Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010849.1 Corchorus capsularis cultivar CVL-1 contig10870, 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: 51770
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:11947 original size:21 final size:21
Alignment explanation
Indices: 11904--11947 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11894 ATAAACCTTG
* *
11904 ATTAATTTGTTTTTAATGCTA
1 ATTAATTTATTTTAAATGCTA
11925 ATTAATTTAATTTTAAATG-TA
1 ATTAATTT-ATTTTAAATGCTA
11946 AT
1 AT
11948 CATATGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTAATTTATTTTAAATGCTA
Found at i:13692 original size:14 final size:14
Alignment explanation
Indices: 13673--13701 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13663 GAAATATAAC
13673 AATAAATAATAATA
1 AATAAATAATAATA
13687 AATAAATAATAATA
1 AATAAATAATAATA
13701 A
1 A
13702 TGGAGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAATAATAATA
Found at i:14527 original size:8 final size:8
Alignment explanation
Indices: 14514--14545 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
14504 AATGGGGGGT
14514 GGCCAAAC
1 GGCCAAAC
14522 GGCCAAAC
1 GGCCAAAC
14530 GGCCAAAC
1 GGCCAAAC
14538 GGCCAAAC
1 GGCCAAAC
14546 CGTCATGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.38, G:0.25, T:0.00
Consensus pattern (8 bp):
GGCCAAAC
Found at i:29203 original size:2 final size:2
Alignment explanation
Indices: 29196--29231 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29186 AAAAGCTGCC
*
29196 TA TA TA TA TA TA TA TA GA 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
29232 ATTATTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30698 original size:11 final size:11
Alignment explanation
Indices: 30682--30706 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30672 AATCAAGTTT
30682 TGTTATAAGTA
1 TGTTATAAGTA
30693 TGTTATAAGTA
1 TGTTATAAGTA
30704 TGT
1 TGT
30707 AGATTCAATG
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (11 bp):
TGTTATAAGTA
Found at i:43301 original size:13 final size:13
Alignment explanation
Indices: 43285--43311 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43275 TTATTCAAAA
43285 TCAAAATTCTTTT
1 TCAAAATTCTTTT
43298 TCAAAATTCTTTT
1 TCAAAATTCTTTT
43311 T
1 T
43312 TTGGGCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TCAAAATTCTTTT
Found at i:47116 original size:18 final size:18
Alignment explanation
Indices: 47077--47118 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
47067 TCAGCCAAAC
* *
47077 AGAAAAGAAGAAGAGAAT
1 AGAAAAGAAGAAGAAAAA
47095 AGAAAAGAA-AAGAAAAGA
1 AGAAAAGAAGAAGAAAA-A
47113 AGAAAA
1 AGAAAA
47119 TCGAAAGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (18 bp):
AGAAAAGAAGAAGAAAAA
Found at i:47124 original size:25 final size:23
Alignment explanation
Indices: 47077--47124 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
47067 TCAGCCAAAC
*
47077 AGAAAAGAAGAAGAGAATAGAAA
1 AGAAAAGAAGAAGAAAATAGAAA
*
47100 AGAAAAGAAAAGAAGAAAATCGAAA
1 AGAAAAG--AAGAAGAAAATAGAAA
47125 GACGAGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.71, C:0.02, G:0.23, T:0.04
Consensus pattern (23 bp):
AGAAAAGAAGAAGAAAATAGAAA
Found at i:47850 original size:12 final size:12
Alignment explanation
Indices: 47813--47874 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
47803 AGCGAATTCT
*
47813 TTATGAAAATCA
1 TTATAAAAATCA
**
47825 TTAT-AATTTCA
1 TTATAAAAATCA
47836 TTATAAAAATCA
1 TTATAAAAATCA
**
47848 -T-T-AATTTCA
1 TTATAAAAATCA
47857 TTATAAAAATCA
1 TTATAAAAATCA
47869 TTATAA
1 TTATAA
47875 TTTCAATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 11 0.29
12 20 0.53
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (12 bp):
TTATAAAAATCA
Found at i:47854 original size:21 final size:23
Alignment explanation
Indices: 47813--47885 Score: 114
Period size: 21 Copynumber: 3.2 Consensus size: 23
47803 AGCGAATTCT
*
47813 TTATGAAAATCATTATAATTTCA
1 TTATAAAAATCATTATAATTTCA
47836 TTATAAAAATCA-T-TAATTTCA
1 TTATAAAAATCATTATAATTTCA
47857 TTATAAAAATCATTATAATTTCAA
1 TTATAAAAATCATTATAATTTC-A
47881 TTATA
1 TTATA
47886 TTTATTTATA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 20 0.43
22 2 0.04
23 18 0.39
24 6 0.13
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (23 bp):
TTATAAAAATCATTATAATTTCA
Found at i:49439 original size:7 final size:7
Alignment explanation
Indices: 49427--49453 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
49417 AATTCTATTC
49427 CTCTAGG
1 CTCTAGG
49434 CTCTAGG
1 CTCTAGG
49441 CTCTAGG
1 CTCTAGG
49448 CTCTAG
1 CTCTAG
49454 CATTTCCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (7 bp):
CTCTAGG
Found at i:49647 original size:13 final size:14
Alignment explanation
Indices: 49629--49657 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49619 AGAGCGTCAT
49629 ATATATAATA-ATA
1 ATATATAATATATA
49642 ATATATAATATATA
1 ATATATAATATATA
49656 AT
1 AT
49658 TAATATCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATAATATATA
Found at i:49651 original size:7 final size:7
Alignment explanation
Indices: 49629--49657 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49619 AGAGCGTCAT
49629 ATATATA
1 ATATATA
49636 ATA-ATA
1 ATATATA
49642 ATATATA
1 ATATATA
49649 ATATATA
1 ATATATA
49656 AT
1 AT
49658 TAATATCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATATA
Done.