Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001884.1 Kokia drynarioides strain JFW-HI SEQ_113656, 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: 1968
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Found at i:348 original size:97 final size:92
Alignment explanation
Indices: 230--475 Score: 278
Period size: 93 Copynumber: 2.6 Consensus size: 92
220 CTTTTACAGC
* *
230 TTCGGTTCCTTAAAGTGTTCAAGACGATCCATTTCTTCGAGTAATTTTTCGAACATAACTTCTAA
1 TTCGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAA-TTTTCGAACATAACATCT-A
295 AGTTGTCAAACCTTTACGAGTTCTTTTCTAAA
64 AG--G-CAAACCTTTACGAGTTCTTTTCTAAA
* * * * * ** * *
327 TTCGGTTCATTAAAGTCTTCAAGATGATCCATTCCTTCGAGTAACTTTCCAAACATTCCATGTGA
1 TTCGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAA-TTTTCGAACATAACATCTAA
* * *
392 GGGAACCCTTTACGAGTTCTTTTTTAAA
65 GGCAAACCTTTACGAGTTCTTTTCTAAA
*
420 TCCGGTTCCTTGAAA-TGTTCAAGACGATCCATTCCTTCGAGTAATTTTCTGAACAT
1 TTCGGTTCCTT-AAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTC-GAACAT
476 TCCATGCGTG
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
92 4 0.03
93 64 0.51
94 4 0.03
96 2 0.02
97 52 0.41
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (92 bp):
TTCGGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAATTTTCGAACATAACATCTAAG
GCAAACCTTTACGAGTTCTTTTCTAAA
Found at i:781 original size:216 final size:216
Alignment explanation
Indices: 400--1968 Score: 1816
Period size: 216 Copynumber: 7.3 Consensus size: 216
390 GAGGGAACCC
* * * * * *
400 TTTACGAGTTCTTTTTTAAATCCGGTTCCTTGAAA-TGTTCAAGACGATCCATTCCTTCGAGTAA
1 TTTACGAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGACGATCCAATCCTTCGAGCAA
* ** * *
464 TTTTCTGAACATTCCATGCGT-GGGAAATTTCATCATTTGGTCTAAATAGTTTTTCGTTGTT-TA
65 TTTTCCGAACATTCCATGC-TAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATT-TTGTA
* * *
527 AACAAGTTTTGATCTTTGAATTAAAGACTTATTTACGTGCGAATTGTTTCTCTCTTGGTTATTGG
128 AACAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGG
* * * *
592 ATGAAGTTTCGAACATGTCAAACT
193 ACGAACTTCCGAACTTGTCAAACT
* * *
616 TTTACGTGTTCTTTTATAGCTTCGGTTCCTTAAAGTATTCAAGATGATCCAATCCTTCGAGCAAT
1 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAAT
* * * * * * * *
681 TTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCTAAAGAGTTTGTCATTTAGTAAAC
66 TTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
* ** *
746 AAATTTTGGCCTTTGAATTAAAAATTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGACG
131 AAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGACG
*
811 AACTTCCGAACTTGTCAAATT
196 AACTTCCGAACTTGTCAAACT
* * * * * * * * * *
832 TTTACAAGTTCTTTT-TAAATTCAGTTCCTTAAAGTGTCCAAGATGATCC-ATTCGTAGAGTAAT
1 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAAT
** * *
895 TCCCCGACCATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTATT-TCATTTTGTAAA
66 TTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGT-TTGTCATTTTGTAAA
* * * *
959 CAAGTTTTAATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGAC
130 CAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGAC
*
1024 GAACTTCCAAACTTGTCAAACT
195 GAACTTCCGAACTTGTCAAACT
* * * * *
1046 TTTACGAGTTCTTTTTTAACTTCGGTTTCTTAAAATATTCAAGATGATCCAATCTTTCGAGCAAA
1 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGC-AA
* * * * * *
1111 TTTT-CAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCTAAAGAGTTTGTCA-TTTGTAAA
65 TTTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
** *
1174 CAAGTTTTGGCCTTTGAATT-AAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTGTTGGAC
130 CAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGAC
* *
1238 GAACTTCTGAATTTGTCAAACT
195 GAACTTCCGAACTTGTCAAACT
* * * * * * * *
1260 TTTACGAGTTCTTTTTTAA-ATCTGGTTCCTTAAAGTGTTCAACACAATCCATTCCTTTGAGTAA
1 TTTACGAGTTCTTTTATAACTTC-GGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAA
* * ** * * * *
1324 TTTTCCAAACGTTCCATGAGAGGGAAATCGCACCATTTGGCCTAAATAGTTTCTCATTTTATAAA
65 TTTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* * * * * * * *
1389 CAAGTTTTGATCTTCGAATTAAAAGCTTATTTACATGTGAATTGTGTGTCTCTTGGTTTTTGGAT
130 CAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGAC
*
1454 GAACTTCCAAACTTGTCAAACT
195 GAACTTCCGAACTTGTCAAACT
* * * *
1476 TTTACGAGTTCTTTCATAACTTCAGTTCCATAAAGTATTCAAGACGATCCAATCCATCGAGCAAT
1 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAAT
* * * * * *
1541 TTTCCGAACATTACATTCTCGGGAAGTTGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAAC
66 TTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
* *
1606 AAGTTTTG-TCATTCGAATTAAAAACTTATTTACGTGAAAATTGTTTCTCTCTTGGTTGTTGGAC
131 AAGTTTTGATC-TTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGAC
* *
1670 GAACTTTCGAACTTGTCACACT
195 GAACTTCCGAACTTGTCAAACT
* * * * * * *
1692 TTTACGAGTTCTTTTTTAA-ATCTAGTTCCTTAAAGTGTT-AAGACGATCCATTACTTCGAGTAA
1 TTTACGAGTTCTTTTATAACTTC-GGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAA
* * * *
1755 TTTTCCGAACATTCCAAGCGAGGGAAATCGCATAATTTGGTCTAAATAGTTTTTCATTTTGTAAA
65 TTTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
** * * *
1820 CAAGTTTTGATCTTTGAATTAAAAACTTATTTAAATGAGAATTGTTTGTCTCTTGGTTCTTGGAT
130 CAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGAC
1885 GAACTTCCGAACTTGTCAAACT
195 GAACTTCCGAACTTGTCAAACT
* * * *
1907 TTTACGACTTCTTTTACAACTTCGATTCCTTAAAGTATTTAAGACGA-CCAATCCTTCGAGCA
1 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCA
Statistics
Matches: 1125, Mismatches: 210, Indels: 37
0.82 0.15 0.03
Matches are distributed among these distances:
213 8 0.01
214 297 0.26
215 310 0.28
216 504 0.45
217 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (216 bp):
TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAAT
TTTCCGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
AAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTGTTGGACG
AACTTCCGAACTTGTCAAACT
Found at i:1090 original size:430 final size:431
Alignment explanation
Indices: 400--1968 Score: 2272
Period size: 430 Copynumber: 3.6 Consensus size: 431
390 GAGGGAACCC
**
400 TTTACGAGTTCTTTTTTAAATCCGGTTCCTTGAAA-TGTTCAAGACGATCCATTCCTTCGAGTAA
1 TTTACGAGTTCTTTTTTAAATCTAGTTCCTT-AAAGTGTTCAAGACGATCCATTCCTTCGAGTAA
* * ** *
464 TTTTCTGAACATTCCATGCGTGGGAAATTTCATCATTTGGTCTAAATAGTTTTTCGTTGTT-TAA
65 TTTTCCGAACATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATT-TTGTAA
* * * * *
528 ACAAGTTTTGATCTTTGAATTAAAGACTTATTTACGTGCGAATTGTTTCTCTCTTGGTTATTGGA
129 ACAAGTTTTGATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGA
* * * * * *
593 TGAAGTTTCGAACATGTCAAACTTTTACGTGTTCTTTTATAGCTTCGGTTCCTTAAAGTATTCAA
194 TGAACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA
*
658 GATGATCCAATCCTTCGAGCAATTTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCT
259 GACGATCCAATCCTTCGAGCAATTTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCT
* *
723 AAAGAGTTTGTCATTTAGTAAACAAATTTTGGCCTTTGAATTAAAAATTTATTTACGTGAGAATT
324 AAAGAGTTTGTCATTT-GTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACGTGAGAATT
*
788 GTTTCTCTCTTGGTTGTTGGACGAACTTCCGAACTTGTCAAATT
388 GTTTCTCTCTTGGTTGTTGGACGAACTTCCGAACTTGTCAAACT
* * * * *
832 TTTACAAGTTC-TTTTTAAAT-TCAGTTCCTTAAAGTGTCCAAGATGATCCATT-CGTAGAGTAA
1 TTTACGAGTTCTTTTTTAAATCT-AGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAA
** * *
894 TTCCCCGACCATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTATTTCATTTTGTAAA
65 TTTTCCGAACATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAA
* *
959 CAAGTTTTAATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGAC
130 CAAGTTTTGATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGAT
* * *
1024 GAACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTTTAACTTCGGTTTCTTAAAATATTCAAG
195 GAACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG
* * *
1089 ATGATCCAATCTTTCGAGCAAATTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCTA
260 ACGATCCAATCCTTCGAGCAATTTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCTA
1154 AAGAGTTTGTCATTTGTAAACAAGTTTTGGCCTTTGAATT-AAAACTTATTTACGTGAGAATTGT
325 AAGAGTTTGTCATTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * *
1218 TTCTCTATTGGTTGTTGGACGAACTTCTGAATTTGTCAAACT
390 TTCTCTCTTGGTTGTTGGACGAACTTCCGAACTTGTCAAACT
* * * *
1260 TTTACGAGTTCTTTTTTAAATCTGGTTCCTTAAAGTGTTCAACACAATCCATTCCTTTGAGTAAT
1 TTTACGAGTTCTTTTTTAAATCTAGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAAT
* * * * * * *
1325 TTTCCAAACGTTCCATGAGAGGGAAATCGCACCATTTGGCCTAAATAGTTTCTCATTTTATAAAC
66 TTTCCGAACATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAC
* * * * *
1390 AAGTTTTGATCTTCGAATTAAAAGCTTATTTACATGTGAATTGTGTGTCTCTTGGTTTTTGGATG
131 AAGTTTTGATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGATG
* * *
1455 AACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTCATAACTTCAGTTCCATAAAGTATTCAAGA
196 AACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * *
1520 CGATCCAATCCATCGAGCAATTTTCCGAACATTACATTCTCGGGAAGTTGCATCATTTGGTCTAA
261 CGATCCAATCCTTCGAGCAATTTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCTAA
* * * * *
1585 AAAGTTTGTCATTTTGTAAACAAGTTTTGTCATTCGAATTAAAAACTTATTTACGTGAAAATTGT
326 AGAGTTTGTCA-TTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* *
1650 TTCTCTCTTGGTTGTTGGACGAACTTTCGAACTTGTCACACT
390 TTCTCTCTTGGTTGTTGGACGAACTTCCGAACTTGTCAAACT
*
1692 TTTACGAGTTCTTTTTTAAATCTAGTTCCTTAAAGTGTT-AAGACGATCCATTACTTCGAGTAAT
1 TTTACGAGTTCTTTTTTAAATCTAGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAAT
* *
1756 TTTCCGAACATTCCAAGCGAGGGAAATCGCATAATTTGGTCTAAATAGTTTTTCATTTTGTAAAC
66 TTTCCGAACATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAC
* * *
1821 AAGTTTTGATCTTTGAATTAAAAACTTATTTAAATGAGAATTGTTTGTCTCTTGGTTCTTGGATG
131 AAGTTTTGATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGATG
* * * * *
1886 AACTTCCGAACTTGTCAAACTTTTACGACTTCTTTTACAACTTCGATTCCTTAAAGTATTTAAGA
196 AACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
1951 CGA-CCAATCCTTCGAGCA
261 CGATCCAATCCTTCGAGCA
Statistics
Matches: 1009, Mismatches: 120, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
428 71 0.07
429 60 0.06
430 517 0.51
431 253 0.25
432 108 0.11
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (431 bp):
TTTACGAGTTCTTTTTTAAATCTAGTTCCTTAAAGTGTTCAAGACGATCCATTCCTTCGAGTAAT
TTTCCGAACATTCCATGCGAGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAC
AAGTTTTGATCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTTGGATG
AACTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
CGATCCAATCCTTCGAGCAATTTTTCAAACATTACATGCTCGGGAAGTCGAATCATTTGGTCTAA
AGAGTTTGTCATTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
TCTCTCTTGGTTGTTGGACGAACTTCCGAACTTGTCAAACT
Done.