Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018280.1 Corchorus olitorius cultivar O-4 contig18313, 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: 33398
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Found at i:90 original size:25 final size:25
Alignment explanation
Indices: 1--83 Score: 121
Period size: 25 Copynumber: 3.3 Consensus size: 25
* *
1 CGTTTACTAAACGCAAACACAGGTT
1 CGTTTGCTAAACGCAAACACAGGCT
* *
26 CGTTTTCCAAACGCAAACACAGGCT
1 CGTTTGCTAAACGCAAACACAGGCT
*
51 CGTTTGCTAAACGCAAGCACAGGCT
1 CGTTTGCTAAACGCAAACACAGGCT
76 CGTTTGCT
1 CGTTTGCT
84 CAGCGCACGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (25 bp):
CGTTTGCTAAACGCAAACACAGGCT
Found at i:914 original size:16 final size:16
Alignment explanation
Indices: 892--931 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
882 CGGTCCCCGC
892 AATCCGCTTGATCTTA
1 AATCCGCTTGATCTTA
*
908 TATCCGCTTGATCTTA
1 AATCCGCTTGATCTTA
924 AATCCGCT
1 AATCCGCT
932 GCAACCAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (16 bp):
AATCCGCTTGATCTTA
Found at i:6212 original size:25 final size:24
Alignment explanation
Indices: 6184--6240 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
6174 GTGGATTGTA
* *
6184 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTAAAGAATTAA-ACATT
6209 AAATAAATTAAAGAATTAAACATT
1 AAATAAATTAAAGAATTAAACATT
6233 AAA-AAATT
1 AAATAAATT
6241 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (24 bp):
AAATAAATTAAAGAATTAAACATT
Found at i:7234 original size:105 final size:105
Alignment explanation
Indices: 6999--7190 Score: 269
Period size: 105 Copynumber: 1.8 Consensus size: 105
6989 AGTAAAATGG
* *
6999 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTATTTGAGT
1 TAAAAAT-AAATAGGTATAAGGACATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGT
*** * *
7064 AAAACTATAAAAGTATATTTAAAAATTCTAATATATAAAAA
65 AAAACTATAAAAGTATAAACAAAAATTCTAAGAAATAAAAA
*
7105 TAAAAATCAAATAGTTATAAGGACATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGT
1 TAAAAAT-AAATAGGTATAAGGACATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGT
* *
7169 AAAACTATGAAAGTTTAAACAA
65 AAAACTATAAAAGTATAAACAA
7191 TGACATTTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 39 0.51
106 38 0.49
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (105 bp):
TAAAAATAAATAGGTATAAGGACATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTA
AAACTATAAAAGTATAAACAAAAATTCTAAGAAATAAAAA
Found at i:8899 original size:37 final size:37
Alignment explanation
Indices: 8851--8921 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
8841 AGTTATCGGG
*
8851 AAAAAAGGACATGACTATGGAGAAGGCAGAATAGGGA
1 AAAAAAGGACATGAATATGGAGAAGGCAGAATAGGGA
*
8888 AAAAAATGACATGAATATGGAGAAGGCAGAATAG
1 AAAAAAGGACATGAATATGGAGAAGGCAGAATAG
8922 TACATATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.30, T:0.13
Consensus pattern (37 bp):
AAAAAAGGACATGAATATGGAGAAGGCAGAATAGGGA
Found at i:31202 original size:325 final size:324
Alignment explanation
Indices: 30349--31216 Score: 811
Period size: 331 Copynumber: 2.6 Consensus size: 324
30339 CCATGATGGT
* * * * * *
30349 AAAAA-TGACCCGAAATATTTTTCCTCAATTTTTGGTAAAAATACTCA-ACATATATATATATAT
1 AAAAATTGACCCAAAAGATATTTCCTCAATTCTTAGAAAAAATACTCATA-A-A-A-A-ATATAT
* * *
30412 ATAATTCAACACCAAAAAGATTG-AAGGATTTTTCACGCTTTTTATATCGTTT-TTCATATTTTT
61 A-AATTCAACACCAAAAAGATTGAAAGG-CTTTTCACGCTTCTAATATCGTTTATT--T-TTTTT
* *
30475 CTGAATTAATTTCTAATTAAATCGAAACTTA-ATTTAGATGCACATAAAAACAAATCCTTAAATC
121 C-GAATTAATTTCTAATTAAATCGAAAC-AAGATTTAGATGCTCATAAAAACAAATCCTTAAAT-
** * **
30539 CAATGTGGCTGAGAAGTGATTAGATGAATAAAAATTTATAAAGAAGTTTCGGTGCCAAAAATCAT
183 CAATGTGGCTGAGATTTGATTAGATGAATAAAAATTTACAAAGAAGTTTCGGTGAAAAAAATCAT
* * ** *
30604 GCAAAATAGAGCCATGGCCCTGTAACATGTTTTTAGCCAAAACCGTGATGGTAGTACACGATTTC
248 GCAAAATAGAGCCAGGGCCCTGGAACACATTTTTAGCCAAAACCGTGAT-GTAGTACAC-ATATC
30669 GGCTAAAATTTGGC
311 GGCTAAAATTTGGC
* * * **
30683 AAAAATTGTCCCGAAAGATATTTCCTCAATTCTTGGCTAAAATACTCATAAAAAATATAT-AATT
1 AAAAATTGACCCAAAAGATATTTCCTCAATTCTTAGAAAAAATACTCATAAAAAATATATAAATT
* * * ** *
30747 CGACATCAAAAAGATTGAAGGGCTTTGAACGCTTCTAATATTGTTTTTCCAATTTTTTTTCGAAT
66 CAACACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCG--TTT---ATTTTTTTTCGAAT
* * *
30812 TAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAATA-AAATCCTTAAATCTAATGT
126 TAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAA-ACAAATCCTTAAATC-AATGT
* * *
30876 GGCTGAGATTTGGTTAGATGAATATAGATATTT-CAAAG-AGTTTTGGT-AAAAAAATTCATGCA
189 GGCTGAGATTTGATTAGATGAATA-A-AAATTTACAAAGAAGTTTCGGTGAAAAAAA-TCATGCA
*
30938 AAACT-GAGCC-GGG-CCTCGGAACGCATTTTTAGCCGAAAACTACGATGAT-TAGTACA-A-AT
251 AAA-TAGAGCCAGGGCCCT-GGAACACATTTTTAGCC-AAAAC--CG-TGATGTAGTACACATAT
*
30997 -GGCT-AAATTTTGC
310 CGGCTAAAATTTGGC
* * * * *
31010 AAAAATTGACCTAAAAGATTTTTCCTCGATT-TATATAAAAAATACTCATAAAAGATATATAAAT
1 AAAAATTGACCCAAAAGATATTTCCTCAATTCT-TAGAAAAAATACTCATAAAAAATATATAAAT
* * * * *
31074 TCAACGCCAAAAAAATTGAAAGCCTTGTTCACGCTTCTAATATCGTTTATTTTATTTCAAAATTA
65 TCAACACCAAAAAGATTGAAAGGCTT-TTCACGCTTCTAATATCGTTTATTTTTTTTC-GAATTA
* **
31139 ACTTCTAATTAAATCGAAACAAGATTTAGAAACTCATAAAAACAAATCCTTAAATACAATGTGGC
128 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAAT-CAATGTGGC
31204 TGAGATTTGATTA
192 TGAGATTTGATTA
31217 TATATATATA
Statistics
Matches: 444, Mismatches: 63, Indels: 63
0.78 0.11 0.11
Matches are distributed among these distances:
324 10 0.02
325 72 0.16
326 2 0.00
327 59 0.13
328 27 0.06
329 53 0.12
330 26 0.06
331 115 0.26
332 21 0.05
333 9 0.02
334 10 0.02
335 39 0.09
336 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (324 bp):
AAAAATTGACCCAAAAGATATTTCCTCAATTCTTAGAAAAAATACTCATAAAAAATATATAAATT
CAACACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTATTTTTTTTCGAATTAATT
TCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCAATGTGGCTGAG
ATTTGATTAGATGAATAAAAATTTACAAAGAAGTTTCGGTGAAAAAAATCATGCAAAATAGAGCC
AGGGCCCTGGAACACATTTTTAGCCAAAACCGTGATGTAGTACACATATCGGCTAAAATTTGGC
Found at i:32713 original size:16 final size:16
Alignment explanation
Indices: 32694--32737 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
32684 ACCCGCCCGA
*
32694 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
32710 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
32726 ACCCGAACCCGA
1 ACCCGAACCCGA
32738 CCCGAGACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.41, G:0.16, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:32896 original size:2 final size:2
Alignment explanation
Indices: 32859--32885 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32849 AAACTACTAA
32859 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
32886 AAACTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33200 original size:31 final size:31
Alignment explanation
Indices: 33129--33200 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
33119 GTCTATCAAC
*
33129 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
33160 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
33190 GTTTTAATTTG
1 -TTTTAATTTG
33201 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Done.