Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 7 of 163
Found at i:2062381 original size:13 final size:13
Alignment explanation
Indices: 2062363--2062387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2062353 TTTTGGACCG
2062363 TATTATTATTATT
1 TATTATTATTATT
2062376 TATTATTATTAT
1 TATTATTATTAT
2062388 AAAAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:2062765 original size:20 final size:21
Alignment explanation
Indices: 2062740--2062778 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2062730 AAATTCAAAC
2062740 TCGAACCTTGAACC-TGAATT
1 TCGAACCTTGAACCATGAATT
*
2062760 TCGAACTTTGAACCATGAA
1 TCGAACCTTGAACCATGAA
2062779 CAATTTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TCGAACCTTGAACCATGAATT
Found at i:2063495 original size:16 final size:17
Alignment explanation
Indices: 2063461--2063497 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2063451 TTGGATATTG
2063461 TATTAAACTTATTTTAT
1 TATTAAACTTATTTTAT
2063478 TATTAAA-TT-TTGTTAT
1 TATTAAACTTATT-TTAT
2063494 TATT
1 TATT
2063498 TTAGAGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 10 0.53
17 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTAAACTTATTTTAT
Found at i:2064193 original size:23 final size:22
Alignment explanation
Indices: 2064138--2064227 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 22
2064128 ATTATATTGT
*
2064138 TGTTTTGG-TGCTATTTTTTTGC
1 TGTTTTGGTTGCTA-TTTTTTAC
2064160 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
*
2064182 TG-TTTGATGTTG-T-GTTTTTAC
1 TGTTTTG--GTTGCTATTTTTTAC
*
2064203 TGTTTTGG--G-TTTTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
2064222 TGTTTT
1 TGTTTT
2064228 TGTTATTATT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
20 1 0.02
21 13 0.22
22 22 0.37
23 9 0.15
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:2064239 original size:20 final size:19
Alignment explanation
Indices: 2064151--2064227 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 19
2064141 TTTGGTGCTA
*
2064151 TTTTTTTGCTGTTTTGGTTGCT
1 TTTTTTTACTGTTTTGG--G-T
* *
2064173 ATTTTTTACTG-TTTGATGT
1 TTTTTTTACTGTTTTG-GGT
2064192 TGTGTTTTTACTGTTTTGGGT
1 T-T-TTTTTACTGTTTTGGGT
2064213 TTTTTTTACTGTTTT
1 TTTTTTTACTGTTTT
2064228 TGTTATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 14 0.30
20 3 0.07
21 16 0.35
22 13 0.28
ACGTcount: A:0.06, C:0.06, G:0.19, T:0.68
Consensus pattern (19 bp):
TTTTTTTACTGTTTTGGGT
Found at i:2064258 original size:21 final size:21
Alignment explanation
Indices: 2064225--2064272 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2064215 TTTTTACTGT
*
2064225 TTTTGTTATTATTTTGGTGCTA
1 TTTT-TTACTATTTTGGTGCTA
* *
2064247 TTTTTTACTATTTTTGTGCTG
1 TTTTTTACTATTTTGGTGCTA
2064268 TTTTT
1 TTTTT
2064273 ATTGTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.10, C:0.06, G:0.15, T:0.69
Consensus pattern (21 bp):
TTTTTTACTATTTTGGTGCTA
Found at i:2064258 original size:24 final size:24
Alignment explanation
Indices: 2064231--2064307 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 24
2064221 CTGTTTTTGT
2064231 TATTATTTTGGTGCTATTTTTTAC
1 TATTATTTTGGTGCTATTTTTTAC
* *
2064255 TA-T-TTTT-GTGCT-GTTTTTAT
1 TATTATTTTGGTGCTATTTTTTAC
* * *
2064275 TGTTATTTTTGTTTCTATTTTTT-C
1 TATTA-TTTTGGTGCTATTTTTTAC
2064299 TATTATTTT
1 TATTATTTT
2064308 TGCTACTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 11
0.68 0.14 0.19
Matches are distributed among these distances:
20 7 0.17
21 6 0.15
22 4 0.10
23 9 0.22
24 9 0.22
25 5 0.12
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.70
Consensus pattern (24 bp):
TATTATTTTGGTGCTATTTTTTAC
Found at i:2064281 original size:44 final size:45
Alignment explanation
Indices: 2064221--2064311 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
2064211 GTTTTTTTTA
*
2064221 CTGTTTTTGTTATTA-TTTTGGTGCTATTTTTTACTATT-TTTGTG
1 CTGTTTTTATTATTATTTTTGGTGCTATTTTTT-CTATTATTTGTG
* * * *
2064265 CTGTTTTTATTGTTATTTTTGTTTCTATTTTTTCTATTATTTTTG
1 CTGTTTTTATTATTATTTTTGGTGCTATTTTTTCTATTATTTGTG
2064310 CT
1 CT
2064312 ACTATTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.11, C:0.08, G:0.12, T:0.69
Consensus pattern (45 bp):
CTGTTTTTATTATTATTTTTGGTGCTATTTTTTCTATTATTTGTG
Found at i:2064328 original size:24 final size:23
Alignment explanation
Indices: 2064269--2064331 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
2064259 TTTGTGCTGT
* * *
2064269 TTTTATTGTTATTTTTGTTTCTA
1 TTTTGTTGTTATTTTTGCTACTA
* *
2064292 TTTTTTCTATTATTTTTGCTACTA
1 TTTTGT-TGTTATTTTTGCTACTA
2064316 TTTTGGTTGTTATTTT
1 TTTT-GTTGTTATTTT
2064332 GATTGTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 5 0.16
24 26 0.81
25 1 0.03
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (23 bp):
TTTTGTTGTTATTTTTGCTACTA
Found at i:2067546 original size:48 final size:48
Alignment explanation
Indices: 2067475--2067662 Score: 293
Period size: 48 Copynumber: 4.1 Consensus size: 48
2067465 TAAATATACA
* *
2067475 TAAATTTGAAATTTAATTGACATTATGAATATGCTTTAAGTCAAATGT
1 TAAATTTGAAATTTAATTGACATTGTGAATATGCTTCAAGTCAAATGT
2067523 TAAATTTGAAATTTAATTGACATTGTGAATATGCTTCAAGTCAAATGT
1 TAAATTTGAAATTTAATTGACATTGTGAATATGCTTCAAGTCAAATGT
2067571 TAAATTTGAAATTTAATTGACATTGTG---A---TT--AGTCAAATGT
1 TAAATTTGAAATTTAATTGACATTGTGAATATGCTTCAAGTCAAATGT
*
2067611 TAAATTTGAAATTTAATTAACATTGTGAATATGCTTCAAGTCAAATGT
1 TAAATTTGAAATTTAATTGACATTGTGAATATGCTTCAAGTCAAATGT
2067659 TAAA
1 TAAA
2067663 GTAAAATAAA
Statistics
Matches: 129, Mismatches: 3, Indels: 16
0.87 0.02 0.11
Matches are distributed among these distances:
40 36 0.28
42 2 0.02
43 1 0.01
45 1 0.01
46 2 0.02
48 87 0.67
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (48 bp):
TAAATTTGAAATTTAATTGACATTGTGAATATGCTTCAAGTCAAATGT
Found at i:2067606 original size:40 final size:40
Alignment explanation
Indices: 2067561--2067638 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
2067551 ATATGCTTCA
*
2067561 AGTCAAATGTTAAATTTGAAATTTAATTGACATTGTGATT
1 AGTCAAATGTTAAATTTGAAATTTAATTAACATTGTGATT
2067601 AGTCAAATGTTAAATTTGAAATTTAATTAACATTGTGA
1 AGTCAAATGTTAAATTTGAAATTTAATTAACATTGTGA
2067639 ATATGCTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (40 bp):
AGTCAAATGTTAAATTTGAAATTTAATTAACATTGTGATT
Found at i:2068453 original size:22 final size:20
Alignment explanation
Indices: 2068425--2068481 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
2068415 CCTGATAATT
2068425 AAAAAATATAAAAAAATTAG
1 AAAAAATATAAAAAAATTAG
**
2068445 ATATAAAAT-TTTAAAAATTAG
1 A-A-AAAATATAAAAAAATTAG
2068466 AAAATAA-ATAAAAAAA
1 AAAA-AATATAAAAAAA
2068482 GTTTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 12 0.41
22 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAAAATATAAAAAAATTAG
Found at i:2070490 original size:24 final size:24
Alignment explanation
Indices: 2070453--2070498 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
2070443 TTTCCTGTTT
2070453 ATTATTATTATTTTTTAGAAAATA
1 ATTATTATTATTTTTTAGAAAATA
2070477 ATTATT-TTATTTTTTAGAAAAT
1 ATTATTATTATTTTTTAGAAAAT
2070499 TCTTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTATTATTATTTTTTAGAAAATA
Found at i:2074471 original size:67 final size:70
Alignment explanation
Indices: 2074376--2074541 Score: 214
Period size: 67 Copynumber: 2.4 Consensus size: 70
2074366 TTATTTATTT
* * ***
2074376 ATAAT-AATAAATAAATAATAAAACAAAATTAATAATATTTTACATTTATTTAT-TT-ATATTCA
1 ATAATAAATAAATAAATAATAAAATAAAATAAATAATATTTTACATTTATTTATGTTCATAAAAA
2074438 TAA-A
66 TAATA
* * *
2074442 ATAATAAATAAATAAATAATAAAATAAAATAAATATTATTTTATATTTATTTTTGTTCATAAAAA
1 ATAATAAATAAATAAATAATAAAATAAAATAAATAATATTTTACATTTATTTATGTTCATAAAAA
2074507 TAATA
66 TAATA
*
2074512 ATAATAAATAAATAAATAAAAATAATAAAA
1 ATAATAAATAAATAAATAATAA-AATAAAA
2074542 ATGGAATTGA
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
66 5 0.06
67 43 0.50
68 2 0.02
69 7 0.08
70 22 0.26
71 7 0.08
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (70 bp):
ATAATAAATAAATAAATAATAAAATAAAATAAATAATATTTTACATTTATTTATGTTCATAAAAA
TAATA
Found at i:2074540 original size:9 final size:9
Alignment explanation
Indices: 2074500--2074543 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
2074490 ATTTTTGTTC
2074500 ATAAAAATA
1 ATAAAAATA
*
2074509 ATAATAATA
1 ATAAAAATA
*
2074518 A-ATAAATAA
1 ATAAAAAT-A
2074527 ATAAAAATA
1 ATAAAAATA
2074536 ATAAAAAT
1 ATAAAAAT
2074544 GGAATTGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 4 0.14
9 20 0.69
10 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
ATAAAAATA
Found at i:2075229 original size:80 final size:80
Alignment explanation
Indices: 2075061--2076749 Score: 2836
Period size: 80 Copynumber: 21.2 Consensus size: 80
2075051 TATAACTATA
* * * * *
2075061 AGGGTAAAAGATTAGATTGT-TTCAACCTGCCCCATGGTCGAGGT--AAGATCTGATGGTCTTCA
1 AGGGTAAAAGATTGGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCA
*
2075123 ATC-TGCCCTTTGGTT
65 ATCTTGCCCTCTGGTT
* * * *
2075138 AGGGTAAAAGATTGGATTTTTTTAATCTGCCCCATGATCGGAGTAAAAGATCAGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2075203 TCTTGCCCTCTAGTT
66 TCTTGCCCTCTGGTT
* *
2075218 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGATTTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2075283 TCTTGCCCTCTAGTT
66 TCTTGCCCTCTGGTT
* * *
2075298 AGGATAAAAGATTGGATTTCTTCAATCTGTCCCATGATCGGGGTAGAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2075363 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
*
2075378 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2075443 TCTT-TCCTCTGGTT
66 TCTTGCCCTCTGGTT
*
2075457 AGGGTAAAAGATTGGATTTCTTCAATTTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2075522 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
* *
2075537 AGGGTAAAAGATTGGATTTCTTCAATTTGCCCCATGATCGGGGTAGAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2075602 TCTT-CCCTCTGGTT
66 TCTTGCCCTCTGGTT
* * *
2075616 AGGGTAAAAGATTAGATTTCTTCAATCTGTCCCATGATCAGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2075681 TCTT-CCCTCTGGTT
66 TCTTGCCCTCTGGTT
* * *
2075695 AGGGTAAAAGATTGGATTTCTTCAATTTGTCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
* * *
2075760 TCTTGCCTTTTAGTT
66 TCTTGCCCTCTGGTT
2075775 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2075840 TCTTGCCCTCTGGTC
66 TCTTGCCCTCTGGTT
*
2075855 AGGGTAAAAGGTTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2075920 TCTTGCCCTCTGGTC
66 TCTTGCCCTCTGGTT
*
2075935 AGGGTAAAAGGTTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
* *
2076000 TCTTGCACTCTAGTT
66 TCTTGCCCTCTGGTT
*
2076015 AAGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2076080 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
2076095 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2076160 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
2076175 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2076240 TCTTGCCCTCTAGTT
66 TCTTGCCCTCTGGTT
*
2076255 AGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2076320 TCTT-CCCTCTGGTT
66 TCTTGCCCTCTGGTT
* *
2076334 AGGGTAAAAGATAGGATTTCTTCAATCTGCCCCATGATTGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2076399 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
* *
2076414 AGGGTAAAAGATTGAATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2076479 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
2076494 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
2076559 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGGTT
*
2076574 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
* *
2076639 TTTTGCCCTCTAGTT
66 TCTTGCCCTCTGGTT
* * * * *
2076654 AGGGTAAAAGATTGGATTTTTTCAATTTGCCCCATGATAGGGGTAAAAGATCTGATGGTTTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
2076719 TCTTGCCCTCTGGTG
66 TCTTGCCCTCTGGTT
2076734 AGGGTAAAAGATTGGA
1 AGGGTAAAAGATTGGA
2076750 GGTTGTAATT
Statistics
Matches: 1524, Mismatches: 81, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
76 1 0.00
77 36 0.02
79 320 0.21
80 1167 0.77
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (80 bp):
AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
TCTTGCCCTCTGGTT
Found at i:2076889 original size:50 final size:50
Alignment explanation
Indices: 2076835--2076980 Score: 202
Period size: 50 Copynumber: 2.9 Consensus size: 50
2076825 TTTAAATGAC
* * * * *
2076835 TGAGATTTGCCATTACAGCTTCATTCTGCCCCTCTACAGCTTTAGGTGTA
1 TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
* *
2076885 TGAGATTTGACATTGCGGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
1 TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
* * *
2076935 TGAGATTTACCATTGTAGTTTCAATCTGCACCTCCACCGCTTTAGG
1 TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGG
2076981 GGTAAAAGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (50 bp):
TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
Found at i:2077913 original size:6 final size:6
Alignment explanation
Indices: 2077904--2077954 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
2077894 TCAACCTCCC
* *
2077904 CTTTTT CTTTTT CTTTTCTT CTTTTT CCTTTT CTTTGT CTTTTTT CTTTTT
1 CTTTTT CTTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT C-TTTTT CTTTTT
2077955 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 24 0.63
7 11 0.29
8 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:2077927 original size:20 final size:20
Alignment explanation
Indices: 2077904--2077954 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2077894 TCAACCTCCC
2077904 CTTTTTCTTTTTCTTT-TCTT
1 CTTTTTCTTTTTCTTTGTC-T
*
2077924 CTTTTTCCTTTTCTTTGTCT
1 CTTTTTCTTTTTCTTTGTCT
2077944 -TTTTTCTTTTT
1 CTTTTTCTTTTT
2077955 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.36
20 16 0.57
21 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (20 bp):
CTTTTTCTTTTTCTTTGTCT
Found at i:2077934 original size:15 final size:14
Alignment explanation
Indices: 2077908--2077954 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
2077898 CCTCCCCTTT
2077908 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
*
2077922 TTCTTTTTC-CTT-
1 TTCTTTTTCTTTTC
*
2077934 TTCTTTGTCTTTT-
1 TTCTTTTTCTTTTC
2077947 TTCTTTTT
1 TTCTTTTT
2077955 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:2077955 original size:26 final size:26
Alignment explanation
Indices: 2077906--2077954 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2077896 AACCTCCCCT
*
2077906 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
2077932 TTTTCTTTGTCTTTT-TTCTTTTT
1 TTTTCTTTGTCTTTTCTTCTTTTT
2077955 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTCTTTGTCTTTTCTTCTTTTTCC
Found at i:2083093 original size:4 final size:4
Alignment explanation
Indices: 2083082--2083122 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
2083072 TATATTCATA
2083082 AAAT -AAT AAAT AAAT AAAT AAAT -AAT AAAAT AAAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT A
2083123 TTATTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 6 0.18
4 20 0.59
5 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2083108 original size:67 final size:67
Alignment explanation
Indices: 2083022--2083173 Score: 236
Period size: 67 Copynumber: 2.3 Consensus size: 67
2083012 TTATTTATTT
*
2083022 ATAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATATTCAT-AAAA
1 ATAATAAATAAATAAATAATAAAACAAAATAAATATTATTTTACATTTATTTATATTCATAAAAA
2083085 TA
66 TA
* * * *
2083087 ATAAATAAATAAATAAATAATAAAATAAAATAAATATTATTTTATATTTATTTTTGTTCATAAAA
1 AT-AATAAATAAATAAATAATAAAACAAAATAAATATTATTTTACATTTATTTATATTCATAAAA
2083152 ATA
65 ATA
2083155 ATAATAAATAAATAAATAA
1 ATAATAAATAAATAAATAA
2083174 AAATAATAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
65 2 0.03
66 3 0.04
67 66 0.84
68 8 0.10
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.39
Consensus pattern (67 bp):
ATAATAAATAAATAAATAATAAAACAAAATAAATATTATTTTACATTTATTTATATTCATAAAAA
TA
Found at i:2083173 original size:18 final size:17
Alignment explanation
Indices: 2083150--2083183 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2083140 TTGTTCATAA
*
2083150 AAATAATAATAAATAAAT
1 AAATAAAAAT-AATAAAT
2083168 AAATAAAAATAATAAA
1 AAATAAAAATAATAAA
2083184 AATGGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAATAATAAAT
Found at i:2103882 original size:30 final size:30
Alignment explanation
Indices: 2103846--2103911 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2103836 AAGAGGACTA
*
2103846 TTTTGTCAC-TTTTCATAACTTTAGTAACTG
1 TTTTGTCACATTTTCA-AACTTCAGTAACTG
* *
2103876 TTTTGTCACATTTTCAAAGTTCAGTGACTG
1 TTTTGTCACATTTTCAAACTTCAGTAACTG
2103906 TTTTGT
1 TTTTGT
2103912 TAAATGTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (30 bp):
TTTTGTCACATTTTCAAACTTCAGTAACTG
Found at i:2109564 original size:19 final size:21
Alignment explanation
Indices: 2109542--2109587 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
2109532 AAAATGTTTG
2109542 TAAAAAAATAAATTA-AA-AT
1 TAAAAAAATAAATTATAACAT
**
2109561 TAAAAGCATAAATTATAACAT
1 TAAAAAAATAAATTATAACAT
2109582 TAAAAA
1 TAAAAA
2109588 TAAAGAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 13 0.59
20 2 0.09
21 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAAAATAAATTATAACAT
Found at i:2119103 original size:21 final size:22
Alignment explanation
Indices: 2119060--2119103 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2119050 TATTTAAAAA
*
2119060 AATAAATATGATTAAAATTTAT
1 AATAAATATGATTAAAATATAT
* *
2119082 AATAAA-ATTATTCAAATATAT
1 AATAAATATGATTAAAATATAT
2119103 A
1 A
2119104 TATATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AATAAATATGATTAAAATATAT
Found at i:2120890 original size:17 final size:17
Alignment explanation
Indices: 2120843--2120893 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2120833 GAAACATTTA
2120843 TTTTAATGTTTTAGTATT
1 TTTTAATGTTTTA-TATT
*
2120861 TTTT-ATGTATTATATAT
1 TTTTAATGTTTTATAT-T
2120878 TTTTAAT-TTTTATATT
1 TTTTAATGTTTTATATT
2120894 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 4 0.14
17 19 0.66
18 6 0.21
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTAATGTTTTATATT
Found at i:2127269 original size:12 final size:12
Alignment explanation
Indices: 2127252--2127283 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2127242 CGTATTATTT
2127252 AATTATTGCATC
1 AATTATTGCATC
2127264 AATTATTGCATC
1 AATTATTGCATC
2127276 AATTATTG
1 AATTATTG
2127284 TAAAAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (12 bp):
AATTATTGCATC
Found at i:2135896 original size:11 final size:11
Alignment explanation
Indices: 2135882--2135928 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
2135872 ATTCTCTCAC
2135882 TATTTTGTTAT
1 TATTTTGTTAT
***
2135893 TATTTCACTAT
1 TATTTTGTTAT
*
2135904 TA-TTTGTTAC
1 TATTTTGTTAT
2135914 TATTTTGTTAT
1 TATTTTGTTAT
2135925 TATT
1 TATT
2135929 GTTTTAATAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
10 6 0.22
11 21 0.78
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:2135911 original size:21 final size:19
Alignment explanation
Indices: 2135867--2135918 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2135857 TGCTATTTGC
* *
2135867 TTGTTATTCTCTCACTATT
1 TTGTTATTATTTCACTATT
2135886 TTGTTATTATTTCACTATTAT
1 TTGTTATTATTTCACTA-T-T
*
2135907 TTGTTACTATTT
1 TTGTTATTATTT
2135919 TGTTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 15 0.54
20 1 0.04
21 12 0.43
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (19 bp):
TTGTTATTATTTCACTATT
Found at i:2144763 original size:32 final size:32
Alignment explanation
Indices: 2144727--2144799 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
2144717 ATTGTTTTCC
2144727 TTTTGTGTTTTAAGTGGATTTGTATCCTCTAT
1 TTTTGTGTTTTAAGTGGATTTGTATCCTCTAT
2144759 TTTTGTGTTTTAAGTGGATTTGTATCCTCTAT
1 TTTTGTGTTTTAAGTGGATTTGTATCCTCTAT
2144791 TTTTGTGTT
1 TTTTGTGTT
2144800 ATAAAATCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.14, C:0.08, G:0.19, T:0.59
Consensus pattern (32 bp):
TTTTGTGTTTTAAGTGGATTTGTATCCTCTAT
Found at i:2147084 original size:19 final size:19
Alignment explanation
Indices: 2147057--2147093 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2147047 TTAATATTAA
*
2147057 TATTTCAATAATAAATATT
1 TATTACAATAATAAATATT
*
2147076 TATTACAATTATAAATAT
1 TATTACAATAATAAATAT
2147094 AATAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTACAATAATAAATATT
Found at i:2150472 original size:16 final size:16
Alignment explanation
Indices: 2150448--2150485 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2150438 ATAATTAAAA
2150448 TTAAAT-AAAAATACAT
1 TTAAATAAAAAATA-AT
*
2150464 TTAATTAAAAAATAAT
1 TTAAATAAAAAATAAT
2150480 TTAAAT
1 TTAAAT
2150486 TAGTTACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATAAAAAATAAT
Found at i:2152693 original size:48 final size:49
Alignment explanation
Indices: 2152602--2152712 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
2152592 GTTTAAACGG
* * *
2152602 TCACGGGTTGAAGTATAACTAGGGTTTCCAATTGACAGTGGTTAAGCGA
1 TCACAGGTTGAAGTATAACTACGGTCTCCAATTGACAGTGGTTAAGCGA
* * * *
2152651 TCACAGGTTGAAGTATAACTCCGG-CTCCAATTGGCGGTGGTTATGCGA
1 TCACAGGTTGAAGTATAACTACGGTCTCCAATTGACAGTGGTTAAGCGA
* *
2152699 TCATAGGTTCAAGT
1 TCACAGGTTGAAGT
2152713 TTCATAATAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
48 32 0.60
49 21 0.40
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (49 bp):
TCACAGGTTGAAGTATAACTACGGTCTCCAATTGACAGTGGTTAAGCGA
Found at i:2170157 original size:2 final size:2
Alignment explanation
Indices: 2170150--2170205 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
2170140 AGAAGTAATC
2170150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2170192 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
2170206 AAACCTTTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2171218 original size:14 final size:14
Alignment explanation
Indices: 2171199--2171228 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2171189 TTGATGTTAG
*
2171199 AATTATATATTTAT
1 AATTATATATTAAT
2171213 AATTATATATTAAT
1 AATTATATATTAAT
2171227 AA
1 AA
2171229 GAAGATATCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATATATTAAT
Found at i:2178199 original size:46 final size:45
Alignment explanation
Indices: 2178128--2178238 Score: 150
Period size: 46 Copynumber: 2.4 Consensus size: 45
2178118 TTCTTTGAAA
* * *
2178128 TTTGAAAAAAGGGATTTTTTTTAAAGGGTAAAGAAGAAGAAATGAC
1 TTTGAAAAAA-GGATTTTTTCTAAAGGATAAAAAAGAAGAAATGAC
* *
2178174 TTTGGAAAAAGGATTTCTTTCTAAAGGATAAAAAAGAAGAAATGGC
1 TTTGAAAAAAGGATTT-TTTCTAAAGGATAAAAAAGAAGAAATGAC
*
2178220 TTTGAAAAAAGGGTTTTTT
1 TTTGAAAAAAGGATTTTTT
2178239 TTTTTTTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
45 9 0.16
46 48 0.84
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.31
Consensus pattern (45 bp):
TTTGAAAAAAGGATTTTTTCTAAAGGATAAAAAAGAAGAAATGAC
Found at i:2178385 original size:20 final size:20
Alignment explanation
Indices: 2178348--2178392 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2178338 TAGTAAATGC
**
2178348 AAAAGTAAGGAAGAAAAAAA
1 AAAAGTAAAAAAGAAAAAAA
*
2178368 AAAAGTAAAAAAGTAAAAAA
1 AAAAGTAAAAAAGAAAAAAA
*
2178388 GAAAG
1 AAAAG
2178393 AAGCTTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAAGTAAAAAAGAAAAAAA
Found at i:2178792 original size:17 final size:17
Alignment explanation
Indices: 2178754--2178794 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2178744 TAATTCTTTT
2178754 TAAAATTAATGAAACAA
1 TAAAATTAATGAAACAA
*
2178771 T-AAATTAAT-ATAACGA
1 TAAAATTAATGA-AACAA
2178787 TAAAATTA
1 TAAAATTA
2178795 CACTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (17 bp):
TAAAATTAATGAAACAA
Found at i:2180285 original size:21 final size:20
Alignment explanation
Indices: 2180248--2180287 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2180238 TGTGAACTAC
*
2180248 TTAAAAACAATTGAATCAAA
1 TTAAAAACAATTAAATCAAA
*
2180268 TTAAAAATCGATTAAATCAA
1 TTAAAAA-CAATTAAATCAA
2180288 TGATTAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (20 bp):
TTAAAAACAATTAAATCAAA
Found at i:2181209 original size:7 final size:7
Alignment explanation
Indices: 2181197--2181221 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2181187 ATTTATTTTG
2181197 TAATTAA
1 TAATTAA
2181204 TAATTAA
1 TAATTAA
2181211 TAATTAA
1 TAATTAA
2181218 TAAT
1 TAAT
2181222 CGTTTAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:2183435 original size:25 final size:25
Alignment explanation
Indices: 2183386--2183445 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2183376 AGTCACAAAT
2183386 TTGAATTCATTATAAAAAAACATTA
1 TTGAATTCATTATAAAAAAACATTA
* *
2183411 TTGATTTCATTAT-AAAAATCAATTA
1 TTGAATTCATTATAAAAAAAC-ATTA
2183436 TTTGAATTCA
1 -TTGAATTCA
2183446 ATCTATACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.20
25 16 0.53
26 8 0.27
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (25 bp):
TTGAATTCATTATAAAAAAACATTA
Found at i:2188793 original size:3 final size:3
Alignment explanation
Indices: 2188785--2188822 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2188775 TTTAGCGTGA
2188785 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2188823 AGTAGAGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2190018 original size:31 final size:31
Alignment explanation
Indices: 2189982--2190042 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2189972 ATCTGGTAGC
*
2189982 TTAAATAAAAAC-TTTTGAGTAGTTCAGTGAT
1 TTAAATAAAAACATTTT-AATAGTTCAGTGAT
*
2190013 TTAAATTAAAACATTTTAATAGTTCAGTGA
1 TTAAATAAAAACATTTTAATAGTTCAGTGA
2190043 CTAAATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (31 bp):
TTAAATAAAAACATTTTAATAGTTCAGTGAT
Found at i:2192280 original size:2 final size:2
Alignment explanation
Indices: 2192273--2192313 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2192263 TTTATTAGTT
2192273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2192314 TCTAGTTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2192889 original size:11 final size:11
Alignment explanation
Indices: 2192875--2192902 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2192865 TTAAAATAAT
2192875 TATAAATACAG
1 TATAAATACAG
2192886 TATAAATACAG
1 TATAAATACAG
2192897 TATAAA
1 TATAAA
2192903 AATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (11 bp):
TATAAATACAG
Found at i:2193347 original size:19 final size:18
Alignment explanation
Indices: 2193325--2193360 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2193315 GGATAAAGAA
*
2193325 AATATTAGATATTAAATTG
1 AATATTA-AAATTAAATTG
2193344 AATATTAAAATTAAATT
1 AATATTAAAATTAAATT
2193361 CAGGTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (18 bp):
AATATTAAAATTAAATTG
Found at i:2209362 original size:26 final size:26
Alignment explanation
Indices: 2209322--2209467 Score: 103
Period size: 26 Copynumber: 5.1 Consensus size: 26
2209312 CTTATTAAAT
*
2209322 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* *
2209348 TTTAATAAAAATATTAATTAATTTAATTATAT
1 TTTAAT--AAA-ATT-ATT-A-TTAAATATAA
*
2209380 TTTAATATAATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* *
2209406 TTTAATAAAATAATATATAATTTAATAATATT
1 TTTAATAAAAT--TAT-T-ATTAAAT-ATA-A
*
2209438 TTTAATATAATTATTATTAAAATATGAA
1 TTTAATAAAATTATTATT-AAATAT-AA
2209466 TT
1 TT
2209468 AGTAAAAATT
Statistics
Matches: 94, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
26 24 0.26
27 1 0.01
28 15 0.16
29 12 0.13
30 14 0.15
31 4 0.04
32 24 0.26
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAA
Found at i:2209384 original size:32 final size:31
Alignment explanation
Indices: 2209331--2209457 Score: 92
Period size: 32 Copynumber: 4.3 Consensus size: 31
2209321 TTTTAATAAG
2209331 ATTATT-A-TTAAATATAATTTAATAAAAAT
1 ATTATTAATTTAAATATAATTTAATAAAAAT
* * *
2209360 ATTAATTAATTTAATTATATTTTAAT--ATA-
1 ATT-ATTAATTTAAATATAATTTAATAAAAAT
2209389 ATTATT-A-TTAAATATAATTTAAT-AAAAT
1 ATTATTAATTTAAATATAATTTAATAAAAAT
* * * *
2209417 AATATATAATTT-AATAATATTTTTAATATAATT
1 ATTAT-TAATTTAAAT-ATA-ATTTAATAAAAAT
2209450 ATTATTAA
1 ATTATTAA
2209458 AATATGAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
26 14 0.18
27 3 0.04
28 7 0.09
29 7 0.09
30 9 0.12
31 6 0.08
32 23 0.30
33 7 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTATTAATTTAAATATAATTTAATAAAAAT
Found at i:2209393 original size:58 final size:58
Alignment explanation
Indices: 2209315--2209485 Score: 215
Period size: 58 Copynumber: 2.9 Consensus size: 58
2209305 GATTATTCTT
* *
2209315 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTA
2209373 ATTATATTTTAATATAATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
* * *
2209430 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
2209486 TAATATTAGA
Statistics
Matches: 101, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
57 20 0.20
58 56 0.55
59 11 0.11
60 9 0.09
61 5 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
Found at i:2209479 original size:25 final size:24
Alignment explanation
Indices: 2209450--2209500 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2209440 TAATATAATT
*
2209450 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
2209475 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
2209499 AT
1 AT
2209501 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:2209580 original size:83 final size:83
Alignment explanation
Indices: 2209481--2209647 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
2209471 AAAAATTATA
2209481 ATATATAATATTAGAAAAATAATATATAACCTATTTTTTTAGTTTTAAATTATGATGCATATATA
1 ATATATAATATTAGAAAAATAATATATAACCTATTTTTTTAGTTTTAAATTATGATGCATATATA
2209546 ATATGCTTAAATATCATT
66 ATATGCTTAAATATCATT
2209564 ATATATAATATTAGAAAAATAATATATAACCTATTTTTTTAGTTTTAAATTATGATGCATATATA
1 ATATATAATATTAGAAAAATAATATATAACCTATTTTTTTAGTTTTAAATTATGATGCATATATA
2209629 ATATGCTTAAATATCATT
66 ATATGCTTAAATATCATT
2209647 A
1 A
2209648 ACAAAATAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (83 bp):
ATATATAATATTAGAAAAATAATATATAACCTATTTTTTTAGTTTTAAATTATGATGCATATATA
ATATGCTTAAATATCATT
Found at i:2212996 original size:20 final size:21
Alignment explanation
Indices: 2212959--2212998 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2212949 ACCTTAAATT
2212959 CCTTAGATCCCAAAATCCTAA
1 CCTTAGATCCCAAAATCCTAA
*
2212980 CCTTAGA-CCCAAGATCCTA
1 CCTTAGATCCCAAAATCCTA
2212999 CGCCCTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (21 bp):
CCTTAGATCCCAAAATCCTAA
Found at i:2213701 original size:2 final size:2
Alignment explanation
Indices: 2213694--2213727 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2213684 GTGAAAAATA
2213694 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
2213728 TATGTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2218115 original size:29 final size:30
Alignment explanation
Indices: 2218068--2218124 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2218058 TTGACTTAAT
* * *
2218068 ATGCAATTGTATACATG-AATTTTAAATTG
1 ATGCAATTATACACATGAAATTCTAAATTG
*
2218097 ATGCAATTATACACGTGAAATTCTAAAT
1 ATGCAATTATACACATGAAATTCTAAAT
2218125 ATGGTTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (30 bp):
ATGCAATTATACACATGAAATTCTAAATTG
Found at i:2227098 original size:2 final size:2
Alignment explanation
Indices: 2227091--2227135 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2227081 CCAAAGCTAA
2227091 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2227133 AG A
1 AG A
2227136 ATGGAACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2235074 original size:6 final size:6
Alignment explanation
Indices: 2235063--2235089 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2235053 AGAGAAGACT
2235063 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
2235090 ATATGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:2244103 original size:144 final size:144
Alignment explanation
Indices: 2243837--2244103 Score: 356
Period size: 144 Copynumber: 1.9 Consensus size: 144
2243827 GGCGCCAAAC
* *
2243837 TTGAAAACAAAGCCTCCAGATCAGGTGGTTGAAAGAATCCATTCCTCGGTGGCTCTCTCTTCATA
1 TTGAAAACAAAGCCTCCAGATCAGGTGGATGAAAGAATCCATTCCTCGGTGACTCTCTCTTCATA
* * * **
2243902 TAAACTGCTTGTTTCATCTTCGGCGCCGGCGGACATAGCGGAGGGGCTGCCTTTTGTGTTTGCCG
66 TAAACTGCTTGTTTCATCTTCGGCGCCGCCGGACACAGCGGAGGGGCCGCCGCTTGTGTTTGCCG
2243967 CATCGAGGTCGTAT
131 CATCGAGGTCGTAT
* * * * * *
2243981 TTGAAAACAAAGCTTCGAGATCAGGTGGATGAAAGAATCCATTCTTGGGTGACTTTCTCTTTATA
1 TTGAAAACAAAGCCTCCAGATCAGGTGGATGAAAGAATCCATTCCTCGGTGACTCTCTCTTCATA
* * * * *
2244046 TGAA-TCGCTTGTTTCTTCTTCGGTGCCGCCGGACACGGCGGAGGGGCCGTCGCTTGTG
66 TAAACT-GCTTGTTTCATCTTCGGCGCCGCCGGACACAGCGGAGGGGCCGCCGCTTGTG
2244104 ACCGCCGCCT
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
143 1 0.01
144 103 0.99
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (144 bp):
TTGAAAACAAAGCCTCCAGATCAGGTGGATGAAAGAATCCATTCCTCGGTGACTCTCTCTTCATA
TAAACTGCTTGTTTCATCTTCGGCGCCGCCGGACACAGCGGAGGGGCCGCCGCTTGTGTTTGCCG
CATCGAGGTCGTAT
Found at i:2250599 original size:4 final size:4
Alignment explanation
Indices: 2250592--2250638 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
2250582 ATATAATATA
*
2250592 TATG TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
2250639 TCATGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:2269087 original size:20 final size:21
Alignment explanation
Indices: 2269043--2269087 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2269033 CATAAACAAG
* * *
2269043 AAAAGCCAGGAACTTTTTTTT
1 AAAACCCAGGAACTATTTTTA
2269064 AAAACCCAGGAA-TATTTTTA
1 AAAACCCAGGAACTATTTTTA
2269084 AAAA
1 AAAA
2269088 AAACCCCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (21 bp):
AAAACCCAGGAACTATTTTTA
Found at i:2271466 original size:16 final size:17
Alignment explanation
Indices: 2271444--2271488 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2271434 ATCGGATCCA
2271444 ATAATTATAATTAAAAT
1 ATAATTATAATTAAAAT
*
2271461 -TAATTATTA-TAAAAT
1 ATAATTATAATTAAAAT
*
2271476 AAAATTA-AATTAA
1 ATAATTATAATTAA
2271489 TAGTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATTATAATTAAAAT
Found at i:2274311 original size:19 final size:18
Alignment explanation
Indices: 2274287--2274336 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2274277 ACTATACATG
*
2274287 AATTTTAATTTAATATATT
1 AATTTTAATTTAATAT-GT
2274306 AATTTTAATTT--TATGT
1 AATTTTAATTTAATATGT
2274322 AATTTTAATCTTAAT
1 AATTTTAAT-TTAAT
2274337 TAATTTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.37
17 5 0.19
19 12 0.44
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTTTAATTTAATATGT
Found at i:2274340 original size:16 final size:15
Alignment explanation
Indices: 2274291--2274342 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
2274281 TACATGAATT
*
2274291 TTAA-TTTAATAT-A
1 TTAATTTTAATTTAA
*
2274304 TTAATTTTAATTTTA
1 TTAATTTTAATTTAA
2274319 TGTAATTTTAATCTTAA
1 T-TAATTTTAAT-TTAA
2274336 TTAATTT
1 TTAATTT
2274343 ATACAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 4 0.12
14 7 0.21
15 2 0.06
16 16 0.48
17 4 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TTAATTTTAATTTAA
Found at i:2276289 original size:17 final size:16
Alignment explanation
Indices: 2276225--2276290 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
2276215 TAATTTAATC
2276225 ATATAAAATTTA-TAA
1 ATATAAAATTTATTAA
*
2276240 AGATATAAA-TTATTAA
1 ATATA-AAATTTATTAA
*
2276256 AT-TGAAATTATATTTAA
1 ATATAAAATT-TA-TTAA
2276273 ATATAAAATTTAATTAA
1 ATATAAAATTT-ATTAA
2276290 A
1 A
2276291 ACTGACCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 3 0.08
15 9 0.22
16 9 0.22
17 12 0.30
18 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATAAAATTTATTAA
Found at i:2276451 original size:3 final size:3
Alignment explanation
Indices: 2276443--2276468 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2276433 GGTGGAGCAT
2276443 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2276469 TGTGTTTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2276596 original size:30 final size:30
Alignment explanation
Indices: 2276552--2276616 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
2276542 TAATAAAGAT
* *
2276552 AAAATTTTATTTTAATCTTTTTAAGAA-TATA
1 AAAATTTGATTTTAA--TTTTTAAAAATTATA
2276583 AAAATTTGA-TTTAATTTTTAAAAATTATA
1 AAAATTTGATTTTAATTTTTAAAAATTATA
2276612 AAAAT
1 AAAAT
2276617 ATAAACTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.29
29 9 0.29
30 5 0.16
31 8 0.26
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAATTTGATTTTAATTTTTAAAAATTATA
Found at i:2279091 original size:27 final size:25
Alignment explanation
Indices: 2279040--2279091 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
2279030 CTTTTTTTCC
* *
2279040 CTTTTTTTTTTTTAATTTCCCAAAA
1 CTTTTTTTTTTATAATTTACCAAAA
*
2279065 CTTTTTTGTTTCTATAATTTACTAAAA
1 CTTTTTT-TTT-TATAATTTACCAAAA
2279092 GCCTTATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 12 0.55
ACGTcount: A:0.27, C:0.13, G:0.02, T:0.58
Consensus pattern (25 bp):
CTTTTTTTTTTATAATTTACCAAAA
Found at i:2284054 original size:22 final size:22
Alignment explanation
Indices: 2284029--2284071 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2284019 AATTTGTTTT
*
2284029 TTGCTGCCATTTTATTATTATA
1 TTGCTACCATTTTATTATTATA
* *
2284051 TTGCTACTATTTTGTTATTAT
1 TTGCTACCATTTTATTATTAT
2284072 TATTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTATTATTATA
Found at i:2285465 original size:23 final size:22
Alignment explanation
Indices: 2285439--2285495 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2285429 TTTTTATATT
*
2285439 AAATTTTTAAATATTATTTGATC
1 AAATTTTTAAATATT-TTTGATA
** *
2285462 AAATTTCAAAATATTTTTTATA
1 AAATTTTTAAATATTTTTGATA
2285484 AATATTTTTAAA
1 AA-ATTTTTAAA
2285496 AGTAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATTTTTAAATATTTTTGATA
Found at i:2288936 original size:31 final size:30
Alignment explanation
Indices: 2288886--2289013 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 30
2288876 ACATGCATTT
* *
2288886 CCCTTGAAATTTTTAAAAATTTTAATTA-A
1 CCCTTTAAATTTTTGAAAATTTTAATTAGA
2288915 GCCCTTTAAATTTTTTGAAAATTTTAATTAGA
1 -CCCTTTAAA-TTTTTGAAAATTTTAATTAGA
* * *
2288947 CCCTCTAAAAATTTTGAAAAAAATTTAATTAGA
1 CCCT-TTAAATTTTTG--AAAATTTTAATTAGA
* * * *
2288980 CTCCTTGAAGTTTTTGACAATTTTAAGTAGA
1 C-CCTTTAAATTTTTGAAAATTTTAATTAGA
2289011 CCC
1 CCC
2289014 CCTAATACTT
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
30 10 0.12
31 40 0.49
32 5 0.06
33 23 0.28
34 3 0.04
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (30 bp):
CCCTTTAAATTTTTGAAAATTTTAATTAGA
Found at i:2297584 original size:117 final size:117
Alignment explanation
Indices: 2297362--2297599 Score: 307
Period size: 117 Copynumber: 2.0 Consensus size: 117
2297352 TGTCTCACGG
* * * * * * *
2297362 TTTCGTTATATTGAAGCTCCCAATCCCGTAAACTACTGTCCTTGGAGTTAATTTTCTCTAGAAGG
1 TTTCCTTATATCGAAGCTCCCAATCCCGCAAACTACCGTCCTTGGAGTCAATTTTCGCTACAAGG
* * *
2297427 CCATCGACGACTCCTTGAAGAGCTGCGGTCGTCTCATCATATTTATGTTCCA
66 CCATCAACGACTCCTCGAAGAGCTGCCGTCGTCTCATCATATTTATGTTCCA
* *
2297479 TTTCCTTATATCGAATCTCCCAATGCCGCAAACTACCGTCCTTGGAGTCAACTTTT-GCTACAAG
1 TTTCCTTATATCGAAGCTCCCAATCCCGCAAACTACCGTCCTTGGAGTCAA-TTTTCGCTACAAG
* * * **
2297543 GCCATCAACGAGTTCTCGAAGAGCTGCCGTTGTCTTGTCATATTTATGTTCCA
65 GCCATCAACGACTCCTCGAAGAGCTGCCGTCGTCTCATCATATTTATGTTCCA
2297596 TTTC
1 TTTC
2297600 GGACAACTGT
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
117 99 0.96
118 4 0.04
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (117 bp):
TTTCCTTATATCGAAGCTCCCAATCCCGCAAACTACCGTCCTTGGAGTCAATTTTCGCTACAAGG
CCATCAACGACTCCTCGAAGAGCTGCCGTCGTCTCATCATATTTATGTTCCA
Found at i:2299335 original size:50 final size:51
Alignment explanation
Indices: 2299259--2299369 Score: 163
Period size: 50 Copynumber: 2.2 Consensus size: 51
2299249 TGCGTAAATG
* *
2299259 TTGATAGAATGTGTAAGTATTGTGGGTTAAATATGTTAAATCATGATCAAA
1 TTGATAGAATGTGTAAGTATTGTGGGTTAAATATATTAAATCAAGATCAAA
* *
2299310 TTGATA-AATGTGCTAA-TGTTGTGGGTTAAATTTATTAAATCAAGATCAAA
1 TTGATAGAATGTG-TAAGTATTGTGGGTTAAATATATTAAATCAAGATCAAA
2299360 TTGATAGAAT
1 TTGATAGAAT
2299370 ATATGAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
50 42 0.78
51 12 0.22
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (51 bp):
TTGATAGAATGTGTAAGTATTGTGGGTTAAATATATTAAATCAAGATCAAA
Found at i:2303636 original size:25 final size:26
Alignment explanation
Indices: 2303608--2303660 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
2303598 AAGATTAGGT
* *
2303608 TTTTTATT-TTTATTTTCTATTATTA
1 TTTTTATTATTTATTGTCTATTAGTA
2303633 -TTTTATTATTTATTGTCTATTAGTA
1 TTTTTATTATTTATTGTCTATTAGTA
2303658 TTT
1 TTT
2303661 AATTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 15 0.62
26 2 0.08
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTTATTATTTATTGTCTATTAGTA
Found at i:2306673 original size:594 final size:583
Alignment explanation
Indices: 2305518--2306689 Score: 1968
Period size: 584 Copynumber: 2.0 Consensus size: 583
2305508 AATTTTGTGT
* *
2305518 TTTAAGAAACACAATACCTTTAGAATAAAAACTGATAAAAATTATACAACATAAAAGCTAAAAGA
1 TTTAAGAAACACAATACCTTAAGAATAAAAACTGATAAAAATTATACAACATAAAAGCCAAAAGA
*
2305583 AGAGTAGCGAATCTGAATTAGAATAGATAAATAATCACTGTTTGATAAAAATATATGCAGCATAA
66 AGAGTAGCGAATCTAAATTAGAATAGATAAATAATCACTGTTTGATAAAAATATATGCAGCATAA
* *
2305648 TGAAGTTAAAACACTAAGGTTTTAAAATATTACACGGGTCTAATTTAATGGTTAAGTTAACGATT
131 TGAAGTTAAAACACTAAGGTTTTAAAATATTACACGGGTCTAATTTAATAGTTAAATTAACGATT
* *
2305713 TTAGGAATGGAAGAACTTTATTGATATAGACTCGATAGTTTGAAGATGTAATTAGAATGTTTTAA
196 TTAGGAACGGAAGAACTTTATTGATATAGACTCGATAGTTTGAAGATGTAATTAGAATGTTTGAA
2305778 TATTTGAGGACTAATTTAAAATGTTTGAAAAATATGGTGTAATTAACTCTTAAAATTTGGACATT
261 TATTTGAGGACTAATTTAAAATGTTTGAAAAATATGGTGTAATTAACTCTTAAAATTTGGACATT
* *
2305843 TTATTGAATGGACATTTTTTTTAGTGAATTCGCGGTTCGGATTTATTTTTGACCCACTACTTAAA
326 TTATTGAATGGACATTTTTTTGAGTGAATTAGCGGTTCGGATTTATTTTTGACCCACTACTTAAA
*
2305908 TGTAAGGTAAATTACACCAATAGTCATGCAAGTATTCGAATATTTTCATTTTAGTCACTTGAAAA
391 TGTAAGGTAAATTACACCAATAGTCATCCAAGTATTCGAATATTTTCATTTTAGTCACTTGAAAA
* *
2305973 CAAATAAAATTTTAATTTAGTCACTGTTGTTAGAGAAATTGAATTTTTTTAATCACTGTGATGCT
456 CAAATAAAATTTCAATTTAGTCACTGTTATTAGAGAAATTGAATTTTTTTAATCACTGTGATGCT
* *
2306038 AATGTAGCATTTTCTTTCTTTTGACAAAATAACATATTTAACCCTCAACATTTGTACAACATA
521 AATGTAGCATTTTCTTTCTTTTGACAAAATAACAAATTTAACCCTCAACATTTATACAACATA
*
2306101 TTTAAGAAAACACAATACCTTAAGAATAAAAACTGATAAAAATTATACAACATAAAAGCCGAAAG
1 TTTAAG-AAACACAATACCTTAAGAATAAAAACTGATAAAAATTATACAACATAAAAGCCAAAAG
2306166 AAGAGTAGCGAATCTAAATTAGAATAGATAAATAATCACTGTTTGATAAAAATATATGCAGCATA
65 AAGAGTAGCGAATCTAAATTAGAATAGATAAATAATCACTGTTTGATAAAAATATATGCAGCATA
*
2306231 ATGAAGTTAAAACATTAAGGTTTTAAAATATTACACGGGTCTAATTTAATAGTTAAATTAACGAT
130 ATGAAGTTAAAACACTAAGGTTTTAAAATATTACACGGGTCTAATTTAATAGTTAAATTAACGAT
* *
2306296 TTTAGGAACGGAAGAACTTTGTTGATATGGACTCGATAGTTTGAAGATGTAATTAGAATGTTTGA
195 TTTAGGAACGGAAGAACTTTATTGATATAGACTCGATAGTTTGAAGATGTAATTAGAATGTTTGA
* *
2306361 ATATTTGAGGACTAATTTAAAATGAGGGTTATAGTTTGAGAAGTATGGTGTAATTAACTCTTAAA
260 ATATTTGAGGACTAATTT--AA--A-----AT-GTTTGAAAAATATGGTGTAATTAACTCTTAAA
* * * *
2306426 ATTTTGACTTTTTATTGAATGGTCATTTTTTTGAGTGAATTAGCGGTTTGGATTTATTTTTGACC
315 ATTTGGACATTTTATTGAATGGACATTTTTTTGAGTGAATTAGCGGTTCGGATTTATTTTTGACC
* *
2306491 CACTACTTAAATGTGAGGTAAATTCCACCAATAGTCATCCAAGTATTCGAATATTTTCATTTTAG
380 CACTACTTAAATGTAAGGTAAATTACACCAATAGTCATCCAAGTATTCGAATATTTTCATTTTAG
2306556 TCACTTGAAAACAAATAAAATTTCAATTTAGTCACTGTTATTAGAGAAATTGAA-TTTTTTAATC
445 TCACTTGAAAACAAATAAAATTTCAATTTAGTCACTGTTATTAGAGAAATTGAATTTTTTTAATC
* * *
2306620 ACTGTGATGTTAATGTAGCGTTTTTCTTTCTTTTGACAAAATAACAAATTTAACTCTCAACATTT
510 ACTGTGATGCTAATGTAGC-ATTTTCTTTCTTTTGACAAAATAACAAATTTAACCCTCAACATTT
2306685 ATACA
574 ATACA
2306690 TTCTATCAAT
Statistics
Matches: 548, Mismatches: 29, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
583 6 0.01
584 260 0.47
586 2 0.00
588 1 0.00
593 30 0.05
594 249 0.45
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (583 bp):
TTTAAGAAACACAATACCTTAAGAATAAAAACTGATAAAAATTATACAACATAAAAGCCAAAAGA
AGAGTAGCGAATCTAAATTAGAATAGATAAATAATCACTGTTTGATAAAAATATATGCAGCATAA
TGAAGTTAAAACACTAAGGTTTTAAAATATTACACGGGTCTAATTTAATAGTTAAATTAACGATT
TTAGGAACGGAAGAACTTTATTGATATAGACTCGATAGTTTGAAGATGTAATTAGAATGTTTGAA
TATTTGAGGACTAATTTAAAATGTTTGAAAAATATGGTGTAATTAACTCTTAAAATTTGGACATT
TTATTGAATGGACATTTTTTTGAGTGAATTAGCGGTTCGGATTTATTTTTGACCCACTACTTAAA
TGTAAGGTAAATTACACCAATAGTCATCCAAGTATTCGAATATTTTCATTTTAGTCACTTGAAAA
CAAATAAAATTTCAATTTAGTCACTGTTATTAGAGAAATTGAATTTTTTTAATCACTGTGATGCT
AATGTAGCATTTTCTTTCTTTTGACAAAATAACAAATTTAACCCTCAACATTTATACAACATA
Found at i:2306821 original size:17 final size:18
Alignment explanation
Indices: 2306799--2306838 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2306789 CAAATGGAAC
*
2306799 AAAAATTTAAAAA-AAAT
1 AAAAATTCAAAAATAAAT
*
2306816 AAAAATTCAAAAATACAT
1 AAAAATTCAAAAATAAAT
2306834 AAAAA
1 AAAAA
2306839 CAAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATTCAAAAATAAAT
Found at i:2308082 original size:18 final size:18
Alignment explanation
Indices: 2308059--2308096 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2308049 TAAATTTTTA
2308059 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
2308077 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
2308095 AA
1 AA
2308097 AATTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:2311401 original size:19 final size:20
Alignment explanation
Indices: 2311369--2311407 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2311359 AAACTCGATA
2311369 TTTTTTTTACTTCTTCAATTC
1 TTTTTTTTA-TTCTTCAATTC
*
2311390 TTTTTTTT-TTCTTGAATT
1 TTTTTTTTATTCTTCAATT
2311408 ATAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTTTATTCTTCAATTC
Found at i:2314003 original size:51 final size:51
Alignment explanation
Indices: 2313890--2314004 Score: 124
Period size: 51 Copynumber: 2.3 Consensus size: 51
2313880 CACATAATTG
* * *
2313890 TTGACAAAATGTGTAAATATTGCTGGATAAATTTGTTAAATTAGGATCAAA
1 TTGACAAAATGTGAAAATATTGCTGGATAAATTTGTTAAATCAAGATCAAA
*** * * * *
2313941 TTGATGGAATGTGAAAATGTTG-TGGGTTATATTTGTTATATCAAGATCAAA
1 TTGACAAAATGTGAAAATATTGCT-GGATAAATTTGTTAAATCAAGATCAAA
2313992 TTGACAAAATGTG
1 TTGACAAAATGTG
2314005 TAACCTTTGA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
50 1 0.02
51 49 0.98
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (51 bp):
TTGACAAAATGTGAAAATATTGCTGGATAAATTTGTTAAATCAAGATCAAA
Found at i:2321167 original size:17 final size:18
Alignment explanation
Indices: 2321147--2321186 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2321137 TAAATGGAAC
*
2321147 AAAAATTTAAAAA-AAAT
1 AAAAATTCAAAAATAAAT
*
2321164 AAAAATTCAAAAATACAT
1 AAAAATTCAAAAATAAAT
2321182 AAAAA
1 AAAAA
2321187 CAAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATTCAAAAATAAAT
Found at i:2327382 original size:101 final size:101
Alignment explanation
Indices: 2327211--2327419 Score: 283
Period size: 101 Copynumber: 2.1 Consensus size: 101
2327201 GAGGCACTGG
* * * *
2327211 GTGCCAATTTATTTCGGTTTAACCGATGAGGCACTAGGTGTCAACTTTATTTTAAAGCATGACGC
1 GTGCCAATTTACTTCGGTTTAACCGATGAGACACTAGGTGTCAACCTTATTTTAAAGCAGGACGC
**
2327276 AATTTATTACTTTGGATTTATCCGATGAGGCACAAA
66 AATTTATTACTTCAGATTTATCCGATGAGGCACAAA
* * ** * *
2327312 GTGCCAATTTACTTCGGTTTAATCGATGAGACACTGGGTGTCAACCTTATTTTAGTGCAGGGCGT
1 GTGCCAATTTACTTCGGTTTAACCGATGAGACACTAGGTGTCAACCTTATTTTAAAGCAGGACGC
* * *
2327377 GATTTATTACTTCAGATTTATTCGATGAGGCACAGA
66 AATTTATTACTTCAGATTTATCCGATGAGGCACAAA
2327413 GTGCCAA
1 GTGCCAA
2327420 ACCGATGTGA
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (101 bp):
GTGCCAATTTACTTCGGTTTAACCGATGAGACACTAGGTGTCAACCTTATTTTAAAGCAGGACGC
AATTTATTACTTCAGATTTATCCGATGAGGCACAAA
Found at i:2339643 original size:32 final size:30
Alignment explanation
Indices: 2339607--2339668 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
2339597 CCTCGAATTT
*
2339607 TTCAAG-TTCAAATTATTTTAGATTCAAATCAA
1 TTCAAGTTTC-AATTA-TTTAAATT-AAATCAA
2339639 TTCAAGTTTCAATTATTTAAATTAAATCAA
1 TTCAAGTTTCAATTATTTAAATTAAATCAA
2339669 AATTGAGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 7 0.25
31 7 0.25
32 11 0.39
33 3 0.11
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (30 bp):
TTCAAGTTTCAATTATTTAAATTAAATCAA
Found at i:2343702 original size:92 final size:93
Alignment explanation
Indices: 2343576--2343757 Score: 285
Period size: 92 Copynumber: 2.0 Consensus size: 93
2343566 AATCAAATTA
* * * **
2343576 AAAACAAGGAAAATGACCGTCCAATTCCAAATTCTGAAGTGAACAACGGCCAAAGAGATGGAAAC
1 AAAACAAGGAAAAAGACCCTCCAATTCCAAATTCTCAAGTGAACAAAAGCCAAAGAGATGGAAAC
*
2343641 AGATCTGTAAAAAATTGG-AAAAAATCT
66 AGAGCTGTAAAAAATTGGCAAAAAATCT
* *
2343668 AAAACAAGGAAAAAGACCCTCCAATTCCAAATTCTCAAGTGAAGAAAAGCGAAAGAGATGGAAAC
1 AAAACAAGGAAAAAGACCCTCCAATTCCAAATTCTCAAGTGAACAAAAGCCAAAGAGATGGAAAC
2343733 AGAGCTGTAAAAAATTGGCAAAAAA
66 AGAGCTGTAAAAAATTGGCAAAAAA
2343758 ATAAAGAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 75 0.93
93 6 0.07
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.15
Consensus pattern (93 bp):
AAAACAAGGAAAAAGACCCTCCAATTCCAAATTCTCAAGTGAACAAAAGCCAAAGAGATGGAAAC
AGAGCTGTAAAAAATTGGCAAAAAATCT
Found at i:2344343 original size:16 final size:17
Alignment explanation
Indices: 2344315--2344349 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2344305 AAATCATTTC
2344315 AAGTTTGATTTATTTTA
1 AAGTTTGATTTATTTTA
2344332 AAGTTTGA-TTATTTTA
1 AAGTTTGATTTATTTTA
2344348 AA
1 AA
2344350 TTTAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (17 bp):
AAGTTTGATTTATTTTA
Found at i:2345777 original size:124 final size:125
Alignment explanation
Indices: 2345550--2345789 Score: 349
Period size: 124 Copynumber: 1.9 Consensus size: 125
2345540 TCTACATAGA
*
2345550 GAAAAGAGTTGCATATGCTGAGATTCGACCTTGCTACTTCTTAAAAGAGAATGCTATGAACCTAT
1 GAAAAGAGTTGCATATGCTGAGATTCGACCTTGCTA--TCTTAAAAGAGAATGCTATGAAACTAT
** * *
2345615 CAAACTTGTTTTTCTGGACCTTTCATTTTCTTATAGTACTCGTACATGAAACTTTGACTCTC
64 CAAACTTGTTTTTCCAGACCTTTCATTTTCTTAAAGTACTCATACATGAAACTTTGACTCTC
* * *
2345677 GAAAAGGGTTGCATATGTTGAGATTCGACTTTGCTA-CTTAAAAGAGAATGCTATGAAACTATCA
1 GAAAAGAGTTGCATATGCTGAGATTCGACCTTGCTATCTTAAAAGAGAATGCTATGAAACTATCA
* *
2345741 AGCTTGTTTTTCCAGACCATTT-ATTTTCTTAAAGTACTCATATATGAAA
66 AACTTGTTTTTCCAGACC-TTTCATTTTCTTAAAGTACTCATACATGAAA
2345790 AACTTTCGGA
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
124 66 0.65
125 3 0.03
127 33 0.32
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (125 bp):
GAAAAGAGTTGCATATGCTGAGATTCGACCTTGCTATCTTAAAAGAGAATGCTATGAAACTATCA
AACTTGTTTTTCCAGACCTTTCATTTTCTTAAAGTACTCATACATGAAACTTTGACTCTC
Found at i:2350314 original size:20 final size:20
Alignment explanation
Indices: 2350289--2350326 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2350279 TTATATACAA
*
2350289 ACATATTTAAAATTTAATTC
1 ACATATTTAAAATATAATTC
*
2350309 ACATATTTTAAATATAAT
1 ACATATTTAAAATATAAT
2350327 CCACGTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
ACATATTTAAAATATAATTC
Found at i:2351051 original size:21 final size:21
Alignment explanation
Indices: 2351025--2351064 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2351015 AGACCCAGAA
2351025 GGAGACCTTGAAT-ATCTACCT
1 GGAGACCTTG-ATGATCTACCT
2351046 GGAGACCTTGATGATCTAC
1 GGAGACCTTGATGATCTAC
2351065 ACAGAGATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
GGAGACCTTGATGATCTACCT
Found at i:2358685 original size:14 final size:14
Alignment explanation
Indices: 2358662--2358695 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2358652 TACAATATCT
*
2358662 AAATAATAACAATA
1 AAATAGTAACAATA
2358676 AAATAGTAACAATA
1 AAATAGTAACAATA
*
2358690 TAATAG
1 AAATAG
2358696 CAAAACATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:2359661 original size:21 final size:21
Alignment explanation
Indices: 2359637--2359685 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2359627 TCAACATATA
2359637 GAAATAAATATATATATT-GTT
1 GAAATAAAT-TATATATTAGTT
*
2359658 GAAATTAATTATATATTAGTT
1 GAAATAAATTATATATTAGTT
*
2359679 AAAATAA
1 GAAATAA
2359686 TGAAAAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (21 bp):
GAAATAAATTATATATTAGTT
Found at i:2359686 original size:20 final size:20
Alignment explanation
Indices: 2359647--2359686 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2359637 GAAATAAATA
*
2359647 TATATATTGTTGAAATTAAT
1 TATATATTGTTGAAAATAAT
2359667 TATATATTAGTT-AAAATAAT
1 TATATATT-GTTGAAAATAAT
2359687 GAAAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
TATATATTGTTGAAAATAAT
Found at i:2360078 original size:16 final size:16
Alignment explanation
Indices: 2360053--2360086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2360043 ATAAGTTTTC
*
2360053 ATATAGTTTTTTATAA
1 ATATAGTTTTATATAA
*
2360069 ATATATTTTTATATAA
1 ATATAGTTTTATATAA
2360085 AT
1 AT
2360087 CTTTATGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATATAGTTTTATATAA
Found at i:2362367 original size:2 final size:2
Alignment explanation
Indices: 2362360--2362391 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2362350 AAATAACTGC
2362360 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
2362392 GTAAAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2366243 original size:18 final size:17
Alignment explanation
Indices: 2366224--2366269 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
2366214 TCCCTTCTCT
2366224 TCTCCTTTTCCCTCGCC
1 TCTCCTTTTCCCTCGCC
*
2366241 T-T-CTTTTCCCTCTCCC
1 TCTCCTTTTCCCTC-GCC
*
2366257 TCTCTTTTTCCCT
1 TCTCCTTTTCCCT
2366270 TTCCCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 10 0.42
16 4 0.17
17 2 0.08
18 8 0.33
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (17 bp):
TCTCCTTTTCCCTCGCC
Found at i:2366272 original size:6 final size:6
Alignment explanation
Indices: 2366263--2366370 Score: 94
Period size: 6 Copynumber: 17.8 Consensus size: 6
2366253 TCCCTCTCTT
* * * * *
2366263 TTTCCC TTTCCC TTTCTC TTTCTC TTTCTC TTTCTC TTTCCC --TCTC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC
* * * *
2366309 TCTCCC TTTCTC TCTCTC TTTCCC TTTCCC TTTCCC TTTCACGC TTTTCCC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTC-C-C -TTTCCC
2366360 TTTCCC TTTCC
1 TTTCCC TTTCC
2366371 TTCTCCCTAG
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
4 3 0.03
6 77 0.88
7 2 0.02
8 2 0.02
9 4 0.05
ACGTcount: A:0.01, C:0.44, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTCCC
Found at i:2366274 original size:18 final size:17
Alignment explanation
Indices: 2366242--2366339 Score: 73
Period size: 18 Copynumber: 5.9 Consensus size: 17
2366232 TCCCTCGCCT
*
2366242 TCTTTTCCCTCTCCCTC
1 TCTTTTCCCTTTCCCTC
*
2366259 TCTTTTTCCCTTTCCCTT
1 TC-TTTTCCCTTTCCCTC
*
2366277 TCTCTTTCTC-TT---TC
1 TCT-TTTCCCTTTCCCTC
*
2366291 TC-TTTCTCTTTCCCTC
1 TCTTTTCCCTTTCCCTC
* *
2366307 TC-TCTCCCTTTCTCTC
1 TCTTTTCCCTTTCCCTC
2366323 TCTCTTTCCCTTTCCCT
1 TCT-TTTCCCTTTCCCT
2366340 TTCCCTTTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.09
13 2 0.03
14 3 0.05
16 17 0.27
17 5 0.08
18 31 0.48
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
TCTTTTCCCTTTCCCTC
Found at i:2366377 original size:12 final size:11
Alignment explanation
Indices: 2366263--2366433 Score: 78
Period size: 12 Copynumber: 14.5 Consensus size: 11
2366253 TCCCTCTCTT
2366263 TTTCCCTTTCCC
1 TTTCCCTTT-CC
*
2366275 TTTCTCTTTCTC
1 TTTCCCTTTC-C
*
2366287 TTTCTCTTTCTC
1 TTTCCCTTTC-C
*
2366299 TTTCCCTCT-C
1 TTTCCCTTTCC
*
2366309 TCTCCCTTTCTC
1 TTTCCCTTTC-C
* *
2366321 TCTCTCTTTCCC
1 TTTCCCTTT-CC
2366333 TTTCCCTTTCCC
1 TTTCCCTTT-CC
2366345 TTTCACGCTTTTCCC
1 TTTC-C-C-TTT-CC
2366360 TTTCCCTTTCC
1 TTTCCCTTTCC
**
2366371 TTCTCCCTAGCTC
1 TT-TCCCTTTC-C
*
2366384 TTTCCCTCTCC
1 TTTCCCTTTCC
*
2366395 TTTTCCTTCTCTC
1 TTTCCCTT-TC-C
* *
2366408 GTTCCCTAT-C
1 TTTCCCTTTCC
2366418 TTT-CCTTTCC
1 TTTCCCTTTCC
*
2366428 CTTCCC
1 TTTCCC
2366434 CTATCTCGAT
Statistics
Matches: 126, Mismatches: 20, Indels: 27
0.73 0.12 0.16
Matches are distributed among these distances:
9 4 0.03
10 14 0.11
11 14 0.11
12 70 0.56
13 12 0.10
14 2 0.02
15 10 0.08
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.51
Consensus pattern (11 bp):
TTTCCCTTTCC
Found at i:2366736 original size:16 final size:18
Alignment explanation
Indices: 2366711--2366745 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2366701 AACTAAATTA
2366711 AAAAATGAAATTAA-AAC
1 AAAAATGAAATTAAGAAC
2366728 AAAAA-GAAATTAAGAAC
1 AAAAATGAAATTAAGAAC
2366745 A
1 A
2366746 GTGGAACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAATGAAATTAAGAAC
Found at i:2367067 original size:42 final size:42
Alignment explanation
Indices: 2367020--2367100 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
2367010 TTTATACTTA
* *
2367020 AATTTGA-CATTTTTTTTAAGTTGGTATTTAATTTTTTTTGAG
1 AATTTGATC-TTTTTCTTAAGTTGATATTTAATTTTTTTTGAG
*
2367062 AATTTGATTCTTTTTCTTAATTTGATATTTAATTTTTTT
1 AATTTGA-TCTTTTTCTTAAGTTGATATTTAATTTTTTT
2367101 CGATGTACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 7 0.21
43 26 0.76
44 1 0.03
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (42 bp):
AATTTGATCTTTTTCTTAAGTTGATATTTAATTTTTTTTGAG
Found at i:2367271 original size:21 final size:21
Alignment explanation
Indices: 2367243--2367299 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
2367233 CAATTACTTT
* *
2367243 TAATTTTATTTATTTAATTAA
1 TAATTTTATTAATTTAAATAA
* *
2367264 TTATTTTATTAATTAAAATAA
1 TAATTTTATTAATTTAAATAA
2367285 TAATTTT-TTAATTTA
1 TAATTTTATTAATTTA
2367300 GGTTTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTTTATTAATTTAAATAA
Found at i:2375551 original size:14 final size:13
Alignment explanation
Indices: 2375530--2375563 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2375520 TTTCAAAACC
2375530 TAAATTATATTAT
1 TAAATTATATTAT
*
2375543 TACAATTATATTTT
1 TA-AATTATATTAT
2375557 TAAATTA
1 TAAATTA
2375564 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAATTATATTAT
Found at i:2376729 original size:21 final size:23
Alignment explanation
Indices: 2376705--2376748 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2376695 ACATAACAAT
2376705 TATAA-TTTATAAATTT-AAATA
1 TATAATTTTATAAATTTGAAATA
*
2376726 TATAATTTTATATATTTGAAATA
1 TATAATTTTATAAATTTGAAATA
2376749 AATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATAATTTTATAAATTTGAAATA
Found at i:2389914 original size:15 final size:17
Alignment explanation
Indices: 2389886--2389922 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2389876 AAATTTTAAG
2389886 GATTTGAGGAAGTAAAA
1 GATTTGAGGAAGTAAAA
2389903 -ATTTGA-GAAGTAAAA
1 GATTTGAGGAAGTAAAA
2389918 GATTT
1 GATTT
2389923 TGAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
GATTTGAGGAAGTAAAA
Found at i:2392087 original size:11 final size:13
Alignment explanation
Indices: 2392059--2392091 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
2392049 AATAATTATG
2392059 ATATTATAATTAA
1 ATATTATAATTAA
2392072 ATATTATAA-T-A
1 ATATTATAATTAA
2392083 ATATTATAA
1 ATATTATAA
2392092 CGTGAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 1 0.05
13 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTATAATTAA
Found at i:2395440 original size:13 final size:11
Alignment explanation
Indices: 2395402--2395452 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
2395392 TTTTTTTCAA
2395402 AAAAAAAAGAT-
1 AAAAAAAA-ATC
2395413 AATAAAAAAATC
1 AA-AAAAAAATC
2395425 AAAAAAAAATC
1 AAAAAAAAATC
**
2395436 CCAAAAAAAT-
1 AAAAAAAAATC
2395446 AAAAAAA
1 AAAAAAA
2395453 GTAAGTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 5 0.15
11 21 0.62
12 8 0.24
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:2399253 original size:34 final size:34
Alignment explanation
Indices: 2399210--2399281 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
2399200 GCTTATGGAT
*
2399210 AAAATTTGAAATTAGTTATTGTCAATGTAAAGAA
1 AAAATTTGAAATTAGTCATTGTCAATGTAAAGAA
2399244 AAAATTTGAAATTAGTCATTGTCAATGTAAAGAA
1 AAAATTTGAAATTAGTCATTGTCAATGTAAAGAA
2399278 AAAA
1 AAAA
2399282 CTAAAATTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (34 bp):
AAAATTTGAAATTAGTCATTGTCAATGTAAAGAA
Found at i:2401530 original size:13 final size:13
Alignment explanation
Indices: 2401509--2401542 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2401499 TAAATAATAT
2401509 AATAATAATCCTA
1 AATAATAATCCTA
*
2401522 AATATTAATCCTA
1 AATAATAATCCTA
*
2401535 AAAAATAA
1 AATAATAA
2401543 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:2405895 original size:12 final size:12
Alignment explanation
Indices: 2405878--2405903 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2405868 TGGTAGCTCA
2405878 TGACCCAAATGT
1 TGACCCAAATGT
2405890 TGACCCAAATGT
1 TGACCCAAATGT
2405902 TG
1 TG
2405904 GGGGAGGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (12 bp):
TGACCCAAATGT
Found at i:2414231 original size:16 final size:17
Alignment explanation
Indices: 2414210--2414245 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2414200 TTTGTCGAAT
2414210 AAAAATAATGACA-AAA
1 AAAAATAATGACATAAA
*
2414226 AAAAATAATGTCATAAA
1 AAAAATAATGACATAAA
2414243 AAA
1 AAA
2414246 TAGTATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAAATAATGACATAAA
Found at i:2425210 original size:63 final size:65
Alignment explanation
Indices: 2425121--2425294 Score: 207
Period size: 63 Copynumber: 2.7 Consensus size: 65
2425111 TATTTTGATT
*
2425121 ATTTATTTATTTATATTCATAAAATAAT-A-AATAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAGAATAAATAATAAAACAAAATAAATATTATTTTAC
* * *
2425184 ATTTATTTATTTATGTTCATACAATAATAAATGAATAAATAATAAAATAAAATAAATATTATTTT
1 ATTTATTTATTTATATTCATAAAATAAT-AA-GAATAAATAATAAAACAAAATAAATATTATTTT
2425249 --
64 AC
* *
2425249 A--TATTTATTTATATTTATAAAAATAATAATAAATAAATAAATAAAA
1 ATTTATTTATTTATATTCAT-AAAATAATAA-GAATAAAT-AATAAAA
2425295 AGAATAAGAA
Statistics
Matches: 97, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
63 51 0.53
64 14 0.14
65 2 0.02
67 30 0.31
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (65 bp):
ATTTATTTATTTATATTCATAAAATAATAAGAATAAATAATAAAACAAAATAAATATTATTTTAC
Found at i:2425227 original size:67 final size:63
Alignment explanation
Indices: 2425121--2425294 Score: 208
Period size: 67 Copynumber: 2.7 Consensus size: 63
2425111 TATTTTGATT
*
2425121 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATTATTTTAC
* * *
2425184 ATTTATTTATTTATGTTCATACAATAATAAATGAATAAATAATAAAATAAAATAAATATTATTTT
1 ATTTATTTATTTATATTCAT--AA-AAT-AATAAATAAATAATAAAACAAAATAAATATTATTTT
*
2425249 AT
62 AC
* *
2425251 ATTTATTTATATT-TA-TAAAAATAATAATAAATAAATAAATAAAA
1 ATTTATTTAT-TTATATTCATAA-AATAATAAATAAAT-AATAAAA
2425295 AGAATAAGAA
Statistics
Matches: 96, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
63 29 0.30
64 13 0.14
65 2 0.02
66 5 0.05
67 45 0.47
68 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (63 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATTATTTTAC
Found at i:2428054 original size:11 final size:11
Alignment explanation
Indices: 2428038--2428068 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2428028 TTAACTATGC
2428038 AAATTTAATAT
1 AAATTTAATAT
*
2428049 AAATTTATTAT
1 AAATTTAATAT
2428060 AAATTTAAT
1 AAATTTAAT
2428069 TCCCAGAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTTAATAT
Found at i:2437127 original size:29 final size:30
Alignment explanation
Indices: 2437083--2437140 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
2437073 GAACCCACCA
* *
2437083 TTTTTTTTTTTAAATTGGGTCCACTATTTG
1 TTTTTTTTCTTAAATTGGATCCACTATTTG
2437113 TTTTTTTTCTT-AATTGGATCCACTATTT
1 TTTTTTTTCTTAAATTGGATCCACTATTT
2437141 ATGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTTTTTCTTAAATTGGATCCACTATTTG
Found at i:2439284 original size:22 final size:22
Alignment explanation
Indices: 2439259--2439300 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2439249 AAATGATACC
2439259 AAAACAGT-GAGAAAACAACAAG
1 AAAACAGTAG-GAAAACAACAAG
*
2439281 AAAATAGTAGGAAAACAACA
1 AAAACAGTAGGAAAACAACA
2439301 TATTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.64, C:0.12, G:0.17, T:0.07
Consensus pattern (22 bp):
AAAACAGTAGGAAAACAACAAG
Found at i:2446971 original size:15 final size:15
Alignment explanation
Indices: 2446947--2446976 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2446937 AACCCACATT
2446947 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
2446962 CATTTGAACCAAACC
1 CATTTAAACCAAACC
2446977 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:2447039 original size:21 final size:21
Alignment explanation
Indices: 2447013--2447060 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2447003 AGTCAAACCA
2447013 TTGACTGGCGTTGACCGACCG
1 TTGACTGGCGTTGACCGACCG
* **
2447034 TTGACTGGTGTTGATTGACCG
1 TTGACTGGCGTTGACCGACCG
2447055 TTGACT
1 TTGACT
2447061 TTTTTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGACTGGCGTTGACCGACCG
Found at i:2448115 original size:3 final size:3
Alignment explanation
Indices: 2448103--2448156 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
2448093 TATTCTATTC
2448103 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2448150 TAT TAT T
1 TAT TAT T
2448157 TTGGGATGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:2453859 original size:15 final size:15
Alignment explanation
Indices: 2453835--2453864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2453825 AACCCACATT
2453835 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
2453850 CATTTGAACCAAACC
1 CATTTAAACCAAACC
2453865 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:2460711 original size:17 final size:17
Alignment explanation
Indices: 2460689--2460727 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2460679 AGGTGGAGAA
* * *
2460689 CTTGTTTGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
2460706 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
2460723 CTTGT
1 CTTGT
2460728 CAAAGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:2469269 original size:29 final size:30
Alignment explanation
Indices: 2469226--2469442 Score: 118
Period size: 30 Copynumber: 7.3 Consensus size: 30
2469216 ACCCGAGGGC
*
2469226 AAAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAAATGGTAATTTTGGAGAAATCGGGGTT
* * *
2469256 AAAAATGG-AATTTT--AAAAGATTAGGGGGT
1 AAAAATGGTAATTTTGGAGAA-A-TCGGGGTT
* *
2469285 -AAAATGGTAATTTTTGGTGAAATTGGGGTT
1 AAAAATGGTAA-TTTTGGAGAAATCGGGGTT
* *
2469315 AAAAATGG-AATTTT--AGAAGCTTCGGGGGT
1 AAAAATGGTAATTTTGGAGAA--ATCGGGGTT
*
2469344 -AAAATGGTAATTTTTGGCA-AATTCGGGGTT
1 AAAAATGGTAA-TTTTGG-AGAAATCGGGGTT
* * *
2469374 AAAAATAG-AATTTT--AGAAGCTTCGGGGGGGGT
1 AAAAATGGTAATTTTGGAGAA--ATC---GGGGTT
*
2469406 -AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAAATGGTAATTTTGGAGAAATCGGGGTT
2469435 AAAAATGG
1 AAAAATGG
2469443 GATTTAGGAA
Statistics
Matches: 143, Mismatches: 19, Indels: 50
0.67 0.09 0.24
Matches are distributed among these distances:
26 1 0.01
27 7 0.05
28 15 0.10
29 38 0.27
30 41 0.29
31 20 0.14
32 17 0.12
33 1 0.01
34 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (30 bp):
AAAAATGGTAATTTTGGAGAAATCGGGGTT
Found at i:2469300 original size:59 final size:58
Alignment explanation
Indices: 2469227--2469447 Score: 309
Period size: 59 Copynumber: 3.7 Consensus size: 58
2469217 CCCGAGGGCA
* *
2469227 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTAGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTAGGGGGT
* *
2469285 AAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTAGGGGGT
* * *
2469344 AAAATGGTAATTTTTGG-CAAATTCGGGGTTAAAAATAGAATTTTAGAAGCTTCGGGGGGGGT
1 AAAATGGTAA-TTTTGGTGAAA-TCGGGGTTAAAAATGGAATTTTAGAAGCTT---AGGGGGT
*
2469406 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGGATTT
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTT
2469448 AGGAAAGTTT
Statistics
Matches: 146, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
58 13 0.09
59 89 0.61
61 25 0.17
62 19 0.13
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTAGGGGGT
Done.