Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016129.1 Corchorus capsularis cultivar CVL-1 contig16150, 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: 7510
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:3871 original size:9 final size:9
Alignment explanation
Indices: 3859--3910 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
3849 AAAAGTCAAT
*
3859 AAAGATGAA
1 AAAGAAGAA
*
3868 AAAGATGCAA
1 AAAGAAG-AA
* *
3878 AAAAAAAAA
1 AAAGAAGAA
3887 AAAGAAGAA
1 AAAGAAGAA
*
3896 AAAAAAGAA
1 AAAGAAGAA
3905 AAAGAA
1 AAAGAA
3911 AAGAAAGTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 29 0.83
10 6 0.17
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:3887 original size:18 final size:19
Alignment explanation
Indices: 3865--3910 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
3855 CAATAAAGAT
*
3865 GAAAAAGATGCAAAAAAAAA
1 GAAAAAGAAG-AAAAAAAAA
3885 -AAAAAGAAG-AAAAAAAA
1 GAAAAAGAAGAAAAAAAAA
3902 GAAAAAGAA
1 GAAAAAGAA
3911 AAGAAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
GAAAAAGAAGAAAAAAAAA
Found at i:3890 original size:19 final size:18
Alignment explanation
Indices: 3866--3910 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3856 AATAAAGATG
*
3866 AAAAAGATGCAAAAAAAAA
1 AAAAAGAAG-AAAAAAAAA
*
3885 AAAAAGAAGAAAAAAAAG
1 AAAAAGAAGAAAAAAAAA
3903 AAAAAGAA
1 AAAAAGAA
3911 AAGAAAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGAAAAAAAAA
Found at i:3897 original size:12 final size:11
Alignment explanation
Indices: 3876--3916 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3866 AAAAAGATGC
3876 AAAA-AAAAAA
1 AAAAGAAAAAA
3886 AAAAGAAGAAAA
1 AAAAGAA-AAAA
*
3898 AAAAGAAAAAG
1 AAAAGAAAAAA
3909 AAAAGAAA
1 AAAAGAAA
3917 GTGAAAGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.14
11 13 0.46
12 11 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:3899 original size:20 final size:20
Alignment explanation
Indices: 3876--3916 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3866 AAAAAGATGC
*
3876 AAAAAAA-AAAAAAAGAAGA
1 AAAAAAAGAAAAAAAAAAGA
*
3895 AAAAAAAGAAAAAGAAAAGA
1 AAAAAAAGAAAAAAAAAAGA
3915 AA
1 AA
3917 GTGAAAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAAAGA
Found at i:3923 original size:15 final size:15
Alignment explanation
Indices: 3878--3917 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3868 AAAGATGCAA
*
3878 AAAAAAAAAAAAGAAG
1 AAAAAAAAGAAA-AAG
3894 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
3909 AAAAGAAAG
1 AAAAAAAAG
3918 TGAAAGGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:3928 original size:23 final size:22
Alignment explanation
Indices: 3909--3952 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
3899 AAAGAAAAAG
3909 AAAAGAAAGTGAAAGGGAAAATTA
1 AAAAGAAAGTGAAA-GGAAAA-TA
3933 AAAAGAAAGTGAAAGGAAAA
1 AAAAGAAAGTGAAAGGAAAA
3953 GAAGGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (22 bp):
AAAAGAAAGTGAAAGGAAAATA
Found at i:4699 original size:51 final size:50
Alignment explanation
Indices: 4554--4700 Score: 231
Period size: 50 Copynumber: 2.9 Consensus size: 50
4544 TCAAAACAAG
4554 AAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAAAAT
1 AAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAAAAT
* *
4604 AAGATTGCATTCCATTTGTGAGTTCAATATTAAAATTCGATTTTCAAGAT
1 AAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAAAAT
* * * *
4654 AAGATTGCATTCCATTTTGTGAGTCCAAAATCAAAATTTGCTTTTCA
1 AAGATTGCATTCCA-TTTGTGAGTTCAATATCAAAATTCGATTTTCA
4701 GAGGGTGTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 62 0.70
51 27 0.30
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (50 bp):
AAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAAAAT
Found at i:5402 original size:69 final size:70
Alignment explanation
Indices: 5214--5414 Score: 341
Period size: 70 Copynumber: 2.9 Consensus size: 70
5204 AACACTTTGA
* * *
5214 CTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAACATTGGTTCCATTCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCATTC
5279 AGGGG
66 AGGGG
* *
5284 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAGGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCATTC
5349 AGGGG
66 AGGGG
*
5354 CTTTTCCACAAG-CAAACTCGTTTCCATACGAGTCAGTTCAAGCGTTGGTTCCATCCAAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCA
5415 ACATGGACTT
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
69 47 0.38
70 77 0.62
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (70 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCATTC
AGGGG
Found at i:5646 original size:28 final size:28
Alignment explanation
Indices: 5615--5673 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
5605 ATTTCAATTC
5615 TTCAAATT-C-AATCCTTCAATGCTTCAAT
1 TTCAAATTCCAAATCC--CAATGCTTCAAT
*
5643 TTCAAATTCCAAATGCCAATGCTTCAAT
1 TTCAAATTCCAAATCCCAATGCTTCAAT
5671 TTC
1 TTC
5674 GCTTCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.82
29 1 0.04
30 4 0.14
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (28 bp):
TTCAAATTCCAAATCCCAATGCTTCAAT
Found at i:5684 original size:22 final size:22
Alignment explanation
Indices: 5659--5830 Score: 82
Period size: 22 Copynumber: 7.5 Consensus size: 22
5649 TTCCAAATGC
*
5659 CAATGCTTCAATTTCGC-TTCTT
1 CAATACTTCAATTTC-CATTCTT
*
5681 CAATACTTCAATTTCCATTTTT
1 CAATACTTCAATTTCCATTCTT
* *
5703 CAATTCTTCAATTTCAATAT-TT
1 CAATACTTCAATTTCCAT-TCTT
* * * *
5725 TAATGCTTCAGTTT-CAAT-TT
1 CAATACTTCAATTTCCATTCTT
*
5745 CAATACTTCAAGTTCGATCATTCAATT
1 CAATACTTCAATTTC---CATTC--TT
* * *
5772 CAATGCTTCAATTTATCTTTCTT
1 CAATACTTCAATTT-CCATTCTT
* * *
5795 CAATTCTTCAATCATCCAATGCTT
1 CAATACTTCAAT-TTCC-ATTCTT
*
5819 CAATTCTTCAAT
1 CAATACTTCAAT
5831 AATTCAATGC
Statistics
Matches: 115, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
20 13 0.11
21 2 0.02
22 47 0.41
23 15 0.13
24 20 0.17
25 4 0.03
27 14 0.12
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (22 bp):
CAATACTTCAATTTCCATTCTT
Found at i:5801 original size:8 final size:8
Alignment explanation
Indices: 5790--5847 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
5780 CAATTTATCT
5790 TTCTTCAA
1 TTCTTCAA
5798 TTCTTCAA
1 TTCTTCAA
*
5806 -TCATCCAA
1 TTC-TTCAA
*
5814 TGCTTCAA
1 TTCTTCAA
5822 TTCTTCAA
1 TTCTTCAA
**
5830 TAATTCAA
1 TTCTTCAA
*
5838 TGCTTCAA
1 TTCTTCAA
5846 TT
1 TT
5848 TACTTCAATG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
7 2 0.05
8 36 0.92
9 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.43
Consensus pattern (8 bp):
TTCTTCAA
Found at i:5822 original size:24 final size:24
Alignment explanation
Indices: 5792--5862 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
5782 ATTTATCTTT
*
5792 CTTCAATTCTTCAATCATCCAATG
1 CTTCAATTCTTCAATAATCCAATG
*
5816 CTTCAATTCTTCAATAATTCAATG
1 CTTCAATTCTTCAATAATCCAATG
*
5840 CTTCAATTTACTTCAATGATCCA
1 CTTCAA-TT-CTTCAATAATCCA
5863 GGGTGATCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 28 0.68
25 2 0.05
26 11 0.27
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (24 bp):
CTTCAATTCTTCAATAATCCAATG
Found at i:5830 original size:16 final size:16
Alignment explanation
Indices: 5790--5856 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
5780 CAATTTATCT
*
5790 TTCTTCAATTCTTCAA
1 TTCTTCAATACTTCAA
* *
5806 -TCATCCAATGCTTCAA
1 TTC-TTCAATACTTCAA
*
5822 TTCTTCAATAATTCAA
1 TTCTTCAATACTTCAA
*
5838 TGCTTCAATTTACTTCAA
1 TTCTTCAA--TACTTCAA
5856 T
1 T
5857 GATCCAGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
15 2 0.05
16 28 0.70
17 2 0.05
18 8 0.20
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (16 bp):
TTCTTCAATACTTCAA
Found at i:5960 original size:28 final size:26
Alignment explanation
Indices: 5919--5973 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
5909 TCAATGCCCC
*
5919 AGTTTCAATTTCAATTCTTCAACTTT
1 AGTTTCAATTTCAATGCTTCAACTTT
*
5945 AGTTTCAATTCCTCAATGCTTCAATTTT
1 AGTTTCAATT--TCAATGCTTCAACTTT
5973 A
1 A
5974 ATTCTTCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
28 15 0.60
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.47
Consensus pattern (26 bp):
AGTTTCAATTTCAATGCTTCAACTTT
Found at i:5976 original size:22 final size:22
Alignment explanation
Indices: 5922--6120 Score: 138
Period size: 22 Copynumber: 8.9 Consensus size: 22
5912 ATGCCCCAGT
5922 TTCAATTTCAATTCTTCAA--C
1 TTCAATTTCAATTCTTCAATGC
* * *
5942 TTTAGTTTCAATTCCTCAATGC
1 TTCAATTTCAATTCTTCAATGC
* **
5964 TTCAATTTTAATTCTTCAGCGC
1 TTCAATTTCAATTCTTCAATGC
*
5986 TTCAATTTCAATACTTCAAT--
1 TTCAATTTCAATTCTTCAATGC
* *
6006 TTCAATTCTTTAAATTCCAAATGCCAATGC
1 TTCAA---TTTCAATT-C---T-TCAATGC
* **
6036 TTCAATTTCAATCCTTCAATAT
1 TTCAATTTCAATTCTTCAATGC
* *
6058 TTCAATTTCAATTTTTCAATGT
1 TTCAATTTCAATTCTTCAATGC
6080 TTCAATTTCAATAT-TTCAATGC
1 TTCAATTTCAAT-TCTTCAATGC
* *
6102 TTCAAATCCAATTCTTCAA
1 TTCAATTTCAATTCTTCAA
6121 ATTCCAAATG
Statistics
Matches: 138, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
20 21 0.15
21 1 0.01
22 90 0.65
23 8 0.06
24 1 0.01
26 1 0.01
27 7 0.05
28 4 0.03
30 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (22 bp):
TTCAATTTCAATTCTTCAATGC
Found at i:6011 original size:14 final size:14
Alignment explanation
Indices: 5985--6011 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5975 TTCTTCAGCG
5985 CTTCAATTTCAATA
1 CTTCAATTTCAATA
5999 CTTCAATTTCAAT
1 CTTCAATTTCAAT
6012 TCTTTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (14 bp):
CTTCAATTTCAATA
Found at i:6052 original size:14 final size:14
Alignment explanation
Indices: 6030--6229 Score: 58
Period size: 14 Copynumber: 14.8 Consensus size: 14
6020 TTCCAAATGC
6030 CAATGCTTCAATTT
1 CAATGCTTCAATTT
*
6044 CAATCCTTCAATATTT
1 CAATGCTTC-A-ATTT
6060 CAAT--TTCAATTTTT
1 CAATGCTTCAA--TTT
*
6074 CAATGTTTCAATTT
1 CAATGCTTCAATTT
6088 CAA----T--ATTT
1 CAATGCTTCAATTT
* *
6096 CAATGCTTCAAATC
1 CAATGCTTCAATTT
* *
6110 CAATTCTTCAAATTC
1 CAATGCTTC-AATTT
6125 CAAATG--TCAATGTTT
1 C-AATGCTTCAA--TTT
*
6140 CAAT--TTCAAAATGT
1 CAATGCTTC--AATTT
6154 CAATGCTTCAATTT
1 CAATGCTTCAATTT
* *
6168 C---GATTC--TTC
1 CAATGCTTCAATTT
*
6177 CATTGCTTCAATTT
1 CAATGCTTCAATTT
*
6191 CAATTCTTCGAA-TT
1 CAATGCTTC-AATTT
*
6205 CAATGTTTCAATTT
1 CAATGCTTCAATTT
*
6219 CAATTCTTCAA
1 CAATGCTTCAA
6230 AGCCTCCTTC
Statistics
Matches: 139, Mismatches: 19, Indels: 56
0.65 0.09 0.26
Matches are distributed among these distances:
8 7 0.05
9 3 0.02
10 1 0.01
11 4 0.03
12 6 0.04
13 5 0.04
14 81 0.58
15 11 0.08
16 21 0.15
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.43
Consensus pattern (14 bp):
CAATGCTTCAATTT
Found at i:6076 original size:36 final size:35
Alignment explanation
Indices: 5922--6099 Score: 108
Period size: 36 Copynumber: 4.8 Consensus size: 35
5912 ATGCCCCAGT
*
5922 TTCAATTTCAATTCTTCAACTTTAGTTTCAATTCCTCAATGC
1 TTCAATTTCAA-TCTTCAA---TA-TTTCAATT--TCAATAC
* ****
5964 TTCAATTTTAATTCTTCAGCGCTTCAATTTCAATAC
1 TTCAATTTCAA-TCTTCAATATTTCAATTTCAATAC
* * ** *
6000 TTCAATTTCAATTCTTTAA-ATTCCAAATGCCAATGC
1 TTCAATTTCAA-TCTTCAATATTTC-AATTTCAATAC
**
6036 TTCAATTTCAATCCTTCAATATTTCAATTTCAATTT
1 TTCAATTTCAAT-CTTCAATATTTCAATTTCAATAC
6072 TTCAATGTTTCAAT-TTCAATATTTCAAT
1 TTCAA--TTTCAATCTTCAATATTTCAAT
6100 GCTTCAAATC
Statistics
Matches: 110, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
35 3 0.03
36 72 0.65
37 4 0.04
38 14 0.13
42 17 0.15
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.46
Consensus pattern (35 bp):
TTCAATTTCAATCTTCAATATTTCAATTTCAATAC
Found at i:6165 original size:22 final size:22
Alignment explanation
Indices: 6110--6168 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
6100 GCTTCAAATC
* * *
6110 CAATTCTTCAAATTCCAAATGT
1 CAATGCTTCAATTTCAAAATGT
*
6132 CAATGTTTCAATTTCAAAATGT
1 CAATGCTTCAATTTCAAAATGT
6154 CAATGCTTCAATTTC
1 CAATGCTTCAATTTC
6169 GATTCTTCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (22 bp):
CAATGCTTCAATTTCAAAATGT
Done.