Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012187.1 Kokia drynarioides strain JFW-HI SEQ_127188, 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, 779
Length: 1299
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:631 original size:217 final size:212
Alignment explanation
Indices: 1--1299 Score: 1249
Period size: 217 Copynumber: 6.1 Consensus size: 212
* * * *
1 GCATCATTT-TTCTAAATTGTTTGTCATTTTGTAAACAAGTTATGGTATTT---TTAAAACTTAT
1 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAACTTAT
* * *
62 TTACGTGAGAATTGTTTCTCTCTTTTTGTTCTTGGATGAACTTCCAGACTTTTCAAACTTTTACG
66 TTACGTGAGAATT-TTT-TCTC-TTTGGTTCTTGGACGAACTTCCAAAC-TTTCAAACTTTTACG
* * *
127 AGTTCATTTATAAC-TCCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTT-T
127 AGTTCTTTTATAACTTCC-GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT
*
190 GAACATTCCATTCTCGGGAAATC
191 -AACATTCCATGCTCGGGAAATC
* * * * * * ** *
213 GCATCATTTAGTCTAAATAGGTCT-TAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACAT
1 GCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAA-AACTT
* * * * * * *
277 ATTTTCCTGA-AGA-TTTTT-TC-TTGGCTGTTGGACGAACTTCAAAACATTTCATACGTTTACG
64 ATTTACGTGAGA-ATTTTTTCTCTTTGGTTCTTGGACGAACTTCCAAAC-TTTCAAACTTTTACG
** * * * *
338 AGTTCTTTTATAAC-TCCGTTCCTTGCAGTATTCAGGACAATCCATTCCTTTGAGGAATTTTCTG
127 AGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT-
402 AACATTCCATGCTCGGGAAATC
191 AACATTCCATGCTCGGGAAATC
* * * *
424 GCATCATTTGGTCGAAATAGTTTGTCATTTTGTAAAAAAACTTTTGGTCTTTGAATTAAATACTT
1 GCATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAACAAGTTTTGGTCTTTAAATTAAA-ACTT
*
489 ATTTACGTGAGAATTTTTTCTCGTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACG
64 ATTTACGTGAGAATTTTTTCTC-TTTGGTTCTTGGACGAACTTCCAAACTT-TCAAACTTTTACG
* * * * *
554 AGTTCTTTTATAATTTCAGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTGCA
127 AGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-CT
*
619 AACATTCCATGCTCGGAAAATC
191 AACATTCCATGCTCGGGAAATC
* *
641 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGGTTTTGTTGC-TTGAATTAAAAACT
1 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-GTTTTGGT-CTTTAAATT-AAAACT
** * * * * *
704 TATTTACGTGAGAATCATTTCTCTCTTGTTTCTTGGACAAACTTTCGAACTAGTCAAACTTTTAC
63 TATTTACGTGAGAATTTTTTCTCT-TTGGTTCTTGGACGAACTTCCAAACT-TTCAAACTTTTAC
* * * * * *
769 AAGTTCTTTTATAACTTCGGTTCCTTACAGTATTCAAGACGATACATTCCTTCTAGCAACTTTCT
126 GAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC-
* * *
834 TAACATTCTATGCT-AGAAATATC
190 TAACATTCCATGCTCGGGAA-ATC
* * *
857 GCATCATTT-TTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTTTAAACTTA
1 GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAA-TTAAAACTTA
* * *
921 TTTACGTGAGAATTGTTTCWCTCTCTTT-GTTCTTWGATGAACTTCCAAACTTGTCATACTTTTA
65 TTTACGTGAGAATT-TTT---TCTCTTTGGTTCTTGGACGAACTTCCAAACTT-TCAAACTTTTA
* * * * * *
985 CGAGKTCWTTTATAACTYCKGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTT-
125 CGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC
*
1049 TGAACATTCCATTCTCGGGAAATC
190 T-AACATTCCATGCTCGGGAAATC
* * * * * * ** *
1073 GCATCATTTAGTCTAAATAGGTCT-TAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACAT
1 GCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAA-AACTT
* * * * * * *
1137 ATTTTCTTGAGGA-TTTTT-TC-TTGGCTGTTGGACGAACTTCAAAACATTTCATACTTTTACGA
64 ATTTACGTGAGAATTTTTTCTCTTTGGTTCTTGGACGAACTTCCAAAC-TTTCAAACTTTTACGA
* ** * * * *
1199 GTTCTTTTATAAC-TCCTTTCCTTGCAGTATTCAGGACAATCCATTCCATCAAGCAATTTTCTGA
128 GTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT-A
1263 ACATTCCATGCTCGGGAAATC
192 ACATTCCATGCTCGGGAAATC
1284 GCATCATTTGGTCTAA
1 GCATCATTTGGTCTAA
Statistics
Matches: 899, Mismatches: 146, Indels: 85
0.80 0.13 0.08
Matches are distributed among these distances:
210 81 0.09
211 179 0.20
212 41 0.05
213 36 0.04
214 7 0.01
215 72 0.08
216 234 0.26
217 238 0.26
218 6 0.01
219 5 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (212 bp):
GCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAACTTAT
TTACGTGAGAATTTTTTCTCTTTGGTTCTTGGACGAACTTCCAAACTTTCAAACTTTTACGAGTT
CTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTAACAT
TCCATGCTCGGGAAATC
Found at i:965 original size:433 final size:423
Alignment explanation
Indices: 1--1292 Score: 1489
Period size: 427 Copynumber: 3.0 Consensus size: 423
* *
1 GCATCATTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTATGGT-ATT--TTTAAAACTTATT
1 GCATCATTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAATTTAAAACTTATT
* *
63 TACGTGAGAATTGTTTCTCTCTTTTTGTTCTTGGATGAACTTCCAGACTTTTCAAACTTTTACGA
66 TACGTGAGAATTGTTTC-CTCTCTTTGTTCTTGGATGAACTTCCA-ACTTATCAAACTTTTACGA
*
128 GTTCATTTATAACTCCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTTTGAA
129 GTTCATTTATAACTCCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTTTGAA
*
193 CATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATAGGTCTTAATTTTGTAAACGAGTTTTG
194 CATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATA-GTCTTAATTTTGTAAAAGAGTTTTG
* * * *
258 ATCATTAAAACAAGAACATATTTTCCTGAAGATTTTTTCTTGGCTGTTGGACGAACTTCAAAACA
258 ATCATTAAAACAAAAACATATTTACCTGAAGATTTTTTCTTGGCTCTTGGACAAACTTCAAAACA
* * * * * *
323 TTTCATACGTTTACGAGTTCTTTTATAACTCCGTTCCTTGCAGTATTCAGGACAATCCATTCCTT
323 TGTCAAACGTTTACAAGTTCTTTTATAACTCCGTTCCTTACAGTATTCAAGACAATACATTCCTT
* * * *
388 TGAGGAATTTTCTGAACATTCCATGCTCGGGAAATC
388 TGAGCAACTTTCTGAACATTCCATGCTCAGAAAATC
* * * * *
424 GCATCATTTGGTCGAAATAGTTTGTCATTTTGTAAAAAAACTTTTGGTCTTTGAA-TTAAATACT
1 GCATCATTT-TTCTAAATTGTTTGTCATTTTGT-AAACAAGTTTTGGTCTTT-AATTTAAA-ACT
*
488 TATTTACGTGAGAATT-TTT--TCTCGTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTT
62 TATTTACGTGAGAATTGTTTCCTCTC-TTT-GTTCTTGGATGAACTTCC-AACTTATCAAACTTT
* * * * ** *
550 TACGAGTTCTTTTATAATTTCAGTTCCATAAAGTATTCAAGACGATCCATTCCTTCAAGCAA-TT
124 TACGAGTTCATTTATAACTCCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTT
* * * * *
614 TTGCAAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAA-
189 TTG--AACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATAGTCT-TAATTTTGTAAAAG
* * ** * * **
678 AGGTTTTGTTGC-TTGAATTAAAAACTTATTTACGTG-AGAATCATTTCTCTCTTGTTTCTTGGA
251 A-GTTTTGAT-CATTAAAACAAAAACATATTTACCTGAAG-AT--TTT-T-TCTTGGCTCTTGGA
* * *
741 CAAACTTTC-GAAC-TAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTTACAGTATTC
309 CAAAC-TTCAAAACAT-GTCAAACGTTTACAAGTTCTTTTATAAC-TCCGTTCCTTACAGTATTC
* * *
804 AAGACGATACATTCCTTCT-AGCAACTTTCTTAACATTCTATGCT-AGAAATATC
371 AAGACAATACATTCCTT-TGAGCAACTTTCTGAACATTCCATGCTCAGAAA-ATC
*
857 GCATCATTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTTTAAACTTAT
1 GCATCATTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGGTCTTT-AATTTAAAACTTAT
* * *
922 TTACGTGAGAATTGTTTCWCTCTCTTTGTTCTTWGATGAACTTCCAAACTTGTCATACTTTTACG
65 TTACGTGAGAATTGTTTC-CTCTCTTTGTTCTTGGATGAACTTCC-AACTTATCAAACTTTTACG
* * * *
987 AGKTCWTTTATAACTYCKGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTTTGA
128 AGTTCATTTATAACTCCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTTTGA
*
1052 ACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATAGGTCTTAATTTTGTAAACGAGTTTT
193 ACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATA-GTCTTAATTTTGTAAAAGAGTTTT
* * * * * *
1117 GATCATTAAAACAAGAACATATTTTCTTGAGGATTTTTTCTTGGCTGTTGGACGAACTTCAAAAC
257 GATCATTAAAACAAAAACATATTTACCTGAAGATTTTTTCTTGGCTCTTGGACAAACTTCAAAAC
* * * * * * * * *
1182 ATTTCATACTTTTACGAGTTCTTTTATAACTCCTTTCCTTGCAGTATTCAGGACAATCCATTCCA
322 ATGTCAAACGTTTACAAGTTCTTTTATAACTCCGTTCCTTACAGTATTCAAGACAATACATTCCT
** * * *
1247 TCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATC
387 TTGAGCAACTTTCTGAACATTCCATGCTCAGAAAATC
1284 GCATCATTT
1 GCATCATTT
1293 GGTCTAA
Statistics
Matches: 721, Mismatches: 109, Indels: 74
0.80 0.12 0.08
Matches are distributed among these distances:
423 9 0.01
424 20 0.03
425 14 0.02
426 10 0.01
427 156 0.22
428 130 0.18
429 22 0.03
430 6 0.01
431 40 0.06
432 147 0.20
433 154 0.21
434 9 0.01
435 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (423 bp):
GCATCATTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTAATTTAAAACTTATT
TACGTGAGAATTGTTTCCTCTCTTTGTTCTTGGATGAACTTCCAACTTATCAAACTTTTACGAGT
TCATTTATAACTCCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTTTGAACA
TTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATAGTCTTAATTTTGTAAAAGAGTTTTGATC
ATTAAAACAAAAACATATTTACCTGAAGATTTTTTCTTGGCTCTTGGACAAACTTCAAAACATGT
CAAACGTTTACAAGTTCTTTTATAACTCCGTTCCTTACAGTATTCAAGACAATACATTCCTTTGA
GCAACTTTCTGAACATTCCATGCTCAGAAAATC
Done.