Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007975.1 Kokia drynarioides strain JFW-HI SEQ_122625, 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: 34995
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:7525 original size:15 final size:15
Alignment explanation
Indices: 7505--7543 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
7495 GATCAAAATG
*
7505 TAATTTTACTTTTAT
1 TAATTTTAATTTTAT
*
7520 TAATTTTAATTTTAA
1 TAATTTTAATTTTAT
*
7535 AAATTTTAA
1 TAATTTTAA
7544 AAGATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTTAATTTTAT
Found at i:9643 original size:21 final size:22
Alignment explanation
Indices: 9607--9661 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
9597 AATTTAATCT
* *
9607 TTTTCTTTTATGTTTT-TTAAC
1 TTTTCTTTTTTCTTTTGTTAAC
* *
9628 TTTTCTTTTTTCTTTTGTTTAT
1 TTTTCTTTTTTCTTTTGTTAAC
9650 TTTTCATTTTTT
1 TTTTC-TTTTTT
9662 TCTACTTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 14 0.50
22 8 0.29
23 6 0.21
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTTGTTAAC
Found at i:18401 original size:80 final size:80
Alignment explanation
Indices: 18266--18458 Score: 262
Period size: 80 Copynumber: 2.4 Consensus size: 80
18256 AAGTTATGTT
* * * * *
18266 TGATAAAGTTCAAGCTTCGGCTTAGCAGGCTATAAGCCGGTGGTAAAATTCAAGCTA-CACCTTA
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGCTGATAAAATTAAAGCTATCA-CTTA
*
18330 GCAGGCTTTAAGCTAG
65 GCAGGCTATAAGCTAG
* * *
18346 TGATAAAATTCAAGCTACGGCTTAGTAGGCTATAAGCCGCTGATAAAGTTAAAGCTATGACTTAG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGCTGATAAAATTAAAGCTATCACTTAG
* *
18411 CAGGCTATGAGCTGG
66 CAGGCTATAAGCTAG
*
18426 TGATAAAATACAAGCTACGGCTTAGCAGGCTAT
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTAT
18459 GAACCGATGT
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 98 0.99
81 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (80 bp):
TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGCTGATAAAATTAAAGCTATCACTTAG
CAGGCTATAAGCTAG
Found at i:18460 original size:40 final size:40
Alignment explanation
Indices: 18266--18458 Score: 233
Period size: 40 Copynumber: 4.8 Consensus size: 40
18256 AAGTTATGTT
* *
18266 TGATAAAGTTCAAGCTTCGGCTTAGCAGGCTATAAGCCGG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* ** * **
18306 TGGTAAAATTCAAGCTACACCTTAGCAGGCTTTAAGCTAG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* *
18346 TGATAAAATTCAAGCTACGGCTTAGTAGGCTATAAGCCGC
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* * * * * *
18386 TGATAAAGTTAAAGCTATGACTTAGCAGGCTATGAGCTGG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
*
18426 TGATAAAATACAAGCTACGGCTTAGCAGGCTAT
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTAT
18459 GAACCGATGT
Statistics
Matches: 124, Mismatches: 29, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 124 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (40 bp):
TGATAAAATTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
Found at i:18480 original size:40 final size:38
Alignment explanation
Indices: 18269--18480 Score: 136
Period size: 40 Copynumber: 5.3 Consensus size: 38
18259 TTATGTTTGA
* *
18269 TAAAGTTCAAGCTTCGGCTTAGCAGGCTATAAGCCGGTGGT
1 TAAA-TTCAAGCTACGGCTTAGCAGGCTATAA-CCGAT-GT
* ** * * *
18310 AAAATTCAAGCTACACCTTAGCAGGCTTTAAGCTAGTGAT
1 TAAATTCAAGCTACGGCTTAGCAGGCTATAACCGA-TG-T
* * * *
18350 AAAATTCAAGCTACGGCTTAGTAGGCTATAAGCCGCTGA
1 TAAATTCAAGCTACGGCTTAGCAGGCTATAA-CCGATGT
* * * * * *
18389 TAAAGTTAAAGCTATGACTTAGCAGGCTATGAGCTGGTGAT
1 TAAA-TTCAAGCTACGGCTTAGCAGGCTAT-AACCGATG-T
* *
18430 AAAATACAAGCTACGGCTTAGCAGGCTATGAACCGATGTT
1 TAAATTCAAGCTACGGCTTAGCAGGCTAT-AACCGATG-T
*
18470 TAAACTCAAGC
1 TAAATTCAAGC
18481 CAAGTCTGTA
Statistics
Matches: 128, Mismatches: 37, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
39 5 0.04
40 115 0.90
41 8 0.06
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (38 bp):
TAAATTCAAGCTACGGCTTAGCAGGCTATAACCGATGT
Found at i:19224 original size:24 final size:21
Alignment explanation
Indices: 19192--19256 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
19182 TCAAGTCATA
*
19192 TAAACCCAAACCCTTATAAACC
1 TAAACCCAAACCCTTTTAAA-C
19214 TTTAAACCCAAACCCTTTTAAAC
1 --TAAACCCAAACCCTTTTAAAC
19237 TAAACCCAAACCCTTTTAAA
1 TAAACCCAAACCCTTTTAAA
19257 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 20 0.50
23 1 0.03
24 19 0.47
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCAAACCCTTTTAAAC
Found at i:19647 original size:21 final size:21
Alignment explanation
Indices: 19623--19663 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19613 CTGATGATTT
* *
19623 ACCTTCTCCTCCACCTGTTCA
1 ACCTACTCCTCCACCAGTTCA
*
19644 ACCTACTCCTGCACCAGTTC
1 ACCTACTCCTCCACCAGTTC
19664 TGAGAGTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.07, T:0.29
Consensus pattern (21 bp):
ACCTACTCCTCCACCAGTTCA
Found at i:23477 original size:116 final size:116
Alignment explanation
Indices: 23340--23571 Score: 455
Period size: 116 Copynumber: 2.0 Consensus size: 116
23330 TGAAAACAAG
23340 TTTGTTTAATTAAAATTTAATTTAATTGAAAGACCAATTATGAAATTGGATCCTCTTTAAATGGC
1 TTTGTTTAATTAAAATTTAATTTAATTGAAAGACCAATTATGAAATTGGATCCTCTTTAAATGGC
*
23405 CTAATAATAGAAATGATGTGAAACTCTTTAGATTTTGAGAAATTGTAATTA
66 CTAATAATAGAAATGATGTGAAACTCTTTAGATTTTGAGAAATTGCAATTA
23456 TTTGTTTAATTAAAATTTAATTTAATTGAAAGACCAATTATGAAATTGGATCCTCTTTAAATGGC
1 TTTGTTTAATTAAAATTTAATTTAATTGAAAGACCAATTATGAAATTGGATCCTCTTTAAATGGC
23521 CTAATAATAGAAATGATGTGAAACTCTTTAGATTTTGAGAAATTGCAATTA
66 CTAATAATAGAAATGATGTGAAACTCTTTAGATTTTGAGAAATTGCAATTA
23572 AATCCTAATA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (116 bp):
TTTGTTTAATTAAAATTTAATTTAATTGAAAGACCAATTATGAAATTGGATCCTCTTTAAATGGC
CTAATAATAGAAATGATGTGAAACTCTTTAGATTTTGAGAAATTGCAATTA
Found at i:25635 original size:26 final size:26
Alignment explanation
Indices: 25606--25660 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
25596 ATTGTCATGT
25606 ATAGATTTTGCAAGATGAGAATTTAA
1 ATAGATTTTGCAAGATGAGAATTTAA
25632 ATAGATTTTGCAAGATGAGAATTTAA
1 ATAGATTTTGCAAGATGAGAATTTAA
25658 ATA
1 ATA
25661 AGAGTCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.35
Consensus pattern (26 bp):
ATAGATTTTGCAAGATGAGAATTTAA
Found at i:25655 original size:16 final size:16
Alignment explanation
Indices: 25610--25655 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 16
25600 TCATGTATAG
25610 ATTTTGCAAGATGAGA
1 ATTTTGCAAGATGAGA
25626 A-TTT--AA-AT-AG-
1 ATTTTGCAAGATGAGA
25636 ATTTTGCAAGATGAGA
1 ATTTTGCAAGATGAGA
25652 ATTT
1 ATTT
25656 AAATAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
10 1 0.04
11 5 0.21
12 2 0.08
13 4 0.17
14 2 0.08
15 5 0.21
16 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (16 bp):
ATTTTGCAAGATGAGA
Found at i:27514 original size:30 final size:30
Alignment explanation
Indices: 27467--27534 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
27457 ATATGTTGAT
27467 ACATTGT-ACTAATTAGAAATGATGTAGTG
1 ACATTGTCACTAATTAGAAATGATGTAGTG
*
27496 ACATTGTCACTGATTAGAAATGATGTAGTG
1 ACATTGTCACTAATTAGAAATGATGTAGTG
27526 ACATTGTCA
1 ACATTGTCA
27535 TTGGTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 7 0.19
30 30 0.81
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (30 bp):
ACATTGTCACTAATTAGAAATGATGTAGTG
Found at i:28106 original size:2 final size:2
Alignment explanation
Indices: 28101--28134 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28091 TATATATATA
28101 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28135 AGAAGGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34517 original size:63 final size:63
Alignment explanation
Indices: 34418--34540 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
34408 GATGTTCCAC
34418 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCACTTG
1 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCACTTG
34481 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCAC
1 CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCAC
34541 CTGAACTTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (63 bp):
CTGATGTTTCTGCCCTTTCTGATAAAGAAGAGGATACCCCTGCTGCTGAAATTGATCCACTTG
Done.