Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008922.1 Kokia drynarioides strain JFW-HI SEQ_123613, 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: 5289
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:486 original size:26 final size:26
Alignment explanation
Indices: 457--511 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
447 CACCCAGGAA
*
457 TGTCGCTGCATTAACATGTCCAAAAT
1 TGTCGCTGCATGAACATGTCCAAAAT
*
483 TGTCGCTGCATGAACGTGTCCAAAAT
1 TGTCGCTGCATGAACATGTCCAAAAT
509 TGT
1 TGT
512 GCCCAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAAAAT
Found at i:1621 original size:26 final size:26
Alignment explanation
Indices: 1516--1615 Score: 121
Period size: 26 Copynumber: 3.8 Consensus size: 26
1506 GACTAGGGCG
*
1516 CAATTCTTGACATGCTCATGCAGTGA
1 CAATTCTGGACATGCTCATGCAGTGA
* *
1542 CAACTCTGGACATGTTCATGCAGTGA
1 CAATTCTGGACATGCTCATGCAGTGA
* * * *
1568 TAATTCTGGACAAGTTTC-TACAGTGA
1 CAATTCTGGACATG-CTCATGCAGTGA
1594 CAATTCTGGACATGCTCATGCA
1 CAATTCTGGACATGCTCATGCA
1616 ACGACATTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
25 2 0.03
26 56 0.92
27 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (26 bp):
CAATTCTGGACATGCTCATGCAGTGA
Found at i:4290 original size:356 final size:356
Alignment explanation
Indices: 3637--4324 Score: 1333
Period size: 356 Copynumber: 1.9 Consensus size: 356
3627 GCACCCTTGT
**
3637 TTTCTACTGTTGCTTTTCACTTTCTTTTTCTTGTATCTGCTTCCTTTACTGTGGGAATATCTGTC
1 TTTCTACTGTTGCTTTTCACTTTCTTTTTCTTGTATCTGCTTCCTTTACTGTGGGAATATCTAAC
3702 CCTCAAGTCATTCTTTCGATTAATGCTTCATTTATAAAGCCCTTGTTCTCCAAGATCTCTTCTCC
66 CCTCAAGTCATTCTTTCGATTAATGCTTCATTTATAAAGCCCTTGTTCTCCAAGATCTCTTCTCC
3767 ATCACGGGGTACAACTCCCCTTTGCTGGCACAACTGCACTACCAGTGAGGGAAACACAAATATTC
131 ATCACGGGGTACAACTCCCCTTTGCTGGCACAACTGCACTACCAGTGAGGGAAACACAAATATTC
3832 CCCTTTGTCTGGTAGCACAGTCAGTAATCTCTTAGTGCAATATTGCCTCGACATCAATTTTTCTT
196 CCCTTTGTCTGGTAGCACAGTCAGTAATCTCTTAGTGCAATATTGCCTCGACATCAATTTTTCTT
3897 CCCTTAATGATGGAATGTATCAGACACATTCGATCAAAGGTGACAGTTGTTCTATGTGTTGAAGG
261 CCCTTAATGATGGAATGTATCAGACACATTCGATCAAAGGTGACAGTTGTTCTATGTGTTGAAGG
3962 CAACAATAAGAAAATGCTAAAATATAACAAG
326 CAACAATAAGAAAATGCTAAAATATAACAAG
3993 TTTCTACTGTTGCTTTTCACTTTCTTTTTCTTGTATCTGCTTCCTTTACTGTGGGAATATCTAAC
1 TTTCTACTGTTGCTTTTCACTTTCTTTTTCTTGTATCTGCTTCCTTTACTGTGGGAATATCTAAC
4058 CCTCAAGTCATTCTTTCGATTAATGCTTCATTTATAAAGCCCTTGTTCTCCAAGATCTCTTCTCC
66 CCTCAAGTCATTCTTTCGATTAATGCTTCATTTATAAAGCCCTTGTTCTCCAAGATCTCTTCTCC
*
4123 ATCACGGGGTACAACTCCCCTTTGCTGGCACAACTGCATTACCAGTGAGGGAAACACAAATATTC
131 ATCACGGGGTACAACTCCCCTTTGCTGGCACAACTGCACTACCAGTGAGGGAAACACAAATATTC
4188 CCCTTTGTCTGGTAGCACAGTCAGTAATCTCTTAGTGCAATATTGCCTCGACAT-AAGTTTTTCT
196 CCCTTTGTCTGGTAGCACAGTCAGTAATCTCTTAGTGCAATATTGCCTCGACATCAA-TTTTTCT
4252 TCCCTTAATGATGGAATGTATCAGACACATTCGATCAAAGGTGACAGTTGTTCTATGTGTTGAAG
260 TCCCTTAATGATGGAATGTATCAGACACATTCGATCAAAGGTGACAGTTGTTCTATGTGTTGAAG
4317 GCAACAAT
325 GCAACAAT
4325 CTGCAGTTCA
Statistics
Matches: 328, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
355 2 0.01
356 326 0.99
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (356 bp):
TTTCTACTGTTGCTTTTCACTTTCTTTTTCTTGTATCTGCTTCCTTTACTGTGGGAATATCTAAC
CCTCAAGTCATTCTTTCGATTAATGCTTCATTTATAAAGCCCTTGTTCTCCAAGATCTCTTCTCC
ATCACGGGGTACAACTCCCCTTTGCTGGCACAACTGCACTACCAGTGAGGGAAACACAAATATTC
CCCTTTGTCTGGTAGCACAGTCAGTAATCTCTTAGTGCAATATTGCCTCGACATCAATTTTTCTT
CCCTTAATGATGGAATGTATCAGACACATTCGATCAAAGGTGACAGTTGTTCTATGTGTTGAAGG
CAACAATAAGAAAATGCTAAAATATAACAAG
Done.