Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 2 of 125
Found at i:429120 original size:31 final size:31
Alignment explanation
Indices: 429079--429158 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 31
429069 ATTAAATTGA
* *
429079 AAATCTTAGGTACCAATTTGAACATTGAAGCC
1 AAAT-TTAGGTACCAAATTGAACAATGAAGCC
429111 AAATTTAGGTACCAAATTGAACAATGAAGCC
1 AAATTTAGGTACCAAATTGAACAATGAAGCC
429142 AAATTTAGGTACCAAAT
1 AAATTTAGGTACCAAAT
429159 AGTATATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 42 0.91
32 4 0.09
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (31 bp):
AAATTTAGGTACCAAATTGAACAATGAAGCC
Found at i:430161 original size:19 final size:19
Alignment explanation
Indices: 430137--430180 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
430127 TTATGATATT
*
430137 AAATAACAATAAATAATA-A
1 AAATAACAA-AAATAAAATA
*
430156 AAATAACCAAAATAAAATA
1 AAATAACAAAAATAAAATA
430175 AAATAA
1 AAATAA
430181 AATTTAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATAACAAAAATAAAATA
Found at i:433691 original size:15 final size:15
Alignment explanation
Indices: 433671--433705 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
433661 GCACTTATAG
433671 TATGAATAACTTGAA
1 TATGAATAACTTGAA
433686 TATGAATAACTTGAA
1 TATGAATAACTTGAA
433701 TATGA
1 TATGA
433706 CGTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (15 bp):
TATGAATAACTTGAA
Found at i:439215 original size:8 final size:9
Alignment explanation
Indices: 439194--439218 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
439184 TTTCTATTTG
439194 TTTTTAATA
1 TTTTTAATA
439203 TTTTTAATA
1 TTTTTAATA
439212 TTTTTAA
1 TTTTTAA
439219 ATGCAAGTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:450605 original size:58 final size:58
Alignment explanation
Indices: 450539--450654 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
450529 CTGATGATCA
450539 GTGTAAAAAATCAGAGAAGAAAATTGTTTGGATTTTGGTTCAAAGATTCATGACATTC
1 GTGTAAAAAATCAGAGAAGAAAATTGTTTGGATTTTGGTTCAAAGATTCATGACATTC
450597 GTGTAAAAAATCAGAGAAGAAAATTGTTTGGATTTTGGTTCAAAGATTCATGACATTC
1 GTGTAAAAAATCAGAGAAGAAAATTGTTTGGATTTTGGTTCAAAGATTCATGACATTC
450655 AAAGTTGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (58 bp):
GTGTAAAAAATCAGAGAAGAAAATTGTTTGGATTTTGGTTCAAAGATTCATGACATTC
Found at i:455076 original size:28 final size:28
Alignment explanation
Indices: 455045--455100 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
455035 TATATGGTAT
455045 AATTTA-AAATGAAAATTAAAAAAATTAC
1 AATTTACAAAT-AAAATTAAAAAAATTAC
* *
455073 AATTTAGCACATAAATTTAAAAAAATTA
1 AATTTA-CAAATAAAATTAAAAAAATTA
455101 AAGAATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 15 0.62
30 3 0.12
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (28 bp):
AATTTACAAATAAAATTAAAAAAATTAC
Found at i:456486 original size:52 final size:52
Alignment explanation
Indices: 456402--456532 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
456392 TGAAAAAGGG
* *
456402 TCCGATGACTAAGTGTCATCGTAAGTATATGAATCCTTCATGGATTATAAGA
1 TCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTATAAGA
* *
456454 TCCGATGACTAAGTATCATCGTGAGTACATGAATCCTTCATGGATTATAAGG
1 TCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTATAAGA
*
456506 TCCGATGATTAAGTGTCATCGTGAGTA
1 TCCGATGACTAAGTGTCATCGTGAGTA
456533 TTAAATGTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (52 bp):
TCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCATGGATTATAAGA
Found at i:469700 original size:21 final size:20
Alignment explanation
Indices: 469658--469719 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
469648 ATTAGAATGT
**
469658 AAAA-ATTAAATTAAAAGCA
1 AAAATATTAAATTAAAATAA
469677 AAAATATTAAAATTAAAATAA
1 AAAATATT-AAATTAAAATAA
* *
469698 AAAATGTCTAAATTAATATAA
1 AAAATAT-TAAATTAAAATAA
469719 A
1 A
469720 TAAAGTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 28 0.78
22 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (20 bp):
AAAATATTAAATTAAAATAA
Found at i:474941 original size:20 final size:21
Alignment explanation
Indices: 474906--474948 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
474896 ATATGCAAAA
474906 AAAAAAAAAAGTGTTCAACTAT
1 AAAAAAAAAAG-GTTCAACTAT
*
474928 AAAAAAAAAA-GTTCAATTAT
1 AAAAAAAAAAGGTTCAACTAT
474948 A
1 A
474949 TTGTAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAAAAAAAGGTTCAACTAT
Found at i:483687 original size:2 final size:2
Alignment explanation
Indices: 483680--483717 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
483670 TTAATTAGTA
483680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
483718 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:485547 original size:42 final size:43
Alignment explanation
Indices: 485484--485635 Score: 148
Period size: 43 Copynumber: 3.6 Consensus size: 43
485474 CGCAAAAAAT
* * * * *
485484 GCCGCTAAAGAACATGGTCTTTAGTGGCGTTTA-GATACAAAC
1 GCCGCTAAAGAACATGTTCTTTAGTGACGCTTATCACACAAAC
* * *
485526 GCCGCTAAAGACCATATTCTTTAGTGACGCTTATCCCACAAAC
1 GCCGCTAAAGAACATGTTCTTTAGTGACGCTTATCACACAAAC
* * *
485569 GCCGCTAAAGATCATGTTCTTTAGCAGCAC-TTTATCA-ACAAAC
1 GCCGCTAAAGAACATGTTCTTTAG-TG-ACGCTTATCACACAAAC
* *
485612 GCCGCTAAAGAATATGGTCTTTAG
1 GCCGCTAAAGAACATGTTCTTTAG
485636 CATTGCTTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
42 28 0.31
43 55 0.60
44 6 0.07
45 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
GCCGCTAAAGAACATGTTCTTTAGTGACGCTTATCACACAAAC
Found at i:485633 original size:43 final size:43
Alignment explanation
Indices: 485484--485662 Score: 134
Period size: 43 Copynumber: 4.2 Consensus size: 43
485474 CGCAAAAAAT
* ** * *
485484 GCCGCTAAAGAACATGGTCTTTAGTGGC-GTTTA-GATACAAAC
1 GCCGCTAAAGATCATGGTCTTTAGCAGCACTTTATCA-ACAAAC
* ** * * *
485526 GCCGCTAAAGACCATATTCTTTAG-TG-ACGCTTATCCCACAAAC
1 GCCGCTAAAGATCATGGTCTTTAGCAGCAC-TTTAT-CAACAAAC
*
485569 GCCGCTAAAGATCATGTTCTTTAGCAGCACTTTATCAACAAAC
1 GCCGCTAAAGATCATGGTCTTTAGCAGCACTTTATCAACAAAC
*** * *
485612 GCCGCTAAAGAAT-ATGGTCTTTAGCATTGCTTTTTCCACAAAC
1 GCCGCTAAAG-ATCATGGTCTTTAGCAGCACTTTATCAACAAAC
485655 GCCGCTAA
1 GCCGCTAA
485663 TATTAACAGA
Statistics
Matches: 111, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 24 0.22
43 77 0.69
44 7 0.06
45 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
GCCGCTAAAGATCATGGTCTTTAGCAGCACTTTATCAACAAAC
Found at i:491243 original size:18 final size:18
Alignment explanation
Indices: 491220--491262 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
491210 TAAAGCCATC
491220 AACAACTAGATGTTCGTA
1 AACAACTAGATGTTCGTA
491238 AACAACTAGATGTTCGTA
1 AACAACTAGATGTTCGTA
*
491256 TACAACT
1 AACAACT
491263 TCACGAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (18 bp):
AACAACTAGATGTTCGTA
Found at i:491730 original size:8 final size:8
Alignment explanation
Indices: 491719--491754 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
491709 ATTAAATATT
491719 TAATTAAA
1 TAATTAAA
491727 TAATTAAATA
1 TAATT-AA-A
491737 TAATTAAA
1 TAATTAAA
491745 TAATTAAA
1 TAATTAAA
491753 TA
1 TA
491755 TTTTGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.62
9 4 0.15
10 6 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAATTAAA
Found at i:491763 original size:22 final size:20
Alignment explanation
Indices: 491706--491768 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 20
491696 GTTATTTTTT
491706 ATAATTAAATATTTAATTAA
1 ATAATTAAATATTTAATTAA
491726 ATAATTAAATA--TAATTAA
1 ATAATTAAATATTTAATTAA
491744 ATAATTAAATATTTTGAATTAA
1 ATAATTAAATA-TTT-AATTAA
491766 ATA
1 ATA
491769 TTTGGGTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 18 0.46
20 11 0.28
21 1 0.03
22 9 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATTAAATATTTAATTAA
Found at i:491810 original size:4 final size:4
Alignment explanation
Indices: 491788--491852 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
491778 TCTTTAATAT
* * * *
491788 TTAA ATAA TTAA ATAA TTAA TTAA TT-A TTAA TTAA TTGGA TTGAT TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT-AA TT-AA TTAA
* *
491837 ATAA TTAA ATAA TTAA
1 TTAA TTAA TTAA TTAA
491853 GTATTTGGGC
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
3 3 0.06
4 38 0.81
5 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (4 bp):
TTAA
Found at i:491852 original size:34 final size:34
Alignment explanation
Indices: 491799--492006 Score: 139
Period size: 34 Copynumber: 5.7 Consensus size: 34
491789 TAAATAATTA
* * * *
491799 AATAATTAATTAATTATTAATTAATTGGATTGATTTA
1 AATAATTAAATAATTA--AA-TAATTGGGTTGTTTTT
* * *
491836 AATAATTAAATAATTAAGTATTTGGGCTGTTTTT
1 AATAATTAAATAATTAAATAATTGGGTTGTTTTT
*
491870 AATAATTAAATAATTAAATATTTGGGTTGTTTTT
1 AATAATTAAATAATTAAATAATTGGGTTGTTTTT
* **
491904 AATATTTAAATAAATAAATAATTAATTAATT-AATTGGGTTGATTT
1 -A-A--T-AAT---TAAATAATTAAATAATTGGGTT--GTT--TTT
* * *
491949 AAATAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AAT-AATTAAATAATTAAATAATTGGGTTGTTTTT
491984 AATAATTAAATAATTAAATAATT
1 AATAATTAAATAATTAAATAATT
492007 AAATATTTGA
Statistics
Matches: 136, Mismatches: 22, Indels: 29
0.73 0.12 0.16
Matches are distributed among these distances:
34 61 0.45
35 7 0.05
36 1 0.01
37 18 0.13
38 16 0.12
39 5 0.04
41 5 0.04
42 15 0.11
43 4 0.03
44 1 0.01
45 3 0.02
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (34 bp):
AATAATTAAATAATTAAATAATTGGGTTGTTTTT
Found at i:491941 original size:80 final size:80
Alignment explanation
Indices: 491834--492008 Score: 260
Period size: 80 Copynumber: 2.2 Consensus size: 80
491824 TGGATTGATT
* * * * *
491834 TAAATAATTAAATAATTAAGTATTTGGGCTGTTTTTAATAATTAAATAATTAAATATTTGGGTTG
1 TAAATAAATAATTAATTAAGTAATTGGGCTGATTTAAATAATTAAATAATTAAATATTTGGGTTG
*
491899 TTTTTAATATTTAAA
66 TTTTTAATAATTAAA
* * *
491914 TAAATAAATAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGGGTTG
1 TAAATAAATAATTAATTAAGTAATTGGGCTGATTTAAATAATTAAATAATTAAATATTTGGGTTG
491979 TTTTTAATAATTAAA
66 TTTTTAATAATTAAA
*
491994 TAATTAAATAATTAA
1 TAAATAAATAATTAA
492009 ATATTTGAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (80 bp):
TAAATAAATAATTAATTAAGTAATTGGGCTGATTTAAATAATTAAATAATTAAATATTTGGGTTG
TTTTTAATAATTAAA
Found at i:491997 original size:8 final size:8
Alignment explanation
Indices: 491984--492011 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
491974 GGTTGTTTTT
491984 AATAATTA
1 AATAATTA
491992 AATAATTA
1 AATAATTA
492000 AATAATTA
1 AATAATTA
492008 AATA
1 AATA
492012 TTTGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAATTA
Found at i:492021 original size:13 final size:13
Alignment explanation
Indices: 492003--492027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
491993 ATAATTAAAT
492003 AATTAAATATTTG
1 AATTAAATATTTG
492016 AATTAAATATTT
1 AATTAAATATTT
492028 TGTTGTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AATTAAATATTTG
Found at i:492057 original size:4 final size:4
Alignment explanation
Indices: 492043--492072 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
492033 TTTTTAATAT
*
492043 TTAA ATAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
492073 GGGTTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:492140 original size:34 final size:34
Alignment explanation
Indices: 492052--492277 Score: 127
Period size: 34 Copynumber: 6.5 Consensus size: 34
492042 TTTAAATAAT
* * *
492052 TAATTAATTAATTAATTAATTGGGTTGATTTAAA
1 TAATTAAATAATTAAATATTTGGGTTGATTTAAA
* * *
492086 TAATTAAATAATTAAGTATTTGGGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGGTTGATTTAAA
*
492120 TAATTAAATAATTAAATA-TT---TTGAATTAAA
1 TAATTAAATAATTAAATATTTGGGTTGATTTAAA
* *** ** * *** * *
492150 TATTTGGGTTGTTTTTAATATTTAAATAAATAAATAAATAAA
1 TAATT-AAAT-AATTAAATATTTGGGT---T-GAT--TTAAA
* * *
492192 TAATTAATTAATTAATTAATTGGGTTGATTTAAA
1 TAATTAAATAATTAAATATTTGGGTTGATTTAAA
* * *
492226 TAATTAAATAATTAAGTATTTGGGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGGTTGATTTAAA
492260 TAATTAAATAATTAAATA
1 TAATTAAATAATTAAATA
492278 ATTAATTAAT
Statistics
Matches: 142, Mismatches: 38, Indels: 24
0.70 0.19 0.12
Matches are distributed among these distances:
30 11 0.08
31 1 0.01
32 6 0.04
33 4 0.03
34 96 0.68
36 3 0.02
37 1 0.01
39 1 0.01
40 9 0.06
41 2 0.01
42 8 0.06
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.46
Consensus pattern (34 bp):
TAATTAAATAATTAAATATTTGGGTTGATTTAAA
Found at i:492268 original size:84 final size:84
Alignment explanation
Indices: 492174--492445 Score: 526
Period size: 84 Copynumber: 3.2 Consensus size: 84
492164 TTAATATTTA
* *
492174 AATAAATAAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
1 AATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
492239 AAGTATTTGGGTTGTTTTT
66 AAGTATTTGGGTTGTTTTT
492258 AATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
1 AATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
492323 AAGTATTTGGGTTGTTTTT
66 AAGTATTTGGGTTGTTTTT
492342 AATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
1 AATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
492407 AAGTATTTGGGTTGTTTTT
66 AAGTATTTGGGTTGTTTTT
492426 AATAATTAAATAATTAAATA
1 AATAATTAAATAATTAAATA
492446 TTTTGAATTA
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 186 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (84 bp):
AATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAATT
AAGTATTTGGGTTGTTTTT
Found at i:492271 original size:8 final size:8
Alignment explanation
Indices: 492258--492408 Score: 68
Period size: 8 Copynumber: 18.1 Consensus size: 8
492248 GGTTGTTTTT
492258 AATAATTA
1 AATAATTA
492266 AATAATTA
1 AATAATTA
492274 AATAATTA
1 AATAATTA
*
492282 ATTAATTA
1 AATAATTA
* *
492290 ATTAATTGG
1 AATAATT-A
** *
492299 GTTGATTTA
1 AAT-AATTA
492308 AATAATTA
1 AATAATTA
492316 AATAATTA
1 AATAATTA
* * *
492324 AGTATTTGG
1 AATAATT-A
** ** *
492333 GTTGTTTTT
1 AAT-AATTA
492342 AATAATTA
1 AATAATTA
492350 AATAATTA
1 AATAATTA
492358 AATAATTA
1 AATAATTA
*
492366 ATTAATTA
1 AATAATTA
* *
492374 ATTAATTGG
1 AATAATT-A
** *
492383 GTTGATTTA
1 AAT-AATTA
492392 AATAATTA
1 AATAATTA
492400 AATAATTA
1 AATAATTA
492408 A
1 A
492409 GTATTTGGGT
Statistics
Matches: 109, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
8 92 0.84
9 8 0.07
10 9 0.08
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (8 bp):
AATAATTA
Found at i:492275 original size:50 final size:50
Alignment explanation
Indices: 492221--492324 Score: 163
Period size: 50 Copynumber: 2.1 Consensus size: 50
492211 TTGGGTTGAT
* * *
492221 TTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAA
1 TTAAATAATTAAATAATTAAGTAATTGGGTTGATTTAAATAATTAAATAA
* *
492271 TTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAA
1 TTAAATAATTAAATAATTAAGTAATTGGGTTGATTTAAATAATTAAATAA
492321 TTAA
1 TTAA
492325 GTATTTGGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (50 bp):
TTAAATAATTAAATAATTAAGTAATTGGGTTGATTTAAATAATTAAATAA
Found at i:492285 original size:4 final size:4
Alignment explanation
Indices: 492256--492380 Score: 60
Period size: 4 Copynumber: 31.5 Consensus size: 4
492246 TGGGTTGTTT
* * ** *
492256 TTAA -TAA TTAA ATAA TTAA ATAA TTAA TTAA TTAA TTAA TTGGG TTGAT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT-AA TT-AA
* * * * ** * *
492305 TTAA ATAA TTAA ATAA TTAA GTAT TTGGG TT-G TT-T TTAA -TAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TT-AA TTAA TTAA TTAA TTAA TTAA
* *
492351 ATAA TTAA ATAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
492381 GGGTTGATTT
Statistics
Matches: 92, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
3 11 0.12
4 74 0.80
5 7 0.08
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (4 bp):
TTAA
Found at i:492309 original size:34 final size:34
Alignment explanation
Indices: 492271--492364 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 34
492261 AATTAAATAA
* *
492271 TTAAATAATTAATTAATTAATTAATTGGGTTGAT
1 TTAAATAATTAAATAATTAAATAATTGGGTTGAT
* * *
492305 TTAAATAATTAAATAATTAAGTATTTGGGTTGTT
1 TTAAATAATTAAATAATTAAATAATTGGGTTGAT
*
492339 TTTAATAATTAAATAATTAAATAATT
1 TTAAATAATTAAATAATTAAATAATT
492365 AATTAATTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.47
Consensus pattern (34 bp):
TTAAATAATTAAATAATTAAATAATTGGGTTGAT
Found at i:492359 original size:50 final size:50
Alignment explanation
Indices: 492305--492408 Score: 163
Period size: 50 Copynumber: 2.1 Consensus size: 50
492295 TTGGGTTGAT
* * *
492305 TTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAA
1 TTAAATAATTAAATAATTAAGTAATTGGGTTGATTTAAATAATTAAATAA
* *
492355 TTAAATAATTAATTAATTAATTAATTGGGTTGATTTAAATAATTAAATAA
1 TTAAATAATTAAATAATTAAGTAATTGGGTTGATTTAAATAATTAAATAA
492405 TTAA
1 TTAA
492409 GTATTTGGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (50 bp):
TTAAATAATTAAATAATTAAGTAATTGGGTTGATTTAAATAATTAAATAA
Found at i:492393 original size:34 final size:34
Alignment explanation
Indices: 492355--492560 Score: 142
Period size: 34 Copynumber: 6.3 Consensus size: 34
492345 AATTAAATAA
*
492355 TTAAATAATTAATTAATTAATTAATTGGGTTGAT
1 TTAAATAATTAAATAATTAATTAATTGGGTTGAT
* * *
492389 TTAAATAATTAAATAATTAAGTATTTGGGTTGTT
1 TTAAATAATTAAATAATTAATTAATTGGGTTGAT
* * *
492423 TTTAATAATTAAATAATTAAAT-ATT---TTGAA
1 TTAAATAATTAAATAATTAATTAATTGGGTTGAT
* ** ** * *
492453 TTAAATATTTAGGTTGTT-TTTAATAT---TT-AA
1 TTAAATAATTAAATAATTAATTAAT-TGGGTTGAT
* * *
492483 ATAAATAAATAATTAATTAATTAATTGGGTTGAT
1 TTAAATAATTAAATAATTAATTAATTGGGTTGAT
* * * *
492517 TTAAGTAATTAAATAATTAAGTATTTGGGTTGTT
1 TTAAATAATTAAATAATTAATTAATTGGGTTGAT
*
492551 TTAACTAATT
1 TTAAATAATT
492561 TAAAATTTAA
Statistics
Matches: 131, Mismatches: 34, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
29 1 0.01
30 31 0.24
31 8 0.06
33 4 0.03
34 87 0.66
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (34 bp):
TTAAATAATTAAATAATTAATTAATTGGGTTGAT
Found at i:492571 original size:128 final size:130
Alignment explanation
Indices: 492319--492560 Score: 391
Period size: 128 Copynumber: 1.9 Consensus size: 130
492309 ATAATTAAAT
* * * *
492319 AATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATAATTAATTAATTAATTAATTGGG
1 AATTAAATATTTAGGTTGTTTTTAATAATT--ATAAATAAATAAATAATTAATTAATTAATTGGG
492384 TTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTT
64 TTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTT
492449 TG
129 TG
492451 AATTAAATATTTAGGTTGTTTTTAAT-ATT-TAAATAAATAAATAATTAATTAATTAATTGGGTT
1 AATTAAATATTTAGGTTGTTTTTAATAATTATAAATAAATAAATAATTAATTAATTAATTGGGTT
*
492514 GATTTAAGTAATTAAATAATTAAGTATTTGGGTTG-TTTTAACTAATT
66 GATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAA-TAATT
492561 TAAAATTTAA
Statistics
Matches: 104, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
127 6 0.06
128 71 0.68
131 3 0.03
132 24 0.23
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (130 bp):
AATTAAATATTTAGGTTGTTTTTAATAATTATAAATAAATAAATAATTAATTAATTAATTGGGTT
GATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATAATTAAATATTTTG
Found at i:492745 original size:10 final size:10
Alignment explanation
Indices: 492730--492756 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
492720 TTCCTATTTT
492730 GAATTTATTA
1 GAATTTATTA
492740 GAATTTATTA
1 GAATTTATTA
492750 GAATTTA
1 GAATTTA
492757 AAAGATTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (10 bp):
GAATTTATTA
Found at i:494369 original size:15 final size:15
Alignment explanation
Indices: 494349--494392 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
494339 GGAGGAGGAG
494349 AGGGATTTAGAAATT
1 AGGGATTTAGAAATT
*
494364 AGGGATTTAGAATTT
1 AGGGATTTAGAAATT
* *
494379 AGGAATTTCGAAAT
1 AGGGATTTAGAAAT
494393 CTGTTTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (15 bp):
AGGGATTTAGAAATT
Found at i:494514 original size:41 final size:39
Alignment explanation
Indices: 494469--494574 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 39
494459 GTGCTTTCAT
*
494469 ATAAGCGCCGCTATTACTCTGATCTTCAGCGGCGCTTCTCC
1 ATAAGCGCCGCTATTGCTCT-ATCTT-AGCGGCGCTTCTCC
* *
494510 ATAAGCGCCGCTATTGCTCCATCTGTAGCGGCGCTTTTCC
1 ATAAGCGCCGCTATTGCTCTATCT-TAGCGGCGCTTCTCC
*
494550 ATAAGCGCCGCTGTTGCTCTATCTT
1 ATAAGCGCCGCTATTGCTCTATCTT
494575 TTGCGGCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.02
40 39 0.66
41 19 0.32
ACGTcount: A:0.16, C:0.32, G:0.21, T:0.31
Consensus pattern (39 bp):
ATAAGCGCCGCTATTGCTCTATCTTAGCGGCGCTTCTCC
Found at i:494551 original size:40 final size:39
Alignment explanation
Indices: 494469--494587 Score: 141
Period size: 40 Copynumber: 3.0 Consensus size: 39
494459 GTGCTTTCAT
* * *
494469 ATAAGCGCCGCTATTACTCTGATCTTCAGCGGCGCTTCTCC
1 ATAAGCGCCGCTATTGCTC-CATCTT-AGCGGCGCTTTTCC
494510 ATAAGCGCCGCTATTGCTCCATCTGTAGCGGCGCTTTTCC
1 ATAAGCGCCGCTATTGCTCCATCT-TAGCGGCGCTTTTCC
* * *
494550 ATAAGCGCCGCTGTTGCTCTATCTTTTGCGGCG-TTTTC
1 ATAAGCGCCGCTATTGCTCCATC-TTAGCGGCGCTTTTC
494588 TGCCCAAACG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
39 5 0.07
40 45 0.64
41 20 0.29
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (39 bp):
ATAAGCGCCGCTATTGCTCCATCTTAGCGGCGCTTTTCC
Found at i:517798 original size:3 final size:3
Alignment explanation
Indices: 517790--517825 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
517780 CAGGTTGAGT
517790 TTC TTC TTC TTC TTC TTC TTTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TT
517826 TTTTTGCAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:517813 original size:19 final size:19
Alignment explanation
Indices: 517789--517825 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
517779 TCAGGTTGAG
517789 TTTCTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTCTTC
517808 TTTCTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTTCTT
517826 TTTTTGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCTTCTTCTTCTTCTTC
Found at i:517814 original size:16 final size:16
Alignment explanation
Indices: 517793--517826 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
517783 GTTGAGTTTC
517793 TTCTTCTTCTTCTTCT
1 TTCTTCTTCTTCTTCT
517809 TTCTTCTTCTTCTTCT
1 TTCTTCTTCTTCTTCT
517825 TT
1 TT
517827 TTTTGCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTCTTCTTCTTCT
Found at i:524660 original size:2 final size:2
Alignment explanation
Indices: 524653--524697 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
524643 AATTATTCAA
*
524653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
524695 AT A
1 AT A
524698 ATTTGCTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:525093 original size:14 final size:15
Alignment explanation
Indices: 525074--525102 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
525064 GTATGTATGT
525074 ATATTTT-AATATAC
1 ATATTTTAAATATAC
525088 ATATTTTAAATATAC
1 ATATTTTAAATATAC
525103 TCTTCGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTTTAAATATAC
Found at i:532271 original size:29 final size:30
Alignment explanation
Indices: 532233--532298 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
532223 TAAGAACTGG
*
532233 ATCAAATTAGTCACTATATTATT-AAATGA
1 ATCAAATTAGTCACTATATTATTAAAAAGA
* ** *
532262 ATCAATTTAGTTTCTATATTTTTAAAAAGA
1 ATCAAATTAGTCACTATATTATTAAAAAGA
532292 ATCAAAT
1 ATCAAAT
532299 AAATCCAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (30 bp):
ATCAAATTAGTCACTATATTATTAAAAAGA
Found at i:536797 original size:1 final size:1
Alignment explanation
Indices: 536791--536819 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
536781 AATGAAATGC
536791 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
536820 GAGCTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:537352 original size:19 final size:19
Alignment explanation
Indices: 537312--537353 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
537302 ATTAGTAAAA
*
537312 TAATATATAACTATATTTT
1 TAATATATAAATATATTTT
*
537331 TAATATA-AAATATTTTTCT
1 TAATATATAAATATATTT-T
537350 TAAT
1 TAAT
537354 CCTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATAAATATATTTT
Found at i:541633 original size:29 final size:30
Alignment explanation
Indices: 541601--541659 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
541591 TGTGGTTTAA
*
541601 TGTGGAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
541630 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
541660 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:541668 original size:30 final size:29
Alignment explanation
Indices: 541606--541668 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
541596 TTTAATGTGG
*
541606 AATTGTATACATGAACTTTGATTTTGTGC
1 AATTGTATACATGAACTTTGATTTTGTCC
* *
541635 AATTTTATACATGAAATTTTGA-TTTGATCC
1 AATTGTATACATG-AACTTTGATTTTG-TCC
541665 AATT
1 AATT
541669 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.46
Consensus pattern (29 bp):
AATTGTATACATGAACTTTGATTTTGTCC
Found at i:551536 original size:20 final size:20
Alignment explanation
Indices: 551499--551536 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
551489 GAATAATAAG
*
551499 AAGTTTATTGTTTTATTTAA
1 AAGTTTATTGTTTAATTTAA
551519 AAGTTTA-TGTTTGAATTT
1 AAGTTTATTGTTT-AATTT
551537 TCTAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
AAGTTTATTGTTTAATTTAA
Found at i:554106 original size:22 final size:23
Alignment explanation
Indices: 554068--554111 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
554058 TTTAAAATTT
554068 AATTTATATATTTTATTTTTTAA
1 AATTTATATATTTTATTTTTTAA
*
554091 AATTTA-ATTTTTTATTTTTTA
1 AATTTATATATTTTATTTTTTA
554112 GATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
AATTTATATATTTTATTTTTTAA
Found at i:554120 original size:29 final size:28
Alignment explanation
Indices: 554058--554131 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
554048 TCTTCGTAAA
**
554058 TTTAAAATTTAATTTATATATTTTATTT
1 TTTAAAATTTAATTTATATATTTTAGAT
* *
554086 TTTAAAATTTAATTTTTTATTTTTTAGAT
1 TTTAAAATTTAA-TTTATATATTTTAGAT
554115 TTTAAAATTTAAATTTA
1 TTTAAAATTT-AATTTA
554132 AGTATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 12 0.31
29 25 0.64
30 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTAAAATTTAATTTATATATTTTAGAT
Found at i:558518 original size:2 final size:2
Alignment explanation
Indices: 558511--558535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
558501 TAATGCCGAG
558511 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
558536 TTGGTTAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:572066 original size:18 final size:18
Alignment explanation
Indices: 572043--572085 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
572033 GAATATGTTT
572043 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
572061 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
572079 TTAATTA
1 TTAATTA
572086 CACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:578651 original size:19 final size:19
Alignment explanation
Indices: 578623--578661 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
578613 TTTATTAAAA
*
578623 TTTCATCCATTAAACTAAT
1 TTTCACCCATTAAACTAAT
578642 TTTCACCCATTAAACTAAT
1 TTTCACCCATTAAACTAAT
578661 T
1 T
578662 GTCTGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTCACCCATTAAACTAAT
Found at i:581492 original size:6 final size:6
Alignment explanation
Indices: 581478--581544 Score: 75
Period size: 6 Copynumber: 11.2 Consensus size: 6
581468 TCTAAATTTG
* * *
581478 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA ATTAGATA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-A-A TTTAAA TTTAAA
581526 TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
581545 AAAGATTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 8 0.16
6 37 0.73
7 2 0.04
8 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:581500 original size:27 final size:25
Alignment explanation
Indices: 581454--581503 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
581444 GACTTTTGAG
581454 TTAAATTGATTTTTTCTAAATTTGT
1 TTAAATTGATTTTTTCTAAATTTGT
581479 TTAAATTTAGATTTATTT-TAAATTT
1 TTAAA-TT-GATTT-TTTCTAAATTT
581504 AAAATTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
27 12 0.55
28 3 0.14
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (25 bp):
TTAAATTGATTTTTTCTAAATTTGT
Found at i:581511 original size:23 final size:20
Alignment explanation
Indices: 581495--581543 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 20
581485 TTAGATTTAT
581495 TTTAAATTTAAAATTAGATA
1 TTTAAATTTAAAATTAGATA
*
581515 TTTAAATTT-AATTTA-A-A
1 TTTAAATTTAAAATTAGATA
581532 TTTAAATTTAAA
1 TTTAAATTTAAA
581544 TAAAGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 10 0.37
18 3 0.11
19 5 0.19
20 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAATTTAAAATTAGATA
Found at i:583481 original size:161 final size:163
Alignment explanation
Indices: 583160--583484 Score: 458
Period size: 161 Copynumber: 2.0 Consensus size: 163
583150 AATTTTAATT
** **
583160 GGTTTATAATTTAGTCCTTTGACTATTTGACTGTGCCAGAGGTTGCCACGTGTCATGTATTGGAT
1 GGTTTATAAACTAGTCCTTTGACTATTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTGGAT
* *
583225 TATTTATGCATTTAGTCCTTTTTTATTTTTTATTTGTTTTAATTTAATCCCCAAATCAACTTTAT
66 TATTCATGCATTTAGTCCTTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTAT
** *
583290 TTTAATTATGAAATTGGCCCAATAATTTTTCAA
131 TTTAATTACAAAATTGGCCCAAAAATTTTTCAA
* * *
583323 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCAT-TCTTTGAT
1 GGTTTATAAACTAGTCCTTTGACTATTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTGGAT
* * ** *
583387 TATTCCTTCATTTAGTCC-TTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTT-T
66 TATTCATGCATTTAGTCCTTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTAT
*
583450 ATTTAATTACAAAATTGGTCCAAAAATTTTTCAA
131 -TTTAATTACAAAATTGGCCCAAAAATTTTTCAA
583484 G
1 G
583485 ATTTCCAAAT
Statistics
Matches: 143, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
160 1 0.01
161 70 0.49
162 21 0.15
163 51 0.36
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (163 bp):
GGTTTATAAACTAGTCCTTTGACTATTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTGGAT
TATTCATGCATTTAGTCCTTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTAT
TTTAATTACAAAATTGGCCCAAAAATTTTTCAA
Found at i:583647 original size:30 final size:30
Alignment explanation
Indices: 583613--583708 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
583603 AAACTTTTCC
*
583613 AAAATTATATTTTAAACCCCGATTTCACCG
1 AAAATTATATTTTAAACCCCGATTTCATCG
* * ** * *
583643 AAAATTACTGTTTT-ACCCCCGA-AGCTTCT
1 AAAATTA-TATTTTAAACCCCGATTTCATCG
**
583672 AAAATTCCATTTTAAACCCCGATTTCATCG
1 AAAATTATATTTTAAACCCCGATTTCATCG
583702 AAAATTA
1 AAAATTA
583709 CCATTTTACC
Statistics
Matches: 47, Mismatches: 16, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
28 4 0.09
29 15 0.32
30 23 0.49
31 5 0.11
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAATTATATTTTAAACCCCGATTTCATCG
Found at i:583889 original size:178 final size:176
Alignment explanation
Indices: 583584--584128 Score: 746
Period size: 178 Copynumber: 3.1 Consensus size: 176
583574 AATTGTCCAG
* *
583584 AAATTA-CATTTTACCCCCGAAACTTTTCCAAAATT--ATATTTTAAACCCCGATTTCACCGAAA
1 AAATTACCATTTTACCCCCGAAACTTTTCTAAAATTCCAT-TTTTAAA-CCCGATTTCACCAAAA
**
583646 ATTACTGTTTTACCCCCGAAGCTTCTAAAATTCCATTTTAAACCCCGATTTCATCGAAAATTACC
64 ATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTT-AACCCCGATTTCATCGAAAATTACC
583711 ATTTTACCCTCGAATCTTTTAAAATTCTATTTTAACCTCGATTTCACCAA
128 ATTTTACCCTCGAATCTTTTAAAATTCTATTTTAACC-CGATTTCACCAA
* * *
583761 AAATTACCATTTTACCCCTGAATCTTTTTTAAAATTCCATTTTTAAACCCGATTTCACCAAAAAT
1 AAATTACCATTTTACCCCCGAAACTTTTCTAAAATTCCATTTTTAAACCCGATTTCACCAAAAAT
583826 TACCATTTTACCCCCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCATCGAAAATTACCAT
66 TACCATTTTACCCCCGAAGCTTCTAAAATTCCAT-TTTAACCCCGATTTCATCGAAAATTACCAT
* * *
583891 TTTACCC-CTGAATCTCTTAAATTTCCATTTTTAACCCGATTTCACCAA
130 TTTACCCTC-GAATCTTTTAAAATTCTA-TTTTAACCCGATTTCACCAA
*
583939 AAATTACCATTTTACCCCC-AAAGC--TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
1 AAATTACCATTTTACCCCCGAAA-CTTTTCTAAAATTCCATTTTTAAACCCGATTTCACCAAAAA
* * * ** *
584001 TTACCATTTTACCCCCAAAGCTTCTAAAATTCTATTTTTAACCCCAATTTCCCCAAAAATTACCA
65 TTACCATTTTACCCCCGAAGCTTCTAAAATTCCA-TTTTAACCCCGATTTCATCGAAAATTACCA
* * *
584066 TTTTACCCTCGAAGCTTCTAAAATTCCGT-TTTTAACCCCGATTTCACCGA
129 TTTTACCCTCGAATCTTTTAAAATT-C-TATTTTAA-CCCGATTTCACCAA
584116 AAATTACCATTTT
1 AAATTACCATTTT
584129 GCCCTCGGGT
Statistics
Matches: 330, Mismatches: 26, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
176 118 0.36
177 38 0.12
178 154 0.47
179 18 0.05
180 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (176 bp):
AAATTACCATTTTACCCCCGAAACTTTTCTAAAATTCCATTTTTAAACCCGATTTCACCAAAAAT
TACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTAACCCCGATTTCATCGAAAATTACCATT
TTACCCTCGAATCTTTTAAAATTCTATTTTAACCCGATTTCACCAA
Found at i:583963 original size:117 final size:117
Alignment explanation
Indices: 583584--584128 Score: 709
Period size: 117 Copynumber: 4.6 Consensus size: 117
583574 AATTGTCCAG
* * **
583584 AAATTA-CATTTTACCCCCGAAACTTTTCCAAAATTATATTTTAAACCCCGATTTCACCGAAAAT
1 AAATTACCATTTTACCCCCGAAGC--TTCTAAAATTCCATTTT-AACCCCGATTTCACCGAAAAT
** * * *
583648 TACTGTTTTACCCCCGAAGCTTCTAAAATTCCATTTTAAACCCCGATTTCATCGA
63 TACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * * * * *
583703 AAATTACCATTTTACCCTCGAATCTTTTAAAATTCTATTTTAACCTCGATTTCACCAAAAATTAC
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTAACCCCGATTTCACCGAAAATTAC
* * * *
583768 CATTTTACCCCTGAATCTTTTTTAAAATTCCATTTTTAAACCCGATTTCACCAA
66 CATTTTACCCCCGAAGC--TTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
*
583822 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCATCGAAAATTA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCAT-TTTAACCCCGATTTCACCGAAAATTA
* * *
583887 CCATTTTACCCCTGAATC-TCTTAAATTTCCATTTTTAA-CCCGATTTCACCAA
65 CCATTTTACCCCCGAAGCTTC-TAAAATTCCATTTTTAACCCCGATTTCACCAA
* *
583939 AAATTACCATTTTACCCCCAAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCA-TTTTAACCCCGATTTCACCGAAAATTA
* * * *
584004 CCATTTTACCCCCAAAGCTTCTAAAATTCTATTTTTAACCCCAATTTCCCCAA
65 CCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* *
584057 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCC-ATTTTAACCCCGATTTCACCGAAAATTA
584122 CCATTTT
65 CCATTTT
584129 GCCCTCGGGT
Statistics
Matches: 378, Mismatches: 39, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
117 140 0.37
118 112 0.30
119 70 0.19
120 56 0.15
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (117 bp):
AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTAACCCCGATTTCACCGAAAATTAC
CATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
Found at i:584135 original size:59 final size:59
Alignment explanation
Indices: 583584--584128 Score: 711
Period size: 59 Copynumber: 9.2 Consensus size: 59
583574 AATTGTCCAG
* * ** * *
583584 AAATTA-CATTTTACCCCCGAAACTTTTCCAAAATTATATTTTAAACCCCGATTTCACCGA
1 AAATTACCATTTTACCCCCGAAGC--TTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
** * * *
583644 AAATTACTGTTTTACCCCCGAAGCTTCTAAAATTCCATTTTAAACCCCGATTTCATCGA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * * * *
583703 AAATTACCATTTTACCCTCGAATCTTTTAAAATTCTA-TTTTAACCTCGATTTCACCAA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * * *
583761 AAATTACCATTTTACCCCTGAATCTTTTTTAAAATTCCATTTTTAAACCCGATTTCACCAA
1 AAATTACCATTTTACCCCCGAAGC--TTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * *
583822 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCATCGA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * *
583881 AAATTACCATTTTACCCCTGAATC-TCTTAAATTTCCATTTTTAA-CCCGATTTCACCAA
1 AAATTACCATTTTACCCCCGAAGCTTC-TAAAATTCCATTTTTAACCCCGATTTCACCAA
*
583939 AAATTACCATTTTACCCCCAAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * * *
583998 AAATTACCATTTTACCCCCAAAGCTTCTAAAATTCTATTTTTAACCCCAATTTCCCCAA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * *
584057 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCGA
1 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
584116 AAATTACCATTTT
1 AAATTACCATTTT
584129 GCCCTCGGGT
Statistics
Matches: 429, Mismatches: 49, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
58 90 0.21
59 266 0.62
60 18 0.04
61 55 0.13
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (59 bp):
AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
Found at i:596186 original size:69 final size:69
Alignment explanation
Indices: 595994--596863 Score: 1185
Period size: 69 Copynumber: 12.5 Consensus size: 69
595984 TTGCAGATCT
* * * *
595994 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAGCATGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596058 AGAG
66 AGAG
* * * * *
596062 CAACGTCGTCCCCTTGAAATTGAAGTAGAG-TGGATAACATGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596126 AGAG
66 AGAG
* * *
596130 CAACGTCATCCCCTTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGT
1 CAACGTCATCCTC-TTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGT
596194 AAGAG
65 AAGAG
* *
596199 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596264 AGAG
66 AGAG
* *
596268 CAACGACATCCTCTTGAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596333 AGAG
66 AGAG
*
596337 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596402 AGAG
66 AGAG
* *
596406 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596471 AGAG
66 AGAG
* * *
596475 CAACGTCATCCTCTCGAAATTGAAGTAGAATTGGATATCGGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596540 AGAG
66 AGAG
* *
596544 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596609 AGAG
66 AGAG
* * * *
596613 CAACGGCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAGATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
596678 AGAG
66 AGAG
* * *** * * * * *
596682 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACATAACGTCATCCCCTTTAAATTGACG
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTAT-CTC-TGAAATTGAAG
*
596746 TAGAGTGGAT
64 TA-A---GAG
* * * * *
596756 AACACGTCTTCATCC-CTTGGAATTGAAGTAGAG-TGGATAGCACGTCTTCATCTCTGAAATTGA
1 CA-ACG---TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGA
596819 AGTAAGAG
62 AGTAAGAG
* *
596827 CAATGTCATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATA
596864 GCAAAGTCTC
Statistics
Matches: 729, Mismatches: 59, Indels: 27
0.89 0.07 0.03
Matches are distributed among these distances:
67 6 0.01
68 122 0.17
69 530 0.73
70 11 0.02
71 4 0.01
74 4 0.01
75 14 0.02
76 2 0.00
77 30 0.04
78 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (69 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
AGAG
Found at i:596532 original size:38 final size:36
Alignment explanation
Indices: 596145--596608 Score: 192
Period size: 31 Copynumber: 13.4 Consensus size: 36
596135 TCATCCCCTT
* *
596145 TGAAATTGAAGTAG-AGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGAT-A-TCGTCTTTATCTC
* * **
596182 TGAAATTGAAGTA-AGA--GCA-A-CGTCATCCTCTC
1 TGAAATTGAAGTAGA-ATTGGATATCGTCTTTATCTC
*
596214 -GAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGATATC--GTCTTTATCTC
* * * **
596251 TGAAATTGAAGTA-AGA--GCA-A-CGACATCCTCT-
1 TGAAATTGAAGTAGA-ATTGGATATCGTCTTTATCTC
*
596282 TGAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGATATC--GTCTTTATCTC
* * **
596320 TGAAATTGAAGTA-AGA--GCA-A-CGTCATCCTCTC
1 TGAAATTGAAGTAGA-ATTGGATATCGTCTTTATCTC
*
596352 -GAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGATATC--GTCTTTATCTC
* * **
596389 TGAAATTGAAGTA-AGA--GCA-A-CGTCATCCTCT-
1 TGAAATTGAAGTAGA-ATTGGATATCGTCTTTATCTC
*
596420 TGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGATATC--GTCTTTATCTC
* * * **
596458 CGAAATTGAAGTA-AGA--GCA-A-CGTCATCCTCTC
1 TGAAATTGAAGTAGA-ATTGGATATCGTCTTTATCTC
596490 -GAAATTGAAGTAGAATTGGATATCGGGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGATATC--GTCTTTATCTC
* * **
596527 TGAAATTGAAGTA-AGA--GCA-A-CGTCATCCTCTC
1 TGAAATTGAAGTAGA-ATTGGATATCGTCTTTATCTC
*
596559 -GAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTC
1 TGAAATTGAAGTAGAATTGGATATC--GTCTTTATCTC
596596 TGAAATTGAAGTA
1 TGAAATTGAAGTA
596609 AGAGCAACGG
Statistics
Matches: 312, Mismatches: 60, Indels: 109
0.65 0.12 0.23
Matches are distributed among these distances:
31 75 0.24
32 52 0.17
33 12 0.04
34 12 0.04
35 11 0.04
36 12 0.04
37 63 0.20
38 75 0.24
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (36 bp):
TGAAATTGAAGTAGAATTGGATATCGTCTTTATCTC
Found at i:596787 original size:38 final size:39
Alignment explanation
Indices: 596687--596822 Score: 170
Period size: 39 Copynumber: 3.6 Consensus size: 39
596677 AAGAGCAACG
*** *
596687 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACATAACG
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* *
596726 TCATCCCCTTTAAATTGACGTAGAGTGGATAACACGTCT
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* *
596765 TCAT-CCCTTGGAATTGAAGTAGAGTGGATAGCACGTCT
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
596803 TCAT-CTC-TGAAATTGAAGTA
1 TCATCCCCTTGAAATTGAAGTA
596823 AGAGCAATGT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
37 12 0.14
38 36 0.42
39 37 0.44
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (39 bp):
TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
Found at i:597169 original size:6 final size:6
Alignment explanation
Indices: 597155--597221 Score: 75
Period size: 6 Copynumber: 11.2 Consensus size: 6
597145 TCTAAATTTG
* * *
597155 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA ATTAGATA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-A-A TTTAAA TTTAAA
597203 TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
597222 AAAGATTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 8 0.16
6 37 0.73
7 2 0.04
8 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:597177 original size:27 final size:25
Alignment explanation
Indices: 597131--597180 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
597121 GACTTTTGAG
597131 TTAAATTGATTTTTTCTAAATTTGT
1 TTAAATTGATTTTTTCTAAATTTGT
597156 TTAAATTTAGATTTATTT-TAAATTT
1 TTAAA-TT-GATTT-TTTCTAAATTT
597181 AAAATTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
27 12 0.55
28 3 0.14
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (25 bp):
TTAAATTGATTTTTTCTAAATTTGT
Found at i:597188 original size:23 final size:20
Alignment explanation
Indices: 597172--597220 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 20
597162 TTAGATTTAT
597172 TTTAAATTTAAAATTAGATA
1 TTTAAATTTAAAATTAGATA
*
597192 TTTAAATTT-AATTTA-A-A
1 TTTAAATTTAAAATTAGATA
597209 TTTAAATTTAAA
1 TTTAAATTTAAA
597221 TAAAGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 10 0.37
18 3 0.11
19 5 0.19
20 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAATTTAAAATTAGATA
Found at i:599010 original size:163 final size:162
Alignment explanation
Indices: 598830--599143 Score: 461
Period size: 163 Copynumber: 1.9 Consensus size: 162
598820 AATTTTAATT
** **
598830 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGTTGCCACGTGTCATGT-ATTGGA
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCAT-TCATTGGA
* *
598894 TTATTTATGCATTTAGTCCTTTTTTATTTTTTATTTGTTTTAATTTAATCCCCAAATCAAC-TTT
65 TTATTCATGCATTTAGTCC-TTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTT
*
598958 ATTTTAATTACGAAATTGGCCCAATAATTTTTCAA
129 A-TTTAATTACAAAATTGGCCCAATAATTTTTCAA
*
598993 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTCTTTGGAT
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTCATTGGAT
* * ** *
599058 TATTCCTTCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTAT
66 TATTCATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTAT
*
599123 TTAATTACAAAATTGGTCCAA
131 TTAATTACAAAATTGGCCCAA
599144 ATTTTTTTCA
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
162 58 0.43
163 77 0.57
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.46
Consensus pattern (162 bp):
GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTCATTGGAT
TATTCATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTAT
TTAATTACAAAATTGGCCCAATAATTTTTCAA
Found at i:599345 original size:59 final size:59
Alignment explanation
Indices: 599253--599854 Score: 789
Period size: 59 Copynumber: 10.2 Consensus size: 59
599243 AATTGTCCAG
* ** * *
599253 AAATTA-CATTTTACCC-CGAAACTTTTCCAAAATTATATTTTTAACCCCGATTTCATCAA
1 AAATTACCATTTTACCCTCGAAGCTTTT--AAAATTCCATTTTTAACCCCGATTTCACCGA
* *
599312 AAATTACCATTTTACCCTCGAATCTTTTAAAATT-C-TGTTTTAACCCCGATTTCATCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCAT-TTTTAACCCCGATTTCACCGA
* * * *
599370 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTGTTTAACCCCGATTTCACCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* * *
599429 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTTCATCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* * ** *
599488 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAAACCCGATTTCACCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* * * *
599547 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCATCAA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* * * ** * *
599606 AAATTACCATTTTACCCCCGAATCTCTTAAAATTCTGTTTTTAACCTCGATTTCATCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* *
599665 AAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* * *
599724 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATTTTTAACCTCGATTTCCCCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
* ** *
599783 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCTGTTTTTAACCTCGATTTCACCGA
1 AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
*
599842 AAATTACCGTTTT
1 AAATTACCATTTT
599855 GCCCCCGGGT
Statistics
Matches: 483, Mismatches: 55, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
57 1 0.00
58 53 0.11
59 409 0.85
60 11 0.02
61 9 0.02
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (59 bp):
AAATTACCATTTTACCCTCGAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGA
Found at i:599582 original size:177 final size:177
Alignment explanation
Indices: 599253--599861 Score: 875
Period size: 177 Copynumber: 3.4 Consensus size: 177
599243 AATTGTCCAG
* * * *
599253 AAATTA-CATTTTACCC-CGAAACTTTTCCAAAATTATATTTTTAACCCCGATTTCATCAAAAAT
1 AAATTACCATTTTACCCTCGAAGC--TTCTAAAATTCTATTTTTAACCCCGATTTCATCGAAAAT
* *
599316 TACCATTTTACCCTCGAATCTTTTAAAATTCTG-TTTTAACCCCGATTTCATCGAAAATTACCAT
64 TACCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCACCGAAAATTACCAT
* * * * *
599380 TTTACCCCCGAATCTTTTAAAATTCCGTGTTTAACCCCGATTTCACCGA
129 TTTACCCTCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCACCGA
* *
599429 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTTCATCGAAAATTA
1 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCATCGAAAATTA
*
599494 CCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAAACCCGATTTCACCGAAAATTACCATTT
66 CCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCACCGAAAATTACCATTT
* *
599559 TACCCTCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCATCAA
131 TACCCTCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCACCGA
* * * *
599606 AAATTACCATTTTACCCCCGAATC-TCTTAAAATTCTGTTTTTAACCTCGATTTCATCGAAAATT
1 AAATTACCATTTTACCCTCGAAGCTTC-TAAAATTCTATTTTTAACCCCGATTTCATCGAAAATT
* * **
599670 ACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATT
65 ACCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCACCGAAAATTACCATT
* * *
599735 TTACCCTCGAAGCTTCTAAAATTCCATTTTTAACCTCGATTTCCCCGA
130 TTACCCTCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCACCGA
* * *
599783 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCTGTTTTTAACCTCGATTTCACCGAAAATTA
1 AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCATCGAAAATTA
* *
599848 CCGTTTTGCCCCCG
66 CCATTTTACCCCCG
599862 GGTATCCATA
Statistics
Matches: 390, Mismatches: 38, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
176 74 0.19
177 309 0.79
178 7 0.02
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (177 bp):
AAATTACCATTTTACCCTCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCATCGAAAATTA
CCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCACCGAAAATTACCATTT
TACCCTCGAAGCTTCTAAAATTCCATCTTTAACCCCGATTTCACCGA
Found at i:604690 original size:31 final size:31
Alignment explanation
Indices: 604654--604728 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
604644 TACAAATTGG
* *
604654 TCACTGAATTGTTTGAAAGTTTTCATTTAAT
1 TCACTGAATTGTTTGAAAATTTTCATTTAAA
* * *
604685 TCACTGAACTATTTGAAAATTTTTATTTAAA
1 TCACTGAATTGTTTGAAAATTTTCATTTAAA
* *
604716 TCAATGAGTTGTT
1 TCACTGAATTGTT
604729 AAGTTTTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
TCACTGAATTGTTTGAAAATTTTCATTTAAA
Found at i:606368 original size:18 final size:18
Alignment explanation
Indices: 606345--606379 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
606335 TTATTTTAAA
606345 ATTAAAAAATATAAAATT
1 ATTAAAAAATATAAAATT
606363 ATTAAAAAATATAAAAT
1 ATTAAAAAATATAAAAT
606380 ATATCTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAAAAAATATAAAATT
Found at i:606371 original size:26 final size:27
Alignment explanation
Indices: 606333--606383 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
606323 GGAATTAATT
**
606333 AATTATTTTAAAAT-TAAAAAATATAA
1 AATTATTAAAAAATATAAAAAATATAA
*
606359 AATTATTAAAAAATATAAAATATAT
1 AATTATTAAAAAATATAAAAAATAT
606384 CTTTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATTATTAAAAAATATAAAAAATATAA
Found at i:615048 original size:30 final size:31
Alignment explanation
Indices: 615012--615069 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
615002 GACCAAAAAA
*
615012 AAGTTTAGGCCC-AATGTGAAAACAATTGCT
1 AAGTTTAGACCCTAATGTGAAAACAATTGCT
*
615042 AAGTTTAGACCCTAATGTGAGAACAATT
1 AAGTTTAGACCCTAATGTGAAAACAATT
615070 ATCAAGTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (31 bp):
AAGTTTAGACCCTAATGTGAAAACAATTGCT
Found at i:617392 original size:19 final size:19
Alignment explanation
Indices: 617344--617398 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
617334 GCTTATGCGT
*
617344 CAGGATGCACTTCGTGTGC
1 CAGGATGCACTTCGTGAGC
* * *
617363 TAGATATGCACTTTGTGAGC
1 CAG-GATGCACTTCGTGAGC
617383 CAGGATGCACTTCGTG
1 CAGGATGCACTTCGTG
617399 TGTTAGTATG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (19 bp):
CAGGATGCACTTCGTGAGC
Found at i:617409 original size:19 final size:19
Alignment explanation
Indices: 617348--617410 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
617338 ATGCGTCAGG
617348 ATGCACTTCGTGTGCTAGAT
1 ATGCACTTCGTGTGCTAG-T
* * * *
617368 ATGCACTTTGTGAGCCAGG
1 ATGCACTTCGTGTGCTAGT
*
617387 ATGCACTTCGTGTGTTAGT
1 ATGCACTTCGTGTGCTAGT
617406 ATGCA
1 ATGCA
617411 AATACGTGTC
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (19 bp):
ATGCACTTCGTGTGCTAGT
Found at i:630849 original size:29 final size:30
Alignment explanation
Indices: 630815--630882 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
630805 TAAAATTCCG
* *
630815 TGTATAAAATTATACA-CAATCAAAATTTA
1 TGTATAAAATTACACATAAATCAAAATTTA
630844 TGTATAAAATTACACATTAAATCAAAATTTA
1 TGTATAAAATTACACA-TAAATCAAAATTTA
*
630875 TTTATAAA
1 TGTATAAA
630883 TTTGAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (30 bp):
TGTATAAAATTACACATAAATCAAAATTTA
Found at i:632394 original size:156 final size:156
Alignment explanation
Indices: 632080--632530 Score: 679
Period size: 156 Copynumber: 2.9 Consensus size: 156
632070 CAGAATAATC
* *
632080 AAACAGTGACACGTGATGCCACATATACCTCATCCTGATGTATAGTGACTAGTTTTTAACAATAG
1 AAACAGTGACACATGATGCCACATATACCTCATCCTGATGTATAGTGACCAGTTTTTAACAATAG
** * *
632145 AAATGGATG-AATTTTTAATAGAATGACTAGTTTATTCTTTGATCTAACCTACTGGAACTAATTT
66 AAATGGATGAAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
* * * *
632209 GCCCGTATTTTGAGTAGAGGGGGCAA
131 GCCCATTTTTTGAGTAGAAGGGACAA
** * * *
632235 AAACAGTGACACATGATGCCATGTATATCTCATCTTGATGTATAGTGACCAGTTTTTAACGATAG
1 AAACAGTGACACATGATGCCACATATACCTCATCCTGATGTATAGTGACCAGTTTTTAACAATAG
632300 AAATGGATGAAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
66 AAATGGATGAAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
* *
632365 GCTCATTTTTTTAGTAGAAGGGACAA
131 GCCCATTTTTTGAGTAGAAGGGACAA
* *
632391 AAACAGTGACACATGATGCCACATATACCTCATCCTGACGTATAGTGACCAGTTTTTAATAATAG
1 AAACAGTGACACATGATGCCACATATACCTCATCCTGATGTATAGTGACCAGTTTTTAACAATAG
* * * *
632456 AAATGGATGAAATTTTTAATAGAATGACTAATTTGCTCTTTGATCTAATCTAGTAGAATTAATTT
66 AAATGGATGAAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
*
632521 ACCCATTTTT
131 GCCCATTTTT
632531 AGAATAGAGA
Statistics
Matches: 265, Mismatches: 30, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
155 67 0.25
156 198 0.75
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (156 bp):
AAACAGTGACACATGATGCCACATATACCTCATCCTGATGTATAGTGACCAGTTTTTAACAATAG
AAATGGATGAAATTTTTAATAGAATGACTAGTTTGCTCTTTGATCTAACCTAATAGAACTAATTT
GCCCATTTTTTGAGTAGAAGGGACAA
Found at i:644066 original size:7 final size:7
Alignment explanation
Indices: 644054--644085 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
644044 AATTTTCGAT
644054 AACAAAA
1 AACAAAA
644061 AACAAAA
1 AACAAAA
644068 AACAAAA
1 AACAAAA
644075 AA-AAAA
1 AACAAAA
644081 AACAA
1 AACAA
644086 GTAGAGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AACAAAA
Found at i:644080 original size:13 final size:14
Alignment explanation
Indices: 644054--644085 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
644044 AATTTTCGAT
644054 AACAAAAAACAAAA
1 AACAAAAAACAAAA
644068 AACAAAAAA-AAAA
1 AACAAAAAACAAAA
644081 AACAA
1 AACAA
644086 GTAGAGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AACAAAAAACAAAA
Found at i:644904 original size:12 final size:11
Alignment explanation
Indices: 644869--644926 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
644859 TAATATTTAA
*
644869 AAATATAATAC
1 AAATATAATAT
*
644880 AAACATAATAT
1 AAATATAATAT
644891 AAATATATATAT
1 AAATATA-ATAT
644903 AAATAT-AT-T
1 AAATATAATAT
*
644912 AAAT-TCATAT
1 AAATATAATAT
644922 AAATA
1 AAATA
644927 AATTATTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 1 0.03
9 7 0.17
10 7 0.17
11 15 0.38
12 10 0.25
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:645115 original size:21 final size:20
Alignment explanation
Indices: 645081--645119 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
645071 AAATTATCGT
*
645081 TTAAATAGTAAAATTATAAG
1 TTAAATAATAAAATTATAAG
645101 TTAATATAATAAAATTATA
1 TTAA-ATAATAAAATTATA
645120 TTTTGATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTAAATAATAAAATTATAAG
Found at i:648846 original size:103 final size:104
Alignment explanation
Indices: 648690--649249 Score: 738
Period size: 104 Copynumber: 5.4 Consensus size: 104
648680 CTAGCAATAA
* * * * *
648690 CTAAAAGCCACCAATTTTAAGCTGTAAACCCATAAATCTCTTCCATTGTTTAACAATGAACAATC
1 CTAAAA-CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACTGTTTAACAATCAACAATA
* **
648755 ACCCCATTTCATTAATCCGCTAGCAAAAACTAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
*
648795 CTAAAACCACCAATTTTAAGCT-TAAACCCACAAATTTCCTCCACTGTTTAACAATCAACAATAA
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACTGTTTAACAATCAACAATAA
* *
648859 CCTCATTTCATTAATCCACTAGCAATTACT-AAACCCAG
66 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* ** * ** *
648897 CTGAAACCACCAATTTTTAAGCTGTAAACCCATAAAACTCCTACAAAGTTTAACTATCAACAATA
1 CTAAAACCACCAA-TTTTAAGCTGTAAACCCATAAATTTCCTCCACTGTTTAACAATCAACAATA
* *
648962 ACCCCATTTCATTAATCCATTATCAATTACTAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* *
649002 CTAAAACCACC-ATTTTAAGCTGTAAACCCATAAATTTCCTCCACGGTTTAACAATCAACAATCA
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACTGTTTAACAATCAACAATAA
* *
649066 CCCCATTTCATTGATCCACTAGCAATTACTAAAATCTAG
66 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* *
649105 CT-AAACTCACCAATTTTAAGCTGTAAACCCATAAAATTCCTACA-TAGTTTAACAATCAACAAT
1 CTAAAAC-CACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACT-GTTTAACAATCAACAAT
649168 AACCCCATTTCATTAATCCACT-GTCAATTACTAAAATCCAG
64 AACCCCATTTCATTAATCCACTAG-CAATTACTAAAATCCAG
** * * *
649209 CTAAAGTCATCAATTTTAAGCTGTGAAGCCA-AAATTATCCT
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATT-TCCT
649250 AAAAAAAGAC
Statistics
Matches: 399, Mismatches: 47, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
102 23 0.06
103 162 0.41
104 189 0.47
105 25 0.06
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.28
Consensus pattern (104 bp):
CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACTGTTTAACAATCAACAATAA
CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
Found at i:649053 original size:207 final size:204
Alignment explanation
Indices: 648541--649249 Score: 890
Period size: 207 Copynumber: 3.5 Consensus size: 204
648531 CATAGTTTTA
* * * * *
648541 AGTTTCAACAATAAATAATCACTCCATTTCATTAACCCACTAGCAAATACTAAAATCCAGCTAAA
1 AGTTT-AACAATCAACAATAACCCCATTTCATTAATCCACTAGCAAATACTAAAATCCAGCTAAA
* * * *
648606 ACAACCAATTTTAAGCTGTAAACCCATAAATTTTCTCCATAGTTT---AATCAACAATTACCCCA
65 ACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACAGTTTAACAATCAACAATAACCCCA
*
648668 TTTCATTATCCACTAGCAATAACTAAA-A---G---CCACCAATTTTAAGCTGTAAACCCATAAA
130 TTTCATTATCCACTAGCAATTACTAAACAGCTGAAACCACCAATTTTAAGCTGTAAACCCATAAA
* * *
648726 TCTCTTCCAT
195 ACTCCTACAT
* * * * *
648736 TGTTTAACAATGAACAATCACCCCATTTCATTAATCCGCTAGCAAAAACTAAAATCCAGCTAAAA
1 AGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAAATACTAAAATCCAGCTAAAA
* * *
648801 CCACCAATTTTAAGCT-TAAACCCACAAATTTCCTCCACTGTTTAACAATCAACAATAACCTCAT
66 CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACAGTTTAACAATCAACAATAACCCCAT
648865 TTCATTAATCCACTAGCAATTACTAAACCCAGCTGAAACCACCAATTTTTAAGCTGTAAACCCAT
131 TTCATT-ATCCACTAGCAATTACTAAA--CAGCTGAAACCACCAA-TTTTAAGCTGTAAACCCAT
*
648930 AAAACTCCTACAA
192 AAAACTCCTACAT
* * * *
648943 AGTTTAACTATCAACAATAACCCCATTTCATTAATCCATTATCAATTACTAAAATCCAGCTAAAA
1 AGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAAATACTAAAATCCAGCTAAAA
* *
649008 CCACC-ATTTTAAGCTGTAAACCCATAAATTTCCTCCACGGTTTAACAATCAACAATCACCCCAT
66 CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACAGTTTAACAATCAACAATAACCCCAT
649072 TTCATTGATCCACTAGCAATTACTAAAATCTAGCT-AAACTCACCAATTTTAAGCTGTAAACCCA
131 TTCATT-ATCCACTAGCAATTACT-AAA-C-AGCTGAAAC-CACCAATTTTAAGCTGTAAACCCA
*
649136 TAAAATTCCTACAT
191 TAAAACTCCTACAT
*
649150 AGTTTAACAATCAACAATAACCCCATTTCATTAATCCACT-GTCAATTACTAAAATCCAGCTAAA
1 AGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAG-CAAATACTAAAATCCAGCTAAA
** * * *
649214 GTCATCAATTTTAAGCTGTGAAGCCA-AAATTATCCT
65 ACCACCAATTTTAAGCTGTAAACCCATAAATT-TCCT
649250 AAAAAAAGAC
Statistics
Matches: 449, Mismatches: 44, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
193 23 0.05
194 69 0.15
195 4 0.01
196 22 0.05
197 19 0.04
200 1 0.00
203 1 0.00
206 17 0.04
207 259 0.58
208 34 0.08
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.28
Consensus pattern (204 bp):
AGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAAATACTAAAATCCAGCTAAAA
CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCACAGTTTAACAATCAACAATAACCCCAT
TTCATTATCCACTAGCAATTACTAAACAGCTGAAACCACCAATTTTAAGCTGTAAACCCATAAAA
CTCCTACAT
Found at i:652744 original size:31 final size:31
Alignment explanation
Indices: 652709--652777 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
652699 TATATTATCC
* * *
652709 GGTATCTGAATTTGGCTTCAATATTTAACTT
1 GGTATATGAATTTGACTTCAATATTCAACTT
* * *
652740 GGTATATGAGTTTGACTTCAATGTTCAATTT
1 GGTATATGAATTTGACTTCAATATTCAACTT
652771 GGTATAT
1 GGTATAT
652778 AAGTTTTCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (31 bp):
GGTATATGAATTTGACTTCAATATTCAACTT
Found at i:652783 original size:31 final size:31
Alignment explanation
Indices: 652719--652783 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
652709 GGTATCTGAA
* * *
652719 TTTGGCTTCAATATTTAACTTGGTATATGAG
1 TTTGACTTCAATATTCAACTTGGTATATAAG
* *
652750 TTTGACTTCAATGTTCAATTTGGTATATAAG
1 TTTGACTTCAATATTCAACTTGGTATATAAG
652781 TTT
1 TTT
652784 TCTCAAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (31 bp):
TTTGACTTCAATATTCAACTTGGTATATAAG
Found at i:671645 original size:55 final size:54
Alignment explanation
Indices: 671545--671651 Score: 187
Period size: 55 Copynumber: 2.0 Consensus size: 54
671535 TACCATATGC
*
671545 TTTTGCGATGTGTGGGTCTCTCCCACCATGAGTACTATGCCTTGTGTGGATTGT
1 TTTTGCGATGTGTGGGTCCCTCCCACCATGAGTACTATGCCTTGTGTGGATTGT
*
671599 TTTTGCGATGTGTGGGTCCCTCCTCACCATGAGTACTATGCTTTGTGTGGATT
1 TTTTGCGATGTGTGGGTCCCTCC-CACCATGAGTACTATGCCTTGTGTGGATT
671652 TTGTCTAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 22 0.44
55 28 0.56
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (54 bp):
TTTTGCGATGTGTGGGTCCCTCCCACCATGAGTACTATGCCTTGTGTGGATTGT
Found at i:674804 original size:6 final size:6
Alignment explanation
Indices: 674775--674807 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
674765 TGTGTGTTTG
*
674775 TGTGTA TGTGCA TGTGTA TGTGTA TGTGTA TGT
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGT
674808 ATGTATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.03, G:0.33, T:0.48
Consensus pattern (6 bp):
TGTGTA
Found at i:676333 original size:44 final size:44
Alignment explanation
Indices: 676270--676355 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
676260 AACATTCATG
*
676270 TAGAATTACAACTTCCACATGTTTAAAAAATACTTGTATTCGCA
1 TAGAATTACAACTTCCACATATTTAAAAAATACTTGTATTCGCA
*
676314 TAGAATTACAACTTCCACATATTTGAAAAATACTTGTATTCG
1 TAGAATTACAACTTCCACATATTTAAAAAATACTTGTATTCG
676356 ACACATTCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (44 bp):
TAGAATTACAACTTCCACATATTTAAAAAATACTTGTATTCGCA
Found at i:682214 original size:37 final size:37
Alignment explanation
Indices: 682164--682237 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
682154 TCGCTGACGG
682164 AATAACCTGACAGTTACATGTAACGTGCCACGTGTAT
1 AATAACCTGACAGTTACATGTAACGTGCCACGTGTAT
682201 AATAACCTGACAGTTACATGTAACGTGCCACGTGTAT
1 AATAACCTGACAGTTACATGTAACGTGCCACGTGTAT
682238 CTCACAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (37 bp):
AATAACCTGACAGTTACATGTAACGTGCCACGTGTAT
Found at i:684692 original size:18 final size:18
Alignment explanation
Indices: 684656--684735 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
684646 TTCTATTTCT
* *
684656 TCTTCTTCCTCCTCCTCC
1 TCTTCTTCTTCTTCCTCC
* *
684674 TCCTCTTCTTCTTCTTCC
1 TCTTCTTCTTCTTCCTCC
*
684692 TCTTCTTCTTCTACCTCC
1 TCTTCTTCTTCTTCCTCC
* * *
684710 ACTTCTTCATAC-TCCACC
1 TCTTCTTC-TTCTTCCTCC
684728 TCTTCTTC
1 TCTTCTTC
684736 CATAGTCTCC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
18 47 0.96
19 2 0.04
ACGTcount: A:0.06, C:0.46, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTTCTTCTTCTTCCTCC
Found at i:684714 original size:15 final size:15
Alignment explanation
Indices: 684681--684733 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
684671 TCCTCCTCTT
* **
684681 CTTCTTCTTCCTCTT
1 CTTCTTCTACCTCCA
684696 CTTCTTCTACCTCCA
1 CTTCTTCTACCTCCA
684711 CTTCTTCATA-CTCCA
1 CTTCTTC-TACCTCCA
*
684726 CCTCTTCT
1 CTTCTTCT
684734 TCCATAGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 1 0.03
15 30 0.91
16 2 0.06
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
CTTCTTCTACCTCCA
Found at i:684717 original size:3 final size:3
Alignment explanation
Indices: 684638--684703 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
684628 GATATCTTGA
* * * * * *
684638 TCT TCC TCT TCT AT-T TCT TCT TCT TCC TCC TCC TCC TCC TCT TCT
1 TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
684683 TCT TCT TCC TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT
684704 ACCTCCACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.96
4 1 0.02
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (3 bp):
TCT
Found at i:687408 original size:17 final size:17
Alignment explanation
Indices: 687380--687414 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
687370 TTAATTTTTT
687380 TATTTTTAATTTT-AAA
1 TATTTTTAATTTTCAAA
687396 TATTTTATAATTTTCAAA
1 TATTTT-TAATTTTCAAA
687414 T
1 T
687415 TATTAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTAATTTTCAAA
Found at i:695982 original size:100 final size:100
Alignment explanation
Indices: 695779--696431 Score: 790
Period size: 100 Copynumber: 6.5 Consensus size: 100
695769 ATATATGGAC
* * * * *
695779 GTAATTATCCTGTATCACAGCCATCACACGATATCTCTCAACGCAAGGGTCGATATCATCAAATT
1 GTAATTATCCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGA-ATGATCAAATT
* *
695844 AAAACTACATATTACATAACCATGATTCATATATAA
65 AAGACTACATATTACATAACCATGATTCATATACAA
*
695880 GTAATTATCCTGTATCACCGCCATCGCACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTA
1 GTAATTATCCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTA
695945 AGACTACATATTACATAACCATGATTCATATACAA
66 AGACTACATATTACATAACCATGATTCATATACAA
* * * * *
695980 GTAATAATCCCT-TATCAACACCATCACACGATTTCTCTCGAGGCAAGGATCGAATGAGCAAATT
1 GTAATTAT-CCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATT
*
696044 AAGACTACATATTACATAACCATGATTCATATTCAA
65 AAGACTACATATTACATAACCATGATTCATATACAA
* ** * * * * * * * *
696080 GTAAATATCCCATATCATCGCCACCACACAATTGCTCTTAAGGCGAGGATCAAATGATCAAATCA
1 GTAATTATCCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTA
*
696145 AGACTACATATTGCATAACCATGATTCATATACAA
66 AGACTACATATTACATAACCATGATTCATATACAA
* * * * *
696180 GTAATAATCCCT-TATCACCACCGTCACACGATTTCTCTCGAGGCAAGGATTGAATGATCAAATT
1 GTAATTAT-CCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATT
696244 AAGACTACATATTACATAACCATGATTCATATACAA
65 AAGACTACATATTACATAACCATGATTCATATACAA
* * * * * ** * * *
696280 ATAAATATCCTAT-TCATCGCCACCACATAATTTCTCTTAAGGCAAGGATCAAATGATCAAATCA
1 GTAATTATCCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTA
* * *
696344 AAACTGCATATTACATAACCATGATTCAAATACAA
66 AGACTACATATTACATAACCATGATTCATATACAA
* * * * * * * *
696379 GCAATTATCCCGTATCATCACCACCTCATGATTTCTCTCAAAGCAAGGATCGA
1 GTAATTATCCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGA
696432 TACAGTTTAA
Statistics
Matches: 472, Mismatches: 75, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
99 85 0.18
100 334 0.71
101 53 0.11
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (100 bp):
GTAATTATCCTGTATCACCGCCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTA
AGACTACATATTACATAACCATGATTCATATACAA
Found at i:696181 original size:200 final size:200
Alignment explanation
Indices: 695791--696431 Score: 892
Period size: 200 Copynumber: 3.2 Consensus size: 200
695781 AATTATCCTG
* * * * *
695791 TATC-ACAGCCATCACACGATATCTCTCAACGCAAGGGTCGATATCATCAAATTAAAACTACATA
1 TATCAACA-CCATCACACGATTTCTCTCAAGGCAAGGATCGA-ATGATCAAATTAAGACTACATA
* * * * * * *
695855 TTACATAACCATGATTCATATAT-AAGTAATTATCCTGTATCACCGCCATCGCACGATTTCTCTC
64 TTACATAACCATGATTCATAT-TCAAGTAAATATCCTATATCATCGCCACCACACAATTTCTCTT
* *
695919 AAGGCAAGGATCGAATGATCAAATTAAGACTACATATTACATAACCATGATTCATATACAAGTAA
128 AAGGCAAGGATCAAATGATCAAATCAAGACTACATATTACATAACCATGATTCATATACAAGTAA
695984 TAATCCCT
193 TAATCCCT
* *
695992 TATCAACACCATCACACGATTTCTCTCGAGGCAAGGATCGAATGAGCAAATTAAGACTACATATT
1 TATCAACACCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATT
* *
696057 ACATAACCATGATTCATATTCAAGTAAATATCCCATATCATCGCCACCACACAATTGCTCTTAAG
66 ACATAACCATGATTCATATTCAAGTAAATATCCTATATCATCGCCACCACACAATTTCTCTTAAG
* *
696122 GCGAGGATCAAATGATCAAATCAAGACTACATATTGCATAACCATGATTCATATACAAGTAATAA
131 GCAAGGATCAAATGATCAAATCAAGACTACATATTACATAACCATGATTCATATACAAGTAATAA
696187 TCCCT
196 TCCCT
* * * *
696192 TATCACCACCGTCACACGATTTCTCTCGAGGCAAGGATTGAATGATCAAATTAAGACTACATATT
1 TATCAACACCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATT
* * *
696257 ACATAACCATGATTCATATACAAATAAATATCCTAT-TCATCGCCACCACATAATTTCTCTTAAG
66 ACATAACCATGATTCATATTCAAGTAAATATCCTATATCATCGCCACCACACAATTTCTCTTAAG
* * * * *
696321 GCAAGGATCAAATGATCAAATCAAAACTGCATATTACATAACCATGATTCAAATACAAGCAATTA
131 GCAAGGATCAAATGATCAAATCAAGACTACATATTACATAACCATGATTCATATACAAGTAATAA
*
696386 TCCCG
196 TCCCT
* * * * *
696391 TATCATCACCACCTCATGATTTCTCTCAAAGCAAGGATCGA
1 TATCAACACCATCACACGATTTCTCTCAAGGCAAGGATCGA
696432 TACAGTTTAA
Statistics
Matches: 393, Mismatches: 45, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
199 122 0.31
200 235 0.60
201 33 0.08
202 3 0.01
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (200 bp):
TATCAACACCATCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATT
ACATAACCATGATTCATATTCAAGTAAATATCCTATATCATCGCCACCACACAATTTCTCTTAAG
GCAAGGATCAAATGATCAAATCAAGACTACATATTACATAACCATGATTCATATACAAGTAATAA
TCCCT
Found at i:698126 original size:5 final size:5
Alignment explanation
Indices: 698118--698149 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
698108 TTAATCTAAT
698118 TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
698150 CATAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:699575 original size:7 final size:7
Alignment explanation
Indices: 699563--699593 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
699553 GGCGGATGGG
699563 AAGTGGA
1 AAGTGGA
699570 AAGTGGA
1 AAGTGGA
699577 AAGTGGA
1 AAGTGGA
699584 AAGTGGA
1 AAGTGGA
699591 AAG
1 AAG
699594 GAAGTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (7 bp):
AAGTGGA
Found at i:706499 original size:15 final size:16
Alignment explanation
Indices: 706463--706497 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
706453 TTTTTATAGA
*
706463 AAAAAT-AATTATATC
1 AAAAATAAATAATATC
706478 AAAAATAAATAATATC
1 AAAAATAAATAATATC
706494 AAAA
1 AAAA
706498 TATTCAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAATAATATC
Found at i:724742 original size:19 final size:20
Alignment explanation
Indices: 724705--724745 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
724695 TATAATAAAA
*
724705 AAATAAGCAAAAGTTCAAGT
1 AAATAAGCAAAAGTCCAAGT
*
724725 AAATAA-CATAAGTCCAAGT
1 AAATAAGCAAAAGTCCAAGT
724744 AA
1 AA
724746 CAACAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (20 bp):
AAATAAGCAAAAGTCCAAGT
Found at i:728573 original size:4 final size:4
Alignment explanation
Indices: 728564--728590 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
728554 AATAATTAAA
728564 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
728591 ATGTAATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:731691 original size:28 final size:28
Alignment explanation
Indices: 731651--731723 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
731641 ATTGGAGTTG
* *
731651 AAAATGAG-AATTTTGGATACCCGAGG-GT
1 AAAAT-AGTAATTTTGGACACCCG-GGAGC
*
731679 AAAATAGTAATTTTGGACACTCGGGAGC
1 AAAATAGTAATTTTGGACACCCGGGAGC
*
731707 AAAATGGTAATTTTGGA
1 AAAATAGTAATTTTGGA
731724 AAAGTTTGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 4 0.10
28 35 0.90
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (28 bp):
AAAATAGTAATTTTGGACACCCGGGAGC
Found at i:731769 original size:29 final size:29
Alignment explanation
Indices: 731707--731931 Score: 133
Period size: 30 Copynumber: 7.6 Consensus size: 29
731697 ACTCGGGAGC
*
731707 AAAATGGTAATTTTGGAAAAGTTTG-GGGTCA
1 AAAATGG-AATTTTTG-AAAGTTTGAGGGT-A
*
731738 AAAAAGGAATTTTTGAAAGTTTGAGGGT-
1 AAAATGGAATTTTTGAAAGTTTGAGGGTA
* * *
731766 AAAATGGTAATTTTTGGAGAA--ATCATGGTCA
1 AAAATGG-AATTTTT-GA-AAGTTTGAGGGT-A
* *
731797 AAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGAAAGTTTGAGGGTA
* * *
731826 AAAATGTATTTTTTGGAAAATTTG-GGGTTA
1 AAAATGGAATTTTT-GAAAGTTTGAGGG-TA
* * *
731856 AAAATAGAA-TTTTGGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGAAAGTTTGAGGGTA
* **
731883 AAAATGTAATTTTTGGAAAGTTCAAGGGGT-
1 AAAATGGAATTTTT-GAAAGTTTGA-GGGTA
*
731913 AAAATGGTATTTTTAGAAA
1 AAAATGGAATTTTT-GAAA
731932 AATCAAGGTC
Statistics
Matches: 152, Mismatches: 28, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
27 7 0.05
28 19 0.12
29 52 0.34
30 59 0.39
31 15 0.10
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAAGTTTGAGGGTA
Found at i:731770 original size:59 final size:58
Alignment explanation
Indices: 731707--731901 Score: 229
Period size: 59 Copynumber: 3.3 Consensus size: 58
731697 ACTCGGGAGC
*
731707 AAAATGGTAA-TTTTGGAAAAGTTTGGGGTCAAAAAAGGAATTTTTGAAAGTTTGAGGGT
1 AAAAT-GTAATTTTTGGAAAA-TTTGGGGTCAAAAAAGGAATTTTTGGAAGTTTGAGGGT
* * *
731766 AAAATGGTAATTTTTGGAGAAATCAT--GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAT-GTAATTTTTGGA-AAAT-TTGGGGTCAAAAAAGGAATTTTTGGAAGTTTGAGGGT
* * *
731825 AAAAATGTATTTTTTGGAAAATTTGGGGTTAAAAATA-GAA-TTTTGGAAGTTCGAGGGT
1 -AAAATGTAATTTTTGGAAAATTTGGGGTCAAAAA-AGGAATTTTTGGAAGTTTGAGGGT
731883 AAAATGTAATTTTTGGAAA
1 AAAATGTAATTTTTGGAAA
731902 GTTCAAGGGG
Statistics
Matches: 118, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
57 19 0.16
58 20 0.17
59 62 0.53
60 13 0.11
61 4 0.03
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAAATTTGGGGTCAAAAAAGGAATTTTTGGAAGTTTGAGGGT
Found at i:731974 original size:29 final size:28
Alignment explanation
Indices: 731738--732005 Score: 137
Period size: 30 Copynumber: 9.2 Consensus size: 28
731728 TTTGGGGTCA
* * * *
731738 AAAAAGGAATTTTTGAAAGTTTGAGGGT
1 AAAATGGAATTTTTGGAAGTTCGGGGGT
** **
731766 AAAATGGTAATTTTTGGAGAAATC-ATGGT
1 AAAATGG-AATTTTTGGA-AGTTCGGGGGT
*
731795 CAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 --AAAATGGAATTTTTGGAAGTTCGGGGGT
* * * * *
731825 AAAAATGTATTTTTTGGAAAATTTGGGGTT
1 -AAAATGGAATTTTTGG-AAGTTCGGGGGT
* *
731855 AAAAATAGAA-TTTTGGAAGTTCGAGGGT
1 -AAAATGGAATTTTTGGAAGTTCGGGGGT
* *
731883 AAAATGTAATTTTTGGAAAGTTCAAGGGGT
1 AAAATGGAATTTTTGG-AAGTTC-GGGGGT
* * ** **
731913 AAAATGGTATTTTTAGAAAAATC-AAGGT
1 AAAATGGAATTTTT-GGAAGTTCGGGGGT
*
731941 CAAAAGTGGAATTTTTTGAAGTTCGGGGGT
1 -AAAA-TGGAATTTTTGGAAGTTCGGGGGT
* *
731971 AAAATAGTAATTTTTGGAGAGATCGGGGGT
1 AAAAT-GGAATTTTTGGA-AGTTCGGGGGT
*
732001 CAAAT
1 AAAAT
732006 ATAATTTTGA
Statistics
Matches: 181, Mismatches: 44, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
27 7 0.04
28 24 0.13
29 64 0.35
30 78 0.43
31 8 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:732010 original size:29 final size:29
Alignment explanation
Indices: 731675--732013 Score: 119
Period size: 29 Copynumber: 11.6 Consensus size: 29
731665 GGATACCCGA
*
731675 GGGTAAAATAGTAA-TTTTGGACA-CTCGG
1 GGGTAAAATAGTAATTTTTGGA-AGATCGG
* * * * **
731703 GAGCAAAATGGTAA-TTTTGGAAAAGTTTG
1 GGGTAAAATAGTAATTTTTGGAAGA-TCGG
* * * * * *
731732 GGGTCAAAAAAGGAATTTTTGAAAGTTTGA
1 GGGT-AAAATAGTAATTTTTGGAAGATCGG
* * *
731762 GGGTAAAATGGTAATTTTTGGAGAAATC-A
1 GGGTAAAATAGTAATTTTTGGA-AGATCGG
* * * *
731791 TGGTCAAAA-ATGGAATTTTTGGAAGTTTGG
1 GGGT-AAAATA-GTAATTTTTGGAAGATCGG
* * *
731821 GGGTAAAA-ATGTATTTTTTGGAAAATTTGG
1 GGGTAAAATA-GTAATTTTTGGAAGA-TCGG
* * *
731851 GGTTAAAAATAG-AA-TTTTGGAAGTTCGA
1 GGGT-AAAATAGTAATTTTTGGAAGATCGG
* *
731879 GGGTAAAAT-GTAATTTTTGGAAAGTTCAAG
1 GGGTAAAATAGTAATTTTTGG-AAGATC-GG
* * * *
731909 GGGTAAAATGGT-ATTTTTAGAAAAATC-A
1 GGGTAAAATAGTAATTTTT-GGAAGATCGG
* * * *
731937 AGGTCAAAAGT-GGAATTTTTTGAAGTTCGG
1 GGGT-AAAA-TAGTAATTTTTGGAAGATCGG
731967 GGGTAAAATAGTAATTTTTGGAGAGATCGG
1 GGGTAAAATAGTAATTTTTGGA-AGATCGG
*
731997 GGGTCAAATA-TAATTTT
1 GGGTAAAATAGTAATTTT
732014 GAAATAGTTT
Statistics
Matches: 228, Mismatches: 60, Indels: 45
0.68 0.18 0.14
Matches are distributed among these distances:
26 1 0.00
27 8 0.04
28 33 0.14
29 85 0.37
30 85 0.37
31 15 0.07
32 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGTAAAATAGTAATTTTTGGAAGATCGG
Found at i:733084 original size:3 final size:3
Alignment explanation
Indices: 733076--733146 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
733066 CGACCTCCCT
* *
733076 TTA TTA TTA TTA TTA TTAA CTA TTA TTA TTA ATA TTTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * *
733122 TAA ATA ATA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA
733147 ATGTCTTTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:733101 original size:13 final size:12
Alignment explanation
Indices: 733076--733146 Score: 71
Period size: 10 Copynumber: 6.2 Consensus size: 12
733066 CGACCTCCCT
*
733076 TTATTATTATTA
1 TTATTAATATTA
733088 TTATTAACTATTA
1 TTATTAA-TATTA
733101 TTATTAATA-T-
1 TTATTAATATTA
733111 TTATT-ATATTA
1 TTATTAATATTA
* *
733122 TAAATAATATTA
1 TTATTAATATTA
733134 TTA--AATATTA
1 TTATTAATATTA
733144 TTA
1 TTA
733147 ATGTCTTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
9 3 0.06
10 16 0.31
11 4 0.08
12 16 0.31
13 12 0.24
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:733101 original size:16 final size:15
Alignment explanation
Indices: 733080--733146 Score: 59
Period size: 16 Copynumber: 4.5 Consensus size: 15
733070 CTCCCTTTAT
*
733080 TATTATTATTATTAAC
1 TATTATTATTA-TAAA
**
733096 TATTATTATTAATATT
1 TATTATTATT-ATAAA
733112 TATTA-TATTATAAA
1 TATTATTATTATAAA
*
733126 TAATATTA-T-TAAA
1 TATTATTATTATAAA
733139 TATTATTA
1 TATTATTA
733147 ATGTCTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
13 11 0.26
14 8 0.19
15 6 0.14
16 17 0.40
17 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTATTATAAA
Found at i:733846 original size:17 final size:17
Alignment explanation
Indices: 733821--733914 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
733811 TTAAAATTTT
733821 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
*
733839 ATTTAAAAAAAATTTAA
1 ATTTAAAATAAATTTAA
* * **
733856 ACTTCAAATAAGCTTAA
1 ATTTAAAATAAATTTAA
*
733873 ATTTACAATAAATTTAA
1 ATTTAAAATAAATTTAA
* *
733890 ACTTAAAAT-AATTAAA
1 ATTTAAAATAAATTTAA
*
733906 AATTAAAAT
1 ATTTAAAAT
733915 CTAAAATTGG
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 14 0.23
17 43 0.70
18 4 0.07
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:733865 original size:34 final size:34
Alignment explanation
Indices: 733826--733913 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
733816 ATTTTATTTC
733826 AAAATAAATTTAAATTTAAAAAAAATTTAAACTT
1 AAAATAAATTTAAATTTAAAAAAAATTTAAACTT
* ** * *
733860 CAAATAAGCTTAAATTTACAATAAATTTAAACTT
1 AAAATAAATTTAAATTTAAAAAAAATTTAAACTT
* *
733894 AAAAT-AATTAAAAATTAAAA
1 AAAATAAATTTAAATTTAAAA
733914 TCTAAAATTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 10 0.23
34 33 0.77
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAAAAAATTTAAACTT
Found at i:737890 original size:13 final size:14
Alignment explanation
Indices: 737872--737901 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
737862 GCTCACATAA
737872 AAAAAAACT-AAAT
1 AAAAAAACTCAAAT
737885 AAAAAAACTCAAAT
1 AAAAAAACTCAAAT
737899 AAA
1 AAA
737902 CTCGATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAAACTCAAAT
Found at i:739697 original size:7 final size:7
Alignment explanation
Indices: 739685--739709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
739675 CTTTCTTTTA
739685 TTTTATT
1 TTTTATT
739692 TTTTATT
1 TTTTATT
739699 TTTTATT
1 TTTTATT
739706 TTTT
1 TTTT
739710 CATATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:747869 original size:31 final size:31
Alignment explanation
Indices: 747832--747914 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 31
747822 TATTTGTTTA
*
747832 AATGTATATAACTGAATCAAAATCAAAATTT
1 AATGTATATAACTGAACCAAAATCAAAATTT
* ** * *
747863 TATGTATATATTTGAACCACAATCAAAGTTT
1 AATGTATATAACTGAACCAAAATCAAAATTT
* * *
747894 AATGTGTATAATTGTACCAAA
1 AATGTATATAACTGAACCAAA
747915 TTAAAGTGTA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.35
Consensus pattern (31 bp):
AATGTATATAACTGAACCAAAATCAAAATTT
Found at i:754244 original size:13 final size:13
Alignment explanation
Indices: 754226--754250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
754216 ATGAAATGTG
754226 ATTTCAATTTTAA
1 ATTTCAATTTTAA
754239 ATTTCAATTTTA
1 ATTTCAATTTTA
754251 TAGGGATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTCAATTTTAA
Found at i:755182 original size:150 final size:150
Alignment explanation
Indices: 754686--755187 Score: 643
Period size: 151 Copynumber: 3.3 Consensus size: 150
754676 ATTCAAGGAC
** * *
754686 CGTGTTTCAAAAATTAACTTAGTTTGCATTTTGTGTTTGAAATTGAAGTTTGAGATCGAAGTTGT
1 CGTGTTTCAAATGTTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATCGAAGTTGT
* ** * * * * *
754751 TAGGACCAAGGTTCTGTATATTCGGGAGCGGAGTGTTGGGATGGGAAGCACTTCCTGATTGGTTT
66 TAAGAATAAAGTTCTGTTTATTCGGGAGCTGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTAT
*
754816 GAATTCGTAATCTTAAAGCAT
131 GAATTCGTAATCATAAAG-AT
* * * *
754837 CATGTTTCGAAA-GTTAACTTAGTTTGTATTGTGTGTTCGAAATCGAAGTTTGAGATCAAAGTTG
1 CGTGTTTC-AAATGTTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATCGAAGTTG
* * * *
754901 TTAAGAATACAGTTCTGTTTATTTGGGAG-TGGAGTGTAGGGATGGGAAGTATTTCCTGATTGGT
65 TTAAGAATAAAGTTCTGTTTATTCGGGAGCT-GAGTGTTGGGATGGGAAGTACTTCCTGATTGGT
754965 ATGAATTCGTAATCATAAATGAT
129 ATGAATTCGTAATCATAAA-GAT
* *
754988 CGTGTTTCGAATGTTAAC-TAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATTGAAGTTG
1 CGTGTTTCAAATGTTAACTTA-GTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATCGAAGTTG
** * * * *
755052 TTAAGAATATTGTTCTGTTTGTTCGGGAGCTGAGTGTTGGAATGGGTAGTA-TTCCCGATTGGTA
65 TTAAGAATAAAGTTCTGTTTATTCGGGAGCTGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTA
*
755116 TGAATTTGTAATCATAAACGAT
130 TGAATTCGTAATCATAAA-GAT
*
755138 CGTGTTTCAAATGTTAACTTGGTTTGCATTTTGTGTTCGAAATCGAAGTT
1 CGTGTTTCAAATGTTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTT
755188 AAGAATCCGG
Statistics
Matches: 306, Mismatches: 38, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
150 82 0.27
151 219 0.72
152 5 0.02
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (150 bp):
CGTGTTTCAAATGTTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATCGAAGTTGT
TAAGAATAAAGTTCTGTTTATTCGGGAGCTGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTAT
GAATTCGTAATCATAAAGAT
Found at i:757651 original size:18 final size:18
Alignment explanation
Indices: 757630--757668 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
757620 ACAGCAAGAA
*
757630 TTTCAAATAAGTTTATTT
1 TTTCAAATAAATTTATTT
**
757648 TTTCATTTAAATTTATTT
1 TTTCAAATAAATTTATTT
757666 TTT
1 TTT
757669 GAATCTTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTCAAATAAATTTATTT
Found at i:763243 original size:14 final size:14
Alignment explanation
Indices: 763224--763253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
763214 CTTGATAATC
*
763224 ATGTGATTAATTGA
1 ATGTGATGAATTGA
763238 ATGTGATGAATTGA
1 ATGTGATGAATTGA
763252 AT
1 AT
763254 ATAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
ATGTGATGAATTGA
Found at i:765727 original size:14 final size:14
Alignment explanation
Indices: 765708--765737 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
765698 CTTGATAATC
*
765708 ATGTGATTAATTGA
1 ATGTGATGAATTGA
765722 ATGTGATGAATTGA
1 ATGTGATGAATTGA
765736 AT
1 AT
765738 ATAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
ATGTGATGAATTGA
Found at i:772145 original size:70 final size:67
Alignment explanation
Indices: 772022--772154 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
772012 ATAAACAATA
* * * *
772022 TAATGGTTTTGCCTTTTAACTTAATGGATAAACATTTATCAAAATGATATAATTTTACCTTTTAA
1 TAATGATTTTGACTTTTAACTTAAAGGATAAACATTTATCAAAACGATATAATTTTACCTTTTAA
772087 CT
66 CT
*
772089 TAATGATTTTGACTTTTAACTTTAGAAAGGATAAACATTTATCAAAACGATGTAATTTTACCTTT
1 TAATGATTTTGACTTTTAAC-TT--AAAGGATAAACATTTATCAAAACGATATAATTTTACCTTT
772154 T
63 T
772155 CTTATTCGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 18 0.31
68 2 0.03
70 38 0.66
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTAAAGGATAAACATTTATCAAAACGATATAATTTTACCTTTTAA
CT
Found at i:772727 original size:29 final size:30
Alignment explanation
Indices: 772677--772737 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
772667 AATCTATATC
772677 TTTATAATTTTTAAAAAATTAAAT-TAAATT
1 TTTATAATTTTTAAAAAATTAAATAT-AATT
* * *
772707 TTTAT-ATTTTTTAGAATTTAAATATAATT
1 TTTATAATTTTTAAAAAATTAAATATAATT
772736 TT
1 TT
772738 ATCATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAATTAAATATAATT
Found at i:776830 original size:14 final size:14
Alignment explanation
Indices: 776811--776840 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
776801 CTTGATAATC
*
776811 ATGTGATTAATTGA
1 ATGTGATGAATTGA
776825 ATGTGATGAATTGA
1 ATGTGATGAATTGA
776839 AT
1 AT
776841 ATAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
ATGTGATGAATTGA
Found at i:779312 original size:14 final size:14
Alignment explanation
Indices: 779293--779322 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
779283 CTTGATAATC
*
779293 ATGTGATTAATTGA
1 ATGTGATGAATTGA
779307 ATGTGATGAATTGA
1 ATGTGATGAATTGA
779321 AT
1 AT
779323 ATAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
ATGTGATGAATTGA
Done.