Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013366.1 Kokia drynarioides strain JFW-HI SEQ_128389, 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: 41348
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1713 original size:42 final size:42
Alignment explanation
Indices: 1666--1747 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
1656 ACGCACAGTG
1666 TTAAAAAGAAACATCTTTTAAAGTAAGGTAACCATGGAAGTC
1 TTAAAAAGAAACATCTTTTAAAGTAAGGTAACCATGGAAGTC
1708 TTAAAAAGAAACATCTTTTAAAGTAAGGTAACCATGGAAG
1 TTAAAAAGAAACATCTTTTAAAGTAAGGTAACCATGGAAG
1748 GGGGAAGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (42 bp):
TTAAAAAGAAACATCTTTTAAAGTAAGGTAACCATGGAAGTC
Found at i:5512 original size:31 final size:31
Alignment explanation
Indices: 5474--5587 Score: 104
Period size: 32 Copynumber: 3.6 Consensus size: 31
5464 AATTTTGGAT
* *
5474 CCTTAAAAATTGAAGAAAATTTTTTTAGATC
1 CCTTAAAAATTGAAAAAAATTTTTTTAGACC
* * *
5505 CCTTAAAAGTTGGTAAAACAATTTTTTGAG-CC
1 CCTTAAAAATT-G-AAAAAAATTTTTTTAGACC
** * * *
5537 CCTTAAAACCTGAAAAAAATGATTTTTGGGCC
1 CCTTAAAAATTGAAAAAAAT-TTTTTTAGACC
5569 CCTTAAAAATTGAAAAAAA
1 CCTTAAAAATTGAAAAAAA
5588 ATTTGGACCC
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
30 7 0.11
31 16 0.24
32 30 0.45
33 13 0.20
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (31 bp):
CCTTAAAAATTGAAAAAAATTTTTTTAGACC
Found at i:9661 original size:24 final size:24
Alignment explanation
Indices: 9595--9663 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
9585 ACAAAGATTT
*
9595 TTATACTAATAAATGTCAAATATA
1 TTATACTAATAAATGTTAAATATA
9619 TTATACTAATAAATGTTAAATATA
1 TTATACTAATAAATGTTAAATATA
*
9643 TTATACTAATAAATATTAAAT
1 TTATACTAATAAATGTTAAAT
9664 CTTTTAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (24 bp):
TTATACTAATAAATGTTAAATATA
Found at i:17381 original size:2 final size:2
Alignment explanation
Indices: 17374--17403 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17364 ATAAAATTTA
17374 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17404 CTACTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20552 original size:20 final size:21
Alignment explanation
Indices: 20499--20558 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
20489 CTCTCAACAA
20499 AATTTATAAAATAATTTCAAAAT
1 AATTTATAAAA-AA-TTCAAAAT
20522 AAATTT-T--AAAATTCAAAAT
1 -AATTTATAAAAAATTCAAAAT
20541 -ATTTATAAAAAATTCAAA
1 AATTTATAAAAAATTCAAA
20559 TTTTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 8 0.24
20 12 0.36
21 2 0.06
23 1 0.03
24 5 0.15
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTATAAAAAATTCAAAAT
Found at i:25598 original size:117 final size:118
Alignment explanation
Indices: 25469--25716 Score: 385
Period size: 117 Copynumber: 2.1 Consensus size: 118
25459 GAGTAAAATA
* *
25469 GTAATTTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCTG-GTGTGAAATGGTAA
1 GTAA-TTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC-GAGGGTAAAATGGTAA
* * *
25533 TTTTTAGAAGTTTCGGGGT-AAAAATGAGATTTTTGGAAGTTC-AGGGGTAAAGGG
64 TTTTTAGAAATTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGA-GGGTAAAAGG
25587 GTAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATT
1 GTAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATT
* *
25652 TTTAGAAATTTTGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATG
66 TTTAGAAATTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAGG
25705 GTAATTTTTGGA
1 GTAATTTTTGGA
25717 CAGCCTAGGG
Statistics
Matches: 120, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
116 1 0.01
117 71 0.59
118 47 0.39
119 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (118 bp):
GTAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATT
TTTAGAAATTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAGG
Found at i:25632 original size:59 final size:59
Alignment explanation
Indices: 25343--25716 Score: 363
Period size: 59 Copynumber: 6.4 Consensus size: 59
25333 CGGATGCACG
* ** * * * * *
25343 GGGTAAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATG-GAATTTT-AAACATTCGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAA-GTTCGA
* * * * * * *
25401 GGGTAAAAGGGTAA-CTTT-GAGAGTTTCGAGGTCGAAAACG-GAGTCTTCGGACA--TCCA
1 GGGTAAAATGGTAATTTTTGGA-AGTTTCGAGGTCAAAAATGAGA-TTTTTGGA-AGTTCGA
* *
25458 GGAGTAAAATAGTAATTTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCTG-
1 GG-GTAAAATGGTAA-TTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTC-GA
* * * *
25519 GTGTGAAATGGTAATTTTTAGAAGTTTCGGGGT-AAAAATGAGATTTTTGGAAGTTC-A
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGA
** *
25576 GGGGTAAAGGGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGA
1 -GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGA
* * *
25636 GGGTAAAATGGTAATTTTTAGAAATTTTGAGGTCAAAAATGAGATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGA
25695 GGGTAAAATGGTAATTTTTGGA
1 GGGTAAAATGGTAATTTTTGGA
25717 CAGCCTAGGG
Statistics
Matches: 258, Mismatches: 42, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
56 2 0.01
57 22 0.09
58 74 0.29
59 115 0.45
60 38 0.15
61 7 0.03
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGA
Found at i:25711 original size:29 final size:29
Alignment explanation
Indices: 25461--25716 Score: 185
Period size: 29 Copynumber: 8.7 Consensus size: 29
25451 ACATCCAGGA
*
25461 GTAAAATAGTAATTTTTTGGAAGTTTCGA-G
1 GTAAAATGGTAA-TTTTTGGAAG-TTCGAGG
* *
25491 GTCAAAAATGG-GATTTTTGGAAGTTCTG-GT
1 GT--AAAATGGTAATTTTTGGAAGTTC-GAGG
* *
25521 GTGAAATGGTAATTTTTAGAAGTTTCG-GG
1 GTAAAATGGTAATTTTTGGAAG-TTCGAGG
25550 GTAAAAAT-G-AGATTTTTGGAAGTTC-AGGG
1 GT-AAAATGGTA-ATTTTTGGAAGTTCGA-GG
**
25579 GTAAAGGGGTAATTTTTGGAAGTTTCGA-G
1 GTAAAATGGTAATTTTTGGAAG-TTCGAGG
*
25608 GTCAAAAATGG-GATTTTTGGAAGTTCGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTCGAGG
* * *
25638 GTAAAATGGTAATTTTTAGAAATTTTGA-G
1 GTAAAATGGTAATTTTT-GGAAGTTCGAGG
25667 GTCAAAAAT-G-AGATTTTTGGAAGTTCGAGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTCGAGG
25697 GTAAAATGGTAATTTTTGGA
1 GTAAAATGGTAATTTTTGGA
25717 CAGCCTAGGG
Statistics
Matches: 180, Mismatches: 21, Indels: 51
0.71 0.08 0.20
Matches are distributed among these distances:
28 25 0.14
29 79 0.44
30 58 0.32
31 12 0.07
32 6 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAAGTTCGAGG
Found at i:26752 original size:3 final size:3
Alignment explanation
Indices: 26744--26832 Score: 81
Period size: 3 Copynumber: 28.7 Consensus size: 3
26734 TTAATTAATG
* * * *
26744 TTA TTA TTA ATA TTA TTA TTGA TGTCA TTA TTA TTA TTG TCA TTA ATA
1 TTA TTA TTA TTA TTA TTA TT-A T-T-A TTA TTA TTA TTA TTA TTA TTA
* *
26792 TTG TTAA TGA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
26833 GCCAATATAA
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 1 0.01
3 61 0.88
4 4 0.06
5 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:26752 original size:12 final size:12
Alignment explanation
Indices: 26737--26857 Score: 89
Period size: 12 Copynumber: 10.1 Consensus size: 12
26727 TTCTTTTTTA
*
26737 ATTAATGTTATT
1 ATTAATATTATT
26749 ATTAATATTATT
1 ATTAATATTATT
* * *
26761 ATTGATGTCATT
1 ATTAATATTATT
* * *
26773 ATTATTATTGTC
1 ATTAATATTATT
*
26785 ATTAATATTGTT
1 ATTAATATTATT
* *
26797 AATGATATTATT
1 ATTAATATTATT
*
26809 ATTATTATTATT
1 ATTAATATTATT
*
26821 ATTATTATTATT
1 ATTAATATTATT
*** *
26833 GCCAATATAATT
1 ATTAATATTATT
*
26845 AATAATATTATT
1 ATTAATATTATT
26857 A
1 A
26858 ATGACATTTT
Statistics
Matches: 82, Mismatches: 27, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 82 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (12 bp):
ATTAATATTATT
Found at i:27559 original size:6 final size:6
Alignment explanation
Indices: 27540--27612 Score: 55
Period size: 6 Copynumber: 12.5 Consensus size: 6
27530 AAATCCATTC
**
27540 AAATTT -AA-TT AAATTT AAATTT AAAGCAT AAATTT AAATTT AACA--T
1 AAATTT AAATTT AAATTT AAATTT AAA-TTT AAATTT AAATTT AA-ATTT
* **
27586 AAATTT AAATTC AAAAAT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
27613 CCAATTTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 3 0.06
5 7 0.14
6 36 0.71
7 5 0.10
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (6 bp):
AAATTT
Found at i:27579 original size:35 final size:35
Alignment explanation
Indices: 27540--27612 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
27530 AAATCCATTC
* * *
27540 AAATTTAA-TTAAATTTAAATTTAAAGCATAAATTT
1 AAATTTAACATAAATTTAAATTCAAA-AATAAATTT
27575 AAATTTAACATAAATTTAAATTCAAAAATAAATTT
1 AAATTTAACATAAATTTAAATTCAAAAATAAATTT
27610 AAA
1 AAA
27613 CCAATTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 19 0.56
36 15 0.44
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (35 bp):
AAATTTAACATAAATTTAAATTCAAAAATAAATTT
Found at i:27607 original size:18 final size:17
Alignment explanation
Indices: 27549--27612 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 17
27539 CAAATTTAAT
27549 TAAATTTAAATTTAAAGCA
1 TAAATTTAAA-TTAAA-CA
*
27568 TAAATTTAAATTTAACA
1 TAAATTTAAATTAAACA
*
27585 TAAATTTAAATTCAAAAA
1 TAAATTTAAATT-AAACA
27603 TAAATTTAAA
1 TAAATTTAAA
27613 CCAATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
17 14 0.34
18 17 0.41
19 10 0.24
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTAAACA
Found at i:28501 original size:86 final size:86
Alignment explanation
Indices: 28356--28565 Score: 303
Period size: 86 Copynumber: 2.4 Consensus size: 86
28346 CGTGGGTTTG
** * * * * * *
28356 ATTTGGTCTTCTTCTTAGTATCTCATCGGGAAGATGACTGCGTCATTTGTTTCAATCCGCTTCTC
1 ATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACTGCGTCATCTGTTTCAATCCGCTTCTC
28421 TATATCTCATAAGGAAGACGA
66 TATATCTCATAAGGAAGACGA
* *
28442 ATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACTGCGTCGTCTGTTTCAATCCGCTTCTT
1 ATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACTGCGTCATCTGTTTCAATCCGCTTCTC
* *
28507 TGTATCTCATCAGGAAGACGA
66 TATATCTCATAAGGAAGACGA
*
28528 ATTTAGTCCACTTCTCAGTATTTCATCAGGAAGCTAAC
1 ATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAAC
28566 CTTTTTATCA
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 111 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (86 bp):
ATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACTGCGTCATCTGTTTCAATCCGCTTCTC
TATATCTCATAAGGAAGACGA
Found at i:40654 original size:15 final size:16
Alignment explanation
Indices: 40636--40675 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
40626 TATTATTAAT
40636 ATTATTATTGA-TGTC
1 ATTATTATTGATTGTC
40651 ATTATTATT-ATTGTC
1 ATTATTATTGATTGTC
*
40666 ATTAATATTG
1 ATTATTATTG
40676 TTAATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (16 bp):
ATTATTATTGATTGTC
Done.