Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010234.1 Kokia drynarioides strain JFW-HI SEQ_125065, 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: 19834
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:214 original size:15 final size:15
Alignment explanation
Indices: 196--266 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
186 TTTTGGGTAG
196 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
211 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
* *
226 TCTGTAACTGGGCCA
1 TTTGTAATTGGGCCA
*
241 TTTGTTATTGGGCCA
1 TTTGTAATTGGGCCA
256 TTTGTAATTGG
1 TTTGTAATTGG
267 ACTTTGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:221 original size:30 final size:29
Alignment explanation
Indices: 196--278 Score: 107
Period size: 30 Copynumber: 2.9 Consensus size: 29
186 TTTTGGGTAG
196 TTTGTAATTGGGCCATTTGTATTTGGGCCA
1 TTTGTAATTGGGCCATTTGT-TTTGGGCCA
* *
226 TCTGTAACTGGGCCATTTGTTATTGGGCCA
1 TTTGTAATTGGGCCATTTGTT-TTGGGCCA
*
256 TTTGTAATT-GGAC-TTTGTTTTGG
1 TTTGTAATTGGGCCATTTGTTTTGG
279 ATTTTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.09
28 6 0.13
29 4 0.09
30 33 0.70
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.45
Consensus pattern (29 bp):
TTTGTAATTGGGCCATTTGTTTTGGGCCA
Found at i:320 original size:17 final size:17
Alignment explanation
Indices: 298--413 Score: 124
Period size: 17 Copynumber: 7.4 Consensus size: 17
288 TTGGACTTTC
* *
298 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
315 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
332 TAAATTTAAATTT---A
1 TAAATTTAAATTTAAAA
*
346 -AAA--TAAACTT--AA
1 TAAATTTAAATTTAAAA
*
358 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
375 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
392 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
408 TAAATT
1 TAAATT
414 CAATTTCCAA
Statistics
Matches: 86, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
11 6 0.07
12 1 0.01
13 6 0.07
14 1 0.01
15 6 0.07
16 8 0.09
17 58 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:324 original size:6 final size:6
Alignment explanation
Indices: 298--408 Score: 83
Period size: 6 Copynumber: 18.8 Consensus size: 6
288 TTGGACTTTC
* *
298 TAAATT TAATTT TATAA-- TAAATT TAAATT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
344 TAAA-A TAAACTT AATAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A
1 TAAATT TAAA-TT --TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT
*
392 TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAAT
409 AAATTCAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
4 5 0.06
5 15 0.18
6 54 0.64
7 4 0.05
8 2 0.02
9 4 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:363 original size:43 final size:43
Alignment explanation
Indices: 312--400 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
302 TTTAATTTTA
312 TAATAAATTTAAATTTAAAATAAATTTAAATTTAAAATAAACT
1 TAATAAATTTAAATTTAAAATAAATTTAAATTTAAAATAAACT
*
355 TAATAAATTTAAATTTCAAATAAATTTAAATTTAAAATAAACT
1 TAATAAATTTAAATTTAAAATAAATTTAAATTTAAAATAAACT
398 TAA
1 TAA
401 ATTTAAATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (43 bp):
TAATAAATTTAAATTTAAAATAAATTTAAATTTAAAATAAACT
Found at i:366 original size:26 final size:25
Alignment explanation
Indices: 330--390 Score: 90
Period size: 26 Copynumber: 2.5 Consensus size: 25
320 TTAAATTTAA
330 AATAAATTTAAATTTAAAATAAACTT
1 AATAAATTTAAATTTAAAATAAA-TT
*
356 AATAAATTTAAATTTCAAATAAATT
1 AATAAATTTAAATTTAAAATAAATT
381 --TAAATTTAAA
1 AATAAATTTAAA
391 ATAAACTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 10 0.29
25 2 0.06
26 22 0.65
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
AATAAATTTAAATTTAAAATAAATT
Found at i:377 original size:60 final size:59
Alignment explanation
Indices: 298--411 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 59
288 TTGGACTTTC
* *
298 TAAATTTAATTTTATAATAAATTTAAATTTAAAATAAATTTAAATTTAAAATAAACTTAA
1 TAAATTTAATTTCATAATAAATTTAAATTTAAAATAAACTTAAATTT-AAATAAACTTAA
358 TAAATTTAAATTTCA-AATAAATTTAAATTTAAAATAAACTTAAATTTAAATAAA
1 TAAATTT-AATTTCATAATAAATTTAAATTTAAAATAAACTTAAATTTAAATAAA
412 TTCAATTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
59 7 0.14
60 38 0.75
61 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (59 bp):
TAAATTTAATTTCATAATAAATTTAAATTTAAAATAAACTTAAATTTAAATAAACTTAA
Found at i:425 original size:16 final size:17
Alignment explanation
Indices: 298--426 Score: 109
Period size: 17 Copynumber: 8.2 Consensus size: 17
288 TTGGACTTTC
*
298 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
*
315 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTCAAA
332 TAAATTTAAATTT---A
1 TAAATTTAAATTTCAAA
*
346 -AAA--TAAACTT--AA
1 TAAATTTAAATTTCAAA
358 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
375 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTCAAA
*
392 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
408 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
424 TAA
1 TAA
427 GTCCAGACAA
Statistics
Matches: 97, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
11 6 0.06
12 1 0.01
13 6 0.06
14 1 0.01
15 13 0.13
16 12 0.12
17 52 0.54
18 6 0.06
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:2422 original size:24 final size:24
Alignment explanation
Indices: 2393--2445 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
2383 ACTTAATTTC
2393 TCCTTAATTTAGTGTATAATTTGT
1 TCCTTAATTTAGTGTATAATTTGT
2417 TCCTTAATTTAGTGTATAATTTGT
1 TCCTTAATTTAGTGTATAATTTGT
2441 TCCTT
1 TCCTT
2446 TTTTGTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (24 bp):
TCCTTAATTTAGTGTATAATTTGT
Found at i:7415 original size:3 final size:3
Alignment explanation
Indices: 7407--7441 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
7397 ATTTTAATTG
* *
7407 ATA ATA ATA ATA ATA ATA ATA ATT ATT ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7442 GAAGACATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:8893 original size:59 final size:59
Alignment explanation
Indices: 8787--9224 Score: 630
Period size: 59 Copynumber: 7.4 Consensus size: 59
8777 TTCGAATGTA
* * * * * *
8787 CGGGGGCAAAATGGT-AGTTTTGGAGGGTTCAGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
8845 CGGGGGTAAAATGGTAATTTTTATAAGGTTAGGGGTCAAAAATGGGATTTTTGGAAG-T
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
8903 CTGGCGGTAAAATGGTAATTTTTAGAAGGTCTC-GGGTCAAAAATGGAATTTTTGGAAGTT
1 C-GGGGGTAAAATGGTAATTTTTAGAAGGT-TCGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
8963 CGGGGGTAAAATGGTAATTTTTAGAATGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
9022 CGGGGATGAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* ** *
9081 TGGGGGTAAAATGGTAATTTTTAGAAGGTTTTGGGTCAAAAATGGGATTTTTGGAAATT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
9140 CGGGGATAAAACGGTAATTTTTAGATGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
9199 CGGGTGTAAAATGGTAATTTTTAGAA
1 CGGGGGTAAAATGGTAATTTTTAGAA
9225 AGTTTAGGGA
Statistics
Matches: 336, Mismatches: 39, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
58 18 0.05
59 315 0.94
60 3 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:10549 original size:22 final size:22
Alignment explanation
Indices: 10521--10579 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
10511 AGTAATAATA
10521 TGCAAGTTGCAGCCGGTGGCAG
1 TGCAAGTTGCAGCCGGTGGCAG
10543 TGCAAGTTGCAGCCGGTGGCAG
1 TGCAAGTTGCAGCCGGTGGCAG
*
10565 TGCAAGTTGGAGCCG
1 TGCAAGTTGCAGCCG
10580 AAGATGGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.19
Consensus pattern (22 bp):
TGCAAGTTGCAGCCGGTGGCAG
Found at i:10739 original size:17 final size:18
Alignment explanation
Indices: 10714--10755 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
10704 GATCGGACCC
* *
10714 TTTTAGGTTTAGGG-TTA
1 TTTTGGGTTTAGGGCTGA
*
10731 TTTTGGGTTTGGGGCTGA
1 TTTTGGGTTTAGGGCTGA
10749 TTTTGGG
1 TTTTGGG
10756 CCACTTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (18 bp):
TTTTGGGTTTAGGGCTGA
Found at i:10874 original size:17 final size:16
Alignment explanation
Indices: 10833--10906 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
10823 TTGGACTTTC
*
10833 TAAATTTAATTTTTATAA
1 TAAATTTAA-ATTTA-AA
10851 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
*
10868 CAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
10885 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
10901 TAAATT
1 TAAATT
10907 CGATTTCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
16 8 0.16
17 31 0.63
18 10 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:10894 original size:34 final size:34
Alignment explanation
Indices: 10834--10906 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
10824 TGGACTTTCT
* * *
10834 AAATTTAATTTTTATAATAAATTTAAATTTCAAAC
1 AAATTTAATATTTAAAATAAACTTAAATTT-AAAC
*
10869 AAATTTAA-ATTTAAAATAAACTTAAATTTAAAT
1 AAATTTAATATTTAAAATAAACTTAAATTTAAAC
10902 AAATT
1 AAATT
10907 CGATTTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 8 0.24
34 18 0.53
35 8 0.24
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (34 bp):
AAATTTAATATTTAAAATAAACTTAAATTTAAAC
Found at i:12160 original size:27 final size:27
Alignment explanation
Indices: 12130--12189 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
12120 CCAAGAATTT
*
12130 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
* *
12157 TATTAAAAGGAGGGTCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
12184 TCATTA
1 T-ATTA
12190 GTTGAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.