Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007399.1 Corchorus olitorius cultivar O-4 contig07424, 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, 670
Length: 1118
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Found at i:524 original size:39 final size:39
Alignment explanation
Indices: 481--927 Score: 263
Period size: 39 Copynumber: 11.2 Consensus size: 39
471 CAAAGACTTG
*
481 AGCAGGTTTGCTTAAACAGAAATTCTAAACAAGGACCTA
1 AGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTA
* * ** *
520 AGCAGGTTTGCTTAAAC-GAGATTCTAAATGTA-GA-CTT
1 AGCAGGTTTACTTAAACAGAAATTCTAAA-CAAGGACCTA
* * *
557 AGCAGGTTCACTTAAACGGAAATTCTAAAC-AGTGACCTG
1 AGCAGGTTTACTTAAACAGAAATTCTAAACAAG-GACCTA
* *
596 AGCAGGTTTTACTTGAAC-GAGAATTCTAAATAAGGACCTA
1 AGCAGG-TTTACTTAAACAGA-AATTCTAAACAAGGACCTA
* * * *
636 AGCAGGTTTGCTT--ACATGAGATTCTGAACGAGGACCTA
1 AGCAGGTTTACTTAAACA-GAAATTCTAAACAAGGACCTA
* *
674 AGCAGGTTTTCTTAAACAGAAATTCTAATGAGATTCTAAACATAGACCTA
1 AGCAGGTTTACTTAAACAGAAATTCT-A--A-A--C---A-A-GGACCTA
* * * ** *
724 AGCAGGTTTCCTTGATCA-AAGCTCTAAGC-AGAGATCCTA
1 AGCAGGTTTACTTAAACAGAAATTCTAAACAAG-GA-CCTA
* * *
763 AGCAGGTTCACTTAAACAGAAATTTTACACAAGGACCTA
1 AGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTA
* * * *
802 AGCAGGTTCAATTAAAC-GAAACTCCTAAACGTA-GACCTA
1 AGCAGGTTTACTTAAACAGAAA-TTCTAAAC-AAGGACCTA
* * ** * *
841 AGCAGGTTCACTTAAACGGGCATTCTACACAAGAACCTA
1 AGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTA
* *
880 AACAGGTTTGA-TTGAAC-GAAAGTTCTAAACAAGGACCTA
1 AGCAGGTTT-ACTTAAACAGAAA-TTCTAAACAAGGACCTA
919 AGCAGGTTT
1 AGCAGGTTT
928 GCTAAGATAA
Statistics
Matches: 316, Mismatches: 59, Indels: 66
0.72 0.13 0.15
Matches are distributed among these distances:
36 1 0.00
37 19 0.06
38 61 0.19
39 154 0.49
40 44 0.14
41 4 0.01
42 1 0.00
43 2 0.01
45 1 0.00
46 1 0.00
48 1 0.00
49 6 0.02
50 21 0.07
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (39 bp):
AGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTA
Found at i:579 original size:76 final size:74
Alignment explanation
Indices: 473--701 Score: 237
Period size: 76 Copynumber: 3.0 Consensus size: 74
463 AAACGGAACA
*
473 AAGACTTGAGCAGGTTTGCTTAAACAGAAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACG
1 AAGACTT-AGCAGGTTTGCTTAAACAGAAATTCTAAAC-AGGACCTAAGCAGGTTTACTTAAACG
538 AGATTCTAAAT
64 AGATTCTAAAT
* ** * * *
549 GTAGACTTAGCAGGTTCACTTAAACGGAAATTCTAAACAGTGACCTGAGCAGGTTTTACTTGAAC
1 -AAGACTTAGCAGGTTTGCTTAAACAGAAATTCTAAACAG-GACCTAAGCAGG-TTTACTTAAAC
614 GAGAATTCTAAAT
63 GAG-ATTCTAAAT
* * * *
627 AAGGACCTAAGCAGGTTTGCTT--ACATGAGATTCTGAACGAGGACCTAAGCAGGTTTTCTTAAA
1 AA-GA-CTTAGCAGGTTTGCTTAAACA-GAAATTCTAAAC-AGGACCTAAGCAGGTTTACTTAAA
*
690 CAGAAATTCTAA
62 C-GAGATTCTAA
702 TGAGATTCTA
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
75 2 0.02
76 38 0.30
77 37 0.29
78 34 0.27
79 15 0.12
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (74 bp):
AAGACTTAGCAGGTTTGCTTAAACAGAAATTCTAAACAGGACCTAAGCAGGTTTACTTAAACGAG
ATTCTAAAT
Found at i:582 original size:38 final size:36
Alignment explanation
Indices: 473--701 Score: 152
Period size: 38 Copynumber: 5.9 Consensus size: 36
463 AAACGGAACA
473 AAGACTTGAGCAGGTTTGCTTAAACAGAAATTCTAAAC
1 AAGACTT-AGCAGGTTTGCTTAAAC-GAAATTCTAAAC
* * *
511 AAGGACCTAAGCAGGTTTGCTTAAACGAGATTCTAAATG
1 AA-GA-CTTAGCAGGTTTGCTTAAACGAAATTCTAAA-C
* **
550 TAGACTTAGCAGGTTCACTTAAACGGAAATTCTAAAC
1 AAGACTTAGCAGGTTTGCTTAAAC-GAAATTCTAAAC
* * * * *
587 AGTGACCTGAGCAGGTTTTACTTGAACGAGAATTCTAAAT
1 A-AGA-CTTAGCAGG-TTTGCTTAAACGA-AATTCTAAAC
* * * * *
627 AAGGACCTAAGCAGGTTTGCTTACATGAGATTCTGAAC
1 AA-GA-CTTAGCAGGTTTGCTTAAACGAAATTCTAAAC
* * *
665 GAGGACCTAAGCAGGTTTTCTTAAACAGAAATTCTAA
1 -AAGA-CTTAGCAGGTTTGCTTAAAC-GAAATTCTAA
702 TGAGATTCTA
Statistics
Matches: 150, Mismatches: 30, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
37 17 0.11
38 53 0.35
39 48 0.32
40 32 0.21
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (36 bp):
AAGACTTAGCAGGTTTGCTTAAACGAAATTCTAAAC
Found at i:637 original size:116 final size:116
Alignment explanation
Indices: 479--926 Score: 316
Period size: 117 Copynumber: 3.8 Consensus size: 116
469 AACAAAGACT
*
479 TGAGCAGGTTTGCTTAAACAGAAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACGAGATTC
1 TGAGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACGAGATTC
* * *
544 TAAATGTA-GA-CTTAGCAGGTTCACTTAAACGGAAATTCTAAACAGTGACC
66 TAAACG-AGGACCTAAGCAGGTTCACTTAAACAGAAATTCTAAACAGTGACC
* * * *
594 TGAGCAGGTTTTACTTGAAC-GAGAATTCTAAATAAGGACCTAAGCAGGTTTGCTTACATGAGAT
1 TGAGCAGG-TTTACTTAAACAGA-AATTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACGAGAT
* ** *
658 TCTGAACGAGGACCTAAGCAGGTTTTCTTAAACAGAAATTCTAATGAGATTCTAAACATAGACC
64 TCTAAACGAGGACCTAAGCAGGTTCACTTAAACAGAAATTCT-A--A-A--C---A-GT-GACC
* * * * ** * ** *
722 TAAGCAGGTTTCCTTGATCA-AAGCTCTAAGC-AGAGATCCTAAGCAGGTTCACTTAAACAGAAA
1 TGAGCAGGTTTACTTAAACAGAAATTCTAAACAAG-GA-CCTAAGCAGGTTTGCTTAAAC-GAGA
* * * * *
785 TTTTACACAAGGACCTAAGCAGGTTCAATTAAAC-GAAACTCCTAAAC-GTAGACC
63 TTCTAAACGAGGACCTAAGCAGGTTCACTTAAACAGAAA-TTCTAAACAGT-GACC
* * * ** * * * * * *
839 TAAGCAGGTTCACTTAAACGGGCATTCTACACAAGAACCTAAACAGGTTTGATTGAACGAAAGTT
1 TGAGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACGAGA-TT
*
904 CTAAACAAGGACCTAAGCAGGTT
65 CTAAACGAGGACCTAAGCAGGTT
927 TGCTAAGATA
Statistics
Matches: 258, Mismatches: 52, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
115 11 0.04
116 59 0.23
117 85 0.33
118 7 0.03
119 2 0.01
120 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 1 0.00
125 3 0.01
126 9 0.03
127 33 0.13
128 44 0.17
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (116 bp):
TGAGCAGGTTTACTTAAACAGAAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACGAGATTC
TAAACGAGGACCTAAGCAGGTTCACTTAAACAGAAATTCTAAACAGTGACC
Done.