Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013889.1 Kokia drynarioides strain JFW-HI SEQ_128917, 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: 10139
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:387 original size:13 final size:13
Alignment explanation
Indices: 369--408 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
359 ATAAAATATT
369 ATTAATAATAATA
1 ATTAATAATAATA
*
382 ATTAATATTAATA
1 ATTAATAATAATA
* *
395 ATAAATAAAAATA
1 ATTAATAATAATA
408 A
1 A
409 AGCCATGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTAATAATAATA
Found at i:2438 original size:30 final size:29
Alignment explanation
Indices: 2394--2500 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 29
2384 AAGAATTTGA
* *
2394 GGTCAAAATGTGATTTTAGGAAAGTTTTAC
1 GGTCAAAATATGATTTT-GGAAAGTTTAAC
* *
2424 GGTTAAAATATGATTTTGTGAAAGTTTAAG
1 GGTCAAAATATGATTTTG-GAAAGTTTAAC
***
2454 GGTCAAAATATGATTTTGGGAAAGTTTGGG
1 GGTCAAAATATGATTTT-GGAAAGTTTAAC
*
2484 GGTCAAAATGTGATTTT
1 GGTCAAAATATGATTTT
2501 TAGATAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.01
30 65 0.97
31 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
GGTCAAAATATGATTTTGGAAAGTTTAAC
Found at i:4811 original size:37 final size:37
Alignment explanation
Indices: 4761--4899 Score: 179
Period size: 37 Copynumber: 3.8 Consensus size: 37
4751 ATTGTTTCAA
* * * *
4761 TCCACTTCTCTGTATCTCATGAAGAAGATGGATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* * *
4798 TCCACTTCTCTGTATCTTATTAGGAAGGCGAATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* * * *
4835 TCCACTTCTTTGTACCTTATCAGGAAGGCGAATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
4872 TCCACTTCTCTGTATCTCATCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAGGAAGA
4900 TGACCAATTT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 89 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (37 bp):
TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
Found at i:5031 original size:37 final size:37
Alignment explanation
Indices: 4989--5097 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
4979 TTGCTTCATT
* *
4989 AATTTGATCCACTTCTCTGTATCTCATCAGGAAGACG
1 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACG
* ** * *
5026 GATTTGGGGTACTTCTTTGTATCTCATCATGAAGACG
1 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACG
5063 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
1 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
5098 TGATCTCTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (37 bp):
AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACG
Found at i:5067 original size:198 final size:198
Alignment explanation
Indices: 4792--5467 Score: 714
Period size: 198 Copynumber: 3.4 Consensus size: 198
4782 AAGAAGATGG
* * * * * * * *
4792 ATTTGGTCCACTTCTCTGTATCTTATTAGGAAGGCGAATTTGGTCCACTTCTTTGTACCTTATCA
1 ATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGGCCACTTCTTTGTATCTCATCA
* *
4857 GGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCAATTTATTGCTTTTACC
66 GGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTTACC
*
4922 CACTTCTTTGTATCTCATCAAGAAAATGGGGGTGTGAAGTTTCACTTACATTAAGCTTTGCTTCA
131 CACTTCTTTGTATCTCATCAAGAAAATGGGGGTGTGAAGTTTCACTCACATTAAGCTTTGCTTCA
4987 TTA
196 TTA
* * **
4990 ATTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGGGTACTTCTTTGTATCTCATCA
1 ATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGGCCACTTCTTTGTATCTCATCA
* * * * *
5055 TGAAGACGAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCTCTTTATTGCTTTAACC
66 GGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTTACC
* *
5120 CACCTT-TTTGTATCTCATC-AGAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTT
131 CA-CTTCTTTGTATCTCATCAAGAAA-ATGGGGGTGTGAAGTTTCACTCACATTAAGCTTTGCTT
* *
5183 TATTG
194 CATTA
* * * * * ***
5188 ATTTGGTCTACATCTCTAAATCTCATCTGGAAGATGACTGCCTCATTGATTTAATCCACTT-TTC
1 ATTTGATCCACTTCTCTATATCTCATCAGG-A-A-GAC-G----A---ATTTGGGCCACTTCTT-
* * * * * * * *
5252 TGTATCTCTTTAGGAAGATGAATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGACCGCCTT
54 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTT
* * * * *
5317 ATT--TTTTGGACCAACTTCTCTGTATCTCATCAAGAAGATGGAGGTGTGAAGTTTTACTCACAT
119 ATTGCTTTT--ACCCACTTCTTTGTATCTCATCAAGAAAATGGGGGTGTGAAGTTTCACTCACAT
* *
5380 TTAGCTTTGCTTCATTT
182 TAAGCTTTGCTTCATTA
* ** *
5397 ATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGTATCTCATCA
1 ATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGGCCACTTCTTTGTATCTCATCA
5462 GGAAGA
66 GGAAGA
5468 TGACCACTTT
Statistics
Matches: 392, Mismatches: 67, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
197 5 0.01
198 216 0.55
199 5 0.01
200 1 0.00
201 4 0.01
202 1 0.00
205 1 0.00
206 2 0.01
207 4 0.01
208 6 0.02
209 143 0.36
210 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (198 bp):
ATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGGCCACTTCTTTGTATCTCATCA
GGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTTACC
CACTTCTTTGTATCTCATCAAGAAAATGGGGGTGTGAAGTTTCACTCACATTAAGCTTTGCTTCA
TTA
Found at i:5422 original size:209 final size:209
Alignment explanation
Indices: 5056--5433 Score: 503
Period size: 209 Copynumber: 1.8 Consensus size: 209
5046 ATCTCATCAT
* * * *
5056 GAAGACGAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCTCTTTATTGCTTTAACCC
1 GAAGACGAATTTGGTCTACTTCTCTGCATCTCATCAGGAAGATGACCGCCTTATTGCTTTAACCC
* * * * *
5121 ACCTTTTTGTATCTCATCAGAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTTAT
66 AACTTTCTGTATCTCATCAGAAAGATGGAGGTGTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
* * *
5186 TGATTTGGTCTACATCTCTAAATCTCATCTGGAAGATGACTGCCTCATTGATTTAATCCACTTTT
131 TGATTTGATCCACATCTCTAAATCTCATCAGGAAGATGACTGCCTCATTGATTTAATCCACTTTT
5251 CTGTATCTCTTTAG
196 CTGTATCTCTTTAG
* * * *
5265 GAAGATGAATTTGGT-TCACTTCTCTGCATCTCGTCAGGAAGATGACCGCCTTATT-TTTTGGA-
1 GAAGACGAATTTGGTCT-ACTTCTCTGCATCTCATCAGGAAGATGACCGCCTTATTGCTTT-AAC
* *
5327 CCAACTTCTCTGTATCTCATCA-AGAAGATGGAGGTGTGAAGTTTTACTCACATTTAGCTTTGCT
64 CCAACTT-TCTGTATCTCATCAGA-AAGATGGAGGTGTGAAGTTTCACTCACATTGAGCTTTGCT
* * *
5391 TCATTTATTTGATCCACTTCTCTATATCTCATCAGGAAGATGA
127 TCATTGATTTGATCCACATCTCTAAATCTCATCAGGAAGATGA
5434 ATTTGGTTCA
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
208 11 0.08
209 133 0.92
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (209 bp):
GAAGACGAATTTGGTCTACTTCTCTGCATCTCATCAGGAAGATGACCGCCTTATTGCTTTAACCC
AACTTTCTGTATCTCATCAGAAAGATGGAGGTGTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
TGATTTGATCCACATCTCTAAATCTCATCAGGAAGATGACTGCCTCATTGATTTAATCCACTTTT
CTGTATCTCTTTAG
Found at i:5506 original size:161 final size:161
Alignment explanation
Indices: 5230--5536 Score: 461
Period size: 161 Copynumber: 1.9 Consensus size: 161
5220 GATGACTGCC
* * * *
5230 TCATTGATTTAATCCACTTTTCTGTATCTCTTTAGGAAGATGAATTTGGTTCACTTCTCTGCATC
1 TCATTGATTTAATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGCATC
* * * *
5295 TCGTCAGGAAGATGACCGCCTTATTTTTTGGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
66 TCATCAGGAAGATGACCACCTTATTGTTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
*
5360 GTGTGAAGTTTTACTCACATTTAGCTTTGCT
131 GTGTGAAGTTTCACTCACATTTAGCTTTGCT
* * *
5391 TCATTTATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGTATC
1 TCATTGATTTAATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGCATC
* * *
5456 TCATCAGGAAGATGACCACTTTATTGTTTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGAG
66 TCATCAGGAAGATGACCACCTTATTGTTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
* *
5521 TTTTGAAGTTTCACTC
131 GTGTGAAGTTTCACTC
5537 GTATTGAACT
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
161 129 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (161 bp):
TCATTGATTTAATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGCATC
TCATCAGGAAGATGACCACCTTATTGTTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
GTGTGAAGTTTCACTCACATTTAGCTTTGCT
Found at i:5574 original size:161 final size:161
Alignment explanation
Indices: 5230--5592 Score: 458
Period size: 161 Copynumber: 2.3 Consensus size: 161
5220 GATGACTGCC
* * * * *
5230 TCATTGATTTAATCCACTTTTCTGTATCTCTTTAGGAAGATGAATTTGGTTCACTTCTCTGCATC
1 TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTGCATC
* * * *
5295 TCGTCAGGAAGATGACCGCCTTATTTTTTGGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
66 TCATCAGGAAGATGACCACCTTATTGTTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
* * * *
5360 GTGTGAAGTTTTACTCACATTTAGCTTTGCT
131 GTGTGAAGTTTCACTCACATTGAACTTTGCA
* *
5391 TCATTTATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGTATC
1 TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTGCATC
* * *
5456 TCATCAGGAAGATGACCACTTTATTGTTTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGAG
66 TCATCAGGAAGATGACCACCTTATTGTTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
* * **
5521 TTTTGAAGTTTCACTCGTATTGAACTTCT-CA
131 GTGTGAAGTTTCACTCACATTGAACTT-TGCA
* * *** *
5552 TCATTTTTTTGGTTTGCTTCTCTGTATCTCATTAGGAAGAT
1 TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGAT
5593 AACCTTTTGA
Statistics
Matches: 172, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
161 171 0.99
162 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (161 bp):
TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTGCATC
TCATCAGGAAGATGACCACCTTATTGTTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG
GTGTGAAGTTTCACTCACATTGAACTTTGCA
Done.