Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024620.1 Corchorus olitorius cultivar O-4 contig24653, 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: 36865
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1137 original size:2 final size:2
Alignment explanation
Indices: 1130--1154 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1120 TACTATTTAG
1130 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1155 GGGCTTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2061 original size:34 final size:35
Alignment explanation
Indices: 2021--2189 Score: 189
Period size: 34 Copynumber: 4.7 Consensus size: 35
2011 TCAATATTCG
2021 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
* * *
2056 -AGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCC-ACCAGGTTTT
* *
2091 AAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCA-CCAGGTTTT
* * * *
2127 CAAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTCT
1 --AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
*
2164 -AGTTTTCAATTTAGGGAAAGTTCCCA
1 AAGTTTTCAAATT-GGGAAAGTTCCCA
2190 TCATTTTCAG
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 32 0.28
35 22 0.19
36 30 0.26
37 7 0.06
38 24 0.21
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (35 bp):
AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
Found at i:2219 original size:74 final size:75
Alignment explanation
Indices: 2051--2230 Score: 192
Period size: 74 Copynumber: 2.4 Consensus size: 75
2041 TTCCCACCAG
* * *
2051 GTTTTAGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCC
1 GTTTTAG--TTTAAATTGGGAAAGTTCCCATCAAGGTTCTAAGTTTTCAAATTGGGAAAGTTCCC
2116 ATTCAGTTTTTCA
64 ATTCAG-TTTTCA
*** *
2129 AAATT--TTTAAATTGGGAAAGTTCCCATC-AGGTTCT-AGTTTTCAATTTAGGGAAAGTTCCCA
1 GTTTTAGTTTAAATTGGGAAAGTTCCCATCAAGGTTCTAAGTTTTCAAATT-GGGAAAGTTCCCA
2190 -TCA-TTTTCA
65 TTCAGTTTTCA
*
2199 GTTTTAGTTTCCAAAGTGGGAAAGTTCCCATC
1 GTTTTAGTTT--AAATTGGGAAAGTTCCCATC
2231 GAAAATTAGT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
70 8 0.09
72 17 0.20
73 18 0.21
74 41 0.48
78 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (75 bp):
GTTTTAGTTTAAATTGGGAAAGTTCCCATCAAGGTTCTAAGTTTTCAAATTGGGAAAGTTCCCAT
TCAGTTTTCA
Found at i:2249 original size:108 final size:106
Alignment explanation
Indices: 2021--2250 Score: 232
Period size: 108 Copynumber: 2.1 Consensus size: 106
2011 TCAATATTCG
* * *
2021 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTTAAATTGGGAAAGTTCCCAACAAG
1 AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTCTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
* * ***
2086 TTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTT
66 TTTTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAATT
* * * * *
2127 CAAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTCTAGTTTTCAATTTAGGGAAAGTTCCCATC
1 --AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTCTAGTTTTCAAATT-GGGAAAGTTCCCAAC
** *
2192 ATTTTCAGTTTTAGTTTCCAAAGTGGGAAAGTTCCCA-TC-GAAAATT
63 AAGTT---TTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAG-AAATT
2238 -AGTTTTAAAATTG
1 AAGTTTTAAAATTG
2251 AGTCGTTTTA
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
108 52 0.52
109 17 0.17
110 1 0.01
111 4 0.04
112 26 0.26
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (106 bp):
AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTCTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
TTTTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAATT
Found at i:8395 original size:26 final size:26
Alignment explanation
Indices: 8366--8427 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
8356 CAAGCCAGTA
*
8366 ATTGAAGCAATTTCAATTACAATTTC
1 ATTGAAGCAATTTCAACTACAATTTC
*
8392 ATTGAAGCAATTTCAGCTACAATTTC
1 ATTGAAGCAATTTCAACTACAATTTC
8418 ATTGAAGCAA
1 ATTGAAGCAA
8428 CCCCTCCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (26 bp):
ATTGAAGCAATTTCAACTACAATTTC
Found at i:14116 original size:21 final size:21
Alignment explanation
Indices: 14077--14124 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
14067 ATTAAAGCAT
14077 ACAAAACAAAAAATAATATAA
1 ACAAAACAAAAAATAATATAA
* *
14098 ATAAAACTAAGAAAT-ATATAA
1 ACAAAAC-AAAAAATAATATAA
14119 ACAAAA
1 ACAAAA
14125 TGTTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.17
Consensus pattern (21 bp):
ACAAAACAAAAAATAATATAA
Found at i:27714 original size:11 final size:11
Alignment explanation
Indices: 27698--27723 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27688 AGATAATTTC
27698 TTTTCTTCTAG
1 TTTTCTTCTAG
27709 TTTTCTTCTAG
1 TTTTCTTCTAG
27720 TTTT
1 TTTT
27724 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:28514 original size:15 final size:15
Alignment explanation
Indices: 28484--28525 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
28474 TTACTTTGCT
28484 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
28500 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
28515 TTGCTTTCTGT
1 TTGTTTTCTGT
28526 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:36355 original size:38 final size:36
Alignment explanation
Indices: 36312--36431 Score: 132
Period size: 36 Copynumber: 3.2 Consensus size: 36
36302 AAAAGGAGCT
* * *
36312 AAAAAAAATTGGACCTAAAATAGAGAGAGGTCGAAA
1 AAAAAAAATTGGACCTAAAATAGAAAGAAGTCAAAA
* * *
36348 AATAAAAACTGGACCTAAAATAGAAATAAGTCCAAAA
1 AAAAAAAATTGGACCTAAAATAGAAAGAAGT-CAAAA
* * *
36385 AGAAAAAAATTGGGCCTAAAACAGAAAGATGTCAAAA
1 A-AAAAAAATTGGACCTAAAATAGAAAGAAGTCAAAA
36422 AAAAAGAAAT
1 AAAAA-AAAT
36432 AAAAAAGGAG
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
36 30 0.43
37 15 0.22
38 24 0.35
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (36 bp):
AAAAAAAATTGGACCTAAAATAGAAAGAAGTCAAAA
Found at i:36799 original size:2 final size:2
Alignment explanation
Indices: 36794--36865 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
36784 TATATATATA
36794 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36836 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.