Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008949.1 Corchorus capsularis cultivar CVL-1 contig08970, 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: 5485
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Found at i:2517 original size:22 final size:23
Alignment explanation
Indices: 2486--2533 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
2476 ATCAGTAAAG
2486 AAAAGAGTAAAATG-GTAATCAGT
1 AAAAGAGTAAAA-GAGTAATCAGT
2509 AAAA-AGTAAAAGAGTAATCAGT
1 AAAAGAGTAAAAGAGTAATCAGT
2531 AAA
1 AAA
2534 GAAAAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.58, C:0.04, G:0.19, T:0.19
Consensus pattern (23 bp):
AAAAGAGTAAAAGAGTAATCAGT
Found at i:2534 original size:14 final size:14
Alignment explanation
Indices: 2517--2575 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2507 GTAAAAAGTA
2517 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
*
2531 AAAGA--AA-AAGT
1 AAAGAGTAATCAGT
*
2542 AGAAGAGTATTCA-T
1 A-AAGAGTAATCAGT
2556 ACAAGAGTAATCAGT
1 A-AAGAGTAATCAGT
2571 AAAGA
1 AAAGA
2576 AAAATGGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
11 4 0.11
12 6 0.17
14 22 0.63
15 3 0.09
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (14 bp):
AAAGAGTAATCAGT
Found at i:2600 original size:89 final size:84
Alignment explanation
Indices: 2455--2625 Score: 213
Period size: 89 Copynumber: 2.0 Consensus size: 84
2445 AATTTCATGC
2455 AAGAGTATTCATACAAGAGTAATCAGTAAAGAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAA
1 AAGAGTATTCATACAAGAGTAATCAGTAAAGAAAAGAGTAAAA-GGTAAT-AGT--AAAGT-AAA
*
2520 GAGTAATCAGTAAAGAAAAAGTAG
61 GAGTAATCAGCAAAGAAAAAGTAG
2544 AAGAGTATTCATACAAGAGTAATCAGTAAAGAAAA-ATGGT-AAAGAGTAGAGT-GTAAAGTAAA
1 AAGAGTATTCATACAAGAGTAATCAGTAAAGAAAAGA--GTAAAAG-GTA-A-TAGTAAAGTAAA
*
2606 GAGTAATCAGCAAAGTAAAA
61 GAGTAATCAGCAAAGAAAAA
2626 TGGTAAAAAG
Statistics
Matches: 75, Mismatches: 2, Indels: 13
0.83 0.02 0.14
Matches are distributed among these distances:
86 21 0.28
87 5 0.07
88 2 0.03
89 43 0.57
90 3 0.04
91 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (84 bp):
AAGAGTATTCATACAAGAGTAATCAGTAAAGAAAAGAGTAAAAGGTAATAGTAAAGTAAAGAGTA
ATCAGCAAAGAAAAAGTAG
Found at i:2608 original size:46 final size:43
Alignment explanation
Indices: 2494--2638 Score: 133
Period size: 46 Copynumber: 3.4 Consensus size: 43
2484 AGAAAAGAGT
**
2494 AAAATGGTAATCAGTAA--AAAGTAAAAGAGTAATCAGTAAAGA
1 AAAATGGTAAAGAGTAATTAAAGT-AAAGAGTAATCAGTAAAGA
*
2536 AAAA--GTAGAAGAGT-ATT-CA-TACAAGAGTAATCAGTAAAGA
1 AAAATGGTA-AAGAGTAATTAAAGTA-AAGAGTAATCAGTAAAGA
* *
2576 AAAATGGTAAAGAGTAGAGTGTAAAGTAAAGAGTAATCAGCAAAGT
1 AAAATGGTAAAGAGTA-A-T-TAAAGTAAAGAGTAATCAGTAAAGA
*
2622 AAAATGGTAAAAAGTAA
1 AAAATGGTAAAGAGTAA
2639 AAGAATAATC
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
39 1 0.01
40 27 0.32
41 11 0.13
42 7 0.08
43 1 0.01
44 1 0.01
45 2 0.02
46 32 0.38
47 2 0.02
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.19
Consensus pattern (43 bp):
AAAATGGTAAAGAGTAATTAAAGTAAAGAGTAATCAGTAAAGA
Found at i:2745 original size:16 final size:16
Alignment explanation
Indices: 2726--2759 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2716 GTAAGAAGGT
*
2726 AATCAGTAAAGAGTAA
1 AATCAGCAAAGAGTAA
2742 AATCAGCAAAGAGTAA
1 AATCAGCAAAGAGTAA
2758 AA
1 AA
2760 AAGTAATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (16 bp):
AATCAGCAAAGAGTAA
Found at i:2848 original size:21 final size:19
Alignment explanation
Indices: 2772--2859 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 19
2762 GTAATCGATA
*
2772 AAAGATAATCAGTAAGAGTAA
1 AAAG-TAATCAGTAAGAGT-C
*
2793 AACAGTAACCAGTAAGAG-C
1 AA-AGTAATCAGTAAGAGTC
*
2812 AAAGTGATGATTAGTAAGAGTC
1 AAAGT-A--ATCAGTAAGAGTC
*
2834 AATTAGTAATCAGTAAAGAGTA
1 AA--AGTAATCAGT-AAGAGTC
2856 AAAG
1 AAAG
2860 GTGATAAGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
18 3 0.06
19 3 0.06
20 2 0.04
21 28 0.53
22 13 0.25
23 1 0.02
24 3 0.06
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (19 bp):
AAAGTAATCAGTAAGAGTC
Found at i:2970 original size:29 final size:28
Alignment explanation
Indices: 2909--2972 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
2899 GTGGTAACAA
*
2909 ATAAAAGAGAGTAAGAAAAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAGAGTAAATG
*
2937 GTAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGT--AAATG
2966 ATAAAAG
1 ATAAAAG
2973 TAGCAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 16 0.53
28 5 0.17
29 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (28 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAATG
Found at i:4507 original size:42 final size:42
Alignment explanation
Indices: 4452--4550 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
4442 TTGTATATGG
* * * **
4452 TGCATCTATCATGCATTGTCCATTTC-TTTGTATATATGTTCA
1 TGCATCCATCATGCATTATCC-TTTCATTGGTATATATGCCCA
* *
4494 TGCATCGATCATGCATTATCCTTTCATTGGTATATGTGCCCA
1 TGCATCCATCATGCATTATCCTTTCATTGGTATATATGCCCA
4536 TGCATCCATCATGCA
1 TGCATCCATCATGCA
4551 CTCACTTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (42 bp):
TGCATCCATCATGCATTATCCTTTCATTGGTATATATGCCCA
Done.