Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_534.0, 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: 12624
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.29
Warning! 2696 characters in sequence are not A, C, G, or T
Found at i:1180 original size:171 final size:169
Alignment explanation
Indices: 152--2049 Score: 1163
Period size: 170 Copynumber: 11.2 Consensus size: 169
142 NNNNNNNNNN
* * * * * *
152 TTTAAAGTGAGTAATCAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTACTAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
** * ** * * *
217 ATGGCTTTTCTTCACGTTTC-CTAAGACAAACATTCAATTATAGTTTGTTTTAACCAAAAATACA
66 ATGAATTTTCTTCACATTTCTC-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATA
********** *
281 AAACAATTCAACTTAAAATCAANNNNNNNNNNATAAAACCA
130 AAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * ** * * ***
322 TTTAAAGTGAGTAATAAGACTTTTAAAAGAATAAGAGACTATAAATGGACATTTT-TTAAAAAT-
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAC-TTTTCTTGCCAATG
** * * * * * *
385 ATATG-GGTTT-TTCTACATGTTTTCCTAGGTAGGCCA-TCAA-TATAGTTTG-TTTAATCAAAT
65 A-ATGAATTTTCTTC-ACAT-TTCT-CAAGGTA-GACATTCAATTATAGTCTGTTTTAACCAAAA
* * * *
445 GTAAAAAAAATT-AAC-TAAAAT-AA-TATTG-GATAATAAAACCA
125 ATATAAAAAATTCAACTTAAAATCAATTA-TGAGATTATAAAACTA
* * ** **
486 TTTAAAGTGAGTAATAAGGCTTTTGAA-GATATGGGAGGTTATAAAT-GAACTTTTCTTTTCAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGA-ATGGGTGACTATAAATAG-ACTTTTCTTGCCAAT
* * ** * * *
549 GAA-CACCTTTCTCTTCGTA-TTCTTGAA-GTAGACATTCAATTATAATCAGTTTTAACCAAAAA
64 GAATGA-ATTT-TCTTCACATTTC-TCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAA
* ** * * * * *
611 TGTAAAAATAATTGTACATAAAATCAATTTTGAGATAACAAAACCA
126 TAT-AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* ** *
657 TTT-----GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCAAGCTAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
** * * ********* * * *
717 ATGCCTTTTTCTTCATATTTCT-AGAAGTAGACANNNNNNNNNNA-TCTATTTTGACCAATAATG
66 ATG-AATTTTCTTCACATTTCTCA-AGGTAGACA-TTCAATTATAGTCTGTTTTAACCAA-AA-A
* *** *
780 TAAAAAAAATT-ATAGC-TAAAATCAATTATGAGATTATAGTCCGA
126 TATAAAAAATTCA-A-CTTAAAATCAATTATGAGATTATAAAACTA
* * * * ** *
824 GTTAAAGCTAGTAATAAGACTTTTGAAAGAATGGAAGACTATAAATAGACTTTTCTTGCGAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
** * * * *
889 ATGCTTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATATA
66 ATG-AATTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT-
* * * * *
954 AAAAAAATTGAGCTTAAAATTAATTTTGAGATTATAAAACCA
129 -AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * *
996 TTTAAAGTGAGTAATAAGGC-TTTGAAGGAATGGGTGACTACAAATAGACTTTTTTTTGCCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAC-TTTTCTTGCCAATG
* * * * * *
1060 AATGAATTTCTCTTCACATTTCTCAAGGCAAACATTCAGTTGTAGTCTGTTTTAACCAAAGATGT
65 AATGAATTT-TCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT
* **
1125 AGTAAAATTCAAGATAAAATCAATTATGAGATTATAAAACTA
129 A-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
*** * *
1167 TTTAAA-CTGAGTAAT-A-GCTTTTGAAGGAATGAAAGACTATAAATGGACTTTT-TTTCCAAAT
1 TTTAAAGC-GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCC-AAT
* ** * ** * *
1228 AAAT-AGGTTT-TTCAACATGTTTTCTAAGACAGGCATTCAATTATAGTCTGTTTTAAGCAAAAA
64 GAATGAATTTTCTTC-ACAT-TTCTC-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAA
* * * *
1291 TATAAAAAATTCAACTCAAAATCTATTGTGAGATTATAAAACTG
126 TATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * *
1335 TTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATGGACTTTTCTTACCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
* * ** * * * * *
1400 ATGTATTTTTTTCATGTTTCTCAAGATAGACATTCAATTATAATATGTTTTAACCAAAAATGTTC
66 ATGAATTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT-ATA
1465 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCT-
130 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTA
* * * * ** *
1505 TTTAAAGCGAGTAATAAGACTTTTTAAGGAATGGGTGACTATAAATAGATTTTTCCTATCAATAA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
* * ** * * * * * * *
1570 ATGCCATTTTCTTCATATTTCTTGAGTTAAACATTCAATTATAAT-TTTTTTAACTAATAATTTA
66 ATG-AATTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT-
* ** * *
1634 AAACAAATTGAACCCAAAATCAATTATAAGATTATAAAACCA
129 AAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * ** *
1676 TTTAAAGCAAGTAATAAGTCTTTTGAAGGAATAAGAGACTATAAAT-GACCTTTTCTTGCCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGA-CTTTTCTTGCCAATG
* * * *
1740 AA--AATTTTTTTCCTCACGTTTCTTAAGGTAGACATTCAA-TATAGTGTAG-TTTAACCAAAAA
65 AATGAA---TTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCT-GTTTTAACCAAAAA
* * *
1801 TATAAAAAATTTTAACTTAAAATCTATTATGAGATTATAAAACCA
126 TATAAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * *
1846 TTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTCTT-CTCGATA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGC-CAATG
* * ** *
1910 AAT-AACTTTTTCTAT-ACATTT-T-ATGAGGCAGGCATTCAATTATAGTCTGTTTTAATGAAGA
65 AATGAA--TTTTCT-TCACATTTCTCA--AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAA
* *
1971 ATGTAAAACAATTCAACTTAAAATCAATAATGAGATTATAAAA-TAA
125 ATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACT-A
*
2017 TTTAAAGCGAGTAATAAGGCGTTTGAAGGAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG
2050 ATAGGCTATA
Statistics
Matches: 1357, Mismatches: 283, Indels: 175
0.75 0.16 0.10
Matches are distributed among these distances:
162 3 0.00
163 14 0.01
164 63 0.05
165 17 0.01
166 69 0.05
167 70 0.05
168 76 0.06
169 117 0.09
170 365 0.27
171 359 0.26
172 202 0.15
173 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
ATGAATTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAA
AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
Found at i:1298 original size:341 final size:338
Alignment explanation
Indices: 578--2090 Score: 1187
Period size: 341 Copynumber: 4.4 Consensus size: 338
568 TTCTTGAAGT
* * * * ** *
578 AGACATTCAATTATAATCAGTTTTAACCAAAAATGTAAAAATAATTGTACAT-AAAATCAATTTT
1 AGACATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAA-AATTCAAC-TCAAAATCAATTAT
* *
642 GAGATAACAAAACCATTT-----GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
64 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GAC
** * ** ** * ******** * *
702 TTTTCAAGCTAATGAATGCCTTTTTCTTCATATTTCT-AGAAGTAGACANNNNNNNNNNA-TCTA
128 TTTTCTTGCCAATGAATG-AATTTTCTTCACGTTTCTCA-AGGTAGACA--TTCATTATAGTATG
* * *** * *
765 TTTTGACCAATAATGTAAAAAAAATT-ATAGC-TAAAATCAATTATGAGATTATAGTCCGAGTTA
189 TTTTAACCAAAAATGT--AAAAAATTCA-A-CTTAAAATCAATTATGAGATTATAAAACTATTTA
* * * * * *
828 AAGCTAGTAATAAGACTTTTGAAAGAATGGAAGACTATAAATAGACTTTTCTTGCGAATGAATGC
250 AAGCGAGTAATAAGACTTTTGAAGGAATGAAAGACTATAAATAGACTTTTCTTCCAAATAAATGC
* ** ** *
893 TTTTTTCTTCACGTTTCTTAAGGT
315 CTTTTTCAACATTTTTCTTAAGGC
* * * * * *
917 AGACATTCAATTATAGTCTATTTTAACTAAAAATATAAAAAAAATTGAGCTTAAAATTAATTTTG
1 AGACATTCAATTATAGTCTGTTTTAACTAAAAATAT-AAAAAAATTCAACTCAAAATCAATTATG
* *
982 AGATTATAAAACCATTTAAAGTGAGTAATAAGGC-TTTGAAGGAATGGGTGACTACAAATAGACT
65 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GAC-
* * * * * *
1046 TTTTTTTGCCAATGAATGAATTTCTCTTCACATTTCTCAAGGCAAACATTCAGTTGTAGTCTGTT
128 TTTTCTTGCCAATGAATGAATTT-TCTTCACGTTTCTCAAGGTAGACATTCA-TTATAGTATGTT
* * **
1111 TTAACCAAAGATGTAGTAAAATTCAAGATAAAATCAATTATGAGATTATAAAACTATTTAAA-CT
191 TTAACCAAAAATGTA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC-
* * *
1175 GAGTAAT-AG-CTTTTGAAGGAATGAAAGACTATAAATGGACTTTTTTTCCAAATAAATAG-GTT
254 GAGTAATAAGACTTTTGAAGGAATGAAAGACTATAAATAGACTTTTCTTCCAAATAAAT-GCCTT
*
1237 TTTCAACATGTTTTC-TAAGAC
318 TTTCAACAT-TTTTCTTAAGGC
* * *
1258 AGGCATTCAATTATAGTCTGTTTTAAGC-AAAAATAT-AAAAAATTCAACTCAAAATCTATTGTG
1 AGACATTCAATTATAGTCTGTTTTAA-CTAAAAATATAAAAAAATTCAACTCAAAATCAATTATG
** * * *
1321 AGATTATAAAACTGTTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATGGACT
65 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACT
* * * * * *
1386 TTTCTTACCAATGAATGTATTTTTTTCATGTTTCTCAAGATAGACATTCAATTATAATATGTTTT
129 TTTCTTGCCAATGAATGAATTTTCTTCACGTTTCTCAAGGTAGACATTC-ATTATAGTATGTTTT
*
1451 AACCAAAAATGTTCAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCT-TTTAAAGCGA
193 AACCAAAAATG-TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTATTTAAAGCGA
* *** * *
1515 GTAATAAGACTTTTTAAGGAATGGGTGACTATAAATAGATTTTTCCTAT-C-AATAAATGCCATT
256 GTAATAAGACTTTTGAAGGAATGAAAGACTATAAATAGACTTTT-CT-TCCAAATAAATGCCTTT
** * * **
1578 TTCTTCATATTTCTTGAGTT
319 TTCAACATTTTTCTTAAGGC
* * * * * * * *
1598 AAACATTCAATTATAAT-TTTTTTAACTAATAATTTAAAACAAATTGAACCCAAAATCAATTATA
1 AGACATTCAATTATAGTCTGTTTTAACTAAAAATATAAAA-AAATTCAACTCAAAATCAATTATG
* * ** *
1662 AGATTATAAAACCATTTAAAGCAAGTAATAAGTCTTTTGAAGGAATAAGAGACTATAAATGACCT
65 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGA-CT
* * * *
1727 TTTCTTGCCAATGAA--AATTTTTTTCCTCACGTTTCTTAAGGTAGACATTCAATATAGTGTAG-
129 TTTCTTGCCAATGAATGAA---TTTTCTTCACGTTTCTCAAGGTAGACATTCATTATAGTAT-GT
* * * *
1789 TTTAACCAAAAATATAAAAAATTTTAACTTAAAATCTATTATGAGATTATAAAACCATTTAAAGC
190 TTTAACCAAAAATGTAAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * ** * * **
1854 GAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTCTTCTC-GATAAATAACTT
254 GAGTAATAAGACTTTTGAAGGAATGAAAGACTATAAATAGACTTTTCTTC-CAAATAAATGCCTT
* *
1918 TTTCTATACA-TTTT-ATGAGGC
318 TTTC-A-ACATTTTTCTTAAGGC
* * * * * *
1939 AGGCATTCAATTATAGTCTGTTTTAA-TGAAGAATGTAAAACAATTCAACTTAAAATCAATAATG
1 AGACATTCAATTATAGTCTGTTTTAACT-AAAAATATAAAAAAATTCAACTCAAAATCAATTATG
** * * * *
2003 AGATTATAAAATAATTTAAAGCGAGTAATAAGGCGTTTGAAGGAAT-GATAGGCTATAAATGAAT
65 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGT-GACTATAAATG-AC
* * *
2067 TTTTCTTCCCAATGGATGACTTTT
128 TTTTCTTGCCAATGAATGAATTTT
2091 TCTANNNNNN
Statistics
Matches: 945, Mismatches: 179, Indels: 99
0.77 0.15 0.08
Matches are distributed among these distances:
338 91 0.10
339 164 0.17
340 109 0.12
341 385 0.41
342 58 0.06
343 76 0.08
344 61 0.06
345 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (338 bp):
AGACATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAAATTCAACTCAAAATCAATTATGA
GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGACTTT
TCTTGCCAATGAATGAATTTTCTTCACGTTTCTCAAGGTAGACATTCATTATAGTATGTTTTAAC
CAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
AAGACTTTTGAAGGAATGAAAGACTATAAATAGACTTTTCTTCCAAATAAATGCCTTTTTCAACA
TTTTTCTTAAGGC
Found at i:1384 original size:170 final size:168
Alignment explanation
Indices: 152--2063 Score: 1173
Period size: 171 Copynumber: 11.3 Consensus size: 168
142 NNNNNNNNNN
* * * * *
152 TTTAAAGTGAGTAATCAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTACTAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTTTT-CCAATAA
** * ** * * *
217 AT-GGCTTTTCTTCACGTTTCCTAAGACAAACATTCAATTATAGTTTGTTTTAACCAAAAATACA
65 ATAGTTTTTTCTTCATGTTT-CTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATA
********** *
281 AAACAATTCAACTTAAAATCAANNNNNNNNNNATAAAACCA
129 AAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * * ***
322 TTTAAAGTGAGTAATAAGACTTTTAAAAGAATAAGA-GACTATAAATGGACATTTTTTAAAAATA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAAATGGAC-TTTTTTTCCAATA
* * * * * * * **
386 TATGGGTTTTTCTACATGTTTTCCT-AGGTAGGCCA-TCAA-TATAGTTTG-TTTAATCAAATGT
64 AATAGTTTTTTCTTCATG-TTT-CTAAGGTA-GACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * *
447 AAAAAAAATT-AAC-TAAAAT-AA-TATTG-GATAATAAAACCA
126 ATAAAAAATTCAACTTAAAATCAATTA-TGAGATTATAAAACTA
* ** * *
486 TTTAAAGTGAGTAATAAGGCTTTTGAA-GATATGGGA-GGTTATAAATGAACTTTTCTTTTCAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGA-AT-GGATGACTATAAATGGACTTTT-TTTCCAAT
* * ** * * *
549 GAACACCTTTCTCTTC--GTATTCTTGAA-GTAGACATTCAATTATAATCAGTTTTAACCAAAAA
63 AAATAGTTTTTTCTTCATGT-TTC-T-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAA
* ** * * * * *
611 TGTAAAAATAATTGTACATAAAATCAATTTTGAGATAACAAAACCA
125 TAT-AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* *** * *
657 TTT-----GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCAAGCTAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTT-TTTCCAATAA
* * * ********* * * *
717 AT-GCCTTTTTCTTCATATTTCTAGAAGTAGACANNNNNNNNNNA-TCTATTTTGACCAATAATG
65 ATAG-TTTTTTCTTCATGTTTCTA-AGGTAGACA-TTCAATTATAGTCTGTTTTAACCAA-AA-A
* *** *
780 TAAAAAAAATT-ATAGC-TAAAATCAATTATGAGATTATAGTCCGA
125 TATAAAAAATTCA-A-CTTAAAATCAATTATGAGATTATAAAACTA
* * * * * * * * *
824 GTTAAAGCTAGTAATAAGACTTTTGAAAGAATGGAAGACTATAAATAGACTTTTCTTGCGAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTT-TTTCCAATAA
* * *
889 AT-GCTTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATAT
65 ATAG-TTTTTTCTTCATGTTTC-TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT
* * * * *
953 AAAAAAAATTGAGCTTAAAATTAATTTTGAGATTATAAAACCA
128 --AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * * *
996 TTTAAAGTGAGTAATAAGGC-TTTGAAGGAATGGGTGACTACAAATAGACTTTTTTTTGCCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGAC-TTTTTTT-CCAATA
* * ** * * * * * *
1060 AAT-GAATTTCTCTTCACATTTCTCAAGGCAAACATTCAGTTGTAGTCTGTTTTAACCAAAGATG
64 AATAG-TTTTTTCTTCATGTTTCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATA
* **
1124 TAGTAAAATTCAAGATAAAATCAATTATGAGATTATAAAACTA
127 TA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* *
1167 TTTAAA-CTGAGTAAT-A-GCTTTTGAAGGAATGAAAGACTATAAATGGACTTTTTTTCCAAATA
1 TTTAAAGC-GAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTTTTCC-AATA
* ** ** * *
1229 AATAGGTTTTTCAACATGTTTTCTAAGACAGGCATTCAATTATAGTCTGTTTTAAGCAAAAATAT
64 AATAGTTTTTTCTTCATG-TTTCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT
* * * *
1294 AAAAAATTCAACTCAAAATCTATTGTGAGATTATAAAACTG
128 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * *
1335 TTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGATGACTATAAATGGACTTTTCTTACCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTT-TTTCCAATAA
* * * *
1400 AT-GTATTTTT-TTCATGTTTCTCAAGATAGACATTCAATTATAATATGTTTTAACCAAAAATGT
65 ATAGT-TTTTTCTTCATGTTTCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT-A
*
1463 TCAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCT-
127 TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CTA
* * * *
1505 TTTAAAGCGAGTAATAAGACTTTTTAAGGAATGGGTGACTATAAATAGA-TTTTTCCTAT-CAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTT--T-TCCAAT
** * * * * * * * *
1568 AAAT-GCCATTTTCTTCATATTTCTTGAGTTAAACATTCAATTATAAT-TTTTTTAACTAATAAT
63 AAATAG-TTTTTTCTTCATGTTTC-TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * ** * *
1631 TTAAAACAAATTGAACCCAAAATCAATTATAAGATTATAAAACCA
126 AT-AAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * * *
1676 TTTAAAGCAAGTAATAAGTCTTTTGAAGGAATAAGA-GACTATAAAT-GACCTTTTCTTGCCAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAAATGGA-CTTTT-TTTCCAAT
* * * *
1739 GAAA-ATTTTTTTCCTCACGTTTCTTAAGGTAGACATTCAA-TATAGTGTAG-TTTAACCAAAAA
63 -AAATAGTTTTTTCTTCATGTTTC-TAAGGTAGACATTCAATTATAGTCT-GTTTTAACCAAAAA
* * *
1801 TATAAAAAATTTTAACTTAAAATCTATTATGAGATTATAAAACCA
125 TATAAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACTA
* * *
1846 TTTAAAGCGAGTAATAAGGCTTTTGAAGAAAT-GAGTGACTATAAATGGACTTTTCTTCTCGATA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGA-TGACTATAAATGGACTTTTTTTC-CAATA
** * * * * ** * *
1910 AATAACTTTTTCTATACAT-TTTATGAGGCAGGCATTCAATTATAGTCTGTTTTAATGAAGAATG
64 AATAGTTTTTTCT-T-CATGTTTCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATA
*
1974 TAAAACAATTCAACTTAAAATCAATAATGAGATTATAAAA-TAA
127 TAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACT-A
* *
2017 TTTAAAGCGAGTAATAAGGCGTTTGAAGGAAT-GATAGGCTATAAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAT-GACTATAAATG
2064 AATTTTTCTT
Statistics
Matches: 1368, Mismatches: 281, Indels: 185
0.75 0.15 0.10
Matches are distributed among these distances:
161 2 0.00
162 7 0.01
163 13 0.01
164 69 0.05
165 15 0.01
166 64 0.05
167 58 0.04
168 71 0.05
169 132 0.10
170 354 0.26
171 366 0.27
172 213 0.16
173 4 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTTTTCCAATAAA
TAGTTTTTTCTTCATGTTTCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAA
AAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
Found at i:3679 original size:170 final size:161
Alignment explanation
Indices: 3397--3706 Score: 325
Period size: 170 Copynumber: 1.9 Consensus size: 161
3387 NNNNNNNNNN
* ** ***
3397 TTCAACTTAAAATCAATAATGAGATTATAAAACTATTTAAAGTGAGTAATAAGATGTTTGAAGGA
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACACTTGAAGGA
* * * *
3462 TTGAGAGACTATAAATGGACTTTTCTTCCCAATGAATGGCTTTTTCTACACATTT-TTGAGCCAA
66 ATGAGAGACTATAAATGAACTTTTCTTCCCAATGAATGACTTTTTCTACACATTTCCTGAGCCAA
3526 GCATTCAANNNNNNNNNNTTTTAATGAAGAATATAAAAAAA
131 GCATTCAA----------TTTTAATGAAGAATATAAAAAAA
* * * * *
3567 TTCAACTTAAAATCTATTATGAGATTGTAACACCATTTAAAGCAAGTAATAAGGCACTTGAAGGA
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACACTTGAAGGA
* * ** * * *
3632 ATGGGAGACTATAAATGAATTTTTCTTCTTAATGAATTACTTTTTCTATATATTTCCTGAGCCAA
66 ATGAGAGACTATAAATGAACTTTTCTTCCCAATGAATGACTTTTTCTACACATTTCCTGAGCCAA
3697 GCATTCAATT
131 GCATTCAATT
3707 ATAGTCTGTT
Statistics
Matches: 117, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
161 2 0.02
170 99 0.85
171 16 0.14
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (161 bp):
TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACACTTGAAGGA
ATGAGAGACTATAAATGAACTTTTCTTCCCAATGAATGACTTTTTCTACACATTTCCTGAGCCAA
GCATTCAATTTTAATGAAGAATATAAAAAAA
Found at i:5582 original size:171 final size:170
Alignment explanation
Indices: 4706--6577 Score: 1725
Period size: 171 Copynumber: 10.9 Consensus size: 170
4696 NNNNNNNNNN
* * * *
4706 AAAAATTTAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * *
4771 AAGGATTGGGTGACTATAAATGGACTTTTCTTAAC-AATAAATACCTTTTTCTTCATGTTTATCG
66 AAGGA-AGAGTGACTATAAATGGACTTTTCTT-GCTAATGAATGCCTTTTTCTTCATGTTTCTCG
* * * *
4835 AGGTAAACATTCAATTATAATCTATTTTAACTAATAAT-TCAA
129 AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT-AA
* * * * * * * *
4877 TAGAAATTGAACCTAAAA-CCATCTATGAGATTATAAAACCTTTTAAAGTGAGCAATAAGGCTTA
1 -AAAAATTCAACTTAAAATCAAT-TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * **
4941 TGAAGAAATGAGTGACTATAAATGGACTTTTGTTGCTAATGAATGCC-TTTTCTTCACATTTCTC
64 TGAAGGAA-GAGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTC
* * * * *
5005 AATGTAGACATTCAATTATAATCTATTTTAACTAAAAAAGTAAGA
128 GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT-A-A
* * * * *
5050 AAAAATTGAGCTTAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * * * *
5115 AAGGAGTGGGTGACTATAAATAGACTGTTCATGCAAATGAATTCATTTTTCTTCATGTTTC-CTA
66 AAGGA-AGAGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTCGA
* * *
5179 TGGTAGACATTCAATTATAGTCTTTTTTAACAAAAAATGTAA
130 -GGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
* * * * *
5221 AATAATTCAACTTAAAATTAATTATGAGATTAT-AAACTATTTAAAGCGAGTAATGAGACTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* ** * * * * * * *
5285 AAGGAATGGGTGACTGCAAATAGACTTTTCTTCCTAATGAATGCC-TTTTCATGATATTTTTTGA
66 AAGGAA-GAGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTCGA
* * * * * ** * *
5349 AGCAAATATTCAAGTATGGTCTGTTTTAACTAAAAATGTAG
130 GGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
* * *
5390 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTA
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * *
5455 AAGGAACAGTAGACTATAAATGGACTTTTCTTGCTAATGGATGCTTTTTTCTTTACT-TTTCTTG
66 AAGGAAGAGT-GACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCA-TGTTTCTCG
* *
5519 AGGTAGACATTCAATTATAGTTTGTTTTAACCAAACAA-GTAA
129 AGGTAGACATTCAATTATAATCTGTTTTAACCAAA-AATGTAA
* * * * * * *
5561 AAAAATTCAACTTATAATCAATTATGAGATTGTAAAACCATTTAAACCAAGCAATATGGCTTTTA
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * ** *
5626 AAGGAACATGTGACTATAAATGAACTTTTCTTG-TCAATCAATGCCTTTTTC-TCTATGTGACAC
66 AAGGAAGA-GTGACTATAAATGGACTTTTCTTGCT-AATGAATGCCTTTTTCTTC-ATGTTTCTC
* * * *
5689 GAGGTAGATATTCAATTATAATCTCTTTTAACAAAAAATATGAAA
128 GAGGTAGACATTCAATTATAATCTGTTTTAAC-CAAAA-ATGTAA
* * * * * *
5734 AAAAATTGAACATAAAATCAAATT-TGTGATTATAAAACCATTTAAA-CAGAGCAATATGTCTTT
1 AAAAATTCAACTTAAAATC-AATTATGAGATTATAAAACCATTTAAAGC-GAGTAATAAGGCTTT
* *
5797 TGAAGGAATGTGTGACTATAAATGGACTTTT-TCTGCTAATGAATGCCTTTTTCTTCATGTTTTT
64 TGAAGGAA-GAGTGACTATAAATGGACTTTTCT-TGCTAATGAATGCCTTTTTCTTCATGTTTCT
* * * * *
5861 CAAGTTAGACATTAAATTATAATCTGTGTTT-ACTAATAATGTAA
127 CGAGGTAGACATTCAATTATAATCTGT-TTTAACCAAAAATGTAA
* * * * * *
5905 AACCAATTGAACCTAAAATCAATTATAAAATTATAAAACCATTTATAGCGAGTAATAAGGCTTTT
1 AA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * *
5970 AAAGGAATATGTGACTATAAATGGACTTTTCTGGCCAATGAATGCCTTTTTCTTCATATTTCACG
65 GAAGGAAGA-GTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTCG
*
6035 AGGTAAACA-TCAATTATAATCTGTTTTAACCAAAAATGTAA
129 AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
* * *
6076 AAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTACTAAGGATTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * *
6141 AACGAATGGGTGATTATAAATGGACTTTTCTTGATAATGAATGCCTTTTTCTTCATTTTTCCCAA
66 AAGGAA-GAGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTCGA
* * * *
6206 GGCAGACATTCAATTATAGTCTATTTTAATCAAAAATGTAA
130 GGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
* * * *
6247 AAAAACTCAACTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGGTTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * * ** * * *
6312 AAAGAATG-G-GAAGCTATCAATGTACTTTTTTTACAAATAAATGAGTTTTTCTACATGTTTTTT
66 AAGGAA-GAGTG-A-CTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTC
* * * *
6375 GAGGGAGACATTCAATTATAATCTGTTTTAGCTAAAAATATAAA
128 GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT-AA
* *
6419 AAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCATTTAAAGCAAGTAATAA-GCTTTTT
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTT
* * * * ** * * *
6483 GAAAGAATGAGAGACTATAAATGGACTTTTCTTAC-AAGTAAATGGGTTTTTCTACACGTTTCTT
65 GAAGGAA-GAGTGACTATAAATGGACTTTTCTTGCTAA-TGAATGCCTTTTTCTTCATGTTTCTC
* * *
6547 GAGGCA-AGCATTCAATTATAGTCTATTTTAA
128 GAGGTAGA-CATTCAATTATAATCTGTTTTAA
6578 TGAAANNNNN
Statistics
Matches: 1403, Mismatches: 251, Indels: 92
0.80 0.14 0.05
Matches are distributed among these distances:
169 77 0.05
170 245 0.17
171 460 0.33
172 433 0.31
173 177 0.13
174 11 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAAGAGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTCGAG
GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
Found at i:6216 original size:686 final size:676
Alignment explanation
Indices: 4706--6512 Score: 1925
Period size: 686 Copynumber: 2.6 Consensus size: 676
4696 NNNNNNNNNN
* * *
4706 AAAAATTTAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * * * * *
4771 AAGGATTGGGTGACTATAAATGGACTTTTCTTAACAATAAATACCTTTTTCTTCATGTTTATCGA
66 AAGGAATGGGTGACTATAAATGGACTTTTCTTGATAATGAATGCCTTTTTCTTCATTTTTCTCGA
* * * * * * * * *
4836 GGTAAACATTCAATTATAATCTATTTTAACTAATAATTCAATAGAAATTGAACCTAAAACCATCT
131 GGTAGACATTCAATTATAGTCTATTTTAAC-AAAAAGT-AA-AAAAATTCAACTTAAATCAAT-T
* * * * *
4901 ATGAGATTATAAAACCTTTTAAAGTGAGCAATAAGGCTTATGAAGAAATGAGTGACTATAAATGG
192 ATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTAAAGAAAT--GTGACTATAAATGA
* * * * *
4966 ACTTTTGTTG-CTAATGAATGCCTTTTCTTCACAT-TTCTCAATGTAGACATTCAATTATAATCT
255 ACTTTT-TTGTCAAATAAATGCC-TTT-TTCTCATGTTCTCGAGGTAGACATTCAATTATAATCT
* * * *
5029 ATTTTAACTAAAAAAGTA-AGAAAAAATTGAGCTTAAAATTAATTTTGAGATTATAAAACCATTT
317 ATTTTAAC-AAAAAA-TATAAAAAAAATTGAACTTAAAATCAAATTTGAGATTATAAAACCATTT
** * * * *
5093 AAAGTGAGTAATAAGGCTTTTGAAGGAGTGGGTGACTATAAATAGAC-TGTTCATGCAAATGAAT
380 AAACAGAGTAATAA-GCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTCATGCAAATGAAT
* * * * *
5157 TCATTTTTCTTCATGTTTCCTATGGTAGACATTCAATTATAGTCTTTTTTAACAAAAAATGTAAA
444 GCATTTTTCTTCATGTTTCCTAAGGTAGACATTAAATTATAATCTTGTTTAACAAAAAATGTAAA
* * * * * * * *
5222 ATAATTCAACTTAAAATTAATTATGAGATTATAAACTATTTAAAGCGAGTAATGAGACTTTTGAA
509 ACAATTCAACCTAAAATCAATTATAAAATTATAAACCATTTAAAGCGAGTAATAAGACTTTTAAA
* * * * ***
5287 GGAATGGGTGACTGCAAATAGACTTTTCTTCCTAATGAATGCCTTTTCATGATATTTTTTGAAGC
574 GGAATAGGTGACTACAAATAGACTTTTCTGCCTAATGAATGCCTTTTCATCATATTTCACGAAGC
* ** * *
5352 AAATATTCAAGTATGGTCTGTTTTAACTAAAAATGTAG
639 AAACATTCAAGTATAATCTGTTTTAACCAAAAATGTAA
* *
5390 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTA
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
** * * * * * *
5455 AAGGAA-CAGTAGACTATAAATGGACTTTTCTTGCTAATGGATGCTTTTTTCTTTACTTTTCTTG
66 AAGGAATGGGT-GACTATAAATGGACTTTTCTTGATAATGAATGCCTTTTTCTTCATTTTTCTCG
* *
5519 AGGTAGACATTCAATTATAGTTTGTTTTAACCAAACAAGTAAAAAAATTCAACTTATAATCAATT
130 AGGTAGACATTCAATTATAGTCTATTTTAA-CAAA-AAGTAAAAAAATTCAACTTA-AATCAATT
* * * *
5584 ATGAGATTGTAAAACCATTTAAACCAAGCAATATGGCTTTTAAAGGAACATGTGACTATAAATGA
192 ATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTAAA-GAA-ATGTGACTATAAATGA
* * * *
5649 ACTTTTCTTGTC-AATCAATGCCTTTTTCTCTATGTGACACGAGGTAGATATTCAATTATAATCT
255 ACTTTT-TTGTCAAATAAATGCCTTTTTCTC-ATGT-TCTCGAGGTAGACATTCAATTATAATCT
* * *
5713 CTTTTAACAAAAAATATGAAAAAAAATTGAACATAAAATCAAATTTGTGATTATAAAACCATTTA
317 ATTTTAACAAAAAATAT-AAAAAAAATTGAACTTAAAATCAAATTTGAGATTATAAAACCATTTA
* * * *
5778 AACAGAGCAATATGTCTTTTGAAGGAATGTGTGACTATAAATGGACTTTTTC-TGCTAATGAATG
381 AACAGAGTAATAAG-CTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTCATGCAAATGAATG
* * * * *
5842 CCTTTTTCTTCATGTTT-TTCAAGTTAGACATTAAATTATAATCTGTGTTT-ACTAATAATGTAA
445 CATTTTTCTTCATGTTTCCT-AAGGTAGACATTAAATTATAATCT-TGTTTAACAAAAAATGTAA
* * *
5905 AACCAATTGAACCTAAAATCAATTATAAAATTATAAAACCATTTATAGCGAGTAATAAGGCTTTT
508 AA-CAATTCAACCTAAAATCAATTATAAAATTAT-AAACCATTTAAAGCGAGTAATAAGACTTTT
* * * *
5970 AAAGGAATATGTGACTATAAATGGACTTTTCTGGCC-AATGAATGCCTTTTTCTTCATATTTCAC
571 AAAGGAATAGGTGACTACAAATAGACTTTTCT-GCCTAATGAATGCC-TTTTCATCATATTTCAC
* * *
6034 GAGGTAAACA-TCAATTATAATCTGTTTTAACCAAAAATGTAA
634 GAAGCAAACATTCAAGTATAATCTGTTTTAACCAAAAATGTAA
* * * *
6076 AAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTACTAAGGATTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * *
6141 AACGAATGGGTGATTATAAATGGACTTTTCTTGATAATGAATGCCTTTTTCTTCATTTTTCCCAA
66 AAGGAATGGGTGACTATAAATGGACTTTTCTTGATAATGAATGCCTTTTTCTTCATTTTTCTCGA
* *
6206 GGCAGACATTCAATTATAGTCTATTTTAATCAAAAATGTAAAAAAACTCAACTTAAAATCAATTA
131 GGTAGACATTCAATTATAGTCTATTTTAA-CAAAAA-GTAAAAAAATTCAACTT-AAATCAATTA
* * * * * * *
6271 TAAGATTATAAAACTATTTAAAGCGAGTAATAAGGTTTTTGAAAG-AATGGGAAGCTATCAATGT
193 TGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTT-AAAGAAATGTG-A-CTATAAATGA
** * * *
6335 ACTTTTTT-TACAAATAAATGAGTTTTTCTACATGTTTTTTGAGGGAGACATTCAATTATAATCT
255 ACTTTTTTGT-CAAATAAATGCCTTTTTCT-CATG-TTCTCGAGGTAGACATTCAATTATAATCT
* * * * *
6399 GTTTTAGCTAAAAATATAAAAAAAATTCAACTTAAAATC-AATTATGAGATTACAAAACCATTTA
317 ATTTTAACAAAAAATATAAAAAAAATTGAACTTAAAATCAAATT-TGAGATTATAAAACCATTTA
* *
6463 AAGCA-AGTAATAAGCTTTTTGAAAGAATGAGAGACTATAAATGGACTTTT
381 AA-CAGAGTAATAAGC-TTTTGAAGGAATGAGTGACTATAAATGGACTTTT
6513 CTTACAAGTA
Statistics
Matches: 931, Mismatches: 159, Indels: 65
0.81 0.14 0.06
Matches are distributed among these distances:
681 4 0.00
682 7 0.01
683 90 0.10
684 322 0.35
685 124 0.13
686 355 0.38
687 29 0.03
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (676 bp):
AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
AAGGAATGGGTGACTATAAATGGACTTTTCTTGATAATGAATGCCTTTTTCTTCATTTTTCTCGA
GGTAGACATTCAATTATAGTCTATTTTAACAAAAAGTAAAAAAATTCAACTTAAATCAATTATGA
GATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTAAAGAAATGTGACTATAAATGAACTTTT
TTGTCAAATAAATGCCTTTTTCTCATGTTCTCGAGGTAGACATTCAATTATAATCTATTTTAACA
AAAAATATAAAAAAAATTGAACTTAAAATCAAATTTGAGATTATAAAACCATTTAAACAGAGTAA
TAAGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTCATGCAAATGAATGCATTTTTCTTC
ATGTTTCCTAAGGTAGACATTAAATTATAATCTTGTTTAACAAAAAATGTAAAACAATTCAACCT
AAAATCAATTATAAAATTATAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGGAATAGGTGAC
TACAAATAGACTTTTCTGCCTAATGAATGCCTTTTCATCATATTTCACGAAGCAAACATTCAAGT
ATAATCTGTTTTAACCAAAAATGTAA
Found at i:9263 original size:172 final size:171
Alignment explanation
Indices: 8698--9701 Score: 483
Period size: 170 Copynumber: 5.9 Consensus size: 171
8688 NNNNNNNNNN
* * * * * ** *
8698 CAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATTTGTGACTACA
1 CAATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGAGTGACTATA
* * * * *
8763 AATAGACTTTTGTTGCCAATGACTACC-TTTTCTTGACAT-TTTC-TGAAG-TAGACAATCAATT
66 AATAGACTTTTCTTGCCAATGAATGCCTTTTTCTT---ATGTTTCACG-AGTTAGACATTCAATT
* * * * * *
8824 ATAGTCTATTTTAACTAAAACTGT-AAAAAAATTCAACTTAAAAT
127 ATAATCTATTTTCACAAAAAATGTAAAAAAAATTGAACATAAAAT
* * ** * * * * * ***
8868 CAATCATTAGATTATAAAATAATTTTAAGTGAGTAATAAGGCTTTCGAAGGAATGAGAGACTNNN
1 CAATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGAGTGACTATA
******* * * * * * ** * *
8933 NNNNNNNTTTTCTTACAAATAAATAG-GTTTTTCTATACGTTTC-CTGAGGCA-AGCATTTAACT
66 AATAGACTTTTCTTGCCAATGAAT-GCCTTTTTCT-TATGTTTCAC-GAGTTAGA-CATTCAATT
* * ** * * * * *
8995 ATAGTCTATTTTAATGAAAACTG--CAAAAAATTCAACTTAGAAT
127 ATAATCTATTTTCACAAAAAATGTAAAAAAAATTGAACATAAAAT
* * **********
9038 CAATTATGAGATTATAAAACCATTTAAACCA-AGTAATNNNNNNNNNNAAGGAATGAGTGACTAT
1 CAATTATAAGATTATAAAACCATTTAAA-GAGAGTAATAAAGCTTTTGAAGGAATGAGTGACTAT
* * * * *
9102 AAATGGACTTTTCTTGCCAATCATTGCCTTTTTCTCTATGTGTCACGAGGTAGACATTCAATTAT
65 AAATAGACTTTTCTTGCCAATGAATGCCTTTTTCT-TATGTTTCACGAGTTAGACATTCAATTAT
* *
9167 AATCTCTTTTCACAAAAAATGTAAAAAAAATTTAACATAAAAT
129 AATCTATTTTCACAAAAAATGTAAAAAAAATTGAACATAAAAT
** *
9210 CAAATT-TGTGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGCGTGACTAT
1 C-AATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGAGTGACTAT
* * * * **
9274 AAATAGACTTTTCCTACCAATGAATGTCTTTTTCTTCACGTTTTTCGAGTTAGACATTCAATTAT
65 AAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTT-ATGTTTCACGAGTTAGACATTCAATTAT
* * * ** * *
9339 AATCTATTTTTACCAATAATGTAAAACTAATTGAGCCTAAAAT
129 AATCTATTTTCACAAAAAATGTAAAAAAAATTGAACATAAAAT
* *********** *
9382 CAATTATAAGATTATAAAACCATTTAAAGTGNNNNNNNNNNTTTTTGAAGGAATGGGTGACTATA
1 CAATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGAGTGACTATA
* * *
9447 AATAGACTTTTTCTGGCCATTGAATGCCTTTTTCTTTATGTTTCACGAGTTAAACATTCAATTAT
66 AATAGAC-TTTTCTTGCCAATGAATGCCTTTTTC-TTATGTTTCACGAGTTAGACATTCAATTAT
*** * * * * * * **
9512 AATCTGCGTTAACTAAAAATAT-AAAAAAACTCAACTTAAANN
129 AATCTATTTTCACAAAAAATGTAAAAAAAATTGAACATAAAAT
******** * * * * * *
9554 NNNNNNNNAGATTATAAAAGCATTTAAAGCGAGTACT-AAGGTTTTGAACGAATG-GATGATTAT
1 CAATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGAG-TGACTAT
** * **
9617 AAATAGACTTTTCTTGATAATGAATGCCTTTTTCTTCATGTTTTC-CAAGGCAGACATTCAATTA
65 AAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTT-ATG-TTTCACGAGTTAGACATTCAATTA
* * *
9681 TAGTCTATTTTAACCAAAAAT
128 TAATCTATTTTCACAAAAAAT
9702 NNNNNNNNNN
Statistics
Matches: 620, Mismatches: 192, Indels: 44
0.72 0.22 0.05
Matches are distributed among these distances:
169 4 0.01
170 245 0.40
171 73 0.12
172 232 0.37
173 64 0.10
174 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
CAATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAAGCTTTTGAAGGAATGAGTGACTATA
AATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTATGTTTCACGAGTTAGACATTCAATTATAA
TCTATTTTCACAAAAAATGTAAAAAAAATTGAACATAAAAT
Found at i:10201 original size:171 final size:170
Alignment explanation
Indices: 9809--11121 Score: 624
Period size: 171 Copynumber: 7.7 Consensus size: 170
9799 NNNTTGTAAA
* * * * * *
9809 AAAAGTCCATTGATAGCCTC-CCATTCTTTCAAAAACTTTATTACTTGCTTTAAATGGTTTTATA
1 AAAAGTCCATTTATAG--TCACCATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATA
* * *
9873 ATCTTATAATTGATTTTAACTTGAGTTTTTTTTATATTTTTGGTTAAAATAGACTATAATTGAAT
64 ATCTTATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAAT
* * * * *****
9938 GTTTGCCTTGGGAAAGATGAAGAAAAAGGCATTCATTNNNNNNN
129 GTCTACCTTGAGAAACATGAAGAAAAAGGCATTCATT--GGCAG
*** * * * * *
9982 NNNA-TCCATTTATAATCACCCATTCGTTCAACATCCTTAGTACTCGCTTTAAAAGGTTCTATAA
1 AAAAGTCCATTTATAGTCA-CCATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATAA
* *
10046 TCTCATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTAGTTAAAATAGATTATAATTG-ATG
65 TCTTATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAATG
*
10110 TCTACCTTGTGAAACATGAAGAAAAAGGCATTCATTGGCCAG
130 TCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGG-CAG
**********
10152 AAAAGTCCATTTATAGTCACCTATTCCTNNNNNNNNNNTATTACTCGCTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCACC-ATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATAA
** * * ** * * *
10217 TCTTATAATTGATTTTAGGTTCAATTGGTTTTGCATTATTGGTAAAAATAGATTATAATTGAATG
65 TCTTATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAATG
* * **
10282 TCTAACTCGAGAAACATGAAGAAAAATACATTCATTGGCAGG
130 TCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCA-G
* * * * * **********
10324 AAAAGTTCATTTATAGTCACGCATTCCTTCAAAAGCCATATTACTCTCTNNNNNNNNNNTTATAA
1 AAAAGTCCATTTATAGTCAC-CATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATAA
** * ** * * *
10389 TCACA-AATATAATTTTATGTTTAATTTTTTTTTACATTTTT--TTAAAAGAGATTATAATTGAA
65 TCTTATAAT-TGATTTTA-AATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAA
* * * * *
10451 TGTTTACC-TCATGACACAT-AGAGAAAAAGGCATTGATTGACAAG
128 TGTCTACCTTGA-GAAACATGA-AGAAAAAGGCATTCATTGGC-AG
* ** ** * * * * *
10495 AAACGTTTATTTATAGTCACTTGTTCCTTTAAAAGCCATTA-TACTTGGTTTAAATGGTTTTATA
1 AAAAGTCCATTTATAGTCAC-CATTCCTTCAACATCC-TTATTACTCGCTTTAAATGGTTTTATA
* * ********** * * *
10559 AT-TTCATTATTGATTCT-NNNNNNNNNNTTTTTACTTTTTTGGTTAAAATAAACTATAATTGAA
64 ATCTT-ATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAA
** * ** * * *
10622 TGTCTACCTCAAAGAAAGAAAAAGAAAAAAGCATCCATTAGCAAG
128 TGTCTACCT-TGAGAAACATGAAGAAAAAGGCATTCATTGGC-AG
* ** * * **********
10667 AAAAGTCCATTTATATTCTGTCATTCCTTCAAAAGCCTTATTACTCGCTTTANNNNNNNNNNTAA
1 AAAAGTCCATTTATAGTC-ACCATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATAA
* * * * * * ** * * * *
10732 TCTCATAATTGATTTTCAGTTGA-ATTTTTCTATATTTTTAATTGAAACAGACTATGATTGAATG
65 TCTTATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAATG
* * * * * * * *
10796 TCTGCTTTG-GAAAATATCATG-AAAAGGAATTTATTAGCAAG
130 TCTACCTTGAG-AAACATGAAGAAAAAGGCATTCATTGGC-AG
* * * * * * *
10837 AAAATTCTATTTACAGTCACTCATTCCTTCAAAAGCTTTATTACTCGCTTTAAATAGTTTTATAA
1 AAAAGTCCATTTATAGTCAC-CATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATAA
* * * * * * *
10902 TCTTATAATTGATTTTAAGTTGA-ATTATTTTATATTTTTTGTTAAAACAGACTATAATTGAATG
65 TCTTATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAATG
* * * *** * *
10966 TCTACCATGGGAAACGTGAAGAAAAATAAATTTATTTGCATG
130 TCTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCA-G
* ** * * *
11008 AACAGTCTGTTTATAGTCACCCACTCCTTCAAAAGCCTTATTACTCAG-TTTAAATGGTTTTATA
1 AAAAGTCCATTTATAGTCA-CCATTCCTTCAACATCCTTATTACTC-GCTTTAAATGGTTTTATA
* * ** * * *
11072 ATCTCAAAATTGATTTTAAGCTCAATTTTTTCTTACTTTTTTGGTTAAAA
64 ATCTTATAATTGATTTTAAATTGAGTTTTTT-TTACATTTTTGGTTAAAA
11122 AAATGTAAAC
Statistics
Matches: 847, Mismatches: 259, Indels: 68
0.72 0.22 0.06
Matches are distributed among these distances:
169 12 0.01
170 140 0.17
171 352 0.42
172 307 0.36
173 36 0.04
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.39
Consensus pattern (170 bp):
AAAAGTCCATTTATAGTCACCATTCCTTCAACATCCTTATTACTCGCTTTAAATGGTTTTATAAT
CTTATAATTGATTTTAAATTGAGTTTTTTTTACATTTTTGGTTAAAATAGATTATAATTGAATGT
CTACCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCAG
Found at i:11648 original size:170 final size:168
Alignment explanation
Indices: 11116--11682 Score: 565
Period size: 170 Copynumber: 3.3 Consensus size: 168
11106 ACTTTTTTGG
* * * * * *
11116 TTAA-AAAAATGTAAACAAAATTGAGCTTAAAATCAATTTTCAGATTATAAAACCATTTAAACTG
1 TTAATAAAAATGT-AA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTG
* *
11180 AGTAATAAGGCTTTTGAAAGAATGGGTA-ACTATAAATAGACCTTTCTTACCAATGAATGAATTT
64 AGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATAGACTTTTCTTACCAATGAATG-ATTT
* ** *
11244 TTCT-TCACGTTTCTTGAGGTAAGCATTCAATTACAGC-CGGTTT
127 TTCTAT-ATGTTTCTAAAGGTAAGCATTCAATTATAGCTC--TTT
*
11287 TTAATAAAAAATGTAAAATAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCG
1 TTAAT-AAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTG
* * * * * **
11352 AGTAATAAGGCTTTTGAAGGAATAGGTGACTACAAATGGACTTTTCTTCCCAATGAATGCCTTTT
64 AGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTACCAATGAATGATTTTT
* * * *
11417 CTTGATAT-TTTCTGAA-GCAAACATTCAATTAT-GATCTGTT
129 C-T-ATATGTTTCTAAAGGTAAGCATTCAATTATAGCTCT-TT
* * *
11457 TTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATCATTAGATTATAAAACTATTTAAAGTG
1 TTAA-TAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTG
* * * *
11522 AGTAATAAGGCTTTCGAAGGAATGGGAGACTATAAATAGACTTTTCTTACAAATAAATAGGTTTT
64 AGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTACCAATGAAT-GATTTT
* * * * *
11587 TCTATATGTTTCCAAAGGTAGGCATTTAACTATAG-TTTATT
128 TCTATATGTTTCTAAAGGTAAGCATTCAATTATAGCTCT-TT
* * * *
11628 TTAATGAAAACTATAAAAAATTCAACTTAGATTCAATTATGAGATTATAAAACTA
1 TTAAT-AAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
11683 NNNNNNNNNN
Statistics
Matches: 327, Mismatches: 53, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
169 5 0.02
170 151 0.46
171 61 0.19
172 100 0.31
173 9 0.03
174 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
TTAATAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
TAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTACCAATGAATGATTTTTCT
ATATGTTTCTAAAGGTAAGCATTCAATTATAGCTCTTT
Done.