Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013997.1 Kokia drynarioides strain JFW-HI SEQ_129028, 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: 28177
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:6591 original size:64 final size:63
Alignment explanation
Indices: 6499--6670 Score: 281
Period size: 64 Copynumber: 2.7 Consensus size: 63
6489 TTATTTATTT
*
6499 ATTTATTTATCTATATTCATAAAATAATAAATAAATAATAAAACAAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAAC-AAAATTAATATTATTTTAC
* *
6563 ATTTATTTATTTATATTCATACAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAT
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
*
6626 ATTTATTTATTTATATTCATAAAAATAATGAATAAATAAATAAAA
1 ATTTATTTATTTATATTCAT-AAAATAATAAATAAAT-AATAAAA
6671 ATAATAAGAA
Statistics
Matches: 101, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
63 38 0.38
64 56 0.55
65 7 0.07
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (63 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
Found at i:6654 original size:53 final size:60
Alignment explanation
Indices: 6524--6642 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 60
6514 TTCATAAAAT
6524 AATAAATAAATAATAAAACAAAAATTAATATTATTTTACATTTATTTATTTATATTCATAC
1 AATAAATAAATAATAAAACAAAAATTAATATTATTTTACATTTATTTATTTATATT-ATAC
*
6585 AATAATAAATAAATAATAAAAC-AAAATTAATATTATTTTATATTTATTTATTTATATT
1 ---AATAAATAAATAATAAAACAAAAATTAATATTATTTTACATTTATTTATTTATATT
6643 CATAAAAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
63 35 0.65
64 19 0.35
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (60 bp):
AATAAATAAATAATAAAACAAAAATTAATATTATTTTACATTTATTTATTTATATTATAC
Found at i:6670 original size:21 final size:19
Alignment explanation
Indices: 6644--6688 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
6634 ATTTATATTC
*
6644 ATAAAAATAATGAATAAATAA
1 ATAAAAATAAT-AAGAAA-AA
6665 ATAAAAATAATAAGAAAAA
1 ATAAAAATAATAAGAAAAA
6684 ATAAA
1 ATAAA
6689 TTAGGTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 5 0.22
21 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
ATAAAAATAATAAGAAAAA
Found at i:7263 original size:40 final size:40
Alignment explanation
Indices: 7217--7625 Score: 366
Period size: 40 Copynumber: 10.3 Consensus size: 40
7207 ATTGAATTGT
* *
7217 TTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGAATAGTC
1 TTCAATCTGCCCTC-TGGTCGGGGTAAGAGATCGGATGGTC
** * * * *
7257 TTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGAATTG-C
1 TTCAATCTGCCCTCTGGTCGGGGTAAGAGATCGGATGGTC
* * *
7296 TTCAATCTGCCAC-ATGGTCAGGGTAAGAGATCAGATGGTC
1 TTCAATCTGCC-CTCTGGTCGGGGTAAGAGATCGGATGGTC
* * *** * *** *
7336 TTCAATCTACCCTCTAGTTAAGGTAAAAGATTAAATTG-C
1 TTCAATCTGCCCTCTGGTCGGGGTAAGAGATCGGATGGTC
*
7375 TTCAATCTACCC-CATGGTCGGGGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCTC-TGGTCGGGGTAAGAGATCGGATGGTC
* * ** * * *
7415 TTTAATCTACCCTCTGGTTAGGGTAAAAGATTGGATTG-C
1 TTCAATCTGCCCTCTGGTCGGGGTAAGAGATCGGATGGTC
*
7454 TTCAATCAGCCC-CATGGTCGGGGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCTC-TGGTCGGGGTAAGAGATCGGATGGTC
* * *
7494 TTCAATATGCCCTCTGGTCGAGGTAAAAGATCGGATGGTC
1 TTCAATCTGCCCTCTGGTCGGGGTAAGAGATCGGATGGTC
* * *
7534 TTCAATTTG-CCTCATGGTCGGGGTAAGAGATTGGTTGGTC
1 TTCAATCTGCCCTC-TGGTCGGGGTAAGAGATCGGATGGTC
* * *
7574 TTCAATCTACCCTCTAGTCGGGGTAAGAGATCGGTTGGTC
1 TTCAATCTGCCCTCTGGTCGGGGTAAGAGATCGGATGGTC
7614 TTCAATCTGCCC
1 TTCAATCTGCCC
7626 ATTTCAGCTT
Statistics
Matches: 299, Mismatches: 58, Indels: 24
0.78 0.15 0.06
Matches are distributed among these distances:
38 2 0.01
39 92 0.31
40 198 0.66
41 7 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
TTCAATCTGCCCTCTGGTCGGGGTAAGAGATCGGATGGTC
Found at i:7337 original size:79 final size:79
Alignment explanation
Indices: 7198--7588 Score: 541
Period size: 79 Copynumber: 4.9 Consensus size: 79
7188 ATAGTTTTAG
* * *
7198 GGGTAAAAGATTGAATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATAGTCTTCAAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
7263 CTGCCCTCTGGTTA
66 CTACCCTCTGGTTA
* * *
7277 GGGTAAAAGATTGAATTGCTTCAATCTGCCACATGGTCAGGGTAAGAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
7342 CTACCCTCTAGTTA
66 CTACCCTCTGGTTA
* * * *
7356 AGGTAAAAGATTAAATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
7421 CTACCCTCTGGTTA
66 CTACCCTCTGGTTA
* *
7435 GGGTAAAAGATTGGATTGCTTCAATCAGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* * *
7500 ATGCCCTCTGG-TC
66 CTACCCTCTGGTTA
* * * * * * *
7513 GAGGTAAAAGATCGGATGGTCTTCAATTTGCCTCATGGTCGGGGTAAGAGATTGGTTGGTCTTCA
1 G-GGTAAAAGATTGAATTG-CTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCA
7578 ATCTACCCTCT
64 ATCTACCCTCT
7589 AGTCGGGGTA
Statistics
Matches: 276, Mismatches: 34, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
78 2 0.01
79 225 0.82
80 49 0.18
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (79 bp):
GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
CTACCCTCTGGTTA
Found at i:7700 original size:50 final size:50
Alignment explanation
Indices: 7656--7789 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
7646 AGATTCATCC
7656 TTGAGACTTCAATCTACCCCTCTACAGCTTTAGGTGA-ATGAGATTCGCCA
1 TTGAGACTTCAATCTACCCCTCTACAGCTTTAGGT-ATATGAGATTCGCCA
* * * *
7706 TTGCGGCTTCAATCTGCCCCTTTACAGCTTTAGGTATATGAGATTCGCCA
1 TTGAGACTTCAATCTACCCCTCTACAGCTTTAGGTATATGAGATTCGCCA
* * * ** *
7756 TCGTGGCTTCAATCTATTCCTTTACAGCTTTAGG
1 TTGAGACTTCAATCTACCCCTCTACAGCTTTAGG
7790 GGTATAATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 73 0.99
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (50 bp):
TTGAGACTTCAATCTACCCCTCTACAGCTTTAGGTATATGAGATTCGCCA
Found at i:12614 original size:31 final size:31
Alignment explanation
Indices: 12568--12647 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
12558 CATCTTTCTC
12568 AAACTTT-T-AATGCATGAAAATGCGATACA
1 AAACTTTATGAATGCATGAAAATGCGATACA
* *
12597 AAACTTTATGAATGCATGAAAATGCGATGCG
1 AAACTTTATGAATGCATGAAAATGCGATACA
*
12628 AAA-TTTGATGAATACATGAA
1 AAACTTT-ATGAATGCATGAA
12648 TGCATATGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 7 0.16
30 4 0.09
31 34 0.76
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATGCGATACA
Found at i:21371 original size:51 final size:51
Alignment explanation
Indices: 21288--21422 Score: 216
Period size: 51 Copynumber: 2.6 Consensus size: 51
21278 CTATAAACGA
* **
21288 AAAGGTCCGATGATTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTACGGATT
* *
21339 AAAGGTCTGATGACTAAGTGTCATTGTCAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTACGGATT
*
21390 AAAGGTCCAATGACTAAGTGTCATTGTGAGTAA
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAA
21423 GTGTCATCGT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTACGGATT
Found at i:21425 original size:16 final size:16
Alignment explanation
Indices: 21404--21438 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21394 GTCCAATGAC
*
21404 TAAGTGTCATTGTGAG
1 TAAGTGTCATCGTGAG
21420 TAAGTGTCATCGTGAG
1 TAAGTGTCATCGTGAG
21436 TAA
1 TAA
21439 ATGAATCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.34
Consensus pattern (16 bp):
TAAGTGTCATCGTGAG
Found at i:21461 original size:67 final size:67
Alignment explanation
Indices: 21348--21486 Score: 206
Period size: 67 Copynumber: 2.1 Consensus size: 67
21338 TAAAGGTCTG
* * * *
21348 ATGACTAAGTGTCATTGTCAGTAAATGAATCCTTTACGGATTAAAGGTCCAATGACTAAGTGTCA
1 ATGAGTAAGTGTCATCGTCAGTAAATGAATCCTTTACGGATTAAAGGTCCAATAACTAAGTATCA
21413 TT
66 TT
* * * *
21415 GTGAGTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAACTAAGTATCA
1 ATGAGTAAGTGTCATCGTCAGTAAATGAATCCTTTACGGATTAAAGGTCCAATAACTAAGTATCA
21480 TT
66 TT
21482 ATGAG
1 ATGAG
21487 CAAATGAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (67 bp):
ATGAGTAAGTGTCATCGTCAGTAAATGAATCCTTTACGGATTAAAGGTCCAATAACTAAGTATCA
TT
Found at i:21497 original size:51 final size:51
Alignment explanation
Indices: 21420--21686 Score: 257
Period size: 51 Copynumber: 5.2 Consensus size: 51
21410 TCATTGTGAG
**
21420 TAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAAC
1 TAAGTGTCATTATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAAC
* * * * *
21471 TAAGTATCATTATGAGCAAATGAATCCTTTACGGATTAAATGTCTGATAAC
1 TAAGTGTCATTATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAAC
** * * *
21522 TAAGTGTCACCATGAGTAAATGAATCTTTTATGGACTAAAGGTCCGATGAC
1 TAAGTGTCATTATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAAC
* * * * * *
21573 TAAGTGTCATTGTGAGTAAATGAATCCATGATGGATTAAGGGTTCGATGAC
1 TAAGTGTCATTATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAAC
** ** * * ** *
21624 TTTGTGTCATCGTGAGTATATGAATTCCTATATGGAACAAGAGGTCCGATGAC
1 TAAGTGTCATTATGAGTAAATGAA-TCCTTTATGGATTAA-AGGTCCGATAAC
21677 TATA-TGTCAT
1 TA-AGTGTCAT
21687 CGTGAGTATT
Statistics
Matches: 174, Mismatches: 39, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
51 147 0.84
52 10 0.06
53 17 0.10
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (51 bp):
TAAGTGTCATTATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAAC
Found at i:21510 original size:118 final size:118
Alignment explanation
Indices: 21302--21530 Score: 350
Period size: 118 Copynumber: 1.9 Consensus size: 118
21292 GTCCGATGAT
* * * *
21302 TAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAGGTCTGATGACTAAGTGTCATTGTC
1 TAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATAACTAAGTATCATTATC
* *
21367 AGTAAATGAATCCTTTACGGATTAAAGGTCCAATGACTAAGTGTCATTGTGAG
66 AGCAAATGAATCCTTTACGGATTAAAGGTCCAATAACTAAGTGTCATTGTGAG
* * *
21420 TAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAACTAAGTATCATTATG
1 TAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATAACTAAGTATCATTATC
* **
21485 AGCAAATGAATCCTTTACGGATTAAATGTCTGATAACTAAGTGTCA
66 AGCAAATGAATCCTTTACGGATTAAAGGTCCAATAACTAAGTGTCA
21531 CCATGAGTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 99 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (118 bp):
TAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATAACTAAGTATCATTATC
AGCAAATGAATCCTTTACGGATTAAAGGTCCAATAACTAAGTGTCATTGTGAG
Found at i:21609 original size:102 final size:102
Alignment explanation
Indices: 21420--21694 Score: 313
Period size: 102 Copynumber: 2.7 Consensus size: 102
21410 TCATTGTGAG
* * * *
21420 TAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCGATAACTAAGTATCATTATG
1 TAAGTGTCATCGTGAGTAAATGAATCCTTTATGGACTAAAGGTCCGATGACTAAGTGTCATTGTG
* * * *
21485 AGCAAATGAATCCTTTACGGATTAAATG-TCTGATAAC
66 AGTAAATGAATCCATGACGGATTAAAGGTTC-GATAAC
* * *
21522 TAAGTGTCACCATGAGTAAATGAATCTTTTATGGACTAAAGGTCCGATGACTAAGTGTCATTGTG
1 TAAGTGTCATCGTGAGTAAATGAATCCTTTATGGACTAAAGGTCCGATGACTAAGTGTCATTGTG
* * *
21587 AGTAAATGAATCCATGATGGATTAAGGGTTCGATGAC
66 AGTAAATGAATCCATGACGGATTAAAGGTTCGATAAC
** * *
21624 TTTGTGTCATCGTGAGTATATGAATTCCTATATGGAAC-AAGAGGTCCGATGACTATA-TGTCAT
1 TAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGG-ACTAA-AGGTCCGATGACTA-AGTGTCAT
*
21687 CGTGAGTA
62 TGTGAGTA
21695 TTAAATGAAA
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
102 104 0.71
103 12 0.08
104 29 0.20
105 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.32
Consensus pattern (102 bp):
TAAGTGTCATCGTGAGTAAATGAATCCTTTATGGACTAAAGGTCCGATGACTAAGTGTCATTGTG
AGTAAATGAATCCATGACGGATTAAAGGTTCGATAAC
Done.