Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013353.1 Kokia drynarioides strain JFW-HI SEQ_128376, 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: 75477
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:129 original size:30 final size:30
Alignment explanation
Indices: 73--129 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
63 TTTTATAAAT
*
73 AATTAATATTAAATATTTAGATATATTTAA
1 AATTAATATTAAATATTTAGAAATATTTAA
**
103 AATTAATATTTCATATATTA-AAATATT
1 AATTAATATTAAATAT-TTAGAAATATT
130 AACAAGAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.87
31 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AATTAATATTAAATATTTAGAAATATTTAA
Found at i:7938 original size:6 final size:6
Alignment explanation
Indices: 7916--7950 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
7906 AAACTGCACA
* *
7916 TGTATC TGTTTC TGTATC CGTATC TGTATC TGTAT
1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTAT
7951 GTGAATCTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (6 bp):
TGTATC
Found at i:14170 original size:92 final size:92
Alignment explanation
Indices: 14013--14193 Score: 353
Period size: 92 Copynumber: 2.0 Consensus size: 92
14003 GTACTTCTTC
14013 TTAACTCCCTCAAACTTATTTTCAGAGAATATTCTGGATCGAATGAGTCTATTGTTTGGGACAAT
1 TTAACTCCCTCAAACTTATTTTCAGAGAATATTCTGGATCGAATGAGTCTATTGTTTGGGACAAT
14078 TTAAAGACAAATATAAGAGAAGGCTTT
66 TTAAAGACAAATATAAGAGAAGGCTTT
14105 TTAACTCCCTCAAACTTATTTTCAGAGAATATTCTGGATCGAATGAGTCTATTGTTTGGGACAAT
1 TTAACTCCCTCAAACTTATTTTCAGAGAATATTCTGGATCGAATGAGTCTATTGTTTGGGACAAT
*
14170 TTAAAGACAATTATAAGAGAAGGC
66 TTAAAGACAAATATAAGAGAAGGC
14194 ATTACTTATT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (92 bp):
TTAACTCCCTCAAACTTATTTTCAGAGAATATTCTGGATCGAATGAGTCTATTGTTTGGGACAAT
TTAAAGACAAATATAAGAGAAGGCTTT
Found at i:15937 original size:27 final size:26
Alignment explanation
Indices: 15890--15945 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
15880 TAACAGCCCG
***
15890 TTTTTTAGTGGTGTTGGAAATAATGA
1 TTTTTTAGTGGTGTCAAAAATAATGA
*
15916 TTTTTTCAGTGGTGTCAAAAATAGTGA
1 TTTTTT-AGTGGTGTCAAAAATAATGA
15943 TTT
1 TTT
15946 CGGGATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (26 bp):
TTTTTTAGTGGTGTCAAAAATAATGA
Found at i:19460 original size:30 final size:30
Alignment explanation
Indices: 19425--19549 Score: 110
Period size: 30 Copynumber: 4.2 Consensus size: 30
19415 ATTTTATTTT
* *
19425 AAAATTCAAACTTGACCCCTAATCTTTCCA
1 AAAATTCAAATTTGACCCCTAAACTTTCCA
* * *
19455 AAAATTCTAATTTG-GCCCTCAAAATTTCCA
1 AAAATTCAAATTTGACCCCT-AAACTTTCCA
** * * *
19485 AAAATTTGAATTTAACCCCTGACCTTTCCA
1 AAAATTCAAATTTGACCCCTAAACTTTCCA
* * *
19515 AAGATTTAAATTT-AACCCTAAACTTTCCA
1 AAAATTCAAATTTGACCCCTAAACTTTCCA
19544 AAAATT
1 AAAATT
19550 TGAATTTGTC
Statistics
Matches: 75, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
29 22 0.29
30 49 0.65
31 4 0.05
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAATTCAAATTTGACCCCTAAACTTTCCA
Found at i:19473 original size:29 final size:29
Alignment explanation
Indices: 19441--19556 Score: 126
Period size: 30 Copynumber: 3.9 Consensus size: 29
19431 CAAACTTGAC
* **
19441 CCCTAATCTTTCCAAAAATTCT-AATTTGG
1 CCCTAAACTTTCCAAAAATT-TGAATTTAA
*
19470 CCCTCAAAATTTCCAAAAATTTGAATTTAA
1 CCCT-AAACTTTCCAAAAATTTGAATTTAA
* * * *
19500 CCCCTGACCTTTCCAAAGATTTAAATTTAA
1 -CCCTAAACTTTCCAAAAATTTGAATTTAA
19530 CCCTAAACTTTCCAAAAATTTGAATTT
1 CCCTAAACTTTCCAAAAATTTGAATTT
19557 GTCCCCCAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 28 0.39
30 39 0.55
31 4 0.06
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTTGAATTTAA
Found at i:19527 original size:60 final size:59
Alignment explanation
Indices: 19439--19556 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
19429 TTCAAACTTG
* **
19439 ACCCCTAATCTTTCCAAAAATTCTAATTTGGCCCTCAAAATTTCCAAAAATTTGAATTTA
1 ACCCCTAACCTTTCCAAAAATTCTAATTTAACCCT-AAAATTTCCAAAAATTTGAATTTA
* * *
19499 ACCCCTGACCTTTCCAAAGATT-TAAATTTAACCCTAAACTTTCCAAAAATTTGAATTT
1 ACCCCTAACCTTTCCAAAAATTCT-AATTTAACCCTAAAATTTCCAAAAATTTGAATTT
19557 GTCCCCCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 23 0.45
60 28 0.55
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (59 bp):
ACCCCTAACCTTTCCAAAAATTCTAATTTAACCCTAAAATTTCCAAAAATTTGAATTTA
Found at i:27343 original size:16 final size:17
Alignment explanation
Indices: 27324--27357 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27314 AAAATGATGA
27324 AATGA-AAAAAAAATGC
1 AATGATAAAAAAAATGC
*
27340 AATGATAATAAAAATGC
1 AATGATAAAAAAAATGC
27357 A
1 A
27358 TTAAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (17 bp):
AATGATAAAAAAAATGC
Found at i:38631 original size:19 final size:19
Alignment explanation
Indices: 38594--38631 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38584 GGGTTTAGGA
*
38594 AAAATAAATTTTTGAGAGG
1 AAAATAAAGTTTTGAGAGG
38613 AAAATAAAAGTTTTG-GAGG
1 AAAAT-AAAGTTTTGAGAGG
38632 GAAAGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
AAAATAAAGTTTTGAGAGG
Found at i:38634 original size:20 final size:19
Alignment explanation
Indices: 38594--38635 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
38584 GGGTTTAGGA
*
38594 AAAATAAATTTTTGAGAGG
1 AAAATAAATTTTGGAGAGG
38613 AAAATAAAAGTTTTGGAG-GG
1 AAAAT-AAA-TTTTGGAGAGG
38633 AAA
1 AAA
38636 GTAATAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (19 bp):
AAAATAAATTTTGGAGAGG
Found at i:42405 original size:31 final size:29
Alignment explanation
Indices: 42341--42405 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
42331 TCAAGTTACA
* *
42341 TTTTAATCACTTATATTTGAAATGTTACG
1 TTTTAATCACTTACATTTGAAATGTAACG
* *
42370 TTTTAATCACTTACGTTATCGAATTGTAACG
1 TTTTAATCACTTACATT-T-GAAATGTAACG
42401 TTTTA
1 TTTTA
42406 GTCATTGAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.50
30 1 0.03
31 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (29 bp):
TTTTAATCACTTACATTTGAAATGTAACG
Found at i:51792 original size:29 final size:29
Alignment explanation
Indices: 51733--51792 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
51723 TATGGTTTAA
* * *
51733 TGTGTAATTATATACATGAACTTTGATTT
1 TGTGCAATTATATACATGAAATTTGAATT
* *
51762 TGTGCAATTTTATACATGAAATTTTAATT
1 TGTGCAATTATATACATGAAATTTGAATT
51791 TG
1 TG
51793 ATCAAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (29 bp):
TGTGCAATTATATACATGAAATTTGAATT
Found at i:56360 original size:18 final size:18
Alignment explanation
Indices: 56337--56391 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
56327 AATTTATATG
56337 AAAATCC-CAACAGGATTT
1 AAAATCCTCAA-AGGATTT
**
56355 AAAATCCTTGAAGGATTT
1 AAAATCCTCAAAGGATTT
**
56373 AAAATCCTTGAAGGATTT
1 AAAATCCTCAAAGGATTT
56391 A
1 A
56392 GAGTTTCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 33 0.97
19 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (18 bp):
AAAATCCTCAAAGGATTT
Found at i:57942 original size:326 final size:326
Alignment explanation
Indices: 57349--58004 Score: 1125
Period size: 326 Copynumber: 2.0 Consensus size: 326
57339 TAATGCAACA
*
57349 TGTATAGCTCAATTGAAGAGTGGTTACATAAAAGGTGACAGGACGAAACATATTTCACCAAAATT
1 TGTATAGCTCAATTGAAGAGTGGTTACATAAAAGGTGACAGAACGAAACATATTTCACCAAAATT
57414 ATTTTTCACTCATGATATTGAGAAGAAAGGTGACATAAAAGTTCAACAAATTCATTCTAGTGATA
66 ATTTTTCACTCATGATATTGAGAAGAAAGGTGACATAAAAGTTCAACAAATTCATTCTAGTGATA
* *
57479 ATTTAGCAGATCTTTTTACCAAAACACTGTCAACTTCAACATTTGAAAGACTACTAGATAAGATT
131 ATTTAGCAGATCTTTTTACCAAAACACTATCAACTTCAACATTTGAAAGACTACTAGATAAGACT
* ***
57544 AGAATGTGTCGACTCCAAGATATAATACGATGTTGTCATTAGGGGAGTCTAAAATACGTTGTACT
196 AGAATGTGTCGACTCAAAGATATAATACGATGTTGTCATTAGGGGAGTCTAAAATACGCCATACT
57609 CTTTTCCTTTAACCAAGGTTTTGTCCCACTAAGTTTTCTTGGTAAAAGGTTTTTAACGAGGTAGC
261 CTTTTCCTTTAACCAAGGTTTTGTCCCACTAAGTTTTCTTGGTAAAAGGTTTTTAACGAGGTAGC
57674 T
326 T
* *
57675 TGTATAGCTCAATTGAAGAGTGGTTACATAAAATGTGACAGAACGAAACGTATTTCACCAAAATT
1 TGTATAGCTCAATTGAAGAGTGGTTACATAAAAGGTGACAGAACGAAACATATTTCACCAAAATT
* * *
57740 ATTTTTCACTCATGATCTTGAGGAGAAAGGTGACA-AAGAAGTTCAACAAATTCGTTCTAGTGAT
66 ATTTTTCACTCATGATATTGAGAAGAAAGGTGACATAA-AAGTTCAACAAATTCATTCTAGTGAT
57804 AATTTAGCAGATCTTTTTACCAAAACACTATCAACTTCAACATTTGAAAGACTACTAGATAAGAC
130 AATTTAGCAGATCTTTTTACCAAAACACTATCAACTTCAACATTTGAAAGACTACTAGATAAGAC
* *
57869 TGGAATGTGTCGACTCAAAGATATAATATGATGTTGTCATTAGGGGAGTCTAAAATACGCCATAC
195 TAGAATGTGTCGACTCAAAGATATAATACGATGTTGTCATTAGGGGAGTCTAAAATACGCCATAC
* ** * *
57934 TCTTTTCCTTTAACCAAGTTTTTGTCCCACTGGGTTTTCTTGGTGAAAGGTTTTTACCGAGGTAG
260 TCTTTTCCTTTAACCAAGGTTTTGTCCCACTAAGTTTTCTTGGTAAAAGGTTTTTAACGAGGTAG
57999 CT
325 CT
58001 TGTA
1 TGTA
58005 ATAGGAGATT
Statistics
Matches: 310, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
325 2 0.01
326 308 0.99
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (326 bp):
TGTATAGCTCAATTGAAGAGTGGTTACATAAAAGGTGACAGAACGAAACATATTTCACCAAAATT
ATTTTTCACTCATGATATTGAGAAGAAAGGTGACATAAAAGTTCAACAAATTCATTCTAGTGATA
ATTTAGCAGATCTTTTTACCAAAACACTATCAACTTCAACATTTGAAAGACTACTAGATAAGACT
AGAATGTGTCGACTCAAAGATATAATACGATGTTGTCATTAGGGGAGTCTAAAATACGCCATACT
CTTTTCCTTTAACCAAGGTTTTGTCCCACTAAGTTTTCTTGGTAAAAGGTTTTTAACGAGGTAGC
T
Found at i:60033 original size:20 final size:20
Alignment explanation
Indices: 60008--60045 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59998 CATTAATTAA
60008 AATTTTGTGG-TTAAATTGGG
1 AATTTTG-GGATTAAATTGGG
60028 AATTTTGGGATTAAATTG
1 AATTTTGGGATTAAATTG
60046 TTTAGTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (20 bp):
AATTTTGGGATTAAATTGGG
Found at i:68758 original size:195 final size:193
Alignment explanation
Indices: 68384--68825 Score: 462
Period size: 195 Copynumber: 2.3 Consensus size: 193
68374 TACCAGAACT
* * * * * * * *
68384 CGATGTTGCTCACACGAGCTGTCGAGGAGTTGCAACATATGGGGCACCTTAACCATTGGTACGAT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATAT-GCGTACCTCAGCCATTGATACGAT
* * ** *
68449 GTCTGTCTATATAATTGTCTCCTAACGATGCTGCTCACATGAGCTGTCAGGTGTATGCACTTATG
65 ATCTGTCTATATAATTGTCTCCTAACGATGCTGCTCACACGAGCTGTCAGGAATATGCACTTAAG
* * * ** *
68514 TATAAGTCTCAGCCATCTTAGGGCCTATAATCCATTTTAGGACTCATATCTCTTTTTTCGATTCA
130 CATAAATCTCAGCCATCGTAGGAACTATAATCCATTTTAGGACTCATATCTCTTTTTT-GACTCA
* * *
68579 TGATGCTGCTCACACAAGCTGTCGAGGACTCGCAACATATGCAGTACCTCAGCCATTGATACGGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGC-GTACCTCAGCCATTGATACGAT
* * * *
68644 ATTTGTGC-ATATAATTGT-TCCTTAACGATTCTGCTCACACGAGCTAT-TGAGAATATGCA-TT
65 ATCTGT-CTATATAATTGTCTCC-TAACGATGCTGCTCACACGAGCTGTCAG-GAATATGCACTT
*
68705 CAAGCATAAATCT-AGCCATCGTAGGAACTATAATCCATTTTAGGATTTCATATCTCTTTTTTGA
127 -AAGCATAAATCTCAGCCATCGTAGGAACTATAATCCATTTTAGGA-CTCATATCTCTTTTTTGA
68769 CTCA
190 CTCA
* ** * * * *
68773 CGGTGCCACTCACATGAGCTATCAAGGACTCGTAACATATGCGATACCTCAGC
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCG-TACCTCAGC
68826 GTCAGTTTCA
Statistics
Matches: 204, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
193 1 0.00
194 83 0.41
195 119 0.58
196 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (193 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGTACCTCAGCCATTGATACGATA
TCTGTCTATATAATTGTCTCCTAACGATGCTGCTCACACGAGCTGTCAGGAATATGCACTTAAGC
ATAAATCTCAGCCATCGTAGGAACTATAATCCATTTTAGGACTCATATCTCTTTTTTGACTCA
Found at i:73473 original size:28 final size:28
Alignment explanation
Indices: 73436--73512 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
73426 TTTAGAGTTC
73436 GCCACAAAGGTTCACTTTACAAAGTATA
1 GCCACAAAGGTTCACTTTACAAAGTATA
73464 GCCACAAAGGTTCACTTTACAAAGTATA
1 GCCACAAAGGTTCACTTTACAAAGTATA
73492 GCCACAAAGGCTTC-CTTTACA
1 GCCACAAAGG-TTCACTTTACA
73513 GAATTTAAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 45 0.94
29 3 0.06
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (28 bp):
GCCACAAAGGTTCACTTTACAAAGTATA
Done.