Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001808.1 Corchorus olitorius cultivar O-4 contig01808, 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: 7721
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Found at i:7349 original size:40 final size:40
Alignment explanation
Indices: 7305--7690 Score: 202
Period size: 40 Copynumber: 9.3 Consensus size: 40
7295 TTTCTAGCTA
* *
7305 GGAAGGGCAAACTAGTAGACTAAACAACACCTTCCGGTGG
1 GGAAGGGCAAACTAGGAGACTAAACAACACCTTCCGATGG
* *
7345 GGAAGCGCAAACT-GGAATGTAAACAACACTGGACAACACCTTCCGATGG
1 GGAAGGGCAAACTAGG-A-G---ACTA-A----ACAACACCTTCCGATGG
* * **
7394 GGAAGGGCAAA-TTGG-GTATGTAAACAACACCTTCC-AGTTA
1 GGAAGGGCAAACTAGGAG-A-CTAAACAACACCTTCCGA-TGG
* * *
7434 GGAAAGGCGAACTAGGA-A-TACAGACAACACCTTCCGGTGG
1 GGAAGGGCAAACTAGGAGACTA-A-ACAACACCTTCCGATGG
* * *
7474 GGAAGGGCAAAC-AGGGAAATGTAAACAACACCTTCCGATGA
1 GGAAGGGCAAACTA-GGAGA-CTAAACAACACCTTCCGATGG
* * * *
7515 GGAAGGGCAAACT-GGAAATGTAAAAAACACCTTCCGGTGG
1 GGAAGGGCAAACTAGGAGA-CTAAACAACACCTTCCGATGG
** *
7555 GGAAGGGCAAACTAGGGATGTGTAAACAACACCTTCCGATGA
1 GGAAGGGCAAACTA-GGA-GACTAAACAACACCTTCCGATGG
* * * * *
7597 GGAAGGACAAA-TTGGTAAATGCT-GACAACACCTTCCGATGA
1 GGAAGGGCAAACTAGG-AGA--CTAAACAACACCTTCCGATGG
* * *
7638 GAAAGAGCAAACTAGGAGAAGCT-GACAACACCTTCCGAT-G
1 GGAAGGGCAAACTAGGAG-A-CTAAACAACACCTTCCGATGG
7678 GGAAGGGCAAACT
1 GGAAGGGCAAACT
7691 GGACAAAGGC
Statistics
Matches: 273, Mismatches: 42, Indels: 62
0.72 0.11 0.16
Matches are distributed among these distances:
38 2 0.01
39 4 0.01
40 112 0.41
41 79 0.29
42 37 0.14
43 2 0.01
44 5 0.02
45 2 0.01
46 1 0.00
48 1 0.00
49 28 0.10
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.15
Consensus pattern (40 bp):
GGAAGGGCAAACTAGGAGACTAAACAACACCTTCCGATGG
Found at i:7404 original size:49 final size:50
Alignment explanation
Indices: 7328--7423 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
7318 AGTAGACTAA
*
7328 ACAACACCTTCCGGTGGGGAAGCGCAAACT-GGAATGTAAACAACACTGG
1 ACAACACCTTCCGATGGGGAAGCGCAAACTGGGAATGTAAACAACACTGG
* * *
7377 ACAACACCTTCCGATGGGGAAGGGCAAATTGGGTATGTAAACAACAC
1 ACAACACCTTCCGATGGGGAAGCGCAAACTGGGAATGTAAACAACAC
7424 CTTCCAGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 27 0.64
50 15 0.36
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (50 bp):
ACAACACCTTCCGATGGGGAAGCGCAAACTGGGAATGTAAACAACACTGG
Found at i:7519 original size:41 final size:41
Alignment explanation
Indices: 7377--7721 Score: 262
Period size: 40 Copynumber: 8.5 Consensus size: 41
7367 ACAACACTGG
* ** *
7377 ACAACACCTTCCGATGGGGAAGGGCAAATTGGG-TATGTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACAGGGAAATGTAA
* * * ** *
7417 ACAACACCTTCC-AGTTAGGAAAGGCGAACTA-GG-AATACAG
1 ACAACACCTTCCGA-TGAGGAAGGGCAAAC-AGGGAAATGTAA
* *
7457 ACAACACCTTCCGGTGGGGAAGGGCAAACAGGGAAATGTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACAGGGAAATGTAA
*
7498 ACAACACCTTCCGATGAGGAAGGGCAAAC-TGGAAATGTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACAGGGAAATGTAA
* * * **
7538 AAAACACCTTCCGGTGGGGAAGGGCAAACTAGGGATGTGTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAAC-AGGGAAATGTAA
* ** * *
7580 ACAACACCTTCCGATGAGGAAGGACAAATTGGTAAATGCT-G
1 ACAACACCTTCCGATGAGGAAGGGCAAACAGGGAAATG-TAA
* * *
7621 ACAACACCTTCCGATGAGAAAGAGCAAACTA-GGAGAA-GCT-G
1 ACAACACCTTCCGATGAGGAAGGGCAAAC-AGGGA-AATG-TAA
* * **
7662 ACAACACCTTCCGATG-GGAAGGGCAAAC-TGGACAAAGGCA
1 ACAACACCTTCCGATGAGGAAGGGCAAACAGGGA-AATGTAA
*
7702 ACAACACCTCCCGATGAGGA
1 ACAACACCTTCCGATGAGGA
Statistics
Matches: 242, Mismatches: 49, Indels: 27
0.76 0.15 0.08
Matches are distributed among these distances:
39 7 0.03
40 114 0.47
41 86 0.36
42 35 0.14
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (41 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACAGGGAAATGTAA
Found at i:7544 original size:81 final size:82
Alignment explanation
Indices: 7376--7693 Score: 341
Period size: 81 Copynumber: 3.9 Consensus size: 82
7366 AACAACACTG
* * *
7376 GACAACACCTTCCGATGGGGAAGGGCAAA-TTGGG-TATGTAAACAACACCTTCC-AGTTAGGAA
1 GACAACACCTTCCGATGGGGAAGGGCAAACTAGGGAAATGTAAACAACACCTTCCGA-TGAGGAA
* * **
7438 AGGCGAACTAGG-AATACA
65 GGGCAAACT-GGAAATGTA
*
7456 GACAACACCTTCCGGTGGGGAAGGGCAAAC-AGGGAAATGTAAACAACACCTTCCGATGAGGAAG
1 GACAACACCTTCCGATGGGGAAGGGCAAACTAGGGAAATGTAAACAACACCTTCCGATGAGGAAG
7520 GGCAAACTGGAAATGTA
66 GGCAAACTGGAAATGTA
* * * **
7537 AAAAACACCTTCCGGTGGGGAAGGGCAAACTAGGGATGTGTAAACAACACCTTCCGATGAGGAAG
1 GACAACACCTTCCGATGGGGAAGGGCAAACTAGGGAAATGTAAACAACACCTTCCGATGAGGAAG
* *
7602 GACAAATTGGTAAATGCT-
66 GGCAAACTGG-AAATG-TA
* * * *
7620 GACAACACCTTCCGATGAGAAAGAGCAAACTA-GGAGAA-GCT-GACAACACCTTCCGATG-GGA
1 GACAACACCTTCCGATGGGGAAGGGCAAACTAGGGA-AATG-TAAACAACACCTTCCGATGAGGA
7681 AGGGCAAACTGGA
64 AGGGCAAACTGGA
7694 CAAAGGCAAC
Statistics
Matches: 204, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
80 34 0.17
81 76 0.37
82 61 0.30
83 32 0.16
84 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (82 bp):
GACAACACCTTCCGATGGGGAAGGGCAAACTAGGGAAATGTAAACAACACCTTCCGATGAGGAAG
GGCAAACTGGAAATGTA
Found at i:7634 original size:123 final size:120
Alignment explanation
Indices: 7376--7721 Score: 324
Period size: 123 Copynumber: 2.8 Consensus size: 120
7366 AACAACACTG
* * ** * * *
7376 GACAACACCTTCCGATGGGGAAGGGCAAATTGGGTATGTAAACAACACCTTCCAGTTAGGAAAGG
1 GACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGTAAACAACACCTTCC-GGTGGGAAGGG
* * * * *
7441 CGAACTAGGAATACAGACAACACCTTCCGGTGGGGAAGGGCAAACAGGGAAATGTA
65 CAAACTAGGAATACAAACAACACCTTCCGATGAGGAAGGACAAACAGGGAAATGTA
* *
7497 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGTAAAAAACACCTTCCGGTGGGGAAGGG
1 GACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGTAAACAACACCTTCCGGT-GGGAAGGG
* ** ** *
7562 CAAACTAGGGATGTGTAAACAACACCTTCCGATGAGGAAGGACAAATTGGTAAATGCT-
65 CAAACTA-GGA-ATACAAACAACACCTTCCGATGAGGAAGGACAAACAGGGAAATG-TA
* * * *
7620 GACAACACCTTCCGATGAGAAAGAGCAAACTAGGAGAA-GCT-GACAACACCTTCCGATGGGAAG
1 GACAACACCTTCCGATGAGGAAGGGCAAACT-GGA-AATG-TAAACAACACCTTCCGGTGGGAAG
* *
7683 GGCAAACT-GGACAAAGGC-AACAACACCTCCCGATGAGGA
63 GGCAAACTAGGA-ATA--CAAACAACACCTTCCGATGAGGA
Statistics
Matches: 184, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
120 2 0.01
121 62 0.34
122 23 0.12
123 76 0.41
124 18 0.10
125 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (120 bp):
GACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGTAAACAACACCTTCCGGTGGGAAGGGC
AAACTAGGAATACAAACAACACCTTCCGATGAGGAAGGACAAACAGGGAAATGTA
Done.