Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004192.1 Kokia drynarioides strain JFW-HI SEQ_117425, 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, 870
Length: 1451
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Found at i:383 original size:216 final size:216
Alignment explanation
Indices: 1--1445 Score: 1596
Period size: 216 Copynumber: 6.7 Consensus size: 216
* * * * *
1 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
1 TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
* * * * *
66 TTTTGGTCTTTGAATTAAACACTTATTTACATGAGAATTGTTTCTTTCTTT-CTCTTTGTACGAA
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTC-TTGGACGAA
* *
130 CTTTCGAACTTGTCAAACTTCTACGAGTTACTTTT-TAACTTCGGTTCCCTAAAGTATTCAATAA
130 CTTTCGAACTTGTCAAACTTTTACGAGTTA-TTTTATAACTTCGGTTCCCTAAAGTATTCAAGAA
*
194 GATCCATTCCTTTGAGCAATCTT
194 GATCCATTCCTTTGAGCAATTTT
* * * * *
217 TCAAACATTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAATTTGTTATTTTGCAAACAAG
1 TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
* * *
282 TTTTGCTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTATCTCTTTGTTCTTGGACGAAC
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAC
* * * * * * *
347 TTTTGAACTTTTCAAACTTTTAAGAGTTATTTTTTAACTTCAGTTCCCTGAAGTATTCAACAAGA
131 TTTCGAACTTGTCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCTAAAGTATTCAAGAAGA
*
412 TCCATTCCTTTGAGAAATTTT
196 TCCATTCCTTTGAGCAATTTT
* * * * * * * * **
433 TCGAATATTCCATCCTTGGTAAATCACTTCATTTGGTCTAAATAATTTGTCATTTTGTATCCAAG
1 TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
*
498 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAG
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAC
* * * * * *
563 TTTCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACTTCGGATCCTTGAAGTATTCAAGACGA
131 TTTCGAACTTGTCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCTAAAGTATTCAAGAAGA
628 TCCATT-CTTTCGAGCAATTTT
196 TCCATTCCTTT-GAGCAATTTT
* * * * *
649 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
1 TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
* * *
714 TTTTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG-TCTTTGTATGAA
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTC-TTGGACGAA
* * **
778 CTTTCGAAGTTGTCAAACTTTTACGAGTTACTTTT-TAACTTCGGTTCCCTAAAGTATTTAACTA
130 CTTTCGAACTTGTCAAACTTTTACGAGTTA-TTTTATAACTTCGGTTCCCTAAAGTATTCAAGAA
* * *
842 GATCCATTCCATAGAGAAATTTT
194 GATCCATTCCTTTGAGCAATTTT
** * * *
865 TTGAACATTCCATGCTCGAGAAATAGCATCATTTGGTCTAACTAGTTTGTCATTTTGTAAACAAG
1 TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
** * * * * * * * *
930 TTTTATTTTTTGAATTAAGAACTTATTTATGAGAGAATTGTATCACACTTGGTT-TATGGACGAA
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCT-TGGACGAA
** * * * * * *** * * *
994 CTCCCGAACTTGGCAAACTTTGAGGAGATCTTTTATAACTTAACTTCCTTAATGTATTTC-AGAC
130 CTTTCGAACTTGTCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCTAAAGTA-TTCAAGAA
* *
1058 GACCCATTCCTTTGAGCCA-TTT
194 GATCCATTCCTTTGAGCAATTTT
* * * *
1080 TCTAAACATTCAATGCT-GGAGAAATTGCATCATTTGGTCTAAAGAGTTTGTCATTTCGTAAACA
1 TC-AAACATTCCATGCTCGG-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* **
1144 AGTTTTGGTCTTGGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTACTTCTTGGACGA
64 AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGA
* * * * * * *
1209 ACTTTCGAACGTGTCAAACTTTTACAACTTCTTTTATAACTTTC-GTTCCTTAAAGCATTCAAGG
129 ACTTTCGAACTTGTCAAACTTTTACGAGTTATTTTATAAC-TTCGGTTCCCTAAAGTATTCAAGA
* * * *
1273 CGATCCATTCCTTCGAGTAGTTTT
193 AGATCCATTCCTTTGAGCAATTTT
* * ** * * * *
1297 CCAAACATTCCTTGCTCAAGAAATCGCATCATTTAGTCTGAATAGATTGTCGTTTTGTAAACAAG
1 TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
* * * * * *
1362 TTTTGGTCGTTGTATTAGAAAGTTATTTACGTGAGAATTGTTTCTCTCTTTGTTTTTGGATGAAC
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAC
* * *
1427 TTCCAAACTAGTCAAACTT
131 TTTCGAACTTGTCAAACTT
1446 CTACAA
Statistics
Matches: 1022, Mismatches: 190, Indels: 34
0.82 0.15 0.03
Matches are distributed among these distances:
215 23 0.02
216 981 0.96
217 18 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (216 bp):
TCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAG
TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAC
TTTCGAACTTGTCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCTAAAGTATTCAAGAAGA
TCCATTCCTTTGAGCAATTTT
Found at i:1243 original size:648 final size:647
Alignment explanation
Indices: 1--1449 Score: 1874
Period size: 648 Copynumber: 2.2 Consensus size: 647
1 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
1 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
* * * * *
66 TTTTGGTCTTTGAATTAAACACTTATTTACATGAGAATTGTTTCTTTCTTTCTCTTTGTACGAAC
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTATGAAC
131 TTTCGAACTTGTCAAACTTCTACGAGTTACTTTTTAACTTCGGTTCCCTAAAGTATTCAATAAGA
131 TTTCGAACTTGTCAAACTTCTACGAGTTACTTTTTAACTTCGGTTCCCTAAAGTATTCAATAAGA
* * * * *
196 TCCATTCCTTTGAGCAATCTTTCAAACATTCCATGCTTGGGAAATCACATCATTTGGTCTAAATA
196 TCCATTCCATAGAGAAATCTTTCAAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATA
* * * * *
261 ATTTGTTATTTTGCAAACAAGTTTTGCTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTA
261 ATTTGTCATTTTGCAAACAAGTTTTACTCTTTGAATTAAAAACTTATTTACGAGAGAATTGTTCA
* * *** ** * * * * *
326 TCTCTTTGTTCTTGGACGAACTTTTGAACTTTTCAAACTTTTAAGAGTTATTTTTTAACTTCAGT
326 TCACTTGGTTCTTGGACGAACTCCCGAACTTGGCAAACTTTGAAGAGATATTTTATAACTTAACT
* * * * *
391 TCCCTGAAGTATTCAACAAGATCCATTCCTTTGAGAAATTTTTCGAATATTCCATCCTTGGTAAA
391 TCCCTGAAGTATTCAAC-AGACCCATTCCTTTGAGAAATTTTTCAAACATTCAATCCTTGGGAAA
* * * ** *
456 TCACTTCATTTGGTCTAAATAATTTGTCATTTTGTATCCAAGTTTTGGTCTTTGAATTAAAAACT
455 TCACATCATTTGGTCTAAAGAATTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAATTAAAAACT
** * *
521 TATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAGTTTCGAACTTGTCAAACTTTTAC
520 TATTTACGTGAGAATTGTTTCTCTCTTACTTCTTGGACGAACTTTCGAACGTGTCAAACTTTTAC
* * * * *
586 TAGTTCTTTTATAAC-TTCGGATCCTTGAAGTATTCAAGACGATCCATTCTTTCGAGCAATTTT
585 AACTTCTTTTATAACTTTC-GATCCTTAAAGCATTCAAGACGATCCATTCCTTCGAGCAATTTT
649 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
1 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
*
714 TTTTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTATGAAC
66 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTATGAAC
* * *
779 TTTCGAAGTTGTCAAACTTTTACGAGTTACTTTTTAACTTCGGTTCCCTAAAGTATTTAACT-AG
131 TTTCGAACTTGTCAAACTTCTACGAGTTACTTTTTAACTTCGGTTCCCTAAAGTATTCAA-TAAG
* ** *
843 ATCCATTCCATAGAGAAATTTTTTGAACATTCCATGCTCGAGAAAT-AGCATCATTTGGTCTAAC
195 ATCCATTCCATAGAGAAATCTTTCAAACATTCCATGCTCGAGAAATCA-CATCATTTGGTCTAAA
* * * * * *
907 TAGTTTGTCATTTTGTAAACAAGTTTTATTTTTTGAATTAAGAACTTATTTATGAGAGAATTGTA
259 TAATTTGTCATTTTGCAAACAAGTTTTACTCTTTGAATTAAAAACTTATTTACGAGAGAATTGT-
* *
972 TCA-CACTTGGTT-TATGGACGAACTCCCGAACTTGGCAAACTTTGAGGAGATCTTTTATAACTT
323 TCATCACTTGGTTCT-TGGACGAACTCCCGAACTTGGCAAACTTTGAAGAGATATTTTATAACTT
* ** *
1035 AACTT-CCTTAATGTATTTCAGAC-GACCCATTCCTTTGAGCCA-TTTTCTAAACATTCAATGC-
387 AACTTCCCTGAA-GTA-TTCA-ACAGACCCATTCCTTTGAGAAATTTTTC-AAACATTCAATCCT
** *
1096 TGGAGAAATTGCATCATTTGGTCTAAAGAGTTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAAT
448 TGG-GAAATCACATCATTTGGTCTAAAGAATTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAAT
1161 TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTACTTCTTGGACGAACTTTCGAACGTGTCAA
512 TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTACTTCTTGGACGAACTTTCGAACGTGTCAA
* * *
1226 ACTTTTACAACTTCTTTTATAACTTTCGTTCCTTAAAGCATTCAAGGCGATCCATTCCTTCGAGT
577 ACTTTTACAACTTCTTTTATAACTTTCGATCCTTAAAGCATTCAAGACGATCCATTCCTTCGAGC
*
1291 AGTTTT
642 AATTTT
* * * ** * * * * * *
1297 CCAAACATTCCTTGCTCAAGAAATCGCATCATTTAGTCTGAA-TAGATTGTCGTTTTGTAAACAA
1 TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCT-AATTAGTTTGTCATTTTGCAAACAA
* * * * * *
1361 GTTTTGGTCGTTGTATTAGAAAGTTATTTACGTGAGAATTGTTTCTCTCTTTGTTTTTGGATGAA
65 GTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTATGAA
* * *
1426 CTTCCAAACTAGTCAAACTTCTAC
130 CTTTCGAACTTGTCAAACTTCTAC
1450 AA
Statistics
Matches: 693, Mismatches: 97, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
647 15 0.02
648 664 0.96
649 12 0.02
650 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (647 bp):
TCAAACATTTCATGCTCGGGAGATCGCATCATTTGGCCTAATTAGTTTGTCATTTTGCAAACAAG
TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTATGAAC
TTTCGAACTTGTCAAACTTCTACGAGTTACTTTTTAACTTCGGTTCCCTAAAGTATTCAATAAGA
TCCATTCCATAGAGAAATCTTTCAAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATA
ATTTGTCATTTTGCAAACAAGTTTTACTCTTTGAATTAAAAACTTATTTACGAGAGAATTGTTCA
TCACTTGGTTCTTGGACGAACTCCCGAACTTGGCAAACTTTGAAGAGATATTTTATAACTTAACT
TCCCTGAAGTATTCAACAGACCCATTCCTTTGAGAAATTTTTCAAACATTCAATCCTTGGGAAAT
CACATCATTTGGTCTAAAGAATTTGTCATTTCGTAAACAAGTTTTGGTCTTGGAATTAAAAACTT
ATTTACGTGAGAATTGTTTCTCTCTTACTTCTTGGACGAACTTTCGAACGTGTCAAACTTTTACA
ACTTCTTTTATAACTTTCGATCCTTAAAGCATTCAAGACGATCCATTCCTTCGAGCAATTTT
Done.