Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020984.1 Corchorus olitorius cultivar O-4 contig21017, 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: 9139
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:485 original size:16 final size:16
Alignment explanation
Indices: 428--487 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
418 GTCGGGTTGA
*
428 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTAATT
* * **
444 TTGGGTTTGGGTCGTT
1 TCGGGTTCGGGTAATT
*
460 T-GGATTCGGGTAATT
1 TCGGGTTCGGGTAATT
475 TCGGGTTCGGGTA
1 TCGGGTTCGGGTA
488 CCCAAAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 11 0.31
16 24 0.69
ACGTcount: A:0.08, C:0.12, G:0.40, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:1267 original size:22 final size:22
Alignment explanation
Indices: 1237--1288 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1227 AATTCTTGCT
* *
1237 TCTTGAAATAATTCTTCAATGA-
1 TCTTCAAATAA-TCTTCAATAAG
*
1259 TCTTCAAATTATCTTCAATAAG
1 TCTTCAAATAATCTTCAATAAG
1281 TCTTCAAA
1 TCTTCAAA
1289 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAATAAG
Found at i:4913 original size:29 final size:29
Alignment explanation
Indices: 4880--4981 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
4870 GATCACCTAC
* *
4880 GGGCATTTTGGTCATTTTCAAAAATCCAG
1 GGGCATTTTAGTCATTTTCAAAAATCCAA
*
4909 GGGCATTTTAGTCATTTTCAAAAATCCAC
1 GGGCATTTTAGTCATTTTCAAAAATCCAA
*
4938 GGGCATTTTAGTCATTTTC--ACATCCAA
1 GGGCATTTTAGTCATTTTCAAAAATCCAA
4965 GGGCATTTTAGTCATTT
1 GGGCATTTTAGTCATTT
4982 GCGCATTCAG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 23 0.33
29 46 0.67
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (29 bp):
GGGCATTTTAGTCATTTTCAAAAATCCAA
Found at i:4995 original size:27 final size:27
Alignment explanation
Indices: 4880--4996 Score: 126
Period size: 29 Copynumber: 4.2 Consensus size: 27
4870 GATCACCTAC
* *
4880 GGGCATTTTGGTCATTTTCAAAAATCCAG
1 GGGCATTTTAGTCATTTTC--ACATCCAG
* *
4909 GGGCATTTTAGTCATTTTCAAAAATCCAC
1 GGGCATTTTAGTCATTTTC--ACATCCAG
*
4938 GGGCATTTTAGTCATTTTCACATCCAA
1 GGGCATTTTAGTCATTTTCACATCCAG
* * *
4965 GGGCATTTTAGTCATTTGCGCATTCAG
1 GGGCATTTTAGTCATTTTCACATCCAG
4992 GGGCA
1 GGGCA
4997 CGTTGGTCAT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 34 0.43
29 46 0.57
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (27 bp):
GGGCATTTTAGTCATTTTCACATCCAG
Found at i:8101 original size:11 final size:11
Alignment explanation
Indices: 8085--8110 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8075 ATAGAGTAAT
8085 AAAAGAAAAAG
1 AAAAGAAAAAG
8096 AAAAGAAAAAG
1 AAAAGAAAAAG
8107 AAAA
1 AAAA
8111 AGGTAAGAAT
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:8773 original size:31 final size:31
Alignment explanation
Indices: 8738--8809 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
8728 AAAAAGATTG
8738 TTTTTCAAAAAGACAAGTGTTCTCTTATGCA
1 TTTTTCAAAAAGACAAGTGTTCTCTTATGCA
*
8769 TTTTTCAAAAAGGCAAGTGTTCTCTTATGCA
1 TTTTTCAAAAAGACAAGTGTTCTCTTATGCA
*
8800 GTTTTCAAAA
1 TTTTTCAAAA
8810 GAAATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTTTCAAAAAGACAAGTGTTCTCTTATGCA
Found at i:8873 original size:21 final size:21
Alignment explanation
Indices: 8833--8873 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8823 GTAATCAAGA
*
8833 GTTTTCAAGATTTAAATAGAG
1 GTTTTCAAGATTCAAATAGAG
8854 GTTTTCAA-ATTCAAACTAGA
1 GTTTTCAAGATTCAAA-TAGA
8874 CTTAGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
GTTTTCAAGATTCAAATAGAG
Done.