Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014774.1 Kokia drynarioides strain JFW-HI SEQ_129815, 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: 91040
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 284 characters in sequence are not A, C, G, or T
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--35 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 ACCTT
6 TA 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 TA
36 AAGAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8529 original size:47 final size:48
Alignment explanation
Indices: 8460--8551 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
8450 CCAAATAACA
* * *
8460 ATTGCAATTAGTATACTAAAATAGTCCATCGAAG-TTATACCTTTCCC
1 ATTGCAATCAGTATACGAAAATAGCCCATCGAAGTTTATACCTTTCCC
8507 ATTGCAATCAGTGA-ACGAAAATAGCCCATCGAAGTTTTATACCTT
1 ATTGCAATCAGT-ATACGAAAATAGCCCATCGAAG-TTTATACCTT
8552 CAGACGCCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
47 29 0.74
48 1 0.03
49 9 0.23
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (48 bp):
ATTGCAATCAGTATACGAAAATAGCCCATCGAAGTTTATACCTTTCCC
Found at i:15126 original size:17 final size:17
Alignment explanation
Indices: 15100--15138 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
15090 TAAAAAAGAA
*
15100 TTATACAATATCTTTT-T
1 TTATAAAATAT-TTTTAT
15117 TTATAAAATATTTTTAT
1 TTATAAAATATTTTTAT
15134 TTATA
1 TTATA
15139 TACATGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATAAAATATTTTTAT
Found at i:17378 original size:29 final size:32
Alignment explanation
Indices: 17324--17389 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 32
17314 AATAGTTCAT
*
17324 ATTTTTTATAATTTTTAAAGGATT-AAAT-TA
1 ATTTTTTATAATTTTGAAAGGATTAAAATATA
* *
17354 ATTTTTTATCATTTTGAGAGG-TTAAAATATA
1 ATTTTTTATAATTTTGAAAGGATTAAAATATA
17385 ATTTT
1 ATTTT
17390 ACTGTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 22 0.71
31 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (32 bp):
ATTTTTTATAATTTTGAAAGGATTAAAATATA
Found at i:20401 original size:2 final size:2
Alignment explanation
Indices: 20394--20418 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20384 TTCGGCTGCA
20394 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20419 ACCAAAGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30890 original size:153 final size:153
Alignment explanation
Indices: 30612--31071 Score: 821
Period size: 153 Copynumber: 3.0 Consensus size: 153
30602 TCTCTTAGTT
*
30612 GCTTTCTGCTTTAAAAGAAAAGGTAACCTTAGTTTGGGTTATCTGACAGATTAAAAGTAGTCCAA
1 GCTTTCTGCTTTAAAAGAAAAGGTAAACTTAGTTTGGGTTATCTGACAGATTAAAAGTAGTCCAA
*
30677 AGGATTCGGAAGAATCGGTCCCTGGTAATTCTCTTTCTCGAACTGCTTCATGTGACAAGGTAGGT
66 AGGATACGGAAGAATCGGTCCCTGGTAATTCTCTTTCTCGAACTGCTTCATGTGACAAGGTAGGT
*
30742 CAAAGATTTCCAAGTAGCTTTCA
131 CAAATATTTCCAAGTAGCTTTCA
* *
30765 GCTTTCTGCTTTAAAAGAAAAGGTAAACTTAGTTTGGGTTATCTGACAGATTAAATGTAGTTCAA
1 GCTTTCTGCTTTAAAAGAAAAGGTAAACTTAGTTTGGGTTATCTGACAGATTAAAAGTAGTCCAA
30830 AGGATACGGAAGAATCGGTCCCTGGTAATTCTCTTTCTCGAACTGCTTCATGTGACAAGGTAGGT
66 AGGATACGGAAGAATCGGTCCCTGGTAATTCTCTTTCTCGAACTGCTTCATGTGACAAGGTAGGT
*
30895 CAAATATTTCCAAGTAGCTTTGA
131 CAAATATTTCCAAGTAGCTTTCA
30918 GCTTTCTGCTTTAAAAGAAAAGGTAAACTTAGTTTGGGTTATCTGACAGATTAAAAGTAGTCCAA
1 GCTTTCTGCTTTAAAAGAAAAGGTAAACTTAGTTTGGGTTATCTGACAGATTAAAAGTAGTCCAA
* * * * *
30983 TGGATATGGAAGAATCGGTCCCTGATAATTCTCTTTCTCAAACTGCTTCATGTGACAAGGTGGGT
66 AGGATACGGAAGAATCGGTCCCTGGTAATTCTCTTTCTCGAACTGCTTCATGTGACAAGGTAGGT
31048 CAAATATTTCCAAGTAGCTTTCA
131 CAAATATTTCCAAGTAGCTTTCA
31071 G
1 G
31072 TTATTGCTTC
Statistics
Matches: 293, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 293 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (153 bp):
GCTTTCTGCTTTAAAAGAAAAGGTAAACTTAGTTTGGGTTATCTGACAGATTAAAAGTAGTCCAA
AGGATACGGAAGAATCGGTCCCTGGTAATTCTCTTTCTCGAACTGCTTCATGTGACAAGGTAGGT
CAAATATTTCCAAGTAGCTTTCA
Found at i:47258 original size:53 final size:53
Alignment explanation
Indices: 47147--47435 Score: 454
Period size: 53 Copynumber: 5.5 Consensus size: 53
47137 TTCTCATTTA
* *
47147 ATACTCACGATGACACATAGTCATCAGACCT-TTAATTCGCAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGGATTCAT
* *
47199 ATACTCACGATGACACATAGTCATTAGACCTGTTAATCCGTAATAGGATTCTT
1 ATACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGGATTCAT
* * * *
47252 ATACTCACGATGACACATAGTCATCGGACTTATCAATCCGTAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGGATTCAT
* *
47305 ATACTCACGATGACATATAGTCATCGGACCTGTTAATCCGTAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGGATTCAT
* * *
47358 ATACTCACGATGACACATAGTCATCAAACCTGTTAATCTGTAATGGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGGATTCAT
47411 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
47436 GAACCTTTTA
Statistics
Matches: 217, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
52 30 0.14
53 187 0.86
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (53 bp):
ATACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGGATTCAT
Found at i:59777 original size:14 final size:14
Alignment explanation
Indices: 59758--59788 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59748 TTAATTATTT
59758 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
59772 TTTAATTAATTAAA
1 TTTAATTAAATAAA
59786 TTT
1 TTT
59789 TCTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:61461 original size:6 final size:6
Alignment explanation
Indices: 61450--61479 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
61440 TGTACGGCGA
61450 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC
1 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC
61480 CAACTGTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
TGGCAC
Found at i:63255 original size:26 final size:26
Alignment explanation
Indices: 63224--63283 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
63214 TTTTTTGAAC
63224 CGAGTCGAGTGAAATAAAATTCAAAT
1 CGAGTCGAGTGAAATAAAATTCAAAT
* * *
63250 CGAGTCAAGTGAAATTAAATTCAATT
1 CGAGTCGAGTGAAATAAAATTCAAAT
*
63276 CAAGTCGA
1 CGAGTCGA
63284 ATCGAGTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (26 bp):
CGAGTCGAGTGAAATAAAATTCAAAT
Found at i:63516 original size:18 final size:19
Alignment explanation
Indices: 63495--63534 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
63485 TTTTAAAAAA
*
63495 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGAAATTTT
*
63513 TATAAATATTTTAAATTTT
1 TATAAATATTTGAAATTTT
63532 TAT
1 TAT
63535 TGAGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:68430 original size:18 final size:18
Alignment explanation
Indices: 68407--68443 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
68397 TGACTTTTCG
*
68407 AATTCGAATAATTCAAAT
1 AATTCGAATAAATCAAAT
68425 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
68443 A
1 A
68444 TTAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:77173 original size:23 final size:23
Alignment explanation
Indices: 77129--77173 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
77119 GTACTCTAAT
*
77129 ATAAATATTAAAATAATGTTAAG
1 ATAAATATTAAAATAATATTAAG
*
77152 ATAACTATATAAAA-AATATTAA
1 ATAAATAT-TAAAATAATATTAA
77174 ATATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
ATAAATATTAAAATAATATTAAG
Found at i:78392 original size:19 final size:18
Alignment explanation
Indices: 78364--78421 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
78354 TTTTTATCTA
*
78364 AATTTCTTTAAAAAAATT
1 AATTTTTTTAAAAAAATT
*
78382 CAATTTTTTT--AAATATT
1 -AATTTTTTTAAAAAAATT
*
78399 ATTTTTTTTAAAAAAATTT
1 AATTTTTTTAAAAAAA-TT
78418 AATT
1 AATT
78422 CAATTGTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.26
17 6 0.19
18 4 0.13
19 13 0.42
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTTTTAAAAAAATT
Found at i:87451 original size:29 final size:30
Alignment explanation
Indices: 87418--87474 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
87408 TGATTCATTG
* *
87418 TGCAATTTGATATATG-AACTTTAATTTAA
1 TGCAATTTGACACATGAAACTTTAATTTAA
*
87447 TGCAATTTTACACATGAAACTTTAATTT
1 TGCAATTTGACACATGAAACTTTAATTT
87475 TGATTCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (30 bp):
TGCAATTTGACACATGAAACTTTAATTTAA
Found at i:88696 original size:46 final size:45
Alignment explanation
Indices: 88607--88700 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 45
88597 TAAGACTTTG
* * **
88607 TTTAAGTTTAAATTCTATTTTTAGGATTATTATTATATTGTTTAGA
1 TTTAAGTTTAAATTCTATTTTTAGCATTATAATTATAGAGTTTA-A
*
88653 TTTAATTTTAAATT-TATCTTTTAAGCATTATAATT-TAGAGTTTAA
1 TTTAAGTTTAAATTCTAT-TTTT-AGCATTATAATTATAGAGTTTAA
88698 TTT
1 TTT
88701 GGATCCAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
45 7 0.17
46 24 0.59
47 10 0.24
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (45 bp):
TTTAAGTTTAAATTCTATTTTTAGCATTATAATTATAGAGTTTAA
Done.