Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011980.1 Corchorus olitorius cultivar O-4 contig12013, 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: 15730
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1881 original size:22 final size:22
Alignment explanation
Indices: 1851--2062 Score: 137
Period size: 22 Copynumber: 9.6 Consensus size: 22
1841 TCCAACGTAG
* *
1851 AAATATTGATAATCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* *
1874 AAATTTGATAACCTCATTATG-
1 AAATTTGATAACCACACTATGA
* *
1895 AAATCTGGATAACCAGC-TTATGA
1 AAAT-TTGATAACCA-CACTATGA
* *
1918 AAATTTGATAACCACATTGTGA
1 AAATTTGATAACCACACTATGA
* * *
1940 AATTTTGATAATCACATTATGA
1 AAATTTGATAACCACACTATGA
* * * *
1962 AATTTTGATAACCTCAGTGTG-
1 AAATTTGATAACCACACTATGA
* * * *
1983 AAATTGTGATAATCTCCCTATTA
1 AAATT-TGATAACCACACTATGA
* *
2006 AATTTTGATAATCACACTAT-A
1 AAATTTGATAACCACACTATGA
*
2027 AAA-TTGGTAACCACACTATGAAA
1 AAATTTGATAACCACACTATG--A
2050 AAATTTGATAACC
1 AAATTTGATAACC
2063 TCCTCATAAA
Statistics
Matches: 151, Mismatches: 28, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
20 14 0.09
21 12 0.08
22 100 0.66
23 17 0.11
24 8 0.05
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:1919 original size:44 final size:43
Alignment explanation
Indices: 1871--2064 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 43
1861 AATCACACTG
*
1871 TGAAAATTTGATAACCTCATTATGAAATCTGGATAACCAGC-TTA
1 TGAAAATTTGATAACCTCATTGTGAAAT-TGGATAACCA-CATTA
* * *
1915 TGAAAATTTGATAACCACATTGTGAAATTTTGATAATCACATTA
1 TGAAAATTTGATAACCTCATTGTGAAA-TTGGATAACCACATTA
* * * * **
1959 TGAAATTTTGATAACCTCAGTGTGAAATTGTGATAATCTCCCTA
1 TGAAAATTTGATAACCTCATTGTGAAATTG-GATAACCACATTA
* * * * * * * *
2003 TTAAATTTTGATAATCACACTATAAAATTGG-TAACCACACTA
1 TGAAAATTTGATAACCTCATTGTGAAATTGGATAACCACATTA
2045 TGAAAAAATTTGATAACCTC
1 TG--AAAATTTGATAACCTC
2065 CTCATAAAAT
Statistics
Matches: 121, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
42 9 0.07
43 4 0.03
44 107 0.88
45 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (43 bp):
TGAAAATTTGATAACCTCATTGTGAAATTGGATAACCACATTA
Found at i:1985 original size:66 final size:64
Alignment explanation
Indices: 1850--2049 Score: 181
Period size: 66 Copynumber: 3.1 Consensus size: 64
1840 CTCCAACGTA
* * * *
1850 GAAATATTGATAATCACACTGTGAAAATTTGATAACCTCATTATGAAATCTGGATAACCAGCTTA
1 GAAAT-TTGATAATCACACTGTGAAATTTTGATAATCACATTATGAAATTTGGATAACCAGC-TA
1915 T
64 T
* * *
1916 GAAAATTTGATAACCACATTGTGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCAG-T
1 G-AAATTTGATAATCACACTGTGAAATTTTGATAATCACATTATGAAATTTGGATAA-C-CAGCT
*
1980 GT
63 AT
* * * * * * *
1982 GAAATTGTGATAATCTCCCTATTAAATTTTGATAATCACACTAT-AAAATTGG-TAACCACACTA
1 GAAATT-TGATAATCACACTGTGAAATTTTGATAATCACATTATGAAATTTGGATAACCA-GCTA
2045 T
64 T
2046 GAAA
1 GAAA
2050 AAATTTGATA
Statistics
Matches: 109, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 9 0.08
65 11 0.10
66 78 0.72
67 5 0.05
68 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (64 bp):
GAAATTTGATAATCACACTGTGAAATTTTGATAATCACATTATGAAATTTGGATAACCAGCTAT
Found at i:2276 original size:22 final size:22
Alignment explanation
Indices: 2248--2305 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2238 CCTCCCTATG
* *
2248 AAATTTTGTTAA-CATACTTATA
1 AAATTTTGATAACCA-AATTATA
2270 AAATTTTGATAACCAAATTATA
1 AAATTTTGATAACCAAATTATA
* *
2292 AAATATCGATAACC
1 AAATTTTGATAACC
2306 TTCGTATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCAAATTATA
Found at i:2402 original size:44 final size:45
Alignment explanation
Indices: 2354--2460 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 45
2344 ATAATCTTTT
** * *
2354 TATGAAATTTTTG-TAATTTCTACATAAAATTTTGATAACTACAC
1 TATGAAATTTTTGATAACCTCCACATAAAATTTTGATAACCACAC
* * * *
2398 TATG-AAGTTTTGATAACCTCCATATGAAATTTTGGTAACCACAC
1 TATGAAATTTTTGATAACCTCCACATAAAATTTTGATAACCACAC
*
2442 TATGAAA-TATTGATAACCT
1 TATGAAATTTTTGATAACCT
2461 TCCTATGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 7 0.13
44 43 0.83
45 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (45 bp):
TATGAAATTTTTGATAACCTCCACATAAAATTTTGATAACCACAC
Found at i:2467 original size:22 final size:22
Alignment explanation
Indices: 2380--2459 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
2370 TTTCTACATA
*
2380 AAATTTTGATAACTACACTATG
1 AAATTTTGATAACCACACTATG
* *
2402 AAGTTTTGATAACCTC-CATATG
1 AAATTTTGATAACCACAC-TATG
*
2424 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
*
2446 AAATATTGATAACC
1 AAATTTTGATAACC
2460 TTCCTATGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:15186 original size:14 final size:12
Alignment explanation
Indices: 15143--15175 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
15133 CATATGTACT
15143 AATA-ATAA-TA
1 AATATATAATTA
15153 AATATATAATTA
1 AATATATAATTA
15165 AATATATAATT
1 AATATATAATT
15176 TATAATCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 4 0.19
12 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATATATAATTA
Done.