Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012156.1 Corchorus olitorius cultivar O-4 contig12189, 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: 30342
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:6106 original size:30 final size:30
Alignment explanation
Indices: 6034--6111 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
6024 TTGCTTATTT
* *
6034 TATCTTTC-AATTG-TTGATTTGAATTGCCA
1 TATCTTGCTAATTGATTGA-TTGAATTGCAA
6063 TATCTTGCT-ATTGATTGATTGAATTGCAA
1 TATCTTGCTAATTGATTGATTGAATTGCAA
*
6092 TTAT-TTGTTAATTGATTGAT
1 -TATCTTGCTAATTGATTGAT
6112 AGATTGTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (30 bp):
TATCTTGCTAATTGATTGATTGAATTGCAA
Found at i:6887 original size:22 final size:24
Alignment explanation
Indices: 6835--6888 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
6825 CTTGAAAAAA
*
6835 AAAAGAAGAGAAAAAACTTGCAAT
1 AAAAGAAGAAAAAAAACTTGCAAT
* *
6859 ATCAAGAATAAAAAAAAC-TG-AAT
1 A-AAAGAAGAAAAAAAACTTGCAAT
6882 AAAAGAA
1 AAAAGAA
6889 CAATTCGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.20
23 4 0.16
24 3 0.12
25 13 0.52
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAAGAAGAAAAAAAACTTGCAAT
Found at i:12445 original size:11 final size:11
Alignment explanation
Indices: 12429--12454 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12419 CCTTTGCCTA
12429 AAAACTAGAAG
1 AAAACTAGAAG
12440 AAAACTAGAAG
1 AAAACTAGAAG
12451 AAAA
1 AAAA
12455 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:14848 original size:16 final size:15
Alignment explanation
Indices: 14827--14874 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
14817 AGGAATAGGC
14827 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
14842 TAATCAATCAAAGCAA
1 -AATCAATCAAAGCAA
14858 AA-CAATGCAAAG-AA
1 AATCAAT-CAAAGCAA
14872 AAT
1 AAT
14875 GAATAGATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 15 0.50
ACGTcount: A:0.60, C:0.17, G:0.08, T:0.15
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:19177 original size:142 final size:141
Alignment explanation
Indices: 18905--19183 Score: 504
Period size: 142 Copynumber: 2.0 Consensus size: 141
18895 GCCTAGTGAT
* *
18905 GCGAATCTAGTTTGTTAGATTCAAATCTATCCTTAAAAAGACTCCAAAGATCTACTTGACAACTT
1 GCGAATCTAGTTTGTTAAATACAAATCTATCCTTAAAAAGACTCCAAAGATCTACTTGACAACTT
18970 CAACTTCTAGATTTGTATGAAGAATCGATAAACCTAACCAAGCTTCTTCTTCGTTCGTCGCCTTT
66 CAACTTCTAGATTTGTATGAAGAATCGATAAACCTAACCAAGCTTCTTCTTCGTTCGTCGCCTTT
19035 GATGGATTGAC
131 GATGGATTGAC
* *
19046 GCGAATCTAGTTGTGTTAAATACAAATCTATCCTTGAAAAGCCTCCAAAGATCTACTTGACAACT
1 GCGAATCTAGTT-TGTTAAATACAAATCTATCCTTAAAAAGACTCCAAAGATCTACTTGACAACT
*
19111 TCAACTTCTAGATTTGTATGAAGAATCGATAAACCTAACCAAGCTTCTTCTTCGTTCGTCGGCTT
65 TCAACTTCTAGATTTGTATGAAGAATCGATAAACCTAACCAAGCTTCTTCTTCGTTCGTCGCCTT
19176 TGATGGAT
130 TGATGGAT
19184 AATTAGACCT
Statistics
Matches: 132, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
141 12 0.09
142 120 0.91
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (141 bp):
GCGAATCTAGTTTGTTAAATACAAATCTATCCTTAAAAAGACTCCAAAGATCTACTTGACAACTT
CAACTTCTAGATTTGTATGAAGAATCGATAAACCTAACCAAGCTTCTTCTTCGTTCGTCGCCTTT
GATGGATTGAC
Found at i:20004 original size:30 final size:29
Alignment explanation
Indices: 19968--20052 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 29
19958 CATCTTCAAG
19968 TCCATGATAAGTCCTTGGTGC-ATCATTCCC
1 TCCATGATAAG-CCTTGG-GCGATCATTCCC
19998 TCCATGATAAGCCTTGGGCGTATCATTCCC
1 TCCATGATAAGCCTTGGGCG-ATCATTCCC
20028 TCCATGATAAGCCTTGGGCGCATCA
1 TCCATGATAAGCCTTGGGCG-ATCA
20053 CCTAGTTGTG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
28 2 0.04
29 6 0.12
30 44 0.85
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.29
Consensus pattern (29 bp):
TCCATGATAAGCCTTGGGCGATCATTCCC
Found at i:22822 original size:32 final size:32
Alignment explanation
Indices: 22770--22954 Score: 226
Period size: 32 Copynumber: 5.5 Consensus size: 32
22760 AAAAAGCAGT
* **
22770 TAAATATAGCGGCGCTTTGTTCTGAAGACGCCGC
1 TAAATA-AG-GGCGTTTTGTTCTTCAGACGCCGC
22804 TAAATAAGGGCGTTTTGTTCTTCAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTTCAGACGCCGC
* *
22836 TAAATAAGGGCGTTTTGTTCTTCAGACGTCAC
1 TAAATAAGGGCGTTTTGTTCTTCAGACGCCGC
* *
22868 TAAATAAGGGCGTTTTGTTTTTTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTTCAGACGCCGC
22900 TAAATAAGGGCGTTTTGTTCTTTGTTCTTTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTC----TTC---AGACGCCGC
22939 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
22955 CTTTTCACAT
Statistics
Matches: 133, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
32 98 0.74
33 2 0.02
34 6 0.05
36 2 0.02
39 25 0.19
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTTCAGACGCCGC
Found at i:26691 original size:31 final size:31
Alignment explanation
Indices: 26656--26749 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
26646 TTTCATTTCC
* *
26656 ACTTAGCGGCGTCTGGTGTTTAAACGCTGCT
1 ACTTAGCGGCGTCTGATGTTTAAACGCCGCT
*
26687 ACTTAGCGGCGTTTGATGTTTAAACGCCGCT
1 ACTTAGCGGCGTCTGATGTTTAAACGCCGCT
*
26718 ACTTAGCGGCGTCTGATGTTTAAGCGCCGCT
1 ACTTAGCGGCGTCTGATGTTTAAACGCCGCT
26749 A
1 A
26750 TCTATTATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (31 bp):
ACTTAGCGGCGTCTGATGTTTAAACGCCGCT
Found at i:26935 original size:31 final size:31
Alignment explanation
Indices: 26875--26935 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
26865 TTCTTTCGAA
*
26875 ACGCCACTAAATGGCAGCGTCCCTTTGTCAG
1 ACGCCACTAAATGGCAGCGTCCCTATGTCAG
* **
26906 ACGCCACTAAATGGCGGCGTCTGTATGTCA
1 ACGCCACTAAATGGCAGCGTCCCTATGTCA
26936 TATAGCGGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (31 bp):
ACGCCACTAAATGGCAGCGTCCCTATGTCAG
Done.