Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398899.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2181.0, 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: 15414
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.31
Warning! 2074 characters in sequence are not A, C, G, or T
Found at i:3187 original size:171 final size:158
Alignment explanation
Indices: 3010--3320 Score: 333
Period size: 169 Copynumber: 1.9 Consensus size: 158
3000 TAGGCTTTTA
* * *
3010 AAGGAATAGGTAACTATAAATGGA-CTTCTCTTGCTAGTGAATGTCTTTTTCTTCATATTTCTTG
1 AAGGAATAGGTAACTATAAATGGACCTT-TCTTGCTAATGAA--TCTTTTTCTTCACATTTCTCG
* * *
3074 AGGCAAACATTCAATTATAGTCTGCTT-TAACTAAAAATGTGAAAA-AAGTT-AACTTAATATCA
63 AGACAAACATTCAATTATAATCTG-TTCTAAC-AAAAATGT-AAAAGAA-TTCAACTTAAAATCA
* *
3136 ATTATGAGATTATAAAATCATTTAAAGCAAGNNNNNNNNNNTTTG
124 ATTATCAAATTATAAAATCATTTAAAGCAAG----------TTTG
* * *
3181 AAGGAATGGGTGACTATAAATGGACCTTTCTTGCTAATGAATCTTTTTTTTCACATTTCTCGAGA
1 AAGGAATAGGTAACTATAAATGGACCTTTCTTGCTAATGAATCTTTTTCTTCACATTTCTCGAGA
*
3246 CAAACATTCAATTATAATCTGTTCTAACAAAAATGTAAAAGAATTCAACTTAAAATCAATTTTCA
66 CAAACATTCAATTATAATCTGTTCTAACAAAAATGTAAAAGAATTCAACTTAAAATCAATTATCA
3311 AATTATAAAA
131 AATTATAAAA
3321 CTATTTACAG
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
167 6 0.05
168 37 0.30
169 44 0.35
171 34 0.27
172 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35
Consensus pattern (158 bp):
AAGGAATAGGTAACTATAAATGGACCTTTCTTGCTAATGAATCTTTTTCTTCACATTTCTCGAGA
CAAACATTCAATTATAATCTGTTCTAACAAAAATGTAAAAGAATTCAACTTAAAATCAATTATCA
AATTATAAAATCATTTAAAGCAAGTTTG
Found at i:3696 original size:171 final size:170
Alignment explanation
Indices: 2110--4209 Score: 869
Period size: 171 Copynumber: 12.3 Consensus size: 170
2100 NNNNNNNNNN
* * *
2110 AATTATGAGATTATAAAACCATTTAAAGGGAGTAGTAAGGCTTTTGAAGGAATAGGTGGCTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
** * *** * *
2175 ATAGACTTTTCTTGTCAATTAAAAAACTTTTTCTTCATG-TTTCTC-AAGGTAGATATTCAATTA
66 ATAGACTTTTCTTACCAA-TGAATGTCTTTTTCTTCATGTTTTC-CGAA-GCAGACATTCAATTA
** * * * * *****
2238 TAGTCTATTTTAACTAAAAATAT-GAAAAATTTAACTTANNNNN
128 TAACCT-GTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATT
***** * ** *
2281 NNNNNTGAGATTATAAAACCATTTAAAACTCGTAATAAGGCTTTTGAAGGAATAGGTGGCTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * * * * *
2346 AT-GAAATTTTCTTATCAATGAATAGT-TTTTT-TTCATGTTTTTCGAGGTAAATATTCAATTAT
66 ATAG-ACTTTTCTTACCAATGAAT-GTCTTTTTCTTCATGTTTTCCGAAGCAGACATTCAATTAT
* * *
2408 AGCCTGTTT--CTAAGAAACTGTAAAAAGATTCAACTTAGAATT
129 AACCTGTTTAACTAA-AAA-TGTAAAAAAATTCAACTTAAAATT
* * * * * * *
2450 AATTATGAGATTATAAAACCATTTAAAGTGAGTAACATGGCATTTGACGGGATTGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * *
2515 AT-GAGCATTTCTTACCAATGAATGCCTTCTTCTTCATGTTTCCCGAAGCCA-ACATTCAATTAT
66 ATAGA-CTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTTCCGAAG-CAGACATTCAATTAT
** * * * * *******
2578 AATTTTTTTTACTAAAAATGTAAAAATATTCAAATNNNNNNN
129 AACCTGTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATT
*** * * * * *
2620 NNNTATGTGATTATAAAACCATCTAAAGCGAGTAATAAGGCTTTTGAAGG-CTTGAGTGAATATA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GTGACTATA
* * * * * * * * *
2684 AACACACTTTT-TACACCAAT-AGATGACTTTTGCTTTATG-TTTCCCAGGGCAGACATTCAATC
65 AATAGACTTTTCT-TACCAATGA-ATGTCTTTTTCTTCATGTTTTCCGA-AGCAGACATTCAATT
* * * *
2746 ATAACATATTATAA-TCAAAACTGTCAAAAAATTTC-ACTTAAAATT
127 ATAACCTGTT-TAACT-AAAAATGT-AAAAAAATTCAACTTAAAATT
* **********
2791 AATTATGAGATTATAAAACCATTTAAAGTGAGTAANNNNNNNNNNGAAGGAATAGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * * * * *
2856 ATAGACTTTTCTTGCCAATGAATGGCATTTTATTCATGTTCT-CTAAGACAGACATTTAATTATA
66 ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTTCCGAAG-CAGACATTCAATTATA
* * * *
2920 GCCTTTTTTAACCAAAAATGTAAAAAACAAATT-AACTTAAAATC
130 ACC-TGTTTAACTAAAAATGT--AAAA-AAATTCAACTTAAAATT
********** * * *
2964 AATTATGAGATNNNNNNNNNNTTTAAAGCGAGTAATTAGGCTTTTAAAGGAATAGGTAACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * * * * * * *
3029 ATGGACTTCTCTTGCTAGTGAATGTCTTTTTCTTCAT-ATTTCTTGAGGCAAACATTCAATTATA
66 ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTTC-CGAAGCAGACATTCAATTATA
** * * *
3093 GTCTGCTTTAACTAAAAATGTGAAAAAAGTT-AACTTAATATC
130 ACCTG-TTTAACTAAAAATGT-AAAAAAATTCAACTTAAAATT
* * ********** *
3135 AATTATGAGATTATAAAATCATTTAAAGCAAGNNNNNNNNNNTTTGAAGGAATGGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * * * ** *
3200 ATGGACCTTTCTTGCTAATGAA--TCTTTTTTTTCA-CATTTCTCG-AGACAAACATTCAATTAT
66 ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTTC-CGAAG-CAGACATTCAATTAT
* * *
3261 AATCTGTTCTAAC-AAAAATGTAAAAGAATTCAACTTAAAATC
129 AACCTGTT-TAACTAAAAATGTAAAAAAATTCAACTTAAAATT
* * * * * * * * * *
3303 AATTTTCAAATTATAAAACTATTTACAGTGATTAATAAGGCTTTTGAAGGAATGGGTGGCTATAG
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * * * * *
3368 ATAGACTTTTCATATCAACGAATGTCTTTTTCTTTATGTGTCTT--GAGGCATACATTTAATTAT
66 ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGT-T-TTCCGAAGCAGACATTCAATTAT
* * * *
3431 AATCTATTTAAATAAAAAATATAAAAAAATTCAACTTAAAATCT
129 AACCTGTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAAT-T
************************
3475 -ATTATGAGATTATAAAACCANNNNNNNNNNNNNNNNNNNNNNNNGAAGGAATAGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * * *
3539 ATGGACTTTTCTTACCAATGAATGTCTTTTTCTTTATATTTTCCAAAGTAGACATTCAATTATAA
66 ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTTCCGAAGCAGACATTCAATTATAA
*
3604 CCTGTTGTAACTAAAAATGTAAAAAAATTCAACTCAAAATT
131 CCTGTT-TAACTAAAAATGTAAAAAAATTCAACTTAAAATT
* * * **********
3645 AATTACGAGATTATAAAAGCATTTACAGCGAGTAATAAGGCTTTTGAAGGAATNNNNNNNNNNAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
** * * *
3710 ATAGACTTTTCTTACCAATGAAT-TCCTTTTTCTTCACATTTCCCTAAGCAGACATTAAATTATA
66 ATAGACTTTTCTTACCAATGAATGT-CTTTTTCTTCATGTTTTCCGAAGCAGACATTCAATTATA
* * * * *
3774 ATCTGTTCTAACCAAAAATGTAAAAATATTCAACTTGAAATC
130 ACCTGTT-TAACTAAAAATGTAAAAAAATTCAACTTAAAATT
* * *********** * * * *
3816 AATTATGCGAGTATAAAAANNNNNNNNNNGAGTGATAAGGCTTTTGAAAGAATGGGTGATTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
** *
3881 ATAGACTTTTCTT-CCAATGAATG-CATTTTTCTTCATG-TTTCTTAAGGTCA-AAATTCAATTA
66 ATAGACTTTTCTTACCAATGAATGTC-TTTTTCTTCATGTTTTCCGAA-G-CAGACATTCAATTA
* * ********** ** *
3942 TAATCTGTTTTAACCAAANNNNNNNNNNAATTTGACTTAAAATC
128 TAACCTG-TTTAACTAAAAATGTAAAAAAATTCAACTTAAAATT
** * *
3986 AATTATGCA-ATTATAAAACTTTTTAAAGCAAGTAATAAGG-TTTTCGAAGGAATGGGTGACTAT
1 AATTATG-AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-GAAGGAATAGGTGACTAT
* ** * * * * *
4049 AAAT-GAACTTTTCTT-CTCAATTAATCACTTTTTGTACACG-TTTCCAAAGATAGACATTCAAT
64 AAATAG-ACTTTTCTTAC-CAATGAATGTCTTTTTCTTCATGTTTTCCGAAG-CAGACATTCAAT
* * * ** * *
4111 TATAATCTATTTTAAC-AAAACATATGGAAAAACTCAACTTAAATTT
126 TATAACCT-GTTTAACTAAAA-ATGTAAAAAAATTCAACTTAAAATT
* * ** *
4157 AATTATGAGATTGTAAAACGATTTATAA-TAAGTAATAAGGCTTTTAAAGGAAT
1 AATTATGAGATTATAAAACCATTTA-AAGCGAGTAATAAGGCTTTTGAAGGAAT
4210 GGNNNNNNNN
Statistics
Matches: 1404, Mismatches: 456, Indels: 138
0.70 0.23 0.07
Matches are distributed among these distances:
166 4 0.00
167 10 0.01
168 87 0.06
169 180 0.13
170 299 0.21
171 661 0.47
172 44 0.03
173 117 0.08
174 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTTTCCGAAGCAGACATTCAATTATAA
CCTGTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATT
Found at i:5735 original size:171 final size:170
Alignment explanation
Indices: 5541--5927 Score: 404
Period size: 171 Copynumber: 2.3 Consensus size: 170
5531 NNNNNNNNNA
* * * **
5541 GAGTAATAAAGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCATATTAATAAACGT-CTT
1 GAGTAGTAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCATACCAATAAA-GTCCTT
*** * * *
5605 TTTCTTCATATTTCTTGAGGTAGACATTCAATTATAACTTGTTTTAACTAAAAATGTAAAAAAAT
65 TTTCTTCATATTTCCCCAAGCAGACATTCAATTATAACTTGTTTTAACTAAAAATATAAAAAAAT
* *
5670 TCAACTCAAAATCAATTA-CAAGATTATAAAACCATTTACAGC
130 TCAACTCAAAATCAATTAGCAAG--TATAAAAACATTTAAAGC
* * * * *
5712 GAGTAGTAAGGCTTTTAAAGGAAT-ATTTGACTATAAATGAACTTTTCTTACCAATGAATTCCTT
1 GAGTAGTAAGGCTTTTAAAGGAATGA-GTGACTATAAATGGACTTTTCATACCAATAAAGTCCTT
* * * * * *
5776 TTTCTTCATGTTTCCCCAAGCAGACATTTAATTATAATTTGTTTTAATTAAAAATATAAATATAT
65 TTTCTTCATATTTCCCCAAGCAGACATTCAATTATAACTTGTTTTAACTAAAAATATAAAAAAAT
* * *
5841 TCAACTTAAAATCAATTATGCAAGTATAAAAATATTTAAAGT
130 TCAACTCAAAATCAATTA-GCAAGTATAAAAACATTTAAAGC
* * * * *
5883 GAGT-GACAAGGCTTTTAAAAGAATGGGTGACTGTAAATTGACTTT
1 GAGTAG-TAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTT
5928 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 34, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
170 3 0.02
171 169 0.96
173 4 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
GAGTAGTAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCATACCAATAAAGTCCTTT
TTCTTCATATTTCCCCAAGCAGACATTCAATTATAACTTGTTTTAACTAAAAATATAAAAAAATT
CAACTCAAAATCAATTAGCAAGTATAAAAACATTTAAAGC
Found at i:6789 original size:171 final size:171
Alignment explanation
Indices: 6341--7605 Score: 736
Period size: 171 Copynumber: 7.4 Consensus size: 171
6331 CAAAAAGATA
* * * * * * * * *
6341 AAAAAATTCAACTTAGAGTCAATTATGAGGTGATAAAACCATTGAAAGTGAGTAATAAGGCATTC
1 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * *
6406 GAAGGAAT-TGGTGACCATAAACGGGCTTTTCTTGCCAATGAATTTCTTTTTCTTCATGTTTCTT
66 AAAGGAATAT-GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTC
*
6470 GAGGCAAACATTCAATTATAGTTTGTTCTAACTAAAAATGTT
130 GAGGCAAACATTCAATTATAGTTTGTTCTAACTAAAAATGTG
* * *
6512 AAAAAATGT-ACCTT-AAATCAATTTTC-AAATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
1 AAAAAAT-TCAACTTAAAATCAA-TTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * * ** *
6574 TTAAATGAATGA-GAGACTAGAAATGGACTTTT-TTTCCTAATGAATGGCTTTTTCTTTATGTTT
64 TTAAAGGAAT-ATGTGACTATAAATGGACTTTTCTTGCC-AATGAATATCTTTTTCTTCATGTTT
* * * * *
6637 CTCGATGTAAACATTCAATTTTAGTTTGTTTTAACTAAAACTGTG
127 CTCGAGGCAAACATTCAATTATAGTTTGTTCTAACTAAAAATGTG
* * * *
6682 AAAAAATTCAATTTAAAACCAATTACGAGATTATAAAATCATTTAAAGCAAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* **********
6747 AAAGGAATATGTGGCTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTNNNNNNNNNNCG
66 AAAGGAATATGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCG
* * * * ** * *
6812 AGGTAGACATTCAATTATAATCTGTGT-TAAAGAAAAATATA
131 AGGCAAACATTCAATTATAGTTTGT-TCTAACTAAAAATGTG
* * * *** * * *
6853 AAAAAATTTAACTTAAAATTAATTATGAGGCGATAAAACTATTGAGAGCGAGTAATAAGG-TTTT
1 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * * * * * *
6917 CGAA-G-ATATGGGTGAGTATAAGTGAACTTTT-TTAGTCAAGGAATAGCTATTTCATCATGTTC
66 -AAAGGAATAT--GTGACTATAAATGGACTTTTCTT-GCCAATGAATATCTTTTTCTTCATGTTT
* * * * * * *
6979 CTTGAGGTAGACATTTAATTATAATCTGTT-TGAACTAAAAATGTA
127 CTCGAGGCAAACATTCAATTATAGTTTGTTCT-AACTAAAAATGTG
* * * * * ********** *
7024 AAAAAAGTGAACCTAAAATCAATTATGAGATTACAANNNNNNNNNNAGTGAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * * * * *
7089 AAAGGAACAGGTGGCTATAAACGAACTTTTCTTACCAATGAAT-GCTTTTTTTCTCATGTTTCTT
66 AAAGGAATATGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCT-TCATGTTTCTC
* * * * *
7153 GAGGTAGACATTCAATTATAGTCTGTT-T-GCATAGAAAATGTA
130 GAGGCAAACATTCAATTATAGTTTGTTCTAAC-TA-AAAATGTG
********** * *
7195 AAAAAATTCAACTTAANNNNNNNNNNGAGATTATAAAACTATTTAAAGCGAGTAGTAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
** ** * * * * * *
7260 GGAGGAATGGGTGACTATAAAGGGACTTTTCTTGCTAATGACTCTCTTTTTCTTCACGTTTCTCA
66 AAAGGAATATGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCG
** * * * * *
7325 AGATAGACATTCAATTATAATTTGTTCTAACCAAAAAGGTA
131 AGGCAAACATTCAATTATAGTTTGTTCTAACTAAAAATGTG
* * * * *
7366 AAAAAATT-ATACCTAAAATCAATTATGAGATAATAAAACCATTTGAAGTGAGTAATAAGGCTTT
1 AAAAAATTCA-ACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * *
7430 TGAAA-GAATGA-GTGACTATAAACGGACTTTTCTTGTCAATAAATGTCTTTTT-TTCACGTTTC
65 T-AAAGGAAT-ATGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTC
* * ** * *
7492 TCGAGGTAGACATTCGCTTATAATCTGCTT-TAACTAAAAATGT-
128 TCGAGGCAAACATTCAATTATAGTTTG-TTCTAACTAAAAATGTG
* * * *** * *
7535 AAAAGTATTCAAATTAAAATTAATTATTTGATTATAAAACTATTTAAAGCGAGTAATAAGACTTT
1 AAAA-AATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
*
7600 TGAAGG
65 TAAAGG
7606 CTTGAGTGAC
Statistics
Matches: 832, Mismatches: 229, Indels: 67
0.74 0.20 0.06
Matches are distributed among these distances:
169 16 0.02
170 241 0.29
171 549 0.66
172 23 0.03
173 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.34
Consensus pattern (171 bp):
AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
AAAGGAATATGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCG
AGGCAAACATTCAATTATAGTTTGTTCTAACTAAAAATGTG
Found at i:9175 original size:170 final size:170
Alignment explanation
Indices: 7744--9179 Score: 755
Period size: 171 Copynumber: 8.4 Consensus size: 170
7734 NNNNNNNNNA
* * * *
7744 TTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATACAACCATTTATAG
1 TTTTAAACAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * ** * * *
7809 TGAGTAATAAGGGTTTTGAAGGAATG-GATGGCTATAAATAAACTTTTCATGCCAATGAATGCCT
65 TGAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGGACTTTTCTTGCTAATGAATACCT
* * * * ** * *
7873 TTTTCTTGATATTTCTCAAGATAAACATTCAATTATAGTTTG
129 TTTTTTTCATGTTTCTCGAGGCAAACATTCAATTATAATCTG
** ********* * * *
7915 TTTTAATTANNNNNNNNNNAAAATTTAACTTAAAATCAATTATGCGATTATAAAACCTTTTAAAG
1 TTTTAAACA-AAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * * * *
7980 TGAGCAATAATGTTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCGT-CGTAATGAAT-GCT
65 TGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGC-TAATGAATACCT
* * *
8043 TTTTGTAT-ATGTTTC-CTGAGACAGACATTCAATTATAATCTG
129 TTTT-TTTCATGTTTCTC-GAGGCAAACATTCAATTATAATCTG
* * * **********
8085 TTTT-AACTAAAAATGTAGAAAAACTCAACTTAAATTTAATNNNNNNNNNNTAAAACCATTTAAA
1 TTTTAAAC-AAAAATGTA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * * * *
8149 GTAAGTAATAATGCTTTTGAAGGAAT-AGAAGACTATAAATGAAATTTTCTTGCCAATCACTATC
64 GTGAGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATGGACTTTTCTTGCTAATGAATACC
* * * * * *
8213 TTTTTCTTCATGTTTCTTGAAGTAGACA-TCGAGTTATAATCTG
128 TTTTTTTTCATGTTTCTCGAGGCAAACATTC-AATTATAATCTG
* * * ***
8256 TGTT-AACCAAAAT-TAAAAAAATTTCAACATAAAATCAATTATGAGATTATAAAACCATTTNNN
1 TTTTAAACAAAAATGT-AAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
******* * * * * *
8319 NNNNNNNATAAGGCTTTTGAAGAAATTG-GTGACTATAAACGGACTTTTCTT-TTCAATTAATAC
64 GTGAGTAATAAGGCTTTTGAAGGAA-TGAGAGACTATAAATGGACTTTTCTTGCT-AATGAATAC
* * * *
8382 CTTTTTATTCACGTTTCTTGAGGTAAACATTCAATTATAATCTG
127 CTTTTTTTTCATGTTTCTCGAGGCAAACATTCAATTATAATCTG
********** * *
8426 NNNNNNNNNNAAATGTAAAACAATTCAACTTAAAATTAACTT-TGAGATTATAAAATCATTTAAA
1 TTTTAAACAAAAATGTAAAA-AATTCAACTTAAAATCAA-TTATGAGATTATAAAACCATTTAAA
* ** * * * * *
8490 GTGAGTAATAAGGCTTTTTAAAAAATAAGTGGCTATAAAT-TATCTTTTCTTG-TCAAT-AACTG
64 GTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGA-CTTTTCTTGCT-AATGAA-TA
* * *
8552 TCTTTTTCTTT-ATGTTTCTTGAGGCAAACATTCAATTATAGTCTG
126 CCTTTTT-TTTCATGTTTCTCGAGGCAAACATTCAATTATAATCTG
* * * *
8597 CTTTAATA-AAAAATATAAAAAATTCAACTTAAAATTAATGATGAGATTATAAAACCATTTAAAG
1 TTTTAA-ACAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* ********* * * * * * * * *
8661 -CANNNNNNNNNNCTTTTGAAGGAATGGGTGACTATAATTGGACTTTTTTTACCAATGACTACAT
65 TGA-GTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCTAATGAATACCT
* * *
8725 TTTCTCTTCATGTTTC-CTGAGGCAAACATTCAATTATAGTTTG
129 TTT-TTTTCATGTTTCTC-GAGGCAAACATTCAATTATAATCTG
** * * * *
8768 TTTTAAGTAAAAATATAAAAGAATTCAACTTAAAACCAATTGTGAGTTTATAAAACCATTTAAAG
1 TTTTAAACAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
********** * * *
8833 TGAGTAATAAGGNNNNNNNNNNAAT-AGATGACTATAAATGGACTTTTCTT-ATAAATAAATA-G
65 TGAGTAATAAGGCTTTTGAAGGAATGAGA-GACTATAAATGGACTTTTCTTGCT-AATGAATACC
* * * * * * * *
8895 TTTTTTCTTCACGTTTC-CTAGGGTAGATATTTAATTGTAATAT-
128 TTTTTT-TTCATGTTTCTCGA-GGCAAACATTCAATTATAATCTG
* * * * * *
8938 ATTTCACCAAAAATGTAAAAAAAATTTAACTGAAAATCAAATT-TGAGATTATAAAACCATATAA
1 TTTTAAACAAAAATGT--AAAAAATTCAACTTAAAATC-AATTATGAGATTATAAAACCATTTAA
* * *
9002 AGTGAATAATAAGGTTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCTAATGACTACC
63 AGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCTAATGAATACC
* * * *
9067 TTTTTTTTCATGTTTCTCAAGGGAGACATTCAATTATAGTCTG
128 TTTTTTTTCATGTTTCTCGAGGCAAACATTCAATTATAATCTG
* *
9110 TTTTAAACAAAAATGTAAAAAATTTAACTTAAAATCAATTATGAGTTTATAAAACCATTTAAAGT
1 TTTTAAACAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGT
9175 GAGTA
66 GAGTA
9180 NNNNNNNNNN
Statistics
Matches: 931, Mismatches: 281, Indels: 107
0.71 0.21 0.08
Matches are distributed among these distances:
169 15 0.02
170 361 0.39
171 446 0.48
172 108 0.12
173 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.36
Consensus pattern (170 bp):
TTTTAAACAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGT
GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCTAATGAATACCTTT
TTTTTCATGTTTCTCGAGGCAAACATTCAATTATAATCTG
Found at i:10324 original size:171 final size:168
Alignment explanation
Indices: 9747--14211 Score: 1013
Period size: 171 Copynumber: 26.2 Consensus size: 168
9737 NNNNNNNNNN
* * *
9747 AATCAATTATGAGATTATAAAAGT-ATTTAAAGGGAGTAGTAAGGCTTTTGAGGGAAT-AGGTGA
1 AATCAATTATGAGATTATAAAA-TCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGA-GTGA
* * * * * *** * **
9810 TTATAAATAAACTTTTTTTGCTAATTAAAAAACTT-TTCTGCACGTTTCTCGAGATAGACATTCA
63 CTATAAATAAACTTTTCTTACCAA-TGAATGCCTTCTTCT-CACGTTTCCCGAGGCAGACATTCA
* * ** * *
9874 ATTATAGTCTATTTTAACTAAAAATGTGGAACAATTCAATTTAA
126 ATTATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
********** * * * *
9918 AATCAATTATGAGATTATNNNNNNNNNNAAAGCGATTAATAAGGCTTTTGAACGG-ATGGGTGGC
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAA-GGAATGAGTGAC
** * * * * * ** * *
9982 TATAAATGGACTTTTCTTATCAATGAATACCTTTTTCTTTATGTTTCTTGAGGAAGATATTCAAT
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
** * * *
10047 TATAGCCTGTTTGTAA-GAAAATGTAAAAAAATTCAATTTAG
128 TATAATCTGTTT-TAACAAAAATGTAAAAAAATTCAAATTAA
** * * ** * * * *
10088 AATTGATTATGAGATTATAAAACCATTTAAAGTGAGTAGTGCGGCATTTGATGGGATGGGTGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAAT-AAGCTTTTGAAGGAATGAGTGACT
* *
10153 ATAAATAAACTTTTTTTACCAATGAATGCGTTCTTCTTCACGTTTCCCGAGGCCA-ACATTCAAT
65 ATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGG-CAGACATTCAAT
* * *
10217 TGTAAT-TTTTTTTACGAAAAATGTAAAAAAAAATT-AAATTAA
128 TATAATCTGTTTTAAC-AAAAATGT--AAAAAAATTCAAATTAA
* *
10259 AATCAATTTTGAGATTATAAAATCATTTAAAGTGAATAATAATGCTTTTGAAGGAATGAGTGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACT
** * * * * ** * **
10324 ATAAATGGACTTTTCTTGCTAGTGAATGCCTTTTTCTCACGTTTCTTGAGGTAGACATTTGATTA
65 ATAAATAAACTTTTCTTACCAATGAATGCCTTCTTCTCACGTTTCCCGAGGCAGACATTCAATTA
* *
10389 TAATCTGTTTTAACCAAAATGTAAAAATATTCAAATTAA
130 TAATCTGTTTTAACAAAAATGTAAAAAAATTCAAATTAA
* * * ** * *
10428 AATCAATTATGTGATTATAAAATCATCTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTGAAT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAG-CTTTTGAAGGAATGAGTGACT
* * * * * * * ** * ** * *
10493 ATAAACACACTTTTCATGCCAAT-AGATG-ATTTTTGCTTTATATTTTCTAAAGAAGACATTCAA
65 ATAAATAAACTTTTCTTACCAATGA-ATGCCTTCTT-C-TCACGTTTCCCGAGGCAGACATTCAA
* * * * * * * * *
10556 TCATATTATATTTCAATCCATATTGTAAAAAAAATTCAACTTAA
127 TTATAATCTGTTTTAA-CAAAAATGT-AAAAAAATTCAAATTAA
********** * * * *
10600 AATCAATTANNNNNNNNNNAAATCATTTAAAGTAAGTAATAAGATTTTTGAAAGAATGGGTGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAG-CTTTTGAAGGAATGAGTGACT
*** * * * * *
10665 ATAAATGGGCTTTTCTTGCCAATGAAGTGCATT-TTCTTCATGTTTTCAGAGGCA-AGCATTCAA
65 ATAAATAAACTTTTCTTACCAATGAA-TGCCTTCTTC-TCACGTTTCCCGAGGCAGA-CATTCAA
** * * **********
10728 TTATAGCCTTTTTTAACAAAAAATATAAANNNNNNNNNNTTAA
127 TTATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
* ** * * * *
10771 AATCAATTATGACATTATAAAGCCATTTAAAGCGAGTAATTAGGTTTTTGAAGGAAT-AGGCGAC
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAA-TAAGCTTTTGAAGGAATGA-GTGAC
*** * * * * * ** *
10835 TATAAATGGGCTTCTCTTGCCAATGAATACCTTTTTCTTCACATTTCTTGAGACAGACATTCAAT
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
** * * * *
10900 TATAGCCTATTTTAACTGAAAATGTGAAAAAATAT-AACTTAA
128 TATAATCTGTTTTAAC-AAAAATGTAAAAAAAT-TCAAATTAA
* ********** ** *
10942 AATCAATTATGGGATTATANNNNNNNNNNAAGCAAGTAATAAGGCTTTTGAAGGAATGAATGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACT
* ** * * * * * * * * ** * *
11007 ATAATTGGACCTTTCGTGCTAATGAATACCTTTTTTTCATGTTTCCTAAGGTAAACATTCAATTA
65 ATAAATAAACTTTTCTTACCAATGAATGCCTTCTTCTCACGTTTCCCGAGGCAGACATTCAATTA
** * * ** * *
11072 TAATCTAATCTAA-AAAAATATAAACGAATGCAATTTAA
130 TAATCTGTTTTAACAAAAATGTAAAAAAATTCAAATTAA
* ** * * * * * *
11110 AATCAATTTTGAGATTATAAAGCCAATTACAGTGAGTAATAAGACTTTTAAAAGAATGGGTGGCT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAG-CTTTTGAAGGAATGAGTGACT
** ** * * * * * * ****
11175 ATGGATGGACTTTTCATATCAATGAATGCCTTTTTTTTTACATTTTTTAAGGCAGACATTCAATT
65 ATAAATAAACTTTTCTTACCAATGAATGCC-TTCTTCTCACGTTTCCCGAGGCAGACATTCAATT
* * ********* *
11240 ATAGTCTATTTTNNNNNNNNNNGTAAAAAAATTCAACTTAA
129 ATAATCTGTTTT-AACAAAAATGTAAAAAAATTCAAATTAA
** * **********
11281 AATCTGTTATGAGATTATAAAACCATTTAAA-TCGAGTAATAAGGCTTTTGANNNNNNNNNNGAC
1 AATCAATTATGAGATTATAAAATCATTTAAAGT-GAGTAATAA-GCTTTTGAAGGAATGAGTGAC
* * ** * ** *
11345 TATAAATGAACTTTTCTTACCAATGAATGCCTTTTTCTTCATATTGCTTGAGGTAGACATTCAAT
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
* * * *
11410 TATAACCTGTTTTAACTAAAAATGTAAAAAAATTCAACTCAN
128 TATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
********** * ** * * *
11452 NNNNNNNNNCGAGATTATAAAA-CTATTTACAGCAAGTAATAAGGCTTTTGAAAGAATTACTGAC
1 AATCAATTATGAGATTATAAAATC-ATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGAC
* * * * * * * *
11516 TATAAATAGACTTTTCTTACCAATAAATTCTTTTTTCTTCATGTTTCCCCAAGCA-ACCATTCAA
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGA-CATTCAA
* * ********* * *
11580 TTATAGTCTATTTTAACAANNNNNNNNNNAATATTCAACTTAA
127 TTATAATCTGTTTTAACAA-AAATGTAAAAAAATTCAAATTAA
* * * *
11623 AATTAATTATGCA-AGTATAAAAAT-ATTTAAAGTGAGTGATAAAGCTTTTGAAAGAATGAGTGA
1 AATCAATTATG-AGATTAT-AAAATCATTTAAAGTGAGTAAT-AAGCTTTTGAAGGAATGAGTGA
* ********** * * * * * * *
11686 CTATAAATAGANNNNNNNNNNCAATGAATACCTTTTTCTTCATGTTTCTCAAGGCAGATATTTAA
63 CTATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAA
* * * * *
11751 TAATAATCTTTTTTAACAAAAAATGTAAAACAATTCGACTTAA
127 TTATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
** * ** * * *
11794 AATCAATTATGCTATTATAAAATCTTTTAAAGCAAGCAATAAGGCTTTTGAAGAAATGGGTGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACT
* * * * ** * * * * ** *
11859 ATATATAGACTTTTCTT-CTTAATTAATGGTTTTTTGTACACATTTCCCTAGTTAAACATTCAAT
65 ATAAATAAACTTTTCTTAC-CAATGAATGCCTTCTTCT-CACGTTTCCCGAGGCAGACATTCAAT
* * **********
11923 TATAATCAGTTTTAACTAAAAATGTAGAAAANNNNNNNNNNA
128 TATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
* * * * * * *
11965 ATTTAATTATGAGATTATAAAATCGTTTAAAGTAAGTAATAAGGCTTTTAAAGGAAAG-GATAAC
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAG-TGAC
** * * ** * * * * ***********
12029 TATAAATGGACTTTTCTTGCCAATGACTATCTTTTTCTTCATGTTTCTCAAGGTNNNNNNNNNNT
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
* *
12094 TATAATCTGTGTTAACCAAAAA-GATAAAAAAAAATTCAACTTAA
128 TATAATCTGTTTTAA-CAAAAATG-T--AAAAAAATTCAAATTAA
* ********** * * *
12138 AGTCAATTNNNNNNNNNNAAAACCATTGAAAGTGAGTAATAAGGCATTTGAAGGAATTG-GTGAC
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAA-TGAGTGAC
* ** ** * ** * *** ** * *
12202 CATAAATGGACTTTTCTTGTCAACGAATTTCTTTTTCTTCACGTTTCTTAAGAAAAATATTCAAT
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
* * * *
12267 TATAATTTGTTGTAACCAAAAATGTAAAAAAATTGAACTTAA
128 TATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAAATTAA
* * * * * *
12309 AAACAATTTTGAGATTAGAAAACCATTTAAAGT-AGGTAATAAGGCTTTTAAAGGAATGAGAGAC
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGA-GTAATAA-GCTTTTGAAGGAATGAGTGAC
* * * * * * * * * *
12373 TAGAAATAGACTTCTCTTTCGAATGAATGGCTTTTTCTACATGTTTCTCGAGGTA-AGCATTCAA
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTCT-CACGTTTCCCGAGGCAGA-CATTCAA
* * * *
12437 TAATAGTCTGTTTTAAGAAAAATGATAAAAACAATTCAACTTAA
127 TTATAATCTGTTTTAACAAAAATG-TAAAAA-AATTCAAATTAA
********** ** * * *
12481 AATCAATTATGAGANNNNNNNNNNATTTAAAGCAAATAATAAAGCTTTTGAAGTAATGAGTGGCT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAAT-AAGCTTTTGAAGGAATGAGTGACT
** * * * * *** *
12546 ATAAATGGACTTTTCTT-CTAATGAACAT-CTTTTTTTTCACGTTTCTTAAGGCAAACATTCAAT
65 ATAAATAAACTTTTCTTACCAATG-A-ATGCCTTCTTCTCACGTTTCCCGAGGCAGACATTCAAT
* * * *
12609 TATAATCTGTTCTAACCAAAAATGTGAAAAAATTTAACTTAA
128 TATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAAATTAA
* * * * *
12651 AATCAATTTTGATATTATAAAA-CTAATTAAAGTGAGTAATAAGGCTTTTAAAGGAATAAGTTG-
1 AATCAATTATGAGATTATAAAATC-ATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAG-TGA
* * * * * * * * * * *
12714 CTATAAATAGACTTTTCATATCAATAAATGTCTTTTTCTTCACATTTCTCAATGCAGATATTCAA
63 CTATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAA
* * ********* * *
12779 TTATAGTTTGTTTNNNNNNNNNNTGTGAAAAAATTCAACTTAA
127 TTATAATCTGTTT-TAACAAAAATGTAAAAAAATTCAAATTAA
* ** * * *
12822 AA-CTAATTATGAGA-TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTAAAGAAAT-AGGTGG
1 AATC-AATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGA-GTGA
* * * * * * * * *
12884 CTATAAATAAACTTTTCTTATCAATGAATATCTTTTTTTTTACGTTTCTCGAGGTAGAGATTCAA
63 CTATAAATAAACTTTTCTTACCAATGAAT-GCCTTCTTCTCACGTTTCCCGAGGCAGACATTCAA
* * * * *
12949 TTATAATCTGTGTTAATAAAAAATATAAAAAAATTTAACTTAA
127 TTATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAAATTAA
* * * * * * *
12992 AATCAATTATGA-AGTGATAAAA-CTATTGAGAGTGAGTAGTAAGGCTTTCGAAGGTATGGGTGA
1 AATCAATTATGAGA-TTATAAAATC-ATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGA
* * * * * * * *
13055 CTATAAGTGAACTTTTTCAGTA--AATGAATGGCTTTTTCATCACG-TTCCTTGAGGTATACATT
63 CTATAAATAAAC-TTTTC-TTACCAATGAATGCCTTCTTC-TCACGTTTCC-CGAGGCAGACATT
*
13117 CAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTC-AATCATAA
124 CAATTATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAAT--TAA
* ********** * *
13164 AATTAATTATGAGATTATAAAA-CTATTTANNNNNNNNNNTAAGGCTTTTAAAGAAATTG-GTGA
1 AATCAATTATGAGATTATAAAATC-ATTTAAAGTGAGTAATAA-GCTTTTGAAGGAA-TGAGTGA
** * * ** *
13227 CTATAAACGAACTTTTCTTACTAATGAATGCCTTTTTTCTCACGTTTCTTGAGGCTG----T---
63 CTATAAATAAACTTTTCTTACCAATGAATGCC-TTCTTCTCACGTTTCCCGAGGCAGACATTCAA
*
13285 TT-TAATC-G--------AAAATGTAAAAAAATTCAACTTAA
127 TTATAATCTGTTTTAACAAAAATGTAAAAAAATTCAAATTAA
********** ** * * *
13317 AATCAATTNNNNNNNNNNAAAA-CTATTTAAAGCAAGTAGTAAGGCTTTTGGAGGAATGGGTGAC
1 AATCAATTATGAGATTATAAAATC-ATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGAC
** * * * * * * *** * *
13381 TATAAATGGACTTTTCTCACTAATGACT-CTCTTTTTCTTTACGTTTCTCGAAATAGACGTTTAA
64 TATAAATAAACTTTTCTTACCAATGAATGC-CTTCTTC-TCACGTTTCCCGAGGCAGACATTCAA
* * * **
13445 TTATAATTTCTTTTAACTAAAAAAGTAAAAAAATT-ATACCTAA
127 TTATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCA-AATTAA
* * *********
13488 AATTAATTATAAGATTATAAAA-CTATTTAAAGTGAGNNNNNNNNNNTTTGAAGGAATGAGTGAC
1 AATCAATTATGAGATTATAAAATC-ATTTAAAGTGAG-TAATAAGCTTTTGAAGGAATGAGTGAC
* ** * *** * * * * ** * *
13552 TGTAAATGGACTTTTTTTGTAAATAAATACCTT-TTTTCACATTTCTTGAGGCAGATATTCGATT
64 TATAAATAAACTTTTCTTACCAATGAATGCCTTCTTCTCACGTTTCCCGAGGCAGACATTCAATT
* * * *
13616 ATAATCTATTTTAACTAAAAATATAAAAATATTTAAATTAA
129 ATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
** * * **
13657 AATCAATTATTTGATTATAAAATCATTCAAAGCGAGTAATAAGGCTTTTGAAGGCTTGAGTGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACT
** ** * * * * *
13722 ATAAATGCACTTTTCACACCAATGGATAG-CTTTTTCTTCATGTTTCCCTAGGCAAACATTCAAT
65 ATAAATAAACTTTTCTTACCAATGAAT-GCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
* * * * *
13786 CATAATATATTTTAATCAAAAATATTAAAAAAAATTCAACTTAA
128 TATAATCTGTTTTAA-CAAAAAT-GT-AAAAAAATTCAAATTAA
* * * * * * * *
13830 AATCAATTATGAGACTATACAACCATTTATAGTGAGTAATAAGGGTTCTGAAGGAATGGGTAACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACT
** * * * * ** * * * **
13895 ATAAATGGACTTTTCATGCCAATGAATACCTTTTTCTTCATATTTCTCAACGTTGACATTCAATT
65 ATAAATAAACTTTTCTTACCAATGAATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAATT
* * * * * *
13960 ATAGTTTGTTTTAACAAAAAATATGAAAAAATTCAACTTAN
129 ATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAATTAA
********* * ** * * *
14001 NNNNNNNNNTGAGATTATAAAACCATTTACTGCGAGTAATAAGGC-TTTGAAGGAATAACTGACT
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACT
* * * * * * * *
14065 ATAAATAGACTTTT-TTATCAATGAGAT-CCTTTTTCTTCACGTTTCCCCAAGCAAATATTTAAT
65 ATAAATAAACTTTTCTTACCAATGA-ATGCCTTCTTC-TCACGTTTCCCGAGGCAGACATTCAAT
* * *
14128 TATAAACTGTTCTAACCAAAAT-TATAAAAATATT-AAACTTAA
128 TATAATCTGTTTTAACAAAAATGTA-AAAAA-ATTCAAA-TTAA
* * *
14170 AATCAATTATGAGATTATAAAACCTTTTAAAGTAAGTAATAA
1 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAA
14212 NNNNNNNNNN
Statistics
Matches: 3101, Mismatches: 1042, Indels: 304
0.70 0.23 0.07
Matches are distributed among these distances:
152 9 0.00
153 77 0.02
154 17 0.01
155 2 0.00
157 1 0.00
160 2 0.00
161 4 0.00
164 5 0.00
165 2 0.00
167 2 0.00
168 111 0.04
169 328 0.11
170 497 0.16
171 1454 0.47
172 314 0.10
173 270 0.09
174 6 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGCTTTTGAAGGAATGAGTGACTA
TAAATAAACTTTTCTTACCAATGAATGCCTTCTTCTCACGTTTCCCGAGGCAGACATTCAATTAT
AATCTGTTTTAACAAAAATGTAAAAAAATTCAAATTAA
Found at i:13120 original size:341 final size:329
Alignment explanation
Indices: 12505--13124 Score: 660
Period size: 341 Copynumber: 1.8 Consensus size: 329
12495 NNNNNNNNNN
* * ** *
12505 ATTTAAAGCAAATAATAAAGCTTTTGAAGTAATGAGTGGCTATAAATGGACTTTTCTTCTAATGA
1 ATTTAAAGCAAATAATAAAGCTTTTAAAGAAATGAGTGGCTATAAATAAACTTTTCTTATAATGA
* * * *
12570 ACATCTTTTTTTTCACGTTTCTTAAGGCAAACATTCAATTATAATCTGTTCTAACCAAAAATGTG
66 ACATCTTTTTTTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAAATATA
* * *
12635 AAAAAATTTAACTTAAAATCAATTTTGATATTATAAAACTAATTAAAGTGAGTAATAAGGCTTTT
131 AAAAAATTTAACTTAAAATCAATTATGATATGATAAAACTAATTAAAGTGAGTAATAAGGCTTTC
* * * *
12700 AAAGGAATAAGTTGCTATAAATAGACTTTTCATATCAATAAATGTCTTTTTCTTCACATTTCTCA
196 AAAGGAATAAGGTGCTATAAATAGACTTTTCATA-CAATAAATGGCTTTTTCATCACATTCCTCA
* *
12765 ATGCAGATATTCAATTATAGTTTGTTTNNNNNNNNNNTGTGAAAAAATTCAACTTAAAACTAATT
260 AGGCAGACATTCAATTATAGTTTGTTT----------TGTGAAAAAATTCAACTTAAAACTAATT
12830 ATGAGATATAAAACC
315 ATGAGATATAAAACC
* *
12845 ATTTAAAGCAAGTAATAAGGCTTTTAAAGAAAT-AGGTGGCTATAAATAAACTTTTCTTATCAAT
1 ATTTAAAGCAAATAATAAAGCTTTTAAAGAAATGA-GTGGCTATAAATAAACTTTTCTTAT-AAT
* * * * * * *
12909 GAATATCTTTTTTTTTACGTTTCTCGAGGTAGAGATTCAATTATAATCTGTGT-TAATAAAAAAT
64 GAACATCTTTTTTTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGT-TCTAACAAAAAAT
* *
12973 ATAAAAAAATTTAACTTAAAATCAATTATGA-AGTGATAAAACT-ATTGAGAGTGAGTAGTAAGG
128 ATAAAAAAATTTAACTTAAAATCAATTATGATA-TGATAAAACTAATT-AAAGTGAGTAATAAGG
* * * * *
13036 CTTTCGAAGGTAT-GGGTGACTATAAGT-GAACTTTTTCAGTA-AATGAATGGCTTTTTCATCAC
191 CTTTCAAAGGAATAAGGTG-CTATAAATAG-AC-TTTTCA-TACAATAAATGGCTTTTTCATCAC
* ** * *
13098 GTTCCTTGAGGTATACATTCAATTATA
252 ATTCCTCAAGGCAGACATTCAATTATA
13125 ATCTATTTTA
Statistics
Matches: 232, Mismatches: 39, Indels: 17
0.81 0.14 0.06
Matches are distributed among these distances:
339 1 0.00
340 59 0.25
341 163 0.70
342 7 0.03
343 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (329 bp):
ATTTAAAGCAAATAATAAAGCTTTTAAAGAAATGAGTGGCTATAAATAAACTTTTCTTATAATGA
ACATCTTTTTTTTCACGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAAATATA
AAAAAATTTAACTTAAAATCAATTATGATATGATAAAACTAATTAAAGTGAGTAATAAGGCTTTC
AAAGGAATAAGGTGCTATAAATAGACTTTTCATACAATAAATGGCTTTTTCATCACATTCCTCAA
GGCAGACATTCAATTATAGTTTGTTTTGTGAAAAAATTCAACTTAAAACTAATTATGAGATATAA
AACC
Found at i:13956 original size:173 final size:171
Alignment explanation
Indices: 13616--14211 Score: 418
Period size: 173 Copynumber: 3.5 Consensus size: 171
13606 ATATTCGATT
* * * * ** * *
13616 ATAATCTATTTTAACTAAAAATAT-AAAAATATTTAAATTAAAATCAATTATTTGATTATAAAAT
1 ATAATATATTTTAAC-AAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAAC
* ** *
13680 CATTCAAAGCGAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGCACTTTTCACACCAAT
65 CATTCAAAGCGAGTAATAAGGCTTCTGAAGGAATGAGTAACTATAAATGCACTTTTCACACCAAT
* * * * *
13745 GGATAGCTTTTTCTTCATGTTTCCCTAGGCAAACATTCAATC
130 GAATACCTTTTTCTTCATATTTCCCAACGCAAACATTCAATC
*
13787 ATAATATATTTTAATCAAAAATATTAAAAAAAATTCAACTTAAAATCAATTATGAGACTATACAA
1 ATAATATATTTTAA-CAAAAATA-TAAAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAA
* * * * * * **
13852 CCATTTATAGTGAGTAATAAGGGTTCTGAAGGAATGGGTAACTATAAATGGACTTTTCATGCCAA
64 CCATTCAAAGCGAGTAATAAGGCTTCTGAAGGAATGAGTAACTATAAATGCACTTTTCACACCAA
* *** *
13917 TGAATACCTTTTTCTTCATATTTCTCAACGTTGACATTCAATT
129 TGAATACCTTTTTCTTCATATTTCCCAACGCAAACATTCAATC
* * * * ********** *
13960 ATAGTTTGTTTTAACAAAAA-ATATGAAAAAATTCAACTTANNNNNNNNNNTGAGATTATAAAAC
1 ATAATATATTTTAACAAAAATATA-AAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAAC
* ** * * * ** *
14024 CATTTACTGCGAGTAATAAGGCTT-TGAAGGAATAACTGACTATAAATAG-ACTTTT-TTATCAA
65 CATTCAAAGCGAGTAATAAGGCTTCTGAAGGAATGAGTAACTATAAAT-GCACTTTTCACACCAA
** * * *
14086 TGAGAT-CCTTTTTCTTCACGTTTCCCCAA-GCAAATATTTAATT
129 TGA-ATACCTTTTTCTTCATATTT-CCCAACGCAAACATTCAATC
* * * * * *
14129 ATAA-ACTGTTCTAACCAAAAT-TATAAAAATATTAAACTTAAAATCAATTATGAGATTATAAAA
1 ATAATA-TATTTTAACAAAAATATA-AAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAA
* * **
14192 CCTTTTAAAGTAAGTAATAA
64 CCATTCAAAGCGAGTAATAA
14212 NNNNNNNNNN
Statistics
Matches: 328, Mismatches: 88, Indels: 20
0.75 0.20 0.05
Matches are distributed among these distances:
169 90 0.27
170 33 0.10
171 69 0.21
172 8 0.02
173 128 0.39
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.35
Consensus pattern (171 bp):
ATAATATATTTTAACAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAACC
ATTCAAAGCGAGTAATAAGGCTTCTGAAGGAATGAGTAACTATAAATGCACTTTTCACACCAATG
AATACCTTTTTCTTCATATTTCCCAACGCAAACATTCAATC
Found at i:14984 original size:171 final size:169
Alignment explanation
Indices: 14705--15042 Score: 374
Period size: 171 Copynumber: 2.0 Consensus size: 169
14695 NNNNNNNNNN
* * *
14705 TTAAAGTAAGTAATAATGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCCTACCAATCAT
1 TTAAAGTAAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCCTACCAATAAA
** ** * * ** * * *
14770 TGCCTTTTTCTTTATTTTTTTTGAGGTAGACATTAAGTTATAATCTGTGTT-AACCAAAAATGAA
66 AACCTTTTAATTCATGTTTCCTAAGGCAAACATTAAGTTATAAT-T-TGTTCAACCAAAAATGAA
*
14834 AAAAAATTCAACATAAAATTAATTATGAGATGATAAAACCA
129 AAAAAATTCAACATAAAATCAATTATGAGATGATAAAACCA
* * * **
14875 TTAAACGTAAGTAATAAGGCTTTTGAATGAATGGGTGACTATAAATGGACTTTTCTTGTCAATAA
1 TTAAA-GTAAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCCTACCAATAA
* * *
14940 AAACCTTTTAATTCATGTTTCCTAAGGCAAACATTCAA-TTATAATTTGTTCCAACTAAAACTGT
65 AAACCTTTTAATTCATGTTTCCTAAGGCAAACATT-AAGTTATAATTTGTT-CAACCAAAAATGA
* * * *
15004 AAAAAAATTCATCTTAAAATCAATTTTGAGATTATAAAA
128 AAAAAAATTCAACATAAAATCAATTATGAGATGATAAAA
15043 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
169 4 0.03
170 6 0.04
171 125 0.91
172 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
TTAAAGTAAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATGGACTTTTCCTACCAATAAA
AACCTTTTAATTCATGTTTCCTAAGGCAAACATTAAGTTATAATTTGTTCAACCAAAAATGAAAA
AAAATTCAACATAAAATCAATTATGAGATGATAAAACCA
Done.