Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022728.1 Corchorus olitorius cultivar O-4 contig22761, 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: 8698
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1249 original size:14 final size:15
Alignment explanation
Indices: 1230--1259 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1220 CAATCAAAGC
1230 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
1244 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
1259 A
1 A
1260 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:1679 original size:21 final size:21
Alignment explanation
Indices: 1655--1709 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1645 GGGCATGGAT
* * *
1655 GGTGCTGGCACGGGCTTAGCC
1 GGTGGTGGCACGGGATTAACC
1676 GGTGGTGGCACGGGATTAACC
1 GGTGGTGGCACGGGATTAACC
1697 GGTGGTGGCACGG
1 GGTGGTGGCACGG
1710 TGAATAGCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGGTGGCACGGGATTAACC
Found at i:1727 original size:22 final size:21
Alignment explanation
Indices: 1655--1721 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1645 GGGCATGGAT
* **
1655 GGTGCTGGCACGGGCTTAGCC
1 GGTGGTGGCACGGGAATAGCC
* *
1676 GGTGGTGGCACGGGATTAACC
1 GGTGGTGGCACGGGAATAGCC
1697 GGTGGTGGCACGGTGAATAGCC
1 GGTGGTGGCACGG-GAATAGCC
1719 GGT
1 GGT
1722 AATGGCTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 31 0.77
22 9 0.22
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (21 bp):
GGTGGTGGCACGGGAATAGCC
Found at i:4177 original size:24 final size:25
Alignment explanation
Indices: 4141--4195 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
4131 ATAAATAAAA
* *
4141 TTTTTTATGACGCAGAAA-T-TTTT
1 TTTTTTATAACGCACAAACTCTTTT
4164 TTTTTATATAACGCACAAACTCTTTT
1 TTTTT-TATAACGCACAAACTCTTTT
4190 TTTTTT
1 TTTTTT
4196 CAAAAACGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 11 0.41
25 2 0.07
26 9 0.33
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (25 bp):
TTTTTTATAACGCACAAACTCTTTT
Found at i:4290 original size:21 final size:21
Alignment explanation
Indices: 4265--4333 Score: 59
Period size: 26 Copynumber: 3.0 Consensus size: 21
4255 AAAACGGAAA
4265 AGAAATTTTTTTTTATGACGC
1 AGAAATTTTTTTTTATGACGC
*
4286 AGAAACAAATTTTTTTTTTATGACAC
1 AG----AAA-TTTTTTTTTATGACGC
*
4312 A-AAATTTTTTTTTTTCGACGC
1 AGAAATTTTTTTTTAT-GACGC
4333 A
1 A
4334 AAACACAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
20 10 0.26
21 10 0.26
25 3 0.08
26 16 0.41
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (21 bp):
AGAAATTTTTTTTTATGACGC
Found at i:4744 original size:16 final size:15
Alignment explanation
Indices: 4706--4747 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
4696 ACAGAGGTTG
4706 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4721 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4736 ACTAGAAAACAA
1 AC-AGAAAACAA
4748 AGCAGAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:6157 original size:30 final size:31
Alignment explanation
Indices: 6118--6177 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
6108 CAATTCTTCC
*
6118 TCTTGAAATAAATCTTC-AATGGTCTTCAAG
1 TCTTCAAATAAATCTTCAAATGGTCTTCAAG
*
6148 TCTTCAAATAAGTCTTCAAATGGTCTTCAA
1 TCTTCAAATAAATCTTCAAATGGTCTTCAA
6178 ACACGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (31 bp):
TCTTCAAATAAATCTTCAAATGGTCTTCAAG
Found at i:6175 original size:11 final size:11
Alignment explanation
Indices: 6130--6178 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 11
6120 TTGAAATAAA
6130 TCTTC-AATGG
1 TCTTCAAATGG
6140 TCTTC-AA--G
1 TCTTCAAATGG
*
6148 TCTTCAAATAAG
1 TCTTCAAAT-GG
6160 TCTTCAAATGG
1 TCTTCAAATGG
6171 TCTTCAAA
1 TCTTCAAA
6179 CACGAACTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 7 0.21
11 9 0.26
12 10 0.29
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (11 bp):
TCTTCAAATGG
Done.