Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018711.1 Corchorus olitorius cultivar O-4 contig18744, 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: 4985
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:55 original size:39 final size:39
Alignment explanation
Indices: 1--296 Score: 432
Period size: 39 Copynumber: 7.6 Consensus size: 39
** * * *
1 AAAGTTGGTTGGAAACATGCCATATTTTCAGCATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
** *
40 AAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
79 -AAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
*
117 AAAGTTGACTGGAAACAGGTCATCTCTTCAGCATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
** *
156 AAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
* *
195 AAAGTTGACTGGAAACAGGTCATCTCTTCAACATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
* **
234 AAAGTTGACTGGAAACAGGTCATCTTTTTAATATTTATC
1 AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
273 AAAGTTGACTGGAAACAGGTCATC
1 AAAGTTGACTGGAAACAGGTCATC
297 CCTTCTCATT
Statistics
Matches: 238, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 35 0.15
39 203 0.85
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (39 bp):
AAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATC
Found at i:355 original size:33 final size:33
Alignment explanation
Indices: 316--530 Score: 251
Period size: 33 Copynumber: 6.5 Consensus size: 33
306 TTTTAATTTC
316 GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
1 GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
349 GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
1 GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
* * *
382 GACCTCAGACAGGTCTTTCTCAGTTTTAA-TTTC-
1 GACCTCAGACAGGTCTTTATC--TTTCAAGTTCCA
* *
415 GACCTCAGACATGTCTTTATCTTCCAAGTTCCA
1 GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
** * *
448 GACCTCAGACAGGTCTTCCTCAGTTTTAAATT-C-
1 GACCTCAGACAGGTCTTTATC--TTTCAAGTTCCA
* * *
481 GACCTCAGACAGGTCTTTATCTTT-TAGTTTCG
1 GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
513 GACCTCAGACAGGTCTTT
1 GACCTCAGACAGGTCTTT
531 CTTAGTTTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.02
31 8 0.05
32 21 0.13
33 109 0.70
34 4 0.03
35 11 0.07
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.35
Consensus pattern (33 bp):
GACCTCAGACAGGTCTTTATCTTTCAAGTTCCA
Found at i:411 original size:99 final size:97
Alignment explanation
Indices: 299--530 Score: 324
Period size: 99 Copynumber: 2.4 Consensus size: 97
289 AGGTCATCCC
*
299 TTCTCATTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTC
1 TTCTCA-TTTTAATTTCGACCTCAGACAGGTCTTTATCTTCCAAGTTCCAGACCTCAGACAGGTC
* *
364 TTTATC-TTTCAAGTTCCAGACCTCAGACAGGTCT
65 TTCATCATTTCAAATT-C-GACCTCAGACAGGTCT
*
398 TTCTCAGTTTTAATTTCGACCTCAGACATGTCTTTATCTTCCAAGTTCCAGACCTCAGACAGGTC
1 TTCTCA-TTTTAATTTCGACCTCAGACAGGTCTTTATCTTCCAAGTTCCAGACCTCAGACAGGTC
* *
463 TTCCTCAGTTTTAAATTCGACCTCAGACAGGTCT
65 TTCATCA-TTTCAAATTCGACCTCAGACAGGTCT
* *
497 TTATC-TTTTAGTTTCGGACCTCAGACAGGTCTTT
1 TTCTCATTTTAATTTC-GACCTCAGACAGGTCTTT
531 CTTAGTTTTT
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
97 9 0.08
98 17 0.14
99 86 0.72
100 1 0.01
101 7 0.06
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (97 bp):
TTCTCATTTTAATTTCGACCTCAGACAGGTCTTTATCTTCCAAGTTCCAGACCTCAGACAGGTCT
TCATCATTTCAAATTCGACCTCAGACAGGTCT
Found at i:549 original size:66 final size:65
Alignment explanation
Indices: 316--539 Score: 299
Period size: 66 Copynumber: 3.4 Consensus size: 65
306 TTTTAATTTC
* * *
316 GACCTCAGACAGGTCTTTATC--TTTCAAGTTCCAGACCTCAGACAGGTCTTTATCTTTCAAGTT
1 GACCTCAGACAGGTCTTTCTCAGTTTTAAATT-C-GACCTCAGACAGGTCTTTATCTTT-AAGTT
379 CCA
63 CCA
* * *
382 GACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACATGTCTTTATCTTCCAAGTTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTTAAATTCGACCTCAGACAGGTCTTTATCTT-TAAGTTCC
447 A
65 A
* * * *
448 GACCTCAGACAGGTCTTCCTCAGTTTTAAATTCGACCTCAGACAGGTCTTTATCTTTTAGTTTCG
1 GACCTCAGACAGGTCTTTCTCAGTTTTAAATTCGACCTCAGACAGGTCTTTATCTTTAAGTTCCA
*
513 GACCTCAGACAGGTCTTTCTTAGTTTT
1 GACCTCAGACAGGTCTTTCTCAGTTTT
540 TAAGGTCGAC
Statistics
Matches: 141, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
65 30 0.21
66 103 0.73
67 1 0.01
68 7 0.05
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (65 bp):
GACCTCAGACAGGTCTTTCTCAGTTTTAAATTCGACCTCAGACAGGTCTTTATCTTTAAGTTCCA
Done.