Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398822.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2106.0, 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: 29920
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.25
Warning! 9326 characters in sequence are not A, C, G, or T
Found at i:1286 original size:171 final size:168
Alignment explanation
Indices: 667--1500 Score: 608
Period size: 171 Copynumber: 4.9 Consensus size: 168
657 NNNNNNNNNN
* * * * * *
667 GAATGTCTACCTTA-AGAAACATGAATAAAAGGGCATTCATTGGGAAGAAAAGTCAATTTATAGT
1 GAATGTGTACC-TAGAGAAACATAAAGAAAA-AGCATTCATT-AGAAGAAAAGTCCATTTATAGT
* ** * *
731 CACCCATTCCTT-AAGAAGGCTTATTACTTGCTTTAAACCGTTTTATAATC-CTATAACTAACTT
63 CACCCATTCCTTCAA-AA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTC-ATAACTGATTT
* ** *
794 TAAGTTCAATTGTTTTACA-TTTTTTTTAAAA-ATAGACTATAATT
125 TAAGTTGAATTGTTTTACACTTTTGGTTAAAACA-A-ACAATAATT
* * * * *
838 GAATGTCTACC-ATGAGAAACGTGAAGAAAAACGCATTCATTGACAAAAAAAAGTCCATTTATAG
1 GAATGTGTACCTA-GAGAAACATAAAGAAAAA-GCATTCATT-A-GAAGAAAAGTCCATTTATAG
* * * * * * ******
902 TCACCCATTCCATCAAAAGACTGATTACTCGCTTGAAATCGTTTTATAATCTCCTAATTNNNNNN
62 TCACCCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTT
**** * * ** * * * *
967 NNNNTGAATTATTTTACATTTTTCATTAAAAGAAACCACAACT
126 AAGTTGAATTGTTTTACACTTTTGGTTAAAACAAACAATAATT
* * * *
1010 GAATGTGT-CTTAG-GAAACGTAAAGTGAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTC
1 GAATGTGTACCTAGAGAAACATAAAG-AAAAAGCATTCATTAG-AAGAAAAGTCCATTTATAGTC
** * * ** *
1073 ACTTATTCCCTCAAAAGGTGTATTAGACGTTTTAAATAGTTTTATAATCTCATAACTGATTTTAA
64 ACCCATTCCTTCAAAAGCT-TATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAA
***********
1138 GTTGAATTGTTTTACACNNNNNNNNNNNACAAACAATAATT
128 GTTGAATTGTTTTACACTTTTGGTTAAAACAAACAATAATT
1179 GAATGTGTACCTAGAGAAACATAAAGAAACAAGCATTCATTAAGAAGAAAAGTCCATTTATAGTC
1 GAATGTGTACCTAGAGAAACATAAAGAAA-AAGCATTCATT-AGAAGAAAAGTCCATTTATAGTC
* * *
1244 ACCCATTCCTTAAAAATGCTTATTACTCGCTTTAACTAGTTTTATAATCTCATTACTGATTTTAA
64 ACCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAA
* * *
1309 GTTGAA--GTTTTCCACATTTTTGGTTAAAACAGACTATAATT
128 GTTGAATTGTTTT--ACACTTTTGGTTAAAACAAACAATAATT
* ** * * * *
1350 GAATGTCTACCTCCATAAACATAAAGAAAAAGGGATTCATTGACAAGAAAAGTCCATTTATAATC
1 GAATGTGTACCTAGAGAAACATAAAGAAAAA-GCATTCATT-AGAAGAAAAGTCCATTTATAGTC
* * * * * *
1415 ACCGATTCCTTCAAAAGGCTTATTACTCGCTTCAAATGGTTTTATAATCTCTTAATTTATTTTAA
64 ACCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAA
*
1480 GTTGAATTGTTTTACATTTTT
128 GTTGAATTGTTTTACACTTTT
1501 TNNNNNNNNN
Statistics
Matches: 517, Mismatches: 123, Indels: 46
0.75 0.18 0.07
Matches are distributed among these distances:
168 1 0.00
169 99 0.19
170 27 0.05
171 279 0.54
172 91 0.18
173 19 0.04
174 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.34
Consensus pattern (168 bp):
GAATGTGTACCTAGAGAAACATAAAGAAAAAGCATTCATTAGAAGAAAAGTCCATTTATAGTCAC
CCATTCCTTCAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTT
GAATTGTTTTACACTTTTGGTTAAAACAAACAATAATT
Found at i:3987 original size:172 final size:172
Alignment explanation
Indices: 3802--4125 Score: 479
Period size: 172 Copynumber: 1.9 Consensus size: 172
3792 NNNNNNNNNA
* * * * *
3802 AAGAAAAAGAGATTCATTAGCAAGAAAAGTCTATTTATAGCCACTCATTCCTTCAAAAGGCTTAC
1 AAGAAAAAGAGATTCATTAGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTCAAAAAGCATAC
* * * *
3867 TACTCGCTTTAAATAGTTTTATCATCTCATAACTA-ATTTTAAGTTGAATGTTTTTACATTTTTG
66 TACTCGCTTTAAACAGTTTTATAATCTCATAA-TAGATTTTAAGTGGAATGTTTTTAAATTTTTG
* *
3931 GGTAAAACAGACTATAATTGAATACATACCATTTAGAAACATT
130 GGTAAAACAAACAATAATTGAATACATACCATTTAGAAACATT
* * *
3974 AAGAAAAAGAGATTCATTGGAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAAGCATAT
1 AAGAAAAAGAGATTCATTAGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTCAAAAAGCATAC
* *
4039 TACTCGCTTTAAACGGTTTTATAATCTCATAATAGATTTTAAGTGGAATTTTTTTAAATTTTTGG
66 TACTCGCTTTAAACAGTTTTATAATCTCATAATAGATTTTAAGTGGAATGTTTTTAAATTTTTGG
*
4104 TTAAAACAAACAATAATTGAAT
131 GTAAAACAAACAATAATTGAAT
4126 GTCTACCTCA
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
171 2 0.01
172 132 0.99
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (172 bp):
AAGAAAAAGAGATTCATTAGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTCAAAAAGCATAC
TACTCGCTTTAAACAGTTTTATAATCTCATAATAGATTTTAAGTGGAATGTTTTTAAATTTTTGG
GTAAAACAAACAATAATTGAATACATACCATTTAGAAACATT
Found at i:6024 original size:171 final size:166
Alignment explanation
Indices: 5738--6234 Score: 442
Period size: 171 Copynumber: 2.9 Consensus size: 166
5728 ACAACAAACA
* * * *
5738 ATAATTGAATGTGTACCTAGAGAAACGTAAAG-AAACAAGCACTGATTGGCATGAAAAGTCCATT
1 ATAATTGAATGT-TACCT-GAGAAACATGAAGAAAAC-AGCATTGATTGGCAAGAAAAGTCCATT
* * * * * *
5802 TCTAGTCACCCATTCCTTAAGATGGCTTATCACTTGCTTTCAATAGTTTTATAATCTCATAACAG
63 TATAGTCA-CCATTCCTTCAGA-AGCTTAT-ACTTACTTTAAATGGTTTTATAATCTCATAACAG
* *
5867 ACTTTAAGTTGAATTTTTTTACATTTTCAGTTAAAACAGACT
125 ATTTTAAGTTGAATTATTTTACATTTTCAGTTAAAACAGACT
*
5909 ATAATTGAATGTTTACCATGAGAAACATGAAGAAAACAGCATTGATTGACAAGAAAAGTCCATTT
1 ATAATTGAATG-TTACC-TGAGAAACATGAAGAAAACAGCATTGATTGGCAAGAAAAGTCCATTT
* * * * **
5974 ATAGTCACTCATTCCTTCAGAAGCCTTAGTACTCACCTTAAATGGTTTTATAATCTCCTGATTGA
64 ATAGTCAC-CATTCCTTCAGAAG-CTTA-TACTTACTTTAAATGGTTTTATAATCTCATAACAGA
**********
6039 TTTTAAGTTGAATTATTTTANNNNNNNNNNTAAAACAGACT
126 TTTTAAGTTGAATTATTTTACATTTTCAGTTAAAACAGACT
* * * * * * *
6080 ACAATTGAATG-TATCTTGGGAAATATGAAGAAAAAAGCATTCATTGGCCAGAAAAGTCCATTTA
1 ATAATTGAATGTTA-CCTGAGAAACATGAAGAAAACAGCATTGATTGGCAAGAAAAGTCCATTTA
* * * *
6144 TAGTCACCTATTCATTCAAAAAGTTTATTACTTACTTTAAATGGTTTTATAATCTTATAACTA-A
65 TAGTCACC-ATTCCTTC-AGAAGCTTA-TACTTACTTTAAATGGTTTTATAATCTCATAAC-AGA
* *
6208 TTTTAACTTGAATTGTTTTACACTTTT
126 TTTTAAGTTGAATTATTTTACA-TTTT
6235 GGTTACAGCA
Statistics
Matches: 259, Mismatches: 56, Indels: 23
0.77 0.17 0.07
Matches are distributed among these distances:
168 1 0.00
169 107 0.41
170 7 0.03
171 137 0.53
172 7 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.35
Consensus pattern (166 bp):
ATAATTGAATGTTACCTGAGAAACATGAAGAAAACAGCATTGATTGGCAAGAAAAGTCCATTTAT
AGTCACCATTCCTTCAGAAGCTTATACTTACTTTAAATGGTTTTATAATCTCATAACAGATTTTA
AGTTGAATTATTTTACATTTTCAGTTAAAACAGACT
Found at i:9179 original size:340 final size:334
Alignment explanation
Indices: 8770--10350 Score: 1518
Period size: 340 Copynumber: 4.7 Consensus size: 334
8760 ATAAACTATA
* *
8770 ATTGAATGTCTACC-ATGAGAAACATGAAGAAAACAGCATTTATTGACAAGAAAAGTCCATTTAT
1 ATTGAATGTCTACCTA-GAGAAACATGAAGAAAA-AGCATTCATTGGCAAGAAAAGT-CATTTAT
* * * * *
8834 AGTCACCCATTCATTCAAAAGCCTTAGTACTCGCCTTAAATAGTTTTATAATCTCCTAATTGATT
63 AGTCACCCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATT
** * *
8899 TTAAGTTGAATTATTTTGTATTTTTCATTAAAACAGACTACAATTGAATGTGCCCTGGGAAATAT
127 TTAAGTTGAATT-TTTTACATTTTT-ATTAAAACAGACTACAATTGAATGTGCCCTGAGAAACAT
* * * * *
8964 GAAGAAAAAAGCATTCATAGGCAAGGAAAGTCCAGTTATAGTCACCTATTCATTCAAAAGGTTTA
190 GAAGAAAAAAGCATTCATAGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTA
* * * *
9029 TTACTTACTTTAAATGGTTTTAGAATCTCATAACTGATTTTAACTTAAATTGTTTTACACTTTTG
255 TTACTCACTTTAAATGGTTTTAGAATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTTTTG
*
9094 GTTATAGAAA-ACAATG
320 ATTA-A-AAAGACAATG
* * *
9110 ATTGAATGTTTACCTAGAGAAACGTAAAGAAACAAGCATTCATTGGCAAGAAAAGTACATTTATA
1 ATTGAATGTCTACCTAGAGAAACATGAAGAAA-AAGCATTCATTGGCAAGAAAAGT-CATTTATA
* * * * *
9175 GTCACTCATTCCTTAAAAAGGCTTATTACTCGCTTTAACTTGTTTTATAATCTCATTACTGATTT
64 GTCACCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTT
* * * * *
9240 TAAGTTGAATTTTTCTGCATTTTTGGTTAAAATAGACTACAATTGAATGTG-TCTGAAGAAACGT
128 TAAGTTGAATTTTT-TACATTTTT-ATTAAAACAGACTACAATTGAATGTGCCCTG-AGAAACAT
* * *
9304 GTAGATAAAAA-CATTCATCGGCAAGAAAAGTCAATTTATAGTCACCCATTCCTTCAAAAGGCTT
190 GAAGA-AAAAAGCATTCATAGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTT
* * *
9368 ATTACTCGCTTTAAATGGTTTT-GTAATCTCATACCTGATTTTAAGTTGAATTGTTTGACATTTT
254 ATTACTCACTTTAAATGGTTTTAG-AATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTTT
* *
9432 TGATTACCACAA-ACAATA
318 TGATTA--AAAAGACAATG
* * * *
9450 ATTGAATGTGTACCTTGAGAAACATGAAGAAATAAGCATTCATTGGCAAAAAAAGTTCATTTACA
1 ATTGAATGTCTACCTAGAGAAACATGAAGAAA-AAGCATTCATTGGCAAGAAAAG-TCATTTATA
* * * * *
9515 GTCACCAATTCTTTCAAAATGCTTATTACTCGCTTTAATTAGTTTTATAATCTCAGAACTTATTT
64 GTCACCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTT
* * * *
9580 TATGTTGAATTTTTCTACATTTTTGGTTAAAATAGACT---A-T--A---------AGAAACGTG
128 TAAGTTGAATTTTT-TACATTTTT-ATTAAAACAGACTACAATTGAATGTGCCCTGAGAAACATG
* * *
9630 AGGAAAAAAGCATTCATTATG-AAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTA
191 AAGAAAAAAGCATTCA-TAGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTA
* *
9694 TTACTCACTTTAAATGGTTTGATAATCTCATAACTGATTTTATA-TTGAA-TGTTTTACATTTTT
255 TTACTCACTTTAAATGGTTTTAGAATCTCATAACTGATTTTA-AGTTGAATTGTTTTACATTTTT
*
9757 GGTTAAAACAGACAAT-
319 GATTAAAA-AGACAATG
* * *
9773 ATTTGAATGTCT-CCGTCA-AGAAACGTGAAGAAAAGGGCATTCATTGACAAGAAAAGTCTATTT
1 A-TTGAATGTCTACC-T-AGAGAAACATGAAGAAAA-AGCATTCATTGGCAAGAAAAGTC-ATTT
** * *
9836 ATAGTCACCCATTCCCTAAAAAAGCTTATTACTCGCTTTAAATGGTTTGATAATCTCATAACTGA
61 ATAGTCACCCATT-CCTTCAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGA
** * * * *
9901 CCTGAAGTTGAATTTTTTTAAATTTTTACTTAAAACAGACTATAATTGAATGT-CTAACTTGAGA
125 TTTTAAGTTGAA-TTTTTTACATTTTTA-TTAAAACAGACTACAATTGAATGTGC---CCTGAGA
** * * *
9965 AACATGAAGAAAAAGAG-ATTGTTTGGAAAGAAAAGTCCATTTACAGTCACCCATTCCTTCAAAA
185 AACATGAAGAAAAA-AGCATTCATAGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* * * * * * * *
10029 GCCTTATTACTCGCTTTAAATGGTTTTATAATATCCTAA-TCGATTTGAAGTTGAATTCTTTAAC
249 GGCTTATTACTCACTTTAAATGGTTTTAGAATCTCATAACT-GATTTTAAGTTGAATTGTTTTAC
*
10093 ATTTTTCATTAAAAAAGACTACA-G
313 ATTTTTGATT-AAAAAGAC-A-ATG
* * * *
10117 -TTGAACGTGTACCTCGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCATTTTATA
1 ATTGAATGTCTACCTAGAGAAACATGAAG-AAAAAGCATTCATTGGCAAGAAAAGTCA-TTTATA
* * * *
10181 GTCTCTCATTCCTTCAAAAGGTTTATTACTCGCTTTAAAT-GATTTTATAATCTCGTAACTGATT
64 GTCACCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAG-TTTTATAATCTCATAACTGATT
* * * * * * * *
10245 TTCAGCTGAATTGGTTTACATTTGTAGTTAAAACACACAATAATTGAATGTGTACCTTGAGAAAC
127 TTAAGTTGAATT-TTTTACATTTTTA-TTAAAACAGACTACAATTGAATGTG--CCCTGAGAAAC
* * *
10310 ATGAAGAAAAAAGTATTCATTGACAAGAAAAGTCCATTTAT
188 ATGAAGAAAAAAGCATTCATAGGCAAGAAAAGTCCATTTAT
10351 NNNNNNNNNN
Statistics
Matches: 1035, Mismatches: 146, Indels: 118
0.80 0.11 0.09
Matches are distributed among these distances:
322 2 0.00
323 7 0.01
324 148 0.14
325 111 0.11
326 3 0.00
327 1 0.00
328 1 0.00
330 1 0.00
334 1 0.00
336 1 0.00
337 1 0.00
339 7 0.01
340 424 0.41
341 121 0.12
342 193 0.19
343 11 0.01
344 1 0.00
345 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (334 bp):
ATTGAATGTCTACCTAGAGAAACATGAAGAAAAAGCATTCATTGGCAAGAAAAGTCATTTATAGT
CACCCATTCCTTCAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAA
GTTGAATTTTTTACATTTTTATTAAAACAGACTACAATTGAATGTGCCCTGAGAAACATGAAGAA
AAAAGCATTCATAGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTC
ACTTTAAATGGTTTTAGAATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTTTTGATTAAA
AAGACAATG
Found at i:9229 original size:171 final size:170
Alignment explanation
Indices: 8741--10350 Score: 1551
Period size: 171 Copynumber: 9.5 Consensus size: 170
8731 AACAGACTTT
** * * *
8741 TTTTACATTTTCAGTTAAAATAAACTATAATTGAATGTCTACC-ATGAGAAACATGAAGAAAACA
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTA-GAGAAACATGAAGAAAA-A
* * * * * *
8805 GCATTTATTGACAAGAAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCCTTAGTACTCGCCT
64 GCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * * *
8870 TAAATAGTTTTATAATCTCCTAATTGATTTTAAGTTGAATTA
129 TAAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
** ** * * * *
8912 TTTTGTATTTTTCATTAAAACAGACTACAATTGAATGTGC--CCT-GGGAAATATGAAGAAAAAA
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGT-CTACCTAGAGAAACATGAAG-AAAAA
* * * * * * **
8974 GCATTCATAGGCAAGGAAAGTCCAGTTATAGTCACCTATTCATTCAAAAGGTTTATTACTTACTT
64 GCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * *
9039 TAAATGGTTTTAGAATCTCATAACTGATTTTAACTTAAATTG
129 TAAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
* * * * *
9081 TTTTACACTTTTGGTTATAGAA-A-ACAATGATTGAATGTTTACCTAGAGAAACGTAAAGAAACA
1 TTTTACATTTTTGGTTA-A-AACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAGAAA-A
* * *
9144 AGCATTCATTGGCAAGAAAAGTACATTTATAGTCACTCATTCCTTAAAAAGGCTTATTACTCGCT
63 AGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCT
* * *
9209 TTAACTTGTTTTATAATCTCATTACTGATTTTAAGTTGAATT-
128 TTAAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
* * * * * * *
9251 TTTCTGCATTTTTGGTTAAAATAGACTACAATTGAATGTGT--CT-GAAGAAACGTGTAGATAAA
1 TTT-TACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAG-AGAAACATGAAGA-AAA
* * *
9313 AACATTCATCGGCAAGAAAAGTCAATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCT
63 AGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCT
* *
9378 TTAAATGGTTTTGTAATCTCATACCTGATTTTAAGTTGAATTG
128 TTAAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
* * ** * * *
9421 TTTGACATTTTTGATTACCACAAACAATAATTGAATGTGTACCTTGAGAAACATGAAGAAATAAG
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAGAAA-AAG
* * * * * *
9486 CATTCATTGGCAAAAAAAGTTCATTTACAGTCACCAATTCTTTCAAAATGCTTATTACTCGCTTT
65 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
* * * * *
9551 AATTAGTTTTATAATCTCAGAACTTATTTTATGTTGAATT-
130 AAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
* * *
9591 TTTCTACATTTTTGGTTAAAATAGACTATAA--GAA-----ACGT-GAG------G-A-AAAAAG
1 TTT-TACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAGAAAAAG
* * *
9640 CATTCATTATG-AAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCACTT
65 CATTCATT-GGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
*
9704 TAAATGGTTTGATAATCTCATAACTGATTTTATA-TTGAA-TG
129 TAAATGGTTTTATAATCTCATAACTGATTTTA-AGTTGAATTG
* *
9745 TTTTACATTTTTGGTTAAAACAGACAATATTTGAATGTCT-CCGTCA-AGAAACGTGAAGAAAAG
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACC-T-AGAGAAACATGAAGAAAA-
* * * * * *
9808 GGCATTCATTGACAAGAAAAGTCTATTTATAGTCACCCATTCCCTAAAAAAGCTTATTACTCGCT
63 AGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCT
* ** * *
9873 TTAAATGGTTTGATAATCTCATAACTGACCTGAAGTTGAATTT
128 TTAAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
* ** * * *
9916 TTTTAAATTTTTACTTAAAACAGACTATAATTGAATGTCTAACTTGAGAAACATGAAGAAAAAGA
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAGAAAAAG-
* ** * * *
9981 GATTGTTTGGAAAGAAAAGTCCATTTACAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
65 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
* * * *
10046 AAATGGTTTTATAATATCCTAA-TCGATTTGAAGTTGAATTC
130 AAATGGTTTTATAATCTCATAACT-GATTTTAAGTTGAATTG
* ** * * * * * * *
10087 TTTAACATTTTTCATTAAAAAAGACTACAGTTGAACGTGTACCTCGAGAAACATGAAGAAAAAAG
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAG-AAAAAG
* * * *
10152 TATTCATTGGCAAGAAAAGT-CATTTTATAGTCTCTCATTCCTTCAAAAGGTTTATTACTCGCTT
65 CATTCATTGGCAAGAAAAGTCCA-TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * * *
10216 TAAATGATTTTATAATCTCGTAACTGATTTTCAGCTGAATTG
129 TAAATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
* * * * * *
10258 GTTTACATTTGTAGTTAAAACACACAATAATTGAATGTGTACCTTGAGAAACATGAAGAAAAAAG
1 TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAG-AAAAAG
* *
10323 TATTCATTGACAAGAAAAGTCCATTTAT
65 CATTCATTGGCAAGAAAAGTCCATTTAT
10351 NNNNNNNNNN
Statistics
Matches: 1177, Mismatches: 209, Indels: 106
0.79 0.14 0.07
Matches are distributed among these distances:
153 25 0.02
154 93 0.08
155 7 0.01
156 1 0.00
157 1 0.00
159 1 0.00
160 1 0.00
161 2 0.00
163 3 0.00
164 3 0.00
167 1 0.00
168 2 0.00
169 272 0.23
170 123 0.10
171 630 0.54
172 12 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (170 bp):
TTTTACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTAGAGAAACATGAAGAAAAAGC
ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTA
AATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTG
Found at i:9665 original size:154 final size:153
Alignment explanation
Indices: 9467--9769 Score: 419
Period size: 154 Copynumber: 2.0 Consensus size: 153
9457 GTGTACCTTG
* * *
9467 AGAAACATGAAGAAATAAGCATTCATTGGCAAAAAAAGTTCATTTACAGTCACCAATTCTTTCAA
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAAAAAAGTCCATTTACAGTCACCAATTCCTTCAA
* * * * * * *
9532 AATGCTTATTACTCGCTTTAATTAGTTTTATAATCTCAGAACTTATTTTATGTTGAATTTTTCTA
66 AAGGCTTATTACTCACTTTAAATAGTTTGATAATCTCAGAACTGATTTTATATTGAATGTTT-TA
*
9597 CATTTTTGGTTAAAATAGACTATA
130 CATTTTTGGTTAAAACAGACTATA
* * * * *
9621 AGAAACGTGAGGAAAAAAGCATTCATTATG-AAAAAAAGTCCATTTATAGTCACCCATTCCTTCA
1 AGAAACATGAAGAAAAAAGCATTCATT-GGCAAAAAAAGTCCATTTACAGTCACCAATTCCTTCA
* *
9685 AAAGGCTTATTACTCACTTTAAATGGTTTGATAATCTCATAACTGATTTTATATTGAATGTTTTA
65 AAAGGCTTATTACTCACTTTAAATAGTTTGATAATCTCAGAACTGATTTTATATTGAATGTTTTA
9750 CATTTTTGGTTAAAACAGAC
130 CATTTTTGGTTAAAACAGAC
9770 AATATTTGAA
Statistics
Matches: 130, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
153 21 0.16
154 108 0.83
155 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (153 bp):
AGAAACATGAAGAAAAAAGCATTCATTGGCAAAAAAAGTCCATTTACAGTCACCAATTCCTTCAA
AAGGCTTATTACTCACTTTAAATAGTTTGATAATCTCAGAACTGATTTTATATTGAATGTTTTAC
ATTTTTGGTTAAAACAGACTATA
Found at i:10084 original size:495 final size:500
Alignment explanation
Indices: 8651--10350 Score: 1445
Period size: 495 Copynumber: 3.4 Consensus size: 500
8641 NNNNNNNNNN
* * * * * *
8651 ATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTT-AAGATGGCTTATCACTAGCTTTTAAT
1 ATTGGCAAGAAAAGT-CATTTATAGTCACTCATTCCTTCAA-AAGGCTTATTACTCGCTTTAAAT
* * * ** * * *
8715 AGTTTTATAATCTCATAAC--A---GACTT---T-TTTTACATTTTCAGTTAAAATAAACTATAA
64 GGTTTTATAATCTCATAACTGATTTTAATTGAATGTTTTACATTTTTGGTTAAAACAGACAATAA
* * * * *
8771 TTGAATGTCTACCAT-GAGAAACATGAAGAAAACAGCATTTATTGACAAGAAAAGTCCATTTATA
129 TTGAATGTGT-CC-TCAAGAAACGTGAAGAAAA-AGCATTCATTGACAAGAAAAGTCAATTTATA
* ** * * * * * * **
8835 GTCACCCATT-CATTCAAAAGCCTTAGTACTCGCCTTAAATAGTTTTATAATCTCCTAATTGATT
191 GTCACCCATTCCCTAAAAAAG-CTTATTACTCGCTTTAAATGGTTTTGTAATCTCATAACTGACC
* * * * * * * * *
8899 TTAAGTTGAATTATTTTG-TATTTTTCATTAAAACAGACTACAATTGAATGTGC---CCTGGGAA
255 TGAAGTTGAATT-GTTTGAAATTTTTGATTAAAACAAACAATAATTGAATGT-CTAACTTGAGAA
* * * ** * * * * *
8960 ATATGAAGAAAAAAGCATTCATAGGCAAGGAAAGTCCAGTTATAGTCACCTATTCATTCAAAAGG
318 ACATGAAGAAATAAGCATTCATTGGCAAAAAAAGTCCATTTACAGTCACCAATTCCTTCAAAATG
* ** * * * * * * * * *
9025 TTTATTACTTACTTTAAATGGTTTTAGAATCTCATAACTGATTTTAACTTAAATTGTTTTACACT
383 CTTATTACTCGCTTTAAATAGTTTTATAATATCAGAACTGATTTGAAGTTGAATTCTTTAACA-T
* * * * * * * *
9090 TTTGGTTATAGAAAACAATGATTGAATGTTTAC-CTAGAGAAACGTAAAGAAACAAGCATTC
447 TTT--TCAT-TAAAAGACT-AATGAACG--TACTC-A-AGAAACGTGAAGAAAAAAGCATTC
* * *
9151 ATTGGCAAGAAAAGTACATTTATAGTCACTCATTCCTTAAAAAGGCTTATTACTCGCTTTAACTT
1 ATTGGCAAGAAAAGT-CATTTATAGTCACTCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATG
* * * * * *
9216 GTTTTATAATCTCATTACTGATTTTAAGTTGAATTTTTCTGCATTTTTGGTTAAAATAGACTACA
65 GTTTTATAATCTCATAACTGATTTTAA-TTGAATGTTT-TACATTTTTGGTTAAAACAGACAATA
* * * * *
9281 ATTGAATGTGT-CTGAAGAAACGTGTAGATAAAAACATTCATCGGCAAGAAAAGTCAATTTATAG
128 ATTGAATGTGTCCTCAAGAAACGTGAAGA-AAAAGCATTCATTGACAAGAAAAGTCAATTTATAG
* * * * ** *
9345 TCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTGTAATCTCATACCTGATTTT
192 TCACCCATTCCCTAAAAAAGCTTATTACTCGCTTTAAATGGTTTTGTAATCTCATAACTGACCTG
* ** * *
9410 AAGTTGAATTGTTTGACATTTTTGATTACCACAAACAATAATTGAATGTGTACCTTGAGAAACAT
257 AAGTTGAATTGTTTGAAATTTTTGATTAAAACAAACAATAATTGAATGTCTAACTTGAGAAACAT
* *
9475 GAAGAAATAAGCATTCATTGGCAAAAAAAGTTCATTTACAGTCACCAATTCTTTCAAAATGCTTA
322 GAAGAAATAAGCATTCATTGGCAAAAAAAGTCCATTTACAGTCACCAATTCCTTCAAAATGCTTA
* * * * * *
9540 TTACTCGCTTTAATTAGTTTTATAATCTCAGAACTTATTTTATGTTGAATT-TTTCTACATTTTT
387 TTACTCGCTTTAAATAGTTTTATAATATCAGAACTGATTTGAAGTTGAATTCTTT-AACATTTTT
** *
9604 GGTT-AAA-A-T-A-G-AC-TA-T-AAGAAACGTGAGGAAAAAAGCATTC
451 CATTAAAAGACTAATGAACGTACTCAAGAAACGTGAAGAAAAAAGCATTC
* * * *
9645 ATTATG-AAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCACTTTAAAT
1 ATT-GGCAAGAAAAGT-CATTTATAGTCACTCATTCCTTCAAAAGGCTTATTACTCGCTTTAAAT
*
9709 GGTTTGATAATCTCATAACTGATTTTATATTGAATGTTTTACATTTTTGGTTAAAACAGACAATA
64 GGTTTTATAATCTCATAACTGATTTTA-ATTGAATGTTTTACATTTTTGGTTAAAACAGACAATA
* * * *
9774 TTTGAATGTCTCCGTCAAGAAACGTGAAGAAAAGGGCATTCATTGACAAGAAAAGTCTATTTATA
128 ATTGAATGTGTCC-TCAAGAAACGTGAAGAAAA-AGCATTCATTGACAAGAAAAGTCAATTTATA
9839 GTCACCCATTCCCTAAAAAAGCTTATTACTCGCTTTAAATGG-TTTGATAATCTCATAACTGACC
191 GTCACCCATTCCCTAAAAAAGCTTATTACTCGCTTTAAATGGTTTTG-TAATCTCATAACTGACC
* * * *
9903 TGAAGTTGAATTTTTTTAAATTTTT-ACTTAAAACAGACTATAATTGAATGTCTAACTTGAGAAA
255 TGAAGTTGAATTGTTTGAAATTTTTGA-TTAAAACAAACAATAATTGAATGTCTAACTTGAGAAA
* ** *
9967 CATGAAGAAA-AAGAGATTGTTTGG-AAAGAAAAGTCCATTTACAGTCACCCATTCCTTCAAAA-
319 CATGAAGAAATAAG-CATTCATTGGCAAA-AAAAGTCCATTTACAGTCACCAATTCCTTCAAAAT
* **
10029 GCCTTATTACTCGCTTTAAATGGTTTTATAATATCCTAA-TCGATTTGAAGTTGAATTCTTTAAC
382 G-CTTATTACTCGCTTTAAATAGTTTTATAATATCAGAACT-GATTTGAAGTTGAATTCTTTAAC
* * *
10093 ATTTTTCATTAAAAAAGACTACAGTTGAACGTGTACCTCGAGAAACATGAAGAAAAAAGTATTC
445 ATTTTTCATT--AAAAGACTA-A--TGAAC--GTA-CTCAAGAAACGTGAAGAAAAAAGCATTC
* *
10157 ATTGGCAAGAAAAGTCATTTTATAGTCTCTCATTCCTTCAAAAGGTTTATTACTCGCTTTAAATG
1 ATTGGCAAGAAAAGTCA-TTTATAGTCACTCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATG
* * ** * * * *
10222 ATTTTATAATCTCGTAACTGATTTTCAGCTGAATTGGTTTACATTTGTAGTTAAAACACACAATA
65 GTTTTATAATCTCATAACTGATTTT-AATTGAA-TGTTTTACATTTTTGGTTAAAACAGACAATA
** * * *
10287 ATTGAATGTGTACCTTGAGAAACATGAAGAAAAAAGTATTCATTGACAAGAAAAGTCCATTTAT
128 ATTGAATGTGT-CCTCAAGAAACGTGAAG-AAAAAGCATTCATTGACAAGAAAAGTCAATTTAT
10351 NNNNNNNNNN
Statistics
Matches: 982, Mismatches: 162, Indels: 99
0.79 0.13 0.08
Matches are distributed among these distances:
493 31 0.03
494 126 0.13
495 251 0.26
496 3 0.00
497 2 0.00
498 3 0.00
499 1 0.00
500 72 0.07
501 3 0.00
502 2 0.00
504 1 0.00
505 3 0.00
506 7 0.01
508 7 0.01
509 125 0.13
510 19 0.02
511 143 0.15
512 101 0.10
513 76 0.08
514 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (500 bp):
ATTGGCAAGAAAAGTCATTTATAGTCACTCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGG
TTTTATAATCTCATAACTGATTTTAATTGAATGTTTTACATTTTTGGTTAAAACAGACAATAATT
GAATGTGTCCTCAAGAAACGTGAAGAAAAAGCATTCATTGACAAGAAAAGTCAATTTATAGTCAC
CCATTCCCTAAAAAAGCTTATTACTCGCTTTAAATGGTTTTGTAATCTCATAACTGACCTGAAGT
TGAATTGTTTGAAATTTTTGATTAAAACAAACAATAATTGAATGTCTAACTTGAGAAACATGAAG
AAATAAGCATTCATTGGCAAAAAAAGTCCATTTACAGTCACCAATTCCTTCAAAATGCTTATTAC
TCGCTTTAAATAGTTTTATAATATCAGAACTGATTTGAAGTTGAATTCTTTAACATTTTTCATTA
AAAGACTAATGAACGTACTCAAGAAACGTGAAGAAAAAAGCATTC
Found at i:11710 original size:171 final size:170
Alignment explanation
Indices: 11195--12081 Score: 890
Period size: 171 Copynumber: 5.2 Consensus size: 170
11185 NNNNNNNNAC
* * * * *
11195 AATTCAACTTAAAGTCAGTTATAAGATTATAAAACCATTTAAAGCAAGTAATAAGCCTTATT-AA
1 AATTCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAACCTT-TTGAA
* * * * * ** **
11259 GGAATGGGTGACTAGAAATGGACTTTTCTTGCCAATGAAT-TCCCTTTTATTCACCTTTCTTGAG
65 GAAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATCT-CTTTTTCTTCATGTTTCTCAAG
* * ** **
11323 GTAGACATTCAACTATTGTCTG-TTT---T---AA--CCAAA
129 GTACACATTCAATTATAATCTGTTTTAAGTAAAAATGTAAAA
*
11356 AATTCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAG
1 AATTCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAACCTTTTGAAG
* * * * *
11421 AAATGGGTGACTATAAATAGACTTTTCTTGCTAATGAATCTCTTTTT-TTTATGTTTCTCGAGGT
66 AAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTTTTCTTCATGTTTCTCAAGGT
* *
11485 AGACATTCAATTATAATCTGTTTT-AGCCAAAAAATGTAAAA
131 ACACATTCAATTATAATCTGTTTTAAG--TAAAAATGTAAAA
* * * *
11526 AACTCTGACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCAAGTAATAAACCTTTTAAA
1 AATTC-AACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAACCTTTTGAA
* * *
11591 GTAATGAGTGACTATAAATCGACTTTTCTTGCCAATGAATGCT-TTTTTCTTCACGTTTCTCAAG
65 GAAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-CTCTTTTTCTTCATGTTTCTCAAG
** * *
11655 GTACACATTCAATTATTGTCTGTTTTAAGTAAAAGTGTAAACC
129 GTACACATTCAATTATAATCTGTTTTAAGTAAAAATGTAAA-A
** * * *
11698 AATTCAACTTAAAATCAGTTACAAGATTATAAAATTATTTAAAGCGAGGAATAAACGTTTTGAAG
1 AATTCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAACCTTTTGAAG
* * * * *
11763 GAATGAGTGTCTATAAATGGACTTTTCTTGCCAAGGAATGCT-TTTTTCTTAATGTTTCTCGAGG
66 AAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-CTCTTTTTCTTCATGTTTCTCAAGG
* * *
11827 TACACGTTCAATTGTAATCTGTTTTAA-TGAAAAATGTGAAAC
130 TACACATTCAATTATAATCTGTTTTAAGT-AAAAATGT-AAAA
* * * * * * **
11869 AATTCAACTTCAAATAAATTAGGATATTATAAAA-TCATTTGAAGCGAGTAATAAGGCTTTTGAA
1 AATTCAACTTAAAATCAGTTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAACCTTTTGAA
* * ** *
11933 GAAATGGGTGACTGTAAATGGACTTTTCTTTACAAAGAATCTCTTTTTCTTCATGTTTCTCAAGG
65 GAAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTTTTCTTCATGTTTCTCAAGG
* * * * *
11998 TAAACATTCTATTACAGTCTGTTTTAACTAAAAATGTAAAAA
130 TACACATTCAATTATAATCTGTTTTAAGTAAAAATGT-AAAA
* * *
12040 AATTCAACTCAAAGTCAGTTATGAGATTATAAAACCATTTAA
1 AATTCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAA
12082 NNNNNNNNNN
Statistics
Matches: 608, Mismatches: 95, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
160 32 0.05
161 101 0.17
162 1 0.00
168 2 0.00
170 11 0.02
171 414 0.68
172 45 0.07
173 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (170 bp):
AATTCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAACCTTTTGAAG
AAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTTTTCTTCATGTTTCTCAAGGT
ACACATTCAATTATAATCTGTTTTAAGTAAAAATGTAAAA
Found at i:12739 original size:171 final size:171
Alignment explanation
Indices: 12427--12974 Score: 602
Period size: 170 Copynumber: 3.2 Consensus size: 171
12417 NNNNNNNNNN
* * * * * *
12427 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTATCAATGAATTCTTGTAT-GTACACGT
1 CTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATCCTTGTTTCCTACATGT
* * * **
12491 TTCTCAAGG--CACATTCGATTTTAGTCTGTTTTAATAAAAAATGTAAAACAATTCAACTTAAAA
66 TTCTGAAGGTACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAA
* * *
12554 TAAATTAA-GAGATTATAAAACCATTTAAAGCGAGTAATAAGG
131 T-CAGTAATGAGATTATAAAACCATTTAAAGTGAGTAATAA-G
*
12596 CTTTTGAAGGAATGGGTGACTATAAATGAACTTTTTTTGTCAATGAATCCCTT-TTTCCT-CATG
1 CTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAAT-CCTTGTTTCCTACATG
* * *
12659 TTTATGAAGGTAGACATTCAATTAAAGTCTGTTTTAACCAAAAATGTAGAAA-AATTCAACTTAA
65 TTTCTGAAGGTACACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAACAATTCAACTTAA
* *
12723 AATCAGTAATGAGATTATAAAACCAGTTAAAGTGAGTGATAAG
129 AATCAGTAATGAGATTATAAAACCATTTAAAGTGAGTAATAAG
* * * *
12766 CATTTTTAAGGAATGGGTGACTATAAATGAAC-TTTCTTGCCAATGAATGCTTGTTTCTTTACAT
1 C-TTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATCCTTGTTTC-CTACAT
* * * *
12830 -TTCTCTG--GGTACACATTCAATTATTGT-TCGTTGTAACCAAAAGTGTAAAACAATTTAACTT
64 GTT-TCTGAAGGTACACATTCAATTATAGTCT-GTTTTAACCAAAAATGTAAAACAATTCAACTT
** *
12891 AAAATCAGGT-ATGAGATTATAAAACCATTTATAA-TGTCTAATACAC
127 AAAATCA-GTAATGAGATTATAAAACCATTTA-AAGTGAGTAATA-AG
* *
12937 CTTTTGAAGGAATAGGTGACTATAAATGACCTTTTCTT
1 CTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT
12975 NNNNNNNNNN
Statistics
Matches: 322, Mismatches: 40, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
169 65 0.20
170 130 0.40
171 118 0.37
172 9 0.03
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (171 bp):
CTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATCCTTGTTTCCTACATGT
TTCTGAAGGTACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAA
TCAGTAATGAGATTATAAAACCATTTAAAGTGAGTAATAAG
Found at i:14147 original size:171 final size:170
Alignment explanation
Indices: 13562--14316 Score: 847
Period size: 171 Copynumber: 4.4 Consensus size: 170
13552 NNNNNNNNNN
* * * * * * * **
13562 ATAATTGAATGTGTACCTAGAGAAACATGAACAAACAAGCATTCATTGGCGAGAAAAGTCCATTT
1 ATAATTGAATGTCTAACTTGAGAAACGTGAAGAAAAAAGCATTCTTTGGAAAGAAAAGTCCATTT
* * *
13627 ATAGTCACTCATTCCTTAAAAATGCTTATTACTCGCTTTAACTGGTTTTATAATCTCATAACTTA
66 ATAGTCACCCATTCCTTAAAAA-GCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAACTGA
* *
13692 TTTTAAGTTGAATGTTTCTACATTTTTGGTTAAAATAGACT
130 TTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGACT
* * * *
13733 ATAATTGAATGTGC-AACTTGAGAAACATGAAGAAAAAAGCATTCATTAGGAAAAAAAAGTTCAT
1 ATAATTGAATGT-CTAACTTGAGAAACGTGAAGAAAAAAGCATTC-TTTGGAAAGAAAAGTCCAT
* *
13797 TTATAGTCACCCATTTCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTATAATCTC--AACT
64 TTATAGTCACCCATTCCTT-AAAAAGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAACT
* * *
13860 GATTTTATGTTGAA-TTTTTTACATTTTTGGTTAAAACAGACA
128 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGACT
* * ** * ** * * *
13902 ATATTTGAATGTCTACCTCAAGAAACGTGAAGAACAGGGCAATCATT-GACAAGAAAAGTCTATT
1 ATAATTGAATGTCTAACTTGAGAAACGTGAAGAAAAAAGCATTCTTTGGA-AAGAAAAGTCCATT
*
13966 TATAGTCACCCATTCCTTGAAAAAGCTTATTACTCGCTTTAAATGGTTTGATAATCTCATAACTG
65 TATAGTCACCCATTCCTT-AAAAAGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAACTG
* * * *
14031 ACTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAGTAGGCT
129 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGACT
*
14073 ATAATTGAATGTCTAACTTGAGAAACGCGAAGAAAAAAAG-ATTCTTTGGAAAGAAAAGTCCATT
1 ATAATTGAATGTCTAACTTGAGAAACGTGAAG-AAAAAAGCATTCTTTGGAAAGAAAAGTCCATT
* * * * *
14137 TACAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCCTAATTG
65 TATAGTCACCCATTCCTTAAAAAG-CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAACTG
* * * ** * *
14202 ATTTGAAGTTGAATTCTTTCACATTTTTCATTAAAACACACT
129 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGACT
* * * * * * * * * *
14244 ACAGTTGAACGTATACCTCGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCTTTT
1 ATAATTGAATGTCTAACTTGAGAAACGTGAAGAAAAAAGCATTCTTTGGAAAGAAAAGTCCATTT
14309 ATAGTCAC
66 ATAGTCAC
14317 NNNNNNNNNN
Statistics
Matches: 487, Mismatches: 85, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
167 2 0.00
168 67 0.14
169 57 0.12
170 44 0.09
171 244 0.50
172 69 0.14
173 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (170 bp):
ATAATTGAATGTCTAACTTGAGAAACGTGAAGAAAAAAGCATTCTTTGGAAAGAAAAGTCCATTT
ATAGTCACCCATTCCTTAAAAAGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAACTGAT
TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGACT
Found at i:15670 original size:15 final size:16
Alignment explanation
Indices: 15647--15679 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
15637 TTTTAATAAA
15647 AAATATAAAAT-AATT
1 AAATATAAAATCAATT
*
15662 AAATTTAAAATCAATT
1 AAATATAAAATCAATT
15678 AA
1 AA
15680 GAGATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATAAAATCAATT
Found at i:16941 original size:21 final size:21
Alignment explanation
Indices: 16912--16952 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16902 GAATAGGTGA
16912 CTATAAATGCACTTTTCTTCC
1 CTATAAATGCACTTTTCTTCC
* **
16933 CTATGAATGCTTTTTTCTTC
1 CTATAAATGCACTTTTCTTC
16953 ACGTTTCCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (21 bp):
CTATAAATGCACTTTTCTTCC
Found at i:17585 original size:171 final size:172
Alignment explanation
Indices: 16613--17588 Score: 551
Period size: 171 Copynumber: 5.7 Consensus size: 172
16603 NNNNCTTCAC
* * * * * *
16613 GTTTCTCAAGGTAGGCATTCAATTATAGTCTATTTTAATCAAAAATGTAGAAAAATTCAACATAA
1 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAA
* * * ** ********** *
16678 AATCA-GTAATGAGATTATAAAATCAGATAANNNNNNNNNNAAGCCTTTTTAAGGAATG-GGTGA
66 AAT-ATGTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGGTGA
* * * * * *
16741 CTATAAATGGACTTTTCATGCTAATGAGTG-CTTGTTTTTTTAT
130 CTATAAATGGACTTTTCTTGCCAATGAATGCCAT-TTTATTAAT
** * * * * * * * *
16784 GTTTCTCTAGGTAAACATTCAATTATTGTTTGTTGTAACCAAAAGTGTAAAACAATTCAACTTAA
1 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAA
* ********** *
16849 AAT-TAGTTATGAGATTATAAAACNNNNNNNNNNGAGTAATAAACCTTTTGAAGGAAT-AGGTGA
66 AATAT-GTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGGTGA
* * * ** * * *
16912 CTATAAATGCACTTTTCTTCCCTATGAATGCTTTTTTCTTCAC
130 CTATAAATGGACTTTTCTTGCCAATGAATGCCATTTTATTAAT
** * * * * *
16955 GTTTCCCAA-G-ACACATTCAATTGTAGTCTGTTTTAATGAAAAATATAAAACAATTCAACTCAA
1 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAA
* *** * * * * *
17018 AATCA-ATTAGGTGATTAGAAAACGATTTCAAGCGAGTAATAAGGCTTTTGATGGAATG-GGTGA
66 AAT-ATGTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGGTGA
* * * * * *
17081 CTATAAATGAACTTTTCTAGTCAATGAATGCCTTTTTCTTCAT
130 CTATAAATGGACTTTTCTTGCCAATGAATGCCATTTTATTAAT
* * * ********** * *
17124 GTTTCTCATGGTATACATTCAATTATANNNNNNNNNNA-CTAAAAATGTAAAACAATTCAACTTA
1 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATC-AAAAATATAAAAAAATTCAACTTA
* * * * * *
17188 AAGTCA-GTTATAAGATTATAGAACGATTTAAAGCAAGTAATTAGCCTTCTT-AAAGAAT-AGGT
65 AAAT-ATGTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTT-TTGAAGGAATGAGGT
*
17250 GACTATAAATGGACTTTTCTTGCCAATGAATGCCATTTTATTCAT
128 GACTATAAATGGACTTTTCTTGCCAATGAATGCCATTTTATTAAT
* * * * **
17295 GTTTCTTAAGGTAGACATTTAATTATTGTCTGTTTTAATCAAAAATTTTGAAAAATTCAACTTAA
1 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAA
* * * **********
17360 AATCTGTTATGAGATTATAAAACCGTTTAAAGCGAGTANNNNNNNNNNTGAAGGAATGA-GTGAC
66 AATATGTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGGTGAC
* ** *
17424 TATAAATGGACTTTTCTTTCCAATGAAT-CTTTTTTTCTTAAT
131 TATAAATGGACTTTTCTTGCCAATGAATGC-CATTTTATTAAT
**********
17466 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTNNNNNNNNNNAATATAAAAAAATTCAACTTAA
1 GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAA
*
17531 AATATGTTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATG
66 AATATGTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATG
17589 GANNNNNNNN
Statistics
Matches: 605, Mismatches: 183, Indels: 34
0.74 0.22 0.04
Matches are distributed among these distances:
169 129 0.21
170 4 0.01
171 466 0.77
172 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.34
Consensus pattern (172 bp):
GTTTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAA
AATATGTTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGGTGAC
TATAAATGGACTTTTCTTGCCAATGAATGCCATTTTATTAAT
Found at i:19433 original size:171 final size:171
Alignment explanation
Indices: 19145--20146 Score: 997
Period size: 171 Copynumber: 5.9 Consensus size: 171
19135 NNNNNNNNNN
* * * *
19145 TTTATAGTCACTCATTCCTTCAGAAGGTTTATTACTCGCTTTAAATGATTTTATAATCTCGTAAC
1 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAC
* * * * * *
19210 TGATTTTCA-TCTGAATTGGTTTACATTTTTAGTTAAAACACACAATAATTGAATGTGTACCTTG
66 TGATTTTAAGT-TGAATTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTG
* * *
19274 AGAAATGTGAAGAAAAAAGTACTCATTGACAAGAAAAGTCCA
130 AGAAATGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCA
* * * *
19316 TTTATAGTCACCCATTGCTTTAAAAGACTTATTACTCACTTTAAAT-AGTTTTATAATCTCATAA
1 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGA-TTTTATAATCTCATAA
*** * * *
19380 CTGATTTTAAGCCAAATTGTTTTACATTTTTGGTTAAAACAGACTACAATTGAATATCTACCTTT
65 CTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTG
* * *
19445 ATAAGCAT-T-AAG-AAAAGGGATTCATTGGCAAGAAAAGTCCA
130 AGAA--ATGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCA
* * * *
19486 TTTATAGTCGCCCATTCCCTCAAAAGGCTTATTACTCGTTTTAAACGATTTTATAATCTCATAA-
1 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAC
* * * *
19550 TAGATTTTAAGTTGAATTTTTTTAAATTTTTGATTAAAACAGA-TAATAATTGAATGTCTACCTC
66 T-GATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAACAGACT-ATAATTGAATGTCTACCTT
* * * *
19614 AAGAAATGTGAA-TAAAAGAGCATCCATTGGCAAGAAAAGTCCA
129 GAGAAATGTGAAGAAAAAG-GCATTCATTGACAAGAAAAGTCCA
* * * *
19657 TTTATAGTCACCCATTCCTTAAAAAGGCTTATTACTTGCTTTAAATGGTTTGATAATCTCATAAC
1 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAC
* * * * * **
19722 TAACTTTAAGTTAAATT-TTCTTACATTTTTGGTTAAAAAAGACTATAATTGAATGTCCACCACG
66 TGATTTTAAGTTGAATTGTT-TTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTG
* *
19786 AGAAACGTGAAGAAAAAGGCATTCATTGAAAAGAAAAGTCCA
130 AGAAATGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCA
* *** * *
19828 TTTATAGTCACCCATTCCTTTAAAA-AAATATTACTCGCTTGAAATGGTTTTATAATCTTC-TAA
1 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGATTTTATAATC-TCATAA
* * * * ** ** * * ** *
19891 TTCATTATAAGTCGAACCGTTTTACATTTTTCTTTAAAACACACTACAAGAGAATGTGT--CTTG
65 CTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTG
* * *
19954 CGAAACGTGAAGAAAAAGGCATTTATTGACAAGAAAAGTCCA
130 AGAAATGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCA
* * * * * * *
19996 CTTATAGTTACCTATTCCTTCAAAAGGTTTATTACTTGCTTTAAATGATTTTATAATCTTATAAA
1 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAC
* * * * * * * * *
20061 TTATTTTAAGTTGAATTGTTTTATACTTTTGGTTACAACAAACAATAATTAAATGTGTACCTAGA
66 TGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGA
* *
20126 GAAACGT-ATAGAAACAGGCAT
131 GAAATGTGA-AGAAAAAGGCAT
20147 NNNNNNNNNN
Statistics
Matches: 681, Mismatches: 128, Indels: 44
0.80 0.15 0.05
Matches are distributed among these distances:
168 65 0.10
169 74 0.11
170 212 0.31
171 320 0.47
172 8 0.01
173 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAC
TGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGA
GAAATGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCA
Found at i:19774 original size:341 final size:337
Alignment explanation
Indices: 19145--20095 Score: 1009
Period size: 341 Copynumber: 2.8 Consensus size: 337
19135 NNNNNNNNNN
* * *
19145 TTTATAGTCACTCATTCCTTCAGAAGGTTTATTACTCGCTTTAAATGATTTTATAATCTCGTAAC
1 TTTATAGTCACCCATTCCTTCAAAAGGATTATTACTCGCTTTAAATGATTTTATAATCTC-TAA-
* * * *
19210 TGATTTTCA-TCTGAATTGGTTTACATTTTTAGTTAAAACACACAATAATTGAATGTGTACCTTG
64 TGATTTTAAGT-TGAATTGTTTTACATTTTTA-TTAAAACACATAATAATTGAATGTGTACC-TC
* * *
19274 AGAAATGTGAAGAAAAAAGTA-CTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTGCTTTA
126 AGAAATGTGAAG-AAAAAGCATC-CATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTAA
* ** * * **
19338 AAAGACTTATTACTCACTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGCCAAATTGTTTT
189 AAAGGCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAACTAATTTTAAGTTAAATTGTTTT
* * *** * * * *
19403 ACATTTTTGGTTAAAACAGACTACAATTGAATATCTACCTTTATAAGCATTAAG-AAAAGGGATT
254 ACATTTTTGGTTAAAAAAGACTACAATTGAATATCCACCACGAGAAACATGAAGAAAAAGGCATT
**
19467 CATTGGCAAGAAAAGTCCA
319 CATTGAAAAGAAAAGTCCA
* * * * *
19486 TTTATAGTCGCCCATTCCCTCAAAAGGCTTATTACTCGTTTTAAACGATTTTATAATCTCATAAT
1 TTTATAGTCACCCATTCCTTCAAAAGGATTATTACTCGCTTTAAATGATTTTATAATCTC-TAAT
* * * *
19551 AGATTTTAAGTTGAATTTTTTTAAATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTCAA
65 -GATTTTAAGTTGAATTGTTTTACATTTTT-ATTAAAACACATAATAATTGAATGTGTACCTC-A
* *
19616 GAAATGTGAATAAAAGAGCATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTAAAA
127 GAAATGTGAAGAAAA-AGCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTAAAA
* *
19681 AGGCTTATTACTTGCTTTAAATGGTTTGATAATCTCATAACTAACTTTAAGTTAAATT-TTCTTA
191 AGGCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAACTAATTTTAAGTTAAATTGTT-TTA
* * *
19745 CATTTTTGGTTAAAAAAGACTATAATTGAATGTCCACCACGAGAAACGTGAAGAAAAAGGCATTC
255 CATTTTTGGTTAAAAAAGACTACAATTGAATATCCACCACGAGAAACATGAAGAAAAAGGCATTC
19810 ATTGAAAAGAAAAGTCCA
320 ATTGAAAAGAAAAGTCCA
* * * * *
19828 TTTATAGTCACCCATTCCTTTAAAA-AAATATTACTCGCTTGAAATGGTTTTATAATCTTCTAAT
1 TTTATAGTCACCCATTCCTTCAAAAGGATTATTACTCGCTTTAAATGATTTTATAATC-TCTAA-
* * * ** * * ** *
19892 TCATTATAAGTCGAACCGTTTTACATTTTTCTTTAAAACACACT-ACAAGAGAATGTGT-CTTGC
64 TGATTTTAAGTTGAATTGTTTTACATTTTT-ATTAAAACACA-TAATAATTGAATGTGTACCT-C
* ** * * * *
19955 -GAAACGTGAAGAAAAAGGCATTTATTGACAAGAAAAGTCCACTTATAGTTACCTATTCCTTCAA
126 AGAAATGTGAAGAAAAA-GCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTAAA
* * * * * *
20019 AAGGTTTATTACTTGCTTTAAATGATTTTATAATCTTATAAATTATTTTAAGTTGAATTGTTTTA
190 AAGGCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAACTAATTTTAAGTTAAATTGTTTTA
* *
20084 TACTTTTGGTTA
255 CATTTTTGGTTA
20096 CAACAAACAA
Statistics
Matches: 508, Mismatches: 88, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
338 1 0.00
339 117 0.23
340 12 0.02
341 323 0.64
342 55 0.11
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (337 bp):
TTTATAGTCACCCATTCCTTCAAAAGGATTATTACTCGCTTTAAATGATTTTATAATCTCTAATG
ATTTTAAGTTGAATTGTTTTACATTTTTATTAAAACACATAATAATTGAATGTGTACCTCAGAAA
TGTGAAGAAAAAGCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTAAAAAGGCT
TATTACTTGCTTTAAATGGTTTTATAATCTCATAACTAATTTTAAGTTAAATTGTTTTACATTTT
TGGTTAAAAAAGACTACAATTGAATATCCACCACGAGAAACATGAAGAAAAAGGCATTCATTGAA
AAGAAAAGTCCA
Found at i:23453 original size:171 final size:171
Alignment explanation
Indices: 23150--23829 Score: 832
Period size: 171 Copynumber: 4.0 Consensus size: 171
23140 GAAGAAAAGT
*
23150 TTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAATTGAATTGTTTTACATTT
1 TTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTT
* * * * *
23215 TTGGTTACAACAAACAATAATTGAATGTGTACCACGAGAAACGTAAAGAAACAAGCATTCGTTGG
66 TTGGTTAAAACAAACAATAATTGAATGTCTACCTCGAGAAACGTAAAGAAACAAGGATTCATTGG
* * * * *
23280 CAAGAAAAGTCTATTTAAAGTCATCCATTACTTAAAAAGTC
131 CAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGGC
** * * *
23321 TTATTACTCGCTTTATCTAGTTTTATAATCTCATTATTGATTTTAAGTTGAATT-TTTCTATATT
1 TTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATTGTTT-TACATT
** * * * * * *
23385 TTTTATTAAAACAGAA-TATAATTGAATGCCTACCTTGAGAAACATGAAGAAA-AAGGGATTAAT
65 TTTGGTTAAAACA-AACAATAATTGAATGTCTACCTCGAGAAACGTAAAGAAACAA-GGATTCAT
** *
23448 TGGCAAGAAAAGTCCATTCCTAGTCACCCATTCCTTCAAAAGGC
128 TGGCAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGGC
* * * *
23492 CTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTGGATTGTTTTAAATTT
1 TTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTT
* * * * * * * *
23557 CT--TTAAAACAGACAATAACTGAATGTCAACCTCAAGAAACGTGAATAAA-AGGGCATTCATTG
66 TTGGTTAAAACAAACAATAATTGAATGTCTACCTCGAGAAACGTAAAGAAACAAGG-ATTCATTG
* * *
23619 GTAAGAAAAGTCTATTTATAGTCACCCATTACTTTAAAAGGC
130 GCAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGGC
* * * *
23661 TTATTACTCACTTTAAATAGTTTTATAATCTTATAACTGATTTTAAGTTGAATTTTTTTACACTT
1 TTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTT
* * *
23726 TTGGTTATAACAAACAATAATTGAATGTGTACCTCGAGAAACGTAAAGAAACAAGTATTCATTGG
66 TTGGTTAAAACAAACAATAATTGAATGTCTACCTCGAGAAACGTAAAGAAACAAGGATTCATTGG
*
23791 CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
131 CAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAG
23830 CCNNNNNNNN
Statistics
Matches: 424, Mismatches: 76, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
168 3 0.01
169 138 0.33
170 5 0.01
171 271 0.64
172 7 0.02
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
TTATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATTGTTTTACATTT
TTGGTTAAAACAAACAATAATTGAATGTCTACCTCGAGAAACGTAAAGAAACAAGGATTCATTGG
CAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGGC
Found at i:23792 original size:340 final size:341
Alignment explanation
Indices: 23151--23829 Score: 907
Period size: 340 Copynumber: 2.0 Consensus size: 341
23141 AAGAAAAGTT
* * *
23151 TATTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAAATTGAATTGTTTTACATTTT
1 TATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAATTGAATTGTTTTAAATTTC
* * ** * *
23216 TGGTTACAACAAACAATAATTGAATGTGTACCACGAGAAACGTAAAGAAACAAGCATTCGTTGGC
66 T-GTTAAAACAAACAATAACTGAATGTCAACCACAAGAAACGTAAAGAAACAAGCATTCATTGGC
* * * **
23281 AAGAAAAGTCTATTTAAAGTCATCCATTACTTAAAAAGTCTTATTACTCGCTTTATCTAGTTTTA
130 AAGAAAAGTCTATTTAAAGTCACCCATTACTTAAAAAGGCTTATTACTCACTTTAAATAGTTTTA
* * * * * *
23346 TAATCTCATTATTGATTTTAAGTTGAATTTTTCTATATTTTTTATTAAAACAGAATATAATTGAA
195 TAATCTCATAACTGATTTTAAGTTGAATTTTTCTACACTTTTGATTAAAACAGAAAATAATTGAA
* * *
23411 TGCCTACCTTGAGAAACATGAAGAAAAAGGGATTAATTGGCAAGAAAAGTCCATTCCTAGTCACC
260 TGCCTACCTCGAGAAACATAAAGAAAAAGGGATTAATTGGCAAGAAAAGTCCATTCATAGTCACC
23476 CATTCCTTCAAAAGGCC
325 CATTCCTTCAAAAGGCC
* *
23493 TATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTGGATTGTTTTAAATTTC
1 TATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAATTGAATTGTTTTAAATTTC
* * * * * *
23558 T-TTAAAACAGACAATAACTGAATGTCAACCTCAAGAAACGTGAATAAA-AGGGCATTCATTGGT
66 TGTTAAAACAAACAATAACTGAATGTCAACCACAAGAAACGTAAAGAAACA-AGCATTCATTGGC
* *
23621 AAGAAAAGTCTATTTATAGTCACCCATTACTTTAAAAGGCTTATTACTCACTTTAAATAGTTTTA
130 AAGAAAAGTCTATTTAAAGTCACCCATTACTTAAAAAGGCTTATTACTCACTTTAAATAGTTTTA
* * * *
23686 TAATCTTATAACTGATTTTAAGTTGAATTTTTTTACACTTTTGGTTATAACA-AACAATAATTGA
195 TAATCTCATAACTGATTTTAAGTTGAATTTTTCTACACTTTTGATTAAAACAGAA-AATAATTGA
** * * * *
23750 ATGTGTACCTCGAGAAACGTAAAGAAACAA-GTATTCATTGGCAAGAAAAGTCCATTTATAGTCA
259 ATGCCTACCTCGAGAAACATAAAGAAA-AAGGGATTAATTGGCAAGAAAAGTCCATTCATAGTCA
23814 CCCATTCCTTCAAAAG
323 CCCATTCCTTCAAAAG
23830 CCNNNNNNNN
Statistics
Matches: 291, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
339 3 0.01
340 225 0.77
341 2 0.01
342 61 0.21
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (341 bp):
TATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAATTGAATTGTTTTAAATTTC
TGTTAAAACAAACAATAACTGAATGTCAACCACAAGAAACGTAAAGAAACAAGCATTCATTGGCA
AGAAAAGTCTATTTAAAGTCACCCATTACTTAAAAAGGCTTATTACTCACTTTAAATAGTTTTAT
AATCTCATAACTGATTTTAAGTTGAATTTTTCTACACTTTTGATTAAAACAGAAAATAATTGAAT
GCCTACCTCGAGAAACATAAAGAAAAAGGGATTAATTGGCAAGAAAAGTCCATTCATAGTCACCC
ATTCCTTCAAAAGGCC
Found at i:24643 original size:171 final size:169
Alignment explanation
Indices: 23932--24819 Score: 663
Period size: 171 Copynumber: 5.2 Consensus size: 169
23922 NNNNNNNNNN
23932 AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAG-TTAAGTTTTTTT
1 AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTTAA-TTTTTTT
* * * ********* *
23996 ACATTTCTT-ATTAAAACAGACAATAACTGAATGTCAACCTCNNNNNNNNNNAATAAAAGGGCAT
65 ACATTT-TTGGTTAAAACAGACAATAATTGAATGTCTACCTC-AAGAAACATAATAAAA-GACAT
* * * *
24060 TCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTACTTTAC
127 TCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
* ********** ** *
24103 AAGGCTTATTACTCCCTTTAAATAGTTTTATAATCTCANNNNNNNNNNTAAGTCAAATGTTTTTA
1 AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTTAATTTTTTTA
* * * * * * * * * *
24168 CATTTTTGGCTAAAACAAACTATAATTAAATGTCTATCTTAAGAAACATAAAAAAAAAGATTCGT
66 CATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATAATAAAAGACATTCAT
* * **
24233 TAGCAAGAAAAGTCTATTTATAGTCGTCCATTCCTTCAA
131 TGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
* * * *
24272 AAGGCTTATTACTCACTTTAAATAGTTTTATAATCTCATCACATATTTTAAGTTGAATTTTTTTA
1 AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTTAATTTTTTTA
* * * * ** * * **
24337 CATTTTTGGGTAACACAGACTATAATTGAATGCCTACCTTTAGAAAAATTAAGAAAAAGGGATTC
66 CATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACA-TAA-TAAAAGACATTC
*
24402 ATTGGCAA-AAACAGTACATTTATAGTCACCCATTCCTTCAA
129 ATTGGCAAGAAA-AGTCCATTTATAGTCACCCATTCCTTCAA
********** ** *
24443 AAGGCTTATTNNNNNNNNNNAACGGTTTTATAATCTCATAACAGATTTTAAGTTTAATTTTTTAA
1 AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTTAATTTTTTTA
* *
24508 AATTTTTGGTTAAAACGGACAATAATTGAATGTCTACCTCAAGAAACATGAATAAAAGCACATTC
66 CATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACAT-AATAAAAG-ACATTC
24573 ATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTT-AA
129 ATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
* * * * * * **********
24613 GAAGGCTGATTACTTGCTTTAAATGGTTTTATAATCTTATAACTGACTTTAAGTTGNNNNNNNNN
1 -AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTTAATTTTTTT
* * * * ** * *
24678 NCATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCAT-GAGAAATGTGAAGAAAAAGGCAT
65 ACATTTTTGGTTAAAACAGACAATAATTGAATGTCTACC-TCAAGAAACAT-AA-TAAAAGACAT
* *
24742 TCATTGACGAA-AAAAGTCCATTTATAGTCACCCATTCCATCAA
127 TCATTGGC-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
* * * *
24785 AAGCCCTATTACTCGCTTGAAATCGTTTTATAATC
1 AAGGCTTATTACTCGCTTTAAATAGTTTTATAATC
24820 GCCTATTTTA
Statistics
Matches: 557, Mismatches: 147, Indels: 26
0.76 0.20 0.04
Matches are distributed among these distances:
169 127 0.23
170 22 0.04
171 393 0.71
172 15 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.34
Consensus pattern (169 bp):
AAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAACAGATTTTAAGTTTAATTTTTTTA
CATTTTTGGTTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACATAATAAAAGACATTCAT
TGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
Found at i:26608 original size:171 final size:171
Alignment explanation
Indices: 26323--26638 Score: 411
Period size: 171 Copynumber: 1.8 Consensus size: 171
26313 NNNNNNNCTC
* *
26323 ATAACTGATTTTAAGTCAAATGTTTTTATATTTTTGGCTAAAACAGACTATAATTGAATGTCTAC
1 ATAACTGATTTTAAGTCAAATGTTTTTATATTTTTGGCTAAAACAGACTATAATTGAATGCCGAC
* **********
26388 CTTGAGAAACGTAAAGAAAAAGANNNNNNNNNNCAAGAAAAGTCCATTTATAGTCACCCATTCCT
66 CTTGAGAAACATAAAGAAAAAGAGATTTATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
*
26453 TCAAAAGGCTTATTATTCGGTTTAAATAGTTTTATAATCTT
131 TCAAAAGCCTTATTATTCGGTTTAAATAGTTTTATAATCTT
* * *
26494 ATAACTGATTTTAAG-CTGAATTTTTTTACTTTTTTTGG-TAAAACAGACTATAATTGAATGCCG
1 ATAACTGATTTTAAGTC-AAATGTTTTTA-TATTTTTGGCTAAAACAGACTATAATTGAATGCCG
* * *
26557 ACCTTTAGAAACATTAAGAAAAAGAGATTTATTGGCAAGAAAAGTCCATTTATAGTCACTCATTC
64 ACCTTGAGAAACATAAAGAAAAAGAGATTTATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC
*
26622 CTTCAATAGCCTTATTA
129 CTTCAAAAGCCTTATTA
26639 CTNNNNNNNN
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
170 1 0.01
171 113 0.93
172 8 0.07
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.35
Consensus pattern (171 bp):
ATAACTGATTTTAAGTCAAATGTTTTTATATTTTTGGCTAAAACAGACTATAATTGAATGCCGAC
CTTGAGAAACATAAAGAAAAAGAGATTTATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
TCAAAAGCCTTATTATTCGGTTTAAATAGTTTTATAATCTT
Done.