Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008967.1 Corchorus capsularis cultivar CVL-1 contig08988, 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: 12131
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:617 original size:6 final size:6
Alignment explanation
Indices: 579--613 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
569 CTCATTCTAG
* *
579 TTAAAA TTAAAA TTAAAA TTAAAA ATAAAT TTAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
614 TTTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TTAAAA
Found at i:4016 original size:133 final size:132
Alignment explanation
Indices: 3857--4275 Score: 572
Period size: 150 Copynumber: 3.0 Consensus size: 132
3847 ATCCTTTTAC
3857 AAAAATAAATCTTAAAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCCGAG
1 AAAAATAAATCTT-AAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCCGAG
3922 AAGTCAAGGATTAACATACCCTAATCCTTTTACAAAAAAAAAACAAAACAACGTGAACTAACACC
65 AAGTCAAGGATTAACATACCCTAATCCTTTTACAAAAAAAAAA-AAAACAACGTGAACTAACACC
3987 AACA
129 AACA
3991 AAAAATAAATCTTAAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCC-AGG
1 AAAAATAAATCTTAAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCCGA-G
4055 AAGTCAAGGATTAACATACCCTAATCCTTTTACAAAAATAAATCCTTTTATAAAAAAAAAAACAA
65 AAGTCAAGGATTAACATACCCTAATCCTTTTAC--------A-------A-AAAA-AAAAAA-AA
4120 CAACGTGAACTAACACCAACA
112 CAACGTGAACTAACACCAACA
* *
4141 GAAAATAAATCTTAAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCCGGGA
1 AAAAATAAATCTTAAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCCGAGA
* *
4206 AGTCAAGGATTAACATACCCTAATCTTTTTTTAC-AAAAAAAAAAAAACCACGTGAACTAACACC
66 AGTCAAGGATTAACATACCCTAATC--CTTTTACAAAAAAAAAAAAAACAACGTGAACTAACACC
*
4270 TACA
129 AACA
4274 AA
1 AA
4276 TTAAAATTCC
Statistics
Matches: 257, Mismatches: 6, Indels: 45
0.83 0.02 0.15
Matches are distributed among these distances:
132 1 0.00
133 104 0.40
134 19 0.07
135 4 0.02
136 1 0.00
141 1 0.00
148 1 0.00
149 6 0.02
150 114 0.44
152 6 0.02
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (132 bp):
AAAAATAAATCTTAAAAAAATAAAGAAAAAACGTAAACAAGCACCAACAAATTAAAATTCCGAGA
AGTCAAGGATTAACATACCCTAATCCTTTTACAAAAAAAAAAAAAACAACGTGAACTAACACCAA
CA
Found at i:10893 original size:2 final size:2
Alignment explanation
Indices: 10888--10922 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10878 TATATATATA
10888 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
10923 TTCGCTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Done.