Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017863.1 Corchorus olitorius cultivar O-4 contig17896, 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: 61375
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:46991 original size:22 final size:23
Alignment explanation
Indices: 46952--46994 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
46942 AATCCTAATC
46952 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
46975 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
46995 ACTCCTCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:49925 original size:45 final size:45
Alignment explanation
Indices: 49853--49982 Score: 190
Period size: 45 Copynumber: 2.9 Consensus size: 45
49843 AATCTTTTTC
* * * * *
49853 CATCAATG-ACAAACTCAGACTCCTCTCCCTCACAAACAAATTCTT
1 CATCAA-GAACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTT
49898 CATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTT
1 CATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTT
*
49943 CATCAAGAACAAAATCAGAATCTTCTCCTTTACAAACAAA
1 CATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAA
49983 GAAAAGATCT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 1 0.01
45 77 0.99
ACGTcount: A:0.42, C:0.30, G:0.05, T:0.24
Consensus pattern (45 bp):
CATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTT
Found at i:50740 original size:22 final size:23
Alignment explanation
Indices: 50701--50743 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
50691 AATCCTAATC
50701 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
50724 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
50744 ACTCCTCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:51436 original size:15 final size:15
Alignment explanation
Indices: 51411--51445 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51401 ACTAACTCAA
*
51411 CAAACTCAACTGACT
1 CAAACTAAACTGACT
*
51426 TAAACTAAACTGACT
1 CAAACTAAACTGACT
51441 CAAAC
1 CAAAC
51446 ATTCAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.20
Consensus pattern (15 bp):
CAAACTAAACTGACT
Found at i:53299 original size:15 final size:14
Alignment explanation
Indices: 53281--53340 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
53271 AAGATGTTGT
53281 TGAGGACGATGATGA
1 TGAGGA-GATGATGA
*
53296 TGA-G-GATGGTGA
1 TGAGGAGATGATGA
*
53308 CGAGGATGATGATGA
1 TGAGGA-GATGATGA
*
53323 TGAGGAGGATGAGGA
1 TGAGGA-GATGATGA
53338 TGA
1 TGA
53341 AGCTTCATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 9 0.25
13 1 0.03
14 1 0.03
15 25 0.69
ACGTcount: A:0.32, C:0.03, G:0.45, T:0.20
Consensus pattern (14 bp):
TGAGGAGATGATGA
Found at i:53309 original size:21 final size:21
Alignment explanation
Indices: 53285--53324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53275 TGTTGTTGAG
*
53285 GACGATGATGATGAGGATGGT
1 GACGAGGATGATGAGGATGGT
*
53306 GACGAGGATGATGATGATG
1 GACGAGGATGATGAGGATG
53325 AGGAGGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.42, T:0.23
Consensus pattern (21 bp):
GACGAGGATGATGAGGATGGT
Found at i:53321 original size:18 final size:18
Alignment explanation
Indices: 53294--53340 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
53284 GGACGATGAT
*
53294 GATGAGGATGGTGACGAG
1 GATGAGGATGATGACGAG
* *
53312 GATGATGATGATGAGGAG
1 GATGAGGATGATGACGAG
53330 GATGAGGATGA
1 GATGAGGATGA
53341 AGCTTCATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.47, T:0.19
Consensus pattern (18 bp):
GATGAGGATGATGACGAG
Found at i:55584 original size:42 final size:42
Alignment explanation
Indices: 55499--55593 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
55489 GGCATACTGA
* * * * *
55499 TCATCCTCATCTACATGCGCTTTAGCATATTTGTCTTCTTCC
1 TCATCCTCCTCTACATGCGCTTTAGCATATCTATCATCCTCC
55541 TCATCCTCCTCTACATGTC-CTTTAGCATATCTATCATCCTCC
1 TCATCCTCCTCTACATG-CGCTTTAGCATATCTATCATCCTCC
*
55583 TCTTCCTCCTC
1 TCATCCTCCTC
55594 CAGATGACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.16, C:0.37, G:0.06, T:0.41
Consensus pattern (42 bp):
TCATCCTCCTCTACATGCGCTTTAGCATATCTATCATCCTCC
Found at i:60884 original size:39 final size:40
Alignment explanation
Indices: 60828--60908 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
60818 TTTAATTCCT
*
60828 ATGTAATATATATAATAAGTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
60868 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
60907 AT
1 AT
60909 TCTTAGGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.