Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017316.1 Corchorus olitorius cultivar O-4 contig17349, 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: 11227
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:6480 original size:36 final size:36
Alignment explanation
Indices: 6397--6889 Score: 615
Period size: 36 Copynumber: 14.1 Consensus size: 36
6387 ATTTGAGATG
* * * *
6397 CTTCAGTTCATTTCAGTTGACCCAGGGTGGTCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6433 -TTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
6468 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6504 CTTCAGTTTATTTCAATTGACCCAGGGC-AGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGA-TCTTTT
* * *
6539 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTGTTTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT-T
* *
6576 -TT-AGTTTATTTCAGTTGATCCAGGGCGACCCTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6610 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTTT
1 CTTCAGTTTAT-TTCAGTTGATCCAGGGCGATCTTTT
* *
6646 CTTCAGTTTATTTCAGTTGATCCAGGACGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6681 CTTCAGCTTATTTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6717 CTTCAGTTTATTTCAGTTGAACCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6753 CTTCAGTTTATTTCAATTGATCCAGGGCGATC--TT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6787 -TTC-------TTCAGTTGATCTAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * *
6815 CTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6851 CTTCAGTTTATTTCAATTGATCGAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
6887 CTT
1 CTT
6890 TAATTGATCC
Statistics
Matches: 402, Mismatches: 35, Indels: 40
0.84 0.07 0.08
Matches are distributed among these distances:
26 19 0.05
28 2 0.00
29 3 0.01
33 3 0.01
34 3 0.01
35 126 0.31
36 243 0.60
37 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:6540 original size:71 final size:72
Alignment explanation
Indices: 6397--6889 Score: 606
Period size: 71 Copynumber: 7.0 Consensus size: 72
6387 ATTTGAGATG
* * * *
6397 CTTCAGTTCATTTCAGTTGACCCAGGGTGGTCTTTT-TTCAGTTTATTTCAGTTGACCCAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
6461 ATCTTTT
66 ATCTTTT
*
6468 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGACCCAGGGC-
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
6532 AGTC-TTT
66 A-TCTTTT
* * * *
6539 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTGTTTAT-TT-AGTTTATTTCAGTTGATCCAGGGC
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT-TCTTCAGTTTATTTCAGTTGACCCAGGGC
* *
6602 GACCCTTT
65 GATCTTTT
* * * *
6610 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGAC
1 CTTCAGTTTAT-TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGC
*
6674 GGTC-TTT
65 GATCTTTT
* *
6681 CTTCAGCTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGAACCAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
6746 ATCTTTT
66 ATCTTTT
* *
6753 CTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTGA--TC---T-----AGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
6808 ATCTTTT
66 ATCTTTT
* * * * * *
6815 CTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTCAGTTTATTTCAATTGATCGAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
6880 ATCTTTT
66 ATCTTTT
6887 CTT
1 CTT
6890 TAATTGATCC
Statistics
Matches: 371, Mismatches: 31, Indels: 39
0.84 0.07 0.09
Matches are distributed among these distances:
62 56 0.15
64 2 0.01
67 2 0.01
70 28 0.08
71 165 0.44
72 118 0.32
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (72 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
ATCTTTT
Found at i:6655 original size:107 final size:107
Alignment explanation
Indices: 6397--6885 Score: 574
Period size: 107 Copynumber: 4.7 Consensus size: 107
6387 ATTTGAGATG
* * * * * * *
6397 CTTCAGTTCATTTCAGTTGACCCAGGGTGGT-CTTTTTTCAGTTTATTTCAGTTGACCCAGGGCG
1 CTTCAGTTTATTTCAATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
*
6461 ATCTTT-TCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
66 GTCTTTAT-TT-AGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* *
6504 CTTCAGTTTATTTCAATTGACCCAGGGC-AGT-CTTTCTTCAGTTTATTTCAGTTGACCCAGGGC
1 CTTCAGTTTATTTCAATTGATCCAGGGCGA-TCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGC
* * *
6567 GGTGTTTATTTAGTTTATTTCAGTTGATCCAGGGCGACCCTTT
65 GGTCTTTATTTAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
6610 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGAC
1 CTTCAGTTTAT-TTCAATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGC
* * *
6674 GGTCTTTCTTCAGCTTATTTCAGTTGATCCAGGGCGATCTTTT
65 GGTCTTTATTTAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * *
6717 CTTCAGTTTATTTCAGTTGAACCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGC-
1 CTTCAGTTTATTTCAATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
* * *
6781 G-----ATCT--TTT-CTTCAGTTGATCTAGGGCGATCTTTT
66 GTCTTTATTTAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
6815 CTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTCAGTTTATTTCAATTGATCGAGGGCG
1 CTTCAGTTTATTTCAATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
*
6880 ATCTTT
66 GTCTTT
6886 TCTTTAATTG
Statistics
Matches: 335, Mismatches: 35, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
98 83 0.25
99 2 0.01
101 1 0.00
106 58 0.17
107 190 0.57
108 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (107 bp):
CTTCAGTTTATTTCAATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
GTCTTTATTTAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:6806 original size:62 final size:62
Alignment explanation
Indices: 6728--6858 Score: 226
Period size: 62 Copynumber: 2.1 Consensus size: 62
6718 TTCAGTTTAT
*
6728 TTCAGTTGAACCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTC
1 TTCAGTTGAACCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTC
* * *
6790 TTCAGTTGATCTAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTC
1 TTCAGTTGAACCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTC
6852 TTCAGTT
1 TTCAGTT
6859 TATTTCAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (62 bp):
TTCAGTTGAACCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTC
Found at i:6820 original size:26 final size:26
Alignment explanation
Indices: 6764--6822 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
6754 TTCAGTTTAT
*
6764 TTCAATTGATCCAGGGCGATCTTTTC
1 TTCAGTTGATCCAGGGCGATCTTTTC
*
6790 TTCAGTTGATCTAGGGCGATCTTTTC
1 TTCAGTTGATCCAGGGCGATCTTTTC
6816 TTCAGTT
1 TTCAGTT
6823 TATTTCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (26 bp):
TTCAGTTGATCCAGGGCGATCTTTTC
Found at i:6861 original size:98 final size:98
Alignment explanation
Indices: 6692--6966 Score: 392
Period size: 98 Copynumber: 2.8 Consensus size: 98
6682 TTCAGCTTAT
*
6692 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGAACCAGGGCGATCTTTTCTTC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
6757 AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
66 AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
* * * *
6790 TTCAGTTGATCTAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
*
6855 AGTTTATTTCAATTGATCGAGGGCGATCTTTTC
66 AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
* * * * * * * * * *
6888 TTTAATTGATCCAGGGTGATC-TTTCCTCAATTTACTTCAGTAGATCCAGGGTGATCTTCTCTGC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
6952 AGTTTA-TTCAATTGA
66 AGTTTATTTCAATTGA
6967 CTGCAAAATG
Statistics
Matches: 157, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 9 0.06
97 39 0.25
98 109 0.69
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (98 bp):
TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
AGTTTATTTCAATTGATCCAGGGCGATCTTTTC
Found at i:6919 original size:25 final size:26
Alignment explanation
Indices: 6863--6919 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
6853 TCAGTTTATT
* *
6863 TCAATTGATCGAGGGCGATCTTTTCT
1 TCAATTGATCCAGGGCGATCTTTTCC
* *
6889 TTAATTGATCCAGGGTGATC-TTTCC
1 TCAATTGATCCAGGGCGATCTTTTCC
6914 TCAATT
1 TCAATT
6920 TACTTCAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (26 bp):
TCAATTGATCCAGGGCGATCTTTTCC
Found at i:7268 original size:30 final size:30
Alignment explanation
Indices: 7228--7980 Score: 1010
Period size: 30 Copynumber: 25.1 Consensus size: 30
7218 TGCTTTATCA
* * * * *
7228 GCTTT-TTTTAACCCTGGTGGAGGATCCTA
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7257 GCTTTATTTTAATCCTATTTGAGGATCATC
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * *
7287 GCTTTATTCTAATCATGTTTAAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7317 GCTTTATGTTAATCCT-TGTTGAGGATCGTT
1 GCTTTATTTTAATCCTGT-TTGAGGATCATT
* **
7347 GCTTTATTTTAATCCTGGTTGAGGATTGTT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
7377 GCTTTATTTTAATCATGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
** *
7407 GCTTTATGCTAATCCTGTTTGAGGAGCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * *
7437 GCTTTATGTTAATCCTGGTTGAGGATCGTT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
7467 GCTTTATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7497 TCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7527 GCTATATTTTAATCCTGTTTGACGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7557 ACTATATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
7587 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7617 GCTATATTTTAATTCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
7647 GCTATATTTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
7677 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
7707 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7737 GCTATATTTTAATCTTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7767 GCTATATTGTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
*
7797 GCTTTATGTTAATCCTGTTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* * * *
7827 GCTATATTTTAATCCTGATTGAGGGTCGTT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7857 GCTTTATTTTAATCCTGATTGAGGATCTTT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7887 GCTTTATTCTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
* *
7917 GCTTCATTTTAATCCTGGTTGAGGATCATT
1 GCTTTATTTTAATCCTGTTTGAGGATCATT
7947 GCTTTATTTTAATCCTGGTTT-AGGGA-CATT
1 GCTTTATTTTAATCCT-GTTTGA-GGATCATT
7977 GCTT
1 GCTT
7981 CATCAATTAA
Statistics
Matches: 645, Mismatches: 74, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
29 6 0.01
30 633 0.98
31 6 0.01
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (30 bp):
GCTTTATTTTAATCCTGTTTGAGGATCATT
Found at i:8571 original size:58 final size:54
Alignment explanation
Indices: 8501--8688 Score: 146
Period size: 58 Copynumber: 3.3 Consensus size: 54
8491 CACCTAAGAT
8501 ATTTTGGTCATTTTTCACATTCAATGGCATTATGGTCATTTTAAGTTCATTCAGGGGC
1 ATTTTGGTCATTTTTCACATTCAATGGCATTATGGTCATTTT--G--CATTCAGGGGC
* * * * *
8559 ATTTTGGTCATTTTCGCATATTC-ATGGTTATTTTGGTCATTTCTGCATATCTAGGGGT
1 ATTTTGGTCATTTT-TCACATTCAATGG-CATTATGGTCATTT-TGCAT-TC-AGGGGC
* * * **
8617 ATTTTTGTCATTTCT-GCATATCTAGGGGCATTATGGTCATTTTTGCACATTCAGGGGC
1 ATTTTGGTCATTTTTCACAT-TC-AATGGCATTATGGTCA-TTTTG--CATTCAGGGGC
8675 ATTTTGGTCATTTT
1 ATTTTGGTCATTTT
8689 AAGTTCACAT
Statistics
Matches: 102, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
56 5 0.05
57 4 0.04
58 64 0.63
59 25 0.25
60 4 0.04
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (54 bp):
ATTTTGGTCATTTTTCACATTCAATGGCATTATGGTCATTTTGCATTCAGGGGC
Found at i:8591 original size:29 final size:30
Alignment explanation
Indices: 8553--8688 Score: 149
Period size: 29 Copynumber: 4.7 Consensus size: 30
8543 AAGTTCATTC
8553 AGGGGCATTTTGGTCATTTTC-GCATAT-T
1 AGGGGCATTTTGGTCATTTTCTGCATATCT
* **
8581 CATGGTTATTTTGGTCA-TTTCTGCATATCT
1 -AGGGGCATTTTGGTCATTTTCTGCATATCT
* *
8611 AGGGGTATTTTTGTCA-TTTCTGCATATCT
1 AGGGGCATTTTGGTCATTTTCTGCATATCT
* *
8640 AGGGGCATTATGGTCATTTT-TGCACAT-T
1 AGGGGCATTTTGGTCATTTTCTGCATATCT
8668 CAGGGGCATTTTGGTCATTTT
1 -AGGGGCATTTTGGTCATTTT
8689 AAGTTCACAT
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.05
29 83 0.90
30 4 0.04
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.45
Consensus pattern (30 bp):
AGGGGCATTTTGGTCATTTTCTGCATATCT
Found at i:8834 original size:37 final size:36
Alignment explanation
Indices: 8780--8853 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
8770 GCACCTTTGG
* *
8780 CATTTTTAGTAATTTAACATTGTTGGCATTTTTGCA
1 CATTTTTAGTAACTTAACATTGTTGGCATTGTTGCA
*
8816 CATTTCTTAGTAACTTAACATTGTTTGCATTGTTGCA
1 CATTT-TTAGTAACTTAACATTGTTGGCATTGTTGCA
8853 C
1 C
8854 TCTAATCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 5 0.15
37 29 0.85
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (36 bp):
CATTTTTAGTAACTTAACATTGTTGGCATTGTTGCA
Done.