Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021498.1 Corchorus olitorius cultivar O-4 contig21531, 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: 2383
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Found at i:1293 original size:28 final size:28
Alignment explanation
Indices: 1262--1809 Score: 332
Period size: 28 Copynumber: 19.6 Consensus size: 28
1252 GTCATTTTTG
*
1262 TCTTCGAGAGCGTACTACCTCTTCGCGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* *
1290 TCTTTGGGAGCGTACTACCGCTTCGC-A
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * *
1317 CTCTCTGGGAGCGTACTACCTCTTTGCGA
1 -TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * *
1346 TCCTTGAGAGCGTACTACCACCTCGAGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * **
1374 GCTTGGAGGAGGCGTTCTACCAATTCGCGA
1 TCTTTGA-GA-GCGTACTACCTCTTCGCGA
* * *
1404 GCTTTG-GGGCGTACTACCGCTTCGC-A
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* **
1430 CTCTTTGGGAGCGTACTACGCAT-TT-TTG-
1 -TCTTTGAGAGCGTACTAC-C-TCTTCGCGA
*
1458 TCTTCGAGAGCGTACTACCTCTTCGCGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* *
1486 TCTTTGGGAGCGTACTACCTCTTTGCGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* *
1514 TCCTTGAGAGCGTACTA-CTGCTTCGCGG
1 TCTTTGAGAGCGTACTACCT-CTTCGCGA
* * * *
1542 TCGTTGGGAGCGTACTA-CTGCTTCACGC
1 TCTTTGAGAGCGTACTACCT-CTTCGCGA
* * * *
1570 TCTTTGGGAGCGTACTACCGCTTCACGC
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * *
1598 TCTTTGGGAGCGTACTACCACCTCGAGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * *
1626 GCTTGGAGGGCGTACTACCAT-TTCGTGA
1 TCTTTGAGAGCGTACTACC-TCTTCGCGA
* * *
1654 ACTTTGA-AGCGTACTACCACTTTGCGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * *
1681 TCCTTGAGAGCGTACTACCACCTCGGGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * *
1709 GCTTGGAGGGAGTACTACCAT-TTCGCGA
1 TCTTTGAGAGCGTACTACC-TCTTCGCGA
* * *
1737 ACTTTGAG-GCGTACTACCACTTCGAGA
1 TCTTTGAGAGCGTACTACCTCTTCGCGA
* * * *
1764 GCTTGGAGGGTGTACTACCAT-TTCGCGA
1 TCTTTGAGAGCGTACTACC-TCTTCGCGA
* *
1792 ACTTT-AGGAGCGTTCTAC
1 TCTTTGA-GAGCGTACTAC
1810 GCCTTAGGAT
Statistics
Matches: 405, Mismatches: 93, Indels: 44
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.00
26 4 0.01
27 81 0.20
28 292 0.72
29 7 0.02
30 20 0.05
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.28
Consensus pattern (28 bp):
TCTTTGAGAGCGTACTACCTCTTCGCGA
Found at i:1641 original size:168 final size:168
Alignment explanation
Indices: 1297--1759 Score: 496
Period size: 167 Copynumber: 2.8 Consensus size: 168
1287 CGATCTTTGG
* *
1297 GAGCGTACTACCGCTTCGC-ACTCTCTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTAC
1 GAGCGTACTACCTCTTCGCGA-TCTTTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTAC
* *
1361 TACCACCTCGAGAGCTTGGAGGAGGCGTTCTACCAATTCGCGAGCTTTGGGGCGTACTACCGCTT
65 TACCACCTCGAGAGCTTGGAGGAGGCGTACTACCAATTCACGAGCTTTGGGGCGTACTACCGCTT
* * *** *
1426 CGCACTCTTTGGGAGCGTACTACGCATTTTTGTCTTCGA
130 CACACTCTTTGGGAGCGTACTACGCACTCGAGGCTTCGA
1465 GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACT
1 GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACT
** * * *** **
1530 ACTGCTTCGCG-GTCGTT-G-GGA-GCGTACTACTGCTTCACGCTCTTTGGGAGCGTACTACCGC
66 ACCACCTCGAGAG-C-TTGGAGGAGGCGTACTACCAATTCACGAGCTTTGGG-GCGTACTACCGC
* *
1591 TTCACGCTCTTTGGGAGCGTACTAC-CACCTCGAGAGCTTGGA
128 TTCACACTCTTTGGGAGCGTACTACGCA-CTCGAG-GCTTCGA
* * * * *
1633 GGGCGTACTACCAT-TTCGTGAACTTT-GAAGCGTACTACCACTTTGCGATCCTTGAGAGCGTAC
1 GAGCGTACTACC-TCTTCGCGATCTTTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTAC
* * * * * * *
1696 TACCACCTCGGGAGCTTGGA-G-GGAGTACTACCATTTCGCGAACTTTGAGGCGTACTACCACTT
65 TACCACCTCGAGAGCTTGGAGGAGGCGTACTACCAATTCACGAGCTTTGGGGCGTACTACCGCTT
1759 C
130 C
1760 GAGAGCTTGG
Statistics
Matches: 245, Mismatches: 39, Indels: 24
0.80 0.13 0.08
Matches are distributed among these distances:
166 38 0.16
167 106 0.43
168 97 0.40
169 4 0.02
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (168 bp):
GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACT
ACCACCTCGAGAGCTTGGAGGAGGCGTACTACCAATTCACGAGCTTTGGGGCGTACTACCGCTTC
ACACTCTTTGGGAGCGTACTACGCACTCGAGGCTTCGA
Found at i:1699 original size:83 final size:83
Alignment explanation
Indices: 1324--1758 Score: 380
Period size: 83 Copynumber: 5.2 Consensus size: 83
1314 GCACTCTCTG
*
1324 GGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGAGGCGT
1 GGAGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGA-G-GGCGT
* * *
1389 TCTACCAATTCGCGAGCTTT
64 ACTACCATTTCGCGAACTTT
* * * * * * *** * * *
1409 GGGGCGTACTACCGCTTCGC-ACTCTTTGGGAGCGTACTACGCA-TTTTTG-TCTTCGAGAGCGT
1 GGAGCGTACTACCACTTTGCGA-TCCTTGAGAGCGTACTAC-CACCTCGAGAGCTTGGAGGGCGT
*
1471 ACTACC-TCTTCGCGATCTTT
64 ACTACCAT-TTCGCGAACTTT
* ** * * *
1491 GGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACTGCTTCGCG-GTCGTTGG-GAGCG
1 -GGAGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAG-C-TTGGAGGGCG
*** * **
1554 TACTACTGCTTCACGCTCTTT
63 TACTACCATTTCGCGAACTTT
* ** * * *
1575 GGGAGCGTACTACCGCTTCACGCTCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTA
1 -GGAGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTA
*
1640 CTACCATTTCGTGAACTTT
65 CTACCATTTCGCGAACTTT
* * *
1659 GAAGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGGGAGTAC
1 GGAGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTAC
1724 TACCATTTCGCGAACTTT
66 TACCATTTCGCGAACTTT
1742 -GAGGCGTACTACCACTT
1 GGA-GCGTACTACCACTT
1759 CGAGAGCTTG
Statistics
Matches: 278, Mismatches: 60, Indels: 26
0.76 0.16 0.07
Matches are distributed among these distances:
82 21 0.08
83 128 0.46
84 88 0.32
85 39 0.14
86 2 0.01
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.28
Consensus pattern (83 bp):
GGAGCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTAC
TACCATTTCGCGAACTTT
Found at i:1749 original size:55 final size:56
Alignment explanation
Indices: 1664--1809 Score: 199
Period size: 55 Copynumber: 2.6 Consensus size: 56
1654 ACTTTGAAGC
* * *
1664 GTACTACCACTTT-GCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGGGA
1 GTACTACCA-TTTCGCGAACTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGA
* *
1720 GTACTACCATTTCGCGAACTTTGAG-GCGTACTACCACTTCGAGAGCTTGGAGGGT
1 GTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGA
*
1775 GTACTACCATTTCGCGAACTTT-AGGAGCGTTCTAC
1 GTACTACCATTTCGCGAACTTTGA-GAGCGTACTAC
1810 GCCTTAGGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
54 1 0.01
55 53 0.65
56 27 0.33
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (56 bp):
GTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGA
Done.