Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399276.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2545.0, 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: 13735
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.28
Warning! 3458 characters in sequence are not A, C, G, or T
Found at i:555 original size:171 final size:171
Alignment explanation
Indices: 1--1485 Score: 855
Period size: 171 Copynumber: 8.7 Consensus size: 171
* * ** * *
1 TTCAACTTAAAATCAATTATGAGACTATAAAACCATTTAAAGTGAGTAATAAGCCTTTCAAAGGT
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* * * * * * * * * * *
66 TTAGGTAACTAT-AATAGACTTTTCTTTCTAATGAATGGCTTTTGCATCATGTTTCCTGAA-GTA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTT-CTCAAGGCA
* * * * * * **
129 GACACTCAATTATAATATATTGTAACAAAAAATGTAAAAATTT
130 AACACTCAATTATAATCTGTTTTAACTAAAAATATAAAAA-AA
* * * *
172 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACCAGTAATAAGGCTTTGGAAA-G
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT-CAAAGG
* ********** * *
236 CATGGGTGAATATAAATGGACTTNNNNNNNNNNTGAAT-AGCTTTTTCTTCATGTTT-TCTATGA
65 CATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGA-CTTTTTCTTCATGTTTCTC-AAGG
* * * * * * *
299 CAGACATTTAAATACAATTTGTTTTAACCAAAAATATAAAAAAA
128 CAAACACTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAA
** ********************** *
343 TTTGACTTAAAATNNNNNNNNNNNNNNNNNNNNNNTTTAAAGTAAGTAATAAGGCTTTCAAAGGC
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* * * * * **
408 ATGGGTGACTATAAATGGACTTTTTTTGCCTATGAATCACGTTTTCTTCACGTTTCTTGAGGCAA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGGCAA
*
473 ACACTCAATTATAATCTGTTTTAACTAAAAATATAAAATAA
131 ACACTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAA
* * * * *
514 TTCAACTTAAAATCAATAATGAGATTATAAAATCATTTAAAGTAAGTAATAAAGCTTTAAAAGGA
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* * * * * *
579 ATGGGTGGCTATAAATGGAC-ATTCTTGTCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGAAA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGGCAA
** *
643 ACACTCAATTATAATCTGTTTTGGCTAAAAATGTAAAAAAATTA
131 ACACTCAATTATAATCTGTTTTAACTAAAAATAT-AAAAAA--A
* * ********** *
687 TTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAANNNNNNNNNNAGGCTTTGAAAGGC
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* ** * * *
752 ATGGGTGACTATAAATGGACTTTTCTTACTTATGAATCA-TGTTTTCTTCATGTTTTTCGAGGCA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACT-TTTTCTTCATGTTTCTCAAGGCA
* *
816 AACACTCAATTATAATCT-ATTT-AGTCAAAAATATAAAAAAA
130 AACACTCAATTATAATCTGTTTTAACT-AAAAATATAAAAAAA
* * * * * * * * **
857 ATCAGCTTAAAATCAATTATGATATTGTAAAACCATTTAGAGCGAGTAATAAAGCTTTGGAAGGC
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* * *
922 ATGGGTGACTATAAATGGACTTCTCTTG-CACTTGAAT-AGTTTTTTCTTCATGTTTC-CTAAGG
66 ATGGGTGACTATAAATGGACTTTTCTTGCCA-ATGAATGA-CTTTTTCTTCATGTTTCTC-AAGG
* * * * * * *
984 TAGA-ATTCAAATATAATCTATTTTAACCAAAAA-AGAAAAAAA
128 CAAACACTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAA
** * * * * * *
1026 TTTGACGT-AAATCAATAATGAGATTATAAAACCATTTGAAGTAAGTAATAAGTCCTCCAAAGGC
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* * ** * * **
1090 ATGAGTGACTATGAATAAACTTTT-TCTGCCAAT-ATATGGCTTTTTCTTCATGTTTCCCAAAAC
66 ATGGGTGACTATAAATGGACTTTTCT-TGCCAATGA-ATGACTTTTTCTTCATGTTTCTCAAGGC
* * * * *
1153 AAACATTCAACTATAAACTATTTTCA-TAAAAAATATAAAAAAA
129 AAACACTCAATTATAATCTGTTTTAACT-AAAAATATAAAAAAA
********** * * ** **
1196 TTCAACTTAAAANNNNNNNNNNGATTATAAAACCATTTCAAGCGAGTAATAAATCTTTGGAAGGC
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
** * * **
1261 ATATGTGGCTATAAATGGACTTTTCTTGCCAATGAAT-AGCTTTTTCTTCATGTTTCTCCAGATA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGA-CTTTTTCTTCATGTTTCTCAAGGCA
* * * *
1325 GACATTCAAATATAATATGTTTTAA-T----A-A-AAAAAAA
130 AACACTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAA
* * * * * * *
1360 TT-GACTTGAAATCAGTAATGAGATTATAAAACCATTTGAAGCAAGTAATAAGGCCTCCAAAGGT
1 TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
* * * * **
1424 ATGGGTGACTACAAATAGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTCAAGG
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGG
1486 TNNNNNNNNN
Statistics
Matches: 976, Mismatches: 305, Indels: 74
0.72 0.23 0.05
Matches are distributed among these distances:
163 91 0.09
164 9 0.01
165 1 0.00
166 1 0.00
167 2 0.00
168 87 0.09
169 53 0.05
170 186 0.19
171 343 0.35
172 73 0.07
173 82 0.08
174 48 0.05
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.33
Consensus pattern (171 bp):
TTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGC
ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGGCAA
ACACTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAA
Found at i:937 original size:170 final size:170
Alignment explanation
Indices: 378--1076 Score: 596
Period size: 170 Copynumber: 4.1 Consensus size: 170
368 NNNNNNNNNN
* * * * *
378 TTTAAAGTAAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTTTTGCCTATGA
1 TTTAAAGCAAGTAATAAAGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTT-CTTATGA
* * *
443 ATCACGTTTTCTTCACGTTTCTT-GAGGCAAACACTCAATTATAATCTGTTTTA-ACTAAAAATA
65 ATCATGTTTTCTTCATGTTT-TTCGAGGCAAACACTCAATTATAATCT-ATTTAGACTAAAAATA
* * *
506 TAAAATAATTCAACTTAAAATCAATAATGAGATTATAAAATCA
128 TAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAATCA
* * * * * * *
549 TTTAAAGTAAGTAATAAAGCTTTAAAAGGAATGGGTGGCTATAAATGGAC-ATTCTTGTCAATGA
1 TTTAAAGCAAGTAATAAAGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTCT-TATGA
* * * * * * * *
613 ATGGC-T-TTTTCTTCATGCTTCTCAAGGAAAACACTCAATTATAATCTGTTTTGGCTAAAAATG
65 AT--CATGTTTTCTTCATGTTTTTCGAGGCAAACACTCAATTATAATCTATTTAGACTAAAAATA
676 TAAAAAAATTATTCAACTTAAAATCAATTATGAGATTATAAAATCA
128 TAAAAAAA--A-TCAACTTAAAATCAATTATGAGATTATAAAATCA
********** *
722 TTTAAANNNNNNNNNNAGGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTACTTATGA
1 TTTAAAGCAAGTAATAAAGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTT-CTTATGA
*
787 ATCATGTTTTCTTCATGTTTTTCGAGGCAAACACTCAATTATAATCTATTTAGTC-AAAAATATA
65 ATCATGTTTTCTTCATGTTTTTCGAGGCAAACACTCAATTATAATCTATTTAGACTAAAAATATA
* * * *
851 AAAAAAATCAGCTTAAAATCAATTATGATATTGTAAAACCA
130 AAAAAAATCAACTTAAAATCAATTATGAGATTATAAAATCA
* * * * *
892 TTTAGAGCGAGTAATAAAGCTTTGGAAGGCATGGGTGACTATAAATGGACTTCTCTTGCACT-TG
1 TTTAAAGCAAGTAATAAAGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTT-C-TTATG
* * * * * * * *
956 AAT-AGTTTTTTCTTCATG-TTTCCTAAGGTAGA-ATTCAAATATAATCTATTTTA-ACCAAAAA
64 AATCA-TGTTTTCTTCATGTTTTTC-GAGGCAAACACTCAATTATAATCTA-TTTAGACTAAAAA
* * ** * * *
1017 -AGAAAAAAATTTGACGT-AAATCAATAATGAGATTATAAAACCA
126 TATAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAATCA
* *
1060 TTTGAAGTAAGTAATAA
1 TTTAAAGCAAGTAATAA
1077 GTCCTCCAAA
Statistics
Matches: 423, Mismatches: 88, Indels: 37
0.77 0.16 0.07
Matches are distributed among these distances:
168 36 0.09
169 35 0.08
170 164 0.39
171 48 0.11
172 2 0.00
173 84 0.20
174 53 0.13
175 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
TTTAAAGCAAGTAATAAAGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTCTTATGAA
TCATGTTTTCTTCATGTTTTTCGAGGCAAACACTCAATTATAATCTATTTAGACTAAAAATATAA
AAAAAATCAACTTAAAATCAATTATGAGATTATAAAATCA
Found at i:2244 original size:170 final size:168
Alignment explanation
Indices: 1815--2572 Score: 501
Period size: 171 Copynumber: 4.5 Consensus size: 168
1805 AAGCAGACAT
* * * * * * * *
1815 TCAAATATAACCTATTTTAATAAAAAATATAAAAAAATT-AACTAAAAATCAATAATGAGATTAT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGT
* * * * *
1879 TAAACCATTTAAAGCGAGTAATAAAGCTTTGGAAGGTATG-GATGGCTATAAATGGACTTTTCTT
66 AAAACCATTTAAAGCGAGTAATAAGGCTTTGAAAGGCATGAG-TGACTATAAATGGACTTTTCTT
********* ** *
1943 GCCNNNNNNNNNNTTTTTCTTCATGTTTC-CTAAGGTAAACAT
130 G-C--TATGAATCATTTTCTTCATGTTTCTC-AAGACAAACAC
* * * * * ***********
1985 TCAATTATAATTTGTTTTAACTAAAAATATAAAAAAATTTAATTTAAAATCAANNNNNNNNNNAT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGT
*
2050 AAAACTATTTAAAGCGAGTAATAAGGCTTTGAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
66 AAAACCATTTAAAGCGAGTAATAAGGCTTTGAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
2115 CCTATGAATCATATTTCTTTCATGTTTCTCAAGACAAACAC
131 -CTATGAATCAT-TTTC-TTCATGTTTCTCAAGACAAACAC
* * * * ***
2156 TCAATTGTAATCTGTTCTAAC-CAAAATATAAAAAAATTCAACTTAAAATTTTTTATGAGATTGT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGT
* *
2220 AAAACCATTTAAAGCGAGTAATAAGACTTTGAAAGGCAT-AATGGACTATAAATGGA-TATTTCT
66 AAAACCATTTAAAGCGAGTAATAAGGCTTTGAAAGGCATGAGT-GACTATAAATGGACT-TTTCT
* * * * *
2283 TGGCAACGATTGGC-TTCTTCTTCATGTTTCTCGAGGTCAATACA-
129 T-GCTATGAAT--CATT-TTCTTCATGTTTCTC-AAGACAA-ACAC
* * * * ********** *
2327 T-AATTATAATCTATTTTCACTAAAAATGTAAAGAAATTCAACTTAAAATCNNNNNNNNNNTTAT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGT
* ** * *
2391 AAAATCATTTAAAGCGAGTAATATTGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTGTTG
66 AAAACCATTTAAAGCGAGTAATAAGGCTTTGAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * *
2456 CTAATGAATGACTTTTTCTTCATATTT-TCCGAGGCAACCAC
131 CT-ATGAAT--CATTTTCTTCATGTTTCT-CAAGACAAACAC
* * *
2497 TCAATTATATTCTGTTTTGACAAAAAATGTAAAAAAATTCAACTTAATATCAATTATGAGATTGT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGT
*
2562 AAAACTATTTA
66 AAAACCATTTA
2573 NNNNNNNNNN
Statistics
Matches: 449, Mismatches: 118, Indels: 41
0.74 0.19 0.07
Matches are distributed among these distances:
169 6 0.01
170 160 0.36
171 273 0.61
172 10 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.34
Consensus pattern (168 bp):
TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTGT
AAAACCATTTAAAGCGAGTAATAAGGCTTTGAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
CTATGAATCATTTTCTTCATGTTTCTCAAGACAAACAC
Found at i:4245 original size:171 final size:170
Alignment explanation
Indices: 3924--4642 Score: 479
Period size: 171 Copynumber: 4.2 Consensus size: 170
3914 NNNNNNNNNN
* * * * * * *
3924 AGTCCATTTATAGCCACCCATGCCTTTC-AAAGCTTTA-TTACTCGCTTTAAATGGCTTTATAAT
1 AGTCCATTTATAGTCACCCACGCC-TTCAAAAGC-CTACTTGCTCCCTCTAAATGGTTTTATAAT
* * * * * * * * *
3987 CTCATTATTGATTTTGAGATGGATTTTTTTATATTTTTTATTAAAATAGTTTATATTTGAATGTC
64 CTCATAATTAATTTTGAG-TAGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAGTGTT
*
4052 TGCCTTG-GAAAACATAAAGAAAAAGCCATTCATTGATAAGAAA
128 TGCCTTGAG-AAACATGAAGAAAAAGCCATTCATTGATAAGAAA
* * * ********** *
4095 AGTCCACTTATAGTCACCCATGCCTTCCAAAGCCTNNNNNNNNNNTCTAAATGGTTTTACAATCT
1 AGTCCATTTATAGTCACCCACGCCTTCAAAAGCCTACTTGCTCCCTCTAAATGGTTTTATAATCT
* * *
4160 CATAATTAATTTTGAGTAGAAATTTTTTATATTTTTAATTAAAACAGATTATAGTTGAGTGTTTT
66 CATAATTAATTTTGAGTAG-AATTTTTTATATTTTTTATTAAAACAGATTATAATTGAGTGTTTG
* * *
4225 CCTTGAGAAACGTGAAGAAAACATG--ATTTATTGACAAGAAA
130 CCTTGAGAAACATGAAGAAAA-A-GCCATTCATTGATAAGAAA
* ** * *
4266 AGTCCATTTATAATCATGCACGCCTTCAAAAGCCTACTTGCTCCCTTTAAATGGTTCTATAATCT
1 AGTCCATTTATAGTCACCCACGCCTTCAAAAGCCTACTTGCTCCCTCTAAATGGTTTTATAATCT
* * * * * *
4331 CATAATTAATTTTAAGTTGAATTGTTTTTTCATTTTTTGTCAAAACAGATTGTAATTGAGTGTTT
66 CATAATTAATTTTGAGTAGAATT-TTTTAT-ATTTTTTATTAAAACAGATTATAATTGAGTGTTT
* *
4396 GCCTTAAGAAGCATGAAGAAAAAGCCATTCATT-AGTAAGAAA
129 GCCTTGAGAAACATGAAGAAAAAGCCATTCATTGA-TAAGAAA
* ********** * * * * *
4438 AGTCCATTTATAGCCNNNNNNNNNNTCCAAAGCTTTA-TTACTCGCT-TACATGGTTTTATAATC
1 AGTCCATTTATAGTCACCCACGCCTTCAAAAGC-CTACTTGCTCCCTCTAAATGGTTTTATAATC
* * * * * *
4501 TCATTATTGATTTTGAGATA-AATTTTTT-TACATTTTTAGTTAAAATAGATTATATTTGAATGT
65 TCATAATTAATTTTGAG-TAGAATTTTTTATA-TTTTTTA-TTAAAACAGATTATAATTGAGTGT
* * * * * *
4564 CTGCCTTG-GAAAACATAAAGAAAAAGTCATTAATTGACAAGAGA
127 TTGCCTTGAG-AAACATGAAGAAAAAGCCATTCATTGATAAGAAA
* * * * *
4608 AGTTCACTTATAGTCACTCATGCCTTCCAAAGCCT
1 AGTCCATTTATAGTCACCCACGCCTTCAAAAGCCT
4643 TATTACTCGC
Statistics
Matches: 417, Mismatches: 114, Indels: 36
0.74 0.20 0.06
Matches are distributed among these distances:
168 1 0.00
169 8 0.02
170 86 0.21
171 230 0.55
172 89 0.21
173 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.37
Consensus pattern (170 bp):
AGTCCATTTATAGTCACCCACGCCTTCAAAAGCCTACTTGCTCCCTCTAAATGGTTTTATAATCT
CATAATTAATTTTGAGTAGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAGTGTTTGC
CTTGAGAAACATGAAGAAAAAGCCATTCATTGATAAGAAA
Found at i:10064 original size:171 final size:170
Alignment explanation
Indices: 8740--10132 Score: 992
Period size: 170 Copynumber: 8.2 Consensus size: 170
8730 NNNNNNNNNN
* * * * *
8740 AAAGCCTTATTACTCGCTTTAAATGATTTTATAATTTCATAATTGATTTTAAG-TCAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTAATTTT-AGTTGAA-TTTTTT
* * *
8804 TACA-TTTTAGTTAAAAAAGACTATAATTGAATGTCGACCTTGAGAAACATGAAGAAACAA-GCA
64 TACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAA-AAGGCA
* * * *
8867 TTCATTAGCAAA-AAAAGT-CTATTTATAGTCTCCTATTCTTTCA
128 TTCATT-GGAAAGAAAAGTAC-ATTTATAGTCACCCATTCCTTCA
* * ********** * *
8910 AAATCCTTATTACTCGCTTTAAATGATTTTATNNNNNNNNNNTTGATTTTAGGTTCAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTAATTTTA-GTTGAA-TTTTTT
* * * * * * * **
8975 TACATTATTAGTTCAAACTGATTATAATTGAATGTCGACCTTGTGAAATGTGAAGAAAAAGGCAT
64 TACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCAT
* * *******
9040 TCATTGGCAAGAAAAGT-CTATTTGTAGTCACCCATNNNNNNN
129 TCATTGGAAAGAAAAGTAC-ATTTATAGTCACCCATTCCTTCA
*** * * * * * *
9082 NNNGCCTTATTACTCGCTTTAAATGGTTTTAGAATATTGAAAA-TGATTTGAAGTTG-ATTTTGT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT-CTCAAAATTAATTT-TAGTTGAATTTTTT
** * ** * * * *
9145 TACATTTTTTATTAAAACAAACTATAATTGAATGTCTGGCTCGAAAAACGTGAAGAAACAA-GTA
64 TACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAA-AAGGCA
* * * * * * *
9209 TTCATTGAAAAGAAAAGAATATTTATACTCTCCTATTCCTTCG
128 TTCATTGGAAAGAAAAGTACATTTATAGTCACCCATTCCTTCA
* * * * * * *
9252 AAACCCTTATTACTCGCTTTAAATAGTTTTAGAATATCGAAAA-TGATTTGAAGTTG-ATTTTGT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC-AAAATTAATTT-TAGTTGAATTTTTT
* * ** *
9315 TACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGA-CTCGAAAAAGGTGAAGAAACAA-GT
64 TACATTTTTGGTTAAAACAGACTATAATTGAATGTCT-ACCTTGAGAAACATGAAGAAA-AAGGC
* * * * *
9378 ATTCATTGGAAAGAAAAGTATATTTATACTCTCCTATTCCTTCG
127 ATTCATTGGAAAGAAAAGTACATTTATAGTCACCCATTCCTTCA
* * * *
9422 AAAGCCTTATTACTCGCTTTAATTCGTTTTATAATCT-AATAATTGATTTTAGTAGAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAA-AATTAATTTTAGTTGAATTTTTTT
* * * * * * *
9486 ACATTTTT-ATTAAAACAGACAATAATCGTATGTCTACCTTGAGAAACACGAAGAGAAAGGCAGT
65 ACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATT
* * * * * *
9550 CGTTGGTAAGAAAAGTTCATTTATTGTCAACCATTCCTTTA
130 CATTGGAAAGAAAAGTACATTTATAGTCACCCATTCCTTCA
* **********
9591 AAAGTCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTANNNNNNNNNNAAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTA-ATTTTAGTTGAATTTTTTT
* * ** * **
9656 ATATTTCTCATTAAAACAGACTATAATTGAATGTCTACCTCG-GTAAACATGAAGAAAAACACAT
65 ACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAG-AAACATGAAGAAAAAGGCAT
** * * *
9720 TCATTTAAAAGAGAAA-TCCATTTATAGTCTCCCATTCTTTCA
129 TCATTGGAAAGA-AAAGTACATTTATAGTCACCCATTCCTTCA
* *
9762 AAAGCCTTATTACT--C--TAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTAATTTT-AGTTGAA--TTTTT
* * * * * ** *
9823 TTACTTTTTTAGTGAAAACAGATTATAATTGAATGTTTAAGTTGAGAAACATGAAGAAAAAGGTA
63 TTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCA
* *
9888 TTCATTGGCAAGAAAAGTACATTTATTGTCACCCATTCCTTCA
128 TTCATTGGAAAGAAAAGTACATTTATAGTCACCCATTCCTTCA
********** *
9931 AAAGCCTTATTACTCGCTTTAAATGGNNNNNNNNNNTCATAATTAATTTTAGGTTGAATTTTTTT
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTAATTTTA-GTTGAATTTTTTT
* * *
9996 ACATTTTTGGTTAGAACAGACTATAATTGAATGTCTACGTTGAGAAATATGAAGAAAAAGGCATT
65 ACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATT
* ** * * *
10061 CATTAGCCAGAAAAGTCCATTTATAGTAACTCATTCCTTCA
130 CATTGGAAAGAAAAGTACATTTATAGTCACCCATTCCTTCA
* *
10102 AAAGCCTTATTACTCGTTTTAAATAGTTTTA
1 AAAGCCTTATTACTCGCTTTAAATGGTTTTA
10133 NNNNNNNNNN
Statistics
Matches: 965, Mismatches: 227, Indels: 61
0.77 0.18 0.05
Matches are distributed among these distances:
167 28 0.03
168 8 0.01
169 216 0.22
170 343 0.36
171 231 0.24
172 114 0.12
173 25 0.03
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.37
Consensus pattern (170 bp):
AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTAATTTTAGTTGAATTTTTTTA
CATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCATTC
ATTGGAAAGAAAAGTACATTTATAGTCACCCATTCCTTCA
Found at i:11516 original size:171 final size:161
Alignment explanation
Indices: 11159--11572 Score: 314
Period size: 171 Copynumber: 2.4 Consensus size: 161
11149 NNNNNCTTGA
** * * *
11159 GAAACATGAAGAAAAAGGTAGTCATT-AGCAGGAAAAGTTTATTTATAGTCACTCATTCCTTTAA
1 GAAACATGAAGAAAAAACTATTCATTAAG-AAGAAAAG-TTATTTATAGTCACTCATTCCTTCAA
* *
11223 AATCCTTATTACTCACTTTAAAAGGTTTTATAATCTCATNNNNNNNNNNAAGCTGAATTTTTTTA
64 AACCCTTATTACTCACTTTAAAAGGTTTTATAATCTCAT---------AAAGCTGAATTTTTTTA
* * * * *
11288 CATTTTTCGTTAAAACAAGCTATAATTGAATATTAACTTTAT
120 CATTTTTCATTAAAACAAGATATAATTGAATACTAACTTCAG
* ** *
11330 GAAACATGAAGAAAAAGGC-ATTCATTGTGAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA
1 GAAACATGAAGAAAAA-ACTATTCATTAAGAAGAAAAGT-TATTTATAGTCACTCATTCCTTCAA
* * * *
11394 AACCCTTATTACTCATTTTAAATGGTTTTATAATCTCATANNNNNNNNNNAGTTGAATTTTTTTA
64 AACCCTTATTACTCACTTTAAAAGGTTTTATAATCTCATA---------AAGCTGAATTTTTTTA
* * *
11459 CATTTTTTATTAAAACAA-ATAATAATTGAATCCCTGAC-TCAG
120 CATTTTTCATTAAAACAAGAT-ATAATTGAAT-ACTAACTTCAG
** * * *
11501 GAAATGTGTAGAAAAAACTATTCATTAAGAAAAAAAGTTCATTTACAGTCACTCATTCCTTCAAA
1 GAAACATGAAGAAAAAACTATTCATTAAGAAGAAAAGTT-ATTTATAGTCACTCATTCCTTCAAA
*
11566 AGCCTTA
65 ACCCTTA
11573 NNNNNNNNNN
Statistics
Matches: 197, Mismatches: 30, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
170 4 0.02
171 188 0.95
172 5 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.34
Consensus pattern (161 bp):
GAAACATGAAGAAAAAACTATTCATTAAGAAGAAAAGTTATTTATAGTCACTCATTCCTTCAAAA
CCCTTATTACTCACTTTAAAAGGTTTTATAATCTCATAAAGCTGAATTTTTTTACATTTTTCATT
AAAACAAGATATAATTGAATACTAACTTCAG
Found at i:11869 original size:513 final size:491
Alignment explanation
Indices: 10933--11901 Score: 1024
Period size: 513 Copynumber: 1.9 Consensus size: 491
10923 GTTAATTTTG
*
10933 AGTTGAATTTTTTTACATTTTTCATTAAAACAAACAATAATTGAATCCCTGACTTAGGAAATGTG
1 AGTTGAATTTTTTTACATTTTTCATTAAAACAAACAATAATTGAATCCCTGACTCAGGAAATGTG
* * * **********
10998 TAGAAAAAACTATTCATTGAGAAGAAAAGTTCATTTATAGTCACCCANNNNNNNNNNAGCCTTAT
66 TAGAAAAAACTATTCATTAAGAAAAAAAGTTCATTTACAGTCACCCATTCCTTCAAAAGCCTTAT
* * *
11063 TACTCGCTTTCAATGGTTTTATAATCTCATGATTGATTTTAAGTCATTGTTTTACACTTTTGATT
131 TACTCGCTTTAAATAGTTTTATAATCTCATGATTGATTTTAAGTCATTATTTTACACTTTTGATT
*
11128 AAAACAGATAATAATTNNNNNNNNNNCTTGAGAAACATGAAGAAAAAGGTAGTCATTAGCAGGAA
196 AAAACAGATAATAATT----------CTTGAGAAACATGAAGAAAAAGGTAGTCATTAGCAAGAA
* * *
11193 AAGTTTATTTATAGTCACTCATTCCTTTAAAATCCTTATTACTCACTTTAAAAGGTTTTATAATC
251 AAGTTCATTTATAGTCACTCATTCCTTTAAAACCCTTATTACTCACTGTAAAAGGTTTTATAATC
********** *
11258 TCATNNNNNNNNNNAAGCTGAATTTTTTTACATTTTTCGTTAAAACAAGCTATAATTGAATATTA
316 TCATAATTGATTTTAAGCTGAATTTTTTTACATTTTTCGTTAAAACAAACTATAATTGAATATTA
* *
11323 ACTTTATGAAACATGAAGAAAAAGGCATTCATTGTGAAGAAAAGTCTATTTATAGTCACCCATTC
381 ACCTTATGAAACATGAAGAAAAAGGCATTCATTGTCAAGAAAAGTCTATTTATAGTCACCCATTC
11388 CTTCAAAACCCTTATTACTCATTTTAAATGGTTTTATAATCTCATA
446 CTTCAAAACCCTTATTACTCATTTTAAATGGTTTTATAATCTCATA
* *
11434 NNNNNNNNNNAGTTGAATTTTTTTACATTTTTTATTAAAACAAATAATAATTGAATCCCTGACTC
1 ----------AGTTGAATTTTTTTACATTTTTCATTAAAACAAACAATAATTGAATCCCTGACTC
*
11499 AGGAAATGTGTAGAAAAAACTATTCATTAAGAAAAAAAGTTCATTTACAGTCACTCATTCCTTCA
56 AGGAAATGTGTAGAAAAAACTATTCATTAAGAAAAAAAGTTCATTTACAGTCACCCATTCCTTCA
********** *
11564 AAAGCCTTANNNNNNNNNNTAAATAGTTTTATAATCTCATGATTGATTTTAAGTTATATTATTTT
121 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATGATTGATTTTAAG-T-CATTATTTT
11629 ACACTTTTGATTAAAACAGATAATAATTNNNNNNNNNNCTTGAGAAACATGAAGAAAAAGGTAGT
184 ACACTTTTGATTAAAACAGATAATAATT----------CTTGAGAAACATGAAGAAAAAGGTAGT
* *
11694 CATTGGCAAGAAAAGTTCATTTATAGTTAC-CTATTCCTTTAAAACCCTTATTAC-CTACTGTAA
239 CATTAGCAAGAAAAGTTCATTTATAGTCACTC-ATTCCTTTAAAACCCTTATTACTC-ACTGTAA
* ********** * *
11757 ATGGTTTTATAATCTCATAATTGATTTTAANNNNNNNNNNTTTATATTTTTGGTTAAAACAAACT
302 AAGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTTCGTTAAAACAAACT
* *
11822 ATAATTGAATATTTACCTTATGAAAGATGAAGAAAAAGGCATTCATTGTCAAGAAAAGTCTATTT
367 ATAATTGAATATTAACCTTATGAAACATGAAGAAAAAGGCATTCATTGTCAAGAAAAGTCTATTT
*
11887 ATAGTCACCTATTCC
432 ATAGTCACCCATTCC
11902 NNNNNNNNNN
Statistics
Matches: 388, Mismatches: 66, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
511 144 0.37
512 3 0.01
513 241 0.62
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.35
Consensus pattern (491 bp):
AGTTGAATTTTTTTACATTTTTCATTAAAACAAACAATAATTGAATCCCTGACTCAGGAAATGTG
TAGAAAAAACTATTCATTAAGAAAAAAAGTTCATTTACAGTCACCCATTCCTTCAAAAGCCTTAT
TACTCGCTTTAAATAGTTTTATAATCTCATGATTGATTTTAAGTCATTATTTTACACTTTTGATT
AAAACAGATAATAATTCTTGAGAAACATGAAGAAAAAGGTAGTCATTAGCAAGAAAAGTTCATTT
ATAGTCACTCATTCCTTTAAAACCCTTATTACTCACTGTAAAAGGTTTTATAATCTCATAATTGA
TTTTAAGCTGAATTTTTTTACATTTTTCGTTAAAACAAACTATAATTGAATATTAACCTTATGAA
ACATGAAGAAAAAGGCATTCATTGTCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAACC
CTTATTACTCATTTTAAATGGTTTTATAATCTCATA
Found at i:13026 original size:171 final size:171
Alignment explanation
Indices: 12645--13430 Score: 590
Period size: 171 Copynumber: 4.6 Consensus size: 171
12635 NNNNNNNNNN
* *
12645 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTGTAATCTCATAATTGATTTTGAA-TTGAA-A
1 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTT-AAGTTGAATT
* ** * ** ** *
12708 TTTTGCATTTTTGGTTAAAACAAACTATAATTGAATGTCTTCCTTGAGAAACATGAAGAAAAAAG
65 TTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTGGCTCAAGAAACATGAAGAAAAAAC
* * * * *
12773 TATTCACTA-TCAAGAAAAGTCTATTTATAGTCACCCATTCT
130 TATTCATTAGACAACAAAAGTCTATTTACAGTCACCCATTCC
********** *
12814 TTCAAAAGCCTTANNNNNNNNNNTAAATGGTTTTATAATCTCATAATTGATTTTCAGTTGAATTT
1 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT
* * ** *
12879 TTATACTTTTTTCATTAAAACAAACTATAATTGAATGCCTGGCTCAAAAAATGTGCAGAAAAAAC
66 TT-TACATTTTTCATTAAAACAAACTATAATTGAATGCCTGGCTCAAGAAACATGAAGAAAAAAC
* * **
12944 TATTCTTTGAGACAA-AAAGGTC-ATTTACAGTCACTTATTCC
130 TATTCATT-AGACAACAAAAGTCTATTTACAGTCACCCATTCC
* * * *
12985 TTCAAAAGCCTTATTACTCGTTTTAAATAGTTTTCTAATCTCATAATTAATTTTGAGTTGAATGT
1 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT-T
* * ** **
13050 TTTTACATTTTT-AGTTTAAAA-AGACTATAATTGAATGTCTATCTTGAGAAACATGAAGAAAAA
65 TTTTACATTTTTCA--TTAAAACAAACTATAATTGAATGCCTGGCTCAAGAAACATGAAGAAAAA
*
13113 GAC-ATTCATT-GACAACAAAAGTCTATTTATAGTCACCCATTCC
128 -ACTATTCATTAGACAACAAAAGTCTATTTACAGTCACCCATTCC
********************
13156 TTCAAAAGCCTTANNNNNNNNNNNNNNNNNNNNTATAATCTCATAATTGATTTTAAGTTGAATTT
1 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TT
* * * ** * *
13221 TTTTACTTTTTTCATTAAAACAGATTATAATTGAATGCCTGGCTCAAGAAATGTGTAGAAAAAAT
65 TTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTGGCTCAAGAAACATGAAGAAAAAAC
* *
13286 TATTCATT--ACGAAGAAATG-CTAATTTACAGTCACCCATTCC
130 TATTCATTAGAC-AACAAAAGTCT-ATTTACAGTCACCCATTCC
* * * * * *
13327 TTTAAAAGCCTTATTATTCGCTTTAAATGATTTTATAATCTCTTAATTTATTTTAAGTTGAATTT
1 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA---
* * *
13392 TTTTTTTCATTTTT-AGTTTAAACAGACTATAATTGAATG
63 TTTTTTACATTTTTCA-TTAAAACAAACTATAATTGAATG
13431 TCTATCTTGA
Statistics
Matches: 468, Mismatches: 129, Indels: 36
0.74 0.20 0.06
Matches are distributed among these distances:
168 1 0.00
169 53 0.11
170 21 0.04
171 334 0.71
172 22 0.05
173 37 0.08
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (171 bp):
TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT
TTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTGGCTCAAGAAACATGAAGAAAAAACT
ATTCATTAGACAACAAAAGTCTATTTACAGTCACCCATTCC
Found at i:13275 original size:342 final size:330
Alignment explanation
Indices: 12645--13441 Score: 861
Period size: 342 Copynumber: 2.3 Consensus size: 330
12635 NNNNNNNNNN
* * * *
12645 TTCAAAAGCCTTATTACTCGTTTTAAATGGTTTTGTAATCTCATAATTGATTTTGAATTGAA-AT
1 TTCAAAAGCCTTATTACTCGTTTTAAAT-GTTTTATAATCTCATAATTAATTTTGAGTTGAATTT
* * *
12709 TTTGCATTTTT-GGTTAAAACAAACTATAATTGAATGTCT-TCCTTGAGAAACATGAAGAAAAAA
65 TTTACATTTTTAGTTTAAAA-AGACTATAATTGAATGTCTAT-CTTGAGAAACATGAAGAAAAAA
* * *
12772 GTATTCACTATCAAGAAAAGTCTATTTATAGTCACCCATTCTTTCAAAAGCCTTANNNNNNNNNN
128 GCATTCACTATCAACAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTA----------
*
12837 TAAATGGTTTTATAATCTCATAATTGATTTTCAGTTGAATTTTTATACTTTTTTCATTAAAACAA
183 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTATACTTTTTTCATTAAAACAA
* *
12902 ACTATAATTGAATGCCTGGCTCAAAAAATGTGCAGAAAAAACTATTCTTTGA-GACA-AAAAGGT
248 ACTATAATTGAATGCCTGGCTCAAAAAATGTGCAGAAAAAACTATTCATT-ACGA-AGAAAAGCT
* **
12965 CATTTACAGTCACTTATTCC
311 AATTTACAGTCACCCATTCC
*
12985 TTCAAAAGCCTTATTACTCGTTTTAAATAGTTTTCTAATCTCATAATTAATTTTGAGTTGAATGT
1 TTCAAAAGCCTTATTACTCGTTTTAAAT-GTTTTATAATCTCATAATTAATTTTGAGTTGAAT-T
13050 TTTTACATTTTTAGTTTAAAAAGACTATAATTGAATGTCTATCTTGAGAAACATGAAG-AAAAAG
64 TTTTACATTTTTAGTTTAAAAAGACTATAATTGAATGTCTATCTTGAGAAACATGAAGAAAAAAG
*
13114 ACATTCATTGA-CAACAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTANNNNNNNNN
129 -CATTCACT-ATCAACAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTA---------
********** *
13178 NNNNNNNNNNNTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTTTTTTCATTAAAACA
183 -TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTATACTTTTTTCATTAAAACA
* * * * * *
13243 GATTATAATTGAATGCCTGGCTCAAGAAATGTGTAGAAAAAATTATTCATTACGAAGAAATGCTA
247 AACTATAATTGAATGCCTGGCTCAAAAAATGTGCAGAAAAAACTATTCATTACGAAGAAAAGCTA
13308 ATTTACAGTCACCCATTCC
312 ATTTACAGTCACCCATTCC
* * * * * *
13327 TTTAAAAGCCTTATTATTCGCTTTAAATGATTTTATAATCTCTTAATTTATTTTAAGTTGAATTT
1 TTCAAAAGCCTTATTACTCGTTTTAAATG-TTTTATAATCTCATAATTAATTTTGAGTTGAA---
* *
13392 TTTTTTTCATTTTTAGTTTAAACAGACTATAATTGAATGTCTATCTTGAG
62 TTTTTTACATTTTTAGTTTAAAAAGACTATAATTGAATGTCTATCTTGAG
13442 NNNNNNNNNN
Statistics
Matches: 401, Mismatches: 44, Indels: 20
0.86 0.09 0.04
Matches are distributed among these distances:
340 58 0.14
341 9 0.02
342 277 0.69
343 9 0.02
344 47 0.12
345 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (330 bp):
TTCAAAAGCCTTATTACTCGTTTTAAATGTTTTATAATCTCATAATTAATTTTGAGTTGAATTTT
TTACATTTTTAGTTTAAAAAGACTATAATTGAATGTCTATCTTGAGAAACATGAAGAAAAAAGCA
TTCACTATCAACAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATAAATGGTTTTAT
AATCTCATAATTGATTTTAAGTTGAATTTTTATACTTTTTTCATTAAAACAAACTATAATTGAAT
GCCTGGCTCAAAAAATGTGCAGAAAAAACTATTCATTACGAAGAAAAGCTAATTTACAGTCACCC
ATTCC
Done.