Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399395.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2661.0, 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: 6549
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 1454 characters in sequence are not A, C, G, or T
Found at i:379 original size:172 final size:166
Alignment explanation
Indices: 1--417 Score: 484
Period size: 169 Copynumber: 2.4 Consensus size: 166
* * * *
1 AAATCAATTATGAGA-TTATAAAACCATTTAAAGCGAGTAATAAGTCTTTTGAAGCAATGGCACA
1 AAATCAATTATGA-ATTTATAAAA-CATTTAAAGCGAGTAAT-AGGCTTTTGAAGGAATAG-AGA
* * * * * *
65 CTATAAGTAGACTTTTGTTGTCAGTGAATTCTTTTTTCTTGCATTTCTCATGGTAGCATTCAATT
62 CTATAAGTGGACCTTTCTTGCCAATGAATTCTTTTTCCTTGCATTTCTCATGGTAGCATTCAATT
* * *
130 ATAGTCTATTTTAACAAAAAATGTAAAATAACTGAACTTA
127 ATAGTCTATCTTAACAAAAAATGTAAAAAAACTAAACTTA
*
170 AAATCAATTATGAGTTTATAAAACTATTTAAAGCGAGTAATAGGACTTTTGAAGGAATAAGAGAC
1 AAATCAATTATGAATTTATAAAAC-ATTTAAAGCGAGTAATAGG-CTTTTGAAGGAAT-AGAGAC
*
235 TATAAGTGGACCTTTCTTGCCAATGAATAT-TTTTTCCTT-CATGATTCTTGA-GGTAGGCATTC
63 TATAAGTGGACCTTTCTTGCCAATGAAT-TCTTTTTCCTTGCAT--TTC-TCATGGTA-GCATTC
*
297 AATTATAGTCTATCTTAATC-AAAAATGTGAAAAAAATTAAACTTA
123 AATTATAGTCTATCTTAA-CAAAAAATGT-AAAAAAACTAAACTTA
*
342 AAATCAATTATGAATTTATAAAATCATTTATAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGAC
1 AAATCAATTATGAATTTATAAAA-CATTTAAAGCGAGTAAT-AGGCTTTTGAAGGAAT-AGAGAC
*
407 TATAAATGGAC
63 TATAAGTGGAC
418 TTNNNNNNNN
Statistics
Matches: 215, Mismatches: 20, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
168 6 0.03
169 83 0.39
170 9 0.04
171 33 0.15
172 80 0.37
173 4 0.02
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (166 bp):
AAATCAATTATGAATTTATAAAACATTTAAAGCGAGTAATAGGCTTTTGAAGGAATAGAGACTAT
AAGTGGACCTTTCTTGCCAATGAATTCTTTTTCCTTGCATTTCTCATGGTAGCATTCAATTATAG
TCTATCTTAACAAAAAATGTAAAAAAACTAAACTTA
Found at i:1795 original size:12 final size:12
Alignment explanation
Indices: 1778--1807 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1768 AATTATGAGA
1778 TTATAGTCTACT
1 TTATAGTCTACT
1790 TTATAGTCTACT
1 TTATAGTCTACT
1802 TTATAG
1 TTATAG
1808 CATTCAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (12 bp):
TTATAGTCTACT
Found at i:2632 original size:172 final size:170
Alignment explanation
Indices: 1849--2760 Score: 748
Period size: 172 Copynumber: 5.3 Consensus size: 170
1839 TGAGGTACAT
** * * *
1849 ATTCAATTATAGTCTACTTTAACTATAAATATAAAAACATTGAACTTAAAATCAATTATGAGATT
1 ATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATT
********** * * *
1914 ATAGANNNNNNNNNNA-CGAGTAATAAGGCTTTTGAAGGAATGAGAAACTATAAATGGATTTTTC
66 ATA-AAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTC
* * * * * *
1978 CTACCAATGAATACTTTTTTATTCATGTTTCTCAAGGTAGAT
130 TTGCCAATGAATAC-TTTTCATTCATGATTCTTAAGGTAGAC
* * *
2020 ATTCAATTATAGTCTGTTTTAAAC-AAAAATGTAAAGAAAATTGAACATAAAATCGATTTTGAGA
1 ATTCAATTATAGTCTGTTTT-AACTAAAAATGTAAA-AAAATTGAACTTAAAATCAATTATGAGA
* ** * ********** *
2084 TAATAAAATAATTTAATA-CGAGTAATAAGGCTTTTGAAGGAATGAGNNNNNNNNNNTTGACTTT
64 TTATAAAACCATTTAA-AGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTT
* *
2148 TCTTGCCAATGAATGCTTTTCTCTTC-T-ATTTCTTAAGGTAGAC
128 TCTTGCCAATGAATACTTTTC-ATTCATGA-TTCTTAAGGTAGAC
* * * * *
2191 ATTTAATTATAGTGTGTTTTAACAAAAAATGTGAAAAAATTGAACTTAAAATTAATTATGAGATT
1 ATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATT
********** * * *
2256 ATANNNNNNNNNNAAGCGAGTAATAAGGCTTTTGAAAGAATGAGAGACTATAAATAGACTTTTCT
66 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCT
*** * **
2321 CATCAATGAATACTTTT--TTCTTGTATTTCTCGAGGTAG-C
131 TGCCAATGAATACTTTTCATTCATG-A-TTCTTAAGGTAGAC
* * * *
2360 ATTCAATTATAGTCTATTTTAA-TCAAAAATATAAAAAAAATGAACTTAAAATCAATCATGAGAT
1 ATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGAT
* * *
2424 TATAAAACCATTTAAAGCGAA-TAATAGGGTTTTTGAAGGAATCAGAGACTATAAATGGACTTTT
65 TATAAAACCATTTAAAGC-AAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT
* *
2488 CTTGCCAATGAATACTTTTGCCTTCATGATTCTTGAGGTAGAC
129 CTTGCCAATGAATACTTTT-CATTCATGATTCTTAAGGTAGAC
* * * * *
2531 ATTCAATTATAGTCTGTCTGAACTAAAAATGTGAAAAAAATTAAACTTCAAATCAATTATTA-AT
1 ATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAAATTGAACTTAAAATCAATTATGAGA-
* * * *
2595 TTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATTAGAGACTATAAATGGGCTTAT
64 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT
* * ** * * * *
2660 CTTGCTAATAAATTTTTTTTATTCACGTTTATTAAGGTAGAC
129 CTTGCCAATGAATACTTTTCATTCATGATTCTTAAGGTAGAC
* *
2702 ATTCAATTATAGTCTGCTTTAACTAAAAATGTAAAAAAAATTAAACTTAAAATCAATTA
1 ATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAAATTGAACTTAAAATCAATTA
2761 NNNNNNNNNN
Statistics
Matches: 586, Mismatches: 135, Indels: 40
0.77 0.18 0.05
Matches are distributed among these distances:
167 3 0.01
168 1 0.00
169 118 0.20
170 106 0.18
171 175 0.30
172 183 0.31
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.34
Consensus pattern (170 bp):
ATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATT
ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCT
TGCCAATGAATACTTTTCATTCATGATTCTTAAGGTAGAC
Found at i:2741 original size:171 final size:171
Alignment explanation
Indices: 1934--2760 Score: 543
Period size: 171 Copynumber: 4.8 Consensus size: 171
1924 NNNNNACGAG
* * * * * * * * **
1934 TAATAAGGCTTTTGAAGGAATGAGAAACTATAAATGGATTTTTCCTACCAATGAATACTTTTTTA
1 TAATAAGACTTTTGAAGGAATCAGAGACTATAAATGGACTTATCTTGCCAATAAATACTTTTGCA
* * * * * * *
1999 TTCATGTTTCTCAAGGTAGATATTCAATTATAGTCTGTTTTAAAC-AAAAATGTAAAGAAAATTG
66 TTCACGATTATTAAGGTAGACATTCAATTATAGTCTG-TTT-AACTAAAAATGTAAAAAAAATTA
* * * * ** *
2063 AACATAAAATCGATTTTGAGATAATAAAATAATTTAATA-CGAG
129 AACTTAAAATCAATTATGAGATTATAAAACCATTTAA-AGCGAA
* * ********** * * * *
2106 TAATAAGGCTTTTGAAGGAATGAGNNNNNNNNNNTTGACTTTTCTTGCCAATGAATGCTTTT-CT
1 TAATAAGACTTTTGAAGGAATCAGAGACTATAAATGGACTTATCTTGCCAATAAATACTTTTGC-
* * * * * * *
2170 CTTCTA--TTTCTTAAGGTAGACATTTAATTATAGTGTGTTTTAACAAAAAATGT-GAAAAAATT
65 ATTC-ACGATTATTAAGGTAGACATTCAATTATAGTCTG-TTTAACTAAAAATGTAAAAAAAATT
* * ********** *
2232 GAACTTAAAATTAATTATGAGATTATANNNNNNNNNNAAGCGAG
128 AAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAA
* * * * * *** *
2276 TAATAAGGCTTTTGAAAGAATGAGAGACTATAAATAGACTTTTCTCATCAATGAATACTTTT---
1 TAATAAGACTTTTGAAGGAATCAGAGACTATAAATGGACTTATCTTGCCAATAAATACTTTTGCA
** * * *
2338 TTCTTGTATT-TCTCGAGGTAG-CATTCAATTATAGTCTATTTTAA-TCAAAAATATAAAAAAAA
66 TTCACG-ATTAT-T-AAGGTAGACATTCAATTATAGTCT-GTTTAACT-AAAAATGTAAAAAAAA
* *
2400 -TGAACTTAAAATCAATCATGAGATTATAAAACCATTTAAAGCGAA
126 TTAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAA
* ** * * *
2445 TAATAGGGTTTTTGAAGGAATCAGAGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTGCC
1 TAATAAGACTTTTGAAGGAATCAGAGACTATAAATGGACTTATCTTGCCAATAAATACTTTTGCA
* * * * *
2510 TTCATGATTCTTGAGGTAGACATTCAATTATAGTCTGTCTGAACTAAAAATGTGAAAAAAATTAA
66 TTCACGATTATTAAGGTAGACATTCAATTATAGTCTGT-TTAACTAAAAATGTAAAAAAAATTAA
* *
2575 ACTTCAAATCAATTATTA-ATTTATAAAACCATTTAAAGC-AA
130 ACTTAAAATCAATTATGAGA-TTATAAAACCATTTAAAGCGAA
* * * * **
2616 GTAATAAGACTTTTGAAGGAATTAGAGACTATAAATGGGCTTATCTTGCTAATAAAT-TTTTTTT
1 -TAATAAGACTTTTGAAGGAATCAGAGACTATAAATGGACTTATCTTGCCAATAAATACTTTTGC
*
2680 ATTCACGTTTATTAAGGTAGACATTCAATTATAGTCTGCTTTAACTAAAAATGTAAAAAAAATTA
65 ATTCACGATTATTAAGGTAGACATTCAATTATAGTCTG-TTTAACTAAAAATGTAAAAAAAATTA
2745 AACTTAAAATCAATTA
129 AACTTAAAATCAATTA
2761 NNNNNNNNNN
Statistics
Matches: 520, Mismatches: 112, Indels: 47
0.77 0.16 0.07
Matches are distributed among these distances:
167 3 0.01
168 1 0.00
169 116 0.22
170 103 0.20
171 154 0.30
172 142 0.27
173 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.35
Consensus pattern (171 bp):
TAATAAGACTTTTGAAGGAATCAGAGACTATAAATGGACTTATCTTGCCAATAAATACTTTTGCA
TTCACGATTATTAAGGTAGACATTCAATTATAGTCTGTTTAACTAAAAATGTAAAAAAAATTAAA
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAA
Found at i:3553 original size:172 final size:173
Alignment explanation
Indices: 3278--3591 Score: 443
Period size: 172 Copynumber: 1.8 Consensus size: 173
3268 TTATGAGATA
* * *
3278 ATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATAAAAGACTATAAATGGACTCTTCT
1 ATAAAACCATTTAAAGCCAGTAAGAAGCCTTTTGAAAGAATAAAAGACTATAAAAGGACTCTTCT
*** *
3343 TGCTAATGAATGCTTTTTTCTTCATGATTCTCGAGGTAGGTTTTCAATTATAGTCTGTTTTAACT
66 TGCTAATGAATGCTTTTTTCTTCATGATTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACT
*
3408 AAAAATGTGAAAAAAATTGAACTTAAAAATCAATTACGAATTT
131 AAAAATGAGAAAAAAATTGAACTTAAAAATCAATTACGAATTT
* * * ** * *
3451 ATAAAACCATTTAAAGCCAGTAAGAAGGCTTTTGAAGGGATGGAAGATTATAAAAGGACTTTTCT
1 ATAAAACCATTTAAAGCCAGTAAGAAGCCTTTTGAAAGAATAAAAGACTATAAAAGGACTCTTCT
* * *
3516 TGC-AATGGATGTTTTTTTC-TCTATGATTCTCGAGGTAGACATTCAATTGTAGTCTATTTTAAC
66 TGCTAATGAATGCTTTTTTCTTC-ATGATTCTCGAGGTAGACATTCAATTATAGTCTATTTTAAC
3579 TAAAAATGAGAAA
130 TAAAAATGAGAAA
3592 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
171 2 0.02
172 62 0.51
173 58 0.48
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (173 bp):
ATAAAACCATTTAAAGCCAGTAAGAAGCCTTTTGAAAGAATAAAAGACTATAAAAGGACTCTTCT
TGCTAATGAATGCTTTTTTCTTCATGATTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACT
AAAAATGAGAAAAAAATTGAACTTAAAAATCAATTACGAATTT
Found at i:4257 original size:172 final size:171
Alignment explanation
Indices: 3759--5901 Score: 1804
Period size: 172 Copynumber: 12.5 Consensus size: 171
3749 NNNNNNNNNN
* * * *
3759 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAA-GAAAAAAACAT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAA-A-
* * ********** * * *
3823 TTAAACTTAAAATCAATTTTGNNNNNNNNNNACCATTTAAACCGAGTAATAAGGTTTTTTAAGGA
64 TTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* *
3888 AT-GAGAGACTATAAATAGG-CTTTTCTTTCCAATGAATGCCTTT
129 ATGGA-AGACTATAAAT-GGACTTTTCTTGCCAATGAATGCTTTT
* * * * *
3931 TTCTCCATGTTTCTTAAGTTAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAAAATT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATT
* * * * * *
3996 GAACATAAATTCAATTTTGAGA-TAGTAAAACTATTTAGAGCGAGTAATAAGGCTTTTGAATGAA
66 GAACTTAAAATCAATTATGAGATTA-TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
** * *
4060 TGGGCGACTATAAATAGACTTTTCTT-CTTAATGAATGCTTTT
130 TGGAAGACTATAAATGGACTTTTCTTGC-CAATGAATGCTTTT
* * * *
4102 TTCTTCATGATTCTCAAGGTAGACATTCAATTGTAGTATGTTTTAA-TCAAAAATGTGAAAAAAA
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACT-AAAAATGT-AAAAAAA
* * * * *
4166 TTGAACTTAAAATCAACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAAGA
64 TTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * **********
4231 ATGGAAGAATATAAATGGATTTTTCTTGCCANNNNNNNNNNTT
129 ATGGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * *
4274 TTCTTCATGTTTCTCGAGGTAGATATTCAATTATAGCCTATTTTAAGC-AAAAATGTATAAAAAA
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAA-CTAAAAATGTA-AAAAAA
* * *
4338 TTGAACTTAAAATCAATTATGA-ATTTATAAAACTATTTCAAGCGAGTAATAAGGCATTTGAAGG
64 TTGAACTTAAAATCAATTATGAGA-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * ** *
4402 AAT-GAGAGATTATAAATAGACTTTTCTTGTTAATAAATGCTTTT
128 AATGGA-AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
** * * * *
4446 TTCTTCACATTTCTCAAGGTACACCTTCAATTATAGTCTGTTTTAA-TCAAAAATATAAAAAAAT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACT-AAAAATGTAAAAAAAT
* ********** * * * *
4510 TCAANNNNNNNNNNATTACGAGATTATAAAACTATTTAAAGCGAGTAATAAAGCTTTTGAAAGAA
65 TGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
* * * *
4575 TGGGAGACTCTAAATGGACGTTTCTTGTCAATGAATGCTTTT
130 TGGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* *
4617 TTCTTCCA--TTTCTTAAGGTAG-CATTCAATTATAGTGTATTTTAACTAAAAATGTAAAAGAAA
1 TTCTT-CATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATGTAAAA-AAA
* ********** * * **
4679 TTAAACTTAAAATCAATTATGAGANNNNNNNNNNATTTGAAGCGAGTAATAAGCCTTTTGAAACA
64 TTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* *
4744 ATGGAAGACTATAAATGGACTCTTCTTACCAATGAATGCTTTT
129 ATGGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* *** *
4787 TTCTTCATGATTCTTGGGGTA-AGCTTTCAATTATAGTCTATTTTAACTAAAAATGTGAAAAAAA
1 TTCTTCATGTTTCTCAAGGTAGA-CATTCAATTATAGTCTATTTTAACTAAAAATGT--AAAAAA
**
4851 ATTGAACTTAAAAATCAATT-TCGA-ATTTATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGA
63 ATTGAACTT-AAAATCAATTAT-GAGA-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA
* * *
4914 AGGGATGGAAGACTATAAAAGGGCTTTTCTTGCCAATGAATGCTTTT
125 AGGAATGGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * ** * * *
4961 TTCTTCATGATTCTCGAGGTAGATATTCAATTGTAGTCGGTTTTAACTACAAAGGAGAAAAAAAT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATG-TAAAAAAAT
* **********
5026 TAAACTTAAAATCAATTATGAGATTANNNNNNNNNNTAAAGCGAGTAATAAGGCTTTTGAAGGAA
65 TGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
* *
5091 TGGAAGAATATAAATGGACTTTTCTTGCTAATGAATG-TTTT
130 TGGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * *
5132 TCTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACTAAAAAAGAAAAAAAAA
1 T-TCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATG-TAAAAAAA
* * * * * * *
5197 TTTAAACTTAAAATCAATT-T-TG-TCAT-TAACCATTTACAGCAAGTAATAAGGCTTTTTAAGG
64 -TTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* *
5258 AAT-GAGAGACTATAAATAGACTTTTCTTGCCAATGAAT-ATCTTT
128 AATGGA-AGACTATAAATGGACTTTTCTTGCCAATGAATGCT-TTT
* * * * **
5302 TTCTTCATATTTCTTAAGTTAGACATTCAATTATAGTCTATTTTAACAAAAAAATGTAAAAACTT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAAC-TAAAAATGTAAAAAAAT
* * * * * *
5367 TGAACATAAAATTAATTTTGAGATAATAAAACTATTTAAAGCGAGTAATAAGGCTCTTGAAGGAA
65 TGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
**********
5432 TAGG-AGACTATAAANNNNNNNNNNTTGCCAATGAATGCTTTT
130 T-GGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * * * *
5474 TTCCTCAT-TTTTTTAAGGTAGATATTCAATTATAGCCTGTTTTAACTAAAAATATGAAAACAAA
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACT-AAAA-ATGTAAA-AAA
* * * * *
5538 ATTAAACTTAAAATCAATTATGA-ATCTATAAAATCATTTAAAGTGAGGAATAAGACTTTTGAAG
63 ATTGAACTTAAAATCAATTATGAGAT-TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * * *
5602 GTATAGG-AGATTATAAATGGACTTATCTTGCCAATAAATGCTTTT
127 GAAT-GGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* ** * * * *
5647 TTCTTCATGTTTGTTGAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAAATATAAAAATATT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATT
* * * *
5712 GAACTTAAAATAAATTATGAGATTATAGAACCATTTAAAACGAGTAATAAGGCTTTTGAAAGAAT
66 GAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
* *
5777 -GAGAGACTATAAATGGATTTTTCTTGCCAAAGAATGCTTTT
131 GGA-AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * * * *
5818 TTATTCATGTTTCTCAAGGTAAACATTGAACTATAATCTATTTTAACCAAAAATATTAAAAAAAT
1 TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAAT-GTAAAAAAA-
* *
5883 TTGAGCATAAAATCAATTA
64 TTGAACTTAAAATCAATTA
5902 AGTGGGTAAT
Statistics
Matches: 1562, Mismatches: 352, Indels: 113
0.77 0.17 0.06
Matches are distributed among these distances:
168 17 0.01
169 138 0.09
170 111 0.07
171 410 0.26
172 562 0.36
173 166 0.11
174 157 0.10
175 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATT
GAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
GGAAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
Found at i:4867 original size:515 final size:514
Alignment explanation
Indices: 3854--5900 Score: 1488
Period size: 515 Copynumber: 4.0 Consensus size: 514
3844 NNNNNNNNNN
* * *
3854 ACCATTTAAACCGAGTAATAAGGTTTTTTAAGGAATGAGAGACTATAAATAGGCTTTTCTT-TCC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGGCTTTTCTTGT-C
* * ** * * *
3918 AATGAATGCCTTTTTCTCCATGTTTCTTAAGTTAGACATTCAATTATAGTCTATTTTAACCAAAA
65 AATGAATGCTTTTTTCTTCACATTTCTCAAGGTACACATTCAATTATAGTCTATTTTAACCAAAA
* ** * *
3983 ATATAAAAAAATTGAACATAAATTCAATTTTGAGATAGTAAAACTATTTAGAGCGAGTAATAAGG
130 ATATAAAAAAATTCAACATAAATTCAATTACGAGATAGTAAAACTATTTAAAGCGAGTAATAAAG
* * * *
4048 CTTTTGAATGAATGGGCGACTATAAATAGACTTTTCTTCTTAATGAATGCTTTTTTCTTCATGAT
195 CTTTTGAAAGAATGGGAGACTATAAATAGACGTTTCTTCTCAATGAATGCTTTTTTCTTCAT-AT
* * *
4113 TCTCAAGGTAGACATTCAATTGTAGTATGTTTTAATCAAAAATGTGAAAAAAATTGAACTTAAAA
259 TCTCAAGGTAGACATTCAATTATAGTATATTTTAATCAAAAATGTGAAAAAAATTAAACTTAAAA
*
4178 TCAACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAAGAATGGAAGAATAT
324 TCAACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAACAATGGAAGAATAT
* * * ********** *
4243 AAATGGATTTTTCTTGCCANNNNNNNNNNTTTTCTTCATGTTTCTCGAGGTAGATATTCAATTAT
389 AAATGGACTCTTCTTACCAATGAATGCTTTTTTCTTCATGATTCTCGAGGTAGATATTCAATTAT
*
4308 AGCCTATTTTAAGCAAAAATGTATAAAAAATTGAACTTAAAATCAATTAT-GAATTTATAAA
454 AGCCTATTTTAAGCAAAAATGTAAAAAAAATTGAACTTAAAATCAATT-TCGAATTTATAAA
* * * * * *
4369 ACTATTTCAAGCGAGTAATAAGGCATTTGAAGGAATGAGAGATTATAAATAGACTTTTCTTGTTA
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGGCTTTTCTTGTCA
* * * *
4434 ATAAATGCTTTTTTCTTCACATTTCTCAAGGTACACCTTCAATTATAGTCTGTTTTAATCAAAAA
66 ATGAATGCTTTTTTCTTCACATTTCTCAAGGTACACATTCAATTATAGTCTATTTTAACCAAAAA
**********
4499 TATAAAAAAATTCAANNNNNNNNNNATTACGAGATTA-TAAAACTATTTAAAGCGAGTAATAAAG
131 TATAAAAAAATTCAACATAAATTCAATTACGAGA-TAGTAAAACTATTTAAAGCGAGTAATAAAG
* * *
4563 CTTTTGAAAGAATGGGAGACTCTAAATGGACGTTTCTTGTCAATGAATGCTTTTTTCTTCCAT-T
195 CTTTTGAAAGAATGGGAGACTATAAATAGACGTTTCTTCTCAATGAATGCTTTTTTCTT-CATAT
* *
4627 TCTTAAGGTAG-CATTCAATTATAGTGTATTTTAA-CTAAAAATGT-AAAAGAAATTAAACTTAA
259 TCTCAAGGTAGACATTCAATTATAGTATATTTTAATC-AAAAATGTGAAAA-AAATTAAACTTAA
* * ********** * * *
4689 AATCAATTATGAGANNNNNNNNNNATTTGAAGCGAGTAATAAGCCTTTTGAAACAATGGAAGACT
322 AATCAACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAACAATGGAAGAAT
* * *
4754 ATAAATGGACTCTTCTTACCAATGAATGCTTTTTTCTTCATGATTCTTGGGGTAAGCT-TTCAAT
387 ATAAATGGACTCTTCTTACCAATGAATGCTTTTTTCTTCATGATTCTCGAGGT-AGATATTCAAT
*
4818 TATAGTCTATTTTAA-CTAAAAATGTGAAAAAAAATTGAACTTAAAAATCAATTTCGAATTTATA
451 TATAGCCTATTTTAAGC-AAAAATGT-AAAAAAAATTGAACTT-AAAATCAATTTCGAATTTATA
4882 AA
513 AA
** * *
4884 ACCATTTAAAGTAAGTAATAAGGCTTTTGAAGGGATG-GAAGACTATAAA-AGGGCTTTTCTTGC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATA-GGCTTTTCTTGT
* * * * * ** *
4947 CAATGAATGCTTTTTTCTTCATGA-TTCTCGAGGTAGATATTCAATTGTAGTCGGTTTTAACTAC
64 CAATGAATGCTTTTTTCTTCA-CATTTCTCAAGGTACACATTCAATTATAGTCTATTTTAACCA-
** * * * * * ********
5011 AAAGGAGAAAAAAATTAAACTTAAAATCAATTATGAGAT--TANNNNNNNNNNTAAAGCGAGTAA
127 AAAATATAAAAAAATTCAACATAAATTCAATTACGAGATAGTA--AAACTATTTAAAGCGAGTAA
* * * * * *
5074 TAAGGCTTTTGAAGGAATGGAAGAATATAAATGGACTTTTCTTGCT-AATGAATG-TTTTTCTCT
190 TAAAGCTTTTGAAAGAATGGGAGACTATAAATAGACGTTTCTT-CTCAATGAATGCTTTTT-TCT
* * * **
5137 TCACGT-TTCTCAAGGTAGACATTCAATTATAATCTATTTTAA-CTAAAAAAGAAAAAAAAATTT
253 TCA--TATTCTCAAGGTAGACATTCAATTATAGTATATTTTAATC-AAAAATGTGAAAAAAA-TT
* ** ** * * * * **
5200 AAACTTAAAATCAATTTTG-TCAT-T--AACCATTTACAGCAAGTAATAAGGCTTTTTAAGGAAT
314 AAACTTAAAATCAACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAACAAT
* * * * * ** *
5261 -GAGAGACTATAAATAGACTTTTCTTGCCAATGAAT-ATCTTTTTCTTCAT-ATTTCTTAAGTTA
379 GGA-AGAATATAAATGGACTCTTCTTACCAATGAATGCT-TTTTTCTTCATGA-TTCTCGAGGTA
* * ** * * *
5323 GACATTCAATTATAGTCTATTTTAA-CAAAAAAATGT-AAAAACTTTGAACATAAAATTAATTTT
441 GATATTCAATTATAGCCTATTTTAAGC--AAAAATGTAAAAAAAATTGAACTTAAAATCAATTTC
*
5386 GAGA-TAATAAA
504 GA-ATTTATAAA
* * ********** *
5397 ACTATTTAAAGCGAGTAATAAGGCTCTTGAAGGAAT-AGGAGACTATAAANNNNNNNNNNTTGCC
1 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATAGGCTTTTCTTGTC
* * * * * * * * *
5461 AATGAATGCTTTTTTCCTCA-TTTTTTTAAGGTAGATATTCAATTATAGCCTGTTTTAACTAAAA
65 AATGAATGCTTTTTTCTTCACATTTCTCAAGGTACACATTCAATTATAGTCTATTTTAACCAAAA
* * * * * *
5525 ATATGAAAACAAAATTAAACTTAAAATCAATTATGA-ATCTA-TAAAA-TCATTTAAAGTGAGGA
130 ATAT--AAA-AAAATTCAACATAAATTCAATTACGAGA--TAGTAAAACT-ATTTAAAGCGAGTA
* * * * * *
5587 AT-AAGACTTTTGAAGGTATAGGAGATTATAAATGGAC-TTATCTTGC-CAATAAATGCTTTTTT
189 ATAAAG-CTTTTGAAAGAATGGGAGACTATAAATAGACGTT-TCTT-CTCAATGAATGCTTTTTT
* * ** * * * * * *
5649 CTTCATGTTTGTTGAGGTAGACATTCAATTATAGTCTCTTTTAACCAAAAATAT-AAAAATATTG
251 CTTCAT-ATTCTCAAGGTAGACATTCAATTATAGTATATTTTAATCAAAAATGTGAAAAAAATTA
* * * * * * * *
5713 AACTTAAAATAAATTATGAGATTATAGAACCATTTAAAACGAGTAATAAGGCTTTTGAAAGAAT-
315 AACTTAAAATCAACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAACAATG
* * * * * * * * * *
5777 GAGAGACTATAAATGGATTTTTCTTGCCAAAGAATGCTTTTTTATTCATGTTTCTCAAGGTAAAC
380 GA-AGAATATAAATGGACTCTTCTTACCAATGAATGCTTTTTTCTTCATGATTCTCGAGGTAGAT
* * ** * * * * *
5842 ATTGAACTATAATCTATTTTAACCAAAAATATTAAAAAAATTTGAGCATAAAATCAATT
444 ATTCAATTATAGCCTATTTTAAGCAAAAAT-GTAAAAAAAATTGAACTTAAAATCAATT
5901 AAGTGGGTAA
Statistics
Matches: 1230, Mismatches: 246, Indels: 110
0.78 0.16 0.07
Matches are distributed among these distances:
511 4 0.00
512 58 0.05
513 252 0.20
514 174 0.14
515 443 0.36
516 206 0.17
517 37 0.03
518 32 0.03
519 24 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (514 bp):
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGGCTTTTCTTGTCA
ATGAATGCTTTTTTCTTCACATTTCTCAAGGTACACATTCAATTATAGTCTATTTTAACCAAAAA
TATAAAAAAATTCAACATAAATTCAATTACGAGATAGTAAAACTATTTAAAGCGAGTAATAAAGC
TTTTGAAAGAATGGGAGACTATAAATAGACGTTTCTTCTCAATGAATGCTTTTTTCTTCATATTC
TCAAGGTAGACATTCAATTATAGTATATTTTAATCAAAAATGTGAAAAAAATTAAACTTAAAATC
AACTAAGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAACAATGGAAGAATATAA
ATGGACTCTTCTTACCAATGAATGCTTTTTTCTTCATGATTCTCGAGGTAGATATTCAATTATAG
CCTATTTTAAGCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTTCGAATTTATAAA
Done.