Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402105.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_52.0, 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: 35315
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 13349 characters in sequence are not A, C, G, or T
Found at i:4127 original size:172 final size:172
Alignment explanation
Indices: 3899--5049 Score: 1213
Period size: 172 Copynumber: 6.7 Consensus size: 172
3889 TAAGCCTTTG
* * * * * * * ** *
3899 AAAGACTTATCACTTGCTTTAAATGGTTTAATAATCTCAAAATTGATACTAGGTTGATTTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATTTTTTT
** * * *
3964 ACATTTTTGGTTAATGCATACTAGAATTGAGTGTCTACCTTGAGAAACATGAAGAAAAAAGCATT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATT
** * *
4029 CATTTTCAAGAAAAGTCTAATTATAGTCACCCATACTTTCAA
131 CATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
* * *
4071 AAAGTCTTATTACTTGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATATTTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATTTTTTT
* * * * * * *
4136 ATATTTTTGGATAAAATAGACTATAATTGAATGTCTACCTTTAGAAACGTGAAGAAAAAAATATT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATT
*
4201 CATTAGCAAGAAAAGTCTAATTATAGTCACCCATACCTTCAA
131 CATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
* * *
4243 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATATCATAATTGATTTTAGATTGAATATTTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATTTTTTT
* * * * * * * * *
4308 ATATTTTTGGATAAAATATACTATAATTGATTGTGTACCTTTG-GAAACATGAAGAAAGAAGCAT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACC-TTGAGAAACATGAAGAAAAAAGTAT
* * * *
4372 TCATTGGTAAAAAAAGTC-ATTTATAGTTACCCATACCTTCAA
130 TCATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
** * ** * *
4414 AAAGATTTATTACTCGCTCTAAATAGTTTTATAATACCATAAATGATTTTAGGTTGAAGTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATTTTTTT
* * * * * *
4479 ACATTTTTAGTTAAAACAGACTAGAATTAAATGTTTACCTTGGGAAACGTGAAGAAAAAGGTATT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATT
* **
4544 CATTAGCAAAAAAAGTCTATTTATAGTCACCCATTTCTTCAA
131 CATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
** * * *
4586 AAAGATTTATTACTCGCTTTAAATAGTTTTATATTGCCATAATTGATTTTAGGTTAAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATTTTTTT
* * * * *
4651 ACATTTTTAGTTAAAACAGACTAGAATTGAATGTTTGCCTT-AGGAAACATAAAGAAAAAGGTAT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGA-GAAACATGAAGAAAAAAGTAT
* * * **
4715 TCATTAACAA-AAAAGTCCATTTAGAGTCACCCATTTCTTC-A
130 TCATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
* * * * *
4756 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTACGTTTGAATTGTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTA-GGTTGAATT-TTT
* * * * * *
4820 GTACTTTTTTGATTAAAATAGACTAGAATTTAATGTCTACCTTGAGAAAAATGAAGAAAAAAGTA
64 TTACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTA
* * *
4885 TTCATTTGCAAG-AAAGTCCATTTATAGTCACCCGTACCTTC-A
129 TTCATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
* * * * * * * * * * *
4927 AGAGCCTTATTACTTGCTTTTAACACTTTTGTGATGCCATAATTCATTTTACAGTT-AAATTTTT
1 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTA-GGTTGAATTTTTT
* * * ** *
4991 TAAAGTTTTTGGTTAAAACAGACTATAATTGAATGTTTACCTCAAGAAACATAAAGAAA
65 TACA-TTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAA
5050 NNNNNNNNNN
Statistics
Matches: 832, Mismatches: 137, Indels: 21
0.84 0.14 0.02
Matches are distributed among these distances:
169 4 0.00
170 54 0.06
171 341 0.41
172 431 0.52
173 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (172 bp):
AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATTTTTTT
ACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATT
CATTAGCAAGAAAAGTCTATTTATAGTCACCCATACCTTCAA
Found at i:4463 original size:343 final size:337
Alignment explanation
Indices: 3899--5032 Score: 1195
Period size: 343 Copynumber: 3.3 Consensus size: 337
3889 TAAGCCTTTG
* * * * * ** * * *
3899 AAAGACTTATCACTTGCTTTAAATGGTTTAATAAT-CTCAAAATTGATACTAGGTTGATTTTTTT
1 AAAGACTTATTACTCGCTTTAAATAGTTTTATAATGC-CATAATTGATTTTAGATTAAATTTTTT
** * * *
3963 TACATTTTTGGTTAATGCATACTAGAATTGAGTGTCTACC-TTGAGAAACATGAAGAAAAAAGCA
65 TACATTTTTGGTTAAAACAGACTAGAATTGAATGTTTACCTTTG-GAAACATGAAG-AAAAAGCA
* * * *
4027 TTCATTTTCAAGAAAAGTCTAATTATAGTCACCCATACTTTCAAAAAGTCTTATTACTTGCTTTA
128 TTCA-TTT-AAAAAAAGTC-ATTTATAGTCACCCATACCTTCAAAAAGT-TTATTACTCGCTTTA
* * *
4092 AATAGTTTTATAATGTCATAATTGATTTTAGGTTGAATATTTTTATATTTTTGGATAAAATAGAC
189 AATAGTTTTATAAT-CCATAAATGATTTTAGGTTGAAT-TTTTTATATTTTTAGATAAAATAGAC
* * * * *
4157 TATAATTGAATGTCTACCTTTAGAAACGTGAAGAAAAAAATATTCATTAGCAAGAAAAGTCTAAT
252 TAGAATTAAATGTCTACCTTGAGAAACGTGAAGAAAAAAGTATTCATTAGCAAGAAAAGTCTATT
4222 TATAGTCACCCATACCTTCAA
317 TATAGTCACCCATACCTTCAA
* ** * *
4243 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATATCATAATTGATTTTAGATTGAATATTTTT
1 AAAGACTTATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAGATTAAATTTTTTT
* * * * * * *
4308 ATATTTTTGGATAAAATATACTATAATTGATTGTGTACCTTTGGAAACATGAAGAAAGAAGCATT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTTTACCTTTGGAAACATGAAGAAA-AAGCATT
* *
4373 CATTGGTAAAAAAAGTCATTTATAGTTACCCATACCTTCAAAAAGATTTATTACTCGCTCTAAAT
130 CATT--TAAAAAAAGTCATTTATAGTCACCCATACCTTCAAAAAG-TTTATTACTCGCTTTAAAT
* * *
4438 AGTTTTATAATACCATAAATGATTTTAGGTTGAAGTTTTTTACATTTTTAGTTAAAACAGACTAG
192 AGTTTTATAAT-CCATAAATGATTTTAGGTTGAA-TTTTTTATATTTTTAGATAAAATAGACTAG
* * * *
4503 AATTAAATGTTTACCTTGGGAAACGTGAAGAAAAAGGTATTCATTAGCAAAAAAAGTCTATTTAT
255 AATTAAATGTCTACCTTGAGAAACGTGAAGAAAAAAGTATTCATTAGCAAGAAAAGTCTATTTAT
**
4568 AGTCACCCATTTCTTCAA
320 AGTCACCCATACCTTCAA
* * *
4586 AAAGATTTATTACTCGCTTTAAATAGTTTTATATTGCCATAATTGATTTTAGGTTAAATTTTTTT
1 AAAGACTTATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAGATTAAATTTTTTT
* * * * *
4651 ACATTTTTAGTTAAAACAGACTAGAATTGAATGTTTGCCTTAGGAAACATAAAGAAAAAGGTATT
66 ACATTTTTGGTTAAAACAGACTAGAATTGAATGTTTACCTTTGGAAACATGAAGAAAAA-GCATT
* * ** * *
4716 CATTAACAAAAAAGTCCATTTAGAGTCACCCATTTCTTC-AAAAGCCTTATTACTCACTTTAAAT
130 CATTTA-AAAAAAGT-CATTTATAGTCACCCATACCTTCAAAAAG-TTTATTACTCGCTTTAAAT
* * * * *
4780 GGTTTTATAATCTCA-AAATTGA-TTTACGTTTGAATTGTTTGTACTTTTTTGATTAAAATAGAC
192 AGTTTTATAATC-CATAAA-TGATTTTA-GGTTGAATTTTTTATA-TTTTTAGA-TAAAATAGAC
* ** * *
4843 TAGAATTTAATGTCTACCTTGAGAAAAATGAAGAAAAAAGTATTCATTTGCAAG-AAAGTCCATT
252 TAGAATTAAATGTCTACCTTGAGAAACGTGAAGAAAAAAGTATTCATTAGCAAGAAAAGTCTATT
*
4907 TATAGTCACCCGTACCTTC-A
317 TATAGTCACCCATACCTTCAA
* * * * * * * * * *
4927 AGAGCCTTATTACTTGCTTTTAACACTTTTGTGATGCCATAATTCATTTTACAGTTAAA-TTTTT
1 AAAGACTTATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAGA-TTAAATTTTTT
* *
4991 TAAAGTTTTTGGTTAAAACAGACTATAATTGAATGTTTACCT
65 TACA-TTTTTGGTTAAAACAGACTAGAATTGAATGTTTACCT
5033 CAAGAAACAT
Statistics
Matches: 663, Mismatches: 110, Indels: 36
0.82 0.14 0.04
Matches are distributed among these distances:
341 64 0.10
342 122 0.18
343 359 0.54
344 114 0.17
345 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (337 bp):
AAAGACTTATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAGATTAAATTTTTTT
ACATTTTTGGTTAAAACAGACTAGAATTGAATGTTTACCTTTGGAAACATGAAGAAAAAGCATTC
ATTTAAAAAAAGTCATTTATAGTCACCCATACCTTCAAAAAGTTTATTACTCGCTTTAAATAGTT
TTATAATCCATAAATGATTTTAGGTTGAATTTTTTATATTTTTAGATAAAATAGACTAGAATTAA
ATGTCTACCTTGAGAAACGTGAAGAAAAAAGTATTCATTAGCAAGAAAAGTCTATTTATAGTCAC
CCATACCTTCAA
Found at i:5448 original size:172 final size:172
Alignment explanation
Indices: 5160--5523 Score: 383
Period size: 172 Copynumber: 2.1 Consensus size: 172
5150 GGAATGGGTG
* * * * * *
5160 ACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTGCATTTCTAGAGGTAGACATTGA
1 ACTATAAATGGACTTTTCTTACAAATGAATACCTTTTTCTTTACATTTCTAGAAGTAGACATTCA
*
5225 ATTATAGTCTATTTTAACCAAAAACGTAAAAAAATTCAACCGCAAAATCAATTAT-AGCATCACA
66 ATTATAGTCTATTTTAACCAAAAACGTAAAAAAATTCAAACGCAAAATCAATTATGAG-ATCACA
* * * *
5289 AAACTATTTAAAGCAAGTAGTAAGGCTTTTGAAGGTACGGGTA
130 AAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGTACGGATA
* * ** *
5332 ATTATAAATGGACTTTTCTTACAAATGAATACTTTTTTCTTTATTTTTCTCA-AATTAGACATTC
1 ACTATAAATGGACTTTTCTTACAAATGAATACCTTTTTCTTTACATTTCT-AGAAGTAGACATTC
* * * * * * * * * * *
5396 TATTCTGGTCTATTTTAACTAAAAATGTACAAAGAATTCAAATG-TAAATCAATTTTGAGATTAT
65 AATTATAGTCTATTTTAACCAAAAACGTA-AAAAAATTCAAACGCAAAATCAATTATGAGATCAC
** ** * *
5460 AATGCCATTTAAAGTGAGTAATAAGGCTTTTGAAAGTATGGATT
129 AAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGTACGGATA
5504 ACTATAAATGGACTTTTCTT
1 ACTATAAATGGACTTTTCTT
5524 GGCAATGAAN
Statistics
Matches: 155, Mismatches: 34, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
172 141 0.91
173 14 0.09
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (172 bp):
ACTATAAATGGACTTTTCTTACAAATGAATACCTTTTTCTTTACATTTCTAGAAGTAGACATTCA
ATTATAGTCTATTTTAACCAAAAACGTAAAAAAATTCAAACGCAAAATCAATTATGAGATCACAA
AACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGTACGGATA
Found at i:18146 original size:172 final size:172
Alignment explanation
Indices: 17432--18209 Score: 729
Period size: 171 Copynumber: 4.5 Consensus size: 172
17422 NNNNNNNNNN
* *
17432 GTAGACATTCAATTATAATATATTTTAACCAAAAATGTATAAAGAATTCAAATTTAAATCAATTT
1 GTAGACATTCAATTATAGTATATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTT
* * * * *
17497 TGAGAATATAAAACCATTTACAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGA
66 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGA
* * * ** *
17562 CTTTTATTGCTAATGAATGCCTTTTGT-TT-ACGTTTCTTGAG
131 CTTTTCTTGCCAATGAATTCCTTTT-TCTTCATATTTCTTAAG
* * * * * * * *
17603 GTAGACATTGAATTATAGTATGTTTTAGCCAAAAACGTA-AAACAATTCAACAGTAAAATCAACT
1 GTAGACATTCAATTATAGTATATTTTAACCAAAAATGTACAAAGAATTCAA-ATTTAAATCAATT
* * ** * * * *
17667 ATG-GCATTACAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGCTACGGGTGACAATAAATG
65 TTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATG
* ********** *
17731 GACTTTTCTTGCAAATGANNNNNNNNNNCTTCATTTTTCTTAAG
129 GACTTTTCTTGCCAATGAATTCCTTTTTCTTCATATTTCTTAAG
* * * * *
17775 GTAGACATTTAATTCTAGTTTATTTTAACCAAAAATGTATAAAGAATTCAAATGTAAATCAATTT
1 GTAGACATTCAATTATAGTATATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTT
***************** *
17840 TGAGATTATNNNNNNNNNNNNNNNNNGTAATAAGGCTTTTGAAGGTATGGGTGACTAT-AATGGA
66 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGA
* *
17904 CTTTTCTTGCCAATGAATTCCTTTTTCTTCATATATCTGAAG
131 CTTTTCTTGCCAATGAATTCCTTTTTCTTCATATTTCTTAAG
* * * * *
17946 GTAGACATTCAATTATAATCTGTTTTAACCAAATATGTACAAAGAATTTAAATTTAAATCAATTT
1 GTAGACATTCAATTATAGTATATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTT
* ** * * * * *
18011 TGAGAATATAAAATTATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGCGTAACTAGAAATTGA
66 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGA
*
18076 CTTTTCTTGCCAATGAATTCCTTTTTCTTCATATTTCTCAAG
131 CTTTTCTTGCCAATGAATTCCTTTTTCTTCATATTTCTTAAG
* * * * *
18118 GTAGACATTCAATTGTAGTCTATTTTAACCAAAAATGTACAAAAAATTTAAATGTAAATCAATTT
1 GTAGACATTCAATTATAGTATATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTT
18183 TGAGATTATAAAACCATTTAAAGTGAG
66 TGAGATTATAAAACCATTTAAAGTGAG
18210 NNNNNNNNNN
Statistics
Matches: 472, Mismatches: 128, Indels: 13
0.77 0.21 0.02
Matches are distributed among these distances:
170 11 0.02
171 238 0.50
172 212 0.45
173 11 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (172 bp):
GTAGACATTCAATTATAGTATATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTT
TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGA
CTTTTCTTGCCAATGAATTCCTTTTTCTTCATATTTCTTAAG
Found at i:21499 original size:172 final size:171
Alignment explanation
Indices: 21078--22911 Score: 1086
Period size: 172 Copynumber: 10.7 Consensus size: 171
21068 NNNNNNNNNN
* * * * *
21078 TAAATCAATTTTGACAATATAAAACTATTTAAAGTGAGTAATAAGGCCTTTAAAAGAATGGGTGA
1 TAAATCAATTTTG-GAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
* * * * * *
21143 TTATAAATGTACTTTTCTTAC-CAATGAATGCCTTTTTCTTTACGA-TTCTCAAGGTAAAAATTC
65 CTATAAATGGACTTTTCTT-CTCAATGAATGCCTTTTTCTTCAC-ATTTCTCAAGGTAGACATTG
* * ** * * *
21206 AATTATAGTCTATTTTAACTTAAAATGTAAAAAACAATTCAACCTT
128 AATTATAATCTGTTTTAACCAAAAATGT-ACAAAGAATTCAA-ATT
* * * * * * * * *
21252 GAAATCAATTATGGCATTACAAAACCATTTAAAGTAAGTGATAAAGCTTTTGAAAGTG--TGGAT
1 TAAATCAATTTTGG-AATATAAAACCATTTAAAGTGAGTAACAAGGCTTTT-AAAG-GAATGGGT
* * *
21315 GACTATAAATGGACTTTTCTTACT-AATGACTTCCTTTTTCTTCACATTTCTTAAGGTAGACATT
63 GACTATAAATGGACTTTTCTT-CTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATT
* * *
21379 TAATTATAATCTGTTTTAACCAAAAATATACGAAGAATTCAAATT
127 GAATTATAATCTGTTTTAACCAAAAATGTACAAAGAATTCAAATT
**********
21424 TAAATCAATTTTGTGAATATAAAACCATTTAAAGTGANNNNNNNNNNTTTTAAAGGAATGGGTGA
1 TAAATCAATTTTG-GAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
* ** * **
21489 CTATAAATGGACTTGTCTTGGCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAGACATTGAA
65 CTATAAATGGACTTTTCTTCTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTGAA
* * * **
21554 TTATAGTCTGTTTTAACCAAAAACGTA-AAAAAATTCAACCGT
130 TTATAATCTGTTTTAACCAAAAATGTACAAAGAATTCAA-ATT
* * * ** * * * * * *
21596 AAAATCAATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAGGGTTTTGAAGGTACGAGTGA
1 TAAATCAATTTTGG-AATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
* * * * * *
21661 CTATAAATAGACTTTTCTTGTCGATGAATTCTTTTTTCTTCACATTTCTCAATGTAGACATTCG-
65 CTATAAATGGACTTTTCTTCTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATT-GA
* *
21725 ATTATAATCAGTTTTAACCAAAAATGTACAAAGAATTGAAATT
129 ATTATAATCTGTTTTAACCAAAAATGTACAAAGAATTCAAATT
* *
21768 TAAATCAATTTTGAGAATATAAAATCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATAGGTGA
1 TAAATCAATTTTG-GAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
* * * ** *
21833 CTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTTATGTTTCTCGAGGTAGACATTGAA
65 CTATAAATGGACTTTTCTTCTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTGAA
* * ** ***
21898 TTATAGTCTATTTTAACCAAAAACATA-AAA-ATATTCAGCCGT
130 TTATAATCTGTTTTAACCAAAAATGTACAAAGA-ATTCA-AATT
* * * * * ** * * * *
21940 AAAATCAATTATGGCATTACAAAACTATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGGGTGA
1 TAAATCAATTTTGG-AATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
* * * * ** *
22005 CTATAAATAGACTTTTCTTAC-AAATGAATACTTTTTTCTTCATTTTTCTCAAGGTAGACATTAA
65 CTATAAATGGACTTTTCTT-CTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTGA
* * * * * * *
22069 ACTCTAGTTTATTTAAACCAAAAATGTACAAAGAATTCAAATG
129 ATTATAATCTGTTTTAACCAAAAATGTACAAAGAATTCAAATT
* * * * * *
22112 TAAATCAATTTTGAGATTATAAAACCATATAGAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGA
1 TAAATCAATTTTG-GAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
* ** * * *
22177 CTATAAATGGACTTTTCTTGC-CAATAAATATCTTTTTCTTCACGTTTGCT-AAGGCAGACATTC
65 CTATAAATGGACTTTTCTT-CTCAATGAATGCCTTTTTCTTCACATTT-CTCAAGGTAGACATTG
* * * **
22240 AATTCTAGTCTGTTTTAACAAAAAATGTA-AAA-ATATTCAACCT
128 AATTATAATCTGTTTTAACCAAAAATGTACAAAGA-ATTCAAATT
* ** * * * * * *
22283 AAAATCAATGAT-GACATTATCAAACTATTTAAAGCGAGTAATAAAGCTTTTTTAA-GATATGGG
1 TAAATCAATTTTGGA-A-TATAAAACCATTTAAAGTGAGTAACAAGGC-TTTTAAAGGA-ATGGG
* * * ** * *
22346 CGACTATAATTAGACTTTTCTTAC-CAATCG-ATGATTTTTTCTTCACGTTTCTGAAGGTAGACA
62 TGACTATAAATGGACTTTTCTT-CTCAAT-GAATGCCTTTTTCTTCACATTTCTCAAGGTAGACA
* * * * ***
22409 TTCAATT-TCAGTCAT-TTTTATCCAAAAATGTA-AAA-ATAGTCAGCCT
125 TTGAATTAT-AATC-TGTTTTAACCAAAAATGTACAAAGA-ATTCAAATT
* * * * ** * * *
22455 AAAATCAATTAT-GACCTTATAAAACTATTTAAAGCAAGTAATAAGGCTTTTTGAAA-GTATAGG
1 TAAATCAATTTTGGA--ATATAAAACCATTTAAAGTGAGTAACAAGGC-TTTT-AAAGGAATGGG
* * * * * *
22518 TGACTATAATTAGACTTTTCTTGTCAATGAATGCGTTTTTCTTCACGTTTCTCAAGGTAAACATT
62 TGACTATAAATGGACTTTTCTTCTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATT
* * * * ** * **
22583 CAATTCTAGTTTGTTTTAATAAAAAATGTA-AAAAAATTCAACCT
127 GAATTATAATCTGTTTTAACCAAAAATGTACAAAGAATTCAAATT
* * * ** ** * ** **
22627 AAAATTAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATTAGGCTTTCAAAGGCTTGATTGA
1 TAAATCAATTTTG-GAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGA
** * * ** ** * *
22692 CTATAAAT-GATCTTTT-TGTGCT-AATGGTTGGCTTTTGCTTCATGTACCCCAAGGTCGACATT
65 CTATAAATGGA-CTTTTCT-T-CTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATT
* ** * * *
22754 CAATTATAGCCTTTTTTTAATCAAAAATGTTA-AAA-AATTC-AACT
127 GAATTATAATC-TGTTTTAACCAAAAATG-TACAAAGAATTCAAATT
* ** * * * * * * *
22798 TAAATTCATTTTTGAGGTTGTATAGCCATTTAAAGTAAGTAATAAGGCTTTTGAAGAAATGGGTG
1 TAAA-TCAATTTTG-GAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTG
* * *
22863 ACTATAAAGGGACTTTTCTTGC-CAATGAATACCTTTTTCTTCACGTTTC
64 ACTATAAATGGACTTTTCTT-CTCAATGAATGCCTTTTTCTTCACATTTC
22912 CTAAGGCATA
Statistics
Matches: 1321, Mismatches: 288, Indels: 104
0.77 0.17 0.06
Matches are distributed among these distances:
169 2 0.00
170 9 0.01
171 135 0.10
172 999 0.76
173 49 0.04
174 123 0.09
175 3 0.00
176 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (171 bp):
TAAATCAATTTTGGAATATAAAACCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATGGGTGAC
TATAAATGGACTTTTCTTCTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTGAAT
TATAATCTGTTTTAACCAAAAATGTACAAAGAATTCAAATT
Found at i:21746 original size:344 final size:343
Alignment explanation
Indices: 20913--22981 Score: 1804
Period size: 344 Copynumber: 6.0 Consensus size: 343
20903 NNNNNNNNNN
* * * * * * *
20913 ATTATGGCATTACAAAACTATTTCAAGCAAGTGATAATGCTTTTGAAGGTGTGGGTGACTATAAA
1 ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGAGTGACTATAAA
* * * * *
20978 TGGACTTTTCTTACCAATGAAGTCCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAAT
66 TAGACTTTTCTTACAAATGAATTCTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAAT
* *********************** * *
21043 CTGTTTTAACCANNNNNNNNNNNNNNNNNNNNNNNTAAATCAATTTTGACAATATAAAACTATTT
131 CAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGAATATAAAACCATTT
* * * * * *
21108 AAAGTGAGTAATAAGGCCTTTAAAAGAATGGGTGATTATAAATGTACTTTTCTTACCAATGAATG
196 AAAGTGAGTAAAAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * **
21173 CCTTTTTCTTTACGATTCTCAAGGTAAAAATTCAATTATAGTCTATTTTAACTTAAAATGTAAAA
261 CCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGT-AAA
*
21238 AACAATTCAACCTTGAAATCA
325 AA-AATTCAACC-TAAAATCA
* * * * *
21259 ATTATGGCATTACAAAACCATTTAAAGTAAGTGATAAAGCTTTTGAAAGTGTG-GATGACTATAA
1 ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGAG-TGACTATAA
* * * * * *
21323 ATGGACTTTTCTTACTAATGACTTCCTTTTTCTTCACATTTCTTAAGGTAGACATTTAATTATAA
65 ATAGACTTTTCTTACAAATGAATTCTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAA
* * * *
21388 TCTGTTTTAACCAAAAATATACGAAGAATTCAAATTTAAATCAATTTTGTGAATATAAAACCATT
130 TCAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGAATATAAAACCATT
********** * *
21453 TAAAGTGANNNNNNNNNNTTTTAAAGGAATGGGTGACTATAAATGGACTTGTCTTGGCAATGAAT
195 TAAAGTGAGTAAAAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * *
21518 GCCTTTTTCTTTATGTTTCTCAAGGTAGACATTGAATTATAGTCTGTTTTAACCAAAAACGTAAA
260 GCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAA
21583 AAAATTCAACCGTAAAATCA
325 AAAATTCAACC-TAAAATCA
* * *
21603 ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAGGGTTTTGAAGGTACGAGTGACTATAAA
1 ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGAGTGACTATAAA
* * * *
21668 TAGACTTTTCTTGTC-GATGAATTCTTTTTTCTTCACATTTCTCAATGTAGACATTCGATTATAA
66 TAGACTTTTCTT-ACAAATGAATTCTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAA
* *
21732 TCAGTTTTAACCAAAAATGTACAAAGAATTGAAATTTAAATCAATTTTGAGAATATAAAATCATT
130 TCAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGAATATAAAACCATT
* * *
21797 TAAAGTGAGTAACAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
195 TAAAGTGAGTAAAAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * * **
21862 GCTTTTTTCTTTATGTTTCTCGAGGTAGACATTGAATTATAGTCTATTTTAACCAAAAACATAAA
260 GCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAA
* *
21927 AATATTCAGCCGTAAAATCA
325 AAAATTCAACC-TAAAATCA
* * *
21947 ATTATGGCATTACAAAACTATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGGGTGACTATAAA
1 ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGAGTGACTATAAA
* ** * * * *
22012 TAGACTTTTCTTACAAATGAATACTTTTTTCTTCATTTTTCTCAAGGTAGACATTAAACTCTAGT
66 TAGACTTTTCTTACAAATGAATTCTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATA-A
* * * * *
22077 TTA-TTTAAACCAAAAATGTACAAAGAATTCAAATGTAAATCAATTTTGAGATTATAAAACCATA
130 TCAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGAATATAAAACCATT
* * * * *
22141 TAGAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAAT
195 TAAAGTGAGTAAAAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
** * * *
22206 ATCTTTTTCTTCACGTTTGCT-AAGGCAGACATTCAATTCTAGTCTGTTTTAACAAAAAATGTAA
260 GCCTTTTTCTTTACGTTT-CTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAA
*
22270 AAATATTCAACCTAAAATCA
324 AAAAATTCAACCTAAAATCA
* * * * * * * * *
22290 ATGATGACATTATCAAACTATTTAAAGCGAGTAATAAAGCTTTTTTAAGATATGGGCGACTATAA
1 ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAAGC-TTTTGAAGGTATGAGTGACTATAA
* * ** * *
22355 TTAGACTTTTCTTACCAATCG-ATGATTTTTTCTTCACGTTTCTGAAGGTAGACATTCAATT-TC
65 ATAGACTTTTCTTACAAAT-GAATTCTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTAT-
* * * * *** * * *** *
22418 AGTCATTTTTATCCAAAAATGTA-AAA-ATAGTCAGCCTAAAATCAATTATGACCTTATAAAACT
128 AATCAGTTTTAACCAAAAATGTACAAAGA-ATTCAAATTTAAATCAATTTTGAGAATATAAAACC
** * * * * * *
22481 ATTTAAAGCAAGTAATAAGGCTTTTTGAAA-GTATAGGTGACTATAATTAGACTTTTCTTGTCAA
192 ATTTAAAGTGAGTAAAAAGGC-TTTT-AAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAA
* * * * * *
22545 TGAATGCGTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTCTAGTTTGTTTTAATAAAAAAT
255 TGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAT
*
22610 GTAAAAAAATTCAACCTAAAATTA
320 GTAAAAAAATTCAACCTAAAATCA
* * * ** *
22634 ATTTTGAG-ATTATAAAACCATTTAAAGCAAGTAATTAGGCTTTCAAAGGCT-TGATTGACTATA
1 ATTATG-GCATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGG-TATGAGTGACTATA
* * * * ** ** * *
22697 AAT-GATCTTTT-TGTGCTAATG-GTTGGC-TTTTGCTTCATGTACCCCAAGGTCGACATTCAAT
64 AATAGA-CTTTTCT-TACAAATGAATT--CTTTTTTCTTCACATTTCTCAAGGTAGACATTCAAT
** ** * * * ** *
22758 TATAGCCTTTTTTTAATCAAAAATGTTA-AAA-AATTC-AACTTAAATTCATTTTTGAGGTTGTA
125 TATAATC-AGTTTTAACCAAAAATG-TACAAAGAATTCAAATTTAAA-TCAATTTTGAGAATATA
* * * * * * *
22820 TAGCCATTTAAAGTAAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAAGGGACTTTTCTTGC
187 AAACCATTTAAAGTGAGTAAAAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGC
* * * * * * * *
22885 CAATGAATACCTTTTTCTTCACGTTTC-CTAAGGCATACA--CAAATTATATTCGGTTCTAACCA
252 CAATGAATGCCTTTTTCTTTACGTTTCTC-AAGGTAGACATTC-AATTATAGTCTGTTTTAACAA
* * *
22947 AAAACGTCAAAAAATTCAATCTAAAATCA
315 AAAATGTAAAAAAATTCAACCTAAAATCA
22976 ATTATG
1 ATTATG
22982 ACGTTATACN
Statistics
Matches: 1424, Mismatches: 272, Indels: 58
0.81 0.16 0.03
Matches are distributed among these distances:
341 1 0.00
342 53 0.04
343 218 0.15
344 875 0.61
345 21 0.01
346 256 0.18
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (343 bp):
ATTATGGCATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGAGTGACTATAAA
TAGACTTTTCTTACAAATGAATTCTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAAT
CAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGAATATAAAACCATTT
AAAGTGAGTAAAAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
CCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAA
AAATTCAACCTAAAATCA
Found at i:22831 original size:516 final size:506
Alignment explanation
Indices: 21079--22911 Score: 1481
Period size: 516 Copynumber: 3.5 Consensus size: 506
21069 NNNNNNNNNT
* * * ** ** ** * *
21079 AAATCAATTTTGACAATATAAAACTATTTAAAGTGAGTAATAAGGCCTTTAAAAGAATGGGTGAT
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATAAGG-CTTTTGAAGGTTGAGTGAC
* * * * * * ** *
21144 TATAAAT-GTACTTTTCTTACCAATGAATGCCTTTTTCTTTACGATTCTCAAGGTAAAAATTCAA
65 TATAAATAG-ACTTTTCTTGCTAATG-AT-TCTTTTTCTTCACGTTTCCCAAGGTCGACATTCAA
* * *
21208 TTATAGTCTATTTTAACTTAAAATGTAAAAAACAATTCAACCTTGAAATCAATTATG-GCATTAC
127 TTATAGTCTGTTTTAAC-AAAAATGT--AAAA-AATTCAA-CTT-AAATCAATTTTGAG-ATTA-
* * * * ** * *
21272 AAAACCATTTAAAGTAAGTGATAAAGCTTTTGAAAGTGTGGATGACTATAAATGGACTTTTCTTA
184 TAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGAATGGGTGACTATAAATGGACTTTTCTTG
* * *** * ** * * *
21337 CTAATGACTTCCTTTTTCTTCACATTTCTTAAGGTAGACATTTAATTATAATCTGTTTTAACCAA
248 CCAATGAATGATTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACCAA
* *** * * ** * * * ** ***
21402 AAATATACGAAGAAT--TCA-AATTTAAATCAATTTTGTGAATATAAAACCATTTAAAGTGANNN
313 AAACATA--AA-AATAGTCAGCCGTAAAATCAATTATGACATTACAAAACTATTTAAAGCAAGTA
******* * * * * *
21464 NNNNNNNTTTT-AAAGGAATGGGTGACTATAAATGGACTTGTCTTGGCAATGAATGCCTTTTTCT
375 ATAAAGCTTTTGAAA-GTATAGGTGACTATAAATAGACTTTTCTTGACAATGAATGCCTTTTTCT
* * * * *
21528 TTATGTTTCTCAAGGTAGACATTGAATTATAGTCTGTTTTAACCAAAAACGTAAAAAAATTCAAC
439 TCATGTTTCTCAAGGTAGACATTAAATTCTAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAAC
21593 CGTA
504 C-TA
* * *
21597 AAATCAATTATG-GCATTATAAAACCATTTAAAGCAAGTAATAAGGGTTTTGAAGGTACGAGTGA
1 AAATCAATTTTGAG-ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGT-TGAGTGA
* * * * * *
21661 CTATAAATAGACTTTTCTTG-TCGATGAATTCTTTTTTCTTCACATTTCTCAATGTAGACATTCG
64 CTATAAATAGACTTTTCTTGCT-AATG-ATTC-TTTTTCTTCACGTTTCCCAAGGTCGACATTCA
* * * * *
21725 ATTATAATCAGTTTTAACCAAAAATGTACAAAGAATTGAAATTTAAATCAATTTTGAGAATATAA
126 ATTATAGTCTGTTTTAA-CAAAAATGTA-AAA-AATT-CAACTTAAATCAATTTTGAGATTAT-A
* * * *
21790 AATCATTTAAAGTGAGTAACAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGTC
186 AACCATTTAAAGTGAGTAATAAGGCTTTTAAA-GAATGGGTGACTATAAATGGACTTTTCTTGCC
* * * *
21855 AATGAATGCTTTTTTCTTTATGTTTCTCGAGGTAGACATTGAATTATAGTCTATTTTAACCAAAA
250 AATGAATGATTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACCAAAA
* *
21920 ACATAAAAATATTCAGCCGTAAAATCAATTATGGCATTACAAAACTATTTAAAGCAAGTAATAAA
315 ACATAAAAATAGTCAGCCGTAAAATCAATTATGACATTACAAAACTATTTAAAGCAAGTAATAAA
* * * * *
21985 GCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTT-ACAAATGAATACTTTTTTCTTCATT
380 GCTTTTGAAAGTATAGGTGACTATAAATAGACTTTTCTTGAC-AATGAATGCCTTTTTCTTCATG
* * * * * *
22049 TTTCTCAAGGTAGACATTAAACTCTAGTTTATTTAAACCAAAAATGTACAAAGAATTCAA-ATGT
444 TTTCTCAAGGTAGACATTAAATTCTAGTTTGTTTTAACCAAAAATGTA-AAAAAATTCAACCT-A
* * ** ** *
22113 AAATCAATTTTGAGATTATAAAACCATATAGAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAG-GTTGAGTGAC
* * * * *
22178 TATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCACGTTTGCTAAGG-CAGACATTCAA
65 TATAAATAGACTTTTCTTGCTAAT-GAT-TCTTTTTCTTCACGTTTCCCAAGGTC-GACATTCAA
* * ** *
22242 TTCTAGTCTGTTTTAACAAAAAATGTAAAAATATTCAACCTAAAATCAATGATGACATTATCAAA
127 TTATAGTCTGTTTTAAC-AAAAATGTAAAAA-ATTCAA-CTTAAATCAATTTTGAGATTAT-AAA
* * * * * * * *
22307 CTATTTAAAGCGAGTAATAAAGCTTTTTTAAGATATGGGCGACTATAATTAGACTTTTCTTACCA
188 CCATTTAAAGTGAGTAATAAGGC-TTTTAAAGA-ATGGGTGACTATAAATGGACTTTTCTTGCCA
*
22372 ATCG-ATGATTTTTTCTTCACGTTTCT-GAAGGTAGACATTCAATT-TCAGTC-ATTTTTATCCA
251 AT-GAATGATTTTTTCTTCACGTTTCTCG-AGGTAGACATTCAATTAT-AGTCTA-TTTTAACCA
** * *
22433 AAAATGTAAAAATAGTCAGCC-TAAAATCAATTATGACCTTATAAAACTATTTAAAGCAAGTAAT
312 AAAACATAAAAATAGTCAGCCGTAAAATCAATTATGACATTACAAAACTATTTAAAGCAAGTAAT
* * * *
22497 AAGGCTTTTTGAAAGTATAGGTGACTATAATTAGACTTTTCTTGTCAATGAATGCGTTTTTCTTC
377 AAAGC-TTTTGAAAGTATAGGTGACTATAAATAGACTTTTCTTGACAATGAATGCCTTTTTCTTC
* * * **
22562 ACGTTTCTCAAGGTAAACATTCAATTCTAGTTTGTTTTAATAAAAAATGTAAAAAAATTCAACCT
441 ATGTTTCTCAAGGTAGACATTAAATTCTAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACCT
22627 A
506 A
* * ** *
22628 AAATTAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATTAGGCTTTCAAAGGCTTGATTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGG-TTGAGTGAC
* * * **
22693 TATAAAT-GATCTTTT-TGTGCTAATGGTTGGCTTTTGCTTCATGTACCCCAAGGTCGACATTCA
65 TATAAATAGA-CTTTTCT-TGCTAATGATT--CTTTTTCTTCACGTTTCCCAAGGTCGACATTCA
* * * * *
22756 ATTATAGCCTTTTTTTAATCAAAAATGTTAAAAAATTCAACTTAAATTCATTTTTGAGGTTGTAT
126 ATTATAGTC-TGTTTTAA-CAAAAATG-TAAAAAATTCAACTTAAA-TCAATTTTGAGATTATA-
* * * *
22821 AGCCATTTAAAGTAAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAAGGGACTTTTCTTGCC
186 AACCATTTAAAGTGAGTAATAAGGCTTTTAAAG-AATGGGTGACTATAAATGGACTTTTCTTGCC
*
22886 AATGAAT-ACCTTTTTCTTCACGTTTC
250 AATGAATGA-TTTTTTCTTCACGTTTC
22912 CTAAGGCATA
Statistics
Matches: 1048, Mismatches: 217, Indels: 103
0.77 0.16 0.08
Matches are distributed among these distances:
513 4 0.00
514 11 0.01
515 272 0.26
516 605 0.58
517 41 0.04
518 113 0.11
519 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (506 bp):
AAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGTTGAGTGACT
ATAAATAGACTTTTCTTGCTAATGATTCTTTTTCTTCACGTTTCCCAAGGTCGACATTCAATTAT
AGTCTGTTTTAACAAAAATGTAAAAAATTCAACTTAAATCAATTTTGAGATTATAAACCATTTAA
AGTGAGTAATAAGGCTTTTAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGATT
TTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAACATAAAAATA
GTCAGCCGTAAAATCAATTATGACATTACAAAACTATTTAAAGCAAGTAATAAAGCTTTTGAAAG
TATAGGTGACTATAAATAGACTTTTCTTGACAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTA
GACATTAAATTCTAGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACCTA
Found at i:24272 original size:173 final size:162
Alignment explanation
Indices: 23760--24251 Score: 391
Period size: 173 Copynumber: 2.9 Consensus size: 162
23750 NNNNNNNNGG
* * * * * *
23760 TTCTCATGATAGACATTGAATTATAGTATGTTTTAACCAAAAACATAAAAAAATTCAACCGTAAA
1 TTCTCAAGGTAGACATTAAATTATAGT-TATTTTAACCAAAAAC-TTAAAAAATTCAACTGTAAA
* * * * *
23825 ATCAATTATGGTATTACAAAACCA-TTTAAAGTAAGTACTAAGGCTTTTGAAGGTACGAGTGACT
64 ATCAATTATTGCATTACAAAACCATTTTAAAGTAAGTAATAAGGCTTTTGAAGGTATGGGTGACT
* * * *
23889 GTAAATGTACTTTTATTNNNNNNNNNNTCCTTTTTCTTCACAT
129 ATAAATGAACTTTTCTT---------TTCCTTTTTCTTCACAT
* * * * * *
23932 TTCTCAAGGTAGACATTCAATTATAAATTATTTTAACCAAAAAATGCACAACAAATTCAAAT-TT
1 TTCTCAAGGTAGACATTAAATTAT-AGTTATTTTAACCAAAAACT-TA-AA-AAATTCAACTGTA
* * * * * * * * *
23996 AAATCAATT-TTGAGAATATAGAACTATTTGAAA-TGAGTAATAAGGCTTTTAAAGGAATGGGTG
62 AAATCAATTATTG-CATTACAAAACCATTTTAAAGTAAGTAATAAGGCTTTTGAAGGTATGGGTG
* * *
24059 ACTATAAATGAACTTTTCTTTNNNNNNNNNNCCTTTTTCTTTACGT
126 ACTATAAATGAACTTTTCTTT---------TCCTTTTTCTTCACAT
*
24105 TTCTCTAGGTAGACATTAAATTATAGTCTATTTTAACCAAAAACTTAAAAACATTCAACTGTAAA
1 TTCTCAAGGTAGACATTAAATTATAGT-TATTTTAACCAAAAACTTAAAAA-ATTCAACTGTAAA
24170 ATCAATTATTGCATTACAAAACCATTTTAAAGTAAGTAATAAGGCTTTTGAAGGTATGGGTGACT
64 ATCAATTATTGCATTACAAAACCATTTTAAAGTAAGTAATAAGGCTTTTGAAGGTATGGGTGACT
24235 ATAAAT-AGACTTTTCTT
129 ATAAATGA-ACTTTTCTT
24252 NNNNNNNNNN
Statistics
Matches: 253, Mismatches: 46, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
170 2 0.01
171 10 0.04
172 66 0.26
173 162 0.64
174 13 0.05
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35
Consensus pattern (162 bp):
TTCTCAAGGTAGACATTAAATTATAGTTATTTTAACCAAAAACTTAAAAAATTCAACTGTAAAAT
CAATTATTGCATTACAAAACCATTTTAAAGTAAGTAATAAGGCTTTTGAAGGTATGGGTGACTAT
AAATGAACTTTTCTTTTCCTTTTTCTTCACAT
Found at i:24347 original size:173 final size:162
Alignment explanation
Indices: 23917--24353 Score: 360
Period size: 173 Copynumber: 2.6 Consensus size: 162
23907 NNNNNNNNNT
* ** *
23917 CCTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAAATTATTTTAACCAAAAAATGCACA
1 CCTTTTTCTTCACATTTCTCAAGGTAGACATTAAATTATAGTTTATTTTAACC-AAAAATGTACA
* * * * *
23982 ACAAATTCAAATTTAAATCAATTTTGAGAATATAGAACTATTTGAAATGAGTAATAAGGCTTTTA
65 A-AAATTCAAATTTAAATCAATTTTGACAATACAAAACCATTTGAAATAAGTAATAAGGCTTTTA
*
24047 AAGGAATGGGTGACTATAAATGAACTTTTCTTTNNNNNNNNNN
129 AAGGAATGGGTGACTATAAATGAACTTTTCTTT---------A
* * * *
24090 CCTTTTTCTTTACGTTTCTCTAGGTAGACATTAAATTATAGTCTATTTTAACCAAAAACT-TA-A
1 CCTTTTTCTTCACATTTCTCAAGGTAGACATTAAATTATAGTTTATTTTAACCAAAAA-TGTACA
* * * *
24153 AAACATTCAACTGTAAAATCAATTATTG-CATTACAAAACCATTTTAAAGTAAGTAATAAGGCTT
65 AAA-ATTCAAAT-TTAAATCAATT-TTGACAATACAAAACCATTTGAAA-TAAGTAATAAGGCTT
* * *
24217 TTGAAGGTATGGGTGACTATAAAT-AGACTTTTCTTNNNNNNNNNNA
126 TTAAAGGAATGGGTGACTATAAATGA-ACTTTTCTT---------TA
* ** * * *
24263 CTTTTTTCTTCATTTTTCTCAAGGTAGGCATTAAATTCTAGTTTATTTTAGCCAAAAATGTACAA
1 CCTTTTTCTTCACATTTCTCAAGGTAGACATTAAATTATAGTTTATTTTAACCAAAAATGTACAA
24328 AGAATTCAAATTTAAATCAATTTTGA
66 A-AATTCAAATTTAAATCAATTTTGA
24354 GATTATAANN
Statistics
Matches: 213, Mismatches: 32, Indels: 38
0.75 0.11 0.13
Matches are distributed among these distances:
170 2 0.01
171 9 0.04
172 35 0.16
173 156 0.73
174 10 0.05
175 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.36
Consensus pattern (162 bp):
CCTTTTTCTTCACATTTCTCAAGGTAGACATTAAATTATAGTTTATTTTAACCAAAAATGTACAA
AAATTCAAATTTAAATCAATTTTGACAATACAAAACCATTTGAAATAAGTAATAAGGCTTTTAAA
GGAATGGGTGACTATAAATGAACTTTTCTTTA
Done.