Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005954.1 Kokia drynarioides strain JFW-HI SEQ_120348, 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: 1772
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Found at i:652 original size:215 final size:216
Alignment explanation
Indices: 1--1772 Score: 2095
Period size: 215 Copynumber: 8.2 Consensus size: 216
* * **
1 TCATTTTATAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTGACA
1 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTC-
* * * ** *
66 TGGGTT-TTGGACAAACTTCCGATCTTGTCGAACTTTTACGAGTTCTTTTATAAAATCTATTCCT
65 TTGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCT
* * * * *
130 TAAAGTAATGAAGACGATGCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCAC
130 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCAC
195 ATCATTTGGTCTAAATA-TGTTG
195 ATCATTTGGTCTAAATAGT-TTG
* * * * *
217 TCATTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTGTTTACGTGAGTATTGTTTCTCTCT
1 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
* * * * * *
282 TGGTTCTTGGACGAACTTCTGAACTTGTGAAACTTTTACGGGTTCTTTTATAACTTCTATTCGTT
66 TGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * **
347 AAAGTA-T-AAGACGATCCATTCCTTCAACCAATTTTTCGAACATTTGATGCTCGAGAAATCACA
131 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCACA
*
410 TCATTTGCTCTAAATAGTTTG
196 TCATTTGGTCTAAATAGTTTG
* *
431 TCATTTTTTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
1 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
* *
496 TGGTTCTTGGACGAACTT-CGATCTTGTCAAACTTTTACGAGTTCCTTCATAACTTCGATTCCTT
66 TGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * *
560 AAAGTATTCAAGATGATCCATTCCTTCGAGCAGTTTTTCGAACATTCCATGCTCGAAAAATCACA
131 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCACA
* * *
625 TCATTCGGTGTAAATAGTTTT
196 TCATTTGGTCTAAATAGTTTG
* * * * * * * *
646 TCATTTTGTGAAA-AAGTTTTGGTGTTTAAATCAAAAACTTATTTACGTGGGAATTGTTCCTCTC
1 TCATTTTGT-AAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTC
* * *
710 TTGGTTCTTGGACGAACTTCCAATGTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCAT
65 TTGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCT
* * ** * * * * *
775 TAAATTGTTCAAGATAATCCATTCCTTGGATCAATTTTTTC-AACATTCCATGCACGGGAAATCG
130 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTTCGAACATTCCATGCTCGAGAAATCA
839 CATCATTTGGTCTAAATAGTTTG
194 CATCATTTGGTCTAAATAGTTTG
* *
862 TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCGTATTTACGTGAGAATTATTTCTCTCT
1 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
* * *
927 TGGTTGTTGGACGAACTT-CGATCTGGTCAAATTTTTACGAGTTCTTTTATAACTTCGATTCCTT
66 TGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * * * * *
991 AAAGTATTCAAGACGATCCATTCCTTCGATCAATTTTCCGAATATTCCATTCTCGTGAAATCGCA
131 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCACA
*
1056 TCATTTAGTCTAAATAGATTT-
196 TCATTTGGTCTAAATAG-TTTG
* * * * *
1077 TCATATTT-TAAA-AATGTTTTGGTCTTTGGATTAAAGA-CTGATTTATGTGAGAATTATTTATC
1 TCAT-TTTGTAAACAA-CTTTTGGTCTTTGAATTAAA-ATCTTATTTACGTGAGAATTATTTCTC
* * * * * *
1139 TCTTGATTCTAT-GACGAACTTCCGAACTTGTAAAACTTTTACAAATTCTTTTATAACTTC-CTT
63 TCTTGGTTCT-TGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATT
* * * * * * ** *
1202 CATTAAAGTATTCAAGATGGTCCATTCCTTTGTGAAATTTGCCAAACATTCCATGCTC-AGGAAA
127 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGA-GAAA
*
1266 TCACATCATTTGGTATAAATAGTTTG
191 TCACATCATTTGGTCTAAATAGTTTG
* * * *
1292 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTTTTTCTCACA
1 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
* * * **
1357 TGGTTTTTGGACAAACTTCCGATCTTGTCGAACTTTCGCGAGTTCTTTTATAACTTCGATTCCTT
66 TGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * * * * * * * *
1422 AAAGTAATGAAGACGATGCATTCCATCTAACAATTTTCCGAACATTTCATGCTCGAGAAATCAAA
131 AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCACA
1487 TCATTTGGTCTAAAATAGTTTG
196 TCATTTGGTCT-AAATAGTTTG
* * * * * *
1509 TCAGTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTATTTGCGTGAGTATTGTTTCTCTCT
1 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
* * *
1574 TGGTTCTTGGATGAACTTCCGAACTTGTCAAACTTTTAC-AGGTTCTTTCATAACTTCGATTCCT
66 TGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGA-GTTCTTTTATAACTTCGATTCCT
* * * * * *
1638 TAAAGTATTCAAGATGATCCATTCCTTCAAGCAATTTTTTGAGCATTCCAAGCTCGAAAAATCAC
130 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCAC
*
1703 ATCATTCGGTCTAAATAGTTTG
195 ATCATTTGGTCTAAATAGTTTG
* * * * *
1725 TCATTTTGCGAAA-AAGTTTTGGTGTTTAAATCGAAAA-CTTATTTACGT
1 TCATTTTG-TAAACAACTTTTGGTCTTTGAAT-TAAAATCTTATTTACGT
Statistics
Matches: 1315, Mismatches: 214, Indels: 54
0.83 0.14 0.03
Matches are distributed among these distances:
213 44 0.03
214 159 0.12
215 478 0.36
216 438 0.33
217 196 0.15
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (216 bp):
TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
TGGTTCTTGGACGAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
AAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCACA
TCATTTGGTCTAAATAGTTTG
Found at i:981 original size:431 final size:432
Alignment explanation
Indices: 1--1732 Score: 2195
Period size: 431 Copynumber: 4.0 Consensus size: 432
* * *
1 TCATTTTATAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTGACA
1 TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTCAC-
* * ** *
66 TGGGTTTTGGACAAACTTCCGATCTTGTCGAACTTTTACGAGTTCTTTTATAAAATCTATTCCTT
65 TTGGTTTTGGACAAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * ** *
131 AAAGTAATGAAGACGATGCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCACA
130 AAAGTAATCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACA
*
196 TCATTTGGTCTAAATA-TGTTGTCATTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTGTT
195 TCATTTGGTCTAAATAGT-TTGTCATTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTATT
* * * *
260 TACGTGAGTATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTGAAACTTTTACGGGT
259 TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGT
* * * * *
325 TCTTTTATAACTTCTATTCGTTAAAGTA-T-AAGACGATCCATTCCTTCAACCAA-TTTTTCGAA
324 TCTTTTATAACTTCGATTCATTAAAGTATTCAAGATGATCCATTCCTTCAATCAATTTTTTCAAA
** *
387 CATTTGATGCTCGAGAAATCACATCATTTGCTCTAAATAGTTTG
389 CATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTG
* * *
431 TCATTTTTTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACGTGAGAATTATTTCTCTCT
1 TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTCACT
* * *
496 TGGTTCTTGGACGAACTT-CGATCTTGTCAAACTTTTACGAGTTCCTTCATAACTTCGATTCCTT
66 TGGTT-TTGGACAAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * * * *
560 AAAGTATTCAAGATGATCCATTCCTTCGAGCAGTTTTTCGAACATTCCATGCTCGAAAAATCACA
130 AAAGTAATCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACA
* * * * * *
625 TCATTCGGTGTAAATAGTTTTTCATTTTGTGAAA-AAGTTTTGGTGTTTAAATCAAAAACTTATT
195 TCATTTGGTCTAAATAGTTTGTCATTTTGT-AAACAACTTTTGGTGTTTGAATTAAAAACTTATT
* * *
689 TACGTGGGAATTGTTCCTCTCTTGGTTCTTGGACGAACTTCC-AATGTTGTCAAACTTTTACGAG
259 TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAA-CTTGTCAAACTTTTACGAG
* * * **
753 TTCTTTTATAACTTCGATTCATTAAATTGTTCAAGATAATCCATTCCTTGGATCAATTTTTTC-A
323 TTCTTTTATAACTTCGATTCATTAAAGTATTCAAGATGATCCATTCCTTCAATCAATTTTTTCAA
* * *
817 ACATTCCATGCACGGGAAATCGCATCATTTGGTCTAAATAGTTTG
388 ACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTG
* * *
862 TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCGTATTTACGTGAGAATTATTTCTCTCT
1 TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTCACT
* * *
927 TGGTTGTTGGACGAACTT-CGATCTGGTCAAATTTTTACGAGTTCTTTTATAACTTCGATTCCTT
66 TGGTT-TTGGACAAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * * * * *
991 AAAGTATTCAAGACGATCCATTCCTTCGATCAATTTTCCGAATATTCCATTCTCGTGAAATCGCA
130 AAAGTAATCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACA
* * * * * *
1056 TCATTTAGTCTAAATAGATTT-TCATATTT-TAAA-AATGTTTTGGTCTTTGGATTAAAGACTGA
195 TCATTTGGTCTAAATAG-TTTGTCAT-TTTGTAAACAA-CTTTTGGTGTTTGAATTAAAAACTTA
* * * * * *
1118 TTTATGTGAGAATTATTTATCTCTTGATTCTAT-GACGAACTTCCGAACTTGTAAAACTTTTACA
257 TTTACGTGAGAATTGTTTCTCTCTTGGTTCT-TGGACGAACTTCCGAACTTGTCAAACTTTTACG
* * * ** * * **
1182 AATTCTTTTATAACTTC-CTTCATTAAAGTATTCAAGATGGTCCATTCCTT-TGTGAAATTTGCC
321 AGTTCTTTTATAACTTCGATTCATTAAAGTATTCAAGATGATCCATTCCTTCAATCAATTTTTTC
*
1245 AAACATTCCATGCTC-AGGAAATCACATCATTTGGTATAAATAGTTTG
386 AAACATTCCATGCTCGA-GAAATCACATCATTTGGTCTAAATAGTTTG
* * *
1292 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTTTTTCTCACA
1 TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTCACT
* **
1357 TGGTTTTTGGACAAACTTCCGATCTTGTCGAACTTTCGCGAGTTCTTTTATAACTTCGATTCCTT
66 TGG-TTTTGGACAAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTT
* * * * * * *
1422 AAAGTAATGAAGACGATGCATTCCATCTAACAATTTTCCGAACATTTCATGCTCGAGAAATCAAA
130 AAAGTAATCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACA
*
1487 TCATTTGGTCTAAAATAGTTTGTCAGTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTATT
195 TCATTTGGTCT-AAATAGTTTGTCATTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTATT
* * *
1552 TGCGTGAGTATTGTTTCTCTCTTGGTTCTTGGATGAACTTCCGAACTTGTCAAACTTTTAC-AGG
259 TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGA-G
* * * *
1616 TTCTTTCATAACTTCGATTCCTTAAAGTATTCAAGATGATCCATTCCTTCAAGCAATTTTTT-GA
323 TTCTTTTATAACTTCGATTCATTAAAGTATTCAAGATGATCCATTCCTTCAATCAATTTTTTCAA
* * * *
1680 GCATTCCAAGCTCGAAAAATCACATCATTCGGTCTAAATAGTTTG
388 ACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTG
1725 TCATTTTG
1 TCATTTTG
1733 CGAAAAAGTT
Statistics
Matches: 1120, Mismatches: 157, Indels: 47
0.85 0.12 0.04
Matches are distributed among these distances:
428 2 0.00
429 239 0.21
430 222 0.20
431 456 0.41
432 116 0.10
433 79 0.07
434 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (432 bp):
TCATTTTGTAAACAACATTTGGTCTTTGAATTAAAATCTTATTTACATGAGAATTATTTCTCACT
TGGTTTTGGACAAACTTCCGATCTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCTTA
AAGTAATCAAGACGATCCATTCCTTCGAGCAATTTTCCGAACATTCCATGCTCGAGAAATCACAT
CATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTGTTTGAATTAAAAACTTATTTA
CGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTC
TTTTATAACTTCGATTCATTAAAGTATTCAAGATGATCCATTCCTTCAATCAATTTTTTCAAACA
TTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTG
Done.