Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010143.1 Corchorus capsularis cultivar CVL-1 contig10164, 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: 35192
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2002 original size:2 final size:2
Alignment explanation
Indices: 1995--2028 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1985 TCTAAGATAA
1995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2029 CCTTTGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2186 original size:6 final size:6
Alignment explanation
Indices: 2175--2215 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
2165 AGAAACCCTA
*
2175 TGTGAC TGTGAC TGTGAC TGTGAC TGTGAC TGTGAT TGTGA
1 TGTGAC TGTGAC TGTGAC TGTGAC TGTGAC TGTGAC TGTGA
2216 AAATTGGGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.12, G:0.34, T:0.37
Consensus pattern (6 bp):
TGTGAC
Found at i:5153 original size:3 final size:3
Alignment explanation
Indices: 5140--5176 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
5130 TTTAATCCAG
5140 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5177 CCGTAAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:9329 original size:13 final size:14
Alignment explanation
Indices: 9311--9340 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9301 TCTATTGTAG
9311 ACTCAACAAACT-A
1 ACTCAACAAACTCA
9324 ACTCAACAAACTCA
1 ACTCAACAAACTCA
9338 ACT
1 ACT
9341 GACTCAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (14 bp):
ACTCAACAAACTCA
Found at i:9350 original size:15 final size:15
Alignment explanation
Indices: 9330--9364 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9320 ACTAACTCAA
*
9330 CAAACTCAACTGACT
1 CAAACTAAACTGACT
*
9345 CAAACTAAACTGGCT
1 CAAACTAAACTGACT
9360 CAAAC
1 CAAAC
9365 ATCCAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (15 bp):
CAAACTAAACTGACT
Found at i:10456 original size:26 final size:26
Alignment explanation
Indices: 10420--10470 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
10410 TTCATACTTA
10420 CAACATTAATTAGTTTGGGGAGGAAT
1 CAACATTAATTAGTTTGGGGAGGAAT
10446 CAACATTAATTAGTTTGGGGAGGAA
1 CAACATTAATTAGTTTGGGGAGGAA
10471 ATCTAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (26 bp):
CAACATTAATTAGTTTGGGGAGGAAT
Found at i:15700 original size:12 final size:12
Alignment explanation
Indices: 15683--15712 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15673 TAGAGTTTTG
15683 GAGGATATTGAA
1 GAGGATATTGAA
*
15695 GAGGATATTGAG
1 GAGGATATTGAA
15707 GAGGAT
1 GAGGAT
15713 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (12 bp):
GAGGATATTGAA
Found at i:20218 original size:30 final size:30
Alignment explanation
Indices: 20184--20250 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
20174 TGTATTAATC
**
20184 AAATGAATCGGGATTACAAATATTAGATGA
1 AAATGAATCAAGATTACAAATATTAGATGA
20214 AAATGAATCAAGATTACAAATATTAGATGA
1 AAATGAATCAAGATTACAAATATTAGATGA
20244 AAGATGA
1 AA-ATGA
20251 CCCATCCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (30 bp):
AAATGAATCAAGATTACAAATATTAGATGA
Found at i:21544 original size:27 final size:28
Alignment explanation
Indices: 21496--21558 Score: 110
Period size: 27 Copynumber: 2.2 Consensus size: 28
21486 TGTTTCCTAT
21496 TTTCCTCTAAAAAAAACCCTAGCATGTGC
1 TTTCCTCT-AAAAAAACCCTAGCATGTGC
21525 TTTCCTCT-AAAAAACCCTAGCATGTGC
1 TTTCCTCTAAAAAAACCCTAGCATGTGC
21552 TTTCCTC
1 TTTCCTC
21559 CCCAGAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 26 0.76
29 8 0.24
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (28 bp):
TTTCCTCTAAAAAAACCCTAGCATGTGC
Found at i:30442 original size:2 final size:2
Alignment explanation
Indices: 30435--30464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30425 ATGCTTTTCA
30435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30465 CTTACACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31386 original size:3 final size:3
Alignment explanation
Indices: 31380--31439 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
31370 AAAAAAAAAA
31380 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31428 TAT TAT TAT TAT
1 TAT TAT TAT TAT
31440 ATACTAGTAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.