Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006137.1 Kokia drynarioides strain JFW-HI SEQ_120671, 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: 3621
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Found at i:424 original size:39 final size:40
Alignment explanation
Indices: 358--460 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
348 CCTACCATCG
* * * ** *
358 CTCTCCCTCTTCCCCACTAGT-CTTCCCC-CTACTCTGATT
1 CTCTCCCTCTCCCCCAC-CGTCCCTCCCCTCTACTCCAATC
*
397 CTCTCCCTCTCCCCCACCGTCCCTCCCCTTTACTCCAATC
1 CTCTCCCTCTCCCCCACCGTCCCTCCCCTCTACTCCAATC
*
437 CTTTCCCTCTCCCCCACCGTCCCT
1 CTCTCCCTCTCCCCCACCGTCCCT
461 TTCCCTTTGC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.04
39 22 0.41
40 30 0.56
ACGTcount: A:0.09, C:0.56, G:0.04, T:0.31
Consensus pattern (40 bp):
CTCTCCCTCTCCCCCACCGTCCCTCCCCTCTACTCCAATC
Found at i:1422 original size:423 final size:423
Alignment explanation
Indices: 636--1482 Score: 1545
Period size: 423 Copynumber: 2.0 Consensus size: 423
626 GGATTGTGGC
636 AACCACAATTGCCTTTGCTGCATTCCTCTTCTCAGACCACTTCTAATAAGCTTCTGTCTTTCTTT
1 AACCACAATTGCCTTTGCTGCATTCCTCTTCTCAGACCACTTCTAATAAGCTTCTGTCTTTCTTT
*
701 CACATCTTCTTCTTTTCCTTATCAAAATGACAACTTTAACATATTTGGTAGAAACAACAATGGTA
66 CACATCTTCTTCTTTTCCTTATCAAAATGACAACTTTAAAATATTTGGTAGAAACAACAATGGTA
* * *
766 GAAGAGACCTCCACAGCAACGTAGGTAAACAAAAGCTCATTCTAAAAATTGAAAAAAAGCCTTTC
131 GAAGAGACCTCCACAACAACGTAGGTAAACAAAAGCCCATTCTAAAAATTGAAAAAAAGACTTTC
* *
831 TTTTATATGAAAATTTGAAAAACCATAGCTTTGTTCAAATTTTGAGAAATATGGTAAAGCTAACC
196 TTTTATATGAAAATTTGAAAAACCATAGCTTTGTTCAAAATTTGAGAAATAAGGTAAAGCTAACC
896 CTTTTATGTTTTGAGACAAAATGGAGTGTCTGAGCTCAACATAGTTAAAGGATTTAGTCAGGTTC
261 CTTTTATGTTTTGAGACAAAATGGAGTGTCTGAGCTCAACATAGTTAAAGGATTTAGTCAGGTTC
961 CTAAAACATTCTCTTATTCTCCAATTCAATTCAAAGATATTGTAGAGAAAGTAAAGCAAATGGGG
326 CTAAAACATTCTCTTATTCTCCAATTCAATTCAAAGATATTGTAGAGAAAGTAAAGCAAATGGGG
1026 TTCAGTCCAGAGAGGTTTACTTTTATTTTAGCT
391 TTCAGTCCAGAGAGGTTTACTTTTATTTTAGCT
1059 AACCACAATTGCCTTTGCTGCATTCCTCTTCTC-GCACCACTTCTAATAAGCTTCTGTCTTTCTT
1 AACCACAATTGCCTTTGCTGCATTCCTCTTCTCAG-ACCACTTCTAATAAGCTTCTGTCTTTCTT
1123 TCACATCTTCTTCTTTTCCTTATCAAAATGACAACTTTATAAATATTTGGTAGAAACAACAATGG
65 TCACATCTTCTTCTTTTCCTTATCAAAATGACAACTTTA-AAATATTTGGTAGAAACAACAATGG
*
1188 TAGAAGAGACCTCCACAACCACGTAGGTAAACAAAAGCCCATTCTAAAAATTGAAAAAAA-ACTT
129 TAGAAGAGACCTCCACAACAACGTAGGTAAACAAAAGCCCATTCTAAAAATTGAAAAAAAGACTT
1252 TCTTTTATATGAAAATTTGAAAAACCATAGCTTTGTTCAAAATTTGAGAAATAAGGTAAAGCTAA
194 TCTTTTATATGAAAATTTGAAAAACCATAGCTTTGTTCAAAATTTGAGAAATAAGGTAAAGCTAA
* **
1317 CCCTTTTATGTTTTGAGACAAAATGGAGTGTCTGAGCTTAACATAGTTAAAGGATTTAGTTGGGT
259 CCCTTTTATGTTTTGAGACAAAATGGAGTGTCTGAGCTCAACATAGTTAAAGGATTTAGTCAGGT
* *
1382 TCCTAAGACATTCTTTTATTCTCCAATTCAATTCAAAGATATTGTAGAGAAAGTAAAGCAAATGG
324 TCCTAAAACATTCTCTTATTCTCCAATTCAATTCAAAGATATTGTAGAGAAAGTAAAGCAAATGG
*
1447 GGTTCAGTCCAGAGTGGTTTACTTTTATTTTAGCT
389 GGTTCAGTCCAGAGAGGTTTACTTTTATTTTAGCT
1482 A
1 A
1483 TTACTATTTT
Statistics
Matches: 409, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
422 1 0.00
423 327 0.80
424 81 0.20
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (423 bp):
AACCACAATTGCCTTTGCTGCATTCCTCTTCTCAGACCACTTCTAATAAGCTTCTGTCTTTCTTT
CACATCTTCTTCTTTTCCTTATCAAAATGACAACTTTAAAATATTTGGTAGAAACAACAATGGTA
GAAGAGACCTCCACAACAACGTAGGTAAACAAAAGCCCATTCTAAAAATTGAAAAAAAGACTTTC
TTTTATATGAAAATTTGAAAAACCATAGCTTTGTTCAAAATTTGAGAAATAAGGTAAAGCTAACC
CTTTTATGTTTTGAGACAAAATGGAGTGTCTGAGCTCAACATAGTTAAAGGATTTAGTCAGGTTC
CTAAAACATTCTCTTATTCTCCAATTCAATTCAAAGATATTGTAGAGAAAGTAAAGCAAATGGGG
TTCAGTCCAGAGAGGTTTACTTTTATTTTAGCT
Found at i:1893 original size:22 final size:19
Alignment explanation
Indices: 1859--1906 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
1849 AAATCAGAGT
* *
1859 AGGGGGAGGATGGTGGGGA
1 AGGGAGAGGATGGTAGGGA
1878 TCAGGGAGAGCGATGGTAGGGA
1 --AGGGAGAG-GATGGTAGGGA
1900 AGGGAGA
1 AGGGAGA
1907 TGAGAAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.27, C:0.04, G:0.58, T:0.10
Consensus pattern (19 bp):
AGGGAGAGGATGGTAGGGA
Done.