Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019144.1 Corchorus olitorius cultivar O-4 contig19177, 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: 5171
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Found at i:1957 original size:11 final size:11
Alignment explanation
Indices: 1941--1965 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1931 ACTCTTTTAG
1941 TGTTTTTCTCT
1 TGTTTTTCTCT
1952 TGTTTTTCTCT
1 TGTTTTTCTCT
1963 TGT
1 TGT
1966 CTCCGGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (11 bp):
TGTTTTTCTCT
Found at i:2680 original size:58 final size:58
Alignment explanation
Indices: 2584--2698 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
2574 ATTAATCAAA
*
2584 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * *
2642 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCAAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGC
2699 ATGATGCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:4012 original size:36 final size:36
Alignment explanation
Indices: 3965--4034 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3955 TTCAATAACC
* *
3965 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
4001 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
4035 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:4920 original size:205 final size:204
Alignment explanation
Indices: 4550--4965 Score: 676
Period size: 203 Copynumber: 2.0 Consensus size: 204
4540 GCTTAATAAC
* *
4550 TTTATGAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAAAAAAGTTGTAGTGAATAA
* * *
4615 GATACAATATATTATTATTATATATATAACTATATCAAAAAAAAAGTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTATATATATAACTATATCAAAAAAAAAGTAGTTGAACATTAGTGGTT
4680 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-A-AAAGATATTAAAG
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAGATATT-AAG
*
4743 ATCCGATTTA
195 ACCCGATTTA
* *
4753 TTTATCAATGGTGAATGTTATTAATTTTTTAATTCTAAGATTACTAAAAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAAAAAAGTTGTAGTGAATAA
*
4818 GATACAACACATTACTATTATATATATAGAACTATA-CAAAAAAAAAATTAGTTGAACATTAGTG
66 GATACAACACATTACTATTATATATAT--AACTATATC-AAAAAAAAAGTAGTTGAACATTAGTG
4882 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAATTAAAGATAT
128 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-AA-TAAAGATAT
4947 TAAGACCCGATTTA
191 TAAGACCCGATTTA
4961 TTTAT
1 TTTAT
4966 TATTAAGGAA
Statistics
Matches: 197, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
203 85 0.43
204 1 0.01
205 84 0.43
207 1 0.01
208 17 0.09
209 9 0.05
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (204 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAAAAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATATCAAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAGATATTAAGA
CCCGATTTA
Done.