Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017031.1 Corchorus olitorius cultivar O-4 contig17064, 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: 17709
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Found at i:2960 original size:29 final size:29
Alignment explanation
Indices: 2918--3092 Score: 332
Period size: 29 Copynumber: 6.0 Consensus size: 29
2908 CAAGTTTTCG
2918 AGTTTTCAATTTAGGGAAAGATCCCATCA
1 AGTTTTCAATTTAGGGAAAGATCCCATCA
2947 AGTTTTCAATTTAGGGAAAGATCCCATCA
1 AGTTTTCAATTTAGGGAAAGATCCCATCA
2976 AGTTTTCAATTTAGGGAAAGATCCCATCA
1 AGTTTTCAATTTAGGGAAAGATCCCATCA
3005 AGTTTTCAATTTAGGGAAAGATCCCATCA
1 AGTTTTCAATTTAGGGAAAGATCCCATCA
3034 AGTTTTCAAATTTAGGGAAAGATCCCATCA
1 AGTTTTC-AATTTAGGGAAAGATCCCATCA
*
3064 AGTTTTCAATTTAGGGAAAGTTCCCATCA
1 AGTTTTCAATTTAGGGAAAGATCCCATCA
3093 TTTTAAGTTT
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
29 115 0.80
30 29 0.20
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (29 bp):
AGTTTTCAATTTAGGGAAAGATCCCATCA
Found at i:8614 original size:54 final size:54
Alignment explanation
Indices: 8515--8617 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
8505 GATGGGGGTC
*
8515 ACTTAAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAAAA
1 ACTTAAGTTGAAAACCCGAAAAGGGCGGCTCAAGGGAAGGATGGAAAAGGAAAA
* * *
8569 ACTTGAGTTGAAAACCCGCAAAGGGCGGCTCAAGCGGAA-GTTGGAAAAG
1 ACTTAAGTTGAAAACCCGAAAAGGGCGGCTCAAG-GGAAGGATGGAAAAG
8618 ACATAGTCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 41 0.93
55 3 0.07
ACGTcount: A:0.40, C:0.16, G:0.31, T:0.14
Consensus pattern (54 bp):
ACTTAAGTTGAAAACCCGAAAAGGGCGGCTCAAGGGAAGGATGGAAAAGGAAAA
Found at i:9707 original size:58 final size:58
Alignment explanation
Indices: 9523--10038 Score: 597
Period size: 58 Copynumber: 8.6 Consensus size: 58
9513 AATTCATCAG
* *
9523 AGATGGATTTGAAGACAGTTCCTAAAAAGATTTTAAGATTCAAGGCTAAAGACAGCTCAC
1 AGATGGATCTGAAGACAGTTCCT-AAAAGATTTTAAGATT-AAGGCTGAAGACAGCTCAC
*
9583 AGATGGATCTGAAGACAGTTCCTAAAAAGATTTTAAGATTTAAGGCTGAAGACAGCTCAT
1 AGATGGATCTGAAGACAGTTCCT-AAAAGATTTTAAGA-TTAAGGCTGAAGACAGCTCAC
9643 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
*
9701 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGATAGCTCAC
1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
9759 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
* * * ** * * *
9817 AGATGGATCTGAAGACAGTTCCTAAAATATTTTAAGAGTGAGTATGAAAACGGCTCAT
1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
* * * * * * *
9875 AGACGGGTTCTGAAGACAGTTCCTGAATGATATTTAAGAGTGAA-TCT-AAGAACAGTTCAC
1 AGA-TGGATCTGAAGACAGTTCCTAAAAGAT-TTTAAGA-TTAAGGCTGAAG-ACAGCTCAC
* * * * * *
9935 AAAGATGGGTTCTGAAGACAGTTCCTAAAAGGTAATTAAGAGTGAA-TCTGAAGACAGTTCAC
1 --AGAT-GGATCTGAAGACAGTTCCTAAAAGAT-TTTAAGA-TTAAGGCTGAAGACAGCTCAC
* * *
9997 GAAGATAGGTTTTGAAGACAATTCCTGAAAAGAGTTTTAAGA
1 --AGAT-GGATCTGAAGACAGTTCCT-AAAAGA-TTTTAAGA
10039 ACGAATTGCA
Statistics
Matches: 407, Mismatches: 38, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
58 187 0.46
59 38 0.09
60 92 0.23
61 3 0.01
62 72 0.18
63 14 0.03
64 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (58 bp):
AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTAAGGCTGAAGACAGCTCAC
Found at i:10058 original size:63 final size:62
Alignment explanation
Indices: 9880--10058 Score: 175
Period size: 62 Copynumber: 2.9 Consensus size: 62
9870 CTCATAGACG
* * * * * ** *
9880 GGTTCTGAAGACAGTTCCTGAATGATATTTAAGAGTGAATCT-AAGAACAGTTCACAAAGATG
1 GGTTCTGAAGACAATTCCTAAAAGGTAATTAAGAACGAATCTGAAG-ACAGTTCACAAAGATA
* ** *
9942 GGTTCTGAAGACAGTTCCTAAAAGGTAATTAAGAGTGAATCTGAAGACAGTTCACGAAGATA
1 GGTTCTGAAGACAATTCCTAAAAGGTAATTAAGAACGAATCTGAAGACAGTTCACAAAGATA
* *
10004 GGTTTTGAAGACAATTCCTGAAAAGAGT-TTTAAGAACGAAT-TGCAAGACAGTTCA
1 GGTTCTGAAGACAATTCCT-AAAAG-GTAATTAAGAACGAATCTG-AAGACAGTTCA
10059 TGAAAGTGAT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
62 71 0.70
63 29 0.28
64 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (62 bp):
GGTTCTGAAGACAATTCCTAAAAGGTAATTAAGAACGAATCTGAAGACAGTTCACAAAGATA
Found at i:11752 original size:2 final size:2
Alignment explanation
Indices: 11741--11770 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11731 AAAAACAGGC
*
11741 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11771 GTCCTACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12899 original size:2 final size:2
Alignment explanation
Indices: 12892--12922 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12882 ACTTTGTTTG
12892 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12923 TAAATAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.