Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 4 of 21
Found at i:373576 original size:42 final size:42
Alignment explanation
Indices: 373529--373611 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
373519 TTACTTTCAT
*
373529 ATGTAAATTTTATTAAATTTTATAATTACAATATGTGAAGTG
1 ATGTAAATTTTATTAAATTTTATAATTACAATATATGAAGTG
* *
373571 ATGTAAATTTTATTAATTTTTATAATTATAATATATGAAGT
1 ATGTAAATTTTATTAAATTTTATAATTACAATATATGAAGT
373612 AATTGTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (42 bp):
ATGTAAATTTTATTAAATTTTATAATTACAATATATGAAGTG
Found at i:375776 original size:35 final size:35
Alignment explanation
Indices: 375730--375800 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
375720 GTCGGGGTAG
375730 TAATTCCTTCTCCACTTTGGAGTAGGATTCTCCTT
1 TAATTCCTTCTCCACTTTGGAGTAGGATTCTCCTT
375765 TAATTCCTTCTCCACTTTGGAGTAGGATTCTCCTT
1 TAATTCCTTCTCCACTTTGGAGTAGGATTCTCCTT
375800 T
1 T
375801 CTTTTCATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (35 bp):
TAATTCCTTCTCCACTTTGGAGTAGGATTCTCCTT
Found at i:378520 original size:21 final size:21
Alignment explanation
Indices: 378494--378538 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
378484 CAAAATACAC
* *
378494 AAAGGGATA-GATTTCTGTGTA
1 AAAGGGA-ACGATCTCTATGTA
378515 AAAGGGAACGATCTCTATGTA
1 AAAGGGAACGATCTCTATGTA
378536 AAA
1 AAA
378539 AAAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (21 bp):
AAAGGGAACGATCTCTATGTA
Found at i:379896 original size:24 final size:25
Alignment explanation
Indices: 379843--379900 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
379833 TTTTATTTAT
379843 ATTTT-ATTATTTAATATAAATATA
1 ATTTTAATTATTTAATATAAATATA
*
379867 ATTTTTAATTATTT-AT-TATATATA
1 A-TTTTAATTATTTAATATAAATATA
379891 CATTTTAATT
1 -ATTTTAATT
379901 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 16 0.53
25 7 0.23
26 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTAATTATTTAATATAAATATA
Found at i:380343 original size:18 final size:16
Alignment explanation
Indices: 380304--380339 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
380294 ATATTTATGA
380304 ATATAA-TTTTAATAT
1 ATATAATTTTTAATAT
*
380319 ATATAATTTTTAGTAT
1 ATATAATTTTTAATAT
380335 ATATA
1 ATATA
380340 TAATATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATAATTTTTAATAT
Found at i:380758 original size:19 final size:19
Alignment explanation
Indices: 380698--380759 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
380688 TATAAATTTA
*
380698 AATTAATTTGATTTAAAT-T
1 AATT-ATTTTATTTAAATAT
380717 -ATTATTTT-TTAATAAA-AT
1 AATTATTTTATT--TAAATAT
*
380735 TATTATTTTATTTAAATAT
1 AATTATTTTATTTAAATAT
380754 AATTAT
1 AATTAT
380760 AAAATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 2 0.06
17 4 0.11
18 12 0.34
19 15 0.43
20 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTATTTTATTTAAATAT
Found at i:383265 original size:2 final size:2
Alignment explanation
Indices: 383258--383291 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
383248 CAGCCATACC
383258 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
383292 GGGTTAAATA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:387455 original size:12 final size:12
Alignment explanation
Indices: 387438--387464 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
387428 TAAATAAATA
387438 AATCATAAAACC
1 AATCATAAAACC
387450 AATCATAAAACC
1 AATCATAAAACC
387462 AAT
1 AAT
387465 GCAGGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (12 bp):
AATCATAAAACC
Found at i:387887 original size:38 final size:37
Alignment explanation
Indices: 387832--387906 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
387822 TTTTTTTCTT
* *
387832 TTCACAGCTTGAAGAAGAAATTGAAACCCTAATTAAAC
1 TTCACAGCTGGAAGAAGAAAATG-AACCCTAATTAAAC
* *
387870 TTCACAGCTGGAGGAAGAAAATGAAGCCTAATTAAAC
1 TTCACAGCTGGAAGAAGAAAATGAACCCTAATTAAAC
387907 CCAAATAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 13 0.39
38 20 0.61
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (37 bp):
TTCACAGCTGGAAGAAGAAAATGAACCCTAATTAAAC
Found at i:388102 original size:15 final size:15
Alignment explanation
Indices: 388084--388143 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
388074 TAATTTTTTA
388084 AATTTAAATTAATTT
1 AATTTAAATTAATTT
388099 AATTTAAATTATTATTT
1 AATTTAAATTA--ATTT
*
388116 AATAATAAATT--TTT
1 AAT-TTAAATTAATTT
388130 -ATTTAAATTTAATT
1 AATTTAAA-TTAATT
388144 ATAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
12 4 0.11
13 4 0.11
14 3 0.08
15 13 0.35
17 7 0.19
18 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTAAATTAATTT
Found at i:388157 original size:21 final size:21
Alignment explanation
Indices: 388133--388172 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
388123 AATTTTTATT
388133 TAAAT-TTAATTATAAAAAAAA
1 TAAATATTAA-TATAAAAAAAA
388154 TAAATATTAATATAAAAAA
1 TAAATATTAATATAAAAAA
388173 TAATGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATATTAATATAAAAAAAA
Found at i:388313 original size:21 final size:20
Alignment explanation
Indices: 388289--388335 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
388279 ATTTAATTTA
* *
388289 TAAATATTTTTATTTTATATT
1 TAAATATTTTAAATTT-TATT
388310 TAAATTATTTTAAATTTTATT
1 TAAA-TATTTTAAATTTTATT
388331 TAAAT
1 TAAAT
388336 TAAATTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TAAATATTTTAAATTTTATT
Found at i:388317 original size:11 final size:11
Alignment explanation
Indices: 388303--388337 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
388293 TATTTTTATT
388303 TTATATTTAAA
1 TTATATTTAAA
388314 TTAT-TTTAAA
1 TTATATTTAAA
*
388324 TTTTATTTAAA
1 TTATATTTAAA
388335 TTA
1 TTA
388338 AATTCGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTATATTTAAA
Found at i:388336 original size:21 final size:21
Alignment explanation
Indices: 388278--388337 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
388268 TTTAGATCGT
* * *
388278 AATTTAATTTATAAATATTTTT
1 AATTTTATTTA-AATTATTTTA
*
388300 ATTTTATATTTAAATTATTTTA
1 AATTT-TATTTAAATTATTTTA
388322 AATTTTATTTAAATTA
1 AATTTTATTTAAATTA
388338 AATTCGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 11 0.34
22 16 0.50
23 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTATTTAAATTATTTTA
Found at i:389295 original size:27 final size:26
Alignment explanation
Indices: 389265--389329 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
389255 ATAAAATAAT
* * *
389265 AAAACAAAAATAATTAAGAAAATTTTAA
1 AAAATAAAAA-AATT-AGAAAAATTCAA
389293 AAAATAAAAAAATTAGAAAAATTCAAA
1 AAAATAAAAAAATTAGAAAAATTC-AA
389320 AAAATAAAAA
1 AAAATAAAAA
389330 TAAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.24
27 16 0.48
28 9 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (26 bp):
AAAATAAAAAAATTAGAAAAATTCAA
Found at i:389980 original size:22 final size:24
Alignment explanation
Indices: 389953--389996 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
389943 TATAAATTTT
389953 AATAAA-TTAATA-ATTTATATTA
1 AATAAATTTAATATATTTATATTA
389975 AATAAATTTAATATATTTATAT
1 AATAAATTTAATATATTTATAT
389997 ATTTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATAAATTTAATATATTTATATTA
Found at i:389981 original size:32 final size:32
Alignment explanation
Indices: 389944--390006 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
389934 ATATATTTTT
389944 ATAAATTTTAATAAATTAATA-ATTTATATTAA
1 ATAAA-TTTAATAAATTAATATATTTATATTAA
* *
389976 ATAAATTTAATATATTTATATATTTATATTA
1 ATAAATTTAATAAATTAATATATTTATATTA
390007 TATTTGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATAAATTTAATAAATTAATATATTTATATTAA
Found at i:390032 original size:23 final size:25
Alignment explanation
Indices: 390002--390052 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
389992 TATATATTTA
*
390002 TATTATATT-TGTGTT-ATTTTTTT
1 TATTATATTGTATGTTAATTTTTTT
*
390025 TATTATATTGTATTTTAATTTTTTT
1 TATTATATTGTATGTTAATTTTTTT
390050 TAT
1 TAT
390053 CATGTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 4 0.17
25 11 0.46
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (25 bp):
TATTATATTGTATGTTAATTTTTTT
Found at i:391003 original size:24 final size:23
Alignment explanation
Indices: 390970--391032 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
390960 TTTTTCTCCA
* *
390970 TTTTTGCTTTC-TTTCTCTCTCTTT
1 TTTTTTCTTTCTTTTC-CT-TCCTT
390994 TTTTTTCTTTCCTTTTCCTTCCTT
1 TTTTTTCTTT-CTTTTCCTTCCTT
*
391018 TTCTTTCTTTCTTTT
1 TTTTTTCTTTCTTTT
391033 TCTTTATTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 5 0.15
24 22 0.65
25 3 0.09
26 4 0.12
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTTCTTTCTTTTCCTTCCTT
Found at i:392134 original size:22 final size:21
Alignment explanation
Indices: 392079--392134 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
392069 GCTTAAAAAA
392079 TAAATAATAAATAATTTTTTAT
1 TAAATAA-AAATAATTTTTTAT
**
392101 TAAATATGAATAATTTTTTAATT
1 TAAATAAAAATAATTTTTT-A-T
392124 TAAA-AAAAATA
1 TAAATAAAAATA
392135 TATAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 12 0.43
23 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAATAAAAATAATTTTTTAT
Found at i:395802 original size:17 final size:16
Alignment explanation
Indices: 395735--395827 Score: 60
Period size: 16 Copynumber: 6.0 Consensus size: 16
395725 TGGAGTGTAG
395735 ATATTTATAT-ATTTT
1 ATATTTATATAATTTT
395750 ATAATGTTATA-AA---T
1 AT-AT-TTATATAATTTT
*
395764 ATATTTA-AAATATTTT
1 ATATTTATATA-ATTTT
395780 ATATTTATATAATTTT
1 ATATTTATATAATTTT
395796 AATATTT-TAATAA-TTT
1 -ATATTTAT-ATAATTTT
395812 ATA-TTATATAAATTTT
1 ATATTTATAT-AATTTT
395828 TAAAAATATA
Statistics
Matches: 63, Mismatches: 1, Indels: 27
0.69 0.01 0.30
Matches are distributed among these distances:
11 1 0.02
12 4 0.06
13 3 0.05
14 7 0.11
15 8 0.13
16 22 0.35
17 18 0.29
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
ATATTTATATAATTTT
Found at i:397053 original size:17 final size:17
Alignment explanation
Indices: 397014--397053 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
397004 TTTTCCACTA
397014 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
*
397031 TATTTCTTTCTTT-TCTC
1 TTTTTCTTTCTTTCT-TC
397048 TTTTTC
1 TTTTTC
397054 CCTCAAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:399610 original size:20 final size:21
Alignment explanation
Indices: 399585--399623 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
399575 AATTCAATTC
399585 AAATAAT-TATTTATTTAATA
1 AAATAATATATTTATTTAATA
*
399605 AAATAATATTTTTATTTAA
1 AAATAATATATTTATTTAA
399624 ATTTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAATATATTTATTTAATA
Found at i:400130 original size:19 final size:18
Alignment explanation
Indices: 400072--400130 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
400062 CAAGATATTG
400072 ATTTTTTA-AATTTTTTAATT
1 ATTTTTTATAA-TTTTT--TT
*
400092 ATTTTTTATGATTATTTTT
1 ATTTTTTATAATT-TTTTT
400111 ATTTTTTATAATTTTCTTT
1 ATTTTTTATAATTTT-TTT
400130 A
1 A
400131 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.06
19 18 0.53
20 10 0.29
21 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTATAATTTTTTT
Found at i:400216 original size:24 final size:23
Alignment explanation
Indices: 400197--400243 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
400187 TTATTTTATT
*
400197 TATTTAATATTTAATAATTTTAAA
1 TATTAAATATTT-ATAATTTTAAA
*
400221 TATTAAATATTTATGATTTTAAA
1 TATTAAATATTTATAATTTTAAA
400244 ACTTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTAAATATTTATAATTTTAAA
Found at i:400402 original size:29 final size:28
Alignment explanation
Indices: 400339--400423 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 28
400329 TGTGTTTAAT
* * *
400339 ATATAAAAAAAT-TTTAAAATATTGATGA
1 ATATAAAATAATATATAAAATATTTAT-A
*
400367 ATTTAAAATAATATATAAAATATTTATA
1 ATATAAAATAATATATAAAATATTTATA
400395 CATATAAATATTAA-A-ATAAAA-ATTTATA
1 -ATATAAA-A-TAATATATAAAATATTTATA
400423 A
1 A
400424 ATCTACTGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 18 0.38
29 24 0.50
30 2 0.04
31 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (28 bp):
ATATAAAATAATATATAAAATATTTATA
Found at i:402438 original size:31 final size:31
Alignment explanation
Indices: 402369--402445 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
402359 TATTTGATCA
* *
402369 ATTTAATTTAAATTATTATTTTTTTGAATTG
1 ATTTAATTTAAATTATTATTTTTATAAATTG
*
402400 ATCTAATTTAAATTATTATTTTTAATAAATT-
1 ATTTAATTTAAATTATTATTTTT-ATAAATTG
*
402431 TTTTAATTT-AATTAT
1 ATTTAATTTAAATTAT
402446 AAAATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 6 0.15
31 29 0.73
32 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (31 bp):
ATTTAATTTAAATTATTATTTTTATAAATTG
Found at i:402840 original size:28 final size:27
Alignment explanation
Indices: 402794--402877 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 27
402784 TTTGTTTATA
*
402794 AAAAATGGTGGTTATTTTGTGTTTGTC
1 AAAAATGGTGGTTATTTTGTATTTGTC
*
402821 AAAAATGGTGGTTTTCTTTGTATTTGTC
1 AAAAATGGTGGTTAT-TTTGTATTTGTC
* * * *
402849 AAATATGGAGGCT-TGTT-TATTTGTC
1 AAAAATGGTGGTTATTTTGTATTTGTC
402874 AAAA
1 AAAA
402878 TTTGTGGCTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
25 11 0.22
26 2 0.04
27 15 0.31
28 21 0.43
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (27 bp):
AAAAATGGTGGTTATTTTGTATTTGTC
Found at i:402958 original size:20 final size:20
Alignment explanation
Indices: 402933--402978 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
402923 AAATAGAGGC
402933 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCCTCCCTCTCAAGTA
* * **
402953 TCCCTCGTCCTTCTCTTGTA
1 TCCCTCCTCCCTCTCAAGTA
402973 TCCCTC
1 TCCCTC
402979 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.48, G:0.07, T:0.37
Consensus pattern (20 bp):
TCCCTCCTCCCTCTCAAGTA
Found at i:406429 original size:594 final size:594
Alignment explanation
Indices: 405301--406468 Score: 2264
Period size: 594 Copynumber: 2.0 Consensus size: 594
405291 CTTTTTATGG
*
405301 GAATCACACATGGAGTGAAGGGATTCTGACTTTGGTGCTTAGACACAAAGAAGATAATCTGTAGC
1 GAATCACACATGGAGTGAAGGGATTCCGACTTTGGTGCTTAGACACAAAGAAGATAATCTGTAGC
405366 AGAGATGTTACCTTTAATGAATCTGCCATGTTGAAGAAGGTAACAATTGGAGTTGTTCAGACAAG
66 AGAGATGTTACCTTTAATGAATCTGCCATGTTGAAGAAGGTAACAATTGGAGTTGTTCAGACAAG
* *
405431 TAGTACTCCGCAGCAGGTGGAGTATACTCCAAAACAAGTAGAGTTTCAACAGGTTAAGATTAGCC
131 TAGTACTCCGCAGCAGGTGGAGTATACTCCAAAACAAGTAGAGTTTCAACAGATAAAGATTAGCC
*
405496 TAGCAAGCAATGCAACTGATTCTCCAATTCAAATGGAAGAGTCACAAGATAAAGAGGTTCAAACC
196 CAGCAAGCAATGCAACTGATTCTCCAATTCAAATGGAAGAGTCACAAGATAAAGAGGTTCAAACC
*
405561 CAAGAACCATTTGAGACACCAGAACCACTTGCAGTTACAAGGCCAATGAGAGAAATTCGTAGACC
261 CAAGAACCATTTGAGACACCAGAACCACTTGCAGTTACAAGGCCAAGGAGAGAAATTCGTAGACC
405626 TGCTCGATTTACTGATATGGTGGCCTATGCCCTTCCAGTTGTTGATGATGATATTCCTATCACTT
326 TGCTCGATTTACTGATATGGTGGCCTATGCCCTTCCAGTTGTTGATGATGATATTCCTATCACTT
405691 ATCAAGAAGCAATGCAAAGCTTAGAAACTGACAAGTGGAAAAACGCCATGGATGAAGAAATGGAG
391 ATCAAGAAGCAATGCAAAGCTTAGAAACTGACAAGTGGAAAAACGCCATGGATGAAGAAATGGAG
405756 TCTCTCCGGAAGAACAACACCTGGGAGTTGACACAATTACCAAAAGGTAAAAAGGCAATTGGATG
456 TCTCTCCGGAAGAACAACACCTGGGAGTTGACACAATTACCAAAAGGTAAAAAGGCAATTGGATG
405821 CAAGTGGGTATTTGTAAAGAAAGATGAATCTTCTAGCAAGAAAGATGTTCGCTATGTTACCTTTA
521 CAAGTGGGTATTTGTAAAGAAAGATGAATCTTCTAGCAAGAAAGATGTTCGCTATGTTACCTTTA
405886 AAGAAAGAT
586 AAGAAAGAT
405895 GAATCACACATGGAGTGAAGGGATTCCGACTTTGGTGCTTAGACACAAAGAAGATAATCTGTAGC
1 GAATCACACATGGAGTGAAGGGATTCCGACTTTGGTGCTTAGACACAAAGAAGATAATCTGTAGC
405960 AGAGATGTTACCTTTAATGAATCTGCCATGTTGAAGAAGGTAACAATTGGAGTTGTTCAGACAAG
66 AGAGATGTTACCTTTAATGAATCTGCCATGTTGAAGAAGGTAACAATTGGAGTTGTTCAGACAAG
*
406025 TAGTACTCCGCAGCAGGTGGAGTATACTCCAAAACAAGTGGAGTTTCAACAGATAAAGATTAGCC
131 TAGTACTCCGCAGCAGGTGGAGTATACTCCAAAACAAGTAGAGTTTCAACAGATAAAGATTAGCC
*
406090 CAGCAAGCAATGCAACTGATTCTCCAATTCAAATGGAAGAGTCACAAGATGAAGAGGTTCAAACC
196 CAGCAAGCAATGCAACTGATTCTCCAATTCAAATGGAAGAGTCACAAGATAAAGAGGTTCAAACC
406155 CAAGAACCATTTGAGACACCAGAACCACTTGCAGTTACAAGGCCAAGGAGAGAAATTCGTAGACC
261 CAAGAACCATTTGAGACACCAGAACCACTTGCAGTTACAAGGCCAAGGAGAGAAATTCGTAGACC
*
406220 TGCTCGATTTCCTGATATGGTGGCCTATGCCCTTCCAGTTGTTGATGATGATATTCCTATCACTT
326 TGCTCGATTTACTGATATGGTGGCCTATGCCCTTCCAGTTGTTGATGATGATATTCCTATCACTT
406285 ATCAAGAAGCAATGCAAAGCTTAGAAACTGACAAGTGGAAAAACGCCATGGATGAAGAAATGGAG
391 ATCAAGAAGCAATGCAAAGCTTAGAAACTGACAAGTGGAAAAACGCCATGGATGAAGAAATGGAG
406350 TCTCTCCGGAAGAACAACACCTGGGAGTTGACACAATTACCAAAAGGTAAAAAGGCAATTGGATG
456 TCTCTCCGGAAGAACAACACCTGGGAGTTGACACAATTACCAAAAGGTAAAAAGGCAATTGGATG
406415 CAAGTGGGTATTTGTAAAGAAAGATGAATCTTCTAGCAAGAAAGATGTTCGCTA
521 CAAGTGGGTATTTGTAAAGAAAGATGAATCTTCTAGCAAGAAAGATGTTCGCTA
406469 CAAGGCAAGA
Statistics
Matches: 566, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
594 566 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (594 bp):
GAATCACACATGGAGTGAAGGGATTCCGACTTTGGTGCTTAGACACAAAGAAGATAATCTGTAGC
AGAGATGTTACCTTTAATGAATCTGCCATGTTGAAGAAGGTAACAATTGGAGTTGTTCAGACAAG
TAGTACTCCGCAGCAGGTGGAGTATACTCCAAAACAAGTAGAGTTTCAACAGATAAAGATTAGCC
CAGCAAGCAATGCAACTGATTCTCCAATTCAAATGGAAGAGTCACAAGATAAAGAGGTTCAAACC
CAAGAACCATTTGAGACACCAGAACCACTTGCAGTTACAAGGCCAAGGAGAGAAATTCGTAGACC
TGCTCGATTTACTGATATGGTGGCCTATGCCCTTCCAGTTGTTGATGATGATATTCCTATCACTT
ATCAAGAAGCAATGCAAAGCTTAGAAACTGACAAGTGGAAAAACGCCATGGATGAAGAAATGGAG
TCTCTCCGGAAGAACAACACCTGGGAGTTGACACAATTACCAAAAGGTAAAAAGGCAATTGGATG
CAAGTGGGTATTTGTAAAGAAAGATGAATCTTCTAGCAAGAAAGATGTTCGCTATGTTACCTTTA
AAGAAAGAT
Found at i:408007 original size:28 final size:27
Alignment explanation
Indices: 407952--408022 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
407942 GCCACCCATT
407952 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
407979 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
408007 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
408023 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:408131 original size:20 final size:20
Alignment explanation
Indices: 408106--408144 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
408096 GGCTCTCTCC
408106 TCCCTCTCAAGTATCCCTCA
1 TCCCTCTCAAGTATCCCTCA
**
408126 TCCCTCTCTTGTATCCCTC
1 TCCCTCTCAAGTATCCCTC
408145 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.46, G:0.05, T:0.36
Consensus pattern (20 bp):
TCCCTCTCAAGTATCCCTCA
Found at i:410938 original size:5 final size:5
Alignment explanation
Indices: 410928--410952 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
410918 TTTCCTTGTC
410928 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
410953 AAATTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:412101 original size:35 final size:37
Alignment explanation
Indices: 412057--412128 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
412047 ATGCGTTCGG
*
412057 TTTAGTTT-AAATT-ATTATTTAATAATAAA-AAATATT
1 TTTAGTTTAAAATTAATTA--TAAAAATAAATAAATATT
412093 TTTA-TTTAAAATTAATTATAAAAATAAATAAATATT
1 TTTAGTTTAAAATTAATTATAAAAATAAATAAATATT
412129 AATATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 12 0.38
36 16 0.50
37 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTAGTTTAAAATTAATTATAAAAATAAATAAATATT
Found at i:412134 original size:22 final size:22
Alignment explanation
Indices: 412099--412140 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
412089 TATTTTTATT
412099 TAAAATTAATTATAAAAATAAA
1 TAAAATTAATTATAAAAATAAA
412121 TAAATATTAA-TATAAAAATA
1 TAAA-ATTAATTATAAAAATA
412141 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTAATTATAAAAATAAA
Found at i:412340 original size:31 final size:31
Alignment explanation
Indices: 412302--412361 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
412292 AAATTACGTG
*
412302 GGATAATGCATTTACAGTTAATAAAGATATT
1 GGATAATGCATTTACAATTAATAAAGATATT
*
412333 GGATAATGCATTTACAATTAGTAAAGATA
1 GGATAATGCATTTACAATTAATAAAGATA
412362 ATGTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (31 bp):
GGATAATGCATTTACAATTAATAAAGATATT
Found at i:412892 original size:63 final size:63
Alignment explanation
Indices: 412773--412910 Score: 163
Period size: 63 Copynumber: 2.2 Consensus size: 63
412763 TATAATTTAA
* * * *
412773 AAGAAAATATTAAAATATTAAAATTGACATAAAACAGTAAATGGGATAATATATTATTTTCAC
1 AAGAAAATATTTAAATATTAAAATTAACATAAAACAGTAAATGGGATAATACATTATCTTCAC
* * * * *
412836 AA-AAAATTATTTAAATATTAAAATTAACCTAATAA-TGTAAATGTGATAATGCATTATCTTCGC
1 AAGAAAA-TATTTAAATATTAAAATTAACATAA-AACAGTAAATGGGATAATACATTATCTTCAC
412899 AAGAAAATATTT
1 AAGAAAATATTT
412911 GTTGTGTAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
62 4 0.06
63 53 0.84
64 6 0.10
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (63 bp):
AAGAAAATATTTAAATATTAAAATTAACATAAAACAGTAAATGGGATAATACATTATCTTCAC
Found at i:413305 original size:2 final size:2
Alignment explanation
Indices: 413298--413330 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
413288 TATCATTTGG
413298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
413331 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:413335 original size:2 final size:2
Alignment explanation
Indices: 413330--413363 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
413320 ATATATATAT
413330 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
413364 TTAATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:416667 original size:14 final size:14
Alignment explanation
Indices: 416648--416677 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
416638 TTTAGTTGTG
*
416648 TTATTATTTTTTTA
1 TTATTATTATTTTA
416662 TTATTATTATTTTA
1 TTATTATTATTTTA
416676 TT
1 TT
416678 GATAAAAACT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:418090 original size:7 final size:8
Alignment explanation
Indices: 418055--418112 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 8
418045 GATCATGGAA
418055 TAAAATTAT
1 TAAAA-TAT
*
418064 TAAATTAT
1 TAAAATAT
418072 TATAAATAT
1 TA-AAATAT
418081 TAAAAT-T
1 TAAAATAT
418088 T-AAATAT
1 TAAAATAT
*
418095 T-AAATTT
1 TAAAATAT
418102 ATAAAATAT
1 -TAAAATAT
418111 TA
1 TA
418113 TTTTTTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 4 0.10
7 9 0.22
8 12 0.29
9 16 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TAAAATAT
Found at i:418327 original size:30 final size:28
Alignment explanation
Indices: 418292--418347 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
418282 ATGTAAAATT
* *
418292 TTAAATTGATTGATATTTTTATCATATAAA
1 TTAAATAGATTAAT-TTTTTAT-ATATAAA
418322 TTAAATAGATTAATTTTTTATATATA
1 TTAAATAGATTAATTTTTTATATATA
418348 CTTAACGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 7 0.29
30 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (28 bp):
TTAAATAGATTAATTTTTTATATATAAA
Found at i:418915 original size:17 final size:18
Alignment explanation
Indices: 418881--418920 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
418871 GAGCAGCCCG
*
418881 TTTTTAAATAAGCTCAAT
1 TTTTTAAATAAACTCAAT
*
418899 TTTTTAACTAAAC-CAAT
1 TTTTTAAATAAACTCAAT
418916 TTTTT
1 TTTTT
418921 TGTTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTTAAATAAACTCAAT
Found at i:419896 original size:35 final size:34
Alignment explanation
Indices: 419839--419910 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
419829 TGTTCAAAAA
* * *
419839 TTAAATTGAATTGTAATAAAATTTTAATTTTTAAT
1 TTAAATTGAATTGAAATAAAATTTAAAATTTT-AT
*
419874 TTAAATTTGAATT-AAATTAAATTTAAAATTTTAT
1 TTAAA-TTGAATTGAAATAAAATTTAAAATTTTAT
419908 TTA
1 TTA
419911 TTATTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 5 0.16
35 20 0.62
36 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (34 bp):
TTAAATTGAATTGAAATAAAATTTAAAATTTTAT
Found at i:419954 original size:24 final size:24
Alignment explanation
Indices: 419889--419952 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 24
419879 TTTGAATTAA
*
419889 ATTAAATTTAAAATTTTATTTATT
1 ATTAAATTTAAAATATTATTTATT
*
419913 ATTTATTATTGTAAAATATTATGTTATT
1 A-TTA-AATT-TAAAATATTAT-TTATT
419941 ATTAAATTTAAA
1 ATTAAATTTAAA
419953 TAAAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 1 0.03
25 7 0.21
26 6 0.18
27 13 0.39
28 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (24 bp):
ATTAAATTTAAAATATTATTTATT
Found at i:421455 original size:12 final size:12
Alignment explanation
Indices: 421437--421483 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
421427 AATAATAAAC
421437 ATAATAAATATT
1 ATAATAAATATT
*
421449 ATTAT-AATAATT
1 ATAATAAAT-ATT
*
421461 ATCAATAAATATA
1 AT-AATAAATATT
421474 ATAATAAATA
1 ATAATAAATA
421484 ATAACAAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.10
12 17 0.59
13 6 0.21
14 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATAAATATT
Found at i:423331 original size:23 final size:22
Alignment explanation
Indices: 423274--423335 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
423264 ATTAAATTTA
423274 ATGATATTAAAATATAATATAATT
1 ATGAT-TT-AAATATAATATAATT
* **
423298 ATACAAGTAAATATAATATAAATT
1 AT-GATTTAAATATAATAT-AATT
423322 ATGATTTAAA-ATAA
1 ATGATTTAAATATAA
423336 AAAAGTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
22 4 0.13
23 16 0.53
24 9 0.30
25 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
ATGATTTAAATATAATATAATT
Found at i:423333 original size:24 final size:23
Alignment explanation
Indices: 423274--423334 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
423264 ATTAAATTTA
423274 ATGATATTAAAATATAATATAATT
1 ATGAT-TTAAAATATAATATAATT
* **
423298 ATACAAGT-AAATATAATATAAATT
1 AT-GATTTAAAATATAATAT-AATT
423322 ATGATTTAAAATA
1 ATGATTTAAAATA
423335 AAAAAGTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
23 13 0.46
24 14 0.50
25 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
ATGATTTAAAATATAATATAATT
Found at i:425137 original size:17 final size:17
Alignment explanation
Indices: 425117--425155 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
425107 AGAAAACTAA
425117 AATATGATA-AAAAATAT
1 AATATGATATAAAAA-AT
425134 AATATGATATAAAAAAT
1 AATATGATATAAAAAAT
425151 AATAT
1 AATAT
425156 AAATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AATATGATATAAAAAAT
Found at i:425218 original size:32 final size:33
Alignment explanation
Indices: 425158--425223 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
425148 AATAATATAA
* *
425158 ATATAATATTAATAGATGAATATTTTAAAATTT
1 ATATAATATAAATAGATGAATATATTAAAATTT
* *
425191 ATATAATATAAAT-GATTAATATATTAAACTTT
1 ATATAATATAAATAGATGAATATATTAAAATTT
425223 A
1 A
425224 AATATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (33 bp):
ATATAATATAAATAGATGAATATATTAAAATTT
Found at i:425613 original size:19 final size:19
Alignment explanation
Indices: 425566--425619 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
425556 AAAAAAAAAA
425566 AAAAATTATTTTTAT-TTT
1 AAAAATTATTTTTATATTT
425584 ATATAAA-TATTTTTATATTT
1 A-A-AAATTATTTTTATATTT
*
425604 AAAAATTATTTATATA
1 AAAAATTATTTTTATA
425620 AAATATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 20 0.65
20 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAAATTATTTTTATATTT
Found at i:425624 original size:32 final size:31
Alignment explanation
Indices: 425581--425699 Score: 97
Period size: 32 Copynumber: 3.8 Consensus size: 31
425571 TTATTTTTAT
*
425581 TTTATATAAATATTTTTATAT-TTAAAAATTA
1 TTTATATAAATATATTTATATATT-AAAATTA
425612 TTTATATAAAATATATTTATATATTAAAATTA
1 TTTATAT-AAATATATTTATATATTAAAATTA
* *
425644 -TTATTTTTAATATAATTTA-A-A-TAAAATT-
1 TTTA-TATAAATAT-ATTTATATATTAAAATTA
* *
425672 TTTAAATACAATATATTATAGATATTAA
1 TTTATATA-AATATATT-TATATATTAA
425700 TTTTTATTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
28 4 0.06
29 17 0.24
30 2 0.03
31 17 0.24
32 30 0.42
33 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TTTATATAAATATATTTATATATTAAAATTA
Found at i:425628 original size:15 final size:15
Alignment explanation
Indices: 425581--425634 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
425571 TTATTTTTAT
*
425581 TTTATAT-AAATATT
1 TTTATATAAAATATA
425595 TTTATATTTAAAA-ATTA
1 TTTATA--TAAAATA-TA
425612 TTTATATAAAATATA
1 TTTATATAAAATATA
425627 TTTATATA
1 TTTATATA
425635 TTAAAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 6 0.18
15 15 0.44
16 3 0.09
17 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTATATAAAATATA
Found at i:425629 original size:47 final size:47
Alignment explanation
Indices: 425578--425670 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 47
425568 AAATTATTTT
* * *
425578 TATTT-TATA-TAAATATTTTTATATTTAAAAATTATTTATATAAAATA
1 TATTTATATATTAAA-ATTATTAT-TTTAAAAATAATTTAAATAAAATA
* *
425625 TATTTATATATTAAAATTATTATTTTTAATATAATTTAAATAAAAT
1 TATTTATATATTAAAATTATTATTTTAAAAATAATTTAAATAAAAT
425671 TTTTAAATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 24 0.62
48 11 0.28
49 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (47 bp):
TATTTATATATTAAAATTATTATTTTAAAAATAATTTAAATAAAATA
Found at i:426410 original size:16 final size:16
Alignment explanation
Indices: 426391--426421 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
426381 AAATTTAAAT
*
426391 ATTTTTAAATATTTTA
1 ATTTTTAAAAATTTTA
426407 ATTTTTAAAAATTTT
1 ATTTTTAAAAATTTT
426422 CACACATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTAAAAATTTTA
Found at i:429295 original size:13 final size:13
Alignment explanation
Indices: 429262--429306 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
429252 TTAAAAAATT
429262 ATAAAATAAATAAA
1 ATAAAAT-AATAAA
*
429276 ATAAAATAATAAC
1 ATAAAATAATAAA
*
429289 ATCAAAT-ATAAA
1 ATAAAATAATAAA
429301 ATAAAA
1 ATAAAA
429307 ATATTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.33
13 11 0.41
14 7 0.26
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAATAATAAA
Found at i:434215 original size:14 final size:13
Alignment explanation
Indices: 434186--434220 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
434176 TTAATTTTTT
*
434186 TTTAGTATTTATA
1 TTTAATATTTATA
434199 TTTAATATTTCATA
1 TTTAATATTT-ATA
434213 TTTAATAT
1 TTTAATAT
434221 GTATTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:435204 original size:16 final size:15
Alignment explanation
Indices: 435183--435271 Score: 83
Period size: 16 Copynumber: 5.7 Consensus size: 15
435173 AGCAAAAGCA
435183 AATTTAATTTTAAAAT
1 AATTTAA-TTTAAAAT
435199 AATTTAAATTTAAAAT
1 AATTT-AATTTAAAAT
435215 --TTTAAAAATTTAAAAT
1 AATTT---AATTTAAAAT
* *
435231 TATTTAATTTAAATT
1 AATTTAATTTAAAAT
*
435246 AAATTAATTTAAAATT
1 AATTTAATTTAAAA-T
435262 AATTTAATTT
1 AATTTAATTT
435272 GTTGAATTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
14 3 0.05
15 20 0.32
16 34 0.55
17 2 0.03
18 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTAATTTAAAAT
Found at i:435206 original size:10 final size:10
Alignment explanation
Indices: 435191--435268 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
435181 CAAATTTAAT
435191 TTTAAAATAA
1 TTTAAAATAA
*
435201 TTTAAATTTAAAA
1 TTTAAA---ATAA
*
435214 TTTTAAA-AA
1 TTTAAAATAA
*
435223 TTTAAAATTA
1 TTTAAAATAA
**
435233 TTTAATTTAA
1 TTTAAAATAA
* *
435243 ATTAAATTAA
1 TTTAAAATAA
435253 TTTAAAATTAA
1 TTTAAAA-TAA
435264 TTTAA
1 TTTAA
435269 TTTGTTGAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
9 8 0.15
10 28 0.54
11 8 0.15
13 8 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:435855 original size:2 final size:2
Alignment explanation
Indices: 435848--435873 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
435838 ATAAAGATTT
435848 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
435874 AATAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:436631 original size:104 final size:99
Alignment explanation
Indices: 436523--436711 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 99
436513 TTCTAACTTA
* * *
436523 ATTTTAACTACAAAATATAAATAAATATATGTTATTTAATATAATTTAATTTGAAATTAACTTTT
1 ATTTTAAATACAAAATATAAATAAATATATATTATTTAACATAATTTAA-TT--AATTAA-TTTT
436588 ATTAATAATTAAAAATTATAAAAAATTAGAAAACCCTTC
62 ATTAAT-ATTAAAAATTATAAAAAATTAGAAAACCCTTC
* * *
436627 ATTTTAAATACAAATTTTAAATAAATATTTATTATTTAACATAATTTAATTAATTAATTTTATTA
1 ATTTTAAATACAAAATATAAATAAATATATATTATTTAACATAATTTAATTAATTAATTTTATTA
*
436692 ATATTTAAAATTATAAAAAA
66 ATATTAAAAATTATAAAAAA
436712 AATAAAAAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
99 17 0.22
100 10 0.13
101 6 0.08
103 2 0.03
104 43 0.55
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (99 bp):
ATTTTAAATACAAAATATAAATAAATATATATTATTTAACATAATTTAATTAATTAATTTTATTA
ATATTAAAAATTATAAAAAATTAGAAAACCCTTC
Found at i:437289 original size:22 final size:21
Alignment explanation
Indices: 437264--437324 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
437254 ATTTTTATTT
437264 AAATTTAATAATAAATATATAA
1 AAATTTAATAATAAATA-ATAA
*
437286 AAATATGAAT-ATAAA-AATAA
1 AAAT-TTAATAATAAATAATAA
* *
437306 TATTTTAATAATATAATAA
1 AAATTTAATAATA-AATAA
437325 ATAATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.13
20 9 0.29
21 3 0.10
22 11 0.35
23 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTTAATAATAAATAATAA
Found at i:442986 original size:11 final size:11
Alignment explanation
Indices: 442958--442990 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
442948 GGTATTTTGA
442958 AAATAATATA-
1 AAATAATATAT
*
442968 AAAAAATATAT
1 AAATAATATAT
442979 AAATAATATAT
1 AAATAATATAT
442990 A
1 A
442991 TTTGATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATAATATAT
Found at i:444262 original size:18 final size:20
Alignment explanation
Indices: 444219--444262 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
444209 AAACATCAAC
444219 AAATAACTTATTAAAAATAT
1 AAATAACTTATTAAAAATAT
*
444239 ATATAA-TTATTAAAAA-AT
1 AAATAACTTATTAAAAATAT
444257 AAATAA
1 AAATAA
444263 AAAAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAACTTATTAAAAATAT
Found at i:444596 original size:26 final size:26
Alignment explanation
Indices: 444557--444608 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
444547 CAAAATTAAC
*
444557 TTAAATGATCTAATTTATTAATAATA
1 TTAAATGATCTAATTTATTAACAATA
* *
444583 TTAAGTGATTTAATTTATTAACAATA
1 TTAAATGATCTAATTTATTAACAATA
444609 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (26 bp):
TTAAATGATCTAATTTATTAACAATA
Found at i:447859 original size:14 final size:14
Alignment explanation
Indices: 447840--447896 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
447830 AATATGATAT
447840 AAATTTATATATTA
1 AAATTTATATATTA
447854 AAATTTATATAATATA
1 AAATTTATAT-AT-TA
*
447870 AATTATTAATATATTA
1 AA--ATTTATATATTA
447886 AAATTTATATA
1 AAATTTATATA
447897 AATATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 18 0.49
15 2 0.05
16 8 0.22
17 2 0.05
18 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTATATATTA
Found at i:447871 original size:16 final size:16
Alignment explanation
Indices: 447831--447919 Score: 73
Period size: 16 Copynumber: 5.7 Consensus size: 16
447821 AATAATTAAA
*
447831 ATATGATAT-AAATTT
1 ATATAATATAAAATTT
447846 ATAT-AT-TAAAATTT
1 ATATAATATAAAATTT
*
447860 ATATAATATAAATTATT
1 ATATAATATAAAAT-TT
447877 A-AT-ATATTAAAATTT
1 ATATAATA-TAAAATTT
447892 ATATAAATATAAAATATT
1 ATAT-AATATAAAAT-TT
*
447910 TTA-AATATAA
1 ATATAATATAA
447920 TTATAATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
13 1 0.02
14 12 0.19
15 12 0.19
16 21 0.34
17 9 0.15
18 7 0.11
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (16 bp):
ATATAATATAAAATTT
Found at i:447887 original size:32 final size:30
Alignment explanation
Indices: 447831--447909 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 30
447821 AATAATTAAA
*
447831 ATATGATATAAAT-TTATATATTAAAATTT
1 ATATAATATAAATATTATATATTAAAATTT
447860 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAA-TATT-ATATATTAAAATTT
447892 ATATAAATATAAAATATT
1 ATAT-AATAT-AAATATT
447910 TTAAATATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 11 0.25
30 1 0.02
31 2 0.05
32 18 0.41
33 9 0.20
34 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATAATATAAATATTATATATTAAAATTT
Found at i:447893 original size:18 final size:17
Alignment explanation
Indices: 447830--447919 Score: 56
Period size: 14 Copynumber: 5.5 Consensus size: 17
447820 AAATAATTAA
447830 AATATGATATAAATTTA-T
1 AATAT-ATA-AAATTTATT
447848 -ATAT-TAAAATTTA-T
1 AATATATAAAATTTATT
447862 -ATA-ATATAAA-TTATT
1 AATATATA-AAATTTATT
447877 AATATATTAAAATTTATAT
1 AATATA-TAAAATTTAT-T
447896 AA-ATATAAAATATT-TT
1 AATATATAAAAT-TTATT
447912 AA-ATATAA
1 AATATATAA
447920 TTATAATATA
Statistics
Matches: 63, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
14 16 0.25
15 6 0.10
16 12 0.19
17 15 0.24
18 11 0.17
19 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
AATATATAAAATTTATT
Found at i:450044 original size:42 final size:42
Alignment explanation
Indices: 449971--450051 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
449961 ATATTAAATA
449971 TTTAAATATTTTTTAAATTAATTAATATATATTATATTTATT
1 TTTAAATATTTTTTAAATTAATTAATATATATTATATTTATT
* *
450013 TTTAAA-ATTTTTATATATTTAA-TAATTTATATTATATTT
1 TTTAAATATTTTT-TA-AATTAATTAATATATATTATATTT
450052 TTTATAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 6 0.17
42 24 0.69
43 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (42 bp):
TTTAAATATTTTTTAAATTAATTAATATATATTATATTTATT
Found at i:450048 original size:19 final size:19
Alignment explanation
Indices: 449992--450051 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
449982 TTTAAATTAA
*
449992 TTAATATATATTATATTTATTT
1 TTAATA-AT-TTATA-TTATAT
*
450014 TTAA-AATTTTTA-TATAT
1 TTAATAATTTATATTATAT
450031 TTAATAATTTATATTATAT
1 TTAATAATTTATATTATAT
450050 TT
1 TT
450052 TTTATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 8 0.24
18 7 0.21
19 11 0.33
20 2 0.06
21 1 0.03
22 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATAATTTATATTATAT
Found at i:450797 original size:14 final size:15
Alignment explanation
Indices: 450780--450839 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 15
450770 GTGATAATTT
450780 TAAATATAAT-TATA
1 TAAATATAATATATA
450794 TAAATATAATATATA
1 TAAATATAATATATA
450809 T-AA-A-AATAT-TA
1 TAAATATAATATATA
*
450820 -AAATATAATATAAA
1 TAAATATAATATATA
450834 TAAATA
1 TAAATA
450840 ATTTAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 4 0.10
12 6 0.15
13 6 0.15
14 13 0.33
15 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATAATATATA
Found at i:450826 original size:20 final size:23
Alignment explanation
Indices: 450801--450858 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
450791 ATATAAATAT
450801 AATATATATAA-AAAT-A-TTAA
1 AATATATATAATAAATAATTTAA
450821 AATATAATATAAATAAATAATTTAA
1 AATAT-ATAT-AATAAATAATTTAA
*
450846 AATTTATATAATA
1 AATATATATAATA
450859 TTAATTACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.16
21 4 0.12
22 2 0.06
23 8 0.25
24 5 0.16
25 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATATATAATAAATAATTTAA
Found at i:450829 original size:25 final size:25
Alignment explanation
Indices: 450785--450856 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
450775 AATTTTAAAT
*
450785 ATAATTATATAAATATAATATATATAA
1 ATAATT-TA-AAATATAATATAAATAA
450812 A-AATATTAAAATATAATATAAATAA
1 ATAAT-TTAAAATATAATATAAATAA
*
450837 ATAATTTAAAAT-TTATATAA
1 ATAATTTAAAATATAATATAA
450857 TATTAATTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 7 0.17
25 24 0.59
26 8 0.20
27 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATTTAAAATATAATATAAATAA
Found at i:450854 original size:29 final size:31
Alignment explanation
Indices: 450822--450896 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 31
450812 AAATATTAAA
450822 ATATAATATAAATAAATAATTTA-AAA-TTT
1 ATATAATATAAATAAATAATTTACAAATTTT
* * *
450851 ATATAATATTAATTACTAATTTATCAAATTTTT
1 ATATAATATAAATAAATAATTTA-CAAA-TTTT
450884 ATATAAATATAAA
1 ATAT-AATATAAA
450897 ATATTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 20 0.54
31 3 0.08
33 7 0.19
34 7 0.19
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATAATATAAATAAATAATTTACAAATTTT
Found at i:450900 original size:7 final size:8
Alignment explanation
Indices: 450883--450957 Score: 55
Period size: 8 Copynumber: 8.8 Consensus size: 8
450873 ATCAAATTTT
450883 TATATAAA
1 TATATAAA
450891 TATA-AAA
1 TATATAAA
*
450898 TATTTTAAA
1 TA-TATAAA
*
450907 TAAAATAAAA
1 T-ATAT-AAA
450917 TATATAATTA
1 TATATAA--A
450927 TATTATAAA
1 TA-TATAAA
450936 TATATAAA
1 TATATAAA
450944 T-TACTAAA
1 TATA-TAAA
450952 TATATA
1 TATATA
450958 TAAATTAGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
7 7 0.13
8 21 0.39
9 13 0.24
10 8 0.15
11 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:450902 original size:21 final size:20
Alignment explanation
Indices: 450878--450919 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
450868 AATTTATCAA
*
450878 ATTTTTATATAAATATAAAAT
1 ATTTTTAAATAAA-ATAAAAT
450899 A-TTTTAAATAAAATAAAAT
1 ATTTTTAAATAAAATAAAAT
450918 AT
1 AT
450920 ATAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 10 0.53
21 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTTTAAATAAAATAAAAT
Found at i:450921 original size:21 final size:20
Alignment explanation
Indices: 450876--450919 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
450866 CTAATTTATC
*
450876 AAAT-TTTTATATAAATATA
1 AAATATTTTAAATAAATATA
450895 AAATATTTTAAATAAA-ATA
1 AAATATTTTAAATAAATATA
450914 AAATAT
1 AAATAT
450920 ATAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATTTTAAATAAATATA
Found at i:451197 original size:29 final size:27
Alignment explanation
Indices: 451145--451217 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
451135 AGTTGTAATA
*
451145 AAAAAATAATTTAATACTTTTATTATT
1 AAAAAATAATTTTATACTTTTATTATT
* *
451172 AAATTAAATAATTTTAT-TTTTATATTTTT
1 AAA--AAATAATTTTATACTTT-TATTATT
451201 AAAAATATAATTTTATA
1 AAAAA-ATAATTTTATA
451218 ATAATATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 5 0.13
28 13 0.34
29 20 0.53
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAAAATAATTTTATACTTTTATTATT
Found at i:451249 original size:18 final size:17
Alignment explanation
Indices: 451204--451249 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
451194 TATTTTTAAA
451204 AATATAATTTT-ATAAT
1 AATATAATTTTAATAAT
* *
451220 AATATTTATTTAAATAAT
1 AATA-TAATTTTAATAAT
451238 AATATAATTTTA
1 AATATAATTTTA
451250 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 11 0.46
18 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATAATTTTAATAAT
Found at i:451952 original size:17 final size:17
Alignment explanation
Indices: 451932--451976 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
451922 TACAAATTAA
451932 AATAAA-AATATTTAAAT
1 AATAAATAA-ATTTAAAT
451949 AATAAATAAATTTAAAT
1 AATAAATAAATTTAAAT
**
451966 TTTAAATAAAT
1 AATAAATAAAT
451977 GAAGGGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATAAATTTAAAT
Found at i:452791 original size:15 final size:17
Alignment explanation
Indices: 452771--452810 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
452761 CAAAAAAATT
452771 TAAATTTTT-TTATA-A
1 TAAATTTTTATTATATA
*
452786 TAAATTTTTATTATATC
1 TAAATTTTTATTATATA
452803 TAAATTTT
1 TAAATTTT
452811 GAATAACCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 5 0.23
17 8 0.36
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TAAATTTTTATTATATA
Found at i:453070 original size:18 final size:18
Alignment explanation
Indices: 453047--453089 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
453037 TTATTGCATA
*
453047 TTTTAATTTACGATTTTT
1 TTTTAACTTACGATTTTT
**
453065 TTTTAACTTGTGATTTTT
1 TTTTAACTTACGATTTTT
453083 TATTTAA
1 T-TTTAA
453090 ATAGGTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTAACTTACGATTTTT
Found at i:453677 original size:16 final size:17
Alignment explanation
Indices: 453656--453688 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
453646 TGAGTTAAGA
453656 ATTTATTGATT-ATTTT
1 ATTTATTGATTAATTTT
*
453672 ATTTATTTATTAATTTT
1 ATTTATTGATTAATTTT
453689 TAATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTATTGATTAATTTT
Found at i:454337 original size:44 final size:44
Alignment explanation
Indices: 454274--454360 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
454264 TTCTTTTACT
454274 TAAAGCATATATATTATTAGAAACTAATCTGACCCAGGCCGATA
1 TAAAGCATATATATTATTAGAAACTAATCTGACCCAGGCCGATA
454318 TAAAGCATATATATTATTAGAAACTAATCTGACCCAGGCCGAT
1 TAAAGCATATATATTATTAGAAACTAATCTGACCCAGGCCGAT
454361 CAAGTTGACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (44 bp):
TAAAGCATATATATTATTAGAAACTAATCTGACCCAGGCCGATA
Found at i:457016 original size:14 final size:15
Alignment explanation
Indices: 456979--457015 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
456969 ATTGTGCTAA
*
456979 AATATTTTTAAAAAT
1 AATATTTTAAAAAAT
456994 AATATTTTAAAAAAT
1 AATATTTTAAAAAAT
*
457009 TATATTT
1 AATATTT
457016 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTTTAAAAAAT
Found at i:457054 original size:23 final size:24
Alignment explanation
Indices: 457006--457062 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
456996 TATTTTAAAA
457006 AATTATATTTATATTTTTATATCAT
1 AATTATA-TTATATTTTTATATCAT
*
457031 ATTTATATTAT-TTTTTAT-TACAT
1 AATTATATTATATTTTTATAT-CAT
457054 AATTATATT
1 AATTATATT
457063 TTATATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 18 0.62
24 4 0.14
25 6 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTATATTATATTTTTATATCAT
Found at i:457061 original size:29 final size:29
Alignment explanation
Indices: 457029--457100 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
457019 TTTTTATATC
* *
457029 ATATTTATATTATTTTTTATTACA-TAATT
1 ATATTTATATTATATTTTAATACATTAA-T
*
457058 ATATTT-TATATAAATTTTAATACATTAAT
1 ATATTTATAT-TATATTTTAATACATTAAT
457087 A-ATTTATATTATAT
1 ATATTTATATTATAT
457101 AAAATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
28 11 0.31
29 22 0.61
30 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
ATATTTATATTATATTTTAATACATTAAT
Found at i:457124 original size:32 final size:34
Alignment explanation
Indices: 457047--457110 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
457037 ATTATTTTTT
*
457047 ATTACATAA-TTATATTTTATATAAATTTTAATAC
1 ATTA-ATAATTTATATTATATATAAATTTTAATAC
457081 ATTAATAATTTATATTATATA-AAATTTTAA
1 ATTAATAATTTATATTATATATAAATTTTAA
457111 ATAATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (34 bp):
ATTAATAATTTATATTATATATAAATTTTAATAC
Found at i:457159 original size:12 final size:12
Alignment explanation
Indices: 457132--457167 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
457122 TTACATTACA
457132 TTTATATTAT-T
1 TTTATATTATAT
*
457143 TTTATATCATAT
1 TTTATATTATAT
457155 TTTATATTATAT
1 TTTATATTATAT
457167 T
1 T
457168 AATTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:458278 original size:25 final size:25
Alignment explanation
Indices: 458224--458279 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
458214 AAATAAAAAG
*
458224 ATAAATATAAAAATAAATATATTTA
1 ATAAATATAAAAATAAATATAATTA
* * *
458249 GTAAATA-AAAAATGATTAATAATTA
1 ATAAATATAAAAATAAAT-ATAATTA
458274 ATAAAT
1 ATAAAT
458280 GGACATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (25 bp):
ATAAATATAAAAATAAATATAATTA
Found at i:459147 original size:6 final size:6
Alignment explanation
Indices: 459136--459164 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
459126 ATGTTAAATA
459136 AATTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTT
459165 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:460052 original size:22 final size:22
Alignment explanation
Indices: 460024--460070 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
460014 ATAAATATTT
460024 AAATATATCAAAT-ATAAATAAA
1 AAATATATC-AATCATAAATAAA
*
460046 AAATATATCTATCATAAATAAA
1 AAATATATCAATCATAAATAAA
460068 AAA
1 AAA
460071 ATTAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATATATCAATCATAAATAAA
Found at i:460232 original size:22 final size:23
Alignment explanation
Indices: 460202--460245 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
460192 ATTTTACTAA
*
460202 TAATTAAATAAAATT-AATTTAT
1 TAATGAAATAAAATTCAATTTAT
*
460224 TAATGAAATCAAATTCAATTTA
1 TAATGAAATAAAATTCAATTTA
460246 ATTGATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (23 bp):
TAATGAAATAAAATTCAATTTAT
Found at i:460476 original size:20 final size:20
Alignment explanation
Indices: 460451--460494 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
460441 CCAAAAGCCC
460451 ATTTAATATTTTAATTAATT
1 ATTTAATATTTTAATTAATT
460471 ATTTAATATTTTAATTAATT
1 ATTTAATATTTTAATTAATT
460491 ATTT
1 ATTT
460495 CATAGTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATATTTTAATTAATT
Found at i:461379 original size:14 final size:14
Alignment explanation
Indices: 461362--461391 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
461352 TATAAAAATT
461362 TAAAATTTGAATCA
1 TAAAATTTGAATCA
461376 TAAAATTTGAATCA
1 TAAAATTTGAATCA
461390 TA
1 TA
461392 TGATCCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TAAAATTTGAATCA
Found at i:467249 original size:21 final size:20
Alignment explanation
Indices: 467207--467249 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
467197 TTGATTTGAA
*
467207 TTCAGATAAAAATATTAAAT
1 TTCAGATAAAAATAATAAAT
* *
467227 TTCATATAAAAATTAATATAT
1 TTCAGATAAAAA-TAATAAAT
467248 TT
1 TT
467250 AAATTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (20 bp):
TTCAGATAAAAATAATAAAT
Found at i:467253 original size:14 final size:14
Alignment explanation
Indices: 467236--467280 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
467226 TTTCATATAA
467236 AAATTAATATATTT
1 AAATTAATATATTT
*
467250 AAATTTTATATATTT
1 AAA-TTAATATATTT
467265 AAATATAA-ATATTT
1 AAAT-TAATATATTT
467279 AA
1 AA
467281 TCTATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTAATATATTT
Found at i:467308 original size:35 final size:35
Alignment explanation
Indices: 467230--467334 Score: 131
Period size: 35 Copynumber: 2.9 Consensus size: 35
467220 ATTAAATTTC
* * *
467230 ATATAAA-AATTAATATATTTAAATTTTATATATTTAA
1 ATATAAATATTTAATCTA-TTATATTTT-TAT-TTTAA
467267 ATATAAATATTTAATCTATTATATTTTTATTTTAA
1 ATATAAATATTTAATCTATTATATTTTTATTTTAA
**
467302 ATATAAATATTTAATCCGTTATATTTTTATTTT
1 ATATAAATATTTAATCTATTATATTTTTATTTT
467335 GTTCCATCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 36 0.58
36 3 0.05
37 15 0.24
38 8 0.13
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (35 bp):
ATATAAATATTTAATCTATTATATTTTTATTTTAA
Found at i:467433 original size:2 final size:2
Alignment explanation
Indices: 467426--467452 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
467416 TACATCAATT
467426 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 T
467453 TTTAACTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:468449 original size:2 final size:2
Alignment explanation
Indices: 468442--468471 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
468432 CATTAAATTT
468442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
468472 CAGATACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:468607 original size:2 final size:2
Alignment explanation
Indices: 468552--468593 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
468542 TGTCGATCTT
* * *
468552 TA TA TA TA CA TT TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
468594 AATTGATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:468615 original size:26 final size:24
Alignment explanation
Indices: 468586--468633 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
468576 TATACATATA
468586 TATATATAAATTGATTTATATAAATG
1 TATA-ATAAATTGATTT-TATAAATG
* *
468612 TATAATTAATTTATTTTATAAA
1 TATAATAAATTGATTTTATAAA
468634 CTTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TATAATAAATTGATTTTATAAATG
Found at i:469064 original size:3 final size:3
Alignment explanation
Indices: 469056--469101 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
469046 GTAAATAGGA
469056 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
469102 GTTGGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:469566 original size:14 final size:16
Alignment explanation
Indices: 469547--469578 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
469537 TTACAATTTT
469547 ATATTT-TTAA-TATA
1 ATATTTCTTAATTATA
469561 ATATTTCTTAATTATA
1 ATATTTCTTAATTATA
469577 AT
1 AT
469579 TAATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTCTTAATTATA
Found at i:471723 original size:25 final size:27
Alignment explanation
Indices: 471691--471747 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
471681 AATATGATTC
471691 AAAT-TTAAT-TACAAAT-TTATAT-AT
1 AAATATTAATATA-AAATATTATATAAT
471715 AAATATTAATATAAAATAATTATATAAT
1 AAATATTAATATAAAAT-ATTATATAAT
471743 AAATA
1 AAATA
471748 AATATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 4 0.14
25 9 0.32
26 2 0.07
27 6 0.21
28 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATATTAATATAAAATATTATATAAT
Found at i:471736 original size:14 final size:14
Alignment explanation
Indices: 471704--471781 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 14
471694 TTTAATTACA
*
471704 AATTTATATATAAAT
1 AATTAATATA-AAAT
471719 -ATTAATATAAAAT
1 AATTAATATAAAAT
471732 AATT-ATATAATAAAT
1 AATTAATAT-A-AAAT
* *
471747 AAATATATTTAAAAT
1 AATTA-ATATAAAAT
*
471762 AATAAAT-TAAAAT
1 AATTAATATAAAAT
*
471775 TATTAAT
1 AATTAAT
471782 CGAATCTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
13 19 0.37
14 14 0.27
15 14 0.27
16 1 0.02
17 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAATATAAAAT
Found at i:471993 original size:20 final size:19
Alignment explanation
Indices: 471965--472018 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
471955 CTGCTCGTAC
*
471965 TTAATATATTTTATTTTATT
1 TTAAAATATTTTATTTTA-T
471985 TTAAAATATTTTATATTTAT
1 TTAAAATATTTTAT-TTTAT
*
472005 ATAAAAT-TTTTATT
1 TTAAAATATTTTATT
472019 AATAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 6 0.19
20 20 0.65
21 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAAAATATTTTATTTTAT
Found at i:472029 original size:15 final size:15
Alignment explanation
Indices: 471978--472040 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 15
471968 ATATATTTTA
* *
471978 TTTTATTTTAAAATAT
1 TTTTATTATATAA-AT
471994 TTTATATTTATATAAAAT
1 TTT-TA-TTATAT-AAAT
472012 TTTTATTA-ATAAAT
1 TTTTATTATATAAAT
472026 TTTTATTATATAAAT
1 TTTTATTATATAAAT
472041 CAATAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 12 0.29
15 8 0.20
16 6 0.15
17 4 0.10
18 9 0.22
19 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATTATATAAAT
Found at i:472055 original size:18 final size:19
Alignment explanation
Indices: 472032--472073 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
472022 AAATTTTTAT
472032 TATATAA-ATCAATA-AATA
1 TATATAATAT-AATATAATA
472050 TATATAATATAATATAATA
1 TATATAATATAATATAATA
472069 T-TATA
1 TATATA
472074 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATAATATAATATAATA
Found at i:472068 original size:23 final size:22
Alignment explanation
Indices: 472018--472068 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
472008 AAATTTTTAT
* * *
472018 TAATAAATTTTTATTATATAAA
1 TAATAAATATATATAATATAAA
472040 TCAATAAATATATATAATATAATA
1 T-AATAAATATATATAATATAA-A
472064 TAATA
1 TAATA
472069 TTATATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 21 0.88
24 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATATATATAATATAAA
Found at i:472088 original size:19 final size:20
Alignment explanation
Indices: 472062--472109 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
472052 TATAATATAA
472062 TATAATATTAT-ATTATTTT
1 TATAATATTATAATTATTTT
* * *
472081 TATTATATTTTAATTTTTTT
1 TATAATATTATAATTATTTT
472101 TATAATATT
1 TATAATATT
472110 TCCGTTGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATAATATTATAATTATTTT
Found at i:479525 original size:18 final size:19
Alignment explanation
Indices: 479490--479527 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
479480 TAATTTAATT
479490 TTAAAAATTTATATAAAAA
1 TTAAAAATTTATATAAAAA
* *
479509 TTAAAATTTTTTA-AAAAA
1 TTAAAAATTTATATAAAAA
479527 T
1 T
479528 CATATATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAAATTTATATAAAAA
Found at i:479610 original size:23 final size:23
Alignment explanation
Indices: 479568--479613 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
479558 AAATAATTTT
**
479568 AAAATATTTTATATCTTTTAATA
1 AAAATATTTTATATAATTTAATA
*
479591 AAAATATTTTATTTAATTTAATA
1 AAAATATTTTATATAATTTAATA
479614 CACGTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAATATTTTATATAATTTAATA
Found at i:480617 original size:21 final size:21
Alignment explanation
Indices: 480578--480617 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
480568 TAATTTATTG
* * *
480578 TTTTATTTTTTTAAGTTTTAT
1 TTTTATTTATGTAAATTTTAT
480599 TTTTATTTATGTAAATTTT
1 TTTTATTTATGTAAATTTT
480618 TGTTATAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTATTTATGTAAATTTTAT
Found at i:481230 original size:20 final size:19
Alignment explanation
Indices: 481207--481252 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
481197 TTTTTGGCAA
481207 AATTATAATATAAATTTATT
1 AATTATAATATAAATTT-TT
* *
481227 AATTATATTGTAAATTTTT
1 AATTATAATATAAATTTTT
481246 ATATTAT
1 A-ATTAT
481253 GCATACACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTATAATATAAATTTTT
Found at i:481954 original size:3 final size:3
Alignment explanation
Indices: 481946--481982 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
481936 TATTAATATC
481946 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
481983 TCTTTGGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:482427 original size:29 final size:29
Alignment explanation
Indices: 482355--482428 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
482345 TTTAAAAAAT
* *
482355 TTAAAAAATGATAATTTATTTATTATTAAA
1 TTAAAAAAT-ATAATATATTTAATATTAAA
* *
482385 TAAAAATAACATAATATA-TTAATATTAAA
1 TTAAAA-AATATAATATATTTAATATTAAA
482414 GTTAAAAAATATAAT
1 -TTAAAAAATATAAT
482429 TGAATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 17 0.47
30 17 0.47
31 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAAAAAATATAATATATTTAATATTAAA
Found at i:483235 original size:21 final size:20
Alignment explanation
Indices: 483211--483259 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
483201 ATTTTGTAAG
483211 ATTTTTATGTA-ATTTTTATGT
1 ATTTTTAT-TATATTTTTAT-T
* *
483232 ATTTATATTATGTTTTTATT
1 ATTTTTATTATATTTTTATT
483252 ATTTTTAT
1 ATTTTTAT
483260 ATCATGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (20 bp):
ATTTTTATTATATTTTTATT
Found at i:483251 original size:11 final size:12
Alignment explanation
Indices: 483226--483267 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
483216 TATGTAATTT
483226 TTATGTATTTATA
1 TTATGT-TTTATA
483239 TTATGTTTT-TA
1 TTATGTTTTATA
483250 TTAT-TTTTATA
1 TTATGTTTTATA
*
483261 TCATGTT
1 TTATGTT
483268 GAATTTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 4 0.15
11 11 0.42
12 5 0.19
13 6 0.23
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (12 bp):
TTATGTTTTATA
Done.