Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008821.1 Kokia drynarioides strain JFW-HI SEQ_123505, 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: 85906
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:5324 original size:54 final size:53
Alignment explanation
Indices: 5249--5358 Score: 132
Period size: 54 Copynumber: 2.1 Consensus size: 53
5239 GAAAAAGAAG
* * *
5249 AAAATAAATCATGTAAGAAATTTTTAATTTTTAATATAATTTTT-TGAATTTTT
1 AAAATAAATCATGGAAGAAATTTATAACTTTTAATAT-ATTTTTCTGAATTTTT
* * * *
5302 AAAACTAAATCATGGAATAAATTTATAGCTTTTAATATTTTTTTCTTAATTTTT
1 AAAA-TAAATCATGGAAGAAATTTATAACTTTTAATATATTTTTCTGAATTTTT
5356 AAA
1 AAA
5359 TAATTTTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
53 9 0.19
54 39 0.81
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (53 bp):
AAAATAAATCATGGAAGAAATTTATAACTTTTAATATATTTTTCTGAATTTTT
Found at i:5386 original size:20 final size:21
Alignment explanation
Indices: 5363--5413 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
5353 TTTAAATAAT
5363 TTTAATAATTTGA-AAAAAAA
1 TTTAATAATTTGACAAAAAAA
*
5383 TTTAGAT--TTTTACAAAAAAA
1 TTTA-ATAATTTGACAAAAAAA
*
5403 TTTAAAAATTT
1 TTTAATAATTT
5414 TTAACATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 5 0.20
20 15 0.60
21 5 0.20
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
TTTAATAATTTGACAAAAAAA
Found at i:5414 original size:21 final size:20
Alignment explanation
Indices: 5349--5414 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
5339 TTTTTTTCTT
* * * *
5349 AATTTTTAAATAATTTTAAT
1 AATTTTAAAAAAAATTTAAA
* *
5369 AATTTGAAAAAAAATTT-AG
1 AATTTTAAAAAAAATTTAAA
*
5388 ATTTTTACAAAAAAATTTAAA
1 AATTTTA-AAAAAAATTTAAA
5409 AATTTT
1 AATTTT
5415 TAACATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
19 6 0.17
20 23 0.66
21 6 0.17
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAAAAATTTAAA
Found at i:25419 original size:23 final size:23
Alignment explanation
Indices: 25393--25558 Score: 156
Period size: 23 Copynumber: 7.1 Consensus size: 23
25383 ACACTAGTCC
25393 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
25416 GCTCTATGATTAGTATTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
25439 GCTCTCT-ATTTAGCACTATCTAT
1 GCTCTCTGA-TTAGCACTGTGTGT
* *
25462 GCTCTATGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
25485 GCTCTCTGTTTAGCA-TGTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
* *
25508 GCTCTCTGTTATTAACACTTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
25533 GCTCTCTGATTAGCACTTTGTAT
1 GCTCTCTGATTAGCACTGTGTGT
25556 GCT
1 GCT
25559 TAGTACTTTG
Statistics
Matches: 115, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
22 5 0.04
23 92 0.80
25 15 0.13
26 3 0.03
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:25598 original size:22 final size:23
Alignment explanation
Indices: 25558--25604 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
25548 CTTTGTATGC
* *
25558 TTAGTACTTTGTGTACTCTCTGT
1 TTAGTACTTCGTGTACTCTCCGT
25581 TTAGTACTTCG-GTACTCTCCGT
1 TTAGTACTTCGTGTACTCTCCGT
25603 TT
1 TT
25605 GTTCCGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (23 bp):
TTAGTACTTCGTGTACTCTCCGT
Found at i:28780 original size:23 final size:23
Alignment explanation
Indices: 28741--28833 Score: 107
Period size: 23 Copynumber: 4.1 Consensus size: 23
28731 ATAAAACATT
*
28741 ATGGCAGGAAAGTTACAAATATA
1 ATGGCAGGAGAGTTACAAATATA
* * *
28764 ATGGCAAGAGAGCTACAAACATA
1 ATGGCAGGAGAGTTACAAATATA
** * *
28787 ATGATAGGAGAGTTACGAATACA
1 ATGGCAGGAGAGTTACAAATATA
28810 ATGGCAGGAGAGTTACAAA-ATA
1 ATGGCAGGAGAGTTACAAATATA
28832 AT
1 AT
28834 AATAATAATT
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
22 4 0.07
23 51 0.93
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (23 bp):
ATGGCAGGAGAGTTACAAATATA
Found at i:28813 original size:46 final size:45
Alignment explanation
Indices: 28746--28833 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
28736 ACATTATGGC
*
28746 AGGAAAGTTACAAATATAATGGCAAGAGAGCTACAAACATAATGAT
1 AGGAAAGTTACAAATACAATGGCAAGAGAGCTACAAA-ATAATGAT
* * * *
28792 AGGAGAGTTACGAATACAATGGCAGGAGAGTTACAAAATAAT
1 AGGAAAGTTACAAATACAATGGCAAGAGAGCTACAAAATAAT
28834 AATAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 5 0.14
46 32 0.86
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (45 bp):
AGGAAAGTTACAAATACAATGGCAAGAGAGCTACAAAATAATGAT
Found at i:29383 original size:24 final size:22
Alignment explanation
Indices: 29356--29408 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
29346 GAATAATCAA
*
29356 ATAATTCCAGCAAGAGTTTGTTAT
1 ATAACTCCAG-AA-AGTTTGTTAT
**
29380 ATAACTCTTGAAAGTTTGTTAT
1 ATAACTCCAGAAAGTTTGTTAT
29402 ATAACTC
1 ATAACTC
29409 TTTTTCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 2 0.08
24 7 0.27
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ATAACTCCAGAAAGTTTGTTAT
Found at i:29581 original size:3 final size:3
Alignment explanation
Indices: 29573--29615 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
29563 AATTCAAAAG
29573 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29616 AAGAAACCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:34382 original size:52 final size:52
Alignment explanation
Indices: 34281--34572 Score: 370
Period size: 52 Copynumber: 5.6 Consensus size: 52
34271 AAATGCAAAA
** *
34281 AGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACGGATTATG
* * * *
34334 AGATCCGATGATTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
34386 AGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* ** *
34438 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATTTTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
34490 AGGTCCGATGACTATGTGTCATCGTAAGCATATGGATCCTTTTACGGCTT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
* * * *
34542 AAGTCTGATGACTTTGTGTTATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
34573 TAAATAGGAA
Statistics
Matches: 210, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
52 178 0.85
53 32 0.15
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:39616 original size:79 final size:78
Alignment explanation
Indices: 39467--39621 Score: 204
Period size: 79 Copynumber: 2.0 Consensus size: 78
39457 TAAAATATAT
* * * ** *
39467 TGTAGCATTTAATATTATGTTATTAGTTAAAAGAGTAAGTAATCTCACATTGTTTAAGAACAATC
1 TGTAGCATTTAATATTATATTATTAGTTAAAAAAGGAAACAATCTCACATTATTTAAGAACAATC
39532 TTCAAATGGATAG
66 TTCAAATGGATAG
* * *
39545 TGTAGCATTTAATCTTATATTGTTAGTTAAAAAAAGGAAACAATCTCACATTATTTAGGAACAAG
1 TGTAGCATTTAATATTATATTATTAGTT-AAAAAAGGAAACAATCTCACATTATTTAAGAACAA-
39610 T-TTCAAATGGAT
64 TCTTCAAATGGAT
39622 TATGAATTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
78 25 0.38
79 40 0.61
80 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (78 bp):
TGTAGCATTTAATATTATATTATTAGTTAAAAAAGGAAACAATCTCACATTATTTAAGAACAATC
TTCAAATGGATAG
Found at i:42500 original size:30 final size:30
Alignment explanation
Indices: 42466--42530 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
42456 ACTTATTTTA
*
42466 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
42496 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
42526 TTGTT
1 TTGTT
42531 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGGCAT
Found at i:46164 original size:28 final size:30
Alignment explanation
Indices: 46112--46169 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
46102 CATGCATTTG
*
46112 GAATTTAACTTTTTTATTTTTTATTTTAAA
1 GAATTTAACTTTTTTATTTTCTATTTTAAA
*
46142 GAATTT-AGTTTTTT-TTTTCTATTTTAAA
1 GAATTTAACTTTTTTATTTTCTATTTTAAA
46170 ATATAAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 13 0.50
29 7 0.27
30 6 0.23
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (30 bp):
GAATTTAACTTTTTTATTTTCTATTTTAAA
Found at i:51607 original size:17 final size:18
Alignment explanation
Indices: 51582--51619 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
51572 ATAGAATTAA
*
51582 AATTGAATTGAA-AAAAT
1 AATTGAATTCAATAAAAT
*
51599 AATTTAATTCAATAAAAT
1 AATTGAATTCAATAAAAT
51617 AAT
1 AAT
51620 ATTTTGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AATTGAATTCAATAAAAT
Found at i:58559 original size:25 final size:26
Alignment explanation
Indices: 58504--58559 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
58494 AATTTAATGA
* * *
58504 ATTTATATATTTATAATTTTGAGGAGT
1 ATTT-TATATATATAATTTTGAGAAAT
58531 -TTTTATATATATAATTTTGA-AAAT
1 ATTTTATATATATAATTTTGAGAAAT
58555 ATTTT
1 ATTTT
58560 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 2 0.08
25 20 0.80
26 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (26 bp):
ATTTTATATATATAATTTTGAGAAAT
Found at i:59176 original size:10 final size:9
Alignment explanation
Indices: 59161--59185 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59151 ATATCCACAT
59161 AAAAAAAAG
1 AAAAAAAAG
59170 AAAAAAAAG
1 AAAAAAAAG
59179 AAAAAAA
1 AAAAAAA
59186 CTATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:62847 original size:2 final size:2
Alignment explanation
Indices: 62840--62874 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
62830 CTTAGTAGGA
62840 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
62875 ATGTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:79161 original size:25 final size:25
Alignment explanation
Indices: 79133--79187 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
79123 GTATAAAAGC
79133 AAAATGAATTATTAAATT-T-AAAATT
1 AAAAT-AATTA-TAAATTATAAAAATT
* *
79158 AAAATATTTATAACTTATAAAAATT
1 AAAATAATTATAAATTATAAAAATT
79183 AAAAT
1 AAAAT
79188 TATTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 16 0.62
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATAATTATAAATTATAAAAATT
Found at i:79634 original size:104 final size:104
Alignment explanation
Indices: 79454--79663 Score: 402
Period size: 104 Copynumber: 2.0 Consensus size: 104
79444 AGAAATATAC
79454 TGAAGTTCACCAATTATGCGGAGGTGATTTTCCTTTTCCTATTTCTAGGTGCAAGCCTTCTAGCA
1 TGAAGTTCACCAATTATGCGGAGGTGATTTTCCTTTTCCTATTTCTAGGTGCAAGCCTTCTAGCA
**
79519 AGTGACGTACTTTGAACCCATTCCAAACACAGATGGAGA
66 AGTGAAATACTTTGAACCCATTCCAAACACAGATGGAGA
79558 TGAAGTTCACCAATTATGCGGAGGTGATTTTCCTTTTCCTATTTCTAGGTGCAAGCCTTCTAGCA
1 TGAAGTTCACCAATTATGCGGAGGTGATTTTCCTTTTCCTATTTCTAGGTGCAAGCCTTCTAGCA
79623 AGTGAAATACTTTGAACCCATTCCAAACACAGATGGAGA
66 AGTGAAATACTTTGAACCCATTCCAAACACAGATGGAGA
79662 TG
1 TG
79664 GATCAATGTC
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (104 bp):
TGAAGTTCACCAATTATGCGGAGGTGATTTTCCTTTTCCTATTTCTAGGTGCAAGCCTTCTAGCA
AGTGAAATACTTTGAACCCATTCCAAACACAGATGGAGA
Found at i:81104 original size:3 final size:3
Alignment explanation
Indices: 81096--81123 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
81086 TATTTGAAAA
81096 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
81124 TATTCAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.