Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010869.1 Kokia drynarioides strain JFW-HI SEQ_125837, 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: 237692
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:495 original size:18 final size:19
Alignment explanation
Indices: 456--495 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
446 GTGATGCTAC
456 TTGATCTGTTAACACTTGT
1 TTGATCTGTTAACACTTGT
475 TTGATCTGTTAACAC-TGT
1 TTGATCTGTTAACACTTGT
493 TTG
1 TTG
496 GGATTTAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGATCTGTTAACACTTGT
Found at i:2697 original size:11 final size:11
Alignment explanation
Indices: 2643--2711 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
2633 TTCTGAGTTG
2643 TATGTTGTG-TT
1 TATGTTG-GCTT
2654 T-TGTTGGCTT
1 TATGTTGGCTT
* *
2664 TATGATGACTT
1 TATGTTGGCTT
*
2675 TATGTCT-ACTT
1 TATGT-TGGCTT
2686 TATGTTGGCTT
1 TATGTTGGCTT
2697 TAATGTTGGCTT
1 T-ATGTTGGCTT
2709 TAT
1 TAT
2712 ATTAGATGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 1 0.02
10 9 0.18
11 27 0.55
12 12 0.24
ACGTcount: A:0.14, C:0.09, G:0.22, T:0.55
Consensus pattern (11 bp):
TATGTTGGCTT
Found at i:3856 original size:12 final size:12
Alignment explanation
Indices: 3828--3863 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
3818 GGTTGTTATT
*
3828 TTGAACTGTTT-
1 TTGAACTTTTTG
3839 TTGAACTTTTTG
1 TTGAACTTTTTG
3851 TTGAACTTTTTG
1 TTGAACTTTTTG
3863 T
1 T
3864 AAAGTTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (12 bp):
TTGAACTTTTTG
Found at i:4160 original size:16 final size:16
Alignment explanation
Indices: 4135--4175 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
4125 ACAACCAAAC
*
4135 CAACAGCCATGAGAAG
1 CAACAACCATGAGAAG
*
4151 TAACAACCATGAGAAG
1 CAACAACCATGAGAAG
4167 CAACAACCA
1 CAACAACCA
4176 ACAAAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (16 bp):
CAACAACCATGAGAAG
Found at i:4907 original size:31 final size:31
Alignment explanation
Indices: 4872--4947 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
4862 TAAAAGCAAA
*
4872 AAGAA-TACACTAACCATTTACAAATATAAAC
1 AAGAACTACAATAA-CATTTACAAATATAAAC
* * *
4903 AAGAACTACAATAATATTTACGAATATAAAT
1 AAGAACTACAATAACATTTACAAATATAAAC
* *
4934 AGGATCTACAATAA
1 AAGAACTACAATAA
4948 AAAATTGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 31 0.82
32 7 0.18
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (31 bp):
AAGAACTACAATAACATTTACAAATATAAAC
Found at i:6821 original size:31 final size:29
Alignment explanation
Indices: 6786--6855 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
6776 ATCTTAAAAT
*
6786 TATACATGAATTATAGTTTAATGTGTAATTG
1 TATACATGAATTATAATTT--TGTGTAATTG
* * *
6817 TATACATAAATTTTAATTTTGTGTAATTT
1 TATACATGAATTATAATTTTGTGTAATTG
*
6846 TATAAATGAA
1 TATACATGAA
6856 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (29 bp):
TATACATGAATTATAATTTTGTGTAATTG
Found at i:6839 original size:29 final size:30
Alignment explanation
Indices: 6807--6865 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
6797 TATAGTTTAA
*
6807 TGTGTAATTGTATACAT-AAATTTTAATTT
1 TGTGTAATTGTATAAATGAAATTTTAATTT
* *
6836 TGTGTAATTTTATAAATGAAATTTTGATTT
1 TGTGTAATTGTATAAATGAAATTTTAATTT
6866 GATATAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.53
Consensus pattern (30 bp):
TGTGTAATTGTATAAATGAAATTTTAATTT
Found at i:23153 original size:10 final size:10
Alignment explanation
Indices: 23140--23169 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
23130 TATTTTTTGC
23140 CTTTTTCTTT
1 CTTTTTCTTT
23150 CTTTTTCTTT
1 CTTTTTCTTT
*
23160 TTTTTTCTTT
1 CTTTTTCTTT
23170 GGGTTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:29455 original size:2 final size:2
Alignment explanation
Indices: 29450--29475 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29440 TAAATATTTA
29450 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
29476 CAATTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30638 original size:32 final size:32
Alignment explanation
Indices: 30592--30653 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
30582 AAAAAATTGT
*
30592 TATTTTTTGTTGTTTT-TTACTATTTTGCTGC
1 TATTTTTTGTTGTTTTCTCACTATTTTGCTGC
*
30623 TATTTTCTTGTTGTTTTCTCATTATTTTGCT
1 TATTTT-TTGTTGTTTTCTCACTATTTTGCT
30654 ACCATTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 6 0.22
32 10 0.37
33 11 0.41
ACGTcount: A:0.10, C:0.11, G:0.11, T:0.68
Consensus pattern (32 bp):
TATTTTTTGTTGTTTTCTCACTATTTTGCTGC
Found at i:37192 original size:19 final size:20
Alignment explanation
Indices: 37161--37199 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
37151 TTTATAATAC
*
37161 TTTATATTATTATGTTATTT
1 TTTATATTATTATGTAATTT
37181 TTTATA-TATTATGTAATTT
1 TTTATATTATTATGTAATTT
37200 AAAACATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTATATTATTATGTAATTT
Found at i:37266 original size:22 final size:22
Alignment explanation
Indices: 37228--37274 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
37218 AATCTATACT
*
37228 AAATATATAATACAAATA-TTA
1 AAATATAAAATACAAATATTTA
*
37249 AAATAATAAAATATAAATATTTA
1 AAAT-ATAAAATACAAATATTTA
37272 AAA
1 AAA
37275 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAAAATACAAATATTTA
Found at i:43144 original size:16 final size:15
Alignment explanation
Indices: 43123--43152 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43113 TTTATGACAA
43123 ATATCTATCTATATTC
1 ATATCTAT-TATATTC
43139 ATATCTATTATATT
1 ATATCTATTATATT
43153 TAAGTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATCTATTATATTC
Found at i:44940 original size:18 final size:17
Alignment explanation
Indices: 44898--44940 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
44888 TTTTTAAGTT
*
44898 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
44915 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
44933 TATAATTT
1 TATAATTT
44941 AAAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:45100 original size:20 final size:19
Alignment explanation
Indices: 45054--45101 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
45044 AAAATTATAT
45054 AAAATT-AT-TAAATATTA
1 AAAATTAATATAAATATTA
*
45071 GAAATATAATATAAATATTAA
1 AAAAT-TAATATAAATATT-A
45092 AAAATTAATA
1 AAAATTAATA
45102 CGGGCGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 1 0.04
19 2 0.08
20 13 0.52
21 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTAATATAAATATTA
Found at i:45429 original size:16 final size:17
Alignment explanation
Indices: 45408--45450 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
45398 AAATTATAGA
*
45408 GATTAAATTTTAAA-TT
1 GATTAAATTTAAAATTT
*
45424 GATTAAAATTAAAATTT
1 GATTAAATTTAAAATTT
45441 GACTTAAATT
1 GA-TTAAATT
45451 ATCGATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 4 0.18
18 6 0.27
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (17 bp):
GATTAAATTTAAAATTT
Found at i:46639 original size:20 final size:22
Alignment explanation
Indices: 46614--46671 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
46604 TAATGATCAG
*
46614 AGTAAGTAAATT-TT-GAACTC
1 AGTAAGTAAATTATTAGAAATC
46634 AGTAAGTAAATTATTACGAAATC
1 AGTAAGTAAATTATTA-GAAATC
*
46657 AGTAAGCAAATTATT
1 AGTAAGTAAATTATT
46672 TTGAGCTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 12 0.36
21 2 0.06
23 19 0.58
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
AGTAAGTAAATTATTAGAAATC
Found at i:46681 original size:23 final size:23
Alignment explanation
Indices: 46623--46687 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
46613 GAGTAAGTAA
*
46623 ATTTTGAACTCAGTAAGTAAATT
1 ATTTTGAACTCAGTAAGCAAATT
** *
46646 ATTACGAAATCAGTAAGCAAATT
1 ATTTTGAACTCAGTAAGCAAATT
*
46669 ATTTTGAGCTCAGTAAGCA
1 ATTTTGAACTCAGTAAGCA
46688 TATCTAAGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (23 bp):
ATTTTGAACTCAGTAAGCAAATT
Found at i:68732 original size:20 final size:20
Alignment explanation
Indices: 68703--68740 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
68693 ACATTAAACT
* *
68703 AAAAATAATATAAATAATTC
1 AAAAAAAATAAAAATAATTC
68723 AAAAAAAATAAAAATAAT
1 AAAAAAAATAAAAATAAT
68741 ATTGGTGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAAAATAAAAATAATTC
Found at i:68734 original size:29 final size:30
Alignment explanation
Indices: 68668--68742 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
68658 AATTTTAAAT
*
68668 AAATGAAAAAT-ATATAAATTATTAAACATTA
1 AAAT-AAAAATAATATAAATAATTAAACA-TA
*
68699 AACTAAAAATAATATAAATAATTCAAA-A-A
1 AAATAAAAATAATATAAATAATT-AAACATA
68728 AAATAAAAATAATAT
1 AAATAAAAATAATAT
68743 TGGTGGGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 15 0.38
30 6 0.15
31 15 0.38
32 3 0.08
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (30 bp):
AAATAAAAATAATATAAATAATTAAACATA
Found at i:75981 original size:3 final size:3
Alignment explanation
Indices: 75968--75998 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
75958 AGTTGATTGG
75968 TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
75999 ATTTTAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:76363 original size:13 final size:13
Alignment explanation
Indices: 76331--76369 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
76321 AACTAAATTT
76331 TTATATATTATAAA
1 TTATATATT-TAAA
*
76345 AT-TATATTTAAA
1 TTATATATTTAAA
76357 TTATATATTTAAA
1 TTATATATTTAAA
76370 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 16 0.73
14 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATATATTTAAA
Found at i:77274 original size:15 final size:15
Alignment explanation
Indices: 77247--77288 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
77237 TATAATAGTA
*
77247 AATTTAGTTTTTAAT
1 AATTTAATTTTTAAT
*
77262 -ATTTAAATTTTTATT
1 AATTT-AATTTTTAAT
77277 AATTTAATTTTT
1 AATTTAATTTTT
77289 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
AATTTAATTTTTAAT
Found at i:82515 original size:2 final size:2
Alignment explanation
Indices: 82467--82496 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
82457 AAAATTTGAA
82467 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
82497 TAATTTGCTA
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:91427 original size:30 final size:31
Alignment explanation
Indices: 91385--91450 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
91375 TAGTAAAAAT
91385 AAAATTATATTTA-TCCTTTTAAAAATGATA
1 AAAATTATATTTAGTCCTTTTAAAAATGATA
* *
91415 AAAATT-TGATTTAGTCTTTTTAAAAATTATA
1 AAAATTAT-ATTTAGTCCTTTTAAAAATGATA
91446 AAAAT
1 AAAAT
91451 ATAGGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 1 0.03
30 11 0.34
31 20 0.62
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (31 bp):
AAAATTATATTTAGTCCTTTTAAAAATGATA
Found at i:95048 original size:102 final size:101
Alignment explanation
Indices: 94862--95048 Score: 234
Period size: 102 Copynumber: 1.8 Consensus size: 101
94852 AATTTATATG
* * *
94862 ATATAAAATTAAATATATATTATTCAAGCACAATGACCTAACTTGATAACTGAAGGTGATTAAGT
1 ATATAAAATTAAATATATATTATTCAAGCACAATAACCTAACTCGATAACTAAAGGTGATTAAGT
* *
94927 CGATTAACTGATCGACCTAATTTCAAATTATTTAAA
66 CGATTAACTAACCGACCTAATTTCAAATTATTTAAA
* * * *
94963 ATATATAAATTAAATATATATTATTCAATCTCAATAACCT-AGTCCGATAATTAAAGGTGATTAA
1 ATATA-AAATTAAATATATATTATTCAAGCACAATAACCTAACT-CGATAACTAAAGGTGATTAA
* *
95027 GTCGGTTAA-TCAACCGGCCTAA
64 GTCGATTAACT-AACCGACCTAA
95049 AGCCAATTCA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
101 8 0.11
102 64 0.89
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (101 bp):
ATATAAAATTAAATATATATTATTCAAGCACAATAACCTAACTCGATAACTAAAGGTGATTAAGT
CGATTAACTAACCGACCTAATTTCAAATTATTTAAA
Found at i:97277 original size:19 final size:20
Alignment explanation
Indices: 97255--97292 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
97245 ACAAAAAAAA
*
97255 AAAATATTTAAAAA-ATTAT
1 AAAAGATTTAAAAATATTAT
*
97274 AAAAGCTTTAAAAATATTA
1 AAAAGATTTAAAAATATTA
97293 ATTTTGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAGATTTAAAAATATTAT
Found at i:108909 original size:38 final size:38
Alignment explanation
Indices: 108837--108927 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
108827 AAAATAAAAA
* * *
108837 AATTGGTTTAATCGGTTTGTTCAATCGATCAATTTGACT
1 AATTGGTTTAAT-TGTCTGTTCAATCAATCAATTTGACT
*
108876 AATTGGTTTAATTGTCTGTTCAATCAA-CTAATTTGATT
1 AATTGGTTTAATTGTCTGTTCAATCAATC-AATTTGACT
* *
108914 AATCGGTTCAATTG
1 AATTGGTTTAATTG
108928 ATTCATGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.02
38 32 0.71
39 12 0.27
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (38 bp):
AATTGGTTTAATTGTCTGTTCAATCAATCAATTTGACT
Found at i:125316 original size:20 final size:21
Alignment explanation
Indices: 125275--125317 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
125265 TATGTTAAGT
*
125275 CAAATTTTGATATTTGTCTCG
1 CAAATTTTGATATTAGTCTCG
125296 CAAATTTGTGAT-TTAGT-TCG
1 CAAATTT-TGATATTAGTCTCG
125316 CA
1 CA
125318 TTGTCCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (21 bp):
CAAATTTTGATATTAGTCTCG
Found at i:144233 original size:20 final size:19
Alignment explanation
Indices: 144210--144269 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
144200 AATTTCTACA
*
144210 AAATTTAAATAATATTTTAT
1 AAATTTTAATAATATTTT-T
*
144230 AAATTTTAATAACATTTTT
1 AAATTTTAATAATATTTTT
144249 ACAATTTTAA-AATATTTTT
1 A-AATTTTAATAATATTTTT
144268 AA
1 AA
144270 TAATATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 11 0.31
20 24 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTTAATAATATTTTT
Found at i:144241 original size:10 final size:11
Alignment explanation
Indices: 144212--144277 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
144202 TTTCTACAAA
*
144212 ATTTAAATAAT
1 ATTTTAATAAT
144223 ATTTT-ATAA-
1 ATTTTAATAAT
*
144232 ATTTTAATAAC
1 ATTTTAATAAT
144243 ATTTT--TACA-
1 ATTTTAATA-AT
144252 ATTTTAA-AAT
1 ATTTTAATAAT
144262 ATTTTTAATAAT
1 A-TTTTAATAAT
144274 ATTT
1 ATTT
144278 AATTTATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
9 13 0.28
10 11 0.24
11 18 0.39
12 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTTAATAAT
Found at i:144271 original size:9 final size:9
Alignment explanation
Indices: 144219--144334 Score: 51
Period size: 9 Copynumber: 12.1 Consensus size: 9
144209 AAAATTTAAA
144219 TAATATTTT
1 TAATATTTT
144228 ATAA-ATTTT
1 -TAATATTTT
*
144237 AATAACATTTT
1 --TAATATTTT
144248 TACA-ATTTT
1 TA-ATATTTT
*
144257 AAAATATTTT
1 -TAATATTTT
*
144267 TAATAATATT
1 TAAT-ATTTT
144277 TAAT-TTATT
1 TAATATT-TT
*
144286 TAATAATTT
1 TAATATTTT
*
144295 AAATATTTT
1 TAATATTTT
144304 TACA-ATTTT
1 TA-ATATTTT
*
144313 TGTATATTTT
1 T-AATATTTT
144323 TGAATACTTTT
1 T-AATA-TTTT
144334 T
1 T
144335 TCGATTTTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
8 1 0.01
9 39 0.46
10 34 0.40
11 10 0.12
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (9 bp):
TAATATTTT
Found at i:144310 original size:17 final size:18
Alignment explanation
Indices: 144243--144311 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
144233 TTTTAATAAC
144243 ATTTTT-ACAATTTTAAAAT
1 ATTTTTAACAA-TTT-AAAT
* *
144262 ATTTTTAATAATATTTAAT
1 ATTTTTAACAAT-TTAAAT
*
144281 -TTATTTAATAATTTAAAT
1 ATT-TTTAACAATTTAAAT
144299 ATTTTT-ACAATTT
1 ATTTTTAACAATTT
144312 TTGTATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 6 0.14
18 10 0.24
19 21 0.50
20 5 0.12
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTTAACAATTTAAAT
Found at i:146409 original size:27 final size:27
Alignment explanation
Indices: 146379--146431 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
146369 TAAAAAAACC
146379 ATATATTATT-TTTAATTTAATATTTAG
1 ATAT-TTATTCTTTAATTTAATATTTAG
* * *
146406 ATATTTTTTCTTTTATTTAATTTTTA
1 ATATTTATTCTTTAATTTAATATTTA
146432 AATTTAGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (27 bp):
ATATTTATTCTTTAATTTAATATTTAG
Found at i:155645 original size:27 final size:25
Alignment explanation
Indices: 155607--155661 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
155597 CTCATTTTCC
*
155607 TTTTTTTTTTTTATCTTTTTAAATGT
1 TTTTTTTTTTTTATCTTTTAAAAT-T
*
155633 TTTTTATTTTTTTTTCTTTTAAAATT
1 TTTTT-TTTTTTTATCTTTTAAAATT
155659 TTT
1 TTT
155662 GAGAAGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTTTTTTTTTTATCTTTTAAAATT
Found at i:158237 original size:50 final size:50
Alignment explanation
Indices: 158174--158269 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
158164 ATATTTAGAG
*
158174 CGGTGAACTCCCTTAACCATCAAACCATTATATGAGATTCATAATTATGA
1 CGGTGAACACCCTTAACCATCAAACCATTATATGAGATTCATAATTATGA
* **
158224 CGGTGAACACCCTTGACCATCAAATTATTATATGAGATTCATAATT
1 CGGTGAACACCCTTAACCATCAAACCATTATATGAGATTCATAATT
158270 TGATAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (50 bp):
CGGTGAACACCCTTAACCATCAAACCATTATATGAGATTCATAATTATGA
Found at i:158787 original size:202 final size:203
Alignment explanation
Indices: 158431--158860 Score: 704
Period size: 202 Copynumber: 2.1 Consensus size: 203
158421 ATATATATAT
*
158431 ATTGGGTGTGTTTATCCAAATTGTAGAAAATAATGGGAAGGAAAGCCTTCAGTTTGCGCATGGGA
1 ATTGGGTGTGTTTATCCAAATTGTAGAAAATAATGGGAAGGAAAGCCTTCACTTTGCGCATGGGA
* *
158496 TGTGAACAAAAAAAATCATACAACAACGGTTTTAACAATTCAGTGATGTAAATGAAAATTTTCGA
66 TGTGAACAAAAAAAATCATACAACAACGGTTTTAACAACTCAGTGATGTAAATGAAAACTTTCGA
* * *
158561 ATAGTTCAGTGATTATTTTGTAAC-TTTTGAAGTTAAGTAACCAAAATATAAACTTATTAATAGT
131 ATAGTTCAATGATTATTCTGTAACTTTTTGAAGTTAAGTAACCAAAATATAAACTTACTAATAGT
158625 TTAATGAC
196 TTAATGAC
* *
158633 ATTGGATGTGTTTATCCAAATTGTAGAAAATAA-GAGGAAGGAAAGCCTTTACTTTGCGCA-GGA
1 ATTGGGTGTGTTTATCCAAATTGTAGAAAATAATG-GGAAGGAAAGCCTTCACTTTGCGCATGG-
* *
158696 GATGTGAACAAAAAAAGTCATACAACAACGGTTTTAACAGCTCAGTGATGTAAATGAAAACTTTC
64 GATGTGAACAAAAAAAATCATACAACAACGGTTTTAACAACTCAGTGATGTAAATGAAAACTTTC
*
158761 GAATAGTTTAATGATTATTCTGTAACTTTTTGAAGTTAAGTAACCAAAATATAAACTTACTAATA
129 GAATAGTTCAATGATTATTCTGTAACTTTTTGAAGTTAAGTAACCAAAATATAAACTTACTAATA
158826 GTTTAATGAC
194 GTTTAATGAC
*
158836 ATTGGGTGTAATTTATCCAAATTGT
1 ATTGGGTGT-GTTTATCCAAATTGT
158861 TTTAATCAAA
Statistics
Matches: 211, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
201 3 0.01
202 139 0.66
203 55 0.26
204 14 0.07
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (203 bp):
ATTGGGTGTGTTTATCCAAATTGTAGAAAATAATGGGAAGGAAAGCCTTCACTTTGCGCATGGGA
TGTGAACAAAAAAAATCATACAACAACGGTTTTAACAACTCAGTGATGTAAATGAAAACTTTCGA
ATAGTTCAATGATTATTCTGTAACTTTTTGAAGTTAAGTAACCAAAATATAAACTTACTAATAGT
TTAATGAC
Found at i:167854 original size:22 final size:21
Alignment explanation
Indices: 167813--167856 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
167803 TTCAAGTTAT
167813 TTTTATTATTTTAAATATAAA
1 TTTTATTATTTTAAATATAAA
*
167834 TTTT-TTATCTTTATATCATAAA
1 TTTTATTAT-TTTAAAT-ATAAA
167856 T
1 T
167857 AATTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 10 0.50
22 6 0.30
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATTATTTTAAATATAAA
Found at i:191989 original size:34 final size:34
Alignment explanation
Indices: 191946--192010 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
191936 TGATTGATGC
*
191946 ATAAAATATTATTTTAACTTTCTACCCGGAGAGA
1 ATAAAATATTATTTTAACTTTCTACCAGGAGAGA
191980 ATAAAATATTATTTTAACTTTCTACCAGGAG
1 ATAAAATATTATTTTAACTTTCTACCAGGAG
192011 TTATTCTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (34 bp):
ATAAAATATTATTTTAACTTTCTACCAGGAGAGA
Found at i:203030 original size:21 final size:22
Alignment explanation
Indices: 202997--203037 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
202987 ATTTTCTGGG
*
202997 TATTTTAGCATTTGG-TTTTCA
1 TATTTTAGAATTTGGATTTTCA
*
203018 TATTTTATAATTTGGATTTT
1 TATTTTAGAATTTGGATTTT
203038 TTCTTGGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.05, G:0.12, T:0.61
Consensus pattern (22 bp):
TATTTTAGAATTTGGATTTTCA
Found at i:207273 original size:85 final size:85
Alignment explanation
Indices: 207130--207300 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
207120 TGTCTTCTAA
*
207130 ATTGGAAAGCACAAATTGTGCTCTTAAAGTTGGTATATTTAGAATGTGATTGATTAGAGAAATAG
1 ATTGGAAAGCACAAATTGTGCCCTTAAAGTTGGTATATTTAGAATGTGATTGATTAGAGAAATAG
207195 TTGAGATGAAAAAAAGGGTT
66 TTGAGATGAAAAAAAGGGTT
207215 ATTGGAAAGCACAAATTGTGCCCTTAAAGTTGGTATATTTAGAATGTGATTGATTAGAGAAATAG
1 ATTGGAAAGCACAAATTGTGCCCTTAAAGTTGGTATATTTAGAATGTGATTGATTAGAGAAATAG
207280 TTGAGATGAAAAAAAGGGTT
66 TTGAGATGAAAAAAAGGGTT
207300 A
1 A
207301 CTATTTGATG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (85 bp):
ATTGGAAAGCACAAATTGTGCCCTTAAAGTTGGTATATTTAGAATGTGATTGATTAGAGAAATAG
TTGAGATGAAAAAAAGGGTT
Found at i:208734 original size:15 final size:16
Alignment explanation
Indices: 208714--208747 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
208704 TAATTTTTAA
208714 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
208729 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
208745 AAA
1 AAA
208748 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:209189 original size:16 final size:16
Alignment explanation
Indices: 209177--209225 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
209167 ATTTTTGTTC
209177 AATTTGATATTTGGTT
1 AATTTGATATTTGGTT
* *
209193 AATTTGATAACTTGATT
1 AATTTGAT-ATTTGGTT
209210 AATTTG--ATTTGGTT
1 AATTTGATATTTGGTT
209224 AA
1 AA
209226 ATCAAATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 8 0.29
16 8 0.29
17 12 0.43
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (16 bp):
AATTTGATATTTGGTT
Found at i:221806 original size:32 final size:32
Alignment explanation
Indices: 221765--221830 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
221755 CATTTTAGAC
221765 CTCATCATCTATAACTTTATTGTTTTCTCATT
1 CTCATCATCTATAACTTTATTGTTTTCTCATT
221797 CTCATCATCTATAACTTTATTGTTTTCTCATT
1 CTCATCATCTATAACTTTATTGTTTTCTCATT
221829 CT
1 CT
221831 TTGTTTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.53
Consensus pattern (32 bp):
CTCATCATCTATAACTTTATTGTTTTCTCATT
Found at i:225818 original size:14 final size:14
Alignment explanation
Indices: 225796--225825 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
225786 TTAATAACAA
*
225796 AAATGAATGAATTT
1 AAATCAATGAATTT
225810 AAATCAATGAATTT
1 AAATCAATGAATTT
225824 AA
1 AA
225826 CATTTGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.33
Consensus pattern (14 bp):
AAATCAATGAATTT
Done.