Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016992.1 Corchorus olitorius cultivar O-4 contig17025, 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: 45129
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1710 original size:23 final size:23
Alignment explanation
Indices: 1684--1737 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
1674 GTACATCTGT
1684 TTGTA-TGTAGGCATAAAATGTTA
1 TTGTATTG-AGGCATAAAATGTTA
1707 TTGTATTGAGGCATAAAATGTTA
1 TTGTATTGAGGCATAAAATGTTA
1730 TTGTATTG
1 TTGTATTG
1738 GTGCTATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (23 bp):
TTGTATTGAGGCATAAAATGTTA
Found at i:10167 original size:6 final size:6
Alignment explanation
Indices: 10156--10188 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
10146 CTGTTAGGGT
10156 CTTGAG CTTGAG CTTGAG CTTGAG CTTGAG CTT
1 CTTGAG CTTGAG CTTGAG CTTGAG CTTGAG CTT
10189 CATCTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.36
Consensus pattern (6 bp):
CTTGAG
Found at i:13034 original size:4 final size:4
Alignment explanation
Indices: 13020--13054 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
13010 CTAGCACCTA
* *
13020 TTTC GTTC TTTC TTTC TTTC TTTC TTTC TTCC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
13055 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:18210 original size:9 final size:10
Alignment explanation
Indices: 18192--18249 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
18182 AATAAAAATA
18192 ATTTAT-TAT
1 ATTTATATAT
18201 ATTTTATATAT
1 A-TTTATATAT
* *
18212 ATCATAAATAT
1 AT-TTATATAT
18223 ATTT-TATAT
1 ATTTATATAT
18232 -TTTATATAT
1 ATTTATATAT
*
18241 ATATATATA
1 ATTTATATA
18250 GAATCCTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 3 0.08
9 10 0.26
10 14 0.36
11 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTATATAT
Found at i:26070 original size:6 final size:6
Alignment explanation
Indices: 26059--26089 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
26049 CTACAGTGGT
26059 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA G
1 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA G
26090 AACGAGGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:26507 original size:20 final size:18
Alignment explanation
Indices: 26466--26509 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
26456 CGAGATTGTA
26466 ATATATATATTATAATAC
1 ATATATATATTATAATAC
26484 ATATATATA-TATAATGAC
1 ATATATATATTATAAT-AC
26502 ATATATAT
1 ATATATAT
26510 GAGGATACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATATATATTATAATAC
Found at i:34056 original size:24 final size:24
Alignment explanation
Indices: 34029--34079 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
34019 CCCATTGCTA
*
34029 TGATACCAGACAATCCCGTGGCTC
1 TGATACCAGACAATCCCGTGGATC
*
34053 TGATACCAGGCAATCCCGTGGATC
1 TGATACCAGACAATCCCGTGGATC
34077 TGA
1 TGA
34080 GGAATTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (24 bp):
TGATACCAGACAATCCCGTGGATC
Found at i:34392 original size:32 final size:33
Alignment explanation
Indices: 34322--34397 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 33
34312 TTATTCAACT
34322 CCACGATTCTCTCCCCCCTCTCTATCCATATCAC
1 CCACGATTCTCTCCCCCCTCTCTATCCA-ATCAC
*
34356 CCACGATTCTCTCCTCCCTCTCTATCC-ATCAC
1 CCACGATTCTCTCCCCCCTCTCTATCCAATCAC
34388 CCACGATTCT
1 CCACGATTCT
34398 TCCAAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 15 0.37
34 26 0.63
ACGTcount: A:0.17, C:0.49, G:0.04, T:0.30
Consensus pattern (33 bp):
CCACGATTCTCTCCCCCCTCTCTATCCAATCAC
Found at i:35246 original size:2 final size:2
Alignment explanation
Indices: 35239--35266 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35229 CATAACATAC
35239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35267 CAAAATCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38055 original size:8 final size:9
Alignment explanation
Indices: 38019--38056 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
38009 CCCAAATTAC
38019 TTATGGAAA
1 TTATGGAAA
*
38028 TTAAGGAAA
1 TTATGGAAA
38037 TTATGGAAA
1 TTATGGAAA
38046 TTAT-GAAA
1 TTATGGAAA
38054 TTA
1 TTA
38057 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:39475 original size:50 final size:47
Alignment explanation
Indices: 39345--39487 Score: 155
Period size: 49 Copynumber: 3.0 Consensus size: 47
39335 CAAGCAATCC
* * *
39345 TTTACTTTTCA-CTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATC-GCACTTTTTCTCAATTTTTA-GACAAAATTGATCT
* *
39393 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAAGACAAAATTGATCT
1 TTTAATTTTCA-TCGCA-CTTTTTCTCAATTTTT--AGACAAAATTGATCT
* *
39443 TTTAATTTTCATCGCACTTTTTATCAATTTTTTGACAAAATTGAT
1 TTTAATTTTCATCGCACTTTTTCTCAATTTTTAGACAAAATTGAT
39488 TGGCACGCTC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
47 17 0.21
48 6 0.08
49 31 0.39
50 19 0.24
51 7 0.09
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATCGCACTTTTTCTCAATTTTTAGACAAAATTGATCT
Found at i:41924 original size:14 final size:14
Alignment explanation
Indices: 41905--41943 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41895 GTTTCAACCA
41905 ATATATATACATAC
1 ATATATATACATAC
** *
41919 ATATATATGTATAT
1 ATATATATACATAC
41933 ATATATATACA
1 ATATATATACA
41944 CACACACACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:43488 original size:15 final size:15
Alignment explanation
Indices: 43447--43496 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
43437 TGCTAGGGTG
*
43447 AATGGTGCAAACAAC
1 AATGGTGCGAACAAC
43462 AATGGTGCGAACAAC
1 AATGGTGCGAACAAC
* *
43477 AATGGTGTGAACAAT
1 AATGGTGCGAACAAC
43492 AATGG
1 AATGG
43497 AAATGGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (15 bp):
AATGGTGCGAACAAC
Done.