Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002324.1 Corchorus olitorius cultivar O-4 contig02324, 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: 3711
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2130 original size:22 final size:22
Alignment explanation
Indices: 2087--2498 Score: 93
Period size: 22 Copynumber: 18.6 Consensus size: 22
2077 TATTTTTATG
*
2087 AAATTTT-ATAATC-AC-TATA
1 AAATTTTGATAACCTACATATA
2106 AAATTTTGATAACCTACATATA
1 AAATTTTGATAACCTACATATA
*
2128 AAATTTTGATAA-TTACAATATA
1 AAATTTTGATAACCTAC-ATATA
* * *** *
2150 AAGTTTTTATGATGATACTTA-A
1 AAATTTTGAT-AACCTACATATA
* * *
2172 AAATTTCGAGAACC-ACTATATG
1 AAATTTTGATAACCTAC-ATATA
* * * *
2194 AAATTTTGTTAACTTCCCTATA
1 AAATTTTGATAACCTACATATA
* * *
2216 AAATTTTG-TTACACTCCCTATA
1 AAATTTTGATAAC-CTACATATA
* * *
2238 AAATTTTTAATAACC-ACCTAATG
1 AAA-TTTTGATAACCTACAT-ATA
*
2261 AAATTTTGATAACC-ACCTTATGA
1 AAATTTTGATAACCTA-CATAT-A
* *
2284 AAA-TTTGATAACCAACCTCCCAATA
1 AAATTTTGATAACCTACAT----ATA
* * *
2309 AAATGTTGGTAAGCGC-ACATTATG
1 AAATTTTGATAA-C-CTACA-TATA
** * *
2333 AAATTTTGATAATTTTCCTATA
1 AAATTTTGATAACCTACATATA
* * * *
2355 AAATATTGGTAATC-ACATTATG
1 AAATTTTGATAACCTACA-TATA
* *
2377 AAATTTTGATAACCATAC-CATG
1 AAATTTTGATAACC-TACATATA
* *
2399 AAATTGTGAT-ACCT-CACTATG
1 AAATTTTGATAACCTACA-TATA
* * *
2420 AAATTTTTATAAACCTCCCTATA
1 AAATTTTGAT-AACCTACATATA
* * * * *
2443 AAATTTTGATAACATGCTTTTG
1 AAATTTTGATAACCTACATATA
*
2465 AAATTTTGATAACCT-CAT-GA
1 AAATTTTGATAACCTACATATA
*
2485 AATTTTTGATAACC
1 AAATTTTGATAACC
2499 ATGTTATGAA
Statistics
Matches: 289, Mismatches: 71, Indels: 65
0.68 0.17 0.15
Matches are distributed among these distances:
19 8 0.03
20 21 0.07
21 28 0.10
22 157 0.54
23 37 0.13
24 21 0.07
25 4 0.01
26 8 0.03
27 3 0.01
28 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTACATATA
Found at i:2441 original size:23 final size:23
Alignment explanation
Indices: 2377--2454 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
2367 TCACATTATG
* *
2377 AAATTTTGAT-AACCAT-ACCATG
1 AAATTTTGATAAACC-TCACTATA
* *
2399 AAATTGTGAT--ACCTCACTATG
1 AAATTTTGATAAACCTCACTATA
* *
2420 AAATTTTTATAAACCTCCCTATA
1 AAATTTTGATAAACCTCACTATA
2443 AAATTTTGATAA
1 AAATTTTGATAA
2455 CATGCTTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.02
21 16 0.35
22 9 0.20
23 20 0.43
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCACTATA
Found at i:2519 original size:22 final size:22
Alignment explanation
Indices: 2372--2519 Score: 85
Period size: 22 Copynumber: 6.8 Consensus size: 22
2362 GGTAATCACA
*
2372 TTATGAAATTTTGATAACCATA
1 TTATGAAATTTTGATAACCATG
** * *
2394 CCATGAAATTGTGAT-ACC-TCA
1 TTATGAAATTTTGATAACCAT-G
* * *
2415 CTATGAAATTTTTATAAACC-TCC
1 TTATGAAATTTTGAT-AACCAT-G
* *
2438 CTATAAAATTTTGATAA-CATG
1 TTATGAAATTTTGATAACCATG
*
2459 CTTTTGAAATTTTGATAACC---
1 -TTATGAAATTTTGATAACCATG
*
2479 TCATGAAATTTTTGATAACCATG
1 TTATGAAA-TTTTGATAACCATG
*
2502 TTATGAAATTATGATAAC
1 TTATGAAATTTTGATAAC
2520 ATCCCTATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.06
20 12 0.12
21 17 0.17
22 38 0.38
23 26 0.26
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCATG
Done.