Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009064.1 Corchorus capsularis cultivar CVL-1 contig09085, 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: 20542
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1987 original size:33 final size:32
Alignment explanation
Indices: 1950--2054 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 32
1940 CCAAGCGATT
* *
1950 GCCGGT-TGTGGCCGGACATGTCCATGTCGCGTG
1 GCCGGTGT-TGGCCGGGCATCTCCA-GTCGCGTG
*
1983 GCCGGTGTTGGCCGGGCATCTCCGAGTCACGTG
1 GCCGGTGTTGGCCGGGCATCTCC-AGTCGCGTG
* *
2016 GCCGGTGTTGGCCGGGCTTCTCCAAGTCGCATG
1 GCCGGTGTTGGCCGGGCATCTCC-AGTCGCGTG
2049 GCCGGT
1 GCCGGT
2055 CACTAGTGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 61 0.97
34 2 0.03
ACGTcount: A:0.09, C:0.30, G:0.39, T:0.23
Consensus pattern (32 bp):
GCCGGTGTTGGCCGGGCATCTCCAGTCGCGTG
Found at i:7556 original size:9 final size:8
Alignment explanation
Indices: 7522--7555 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
7512 GAATCGGCTA
7522 TGAATTTT
1 TGAATTTT
*
7530 TGAAGTTTC
1 TGAA-TTTT
7539 TGAATTTT
1 TGAATTTT
7547 TGAATTTT
1 TGAATTTT
7555 T
1 T
7556 TTAAGAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:8558 original size:33 final size:32
Alignment explanation
Indices: 8521--8627 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
8511 CGCCAGGCGA
* *
8521 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGGCATCTCCA-GTCGCG
*
8554 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
* *
8587 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
8620 TGGCCGGT
1 TGGCCGGT
8628 CACTAGTGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 63 0.97
34 2 0.03
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGGCATCTCCAGTCGCG
Found at i:11221 original size:21 final size:21
Alignment explanation
Indices: 11195--11234 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11185 AAAGTGAAGT
11195 AAAGAGTAATCAGTAAAGAGC
1 AAAGAGTAATCAGTAAAGAGC
*
11216 AAAGAGTAATTAGTAAAGA
1 AAAGAGTAATCAGTAAAGA
11235 AAAATGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAGAGTAATCAGTAAAGAGC
Found at i:11271 original size:15 final size:14
Alignment explanation
Indices: 11249--11283 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
11239 TGGTCACGAA
11249 TAAAGAGTAATCAG
1 TAAAGAGTAATCAG
11263 TAGAAGAGTAATCAG
1 TA-AAGAGTAATCAG
11278 TAAAGA
1 TAAAGA
11284 CAAAAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.20
Consensus pattern (14 bp):
TAAAGAGTAATCAG
Found at i:11343 original size:22 final size:21
Alignment explanation
Indices: 11318--11545 Score: 176
Period size: 22 Copynumber: 10.5 Consensus size: 21
11308 AGTAAGAGTA
*
11318 AAAAGGTAATATGGTAAAAAGT
1 AAAAGGTAAT-TAGTAAAAAGT
* **
11340 AAAAGGTAATCAGTAAAGGGT
1 AAAAGGTAATTAGTAAAAAGT
*
11361 CAAATGGTAATTAGTAAAAAGT
1 -AAAAGGTAATTAGTAAAAAGT
11383 AAAATGGTAATTAGT-AAAAGTT
1 AAAA-GGTAATTAGTAAAAAG-T
* *
11405 AAAAGAGTAATCAGTAGAAAGT
1 AAAAG-GTAATTAGTAAAAAGT
* * *
11427 AATA-GTAATCAGTAAGAAG-
1 AAAAGGTAATTAGTAAAAAGT
* * *
11446 CAATGGTAATTAGTAAAAAAAT
1 AAAAGGTAATTAGT-AAAAAGT
11468 AAAAAGGTAATTAGTAAAAAGT
1 -AAAAGGTAATTAGTAAAAAGT
*
11490 AAAATAGTAATTAG-AAAAGAGT
1 AAAA-GGTAATTAGTAAAA-AGT
**
11512 AAAATGGTAATCGGTAAAAAAGT
1 AAAA-GGTAATTAGT-AAAAAGT
11535 AAAAGAGTAAT
1 AAAAG-GTAAT
11546 CAGCAAAGAA
Statistics
Matches: 165, Mismatches: 27, Indels: 27
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.01
20 21 0.13
21 28 0.17
22 83 0.50
23 28 0.17
24 4 0.02
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (21 bp):
AAAAGGTAATTAGTAAAAAGT
Found at i:11454 original size:20 final size:21
Alignment explanation
Indices: 11410--11461 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
11400 AAGTTAAAAG
*
11410 AGTAATCAGT-AGAAAGTAAT
1 AGTAATCAGTAAGAAAGCAAT
11430 AGTAATCAGTAAG-AAGCAAT
1 AGTAATCAGTAAGAAAGCAAT
* *
11450 GGTAATTAGTAA
1 AGTAATCAGTAA
11462 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (21 bp):
AGTAATCAGTAAGAAAGCAAT
Found at i:11573 original size:7 final size:7
Alignment explanation
Indices: 11561--11585 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11551 AAGAAAAATG
11561 GTAAAGA
1 GTAAAGA
11568 GTAAAGA
1 GTAAAGA
11575 GTAAAGA
1 GTAAAGA
11582 GTAA
1 GTAA
11586 TCAACAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (7 bp):
GTAAAGA
Found at i:11585 original size:151 final size:151
Alignment explanation
Indices: 11316--11588 Score: 324
Period size: 151 Copynumber: 1.8 Consensus size: 151
11306 ATAGTAAGAG
* * * * * *
11316 TAAAAAGGTAATATGGTAAAAAGTAAAAGGTAATCAGTAAAGGGTCAAATGGTAATTAGTAAAAA
1 TAAAAAGGTAATATAGTAAAAAGTAAAAAGTAATCAGAAAAGAGTAAAATGGTAATCAGTAAAAA
* * * *
11381 GTAAAATGGTAATTAGTAAAAGTTAAAAGAGTAATCAGTAGAAAGTAATAGTAATCAGTAAGAAG
66 GTAAAATGGTAATCAGTAAAAGTAAAAAGAGTAAACAGTAGAAAGTAAGAGTAATCAGTAAGAAG
11446 CAATGGTAATTAGTAAAAAAA
131 CAATGGTAATTAGTAAAAAAA
* *
11467 TAAAAAGGTAAT-TAGTAAAAAGTAAAATAGTAATTAGAAAAGAGTAAAATGGTAATCGGTAAAA
1 TAAAAAGGTAATATAGTAAAAAGTAAAA-AGTAATCAGAAAAGAGTAAAATGGTAATCAGT-AAA
* *
11531 AAGTAAAA-GAGTAATCAG-CAAAG-AAAAATG-GTAAAGAGTA-AAGAGTAAAGAGTAATCA
64 AAGTAAAATG-GTAATCAGTAAAAGTAAAAA-GAGTAAACAGTAGAA-AGT-AAGAGTAATCA
11589 ACAAAGGAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
149 2 0.02
150 29 0.28
151 53 0.52
152 18 0.18
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (151 bp):
TAAAAAGGTAATATAGTAAAAAGTAAAAAGTAATCAGAAAAGAGTAAAATGGTAATCAGTAAAAA
GTAAAATGGTAATCAGTAAAAGTAAAAAGAGTAAACAGTAGAAAGTAAGAGTAATCAGTAAGAAG
CAATGGTAATTAGTAAAAAAA
Found at i:11654 original size:14 final size:14
Alignment explanation
Indices: 11536--11671 Score: 59
Period size: 14 Copynumber: 9.6 Consensus size: 14
11526 TAAAAAAGTA
*
11536 AAAGAGTAATCAGC
1 AAAGAGTAATCAGT
** *
11550 AAAGAAAAAT-GGT
1 AAAGAGTAATCAGT
**
11563 AAAGAGTAAAGAGT
1 AAAGAGTAATCAGT
**
11577 AAAGAGTAATCAAC
1 AAAGAGTAATCAGT
11591 AAAGGAAACGGTAATCAGT
1 AAA-G--A--GTAATCAGT
*
11610 AAAGA--AA-AAGT
1 AAAGAGTAATCAGT
*
11621 AAAAGAGTATTCAG-
1 -AAAGAGTAATCAGT
11635 ACAAGAGTAATCAGT
1 A-AAGAGTAATCAGT
**
11650 AAAGAAAAATC-GT
1 AAAGAGTAATCAGT
11663 AAAGAGTAA
1 AAAGAGTAA
11672 AGAGTAAAGT
Statistics
Matches: 88, Mismatches: 22, Indels: 25
0.65 0.16 0.19
Matches are distributed among these distances:
11 3 0.03
12 7 0.08
13 18 0.20
14 43 0.49
15 4 0.05
16 1 0.01
17 1 0.01
18 1 0.01
19 10 0.11
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.15
Consensus pattern (14 bp):
AAAGAGTAATCAGT
Found at i:11675 original size:34 final size:34
Alignment explanation
Indices: 11637--12006 Score: 233
Period size: 34 Copynumber: 11.1 Consensus size: 34
11627 GTATTCAGAC
*
11637 AAGAGTAATCAGTAAAGAAAAATCGTAAAGAGTA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
** * * *
11671 AAGAGTAA--AGTAAAGAGTAAT--CAACAAAGGA
1 AAGAGTAATCAGTAAAGAAAAATGGTAA-AGAGTA
* * **
11702 AATG-GTAATCAGT-AAGGAAAACGAAAAAGAGCATTCA
1 AA-GAGTAATCAGTAAAGAAAAATGGTAAAGAG---T-A
11739 GACAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
1 -A-A-GAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
* * *
11776 AAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
* * *
11810 AAAAGTAATCAGTAAAGAAAAAGGGTAAAGTGTA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
* *
11844 AAGAGTAA--AG-AGAAGAGAAATCAGT-AA-AG--
1 AAGAGTAATCAGTA-AAGAAAAAT-GGTAAAGAGTA
* *
11873 AA-A--AAT-GGTAAAGATTAAA-GAGT--AGAGTA
1 AAGAGTAATCAGTAAAGA-AAAATG-GTAAAGAGTA
* * *
11902 AAGAGTAATCAGCAAAGGAAAATGGTAAAGAGTG
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
* *
11936 AAGAG-AAGTCAGTAAAGAAGAATGGTGAAGAGTA
1 AAGAGTAA-TCAGTAAAGAAAAATGGTAAAGAGTA
11970 AAGAGTAATCCAGTAAAGAAAAATGGTAAAGAGTA
1 AAGAGTAAT-CAGTAAAGAAAAATGGTAAAGAGTA
12005 AA
1 AA
12007 ATATTAATCA
Statistics
Matches: 257, Mismatches: 46, Indels: 65
0.70 0.12 0.18
Matches are distributed among these distances:
26 3 0.01
27 9 0.04
28 5 0.02
29 4 0.02
30 3 0.01
31 12 0.05
32 36 0.14
33 16 0.06
34 111 0.43
35 28 0.11
36 1 0.00
37 2 0.01
38 2 0.01
39 2 0.01
40 9 0.04
41 14 0.05
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (34 bp):
AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTA
Found at i:11690 original size:46 final size:46
Alignment explanation
Indices: 11637--11940 Score: 153
Period size: 46 Copynumber: 6.8 Consensus size: 46
11627 GTATTCAGAC
* *
11637 AAGAGTAATCAGTAAAGAAAAATCGTAAAGAGTAAAGAGTAAAGTA
1 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
* * ** * *
11683 AAGAGTAATCAACAAAG-GAAATGGTAATCAGT-AAG-GAAAACGAAA
1 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAGTAAA-G-TA
* * ** * *
11728 AAGAGCATTCAG-ACAAGAGTAATCAGTAAAGA-AAAATG-GTAAAGAGTA
1 AAGAGTAATCAGCA-AAGAAAAAT-GGTAAAGAGTAAA-GAGT-AA-AGTA
* * *
11776 AAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAAAAAGTAATCAGTA
1 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAGTAA--AGTA
** * *
11824 AAGA--AA--A--AGGGTAAAGT-GTAAAGAGTAAAGAG--AAG--
1 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
* * *
11859 -AGA--AATCAGTAAAGAAAAATGGTAAAGATTAAAGAGTAGAGTA
1 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
* *
11902 AAGAGTAATCAGCAAAGGAAAATGGTAAAGAGTGAAGAG
1 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAG
11941 AAGTCAGTAA
Statistics
Matches: 190, Mismatches: 43, Indels: 50
0.67 0.15 0.18
Matches are distributed among these distances:
34 5 0.03
36 1 0.01
37 2 0.01
38 6 0.03
39 15 0.08
41 15 0.08
42 7 0.04
43 4 0.02
44 9 0.05
45 24 0.13
46 50 0.26
47 15 0.08
48 32 0.17
49 4 0.02
50 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (46 bp):
AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
Found at i:11715 original size:105 final size:105
Alignment explanation
Indices: 11537--11929 Score: 426
Period size: 105 Copynumber: 3.7 Consensus size: 105
11527 AAAAAAGTAA
*
11537 AAGAGTAATCAGCAAAGAAAAATGGTAAAGAGT-AA-AG---AGTAAAGAGTAATCAACAAAGGA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGA
*
11597 AACGGTAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGAC
66 AATGGTAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGAC
*
11637 AAGAGTAATCAGTAAAGAAAAATCGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGA
* * * *
11702 AATGGTAATCAGTAAGGAAAACGAAAAAGAGCATTCAGAC
66 AATGGTAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGAC
* * *
11742 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAGTA-AAATGGTAA-A
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAA--AGTAAAG-AGTAAT--CAACA
* ** * *
11805 AAGTAAAAAGTAATCAGTAAAGAAAAAGGGTAAAGTGTAAAGAGTA--AAGAG
61 AAGGAAATGGTAATCAGTAAAGAAAAA--GT--A----AAAGAGTATTCAGAC
* * * *
11856 AAGAGAAATCAGTAAAGAAAAATGGTAAAGATTAAAGAGTAGAGTAAAGAGTAATCAGCAAAGGA
1 AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGG-
11921 AAATGGTAA
65 AAATGGTAA
11930 AGAGTGAAGA
Statistics
Matches: 242, Mismatches: 30, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
100 31 0.13
101 2 0.01
102 2 0.01
105 99 0.41
107 9 0.04
108 24 0.10
109 2 0.01
110 2 0.01
111 5 0.02
112 17 0.07
114 42 0.17
116 7 0.03
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.16
Consensus pattern (105 bp):
AAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGA
AATGGTAATCAGTAAAGAAAAAGTAAAAGAGTATTCAGAC
Found at i:11778 original size:7 final size:7
Alignment explanation
Indices: 11766--11909 Score: 58
Period size: 7 Copynumber: 21.6 Consensus size: 7
11756 AAGAAAAATG
11766 GTAAAGA
1 GTAAAGA
11773 GTAAAGA
1 GTAAAGA
**
11780 GTAATCA
1 GTAAAGA
*
11787 G-CAA-A
1 GTAAAGA
11792 GTAAA-A
1 GTAAAGA
*
11798 TGGTAAAAA
1 --GTAAAGA
*
11807 GTAAAAA
1 GTAAAGA
**
11814 GTAATCA
1 GTAAAGA
11821 GTAAAGA
1 GTAAAGA
* *
11828 -AAAAGG
1 GTAAAGA
*
11834 GTAAAGT
1 GTAAAGA
11841 GTAAAGA
1 GTAAAGA
11848 GTAAAGA
1 GTAAAGA
11855 G--AAGA
1 GTAAAGA
*
11860 G-AAATCA
1 GTAAA-GA
11867 GTAAAGA
1 GTAAAGA
*
11874 -AAAATG-
1 GTAAA-GA
11880 GTAAAGA
1 GTAAAGA
*
11887 TTAAAGA
1 GTAAAGA
11894 GT--AGA
1 GTAAAGA
11899 GTAAAGA
1 GTAAAGA
11906 GTAA
1 GTAA
11910 TCAGCAAAGG
Statistics
Matches: 104, Mismatches: 20, Indels: 26
0.69 0.13 0.17
Matches are distributed among these distances:
5 12 0.12
6 14 0.13
7 69 0.66
8 8 0.08
9 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (7 bp):
GTAAAGA
Found at i:12019 original size:35 final size:34
Alignment explanation
Indices: 11896--12019 Score: 119
Period size: 34 Copynumber: 3.6 Consensus size: 34
11886 ATTAAAGAGT
* *
11896 AGAGT-AAAGAGTAATCAGCAAAGGAAAATGGTAA
1 AGAGTAAAAGA-TAATCAGTAAAGAAAAATGGTAA
* * * *
11930 AGAGTGAAGAGA-AGTCAGTAAAGAAGAATGGTGA
1 AGAGT-AAAAGATAATCAGTAAAGAAAAATGGTAA
11964 AGAGT-AAAGAGTAATCCAGTAAAGAAAAATGGTAA
1 AGAGTAAAAGA-TAAT-CAGTAAAGAAAAATGGTAA
*
11999 AGAGTAAAATATTAATCAGTA
1 AGAGTAAAAGA-TAATCAGTA
12020 GAAGGTAATG
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
32 4 0.06
34 29 0.40
35 27 0.38
36 12 0.17
ACGTcount: A:0.52, C:0.05, G:0.26, T:0.18
Consensus pattern (34 bp):
AGAGTAAAAGATAATCAGTAAAGAAAAATGGTAA
Done.