Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016113.1 Corchorus capsularis cultivar CVL-1 contig16134, 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: 9823
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Found at i:3210 original size:21 final size:21
Alignment explanation
Indices: 3186--3233 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3176 CTATTATCGC
*
3186 TTTTGCTCTTACCGATTACTG
1 TTTTACTCTTACCGATTACTG
* *
3207 TTTTACTCTTACTGATTAC-C
1 TTTTACTCTTACCGATTACTG
3227 TTTTACT
1 TTTTACT
3234 GATTACTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.17, C:0.23, G:0.08, T:0.52
Consensus pattern (21 bp):
TTTTACTCTTACCGATTACTG
Found at i:3232 original size:14 final size:14
Alignment explanation
Indices: 3215--3262 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
3205 TGTTTTACTC
3215 TTACTGATTACCTT
1 TTACTGATTACCTT
*
3229 TTACTGATTACTATT
1 TTACTGATTAC-CTT
*
3244 TTACTGATTATCTT
1 TTACTGATTACCTT
3258 TTACT
1 TTACT
3263 TTTTACTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (14 bp):
TTACTGATTACCTT
Found at i:3239 original size:21 final size:21
Alignment explanation
Indices: 3167--3240 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
3157 TTTTTCTCTC
3167 TACTGATTACT-ATTATCGCTTT
1 TACT-ATTACTGATTA-CGCTTT
* * *
3189 TGCTCTTACCGATTACTG-TTT
1 TACTATTACTGATTAC-GCTTT
*
3210 TACTCTTACTGATTAC-CTTT
1 TACTATTACTGATTACGCTTT
3230 TACTGATTACT
1 TACT-ATTACT
3241 ATTTTACTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
20 7 0.17
21 27 0.64
22 8 0.19
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.49
Consensus pattern (21 bp):
TACTATTACTGATTACGCTTT
Found at i:3275 original size:14 final size:14
Alignment explanation
Indices: 3215--3259 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
3205 TGTTTTACTC
*
3215 TTACTGATTACCTT
1 TTACTGATTACTTT
3229 TTACTGATTACTATT
1 TTACTGATTACT-TT
3244 TTACTGATTATCTTT
1 TTACTGATTA-CTTT
3259 T
1 T
3260 ACTTTTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 11 0.39
15 15 0.54
16 2 0.07
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (14 bp):
TTACTGATTACTTT
Found at i:3295 original size:44 final size:43
Alignment explanation
Indices: 3236--3473 Score: 171
Period size: 43 Copynumber: 5.3 Consensus size: 43
3226 CTTTTACTGA
* *
3236 TTACTATTTTACTGATTATCTTTTACTTTTTACTGATTACCATT
1 TTACT-TTTTACTGATTATCTTTTGCTTTTTACTGATTACCTTT
* * *
3280 TTACTCTTTTTCTGATTACCATTTTCTGCTCCCTTTTTTACTGGTTA-CTTT
1 TTACT-TTTTACTGATTATC--TTT-TG----C-TTTTTACTGATTACCTTT
* **
3331 TTAGTTTTTACTGATTGCCTTTTGCTTTTTA-TCGATTACCTTT
1 TTACTTTTTACTGATTATCTTTTGCTTTTTACT-GATTACCTTT
* * *
3374 TTACTTTTTGCTGATTAGCTTTTTGCTCTTTACTGATTACCTTT
1 TTACTTTTTACTGATTATC-TTTTGCTTTTTACTGATTACCTTT
* * * *
3418 TTAC-TCTTACTAATT-TCCTTTTGCTTCTTACTTATTACCCTTT
1 TTACTTTTTACTGATTAT-CTTTTGCTTTTTACTGATTA-CCTTT
*
3461 TTAC-TCTTACTGA
1 TTACTTTTTACTGA
3474 GTACTATTTA
Statistics
Matches: 157, Mismatches: 23, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
41 1 0.01
42 26 0.17
43 46 0.29
44 42 0.27
45 1 0.01
46 3 0.02
47 3 0.02
48 3 0.02
50 12 0.08
51 8 0.05
52 12 0.08
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (43 bp):
TTACTTTTTACTGATTATCTTTTGCTTTTTACTGATTACCTTT
Found at i:3352 original size:22 final size:23
Alignment explanation
Indices: 3242--3463 Score: 132
Period size: 21 Copynumber: 9.9 Consensus size: 23
3232 CTGATTACTA
*
3242 TTTTACTGATTATC-TTTTA-CT
1 TTTTACTGATTACCTTTTTAGCT
*
3263 TTTTACTGATTACCATTTTA-CT
1 TTTTACTGATTACCTTTTTAGCT
*
3285 CTTTTTCTGATTACCATTTTCT-GCTCCCTT
1 -TTTTACTGATTACC-TTTT-TAG----C-T
*
3315 TTTTACTGGTTA-CTTTTTAG-T
1 TTTTACTGATTACCTTTTTAGCT
*
3336 TTTTACTGATTGCC-TTTT-GCT
1 TTTTACTGATTACCTTTTTAGCT
3357 TTTTA-TCGATTACCTTTTTA-CT
1 TTTTACT-GATTACCTTTTTAGCT
* *
3379 TTTTGCTGATTAGCTTTTT-GCT
1 TTTTACTGATTACCTTTTTAGCT
*
3401 CTTTACTGATTACCTTTTTA-C-
1 TTTTACTGATTACCTTTTTAGCT
* * *
3422 TCTTACTAATTTCC-TTTT-GCT
1 TTTTACTGATTACCTTTTTAGCT
* *
3443 TCTTACTTATTACCCTTTTTA
1 TTTTACTGATTA-CCTTTTTA
3464 CTCTTACTGA
Statistics
Matches: 158, Mismatches: 19, Indels: 45
0.71 0.09 0.20
Matches are distributed among these distances:
20 7 0.04
21 60 0.38
22 50 0.32
23 18 0.11
24 3 0.02
25 1 0.01
26 1 0.01
27 5 0.03
28 1 0.01
29 11 0.07
30 1 0.01
ACGTcount: A:0.15, C:0.20, G:0.08, T:0.57
Consensus pattern (23 bp):
TTTTACTGATTACCTTTTTAGCT
Found at i:3427 original size:21 final size:21
Alignment explanation
Indices: 3364--3473 Score: 105
Period size: 22 Copynumber: 5.1 Consensus size: 21
3354 GCTTTTTATC
* *
3364 GATTACCTTTTTACTTTTTGCT
1 GATTACCTTTTTAC-TCTTACT
* *
3386 GATTAGCTTTTTGCTCTTTACT
1 GATTACCTTTTTACTC-TTACT
3408 GATTACCTTTTTACTCTTACT
1 GATTACCTTTTTACTCTTACT
* * *
3429 AATTTCC-TTTTGCTTCTTACT
1 GATTACCTTTTTAC-TCTTACT
*
3450 TATTACCCTTTTTACTCTTACT
1 GATTA-CCTTTTTACTCTTACT
3472 GA
1 GA
3474 GTACTATTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.07
21 21 0.30
22 40 0.56
23 5 0.07
ACGTcount: A:0.16, C:0.22, G:0.07, T:0.55
Consensus pattern (21 bp):
GATTACCTTTTTACTCTTACT
Found at i:3542 original size:22 final size:22
Alignment explanation
Indices: 3517--3569 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3507 GACTACCTTC
* * *
3517 TTACTTTTTACTGATTACTATT
1 TTACTCTTTACTAATTACCATT
3539 TTACTCTTTACTAATTACCATT
1 TTACTCTTTACTAATTACCATT
*
3561 TTACCCTTT
1 TTACTCTTT
3570 TAGATACCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.55
Consensus pattern (22 bp):
TTACTCTTTACTAATTACCATT
Found at i:3780 original size:22 final size:24
Alignment explanation
Indices: 3753--3796 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
3743 TTAACCACTC
3753 AACTCTTAATTAT-GA-TCACTTT
1 AACTCTTAATTATCGATTCACTTT
3775 AACTCTTAATTATCGATTCACT
1 AACTCTTAATTATCGATTCACT
3797 GATTACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (24 bp):
AACTCTTAATTATCGATTCACTTT
Found at i:3983 original size:54 final size:55
Alignment explanation
Indices: 3879--3992 Score: 160
Period size: 55 Copynumber: 2.1 Consensus size: 55
3869 TATCTTTTAC
* * *
3879 CTGA-TTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACCCTAATTAATCTCTTTTTACTTAATTA
* * *
3933 CTGATTTACTGATTACTGCTACTTTGACCCTAATTAATCTC-TTTTACTTAATTA
1 CTGATTTACTGATTACTACTACCTTAACCCTAATTAATCTCTTTTTACTTAATTA
3987 CTGATT
1 CTGATT
3993 GCCCCCTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 23 0.43
55 30 0.57
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (55 bp):
CTGATTTACTGATTACTACTACCTTAACCCTAATTAATCTCTTTTTACTTAATTA
Found at i:4757 original size:101 final size:102
Alignment explanation
Indices: 4647--4905 Score: 358
Period size: 101 Copynumber: 2.5 Consensus size: 102
4637 AAGGGTGACA
* * *
4647 TTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAATGGTTAAATCTTTATTCATTAACC
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTCACTAACC
4712 ACCCTAAAAATTCAATCTTTTACTCAAAGATAACA-T
66 ACCCTAAAAATTCAATCTTTTACTCAAAGATAACATT
* * * * * * **
4748 TTTTGTTTACCGATTACTTAAAAATTGAATCTTTTGTTTAAAGGTTAAATCTTTATTTACTAATT
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTCACTAACC
* *
4813 ACCCTAAAAATTCAATCTTTTACTCAAAGATGATATT
66 ACCCTAAAAATTCAATCTTTTACTCAAAGATAACATT
* *
4850 TTTTATTTACCAATTTGCTTAAAAATTCAATCTTTTCATTCAAAGGTTACATCTTT
1 TTTTATTTACCAA-TTACTTAAAAATTCAATCTTTT-ATTCAAAGGTTAAATCTTT
4906 TAGCAAAAGG
Statistics
Matches: 135, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
101 87 0.64
102 12 0.09
103 20 0.15
104 16 0.12
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (102 bp):
TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTCACTAACC
ACCCTAAAAATTCAATCTTTTACTCAAAGATAACATT
Found at i:4832 original size:51 final size:50
Alignment explanation
Indices: 4648--4905 Score: 239
Period size: 51 Copynumber: 5.1 Consensus size: 50
4638 AGGGTGACAT
*
4648 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAATGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * ** * * * *
4698 TTTATTCATTAACCACCCTAAAAATTCAATCTTTTACTCAAA-GATAACATT
1 TTTATTTACTAATTA-CTTAAAAATTCAATCTTTTATTCAAAGGTTAA-ATC
* ** * * *
4749 TTTGTTTACCGATTACTTAAAAATTGAATCTTTTGTTTAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * * * * *
4799 TTTATTTACTAATTACCCTAAAAATTCAATCTTTTACTCAAAGATGATATTT
1 TTTATTTACTAATTA-CTTAAAAATTCAATCTTTTATTCAAAGGTTA-AATC
* * *
4851 TTTATTTACCAATTTGCTTAAAAATTCAATCTTTTCATTCAAAGGTTACATC
1 TTTATTTACTAA-TTACTTAAAAATTCAATCTTTT-ATTCAAAGGTTAAATC
4903 TTT
1 TTT
4906 TAGCAAAAGG
Statistics
Matches: 157, Mismatches: 44, Indels: 12
0.74 0.21 0.06
Matches are distributed among these distances:
50 50 0.32
51 61 0.39
52 35 0.22
53 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
Found at i:7889 original size:17 final size:17
Alignment explanation
Indices: 7867--7899 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7857 TAGATAAATA
*
7867 ATAGTATTAAATAGATG
1 ATAGTACTAAATAGATG
7884 ATAGTACTAAATAGAT
1 ATAGTACTAAATAGAT
7900 AATAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
ATAGTACTAAATAGATG
Done.