Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014121.1 Kokia drynarioides strain JFW-HI SEQ_129154, 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: 20623
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Found at i:1352 original size:18 final size:18
Alignment explanation
Indices: 1331--1437 Score: 64
Period size: 18 Copynumber: 5.9 Consensus size: 18
1321 AAATTTATTA
1331 TTTTAGAATTTTTTAAAT
1 TTTTAGAATTTTTTAAAT
*
1349 TTTT-TAATTTATTTATATAT
1 TTTTAGAATTT-TTTA-A-AT
* *
1369 TCTTAAGAATTTTTT-TAT
1 T-TTTAGAATTTTTTAAAT
** *
1387 TTTTA-AA-AATATAAA-
1 TTTTAGAATTTTTTAAAT
1402 TTTTAGAATTTTTATAAAT
1 TTTTAGAATTTTT-TAAAT
1421 ATTTT-GAATTTTTTAAA
1 -TTTTAGAATTTTTTAAA
1438 ATTATTTTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 22
0.66 0.12 0.22
Matches are distributed among these distances:
15 7 0.11
16 5 0.08
17 9 0.14
18 19 0.29
19 9 0.14
20 7 0.11
21 5 0.08
22 5 0.08
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTTAGAATTTTTTAAAT
Found at i:1431 original size:19 final size:19
Alignment explanation
Indices: 1396--1452 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
1386 TTTTTAAAAA
*
1396 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
1414 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
1433 T-TAAAATTATTTTAAATTTT
1 TAT-AAA-TATTTTGAATTTT
1453 CTGTAAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 14 0.41
20 12 0.35
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:1433 original size:20 final size:20
Alignment explanation
Indices: 1396--1452 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1386 TTTTTAAAAA
*
1396 TATAAAT-TTTAGAA-TTTT
1 TATAAATATTTTGAATTTTT
1414 TATAAATATTTTGAATTTTT
1 TATAAATATTTTGAATTTTT
*
1434 TA-AAATTATTTTAAATTTT
1 TATAAA-TATTTTGAATTTT
1453 CTGTAAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.21
19 9 0.26
20 18 0.53
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TATAAATATTTTGAATTTTT
Found at i:1995 original size:18 final size:19
Alignment explanation
Indices: 1972--2007 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1962 TAATGTTTTC
*
1972 ATTTTTTAAAAT-AAAAAT
1 ATTTTTGAAAATGAAAAAT
1990 ATTTTTGAAAATGAAAAA
1 ATTTTTGAAAATGAAAAA
2008 GAAAAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
ATTTTTGAAAATGAAAAAT
Found at i:2357 original size:19 final size:19
Alignment explanation
Indices: 2333--2370 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2323 ATTGCACATT
*
2333 AAATCAAAATTCATGTATA
1 AAATCAAAATTCATATATA
2352 AAATCAAAATTCATATATA
1 AAATCAAAATTCATATATA
2371 GTTTATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATCAAAATTCATATATA
Found at i:4707 original size:102 final size:102
Alignment explanation
Indices: 4522--4712 Score: 276
Period size: 102 Copynumber: 1.9 Consensus size: 102
4512 TATTATTAAT
* * *
4522 TAATATTATTTATTTGGATGCAATAGTAAAGTACATCTCACCCTTAAGAAAAAATATAAATTTAA
1 TAATATTACTTATTTGGATGCAATAGTAAAATACATCTCACCCTTAAGAAAAAATATAAATTCAA
* *
4587 ATTTTAAAGACGATATTAATAGAAAAATACAACAACA
66 ATTTTAAAAACGACATTAATAGAAAAATACAACAACA
* * * * *
4624 TAATATTACTTATTTGGATGCAATGGTAAAATATATCTCACCCTTAA-AAGAAAATATGAGTTCG
1 TAATATTACTTATTTGGATGCAATAGTAAAATACATCTCACCCTTAAGAA-AAAATATAAATTCA
4688 AATTTTAAAAACGACATTAATAGAA
65 AATTTTAAAAACGACATTAATAGAA
4713 GAAACAATCA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 2 0.03
102 76 0.97
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (102 bp):
TAATATTACTTATTTGGATGCAATAGTAAAATACATCTCACCCTTAAGAAAAAATATAAATTCAA
ATTTTAAAAACGACATTAATAGAAAAATACAACAACA
Found at i:17892 original size:475 final size:475
Alignment explanation
Indices: 17002--17952 Score: 1884
Period size: 475 Copynumber: 2.0 Consensus size: 475
16992 GCGCTAATTT
17002 CTCTCGCTCTACATTGGTGGATAAAGCACATCAGTCGCGCGGTCCATTGGGTGAGAGCTAATTTG
1 CTCTCGCTCTACATTGGTGGATAAAGCACATCAGTCGCGCGGTCCATTGGGTGAGAGCTAATTTG
17067 TTTTTAAATCTTATAAAAATTCCCTAAATTATTATTTTTATTATTATTAATGACAAAAGTGCATA
66 TTTTTAAATCTTATAAAAATTCCCTAAATTATTATTTTTATTATTATTAATGACAAAAGTGCATA
17132 TTTAAAATTTAATTTAAAAAACAAAATTTACTTTAAATATAATTAAAAAGGACTTTTGGAACTTA
131 TTTAAAATTTAATTTAAAAAACAAAATTTACTTTAAATATAATTAAAAAGGACTTTTGGAACTTA
17197 AAAAACTAACTTACAACTCAAATTTTCTATATATACTTCCGTACCTATTTTTATGTTATATATAT
196 AAAAACTAACTTACAACTCAAATTTTCTATATATACTTCCGTACCTATTTTTATGTTATATATAT
17262 CATTCATATCTAATCTAATATATACACTAAAGTAATATATTGAAGCAATTTCGGAAATTTCATGT
261 CATTCATATCTAATCTAATATATACACTAAAGTAATATATTGAAGCAATTTCGGAAATTTCATGT
17327 TCAATGTCAGTTCATAGCAGAAAATTGAAATTATGTAAATGTGTTGGGAGAAATTTTTAGGTTTT
326 TCAATGTCAGTTCATAGCAGAAAATTGAAATTATGTAAATGTGTTGGGAGAAATTTTTAGGTTTT
*
17392 TTGGGGCATTCTAAGATGTATAAATATCAAATATGAGAAGAGGGGTGTAAGTCGTCATAGAATAT
391 TTGGGGCATTCTAAGACGTATAAATATCAAATATGAGAAGAGGGGTGTAAGTCGTCATAGAATAT
17457 TGAAGAAAACAACGGGAAAA
456 TGAAGAAAACAACGGGAAAA
17477 CTCTCGCTCTACATTGGTGGATAAAGCACATCAGTCGCGCGGTCCATTGGGTGAGAGCTAATTTG
1 CTCTCGCTCTACATTGGTGGATAAAGCACATCAGTCGCGCGGTCCATTGGGTGAGAGCTAATTTG
17542 TTTTTAAATCTTATAAAAATTCCCTAAATTATTATTTTTATTATTATTAATGACAAAAGTGCATA
66 TTTTTAAATCTTATAAAAATTCCCTAAATTATTATTTTTATTATTATTAATGACAAAAGTGCATA
17607 TTTAAAATTTAATTTAAAAAACAAAATTTACTTTAAATATAATTAAAAAGGACTTTTGGAACTTA
131 TTTAAAATTTAATTTAAAAAACAAAATTTACTTTAAATATAATTAAAAAGGACTTTTGGAACTTA
17672 AAAAACTAACTTACAACTCAAATTTTCTATATATACTTCCGTACCTATTTTTATGTTATATATAT
196 AAAAACTAACTTACAACTCAAATTTTCTATATATACTTCCGTACCTATTTTTATGTTATATATAT
17737 CATTCATATCTAATCTAATATATACACTAAAGTAATATATTGAAGCAATTTCGGAAATTTCATGT
261 CATTCATATCTAATCTAATATATACACTAAAGTAATATATTGAAGCAATTTCGGAAATTTCATGT
*
17802 TCAATGTCAGTTCATAGCAGAAAATTGAAATTATGTAAATGTGTTGGGAGAAATTTTTTGGTTTT
326 TCAATGTCAGTTCATAGCAGAAAATTGAAATTATGTAAATGTGTTGGGAGAAATTTTTAGGTTTT
17867 TTGGGGCATTCTAAGACGTATAAATATCAAATATGAGAAGAGGGGTGTAAGTCGTCATAGAATAT
391 TTGGGGCATTCTAAGACGTATAAATATCAAATATGAGAAGAGGGGTGTAAGTCGTCATAGAATAT
17932 TGAAGAAAACAACGGGAAAA
456 TGAAGAAAACAACGGGAAAA
17952 C
1 C
17953 ACCATTGAAG
Statistics
Matches: 474, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
475 474 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (475 bp):
CTCTCGCTCTACATTGGTGGATAAAGCACATCAGTCGCGCGGTCCATTGGGTGAGAGCTAATTTG
TTTTTAAATCTTATAAAAATTCCCTAAATTATTATTTTTATTATTATTAATGACAAAAGTGCATA
TTTAAAATTTAATTTAAAAAACAAAATTTACTTTAAATATAATTAAAAAGGACTTTTGGAACTTA
AAAAACTAACTTACAACTCAAATTTTCTATATATACTTCCGTACCTATTTTTATGTTATATATAT
CATTCATATCTAATCTAATATATACACTAAAGTAATATATTGAAGCAATTTCGGAAATTTCATGT
TCAATGTCAGTTCATAGCAGAAAATTGAAATTATGTAAATGTGTTGGGAGAAATTTTTAGGTTTT
TTGGGGCATTCTAAGACGTATAAATATCAAATATGAGAAGAGGGGTGTAAGTCGTCATAGAATAT
TGAAGAAAACAACGGGAAAA
Found at i:19064 original size:15 final size:14
Alignment explanation
Indices: 19017--19068 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
19007 TTTCAGGAAT
19017 AACTATGTTTAGAAC
1 AACT-TGTTTAGAAC
*
19032 AATCATTGTTTGGAAC
1 AA-C-TTGTTTAGAAC
19048 AACTTGTATTAGAAC
1 AACTTGT-TTAGAAC
19063 AA-TTGT
1 AACTTGT
19069 GTTATTCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 12 0.38
17 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (14 bp):
AACTTGTTTAGAAC
Found at i:19992 original size:39 final size:40
Alignment explanation
Indices: 19949--20031 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
19939 AGTAACAGCG
* *
19949 TTTTTCCATAAACGCCGCAAAAGGTAAAGCAATAGCTGCT
1 TTTTTCCAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
**
19989 TTTTTTTAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
1 TTTTTCCAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
20029 TTT
1 TTT
20032 GTAGGAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (40 bp):
TTTTTCCAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
Found at i:20098 original size:41 final size:40
Alignment explanation
Indices: 19998--20232 Score: 177
Period size: 41 Copynumber: 5.8 Consensus size: 40
19988 TTTTTTTTAA
* * * * **
19998 AAACGCCGCAAAAGGT-AAAGCAATAGCGGCTTTTGTAGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAATAGG
* *
20037 AAAAATGCCGCTAAAAGTCAGAGCATTAGCGGCGTTAATGAGG
1 --AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAAT-AGG
** *
20080 AAACGCCGCTAAAGGTCAGAGCATTAGCAACGTTTATGAGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAAT-AGG
* * * * *
20121 AAACACCACTAAAGGTCAGAGCATTAGCGACGTTTACTAGA
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCG-TTAATAGG
* * * * *
20162 AAACGCTGCTAAAGGTAAGAGCATTAGTGGTGTTTATAGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAATAGG
* * *
20202 AAAAACACCGCTAAAGGTTA-AGCAATAGCGG
1 --AAACGCCGCTAAAGGTCAGAGCATTAGCGG
20233 GATTTTCCCA
Statistics
Matches: 155, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
40 5 0.03
41 114 0.74
42 33 0.21
43 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (40 bp):
AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAATAGG
Found at i:20231 original size:82 final size:83
Alignment explanation
Indices: 19997--20219 Score: 240
Period size: 82 Copynumber: 2.7 Consensus size: 83
19987 CTTTTTTTTA
* * * ** *
19997 AAAACGCCGCAAAAGGTAA-AGCAATAGCGGCT-TTTGTAGGAAAAATGCCGCTAAAAGTCAGAG
1 AAAACGCCGCTAAAGGTAAGAGCATTAGCGG-TGTTTATAGGAAAAACACCGCTAAAGGTCAGAG
*
20060 CATTAGCGGCGTTAATGAG
65 CATTAGCGACGTTAATGAG
* * *** *
20079 GAAACGCCGCTAAAGGTCAGAGCATTAGCAACGTTTATGAGG--AAACACCACTAAAGGTCAGAG
1 AAAACGCCGCTAAAGGTAAGAGCATTAGCGGTGTTTAT-AGGAAAAACACCGCTAAAGGTCAGAG
*
20142 CATTAGCGACGTTTACT-AG
65 CATTAGCGACG-TTAATGAG
* *
20161 AAAACGCTGCTAAAGGTAAGAGCATTAGTGGTGTTTATAGGAAAAACACCGCTAAAGGT
1 AAAACGCCGCTAAAGGTAAGAGCATTAGCGGTGTTTATAGGAAAAACACCGCTAAAGGT
20220 TAAGCAATAG
Statistics
Matches: 113, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
81 3 0.03
82 76 0.67
83 31 0.27
84 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (83 bp):
AAAACGCCGCTAAAGGTAAGAGCATTAGCGGTGTTTATAGGAAAAACACCGCTAAAGGTCAGAGC
ATTAGCGACGTTAATGAG
Found at i:20562 original size:31 final size:28
Alignment explanation
Indices: 20526--20605 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 28
20516 AATTAAATCA
20526 AAATTAAAGTTTCGTGTATACATGTGAACC
1 AAATTAAAGTTTCGTGTATA-AT-TGAACC
* * *
20556 ATAATTAGAAATTCACGTGTATAATTGCACC
1 A-AATTA-AAGTT-TCGTGTATAATTGAACC
*
20587 AAATTAAAG-TTCATGTATA
1 AAATTAAAGTTTCGTGTATA
20606 TAATTGCACA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 7 0.17
28 1 0.02
29 2 0.05
30 6 0.15
31 11 0.27
32 6 0.15
33 8 0.20
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (28 bp):
AAATTAAAGTTTCGTGTATAATTGAACC
Found at i:20607 original size:29 final size:29
Alignment explanation
Indices: 20526--20614 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
20516 AATTAAATCA
* * *
20526 AAATTAAAGTTTCGTGTATA-CATGTGAACC
1 AAATTAAAG-TTCATGTATATAAT-TGCACC
* * *
20556 ATAATTAGAAATTCACGTGTATAATTGCACC
1 A-AATTA-AAGTTCATGTATATAATTGCACC
20587 AAATTAAAGTTCATGTATATAATTGCAC
1 AAATTAAAGTTCATGTATATAATTGCAC
20615 ATTAAATCA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
29 19 0.40
30 6 0.13
31 18 0.38
32 4 0.09
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATATAATTGCACC
Done.