Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015632.1 Corchorus olitorius cultivar O-4 contig15665, 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: 26835
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2206 original size:15 final size:15
Alignment explanation
Indices: 2186--2239 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
2176 GATCAAATGA
*
2186 GGAGGGGTAGGGTGG
1 GGAGGGGTAGGGTAG
*
2201 GGAGGGGTGGGGTAG
1 GGAGGGGTAGGGTAG
* *
2216 GGAGGGGGAGGGTTTG
1 GGAGGGGTAGGG-TAG
2232 GGAGGGGT
1 GGAGGGGT
2240 TTTAGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 23 0.72
16 9 0.28
ACGTcount: A:0.13, C:0.00, G:0.72, T:0.15
Consensus pattern (15 bp):
GGAGGGGTAGGGTAG
Found at i:2228 original size:20 final size:20
Alignment explanation
Indices: 2189--2227 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2179 CAAATGAGGA
*
2189 GGGGTAGGGTGGGGAGGGGT
1 GGGGTAGGGGGGGGAGGGGT
2209 GGGGTAGGGAGGGGGAGGG
1 GGGGTAGGG-GGGGGAGGG
2228 TTTGGGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.13, C:0.00, G:0.77, T:0.10
Consensus pattern (20 bp):
GGGGTAGGGGGGGGAGGGGT
Found at i:2685 original size:17 final size:17
Alignment explanation
Indices: 2659--2691 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2649 GGGCAAGAAA
*
2659 TAAAATATAAATTATTT
1 TAAAAAATAAATTATTT
2676 TAAAAAATAAATTATT
1 TAAAAAATAAATTATT
2692 ATATATTCCT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAAATAAATTATTT
Found at i:2805 original size:22 final size:22
Alignment explanation
Indices: 2758--2805 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2748 TAAAAATTAT
* *
2758 ATTATATTATTATATTTATTTT
1 ATTATATTATTAGATTTATTTC
*
2780 ATTATTTTATTAGATTT-TATTC
1 ATTATATTATTAGATTTAT-TTC
2802 ATTA
1 ATTA
2806 AGGACAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTATATTATTAGATTTATTTC
Found at i:4447 original size:3 final size:3
Alignment explanation
Indices: 4439--4472 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4429 GCGGGGAAAA
*
4439 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4473 GTTGTTGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4791 original size:108 final size:109
Alignment explanation
Indices: 4637--4941 Score: 359
Period size: 110 Copynumber: 2.8 Consensus size: 109
4627 ATTTTCTTTC
*
4637 TCTAAAACCCTATG-TAATGGTGTTACAAATATTTGAGATTTACCCTTTTAAAAAATAAAACATT
1 TCTAAAACCCTATGATAAT-GTGTTTCAAA-ATTTGAGATTTACCCTTTT-AAAAATAAAACATT
* ** *
4701 TTTATCGTTGGGGCTAAACCTTA-TTATAAGTGTTTAAAATTA-TTT
63 TTTATAGTTGGGGCTAAACCTTAGGGATAAGTATTTAAAATTATTTT
* * * * *
4746 TCTAAAACCCTAGGATAATGTGTTTCGAAATTTGAGATTTACCCTTTTGACAAACATAACATTTT
1 TCTAAAACCCTATGATAATGTGTTTCAAAATTTGAGATTTACCCTTTT-AAAAATAAAACATTTT
* * *
4811 TATAATTGGGGCTAAACCTTAGGGATAGGTATTTAAACTTATTTT
65 TATAGTTGGGGCTAAACCTTAGGGATAAGTATTTAAAATTATTTT
** * *
4856 TCTAAAATTCTATGATAAT-TGGTCTT-AAAATTTAAGATTTACCCTTTTAAATATAAAACATTT
1 TCTAAAACCCTATGATAATGT-GT-TTCAAAATTTGAGATTTACCCTTTTAAAAATAAAACA-TT
4919 TTTATAGTTGGGGCTAAACCTTA
63 TTTATAGTTGGGGCTAAACCTTA
4942 ATTAATTGTT
Statistics
Matches: 166, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
108 51 0.31
109 44 0.27
110 69 0.42
111 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (109 bp):
TCTAAAACCCTATGATAATGTGTTTCAAAATTTGAGATTTACCCTTTTAAAAATAAAACATTTTT
ATAGTTGGGGCTAAACCTTAGGGATAAGTATTTAAAATTATTTT
Found at i:7318 original size:30 final size:30
Alignment explanation
Indices: 7221--7306 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
7211 TTCAAAGGAT
7221 GATTTTGACCCAGATGAGGATCCCGAAGAG
1 GATTTTGACCCAGATGAGGATCCCGAAGAG
* *
7251 GATTTTGACCCGGACGAGGATCCCGAAGAG
1 GATTTTGACCCAGATGAGGATCCCGAAGAG
*
7281 GATTTTGACCCAAATGAGGATCCCGA
1 GATTTTGACCCAGATGAGGATCCCGA
7307 GGAAGAGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (30 bp):
GATTTTGACCCAGATGAGGATCCCGAAGAG
Found at i:21637 original size:211 final size:211
Alignment explanation
Indices: 21265--21687 Score: 810
Period size: 211 Copynumber: 2.0 Consensus size: 211
21255 AGAAACCTCC
*
21265 AACATAGAATTAATATCCCTCTTGACAACAATAACATGGATCATTTATATCTAAAGATTATGAAA
1 AACATAGAATTAATATCCCTCTTGACAACAATAACATGGATCATTGATATCTAAAGATTATGAAA
21330 ACAATGGATAGCTTGCTTGGAATTTAATCCTAAATTACCTTAATTAGATAAAGCTCTTGATCCAG
66 ACAATGGATAGCTTGCTTGGAATTTAATCCTAAATTACCTTAATTAGATAAAGCTCTTGATCCAG
21395 TGTGAATTATCCCTTTTATTCTTTAAATAATTACCTCTTGATCCAGTGTGATAATTACTCAAGAA
131 TGTGAATTATCCCTTTTATTCTTTAAATAATTACCTCTTGATCCAGTGTGATAATTACTCAAGAA
21460 TAAAGCATTAAGATCT
196 TAAAGCATTAAGATCT
21476 AACATAGAATTAATATCCCTCTTGACAACAATAACATGGATCATTGATATCTAAAGATTATGAAA
1 AACATAGAATTAATATCCCTCTTGACAACAATAACATGGATCATTGATATCTAAAGATTATGAAA
*
21541 ACAGTGGATAGCTTGCTTGGAATTTAATCCTAAATTACCTTAATTAGATAAAGCTCTTGATCCAG
66 ACAATGGATAGCTTGCTTGGAATTTAATCCTAAATTACCTTAATTAGATAAAGCTCTTGATCCAG
* *
21606 TGTGAATTATCCCTTTTATTTTTTGAATAATTACCTCTTGATCCAGTGTGATAATTACTCAAGAA
131 TGTGAATTATCCCTTTTATTCTTTAAATAATTACCTCTTGATCCAGTGTGATAATTACTCAAGAA
21671 TAAAGCATTAAGATCT
196 TAAAGCATTAAGATCT
21687 A
1 A
21688 GTAATTTACA
Statistics
Matches: 208, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 208 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (211 bp):
AACATAGAATTAATATCCCTCTTGACAACAATAACATGGATCATTGATATCTAAAGATTATGAAA
ACAATGGATAGCTTGCTTGGAATTTAATCCTAAATTACCTTAATTAGATAAAGCTCTTGATCCAG
TGTGAATTATCCCTTTTATTCTTTAAATAATTACCTCTTGATCCAGTGTGATAATTACTCAAGAA
TAAAGCATTAAGATCT
Found at i:22737 original size:19 final size:18
Alignment explanation
Indices: 22704--22739 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22694 TTGAAATTAT
*
22704 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
22722 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
22740 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:25294 original size:20 final size:21
Alignment explanation
Indices: 25256--25294 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25246 TCCTTGTCGA
25256 CGATTTGCTCCTCTCTTTAGC
1 CGATTTGCTCCTCTCTTTAGC
25277 CGATTATGCT-CT-TCTTTA
1 CGATT-TGCTCCTCTCTTTA
25295 TTCGGCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.13, C:0.28, G:0.13, T:0.46
Consensus pattern (21 bp):
CGATTTGCTCCTCTCTTTAGC
Done.