Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002331.1 Kokia drynarioides strain JFW-HI SEQ_114379, 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: 88234
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:316 original size:19 final size:20
Alignment explanation
Indices: 294--341 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
284 CAAACTCTTG
294 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
313 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
333 -TAAT-ATTAA
1 ATAATAATTAA
342 GAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:10668 original size:66 final size:66
Alignment explanation
Indices: 10562--10694 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
10552 GAGTGGCTCG
10562 TAGTATGAATTCTAGGCATCATATTTCTTTTAATAATTGTAACATAATGATTGAACAATTTTACC
1 TAGTATGAATTCTAGGCATCATATTTCTTTTAATAATTGTAACATAATGATTGAACAATTTTACC
10627 A
66 A
10628 TAGTATGAATTCTAGGCATCATATTTCTTTTAATAATTGTAACATAATGATTGAACAATTTTACC
1 TAGTATGAATTCTAGGCATCATATTTCTTTTAATAATTGTAACATAATGATTGAACAATTTTACC
10693 A
66 A
10694 T
1 T
10695 TTTCAATTAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (66 bp):
TAGTATGAATTCTAGGCATCATATTTCTTTTAATAATTGTAACATAATGATTGAACAATTTTACC
A
Found at i:36921 original size:27 final size:28
Alignment explanation
Indices: 36848--36923 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
36838 ATGTATAGAA
36848 TATAGCTCA-TTCGAGCCCAGAACAAAG
1 TATAGCTCATTTCGAGCCCAGAACAAAG
* *
36875 TTTAGTTCATTT-GAGCCCAGAACAAAG
1 TATAGCTCATTTCGAGCCCAGAACAAAG
*
36902 TA-ATGCTCCTTTCGAG-CCAGAA
1 TATA-GCTCATTTCGAGCCCAGAA
36924 ATAGAACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 1 0.02
27 35 0.85
28 5 0.12
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (28 bp):
TATAGCTCATTTCGAGCCCAGAACAAAG
Found at i:43304 original size:26 final size:26
Alignment explanation
Indices: 43266--43339 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
43256 GTTACGCTCC
* *
43266 TTTCAAGCTAGAA-ACAGAATAACGCT
1 TTTCGAGCTAGAACACAGAAT-ACGAT
* * *
43292 TTTCGAGCCAGAACATAGAGTACGAT
1 TTTCGAGCTAGAACACAGAATACGAT
*
43318 TTTACGAGCTAGAATACAGAAT
1 TTT-CGAGCTAGAACACAGAAT
43340 TACTCCTCGA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
26 18 0.49
27 19 0.51
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (26 bp):
TTTCGAGCTAGAACACAGAATACGAT
Found at i:46611 original size:23 final size:23
Alignment explanation
Indices: 46581--46638 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
46571 ATGATTTGTA
46581 GATTATTTCAAAACCTTGAAATT
1 GATTATTTCAAAACCTTGAAATT
46604 GATTATTTCAAAACCTTGAAATT
1 GATTATTTCAAAACCTTGAAATT
46627 GATTATTTCAAA
1 GATTATTTCAAA
46639 GTTTTATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (23 bp):
GATTATTTCAAAACCTTGAAATT
Found at i:46908 original size:33 final size:31
Alignment explanation
Indices: 46851--46920 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
46841 GATAATGTGC
*
46851 TAAGTAGTCATAGATTCCTATAATAATATAT
1 TAAGTAGTCATAGATTCCGATAATAATATAT
*
46882 TAAGTAGTCATATAGATTCCGGTAATAATATAT
1 TAAGTAGTC--ATAGATTCCGATAATAATATAT
*
46915 TGAGTA
1 TAAGTA
46921 ATCACAACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 9 0.26
33 25 0.74
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (31 bp):
TAAGTAGTCATAGATTCCGATAATAATATAT
Found at i:52522 original size:21 final size:22
Alignment explanation
Indices: 52468--52523 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
52458 ATTCAAAAAT
*
52468 AGTGCAGACTTCTATCGATACCT
1 AGTG-AGACTTCTATCGATACCA
* *
52491 AG-GACAGTTCTATCGATA-CA
1 AGTGAGACTTCTATCGATACCA
52511 AGTGAGACTTCTA
1 AGTGAGACTTCTA
52524 CAGAAACAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 1 0.04
23 2 0.07
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (22 bp):
AGTGAGACTTCTATCGATACCA
Found at i:75866 original size:96 final size:96
Alignment explanation
Indices: 75702--75891 Score: 362
Period size: 96 Copynumber: 2.0 Consensus size: 96
75692 TTTATAAGTC
* *
75702 ATATCCTTTCTATCCATTTATTTCATTACCATTATACAATTCCAAGTTCTTAACTTAATTTTTCC
1 ATATCCTTTCTATCCATTTATTTCATTACCATTATACAATTCCAAATTCTTAACTTAATTTTCCC
75767 TTTCTCGTAAAAGTACCTATTTAGACTATTT
66 TTTCTCGTAAAAGTACCTATTTAGACTATTT
75798 ATATCCTTTCTATCCATTTATTTCATTACCATTATACAATTCCAAATTCTTAACTTAATTTTCCC
1 ATATCCTTTCTATCCATTTATTTCATTACCATTATACAATTCCAAATTCTTAACTTAATTTTCCC
75863 TTTCTCGTAAAAGTACCTATTTAGACTAT
66 TTTCTCGTAAAAGTACCTATTTAGACTAT
75892 CGAGAATTCA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.46
Consensus pattern (96 bp):
ATATCCTTTCTATCCATTTATTTCATTACCATTATACAATTCCAAATTCTTAACTTAATTTTCCC
TTTCTCGTAAAAGTACCTATTTAGACTATTT
Found at i:76125 original size:30 final size:30
Alignment explanation
Indices: 76063--76126 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
76053 AATTACACCA
* * *
76063 ACAGTCACTCAACTTTGATGCAACTGACAAG
1 ACAGTCACTCAACTTTGA-GAAAATAACAAG
76094 ACAGTCACTCAACTTTCGA-AAAATAACAAG
1 ACAGTCACTCAACTTT-GAGAAAATAACAAG
76124 ACA
1 ACA
76127 ATCATCCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 11 0.38
31 16 0.55
32 2 0.07
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.20
Consensus pattern (30 bp):
ACAGTCACTCAACTTTGAGAAAATAACAAG
Found at i:76298 original size:3 final size:3
Alignment explanation
Indices: 76290--76429 Score: 102
Period size: 3 Copynumber: 46.7 Consensus size: 3
76280 ATCTCCATTT
* * * * * * *
76290 CTC CTC CTC CTC CTC CTC CTC CTT CTT CTC CTT CTT CTT CTT CTC CTT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * *
76338 CTC CTT CTC CTT CTC CTT CTC CTC CTC CTC CTC CTC CTC GTT CTC CTTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C-TC
* * * * * *
76387 C-C CTT CTC CTT TTG CTT CTT CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
76430 TCTTCTTCTA
Statistics
Matches: 111, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
2 2 0.02
3 106 0.95
4 3 0.03
ACGTcount: A:0.00, C:0.54, G:0.01, T:0.45
Consensus pattern (3 bp):
CTC
Found at i:76405 original size:48 final size:48
Alignment explanation
Indices: 76330--76424 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
76320 CTTCTTCTTC
*
76330 TTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTCCTCCTCCTCCTCCTCG
1 TTCTCCTTCCCCTTCTCCTTCTCCTTCTCCTCCTCCTCCTCCTCCTCG
* * *
76378 TTCTCCTTCCCCTTCTCCTTTTGCTTCTTCTCCTCCTCCTCCTCCTC
1 TTCTCCTTCCCCTTCTCCTTCTCCTTCTCCTCCTCCTCCTCCTCCTC
76425 CTCCTTCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.00, C:0.53, G:0.02, T:0.45
Consensus pattern (48 bp):
TTCTCCTTCCCCTTCTCCTTCTCCTTCTCCTCCTCCTCCTCCTCCTCG
Found at i:77143 original size:21 final size:19
Alignment explanation
Indices: 77119--77161 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
77109 TTACCCTAAA
*
77119 AAATAGCATCTAAATTACTAC
1 AAATAGAATC-AAA-TACTAC
*
77140 AAATAGAATCAAATATTAC
1 AAATAGAATCAAATACTAC
77159 AAA
1 AAA
77162 AACACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATAGAATCAAATACTAC
Found at i:83657 original size:17 final size:17
Alignment explanation
Indices: 83637--83678 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
83627 ATTTATATCG
83637 AAATTTTATTAATAAGA
1 AAATTTTATTAATAAGA
*
83654 AAA-TTTATTAATAATA
1 AAATTTTATTAATAAGA
*
83670 AATTTTTAT
1 AAATTTTAT
83679 GTTAAGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATTTTATTAATAAGA
Found at i:83764 original size:2 final size:2
Alignment explanation
Indices: 83747--83781 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
83737 ATACTTTTAG
*
83747 TA TA TA TT TA TA -A 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 TA TA TA
83782 AGTAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:85684 original size:26 final size:27
Alignment explanation
Indices: 85635--85735 Score: 75
Period size: 26 Copynumber: 3.7 Consensus size: 27
85625 TTTTCCAACA
85635 CTTATATATATATATATTATTTTTATT
1 CTTATATATATATATATTATTTTTATT
*
85662 CTTAT-TATATATCT-TTATTTTTTATAT
1 CTTATATATATATATATTA-TTTTTAT-T
* * ***
85689 ATT-TCTA-ATGCGTATTATACTTTTATT
1 CTTATATATATATATATTAT--TTTTATT
85716 CTTTATATATATATATATTA
1 C-TTATATATATATATATTA
85736 CTTTATCATA
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
25 3 0.05
26 20 0.36
27 14 0.25
28 8 0.15
29 3 0.05
30 7 0.13
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (27 bp):
CTTATATATATATATATTATTTTTATT
Found at i:85688 original size:17 final size:19
Alignment explanation
Indices: 85656--85690 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
85646 ATATATTATT
85656 TTTATTCTTATTATATATC
1 TTTATTCTTATTATATATC
85675 TTTATT-TT-TTATATAT
1 TTTATTCTTATTATATAT
85691 TTCTAATGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTCTTATTATATATC
Found at i:85737 original size:28 final size:28
Alignment explanation
Indices: 85636--85739 Score: 76
Period size: 28 Copynumber: 3.8 Consensus size: 28
85626 TTTCCAACAC
*
85636 TTATATATATATATATTATTTTTATTC-
1 TTATATATATATATATTACTTTTATTCT
* * *
85663 TTAT-TATATATCT-TTATTTTTTATATAT
1 TTATATATATATATATTA-CTTTTAT-TCT
* *
85691 TTCTA-ATGCGTAT-TA-TACTTTTATTCT
1 TTATATAT--ATATATATTACTTTTATTCT
85718 TTATATATATATATATTACTTT
1 TTATATATATATATATTACTTT
85740 ATCATAACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
25 3 0.05
26 18 0.31
27 13 0.22
28 19 0.32
29 3 0.05
30 3 0.05
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATATATATATATATTACTTTTATTCT
Done.