Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014920.1 Kokia drynarioides strain JFW-HI SEQ_129963, 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: 43664
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 201 characters in sequence are not A, C, G, or T
Found at i:760 original size:17 final size:17
Alignment explanation
Indices: 738--832 Score: 111
Period size: 17 Copynumber: 5.5 Consensus size: 17
728 ACTTTTTAAT
*
738 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
755 ATTTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
* *
773 AATTTAAACTTAAAACA
1 AATTTAAATTTAAAATA
*
790 AGTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
807 AATTT-AATCTTAAAATAA
1 AATTTAAAT-TTAAAAT-A
825 AATTTAAA
1 AATTTAAA
833 AAGTAGGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.05
17 40 0.62
18 20 0.31
19 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:777 original size:35 final size:34
Alignment explanation
Indices: 738--821 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 34
728 ACTTTTTAAT
* * * *
738 AATTTAAATTTAGAATAATTTTAAATTTAAAAATA
1 AATTTAAACTTAAAACAAGTTTAAATTT-AAAATA
773 AATTTAAACTTAAAACAAGTTTAAATTTAAAATA
1 AATTTAAACTTAAAACAAGTTTAAATTTAAAATA
*
807 AATTTAATCTTAAAA
1 AATTTAAACTTAAAA
822 TAAAATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 20 0.45
35 24 0.55
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (34 bp):
AATTTAAACTTAAAACAAGTTTAAATTTAAAATA
Found at i:3549 original size:25 final size:25
Alignment explanation
Indices: 3502--3549 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3492 CACAAATCAC
*
3502 AAACCAAAACTAAAATTATAACCCT
1 AAACCAAAACTAAAATTAGAACCCT
*
3527 AAACCAAAAC-CAAATCTAGAACC
1 AAACCAAAACTAAAAT-TAGAACC
3550 TCGAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (25 bp):
AAACCAAAACTAAAATTAGAACCCT
Found at i:9057 original size:20 final size:20
Alignment explanation
Indices: 9033--9077 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
9023 CTATTTTTTA
*
9033 ATTTTTATGAA-TTATATAT
1 ATTTTTATGAATTTATAAAT
9052 ATTTTT-TGAATTTTATAAAT
1 ATTTTTATGAA-TTTATAAAT
9072 ATTTTT
1 ATTTTT
9078 TATATATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 6 0.26
20 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTTTATGAATTTATAAAT
Found at i:18459 original size:22 final size:21
Alignment explanation
Indices: 18431--18482 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
18421 CATTGAAATA
*
18431 TTAGGGTTTGGGGTTTTAAGAT
1 TTAGGGTTTAGGG-TTTAAGAT
*
18453 TTAGGGTTTAGGGTTTAAGGT
1 TTAGGGTTTAGGGTTTAAGAT
18474 TTAGAGGTT
1 TTAG-GGTT
18483 AGATGTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTTAAGAT
Found at i:18462 original size:7 final size:7
Alignment explanation
Indices: 18431--18682 Score: 119
Period size: 7 Copynumber: 35.9 Consensus size: 7
18421 CATTGAAATA
18431 TTAGGGT
1 TTAGGGT
*
18438 TTGGGGTT
1 TTAGGG-T
* *
18446 TTAAGAT
1 TTAGGGT
18453 TTAGGGT
1 TTAGGGT
18460 TTAGGGT
1 TTAGGGT
*
18467 TTAAGGT
1 TTAGGGT
18474 TTAGAGG-
1 TTAG-GGT
*
18481 TTA-GAT
1 TTAGGGT
*
18487 GTAGGGT
1 TTAGGGT
*
18494 TT-GGGG
1 TTAGGGT
18500 TTAGGGT
1 TTAGGGT
18507 TTAGGGT
1 TTAGGGT
*
18514 TTAGGTT
1 TTAGGGT
18521 TTAAGGG-
1 TT-AGGGT
18528 TTAGGGGT
1 TTA-GGGT
**
18536 CGAGGGGT
1 TTA-GGGT
*
18544 TTAGGGA
1 TTAGGGT
18551 TT-GGAGT
1 TTAGG-GT
*
18558 TTAAGGT
1 TTAGGGT
18565 TT-GAGG-
1 TTAG-GGT
18571 TTAGGGT
1 TTAGGGT
**
18578 TTAAAG-
1 TTAGGGT
*
18584 TTAAGGT
1 TTAGGGT
* *
18591 TTTGGGA
1 TTAGGGT
*
18598 TCAGAGGT
1 TTAG-GGT
*
18606 TAAGGG-
1 TTAGGGT
*
18612 TTAGGGC
1 TTAGGGT
18619 TTAGAGG-
1 TTAG-GGT
18626 TTAGGGT
1 TTAGGGT
*
18633 TTATGGT
1 TTAGGGT
*
18640 TTAAGGT
1 TTAGGGT
18647 TTAAAGGGT
1 TT--AGGGT
18656 TTAGGGT
1 TTAGGGT
18663 TTAGGGT
1 TTAGGGT
*
18670 CTAGGGT
1 TTAGGGT
*
18677 CTAGGG
1 TTAGGG
18683 CTCGGGGCTC
Statistics
Matches: 186, Mismatches: 39, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
5 1 0.01
6 26 0.14
7 129 0.69
8 24 0.13
9 6 0.03
ACGTcount: A:0.20, C:0.02, G:0.40, T:0.37
Consensus pattern (7 bp):
TTAGGGT
Found at i:28371 original size:29 final size:27
Alignment explanation
Indices: 28314--28371 Score: 62
Period size: 29 Copynumber: 2.1 Consensus size: 27
28304 TTTTTAAAAC
* *
28314 TTATTTTTTTATAATATTAATGATTTT
1 TTATTTTTTTATAATATTAATAATGTT
* *
28341 TTATTTTTATATATAATTTTTATAATGTT
1 TTATTTTT-T-TATAATATTAATAATGTT
28370 TT
1 TT
28372 TGAATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 8 0.32
28 1 0.04
29 16 0.64
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (27 bp):
TTATTTTTTTATAATATTAATAATGTT
Found at i:39924 original size:62 final size:60
Alignment explanation
Indices: 39556--40178 Score: 504
Period size: 62 Copynumber: 10.3 Consensus size: 60
39546 TGGGTGTTAA
* * * ** *
39556 CCATGCAATGGTCGACACTCCTTTTTAATCTGATAAAAAAA-TT-AA-AATTTTGAATGTTGG
1 CCATGCAATGGCCGACAC-CCCTTTT-ATCAGATAAAAAAATTTCAATTTTTTTG-GTGTTGG
* * ** * * *
39616 TCATGCAATAGTTGACACCCCTTTTTTGTCAGAT-AAAAAA-TACAATTTTTTTTGTGTTGG
1 CCATGCAATGGCCGACACCCC--TTTTATCAGATAAAAAAATTTCAATTTTTTTGGTGTTGG
* * * * * * *
39676 TCATACAATGGCCAACACCTCTATTTATCTGATAAAAAAA--TCAAATTTTTGGGTGTT-G
1 CCATGCAATGGCCGACACCCCT-TTTATCAGATAAAAAAATTTCAATTTTTTTGGTGTTGG
* ** * *
39734 ACATGCAATGATCGACACCCCCTTTTTTATTAGAT--AAAAATTTTAA-TTTTTTGGTGTTGG
1 CCATGCAATGGCCGACA-CCCC--TTTTATCAGATAAAAAAATTTCAATTTTTTTGGTGTTGG
* * *
39794 CCATGCAATGGCCGACACCCCTATTTATCTGATAAAAAAAATT-AATTTTTTGGGTGTTGG
1 CCATGCAATGGCCGACACCCCT-TTTATCAGATAAAAAAATTTCAATTTTTTTGGTGTTGG
* * *
39854 CCATGCAATGGCCGACATCCCCTTTTCTCAGATAAAAAAATTTCAATTTTTTTTGGTATTGA
1 CCATGCAATGGCCGACA-CCCCTTTTATCAGATAAAAAAATTTCAA-TTTTTTTGGTGTTGG
* * *
39916 CCATGCAATGGTCGACACCCCTATTTATCTGATAAAAAAAATTCAAATTTTTTTGGTGTTGG
1 CCATGCAATGGCCGACACCCCT-TTTATCAGATAAAAAAATTTC-AATTTTTTTGGTGTTGG
* * * * *
39978 CCATGCAATGGTCGACCCTCCCTTTTTTCAGATAAAAAAATCTCAAATTTTTTTTGTGTTGG
1 CCATGCAATGGCCGACAC-CCCTTTTATCAGATAAAAAAATTTC-AATTTTTTTGGTGTTGG
* * * *
40040 TCATGTAATGGCCGACACCCCCTTTTCTCAGATAAAAAAATTTCAAACTTTTTTGGTGTTGG
1 CCATGCAATGGCCGACA-CCCCTTTTATCAGATAAAAAAATTTC-AATTTTTTTGGTGTTGG
* ** *
40102 CCATGCAATTGCCGACACCCTCTTTTTATTTGGT-AAAAAA-TT-AA-TTTTTTGGTGTTGG
1 CCATGCAATGGCCGACACCC-C-TTTTATCAGATAAAAAAATTTCAATTTTTTTGGTGTTGG
* * *
40160 CAATGTAATGGTCGACACC
1 CCATGCAATGGCCGACACC
40179 AACTTCCTCT
Statistics
Matches: 461, Mismatches: 77, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
57 1 0.00
58 56 0.12
59 52 0.11
60 129 0.28
61 26 0.06
62 183 0.40
63 14 0.03
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (60 bp):
CCATGCAATGGCCGACACCCCTTTTATCAGATAAAAAAATTTCAATTTTTTTGGTGTTGG
Found at i:40031 original size:124 final size:122
Alignment explanation
Indices: 39556--40178 Score: 609
Period size: 124 Copynumber: 5.2 Consensus size: 122
39546 TGGGTGTTAA
* * * * * *
39556 CCATGCAATGGTCGACACTCCTTTTTAATCTGAT-AAAAAAATT-AAA-ATTTTGAATGTTGGTC
1 CCATGCAATGGCCGACACCCCTATTT-ATCTGATAAAAAAAATTCAAATTTTTTG-GTGTTGGCC
* * * * *
39618 ATGCAATAGTTGACACCCCTTTTTTGTCAGAT-AAAAAATAC-AATTTTTTTTGTGTTGG
64 ATGCAATGGTCGACACCCCCTTTTT-TCAGATAAAAAAATTCAAATTTTTTTGGTGTTGG
* * * * * *
39676 TCATACAATGGCCAACACCTCTATTTATCTGAT-AAAAAAA-TCAAATTTTTGGGTGTT-GACAT
1 CCATGCAATGGCCGACACCCCTATTTATCTGATAAAAAAAATTCAAATTTTTTGGTGTTGGCCAT
* * **
39738 GCAATGATCGACACCCCCTTTTTT-A-TTAGATAAAAATTTTAA-TTTTTTGGTGTTGG
66 GCAATGGTCGACACCCCCTTTTTTCAGATA-A-AAAAATTCAAATTTTTTTGGTGTTGG
39794 CCATGCAATGGCCGACACCCCTATTTATCTGATAAAAAAAATT--AATTTTTTGGGTGTTGGCCA
1 CCATGCAATGGCCGACACCCCTATTTATCTGATAAAAAAAATTCAAATTTTTT-GGTGTTGGCCA
* * * * * *
39857 TGCAATGGCCGACATCCCCTTTTCTCAGATAAAAAAATTTCAATTTTTTTTGGTATTGA
65 TGCAATGGTCGACACCCCCTTTTTTCAGATAAAAAAA-TTCAAATTTTTTTGGTGTTGG
*
39916 CCATGCAATGGTCGACACCCCTATTTATCTGATAAAAAAAATTCAAATTTTTTTGGTGTTGGCCA
1 CCATGCAATGGCCGACACCCCTATTTATCTGATAAAAAAAATTCAAA-TTTTTTGGTGTTGGCCA
*
39981 TGCAATGGTCGAC-CCTCCCTTTTTTCAGATAAAAAAATCTCAAATTTTTTTTGTGTTGG
65 TGCAATGGTCGACACC-CCCTTTTTTCAGATAAAAAAAT-TCAAATTTTTTTGGTGTTGG
* * * * *
40040 TCATGTAATGGCCGACACCCCCT-TTTCTCAGATAAAAAAATTTCAAACTTTTTTGGTGTTGGCC
1 CCATGCAATGGCCGACA-CCCCTATTTATCTGATAAAAAAAATTCAAA-TTTTTTGGTGTTGGCC
* * * ** *
40104 ATGCAATTGCCGACACCCTCTTTTTATTTGGT-AAAAAATT--AA-TTTTTTGGTGTTGG
64 ATGCAATGGTCGACACCCCCTTTTT-TCAGATAAAAAAATTCAAATTTTTTTGGTGTTGG
* * *
40160 CAATGTAATGGTCGACACC
1 CCATGCAATGGCCGACACC
40179 AACTTCCTCT
Statistics
Matches: 421, Mismatches: 60, Indels: 45
0.80 0.11 0.09
Matches are distributed among these distances:
115 1 0.00
116 1 0.00
117 2 0.00
118 79 0.19
119 38 0.09
120 80 0.19
121 7 0.02
122 56 0.13
123 3 0.01
124 138 0.33
125 16 0.04
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (122 bp):
CCATGCAATGGCCGACACCCCTATTTATCTGATAAAAAAAATTCAAATTTTTTGGTGTTGGCCAT
GCAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTCAAATTTTTTTGGTGTTGG
Found at i:43656 original size:84 final size:84
Alignment explanation
Indices: 43422--43664 Score: 375
Period size: 81 Copynumber: 2.9 Consensus size: 84
43412 ATTTAAAATC
*
43422 TGATAAAAATTATAATATAATAATAATTGTTAATTTAAATATTTAAAATTAATAAATAACGTATT
1 TGATAAAAATTATAATATAATAATAATTGTTAATTTAAATATTTAAAATTAATAAATAATGTATT
43487 GTCAAATCAACACATTATT
66 GTCAAATCAACACATTATT
* * *
43506 TAATAAAAATTATAATATAATAAT--TT-TTTATTTAAATATTTAAATTTAATAAATAATGTATT
1 TGATAAAAATTATAATATAATAATAATTGTTAATTTAAATATTTAAAATTAATAAATAATGTATT
* *
43568 GTCAAATCAATATATTATT
66 GTCAAATCAACACATTATT
* * *
43587 TGATAAAAATTATAATATAATAATAATTGTTGATTTAACTATTTAAAATTAATAAATAATATATT
1 TGATAAAAATTATAATATAATAATAATTGTTAATTTAAATATTTAAAATTAATAAATAATGTATT
43652 GTCAAAATCAACA
66 GTC-AAATCAACA
Statistics
Matches: 143, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
81 73 0.51
82 2 0.01
83 2 0.01
84 58 0.41
85 8 0.06
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (84 bp):
TGATAAAAATTATAATATAATAATAATTGTTAATTTAAATATTTAAAATTAATAAATAATGTATT
GTCAAATCAACACATTATT
Done.