Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002964.1 Kokia drynarioides strain JFW-HI SEQ_115438, 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: 2004
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:389 original size:216 final size:213
Alignment explanation
Indices: 5--1999 Score: 1872
Period size: 216 Copynumber: 9.3 Consensus size: 213
1 TCAG
*
5 GCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
1 GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
** * * * *
70 TAAAAAACTTTTGGTGTTTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTTTTTGTTTTT
66 TAAAAAGGTTTTGGTCTTTGAATTAAA-ACTTATTTACGTGAGAATT-TTTCTCTCTTGGTTCTT
* * ** * *
135 GGACGAACTTCCGAACTTA-TCAAACTTTTAGGAGTTCTTTTATAATTTTAGTTTCGTAAAGTAT
129 GGACGAACTTTCGAAC-TAGTCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAGTAT
199 TCAAGACGATCCATTCCTTCGA
192 TCAAGACGATCCATTCCTTCGA
221 GCAATTATTC-GAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
1 GCAATT-TTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
* * *
285 GTAAAAAGGTTTTGTTGC-TTGAATTAATAACTTATTTACGTGAGAAATATTTCTCTCTTGGTCC
65 GTAAAAAGGTTTTGGT-CTTTGAATTAA-AACTTATTTACGTGAG-AATTTTTCTCTCTTGGTTC
* *
349 TTGGACCAACTTTCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCC-T----TA
127 TTGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAGTA
* * *
409 CTCAAGACGATACATTCCTTCTA
191 TTCAAGACGATCCATTCCTTCGA
* * * * * *
432 GCAACTTTCTTAACATTCTATGCT-AGATAAATCGCATCATTT-TTCTAAATTGTTTGTCATTTT
1 GCAATTTTCTGAACATTCCATGCTCGGA-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
* * *
495 GTAAACAA-GTTTTGTTCTTTAAATTTAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGT
65 GTAAA-AAGGTTTTGGTCTTTGAA-TTAAAACTTATTTACGTGAGAA-T-TTT-TCTCTCTTGGT
* * * * * *
559 TCTTTGATGAACTTCCAAACTTGCCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAG
125 TCTTGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAG
* *
624 TATTCAAGACGTTCCATTCCTTTGA
189 TATTCAAGACGATCCATTCCTTCGA
* * * * * *
649 GGAATTTT-TGAACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATAGGTCT-TAATTTT
1 GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTT
* * * * ** * * * * * *
712 GT-AAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGA-TTTT-T-TCTTGGCTGT
65 GTAAAAAG-GTTTTGGTCTTTGAATTAA-AACTTATTTACGTGAGAATTTTTCTCTCTTGGTTCT
* * * * **
773 TGGACGAAC-TTCAAAAC-ATTTCAAACTTTTACGAGTTCTTTTATAACTCAGTTCCTTGCAGTA
128 TGGACGAACTTTC-GAACTA-GTCAAACTTTTACGAGTTCTTTTATAATTCGGTTCCTTAAAGTA
* *
836 TTCAAGACGATCCATTCCATCAA
191 TTCAAGACGATCCATTCCTTCGA
* * *
859 GCAATTTTCTGAACATTCCATGCTCGGGAAATCGGACCATTTGGTCTAAATAGTTTGTCATTTTG
1 GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
** *
924 TAAAAAACTTTTGGTCTTTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTT
66 TAAAAAGGTTTTGGTCTTTGAATTAAA-ACTTATTTACGTGAGAATT-TTTCTCTCTTGGTTCTT
* *
989 GGACGAAC-TTCTGAACTTA-TCAAACTTTTACGAGTTCTTTTATAATTTCAGTTCCATAAAGTA
129 GGACGAACTTTC-GAAC-TAGTCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAGTA
*
1052 TTCTAGACGATCCATTCCTTCGA
191 TTCAAGACGATCCATTCCTTCGA
* * * *
1075 GCAATTTTTCT-AACATTCCATGCTTGGGAAATCGTATCATTTGGTCTAAATAATTTTGTCATTT
1 GCAA-TTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAAT-AGTTTGTCATTT
* * * * *
1139 TGTTAAAAGGTTTTGTTGTTTGAATTATAAACTTATTTACCTGAGAATTGCTTCTCTCTTGGTTC
64 TGTAAAAAGGTTTTGGTCTTTGAATTA-AAACTTATTTACGTGAGAATT-TTTCTCTCTTGGTTC
* * * * * *
1204 TTGGACGAACTTTCGAACTAGTCAAACTTTTACAAGTTCTCTCATATCTTTGGCTCCTTAAAGTA
127 TTGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATA-ATTCGGTTCCTTAAAGTA
1269 TTCAAGACGATCCATTCCTTCGA
191 TTCAAGACGATCCATTCCTTCGA
* * * * * * * *
1292 GCAATTTTCTAAACATTCAATTCT-TGAGAAATGGCAGCATTTGGTCTCAAGAGTTTGTCATTTT
1 GCAATTTTCTGAACATTCCATGCTCGGA-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
* * * * * *
1356 -AAAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTT-TCGCTTGGTTCA
65 GTAAAA-AGGTTTTGGTCTTTGAAT-TAAAACTTATTTACGTGAGAATTTTTCTCTCTTGGTTCT
* * * * * *
1419 TGGACAAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTACAGTTT
128 TGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAGTAT
* *
1484 TCAAGACGATACA-TCCTTCTA
192 TCAAGACGATCCATTCCTTCGA
* * * * * *
1505 GCAACTTTCTTAACATTCTATGCTCGAAAAATCGCATCATTT-TTCTAAAT--TGTGTCATTTTG
1 GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
* *
1567 TAAACAA-GTTTTGGTCTTTAAATTTAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTT
66 TAAA-AAGGTTTTGGTCTTTGAA-TTAAAACTTATTTACGTGAGAA-T-TTT-TCTCTCTTGGTT
* * * * ** * * *
1631 CTTGTATGAACTTCCAAACTTTTCAAACTTTTACGAGTTCATTTAAAACTCCGGTTCCTTAAAGT
126 CTTGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAA-TTCGGTTCCTTAAAGT
*
1696 ATTCAAGACGATCCATTCCTTTGA
190 ATTCAAGACGATCCATTCCTTCGA
* * * * * * *
1720 GGAATTTT-TGAACATTCCATTCTCGGAAAATCACATCATTTAGTCAAAATAGGTCT-TAATTTT
1 GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTT
* * * * * ** * * * * * * *
1783 GT-GAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGGGGA-TTTT-T-TCTTGGCTGT
65 GTAAAAAG-GTTTTGGTCTTTGAATTAA-AACTTATTTACGTGAGAATTTTTCTCTCTTGGTTCT
* * * * **
1844 TGGACGAAC-TTCAGAAC-ATTTCAAACTTTTACGAGTTCTTTTATAACTCCGTCCCTTGCAGTA
128 TGGACGAACTTTC-GAACTA-GTCAAACTTTTACGAGTTCTTTTATAATTCGGTTCCTTAAAGTA
* *
1907 TTCAAGACGATCCATTCCATCAA
191 TTCAAGACGATCCATTCCTTCGA
* *
1930 GCAATTTT-TGAACTTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
1 GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
1994 TAAAAA
66 TAAAAA
2000 ACTTT
Statistics
Matches: 1459, Mismatches: 252, Indels: 141
0.79 0.14 0.08
Matches are distributed among these distances:
209 6 0.00
210 232 0.16
211 227 0.16
212 74 0.05
213 46 0.03
214 185 0.13
215 76 0.05
216 316 0.22
217 287 0.20
218 10 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (213 bp):
GCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
TAAAAAGGTTTTGGTCTTTGAATTAAAACTTATTTACGTGAGAATTTTTCTCTCTTGGTTCTTGG
ACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTTATAATTCGGTTCCTTAAAGTATTCAA
GACGATCCATTCCTTCGA
Found at i:1567 original size:643 final size:644
Alignment explanation
Indices: 5--1992 Score: 2074
Period size: 643 Copynumber: 3.1 Consensus size: 644
1 TCAG
*
5 GCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
1 GCAATTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT-
* * * * * * *
70 TAAAA-AACTTTTGGTGTTTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTTTTTGTTTT
65 AAAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTC--TTGGTTCT
* * * * * *
134 TGGACGAACTTCCGAACTTATCAAACTTTTAGGAGTTCTTTTATAATTTTAGTTTCGTAAAGTAT
128 TGGACGAACTTCCGAACTT-TCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTAT
*
199 TCAAGACGATCCATTCCTTCGAGCAATTATTC-GAACATTCCATGCTCGGAAAATCGCATCATTT
192 TCAAGACGATCCATTCCTTCAAGCAATT-TTCTGAACATTCCATGCTCGGAAAATCGCATCATTT
* *
263 GGTCTAAATAGTTTGTCATTTTGTAAAAAGGTTTTGTTGC-TTGAATT-AATAACTTATTTACGT
256 GGTCTAAATA-TTTGTCATTTTGTAAAAAAGTTTTGGT-CTTTGAATTAAAT-ACTTATTTACGT
* * * * * *
326 GAGAAATATTTCTCTCTTGGTCCTTGGACCAACTT-TCGAAC-TAGTCAAACTTTTACAAGTTCT
318 GAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCT-GAACTTA-TCAAACTTTTACGAGTTCT
* * * *
389 TTTATAACTTCGGTTCCT----TACTCAAGACGATACATTCCTTCTAGCAA-CTTTCTTAACATT
381 TTTATAACTTCGGTTCCTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTC-TAACATT
* * *
449 CTATGCTAGATAAATCGCATCATTTTTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGTTCTT
445 CCATGCTAGAGAAATCGCATCATTTGTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGTTCTT
* * * * *
514 TAAATTTAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTTGATGAACTTCCAAAC
510 TAAATTTAAAACTTATTTACCTGAGAATTGTCTCTCTCTCTTGGTTCTTGGACGAACTTCCAAAC
* * * * * *
579 TTGCCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGTTCCATTCC
575 TAGCCAAACTTTTACAAGTTCTCTCATAACTTCGGCTCCTTAAAGTATTCAAGACGATCCATTCC
*
644 TTTGA
640 TTCGA
* * * *
649 GGAATTTT-TGAACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAATAGGTCT-TAATTTT
1 GCAATTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTT
** * * * * * * * * * * * *
712 GTAAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGATT-TTT-TCTTGGCTGTTG
65 AAAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTCTTG
** *
775 GACGAACTTCAAAACATTTCAAACTTTTACGAGTTCTTTTATAAC-TCAGTTCCTTGCAGTATTC
130 GACGAACTTCCGAAC-TTTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTC
* * * *
839 AAGACGATCCATTCCATCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGGACCATTTGGT
194 AAGACGATCCATTCCTTCAAGCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGT
*
904 CTAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAATACTTATTTACGTGAGAA
259 CTAAATA-TTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAATACTTATTTACGTGAGAA
969 TTGTTTCTCTTTTGGTTCTTGGACGAACTTCTGAACTTATCAAACTTTTACGAGTTCTTTTATAA
323 TTGTTTCTCTTTTGGTTCTTGGACGAACTTCTGAACTTATCAAACTTTTACGAGTTCTTTTATAA
* * *
1034 TTTCAGTTCCATAAAGTATTCTAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCT
388 CTTCGGTTCC-TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCT
* * * * * *
1099 TGGGAAATCGTATCATTTGGTCTAAATAAT-TTTGTCATTTTGTTAAA-AGGTTTTGTTGTTTGA
452 AGAGAAATCGCATCATTT-GTCTAAAT--TGTTTGTCATTTTG-TAAACAAGTTTTGTTCTTTAA
* *
1162 A-TTATAAACTTATTTACCTGAGAATTG-CT-TCTCTCTTGGTTCTTGGACGAACTTTCGAACTA
513 ATTTA-AAACTTATTTACCTGAGAATTGTCTCTCTCTCTTGGTTCTTGGACGAACTTCCAAACTA
* * *
1224 GTCAAACTTTTACAAGTTCTCTCATATCTTTGGCTCCTTAAAGTATTCAAGACGATCCATTCCTT
577 GCCAAACTTTTACAAGTTCTCTCATAACTTCGGCTCCTTAAAGTATTCAAGACGATCCATTCCTT
1289 CGA
642 CGA
* * * * * * * *
1292 GCAATTTTCTAAACATTCAATTCTTGAGAAATGGCAGCATTTGGTCTCAAGAGTTTGTCATTTTA
1 GCAATTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTA
* *
1357 AAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCGCTTGGTTCATGG
66 AAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTCTTGG
* * * *
1422 ACAAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTACAGTTTTCA
131 ACGAACTTCCGAACTT-TCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTCA
* * * * * * *
1487 AGACGATACA-TCCTTCTAGCAACTTTCTTAACATTCTATGCTCGAAAAATCGCATCATTT-TTC
195 AGACGATCCATTCCTTCAAGCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTC
* * *
1550 TAAAT-TGTGTCATTTTGTAAACAAGTTTTGGTCTTTAAATTTAAA-ACTTATTTACGTGAGAAT
260 TAAATATTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAA-TTAAATACTTATTTACGTGAGAAT
* * * ** * * *
1613 TGTTTCTCTCTCTTTGTTCTTGTATGAACTTCCAAACTTTTCAAACTTTTACGAGTTCATTTAAA
324 TGTTTCTCT-T-TTGGTTCTTGGACGAACTTCTGAACTTATCAAACTTTTACGAGTTCTTTTATA
* * * * *
1678 ACTCCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTTT-GAACATTCCATTC
387 ACTTCGGTTCC-TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGC
* * * * * * * * * *
1742 TCG-GAAAATCACATCATTTAGTCAAAATAGGTCT-TAATTTTGTGAACGAGTTTTGATCATTAA
451 TAGAG-AAATCGCATCATTT-GTCTAAAT-TGTTTGTCATTTTGTAAACAAGTTTTGTTCTTTAA
** * * * * * *
1805 A-ACAAGAACATATTTTCCTGGGGA-T-T-T-T-T-TCTTGGCTGTTGGACGAACTT-CAGAAC-
513 ATTTAA-AACTTATTTACCTGAGAATTGTCTCTCTCTCTTGGTTCTTGGACGAACTTCCA-AACT
** * * * * * **
1861 ATTTCAAACTTTTACGAGTTCTTTTATAACTCCGTC-CCTTGCAGTATTCAAGACGATCCATTCC
576 A-GCCAAACTTTTACAAGTTCTCTCATAACTTCGGCTCCTTAAAGTATTCAAGACGATCCATTCC
* *
1925 ATCAA
640 TTCGA
* *
1930 GCAATTTT-TGAACTTTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
1 GCAATTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
1993 GTAAAAAACT
Statistics
Matches: 1116, Mismatches: 193, Indels: 77
0.81 0.14 0.06
Matches are distributed among these distances:
637 49 0.04
638 227 0.20
639 100 0.09
640 3 0.00
641 4 0.00
642 11 0.01
643 315 0.28
644 141 0.13
645 148 0.13
646 92 0.08
647 26 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (644 bp):
GCAATTTTCTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTA
AAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTCTTGG
ACGAACTTCCGAACTTTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTACAGTATTCAA
GACGATCCATTCCTTCAAGCAATTTTCTGAACATTCCATGCTCGGAAAATCGCATCATTTGGTCT
AAATATTTGTCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAATACTTATTTACGTGAGAATTG
TTTCTCTTTTGGTTCTTGGACGAACTTCTGAACTTATCAAACTTTTACGAGTTCTTTTATAACTT
CGGTTCCTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTAGAG
AAATCGCATCATTTGTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGTTCTTTAAATTTAAAA
CTTATTTACCTGAGAATTGTCTCTCTCTCTTGGTTCTTGGACGAACTTCCAAACTAGCCAAACTT
TTACAAGTTCTCTCATAACTTCGGCTCCTTAAAGTATTCAAGACGATCCATTCCTTCGA
Done.