Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011310.1 Kokia drynarioides strain JFW-HI SEQ_126290, 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: 4949
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Found at i:821 original size:29 final size:29
Alignment explanation
Indices: 775--1364 Score: 324
Period size: 29 Copynumber: 20.1 Consensus size: 29
765 CCCTGGAGGT
*
775 CCCT-AAACCTTCC-AAAATTGCCATTTTA
1 CCCTCAAA-CTTCCAAAAATTCCCATTTTA
803 CCCTCAAACTTCCAAAAA-TCCCATTTTAAA
1 CCCTCAAACTTCCAAAAATTCCCATTTT--A
* * *
833 CCCTGAACCTTCCAAAAATTACCATTTTA
1 CCCTCAAACTTCCAAAAATTCCCATTTTA
* * * *
862 CCCCCAAACTTTCAAAAAATCTCATTTTGA
1 CCCTCAAACTTCCAAAAATTCCCATTTT-A
* *** *
892 CCC-CGAACCTGGTAAAAATTACCATTTTAA
1 CCCTC-AAACTTCCAAAAATTCCCATTTT-A
* *
922 CCC-CGAACTTCCAAAAAATCCCATTTTGA
1 CCCTCAAACTTCCAAAAATTCCCATTTT-A
* * *
951 CCC-CGAACCTTCCAAAAATTACTATTTTA
1 CCCTC-AAACTTCCAAAAATTCCCATTTTA
*
980 CCCTCGAACTTCCAAAAA-TCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCCA-TTTT-A
* * **
1010 CCC-CGAACCTCCCAAAAAATT-TTATTTTA
1 CCCTC-AAACTTCC-AAAAATTCCCATTTTA
*
1039 CACCTCGAACTTCCAAAAA--CCCATTTTTAA
1 C-CCTCAAACTTCCAAAAATTCCCA-TTTT-A
* * *
1069 CCC-CGAACCTTCAAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTCCCATTTTA
* * *
1098 CCCCCGAACTTCCAAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCCA-TTTT-A
**
1129 CCC-CAAACCTTCCAAAAATGACCATTTTA
1 CCCTCAAA-CTTCCAAAAATTCCCATTTTA
* *
1158 CCCTCAAACTTCTAAAAAGTCCCATTTTTTA
1 CCCTCAAACTTCCAAAAATTCCCA--TTTTA
* *
1189 CCC-CAAGCCTTCC--AAAGTCCCATTTTTTA
1 CCCTCAA-ACTTCCAAAAATTCCCA--TTTTA
* ** **
1218 CTCC-GAGCCTTCCAAAAATGACCATTTTA
1 C-CCTCAAACTTCCAAAAATTCCCATTTTA
* * *
1247 CCCCCGAACTTCC-AAAAGTCCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCCA-TTTTA
*
1276 CCCT-AAACCTTCCAAAAATTACCA-TTTA
1 CCCTCAAA-CTTCCAAAAATTCCCATTTTA
*
1304 CCCTCGAACTTCCAAAAA-TCCCATTCTTGA
1 CCCTCAAACTTCCAAAAATTCCCATT-TT-A
* * *
1334 CCCTGAACCTTCC-AAAATTACCATTTTA
1 CCCTCAAACTTCCAAAAATTCCCATTTTA
1362 CCC
1 CCC
1365 CCGAACATTT
Statistics
Matches: 433, Mismatches: 87, Indels: 84
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.01
28 56 0.13
29 185 0.43
30 134 0.31
31 53 0.12
32 1 0.00
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.29
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCCATTTTA
Found at i:871 original size:59 final size:59
Alignment explanation
Indices: 780--1204 Score: 513
Period size: 59 Copynumber: 7.2 Consensus size: 59
770 GAGGTCCCTA
* * ** *
780 AACCTTCC-AAAATTGCCATTTTACCCTCAAACTTCCAAAAATCCCATTTTAAACCCTG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
838 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTTCAAAAAATCTCA-TTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAAATCCCATTTTTGACCCCG
***
897 AACCTGGTAAAAATTACCATTTTAACCC-CGAACTTCCAAAAAATCCCA-TTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTT-ACCCTCGAACTTCC-AAAAATCCCATTTTTGACCCCG
*
956 AACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* ** *
1015 AACCTCCCAAAAAATT-TTATTTTACACCTCGAACTTCCAAAAA-CCCATTTTTAACCCCG
1 AACCTTCC-AAAAATTACCATTTTAC-CCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
1074 AACCTTCAAAAAATTACCATTTTACCCCCGAACTTCCAAAAAATCCCATTTTTGACCCCA
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCC-AAAAATCCCATTTTTGACCCCG
* * * *
1134 AACCTTCCAAAAATGACCATTTTACCCTCAAACTTCTAAAAAGTCCCATTTTTTACCCC-
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAA-TCCCATTTTTGACCCCG
1193 AAGCCTTCCAAA
1 AA-CCTTCCAAA
1205 GTCCCATTTT
Statistics
Matches: 321, Mismatches: 33, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
58 43 0.13
59 168 0.52
60 110 0.34
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.28
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:3911 original size:30 final size:30
Alignment explanation
Indices: 3875--3937 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
3865 GCTTGTTCTT
3875 CCTAATACAATAAATTAGGTTGAATTTCAA
1 CCTAATACAATAAATTAGGTTGAATTTCAA
*
3905 CCTAATACGATAAATTAGGTTGAATTTCAA
1 CCTAATACAATAAATTAGGTTGAATTTCAA
3935 CCT
1 CCT
3938 CTTTTGCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (30 bp):
CCTAATACAATAAATTAGGTTGAATTTCAA
Done.