Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017235.1 Corchorus olitorius cultivar O-4 contig17268, 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: 15182
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:661 original size:79 final size:79
Alignment explanation
Indices: 506--790 Score: 495
Period size: 79 Copynumber: 3.6 Consensus size: 79
496 ATAATCGTAA
506 TACTCCTAATCAA-T--TAATGTAGTACGAGGGTAGGCGAAGGAAAGCAATTATATTTGCATTAG
1 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGG--A--AA-TATATTTGCATTAG
568 TTAGCTACAGGTGGGTTAG
61 TTAGCTACAGGTGGGTTAG
587 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAATATATTTGCATTAGTTAGC
1 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAATATATTTGCATTAGTTAGC
652 TACAGGTGGGTTAG
66 TACAGGTGGGTTAG
666 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAATATATTTGCATTAGTTAGC
1 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAATATATTTGCATTAGTTAGC
*
731 TACAGGTTGGTTAG
66 TACAGGTGGGTTAG
745 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAA
1 TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAA
791 GCAATTATAT
Statistics
Matches: 200, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
79 157 0.79
80 2 0.01
81 13 0.06
82 2 0.01
84 26 0.13
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (79 bp):
TACTCCTAATCAATTAATAATGTAGTACGAGGGTAGGCGAAGGAAATATATTTGCATTAGTTAGC
TACAGGTGGGTTAG
Found at i:1131 original size:33 final size:33
Alignment explanation
Indices: 1094--1156 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1084 AACCCAGATT
*
1094 TGACCCGAAATCC-AAACGACCCGAACCCGAAAA
1 TGACCC-AAACCCAAAACGACCCGAACCCGAAAA
*
1127 TGACCCAAACCCAAAATGACCCGAACCCGA
1 TGACCCAAACCCAAAACGACCCGAACCCGA
1157 TCAACCCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.06
Consensus pattern (33 bp):
TGACCCAAACCCAAAACGACCCGAACCCGAAAA
Found at i:1144 original size:16 final size:16
Alignment explanation
Indices: 1063--1154 Score: 62
Period size: 16 Copynumber: 5.6 Consensus size: 16
1053 AATCCGCCCA
* *
1063 ACCCGAAACCGAAACTG
1 ACCC-AAACCCAAAATG
**
1080 ACCC-AACCCAGATTTG
1 ACCCAAACCCA-AAATG
* *
1096 ACCCGAAATCC-AAACG
1 ACCC-AAACCCAAAATG
*
1112 ACCCGAACCCGAAAATG
1 ACCCAAACCC-AAAATG
1129 ACCCAAACCCAAAATG
1 ACCCAAACCCAAAATG
*
1145 ACCCGAACCC
1 ACCCAAACCC
1155 GATCAACCCG
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
15 9 0.16
16 28 0.48
17 17 0.29
18 4 0.07
ACGTcount: A:0.40, C:0.39, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCAAACCCAAAATG
Found at i:2639 original size:16 final size:16
Alignment explanation
Indices: 2618--2652 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2608 AAAAAATGAA
2618 CCGTAACGACCCGAAC
1 CCGTAACGACCCGAAC
2634 CCGTAACGACCCGAAC
1 CCGTAACGACCCGAAC
2650 CCG
1 CCG
2653 AAAACCCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.46, G:0.20, T:0.06
Consensus pattern (16 bp):
CCGTAACGACCCGAAC
Found at i:5069 original size:24 final size:24
Alignment explanation
Indices: 5042--5090 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5032 CACATGTCCT
5042 TGATTTTGCCCTAAACCATCAATC
1 TGATTTTGCCCTAAACCATCAATC
*
5066 TGATTTTGCCCTAAACCATTAATC
1 TGATTTTGCCCTAAACCATCAATC
5090 T
1 T
5091 CCATCAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.37
Consensus pattern (24 bp):
TGATTTTGCCCTAAACCATCAATC
Found at i:5868 original size:21 final size:22
Alignment explanation
Indices: 5844--5887 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5834 TGATTATTAG
5844 ATAATATATA-TTAACTAATAA
1 ATAATATATATTTAACTAATAA
*
5865 ATAATATATATTTAATTAATAA
1 ATAATATATATTTAACTAATAA
5887 A
1 A
5888 ATGGGCGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATATATATTTAACTAATAA
Found at i:7344 original size:68 final size:67
Alignment explanation
Indices: 7232--7367 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 67
7222 CCAGTACTCA
* **
7232 ACTAAAAACTTCATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTTACCATTTT
1 ACTAAAAACTTCATTGTTATTTAATTAAATCTAATATCCATATAACTATTTTATTTTACCA-TTT
7297 ACT
65 ACT
7300 ACTAAAAAC-TCTATTGTTATTTAATTAAATCTAATATCCATATAACTATTTTATTTTACCATTT
1 ACTAAAAACTTC-ATTGTTATTTAATTAAATCTAATATCCATATAACTATTTTATTTTACCATTT
7364 ACT
65 ACT
7367 A
1 A
7368 TTTTAATTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
67 9 0.14
68 55 0.86
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.49
Consensus pattern (67 bp):
ACTAAAAACTTCATTGTTATTTAATTAAATCTAATATCCATATAACTATTTTATTTTACCATTTA
CT
Found at i:10081 original size:66 final size:64
Alignment explanation
Indices: 9998--10128 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 64
9988 CTGGGATTGA
*
9998 TGCAGGCTGTGTTGCGATTTGAGTTTCTGGCAAGGGAACTGGCTGAGGTAATAACTCTCTCTGTT
1 TGCAGGCTGTGGTGCGATTTGAGTTTCTGGCAAGGG-ACTGGCTGAGGT-ATAACTCTCTCTGTT
10063 G
64 G
*
10064 TGCAGGCTGTGGTGCGATTTGAGTTTCTGGCAAGGGACTGGCTGAGGTATAATTCTCTCTGTTG
1 TGCAGGCTGTGGTGCGATTTGAGTTTCTGGCAAGGGACTGGCTGAGGTATAACTCTCTCTGTTG
10128 T
1 T
10129 ACATTAGCAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 16 0.25
65 12 0.19
66 35 0.56
ACGTcount: A:0.17, C:0.16, G:0.33, T:0.34
Consensus pattern (64 bp):
TGCAGGCTGTGGTGCGATTTGAGTTTCTGGCAAGGGACTGGCTGAGGTATAACTCTCTCTGTTG
Found at i:14602 original size:14 final size:14
Alignment explanation
Indices: 14583--14610 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14573 TTTTTCTTCT
14583 AAAAATTAGGTTCA
1 AAAAATTAGGTTCA
14597 AAAAATTAGGTTCA
1 AAAAATTAGGTTCA
14611 GTGGACAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAAATTAGGTTCA
Done.