Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397724.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1022.0, 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: 14879
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.24
Warning! 5146 characters in sequence are not A, C, G, or T
Found at i:7218 original size:15 final size:16
Alignment explanation
Indices: 7194--7233 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
7184 ATAATCTCAA
*
7194 AATTCATTT-AATTTG
1 AATTCTTTTAAATTTG
7209 AATTCTTTTAAATTTG
1 AATTCTTTTAAATTTG
7225 AATTCTTTT
1 AATTCTTTT
7234 TACATTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (16 bp):
AATTCTTTTAAATTTG
Found at i:7406 original size:16 final size:16
Alignment explanation
Indices: 7354--7410 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
7344 TTTATTACTC
7354 AATTTAAATTGTTTTA
1 AATTTAAATTGTTTTA
*
7370 TAATCTCATAATTGATTTTA
1 -AAT-TTA-AATTG-TTTTA
*
7390 AGTTTAAATTGTTTTA
1 AATTTAAATTGTTTTA
7406 AATTT
1 AATTT
7411 TTAGTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 9 0.27
17 8 0.24
18 4 0.12
19 7 0.21
20 5 0.15
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (16 bp):
AATTTAAATTGTTTTA
Found at i:7534 original size:172 final size:171
Alignment explanation
Indices: 7296--7723 Score: 491
Period size: 172 Copynumber: 2.5 Consensus size: 171
7286 AAGAAAAATG
* * * *
7296 TTCATTGGCAAGAGAAGTCCATTTATAGTCAGCCATTCCTTCAAAAGCTTTATTACTCAATTTAA
1 TTCATTGGTAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCCTTATTACTCACTTTAA
* * * * *
7361 ATTGTTTTATAATCTCATAATTGATTTTAAGTTTAAATTGTTT-TA-AATTTTTAGTTAAAATAT
65 ATGGTTTTATAATCTCAAAATTGA-TTTAAATTTAAATTCTTTGTACAATTTTTA-TTAAAACAT
* ** * *
7424 ATTATAATTAAATGTCTAACTTGAGAAACGTGAAGAAAAAGACA
128 ATTAGAATTAAATGTCTAACTCAAGAAACATAAAGAAAAAGACA
* * * *
7468 TTCATTGGTAAGAAAAGTCTAGTTATAGCCACACATTCCTTTAAAAGCCTTATTACTCACTTTAA
1 TTCATTGGTAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATTACTCACTTTAA
* * * * *
7533 ATGGTTTTGTATTCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTTATTAAAACATCT
65 ATGGTTTTATAATCTCAAAATTGATTTAAATTTAAATTCTTTGTACAATTTTTATTAAAACATAT
* * * **
7598 TAGAGTTGAATGTCTACCTCAAGAAACATAAAGAAAAAGGTA
130 TAGAATTAAATGTCTAACTCAAGAAACATAAAGAAAAAGACA
* * * **
7640 TTCATTGGTAAGAATAGTCCATTTGTAGTTACTTGTTCCTTCAAAAGCCTTATTACTCACTTTAA
1 TTCATTGGTAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATTACTCACTTTAA
*
7705 ATGGCTTTATAATCTCAAA
65 ATGGTTTTATAATCTCAAA
7724 NNNNNNNNNN
Statistics
Matches: 212, Mismatches: 41, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
171 16 0.08
172 189 0.89
173 7 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
TTCATTGGTAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
TGGTTTTATAATCTCAAAATTGATTTAAATTTAAATTCTTTGTACAATTTTTATTAAAACATATT
AGAATTAAATGTCTAACTCAAGAAACATAAAGAAAAAGACA
Found at i:9608 original size:172 final size:171
Alignment explanation
Indices: 8506--9637 Score: 657
Period size: 171 Copynumber: 6.7 Consensus size: 171
8496 NNNNNNNNNN
* * * * ** * *
8506 TACTCACTTTATATGATTTTAGAATCTCATAATTGATTTTAGGTTGAATT-TTTTGACGTTTTTG
1 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTT-ACATTTTTA
* * * * * *
8570 GTTAGAGAA-A-AATGTAATTGAA--TCTGCCTTGGGAAACATGAAGAAGAAGGTATTCATTGGC
65 GTTA-A-AACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGC
* * **********
8631 AAGAAAAGT-TCATTTATAGTCACCCATTCNNNNNNNNNNCTTAT
128 AAGAAAAGTCT-ATTTATAGTCACCAATGCCTTCAAAAGCCTTAT
* * * *
8675 TACTCACTTTAAATGGTTTTATAATCTCAAGATTGATTTTAAGTTGGATTCTTTTACATTTTTTG
1 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTTACATTTTTAG
* * * * * * ** *
8740 TTAAGAA-ACG-CTATAATTGTATGTCTGCCTTG-G-----GGATGTAAAA-GCAACCATTGACA
66 TTAA-AACA-GATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCA
* *
8796 CA-AAAAGTCCATTTATAGTCACTTAA-GCCTTCAAAAGCCTTAT
129 -AGAAAAGTCTATTTATAGTCAC-CAATGCCTTCAAAAGCCTTAT
** * * * * ********
8839 TACATGGC-TTAAACGGTTTCATAAAC-CAATAATT-ATTTTTAAGTTGAATAT-TTNNNNNNNN
1 TAC-TCACTTTAAATGGTTTTATAATCTCAA-AATTGA-TTTTAAATTGAAT-TCTTTTACATTT
*** * * ** * *
8900 NNGGTTAAAACAGACTAGAATTGAATGT-TCACCTCAAGAAACATGATGAAAAAAGCATTCATTG
62 TTAGTTAAAACAGATTATAATTGAATGTCT-ACCTTGAGAAACATGAAGAAAAAGGCATTCATTG
* * * * * *
8964 GCAAGAAAAGCCCATTTACAGTCACCCATACATTCAAAAGCCTTAT
126 GCAAGAAAAGTCTATTTATAGTCACCAATGCCTTCAAAAGCCTTAT
* * * * * * * * * *
9010 TACTCGCTTTAAATGATTTTTTAGTGTCATAAA-TGATTTTATATTGAATTGTTTTTCAGTTTTG
1 TACTCACTTTAAATGGTTTTATAATCTCA-AAATTGATTTTAAATTGAATTCTTTTACATTTTTA
* * * *
9074 GTTAAAACAGATTATAATTGTATGTCTACCTTAAGAAACATGAAG-AAAAGGATATTCATTGGCT
65 GTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGG-CATTCATTGGCA
* * *******
9138 AGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAANNNNNNN
129 AGAAAAGTCTATTTATAGTCACCAATGCCTTCAAAAGCCTTAT
*** * * * * * *
9181 NNNTCGCTGTAAAAGGTTTTATAATCTCATAATTGATTTTGAATTGAATTCTTTTACATATTTAG
1 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTTACATTTTTAG
** *
9246 TTAAAACAGATTATAATTGAATGTCTA-CTTCGAGAAATGTTAAGAAAAAGGCATTCATTGGCAA
66 TTAAAACAGATTATAATTGAATGTCTACCTT-GAGAAACATGAAGAAAAAGGCATTCATTGGCAA
* *
9310 GAAAAGTCTATTTATAGTCAACCATTG-CTTCAAAAGTCTTAT
130 GAAAAGTCTATTTATAGTC-ACCAATGCCTTCAAAAGCCTTAT
** * * * * *
9352 TGTTCACTTTAAATCGTTTTACAATCTCAAAATTAATTTTAAGTTCAAATT-TATTTACATTTTT
1 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATT-GAATTCT-TTTACATTTTT
********** * ** *
9416 AGTTNNNNNNNNNNATAATTGAATGTCTAGCTTGAGAAACATGAAGAAAAAGGCATTTGTTGGTA
64 AGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCA
*
9481 AGAAAAG-CTCATTTATAGTCACCAATGCCTTTAAAAGCCTTAT
129 AGAAAAGTCT-ATTTATAGTCACCAATGCCTTCAAAAGCCTTAT
* **
9524 TACTCACTTTAAATGGTTTTATAGTCTCAAAATTG-TTTTAAATTTGAATTCTTTGTATGTTTTT
1 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAA-TTGAATTCTTT-TACATTTTT
* *
9588 AGTGAAAACAGATTATAATTGATTGTCTACCTTGAGAAACATGAAGAAAA
64 AGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAA
9638 GGTCTTTCNN
Statistics
Matches: 722, Mismatches: 198, Indels: 83
0.72 0.20 0.08
Matches are distributed among these distances:
163 8 0.01
164 89 0.12
165 12 0.02
168 5 0.01
169 62 0.09
170 29 0.04
171 332 0.46
172 181 0.25
173 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.36
Consensus pattern (171 bp):
TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTTACATTTTTAG
TTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCAAG
AAAAGTCTATTTATAGTCACCAATGCCTTCAAAAGCCTTAT
Found at i:10787 original size:171 final size:171
Alignment explanation
Indices: 10474--11579 Score: 909
Period size: 171 Copynumber: 6.5 Consensus size: 171
10464 AGCCAACCAT
* * * ** *
10474 TTGGCATGAAAAGTTCATTTATAGTCACTCA-AGCCTTTGAAAGCCTTATTAC-CAATTTAAATG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATA-CCTTCAAAAGCCTTATTACTCACTTTAAATG
* * ** * *
10537 GTTTCATTAACTA--ATAATAT-TTTTTAAGTTGCCTATTTTTACATTTTTGGTTCAAACAGACT
65 GTTTTA-TAA-TATCATAAT-TGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAACT
* * * * * ***
10599 AGAATTGTATATCTACCTTAAGAAACATGTAGAAAAAAGCATNNN
127 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAAGCATTCA
******* * * * *
10644 NNNNNNNGAAAAGTCCATTTATAGTCACCTATACCTTTAAAAGTCTTATTACTTACTTTAAATGG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCACTTTAAATGG
* *
10709 TTTTTTAATATCATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAATTATAA
66 TTTTATAATATCATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAACTATAA
* * *
10774 TTGGATGTCTACCTCAAGAAACATGAAG-AAAAGGATATTCA
131 TTGAATGTCTACCTCAAGAAACATGAAGAAAAAAG-CATTCA
* * ** * * *
10815 TTGGCAAGAAAAGTCTATTTATAGCCACCCATTTCTTCAAAAACCTTATTACTCACTGTAAATGA
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCACTTTAAATGG
* * * * * * *
10880 TTTTGTAATCTCATAATTGATTTTAGGTTGAATTTTTTTA-AGTTTTTGGTTAGAACAGATTATA
66 TTTTATAATATCATAATTGATTTTAAGTTGAATATTTTTACA-TTTTTGGTTAAAACAAACTATA
* ** *** * *
10944 ATTGAATATCGGCCTTGGGAAACATGAAGAAAAAGGTATTCA
130 ATTGAATGTCTACCTCAAGAAACATGAAGAAAAAAGCATTCA
* * * * *
10986 TTGGCAAGAAAAGTCCATTTATAGTTACCCATTCCATCAAAAGGCTTATTACTCACTTTAAATAG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCACTTTAAATGG
* * * * * *
11051 TTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTTACATTTTTAGTTAAGAA-AAGCTATA
66 TTTTATAATATCATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAA-AACAAACTATA
* ** * * **
11115 ATTGAATGTCTGCCTCGGGGAACGA-GAAG-CAAAAGCCAACCA
130 ATTGAATGTCTACCTCAAGAAAC-ATGAAGAAAAAAG-CATTCA
* * **
11157 TTGGCACA-AAAAGTCCATTTATAGTCACTCA-AGCCTTCGAAAGCCTTATTACATGGC-TTAAA
1 TTGGCA-AGAAAAGTCCATTTATAGTCACCCATA-CCTTCAAAAGCCTTATTAC-TCACTTTAAA
* *
11219 TGGTTTCATAA-ACTAATAATT-ATTTTTAAGTTGAATATTTTTACATTTTTGGTTAAAA-AAGA
63 TGGTTTTATAATA-TCATAATTGA-TTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAA-A
* * **
11281 CTAGAATTGAATGTCTACCTCAAGAAATATGATTAAAAAAGCATTCA
125 CTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAAGCATTCA
* * ** *
11328 TTGGAAAGAAAAGTCCATTTATAGACACCCATATATTCAAAAGCCTTATCACTCACTTTAAATGG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCACTTTAAATGG
* * * * * * *
11393 TTCTATAGTGTCATATTTGATTTTAAGTTGAAT-TTGTTTATAGTTTTGGTTAAAACAGA-TAAT
66 TTTTATAATATCATAATTGATTTTAAGTTGAATATT-TTTACATTTTTGGTTAAAACAAACT-AT
* * * * *
11456 AATTGGATGTCTACCTCGAGAAACATGAAG-AAAAGGATATTTA
129 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAAG-CATTCA
* * *** * * *
11499 TTGGCAAAAAAAGTCCATTTATAGTCATCCATTTTTTCAAAAGCCTTATTACTCGCTGTAAAAGG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCACTTTAAATGG
*
11564 TTTTATAATCTCATAA
66 TTTTATAATATCATAA
11580 NNNNNNNNNN
Statistics
Matches: 747, Mismatches: 160, Indels: 57
0.77 0.17 0.06
Matches are distributed among these distances:
169 2 0.00
170 69 0.09
171 655 0.88
172 21 0.03
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (171 bp):
TTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCACTTTAAATGG
TTTTATAATATCATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAACTATAA
TTGAATGTCTACCTCAAGAAACATGAAGAAAAAAGCATTCA
Found at i:11206 original size:342 final size:340
Alignment explanation
Indices: 10482--11579 Score: 1061
Period size: 342 Copynumber: 3.2 Consensus size: 340
10472 ATTTGGCATG
* *** ** ** * *
10482 AAAAGTTCATTTATAGTCACTCAAGCCTTTGAAAGCCTTATTAC-CAATTTAAATGGTTTCATTA
1 AAAAGTCCATTTATAGTCACTCATTTCTTCAAAAGCCTTATTACTCGCTGTAAATGGTTTTA-TA
* ** * * *
10546 A-CTAATAA-TATTTTTTAAGTTGCCTATTTTTACATTTTTGGTTCAAACAGACTAGAATTGTAT
65 ATCTCATAATTA-TTTTTAAGTTGAATATTTTTACATTTTTGGTTAAAAAAGACTAGAATTGAAT
* * * ********** *
10609 ATCTACCTTAAGAAACATGTAGAAAAAAGCATNNNNNNNNNNGAAAAGTCCATTTATAGTCACCT
129 ATCGACCTCAAGAAACATGAAGAAAAAAGCATTCATTGGAAAGAAAAGTCCATTTATAGTCACCC
* * * * * *
10674 ATACCTTTAAAAGTCTTATTACTTACTTTAAATGGTTTTTTAATATCATAATTGATTTTAAGTTG
194 ATTCCATCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATATCATAATTGATTTTAAGTTG
* *
10739 AATATTTTTACATTTTTGGTTAAAACAA-ATTATAATTGGATGTCTACCTCAAGAAACATGAAGA
259 AATTTTTTTACATTTTTGGTTAAAA-AAGA-TATAATTGGATGTCTACCTCGAGAAACATGAAGA
10803 AAAGGATATTCATTGGCAA
322 AAAGGATATTCATTGGCAA
* * * * * * *
10822 GAAAAGTCTATTTATAGCCACCCATTTCTTCAAAAACCTTATTACTCACTGTAAATGATTTTGTA
1 -AAAAGTCCATTTATAGTCACTCATTTCTTCAAAAGCCTTATTACTCGCTGTAAATGGTTTTATA
* * * * * *
10887 ATCTCATAATTGA-TTTTAGGTTGAATTTTTTTA-AGTTTTTGGTTAGAACAGATTATAATTGAA
65 ATCTCATAATT-ATTTTTAAGTTGAATATTTTTACA-TTTTTGGTTAAAAAAGACTAGAATTGAA
* *** * * * *
10950 TATCGGCCTTGGGAAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCCATTTATAGTTACC
128 TATCGACCTCAAGAAACATGAAGAAAAAAGCATTCATTGGAAAGAAAAGTCCATTTATAGTCACC
* * * *
11015 CATTCCATCAAAAGGCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTT
193 CATTCCATCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATATCATAATTGATTTTAAGTT
* * * * * * *
11080 GATTTTTTTTACATTTTTAGTTAAGAAAAGCTATAATTGAATGTCTGCCTCGGGGAACGA-GAAG
258 GAATTTTTTTACATTTTTGGTTAA-AAAAGATATAATTGGATGTCTACCTCGAGAAAC-ATGAAG
* *
11144 CAAAAGCCA-A-CCATTGGCACA
321 -AAAAG-GATATTCATTGGCA-A
*** * * *
11165 AAAAGTCCATTTATAGTCACTCAAGCCTTCGAAAGCCTTATTACATGGCT-TAAATGGTTTCATA
1 AAAAGTCCATTTATAGTCACTCATTTCTTCAAAAGCCTTATTAC-TCGCTGTAAATGGTTTTATA
* * *
11229 AACTAATAATTATTTTTAAGTTGAATATTTTTACATTTTTGGTTAAAAAAGACTAGAATTGAATG
65 ATCTCATAATTATTTTTAAGTTGAATATTTTTACATTTTTGGTTAAAAAAGACTAGAATTGAATA
* * ** *
11294 TCTACCTCAAGAAATATGATTAAAAAAGCATTCATTGGAAAGAAAAGTCCATTTATAGACACCCA
130 TCGACCTCAAGAAACATGAAGAAAAAAGCATTCATTGGAAAGAAAAGTCCATTTATAGTCACCCA
* * * * *
11359 TAT--ATTCAAAAGCCTTATCACTCACTTTAAATGGTTCTATAGTGTCATATTTGATTTTAAGTT
195 T-TCCA-TCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATATCATAATTGATTTTAAGTT
* * * *
11422 GAATTTGTTTATAGTTTTGGTTAAAACAGATAATAATTGGATGTCTACCTCGAGAAACATGAAGA
258 GAATTTTTTTACATTTTTGGTTAAAAAAGAT-ATAATTGGATGTCTACCTCGAGAAACATGAAGA
*
11487 AAAGGATATTTATTGGCAAA
322 AAAGGATATTCATTGGC-AA
* *
11507 AAAAGTCCATTTATAGTCA-TCCATTTTTTCAAAAGCCTTATTACTCGCTGTAAAAGGTTTTATA
1 AAAAGTCCATTTATAGTCACT-CATTTCTTCAAAAGCCTTATTACTCGCTGTAAATGGTTTTATA
11571 ATCTCATAA
65 ATCTCATAA
11580 NNNNNNNNNN
Statistics
Matches: 603, Mismatches: 131, Indels: 45
0.77 0.17 0.06
Matches are distributed among these distances:
340 1 0.00
341 57 0.09
342 526 0.87
343 17 0.03
344 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (340 bp):
AAAAGTCCATTTATAGTCACTCATTTCTTCAAAAGCCTTATTACTCGCTGTAAATGGTTTTATAA
TCTCATAATTATTTTTAAGTTGAATATTTTTACATTTTTGGTTAAAAAAGACTAGAATTGAATAT
CGACCTCAAGAAACATGAAGAAAAAAGCATTCATTGGAAAGAAAAGTCCATTTATAGTCACCCAT
TCCATCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATATCATAATTGATTTTAAGTTGAA
TTTTTTTACATTTTTGGTTAAAAAAGATATAATTGGATGTCTACCTCGAGAAACATGAAGAAAAG
GATATTCATTGGCAA
Found at i:11504 original size:513 final size:513
Alignment explanation
Indices: 10652--11576 Score: 1242
Period size: 513 Copynumber: 1.8 Consensus size: 513
10642 NNNNNNNNNG
* * * **
10652 AAAAGTCCATTTATAGTCACCTATACCTTTAAAAGTCTTATTACTTACTTTAAATGGTTTTTTAA
1 AAAAGTCCATTTATAGTCACCTATACCTTCAAAAGCCTTATTACTGACTTTAAATGGTTTCATAA
* * * *
10717 TATCATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAATTATAATTGGATGT
66 TATAATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAACTAGAATTGAATGT
* * * * *
10782 CTACCTCAAGAAACATGAAGAAAAGGATATTCATTGGCAAGAAAAGTCTATTTATAGCCACCCAT
131 CTACCTCAAGAAACATGAAGAAAAAGACATTCATTGGAAAGAAAAGTCCATTTATAGACACCCAT
* * * * * *
10847 TTCTTCAAAAACCTTATTACTCACTGTAAATGATTTTGTAATCTCATAATTGATTTTAGGTTGAA
196 ATATTCAAAAACCTTATCACTCACTGTAAATGATTCTATAATCTCATAATTGATTTTAAGTTGAA
* * * * * *
10912 TTTTTTTAAGTTTTTGGTTAGAACAGATTATAATTGAATATCGGCCTTGGGAAACATGAAGAAAA
261 TTTGTTTAAGTTTTTGGTTAAAACAGATAATAATTGAATATCGACCTCGAGAAACATGAAGAAAA
* * *
10977 AGGTATTCATTGGCAAGAAAAGTCCATTTATAGTTACCCATTCCATCAAAAGGCTTATTACTCAC
326 AGGTATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCTTATTACTCAC
*
11042 TTTAAATA-GTTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTTACATTTTTAGTTAAGA
391 TGTAAA-AGGTTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTTACATTTTTAGTTAAGA
11106 AAAGCTATAATTGAATGTCTGCCTCGGGGAACGAGAAGCAAAAGCCAACCATTGGCACA
455 AAAGCTATAATTGAATGTCTGCCTCGGGGAACGAGAAGCAAAAGCCAACCATTGGCACA
* *
11165 AAAAGTCCATTTATAGTCA-CTCA-AGCCTTCGAAAGCCTTATTACATGGC-TTAAATGGTTTCA
1 AAAAGTCCATTTATAGTCACCT-ATA-CCTTCAAAAGCCTTATTAC-TGACTTTAAATGGTTTCA
11227 TAA-ACTAATAATT-ATTTTTAAGTTGAATATTTTTACATTTTTGGTTAAAA-AAGACTAGAATT
63 TAATA-TAATAATTGA-TTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAA-ACTAGAATT
*
11289 GAATGTCTACCTCAAGAAATATGATTA-AAAAAG-CATTCATTGGAAAGAAAAGTCCATTTATAG
125 GAATGTCTACCTCAAGAAACATGA--AGAAAAAGACATTCATTGGAAAGAAAAGTCCATTTATAG
* * * * * *
11352 ACACCCATATATTCAAAAGCCTTATCACTCACTTTAAATGGTTCTATAGTGTCATATTTGATTTT
188 ACACCCATATATTCAAAAACCTTATCACTCACTGTAAATGATTCTATAATCTCATAATTGATTTT
* * *
11417 AAGTTGAATTTGTTTATAG-TTTTGGTTAAAACAGATAATAATTGGATGTCTACCTCGAGAAACA
253 AAGTTGAATTTGTTTA-AGTTTTTGGTTAAAACAGATAATAATTGAATATCGACCTCGAGAAACA
* * ***
11481 TGAAG-AAAAGGATATTTATTGGCAAAAAAAGTCCATTTATAGTCATCCATTTTTTCAAAAGCCT
317 TGAAGAAAAAGG-TATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCT
*
11545 TATTACTCGCTGTAAAAGGTTTTATAATCTCA
381 TATTACTCACTGTAAAAGGTTTTATAATCTCA
11577 TAANNNNNNN
Statistics
Matches: 353, Mismatches: 48, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
512 14 0.04
513 329 0.93
514 9 0.03
515 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (513 bp):
AAAAGTCCATTTATAGTCACCTATACCTTCAAAAGCCTTATTACTGACTTTAAATGGTTTCATAA
TATAATAATTGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAACAAACTAGAATTGAATGT
CTACCTCAAGAAACATGAAGAAAAAGACATTCATTGGAAAGAAAAGTCCATTTATAGACACCCAT
ATATTCAAAAACCTTATCACTCACTGTAAATGATTCTATAATCTCATAATTGATTTTAAGTTGAA
TTTGTTTAAGTTTTTGGTTAAAACAGATAATAATTGAATATCGACCTCGAGAAACATGAAGAAAA
AGGTATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCTTATTACTCAC
TGTAAAAGGTTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTTACATTTTTAGTTAAGAA
AAGCTATAATTGAATGTCTGCCTCGGGGAACGAGAAGCAAAAGCCAACCATTGGCACA
Found at i:12020 original size:171 final size:171
Alignment explanation
Indices: 11720--12045 Score: 408
Period size: 171 Copynumber: 1.9 Consensus size: 171
11710 ACTTTAAATG
* * * *
11720 GTTTTGTAATGTCATAATTGATTTTAGGTTGAATGTTTTTACATTTTTAGTTGAAACAGACTATA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAGACTATA
* * **
11785 ATTGAATGTCAATCTCAAGGAACATAAAGAAAAAGGTGTTCATTGGCAAGAAAAGTACATTTATA
66 ATTGAATGTCAACCTCAAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAAAAGTACATTTATA
* * *
11850 GTCTCTCATT-CCTTCAAAAGCCTTAATACTTGCTGTAAAAA
131 GTCACCCATTATC-TCAAAAGCCTTAATACTTGCTGTAAAAA
*
11891 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGA-TAAT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAGACT-AT
* * ** ** * *
11955 AATTGACTGT-ATACCTCGAGAAATGTCTAGAGAAAGGCATTCATTGGCAAGAAAAGCT-TATTT
65 AATTGAATGTCA-ACCTCAAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAAAAG-TACATTT
12018 ATAGTCACCCATTATCTCAAAAGCCTTA
128 ATAGTCACCCATTATCTCAAAAGCCTTA
12046 TTGCTCACTT
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 2 0.02
171 127 0.97
172 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (171 bp):
GTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAGACTATA
ATTGAATGTCAACCTCAAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAAAAGTACATTTATA
GTCACCCATTATCTCAAAAGCCTTAATACTTGCTGTAAAAA
Found at i:14264 original size:172 final size:161
Alignment explanation
Indices: 14071--14392 Score: 301
Period size: 171 Copynumber: 1.9 Consensus size: 161
14061 NNNNNNNNNN
* * * *
14071 GTTTTATATTCTCAAAATTGATTTAAATTTGAATTCTTTGCAGGTTTTTAGTTAAAACAT-ATTA
1 GTTTTATAATCTCAAAATTGATTTAAAGTTGAATT-TTTGAACGTTTTTAGTTAAAAC-TGATTA
* * * * *
14135 TAATTGAATGTTTAGCTCGA-GAAATGTGAAG-AAAAGGTCTTTCATTGGCAAGAAAAGTCCATT
64 TAATTGAATATCT-GCTCGACGAAACGTGAAGAAAAAGGT-ATTCATTAGCAAGAAAAGTCCATT
14198 TACAGTCAGC-CATTCCTTCAAAAGCCTTATNNNNNNNNNNAAATG
127 TACAGTCA-CTCATTCCTTCAAAAGCCTTAT----------AAATG
* * * * * *
14243 GTTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTAACGTTTTTGGTTAGAACTGATTATA
1 GTTTTATAATCTCAAAATTGATTTAAAGTTGAATTTTTGAACGTTTTTAGTTAAAACTGATTATA
* ** *
14308 ATTGAATATCTGTTTTACGAAACGTGAAGAAAAAGGTATTCATTAGCAAGAAAAGTCCATTTATA
66 ATTGAATATCTGCTCGACGAAACGTGAAGAAAAAGGTATTCATTAGCAAGAAAAGTCCATTTACA
*
14373 GTCACTTATTCCTTCAAAAG
131 GTCACTCATTCCTTCAAAAG
14393 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
170 5 0.04
171 84 0.67
172 37 0.29
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.37
Consensus pattern (161 bp):
GTTTTATAATCTCAAAATTGATTTAAAGTTGAATTTTTGAACGTTTTTAGTTAAAACTGATTATA
ATTGAATATCTGCTCGACGAAACGTGAAGAAAAAGGTATTCATTAGCAAGAAAAGTCCATTTACA
GTCACTCATTCCTTCAAAAGCCTTATAAATG
Done.