Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014342.1 Kokia drynarioides strain JFW-HI SEQ_129379, 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: 53755
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:13356 original size:56 final size:55
Alignment explanation
Indices: 13270--13452 Score: 154
Period size: 65 Copynumber: 3.1 Consensus size: 55
13260 AGAGATTTTG
* *
13270 AAAAAAAAAAA-TTGATGTT-GGCTATTGCATGGCCGACACCTCTTTTTTAATCTAA
1 AAAAAAAAAAATTTGGTGTTAGTC-ATTGCATGGCCGACACCTCTTTTTT-ATCTAA
* *
13325 CAAAAAAAAAATTTGGTGTTAGTCATTGCATGGCTGACACCATCTTTTTGTATCTGATA
1 AAAAAAAAAAATTTGGTGTTAGTCATTGCATGGCCGACACC-TCTTTTT-TATCT-A-A
* ** * *
13384 GAAAAAAATTCAAAATTTTTGGTATTAGTCATTGCATGATCGACACCCCTTTTTTATCTGA
1 -AAAAAAA---AAAA--TTTGGTGTTAGTCATTGCATGGCCGACACCTCTTTTTTATCTAA
*
13445 TAAAAAAA
1 AAAAAAAA
13453 TTCAAATTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
55 10 0.10
56 23 0.22
57 14 0.13
58 2 0.02
59 1 0.01
60 12 0.12
61 1 0.01
63 9 0.09
64 6 0.06
65 26 0.25
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (55 bp):
AAAAAAAAAAATTTGGTGTTAGTCATTGCATGGCCGACACCTCTTTTTTATCTAA
Found at i:13412 original size:65 final size:61
Alignment explanation
Indices: 13336--13572 Score: 179
Period size: 61 Copynumber: 3.9 Consensus size: 61
13326 AAAAAAAAAA
* * *
13336 TTTGGTGTTAGTCATTGCATG-GCTGACACCATCTTTTTGTATCTGATAGAAAAAAATTCAAAAT
1 TTTGGTATTAGTCATTGCATGATC-GACACC-CCTTTTT-TATCTGAT--AAAAAAATTCAAAAT
13400 T
61 T
13401 TTTGGTATTAGTCATTGCATGATCGACACCCCTTTTTTATCTGATAAAAAAATTC-AAATT
1 TTTGGTATTAGTCATTGCATGATCGACACCCCTTTTTTATCTGATAAAAAAATTCAAAATT
* * * * * *
13461 TTT--T-TTGGT-GTTGGCTATGCATTGAC-CGCC-TTTTTATATGATAAAAAAAATCAAAATT
1 TTTGGTATTAGTCATT-GC-ATG-ATCGACACCCCTTTTTTATCTGATAAAAAAATTCAAAATT
* * * * **
13519 TTTGGTGTTGGCCATTGCATG-GCTGACATTACC-TTTTTATCTGATAAAAAAATT
1 TTTGGTATTAGTCATTGCATGATC-GACA-CCCCTTTTTTATCTGATAAAAAAATT
13573 TAATTTTTTT
Statistics
Matches: 143, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
56 2 0.01
57 26 0.18
58 15 0.10
59 8 0.06
60 12 0.08
61 37 0.26
62 2 0.01
63 8 0.06
64 6 0.04
65 26 0.18
66 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (61 bp):
TTTGGTATTAGTCATTGCATGATCGACACCCCTTTTTTATCTGATAAAAAAATTCAAAATT
Found at i:13536 original size:118 final size:121
Alignment explanation
Indices: 13370--13585 Score: 298
Period size: 118 Copynumber: 1.8 Consensus size: 121
13360 GACACCATCT
* * * *
13370 TTTTGTATCTGATAGAAAAAAATTCAAAATTTTTGGTATTAGTCATTGCAT-GATCGACA-CCCC
1 TTTTGTATATGATAGAAAAAAATTCAAAATTTTTGGTATTAGCCATTGCATGGCT-GACATCACC
13433 TTTTTTATCTGATAAAAAAATTCAAATTTTTTTTGGTGTTGGCTATGCATTGACCGCC
65 -TTTTTATCTGATAAAAAAATTCAAATTTTTTTTGGTGTTGGCTATGCATTGACCGCC
* * *
13491 TTTT-TATATGATA-AAAAAAA-TCAAAATTTTTGGTGTTGGCCATTGCATGGCTGACATTACCT
1 TTTTGTATATGATAGAAAAAAATTCAAAATTTTTGGTATTAGCCATTGCATGGCTGACATCACCT
* *
13553 TTTTATCTGATAAAAAAATTTAATTTTTTTTTG
66 TTTTATCTGATAAAAAAATTCAAATTTTTTTTG
13586 TTTTTTATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 61 0.73
119 11 0.13
120 8 0.10
121 4 0.05
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (121 bp):
TTTTGTATATGATAGAAAAAAATTCAAAATTTTTGGTATTAGCCATTGCATGGCTGACATCACCT
TTTTATCTGATAAAAAAATTCAAATTTTTTTTGGTGTTGGCTATGCATTGACCGCC
Found at i:13600 original size:35 final size:36
Alignment explanation
Indices: 13552--13623 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
13542 TGACATTACC
* *
13552 TTTTTATCTGATAAAAAAATT-TAATTTTTTTTTGT
1 TTTTTATCTGATAAAAAAATTCAAATTTTTTTGTGT
13587 TTTTTAT-TAGATAAAAAAATTCAAATTTTTTTGTGT
1 TTTTTATCT-GATAAAAAAATTCAAATTTTTTTGTGT
13623 T
1 T
13624 AGTCATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 19 0.58
36 13 0.39
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (36 bp):
TTTTTATCTGATAAAAAAATTCAAATTTTTTTGTGT
Found at i:15723 original size:18 final size:17
Alignment explanation
Indices: 15700--15763 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
15690 GAGAAACATG
15700 GAAGGAGAAACCATGGGA
1 GAAGGAGAAACC-TGGGA
*
15718 GAAGGAGAAATGCTGGGA
1 GAAGGAGAAA-CCTGGGA
* *
15736 GGAGGAGAAGTCCTGGGA
1 GAAGGAGAA-ACCTGGGA
*
15754 GGAGGAGAAA
1 GAAGGAGAAA
15764 TACTAGAACG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 38 0.97
19 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.45, T:0.08
Consensus pattern (17 bp):
GAAGGAGAAACCTGGGA
Found at i:21692 original size:32 final size:32
Alignment explanation
Indices: 21646--21714 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
21636 TTGCTAGAAA
21646 TCAAACACTCGATTTTCCTACCGGTACTCAAT
1 TCAAACACTCGATTTTCCTACCGGTACTCAAT
* * *
21678 TCAAACGCTTGATTTTCCTACCGGTACTCGAT
1 TCAAACACTCGATTTTCCTACCGGTACTCAAT
21710 TCAAA
1 TCAAA
21715 ACTAAGAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (32 bp):
TCAAACACTCGATTTTCCTACCGGTACTCAAT
Found at i:26720 original size:4 final size:4
Alignment explanation
Indices: 26711--26755 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
26701 TCTAGTTCAT
26711 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
26756 CATATATGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:27707 original size:14 final size:14
Alignment explanation
Indices: 27681--27722 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
27671 CTATTATCTT
27681 GAAA-TTATGAAAA
1 GAAATTTATGAAAA
*
27694 GAAATTTATCAAAA
1 GAAATTTATGAAAA
27708 -AAATATTATGAAAA
1 GAAAT-TTATGAAAA
27722 G
1 G
27723 GGCAAGGCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (14 bp):
GAAATTTATGAAAA
Found at i:28541 original size:45 final size:46
Alignment explanation
Indices: 28492--28583 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
28482 AAAATCCATA
28492 TATATCCAGATATA-TGTTTTTACCTAGTACAATCTTTGAACATGT
1 TATATCCAGATATAGTGTTTTTACCTAGTACAATCTTTGAACATGT
28537 TATATCCAGATATAGTGTTTTTACCTAGTACAATCTTTGAACATGT
1 TATATCCAGATATAGTGTTTTTACCTAGTACAATCTTTGAACATGT
28583 T
1 T
28584 TTTTTCCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 14 0.30
46 32 0.70
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (46 bp):
TATATCCAGATATAGTGTTTTTACCTAGTACAATCTTTGAACATGT
Found at i:34245 original size:22 final size:20
Alignment explanation
Indices: 34203--34245 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
34193 CCACATTAAT
*
34203 TTCATAATTTATCTTTACAA
1 TTCATAATTTATCTTGACAA
*
34223 TTCATAATTCATATCTTGCCAA
1 TTCATAATT--TATCTTGACAA
34245 T
1 T
34246 GATGAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.47
Consensus pattern (20 bp):
TTCATAATTTATCTTGACAA
Found at i:34537 original size:24 final size:22
Alignment explanation
Indices: 34510--34662 Score: 79
Period size: 22 Copynumber: 6.9 Consensus size: 22
34500 ATTATATTAT
34510 TGTTTTGGTGCTGATTTTTTTTGC
1 TGTTTTGGTG-TG-TTTTTTTTGC
*
34534 TGTTTTGGT-TGTTATTTTTTGT
1 TGTTTTGGTGTGTT-TTTTTTGC
* *
34556 TGTTTTGGTGT-TGTGTTTTTAC
1 TGTTTTGGTGTGT-TTTTTTTGC
*
34578 TGTTTTGGTGAT-TTTTTTAT--
1 TGTTTTGGTG-TGTTTTTTTTGC
**
34598 TGTTTTGGT-TGCTGTTTTGGTGC
1 TGTTTTGGTGTG-T-TTTTTTTGC
**
34621 TGTTTTTAT-TGTTATTTTTGTTGC
1 TGTTTTGGTGTG-T-TTTTT-TTGC
*
34645 TGTTTTGGT-TGTTATTTT
1 TGTTTTGGTGTGTTTTTTT
34663 AGTTGTTTGG
Statistics
Matches: 102, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.01
20 10 0.10
21 8 0.08
22 43 0.42
23 19 0.19
24 21 0.21
ACGTcount: A:0.05, C:0.04, G:0.24, T:0.67
Consensus pattern (22 bp):
TGTTTTGGTGTGTTTTTTTTGC
Found at i:34613 original size:12 final size:12
Alignment explanation
Indices: 34598--34655 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
34588 ATTTTTTTAT
34598 TGTTTTGGTTGC
1 TGTTTTGGTTGC
34610 TGTTTTGG-TGC
1 TGTTTTGGTTGC
** *
34621 TGTTTTTATTGT
1 TGTTTTGGTTGC
* *
34633 TATTTTTGTTGC
1 TGTTTTGGTTGC
34645 TGTTTTGGTTG
1 TGTTTTGGTTG
34656 TTATTTTAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.03, C:0.05, G:0.28, T:0.64
Consensus pattern (12 bp):
TGTTTTGGTTGC
Found at i:34614 original size:32 final size:31
Alignment explanation
Indices: 34577--34670 Score: 98
Period size: 35 Copynumber: 2.8 Consensus size: 31
34567 TGTGTTTTTA
34577 CTGTTTTGGTGATTTTTTTATTGTTTTGGTTG
1 CTGTTTTGGTG-TTTTTTTATTGTTTTGGTTG
* *
34609 CTGTTTTGGTGCTGTTTTTATTGTTATTTTTGTTG
1 CTGTTTTGGTG-TTTTTTTATTG---TTTTGGTTG
*
34644 CTGTTTTGGTTGTTATTTTAGTTGTTT
1 CTGTTTTGG-TGTTTTTTTA-TTGTTT
34671 GGATGTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
32 21 0.40
33 3 0.06
35 23 0.44
36 5 0.10
ACGTcount: A:0.06, C:0.04, G:0.23, T:0.66
Consensus pattern (31 bp):
CTGTTTTGGTGTTTTTTTATTGTTTTGGTTG
Found at i:34651 original size:35 final size:32
Alignment explanation
Indices: 34577--34653 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 32
34567 TGTGTTTTTA
*
34577 CTGTTTTGGTGATTTTTTTATTGTTTTGGTTG
1 CTGTTTTGGTGATGTTTTTATTGTTTTGGTTG
* *
34609 CTGTTTTGGTGCTGTTTTTATTGTTATTTTTGTTG
1 CTGTTTTGGTGATGTTTTTATTG---TTTTGGTTG
34644 CTGTTTTGGT
1 CTGTTTTGGT
34654 TGTTATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 21 0.54
35 18 0.46
ACGTcount: A:0.05, C:0.05, G:0.25, T:0.65
Consensus pattern (32 bp):
CTGTTTTGGTGATGTTTTTATTGTTTTGGTTG
Found at i:34667 original size:24 final size:22
Alignment explanation
Indices: 34526--34692 Score: 121
Period size: 22 Copynumber: 7.6 Consensus size: 22
34516 GGTGCTGATT
34526 TTTTTTGCTGTTTTGGTTGTTA
1 TTTTTTGCTGTTTTGGTTGTTA
* *
34548 TTTTTTGTTGTTTTGG-TGTTG
1 TTTTTTGCTGTTTTGGTTGTTA
* *
34569 TGTTTTTACTGTTTTGG-TGAT-
1 T-TTTTTGCTGTTTTGGTTGTTA
** * *
34590 TTTTTTATTGTTTTGGTTGCTG
1 TTTTTTGCTGTTTTGGTTGTTA
* **
34612 TTTTGGTGCTGTTTTTATTGTTA
1 TTTT-TTGCTGTTTTGGTTGTTA
34635 TTTTTGTTGCTGTTTTGGTTGTTA
1 -TTTT-TTGCTGTTTTGGTTGTTA
* * *
34659 -TTTTAGTTG-TTTGGATGTTA
1 TTTTTTGCTGTTTTGGTTGTTA
34679 TTTTTATGC-GTTTT
1 TTTTT-TGCTGTTTT
34693 TATTATTGTT
Statistics
Matches: 115, Mismatches: 22, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
20 24 0.21
21 18 0.16
22 42 0.37
23 11 0.10
24 20 0.17
ACGTcount: A:0.07, C:0.04, G:0.23, T:0.66
Consensus pattern (22 bp):
TTTTTTGCTGTTTTGGTTGTTA
Found at i:34672 original size:87 final size:88
Alignment explanation
Indices: 34506--34685 Score: 194
Period size: 87 Copynumber: 2.0 Consensus size: 88
34496 AAAAATTATA
** *
34506 TTATTGTTTTGGTGCTGATTTTTTTTGCTGTTTTGGTTGTTATTTTTTGTTGTTTTGGTGTTGTG
1 TTATTGTTTTGGTGCTGA-TTTTGGTGCTGTTTTGATTGTTATTTTTTGTTGTTTTGGTGTTGTG
34571 TTTTTACTGTTTTGG-TGATT-TTT
65 TTTTTACTGTTTTGGATG-TTATTT
* *
34594 TTATTGTTTTGGTTGCTG-TTTTGGTGCTGTTTTTATTGTTA-TTTTTGTTGCTGTTTTG-GTTG
1 TTATTGTTTTGG-TGCTGATTTTGGTGCTGTTTTGATTGTTATTTTTTGTTG-T-TTTGGTGTTG
*
34656 T-TATTTTAGT-TGTTTGGATGTTATTT
63 TGT-TTTTACTGT-TTTGGATGTTATTT
34682 TTAT
1 TTAT
34686 GCGTTTTTAT
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
86 11 0.14
87 38 0.48
88 25 0.32
89 5 0.06
ACGTcount: A:0.07, C:0.03, G:0.23, T:0.66
Consensus pattern (88 bp):
TTATTGTTTTGGTGCTGATTTTGGTGCTGTTTTGATTGTTATTTTTTGTTGTTTTGGTGTTGTGT
TTTTACTGTTTTGGATGTTATTT
Found at i:37552 original size:72 final size:71
Alignment explanation
Indices: 37453--37615 Score: 191
Period size: 72 Copynumber: 2.3 Consensus size: 71
37443 TGTAATTCAG
* * * * *
37453 TGAATTAGTTTGATCATTGATTCTTTATTCTGTTAATCAATAGAGGATAATTGGTAAACTGTACT
1 TGAATTAGATAGATCATT-AGT-TTTATTCTGTTAATCAATAGAGGATAATTGATAAACTGTAAT
*
37518 TAAATCAA
64 CAAATCAA
* * * *
37526 TGAATTAGATAAGATCATTAGTTTTATTCTTTTAATCAATAGAGGGTGATTGATAATCTGTAATC
1 TGAATTAGAT-AGATCATTAGTTTTATTCTGTTAATCAATAGAGGATAATTGATAAACTGTAATC
*
37591 AAATCAG
65 AAATCAA
*
37598 TGAATTAGATTGATCATT
1 TGAATTAGATAGATCATT
37616 GATTTCTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
71 7 0.09
72 52 0.68
73 11 0.14
74 7 0.09
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (71 bp):
TGAATTAGATAGATCATTAGTTTTATTCTGTTAATCAATAGAGGATAATTGATAAACTGTAATCA
AATCAA
Found at i:42869 original size:36 final size:36
Alignment explanation
Indices: 42829--42902 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
42819 AATGTTCATG
42829 TTATTTTAGTCACATGCTCTGAGCAAAACATATATA
1 TTATTTTAGTCACATGCTCTGAGCAAAACATATATA
42865 TTATTTTAGTCACATGCTCTGAGCAAAACATATATA
1 TTATTTTAGTCACATGCTCTGAGCAAAACATATATA
42901 TT
1 TT
42903 TCTTGTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (36 bp):
TTATTTTAGTCACATGCTCTGAGCAAAACATATATA
Done.