Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007093.1 Kokia drynarioides strain JFW-HI SEQ_121702, 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, 756
Length: 1260
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:454 original size:216 final size:215
Alignment explanation
Indices: 1--537 Score: 675
Period size: 216 Copynumber: 2.5 Consensus size: 215
* * * * *
1 GTGAGAATTATTTCTCTCTTGGTTCTTCGACAAACTTTCAAACTTGTCAAACTTTTACAAGTTCT
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTACGAGTTCT
* * * * * * * *
66 TTTATAACTTTGGTTCCTTAAAGTATTCAAGTCTATTCATTCTTTCAACCACTTTTCGAACATTT
66 TTGATAACTTTGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCAACAAATTTTCGAACATTC
*
131 AATGCTCTGGAAATTGCATCATTTCGTCCAAATAGTTTGTCAGTTTGTAAACAACTTTTGCTCTT
131 AATGCTCGGGAAATTGCATCATTTCGTCCAAATAGTTTGTCAGTTTGTAAACAACTTTTGCTCTT
* * *
196 TGAATTAAGAACTGATTTAC
196 TGAAATAAAAACTGATATAC
* * *
216 ATGAGAATTGCTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTAGTCAAACTTTTACGAGTTCT
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTACGAGTTCT
* * * * * *
281 TAGATAACTTAGTTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGAGAAATTTTCTAAGCATT
66 TTGATAACTTTGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCAACAAATTTTCGAA-CATT
* * * * *
346 CCATGCTCGGGAAATCT-CATGATTT-GTTCCAAATAGTTTGTCATTTTGTAAGCAACTTTTGGT
130 CAATGCTCGGGAAAT-TGCATCATTTCG-TCCAAATAGTTTGTCAGTTTGTAAACAACTTTTGCT
*
409 CTTTGAAATAAAAACTTATATAC
193 CTTTGAAATAAAAACTGATATAC
* ** * *
432 GTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTCTGAACTTCTCATACTTTTACGAGTTCT
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTACGAGTTCT
*
497 TTGATAACTTTGGTTCCTTAGAGTATTCAAGA-AGATCCATT
66 TTGATAACTTTGGTTCCTTAAAGTATTCAAGACA-ATCCATT
538 ATCTTTTGAT
Statistics
Matches: 274, Mismatches: 44, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
215 106 0.39
216 167 0.61
217 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (215 bp):
GTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACTTTTACGAGTTCT
TTGATAACTTTGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCAACAAATTTTCGAACATTC
AATGCTCGGGAAATTGCATCATTTCGTCCAAATAGTTTGTCAGTTTGTAAACAACTTTTGCTCTT
TGAAATAAAAACTGATATAC
Found at i:797 original size:309 final size:309
Alignment explanation
Indices: 238--842 Score: 887
Period size: 309 Copynumber: 2.0 Consensus size: 309
228 TCTCTCTTGG
* *
238 TTCTTGGACGAACTTCCAAACTAGTCAAACTTTTACGAGTTCTTAGATAACTTAGTTTCCTTAAA
1 TTCTTGGACGAACCTCCAAACTAGTCAAACATTTACGAGTTCTTAGATAACTTAGTTTCCTTAAA
* * *
303 GTATTCAAGACAATCCATTCCTTCGAGAAATTTTCTAAGCATTCCATGCTCGGGAAATCTCATGA
66 GTATTCAAGACAATCCATTCCTTCAAGAAATTTTCTAAGCATTCCATGCTCAGGAAATCTCATCA
* *
368 TTTGTTCCAAATAGTTTGTCATTTTGTAAGCAACTTTTGGTCTTTGAAATAAAAACTTATATACG
131 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAATAAAAACTTATATACG
* * *
433 TGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTCTGAACTTCTCATACTTTTACGAGTTCTT
196 TGAGAATTATTTCTCTCTTGGTTCTCGGACGAACTTCTGAAATTCTCAAACTTTTACGAGTTCTT
* * *
498 TGATAACTTTGGTTCCTTAGAGTATTCAAGAAGATCCATTATCTTTTGA
261 TGATAACATCGGTTCCTTAAAGTATTCAAGAAGATCCATTATCTTTTGA
* ** *
547 TTCTTGGACGAACACT-CAAACTTGTCAAACATTTACGAGTTCTTTTATAACTT-CTGTTCCTTA
1 TTCTTGGACGAAC-CTCCAAACTAGTCAAACATTTACGAGTTCTTAGATAACTTAGT-TTCCTTA
* * * *
610 AAGTATTCAAGACGATTCATTCCTTCAAGCAATTTTCTGAAG-ATTTCATGCTCAGGAAAT-TGC
64 AAGTATTCAAGACAATCCATTCCTTCAAGAAATTTTCT-AAGCATTCCATGCTCAGGAAATCT-C
* * *
673 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATT
127 ATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAATAAAAACTTATA
*
738 TACGTGAGAATTATTTCTCTCTTGGTTCAT-GGACGAACTTCTGAAATTTTCAAACTTTTACGAG
192 TACGTGAGAATTATTTCTCTCTTGGTTC-TCGGACGAACTTCTGAAATTCTCAAACTTTTACGAG
* *
802 TTCTTTTATAACATCGGTTCCTTAAAGTATTCAAGATGATC
256 TTCTTTGATAACATCGGTTCCTTAAAGTATTCAAGAAGATC
843 GATTCCTTCG
Statistics
Matches: 264, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
308 2 0.01
309 257 0.97
310 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (309 bp):
TTCTTGGACGAACCTCCAAACTAGTCAAACATTTACGAGTTCTTAGATAACTTAGTTTCCTTAAA
GTATTCAAGACAATCCATTCCTTCAAGAAATTTTCTAAGCATTCCATGCTCAGGAAATCTCATCA
TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAATAAAAACTTATATACG
TGAGAATTATTTCTCTCTTGGTTCTCGGACGAACTTCTGAAATTCTCAAACTTTTACGAGTTCTT
TGATAACATCGGTTCCTTAAAGTATTCAAGAAGATCCATTATCTTTTGA
Found at i:1074 original size:215 final size:213
Alignment explanation
Indices: 547--1245 Score: 936
Period size: 216 Copynumber: 3.2 Consensus size: 213
537 TATCTTTTGA
** *
547 TTCTTGGACGAACACTCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCTGTTCCTTAAA
1 TTCTTGGACGAACTTTCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCTTAAA
* * * * * *
612 GTATTCAAGACGATTCATTCCTTCAAGCAATTTTCTGAAGATTTCATGCTCAGGAAATTGCATCA
65 GTATTCAAGACGATCCATTCCTTCAAGCAATTTTTTGAACA-TTCCTGCTCGGGAAATCGCATCA
*
677 TTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACG
129 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACG
*
742 TGAGAATTATTTCTCTCTTGG
194 TGAGAA-TGTTTCTCTCTTGG
* * * *
763 TTCATGGACGAACTTCTGAAA-TTTTCAAACTTTTACGAGTTCTTTTATAACATCGGTTCCTTAA
1 TTCTTGGACGAACTT-TCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC-GTTCCTTAA
* * *
827 AGTATTCAAGATGATCGATTCCTTCGAGCAATTTTTTGAACATTCCTGGCTCGGGAAATCGCATC
64 AGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTTGAACATTCCT-GCTCGGGAAATCGCATC
* * ** *
892 ATCTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTGGGTCTTTGAATTAAAAACTTCCTTAG
128 ATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAC
957 GTGAGAATGTTTCTCTCTTGG
193 GTGAGAATGTTTCTCTCTTGG
* * *
978 TTCTTGGTCGAACTTTCAAAGTTGTCAAACTTTTACGAGTTATTTTATAACTTCGATTCCTTAAA
1 TTCTTGGACGAACTTTCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG-TTCCTTAAA
* *
1043 GTATTCAAGACAATCCATTCCTTCAAGCAATTTTTTGAACATTCCATGCTTGGGAAATCGCATCA
65 GTATTCAAGACGATCCATTCCTTCAAGCAATTTTTTGAACATTCC-TGCTCGGGAAATCGCATCA
* * * *
1108 TTTGGTCCAAATAGTTTGTCATTTTATAAACAACTTTTGCTCTTTGAAATAAAAACTTATTTACC
129 TTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACG
*
1173 TGAGAAATGTTTCTCTATTGG
194 TGAG-AATGTTTCTCTCTTGG
* * * * * *
1194 TTCTT-CACCAAACTTCCGAACATGTCAAACTTTTAAGAGTT-TTTTATAACTT
1 TTCTTGGA-CGAACTTTCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
1246 TGTTTCCTAA
Statistics
Matches: 423, Mismatches: 53, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
214 5 0.01
215 198 0.47
216 216 0.51
217 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (213 bp):
TTCTTGGACGAACTTTCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGTTCCTTAAAG
TATTCAAGACGATCCATTCCTTCAAGCAATTTTTTGAACATTCCTGCTCGGGAAATCGCATCATT
TGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTG
AGAATGTTTCTCTCTTGG
Done.