Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014186.1 Kokia drynarioides strain JFW-HI SEQ_129219, 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: 74698
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:54 original size:16 final size:16
Alignment explanation
Indices: 9--58 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1 AACCTAGC
*
9 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
25 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
39 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
55 TAAT
1 TAAT
59 ATCTCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:1443 original size:43 final size:43
Alignment explanation
Indices: 1361--1445 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
1351 ATTAACATGT
* * *
1361 TAAATTATATTATTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATAGTATTTGACTCGTATTAATATGCTTGCATGTTAC
*
1404 TAAATTATAGTACTTT-ACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATAGTA-TTTGACTCGTATTAATATGCTTG-CATGTTA
1446 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.08
43 30 0.83
44 3 0.08
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (43 bp):
TAAATTATAGTATTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:2079 original size:45 final size:45
Alignment explanation
Indices: 2013--2149 Score: 186
Period size: 45 Copynumber: 3.0 Consensus size: 45
2003 GCATAGCTCA
2013 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *
2058 TCAAGCCAAGGATATCGGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * * *
2103 TCAAGGGAAGGATATCAAG-CTGAGTTTGACGAGTCATCGCGATAC
1 TCAAGCCAAGGATATC-AGCCTCAGTTTGACGAGCCACCGCAATAC
2148 TC
1 TC
2150 TATTCCTCTC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 80 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:2170 original size:21 final size:21
Alignment explanation
Indices: 2144--2186 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2134 AGTCATCGCG
*
2144 ATACTCTATTCCTCTCG-GGCA
1 ATACTCTACTCCTC-CGAGGCA
2165 ATACTCTACTCCTCCGAGGCA
1 ATACTCTACTCCTCCGAGGCA
2186 A
1 A
2187 ATAGACCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (21 bp):
ATACTCTACTCCTCCGAGGCA
Found at i:5623 original size:4 final size:4
Alignment explanation
Indices: 5601--5666 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
5591 AACATATTAC
* * * * * *
5601 CTTT CTCT CCTT C-TT CTTT CTTTT CTCT CCTT CTTC CTTT CTTT CCTT
1 CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT
5649 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
5667 CCGTTTATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
3 3 0.06
4 38 0.79
5 7 0.15
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:5627 original size:20 final size:20
Alignment explanation
Indices: 5602--5661 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
5592 ACATATTACC
5602 TTTCTCTCCTTCTTCTTTCT
1 TTTCTCTCCTTCTTCTTTCT
5622 TTTCTCTCCTTCTTCCTTTC-
1 TTTCTCTCCTTCTT-CTTTCT
*
5642 TTTC-CTTCTT-TTCTTTCT
1 TTTCTCTCCTTCTTCTTTCT
5660 TT
1 TT
5662 CTTTCCCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 5 0.14
18 4 0.11
19 5 0.14
20 18 0.49
21 5 0.14
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTCTCCTTCTTCTTTCT
Found at i:5663 original size:13 final size:13
Alignment explanation
Indices: 5614--5665 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
5604 TCTCTCCTTC
5614 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
* *
5627 CTCCTTCTTCCTTTCT
1 -TTC-T-TTCTTTTCT
*
5643 TTCCTTCTTTTCT
1 TTCTTTCTTTTCT
5656 TTCTTTCTTT
1 TTCTTTCTTT
5666 CCCGTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 17 0.57
14 2 0.07
15 3 0.10
16 8 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCTTTCTTTTCT
Found at i:8455 original size:15 final size:15
Alignment explanation
Indices: 8435--8464 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8425 CTTTCAGATT
8435 GAAAACATAAATTCG
1 GAAAACATAAATTCG
*
8450 GAAAACATCAATTCG
1 GAAAACATAAATTCG
8465 TACACTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (15 bp):
GAAAACATAAATTCG
Found at i:9249 original size:19 final size:20
Alignment explanation
Indices: 9218--9255 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
9208 TATTTTATTT
*
9218 TAAAATATAATTATAAATAA
1 TAAAATATAATTAAAAATAA
9238 TAAAAT-TAATTAAAAATA
1 TAAAATATAATTAAAAATA
9256 TTTAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAATATAATTAAAAATAA
Found at i:9261 original size:20 final size:20
Alignment explanation
Indices: 9216--9264 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
9206 TATATTTTAT
*
9216 TTTAAAATATAATTATAAATA
1 TTTAAAAT-TAATTAAAAATA
*
9237 -ATAAAATTAATTAAAAATA
1 TTTAAAATTAATTAAAAATA
9256 TTTAAAATT
1 TTTAAAATT
9265 GATTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAATTAATTAAAAATA
Found at i:19376 original size:6 final size:6
Alignment explanation
Indices: 19365--19396 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
19355 TTTATTGAGT
*
19365 CTAAGG CTAAGG CTAAGA CTAAGG CTAAGG CT
1 CTAAGG CTAAGG CTAAGG CTAAGG CTAAGG CT
19397 TTATAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (6 bp):
CTAAGG
Found at i:21348 original size:2 final size:2
Alignment explanation
Indices: 21341--21370 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21331 AACTCCATGG
21341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21371 GAGTTTGTTT
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):
AT
Found at i:22398 original size:20 final size:21
Alignment explanation
Indices: 22358--22399 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
22348 TACAACCCAC
*
22358 GCACACATGATAATTTTAATA
1 GCACACATGATAATCTTAATA
*
22379 GCACACAT-ATGATCTTAATA
1 GCACACATGATAATCTTAATA
22399 G
1 G
22400 TATTTACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (21 bp):
GCACACATGATAATCTTAATA
Found at i:25011 original size:13 final size:13
Alignment explanation
Indices: 24993--25017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24983 AAAAAATTAA
24993 TTTTAATTAATAT
1 TTTTAATTAATAT
25006 TTTTAATTAATA
1 TTTTAATTAATA
25018 AATATATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAATTAATAT
Found at i:25107 original size:19 final size:18
Alignment explanation
Indices: 25083--25122 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
25073 TATAAATAAA
* *
25083 ATAATAAATATGTAATTAT
1 ATAATAAAAATAT-ATTAT
25102 ATAATAAAAATATATTAT
1 ATAATAAAAATATATTAT
25120 ATA
1 ATA
25123 TCATTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAATAAAAATATATTAT
Found at i:46846 original size:5 final size:5
Alignment explanation
Indices: 46808--46842 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
46798 ATTAAAATCA
*
46808 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC CTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
46843 CTTTGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:50413 original size:21 final size:20
Alignment explanation
Indices: 50371--50422 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
50361 AATAAATAAC
**
50371 TTTTAAT-TTACTATGTCTA
1 TTTTAATGTTACTATGTAAA
50390 TTTTAATTGTTACTATGTAAA
1 TTTTAA-TGTTACTATGTAAA
50411 TTTCTAATGTTA
1 TTT-TAATGTTA
50423 TGAATATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.21
20 1 0.04
21 18 0.64
22 3 0.11
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTTAATGTTACTATGTAAA
Found at i:54608 original size:12 final size:12
Alignment explanation
Indices: 54577--54602 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54567 TAACTTTGAG
54577 ATGGATTTATTT
1 ATGGATTTATTT
54589 ATGGATTTATTT
1 ATGGATTTATTT
54601 AT
1 AT
54603 TTATTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (12 bp):
ATGGATTTATTT
Found at i:54798 original size:25 final size:25
Alignment explanation
Indices: 54744--54799 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
54734 TTAAAATAAT
*
54744 TTTAAATTGTTTAATTTTTAATCTA
1 TTTAAATTATTTAATTTTTAATCTA
*
54769 ATTAAATATATTTAA-TTTT-ATCATA
1 TTTAAAT-TATTTAATTTTTAATC-TA
54794 TTTAAA
1 TTTAAA
54800 AAATGTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 17 0.65
26 6 0.23
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTAAATTATTTAATTTTTAATCTA
Found at i:59137 original size:27 final size:27
Alignment explanation
Indices: 59105--59163 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
59095 CAAACTACCA
59105 TTGAGGTGGTGAAGTTACTTGCCATAT
1 TTGAGGTGGTGAAGTTACTTGCCATAT
59132 TTGAGGTGGTGAAGTTACTTGCCATAT
1 TTGAGGTGGTGAAGTTACTTGCCATAT
59159 TTGAG
1 TTGAG
59164 TTGGCAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (27 bp):
TTGAGGTGGTGAAGTTACTTGCCATAT
Found at i:63621 original size:22 final size:23
Alignment explanation
Indices: 63577--63625 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
63567 CCAACGAGTG
*
63577 GTTTTAGTGGAAAAGAAAATGAT
1 GTTTCAGTGGAAAAGAAAATGAT
63600 GTTTCAGTGGAAAAG-AAATGAT
1 GTTTCAGTGGAAAAGAAAATGAT
63622 GTTT
1 GTTT
63626 ATTTTAGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.33
Consensus pattern (23 bp):
GTTTCAGTGGAAAAGAAAATGAT
Found at i:64364 original size:3 final size:3
Alignment explanation
Indices: 64356--64380 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
64346 AACTGGTGTT
64356 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
64381 ATATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71104 original size:18 final size:19
Alignment explanation
Indices: 71064--71108 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
71054 GGCAGCCATA
*
71064 AATTAAAAAATAAAAATCT
1 AATTTAAAAATAAAAATCT
71083 --TTTAAAAATAAAAAT-T
1 AATTTAAAAATAAAAATCT
71099 AATTTAAAAA
1 AATTTAAAAA
71109 AGTATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTTAAAAATAAAAATCT
Done.