Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014790.1 Corchorus capsularis cultivar CVL-1 contig14811, 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: 27973
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:89 original size:41 final size:41
Alignment explanation
Indices: 41--123 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
31 TTTACAGTGA
* *
41 TAATTAATTTATAGATTACTCATTCTGTCCCTTTTTATAAG
1 TAATTAATTTATAGATTACTCATTCTATCCATTTTTATAAG
82 TAATTAATTTATAGATTACTCATTCTATCCATTTTTATAAG
1 TAATTAATTTATAGATTACTCATTCTATCCATTTTTATAAG
123 T
1 T
124 CTCTTTTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.49
Consensus pattern (41 bp):
TAATTAATTTATAGATTACTCATTCTATCCATTTTTATAAG
Found at i:261 original size:22 final size:22
Alignment explanation
Indices: 215--263 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
205 TGCCTTTTTT
*
215 TCTCT-CTCCCCCCACTTAATC
1 TCTCTCCTCCCCCCACTTAATA
*
236 TCTCTCCTCCTCCCAC-TAACTA
1 TCTCTCCTCCCCCCACTTAA-TA
258 TCTCTC
1 TCTCTC
264 TACATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTCTCCTCCCCCCACTTAATA
Found at i:7680 original size:25 final size:25
Alignment explanation
Indices: 7617--7686 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 25
7607 TTTACTATCT
7617 TAAATATAAT-ATATATTATTAAATAA
1 TAAATA-AATAATATATT-TTAAATAA
7643 -ATAAT-AA-AA-ATATTTTAAATAA
1 TA-AATAAATAATATATTTTAAATAA
7665 TAAATAAATAATATATATTTAA
1 TAAATAAATAATATAT-TTTAA
7687 TTACTAAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
22 11 0.30
23 8 0.22
24 5 0.14
25 5 0.14
26 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAATAAATAATATATTTTAAATAA
Found at i:9581 original size:272 final size:266
Alignment explanation
Indices: 9058--9603 Score: 665
Period size: 272 Copynumber: 2.0 Consensus size: 266
9048 TTCCAAGTGG
* *
9058 ATTAGCCCACGCTTATGCTGTAGGCAAAATTTTCAAATTTGAACATGGGTTTACACATAAATAGG
1 ATTAGCCCACACTTATGCTGCAGGCAAAATTTTCAAATTTGAACATGGGTTTACACATAAATAGG
* * *
9123 CCCGTTGAATCTGAACTTACTAATAAGTCTATTATTATATTATTATTATAACTTTAAACACATAG
66 CCCATTGAATCTGAACTTACTAATAAATCTATTATTATATTATTATTATAAATTTAAACACATAG
* * *
9188 ATACAAGACAAAATTTGGGTTATTATCTCTATCGTAAAAAAAAAAGTAGATTGTGAGTTTTAATA
131 ATAAAAGACAAAAATTGGGTTATTATATCTATCGT-AAAAAAAAAGTAGATTGTGAGTTTTAATA
9253 ATTTTGGTGGGTACTCATCAAATAATATATAAGAGTATATAATATATATATATATATATAAGATT
195 ATTTTGGTGGGTAC-CATCAAATAATATAT-A-AGTATAT-A-ATATATATATATATATAAGATT
*
9318 CTCATATATATT
255 ATCATATATATT
* * ** **
9330 ATTAGCCCACACTTATGCTGCAGGTAAAATTTTGAAATTTGAACATGGGTTTACATGTGTATAGG
1 ATTAGCCCACACTTATGCTGCAGGCAAAATTTTCAAATTTGAACATGGGTTTACACATAAATAGG
* * *
9395 TCCATTGAAATTTGGACTTACTAATAAATCTGTTATTATATTATTATTATTATCATTATAAATTT
66 CCCATTG-AATCTGAACTTACTAATAAATC---TA-T-TATTA-TATTA-T-T-ATTATAAATTT
* *
9460 AAACACATAGATAAAAGATAAAAATTGGGTTGTTATATCTATCGT-AAAAAAAAGTAGATTGTGA
121 AAACACATAGATAAAAGACAAAAATTGGGTTATTATATCTATCGTAAAAAAAAAGTAGATTGTGA
* * * *
9524 GTTTTAGTAATTTTGGTAGGGTA-C-TCAAATAATATAT-AGTA-GT-ATATA-GTGTATATATA
186 GTTTTAATAATTTTGGT-GGGTACCATCAAATAATATATAAGTATATAATATATATATATATATA
*
9583 AGATTATCATATTTATT
250 AGATTATCATATATATT
9600 ATTA
1 ATTA
9604 TTTATAATTA
Statistics
Matches: 238, Mismatches: 25, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
270 28 0.12
271 5 0.02
272 62 0.26
273 19 0.08
274 1 0.00
275 4 0.02
276 2 0.01
277 1 0.00
278 18 0.08
279 6 0.03
280 36 0.15
281 6 0.03
282 50 0.21
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (266 bp):
ATTAGCCCACACTTATGCTGCAGGCAAAATTTTCAAATTTGAACATGGGTTTACACATAAATAGG
CCCATTGAATCTGAACTTACTAATAAATCTATTATTATATTATTATTATAAATTTAAACACATAG
ATAAAAGACAAAAATTGGGTTATTATATCTATCGTAAAAAAAAAGTAGATTGTGAGTTTTAATAA
TTTTGGTGGGTACCATCAAATAATATATAAGTATATAATATATATATATATATAAGATTATCATA
TATATT
Found at i:11490 original size:25 final size:25
Alignment explanation
Indices: 11461--11517 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
11451 TCTTTTCTAC
*
11461 TAGTTGTTTTTTACTATGTGTTTAA
1 TAGTTGTTTTCTACTATGTGTTTAA
11486 TAGTTGTTTTCTACTATGTGTTTAA
1 TAGTTGTTTTCTACTATGTGTTTAA
11511 TAGTTGT
1 TAGTTGT
11518 AACAAGTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.05, G:0.18, T:0.58
Consensus pattern (25 bp):
TAGTTGTTTTCTACTATGTGTTTAA
Found at i:13113 original size:25 final size:25
Alignment explanation
Indices: 13085--13133 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13075 CTTCCAAGAA
13085 AAGATGTGGTTGGATAGAAAGAGTT
1 AAGATGTGGTTGGATAGAAAGAGTT
*
13110 AAGATGTGGTTGGATAGATAGAGT
1 AAGATGTGGTTGGATAGAAAGAGT
13134 AATTCAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.29
Consensus pattern (25 bp):
AAGATGTGGTTGGATAGAAAGAGTT
Found at i:13581 original size:30 final size:29
Alignment explanation
Indices: 13540--13608 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
13530 TAAATTGGCC
* *
13540 CCATGAACTATTGTGTCAAGGACGTTTTG
1 CCATAAACTATTGTGTCAAGGACATTTTG
*
13569 TCCATAAACTATTGTGTCAATGACATTTTG
1 -CCATAAACTATTGTGTCAAGGACATTTTG
13599 CACATAAACT
1 C-CATAAACT
13609 TCAAATTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (29 bp):
CCATAAACTATTGTGTCAAGGACATTTTG
Found at i:13667 original size:31 final size:31
Alignment explanation
Indices: 13610--13688 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
13600 ACATAAACTT
* *
13610 CAAATTAGGACATTTCGCCCTCTGAACAT-C
1 CAAATTAGGACATTTTGCCCTATGAACATCC
*
13640 CAAATTCAGGACATTTTGTCCC-ATGAACTTCC
1 CAAATT-AGGACATTTTG-CCCTATGAACATCC
*
13672 CAAATTTAAGACATTTT
1 CAAA-TTAGGACATTTT
13689 TCCTAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 6 0.15
31 16 0.39
32 17 0.41
33 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (31 bp):
CAAATTAGGACATTTTGCCCTATGAACATCC
Found at i:25299 original size:21 final size:20
Alignment explanation
Indices: 25269--25321 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
25259 ACTAGCGCTG
*
25269 GGCGCCCATGTGGTATGCTT
1 GGCGCCCATGTGGTATGCCT
*
25289 GGCGCCCCATGTGGTTTGCCT
1 GGCG-CCCATGTGGTATGCCT
*
25310 CGCGACCCATGT
1 GGCG-CCCATGT
25322 ACTCCAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.26
Consensus pattern (20 bp):
GGCGCCCATGTGGTATGCCT
Done.