Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005340.1 Kokia drynarioides strain JFW-HI SEQ_119296, 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: 48927
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:1204 original size:6 final size:6
Alignment explanation
Indices: 1193--1237 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1183 TGATCAAAAT
* * *
1193 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
1238 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:9817 original size:4 final size:4
Alignment explanation
Indices: 9808--9963 Score: 114
Period size: 4 Copynumber: 38.0 Consensus size: 4
9798 TTAAAAATAT
* * * * *
9808 TTTA TTTA TTTA TTTA ATTA TTTGT TTTA TTTA ATTA GTTA GTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * * *
9857 TATA TCTA GTTA TTTA TTTA TTTTA TGTA TTTA GTTA TTTTT TTTA TTTTG
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
* * ** *
9908 TTTA TTTA GTTA TTTA TTTA CTTA TTTA CCTA GTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
9956 CTTA TTTA
1 TTTA TTTA
9964 CTTACATCGT
Statistics
Matches: 117, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
4 105 0.90
5 12 0.10
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:9855 original size:41 final size:41
Alignment explanation
Indices: 9809--9963 Score: 107
Period size: 41 Copynumber: 3.8 Consensus size: 41
9799 TAAAAATATT
*
9809 TTATTTATTTATTTAATTATTTGTTTTATTTAAT-TAGTTAG
1 TTATTTATTTATTTAATTATTT-ATTTATTTAATGTAGTTAG
* * * * *
9850 TTATTTATATATCTAGTTATTTATTTATTTTATGTATTTAG
1 TTATTTATTTATTTAATTATTTATTTATTTAATGTAGTTAG
* ** * * * *
9891 TTATTTTTTTTATTTTGTTTATTTAGTTATTT-ATTTACTTAT
1 TTA-TTTATTTA-TTTAATTATTTATTTATTTAATGTAGTTAG
** * * *
9933 TTACCTAGTTATTTATTTATTTACTTATTTA
1 TTATTTATTTATTTAATTATTTATTTATTTA
9964 CTTACATCGT
Statistics
Matches: 89, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
40 26 0.29
41 32 0.36
42 16 0.18
43 15 0.17
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (41 bp):
TTATTTATTTATTTAATTATTTATTTATTTAATGTAGTTAG
Found at i:9889 original size:17 final size:17
Alignment explanation
Indices: 9867--9927 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
9857 TATATCTAGT
9867 TATTTATTTATTTTATG
1 TATTTATTTATTTTATG
* * *
9884 TATTTAGTTATTTTTTT
1 TATTTATTTATTTTATG
*
9901 TATTTTGTTTA-TTTA-G
1 TA-TTTATTTATTTTATG
9917 TTATTTATTTA
1 -TATTTATTTA
9928 CTTATTTACC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.21
17 21 0.62
18 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (17 bp):
TATTTATTTATTTTATG
Found at i:10011 original size:31 final size:31
Alignment explanation
Indices: 9973--10051 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
9963 ACTTACATCG
*
9973 TAAAATTTATCTAGTTACTTATTTACTAAGT
1 TAAAATTTATATAGTTACTTATTTACTAAGT
* * *
10004 TAAAATTTATTTAATTACTTATTTACTTAGT
1 TAAAATTTATATAGTTACTTATTTACTAAGT
*
10035 TAGAATTTATATAGTTA
1 TAAAATTTATATAGTTA
10052 TTGTATAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (31 bp):
TAAAATTTATATAGTTACTTATTTACTAAGT
Found at i:25698 original size:91 final size:91
Alignment explanation
Indices: 25525--25824 Score: 388
Period size: 91 Copynumber: 3.3 Consensus size: 91
25515 CTCCAGTTTA
* * * * * * * *
25525 TGGATAAACCACTAGTG-TTGCAGGTTAATATGCTATTAGTAGTTGTGAGTACACAACAACTTTG
1 TGGATAAACCACGAGTGTTTGCATGTTAATATGCTGTTAGTGGTTATGAATACACAATAAGTTTG
** ** *
25589 CAGATAATAATTGTCAGTATAAGGTG
66 CAGATAATAGCTACCAGTATAAGTTG
* * * *
25615 TGGTTAAACCACGAGTGCTTGCATGTTAATATGATGTTAGTGGTTATGAATACACAATGAGTTTG
1 TGGATAAACCACGAGTGTTTGCATGTTAATATGCTGTTAGTGGTTATGAATACACAATAAGTTTG
25680 CAGATAATAGCTACCAGTATAAGTTG
66 CAGATAATAGCTACCAGTATAAGTTG
* * * *
25706 TGGATAAACCACAAGTGTTTGCATGTTAATACGCTGTCAATGGTTATGAATACACAATAAGTTTG
1 TGGATAAACCACGAGTGTTTGCATGTTAATATGCTGTTAGTGGTTATGAATACACAATAAGTTTG
*
25771 CAGATAATAGCTACCAATATAAGTTG
66 CAGATAATAGCTACCAGTATAAGTTG
25797 TGGATAAACCACGAGTGTTTGCA-GTTAA
1 TGGATAAACCACGAGTGTTTGCATGTTAA
25825 AATTGTCAAT
Statistics
Matches: 183, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
90 20 0.11
91 163 0.89
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (91 bp):
TGGATAAACCACGAGTGTTTGCATGTTAATATGCTGTTAGTGGTTATGAATACACAATAAGTTTG
CAGATAATAGCTACCAGTATAAGTTG
Found at i:25820 original size:47 final size:47
Alignment explanation
Indices: 25675--25820 Score: 140
Period size: 47 Copynumber: 3.2 Consensus size: 47
25665 TACACAATGA
*
25675 GTTTGCAGATAATAGCTACCAGTATAAGTTGTGGATAAACCACAAGT
1 GTTTGCAGATAATAGCTACCAATATAAGTTGTGGATAAACCACAAGT
* ** * * * * * *
25722 GTTTGCATGTTAATACGCTGTC-A-AT-GGTTATGAATACACAATAA--
1 GTTTGCA-GATAATA-GCTACCAATATAAGTTGTGGATAAACCACAAGT
*
25766 GTTTGCAGATAATAGCTACCAATATAAGTTGTGGATAAACCACGAGT
1 GTTTGCAGATAATAGCTACCAATATAAGTTGTGGATAAACCACAAGT
25813 GTTTGCAG
1 GTTTGCAG
25821 TTAAAATTGT
Statistics
Matches: 72, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
42 4 0.06
43 7 0.10
44 9 0.12
45 12 0.17
46 13 0.18
47 17 0.24
48 6 0.08
49 4 0.06
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (47 bp):
GTTTGCAGATAATAGCTACCAATATAAGTTGTGGATAAACCACAAGT
Found at i:28912 original size:24 final size:23
Alignment explanation
Indices: 28852--28912 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
28842 AAATAAATTT
28852 TATAAATTTATATT-ACATAAAC
1 TATAAATTTATATTCACATAAAC
** *
28874 TATAAATAAAAATTCATCATAAAC
1 TATAAATTTATATTCA-CATAAAC
28898 T-TAAAATTTATATTC
1 TAT-AAATTTATATTC
28913 TTTAATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 11 0.37
23 2 0.07
24 17 0.57
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAAATTTATATTCACATAAAC
Found at i:29442 original size:16 final size:14
Alignment explanation
Indices: 29414--29457 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
29404 AAGTTAAATA
*
29414 AATATTAATTTTTTT
1 AATATTAA-ATTTTT
29429 AATAATTAAATTTTT
1 AAT-ATTAAATTTTT
29444 AATATTAAAATTTT
1 AATATT-AAATTTT
29458 CTTTCACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 18 0.69
16 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATATTAAATTTTT
Found at i:29597 original size:13 final size:13
Alignment explanation
Indices: 29579--29603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29569 AAAGTAAGTT
29579 TGTAAATATTATC
1 TGTAAATATTATC
29592 TGTAAATATTAT
1 TGTAAATATTAT
29604 TATTTAATAT
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:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TGTAAATATTATC
Found at i:31264 original size:100 final size:101
Alignment explanation
Indices: 31146--31330 Score: 237
Period size: 100 Copynumber: 1.8 Consensus size: 101
31136 CAAGTTGGCG
* * ** **
31146 AGCGTAAACGCATATATAAAATGACGAACGTAAATGTGTGCAAGCTGGTGAGCATAAACACATAT
1 AGCGTAAACGCATATATAAAATGAAGAACGTAAACGAATGCAAGCTGGCAAGCATAAACACATAT
*
31211 ATA-AGTTGACGAGCGTAAACATGAGCAAGCTAGCA
66 ATATAGCTGACGAGCGTAAACATGAGCAAGCTAGCA
* ** ** * *
31246 AGCGTAAACTCATATATAAGCTGAAGAGTGTAAACGAATGCAAGCTGGCAAGCGTAAACGCATAT
1 AGCGTAAACGCATATATAAAATGAAGAACGTAAACGAATGCAAGCTGGCAAGCATAAACACATAT
31311 ATATAGCTGACGAGCGTAAA
66 ATATAGCTGACGAGCGTAAA
31331 AGTATGAAAG
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
100 55 0.79
101 15 0.21
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (101 bp):
AGCGTAAACGCATATATAAAATGAAGAACGTAAACGAATGCAAGCTGGCAAGCATAAACACATAT
ATATAGCTGACGAGCGTAAACATGAGCAAGCTAGCA
Found at i:31265 original size:50 final size:49
Alignment explanation
Indices: 31135--31330 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 49
31125 CTGGACGTAT
* * ** * * *
31135 GCAAGTTGGCGAGCGTAAACGCATATATAAAATGACGAACGTAAATGTGT
1 GCAAGCTGGCAAGCGTAAACGCATATATAAGCTGACGAGCGTAAA-CTGA
** * * *
31185 GCAAGCTGGTGAGCATAAACACATATATAAGTTGACGAGCGTAAACATGA
1 GCAAGCTGGCAAGCGTAAACGCATATATAAGCTGACGAGCGTAAAC-TGA
* * * *
31235 GCAAGCTAGCAAGCGTAAACTCATATATAAGCTGAAGAGTGTAAAC-GAA
1 GCAAGCTGGCAAGCGTAAACGCATATATAAGCTGACGAGCGTAAACTG-A
31284 TGCAAGCTGGCAAGCGTAAACGCATATATATAGCTGACGAGCGTAAA
1 -GCAAGCTGGCAAGCGTAAACGCATATATA-AGCTGACGAGCGTAAA
31331 AGTATGAAAG
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 105 0.87
51 14 0.12
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (49 bp):
GCAAGCTGGCAAGCGTAAACGCATATATAAGCTGACGAGCGTAAACTGA
Found at i:38283 original size:52 final size:52
Alignment explanation
Indices: 38201--38544 Score: 537
Period size: 52 Copynumber: 6.6 Consensus size: 52
38191 TTCACATTTA
* * * * * *
38201 ATACTCACGATAACATATTA-TCATCAGACCTCATAATTCGAAAAAGATTCAT
1 ATACTCACGATGACACA-TAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
**
38253 ATACTCACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
*
38305 ATACTCACGATGACACATAGTCATTGGACCTTATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
*
38357 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
* * *
38409 ATACTCACGATGACACATAGTCATTGGACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
*
38461 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
*
38513 ATACTCACGGTGACACATAGTCATCGGACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
38545 TTGCATTTAT
Statistics
Matches: 275, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
51 2 0.01
52 273 0.99
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAAGATTCAT
Found at i:41429 original size:17 final size:17
Alignment explanation
Indices: 41407--41441 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41397 GTTGGTAAGC
41407 TTTGATAATGTTTCAAG
1 TTTGATAATGTTTCAAG
41424 TTTGATAATGTTTCAAG
1 TTTGATAATGTTTCAAG
41441 T
1 T
41442 AGGCATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.49
Consensus pattern (17 bp):
TTTGATAATGTTTCAAG
Found at i:42735 original size:22 final size:22
Alignment explanation
Indices: 42710--42758 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
42700 TTTAAATAAA
*
42710 AAAAAT-ATAAATCTAAAAATTT
1 AAAAATAATAAATC-AAAAATTC
* *
42732 AAAATTAATAATTCAAAAATTC
1 AAAAATAATAAATCAAAAATTC
42754 AAAAA
1 AAAAA
42759 ATAGAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATAATAAATCAAAAATTC
Found at i:42986 original size:21 final size:21
Alignment explanation
Indices: 42960--43000 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42950 AAAATATTGA
*
42960 TCAACATCGATTAATGATCAG
1 TCAACACCGATTAATGATCAG
*
42981 TCAACACCGGTTAATGATCA
1 TCAACACCGATTAATGATCA
43001 ACCAAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (21 bp):
TCAACACCGATTAATGATCAG
Found at i:45347 original size:53 final size:53
Alignment explanation
Indices: 45289--45395 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
45279 TTTTTACTTG
45289 AATTCTGCAGATCTTAGTTTTGGTTTTAGTAGGAGATAGTGCTGAACTTCCAT
1 AATTCTGCAGATCTTAGTTTTGGTTTTAGTAGGAGATAGTGCTGAACTTCCAT
45342 AATTCTGCAGATCTTAGTTTTGGTTTTAGTAGGAGATAGTGCTGAACTTCCAT
1 AATTCTGCAGATCTTAGTTTTGGTTTTAGTAGGAGATAGTGCTGAACTTCCAT
45395 A
1 A
45396 GTTGAAAATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (53 bp):
AATTCTGCAGATCTTAGTTTTGGTTTTAGTAGGAGATAGTGCTGAACTTCCAT
Done.