Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001467.1 Kokia drynarioides strain JFW-HI SEQ_112991, 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: 1712
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:775 original size:282 final size:279
Alignment explanation
Indices: 1--1712 Score: 1818
Period size: 282 Copynumber: 6.1 Consensus size: 279
*
1 TGTACTTGTTGATTTGTGCGGATTTCGTCCCACTATTTTTATTTACTCGTAGCATTCAAATTGGC
1 TGTACTTGTTGATTTGTGCGGATTTGGT-CC-CTATTTTTATTTACTCGTAGCATTCAAATTGGC
* * *
66 GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATTAAATCAACGAAGAATCTCCCTGCCAAATTC
64 GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTACCAAATAC
* *
131 AAGCAGCTCAATCACATGCATTTGACTTGAAACCGCCGCGTAAGATGGCAATTTTAAAATAAAAG
129 AAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCGCGTAAGATGGCAGTTTTAAAATAAAAG
* *
196 AGAAAATA-TTTTTTATATCAAGAACGTCGCGTGTCAGAATCCAAAGAAGCAAATATTATTTTAG
194 AGAAAATATTTTTTTATATCAAGAACGCCGCGTGTCAGAAT-CAAAGAAACAAATATTATTTTAG
260 CTTAAATTTTAAGAATAGTCCT
258 CTTAAATTTTAAGAATAGTCCT
* * *
282 TGTACTTGTTAATTTCTGCGGACTTT-GTCCCTCATTTTTTATTTACTCGTAGCATTGAAATTGG
1 TGTACTTGTTGATTTGTGCGGA-TTTGGTCCCT-A-TTTTTATTTACTCGTAGCATTCAAATTGG
* * * * * * *
346 CCTCTTATGTTT--GACAAAAAA-ACAAAATAGATGAAATCAAAGAAGAATCTCCCTGCCAAATA
63 CGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTACCAAATA
* * * * *
408 CAATCAGCTCCATCACATGCATTTAACTGGAAACTGCCGCGTAAGATGGCAGTTTTAAAGTAAAA
128 CAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCGCGTAAGATGGCAGTTTTAAAATAAAA
* * * * * *
473 GAGAAAATATTTTCTTATATCAAGAACGCCGCGTGTCAAAATCAAGAGAAACAAGTAGTACTTCA
193 GAGAAAATATTTTTTTATATCAAGAACGCCGCGTGTCAGAATCAA-AGAAACAAATATTATTTTA
*
538 GTTTAAATTTTAAGAATAGTCCT
257 GCTTAAATTTTAAGAATAGTCCT
561 TGTACTTGTTGATTTGTGCGGATTTGGTCCTACTATTTTTATTTACTCGTAGCATTCAAATTGGC
1 TGTACTTGTTGATTTGTGCGGATTTGGTCC--CTATTTTTATTTACTCGTAGCATTCAAATTGGC
* * **
626 GTCTTATCTTTGAGAAAAAAAATAGAAAATGGATGAAATCAACGAAGAATCTCCCTGCCAAATTT
64 GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTACCAAATAC
* * * *
691 AAGCCGCTCAATCACATGCATTTAACTTGAATCCGCCACGTAAGATGTCAGTTTTAAAATAAAAG
129 AAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCGCGTAAGATGGCAGTTTTAAAATAAAAG
* * * **
756 AGAAAATATTTTTTTATATCAAGAATGCTGCGTGTCAAAATCCAAATTAACAAATATTATTTTAG
194 AGAAAATATTTTTTTATATCAAGAACGCCGCGTGTCAGAAT-CAAAGAAACAAATATTATTTTAG
*
821 CTTAAATTTTAAGATTAGTCCT
258 CTTAAATTTTAAGAATAGTCCT
* * * * * *
843 TGTACGTGTTGATTTGTGCAGATTTGGTCCCACTAATTTTATTTACTCATAGCATTCAAATCGGG
1 TGTACTTGTTGATTTGTGCGGATTTGGT-CC-CTATTTTTATTTACTCGTAGCATTCAAATTGGC
* *
908 GTCTTATCTTTGAGAAAAAAAAGAAGAAAATTGATGAAATCAACGAAGAATCTTCCTACCAAATA
64 GTCTTATCTTTGAGAAAAAAAA-TAGAAAATTGATGAAATCAACGAAGAATCTCCCTACCAAATA
* * ** * * * **
973 CAAGCAGCTCAGTCACATG-ATATTATA-TTAAAATGGCTC-CGTTAGATGACCGTTTTAGGATA
128 CAAGCAGCTCAATCACATGCAT-TTA-ACTTGAAACCGC-CGCGTAAGATGGCAGTTTTAAAATA
* ** * * *** * * **
1035 AAAAAGAATTTATTATTTTTATATTAAAAATATCGCATGTCAGAGTCGAGTGAAACAAATATTAT
190 AAAGAGAAAATATT-TTTTTATATCAAGAACGCCGCGTGTCAGAATC-AAAGAAACAAATATTAT
* * ** *
1100 TCTAGGTTTGATTCTAAGAATAGTCCT
253 TTTAGCTTAAATTTTAAGAATAGTCCT
* * * * * * * * *
1127 TTTACTTATCGATTTGGGCGGATTTGCTCCCTTTATTTGTATTTACTTGTAGAATTCAAATTGAC
1 TGTACTTGTTGATTTGTGCGGATTTGGTCCC--TATTTTTATTTACTCGTAGCATTCAAATTGGC
** * * * *
1192 GTCTTAAGTTTGAG-AAAACAA-ACAATATTGATGAAATCGACGAAGAATC-CGCCTACCAAATA
64 GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTC-CCTACCAAATA
** * * * * ** *
1254 CAAGCAGCTCTGTCACATGCAATTATCTTAAAACCGCCGCATAAGACAGCAGTCTTAAAATAAAA
128 CAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCGCGTAAGATGGCAGTTTTAAAATAAAA
* ** * ** * * * * *
1319 AAGAATTTATTATTTATTATATCAAAAATTCCGTGTGTTAGAGTGAAGTGAAACAAATATTATTT
193 GAGAAAATATT-TTT-TTATATCAAGAACGCCGCGTGTCAGAATCAA-AGAAACAAATATTATTT
*
1384 TAGCTTAAATTCTAAGAATAGTCCT
255 TAGCTTAAATTTTAAGAATAGTCCT
* * * ** * * * *
1409 AGTATTTCTTGATTTGCACAGATTTGGTCCCTCATTTTTTATTTACTCGTAGCATTGAAAATAGC
1 TGTACTTGTTGATTTGTGCGGATTTGGTCCCT-A-TTTTTATTTACTCGTAGCATTCAAATTGGC
* ** * *
1474 TTCTTAAGTTTGAGAAAAAAACT---AAATAGATGAAATCCAA-GAAGAATCTCCCTACCAAATA
64 GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAAT-CAACGAAGAATCTCCCTACCAAATA
** *
1535 CAA-CAGCTCCGTCACATGCATTTAACTTGAAACCGTCGCGTAAGATGGCAGTTTTAAAATAAAA
128 CAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCGCGTAAGATGGCAGTTTTAAAATAAAA
* * * * *
1599 CAGAAAATATTTTTTTTATATCAAGAACGTCGTGTGTCAGAATCTAAAGAAACAAATATAACTTT
193 GAGAAAATA-TTTTTTTATATCAAGAACGCCGCGTGTCAGAATC-AAAGAAACAAATATTATTTT
*
1664 AGTTTAAATTTTAAGAATAGTCCT
256 AGCTTAAATTTTAAGAATAGTCCT
1688 TGTACTTGTTGATTTGTGCGGATTT
1 TGTACTTGTTGATTTGTGCGGATTT
Statistics
Matches: 1194, Mismatches: 202, Indels: 72
0.81 0.14 0.05
Matches are distributed among these distances:
278 109 0.09
279 215 0.18
280 69 0.06
281 204 0.17
282 371 0.31
283 110 0.09
284 116 0.10
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (279 bp):
TGTACTTGTTGATTTGTGCGGATTTGGTCCCTATTTTTATTTACTCGTAGCATTCAAATTGGCGT
CTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTACCAAATACAA
GCAGCTCAATCACATGCATTTAACTTGAAACCGCCGCGTAAGATGGCAGTTTTAAAATAAAAGAG
AAAATATTTTTTTATATCAAGAACGCCGCGTGTCAGAATCAAAGAAACAAATATTATTTTAGCTT
AAATTTTAAGAATAGTCCT
Found at i:1376 original size:566 final size:556
Alignment explanation
Indices: 1--1712 Score: 1771
Period size: 561 Copynumber: 3.0 Consensus size: 556
* * *
1 TGTACTTGTTGATTTGTGCGGATTT-CGTCCCACTATTTTTATTTACTCGTAGCATTCAAATTGG
1 TGTACTTATCGATTTGTGCGGATTTGC-TCCCTCTATTTTTATTTACTCGTAGCATTCAAATTGG
*
65 CGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATTAAATCAACGAAGAATCTCCCTGCCAAATT
65 CGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTGCCAAATT
* *
130 CAAGCAGCTCAATCACATGCATTTGACTTGAAACCGCCGCGTAAGATGGCAATTTTAAAATAAAA
130 CAAGCAGCTCAATCACATGCATTT-ACTTGAAACCGCCGCGTAAGA-AGCAGTTTTAAAATAAAA
* ** * *
195 GAGAA-AATATTTTTTATATCAAGAACGT-CGCGTGTCAGAATCCAAAGAAGCAAATATTATTTT
193 GAGAATATTA-TTTTTATATCAA-AAATTCCGCGTGTCAGAATCCAATGAAACAAATATTATTTT
* * *
258 AGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTAATTTCTGCGGACTTT-GTCCCTCATTTTTT
256 AGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCAGA-TTTGGTCCCTCATTTTTT
* *
322 ATTTACTCGTAGCATTGAAATTGGCCTCTTATGTTTGA-CAAAAAAACAAAATAGATGAAATCAA
320 ATTTACTCGTAGCATT-AAAATGGCCTCTTATGTTTGAGAAAAAAAACAAAATAGATGAAATC-A
* *
386 AGAAGAATCTCCCTGCCAAATACAATCAGCTCCA-TCACATGCATTTAACTGGAAACTGCCGCGT
383 AGAAGAATCTCCCTACCAAATACAA-CAGCT-CAGTCACATGCATTTAACTGGAAAATGCCGCGT
* * * * *
450 AAGATGGCAGTTTTAAAGTAAAAGAGAAAATATTTTCTTATATCAAGAACGCCGCGTGTCAAAAT
446 AAGATGACAGTTTTAAAGTAAAAAAGAAAATATTTTCTTATATCAAAAACACCGCATGTCAAAAT
* *
515 CAAGAGAAACAAGTAGTACTTCAGTTTAAATTTTAAGAATAGTCCT
511 CAAGAGAAACAAATAGTACTTCAGTTTAAATTCTAAGAATAGTCCT
* * *
561 TGTACTTGTTGATTTGTGCGGATTTGGT-CCTACTATTTTTATTTACTCGTAGCATTCAAATTGG
1 TGTACTTATCGATTTGTGCGGATTTGCTCCCT-CTATTTTTATTTACTCGTAGCATTCAAATTGG
*
625 CGTCTTATCTTTGAGAAAAAAAATAGAAAATGGATGAAATCAACGAAGAATCTCCCTGCCAAATT
65 CGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTGCCAAATT
* * * * *
690 TAAGCCGCTCAATCACATGCATTTAACTTGAATCCGCCACGTAAGATGTCAGTTTTAAAATAAAA
130 CAAGCAGCTCAATCACATGCATTT-ACTTGAAACCGCCGCGTAAGAAG-CAGTTTTAAAATAAAA
* * * * *
755 GAGAAAATATT-TTTTTATATCAAGAATGCTGCGTGTCAAAATCCAAAT-TAACAAATATTATTT
193 GAG--AATATTATTTTTATATCAAAAATTCCGCGTGTCAGAATCC-AATGAAACAAATATTATTT
* * * *
818 TAGCTTAAATTTTAAGATTAGTCCTTGTACGTGTTGATTTGTGCAGATTTGGTCCCAC-TAATTT
255 TAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCAGATTTGGTCCCTCAT-TTTT
* * ** * * *
882 TATTTACTCATAGCATTCAAATCGGGGTCTTATCTTTGAGAAAAAAAAGAAGAAAATTGATGAAA
319 TATTTACTCGTAGCATTAAAAT-GGCCTCTTATGTTTGAG--AAAAAA-AACAAAATAGATGAAA
* *
947 TCAACGAAGAATCTTCCTACCAAATACAAGCAGCTCAGTCACATG-ATATTATA-T-TAAAATGG
380 TCAA-GAAGAATCTCCCTACCAAATACAA-CAGCTCAGTCACATGCAT-TTA-ACTGGAAAAT-G
* * * ** * * * *
1009 CTC-CGTTAGATGACCGTTTT-AGGATAAAAAAGAATTTATTATTTTTATATTAAAAATATCGCA
440 C-CGCGTAAGATGACAGTTTTAAAG-TAAAAAAGAAAATATT-TTCTTATATCAAAAACACCGCA
* * * * * *
1072 TGTCAGAGTCGAGTGAAACAAATATTA-TTCTAGGTTT-GATTCTAAGAATAGTCCT
502 TGTCAAAATCAAGAGAAACAAATAGTACTTC-A-GTTTAAATTCTAAGAATAGTCCT
* * * * * * *
1127 TTTACTTATCGATTTGGGCGGATTTGCTCCCTTTATTTGTATTTACTTGTAGAATTCAAATTGAC
1 TGTACTTATCGATTTGTGCGGATTTGCTCCCTCTATTTTTATTTACTCGTAGCATTCAAATTGGC
** * * * * * *
1192 GTCTTAAGTTTGAG-AAAACAA-ACAATATTGATGAAATCGACGAAGAATC-CGCCTACCAAATA
66 GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTC-CCTGCCAAATT
** * * * *
1254 CAAGCAGCTCTGTCACATGCAATTATCTTAAAACCGCCGCATAAGACAGCAGTCTTAAAATAAAA
130 CAAGCAGCTCAATCACATGCATTTA-CTTGAAACCGCCGCGTAAGA-AGCAGTTTTAAAATAAAA
* * * * *
1319 AAGAATTTATTATTTATTATATCAAAAATTCCGTGTGTTAGAGT-GAAGTGAAACAAATATTATT
193 GAGAA--TATTATTT-TTATATCAAAAATTCCGCGTGTCAGAATCCAA-TGAAACAAATATTATT
* * * * **
1383 TTAGCTTAAATTCTAAGAATAGTCCTAGTATTTCTTGATTTGCACAGATTTGGTCCCTCATTTTT
254 TTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCAGATTTGGTCCCTCATTTTT
* * * *
1448 TATTTACTCGTAGCATTGAAAATAGCTTCTTAAGTTTGAG-AAAAAAACTAAATAGATGAAATCC
319 TATTTACTCGTAGCATT-AAAATGGCCTCTTATGTTTGAGAAAAAAAACAAAATAGATGAAAT-C
* * ** *
1512 AAGAAGAATCTCCCTACCAAATACAACAGCTCCGTCACATGCATTTAACTTGAAACCGTCGCGTA
382 AAGAAGAATCTCCCTACCAAATACAACAGCTCAGTCACATGCATTTAACTGGAAAATGCCGCGTA
* * * * * ** ** *
1577 AGATGGCAGTTTTAAAATAAAACAGAAAATATTTTTTTTATATCAAGAACGTCGTGTGTCAGAAT
447 AGATGACAGTTTTAAAGTAAAAAAGAAAATA-TTTTCTTATATCAAAAACACCGCATGTCAAAAT
* *
1642 CTAA-AGAAACAAATA-TAACTTTAGTTTAAATTTTAAGAATAGTCCT
511 C-AAGAGAAACAAATAGT-ACTTCAGTTTAAATTCTAAGAATAGTCCT
* *
1688 TGTACTTGTTGATTTGTGCGGATTT
1 TGTACTTATCGATTTGTGCGGATTT
Statistics
Matches: 950, Mismatches: 154, Indels: 95
0.79 0.13 0.08
Matches are distributed among these distances:
559 3 0.00
560 195 0.21
561 236 0.25
562 54 0.06
563 12 0.01
564 108 0.11
565 97 0.10
566 233 0.25
567 12 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (556 bp):
TGTACTTATCGATTTGTGCGGATTTGCTCCCTCTATTTTTATTTACTCGTAGCATTCAAATTGGC
GTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAAATCAACGAAGAATCTCCCTGCCAAATTC
AAGCAGCTCAATCACATGCATTTACTTGAAACCGCCGCGTAAGAAGCAGTTTTAAAATAAAAGAG
AATATTATTTTTATATCAAAAATTCCGCGTGTCAGAATCCAATGAAACAAATATTATTTTAGCTT
AAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCAGATTTGGTCCCTCATTTTTTATTTAC
TCGTAGCATTAAAATGGCCTCTTATGTTTGAGAAAAAAAACAAAATAGATGAAATCAAGAAGAAT
CTCCCTACCAAATACAACAGCTCAGTCACATGCATTTAACTGGAAAATGCCGCGTAAGATGACAG
TTTTAAAGTAAAAAAGAAAATATTTTCTTATATCAAAAACACCGCATGTCAAAATCAAGAGAAAC
AAATAGTACTTCAGTTTAAATTCTAAGAATAGTCCT
Done.