Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024156.1 Corchorus olitorius cultivar O-4 contig24189, 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: 6536
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Found at i:5743 original size:27 final size:26
Alignment explanation
Indices: 5711--5804 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 26
5701 AATTTTACCC
*
5711 TTTAATTACCAAATTTCATTTCCATT
1 TTTAATTACCAAATTTCATTTACATT
* *
5737 CTTTAATTATCCAATTTTACCAATTAC-TT
1 -TTTAATTA-CCAAATTT--CATTTACATT
*
5766 TTTAATTACCCAATTTCATTTTTAC-TT
1 TTTAATTACCAAATTTCA--TTTACATT
5793 TTTAATTACCAA
1 TTTAATTACCAA
5805 GTTGACCAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.04
27 31 0.56
28 15 0.27
29 2 0.04
30 5 0.09
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTAATTACCAAATTTCATTTACATT
Found at i:5770 original size:28 final size:27
Alignment explanation
Indices: 5738--5824 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
5728 ATTTCCATTC
*
5738 TTTAATTATCCAATTTTACCAATTACTT
1 TTTAATTA-CCAATTTCACCAATTACTT
***
5766 TTTAATTACCCAATTTCA-TTTTTACTT
1 TTTAATTA-CCAATTTCACCAATTACTT
* * *
5793 TTTAATTACCAAGTTGACCAATTTCCTT
1 TTTAATTACCAATTTCACCAA-TTACTT
5821 TTTA
1 TTTA
5825 CTCTTTGATT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 7 0.15
27 14 0.30
28 25 0.54
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTAATTACCAATTTCACCAATTACTT
Found at i:5797 original size:55 final size:55
Alignment explanation
Indices: 5711--5824 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 55
5701 AATTTTACCC
* *
5711 TTTAATTACCAAATTTCATTTCCATTCTTTAATTATCCAATTTTACCAA-TTACTT
1 TTTAATTACCAAATTTCATTTCCATTCTTTAATTA-CCAAGTTGACCAATTTACTT
* ** *
5766 TTTAATTACCCAATTTCATTTTTACTT-TTTAATTACCAAGTTGACCAATTTCCTT
1 TTTAATTACCAAATTTCATTTCCA-TTCTTTAATTACCAAGTTGACCAATTTACTT
5821 TTTA
1 TTTA
5825 CTCTTTGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
54 11 0.22
55 38 0.75
56 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (55 bp):
TTTAATTACCAAATTTCATTTCCATTCTTTAATTACCAAGTTGACCAATTTACTT
Found at i:6155 original size:54 final size:53
Alignment explanation
Indices: 6097--6259 Score: 188
Period size: 54 Copynumber: 3.0 Consensus size: 53
6087 TTTAATTTTC
6097 ATTC-TTTAATTACCAAATTCTTTTTACTTTACCAAATTTCTTTTTAATTACCAA
1 ATTCTTTTAATTACC-AATTCTTTTTACTTTACC-AATTTCTTTTTAATTACCAA
* *
6151 ATTCTTTTATAGTTACCAATTCTTTTTACTTTATCGA-TTCTTTTTAATTACCAA
1 ATTCTTTTA-A-TTACCAATTCTTTTTACTTTACCAATTTCTTTTTAATTACCAA
* * * *
6205 ATTCTTTTTTAGTTACCAATTCTTTATATTTTA-CAATTCTTTTTTTAATTACCAA
1 ATTC--TTTTAATTACCAATTCTTTTTACTTTACCAATT-TCTTTTTAATTACCAA
6260 TTTTACTTTC
Statistics
Matches: 95, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
53 2 0.02
54 45 0.47
55 20 0.21
56 23 0.24
57 5 0.05
ACGTcount: A:0.28, C:0.17, G:0.02, T:0.53
Consensus pattern (53 bp):
ATTCTTTTAATTACCAATTCTTTTTACTTTACCAATTTCTTTTTAATTACCAA
Found at i:6157 original size:18 final size:18
Alignment explanation
Indices: 6101--6259 Score: 139
Period size: 18 Copynumber: 8.7 Consensus size: 18
6091 ATTTTCATTC
6101 TTTAATTACCAAATTCTT
1 TTTAATTACCAAATTCTT
*
6119 TTTACTTTACCAAATTTCTT
1 TTTA-ATTACCAAA-TTCTT
6139 TTTAATTACCAAATTCTT
1 TTTAATTACCAAATTCTT
*
6157 TTATAGTTACC-AATTCTT
1 TT-TAATTACCAAATTCTT
* * *
6175 TTTACTTTATC-GATTCTT
1 TTTA-ATTACCAAATTCTT
6193 TTTAATTACCAAATTCTTT
1 TTTAATTACCAAATTC-TT
*
6212 TTTAGTTACC-AATTCTT
1 TTTAATTACCAAATTCTT
* *
6229 TATATTTTA-C-AATTCTTTT
1 TTTA-ATTACCAAATTC--TT
6248 TTTAATTACCAA
1 TTTAATTACCAA
6260 TTTTACTTTC
Statistics
Matches: 116, Mismatches: 14, Indels: 20
0.77 0.09 0.13
Matches are distributed among these distances:
17 17 0.15
18 49 0.42
19 40 0.34
20 10 0.09
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAATTACCAAATTCTT
Found at i:6278 original size:27 final size:26
Alignment explanation
Indices: 6248--6332 Score: 94
Period size: 27 Copynumber: 3.5 Consensus size: 26
6238 CAATTCTTTT
6248 TTTAATTACCAATTTTACTTTCACTCC
1 TTTAATTACCAATTTTACTTT-ACTCC
*
6275 TTTAATTACCAA-ATT-C-TT--T--
1 TTTAATTACCAATTTTACTTTACTCC
6294 TTTAATTACCAATTTTACTTTTACTCC
1 TTTAATTACCAATTTTAC-TTTACTCC
6321 TTTAATTACCAA
1 TTTAATTACCAA
6333 ATTCATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 12 0.25
20 2 0.04
21 2 0.04
23 2 0.04
24 2 0.04
25 2 0.04
26 2 0.04
27 24 0.50
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTAATTACCAATTTTACTTTACTCC
Found at i:6299 original size:19 final size:19
Alignment explanation
Indices: 6275--6391 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 19
6265 CTTTCACTCC
6275 TTTAATTACCAAATTCTTT
1 TTTAATTACCAAATTCTTT
*
6294 TTTAATTACCAATTTTACTTTTACT
1 TTTAATTACCAA-ATT-C--TT--T
*
6319 CCTTTAATTACCAAATTCATT
1 --TTTAATTACCAAATTCTTT
* * *
6340 TTTAATTTATC-GATTTTTT
1 TTTAA-TTACCAAATTCTTT
6359 TTTAAATTACCAAATTCCTTT
1 TTT-AATTACCAAATT-CTTT
6380 TTTAATTACCAA
1 TTTAATTACCAA
6392 CTTTACTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
19 29 0.38
20 20 0.26
21 8 0.11
23 3 0.04
25 2 0.03
26 2 0.03
27 12 0.16
ACGTcount: A:0.31, C:0.16, G:0.01, T:0.52
Consensus pattern (19 bp):
TTTAATTACCAAATTCTTT
Found at i:6301 original size:46 final size:45
Alignment explanation
Indices: 6239--6447 Score: 229
Period size: 46 Copynumber: 4.7 Consensus size: 45
6229 TATATTTTAC
6239 AATTCTTTTTTTAATTACCAATTTTACTTTCACTCCTTTAATTACCA
1 AATTC-TTTTTTAATTACCAATTTTACTTTCACT-CTTTAATTACCA
*
6286 AATTCTTTTTTAATTACCAATTTTACTTTTACTCCTTTAATTACCA
1 AATTCTTTTTTAATTACCAATTTTACTTTCACT-CTTTAATTACCA
* * * *
6332 AATTCATTTTTAATTTATCGA-TTT--TTT---T-TTAAATTACCA
1 AATTCTTTTTTAA-TTACCAATTTTACTTTCACTCTTTAATTACCA
* * **
6371 AATTCCTTTTTTAATTACCAACTTTACTTTTACTCTTTTTTTACCA
1 AATT-CTTTTTTAATTACCAATTTTACTTTCACTCTTTAATTACCA
6417 AA-T-TTTTTTAATTACCAATTTTACTTTCACT
1 AATTCTTTTTTAATTACCAATTTTACTTTCACT
6448 TTACTTTATT
Statistics
Matches: 140, Mismatches: 13, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
39 19 0.14
40 11 0.08
41 1 0.01
42 3 0.02
43 26 0.19
44 3 0.02
45 2 0.01
46 65 0.46
47 10 0.07
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (45 bp):
AATTCTTTTTTAATTACCAATTTTACTTTCACTCTTTAATTACCA
Found at i:6380 original size:20 final size:20
Alignment explanation
Indices: 6324--6391 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
6314 TTACTCCTTT
6324 AATTACCAAATTCATTTTTA
1 AATTACCAAATTCATTTTTA
* * * **
6344 ATTTATC-GATTTTTTTTTA
1 AATTACCAAATTCATTTTTA
* *
6363 AATTACCAAATTCCTTTTTT
1 AATTACCAAATTCATTTTTA
6383 AATTACCAA
1 AATTACCAA
6392 CTTTACTTTT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.34, C:0.15, G:0.01, T:0.50
Consensus pattern (20 bp):
AATTACCAAATTCATTTTTA
Found at i:6400 original size:21 final size:21
Alignment explanation
Indices: 6356--6401 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6346 TTATCGATTT
*
6356 TTTTTTAAATTACCAAATTCC
1 TTTTTTAAATTACCAAATTAC
*
6377 TTTTTT-AATTACCAACTTTAC
1 TTTTTTAAATTACCAA-ATTAC
6398 TTTT
1 TTTT
6402 ACTCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTTTAAATTACCAAATTAC
Done.