Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021699.1 Corchorus olitorius cultivar O-4 contig21732, 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: 7822
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Found at i:104 original size:39 final size:39
Alignment explanation
Indices: 53--500 Score: 217
Period size: 39 Copynumber: 11.8 Consensus size: 39
43 TAGCAGAGAT
* * * * **
53 CCTAAGCAGGTTTACTTTAATGATAATTCTAAATAGTGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
*
92 CCTAAACAGGTTTACTTAAACGAAAATTCTAAACAAAGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
*** * * * ***
131 CCTAAGCAGGTTTAAACAAACG-AGATTCTTAGCGGGGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
* ** ***
169 CCTAAGCAGGTTTTC-TAAA-GCAGAAATTCTAGGCCGGGA
1 CCTAAGCAGGTTTACTTAAACG-A-AAATTCTAAACAAAGA
* * * *
208 CCTAAGCAGGTTTTCTTAGATG-AAATTCTAAACATAGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
** * * *
246 CCTAAGCAGGTTTACTTAAACG-AAGCTCTAAGCAGAGG
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
* * * ** *
284 CCTAAGCAGGTTTACTAAAATGGAAATTCTAAAGGAGGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
* * * * * **
323 CCTAAGCAGGTTTACTTAAATGGCAACTT-TATATAGGGA
1 CCTAAGCAGGTTTACTTAAA-CGAAAATTCTAAACAAAGA
* * * * *
362 CCTAAGCAGGTTTACTT-GACCAAAACTCTAAGCAGAGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
* * *
400 TCCTAAACAGGTTTACTTAAACG--------GAACAGAGA
1 -CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
* * * *
432 CCTAAGCAGGTTTGCTTAAACGGAGATTCTAAACAAGGA
1 CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
* *
471 CCTACGCAGGTTTTA-TTAAACGCAAATTCT
1 CCTAAGCAGG-TTTACTTAAACGAAAATTCT
501 GATGAGATTT
Statistics
Matches: 310, Mismatches: 80, Indels: 38
0.72 0.19 0.09
Matches are distributed among these distances:
31 20 0.06
32 7 0.02
36 1 0.00
37 6 0.02
38 91 0.29
39 171 0.55
40 13 0.04
41 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (39 bp):
CCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAAAGA
Found at i:248 original size:77 final size:77
Alignment explanation
Indices: 167--342 Score: 198
Period size: 77 Copynumber: 2.3 Consensus size: 77
157 TCTTAGCGGG
* * * * * * *
167 GACCTAAGCAGGTTTTC-TAAAGCAGAAATTCTAGGCCG-GGACCTAAGCAGGTTTTCTTAGAT-
1 GACCTAAGCAGGTTTACTTAAA-C-GAAACTCTAAGCAGAGG-CCTAAGCAGGTTTACTAAAATG
229 GAAATTCTAAA-CATA
63 GAAATTCTAAAGCA-A
*
244 GACCTAAGCAGGTTTACTTAAACGAAGCTCTAAGCAGAGGCCTAAGCAGGTTTACTAAAATGGAA
1 GACCTAAGCAGGTTTACTTAAACGAAACTCTAAGCAGAGGCCTAAGCAGGTTTACTAAAATGGAA
* *
309 ATTCTAAAGGAG
66 ATTCTAAAGCAA
321 GACCTAAGCAGGTTTACTTAAA
1 GACCTAAGCAGGTTTACTTAAA
343 TGGCAACTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
76 28 0.33
77 52 0.61
78 5 0.06
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (77 bp):
GACCTAAGCAGGTTTACTTAAACGAAACTCTAAGCAGAGGCCTAAGCAGGTTTACTAAAATGGAA
ATTCTAAAGCAA
Found at i:267 original size:115 final size:116
Alignment explanation
Indices: 90--342 Score: 282
Period size: 115 Copynumber: 2.2 Consensus size: 116
80 TCTAAATAGT
90 GACCTAAACAGGTTTACTTAAACGAAAATTCTAAACAAAGACCTAAGCAGGTTTAAACAAACG-A
1 GACCTAAACAGGTTTACTTAAACGAAAATTCTAAACAAAGACCTAAGCAGGTTTAAACAAACGAA
* * * *
154 GATTCTTAGC-GGGGACCTAAGCAGGTTTTCTAAAGCAGAAATTCTAGGCCGG
66 G-CTCTAAGCAGAGG-CCTAAGCAGGTTTACTAAAGCAGAAATTCTAGGCCGG
* * * * * ***
206 GACCTAAGCAGGTTTTCTTAGATG-AAATTCTAAACATAGACCTAAGCAGGTTTACTTAAACGAA
1 GACCTAAACAGGTTTACTTAAACGAAAATTCTAAACAAAGACCTAAGCAGGTTTAAACAAACGAA
*** *
270 GCTCTAAGCAGAGGCCTAAGCAGGTTTACTAAAATGGAAATTCTAAAGG--AG
66 GCTCTAAGCAGAGGCCTAAGCAGGTTTACTAAAGCAGAAATTCT--AGGCCGG
*
321 GACCTAAGCAGGTTTACTTAAA
1 GACCTAAACAGGTTTACTTAAA
343 TGGCAACTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
115 87 0.76
116 25 0.22
117 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (116 bp):
GACCTAAACAGGTTTACTTAAACGAAAATTCTAAACAAAGACCTAAGCAGGTTTAAACAAACGAA
GCTCTAAGCAGAGGCCTAAGCAGGTTTACTAAAGCAGAAATTCTAGGCCGG
Found at i:442 original size:31 final size:32
Alignment explanation
Indices: 394--455 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
384 AAACTCTAAG
394 CAGAGATCCTAAACAGGTTTACTTAAACGGAA
1 CAGAGATCCTAAACAGGTTTACTTAAACGGAA
* *
426 CAGAGA-CCTAAGCAGGTTTGCTTAAACGGA
1 CAGAGATCCTAAACAGGTTTACTTAAACGGA
456 GATTCTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (32 bp):
CAGAGATCCTAAACAGGTTTACTTAAACGGAA
Found at i:534 original size:50 final size:49
Alignment explanation
Indices: 454--633 Score: 227
Period size: 50 Copynumber: 3.6 Consensus size: 49
444 TGCTTAAACG
* * *
454 GAGATTCTAAAC-AAGGACCTACGCAGGTTTTATTAAACGCAAATTCTGAT
1 GAGATTCTAAACGTA-GACCTAAGCAGGTTTTCTTAAACG-AAATTCTGAT
* * ** *
504 GAGATTTTAGACGGGGGCCTAAGCAGGTTTTCTTAAACAGAAATTCTGAT
1 GAGATTCTAAACGTAGACCTAAGCAGGTTTTCTTAAAC-GAAATTCTGAT
* *
554 GAGATTCTAAACGTAGACCTAAGCGGGTTTTCTTAAACATAAATTCTGAT
1 GAGATTCTAAACGTAGACCTAAGCAGGTTTTCTTAAAC-GAAATTCTGAT
604 GAGATTCTAAACGTAGACCTAAGCAGGTTT
1 GAGATTCTAAACGTAGACCTAAGCAGGTTT
634 ACTAAGTTAA
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
50 112 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (49 bp):
GAGATTCTAAACGTAGACCTAAGCAGGTTTTCTTAAACGAAATTCTGAT
Found at i:1179 original size:2 final size:2
Alignment explanation
Indices: 1172--1200 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1162 AGACGAAGAG
1172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1201 AAGAGGGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.