Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012089.1 Corchorus capsularis cultivar CVL-1 contig12110, 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: 30552
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1752 original size:18 final size:19
Alignment explanation
Indices: 1707--1754 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1697 AAAGTTTTTC
*
1707 TTTTCTTTTCTGCCCTAAA
1 TTTTATTTTCTGCCCTAAA
*
1726 TTTTTTTTTCT-CCC-AAA
1 TTTTATTTTCTGCCCTAAA
1743 TTCTTATTTTCT
1 TT-TTATTTTCT
1755 TCTTTTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.19
18 11 0.42
19 10 0.38
ACGTcount: A:0.15, C:0.23, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATTTTCTGCCCTAAA
Found at i:14230 original size:34 final size:33
Alignment explanation
Indices: 14161--14263 Score: 145
Period size: 34 Copynumber: 3.1 Consensus size: 33
14151 TTTGCTCAAC
14161 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
14194 TTGTAAAGGCGTGATGAAGGCCCGTGTAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTG-AACTTCA
* * * * *
14228 TTGTAACGACATGATAAAGGCCCG-CAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
14260 TTGT
1 TTGT
14264 TTGTAAGAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.17
33 26 0.41
34 27 0.42
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (33 bp):
TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
Found at i:25125 original size:18 final size:19
Alignment explanation
Indices: 25102--25140 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
25092 TTCTTGAAAT
*
25102 AATTCTTC-AATTGTCTTC
1 AATTCTTCAAATTATCTTC
25120 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
25139 AA
1 AA
25141 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:25139 original size:11 final size:11
Alignment explanation
Indices: 25123--25152 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
25113 TGTCTTCAAT
*
25123 TCTTCAAATTA
1 TCTTCAAATAA
25134 TCTTCAAATAA
1 TCTTCAAATAA
25145 TCTTCAAA
1 TCTTCAAA
25153 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:25151 original size:22 final size:22
Alignment explanation
Indices: 25093--25152 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
25083 AATTCTTGCT
* *
25093 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
25115 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
25134 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
25153 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 3 0.09
21 3 0.09
22 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:26282 original size:14 final size:14
Alignment explanation
Indices: 26263--26291 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26253 TCAATGAATC
26263 AAACATTCTTAAAA
1 AAACATTCTTAAAA
26277 AAACATTCTTAAAA
1 AAACATTCTTAAAA
26291 A
1 A
26292 TTCTAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AAACATTCTTAAAA
Found at i:26594 original size:21 final size:19
Alignment explanation
Indices: 26562--26600 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
26552 CAATCAAGCA
26562 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
26581 AATCATAGTATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
26601 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:28157 original size:15 final size:15
Alignment explanation
Indices: 28136--28193 Score: 98
Period size: 15 Copynumber: 3.9 Consensus size: 15
28126 TATCCAACTT
*
28136 GCTCATCTTCTTGTG
1 GCTCATCTTCTGGTG
*
28151 ACTCATCTTCTGGTG
1 GCTCATCTTCTGGTG
28166 GCTCATCTTCTGGTG
1 GCTCATCTTCTGGTG
28181 GCTCATCTTCTGG
1 GCTCATCTTCTGG
28194 CTTAGCAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41
Consensus pattern (15 bp):
GCTCATCTTCTGGTG
Found at i:29298 original size:17 final size:18
Alignment explanation
Indices: 29276--29314 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29266 CCTAAATTTA
29276 TTTTCGACAC-AATTTTT
1 TTTTCGACACAAATTTTT
*
29293 TTTTCGACGCAAATTTTT
1 TTTTCGACACAAATTTTT
29311 TTTT
1 TTTT
29315 TTTTAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTTCGACACAAATTTTT
Found at i:29648 original size:6 final size:6
Alignment explanation
Indices: 29637--29662 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29627 CAAAATTAAT
29637 TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TA
29663 CGGCAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Done.