Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011797.1 Kokia drynarioides strain JFW-HI SEQ_126792, 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: 61148
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:2463 original size:17 final size:16
Alignment explanation
Indices: 2441--2472 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2431 AAAGTTAGTG
2441 GCTTAAGTTAAGGTTAA
1 GCTTAAGTT-AGGTTAA
2458 GCTTAAGTTAGGTTA
1 GCTTAAGTTAGGTTA
2473 TATTTTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
GCTTAAGTTAGGTTAA
Found at i:2524 original size:20 final size:21
Alignment explanation
Indices: 2501--2544 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2491 TGTCTGTTTA
*
2501 AAAATATTTATTTTTAT-ATT
1 AAAATATATATTTTTATAATT
*
2521 AAAATGTATATTTTTATAATT
1 AAAATATATATTTTTATAATT
2542 AAA
1 AAA
2545 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AAAATATATATTTTTATAATT
Found at i:8520 original size:18 final size:18
Alignment explanation
Indices: 8481--8522 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
8471 ATTTTTCTCT
* *
8481 CTTTATTTTTTCTATTTT
1 CTTTATTTTTTCTACTTC
*
8499 CTTTTTTTTTTCTACTTC
1 CTTTATTTTTTCTACTTC
8517 CTTTAT
1 CTTTAT
8523 AACATCTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTATTTTTTCTACTTC
Found at i:11423 original size:19 final size:20
Alignment explanation
Indices: 11399--11456 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
11389 TTGAAATCTT
*
11399 TTTATTTTTGTAAATTTA-A
1 TTTATTTTTATAAATTTACA
**
11418 TTTATTTCAATAAATTTCACA
1 TTTATTTTTATAAATTT-ACA
*
11439 TTTAATTTTATAAATTTA
1 TTTATTTTTATAAATTTA
11457 TTACACAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 15 0.48
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTATTTTTATAAATTTACA
Found at i:11972 original size:14 final size:15
Alignment explanation
Indices: 11937--11972 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
11927 CTTCCCTTTA
11937 ATTTTT-ATTTATTT
1 ATTTTTAATTTATTT
11951 ATTTTTAATTTATTT
1 ATTTTTAATTTATTT
11966 -TTTTTAA
1 ATTTTTAA
11973 AAGCAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTAATTTATTT
Found at i:12920 original size:37 final size:37
Alignment explanation
Indices: 12870--12947 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
12860 GGTTAATAAA
12870 ATTGGAAGTTTCATGCTGTGCATTGTGCAAACAATAC
1 ATTGGAAGTTTCATGCTGTGCATTGTGCAAACAATAC
12907 ATTGGAAGTTTCATGCTGTGCATTGTGCAAACAATAC
1 ATTGGAAGTTTCATGCTGTGCATTGTGCAAACAATAC
12944 ATTG
1 ATTG
12948 ATTAATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (37 bp):
ATTGGAAGTTTCATGCTGTGCATTGTGCAAACAATAC
Found at i:24953 original size:22 final size:21
Alignment explanation
Indices: 24901--24953 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
24891 TGTTGAATCG
24901 GATTTTTTATAAAAATTTAAA
1 GATTTTTTATAAAAATTTAAA
* * *
24922 GATATTTTTATGAAATTTTAAT
1 GAT-TTTTTATAAAAATTTAAA
24944 GATTTATTTA
1 GATTT-TTTA
24954 ATCAAATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (21 bp):
GATTTTTTATAAAAATTTAAA
Found at i:33458 original size:16 final size:14
Alignment explanation
Indices: 33430--33464 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
33420 TAAAAAAACC
33430 TTAAAAATTAAAAT
1 TTAAAAATTAAAAT
33444 TTAAAAGATTGAAAAT
1 TTAAAA-ATT-AAAAT
33460 TTAAA
1 TTAAA
33465 TTTCCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 3 0.16
16 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (14 bp):
TTAAAAATTAAAAT
Found at i:43058 original size:64 final size:61
Alignment explanation
Indices: 42928--43063 Score: 191
Period size: 64 Copynumber: 2.2 Consensus size: 61
42918 TTAATATAAC
*
42928 ATTTGGTACTTGAACTTGACACTTTTTTTTGAATTTGGTACCTAAACTTTTTTGAGACTCA
1 ATTTGGTACCTGAACTTGACACTTTTTTTTGAATTTGGTACCTAAACTTTTTTGAGACTCA
* * * * *
42989 ATTTGGTACCTGAACTTGACATTTTTTTTTTCTAATTTGGTACCTAAGCATTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACA-CTTTTTTTT-GAATTTGGTACCTAAAC-TTTTTTGAGACTCA
43053 ATTTGGTACCT
1 ATTTGGTACCT
43064 AAATTTATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
61 20 0.30
62 8 0.12
63 15 0.23
64 23 0.35
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.48
Consensus pattern (61 bp):
ATTTGGTACCTGAACTTGACACTTTTTTTTGAATTTGGTACCTAAACTTTTTTGAGACTCA
Found at i:43321 original size:31 final size:31
Alignment explanation
Indices: 43264--43322 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
43254 ATTGGACCCC
*
43264 AAAAAGTGTCAAGTTTAGATATTAAATTAAG
1 AAAAAGTGTCAAGTTTAGATACTAAATTAAG
*
43295 AAAAAGTTTCAAGTTT-GAGTACTAAATT
1 AAAAAGTGTCAAGTTTAGA-TACTAAATT
43323 GGATCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGATACTAAATTAAG
Found at i:44361 original size:30 final size:30
Alignment explanation
Indices: 44291--44370 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
44281 TCAATATGTT
** * *
44291 ATAAAAAAATATTAAAAATTACATAAAATC
1 ATAAAAATTTATTAAAAAATACAAAAAATC
* *
44321 TTTAAAATTTATTAAAAAATA-AAAAAATC
1 ATAAAAATTTATTAAAAAATACAAAAAATC
*
44350 ATAAAAGATTTATAAAAAAAT
1 ATAAAA-ATTTATTAAAAAAT
44371 CTTTAAAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 11 0.28
30 29 0.73
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (30 bp):
ATAAAAATTTATTAAAAAATACAAAAAATC
Found at i:44368 original size:21 final size:21
Alignment explanation
Indices: 44339--44387 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
44329 TTATTAAAAA
44339 ATAAAAAAATCATAAAAGATTT
1 ATAAAAAAATCATAAAA-ATTT
* *
44361 ATAAAAAAATCTTTAAAATTT
1 ATAAAAAAATCATAAAAATTT
44382 ATAAAA
1 ATAAAA
44388 TATATAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAAAAAAATCATAAAAATTT
Found at i:45500 original size:29 final size:29
Alignment explanation
Indices: 45468--45606 Score: 118
Period size: 29 Copynumber: 4.7 Consensus size: 29
45458 TTCGTGGTCA
* *
45468 AAAATGGAAGTTTTGGAGGTTCGGGGGGT
1 AAAATGGAATTTTTGGAAGTTCGGGGGGT
** *
45497 AAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTCGGGGGGT
* * ***
45526 AAAATGGAATTTTTGAAAGTTTCGAGGTAA
1 AAAATGGAATTTTTGGAAG-TTCGGGGGGT
* * *
45556 AAAATGGGATTTTTGGAAGTTC-GAGAGT
1 AAAATGGAATTTTTGGAAGTTCGGGGGGT
*
45584 AAAAATGGAATTTTCGGACAGTT
1 -AAAATGGAATTTTTGGA-AGTT
45607 TAGGGACCTC
Statistics
Matches: 86, Mismatches: 21, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
28 1 0.01
29 60 0.70
30 25 0.29
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGGT
Found at i:45549 original size:88 final size:90
Alignment explanation
Indices: 45437--45607 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 90
45427 GGGAAGGGGC
* * * * *
45437 AAAATGGTAATTTTTAAAAGTTTCGTGGTCAAAAATGGAAGTTTTGGAGGTTCGGGGGGT-AAAA
1 AAAATGGTAATTTTTAAAAGTTTCGAGGTAAAAAATGGAAGTTTTGGAAGTTC-GAGAGTAAAAA
*
45501 TGGAATTTTTGGA-AGTTTTGGGGTT
65 TGGAATTTTCGGACAGTTTTGGGGTT
* * *
45526 AAAATGG-AATTTTTGAAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCGAGAGTAAAAAT
1 AAAATGGTAATTTTTAAAAGTTTCGAGGTAAAAAATGGAAGTTTTGGAAGTTCGAGAGTAAAAAT
45590 GGAATTTTCGGACAGTTT
66 GGAATTTTCGGACAGTTT
45608 AGGGACCTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
87 4 0.06
88 55 0.77
89 12 0.17
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (90 bp):
AAAATGGTAATTTTTAAAAGTTTCGAGGTAAAAAATGGAAGTTTTGGAAGTTCGAGAGTAAAAAT
GGAATTTTCGGACAGTTTTGGGGTT
Found at i:47175 original size:17 final size:17
Alignment explanation
Indices: 47153--47231 Score: 99
Period size: 17 Copynumber: 4.7 Consensus size: 17
47143 TAAATAAATT
47153 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
47170 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
47187 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
* **
47204 TAAACTT-AATTAAAAA
1 TAAATTTAAATTTCAAA
*
47220 AAAATTTAAATT
1 TAAATTTAAATT
47232 CTGTTGGGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
16 12 0.22
17 42 0.76
18 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:47175 original size:23 final size:23
Alignment explanation
Indices: 47140--47187 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
47130 ATTGGACATT
47140 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
47162 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
47186 AT
1 AT
47188 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:47196 original size:23 final size:23
Alignment explanation
Indices: 47145--47204 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
47135 ACATTATTTA
**
47145 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
47168 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
47192 -TTAAATTTCAAAT
1 AATAAATTT-AAAT
47205 AAACTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:47204 original size:7 final size:6
Alignment explanation
Indices: 47147--47204 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
47137 ATTATTTAAA
47147 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
47193 TAAATT TCAAAT
1 TAAATT T-AAAT
47205 AAACTTAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
4 5 0.11
5 3 0.07
6 28 0.62
7 9 0.20
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:47207 original size:11 final size:10
Alignment explanation
Indices: 47140--47197 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
47130 ATTGGACATT
47140 ATTTAAATAA
1 ATTTAAATAA
47150 ATTTAAATTTAA
1 ATTTAAA--TAA
47162 ATTTATAATAA
1 ATTTA-AATAA
47173 ATTTAAAT--
1 ATTTAAATAA
*
47181 -TTCAAATAA
1 ATTTAAATAA
47190 ATTTAAAT
1 ATTTAAAT
47198 TTCAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:59756 original size:30 final size:30
Alignment explanation
Indices: 59709--59899 Score: 221
Period size: 29 Copynumber: 6.4 Consensus size: 30
59699 CGGGCGAGGT
*
59709 AAAATGGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTCA
* *
59740 AAAATGGAAGTTTT-GAAGGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAA-GTTTTGGGGTCA
* *
59769 AAAATGGAATTTTTGGAAGTTTTAGGGTTGA
1 AAAATGGAATTTTTGGAAGTTTT-GGGGTCA
* *
59800 AAAA-AGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
59829 AAATTGGATTTTTTGGAAGTTTTGGGGTC-
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
59858 AAAATGGGATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
59887 AAAATGGAATTTT
1 AAAATGGAATTTT
59900 CAGACAGTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
29 63 0.47
30 60 0.44
31 12 0.09
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTCA
Found at i:59789 original size:59 final size:59
Alignment explanation
Indices: 59598--59899 Score: 235
Period size: 59 Copynumber: 5.1 Consensus size: 59
59588 GCAAAATGAT
* * * * * * *
59598 AATTTTGGGAAATTTTGGGGTTAAAAATGGAATATTTAGACA-TTTAGGGGT-AAAAGGG
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAATGG
* * * * * * *
59656 TAA-TTTT-GAGAGTTTCGAGGTTAAAAATAGAGTTTTTGG-ACTTCGGGCGAGGT-AAAATGG
1 -AATTTTTGGA-AGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT-TGG-G-GGTAAAAATGG
* *
59716 TAATTTTTGAAAGTTTTGGGGTCAAAAATGGAAGTTTT-GAAGGTTTGGGGGTAAAAATGG
1 -AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAA-GTTTGGGGGTAAAAATGG
* * * ** *
59776 AATTTTTGGAAGTTTTAGGGTTGAAAAA-AGAATTTTTGGAAGTTTTAGGGTCAAAATTGG
1 AATTTTTGGAAGTTTT-GGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGG
* *
59836 ATTTTTTGGAAGTTTTGGGGTC-AAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGG
59894 AATTTT
1 AATTTT
59900 CAGACAGTTT
Statistics
Matches: 192, Mismatches: 37, Indels: 29
0.74 0.14 0.11
Matches are distributed among these distances:
56 1 0.01
57 4 0.02
58 42 0.22
59 59 0.31
60 55 0.29
61 28 0.15
62 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (59 bp):
AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGG
Done.