Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005831.1 Corchorus capsularis cultivar CVL-1 contig05849, 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, 844
Length: 1408
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Found at i:273 original size:15 final size:15
Alignment explanation
Indices: 250--279 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
240 ATCGGTTGAA
*
250 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
265 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
280 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:997 original size:22 final size:21
Alignment explanation
Indices: 953--996 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
943 GGAATCTGGA
953 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
* *
974 TTGCTAAATACCGCTCCCCTT
1 TTGCTAAACACCGCCCCCCTT
995 TT
1 TT
997 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:1096 original size:10 final size:10
Alignment explanation
Indices: 1083--1108 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1073 CATTTCTAAC
1083 AACTTCTTCA
1 AACTTCTTCA
1093 AACTTCTTCA
1 AACTTCTTCA
1103 AACTTC
1 AACTTC
1109 ATTTCTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:1170 original size:22 final size:22
Alignment explanation
Indices: 1145--1262 Score: 60
Period size: 26 Copynumber: 4.8 Consensus size: 22
1135 TCCTTCATTT
1145 TAATCATAAACTAATTAAATAC
1 TAATCATAAACTAATTAAATAC
*
1167 TAATTAATCATAAACTAATTAGATAC
1 ----TAATCATAAACTAATTAAATAC
*
1193 TAATTAAACATAAACTAA-TAAACTAAG
1 TAA-T---CATAAACTAATTAAA-T-AC
* *
1220 TAATTTTAATTAACTAATTAAA-AC
1 TAA---TCATAAACTAATTAAATAC
1244 TAATCATAAAACTAATTAA
1 TAATCAT-AAACTAATTAA
1263 TATTAAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
21 3 0.04
22 13 0.18
23 1 0.01
24 4 0.05
25 3 0.04
26 40 0.54
27 8 0.11
29 2 0.03
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATCATAAACTAATTAAATAC
Found at i:1173 original size:26 final size:26
Alignment explanation
Indices: 1144--1211 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
1134 TTCCTTCATT
1144 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
1170 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
1196 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
1212 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:1174 original size:15 final size:15
Alignment explanation
Indices: 1144--1211 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
1134 TTCCTTCATT
1144 TTAATCATAAACTAA
1 TTAATCATAAACTAA
1159 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
1170 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
1185 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
1196 TTAAACATAAACTAA
1 TTAATCATAAACTAA
1211 T
1 T
1212 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Done.