Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006046.1 Kokia drynarioides strain JFW-HI SEQ_120512, 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, 968
Length: 1614
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Found at i:379 original size:216 final size:216
Alignment explanation
Indices: 11--1613 Score: 1554
Period size: 216 Copynumber: 7.5 Consensus size: 216
1 CTTGTAAATT
* * * * * * *
11 TTTGAAAAGTTTGAAAGTTAATCCAAGATCCAAGAGAGAAA-ATATTCTCATGCAAATAAATTTT
1 TTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACA-ATTCTCACGTAAATAAGTTTT
* * * * * * * *
75 AAATTCAAACG-CAAAAAGCTGTTTACCATATGACAAACTATTTTGACCAAATGATGCAATTT-T
65 TAATTCAAA-GACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCT
* * * * *
138 CCGAGAATGGAATGTTCGAAAAATGGGTCGAAGGAATGCATCTTCTTAAATACTATT-AGGAACC
129 -CGAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCTTGAATACT-TTAAGGAACC
* **
202 AAAGTTATAAAAGAACTTGTAAATT
192 AAAGTTATAAAAGAACTCGTAAAAG
* * ***
227 TTTGAAAAGTTCGGAAGTTCATCCAAGAACTGGGAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
*
292 AATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATTATGCGATTTCTCG
66 AATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCTCG
357 AGCATGGAATGTTC-AGAAAATGGCTC--A--AAT-GA--GTCTTGAATACTTTAAGGAACCAAA
131 AGCATGGAATGTTCGA-AAAATGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAA
*
414 GTTGTAAAAGAACTCGTAAAAG
195 GTTATAAAAGAACTCGTAAAAG
* * * * *
436 TTTGACTAGTTCGTAAGTTCGTCCGAGAACCAAGAGAGAATCAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * *
501 AATTTAAAGACCAAAATTTGTTTACAAAATCACAAACTATTTAGACCAAAAGATGCGATTTC-CG
66 AATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCTC-
* * * *
565 GAGCTTGGAATGTTC-AGAAAATGGCTCAAAGGAATGGA-CAATCTTGAATACTTTGAGGAACCA
130 GAGCATGGAATGTTCGA-AAAATGGCTCGAAGGAATGGATC-GTCTTGAATACTTTAAGGAACCA
*
628 AAGTGATAAAAGAACTCGTAAAAG
193 AAGTTATAAAAGAACTCGTAAAAG
* * * ** *
652 TTCT-ACTAGTTCGTAAGTTCGTCCTCGAACCACA-AGAGAAACAATTCTCACGTAAATAGGTTT
1 TT-TGACAAGTTCGAAAGTTCATCCAAGAACCA-AGAGAGAAACAATTCTCACGTAAATAAGTTT
* * * * * * * *
715 TTAATTCAAAGACTAAAAGTTGTTTATATAATGAAAAAGTTTTTAGACCGAATGATACGA-TTCC
64 TTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCT
* * * ** * * * **
779 CGAACATGAAAAGTTCGAAAAATTGG-TCGAAAAAATGGATCGTCTTGAGTACTCTCAGGAACTT
129 CGAGCATGGAATGTTCGAAAAA-TGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCA
* * ** *
843 AAGTTACAAAAGAGCTATTAAATG
193 AAGTTATAAAAGAACTCGTAAAAG
* * * * * * *
867 TTCCG-CAAGTACGGAAGTTCATCCAAAAACCATGAGAGAAACATTTCTCACGTAAACAAGTTTT
1 TT-TGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * * * *
931 TAATTCAAATACCAAAAATTGTTTAGAAAATGATAACCTATTTAGACCAAATGATGTC-ATTTCT
65 TAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATG-CGATTTCT
* * * * * ** * * *
995 CGAGCATGGAATGCTT-GAAAAATTGCACAAAGGAATGAACCACCTTTAATAGTTTAAGGAACCG
129 CGAGCATGGAATG-TTCGAAAAATGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCA
* *
1059 AAGTTATAAAGGAACTGGTAAAAAG
193 AAGTTATAAAAGAACTCGT-AAAAG
* * * *
1084 TTT-ATCAAGTT-TAGAAGTTCGTCCAAGAACCAA-AGAGAAACAATTGTCATGTAAAT-A-TTT
1 TTTGA-CAAGTTCGA-AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT
* * * * * *
1144 TTAATTCAAAGACGAAAAGTTGATTACAAAATGGAAAACTATTTAGACCAAACGATGCGATTCCC
64 TTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCT
* * * * * ***
1209 CGAGCGTAGAATGTTCGAAAAATTGCTCGAAAGATTGGATCGTCTTGAATACTTTAAGGAATTGA
129 CGAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAA
*
1274 AGTTATAAAAGAACTCATAAAAG
194 AGTTATAAAAGAACTCGTAAAAG
* * * * * *
1297 CTTGACAAGCTCGAAAGTTCAGCCAAGAACAAAGAGAGAAATAGTTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * ** * * * *
1362 GATTCAAAGAGCAAAAGTTGTTTATGAAATGACAAACTATTTAGACCAAATAATGCGATTTTTAG
66 AATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCTCG
* * * * *
1427 AGCATTGAATGTTCGAAAAACTGG-TCGAAGG-ATAGGATCGGCTTGAATAATTTAAGGAATCGA
131 AGCATGGAATGTTCGAAAAA-TGGCTCGAAGGAAT-GGATCGTCTTGAATACTTTAAGGAACCAA
*
1490 AGTTATAAAAGAACTCGTCAAAG
194 AGTTATAAAAGAACTCGTAAAAG
* * * *
1513 TTTGACAAGCTCGAAAGGTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTC
1 TTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
*
1578 AATTCAAAGACCAAAAGTTGTTTACAAAATTAAAAA
66 AATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAA
1614 A
Statistics
Matches: 1130, Mismatches: 219, Indels: 76
0.79 0.15 0.05
Matches are distributed among these distances:
208 3 0.00
209 176 0.16
211 2 0.00
212 3 0.00
213 34 0.03
214 142 0.13
215 166 0.15
216 569 0.50
217 35 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (216 bp):
TTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
AATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCTCG
AGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAG
TTATAAAAGAACTCGTAAAAG
Found at i:1385 original size:430 final size:422
Alignment explanation
Indices: 23--1613 Score: 1498
Period size: 430 Copynumber: 3.7 Consensus size: 422
13 TGAAAAGTTT
* * * * * * *
23 GAAAGTTAATCCAAGATCCAAGAGAGAAA-ATATTCTCATGCAAATAAATTTTAAATTC-AA-AC
1 GAAAGTTCAGCCAAGAACCAAGAGAGAAATA-ATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* ** * * * *
85 GCAAAAAGCTGTTTACCATATGACAAACTATTTTGACCAAATGATGCAATTT-TCCGAGAATGGA
65 -CAAAAA-TTGTTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCT-CGAGCATGGA
* * * * * ** * * *
149 ATGTTCGAAAAATGGGTCGAAGGAATGCATCTTCTTAAATACTATT-AGGAACCAAAGTTATAAA
127 ATGTT-GAAAAATTGCTCAAAGGAATGGACCACCTTGAATAAT-TTAAGGAACCGAAGTTATAAA
* ** * * * ***
213 AGAACTTGTAAATTTTTGAAAAGTTCGGAAGTTCATCCAAGAACTGGGAGAGAAACAATTCTCAC
190 AGAACTCGTAAAAGTTT-ACAAGTTCGAAAGTTCGTCCAAGAAC-CAAAGAGAAACAATTCTCAC
278 GTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAAT
253 GTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAAT
* * *
343 TATGCGATTTCTCGAGCATGGAATGTTC-AGAAAATGGCTC--AAAT-GA--GTCTTGAATACTT
318 GATGCGA-TTCCCGAGCAT-GAATGTTCGA-AAAATTGCTCGAAAATGGATCGTCTTGAATACTT
** * * *
402 TAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTTGACTAGTTC
380 TAAGGAA-TTAAGTTATAAAAGAACTCATAAAAG-TTGACAAG-TC
* * *
448 GTAAGTTC-GTCCGAGAACCAAGAGAG-AATCAATTCTCACGTAAATAAGTTTTTAATTTAAAGA
1 GAAAGTTCAG-CCAAGAACCAAGAGAGAAAT-AATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * * *
511 CCAAAATTTGTTTACAAAATCACAAACTATTTAGACCAAAAGATGCGATTTC-CGGAGCTTGGAA
64 CCAAAAATTGTTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAA
* * * * * * * *
575 TGTTCAGAAAATGGCTCAAAGGAATGGACAATCTTGAATACTTTGAGGAACCAAAGTGATAAAAG
128 TGTTGA-AAAATTGCTCAAAGGAATGGACCACCTTGAATAATTTAAGGAACCGAAGTTATAAAAG
* * **
640 AACTCGTAAAAGTTCTACTAGTTCGTAAGTTCGTCCTCGAACCACAAGAGAAACAATTCTCACGT
192 AACTCGTAAAAGTT-TACAAGTTCGAAAGTTCGTCCAAGAACCA-AAGAGAAACAATTCTCACGT
* * * * * * *
705 AAATAGGTTTTTAATTCAAAGACTAAAAGTTGTTTATATAATGAAAAAGTTTTTAGACCGAATGA
255 AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGA
* * * * * * *
770 TACGATTCCCGAACATGAAAAGTTCGAAAAATTGGTCGAAAAAATGGATCGTCTTGAGTACTCTC
320 TGCGATTCCCGAGCATG-AATGTTCGAAAAATTGCTCG--AAAATGGATCGTCTTGAATACTTTA
* * *
835 AGGAACTTAAGTTACAAAAGAGCT-ATTAAATGTTCCG-CAAGTAC
382 AGGAA-TTAAGTTATAAAAGAACTCA-TAAAAGTT--GACAAGT-C
* * * * * * * *
879 GGAAGTTCATCCAAAAACCATGAGAGAAACATTTCTCACGTAAACAAGTTTTTAATTCAAATACC
1 GAAAGTTCAGCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* *
944 AAAAATTGTTTAGAAAATGATAACCTATTTAGACCAAATGATGTC-ATTTCTCGAGCATGGAATG
66 AAAAATTGTTTAGAAAATGACAAACTATTTAGACCAAATGATG-CGATTTCTCGAGCATGGAATG
* * * * *
1008 CTTGAAAAATTGCACAAAGGAATGAACCACCTTTAATAGTTTAAGGAACCGAAGTTATAAAGGAA
130 -TTGAAAAATTGCTCAAAGGAATGGACCACCTTGAATAATTTAAGGAACCGAAGTTATAAAAGAA
* * * *
1073 CTGGTAAAAAGTTTATCAAGTT-TAGAAGTTCGTCCAAGAACCAAAGAGAAACAATTGTCATGTA
194 CTCGT-AAAAGTTTA-CAAGTTCGA-AAGTTCGTCCAAGAACCAAAGAGAAACAATTCTCACGTA
* * * *
1137 AAT-A-TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGGAAAACTATTTAGACCAAACGAT
256 AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGAT
*
1200 GCGATTCCCCGAGCGTAGAATGTTCGAAAAATTGCTCGAAAGATTGGATCGTCTTGAATACTTTA
321 GCGATT-CCCGAGCAT-GAATGTTCGAAAAATTGCTCGAAA-A-TGGATCGTCTTGAATACTTTA
1265 AGGAATTGAAGTTATAAAAGAACTCATAAAAGCTTGACAAGCTC
382 AGGAATT-AAGTTATAAAAGAACTCATAAAAG-TTGACAAG-TC
* * * *
1309 GAAAGTTCAGCCAAGAACAAAGAGAGAAATAGTTCTCACGTAAATAAGTTTTTGATTCAAAGAGC
1 GAAAGTTCAGCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * * *
1374 AAAAGTTGTTTATG-AAATGACAAACTATTTAGACCAAATAATGCGATTTTTAGAGCATTGAATG
66 AAAAATTGTTTA-GAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATG
* * * * ** *
1438 TTCGAAAAACTGGTCGAAGG-ATAGGATCGGCTTGAATAATTTAAGGAATCGAAGTTATAAAAGA
130 TT-GAAAAATTGCTCAAAGGAAT-GGACCACCTTGAATAATTTAAGGAACCGAAGTTATAAAAGA
* * * * *
1502 ACTCGTCAAAGTTTGACAAGCTCGAAAGGTCATCCAAAAACCAAGAGAGAAACAATTCTCACGTA
193 ACTCGTAAAAGTTT-ACAAGTTCGAAAGTTCGTCCAAGAACCAA-AGAGAAACAATTCTCACGTA
* *
1567 AATAAGTTTTCAATTCAAAGACCAAAAGTTGTTTACAAAATTAAAAA
256 AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAA
1614 A
Statistics
Matches: 948, Mismatches: 168, Indels: 93
0.78 0.14 0.08
Matches are distributed among these distances:
423 1 0.00
424 29 0.03
425 250 0.26
426 9 0.01
427 2 0.00
428 7 0.01
429 94 0.10
430 256 0.27
431 228 0.24
432 72 0.08
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (422 bp):
GAAAGTTCAGCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
AAAAATTGTTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGT
TGAAAAATTGCTCAAAGGAATGGACCACCTTGAATAATTTAAGGAACCGAAGTTATAAAAGAACT
CGTAAAAGTTTACAAGTTCGAAAGTTCGTCCAAGAACCAAAGAGAAACAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGAT
TCCCGAGCATGAATGTTCGAAAAATTGCTCGAAAATGGATCGTCTTGAATACTTTAAGGAATTAA
GTTATAAAAGAACTCATAAAAGTTGACAAGTC
Done.