Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009314.1 Kokia drynarioides strain JFW-HI SEQ_124021, 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: 26183
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:2805 original size:14 final size:14
Alignment explanation
Indices: 2786--2837 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
2776 TCTTGAAAAA
**
2786 AAAAATAAGGAAGT
1 AAAAATAAAAAAGT
2800 AAAAATAAAAAAGT
1 AAAAATAAAAAAGT
2814 AAAAAAGTAAAAAAAGT
1 -AAAAA-T-AAAAAAGT
*
2831 GAAAATA
1 AAAAATA
2838 CAAGACCCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 13 0.41
15 6 0.19
16 5 0.16
17 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAAAGT
Found at i:2835 original size:8 final size:8
Alignment explanation
Indices: 2796--2827 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2786 AAAAATAAGG
2796 AAGT-AAA
1 AAGTAAAA
2803 AA-TAAAA
1 AAGTAAAA
2810 AAGTAAAA
1 AAGTAAAA
2818 AAGTAAAA
1 AAGTAAAA
2826 AA
1 AA
2828 AGTGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
6 1 0.04
7 7 0.30
8 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (8 bp):
AAGTAAAA
Found at i:5369 original size:12 final size:12
Alignment explanation
Indices: 5356--5456 Score: 84
Period size: 12 Copynumber: 8.8 Consensus size: 12
5346 CTAAATAACC
*
5356 AAAATAACAACC
1 AAAATAACAACA
*
5368 AAAACAACAACA
1 AAAATAACAACA
*
5380 AGAAT---AACA
1 AAAATAACAACA
*
5389 ATAA-AACAACA
1 AAAATAACAACA
**
5400 AAAATTGCAACA
1 AAAATAACAACA
* *
5412 AAAATAACAGCT
1 AAAATAACAACA
5424 AAAATAACAACA
1 AAAATAACAACA
* *
5436 AAAACAACAATA
1 AAAATAACAACA
5448 AAAATAACA
1 AAAATAACA
5457 TCATCAAAAC
Statistics
Matches: 68, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
9 7 0.10
11 7 0.10
12 54 0.79
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:5385 original size:24 final size:23
Alignment explanation
Indices: 5355--5456 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 23
5345 TCTAAATAAC
*
5355 CAAAATAACAACCAAAACAACAA
1 CAAAATAACAACAAAAACAACAA
*
5378 CAAGAATAACAA-TAAAACAAC-A
1 CAA-AATAACAACAAAAACAACAA
** * *
5400 -AAAATTGCAACAAAAATAACAG
1 CAAAATAACAACAAAAACAACAA
5422 CTAAAATAACAACAAAAACAACAA
1 C-AAAATAACAACAAAAACAACAA
*
5446 TAAAAATAACA
1 -CAAAATAACA
5457 TCATCAAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.10
21 9 0.15
22 1 0.02
23 11 0.18
24 35 0.56
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.10
Consensus pattern (23 bp):
CAAAATAACAACAAAAACAACAA
Found at i:13904 original size:63 final size:62
Alignment explanation
Indices: 13772--13905 Score: 164
Period size: 63 Copynumber: 2.1 Consensus size: 62
13762 TTTAAGTTAT
** *
13772 ATTTGCATTTTCATTTTCATTTTGGAGAAAAGCACATTCTTTTTCAAACGATTCTGTTTCTCC
1 ATTT-CATTTTCATTTTCATTTTGGAGAAAAGCACATAATTTTTCAAACGATTCTATTTCTCC
* *
13835 ATTTTCATTTTCATTTTCATTTTGGAGAAAA-C-CATAATTATTTCCAAATGTTTCATATTTCTC
1 A-TTTCATTTTCATTTTCATTTTGGAGAAAAGCACATAATT-TTT-CAAACGATTC-TATTTCTC
13898 C
62 C
13899 ATTTCAT
1 ATTTCAT
13906 CATTTATATT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
61 5 0.08
62 4 0.06
63 41 0.66
64 12 0.19
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (62 bp):
ATTTCATTTTCATTTTCATTTTGGAGAAAAGCACATAATTTTTCAAACGATTCTATTTCTCC
Found at i:18434 original size:20 final size:20
Alignment explanation
Indices: 18411--18456 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
18401 TGGGTTTATG
18411 ATATATATT-ATAAAAATAAT
1 ATATATATTCATAAAAA-AAT
18431 ATAT-TAATTCATAAAAAAAT
1 ATATAT-ATTCATAAAAAAAT
18451 AT-TATA
1 ATATATA
18457 GTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATATATTCATAAAAAAAT
Found at i:21728 original size:29 final size:27
Alignment explanation
Indices: 21658--21732 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 27
21648 TTTTTGATTC
* *
21658 AATTTGATACTTGAATTTGACATTTTTT
1 AATTTG-TACTTAAACTTGACATTTTTT
*
21686 AATTTGGTAATTAAACTTGACAATTTTTT
1 AATTT-GTACTTAAACTTGAC-ATTTTTT
21715 ATATTTGTACTTAAACTT
1 A-ATTTGTACTTAAACTT
21733 TTTGGGGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 16 0.40
29 20 0.50
30 4 0.10
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (27 bp):
AATTTGTACTTAAACTTGACATTTTTT
Found at i:22071 original size:60 final size:59
Alignment explanation
Indices: 21937--22121 Score: 218
Period size: 60 Copynumber: 3.2 Consensus size: 59
21927 AATAAATTTT
** * * * * *
21937 GGTACCAAATTGAATCTAAAAAAAA-CTTAGGAACCAAATTAGGAAAAAATGCCAAGTTCA
1 GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTA--AGAAAATGTCAAGTTCA
* * *
21997 AGTATCAAACTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAAGTGTCAAGTTCA
1 GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAA-TGTCAAGTTCA
22057 GGTACCAAATTGGGT-C--AAAAAAGTTTAGGTACCAAATT-AGAAAATGTCAAGTTCA
1 GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAATGTCAAGTTCA
22112 GGTACCAAAT
1 GGTACCAAAT
22122 GTTATATAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
55 21 0.19
56 6 0.05
57 22 0.20
59 6 0.05
60 41 0.37
61 14 0.13
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (59 bp):
GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAATGTCAAGTTCA
Found at i:25007 original size:97 final size:97
Alignment explanation
Indices: 24832--25007 Score: 248
Period size: 97 Copynumber: 1.8 Consensus size: 97
24822 AACTTTGGAA
** *
24832 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTCGCACCTAGTAAGTTAAGGCACAGATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
24897 GAATCAGAGATAAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAGAAACATTGCCTCGATTT
* * *
24929 AAGGGTATTCGATTAT-TCCGATTTGAAGAAAAATCGTACCTAGTAAGTTAAGGCATAAATTTTC
1 AAGGATATTCGATTATCT-CGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTC
24993 AAAACTC-GAAATAAA
65 AAAA-TCAGAAATAAA
25008 AGAATATTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
96 1 0.01
97 66 0.96
98 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAGAAACATTGCCTCGATTT
Found at i:25383 original size:28 final size:29
Alignment explanation
Indices: 25352--25431 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
25342 ACTTTGGGGG
25352 CAAAATGGTTATTTTTGGAA-AAAAGGGT
1 CAAAATGGTTATTTTTGGAAGAAAAGGGT
* **
25380 CAAAAATGGAT-TTTTTGGAAGTTTAAGGGT
1 C-AAAATGGTTATTTTTGGAAG-AAAAGGGT
*
25410 -AAAATGGTAATTTTTGG-AGAAA
1 CAAAATGGTTATTTTTGGAAGAAA
25432 TCATGGTCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.02
28 19 0.46
29 15 0.37
30 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
CAAAATGGTTATTTTTGGAAGAAAAGGGT
Found at i:25540 original size:30 final size:30
Alignment explanation
Indices: 25391--25542 Score: 93
Period size: 30 Copynumber: 5.1 Consensus size: 30
25381 AAAAATGGAT
*
25391 TTTTTGGAAGTTTAAGGGTAAAATGGT-AA
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAAA
** * *
25420 TTTTTGGAGAAATCA-TGGTCAAAAAT-G-AAA
1 TTTTTGGA-AGTTTAGGGGT--AAAATGGTAAA
* * *
25450 TTTTTGGAAGTTTGGGGGTAAAACGGT-AT
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAAA
** * * *
25479 TTTTTGGAGAAATCATGGTTAAAAAT-G-AAA
1 TTTTTGGA-AGTTTAGGGGT-AAAATGGTAAA
25509 TTTTTGGAAGTTTAGGGGTAAAATGGTAAA
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAAA
25539 TTTT
1 TTTT
25543 GGAGAAATCG
Statistics
Matches: 87, Mismatches: 24, Indels: 23
0.65 0.18 0.17
Matches are distributed among these distances:
28 9 0.10
29 30 0.34
30 39 0.45
31 9 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
TTTTTGGAAGTTTAGGGGTAAAATGGTAAA
Found at i:25542 original size:29 final size:29
Alignment explanation
Indices: 25392--25545 Score: 75
Period size: 29 Copynumber: 5.2 Consensus size: 29
25382 AAAATGGATT
* *
25392 TTTTGGAAGTTTAAGGGTAAAATGGTAAT
1 TTTTGGAAGTTTAGGGGTAAAATGGTAAA
** * *
25421 TTTTGGAGAAATCA-TGGTCAAAAAT-G-AAA
1 TTTTGGA-AGTTTAGGGGT--AAAATGGTAAA
* * **
25450 TTTTTGGAAGTTTGGGGGTAAAACGGTATT
1 -TTTTGGAAGTTTAGGGGTAAAATGGTAAA
** * * *
25480 TTTTGGAGAAATCATGGTTAAAAAT-G-AAA
1 TTTTGGA-AGTTTAGGGGT-AAAATGGTAAA
25509 TTTTTGGAAGTTTAGGGGTAAAATGGTAAA
1 -TTTTGGAAGTTTAGGGGTAAAATGGTAAA
25539 TTTTGGA
1 TTTTGGA
25546 GAAATCGGGG
Statistics
Matches: 86, Mismatches: 27, Indels: 24
0.63 0.20 0.18
Matches are distributed among these distances:
28 9 0.10
29 37 0.43
30 31 0.36
31 9 0.10
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGGTAAAATGGTAAA
Found at i:25569 original size:29 final size:29
Alignment explanation
Indices: 25480--25571 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
25470 AAACGGTATT
** *
25480 TTTTGGAGAAATCATGGTTAAAAATGAAA
1 TTTTGGAGAAATCGGGGTTAAAAATGGAA
** *
25509 TTTTTGGA-AGTTTAGGGG-T-AAAATGGTAAA
1 -TTTTGGAGA-AATCGGGGTTAAAAATGG--AA
25539 TTTTGGAGAAATCGGGGTTAAAAATGGAA
1 TTTTGGAGAAATCGGGGTTAAAAATGGAA
25568 TTTT
1 TTTT
25572 TGAAAAGTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
28 6 0.13
29 20 0.43
30 14 0.30
31 7 0.15
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
TTTTGGAGAAATCGGGGTTAAAAATGGAA
Found at i:25573 original size:30 final size:31
Alignment explanation
Indices: 25410--25573 Score: 110
Period size: 30 Copynumber: 5.5 Consensus size: 31
25400 GTTTAAGGGT
** *
25410 AAAATGGTAATTTTTGGAGAAATCATGGTCA
1 AAAATGGTAATTTTTGGAGAAATCGGGGTTA
* ** * *
25441 AAAAT-GAAATTTTTGGA-AGTTTGGGGGT-
1 AAAATGGTAATTTTTGGAGAAATCGGGGTTA
* * **
25469 AAAACGGTATTTTTTGGAGAAATCATGGTTA
1 AAAATGGTAATTTTTGGAGAAATCGGGGTTA
* ** *
25500 AAAAT-GAAATTTTTGGA-AGTTTAGGGG-T-
1 AAAATGGTAATTTTTGGAGA-AATCGGGGTTA
*
25528 AAAATGGTAAATTTTGGAGAAATCGGGGTTA
1 AAAATGGTAATTTTTGGAGAAATCGGGGTTA
25559 AAAATGG-AATTTTTG
1 AAAATGGTAATTTTTG
25574 AAAAGTTTGG
Statistics
Matches: 94, Mismatches: 31, Indels: 17
0.66 0.22 0.12
Matches are distributed among these distances:
28 9 0.10
29 31 0.33
30 38 0.40
31 16 0.17
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAGAAATCGGGGTTA
Found at i:25586 original size:59 final size:59
Alignment explanation
Indices: 25291--25586 Score: 359
Period size: 59 Copynumber: 5.1 Consensus size: 59
25281 GGACACTTTG
* * * *
25291 GGGGTAAAA-GGTAA-TTTTGGAAAAATCAGGGTCAAAAATGAAATTTTTAGAACTTTG
1 GGGGTAAAATGGTAATTTTTGGAGAAATCAGGGTCAAAAATGAAATTTTTGGAAGTTTA
* * * * *
25348 GGGGCAAAATGGTTATTTTTGGA-AAA-AAGGGTCAAAAATGGATTTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAGAAATCAGGGTCAAAAATGAAATTTTTGGAAGTTTA
* * *
25405 AGGGTAAAATGGTAATTTTTGGAGAAATCATGGTCAAAAATGAAATTTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGAGAAATCAGGGTCAAAAATGAAATTTTTGGAAGTTTA
* * * *
25464 GGGGTAAAACGGTATTTTTTGGAGAAATCATGGTTAAAAATGAAATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAGAAATCAGGGTCAAAAATGAAATTTTTGGAAGTTTA
* * * * *
25523 GGGGTAAAATGGTAAATTTTGGAGAAATCGGGGTTAAAAATGGAATTTTTGAAAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGAGAAATCAGGGTCAAAAATGAAATTTTTG-GAAGTTTA
25582 GGGGT
1 GGGGT
25587 CGAAAATATG
Statistics
Matches: 206, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
57 53 0.26
58 10 0.05
59 137 0.67
60 6 0.03
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGAGAAATCAGGGTCAAAAATGAAATTTTTGGAAGTTTA
Done.