Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007989.1 Kokia drynarioides strain JFW-HI SEQ_122641, 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: 26455
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1032 original size:22 final size:20
Alignment explanation
Indices: 1000--1053 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
990 TTAATATTAG
1000 TTTATCAAATTAAACTA-AAAA
1 TTTA-CAAATTAAA-TATAAAA
*
1021 TATTACCAAATTTAATATAAAA
1 T-TTA-CAAATTAAATATAAAA
1043 TTTACAAATTA
1 TTTACAAATTA
1054 TATAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.21
21 6 0.21
22 16 0.57
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTACAAATTAAATATAAAA
Found at i:1052 original size:20 final size:20
Alignment explanation
Indices: 1017--1060 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
1007 AATTAAACTA
1017 AAAATATTACCAAATTTAATAT
1 AAAATATTACCAAA-TT-ATAT
1039 AAAAT-TTA-CAAATTATAT
1 AAAATATTACCAAATTATAT
1057 AAAA
1 AAAA
1061 GAAATTAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.36
19 2 0.09
20 4 0.18
21 3 0.14
22 5 0.23
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATATTACCAAATTATAT
Found at i:2496 original size:16 final size:16
Alignment explanation
Indices: 2472--2502 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2462 TGAATTGATT
*
2472 TTTTTTAATTTTTAAA
1 TTTTATAATTTTTAAA
2488 TTTTATAATTTTTAA
1 TTTTATAATTTTTAA
2503 TAATTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATAATTTTTAAA
Found at i:6245 original size:20 final size:20
Alignment explanation
Indices: 6194--6245 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
6184 TAATATAAAA
**
6194 TAATATTTAAATATTATTTTT
1 TAATA-TTAAATATTATCCTT
* **
6215 TGATAGAAAATATTATCCTT
1 TAATATTAAATATTATCCTT
6235 TAATATTAAAT
1 TAATATTAAAT
6246 TCATGTGAAA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (20 bp):
TAATATTAAATATTATCCTT
Found at i:7033 original size:40 final size:40
Alignment explanation
Indices: 6988--7067 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
6978 AAAATAAAAT
6988 TGGATACATATATTTATAAGTATAATAAATATGAAACAAA
1 TGGATACATATATTTATAAGTATAATAAATATGAAACAAA
7028 TGGATACATATATTTATAAGTATAATAAATATGAAACAAA
1 TGGATACATATATTTATAAGTATAATAAATATGAAACAAA
7068 AACAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (40 bp):
TGGATACATATATTTATAAGTATAATAAATATGAAACAAA
Found at i:23525 original size:59 final size:59
Alignment explanation
Indices: 23462--23742 Score: 352
Period size: 59 Copynumber: 4.8 Consensus size: 59
23452 AATTCGAGTT
* * * *
23462 AAAAATGGAATTTGT-AAAGGTTTGAGGATAAAAATGGAATTTTTGGAAGTTTCAAGATC
1 AAAAATGGAATTTTTGAAA-GTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTC
* * *
23521 AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGT-
1 AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTC
* * *
23579 TAAAATGGAATTTTTGGAAGTTC-AGGGGTAAAAATGGAATTTTTGGAGGTTTCAAGGTC
1 AAAAATGGAATTTTTGAAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTC
* * * * * *
23638 AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTC
* * *
23697 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAATATGGAAGTTTTGG
1 AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGG
23743 GGTCTAAAAT
Statistics
Matches: 195, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.01
58 50 0.26
59 140 0.72
60 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTC
Found at i:23527 original size:30 final size:29
Alignment explanation
Indices: 23461--23819 Score: 316
Period size: 29 Copynumber: 12.5 Consensus size: 29
23451 GAATTCGAGT
* * * *
23461 TAAAAATGGAATTTGT-AAAGGTTTGAGGA
1 TAAAAATGGAATTTTTGGAA-GTTTCAGGG
* *
23490 TAAAAATGGAATTTTTGGAAGTTTCAAGA
1 TAAAAATGGAATTTTTGGAAGTTTCAGGG
*
23519 TCAAAAATGGAATTTTTGAAAG-TTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTC-AGGG
* *
23549 TAAAAATGGAATTTTTAGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCAGGG
*
23578 TTAAAATGGAATTTTTGGAAG-TTCAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCA-GGG
* *
23607 TAAAAATGGAATTTTTGGAGGTTTCAAGG
1 TAAAAATGGAATTTTTGGAAGTTTCAGGG
23636 TCAAAAATGGAATTTTTGGAAG-TTCAAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTC-AGGG
* *
23666 TAAAAATAGAATTTTTGGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCAGGG
23695 TTAAAAATGGAATTTTTGGAAG-TTCGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTTC-AGGG
* * *
23725 TAAATATGGAAGTTTTGG--G-GTC----
1 TAAAAATGGAATTTTTGGAAGTTTCAGGG
*
23747 T-AAAATGGAATTTTTGGAAGTTT-TGGTG
1 TAAAAATGGAATTTTTGGAAGTTTCAGG-G
* * *
23775 TCGAAAATAGAATTTTTGGAAG-CTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTC-AGGG
*
23805 TAAAAATGTAATTTT
1 TAAAAATGGAATTTT
23820 AGAACAATTT
Statistics
Matches: 273, Mismatches: 34, Indels: 46
0.77 0.10 0.13
Matches are distributed among these distances:
21 14 0.05
22 1 0.00
23 1 0.00
24 1 0.00
27 3 0.01
28 4 0.01
29 148 0.54
30 99 0.36
31 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCAGGG
Found at i:23562 original size:88 final size:86
Alignment explanation
Indices: 23433--23819 Score: 348
Period size: 88 Copynumber: 4.5 Consensus size: 86
23423 TCTCTGTGGT
* * * * * *
23433 AAAATGGTAATTTTGGGAGAATTCGA-GTTAAAAATGGAATTTGTAAAGGTTTGAGGATAAAAAT
1 AAAATGG-AATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTAAA-GTTTAAGGGTAAAAAT
* *
23497 GGAATTTTTGGAAGTTTCAAGATCA
63 GGAATTTTTGGAAGTTTCAGGGT-A
* * *
23522 AAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAATGG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTA-AAGTTTAAGGGTAAAAATGG
23587 AATTTTTGGAAG-TTCAGGGGTA
65 AATTTTTGGAAGTTTCA-GGGTA
* * * *
23609 AAAATGGAATTTTTGGAGGTTTC-AAGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAAT
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTT-AAAGTTTAAGGGTAAAAAT
* *
23673 AGAATTTTTGGAAGTTTTAGGGTTA
63 GGAATTTTTGGAAGTTTCAGGG-TA
* * *
23698 AAAATGGAATTTTTGGAAGTTCGAGGGTAAATATGGAAGTTTT---G-----GGGTCTAAAATGG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAAAGTTTAAGGGT-AAAAATGG
* *
23755 AATTTTTGGAAGTTT-TGGTGTCG
65 AATTTTTGGAAGTTTCAGG-GT-A
* * *
23778 AAAATAGAATTTTTGGAAGCTCGAGGGTAAAAATGTAATTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
23820 AGAACAATTT
Statistics
Matches: 254, Mismatches: 32, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
79 7 0.03
80 59 0.23
84 1 0.00
87 32 0.13
88 119 0.47
89 36 0.14
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (86 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAAAGTTTAAGGGTAAAAATGGA
ATTTTTGGAAGTTTCAGGGTA
Found at i:23584 original size:117 final size:118
Alignment explanation
Indices: 23459--23742 Score: 387
Period size: 117 Copynumber: 2.4 Consensus size: 118
23449 GAGAATTCGA
*
23459 GTTAAAAATGGAATTTGT-AAAGGTT-TGAGGATAAAAATGGAATTTTTGGAAGTTTCAAGATCA
1 GTTAAAAATGGAATTTGTGAAA-GTTCAG-GGATAAAAATGGAATTTTTGGAAGTTTCAAGATCA
* *
23522 AAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTAGG
64 AAAATGGAATTTTTGAAAGTTCAAGGGTAAAAATAGAATTTTTAGAAGTTTTAGG
* * * * *
23577 GTT-AAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGGAGGTTTCAAGGTCAAA
1 GTTAAAAATGGAATTTGTGAAAGTTCAGGGATAAAAATGGAATTTTTGGAAGTTTCAAGATCAAA
* *
23641 AATGGAATTTTTGGAAGTTCAAGGGTAAAAATAGAATTTTTGGAAGTTTTAGG
66 AATGGAATTTTTGAAAGTTCAAGGGTAAAAATAGAATTTTTAGAAGTTTTAGG
* * * *
23694 GTTAAAAATGGAATTTTTGGAAGTTCGAGGG-TAAATATGGAAGTTTTGG
1 GTTAAAAATGGAATTTGTGAAAGTTC-AGGGATAAAAATGGAATTTTTGG
23743 GGTCTAAAAT
Statistics
Matches: 150, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
117 102 0.68
118 44 0.29
119 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (118 bp):
GTTAAAAATGGAATTTGTGAAAGTTCAGGGATAAAAATGGAATTTTTGGAAGTTTCAAGATCAAA
AATGGAATTTTTGAAAGTTCAAGGGTAAAAATAGAATTTTTAGAAGTTTTAGG
Found at i:25218 original size:24 final size:23
Alignment explanation
Indices: 25181--25227 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
25171 TTGGACTTTG
*
25181 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
25204 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
25228 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:25219 original size:17 final size:17
Alignment explanation
Indices: 25194--25256 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
25184 TAAATAGATT
25194 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
25212 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
* *
25228 GTAAATTTAAACTTAAAA
1 -TAAATTTAAATTTATAA
25246 TAAATTTAAAT
1 TAAATTTAAAT
25257 CCTGTTGGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 3 0.08
17 31 0.77
18 6 0.15
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:25221 original size:6 final size:6
Alignment explanation
Indices: 25191--25256 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
25181 ATTTAAATAG
* *
25191 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
25238 ACTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
25257 CCTGTTGGGC
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.04
5 9 0.19
6 28 0.60
7 8 0.17
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:25613 original size:123 final size:122
Alignment explanation
Indices: 25425--25726 Score: 451
Period size: 123 Copynumber: 2.5 Consensus size: 122
25415 AGCAAGGAAT
* *
25425 AGAGAAGTAGGTCAGACAACGAAACAGTCATCTTCTTGGTGAGATACAGAGAAGTGTACCAAAAT
1 AGAGAAGTAGGTCAAACAACG-AAGAGTCATCTTCTTGGTGAGATACAGAGAAGTGTACCAAAAT
* **
25490 AATGAGGTGAAGCTCAAATGTAAGTGGAACTTCAGCCCCCATCTTCCTAGTGAGATAC
65 AATGAGGTGAAGCTCAAATGTAAGTGAAACTTCAAACCCCATCTTCCTAGTGAGATAC
* *
25548 AGAGAAGTAGGTCAAACAATGAAGTAGTCATTTTCTTGGTGAGATACAGAGAAGTGTACCAAAAT
1 AGAGAAGTAGGTCAAACAACGAAG-AGTCATCTTCTTGGTGAGATACAGAGAAGTGTACCAAAAT
*
25613 AATGAGGTGAAGCTCAAATGTAAGTGAAACTTCAAACCCCATCTTCCTGGTGAGATAC
65 AATGAGGTGAAGCTCAAATGTAAGTGAAACTTCAAACCCCATCTTCCTAGTGAGATAC
* * * * * *
25671 AGAGAAGTTGGTGAAACAACAAAGCGATCATCTTCCTAGTGAGATACAGAGAAGTG
1 AGAGAAGTAGGTCAAACAACGAAGAG-TCATCTTCTTGGTGAGATACAGAGAAGTG
25727 GGTGAAACAA
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
122 3 0.02
123 158 0.98
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (122 bp):
AGAGAAGTAGGTCAAACAACGAAGAGTCATCTTCTTGGTGAGATACAGAGAAGTGTACCAAAATA
ATGAGGTGAAGCTCAAATGTAAGTGAAACTTCAAACCCCATCTTCCTAGTGAGATAC
Found at i:25705 original size:47 final size:47
Alignment explanation
Indices: 25652--25754 Score: 188
Period size: 47 Copynumber: 2.2 Consensus size: 47
25642 CTTCAAACCC
* *
25652 CATCTTCCTGGTGAGATACAGAGAAGTTGGTGAAACAACAAAGCGAT
1 CATCTTCCTAGTGAGATACAGAGAAGTGGGTGAAACAACAAAGCGAT
25699 CATCTTCCTAGTGAGATACAGAGAAGTGGGTGAAACAACAAAGCGAT
1 CATCTTCCTAGTGAGATACAGAGAAGTGGGTGAAACAACAAAGCGAT
25746 CATCTTCCT
1 CATCTTCCT
25755 TGAAGAGTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (47 bp):
CATCTTCCTAGTGAGATACAGAGAAGTGGGTGAAACAACAAAGCGAT
Found at i:26435 original size:2 final size:2
Alignment explanation
Indices: 26428--26455 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26418 TCATACAAGG
26428 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
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.