Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004477.1 Kokia drynarioides strain JFW-HI SEQ_117897, 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: 1708
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Found at i:464 original size:172 final size:171
Alignment explanation
Indices: 179--490 Score: 475
Period size: 172 Copynumber: 1.8 Consensus size: 171
169 AAATAGTTTC
* * * *
179 TCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAACTTATTTAGGTGAGAATTGTTTGTCTCTT
1 TCATTTTGTAAACAACCTTCTGTCTTTGAATTAAAACTTATTTAGGTGAGAATTGTTTGACTATT
** *
244 GGTTTTTGGACAAACATCTGAATTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTA
66 GGTCCTTGGACAAACATCTGAATTGGTAAAACTTTTACAAGTTCTTTTATAACTTAGGTTCCTTA
309 AAGTATTCAAAACGATGCATTCCTTCGAGAAATTTAATTTG
131 AAGTATTCAAAACGATGCATTCCTTCGAGAAATTTAATTTG
*
350 TCATTTTGTAAA-ATACCTTCTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGACTA
1 TCATTTTGTAAACA-ACCTTCTGTCTTTGAATT-AAAACTTATTTAGGTGAGAATTGTTTGACTA
* * * *
414 TTGGTCCTTGGCCGAACATCTGAACTT-GTTAAACTTTTACAAGTTCTTTTATAACTTTGGTTCC
64 TTGGTCCTTGGACAAACATCTGAA-TTGGTAAAACTTTTACAAGTTCTTTTATAACTTAGGTTCC
478 TTAAAGTATTCAA
128 TTAAAGTATTCAA
491 GATGATCCAT
Statistics
Matches: 126, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
170 1 0.01
171 28 0.22
172 95 0.75
173 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.43
Consensus pattern (171 bp):
TCATTTTGTAAACAACCTTCTGTCTTTGAATTAAAACTTATTTAGGTGAGAATTGTTTGACTATT
GGTCCTTGGACAAACATCTGAATTGGTAAAACTTTTACAAGTTCTTTTATAACTTAGGTTCCTTA
AAGTATTCAAAACGATGCATTCCTTCGAGAAATTTAATTTG
Found at i:733 original size:216 final size:216
Alignment explanation
Indices: 346--1301 Score: 1072
Period size: 216 Copynumber: 4.4 Consensus size: 216
336 AGAAATTTAA
* *
346 TTTGTCATTTTGTAAA-ATACCTTCTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTG
1 TTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTG
* * * * * * *
410 ACTATTGGTCCTTGGCCGAACATCTGAACTTGTTAAACTTTTACAAGTTCTTTTATAACTTTGGT
65 TCTATTGGTTCTTGGACGAACATCCGAACTGGTCAAACTTTTACAAGTTCTTTTATAACTTAGGT
* * * * ** * *
475 TCCTTAAAGTATTCAAGATGATCCATACCTTTGAGCAATTTTTCGAACGGTCCATGGTTGAGAAA
130 TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAA
* * *
540 TCATATCATTTTGTCTAATTAG
195 TCACATCATTTGGTCCAATTAG
* * *
562 TTTGTCATTTTTTAAACAACTTTTTTGTATTTGAATTAAAAACTTATTTTGGTGACAATTGTTTG
1 TTTGTCATTTTGTAAACAAC-TTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTG
* *
627 TCTCA-TGGTTCTTGGACGAACATCCGAACTGGT-AAAATTTTACGAGTTCTTTTATAACTTAGG
65 TCT-ATTGGTTCTTGGACGAACATCCGAACTGGTCAAACTTTTACAAGTTCTTTTATAACTTAGG
* * * * * * *
690 TTCCTTAAAGTATTCAAAACGATGCATTCCTTCGAAAAATTTTTTGATCATTCCATTCTCGGGAA
129 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAA
* *
755 ATCGCATCATTTGGTCCAAATAG
194 ATCACATCATTTGGTCCAATTAG
*
778 TTTGTCATTTTGTAAA-ACACTTTTTGTCTTTGAATTAAAAACATATTTTGGTGAGAATTGTTTG
1 TTTGTCATTTTGTAAACA-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTG
* * * ** * * *
842 TCTATTGGTCCTTGGCCGAACTTCTAAACTTGTCAAACTTTTACAAGTTCTTTTATAAGTTCGGT
65 TCTATTGGTTCTTGGACGAACATCCGAACTGGTCAAACTTTTACAAGTTCTTTTATAACTTAGGT
* * * * * * *
907 TCCTTATAGTATTCAAGATGATACATTCCTTCGAGCAACTTTCCGAACATTCCATGCTTG-GTAA
130 TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAG-AA
* *
971 ATCACATCATTTTGCCCAAATT-G
194 ATCACATCATTTGGTCC-AATTAG
* * * *
994 TTTCTCATTATGTAAACAA-TTTTTGGTCTATGAGTTAAAAACTTATTTAT-GTGAGAATAT-TT
1 TTTGTCATTTTGTAAACAACTTTTT-GTCTTTGAATTAAAAACTTATTT-TGGTGAGAAT-TGTT
* * * * * * *
1056 TATCAATTGGTTCTTGAATGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
63 TGTCTATTGGTTCTTGGACGAACATCCGAACTGGTCAAACTTTTACAAGTTCTTTTATAACTTAG
* * *
1121 GTTCCTTAAAGTATGT-AAGACGA-CCTATTCCTTCGAGCAAA-TTTTCGAAAATTCAAAGCTCG
128 GTTCCTTAAAGTAT-TCAAGACGATCC-ATTCCTTCGAG-AAATTTTTCGAACATTCCATGCTCG
** *
1183 AGAAATCGTATCATTTGGACCAATTAG
190 AGAAATCACATCATTTGGTCCAATTAG
* *
1210 TTTGTCATTTTGTAAACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTGT
1 TTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGT
*
1275 CTCTTGGTTCTTGGACGAACATCCGAA
66 CTATTGGTTCTTGGACGAACATCCGAA
1302 TAAAAAAATT
Statistics
Matches: 616, Mismatches: 104, Indels: 40
0.81 0.14 0.05
Matches are distributed among these distances:
214 1 0.00
215 79 0.13
216 454 0.74
217 81 0.13
218 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (216 bp):
TTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGT
CTATTGGTTCTTGGACGAACATCCGAACTGGTCAAACTTTTACAAGTTCTTTTATAACTTAGGTT
CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCATGCTCGAGAAAT
CACATCATTTGGTCCAATTAG
Found at i:1153 original size:432 final size:432
Alignment explanation
Indices: 346--1297 Score: 1249
Period size: 432 Copynumber: 2.2 Consensus size: 432
336 AGAAATTTAA
* * * *
346 TTTGTCATTTTGTAAAATACCTTCTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGA
1 TTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGT
* * *
411 CTATTGGTCCTTGGCCGAACATCTGAACTTGTTAAACTTTTACAAGTTCTTTTATAACTTTGGTT
66 CTATTGGTCCTTGGCCGAACATCTAAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTT
* * * * * *
476 CCTTAAAGTATTCAAGATGATCCATACCTTTGAGCAATTTTTCGAACGGTCCATGGTTGAGAAAT
131 CCTTAAAGTATTCAAGATGATACATACCTTCGAGCAACTTTCCGAACAGTCCATGCTTGAGAAAT
* * * * * * * *
541 CATATCATTTTGTCTAATTAGTTTGTCATTTTTTAAACAACTTTTTTGTATTTGAATTAAAAACT
196 CACATCATTTTGCCAAATTAGTTTCTCATTATGTAAACAACTTTTTGGTATATGAATTAAAAACT
* * *
606 TATTTTGGTGACAATTGTTTGTCTCATGGTTCTTGGACGAACATCCGAACTGGTAAAATTTTACG
261 TATTTTGGTGACAATTGTTTATCTAATGGTTCTTGAACGAACATCCGAACTGGTAAAATTTTACG
* *
671 AGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAAACGATGCATTCCTTCGA-AAAATTTTTT
326 AGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAAACGATCCATTCCTTCGAGAAAA-TTTTC
** * ** * *
735 GATCATTCCATTCTCGGGAAATCGCATCATTTGGTCCAAATAG
390 GAAAATTCAAAGCTCGAGAAATCGCATCATTTGGACCAAATAG
*
778 TTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACATATTTTGGTGAGAATTGTTTGT
1 TTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGT
* *
843 CTATTGGTCCTTGGCCGAACTTCTAAACTTGTCAAACTTTTACAAGTTCTTTTATAAGTTCGGTT
66 CTATTGGTCCTTGGCCGAACATCTAAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTT
* * *
908 CCTTATAGTATTCAAGATGATACATTCCTTCGAGCAACTTTCCGAACATTCCATGCTTG-GTAAA
131 CCTTAAAGTATTCAAGATGATACATACCTTCGAGCAACTTTCCGAACAGTCCATGCTTGAG-AAA
* *
972 TCACATCATTTTGCCCAAATT-GTTTCTCATTATGTAAACAA-TTTTTGGTCTATGAGTTAAAAA
195 TCACATCATTTTG-CCAAATTAGTTTCTCATTATGTAAACAACTTTTTGGTATATGAATTAAAAA
* * * * *
1035 CTTATTTAT-GTGAGAATAT-TTTATC-AATTGGTTCTTGAATGAACTTCCGAACTTGTCAAACT
259 CTTATTT-TGGTGACAAT-TGTTTATCTAA-TGGTTCTTGAACGAACATCCGAACTGGT-AAAAT
* *
1097 TTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATGT-AAGACGA-CCTATTCCTTCGAGCA
320 TTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTAT-TCAAAACGATCC-ATTCCTTCGAGAA
* *
1160 AATTTTCGAAAATTCAAAGCTCGAGAAATCGTATCATTTGGACCAATTAG
383 AATTTTCGAAAATTCAAAGCTCGAGAAATCGCATCATTTGGACCAAATAG
* *
1210 TTTGTCATTTTGT-AAACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTG
1 TTTGTCATTTTGTAAAAC-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTG
* * *
1274 TCTCTTGGTTCTTGGACGAACATC
65 TCTATTGGTCCTTGGCCGAACATC
1298 CGAATAAAAA
Statistics
Matches: 453, Mismatches: 57, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
430 1 0.00
431 67 0.15
432 376 0.83
433 9 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (432 bp):
TTTGTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGT
CTATTGGTCCTTGGCCGAACATCTAAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTT
CCTTAAAGTATTCAAGATGATACATACCTTCGAGCAACTTTCCGAACAGTCCATGCTTGAGAAAT
CACATCATTTTGCCAAATTAGTTTCTCATTATGTAAACAACTTTTTGGTATATGAATTAAAAACT
TATTTTGGTGACAATTGTTTATCTAATGGTTCTTGAACGAACATCCGAACTGGTAAAATTTTACG
AGTTCTTTTATAACTTAGGTTCCTTAAAGTATTCAAAACGATCCATTCCTTCGAGAAAATTTTCG
AAAATTCAAAGCTCGAGAAATCGCATCATTTGGACCAAATAG
Found at i:1430 original size:148 final size:148
Alignment explanation
Indices: 1159--1442 Score: 417
Period size: 148 Copynumber: 1.9 Consensus size: 148
1149 TCCTTCGAGC
* * *
1159 AAATTTTCGAAAATTCAAAGCTCGAGAAATCGTATCATTTGGACCAATTAGTTTGTCATTTTGTA
1 AAATTTTCGAAAATTCAAAGCTCGAGAAACCGCATCATTTGGACCAAATAGTTTGTCATTTTGTA
* *
1224 AACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTGTCTCTTGGTTCTTGG
66 AACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTGTCTATTGGTCCTTGG
1289 ACGAACATCCGAATAAAA
131 ACGAACATCCGAATAAAA
* * ** * * *
1307 AAATTTTCGAACATTCCATTCTCGGGAAACCGCATCATTTTGTCCAAATAGTTTGTCATTTTGTA
1 AAATTTTCGAAAATTCAAAGCTCGAGAAACCGCATCATTTGGACCAAATAGTTTGTCATTTTGTA
* *
1372 GAAC-ACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGGTCCTTG
66 -AACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTGTCTATTGGTCCTTG
*
1436 GCCGAAC
130 GACGAAC
1443 TTTTGAACTT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
148 117 0.98
149 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (148 bp):
AAATTTTCGAAAATTCAAAGCTCGAGAAACCGCATCATTTGGACCAAATAGTTTGTCATTTTGTA
AACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTGTCTATTGGTCCTTGG
ACGAACATCCGAATAAAA
Found at i:1621 original size:364 final size:364
Alignment explanation
Indices: 950--1652 Score: 920
Period size: 364 Copynumber: 1.9 Consensus size: 364
940 AGCAACTTTC
* * * *
950 CGAACATTCCATGCTTGGTAAATCACATCATTTTGCCCAAATTGTTTCTCATTATGTAAACAATT
1 CGAACATTCCATGCTCGGGAAACCACATCATTTTGCCCAAATAGTTTCTCATTATGTAAACAATT
* * *
1015 TTTGGTCTATGAGTTAAAAACTTATTTATGTGAGAATATTTTATCAATTGGTTCTTGAATGAACT
66 TTTGGTCTATGAATTAAAAACTTATTTATGTGAGAATATTTTATCAATTGGTCCTTGAACGAACT
* *
1080 TCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGTATGTAAGACGAC
131 TCCGAACTTCTCAAACTTTTACGAGTTCTTTTATAACTTAGATTCCTTAAAGTATGTAAGACGAC
* * *
1145 CTATTCCTTCGAGCAAATTTTCGAAAATTCAAAGCTCGAGAAATCGTATCATTTGGACCAATTAG
196 CTATTCCTTCGAGCAAATTTTCGAAAATTCAAAGCTCGAGAAATCCTATCAATTGGACCAAATAG
* **
1210 TTTGTCATTTTGTAAACAACTATTTGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTGT
261 TTTATCATTTTGTAAACAACTATTTGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTGT
*
1275 CTCTTGGTTCTTGGACGAACATCCGAATAAAAAAATTTT
326 CTCATGGTTCTTGGACGAACATCCGAATAAAAAAATTTT
* * * * * *
1314 CGAACATTCCATTCTCGGGAAACCGCATCATTTTGTCCAAATAGTTTGTCATTTTGTAGAACACT
1 CGAACATTCCATGCTCGGGAAACCACATCATTTTGCCCAAATAGTTTCTCATTATGTA-AACAAT
* * * **
1379 TTTT-GTCTTTGAATTAAAAACTTATTT-TGGTGAGAAT-TGTTTGTCTATTGGTCCTTGGCCGA
65 TTTTGGTCTATGAATTAAAAACTTATTTAT-GTGAGAATAT-TTTATCAATTGGTCCTTGAACGA
** *
1441 ACTTTTGAACTTCTCAAACTTTTACGAGTTCTTTTATAATTTCA-ATTCCTTAAAGTAT-TCAAG
128 ACTTCCGAACTTCTCAAACTTTTACGAGTTCTTTTATAACTT-AGATTCCTTAAAGTATGT-AAG
* * *
1504 ACGATCC-ATTCCTTCGAG-GAATTTGTCGAACATTGC-ATGCTCGAGAAATCACT-TCAATTGG
191 ACGA-CCTATTCCTTCGAGCAAATTT-TCGAAAATT-CAAAGCTCGAGAAATC-CTATCAATTGG
* * * * *
1565 TCCAAATAGTTTATCATTTTGTAAACAAGTTTTTGTCTTTGAGTTAAAATCTTATTTACATGAGA
252 ACCAAATAGTTTATCATTTTGTAAACAACTATTTGTCTTTGAATTAAAAACTTATTTACATGAGA
1630 ATTGTTTGTCTCATGGTTCTTGG
317 ATTGTTTGTCTCATGGTTCTTGG
1653 CCAAACTTCC
Statistics
Matches: 292, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
363 8 0.03
364 270 0.92
365 14 0.05
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (364 bp):
CGAACATTCCATGCTCGGGAAACCACATCATTTTGCCCAAATAGTTTCTCATTATGTAAACAATT
TTTGGTCTATGAATTAAAAACTTATTTATGTGAGAATATTTTATCAATTGGTCCTTGAACGAACT
TCCGAACTTCTCAAACTTTTACGAGTTCTTTTATAACTTAGATTCCTTAAAGTATGTAAGACGAC
CTATTCCTTCGAGCAAATTTTCGAAAATTCAAAGCTCGAGAAATCCTATCAATTGGACCAAATAG
TTTATCATTTTGTAAACAACTATTTGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTGT
CTCATGGTTCTTGGACGAACATCCGAATAAAAAAATTTT
Found at i:1708 original size:216 final size:215
Alignment explanation
Indices: 1308--1698 Score: 498
Period size: 216 Copynumber: 1.8 Consensus size: 215
1298 CGAATAAAAA
* * * * * *
1308 AATTTTCGAACATTCCATTCTCGGGAAACCGCATCATTTTGTCCAAATAGTTTGTCATTTTGTAG
1 AATTTTCGAACATTCCATGCTCGAGAAACCACATCAATTGGTCCAAATAGTTTATCATTTTGTAG
***
1373 AACACTTTTTGTCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTTGTCTATTGGTCCTTGGC
66 AACACTTTTTGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTGTCTATTGGTCCTTGGC
* *** * * ** *
1438 CGAACTTTTGAACTTCTCAAACTTTTACGAGTTCTTTTATAATTTCAATTCCTTAAAGTATTCAA
131 CAAACTTCCAAACTTCTCAAACTTTTACAAGTTCATGAATAACTTCAATTCCTTAAAGTATTCAA
1503 GACGATCCATTCCTTCGAGG
196 GACGATCCATTCCTTCGAGG
* * *
1523 AATTTGTCGAACATTGCATGCTCGAGAAATCACTTCAATTGGTCCAAATAGTTTATCATTTTGTA
1 AATTT-TCGAACATTCCATGCTCGAGAAACCACATCAATTGGTCCAAATAGTTTATCATTTTGTA
* * * *
1588 -AACAAGTTTTTGTCTTTGAGTTAAAATCTTATTTACATGAGAATTGTTTGTCTCA-TGGTTCTT
65 GAAC-ACTTTTTGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTGTCT-ATTGGTCCTT
* *
1651 GGCCAAACTTCCAAACTTGTCAAAGTTTTACAAGTTCATGAATAACTT
128 GGCCAAACTTCCAAACTTCTCAAACTTTTACAAGTTCATGAATAACTT
1699 AGGTTCCTTA
Statistics
Matches: 146, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
215 8 0.05
216 137 0.94
217 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (215 bp):
AATTTTCGAACATTCCATGCTCGAGAAACCACATCAATTGGTCCAAATAGTTTATCATTTTGTAG
AACACTTTTTGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTGTCTATTGGTCCTTGGC
CAAACTTCCAAACTTCTCAAACTTTTACAAGTTCATGAATAACTTCAATTCCTTAAAGTATTCAA
GACGATCCATTCCTTCGAGG
Done.