Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007831.1 Kokia drynarioides strain JFW-HI SEQ_122467, 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: 46041
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:7614 original size:3 final size:3
Alignment explanation
Indices: 7606--7635 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7596 ATTCGATCTT
7606 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7636 ATAACGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8359 original size:16 final size:16
Alignment explanation
Indices: 8338--8369 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8328 AAAAAAAAAT
8338 ATAAATAAACATGAAA
1 ATAAATAAACATGAAA
*
8354 ATAAATAAAGATGAAA
1 ATAAATAAACATGAAA
8370 TAAGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.19
Consensus pattern (16 bp):
ATAAATAAACATGAAA
Found at i:9261 original size:19 final size:19
Alignment explanation
Indices: 9216--9263 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
9206 ATTTTTATTT
*
9216 TTAAAAAT--CTATTTTTT
1 TTAAAAATCACTATTTTTC
9233 TTAAAAAAATCACTATTTTTC
1 TT--AAAAATCACTATTTTTC
9254 TTAAAAATCA
1 TTAAAAATCA
9264 AAACTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
19 14 0.54
21 10 0.38
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAAAATCACTATTTTTC
Found at i:9455 original size:51 final size:50
Alignment explanation
Indices: 9233--9465 Score: 163
Period size: 51 Copynumber: 4.6 Consensus size: 50
9223 TCTATTTTTT
* * *
9233 TTAAAAAAATCACTA-TTTTTCTTAAAAATCAAAACTTTTATTTTGAAATAA
1 TTAAAAAAATCACAACTTTAT-TTAAAAATCAAAACTTTT-TTTTAAAATAA
* * * ** *
9284 TTAAAAAAA-CATAACTTTGTTTAAATATTTAAACTTTTTCCTTTAAAATGA
1 TTAAAAAAATCACAACTTTATTTAAAAATCAAAACTTTTT--TTTAAAATAA
* ** *
9335 CTAAAAAACAT-A-ATTTTATATTTAAAAATCTAAACTTTCTTTTTAAAA-AA
1 TTAAAAAA-ATCACAACTT-TATTTAAAAATCAAAACTTT-TTTTTAAAATAA
** * * *
9385 AAAAAAAAAGTCACTACTTT-TCTTAAAAATCAAAACTTTTATTTCAAAATAG
1 TTAAAAAAA-TCACAACTTTAT-TTAAAAATCAAAACTTTT-TTTTAAAATAA
*
9437 TTAAAAAAATCAAAACTTTATTTAAAAAT
1 TTAAAAAAATCACAACTTTATTTAAAAAT
9466 TTTAAACTTT
Statistics
Matches: 141, Mismatches: 27, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
49 2 0.01
50 28 0.20
51 79 0.56
52 30 0.21
53 2 0.01
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (50 bp):
TTAAAAAAATCACAACTTTATTTAAAAATCAAAACTTTTTTTTAAAATAA
Found at i:12022 original size:51 final size:51
Alignment explanation
Indices: 11906--12143 Score: 262
Period size: 51 Copynumber: 4.6 Consensus size: 51
11896 TTTCATTTTA
** * * *
11906 TACTCACGATGACA-TATAGTCATCGGACCTCTTGGTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-CTTAATCCACAAAGG-ATTCATT
* ** * *
11959 TACTCACAATGACACAAAGTCATCGGACCCTTAATCCACCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCACAAAGGATTCATT
* ***
12010 TACTCACGATGACACTTAGTCATCGGACCTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCACAAAGGATTCATT
* * * * *
12061 TACTCACAATGACACTTAGTCATTGGACCTTTAATCCGCAAAGGAGTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCACAAAGGATTCATT
*
12112 TACTCACGATGACACTTAGTCATCAGACCCTT
1 TACTCACGATGACACTTAGTCATCGGACCCTT
12144 TCGTTTATAG
Statistics
Matches: 156, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
51 122 0.78
52 9 0.06
53 25 0.16
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTAATCCACAAAGGATTCATT
Found at i:12089 original size:102 final size:104
Alignment explanation
Indices: 11906--12140 Score: 305
Period size: 102 Copynumber: 2.3 Consensus size: 104
11896 TTTCATTTTA
** *
11906 TACTCACGATGACA-TATAGTCATCGGACCTCTTGGTCCATATAGGAATTCATATACTCACAATG
1 TACTCACGATGACACT-TAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACAATG
* * *
11970 ACACAAAGTCATCGGACCCTTAATCCACCATGGATTCATT
65 ACACAAAGTCATCGGACCCTTAATCCACAAAGGAGTCATT
** *
12010 TACTCACGATGACACTTAGTCATCGGACCT-TTAATCTGTAAAGG-ATTCATTTACTCACAATGA
1 TACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACAATGA
** * * *
12073 CACTTAGTCATTGGACCTTTAATCCGCAAAGGAGTCATT
66 CACAAAGTCATCGGACCCTTAATCCACAAAGGAGTCATT
*
12112 TACTCACGATGACACTTAGTCATCAGACC
1 TACTCACGATGACACTTAGTCATCGGACC
12141 CTTTCGTTTA
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
102 77 0.67
103 9 0.08
104 28 0.24
105 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (104 bp):
TACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACAATGA
CACAAAGTCATCGGACCCTTAATCCACAAAGGAGTCATT
Found at i:23005 original size:22 final size:23
Alignment explanation
Indices: 22977--23030 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
22967 AACCTTAAAT
22977 CTAACCCTATAAAATA-AAAACC
1 CTAACCCTATAAAATAGAAAACC
22999 CTAACCCTATAAAATAGAAAACC
1 CTAACCCTATAAAATAGAAAACC
*
23022 ATAACCCTA
1 CTAACCCTA
23031 AACAATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.19
Consensus pattern (23 bp):
CTAACCCTATAAAATAGAAAACC
Found at i:23570 original size:19 final size:20
Alignment explanation
Indices: 23543--23581 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
23533 ATTATTTTTT
*
23543 TTAATATTTAATTTTTTTAA
1 TTAATATTTAAATTTTTTAA
23563 TTAA-ATTTAAATTTTTTAA
1 TTAATATTTAAATTTTTTAA
23582 AAAAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATATTTAAATTTTTTAA
Found at i:23587 original size:19 final size:19
Alignment explanation
Indices: 23548--23588 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
23538 TTTTTTTAAT
* **
23548 ATTTAATTTTTTTAATTAA
1 ATTTAAATTTTTTAAAAAA
23567 ATTTAAATTTTTTAAAAAA
1 ATTTAAATTTTTTAAAAAA
23586 ATT
1 ATT
23589 GAAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATTTTTTAAAAAA
Found at i:24103 original size:14 final size:13
Alignment explanation
Indices: 24084--24122 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
24074 TTGTTTCACT
*
24084 GAAAATAGATTTTG
1 GAAAATA-ATTTTA
24098 GAAAATAATTCTTA
1 GAAAATAATT-TTA
24112 GAAAATAATTT
1 GAAAATAATTT
24123 ATTTTTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (13 bp):
GAAAATAATTTTA
Found at i:35582 original size:19 final size:19
Alignment explanation
Indices: 35559--35609 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
35549 TGAAAAACAA
*
35559 AAAAAAAATAAA-AAAATGAG
1 AAAAAGAATAAAGAAAA--AG
*
35579 AAAAAGAAGAAAGAAAAAG
1 AAAAAGAATAAAGAAAAAG
35598 AAAAAGAATAAA
1 AAAAAGAATAAA
35610 TTGCTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 10 0.37
21 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAAAGAATAAAGAAAAAG
Found at i:35586 original size:6 final size:6
Alignment explanation
Indices: 35550--35605 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
35540 TTAGTCACTT
* * **
35550 GAAAAA CAAAAA -AAAAA TAAAAA -AATGA GAAAAA GAAGAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAA-AAA GAAAAA
35597 GAAAAA GAA
1 GAAAAA GAA
35606 TAAATTGCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 8 0.19
6 28 0.67
7 6 0.14
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:35595 original size:12 final size:12
Alignment explanation
Indices: 35550--35605 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
35540 TTAGTCACTT
*
35550 GAAAAACAAAAA
1 GAAAAAGAAAAA
*
35562 -AAAAATAAAAA
1 GAAAAAGAAAAA
**
35573 -AATGAGAAAAA
1 GAAAAAGAAAAA
35584 GAAGAAAGAAAAA
1 GAA-AAAGAAAAA
35597 GAAAAAGAA
1 GAAAAAGAA
35606 TAAATTGCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 18 0.50
12 8 0.22
13 10 0.28
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (12 bp):
GAAAAAGAAAAA
Found at i:44041 original size:26 final size:25
Alignment explanation
Indices: 43992--44042 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
43982 TTCTAAAAAC
* **
43992 GAAATGAAAATAACTAGAGTTTAAA
1 GAAATGAAAATAACTAAAACTTAAA
44017 GAAATGAAAAATAACTAAAACTTAAA
1 GAAATG-AAAATAACTAAAACTTAAA
44043 TTACAAGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.22
Consensus pattern (25 bp):
GAAATGAAAATAACTAAAACTTAAA
Done.