Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013718.1 Kokia drynarioides strain JFW-HI SEQ_128746, 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: 19766
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:254 original size:15 final size:16
Alignment explanation
Indices: 225--254 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
215 TTTGAGTCTG
225 AAATAAAAATATTAAT
1 AAATAAAAATATTAAT
241 AAATAAAAAT-TTAA
1 AAATAAAAATATTAA
255 AATACCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAATATTAAT
Found at i:280 original size:14 final size:14
Alignment explanation
Indices: 261--342 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 14
251 TTAAAATACC
261 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
* *
275 AGAAATAAAATAAT
1 AAAAATAAAAAAAT
* *
289 ATAAATAACATAAAT
1 AAAAATAA-AAAAAT
304 AAATTAATAAAAAAAT
1 AAA--AATAAAAAAAT
320 ATAAAATTAAATAATAAT
1 A-AAAA-TAAA-AA-AAT
338 AAAAA
1 AAAAA
343 CAATGGGTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.35
15 8 0.15
16 10 0.19
17 13 0.24
18 4 0.07
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:303 original size:23 final size:23
Alignment explanation
Indices: 265--344 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
255 AATACCAAAA
*
265 ATAAAAAAATAGAAATAAAATAAT
1 ATAAAAACATA-AAATAAAATAAT
*
289 ATAAATAACAT-AAATAAATTAAT
1 ATAAA-AACATAAAATAAAATAAT
* * *
312 AAAAAAATATAAAATTAAATAAT
1 ATAAAAACATAAAATAAAATAAT
335 AATAAAAACA
1 -ATAAAAACA
345 ATGGGTTGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 4 0.09
23 25 0.56
24 12 0.27
25 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (23 bp):
ATAAAAACATAAAATAAAATAAT
Found at i:7004 original size:7 final size:7
Alignment explanation
Indices: 6977--7006 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
6967 ATGGTAAGCA
*
6977 AAAATAA
1 AAAATAC
6984 AAAATAC
1 AAAATAC
6991 AAAATAC
1 AAAATAC
6998 AAAATAC
1 AAAATAC
7005 AA
1 AA
7007 GTGCATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAC
Found at i:7153 original size:29 final size:29
Alignment explanation
Indices: 7094--7174 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
7084 GGGTACCCGG
* * *
7094 GGGTAAAATGGTAATTTTAG-ACACTTGA
1 GGGTAAAATGGTAATTTTGGAAAAATTGA
7122 GGGTAAGAATGGTAATTTTGGAAAAATT-A
1 GGGTAA-AATGGTAATTTTGGAAAAATTGA
7151 GGGTGAAAAATGG-AATTTTAGGAA
1 GGGT--AAAATGGTAATTTT-GGAA
7175 CTTCGAGGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 6 0.13
29 24 0.53
30 13 0.29
31 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGAAAAATTGA
Found at i:7241 original size:29 final size:29
Alignment explanation
Indices: 7208--7301 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
7198 TTTTGTGAAA
7208 TCGAGGTCAAAAATAGAATTTTAGAAAGT
1 TCGAGGTCAAAAATAGAATTTTAGAAAGT
* *
7237 TCGAGGGT--AAAATGGTAATTTTTGGTGAAA-T
1 TCGA-GGTCAAAAATAG-AA-TTTT--AGAAAGT
* * *
7268 T-GGGGCCAAAAATAGAATTTTGGAAAGT
1 TCGAGGTCAAAAATAGAATTTTAGAAAGT
7296 TCGAGG
1 TCGAGG
7302 GTGGAAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
27 4 0.08
28 8 0.16
29 15 0.31
30 10 0.20
31 8 0.16
32 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.29
Consensus pattern (29 bp):
TCGAGGTCAAAAATAGAATTTTAGAAAGT
Found at i:7288 original size:59 final size:59
Alignment explanation
Indices: 7106--7318 Score: 225
Period size: 59 Copynumber: 3.6 Consensus size: 59
7096 GTAAAATGGT
* ** * * *
7106 AATTTTAGACACTT-GAGGGTAAGAATGGTAA-TTTTGGAAAAATTAGGGTGAAAAATGG
1 AATTTTAGAAACTTCGAGGGTAA-AATGGTAATTTTTGGTGAAATTGGGGTCAAAAATAG
* * * * * *
7164 AATTTTAGGAACTTCGAGGGCATAATGGTAATTTTTTTGTGAAATCGAGGTCAAAAATAG
1 AATTTTAGAAACTTCGAGGGTAAAATGGTAA-TTTTTGGTGAAATTGGGGTCAAAAATAG
* *
7224 AATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGCCAAAAATAG
1 AATTTTAGAAACTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATAG
* * *
7283 AATTTTGGAAAGTTCGAGGGTGGAAAT-GTAATTTTT
1 AATTTTAGAAACTTCGAGGGT-AAAATGGTAATTTTT
7319 TGGGATACTG
Statistics
Matches: 129, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
58 20 0.16
59 59 0.46
60 50 0.39
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.32
Consensus pattern (59 bp):
AATTTTAGAAACTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATAG
Found at i:7372 original size:29 final size:29
Alignment explanation
Indices: 7328--7462 Score: 85
Period size: 29 Copynumber: 4.6 Consensus size: 29
7318 TTGGGATACT
* *
7328 GGGTTAAAATGGAATTTTGGGAAGTTTAG
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
** *
7357 GGGTAAAAATGTAATTTTTTGGGAA-AATCG
1 GGGTAAAAATGTAA--TTTTGGGAAGTTTAG
* * * *
7387 AGGTAAAAAATGGAATTTTGGAAAGTTCAG
1 GGGT-AAAAATGTAATTTTGGGAAGTTTAG
* * * *
7417 GGGTTAAATTATAA-CTTGGAGAAGTTTAG
1 GGGTAAAAATGTAATTTTGG-GAAGTTTAG
* *
7446 GGGTCAAAATGTGATTT
1 GGGTAAAAATGTAATTT
7463 CTAGACAGTT
Statistics
Matches: 75, Mismatches: 25, Indels: 11
0.68 0.23 0.10
Matches are distributed among these distances:
28 4 0.05
29 43 0.57
30 10 0.13
31 18 0.24
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGGGAAGTTTAG
Found at i:8592 original size:18 final size:20
Alignment explanation
Indices: 8554--8593 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
8544 TGGTCATTGT
*
8554 TATTATTAAATTAATATTGA
1 TATTATTAAATTAATAATGA
8574 TATTATT-AA-TAATAATGA
1 TATTATTAAATTAATAATGA
8592 TA
1 TA
8594 ACTTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTATTAAATTAATAATGA
Found at i:9294 original size:17 final size:17
Alignment explanation
Indices: 9272--9378 Score: 94
Period size: 17 Copynumber: 6.1 Consensus size: 17
9262 TAATATTCAG
9272 TTTTAAATCAAA-TTAAA
1 TTTTAAAT-AAATTTAAA
*
9289 TTTTAATTAAATTTAAA
1 TTTTAAATAAATTTAAA
9306 -TTTAAAGTAAATTTAAA
1 TTTTAAA-TAAATTTAAA
*
9323 TTTAAAAAGATAAATTTAAA
1 TTT--TAA-ATAAATTTAAA
9343 -TTTAAGATAAATTTAAA
1 TTTTAA-ATAAATTTAAA
**
9360 TTAAAAAATAAATTTAAA
1 TT-TTAAATAAATTTAAA
9378 T
1 T
9379 CAATTTAAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
16 8 0.11
17 36 0.47
18 15 0.20
19 4 0.05
20 12 0.16
21 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTTAAATAAATTTAAA
Found at i:9298 original size:11 final size:11
Alignment explanation
Indices: 9281--9387 Score: 65
Period size: 11 Copynumber: 10.3 Consensus size: 11
9271 GTTTTAAATC
9281 AAATTAAATTT
1 AAATTAAATTT
*
9292 TAATTAAATTT
1 AAATTAAATTT
*
9303 AAATTTAAA-GT
1 AAA-TTAAATTT
9314 AAATTTAAATTT
1 AAA-TTAAATTT
9326 AAA--AAGA--T
1 AAATTAA-ATTT
9334 AAATTTAAATTT
1 AAA-TTAAATTT
9346 AAGA-TAAATTT
1 AA-ATTAAATTT
9357 AAATTAAA---
1 AAATTAAATTT
9365 AAA-TAAATTT
1 AAATTAAATTT
*
9375 AAA-TCAATTT
1 AAATTAAATTT
9385 AAA
1 AAA
9388 CCCAACTTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 27
0.71 0.05 0.25
Matches are distributed among these distances:
7 4 0.05
8 7 0.09
9 2 0.03
10 15 0.19
11 37 0.47
12 12 0.15
13 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:9304 original size:6 final size:6
Alignment explanation
Indices: 9284--9378 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
9274 TTAAATCAAA
* * *
9284 TTAAAT TTTAA- TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT TTAAAAAG
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT--AAAT
* * * *
9332 ATAAAT TTAAAT TTAAGA- -TAAAT TTAAAT TAAAAA ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
9379 CAATTTAAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
4 1 0.01
5 11 0.16
6 51 0.75
7 1 0.01
8 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:9344 original size:37 final size:35
Alignment explanation
Indices: 9296--9378 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 35
9286 AAATTTTAAT
9296 TAAATTTAAATTTAA-AGTAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTTAAGA-TAAATTTAAA-TTAAAAA-A
9333 TAAATTTAAATTTAAGATAAATTTAAATTAAAAAA
1 TAAATTTAAATTTAAGATAAATTTAAATTAAAAAA
9368 TAAATTTAAAT
1 TAAATTTAAAT
9379 CAATTTAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
35 12 0.27
36 7 0.16
37 25 0.56
38 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (35 bp):
TAAATTTAAATTTAAGATAAATTTAAATTAAAAAA
Found at i:9383 original size:10 final size:10
Alignment explanation
Indices: 9339--9387 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
9329 AAGATAAATT
9339 TAAATTTAAGA
1 TAAATTTAA-A
9350 TAAATTTAAA
1 TAAATTTAAA
9360 TTAAA---AAA
1 -TAAATTTAAA
9368 TAAATTTAAA
1 TAAATTTAAA
*
9378 TCAATTTAAA
1 TAAATTTAAA
9388 CCCAACTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
7 4 0.12
8 3 0.09
10 13 0.39
11 13 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:14218 original size:7 final size:6
Alignment explanation
Indices: 14203--14255 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
14193 CACTTTTGTC
*
14203 TTTTCT TTTTCT TTTTCT TTTTTT TTTTCAAT TTTTCTT TTTTCT TTTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC--T TTTTC-T TTTTCT TTTTCT
14253 TTT
1 TTT
14256 AAACAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
5 4 0.10
6 26 0.62
7 6 0.14
8 6 0.14
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:15012 original size:5 final size:5
Alignment explanation
Indices: 15002--15095 Score: 109
Period size: 5 Copynumber: 17.8 Consensus size: 5
14992 AGTGCATAAC
*
15002 TAAAA TAAAA TTGAAAA TAAAA T-AAA TAAAA TAAGA TAAAA TAAAA TAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
*
15053 TTGAAAA TAAAA TAAGA TAAAA TAAAA TAAAA TTGAAAA TAAA
1 -T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA TAAA
15096 TATACTAATT
Statistics
Matches: 78, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
4 4 0.05
5 56 0.72
6 6 0.08
7 12 0.15
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:15066 original size:32 final size:32
Alignment explanation
Indices: 15025--15095 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
15015 AAAATAAAAT
15025 AAATAAAATAAGATAAAATAAAATAAAATTGA
1 AAATAAAATAAGATAAAATAAAATAAAATTGA
15057 AAATAAAATAAGATAAAATAAAATAAAATTGA
1 AAATAAAATAAGATAAAATAAAATAAAATTGA
15089 AAATAAA
1 AAATAAA
15096 TATACTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (32 bp):
AAATAAAATAAGATAAAATAAAATAAAATTGA
Found at i:15094 original size:27 final size:28
Alignment explanation
Indices: 15006--15091 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 28
14996 CATAACTAAA
**
15006 ATAAAATTGAAAATAAAATAAATAAAATAAG
1 ATAAAA-T-AAAATAAAATTGA-AAAATAAG
15037 ATAAAATAAAATAAAATTGAAAATAAAATAAG
1 ATAAAATAAAATAAAATTG---A-AAAATAAG
15069 ATAAAATAAAATAAAATTGAAAA
1 ATAAAATAAAATAAAATTGAAAA
15092 TAAATATACT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.06
29 11 0.22
30 1 0.02
31 6 0.12
32 29 0.58
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (28 bp):
ATAAAATAAAATAAAATTGAAAAATAAG
Done.