Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014434.1 Kokia drynarioides strain JFW-HI SEQ_129472, 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: 59171
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:1567 original size:7 final size:7
Alignment explanation
Indices: 1555--1583 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1545 AAAAACCTTC
1555 TTCCCCT
1 TTCCCCT
1562 TTCCCCT
1 TTCCCCT
1569 TT-CCCT
1 TTCCCCT
1575 TTCCCCT
1 TTCCCCT
1582 TT
1 TT
1584 GTTGCAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (7 bp):
TTCCCCT
Found at i:1576 original size:13 final size:13
Alignment explanation
Indices: 1558--1583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1548 AACCTTCTTC
1558 CCCTTTCCCCTTT
1 CCCTTTCCCCTTT
1571 CCCTTTCCCCTTT
1 CCCTTTCCCCTTT
1584 GTTGCAACCT
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:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (13 bp):
CCCTTTCCCCTTT
Found at i:2263 original size:41 final size:41
Alignment explanation
Indices: 2206--2287 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
2196 AAAGAAATGC
*
2206 ATCCATACTTGTCTTGGAGGAGAAAGAAAATGGGAATTAGT
1 ATCCATACTTGTCTTGGAGGAGAAAGAAAATGGAAATTAGT
2247 ATCCATACTTGTCTTGGAGGAGAAAGAAAATGGAAATTAGT
1 ATCCATACTTGTCTTGGAGGAGAAAGAAAATGGAAATTAGT
2288 GTTGAATACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (41 bp):
ATCCATACTTGTCTTGGAGGAGAAAGAAAATGGAAATTAGT
Found at i:3441 original size:24 final size:26
Alignment explanation
Indices: 3414--3461 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
3404 AGAGAAATGT
3414 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
3438 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
3462 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:3554 original size:23 final size:23
Alignment explanation
Indices: 3524--3600 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
3514 ATGCTAGCGC
3524 GCTTACTG-TTCAGCACTAT-GTGT
1 GCTTACTGTTTC-GCACT-TCGTGT
3547 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
3570 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
3593 GCCTACTG
1 GCTTACTG
3601 ATTTGCGCTA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
22 1 0.02
23 47 0.92
24 3 0.06
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:3666 original size:23 final size:22
Alignment explanation
Indices: 3536--3667 Score: 108
Period size: 23 Copynumber: 5.9 Consensus size: 22
3526 TTACTGTTCA
* *
3536 GCACTATGTGTGCTTACTGTTT
1 GCACTATGTGTGCCTACTGATT
* *
3558 CGCACT-TCGTGTGCTTACTGTTT
1 -GCACTAT-GTGTGCCTACTGATT
3581 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTAT-GTGTGCCTACTGA-TT
* **
3605 GCGCTATGTACGCCTACTGATT
1 GCACTATGTGTGCCTACTGATT
3627 GCACTAT-TGTGCCTACTGGATT
1 GCACTATGTGTGCCTACT-GATT
* *
3649 GCACTGTGTGTGCTTACTG
1 GCACTATGTGTGCCTACTG
3668 TTTCCCCATA
Statistics
Matches: 94, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
21 8 0.09
22 20 0.21
23 63 0.67
24 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.39
Consensus pattern (22 bp):
GCACTATGTGTGCCTACTGATT
Found at i:8606 original size:24 final size:24
Alignment explanation
Indices: 8544--8608 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
8534 CTTGTTGAAA
8544 AGCTAGTTTGCTTTTTAATAATAG
1 AGCTAGTTTGCTTTTTAATAATAG
* * * *
8568 AGATTA-ATGGATTTTTAATAGA-AG
1 AG-CTAGTTTGCTTTTTAATA-ATAG
8592 AGCTAGTTTGCTTTTTA
1 AGCTAGTTTGCTTTTTA
8609 GTCTGACGTA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
23 2 0.07
24 25 0.83
25 3 0.10
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (24 bp):
AGCTAGTTTGCTTTTTAATAATAG
Found at i:25714 original size:24 final size:23
Alignment explanation
Indices: 25673--25722 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
25663 GAGTTTAATA
* *
25673 AAGGAGGGGGAAATGGAAATGGAG
1 AAGGAGAGGGAAAGGGAAAT-GAG
* *
25697 AAGGAGAGGGAGAGGGAAGTGAG
1 AAGGAGAGGGAAAGGGAAATGAG
25720 AAG
1 AAG
25723 AAAAAGAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (23 bp):
AAGGAGAGGGAAAGGGAAATGAG
Found at i:27384 original size:29 final size:30
Alignment explanation
Indices: 27333--27392 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
27323 AAAATTGTAC
*
27333 ATTAATTTTGATTTAACGTGTAATTATATAT
1 ATTAATTTTAATTTAAC-TGTAATTATATAT
*
27364 ATTAATTTTAATTTGA-TGTAATTATATAT
1 ATTAATTTTAATTTAACTGTAATTATATAT
27393 GCGAAACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 13 0.48
31 14 0.52
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (30 bp):
ATTAATTTTAATTTAACTGTAATTATATAT
Found at i:27614 original size:30 final size:29
Alignment explanation
Indices: 27580--27637 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
27570 ATAGTTAGAT
27580 AAAATCAAAATTTCATGCATAAAATTACAC
1 AAAATCAAAATTT-ATGCATAAAATTACAC
* *
27610 AAAATCAAAATTTATGTATACAATTACA
1 AAAATCAAAATTTATGCATAAAATTACA
27638 TATTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAATCAAAATTTATGCATAAAATTACAC
Found at i:29565 original size:22 final size:19
Alignment explanation
Indices: 29538--29584 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
29528 AATTTTATTT
*
29538 TTTTAAAAAATACTATAATTAA
1 TTTTAAAAAA-A-TATAA-AAA
29560 TTTTAAAAAAATATAAAAA
1 TTTTAAAAAAATATAAAAA
29579 TTTTAA
1 TTTTAA
29585 TCAAATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 1 0.04
22 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAAAAAAATATAAAAA
Found at i:34609 original size:40 final size:39
Alignment explanation
Indices: 34561--34640 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 39
34551 CTAAAAGATC
34561 ATAACAAAAGAATACTTTAGGTACCTAATTGGGTAAAAA
1 ATAACAAAAGAATACTTTAGGTACCTAATTGGGTAAAAA
*
34600 ATAATCAAAAGAATATTTTAGGTACCTAATTGGGTAAAAA
1 ATAA-CAAAAGAATACTTTAGGTACCTAATTGGGTAAAAA
34640 A
1 A
34641 AAAATAGGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 4 0.10
40 35 0.90
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (39 bp):
ATAACAAAAGAATACTTTAGGTACCTAATTGGGTAAAAA
Found at i:41699 original size:22 final size:21
Alignment explanation
Indices: 41664--41704 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41654 TAAAATTTTA
41664 AAAATTGAAAAATTTAGAAATT
1 AAAATTGAAAAATTT-GAAATT
**
41686 AAAATTGATCAATTTGAAA
1 AAAATTGAAAAATTTGAAA
41705 AGTATGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (21 bp):
AAAATTGAAAAATTTGAAATT
Found at i:53173 original size:23 final size:24
Alignment explanation
Indices: 53126--53173 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
53116 ACTTTACTAC
*
53126 TTATATTAATAGTTTTTGTTCAAA
1 TTATATTAATAGTTTTTCTTCAAA
* *
53150 TTATATTAAT-TTTTTTCTTTAAA
1 TTATATTAATAGTTTTTCTTCAAA
53173 T
1 T
53174 CATGACACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATATTAATAGTTTTTCTTCAAA
Found at i:55732 original size:25 final size:23
Alignment explanation
Indices: 55680--55733 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
55670 ACATTAGCGC
*
55680 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAACACGTCTCGT
55703 GCTCTCTGTTTAACACGTCTCGT
1 GCTCTCTGTTTAACACGTCTCGT
*
55726 GCCCTCTG
1 GCTCTCTG
55734 ATCAGCACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.09, C:0.33, G:0.20, T:0.37
Consensus pattern (23 bp):
GCTCTCTGTTTAACACGTCTCGT
Found at i:55750 original size:23 final size:23
Alignment explanation
Indices: 55724--55871 Score: 133
Period size: 23 Copynumber: 6.4 Consensus size: 23
55714 AACACGTCTC
* *
55724 GTGCCCTCTGATCAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
55747 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
55770 GTACTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
55793 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
55816 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
55841 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
55862 GTACTCTCTG
1 GTGCTCTCTG
55872 TTCGTTCCGT
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
21 13 0.12
22 4 0.04
23 71 0.66
25 14 0.13
26 5 0.05
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:55779 original size:46 final size:45
Alignment explanation
Indices: 55729--55871 Score: 155
Period size: 46 Copynumber: 3.1 Consensus size: 45
55719 GTCTCGTGCC
55729 CTCTGATCAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACT
1 CTCTGATCAGCACTTTGTGTGCTCTCTG-TTAGTACTTTGTGTACT
* * * * * *
55775 CTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCT
1 CTCTGATCAGCACTTTGTGTGCTCTCTG-TTAGTACTTTGTGTACT
* *
55821 CTCTGTTGCCCAGCAC-TTATGTGCTCTCTGTTAGTACTTTG-GTACT
1 CTCTGAT---CAGCACTTTGTGTGCTCTCTGTTAGTACTTTGTGTACT
55867 CTCTG
1 CTCTG
55872 TTCGTTCCGT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
46 54 0.68
47 9 0.11
48 12 0.15
49 4 0.05
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (45 bp):
CTCTGATCAGCACTTTGTGTGCTCTCTGTTAGTACTTTGTGTACT
Found at i:55810 original size:69 final size:66
Alignment explanation
Indices: 55737--55873 Score: 170
Period size: 69 Copynumber: 2.0 Consensus size: 66
55727 CCCTCTGATC
* *
55737 AGCACTTTGTGTGCTCTCTGATT-AGTACTT-TGTGTACTCTCTGATTAGTACTTTGTGTACTCT
1 AGCACTGTGTGTGCTCTCTG-TTCAGCACTTATGTG--CTCTCTG-TTAGTACTTTG-GTACTCT
55800 CTGTTT
61 CTGTTT
55806 AGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCT
1 AGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCT
55871 GTT
63 GTT
55874 CGTTCCGTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
68 2 0.03
69 31 0.51
70 11 0.18
71 7 0.11
72 6 0.10
73 4 0.07
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (66 bp):
AGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGTT
T
Found at i:58718 original size:365 final size:364
Alignment explanation
Indices: 58171--58891 Score: 1379
Period size: 365 Copynumber: 2.0 Consensus size: 364
58161 ATCTGAACAT
58171 GGAGTCATGGTTGATTATTGAAGAAAAAGAATTTCTTTGAGAACTTCAGATGGAAAAGAAGTAGC
1 GGAGTCATGGTTGATTATTGAAGAAAAAGAATTTCTTTGAGAACTTCAGATGGAAAAGAAGTAGC
58236 GGTAATTGGTAAGAAATTCAATGCTTTATCTAATGTAGTCTCTGCAATTAAGGCTTTCAAGATGA
66 GGTAATTGGTAAGAAATTCAATGCTTTATCTAATGTAGTCTCTGCAATTAAGGCTTTCAAGATGA
58301 TTAAGAAAGGGTATAATGCTTTCCTTGCTTATGTTTTGGATACTCGAGTAGAAGATAATGAGATT
131 TTAAGAAAGGGTATAATGCTTTCCTTGCTTATGTTTTGGATACTCGAGTAGAAGATAATGAGATT
58366 AAGAAGATATCGGTGGTACGAGAGTTTCCCGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCT
196 AAGAAGATATCGGTGGTACGAGAGTTTCCCGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCT
58431 TGAAAGAGAAGTTGAATTTGGAATTGATTTAGTACCGAGTACTGCACCGATCTCAATTGCACCTT
261 TGAAAGAGAAGTTGAATTTGGAATTGATTTAGTACCGAGTACTGCACCGATCTCAATTGCACCTT
*
58496 ATCGGATGGCACCGGCAGAGTTAAAAGAATTTCCTTATC
326 ATCGGATGGCACCGACAGAGTTAAAAGAATTTCCTTATC
*
58535 GGAGTCATGGTTGATTATTGAAGAAAAAGAATTTCTTTGAGAACTTCAGATGGAAAAGAAGTAGT
1 GGAGTCATGGTTGATTATTGAAGAAAAAGAATTTCTTTGAGAACTTCAGATGGAAAAGAAGTAGC
*
58600 GGTAATTGGTAAGAAATTTAATGCTTTATCTTAATGTAGTCTCTGCAATTAAGGCTTTCAAGATG
66 GGTAATTGGTAAGAAATTCAATGCTTTATC-TAATGTAGTCTCTGCAATTAAGGCTTTCAAGATG
*
58665 ATTAAGAAAGGGTATAATGCTTTCTTTGCTTATGTTTTGGATACTCGAGTAGAAGATAATGAGAT
130 ATTAAGAAAGGGTATAATGCTTTCCTTGCTTATGTTTTGGATACTCGAGTAGAAGATAATGAGAT
* *
58730 TGAGAAGATATCGGTGGTACGAGAGTTTCTCGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTC
195 TAAGAAGATATCGGTGGTACGAGAGTTTCCCGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTC
58795 TTGAAAGAGAAGTTGAATTTGGAATTGATTTAGTACCGAGTACTGCACCGATCTCAATTGCACCT
260 TTGAAAGAGAAGTTGAATTTGGAATTGATTTAGTACCGAGTACTGCACCGATCTCAATTGCACCT
58860 TATCGGATGGCACCGACAGAGTTAAAAGAATT
325 TATCGGATGGCACCGACAGAGTTAAAAGAATT
58892 GAAGACTCAA
Statistics
Matches: 350, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
364 93 0.27
365 257 0.73
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (364 bp):
GGAGTCATGGTTGATTATTGAAGAAAAAGAATTTCTTTGAGAACTTCAGATGGAAAAGAAGTAGC
GGTAATTGGTAAGAAATTCAATGCTTTATCTAATGTAGTCTCTGCAATTAAGGCTTTCAAGATGA
TTAAGAAAGGGTATAATGCTTTCCTTGCTTATGTTTTGGATACTCGAGTAGAAGATAATGAGATT
AAGAAGATATCGGTGGTACGAGAGTTTCCCGATGTGTTTCTTAAAGAGTTGTCTGGTTTACCTCT
TGAAAGAGAAGTTGAATTTGGAATTGATTTAGTACCGAGTACTGCACCGATCTCAATTGCACCTT
ATCGGATGGCACCGACAGAGTTAAAAGAATTTCCTTATC
Done.