Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013465.1 Corchorus olitorius cultivar O-4 contig13498, 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: 7510
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:2805 original size:13 final size:14
Alignment explanation
Indices: 2787--2849 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 14
2777 CACTCCATCA
2787 AAAAAAATC-AATC
1 AAAAAAATCAAATC
2800 AAAAAAATCAAAAAATC
1 AAAAAAATC---AAATC
*
2817 AAATCAAAGTC-AATC
1 AAA--AAAATCAAATC
2832 AAAAAAATCAAATC
1 AAAAAAATCAAATC
2846 AAAA
1 AAAA
2850 TCAAAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 14 0.34
14 8 0.20
15 7 0.17
17 7 0.17
19 5 0.12
ACGTcount: A:0.70, C:0.14, G:0.02, T:0.14
Consensus pattern (14 bp):
AAAAAAATCAAATC
Found at i:2829 original size:6 final size:5
Alignment explanation
Indices: 2791--2860 Score: 53
Period size: 5 Copynumber: 14.6 Consensus size: 5
2781 CCATCAAAAA
* *
2791 AAATC -AATC AAA-A AAATC AAA-- AAATC AAATC AAAGTC -AATC AAA-A
1 AAATC AAATC AAATC AAATC AAATC AAATC AAATC AAA-TC AAATC AAATC
2836 AAATC AAATC AAAATC AAAATC AAA
1 AAATC AAATC -AAATC -AAATC AAA
2861 AGAGAATTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
3 3 0.06
4 12 0.23
5 25 0.47
6 13 0.25
ACGTcount: A:0.67, C:0.16, G:0.01, T:0.16
Consensus pattern (5 bp):
AAATC
Found at i:2829 original size:19 final size:16
Alignment explanation
Indices: 2804--2860 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 16
2794 TCAATCAAAA
2804 AAATCAAAAAATCAAATC
1 AAATCAAAAAA--AAATC
2822 AAAGTCAATCAAAAAAATC
1 AAA-TCAA--AAAAAAATC
*
2841 AAATCAAAATCAAAATC
1 AAATCAAAA-AAAAATC
2858 AAA
1 AAA
2861 AGAGAATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 7 0.21
19 12 0.35
21 4 0.12
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.16
Consensus pattern (16 bp):
AAATCAAAAAAAAATC
Found at i:2861 original size:12 final size:11
Alignment explanation
Indices: 2790--2860 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 11
2780 TCCATCAAAA
2790 AAAATC-AATC
1 AAAATCAAATC
2800 AAAA--AAATC
1 AAAATCAAATC
2809 AAAAAATCAAATC
1 --AAAATCAAATC
*
2822 AAAGTC-AATC
1 AAAATCAAATC
2832 AAAA--AAATC
1 AAAATCAAATC
2841 -AAATCAAAATC
1 AAAATC-AAATC
2852 AAAATCAAA
1 AAAATCAAA
2861 AGAGAATTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
8 3 0.06
9 8 0.16
10 11 0.22
11 17 0.35
12 5 0.10
13 5 0.10
ACGTcount: A:0.68, C:0.15, G:0.01, T:0.15
Consensus pattern (11 bp):
AAAATCAAATC
Found at i:2861 original size:24 final size:25
Alignment explanation
Indices: 2788--2861 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 25
2778 ACTCCATCAA
2788 AAAAAATC-AATC-AAA--AAAATC
1 AAAAAATCAAATCAAAATCAAAATC
*
2809 AAAAAATCAAATCAAAGTC--AATC
1 AAAAAATCAAATCAAAATCAAAATC
2832 AAAAAAATCAAATCAAAATCAAAATC
1 -AAAAAATCAAATCAAAATCAAAATC
2858 AAAA
1 AAAA
2862 GAGAATTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 8 0.18
22 4 0.09
23 6 0.14
24 18 0.41
25 4 0.09
26 4 0.09
ACGTcount: A:0.69, C:0.15, G:0.01, T:0.15
Consensus pattern (25 bp):
AAAAAATCAAATCAAAATCAAAATC
Found at i:3708 original size:50 final size:50
Alignment explanation
Indices: 3460--3707 Score: 415
Period size: 50 Copynumber: 5.0 Consensus size: 50
3450 GTTTTATAAC
* *
3460 AAAATTGCTTTCCACTTGTGAGTTCAAGATCAAAATTCACTTTTCAAAAT
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
3510 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
3560 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
* *
3610 AAAATTGCTTTCCATTTGTGAGTTCAAGATTAAAATTCGCTTTTCAAAGT
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
** * * *
3660 AAGGTTGCATTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAA
3708 GGGCATTTAA
Statistics
Matches: 188, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 188 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (50 bp):
AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
Found at i:4261 original size:35 final size:35
Alignment explanation
Indices: 4214--4457 Score: 337
Period size: 35 Copynumber: 7.0 Consensus size: 35
4204 TATTTTCCAA
* **
4214 AGATGACTCGGTGTAGCATCTCCAAAGTTGAACTC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
* * * *
4249 GGATGACTCGGTGCAGCATCTTCAAAATTGAACCC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
*
4284 AGATGACTCGGTGTAGCATCTTCAAAATTGAACTC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
*
4319 AGATGACTCGGTGTAGCATCTTCAAAAATGACCTC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
* *
4354 GGATGACTCGGTGTAGCATCTTCAAAAATGAATTC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
*
4389 AGATGACTCGGTGTAGCATCTTCAAAAATGATCTC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
* * * *
4424 GGATGGCTCGATGTAGCATCTTC-AATATGAACTC
1 AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
4458 GGTGGGCTCG
Statistics
Matches: 188, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
34 9 0.05
35 179 0.95
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (35 bp):
AGATGACTCGGTGTAGCATCTTCAAAAATGAACTC
Found at i:4783 original size:27 final size:27
Alignment explanation
Indices: 4732--4783 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
4722 TCAAGAATCT
*
4732 AGGGGCATTTTAGTCATTTGCAGTTTC
1 AGGGGCATTTTAGTCATTTGAAGTTTC
*
4759 AGGGGCATTTTAGTCATTTTAAGTT
1 AGGGGCATTTTAGTCATTTGAAGTT
4784 CACATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTAGTCATTTGAAGTTTC
Found at i:6075 original size:15 final size:16
Alignment explanation
Indices: 6047--6076 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6037 TTTCCCAAAG
6047 AGTTACAGAGAGAAAC
1 AGTTACAGAGAGAAAC
6063 AGTTACA-AGAGAAA
1 AGTTACAGAGAGAAA
6077 GAAAAGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13
Consensus pattern (16 bp):
AGTTACAGAGAGAAAC
Found at i:7492 original size:24 final size:24
Alignment explanation
Indices: 7442--7507 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
7432 ATGGTTTCTG
*
7442 ACTTGGGCTTTTAGATTCCTTGGTGC
1 ACTTGGGCTTTT--ATTCCTTGATGC
*
7468 ACTTGGGCTTTTATTCCTTTATGC
1 ACTTGGGCTTTTATTCCTTGATGC
* *
7492 ATTTGGACCTTTTATT
1 ACTTGG-GCTTTTATT
7508 TAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.43
25 8 0.23
26 12 0.34
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (24 bp):
ACTTGGGCTTTTATTCCTTGATGC
Done.