Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012072.1 Kokia drynarioides strain JFW-HI SEQ_127070, 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: 1736
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.40
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:580 original size:19 final size:18
Alignment explanation
Indices: 558--594 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
548 ATTAAAAAGT
558 CGAGAAAAAAAGAAAAATA
1 CGAGAAAAAAA-AAAAATA
*
577 CGAGAAAAATAAAAAATA
1 CGAGAAAAAAAAAAAATA
595 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (18 bp):
CGAGAAAAAAAAAAAATA
Found at i:584 original size:18 final size:19
Alignment explanation
Indices: 558--594 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
548 ATTAAAAAGT
558 CGAGAAAAAA-AGAAAAATA
1 CGAGAAAAAATA-AAAAATA
577 CGAG-AAAAATAAAAAATA
1 CGAGAAAAAATAAAAAATA
595 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (19 bp):
CGAGAAAAAATAAAAAATA
Found at i:1727 original size:741 final size:689
Alignment explanation
Indices: 307--1736 Score: 2033
Period size: 741 Copynumber: 2.0 Consensus size: 689
297 CAATCCTCTT
307 CCGCCTCTTCCGCCCGCTTTTCGTATCATTTGGTATCAGATTTTGGGCGTTTTAGGTGTTCTTCG
1 CCGCCTCTTCCGCCCGCTTTTCGTATCATTTGGTATCAGATTTTGGGCGTTTTAGGTGTTCTTCG
372 TTGCTTTCTAAACTGATTTCCATTACAAATAGCCAACAAGCAGTTTTTACCTAGTAATTTTTTCG
66 TTGCTTTCTAAACTGATTTCCATTACAAATAGCCAACAAGCAGTTTTTACCTAGTAATTTTTTCG
*
437 GAAAAAAAAATATTTTTGAGTGGTAAACGTTTTTCAATTGTTCTAAAATTTTATATACTGATTCT
131 GAAAAAAAAATATTTTTGAGTGGTAAACGTTTTTCAATTGTTCTAAAATTTTATATACTAATTCT
502 TGGCACTATATTACAGTATAAAAAAATATTTTCCACAAAAAAAGTGATTAAAAAGTCGAGAAAAA
196 TGGCACTATATTACAGTATAAAAAAATATTTTCCACAAAAAAAGTGATTAAAAAGTCGAGAAAAA
567 AAGAAAAATACGAGAAAAATAAAAAATAAAAAAAATATTTTGTGGGTTGAATTTTGTGCCAAAAA
261 AAGAAAAATACGAGAAAAATAAAAAATAAAAAAAATATTTTGTGGGTTGAATTTTGTGCCAAAAA
632 TTTCCATATCAAAAACACATTATTTGGAGAGGATCAAATTTAAATTTAGTGATTTTTGGAAATCA
326 TTTCCATATCAAAAACACATTATTTGGAGAGGATCAAATTTAAATTTAGTGATTTTTGGAAATCA
*
697 AGAACACCTCGAACGAAGTTTGTCAACTTGCTTCACAGTTTTTGGGTTTTAGGATTTCTGCAATT
391 AGAACACCTCGAACGAAGTTTGTCAACTTGCTTCACAGTTTCTGGGTTTTAGGATTTCTGCAATT
762 TTATTGATTCTTAGTTTTAGGTATTAATTTGTTTTTGCTTTTTATTTTTTCTTTTATACATTTTA
456 TTATTGATTCTTAGTTTTAGGTATTAATTTGTTTTTGCTTTTTATTTTTTCTTTTATACATTTTA
827 ACACTTTCTTATTTCTTGTGTTTGTAGGATTAATGAAAGTTGCACCTTCCTTCCTCCGTGCAACA
521 ACACTTTCTTATTTCTTGTGTTTGTAGGATTAATGAAAGTTGCACCTTCCTTCCTCCGTGCAACA
892 CAAATTCTTTGGTGTCTAGTTGATTTTGGATTCATAGTGCTATTAGGATTACTTTGTTAGTTTGA
586 CAAATTCTTTGGTGTCTAGTTGATTTTGGATTCATAGTGCTATTAGGATTACTTTGTTAGTTTGA
957 TTCTAATACATCCTGATTGATTGACATAAATACTTCTAA
651 TTCTAATACATCCTGATTGATTGACATAAATACTTCTAA
************* * ****
996 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCGCCTCTTCCGCCC
1 -------------------------------------CCGCCTCTTCCGCCCG-CTTTTCGTATC
** ** ** * * * *
1061 GCTT--T-TC-GTATCATTT-GGTATCAGATTTTGGGCGTTTTAGGTGTTCTTCGTTGCTTTCTA
28 ATTTGGTATCAG-AT--TTTGGGCGT--TTTA----G-G---T-GTTCTTCG---TTGCTTTCTA
*
1121 AACTGATTTTCATTACAAATAGCCAACAAGCAGTTTTTACCTAGTAATTTTTTCGGAAAAAAAAA
76 AACTGATTTCCATTACAAATAGCCAACAAGCAGTTTTTACCTAGTAATTTTTTCGGAAAAAAAAA
1186 TATTTTTGAGTGGGTAAACGTTTTTCAATTGTTCTAAAATTTTATATACTAATTCTTGGCACTAT
141 TATTTTTGAGT-GGTAAACGTTTTTCAATTGTTCTAAAATTTTATATACTAATTCTTGGCACTAT
1251 ATTACAGTATAAAAAAATATTTTCCACAAAAAAAGTGATTAAAAAGTCGAGAAAAAAAAGAAAAA
205 ATTACAGTATAAAAAAATATTTTCCACAAAAAAAGTGATTAAAAAGTCGAG-AAAAAAAGAAAAA
1316 TACGAGAAAAATAAAAAATAAAAAAAATATTTTGTGGGTTGAATTTTGTGCCAAAAATTTCCATA
269 TACGAGAAAAATAAAAAATAAAAAAAATATTTTGTGGGTTGAATTTTGTGCCAAAAATTTCCATA
1381 TCAAAAACACATTATTTGGAGAGGATCAAATTTAAATTTAGTGATTTTTGGAAATCAAGAACACC
334 TCAAAAACACATTATTTGGAGAGGATCAAATTTAAATTTAGTGATTTTTGGAAATCAAGAACACC
1446 TCGAACGAAGTTTGTCAACTTGCTTCACAGTTTCTGGGTTTTAGGATTTCTGCAATTTTATTGAT
399 TCGAACGAAGTTTGTCAACTTGCTTCACAGTTTCTGGGTTTTAGGATTTCTGCAATTTTATTGAT
1511 TCTTAGTTTTAGGTATTAATTTGTTTTTGCTTTTTATTTTTTCTTTTATACATTTTAACACTTTC
464 TCTTAGTTTTAGGTATTAATTTGTTTTTGCTTTTTATTTTTTCTTTTATACATTTTAACACTTTC
1576 TTATTTCTTGTGTTTGTAGGATTAATGAAAGTTGCACCTTCCTTCCTCCGTGCAACACAAATTCT
529 TTATTTCTTGTGTTTGTAGGATTAATGAAAGTTGCACCTTCCTTCCTCCGTGCAACACAAATTCT
1641 TTGGTGTCTAGTTGATTTTGGATTCATAGTGCTATTAGGATTACTTTGTTAGTTTGATTCTAATA
594 TTGGTGTCTAGTTGATTTTGGATTCATAGTGCTATTAGGATTACTTTGTTAGTTTGATTCTAATA
1706 CATCCTGATTGATTGACATAAATACTTCTAA
659 CATCCTGATTGATTGACATAAATACTTCTAA
Statistics
Matches: 653, Mismatches: 31, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
723 1 0.00
724 4 0.01
725 4 0.01
726 6 0.01
727 9 0.01
731 1 0.00
732 1 0.00
735 1 0.00
736 5 0.01
739 85 0.13
740 103 0.16
741 433 0.66
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.39
Consensus pattern (689 bp):
CCGCCTCTTCCGCCCGCTTTTCGTATCATTTGGTATCAGATTTTGGGCGTTTTAGGTGTTCTTCG
TTGCTTTCTAAACTGATTTCCATTACAAATAGCCAACAAGCAGTTTTTACCTAGTAATTTTTTCG
GAAAAAAAAATATTTTTGAGTGGTAAACGTTTTTCAATTGTTCTAAAATTTTATATACTAATTCT
TGGCACTATATTACAGTATAAAAAAATATTTTCCACAAAAAAAGTGATTAAAAAGTCGAGAAAAA
AAGAAAAATACGAGAAAAATAAAAAATAAAAAAAATATTTTGTGGGTTGAATTTTGTGCCAAAAA
TTTCCATATCAAAAACACATTATTTGGAGAGGATCAAATTTAAATTTAGTGATTTTTGGAAATCA
AGAACACCTCGAACGAAGTTTGTCAACTTGCTTCACAGTTTCTGGGTTTTAGGATTTCTGCAATT
TTATTGATTCTTAGTTTTAGGTATTAATTTGTTTTTGCTTTTTATTTTTTCTTTTATACATTTTA
ACACTTTCTTATTTCTTGTGTTTGTAGGATTAATGAAAGTTGCACCTTCCTTCCTCCGTGCAACA
CAAATTCTTTGGTGTCTAGTTGATTTTGGATTCATAGTGCTATTAGGATTACTTTGTTAGTTTGA
TTCTAATACATCCTGATTGATTGACATAAATACTTCTAA
Done.