Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011000.1 Corchorus capsularis cultivar CVL-1 contig11021, 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: 38433
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Found at i:789 original size:3 final size:3
Alignment explanation
Indices: 781--811 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
771 GTAATTTCTG
781 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
812 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16601 original size:15 final size:16
Alignment explanation
Indices: 16581--16614 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16571 GATTGCTTTC
*
16581 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
16596 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
16612 TTA
1 TTA
16615 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:20743 original size:16 final size:16
Alignment explanation
Indices: 20706--20801 Score: 66
Period size: 16 Copynumber: 5.3 Consensus size: 16
20696 TTTGACCTTC
*
20706 TTACTTAATACCATACT
1 TTACTTAATACCAT-TT
20723 TTACTTAATACCATTT
1 TTACTTAATACCATTT
20739 TTACTCTTTTGTTTAATACCATTT
1 TTA--C-----T-TAATACCATTT
*
20763 TTGACCTTAATACCATGT
1 TT-A-CTTAATACCATTT
*
20781 TTACTTGATACCATTT
1 TTACTTAATACCATTT
20797 TTACT
1 TTACT
20802 CTCTTGTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
16 20 0.31
17 15 0.23
18 13 0.20
19 1 0.02
23 1 0.02
24 14 0.22
25 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (16 bp):
TTACTTAATACCATTT
Found at i:20773 original size:42 final size:42
Alignment explanation
Indices: 20684--20785 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 42
20674 TTTTTTTAAA
20684 TTAATACCATTTTTTGAC-CTTCTTACTTAATACCATACTTTAC
1 TTAATACCA-TTTTT-ACTCTTCTTACTTAATACCATACTTTAC
** *
20727 TTAATACCATTTTTACTCTT-TTGTTTAATACCAT-TTTTGACC
1 TTAATACCATTTTTACTCTTCTTACTTAATACCATACTTT-A-C
*
20769 TTAATACCATGTTTACT
1 TTAATACCATTTTTACT
20786 TGATACCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 3 0.06
41 15 0.29
42 25 0.48
43 9 0.17
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (42 bp):
TTAATACCATTTTTACTCTTCTTACTTAATACCATACTTTAC
Found at i:20803 original size:58 final size:59
Alignment explanation
Indices: 20709--20822 Score: 194
Period size: 58 Copynumber: 1.9 Consensus size: 59
20699 GACCTTCTTA
*
20709 CTTAATACCATACTTTACTTAATACCATTTTTACTCTTTTGTTTAATACCATTTTTGAC
1 CTTAATACCATACTTTACTTAATACCATTTTTACTCTCTTGTTTAATACCATTTTTGAC
* *
20768 CTTAATACCAT-GTTTACTTGATACCATTTTTACTCTCTTGTTTAATACCATTTTT
1 CTTAATACCATACTTTACTTAATACCATTTTTACTCTCTTGTTTAATACCATTTTT
20823 TTTTTACTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 41 0.79
59 11 0.21
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.50
Consensus pattern (59 bp):
CTTAATACCATACTTTACTTAATACCATTTTTACTCTCTTGTTTAATACCATTTTTGAC
Found at i:22201 original size:2 final size:2
Alignment explanation
Indices: 22196--22221 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22186 AAATACACAC
22196 AT 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
22222 TTGTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24410 original size:3 final size:3
Alignment explanation
Indices: 24402--24437 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
24392 GTAATTTCTG
24402 TAT TAT TAT TAT TAT TAT TAT TAT CTATT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT T
24438 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.84
4 4 0.13
5 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:26525 original size:21 final size:21
Alignment explanation
Indices: 26499--26540 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26489 AGTGTCGACC
26499 CAATCA-AGCAATTCAAAGCAT
1 CAATCATAGC-ATTCAAAGCAT
*
26520 CAATCATAGCATTCATAGCAT
1 CAATCATAGCATTCAAAGCAT
26541 ATGAGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
CAATCATAGCATTCAAAGCAT
Found at i:26649 original size:16 final size:16
Alignment explanation
Indices: 26624--26654 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26614 AGGAATAGGC
26624 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
26640 AATCATTCAAAGCAA
1 AATCAATCAAAGCAA
26655 AGAAAAAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:32171 original size:29 final size:29
Alignment explanation
Indices: 32139--32197 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
32129 TGTAACCTCA
32139 TGAAATGAATTTACTAGCTAGCATTAATT
1 TGAAATGAATTTACTAGCTAGCATTAATT
32168 TGAAATGAATTTACTAGCTAGCATTAATT
1 TGAAATGAATTTACTAGCTAGCATTAATT
32197 T
1 T
32198 ATTGATTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TGAAATGAATTTACTAGCTAGCATTAATT
Done.