Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010132.1 Kokia drynarioides strain JFW-HI SEQ_124927, 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: 261070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1476 original size:29 final size:29
Alignment explanation
Indices: 1283--1464 Score: 143
Period size: 29 Copynumber: 6.3 Consensus size: 29
1273 GTTTTTCAAA
* * *
1283 AAAGTCAACGGGTCGATCAATGGTCGATC
1 AAAGTCAACGAGTCGATCAATGATCGGTC
* ** *
1312 AAAGTCAACGAATCGATCAACAATCAGTC
1 AAAGTCAACGAGTCGATCAATGATCGGTC
* * * ** **
1341 AAAGTCAAAGAATCAATCAACAATCAATC
1 AAAGTCAACGAGTCGATCAATGATCGGTC
* * * *
1370 AAAGTCAACG-GATCAATCAACGGTCGATC
1 AAAGTCAACGAG-TCGATCAATGATCGGTC
* *
1399 AAAGTTAAC-AGTTCGATCAATGGTCGGTC
1 AAAGTCAACGAG-TCGATCAATGATCGGTC
*
1428 AAAGTTAACGAGTCGATCAATGATCGGTC
1 AAAGTCAACGAGTCGATCAATGATCGGTC
1457 AAAGTCAA
1 AAAGTCAA
1465 TGGGTCATTC
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 126 0.98
30 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (29 bp):
AAAGTCAACGAGTCGATCAATGATCGGTC
Found at i:3367 original size:6 final size:6
Alignment explanation
Indices: 3358--3384 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3348 TAGGAGTAGG
3358 ATTAGA ATTAGA ATTAGA ATTAGA ATT
1 ATTAGA ATTAGA ATTAGA ATTAGA ATT
3385 TATATTTTGC
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:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATTAGA
Found at i:4411 original size:33 final size:31
Alignment explanation
Indices: 4341--4412 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
4331 AGTAAACAAC
*
4341 ATTTGGGTAAGGTAAAAGATAAAAAAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAAAAAAT
* *
4372 AATTGGGTAAGATAAAAGGTAAAAAATTAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAA--AAAAT
4405 ATTTGGGT
1 ATTTGGGT
4413 TTAGGTTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 23 0.66
33 12 0.34
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (31 bp):
ATTTGGGTAAGATAAAAGATAAAAAAAAAAT
Found at i:4509 original size:37 final size:36
Alignment explanation
Indices: 4442--4511 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
4432 TAATCTTTAG
* *
4442 GGGGAAAATATGGGTAAGGTAAAAGGTTTGGGCTTT
1 GGGGAAAATATGGGTAAAGTAAAAGATTTGGGCTTT
*
4478 GGGGAAAA-ATGGGGTAAAGTAAAAATATTTGGGC
1 GGGGAAAATAT-GGGTAAAGT-AAAAGATTTGGGC
4512 CTGGGTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 2 0.07
36 16 0.55
37 11 0.38
ACGTcount: A:0.36, C:0.03, G:0.37, T:0.24
Consensus pattern (36 bp):
GGGGAAAATATGGGTAAAGTAAAAGATTTGGGCTTT
Found at i:4563 original size:9 final size:9
Alignment explanation
Indices: 4549--4584 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
4539 ATAATATGGT
4549 TTTATTCGA
1 TTTATTCGA
4558 TTTATTCGA
1 TTTATTCGA
*
4567 ATTATTCGA
1 TTTATTCGA
*
4576 GTTATTCGA
1 TTTATTCGA
4585 ATTCGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (9 bp):
TTTATTCGA
Found at i:4573 original size:18 final size:18
Alignment explanation
Indices: 4550--4587 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4540 TAATATGGTT
*
4550 TTATTCGATTTATTCGAA
1 TTATTCGAGTTATTCGAA
4568 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
4586 TT
1 TT
4588 CGAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:8032 original size:18 final size:18
Alignment explanation
Indices: 7992--8043 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
7982 TTTTCAGTTG
*
7992 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
8010 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
8028 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
8044 CTCATCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:17574 original size:41 final size:41
Alignment explanation
Indices: 17523--17600 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
17513 CTGAAAGTAC
*
17523 TTATAGGTGTCATATGATGATATATGGTGATGTTTTGAAAT
1 TTATAGGTGTCATATGATGATATATGGGGATGTTTTGAAAT
* *
17564 TTATGGGTGTCATATGATGATATTTGGGGATGTTTTG
1 TTATAGGTGTCATATGATGATATATGGGGATGTTTTG
17601 GGATGTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.28, T:0.45
Consensus pattern (41 bp):
TTATAGGTGTCATATGATGATATATGGGGATGTTTTGAAAT
Found at i:33188 original size:28 final size:28
Alignment explanation
Indices: 33155--33248 Score: 125
Period size: 28 Copynumber: 3.4 Consensus size: 28
33145 TTTCTTCATT
*
33155 GCTTCACTATGATAGCTCGTACTTCACA
1 GCTTCACTATGATAGCTCGCACTTCACA
* *
33183 GCTTCACTGTGATAGCTCACACTTCACA
1 GCTTCACTATGATAGCTCGCACTTCACA
* * *
33211 GCTTCACTGTAATAGCTTGCACTTCACA
1 GCTTCACTATGATAGCTCGCACTTCACA
*
33239 TCTTCACTAT
1 GCTTCACTAT
33249 ACAAGTTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (28 bp):
GCTTCACTATGATAGCTCGCACTTCACA
Found at i:37094 original size:25 final size:25
Alignment explanation
Indices: 37052--37101 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
37042 TATTTAGATT
37052 AATTAATATTATTATAAAAATATAAA
1 AATTAATATTATTATAAAAAT-TAAA
37078 AATTAA-ATTATGT-TAAAAATTAAA
1 AATTAATATTAT-TATAAAAATTAAA
37102 TTTAGGCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATTAATATTATTATAAAAATTAAA
Found at i:41399 original size:13 final size:15
Alignment explanation
Indices: 41377--41408 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41367 TATATTATTT
41377 TATTATTAATTAA-A
1 TATTATTAATTAACA
41391 TATTA-TAATTAACA
1 TATTATTAATTAACA
41405 TATT
1 TATT
41409 TCCACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTATTAATTAACA
Found at i:42598 original size:25 final size:25
Alignment explanation
Indices: 42570--42640 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 25
42560 AAAGACAAAT
42570 ATATTAATTTGAATATTTTTAA-AAA
1 ATATTAATTT-AATATTTTTAATAAA
*
42595 ATATTTATTTTAA-ATTTTTAATAAA
1 ATA-TTAATTTAATATTTTTAATAAA
42620 ATAAAATTAATTTAATATTTT
1 AT---ATTAATTTAATATTTT
42641 CTATATTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 8 0.21
25 10 0.26
26 6 0.16
27 8 0.21
28 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
ATATTAATTTAATATTTTTAATAAA
Found at i:42633 original size:27 final size:25
Alignment explanation
Indices: 42566--42640 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 25
42556 AATGAAAGAC
42566 AAATATATTAATTTGAATATTTTTAAA
1 AAATA-ATTAATTT-AATATTTTTAAA
* *
42593 AAATATTTATTTTAA-ATTTTTAATA
1 AAATAATTAATTTAATATTTTTAA-A
42618 AAATAAAATTAATTTAATATTTT
1 AAAT--AATTAATTTAATATTTT
42641 CTATATTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 8 0.20
25 7 0.17
26 6 0.15
27 14 0.35
28 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
AAATAATTAATTTAATATTTTTAAA
Found at i:43170 original size:22 final size:20
Alignment explanation
Indices: 43119--43170 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
43109 GAAGGTCGAA
43119 ATTAAATTGTAATTTTTATG
1 ATTAAATTGTAATTTTTATG
43139 ATAGTAAAATTGTAATTTTTAAATG
1 AT--T-AAATTGTAATTTTT--ATG
43164 ATTAAAT
1 ATTAAAT
43171 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 2 0.07
22 5 0.19
23 15 0.56
25 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
ATTAAATTGTAATTTTTATG
Found at i:44413 original size:6 final size:6
Alignment explanation
Indices: 44404--44436 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
44394 CATATATACA
44404 TATATG TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TAT
44437 GTAGTTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:47339 original size:16 final size:15
Alignment explanation
Indices: 47318--47352 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47308 TTAATCACAG
47318 TTAAATACAAAAAAAT
1 TTAAAT-CAAAAAAAT
*
47334 TTAAATCTAAAAAAT
1 TTAAATCAAAAAAAT
47349 TTAA
1 TTAA
47353 GATAATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAATCAAAAAAAT
Found at i:47497 original size:24 final size:24
Alignment explanation
Indices: 47470--47517 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47460 ATGGTGATTA
**
47470 AATTAGTCATTTATGTCGTTTTTT
1 AATTAGTCAAATATGTCGTTTTTT
*
47494 AATTGGTCAAATATGTCGTTTTTT
1 AATTAGTCAAATATGTCGTTTTTT
47518 GAATATTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (24 bp):
AATTAGTCAAATATGTCGTTTTTT
Found at i:48928 original size:29 final size:28
Alignment explanation
Indices: 48890--49055 Score: 109
Period size: 30 Copynumber: 5.6 Consensus size: 28
48880 AGGAAAAACG
48890 GGGTCAAAAATGAAATTTTGAAAAGTTTA
1 GGGTC-AAAATGAAATTTTGAAAAGTTTA
* *
48919 GGGATCAAAATGAAATTTCGAAAAGTTCAA
1 GGG-TCAAAATGAAATTTTGAAAAGTT-TA
* *
48949 GGGTCAAAATCAAATTTTTGGAAAGTTTGA
1 GGGTCAAAATGAAA-TTTTGAAAAGTTT-A
* * * * * *
48979 TGGTTAAAGTCAAATTTT-TAGAGTTTGA
1 GGGTCAAAATGAAATTTTGAAAAGTTT-A
* ** *
49007 GGGACAAAATTGAGTTTTTGGAAAGTTTA
1 GGGTCAAAA-TGAAATTTTGAAAAGTTTA
*
49036 GGGTCCAAAATTGAATTTTT
1 GGGT-CAAAA-TGAAATTTT
49056 AAATAAAATA
Statistics
Matches: 108, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
28 13 0.12
29 47 0.44
30 48 0.44
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (28 bp):
GGGTCAAAATGAAATTTTGAAAAGTTTA
Found at i:55590 original size:17 final size:17
Alignment explanation
Indices: 55568--55623 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
55558 CTTTTGACTT
55568 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
55585 TTAACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
*
55601 TTTAACCTTCCATCTTTC
1 -TTAACCTTCCATCTTCC
55619 TTAAC
1 TTAAC
55624 TTTTCATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.09
16 5 0.16
17 17 0.53
18 4 0.12
20 3 0.09
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:56152 original size:33 final size:34
Alignment explanation
Indices: 56091--56154 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
56081 TGTTATATTA
* * *
56091 TGCTTGCAAGTTTTGTTAAGGGATTACTTATGTT
1 TGCTTGAAAGTTTTGTTAAAGGACTACTTATGTT
56125 TGCTTGAAAG-TTTGTTAAAGGACTACTTAT
1 TGCTTGAAAGTTTTGTTAAAGGACTACTTAT
56155 ATTTATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (34 bp):
TGCTTGAAAGTTTTGTTAAAGGACTACTTATGTT
Found at i:61039 original size:17 final size:17
Alignment explanation
Indices: 61017--61072 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
61007 CTCTTGACTT
61017 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
61034 TTAACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
61050 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
61068 TTAAC
1 TTAAC
61073 TTTTCATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.09
16 5 0.15
17 17 0.52
18 5 0.15
20 3 0.09
ACGTcount: A:0.20, C:0.39, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:61354 original size:19 final size:20
Alignment explanation
Indices: 61330--61375 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
61320 ACCAAAATTT
61330 CATTTTAAATAT-TTTTATA
1 CATTTTAAATATATTTTATA
* * *
61349 CATTTTAATTTTATTTTGTA
1 CATTTTAAATATATTTTATA
61369 CATTTTA
1 CATTTTA
61376 TTTCTTCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (20 bp):
CATTTTAAATATATTTTATA
Found at i:65172 original size:6 final size:6
Alignment explanation
Indices: 65161--65207 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
65151 TGCCTCCCAA
* *
65161 ACCATC ACCATC ACCATC ACCATC ACCATC ACCGTC ACCGTC ACCAT
1 ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCAT
65208 TGCATTCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.30, C:0.49, G:0.04, T:0.17
Consensus pattern (6 bp):
ACCATC
Found at i:71952 original size:37 final size:37
Alignment explanation
Indices: 71910--71980 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
71900 ATGATATATA
71910 TTTTTTCATTTCATTTCATTTCTTTTTGTTTCTTTTT
1 TTTTTTCATTTCATTTCATTTCTTTTTGTTTCTTTTT
* * * *
71947 TTTTTTCGTTTCGTTTCTTTTCTTTTTTTTTCTT
1 TTTTTTCATTTCATTTCATTTCTTTTTGTTTCTT
71981 CCAAACAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.77
Consensus pattern (37 bp):
TTTTTTCATTTCATTTCATTTCTTTTTGTTTCTTTTT
Found at i:71953 original size:22 final size:23
Alignment explanation
Indices: 71928--71975 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
71918 TTTCATTTCA
* *
71928 TTTCTTTTTGTTTCTTTT-TTTT
1 TTTCGTTTCGTTTCTTTTCTTTT
71950 TTTCGTTTCGTTTCTTTTCTTTT
1 TTTCGTTTCGTTTCTTTTCTTTT
71973 TTT
1 TTT
71976 TTCTTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (23 bp):
TTTCGTTTCGTTTCTTTTCTTTT
Found at i:71953 original size:27 final size:27
Alignment explanation
Indices: 71923--71977 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
71913 TTTCATTTCA
*
71923 TTTCATTTC-TTTTTGTTTCTTTTTTTT
1 TTTCATTTCGTTTCT-TTTCTTTTTTTT
*
71950 TTTCGTTTCGTTTCTTTTCTTTTTTTT
1 TTTCATTTCGTTTCTTTTCTTTTTTTT
71977 T
1 T
71978 CTTCCAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (27 bp):
TTTCATTTCGTTTCTTTTCTTTTTTTT
Found at i:73848 original size:37 final size:38
Alignment explanation
Indices: 73763--73851 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 38
73753 AGGGAGAGAG
*
73763 AAATGACTAATAAATGGGAGTAGGTATAGATCGAAGAC
1 AAATGACTAATAAATGGGAGTAGATATAGATCGAAGAC
* * * * *
73801 AAATGTCTAATAAATTGG-GTAGATATAGATTGAATAG
1 AAATGACTAATAAATGGGAGTAGATATAGATCGAAGAC
*
73838 GAATGACTAATAAA
1 AAATGACTAATAAA
73852 GGAGTATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 27 0.63
38 16 0.37
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (38 bp):
AAATGACTAATAAATGGGAGTAGATATAGATCGAAGAC
Found at i:83764 original size:48 final size:48
Alignment explanation
Indices: 83689--83820 Score: 221
Period size: 48 Copynumber: 2.8 Consensus size: 48
83679 TATTTATGCT
83689 TCATTAAGTGTTTT-TTTGTTAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
*
83736 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTTCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
* *
83784 TTATTAACTGTTTTGTTTGTTAAAATGCATCTTTGTT
1 TCATTAAGTGTTTTGTTTGTT-AAATGCATCTTTGTT
83821 AAATGCCTTG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
47 14 0.17
48 51 0.64
49 15 0.19
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
Found at i:83835 original size:49 final size:47
Alignment explanation
Indices: 83691--83835 Score: 186
Period size: 48 Copynumber: 3.0 Consensus size: 47
83681 TTTATGCTTC
* *
83691 ATTAAGTGTTTT-TTTGTTAAATGCATCTTTGTTTAATAATCTGCATC
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATACT-TGCATT
83738 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTT-CATT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAAT-A-CTTGCATT
* * *
83786 ATTAACTGTTTTGTTTGTTAAAATGCATCTTTGTTAAATGCCTTGCATT
1 ATTAAGTGTTTTGTTTGTT-AAATGCATCTTTGTTTAAT-ACTTGCATT
83835 A
1 A
83836 ATTCATCAGC
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
47 12 0.14
48 49 0.56
49 25 0.29
50 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (47 bp):
ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATACTTGCATT
Found at i:84349 original size:80 final size:79
Alignment explanation
Indices: 84261--84417 Score: 224
Period size: 80 Copynumber: 2.0 Consensus size: 79
84251 AGAGAAATGT
* * * * * * *
84261 CATGCCTTTTCAGCTGCATTAGATCCTAATGAAAAGACATGACTCATTGGCTTTCTTACAGGAGT
1 CATGCCTTTTCAACTACATCAGATCCTAATGAAAAGACATGACTCATTAGCTTCCCTACAAGAGT
84326 TAAAAATGAAATTGC
66 T-AAAATGAAATTGC
* *
84341 CATGCCTTTTCAACTACATCAGATCTTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAGT
1 CATGCCTTTTCAACTACATCAGATCCTAATGAAAAGACATGACTCATTAGCTTCCCTACAAGAGT
84406 TAAAATGAAATT
66 TAAAATGAAATT
84418 AGTGCTTGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 11 0.16
80 57 0.84
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (79 bp):
CATGCCTTTTCAACTACATCAGATCCTAATGAAAAGACATGACTCATTAGCTTCCCTACAAGAGT
TAAAATGAAATTGC
Found at i:90302 original size:53 final size:53
Alignment explanation
Indices: 90222--90324 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
90212 AGAATAAGCA
90222 AATGAAAAGCATTAAATAAAAATCAAAGCAATCTAACAATGAAAGATACTCTT
1 AATGAAAAGCATTAAATAAAAATCAAAGCAATCTAACAATGAAAGATACTCTT
*
90275 AATGAAAAGCATTAAATAAGAATCAAAGCAATCTAACAATGAAAGATACT
1 AATGAAAAGCATTAAATAAAAATCAAAGCAATCTAACAATGAAAGATACT
90325 ATTGTATTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (53 bp):
AATGAAAAGCATTAAATAAAAATCAAAGCAATCTAACAATGAAAGATACTCTT
Found at i:91914 original size:19 final size:17
Alignment explanation
Indices: 91890--91934 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
91880 AATTAATAAA
91890 AAAAATGCAATGACAAAAT
1 AAAAATGCAATG--AAAAT
* *
91909 AAAAATGGAATGATAAT
1 AAAAATGCAATGAAAAT
91926 AAAAATGCA
1 AAAAATGCA
91935 TACAAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.62, C:0.07, G:0.13, T:0.18
Consensus pattern (17 bp):
AAAAATGCAATGAAAAT
Found at i:99093 original size:23 final size:23
Alignment explanation
Indices: 99063--99108 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
99053 ACACCAGGGT
99063 TAGTCTTTACCTGTGTAGAATGA
1 TAGTCTTTACCTGTGTAGAATGA
*
99086 TAGTCTTTACTTGTGTAGAATGA
1 TAGTCTTTACCTGTGTAGAATGA
99109 GAGATTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (23 bp):
TAGTCTTTACCTGTGTAGAATGA
Found at i:104981 original size:21 final size:21
Alignment explanation
Indices: 104942--104982 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
104932 TGCATATAAG
*
104942 CAACCACAAATTGAAGGGCAA
1 CAACCACAAACTGAAGGGCAA
* *
104963 CAACCACTAACTGAGGGGCA
1 CAACCACAAACTGAAGGGCA
104983 GAAGAGACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (21 bp):
CAACCACAAACTGAAGGGCAA
Found at i:108027 original size:24 final size:24
Alignment explanation
Indices: 108000--108053 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
107990 ACAAACAATT
108000 CATTTTATATTACAATTGCACTGA
1 CATTTTATATTACAATTGCACTGA
* *
108024 CATTTTGTATTACATTTGCACTGA
1 CATTTTATATTACAATTGCACTGA
108048 CATTTT
1 CATTTT
108054 TTACTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (24 bp):
CATTTTATATTACAATTGCACTGA
Found at i:115866 original size:18 final size:19
Alignment explanation
Indices: 115843--115885 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
115833 TTTAAAGCAC
* *
115843 AAGAAGAATAAGGAAA-AG
1 AAGAAGAAGAAGGAAATAA
115861 AAGAAG-AGAAGGAAATAA
1 AAGAAGAAGAAGGAAATAA
115879 AAGAAGA
1 AAGAAGA
115886 TGTTACCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (19 bp):
AAGAAGAAGAAGGAAATAA
Found at i:118370 original size:24 final size:25
Alignment explanation
Indices: 118341--118395 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
118331 ACAATCAATT
118341 AATTTTATATTACAATTGCACTGAC
1 AATTTTATATTACAATTGCACTGAC
* *
118366 -ATTTTGTATTACATTTGCACTGAC
1 AATTTTATATTACAATTGCACTGAC
118390 AATTTT
1 AATTTT
118396 TACTCTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (25 bp):
AATTTTATATTACAATTGCACTGAC
Found at i:127285 original size:34 final size:34
Alignment explanation
Indices: 127237--127430 Score: 271
Period size: 34 Copynumber: 5.7 Consensus size: 34
127227 GATTAACCAT
*
127237 CCAACACACAAAATGCTCGTAAGAGCTAGTCCAA
1 CCAACACACCAAATGCTCGTAAGAGCTAGTCCAA
*
127271 CCAACACACCAAATGCTCATAAGAGCTAGTCCAA
1 CCAACACACCAAATGCTCGTAAGAGCTAGTCCAA
* * * *
127305 CCAACACACCAAATGTTCGTAATAGCTAGTGCAT
1 CCAACACACCAAATGCTCGTAAGAGCTAGTCCAA
* * * *
127339 CTAACACACCAAATACTTGTATGAGCTAGTCCAA
1 CCAACACACCAAATGCTCGTAAGAGCTAGTCCAA
* *
127373 CCAACACACCAAATGTTCGTAAGAGCTAGTCCAT
1 CCAACACACCAAATGCTCGTAAGAGCTAGTCCAA
*
127407 CCAACACACCAAATGCTTGTAAGA
1 CCAACACACCAAATGCTCGTAAGA
127431 TGTAGCCTAT
Statistics
Matches: 137, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 137 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (34 bp):
CCAACACACCAAATGCTCGTAAGAGCTAGTCCAA
Found at i:127443 original size:34 final size:34
Alignment explanation
Indices: 127233--127449 Score: 262
Period size: 34 Copynumber: 6.4 Consensus size: 34
127223 ACACGATTAA
* *
127233 CCATCCAACACACAAAATGCTCGTAAGAGCTAGT
1 CCATCCAACACACCAAATGCTTGTAAGAGCTAGT
* **
127267 CCAACCAACACACCAAATGCTCATAAGAGCTAGT
1 CCATCCAACACACCAAATGCTTGTAAGAGCTAGT
* *
127301 CCAACCAACACACCAAATG-TTCGTAATAGCTAGT
1 CCATCCAACACACCAAATGCTT-GTAAGAGCTAGT
* * * *
127335 GCATCTAACACACCAAATACTTGTATGAGCTAGT
1 CCATCCAACACACCAAATGCTTGTAAGAGCTAGT
*
127369 CCAACCAACACACCAAATG-TTCGTAAGAGCTAGT
1 CCATCCAACACACCAAATGCTT-GTAAGAGCTAGT
127403 CCATCCAACACACCAAATGCTTGTAAGATG-TAG-
1 CCATCCAACACACCAAATGCTTGTAAGA-GCTAGT
127436 CCTATCCAACACAC
1 CC-ATCCAACACAC
127450 AAAAATACTA
Statistics
Matches: 159, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
33 5 0.03
34 149 0.94
35 5 0.03
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTTGTAAGAGCTAGT
Found at i:127447 original size:102 final size:102
Alignment explanation
Indices: 127233--127458 Score: 305
Period size: 102 Copynumber: 2.2 Consensus size: 102
127223 ACACGATTAA
*
127233 CCATCCAACACACAAAATGCTCGTAAGAGCTAGTCCAACCAACACACCAAATGCTCATAAGAGCT
1 CCATCCAACACACAAAATACTCGTAAGAGCTAGTCCAACCAACACACCAAATGCTCATAAGAGCT
*
127298 AGTCCAACCAACACACCAAATGTTCGTAATAGCTAGT
66 AGTCCAACCAACACACCAAATGTTCGTAAGAGCTAGT
* * * * * * *
127335 GCATCTAACACACCAAATACTTGTATGAGCTAGTCCAACCAACACACCAAATGTTCGTAAGAGCT
1 CCATCCAACACACAAAATACTCGTAAGAGCTAGTCCAACCAACACACCAAATGCTCATAAGAGCT
*
127400 AGTCCATCCAACACACCAAATGCTT-GTAAGATG-TAG-
66 AGTCCAACCAACACACCAAATG-TTCGTAAGA-GCTAGT
127436 CCTATCCAACACACAAAAATACT
1 CC-ATCCAACACAC-AAAATACT
127459 ATAACATATC
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
101 1 0.01
102 96 0.90
103 10 0.09
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.19
Consensus pattern (102 bp):
CCATCCAACACACAAAATACTCGTAAGAGCTAGTCCAACCAACACACCAAATGCTCATAAGAGCT
AGTCCAACCAACACACCAAATGTTCGTAAGAGCTAGT
Found at i:131837 original size:18 final size:18
Alignment explanation
Indices: 131803--131839 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
131793 ACTCTTCTAC
*
131803 TTCTAAATGGAGTCAGAA
1 TTCTAAATGGAGACAGAA
*
131821 TTCTAAATGGGGACAGAA
1 TTCTAAATGGAGACAGAA
131839 T
1 T
131840 GCTCCTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (18 bp):
TTCTAAATGGAGACAGAA
Found at i:134206 original size:19 final size:19
Alignment explanation
Indices: 134182--134220 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
134172 AAAGAGAACA
*
134182 TTGTTGTTGATGCCTTATC
1 TTGTTGCTGATGCCTTATC
134201 TTGTTGCTGATGCCTTATC
1 TTGTTGCTGATGCCTTATC
134220 T
1 T
134221 CGAAGGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.18, G:0.21, T:0.51
Consensus pattern (19 bp):
TTGTTGCTGATGCCTTATC
Found at i:136349 original size:74 final size:74
Alignment explanation
Indices: 136228--136369 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
136218 TGTAGGGATA
* ** *
136228 CAATGTATCATTCAAGAGTCTTCAAGTGAATGGACACATTCATTTATGAATGATGAATAATGGTT
1 CAATGTATCATTCAAGAGTCTTCAAATGAATCAACACATTCATTTATGAATGATGAATAATGGCT
136293 GTTTACATT
66 GTTTACATT
* * * * *
136302 CAATGTTTCATTCAAGATTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATGGCT
1 CAATGTATCATTCAAGAGTCTTCAAATGAATCAACACATTCATTTATGAATGATGAATAATGGCT
136367 GTT
66 GTT
136370 CACTTTCATT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (74 bp):
CAATGTATCATTCAAGAGTCTTCAAATGAATCAACACATTCATTTATGAATGATGAATAATGGCT
GTTTACATT
Found at i:143606 original size:41 final size:41
Alignment explanation
Indices: 143560--143641 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
143550 TTTATTTCTT
143560 TCTCTACAAGTTCCTTTTAACCTTTTTACTAAGTTATTATG
1 TCTCTACAAGTTCCTTTTAACCTTTTTACTAAGTTATTATG
*
143601 TCTCTACAAGTTCCTTTTAACCTTTTTACTGAGTTATTATG
1 TCTCTACAAGTTCCTTTTAACCTTTTTACTAAGTTATTATG
143642 GTAAAAACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (41 bp):
TCTCTACAAGTTCCTTTTAACCTTTTTACTAAGTTATTATG
Found at i:147787 original size:22 final size:23
Alignment explanation
Indices: 147748--147791 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
147738 AATTTGGTTT
*
147748 ACTTTTAGTTGCACTGACAATTA
1 ACTTTTAGTTGCAATGACAATTA
147771 ACTTTTA-TTGCAATGACAATT
1 ACTTTTAGTTGCAATGACAATT
147792 TTGATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (23 bp):
ACTTTTAGTTGCAATGACAATTA
Found at i:153533 original size:21 final size:21
Alignment explanation
Indices: 153509--153559 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
153499 TAGAGGTAAG
*
153509 ACTTGTATCCGTAGAAGAGTC
1 ACTTGTATCCGTAGAACAGTC
* *
153530 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCCGTAGAACAGTC
*
153551 ACTTATATC
1 ACTTGTATC
153560 AGTACAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
ACTTGTATCCGTAGAACAGTC
Found at i:161360 original size:79 final size:80
Alignment explanation
Indices: 161215--161366 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 80
161205 ATCGCAAAGC
* **
161215 CCAGCTCTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCACCTAGTGCCTAACGGGTAA
1 CCAGCTCTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCACCTAATGCCTAACGAATAA
*
161280 ACCGCAAAAGTGAGT
66 ACCACAAAAGTGAGT
* * * *
161295 CCAGCTCTAGTTGGATTAACCGAC-AATATCCTTCAAATCCTGGCATCC-AATGCCTAGCGAATA
1 CCAGCTCTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCA-CCTAATGCCTAACGAATA
161358 AACCACAAA
65 AACCACAAA
161367 TGTGTGCCTA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 39 0.62
80 24 0.38
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (80 bp):
CCAGCTCTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCACCTAATGCCTAACGAATAA
ACCACAAAAGTGAGT
Found at i:161384 original size:79 final size:80
Alignment explanation
Indices: 161215--161385 Score: 195
Period size: 79 Copynumber: 2.1 Consensus size: 80
161205 ATCGCAAAGC
* * **
161215 CCAGCTCTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCACCTAGTGCCTAACGGGTAA
1 CCAGCACTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCACCTAATGCCTAACGAATAA
*
161280 ACCGCAAAAGTGAGT
66 ACCACAAAAGTGAGT
* * * * *
161295 CCAGCTCTAGTTGGATTAACCGAC-AATATCCTTCAAATCCTGGCATCC-AATGCCTAGCGAATA
1 CCAGCACTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCA-CCTAATGCCTAACGAATA
* *
161358 AACCACAAATGTGTG-
65 AACCACAAAAGTGAGT
161373 CCTAGCACTAGTT
1 CC-AGCACTAGTT
161386 AGTTAAACTG
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 2 0.03
79 52 0.67
80 24 0.31
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (80 bp):
CCAGCACTAGTTGAATTAACCAACAAATATCCGTCAAATCCTGGCACCTAATGCCTAACGAATAA
ACCACAAAAGTGAGT
Found at i:167008 original size:24 final size:24
Alignment explanation
Indices: 166976--167024 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
166966 AAATTATGGG
166976 TAAGTTTTCATTTTGGTCACTTAA
1 TAAGTTTTCATTTTGGTCACTTAA
167000 TAAGTTTTCATTTTGGTCACTTAA
1 TAAGTTTTCATTTTGGTCACTTAA
167024 T
1 T
167025 TTAAAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
TAAGTTTTCATTTTGGTCACTTAA
Found at i:167064 original size:30 final size:30
Alignment explanation
Indices: 167029--167111 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
167019 CTTAATTTAA
* *
167029 AAAGTTACAATTT-TGTCATTAAACTATTCG
1 AAAGTTAC-ATTTAAGTCACTAAACTATTCG
* *
167059 AAAGTTTTCATTTAAGTCACTGAACTATTCG
1 AAAG-TTACATTTAAGTCACTAAACTATTCG
**
167090 AAAGTTTTTATTTAAGTCACTA
1 AAAG-TTACATTTAAGTCACTA
167112 GGCTATTAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.18
31 37 0.82
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (30 bp):
AAAGTTACATTTAAGTCACTAAACTATTCG
Found at i:167118 original size:31 final size:31
Alignment explanation
Indices: 167050--167110 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
167040 TTTGTCATTA
167050 AACTATTCGAAAGTTTTCATTTAAGTCACTG
1 AACTATTCGAAAGTTTTCATTTAAGTCACTG
*
167081 AACTATTCGAAAGTTTTTATTTAAGTCACT
1 AACTATTCGAAAGTTTTCATTTAAGTCACT
167111 AGGCTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (31 bp):
AACTATTCGAAAGTTTTCATTTAAGTCACTG
Found at i:177331 original size:19 final size:19
Alignment explanation
Indices: 177283--177354 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
177273 TATAATTTTT
*
177283 ATTTATAAAATTATAGAAGTA
1 ATTTAT-AATTTAT-GAAGTA
*
177304 AGTTT-TAATTTATGACA-TT
1 A-TTTATAATTTATGA-AGTA
*
177323 ATTTATAATTTTTGAAGTA
1 ATTTATAATTTATGAAGTA
177342 ATTTATAATTTAT
1 ATTTATAATTTAT
177355 AACGTAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
18 4 0.10
19 26 0.62
20 7 0.17
21 2 0.05
22 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.50
Consensus pattern (19 bp):
ATTTATAATTTATGAAGTA
Found at i:177361 original size:19 final size:19
Alignment explanation
Indices: 177309--177366 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
177299 AAGTAAGTTT
* * *
177309 TAATTTATGACATTATTTA
1 TAATTTATAACGTAATTTA
*
177328 TAATTTTTGAA-GTAATTTA
1 TAATTTAT-AACGTAATTTA
*
177347 TAATTTATAACGTAAATTA
1 TAATTTATAACGTAATTTA
177366 T
1 T
177367 TGAATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (19 bp):
TAATTTATAACGTAATTTA
Found at i:177386 original size:13 final size:13
Alignment explanation
Indices: 177370--177411 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
177360 AAATTATTGA
177370 ATTATTTTATAAT
1 ATTATTTTATAAT
*
177383 ATTATTTTTTAAT
1 ATTATTTTATAAT
*
177396 TTTA-TTTATAA-
1 ATTATTTTATAAT
177407 ATTAT
1 ATTAT
177412 AATACAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 3 0.12
12 6 0.25
13 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATTTTATAAT
Found at i:208627 original size:21 final size:21
Alignment explanation
Indices: 208603--208647 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
208593 ATCCACAACT
208603 CCCTTCAAAGGCTCTAATTTC
1 CCCTTCAAAGGCTCTAATTTC
* *
208624 CCC-TCCAAGGCTTTAATTTC
1 CCCTTCAAAGGCTCTAATTTC
208644 CCCT
1 CCCT
208648 CCAAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.20, C:0.38, G:0.09, T:0.33
Consensus pattern (21 bp):
CCCTTCAAAGGCTCTAATTTC
Found at i:208633 original size:20 final size:20
Alignment explanation
Indices: 208610--208652 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
208600 ACTCCCTTCA
208610 AAGGCTCTAATTTCCCCTCC
1 AAGGCTCTAATTTCCCCTCC
*
208630 AAGGCTTTAATTTCCCCTCC
1 AAGGCTCTAATTTCCCCTCC
208650 AAG
1 AAG
208653 AAAGAGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.30
Consensus pattern (20 bp):
AAGGCTCTAATTTCCCCTCC
Found at i:209839 original size:24 final size:23
Alignment explanation
Indices: 209807--209861 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 23
209797 TGTAAGGGCA
209807 TCTTCTTGTTTTTCATTTTCATTT
1 TCTTCTTGTTTTTCATTTTC-TTT
209831 TCTTCTTGTTTTTCATTTTCTTT
1 TCTTCTTGTTTTTCATTTTCTTT
*
209854 TCCTCTTG
1 TCTTCTTG
209862 AGAACTCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.69
Consensus pattern (23 bp):
TCTTCTTGTTTTTCATTTTCTTT
Found at i:215155 original size:15 final size:15
Alignment explanation
Indices: 215132--215162 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
215122 TCTATACATC
*
215132 TCTTTTCTTTTTTTT
1 TCTTCTCTTTTTTTT
215147 TCTTCTCTTTTTTTT
1 TCTTCTCTTTTTTTT
215162 T
1 T
215163 GTGTGAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TCTTCTCTTTTTTTT
Found at i:216157 original size:15 final size:16
Alignment explanation
Indices: 216134--216166 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
216124 TCAACTGATT
216134 TTTTCTCAGCACCTTC
1 TTTTCTCAGCACCTTC
*
216150 TTTT-TCAGCATCTTC
1 TTTTCTCAGCACCTTC
216165 TT
1 TT
216167 CCTCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.30, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTTCTCAGCACCTTC
Found at i:216423 original size:18 final size:18
Alignment explanation
Indices: 216400--216440 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
216390 AGCATCCTCT
216400 GATGAGAGTTCATAATCA
1 GATGAGAGTTCATAATCA
216418 GATGAGAGTTCATAATCA
1 GATGAGAGTTCATAATCA
216436 GATGA
1 GATGA
216441 TTGGCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (18 bp):
GATGAGAGTTCATAATCA
Found at i:220806 original size:148 final size:149
Alignment explanation
Indices: 220370--221031 Score: 610
Period size: 148 Copynumber: 4.5 Consensus size: 149
220360 ACTGGGTTTG
* * **
220370 CCGTTGCGGCCTCAACCTTTCCTTTCATATCTTCATGGTACCAGATTCGTCGTTGCGAACTCAAT
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGCCGTTGCGGCCTCAAT
* * *
220435 CCTTCCCATAACATCTTTTAAGGTATCGGGTTCACCATTATGGCCTCAACCTTTCCCTTCATATC
66 CCTTCCCATAACATCTTCTAAGGTACCGGGTTCACCATTACGGCCTCAACCTTTCCCTTCATATC
* *
220500 TTCATGGCAC-CAGATTCA
131 TTCAAGGTACTCAGATTCA
* * * * * * *
220518 CCGTTGCGGCCTCAATCCTTT--CTATAACATCTTCTAAGGTACCGGGTTTGCTGTTGCGGCCTC
1 CCGTTGCGGCCTCAA-CCTTTCCCT-TCATATCTTC-ATGGTACCAGATTCGCCGTTGCGGCCTC
* * * * ** * ** * * *
220581 AA-CCTTTCCCTTCATATCTTC-ATGGTACTAGATTCGA-TGTTGCGGCCTTAATCC-TTCCCAT
63 AATCC-TTCCCATAACATCTTCTAAGGTACCGGGTTC-ACCATTACGGCCTCAA-CCTTTCCCTT
* * ** *
220642 AACATCTTCTAAGGTACTGGGA-TCG
125 CATATCTTC-AAGGTACTCAGATTCA
* * * *
220667 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAAATTCACCGTTCCAGCCTCAAT
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGCCGTTGCGGCCTCAAT
* * *
220732 CCTTCCCATAACATCTTCTAAGCTACCGGGTTCACCATTACGACCTCAACCTTTCCTTTCATATC
66 CCTTCCCATAACATCTTCTAAGGTACCGGGTTCACCATTACGGCCTCAACCTTTCCCTTCATATC
* *
220797 TTCACGGTAC-CAAATTCA
131 TTCAAGGTACTCAGATTCA
* * * * *
220815 CCATTGCGGTCTCAACCTTTCCCTTTATATCTTCATGGTACCAGATTCGTCGTTGTGGCCTCAAT
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGCCGTTGCGGCCTCAAT
* ** *
220880 CATTCTTATAACATCTTCTAAGGTACCGGGTTCACTATTACGGCCTCAACCTTTCCCTTCATATC
66 CCTTCCCATAACATCTTCTAAGGTACCGGGTTCACCATTACGGCCTCAACCTTTCCCTTCATATC
*
220945 TTCATGGTACT-AGATTCA
131 TTCAAGGTACTCAGATTCA
* * * * * * * * *
220963 CCGTTGCGACCTCAATCC-TTCCCATAACATCTTCTAAGGTACCGGGTTCGCTGTTACGGCCTCA
1 CCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTC-ATGGTACCAGATTCGCCGTTGCGGCCTCA
221027 A-CCTT
64 ATCCTT
221032 TCCCTTTATC
Statistics
Matches: 398, Mismatches: 98, Indels: 36
0.75 0.18 0.07
Matches are distributed among these distances:
147 2 0.01
148 263 0.66
149 129 0.32
150 4 0.01
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (149 bp):
CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGCCGTTGCGGCCTCAAT
CCTTCCCATAACATCTTCTAAGGTACCGGGTTCACCATTACGGCCTCAACCTTTCCCTTCATATC
TTCAAGGTACTCAGATTCA
Found at i:220829 original size:99 final size:99
Alignment explanation
Indices: 220304--220878 Score: 634
Period size: 99 Copynumber: 5.8 Consensus size: 99
220294 TTTATATTTC
* * ** ** * * * * *
220304 CATGGTACTAGATCCACCGTTGCGATCTTGATCTTTACCATCACATCTTCTAAGGTACTGGGTTT
1 CATGGTACCAGATTCACCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTTC
*
220369 GCCGTTGCGGCCTCAACCTTTCCTTTCATATCTT
66 GCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
** ** * *
220403 CATGGTACCAGATTCGTCGTTGCGAACTCAATCCTTCCCATAACATCTTTTAAGGTATCGGGTTC
1 CATGGTACCAGATTCACCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTTC
* * **
220468 ACCATTATGGCCTCAACCTTTCCCTTCATATCTT
66 GCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
* * * *
220502 CATGGCACCAGATTCACCGTTGCGGCCTCAATCCTTTCTATAACATCTTCTAAGGTACCGGGTTT
1 CATGGTACCAGATTCACCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTTC
*
220567 GCTGTTGCGGCCTCAACCTTTCCCTTCATATCTT
66 GCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
* * * * *
220601 CATGGTACTAGATTCGA-TGTTGCGGCCTTAATCCTTCCCATAACATCTTCTAAGGTACTGGGAT
1 CATGGTACCAGATTC-ACCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTT
220665 CGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
65 CGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
* * * *
220700 CATGGTACCAAATTCACCGTTCCAGCCTCAATCCTTCCCATAACATCTTCTAAGCTACCGGGTTC
1 CATGGTACCAGATTCACCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTTC
* * * * *
220765 ACCATTACGACCTCAACCTTTCCTTTCATATCTT
66 GCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
* * * * * * * * * *
220799 CACGGTACCAAATTCACCATTGCGGTCTCAA-CCTTTCCCTTTATATCTTC-ATGGTACCAGATT
1 CATGGTACCAGATTCACCGTTGCGGCCTCAATCC-TTCCCATAACATCTTCTAAGGTACCGGGTT
* *
220862 CGTCGTTGTGGCCTCAA
65 CGCCGTTGCGGCCTCAA
220879 TCATTCTTAT
Statistics
Matches: 397, Mismatches: 76, Indels: 7
0.83 0.16 0.01
Matches are distributed among these distances:
98 23 0.06
99 373 0.94
100 1 0.00
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.34
Consensus pattern (99 bp):
CATGGTACCAGATTCACCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTTC
GCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT
Found at i:220905 original size:99 final size:99
Alignment explanation
Indices: 220794--221081 Score: 296
Period size: 99 Copynumber: 2.9 Consensus size: 99
220784 TTCCTTTCAT
* * * *
220794 ATCTTC-ACGGTACCAAATTCACCATTGCGGTCTCAACCTTTCCCTTTATATCTTCATGGTACCA
1 ATCTTCTAAGGTACCAAATTCACCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCA
** * * **
220858 GATTCGTCGTTGTGGCCTCAATCATTCTTATAAC
66 GATTCACCGTTGCGACCTCAATCATTCCCATAAC
*** * *
220892 ATCTTCTAAGGTACCGGGTTCACTATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACTA
1 ATCTTCTAAGGTACCAAATTCACCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCA
*
220957 GATTCACCGTTGCGACCTCAATCCTTCCCATAAC
66 GATTCACCGTTGCGACCTCAATCATTCCCATAAC
*** * ** * * *
220991 ATCTTCTAAGGTACCGGGTTCGCTGTTACGGCCTCAACCTTTCCCTT--TATCTCCAAGGTATCA
1 ATCTTCTAAGGTACCAAATTCACCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCA
* * *
221054 AATTCACCTTTGCGACCTCAGTC-TTCCC
66 GATTCACCGTTGCGACCTCAATCATTCCC
221082 TTTCAAACTT
Statistics
Matches: 164, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
96 5 0.03
97 32 0.20
98 6 0.04
99 121 0.74
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (99 bp):
ATCTTCTAAGGTACCAAATTCACCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCA
GATTCACCGTTGCGACCTCAATCATTCCCATAAC
Found at i:220926 original size:247 final size:245
Alignment explanation
Indices: 220571--221073 Score: 704
Period size: 247 Copynumber: 2.0 Consensus size: 245
220561 GGGTTTGCTG
* * *
220571 TTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACTAGATTCGATGTTGCGGCCTTAATCCT
1 TTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGATGTTGCGGCCTCAATCAT
* * * *
220636 TCCCATAACATCTTCTAAGGTACTGGGATCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTC
66 TCCCATAACATCTTCTAAGGTACCGGGATCACCATTACGGCCTCAACCTTTCCCTTCATATCTTC
220701 ATGGTACCAAATTCACCGTTCC-AGCCTCAATCCTTCCCATAACATCTTCTAAGCTACCGGGTTC
131 ATGGTACCAAATTCACCGTTCCGA-CCTCAATCCTTCCCATAACATCTTCTAAGCTACCGGGTTC
* * *
220765 ACCATTACGACCTCAACCTTTCCTTTCATATCTTCACGGTACCAAATTCACCA
195 ACCATTACGACCTCAACCTTTCCCTT--TATCTCCAAGGTACCAAATTCACCA
* * *
220818 TTGCGGTCTCAACCTTTCCCTTTATATCTTCATGGTACCAGATTCG-TCGTTGTGGCCTCAATCA
1 TTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGAT-GTTGCGGCCTCAATCA
** * *
220882 TTCTTATAACATCTTCTAAGGTACCGGGTTCACTATTACGGCCTCAACCTTTCCCTTCATATCTT
65 TTCCCATAACATCTTCTAAGGTACCGGGATCACCATTACGGCCTCAACCTTTCCCTTCATATCTT
* * * *
220947 CATGGTACTAGATTCACCGTTGCGACCTCAATCCTTCCCATAACATCTTCTAAGGTACCGGGTTC
130 CATGGTACCAAATTCACCGTTCCGACCTCAATCCTTCCCATAACATCTTCTAAGCTACCGGGTTC
* ** * * *
221012 GCTGTTACGGCCTCAACCTTTCCCTTTATCTCCAAGGTATCAAATTCACCT
195 ACCATTACGACCTCAACCTTTCCCTTTATCTCCAAGGTACCAAATTCACCA
*
221063 TTGCGACCTCA
1 TTGCGGCCTCA
221074 GTCTTCCCTT
Statistics
Matches: 225, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
245 30 0.13
246 1 0.00
247 193 0.86
248 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (245 bp):
TTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGATGTTGCGGCCTCAATCAT
TCCCATAACATCTTCTAAGGTACCGGGATCACCATTACGGCCTCAACCTTTCCCTTCATATCTTC
ATGGTACCAAATTCACCGTTCCGACCTCAATCCTTCCCATAACATCTTCTAAGCTACCGGGTTCA
CCATTACGACCTCAACCTTTCCCTTTATCTCCAAGGTACCAAATTCACCA
Found at i:229247 original size:26 final size:26
Alignment explanation
Indices: 229196--229247 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
229186 GTTAAAATAA
*
229196 CTTGAAAAAAAAACTGAAGAGCAATT
1 CTTGAAAAAAAAACTAAAGAGCAATT
*
229222 CTTGAAGAAAAAACTCAAAGAG-AATT
1 CTTGAAAAAAAAACT-AAAGAGCAATT
229248 ATTATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (26 bp):
CTTGAAAAAAAAACTAAAGAGCAATT
Found at i:230438 original size:18 final size:19
Alignment explanation
Indices: 230401--230438 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
230391 CTCTCGGCCT
*
230401 TTTCACATATTTTTCCCTCA
1 TTTCACATA-TTTCCCCTCA
230421 TTTCACATA-TTCCCCTCA
1 TTTCACATATTTCCCCTCA
230439 CAAGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTCACATATTTCCCCTCA
Found at i:231925 original size:17 final size:17
Alignment explanation
Indices: 231901--231943 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
231891 ACTCACAGAA
231901 TATTTTTTT-ATTTTTT
1 TATTTTTTTCATTTTTT
*
231917 TATTTTTTTCGTTTTTT
1 TATTTTTTTCATTTTTT
*
231934 TCTTTTTTTC
1 TATTTTTTTC
231944 TCGAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (17 bp):
TATTTTTTTCATTTTTT
Found at i:231943 original size:8 final size:8
Alignment explanation
Indices: 231903--231944 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
231893 TCACAGAATA
*
231903 TTTTTTTA
1 TTTTTTTC
*
231911 TTTTTTTA
1 TTTTTTTC
231919 TTTTTTTC
1 TTTTTTTC
231927 GTTTTTTTC
1 -TTTTTTTC
231936 TTTTTTTC
1 TTTTTTTC
231944 T
1 T
231945 CGAATTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTTTC
Found at i:234279 original size:8 final size:8
Alignment explanation
Indices: 234266--234302 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
234256 ACAAACAAAT
*
234266 TATATATA
1 TATATATG
234274 TATATATG
1 TATATATG
234282 TATATATG
1 TATATATG
*
234290 TATATATT
1 TATATATG
234298 TATAT
1 TATAT
234303 TTAAAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (8 bp):
TATATATG
Found at i:236357 original size:12 final size:11
Alignment explanation
Indices: 236342--236391 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
236332 GGGCTTTTTG
236342 AATTTGGGTTTA
1 AATTTGGG-TTA
*
236354 AA-TTGGGCTTGT
1 AATTTGGG-TT-A
236366 AATTTGGGTTA
1 AATTTGGGTTA
236377 AATTTGGGTTA
1 AATTTGGGTTA
236388 AATT
1 AATT
236392 GTAAATGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 22 0.67
12 6 0.18
13 5 0.15
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.46
Consensus pattern (11 bp):
AATTTGGGTTA
Found at i:248076 original size:19 final size:20
Alignment explanation
Indices: 248043--248081 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
248033 ACCCACAGAA
*
248043 TATTTTTTTTATTTTTCTCG
1 TATTTTTCTTATTTTTCTCG
248063 TATTTTTCTT-TTTTTCTCG
1 TATTTTTCTTATTTTTCTCG
248082 ACTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (20 bp):
TATTTTTCTTATTTTTCTCG
Done.