Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007775.1 Corchorus capsularis cultivar CVL-1 contig07796, 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: 25837
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:2920 original size:30 final size:30
Alignment explanation
Indices: 2884--2943 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2874 AACAAAAGAA
2884 ATTATAAAAACAAACTTTCAAATGATCATG
1 ATTATAAAAACAAACTTTCAAATGATCATG
2914 ATTATAAAAACAAACTTTCAAATGATCATG
1 ATTATAAAAACAAACTTTCAAATGATCATG
2944 TCTATGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (30 bp):
ATTATAAAAACAAACTTTCAAATGATCATG
Found at i:15911 original size:98 final size:98
Alignment explanation
Indices: 15742--15921 Score: 333
Period size: 98 Copynumber: 1.8 Consensus size: 98
15732 AGGGATATCA
15742 GCCTATCCCTTCCTTTTCTAGTACCCAAGCCGGAGCTTGCTTACCTTATACCAAAGGCCTAAGAA
1 GCCTATCCCTTCCTTTTCTAGTACCCAAGCCGGAGCTTGCTTACCTTATACCAAAGGCCTAAGAA
15807 AGTAAAAAATCTACACTTTTCTAGTAGCCAAGG
66 AGTAAAAAATCTACACTTTTCTAGTAGCCAAGG
* *
15840 GCCTATCCCTTCCTTTTCTAGTACCCAAGCCGGAGCTTGTTTACCTTATACCAAGGGCCTAAGAA
1 GCCTATCCCTTCCTTTTCTAGTACCCAAGCCGGAGCTTGCTTACCTTATACCAAAGGCCTAAGAA
*
15905 AGTAAAATATCTACACT
66 AGTAAAAAATCTACACT
15922 AGTCACTGTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (98 bp):
GCCTATCCCTTCCTTTTCTAGTACCCAAGCCGGAGCTTGCTTACCTTATACCAAAGGCCTAAGAA
AGTAAAAAATCTACACTTTTCTAGTAGCCAAGG
Found at i:21157 original size:105 final size:105
Alignment explanation
Indices: 21009--21346 Score: 424
Period size: 105 Copynumber: 3.1 Consensus size: 105
20999 TCTAAATTGA
* *
21009 GCACTCTTCTTTCGCGCGTTGGTAATTGCACATGCTTAAGGGAGTTGCACATGTTCAGAGGAGCA
1 GCACTCTTCTTTCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAGAGGAGCA
21074 TTCGGTGCTCTTCATTAAACATTCTTCACTCGCGCGGTTG
66 TTCGGTGCTCTTCATTAAACATTCTTCACTCGCGCGGTTG
* * * * * * *
21114 GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCA
1 GCACTCTTCTTTCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAGAGGAGCA
* *
21179 TTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGTCGGCACTCTAAATTG
66 TTCGGTGCTCTTCATTAAACATTCTTCACT--CGC-G-CGG---------TTG
* *
21232 AGCACTCTTCTTTCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAAATGAGC
1 -GCACTCTTCTTTCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAGAGGAGC
*
21297 ATTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTG
65 ATTCGGTGCTCTTCATTAAACATTCTTCACTCGCGCGGTTG
21338 GCACTCTTC
1 GCACTCTTC
21347 ATTGAGCACT
Statistics
Matches: 197, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
105 93 0.47
106 3 0.02
107 3 0.02
108 1 0.01
109 3 0.02
115 3 0.02
116 1 0.01
117 3 0.02
118 3 0.02
119 84 0.43
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (105 bp):
GCACTCTTCTTTCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAGAGGAGCA
TTCGGTGCTCTTCATTAAACATTCTTCACTCGCGCGGTTG
Found at i:21297 original size:119 final size:119
Alignment explanation
Indices: 21114--21696 Score: 833
Period size: 119 Copynumber: 4.9 Consensus size: 119
21104 CGCGCGGTTG
* * *
21114 GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCA
1 GCACTCTTCTTTCGCGCATTGGTGATTGCACGTGCTTCGGGGAGTTGCACGTGTTCAGGGGAGCA
* * * **
21179 TTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGTCGGCACTCTAAATTGA
66 TTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
* * * * ***
21233 GCACTCTTCTTTCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAAATGAGCA
1 GCACTCTTCTTTCGCGCATTGGTGATTGCACGTGCTTCGGGGAGTTGCACGTGTTCAGGGGAGCA
21298 TTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
66 TTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
* *
21352 GCACTCTTCTTTCGCACATTGGTGATTGCACATGCTTCGAGGGAGTTGCACGTGTTCAGGGGAGC
1 GCACTCTTCTTTCGCGCATTGGTGATTGCACGTGCTTCG-GGGAGTTGCACGTGTTCAGGGGAGC
* * * * *
21417 ATTCGGTTCTCTTCATTAATCAGTCTTCATTCACGCGGTTGGCACTCTTCATTGA
65 ATTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
* * * *
21472 GCACTCTTCTTTCGCACATTGGTGATTGCACGTGCTTCGAGGAGTTGCACATTTTCAGGGGAGCA
1 GCACTCTTCTTTCGCGCATTGGTGATTGCACGTGCTTCGGGGAGTTGCACGTGTTCAGGGGAGCA
* *
21537 TTCGGTGCTCTTCATTAAGCATTTTTCACTCGCGCGGTTGTCACTCTTCATTGA
66 TTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
* * * * * *
21591 GCGCTTTTCTTTCCCGCATTGGTGATTTCACGTGCTTGGGGGAGTTGCACGTGTTTAGGGGAGCA
1 GCACTCTTCTTTCGCGCATTGGTGATTGCACGTGCTTCGGGGAGTTGCACGTGTTCAGGGGAGCA
* *
21656 TCCGGTGCTCTTCATTAAGCATTCTTCACTCGCCCGGTTGG
66 TTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGG
21697 TCATCATGCG
Statistics
Matches: 410, Mismatches: 53, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
119 301 0.73
120 109 0.27
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (119 bp):
GCACTCTTCTTTCGCGCATTGGTGATTGCACGTGCTTCGGGGAGTTGCACGTGTTCAGGGGAGCA
TTCGGTGCTCTTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
Found at i:21431 original size:239 final size:238
Alignment explanation
Indices: 21114--21693 Score: 872
Period size: 239 Copynumber: 2.4 Consensus size: 238
21104 CGCGCGGTTG
*
21114 GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCA
1 GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCA
21179 TTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGTCGGCACTCTAAATTGAGCACTCTTCTT
66 TTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGTCGGCACTCTAAATTGAGCACTCTTCTT
* * * *
21244 TCGCGCGTTGGTAATTGCACGTGCTTAGGGGAGTTGCACATGTTCAAATGAGCATTCGGTGCTCT
131 TCGCACATTGGTAATTGCACGTGCTTAGAGGAGTTGCACATGTTCAAAGGAGCATTCGGTGCTCT
21309 TCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
196 TCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
* * * *
21352 GCACTCTTCTTTCGCACATTGGTGATTGCACATGCTTCGAGGGAGTTGCACGTGTTCAGGGGAGC
1 GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTT-GGGGGAGTTGCACGTGTTCAGGGGAGC
* * * * **
21417 ATTCGGTTCTCTTCATTAATCAGTCTTCATTCACGCGGTTGGCACTCTTCATTGAGCACTCTTCT
65 ATTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGTCGGCACTCTAAATTGAGCACTCTTCT
* * * **
21482 TTCGCACATTGGTGATTGCACGTGCTTCGAGGAGTTGCACATTTTCAGGGGAGCATTCGGTGCTC
130 TTCGCACATTGGTAATTGCACGTGCTTAGAGGAGTTGCACATGTTCAAAGGAGCATTCGGTGCTC
* *
21547 TTCATTAAGCATTTTTCACTCGCGCGGTTGTCACTCTTCATTGA
195 TTCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
* * * * *
21591 GCGCTTTTCTTTCCCGCATTGGTGATTTCACGTGCTTGGGGGAGTTGCACGTGTTTAGGGGAGCA
1 GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCA
* * * *
21656 TCCGGTGCTCTTCATTAAGCATTCTTCACTCGCCCGGT
66 TTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGT
21694 TGGTCATCAT
Statistics
Matches: 304, Mismatches: 37, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
238 91 0.30
239 213 0.70
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (238 bp):
GCACTCTTCTTTCACGCATTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCA
TTCGGTGCTCTTCATTAATCAGTCTTCACTCGCGCGGTCGGCACTCTAAATTGAGCACTCTTCTT
TCGCACATTGGTAATTGCACGTGCTTAGAGGAGTTGCACATGTTCAAAGGAGCATTCGGTGCTCT
TCATTAAGCATTCTTCACTCGCGCGGTTGGCACTCTTCATTGA
Found at i:21924 original size:106 final size:106
Alignment explanation
Indices: 21749--22007 Score: 450
Period size: 106 Copynumber: 2.5 Consensus size: 106
21739 TCTTTAGTTT
21749 TGAGGTCAAGTATAGAGCTAATCTTTACGATTGCTCGCCCTTTTGACTCGTGCTTTTATTAGGTC
1 TGAGGTCAAGTATAGAGCTAATCTTTACGATTGCTCGCCCTTTTGACTCGTGCTTTTATTAGGTC
21814 GAGGATAGTGAAACCAATCGCTCGCCAATT-AGCATTGGTCC
66 GAGGATAGTGAAACCAATCGCTCGCCAATTAAG-ATTGGTCC
* *
21855 TGAGGTCAAGTATAGAGCTAATCTTTACGATTGCTCGCCCTTTTGACTCGTGCTTTTATTGGGTT
1 TGAGGTCAAGTATAGAGCTAATCTTTACGATTGCTCGCCCTTTTGACTCGTGCTTTTATTAGGTC
* *
21920 GAGGATAGTGAAACCAATCGCTCGCCAATTAAGTTTGGTCT
66 GAGGATAGTGAAACCAATCGCTCGCCAATTAAGATTGGTCC
*
21961 TGAGGTCAAGTATAGAGCTAAT-TTTACAATTGCTCGCCCTTTTGACT
1 TGAGGTCAAGTATAGAGCTAATCTTTACGATTGCTCGCCCTTTTGACT
22008 TGCTGGTCGC
Statistics
Matches: 147, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
105 24 0.16
106 121 0.82
107 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (106 bp):
TGAGGTCAAGTATAGAGCTAATCTTTACGATTGCTCGCCCTTTTGACTCGTGCTTTTATTAGGTC
GAGGATAGTGAAACCAATCGCTCGCCAATTAAGATTGGTCC
Done.