Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003656.1 Kokia drynarioides strain JFW-HI SEQ_116563, 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: 3293
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Found at i:712 original size:15 final size:15
Alignment explanation
Indices: 692--774 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 15
682 GCTTGGAAAA
**
692 TGCGAGCACTGGTGT
1 TGCGAGCACTCATGT
707 TGCGAGCACTCATGT
1 TGCGAGCACTCATGT
**
722 TGCGAGCACTCACAT
1 TGCGAGCACTCATGT
** *
737 TAAGAGCACTAATGT
1 TGCGAGCACTCATGT
* * * *
752 GGCAAACACTCGTGT
1 TGCGAGCACTCATGT
767 TGCGAGCA
1 TGCGAGCA
775 TGAACGAAGG
Statistics
Matches: 49, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (15 bp):
TGCGAGCACTCATGT
Found at i:2377 original size:216 final size:215
Alignment explanation
Indices: 1979--3290 Score: 1282
Period size: 215 Copynumber: 6.1 Consensus size: 215
1969 CAAAAGTTTG
* ** * * *
1979 TCCAAGAACCAAGAGAGAAACAATTTTCACATAAAAAAAGTTTTTAAATCAAAGACCAAAAATTG
1 TCCAAGAACCAAGAGAGAAACAATTCTCATGT-AAATAAGTTTTTAATTCAAAGACCAAAAGTTG
* * * * *
2044 TTTACAAAATGACAAACTTTTTAGACCAACTGATCGTGACTTCCAAAGCATGAAATGTTCGGAAA
65 TTTACAAAATGACAAACTTTTTAGACCAAATGAT-GCGATTTCC-AAGCATGGAATGTTCAGAAA
** * ** * * *
2109 ATAAGTCGAAGGAATGGATCACCTTAAATACTCTTAGGAA-ACGAAGTTATAAAATAACTTGTAA
128 ATTTGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACA-GAAGTTATAAAAGAACTAGTAA
* *
2173 ATGGTTGACAAGTTCGGAAGTTCG
192 ATGTTTGACAAGTTCGGAAGTTCA
* ** *
2197 TACAAGAACCAAGAGAGTGACAATTCTCATGTAAATAAGTTTTTAATTCAAAGGCCAAAAGTTGT
1 TCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
* * * * *
2262 TTACAAATTGACAGACTTTTTAGACCAAATTATGCGATTTCCTAAGCATAGAATGTTTAGAAAAT
66 TTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCC-AAGCATGGAATGTTCAGAAAAT
* * * * * *
2327 TTGTCGAAGGAATAGATCATCTTGAATACTCTTAGGAACAAAAGTTATAAAAGAACTCGTAACTG
130 TTGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACAGAAGTTATAAAAGAACTAGTAAATG
*
2392 TTAGACAAGTTCGGAAGTTCA
195 TTTGACAAGTTCGGAAGTTCA
* * * * *
2413 TCCACGAACCAAGAGAAAAATAATTCTCATGTAAATAAGTTTTTAATTTAAAGA-AAAAAGGTTG
1 TCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAA-GTTG
* * * * * * *
2477 TTTACAAAAGGACAAACTATTTAAACCAAATGATGCAATTTCCCAGCAAGGAATGTTCA-AAAAA
65 TTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCAAGCATGGAATGTTCAGAAAAT
** * * *
2541 TTGCTCAAACTAATGGATCGTCTTGAATACT-TTAAGGAACGGAAGCTATAAAAGAACTTGTAAA
130 TTG-TCAAAGGAATGGATCGTCTTGAATACTCTT-AGGAACAGAAGTTATAAAAGAACTAGTAAA
** * * * *
2605 ACTTTGACTAGGTCGTATGTTCA
193 TGTTTGACAAGTTCGGAAGTTCA
* * * ** * * *
2628 TCCAAGAACCAAGAGAGAAATAATTCTCATGTCAATATGTACTTAGTTCAGAG-CACAAAAGTTA
1 TCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGAC-CAAAAGTTG
* * * *
2692 TTTACAAAATTACAAACTTTTTAGACCAAATGATGCGATTTTCCAGGCATGGAAAGTT-TGAAAA
65 TTTACAAAATGACAAACTTTTTAGACCAAATGATGCGA-TTTCCAAGCATGGAATGTTCAG-AAA
* ** * * *
2756 ATTGGTTGAAGGAATGGATTGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTAGTAAA
128 ATTTGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACAGAAGTTATAAAAGAACTAGTAAA
* *
2821 TGTTTGACGAGTTCGGAAGTTCG
193 TGTTTGACAAGTTCGGAAGTTCA
* * * * * *
2844 TCCAAGAACCAATAGAGAAACAATTGTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAGGTTAT
1 TCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
* * * * * *
2909 ATATAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCTAGCATGGAATGTTCA-AAAAAT
66 TTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCAAGCATGGAATGTTCAGAAAATT
* * * * * *
2973 TGCTAAAATGAATGCATCGTCTTTAATACT-TTCATGAATC-GAAGTTATAAAAGAACTCGTAAA
131 TG-TCAAAGGAATGGATCGTCTTGAATACTCTT-AGGAA-CAGAAGTTATAAAAGAACTAGTAAA
* *
3036 TGTTTAACCAGTTCGGAAGTTCA
193 TGTTTGACAAGTTCGGAAGTTCA
* ***
3059 TCCAAGAACCAAGAGAGAAACAATTCTC-TCATAAA-AAAAATTTAATTCAAAGACCAAAAAGTT
1 TCCAAGAACCAAGAGAGAAACAATTCTCAT-GTAAATAAGTTTTTAATTCAAAGACC-AAAAGTT
* * * * * * *
3122 GTTTACAAGATGACAAAC-TATTATACCAAATGATGTGATTTCCCGATCATGGAATGTT-TGACA
64 GTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTT-CCAAGCATGGAATGTTCAGA-A
* * * * * * *
3185 AATTGGTCAAAGGAATGGATCGTCTTGACTACTATCAAGAACCGAAGTTATTAAAGAACTAGTAA
127 AATTTGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACAGAAGTTATAAAAGAACTAGTAA
* *
3250 ATGTTTGACAAGTTCAGAACTTCA
192 ATGTTTGACAAGTTCGGAAGTTCA
*
3274 TCAAAGAACCAAGAGAG
1 TCCAAGAACCAAGAGAG
3291 GAA
Statistics
Matches: 893, Mismatches: 179, Indels: 47
0.80 0.16 0.04
Matches are distributed among these distances:
214 54 0.06
215 389 0.44
216 357 0.40
217 67 0.08
218 26 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (215 bp):
TCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
TTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCAAGCATGGAATGTTCAGAAAATT
TGTCAAAGGAATGGATCGTCTTGAATACTCTTAGGAACAGAAGTTATAAAAGAACTAGTAAATGT
TTGACAAGTTCGGAAGTTCA
Found at i:2906 original size:431 final size:427
Alignment explanation
Indices: 1979--3290 Score: 1443
Period size: 431 Copynumber: 3.0 Consensus size: 427
1969 CAAAAGTTTG
* * * **
1979 TCCAAGAACCAAGAGAGAAACAATTTTCACATAAAAAAAGTTTTTAAATCAAAGACCAAAAATTG
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGT-AAAAAAGTTTTTAATTCAAAGACCAAAGGTTG
* * * * **
2044 TTTACAAAATGACAAACTTTTTAGACCAACTGATCGTGACTTCCAAAGCATGAAATGTTCGGAAA
65 TTTACAAAATGACAAACTATTTAGACCAAATGAT-GTGATTTCC-AAGCATGGAATGTTCAAAAA
* * ** ** *
2109 ATAAG-TCGAAGGAATGGATCACCTTAAATACTCTTAGGAAACGAAGTTATAAAATAACTTGTAA
128 AT-TGCTCAAAATAATGGATCGTCTTAAATACT-TTAGG-AACGAAGTTATAAAAGAACTTGTAA
* * * ** *
2173 ATGGTTGACAAGTTCGGAAGTTCGTACAAGAACCAAGAGAGTGACAATTCTCATGTAAATAAGTT
190 ATGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCATGT-AATAAGTA
* *
2238 TTTAATTCAAAGGC-CAAAAGTTGTTTAC-AAATTGACAGACTTTTTAGACCAAATTATGCGATT
254 TTTAATTCAAA-GCACAAAAGTTGTTTACAAAATT-ACAAACTTTTTAGACCAAATGATGCGATT
* * * * * *
2301 TCCTAAGCATAGAATGTTT-AGAAAATTTGTCGAAGGAATAGATCATCTTGAATACTCTTAGGAA
317 TCC-AGGCATGGAATGTTTGA-AAAATTGGTCGAAGGAATGGATCGTCTTGAATACTCTCAGGAA
** * * *
2365 CAAAAGTTATAAAAGAACTCGTAACTGTTAGACAAGTTCGGAAGTTCA
380 CCGAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGGAAGTTCA
* * * * * * **
2413 TCCACGAACCAAGAGAAAAATAATTCTCATGTAAATAAGTTTTTAATTTAAAGAAAAAAGGTTGT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAGGTTGT
* * ** * *
2478 TTACAAAAGGACAAACTATTTAAACCAAATGATGCAATTTCCCAGCAAGGAATGTTCAAAAAATT
66 TTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCAAGCATGGAATGTTCAAAAAATT
* * * **
2543 GCTCAAACTAATGGATCGTCTTGAATACTTTAAGGAACGGAAGCTATAAAAGAACTTGTAAAACT
131 GCTCAAAATAATGGATCGTCTTAAATACTTT-AGGAAC-GAAGTTATAAAAGAACTTGTAAATGT
* * * * * * *
2608 TTGACTAGGTCGTATGTTCATCCAAGAACCAAGAGAGAAATAATTCTCATGTCAATATGTACTTA
194 TTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCATGT-AATAAGTATTTA
* * *
2673 GTTCAGAGCACAAAAGTTATTTACAAAATTACAAACTTTTTAGACCAAATGATGCGATTTTCCAG
258 ATTCAAAGCACAAAAGTTGTTTACAAAATTACAAACTTTTTAGACCAAATGATGCGA-TTTCCAG
* * *
2738 GCATGGAAAGTTTGAAAAATTGGTTGAAGGAATGGATTGTCTTGAATACTCTCAGGAACCGAAGT
322 GCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGT
* *
2803 TATAAAAGAACTAGTAAATGTTTGACGAGTTCGGAAGTTCG
387 TATAAAAGAACTAGTAAATGTTTGACAAGTTCGGAAGTTCA
* * *
2844 TCCAAGAACCAATAGAGAAACAATTGTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAGGTTAT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAGGTTGT
* * *
2909 ATATAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCTAGCATGGAATGTTCAAAAAATT
66 TTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCAAGCATGGAATGTTCAAAAAATT
* * * *
2974 GCT-AAAATGAATGCATCGTCTTTAATACTTTCATGAATCGAAGTTATAAAAGAACTCGTAAATG
131 GCTCAAAAT-AATGGATCGTCTTAAATACTTT-AGGAA-CGAAGTTATAAAAGAACTTGTAAATG
* * * * **
3038 TTTAACCAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTC-TCATAAAAAAAATTT
193 TTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAT-GTAATAAGTATTT
* * * * *
3102 AATTCAAAG-ACCAAAAAGTTGTTTACAAGATGACAAAC-TATTATACCAAATGATGTGATTTCC
257 AATTCAAAGCA-C-AAAAGTTGTTTACAAAATTACAAACTTTTTAGACCAAATGATGCGATTTCC
* * * * * * *
3165 CGATCATGGAATGTTTGACAAATTGGTCAAAGGAATGGATCGTCTTGACTACTATCAAGAACCGA
320 AG-GCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGA
* * *
3230 AGTTATTAAAGAACTAGTAAATGTTTGACAAGTTCAGAACTTCA
384 AGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGGAAGTTCA
*
3274 TCAAAGAACCAAGAGAG
1 TCCAAGAACCAAGAGAG
3291 GAA
Statistics
Matches: 729, Mismatches: 136, Indels: 30
0.81 0.15 0.03
Matches are distributed among these distances:
429 7 0.01
430 151 0.21
431 472 0.65
432 18 0.02
433 55 0.08
434 26 0.04
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (427 bp):
TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAGGTTGT
TTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCAAGCATGGAATGTTCAAAAAATT
GCTCAAAATAATGGATCGTCTTAAATACTTTAGGAACGAAGTTATAAAAGAACTTGTAAATGTTT
GACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCATGTAATAAGTATTTAATT
CAAAGCACAAAAGTTGTTTACAAAATTACAAACTTTTTAGACCAAATGATGCGATTTCCAGGCAT
GGAATGTTTGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTCTCAGGAACCGAAGTTATA
AAAGAACTAGTAAATGTTTGACAAGTTCGGAAGTTCA
Done.