Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002689.1 Kokia drynarioides strain JFW-HI SEQ_114958, 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: 12846
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:302 original size:18 final size:20
Alignment explanation
Indices: 258--308 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
248 CCTTTTATTT
*
258 ATTTATTATTATTAATAATA
1 ATTTATTATTATCAATAATA
*
278 ATATTATTATTATCAA-AA-C
1 AT-TTATTATTATCAATAATA
297 ATTTATTATTAT
1 ATTTATTATTAT
309 TTATGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 4 0.14
21 12 0.43
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTATTATTATCAATAATA
Found at i:362 original size:9 final size:9
Alignment explanation
Indices: 334--392 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 9
324 AAAACTTATT
334 TATTATTAA
1 TATTATTAA
343 TGATATCATTAA
1 T-AT-T-ATTAA
*
355 TATTATTAT
1 TATTATTAA
364 TATTATTAAAA
1 TATTATT--AA
*
375 TAGTATTAA
1 TATTATTAA
384 TATTATTAA
1 TATTATTAA
393 GAATTATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 22 0.54
10 3 0.07
11 10 0.24
12 6 0.15
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (9 bp):
TATTATTAA
Found at i:381 original size:20 final size:20
Alignment explanation
Indices: 353--392 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
343 TGATATCATT
* *
353 AATATTATTATTATTATTAA
1 AATAGTATTAATATTATTAA
373 AATAGTATTAATATTATTAA
1 AATAGTATTAATATTATTAA
393 GAATTATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AATAGTATTAATATTATTAA
Found at i:1057 original size:6 final size:6
Alignment explanation
Indices: 1047--1116 Score: 81
Period size: 6 Copynumber: 12.0 Consensus size: 6
1037 TTTGAACTTT
* *
1047 TTTAAT TTTAAA ATTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
1094 -ATAAA TCTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
1117 AAGGGGCCCG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
5 9 0.16
6 46 0.84
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:1079 original size:17 final size:18
Alignment explanation
Indices: 1047--1116 Score: 108
Period size: 17 Copynumber: 4.0 Consensus size: 18
1037 TTTGAACTTT
*
1047 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAAATTAAA
1065 TTTAAATTT-AAATTAAA
1 TTTAAATTTAAAATTAAA
1082 TTTAAATTTAAAA-TAAA
1 TTTAAATTTAAAATTAAA
*
1099 TCTAAATTTAAAATTAAA
1 TTTAAATTTAAAATTAAA
1117 AAGGGGCCCG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 33 0.69
18 15 0.31
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAAAATTAAA
Found at i:1081 original size:23 final size:22
Alignment explanation
Indices: 1060--1117 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
1050 AATTTTAAAA
*
1060 TTAAATTTAAATTTAAATTAAAT
1 TTAAATTTAAA-ATAAATTAAAT
1083 TTAAATTTAAAATAAATCTAAAT
1 TTAAATTTAAAATAAAT-TAAAT
*
1106 TTAAAATTAAAA
1 TTAAATTTAAAA
1118 AGGGGCCCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATTTAAAATAAATTAAAT
Found at i:1445 original size:17 final size:17
Alignment explanation
Indices: 1413--1500 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 17
1403 AAGCTGATTA
*
1413 AAATTTATTTTTAAATTT
1 AAATTTA-TCTTAAATTT
*
1431 AAATTTATCTTAAATTA
1 AAATTTATCTTAAATTT
1448 AAATTTATCTTTTTAAATTT
1 AAATTTATC---TTAAATTT
*
1468 AAATTTAATC-AAAATTT
1 AAATTT-ATCTTAAATTT
* *
1485 AAATTGATATTAAATT
1 AAATTTATCTTAAATT
1501 AAAAACTCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
16 2 0.03
17 33 0.57
18 7 0.12
20 13 0.22
21 3 0.05
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AAATTTATCTTAAATTT
Found at i:1483 original size:37 final size:35
Alignment explanation
Indices: 1409--1489 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 35
1399 GTTTAAGCTG
*
1409 ATTAAAATTTATTTTTAAATTTAAATTTATCTTAA
1 ATTAAAATTTATTTTTAAATTTAAATTTATCTAAA
1444 ATTAAAATTTATCTTTTTAAATTTAAATTTAATC-AAA
1 ATTAAAATTTA--TTTTTAAATTTAAATTT-ATCTAAA
*
1481 ATTTAAATT
1 ATTAAAATT
1490 GATATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 11 0.27
37 27 0.66
38 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (35 bp):
ATTAAAATTTATTTTTAAATTTAAATTTATCTAAA
Found at i:1504 original size:23 final size:23
Alignment explanation
Indices: 1459--1504 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1449 AATTTATCTT
* *
1459 TTTAAATTTAAATTTAATCAAAA
1 TTTAAATTGAAATTAAATCAAAA
* *
1482 TTTAAATTGATATTAAATTAAAA
1 TTTAAATTGAAATTAAATCAAAA
1505 ACTCAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAATTGAAATTAAATCAAAA
Found at i:2296 original size:14 final size:14
Alignment explanation
Indices: 2251--2302 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2241 AACTAGTTTA
2251 ATAAT-AATAAT-G
1 ATAATAAATAATAG
*
2263 ATAATAATATAATAT
1 ATAATAA-ATAATAG
*
2278 TTAATAAATAATAG
1 ATAATAAATAATAG
*
2292 ATAATACATAA
1 ATAATAAATAA
2303 AAAAAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 5 0.16
13 1 0.03
14 20 0.62
15 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (14 bp):
ATAATAAATAATAG
Found at i:9523 original size:16 final size:17
Alignment explanation
Indices: 9504--9536 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9494 CACATTTGCA
*
9504 TTTATTTTTATT-TTTT
1 TTTAATTTTATTATTTT
9520 TTTAATTTTATTATTTT
1 TTTAATTTTATTATTTT
9537 CACAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTAATTTTATTATTTT
Found at i:11452 original size:15 final size:14
Alignment explanation
Indices: 11425--11454 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
11415 AACGAGCTTA
11425 ATAAAATTTAAAAT
1 ATAAAATTTAAAAT
11439 ATAAAATATTAAAAT
1 ATAAAAT-TTAAAAT
11454 A
1 A
11455 AAGTTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATTTAAAAT
Found at i:12578 original size:17 final size:18
Alignment explanation
Indices: 12558--12591 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12548 AATTCTTTCA
*
12558 TTTTTTTTCTT-TTTTAC
1 TTTTATTTCTTCTTTTAC
12575 TTTTATTTCTTCTTTTA
1 TTTTATTTCTTCTTTTA
12592 TAATGTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTCTTCTTTTAC
Done.