Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015696.1 Corchorus olitorius cultivar O-4 contig15729, 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: 3404
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:117 original size:29 final size:29
Alignment explanation
Indices: 75--138 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
65 TAATCATTAA
* * *
75 AATTCCGTCTACCAATATATGTGCTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
104 AATTCCATCTACCAATAAACGTGCTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
133 AATTCC
1 AATTCC
139 TTATAAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (29 bp):
AATTCCATCTACCAATAAACGTGCTACAT
Found at i:1322 original size:15 final size:15
Alignment explanation
Indices: 1302--1330 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1292 ATACATCAAA
1302 GTAAGTCTTGATTCG
1 GTAAGTCTTGATTCG
1317 GTAAGTCTTGATTC
1 GTAAGTCTTGATTC
1331 ATGAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (15 bp):
GTAAGTCTTGATTCG
Found at i:1474 original size:18 final size:18
Alignment explanation
Indices: 1451--1492 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1441 AAGATTAAGG
*
1451 TAATAATAATT-TTACTAC
1 TAATAATAATTATTA-TAA
1469 TAATAATAATTATTATAA
1 TAATAATAATTATTATAA
1487 TAATAA
1 TAATAA
1493 GAAGTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATTATTATAA
Found at i:1507 original size:24 final size:24
Alignment explanation
Indices: 1475--1525 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1465 CTACTAATAA
*
1475 TAATTATTATAATAATAAGAA-GTT
1 TAATAATTATAATAATAA-AATGTT
*
1499 TAATAATTATAATGATAAAATGTT
1 TAATAATTATAATAATAAAATGTT
1523 TAA
1 TAA
1526 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAAATGTT
Found at i:1686 original size:241 final size:241
Alignment explanation
Indices: 1412--1894 Score: 957
Period size: 241 Copynumber: 2.0 Consensus size: 241
1402 AATTTTTGCC
1412 AAGCTTTGTTTTCTTTAATTTTTGTATAAAAGATTAAGGTAATAATAATTTTACTACTAATAATA
1 AAGCTTTGTTTTCTTTAATTTTTGTATAAAAGATTAAGGTAATAATAATTTTACTACTAATAATA
1477 ATTATTATAATAATAAGAAGTTTAATAATTATAATGATAAAATGTTTAACGTAAAAATAATTGTT
66 ATTATTATAATAATAAGAAGTTTAATAATTATAATGATAAAATGTTTAACGTAAAAATAATTGTT
1542 ATTATTTTAGACTTTTTTAATATGGTAATTTTAAAATAAAAAAGGATATTAGATTACATATTAAA
131 ATTATTTTAGACTTTTTTAATATGGTAATTTTAAAATAAAAAAGGATATTAGATTACATATTAAA
1607 CCTTAAAAATAAAACTAAAATTTTAAAATTAAAAAGGGTATTTTAG
196 CCTTAAAAATAAAACTAAAATTTTAAAATTAAAAAGGGTATTTTAG
*
1653 AAGCTTTGTTTTCTTTAATTTTTGTATAAAAGATTAAGGTAATAATAATTTTACTACTACTAATA
1 AAGCTTTGTTTTCTTTAATTTTTGTATAAAAGATTAAGGTAATAATAATTTTACTACTAATAATA
1718 ATTATTATAATAATAAGAAGTTTAATAATTATAATGATAAAATGTTTAACGTAAAAATAATTGTT
66 ATTATTATAATAATAAGAAGTTTAATAATTATAATGATAAAATGTTTAACGTAAAAATAATTGTT
1783 ATTATTTTAGACTTTTTTAATATGGTAATTTTAAAATAAAAAAGGATATTAGATTACATATTAAA
131 ATTATTTTAGACTTTTTTAATATGGTAATTTTAAAATAAAAAAGGATATTAGATTACATATTAAA
1848 CCTTAAAAATAAAACTAAAATTTTAAAATTAAAAAGGGTATTTTAG
196 CCTTAAAAATAAAACTAAAATTTTAAAATTAAAAAGGGTATTTTAG
1894 A
1 A
1895 TATTTTAGGT
Statistics
Matches: 241, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 241 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (241 bp):
AAGCTTTGTTTTCTTTAATTTTTGTATAAAAGATTAAGGTAATAATAATTTTACTACTAATAATA
ATTATTATAATAATAAGAAGTTTAATAATTATAATGATAAAATGTTTAACGTAAAAATAATTGTT
ATTATTTTAGACTTTTTTAATATGGTAATTTTAAAATAAAAAAGGATATTAGATTACATATTAAA
CCTTAAAAATAAAACTAAAATTTTAAAATTAAAAAGGGTATTTTAG
Found at i:1748 original size:24 final size:24
Alignment explanation
Indices: 1716--1766 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1706 CTACTACTAA
*
1716 TAATTATTATAATAATAAGAA-GTT
1 TAATAATTATAATAATAA-AATGTT
*
1740 TAATAATTATAATGATAAAATGTT
1 TAATAATTATAATAATAAAATGTT
1764 TAA
1 TAA
1767 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAAATGTT
Found at i:3249 original size:22 final size:22
Alignment explanation
Indices: 3193--3315 Score: 104
Period size: 22 Copynumber: 5.6 Consensus size: 22
3183 CTCTAACATA
* **
3193 GAAATATTGATAACCTCATTAT
1 GAAATTTTGATAACCTCCCTAT
***
3215 GAAATTCCAATAACCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * *
3237 GAAAATTTGATAATCACACTAT
1 GAAATTTTGATAACCTCCCTAT
* * **
3259 GAACTTTTGATAATCTCTGTAT
1 GAAATTTTGATAACCTCCCTAT
3281 GAAATTTTGATAATCC-CCCTAT
1 GAAATTTTGATAA-CCTCCCTAT
3303 GAAATTTTGATAA
1 GAAATTTTGATAA
3316 TCATACTATA
Statistics
Matches: 78, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
22 77 0.99
23 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAT
Found at i:3282 original size:44 final size:44
Alignment explanation
Indices: 3234--3317 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
3224 ATAACCTCCC
*
3234 TATGAAAATTTGATAATCACACTATGAACTTTTGATAATCTCTG
1 TATGAAAATTTGATAATCACACTATGAAATTTTGATAATCTCTG
* * *
3278 TATGAAATTTTGATAATCCCCCTATGAAATTTTGATAATC
1 TATGAAAATTTGATAATCACACTATGAAATTTTGATAATC
3318 ATACTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (44 bp):
TATGAAAATTTGATAATCACACTATGAAATTTTGATAATCTCTG
Found at i:3324 original size:22 final size:22
Alignment explanation
Indices: 3233--3330 Score: 115
Period size: 22 Copynumber: 4.5 Consensus size: 22
3223 AATAACCTCC
*
3233 CTATGAAAATTTGATAATCACA
1 CTATGAAATTTTGATAATCACA
* * *
3255 CTATGAACTTTTGATAATCTCT
1 CTATGAAATTTTGATAATCACA
* * *
3277 GTATGAAATTTTGATAATCCCC
1 CTATGAAATTTTGATAATCACA
*
3299 CTATGAAATTTTGATAATCATA
1 CTATGAAATTTTGATAATCACA
*
3321 CTATAAAATT
1 CTATGAAATT
3331 GGTAACAACA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACA
Found at i:3330 original size:44 final size:42
Alignment explanation
Indices: 3233--3402 Score: 123
Period size: 44 Copynumber: 3.9 Consensus size: 42
3223 AATAACCTCC
*
3233 CTATGAAAA-TTTGATAATCACACTATGAACTTTTGATAATCT
1 CTAT-AAAATTTTGATAATCACACTATGAAATTTTGATAATCT
* * *
3275 CTGTATGAAATTTTGATAATCCCCCTATGAAATTTTGATAATCAT
1 C--TATAAAATTTTGATAATCACACTATGAAATTTTGATAATC-T
* * *
3320 ACTATAAAA--TTGGTAA-CAACACAATGAAAATTTTGATAACCT
1 -CTATAAAATTTTGATAATC-ACACTATG-AAATTTTGATAATCT
* * * * *
3362 CCTCAAAAAATTATGATAAACACACCATGAAATTTCGATAA
1 -CT-ATAAAATTTTGATAATCACACTATGAAATTTTGATAA
3403 CC
Statistics
Matches: 101, Mismatches: 16, Indels: 20
0.74 0.12 0.15
Matches are distributed among these distances:
41 1 0.01
42 15 0.15
43 21 0.21
44 49 0.49
45 13 0.13
46 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (42 bp):
CTATAAAATTTTGATAATCACACTATGAAATTTTGATAATCT
Done.