Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397481.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_647.0, 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: 13781
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.28
Warning! 3192 characters in sequence are not A, C, G, or T
Found at i:686 original size:171 final size:171
Alignment explanation
Indices: 393--863 Score: 543
Period size: 171 Copynumber: 2.8 Consensus size: 171
383 NNNNNNNNNN
* * **
393 AATCTCATAATTAATTTTAAGTTGAATT-TTTTTATATTTTTGGTTAAAACAGATAATAATTGAA
1 AATCTCATAATTGATTTTAAGTTG-ATTATTTTTACATTTTTCATTAAAACAGATAATAATTGAA
* * * * * * * * * *
457 TGTGTACCTTA-AGAAATGTTGAGAGAAACACATGCATTGGCAAGCAATGTCCATTTATAGTTAC
65 TGTCTA-CATAGAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCAATTTATAGTTAC
* * *
521 CCATTCCTTCAAAAGCCTTATCACTCGCTTTATATGGTTTTAT
129 CCATTCCTTCAAAAGCATTATCACTCGCTTTAAAAGGTTTTAT
* * *
564 AATCTCATAAATGATTTGAAGTTGATTATTTTTACATTTTTCATTAAAACAGACAATAATTGAAT
1 AATCTCATAATTGATTTTAAGTTGATTATTTTTACATTTTTCATTAAAACAGATAATAATTGAAT
* ** * * *
629 GTCTACAAAGAGAAACGCAAAGAAAAATGCATTCATTGGCAAGAAAAGTCTATTTATAGTCT-TC
66 GTCTACATAGAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCAATTTATAGT-TACC
* * * * *
693 TATTCCTTCAAAATCATTATTATTGGCTTTAAAAGGTTTTAT
130 CATTCCTTCAAAAGCATTATCACTCGCTTTAAAAGGTTTTAT
* *
735 AATCTCATAATTGATTTTAAGTTGATTATTTCTACATTTTTCATTCAAACAGATAATAATTGAAT
1 AATCTCATAATTGATTTTAAGTTGATTATTTTTACATTTTTCATTAAAACAGATAATAATTGAAT
* * * * * *
800 GTCAACCTTGAGAAACATTAAGAAAAAGGCATTCATTAGCAAGAAAAGTCAATTTATAGTTACC
66 GTCTACATAGAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCAATTTATAGTTACC
864 NNNNNNNNNN
Statistics
Matches: 250, Mismatches: 46, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
170 6 0.02
171 243 0.97
172 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
AATCTCATAATTGATTTTAAGTTGATTATTTTTACATTTTTCATTAAAACAGATAATAATTGAAT
GTCTACATAGAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCAATTTATAGTTACCC
ATTCCTTCAAAAGCATTATCACTCGCTTTAAAAGGTTTTAT
Found at i:1864 original size:171 final size:170
Alignment explanation
Indices: 1572--2435 Score: 995
Period size: 171 Copynumber: 5.0 Consensus size: 170
1562 NNNNNNNNNN
* * *
1572 CCTTATTACT-GACTTTAAACGGTTTTATAATCTCAAAATTGATTTTAAGTTGAAATTTTTTTTA
1 CCTTATTACTCG-CTTTAAA-AGTTTTATAATCTCATAATTAATTTTAAGTTG-AA-TTTTTTTA
* * * *
1636 TATTTTAGCTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTC
62 TATTTTTGCTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATTAAGAAAAAGGCATTC
* * * *
1701 ATTAGCAAGAAAAGTCCATTTATAGTCTTCTATTTCTTTAAAAG
127 ATTGGCAAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAG
1745 CCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
1 CCTTATTACTCGCTTTAAA-AGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * * *
1810 TTTTGGTTAAAACAGACAATAATTGAATGTGTACCTCAAGAAACGTTGAGAAAAACGCATTCATT
65 TTTTGCTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATTAAGAAAAAGGCATTCATT
* * *
1875 GGCAAGCAAAGTCCATTTATAGTC-ACTCATTCCCTCAAAAG
130 GGCAAGAAAAGTCCATTTATAGTCTCCT-ATTCCTTCAAAAG
* * ** * * *
1916 CCTTGTCACTCGCTTTATATGGTTTTATAATCTCATAATTGATTTTTAAGTTG-ATTAGTTTTAC
1 CCTTATTACTCGCTTTA-AAAGTTTTATAATCTCATAATT-AATTTTAAGTTGAATT-TTTTTAT
* ** ** *
1980 A-TTTTCCTTAAAACAGACAATAATTGAATGTCTA-CAAAGAGAAACACAAAGAAAAAGGTATTC
63 ATTTTTGCTTAAAACAGACAATAATTGAATGTCTACCTCA-AGAAACATTAAGAAAAAGGCATTC
* * *
2043 ATTGGCAAGAAAAATCCATTTATAGTCTTCTATTCCTTCAAAAT
127 ATTGGCAAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAG
* * * *
2087 CATTATTACTGGCTTTAAAAGGTTTTATAATCTCATAGTTAATTTTAAGTTG-ATTATTTTTACA
1 CCTTATTACTCGCTTTAAAA-GTTTTATAATCTCATAATTAATTTTAAGTTGAATT-TTTTTATA
* ** * *
2151 TTTTT-CATTAAAACAGATAATAATTGAATGTCTATTTCCAGAAACGTTAAGAAAAAGGCATTCA
64 TTTTTGC-TTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATTAAGAAAAAGGCATTCA
* * *
2215 TTGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAG
128 TTGGCAAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAG
* *
2258 CCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATATTAAGTTGAATTTTTTTTATA
1 CCTTATTACTCGCTTTAAAA-GTTTTATAATCTCATAATTAATTTTAAGTTGAA-TTTTTTTATA
* * * * ** * * **
2323 TTTTTTGGTTAAAATAGACTATAATTGAATGTCTTCCTTGACAAACATGAAGAAAAAGAAATTCA
64 -TTTTTGCTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATTAAGAAAAAGGCATTCA
*
2388 TTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAG
128 TTGGCAAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAG
2431 CCTTA
1 CCTTA
2436 NNNNNNNNNN
Statistics
Matches: 588, Mismatches: 88, Indels: 30
0.83 0.12 0.04
Matches are distributed among these distances:
170 28 0.05
171 386 0.66
172 30 0.05
173 143 0.24
174 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (170 bp):
CCTTATTACTCGCTTTAAAAGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATATT
TTTGCTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATTAAGAAAAAGGCATTCATTG
GCAAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAG
Found at i:2271 original size:342 final size:342
Alignment explanation
Indices: 1572--2431 Score: 1145
Period size: 342 Copynumber: 2.5 Consensus size: 342
1562 NNNNNNNNNN
* *
1572 CCTTATTACT-GACTTTAAACGGTTTTATAATCTCAAAATTGATTTTAAGTTGAAATTTTTTTTA
1 CCTTATTACTCG-CTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTTG-AATTTTTTTTA
** * *
1636 TATTTTAGCTTAAAACAGACTATAATTGAATGTCTACCTCA-AGAAATATAAAGAAAAAGGCATT
64 TATTTT-GCTTAAAACAGACTATAATTGAATGTCTA-CAAAGAGAAACATAAAGAAAAAGGAATT
* * * *
1700 CATTAGCAAGAAAAGTCCATTTATAGTCTTCTATTTCTTTAAAAGCCTTATTACTCGCTTTAAAT
127 CATTGGCAAGAAAAGTCCATTTATAGTCTTCTATTCCTTCAAAAGCATTATTACTCGCTTTAAAT
* **
1765 AGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATATTTTTGGTTAAAACAGACAAT
192 AGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACAAT
* * *
1830 AATTGAATGTGTACCTCAAGAAACGTTGAGAAAAACGCATTCATTGGCAAGCAAAGTCCATTTAT
257 AATTGAATGTCTACCTCAAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCCATTTAT
*
1895 AGTCACTCATTCCCTCAAAAG
322 AGTCACCCATTCCCTCAAAAG
* * * * ** *
1916 CCTTGTCACTCGCTTTATATGGTTTTATAATCTCATAATTGATTTTTAAGTTG-ATTAGTTTTAC
1 CCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGA-TTTTAAGTTGAATTTTTTTTAT
* * * *
1980 ATTTTCCTTAAAACAGACAATAATTGAATGTCTACAAAGAGAAACACAAAGAAAAAGGTATTCAT
65 ATTTTGCTTAAAACAGACTATAATTGAATGTCTACAAAGAGAAACATAAAGAAAAAGGAATTCAT
* * *
2045 TGGCAAGAAAAATCCATTTATAGTCTTCTATTCCTTCAAAATCATTATTACTGGCTTTAAA-AGG
130 TGGCAAGAAAAGTCCATTTATAGTCTTCTATTCCTTCAAAAGCATTATTACTCGCTTTAAATA-G
* *
2109 TTTTATAATCTCATAGTTAATTTTAAGTTG-ATTATTTTTACATTTTTCATTAAAACAGATAATA
194 TTTTATAATCTCATAATTAATTTTAAGTTGAATT-TTTTTACATTTTTCATTAAAACAGACAATA
** * * *
2173 ATTGAATGTCTATTTCCAGAAACGTTAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATA
258 ATTGAATGTCTACCTCAAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCCATTTATA
*
2238 GTCACCCATTCCTTCAAAAG
323 GTCACCCATTCCCTCAAAAG
*
2258 CCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATATTAAGTTGAATTTTTTTTATA
1 CCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTATA
* * * *** * * *
2323 TTTTTTGGTTAAAATAGACTATAATTGAATGTCTTCCTTGACAAACATGAAGAAAAAGAAATTCA
66 --TTTTGCTTAAAACAGACTATAATTGAATGTCTACAAAGAGAAACATAAAGAAAAAGGAATTCA
* *
2388 TTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGC
129 TTGGCAAGAAAAGTCCATTTATAGTCTTCTATTCCTTCAAAAGC
2432 CTTANNNNNN
Statistics
Matches: 446, Mismatches: 62, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
341 15 0.03
342 282 0.63
343 13 0.03
344 125 0.28
345 11 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (342 bp):
CCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTATA
TTTTGCTTAAAACAGACTATAATTGAATGTCTACAAAGAGAAACATAAAGAAAAAGGAATTCATT
GGCAAGAAAAGTCCATTTATAGTCTTCTATTCCTTCAAAAGCATTATTACTCGCTTTAAATAGTT
TTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACAATAATT
GAATGTCTACCTCAAGAAACGTTAAGAAAAACGCATTCATTGGCAAGAAAAGTCCATTTATAGTC
ACCCATTCCCTCAAAAG
Found at i:4039 original size:168 final size:169
Alignment explanation
Indices: 3702--4056 Score: 466
Period size: 168 Copynumber: 2.1 Consensus size: 169
3692 NNNNNNNNNN
* * * *
3702 TAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGAGAGACTATAAATGGACTGTTCTT
1 TAAAACCATTTAAAGCCAGTAATAAAGCTTTTGAAGAAATGAGAGACTATAAATGGACTGTCCTT
*
3767 ATCAATGAATGGTTCTTTCTTCAAGTTTCTCATGGTAGACATTCAATTATAATCTGTTTTAGACA
66 ATCAATGAA--GTACTTTCTTCAAGTTTCTCATGGTAGACATTCAATTATAATCTGTTTTAGACA
*
3832 AAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTA
129 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * *
3873 TAAAACCTTTTAAAGCCAGTAATAAGGCTTTTGAAGAAATGGGAGACTATAAATGGACT-TCCCT
1 TAAAACCATTTAAAGCCAGTAATAAAGCTTTTGAAGAAATGAGAGACTATAAATGGACTGT-CCT
* * * * * * *
3937 TGTCAATGAA-TACTTTTTTCAGGTTTCTTGA-GGTAGACATTCAATTATAGTCTCTTTTTA-CC
65 TATCAATGAAGTACTTTCTTCAAGTTTC-TCATGGTAGACATTCAATTATAATCT-GTTTTAGAC
* * *
3999 AAAAATTTCAAAAAATTCAACTTAAAATCAGTTATGAGATTA
128 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
4041 TAAAACCATTTAAAGC
1 TAAAACCATTTAAAGC
4057 GAGNNNNNNN
Statistics
Matches: 161, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
168 89 0.55
169 7 0.04
170 1 0.01
171 64 0.40
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (169 bp):
TAAAACCATTTAAAGCCAGTAATAAAGCTTTTGAAGAAATGAGAGACTATAAATGGACTGTCCTT
ATCAATGAAGTACTTTCTTCAAGTTTCTCATGGTAGACATTCAATTATAATCTGTTTTAGACAAA
AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
Found at i:4721 original size:171 final size:171
Alignment explanation
Indices: 4336--5170 Score: 738
Period size: 171 Copynumber: 4.9 Consensus size: 171
4326 NNNNNNATTT
* *
4336 TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAAAGTCTATAAATAGA
1 TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAA-TCTATAAATAGA
* * * * * * * * *
4401 CATTT-CTTGTCAATAAATG-GTCATTTCTTCATGTTTCTCATGGTCAACATTCAATTATATTCT
65 C-TTTCCTTGCCAATGAATGCTTTA-TTCTTCAAGTTTCTCAAGGTAAACATTCAATTACAGTCT
* ** * * *
4464 GCTTTAACCGAAAATAGAAAAAAAATGCAACTTAAAATCAATTA
128 GTTTTAACTAAAAATATAAAAAAAATTCAACCTAAAATCAATTA
* * * * *
4508 TGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGGTTTTGAAGGAATAGGAATCTATAAGTGGA
1 TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAATCTATAAATAGA
* * * * *
4573 CTTTCCTTGCCAATGAATGCTTTATTCTTCAAGTTTTTTAGGGTAGACATTCAATT-CAGTCTAT
65 CTTTCCTTGCCAATGAATGCTTTATTCTTCAAGTTTCTCAAGGTAAACATTCAATTACAGTCTGT
* * * *
4637 TTTAACTAAAAATTTAAAAAAAATTCAA-TTGAAAATCAGTTC
130 TTTAACTAAAAATATAAAAAAAATTCAACCT-AAAATCAATTA
* * * * *
4679 TGAGATTAAAAAATCATTTAAAGCGAGTCATAAGGCTTTTGAAGAAAAGG-GTCACTATAAATAG
1 TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAAT--CTATAAATAG
* * * * * **
4743 ACTTTTCTTGCCAATGAATCCCATTTA--CTTCATGTTTCTAAAGGTAGACATTCAATTATTGTC
64 ACTTTCCTTGCCAATGAAT-GC-TTTATTCTTCAAGTTTCTCAAGGTAAACATTCAATTACAGTC
* * *
4806 TATTTTAA-TAAAAAATATAAAAATAA-TGAACCTAAAATCAATTA
127 TGTTTTAACT-AAAAATATAAAAAAAATTCAACCTAAAATCAATTA
* * * *
4850 TGAGATTATAAAATCGTTTAAAGAGAGTAATAAGTC-TTTGAAAGGAATGAGAGA-CTATAAATG
1 TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTG-AAGGAATG-GA-ATCTATAAATA
* * ** * * *
4913 GACCTTCTTTGATAATGAAAGCATTT-TTCTTTACA-TTTCTCAAGGAAAACATTCAATTACAGT
63 GACTTTCCTTGCCAATGAATGC-TTTATTCTTCA-AGTTTCTCAAGGTAAACATTCAATTACAGT
* *
4976 CTGTTTTAA-TCAAAAATAT-AAAAAAATTAAACCTAATATCAATT-
126 CTGTTTTAACT-AAAAATATAAAAAAAATTCAACCTAAAATCAATTA
**
5020 TAGAGATTATAAAA-CAGTTTAAAATGAGTAATAAGGCTTTTGAAGGAATGAGAGA-CTATAAAT
1 T-GAGATTATAAAATCA-TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GA-ATCTATAAAT
* * * * *
5083 AGACTTTTCTTGCCAATGAAT--TTTTTTCTTCACGTTTCTCCAGGTAAACATTCAATTATAGTC
62 AGACTTTCCTTGCCAATGAATGCTTTATTCTTCAAGTTTCTCAAGGTAAACATTCAATTACAGTC
* *
5146 TGTTTTAACGAAAAATGTAAAAAAA
127 TGTTTTAACTAAAAATATAAAAAAA
5171 TTTAACTTAA
Statistics
Matches: 539, Mismatches: 98, Indels: 54
0.78 0.14 0.08
Matches are distributed among these distances:
168 3 0.01
169 48 0.09
170 27 0.05
171 327 0.61
172 125 0.23
173 9 0.02
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (171 bp):
TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAATCTATAAATAGAC
TTTCCTTGCCAATGAATGCTTTATTCTTCAAGTTTCTCAAGGTAAACATTCAATTACAGTCTGTT
TTAACTAAAAATATAAAAAAAATTCAACCTAAAATCAATTA
Found at i:5056 original size:342 final size:336
Alignment explanation
Indices: 4334--5170 Score: 899
Period size: 342 Copynumber: 2.4 Consensus size: 336
4324 NNNNNNNNAT
*
4334 TTTGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAAAGT-CTATAAAT
1 TTTGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAA--AGAGTACTATAAAT
* * * *
4398 AGACATTTCTTGTCAATAAATGGTCATTTCTTCATGTTTCTCATGGTCAACATTCAATTATAT-T
64 AGACTTTTCTTGCCAATGAA---TCATTTCTTCATGTTTCTCAAGGT-AACATTCAATTAT-TGT
* ** * *
4462 CTGCTTTAACCGAAAATAGAAAAAAAATGCAACTTAAAATCAATTATGAGATTATAAAACCGTTT
124 CTGTTTTAACAAAAAATATAAAAAAAATGCAACCTAAAATCAATTATGAGATTATAAAACCGTTT
* * * * *
4527 AAAGCGAGTAATAAGGGTTTTGAAGGAATAGGAATCTATAAGTGGACTTTCCTTGCCAATGAATG
189 AAAGAGAGTAATAA-GGTTTTGAAGGAATAGGAATCTATAAATGGACCTTCCTTGACAATGAAAG
* * * * * *
4592 CTTTATTCTTCAAGTTTTTTAGGGTAGACATTCAATTCAGTCTATTTTAACTAAAAATTTAAAAA
253 CTTTATTCTTCAAGTTTCTCAAGGAAAACATTCAATTCAGTCTATTTTAACTAAAAATATAAAAA
* * *
4657 AAATTCAATTGAAAATCAG
318 AAATTAAACTGAAAATCAA
* * *
4676 TTCTGAGATTAAAAAATCATTTAAAGCGAGTCATAAGGCTTTTGAAGAAAAGGGTCACTATAAAT
1 TT-TGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAAAGAGT-ACTATAAAT
*
4741 AGACTTTTCTTGCCAATGAATCCCATTTACTTCATGTTTCTAAAGGTAGACATTCAATTATTGTC
64 AGACTTTTCTTGCCAATGAAT--CATTT-CTTCATGTTTCTCAAGGTA-ACATTCAATTATTGTC
* * * *
4806 TATTTTAATAAAAAATATAAAAATAATG-AACCTAAAATCAATTATGAGATTATAAAATCGTTTA
125 TGTTTTAACAAAAAATATAAAAAAAATGCAACCTAAAATCAATTATGAGATTATAAAACCGTTTA
* *
4870 AAGAGAGTAATAA-GTCTTTGAAAGGAAT-GAGAGA-CTATAAATGGACCTTCTTTGATAATGAA
190 AAGAGAGTAATAAGGT-TTTG-AAGGAATAG-GA-ATCTATAAATGGACCTTCCTTGACAATGAA
* *
4932 AGCATTT-TTCTTTACA-TTTCTCAAGGAAAACATTCAATTACAGTCTGTTTTAA-TCAAAAATA
251 AGC-TTTATTCTTCA-AGTTTCTCAAGGAAAACATTCAATT-CAGTCTATTTTAACT-AAAAATA
*
4994 T-AAAAAAATTAAACCT-AATATCAA
312 TAAAAAAAATTAAA-CTGAAAATCAA
** *
5018 TTTAGAGATTATAAAA-CAGTTTAAAATGAGTAATAAGGCTTTTGAAGGAATGAGAG-ACTATAA
1 TTT-GAGATTATAAAATCA-TTTAAAGCGAGTAATAAGGCTTTTGAA-GAA-AAGAGTACTATAA
** * * *
5081 ATAGACTTTTCTTGCCAATGAATTTTTTTCTTCACGTTTCTCCAGGTAAACATTCAATTATAGTC
62 ATAGACTTTTCTTGCCAATGAA-TCATTTCTTCATGTTTCTCAAGGT-AACATTCAATTATTGTC
* *
5146 TGTTTTAACGAAAAATGTAAAAAAA
125 TGTTTTAACAAAAAATATAAAAAAA
5171 TTTAACTTAA
Statistics
Matches: 418, Mismatches: 54, Indels: 48
0.80 0.10 0.09
Matches are distributed among these distances:
340 53 0.13
341 15 0.04
342 197 0.47
343 150 0.36
344 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (336 bp):
TTTGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAAAGAGTACTATAAATAG
ACTTTTCTTGCCAATGAATCATTTCTTCATGTTTCTCAAGGTAACATTCAATTATTGTCTGTTTT
AACAAAAAATATAAAAAAAATGCAACCTAAAATCAATTATGAGATTATAAAACCGTTTAAAGAGA
GTAATAAGGTTTTGAAGGAATAGGAATCTATAAATGGACCTTCCTTGACAATGAAAGCTTTATTC
TTCAAGTTTCTCAAGGAAAACATTCAATTCAGTCTATTTTAACTAAAAATATAAAAAAAATTAAA
CTGAAAATCAA
Found at i:5637 original size:171 final size:171
Alignment explanation
Indices: 5329--6294 Score: 902
Period size: 171 Copynumber: 5.7 Consensus size: 171
5319 NNNNNNNNNN
** *
5329 AGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATCCCTTTTTCTTAACGTTTCTCAA
1 AGGAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAATGGCTTTTTCTTCACGTTTCTCAA
* * * * *
5393 CGTAGATATTTAATTAT-GATCTGTTTTAAT-ATAAAATATTAAAATAATT-AACTTAAAATCAA
65 GGTAGACATTCAATTATAG-TCTATTTTAATGA-AAAATA-TAAAACAATTCAACTTAAAATCAA
* * *
5455 TTATGAGATTATAAAATCTTTTAAAGTGAGTAACAATGCTTTTGA
127 TTATGAGATTATAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGA
* * * * * * *
5500 AGGAATAGGTGAATGTAAATGGACTTTTCTTCTCCACGAATGGCTTTTTCTAT-ATGTTTCTTAA
1 AGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCT-TCACGTTTCTCAA
* * * *
5564 GGTAGACATTTAATTATAGTCTATTTTAATGAAAAATACAAAACAATTTAACTTAAAATTAATTA
65 GGTAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAACAATTCAACTTAAAATCAATTA
** * *
5629 AAAGATTATAGAA-CTATTTAAAACGAGTAACAAGGCTTTTGA
130 TGAGATTATAAAACCT-TTTAAAGCGAGTAACAAGGCTTTTGA
* * * * * * * *
5671 AGAAATGGGTAACAATAAAGGGACTTTTC-TCTCAATGAATGACTTTTTCTACACATTTCCCAAG
1 AGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTCACGTTTCTCAAG
* * * * * * *
5735 GCA-AGCAGTCAATGATAGTCTCTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTG
66 GTAGA-CATTCAATTATAGTCTATTTTAATGAAAAATATAAAACAATTCAACTTAAAATCAATTA
* * *
5799 TGAGATTATAAAACCATTTATAGTGAGTAATC-AGGCTTTTGA
130 TGAGATTATAAAACCTTTTAAAGCGAGTAA-CAAGGCTTTTGA
* * * * * *
5841 AGGAATGAGAGATTATAAATAGACTTTTCTTGTCAATGAATGG-TTCTTTCTTCACGTTTCTCAT
1 AGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTT-TTTCTTCACGTTTCTCAA
* * * * *
5905 GGTAGACATTCAATTATAGTCTGTTTT-AGGTAAAAATGTAAAACAACTCAAATTAAAATCAATT
65 GGTAGACATTCAATTATAGTCTATTTTAATG-AAAAATATAAAACAATTCAACTTAAAATCAATT
* * * * * *
5969 TTGAGATTACAAAACCATTTAAAGCCAGTAATAAGACTTTTGA
129 ATGAGATTATAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGA
* * * * * **
6012 AGGAATGGGAGACTATAAATAGACTTTCCTTATCAAT-AA-GTGCTTCTTTCTTCAGGTTTCTTG
1 AGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATG-GCTT-TTTCTTCACGTTTCTCA
* * ** * * *
6075 ATGTAGACATTCAATTATAGTCTCTTTTAACCAAAAATTTTAAAA-AGTTCAACTTAAAATCAGT
64 AGGTAGACATTCAATTATAGTCTATTTTAATGAAAAA-TATAAAACAATTCAACTTAAAATCAAT
* * * **
6139 TATGAGGTTATAAAACCTTTTAAAGCAAGTAATAATACTTTTGA
128 TATGAGATTATAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGA
* * * *
6183 AGAAATAGGTGACTATAAATGGACTTTTCTTCTTAATGAATGGCTTTTTCTAC-CTGTTTAC-CA
1 AGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTCAC-GTTT-CTCA
* * *
6246 AGGTAGGCATTCAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATT
64 AGGTAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAACAATT
6295 TANNNNNNNN
Statistics
Matches: 647, Mismatches: 124, Indels: 48
0.79 0.15 0.06
Matches are distributed among these distances:
169 2 0.00
170 153 0.24
171 473 0.73
172 18 0.03
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTCACGTTTCTCAAG
GTAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAACAATTCAACTTAAAATCAATTAT
GAGATTATAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGA
Found at i:6210 original size:342 final size:341
Alignment explanation
Indices: 5425--6289 Score: 933
Period size: 341 Copynumber: 2.5 Consensus size: 341
5415 GTTTTAATAT
* *
5425 AAAATATTAAAATAATT-AACTTAAAATCAATTATGAGATTATAAAATCTTTTAAAGTGAGTAAC
1 AAAATATTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAAT
* * *
5489 AATGCTTTTGAAGGAATAGGTGAATGTAAATGGACTTTTCTTCTCCACGAATGGCTTTTTCTAT-
65 AATGCTTTTGAAGGAATAGGTGAATATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCT-TC
* * * ** * * *
5553 ATGTTTCTTAAGGTAGACATTTAATTATAGTCTATTTTAATGAAAAATACAAAACAATTTAACTT
129 ACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAATGAAAAATGTAAAACAACTCAAATT
* * * * * *
5618 AAAATTAATTAAAAGATTATAGAACTATTTAAAACGAGTAACAAGGCTTTTGAAGAAATGGGTAA
194 AAAATCAATTAAAAGATTACAAAACCATTTAAAACCAGTAACAAGACTTTTGAAGAAATGGGTAA
* * *
5683 CAATAAAGGGACTTTTCTCTCAATGAATGACTTTTTCTACACATTTCCCAAGGCAAGCAGTCAAT
259 CAATAAAGAGACTTTCCTATCAATGAATGACTTTTTCTACACATTTCCCAAGGCAAGCAGTCAAT
**
5748 GATAGTCTCTTTTAATGA
324 GATAGTCTCTTTTAACCA
* * * * * *
5766 AAAATGTAAAAAAATTCAACTTAAAATCAATTGTGAGATTATAAAACCATTTATAGTGAGTAATC
1 AAAATATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATA
* * * * *
5831 AGGCTTTTGAAGGAAT-GAGAGATTATAAATAGACTTTTCTTGTCAATGAATGG-TTCTTTCTTC
66 ATGCTTTTGAAGGAATAG-GTGAATATAAATGGACTTTTCTTCTCAATGAATGGCTT-TTTCTTC
* * *
5894 ACGTTTCTCATGGTAGACATTCAATTATAGTCTGTTTT-AGGTAAAAATGTAAAACAACTCAAAT
129 ACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAATG-AAAAATGTAAAACAACTCAAAT
*** * * *
5958 TAAAATCAATTTTGAGATTACAAAACCATTTAAAGCCAGTAATAAGACTTTTGAAGGAATGGG-A
193 TAAAATCAATTAAAAGATTACAAAACCATTTAAAACCAGTAACAAGACTTTTGAAGAAATGGGTA
* * * ** *** * *
6022 GACTATAAATAGACTTTCCTTATCAAT-AAGTG-CTTCTTTCTTCAGGTTTCTTGATG-TAGACA
258 -ACAATAAAGAGACTTTCC-TATCAATGAA-TGACTT-TTTCTACACATTTCCCAAGGCAAG-CA
* *
6084 TTCAATTATAGTCTCTTTTAACCA
318 GTCAATGATAGTCTCTTTTAACCA
* * * * **
6108 AAAATTTTAAAAAGTTCAACTTAAAATCAGTTATGAGGTTATAAAACCTTTTAAAGCAAGTAATA
1 AAAATATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATA
* * * * *
6173 ATACTTTTGAAGAAATAGGTGACTATAAATGGACTTTTCTTCTTAATGAATGGCTTTTTCTAC-C
66 ATGCTTTTGAAGGAATAGGTGAATATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTCAC
*
6237 TGTTTAC-CAAGGTAGGCATTCAATTATAGTCTATTTTAATGAAAAATGTAAAA
131 -GTTT-CTCAAGGTAGACATTCAATTATAGTCTATTTTAATGAAAAATGTAAAA
6290 AAATTTANNN
Statistics
Matches: 429, Mismatches: 80, Indels: 29
0.80 0.15 0.05
Matches are distributed among these distances:
340 11 0.03
341 223 0.52
342 189 0.44
343 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (341 bp):
AAAATATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATA
ATGCTTTTGAAGGAATAGGTGAATATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTCAC
GTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAATGAAAAATGTAAAACAACTCAAATTAA
AATCAATTAAAAGATTACAAAACCATTTAAAACCAGTAACAAGACTTTTGAAGAAATGGGTAACA
ATAAAGAGACTTTCCTATCAATGAATGACTTTTTCTACACATTTCCCAAGGCAAGCAGTCAATGA
TAGTCTCTTTTAACCA
Found at i:7568 original size:171 final size:169
Alignment explanation
Indices: 7254--8468 Score: 1192
Period size: 171 Copynumber: 7.1 Consensus size: 169
7244 NNNNNNNNNN
* *
7254 TTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTTCTACCAATGA
1 TTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGAAGACTATAAATGGACTTTTT-TCCCAATGA
* * * *
7319 AT-CTCATTTTCTTCATGTTTCTAAAGGTAGACATTCAATTATTA-TCTATTTTAATGAAAAATA
65 ATGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTA-TAGTCTGTTTTAATGAAAAATG
* * *
7382 TAAAAATAATCAACTTAAAATCAGTTATGAGATTATCAAACCG
128 TAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACCG
* *
7425 TTTAAAGCGAGTAATAAAGTTTTTGAAGAAATGGAAGACTATAAATGGACTTTCTTTCCCAATGA
1 TTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGAAGACTATAAATGGACTTT-TTTCCCAATGA
* * * * *
7490 ATGCTTTTTTCTTTAGGTTTCTTAAGGAAGACATTCAATTATAGTCTGTTTGAACT-AAAAATGT
65 ATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-TGAAAAATGT
7554 AAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCG
129 AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCG
* * * *
7596 TTTAAAGCAAGTAA-AAAGGCTTTTGAAGGAAT-GAGTGACTATAAATAGACTTTTCTTGCCAAT
1 TTTAAAGCGAGTAATAAA-GCTTTTGAAGGAATGGA-AGACTATAAATGGACTTTT-TTCCCAAT
* * *
7659 GAATCCTTTTTTCTTAATGTTTCTCAAGGTAGACATTTAATTATTA-TCTGTTTTAATGAAAAAT
63 GAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTA-TAGTCTGTTTTAATGAAAAAT
* *
7723 ATTAAAATAATT-AACTTAAAATCAATTATGAGATTATAAAACCT
127 -GTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCG
* * * * * *
7767 TTTAAAGTGAGTAACAATA-CTTTTAAAGGAATAGG-TGAATATAAATGGACTTTTCTTCTCATA
1 TTTAAAGCGAGTAATAA-AGCTTTTGAAGGAAT-GGAAGACTATAAATGGACTTTT-TTCCCA-A
* ** * * * * * *
7830 AGGTTGGC-TTTTTCTACATGTTTCTTAAGGTAGGCATTTAATTATAGTCTATTTTAATAAAAAA
62 TGAAT-GCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAA
* ** * *
7894 AGTGAAAAAATTTTACTTAAAATCAATTATGAGATTATAGAACCA
126 TGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCG
* * * * * * * *
7939 TTTAAAGCGAGTAACAAGGCTTTTGAAAGAATGGGTA-ACAATAAATAGACTTTTCTCTCAATGA
1 TTTAAAGCGAGTAATAAAGCTTTTGAAGGAAT-GGAAGACTATAAATGGACTTTTTTCCCAATGA
* * *
8003 ATGGC-TTTTTCTAT-ACGTTTCCCAAGGCA-AGCATTCAATTATAGTCTGTTTTAATGAAAAAT
65 AT-GCTTTTTTCT-TCATGTTTCTCAAGGTAGA-CATTCAATTATAGTCTGTTTTAATGAAAAAT
* **
8065 ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
127 GT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCG
* * * **
8109 TTTATAGTGAGTAATAAGGCTTTTGAAGGAAT-GAGAGACTATAAATGGACTTTTCTTGTCAATG
1 TTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGA-AGACTATAAATGGACTTTT-TTCCCAATG
* * * * *
8173 AATGGTTTTTTCTTTACGTTTCTCATGGTAGACATTCAATTATAGTCTGTTTTAGCT-AAAAATG
64 AATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTA-ATGAAAAATG
* * *
8237 TAAAACAATTCAAATTAAAATCAATTTTGAGATTATAAAAACTG
128 TAAAA-AATTCAACTTAAAATCAATTATGAGATTAT-AAAACCG
* * *
8281 GTTAAAGTC-AGTAAT-AAGACTTTTGAAGGAAT-GAGAGACTATAAATAGACTTTTCTTACCAA
1 TTTAAAG-CGAGTAATAAAG-CTTTTGAAGGAATGGA-AGACTATAAATGGACTTTT-TTCCCAA
* * ** * * *
8343 TGAGTGCTTTTTTCTTCAAGTTTCTTGATGTAGATATTCAATTATAGTCTTTTTTAACT-AAAAA
62 TGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-TGAAAAA
* * * *
8407 TTTTAAAAAATTCAACTTAAAATCAGTTATGAGGTTATAAAACCT
126 -TGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCG
*
8452 TTTAAAGCAAGTAATAA
1 TTTAAAGCGAGTAATAA
8469 TANNNNNNNN
Statistics
Matches: 879, Mismatches: 126, Indels: 77
0.81 0.12 0.07
Matches are distributed among these distances:
168 1 0.00
169 1 0.00
170 148 0.17
171 437 0.50
172 283 0.32
173 9 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (169 bp):
TTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGAAGACTATAAATGGACTTTTTTCCCAATGAA
TGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAA
AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCG
Found at i:8003 original size:342 final size:338
Alignment explanation
Indices: 7254--8468 Score: 1354
Period size: 342 Copynumber: 3.6 Consensus size: 338
7244 NNNNNNNNNN
* * * *
7254 TTTAAAGCGAGTAATAAAGCTTTTGAAGGAATG-GATGACTATAAATGGACTTTTTCTACCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-TAACTATAAATAGAC-TTTTCTTCCAATG
* * * *
7318 AAT-CTCATTTTCTTCATGTTTCTAAAGGTAGACATTCAATTATTA-TCTATTTTAATGAAAAAT
64 AATGCT-TTTTTCTTAATGTTTCTCAAGGTAGACATTCAATTA-TAGTCTGTTTTAATGAAAAAT
* * * * * *
7381 ATAAAAATAA-TCAACTTAAAATCAGTTATGAGATTATCAAACCGTTTAAAGCGAGTAATAAAGT
127 ATTAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATAAA-C
* * *
7445 TTTTGAAGAAATGGAAGACTATAAATGGAC-TTTCTTTCCCAATGAAT-GCTTTTTTCTTTAGGT
191 TTTTGAAGGAATGG-AGACTATAAATGGACTTTTC-TTCTCAATGAATGGC-TTTTTCTTTACGT
* *
7508 TTCTTAAGGAAGACATTCAATTATAGTCTGTTTGAACTAAAAATGTAAAACAATTCAACTTAAAA
253 TTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAA-TAAAAATGTAAAACAATTCAACTTAAAA
7573 TCAATTATGAGATTATAAAACC
317 TCAATTATGAGATTATAAAACC
* * *
7595 GTTTAAAGCAAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATG
1 -TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATAGACTTTTCTT-CCAATG
* *
7660 AATCCTTTTTTCTTAATGTTTCTCAAGGTAGACATTTAATTATTA-TCTGTTTTAATGAAAAATA
64 AATGCTTTTTTCTTAATGTTTCTCAAGGTAGACATTCAATTA-TAGTCTGTTTTAATGAAAAATA
*
7724 TTAAAATAATT-AACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAACAATACT
128 TTAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATAA-ACT
* * * * ** ** *
7788 TTTAAAGGAATAGGTGAATATAAATGGACTTTTCTTCTCATAAGGTTGGCTTTTTCTACATGTTT
192 TTTGAAGGAAT-GGAGACTATAAATGGACTTTTCTTCTCA-ATGAATGGCTTTTTCTTTACGTTT
* * * * **
7853 CTTAAGGTAGGCATTTAATTATAGTCTATTTTAATAAAAAAAGTGAAAA-AATTTTACTTAAAAT
255 CTTAAGGTAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGT-AAAACAATTCAACTTAAAAT
*
7917 CAATTATGAGATTATAGAACC
318 CAATTATGAGATTATAAAACC
* * * *
7938 ATTTAAAGCGAGTAACAAGGCTTTTGAAAGAATGGGTAACAATAAATAGACTTTTC-TCTCAATG
1 -TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATAGACTTTTCTTC-CAATG
* * *
8002 AATGGC-TTTTTC-TATACGTTTCCCAAGGCA-AGCATTCAATTATAGTCTGTTTTAATGAAAAA
64 AAT-GCTTTTTTCTTA-ATGTTTCTCAAGGTAGA-CATTCAATTATAGTCTGTTTTAATGAAAAA
* *
8064 TA-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTATTTATAGTGAGTAATAAG
126 TATTAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCT-TTTAAAGTGAGTAATAA-
* * *
8127 GCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGTCAATGAATGGTTTTTTCTTTACGT
189 ACTTTTGAAGGAATG-GAGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTTACGT
* * * *
8192 TTCTCATGGTAGACATTCAATTATAGTCTGTTTTAGCTAAAAATGTAAAACAATTCAAATTAAAA
253 TTCTTAAGGTAGACATTCAATTATAGTCTGTTTTA-ATAAAAATGTAAAACAATTCAACTTAAAA
* *
8257 TCAATTTTGAGATTATAAAAAC
317 TCAATTATGAGATTATAAAACC
*
8279 TGGTTAAAGTC-AGTAATAAGACTTTTGAAGGAATGAG-AGACTATAAATAGACTTTTCTTACCA
1 T--TTAAAG-CGAGTAATAAGGCTTTTGAAGGAATGAGTA-ACTATAAATAGACTTTTCTT-CCA
* ** * * *
8342 ATGAGTGCTTTTTTCTTCAA-GTTTCTTGATGTAGATATTCAATTATAGTCTTTTTTAACT-AAA
61 ATGAATGCTTTTTTCTT-AATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-TGAAA
* * * **
8405 AATTTTAAAA-AATTCAACTTAAAATCAGTTATGAGGTTATAAAACCTTTTAAAGCAAGTAATAA
124 AATATTAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATAA
8469 TANNNNNNNN
Statistics
Matches: 742, Mismatches: 97, Indels: 67
0.82 0.11 0.07
Matches are distributed among these distances:
340 5 0.01
341 107 0.14
342 370 0.50
343 241 0.32
344 18 0.02
345 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (338 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATAGACTTTTCTTCCAATGAA
TGCTTTTTTCTTAATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATATTA
AAATAATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGTGAGTAATAAACTTTTG
AAGGAATGGAGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTTTACGTTTCTTAAG
GTAGACATTCAATTATAGTCTGTTTTAATAAAAATGTAAAACAATTCAACTTAAAATCAATTATG
AGATTATAAAACC
Found at i:8224 original size:513 final size:511
Alignment explanation
Indices: 7273--8465 Score: 1387
Period size: 513 Copynumber: 2.3 Consensus size: 511
7263 AGTAATAAAG
* * * * * *
7273 CTTTTGAAGGAATG-GATGACTATAAATGGACTTTT-TCTACCAATGAAT-CTCATTTTCTTCAT
1 CTTTTAAAGGAATGAGA-GAATATAAATAGACTTTTCT-TACCAAAGAGTGCT-TTTTTCTTCAT
* * *
7335 GTTTCTAAAGGTAGACATTCAATTATTA-TCTATTTTAATGAAAAATATAAAAATAATCAACTTA
63 GTTTCTTAAGGTAGACATTCAATTA-TAGTCTATTTTAAT-AAAAAAATAAAAA-ATTCAACTTA
* * *
7399 AAATCAGTTATGAGATTATCAAACCGTTTAAAGCGAGTAATAAAGTTTTTGAAGAAATGGAAGAC
125 AAATCAGTTATGAGATTAT-AAACCATTTAAAGCGAGTAACAAAGCTTTTGAAGAAATGGAAGAC
* * * * * **
7464 TATAAATGGACTTTCTTTCCCAATGAATGCTTTTTTCTTTAGGTTTCTTAAGGAAGACATTCAAT
189 AATAAATAGACTTTCTCTCCCAATGAATGCTTTTTTCTATACGTTTCCCAAGGAAGACATTCAAT
* *
7529 TATAGTCTGTTTGAACTAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAAC
254 TATAGTCTGTTTGAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* *
7594 CGTTTAAAGCAAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAAT
319 CATTTAAAGCAAGTAAAAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCCAAT
* *
7659 GAATCCTTTTTTCTTAATGTTTCTCAAGGTAGACATTTAATTATTATCTGTTTTA-ATGAAAAAT
384 GAATCCTTTTTTCTTAACGTTTCTCAAGGTAGACATTCAATTATTATCTGTTTTAGAT-AAAAAT
* * * * * * *
7723 ATTAAAATAATT-AACTTAAAATCAATTATGAGATTATAAAACCT-TTTAAAGTGAGTAACAATA
448 -GTAAAACAATTCAAATTAAAATCAATTATGAGATTATAAAAACTGGTTAAAGTCAGTAACAAGA
* * *
7786 CTTTTAAAGGAAT-AGGTGAATATAAATGGACTTTTCTT-CTCATAAG-GTTGGC-TTTTTCTAC
1 CTTTTAAAGGAATGA-GAGAATATAAATAGACTTTTCTTAC-CA-AAGAG-T-GCTTTTTTCTTC
* * **
7847 ATGTTTCTTAAGGTAGGCATTTAATTATAGTCTATTTTAATAAAAAAAGTGAAAAAATTTTACTT
61 ATGTTTCTTAAGGTAGACATTCAATTATAGTCTATTTTAATAAAAAAA-T-AAAAAATTCAACTT
* * *
7912 AAAATCAATTATGAGATTATAGAACCATTTAAAGCGAGTAACAAGGCTTTTGAA-AGAATGGGTA
124 AAAATCAGTTATGAGATTATA-AACCATTTAAAGCGAGTAACAAAGCTTTTGAAGA-AAT-GGAA
*
7976 -ACAATAAATAGACTTT-TCTCTCAATGAATGGC-TTTTTCTATACGTTTCCCAAGGCAAG-CAT
186 GACAATAAATAGACTTTCTCTCCCAATGAAT-GCTTTTTTCTATACGTTTCCCAAGG-AAGACAT
*
8037 TCAATTATAGTCTGTTTTAA-TGAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
249 TCAATTATAGTCTGTTTGAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * ** * *
8101 TAAAACTATTTATAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTT
313 TAAAACCATTTAAAGCAAGTAAAAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTT
* ** * * *
8166 GTCAATGAATGGTTTTTTCTTTACGTTTCTCATGGTAGACATTCAATTA-TAGTCTGTTTTAGCT
378 GCCAATGAATCCTTTTTTCTTAACGTTTCTCAAGGTAGACATTCAATTATTA-TCTGTTTTAGAT
*
8230 AAAAATGTAAAACAATTCAAATTAAAATCAATTTTGAGATTATAAAAACTGGTTAAAGTCAGTAA
442 AAAAATGTAAAACAATTCAAATTAAAATCAATTATGAGATTATAAAAACTGGTTAAAGTCAGTAA
*
8295 TAAGA
507 CAAGA
* * * *
8300 CTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTACCAATGAGTGCTTTTTTCTTCAAGTT
1 CTTTTAAAGGAATGAGAGAATATAAATAGACTTTTCTTACCAAAGAGTGCTTTTTTCTTCATGTT
* * * * **
8365 TCTTGATGTAGATATTCAATTATAGTCTTTTTTAACTAAAAATTTTAAAAAATTCAACTTAAAAT
66 TCTTAAGGTAGACATTCAATTATAGTCTATTTTAA-TAAAAA-AATAAAAAATTCAACTTAAAAT
* * *
8430 CAGTTATGAGGTTATAAAACCTTTTAAAGCAAGTAA
129 CAGTTATGAGATTAT-AAACCATTTAAAGCGAGTAA
8466 TAATANNNNN
Statistics
Matches: 575, Mismatches: 77, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
512 15 0.03
513 367 0.64
514 182 0.32
515 10 0.02
516 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (511 bp):
CTTTTAAAGGAATGAGAGAATATAAATAGACTTTTCTTACCAAAGAGTGCTTTTTTCTTCATGTT
TCTTAAGGTAGACATTCAATTATAGTCTATTTTAATAAAAAAATAAAAAATTCAACTTAAAATCA
GTTATGAGATTATAAACCATTTAAAGCGAGTAACAAAGCTTTTGAAGAAATGGAAGACAATAAAT
AGACTTTCTCTCCCAATGAATGCTTTTTTCTATACGTTTCCCAAGGAAGACATTCAATTATAGTC
TGTTTGAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
AGCAAGTAAAAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATCCT
TTTTTCTTAACGTTTCTCAAGGTAGACATTCAATTATTATCTGTTTTAGATAAAAATGTAAAACA
ATTCAAATTAAAATCAATTATGAGATTATAAAAACTGGTTAAAGTCAGTAACAAGA
Found at i:9971 original size:171 final size:171
Alignment explanation
Indices: 9442--11265 Score: 1643
Period size: 171 Copynumber: 10.7 Consensus size: 171
9432 NNNNNNNNNN
* * * **
9442 ACCATTTAAAGCAAGTAATAACGCTTTTGAAGGAATGGGTA-ATTATAAATAAACTTTTC-T-CT
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATGGACTTTTCTTGC-
* * * * * * * **
9504 CTATGAATGGTTTGTTCTACATGTTTC-CAAGCTAGGCATTCAATAATAGTCTCTTTTAATGAAA
64 CAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAA
**********
9568 AATATAAAAAAATTCAACTTAAAATCAATTNNNNNNNNNNAAA
129 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * *
9611 ACCATTTAAAGCGAGTAATAATGCTTTTGAAGGAATGTGAGACTATAAATGGACTTTTCTTACCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
* * * * * * *
9676 ATGAATGATTCTTTCTTCAT-ATTCTCATGGTAGACATTTAATTATAGTCTGTTTTAGCCAAAAA
66 ATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAAA
* * ** * *
9740 TGTAAAATAATTCAACTTAAAATTGATTTTAAGATTATAAA
131 TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
*** * * * * * *
9781 ATTGTTTAAAGCCAGTAATAAGGCTTTTGCAGTAATGGGAGACTATAAATAGACTTTCCTTACCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
* *
9846 ATGAATGCTTTTTTCTT-TTAGTTTCTCAAGGTAGACATTCAATTATAGTTTCTTTTAACCAAAA
66 ATGAATGCTTTTTTCTTCAT-GTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAA
* * * * *
9910 ATTTAAAAAAATTTAACTTAAAATCAGTTCTGAGATTAAAAA
130 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* *
9952 ACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAA-AGGATGACTATAAATGGACTTTT-TCTGC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA-GACTATAAATGGACTTTTCT-TGC
* ** * * * **
10015 CAATGAATCCCATTTTCTTCATGTTTCTAAAGGTAGACATTCAATTATTGTCTATTTTAATGAAA
64 CAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAA
* ***
10080 AGTATAAAAATAA-TCAACTTAAAATCAATTATGAGATTATCNN
129 AATATAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAA
******** * * * * *
10123 NNNNNNNNAAGCGAGTAATAAGGCTTTTAAATGAATGGAAGACTATAAATAGACTTTCCTTGCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
* * ** ** *
10188 ATGAATGCTTTTTTCTTCAGGTTTCTCGAGAAAGACATTCAATTGCAGTCTATTTTAACCAAAAA
66 ATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAAA
* * * *
10253 TATAAAAAATTTTAACTTAAAATCAATTTTAAGATTATAAA
131 TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* ** * * *
10294 ACCGTTTAAAATGAGTAATAAGGCTTTTGAAGGAATGAGAGATTATAAATGGATTTTTCTTGCCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
* * * * * *
10359 ATGAATGCTTTTTTTTTTACGTTTTCTC-AGGTAGACATTCAATTATAGTGTGTTTTAACTAAAA
66 ATGAATGCTTTTTTCTTCATG-TTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAA
* * * *
10423 ATGTAAAAAAATTCAACTTAAAATTAATTATAAAATTATAAA
130 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
10465 ACCATTTAAAGTGAGTAAAAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCAA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
* * * * **
10530 ATGAAT-CTCTTTTTCTTAATGTTTCTTAAGGTAGACATTCAATTATTA-TCTGTTCTAATGAAA
66 ATGAATGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTA-TAGTCTCTTTTAACCAAA
* * * * **
10593 AATGTTAAAATAA-TCAACTTGAAATTAATTATGAGATGGTAAA
129 AAT-ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * ** * *
10636 ACCTTTTAAAGCGATTAACAATGCTTTTGAAGGAACAGGTGAATATAAATGGACTTTTCTT-CTC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGC-C
* * * **
10700 AACGAATGAC-TTTTTCTACATGTTTC-CTAAGGTAGACATTCAATTATAGTCTATTTTAATAAA
65 AATGAATG-CTTTTTTCTTCATGTTTCTC-AAGGTAGACATTCAATTATAGTCTCTTTTAACCAA
* *
10763 AAATATAAAAAAATTTAACTCAAAATCAATTATGAGATTATAAA
128 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * *
10807 ACTATTTAAAGCGACTAACAAGGCTTTTGAAGGAAT----GACTATAAATGGACTTTT-TT-CTC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGC-C
* * * **
10866 AATGAATGGC-TTTTTCTACATGTTTCCCAAGG-AAAGCATTCAATTATAGTCTGC-TTTAATGA
65 AATGAAT-GCTTTTTTCTTCATGTTTCTCAAGGTAGA-CATTCAATTATAGTCT-CTTTTAACCA
* *
10928 AAAATATAAAACAATTCAACTTAAAATCAATTATAAGATTATAAA
127 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * ** *
10973 ACCATTTATAGCGAGTAATAAGGCTTTTGAAGAAATAGGAAACTATAAATAAACTTTTCTTGTCA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
* * * * ** * * *
11038 ATGAATGATTTTTTCTTCATGTTTCTCATGATGGACATTTTATTATTGTCTGTTTTAGCCAAAAA
66 ATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAAA
* * *
11103 -AGTAAAACAATTCAACTTAAAATAAATTTTGAGATTATAAA
131 TA-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * * * * * * *
11144 AGCGTTTAAAGCCAGTAATCAGAG-TTTCGAGGGAATGAGAGACTATAAATAGACTTTCCTTACC
1 ACCATTTAAAGCGAGTAATAAG-GCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCC
*
11208 AATGAGTGCTTTTTTCTTCA-GCTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTA
65 AATGAATGCTTTTTTCTTCATG-TTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTA
11266 NNNNNNNNNN
Statistics
Matches: 1341, Mismatches: 274, Indels: 78
0.79 0.16 0.05
Matches are distributed among these distances:
165 2 0.00
166 127 0.09
167 19 0.01
168 1 0.00
169 55 0.04
170 185 0.14
171 928 0.69
172 23 0.02
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
ATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAAA
TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
Found at i:11721 original size:171 final size:171
Alignment explanation
Indices: 11407--13758 Score: 2143
Period size: 171 Copynumber: 13.7 Consensus size: 171
11397 NNNNNNNNNG
* ** * ** *
11407 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATAAACATTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* ** ** * * * *
11472 CCAATGAATTCCATTTTCTTCACATTTCTCATGGTAGACATTCAATTATTA-TCTATTTTATTGA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTA-TAGTCTGTTTTAATAA
* *
11536 AAAATGTAAAAATAATT-ACCTTAAAATCAATTATGAGATTAT
130 AAAATATAAAAA-AATTCAACTTAAAATCAATTATGAGATTAT
* * * *
11578 CAAACCGTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTCCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * * * *
11643 CCAATAAAT-CTCTTTTTTTTTATGTTTCTCAAGGTAGATATTCAATTATTGTCTGTTTTAATAA
66 CCAATGAATGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAA
* * *
11707 AAAATATTAAAATAA-TCAACTTGAGATCAATTATGAGATTAT
130 AAAATA-TAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * ** * *
11749 AAAACCTTTTAAAGCGAGTAATAATGCTTTTGAAGGAATAAGTGAATATAAATGGACTTTTCTT-
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * * ** * * * *
11813 CTTAACGAATGGC-TTTTTCTACATGTTTCTTGAGGTAGGCATTGAATTATAGTCTATTTTAATG
66 C-CAATGAAT-GCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATA
* * *
11877 AAAAATGTAAAAAAATTTAACTTAAACTCAATTATGAGATTAT
129 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * * *
11920 AGAACCATTTAAATCGAGTAACAATGTTTTTGAAGGAATAGGTA-AGTATAAATGGACTTTTC-T
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGGAGACTATAAATGGACTTTTCTT
* * * * * *
11983 -CTCAATGAATGGCATTTTTT-GT-ATGTTTCCCAAGGCAGATATTCAATTGTAGTTTGTTTTAA
65 GC-CAATGAAT-GC-TTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA
* *
12045 TAAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTAT
127 TAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
12090 AAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGAGACTATAAATGGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * * * ***
12155 TCAATGAATAG-TTTTTTCTTTATATTTCTCATGGTAGACATTCAATTATAGTCTGTTTTAGCCA
66 CCAATGAAT-GCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAA
* * *
12219 AAAATGTAAAATAATTCAACTTAAAATCAATTTTGAGATTAT
130 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
12261 AAAACCGTTTAAAGCCAGTAATAAGACTTTTG-AGAAAATGGGAGACTATAAATAGAC-TTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG-GAATGGGAGACTATAAATGGACTTTTC-T
* * ** * * *
12324 TGCCAATGAGTGCTTTTTTCTTCAGGTTTCTTGATGTAGACATTCAATTATAGTCTCTTTTAACC
64 TGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-T
** * *
12389 AAAATTTTTTAAAAAAA-TCAACTTAAAATCAGTTATGAGATTAT
128 AAAA-AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
12433 AAAACCATTTAAAGCAAGTAATAAGGTTTTTGAAGGAATGAGAGACTATAAATGGACTTTCCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * * * * **
12498 CTAATGAATGCTTTTTTCTTCATGTTTCTCGAGGAAGACATCCAATTTTAGTCTGTTTTAACCAA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAAA
* * *
12563 AAATATAAAACAATTCAACTTAAAAACAATTATGAGATTGT
131 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* ** * * * * *
12604 AAAACCGTTTAAAATGAGTAATAAGACTTTTGAATGAATGGGAGATTATAAATAGACTTTCCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * * *
12669 CCAATGAATGCTTTTTTCTTCACGTTTCTCTAGGTAAACATTCAATTATAGTCTGTTTTAGTAAA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAAA
*
12734 AAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTAT
131 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
12775 ACAATCATTTAACGCAAGTAATAAGACTTTTGAAGAAATGGGTA-ACTATAAAT-GACTTTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATGGACTTTTCTT
* * * * * * * *
12838 -TCAATGAATGGTTTTTTCTAT-ATGTTTCCCAAGCTAGACATTCAATCATAGTCTCTTTTCATG
65 GCCAATGAATGCTTTTTTCT-TCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATA
*
12901 AAAAATATAAAAAAATTCAACTTAAAATCAATTATCAGATTAT
129 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
12944 ACAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA-ACTATAAATAGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* ** * * * **
13008 CCGATGAATGCTTTTTTCTTCACATTTCTCTAGGAAGACATTCTATTATAGTCTGTTTTAACCAA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAAA
** * * *
13073 AAATGCAAAAAAATTCAACTTAAAATCGATTTTGAGATTTT
131 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* ** * ** * * * *
13114 AAAATCGATTTTGA-C-A-TTATAAAATCATTTGAAAAGAGTAAT--AAGGCTTTTGAAGGAATG
1 AAAA-CCATTTAAAGCGAGTAAT-AAGGCTTTTG--AAG-G-AATGGGAGAC-TAT--A--AAT-
** * * * ** *
13174 AGAGACTATAAATTGACTTTTC-TTGCCAACGAATGCTTTTTCTTCATGTTTCTTTAGGTCGACA
54 -G-GACT-T---TT--CTTGCCAATG--AATG-CT--TTTTTCTTCATGTTTCTCAAGGTAGACA
* *
13238 TTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
106 TTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
13302 T
171 T
* * * * *
13303 AAAACCATTTAAAGCAAGTAATAAAGCTTTTAAACGAATGGGAGACTATAATTGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * *** * * * ***
13368 CCAATGAATGGTTTTTTCTTCACGTTTCTCATTATAAACATTCAATGATAGTTTGTTTTAGCCAA
66 CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAAA
* * ** * *
13433 AAATGTAAAATAATTCAACTTAAAATTGATTTTGAAATTAT
131 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
** ** * * *
13474 AAAACTGTTTAAAGTC-AACAATTAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTCCTT
1 AAAACCATTTAAAG-CGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTT
* * * * * * *
13538 GTCAATGAATGCTTTTTTCTTTAGGTTTTTCATGGTAGACATTCAATTATAGTCTCTTTTAATCA
65 GCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAA
* *
13603 AAAATGTAAAAAAATTCAACTTAAAATCAGTTATGAGATTAT
130 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * *
13645 AAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCCTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
* * *
13710 CCAATGAAT-CTCATTTTCTTCATGTTTCTAAAGATAGACATTCAATTAT
66 CCAATGAATGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTAT
13759 CATCTATCTT
Statistics
Matches: 1764, Mismatches: 352, Indels: 130
0.79 0.16 0.06
Matches are distributed among these distances:
168 13 0.01
169 153 0.09
170 295 0.17
171 982 0.56
172 145 0.08
173 22 0.01
174 4 0.00
175 3 0.00
176 2 0.00
177 3 0.00
179 1 0.00
180 8 0.00
181 2 0.00
183 2 0.00
184 2 0.00
185 3 0.00
186 7 0.00
187 6 0.00
188 12 0.01
189 45 0.03
190 51 0.03
191 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (171 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTG
CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAATAAA
AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
Found at i:13117 original size:20 final size:20
Alignment explanation
Indices: 13092--13143 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
13082 AAAATTCAAC
*
13092 TTAAAATCGATTTTGAGATT
1 TTAAAATCGATTTTGACATT
13112 TTAAAATCGATTTTGACATT
1 TTAAAATCGATTTTGACATT
*
13132 ATAAAATC-ATTT
1 TTAAAATCGATTT
13144 GAAAAGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (20 bp):
TTAAAATCGATTTTGACATT
Found at i:13216 original size:190 final size:189
Alignment explanation
Indices: 12959--13306 Score: 545
Period size: 190 Copynumber: 1.8 Consensus size: 189
12949 AATTTAAAGC
* * *
12959 GAGTAATAAGGCTTTTGAAGGAATGGGAACTATAAATAGACTTTTCTTGCCGATGAATGCTTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAACTATAAATAGACTTTTCTTGCCAACGAATGCTTTTT
*
13024 TCTTCACATTTCTCTAGGAAGACATTCTATTATAGTCTGTTTTAACCAAAAATGCAAAAAAATTC
66 TCTTCACATTTCTCTAGGAAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGCAAAAAAATTC
* * *
13089 AACTTAAAATCGATTTTGAGATTTTAAAATCGATTTTGACATTATAAAATCATTTGAAAA
130 AACTTAAAATCAATTATGAGATTATAAAATCGATTTTGACATTATAAAATCATTTGAAAA
*
13149 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATTGACTTTTCTTGCCAACGAATGC-TTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGA-ACTATAAATAGACTTTTCTTGCCAACGAATGCTTTT
** * ** *
13213 TTCTTCATGTTTCTTTAGGTCGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTC
65 TTCTTCACATTTCTCTAGGAAGACATTCAATTATAGTCTGTTTTAACAAAAATGCAAAAAAATTC
13278 AACTTAAAATCAATTATGAGATTATAAAA
130 AACTTAAAATCAATTATGAGATTATAAAA
13307 CCATTTAAAG
Statistics
Matches: 143, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
189 44 0.31
190 70 0.49
191 29 0.20
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (189 bp):
GAGTAATAAGGCTTTTGAAGGAATGAGAACTATAAATAGACTTTTCTTGCCAACGAATGCTTTTT
TCTTCACATTTCTCTAGGAAGACATTCAATTATAGTCTGTTTTAACAAAAATGCAAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAATCGATTTTGACATTATAAAATCATTTGAAAA
Found at i:13753 original size:342 final size:341
Alignment explanation
Indices: 11407--13758 Score: 2363
Period size: 342 Copynumber: 6.8 Consensus size: 341
11397 NNNNNNNNNG
* ** * * ** *
11407 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATAAACATTTCTTG
1 AAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTG
* * ** ** * * *
11472 CCAATGAATTCCATTTTCTTCACATTTCTCATGGTAGACATTCAATTATTA-TCTATTTTATTGA
66 TCAATGAATGCTTTTTTCTTCATGTTTCTCA-GGTAGACATTCAATTA-TAGTCTGTTTTAATCA
* * *
11536 AAAATGTAAAAATAATT-ACCTTAAAATCAATTATGAGATTATCAAACCGTTTAAAGCGAGTAAT
129 AAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* *
11600 AAGGCTTTTAAAGGAATGGGAGACTATAAATGGAC-TTTCCTTGCCAATAAAT-CTCTTTTTTTT
193 AAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCC-TGCCAATGAATGCT-TTTTTCTT
* * * * * * * *
11663 TATGTTTCTCAAGGTAGATATTCAATTATTGTCTGTTTTAATAAAAAATATTAAAATAA-TCAAC
256 CACGTTTCTCAAGATAGACATTCAATTATAGTCTGTTTTAACAAAAAAT-GTAAAAAAATTCAAC
* *
11727 TTGAGATCAATTATGAGATTAT
320 TTAAAATCAATTATGAGATTAT
* * * * *
11749 AAAACCT-TTTAAAGCGAGTAATAATGCTTTTGAAGGAATAAGTGAATATAAATGGACTTTTCTT
1 AAAA-CTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTT
* * * * * * * * *
11813 CTTAACGAATGGC-TTTTTCTACATGTTTCTTGAGGTAGGCATTGAATTATAGTCTATTTTAATG
65 GTCAATGAAT-GCTTTTTTCTTCATGTTTC-TCAGGTAGACATTCAATTATAGTCTGTTTTAATC
* * * * *
11877 AAAAATGTAAAAAAATTTAACTTAAACTCAATTATGAGATTATAGAACCATTTAAATCGAGTAAC
128 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * *
11942 AATGTTTTTGAAGGAATAGGTA-AGTATAAATGGACTTTT-CT-CTCAATGAATGGCATTTTTT-
193 AAGGCTTTTAAAGGAAT-GGGAGACTATAAATGGACTTTTCCTGC-CAATGAAT-GC-TTTTTTC
* * * ** * * * *
12003 GT-ATGTTTCCCAAGGCAGATATTCAATTGTAGTTTGTTTTAATAAAAAATGTAAAAAAATTCAA
254 TTCACGTTTCTCAAGATAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAA
*
12067 CTTAAAATTAATTATGAGATTAT
319 CTTAAAATCAATTATGAGATTAT
* *
12090 AAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGAGACTATAAATGGACTTTTCTTA
1 AAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTG
* * **
12155 TCAATGAATAG-TTTTTTCTTTATATTTCTCATGGTAGACATTCAATTATAGTCTGTTTTAGCCA
66 TCAATGAAT-GCTTTTTTCTTCATGTTTCTCA-GGTAGACATTCAATTATAGTCTGTTTTAATCA
* * * *
12219 AAAATGTAAAATAATTCAACTTAAAATCAATTTTGAGATTATAAAACCGTTTAAAGCCAGTAATA
129 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * *
12284 AGACTTTTGAGAA--AATGGGAGACTATAAATAGAC-TTTCTTTGCCAATGAGTGCTTTTTTCTT
194 AGGCTTTT-A-AAGGAATGGGAGACTATAAATGGACTTTTC-CTGCCAATGAATGCTTTTTTCTT
* * * * ** *
12346 CAGGTTTCTTGATG-TAGACATTCAATTATAGTCTCTTTTAACCAAAATTTTTTAAAAAAA-TCA
256 CACGTTTC-TCAAGATAGACATTCAATTATAGTCTGTTTTAA-CAAAA-AATGTAAAAAAATTCA
*
12409 ACTTAAAATCAGTTATGAGATTAT
318 ACTTAAAATCAATTATGAGATTAT
* * *
12433 AAAACCATTTAAAGCAAGTAATAAGGTTTTTGAAGGAATGAGAGACTATAAATGGACTTTCCTT-
1 AAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTG
* * * * *
12497 ACTAATGAATGCTTTTTTCTTCATGTTTCTCGAGGAAGACATCCAATTTTAGTCTGTTTTAACCA
66 TC-AATGAATGCTTTTTTCTTCATGTTTCTC-AGGTAGACATTCAATTATAGTCTGTTTTAATCA
* * * * * **
12562 AAAATATAAAACAATTCAACTTAAAAACAATTATGAGATTGTAAAACCGTTTAAAATGAGTAATA
129 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * *
12627 AGACTTTTGAATGAATGGGAGATTATAAATAGAC-TTTCCTTGCCAATGAATGCTTTTTTCTTCA
194 AGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCC-TGCCAATGAATGCTTTTTTCTTCA
* * * ** * *
12691 CGTTTCTCTAGGTAAACATTCAATTATAGTCTGTTTTAGTAAAAAATATAAAAAAATTCAAATTA
258 CGTTTCTCAAGATAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTA
12756 AAATCAATTATGAGATTAT
323 AAATCAATTATGAGATTAT
* * * * *
12775 ACAA-TCATTTAACGCAAGTAATAAGACTTTTGAAGAAATGGGTA-ACTATAAAT-GACTTTTCT
1 AAAACT-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATGGACTTTTCT
* * * * * *
12837 T-TCAATGAATGGTTTTTTCTAT-ATGTTTCCCAAGCTAGACATTCAATCATAGTCTCTTTTCAT
64 TGTCAATGAATGCTTTTTTCT-TCATGTTTCTC-AGGTAGACATTCAATTATAGTCTGTTTTAAT
* * * * *
12900 GAAAAATATAAAAAAATTCAACTTAAAATCAATTATCAGATTATACAACAATTTAAAGCGAGTAA
127 CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * *
12965 TAAGGCTTTTGAAGGAATGGGA-ACTATAAATAGACTTTTCTTGCCGATGAATGCTTTTTTCTTC
192 TAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCCTGCCAATGAATGCTTTTTTCTTC
* * * * *
13029 ACATTTCTCTAGGA-AGACATTCTATTATAGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACT
257 ACGTTTCTC-AAGATAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
* * *
13093 TAAAATCGATTTTGAGATTTT
321 TAAAATCAATTATGAGATTAT
*
13114 AAAATCGATTTTGACATTATAAAATCATTTGAAAAGAGTAATAAGGCTTTTGAAGGAATGAGAGA
1 AAAA-C-----T---ATT-T--AA--A---G--CA-AGTAATAAGGCTTTTGAAGGAATGAGAGA
* * * * *
13179 CTATAAATTGACTTTTCTTGCCAACGAATGC-TTTTTCTTCATGTTTCTTTAGGTCGACATTCAA
46 CTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTC-TCAGGTAGACATTCAA
13243 TTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
110 TTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * * *
13307 CCATTTAAAGCAAGTAATAAAGCTTTTAAACGAATGGGAGACTATAATTGGACTTTTCTTGCCAA
175 CCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCCTGCCAA
* ** * * * * *
13372 TGAATGGTTTTTTCTTCACGTTTCTCATTATAAACATTCAATGATAGTTTGTTTTAGCCAAAAAT
240 TGAATGCTTTTTTCTTCACGTTTCTCAAGATAGACATTCAATTATAGTCTGTTTTAACAAAAAAT
* ** * *
13437 GTAAAATAATTCAACTTAAAATTGATTTTGAAATTAT
305 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
13474 AAAACTGTTTAAAGTCAA-CAATTAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTCCTT
1 AAAACTATTTAAAG-CAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTT
* * * *
13538 GTCAATGAATGCTTTTTTCTTTAGGTTTTTCATGGTAGACATTCAATTATAGTCTCTTTTAATCA
65 GTCAATGAATGCTTTTTTCTTCATGTTTCTCA-GGTAGACATTCAATTATAGTCTGTTTTAATCA
*
13603 AAAATGTAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATA
129 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
13668 AGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCCTACCAATGAAT-CTCATTTTCTTCA
194 AGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCCTGCCAATGAATGCT-TTTTTCTTCA
* *
13732 TGTTTCTAAAGATAGACATTCAATTAT
258 CGTTTCTCAAGATAGACATTCAATTAT
13759 CATCTATCTT
Statistics
Matches: 1682, Mismatches: 258, Indels: 140
0.81 0.12 0.07
Matches are distributed among these distances:
339 105 0.06
340 204 0.12
341 325 0.19
342 432 0.26
343 305 0.18
344 11 0.01
346 2 0.00
348 6 0.00
349 1 0.00
350 1 0.00
351 4 0.00
354 1 0.00
356 1 0.00
358 2 0.00
359 114 0.07
360 160 0.10
361 8 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (341 bp):
AAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTG
TCAATGAATGCTTTTTTCTTCATGTTTCTCAGGTAGACATTCAATTATAGTCTGTTTTAATCAAA
AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
GCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCCTGCCAATGAATGCTTTTTTCTTCACGT
TTCTCAAGATAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAA
TCAATTATGAGATTAT
Done.