Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022817.1 Corchorus olitorius cultivar O-4 contig22850, 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: 8101
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Found at i:1097 original size:13 final size:12
Alignment explanation
Indices: 1076--1121 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
1066 ATTAAGAAAT
*
1076 TCAAAAAAATAAA
1 TCAATAAAA-AAA
1089 TCAATAAAAAAAA
1 TCAAT-AAAAAAA
1102 TCAA-AAAAAAA
1 TCAATAAAAAAA
1113 T-AATAAAAA
1 TCAATAAAAA
1122 TCAAAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.07
11 13 0.43
13 11 0.37
14 4 0.13
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
TCAATAAAAAAA
Found at i:1923 original size:50 final size:50
Alignment explanation
Indices: 1726--1912 Score: 268
Period size: 50 Copynumber: 3.7 Consensus size: 50
1716 GAATATTTAC
*
1726 AATAAGATTGCATGCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
* * **
1776 AGA-AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1 A-ATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
**
1826 AACGAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
* * *
1876 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAA
1 AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAA
1913 GGTTGATTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 1 0.01
50 118 0.98
51 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
Found at i:2584 original size:50 final size:50
Alignment explanation
Indices: 2525--3098 Score: 995
Period size: 50 Copynumber: 11.5 Consensus size: 50
2515 CGAATGCTTT
* *
2525 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
2575 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
2625 GGCTTTTCCACAAGCCAAACTCATTTCCGTACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
2675 GGCTTTTCCACAAGCCAAACTTGTTTCCATATGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
2725 AGCTTTTCCATAAGCCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAATTATCAACATA
2776 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
2826 GGCTTTTCCACAAGTCGAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
2876 GGCTTTTCCACAAGCCAAACTCGTCTCCATATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
2926 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
2976 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
3026 GGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
3076 GGCTTTTCCACAAGCCAAACTCG
1 GGCTTTTCCACAAGCCAAACTCG
3099 AGGATCTCTC
Statistics
Matches: 493, Mismatches: 30, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
50 448 0.91
51 45 0.09
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:3407 original size:28 final size:27
Alignment explanation
Indices: 3374--3472 Score: 112
Period size: 28 Copynumber: 3.7 Consensus size: 27
3364 GATCACCCAG
3374 GGGCATTTTGGTCATTTTTCATATTCA
1 GGGCATTTTGGTCATTTTTCATATTCA
* * * *
3401 GTGGCATTATGGTCATTTTT-ACACTAA
1 G-GGCATTTTGGTCATTTTTCATATTCA
*
3428 GGGCATTTTGGTCA-TTTGCATATTCA
1 GGGCATTTTGGTCATTTTTCATATTCA
*
3454 GGGGCATGTTGGTCATTTT
1 -GGGCATTTTGGTCATTTT
3473 GAGTCCACTT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
25 3 0.05
26 16 0.28
27 19 0.33
28 20 0.34
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTCATATTCA
Found at i:3636 original size:25 final size:25
Alignment explanation
Indices: 3607--3654 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3597 GTATTTTGCG
3607 TTCATGTAGCTCAAAGCTAATTTCA
1 TTCATGTAGCTCAAAGCTAATTTCA
*
3632 TTCATGTAGCTCAAATCTAATTT
1 TTCATGTAGCTCAAAGCTAATTT
3655 GACATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (25 bp):
TTCATGTAGCTCAAAGCTAATTTCA
Found at i:7923 original size:16 final size:15
Alignment explanation
Indices: 7885--7926 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
7875 ACAGAGATTG
* *
7885 ACAGAAAGCAATTAA
1 ACAGAAAACAATAAA
7900 ACAGAAAACAATAAA
1 ACAGAAAACAATAAA
7915 ACTAGAAAACAA
1 AC-AGAAAACAA
7927 AGCAGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.67, C:0.14, G:0.10, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATAAA
Done.