Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000942.1 Kokia drynarioides strain JFW-HI SEQ_112106, 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: 32973
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4419 original size:26 final size:27
Alignment explanation
Indices: 4390--4490 Score: 109
Period size: 26 Copynumber: 3.9 Consensus size: 27
4380 CTTTTAAAAA
*
4390 TATTTTTAAGT-TTTTTTTTTTTACAT
1 TATTTCTAAGTCTTTTTTTTTTTACAT
** *
4416 TATTTCTCTGTCTTTTTTTTTTTTC-T
1 TATTTCTAAGTCTTTTTTTTTTTACAT
* *
4442 TNTTTTTAAGT-TTTTTTTTTTTACAT
1 TATTTCTAAGTCTTTTTTTTTTTACAT
**
4468 TATTTCTCTGTCTTTTTTTTTTT
1 TATTTCTAAGTCTTTTTTTTTTT
4491 CTTTTTACCC
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
25 12 0.20
26 24 0.41
27 23 0.39
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.75
Consensus pattern (27 bp):
TATTTCTAAGTCTTTTTTTTTTTACAT
Found at i:4454 original size:52 final size:51
Alignment explanation
Indices: 4392--4496 Score: 194
Period size: 52 Copynumber: 2.1 Consensus size: 51
4382 TTTAAAAATA
4392 TTTTTAAGTTTTTTTTTTTTACATTATTTCTCTGTCTTTTTTTTTTTTCTT
1 TTTTTAAGTTTTTTTTTTTTACATTATTTCTCTGTCTTTTTTTTTTTTCTT
4443 NTTTTTAAGTTTTTTTTTTTTACATTATTTCTCTGTC-TTTTTTTTTTTCTT
1 -TTTTTAAGTTTTTTTTTTTTACATTATTTCTCTGTCTTTTTTTTTTTTCTT
4494 TTT
1 TTT
4497 ACCCTTTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 3 0.06
51 14 0.26
52 36 0.68
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (51 bp):
TTTTTAAGTTTTTTTTTTTTACATTATTTCTCTGTCTTTTTTTTTTTTCTT
Found at i:16126 original size:39 final size:38
Alignment explanation
Indices: 16071--16156 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 38
16061 TCAAATTATA
16071 AAATATTTTGAAAATG-AGGGAAAATTGTTGGAACATTTTC
1 AAATA-TTTGAAAATGAAGGG-AAATTGTTGGAACA-TTTC
*
16111 AAATATTTGAAAATGAAGGGAGATTGTTGGAACATTTC
1 AAATATTTGAAAATGAAGGGAAATTGTTGGAACATTTC
16149 AAATATTT
1 AAATATTT
16157 ATAGTGTTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
38 12 0.27
39 23 0.52
40 9 0.20
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.35
Consensus pattern (38 bp):
AAATATTTGAAAATGAAGGGAAATTGTTGGAACATTTC
Found at i:20487 original size:20 final size:21
Alignment explanation
Indices: 20452--20491 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20442 GCATTTTTCT
*
20452 ATTTACTTTTATTTGTTTCAC
1 ATTTACTTTTAGTTGTTTCAC
20473 ATTTACTTTT-GTTGTTTCA
1 ATTTACTTTTAGTTGTTTCA
20492 AATTCCTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.62
Consensus pattern (21 bp):
ATTTACTTTTAGTTGTTTCAC
Found at i:22860 original size:17 final size:18
Alignment explanation
Indices: 22822--22860 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22812 TGTATTCTTA
**
22822 TTGTCACTGCATTTTGTT
1 TTGTCACTGCATTTCCTT
22840 TTGTCACTGCA-TTCCTT
1 TTGTCACTGCATTTCCTT
22857 TTGT
1 TTGT
22861 TAACTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.10, C:0.21, G:0.15, T:0.54
Consensus pattern (18 bp):
TTGTCACTGCATTTCCTT
Found at i:23024 original size:75 final size:75
Alignment explanation
Indices: 22901--23040 Score: 226
Period size: 75 Copynumber: 1.9 Consensus size: 75
22891 TAATATTGTC
* * * *
22901 AGTGCATTGGGGACAACGCAGATATTAAGTTTGGGGGGAGATATTGTGAAATGGAAATGTAATTA
1 AGTGCATTGGGGACAACGCAAATATTAAGTTTAGGGGGAGATAATGTGAAATGGAAATGCAATTA
22966 TACAATTGAA
66 TACAATTGAA
* *
22976 AGTGCATTGTGGACAATGCAAATATTAAGTTTAGGGGGAGATAATGTGAAATGGAAATGCAATTA
1 AGTGCATTGGGGACAACGCAAATATTAAGTTTAGGGGGAGATAATGTGAAATGGAAATGCAATTA
23041 CACCTACATA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.28
Consensus pattern (75 bp):
AGTGCATTGGGGACAACGCAAATATTAAGTTTAGGGGGAGATAATGTGAAATGGAAATGCAATTA
TACAATTGAA
Found at i:25697 original size:15 final size:15
Alignment explanation
Indices: 25673--25703 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25663 ATAAATAATA
*
25673 TAAAGGGATCAAATC
1 TAAAGAGATCAAATC
25688 TAAAGAGATCAAATC
1 TAAAGAGATCAAATC
25703 T
1 T
25704 GTATAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (15 bp):
TAAAGAGATCAAATC
Found at i:31756 original size:436 final size:435
Alignment explanation
Indices: 30723--32460 Score: 2474
Period size: 436 Copynumber: 4.0 Consensus size: 435
30713 TGCAACTTGC
* *
30723 AAAAGGCTTTAGTTTATTGGCCTTCATAGTAACTTTTTCAAGTTTCACAGCTACTTTTATATATA
1 AAAAGGCTTTAGTTTATTGGCCTTCACAGTAACTTTTTCAAGTTTCACAGCTACTTTTATACATA
* * * * *
30788 CTGATGGTCCTTTCAGGCTACATATACATCACAAATTTAGTTTCCTACTTGGTTGGAACCATG-C
66 CTGGTGGTCCTTTCA-GCTACACATACATAATAAATTTAGTTTCCTACTTGGTTAGAACCATGTC
* * * * *
30852 TTAATTAAACTGCTAATAACAGTGACAGAGTCAAAAAATTTGTTTTG-GGGA-C-AGAACTAAAT
130 -TAATTAAACTGATAATAACAGTGGCAGGGTTAAAAAATTTGTTTTGAGAGATCGA-AACTAAAT
* * * *
30914 TGTAAATTTTTATAATAGTAAAAATGCAATTTCATCATTTTAATAGCATATATTTTTATAATTTT
193 TATATATTTTTATAATAGTAAAAATACAATTTCATCATTTTAATAGC-TATATCTTTATAATTTT
* * *
30979 TAAAGGGTTAAATCAATTTTTTATCATTTTTGAAGGATGAAAGTGCAATTTTACTATTAGTATTT
257 TAAAGGGTTAAATCAAATTTTTATCATTTTTGAAGGATCAAAGTGCAATTTTACTATTACTATTT
31044 TAAAATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACTC
322 TAAAATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACTC
* * * *
31109 CCGGATCTCCATTACACTTCGTTACTGACTACTAAGTCTAACTTTTTGG
387 CCGGATCTCCACTACGCTCCGTCACTGACTACTAAGTCTAACTTTTTGG
*
31158 AAAAGGCTTTAGTTTATTGGCCTTCACCAGTAACTTTTTCAAGTTTCACAGCTGCTTTTATACAT
1 AAAAGGCTTTAGTTTATTGGCCTTCA-CAGTAACTTTTTCAAGTTTCACAGCTACTTTTATACAT
* * *
31223 AC-GGATGGTCCTTTCGAGCTATACATACATAATAAATTTAGTTTTCTACTTGGTTATAACCAT-
65 ACTGG-TGGTCCTTTC-AGCTACACATACATAATAAATTTAGTTTCCTACTTGGTTAGAACCATG
* *
31286 TCCTAATTAAACTGCTAATAACAGTGGC--GGTTAAAAAATTTATTTTGAGAGATCGAAACTAAA
128 T-CTAATTAAACTGATAATAACAGTGGCAGGGTTAAAAAATTTGTTTTGAGAGATCGAAACTAAA
**
31349 TTATATATTTTTATAATAGTAAAAATGTAATTTCATCATTTTAATAGTCTATATCTTTATAATTT
192 TTATATATTTTTATAATAGTAAAAATACAATTTCATCATTTTAATAG-CTATATCTTTATAATTT
*
31414 TTAAAGGGTTAAATCAAATTTTTATCATTTTTGAAGGATGAAAGTGCAATTTTACTATTACTATT
256 TTAAAGGGTTAAATCAAATTTTTATCATTTTTGAAGGATCAAAGTGCAATTTTACTATTACTATT
*
31479 TT-AAATTGTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACT
321 TTAAAATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACT
** *
31543 CTTGGATCTCCACTACGCTCCGTCACTGGCTACTAAGTCTAACTTTTTGG
386 CCCGGATCTCCACTACGCTCCGTCACTGACTACTAAGTCTAACTTTTTGG
* * *
31593 AAAAGGCTTTAGTTTATTGGCCTCCACAGTAACTTTTTCAAGTTTCACAGCTGCTTTTATATATA
1 AAAAGGCTTTAGTTTATTGGCCTTCACAGTAACTTTTTCAAGTTTCACAGCTACTTTTATACATA
* * *
31658 CTGGTGGTCCTTTCAGTCTACATATACATAATAAATTTAGTTTCCTACTTGGTTAAAACTATGTC
66 CTGGTGGTCCTTTCAG-CTACACATACATAATAAATTTAGTTTCCTACTTGGTTAGAACCATGTC
* * * * ** * *
31723 GAATTAAACTGATAATAACAGTGGTAGGGTTAAAAATTTTGTTTTGGGAGGCCGGAACTAAATTT
130 TAATTAAACTGATAATAACAGTGGCAGGGTTAAAAAATTTGTTTTGAGAGATCGAAACTAAATTA
* *
31788 TATATTTTTAAAATAGTAAAAATACAATTTCATCATTTTTATAGC-ATATTACTTTATAATTTTT
195 TATATTTTTATAATAGTAAAAATACAATTTCATCATTTTAATAGCTATA-T-CTTTATAATTTTT
* * *
31852 AAAGAGTTAAATCAAATTTTTATAATTTTTGAAGGATCAAAGTGTAATTTTACTATTACTATTTT
258 AAAGGGTTAAATCAAATTTTTATCATTTTTGAAGGATCAAAGTGCAATTTTACTATTACTATTTT
* * * * * * *
31917 AAAATTTTATAAATCAAAAAGAGTCTAAATTAAAATTGTATCGTTCTAGAATGGACCATGACTTC
323 AAAATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACTCC
* * *
31982 CGGATCTCCACTACGCTCTGTCATTGACTACTAAGTCTAACTTTTTGA
388 CGGATCTCCACTACGCTCCGTCACTGACTACTAAGTCTAACTTTTTGG
* * * * *
32030 AAAATGCTTTAGTTTATTGGCTTTCACAGTAAATTTTTCAAGTTTCATAGCTACTTCTATACATA
1 AAAAGGCTTTAGTTTATTGGCCTTCACAGTAACTTTTTCAAGTTTCACAGCTACTTTTATACATA
* * *
32095 CTGGTGGTCCTTTCCGACTACACATA-ATAATAAATTTAGTTTCCTACTTGGTTGGAACCATGCC
66 CTGGTGGTCCTTTCAG-CTACACATACATAATAAATTTAGTTTCCTACTTGGTTAGAACCATGTC
* * * *
32159 TAATTAAACT-ACTAATAACAGTGGCGGGGTTAAAAATTTTGTTTTGAGAGGTCGGAACTAAATT
130 TAATTAAACTGA-TAATAACAGTGGCAGGGTTAAAAAATTTGTTTTGAGAGATCGAAACTAAATT
* *
32223 ATATATTTTTATAATAGTAAAAATATAATTTCATCATTTTAATAGTCTATATCTTTAAAATTTTT
194 ATATATTTTTATAATAGTAAAAATACAATTTCATCATTTTAATAG-CTATATCTTTATAATTTTT
* *
32288 AAAGGGTTAAATCAAATTTTTATCATTTTTGAAGGATCAAAATGAAATTTTACTATTACTATTTT
258 AAAGGGTTAAATCAAATTTTTATCATTTTTGAAGGATCAAAGTGCAATTTTACTATTACTATTTT
* **
32353 ATAATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATAAACCATGACTCC
323 AAAATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACTCC
* * *
32418 CGGATCTTCACCACGCTCCGTCACTGACTACTAAATCTAACTT
388 CGGATCTCCACTACGCTCCGTCACTGACTACTAAGTCTAACTT
32461 GTTGAAACCA
Statistics
Matches: 1170, Mismatches: 113, Indels: 39
0.89 0.09 0.03
Matches are distributed among these distances:
433 2 0.00
434 131 0.11
435 165 0.14
436 685 0.59
437 184 0.16
438 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (435 bp):
AAAAGGCTTTAGTTTATTGGCCTTCACAGTAACTTTTTCAAGTTTCACAGCTACTTTTATACATA
CTGGTGGTCCTTTCAGCTACACATACATAATAAATTTAGTTTCCTACTTGGTTAGAACCATGTCT
AATTAAACTGATAATAACAGTGGCAGGGTTAAAAAATTTGTTTTGAGAGATCGAAACTAAATTAT
ATATTTTTATAATAGTAAAAATACAATTTCATCATTTTAATAGCTATATCTTTATAATTTTTAAA
GGGTTAAATCAAATTTTTATCATTTTTGAAGGATCAAAGTGCAATTTTACTATTACTATTTTAAA
ATTTTATAAATTATAAAGAGTCTAAATTAAAATTTTACCATTTTAGAATGGACCATGACTCCCGG
ATCTCCACTACGCTCCGTCACTGACTACTAAGTCTAACTTTTTGG
Done.