351970 CAATAACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* *
351997 AAATGACAGTAATACCCCTTGTAGGGAA
1 AAATGACCGTAATACCCC-TGTAGGGTA
* * **
352025 AAATGATCGTAATACCCCTGTAAGAAA
1 AAATGACCGTAATACCCCTGTAGGGTA
*
352052 AAATGATCGTAATACCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
352079 AAATTACCGTAATAACCCTGTAAGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
352106 AAATGATCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
352133 AAATGACCGTAATGCCCCTATAGGATA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * * *
352160 AAATAACCGTAATGCCCCTGAAGGATA
1 AAATGACCGTAATACCCCTGTAGGGTA
352187 AAATGACCGTAATACCC
1 AAATGACCGTAATACCC
352204 TCAAGGTTAT
Statistics
Matches: 216, Mismatches: 44, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
27 192 0.89
28 24 0.11
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (27 bp):
AAATGACCGTAATACCCCTGTAGGGTA
Found at i:352234 original size:23 final size:23
Alignment explanation
Indices: 352208--352278 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
352198 ATACCCTCAA
*
352208 GGTTATATGATTGATTTGTCTGT
1 GGTTATATGACTGATTTGTCTGT
* * *
352231 GGTTAAATGACTGATATGTTTGT
1 GGTTATATGACTGATTTGTCTGT
* *
352254 GTTTGGTATGACTGATTTGTCTGT
1 GGTT-ATATGACTGATTTGTCTGT
352278 G
1 G
352279 ATTTAAACGA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 22 0.58
24 16 0.42
ACGTcount: A:0.18, C:0.06, G:0.28, T:0.48
Consensus pattern (23 bp):
GGTTATATGACTGATTTGTCTGT
Found at i:352507 original size:32 final size:32
Alignment explanation
Indices: 352466--352668 Score: 230
Period size: 32 Copynumber: 6.4 Consensus size: 32
352456 ACTGCGATGC
*
352466 TACTGATGGCTTTGTGCCAATCATATTATCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
***
352498 TACTGATGGCTTTGTGTTTATCATATTACCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
*
352530 TACTGATGGCTTTATGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
***
352562 TACTGATCATTTTGTGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
** * * *
352594 TACTGATGG-TTGTGTGCCGGTCATATCACTGC
1 TACTGATGGCTT-TGTGCCAATCATATTACCGT
* * *
352626 TACTAATGGCTTTGTGCTAATCATATTACTG-
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
*
352657 TACTTATGGCTT
1 TACTGATGGCTT
352669 GTAGTCATTC
Statistics
Matches: 144, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.09
32 129 0.90
33 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCAATCATATTACCGT
Found at i:353937 original size:14 final size:13
Alignment explanation
Indices: 353915--353967 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
353905 AAATTATTAT
*
353915 TTAATTAATTATAA
1 TTAAATAATTA-AA
353929 TTAAATAATTAAA
1 TTAAATAATTAAA
353942 TTTTAAA-AATTAAA
1 --TTAAATAATTAAA
353956 TTAAATCAATTA
1 TTAAAT-AATTA
353968 GTCATTATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 5 0.15
13 2 0.06
14 22 0.65
15 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:354099 original size:9 final size:9
Alignment explanation
Indices: 354085--354109 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
354075 TAATTTGGAA
354085 ATTAATTTG
1 ATTAATTTG
354094 ATTAATTTG
1 ATTAATTTG
354103 ATTAATT
1 ATTAATT
354110 AAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (9 bp):
ATTAATTTG
Found at i:357078 original size:20 final size:20
Alignment explanation
Indices: 357053--357092 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
357043 TATATTAGTG
357053 GGAGACATGATGATTAAGGT
1 GGAGACATGATGATTAAGGT
357073 GGAGACATGATGATTAAGGT
1 GGAGACATGATGATTAAGGT
357093 TTTTCCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (20 bp):
GGAGACATGATGATTAAGGT
Found at i:386979 original size:26 final size:26
Alignment explanation
Indices: 386905--386961 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
386895 ATTACCGTAA
* * * *
386905 ATGTGGAAGCCCATTAAAACTATCTT
1 ATGTGAAAGTCCATCAAGACTATCTT
386931 ATGTGAAAGTCCATCAAGACTATCTT
1 ATGTGAAAGTCCATCAAGACTATCTT
386957 ATGTG
1 ATGTG
386962 GAAGATCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (26 bp):
ATGTGAAAGTCCATCAAGACTATCTT
Found at i:389219 original size:20 final size:20
Alignment explanation
Indices: 389185--389226 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
389175 AACTATTTAA
** *
389185 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
389205 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
389225 AT
1 AT
389227 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:394297 original size:20 final size:20
Alignment explanation
Indices: 394263--394304 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
394253 AACTATTTAA
** *
394263 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
394283 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
394303 AT
1 AT
394305 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:401063 original size:27 final size:26
Alignment explanation
Indices: 400934--401074 Score: 167
Period size: 27 Copynumber: 5.3 Consensus size: 26
400924 CCCTAAAATA
400934 GGTAAAATGACCAAAATA-CCCATAG
1 GGTAAAATGACCAAAATACCCCATAG
* *
400959 GGTAAAATGACCGAAATACCCCTATAA
1 GGTAAAATGACCAAAATACCCC-ATAG
* * *
400986 GGTAAAATGACTAAAATAACCTCATAA
1 GGTAAAATGACCAAAAT-ACCCCATAG
* *
401013 GGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATA-CCCCATAG
401040 GGTAAAATGACCAAAATATCCCCATAG
1 GGTAAAATGACCAAAATA-CCCCATAG
*
401067 GGAAAAAT
1 GGTAAAAT
401075 TACTGTTATA
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
25 17 0.17
26 4 0.04
27 73 0.74
28 4 0.04
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (26 bp):
GGTAAAATGACCAAAATACCCCATAG
Found at i:401088 original size:54 final size:53
Alignment explanation
Indices: 400933--401074 Score: 196
Period size: 54 Copynumber: 2.7 Consensus size: 53
400923 ACCCTAAAAT
*
400933 AGGTAAAATGACCAAAATA-CCCATAGGGTAAAATGACCGAAATACCCCTATA
1 AGGTAAAATGACCAAAATACCCCATAGGGTAAAATGACCGAAATACCCCCATA
* * * *
400985 AGGTAAAATGACTAAAATAACCTCATAAGGTAGAATGACCGAAATACCCCCATA
1 AGGTAAAATGACCAAAAT-ACCCCATAGGGTAAAATGACCGAAATACCCCCATA
* *
401039 GGGTAAAATGACCAAAATATCCCCATAGGGAAAAAT
1 AGGTAAAATGACCAAAATA-CCCCATAGGGTAAAAT
401075 TACTGTTATA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 17 0.22
53 2 0.03
54 57 0.75
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (53 bp):
AGGTAAAATGACCAAAATACCCCATAGGGTAAAATGACCGAAATACCCCCATA
Found at i:403890 original size:36 final size:36
Alignment explanation
Indices: 403843--403912 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
403833 GGAGGAGCAC
403843 ATCAGTCAGAATAGA-CTCAAAAGGCTGCTAAACTGA
1 ATCAGTCAGAATAGATC-CAAAAGGCTGCTAAACTGA
*
403879 ATCAGTCAGAATAGATCCAAAAGGTTGCTAAACT
1 ATCAGTCAGAATAGATCCAAAAGGCTGCTAAACT
403913 AAATAGAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (36 bp):
ATCAGTCAGAATAGATCCAAAAGGCTGCTAAACTGA
Found at i:404002 original size:14 final size:14
Alignment explanation
Indices: 403983--404010 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
403973 TTTTTTTGAC
403983 ATCAACAATGATAT
1 ATCAACAATGATAT
403997 ATCAACAATGATAT
1 ATCAACAATGATAT
404011 TTTAAATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
ATCAACAATGATAT
Found at i:406279 original size:57 final size:59
Alignment explanation
Indices: 406173--406313 Score: 164
Period size: 57 Copynumber: 2.4 Consensus size: 59
406163 GGTAAAAAGG
*
406173 ATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCTCGAAGAATATGTGTGAAAAAT
1 ATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-GAAAAAT
* *
406235 ATCTAGTCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCTAAGAATATGTGG-AAAAT
1 ATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGGAAAAAT
* *
406290 GGATTTAGCCCGGACGGGTAATCC
1 --ATCTAGCCCGGACGGGTGATCC
406314 GAATTAGGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
55 5 0.07
56 1 0.01
57 42 0.60
58 1 0.01
59 1 0.01
61 1 0.01
62 19 0.27
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (59 bp):
ATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGGAAAAAT
Found at i:406548 original size:67 final size:67
Alignment explanation
Indices: 406440--406566 Score: 218
Period size: 67 Copynumber: 1.9 Consensus size: 67
406430 TATTATAGGG
* * *
406440 GATTTAGCCTGGACTGGTAATCTCGCTGTAAGGAATGAGGTTCGCGGGAGTGTGCTCTCTTGCAG
1 GATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTTGCAG
406505 GA
66 GA
*
406507 GATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCT
1 GATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
406567 AAATTGAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.29
Consensus pattern (67 bp):
GATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTTGCAG
GA
Found at i:414714 original size:14 final size:15
Alignment explanation
Indices: 414691--414730 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
414681 ATATATTTGG
414691 ATTAACATTAATAA-
1 ATTAACATTAATAAT
*
414705 ATTAATATTAATAAT
1 ATTAACATTAATAAT
414720 ATTAAACATTA
1 ATT-AACATTA
414731 CTTAATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 3 0.14
16 6 0.27
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAACATTAATAAT
Found at i:417103 original size:3 final size:3
Alignment explanation
Indices: 417083--417165 Score: 54
Period size: 3 Copynumber: 30.0 Consensus size: 3
417073 TTCCATTTTC
* *
417083 TCT TTT TCT TC- TCA TCT TCT TCT T-T TCT TCT T-T TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
417127 CCA T-T TCT TC- TCT TAT TCT TCT TTT TC- TCT TGT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
417166 ACTACCCAGA
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
2 13 0.22
3 47 0.78
ACGTcount: A:0.04, C:0.28, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:417108 original size:19 final size:18
Alignment explanation
Indices: 417086--417137 Score: 67
Period size: 16 Copynumber: 3.1 Consensus size: 18
417076 CATTTTCTCT
417086 TTTTCTTCTCATCTTCTTC
1 TTTTCTTCTCAT-TTCTTC
417105 TTTTCTTCT--TTTCTTC
1 TTTTCTTCTCATTTCTTC
417121 TTTTC-TC-CATTTCTTC
1 TTTTCTTCTCATTTCTTC
417137 T
1 T
417138 CTTATTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.06
16 19 0.61
17 1 0.03
19 9 0.29
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTTCTCATTTCTTC
Found at i:417146 original size:43 final size:44
Alignment explanation
Indices: 417078--417165 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
417068 GCTCCTTCCA
** *
417078 TTTTCTCTTTTTCTTCTCATCTTCTTC-TTTTCTTCTT-TTCTTC
1 TTTTCTCCATTTCTTCTCATATTCTTCTTTTTC-TCTTGTTCTTC
*
417121 TTTTCTCCATTTCTTCTCTTATTCTTCTTTTTCTCTTGTTCTTC
1 TTTTCTCCATTTCTTCTCATATTCTTCTTTTTCTCTTGTTCTTC
417165 T
1 T
417166 ACTACCCAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 27 0.69
44 12 0.31
ACGTcount: A:0.03, C:0.27, G:0.01, T:0.68
Consensus pattern (44 bp):
TTTTCTCCATTTCTTCTCATATTCTTCTTTTTCTCTTGTTCTTC
Found at i:417165 original size:11 final size:11
Alignment explanation
Indices: 417080--417148 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
417070 TCCTTCCATT
*
417080 TTCTCTTTTTC
1 TTCTCTTCTTC
*
417091 TTCTCATCTTC
1 TTCTCTTCTTC
*
417102 TTCTTTTCTTC
1 TTCTCTTCTTC
*
417113 TTTTCTTCTT-
1 TTCTCTTCTTC
*
417123 TTCTCCAT-TTC
1 TTCT-CTTCTTC
*
417134 TTCTCTTATTC
1 TTCTCTTCTTC
417145 TTCT
1 TTCT
417149 TTTTCTCTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 7 0.15
11 39 0.85
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:417478 original size:29 final size:29
Alignment explanation
Indices: 417445--417502 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
417435 TCCTTCACTC
* * * *
417445 TATCTCCTTTCAGCTACTTACTACATACA
1 TATCTCCTTCCAACAACTCACTACATACA
417474 TATCTCCTTCCAACAACTCACTACATACA
1 TATCTCCTTCCAACAACTCACTACATACA
417503 ATACGTGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.31, C:0.34, G:0.02, T:0.33
Consensus pattern (29 bp):
TATCTCCTTCCAACAACTCACTACATACA
Found at i:422773 original size:3 final size:3
Alignment explanation
Indices: 422765--422794 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
422755 GAACTCTGCA
*
422765 CCT CCT CCT CCT CCT CCA CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
422795 GCACCGCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.67, G:0.00, T:0.30
Consensus pattern (3 bp):
CCT
Found at i:422788 original size:15 final size:15
Alignment explanation
Indices: 422768--422799 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
422758 CTCTGCACCT
422768 CCTCCTCCTCCTCCA
1 CCTCCTCCTCCTCCA
*
422783 CCTCCTCCTCCTGCA
1 CCTCCTCCTCCTCCA
422798 CC
1 CC
422800 GCCAACGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.66, G:0.03, T:0.25
Consensus pattern (15 bp):
CCTCCTCCTCCTCCA
Found at i:424075 original size:13 final size:13
Alignment explanation
Indices: 424029--424076 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
424019 TTGGCAATGC
* *
424029 TTTTAAAAAGTGC
1 TTTTGAAAAGTGT
424042 TTTTGAAAAGTGT
1 TTTTGAAAAGTGT
* *
424055 TGTGGAAAAGTGT
1 TTTTGAAAAGTGT
424068 TTTTGAAAA
1 TTTTGAAAA
424077 TTTTAGTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGT
Found at i:424481 original size:9 final size:9
Alignment explanation
Indices: 424453--424487 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
424443 TTCACATCCA
424453 TCTCTCAAC
1 TCTCTCAAC
*
424462 TCTATCAAAC
1 TCTCTC-AAC
424472 TCTCTCAAC
1 TCTCTCAAC
424481 TCTCTCA
1 TCTCTCA
424488 TTTTAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.34
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:441501 original size:11 final size:11
Alignment explanation
Indices: 441487--441514 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
441477 AGTCAAAAAA
441487 TATTTTAATAT
1 TATTTTAATAT
441498 TATTTTAATAT
1 TATTTTAATAT
441509 TATTTT
1 TATTTT
441515 TTGTGCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTAATAT
Found at i:443539 original size:21 final size:21
Alignment explanation
Indices: 443515--443554 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
443505 ATGCTTGAGT
443515 TATATAT-TTTTGGTCATGATA
1 TATATATGTTTTGG-CATGATA
443536 TATATATGTTTTGGCATGA
1 TATATATGTTTTGGCATGA
443555 AGTAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (21 bp):
TATATATGTTTTGGCATGATA
Found at i:447878 original size:20 final size:20
Alignment explanation
Indices: 447829--447884 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
447819 TGTTTATGCT
* * *
447829 AAGTAAATGAAATGGAAAGT
1 AAGTAAATGGAATGGTAAGA
*
447849 AAGTAAATGGAATGGTGAGA
1 AAGTAAATGGAATGGTAAGA
*
447869 AAGTAAATGGAGTGGT
1 AAGTAAATGGAATGGT
447885 TCAAAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.21
Consensus pattern (20 bp):
AAGTAAATGGAATGGTAAGA
Found at i:448983 original size:20 final size:19
Alignment explanation
Indices: 448945--448983 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
448935 CTACAGTCCA
* *
448945 AAACTTTCAACTTTTTCCT
1 AAACTTTCAAATGTTTCCT
448964 AAACTTTCCAAATGTTTCCT
1 AAACTTT-CAAATGTTTCCT
448984 GTTTAGTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.44
Consensus pattern (19 bp):
AAACTTTCAAATGTTTCCT
Found at i:454440 original size:45 final size:43
Alignment explanation
Indices: 454390--454549 Score: 178
Period size: 45 Copynumber: 3.6 Consensus size: 43
454380 TTCCAAAGTG
*
454390 ATGCCATAGTATCTTTCAACTATGGTATTATTCATTGTCGACGTA
1 ATGCCATAGTATCTTTCAACTATGGTCTTATTCATT-TCGA-GTA
* * * * * *
454435 TTGCCATAGTATCTTTCAACTATAGTCTTATTCGTATCATATTTA
1 ATGCCATAGTATCTTTCAACTATGGTCTTATTCATTTC-GA-GTA
*
454480 ATGCCATAGTATCTTTCAACTATGCTCTTATTCATTTCG-GTTAA
1 ATGCCATAGTATCTTTCAACTATGGTCTTATTCATTTCGAG-T-A
*
454524 ATGCCATAGTATCTTTCAACCATGGT
1 ATGCCATAGTATCTTTCAACTATGGT
454550 GTTTCTCGTT
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
43 1 0.01
44 27 0.28
45 67 0.71
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (43 bp):
ATGCCATAGTATCTTTCAACTATGGTCTTATTCATTTCGAGTA
Found at i:462262 original size:29 final size:31
Alignment explanation
Indices: 462201--462261 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
462191 GAAAAAGAAG
462201 AAGTATAAACATATTGGGCCATTTATGTAAA
1 AAGTATAAACATATTGGGCCATTTATGTAAA
*
462232 AAGTA-AAA-ATATTGGGTCATTTAT-TAAA
1 AAGTATAAACATATTGGGCCATTTATGTAAA
462260 AA
1 AA
462262 AATAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 15 0.52
30 3 0.10
31 5 0.17
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.33
Consensus pattern (31 bp):
AAGTATAAACATATTGGGCCATTTATGTAAA
Found at i:462549 original size:32 final size:32
Alignment explanation
Indices: 462508--462613 Score: 119
Period size: 29 Copynumber: 3.4 Consensus size: 32
462498 GTAATCTACC
462508 TTTTTTTATTCAACATTAAAATTTTGATTTTA
1 TTTTTTTATTCAACATTAAAATTTTGATTTTA
* * * **
462540 TTTTTTTATTCAACATT-AAA--GTAACTTCG
1 TTTTTTTATTCAACATTAAAATTTTGATTTTA
*
462569 TTTTTTTATTCAACATTAAAATTTTGTTTTTAA
1 TTTTTTTATTCAACATTAAAATTTTGATTTT-A
*
462602 TTTTTTTTTTCA
1 TTTTTTTATTCA
462614 CACTAACATT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 21 0.36
30 3 0.05
31 3 0.05
32 20 0.34
33 11 0.19
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.59
Consensus pattern (32 bp):
TTTTTTTATTCAACATTAAAATTTTGATTTTA
Found at i:462669 original size:12 final size:12
Alignment explanation
Indices: 462652--462676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
462642 TGTGGTTCTG
462652 TTTTAATTTTTT
1 TTTTAATTTTTT
462664 TTTTAATTTTTT
1 TTTTAATTTTTT
462676 T
1 T
462677 AAAAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:463312 original size:14 final size:14
Alignment explanation
Indices: 463295--463321 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
463285 TTTCCCCCCA
463295 TTTTTTTCTCTTCC
1 TTTTTTTCTCTTCC
463309 TTTTTTTCTCTTC
1 TTTTTTTCTCTTC
463322 AGTAGCACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTCTCTTCC
Found at i:466370 original size:9 final size:9
Alignment explanation
Indices: 466356--466381 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
466346 CTCTCTCTCT
466356 CTTATTTCG
1 CTTATTTCG
466365 CTTATTTCG
1 CTTATTTCG
466374 CTTATTTC
1 CTTATTTC
466382 TAATTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.08, T:0.58
Consensus pattern (9 bp):
CTTATTTCG
Found at i:469983 original size:28 final size:28
Alignment explanation
Indices: 469943--470000 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
469933 ATCAAAAGGT
*
469943 GTTTGTGAAATTTATGATCTTTCTAGAG
1 GTTTGTGAAATTTATGATCCTTCTAGAG
469971 GTTTGTGAAATTTATGATCCTTCTAGAG
1 GTTTGTGAAATTTATGATCCTTCTAGAG
469999 GT
1 GT
470001 GCTATTGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (28 bp):
GTTTGTGAAATTTATGATCCTTCTAGAG
Found at i:474775 original size:45 final size:45
Alignment explanation
Indices: 474711--474913 Score: 187
Period size: 45 Copynumber: 4.5 Consensus size: 45
474701 ACTGGAATGA
* *
474711 ATTGATTATAAAGATGGTTGCTATGTGCTGATTCCTCTAG-GTACC
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCAC-AGTGTACC
* *
474756 ATTGATTATAAAGGTGGTTGCTATATGCTGATTCCACCGTGTACC
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACAGTGTACC
* * * * *
474801 ATTGATTATAAAGGTGGTTTCTATGTGCTGACTCCAC-CTGAAATC
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACAGTG-TACC
** * * * * ** **
474846 ATTGAAAACAAAGGTGGTTTCTATGTGTTGATTCCACCGAATATA
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACAGTGTACC
*
474891 ATTGATTATAAGGGTGG-TGCTAT
1 ATTGATTATAAAGGTGGTTGCTAT
474914 TACTATTCTG
Statistics
Matches: 130, Mismatches: 25, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
44 8 0.06
45 122 0.94
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (45 bp):
ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACAGTGTACC
Found at i:474864 original size:90 final size:90
Alignment explanation
Indices: 474710--474913 Score: 223
Period size: 90 Copynumber: 2.3 Consensus size: 90
474700 TACTGGAATG
* * * ** ** *
474710 AATTGATTATAAAGATGGTTGCTATGTGCTGATTCCTCTAGGTACCATTGATTATAAAGGTGGTT
1 AATTGATTATAAAGGTGGTTGCTATGTGCTGACTCCCCTAGAAACCATTGAAAACAAAGGTGGTT
**
474775 GCTATATGCTGATTCCACCGTGTAC
66 GCTATATGCTGATTCCACCGAATAC
* * *
474800 CATTGATTATAAAGGTGGTTTCTATGTGCTGACTCCACCT-GAAATCATTGAAAACAAAGGTGGT
1 AATTGATTATAAAGGTGGTTGCTATGTGCTGACTCC-CCTAGAAACCATTGAAAACAAAGGTGGT
* * * *
474864 TTCTATGTGTTGATTCCACCGAATAT
65 TGCTATATGCTGATTCCACCGAATAC
*
474890 AATTGATTATAAGGGTGG-TGCTAT
1 AATTGATTATAAAGGTGGTTGCTAT
474914 TACTATTCTG
Statistics
Matches: 93, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
89 5 0.05
90 86 0.92
91 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (90 bp):
AATTGATTATAAAGGTGGTTGCTATGTGCTGACTCCCCTAGAAACCATTGAAAACAAAGGTGGTT
GCTATATGCTGATTCCACCGAATAC
Found at i:480447 original size:5 final size:5
Alignment explanation
Indices: 480437--480499 Score: 126
Period size: 5 Copynumber: 12.6 Consensus size: 5
480427 AAACTACTAT
480437 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
480487 ATATA ATATA ATA
1 ATATA ATATA ATA
480500 AGGTATGCCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:489453 original size:51 final size:50
Alignment explanation
Indices: 489273--489618 Score: 297
Period size: 50 Copynumber: 6.9 Consensus size: 50
489263 TTTTATCATT
* * *
489273 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATTCTA
* * * * * * *
489323 CGGTTCATGTAGTGGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATTCTA
* * *
489373 CGATTCACGTAGTAGCCTTCACATTGTACTACACAGGTGACCAAAAATTCT-
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACC--AAATTCTA
* * * * * *
489424 CGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC-ATTTCCATC
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATT-C-TA
* * *
489475 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAA-GCTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATTCTA
* *** * * * *
489524 TTCGGTACGTATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTC--
1 --CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCA-AATTCTA
* *
489576 CGATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
489619 TCACTTTCAT
Statistics
Matches: 243, Mismatches: 42, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
48 3 0.01
49 5 0.02
50 119 0.49
51 106 0.44
52 8 0.03
53 1 0.00
54 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATTCTA
Found at i:489639 original size:101 final size:99
Alignment explanation
Indices: 489268--489618 Score: 370
Period size: 101 Copynumber: 3.5 Consensus size: 99
489258 GTTACTTTTA
* * ** * **
489268 TCATT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCATG
1 TCATTCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTT-CGGTACACA
* * *
489332 TAGTGGCCTTCACATAGTACTACACACGTGATCAAGT
65 TAGTAGCCTTCACATAGTACTACACATGTGA-CCA-T
* * * * * *
489369 T--TTACGATTCACGTAGTAGCCTTCACATTGTACTACACAGGTGACCAAAAATTCTCGGTACAC
1 TCATTCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-AAACTT-TCGGTACAC
*
489432 ATAGTAGCCTTCACTTAGTACTACACATGTGACCATT
64 ATAGTAGCCTTCACATAGTACTACACATGTGACCA-T
* *
489469 TCCA-TCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAGCTATTCGGTACG
1 T-CATTCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-CT-TTCGGTACA
* * *
489533 TATAGTAGCCTGCACATAGTACTACACATGCGACCCA-
63 CATAGTAGCCTTCACATAGTACTACACATGTGA-CCAT
*
489570 TCATTCCGATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
1 TCATTCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
489619 TCACTTTCAT
Statistics
Matches: 212, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
99 2 0.01
100 44 0.21
101 86 0.41
102 76 0.36
103 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (99 bp):
TCATTCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTTCGGTACACAT
AGTAGCCTTCACATAGTACTACACATGTGACCAT
Found at i:495375 original size:137 final size:135
Alignment explanation
Indices: 495083--495536 Score: 452
Period size: 134 Copynumber: 3.4 Consensus size: 135
495073 CATTCATTAT
* * * * **
495083 GATTGTAAATCGATGAACTCAAAATAAATTGTTCATGATTATAAATCAATGAACATAAGG-CATG
1 GATTGTAAATCAATGAACTCAAAATAAACTGTTCATGATCATAAATCAATGAAC-TTAGGTTGTG
* * * * *
495147 ATCGTAAGTCAACAAGCTTTAATA-GTACCAATT-ATGATCGTAAACCAGTAAACTATTTAAAT-
65 ATCGTAAATCAGCAAGCTTTAATATATACCAATTGA-GATCGTAAATCAGTGAACTATTTAAATG
495209 AGAGTTGC
129 A-AGTTGC
* * * * * *
495217 GATCGTAGATCAGTGAACTCAAAATGAACTGTTCATGATCGTTAATCAATGAACTTAGGTTGTGA
1 GATTGTAAATCAATGAACTCAAAATAAACTGTTCATGATCATAAATCAATGAACTTAGGTTGTGA
* * *
495282 TTGTAAATCAGCAAGCTTTAATATTATTATCAATTGAGATCGTAAATCAGTGAACTATTTGAATG
66 TCGTAAATCAGCAAGCTTTAATA-TA-TACCAATTGAGATCGTAAATCAGTGAACTATTTAAATG
495347 AAGTTGC
129 AAGTTGC
* * * * * * * *
495354 GATTTTAAATCAATGAACTCAAAATGAACTATTCACGAT-AGCAAATCATTGAGCTTAAGTTGTG
1 GATTGTAAATCAATGAACTCAAAATAAACTGTTCATGATCA-TAAATCAATGAACTTAGGTTGTG
* * * * * * *
495418 ATCGTACATCAGCAAGCTTTAATA-ATACCAGTCGTGATCGTAAATCAATGAACTATTTCAATGG
65 ATCGTAAATCAGCAAGCTTTAATATATACCAATTGAGATCGTAAATCAGTGAACTATTTAAATGA
*
495482 AGTTGT
130 AGTTGC
* ** *
495488 GATTATAAATCACCGAACTCAAAATAAATTGTTCATGATCATAAATCAA
1 GATTGTAAATCAATGAACTCAAAATAAACTGTTCATGATCATAAATCAA
495537 CAAACTTTAA
Statistics
Matches: 261, Mismatches: 51, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
133 4 0.02
134 143 0.55
135 2 0.01
137 110 0.42
138 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (135 bp):
GATTGTAAATCAATGAACTCAAAATAAACTGTTCATGATCATAAATCAATGAACTTAGGTTGTGA
TCGTAAATCAGCAAGCTTTAATATATACCAATTGAGATCGTAAATCAGTGAACTATTTAAATGAA
GTTGC
Found at i:495637 original size:206 final size:206
Alignment explanation
Indices: 495359--495741 Score: 507
Period size: 206 Copynumber: 1.9 Consensus size: 206
495349 GTTGCGATTT
* * * * * * *
495359 TAAATCAATGAACTCAAAATGAACTATTCACGATAGCAAATCATTGAGCTTAAGTTGTGATCGTA
1 TAAATCAATGAACTCAAAATGAACTAGTAACGATAGCAAATCAATGAACTTAAGCTGTGACCATA
* * *
495424 CATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAATGAAC-TATTTCAATGGAGTTGT
66 AATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAACGAACTTA-TTCAATGGAGTTGC
* * * * *
495488 GATTATAAATCACCGAACTCAAAATAAATTGTTCATGATCATAAATCAACAAACTTTAATACTAC
130 AATCATAAATCACCAAAATCAAAATAAACTGTTCATGATCATAAATCAACAAACTTTAATACTAC
495553 TAGTCATGATCA
195 TAGTCATGATCA
* * ***
495565 TAAATCAGTGAACTCAAAATGAACTAGTAATGATCTTAAATCAATGAACTTAAGCTGTGACCATA
1 TAAATCAATGAACTCAAAATGAACTAGTAACGATAGCAAATCAATGAACTTAAGCTGTGACCATA
* * *
495630 AATCAGCAAGCTTTAATAATAGCAGTCGTGATTGTAAATCAACGAACTTATTGAATGGAGTTGCA
66 AATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAACGAACTTATTCAATGGAGTTGCA
** * *
495695 ATCATAAATCAGTAAAATCAAAATGAACTGTTCATGATCGTAAATCA
131 ATCATAAATCACCAAAATCAAAATAAACTGTTCATGATCATAAATCA
495742 TGAACTTAAG
Statistics
Matches: 149, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
206 147 0.99
207 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (206 bp):
TAAATCAATGAACTCAAAATGAACTAGTAACGATAGCAAATCAATGAACTTAAGCTGTGACCATA
AATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAACGAACTTATTCAATGGAGTTGCA
ATCATAAATCACCAAAATCAAAATAAACTGTTCATGATCATAAATCAACAAACTTTAATACTACT
AGTCATGATCA
Found at i:495789 original size:133 final size:133
Alignment explanation
Indices: 495561--495933 Score: 469
Period size: 133 Copynumber: 2.8 Consensus size: 133
495551 ACTAGTCATG
* * *
495561 ATCATAAATCAGTGAACTCAAAATGAACTAG-TAATGATCTTAAATCAATGAACTTAAGCTGTGA
1 ATCATAAATCAGTGAACTCAAAATGAACT-GTTCATGATCGTAAATC-ATGAACTTAAGCTATGA
* * * * * *
495625 CCATAAATCAGCAAGCTTTAATAATAGCAGTCGTGATTGTAAATCAACGAACTTATTGAATGGAG
64 TCGTAAATCAGCAAGCTTTAATAATACCAGTCATGATCGTAAATCAACGAACTTATTGAATGAAG
495690 TTGCA
129 TTGCA
* * *
495695 ATCATAAATCAGTAAAATCAAAATGAACTGTTCATGATCGTAAATCATGAACTTAAGCTATGATT
1 ATCATAAATCAGTGAACTCAAAATGAACTGTTCATGATCGTAAATCATGAACTTAAGCTATGATC
* * * * *
495760 GTAAATCAGCGAGCTTTAATAATACCAGTCATAATCATAAATCAATGAACTTTTTGAATGAAGTT
66 GTAAATCAGCAAGCTTTAATAATACCAGTCATGATCGTAAATCAACGAACTTATTGAATGAAGTT
*
495825 GCG
131 GCA
* * ** * * *
495828 ATAATTAATCAACGAACTCAAAATGAACTATTCATGATTGTAAATTAGTGAACTTAAGCTATGAT
1 ATCATAAATCAGTGAACTCAAAATGAACTGTTCATGATCGTAAATCA-TGAACTTAAGCTATGAT
* *
495893 CGTAAACCAGCAAGCTTTAATAATACTAGTCATGATCGTAA
65 CGTAAATCAGCAAGCTTTAATAATACCAGTCATGATCGTAA
495934 TTAGTGAATT
Statistics
Matches: 204, Mismatches: 33, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
133 112 0.55
134 92 0.45
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (133 bp):
ATCATAAATCAGTGAACTCAAAATGAACTGTTCATGATCGTAAATCATGAACTTAAGCTATGATC
GTAAATCAGCAAGCTTTAATAATACCAGTCATGATCGTAAATCAACGAACTTATTGAATGAAGTT
GCA
Found at i:497685 original size:24 final size:24
Alignment explanation
Indices: 497653--497699 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
497643 ATTTCCTTTG
497653 CTCCTAATTGTCAAGCTAACTGTT
1 CTCCTAATTGTCAAGCTAACTGTT
497677 CTCCTAATTGTCAAGCTAACTGT
1 CTCCTAATTGTCAAGCTAACTGT
497700 AGCCCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (24 bp):
CTCCTAATTGTCAAGCTAACTGTT
Found at i:511559 original size:163 final size:162
Alignment explanation
Indices: 511290--511615 Score: 467
Period size: 163 Copynumber: 2.0 Consensus size: 162
511280 AAGTCTTTAG
* * * * *
511290 GCTTCTTGGTTCTCTTTGTCACATCTCGAAATTGGTCTAGAAGTTTCGAGGATAGTTTTGGAATT
1 GCTTCTTCGTTCTCTTTGTCACATCCCGAAATTGGTCTAAAAGTTTCAAGGATAGTTTTGGAACT
* * *
511355 TTATATTGAAATTGAGTACGGAAATTCAAAGTGAGGTAAACCAAAAATATATTTGTTTATGAG-T
66 TTAGATTGAAATTGAGTACAGAAATTCAAAGTGAGGTAAACCAAAAATATATTTGTCTATG-GCT
*
511419 TTTTGAAGTTAAATCAATTTAC-AAAAATAATGT
130 TTTTGAAATTAAATCAATTT-CTAAAAATAATGT
511452 GCTTCTTCGTTCTCTTTGTCACATCCCGAAATTGGGTCTAAAAGTTTCAAGGATAGTTTTGGAAC
1 GCTTCTTCGTTCTCTTTGTCACATCCCGAAATT-GGTCTAAAAGTTTCAAGGATAGTTTTGGAAC
* * * ** * *
511517 TTTGGCTTGAAATTGAGTTCAGAAATTTGAAGTGAGGTAAACCGAAAATATTTTTGTCTATGGCT
65 TTTAGATTGAAATTGAGTACAGAAATTCAAAGTGAGGTAAACCAAAAATATATTTGTCTATGGCT
511582 TTTTGAAATTAAATCAATTTCTAAAAATAATGT
130 TTTTGAAATTAAATCAATTTCTAAAAATAATGT
511615 G
1 G
511616 GAAAAGACCT
Statistics
Matches: 145, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
162 33 0.23
163 112 0.77
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (162 bp):
GCTTCTTCGTTCTCTTTGTCACATCCCGAAATTGGTCTAAAAGTTTCAAGGATAGTTTTGGAACT
TTAGATTGAAATTGAGTACAGAAATTCAAAGTGAGGTAAACCAAAAATATATTTGTCTATGGCTT
TTTGAAATTAAATCAATTTCTAAAAATAATGT
Found at i:516096 original size:11 final size:11
Alignment explanation
Indices: 516080--516107 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
516070 TGGTATTTAT
516080 AGGTGAGGTTG
1 AGGTGAGGTTG
516091 AGGTGAGGTTG
1 AGGTGAGGTTG
516102 AGGTGA
1 AGGTGA
516108 AGCTTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.54, T:0.25
Consensus pattern (11 bp):
AGGTGAGGTTG
Found at i:516575 original size:15 final size:15
Alignment explanation
Indices: 516547--516580 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
516537 TGGACCCACT
516547 ACATAATAAAAATTA
1 ACATAATAAAAATTA
* *
516562 ACATATTAATAATTA
1 ACATAATAAAAATTA
516577 ACAT
1 ACAT
516581 CAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (15 bp):
ACATAATAAAAATTA
Found at i:519451 original size:26 final size:26
Alignment explanation
Indices: 519421--519497 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
519411 AGGAAGTATT
*
519421 CTGTTACTGGCAACTTTGCCGCGATA
1 CTGTTACTGGCAACTTTGCTGCGATA
* *
519447 CTGTTACTGGCAGCTTTGCTGCAATA
1 CTGTTACTGGCAACTTTGCTGCGATA
* *
519473 CTATTTCTGGCAACTTTGCTGCGAT
1 CTGTTACTGGCAACTTTGCTGCGAT
519498 GTTGGTGCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
CTGTTACTGGCAACTTTGCTGCGATA
Found at i:525668 original size:26 final size:26
Alignment explanation
Indices: 525629--525709 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
525619 TGGAGGAAGT
*
525629 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* * **
525655 ATACTGTTATTGGCAGCTTTGTTGTT
1 ATACTGTTACTGGCAGCTTTGCTGCG
*
525681 ATACTGTTACTGGCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTGCG
525707 ATA
1 ATA
525710 TTGGTGTGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:530213 original size:4 final size:4
Alignment explanation
Indices: 530204--530234 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
530194 TTCAAACTTC
530204 AATT AATT AATT AATT AATT AATT AA-T AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
530235 TAAAAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:533501 original size:63 final size:63
Alignment explanation
Indices: 533423--533550 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
533413 TTAACCTTTG
533423 TTAACTAACCAAATTTCATATAAAACTATCACCTAACCATCCACCATAAAGTAAATTGGTAGA
1 TTAACTAACCAAATTTCATATAAAACTATCACCTAACCATCCACCATAAAGTAAATTGGTAGA
*
533486 TTAACTAACCAAATTTCATATAAAACTATCACCTAACCATTCACCATAAAGTAAATTGGTAGA
1 TTAACTAACCAAATTTCATATAAAACTATCACCTAACCATCCACCATAAAGTAAATTGGTAGA
533549 TT
1 TT
533551 TACCACATAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (63 bp):
TTAACTAACCAAATTTCATATAAAACTATCACCTAACCATCCACCATAAAGTAAATTGGTAGA
Found at i:536347 original size:32 final size:32
Alignment explanation
Indices: 536301--536361 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
536291 AATGTTCAAT
* * *
536301 GGTGGAATTGTAAACTTAGAAATAGTAAATAC
1 GGTGGAATTATAAACATAGAAATAATAAATAC
536333 GGTGGAATTATAAACATAGAAATAATAAA
1 GGTGGAATTATAAACATAGAAATAATAAA
536362 GTATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (32 bp):
GGTGGAATTATAAACATAGAAATAATAAATAC
Found at i:543438 original size:44 final size:44
Alignment explanation
Indices: 543389--543474 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
543379 AACAAATCGA
* ** *
543389 GATAACTTCCCCAATCTTATAGTCTTCTCCTAAAATCACTCCGG
1 GATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTCCGG
543433 GATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTCC
1 GATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTCC
543475 AACCTTCCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.29, C:0.36, G:0.06, T:0.29
Consensus pattern (44 bp):
GATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTCCGG
Found at i:555696 original size:25 final size:24
Alignment explanation
Indices: 555620--555704 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 24
555610 ATACATGCAT
* ** *
555620 GCTCATACGAGCTCTGAATTAGTAT
1 GCTCATACGAGCTGT-AATCGGTAA
*
555645 GCTCTTACGAGCTGTAATCGGTAA
1 GCTCATACGAGCTGTAATCGGTAA
555669 GCTCATACGAGCTGAGTAA-CGGTAA
1 GCTCATACGAGCT--GTAATCGGTAA
555694 GCTCATACGAG
1 GCTCATACGAG
555705 TAAATATCAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
24 18 0.35
25 30 0.58
26 4 0.08
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (24 bp):
GCTCATACGAGCTGTAATCGGTAA
Found at i:558637 original size:15 final size:16
Alignment explanation
Indices: 558617--558648 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
558607 GCTTGAGGTT
558617 AAGATTAATT-AATTA
1 AAGATTAATTAAATTA
558632 AAGATTAATTAAATTA
1 AAGATTAATTAAATTA
558648 A
1 A
558649 TTAAGGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AAGATTAATTAAATTA
Found at i:558640 original size:11 final size:11
Alignment explanation
Indices: 558624--558660 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
558614 GTTAAGATTA
558624 ATTAATTAAAG
1 ATTAATTAAAG
558635 ATTAATT-AA-
1 ATTAATTAAAG
*
558644 ATTAATTAAGG
1 ATTAATTAAAG
558655 ATTAAT
1 ATTAAT
558661 GATTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.30
10 3 0.13
11 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (11 bp):
ATTAATTAAAG
Found at i:558648 original size:20 final size:20
Alignment explanation
Indices: 558623--558660 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
558613 GGTTAAGATT
558623 AATTAATTAAAGATTAATTA
1 AATTAATTAAAGATTAATTA
*
558643 AATTAATTAAGGATTAAT
1 AATTAATTAAAGATTAAT
558661 GATTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
AATTAATTAAAGATTAATTA
Found at i:559821 original size:28 final size:29
Alignment explanation
Indices: 559761--559830 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
559751 ACAATTTCAT
* *
559761 CTTGTGTGAGAAAATTCATAAAATGCTAG
1 CTTGTGTGAGCAAATTCATAAAATGCTAA
*
559790 CTTGAGTGAGCAAATTCAT-AAATG-TCAA
1 CTTGTGTGAGCAAATTCATAAAATGCT-AA
559818 CTTGTGTGAGCAA
1 CTTGTGTGAGCAA
559831 CCCTGATCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.03
28 18 0.50
29 17 0.47
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (29 bp):
CTTGTGTGAGCAAATTCATAAAATGCTAA
Found at i:560831 original size:51 final size:51
Alignment explanation
Indices: 560775--560878 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
560765 CCTTGAATAT
*
560775 TTGAAAAACTTCACAAATTAACTATTGATTGATTTAAGGGT-GCTATCGGGA
1 TTGAAAAACTTCACAAATTAACTATTGATTGATTTAAGGATAG-TATCGGGA
* * * *
560826 TTGAAAAGCTTCGCAGATTAACTCTTGATTGATTTAAGGATAGTATCGGGA
1 TTGAAAAACTTCACAAATTAACTATTGATTGATTTAAGGATAGTATCGGGA
560877 TT
1 TT
560879 TCGTTAGCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (51 bp):
TTGAAAAACTTCACAAATTAACTATTGATTGATTTAAGGATAGTATCGGGA
Found at i:566665 original size:24 final size:24
Alignment explanation
Indices: 566638--566685 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
566628 CCTTCACTAT
*
566638 CAACATCGTCCCCACCCTTAGTCC
1 CAACATCGTCCCCACCCTCAGTCC
* *
566662 CAACATCTTCTCCACCCTCAGTCC
1 CAACATCGTCCCCACCCTCAGTCC
566686 TAGAATTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.50, G:0.06, T:0.23
Consensus pattern (24 bp):
CAACATCGTCCCCACCCTCAGTCC
Found at i:579605 original size:10 final size:10
Alignment explanation
Indices: 579590--579620 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
579580 TTGAAAAATT
579590 AATTAATTTA
1 AATTAATTTA
579600 AATTAATTTA
1 AATTAATTTA
*
579610 AAATAATTTA
1 AATTAATTTA
579620 A
1 A
579621 TAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AATTAATTTA
Found at i:593136 original size:51 final size:51
Alignment explanation
Indices: 593077--593182 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
593067 CTTGGATGTG
593077 TGTTTGAGGTTATGGGTTCAAGTATCATTTTTGGGAAAATTCAGTTATTTT
1 TGTTTGAGGTTATGGGTTCAAGTATCATTTTTGGGAAAATTCAGTTATTTT
593128 TGTTTGAGGTTATGGGTTCAAGTATCATTTTTGGGAAAATTCAGTTATTTT
1 TGTTTGAGGTTATGGGTTCAAGTATCATTTTTGGGAAAATTCAGTTATTTT
593179 TGTT
1 TGTT
593183 CCTAGCCCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.48
Consensus pattern (51 bp):
TGTTTGAGGTTATGGGTTCAAGTATCATTTTTGGGAAAATTCAGTTATTTT
Found at i:597426 original size:12 final size:12
Alignment explanation
Indices: 597409--597439 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
597399 CCTCATACTC
597409 CCGTGTACTAGG
1 CCGTGTACTAGG
*
597421 CCGTGTGCTAGG
1 CCGTGTACTAGG
597433 CCGTGTA
1 CCGTGTA
597440 ACAGCCTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.35, T:0.26
Consensus pattern (12 bp):
CCGTGTACTAGG
Found at i:598651 original size:25 final size:25
Alignment explanation
Indices: 598623--598696 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
598613 ACGAGTTATG
*
598623 AATCGGTATGCTCACTCGAACTGTA
1 AATCGGTATGCTCACTCGAGCTGTA
* *
598648 AATCGGTATGCTCTCAT-GAGCTATA
1 AATCGGTATGCTCAC-TCGAGCTGTA
* *
598673 AATCGATATGCTCACACGAGCTGT
1 AATCGGTATGCTCACTCGAGCTGT
598697 GGGTCGGAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 39 0.98
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (25 bp):
AATCGGTATGCTCACTCGAGCTGTA
Found at i:607597 original size:28 final size:28
Alignment explanation
Indices: 607543--607633 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
607533 ATGTAAATAT
*
607543 TATTATTTGTTTAT-ATATATATATGTA
1 TATTATTTTTTTATAATATATATATGTA
*
607570 -ATTATCTTTTTTATAATCTATATATGTA
1 TATTAT-TTTTTTATAATATATATATGTA
* * *
607598 TATAATTTTTTT-TATATATGTACATGTA
1 TATTATTTTTTTATA-ATATATATATGTA
607626 TA-TATTTT
1 TATTATTTT
607634 GTACCTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 5 0.09
27 14 0.26
28 30 0.57
29 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (28 bp):
TATTATTTTTTTATAATATATATATGTA
Found at i:608547 original size:44 final size:44
Alignment explanation
Indices: 608501--609358 Score: 404
Period size: 44 Copynumber: 19.8 Consensus size: 44
608491 AATGCGATCC
* * * *
608501 GCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * * ** *
608545 GCTCTACTACAACTTCAGAGAGATGGGAT-TATTGGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATT-ACTTCAATCT
* * * * * * **
608589 GCTCCACTGTAACCTCAGTGAGATAATATTTGCTT-CTT-GGTCAT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-ATTACTTCAATC-T
* * * * * *
608633 -CTCCGCTGTAACCTCAGGGAGAT-AGACCTGA-T--GT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-ATTACTTCAATCT
* * * * * *
608672 ACTCTACTGCAACTTCAGAGAGATAAGAGCTATTACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * *
608716 GCTCCACTACAACTTCAGGGAGATAGGAT-T-TTCCATCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATT--A-CTTCAATCT
* * * *
608761 G-TCCCATTGCAACTTCAAGGG-GATAAGACCTGCTTAC-TCAGTCT
1 GCT-CCACTGCAACTTC-AGGGAGATAAGATCT-ATTACTTCAATCT
* *** * *
608805 GCTCCGCTGCAACTTCAGGGAGATAAGA-C-CCGA-TGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * * * *
608846 ACTCTACTGCAACTTCAGAGAGATAAAATCTATTACTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* *
608890 GCTCCACTACAACTTCAGGGAGATAAGAT-TATCAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCT
* * *** *
608934 GCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCT
* * * * *
608979 GCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-ATTACTTCAATCT
* * * * * *
609023 ACTCCGCTGCAACTTCAGGGAGATAAGA-C-CTGA-TGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * * * * * *
609064 ACTCTACTGCAACTTCAGAGATATAAGATCTATTACTTTACTCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * **
609108 GCTCCACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAATCT
* * * *** *
609152 ACTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCT
* * * * *
609197 GCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-ATTACTTCAATCT
* ** *** * *
609241 ACTCCGTTGCAACTTCAGGGAGATAAGA-C-CCGA-TGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * ** * * *
609282 ACTCTACTGCAACTTCAGATATATAAGATCTATTACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
* * *
609326 GCTCTACTACAACTTCAGGGAGATAGGAT-TATT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATT
609359 GGCTTCACCG
Statistics
Matches: 606, Mismatches: 169, Indels: 79
0.71 0.20 0.09
Matches are distributed among these distances:
39 1 0.00
40 23 0.04
41 95 0.16
42 9 0.01
43 51 0.08
44 315 0.52
45 100 0.17
46 10 0.02
48 2 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCT
Found at i:608891 original size:85 final size:85
Alignment explanation
Indices: 608646--609350 Score: 293
Period size: 89 Copynumber: 8.1 Consensus size: 85
608636 CGCTGTAACC
* * *
608646 TCAGGGAGAT-AGACCTGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGAGCTATTACTT
1 TCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTACTT
*
608710 TAATCCGCTCCACTACAACT
66 TAATCTGCTCCACTACAACT
* * * * * * *
608730 TCAGGGAGATAGGATTTTCC-ATCTTCGATCT-GTCCCATTGCAACTTCA-AGGGGATAAGACCT
1 TCAGGGAGATAAGA---CCCGA--TGCGATCTACT-CTACTGCAACTTCAGA-GAGATAAGACCT
* * * * *
608792 GCTTAC-TCAGTCTGCTCCGCTGCAACT
59 -ATTACTTTAATCTGCTCCACTACAACT
* *
608819 TCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAAATCTATTACTT
1 TCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTACTT
608884 TAATCTGCTCCACTACAACT
66 TAATCTGCTCCACTACAACT
* * * * * * * * * ** ***
608904 TCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCA
1 TCAGGGAGATAAG---ACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTA
** * *
608969 TCTTCGATCTGCCCCACTGCAACT
63 -CTTTAATCTGCTCCACTACAACT
* * * * * ** *
608993 TCAGGGGGATAAGACCTGCTTACTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGACCTGA-T
1 TCAGGGAGATAAGACCCG-ATGC-GA-TCTACTCTACTGCAACTTCAGAGAGATAAGACCT-ATT
* * * * *
609057 GC---GATCTACTCTACTGCAACT
62 ACTTTAATCTGCTCCACTACAACT
* * * * * * ** * * * * *
609078 TCAGAGATATAAGA-TCTATTACTTTACTCCGCTCCACTACAACTTCAGGGAGATAGGA-TTATC
1 TCAGGGAGATAAGACCCGA-TGC--GA-TCTACTCTACTGCAACTTCAGAGAGATAAGACCTAT-
** * * * *
609141 GGCTTCAATCTACTCCACTGCAACC
61 TACTTTAATCTGCTCCACTACAACT
* * * * * * * *
609166 TCAGGGAGATAAGATTTGCC-ATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGC
1 TCAGGGAGATAAGA---CCCGA--TGCGATCTACTCTACTGCAACTTCAGAGAGATAAGACCT-A
* * * ** *
609230 TTAC-TCAGTCTACTCCGTTGCAACT
60 TTACTTTAATCTGCTCCACTACAACT
* * *
609255 TCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGATATATAAGATCTATTACTT
1 TCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTACTT
* *
609320 TAATCCGCTCTACTACAACT
66 TAATCTGCTCCACTACAACT
609340 TCAGGGAGATA
1 TCAGGGAGATA
609351 GGATTATTGG
Statistics
Matches: 462, Mismatches: 122, Indels: 73
0.70 0.19 0.11
Matches are distributed among these distances:
83 1 0.00
84 22 0.05
85 171 0.37
86 9 0.02
87 5 0.01
88 68 0.15
89 174 0.38
90 7 0.02
91 2 0.00
92 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (85 bp):
TCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTACTT
TAATCTGCTCCACTACAACT
Found at i:608972 original size:218 final size:218
Alignment explanation
Indices: 608681--609357 Score: 1113
Period size: 218 Copynumber: 3.1 Consensus size: 218
608671 TACTCTACTG
* * * * * * * *
608681 CAACTTCAGAGAGATAAGAGCTATTA-CTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGAT
1 CAACTTCAGGGAGATAAGA-TTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGAT
* * * * *
608745 TTTCCATCTTCGATCTGTCCCATTGCAACTTCAAGGGGATAAGACCTGCTTACTCAGTCTGCTCC
65 TTGCCATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTCC
* *
608810 GCTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAAAT
130 GCTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGATATAAGAT
*
608875 CTATTACTTTAATCTGCTCCACTA
195 CTATTACTTTAATCCGCTCCACTA
608899 CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
1 CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
608964 TGCCATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTCCG
66 TGCCATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTCCG
*
609029 CTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGATATAAGATC
131 CTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGATATAAGATC
*
609094 TATTACTTTACTCCGCTCCACTA
196 TATTACTTTAATCCGCTCCACTA
* * *
609117 CAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATT
1 CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
609182 TGCCATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTCCG
66 TGCCATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTCCG
* *
609247 TTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGATATATAAGATC
131 CTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGATATAAGATC
*
609312 TATTACTTTAATCCGCTCTACTA
196 TATTACTTTAATCCGCTCCACTA
*
609335 CAACTTCAGGGAGATAGGATTAT
1 CAACTTCAGGGAGATAAGATTAT
609358 TGGCTTCACC
Statistics
Matches: 432, Mismatches: 26, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
217 4 0.01
218 428 0.99
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (218 bp):
CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
TGCCATCTTCGATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTCCG
CTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAGATATAAGATC
TATTACTTTAATCCGCTCCACTA
Found at i:608991 original size:174 final size:173
Alignment explanation
Indices: 608458--609010 Score: 681
Period size: 174 Copynumber: 3.2 Consensus size: 173
608448 GCTTTCTCTG
* * * * **
608458 TCTGCTCTGCTGCAAC-CCAGGGAAATAAGACCTAATGCGATCCGCTCTACTGCAACTTCAGAGA
1 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGA
* * * **
608522 GATAAGATCTATTACTTTAATCCGCTCTACTACAACTTCAGAGAGATGGGATTATTGGCTTCAAT
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCAGCTTCAAT
* * * *
608587 CTGCTCCACTGTAACCTCAGTGAGATAATATTTGCTTCTT-GG
131 CTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCGA
* * *
608629 TCAT-CTCCGCTGTAACCTCAGGGAGAT-AGACCTGATGTGATCTACTCTACTGCAACTTCAGAG
1 TC-TGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAG
* * * *
608692 AGATAAGAGCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTTTCCATCTTCG
65 AGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAT-CAGCTTCA
* * **
608757 ATCTG-TCCCATTGCAACTTCAAGGG-GATAAGACCTGCTTAC-TC-A
129 ATCTGCT-CCACTGCAACCTC-AGGGAGATAAGATTTGCTT-CTTCGA
*
608801 GTCTGCTCCGCTGCAACTTCAGGGAGATAAGACCCGATGCGATCTACTCTACTGCAACTTCAGAG
1 -TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAG
* * *
608866 AGATAAAATCTATTACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCAGCTTCAA
65 AGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCAGCTTCAA
*
608931 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
130 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTG-CTTCTTCGA
* * *
608976 TCTGCCCCACTGCAACTTCAGGGGGATAAGACCTG
1 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTG
609011 CTTACTCAGT
Statistics
Matches: 322, Mismatches: 45, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
171 96 0.30
172 45 0.14
173 59 0.18
174 121 0.38
175 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (173 bp):
TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGA
GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCAGCTTCAAT
CTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCGA
Found at i:608995 original size:89 final size:86
Alignment explanation
Indices: 608717--609268 Score: 297
Period size: 89 Copynumber: 6.3 Consensus size: 86
608707 CTTTAATCCG
* * * * *
608717 CTCCACTACAACTTCAGGGAGATAGGATTTTCCATCTTCGATCTG-TCCCATTGCAACTTCAAGG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAT-CA-CTTCAATCTGCT-CCACTGCAACTTC-AGG
** *
608781 G-GATAAGACCTGCTTAC-TC-AGTCTG
62 GAGATAAGATTTGC--ACTTCGA-TCTA
* ** * * * * *
608806 CTCCGCTGCAACTTCAGGGAGATAAGA--CCCGA-TGCGATCTACTCTACTGCAACTTCAGAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATC-ACTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * ** *
608868 ATAAAATCTAT-TACTTTAATCTG
65 ATAAGAT-T-TGCACTTCGATCTA
* *
608891 CTCCACTACAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCA-CTTCAATCTGCTCCACTGCAACTTCAGGGAG
*
608956 ATAAGATTTGCCATCTTCGATCTG
65 ATAAGATTTG-CA-CTTCGATCTA
* * ** * * * *
608980 CCCCACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCTACTCCGCTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGGGAGATAAGA--TTATCACTTCAATCTGCTCCACTGCAACTTCAGGGA
** *
609044 GATAAGACCTG-A-TGCGATCTA
64 GATAAGATTTGCACTTCGATCTA
* * * * * * * *
609065 CTCTACTGCAACTTCAGAGATATAAGATCTATTACTTTACTCCGCTCCACTACAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TATCACTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * *
609130 ATAGGATTAT-CGGCTTCAATCTA
65 ATAAGATT-TGC-ACTTCGATCTA
* * *
609153 CTCCACTGCAACCTCAGGGAGATAAGATT-TGCCATCTTCGATCTGCCCCACTGCAACTTCAGGG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAT--CA-CTTCAATCTGCTCCACTGCAACTTCAGGG
* **
609217 GGATAAGACCTGCTTAC-TC-AGTCTA
63 AGATAAGATTTGC--ACTTCGA-TCTA
**
609242 CTCCGTTGCAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
609269 CCCGATGCGA
Statistics
Matches: 353, Mismatches: 82, Indels: 56
0.72 0.17 0.11
Matches are distributed among these distances:
83 1 0.00
84 9 0.03
85 111 0.31
86 7 0.02
87 6 0.02
88 65 0.18
89 149 0.42
90 2 0.01
91 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (86 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTATCACTTCAATCTGCTCCACTGCAACTTCAGGGAGA
TAAGATTTGCACTTCGATCTA
Found at i:610666 original size:13 final size:13
Alignment explanation
Indices: 610630--610665 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
610620 TTTATTTATT
*
610630 TTTTCATTTGTCA
1 TTTTCATTTTTCA
610643 TTTTCATTTTTCA
1 TTTTCATTTTTCA
610656 -TTTCATTTTT
1 TTTTCATTTTT
610666 TTACTCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:616226 original size:28 final size:27
Alignment explanation
Indices: 616187--616244 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
616177 GGTTAATTAT
* *
616187 AAAATAAGTAATATGCAAAATAACTTA
1 AAAATAAATAATATACAAAATAACTTA
* *
616214 AAAATAAAATAATATATAAAGTAACTTA
1 AAAAT-AAATAATATACAAAATAACTTA
616242 AAA
1 AAA
616245 TGATTAGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (27 bp):
AAAATAAATAATATACAAAATAACTTA
Found at i:618371 original size:11 final size:11
Alignment explanation
Indices: 618357--618388 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
618347 TAAAGAGAGC
*
618357 TTTGAGAGGAA
1 TTTGAGAGAAA
618368 TTTGAGAGAAA
1 TTTGAGAGAAA
618379 TTTGAGAGAA
1 TTTGAGAGAA
618389 TATTGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:621781 original size:11 final size:11
Alignment explanation
Indices: 621767--621798 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
621757 TAAAGAGAGC
*
621767 TTTGAGAGGAA
1 TTTGAGAGAAA
621778 TTTGAGAGAAA
1 TTTGAGAGAAA
621789 TTTGAGAGAA
1 TTTGAGAGAA
621799 TATTGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:627876 original size:97 final size:101
Alignment explanation
Indices: 627773--627979 Score: 228
Period size: 104 Copynumber: 2.0 Consensus size: 101
627763 TCGGAGTAAA
* * *
627773 AAAAAAATAATTTTGG-TGATAGGTTTTTAAGTGGC-AGCAGCAATGTAGG-A-A-TTTT-GTTT
1 AAAAAAA-AATTTTGGTTG-CAGGTTTATAAGTGACGA-CAGCAATGTAGGAATATTTTTAGTTT
* *
627832 TTGGTGCCGCCTCCTTCAATGGAGGCACTAAATATCAGT
63 TTGGTGCCACCTCCTTCAATGGAGGCACCAAATATCAGT
* * *
627871 AAAAAAAAATTTTGGTTGCAGGTTTATAATTGACGACATCAATGTAGGAATCTTATTTTTATTTT
1 AAAAAAAAATTTTGGTTGCAGGTTTATAAGTGACGACAGCAATGTAGGAA---TATTTTTAGTTT
* *
627936 TTGGTGCCACCTCTTTCAATGGAGGCACCAAATTTCAGT
63 TTGGTGCCACCTCCTTCAATGGAGGCACCAAATATCAGT
627975 AAAAA
1 AAAAA
627980 TATTTTTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
97 31 0.34
98 11 0.12
102 1 0.01
103 4 0.04
104 43 0.48
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (101 bp):
AAAAAAAAATTTTGGTTGCAGGTTTATAAGTGACGACAGCAATGTAGGAATATTTTTAGTTTTTG
GTGCCACCTCCTTCAATGGAGGCACCAAATATCAGT
Found at i:628285 original size:80 final size:80
Alignment explanation
Indices: 628149--628312 Score: 274
Period size: 80 Copynumber: 2.0 Consensus size: 80
628139 AGTAATAAAA
* *
628149 TTTTCCTTGGTACCTACTCTAGATGTGACGACACCACCAGCTATATACACCACAATGCCGACTTA
1 TTTTCCTTGGTACCTACTCCAGATGTGACGACACCACCAGCTATATACACCACAATGCCAACTTA
628214 ACAAGTGAAGGTTTT
66 ACAAGTGAAGGTTTT
* * * *
628229 TTTTCCTTGGTACCTACTCCAGATGTGATGGCACCACCAGCTATATATACCCCAATGCCAACTTA
1 TTTTCCTTGGTACCTACTCCAGATGTGACGACACCACCAGCTATATACACCACAATGCCAACTTA
628294 ACAAGTGAAGGTTTT
66 ACAAGTGAAGGTTTT
628309 TTTT
1 TTTT
628313 TTTAATCTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (80 bp):
TTTTCCTTGGTACCTACTCCAGATGTGACGACACCACCAGCTATATACACCACAATGCCAACTTA
ACAAGTGAAGGTTTT
Found at i:629706 original size:103 final size:103
Alignment explanation
Indices: 629592--629800 Score: 303
Period size: 103 Copynumber: 2.0 Consensus size: 103
629582 TGTTGTTGTG
* *
629592 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATT-AAAGTTTTGGTGGTA
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAATTTGTTTTATTAAAAGTTTTGGTAGTA
* * *
629656 TTTTATATCAGTTTTTCATTTTTAAGGGAAATAATAATT
66 TTTTATATCAGTTTTTCATATTTAAGGAAAAGAAT-ATT
* * * *
629695 TTTTATTAGGTTTAAGTTTGTATTAAATGTATGGTTAATTTGTTTTATTAAAATTTTTTGTAGTA
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAATTTGTTTTATTAAAAGTTTTGGTAGTA
* *
629760 TTTTATATTAGTTTTTCGTATTTAAGGAAAAGAATATT
66 TTTTATATCAGTTTTTCATATTTAAGGAAAAGAATATT
629798 TTT
1 TTT
629801 GTTGTTGTGT
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 52 0.55
104 42 0.45
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (103 bp):
TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAATTTGTTTTATTAAAAGTTTTGGTAGTA
TTTTATATCAGTTTTTCATATTTAAGGAAAAGAATATT
Found at i:629858 original size:218 final size:221
Alignment explanation
Indices: 629473--629882 Score: 569
Period size: 218 Copynumber: 1.9 Consensus size: 221
629463 TGTGTGTGTG
** **
629473 TTTTATTAAGTTTAAGTTTGTATTAAATGTATGATTTGTTTGTTTTATTATTATTTTTGTAGTAT
1 TTTTATTAAGTTTAAGTTTGTATTAAATGTATGATTAATTTGTTTTATTAAAATTTTTGTAGTAT
* ** * *
629538 CTTATATCAGTTTTCTGTATTTAAGAGAGAATGCTTTTTTTTGTTGTTGTTGTGTTTTATTAGGT
66 CTTATATCAGTTTTCTGTATTTAAGAGAGAAAGC-AATATTTGTTGTTGTTGTGTTTGATTAGGT
* * * *
629603 TTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAAAGTTTTGGTGGTATTTTATATCAGT
130 TTAAGTTTGTATTAAAGGTAAGATTAATTTATTTTATTAAAGTTTTGGTGATATTTTATATCAGT
629668 TTTTCATTTTTAAGGGAAATAATAATT
195 TTTTCATTTTTAAGGGAAATAATAATT
* *
629695 TTTTATTAGGTTTAAGTTTGTATTAAATGTATGGTTAATTTGTTTTATTAAAATTTTTTGTAGTA
1 TTTTATTAAGTTTAAGTTTGTATTAAATGTATGATTAATTTGTTTTATTAAAA-TTTTTGTAGTA
* *
629760 TTTTATATTAGTTTT-TCGTATTTAAG-GA-AAAG-AATATTT-TTGTTGTTGTGTTTGATTAGG
65 TCTTATATCAGTTTTCT-GTATTTAAGAGAGAAAGCAATATTTGTTGTTGTTGTGTTTGATTAGG
* * * *
629820 TTTAAGTTTGTATTAAATGTAAGATTAATTTATTTTATTAATGTTTTTGTTATATTTTATATC
129 TTTAAGTTTGTATTAAAGGTAAGATTAATTTATTTTATTAAAGTTTTGGTGATATTTTATATC
629883 TTATTTAAGG
Statistics
Matches: 165, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
218 75 0.45
219 4 0.02
221 3 0.02
222 50 0.30
223 33 0.20
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (221 bp):
TTTTATTAAGTTTAAGTTTGTATTAAATGTATGATTAATTTGTTTTATTAAAATTTTTGTAGTAT
CTTATATCAGTTTTCTGTATTTAAGAGAGAAAGCAATATTTGTTGTTGTTGTGTTTGATTAGGTT
TAAGTTTGTATTAAAGGTAAGATTAATTTATTTTATTAAAGTTTTGGTGATATTTTATATCAGTT
TTTCATTTTTAAGGGAAATAATAATT
Found at i:631647 original size:22 final size:23
Alignment explanation
Indices: 631599--631654 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
631589 ATGAGGTTAT
* * *
631599 GCTTAATAAAGTGGTTTAATTAG
1 GCTTAATTAAGTGATTTAATTAA
*
631622 GCTTAATTAA-TGATTTATTTAA
1 GCTTAATTAAGTGATTTAATTAA
631644 GCTTAATTAAG
1 GCTTAATTAAG
631655 AAAGTTAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (23 bp):
GCTTAATTAAGTGATTTAATTAA
Found at i:632041 original size:37 final size:37
Alignment explanation
Indices: 631988--632162 Score: 208
Period size: 37 Copynumber: 4.7 Consensus size: 37
631978 TATATCAAGC
* * *
631988 CAAATCTTACTATTATACTGAATGAGGCTTAATCGAG
1 CAAATCTTACTGTTATACTGAATGAAGCTCAATCGAG
*
632025 CAAATCATACTGTTATACTGAATGAAGCTCAA-CTGAG
1 CAAATCTTACTGTTATACTGAATGAAGCTCAATC-GAG
*
632062 CAAATCTTACTGTTATACTGAATGAAGCTCAACCGAG
1 CAAATCTTACTGTTATACTGAATGAAGCTCAATCGAG
* * * * * *
632099 CAAATCTTACAGTTATATTGAATGATGTTTAATTGAG
1 CAAATCTTACTGTTATACTGAATGAAGCTCAATCGAG
* *
632136 CAAAATCCTACTGTTATACTGAGTGAA
1 C-AAATCTTACTGTTATACTGAATGAA
632163 ACTTGAACGA
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
36 1 0.01
37 96 0.81
38 21 0.18
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (37 bp):
CAAATCTTACTGTTATACTGAATGAAGCTCAATCGAG
Found at i:636097 original size:17 final size:19
Alignment explanation
Indices: 636061--636097 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
636051 TAATTAGATG
*
636061 TTTGTGATTGAATTGTATA
1 TTTGTGATTGAATTGAATA
636080 TTTGTG-TT-AATTGAATA
1 TTTGTGATTGAATTGAATA
636097 T
1 T
636098 ACTTTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (19 bp):
TTTGTGATTGAATTGAATA
Found at i:649382 original size:15 final size:16
Alignment explanation
Indices: 649353--649382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
649343 CAAACAGGCT
649353 TTAACACATTATCAAA
1 TTAACACATTATCAAA
649369 TTAACACA-TATCAA
1 TTAACACATTATCAA
649383 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:666675 original size:3 final size:3
Alignment explanation
Indices: 666662--666707 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
666652 TCTTCGGGCT
*
666662 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
666708 TATTATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:666712 original size:3 final size:3
Alignment explanation
Indices: 666706--666751 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
666696 AATAATAATA
666706 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
666752 AGCCCTTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:670759 original size:23 final size:23
Alignment explanation
Indices: 670729--670774 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
670719 GAGGCCTAAC
670729 CTATTTGGAAAACGGATCTTATT
1 CTATTTGGAAAACGGATCTTATT
670752 CTATTTGGAAAACGGATCTTATT
1 CTATTTGGAAAACGGATCTTATT
670775 TTTTGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (23 bp):
CTATTTGGAAAACGGATCTTATT
Found at i:681474 original size:15 final size:16
Alignment explanation
Indices: 681449--681478 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
681439 AGAGAAAAAT
681449 AAAAGTGAAAATGAAG
1 AAAAGTGAAAATGAAG
681465 AAAA-TGAAAATGAA
1 AAAAGTGAAAATGAA
681479 AAAGGCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
AAAAGTGAAAATGAAG
Found at i:681593 original size:36 final size:33
Alignment explanation
Indices: 681528--681594 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
681518 GTGAATGAAG
*
681528 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
681561 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
681595 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:688136 original size:13 final size:13
Alignment explanation
Indices: 688115--688148 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
688105 AGGGTCACAC
688115 GGCCATGTGGCCA
1 GGCCATGTGGCCA
*
688128 GGCCGTGTGGCCA
1 GGCCATGTGGCCA
*
688141 GACCATGT
1 GGCCATGT
688149 ACAATTCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (13 bp):
GGCCATGTGGCCA
Found at i:693036 original size:27 final size:27
Alignment explanation
Indices: 692998--693055 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
692988 TTTGATATTG
*
692998 TACCGGGTATCCGAAAATGGAGATGTC
1 TACCGGGAATCCGAAAATGGAGATGTC
693025 TACCGGGAATCCGAAAATGGAGATGTC
1 TACCGGGAATCCGAAAATGGAGATGTC
693052 TACC
1 TACC
693056 TCTCTCCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (27 bp):
TACCGGGAATCCGAAAATGGAGATGTC
Found at i:703523 original size:31 final size:29
Alignment explanation
Indices: 703488--703565 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
703478 CTAACAGCTC
* *
703488 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
703519 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
703548 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
703566 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Done.