Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012594.1 Corchorus olitorius cultivar O-4 contig12627, 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: 14826
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:218 original size:16 final size:16
Alignment explanation
Indices: 193--266 Score: 96
Period size: 16 Copynumber: 4.6 Consensus size: 16
183 CGGGTTGATC
193 GGGTTCGGGTCATTTT
1 GGGTTCGGGTCATTTT
*
209 GGGTTTGGGTCATTTT
1 GGGTTCGGGTCATTTT
*
225 CGGGTTCGGGTC-GTTT
1 -GGGTTCGGGTCATTTT
* *
241 GGATTCGGGTCATTTC
1 GGGTTCGGGTCATTTT
257 GGGTTCGGGT
1 GGGTTCGGGT
267 ACCCAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
15 10 0.20
16 29 0.59
17 10 0.20
ACGTcount: A:0.05, C:0.14, G:0.41, T:0.41
Consensus pattern (16 bp):
GGGTTCGGGTCATTTT
Found at i:315 original size:17 final size:17
Alignment explanation
Indices: 275--315 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
265 GTACCCAAAA
275 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
292 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
308 TTTCGGGT
1 TTTCGGGT
316 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:2403 original size:11 final size:11
Alignment explanation
Indices: 2387--2418 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2377 AAGCTATAAA
2387 ATAACTAACTC
1 ATAACTAACTC
2398 ATAACTAACTC
1 ATAACTAACTC
*
2409 ATAACAAACT
1 ATAACTAACT
2419 TAACCATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (11 bp):
ATAACTAACTC
Found at i:5491 original size:18 final size:18
Alignment explanation
Indices: 5468--5504 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5458 TAGAACCATG
*
5468 GAAGTTTGGAGTAGTATT
1 GAAGTTTGGAGCAGTATT
5486 GAAGTTTGGAGCAGTATT
1 GAAGTTTGGAGCAGTATT
5504 G
1 G
5505 TGTTGAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.35, T:0.35
Consensus pattern (18 bp):
GAAGTTTGGAGCAGTATT
Found at i:10293 original size:22 final size:22
Alignment explanation
Indices: 10092--10293 Score: 129
Period size: 22 Copynumber: 9.1 Consensus size: 22
10082 AACAATACTG
* ***
10092 TGAAAATTTGATAACCTTATTA
1 TGAAATTTTGATAACCTCCCTA
* * *
10114 TGAAATGGTCGATAACCTCCCTG
1 TGAAAT-TTTGATAACCTCCCTA
* * * * **
10137 TAAAAATTTGATAACCACACGG
1 TGAAATTTTGATAACCTCCCTA
* * * *
10159 TGAAATCTTAATAACCACACTA
1 TGAAATTTTGATAACCTCCCTA
** *
10181 TGAAATTTTGATAACCTCATTG
1 TGAAATTTTGATAACCTCCCTA
*
10203 TGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
*
10225 TAAAATTTTGATAACCT-CCTCA
1 TGAAATTTTGATAACCTCCCT-A
* * *
10247 TAAAATTTTCATAACCACACC-A
1 TGAAATTTTGATAACCTC-CCTA
*
10269 TGAAATTTAGATAACCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
10291 TGA
1 TGA
10294 GAATGAAACC
Statistics
Matches: 138, Mismatches: 37, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
21 5 0.04
22 117 0.85
23 14 0.10
24 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:10377 original size:22 final size:22
Alignment explanation
Indices: 10343--10398 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
10333 GCTCTCCATA
*
10343 AAATTTTCATAACCTCCCTATG
1 AAATTTTCATAACCTCCCTAGG
** * *
10365 AAATTTTGTTAACCTTCTTAGG
1 AAATTTTCATAACCTCCCTAGG
*
10387 AAATTTTAATAA
1 AAATTTTCATAA
10399 GCACAAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (22 bp):
AAATTTTCATAACCTCCCTAGG
Found at i:10498 original size:22 final size:22
Alignment explanation
Indices: 10425--10574 Score: 117
Period size: 22 Copynumber: 6.9 Consensus size: 22
10415 CCTTCCTCCC
10425 TATGAAATTTTG-TAACCTTCT-
1 TATGAAATTTTGATAACCTT-TG
* ****
10446 TATTAAA-TTTGATAACCACAC
1 TATGAAATTTTGATAACCTTTG
*
10467 TATAAAATTTTGATAACCTTTG
1 TATGAAATTTTGATAACCTTTG
* * ***
10489 TATGATATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTTG
* *
10511 TAAGAAATTTTGATAACCTTTT
1 TATGAAATTTTGATAACCTTTG
* * *
10533 TATGAAATTTCGGTAACCTCTG
1 TATGAAATTTTGATAACCTTTG
*
10555 TATGGAATTTTGATAACCTT
1 TATGAAATTTTGATAACCTT
10575 CTCATGTAAT
Statistics
Matches: 96, Mismatches: 30, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
20 4 0.04
21 17 0.18
22 75 0.78
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTG
Found at i:10519 original size:44 final size:42
Alignment explanation
Indices: 10419--10588 Score: 137
Period size: 44 Copynumber: 3.9 Consensus size: 42
10409 TGATAACCTT
* * *
10419 CCTCCCTATGAAATTTTG-TAACCTTCTTATTAAATTTGATAA
1 CCTCCCTAAGAAATTTTGATAACCTT-TTATGAATTTTGATAA
* * *
10461 CCACACTATA-AAATTTTGATAACCTTTGTATGATATTTTGTTAA
1 CCTCCCTA-AGAAATTTTGATAACCTTT-TATGA-ATTTTGATAA
* *
10505 CCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTCGGTAA
1 CCTCCCTAAGAAATTTTGATAACC-TTTTATG-AATTTTGATAA
** * * *
10549 CCTCTGTATGGAATTTTGATAACCTTCTCATGTAATTTTG
1 CCTCCCTAAGAAATTTTGATAACCTT-TTATG-AATTTTG
10589 GTTTGATTGT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
42 15 0.15
43 14 0.14
44 70 0.68
45 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (42 bp):
CCTCCCTAAGAAATTTTGATAACCTTTTATGAATTTTGATAA
Found at i:10585 original size:22 final size:22
Alignment explanation
Indices: 10403--10588 Score: 105
Period size: 22 Copynumber: 8.4 Consensus size: 22
10393 TAATAAGCAC
10403 AAATTTTGATAACCTTCCTCCCTATG
1 AAATTTTGATAACCTT-CT--C-ATG
* *
10429 AAATTTTG-TAACCTTCTTATT
1 AAATTTTGATAACCTTCTCATG
* * *
10450 AAA-TTTGATAACC-ACACTATA
1 AAATTTTGATAACCTTCTC-ATG
*
10471 AAATTTTGATAACCTT-TGTATG
1 AAATTTTGATAACCTTCT-CATG
* * * *
10493 ATATTTTGTTAACC-TCCCTAAG
1 AAATTTTGATAACCTTCTC-ATG
* *
10515 AAATTTTGATAACCTTTTTATG
1 AAATTTTGATAACCTTCTCATG
* * *
10537 AAATTTCGGTAACC-TCTGTATG
1 AAATTTTGATAACCTTCT-CATG
*
10559 GAATTTTGATAACCTTCTCATG
1 AAATTTTGATAACCTTCTCATG
*
10581 TAATTTTG
1 AAATTTTG
10589 GTTTGATTGT
Statistics
Matches: 121, Mismatches: 29, Indels: 24
0.70 0.17 0.14
Matches are distributed among these distances:
20 5 0.04
21 18 0.15
22 77 0.64
23 4 0.03
24 2 0.02
25 7 0.06
26 8 0.07
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACCTTCTCATG
Found at i:10586 original size:66 final size:65
Alignment explanation
Indices: 10425--10588 Score: 145
Period size: 66 Copynumber: 2.5 Consensus size: 65
10415 CCTTCCTCCC
* * * * *
10425 TATGAAATTTTGTAACCTTCTTAT-TAAATTTGATAACCACACTATAAAATTTTGATAACCTTTG
1 TATGGAATTTTGTAACCTTCTCATGTAATTTTGATAACCACACTATAAAATTTCGATAACCTCTG
* * * **** * *
10489 TAT-GATATTTTGTTAACC-TCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTCGGTAACCT
1 TATGGA-ATTTTG-TAACCTTCTC-ATGTAATTTTGATAACCACACTATAAAATTTCGATAACCT
10552 CTG
63 CTG
10555 TATGGAATTTTGATAACCTTCTCATGTAATTTTG
1 TATGGAATTTTG-TAACCTTCTCATGTAATTTTG
10589 GTTTGATTGT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
63 1 0.01
64 11 0.14
65 6 0.08
66 53 0.70
67 5 0.07
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (65 bp):
TATGGAATTTTGTAACCTTCTCATGTAATTTTGATAACCACACTATAAAATTTCGATAACCTCTG
Found at i:12812 original size:16 final size:15
Alignment explanation
Indices: 12774--12815 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
12764 ACAGAGGTTG
12774 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
12789 ACAGAAAATAATTAA
1 ACAGAAAACAATTAA
12804 ACTAGAAAACAA
1 AC-AGAAAACAA
12816 AACAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.