Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005578.1 Kokia drynarioides strain JFW-HI SEQ_119697, 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: 213741
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 152 characters in sequence are not A, C, G, or T
Found at i:3734 original size:18 final size:18
Alignment explanation
Indices: 3711--3753 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3701 GTTCAAGGTG
3711 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
3729 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
*
3747 TGATTAA
1 TAATTAA
3754 ATACTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:6767 original size:10 final size:10
Alignment explanation
Indices: 6679--6766 Score: 117
Period size: 10 Copynumber: 8.7 Consensus size: 10
6669 TAATTTTTAT
6679 TATTTTATAA
1 TATTTTATAA
6689 TATTTTCATAA
1 TATTTT-ATAA
6700 TATTTTATAA
1 TATTTTATAA
*
6710 TATTTCATAA
1 TATTTTATAA
6720 TATTTTATAA
1 TATTTTATAA
*
6730 TATTTCATAA
1 TATTTTATAA
6740 -ATTTTTATAA
1 TA-TTTTATAA
6750 TATTTTAATAA
1 TATTTT-ATAA
6761 -ATTTTA
1 TATTTTA
6767 AGCTTAAACA
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.03
10 53 0.76
11 15 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTTATAA
Found at i:12952 original size:18 final size:17
Alignment explanation
Indices: 12926--12970 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
12916 TACCAAAATT
*
12926 TATTCTATAATAAGATAA
1 TATTTTATAATAA-ATAA
12944 TATTTTATAATAAATAA
1 TATTTTATAATAAATAA
*
12961 AATTTTATAA
1 TATTTTATAA
12971 ATAGTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TATTTTATAATAAATAA
Found at i:12973 original size:18 final size:18
Alignment explanation
Indices: 12931--12970 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
12921 AAATTTATTC
*
12931 TATAATAAGATAATATTT
1 TATAATAAGATAAAATTT
12949 TATAATAA-ATAAAATTT
1 TATAATAAGATAAAATTT
12966 TATAA
1 TATAA
12971 ATAGTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TATAATAAGATAAAATTT
Found at i:13419 original size:16 final size:17
Alignment explanation
Indices: 13400--13432 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13390 ATAATGAAAA
13400 TTTTTTT-A-TTTAAAT
1 TTTTTTTAATTTTAAAT
13415 TTTTTTTAATTTTAAAT
1 TTTTTTTAATTTTAAAT
13432 T
1 T
13433 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTAATTTTAAAT
Found at i:19556 original size:1 final size:1
Alignment explanation
Indices: 19550--19579 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
19540 NNNNNNNNNN
19550 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19580 TCACTACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:31655 original size:17 final size:16
Alignment explanation
Indices: 31614--31656 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
31604 ACCAATTCAC
*
31614 ATTCAATTGTCAATTT
1 ATTCAATTTTCAATTT
*
31630 ATATAAATTTTGCAATTT
1 AT-TCAATTTT-CAATTT
31648 ATTCAATTT
1 ATTCAATTT
31657 AATCTCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 12 0.55
18 8 0.36
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (16 bp):
ATTCAATTTTCAATTT
Found at i:33672 original size:13 final size:14
Alignment explanation
Indices: 33646--33672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33636 TTCTAAATAA
33646 AAAAAATCATTTTT
1 AAAAAATCATTTTT
33660 AAAAAATCATTTT
1 AAAAAATCATTTT
33673 CCGAAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAAATCATTTTT
Found at i:49849 original size:13 final size:13
Alignment explanation
Indices: 49831--49856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49821 ATAATATTAA
49831 TATTATTATTTAT
1 TATTATTATTTAT
49844 TATTATTATTTAT
1 TATTATTATTTAT
49857 AGTTCTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:53003 original size:23 final size:23
Alignment explanation
Indices: 52971--53018 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
52961 ATTTTTAATT
* *
52971 AATATGTACATATTTTAAATATA
1 AATATGTACAAAATTTAAATATA
* *
52994 AATATTTACAAAATTTAAATTTA
1 AATATGTACAAAATTTAAATATA
53017 AA
1 AA
53019 ACATTGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
AATATGTACAAAATTTAAATATA
Found at i:59790 original size:3 final size:3
Alignment explanation
Indices: 59782--59813 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
59772 TTTAATTAGT
59782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59814 TTGCTTCGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:73526 original size:21 final size:23
Alignment explanation
Indices: 73500--73543 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
73490 AATTTTGTTC
73500 AACTTTAA-CTTTTAT-TCAAAA
1 AACTTTAATCTTTTATATCAAAA
*
73521 AACTTTAATTTTTTATATCAAAA
1 AACTTTAATCTTTTATATCAAAA
73544 CATATTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (23 bp):
AACTTTAATCTTTTATATCAAAA
Found at i:73918 original size:12 final size:12
Alignment explanation
Indices: 73901--73925 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73891 AAGCATTAGA
73901 AGGCTCTAAAAG
1 AGGCTCTAAAAG
73913 AGGCTCTAAAAG
1 AGGCTCTAAAAG
73925 A
1 A
73926 ATCATCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
AGGCTCTAAAAG
Found at i:77194 original size:51 final size:51
Alignment explanation
Indices: 77127--77355 Score: 264
Period size: 51 Copynumber: 4.5 Consensus size: 51
77117 AAAGGGATTA
* *
77127 ATGACTAAGTGTCATCGAGAGCAAATGAATCCTTTATGGATTAAAGGTCTG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCTG
* *
77178 ATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAATGGT-TCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCT-G
* * * *
77229 ATAACTAAGTGCCATCGTGAGTAAATGAGTCCTTTATGGATTAAAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCTG
** * * ** *
77280 ATGACTAAGTGTCATCGTGAGTTTATGGATTCCTATATGGAACAAGAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAAT-GAATCCTTTATGGATTAA-AGGTCTG
*
77333 ATGACTACA-TATCATCGTGAGTA
1 ATGACTA-AGTGTCATCGTGAGTA
77356 TTAAATGAAA
Statistics
Matches: 153, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.01
51 111 0.73
52 14 0.09
53 26 0.17
54 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCTG
Found at i:81757 original size:18 final size:19
Alignment explanation
Indices: 81719--81759 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
81709 TCAGACTAAT
*
81719 TTTTGGACTTTTATTTTAG
1 TTTTGGACTTTTATTTGAG
*
81738 TTTTGGATTTTTA-TTGAG
1 TTTTGGACTTTTATTTGAG
81756 TTTT
1 TTTT
81760 TAGTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.66
Consensus pattern (19 bp):
TTTTGGACTTTTATTTGAG
Found at i:84272 original size:18 final size:18
Alignment explanation
Indices: 84249--84283 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
84239 AGAAATAGCT
* *
84249 GCAAAATAATATATAAAA
1 GCAAAAGAATACATAAAA
84267 GCAAAAGAATACATAAA
1 GCAAAAGAATACATAAA
84284 TGTTGAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (18 bp):
GCAAAAGAATACATAAAA
Found at i:84473 original size:22 final size:20
Alignment explanation
Indices: 84424--84475 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
84414 TTTTTTTTAT
*
84424 TAAAT-AAACACGAAATTCA
1 TAAATAAAACAAGAAATTCA
84443 TATATATAAAACAAGAATATTGCA
1 TA-A-ATAAAACAAGAA-ATT-CA
84467 TAAATAAAA
1 TAAATAAAA
84476 ATTTTATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
21 2 0.07
22 14 0.52
23 4 0.15
24 4 0.15
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.25
Consensus pattern (20 bp):
TAAATAAAACAAGAAATTCA
Found at i:86071 original size:30 final size:29
Alignment explanation
Indices: 86037--86108 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
86027 ATAATAATGA
* *
86037 TAAAATTATATTTTAATTTTTTAAAAATAT
1 TAAAATT-TAATTTAATCTTTTAAAAATAT
* *
86067 TAAAAATTTAATTTGATCTTTTAAAATTAT
1 T-AAAATTTAATTTAATCTTTTAAAAATAT
*
86097 AAAAATATTAAT
1 TAAAAT-TTAAT
86109 CATTAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.14
30 24 0.69
31 6 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTTAATTTAATCTTTTAAAAATAT
Found at i:86208 original size:7 final size:7
Alignment explanation
Indices: 86196--86222 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
86186 CAAATTAATA
86196 TGTCGAT
1 TGTCGAT
86203 TGTCGAT
1 TGTCGAT
86210 TGTCGAT
1 TGTCGAT
86217 TGTCGA
1 TGTCGA
86223 AATATCTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (7 bp):
TGTCGAT
Found at i:91931 original size:31 final size:31
Alignment explanation
Indices: 91863--91931 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
91853 TACAATTTGG
* *
91863 TCATTGAACTATTTGAAAGTTTTCATTTAAG
1 TCATTGAACTATTTCAAAGTTTTCATTTAAA
* *
91894 TTATTGAACTA-TTCATAAGTTTTTATTTAAA
1 TCATTGAACTATTTCA-AAGTTTTCATTTAAA
91925 TCATTGA
1 TCATTGA
91932 GATGTTCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (31 bp):
TCATTGAACTATTTCAAAGTTTTCATTTAAA
Found at i:95186 original size:4 final size:4
Alignment explanation
Indices: 95177--95205 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
95167 GATGATTTGA
95177 AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
95206 ATGAAAGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (4 bp):
AGTG
Found at i:96097 original size:11 final size:11
Alignment explanation
Indices: 96081--96106 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
96071 TTGTTATATA
96081 TTTTTTAGAAT
1 TTTTTTAGAAT
96092 TTTTTTAGAAT
1 TTTTTTAGAAT
96103 TTTT
1 TTTT
96107 AGATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTTAGAAT
Found at i:101820 original size:28 final size:29
Alignment explanation
Indices: 101776--101844 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
101766 TTCACGATTA
* *
101776 GACTGTCTGCCATTTTGGCTTGTAC-TTG
1 GACTGTCCGCCACTTTGGCTTGTACTTTG
* *
101804 GATTGTCCGCCACTTTGGCTTGTGCTTTG
1 GACTGTCCGCCACTTTGGCTTGTACTTTG
*
101833 GACTATCCGCCA
1 GACTGTCCGCCA
101845 AATAGTTCGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.12, C:0.26, G:0.25, T:0.38
Consensus pattern (29 bp):
GACTGTCCGCCACTTTGGCTTGTACTTTG
Found at i:107065 original size:396 final size:397
Alignment explanation
Indices: 106552--107347 Score: 1522
Period size: 396 Copynumber: 2.0 Consensus size: 397
106542 TTACCCATTA
*
106552 TCTGCATTTGCCTTCATTTTCCTTTAAAGTTCTATGAAAGATATCATTTTGCTTAAGTGGAATGG
1 TCTGCATTTGCCTTCATTTTCCTTTAAAGATCTATGAAAGATATCATTTTGCTTAAGTGGAATGG
*
106617 TTGGGTGATACTTCTTTAGAACCAGTGATAGAATCAACATATTTTTCCCTTTTAAGTTTGTTGTA
66 TTGGGTGATACTACTTTAGAACCAGTGATAGAATCAACATATTTTTCCCTTTTAAGTTTGTTGTA
*
106682 GGAATTAATGTTCTTTGGAGATAGTCACAGAACTCGTTGAGATGGTCTTCATGTAATTTTGCTAT
131 GGAATTAATGTTCTTTGGAGAAAGTCACAGAACTCGTTGAGATGGTCTTCATGTAATTTTGCTAT
106747 AGGAAGTAATGTTCTTTGGAGATAATCAGTAATCAAAAAACTTGTTGAGATGGTCTTGATGTAAT
196 AGGAAGTAATGTTCTTTGGAGATAATCAGTAATCAAAAAACTTGTTGAGATGGTCTTGATGTAAT
106812 TTTTTGACACTCATAACTCTGAGGGAACTGTATTCTCAATCATGTACTCTGAAGCTCTTTATTTC
261 TTTTTGACACTCATAACTCTGAGGGAACTGTATTCTCAATCATGTACTCTGAAGCTCTTTATTTC
106877 TATCCTAAAAGGTTAATAAAGAACCAATTTTATGAATTGATGATTATTTTATTATATACTTAAAA
326 TATCCTAAAAGGTTAATAAAGAACCAATTTTATGAATTGATGATTATTTTATTATATACTTAAAA
106942 ATAAAGC
391 ATAAAGC
106949 TCTGCATTTGCCTTCATTTTCCTTTAAA-ATCTATGAAAGATATCATTTTGCTTAAGTGGAATGG
1 TCTGCATTTGCCTTCATTTTCCTTTAAAGATCTATGAAAGATATCATTTTGCTTAAGTGGAATGG
*
107013 TTGGGTGATACTACTTTAGAACTAGTGATAGAATCAACATATTTTTCCCTTTTAAGTTTGTTGTA
66 TTGGGTGATACTACTTTAGAACCAGTGATAGAATCAACATATTTTTCCCTTTTAAGTTTGTTGTA
107078 GGAATTAATGTTCTTTGGAGAAAGTCACAGAACTCGTTGAGATGGTCTTCATGTAATTTTGCTAT
131 GGAATTAATGTTCTTTGGAGAAAGTCACAGAACTCGTTGAGATGGTCTTCATGTAATTTTGCTAT
107143 AGGAAGTAATGTTCTTTGGAGATAATCAGTAATCAAAAAACTTGTTGAGATGGTCTTGATGTAAT
196 AGGAAGTAATGTTCTTTGGAGATAATCAGTAATCAAAAAACTTGTTGAGATGGTCTTGATGTAAT
*
107208 TTTTTGACACTCATAATTCTGAGGGAACTGTATTCTCAATCATGTACTCTGAAGCTCTTTATTTC
261 TTTTTGACACTCATAACTCTGAGGGAACTGTATTCTCAATCATGTACTCTGAAGCTCTTTATTTC
* *
107273 TATCCTACAGGGTTAATAAAGAACCAATTTTATGAATTGATGATTATTTTATTATATACTTAAAA
326 TATCCTAAAAGGTTAATAAAGAACCAATTTTATGAATTGATGATTATTTTATTATATACTTAAAA
107338 ATAAAGC
391 ATAAAGC
107345 TCT
1 TCT
107348 ATATATATTT
Statistics
Matches: 392, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
396 364 0.93
397 28 0.07
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (397 bp):
TCTGCATTTGCCTTCATTTTCCTTTAAAGATCTATGAAAGATATCATTTTGCTTAAGTGGAATGG
TTGGGTGATACTACTTTAGAACCAGTGATAGAATCAACATATTTTTCCCTTTTAAGTTTGTTGTA
GGAATTAATGTTCTTTGGAGAAAGTCACAGAACTCGTTGAGATGGTCTTCATGTAATTTTGCTAT
AGGAAGTAATGTTCTTTGGAGATAATCAGTAATCAAAAAACTTGTTGAGATGGTCTTGATGTAAT
TTTTTGACACTCATAACTCTGAGGGAACTGTATTCTCAATCATGTACTCTGAAGCTCTTTATTTC
TATCCTAAAAGGTTAATAAAGAACCAATTTTATGAATTGATGATTATTTTATTATATACTTAAAA
ATAAAGC
Found at i:109792 original size:12 final size:12
Alignment explanation
Indices: 109775--109799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
109765 TTATTACTTA
109775 TTACTTATGTTT
1 TTACTTATGTTT
109787 TTACTTATGTTT
1 TTACTTATGTTT
109799 T
1 T
109800 GTGCTATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTACTTATGTTT
Found at i:112573 original size:20 final size:20
Alignment explanation
Indices: 112545--112598 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
112535 ACCAATTCGG
* * *
112545 ACCAATTGAACTGGCAAAAA
1 ACCAGTTGAACCGGAAAAAA
112565 ACCAGTTGAACCGGAAAAAA
1 ACCAGTTGAACCGGAAAAAA
112585 ACCAGTTGAACCGG
1 ACCAGTTGAACCGG
112599 GTTTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.13
Consensus pattern (20 bp):
ACCAGTTGAACCGGAAAAAA
Found at i:121190 original size:15 final size:14
Alignment explanation
Indices: 121168--121207 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
121158 ATAATTTTTT
*
121168 ACTATAAATTTCAC
1 ACTATAAATTTAAC
121182 ACTTATAAAATTTAAC
1 AC-TAT-AAATTTAAC
121198 ACTATAAATT
1 ACTATAAATT
121208 GAATATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 7 0.30
15 6 0.26
16 10 0.43
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACTATAAATTTAAC
Found at i:126972 original size:19 final size:18
Alignment explanation
Indices: 126940--126991 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
126930 CGGCAAAAAT
*
126940 AAAAGAGAAAG-AAACGAA
1 AAAAGA-AAAGAAAAAGAA
126958 AGAAAGAAAAGGAAAAAGAA
1 A-AAAGAAAA-GAAAAAGAA
126978 AAAAG-AAAGAAAAA
1 AAAAGAAAAGAAAAA
126992 TCTCTCATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 6 0.20
18 7 0.23
19 10 0.33
20 7 0.23
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAGAA
Found at i:127287 original size:4 final size:4
Alignment explanation
Indices: 127280--127306 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
127270 TAAACAAACA
127280 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
127307 TATATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:134327 original size:20 final size:22
Alignment explanation
Indices: 134302--134343 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
134292 TTTATGAGTC
134302 TTATCTCTTGTA-GTTT-GCAA
1 TTATCTCTTGTATGTTTAGCAA
*
134322 TTATCTGTTGTATGTTTAGCAA
1 TTATCTCTTGTATGTTTAGCAA
134344 GTTTAGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (22 bp):
TTATCTCTTGTATGTTTAGCAA
Found at i:135290 original size:30 final size:30
Alignment explanation
Indices: 135254--135441 Score: 288
Period size: 30 Copynumber: 6.3 Consensus size: 30
135244 TGTTTTAGTT
* *
135254 GGTCTCCCAGAAACCGGAGAAGCAGAAGCA
1 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
* *
135284 GGTCTCCCAGAAATCGTAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
* *
135314 GGTCTCCTAGAAATC-ATAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGA-AGAAGCAGGAGCA
135344 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
135374 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
* *
135404 GGTCTCCGAGAAATCGAAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
135434 GGTCTCCC
1 GGTCTCCC
135442 TATTTGCGTC
Statistics
Matches: 146, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 145 0.99
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.30, T:0.11
Consensus pattern (30 bp):
GGTCTCCCAGAAACCGAAGAAGCAGGAGCA
Found at i:142530 original size:148 final size:148
Alignment explanation
Indices: 142262--142558 Score: 594
Period size: 148 Copynumber: 2.0 Consensus size: 148
142252 TTTAATCCAA
142262 TCCGGTTACTATGAATTTGATGTTGCTATGCCATAATCCCAATTTTCTATACATAGAAATCCATT
1 TCCGGTTACTATGAATTTGATGTTGCTATGCCATAATCCCAATTTTCTATACATAGAAATCCATT
142327 ATCAAAAACAATCAGGGCCATCACAATACATTTTTACAAGTTCTCATAGAAAGTATAGTGCATTG
66 ATCAAAAACAATCAGGGCCATCACAATACATTTTTACAAGTTCTCATAGAAAGTATAGTGCATTG
142392 TCATCAAACTTTAACATC
131 TCATCAAACTTTAACATC
142410 TCCGGTTACTATGAATTTGATGTTGCTATGCCATAATCCCAATTTTCTATACATAGAAATCCATT
1 TCCGGTTACTATGAATTTGATGTTGCTATGCCATAATCCCAATTTTCTATACATAGAAATCCATT
142475 ATCAAAAACAATCAGGGCCATCACAATACATTTTTACAAGTTCTCATAGAAAGTATAGTGCATTG
66 ATCAAAAACAATCAGGGCCATCACAATACATTTTTACAAGTTCTCATAGAAAGTATAGTGCATTG
142540 TCATCAAACTTTAACATC
131 TCATCAAACTTTAACATC
142558 T
1 T
142559 GTGTACCAAT
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 149 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (148 bp):
TCCGGTTACTATGAATTTGATGTTGCTATGCCATAATCCCAATTTTCTATACATAGAAATCCATT
ATCAAAAACAATCAGGGCCATCACAATACATTTTTACAAGTTCTCATAGAAAGTATAGTGCATTG
TCATCAAACTTTAACATC
Found at i:164474 original size:19 final size:19
Alignment explanation
Indices: 164452--164494 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
164442 AAAACATAAA
164452 TCTAACGTGAAAAAACCCC
1 TCTAACGTGAAAAAACCCC
164471 TCTAACGTGAAAAAACCCC
1 TCTAACGTGAAAAAACCCC
164490 TCTAA
1 TCTAA
164495 AGAGGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (19 bp):
TCTAACGTGAAAAAACCCC
Found at i:167208 original size:17 final size:17
Alignment explanation
Indices: 167186--167240 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
167176 TATTATTTTG
167186 AAATTTTAAAAATATAT
1 AAATTTTAAAAATATAT
*
167203 AAATTTTAAAAATATAC
1 AAATTTTAAAAATATAT
* *
167220 AAATTAATACAAATATAT
1 AAATT-TTAAAAATATAT
167238 AAA
1 AAA
167241 ATATTATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTTAAAAATATAT
Found at i:179614 original size:8 final size:7
Alignment explanation
Indices: 179587--179612 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
179577 ACTAATATTT
179587 AAAAATA
1 AAAAATA
179594 AAAAATA
1 AAAAATA
179601 AAAAATA
1 AAAAATA
179608 AAAAA
1 AAAAA
179613 ATCCTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:186543 original size:22 final size:23
Alignment explanation
Indices: 186483--186543 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
186473 TTTTAGGTCG
186483 AAATTAAATTATAATTTTTACAA
1 AAATTAAATTATAATTTTTACAA
* * *
186506 TAATAAAAATATAATTTTTA-AA
1 AAATTAAATTATAATTTTTACAA
*
186528 AAATTAAATTAAAATT
1 AAATTAAATTATAATT
186544 ATATTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTAAATTATAATTTTTACAA
Found at i:191303 original size:16 final size:15
Alignment explanation
Indices: 191284--191313 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
191274 TTTTATCTAC
191284 TATTAATAATTAAAAA
1 TATTAATAA-TAAAAA
191300 TATTAATAATAAAA
1 TATTAATAATAAAA
191314 TGAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATTAATAATAAAAA
Found at i:195232 original size:58 final size:57
Alignment explanation
Indices: 195166--195300 Score: 144
Period size: 58 Copynumber: 2.4 Consensus size: 57
195156 TTGCTCTTTA
* * *
195166 AAAATTTTCCAAGTATAAAACAACTCGCAGATTCACATTCCCAACTTATTATCTTAG
1 AAAATTTTCAAAGTATAAAACAACTCGCAAATTCACATTCCCAACATATTATCTTAG
** * * * * * *
195223 AAAATTTTTCAAAAAATAAAATAGCTTGCAAATTCATATTCCCAACATATTCTTTTAG
1 AAAA-TTTTCAAAGTATAAAACAACTCGCAAATTCACATTCCCAACATATTATCTTAG
* *
195281 GAAATTTTCTAAGTATAAAA
1 AAAATTTTCAAAGTATAAAA
195301 TCGCTTGGGA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
57 17 0.27
58 45 0.73
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (57 bp):
AAAATTTTCAAAGTATAAAACAACTCGCAAATTCACATTCCCAACATATTATCTTAG
Found at i:195319 original size:57 final size:58
Alignment explanation
Indices: 195202--195320 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 58
195192 GCAGATTCAC
* *
195202 ATTCCCAACTTATTATCTTAGAAAATTTTTCAAAAAATAAAATAGCTTGCAAATTCAT
1 ATTCCCAACATATTATCTTAGAAAATTTTTCAAAAAATAAAATAGCTTGCAAATTAAT
* * * * ** * **
195260 ATTCCCAACATATTCTTTTAGGAAA-TTTTCTAAGTATAAAATCGCTTGGGAATTAAT
1 ATTCCCAACATATTATCTTAGAAAATTTTTCAAAAAATAAAATAGCTTGCAAATTAAT
195317 ATTC
1 ATTC
195321 AAATTCAATA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
57 29 0.58
58 21 0.42
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (58 bp):
ATTCCCAACATATTATCTTAGAAAATTTTTCAAAAAATAAAATAGCTTGCAAATTAAT
Found at i:195582 original size:27 final size:27
Alignment explanation
Indices: 195523--195582 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
195513 TGTTATCAGT
* *
195523 AAGGGTAACATCCTCGTTCACAAAAGT
1 AAGGGTAACATCCTCATTCACAAAAGG
* * *
195550 AAGGGTAGCATCCTCATTCGCAATAGG
1 AAGGGTAACATCCTCATTCACAAAAGG
*
195577 AGGGGT
1 AAGGGT
195583 CATGTTCGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (27 bp):
AAGGGTAACATCCTCATTCACAAAAGG
Found at i:201876 original size:29 final size:28
Alignment explanation
Indices: 201828--201887 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
201818 AAAAATTAAT
201828 AAATATAAAATTACATTTTAA-CCTCTTA
1 AAATATAAAATTACATTTTAATCCT-TTA
*
201856 AAATGATAAAATTTCGA-TTTAATCCTTTA
1 AAAT-ATAAAATTAC-ATTTTAATCCTTTA
201885 AAA
1 AAA
201888 ACTATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.14
29 20 0.71
30 4 0.14
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (28 bp):
AAATATAAAATTACATTTTAATCCTTTA
Found at i:204649 original size:19 final size:19
Alignment explanation
Indices: 204627--204665 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
204617 AAGCAATAGA
204627 ATTTTTT-TAGGACAATTTT
1 ATTTTTTGTAGGA-AATTTT
*
204646 ATTTTTTGTATGAAATTTT
1 ATTTTTTGTAGGAAATTTT
204665 A
1 A
204666 AAAATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (19 bp):
ATTTTTTGTAGGAAATTTT
Done.