Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015153.1 Corchorus capsularis cultivar CVL-1 contig15174, 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: 40313
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:24 original size:3 final size:3
Alignment explanation
Indices: 4--44 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1 CGT
* *
4 TTC TTT TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
45 GCAGGGCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:882 original size:2 final size:2
Alignment explanation
Indices: 875--899 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
865 CACAAACAAA
875 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
900 ATAATTAAAC
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:3592 original size:65 final size:65
Alignment explanation
Indices: 3487--3723 Score: 350
Period size: 65 Copynumber: 3.6 Consensus size: 65
3477 CTTTTGTTAT
* * * ** * *
3487 ATTAACTCGAATAATTCAAATATCCTCTTTTCACGTGTTTTCTATTCCTGACTCACTATAGTTGG
1 ATTAACTCGAATAATTCGAATATTCTCTTTTCACGCGTTTTCTATTGTTGACTCACTATTGATGG
* * *
3552 ATTAACTCGAATCATTCGAATATTCTAC-TTTCACGCGTTTTCTATTGTTGACTCATTATTGGTG
1 ATTAACTCGAATAATTCGAATATTCT-CTTTTCACGCGTTTTCTATTGTTGACTCACTATTGATG
3616 G
65 G
*
3617 ATTAACTCGAATCATTCGAATATTCTCTTTTCACGCGTTTTCTATTGTTGACTCACTATTGATGG
1 ATTAACTCGAATAATTCGAATATTCTCTTTTCACGCGTTTTCTATTGTTGACTCACTATTGATGG
*
3682 ATTAACTTGAATAATTCGAATATTCTCTTTTCACGCGTTTTC
1 ATTAACTCGAATAATTCGAATATTCTCTTTTCACGCGTTTTC
3724 AATTACATAG
Statistics
Matches: 157, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
64 1 0.01
65 155 0.99
66 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (65 bp):
ATTAACTCGAATAATTCGAATATTCTCTTTTCACGCGTTTTCTATTGTTGACTCACTATTGATGG
Found at i:7456 original size:21 final size:20
Alignment explanation
Indices: 7423--7477 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
7413 TGTATTTGGG
*
7423 CTTATTATTTTTTTTAAGG-C
1 CTTATT-TTTTTTTGAAGGTC
7443 CTTACATTTTTTTTTGAAGGTC
1 CTT--ATTTTTTTTTGAAGGTC
7465 CTTATTTTTTTTT
1 CTTATTTTTTTTT
7478 CCCTTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 13 0.42
21 11 0.35
22 7 0.23
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (20 bp):
CTTATTTTTTTTTGAAGGTC
Found at i:18411 original size:33 final size:33
Alignment explanation
Indices: 18374--18438 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
18364 GCAGTCAACG
18374 AATCAATCACCAGAATCATCACCGCCGCCGAAT
1 AATCAATCACCAGAATCATCACCGCCGCCGAAT
* *
18407 AATCAATCATCGGAATCATCACCGCCGCCGAA
1 AATCAATCACCAGAATCATCACCGCCGCCGAA
18439 GATGGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.35, G:0.14, T:0.15
Consensus pattern (33 bp):
AATCAATCACCAGAATCATCACCGCCGCCGAAT
Found at i:30539 original size:2 final size:2
Alignment explanation
Indices: 30532--30564 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30522 ACAAGGATTT
30532 TA TA TA 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 TA TA TA T
30565 GAGGGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31536 original size:13 final size:13
Alignment explanation
Indices: 31518--31547 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31508 ACTTCACATT
31518 ATAATTAATATAG
1 ATAATTAATATAG
*
31531 ATAATTAGTATAG
1 ATAATTAATATAG
31544 ATAA
1 ATAA
31548 CAACTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (13 bp):
ATAATTAATATAG
Found at i:32501 original size:21 final size:22
Alignment explanation
Indices: 32471--32512 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
32461 GTCTCATCTC
* *
32471 ATATACTAATTA-GATTACTAA
1 ATATAATAATTACCATTACTAA
32492 ATATAATAATTACCATTACTA
1 ATATAATAATTACCATTACTA
32513 TCACAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATAATAATTACCATTACTAA
Found at i:32545 original size:11 final size:11
Alignment explanation
Indices: 32524--32557 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
32514 CACAATGGAT
*
32524 CACGTGCAACG
1 CACGTGTAACG
*
32535 TACGTGTAACG
1 CACGTGTAACG
32546 CACGTGTAACG
1 CACGTGTAACG
32557 C
1 C
32558 TCGTACAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (11 bp):
CACGTGTAACG
Found at i:34678 original size:21 final size:22
Alignment explanation
Indices: 34648--34689 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
34638 ATCTTATCTC
*
34648 ATATACTAATTA-GATTACTAA
1 ATATAATAATTACGATTACTAA
*
34669 ATATAATAATTACTATTACTA
1 ATATAATAATTACGATTACTA
34690 TCACGATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATAATAATTACGATTACTAA
Found at i:38085 original size:11 final size:11
Alignment explanation
Indices: 38071--38108 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38061 ATTCATAACA
38071 AATTTATAATT
1 AATTTATAATT
38082 AATTTATAATT
1 AATTTATAATT
38093 -ATTTGATAATT
1 AATTT-ATAATT
*
38104 TATTT
1 AATTT
38109 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.