Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009640.1 Kokia drynarioides strain JFW-HI SEQ_124357, 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: 1769
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Found at i:630 original size:216 final size:213
Alignment explanation
Indices: 1--1763 Score: 1724
Period size: 216 Copynumber: 8.2 Consensus size: 213
* * * * **
1 AGTATTCAAGACGATGCATTCCTTCTAGCAACTTTCTT-AACATTCTATGCTAGAAAAATCGCAT
1 AGTATTCAAGACGATCCATTCCTTCGAGCAA-TTT-TTGAACATTCCATGCTCGGGAAATCGCAT
* * * * ** * *
65 CATTT-TTCTAAATTGTTTGTAATTTTATAAACTAGTTATGGTATTTA-AATTTAAAACTT-TCT
64 CATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGT-CTTAGAA-TTAAAACTTAT-T
* ** * * *
127 TACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGGATTAACTTCCAAACTTTTCAATA-TTTTTCG
126 TACGTGAGAATTGTTTCTCT-T-TTGGTTCTTGGACGAACTTCCGAACTTATCAA-ACTTTTACG
*
191 AGTTCATTTATAACTCCGGTTCCTTAA
188 AGTTCTTTTATAACTCC-GTTCCTTAA
* * * *
218 AGTATTCAAGACGATCCATTCCTTTGAGGAATTTTTGAACATTCCATTCTCAGGAAATCGCATCA
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTGAACATTCCATGCTCGGGAAATCGCATCA
* * * ** * ** * *
283 TTTAGTCTAAATAGGTCT-TAATTTTGTAAATGAGTTTTGATCATTA-AAGCAAGAACATATTTT
66 TTTGGTCTAAATA-GTTTGTCATTTTGTAAAAAAGTTTTGGTC-TTAGAATTAA-AACTTATTTA
* * * * * *
346 CCTGAGGATT-TTT-TC--TTGGCTGTTGGACGAACTTCAGAACATT-TCATACTTTTACGAGTT
128 CGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAAC-TTATCAAACTTTTACGAGTT
**
406 CTTTTATAACTCCGTTCCTTGC
192 CTTTTATAACTCCGTTCCTTAA
* * * * *
428 AGTATTCAGGACAATCCATTCCATCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATA
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-TGAACATTCCATGCTCGGGAAATCGCATC
* *
493 ATTTGGTCTAAATAGTTTGTCATTTCGTAAAAAAACTTTTGGTCTTAGAATTAAATACTTATTTA
65 ATTTGGTCTAAATAGTTTGTCATTTTGT-AAAAAAGTTTTGGTCTTAGAATTAAA-ACTTATTTA
558 CGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTTC
128 CGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTTC
* * *
623 TTTTATAATTTCAGTTCCATAA
193 TTTTATAA-CTCCGTTCCTTAA
* * **
645 AGTATTCAAGTCGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCGAAAAATCGCATC
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTT-GAACATTCCATGCTCGGGAAATCGCATC
* *
710 ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAATGTTTTGTTGCTT-GAATTAAAAACTTATTTA
65 ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGT-CTTAGAATT-AAAACTTATTTA
* * ** * *
774 CGTGAGAATTATTTCTCTCTTGGTTCTTGGATAAACTTTCGAAC-TAGTCAAACTTTTACAAGTT
128 CGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTA-TCAAACTTTTACGAGTT
** *
838 CTTTTATAACTTTGGTTCCTTAC
192 CTTTTATAAC-TCCGTTCCTTAA
* * * * **
861 AGTATTCAAGACGATACATTCCTTCTAGCAACTTTCTT-AACATTCTATGCTAGAAAAATCGCAT
1 AGTATTCAAGACGATCCATTCCTTCGAGCAA-TTT-TTGAACATTCCATGCTCGGGAAATCGCAT
* * *
925 CATTT-TTCTAAATTGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTA-AATTTAAAACTTATTT
64 CATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTC-TTAGAA-TTAAAACTTATTT
* * * * *
988 ACGTGAGAATTGTTTCTCTCTCTTTGTTCTTAGATGAACTTCCAAACTTGTCAAACTTTTACGAG
127 ACGTGAGAATTGTTTCTCT-T-TTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAG
**
1053 TTCTTTTATAACTTTTGTTCCTTAA
190 TTCTTTTATAAC-TCCGTTCCTTAA
* * * * * *
1078 AGTATTCAAGACGTTCCATTCCTTTGAGGAATTTTTGAACATTCCATTCTCGAGAAATCGCATTA
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTGAACATTCCATGCTCGGGAAATCGCATCA
* * ** * ** * ** * *
1143 TTTAGTCTAAATAGGTCATAATTTTGTAAACGAGTTTTGATCATTA-AAACAAGAACATATTTTC
66 TTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTC-TTAGAATTAA-AACTTATTTAC
* * * * **
1207 CTGAGGATT-TTT-TC--TTGGCTGTTGGACGAACTTCAAAACATT-TCAAACTTTTACGAGTTC
129 GTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAAC-TTATCAAACTTTTACGAGTTC
**
1267 TTTTATAACTCCGTTCCTTGT
193 TTTTATAACTCCGTTCCTTAA
* * *
1288 AGTATTCAAGACGATCCATTCCATC-AGGCAATTTTCTGAACATTCCATGATCGGGAAATAGCAT
1 AGTATTCAAGACGATCCATTCCTTCGA-GCAATTTT-TGAACATTCCATGCTCGGGAAATCGCAT
* *
1352 CATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAATACTTATTTA
64 CATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTAGAATTAAA-ACTTATTTA
* *
1417 CGTGAGAATTTTTTCTCTTTTGGTTCTTGGACGAACTTCTGAACTTATCAAACTTTTACGAGTTC
128 CGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTTC
* * *
1482 TTTTATAATTTCAGTTCCATAA
193 TTTTATAA-CTCCGTTCCTTAA
* * * *
1504 AGTATTCTAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCTTGGGAAATCGTATC
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTT-GAACATTCCATGCTCGGGAAATCGCATC
* * * * * *
1569 ATTTGGTCTAAATATTTTGTCATTTTGTTAAAAGGTTTTGTTGTTTGAATTATAAACTTATTTAC
65 ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTAGAATTA-AAACTTATTTAC
* * * * *
1634 GTGAGAATTGCTTCTCTCTTGGTTCTTGGATGAACTTTCGAAC-TAGTCAAAC-TTTACAAGTTC
129 GTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTA-TCAAACTTTTACGAGTTC
* * *
1697 TTTCATATCTTCGGTTCCTTAA
193 TTTTATAAC-TCCGTTCCTTAA
*
1719 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTAAACATTC
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-TGAACATTC
1764 AATTCT
Statistics
Matches: 1286, Mismatches: 208, Indels: 106
0.80 0.13 0.07
Matches are distributed among these distances:
209 1 0.00
210 80 0.06
211 216 0.17
212 37 0.03
213 5 0.00
214 5 0.00
215 194 0.15
216 433 0.34
217 308 0.24
218 7 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (213 bp):
AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTGAACATTCCATGCTCGGGAAATCGCATCA
TTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTTGGTCTTAGAATTAAAACTTATTTACGT
GAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTTCTTT
TATAACTCCGTTCCTTAA
Found at i:1305 original size:643 final size:643
Alignment explanation
Indices: 1--1769 Score: 1858
Period size: 643 Copynumber: 2.7 Consensus size: 643
* * * *
1 AGTATTCAAGACGATGCATTCCTTCTAGCAACTTTCTT--AACATTCTATGCTAGAAAAATCGCA
1 AGTATTCAAGACGATCCATTCCTTCAAGCAA-TTT-TTCGAACATTCCATGCTCGAAAAATCGCA
* * * * * * * * *
64 TCATTT-TTCTAAATTGTTTGTAATTTTAT-AAACTAGTTATGGTATTTAAATTTAAAACTT-TC
64 TCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAT-GTTTTGGT-CTTGAATTAAAAACTTAT-
* * * * * *
126 TTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGGATTAACTTCCAAACTTTTCAATA-TTTTTC
126 TTACGTGAGAATT-TTT-TCTCTCTTGGTTCTTGGATAAACTTTCGAAC-TATCAA-ACTTTTAC
* ** *
190 GAGTTCATTTATAACTCCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTT-TGAGGAATTTTT
187 GAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCT-AGCAATTTTT
* * * * *
254 GAACATTCCATTCTCAGGAAATCGCATCATTTAGTCTAAATAGGTCT-TAATTTTGTAAATGAGT
251 GAACATTCCATGCT-AGGAAATCGCATCATTTAGTCTAAATATGTTTGTCATTTTGTAAA-AAGT
* ** * * * * * * *
318 TTTGATCATTAAAGCAAGAACATATTTTCCTGAGGA---TTTT-T-TCTTGGCTGTTGGACGAAC
314 TTTGATCTTTAAATTAA-AACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTTGGATGAAC
* ** * *
378 TTCAGAACATT-TCATACTTTTACGAGTTCTTTTATAAC-TCCGTTCCTTGCAGTATTCAGGACA
378 TTCA-AAC-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACG
* * * * *
441 ATCCATTCCATCAAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCTAAAT
441 ATCCATTCCTTCGAGCAATTTTCTGAACATTCCATTCTCGAGAAATCGCATAATTTAGTCTAAAT
* ** * * ** * *
506 AGTTTGTCATTTCGTAAAAAAACTTTTGGTCTTAGAATTAAATACTTATTTACGTGAGAATTGTT
506 AGGTCATAATTTCGTAAAAAAACTTTTGATCTTAGAAACAAATACATATTTACCTGAGAATTGTT
* ** *
571 TCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTTCTTTTATAATTTCA
571 TCTC-TTTGGCTCTTGGACGAACTTCAAAACTTATCAAACTTTTACGAGTTCTTTTATAATCTCA
636 GTTCCATAA
635 GTTCCATAA
*
645 AGTATTCAAGTCGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCGAAAAATCGCATC
1 AGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCGAAAAATCGCATC
*
710 ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAATGTTTTGTTGCTTGAATTAAAAACTTATTTAC
66 ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAATGTTTTGGT-CTTGAATTAAAAACTTATTTAC
* *
775 GTGAGAATTATTTCTCTCTTGGTTCTTGGATAAACTTTCGAACTAGTCAAACTTTTACAAGTTCT
130 GTGAGAATTTTTTCTCTCTTGGTTCTTGGATAAACTTTCGAACTA-TCAAACTTTTACGAGTTCT
* *
840 TTTATAACTTTGGTTCCTTACAGTATTCAAGACGATACATTCCTTCTAGCAACTTTCTT-AACAT
194 TTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCTAGCAA-TTT-TTGAACAT
* * * *
904 TCTATGCTAGAAAAATCGCATCATTT-TTCTAAAT-TGTTTGTCATTTTGTAAACAAGTTTTGGT
257 TCCATGCTAG-GAAATCGCATCATTTAGTCTAAATATGTTTGTCATTTTGTAAA-AAGTTTTGAT
* *
967 CTTTAAATTTAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTAGATGAACTTCCA
320 CTTTAAA-TTAAAACTTATTTACGTGAGAATTGTTT-TCTCTCTTGGTTCTTGGATGAACTT-CA
** *
1032 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTCAAGACGTTCCAT
382 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCAT
* * *
1097 TCCTTTGAGGAATTTT-TGAACATTCCATTCTCGAGAAATCGCATTATTTAGTCTAAATAGGTCA
447 TCCTTCGAGCAATTTTCTGAACATTCCATTCTCGAGAAATCGCATAATTTAGTCTAAATAGGTCA
* ** * * *
1161 TAATTTTGT-AAACGAGTTTTGATCATTA-AAACAAGA-ACATATTTTCCTGAGGATT-TTT-TC
512 TAATTTCGTAAAAAAACTTTTGATC-TTAGAAACAA-ATACATATTTACCTGAGAATTGTTTCTC
* *
1221 -TTGGCTGTTGGACGAACTTCAAAACATT-TCAAACTTTTACGAGTTCTTTTATAA-CTCCGTTC
575 TTTGGCTCTTGGACGAACTTCAAAAC-TTATCAAACTTTTACGAGTTCTTTTATAATCTCAGTTC
* **
1283 CTTGT
639 CATAA
* * * ** *
1288 AGTATTCAAGACGATCCATTCCATCAGGCAA-TTTTCTGAACATTCCATGATCGGGAAATAGCAT
1 AGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTC-GAACATTCCATGCTCGAAAAATCGCAT
** *
1352 CATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAATACTTATTTA
65 CATTTGGTCTAAATAGTTTGTCATTTTGTAAAAATGTTTTGGTC-TTGAATTAAAAACTTATTTA
* **
1417 CGTGAGAATTTTTTCTCTTTTGGTTCTTGGACGAAC-TTCTGAACTTATCAAACTTTTACGAGTT
129 CGTGAGAATTTTTTCTCTCTTGGTTCTTGGATAAACTTTC-GAAC-TATCAAACTTTTACGAGTT
* * * *
1481 CTTTTATAA-TTTCAGTTCCATAAAGTATTCTAGACGATCCATTCCTTCGAGCAATTTTTCGAAC
192 CTTTTATAACTTT-GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCTAGCAATTTTT-GAAC
* * * * *
1545 ATTCCAAGCTTGGGAAATCGTATCATTTGGTCTAAATAT-TTTGTCATTTTGTTAAAAGGTTTTG
255 ATTCCATGC-TAGGAAATCGCATCATTTAGTCTAAATATGTTTGTCATTTTG-TAAAAAGTTTTG
* * * *
1609 TTGTTTGAATTATAAACTTATTTACGTGAGAATTG-CTTCTCTCTTGGTTCTTGGATGAACTTTC
318 ATCTTTAAATTA-AAACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTTGGATGAAC-TTC
* * * * * *
1673 GAACTAGTCAAAC-TTTACAAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGACGATCCA
381 AAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCA
* *
1737 TTCCTTCGAGCAATTTTCTAAACATTCAATTCT
446 TTCCTTCGAGCAATTTTCTGAACATTCCATTCT
Statistics
Matches: 947, Mismatches: 139, Indels: 80
0.81 0.12 0.07
Matches are distributed among these distances:
641 62 0.07
642 68 0.07
643 380 0.40
644 195 0.21
645 60 0.06
646 10 0.01
647 4 0.00
648 33 0.03
649 97 0.10
650 38 0.04
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (643 bp):
AGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTCGAACATTCCATGCTCGAAAAATCGCATC
ATTTGGTCTAAATAGTTTGTCATTTTGTAAAAATGTTTTGGTCTTGAATTAAAAACTTATTTACG
TGAGAATTTTTTCTCTCTTGGTTCTTGGATAAACTTTCGAACTATCAAACTTTTACGAGTTCTTT
TATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCTAGCAATTTTTGAACATTCCA
TGCTAGGAAATCGCATCATTTAGTCTAAATATGTTTGTCATTTTGTAAAAAGTTTTGATCTTTAA
ATTAAAACTTATTTACGTGAGAATTGTTTTCTCTCTTGGTTCTTGGATGAACTTCAAACTTGTCA
AACTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAG
CAATTTTCTGAACATTCCATTCTCGAGAAATCGCATAATTTAGTCTAAATAGGTCATAATTTCGT
AAAAAAACTTTTGATCTTAGAAACAAATACATATTTACCTGAGAATTGTTTCTCTTTGGCTCTTG
GACGAACTTCAAAACTTATCAAACTTTTACGAGTTCTTTTATAATCTCAGTTCCATAA
Done.