Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024689.1 Corchorus olitorius cultivar O-4 contig24722, 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: 20302
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--41 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42 GATGGACTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2059 original size:22 final size:22
Alignment explanation
Indices: 2000--2060 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
1990 GTAACTGGCT
* *
2000 GACAAAACTATCATGGTTTCATA
1 GACAATACTATCATTG-TTCATA
*
2023 GACAAT--TATCCTTGTTCATA
1 GACAATACTATCATTGTTCATA
2043 GACAATACTATCATTGTT
1 GACAATACTATCATTGTT
2061 TTAGATTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.38
21 6 0.19
22 9 0.28
23 5 0.16
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
GACAATACTATCATTGTTCATA
Found at i:2635 original size:21 final size:21
Alignment explanation
Indices: 2609--2650 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2599 GCACAAAGAA
2609 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
2630 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
2651 CCTAAGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:6947 original size:36 final size:36
Alignment explanation
Indices: 6875--6948 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
6865 TTGTGTTCCT
* **
6875 TTAACAATTCATACATTAATATACATCATTTTGTTC
1 TTAACAAATCATACATTAATATACATCATTAGGTTC
* *
6911 TTAACAAATCCTACATTAATATACATTATTAGGTTC
1 TTAACAAATCATACATTAATATACATCATTAGGTTC
6947 TT
1 TT
6949 GCATCAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.43
Consensus pattern (36 bp):
TTAACAAATCATACATTAATATACATCATTAGGTTC
Found at i:10639 original size:24 final size:24
Alignment explanation
Indices: 10607--10670 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
10597 GCACTTCCCA
10607 GTATACTGACTTCTCTGCTGCCTG
1 GTATACTGACTTCTCTGCTGCCTG
*
10631 GTATACTGACCTCTCTGCTGCCTG
1 GTATACTGACTTCTCTGCTGCCTG
* *
10655 GTATGCTGAATTCTCT
1 GTATACTGACTTCTCT
10671 AGGCTATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (24 bp):
GTATACTGACTTCTCTGCTGCCTG
Found at i:10782 original size:3 final size:3
Alignment explanation
Indices: 10776--10813 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
10766 GTGGTGGTGG
10776 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T-A TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
10814 AAGACTTGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:13911 original size:15 final size:16
Alignment explanation
Indices: 13893--13930 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
13883 AGATATGTAT
13893 TATAATATATA-TATA
1 TATAATATATATTATA
13908 TATAA-ATATATTATA
1 TATAATATATATTATA
13923 TACTAATA
1 TA-TAATA
13931 CGGGCAGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 3 0.15
17 1 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATATATATTATA
Found at i:15841 original size:61 final size:63
Alignment explanation
Indices: 15773--15896 Score: 189
Period size: 61 Copynumber: 2.0 Consensus size: 63
15763 TCTTAGTCCT
*
15773 TTAATCATGTATTTATATCATAATTTCTGATTA-TTT-TAATCATGTATTTTAATTATGAATG
1 TTAATCATGTATTTATATCATAATTTCTCATTATTTTCTAATCATGTATTTTAATTATGAATG
* * *
15834 TTAATCATGTATTTATATGATGATTTCTCATTATTTTTCTAATTATGTATTTTAATTATGAAT
1 TTAATCATGTATTTATATCATAATTTCTCATTA-TTTTCTAATCATGTATTTTAATTATGAAT
15897 TAATTGGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 30 0.54
63 3 0.05
64 23 0.41
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.54
Consensus pattern (63 bp):
TTAATCATGTATTTATATCATAATTTCTCATTATTTTCTAATCATGTATTTTAATTATGAATG
Found at i:15891 original size:13 final size:13
Alignment explanation
Indices: 15804--15893 Score: 71
Period size: 13 Copynumber: 7.0 Consensus size: 13
15794 AATTTCTGAT
*
15804 TATTTTAATCATG
1 TATTTTAATTATG
15817 TATTTTAATTATG
1 TATTTTAATTATG
* * *
15830 AATGTTAATCATG
1 TATTTTAATTATG
*
15843 TA-TTTATATGATG
1 TATTTTA-ATTATG
*
15856 -ATTTCTCATTAT-
1 TATTT-TAATTATG
15868 T-TTTCTAATTATG
1 TATTT-TAATTATG
15881 TATTTTAATTATG
1 TATTTTAATTATG
15894 AATTAATTGG
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
12 14 0.23
13 43 0.70
14 4 0.07
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.56
Consensus pattern (13 bp):
TATTTTAATTATG
Done.