Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010836.1 Kokia drynarioides strain JFW-HI SEQ_125803, 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: 14452
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:470 original size:7 final size:7
Alignment explanation
Indices: 458--482 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
448 TATTATTTTT
458 TTAAATA
1 TTAAATA
465 TTAAATA
1 TTAAATA
472 TTAAATA
1 TTAAATA
479 TTAA
1 TTAA
483 TGTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAATA
Found at i:518 original size:9 final size:9
Alignment explanation
Indices: 506--575 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
496 TATTGTCGTC
506 ATTAATATT
1 ATTAATATT
515 ATTAATGA-T
1 ATTAAT-ATT
* *
524 ATTAGTAAT
1 ATTAATATT
*
533 AATAATATT
1 ATTAATATT
*
542 ATTATTATT
1 ATTAATATT
*
551 ATTACCATAATA
1 ATTA--AT-ATT
563 ATTAATATT
1 ATTAATATT
572 ATTA
1 ATTA
576 TTAATGACAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
8 1 0.02
9 36 0.77
10 3 0.06
11 1 0.02
12 6 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (9 bp):
ATTAATATT
Found at i:525 original size:12 final size:12
Alignment explanation
Indices: 508--580 Score: 60
Period size: 12 Copynumber: 6.1 Consensus size: 12
498 TTGTCGTCAT
508 TAATATTATTAA
1 TAATATTATTAA
* *
520 TGATATTAGTAA
1 TAATATTATTAA
* *
532 TAATAATATTAT
1 TAATATTATTAA
*
544 TATTATTATTACCA
1 TAATATTATTA--A
558 TAATA--ATTAA
1 TAATATTATTAA
*
568 TATTATTATTAA
1 TAATATTATTAA
580 T
1 T
581 GACATTTATT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
10 5 0.11
12 37 0.80
14 4 0.09
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (12 bp):
TAATATTATTAA
Found at i:554 original size:27 final size:27
Alignment explanation
Indices: 486--578 Score: 82
Period size: 27 Copynumber: 3.3 Consensus size: 27
476 ATATTAATGT
** *
486 TTATTATTATTATT-GTCGTCATTAATA
1 TTATTATTATTATTAGTAAT-AATAATA
*
513 TTATTAATGA-TATTAGTAATAATAATA
1 TTATT-ATTATTATTAGTAATAATAATA
*
540 TTATTATTATTATTACCATAATAATTAATA
1 TTATTATTATTATTA--GTAATAA-TAATA
570 TTATTATTA
1 TTATTATTA
579 ATGACATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.06
27 25 0.46
28 6 0.11
29 6 0.11
30 14 0.26
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
TTATTATTATTATTAGTAATAATAATA
Found at i:1248 original size:6 final size:6
Alignment explanation
Indices: 1237--1328 Score: 77
Period size: 6 Copynumber: 16.0 Consensus size: 6
1227 AACATTAATA
* *
1237 TAAATT TAAATT TAAACT TAAATT TATAA-- TAAATT TAAATT TTAA-T
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT
* * * * *
1283 TAAACT TAAACT TAAA-A TAAATT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
1329 CTGTTGGATT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
4 2 0.03
5 14 0.20
6 52 0.74
7 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:1269 original size:17 final size:17
Alignment explanation
Indices: 1237--1328 Score: 103
Period size: 17 Copynumber: 5.4 Consensus size: 17
1227 AACATTAATA
* *
1237 TAAATTTAAATTTAAACT
1 TAAATTTAAA-ATAAATT
*
1255 TAAATTTATAATAAATT
1 TAAATTTAAAATAAATT
* * *
1272 TAAATTTTAATTAAACT
1 TAAATTTAAAATAAATT
*
1289 TAAACTTAAAATAAATT
1 TAAATTTAAAATAAATT
*
1306 TAATTTTAAAATAAATT
1 TAAATTTAAAATAAATT
1323 TAAATT
1 TAAATT
1329 CTGTTGGATT
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
17 51 0.85
18 9 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:1288 original size:34 final size:34
Alignment explanation
Indices: 1237--1328 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
1227 AACATTAATA
* *
1237 TAAATTTAAATTTAAACTTAAATTTATAATAAATT
1 TAAATTTTAA-TTAAACTTAAATTTAAAATAAATT
*
1272 TAAATTTTAATTAAACTTAAACTTAAAATAAATT
1 TAAATTTTAATTAAACTTAAATTTAAAATAAATT
* *
1306 T-AATTTTAAAATAAATTTAAATT
1 TAAATTTT-AATTAAACTTAAATT
1329 CTGTTGGATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 6 0.12
34 35 0.70
35 9 0.18
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (34 bp):
TAAATTTTAATTAAACTTAAATTTAAAATAAATT
Found at i:1315 original size:12 final size:12
Alignment explanation
Indices: 1237--1328 Score: 77
Period size: 11 Copynumber: 8.0 Consensus size: 12
1227 AACATTAATA
1237 TAAATTTAAATT
1 TAAATTTAAATT
*
1249 TAAACTTAAATT
1 TAAATTTAAATT
1261 TATAA--TAAATT
1 TA-AATTTAAATT
*
1272 TAAATTTTAA-T
1 TAAATTTAAATT
* *
1283 TAAACTTAAACT
1 TAAATTTAAATT
*
1295 TAAA-ATAAATT
1 TAAATTTAAATT
* *
1306 TAATTTTAAA-A
1 TAAATTTAAATT
1317 TAAATTTAAATT
1 TAAATTTAAATT
1329 CTGTTGGATT
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
10 2 0.03
11 34 0.54
12 25 0.40
13 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:2595 original size:3 final size:3
Alignment explanation
Indices: 2587--2619 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2577 TTGAAAGAAA
2587 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2620 TTCTATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:7051 original size:21 final size:21
Alignment explanation
Indices: 7026--7065 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7016 TCTTTAATAT
7026 TATTAAAATTATAATATTTGA
1 TATTAAAATTATAATATTTGA
* *
7047 TATTAATATTTTAATATTT
1 TATTAAAATTATAATATTT
7066 TTAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TATTAAAATTATAATATTTGA
Found at i:7539 original size:18 final size:20
Alignment explanation
Indices: 7508--7547 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
7498 TGATAGAGTG
*
7508 AAAAAAATCGAAAAGAT-AA
1 AAAAAAATCAAAAAGATGAA
7527 AAAAAAAT-AAAAAGATGAA
1 AAAAAAATCAAAAAGATGAA
7546 AA
1 AA
7548 TATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAAAAATCAAAAAGATGAA
Found at i:12355 original size:62 final size:62
Alignment explanation
Indices: 12258--12382 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
12248 AATACTTCCT
12258 CCACCTTTGTTCTCTGTAATCTCCGACTCTCCACCCCAATTGGGTGAACTGGTCACCACACC
1 CCACCTTTGTTCTCTGTAATCTCCGACTCTCCACCCCAATTGGGTGAACTGGTCACCACACC
12320 CCACCTTTGTTCTCTGTAATCTCCGACTCTCCACCCCAATTGGGTGAACTGGTCACCACACC
1 CCACCTTTGTTCTCTGTAATCTCCGACTCTCCACCCCAATTGGGTGAACTGGTCACCACACC
12382 C
1 C
12383 TCCTCCTTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.19, C:0.39, G:0.14, T:0.27
Consensus pattern (62 bp):
CCACCTTTGTTCTCTGTAATCTCCGACTCTCCACCCCAATTGGGTGAACTGGTCACCACACC
Found at i:13834 original size:5 final size:5
Alignment explanation
Indices: 13824--13859 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
13814 AGCTTCAAAA
*
13824 GTGAT GTGAT GTGAT GAGAT GTGAT GTGAT GTGAT G
1 GTGAT GTGAT GTGAT GTGAT GTGAT GTGAT GTGAT G
13860 AGAGGTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (5 bp):
GTGAT
Found at i:13849 original size:20 final size:20
Alignment explanation
Indices: 13824--13862 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13814 AGCTTCAAAA
13824 GTGATGTGATGTGATGAGAT
1 GTGATGTGATGTGATGAGAT
13844 GTGATGTGATGTGATGAGA
1 GTGATGTGATGTGATGAGA
13863 GGTTCCTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (20 bp):
GTGATGTGATGTGATGAGAT
Done.