Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013102.1 Corchorus capsularis cultivar CVL-1 contig13123, 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: 22014
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1398 original size:17 final size:17
Alignment explanation
Indices: 1373--1406 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1363 CACCCTTCTT
1373 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
1390 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
1407 TAGCCGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:3066 original size:33 final size:33
Alignment explanation
Indices: 3024--3087 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3014 GTTGTTTTTT
*
3024 ATGATACTAAACCTAATTT-GAGTGTTGTTTGCG
1 ATGACACTAAACCTAATTTAG-GTGTTGTTTGCG
* *
3057 ATGACACTAAATCTGATTTAGGTGTTGTTTG
1 ATGACACTAAACCTAATTTAGGTGTTGTTTG
3088 TGATAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (33 bp):
ATGACACTAAACCTAATTTAGGTGTTGTTTGCG
Found at i:3193 original size:30 final size:31
Alignment explanation
Indices: 3124--3206 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 31
3114 CTAATTGTGA
*
3124 TGAAAACAATTATGTTTTGGTTGAACATAGCAT
1 TGAAAATAATTATGTTTTGGTTG-A-ATAGCAT
* * *
3157 TAAAAATAATTTTGTTTTGGTTG-ATGGCAT
1 TGAAAATAATTATGTTTTGGTTGAATAGCAT
* *
3187 TGAAAATAAATCTGTTTTGG
1 TGAAAATAATTATGTTTTGG
3207 GTGACGAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 23 0.53
33 20 0.47
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (31 bp):
TGAAAATAATTATGTTTTGGTTGAATAGCAT
Found at i:4986 original size:23 final size:23
Alignment explanation
Indices: 4952--5004 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
4942 GCACTAGTGA
* *
4952 CCGGCCATGCGACTTGGAGAAGC
1 CCGGCCACGCGACTCGGAGAAGC
*
4975 CCGGCCACGCGACTCGGAGATGC
1 CCGGCCACGCGACTCGGAGAAGC
4998 CCGGCCA
1 CCGGCCA
5005 ACACCGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.38, G:0.34, T:0.09
Consensus pattern (23 bp):
CCGGCCACGCGACTCGGAGAAGC
Found at i:8965 original size:3 final size:3
Alignment explanation
Indices: 8957--8989 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
8947 ATACACTATA
8957 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8990 ATGTACTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9596 original size:39 final size:42
Alignment explanation
Indices: 9502--9607 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
9492 CTCTCTCCCC
* * * *
9502 AAAGTCCCCAAACACATATAACACAGAGGCAACTCTCCTTCT
1 AAAGTCCCTAAACACATATAACACAGAGACAACTCTCATACT
9544 AAAGT-CCTCAAACACATATAACACAGAGAC-A-TCT-ATACT
1 AAAGTCCCT-AAACACATATAACACAGAGACAACTCTCATACT
9583 AAAGTCCCTAAACACATATAACACA
1 AAAGTCCCTAAACACATATAACACA
9608 AGGGCAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 24 0.41
40 6 0.10
41 3 0.05
42 25 0.43
ACGTcount: A:0.44, C:0.29, G:0.08, T:0.19
Consensus pattern (42 bp):
AAAGTCCCTAAACACATATAACACAGAGACAACTCTCATACT
Found at i:17202 original size:53 final size:52
Alignment explanation
Indices: 17123--17226 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 52
17113 GGTGATGTTT
*
17123 GATCACCTATGGTGATCTTCGGTGGTGATCTCAGATCACCCCATTTGGTTAG
1 GATCACCTATGGTAATCTTCGGTGGTGATCTCAGATCACCCCATTTGGTTAG
* *
17175 GATCACCTGTTGGTAATCTTGGGTGGTGATCTCAGATCACCCCATTTGGTTA
1 GATCACCT-ATGGTAATCTTCGGTGGTGATCTCAGATCACCCCATTTGGTTA
17227 CACATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 8 0.17
53 40 0.83
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (52 bp):
GATCACCTATGGTAATCTTCGGTGGTGATCTCAGATCACCCCATTTGGTTAG
Found at i:17306 original size:17 final size:17
Alignment explanation
Indices: 17284--17343 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
17274 CTAAACCAAG
*
17284 GTGATCTAGGATCACCA
1 GTGATCTAGCATCACCA
* **
17301 GTGATCTTGCATCACTT
1 GTGATCTAGCATCACCA
*
17318 GTGATCTTA-CATCATCA
1 GTGATC-TAGCATCACCA
17335 GTGATCTAG
1 GTGATCTAG
17344 AGGGTGATCC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 2 0.06
17 30 0.91
18 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (17 bp):
GTGATCTAGCATCACCA
Found at i:21175 original size:5 final size:5
Alignment explanation
Indices: 21165--21189 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21155 CTATTTCTAA
21165 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
21190 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:21246 original size:16 final size:18
Alignment explanation
Indices: 21217--21249 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
21207 ACTTTTAATC
21217 AATTATATTCATTTTTAT
1 AATTATATTCATTTTTAT
21235 AATTAT-TT-ATTTTTA
1 AATTATATTCATTTTTA
21250 CCATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTATATTCATTTTTAT
Done.