Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007736.1 Corchorus capsularis cultivar CVL-1 contig07757, 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: 12769
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Found at i:307 original size:11 final size:11
Alignment explanation
Indices: 291--315 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
281 CCTGTTCTTC
291 TTTGTTTTTTT
1 TTTGTTTTTTT
302 TTTGTTTTTTT
1 TTTGTTTTTTT
313 TTT
1 TTT
316 TTTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:1216 original size:2 final size:2
Alignment explanation
Indices: 1209--1237 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1199 TAGCTTATCA
1209 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
1238 ATTTGTCACC
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:1276 original size:3 final size:3
Alignment explanation
Indices: 1270--1302 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1260 TTTTTGAAAA
1270 AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
1303 CAATTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1292 original size:16 final size:16
Alignment explanation
Indices: 1271--1301 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1261 TTTTGAAAAA
1271 ATAATAATAATAATAT
1 ATAATAATAATAATAT
1287 ATAATAATAATAATA
1 ATAATAATAATAATA
1302 ACAATTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAATAATAT
Found at i:2086 original size:2 final size:2
Alignment explanation
Indices: 2079--2103 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2069 TAACCAACAA
2079 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 A
2104 ATAATGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2113 original size:12 final size:13
Alignment explanation
Indices: 2078--2119 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
2068 ATAACCAACA
2078 AATATATATATAT
1 AATATATATATAT
2091 -ATATATATATAT
1 AATATATATATAT
* *
2103 AATA-ATGTATAC
1 AATATATATATAT
2115 AATAT
1 AATAT
2120 CATAAGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
AATATATATATAT
Found at i:2292 original size:17 final size:17
Alignment explanation
Indices: 2270--2363 Score: 111
Period size: 17 Copynumber: 5.6 Consensus size: 17
2260 TTCCTACCCT
2270 ACTCACCTGGTACAAAC
1 ACTCACCTGGTACAAAC
* *
2287 ACTCACATGATACAAAC
1 ACTCACCTGGTACAAAC
*
2304 ACTCATCTGGTACAAAC
1 ACTCACCTGGTACAAAC
* *
2321 ACTCACCTGGTGC-AAT
1 ACTCACCTGGTACAAAC
* *
2337 ACTCACCTGGTGC-AAT
1 ACTCACCTGGTACAAAC
2353 ACTCACCTGGT
1 ACTCACCTGGT
2364 GAGGTCACCA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
16 29 0.42
17 40 0.58
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (17 bp):
ACTCACCTGGTACAAAC
Found at i:2342 original size:16 final size:16
Alignment explanation
Indices: 2321--2364 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
2311 TGGTACAAAC
2321 ACTCACCTGGTGCAAT
1 ACTCACCTGGTGCAAT
2337 ACTCACCTGGTGCAAT
1 ACTCACCTGGTGCAAT
2353 ACTCACCTGGTG
1 ACTCACCTGGTG
2365 AGGTCACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (16 bp):
ACTCACCTGGTGCAAT
Found at i:3802 original size:21 final size:21
Alignment explanation
Indices: 3778--3817 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3768 ACTGGAGGGC
3778 TTTACTTCCTGAGGAAGGCGT
1 TTTACTTCCTGAGGAAGGCGT
*
3799 TTTACTTGCTGAGGAAGGC
1 TTTACTTCCTGAGGAAGGC
3818 TAACTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (21 bp):
TTTACTTCCTGAGGAAGGCGT
Found at i:4638 original size:156 final size:155
Alignment explanation
Indices: 4336--4687 Score: 353
Period size: 156 Copynumber: 2.3 Consensus size: 155
4326 CTTCTCACCT
* * *
4336 CAAATTGTCCTT-AATG-AAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAATTT
1 CAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGAGCTG-AATTT
* * *
4399 TTCCAAGGGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACTGAGCTTCCC
65 TTCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTTCCC
* * * *
4464 TTGATGGTGAACTAGGTTT-CTCTCCC
130 TAGATAGAGAACTAGGTTTACAC-CCC
** *
4490 TGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTC-CAACGAAGCTG-A-TT
1 CAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACG-AGCTGAATTT
* *
4552 TTCCACCAGTAGACTTAGATTATTCC-CATAA-AGCTATGGGAAAAATTCTAAGTAAAACCGAAC
65 TTCCA--AG-AGACTTAGAATA-TCCACATAAGA-CTATGGAAAAAATTCTAAGTAAAACCGAAC
* * *
4615 -TCTCTAGCATAGAGAAGTTGGTTTGACACCCC
125 TTCCCTAG-ATAGAGAACTAGGTTT-ACACCCC
* * *
4647 CAAACTGTCCTTTAATTGAAAAACTAGCATAAGTTCTTCAT
1 CAAATTGTCC-TTAAATGAAAAACTAGCATAAGTTTTTCAT
4688 AGTAAGTCTG
Statistics
Matches: 162, Mismatches: 24, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
153 7 0.04
154 10 0.06
155 15 0.09
156 88 0.54
157 12 0.07
158 30 0.19
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (155 bp):
CAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCCAAGTCTCAACGAGCTGAATTTT
TCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTTCCCT
AGATAGAGAACTAGGTTTACACCCC
Done.