Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007122.1 Kokia drynarioides strain JFW-HI SEQ_121733, 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: 5814
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Found at i:274 original size:30 final size:30
Alignment explanation
Indices: 212--564 Score: 150
Period size: 30 Copynumber: 11.9 Consensus size: 30
202 GAAGTCCCTG
** * ***
212 AACTTTTTTAAAATCATATTTTAACTTTCA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
242 AACTTTTCAAAAATCATATTTTGACCCCCA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* *
272 AACATTTCAAAAAT--TCATTTTGA-CCCTA
1 AACTTTTCAAAAATCAT-ATTTTGACCCCCA
* * * * * *
300 AACTTTTAAAAAATTACATTTTAACTCCTA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* * * * * *
330 AACGTTCCAAAAATTCA-AATTTGGCTCCCG
1 AACTTTTCAAAAA-TCATATTTTGACCCCCA
* * * * **
360 CACTTTTCAAAAATTACATTTTAACCCATA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* *
390 AACTTTTCAAAAATCATATTTTAACCCCCT
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* * * **
420 AAC-TTTCTAGAAATCACATTTTGA-CTCTT
1 AACTTTTC-AAAAATCATATTTTGACCCCCA
* * *
449 AAC-TTTCAAAAAAAT-ACATTATGACCACCA
1 AACTTTTC--AAAAATCATATTTTGACCCCCA
** ** ** **
479 AAC-TTTCCCAAATTTTAGAATTGACCCTTA
1 AACTTTTCAAAAATCATA-TTTTGACCCCCA
* *
509 AACTTTTCAAAAATCATATTTTGACCTCCG
1 AACTTTTCAAAAATCATATTTTGACCCCCA
*
539 ATC-TTTCTAAAAATCATATTTTGACC
1 AACTTTTC-AAAAATCATATTTTGACC
565 TTGAACTTTC
Statistics
Matches: 239, Mismatches: 71, Indels: 26
0.71 0.21 0.08
Matches are distributed among these distances:
28 21 0.09
29 42 0.18
30 164 0.69
31 12 0.05
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (30 bp):
AACTTTTCAAAAATCATATTTTGACCCCCA
Found at i:573 original size:29 final size:29
Alignment explanation
Indices: 499--592 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
489 AATTTTAGAA
*
499 TTGACCCTTAAACTTT-TCAAAAATCATATT
1 TTGA-CCTTGAACTTTCT-AAAAATCATATT
* *
529 TTGACCTCCGATCTTTCTAAAAATCATATT
1 TTGACCT-TGAACTTTCTAAAAATCATATT
* * *
559 TTGACCTTGAACTTTCCAAAATTCA-AAT
1 TTGACCTTGAACTTTCTAAAAATCATATT
587 TTGACC
1 TTGACC
593 CCAAACCTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.15
29 17 0.31
30 28 0.52
31 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (29 bp):
TTGACCTTGAACTTTCTAAAAATCATATT
Found at i:650 original size:28 final size:28
Alignment explanation
Indices: 509--650 Score: 79
Period size: 28 Copynumber: 5.0 Consensus size: 28
499 TTGACCCTTA
* * * *
509 AACTTTTCAAAAATCATATTTTGACCTCCG
1 AACTTTCCAAAATTCA-ATTTTAACC-CTG
* * * * *
539 ATCTTTCTAAAAATCATATTTTGACCTTG
1 AACTTTCCAAAATTCA-ATTTTAACCCTG
* * **
568 AACTTTCCAAAATTCAAATTTGACCCCA
1 AACTTTCCAAAATTCAATTTTAACCCTG
* ** *
596 AACCTTCC-AAATTTGATTTCAACCCCTG
1 AACTTTCCAAAATTCAATTTTAA-CCCTG
*
624 AATTTTCCAAAATTCAATTTTAACCCT
1 AACTTTCCAAAATTCAATTTTAACCCT
651 CAAAAGCCCC
Statistics
Matches: 85, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
27 9 0.11
28 28 0.33
29 25 0.29
30 23 0.27
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (28 bp):
AACTTTCCAAAATTCAATTTTAACCCTG
Found at i:730 original size:17 final size:17
Alignment explanation
Indices: 702--754 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
692 AAAATTCAAA
*
702 TTTTTATCATTATTTAG
1 TTTTTTTCATTATTTAG
*
719 TTTTTTTTATTATATTA-
1 TTTTTTTCATTAT-TTAG
*
736 TATTTTTCATTATTT-G
1 TTTTTTTCATTATTTAG
752 TTT
1 TTT
755 GTTTAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.14
17 22 0.76
18 3 0.10
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (17 bp):
TTTTTTTCATTATTTAG
Found at i:1274 original size:104 final size:106
Alignment explanation
Indices: 1066--1328 Score: 343
Period size: 104 Copynumber: 2.5 Consensus size: 106
1056 CGAGAAATTA
* * * * *** **
1066 TGCCCTAACGTGTTAGGTATGATTTTTCTTTGAACCTAAATAATCGAATATCCTATTTGGAACTG
1 TGCCCTAACATG-T-GGTGTGATTTTACCTTGAACCTAAATAATCGAATATCCTATTCAAAACCA
*
1131 AAAATGCTCAATATTCTGTTATTTTAGGGGATTTGAAAAATCG
64 AAAATGCTCAATATTCTGTTATTTTAAGGGATTTGAAAAATCG
* *
1174 TGTCCTAA-A-G-GGTGTGATTTTGCCTTGAACCTAAATAATCGAATATCCTATTCAAAACCAAA
1 TGCCCTAACATGTGGTGTGATTTTACCTTGAACCTAAATAATCGAATATCCTATTCAAAACCAAA
*
1236 TAATGCTCAATATTCTGTTATTTTAAGGGATTTTAAAAATCG
66 -AATGCTCAATATTCTGTTATTTTAAGGGATTTGAAAAATCG
1278 TGCCCTAACATGTTCGGTGTGATTTTACCTTGAACCTAAATAATCGAATAT
1 TGCCCTAACATG-T-GGTGTGATTTTACCTTGAACCTAAATAATCGAATAT
1329 TTCGTTTAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
103 44 0.33
104 46 0.34
105 1 0.01
106 2 0.01
108 7 0.05
109 35 0.26
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (106 bp):
TGCCCTAACATGTGGTGTGATTTTACCTTGAACCTAAATAATCGAATATCCTATTCAAAACCAAA
AATGCTCAATATTCTGTTATTTTAAGGGATTTGAAAAATCG
Found at i:3401 original size:16 final size:16
Alignment explanation
Indices: 3380--3415 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3370 TAACAAGGGA
*
3380 AAGAAGGGAGGAAGAG
1 AAGAAGAGAGGAAGAG
*
3396 AAGAAGAGAGGAATAG
1 AAGAAGAGAGGAAGAG
3412 AAGA
1 AAGA
3416 GAAATTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.03
Consensus pattern (16 bp):
AAGAAGAGAGGAAGAG
Found at i:3693 original size:93 final size:93
Alignment explanation
Indices: 3534--3707 Score: 339
Period size: 93 Copynumber: 1.9 Consensus size: 93
3524 TAATGTACTC
3534 AATTTTATACATTTGTCTTCCGTGCATGCAGCTGTATATTTATTAGTCAAACCAAATCAATGAGC
1 AATTTTATACATTTGTCTTCCGTGCATGCAGCTGTATATTTATTAGTCAAACCAAATCAATGAGC
3599 ATTAATTTTAATTAAAGAGAATGCATTG
66 ATTAATTTTAATTAAAGAGAATGCATTG
*
3627 AATTTTGTACATTTGTCTTCCGTGCATGCAGCTGTATATTTATTAGTCAAACCAAATCAATGAGC
1 AATTTTATACATTTGTCTTCCGTGCATGCAGCTGTATATTTATTAGTCAAACCAAATCAATGAGC
3692 ATTAATTTTAATTAAA
66 ATTAATTTTAATTAAA
3708 AAGATTTTAT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (93 bp):
AATTTTATACATTTGTCTTCCGTGCATGCAGCTGTATATTTATTAGTCAAACCAAATCAATGAGC
ATTAATTTTAATTAAAGAGAATGCATTG
Found at i:3716 original size:15 final size:15
Alignment explanation
Indices: 3696--3734 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3686 ATGAGCATTA
3696 ATTTTAATTAAAAAG
1 ATTTTAATTAAAAAG
*
3711 ATTTT-ATTAAAGAG
1 ATTTTAATTAAAAAG
*
3725 GTTTTAATTA
1 ATTTTAATTA
3735 TCCAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (15 bp):
ATTTTAATTAAAAAG
Found at i:4387 original size:25 final size:25
Alignment explanation
Indices: 4340--4387 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
4330 TTTAAAATTT
*
4340 AAAATTTATTTAAAAAGTCATAAGC
1 AAAATTTATTTAAAAAATCATAAGC
*
4365 AAAATTTA-TTACAAAAATTATAA
1 AAAATTTATTTA-AAAAATCATAA
4388 ACTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAATTTATTTAAAAAATCATAAGC
Found at i:5304 original size:12 final size:12
Alignment explanation
Indices: 5285--5366 Score: 68
Period size: 12 Copynumber: 7.2 Consensus size: 12
5275 TGTTTTCGTC
5285 GTTATTTTTGTT
1 GTTATTTTTGTT
*
5297 GTT-GTTTTGTT
1 GTTATTTTTGTT
5308 GTTATTTTTGTT
1 GTTATTTTTGTT
*
5320 GTT-TTTAATGTT
1 GTTATTT-TTGTT
**
5332 G----TTTTACT
1 GTTATTTTTGTT
*
5340 GTTATTTTGGTT
1 GTTATTTTTGTT
5352 GTTATTTTTGTT
1 GTTATTTTTGTT
5364 GTT
1 GTT
5367 CGGATGTTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
8 3 0.06
9 2 0.04
11 13 0.24
12 36 0.67
ACGTcount: A:0.09, C:0.01, G:0.20, T:0.71
Consensus pattern (12 bp):
GTTATTTTTGTT
Found at i:5320 original size:20 final size:20
Alignment explanation
Indices: 5295--5380 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 20
5285 GTTATTTTTG
5295 TTGTTGTTTTGTTGTTATTT
1 TTGTTGTTTTGTTGTTATTT
*
5315 TTGTTGTTTT-TAATGTTGTTT
1 TTGTTGTTTTGT--TGTTATTT
*
5336 TACTGTTATTTTGGTTGTTATTT
1 T--TGTTGTTTT-GTTGTTATTT
** *
5359 TTGTTGTTCGGATGTTATTT
1 TTGTTGTTTTGTTGTTATTT
5379 TT
1 TT
5381 TATACGTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 21 0.40
21 14 0.26
23 16 0.30
25 1 0.02
ACGTcount: A:0.09, C:0.02, G:0.20, T:0.69
Consensus pattern (20 bp):
TTGTTGTTTTGTTGTTATTT
Found at i:5325 original size:32 final size:31
Alignment explanation
Indices: 5289--5380 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
5279 TTCGTCGTTA
*
5289 TTTTTGTTGTTGTTTTGTTGTTATTTTTGTTG
1 TTTTT-TTGTTGTTTTGATGTTATTTTTGTTG
* *
5321 TTTTTAATGTTGTTTT-ACTGTTATTTTGGTTG
1 TTTTT-TTGTTGTTTTGA-TGTTATTTTTGTTG
**
5353 TTATTTTTGTTGTTCGGATGTTATTTTT
1 TT-TTTTTGTTGTTTTGATGTTATTTTT
5381 TATACGTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
32 45 0.92
33 4 0.08
ACGTcount: A:0.09, C:0.02, G:0.20, T:0.70
Consensus pattern (31 bp):
TTTTTTTGTTGTTTTGATGTTATTTTTGTTG
Done.