Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003411.1 Corchorus capsularis cultivar CVL-1 contig03419, 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, 629
Length: 1049
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Found at i:66 original size:21 final size:20
Alignment explanation
Indices: 1--322 Score: 100
Period size: 21 Copynumber: 14.7 Consensus size: 20
1 AGTAATCAGTAAAAAGTAAGA-
1 AGTAATCAGT-AAAAGTAA-AT
** *
22 AGGTAATCAACAAGAGTAAAAT
1 A-GTAATCAGTAAAAGT-AAAT
*
44 AGTAGTCAGTAGAAAGTAAAT
1 AGTAATCAGTA-AAAGTAAAT
* *
65 AGTAATCAGTAAGAGTAAAAC
1 AGTAATCAGTAAAAGT-AAAT
* *
86 AATAATCGGTAAGAAGTAAA-
1 AGTAATCAGTAA-AAGTAAAT
**
106 AGGCGATCAGTAAAGAGTAAA-
1 A-GTAATCAGTAAA-AGTAAAT
*
127 AGGCTAATCAATAAGAAGTAAA-
1 A-G-TAATCAGTAA-AAGTAAAT
*
149 AGGTAATCAGTAAAAAGCAAA-
1 A-GTAATCAGT-AAAAGTAAAT
* *
170 AGGCAATCAGTAAAAGGTAAAAC
1 A-GTAATCAGTAAAA-GT-AAAT
193 AGTAATCAGTAAAAAAAGGAGTAGAAAAT
1 AGTAATCAGT----AAA--AGT---AAAT
*
222 AGTAATCACTAAAAGAGTAAA-
1 AGTAATCAGT-AAA-AGTAAAT
243 AGGGTAATCAGTAAAAAGTAAGA-
1 A--GTAATCAGT-AAAAGTAA-AT
** *
266 AGGTAATCAACAAGAGTAAAAT
1 A-GTAATCAGTAAAAGT-AAAT
*
288 AGTAATCAGTACAAAGTAAAG
1 AGTAATCAGTA-AAAGTAAAT
*
309 AATAATCAGTAAAA
1 AGTAATCAGTAAAA
323 TAGTGATGGT
Statistics
Matches: 237, Mismatches: 36, Indels: 57
0.72 0.11 0.17
Matches are distributed among these distances:
20 13 0.05
21 112 0.47
22 69 0.29
23 16 0.07
25 4 0.02
26 7 0.03
27 2 0.01
28 1 0.00
29 13 0.05
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (20 bp):
AGTAATCAGTAAAAGTAAAT
Found at i:135 original size:43 final size:43
Alignment explanation
Indices: 3--205 Score: 143
Period size: 43 Copynumber: 4.7 Consensus size: 43
1 AG
* * *
3 TAATCAGTAAAAAGTAAGAAGGTAATCA--ACAAGAGTAAAATAG-
1 TAATCAGTAAGAAGTAA-AAGGCAATCAGTA-AAGAGTAAAA-GGC
* * ***
46 TAGTCAGT-AGAAAGTAAATA-GTAATCAGT-AAGAGTAAAACAA
1 TAATCAGTAAG-AAGTAAA-AGGCAATCAGTAAAGAGTAAAAGGC
* *
88 TAATCGGTAAGAAGTAAAAGGCGATCAGTAAAGAGTAAAAGGC
1 TAATCAGTAAGAAGTAAAAGGCAATCAGTAAAGAGTAAAAGGC
* * * *
131 TAATCAATAAGAAGTAAAAGGTAATCAGTAAAAAGCAAAAGGC
1 TAATCAGTAAGAAGTAAAAGGCAATCAGTAAAGAGTAAAAGGC
* *
174 -AATCAGTAA-AAGGTAAAACAGTAATCAGTAAA
1 TAATCAGTAAGAA-GTAAAA-GGCAATCAGTAAA
206 AAAAGGAGTA
Statistics
Matches: 131, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
41 3 0.02
42 53 0.40
43 75 0.57
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.18
Consensus pattern (43 bp):
TAATCAGTAAGAAGTAAAAGGCAATCAGTAAAGAGTAAAAGGC
Found at i:135 original size:64 final size:64
Alignment explanation
Indices: 49--204 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
39 AAAATAGTAG
* * * * *
49 TCAGTAGAAA-GT-AAATAGTAATCAGTAAG-AGTAAAACAATAATCGGTAAGAAGTAAAAGGCG
1 TCAGTA-AAAGGTAAAACAGTAATCAGTAAGAAGTAAAA-AATAATCAGTAAAAAGCAAAAGGCA
111 A
64 A
* * **
112 TCAGT-AAAGAGTAAAA-GGCTAATCAATAAGAAGTAAAAGGTAATCAGTAAAAAGCAAAAGGCA
1 TCAGTAAAAG-GTAAAACAG-TAATCAGTAAGAAGTAAAAAATAATCAGTAAAAAGCAAAAGGCA
175 A
64 A
176 TCAGTAAAAGGTAAAACAGTAATCAGTAA
1 TCAGTAAAAGGTAAAACAGTAATCAGTAA
205 AAAAAGGAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
61 3 0.04
63 8 0.11
64 53 0.70
65 12 0.16
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (64 bp):
TCAGTAAAAGGTAAAACAGTAATCAGTAAGAAGTAAAAAATAATCAGTAAAAAGCAAAAGGCAA
Done.