Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010278.1 Corchorus capsularis cultivar CVL-1 contig10299, 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: 15111
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4330 original size:33 final size:33
Alignment explanation
Indices: 4293--4399 Score: 144
Period size: 33 Copynumber: 3.2 Consensus size: 33
4283 AGCACTAGAG
* *
4293 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
4326 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
4359 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
4391 AACCGGCCA
1 -ACCGGCCA
4400 TCGCTAGGCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
32 1 0.02
33 64 0.98
ACGTcount: A:0.22, C:0.38, G:0.29, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:5209 original size:36 final size:36
Alignment explanation
Indices: 5169--5271 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 36
5159 CATCGACATA
*
5169 CAAGTCTAGGAGTTCAAGTCGACTTTGGTGGATATT
1 CAAGTCTAGAAGTTCAAGTCGACTTTGGTGGATATT
*
5205 CAAGTCTAGAAGTTCAAGT---C-----TAGA-AGTT
1 CAAGTCTAGAAGTTCAAGTCGACTTTGGTGGATA-TT
5233 CAAGTCTAGAAGTTCAAGTCGACTTTGGTGGATATT
1 CAAGTCTAGAAGTTCAAGTCGACTTTGGTGGATATT
5269 CAA
1 CAA
5272 AGGGGATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
27 1 0.02
28 24 0.44
31 1 0.02
33 1 0.02
36 26 0.48
37 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (36 bp):
CAAGTCTAGAAGTTCAAGTCGACTTTGGTGGATATT
Found at i:5222 original size:14 final size:14
Alignment explanation
Indices: 5203--5252 Score: 100
Period size: 14 Copynumber: 3.6 Consensus size: 14
5193 TTGGTGGATA
5203 TTCAAGTCTAGAAG
1 TTCAAGTCTAGAAG
5217 TTCAAGTCTAGAAG
1 TTCAAGTCTAGAAG
5231 TTCAAGTCTAGAAG
1 TTCAAGTCTAGAAG
5245 TTCAAGTC
1 TTCAAGTC
5253 GACTTTGGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (14 bp):
TTCAAGTCTAGAAG
Found at i:5918 original size:11 final size:11
Alignment explanation
Indices: 5893--5920 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5883 AAAATATCAT
5893 AAAAATAATAA
1 AAAAATAATAA
5904 AAAAATAATAA
1 AAAAATAATAA
5915 AAAAAT
1 AAAAAT
5921 TCGATCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:10189 original size:56 final size:56
Alignment explanation
Indices: 10086--10337 Score: 337
Period size: 56 Copynumber: 4.4 Consensus size: 56
10076 GATAGCTCAC
*
10086 AGATGGA-TCTGAAGACAGTTCCTACAAGATATTAAGAATGAGTATGAAGACTGCTCAT
1 AGATGGATTCTGAAGACAGTTCCTA-AA-A-ATTAAGAATGAGTATGAAGACTGCTCGT
10144 AGATGGATTCTGAAGACAGTTCCTAAAAATTAAGAATGAGTATGAAGACTGCTCGT
1 AGATGGATTCTGAAGACAGTTCCTAAAAATTAAGAATGAGTATGAAGACTGCTCGT
* *
10200 AGATGGGTTTTGAAGACAGTTCCTAAAAATTAAGAATGAGTATGAAGACTGCTCGT
1 AGATGGATTCTGAAGACAGTTCCTAAAAATTAAGAATGAGTATGAAGACTGCTCGT
* * * * * *
10256 AGATGGGTTCTGAAGACAGTTCCTAAAGGAAATCAAGCATGAGTATGACGATTGCTTGT
1 AGATGGATTCTGAAGACAGTTCCT-AA--AAATTAAGAATGAGTATGAAGACTGCTCGT
* *
10315 AGACGGA-TCTGAAGACGGTTCCT
1 AGATGGATTCTGAAGACAGTTCCT
10338 GAAAGCGTAA
Statistics
Matches: 178, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
56 104 0.58
57 3 0.02
58 24 0.13
59 47 0.26
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (56 bp):
AGATGGATTCTGAAGACAGTTCCTAAAAATTAAGAATGAGTATGAAGACTGCTCGT
Found at i:10669 original size:29 final size:29
Alignment explanation
Indices: 10632--10710 Score: 108
Period size: 27 Copynumber: 2.8 Consensus size: 29
10622 ATTAAGGTCG
* **
10632 CCCAAGGGCATTTTGGTCATTTTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTTCACA
10661 CCCAGGGGCATTTTGGTCA--TTTTCACA
1 CCCAGGGGCATTTTGGTCATTTTTTCACA
*
10688 CCCAGGGGCATTTAGGTCATTTT
1 CCCAGGGGCATTTTGGTCATTTT
10711 GGCATTTAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 24 0.55
29 20 0.45
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (29 bp):
CCCAGGGGCATTTTGGTCATTTTTTCACA
Found at i:13646 original size:49 final size:48
Alignment explanation
Indices: 13554--13757 Score: 229
Period size: 49 Copynumber: 4.2 Consensus size: 48
13544 AACTTGTAAC
*
13554 TAAAAGATTGAAGCTTTAAATAACTTA--AA-TAAAAATGTCATCTTTGGG
1 TAAAAGATTGAA-CTTT-AGTAA-TTAGTAAGTAAAAATGTCATCTTTGGG
13602 TAAAAGATTGAACTCTTAGTAATTAGTAAGTAAAAATGGT-ATCTTTGGG
1 TAAAAGATTGAACT-TTAGTAATTAGTAAGTAAAAAT-GTCATCTTTGGG
* * *
13651 TAAAAGATTGAATTTTTAGTAATTAGTAGGT-AAAATGTCATCTTTAGG
1 TAAAAGATTGAA-CTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
* * *
13699 TAAAAGATTGAAACTTTAGGTAATTAGTAAGTAAAGATGTCACCTTTGAG
1 TAAAAGATTG-AACTTTA-GTAATTAGTAAGTAAAAATGTCATCTTTGGG
*
13749 CAAAAGATT
1 TAAAAGATT
13758 TATTTTTAGA
Statistics
Matches: 135, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
46 3 0.02
47 8 0.06
48 43 0.32
49 57 0.42
50 24 0.18
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (48 bp):
TAAAAGATTGAACTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGG
Found at i:13764 original size:97 final size:98
Alignment explanation
Indices: 13585--13777 Score: 268
Period size: 97 Copynumber: 2.0 Consensus size: 98
13575 AACTTAAATA
* * *
13585 AAAATGTCATCTTTGGGTAAAAGATTGAACTCTTAGTAATTAGTAAGTAAAAATGGTATCTTTGG
1 AAAATGTCATCTTTAGGTAAAAGATTGAACTCTTAGTAATTAGTAAGTAAAAATGGTACCTTTGA
*
13650 GTAAAAGATTGAATTTTT-AGTAATTAGTAGGT
66 GCAAAAGATTGAATTTTTAAGTAATTAGTAGGT
*
13682 AAAATGTCATCTTTAGGTAAAAGATTGAAACT-TTAGGTAATTAGTAAGTAAAGAT-GTCACCTT
1 AAAATGTCATCTTTAGGTAAAAGATTG-AACTCTTA-GTAATTAGTAAGTAAAAATGGT-ACCTT
*
13745 TGAGCAAAAGATT-TATTTTTAGAGTAATTAGTA
63 TGAGCAAAAGATTGAATTTTTA-AGTAATTAGTA
13778 AATGGAGATG
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
97 37 0.44
98 37 0.44
99 11 0.13
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.36
Consensus pattern (98 bp):
AAAATGTCATCTTTAGGTAAAAGATTGAACTCTTAGTAATTAGTAAGTAAAAATGGTACCTTTGA
GCAAAAGATTGAATTTTTAAGTAATTAGTAGGT
Found at i:13766 original size:49 final size:50
Alignment explanation
Indices: 13583--13816 Score: 210
Period size: 49 Copynumber: 4.7 Consensus size: 50
13573 ATAACTTAAA
* * * * *
13583 TAAAAATGTCATCTTTGGGTAAAAGATTGAACTCTTA-GTAATTAGTAAG
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAGGTAATTAGTAAG
* * * *
13632 TAAAAATGGT-ATCTTTGGGTAAAAGATTGAATTTTTA-GTAATTAGTAGG
1 TAAAGAT-GTCACCTTTGAGTAAAAGATTGAATTTTTAGGTAATTAGTAAG
* **
13681 TAAA-ATGTCATCTTT-AGGTAAAAGATTGAAACTTTAGGTAATTAGTAAG
1 TAAAGATGTCACCTTTGA-GTAAAAGATTGAATTTTTAGGTAATTAGTAAG
* * *
13730 TAAAGATGTCACCTTTGAGCAAAAGATT-TATTTTTAGAGTAATTAGTAAA
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAG-GTAATTAGTAAG
** * * * *
13780 TGGAGATGTAACCTTTGAATAAGAGATTGAAGTTTTA
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTA
13817 AAAAGTAATT
Statistics
Matches: 156, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.01
48 25 0.16
49 68 0.44
50 54 0.35
51 7 0.04
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (50 bp):
TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAGGTAATTAGTAAG
Found at i:13772 original size:50 final size:51
Alignment explanation
Indices: 13583--13869 Score: 200
Period size: 49 Copynumber: 5.7 Consensus size: 51
13573 ATAACTTAAA
* * * * *
13583 TAAAAATGTCATCTTTGGGTAAAAGATTGAACTCTT--AGTAATTAGTAAG
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAG
* * * *
13632 TAAAAATGGT-ATCTTTGGGTAAAAGATTGAATTTTT--AGTAATTAGTAGG
1 TAAAGAT-GTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAG
* **
13681 TAAA-ATGTCATCTTT-AGGTAAAAGATTGAAACTTTAG-GTAATTAGTAAG
1 TAAAGATGTCACCTTTGA-GTAAAAGATTGAATTTTTAGAGTAATTAGTAAG
* * *
13730 TAAAGATGTCACCTTTGAGCAAAAGATT-TATTTTTAGAGTAATTAGTAAA
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAG
** * * * * * *
13780 TGGAGATGTAACCTTTGAATAAGAGATTGAAGTTTTAAAAAGTAATTTGTGAA-
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAA-TTTT-TAGAGTAATTAGT-AAG
* * * * *
13833 TAAA-ATGTCATCTTTGAATTAAAGTTTGAACTTTTAG
1 TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAG
13870 GCCATTAATA
Statistics
Matches: 193, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
47 2 0.01
48 24 0.12
49 68 0.35
50 55 0.28
51 5 0.03
52 25 0.13
53 12 0.06
54 2 0.01
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (51 bp):
TAAAGATGTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAG
Found at i:14704 original size:55 final size:54
Alignment explanation
Indices: 14644--14948 Score: 490
Period size: 55 Copynumber: 5.6 Consensus size: 54
14634 AAAAAGGGGC
14644 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGATAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAG-TAAGGTAATAGTAATCAGTA
14699 AATCAGTAATTAAGTAAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGT-AAAAAGAGATTAATCAGAG-TAAGGTAATAGTAATCAGTA
14755 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAG-TAAGGTAATAGTAATCAGTA
*
14810 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGT-AAGGTAATAGTAATCAGTA
14865 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG---TCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGT-AAGGTAATAGTAATCAGTA
* * * *
14917 AATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
14949 TAAATTGATA
Statistics
Matches: 241, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
52 34 0.14
54 1 0.00
55 152 0.63
56 54 0.22
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (54 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTAAGGTAATAGTAATCAGTA
Found at i:14946 original size:26 final size:26
Alignment explanation
Indices: 14865--14951 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
14855 GTAATCAGTA
* * * *
14865 AATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAATCAGGTAAAAAGATAGT
* *
14891 AATCAG-AGTCAAGGT-AATAG-TCAGT
1 AATCAGTAATC-AGGTAAAAAGAT-AGT
14916 AAATCAGTAATCAGGTAAAAAGATAGT
1 -AATCAGTAATCAGGTAAAAAGATAGT
14943 AATCAGTAA
1 AATCAGTAA
14952 ATTGATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
25 8 0.17
26 28 0.60
27 10 0.21
28 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (26 bp):
AATCAGTAATCAGGTAAAAAGATAGT
Found at i:14951 original size:34 final size:33
Alignment explanation
Indices: 14911--15024 Score: 106
Period size: 34 Copynumber: 3.3 Consensus size: 33
14901 AAGGTAATAG
*
14911 TCAGTAAATCAGTAATCAGGTAAAAAGATAGTAA
1 TCAGTAAAT-AGTAATAAGGTAAAAAGATAGTAA
* * *
14945 TCAGTAAATTGATAATTAAGAGTCCAGATA-ATAGTAA
1 TCAGTAAATAG-TAA-TAAG-GT--AAAAAGATAGTAA
14982 TCAGTAAATTAGTAATTAA-GTAAAAAGATAGTAA
1 TCAGTAAA-TAGTAA-TAAGGTAAAAAGATAGTAA
15016 TCAGTAAAT
1 TCAGTAAAT
15025 TGATAATTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
33 5 0.08
34 27 0.41
35 5 0.08
36 2 0.03
37 22 0.33
38 5 0.08
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (33 bp):
TCAGTAAATAGTAATAAGGTAAAAAGATAGTAA
Found at i:14979 original size:37 final size:36
Alignment explanation
Indices: 14930--15035 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 36
14920 CAGTAATCAG
14930 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAGA
1 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAGA
* *
14966 GTCCAGATA-ATAGTAATCAGTAAATT-AGTAATT-A-A
1 GT--AAAAAGATAGTAATCAGTAAATTGA-TAATTAAGA
15001 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAG
1 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAG
15036 GGTTAAAGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
33 3 0.05
34 22 0.37
35 5 0.08
36 4 0.07
37 22 0.37
38 3 0.05
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (36 bp):
GTAAAAAGATAGTAATCAGTAAATTGATAATTAAGA
Done.