Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015181.1 Kokia drynarioides strain JFW-HI SEQ_130225, whole genome shotgun sequence
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: 642291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 422 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2609 original size:6 final size:6
Alignment explanation
Indices: 2600--2648 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
2590 CAAATTTATT
** * *
2600 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTTAA TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2647 TT
1 TT
2649 GATTTAAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2614 original size:18 final size:17
Alignment explanation
Indices: 2591--2648 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
2581 AAATTGATTC
2591 AAATTTATTTTTAAATTT
1 AAATTT-TTTTTAAATTT
**
2609 AAATTTGCTTTAAATTT
1 AAATTTTTTTTAAATTT
* *
2626 AAATTTTAATTAAAATTT
1 AAATTTT-TTTTAAATTT
2644 AAATT
1 AAATT
2649 GATTTAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 15 0.44
18 19 0.56
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
AAATTTTTTTTAAATTT
Found at i:2636 original size:29 final size:29
Alignment explanation
Indices: 2578--2643 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2568 TTTTATTAGG
*
2578 TTTAAA-TTGATTCAAATTTATTTTTAAA
1 TTTAAATTTGATTCAAATTTAATTTTAAA
* *
2606 TTTAAATTTGCTTTAAATTTAAATTTT-AA
1 TTTAAATTTGATTCAAATTT-AATTTTAAA
*
2635 TTAAAATTT
1 TTTAAATTT
2644 AAATTGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.19
29 21 0.66
30 5 0.16
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTAAATTTGATTCAAATTTAATTTTAAA
Found at i:2655 original size:17 final size:18
Alignment explanation
Indices: 2603--2662 Score: 70
Period size: 17 Copynumber: 3.4 Consensus size: 18
2593 ATTTATTTTT
*
2603 AAATTTAAATTTGCTTT-
1 AAATTTAAATTTGATTTA
* *
2620 AAATTTAAATTTTAATTA
1 AAATTTAAATTTGATTTA
2638 AAATTTAAA-TTGATTTA
1 AAATTTAAATTTGATTTA
*
2655 AAACTTAA
1 AAATTTAA
2663 TTAAATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
17 27 0.75
18 9 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATTTAAATTTGATTTA
Found at i:3365 original size:3 final size:3
Alignment explanation
Indices: 3359--3468 Score: 87
Period size: 3 Copynumber: 36.0 Consensus size: 3
3349 AATATTAATT
** * * * *
3359 TAA TAA TAA TAA TGG TCA TAA CAA TAAA TGA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
** * *
3405 TAA TAA TAA TAA TAA TAA -ATA TTG TAA TAA TGA TAA TAT TAA TTAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA
*
3451 TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
3469 ATATTTTTTT
Statistics
Matches: 82, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
2 1 0.01
3 75 0.91
4 6 0.07
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4499 original size:29 final size:29
Alignment explanation
Indices: 4453--4746 Score: 233
Period size: 29 Copynumber: 9.8 Consensus size: 29
4443 TTGGAGATCC
* *
4453 CTAAACTATCCAAAAATTACATTTTTACCT
1 CTAAACT-TCCAAAAATTCCATTTTAACCT
*
4483 CTAAACTTCTAAAAATTCCATTTTCAACCT
1 CTAAACTTCCAAAAATTCCATTTT-AACCT
* *
4513 -TAAAACTTCCAAAAATTCCATTTTCACCC
1 CT-AAACTTCCAAAAATTCCATTTTAACCT
* *
4542 CTAAATTTCCAAAAAAAAAAATCCATTTTCAACC-
1 CTAAACTTCC-----AAAAATTCCATTTT-AACCT
* *
4576 CTAAAACTTCCAAAAATTCCATTTTCACCC
1 CT-AAACTTCCAAAAATTCCATTTTAACCT
*
4606 CTAAACTTCCAAAAATTCCATTTTCGACCT
1 CTAAACTTCCAAAAATTCCATTTT-AACCT
* *
4636 CGAAACTTCCAAAAATTCCATTTTTACC-
1 CTAAACTTCCAAAAATTCCATTTTAACCT
*
4664 CTTGAACTTCCAAAAATTCCATTTT-A-CT
1 C-TAAACTTCCAAAAATTCCATTTTAACCT
* *
4692 CCTGAA-TGTCTAAAAATTCCATTTTAACC-
1 -CTAAACT-TCCAAAAATTCCATTTTAACCT
** *
4721 CCGAACTTTCCCAAAATTACCATTTT
1 CTAAAC-TTCCAAAAATT-CCATTTT
4747 GCCCCTGAGA
Statistics
Matches: 221, Mismatches: 22, Indels: 42
0.78 0.08 0.15
Matches are distributed among these distances:
27 2 0.01
28 26 0.12
29 85 0.38
30 83 0.38
34 15 0.07
35 10 0.05
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
CTAAACTTCCAAAAATTCCATTTTAACCT
Found at i:4556 original size:59 final size:59
Alignment explanation
Indices: 4455--4688 Score: 297
Period size: 59 Copynumber: 3.9 Consensus size: 59
4445 GGAGATCCCT
* * * *
4455 AAACTATCCAAAAATTACATTTTTACCTCTAAACTTCTAAAAATTCCATTTTCAACCTTA
1 AAACT-TCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCAACCTTA
* * *
4515 AAACTTCCAAAAATTCCATTTTCACCCCTAAATTTCCAAAAAAAAAAATCCATTTTCAACCCTA
1 AAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCC-----AAAAATTCCATTTTCAACCTTA
* **
4579 AAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCAACCTTA
* * *
4638 AAACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAATTCCATTTT
4689 ACTCCTGAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
59 92 0.60
60 5 0.03
64 56 0.37
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCAACCTTA
Found at i:4584 original size:64 final size:64
Alignment explanation
Indices: 4493--4679 Score: 251
Period size: 64 Copynumber: 3.0 Consensus size: 64
4483 CTAAACTTCT
* *
4493 AAAAATTCCATTTTCAACCTTAAAACTTCCAAAAATTCCATTTTCACCCCTAAATTTCCAAAAA
1 AAAAATTCCATTTTCAACCCTAAAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAA
*
4557 AAAAAATCCATTTTCAACCCTAAAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCC-----
1 AAAAATTCCATTTTCAACCCTAAAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAA
* * * * *
4616 AAAAATTCCATTTTCGA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAA
1 AAAAATTCCATTTTCAACCCT-AAAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAA
4680 TTCCATTTTA
Statistics
Matches: 108, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
58 3 0.03
59 49 0.45
64 56 0.52
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.30
Consensus pattern (64 bp):
AAAAATTCCATTTTCAACCCTAAAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAA
Found at i:4675 original size:123 final size:123
Alignment explanation
Indices: 4451--4679 Score: 343
Period size: 123 Copynumber: 1.9 Consensus size: 123
4441 CCTTGGAGAT
* * * *
4451 CCCTAAACTATCCAAAAATTACATTTTTACCTCTAAACTTCTAAAAATTCCATTTTCAACCTTAA
1 CCCTAAACTATCCAAAAATTACATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCAACCTCAA
*
4516 AACTTCCAAAAATTCCATTTTCACCCCTAAATTTCCAAAAAAAAAAATCCATTTTCAA
66 AACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAAAAAAAATCCATTTTCAA
* * *
4574 CCCTAAAACT-TCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCGACCTCG
1 CCCT-AAACTATCCAAAAATTACATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCAACCTCA
* * *
4638 AAACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAA
65 AAACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAA
4680 TTCCATTTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
123 89 0.95
124 5 0.05
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.31
Consensus pattern (123 bp):
CCCTAAACTATCCAAAAATTACATTTTCACCCCTAAACTTCCAAAAATTCCATTTTCAACCTCAA
AACTTCCAAAAATTCCATTTTCACCCCTAAACTTCCAAAAAAAAAAATCCATTTTCAA
Found at i:11964 original size:2 final size:2
Alignment explanation
Indices: 11959--11986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11949 TAGAGAGATA
11959 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
11987 TTTGAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12275 original size:16 final size:16
Alignment explanation
Indices: 12242--12285 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
12232 TTAAATAATT
**
12242 AATAAAAATATTTTAAA
1 AATAAAAA-ATTAAAAA
12259 AATAAAAAATTAAAAA
1 AATAAAAAATTAAAAA
*
12275 ATTAAAAAATT
1 AATAAAAAATT
12286 CGGTTCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAAAAATTAAAAA
Found at i:12282 original size:9 final size:8
Alignment explanation
Indices: 12256--12285 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12246 AAAATATTTT
12256 AAAAA-TA
1 AAAAATTA
12263 AAAAATTA
1 AAAAATTA
12271 AAAAATTA
1 AAAAATTA
12279 AAAAATT
1 AAAAATT
12286 CGGTTCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATTA
Found at i:12509 original size:60 final size:60
Alignment explanation
Indices: 12378--12499 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
12368 TGATTTTTCT
* *
12378 CTTGAAATTTTTAGAAAATTTTAATTAGACCCCCAAAACTTTTAGAAAATTTCATTATCC
1 CTTGAAATTTTTAGAAAAATATAATTAGACCCCCAAAACTTTTAGAAAATTTCATTATCC
* ** *
12438 CTTGAAATTTTTAGAAAAATATAATTAGGCCCCTTAAA-TTTTA-AAAATTCTCATTATAC
1 CTTGAAATTTTTAGAAAAATATAATTAGACCCCCAAAACTTTTAGAAAATT-TCATTATCC
12497 CTT
1 CTT
12500 TTATTTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 6 0.11
59 16 0.29
60 33 0.60
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (60 bp):
CTTGAAATTTTTAGAAAAATATAATTAGACCCCCAAAACTTTTAGAAAATTTCATTATCC
Found at i:19055 original size:13 final size:13
Alignment explanation
Indices: 19037--19063 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19027 AAAGAATACT
19037 TTAATTGGAGGGC
1 TTAATTGGAGGGC
19050 TTAATTGGAGGGC
1 TTAATTGGAGGGC
19063 T
1 T
19064 AGATTAGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.37, T:0.33
Consensus pattern (13 bp):
TTAATTGGAGGGC
Found at i:30997 original size:16 final size:16
Alignment explanation
Indices: 30976--31006 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
30966 AGAACTAAAC
30976 CAATAACGACTAGTAT
1 CAATAACGACTAGTAT
30992 CAATAACGACTAGTA
1 CAATAACGACTAGTA
31007 CATACCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (16 bp):
CAATAACGACTAGTAT
Found at i:31029 original size:64 final size:64
Alignment explanation
Indices: 30928--31054 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
30918 AGAACTAAAC
30928 CAATAACGACTAGTACATACCACCAACAAGAGTAGAACAGAACTAAACCAATAACGACTAGTAT
1 CAATAACGACTAGTACATACCACCAACAAGAGTAGAACAGAACTAAACCAATAACGACTAGTAT
*
30992 CAATAACGACTAGTACATACCACCAACAAGAGTAGAACAGAACTAAACCAATGACGACTAGTA
1 CAATAACGACTAGTACATACCACCAACAAGAGTAGAACAGAACTAAACCAATAACGACTAGTA
31055 CATACCACTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.15
Consensus pattern (64 bp):
CAATAACGACTAGTACATACCACCAACAAGAGTAGAACAGAACTAAACCAATAACGACTAGTAT
Found at i:35809 original size:20 final size:20
Alignment explanation
Indices: 35780--35824 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
35770 GTACGGGTAG
35780 TGAG-ATGTATCAAGAGATA
1 TGAGTATGTATCAAGAGATA
35799 TGAGTATGTATCAAGAGATA
1 TGAGTATGTATCAAGAGATA
*
35819 CGAGTA
1 TGAGTA
35825 AATCAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (20 bp):
TGAGTATGTATCAAGAGATA
Found at i:37170 original size:37 final size:37
Alignment explanation
Indices: 37120--37192 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
37110 AGGAGCTATG
*
37120 GATAGTTCTAGGCATTGTATCAAAAAGAGCAGATATA
1 GATAGTTATAGGCATTGTATCAAAAAGAGCAGATATA
*
37157 GATAGTTATAGGCATTGTATCAAAAAGATCAGATAT
1 GATAGTTATAGGCATTGTATCAAAAAGAGCAGATAT
37193 GATCAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.29
Consensus pattern (37 bp):
GATAGTTATAGGCATTGTATCAAAAAGAGCAGATATA
Found at i:39628 original size:37 final size:37
Alignment explanation
Indices: 39577--39647 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
39567 TCAGTTGGAA
39577 GAGCTTTTGCTAATATGTCAAAGAAAACACGTCCGAC
1 GAGCTTTTGCTAATATGTCAAAGAAAACACGTCCGAC
* *
39614 GAGCTTTTGTTAATATGTTAAAGAAAACACGTCC
1 GAGCTTTTGCTAATATGTCAAAGAAAACACGTCC
39648 AGCTCGATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (37 bp):
GAGCTTTTGCTAATATGTCAAAGAAAACACGTCCGAC
Found at i:40402 original size:3 final size:3
Alignment explanation
Indices: 40394--40431 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40384 TGACTTTTAA
40394 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40432 AGATGGAGTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45167 original size:2 final size:2
Alignment explanation
Indices: 45160--45186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45150 ATTTGTTAAC
45160 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
45187 CATGGTGGTC
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:45560 original size:2 final size:2
Alignment explanation
Indices: 45553--45582 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45543 GACTACCTTG
45553 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
45583 CTTTACTGAT
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):
AT
Found at i:49485 original size:2 final size:2
Alignment explanation
Indices: 49478--49506 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49468 CCGTATTAGT
49478 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 T
49507 TTAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50736 original size:2 final size:2
Alignment explanation
Indices: 50729--50759 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
50719 AAAAACATTT
50729 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
50760 ACATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:51807 original size:45 final size:45
Alignment explanation
Indices: 51743--51835 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
51733 AATCCGAGAA
* * *
51743 CTGTGATTGCTTACAAGGTATGTCATTTCTTTTACAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGTCATTCCTTTTAAAAAGTTAGCT
51788 CTGTGATTGCTTACAAGGTATGTCATTCCTTTTAAAAAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGTCATTCCTTTTAAAAAGTTAGCT
51833 CTG
1 CTG
51836 GTTTATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (45 bp):
CTGTGATTGCTTACAAGGTATGTCATTCCTTTTAAAAAGTTAGCT
Found at i:61484 original size:31 final size:31
Alignment explanation
Indices: 61418--61484 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
61408 AACAGTCCGG
* *
61418 TGACTTAAATAAAAACTTTCATATAGTTTAG
1 TGACTTAAATAAAAACTTTCATATAGTTCAA
* * *
61449 TGACTTAAATGAAGACTTTTGA-ATAGTTCAA
1 TGACTTAAATAAAAAC-TTTCATATAGTTCAA
61480 TGACT
1 TGACT
61485 ATTTTGTGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCATATAGTTCAA
Found at i:66270 original size:32 final size:32
Alignment explanation
Indices: 66232--66310 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
66222 TTAAATTTTG
66232 GATCATTTCAG-TTT-GAATTGATCTTGAGTTCA
1 GATCATTTCAGATTTAG-ATTG-TCTTGAGTTCA
* *
66264 GATCATTTTAGATTTAGATTGTTTTGAGTTCA
1 GATCATTTCAGATTTAGATTGTCTTGAGTTCA
*
66296 AATCATTTCAGATTT
1 GATCATTTCAGATTT
66311 TGGTCACTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 33 0.80
33 7 0.17
34 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (32 bp):
GATCATTTCAGATTTAGATTGTCTTGAGTTCA
Found at i:73774 original size:19 final size:19
Alignment explanation
Indices: 73750--73788 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
73740 TACTTTAATA
* *
73750 TTTATTAATTTAATATTTT
1 TTTATTAATTGAAAATTTT
*
73769 TTTATTTATTGAAAATTTT
1 TTTATTAATTGAAAATTTT
73788 T
1 T
73789 ATATAGTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATTAATTGAAAATTTT
Found at i:73775 original size:15 final size:15
Alignment explanation
Indices: 73737--73776 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
73727 ATTTATTCTA
73737 TTTTACTTTAATATTT
1 TTTTA-TTTAATATTT
* *
73753 ATTAATTTAATATTT
1 TTTTATTTAATATTT
73768 TTTTATTTA
1 TTTTATTTA
73777 TTGAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATTTAATATTT
Found at i:82976 original size:65 final size:65
Alignment explanation
Indices: 82905--83035 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
82895 GTTAAATTAA
82905 TGATTTTACTAATGAAAAGATATTATTGATATAAATTAAAAAAATTAAGGGTATAATTAGAATAT
1 TGATTTTACTAATGAAAAGATATTATTGATATAAATTAAAAAAATTAAGGGTATAATTAGAATAT
* *
82970 TGATTTTACTAATGAAAGGATATTATTGATATAAATTTAAAAAATTAAGGGTATAATTAGAATAT
1 TGATTTTACTAATGAAAAGATATTATTGATATAAATTAAAAAAATTAAGGGTATAATTAGAATAT
83035 T
1 T
83036 TTAAAGTTGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (65 bp):
TGATTTTACTAATGAAAAGATATTATTGATATAAATTAAAAAAATTAAGGGTATAATTAGAATAT
Found at i:88159 original size:18 final size:18
Alignment explanation
Indices: 88125--88159 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88115 TGAGTTTTTC
*
88125 TCAATCATTTTGATCTCA
1 TCAATCATTCTGATCTCA
*
88143 TCAATCATTCTGCTCTC
1 TCAATCATTCTGATCTC
88160 CATTCATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.43
Consensus pattern (18 bp):
TCAATCATTCTGATCTCA
Found at i:96758 original size:20 final size:20
Alignment explanation
Indices: 96716--96759 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
96706 ATTTGACTAG
* **
96716 TTTTGGGTCTCGATCTCGGT
1 TTTTGGGTCTCGAGCTCAAT
*
96736 TTTTGGTTCTCGAGCTCAAT
1 TTTTGGGTCTCGAGCTCAAT
96756 TTTT
1 TTTT
96760 TATCTCAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTTGGGTCTCGAGCTCAAT
Found at i:104941 original size:20 final size:21
Alignment explanation
Indices: 104918--104957 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
104908 TCTAAACCTC
104918 AAACCTCAAACA-TGAACCCT
1 AAACCTCAAACATTGAACCCT
* *
104938 AAACTTCGAACATTGAACCC
1 AAACCTCAAACATTGAACCC
104958 AAGGTTCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.33, G:0.07, T:0.17
Consensus pattern (21 bp):
AAACCTCAAACATTGAACCCT
Found at i:106129 original size:23 final size:25
Alignment explanation
Indices: 106102--106148 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
106092 GAAAGTATAA
*
106102 AATTTA-A-AAAAAAAATCTAAAAG
1 AATTTAGATAAAAAAAATATAAAAG
*
106125 AATTTAGATTAAAAAAATATAAAA
1 AATTTAGATAAAAAAAATATAAAA
106149 TGGACCAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (25 bp):
AATTTAGATAAAAAAAATATAAAAG
Found at i:106539 original size:5 final size:6
Alignment explanation
Indices: 106508--106544 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
106498 GGGCAAAGGA
106508 GCAAAG GCAAAG GCAAAG GCAAAG GC-AAG GC-AAG GCA
1 GCAAAG GCAAAG GCAAAG GCAAAG GCAAAG GCAAAG GCA
106545 TGCTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.46, C:0.19, G:0.35, T:0.00
Consensus pattern (6 bp):
GCAAAG
Found at i:123628 original size:6 final size:6
Alignment explanation
Indices: 123627--123653 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
123617 GAGAGAGTGA
123627 GAGAGT GAGAGT GAGAGT GAGAGT GAG
1 GAGAGT GAGAGT GAGAGT GAGAGT GAG
123654 GGAGGGACTA
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:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GAGAGT
Found at i:134187 original size:22 final size:22
Alignment explanation
Indices: 134162--134203 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
134152 GTCCTTATAG
134162 TTTT-TTTTTTAAGAATTTAATC
1 TTTTATTTTTT-AGAATTTAATC
*
134184 TTTTATTTTTTAGATTTTAA
1 TTTTATTTTTTAGAATTTAA
134204 AATTTAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTTATTTTTTAGAATTTAATC
Found at i:146062 original size:14 final size:15
Alignment explanation
Indices: 146043--146074 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
146033 CATAATTTCA
146043 TTATGACAAAAC-TG
1 TTATGACAAAACTTG
146057 TTATGACAAAACTTG
1 TTATGACAAAACTTG
146072 TTA
1 TTA
146075 GTAGTAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
TTATGACAAAACTTG
Found at i:146712 original size:19 final size:20
Alignment explanation
Indices: 146690--146727 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
146680 TAATTTGATG
146690 TTTAAATT-ATTTAAAATTT
1 TTTAAATTAATTTAAAATTT
* *
146709 TTTAATTTAATTTTAAATT
1 TTTAAATTAATTTAAAATT
146728 ATTAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAAATTAATTTAAAATTT
Found at i:146726 original size:20 final size:20
Alignment explanation
Indices: 146698--146737 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
146688 TGTTTAAATT
* *
146698 ATTTAAAATTTTTTAATTTA
1 ATTTAAAATTATTAAATTTA
*
146718 ATTTTAAATTATTAAATTTA
1 ATTTAAAATTATTAAATTTA
146738 TTATTATACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAAAATTATTAAATTTA
Found at i:150169 original size:48 final size:47
Alignment explanation
Indices: 150117--150263 Score: 106
Period size: 48 Copynumber: 3.1 Consensus size: 47
150107 AAATATATTC
150117 TTATTATATAATTATATAATTATTAATTTATTTATATAAATAAAGGAG
1 TTATTATATAATTA-ATAATTATTAATTTATTTATATAAATAAAGGAG
* * * * * * * **
150165 TTATTA-AT--TTAAAATATTTTTAATGTAATGATATACATTATA--TT
1 TTATTATATAATTAATA-ATTATTAATTTATTTATATA-AATAAAGGAG
** *
150209 TCTATTATATAATTACATGTTTATTATTTTATTTATATAAATAAAGGAG
1 T-TATTATATAATTA-ATAATTATTAATTTATTTATATAAATAAAGGAG
150258 TTATTA
1 TTATTA
150264 ATTAAAAAGA
Statistics
Matches: 69, Mismatches: 21, Indels: 18
0.64 0.19 0.17
Matches are distributed among these distances:
44 3 0.04
45 24 0.35
46 6 0.09
47 6 0.09
48 28 0.41
49 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (47 bp):
TTATTATATAATTAATAATTATTAATTTATTTATATAAATAAAGGAG
Found at i:154019 original size:19 final size:17
Alignment explanation
Indices: 153987--154021 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
153977 CTTTAATTTT
153987 CAATAATAATAATAATA
1 CAATAATAATAATAATA
154004 CAATATATAATGAATAAT
1 CAATA-ATAAT-AATAAT
154022 TTTTGCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
CAATAATAATAATAATA
Found at i:154134 original size:27 final size:27
Alignment explanation
Indices: 154104--154158 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
154094 GGATTGGATC
154104 AATTTACTCTCTATACGATTAAAAAAA
1 AATTTACTCTCTATACGATTAAAAAAA
154131 AATTTACTCTCTATACGATTAAAAAAA
1 AATTTACTCTCTATACGATTAAAAAAA
154158 A
1 A
154159 TCAAATAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.33
Consensus pattern (27 bp):
AATTTACTCTCTATACGATTAAAAAAA
Found at i:162931 original size:22 final size:23
Alignment explanation
Indices: 162906--162950 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
162896 AACATTTGCT
**
162906 TGTTA-AATTATATCTATTTTTG
1 TGTTATAATTATAAATATTTTTG
162928 TGTTATTAATTATAAATATTTTT
1 TGTTA-TAATTATAAATATTTTT
162951 AATGTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
24 14 0.74
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (23 bp):
TGTTATAATTATAAATATTTTTG
Found at i:168248 original size:17 final size:16
Alignment explanation
Indices: 168216--168250 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
168206 AATAAATAAT
168216 TAAAATATTAAAAAAA
1 TAAAATATTAAAAAAA
168232 TAAAATCATTTAAAAAAA
1 TAAAAT-A-TTAAAAAAA
168250 T
1 T
168251 TATAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 1 0.06
18 10 0.59
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATATTAAAAAAA
Found at i:171029 original size:16 final size:16
Alignment explanation
Indices: 171008--171049 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
170998 GGGCCTGATT
171008 TTTTTATTCAAATT-TA
1 TTTTTA-TCAAATTATA
*
171024 TTTTTA-CAACTTATA
1 TTTTTATCAAATTATA
171039 TTTTTATCAAA
1 TTTTTATCAAA
171050 ATCTTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTATCAAATTATA
Found at i:176167 original size:22 final size:21
Alignment explanation
Indices: 176139--176188 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
176129 TGATCCCTAT
176139 ATTTTTTATTTTGAT-TAATTTA
1 ATTTTTTATTTT-ATGT-ATTTA
* *
176161 ATTTTTTCTTTTATGTTTTTA
1 ATTTTTTATTTTATGTATTTA
176182 ATTTTTT
1 ATTTTTT
176189 TTCTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (21 bp):
ATTTTTTATTTTATGTATTTA
Found at i:179995 original size:29 final size:28
Alignment explanation
Indices: 179957--180301 Score: 177
Period size: 29 Copynumber: 11.8 Consensus size: 28
179947 GAGGTCCCTA
179957 AACTGTCCAAAAATTACATTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTACCC-CG
* * * *
179987 AACTTCCAAAAATCCAGATTTTGACCTCG
1 AACTTCCAAAAAT-TACATTTTTACCCCG
* *
180016 AAACTTCTAAAAATTACCA-TTTTATCCCG
1 -AACTTCCAAAAATTA-CATTTTTACCCCG
* *
180045 AACTTCCAAAAATTCCCATTTTGACCCCG
1 AACTTCCAAAAATT-ACATTTTTACCCCG
*
180074 AAACTT-TAAAAATTACCA-TTTTACCCTCG
1 -AACTTCCAAAAATTA-CATTTTTACCC-CG
** * * *
180103 AACTTCCAAAAATCCCAATTTTGACACTG
1 AACTTCCAAAAATTAC-ATTTTTACCCCG
* *
180132 AAACTTCCAAAAAATACCA-TTTTACCCCTA
1 -AACTTCCAAAAATTA-CATTTTTACCCC-G
** * *
180162 AACTTAAAAAAATCT-CAATTTTAACCCCAA
1 AACTTCCAAAAAT-TAC-ATTTTTACCCC-G
*
180192 AACTTTCAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATTA-CATTTTTA-CCCCG
* * *
180221 AACCTCCAAAAATTCCATTTTTGACTCCG
1 AACTTCCAAAAATTACATTTTT-ACCCCG
**
180250 AAAC-TCTCAAAAATTAC-TATTTTACTCCTA
1 -AACTTC-CAAAAATTACAT-TTTTAC-CCCG
*
180280 AACTTCC-AAAATTCCATTTTTA
1 AACTTCCAAAAATTACATTTTTA
180302 ACCCAGAAAT
Statistics
Matches: 239, Mismatches: 48, Indels: 58
0.69 0.14 0.17
Matches are distributed among these distances:
28 43 0.18
29 98 0.41
30 96 0.40
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (28 bp):
AACTTCCAAAAATTACATTTTTACCCCG
Found at i:180056 original size:58 final size:57
Alignment explanation
Indices: 179956--180330 Score: 334
Period size: 59 Copynumber: 6.4 Consensus size: 57
179946 AGAGGTCCCT
*
179956 AAACTGTCCAAAAATTA-CATTTTTACCCTCGAACTTCCAAAAATCCAGATTTTGACCTCG
1 AAACT-TCTAAAAATTACCA-TTTTACCC-CGAACTTCCAAAAATCCA-ATTTTGACCTCG
* * *
180016 AAACTTCTAAAAATTACCATTTTATCCCGAACTTCCAAAAATTCCCATTTTGACCCCG
1 AAACTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAA-TCCAATTTTGACCTCG
180074 AAACTT-TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACACT-G
1 AAACTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAAT-CCAATTTTGAC-CTCG
* * * ** * * *
180132 AAACTTCCAAAAAATACCATTTTACCCCTAAACTTAAAAAAATCTCAATTTTAACCCCA
1 AAACTTCTAAAAATTACCATTTTACCCC-GAACTTCCAAAAATC-CAATTTTGACCTCG
* *
180191 AAACTT-TCAAAAATTACCATTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA-CTCCG
1 AAACTTCT-AAAAATTACCATTTTA-CCCCGAACTTCCAAAAA-TCCAATTTTGACCT-CG
* ** * * *
180250 AAAC-TCTCAAAAATTACTATTTTACTCCTAAACTTCCAAAATTCCATTTTTAACC-CAG
1 AAACTTCT-AAAAATTACCATTTTAC-CCCGAACTTCCAAAAATCCAATTTTGACCTC-G
* * *
180308 AAA-TTTTCAAAATTACCCTTTTA
1 AAACTTCTAAAAATTACCATTTTA
180331 TCGTCGGATG
Statistics
Matches: 262, Mismatches: 35, Indels: 39
0.78 0.10 0.12
Matches are distributed among these distances:
57 34 0.13
58 84 0.32
59 131 0.50
60 13 0.05
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (57 bp):
AAACTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCAATTTTGACCTCG
Found at i:181514 original size:12 final size:12
Alignment explanation
Indices: 181467--181514 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
181457 TGGCCCATAT
181467 GATCTGACACAC
1 GATCTGACACAC
*
181479 GATTTGACACAAC
1 GATCTGACAC-AC
181492 GATCT-AGCACAC
1 GATCTGA-CACAC
*
181504 GACCTGACACA
1 GATCTGACACA
181515 TAACCGTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (12 bp):
GATCTGACACAC
Found at i:183532 original size:59 final size:60
Alignment explanation
Indices: 183434--183570 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 60
183424 AGACACCCGG
* * *
183434 GGGTAGAACGGTAACTTTTAGAAAAAATCGGGATCAAAAACAAAATTTTTGGACAT-TCGA
1 GGGTAAAACGGTAATTTTTAGAAAAAATCGGGATAAAAAACAAAATTTTTGGACATCT-GA
* * ** *
183494 GGGTAAAATGGTAATTTTTAG-AAAAATTGGGATAAAAAACGGAATTTTTGGACATCTGG
1 GGGTAAAACGGTAATTTTTAGAAAAAATCGGGATAAAAAACAAAATTTTTGGACATCTGA
*
183553 GGGTAAAAGGGTAATTTT
1 GGGTAAAACGGTAATTTT
183571 GAATGTTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 48 0.72
60 19 0.28
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.28
Consensus pattern (60 bp):
GGGTAAAACGGTAATTTTTAGAAAAAATCGGGATAAAAAACAAAATTTTTGGACATCTGA
Found at i:183613 original size:30 final size:30
Alignment explanation
Indices: 183575--183659 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
183565 AATTTTGAAT
* *
183575 GTTTTGGGGT-AAAAAATGAGATTTTAGGGAA
1 GTTTGGGGGTCAAAAAAT-A-ATTTTAGAGAA
*
183606 GTTTGGGGGTCAAAACATAATTTTAGAGAA
1 GTTTGGGGGTCAAAAAATAATTTTAGAGAA
** *
183636 GTTTAAGGGTCAAAACATAATTTT
1 GTTTGGGGGTCAAAAAATAATTTT
183660 TGGATAACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 32 0.67
31 10 0.21
32 6 0.12
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (30 bp):
GTTTGGGGGTCAAAAAATAATTTTAGAGAA
Found at i:183672 original size:30 final size:30
Alignment explanation
Indices: 183612--183673 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
183602 GGAAGTTTGG
**
183612 GGGTCAAAACATAATTTTAGAGAAGTTTAA
1 GGGTCAAAACATAATTTTAGAGAAACTTAA
*
183642 GGGTCAAAACATAATTTTTG-GATAACTTAA
1 GGGTCAAAACATAATTTTAGAGA-AACTTAA
183672 GG
1 GG
183674 ATCTCCAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (30 bp):
GGGTCAAAACATAATTTTAGAGAAACTTAA
Found at i:184803 original size:3 final size:3
Alignment explanation
Indices: 184797--184874 Score: 52
Period size: 3 Copynumber: 26.0 Consensus size: 3
184787 ATTATATTGT
* * * * * *
184797 TTA TTA TTA TTA ATA -AA TTCA TTA CTG TTA TTA TTA ATA TTA TCA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* *
184842 -TA TTCA TCA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
184875 ATGTTCATTC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
2 2 0.03
3 51 0.88
4 5 0.09
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:186472 original size:15 final size:16
Alignment explanation
Indices: 186444--186473 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
186434 CAATTCTTTC
186444 TTCATTGCTTTTATCA
1 TTCATTGCTTTTATCA
186460 TTCATTG-TTTTATC
1 TTCATTGCTTTTATC
186474 TTTGTTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.60
Consensus pattern (16 bp):
TTCATTGCTTTTATCA
Found at i:189532 original size:25 final size:24
Alignment explanation
Indices: 189504--189550 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
189494 AAATCCTTAA
189504 CCTTATAAA-CTTTATTCAAATAAGT
1 CCTTA-AAATCTTTATT-AAATAAGT
*
189529 CCTTAAAATTTTTATTAAATAA
1 CCTTAAAATCTTTATTAAATAA
189551 TCTCATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (24 bp):
CCTTAAAATCTTTATTAAATAAGT
Found at i:189563 original size:24 final size:25
Alignment explanation
Indices: 189514--189564 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
189504 CCTTATAAAC
*
189514 TTTATTCAAATAAGTCCTTAAAATT
1 TTTATTCAAATAAGTCCATAAAATT
*
189539 TTTATT-AAATAA-TCTCATAATATT
1 TTTATTCAAATAAGTC-CATAAAATT
189563 TT
1 TT
189565 ATTTTTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTATTCAAATAAGTCCATAAAATT
Found at i:189712 original size:191 final size:187
Alignment explanation
Indices: 189453--189804 Score: 535
Period size: 191 Copynumber: 1.9 Consensus size: 187
189443 ATATGTATTG
* *
189453 TAGATGAAAATTCAATGCTTTTAAAGAAGGTAATATTTAAAAAATCCTTAACCTTATAAACTTTA
1 TAGATGAAAATTCAATGCTTTTAAAAAAGGTAATATTTAAAAAATCCTTAACCTGATAAACTTTA
* *
189518 TTCAAATAAGTCCTTAAAATTTTTATTAAATAATCTCA-TAATATTTTATTTTTATTCATGTAAG
66 TTCAAATAAGTCCTTAAAATTTTTATTAAATAATCTCACT-ATATTTTATGTTTATTCATGAAAG
* *
189582 TCTTTGATTTAAACTAAAATTGCTTGCCATATCACTTAATAAAACAAAATATTTACTT
130 TCCTTAATTTAAACTAAAATTGCTTGCCATATCACTTAATAAAACAAAATATTTACTT
* * * *
189640 TAGATGAAAATTCAATGTCTTTTAAAAAATGTAATACATTTAAAATAGTCCTTAATCTGATACAC
1 TAGATGAAAATTCAATG-CTTTTAAAAAAGGTAAT--ATTTAAAA-AATCCTTAACCTGATAAAC
* * *
189705 TTTATTCAAATAAGTCCTTATATTTTTTATTAAATAATCTCACTATCTTTTATGTTTATTCATGA
62 TTTATTCAAATAAGTCCTTAAAATTTTTATTAAATAATCTCACTATATTTTATGTTTATTCATGA
189770 AAGTCCTTAATTTAAACTAAAATTGCTTGCCATAT
127 AAGTCCTTAATTTAAACTAAAATTGCTTGCCATAT
189805 AATTCTTAAT
Statistics
Matches: 147, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
187 17 0.12
188 15 0.10
190 8 0.05
191 106 0.72
192 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (187 bp):
TAGATGAAAATTCAATGCTTTTAAAAAAGGTAATATTTAAAAAATCCTTAACCTGATAAACTTTA
TTCAAATAAGTCCTTAAAATTTTTATTAAATAATCTCACTATATTTTATGTTTATTCATGAAAGT
CCTTAATTTAAACTAAAATTGCTTGCCATATCACTTAATAAAACAAAATATTTACTT
Found at i:204891 original size:5 final size:5
Alignment explanation
Indices: 204866--204909 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
204856 TTTGACCTCC
* *
204866 GACGA GAAGA TACGAA GACGA GACGA GACGA GACGA GACGA GAC
1 GACGA GACGA GACG-A GACGA GACGA GACGA GACGA GACGA GAC
204910 AAAGACCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.43, C:0.18, G:0.36, T:0.02
Consensus pattern (5 bp):
GACGA
Found at i:204901 original size:15 final size:16
Alignment explanation
Indices: 204866--204920 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
204856 TTTGACCTCC
* *
204866 GACGAGAAGATACGAA
1 GACGAGACGAGACGAA
204882 GACGAGACGAGACG-A
1 GACGAGACGAGACGAA
*
204897 GACGAGACGAGACAAA
1 GACGAGACGAGACGAA
*
204913 GACCAGAC
1 GACGAGAC
204921 AGCAAGCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 14 0.41
16 20 0.59
ACGTcount: A:0.45, C:0.20, G:0.33, T:0.02
Consensus pattern (16 bp):
GACGAGACGAGACGAA
Found at i:205061 original size:20 final size:21
Alignment explanation
Indices: 205028--205068 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
205018 AATGCGTGTA
*
205028 TTTTCTAATCTTATTTTTTAT
1 TTTTCTAATCTTATTTATTAT
*
205049 TTTTCT-ATTTTATTTATTAT
1 TTTTCTAATCTTATTTATTAT
205069 ATGTGACGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCTAATCTTATTTATTAT
Found at i:213125 original size:29 final size:30
Alignment explanation
Indices: 213072--213139 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
213062 TATTCGCGAA
*
213072 TTTAAAATTTAATCCTTAT-ATTTTTAT-T
1 TTTAAAATTTAATCCTTATAATTTTAATAT
* *
213100 TTTAAGAATTTAATCTTTTTAATTTTAATAT
1 TTTAA-AATTTAATCCTTATAATTTTAATAT
213131 TTTAAAATT
1 TTTAAAATT
213140 GTTAACACTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.15
29 12 0.35
30 11 0.32
31 6 0.18
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTAAAATTTAATCCTTATAATTTTAATAT
Found at i:213455 original size:28 final size:29
Alignment explanation
Indices: 213424--213482 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
213414 TATATCTTTC
213424 ATTTATTAAAACTTTACA-TATA-TTTTAT
1 ATTTATTAAAA-TTTACATTATAGTTTTAT
* * *
213452 ATTTTTTAATATTTATATTATAGTTTTAT
1 ATTTATTAAAATTTACATTATAGTTTTAT
213481 AT
1 AT
213483 ATTACTATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 13 0.50
29 8 0.31
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
ATTTATTAAAATTTACATTATAGTTTTAT
Found at i:213522 original size:2 final size:2
Alignment explanation
Indices: 213517--213568 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
213507 TATTGTAAAT
* *
213517 TA TA TA TA CA AA TA TA TA -A TA TA -A TA TA -A 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
213556 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
213569 AACATAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:213550 original size:19 final size:19
Alignment explanation
Indices: 213517--213568 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
213507 TATTGTAAAT
*
213517 TATATATACA-AATATATA
1 TATATATATATAATATATA
213535 -ATATA-ATATAATATATA
1 TATATATATATAATATATA
*
213552 TATATATATATATTATA
1 TATATATATATAATATA
213569 AACATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 5 0.17
19 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATATATATAATATATA
Found at i:214290 original size:30 final size:31
Alignment explanation
Indices: 214253--214321 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
214243 CATTAAACAC
214253 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACGTTATCGAAAA-GTGACAA
*
214283 AATAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAACGTTATCGAAAAGTGACAA
214314 AACAGTCA
1 AACAGTCA
214322 TTGAAATCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 15 0.44
32 5 0.15
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (31 bp):
AACAGTCACTAACGTTATCGAAAAGTGACAA
Found at i:214509 original size:30 final size:31
Alignment explanation
Indices: 214440--214512 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
214430 GTGTTTAGAA
* *
214440 TTAGTGATTGTTTTGTCATTTTTTGATAACG
1 TTAGTGACTGTTTTGTCAATTTTTGATAACG
214471 TTAGTGACTGTTTTGTCACATTTTT-A-AA-G
1 TTAGTGACTGTTTTGTCA-ATTTTTGATAACG
214500 TTGAGTGACTGTT
1 TT-AGTGACTGTT
214513 GTGTTAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 18 0.47
32 5 0.13
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.51
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTCAATTTTTGATAACG
Found at i:214874 original size:17 final size:16
Alignment explanation
Indices: 214852--214885 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
214842 AATAAATCAT
*
214852 TAAAAAATTATAAAAAA
1 TAAAAAA-TAAAAAAAA
214869 TAAAAAATAAAAAAAA
1 TAAAAAATAAAAAAAA
214885 T
1 T
214886 TAGTTCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAAATAAAAAAAA
Found at i:215244 original size:22 final size:22
Alignment explanation
Indices: 215217--215260 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
215207 AAGTGACATA
*
215217 TAAAAACATAATAAAATATTTTC
1 TAAAAATA-AATAAAATATTTTC
*
215240 TAAAAATAAATATAATATTTT
1 TAAAAATAAATAAAATATTTT
215261 TTATTAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAATAAATAAAATATTTTC
Found at i:218167 original size:25 final size:25
Alignment explanation
Indices: 218106--218186 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 25
218096 GCAAGTATGA
*
218106 AATTGAAAATAAAAATATTAGTAATT
1 AATT-AAAATAAAATTATTAGTAATT
*
218132 AAATTAGAAATAAAATTATTTAATAATT
1 -AATTA-AAATAAAATTA-TTAGTAATT
*
218160 AATT-AAATAGAATTAATTAGTAATT
1 AATTAAAATAAAATT-ATTAGTAATT
218185 AA
1 AA
218187 ATTGATTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
25 19 0.40
26 2 0.04
27 18 0.38
28 8 0.17
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
AATTAAAATAAAATTATTAGTAATT
Found at i:218200 original size:21 final size:21
Alignment explanation
Indices: 218159--218202 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
218149 ATTTAATAAT
218159 TAATTAAATAGAATTAATTAG
1 TAATTAAATAGAATTAATTAG
*
218180 TAATTAAATTG-ATTAAGTTAG
1 TAATTAAATAGAATTAA-TTAG
218201 TA
1 TA
218203 TGTATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
TAATTAAATAGAATTAATTAG
Found at i:221267 original size:6 final size:6
Alignment explanation
Indices: 221256--221287 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
221246 CAACTAGTGT
*
221256 TTGCAG TTGCAG TTGCAG TTGCAG TTACAG TT
1 TTGCAG TTGCAG TTGCAG TTGCAG TTGCAG TT
221288 CCACTTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (6 bp):
TTGCAG
Found at i:232000 original size:15 final size:15
Alignment explanation
Indices: 231980--232008 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
231970 ATTAAAAATA
231980 AAAAAATAATATTTT
1 AAAAAATAATATTTT
231995 AAAAAATAATATTT
1 AAAAAATAATATTT
232009 ATTTTTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAAATAATATTTT
Found at i:232194 original size:17 final size:18
Alignment explanation
Indices: 232172--232213 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
232162 TTGGTATCTT
*
232172 AAAATTTTTAAAA-AATA
1 AAAATTATTAAAATAATA
232189 AAAATTATTAAAATAAT-
1 AAAATTATTAAAATAATA
232206 AAAATTAT
1 AAAATTAT
232214 ATTTTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAAATAATA
Found at i:233118 original size:29 final size:29
Alignment explanation
Indices: 233076--233141 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
233066 ACAGTGGTGT
* *
233076 GCGGACACACGTTGTCAGCAAAACTACCA
1 GCGGGCACACGTTGCCAGCAAAACTACCA
233105 GCGGGCACACGTTGCCAGCAAAACTACCA
1 GCGGGCACACGTTGCCAGCAAAACTACCA
233134 GCGGGCAC
1 GCGGGCAC
233142 GGATAACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.26, T:0.11
Consensus pattern (29 bp):
GCGGGCACACGTTGCCAGCAAAACTACCA
Found at i:233607 original size:45 final size:45
Alignment explanation
Indices: 233554--233644 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
233544 AAAACAAGAG
233554 ATGGTGATTACATTTAATGGAAGTAATGGAAAAAAATAAACTTTT
1 ATGGTGATTACATTTAATGGAAGTAATGGAAAAAAATAAACTTTT
*
233599 ATGGTGATTACATTTAATGGAAGTAATGGAGAAAAATAAACTTTT
1 ATGGTGATTACATTTAATGGAAGTAATGGAAAAAAATAAACTTTT
233644 A
1 A
233645 ATCCTGTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (45 bp):
ATGGTGATTACATTTAATGGAAGTAATGGAAAAAAATAAACTTTT
Found at i:246283 original size:3 final size:3
Alignment explanation
Indices: 246275--246299 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
246265 GTAAAGTTAG
246275 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
246300 ACAGAGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:247214 original size:19 final size:20
Alignment explanation
Indices: 247186--247228 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
247176 TTTGACCATA
*
247186 AAAATCAACAATTTGAAC-C
1 AAAATCAACAACTTGAACTC
*
247205 AAAATTAACAACTTGAACTC
1 AAAATCAACAACTTGAACTC
247225 AAAA
1 AAAA
247229 CGATCTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATCAACAACTTGAACTC
Found at i:259336 original size:28 final size:28
Alignment explanation
Indices: 259304--259372 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
259294 AATAGTTTAT
259304 ATTTTTATATTTTTAAAGGATTAAATTA-
1 ATTTTTATATTTTT-AAGGATTAAATTAC
259332 ATTTTTATTATTTTTAAGGATTAAATTAC
1 ATTTTTA-TATTTTTAAGGATTAAATTAC
*
259361 AATTTTA-ATTTT
1 ATTTTTATATTTT
259373 ACTATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 5 0.13
28 20 0.53
29 13 0.34
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (28 bp):
ATTTTTATATTTTTAAGGATTAAATTAC
Found at i:259674 original size:13 final size:13
Alignment explanation
Indices: 259656--259680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259646 TTAAGTGAAG
259656 ATTAAATTAATTA
1 ATTAAATTAATTA
259669 ATTAAATTAATT
1 ATTAAATTAATT
259681 TTAATGTTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAAATTAATTA
Found at i:260184 original size:19 final size:19
Alignment explanation
Indices: 260142--260184 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
260132 TTGATCCTCA
*
260142 TTTTTTTTTTGTTTTGAGT
1 TTTTTTTTTTCTTTTGAGT
*
260161 ATTTTTTTTTCTTTT-ATGT
1 TTTTTTTTTTCTTTTGA-GT
260180 TTTTT
1 TTTTT
260185 AAACTTTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.07, C:0.02, G:0.09, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTTCTTTTGAGT
Found at i:264920 original size:59 final size:58
Alignment explanation
Indices: 264760--264920 Score: 160
Period size: 59 Copynumber: 2.7 Consensus size: 58
264750 TTTTTTGATC
* * * * * *
264760 CTTGAGTTTTGCTTCAATACTCAATTTAGTACTTAACATTTTTTTGTCCCATTTTAGTA
1 CTTGAGTTTTGCTTCAATATTCAATTTGGTACTTAGC-TTTTTTTGTCCCAATTAAATA
* * * * * * * *
264819 CCTAAGTTTGGCTTCAATTTTCATTTTGGTACCTAAGTTTTTTTTGTCTCAATTAAATA
1 CTTGAGTTTTGCTTCAATATTCAATTTGGTA-CTTAGCTTTTTTTGTCCCAATTAAATA
*
264878 CTTGAGTTTTGCTTCAATGTTCAATTTGGTACTTGAGCTTTTT
1 CTTGAGTTTTGCTTCAATATTCAATTTGGTACTT-AGCTTTTT
264921 GTATTCCGAT
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
58 2 0.03
59 74 0.94
60 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.50
Consensus pattern (58 bp):
CTTGAGTTTTGCTTCAATATTCAATTTGGTACTTAGCTTTTTTTGTCCCAATTAAATA
Found at i:268220 original size:11 final size:11
Alignment explanation
Indices: 268201--268236 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
268191 ATGAAATGGT
268201 AACAAAACAAC
1 AACAAAACAAC
* *
268212 AACATAACAAT
1 AACAAAACAAC
268223 AACAAAACAAC
1 AACAAAACAAC
268234 AAC
1 AAC
268237 GTAACAAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (11 bp):
AACAAAACAAC
Found at i:268225 original size:22 final size:22
Alignment explanation
Indices: 268200--268243 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
268190 AATGAAATGG
268200 TAACAAAACAACAACATAACAA
1 TAACAAAACAACAACATAACAA
*
268222 TAACAAAACAACAACGTAACAA
1 TAACAAAACAACAACATAACAA
268244 GTAGTCAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.23, G:0.02, T:0.09
Consensus pattern (22 bp):
TAACAAAACAACAACATAACAA
Found at i:268242 original size:11 final size:11
Alignment explanation
Indices: 268201--268243 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
268191 ATGAAATGGT
*
268201 AACAAAACAAC
1 AACATAACAAC
*
268212 AACATAACAAT
1 AACATAACAAC
*
268223 AACAAAACAAC
1 AACATAACAAC
*
268234 AACGTAACAA
1 AACATAACAA
268244 GTAGTCAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.67, C:0.23, G:0.02, T:0.07
Consensus pattern (11 bp):
AACATAACAAC
Found at i:269821 original size:3 final size:3
Alignment explanation
Indices: 269806--269839 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
269796 ATGAAGCTGG
* *
269806 TCA TCA GCA TCA TCA TCA TCA GCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
269840 AAACAACAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (3 bp):
TCA
Found at i:269826 original size:15 final size:15
Alignment explanation
Indices: 269806--269839 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
269796 ATGAAGCTGG
269806 TCATCAGCATCATCA
1 TCATCAGCATCATCA
269821 TCATCAGCATCATCA
1 TCATCAGCATCATCA
269836 TCAT
1 TCAT
269840 AAACAACAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (15 bp):
TCATCAGCATCATCA
Found at i:273016 original size:20 final size:20
Alignment explanation
Indices: 272993--273031 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
272983 ATATATAACC
*
272993 CTTATTATATTATTATTTAG
1 CTTATAATATTATTATTTAG
*
273013 CTTATAATTTTATTATTTA
1 CTTATAATATTATTATTTA
273032 TTCATACTAA
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:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
CTTATAATATTATTATTTAG
Found at i:277730 original size:11 final size:11
Alignment explanation
Indices: 277714--277771 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
277704 GATATTTTTG
277714 TATTGTTTTCT
1 TATTGTTTTCT
* *
277725 TGTTGTTTTGT
1 TATTGTTTTCT
* *
277736 TACTATTTTCT
1 TATTGTTTTCT
277747 TATTGTTTTCT
1 TATTGTTTTCT
* * *
277758 CACTGTTTTGT
1 TATTGTTTTCT
277769 TAT
1 TAT
277772 CATTTCATTA
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.10, C:0.10, G:0.12, T:0.67
Consensus pattern (11 bp):
TATTGTTTTCT
Found at i:277765 original size:33 final size:33
Alignment explanation
Indices: 277706--277770 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
277696 CAAAAAATGA
***
277706 TATTTTTGTATTGTTTTCTTGTTGTTTTGTTAC
1 TATTTTTGTATTGTTTTCTCACTGTTTTGTTAC
277739 TATTTTCT-TATTGTTTTCTCACTGTTTTGTTA
1 TATTTT-TGTATTGTTTTCTCACTGTTTTGTTA
277771 TCATTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.12, T:0.68
Consensus pattern (33 bp):
TATTTTTGTATTGTTTTCTCACTGTTTTGTTAC
Found at i:277766 original size:22 final size:22
Alignment explanation
Indices: 277717--277771 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
277707 ATTTTTGTAT
* * *
277717 TGTTTTCTTGTTGTTTTGTTAC
1 TGTTTTCTTATTGTTTTCTCAC
*
277739 TATTTTCTTATTGTTTTCTCAC
1 TGTTTTCTTATTGTTTTCTCAC
*
277761 TGTTTTGTTAT
1 TGTTTTCTTAT
277772 CATTTCATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.09, C:0.11, G:0.13, T:0.67
Consensus pattern (22 bp):
TGTTTTCTTATTGTTTTCTCAC
Found at i:281344 original size:295 final size:295
Alignment explanation
Indices: 280746--281624 Score: 1527
Period size: 295 Copynumber: 3.0 Consensus size: 295
280736 TTGAGGCTTG
* * * *
280746 AACTTGGTAACTATTTCCATATTAAGGCTTGAACTTTTTTTTCA-G--GTTAAGCCTTAAACTTG
1 AACTTGGTAATTATTTCCATATTAAGACTTGAAC-TTTTTTTGAGGAAGTTAAACCTTAAACTTG
* * *
280808 GTAATTGTTTCCATATTGGAGCTTGAACTTTTCTTTTAATATAAGTTAGTCCCTGATATTTCCTT
65 GCAATTGTTTCCATATTGGAGCTTGAACTTTTCTTTTAATATAAGTTTGTCCTTGATATTTCCTT
* * *
280873 GAAAAACTTAAAGTTCAGGCCTCAATGTGAGAATAATTGTCTAGTTTAGGAACTAACTTGGAC--
130 GAAAAACTTAAAGTTCAAGCCCCAATGTGAGAATAATTGTCAAGTTTAGGAACTAACTTGGACAA
* *
280936 -AGAAAAATTCAAGTCCCAATATGAGAAAAATTGTCAAGTTCAAGACTTAACTTGGACTAGGGCT
195 AAGAAAAATTCAAGTCCCAATGTGAGAAAAATTGTCAAGTTCAGGACTTAACTTGGACTAGGGCT
281000 GAGCAAATAAACCGATAAAACCAAAAAATCGATCTA
260 GAGCAAATAAACCGATAAAACCAAAAAATCGATCTA
281036 AACTTGGTAATTATTTCCATATTAAGACTTGAACTTTTTTTGAGGAAGTTAAACCTTAAACTTGG
1 AACTTGGTAATTATTTCCATATTAAGACTTGAACTTTTTTTGAGGAAGTTAAACCTTAAACTTGG
* *
281101 CAATTGTTTTCATATTAGAGCTTGAACTTTTCTTTTAATATAAGTTTGTCCTTGATATTTCCTTG
66 CAATTGTTTCCATATTGGAGCTTGAACTTTTCTTTTAATATAAGTTTGTCCTTGATATTTCCTTG
* *
281166 AAAAACTTAAAGTTCAAGCCCCAACGTGCGAATAATTGTCAAGTTTAGGAACTAACTTGGACAAA
131 AAAAACTTAAAGTTCAAGCCCCAATGTGAGAATAATTGTCAAGTTTAGGAACTAACTTGGACAAA
281231 AGAAAAATTCAAGTCCCAATGTGAGAAAAATTGTCAAGTTCAGGACTTAACTTGGACTAGGGCTG
196 AGAAAAATTCAAGTCCCAATGTGAGAAAAATTGTCAAGTTCAGGACTTAACTTGGACTAGGGCTG
*
281296 AGCAAATAAACCTATAAAACCAAAAAATCGATCTA
261 AGCAAATAAACCGATAAAACCAAAAAATCGATCTA
281331 AACTTGGTAATTATTTCCATATTAAGACTTGAACTTTTTTTGAGGAAGTTAAACCTTAAACTTGG
1 AACTTGGTAATTATTTCCATATTAAGACTTGAACTTTTTTTGAGGAAGTTAAACCTTAAACTTGG
281396 CAATTGTTTCCATATTGGAGCTTGAACTTTTCTTTTAATATAAGTTTGTCCTTGATATTTCCTTG
66 CAATTGTTTCCATATTGGAGCTTGAACTTTTCTTTTAATATAAGTTTGTCCTTGATATTTCCTTG
281461 AAAAACTTAAAGTTCAAGCCCCAATGTGAGAATAATTGTCAAGTTTAGGAACTAACTTGGACAAA
131 AAAAACTTAAAGTTCAAGCCCCAATGTGAGAATAATTGTCAAGTTTAGGAACTAACTTGGACAAA
* * *
281526 AGAAAATTTCAAGTCCCAATGTGAGAAAAATTGTCAAATTCAGAACTTAACTTGGACTAGGGCTG
196 AGAAAAATTCAAGTCCCAATGTGAGAAAAATTGTCAAGTTCAGGACTTAACTTGGACTAGGGCTG
281591 AGCAAATAAACCGATAAAACCAAAAAATCGATCT
261 AGCAAATAAACCGATAAAACCAAAAAATCGATCT
281625 GAATCGATGT
Statistics
Matches: 558, Mismatches: 25, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
289 8 0.01
290 33 0.06
292 134 0.24
295 383 0.69
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (295 bp):
AACTTGGTAATTATTTCCATATTAAGACTTGAACTTTTTTTGAGGAAGTTAAACCTTAAACTTGG
CAATTGTTTCCATATTGGAGCTTGAACTTTTCTTTTAATATAAGTTTGTCCTTGATATTTCCTTG
AAAAACTTAAAGTTCAAGCCCCAATGTGAGAATAATTGTCAAGTTTAGGAACTAACTTGGACAAA
AGAAAAATTCAAGTCCCAATGTGAGAAAAATTGTCAAGTTCAGGACTTAACTTGGACTAGGGCTG
AGCAAATAAACCGATAAAACCAAAAAATCGATCTA
Found at i:289885 original size:4 final size:4
Alignment explanation
Indices: 289876--289906 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
289866 AGGCATTTCA
289876 ATGT ATGT ATGT ATGT ATGT ATGT AATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT -ATGT AT
289907 TGATTGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:291050 original size:134 final size:132
Alignment explanation
Indices: 290812--291053 Score: 324
Period size: 134 Copynumber: 1.8 Consensus size: 132
290802 CCACATCCTT
* * *
290812 ACCCATCTCTTTAGCATTTGAAGAATCTTCTATAAGCTTTGACATCAATTCAACGTCCTCCTCCA
1 ACCCATCTCTTTAGCACTTGAAGAATCTTCTATAAGCTTTGACAACAATTCAACGTCATCCTCCA
* * * *
290877 TATTCATATCTATCTCTTTAGCACTTGGAGAATCTTCTATAAGCTTTGATATCAATTCCATGCTA
66 TAGTCATACCCATCTCTTTAGCACTTGCAGAATCTTCTATAAGCTTTGATATCAATTCCATGCTA
290942 TG
131 TG
* ** **
290944 ACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTTTGGTAACAATTCAGTGTTCAT-CT
1 ACCCATCTCTTTAGCACTTGAAGAATCTTCTATAAGC--TTTGACAACAATTCAACG-TCATCCT
* *
291008 CCATAGTCTTACCCATCTCTTTAGCACTTGCAGAGTCTTCTATAAG
63 CCATAGTCATACCCATCTCTTTAGCACTTGCAGAATCTTCTATAAG
291054 ATCAGTGTTC
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
132 35 0.38
134 55 0.59
135 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (132 bp):
ACCCATCTCTTTAGCACTTGAAGAATCTTCTATAAGCTTTGACAACAATTCAACGTCATCCTCCA
TAGTCATACCCATCTCTTTAGCACTTGCAGAATCTTCTATAAGCTTTGATATCAATTCCATGCTA
TG
Found at i:291071 original size:134 final size:132
Alignment explanation
Indices: 290811--291132 Score: 314
Period size: 134 Copynumber: 2.4 Consensus size: 132
290801 GCCACATCCT
* * ** * *
290811 TACCCATCTCTTTAGCATTTGAAGAATCTTCTATAAGCTTTGACATCAATTCAACGTCCTCCTCC
1 TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTGGTAACAATTCAACGTCATCCTCC
* * * * ** * *
290876 ATATTCATATCTATCTCTTTAGCACTTGGAGAATCTTCTATAAGCTTTGATATCAATTCCATGCT
66 ATAGTCATACCCATCTCTTTAGCACTTGCAGAATCTTCTATAAGCAGTGATATCAACTCCATACT
290941 -A
131 CA
**
290942 TGACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTTTGGTAACAATTCAGTGTTCAT-
1 T-ACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGC--TTTGGTAACAATTCAACG-TCATC
* * *
291006 CTCCATAGTCTTACCCATCTCTTTAGCACTTGCAGAGTCTTCTATAAGATCAGTG-T-TCACCTC
62 CTCCATAGTCATACCCATCTCTTTAGCACTTGCAGAATCTTCTATAAG--CAGTGATATCAACTC
*
291069 CATATTCA
125 CATACTCA
* * * *
291077 TACCCATC-CTGTTGGC-CATTGTAGAATCATCTAAAAGCTTTGGTAGCAATTCAACG
1 TACCCATCTCT-TTAGCAC-TTGTAGAATCTTCTATAAGCTTTGGTAACAATTCAACG
291133 CCCGCCTCAG
Statistics
Matches: 156, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
131 1 0.01
132 50 0.32
133 3 0.02
134 93 0.60
135 6 0.04
136 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (132 bp):
TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTGGTAACAATTCAACGTCATCCTCC
ATAGTCATACCCATCTCTTTAGCACTTGCAGAATCTTCTATAAGCAGTGATATCAACTCCATACT
CA
Found at i:291946 original size:120 final size:120
Alignment explanation
Indices: 291733--291974 Score: 475
Period size: 120 Copynumber: 2.0 Consensus size: 120
291723 CTGTCCGGCG
291733 AAAGGAAATCTAGCATCGGCCGAATTCGACATTCTTGATCCCGCGCGATTAGGAATCATCTCACC
1 AAAGGAAATCTAGCATCGGCCGAATTCGACATTCTTGATCCCGCGCGATTAGGAATCATCTCACC
291798 CTCAACTTGGAGGACTCCTTTCCAATCAGAATTCTACGCAAGTGAATATGTTCGA
66 CTCAACTTGGAGGACTCCTTTCCAATCAGAATTCTACGCAAGTGAATATGTTCGA
*
291853 AAAGGAAATCTAGCATCGGCCGAATTCGACATTCTTGATCCCGCGCGATTAGGAATCATCTTACC
1 AAAGGAAATCTAGCATCGGCCGAATTCGACATTCTTGATCCCGCGCGATTAGGAATCATCTCACC
291918 CTCAACTTGGAGGACTCCTTTCCAATCAGAATTCTACGCAAGTGAATATGTTCGA
66 CTCAACTTGGAGGACTCCTTTCCAATCAGAATTCTACGCAAGTGAATATGTTCGA
291973 AA
1 AA
291975 TTATTAGATA
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (120 bp):
AAAGGAAATCTAGCATCGGCCGAATTCGACATTCTTGATCCCGCGCGATTAGGAATCATCTCACC
CTCAACTTGGAGGACTCCTTTCCAATCAGAATTCTACGCAAGTGAATATGTTCGA
Found at i:292482 original size:18 final size:16
Alignment explanation
Indices: 292421--292484 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 16
292411 TGTAAATTTT
292421 TTTATAGTTTAAT-ATA
1 TTTATA-TTTAATAATA
*
292437 TTTATATTTATTAATA
1 TTTATATTTAATAATA
* *
292453 TTT-GATTAAATAATAA
1 TTTATATTTAATAAT-A
292469 TTTTATATTTAATAAT
1 -TTTATATTTAATAAT
292485 TTCGAGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.34
16 13 0.34
17 3 0.08
18 9 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTATATTTAATAATA
Found at i:293454 original size:21 final size:21
Alignment explanation
Indices: 293403--293456 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
293393 TTGAACCAAT
* * *
293403 AAAAAATTGATATTTAGAAAA
1 AAAAAATTTATTTTTAAAAAA
***
293424 AAATGTTTTATTTTTAAAAAA
1 AAAAAATTTATTTTTAAAAAA
293445 AAAAAATTTATT
1 AAAAAATTTATT
293457 ATGTATCGGT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (21 bp):
AAAAAATTTATTTTTAAAAAA
Found at i:295435 original size:31 final size:31
Alignment explanation
Indices: 295378--295474 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 31
295368 GAACCCCAAA
* * * *
295378 AAATTTAAATACCAACTTAAGAAAAAATATC
1 AAATTTAAGTACAAAATTAAAAAAAAATATC
* *
295409 AAGTTT-AGATA-ACAAATTAAAAAAAAATTGTC
1 AAATTTAAG-TACA-AAATTAAAAAAAAA-TATC
295441 AAATTTAAGTACAAAATTAAAAAAAAA-ATC
1 AAATTTAAGTACAAAATTAAAAAAAAATATC
295471 AAAT
1 AAAT
295475 ATCAATTACT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
30 7 0.13
31 19 0.36
32 24 0.45
33 3 0.06
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (31 bp):
AAATTTAAGTACAAAATTAAAAAAAAATATC
Found at i:296295 original size:30 final size:31
Alignment explanation
Indices: 296235--296303 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
296225 TTATAATTAA
* ** *
296235 ATTTA-TTTTTATAATATATATTTGCCATAT
1 ATTTATTTTTTATAATATAAAAATGCAATAT
296265 ATTTATTTTTTATAATATAAAAAT-CAATAT
1 ATTTATTTTTTATAATATAAAAATGCAATAT
296295 ATTATATTT
1 ATT-TATTT
296304 AAATTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (31 bp):
ATTTATTTTTTATAATATAAAAATGCAATAT
Found at i:296601 original size:26 final size:24
Alignment explanation
Indices: 296549--296601 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
296539 TATTTACATA
* *
296549 TTTTATTAATTTGACTCTTATTTT
1 TTTTATTAATTTGACTCTTAATCT
*
296573 TTTTAATTAAATTTGACTTTTAATCT
1 TTTT-ATT-AATTTGACTCTTAATCT
296599 TTT
1 TTT
296602 AAAAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 3 0.12
26 17 0.71
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTTATTAATTTGACTCTTAATCT
Found at i:304801 original size:21 final size:21
Alignment explanation
Indices: 304765--304809 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
304755 TCTACTTGGT
* *
304765 AAAAGAAACTGATAAATCATAA
1 AAAAAAAACTGATAAAACA-AA
304787 AAAAAAAACTG-TAAAACAAA
1 AAAAAAAACTGATAAAACAAA
304807 AAA
1 AAA
304810 TTTGTGACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.71, C:0.09, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAAAAAACTGATAAAACAAA
Found at i:305425 original size:29 final size:27
Alignment explanation
Indices: 305369--305433 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
305359 CATGTGACAA
305369 AAAAGTTATAAAAAAATAAAAATCAAT
1 AAAAGTTATAAAAAAATAAAAATCAAT
* ** *
305396 AAGAGTTATAAAAAATATTAAATTTTAAT
1 AAAAGTTATAAAAAA-A-TAAAAATCAAT
305425 AAAAGTTAT
1 AAAAGTTAT
305434 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 14 0.45
28 1 0.03
29 16 0.52
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAGTTATAAAAAAATAAAAATCAAT
Found at i:306491 original size:16 final size:16
Alignment explanation
Indices: 306463--306503 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
306453 GAGATCTAGA
*
306463 TAAGATTATAAAT-TT
1 TAAGATTAAAAATATT
306478 TAAGTATTAAAAATATT
1 TAAG-ATTAAAAATATT
306495 TAA-ATTAAA
1 TAAGATTAAA
306504 TTATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TAAGATTAAAAATATT
Found at i:307832 original size:30 final size:30
Alignment explanation
Indices: 307789--307863 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
307779 AGCCTGTATC
* *
307789 TTTATAATATTTAAAGGATTAA-ATCAAAT
1 TTTATCATTTTTAAAGGATTAACATCAAAT
* * * **
307818 TTCTATCATTTTTAAGGGTTTAACGTGTAAT
1 TT-TATCATTTTTAAAGGATTAACATCAAAT
307849 TTTATCATTTTTAAA
1 TTTATCATTTTTAAA
307864 TTAAAATCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 2 0.06
30 28 0.78
31 6 0.17
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTATCATTTTTAAAGGATTAACATCAAAT
Found at i:310315 original size:15 final size:15
Alignment explanation
Indices: 310295--310344 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
310285 ATAAATTTTT
310295 AAATTAATAATAGTA
1 AAATTAATAATAGTA
** *
310310 AAATTACATTTTTGATA
1 AAATTA-ATAATAG-TA
310327 AAATTAATAATAGTA
1 AAATTAATAATAGTA
310342 AAA
1 AAA
310345 ATTATAAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 11 0.41
16 8 0.30
17 8 0.30
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (15 bp):
AAATTAATAATAGTA
Found at i:315997 original size:59 final size:60
Alignment explanation
Indices: 315896--316008 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
315886 GACAAGATTA
* * **
315896 AATAGTTAGATGACCATTTTGTAACTTTTCATAGTTTAGTGACCAAAAAAGAAATTTACT
1 AATAGTTAGATGACCATTTTGTAACTCTTAATAGAATAGTGACCAAAAAAGAAATTTACT
* *
315956 AATAGTTA-TTGACCATTTTGTAACTCTTAATA-AATAGGTGACCAGAAAAGAAA
1 AATAGTTAGATGACCATTTTGTAACTCTTAATAGAATA-GTGACCAAAAAAGAAA
316009 AAAGACCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 2 0.04
59 36 0.78
60 8 0.17
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (60 bp):
AATAGTTAGATGACCATTTTGTAACTCTTAATAGAATAGTGACCAAAAAAGAAATTTACT
Found at i:316961 original size:16 final size:16
Alignment explanation
Indices: 316940--316979 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
316930 ATTGATTAGG
*
316940 GTTGTAATGAAATAGA
1 GTTGTAATGAAATAAA
*
316956 GTTGTAATGTAATAAA
1 GTTGTAATGAAATAAA
316972 GTTGTAAT
1 GTTGTAAT
316980 CAGTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (16 bp):
GTTGTAATGAAATAAA
Found at i:317222 original size:61 final size:63
Alignment explanation
Indices: 317150--317286 Score: 199
Period size: 61 Copynumber: 2.2 Consensus size: 63
317140 TTATTCAATA
* * *
317150 TAATAGAATTATTATTAAATATAATTTGAT-AAAAATGATAATAAATAATTTAATCAT-ATT-T
1 TAATATAATTATTATTAAATATAATTTAATAAAAAATAATAATAAATAATTTAAT-ATCATTCT
* *
317211 TAATATAATTATTATTGAATATAATTTAATAAAAAATAATAATATATAATTTAATATCATTCT
1 TAATATAATTATTATTAAATATAATTTAATAAAAAATAATAATAAATAATTTAATATCATTCT
317274 TAATATAATTATT
1 TAATATAATTATT
317287 TTTATATTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
61 29 0.43
62 25 0.37
63 14 0.21
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (63 bp):
TAATATAATTATTATTAAATATAATTTAATAAAAAATAATAATAAATAATTTAATATCATTCT
Found at i:320380 original size:29 final size:29
Alignment explanation
Indices: 320326--320387 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 29
320316 AATAATGTTA
**
320326 AAAAACTATATAAAATTTTTTAAT-AAAT
1 AAAAACTATATAAAATTTTAAAATAAAAT
320354 AAAAA-TATATAAAATTATTAAATATAAAAT
1 AAAAACTATATAAAATT-TTAAA-ATAAAAT
320384 AAAA
1 AAAA
320388 TAAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 11 0.38
28 8 0.28
29 2 0.07
30 8 0.28
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAACTATATAAAATTTTAAAATAAAAT
Found at i:325234 original size:23 final size:23
Alignment explanation
Indices: 325180--325227 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
325170 TCCGTACTTT
*
325180 TTATATTT-TTTAAATATTTATA
1 TTATATTTAATTAAATATTTATA
*
325202 TTATATTTAATTAATTATTTAT-
1 TTATATTTAATTAAATATTTATA
325224 TTAT
1 TTAT
325228 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATATTTAATTAAATATTTATA
Found at i:335086 original size:20 final size:20
Alignment explanation
Indices: 335061--335110 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
335051 TTTTATGATT
**
335061 TATTAATATTTCTAAGGTTA
1 TATTAATATTTCTAACCTTA
* *
335081 TATTAAAATTTTTAACCTTA
1 TATTAATATTTCTAACCTTA
*
335101 TATCAATATT
1 TATTAATATT
335111 AAAATCTCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (20 bp):
TATTAATATTTCTAACCTTA
Found at i:336637 original size:26 final size:26
Alignment explanation
Indices: 336605--336662 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
336595 TTATTTTATA
*
336605 TTATATTGTTTTA-ATATTTAATAATT
1 TTATATT-TTTTATATATTGAATAATT
* *
336631 TTATATTTTTTATTTATTGAATATTT
1 TTATATTTTTTATATATTGAATAATT
336657 TTATAT
1 TTATAT
336663 AATCATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (26 bp):
TTATATTTTTTATATATTGAATAATT
Found at i:336958 original size:19 final size:19
Alignment explanation
Indices: 336934--336971 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
336924 ATCAACCAAC
336934 CCCAATCCTAATTTAACTT
1 CCCAATCCTAATTTAACTT
336953 CCCAATCCTAATTTAACTT
1 CCCAATCCTAATTTAACTT
336972 TTATGGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (19 bp):
CCCAATCCTAATTTAACTT
Found at i:344380 original size:12 final size:12
Alignment explanation
Indices: 344363--344388 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
344353 AGTTTAATAC
344363 ATATAATATATA
1 ATATAATATATA
344375 ATATAATATATA
1 ATATAATATATA
344387 AT
1 AT
344389 TTTGTTAATT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATAATATATA
Found at i:348799 original size:16 final size:16
Alignment explanation
Indices: 348778--348819 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
348768 TTTTCAAAAA
348778 TAAAAATA-AAAATAT
1 TAAAAATATAAAATAT
*
348793 GTAAAAATTATAATATAT
1 -TAAAAA-TATAAAATAT
348811 TAAAAATAT
1 TAAAAATAT
348820 TATAAAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
TAAAAATATAAAATAT
Found at i:350598 original size:31 final size:33
Alignment explanation
Indices: 350560--350628 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
350550 AAATTTCAAT
* *
350560 AAATAAAAAT-GTATAAA-ATTATT-AAATATTA
1 AAATAAAAATAATATAAATATT-TTAAAAAATTA
350591 AAAT-AAAATAATATAAATATTTTAAAAAATTA
1 AAATAAAAATAATATAAATATTTTAAAAAATTA
350623 AAATAA
1 AAATAA
350629 TATGGAGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 5 0.16
31 12 0.38
32 14 0.44
33 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (33 bp):
AAATAAAAATAATATAAATATTTTAAAAAATTA
Found at i:356033 original size:2 final size:2
Alignment explanation
Indices: 356026--356090 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
356016 CTACAAATAG
356026 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
*
356068 AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
356091 CACATATGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:356952 original size:2 final size:2
Alignment explanation
Indices: 356945--356972 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
356935 CATATCAATG
356945 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
356973 CGAGAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:359412 original size:8 final size:8
Alignment explanation
Indices: 359396--359440 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
359386 ACCGGGAAAT
*
359396 TAGATAGA
1 TAGAGAGA
359404 TAGAGAGA
1 TAGAGAGA
359412 TAGAGAGA
1 TAGAGAGA
359420 TAGAGAGA
1 TAGAGAGA
*
359428 GAGAGAGA
1 TAGAGAGA
*
359436 GAGAG
1 TAGAG
359441 GGGAAGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.40, T:0.11
Consensus pattern (8 bp):
TAGAGAGA
Done.