Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006783.1 Corchorus capsularis cultivar CVL-1 contig06804, 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: 47517
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1136 original size:6 final size:6
Alignment explanation
Indices: 1125--1185 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
1115 CCGTTTGACA
* *
1125 TCGTTT TCGTTTT TCTGTTTT TTGTTT TTG-TT TCGTTT TCGTTT T-GTTT
1 TCGTTT TCG-TTT TC-G-TTT TCGTTT TCGTTT TCGTTT TCGTTT TCGTTT
1174 TCGTTT T-GTTT T
1 TCGTTT TCGTTT T
1186 TGTTGCGCTG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
5 14 0.29
6 23 0.47
7 6 0.12
8 6 0.12
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.74
Consensus pattern (6 bp):
TCGTTT
Found at i:1168 original size:11 final size:11
Alignment explanation
Indices: 1144--1185 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
1134 TTTTTCTGTT
*
1144 TTTTGTTTTTG
1 TTTTGTTTTCG
*
1155 TTTCGTTTTCG
1 TTTTGTTTTCG
1166 TTTTGTTTTCG
1 TTTTGTTTTCG
1177 TTTTGTTTT
1 TTTTGTTTT
1186 TGTTGCGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.00, C:0.07, G:0.17, T:0.76
Consensus pattern (11 bp):
TTTTGTTTTCG
Found at i:1168 original size:17 final size:16
Alignment explanation
Indices: 1144--1189 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
1134 TTTTTCTGTT
1144 TTTTGTTTTTGTTTCG
1 TTTTGTTTTTGTTTCG
1160 TTTTCG-TTTTGTTTTCG
1 TTTT-GTTTTTG-TTTCG
1177 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
1190 GCGCTGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.00, C:0.07, G:0.17, T:0.76
Consensus pattern (16 bp):
TTTTGTTTTTGTTTCG
Found at i:2841 original size:3 final size:3
Alignment explanation
Indices: 2833--2872 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2823 TGATTCGACA
2833 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2873 GAAATGACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:7872 original size:60 final size:60
Alignment explanation
Indices: 7799--7921 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
7789 GCTGTCTATA
7799 GGCAAGACACTGCAATCACAAATATTTTCTATACTGGAGAAATCGCCCAAGGGAAAGAAG
1 GGCAAGACACTGCAATCACAAATATTTTCTATACTGGAGAAATCGCCCAAGGGAAAGAAG
7859 GGCAAGACACTGCAATCACAAATATTTTCTATACTGGAGAAATCGCCCAAGGGAAAGAAG
1 GGCAAGACACTGCAATCACAAATATTTTCTATACTGGAGAAATCGCCCAAGGGAAAGAAG
7919 GGC
1 GGC
7922 TAAATAAAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (60 bp):
GGCAAGACACTGCAATCACAAATATTTTCTATACTGGAGAAATCGCCCAAGGGAAAGAAG
Found at i:24182 original size:11 final size:10
Alignment explanation
Indices: 24164--24213 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 10
24154 GAAGTTCGTG
24164 TTTTGAAGAT
1 TTTTGAAGAT
24174 TTCTTGAAGAT
1 TT-TTGAAGAT
24185 ATTTTGAAGA-
1 -TTTTGAAGAT
24195 -TTTGAAGA-
1 TTTTGAAGAT
24203 -TTTGAAGAT
1 TTTTGAAGAT
24212 TT
1 TT
24214 GAAGACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 16 0.44
10 3 0.08
11 15 0.42
12 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:24231 original size:8 final size:8
Alignment explanation
Indices: 24187--24218 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
24177 TTGAAGATAT
24187 TTTGAAGA
1 TTTGAAGA
24195 TTTGAAGA
1 TTTGAAGA
24203 TTTGAAGA
1 TTTGAAGA
24211 TTTGAAGA
1 TTTGAAGA
24219 CAATTGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (8 bp):
TTTGAAGA
Found at i:32204 original size:2 final size:2
Alignment explanation
Indices: 32197--32224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32187 CTTCCCGAAT
32197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32225 CACTATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33427 original size:17 final size:16
Alignment explanation
Indices: 33405--33443 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
33395 TTTATATATA
33405 AAAAAAACTACCTATT
1 AAAAAAACTACCTATT
*
33421 GAAAAAAACTACTTATT
1 -AAAAAAACTACCTATT
33438 AAAAAA
1 AAAAAA
33444 TATCATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.62, C:0.13, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAAACTACCTATT
Found at i:36532 original size:138 final size:138
Alignment explanation
Indices: 36284--36542 Score: 509
Period size: 138 Copynumber: 1.9 Consensus size: 138
36274 AGATTCACCA
36284 TCTTCGTGAACAAATTTCCATTGCCTGTGTGAAGGTTTAATTACTTCTTAAGGCTATTGCTTGCA
1 TCTTCGTGAACAAATTTCCATTGCCTGTGTGAAGGTTTAATTACTTCTTAAGGCTATTGCTTGCA
*
36349 TATATAGATTATATTCATTTCTTTTTGCTTAGAAGTGCATTTCCAACTAATTCTGTGTGAAGGTG
66 TATATAGATTATATTCATTTCCTTTTGCTTAGAAGTGCATTTCCAACTAATTCTGTGTGAAGGTG
36414 TAATTACT
131 TAATTACT
36422 TCTTCGTGAACAAATTTCCATTGCCTGTGTGAAGGTTTAATTACTTCTTAAGGCTATTGCTTGCA
1 TCTTCGTGAACAAATTTCCATTGCCTGTGTGAAGGTTTAATTACTTCTTAAGGCTATTGCTTGCA
36487 TATATAGATTATATTCATTTCCTTTTGCTTAGAAGTGCATTTCCAACTAATTCTGT
66 TATATAGATTATATTCATTTCCTTTTGCTTAGAAGTGCATTTCCAACTAATTCTGT
36543 AGTCACTTTA
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 120 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (138 bp):
TCTTCGTGAACAAATTTCCATTGCCTGTGTGAAGGTTTAATTACTTCTTAAGGCTATTGCTTGCA
TATATAGATTATATTCATTTCCTTTTGCTTAGAAGTGCATTTCCAACTAATTCTGTGTGAAGGTG
TAATTACT
Done.