Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020990.1 Corchorus olitorius cultivar O-4 contig21023, 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: 14389
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1531 original size:16 final size:17
Alignment explanation
Indices: 1505--1536 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1495 GTGACAAATT
1505 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
1522 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
1537 ACGCAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:11069 original size:375 final size:375
Alignment explanation
Indices: 10622--11396 Score: 1230
Period size: 375 Copynumber: 2.1 Consensus size: 375
10612 TGGTCTCAAG
* * *
10622 AGAAGAAAAAGAGGATGTGGGTGGAGAGGCGAATTAATCTCAAGAGGTAGATCCTCAGCACAGTG
1 AGAAGAAAAAGAGGGTGTGGGTGGAAAGGCGAATTAATCTCAAGAGGTAGATCCTCAGCACAATG
* * * *
10687 TTTATGAAGGTCAGAGCCAAAGTCCATGCAACCCAAACATCTGTAGAAGGGTCCTGATAGTTTTT
66 TTTATGAAGGTCAGAGCCAAAGTCAACGCAACCCAAACAACTGCAGAAGGGTCCTGATAGTTTTT
* * * *
10752 CCCCACATGCGTCGCAACAACAATCATAAAGTAATCTCTTGGTAGGCATTGCAATAAGTAACAAA
131 CCCCACATGCATCGCAACAACAATCATAAAGTAAACTCTCGGTAGGCATTGCAATAAGCAACAAA
* *
10817 GGATGCGGGTGGCTAAAATGTTCGAGCAGAGAAA-TATTTCCAAAAGTGGATAGTGGAAGAAAGG
196 GGATGCGGGTGGCTAAAATGTTCAAGCAGAGAAAGT-TTTCCAAAAGTGGACAGTGGAAGAAAGG
* *
10881 CACAGTAGATGTCTAGGAAGAAATCACAAGTCTTGCATTGAAAAACAAATCCCAAACATTTATAG
260 CACAGTAGATGTCTAGGAAGAAATCACAAGTCTTACAGTGAAAAACAAATCCCAAACATTTATAG
10946 CGACATAAACTACAAAAGCA-TGATTTATCTTCAGGGTATGGTGAACTTGGC
325 CGACATAAACTACAAAAGCATTG-TTTATCTTCAGGGTATGGTGAACTTGGC
*
10997 AGAAGAAAAAGAGGGTGTGGGTGGAAAGGCGGATTAATCTCAAGAGGTAGATCCTCAGCACAATG
1 AGAAGAAAAAGAGGGTGTGGGTGGAAAGGCGAATTAATCTCAAGAGGTAGATCCTCAGCACAATG
11062 TTTATGAAGGTCAGAGCCAAAGTCAACGCAACCCAAACAACTGCAGAAGGGTCCTGATAGTTTTT
66 TTTATGAAGGTCAGAGCCAAAGTCAACGCAACCCAAACAACTGCAGAAGGGTCCTGATAGTTTTT
* * * * *
11127 CCTCACATGCATCGCAACAACAATCATCAAGTAAACTCTCGGTGGGCTTTTCAATAAGCAACAAA
131 CCCCACATGCATCGCAACAACAATCATAAAGTAAACTCTCGGTAGGCATTGCAATAAGCAACAAA
** * *
11192 GGATGTTGGTGGCTACAATGTTCAAGTAGAGAAAGTTTTCCAAAAGTGGACAGTGGAAGAAAGGC
196 GGATGCGGGTGGCTAAAATGTTCAAGCAGAGAAAGTTTTCCAAAAGTGGACAGTGGAAGAAAGGC
* * *
11257 ACAGTCGATGTCTTGGAAGAAATCACAAGTCTTACAGTGAAAAACATATCCCAAACATTTATAGC
261 ACAGTAGATGTCTAGGAAGAAATCACAAGTCTTACAGTGAAAAACAAATCCCAAACATTTATAGC
* * *
11322 GACATAAGCTACAAAAGCATTGTTTATCTTGAGGGTATGGTGAATTTGGC
326 GACATAAACTACAAAAGCATTGTTTATCTTCAGGGTATGGTGAACTTGGC
*
11372 AGAAGAATAAGAGGGTGTGGGTGGA
1 AGAAGAAAAAGAGGGTGTGGGTGGA
11397 TAGGATTATC
Statistics
Matches: 366, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
375 363 0.99
376 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (375 bp):
AGAAGAAAAAGAGGGTGTGGGTGGAAAGGCGAATTAATCTCAAGAGGTAGATCCTCAGCACAATG
TTTATGAAGGTCAGAGCCAAAGTCAACGCAACCCAAACAACTGCAGAAGGGTCCTGATAGTTTTT
CCCCACATGCATCGCAACAACAATCATAAAGTAAACTCTCGGTAGGCATTGCAATAAGCAACAAA
GGATGCGGGTGGCTAAAATGTTCAAGCAGAGAAAGTTTTCCAAAAGTGGACAGTGGAAGAAAGGC
ACAGTAGATGTCTAGGAAGAAATCACAAGTCTTACAGTGAAAAACAAATCCCAAACATTTATAGC
GACATAAACTACAAAAGCATTGTTTATCTTCAGGGTATGGTGAACTTGGC
Found at i:11678 original size:39 final size:39
Alignment explanation
Indices: 11624--11726 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 39
11614 CTCAGGAATG
11624 TGATCATTTTCTTCTTCTGCAGCCTCAGAAATGTCATCT
1 TGATCATTTTCTTCTTCTGCAGCCTCAGAAATGTCATCT
* * ** * *
11663 TGATCAGTTTCTTCTTCTTCTACGGTGTCTGGAATGTCATCT
1 TGATCA--TT-TTCTTCTTCTGCAGCCTCAGAAATGTCATCT
*
11705 TGATCATTTTCTTCTTTTGCAG
1 TGATCATTTTCTTCTTCTGCAG
11727 TCTTAGGAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
39 17 0.33
40 2 0.04
41 2 0.04
42 31 0.60
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.46
Consensus pattern (39 bp):
TGATCATTTTCTTCTTCTGCAGCCTCAGAAATGTCATCT
Found at i:11736 original size:39 final size:39
Alignment explanation
Indices: 11524--11738 Score: 138
Period size: 39 Copynumber: 5.8 Consensus size: 39
11514 AACAAGCTTC
* * * ** *
11524 ATCATTTTCTCCTTCTGTAGTCTCAGGAAAATCATGTTG
1 ATCATTTTCTTCTTTTGCAGTCTCAGGAATGTCATCTTG
* * *
11563 ATCATTTTC-TCCTAT-C--TC-CA-GAATGTCATCTCG
1 ATCATTTTCTTCTTTTGCAGTCTCAGGAATGTCATCTTG
11596 ATCATTTTCTTC---TGCAGTCTCAGGAATG------TG
1 ATCATTTTCTTCTTTTGCAGTCTCAGGAATGTCATCTTG
* * *
11626 ATCATTTTCTTCTTCTGCAGCCTCAGAAATGTCATCTTG
1 ATCATTTTCTTCTTTTGCAGTCTCAGGAATGTCATCTTG
* * *
11665 ATCAGTTTCTTCTTCTT-CTACGGTGTCTGGAATGTCATCTTG
1 ATCATTTTCTTCTT-TTGC-A--GTCTCAGGAATGTCATCTTG
*
11707 ATCATTTTCTTCTTTTGCAGTCTTAGGAATGT
1 ATCATTTTCTTCTTTTGCAGTCTCAGGAATGT
11739 TGTCATCTTG
Statistics
Matches: 135, Mismatches: 21, Indels: 40
0.69 0.11 0.20
Matches are distributed among these distances:
30 13 0.10
31 1 0.01
32 1 0.01
33 32 0.24
34 6 0.04
35 4 0.03
36 5 0.04
38 3 0.02
39 35 0.26
40 2 0.01
41 3 0.02
42 30 0.22
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (39 bp):
ATCATTTTCTTCTTTTGCAGTCTCAGGAATGTCATCTTG
Done.