Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007156.1 Corchorus capsularis cultivar CVL-1 contig07177, 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: 25486
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28 TAATTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4641 original size:8 final size:8
Alignment explanation
Indices: 4630--4661 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
4620 TTATAAAACA
4630 AAAAAAAT
1 AAAAAAAT
4638 AAAAAAAAT
1 -AAAAAAAT
4647 AAAAAAAT
1 AAAAAAAT
4655 AAAAAAA
1 AAAAAAA
4662 AACCCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (8 bp):
AAAAAAAT
Found at i:4641 original size:9 final size:9
Alignment explanation
Indices: 4624--4662 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
4614 ACCAATTTAT
*
4624 AAAACAAAA
1 AAAATAAAA
4633 AAAATAAAA
1 AAAATAAAA
4642 AAAAT-AAA
1 AAAATAAAA
4650 AAAATAAAA
1 AAAATAAAA
4659 AAAA
1 AAAA
4663 ACCCTGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAATAAAA
Found at i:4650 original size:17 final size:17
Alignment explanation
Indices: 4630--4662 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4620 TTATAAAACA
4630 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
4647 AAAAAAATAAAAAAAA
1 AAAAAAATAAAAAAAA
4663 ACCCTGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:6747 original size:3 final size:3
Alignment explanation
Indices: 6739--6772 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
6729 TATAATTTAA
* *
6739 AAT AAT AAT AAT AAT AAT ACT AAT AAT ACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6773 GAAGGCCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7758 original size:1 final size:1
Alignment explanation
Indices: 7752--7785 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
7742 AGACATTGTT
7752 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7786 CTAGTGGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13759 original size:3 final size:3
Alignment explanation
Indices: 13751--13779 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13741 AGGTCATTTT
13751 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13780 GCAAGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18537 original size:22 final size:22
Alignment explanation
Indices: 18512--18555 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18502 TATTATATAT
18512 AAATATAAATCAAATTGAAAAA
1 AAATATAAATCAAATTGAAAAA
*
18534 AAATATGAATCAAATTGAAAAA
1 AAATATAAATCAAATTGAAAAA
18556 TATGAAGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (22 bp):
AAATATAAATCAAATTGAAAAA
Found at i:18556 original size:19 final size:20
Alignment explanation
Indices: 18512--18561 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
18502 TATTATATAT
*
18512 AAATATAAATCAAATTGAAAAA
1 AAATATGAATCAAATTG--AAA
18534 AAATATGAATCAAATTG-AA
1 AAATATGAATCAAATTGAAA
18553 AAATATGAA
1 AAATATGAA
18562 GGTTACTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
22 16 0.59
ACGTcount: A:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (20 bp):
AAATATGAATCAAATTGAAA
Found at i:18910 original size:6 final size:6
Alignment explanation
Indices: 18901--18928 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18891 TGGGAAATGT
18901 AAATTG AAATTG AAATTG AAATTG AAAT
1 AAATTG AAATTG AAATTG AAATTG AAAT
18929 AGGCAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (6 bp):
AAATTG
Found at i:23902 original size:29 final size:29
Alignment explanation
Indices: 23815--23902 Score: 74
Period size: 32 Copynumber: 2.9 Consensus size: 29
23805 ATATAAATTC
*
23815 AAAAT-TAAAATAAATAATAGATAAATAATA
1 AAAATATAAAATAAAAAATAGAT-AAT-ATA
* *
23845 AAAA-ATAAAA-AAATAAATGGTTTAAAATATA
1 AAAATATAAAATAAA-AAATAG---ATAATATA
23876 AAAATATAAAATAAAAAATAGATAATA
1 AAAATATAAAATAAAAAATAGATAATA
23903 CAAACGAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
29 8 0.17
30 13 0.28
31 7 0.15
32 14 0.30
33 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (29 bp):
AAAATATAAAATAAAAAATAGATAATATA
Found at i:25436 original size:2 final size:2
Alignment explanation
Indices: 25431--25463 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
25421 ATTTTTTGTC
25431 AT AT AT AT A- 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
25464 TCCTATAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.