Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010377.1 Corchorus capsularis cultivar CVL-1 contig10398, 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: 30891
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AT AT AT AT AT 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 AT AT AT AT AT A
40 CTTATACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6447 original size:2 final size:2
Alignment explanation
Indices: 6440--6469 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6430 CTTTAACATA
6440 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
6470 CTCATGTTCA
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:13579 original size:4 final size:4
Alignment explanation
Indices: 13562--13591 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
13552 ATGATTTATC
*
13562 AAAT AAAC AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
13592 TAATCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:20461 original size:2 final size:2
Alignment explanation
Indices: 20454--20481 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20444 ACAAGTTGGA
20454 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
20482 TTACTAAAAC
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):
AT
Found at i:22231 original size:19 final size:19
Alignment explanation
Indices: 22207--22265 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
22197 CTGTTTAGCA
*
22207 ACTGTATAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
*
22226 ACTGTACAGATTAGATTAAGT
1 ACTGTACAGATGAGATT-A-T
*
22247 ACTGTGCAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
22266 TGGAGTAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 16 0.47
20 2 0.06
21 16 0.47
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:22251 original size:21 final size:20
Alignment explanation
Indices: 22207--22264 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
22197 CTGTTTAGCA
*
22207 ACTGTATAGATGAGATT-AT
1 ACTGTACAGATGAGATTAAT
*
22226 ACTGTACAGATTAGATTAAGT
1 ACTGTACAGATGAGATTAA-T
*
22247 ACTGTGCAGATGAGATTA
1 ACTGTACAGATGAGATTA
22265 TTGGAGTAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
20 1 0.03
21 17 0.52
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAAT
Found at i:25380 original size:14 final size:14
Alignment explanation
Indices: 25359--25392 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
25349 TGTTCATTTC
25359 ATATATATATACTATA
1 ATATATATA-ACTA-A
25375 ATATATATAACTAA
1 ATATATATAACTAA
25389 ATAT
1 ATAT
25393 TAACCAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATAACTAA
Found at i:26667 original size:2 final size:2
Alignment explanation
Indices: 26660--26708 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
26650 GGGTCCAAGC
26660 TA TA TA TA T- TA T- TA GTA 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 TA TA TA TA TA TA TA
26701 TA TA TA TA
1 TA TA TA TA
26709 AGTTAACAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28808 original size:13 final size:14
Alignment explanation
Indices: 28790--28818 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28780 GTTTCTCTTT
28790 TTCC-TTTTGTTCC
1 TTCCTTTTTGTTCC
28803 TTCCTTTTTGTTCC
1 TTCCTTTTTGTTCC
28817 TT
1 TT
28819 TGTTTATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.28, G:0.07, T:0.66
Consensus pattern (14 bp):
TTCCTTTTTGTTCC
Found at i:29314 original size:4 final size:4
Alignment explanation
Indices: 29305--29332 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29295 ACCTAGGAAG
29305 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
29333 TATATATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Done.