Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012089.1 Kokia drynarioides strain JFW-HI SEQ_127088, 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: 93928
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:114 original size:32 final size:32
Alignment explanation
Indices: 78--140 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
68 AGCCGAAATT
* *
78 AATTAGCCGATTAATGTGTTTCAGGTACATGC
1 AATTAGCCGATTAATATATTTCAGGTACATGC
*
110 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCCGATTAATATATTTCAGGTACATG
141 TATTGATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
AATTAGCCGATTAATATATTTCAGGTACATGC
Found at i:463 original size:11 final size:10
Alignment explanation
Indices: 433--466 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
423 TCTAGCCTAG
*
433 TCCATTCAAC
1 TCCATTCAGC
443 TCCATTCAGC
1 TCCATTCAGC
453 TCCATTTCAGC
1 TCCA-TTCAGC
464 TCC
1 TCC
467 TTACTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.21, C:0.41, G:0.06, T:0.32
Consensus pattern (10 bp):
TCCATTCAGC
Found at i:11995 original size:17 final size:17
Alignment explanation
Indices: 11973--12015 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
11963 ATGCATCTCA
11973 TTTAGTTGTCATTGCAT
1 TTTAGTTGTCATTGCAT
*
11990 TTTAGTTGTCGTTGCAT
1 TTTAGTTGTCATTGCAT
*
12007 TTTACTTGT
1 TTTAGTTGT
12016 TAGTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.56
Consensus pattern (17 bp):
TTTAGTTGTCATTGCAT
Found at i:12647 original size:17 final size:16
Alignment explanation
Indices: 12603--12647 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
12593 ACATATAAAA
12603 AAAAG-AAAAAAAAGG
1 AAAAGCAAAAAAAAGG
*
12618 -AAAGCAAGAAAAAGTG
1 AAAAGCAAAAAAAAG-G
12634 AAAAGCAAAAAAAA
1 AAAAGCAAAAAAAA
12648 AATATATTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 1 0.04
17 12 0.48
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAGCAAAAAAAAGG
Found at i:15863 original size:24 final size:24
Alignment explanation
Indices: 15832--15923 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
15822 CCAAAAAAAA
*
15832 TTAGCTCTTACGAGCCTAGATAGG
1 TTAGCTCTTACGAGCCCAGATAGG
* *
15856 TTAGCTCTTACGAACCCAAATAGG
1 TTAGCTCTTACGAGCCCAGATAGG
* *
15880 TTAGCTCTTATGAGCCCAGATAAG
1 TTAGCTCTTACGAGCCCAGATAGG
*
15904 TTAGCTCATT-TGAGCCCAGA
1 TTAGCTC-TTACGAGCCCAGA
15924 CAAAGTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 58 0.97
25 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGATAGG
Found at i:16097 original size:82 final size:82
Alignment explanation
Indices: 15948--16163 Score: 279
Period size: 82 Copynumber: 2.6 Consensus size: 82
15938 TATACGATAC
**** * * ** *
15948 TGCTCACACAAGCTGATGAGAATATGTAACATATGTAGAAACTCAGCCATAGATACGGTCTAGAA
1 TGCTCACACAAGCTGATGAGAATCCACAACGTATGTAGAAACTCAGCCATCGATACGAACCAGAA
* *
16013 TTACCCACTCATGATTT
66 TTACCCACTCAGGATGT
* *
16030 TGCTTACACAAGCTGATGAGAATCCACAACGTATGTAGAAACTCAGCCATCGATACGAACCATAA
1 TGCTCACACAAGCTGATGAGAATCCACAACGTATGTAGAAACTCAGCCATCGATACGAACCAGAA
*
16095 TTACCCACTTAGGATGT
66 TTACCCACTCAGGATGT
* * *
16112 TACTCACACAAGTTGATGAGAATCCACAACGTATGTAGAAACTCAGTCATCG
1 TGCTCACACAAGCTGATGAGAATCCACAACGTATGTAGAAACTCAGCCATCG
16164 TAAGGGTCTA
Statistics
Matches: 116, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 116 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (82 bp):
TGCTCACACAAGCTGATGAGAATCCACAACGTATGTAGAAACTCAGCCATCGATACGAACCAGAA
TTACCCACTCAGGATGT
Found at i:20751 original size:24 final size:24
Alignment explanation
Indices: 20657--20764 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
20647 ACTGAGTCTT
* *
20657 CCAGA-AATTTAGCTCATACAAGC
1 CCAGATAAGTTAGCTCATACGAGC
* *
20680 CCAGACAAAATTAGCTCATACGAGC
1 CCAGA-TAAGTTAGCTCATACGAGC
* * **
20705 CCAAATAGGTTAGCTTTTACGAGC
1 CCAGATAAGTTAGCTCATACGAGC
*
20729 CCAGATAAGTTAGCTCATTCGAGC
1 CCAGATAAGTTAGCTCATACGAGC
*
20753 CTAGATAGAGTT
1 CCAGATA-AGTT
20765 TAACTAGTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 5 0.07
24 39 0.57
25 24 0.35
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (24 bp):
CCAGATAAGTTAGCTCATACGAGC
Found at i:20924 original size:82 final size:82
Alignment explanation
Indices: 20778--20990 Score: 273
Period size: 82 Copynumber: 2.6 Consensus size: 82
20768 CTAGTATACG
* ** * * * * *
20778 ATGCTGCTCACACAAGGTGATGAGAATCCGTAACATATGCAAAAACTCAGCCATCGATATGGTCC
1 ATGCTGCTCACACAAGCTGATGAGAATCCACAACGTATGTAAAAACTCAGCAATCAATACGGTCC
*
20843 AAAATTACCCACTCACA
66 AAAAGTACCCACTCACA
*
20860 ATGCTGCTCACACAAGCTGATGAGAATCCACAACGTATGTAAAAACTTAGCAATCAATACGGTCC
1 ATGCTGCTCACACAAGCTGATGAGAATCCACAACGTATGTAAAAACTCAGCAATCAATACGGTCC
* * * *
20925 AGAAGTACCTATTCACG
66 AAAAGTACCCACTCACA
* * *
20942 ATACTGCTCACACAAGCTTATGAGAATCCACAACGTATGTAGAAACTCA
1 ATGCTGCTCACACAAGCTGATGAGAATCCACAACGTATGTAAAAACTCA
20991 ACCGTTGTAG
Statistics
Matches: 113, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 113 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (82 bp):
ATGCTGCTCACACAAGCTGATGAGAATCCACAACGTATGTAAAAACTCAGCAATCAATACGGTCC
AAAAGTACCCACTCACA
Found at i:24053 original size:28 final size:28
Alignment explanation
Indices: 24013--24067 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
24003 AATTTAACGA
*
24013 TATGTGGAAGCCTTTGTGGT-TGTTCTAC
1 TATGTGAAAGCCTTTGT-GTCTGTTCTAC
24041 TATGTGAAAGCCTTTGTGTCTGTTCTA
1 TATGTGAAAGCCTTTGTGTCTGTTCTA
24068 TTACATGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.44
Consensus pattern (28 bp):
TATGTGAAAGCCTTTGTGTCTGTTCTAC
Found at i:26133 original size:8 final size:8
Alignment explanation
Indices: 26122--26162 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
26112 CTAATTTGTG
*
26122 TTTTTTTG
1 TTTTTTTA
26130 TTTTTTTA
1 TTTTTTTA
*
26138 TTTTATTA
1 TTTTTTTA
*
26146 TTTTATTA
1 TTTTTTTA
26154 TTTTTTTA
1 TTTTTTTA
26162 T
1 T
26163 CCTGCCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:26547 original size:25 final size:25
Alignment explanation
Indices: 26519--26571 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
26509 AATTTTTACC
26519 TTTAAATTAAATCCATTTATTCT-TT
1 TTTAAATT-AATCCATTTATTCTATT
* *
26544 TTTAAATTAATCCTTTTTTTCTATT
1 TTTAAATTAATCCATTTATTCTATT
26569 TTT
1 TTT
26572 TTATTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAATTAATCCATTTATTCTATT
Found at i:26565 original size:24 final size:25
Alignment explanation
Indices: 26519--26587 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
26509 AATTTTTACC
*
26519 TTTAAATTAAATCCATTTATTC-TTT
1 TTTAAATT-AATCCTTTTATTCATTT
*
26544 TTTAAATTAATCCTTTTTTTCTATTT
1 TTTAAATTAATCCTTTTATTC-ATTT
* *
26570 TTTTATTTAATCCTTTTA
1 TTTAAATTAATCCTTTTA
26588 ATTATCTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.30
25 8 0.22
26 18 0.49
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAATTAATCCTTTTATTCATTT
Found at i:31473 original size:53 final size:53
Alignment explanation
Indices: 31415--31520 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
31405 GAAACCAATA
* *
31415 AAACTTTTATAATTTTTCTCATCAACCCTCTCAAAATATTCATTGCTGGTAAG
1 AAACTTCTATAATTTTTCTCATCAACCCTCTCAAAATATTCATTGCTAGTAAG
31468 AAACTTCTATAATTTTTCTCATCAACCCTCTCAAAATATTCATTGCTAGTAAG
1 AAACTTCTATAATTTTTCTCATCAACCCTCTCAAAATATTCATTGCTAGTAAG
31521 CATTTCACCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (53 bp):
AAACTTCTATAATTTTTCTCATCAACCCTCTCAAAATATTCATTGCTAGTAAG
Found at i:32404 original size:21 final size:22
Alignment explanation
Indices: 32378--32424 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
32368 TTTACCAACA
* *
32378 TTGACTTGATGTTGATTG-ATG
1 TTGACTAGACGTTGATTGAATG
32399 TTGACTAGACGTTGATTGAATG
1 TTGACTAGACGTTGATTGAATG
32421 TTGA
1 TTGA
32425 TCAAACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (22 bp):
TTGACTAGACGTTGATTGAATG
Found at i:32435 original size:22 final size:22
Alignment explanation
Indices: 32388--32446 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
32378 TTGACTTGAT
*
32388 GTTGATTGATGTTGA-CTAGAC
1 GTTGATTGATGTTGATCTAAAC
32409 GTTGATTGAATGTTGATC-AAAC
1 GTTGATTG-ATGTTGATCTAAAC
* *
32431 TTTGATTGGTGTTGAT
1 GTTGATTGATGTTGAT
32447 TGATTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.45
22 17 0.52
23 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (22 bp):
GTTGATTGATGTTGATCTAAAC
Found at i:32650 original size:15 final size:14
Alignment explanation
Indices: 32632--32677 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
32622 TAAAAATTGT
32632 TTTTTAATTTATATA
1 TTTTTAATTTATA-A
*
32647 TTTTTTATTT-TAA
1 TTTTTAATTTATAA
32660 -TTTT-ATTTATAA
1 TTTTTAATTTATAA
32672 TTTTTA
1 TTTTTA
32678 GAATAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
11 4 0.15
12 7 0.26
13 5 0.19
14 2 0.07
15 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTAATTTATAA
Found at i:33188 original size:12 final size:12
Alignment explanation
Indices: 33173--33198 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33163 TTCTTAAAAG
33173 AAAGAAATTTAT
1 AAAGAAATTTAT
33185 AAAGAAATTTAT
1 AAAGAAATTTAT
33197 AA
1 AA
33199 TTGCAACTCC
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAGAAATTTAT
Found at i:36031 original size:73 final size:73
Alignment explanation
Indices: 35944--36080 Score: 256
Period size: 73 Copynumber: 1.9 Consensus size: 73
35934 CTTCATAAAT
*
35944 TTTAGTATATATTTTCTTTTTTGAAAGGAATTCGTTAACCATCGAAAATTATAGACAGTTCCTTA
1 TTTAGTATATATTTTCTTTTTTGAAAGGAATTCGTTAACCATCGAAAATAATAGACAGTTCCTTA
36009 ACTTGTTA
66 ACTTGTTA
*
36017 TTTAGTATATATTTTCTTTTTTGAAAGGAATTCGTTAACCATCGAAAATAATAGACGGTTCCTT
1 TTTAGTATATATTTTCTTTTTTGAAAGGAATTCGTTAACCATCGAAAATAATAGACAGTTCCTT
36081 GTTAGGGTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (73 bp):
TTTAGTATATATTTTCTTTTTTGAAAGGAATTCGTTAACCATCGAAAATAATAGACAGTTCCTTA
ACTTGTTA
Found at i:39973 original size:20 final size:21
Alignment explanation
Indices: 39950--39995 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
39940 GTAAAGTCAG
*
39950 ATGTATCAAAACCTTAGAGA-
1 ATGTATCAAAACCTTAAAGAC
* *
39970 ATGTTTCAATACCTTAAAGAC
1 ATGTATCAAAACCTTAAAGAC
39991 ATGTA
1 ATGTA
39996 CTAGTACCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (21 bp):
ATGTATCAAAACCTTAAAGAC
Found at i:45682 original size:15 final size:15
Alignment explanation
Indices: 45658--45692 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45648 TACATATACT
*
45658 TTTTTTTCTTTTCCC
1 TTTTTCTCTTTTCCC
*
45673 TTTTTCTCTTTTCTC
1 TTTTTCTCTTTTCCC
45688 TTTTT
1 TTTTT
45693 TTTTATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTCTTTTCCC
Found at i:50454 original size:11 final size:11
Alignment explanation
Indices: 50433--50463 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
50423 CTAGTATCTA
50433 TAGATGCTGCAG
1 TAGA-GCTGCAG
50445 TAGAGCTGCAG
1 TAGAGCTGCAG
50456 TAGAGCTG
1 TAGAGCTG
50464 GTAGTTGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.26, C:0.16, G:0.35, T:0.23
Consensus pattern (11 bp):
TAGAGCTGCAG
Found at i:55584 original size:23 final size:22
Alignment explanation
Indices: 55540--55584 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55530 TTTCAAACAA
**
55540 TATCAATACCTCTTCATGATAC
1 TATCAATACCTCTTCAAAATAC
*
55562 TATCAATACCTTCTTTAAAATAC
1 TATCAATACC-TCTTCAAAATAC
55585 CGATACCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (22 bp):
TATCAATACCTCTTCAAAATAC
Found at i:56767 original size:89 final size:89
Alignment explanation
Indices: 56621--56800 Score: 297
Period size: 89 Copynumber: 2.0 Consensus size: 89
56611 AAAATAGTCC
*
56621 TATTTAACAACCAAGCTTAATAATATTCCATAAATAATCAAGAACAACTCAAACTCATCAATGAC
1 TATTTAACAACCAAGCTTAATAATATTCCATAAATAATCAAGAACAACTCAAACTCATAAATGAC
*
56686 TTAATCCTTAACATTTGATAGTTT
66 TTAATCCTTAACATTTGACAGTTT
* * * * *
56710 TATTTAACAATCAAGCTTAATAATATTCCATAAATCATCAAGAACAACTTAAGCTCATAAATGGC
1 TATTTAACAACCAAGCTTAATAATATTCCATAAATAATCAAGAACAACTCAAACTCATAAATGAC
56775 TTAATCCTTAACATTTGACAGTTT
66 TTAATCCTTAACATTTGACAGTTT
56799 TA
1 TA
56801 CAAATTAGCC
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (89 bp):
TATTTAACAACCAAGCTTAATAATATTCCATAAATAATCAAGAACAACTCAAACTCATAAATGAC
TTAATCCTTAACATTTGACAGTTT
Found at i:57111 original size:28 final size:28
Alignment explanation
Indices: 57077--57137 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
57067 AACCATCCAC
57077 TAAAAACCTAAATGGAATATTTACCATT
1 TAAAAACCTAAATGGAATATTTACCATT
57105 TAAAAACCTAAATGGAATATTTACCATT
1 TAAAAACCTAAATGGAATATTTACCATT
57133 TAAAA
1 TAAAA
57138 CCTTTACGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (28 bp):
TAAAAACCTAAATGGAATATTTACCATT
Found at i:62469 original size:21 final size:21
Alignment explanation
Indices: 62445--62484 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
62435 TCCCACATGC
62445 CCATGTGGCTACTCTACACGT
1 CCATGTGGCTACTCTACACGT
62466 CCATGTGGCTACTCTACAC
1 CCATGTGGCTACTCTACAC
62485 ACCCATATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.35, G:0.17, T:0.28
Consensus pattern (21 bp):
CCATGTGGCTACTCTACACGT
Found at i:62490 original size:21 final size:21
Alignment explanation
Indices: 62444--62490 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
62434 ATCCCACATG
*
62444 CCCATGTGGCTACTCTACACG
1 CCCATGTGGCTACTCTACACA
*
62465 TCCATGTGGCTACTCTACACA
1 CCCATGTGGCTACTCTACACA
62486 CCCAT
1 CCCAT
62491 ATGCTCATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (21 bp):
CCCATGTGGCTACTCTACACA
Found at i:70533 original size:2 final size:2
Alignment explanation
Indices: 70523--70554 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
70513 GAAGAAAAAA
*
70523 AT AT CT 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
70555 TATTGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86553 original size:18 final size:18
Alignment explanation
Indices: 86521--86572 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
86511 TTGGGATGAG
86521 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
86537 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
86555 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
86573 TAACTACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:88362 original size:2 final size:2
Alignment explanation
Indices: 88355--88393 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
88345 AACACCCCAC
88355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88394 ATGTAGGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:92223 original size:467 final size:468
Alignment explanation
Indices: 91321--92251 Score: 1517
Period size: 467 Copynumber: 2.0 Consensus size: 468
91311 CAGCAGCAGT
*
91321 TCACCCCTGTAAGACTCCCAAACAAGCTTGGATAAGCTGAAGGAAGAGTTGATGGAGCATGTGCT
1 TCACCCCTGTAAGACTCCCAAACAAGCTTGGATAAGCTGAAGGAAGAGTTAATGGAGCATGTGCT
* *
91386 TGAAGACACTCCACAACTGGAGGGAGTATGTTCAAGAAGAAACAAGACAGTAAAGAACAAGGCAA
66 TGAAGACACTCCACAACAGGAAGGAGTATGTTCAAGAAGAAACAAGACAGTAAAGAACAAGGCAA
91451 GATGTGTTGTCAACCAAGACTTTAAAAGAGGAAAATACTCCATTTGATGAACAAATCTTTGGCAC
131 GATGTGTTGTCAACCAAGACTTTAAAAGAGGAAAATACTCCATTTGATGAACAAATCTTTGGCAC
* * ** *
91516 AAAAGACTGGGATAGTCAAGTGTGTGAGTCAGATTTGGTTGAGGCCAAGGTTGAAAATGAATTGC
196 AAAAGACTAGGATAGTCAAGTGTGTGAGTCAAATTTGGTTGAGGAAAAGGTTGAAAATGAATTGA
* * ** *
91581 TTAGGGAAAGTCAGGTTGAAATAAAGCATCAAAGGACTGCCAAGCTCAAAAAAACTTGATGAATG
261 TTAGGCAAAGTCAGCTTGAAATAAAGCATCAAACAACTGCCAAGCTCAAAAAAACTTGATAAATG
** *
91646 ACTGATATTTGAAGCATGGAGGCCAAGAAGGAGTGTTGAAAATGGCCAACCATCTTGCTATTATG
326 ACTGATATTTGAAGCATGGAGGCCAAGAAGGAGTGTTGAAAACAGCCAACCATCTTGCTATTATA
* * *
91711 CTTTTGTTAAAGTGCTTGCAGATTGTAAAAATGCTGTAACACATATGCTTGCTGTAATAGCAAGA
391 ATTTTGTTAAAGTGCATGCAGATTGTAAAAATGCTGTAACACATATGCTTGCTGTAATAACAAGA
*
91776 TTTGAATATATGC
456 TTTAAATATATGC
* *
91789 TCACCCCTTTAAGACT-CCAAACAAGCTTGGATAAGCTGAAGGAGGAGTTAATGGAGCATGTGCT
1 TCACCCCTGTAAGACTCCCAAACAAGCTTGGATAAGCTGAAGGAAGAGTTAATGGAGCATGTGCT
91853 TGAAGACACTCCACAACAGGAAGGAGTATGTTCAAGAAGAAACAAGACAGTAAAGAACAAGGCAA
66 TGAAGACACTCCACAACAGGAAGGAGTATGTTCAAGAAGAAACAAGACAGTAAAGAACAAGGCAA
* * *
91918 GATGTGTTGTCAACCAAGGCTTTGAAGGAGGAAAATACTCCATTTGATGAACAAATCTTTGGCAC
131 GATGTGTTGTCAACCAAGACTTTAAAAGAGGAAAATACTCCATTTGATGAACAAATCTTTGGCAC
*
91983 AAAAGACTAGGCTAGTCAAGTGTGTGAGTCAAATTTGGTTGAGGAAAAGGTTGAAAATGAATTGA
196 AAAAGACTAGGATAGTCAAGTGTGTGAGTCAAATTTGGTTGAGGAAAAGGTTGAAAATGAATTGA
*
92048 TT-GAGCAAAGTCAGCTTGAAATAAAGTATCAAACAACTGCCAAGCT-AAAAAAATCTTGATAAA
261 TTAG-GCAAAGTCAGCTTGAAATAAAGCATCAAACAACTGCCAAGCTCAAAAAAA-CTTGATAAA
* * * *
92111 TGACTGATATTTGAAGCATGGAGGCCAAGAAGGAGTTTTGAAAACAGCCAACCATGTTGCTGTTC
324 TGACTGATATTTGAAGCATGGAGGCCAAGAAGGAGTGTTGAAAACAGCCAACCATCTTGCTATTA
* *
92176 TAATTTTGTTAAAGTGCATGCAGATTGTAAAAATGTTGTAGCACATATGCTTGCTGTAATAACAA
389 TAATTTTGTTAAAGTGCATGCAGATTGTAAAAATGCTGTAACACATATGCTTGCTGTAATAACAA
*
92241 GGTTTAAATAT
454 GATTTAAATAT
92252 TTGAGAACTT
Statistics
Matches: 427, Mismatches: 34, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
466 8 0.02
467 404 0.95
468 15 0.04
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (468 bp):
TCACCCCTGTAAGACTCCCAAACAAGCTTGGATAAGCTGAAGGAAGAGTTAATGGAGCATGTGCT
TGAAGACACTCCACAACAGGAAGGAGTATGTTCAAGAAGAAACAAGACAGTAAAGAACAAGGCAA
GATGTGTTGTCAACCAAGACTTTAAAAGAGGAAAATACTCCATTTGATGAACAAATCTTTGGCAC
AAAAGACTAGGATAGTCAAGTGTGTGAGTCAAATTTGGTTGAGGAAAAGGTTGAAAATGAATTGA
TTAGGCAAAGTCAGCTTGAAATAAAGCATCAAACAACTGCCAAGCTCAAAAAAACTTGATAAATG
ACTGATATTTGAAGCATGGAGGCCAAGAAGGAGTGTTGAAAACAGCCAACCATCTTGCTATTATA
ATTTTGTTAAAGTGCATGCAGATTGTAAAAATGCTGTAACACATATGCTTGCTGTAATAACAAGA
TTTAAATATATGC
Done.