Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001714.1 Kokia drynarioides strain JFW-HI SEQ_113410, 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: 1670
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:517 original size:216 final size:215
Alignment explanation
Indices: 23--1670 Score: 1529
Period size: 216 Copynumber: 7.7 Consensus size: 215
13 AAAGCTTGGA
* * * * *
23 AAGAACCAAGAGAGAAACAATTCTCACGTAAAT-A-TTTTTAATAT-AAAGACCAAAGGTTGATT
1 AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAAT-TCAAAAACCAAAAGTTGTTT
* * * *
85 GCAAAATGACAAACTATTTAGACCAAATGATGCGATTT-TTCAAGCATGGAATGTTCGACAAATT
65 ACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCT-GAGCATGGAATGTTCGA-AAATT
* * * * * * * * *
149 GCTTGAAGGACTAGATTGTCCTGAATA-TTCTCAA-GAACCAAAGTTATAAAAGAACTCGTAATT
128 GGTCGAAGGAATGGATCGTCTTGAATACTT-T-AAGGAATCAAAGTTATAAAAGAACTCATAAAT
*
212 GTTTGACAAGTT-TGAAAGTTC--CC
191 GTTTGACAAGTTCAG-AAGTTCGTCC
* * *
235 AAGAACCAA-AAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACCACAAGTTATTT
1 AAGAACCAAGAA-AGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTT
* * * * * *
299 ACAAAATAACAAACTTTTTGGACCAAGTGATACTATTTCCTGAGCATGGAATATTCTGAAAATTG
65 ACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTC-GAAAATTG
* * * * * * * *
364 GACGAAGAAATGGATCATCTTGAACACTTTAAGGAACCGAAGATATAAAAGAACTCAAAAATGTT
129 GTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATGTT
*
429 TGACAAGTTCAGAAGTTCATCC
194 TGACAAGTTCAGAAGTTCGTCC
* * * **
451 AAGATCCAACAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAGAGTCATTTA
1 AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA
** **
516 CAAAATGACAAACTTTTTAGACCAAATGATGC-AAATCCTGAGCATATAATGTTCGGAAAATTGG
66 CAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTC-GAAAATTGG
* * * * * *
580 TCGAGGGAATGGATCGCCTTGAACT-CTCTCAGGAACCAAAGTTATAAAAGAACTCGTAAAATGT
130 TCGAAGGAATGGATCGTCTTGAA-TACTTTAAGGAATCAAAGTTATAAAAGAACTCAT-AAATGT
* ** ** *
644 TTGACAATTTTGGGTGTTCGTTC
193 TTGACAAGTTCAGAAGTTCGTCC
* * * *
667 AAGAATCAAGAGAGAAACAATTATCACGTAAATAA----TTAATTCAAAGAA-CAAAAGTTGTTT
1 AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAA-AACCAAAAGTTGTTT
* * * * * ** *
727 ACAAAATGAGAAACTATATAGATCAAATGATGCGACTTCCCAAGCATGGAATGCTCGAAAAATTG
65 ACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCG-AAAATTG
* * * * ** *
792 CTCAAAGAAATGGATCGTCATT-AATACTTTAAGGTATTTAAGTTATAAAAGAACTCATAAATTT
129 GTCGAAGGAATGGATCGTC-TTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATGT
* *
856 TTGACAAGATC-GAAAGTTTGTCC
193 TTGACAAGTTCAG-AAGTTCGTCC
* * * *
879 AAGATA-CAAGAGAGAAATAATTCTCACGTAAATAAGTTTTAAATTCAAAAACCAAAAGTTGTTT
1 AAGA-ACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTT
* * * * * * *
943 ACAAGATGAAAAACTACTTT-GACCAAATGATGCGATTT-CTCAAGAATGGAATGCTCAAAAAAT
65 ACAAAATGACAAACT-TTTTAGACCAAATGATGCGATTTCCT-GAGCATGGAATGTTC-GAAAAT
* * * * * *
1006 TGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGAAATCGAAGTTAGAAAAGAACTCATAAATG
127 TGGTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATG
* *
1071 TTTGACAAGTTCAGAAATTTGTCC
192 TTTGACAAGTTCAGAAGTTCGTCC
* * * * *
1095 AAGAACCAATAGAGAAACAATTCTCATGTAAATAAGTTTTAAATTCAAAGACGAAAAGTTGTTTA
1 AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA
* * * * *
1160 C-AGATGGA-AAACTATTTT-TACCAAATGATTCCATTTTACC-GAGAATGGAATGTTCGAAAAA
66 CAAAAT-GACAAACT-TTTTAGACCAAATGATGCGA-TTT-CCTGAGCATGGAATGTTCG-AAAA
* * * * * *
1221 TTGGTCAAAGGAATGGATCTTCTTAAATA-TTCTCAGGAATCAAAGTTATAAACA-AACTCCTAT
126 TTGGTCGAAGGAATGGATCGTCTTGAATACTT-TAAGGAATCAAAGTTATAAA-AGAACTCATAA
* *
1284 ATGTTTGAGAGGTTCAGAAGTTCGTCC
189 ATGTTTGACAAGTTCAGAAGTTCGTCC
* * * ** *
1311 AAGAACCAAAAAAGAAATAATTCTCATGTAAATAAGTTTTTAATTGAAGCACCACAAGTTGTTTA
1 AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA
* * *
1376 CAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGATCATGGAATGTTCAAAAAACTAG
66 CAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTC-GAAAA-TTG
* * * * *
1441 AT-GAAGGAATGGTTCGTCTTGAATGCTTTAAGGAATCGAAGTTATAAAAGAACTCAAAAATGTT
129 GTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATGTT
* * * *
1505 TGACATGTTCGGAAGTTTGTCA
194 TGACAAGTTCAGAAGTTCGTCC
* * * * *
1527 AAGAACCAATAATGAAACAATTCTCACGTAAA-AAGTTTTTAATTCAAAAACCAAAAGCTATTTA
1 AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA
* * * * *
1591 CAAAATGACAAACTATTTAGACCAAATAATGCAACTTCCCGAGCATGGAATGTTCGAAAAATTGG
66 CAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCG-AAAATTGG
1656 TCGAAGGAATGGATC
130 TCGAAGGAATGGATC
Statistics
Matches: 1180, Mismatches: 207, Indels: 95
0.80 0.14 0.06
Matches are distributed among these distances:
211 2 0.00
212 129 0.11
213 70 0.06
214 136 0.12
215 202 0.17
216 609 0.52
217 31 0.03
218 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (215 bp):
AAGAACCAAGAAAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA
CAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAAAATTGGT
CGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATGTTTG
ACAAGTTCAGAAGTTCGTCC
Found at i:1290 original size:644 final size:640
Alignment explanation
Indices: 23--1670 Score: 1755
Period size: 644 Copynumber: 2.6 Consensus size: 640
13 AAAGCTTGGA
* * * *
23 AAGAACCAAGAGAGAAACAATTCTCACGTAAATATTTTTAATATAAAGACCAAAGGTTGATTGCA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATA--ATTAAT-TAAAGACCAAAAGTTGTTTACA
** *
88 AAATGACAAACTATTTAGACCAAATGATGCGATTTTTCAAGCATGGAATGTTCGACAAATTGCTT
63 AAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGC-T
* * * * * *
153 GAAGGACTAGATTGTCCTGAATA-TTCTCAA-GAACCAAAGTTATAAAAGAACTCGT-AATTGTT
127 GAAGGAATGGATCGT-CTTAATACTT-T-AAGGAATCAAAGTTATAAAAGAACTCATAAATT-TT
* * *
215 TGACAAGTTTGAAAG-TT-CCCAAGAACCAAAAGAGAAACAATTCTCATGTAAATAAGTTTTTAA
188 TGACAAGTTCGAAAGTTTGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
* * * * * * *
278 TTCAAAGACCACAAGTTATTTACAAAAT-AACAAACTTTTTGGACCAAGTGATACTATTTCCTGA
253 TTCAAAAACCAAAAGTTATTTACAAAATGAA-AAACTATTTAGACCAAATGATGCAATTTCC-GA
* ** * * * *
342 GCATGGAATATTCTGAAAATTGGACGAAGAAATGGATCATCTTGAACACTTTAAGGAACCGAAGA
316 GCATGGAATGTTCAAAAAATTGGTCGAAGGAATGGATCATCTTGAACACTCTAAGAAACCGAAGA
* * *
407 TATAAAAGAACTCAAAAATGTTTGACAAGTTCAGAAGTTCATCCAAGATCCAACAAAGAAACAAT
381 TAGAAAAGAACTCAAAAATGTTTGACAAGTTCAGAAATTCATCCAAGAACCAACAAAGAAACAAT
* *
472 TCTCATGTAAATAAGTTTTTAATTCAAAAACCAAGAGTCATTTACAAAATGACAAACTTTTTAGA
446 TCTCATGTAAATAAGTTTTAAATTCAAAAACCAAAAGTCATTTACAAAATGACAAACTTTTTAGA
* * * * * *
537 CCAAATGATGCAAATCCTGAGCATATAATGTTCGGAAAATTGGTCGAGGGAATGGATCGCCTTGA
511 CCAAATGATCCAAATCCTGAGAATAGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGCCTTGA
* * * ** ** *
602 ACTCTCTCAGGAACCAAAGTTATAAAAGAACTCGTAAAATGTTTGACAATTTTGGGTGTTCGTTC
576 AATCTCTCAGGAACCAAAGTTATAAAAGAACTCCTAAAATGTTTGACAAGTTCAGAAGTTCGTCC
* * *
667 AAGAATCAAGAGAGAAACAATTATCACGTAAATAATTAATTCAAAGAACAAAAGTTGTTTACAAA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAATTAATT-AAAGACCAAAAGTTGTTTACAAA
* * * * * *
732 ATGAGAAACTATATAGATCAAATGATGCGACTTCCCAAGCATGGAATGCTCGAAAAATTGCTCAA
65 ATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCT-GA
* * **
797 AGAAATGGATCGTCATTAATACTTTAAGGTATTTAAGTTATAAAAGAACTCATAAATTTTTGACA
129 AGGAATGGATCGTC-TTAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATTTTTGACA
* * * *
862 AGATCGAAAGTTTGTCCAAGATA-CAAGAGAGAAATAATTCTCACGTAAATAAGTTTTAAATTCA
193 AGTTCGAAAGTTTGTCCAAGA-ACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
* * * * *
926 AAAACCAAAAGTTGTTTACAAGATGAAAAACTACTTT-GACCAAATGATGCGATTTCTCAAGAAT
257 AAAACCAAAAGTTATTTACAAAATGAAAAACTA-TTTAGACCAAATGATGCAATTTC-CGAGCAT
* * * * * * *
990 GGAATGCTCAAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTCTCAGAAATCGAAGTTAGA
320 GGAATGTTCAAAAAATTGGTCGAAGGAATGGATCATCTTGAACACTCTAAGAAACCGAAGATAGA
* ** * *
1055 AAAGAACTCATAAATGTTTGACAAGTTCAGAAATTTGTCCAAGAACCAATAGAGAAACAATTCTC
385 AAAGAACTCAAAAATGTTTGACAAGTTCAGAAATTCATCCAAGAACCAACAAAGAAACAATTCTC
* * ** * *
1120 ATGTAAATAAGTTTTAAATTCAAAGACGAAAAGTTGTTTAC-AGATGGA-AAACTATTTT-TACC
450 ATGTAAATAAGTTTTAAATTCAAAAACCAAAAGTCATTTACAAAAT-GACAAACT-TTTTAGACC
** * **
1182 AAATGATTCCATTTTACC-GAGAATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCTTCTT-
513 AAATGA-TCCA-AAT-CCTGAGAATAGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGCCTTG
* * * * *
1245 AAATATTCTCAGGAATCAAAGTTATAAACA-AACTCCT-ATATGTTTGAGAGGTTCAGAAGTTCG
575 AAAT-CTCTCAGGAACCAAAGTTATAAA-AGAACTCCTAAAATGTTTGACAAGTTCAGAAGTTCG
1308 TCC
638 TCC
* * * * * *
1311 AAGAACCAAAAAAGAAATAATTCTCATGTAAATAAGTTTTTAATTGAAGCACCACAAGTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAA----TTAATTAAAG-ACCAAAAGTTGTTTA
* ** * * *
1376 CAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCTGATCATGGAATGTTCAAAAAACTAG
61 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAA-TTG
* * * * * *
1441 ATGAAGGAATGGTTCGTCTTGAATGCTTTAAGGAATCGAAGTTATAAAAGAACTCAAAAATGTTT
125 CTGAAGGAATGGATCGTCTT-AATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATTTTT
* * * *
1506 GACATGTTCGGAAGTTTGTCAAAGAACCAATAA-TGAAACAATTCTCACGTAAA-AAGTTTTTAA
189 GACAAGTTCGAAAGTTTGTCCAAGAACCAA-AAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
* * * *
1569 TTCAAAAACCAAAAGCTATTTACAAAATGACAAACTATTTAGACCAAATAATGCAACTTCCCGAG
253 TTCAAAAACCAAAAGTTATTTACAAAATGAAAAACTATTTAGACCAAATGATGCAA-TTTCCGAG
*
1634 CATGGAATGTTCGAAAAATTGGTCGAAGGAATGGATC
317 CATGGAATGTTCAAAAAATTGGTCGAAGGAATGGATC
Statistics
Matches: 827, Mismatches: 147, Indels: 57
0.80 0.14 0.06
Matches are distributed among these distances:
641 5 0.01
642 128 0.15
643 25 0.03
644 324 0.39
645 72 0.09
646 6 0.01
647 97 0.12
648 166 0.20
649 4 0.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (640 bp):
AAGAACCAAGAGAGAAACAATTCTCACGTAAATAATTAATTAAAGACCAAAAGTTGTTTACAAAA
TGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCTGAAG
GAATGGATCGTCTTAATACTTTAAGGAATCAAAGTTATAAAAGAACTCATAAATTTTTGACAAGT
TCGAAAGTTTGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAA
CCAAAAGTTATTTACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCCGAGCATGGAATG
TTCAAAAAATTGGTCGAAGGAATGGATCATCTTGAACACTCTAAGAAACCGAAGATAGAAAAGAA
CTCAAAAATGTTTGACAAGTTCAGAAATTCATCCAAGAACCAACAAAGAAACAATTCTCATGTAA
ATAAGTTTTAAATTCAAAAACCAAAAGTCATTTACAAAATGACAAACTTTTTAGACCAAATGATC
CAAATCCTGAGAATAGAATGTTCGAAAAATTGGTCAAAGGAATGGATCGCCTTGAAATCTCTCAG
GAACCAAAGTTATAAAAGAACTCCTAAAATGTTTGACAAGTTCAGAAGTTCGTCC
Done.