Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012863.1 Kokia drynarioides strain JFW-HI SEQ_127877, 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: 113114
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 199 characters in sequence are not A, C, G, or T
Found at i:11818 original size:12 final size:12
Alignment explanation
Indices: 11801--11827 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11791 AATTTGCCTC
11801 TTGATTGATCTG
1 TTGATTGATCTG
11813 TTGATTGATCTG
1 TTGATTGATCTG
11825 TTG
1 TTG
11828 TTCTAGATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (12 bp):
TTGATTGATCTG
Found at i:15789 original size:15 final size:17
Alignment explanation
Indices: 15754--15789 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
15744 AAAAATAAAT
15754 TTATATTAATATATATA
1 TTATATTAATATATATA
15771 TTATATTAATA-AT-TA
1 TTATATTAATATATATA
15786 TTAT
1 TTAT
15790 TATTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 2 0.11
17 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTAATATATATA
Found at i:22101 original size:2 final size:2
Alignment explanation
Indices: 22094--22120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22084 CGTGGGCAGC
22094 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
22121 TACAAGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22834 original size:326 final size:326
Alignment explanation
Indices: 22241--22882 Score: 1257
Period size: 326 Copynumber: 2.0 Consensus size: 326
22231 AAGGAGCGTG
*
22241 GAAGTGGATATACTTAAAAGATTTTGTTCTGTTTCATGTTTTGTCTTGCTTGCCCTAAGATTATC
1 GAAGTGGATATACTTAAAAGATTTTGTTCTGTTTCATGTTTTGTCTTGCTTGCCCTAAGATTATA
*
22306 TTACACATCTTGTAAAGATAAAGATACATCAGGTTCCATTGAAATCGTACCACGTTTGCTTCTTC
66 TTACACATCTTGTAAAGATAAAGATACATCAGGTTCCATTGAAACCGTACCACGTTTGCTTCTTC
22371 CTGGTTTTTTATTTAGTTATAATCAAAGATAAATACGTATATATTTAAATAATATTAAATGTTAG
131 CTGGTTTTTTATTTAGTTATAATCAAAGATAAATACGTATATATTTAAATAATATTAAATGTTAG
22436 TAATCAATTTACTCATTCTATTGATTATATTAAAATAATTGGATTTGAGGAGGTGGATTAAAAGA
196 TAATCAATTTACTCATTCTATTGATTATATTAAAATAATTGGATTTGAGGAGGTGGATTAAAAGA
22501 AATAATCGTTCTGACAAAAAAAATGGAGATAGAAATAAAAGATGTTATAAAAAAAAAATGGAGAT
261 AATAATCGTTCTGACAAAAAAAATGGAGATAGAAATAAAAGATGTTATAAAAAAAAAATGGAGAT
22566 A
326 A
22567 GAAGTGGATATACTTAAAAGATTTTGTTCTGTTTCATGTTTTGTCTTGCTTGCCCTAAGATTATA
1 GAAGTGGATATACTTAAAAGATTTTGTTCTGTTTCATGTTTTGTCTTGCTTGCCCTAAGATTATA
22632 TTACACATCTTGTAAAGATAAAGATACATCAGGTTCCATTGAAACCGTACCACGTTTGCTTCTTC
66 TTACACATCTTGTAAAGATAAAGATACATCAGGTTCCATTGAAACCGTACCACGTTTGCTTCTTC
22697 CTGGTTTTTTATTTAGTTATAATCAAAGATAAATACGTATATATTTAAATAATATTAAATGTTAG
131 CTGGTTTTTTATTTAGTTATAATCAAAGATAAATACGTATATATTTAAATAATATTAAATGTTAG
22762 TAATCAATTTACTCATTCTATTGATTATATTAAAATAATTGGATTTGAGGAGGTGGATTAAAAGA
196 TAATCAATTTACTCATTCTATTGATTATATTAAAATAATTGGATTTGAGGAGGTGGATTAAAAGA
*
22827 AATAATCGTTCTGACAAAAAAAATGGAGATAGAAATAAAAGATGTTGTAAAAAAAA
261 AATAATCGTTCTGACAAAAAAAATGGAGATAGAAATAAAAGATGTTATAAAAAAAA
22883 CTTCGGATAT
Statistics
Matches: 313, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
326 313 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (326 bp):
GAAGTGGATATACTTAAAAGATTTTGTTCTGTTTCATGTTTTGTCTTGCTTGCCCTAAGATTATA
TTACACATCTTGTAAAGATAAAGATACATCAGGTTCCATTGAAACCGTACCACGTTTGCTTCTTC
CTGGTTTTTTATTTAGTTATAATCAAAGATAAATACGTATATATTTAAATAATATTAAATGTTAG
TAATCAATTTACTCATTCTATTGATTATATTAAAATAATTGGATTTGAGGAGGTGGATTAAAAGA
AATAATCGTTCTGACAAAAAAAATGGAGATAGAAATAAAAGATGTTATAAAAAAAAAATGGAGAT
A
Found at i:32859 original size:2 final size:2
Alignment explanation
Indices: 32852--32876 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32842 GATAACAATG
32852 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32877 GCTTATGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37402 original size:5 final size:5
Alignment explanation
Indices: 37388--37416 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
37378 AGGGTGAGTC
37388 ATCC- ATCCA ATCCA ATCCA ATCCA ATCCA
1 ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA
37417 GATGTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCCA
Found at i:55908 original size:21 final size:23
Alignment explanation
Indices: 55884--55930 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
55874 TTAATCCTAA
* *
55884 TTAACTCATTTCTTA-TTT-TTT
1 TTAACTCAATTCATACTTTATTT
55905 TTAACTCAATTCATACTTTATTT
1 TTAACTCAATTCATACTTTATTT
55928 TTA
1 TTA
55931 TTCAATTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 3 0.14
23 6 0.27
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.60
Consensus pattern (23 bp):
TTAACTCAATTCATACTTTATTT
Found at i:57820 original size:23 final size:23
Alignment explanation
Indices: 57738--57821 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
57728 TAAACAGAAC
* *
57738 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGTACACAAAGTGCT
**
57760 AAACAGAGAG--CACATAAGCTGGG
1 AAACAGAGAGTACACA-AAG-TGCT
* **
57783 CAACAGAGAACACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTGCT
57806 AAACAGAGAGTACACA
1 AAACAGAGAGTACACA
57822 GTACTGAGCA
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 13 0.28
23 24 0.52
24 3 0.07
25 4 0.09
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (23 bp):
AAACAGAGAGTACACAAAGTGCT
Found at i:57857 original size:23 final size:23
Alignment explanation
Indices: 57827--57945 Score: 161
Period size: 23 Copynumber: 5.2 Consensus size: 23
57817 ACACAGTACT
* *
57827 GAGCACACAAAGTGTTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
57850 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
57873 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
* * *
57896 GAGCACGA-GACGTGCTAAACAAA
1 GAGCAC-ACGAAGTGCTAATCAGA
57919 GAGCACAC-ATAGTGCTAATCAGA
1 GAGCACACGA-AGTGCTAATCAGA
57942 GAGC
1 GAGC
57946 GCGCTAGTGT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
22 2 0.02
23 82 0.96
24 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (23 bp):
GAGCACACGAAGTGCTAATCAGA
Found at i:67070 original size:59 final size:60
Alignment explanation
Indices: 66945--67073 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
66935 AACCCTTTTT
* *
66945 TTTTTTATTATCTAATTTTGATACTTGAACTTTACACTTTTTCCTAATTTGGTACCTAAAC
1 TTTTTT-TTATCCAATTTTGATACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAAC
* * * **
67006 TTTTTTTTATCCAA-TTTGGTATTTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAGT
1 TTTTTTTTATCCAATTTTGATACTTGAACTTGACA-CTTTTTCCTAATTTGGTACCTAAAC
67066 TTTTTTTT
1 TTTTTTTT
67074 TTAGATTCAG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 17 0.28
60 37 0.62
61 6 0.10
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.55
Consensus pattern (60 bp):
TTTTTTTTATCCAATTTTGATACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAAC
Found at i:67332 original size:31 final size:31
Alignment explanation
Indices: 67294--67371 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
67284 GGACCCAAAA
**
67294 AAGTTTAAGTACCAATTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAAATAAAAAAAAGTGTC
**
67325 AAGTTTAAGTACCAAAATAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAAATAAAAAAAAGTGTC
* *
67356 AAGTTTGAGTATCAAA
1 AAGTTTAAGTACCAAA
67372 TTAGACAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAAATAAAAAAAAGTGTC
Found at i:70152 original size:10 final size:10
Alignment explanation
Indices: 70126--70160 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
70116 AAATTTTAAA
*
70126 AAAGAAAAAG
1 AAAGAAAGAG
70136 AAAAGAAAGAG
1 -AAAGAAAGAG
70147 AAAGAAAGAG
1 AAAGAAAGAG
70157 AAAG
1 AAAG
70161 CTCTTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAG
Found at i:70772 original size:20 final size:19
Alignment explanation
Indices: 70747--70813 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 19
70737 AGTATTGTAT
70747 TTATAATTATCATTTATAAA
1 TTATAATTAT-ATTTATAAA
* *
70767 TTATAATCATTTTTCATGAATTA
1 TTATAATTATATTT-AT-AA--A
*
70790 TTATAATTATAATTTAAAAA
1 TTATAATTAT-ATTTATAAA
70810 TTAT
1 TTAT
70814 TTCAACACCA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
19 3 0.08
20 16 0.43
21 2 0.05
22 2 0.05
23 11 0.30
24 3 0.08
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (19 bp):
TTATAATTATATTTATAAA
Found at i:71402 original size:2 final size:2
Alignment explanation
Indices: 71395--71423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
71385 AAACTAAGAA
71395 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
71424 AAAAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:76360 original size:24 final size:24
Alignment explanation
Indices: 76317--76365 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
76307 GGTTCAAGTT
* **
76317 AAATTATAATTTTTGTAATAGTAA
1 AAATAATAATTTTTAAAATAGTAA
*
76341 AAATAATAATTTTTAAAATATTAA
1 AAATAATAATTTTTAAAATAGTAA
76365 A
1 A
76366 TTATTTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAATAATAATTTTTAAAATAGTAA
Done.