Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012138.1 Corchorus capsularis cultivar CVL-1 contig12159, 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: 13261
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:377 original size:200 final size:201
Alignment explanation
Indices: 3--366 Score: 579
Period size: 200 Copynumber: 1.8 Consensus size: 201
1 CT
* * * *
3 ACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTTTAAATTGTTT
1 ACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTAAAATTATTT
** *
68 TGGCAACTACCTAGAGGTCGTTGTGTAAGTGTTTTGGAAACGACTTTTAATCATTTTTAAAACTT
66 TGGCAACTACCTAGAGGTCGTTACGTAAGTGTTTTGGAAACGACATTTAATCATTTTTAAAACTT
* * **
133 ATTCGTAACCAATTAAAAGTGGTTGCGAAATTATTACACAACCAATCAAATGTTGCTACGTAAAA
131 ATCCGTAACCAATTAAAAGTGGTTGCCAAAAAATTACACAACCAATCAAATGTTGCTACGTAAAA
198 GATTTC
196 GATTTC
* *
204 ACAACCAAAACAACATTG-TGCGTAAGGGTTTTCGTAACGACATTTAATCGTTTTAAAATTATTT
1 ACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTAAAATTATTT
* *
268 TGGCAACTACCTAGAGGTCGTTACGTAAGTGTTTTGGAAACGACATTTAATCGTTTTTAAAAGTT
66 TGGCAACTACCTAGAGGTCGTTACGTAAGTGTTTTGGAAACGACATTTAATCATTTTTAAAACTT
333 ATCCGTAACCAATT-AAAGTGGTTGCCAAAAAATT
131 ATCCGTAACCAATTAAAAGTGGTTGCCAAAAAATT
367 TTCGCAACCA
Statistics
Matches: 148, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
199 17 0.11
200 115 0.78
201 16 0.11
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (201 bp):
ACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTAAAATTATTT
TGGCAACTACCTAGAGGTCGTTACGTAAGTGTTTTGGAAACGACATTTAATCATTTTTAAAACTT
ATCCGTAACCAATTAAAAGTGGTTGCCAAAAAATTACACAACCAATCAAATGTTGCTACGTAAAA
GATTTC
Found at i:506 original size:20 final size:20
Alignment explanation
Indices: 481--522 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
471 GCGAACACTC
* *
481 AAGTCGTTGTGTTAGATCTT
1 AAGTCGTTGCGTTAGATATT
501 AAGTCGTTGCGTTAGATATT
1 AAGTCGTTGCGTTAGATATT
521 AA
1 AA
523 ACAACGGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (20 bp):
AAGTCGTTGCGTTAGATATT
Found at i:3160 original size:17 final size:17
Alignment explanation
Indices: 3138--3170 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3128 GTAAGTATAA
*
3138 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
3155 AATTTCATCCATATTA
1 AATTTCATCCATATTA
3171 ATATGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:3362 original size:109 final size:108
Alignment explanation
Indices: 3228--3445 Score: 269
Period size: 109 Copynumber: 2.0 Consensus size: 108
3218 ATTAATCGGA
* **** * * *
3228 TATATTAATTCTTCAATAAAATAATCTGGTTTTACATTATAAATTTTAAGGTTGGGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCCACTTTACATTATAAATTATAAGGCTGAGATATT-GGA
* * *
3293 AAAAA-GAAAA-CCAAAAAATTGATTTAAAGATATTTTTAATTAAT
65 AAAAACAAAAAGCAAAAAAATTGA--TAAAGATATTGTTAATTAAT
* *
3337 TATATTAATTCTTGAACAAAATAATCCCACTTTACATTATAAATTATAAGGCTGAGATATTTGAA
1 TATATTAATTCTTCAACAAAATAATCCCACTTTACATTATAAATTATAAGGCTGAGATATTGGAA
*
3402 AAAACAAAAAGCAAAAAAATTGATAAGGATATTGTTAATTAAT
66 AAAACAAAAAGCAAAAAAATTGATAAAGATATTGTTAATTAAT
3445 T
1 T
3446 TTTACATTAT
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
108 26 0.28
109 56 0.60
110 11 0.12
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (108 bp):
TATATTAATTCTTCAACAAAATAATCCCACTTTACATTATAAATTATAAGGCTGAGATATTGGAA
AAAACAAAAAGCAAAAAAATTGATAAAGATATTGTTAATTAAT
Found at i:4797 original size:2 final size:2
Alignment explanation
Indices: 4781--4819 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
4771 GGAGACAAAA
4781 AT AT -T AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
4820 AACTATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5747 original size:31 final size:30
Alignment explanation
Indices: 5658--5749 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 30
5648 ATTAAACAAA
*
5658 TAAGGATATAATAGGAATATATTAAAAGTTAAT
1 TAAGGGTATAATAGG--TA-ATTAAAAGTTAAT
* * *
5691 TAAGGGTACAATTGGAATATTAAAAGTTAAT
1 TAAGGGTATAATAGGTA-ATTAAAAGTTAAT
5722 TAAGGGTATAATAGGTAATTCAAAAGTT
1 TAAGGGTATAATAGGTAATT-AAAAGTT
5750 TCTGAAAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
30 3 0.06
31 36 0.71
33 12 0.24
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (30 bp):
TAAGGGTATAATAGGTAATTAAAAGTTAAT
Found at i:5789 original size:14 final size:12
Alignment explanation
Indices: 5771--5822 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
5761 GTACTTTTAT
5771 ATATAGTATATAG
1 ATATAG-ATATAG
5784 TATATAGATATAG
1 -ATATAGATATAG
* * *
5797 ATAGATAGATAG
1 ATATAGATATAG
5809 ATATAGATATAG
1 ATATAGATATAG
5821 AT
1 AT
5823 TAACATTAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 20 0.62
13 6 0.19
14 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (12 bp):
ATATAGATATAG
Found at i:6138 original size:2 final size:2
Alignment explanation
Indices: 6131--6159 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6121 ACATACATAC
6131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6160 AGAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9894 original size:3 final size:3
Alignment explanation
Indices: 9886--9954 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
9876 AGGCTCCTTC
* *
9886 CTT CTT CTT CTT CTT CTT CTT CTT CGT CTT CTT CTT CTT CTT CTC CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
9934 CAT ATA CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT
9955 GTCTATGATC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.04, C:0.33, G:0.01, T:0.61
Consensus pattern (3 bp):
CTT
Done.