Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020597.1 Corchorus olitorius cultivar O-4 contig20630, 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: 3441
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Found at i:75 original size:35 final size:34
Alignment explanation
Indices: 35--188 Score: 115
Period size: 35 Copynumber: 4.5 Consensus size: 34
25 AAGAGTTAGG
*
35 ATTATTAAGTATTAATTTAATAATATGATTTATTA
1 ATTATTAATTATTAATTTAATAATAT-ATTTATTA
* *
70 ATTATTAATTATT-ATTTTATCAATA-ATTAAATTTA
1 ATTATTAATTATTAATTTAAT-AATATATT-TA-TTA
* * *
105 GGATTAATAATTAATAATTTAATAATTTAATTTATTA
1 --ATTATTAATTATTAATTTAATAATAT-ATTTATTA
* *
142 ATTATTAATTATTAA--TAATATTATATTCA-TA
1 ATTATTAATTATTAATTTAATAATATATTTATTA
173 A-T-TTAATTTATTAATT
1 ATTATTAA-TTATTAATT
189 AAAAAATAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
29 4 0.04
30 8 0.08
31 3 0.03
32 4 0.04
33 10 0.11
34 7 0.07
35 32 0.34
37 17 0.18
38 7 0.07
39 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTATTAATTATTAATTTAATAATATATTTATTA
Found at i:76 original size:7 final size:7
Alignment explanation
Indices: 35--157 Score: 65
Period size: 7 Copynumber: 17.3 Consensus size: 7
25 AAGAGTTAGG
35 ATTATTA
1 ATTATTA
*
42 AGTATTA
1 ATTATTA
*
49 ATTTAATA
1 A-TTATTA
*
57 A-TATGA
1 ATTATTA
*
63 TTTATTA
1 ATTATTA
70 ATTATTA
1 ATTATTA
77 ATTATTA
1 ATTATTA
* *
84 TTTTATCA
1 -ATTATTA
*
92 ATAATTA
1 ATTATTA
*
99 AAT-TTA
1 ATTATTA
*
105 GGATTAATA
1 --ATTATTA
*
114 ATTAATA
1 ATTATTA
121 A-T-TTA
1 ATTATTA
*
126 ATAATTTA
1 ATTA-TTA
134 ATTTATTA
1 A-TTATTA
142 ATTATTA
1 ATTATTA
149 ATTATTA
1 ATTATTA
156 AT
1 AT
158 AATATTATAT
Statistics
Matches: 86, Mismatches: 20, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
5 3 0.03
6 7 0.08
7 52 0.60
8 20 0.23
9 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (7 bp):
ATTATTA
Found at i:1770 original size:22 final size:22
Alignment explanation
Indices: 1742--1805 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1732 TCAAGCCACC
*
1742 TACTGATTTCCATTTTACTTTT
1 TACTGATTACCATTTTACTTTT
*
1764 TACTGATTACCATTTTA---AT
1 TACTGATTACCATTTTACTTTT
*
1783 TACTGAGTACCATTTTACTTTT
1 TACTGATTACCATTTTACTTTT
1805 T
1 T
1806 GGAACTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 17 0.49
22 18 0.51
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.53
Consensus pattern (22 bp):
TACTGATTACCATTTTACTTTT
Found at i:1787 original size:19 final size:19
Alignment explanation
Indices: 1763--1799 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1753 ATTTTACTTT
*
1763 TTACTGATTACCATTTTAA
1 TTACTGAGTACCATTTTAA
1782 TTACTGAGTACCATTTTA
1 TTACTGAGTACCATTTTA
1800 CTTTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (19 bp):
TTACTGAGTACCATTTTAA
Found at i:1924 original size:35 final size:34
Alignment explanation
Indices: 1884--2058 Score: 167
Period size: 35 Copynumber: 5.0 Consensus size: 34
1874 ATTGCCTTTG
*
1884 ACCTTAATTACTAAATACCATGTTTACT-TTGTTT
1 ACCTTAATTACTAAATACCATTTTTACTATT-TTT
* * *
1918 AGCCTTAATTAATGATTACCAATTTTT-CTACTCTTTT
1 A-CCTTAATTACTAAATACC-ATTTTTACTA-T-TTTT
* * *
1955 CAACTTAATTACTAAATACCATTTTTATTCTTTTT
1 -ACCTTAATTACTAAATACCATTTTTACTATTTTT
*
1990 AACTTTAATTACTAAATACCATTTTTACTATTTTT
1 -ACCTTAATTACTAAATACCATTTTTACTATTTTT
* * *
2025 AACTT-ATTACCAAATACCATTTTTACTCTTTTT
1 ACCTTAATTACTAAATACCATTTTTACTATTTTT
2058 A
1 A
2059 AATTAATACT
Statistics
Matches: 115, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
33 27 0.23
34 4 0.03
35 51 0.44
36 12 0.10
37 19 0.17
38 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (34 bp):
ACCTTAATTACTAAATACCATTTTTACTATTTTT
Found at i:2010 original size:72 final size:69
Alignment explanation
Indices: 1886--2059 Score: 201
Period size: 72 Copynumber: 2.5 Consensus size: 69
1876 TGCCTTTGAC
* * * * *
1886 CTTAATTACTAAATACCATGTTTACTT-TGTTTAGCCTTAATTAATGATTACCAATTTTT-CTAC
1 CTTAATTACTAAATACCATTTTTA-TTCTTTTTAACCTTAATTAATAAATACC-ATTTTTACTA-
1949 TCTTTTCAA
63 T-TTTT-AA
* *
1958 CTTAATTACTAAATACCATTTTTATTCTTTTTAACTTTAATTACTAAATACCATTTTTACTATTT
1 CTTAATTACTAAATACCATTTTTATTCTTTTTAACCTTAATTAATAAATACCATTTTTACTATTT
2023 TTAA
66 TTAA
* *
2027 CTT-ATTACCAAATACCATTTTTACTCTTTTTAA
1 CTTAATTACTAAATACCATTTTTATTCTTTTTAA
2060 ATTAATACTG
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
68 28 0.31
69 5 0.05
70 4 0.04
71 9 0.10
72 45 0.49
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.49
Consensus pattern (69 bp):
CTTAATTACTAAATACCATTTTTATTCTTTTTAACCTTAATTAATAAATACCATTTTTACTATTT
TTAA
Found at i:2695 original size:31 final size:30
Alignment explanation
Indices: 2660--2732 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
2650 TACCGTACAT
*
2660 GTCCCTCTACTTACAAAAAGGGATCAATTTG
1 GTCCCTCTACTTACAAAAACGG-TCAATTTG
* *
2691 GTCCCCCTAC-TACAAAAACTGTCAATTTG
1 GTCCCTCTACTTACAAAAACGGTCAATTTG
* *
2720 GTCCATTTACTTA
1 GTCCCTCTACTTA
2733 TAATTTGGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 15 0.43
30 11 0.31
31 9 0.26
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (30 bp):
GTCCCTCTACTTACAAAAACGGTCAATTTG
Found at i:2717 original size:29 final size:31
Alignment explanation
Indices: 2660--2723 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
2650 TACCGTACAT
* *
2660 GTCCCTCTACTTACAAAAAGGGATCAATTTG
1 GTCCCCCTACTTACAAAAACGGATCAATTTG
*
2691 GTCCCCCTAC-TACAAAAACTG-TCAATTTG
1 GTCCCCCTACTTACAAAAACGGATCAATTTG
2720 GTCC
1 GTCC
2724 ATTTACTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 12 0.40
30 9 0.30
31 9 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (31 bp):
GTCCCCCTACTTACAAAAACGGATCAATTTG
Found at i:2840 original size:12 final size:12
Alignment explanation
Indices: 2825--2857 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2815 TTTCTCCTTC
2825 TGTTTTTGTTGA
1 TGTTTTTGTTGA
2837 TGTTTTTGTTGA
1 TGTTTTTGTTGA
2849 -GTTTGTTGT
1 TGTTT-TTGT
2858 GAGCTTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.06, C:0.00, G:0.27, T:0.67
Consensus pattern (12 bp):
TGTTTTTGTTGA
Found at i:3088 original size:29 final size:30
Alignment explanation
Indices: 3031--3103 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
3021 CACCAAATTG
3031 TAAGTAGAGGGACCAAATTGACAGCTTTTA
1 TAAGTAGAGGGACCAAATTGACAGCTTTTA
* *** *
3061 T-AGTAGAGGGACCAAATTGTCCTTTTTTG
1 TAAGTAGAGGGACCAAATTGACAGCTTTTA
3090 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
3104 TGTACGGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (30 bp):
TAAGTAGAGGGACCAAATTGACAGCTTTTA
Found at i:3098 original size:30 final size:30
Alignment explanation
Indices: 2984--3103 Score: 109
Period size: 31 Copynumber: 4.0 Consensus size: 30
2974 ATATATAATC
*
2984 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGCTTTTG-TAAGTAGAGGGAC-CA
* * **
3015 AATCGACACCAAATTGTAAGTAGAGGGACCA
1 AATTGACAGC-TTTTGTAAGTAGAGGGACCA
*
3046 AATTGACAGCTTTTAT-AGTAGAGGGACCA
1 AATTGACAGCTTTTGTAAGTAGAGGGACCA
* ***
3075 AATTGTCCTTTTTTGTAAGTAGAGGGACC
1 AATTGACAGCTTTTGTAAGTAGAGGGACC
3104 TGTACGGTAT
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
29 24 0.34
30 16 0.23
31 28 0.39
32 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (30 bp):
AATTGACAGCTTTTGTAAGTAGAGGGACCA
Done.