Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007689.1 Corchorus capsularis cultivar CVL-1 contig07710, 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: 19059
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Found at i:2798 original size:62 final size:61
Alignment explanation
Indices: 2701--2928 Score: 248
Period size: 62 Copynumber: 3.7 Consensus size: 61
2691 TGCAAGAACA
*
2701 TGACAAAATTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATTGAAACTATATG-AGAGAATG
1 TGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATT-AAACTA-ATGCAGAGAATG
* * * *
2763 TGACACAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAACTATAATCTAAGTGCAG-GAATG
1 TGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAAT-TAAACTAA-TGCAGAGAATG
* * * *
2825 TGA-AGAAACTGACCCTTTATCTGAAAGGGTATTTTGGGAATACTAAACTAAAATGCA-AGAAGG
1 TGACA-AAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAA-ATTAAACT--AATGCAGAGAATG
**
2888 TGACAAAACCAACCCTTTGTCCGAAAGGGTATTTTTGGGAA
1 TGACAAAACTGACCCTTTGTCCGAAAGGGTA-TTTTGGGAA
2929 TCGAAAGTAC
Statistics
Matches: 141, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
61 2 0.01
62 91 0.65
63 36 0.26
64 12 0.09
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (61 bp):
TGACAAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATTAAACTAATGCAGAGAATG
Found at i:3123 original size:46 final size:46
Alignment explanation
Indices: 3062--3155 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
3052 AAGTAAAAAG
* * * *
3062 AAGTGTCTTTCGTCCGGGAAGGGTGCTTTGGGAAAAAGCAAGTAAA
1 AAGTGCCTTCCGTCCGGGAAGGGTACTTTGGGAAAAAGCAACTAAA
*
3108 AAGTGCCTTCCGTCCGGGAAGGGTATTTTGGGAAAAAGCAACTAAA
1 AAGTGCCTTCCGTCCGGGAAGGGTACTTTGGGAAAAAGCAACTAAA
3154 AA
1 AA
3156 ACAAAATTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (46 bp):
AAGTGCCTTCCGTCCGGGAAGGGTACTTTGGGAAAAAGCAACTAAA
Found at i:3607 original size:6 final size:6
Alignment explanation
Indices: 3596--3623 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3586 AGTTTTCTCC
3596 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
3624 ACCAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:5937 original size:2 final size:2
Alignment explanation
Indices: 5925--5956 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5915 ATCTGCAGGC
*
5925 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5957 TTTTAGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6140 original size:13 final size:13
Alignment explanation
Indices: 6122--6149 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6112 AATGCAAATT
6122 CTATTTCTACCAG
1 CTATTTCTACCAG
6135 CTATTTCTACCAG
1 CTATTTCTACCAG
6148 CT
1 CT
6150 CAATTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.32, G:0.07, T:0.39
Consensus pattern (13 bp):
CTATTTCTACCAG
Found at i:6241 original size:17 final size:18
Alignment explanation
Indices: 6219--6261 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
6209 GATGCTAGAT
6219 TCAATATAAAAGCTAA-A
1 TCAATATAAAAGCTAAGA
**
6236 TCAATACGAAAGCTAAGA
1 TCAATATAAAAGCTAAGA
6254 TGCAATAT
1 T-CAATAT
6262 TGGCCTCTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 2 0.10
19 5 0.24
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (18 bp):
TCAATATAAAAGCTAAGA
Found at i:9019 original size:21 final size:21
Alignment explanation
Indices: 8977--9034 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
8967 TTTAGGGAGC
* *
8977 TTTATTGTAATGATTTAGCCT
1 TTTACTGTAATGATTTACCCT
8998 TTTACTGTAATG-TTATACCCT
1 TTTACTGTAATGATT-TACCCT
9019 TTATGACTTGTAATGA
1 TT-T-AC-TGTAATGA
9035 CATGCTATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 18 0.60
22 1 0.03
23 2 0.07
24 7 0.23
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (21 bp):
TTTACTGTAATGATTTACCCT
Found at i:9634 original size:309 final size:309
Alignment explanation
Indices: 9075--9692 Score: 1209
Period size: 309 Copynumber: 2.0 Consensus size: 309
9065 TTAAGAAAAG
9075 AGGAAGAAGACATTAATACTGTGATGTGGTGAAAAGGGTGTAGTCATTAATCAAGAGAGTTTCAT
1 AGGAAGAAGACATTAATACTGTGATGTGGTGAAAAGGGTGTAGTCATTAATCAAGAGAGTTTCAT
9140 ATTTACAAAGAAAAAGAATAACATATAAAGGTAGCGCCTCGTAATGATGAATACTCTGACGATGT
66 ATTTACAAAGAAAAAGAATAACATATAAAGGTAGCGCCTCGTAATGATGAATACTCTGACGATGT
9205 GATGGCGAGATCTTTGGATTCTTTCGAGAGAAAAACCTACTGTACTGATAGCACCCACTCAGTCT
131 GATGGCGAGATCTTTGGATTCTTTCGAGAGAAAAACCTACTGTACTGATAGCACCCACTCAGTCT
9270 GGATCGCGCCCTACTCCTTTCATCTTCAAGAGATAGCTATGCATCCATTCGCCCTGGCCTCTTTT
196 GGATCGCGCCCTACTCCTTTCATCTTCAAGAGATAGCTATGCATCCATTCGCCCTGGCCTCTTTT
9335 CCTTAAGCCGCCCTTTTCAGGTTTTCGGCTCAAGTTCACCTTTTTCCAT
261 CCTTAAGCCGCCCTTTTCAGGTTTTCGGCTCAAGTTCACCTTTTTCCAT
9384 AGGAAGAAGACATTAATACTGTGATGTGGTGAAAAGGGTGTAGTCATTAATCAAGAGAGTTTCAT
1 AGGAAGAAGACATTAATACTGTGATGTGGTGAAAAGGGTGTAGTCATTAATCAAGAGAGTTTCAT
9449 ATTTACAAAGAAAAAGAATAACATATAAAGGTAGCGCCTCGTAATGATGAATACTCTGACGATGT
66 ATTTACAAAGAAAAAGAATAACATATAAAGGTAGCGCCTCGTAATGATGAATACTCTGACGATGT
9514 GATGGCGAGATCTTTGGATTCTTTCGAGAGAAAAACCTACTGTACTGATAGCACCCACTCAGTCT
131 GATGGCGAGATCTTTGGATTCTTTCGAGAGAAAAACCTACTGTACTGATAGCACCCACTCAGTCT
* *
9579 GGATCGCGCCCTACTCCTTTGATCTTCAAGAGATAGCTCTGCATCCATTCGCCCTGGCCTCTTTT
196 GGATCGCGCCCTACTCCTTTCATCTTCAAGAGATAGCTATGCATCCATTCGCCCTGGCCTCTTTT
*
9644 CCTTAAGCCGCCCTTTTCGGGTTTTCGGCTCAAGTTCACCTTTTTCCAT
261 CCTTAAGCCGCCCTTTTCAGGTTTTCGGCTCAAGTTCACCTTTTTCCAT
9693 CCCTCGCTTT
Statistics
Matches: 306, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
309 306 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (309 bp):
AGGAAGAAGACATTAATACTGTGATGTGGTGAAAAGGGTGTAGTCATTAATCAAGAGAGTTTCAT
ATTTACAAAGAAAAAGAATAACATATAAAGGTAGCGCCTCGTAATGATGAATACTCTGACGATGT
GATGGCGAGATCTTTGGATTCTTTCGAGAGAAAAACCTACTGTACTGATAGCACCCACTCAGTCT
GGATCGCGCCCTACTCCTTTCATCTTCAAGAGATAGCTATGCATCCATTCGCCCTGGCCTCTTTT
CCTTAAGCCGCCCTTTTCAGGTTTTCGGCTCAAGTTCACCTTTTTCCAT
Done.