Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016171.1 Corchorus olitorius cultivar O-4 contig16204, 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: 6198
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Found at i:2994 original size:93 final size:93
Alignment explanation
Indices: 2882--3065 Score: 260
Period size: 93 Copynumber: 2.0 Consensus size: 93
2872 AGTTTTGCAT
* * ** *
2882 GATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATATAGTCAAATCTCAGTCAAATTGGA
1 GATTTTGGGCACCAAGACTCCTTGAAATATCTAAATTCATATAACCAAATCTCAGCCAAATTGGA
2947 TTTAAGGATTTGGTTTTACAAGCATCAA
66 TTTAAGGATTTGGTTTTACAAGCATCAA
* * * * *
2975 GATTTTGGGCACCCAGACTCCTTGAAATATTTAAATTTATCTAACCAAATCTCAGCCACATTGGA
1 GATTTTGGGCACCAAGACTCCTTGAAATATCTAAATTCATATAACCAAATCTCAGCCAAATTGGA
* *
3040 TTTAAGGATTTGTTTTTACGAGCATC
66 TTTAAGGATTTGGTTTTACAAGCATC
3066 TGAATCTTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (93 bp):
GATTTTGGGCACCAAGACTCCTTGAAATATCTAAATTCATATAACCAAATCTCAGCCAAATTGGA
TTTAAGGATTTGGTTTTACAAGCATCAA
Found at i:3557 original size:42 final size:42
Alignment explanation
Indices: 3502--3587 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
3492 TATTGTGGAC
*
3502 AAAAATTGAGGACATATCTTTTGGGTCAATTTTTTTTTACAA
1 AAAAATTGAGGACATATCTTTTAGGTCAATTTTTTTTTACAA
3544 AAAAATTGAGGACATATCTTTTAGGTCAATTTTTTTTTACAA
1 AAAAATTGAGGACATATCTTTTAGGTCAATTTTTTTTTACAA
3586 AA
1 AA
3588 TTTTAGCTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (42 bp):
AAAAATTGAGGACATATCTTTTAGGTCAATTTTTTTTTACAA
Found at i:4379 original size:327 final size:321
Alignment explanation
Indices: 3577--4735 Score: 913
Period size: 327 Copynumber: 3.6 Consensus size: 321
3567 GGTCAATTTT
* * ** * *
3577 TTTTTACAAAATTTTAGCTGAAATCGTGTAATAACCATCACGGTTTTTAACTAAAACCGCTTTCC
1 TTTTTACAAAATTTTAGCTCAAATCGTG-----ACCATCACAGTTTTTGGCTAAAAACGCGTTCC
** * * * * * * *
3642 GGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGGAATATCTATATTCATCT
61 GGGA-CCTAGCTCAGTTTTGCATGATTTTTGGCGCAAATACTCATTGAAATATCTATATTAATCT
* * * * * * **
3707 AGTCAAATCTCAGTCAAATTGGATTTAAGGATTTGGTTTTACAAGCATC-AGAATGTTGTTTCGA
125 AATCAAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTA-AATCATGTTTCGA
* *** ** * *
3771 TTTTAATTCGGGAAA--AA--A-AGGGA-AA-AC-AATATTTTAAGCGTGAAAAG-CCTTTTAA-
189 -TTTAA-TC-AGAAATTAATTAGAAAAATAATACGAATATTAGAAGCATGAAAAGTCC--TCAAT
* * *
3826 TCTTTTTGTG--TTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAA-TTGAGGAAAAATTT
249 TATTTTTG-GCATTGAATTATATATTTTTTATAAGTATTGTGGC-AAAAAGTTGAGGAAAAATCT
* **
3888 TTCAAGTCAA
312 TACGGGTCAA
* * * * *
3898 TTTTTGCAAAATCTTAGCTAAAATCATGTACTAACTATCACAGTTTTTGCCTAAAAACGCGTTCC
1 TTTTTACAAAATTTTAGCTCAAATCGTG-AC---C-ATCACAGTTTTTGGCTAAAAACGCGTTCC
* * * * * ** *
3963 GGGGCCCCAGCTCAGTTTTACATGATTTTTTGCACCCATACTCATTGAAATATCTATATTTATCT
61 -GGGACCTAGCTCAGTTTTGCATGATTTTTGGCGCAAATACTCATTGAAATATCTATATTAATCT
* * *
4028 AA-CAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTTTTTCGAT
125 AATCAAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGAT
* * *
4092 TTAATTAGAAATTAATTCAGAGAAACTAAGATAAACG-ATATTAGAAGCGTGAAAAGTCCTCCAA
190 TTAATCAGAAATTAATT-AGA-AAAAT-A-AT--ACGAATATTAGAAGCATGAAAAGTCCT-CAA
* * * *
4156 -TCTTTTTGGCATTGATTTATA-ATTTTTTTATAAGTATTTTGGCAAAAAATTTGAGGAAAAATC
248 TTATTTTTGGCATTGAATTATATA-TTTTTTATAAGTATTGTGGC-AAAAAGTTGAGGAAAAATC
4219 TTACGGGTCAA
311 TTACGGGTCAA
**
4230 TTTTTTGTAAAATTTTAG-TCCAAATCGTG-CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGG
1 -TTTTTACAAAATTTTAGCT-CAAATCGTGACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGG
*** * *
4293 ACCTAGCTCAGTTTTGCATGATTTTTGGCGTTGATACTCCTTGAAATATCTATATTCATCTAATC
64 ACCTAGCTCAGTTTTGCATGATTTTTGGCGCAAATACTCATTGAAATATCTATATTAATCTAATC
* * * * *
4358 AAATCAAAGCTACAGTGGATTTAAGGATTTGTTTTTACGAGCCTCTGAATCATGTTTCGATTTAA
129 AAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAA
* * * * *
4423 TCATAAATTAATTTGAAAAATAATAGGAATATTAGAAGCATGAAAAGTCCTTAATTATTTTTGGT
194 TCAGAAATTAATTAGAAAAATAATACGAATATTAGAAGCATGAAAAGTCCTCAATTATTTTTGGC
* * * * * * ** *
4488 GTTGAATTATATATTTTTTATGAGTATTGTGGCCAGAAGTTGAGGAAAATTTTTTTGGTTCAA
259 ATTGAATTATATATTTTTTATAAGTATTGTGGCAAAAAGTTGAGGAAAAATCTTACGGGTCAA
* * *
4551 TTTTTACAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACACGTTCC
1 TTTTTACAAAATTTTAGCTCAAATCGTG-----ACCATCACAGTTTTTGGCTAAAAACGCGTTCC
* * * * * * *
4616 GAGGTCCT-GTCTCAGTTTTGCATTATTTTTGGTGCAAAGACTCGTTAAAATATATTTATATTAA
61 G-GGACCTAG-CTCAGTTTTGCATGATTTTTGGCGCAAATACTCATT-GAA-ATATCTATATTAA
* *
4680 TCT-ATCTAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAA
122 TCTAATC-AAATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAA
4736 CTATATATGC
Statistics
Matches: 682, Mismatches: 112, Indels: 80
0.78 0.13 0.09
Matches are distributed among these distances:
317 6 0.01
318 1 0.00
319 7 0.01
320 76 0.11
321 128 0.19
322 61 0.09
323 4 0.01
324 1 0.00
325 4 0.01
326 90 0.13
327 132 0.19
328 6 0.01
329 58 0.09
330 30 0.04
331 35 0.05
332 21 0.03
333 22 0.03
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (321 bp):
TTTTTACAAAATTTTAGCTCAAATCGTGACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGAC
CTAGCTCAGTTTTGCATGATTTTTGGCGCAAATACTCATTGAAATATCTATATTAATCTAATCAA
ATCTAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATC
AGAAATTAATTAGAAAAATAATACGAATATTAGAAGCATGAAAAGTCCTCAATTATTTTTGGCAT
TGAATTATATATTTTTTATAAGTATTGTGGCAAAAAGTTGAGGAAAAATCTTACGGGTCAA
Done.