Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008103.1 Kokia drynarioides strain JFW-HI SEQ_122761, 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: 24678
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:193 original size:30 final size:30
Alignment explanation
Indices: 88--302 Score: 144
Period size: 30 Copynumber: 7.3 Consensus size: 30
78 CATTAAAATC
* *
88 GGGTCAAATTTAAATTTTTGAAAAG-TTAA
1 GGGTCAAATTTGAATTTTTGAAAAGTTTGA
* *
117 TGGTCAAATTGGAATTTTTAGAAAA-TTT-A
1 GGGTCAAATTTGAATTTTT-GAAAAGTTTGA
** * * *
146 GGGGTTGACTTGGAATTTTTAAAAAGTTTGA
1 -GGGTCAAATTTGAATTTTTGAAAAGTTTGA
** *
177 GGGTCAAATTCAAATTTTTGGAAAGTTTTG-
1 GGGTCAAATTTGAATTTTTGAAAAG-TTTGA
207 GGG--AAATTT-AATTTTTTGGAAAA-TTT-A
1 GGGTCAAATTTGAA-TTTTT-GAAAAGTTTGA
* * *
234 GGGGTAAAATTTGGATTTTTGGAAAA-TTTAA
1 -GGGTCAAATTTGAATTTTT-GAAAAGTTTGA
*
265 GGGTCAAATTCGAATTTTTGAAAAGTTTGA
1 GGGTCAAATTTGAATTTTTGAAAAGTTTGA
*
295 GAGTCAAA
1 GGGTCAAA
303 ACATAATTTC
Statistics
Matches: 148, Mismatches: 23, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.03
28 13 0.09
29 30 0.20
30 93 0.63
31 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGAAAAGTTTGA
Found at i:253 original size:88 final size:88
Alignment explanation
Indices: 88--292 Score: 236
Period size: 88 Copynumber: 2.3 Consensus size: 88
78 CATTAAAATC
* * * **
88 GGGTCAAATTTAAATTTTTGAAAAGTTAATGGTCAAATTGGAATTTTTAGAAAATTTAGGGGTTG
1 GGGTCAAATTCAAATTTTTGAAAAGTT-TTGGGCAAATTGGAATTTTTAGAAAATTTAGGGGTAA
*
153 ACTTGGAATTTTT-AAAAAGTTTGA
65 ACTTGGAATTTTTGAAAAA-TTTAA
* * * *
177 GGGTCAAATTCAAATTTTTGGAAAGTTTTGGGGAAATT-TAATTTTTTGGAAAATTTAGGGGTAA
1 GGGTCAAATTCAAATTTTTGAAAAGTTTTGGGCAAATTGGAA-TTTTTAGAAAATTTAGGGGT-A
* *
241 AATTTGG-ATTTTTGGAAAATTTAA
64 AACTTGGAATTTTTGAAAAATTTAA
*
265 GGGTCAAATTCGAATTTTTGAAAAGTTT
1 GGGTCAAATTCAAATTTTTGAAAAGTTT
293 GAGAGTCAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 2 0.02
88 63 0.64
89 34 0.34
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (88 bp):
GGGTCAAATTCAAATTTTTGAAAAGTTTTGGGCAAATTGGAATTTTTAGAAAATTTAGGGGTAAA
CTTGGAATTTTTGAAAAATTTAA
Found at i:2123 original size:111 final size:111
Alignment explanation
Indices: 1935--2136 Score: 291
Period size: 111 Copynumber: 1.8 Consensus size: 111
1925 CACTAATCGC
1935 CATTTCAATGCAAAAATACTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTTGATTGAAGGCA
1 CATTTCAATGCAAAAATACTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTTGATTGAAGGCA
* *
2000 AAGCTTGCATGAATGAAAAAATTAAAAATACCAGTCCACTAACCAT
66 AAGATTGAATGAATGAAAAAATTAAAAATACCAGTCCACTAACCAT
* ** * * *
2046 CATTTCTATGCAAAAATGTTTGAAC-GGGATTGTGAGGTGGATAAAATTTAACTTT-ATTGAAGG
1 CATTTCAATGCAAAAATACTTGAACAGGG-TTGTAAAGTGGATAAAATTGAA-TTTGATTGAAGG
*
2109 CAAAGATTGAATGAATGAGAAAATTAAA
64 CAAAGATTGAATGAATGAAAAAATTAAA
2137 CATTGATCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
110 3 0.04
111 74 0.93
112 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.28
Consensus pattern (111 bp):
CATTTCAATGCAAAAATACTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTTGATTGAAGGCA
AAGATTGAATGAATGAAAAAATTAAAAATACCAGTCCACTAACCAT
Found at i:2483 original size:15 final size:14
Alignment explanation
Indices: 2434--2510 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 14
2424 CACCTCGACC
* *
2434 TCTCCTTTTCTTTT
1 TCTCTTTTTTTTTT
2448 TC-CTTTTTTATTTT
1 TCTCTTTTTT-TTTT
*
2462 T-TATTTTATTTTTT
1 TCTCTTTT-TTTTTT
*
2476 TCTCTTTTCTTTCTT
1 TCTCTTTT-TTTTTT
*
2491 TCTTTTCTTTCTTTTT
1 TCTCTT-TTT-TTTTT
2507 TCTC
1 TCTC
2511 AATTTTTTGG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
13 5 0.10
14 16 0.33
15 18 0.38
16 9 0.19
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTCTTTTTTTTTT
Found at i:2494 original size:13 final size:13
Alignment explanation
Indices: 2478--2504 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2468 TATTTTTTTC
2478 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
2491 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
2504 T
1 T
2505 TTTCTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:2508 original size:20 final size:18
Alignment explanation
Indices: 2438--2509 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 18
2428 TCGACCTCTC
2438 CTTTTCTTTTTCCTTTTTTAT
1 CTTTT-TTTTT-CTTTTTT-T
*
2459 -TTTTTATTTTATTTTTTT
1 CTTTTT-TTTTCTTTTTTT
*
2477 CTCTTTTCTTTCTTTCTTTT
1 CT-TTTTTTTTCTTT-TTTT
2497 CTTTCTTTTTTCT
1 CTTT-TTTTTTCT
2510 CAATTTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.02
19 16 0.38
20 25 0.60
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (18 bp):
CTTTTTTTTTCTTTTTTT
Found at i:6959 original size:12 final size:12
Alignment explanation
Indices: 6932--6974 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
6922 ACAATAAGGT
*
6932 AATAAATTGAGTA
1 AATAAA-TGAATA
6945 AATAAAT-AATCA
1 AATAAATGAAT-A
6957 AATAAATGAATA
1 AATAAATGAATA
6969 AATAAA
1 AATAAA
6975 GAAACAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.07
12 16 0.59
13 9 0.33
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (12 bp):
AATAAATGAATA
Found at i:7079 original size:30 final size:30
Alignment explanation
Indices: 7042--7200 Score: 151
Period size: 30 Copynumber: 5.3 Consensus size: 30
7032 CATTAAAATC
7042 GGGTTAAATTTAAATTTTTGAAAAGTTT-A
1 GGGTTAAATTTAAATTTTTGAAAAGTTTGA
* * *
7071 GGGTTTAAATTCAAATTTTTGGAAAGTTTAA
1 GGG-TTAAATTTAAATTTTTGAAAAGTTTGA
* * *
7102 GGGTTAAATTTGAATTTTTTAGAAAA-TTCGT
1 GGGTTAAATTT-AAATTTTT-GAAAAGTTTGA
* ** *
7133 GGGTAAAATTTGGATTTTTGGAAAGTTTGA
1 GGGTTAAATTTAAATTTTTGAAAAGTTTGA
* * * *
7163 AGGTCAAATTCAAATTTTAGAAAAGTTTGA
1 GGGTTAAATTTAAATTTTTGAAAAGTTTGA
7193 GGGTTAAA
1 GGGTTAAA
7201 ACATAATTTT
Statistics
Matches: 101, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
29 7 0.07
30 67 0.66
31 23 0.23
32 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (30 bp):
GGGTTAAATTTAAATTTTTGAAAAGTTTGA
Found at i:7201 original size:61 final size:61
Alignment explanation
Indices: 7042--7201 Score: 157
Period size: 61 Copynumber: 2.6 Consensus size: 61
7032 CATTAAAATC
* * * *
7042 GGGTTAAATTTAAATTTTTGAAAAGTTT-AGGGTTTAAATTCAAATTTTTGGAAAGTTTAA
1 GGGTCAAATTCAAATTTTAGAAAAGTTTGAGGGTTAAAATTCAAATTTTTGGAAAGTTTAA
* * * * * ***
7102 GGGTTAAATTTGAATTTTTTAGAAAA-TTCGTGGG-TAAAATTTGGATTTTTGGAAAGTTTGAA
1 GGGTCAAA-TTCAA-ATTTTAGAAAAGTTTGAGGGTTAAAATTCAAATTTTTGGAAAGTTT-AA
7164 -GGTCAAATTCAAATTTTAGAAAAGTTTGAGGGTTAAAA
1 GGGTCAAATTCAAATTTTAGAAAAGTTTGAGGGTTAAAA
7202 CATAATTTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
59 10 0.12
60 18 0.22
61 38 0.47
62 14 0.17
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (61 bp):
GGGTCAAATTCAAATTTTAGAAAAGTTTGAGGGTTAAAATTCAAATTTTTGGAAAGTTTAA
Found at i:10665 original size:24 final size:24
Alignment explanation
Indices: 10637--10683 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
10627 TAGACTAATA
10637 AGAGTTTAACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
10661 AGAGTTTAATTGAAACAAATAAA
1 AGAGTTTAACTCAAACAAATAAA
10684 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:10692 original size:24 final size:24
Alignment explanation
Indices: 10641--10699 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
10631 CTAATAAGAG
* * * *
10641 TTTAACTCAAACAAATAAATAGAG
1 TTTAACTGAAACAAATAAACAAAA
*
10665 TTTAATTGAAACAAATAAACAAAA
1 TTTAACTGAAACAAATAAACAAAA
10689 TTTAACTGAAA
1 TTTAACTGAAA
10700 GATATTTCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (24 bp):
TTTAACTGAAACAAATAAACAAAA
Found at i:16490 original size:18 final size:20
Alignment explanation
Indices: 16467--16512 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
16457 TACAAAATAA
*
16467 TCAAAATAATTT-TTAAAAT
1 TCAAAATAATTTATAAAAAT
*
16486 T-AAAAAAATTTATAAAAAT
1 TCAAAATAATTTATAAAAAT
16505 TCAAAATA
1 TCAAAATA
16513 TTTGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAT
Found at i:20356 original size:22 final size:22
Alignment explanation
Indices: 20307--20360 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20297 TGCACTTAAC
*
20307 ATAAAAAAAATTCAAAAATTCA
1 ATAAAAAAAATTCAAAAACTCA
* *
20329 AAAAAAAAAATTCTAAAACT-A
1 ATAAAAAAAATTCAAAAACTCA
20350 TATAAAAAAAA
1 -ATAAAAAAAA
20361 CTAAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (22 bp):
ATAAAAAAAATTCAAAAACTCA
Found at i:22602 original size:29 final size:29
Alignment explanation
Indices: 22560--22745 Score: 160
Period size: 29 Copynumber: 6.3 Consensus size: 29
22550 TGAAATAGTA
*
22560 ATTTTGGGAAAATTCGGGGTTAAAAATGGG
1 ATTTTTGG-AAATTCGGGGTTAAAAATGGG
* * *
22590 ATTCTTAGAAATTCGAGGG-TAAAAATGGA
1 ATTTTTGGAAATTCG-GGGTTAAAAATGGG
* * *
22619 ATTTTTGGAAGTTTTGGGGTCAAAAATGGG
1 ATTTTTGGAA-ATTCGGGGTTAAAAATGGG
* * * *
22649 ATTTTTGGAAGTTTGGGGGTAAAAATGGA
1 ATTTTTGGAAATTCGGGGTTAAAAATGGG
* **
22678 ATTTTTGGAAGTTTCAAGGTTAAAAATGGG
1 ATTTTTGGAA-ATTCGGGGTTAAAAATGGG
* * *
22708 ATTTTTGGAAGTTTAGGGG-TAAAAATGGA
1 ATTTTTGGAA-ATTCGGGGTTAAAAATGGG
22737 ATTTTTGGA
1 ATTTTTGGA
22746 GACCTTTAGG
Statistics
Matches: 128, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
29 70 0.55
30 58 0.45
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAATTCGGGGTTAAAAATGGG
Found at i:22646 original size:30 final size:29
Alignment explanation
Indices: 22606--22745 Score: 208
Period size: 30 Copynumber: 4.8 Consensus size: 29
22596 AGAAATTCGA
*
22606 GGGTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTAG
* *
22635 GGGTCAAAAATGGGATTTTTGGAAGTTTGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTAG
*
22665 GGGTAAAAATGGAATTTTTGGAAGTTTCAA
1 GGGTAAAAATGGAATTTTTGGAAGTTT-AG
* *
22695 GGTTAAAAATGGGATTTTTGGAAGTTTAG
1 GGGTAAAAATGGAATTTTTGGAAGTTTAG
22724 GGGTAAAAATGGAATTTTTGGA
1 GGGTAAAAATGGAATTTTTGGA
22746 GACCTTTAGG
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
29 47 0.47
30 52 0.53
ACGTcount: A:0.32, C:0.01, G:0.31, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTAG
Found at i:22669 original size:59 final size:59
Alignment explanation
Indices: 22572--22745 Score: 258
Period size: 59 Copynumber: 2.9 Consensus size: 59
22562 TTTGGGAAAA
* * * * *
22572 TTCGGGGTTAAAAATGGGATTCTTAGAAATTCGAGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
* *
22631 TTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
** *
22690 TTCAAGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGA
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
22746 GACCTTTAGG
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 103 1.00
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (59 bp):
TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:23289 original size:13 final size:13
Alignment explanation
Indices: 23273--23297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23263 AAAAAACCTC
23273 AAAATCCTCTCAA
1 AAAATCCTCTCAA
23286 AAAATCCTCTCA
1 AAAATCCTCTCA
23298 CCCCTTCTCG
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:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATCCTCTCAA
Found at i:23773 original size:12 final size:12
Alignment explanation
Indices: 23745--23782 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
23735 TTCGTTTTAT
*
23745 TTAT-TTATTTA
1 TTATATTATTAA
23756 TT-TATTATTAA
1 TTATATTATTAA
23767 TTATATTATTAA
1 TTATATTATTAA
23779 TTAT
1 TTAT
23783 TTAATAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 10 0.42
12 13 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTATTAA
Done.