Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009076.1 Corchorus capsularis cultivar CVL-1 contig09097, 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: 18573
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2741 original size:54 final size:53
Alignment explanation
Indices: 2677--2787 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 53
2667 CCATTACACA
* *
2677 CACACACACATGTTTATATGCCTCACTTTATATTTTGTTTTTGGGGTTTGCTCG
1 CACACACACATGTTTATATGCCACACTTTATATTTTG-TTTTGGGGTTTGCTCC
*
2731 CACAGACACATGTTTATATGCCACACTTTATATTTTGTTTTGGGGTTTGCTCC
1 CACACACACATGTTTATATGCCACACTTTATATTTTGTTTTGGGGTTTGCTCC
2784 CACA
1 CACA
2788 TTTCATTACT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 19 0.35
54 35 0.65
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (53 bp):
CACACACACATGTTTATATGCCACACTTTATATTTTGTTTTGGGGTTTGCTCC
Found at i:3902 original size:81 final size:81
Alignment explanation
Indices: 3767--3928 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
3757 ATTTTGCATC
* *
3767 CCCTTGAGTACTTGCTTCCGAATTGATTTTAACACCTCCAAATCAAAACTTGGAAAAAACGCTTT
1 CCCTTGAGTACCTGCTTCCGAATTGATTTTAACACCTCCAAATCAAAACTTGGAAAAAAAGCTTT
3832 ATGGATTATACTAAAA
66 ATGGATTATACTAAAA
3848 CCCTTGAGTACCTGCTTCCGAATTGATTTTAACACCTCCAAATCAAAACTTGGAAAAAAAGCTTT
1 CCCTTGAGTACCTGCTTCCGAATTGATTTTAACACCTCCAAATCAAAACTTGGAAAAAAAGCTTT
3913 ATGGATTATACTAAAA
66 ATGGATTATACTAAAA
3929 TCAAAACTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (81 bp):
CCCTTGAGTACCTGCTTCCGAATTGATTTTAACACCTCCAAATCAAAACTTGGAAAAAAAGCTTT
ATGGATTATACTAAAA
Found at i:3941 original size:39 final size:39
Alignment explanation
Indices: 3887--3967 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
3877 TAACACCTCC
3887 AAATCAAAACTTGGAAAAAAAGCTTTATGGATTATACTA
1 AAATCAAAACTTGGAAAAAAAGCTTTATGGATTATACTA
3926 AAATCAAAACTTGGAAAAAAAGCTTTATGGATTATACTA
1 AAATCAAAACTTGGAAAAAAAGCTTTATGGATTATACTA
3965 AAA
1 AAA
3968 CTTAATTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (39 bp):
AAATCAAAACTTGGAAAAAAAGCTTTATGGATTATACTA
Found at i:4613 original size:20 final size:21
Alignment explanation
Indices: 4588--4626 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4578 TTTAGAAGCA
4588 ATTAATTAAAAAC-ATTAAAC
1 ATTAATTAAAAACAATTAAAC
4608 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAACAATTAA
4627 GGAAGGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAATTAAAAACAATTAAAC
Found at i:12991 original size:12 final size:12
Alignment explanation
Indices: 12974--12998 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12964 GTTGCGGCCT
12974 CTGTGGGAAACG
1 CTGTGGGAAACG
12986 CTGTGGGAAACG
1 CTGTGGGAAACG
12998 C
1 C
12999 ATAAGCTGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.40, T:0.16
Consensus pattern (12 bp):
CTGTGGGAAACG
Found at i:16157 original size:26 final size:26
Alignment explanation
Indices: 16137--16188 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
16127 GAAAAACGCT
16137 CAAATAAAACGCATTAAAAAAAGAATG
1 CAAA-AAAACGCATTAAAAAAAGAATG
*
16164 TAAAAAAACGCATTAAAAAAAGAAT
1 CAAAAAAACGCATTAAAAAAAGAAT
16189 AGCGTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (26 bp):
CAAAAAAACGCATTAAAAAAAGAATG
Found at i:16158 original size:13 final size:13
Alignment explanation
Indices: 16128--16184 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
16118 AAAGTTCAAG
*
16128 AAAAACGC-TCAA
1 AAAAACGCATTAA
16140 ATAAAACGCATTAA
1 A-AAAACGCATTAA
*
16154 AAAAA-GAATGTAA
1 AAAAACGCAT-TAA
16167 AAAAACGCATTAA
1 AAAAACGCATTAA
16180 AAAAA
1 AAAAA
16185 GAATAGCGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.11
13 27 0.71
14 7 0.18
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.14
Consensus pattern (13 bp):
AAAAACGCATTAA
Found at i:16612 original size:30 final size:30
Alignment explanation
Indices: 16545--16616 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
16535 ACACCGAACC
****
16545 GTCAAATAAGCCCCTGAACTATTATTTCAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAAA
* *
16575 -CCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAAA
16604 GTCAAATAAGCCC
1 GTCAAATAAGCCC
16617 TGTTGCCAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (30 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAAA
Done.