Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010493.1 Kokia drynarioides strain JFW-HI SEQ_125402, 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: 11710
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:108 original size:2 final size:2
Alignment explanation
Indices: 101--159 Score: 100
Period size: 2 Copynumber: 29.0 Consensus size: 2
91 GTTGGTTGTA
*
101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
143 AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT A-T AT AT
160 TTTGATATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1649 original size:23 final size:23
Alignment explanation
Indices: 1617--1660 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1607 AATACCATTT
1617 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
1640 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
1661 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:1653 original size:13 final size:11
Alignment explanation
Indices: 1621--1663 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1611 CCATTTTCTA
*
1621 AATAAAATAAT
1 AATAAAATATT
1632 AAT-AAATATCT
1 AATAAAATAT-T
1643 AAGTAAAATATT
1 AA-TAAAATATT
1655 AATAAAATA
1 AATAAAATA
1664 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2441 original size:2 final size:2
Alignment explanation
Indices: 2434--2463 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2424 ATAATATTCT
2434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2464 ATTTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2531 original size:12 final size:11
Alignment explanation
Indices: 2504--2535 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2494 CATTTTAGTT
2504 ATTTTTATATA
1 ATTTTTATATA
2515 A-TTTTATATA
1 ATTTTTATATA
2525 ATTTTT-TATA
1 ATTTTTATATA
2535 A
1 A
2536 GTTATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:2686 original size:19 final size:18
Alignment explanation
Indices: 2646--2688 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2636 TTTTCTATTT
*
2646 TTTTTCTAATTTTTATAG
1 TTTTTCTAATTTTTATAA
2664 TTTTTCTATATTTTT-TACA
1 TTTTTCTA-ATTTTTATA-A
2683 TTTTTC
1 TTTTTC
2689 AAAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTCTAATTTTTATAA
Found at i:3569 original size:88 final size:87
Alignment explanation
Indices: 3477--3687 Score: 259
Period size: 85 Copynumber: 2.4 Consensus size: 87
3467 GAGAAAGGGT
** * *
3477 TTAATTGCTTTTCTTTTGAAAATTTTTGAGGGTTTTTTTGATGCATTTTAAAAGTTTAAGTACTC
1 TTAATTGCTTTT-TTTTGAAAAAGTTTGAGGGCTTTTTTGATGCATTTTAAAAGTTCAAGTACTC
*
3542 AATTAAGT-AAAAAACGTAG-GGCC
65 AATTAAGTCAAAAAA-GGAGAGG-C
* * *
3565 TTAATTGC-TTTTTTT-AAAAAGTTTGAGGACCTTTTTGATGCATTTTGAAAGTTCAAGTACTCA
1 TTAATTGCTTTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATGCATTTTAAAAGTTCAAGTACTCA
*
3628 ATTGAGTGCAAAAAAGGAGAGGC
66 ATTAAGT-CAAAAAAGGAGAGGC
**
3651 TTAATTATTTTTTTTTGAAAAAGTTTGAGGGCTTTTT
1 TTAATTGCTTTTTTTTGAAAAAGTTTGAGGGCTTTTT
3688 ACACCCTTAA
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
85 47 0.45
86 14 0.13
87 18 0.17
88 26 0.25
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (87 bp):
TTAATTGCTTTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATGCATTTTAAAAGTTCAAGTACTCA
ATTAAGTCAAAAAAGGAGAGGC
Found at i:4529 original size:59 final size:59
Alignment explanation
Indices: 4445--4595 Score: 200
Period size: 58 Copynumber: 2.6 Consensus size: 59
4435 AAATAAGATG
* * * * *
4445 TTTTTTTGGTCCAATTAGGTGTCTAAACTTGATC-TCAAGGTTTAATTTGATACTTAAAC
1 TTTTTTTTGTCCAATTAGGTATCTAAACTT-AGCATCAAGATTCAATTTGATACTTAAAC
* *
4504 TTTTTTTTATCCAATGAGGTATCTAAAC-TAGCATCAAGATTCAATTTGATACTTAAAC
1 TTTTTTTTGTCCAATTAGGTATCTAAACTTAGCATCAAGATTCAATTTGATACTTAAAC
*
4562 -TTTTTTTGTCCAATTAGTTATCTAAACTTAGCAT
1 TTTTTTTTGTCCAATTAGGTATCTAAACTTAGCAT
4596 TTTGGTTTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 26 0.32
58 30 0.38
59 24 0.30
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.44
Consensus pattern (59 bp):
TTTTTTTTGTCCAATTAGGTATCTAAACTTAGCATCAAGATTCAATTTGATACTTAAAC
Found at i:5575 original size:56 final size:57
Alignment explanation
Indices: 5444--5820 Score: 199
Period size: 62 Copynumber: 6.5 Consensus size: 57
5434 TTTTTCAGAT
* * *
5444 AAAAAAATTTCAAAATTTTTTTGTGTTGCCCATGTAAT-AGTCGACACCCTTTTT-TTGA
1 AAAAAAATTTC-AAATTTTTTTGTGTTGGCCATGCAATGA-CCGACACCCTTTTTATT-A
* ** * *
5502 AAAAAAAATT-ACTTTTTTTTGTGTGGGCCATGCAATGACCGACACCCTTTTT-TTT
1 AAAAAAATTTCAAATTTTTTTGTGTTGGCCATGCAATGACCGACACCCTTTTTATTA
* * * *
5557 TAAAAAATTTCAAATTTTTTTGGTGTTGG-TATGCAATG---GTC-CCCTTTTTGA-GA
1 AAAAAAATTTCAAATTTTTTT-GTGTTGGCCATGCAATGACCGACACCCTTTTT-ATTA
* ** * *
5610 AAAAAAATTGC--ATTTTTGAGTGTTGGCCATGCAATGGCCGACACTCCCTTTTTCA-GA
1 AAAAAAATTTCAAATTTTTTTGTGTTGGCCATGCAATGACCGACA--CCCTTTTT-ATTA
* * * ***
5667 TAAAAAAATTTTAAATTTTTTTTGTGTTGGCCATGCAATGATCGACACCCCCTGTTCTCGGA
1 -AAAAAAATTTCAAA-TTTTTTTGTGTTGGCCATGCAATGACCGACA--CCCT-TTTTATTA
* * * ** *
5729 TAAAAAAATTTTAAATTTTTTTGGTGTTAGCTATGCAATGATTGACACCCCCTTTTTATTTGG
1 -AAAAAAATTTCAAATTTTTTT-GTGTTGGCCATGCAATGACCGACA--CCCTTTTTA-TT-A
* *
5792 TAAAAAA-TT-AAATTTTTTGGTGTTGGCCA
1 AAAAAAATTTCAAATTTTTTTGTGTTGGCCA
5821 CAACTTCCTC
Statistics
Matches: 253, Mismatches: 45, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
50 7 0.03
51 14 0.06
52 8 0.03
53 11 0.04
54 2 0.01
55 8 0.03
56 52 0.21
57 18 0.07
58 18 0.07
59 8 0.03
60 10 0.04
61 44 0.17
62 53 0.21
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (57 bp):
AAAAAAATTTCAAATTTTTTTGTGTTGGCCATGCAATGACCGACACCCTTTTTATTA
Found at i:5638 original size:107 final size:109
Alignment explanation
Indices: 5425--5706 Score: 302
Period size: 107 Copynumber: 2.5 Consensus size: 109
5415 TTTGCATGGT
* * *
5425 CGACACCCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTT-GTGTTGCCCATGTAATAGTCGAC
1 CGACACCCCTTTTT-AGATAAAAAAATTTC-AAATTTTTTTGGTGTTGGCCATGCAAT-G--GTC
* **
5489 ACCCTTTTTTTGAAAAAAAAATTACTTTTTTTTGTGTGGGCCATGCAATGAC
61 -CCC--TTTTTGAAAAAAAAATTACATTTTTGAGTGTGGGCCATGCAATGAC
** * *
5541 CGACA-CCCTTTTT-TTTTAAAAAATTTCAAATTTTTTTGGTGTTGG-TATGCAATGGTCCCCTT
1 CGACACCCCTTTTTAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCCCCTT
* * *
5603 TTTGAGAAAAAAAATTGCATTTTTGAGTGTTGGCCATGCAATGGC
66 TTTGA-AAAAAAAATTACATTTTTGAGTGTGGGCCATGCAATGAC
* *
5648 CGACACTCCCTTTTTCAGATAAAAAAATTTTAAATTTTTTTTGTGTTGGCCATGCAATG
1 CGACAC-CCCTTTTT-AGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATG
5707 ATCGACACCC
Statistics
Matches: 140, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
106 7 0.05
107 38 0.27
108 3 0.02
109 10 0.07
111 28 0.20
112 24 0.17
113 17 0.12
115 8 0.06
116 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (109 bp):
CGACACCCCTTTTTAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGTCCCCTT
TTTGAAAAAAAAATTACATTTTTGAGTGTGGGCCATGCAATGAC
Found at i:5741 original size:62 final size:61
Alignment explanation
Indices: 5622--5783 Score: 225
Period size: 62 Copynumber: 2.6 Consensus size: 61
5612 AAAAATTGCA
** * *
5622 TTTTTGAGTGTTGGCCATGCAATGGCCGACACTCCCTTTTTCAGATAAAAAAATTTTAAATT
1 TTTTTG-GTGTTGGCCATGCAATGATCGACACCCCCTTTCTCAGATAAAAAAATTTTAAATT
* *
5684 TTTTTTGTGTTGGCCATGCAATGATCGACACCCCCTGTTCTCGGATAAAAAAATTTTAAATT
1 TTTTTGGTGTTGGCCATGCAATGATCGACACCCCCT-TTCTCAGATAAAAAAATTTTAAATT
* * *
5746 TTTTTGGTGTTAGCTATGCAATGATTGACACCCCCTTT
1 TTTTTGGTGTTGGCCATGCAATGATCGACACCCCCTTT
5784 TTATTTGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
61 29 0.33
62 60 0.67
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (61 bp):
TTTTTGGTGTTGGCCATGCAATGATCGACACCCCCTTTCTCAGATAAAAAAATTTTAAATT
Found at i:9613 original size:12 final size:12
Alignment explanation
Indices: 9571--9618 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
9561 ATTTGTGTAA
*
9571 AAATTAATTTGA
1 AAATTAATTTGG
9583 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
9599 AAATTAATTTGG
1 AAATTAATTTGG
9611 AAATTAAT
1 AAATTAAT
9619 GAATATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:9804 original size:48 final size:46
Alignment explanation
Indices: 9751--9899 Score: 106
Period size: 48 Copynumber: 3.4 Consensus size: 46
9741 AAAAAAAATT
9751 ATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATAC
1 ATTATT-TATTACAATTTATATCAAATA-TGTGTTAATTTGACAATAC
* ** *
9799 ATTATTTA-T-CAAATT-T-TC--ATA--T-TTAAAGT-ACAA-ATT
1 ATTATTTATTACAATTTATATCAAATATGTGTTAATTTGACAATA-C
* * *
9835 ATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 ATTATT-TATTACAATTTATATCAAAT-ATGTGTTAATTTGACAATAC
9883 ATTATTTATTA-AATTTA
1 ATTATTTATTACAATTTA
9900 AATATTTAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 30
0.65 0.09 0.26
Matches are distributed among these distances:
35 1 0.01
36 10 0.13
37 7 0.09
38 2 0.03
39 4 0.05
40 1 0.01
41 5 0.07
43 4 0.05
44 2 0.03
45 5 0.07
46 7 0.09
47 11 0.14
48 16 0.21
49 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (46 bp):
ATTATTTATTACAATTTATATCAAATATGTGTTAATTTGACAATAC
Found at i:9843 original size:84 final size:84
Alignment explanation
Indices: 9722--9944 Score: 304
Period size: 84 Copynumber: 2.6 Consensus size: 84
9712 ATTTAAAATT
* *
9722 AATTTAACATTATTTAAATAAAAAAAATTATTATTATATTACAATTTATATCAAATATTGTGTTA
1 AATTTAA-A-TATTTAAAT--AAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTA
9787 ATTTGACAATACATTATTTATCA
62 ATTTGACAATACATTATTTATCA
** * * *
9810 AATTTTCATATTTAAAGT-ACAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
1 AATTTAAATATTTAAA-TAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTAATT
*
9874 TGACAATACATTATTTATTA
65 TGACAATACATTATTTATCA
9894 AATTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCA
1 AATTTAAATATTTAAATAAAAA--ATTATTATTATATTACAATTTTTATCA
9945 TATTTTAAAT
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
83 1 0.01
84 77 0.65
86 34 0.29
87 2 0.02
88 5 0.04
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (84 bp):
AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTAATTT
GACAATACATTATTTATCA
Found at i:10134 original size:20 final size:20
Alignment explanation
Indices: 10106--10148 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10096 ACACCTCAAA
* *
10106 ACCGCCTTTGACTGCCGTTG
1 ACCGACTTTGACTACCGTTG
*
10126 ACCGACTTTGTCTACCGTTG
1 ACCGACTTTGACTACCGTTG
10146 ACC
1 ACC
10149 AAGTTTCGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.35, G:0.21, T:0.30
Consensus pattern (20 bp):
ACCGACTTTGACTACCGTTG
Done.