Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012902.1 Corchorus capsularis cultivar CVL-1 contig12923, 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: 23089
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:2029 original size:24 final size:24
Alignment explanation
Indices: 1979--2029 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1969 GGAGAAATCA
1979 TGAAACAATCTATGTAAATTTTCTT
1 TGAAACAATCTA-GTAAATTTTCTT
* *
2004 TGAAGCAATCTA-TAATATTTTTTT
1 TGAAACAATCTAGTAA-ATTTTCTT
2028 TG
1 TG
2030 GGTGCATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.13
24 9 0.39
25 11 0.48
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (24 bp):
TGAAACAATCTAGTAAATTTTCTT
Found at i:3479 original size:36 final size:37
Alignment explanation
Indices: 3433--3508 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
3423 CCATCAAGTG
* *
3433 AGAATCATTTTGATTTCAA-TGAAGATCAATGGATGGA
1 AGAATCATTTTGAATTCAACGGAA-ATCAATGGATGGA
* *
3470 AGAAT-ATTTTGAATTGAACGGAAATCAATGGTTGGA
1 AGAATCATTTTGAATTCAACGGAAATCAATGGATGGA
3506 AGA
1 AGA
3509 CTTTGATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (37 bp):
AGAATCATTTTGAATTCAACGGAAATCAATGGATGGA
Found at i:3584 original size:48 final size:48
Alignment explanation
Indices: 3505--3623 Score: 184
Period size: 48 Copynumber: 2.5 Consensus size: 48
3495 CAATGGTTGG
* *
3505 AAGACTTTGATTTGAACGAAGATTGGTTAGGAGATGAAGCCAACATTC
1 AAGATTTTGATTTGAACGAAGATTGGGTAGGAGATGAAGCCAACATTC
*
3553 AAGATTTTGATTTGAACGAAGATTGGGTAGGAGATGAAGGCAACATTC
1 AAGATTTTGATTTGAACGAAGATTGGGTAGGAGATGAAGCCAACATTC
* * *
3601 ATGATTTTGATTTAAATGAAGAT
1 AAGATTTTGATTTGAACGAAGAT
3624 CCAGGAGATG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (48 bp):
AAGATTTTGATTTGAACGAAGATTGGGTAGGAGATGAAGCCAACATTC
Found at i:7000 original size:27 final size:27
Alignment explanation
Indices: 6966--7026 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 27
6956 TCTGGAATGA
6966 AAGGGAAAGGGACAATTAAAAAGGAAC
1 AAGGGAAAGGGACAATTAAAAAGGAAC
6993 AAGGGAAAGGGACAATTAAAAAGGAAC
1 AAGGGAAAGGGACAATTAAAAAGGAAC
7020 AGAGGGA
1 A-AGGGA
7027 GTAATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.54, C:0.07, G:0.33, T:0.07
Consensus pattern (27 bp):
AAGGGAAAGGGACAATTAAAAAGGAAC
Found at i:7037 original size:2 final size:2
Alignment explanation
Indices: 7030--7060 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7020 AGAGGGAGTA
7030 AT 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 AT A
7061 ACATAATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7256 original size:65 final size:62
Alignment explanation
Indices: 7140--7266 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 62
7130 GCTCCTCAAA
* * *
7140 CTGCCATAACTTTTTAACTTTCAACTTTTCTTTTGCTTTGTGTCCATGATCAAAATCTTCAATC
1 CTGCCATAACTCTTTAACGTTCAACTTTTCTTTTGCTTTGTGTCAATGATC--AATCTTCAATC
* *
7204 CTGCCATAGCTCTTTATCGTTCAACTTTTCCTTTTG-TTCTGTGTCAATGATCAATCTTCAATC
1 CTGCCATAACTCTTTAACGTTCAACTTTT-CTTTTGCTT-TGTGTCAATGATCAATCTTCAATC
7267 TTTCTTTGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
63 11 0.20
64 27 0.48
65 18 0.32
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.45
Consensus pattern (62 bp):
CTGCCATAACTCTTTAACGTTCAACTTTTCTTTTGCTTTGTGTCAATGATCAATCTTCAATC
Found at i:7518 original size:54 final size:54
Alignment explanation
Indices: 7436--7546 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
7426 TAGAGTTGCC
* *
7436 TATGTTTACTGAAATGAATTAATGATAATATAATTTTATTACACTACTTATAAA
1 TATGTCTACTGAAATGAATTAATGATAATAGAATTTTATTACACTACTTATAAA
*
7490 TATGTCTACTGACATGAATTAATGATAATAGAATTTTATTACACTACTTATAAA
1 TATGTCTACTGAAATGAATTAATGATAATAGAATTTTATTACACTACTTATAAA
7544 TAT
1 TAT
7547 ATCTTTATCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (54 bp):
TATGTCTACTGAAATGAATTAATGATAATAGAATTTTATTACACTACTTATAAA
Found at i:8365 original size:9 final size:10
Alignment explanation
Indices: 8351--8382 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
8341 TTTCTTTGCC
8351 CTTTCTCT-T
1 CTTTCTCTCT
8360 CTTTCTCTCT
1 CTTTCTCTCT
8370 CTTTCT-TCT
1 CTTTCTCTCT
8379 CTTT
1 CTTT
8383 GAGTTATGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (10 bp):
CTTTCTCTCT
Done.