Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016213.1 Corchorus olitorius cultivar O-4 contig16246, 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: 24568
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1199 original size:34 final size:35
Alignment explanation
Indices: 1130--1193 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
1120 GAGCTAAAAA
*
1130 AGACCCTATTTTTATGCCTATTTTACTATGTTTTT
1 AGACCCTATTTTTATGCCTATATTACTATGTTTTT
*
1165 AGACCC-ATTTTTATGCTTA-ATTA-TATGTT
1 AGACCCTATTTTTATGCCTATATTACTATGTT
1194 ATTTTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 6 0.22
33 3 0.11
34 12 0.44
35 6 0.22
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (35 bp):
AGACCCTATTTTTATGCCTATATTACTATGTTTTT
Found at i:2796 original size:15 final size:16
Alignment explanation
Indices: 2765--2804 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
2755 TTACTCTGCT
2765 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
2781 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
2796 TTGCTTTCT
1 TTGTTTTCT
2805 GTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:4092 original size:84 final size:84
Alignment explanation
Indices: 3937--4104 Score: 230
Period size: 84 Copynumber: 2.0 Consensus size: 84
3927 ATGCGACTAT
* * * *
3937 TCTGTGGATCTAGTGGCACTGAAAAACCATGAGTGACCAGAGAATCAGAACAATTTTCCTTTAGA
1 TCTGTGGAGCTAGTGGCACTGAAAAACCATGAGTGACCAAAGAATCAAAACAATTTTCCTGTAGA
4002 AGTAGTGGCACTGAAGAGG
66 AGTAGTGGCACTGAAGAGG
** * * *
4021 TCTGTGGAGCTAGTGGCACT-AAAGAACCATGAGTGGTCAAAGAATCAAAACGATTTTGCTGTGG
1 TCTGTGGAGCTAGTGGCACTGAAA-AACCATGAGTGACCAAAGAATCAAAACAATTTTCCTGTAG
*
4085 AATTAGTGGCACTGAAGAGG
65 AAGTAGTGGCACTGAAGAGG
4105 AAGCATTAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
83 3 0.04
84 70 0.96
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (84 bp):
TCTGTGGAGCTAGTGGCACTGAAAAACCATGAGTGACCAAAGAATCAAAACAATTTTCCTGTAGA
AGTAGTGGCACTGAAGAGG
Found at i:6735 original size:27 final size:28
Alignment explanation
Indices: 6705--6785 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 28
6695 TTTGAATTCA
*
6705 AACTAACTTTGAATGGGA-AATTGACTT
1 AACTAACTTTGAATGGGAGAACTGACTT
*
6732 AACTAGCTTTGAAT-GGAGAACTGACTT
1 AACTAACTTTGAATGGGAGAACTGACTT
* * * *
6759 GACTGACTTGGAATGAGAG-ACTGACTT
1 AACTAACTTTGAATGGGAGAACTGACTT
6786 TGAATGATCC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 3 0.07
27 39 0.87
28 3 0.07
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (28 bp):
AACTAACTTTGAATGGGAGAACTGACTT
Found at i:11099 original size:11 final size:11
Alignment explanation
Indices: 11085--11122 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11075 ATTCATAACA
11085 AATTTATAATT
1 AATTTATAATT
11096 AATTTATAATT
1 AATTTATAATT
11107 -ATTTGATAATT
1 AATTT-ATAATT
*
11118 TATTT
1 AATTT
11123 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:13077 original size:217 final size:217
Alignment explanation
Indices: 12702--13131 Score: 743
Period size: 217 Copynumber: 2.0 Consensus size: 217
12692 GATCAAAAAC
*
12702 GATCCGAATATTCGATTGAACCAATCAATGTCCGGTTCGTTGACTCTCCAAGTTTGTGTCTCATC
1 GATCCGAATATCCGATTGAACCAATCAATGTCCGGTTCGTTGACTCTCCAAGTTTGTGTCTCATC
* *
12767 AGGCCAGATTGGCCTCTAAATCTCGGTTTAACCAATTGAATCGGCTGATCCGATTCAGTTTTGAA
66 AGGCCAGATTGGCCTCCAAATCTCGGTTTAACCAATTGAATCGGCCGATCCGATTCAGTTTTGAA
12832 TTCATTGGTTTTAGGCCTAGCTTTTCTGAAATATTCTTATATCTAGTTTGGCCCAATCAACTATT
131 TTCATTGGTTTTAGGCCTAGCTTTTCTGAAATATTCTTATATCTAGTTTGGCCCAATCAACTATT
*
12897 ATTAATGATGATTGGCGGCCTA
196 ATTAATGATGATTAGCGGCCTA
** *
12919 GATCCGAATATCCGATTGAACCGGTCAATGTCTGGTTCGTTGACTCTCCAAGTTTGTGTCTCATC
1 GATCCGAATATCCGATTGAACCAATCAATGTCCGGTTCGTTGACTCTCCAAGTTTGTGTCTCATC
* * * * *
12984 AGGCCAGATTGGCCTCCAATTGTCGGTTTAACCAATTGAATTGGCCGATCCGGTTCGGTTTTGAA
66 AGGCCAGATTGGCCTCCAAATCTCGGTTTAACCAATTGAATCGGCCGATCCGATTCAGTTTTGAA
*
13049 TTCATTGGTTTTAGGCCTAGCTTTTCTGAAATATTGTTATATCTAGTTTGGCCCAATCAACTATT
131 TTCATTGGTTTTAGGCCTAGCTTTTCTGAAATATTCTTATATCTAGTTTGGCCCAATCAACTATT
13114 ATTAATGATGATTAGCGG
196 ATTAATGATGATTAGCGG
13132 TCTATCATAC
Statistics
Matches: 200, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 200 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (217 bp):
GATCCGAATATCCGATTGAACCAATCAATGTCCGGTTCGTTGACTCTCCAAGTTTGTGTCTCATC
AGGCCAGATTGGCCTCCAAATCTCGGTTTAACCAATTGAATCGGCCGATCCGATTCAGTTTTGAA
TTCATTGGTTTTAGGCCTAGCTTTTCTGAAATATTCTTATATCTAGTTTGGCCCAATCAACTATT
ATTAATGATGATTAGCGGCCTA
Found at i:13908 original size:44 final size:44
Alignment explanation
Indices: 13789--13960 Score: 177
Period size: 44 Copynumber: 3.9 Consensus size: 44
13779 ATAAACGTCA
* *
13789 TTATACAATTTTAATAACCACACAACAAAATTTTGATAGCTTCC
1 TTATACAATTTTGATAACCACACAACAAAATTTTGATAACTTCC
* * * * * **
13833 TCATAAAATTTTGATGATCAAACAATGAAATTTTGATAACTTCC
1 TTATACAATTTTGATAACCACACAACAAAATTTTGATAACTTCC
* * *
13877 TTATACAATTTCGATAACCCCACAACAAAATTTTGATAA-TCTCG
1 TTATACAATTTTGATAACCACACAACAAAATTTTGATAACT-TCC
* * *
13921 TTATATAATTTTGATAACCTCA-ATATAAAATTTTGATAAC
1 TTATACAATTTTGATAACCACACA-ACAAAATTTTGATAAC
13961 CACACTATAA
Statistics
Matches: 102, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
43 2 0.02
44 100 0.98
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (44 bp):
TTATACAATTTTGATAACCACACAACAAAATTTTGATAACTTCC
Found at i:13961 original size:22 final size:22
Alignment explanation
Indices: 13860--13970 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
13850 TCAAACAATG
* **
13860 AAATTTTGATAACTTCCTTATA
1 AAATTTTGATAACCTCAATATA
* * * *
13882 CAATTTCGATAACCCCACA-ACA
1 AAATTTTGATAACCTCA-ATATA
* **
13904 AAATTTTGATAATCTCGTTATA
1 AAATTTTGATAACCTCAATATA
*
13926 TAATTTTGATAACCTCAATATA
1 AAATTTTGATAACCTCAATATA
* *
13948 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCTCAATATA
13970 A
1 A
13971 GTTTTAATAA
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCTCAATATA
Found at i:13980 original size:21 final size:20
Alignment explanation
Indices: 13923--13980 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
13913 TAATCTCGTT
*
13923 ATATAATTTTGATAACCTCA
1 ATATAATTTTGATAACCACA
13943 ATATAAAATTTTGATAACCACA
1 ATAT--AATTTTGATAACCACA
* *
13965 CTATAAGTTTTAATAA
1 ATATAA-TTTTGATAA
13981 TTATTCTACG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 18 0.56
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
ATATAATTTTGATAACCACA
Found at i:14083 original size:22 final size:22
Alignment explanation
Indices: 14049--14148 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
14039 TCTCTTTACG
**
14049 AAATTTTTTTAATCTCACTATA
1 AAATTTTGATAATCTCACTATA
** * *
14071 AAATTTTGATAATCGGATTATG
1 AAATTTTGATAATCTCACTATA
* **
14093 AAATTGTGAT-ATCCTCTTTATA
1 AAATTTTGATAAT-CTCACTATA
* *
14115 AAATTTTAATAACCTCACTATA
1 AAATTTTGATAATCTCACTATA
14137 AAATTTTGATAA
1 AAATTTTGATAA
14149 ATTTCCTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
21 2 0.03
22 56 0.95
23 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCTCACTATA
Found at i:15393 original size:6 final size:6
Alignment explanation
Indices: 15376--15431 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
15366 GTACTTTTAT
15376 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
15423 ATATAG ATA
1 ATATAG ATA
15432 ATAATTATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.10
6 44 0.90
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:17897 original size:14 final size:14
Alignment explanation
Indices: 17878--17906 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17868 TCTATTGAAA
17878 GTGGAGTTAAACCT
1 GTGGAGTTAAACCT
17892 GTGGAGTTAAACCT
1 GTGGAGTTAAACCT
17906 G
1 G
17907 GTGACACGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (14 bp):
GTGGAGTTAAACCT
Done.