Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022271.1 Corchorus olitorius cultivar O-4 contig22304, 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: 15957
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Found at i:9486 original size:69 final size:69
Alignment explanation
Indices: 9408--9536 Score: 179
Period size: 69 Copynumber: 1.9 Consensus size: 69
9398 TTGTCTTTAA
* * * * *
9408 TTATATGTAATTTTAGCATTTG-GTTGCAAGTAATGGTGTTTCTACCATTTTTTCCTTAGTACGT
1 TTATATGTAATTTTAACA-TTGAGATGCAAGTAATGGTGCTCCCACCATTTTTTCCTTAGTACGT
9472 TGTCT
65 TGTCT
* *
9477 TTATATGTAATTTTAACATTGAGATGTAATTAATGGTGCTCCCACCATTTTTTCCTTAGT
1 TTATATGTAATTTTAACATTGAGATGCAAGTAATGGTGCTCCCACCATTTTTTCCTTAGT
9537 TGTTACTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
68 3 0.06
69 49 0.94
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (69 bp):
TTATATGTAATTTTAACATTGAGATGCAAGTAATGGTGCTCCCACCATTTTTTCCTTAGTACGTT
GTCT
Found at i:12165 original size:52 final size:52
Alignment explanation
Indices: 12109--12259 Score: 241
Period size: 52 Copynumber: 2.9 Consensus size: 52
12099 GTTTGAATGC
*
12109 TTTGAAAACCT-GATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAATAT
1 TTTGAAAA-CTAGATGGGAACTTTCCCATTTTGAAAAGACCTAAATTGAATAT
*
12161 TTTGAAAACTAGATGGGAATTTTCCCATTTTGAAAAGACCTAAATTGAATAT
1 TTTGAAAACTAGATGGGAACTTTCCCATTTTGAAAAGACCTAAATTGAATAT
* * *
12213 TTTGAAAACTGGATTGGAACTTTCCCATTTTGGAAAGACCTAAATTG
1 TTTGAAAACTAGATGGGAACTTTCCCATTTTGAAAAGACCTAAATTG
12260 GAAATTAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 90 0.98
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (52 bp):
TTTGAAAACTAGATGGGAACTTTCCCATTTTGAAAAGACCTAAATTGAATAT
Found at i:13244 original size:18 final size:17
Alignment explanation
Indices: 13221--13272 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 17
13211 ATGCCGAAGG
13221 CTTTTTCTCTTGTTTTTT
1 CTTTTT-TCTTGTTTTTT
13239 CTTTTTTCTGTGTTTTTT
1 CTTTTTTCT-TGTTTTTT
13257 CTTGTTTT-TTGTTTTT
1 CTT-TTTTCTTGTTTTT
13273 GTGTTACCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.31
18 18 0.56
19 4 0.12
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.79
Consensus pattern (17 bp):
CTTTTTTCTTGTTTTTT
Found at i:13254 original size:11 final size:10
Alignment explanation
Indices: 13222--13266 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
13212 TGCCGAAGGC
13222 TTTTTCTCTTG
1 TTTTT-TCTTG
13233 TTTTTTC---
1 TTTTTTCTTG
13240 TTTTTTCTGTG
1 TTTTTTCT-TG
13251 TTTTTTCTTG
1 TTTTTTCTTG
13261 TTTTTT
1 TTTTTT
13267 GTTTTTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
7 7 0.23
10 10 0.33
11 13 0.43
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (10 bp):
TTTTTTCTTG
Found at i:15540 original size:28 final size:28
Alignment explanation
Indices: 15509--15585 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
15499 TTAGGATCAC
15509 CTAGGGGCATTTTGGTCATTTTCAAAAT
1 CTAGGGGCATTTTGGTCATTTTCAAAAT
* * * *
15537 CTAGGGGCATTTTAGTCATTTGCATATT
1 CTAGGGGCATTTTGGTCATTTTCAAAAT
15565 C-AGGGGCATTTTGGTCATTTT
1 CTAGGGGCATTTTGGTCATTTT
15586 AAGTCAACGC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 18 0.42
28 25 0.58
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTCAAAAT
Done.