Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397929.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1234.0, 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: 11891
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.27
Warning! 2998 characters in sequence are not A, C, G, or T
Found at i:2303 original size:171 final size:170
Alignment explanation
Indices: 1966--2806 Score: 700
Period size: 171 Copynumber: 4.9 Consensus size: 170
1956 NNNNAGCGAG
* * * * **
1966 TAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGGAAATGAATAG-CTTTTT
1 TAATAA-GATTTTGAAAGAATGGGTGACTATAAATGGACTTTTCCTGCCAATGAA-AGCCTTTTT
*** * *** **
2030 CCACATGTTTCCTGAA-GTAGACATTCAATTA-CGGTCTGTTTTAATGAAAAAT-TAAAAAGAAA
64 TTTCATGTTT-CTCAAGGTAGACATTCAATTATTACTCTGTTTTAA-CCAAAATGTAAAAA-AAA
*
2092 -TCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGTAA
126 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTAA
* ** *
2136 GTAATAAGATTTTGAAAGAATGGGTTACTGCAAATGGACTTTTCCTGCCAATGAAAGTCTTTTTT
1 -TAATAAGATTTTGAAAGAATGGGTGACTATAAATGGACTTTTCCTGCCAATGAAAGCCTTTTTT
* ** * * *
2201 TTCATGTTTTTTGAGGTAGACATTCGATTATTACT-TGTTTTAATCTAAATGTAAAAAAAAATTC
65 TTCATGTTTCTCAAGGTAGACATTCAATTATTACTCTGTTTTAACCAAAATGT-AAAAAAAATTC
* * *
2265 AACTTAAACTCAATTATGAGAGTATAAAACCATTTAAAGCGAA
129 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-TAA
* ********** * ** * * *
2308 TAATAAGGCTTTTNNNNNNNNNNGTGACTATAAATGGACTTTTCTTGGTAATGAATGGCTTTTTC
1 TAATAA-GATTTTGAAAGAATGGGTGACTATAAATGGACTTTTCCTGCCAATGAAAGCCTTTTTT
** * * * ** ***
2373 CACATGTTTC-CTAATGTAAACATTCAATTA-TAGTCTGTTTTAATGAAAAATGT-AAAAAANNN
65 TTCATGTTTCTC-AAGGTAGACATTCAATTATTACTCTGTTTTAA-CCAAAATGTAAAAAAAATT
******* * **
2435 NNNNNNNAAATTAATTATGAGATTATAAAACCATTTAAAGTGGG
128 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGT-AA
* * * * *
2479 TAATAAGATTTTGAAAGAATGGGTTACTATAAATAGACTTTTCTTTCCAATGAAAGCCTCTTTTT
1 TAATAAGATTTTGAAAGAATGGGTGACTATAAATGGACTTTTCCTGCCAATGAAAGCCTTTTTTT
* * * *
2544 TCATATTTTTCAAGGTAGACATTCAATTATTGCT-TGTTTTAACCAAAATGTGAAAAAAATTCAA
66 TCATGTTTCTCAAGGTAGACATTCAATTATTACTCTGTTTTAACCAAAATGTAAAAAAAATTCAA
* *
2608 CTTAAAATCAATTATAAGACTATAAAACCATTTAAAGTGAA
131 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGT-AA
* *
2649 TAATAAGACTTTTGAATGAATGGGTGACTATAAATGGACTTTT-CTAGCCAATGAAGGCCTTTTT
1 TAATAAGA-TTTTGAAAGAATGGGTGACTATAAATGGACTTTTCCT-GCCAATGAAAGCCTTTTT
* *
2713 TTTCATGTTTCTCGAGGTAGACATTCAATTATTA-TCTGTTCTAACCAAAAATGT-AAAAAAATT
64 TTTCATGTTTCTCAAGGTAGACATTCAATTATTACTCTGTTTTAACC-AAAATGTAAAAAAAATT
* *
2776 TAACTTAAAATCAATTATGAGATCATAAAAC
128 CAACTTAAAATCAATTATGAGATTATAAAAC
2807 TNNNNNNNNN
Statistics
Matches: 516, Mismatches: 135, Indels: 38
0.75 0.20 0.06
Matches are distributed among these distances:
169 15 0.03
170 194 0.38
171 225 0.44
172 76 0.15
173 6 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (170 bp):
TAATAAGATTTTGAAAGAATGGGTGACTATAAATGGACTTTTCCTGCCAATGAAAGCCTTTTTTT
TCATGTTTCTCAAGGTAGACATTCAATTATTACTCTGTTTTAACCAAAATGTAAAAAAAATTCAA
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTAA
Found at i:2602 original size:342 final size:331
Alignment explanation
Indices: 1989--2662 Score: 875
Period size: 342 Copynumber: 2.0 Consensus size: 331
1979 GAAGGAATGA
*
1989 GTGACTATAAATGGACTTTTCTTGGAAATGAATAGCTTTTTCCACATGTTTCCTGAAGTAGACAT
1 GTGACTATAAATGGACTTTTCTTGGAAATGAATAGCTTTTTCCACATGTTTCCTGAAGTAAACAT
*
2054 TCAATTACGGTCTGTTTTAATGAAAAATTAAAAAGAAATCAACTTAAAATAAATTATGAGATTAT
66 TCAATTACAGTCTGTTTTAATGAAAAATTAAAAAGAAATCAACTTAAAATAAATTATGAGATTAT
* *
2119 AAAACCATTTAAAGTAAGTAATAAGATTTTGAAAGAATGGGTTACTGCAAATGGACTTTTCCTGC
131 AAAACCATTTAAAGTAAGTAATAAGATTTTGAAAGAATGGGTTACTACAAATAGACTTTTCCTGC
* * * ** * * *
2184 CAATGAAAGTCTTTTTTTTCATGTTTTTTGAGGTAGACATTCGATTATTACTTGTTTTAATCTAA
196 CAATGAAAGCCTCTTTTTTCATATTTTTCAAGGTAGACATTCAATTATTACTTGTTTTAACCAAA
* * *
2249 ATGTAAAAAAAAATTCAACTTAAACTCAATTATGAGAGTATAAAACCATTTAAAGCGAATAATAA
261 ATGT-AAAAAAAATTCAACTTAAAATCAATTATAAGACTATAAAACCATTTAAAGCGAATAATAA
*
2314 GGCTTTT
325 GACTTTT
* *
2321 NNNNNNNNNNGTGACTATAAATGGACTTTTCTTGGTAATGAATGGCTTTTTCCACATGTTTCCT-
1 ----------GTGACTATAAATGGACTTTTCTTGGAAATGAATAGCTTTTTCCACATGTTTCCTG
* ********** *
2385 AATGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAA-ANNNNNNNNNNAAATTAA
56 AA-GTAAACATTCAATTACAGTCTGTTTTAATGAAAAAT-TAAAAAGAAATCAACTTAAAATAAA
** *
2449 TTATGAGATTATAAAACCATTTAAAGTGGGTAATAAGATTTTGAAAGAATGGGTTACTATAAATA
119 TTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGATTTTGAAAGAATGGGTTACTACAAATA
* * *
2514 GACTTTTCTTTCCAATGAAAGCCTCTTTTTTCATATTTTTCAAGGTAGACATTCAATTATTGCTT
184 GACTTTTCCTGCCAATGAAAGCCTCTTTTTTCATATTTTTCAAGGTAGACATTCAATTATTACTT
*
2579 GTTTTAACCAAAATGTGAAAAAAATTCAACTTAAAATCAATTATAAGACTATAAAACCATTTAAA
249 GTTTTAACCAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGACTATAAAACCATTTAAA
*
2644 GTGAATAATAAGACTTTT
314 GCGAATAATAAGACTTTT
2662 G
1 G
2663 AATGAATGGG
Statistics
Matches: 292, Mismatches: 38, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
331 1 0.00
341 63 0.22
342 222 0.76
343 6 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (331 bp):
GTGACTATAAATGGACTTTTCTTGGAAATGAATAGCTTTTTCCACATGTTTCCTGAAGTAAACAT
TCAATTACAGTCTGTTTTAATGAAAAATTAAAAAGAAATCAACTTAAAATAAATTATGAGATTAT
AAAACCATTTAAAGTAAGTAATAAGATTTTGAAAGAATGGGTTACTACAAATAGACTTTTCCTGC
CAATGAAAGCCTCTTTTTTCATATTTTTCAAGGTAGACATTCAATTATTACTTGTTTTAACCAAA
ATGTAAAAAAAATTCAACTTAAAATCAATTATAAGACTATAAAACCATTTAAAGCGAATAATAAG
ACTTTT
Found at i:5215 original size:171 final size:161
Alignment explanation
Indices: 5004--5332 Score: 301
Period size: 171 Copynumber: 2.0 Consensus size: 161
4994 AAAGCGAGTA
* * *
5004 ATAAGGCTTTTGAAGGAATGGATGAAAATAAATAGACTTTTTTTGCCAATG-AAT-C-TCTTTTT
1 ATAAGGCTTTTGAAAGAATGGATGAAAATAAATAGACTTTTCTTGACAA-GAAATGCAT-TTTTT
* *
5066 CTTTGC-GTTTCTCGATGTAGACATTGAATTATAATCTCTTTTAACCAACAAA-TCAAAAAAATT
64 -TTT-CAGTTTCTCGAGGTAGACATTCAATTATAATCTCTTTTAACCAA-AAAGTCAAAAAAATT
*
5129 GAACTTAAAATCAATTTTGAGATTATAAAACTATTT
126 GAACTTAAAATCAATTATGAGATTATAAAACTATTT
** *
5165 ANNNNNNNNNNTAAGGCTTTTGAAAGAATGAGA-GACTATAAATGGACTTTTCTTGACAAGAAAT
1 A----------TAAGGCTTTTGAAAGAATG-GATGAAAATAAATAGACTTTTCTTGACAAGAAAT
* * * * * *
5229 GCATTTTTTTTTCATGTTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTGACCAAAAATGTGA
55 GCATTTTTTTTTCA-GTTTCTCGAGGTAGACATTCAATTATAATCTCTTTTAACCAAAAA-GTCA
* *
5294 AAAAAATTTAACTTAAAATTAATTATGAGATTATAAAAC
118 AAAAAATTGAACTTAAAATCAATTATGAGATTATAAAAC
5333 NNNNNNNNNN
Statistics
Matches: 133, Mismatches: 17, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
161 1 0.01
170 2 0.02
171 48 0.36
172 43 0.32
173 39 0.29
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (161 bp):
ATAAGGCTTTTGAAAGAATGGATGAAAATAAATAGACTTTTCTTGACAAGAAATGCATTTTTTTT
TCAGTTTCTCGAGGTAGACATTCAATTATAATCTCTTTTAACCAAAAAGTCAAAAAAATTGAACT
TAAAATCAATTATGAGATTATAAAACTATTT
Found at i:9232 original size:170 final size:171
Alignment explanation
Indices: 8819--9267 Score: 408
Period size: 170 Copynumber: 2.6 Consensus size: 171
8809 NNNNNNNNNN
*
8819 AAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTTGATGAATGG-TTTTTTTACA
1 AAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTTCTTCTTGATGAATGGTTTTTTTTACA
* * * * * **
8883 TGTTTCCCAAGGCAAGCATTAAATGATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTNN
66 TGTTTCTCAAGGCAGGTATTAAATCATAGTCTATTTTAATGAAAAATGTAAAAAAAATCAACTAT
********
8948 NNNNNNNNTATGAGATTATAAAACTATTTAAAGCAAATAAT
131 AAAAAAATTATGAGATTATAAAACTATTTAAAGCAAATAAT
* * * ** **
8989 AAGGCTTTT-AAAAGAATAAGAGACTATAAATGGACTTTTCTTAC-CAATGAATACTTGTTTCTT
1 AAGGCTTTTGAAGA-AATAGGTGACTATAAATGGACTTTTCTT-CTTGATGAATGGTT-TTT-TT
* * * * *
9052 CACA--TTTCTCAAGGCAGGTATTCAATTATTGTCTGTTTTAATGAAAAATG-AATAAAAAATCA
62 TACATGTTTCTCAAGGCAGGTATTAAATCATAGTCTATTTTAATGAAAAATGTAA-AAAAAATCA
********** ***
9114 ACT-TAAAAAAATTANNNNNNNNNNAAACTATTTAAAGCGGGTAAT
126 ACTATAAAAAAATTATGAGATTATAAAACTATTTAAAGCAAATAAT
*
9159 AGGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTTCTTCTTGATGAATGGTTTTTTTTACA
1 AAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTTCTTCTTGATGAATGGTTTTTTTTACA
* *
9224 TGTTTCTCAAGGTAGGTATTTAATCATAGTCTATTTTAATGAAA
66 TGTTTCTCAAGGCAGGTATTAAATCATAGTCTATTTTAATGAAA
9268 NNNNNNNNNN
Statistics
Matches: 216, Mismatches: 53, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
168 5 0.02
169 6 0.03
170 142 0.66
171 55 0.25
172 3 0.01
173 5 0.02
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.35
Consensus pattern (171 bp):
AAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTTCTTCTTGATGAATGGTTTTTTTTACA
TGTTTCTCAAGGCAGGTATTAAATCATAGTCTATTTTAATGAAAAATGTAAAAAAAATCAACTAT
AAAAAAATTATGAGATTATAAAACTATTTAAAGCAAATAAT
Found at i:9857 original size:170 final size:170
Alignment explanation
Indices: 9376--9955 Score: 591
Period size: 171 Copynumber: 3.4 Consensus size: 170
9366 NNAAATTTTG
* * * * *
9376 TTTACATTTT-GGTTAAAATAGACAATAATTGAATGTTTACCTTCAAAAACATGAAGAAAAAGAC
1 TTTACATTTTCAGTTAAAATAGACAATAATTGAATGTCTACCTTGAGAAACATGAAAAAAAAGAC
** * *
9440 ATTCATCGGAGAGAAAAGTCCATTTATAGTCACCCATT-CTATCAAAAGCCTTACTACTCGCTTT
66 ATTCATTAGA-AGAAAAGTCCATTTATAGTCACCCATTCCT-TC-AAAGCCTTATTACTTGCTTT
* * *
9504 AAATAGTTTAATAATTCTATAATTGATTTTAAGTTCAAGTT-T
128 AAATAGTTTTATAATCCCATAATTGATTTTAAGTTCAAGTTGT
* * * * ** * * * *
9546 TTTACATTTTTCA-TTAAAATAGACTACAATTGAATGCCTACATCAAGAAACGTGCAGAAAAAGC
1 TTTACA-TTTTCAGTTAAAATAGACAATAATTGAATGTCTACCTTGAGAAACATGAAAAAAAAGA
* * * *
9610 CATTCTTTGAGAAGAAAAGTCCATTTATATTCACCTATTCCTTCAAATGTCTTATTACTTGCTTT
65 CATTCATT-AGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA-GCCTTATTACTTGCTTT
* * * *
9675 AAATGGTTTTATACTCCCATAATTGATTTTCAGTTGAA-TTGT
128 AAATAGTTTTATAATCCCATAATTGATTTTAAGTTCAAGTTGT
* * * *
9717 TTTACATTCTT-AGTTAAAACAGACAATAATTGACTATCTATCTTGAGAAACATGAAAAAAAATG
1 TTTACATT-TTCAGTTAAAATAGACAATAATTGAATGTCTACCTTGAGAAACATGAAAAAAAA-G
* *
9781 -CATTCATTAGCAAGAAAAGTCCA-TTACAGTCACCCATTCCTTCAGAAGCCTTATTACTTACTT
64 ACATTCATTAG-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCA-AAGCCTTATTACTTGCTT
* * * * *
9844 TAAATAGTTTTATAATCTCAAAATTGATTTTAACTTCAATTTGC
127 TAAATAGTTTTATAATCCCATAATTGATTTTAAGTTCAAGTTGT
* * ** * *
9888 TTTAAATTTTCAGTCAAAATAGATTATAATTGAATGTCTACCTTGTGAAACATGAAAAAAAAGGC
1 TTTACATTTTCAGTTAAAATAGACAATAATTGAATGTCTACCTTGAGAAACATGAAAAAAAAGAC
9953 ATT
66 ATT
9956 TATTGGCCCA
Statistics
Matches: 333, Mismatches: 63, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
170 83 0.25
171 245 0.74
172 5 0.02
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (170 bp):
TTTACATTTTCAGTTAAAATAGACAATAATTGAATGTCTACCTTGAGAAACATGAAAAAAAAGAC
ATTCATTAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAGCCTTATTACTTGCTTTAAA
TAGTTTTATAATCCCATAATTGATTTTAAGTTCAAGTTGT
Found at i:10259 original size:319 final size:328
Alignment explanation
Indices: 9376--10538 Score: 910
Period size: 319 Copynumber: 3.5 Consensus size: 328
9366 NNAAATTTTG
* * * * * *
9376 TTTACATTTTGGTTAAAATAGACAATAATTGAATGTTTACCTTC-AAAAACATGAAGAAAAAGAC
1 TTTATATTTTTGTTAAAACAGACTATAATTGAATGTCTACC-TCGAGAAACATGAAGAAAAAG-C
* * * * **
9440 ATTCATCGG-AGAGAAAAGTCCATTTATAGTCACCCATTCTATCAAAAGCCTTACTACTCGCTTT
64 ATTCATTGGCA-AGAAAAGTCCATTTATAGTCACCCATTCCATCAGAAGCCTTATTACTTACTTT
* * * * *
9504 AAATAGTTTAATAAT-TCTATAATTGATTTTAAGTTCAAGTTT--TTTACATTTTTCA-TTAAAA
128 AAATAGTTTTATAATCTC-AAAATTGATTTTAACTTCAA-TTTGCTTTA-AATTTTCAGTCAAAA
* * * * * * * * **
9565 TAGACTACAATTGAATGCCTACATCAAGAAACGTGCAGAAAAAGCCATTCTTTGAGAAGAAAAGT
190 CAGATTATAATTGAATGTCTACATTAAGAAACAT--AG----A---A---TATAAGAAGAAGGGT
* * * * * * ** ** * *
9630 CCATTTATATTCACCTATTCCTTCAAATGTCTTATTACTTGCTTTAAATGGTTTTATACTCCCAT
243 CTATTTATA-TCACCCATTCCTACAAAAGCCCTATTACTCACTAGAAATGGTTTTATAATCTCAT
*
9695 AATTGATTTTCAGTTGAATTG-T
307 AATTGATTTTAAGTTG-ATTGTT
* * * * * * * *
9717 TTTACATTCTTAGTTAAAACAGACAATAATTGACTATCTATCTTGAGAAACATGAAAAAAAATGC
1 TTTATATT-TTTGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAA-GC
* * *
9782 ATTCATTAGCAAGAAAAGTCCA-TTACAGTCACCCATTCCTTCAGAAGCCTTATTACTTACTTTA
64 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCATCAGAAGCCTTATTACTTACTTTA
*
9846 AATAGTTTTATAATCTCAAAATTGATTTTAACTTCAATTTGCTTTAAATTTTCAGTCAAAATAGA
129 AATAGTTTTATAATCTCAAAATTGATTTTAACTTCAATTTGCTTTAAATTTTCAGTCAAAACAGA
* ** **
9911 TTATAATTGAATGTCTACCTTGTGAAACAT-G-A-A-AA-AA-AA-GG-C-ATTTAT-TGGCCCA
194 TTATAATTGAATGTCTACATTAAGAAACATAGAATATAAGAAGAAGGGTCTATTTATATCACCCA
* * *
9966 TTTCTTCAAAAGCCTTATTACTCACTAGAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGA
259 TTCCTACAAAAGCCCTATTACTCACTAGAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGA
10031 TTGTT
324 TTGTT
* *
10036 TTTATATTTTTGTTAAAATAGACTATAATTGAATGTCTACCTCGAGAAGCATGAAGAAACAAGCA
1 TTTATATTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAA-AAGCA
** * ** * *
10101 TTCATTGGCAAGAAAAGTAGATTTATAGTCTCTTATTCCCTCAGAAGCCTTATTACTCACTTTAA
65 TTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCATCAGAAGCCTTATTACTTACTTTAA
* ** * ********* *
10166 ATAGTTTTATAATATCAAAATTGATTTTAGGTTCAATTT-TTTTNNNNNNNNNNGTTAAAACAGA
130 ATAGTTTTATAATCTCAAAATTGATTTTAACTTCAATTTGCTTT-AAATTTTCAGTCAAAACAGA
*
10230 TTATAATTGAATGTCTATATTAAGAAACATAAAGAAAAATGTATTAATTGGCAAGAAGGGTCTAT
194 TTATAATTGAATGTCTACATTAAGAAACAT--AG---AA--TA-TAA---G-AAGAAGGGTCTAT
** ** * *
10295 TTATAGTCACCCATTCCTACAAAAGCCCTATTACTTGCTTTAAATGATTTTATAATCTCAAAATT
247 TTATA-TCACCCATTCCTACAAAAGCCCTATTACTCACTAGAAATGGTTTTATAATCTCATAATT
*
10360 GATTTTAAGTTGACTTATT
311 GATTTTAAGTTGA-TTGTT
* * * *
10379 TTT-TATTTTTGGTTAAAACAGACTATAATTGAATGCCTTCCTCGAGAAACATGTAGAAAAAGTA
1 TTTATATTTTT-GTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAG-C
* * *
10443 ATTTATTGAG-AAGAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCTTATTACTTTCTTT
64 ATTCATTG-GCAAGAAAAGTCCATTTATAGTCACCCATTCCATCAGAAGCCTTATTACTTACTTT
* *
10507 TAATAGTTTTATAATCTCATAATTGATTTTAA
128 AAATAGTTTTATAATCTCAAAATTGATTTTAA
10539 NNNNNNNNNN
Statistics
Matches: 666, Mismatches: 117, Indels: 76
0.78 0.14 0.09
Matches are distributed among these distances:
318 70 0.11
319 176 0.26
321 6 0.01
322 2 0.00
323 1 0.00
324 2 0.00
325 2 0.00
326 2 0.00
329 1 0.00
331 3 0.00
336 2 0.00
337 2 0.00
338 2 0.00
339 2 0.00
340 9 0.01
341 82 0.12
342 169 0.25
343 132 0.20
344 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (328 bp):
TTTATATTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGCAT
TCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCATCAGAAGCCTTATTACTTACTTTAAA
TAGTTTTATAATCTCAAAATTGATTTTAACTTCAATTTGCTTTAAATTTTCAGTCAAAACAGATT
ATAATTGAATGTCTACATTAAGAAACATAGAATATAAGAAGAAGGGTCTATTTATATCACCCATT
CCTACAAAAGCCCTATTACTCACTAGAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGATT
GTT
Found at i:10474 original size:171 final size:168
Alignment explanation
Indices: 9962--10538 Score: 563
Period size: 171 Copynumber: 3.4 Consensus size: 168
9952 CATTTATTGG
* * ** * *
9962 CCCATTTCTTCAAAAGCCTTATTACTCACTAGAAATGGTTTTATAATCTCATAATTGATTTTAAG
1 CCCATTCCTACAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAG
* * *
10027 TTGATTGTTTTTATATTTTTGTTAAAATAGACTATAATTGAATGTCTACCTCGAGAAGCATGAAG
66 TTGATT-TTTTTATATTTTTGTTAAAACAGACTATAATTGAATGTCTTCCTCGAGAAACATGAAG
* * ** *
10092 AAACAAGCATTCATTGGCAAGAAAAGTAGATTTATAGTCT
130 AAA-AAGTATTAATTGGCAAGAAAAGTCCATTTATAGTCA
** * * *
10132 CTTATTCCCT-CAGAAGCCTTATTACTCACTTTAAATAGTTTTATAATATCAAAATTGATTTTAG
1 CCCATT-CCTACAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAA
* ******** * * **
10196 GTTCAATTTTTTTNNNNNNNNNNGTTAAAACAGATTATAATTGAATGTCTAT-ATTAAGAAACAT
65 GTT-GATTTTTTT--ATATTTTTGTTAAAACAGACTATAATTGAATGTCT-TCCTCGAGAAACAT
* ** *
10260 AAAGAAAAATGTATTAATTGGCAAGAAGGGTCTATTTATAGTCA
126 GAAGAAAAA-GTATTAATTGGCAAGAAAAGTCCATTTATAGTCA
* **
10304 CCCATTCCTACAAAAGCCCTATTACTTGCTTTAAAT-GATTTTATAATCTCAAAATTGATTTTAA
1 CCCATTCCTACAAAAGCCTTATTACTCACTTTAAATAG-TTTTATAATCTCAAAATTGATTTTAA
*
10368 GTTGACTTATTTTT-TATTTTTGGTTAAAACAGACTATAATTGAATGCCTTCCTCGAGAAACATG
65 GTTGA-TT-TTTTTATATTTTT-GTTAAAACAGACTATAATTGAATGTCTTCCTCGAGAAACATG
* *
10432 TAGAAAAAGTAATTTATTGAG-AAGAAAAGTCCATTTATAGTCA
127 AAGAAAAAGT-ATTAATTG-GCAAGAAAAGTCCATTTATAGTCA
** * *
10475 CCCATTCC-ATCAAAAGCCTTATTACTTTCTTTTAATAGTTTTATAATCTCATAATTGATTTTAA
1 CCCATTCCTA-CAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAA
10539 NNNNNNNNNN
Statistics
Matches: 326, Mismatches: 65, Indels: 31
0.77 0.15 0.07
Matches are distributed among these distances:
170 63 0.19
171 135 0.41
172 123 0.38
173 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (168 bp):
CCCATTCCTACAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAG
TTGATTTTTTTATATTTTTGTTAAAACAGACTATAATTGAATGTCTTCCTCGAGAAACATGAAGA
AAAAGTATTAATTGGCAAGAAAAGTCCATTTATAGTCA
Found at i:10575 original size:171 final size:171
Alignment explanation
Indices: 10293--10654 Score: 415
Period size: 171 Copynumber: 2.1 Consensus size: 171
10283 AGAAGGGTCT
10293 ATTTATAGTCACCCATTCCTACAAAAGCCCTATTACTTGCTTTAAATGATTTTATAATCTCAAAA
1 ATTTATAGTCACCCATTCCTACAAAAGCCCTATTACTTGCTTTAAATGATTTTATAATCTCAAAA
** * * *
10358 TTGATTTTAAGTTGACTTATTTTTTATTTTTGGTTAAAACAGACTATAATTGAATGCCTTCCTC-
66 TTGATTTTAAGTTGACTTATTTTACATTTTTGATTAAAACAGACTATAATTGAATGCATGCCTCA
* * * **
10422 GAGAAACATGTAGAAAAAGTAATTTATTGAGAAGAAAAGTCC
131 G-GAAACATGTAAAAAAAGCAATTCATCAAGAAGAAAAGTCC
* * * *
10464 ATTTATAGTCACCCATTCC-ATCAAAAGCCTTATTACTTTCTTTTAAT-AGTTTTATAATCTCAT
1 ATTTATAGTCACCCATTCCTA-CAAAAGCCCTATTACTTGCTTTAAATGA-TTTTATAATCTCAA
********** * *
10527 AATTGATTTTAANNNNNNNNNNTTTACATTTTTTATTAAAATAGACTATAATTGAATGCATGCCT
64 AATTGATTTTAAGTTGACTTATTTTACATTTTTGATTAAAACAGACTATAATTGAATGCATGCCT
* *
10592 CAGGAAACGTGTAAAAAAAGCCATTCATCAAGAAGAAAAGTCC
129 CAGGAAACATGTAAAAAAAGCAATTCATCAAGAAGAAAAGTCC
*
10635 ATTTATAGTCACCTATTCCT
1 ATTTATAGTCACCCATTCCT
10655 NNNNNNNNNN
Statistics
Matches: 158, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
170 2 0.01
171 155 0.98
172 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.36
Consensus pattern (171 bp):
ATTTATAGTCACCCATTCCTACAAAAGCCCTATTACTTGCTTTAAATGATTTTATAATCTCAAAA
TTGATTTTAAGTTGACTTATTTTACATTTTTGATTAAAACAGACTATAATTGAATGCATGCCTCA
GGAAACATGTAAAAAAAGCAATTCATCAAGAAGAAAAGTCC
Done.