Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399491.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2752.0, 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: 4804
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.31
Warning! 565 characters in sequence are not A, C, G, or T
Found at i:1212 original size:26 final size:28
Alignment explanation
Indices: 1183--1267 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 28
1173 NNNNNNNNAA
*
1183 AATAAAAATAT-TAAAA-TAAAATATAT
1 AATAAAAATATAAAAAATTAAAATATAT
*
1209 AATACAAAA-ATCAAAAATTAAAATA-A-
1 AATA-AAAATATAAAAAATTAAAATATAT
1235 AAT-AAAATATAAAAAATTAAAATTCATAT
1 AATAAAAATATAAAAAATTAAAA-T-ATAT
1264 AATA
1 AATA
1268 TAAGAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 4 0.08
25 13 0.27
26 10 0.21
27 10 0.21
28 8 0.17
29 3 0.06
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (28 bp):
AATAAAAATATAAAAAATTAAAATATAT
Found at i:1246 original size:7 final size:6
Alignment explanation
Indices: 1181--1249 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
1171 NNNNNNNNNN
* * *
1181 AAAATA AAAATA TTAAAATA AAATATA TAATACA AAAATCA AAAATT AAAAT-
1 AAAATA AAAATA --AAAATA AAA-ATA -AAAATA AAAAT-A AAAATA AAAATA
1233 AAAATA AAATATA AAAA
1 AAAATA AAA-ATA AAAA
1250 ATTAAAATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
5 5 0.10
6 21 0.41
7 17 0.33
8 8 0.16
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAATA
Found at i:1704 original size:15 final size:15
Alignment explanation
Indices: 1686--1721 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1676 CTTGCACTGG
*
1686 CATTGCTTGCAATCA
1 CATTGCCTGCAATCA
*
1701 CATTGCCTGTAATCA
1 CATTGCCTGCAATCA
1716 CATTGC
1 CATTGC
1722 ATTGTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (15 bp):
CATTGCCTGCAATCA
Found at i:2599 original size:170 final size:170
Alignment explanation
Indices: 1791--4616 Score: 1405
Period size: 171 Copynumber: 16.6 Consensus size: 170
1781 NNNNNNNNNN
* * * * * * *
1791 TGAGACTATAAAATCATTTAAAGCTAGTAATAAGGCTTTAGAACGCATGGGTAACTATAAATGTA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* ** * * ** ** *
1856 CTTTTCTTGCCAATGAATGAGATTTTT-TT-A-CGTTT-CATGAGTCAGATGTTCAAACATAATC
66 CTTTTCTTGCCAATGAATG-GCTTTTTCTTCATATTTTCCA--AGGCAAACATTCAATTATAATA
* * * * * *
1917 TGTTTGAAGT-ACAAATGTAAAAAAATTCAACTTAAAATCTATAA
128 TATTTTAA-TCAAAAAAGT-AAAAAATTCAACTTAAAATCAATTA
* * * *
1961 TAAGATTATAAAACCATTTAAAGTGAGTGATAAGGCTTTGGAAGGCATGGGTGATTATAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * ** * * * * *
2026 CTTTTCTTGTCAACGAATGGCTTTTT-TTGCACGTTTCCCAAGGTAAATAGTCAATTATAATCTA
66 CTTTTCTTGCCAATGAATGGCTTTTTCTT-CATATTTTCCAAGGCAAACATTCAATTATAATATA
** * * *********
2090 TTTTAGCCAAAAATGTAAAAAAATTTAAC-TAANNNNNNNNNN
130 TTTTAATCAAAAAAGT-AAAAAATTCAACTTAA-AATCAATTA
* * ** * * * ** *** *
2132 TGAAATTATAAAACTATTTAAAGTAAGTGATAAAGTTTTCAAAGGC-TCGCAAGACCATAAATGG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCAT-GGGTGACTATAAATGG
* * * * * ** *** ** * * *
2196 AGTTTTCTTGTCAATGGATAG-TATTTTTTTCACGTTTTTTGAGAAAAATATTCAAATATAATCT
65 ACTTTTCTTGCCAATGAATGGCT-TTTTCTTCATATTTTCCAAGGCAAACATTCAATTATAATAT
* * * * * * *
2260 GTTTTCACCATAAATA-TAAAACAATTCAATTTAAAATCAGTAA
129 ATTTTAATCA-AAAAAGTAAAA-AATTCAACTTAAAATCAATTA
* * * *
2303 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGTCTTTGGAAGGTATGAGTGACTATAAATTGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * * * * * *
2368 CTTTTCTTGCAAATGCATGCCTTTTGCATCA-CTTTTCCTGAA-ACAAACATTTAGTTATAATAT
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCC--AAGGCAAACATTCAATTATAATAT
*
2431 ATTTTAATCAAAAAAGTAAAAAATGCAACTTAAAATCAATTA
129 ATTTTAATCAAAAAAGTAAAAAATTCAACTTAAAATCAATTA
* * * * * *
2473 TGAGATCATAAAAACATTTAAAGCGAGTAATAAGGTTTTGGAAGGTAAGGGTGATTATAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * * * * *
2538 CTTTTGTTGCTAATGAATGGCTTTTTCTTCATATTTTTCGAGGTAGACAATT-AAATATAATATG
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAAAC-ATTCAATTATAATATA
* * * *
2602 TTTTCAT-AAAAAATATAAAACAATTAAACTTAAAATCAATAA
130 TTTTAATCAAAAAA-GTAAAA-AATTCAACTTAAAATCAATTA
* ********** * *
2644 TCAGATTNNNNNNNNNNTTAAAGCGAGTAATAAGGCTTTGAAAGGCATAGGTGACTATAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * ** *
2709 CTTTTATTGCCAATGGATGGCTTTTGCATCACGTTTTCTACA-GCAAACATTCAATTATAATATA
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCA-AGGCAAACATTCAATTATAATATA
*** * *
2773 TTTTAATCAAAATTTTAAAAAAATCAACCTAAAATCAATTA
130 TTTTAATCAAAAAAGTAAAAAATTCAACTTAAAATCAATTA
** * * ** * * * *
2814 CAAGATTATAAAATCAGTTAAAATGAGTAATAAGGTTTTGGAAGGCATGAGTTACTATAAATGGG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * * * * ** *
2879 TTTTTCTTGCCAATGATTGGCCTTCTCTTCACT-TTTT-TAGAGGTAGACATTCAAACATAATCT
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCA-TATTTTCCA-AGGCAAACATTCAATTATAATAT
* * * ** *
2942 GTTTTCACCAAAAATA-TAAAACAATTCAACTTAAAATCTGTAA
129 ATTTTAATCAAAAA-AGTAAAA-AATTCAACTTAAAATCAATTA
* * * *
2985 TGAGATTATAAGACCATTTAAAGCGAGTAATAAGGCCTTCGAAGG-TTGAGGTGACTATAAATGG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATG-GGTGACTATAAATGG
** * * * * ** *********
3049 ACTTTGATTGCCCATGGATGGCTTTTGCATCA-CGTTTCCNNNNNNNNNNATTCAATTATAATAT
65 ACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCC-AAGGCAAACATTCAATTATAATAT
* *
3113 ATTTTAA-CTAAAAAAGTAAAAAAATCTAACTTAAAATTAATTA
129 ATTTTAATC-AAAAAAGTAAAAAATTC-AACTTAAAATCAATTA
* * * * * ** * ** *
3156 TGAAATTACAGAATCATTTAAAGTGAGTAATAACACTTTGCAAGGCATTAGCGACTATAAACT-G
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAA-TGG
* * * * * *
3220 ACTTTTCTTGTCAATGAATGGTTTTTTCTT--TACGTTTCCTAAAGCAAACATT-AATTACAATC
65 ACTTTTCTTGCCAATGAATGGCTTTTTCTTCATA-TTTTCC-AAGGCAAACATTCAATTATAATA
* *
3282 TATTTTAAT-AAAAATGTAAAAAATTCATCTTAAAATCAATTA
128 TATTTTAATCAAAAAAGTAAAAAATTCAACTTAAAATCAATTA
* * * * *
3324 TGAGATTGA-AAAACTATTTAAA-CTGAGTAATAAGGCTTT-CAACG-ACTTGGTTA-TATATAC
1 TGAGATT-ATAAAACCATTTAAAGC-GAGTAATAAGGCTTTGGAAGGCA-TGGGTGACTATA-A-
* *** * * * * * * * *
3384 ATAGACTTTTCTTAATAGTGGATGGCTTTTGCTT-AT-GTTTCCTAAAGTAGACATTGAATTATA
61 ATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCC-AAGGCAAACATTCAATTATA
* *
3447 ATATATTTTAA-CTAAAAAAGTAAAAAAATTTAACTTAAAATCTATTA
125 ATATATTTTAATC-AAAAAAGT-AAAAAATTCAACTTAAAATCAATTA
* * * * *
3494 TGAGATTATAAAACCTTTTAAAGCTAGTTATAAGGCTTAGGAAGGCTTGGGTGACTATAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * ** * * * * * *
3559 CTTTTGTTGCCAATGAATAGG-TTTTTCTTTATA-TTTCTTAGGAAAAACTTTAAAATATTATTT
66 CTTTTCTTGCCAATGAAT-GGCTTTTTCTTCATATTTTCCAAGG-CAAACATTCAATTATAATAT
* * * * *
3622 GTTTTAA-CTAAAAATGTAATAAAATTTAATTTAAAATCAATAA
129 ATTTTAATC-AAAAAAGTAA-AAAATTCAACTTAAAATCAATTA
* ** *** ** * * * * *
3665 TAAGATTATAAAATTATTTAAAATAAGTAGCAAAGCTTTGGAAGGCACGGATGGCTATAAATAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * ** ** * * *
3730 TTTTTCTTGCTAATGAATGGCTTTTTCTTCA-CGTTTCCTAAAACAGACATTCAGTTATGATATA
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCC-AAGGCAAACATTCAATTATAATATA
* *
3794 TTTTAAGT-AAAAATGTAAAAAAATTCAACTTAAAATTAATTA
130 TTTTAA-TCAAAAAAGT-AAAAAATTCAACTTAAAATCAATTA
* * * ** *
3836 TAAGATTATAAAACCATTTGAAGTGAGTAATAAGGCTTTAAAAGGCATGGATGACTATAAATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * * * ** *
3901 CTTTTTTTGCCAATGGATGGCTTTTACATCACATTTCCCAAGATAAACATTTAATTATAATATAT
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAAACATTCAATTATAATATAT
3966 TTTAAT-AAAAAATGTAAAATAAATGT-AACTTAAAATCAATTA
131 TTTAATCAAAAAA-GT-AAA-AAAT-TCAACTTAAAATCAATTA
* * * * * * *
4008 TAAAATTATAAAACCATTTAAAGCAATTAATAAAGCTTCT-AAAGGCATGGGTGACTACAAATGG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT-TGGAAGGCATGGGTGACTATAAATGG
* * * * * * *
4072 ACTTTTTTTACCAAT-ATATGGCTTTTTGC-TCATA-TTTCCTGAGGTAAACAATGAATTTTAAC
65 ACTTTTCTTGCCAATGA-ATGGCTTTTT-CTTCATATTTTCC-AAGGCAAACATTCAATTATAA-
* * * **********
4134 T-TGTTTTAACCAAAAATGTAAAAAAATTCANNNNNNNNNNAATTA
126 TATATTTTAATCAAAAAAGT-AAAAAATTCAACTTAAAATCAATTA
* * * ** * * *
4179 TGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCAAAGGCTTGGGTGACTATAAGTAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * * ** * *
4244 CTTTTCTTGCCAATAAATAG-TTTTCTCTTCATGTTTTCCAAGACAGACATTCAAACATTATCTA
66 CTTTTCTTGCCAATGAATGGCTTTT-TCTTCATATTTTCCAAGGCAAACATTCAATTATAATATA
* * * *
4308 TTTTAAGCAAAAATGTAAAAGAATTCAACTTAAAATCAGTAA
130 TTTTAATCAAAAAAGTAAAA-AATTCAACTTAAAATCAATTA
* * * * * * * *
4350 GGAGATTATAGAACCATTTAAAGTGAGTAATAAGGTTTTGGAAGGCATGGATGATTATAAGTAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
* * * * * * * * **********
4415 CTTTTCTTGCTAATGGATAGCGTTTGCATCACA-TTTCCTAAAGCAAACATTCNNNNNNNNNNTA
66 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCC-AAGGCAAACATTCAATTATAATATA
* * *
4479 TTTTAACCAAAAATGTAAAAATATTTAACTTAAAATCAATTA
130 TTTTAATCAAAAAAGTAAAAA-ATTCAACTTAAAATCAATTA
* * * ** * *
4521 TGGGTTTATAAAACCATTTAAAGCGAGTAAT-A-GCATTTTGGAATGCATGGGAAAATATAAATA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC--TTTGGAAGGCATGGGTGACTATAAATG
* *
4584 GACTTTTCTTGCCAATGAATGGGTTTTCCTTCA
64 GACTTTTCTTGCCAATGAATGGCTTTTTCTTCA
4617 CTCTTTTAGA
Statistics
Matches: 1992, Mismatches: 573, Indels: 181
0.73 0.21 0.07
Matches are distributed among these distances:
166 5 0.00
167 27 0.01
168 84 0.04
169 44 0.02
170 466 0.23
171 1186 0.60
172 169 0.08
173 11 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGA
CTTTTCTTGCCAATGAATGGCTTTTTCTTCATATTTTCCAAGGCAAACATTCAATTATAATATAT
TTTAATCAAAAAAGTAAAAAATTCAACTTAAAATCAATTA
Found at i:3104 original size:341 final size:342
Alignment explanation
Indices: 2245--3921 Score: 1069
Period size: 341 Copynumber: 4.9 Consensus size: 342
2235 TGAGAAAAAT
* *
2245 ATTCAAATATAATCTGTTTTCACCATAAATATAAAACAATTCAATTTAAAATCAGTAATGAGATT
1 ATTCAAATATAATCTGTTTTCACCAAAAATATAAAACAATTCAACTTAAAATCAGTAATGAGATT
* * * * *
2310 ATAAAACCATTTAAAGCGAGTAATAAGTCTTTGGAAGGTATGA-GTGACTATAAATTGACTTTTC
66 ATAAAACCATTTAAAGCGAGTAATAAGGCCTTCGAAGGT-TGAGGTGACTATAAATGGACTTTTA
* * * * * * *
2374 TTGCAAATGCATGCCTTTTGCATCACTTTTCCTGAAACAAACATTTAGTTATAATATATTTTAAT
130 TTGCCAATGGATGGCTTTTGCATCACGTTTCCTAAAACAAACATTCAATTATAATATATTTTAAT
* ** * *
2439 CAAAAAAGTAAAAAATGCAACTTAAAATCAATTATGAGATCATAAAAACATTTAAAGCGAGTAAT
195 CAAAAAAGTAAAAAATGCAACCTAAAATCAATTACAAGATCATAAAAACAGTTAAAACGAGTAAT
* * * * * * *
2504 AAGGTTTTGGAAGGTAAGGGTGATTATAAATGGACTTTTGTTGCTAATGAATGGCTTTTTCTTCA
260 AAGGTTTTGGAAGGCAAGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCCTTCTCTTCA
*
2569 TATTTTTCGAGGTAGACA
325 TATTTTTAGAGGTAGACA
* ** * * *
2587 ATT-AAATATAATATGTTTTCATAAAAAATATAAAACAATTAAACTTAAAATCAATAATCAGATT
1 ATTCAAATATAATCTGTTTTCACCAAAAATATAAAACAATTCAACTTAAAATCAGTAATGAGATT
********** * *
2651 NNNNNNNNNNTTAAAGCGAGTAATAAGG-CTTTGAAAGGCAT-AGGTGACTATAAATGGACTTTT
66 ATAAAACCATTTAAAGCGAGTAATAAGGCCTTCG-AAGG-TTGAGGTGACTATAAATGGACTTTT
* * *
2714 ATTGCCAATGGATGGCTTTTGCATCACGTTTTCTACAGCAAACATTCAATTATAATATATTTTAA
129 ATTGCCAATGGATGGCTTTTGCATCACGTTTCCTAAAACAAACATTCAATTATAATATATTTTAA
*** * * *
2779 TCAAAATTTTAAAAAAAT-CAACCTAAAATCAATTACAAGATTATAAAATCAGTTAAAATGAGTA
194 TCAAAAAAGT-AAAAAATGCAACCTAAAATCAATTACAAGATCATAAAAACAGTTAAAACGAGTA
* * ** *
2843 ATAAGGTTTTGGAAGGCATGAGTTACTATAAATGGGTTTTTCTTGCCAATGATTGGCCTTCTCTT
258 ATAAGGTTTTGGAAGGCAAGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCCTTCTCTT
2908 CACT-TTTTTAGAGGTAGAC-
323 CA-TATTTTTAGAGGTAGACA
* *
2927 ATTCAAACATAATCTGTTTTCACCAAAAATATAAAACAATTCAACTTAAAATCTGTAATGAGATT
1 ATTCAAATATAATCTGTTTTCACCAAAAATATAAAACAATTCAACTTAAAATCAGTAATGAGATT
* *
2992 ATAAGACCATTTAAAGCGAGTAATAAGGCCTTCGAAGGTTGAGGTGACTATAAATGGACTTTGAT
66 ATAAAACCATTTAAAGCGAGTAATAAGGCCTTCGAAGGTTGAGGTGACTATAAATGGACTTTTAT
* **********
3057 TGCCCATGGATGGCTTTTGCATCACGTTTCCNNNNNNNNNNATTCAATTATAATATATTTTAA-C
131 TGCCAATGGATGGCTTTTGCATCACGTTTCCTAAAACAAACATTCAATTATAATATATTTTAATC
* * * * * * * * **
3121 TAAAAAAGTAAAAAAAT-CTAACTTAAAATTAATTATGAA-ATTACAGAATCATTTAAAGTGAGT
196 -AAAAAAGT-AAAAAATGC-AACCTAAAATCAATTA-CAAGATCATAAAAACAGTTAAAACGAGT
*** * ** * * ** *
3184 AATAACACTTTGCAAGGCATTAGCGACTATAAACT-GACTTTTCTTGTCAATGAATGGTTTTTTC
257 AATAAGGTTTTGGAAGGCAAGAGTGACTATAAA-TGGACTTTTCTTGCCAATGAATGGCCTTCTC
* ** * * * *
3248 TTTACGTTTCCTA-AAGCAAAC-
321 TTCATATTT-TTAGAGGTAGACA
* * * ** * * * *
3269 ATT-AATTACAATCTATTTT-AATAAAAATGTAAAA-AATTCATCTTAAAATCAATTATGAGATT
1 ATTCAAATATAATCTGTTTTCACCAAAAATATAAAACAATTCAACTTAAAATCAGTAATGAGATT
* * * * *
3331 GA-AAAACTATTTAAA-CTGAGTAATAAGGCTTTC-AACGACTT--GGTTA-TATATACATAGAC
66 -ATAAAACCATTTAAAGC-GAGTAATAAGGCCTTCGAA-G-GTTGAGGTGACTATA-A-ATGGAC
* *** * * * ** * *
3390 TTTTCTTAATAGTGGATGGCTTTTGC-TTATGTTTCCTAAAGTAGACATTGAATTATAATATATT
125 TTTTATTGCCAATGGATGGCTTTTGCATCACGTTTCCTAAAACAAACATTCAATTATAATATATT
** * * ** * * ** *
3454 TTAA-CTAAAAAAGTAAAAAAATTTAACTTAAAATCTATTATGAGATTATAAAACCTTTTAAAGC
190 TTAATC-AAAAAAGT-AAAAAATGCAACCTAAAATCAATTACAAGATCATAAAAACAGTTAAAAC
* * * * ** * * *
3518 TAGTTATAAGGCTTAGGAAGGCTTGGGTGACTATAAATGGACTTTTGTTGCCAATGAATAGG-TT
253 GAGTAATAAGGTTTTGGAAGGCAAGAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GGCCT
* * ** *
3582 TTTCTTTATATTTCTTAG-GAAAAAC-
317 TCTCTTCATATTT-TTAGAGGTAGACA
* * * * * * * * * * *
3607 TTTAAAATATTATTTGTTTTAACTAAAAATGTAATAA-AATTTAATTTAAAATCAATAATAAGAT
1 ATTCAAATATAATCTGTTTTCACCAAAAATATAA-AACAATTCAACTTAAAATCAGTAATGAGAT
** *** ** * * * * * * *
3671 TATAAAATTATTTAAAATAAGTAGCAAAGCTTTGGAAGG--CACGGATGGCTATAAATAGATTTT
65 TATAAAACCATTTAAAGCGAGTAATAAGGCCTTCGAAGGTTGA-GG-TGACTATAAATGGACTTT
* * * * * * * *
3734 TCTTGCTAATGAATGGCTTTTTCTTCACGTTTCCTAAAACAGACATTCAGTTATGATATATTTTA
128 TATTGCCAATGGATGGCTTTTGCATCACGTTTCCTAAAACAAACATTCAATTATAATATATTTTA
* * * * * * * * * **
3799 AGT-AAAAATGTAAAAAAATTCAACTTAAAATTAATTATAAGATTATAAAACCATTTGAAGTGAG
193 A-TCAAAAAAGT-AAAAAATGCAACCTAAAATCAATTACAAGATCATAAAAACAGTTAAAACGAG
* ** * * *
3863 TAATAAGGCTTTAAAAGGCATG-GATGACTATAAATGGACTTTTTTTGCCAATGGATGGC
256 TAATAAGGTTTTGGAAGGCAAGAG-TGACTATAAATGGACTTTTCTTGCCAATGAATGGC
3922 TTTTACATCA
Statistics
Matches: 1057, Mismatches: 237, Indels: 82
0.77 0.17 0.06
Matches are distributed among these distances:
337 6 0.01
338 151 0.14
339 88 0.08
340 37 0.04
341 517 0.49
342 249 0.24
343 9 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (342 bp):
ATTCAAATATAATCTGTTTTCACCAAAAATATAAAACAATTCAACTTAAAATCAGTAATGAGATT
ATAAAACCATTTAAAGCGAGTAATAAGGCCTTCGAAGGTTGAGGTGACTATAAATGGACTTTTAT
TGCCAATGGATGGCTTTTGCATCACGTTTCCTAAAACAAACATTCAATTATAATATATTTTAATC
AAAAAAGTAAAAAATGCAACCTAAAATCAATTACAAGATCATAAAAACAGTTAAAACGAGTAATA
AGGTTTTGGAAGGCAAGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCCTTCTCTTCAT
ATTTTTAGAGGTAGACA
Found at i:4465 original size:514 final size:510
Alignment explanation
Indices: 3208--4465 Score: 1247
Period size: 514 Copynumber: 2.5 Consensus size: 510
3198 AGGCATTAGC
* * * * * * *
3208 GACTATAAACT-GACTTTTCTTGTCAATGAATGGTTTTTTCTTTACGTTTCCTAAAGCAAACATT
1 GACTATAAA-TAGACTTTTCTTGCCAATAAATAGCTTTTTCTTCACGTTTCCTAAAACAGACATT
*
3272 -AATTACA--ATCTATTTTAA-TAAAAATGTAAAAAATTCATCTTAAAATCAATTATGAGATTGA
65 CAA--ACATGATCTATTTTAAGTAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATT-A
* * * * * *
3333 -AAAACTATTTAAACTGAGTAATAAGGCTTTCAACGACTTGG-TTATATATACATAGACTTTTCT
127 TAAAACCATTTAAAGTGAGTAATAAGGCTTT-AAAGGCATGGATGAT-TATA-ATAGACTTTTCT
** * * ** *
3396 TAATAGTGGATGGCTTTTGC-TTATGTTTCCTAAAGTAGACATTGAATTATAATATATTTTAACT
189 TGCTAATGGATGGCTTTTGCATCACATTTCCTAAAGTAAACATTGAATTATAATATATTTTAACT
* * * * * *
3460 AAAAAAGTAAAAAAATTTAACTTAAAATCTATTATGAGATTATAAAACCTTTTAAAGCTAGTTAT
254 AAAAAAGTAAAAAAATGTAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGCTAATTAT
* * * * * *
3525 AAGGCTTAGGAAGGCTTGGGTGACTATAAATGGACTTTTGTTGCCAATGAATAGGTTTTTCTTTA
319 AAAGCTTAGAAAGGCATGGGTGACTACAAATGGACTTTTGTTACCAATGAATAGGTTTTTCTTCA
* ** * * * *
3590 TATTTCTTAGGAAAAACTTTAAAATATTATTTGTTTTAACTAAAAATGTAATAAAATTTAATTTA
384 TATTTCTGAGGAAAAACAATAAAATATTACTTGTTTTAACCAAAAATGTAAAAAAATTCAATTTA
* * * * **
3655 AAATCAATAATAAGATTATAAAATTATTTAAAATAAGTAGCAAAGCTTTGGAAGGCACGGAT
449 AAATCAATAATAAGATTATAAAACTATTTAAAACAACTAACAAAGCTTTCAAAGGCACGGAT
* * * * *
3717 GGCTATAAATAGATTTTTCTTGCTAATGAATGGCTTTTTCTTCACGTTTCCTAAAACAGACATTC
1 GACTATAAATAGACTTTTCTTGCCAATAAATAGCTTTTTCTTCACGTTTCCTAAAACAGACATTC
*** * * *
3782 AGTTATGATATATTTTAAGTAAAAATGTAAAAAAATTCAACTTAAAATTAATTATAAGATTATAA
66 AAACATGATCTATTTTAAGTAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * *
3847 AACCATTTGAAGTGAGTAATAAGGCTTTAAAAGGCATGGATGACTATAAATGGACTTTTTTTGCC
130 AACCATTTAAAGTGAGTAATAAGGCTTT-AAAGGCATGGATGATTAT-AATAGACTTTTCTTGCT
* * *
3912 AATGGATGGCTTTTACATCACATTTCC-CAAGATAAACATTTAATTATAATATATTTTAA-TAAA
193 AATGGATGGCTTTTGCATCACATTTCCTAAAG-TAAACATTGAATTATAATATATTTTAACTAAA
3975 AAATGTAAAATAAATGTAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGC-AATTAAT
257 AAA-GTAAAA-AAATGTAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGCTAATT-AT
** *
4039 AAAGCTTCTAAAGGCATGGGTGACTACAAATGGACTTTTTTTACCAAT--ATATGGCTTTTTGC-
319 AAAGCTTAGAAAGGCATGGGTGACTACAAATGGACTTTTGTTACCAATGAATA-GG-TTTTT-CT
* * *
4101 TCATATTTCCTGAGG-TAAACAAT-GAATTTTAACTTGTTTTAACCAAAAATGTAAAAAAATTCA
381 TCATATTT-CTGAGGAAAAACAATAAAATATT-ACTTGTTTTAACCAAAAATGTAAAAAAATTCA
********** * * * * * **
4164 NNNNNNNNNNAATTATGAGATTATAAAACTATTTAAAGCAACTAATAAGGCTTTCAAAGGCTTGG
444 ATTTAAAATCAATAATAAGATTATAAAACTATTTAAAACAACTAACAAAGCTTTCAAAGGCACGG
*
4229 GT
509 AT
* * *
4231 GACTATAAGTAGACTTTTCTTGCCAATAAATAG-TTTTCTCTTCATGTTTTCC-AAGACAGACAT
1 GACTATAAATAGACTTTTCTTGCCAATAAATAGCTTTT-TCTTCACG-TTTCCTAAAACAGACAT
* * * * *
4294 TCAAACATTATCTATTTTAAGCAAAAATGTAAAAGAATTCAACTTAAAATCAGTAAGGAGATTAT
64 TCAAACATGATCTATTTTAAGTAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTAT
* * *
4359 AGAACCATTTAAAGTGAGTAATAAGGTTTTGGAAGGCATGGATGATTATAAGTAGACTTTTCTTG
128 AAAACCATTTAAAGTGAGTAATAAGGCTTT-AAAGGCATGGATGATTATAA-TAGACTTTTCTTG
* * *
4424 CTAATGGATAGCGTTTGCATCACATTTCCTAAAGCAAACATT
191 CTAATGGATGGCTTTTGCATCACATTTCCTAAAGTAAACATT
4466 CNNNNNNNNN
Statistics
Matches: 606, Mismatches: 119, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
508 2 0.00
509 54 0.09
510 11 0.02
511 10 0.02
512 104 0.17
513 61 0.10
514 350 0.58
515 14 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (510 bp):
GACTATAAATAGACTTTTCTTGCCAATAAATAGCTTTTTCTTCACGTTTCCTAAAACAGACATTC
AAACATGATCTATTTTAAGTAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGTGAGTAATAAGGCTTTAAAGGCATGGATGATTATAATAGACTTTTCTTGCTAAT
GGATGGCTTTTGCATCACATTTCCTAAAGTAAACATTGAATTATAATATATTTTAACTAAAAAAG
TAAAAAAATGTAACTTAAAATCAATTATAAAATTATAAAACCATTTAAAGCTAATTATAAAGCTT
AGAAAGGCATGGGTGACTACAAATGGACTTTTGTTACCAATGAATAGGTTTTTCTTCATATTTCT
GAGGAAAAACAATAAAATATTACTTGTTTTAACCAAAAATGTAAAAAAATTCAATTTAAAATCAA
TAATAAGATTATAAAACTATTTAAAACAACTAACAAAGCTTTCAAAGGCACGGAT
Done.