Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003247.1 Kokia drynarioides strain JFW-HI SEQ_115897, 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: 2305
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Found at i:395 original size:29 final size:29
Alignment explanation
Indices: 352--518 Score: 116
Period size: 28 Copynumber: 5.8 Consensus size: 29
342 AGAAGGTCCC
352 TAAAC-TCTCTAAAAATTACATTTTGACCCT
1 TAAACTTCTC-AAAAATTACATTTTGA-CCT
* *
382 TAAACTTCTCAAAAATTAAATTTTTACCT
1 TAAACTTCTCAAAAATTACATTTTGACCT
** * *
411 CGAACTTC-CAAAAATTACATTTTGCCCC
1 TAAACTTCTCAAAAATTACATTTTGACCT
** * *
439 CGAACTT-TCCAAAATTTACCATTAT-ATCC-
1 TAAACTTCT-CAAAAATTA-CATTTTGA-CCT
*
468 -AAACTTCTAAAAAATTACATTTTTG-CCT
1 TAAACTTCTCAAAAATTACA-TTTTGACCT
*
496 TAAACTT-TCAAAAATTATATTTT
1 TAAACTTCTCAAAAATTACATTTT
519 TGCCCTTTGC
Statistics
Matches: 110, Mismatches: 17, Indels: 23
0.73 0.11 0.15
Matches are distributed among these distances:
27 8 0.07
28 48 0.44
29 24 0.22
30 26 0.24
31 4 0.04
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAACTTCTCAAAAATTACATTTTGACCT
Found at i:583 original size:29 final size:29
Alignment explanation
Indices: 535--905 Score: 222
Period size: 29 Copynumber: 12.8 Consensus size: 29
525 TTGCCCCCGG
*** *
535 TGTCCAAAAATTATTGTTTTACCCTCGGA
1 TGTCCAAAAATTACCATTTTACCCTCGAA
**
564 TGTCCAAAAATTACCATTTTAGCCC-AAAA
1 TGTCCAAAAATTACCATTTTA-CCCTCGAA
** * * * *
593 CATCTAAAAATTACTATTTTACCCCCGGA
1 TGTCCAAAAATTACCATTTTACCCTCGAA
* * *
622 TGTCCAAAAATTA-AATTTTTAACCTTGAA
1 TGTCCAAAAATTACCA-TTTTACCCTCGAA
* * *
651 CTTTCC-AAAATTACCATTTTATCC-CGGA
1 -TGTCCAAAAATTACCATTTTACCCTCGAA
*
679 TGTCCAAAAATTA-CATTTTTAACCCT-AAA
1 TGTCCAAAAATTACCA-TTTT-ACCCTCGAA
* *
708 CTTTCCAAAAATTACCATTTTACCCCCGAA
1 -TGTCCAAAAATTACCATTTTACCCTCGAA
* * * * *
738 TATCTAAAAATCACAATTTTGCCCTCGAA
1 TGTCCAAAAATTACCATTTTACCCTCGAA
* * * *
767 CT-TTCAAAAACTACCGTTTTACCCCCGAA
1 -TGTCCAAAAATTACCATTTTACCCTCGAA
** *
796 CATCCAAAAATTACCATTTTACCCTTGAA
1 TGTCCAAAAATTACCATTTTACCCTCGAA
** * * *
825 CATCCAAAAATTGCCATTTT--GCTCCAA
1 TGTCCAAAAATTACCATTTTACCCTCGAA
* *
852 GTGTCCAAAAATTATCATTTTACCCTCGGA
1 -TGTCCAAAAATTACCATTTTACCCTCGAA
*
882 TGTCCCAAAATTACTC-TTTTACCC
1 TGTCCAAAAATTAC-CATTTTACCC
906 CCGGGTATCT
Statistics
Matches: 258, Mismatches: 66, Indels: 36
0.72 0.18 0.10
Matches are distributed among these distances:
27 10 0.04
28 33 0.13
29 181 0.70
30 32 0.12
31 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (29 bp):
TGTCCAAAAATTACCATTTTACCCTCGAA
Found at i:975 original size:29 final size:29
Alignment explanation
Indices: 537--979 Score: 124
Period size: 29 Copynumber: 15.3 Consensus size: 29
527 GCCCCCGGTG
** **
537 TCCAAAAATTATTGTTTTACCCTCGGATG
1 TCCAAAAATTATCATTTTACCCTCGGACA
* ***
566 TCCAAAAATTACCATTTTAGCCC-AAAACA
1 TCCAAAAATTATCATTTTA-CCCTCGGACA
* * **
595 TCTAAAAATTA-CTATTTTACCCCCGGATG
1 TCCAAAAATTATC-ATTTTACCCTCGGACA
* * * * *
624 TCCAAAAATTA-AATTTTTAACCTTGAACTT
1 TCCAAAAATTATCA-TTTTACCCTCGGAC-A
* * **
654 TCC-AAAATTACCATTTTATCC-CGGATG
1 TCCAAAAATTATCATTTTACCCTCGGACA
** *
681 TCCAAAAATTA-CATTTTTAACCCT-AAACTT
1 TCCAAAAATTATCA-TTTT-ACCCTCGGAC-A
* * * *
711 TCCAAAAATTACCATTTTACCCCCGAATA
1 TCCAAAAATTATCATTTTACCCTCGGACA
* * * * *
740 TCTAAAAATCA-CAATTTTGCCCTCGAACT
1 TCCAAAAATTATC-ATTTTACCCTCGGACA
* * * * * *
769 TTCAAAAACTACCGTTTTACCCCCGAACA
1 TCCAAAAATTATCATTTTACCCTCGGACA
* * *
798 TCCAAAAATTACCATTTTACCCTTGAACA
1 TCCAAAAATTATCATTTTACCCTCGGACA
** * **
827 TCCAAAAATTGCCATTTTGCTCCAAGTG---
1 TCCAAAAATTATCATTTTAC-CCTCG-GACA
**
855 TCCAAAAATTATCATTTTACCCTCGGATG
1 TCCAAAAATTATCATTTTACCCTCGGACA
* * **
884 TCCCAAAATTACTC-TTTTACCCCCGGGTA
1 TCCAAAAATTA-TCATTTTACCCTCGGACA
* * * *
913 TCTAAAAA--ATGCATTTTTGCCC-CGAACT
1 TCCAAAAATTAT-CA-TTTTACCCTCGGACA
* * *
941 TTCAAAAATTATCATTTTGCCCTCGGGCA
1 TCCAAAAATTATCATTTTACCCTCGGACA
970 TCCAAAAATT
1 TCCAAAAATT
980 GCATATTTGA
Statistics
Matches: 304, Mismatches: 83, Indels: 54
0.69 0.19 0.12
Matches are distributed among these distances:
26 2 0.01
27 10 0.03
28 52 0.17
29 206 0.68
30 32 0.11
31 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTACCCTCGGACA
Found at i:978 original size:86 final size:85
Alignment explanation
Indices: 711--979 Score: 265
Period size: 86 Copynumber: 3.1 Consensus size: 85
701 CCCTAAACTT
*
711 TCCAAAAATTACCATTTTACCCCCGAATATCT-AAAAATCACAATTTTGCCCTCGAACTTTCAAA
1 TCCAAAAATTACCATTTTACCCCCGAATATCTAAAAAAT-GC-ATTTTGCCC-CGAACTTTCAAA
* * * * *
775 AACTACCGTTTTACCCCCGAACA
63 AATTATCATTTTACCCTCGGACA
** * * * * * *
798 TCCAAAAATTACCATTTTACCCTTGAACATCCAAAAATTGCCATTTTGCTCC-AAGTGTCCAAAA
1 TCCAAAAATTACCATTTTACCCCCGAATATCTAAAAAATG-CATTTTGCCCCGAACT-TTCAAAA
**
862 ATTATCATTTTACCCTCGGATG
64 ATTATCATTTTACCCTCGGACA
* **
884 TCCCAAAATTACTC-TTTTACCCCCGGGTATCTAAAAAATGCATTTTTGCCCCGAACTTTCAAAA
1 TCCAAAAATTAC-CATTTTACCCCCGAATATCTAAAAAATGCA-TTTTGCCCCGAACTTTCAAAA
* *
948 ATTATCATTTTGCCCTCGGGCA
64 ATTATCATTTTACCCTCGGACA
970 TCCAAAAATT
1 TCCAAAAATT
980 GCATATTTGA
Statistics
Matches: 144, Mismatches: 32, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
85 5 0.03
86 93 0.65
87 40 0.28
88 6 0.04
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.31
Consensus pattern (85 bp):
TCCAAAAATTACCATTTTACCCCCGAATATCTAAAAAATGCATTTTGCCCCGAACTTTCAAAAAT
TATCATTTTACCCTCGGACA
Done.