Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015215.1 Kokia drynarioides strain JFW-HI SEQ_130259, 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: 135527
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:65 original size:15 final size:15
Alignment explanation
Indices: 45--96 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
35 ATTCAATATT
45 AATATTTTAATAATA
1 AATATTTTAATAATA
*
60 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
79 AATATATTAATAATA
1 AATATTTTAATAATA
94 AAT
1 AAT
97 GTTTATTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 14 0.47
16 1 0.03
17 2 0.07
18 2 0.07
19 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:74 original size:19 final size:19
Alignment explanation
Indices: 47--104 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
37 TCAATATTAA
*
47 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
66 TATTATAATTATAAATA--
1 TATTATAATAATAAATATT
*
83 TA-T-TAATAATAAATGTT
1 TATTATAATAATAAATATT
100 TATTA
1 TATTA
105 GTATATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 10 0.32
16 1 0.03
17 4 0.13
18 1 0.03
19 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:752 original size:21 final size:20
Alignment explanation
Indices: 728--775 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
718 TAACGAAATG
* *
728 ATAGTAAAAAAATGGAAACAA
1 ATAGTAAAAAAAT-AAAAAAA
* *
749 ATAGCAAAACAATAAAAAAA
1 ATAGTAAAAAAATAAAAAAA
769 ATAGTAA
1 ATAGTAA
776 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (20 bp):
ATAGTAAAAAAATAAAAAAA
Found at i:1353 original size:32 final size:31
Alignment explanation
Indices: 1290--1353 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
1280 AATTAATTTA
*
1290 TTTTAAAATTTTGGAAGAATTTAATTAAAAT
1 TTTTAAAATTTTGGAAGAATTTAATGAAAAT
* *
1321 TTTTAAAAATTTTGTAA-AGTTTAATGAGAAAT
1 TTTT-AAAATTTTGGAAGAATTTAATGA-AAAT
1353 T
1 T
1354 CCATTTTCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (31 bp):
TTTTAAAATTTTGGAAGAATTTAATGAAAAT
Found at i:4284 original size:21 final size:21
Alignment explanation
Indices: 4258--4308 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
4248 ATAATAGCAT
*
4258 AATCCAAATATAAAGTTTAGA
1 AATCCAAATATAAAATTTAGA
* *
4279 AATCCAAACATAAAATTTATA
1 AATCCAAATATAAAATTTAGA
4300 AATCCAAAT
1 AATCCAAAT
4309 TACATAATCC
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:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Found at i:5050 original size:18 final size:18
Alignment explanation
Indices: 5027--5062 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5017 CTTCAATTTA
*
5027 ACATAAAGTATATACCAT
1 ACATAAAGCATATACCAT
*
5045 ACATAAAGCATATGCCAT
1 ACATAAAGCATATACCAT
5063 GAGAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.25
Consensus pattern (18 bp):
ACATAAAGCATATACCAT
Found at i:6896 original size:23 final size:22
Alignment explanation
Indices: 6865--6916 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
6855 TCTCCATTTA
*
6865 TTAGAACATATAGTGCTCTCCGT
1 TTAGCACATATA-TGCTCTCCGT
*
6888 TTAGCACATTTATGCTCTCCGT
1 TTAGCACATATATGCTCTCCGT
6910 TTAGCAC
1 TTAGCAC
6917 CTTGCTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (22 bp):
TTAGCACATATATGCTCTCCGT
Found at i:13595 original size:30 final size:31
Alignment explanation
Indices: 13559--13625 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 31
13549 TTTTAATCTT
13559 TAATTTTC-ATATATAATAATGACATTTTTG
1 TAATTTTCAATATATAATAATGACATTTTTG
13589 TAATTTTCATATATATAATAATGACATTTTTG
1 TAATTTTCA-ATATATAATAATGACATTTTTG
13621 TAATT
1 TAATT
13626 ATTGATACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 8 0.23
32 27 0.77
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (31 bp):
TAATTTTCAATATATAATAATGACATTTTTG
Found at i:20706 original size:20 final size:21
Alignment explanation
Indices: 20670--20719 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
20660 TCATTAAGCT
*
20670 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
20690 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
20710 TTAATATAAA
1 TTAAT-TAAA
20720 CAGTGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:32527 original size:31 final size:31
Alignment explanation
Indices: 32425--32538 Score: 89
Period size: 31 Copynumber: 3.8 Consensus size: 31
32415 AATATAACAC
* *
32425 TTAGTACCTGAACTTGACACTTTTTCCTAA-
1 TTAGTACCTAAACTTGACACTTTTTCGTAAT
* * *
32455 TTAGGACCT-AA--T--CTCTTTTTGGTCCAAT
1 TTAGTACCTAAACTTGACACTTTTTCGT--AAT
*
32483 TTGGTA-CTCAAACTTGACACTTTTTCGTAAT
1 TTAGTACCT-AAACTTGACACTTTTTCGTAAT
*
32514 TTAGTACCTAAACTTGACATTTTTT
1 TTAGTACCTAAACTTGACACTTTTT
32539 TAAGTTGGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
25 8 0.12
27 5 0.08
28 4 0.06
29 4 0.06
30 8 0.12
31 24 0.38
32 2 0.03
33 9 0.14
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.43
Consensus pattern (31 bp):
TTAGTACCTAAACTTGACACTTTTTCGTAAT
Found at i:32554 original size:29 final size:31
Alignment explanation
Indices: 32483--32557 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
32473 TTGGTCCAAT
* *
32483 TTGGTACTCAAACTTGACACTTTTTCGTAAT
1 TTGGTACTTAAACTTGACACTTTTTCGTAAG
* * *
32514 TTAGTACCTAAACTTGACA-TTTTT-TTAAG
1 TTGGTACTTAAACTTGACACTTTTTCGTAAG
32543 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
32558 TTTGGGGTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 16 0.43
30 5 0.14
31 16 0.43
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTCGTAAG
Found at i:33356 original size:21 final size:22
Alignment explanation
Indices: 33330--33370 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33320 TCTGTTAAAG
*
33330 GTAGTTAG-TTGTTGTAACTGA
1 GTAGTTAGTTTGCTGTAACTGA
33351 GTAGTTAGTTTGCTGTAACT
1 GTAGTTAGTTTGCTGTAACT
33371 ATTTCAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.44
Consensus pattern (22 bp):
GTAGTTAGTTTGCTGTAACTGA
Found at i:34236 original size:31 final size:31
Alignment explanation
Indices: 34172--34245 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
34162 AATTTGGATC
* * *
34172 TAATTACAATTTTTAAAAAATCGGAAAATTT
1 TAATTAAAATTTATAAAAAATCGGAAAAGTT
*
34203 TAATTAAAATTTATAAAAAATTTGG-AAAGTT
1 TAATTAAAATTTATAAAAAA-TCGGAAAAGTT
34234 TAATTAGAAATT
1 TAATTA-AAATT
34246 CCGTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 29 0.78
32 8 0.22
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (31 bp):
TAATTAAAATTTATAAAAAATCGGAAAAGTT
Found at i:34942 original size:42 final size:42
Alignment explanation
Indices: 34873--35018 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 42
34863 AAGAGTGTGT
* * * * *
34873 GAAAAGCGCGTCCAGCTAGGTGCGCTTTCTGCATAGTTGGCA
1 GAAAAGCTCGTCCAACTAGATGAGCTTTCTGCATAGTTGGTA
* * * *
34915 AAAAAGCTCGTCCAACTAGATGAGCTTT-TCACACAGTTGTTA
1 GAAAAGCTCGTCCAACTAGATGAGCTTTCT-GCATAGTTGGTA
* * *
34957 GGAAAA-CTTGTCCAACTAGACGAGCTTTCTGCGTAGTTGGTA
1 -GAAAAGCTCGTCCAACTAGATGAGCTTTCTGCATAGTTGGTA
* *
34999 GGAAAGCACGTCCAACTAGA
1 GAAAAGCTCGTCCAACTAGA
35019 CGAACTTTTG
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 5 0.06
42 71 0.88
43 5 0.06
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (42 bp):
GAAAAGCTCGTCCAACTAGATGAGCTTTCTGCATAGTTGGTA
Found at i:35019 original size:42 final size:42
Alignment explanation
Indices: 34896--35026 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 42
34886 AGCTAGGTGC
* ** *
34896 GCTTTCTGCATAGTTGGCAAAAAAGCTCGTCCAACTAGATGA
1 GCTTTCTGCATAGTTGGTAGGAAAGCTCGTCCAACTAGACGA
* * * * *
34938 GCTTT-TCACACAGTTGTTAGGAAAACTTGTCCAACTAGACGA
1 GCTTTCT-GCATAGTTGGTAGGAAAGCTCGTCCAACTAGACGA
* *
34980 GCTTTCTGCGTAGTTGGTAGGAAAGCACGTCCAACTAGACGA
1 GCTTTCTGCATAGTTGGTAGGAAAGCTCGTCCAACTAGACGA
*
35022 ACTTT
1 GCTTT
35027 TGCTGACATG
Statistics
Matches: 70, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
41 1 0.01
42 68 0.97
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
GCTTTCTGCATAGTTGGTAGGAAAGCTCGTCCAACTAGACGA
Found at i:38380 original size:18 final size:18
Alignment explanation
Indices: 38357--38399 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
38347 GAATGAATTT
38357 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
38375 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
38393 TTAATTA
1 TTAATTA
38400 CAACTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:42860 original size:30 final size:30
Alignment explanation
Indices: 42819--42878 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42809 TTTTAATAAT
*
42819 TTATATATTTATAATTTTTTA-AAAATTAAA
1 TTATATATTTATAA-TTTCTAGAAAATTAAA
* *
42849 TTATATTTTTATCATTTCTAGAAAATTAAA
1 TTATATATTTATAATTTCTAGAAAATTAAA
42879 ATGCAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (30 bp):
TTATATATTTATAATTTCTAGAAAATTAAA
Found at i:46293 original size:8 final size:8
Alignment explanation
Indices: 46280--46310 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
46270 AACATGACAT
46280 TTTATAAA
1 TTTATAAA
46288 TTTATAAA
1 TTTATAAA
46296 TTTATAAA
1 TTTATAAA
46304 TTTATAA
1 TTTATAA
46311 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTATAAA
Found at i:48686 original size:41 final size:41
Alignment explanation
Indices: 48610--48724 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 41
48600 TTTGGACAGA
** * *
48610 AAACGCCATAAAAAGTAAAGCAATAGCAGTGTTTTTGT--AG
1 AAACGCCGCAAAAAGTAAAGCAATAGCGGCGTTTTT-TCCAG
* *
48650 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTTCCAT
1 AAACGCCGCAAAAAGTAAAGCAATAGCGGCGTTTTTTCCAG
* * *
48691 AAACGCCGCAAAATGTAAAGTAATAACGGCGTTT
1 AAACGCCGCAAAAAGTAAAGCAATAGCGGCGTTT
48725 ATAGGAAAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 31 0.48
41 32 0.50
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (41 bp):
AAACGCCGCAAAAAGTAAAGCAATAGCGGCGTTTTTTCCAG
Found at i:48766 original size:21 final size:20
Alignment explanation
Indices: 48742--48780 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48732 AGCGCCGCTC
*
48742 AAGGTCAGAGCATTAGCGGCA
1 AAGGTCA-AGCAATAGCGGCA
*
48763 AAGGTTAAGCAATAGCGG
1 AAGGTCAAGCAATAGCGG
48781 TGTTTTTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.36, C:0.15, G:0.33, T:0.15
Consensus pattern (20 bp):
AAGGTCAAGCAATAGCGGCA
Found at i:51276 original size:19 final size:18
Alignment explanation
Indices: 51254--51297 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
51244 GGATTATATC
51254 AAATTTGGATATATATAAA
1 AAATTT-GATATATATAAA
* *
51273 AAATTT-ATATTTATATA
1 AAATTTGATATATATAAA
51290 AAATTTGA
1 AAATTTGA
51298 AAATAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (18 bp):
AAATTTGATATATATAAA
Found at i:53562 original size:21 final size:21
Alignment explanation
Indices: 53537--53576 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
53527 TAAAAATAAT
53537 TAAAA-ATAAAAAATATATACA
1 TAAAACATAAAAAAT-TATACA
53558 TAAAACATAAAAAATTATA
1 TAAAACATAAAAAATTATA
53577 AAAAATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAACATAAAAAATTATACA
Found at i:55560 original size:43 final size:43
Alignment explanation
Indices: 55512--55595 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
55502 AATAGTGGTG
* * * *
55512 TTTGTGATAAAAGCGTCGTTAAAGATCATGTTTTTTAGCGGCC
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTTTATAGCGGCC
*
55555 TTTGTGGGAAAAGCGTCGCTAAAGACCATGTTTTATAGCGG
1 TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTTTATAGCGG
55596 TGTTATCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
TTTGTGAGAAAAGCGTCGCTAAAGACCATGTTTTATAGCGGCC
Found at i:63303 original size:14 final size:13
Alignment explanation
Indices: 63269--63310 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
63259 ATTTAGTCAT
*
63269 TTTTTATTTTTA-
1 TTTTAATTTTTAC
63281 TTTTAATTTTTAC
1 TTTTAATTTTTAC
63294 TTTCTAATTTTT-C
1 TTT-TAATTTTTAC
63307 TTTT
1 TTTT
63311 GTTTGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 12 0.44
13 7 0.26
14 8 0.30
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTAATTTTTAC
Found at i:70828 original size:13 final size:13
Alignment explanation
Indices: 70789--70828 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
70779 AGTTTAGCAT
70789 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
70802 TGCTATGGAAAAG
1 TGCTTTTGAAAAG
*
70815 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
70828 T
1 T
70829 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:71124 original size:20 final size:21
Alignment explanation
Indices: 71083--71130 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
71073 ATTTAATCAG
* *
71083 AATATATAAACTATATT-TTT
1 AATATTTAAACTATATTATTA
71103 AATATTTAAA-TATAATTATTA
1 AATATTTAAACTAT-ATTATTA
71124 AATATTT
1 AATATTT
71131 GTAATTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.50
21 9 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTAAACTATATTATTA
Found at i:71184 original size:24 final size:25
Alignment explanation
Indices: 71154--71201 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
71144 AACACGGATG
*
71154 TATTATTTTAAAA-AATGTTTTTAT
1 TATTATTTTAAAATAATGATTTTAT
71178 TATTATTTTAAAATAATGATTTTA
1 TATTATTTTAAAATAATGATTTTA
71202 ATGCATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TATTATTTTAAAATAATGATTTTAT
Found at i:75552 original size:162 final size:162
Alignment explanation
Indices: 75345--75682 Score: 468
Period size: 162 Copynumber: 2.1 Consensus size: 162
75335 CACGTACATA
* * *
75345 TACTTCCCTTAAATTTTGGAGGCTTCTATTTGACACTTCTGAGCCTTGGATTATTTCTTCTAATT
1 TACTTCCCTTAAACTTTGGAGGCTTCTATTTGACACTTCTGAGCCTTGAATTATTTCTTCCAATT
* * * * *
75410 GGGAGCAAT-CTCTTATCTGCAGAGTTTGCAACCTCCCAAGGCTATTAGCAATAGACATTGG-AA
66 GGGAGCAATAC-CATATCTGAAGAGTTTGCAACCTCCCAAGACTATTAACAATAGACA-GGGAAA
*
75473 AGAGATATCTCAAATTATTGCAGTTTTTAACTTT
129 AGAGATAACTCAAATTATTGCAGTTTTTAACTTT
* *
75507 TACTTCCCTTAAACTTTGGAGG-TT-TATGTCTGACGCTTTTGAGCCTTGAATTATTTCTTCCAA
1 TACTTCCCTTAAACTTTGGAGGCTTCTAT-T-TGACACTTCTGAGCCTTGAATTATTTCTTCCAA
* * * *
75570 TTGGGAGCAGTACGATATCTTAAGAGTTTGCAATCTCCCAAGACTATTAACAATAGACAGGGAAA
64 TTGGGAGCAATACCATATCTGAAGAGTTTGCAACCTCCCAAGACTATTAACAATAGACAGGGAAA
75635 AGAGATAACTCAAATTATTGCAGTTTTTAACTTT
129 AGAGATAACTCAAATTATTGCAGTTTTTAACTTT
*
75669 TATTTCCCTTAAAC
1 TACTTCCCTTAAAC
75683 ACAACACTTG
Statistics
Matches: 156, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
160 3 0.02
161 5 0.03
162 147 0.94
163 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (162 bp):
TACTTCCCTTAAACTTTGGAGGCTTCTATTTGACACTTCTGAGCCTTGAATTATTTCTTCCAATT
GGGAGCAATACCATATCTGAAGAGTTTGCAACCTCCCAAGACTATTAACAATAGACAGGGAAAAG
AGATAACTCAAATTATTGCAGTTTTTAACTTT
Found at i:81313 original size:33 final size:31
Alignment explanation
Indices: 81276--81342 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
81266 CCATGTGTGC
*
81276 TTTATGTTAATTTTTTATAATTACTTATCAATT
1 TTTATGTTAATTTTTTAAAATT-CTTAT-AATT
* * *
81309 TTTATTTTATTTTTTTAAAATTTTTATAATT
1 TTTATGTTAATTTTTTAAAATTCTTATAATT
81340 TTT
1 TTT
81343 GAATTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 7 0.23
32 4 0.13
33 19 0.63
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (31 bp):
TTTATGTTAATTTTTTAAAATTCTTATAATT
Found at i:83491 original size:61 final size:60
Alignment explanation
Indices: 83380--83495 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 60
83370 CCAAATTGAA
** * * * * *
83380 CAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTTAAGTTCAAGTATCAAATTGGGC
1 CAAAAAAAAGTTTAAATACCAAATTAAGAAAAAATATCAAATTCAAGTATCAAATTGGGC
* *
83440 CAAAAACAAAGTTTAAATACCAAATTAAGAAAAAATATCAAATTTAGGTATCAAAT
1 CAAAAA-AAAGTTTAAATACCAAATTAAGAAAAAATATCAAATTCAAGTATCAAAT
83496 ATTATATTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 6 0.13
61 40 0.87
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (60 bp):
CAAAAAAAAGTTTAAATACCAAATTAAGAAAAAATATCAAATTCAAGTATCAAATTGGGC
Found at i:94370 original size:2 final size:2
Alignment explanation
Indices: 94363--94388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
94353 TCAATCTTAA
94363 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
94389 GCAAATTGCC
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:118419 original size:20 final size:20
Alignment explanation
Indices: 118394--118439 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
118384 TGACATGAAA
118394 AATACTTTTGAATCAAAAGG
1 AATACTTTTGAATCAAAAGG
118414 AATACTTTTGAATCAAAAGG
1 AATACTTTTGAATCAAAAGG
118434 AATACT
1 AATACT
118440 AAACAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (20 bp):
AATACTTTTGAATCAAAAGG
Found at i:118838 original size:13 final size:12
Alignment explanation
Indices: 118820--118862 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
118810 CTTAAACCAA
118820 ACTTTTTAAAATC
1 ACTTTTTAAAA-C
*
118833 ACTTTTTCAAAGC
1 ACTTTTT-AAAAC
118846 ACTTTATTAAAAC
1 ACTTT-TTAAAAC
118859 ACTT
1 ACTT
118863 ATCAAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (12 bp):
ACTTTTTAAAAC
Found at i:118872 original size:26 final size:26
Alignment explanation
Indices: 118820--118868 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
118810 CTTAAACCAA
*
118820 ACTTTTTAAAATCACTTTTTCAAAGC
1 ACTTTTTAAAATCACTTTATCAAAGC
118846 ACTTTATTAAAA-CAC-TTATCAAA
1 ACTTT-TTAAAATCACTTTATCAAA
118869 AGCAATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 8 0.38
27 6 0.29
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (26 bp):
ACTTTTTAAAATCACTTTATCAAAGC
Found at i:123186 original size:59 final size:59
Alignment explanation
Indices: 123120--123611 Score: 540
Period size: 59 Copynumber: 8.3 Consensus size: 59
123110 CGGATACCAA
* ** * *
123120 GGGGT-AAAATGGTAATTTTGGGAAAATTTGGGGTTAAAAATGGGATTTTTGGAAGTTTG
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* * * *
123179 GGGGTAAAAACGTAATTTTTGGAAATTTTGGGGTCAAAAAT-TGATTTTTGAAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* * * * ** *
123237 AGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTCATAAATGGGATTTTCAAAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* * * * *
123296 AGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAGATGGGATTTTTGGAAGCTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
*
123355 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATGGGATTTTTGAAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* * * ** *
123413 GGGATAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTCAAAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* * * * * * * **
123472 AGGGTAAAAACGGAATTTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTCGAAAATTAA
1 GGGGTAAAAATGGAA-TTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* * * * *
123532 GGGGTAAAAATAGAAATTTTTAGAAGTTTTGAGGTCAAAATTGGGATTTTTGGAAGTTTG
1 GGGGTAAAAAT-GGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
* *
123592 GGGGTAAAAACGAAATTTTT
1 GGGGTAAAAATGGAATTTTT
123612 AGACAATTTA
Statistics
Matches: 369, Mismatches: 59, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
58 101 0.27
59 167 0.45
60 98 0.27
61 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTTTG
Found at i:123611 original size:29 final size:29
Alignment explanation
Indices: 123120--123601 Score: 374
Period size: 29 Copynumber: 16.3 Consensus size: 29
123110 CGGATACCAA
* * *
123120 GGGGT-AAAATGGTAATTTTGGGAAAATTTG
1 GGGGTAAAAATGG-GATTTTTGG-AAGTTTG
*
123150 GGGTTAAAAATGGGATTTTTGGAAGTTTG
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* ** * *
123179 GGGGTAAAAACGTAATTTTTGGAAATTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* *
123208 GGGGTCAAAAAT-TGATTTTTGAAAGTTTG
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
* * * *
123237 AGGGTAAAAATGGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* * *** *
123266 AGGGTCATAAATGGGATTTTCAAAAGTTCG
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
* * *
123296 AGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* * *
123325 GGGGTCAAAGATGGGATTTTTGGAAGCTCG
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
* *
123355 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* * *
123384 GGGGTCAAAATGGGATTTTTGAAAGTTCG
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
*
123413 GGGATAAAAATGGGATTTTTGGAAGTTTTG
1 GGGGTAAAAATGGGATTTTTGGAAG-TTTG
* *** *
123443 GGGTTAAAAATGGGATTTTCAAAAGTTTA
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* * *
123472 AGGGTAAAAACGGAATTTTTTGGAAGTTTCG
1 GGGGTAAAAATGGGA-TTTTTGGAAGTTT-G
* * * * * **
123503 AGGTTAAAAATGGGATTTTCGAAAATTAA
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
** * *
123532 GGGGTAAAAATAGAAATTTTTAGAAGTTTT
1 GGGGTAAAAAT-GGGATTTTTGGAAGTTTG
* *
123562 GAGGTCAAAATTGGGATTTTTGGAAGTTTG
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
123592 GGGGTAAAAA
1 GGGGTAAAAA
123602 CGAAATTTTT
Statistics
Matches: 349, Mismatches: 93, Indels: 21
0.75 0.20 0.05
Matches are distributed among these distances:
28 6 0.02
29 181 0.52
30 138 0.40
31 24 0.07
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTG
Found at i:124616 original size:3 final size:3
Alignment explanation
Indices: 124595--124683 Score: 61
Period size: 3 Copynumber: 29.0 Consensus size: 3
124585 TTTTATTTAT
* * * * * * * * *
124595 TTA TTA ATA TTAA TAA TTA TTA TTA CTG TCA TTA ATA TTA CTA ATG
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
124641 TTA TTA GTA ATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
124684 ACATTATTGC
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
3 60 0.94
4 4 0.06
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:129172 original size:21 final size:21
Alignment explanation
Indices: 129148--129200 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
129138 AATTGGTGAT
*
129148 GATGATGATGATGACGACGAC
1 GATGATGATGACGACGACGAC
*
129169 GATGCTGATGACGACGACGAC
1 GATGATGATGACGACGACGAC
129190 GATGATGATGA
1 GATGATGATGA
129201 ATAGAGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.34, T:0.19
Consensus pattern (21 bp):
GATGATGATGACGACGACGAC
Found at i:129177 original size:18 final size:18
Alignment explanation
Indices: 129151--129197 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
129141 TGGTGATGAT
129151 GATGATGATGACGACGAC
1 GATGATGATGACGACGAC
*
129169 GATGCTGATGACGACGAC
1 GATGATGATGACGACGAC
*
129187 GACGATGATGA
1 GATGATGATGA
129198 TGAATAGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.34, T:0.17
Consensus pattern (18 bp):
GATGATGATGACGACGAC
Found at i:129852 original size:16 final size:16
Alignment explanation
Indices: 129820--129851 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
129810 TATCAATCAT
129820 TAAATATATATTTATA
1 TAAATATATATTTATA
129836 TAAATA-ATATTT-TA
1 TAAATATATATTTATA
129850 TA
1 TA
129852 TCGATATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATATATATTTATA
Found at i:131237 original size:20 final size:20
Alignment explanation
Indices: 131201--131246 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
131191 AAGTTAAAGG
131201 ATTAAATCGAAAAAAATAATA
1 ATTAAATCGAAAAAAATAA-A
*
131222 ATTAAAT-GACAAAAATAAA
1 ATTAAATCGAAAAAAATAAA
131241 ATTAAA
1 ATTAAA
131247 AATATAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 10 0.42
21 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (20 bp):
ATTAAATCGAAAAAAATAAA
Found at i:134367 original size:96 final size:96
Alignment explanation
Indices: 134267--134461 Score: 345
Period size: 96 Copynumber: 2.0 Consensus size: 96
134257 CAATTAAATA
134267 TTTGGAAAAGACTCAAAAGAGTTGACGCCATCTACTTCCTTCACTGAGTCTGACCAATGCAATAC
1 TTTGGAAAAGACTCAAAAGAGTTGACGCCATCTACTTCCTTCACTGAGTCTGACCAATGCAATAC
*
134332 TCAAATTTGAATTTGATTATGAGAGTATTAT
66 TCAAATTTGAATTTGACTATGAGAGTATTAT
* **
134363 TTTGGAAAAGACTCAAAAGAGTTGACGCCATTTACTTCCTTCACTGAGTCTGACCAATTTAATAC
1 TTTGGAAAAGACTCAAAAGAGTTGACGCCATCTACTTCCTTCACTGAGTCTGACCAATGCAATAC
*
134428 TCAAATTTGAATTTGACTATGAGATTATTAT
66 TCAAATTTGAATTTGACTATGAGAGTATTAT
134459 TTT
1 TTT
134462 ATTCATATAT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (96 bp):
TTTGGAAAAGACTCAAAAGAGTTGACGCCATCTACTTCCTTCACTGAGTCTGACCAATGCAATAC
TCAAATTTGAATTTGACTATGAGAGTATTAT
Found at i:134686 original size:17 final size:17
Alignment explanation
Indices: 134660--134707 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
134650 GGAAATCGAA
134660 TTTA-TTTAAATTTATG
1 TTTATTTTAAATTTATG
134676 TTTATTTTAAATTTATG
1 TTTATTTTAAATTTATG
*
134693 TTTATTTGAAATTTA
1 TTTATTTTAAATTTA
134708 AATTTATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTATTTTAAATTTATG
Found at i:134713 original size:17 final size:16
Alignment explanation
Indices: 134658--134731 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 16
134648 TTGGAAATCG
134658 AATTTATTTAAATTTA
1 AATTTATTTAAATTTA
**
134674 TGTTTATTTTAAATTTA
1 AATTTA-TTTAAATTTA
**
134691 TGTTTATTTGAAATTTA
1 AATTTATTT-AAATTTA
*
134708 AATTTATTATAAAAATTA
1 AATTTATT-T-AAATTTA
134726 AATTTA
1 AATTTA
134732 GAAAGTCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.14
17 29 0.59
18 13 0.27
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:134844 original size:17 final size:18
Alignment explanation
Indices: 134812--134850 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
134802 AAAGTGGCCC
134812 AAAATCAACCCCAAACCT
1 AAAATCAACCCCAAACCT
*
134830 AAAAT-AACCCTAAACCT
1 AAAATCAACCCCAAACCT
134847 AAAA
1 AAAA
134851 GGGCCCAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAATCAACCCCAAACCT
Done.