Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013322.1 Kokia drynarioides strain JFW-HI SEQ_128344, 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: 11203
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Found at i:5421 original size:20 final size:21
Alignment explanation
Indices: 5396--5444 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
5386 AAAAAAAGTG
5396 ATAAAAAAGTA-GAGAAAAA-A
1 ATAAAAAA-TACGAGAAAAAGA
5416 AT-AAAAATACGAGAAAAAGA
1 ATAAAAAATACGAGAAAAAGA
5436 A-AAAAAATA
1 ATAAAAAATA
5445 AAAACAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (21 bp):
ATAAAAAATACGAGAAAAAGA
Found at i:5429 original size:19 final size:20
Alignment explanation
Indices: 5398--5444 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5388 AAAAAGTGAT
*
5398 AAAAAAGTA-GAGAAAAA-A
1 AAAAAAATACGAGAAAAAGA
*
5416 ATAAAAATACGAGAAAAAGA
1 AAAAAAATACGAGAAAAAGA
5436 AAAAAAATA
1 AAAAAAATA
5445 AAAACAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 9 0.38
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.09
Consensus pattern (20 bp):
AAAAAAATACGAGAAAAAGA
Found at i:8492 original size:216 final size:216
Alignment explanation
Indices: 8110--11203 Score: 3270
Period size: 216 Copynumber: 14.4 Consensus size: 216
8100 TTGTATCATA
*
8110 GATTGTCATGAATACTTTAAGGAACT-AATGTT-TCTAAAGAACTCA-TAAAAGTTTGTCAAGTT
1 GATTGTCATGAATACTTTAAGGAACTGAA-GTTAT-AAAAGAACT-AGTAAAAGTTTGTCAAGTT
* * * *
8172 CGGAAGTTCATCCAAGAA-TAATGAGAGAAACAATTCTCGCGTAAATAAGTTTTTAATT-AAAGA
63 CGAAAGTTCGTCCAAGAACCAA-GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * *
8235 CGAAAAGTTTTTTACAAATTGACAAACTATTTTAGACCAAATGATGCGATTTCCCGAGCGTGGAA
127 CCAAAAGTTGTTTACAAAATGACAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAA
8300 TGTTCAGAAAATTGCTCGAAGGAATG
191 TGTTCAGAAAATTGCTCGAAGGAATG
* * * * * *
8326 AATTGTCCTGAATACTTTAAGGAACCGAGGTTATAGAAGAACTAGTAAAAGTTTGTTAAGTTCGA
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
* * *
8391 AAGTTCGTCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATAAGTTTTTAATTCAAAGACCAA
66 AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * * * *
8456 AAGTTGTTTAGAAAATGACAAATTATTTAGACCAAATGCTTCGATTTCCCAAGCATGGAATGTTC
131 AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* **
8521 A-ACTAATTGCTTAAAGGAATG
196 AGA-AAATTGCTCGAAGGAATG
* * ** * *
8542 GATTGTCCTGAATACTTTATGGAACCAAAGTTATAGAAGAATTCA-TAAAAGTTTGTCAAGTTCG
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACT-AGTAAAAGTTTGTCAAGTTCG
* * * *
8606 GAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAAGCTTTTAATTCAAAGACCA
65 AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* *
8671 AAAGTTGTTTAGAAAATGACAAACTATTTAGACCAAATGGTGCGATTTCCCGAGCATGGAATGTT
130 AAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT
*
8736 CA-AATAATTGTTC-AATGGAATG
195 CAGAA-AATTGCTCGAA-GGAATG
* * **
8758 GATTGTCTTGAATACTTTATGGAACCAAAGTTA-AATAAGAACTCA-TAAAAGTTTGTCAAGTTC
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAA-AAGAACT-AGTAAAAGTTTGTCAAGTTC
** * ** *
8821 GAAAGTTTATCCAAGAACCAAGAGAGAAACAACTCTCATATAAATAAGTTTTTAATTCAAAAACC
64 GAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* **
8886 AAAAGTTGTTTACAAAATGACAAACTGTTTAGACCAAATGATGCGATTTTTCGAGCATGGAATGT
129 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
** * **
8951 TTGGAAAATTTCTCGGTGGAATG
194 TCAGAAAATTGCTCGAAGGAATG
* * * * * * * **
8974 GATCGTCATGAATTCTTTTAGGAATTGAAGTTTTAAAAGAAGTCGTAAAAGTTCATCAAGTTC-A
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
* * * *
9038 GAAGTTCGTCCAAGAACAAAGAGCGGAACAATTCTCGCGTAAATAAGTTTTTAATTCAAAGA-CA
66 -AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
** *
9102 AAATGTTGTTTACAAAATGACAAACTATTTTAGACCAAATGATGTAATTTCTCGAGCATGGAATG
130 AAA-GTTGTTTACAAAATGACAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATG
* **
9167 TTC-GAAAATTGCTCAAAACAATG
193 TTCAGAAAATTGCTCGAAGGAATG
* * * * ** * *
9190 GATTGTTATGAATATTTTACGGAACTGAAGTTATAAAAGAACTTGTGTAAGTTT-TCCAGCCTCG
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAG-TTCG
* * ** * * * *
9254 GAAGTTCGTCCGAGGCCCAAGACATAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACTA
65 AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* ** * * * *
9319 AAAGTTGTTTACAAAATGATAAACCGTTTAGACCAAATAATAC-ATTTTCACAAGCATGGAATGT
130 AAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA-TTTCCCGAGCATGGAATGT
**
9383 TTGGAAAATTGCTCGAAGGAATG
194 TCAGAAAATTGCTCGAAGGAATG
** * * * * *
9406 GATCATCAAGAATACTTTAAGGAACTGAAGTTTTTAAAGAATCCA-TAAAAGTTTGCCAAGTTCG
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAA-CTAGTAAAAGTTTGTCAAGTTCG
* * *
9470 AAAGTTCGTCCAAGATCCAAGAGAGAAA-AATTCTCACGTAACTAAGTTTTTACTTCAAAGACCA
65 AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * *
9534 AAAGTTGTTTACAAAATAACAAACCATTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTT
130 AAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT
* **
9599 CTGAAAATTAATCGAAGGAATG
195 CAGAAAATTGCTCGAAGGAATG
** * * *
9621 GATCATCGTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAG-TTGCCAAGTTC-A
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
*
9684 GAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
66 -AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * *
9749 ACAA-TTGTTTAGAAAATGACAAACTATTTAAACCAAATGATGCGATTTCTCGAGCATGGAATGT
130 A-AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
* *
9813 TCATAAAATTGCTCGAA-GATATT
194 TCAGAAAATTGCTCGAAGGA-ATG
* * * * * * *
9836 AATTGTCCTAAATGCTTTAAGGAA-TCGAAGTTATAGAAGAACTTGTAAAAGTTTGTCATGTTCG
1 GATTGTCATGAATACTTTAAGGAACT-GAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCG
* * * *
9900 AAAGTTTGTCCAAGATCCAAGAGAGAAACAACTCTGACGTAGAA-AAGTTTTTTAATTCAAAGAC
65 AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTA-AATAAG-TTTTTAATTCAAAGAC
* * * *
9964 CAAAAGTTGTTTAGAAAATGACAAACTATTTAGA-AAAATGATTCAATTTCCCGAGCATGGAATG
128 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATG
** * *
10028 TTTGGGAAATAGCTCGAAGGAATG
193 TTCAGAAAATTGCTCGAAGGAATG
* * * * *
10052 GATTGTTACGAATACTTTCAGGAACT-ACAGTTATAAAAG----A--AACAGTTTGTCAAGTT-T
1 GATTGTCATGAATACTTTAAGGAACTGA-AGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCG
* * * * * * * *
10109 AGAAGTTTGTCAAAGAACCAAGAAAAAAATAGTTCTCACATAAATAAGTTTTTAGTTCAAAGACC
65 A-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * * *
10174 AAAAGTTGTTTACATAATGATAAACCATTTAGACCAAATGATGAGATTTCCCGAGCATGAAAT-T
129 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
** *
10238 TTTGAAATATAT-CTTGAAGGAATG
194 TCAGAAA-AT-TGCTCGAAGGAATG
* *** * * * * ** * * *
10262 TATCACCTTTAATATTTTAAGGGACCAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTGA
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
* * * ** * *
10327 AAGTTTGTCCAAGAACAAAGAGAGAAATAATTCTCGTGTAAATAAGTTTTTATTTCAAAGACGAA
66 AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * *
10392 TAGTTGTTTACAAAATGAAAAACTATTTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
131 AAGTTGTTTACAAAATGACAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT
* * * *
10457 CCGAAAATTACGCAAAGGAATG
195 CAGAAAATTGCTCGAAGGAATG
* * * * * * *
10479 AATTATCCTGAATACTTTAAAGAA-TCAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCG
1 GATTGTCATGAATACTTTAAGGAACT-GAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCG
* * * * *
10543 AAAGTTCGTCCAAGAACAAAGAGAGGAACAATTCTCGCGTAAATAAGTTTTTAATTCAAACACTA
65 AAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
** * * *
10608 ATTGTTGTTTACAAAATAACAAACTATTTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGT
130 AAAGTTGTTTACAAAATGACAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
* *
10673 TTAG----TAGCTCGAAGGAATG
194 TCAGAAAATTGCTCGAAGGAATG
* * * *
10692 GATTGTTATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAGAAGTTTGCCAAGTTCGA
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
* * * *
10757 AAGTTTGTCCAAGATCCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAA
66 AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* *
10822 AAGTTGTTTACAAAATGACAAAAC-ATTTAGACCAAATAATGTGATTT-CC---C----AA-G-T
131 AAGTTGTTTACAAAATGAC-AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT
* * *
10876 CAAAAAATTACTTGAAGGAATG
195 CAGAAAATTGCTCGAAGGAATG
* * * * *
10898 GATCGTCAAT-AATACTATAAGGAACTGAAGTTTTAAAACAAATCA-TAAAAGTTTGTCAAGTTC
1 GATTGTC-ATGAATACTTTAAGGAACTGAAGTTATAAAAGAACT-AGTAAAAGTTTGTCAAGTTC
* * * * * *
10961 GGAAGTTCGTCCGAGATCCTAGAGAGAAACAATTCTCACATAAATATGTTTTTAATTCAAAGACC
64 GAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * *
11026 AAAAGTTGTTTACAAAATAACAAACCATTTAGACCAAATGATGCGATTTGCCGAGCATGGAATGT
129 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
* *
11091 TTAGAAAATTACTCGAAGGAATG
194 TCAGAAAATTGCTCGAAGGAATG
* ** * ** *
11114 GATCGTCATTTATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTACCAAGTTCGG
1 GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
11179 AAGTTCGTCCAAGAACCAAGAGAGA
66 AAGTTCGTCCAAGAACCAAGAGAGA
Statistics
Matches: 2421, Mismatches: 380, Indels: 154
0.82 0.13 0.05
Matches are distributed among these distances:
202 2 0.00
203 1 0.00
204 2 0.00
205 4 0.00
206 160 0.07
207 4 0.00
208 1 0.00
209 54 0.02
210 110 0.05
211 3 0.00
212 21 0.01
213 139 0.06
214 49 0.02
215 344 0.14
216 1170 0.48
217 351 0.14
218 6 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (216 bp):
GATTGTCATGAATACTTTAAGGAACTGAAGTTATAAAAGAACTAGTAAAAGTTTGTCAAGTTCGA
AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
AGAAAATTGCTCGAAGGAATG
Done.