Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011234.1 Corchorus capsularis cultivar CVL-1 contig11255, 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: 11582
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Found at i:2777 original size:14 final size:14
Alignment explanation
Indices: 2743--2800 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
2733 ACTATTAAAA
2743 CAAGAAACTT-TTTT
1 CAAGAAA-TTGTTTT
2757 CAA-AAATTGTTTT
1 CAAGAAATTGTTTT
*
2770 CAAGAAATGGTTTT
1 CAAGAAATTGTTTT
*
2784 C-AGAAATGAGTTTT
1 CAAGAAAT-TGTTTT
2798 CAA
1 CAA
2801 AAAGGTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.05
13 16 0.42
14 19 0.50
15 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (14 bp):
CAAGAAATTGTTTT
Found at i:5207 original size:84 final size:79
Alignment explanation
Indices: 5106--5631 Score: 356
Period size: 70 Copynumber: 7.1 Consensus size: 79
5096 CAAATTAATT
* *
5106 AGATGACTCGGTGTAGCATCTTCAAAGATAGATTCAGTGAATCAGATGACTCGGTGTAGCATATT
1 AGATGACTCGATGTAGCATCTTCAAAGATAGATTC-GTGAATCAGATGACTCGGTGTAGCATCTT
5171 CAAAGATAGATTTGGATTC
65 C-AA-A-AGA-TTGGATTC
* * *
5190 AGATGACTCGGTGTAGCATCCTCAAAGATAGATTCGGTGAATCAGATGAATCGGTGTAGCATCTT
1 AGATGACTCGATGTAGCATCTTCAAAGATAGATTC-GTGAATCAGATGACTCGGTGTAGCATCTT
5255 C-AAA-ATTGGATTC
65 CAAAAGATTGGATTC
* **
5268 GGATGACTCGATGTAGCATCTTTC----ATAG-TT-G-GTTTCAGATGACTCGGTGTAGCATCTT
1 AGATGACTCGATGTAGCATC-TTCAAAGATAGATTCGTGAATCAGATGACTCGGTGTAGCATCTT
5326 CAAAAG-TTGGATTC
65 CAAAAGATTGGATTC
* * *
5340 AGATGACTCGATGTAGCATTTTTC----ATAG-TT-G-G-TTCCAAATGACTCGGTGTAGCATCT
1 AGATGACTCGATGTAGCA-TCTTCAAAGATAGATTCGTGAAT-CAGATGACTCGGTGTAGCATC-
*
5397 TTC-AAAG-TTGGTTTC
63 TTCAAAAGATTGGATTC
* * * * *
5412 AGATGACTCGGTGTAGCATCTTC--A-A-A-ATT-G-GATTCGGATGACTTGGTGCAGCATCTTC
1 AGATGACTCGATGTAGCATCTTCAAAGATAGATTCGTGAATCAGATGACTCGGTGTAGCATCTTC
*
5470 -AAAG-TTGGTTTC
66 AAAAGATTGGATTC
* * * *
5482 AGATGACTCTG-TGTAGCATCTTC--A-A-A-ATT-G-GATTCGGATGACTTGGTGCAGCATCTT
1 AGATGACTC-GATGTAGCATCTTCAAAGATAGATTCGTGAATCAGATGACTCGGTGTAGCATCTT
*
5539 C-AAAG-TTGGTTTC
65 CAAAAGATTGGATTC
* * * **
5552 AGATGACTTGGTGCAGCATCTTC--A-A-AG-TT-G-GTTTCAGATGACTCGGTGTAGCATCTTC
1 AGATGACTCGATGTAGCATCTTCAAAGATAGATTCGTGAATCAGATGACTCGGTGTAGCATCTTC
5610 -AAA-ATTGGATTC
66 AAAAGATTGGATTC
*
5622 GGATGACTCG
1 AGATGACTCG
5632 GTACAATATC
Statistics
Matches: 400, Mismatches: 29, Indels: 40
0.85 0.06 0.09
Matches are distributed among these distances:
69 1 0.00
70 150 0.38
71 54 0.14
72 91 0.23
73 4 0.01
74 2 0.00
75 4 0.01
78 26 0.06
79 3 0.01
80 1 0.00
81 1 0.00
82 1 0.00
84 62 0.16
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (79 bp):
AGATGACTCGATGTAGCATCTTCAAAGATAGATTCGTGAATCAGATGACTCGGTGTAGCATCTTC
AAAAGATTGGATTC
Found at i:5269 original size:43 final size:43
Alignment explanation
Indices: 5106--5258 Score: 238
Period size: 43 Copynumber: 3.6 Consensus size: 43
5096 CAAATTAATT
*
5106 AGATGACTCGGTGTAGCATCTTCAAAGATAGATTCAGTGAATC
1 AGATGACTCGGTGTAGCATCTTCAAAGATAGATTCGGTGAATC
* * *
5149 AGATGACTCGGTGTAGCATATTCAAAGATAGATT-TG-GATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGATAGATTCGGTGAATC
*
5190 AGATGACTCGGTGTAGCATCCTCAAAGATAGATTCGGTGAATC
1 AGATGACTCGGTGTAGCATCTTCAAAGATAGATTCGGTGAATC
*
5233 AGATGAATCGGTGTAGCATCTTCAAA
1 AGATGACTCGGTGTAGCATCTTCAAA
5259 ATTGGATTCG
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 36 0.36
42 2 0.02
43 61 0.62
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (43 bp):
AGATGACTCGGTGTAGCATCTTCAAAGATAGATTCGGTGAATC
Found at i:5283 original size:35 final size:35
Alignment explanation
Indices: 5231--5633 Score: 511
Period size: 35 Copynumber: 11.4 Consensus size: 35
5221 ATTCGGTGAA
* *
5231 TCAGATGAATCGGTGTAGCATCTTCAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * * *
5266 TCGGATGACTCGATGTAGCATCTTTCATAGTTGGTT
1 TCAGATGACTCGGTGTAGCATC-TTCAAAGTTGGAT
5302 TCAGATGACTCGGTGTAGCATCTTCAAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTC-AAAGTTGGAT
* * *
5338 TCAGATGACTCGATGTAGCATTTTTCATAGTTGG-T
1 TCAGATGACTCGGTGTAGCA-TCTTCAAAGTTGGAT
* *
5373 TCCAAATGACTCGGTGTAGCATCTTTCAAAGTTGGTT
1 T-CAGATGACTCGGTGTAGCATC-TTCAAAGTTGGAT
*
5410 TCAGATGACTCGGTGTAGCATCTTCAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * * *
5445 TCGGATGACTTGGTGCAGCATCTTCAAAGTTGGTT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* *
5480 TCAGATGACTCTGTGTAGCATCTTCAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * * *
5515 TCGGATGACTTGGTGCAGCATCTTCAAAGTTGGTT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * *
5550 TCAGATGACTTGGTGCAGCATCTTCAAAGTTGGTT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
*
5585 TCAGATGACTCGGTGTAGCATCTTCAAAATTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
*
5620 TCGGATGACTCGGT
1 TCAGATGACTCGGT
5634 ACAATATCTT
Statistics
Matches: 319, Mismatches: 43, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
35 202 0.63
36 111 0.35
37 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
Found at i:7135 original size:21 final size:21
Alignment explanation
Indices: 7107--7160 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
7097 ACTAGCGCTG
7107 GGCG-CCCATGTGGTAAGCCT
1 GGCGCCCCATGTGGTAAGCCT
**
7127 GGCGCCCCA-GCTGGTTTGCCT
1 GGCGCCCCATG-TGGTAAGCCT
*
7148 CGCGCCCCATGTG
1 GGCGCCCCATGTG
7161 CTCCAGTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.09, C:0.37, G:0.33, T:0.20
Consensus pattern (21 bp):
GGCGCCCCATGTGGTAAGCCT
Done.