Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005816.1 Kokia drynarioides strain JFW-HI SEQ_120100, 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: 4204
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Found at i:279 original size:30 final size:29
Alignment explanation
Indices: 166--566 Score: 314
Period size: 29 Copynumber: 13.6 Consensus size: 29
156 CAAAAATGGG
* *
166 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAATTGTA
* * *
195 ATTTTTGGAAGGTTC-AGGATAAAAAATAAG-A
1 ATTTTTGGAA-GTTCGGGGGT--AAAAT-TGTA
*
226 CTTTTTGGAAGTTCGGGGGTAAAATTGTA
1 ATTTTTGGAAGTTCGGGGGTAAAATTGTA
* * * **
255 ATTTTTGGAAGGTTCGAGGTTAAAAATGGG
1 ATTTTTGGAA-GTTCGGGGGTAAAATTGTA
* * *
285 ATTTTTGGAAGTTCTGGGGTAAAGTGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAATTGTA
* * * *
314 ATTTTTGGAAGGTTCGAGGTTAAAAATGGA
1 ATTTTTGGAA-GTTCGGGGGTAAAATTGTA
*
344 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGGGGGTAAAATTGTA
* ** * *
373 TTTTTTGGAAGGTTTAGGGTTAAAAATG-A
1 ATTTTTGGAA-GTTCGGGGGTAAAATTGTA
*
402 GATTTTTGGAAGTTCGGGGGTAAAATGGT-
1 -ATTTTTGGAAGTTCGGGGGTAAAATTGTA
* * * * *
431 ATTCTTGGAAGGTTTGGGGTTAAAAAATGGA
1 ATTTTTGGAA-GTTCGGGGGT-AAAATTGTA
* *
462 ATTTTTGGAAGTTTGGGGGTAAAATGGT-
1 ATTTTTGGAAGTTCGGGGGTAAAATTGTA
*
490 ATTTTTGGAAGGTTCGGGGTTGAAAA-TG-A
1 ATTTTTGGAA-GTTCGGGGGT-AAAATTGTA
519 GATTTTTGGAAGTTCGGGGGTAAAA-TGATA
1 -ATTTTTGGAAGTTCGGGGGTAAAATTG-TA
549 ATTTTTGGAAGGTTCGGG
1 ATTTTTGGAA-GTTCGGG
567 ACCTCCGGGG
Statistics
Matches: 292, Mismatches: 59, Indels: 41
0.74 0.15 0.10
Matches are distributed among these distances:
28 26 0.09
29 127 0.43
30 111 0.38
31 27 0.09
32 1 0.00
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGGGGGTAAAATTGTA
Found at i:564 original size:59 final size:59
Alignment explanation
Indices: 119--566 Score: 598
Period size: 59 Copynumber: 7.6 Consensus size: 59
109 TCCGGATGCA
* * * * * *
119 CGGGGGCAAAATGGTAGTTTTGGGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTT-TGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTT
* * * * *
179 CGAGGGTAAAATGGTAATTTTTGGAAGGTTCAGGATAAAAAATAAGACTTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGA-TTTTTGGAAGTT
* * *
239 CGGGGGTAAAATTGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTT
* * *
298 CTGGGGTAAAGTGGTAATTTTTGGAAGGTTCGAGGTTAAAAATG-GAATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAG-ATTTTTGGAAGTT
* **
357 CGGGGGTAAAATGGTATTTTTTGGAAGGTTTAGGGTTAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTT
* *
416 CGGGGGTAAAATGGT-ATTCTTGGAAGGTTTGGGGTTAAAAAATG-GAATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT-AAAAATGAG-ATTTTTGGAAGTT
* *
475 TGGGGGTAAAATGGT-ATTTTTGGAAGGTTCGGGGTTGAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTT
*
533 CGGGGGTAAAATGATAATTTTTGGAAGGTTCGGG
1 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGG
567 ACCTCCGGGG
Statistics
Matches: 345, Mismatches: 36, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
58 52 0.15
59 223 0.65
60 70 0.20
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTT
Found at i:1649 original size:34 final size:34
Alignment explanation
Indices: 1593--1675 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
1583 AATGCCTTTT
* * *
1593 TTATTGTTAATTATTATTTTTTTAAAAGATATTA
1 TTATTATTAATTATTATTTTTTTAAAAAAAATTA
1627 TTATTATT-ATTATTATTGTTTTTAAAAAAAATTA
1 TTATTATTAATTATTATT-TTTTTAAAAAAAATTA
* *
1661 TTATTAATAAATATT
1 TTATTATTAATTATT
1676 TTGAAAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 9 0.21
34 28 0.67
35 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (34 bp):
TTATTATTAATTATTATTTTTTTAAAAAAAATTA
Found at i:2347 original size:17 final size:16
Alignment explanation
Indices: 2325--2386 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
2315 TGGACTTTTC
2325 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
2342 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
2359 TAAACTTAAATTTAAAA
1 TAAA-TTTAATTTTAAA
*
2376 TAAATTCAATT
1 TAAATTTAATT
2387 CCCAACGGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 6 0.15
17 25 0.64
18 8 0.21
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:3091 original size:198 final size:199
Alignment explanation
Indices: 2828--3273 Score: 578
Period size: 205 Copynumber: 2.2 Consensus size: 199
2818 GGGTTCTATA
* ** *
2828 TGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTCGTTTGTTTTATCCGCTTCTCTGTA
1 TGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTTGTTCATTTAATCCGCTTCTCTGTA
*
2893 TCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAAGAAGCTAA-TTA-CTTCGA
66 TCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAAGAAGCTAACTTATCTCCGA
* ** *
2956 -CACGCTTCTCAGTATCTCATCAGGGAGCTGTGG-TTCGAAGA-TTTGCTCATGTCGAGCATGGG
131 TC-CGCTTCTCAGTATCTCATCAGGAAGCTG-GGATTCGAAGACTTT-CTCACATCGAGCACGGG
*
3018 TTTGGTT
193 CTTGGTT
* *
3025 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTCATTTCAATCCGCTTCTCTGT
1 TGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTTGTTCATTT-AATCCGCTTCTCTGT
* *
3090 ATCTCATCAGGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTG
65 ATCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAAGAAGCTAA-C--TTA-T-
* * * * **
3155 CTCCGATCTGCTTCTCAGTGTGTCATCAGGAAGCTGGGATTCGAAGACTTTCTCACATCGTGTGC
125 CTCCGATCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGACTTTCTCACATCGAGCAC
3220 GGGCTTGGTT
190 GGGCTTGGTT
* *
3230 TGGTCTTCTTCTCAATATCTCATTAGGGAGCTGACCGCGTTGTT
1 TGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTTGTT
3274 TTGTGGGTAT
Statistics
Matches: 214, Mismatches: 24, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
197 44 0.21
198 67 0.31
202 3 0.01
204 2 0.01
205 94 0.44
206 4 0.02
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (199 bp):
TGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTTGTTCATTTAATCCGCTTCTCTGTA
TCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAAGAAGCTAACTTATCTCCGA
TCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGACTTTCTCACATCGAGCACGGGCTT
GGTT
Done.