Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005894.1 Kokia drynarioides strain JFW-HI SEQ_120233, 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: 27507
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 247 characters in sequence are not A, C, G, or T
Found at i:394 original size:116 final size:116
Alignment explanation
Indices: 202--453 Score: 346
Period size: 116 Copynumber: 2.2 Consensus size: 116
192 GGTAGAACTC
* * * *
202 ATACTTGTA-CAGGTAAAAGTACAG-GATAGGAGAGAGGTTGTTCTTTGACTTGAGTTGTTTCGG
1 ATACTTGTATC-GGTAGAAGTATAGCG-TAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAG
* * *
265 TAATTGTATAACAGGTATCGGTAATTCTATGCATTGAGGTATCGGTAGTTTAA
64 TAATTGTATAACAGGTATCGGTAATTCTATACATTGAGATATCGATAGTTTAA
* *
318 ATGCTTGTATCGGTAGAAGTATAGCGTAGGAGAGAGGTTGTTCTCTGATTTGAGTTGTTTCAGTA
1 ATACTTGTATCGGTAGAAGTATAGCGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAGTA
* * * *
383 GTTGTATAACAGGTATCGGTAGTTTTGTACATTGAGATATCGATAGTTTAA
66 ATTGTATAACAGGTATCGGTAATTCTATACATTGAGATATCGATAGTTTAA
*
434 ATACTTGTATTGGTAGAAGT
1 ATACTTGTATCGGTAGAAGT
454 TGCAAGGTAG
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
116 117 0.98
117 2 0.02
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.37
Consensus pattern (116 bp):
ATACTTGTATCGGTAGAAGTATAGCGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAGTA
ATTGTATAACAGGTATCGGTAATTCTATACATTGAGATATCGATAGTTTAA
Found at i:5168 original size:19 final size:18
Alignment explanation
Indices: 5119--5161 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
5109 TGCAAAAGTA
5119 AAAAATTC-AAAA-ACTAT
1 AAAAATTCTAAAATA-TAT
5136 AAAAATTCTAAAATATAT
1 AAAAATTCTAAAATATAT
5154 ATAAAATT
1 A-AAAATT
5162 TTCAAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATTCTAAAATATAT
Found at i:6558 original size:24 final size:26
Alignment explanation
Indices: 6526--6582 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
6516 CATCTTTGAA
*
6526 AAAAAATTC-AACAAAATAGA-TTTT
1 AAAAAATTCAAAAAAAATAGATTTTT
*
6550 AAAAAATTCAAAAAAAATATATTTTT
1 AAAAAATTCAAAAAAAATAGATTTTT
6576 AAAAAAT
1 AAAAAAT
6583 ATTATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 9 0.31
25 9 0.31
26 11 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAAAATTCAAAAAAAATAGATTTTT
Found at i:6581 original size:16 final size:16
Alignment explanation
Indices: 6560--6608 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
6550 AAAAAATTCA
6560 AAAAAAATATATTTTT
1 AAAAAAATATATTTTT
6576 AAAAAATATTATATTTTT
1 AAAAAA-A-TATATTTTT
* *
6594 TAAAATATATATTTT
1 AAAAAAATATATTTT
6609 GCCGCGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 14 0.48
17 2 0.07
18 13 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAAAATATATTTTT
Found at i:6588 original size:18 final size:16
Alignment explanation
Indices: 6560--6608 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
6550 AAAAAATTCA
*
6560 AAAAAAATATATTTTT
1 AAAAATATATATTTTT
6576 AAAAAATATTATATTTTT
1 -AAAAATA-TATATTTTT
*
6594 TAAAATATATATTTT
1 AAAAATATATATTTT
6609 GCCGCGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.28
17 12 0.41
18 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATATATATTTTT
Found at i:6593 original size:19 final size:20
Alignment explanation
Indices: 6566--6603 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6556 TTCAAAAAAA
6566 ATATATTTTTAAAAAATATT
1 ATATATTTTTAAAAAATATT
*
6586 ATAT-TTTTTAAAATATAT
1 ATATATTTTTAAAAAATAT
6604 ATTTTGCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTTTTAAAAAATATT
Found at i:11482 original size:24 final size:26
Alignment explanation
Indices: 11444--11492 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
11434 CCCTTTTCCC
11444 TTCACCATTAATGAAAGAAAGAGATT
1 TTCACCATTAATGAAAGAAAGAGATT
*
11470 TTCA-CATT-ATGAAAGAGAGAGAT
1 TTCACCATTAATGAAAGAAAGAGAT
11493 AATAACACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 4 0.18
26 4 0.18
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (26 bp):
TTCACCATTAATGAAAGAAAGAGATT
Found at i:12183 original size:16 final size:17
Alignment explanation
Indices: 12152--12184 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12142 TCAAAATTCC
*
12152 CTTATGTTTTTCTTCAT
1 CTTACGTTTTTCTTCAT
12169 CTTACGTTTTT-TTCAT
1 CTTACGTTTTTCTTCAT
12185 TCTGAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.18, G:0.06, T:0.64
Consensus pattern (17 bp):
CTTACGTTTTTCTTCAT
Found at i:20525 original size:88 final size:85
Alignment explanation
Indices: 20284--20524 Score: 240
Period size: 88 Copynumber: 2.8 Consensus size: 85
20274 ATAAAAAATT
* * *
20284 AAAAAAAGCAATTAAGCCC-C-TTTTTTCACTCAATTTGGTACTTGAACTTTAAAATTGCA-ACA
1 AAAAAAAGCAATTAAGCCCTCTTTTTTTCACTCAATTGGGTACTTGAACTTTAAAA-TGTATAAA
*
20346 AAAAGACCCTCAAACTATTAA
65 AAAACACCCTCAAACTATTAA
* * * * * *
20367 AAAAAAAACAATTAAGTCTCTGCTTTTTTTTGCACTCAATTGGATACTTAAATTTTTAAAATGCA
1 AAAAAAAGCAATTAAG-CCCT-C-TTTTTTT-CACTCAATTGGGTACTTGAA-CTTTAAAATGTA
* **
20432 T--AAAAACACCCTCAAACTTTTTC
61 TAAAAAAACACCCTCAAACTATTAA
* *
20455 AAAAAAAGCAATTAAGCCCCTACTTTTTTTCACTTAATTGGGTACTTGAACTTTCAAATGTATAA
1 AAAAAAAGCAATTAAG-CCCT-CTTTTTTTCACTCAATTGGGTACTTGAACTTTAAAATGTATAA
20520 AAAAA
64 AAAAA
20525 AACCTNNNNN
Statistics
Matches: 128, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
83 15 0.12
84 2 0.02
85 10 0.08
86 18 0.14
87 12 0.09
88 43 0.34
89 21 0.16
90 7 0.05
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (85 bp):
AAAAAAAGCAATTAAGCCCTCTTTTTTTCACTCAATTGGGTACTTGAACTTTAAAATGTATAAAA
AAACACCCTCAAACTATTAA
Found at i:20865 original size:18 final size:19
Alignment explanation
Indices: 20818--20885 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
20808 ATTAGAAAAG
20818 AATTTATAAAAATCGTAAA
1 AATTTATAAAAATCGTAAA
* * *
20837 AATATACAAAATTC-TAAA
1 AATTTATAAAAATCGTAAA
* *
20855 ATTTTATAAAAAATCATAAA
1 AATTTAT-AAAAATCGTAAA
*
20875 AAATTATAAAA
1 AATTTATAAAA
20886 GGCATAAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
18 8 0.21
19 21 0.55
20 9 0.24
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (19 bp):
AATTTATAAAAATCGTAAA
Found at i:21104 original size:18 final size:18
Alignment explanation
Indices: 21063--21104 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
21053 TATTACGATA
*
21063 ATTTTTATATTTTTTATG
1 ATTTTTATATTTTTTATC
*
21081 AATTTTATATTTCTTTA-C
1 ATTTTTATATTT-TTTATC
21099 ATTTTT
1 ATTTTT
21105 TAAAATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATATTTTTTATC
Found at i:21116 original size:21 final size:21
Alignment explanation
Indices: 21090--21134 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21080 GAATTTTATA
*
21090 TTTCTTTAC-ATTTTTTAAAAT
1 TTTC-TTACAATTTTATAAAAT
*
21111 TTTCTTGCAATTTTATAAAAT
1 TTTCTTACAATTTTATAAAAT
21132 TTT
1 TTT
21135 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTCTTACAATTTTATAAAAT
Found at i:21473 original size:89 final size:88
Alignment explanation
Indices: 21312--21485 Score: 226
Period size: 89 Copynumber: 2.0 Consensus size: 88
21302 TAGAAGCAGT
** * * *
21312 TCAAGTACCCAATTGAGTGAAAAAAAAAAAAGAGGCTTAATTGTTTTTTTGAAAAAGTTTGATGA
1 TCAAGTACCCAATTGAGTGAAAAAAAAAAAAGAAACTTAATTGCTTTTTTGAAAAAGTTTAAGGA
21377 CATTTTTGATACATTTTGAAAGC
66 CATTTTTGATACATTTTGAAAGC
*
21400 TCAAGTACTCAATTGAGTGCAAAAAAAAAAATA-AAACTTAATCT-CTTTTTTGAAAAAGTTTAA
1 TCAAGTACCCAATTGAGTG-AAAAAAAAAAA-AGAAACTTAAT-TGCTTTTTTGAAAAAGTTTAA
* * *
21463 GGGCTTTTTTGATGCATTTTGAA
63 GGACATTTTTGATACATTTTGAA
21486 TGTTGTAATA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 18 0.24
89 54 0.73
90 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (88 bp):
TCAAGTACCCAATTGAGTGAAAAAAAAAAAAGAAACTTAATTGCTTTTTTGAAAAAGTTTAAGGA
CATTTTTGATACATTTTGAAAGC
Found at i:22092 original size:19 final size:19
Alignment explanation
Indices: 22068--22126 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
22058 GAAAAAAATT
22068 ATAAAAATAAAAAATTTTA
1 ATAAAAATAAAAAATTTTA
**
22087 GA-AAAAATATTAAATTTTA
1 -ATAAAAATAAAAAATTTTA
*
22106 ATAAAATATAAAAAAATTTA
1 ATAAAA-ATAAAAAATTTTA
22126 A
1 A
22127 AATTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.03
19 19 0.59
20 12 0.38
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAAAAATAAAAAATTTTA
Found at i:22119 original size:28 final size:28
Alignment explanation
Indices: 22045--22144 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 28
22035 GCCCTTGCTC
* *
22045 TTATTAAAAATTAGAAAAAAATTATAAAA
1 TTATTAAAAAATATAAAAAAATT-TAAAA
*
22074 --A-TAAAAAATTTTAGAAAAAATATT-AAA
1 TTATTAAAAAA-TATA-AAAAAAT-TTAAAA
22101 TT-TTAATAAAATATAAAAAAATTTAAAA
1 TTATTAA-AAAATATAAAAAAATTTAAAA
*
22129 TTATTAAAAATTATAA
1 TTATTAAAAAATATAA
22145 TTTTTTATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
26 6 0.11
27 8 0.14
28 28 0.49
29 11 0.19
30 4 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
TTATTAAAAAATATAAAAAAATTTAAAA
Found at i:22211 original size:39 final size:39
Alignment explanation
Indices: 22124--22212 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 39
22114 TAAAAAAATT
* **
22124 TAAAATTATTAAAAATTATAATTTTTTATAAAAATCGTA
1 TAAAATTATAAAAAATTATAAAATTTTATAAAAATCGTA
* * *
22163 -AAAA-AATAAAAAATTGTAAAATTTTATAGAAATCGTA
1 TAAAATTATAAAAAATTATAAAATTTTATAAAAATCGTA
22200 TAAAATTATAAAA
1 TAAAATTATAAAA
22213 TGCATCAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
37 27 0.66
38 8 0.20
39 6 0.15
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (39 bp):
TAAAATTATAAAAAATTATAAAATTTTATAAAAATCGTA
Found at i:22429 original size:20 final size:20
Alignment explanation
Indices: 22404--22460 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
22394 TACGATAATT
22404 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
22424 TTTAT-ATTTCTTTAC-ATT
1 TTTATAATTTTTTTACGAAA
*
22442 TTGTATAATTTTCTTACGA
1 TT-TATAATTTTTTTACGA
22461 CTTTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 13 0.45
21 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:22503 original size:20 final size:20
Alignment explanation
Indices: 22472--22524 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
22462 TTTAAAAAAA
22472 TTTATAATTTTTACAATTTTT
1 TTTAT-ATTTTTACAATTTTT
*
22493 TTTATATTTTTCACGATTTTT
1 TTTATATTTTT-ACAATTTTT
*
22514 TCTA-ATTTTTA
1 TTTATATTTTTA
22525 AATATTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 16 0.55
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATATTTTTACAATTTTT
Found at i:22531 original size:20 final size:19
Alignment explanation
Indices: 22476--22531 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
22466 AAAAAATTTA
22476 TAATTTTTACAAT-TTTTTT
1 TAATTTTTA-AATATTTTTT
* **
22495 TATATTTTTCACGATTTTTT
1 TA-ATTTTTAAATATTTTTT
22515 CTAATTTTTAAATATTT
1 -TAATTTTTAAATATTT
22532 GAATTTTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (19 bp):
TAATTTTTAAATATTTTTT
Found at i:24462 original size:8 final size:8
Alignment explanation
Indices: 24449--24473 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
24439 ACTAACCCTT
24449 AATTGGCC
1 AATTGGCC
24457 AATTGGCC
1 AATTGGCC
24465 AATTGGCC
1 AATTGGCC
24473 A
1 A
24474 TTTCTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (8 bp):
AATTGGCC
Found at i:26407 original size:21 final size:19
Alignment explanation
Indices: 26349--26426 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 19
26339 TTTTAAGAAT
*
26349 ATATTAAAAATA-TTTAAAA
1 ATATTAAAAA-ACTATAAAA
*
26368 GTATTAAAAAACTAT-AAA
1 ATATTAAAAAACTATAAAA
*
26386 ATATTAATCAAAACTCTAAAA
1 ATATTAA--AAAACTATAAAA
*
26407 ATACTACAAAAA-TATAAAA
1 ATATTA-AAAAACTATAAAA
26426 A
1 A
26427 CTAGTATGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
18 10 0.21
19 18 0.38
20 11 0.23
21 8 0.17
22 1 0.02
ACGTcount: A:0.63, C:0.08, G:0.01, T:0.28
Consensus pattern (19 bp):
ATATTAAAAAACTATAAAA
Done.