Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005477.1 Kokia drynarioides strain JFW-HI SEQ_119528, 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, 937
Length: 1562
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Found at i:753 original size:216 final size:216
Alignment explanation
Indices: 40--1199 Score: 1401
Period size: 216 Copynumber: 5.4 Consensus size: 216
30 AACGGACATA
* * * * * * *
40 CGAACTAGTCAAACTTTTACAAGTTCTATTATAACTTCGGTTCTTGAGAGCATTCAAGACGATCC
1 CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGTCGATCC
* * *
105 ACTCCGTT-GACCATTTTTTCGAAGATTCCATGATCAGGAAATCGCATCATTTGGTCTAAA-ACG
66 ATTCC-TTCGACCAATTTTTCGAAGATTCCATGATCAGGAAATCGCATCATTTGGTATAAATA-G
* *
168 TTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTTTTTATGTGAGAATTGTTTC
129 TTTGTCATTTTGTAAATAA-CTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTC
* * *
232 TCTCTTGGTTCTTGGATGAAGTTC
193 TCTCTTGGTTCTTGGACGAACTTT
* * *
256 CGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTTGGTTCCTGAGAGTATTCAAGACGATCC
1 CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGTCGATCC
* * *
321 ATTCCTTTGACCAA-TTTTCTGAAGATTCCATTATC-GAGAAATCGCATCATTTGGTAAAAATAG
66 ATTCCTTCGACCAATTTTTC-GAAGATTCCATGATCAG-GAAATCGCATCATTTGGTATAAATAG
* * * * * * * *
384 TTTGCCA-TTTGTAAATAAATTTTGGTGTTTGACTTAAAAACTTTTTTACATTACAAATCTTTCT
129 TTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCT
*
448 CTCTTGGTTCTTGGACGAAGTTT
194 CTCTTGGTTCTTGGACGAACTTT
* * * * * *
471 CGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCAGTCCCTGATAGTAGTCAAGAT-GATC
1 CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAG-TCGATC
** *
535 CATTCCTTCGACCAATTTTTCGATCATTCCATGATCAGGAAATCGTATCATTTGGTATAAATAGT
65 CATTCCTTCGACCAATTTTTCGAAGATTCCATGATCAGGAAATCGCATCATTTGGTATAAATAGT
* * *
600 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTC
130 TTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCTC
665 TCTTGGTTCTTGGACGAACTTT
195 TCTTGGTTCTTGGACGAACTTT
* * * * *
687 TGAACTGGTTAAACATTTACGAGTTATTTTATAACTTCGGTTCTTGAGAGTATTCAAGTCGATCC
1 CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGTCGATCC
* * *
752 ATTCCTTCGACCAATTTTT-GAAGATTCCATGACCGGGAAATCGCATCATTTTGCTCA-AAATAG
66 ATTCCTTCGACCAATTTTTCGAAGATTCCATGATCAGGAAATCGCATCA-TTTGGT-ATAAATAG
* *
815 TTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATT-AAAAGTTTTTTACGTTAGAATTCTTTCT
129 TTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCT
*
879 TTCTTGGTTCTTGGACGAACATTT
194 CTCTTGGTTCTTGGACGAAC-TTT
* * *
903 -GAACTTGTTAAACATTTACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTTAA-TACGATC
1 CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGT-CGATC
** * * * ** * * * *
966 CATTCCTTCGACTTATTTTTCAAACATTTCATTCTCGGGAAATCGCATCACTTGGTCTAAAAAGT
65 CATTCCTTCGACCAATTTTTCGAAGATTCCATGATCAGGAAATCGCATCATTTGGTATAAATAGT
* * * * * **
1031 TTGGCATGTTGTAAAAAACTTTTGGTCTTTGATTTAAAAACTTTTTTACGTGACAATTGGTTCTC
130 TTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCTC
* * *
1096 TCTTGGTTCTCGGACAAACTTC
195 TCTTGGTTCTTGGACGAACTTT
* * * *
1118 CGAACTTGTCAAACATTTATGAGTTCTTTTATAACTTTGGTTTCTAAGAGTATTCAA-TACGATC
1 CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGT-CGATC
1182 CATTCCTTCGACCAATTT
65 CATTCCTTCGACCAATTT
1200 CTTGAATTAA
Statistics
Matches: 815, Mismatches: 111, Indels: 36
0.85 0.12 0.04
Matches are distributed among these distances:
214 1 0.00
215 371 0.46
216 441 0.54
217 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (216 bp):
CGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGTCGATCC
ATTCCTTCGACCAATTTTTCGAAGATTCCATGATCAGGAAATCGCATCATTTGGTATAAATAGTT
TGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCTCT
CTTGGTTCTTGGACGAACTTT
Found at i:862 original size:431 final size:429
Alignment explanation
Indices: 40--1205 Score: 1552
Period size: 431 Copynumber: 2.7 Consensus size: 429
30 AACGGACATA
* * * * * *
40 CGAACTAGTCAAACTTTTACAAGTTCTATTATAACTTCGGTTCTTGAGAGCATTCAAGACGATCC
1 CGAACTTGTCAAACATTTACAAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCC
* * *
105 ACTCCGTT-GACCATTTTTTCGAAGATTCCATGATCAGGAAATCGCATCATTTGGTCTAAAACGT
66 ATTCC-TTCGACCAATTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCTAAAA-GT
*
169 TTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTTTATGTGAGAATTGTTTCTC
129 TTGTCATTTTGTAAAAA-CTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTC
* * *
234 TCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTTGGTTC
193 TCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTGGTTC
* * * * *
299 CTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTCTGAAGATTCCATTATCGAGAAATC
258 TTGAGAGTATTCAAGTCGATCCATTCCTTCGACCAATTTT-TGAAGATTCCATGACCGAGAAATC
* * *
364 GCATCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTGTTTGACTTAAAAACTTTT
322 GCATCATTTGCTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAAAACTTTT
*
429 TTACATTACAAATCTTTCTCTCTTGGTTCTTGGACGAA-GTTT
387 TTACATTACAAATCTTTCTCTCTTGGTTCTTGGACGAACATTT
* * * * * *
471 CGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCAGTCCCTGATAGTAGTCAAGATGATCC
1 CGAACTTGTCAAACATTTACAAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCC
* * *
536 ATTCCTTCGACCAATTTTTCGATCATTCCATGATCAGGAAATCGTATCATTTGGTATAAATAGTT
66 ATTCCTTCGACCAATTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCTAAA-AGTT
* *
601 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCT
130 TGTCATTTTGTAAA-AACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCT
** * * * *
666 CTTGGTTCTTGGACGAACTTTTGAACTGGTTAAACATTTACGAGTTATTTTATAACTTCGGTTCT
194 CTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTGGTTCT
*
731 TGAGAGTATTCAAGTCGATCCATTCCTTCGACCAATTTTTGAAGATTCCATGACCGGGAAATCGC
259 TGAGAGTATTCAAGTCGATCCATTCCTTCGACCAATTTTTGAAGATTCCATGACCGAGAAATCGC
* * * *
796 ATCATTTTGCTCAAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATT-AAAAGTTTT
324 ATCA-TTTGCTAAAAATAGTTTGCCA-TTTGTAAATAAATTTTGGTCTTTGAATTAAAAACTTTT
* * * *
860 TTACGTTAGAATTCTTTCTTTCTTGGTTCTTGGACGAACATTT
387 TTACATTACAAATCTTTCTCTCTTGGTTCTTGGACGAACATTT
* * * *
903 -GAACTTGTTAAACATTTACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTTAATACGATCC
1 CGAACTTGTCAAACATTTACAAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCC
** * * ** * *
967 ATTCCTTCGACTTATTTTTCAAACATTTCATTCTCGGGAAATCGCATCACTTGGTCTAAAAAGTT
66 ATTCCTTCGACCAATTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCT-AAAAGTT
* * * * *
1032 TGGCATGTTGTAAAAAACTTTTGGTCTTTGATTTAAAAACTTTTTTACGTGACAATTGGTTCTCT
130 TGTCATTTTGT-AAAAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCT
* * *
1097 CTTGGTTCTCGGACAAACTTCCGAACTTGTCAAACATTTATGAGTTCTTTTATAACTTTGGTT-T
194 CTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTGGTTCT
*
1161 CTAAGAGTATTCAA-TACGATCCATTCCTTCGACCAATTTCTTGAA
259 -TGAGAGTATTCAAGT-CGATCCATTCCTTCGACCAATTT-TTGAA
1206 TTAAAAAACT
Statistics
Matches: 639, Mismatches: 85, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
430 31 0.05
431 566 0.89
432 42 0.07
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (429 bp):
CGAACTTGTCAAACATTTACAAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCC
ATTCCTTCGACCAATTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCTAAAAGTTT
GTCATTTTGTAAAAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCT
TGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTTGGTTCTTG
AGAGTATTCAAGTCGATCCATTCCTTCGACCAATTTTTGAAGATTCCATGACCGAGAAATCGCAT
CATTTGCTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAAAACTTTTTTAC
ATTACAAATCTTTCTCTCTTGGTTCTTGGACGAACATTT
Found at i:1247 original size:143 final size:143
Alignment explanation
Indices: 1066--1348 Score: 329
Period size: 143 Copynumber: 2.0 Consensus size: 143
1056 TCTTTGATTT
* * * *
1066 AAAAACTTTTTTACGTGACAATTGGTTCTCTCTTGGTTCTCGGACAAACT-TCCGAACTTGTCAA
1 AAAAACTTTATTACGTGACAATTGGTTCTCTATCGGTTCTCGGACAAACTGT-CAAACTTGTCAA
* * * * *
1130 ACATTT-ATGAGTTCTTTTATAACTTTGGTTTCTA-AGAGTATTCAATACGATCCATTCCTTCGA
65 ACATTTCAT-AATTCTTTTATAACTTCGG-TTCCAGAGAGTAGTCAAGACGATCCATTCCTTCGA
1193 CCAATTTCTTGAATTA
128 CCAATTTCTTGAATTA
* * * ** *
1209 AAAAACTTTATTACGTGAGAATTGTTTCTCTATCGGTTCTTGGATGAAGTGTCAAACTTGTCAAA
1 AAAAACTTTATTACGTGACAATTGGTTCTCTATCGGTTCTCGGACAAACTGTCAAACTTGTCAAA
* * * * *
1274 CATTTCCTAATTCTTTTATAACTTCGGTTCCAGATAGTAGTCGAGATGATCCATTCCTTTGACCA
66 CATTTCATAATTCTTTTATAACTTCGGTTCCAGAGAGTAGTCAAGACGATCCATTCCTTCGACCA
*
1339 ATTTTTTGAA
131 ATTTCTTGAA
1349 CATTCCATGC
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
142 4 0.03
143 110 0.95
144 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (143 bp):
AAAAACTTTATTACGTGACAATTGGTTCTCTATCGGTTCTCGGACAAACTGTCAAACTTGTCAAA
CATTTCATAATTCTTTTATAACTTCGGTTCCAGAGAGTAGTCAAGACGATCCATTCCTTCGACCA
ATTTCTTGAATTA
Found at i:1543 original size:359 final size:359
Alignment explanation
Indices: 904--1558 Score: 907
Period size: 359 Copynumber: 1.8 Consensus size: 359
894 CGAACATTTG
* * * * * *
904 AACTTGTTAAACATTTACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTTAATACGATCCAT
1 AACTTGTCAAACATTTACGAATTCTTTTATAACTTCAGTTCCAGAGAGTAGTCAAGACGATCCAT
** * *
969 TCCTTCGACTTATTTTTCAAACATTTCATTCTCGGGAAATCGCATCACTTGGTCTAAAAAGTTTG
66 TCCTTCGACCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCACTTGGTCTAAAAAGTTTG
* *
1034 GCATGTTGTAAAAAACTTTTGGTCTTTGATTTAAAAACTTTTTTACGTGACAATTGGTTCTCTCT
131 GCATGTTGTAAAAAACATTTGGTCTTTGAATTAAAAACTTTTTTACGTGACAATTGGTTCTCTCT
** *
1099 TGGTTCTCGGACAAACTTCCGAACTTGTCAAACATTTATGAGTTCTTTTATAACTTTGGTTTCTA
196 TGGTTCTCGGACAAACTTCCGAACTTGTCAAACATTTATGAAATCTTTTATAACTTTGGTTCCTA
* *
1164 AGAGTATTCAATACGATCCATTCCTTCGACCAATTTCTTGAATTAAAAAACTTTATTACGTGAGA
261 AGAGTAGTCAAGACGATCCATTCCTTCGACCAATTTCTTGAATTAAAAAACTTTATTACGTGAGA
1229 ATTGTTTCTCTATCGGTTCTTGGATGAAGTGTCA
326 ATTGTTTCTCTATCGGTTCTTGGATGAAGTGTCA
* * * * * *
1263 AACTTGTCAAACATTTCCTAATTCTTTTATAACTTCGGTTCCAGATAGTAGTCGAGATGATCCAT
1 AACTTGTCAAACATTTACGAATTCTTTTATAACTTCAGTTCCAGAGAGTAGTCAAGACGATCCAT
* ** * *
1328 TCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAACGTTTG
66 TCCTTCGACCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCACTTGGTCTAAAAAGTTTG
* * * * * *
1393 TCATTTTGTAAAAAGCATTTGGTCTTTGAATTAAAATCTTTTTTACGTGAGAATTGTTTCTCTCT
131 GCATGTTGTAAAAAACATTTGGTCTTTGAATTAAAAACTTTTTTACGTGACAATTGGTTCTCTCT
* ** * *
1458 TGGTTCTTGGATGAAGTTTCGAACTTGTCAAACATTTACT-AAATCTTTTATAACTTTGGTTCCT
196 TGGTTCTCGGACAAACTTCCGAACTTGTCAAACATTTA-TGAAATCTTTTATAACTTTGGTTCCT
* * * *
1522 GATAGTAGTCAAGACGATCCATTTCTTTGACCAATTT
260 AAGAGTAGTCAAGACGATCCATTCCTTCGACCAATTT
1559 TTCG
Statistics
Matches: 252, Mismatches: 43, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
359 251 1.00
360 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (359 bp):
AACTTGTCAAACATTTACGAATTCTTTTATAACTTCAGTTCCAGAGAGTAGTCAAGACGATCCAT
TCCTTCGACCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCACTTGGTCTAAAAAGTTTG
GCATGTTGTAAAAAACATTTGGTCTTTGAATTAAAAACTTTTTTACGTGACAATTGGTTCTCTCT
TGGTTCTCGGACAAACTTCCGAACTTGTCAAACATTTATGAAATCTTTTATAACTTTGGTTCCTA
AGAGTAGTCAAGACGATCCATTCCTTCGACCAATTTCTTGAATTAAAAAACTTTATTACGTGAGA
ATTGTTTCTCTATCGGTTCTTGGATGAAGTGTCA
Done.