Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003606.1 Kokia drynarioides strain JFW-HI SEQ_116493, 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: 9401
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Found at i:237 original size:59 final size:58
Alignment explanation
Indices: 174--332 Score: 144
Period size: 61 Copynumber: 2.7 Consensus size: 58
164 AAAATTTTAA
* **
174 TTTTTACCAAATAAAAAGGAGGTGTCGGTCATTGCATGG-T-CGACATAAAAAAATCGATT
1 TTTTTACCAAACAAAAAGG-GGTGTCGACCATTGCATGGCTAC-ACA-AAAAAAATCGATT
*** *
233 TTTTTATTTAACAAAAAGGGGTGTCGACCATTGCATGGCTAACACAAAAAAAATCTATTTT
1 TTTTTACCAAACAAAAAGGGGTGTCGACCATTGCATGGCT-ACACAAAAAAAATCGA--TT
* * *
294 TTTTTATC-TACAAAAAGAGGGTGTCGATCATTGCATGGC
1 TTTTTACCAAACAAAAAG-GGGTGTCGACCATTGCATGGC
333 CAACACCAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
58 17 0.20
59 26 0.31
60 11 0.13
61 30 0.36
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (58 bp):
TTTTTACCAAACAAAAAGGGGTGTCGACCATTGCATGGCTACACAAAAAAAATCGATT
Found at i:258 original size:58 final size:59
Alignment explanation
Indices: 186--332 Score: 176
Period size: 59 Copynumber: 2.5 Consensus size: 59
176 TTTACCAAAT
*
186 AAAAAGGAGGTGTCGGTCATTGCATGG-T-CGACATAAAAAAATCGATTTTTTTATT-T-AAC
1 AAAAAGG-GGTGTCGATCATTGCATGGCTAC-ACA-AAAAAAATCGATTTTTTT-TTATCAAC
* * *
245 AAAAAGGGGTGTCGACCATTGCATGGCTAACACAAAAAAAATCTATTTTTTTTTATCTAC
1 AAAAAGGGGTGTCGATCATTGCATGGCT-ACACAAAAAAAATCGATTTTTTTTTATCAAC
305 AAAAAGAGGGTGTCGATCATTGCATGGC
1 AAAAAG-GGGTGTCGATCATTGCATGGC
333 CAACACCAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
58 19 0.25
59 26 0.34
60 11 0.14
61 21 0.27
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (59 bp):
AAAAAGGGGTGTCGATCATTGCATGGCTACACAAAAAAAATCGATTTTTTTTTATCAAC
Found at i:317 original size:61 final size:61
Alignment explanation
Indices: 230--700 Score: 302
Period size: 61 Copynumber: 7.8 Consensus size: 61
220 AAAAAAATCG
* * * *
230 ATTTTTTTATTTAACAAAAAGGGGTGTCGACCATTGCATGGCTAACACAAAAAAAATCT-AT
1 ATTTTTTTATCT-ACAAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAAATTTGAA
* * * *
291 TTTTTTTTATCTACAAAAAGAGGGTGTCGATCATTGCATGGCCAACACCAAAAAATTTTGAA
1 ATTTTTTTATCTACAAAAAG-GGGTGTCGACCATTGCATGGCCAACACAAAAAAAATTTGAA
* * **
353 ATTTTTTTATCTGA-AAAAAGGGGTGTC-AGCCATGGCATGACCAACAC-TCAAAAATTT--A
1 ATTTTTTTATCT-ACAAAAAGGGGTGTCGA-CCATTGCATGGCCAACACAAAAAAAATTTGAA
* * * * * *
411 ATTTTTTTATC-AGATAAATAGGGGTGTTGGCCATTGCATAGCAAACACAAAAAAATTTTGAA
1 ATTTTTTTATCTACA-AAA-AGGGGTGTCGACCATTGCATGGCCAACACAAAAAAAATTTGAA
* ** * **
473 ATTTTTTTATCTAAAAAAAGGGAGTGTCGACCACGGCATGACCAACAC-CCAAAAATTTG-A
1 ATTTTTTTATCTACAAAAAGGG-GTGTCGACCATTGCATGGCCAACACAAAAAAAATTTGAA
* * * * *
533 TTTTTTTTATC-AGATAAATAGGGGTGTCCG-CTATTGCATGACCAACAC-CAAAAAA-TTG-A
1 ATTTTTTTATCTACA-AAA-AGGGGTGT-CGACCATTGCATGGCCAACACAAAAAAAATTTGAA
* ** * *
592 A-TTTTTT-T-GACAAAAAGGAGGTGTCGGTCATTGCATGACCAACATC--CAAAAATTTG--
1 ATTTTTTTATCTACAAAAAGG-GGTGTCGACCATTGCATGGCCAACA-CAAAAAAAATTTGAA
* * * *
648 ATTTTTTTATCAGATTAAAAAGGGGTGTCGGCCA-TGCAATGACCAACATCAAA
1 ATTTTTTTATC-TA-CAAAAAGGGGTGTCGACCATTGC-ATGGCCAACA-CAAA
701 TTTTTTTTTC
Statistics
Matches: 332, Mismatches: 49, Indels: 57
0.76 0.11 0.13
Matches are distributed among these distances:
55 5 0.02
56 30 0.09
57 14 0.04
58 22 0.07
59 31 0.09
60 86 0.26
61 90 0.27
62 51 0.15
63 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (61 bp):
ATTTTTTTATCTACAAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAAATTTGAA
Found at i:344 original size:60 final size:58
Alignment explanation
Indices: 245--700 Score: 348
Period size: 60 Copynumber: 7.6 Consensus size: 58
235 TTTATTTAAC
* * * * *
245 AAAAAGGGGTGTCGACCATTGCATGGCTAACACAAAAAAAATCT-ATTTTTTTTTATCTA
1 AAAAAGGGGTGTCGACCATTGCATGACCAACAC-CAAAAAATTTGAATTTTTTTTATC-A
* * *
304 CAAAAAGAGGGTGTCGATCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA
1 -AAAAAG-GGGTGTCGACCATTGCATGACCAACACCAAAAAA-TTTGAATTTTTTTTATC--A
*
367 AAAAAGGGGTGTC-AGCCATGGCATGACCAACACTC-AAAAATTT-AA-TTTTTTTATCA
1 AAAAAGGGGTGTCGA-CCATTGCATGACCAACAC-CAAAAAATTTGAATTTTTTTTATCA
* * * * *
423 GATAAATAGGGGTGTTGGCCATTGCAT-AGCAAACACAAAAAAATTTTGAAATTTTTTTATCTAA
1 -A-AAA-AGGGGTGTCGACCATTGCATGA-CCAACACCAAAAAA-TTTGAATTTTTTTTATC--A
** *
487 AAAAAGGGAGTGTCGACCACGGCATGACCAACACCCAAAAATTTG-ATTTTTTTTATCA
1 AAAAAGGG-GTGTCGACCATTGCATGACCAACACCAAAAAATTTGAATTTTTTTTATCA
* *
545 GATAAATAGGGGTGTCCG-CTATTGCATGACCAACACCAAAAAA-TTGAATTTTTTTGA-C-
1 -A-AAA-AGGGGTGT-CGACCATTGCATGACCAACACCAAAAAATTTGAATTTTTTTTATCA
**
603 AAAAAGGAGGTGTCGGTCATTGCATGACCAACATCC-AAAAATTTG-A-TTTTTTTATCAGA
1 AAAAAGG-GGTGTCGACCATTGCATGACCAACA-CCAAAAAATTTGAATTTTTTTTATC--A
* *
662 TTAAAAAGGGGTGTCGGCCA-TGCAATGACCAACATCAAA
1 --AAAAAGGGGTGTCGACCATTGC-ATGACCAACACCAAA
701 TTTTTTTTTC
Statistics
Matches: 327, Mismatches: 33, Indels: 72
0.76 0.08 0.17
Matches are distributed among these distances:
55 12 0.04
56 31 0.09
57 7 0.02
58 15 0.05
59 38 0.12
60 89 0.27
61 77 0.24
62 54 0.17
63 3 0.01
64 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (58 bp):
AAAAAGGGGTGTCGACCATTGCATGACCAACACCAAAAAATTTGAATTTTTTTTATCA
Found at i:420 original size:181 final size:181
Alignment explanation
Indices: 221--627 Score: 447
Period size: 181 Copynumber: 2.3 Consensus size: 181
211 GGTCGACATA
* * * *
221 AAAAAATCG-ATTTTTTTATTTA-ACAAAAAGGGGTGTCGACCATTGCATGGCTAACACAAAAAA
1 AAAAAATTGAATTTTTTTA-TCAGACAAAAAGGGGTGTCGACCATTGCATAGCAAACACAAAAAA
** * * ** *
284 AATCT-ATTTTTTTTTATCTACAAAAAGAGG-GTGTCGATCATTGCATGGCCAACACCAAAAAAT
65 AATCTGAAATTTTTTTATCTAAAAAAAG-GGAGTGTCGACCACGGCATGACCAACACCAAAAAA-
*
347 TTTGAAATTTTTTTATCTGA-AAAAAGGGGTGTCAGCCATGGCATGACCAACACTC
128 TTTG-AATTTTTTTATCAGATAAAAAGGGGTGTCAGCCATGGCATGACCAACAC-C
* * * * *
402 -AAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTTGGCCATTGCATAGCAAACACAAAAAAA
1 AAAAAATTGAATTTTTTTATCAGACAAAAAGGGGTGTCGACCATTGCATAGCAAACACAAAAAAA
* * *
466 TTTTGAAATTTTTTTATCTAAAAAAAGGGAGTGTCGACCACGGCATGACCAACACCCAAAAATTT
66 ATCTGAAATTTTTTTATCTAAAAAAAGGGAGTGTCGACCACGGCATGACCAACACCAAAAAATTT
* * * * *
531 GATTTTTTTTATCAGATAAATAGGGGTGTCCGCTATTGCATGACCAACACC
131 GAATTTTTTTATCAGATAAAAAGGGGTGTCAGCCATGGCATGACCAACACC
**
582 AAAAAATTGAA-TTTTTT-T--GACAAAAAGGAGGTGTCGGTCATTGCAT
1 AAAAAATTGAATTTTTTTATCAGACAAAAAGG-GGTGTCGACCATTGCAT
628 GACCAACATC
Statistics
Matches: 189, Mismatches: 30, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
177 8 0.04
178 15 0.08
179 1 0.01
180 28 0.15
181 91 0.48
182 46 0.24
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (181 bp):
AAAAAATTGAATTTTTTTATCAGACAAAAAGGGGTGTCGACCATTGCATAGCAAACACAAAAAAA
ATCTGAAATTTTTTTATCTAAAAAAAGGGAGTGTCGACCACGGCATGACCAACACCAAAAAATTT
GAATTTTTTTATCAGATAAAAAGGGGTGTCAGCCATGGCATGACCAACACC
Found at i:472 original size:120 final size:118
Alignment explanation
Indices: 230--700 Score: 451
Period size: 122 Copynumber: 3.9 Consensus size: 118
220 AAAAAAATCG
* * * * * ** * *
230 ATTTTTTTATTTAACAAAAAGGGGTGTCGACCATTGCATGGCTAACACAAAAAAAATCTATTTTT
1 ATTTTTTTATCTGA-AAAAAGGGGTGTCG-CCATGGCATGACCAACAC-TCAAAAATTTA-ATTT
* **
295 TTTTATCTACA-AAA-AGAGGGTGTCGATCATTGCATGGCCAACACCAAAAAATTTTGAA
62 TTTTATC-AGATAAATAG-GGGTGTCGGCCATTGCAT-GCCAACACCAAAAAATTTTGAA
353 ATTTTTTTATCTGAAAAAAGGGGTGTCAGCCATGGCATGACCAACACTCAAAAATTTAATTTTTT
1 ATTTTTTTATCTGAAAAAAGGGGTGTC-GCCATGGCATGACCAACACTCAAAAATTTAATTTTTT
* * *
418 TATCAGATAAATAGGGGTGTTGGCCATTGCATAGCAAACACAAAAAAATTTTGAA
65 TATCAGATAAATAGGGGTGTCGGCCATTGCAT-GCCAACACCAAAAAATTTTGAA
* * * *
473 ATTTTTTTATCTAAAAAAAGGGAGTGTCGACCACGGCATGACCAACACCCAAAAATTTGATTTTT
1 ATTTTTTTATCTGAAAAAAGGG-GTGTCG-CCATGGCATGACCAACACTCAAAAATTT-AATTTT
* *
538 TTTATCAGATAAATAGGGGTGTCCGCTATTGCATGACCAACACCAAAAAA--TTG-A
63 TTTATCAGATAAATAGGGGTGTCGGCCATTGCATG-CCAACACCAAAAAATTTTGAA
* * *
592 A--TTTTT-T-TGACAAAAAGGAGGTGTCGGTCATTGCATGACCAACA-TCCAAAAATTTGATTT
1 ATTTTTTTATCTGA-AAAAAGG-GGTGTC-GCCATGGCATGACCAACACT-CAAAAATTTAATTT
* *
652 TTTTATCAGATTAAAAAGGGGTGTCGGCCA-TGCAATGACCAACATCAAA
62 TTTTATCAGA-TAAATAGGGGTGTCGGCCATTGC-ATG-CCAACACCAAA
701 TTTTTTTTTC
Statistics
Matches: 299, Mismatches: 36, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
115 18 0.06
116 66 0.22
117 7 0.02
119 4 0.01
120 73 0.24
121 42 0.14
122 76 0.25
123 13 0.04
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (118 bp):
ATTTTTTTATCTGAAAAAAGGGGTGTCGCCATGGCATGACCAACACTCAAAAATTTAATTTTTTT
ATCAGATAAATAGGGGTGTCGGCCATTGCATGCCAACACCAAAAAATTTTGAA
Found at i:672 original size:116 final size:116
Alignment explanation
Indices: 292--700 Score: 429
Period size: 116 Copynumber: 3.4 Consensus size: 116
282 AAAATCTATT
* * * *
292 TTTTTTTATC-TACAAAAAGAGGGTGT-CGATCATTGCATGGCCAACACCAAAAAATTTTGAAAT
1 TTTTTTTATCAGATAAAAAG-GGGTGTCCG-CCATTGCATGACCAACACCAAAAAA-TTTGAAAT
* *
355 TTTTTTATCTGAAAAAAGGGGTGTCAGCCATGGCATGACCAACACTCAAAAATTTAA
63 TTTTTTATC--AAAAAAGGGGTGTCGGCCATGGCATGACCAACAC-CAAAAATTTGA
* ** * *
412 TTTTTTTATCAGATAAATAGGGGTGTTGGCCATTGCAT-AGCAAACACAAAAAAATTTTGAAATT
1 TTTTTTTATCAGATAAAAAGGGGTGTCCGCCATTGCATGA-CCAACACCAAAAAA-TTTGAAATT
* *
476 TTTTTATCTAAAAAAAGGGAGTGTCGACCACGGCATGACCAACACCCAAAAATTTGA
64 TTTTTATC--AAAAAAGGG-GTGTCGGCCATGGCATGACCAACA-CCAAAAATTTGA
* *
533 TTTTTTTTATCAGATAAATAGGGGTGTCCGCTATTGCATGACCAACACCAAAAAA-TTG-AATTT
1 -TTTTTTTATCAGATAAAAAGGGGTGTCCGCCATTGCATGACCAACACCAAAAAATTTGAAATTT
* *
596 TTTTGA-C-AAAAAGGAGGTGTCGGTCATTGCATGACCAACATCCAAAAATTTGA
65 TTTT-ATCAAAAAAGG-GGTGTCGGCCATGGCATGACCAACA-CCAAAAATTTGA
* *
649 TTTTTTTATCAGATTAAAAAGGGGTGTCGGCCA-TGCAATGACCAACATCAAA
1 TTTTTTTATCAGA-TAAAAAGGGGTGTCCGCCATTGC-ATGACCAACACCAAA
701 TTTTTTTTTC
Statistics
Matches: 251, Mismatches: 27, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
115 16 0.06
116 69 0.27
117 1 0.00
119 10 0.04
120 68 0.27
121 38 0.15
122 48 0.19
123 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (116 bp):
TTTTTTTATCAGATAAAAAGGGGTGTCCGCCATTGCATGACCAACACCAAAAAATTTGAAATTTT
TTTATCAAAAAAGGGGTGTCGGCCATGGCATGACCAACACCAAAAATTTGA
Found at i:8431 original size:24 final size:24
Alignment explanation
Indices: 8367--8511 Score: 148
Period size: 24 Copynumber: 6.1 Consensus size: 24
8357 ATGTTTTTAT
* * *
8367 TATATTAGCTAGCGAGCGTAAATG
1 TATATCAGCTGGCGAGCGTAAACG
* * *
8391 CATATTAG-TGACGAGCGTAAACG
1 TATATCAGCTGGCGAGCGTAAACG
* * *
8414 TATATCAACTGACGAGCGTAAACA
1 TATATCAGCTGGCGAGCGTAAACG
* * *
8438 CATATTAGCTGGCGAGCGTAAACA
1 TATATCAGCTGGCGAGCGTAAACG
*
8462 TATATTAGCTGGCGAGCGTAAACG
1 TATATCAGCTGGCGAGCGTAAACG
* *
8486 CATATCAGCTGGCGAGCGTAAGCG
1 TATATCAGCTGGCGAGCGTAAACG
8510 TA
1 TA
8512 AACGCATATT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
23 17 0.17
24 85 0.83
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (24 bp):
TATATCAGCTGGCGAGCGTAAACG
Found at i:8478 original size:48 final size:48
Alignment explanation
Indices: 8367--8506 Score: 192
Period size: 48 Copynumber: 2.9 Consensus size: 48
8357 ATGTTTTTAT
* * * *
8367 TATATTAGCTAGCGAGCGTAAATGCATATTAG-TGACGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGGCGAGCGTAAACA
* * * *
8414 TATATCAACTGACGAGCGTAAACACATATTAGCTGGCGAGCGTAAACA
1 TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGGCGAGCGTAAACA
*
8462 TATATTAGCTGGCGAGCGTAAACGCATATCAGCTGGCGAGCGTAA
1 TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGGCGAGCGTAA
8507 GCGTAAACGC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 26 0.33
48 53 0.67
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (48 bp):
TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGGCGAGCGTAAACA
Found at i:8506 original size:72 final size:71
Alignment explanation
Indices: 8368--8506 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 71
8358 TGTTTTTATT
** *
8368 ATATTAGCTAGCGAGCGTAAATGCATATTAGTGACGAGCGTAAACGTATATCAACTGACGAGCGT
1 ATATTAGCTAGCGAGCGTAAACACATATTAGTGACGAGCGTAAACGCATATCAACTGACGAGCGT
8433 AAACAC
66 AAACAC
* * * * *
8439 ATATTAGCTGGCGAGCGTAAACATATATTAGCTGGCGAGCGTAAACGCATATCAGCTGGCGAGCG
1 ATATTAGCTAGCGAGCGTAAACACATATTAG-TGACGAGCGTAAACGCATATCAACTGACGAGCG
8504 TAA
65 TAA
8507 GCGTAAACGC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 27 0.46
72 32 0.54
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (71 bp):
ATATTAGCTAGCGAGCGTAAACACATATTAGTGACGAGCGTAAACGCATATCAACTGACGAGCGT
AAACAC
Done.