Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399879.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3112.0, 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: 18629
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.29
Warning! 4002 characters in sequence are not A, C, G, or T
Found at i:759 original size:171 final size:170
Alignment explanation
Indices: 1--815 Score: 448
Period size: 171 Copynumber: 4.8 Consensus size: 170
* ** * * * *
1 ACAGATTATAATTGAATGTCTACCTTAAAAAACATGAAGAAAAAGATATTCATTAGCAAGAATAG
1 ACAGATTAAAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAAG
* * *** * * * ******
66 TTCATTTATAGTCACCCATTTCTTCAAAAGCTTTTTTACTCGCTTTAAATATTTTTATANNNNNN
66 TCCAATTATAGTCACCCACGCCTTCAAAAGCCTTATTACTCGCTTTAAAT-TATTTATAATCTCA
**** * * *
131 NNNNTGATTTTAAGTTA-AATTTTTT-ACA-TTGTTAGCTAAA
130 TAACTGAATTTAAG-TAGAATTTTTTAAAATTTTTTAG-TAAA
* * * * * *
171 ACAGA-CAATAATTGAATATCTACCTAGGGAAACATGAA-AAAAATATATTCATTGGCAAGAAAA
1 ACAGATTAA-AATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAA
********** * *
234 GTCNNNNNNNNNNCACCCATGCCTTCAAAAGCCTTATTACTTC-CTTTACA-TACTTTTATAATC
65 GTCCAATTATAGTCACCCACGCCTTCAAAAGCCTTATTAC-TCGCTTTAAATTA--TTTATAATC
* * * * * * * *
297 TCATAATTGATTTTAGGTTGAATTTTTTTATA-TTGTTGGCTAAA
127 TCATAACTGAATTTAAGTAGAATTTTTTAAAATTTTTTAG-TAAA
* * * * * **
341 ACAGA-TAATAATTGAATATCTACCTTGGGAAACATGAAGAAATAGATATCCATTGACAAGAAAA
1 ACAGATTAA-AATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAA
* ********** ** * * *
405 GTCCATTTNNNNNNNNNNATACCTTCGAAAGCCTTATTACTCGCTTTGAATTGTTGTATAATCTC
65 GTCCAATTATAGTCACCCACGCCTTCAAAAGCCTTATTACTCGCTTTAAATTATT-TATAATCTC
* *
470 ATAACTGAATTTAAGTTGACTTTTTTAAAATTTTTTAGTAAA
129 ATAACTGAATTTAAGTAGAATTTTTTAAAATTTTTTAGTAAA
* * * * ********** *
512 ATAGATTATAATTGAATGTCTACTTCGGGAAACATGAAGAAAAAGATATTCNNNNNNNNNNATAG
1 ACAGATTAAAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAAG
* *
577 TCCATTTATAGTCACCCACGTCTTCAAAAGCCTTATTACTCGCTTTAAATATATTTATAATCTCA
66 TCCAATTATAGTCACCCACGCCTTCAAAAGCCTTATTACTCGCTTTAAAT-TATTTATAATCTCA
** * * *
642 TAGTTGACTTTAAGTAGAATTTTTCT-ATATTTTTTATTAAA
130 TAACTGAATTTAAGTAGAATTTTT-TAAAATTTTTTAGTAAA
683 ACAGATTAAAATTGAATAG-C-ATCCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAA
1 ACAGATTAAAATTGAAT-GTCTA-CCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAA
* * * * * *
746 AGTCTAATTATAGTCACCCATGCCTTTAAAACCCTTATTACTCACTTTAAATTGTTTTATAATCT
64 AGTCCAATTATAGTCACCCACGCCTTCAAAAGCCTTATTACTCGCTTTAAATT-ATTTATAATCT
811 CATAA
128 CATAA
816 ATAATTTTAA
Statistics
Matches: 493, Mismatches: 135, Indels: 33
0.75 0.20 0.05
Matches are distributed among these distances:
167 1 0.00
168 1 0.00
169 77 0.16
170 86 0.17
171 315 0.64
172 13 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.35
Consensus pattern (170 bp):
ACAGATTAAAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAAG
TCCAATTATAGTCACCCACGCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTATAATCTCAT
AACTGAATTTAAGTAGAATTTTTTAAAATTTTTTAGTAAA
Found at i:2369 original size:170 final size:169
Alignment explanation
Indices: 1560--4128 Score: 2210
Period size: 171 Copynumber: 15.0 Consensus size: 169
1550 NCTTTGAAGC
* * * *
1560 CCTTATTACTCACATTAAATGATTTTATAACCTCATAATTGATTTTGAGTT-AATTTGTTTTATA
1 CCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTGATTTTAAGTTAAATTT-TTTTATA
* * *
1624 TTTTTTATTAAAACAGTTTATAATTGAATGTCTACCTTGAGAAATATGAAGAAAAAGATATCCAT
64 TTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCAT
* *
1689 TGGCAAG-AAAGATCCATTTATAGTCACCCATACCTTCGAAAG
129 TGGCAAGAAAAG-TCTATTTATAGTCA-CCATGCCTTCGAAAG
* *********
1731 CCTTATTATTCGCTTTNNNNNNNNNNATAATCTCATAATTGATTTTAAGCTGAATATTTTTACAT
1 CCTTATTACTCGCTTT-AAATGTTTTATAATCTCATAATTGATTTTAAG-T---TA-----A-AT
* * ** *
1796 TTTTTTACATTTTTTATTAAAATAGATTATAATTGAATGTCCACTTTGAGAAACATGAAGAAAAA
55 TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAA
* * * * * *
1861 GATATTCATTGACAAAAACAATTC-ATTTATAGTCACCCATGCTTTCAAAAG
120 GATATCCATTGGCAAGAA-AAGTCTATTTATAGTCA-CCATGCCTTCGAAAG
* * * *
1912 CCTTATTACTCACCTTAAATGTTTTTGTAATCTCATAGTTGATTTTAAGTTAAATTTTTTTATAT
1 CCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * * * * *
1977 TTTTGATTAAAATAGATAATAATTGAATGTTTGCCTTGAGAAACGTAAAGAAAAAGATATTCATT
65 TTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCATT
* * * *
2042 GGTAAGAAAAGCCTATTTGTAGTCACCGATGCCTTTGAAAG
130 GGCAAGAAAAGTCTATTTATAGTCACC-ATGCCTTCGAAAG
** * * *
2083 CCTTATTAGGCGCTTTAAATGTTTTTATAATCTCATAATTGATTTCAAGCTAAATTTTTTTACAT
1 CCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * * ** * * * * * ** *
2148 TTTTAATTCAAACAAATAATAGCTAAATGTTTGTCTAG-GAAACCCTGAAGAAAAAGCCATTCAT
65 TTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAA-CATGAAGAAAAAGATATCCAT
* * * *
2212 TGGTAAGAAAAGTCTACTTATAGTCACCATTCCTTC-AAAA
129 TGGCAAGAAAAGTCTATTTATAGTCACCATGCCTTCGAAAG
* * * * *
2252 CCTTAATTACTCGCTTTAAATAGTTTAATAATGTCATAAATGATTTTAAGTTGACTTTTTTTA-A
1 CCTT-ATTACTCGCTTTAAAT-GTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATA
* * * * * * * * ** *
2316 ATTTTTAGGTAAAACAGATAATAATTGATTGTTTGTCTCGACAAACATGAAGAAAAAGCCATTCA
64 TTTTTTA-TTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCA
* * * * * *
2381 TTGACAAGAAAAGT-TCATTTATAGTCTCCCGTGCATTTGCAAG
128 TTGGCAAGAAAAGTCT-ATTTATAGTC-ACCATGCCTTCGAAAG
* * *
2424 CCTTAATACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAAGCT-AATTTTTTTCATA
1 CCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTT-ATA
* *
2488 TTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACGTGAAGAAAAAGATAACCAT
64 TTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCAT
2553 TGGCAAGAAAAGTCTATTTATAGTCACCTATGCCTTCGAAAG
129 TGGCAAGAAAAGTCTATTTATAGTCACC-ATGCCTTCGAAAG
* *
2595 CCTTATTATTCGCTTTAAATGGTTTTTTAATCTCATAATT-AGTTTTAAGTTGAAA-TTTTTTAT
1 CCTTATTACTCGCTTTAAAT-GTTTTATAATCTCATAATTGA-TTTTAAGTT-AAATTTTTTTAT
* * * * * *
2658 ATTTTTTATTAAAATACATTATAATTAAATGTCTG-CTTCA-AAAAATGTAAAGAAAAATATATC
63 ATTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATG--AAGAAAAAGATATC
* * * * *
2721 CATTGGTAAGAGAAGTCCATTTATAGTCACCCATACCTTTGTAAA-
126 CATTGGCAAGAAAAGTCTATTTATAGTCA-CCATGCCTTCG-AAAG
** * * * * * * *
2766 CCTTATTACTTACCTTAAATGTTTCTATGACCTTATAATCGACTTTAAGTTGAAA-TGTTTTATA
1 CCTTATTACTCGCTTTAAATGTTT-TATAATCTCATAATTGATTTTAAGTT-AAATTTTTTTATA
* * * *
2830 TTTTTTATTAAAACTA-ATTATAATTGAATGTCTACCATGAGAAACGTGAAGAAAAAGGTATCCA
64 TTTTTTATTAAAAC-AGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCA
* *
2894 TTGGTAAGAAAAGT-TCATTTATACTCACCCATGCCTTCGAAAG
128 TTGGCAAGAAAAGTCT-ATTTATAGTCA-CCATGCCTTCGAAAG
* * *
2937 CCTTATTACTCGCTTTAAATAATTTTATAACCTCATAATTGATTTTAAGTTGAATTTTTTTATAT
1 CCTTATTACTCGCTTTAAAT-GTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * **
3002 TTTTTATTAAAATAGATTATAATTGAATATTTGCCTCAAGAAACATGAAG----A-ATATCCATT
65 TTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCATT
* * *
3062 GGCAAGAAATGT-TCATTTATACTCACTCATGCCTTCGGAAG
130 GGCAAGAAAAGTCT-ATTTATAGTCAC-CATGCCTTCGAAAG
* * * *
3103 CCTTATTACTCGCTTTAAATAGTTTTGTAGTCTCATAATT-AGTTTTAAGTTAAATTATTTTACA
1 CCTTATTACTCGCTTTAAAT-GTTTTATAATCTCATAATTGA-TTTTAAGTTAAATTTTTTTATA
* ** * * * * *
3167 ATTTTTATCCAAACATATTATATTTAAATGTCTACCTCGAGAAACATGAAGAAAAAGATATCCAT
64 TTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCAT
* *
3232 T-GCTAAGAAAAGTCCATTTATAGTCACCAATGCCGTCGAAAG
129 TGGC-AAGAAAAGTCTATTTATAGTCACC-ATGCCTTCGAAAG
* * * *
3274 CATTATTACTCACTTTAAATAATTTTATAATCTCATAATTGATTTTAATTTAAA-TTTTTTATAT
1 CCTTATTACTCGCTTTAAAT-GTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* **
3338 TTTTTATTAAAACAGATTATAATTAAATGTCTATCTTGAGAAACATGAAGAAAAAGATATCCATT
65 TTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCATT
* * * * *
3403 GACAAGAAAAGTCTATTGATAGTCGCCCATGCCTTCGGAAT
130 GGCAAGAAAAGTCTATTTATAGTC-ACCATGCCTTCGAAAG
*
3444 CCTTATTACTCGCTTTAGATGATTTTATAATCTCATAATTGATTTTAAGTTAAA-TTTTTTATAT
1 CCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * *
3508 TTTTTATTAAAACAGAATT-TAATTGAATGTCTGTCTTGTGAAACTTGAAGAAAAAGATATCCAT
65 TTTTTATTAAAACAG-ATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCAT
*
3572 TGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAG
129 TGGCAAGAAAAGTCTATTTATAGTCA-CCATGCCTTCGAAAG
* * * * *
3614 TCTTATCACTCG-TGTTAAATAGTTTCATAATCTCGTAATTGATTTTAAGTTAAATTTTTTTCTA
1 CCTTATTACTCGCT-TTAAAT-GTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATA
* * * ** * *
3678 TTTTTTATTAAAATAGATTATAATTGAATGTTTACCTTGAGAAATGTAAAGAAAAAGATATTCAT
64 TTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCAT
* * *
3743 TGGCAAAAAAAGT-TCATTTATAGTCACCGACGCCTTCAAAAG
129 TGGCAAGAAAAGTCT-ATTTATAGTCACC-ATGCCTTCGAAAG
* ********* * * *
3785 CCTTTTTACTCGCTTTANNNNNNNNNNTAATCTCATAATGGATTTTAAGTTGAATTTTTTTACAT
1 CCTTATTACTCGCTTTA-AATGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * * * ** * * *
3850 TTTTGATTAAAATAGATAATAATTGAATATCTACCTCAAGAAACGTAAAGAAAAAGATATACATT
65 TTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCATT
* * * * * ** * *
3915 GGCAAGAATAGACCATCTATTGTTGCCTAAGCCTTCAAAAG
130 GGCAAGAAAAGTCTATTTATAGTCACC-ATGCCTTCGAAAG
* ********* *
3956 CCTTATTACTCGCTTTAAATATNNNNNNNNNNTCATAATTGATTTTAAGTTAAATTTTTTTACAT
1 CCTTATTACTCGCTTTAAATGT-TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * ** ** * * * * * * * *
4021 TGTCTGCTAAAATTGATAATAATCGAATATCTACCCT-AGGAAACGTGCAGAAATAGATATCCAT
65 TTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGA-GAAACATGAAGAAAAAGATATCCAT
* * *
4085 TGGCAAGAAAAGGCCATTTATAGTCACCAATGCCTTCAAAAG
129 TGGCAAGAAAAGTCTATTTATAGTCACC-ATGCCTTCGAAAG
4127 CC
1 CC
4129 NNNNNNNNNN
Statistics
Matches: 1966, Mismatches: 357, Indels: 150
0.79 0.14 0.06
Matches are distributed among these distances:
165 2 0.00
166 139 0.07
167 1 0.00
169 20 0.01
170 451 0.23
171 1166 0.59
172 38 0.02
173 7 0.00
175 1 0.00
177 2 0.00
180 1 0.00
181 129 0.07
182 7 0.00
183 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
CCTTATTACTCGCTTTAAATGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATT
TTTTATTAAAACAGATTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGATATCCATTG
GCAAGAAAAGTCTATTTATAGTCACCATGCCTTCGAAAG
Found at i:5789 original size:171 final size:170
Alignment explanation
Indices: 5571--6711 Score: 530
Period size: 171 Copynumber: 6.7 Consensus size: 170
5561 NNNNNNNNNN
* * * *
5571 AATAAGGCTTTCGAAGGCATGGGTAAGTATAAATGAACTTTTCTTACCAATGGATACCTTTTTTT
1 AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTT
* *
5636 TCACGTTTCTCAACGTAGACATTCAATTATAAT-CAGTTTTAATAAAAAATATAAAACATTTCAA
66 TCACGTTTCTCAA-GCAGACATTCAATTATAATGCA-TTTTAATAAAAAATATAAAAAATTTCAA
** * * * * *
5700 CTTAAAGTCAATTATAAGGTCATAGAAA-CATTTAAGGTAAGT
129 CTTAAAACCAATTATAAGATCA-AAAAACCATTTAAAGCAAAT
** * * *
5742 AATAAGGCTCACGAAGGTATGGGTGATTATAAATGGACTTCTCTTACCAATGGATATCTTTTTCT
1 AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTT-T
* * * *
5807 TT-ACATTTTTTGAAGCAGACATTCAATTATAATGTATTTTAATAAAAAATATAAAAAATTTCAA
65 TTCAC-GTTTCTCAAGCAGACATTCAATTATAATGCATTTTAATAAAAAATATAAAAAATTTCAA
* *
5871 CTTAAAACCAATTATGAGATTAAAAAACCATTTAAAGCAAAT
129 CTTAAAACCAATTATAAGATCAAAAAACCATTTAAAGCAAAT
* * * * * *
5913 AATAAGGCTTTCGAAAGCATGTGTGACTATAAATAGACTTTTCTTGCCAATGGTTATCTTTTTCT
1 AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTT
************* *
5978 TCACGTTTCTCNNNNNNNNNNNNNNATTATAAT-CTGTTTTAATAAAAAATATAAAAAAATTT-A
66 TCACGTTTCTC-AAGCAGACATTCAATTATAATGC-ATTTTAATAAAAAATAT-AAAAAATTTCA
* * * * * * * * *
6041 ACTTAAAATCATTTATGAGGTTATAAAATCATTTAAAGCGAGT
128 ACTTAAAACCAATTATAAGATCAAAAAACCATTTAAAGCAAAT
* * * * * * * * * * *
6084 ATTAAGGCTTGCAAATGCACGAGAGACTATAAATGAACTTTGCTT--GAAT-G--A-CTTTTTCT
1 AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTT
* * * * * * * * **
6143 TCATGTTTGTCGAGACACACAATCAATTATTAT-C-TGTTTTATCAAAAAATTTAAAAAAAGTCA
66 TCACGTTTCTCAAG-CAGACATTCAATTATAATGCAT-TTTAAT-AAAAAATATAAAAAATTTCA
*********** * ** * * *
6206 ACTTAAAANNNNNNNNNNCATTATTAAACTATTTAAAGCGAGT
128 ACTTAAAACCAATTATAAGATCAAAAAACCATTTAAAGCAAAT
* * * * * * ** *
6249 AATAAAGG-TTTTGAAGGAATGAGTGACTATAAGTAGACTTTTCTTGCCAATGGATGGCTTTTTC
1 AAT-AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTT
* * * ** * *** * * *
6313 TTCAAGTTT-TCCTAGACAAACATTCAGCTATTATTTGTTTGAATTAAAAATGTAAAACAATTT-
65 TTCACGTTTCT-CAAG-CAGACATTCAATTATAATGCATTTTAATAAAAAATATAAAA-AATTTC
* * * * * * *
6376 AGCTTGAAATCAATTATGAGATTATAAAAA-CATTTAAAGCGACT
127 AACTTAAAACCAATTATAAGATCA-AAAAACCATTTAAAGCAAAT
* * * * * *
6420 AATAAAGCTTTCAAAGGCATCGGCGACTACAAATAGG-CTTTTCTTACCAATGAATATCTTTTTC
1 AATAAGGCTTTCGAAGGCATGGGTGACTATAAAT-GGACTTTTCTTACCAATGGATATCTTTTT-
* *
6484 TTT-ACGTTTCTTCAGGCAGACATTCAATTATTAT-CTATTTTAATAAAAAATATAAAAAAATTT
64 TTTCACGTTTC-TCAAGCAGACATTCAATTATAATGC-ATTTTAATAAAAAATAT-AAAAAATTT
* * * *********** * ** *
6547 -AACTTAAAATCAACTATGAGNNNNNNNNNNTATTTAAGGTGAGT
126 CAACTTAAAACCAATTATAAGATCAAAAAACCATTTAAAGCAAAT
* *
6591 AATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGA-TCTTTCTTACCAATGGATATCTTTTTC
1 AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT-TTTCTTACCAATGGATATCTTTTTT
* * * *
6655 TTCATGTTTTTCAAGGTAGACATTTAATTATAAATTG--TTTTAATAAAAAATATAAAA
65 TTCACGTTTCTCAA-GCAGACATTCAATTAT-AA-TGCATTTTAATAAAAAATATAAAA
6712 CAAATTAACT
Statistics
Matches: 726, Mismatches: 205, Indels: 79
0.72 0.20 0.08
Matches are distributed among these distances:
163 1 0.00
164 12 0.02
165 90 0.12
166 5 0.01
167 3 0.00
168 2 0.00
169 3 0.00
170 26 0.04
171 542 0.75
172 39 0.05
173 3 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTT
TCACGTTTCTCAAGCAGACATTCAATTATAATGCATTTTAATAAAAAATATAAAAAATTTCAACT
TAAAACCAATTATAAGATCAAAAAACCATTTAAAGCAAAT
Found at i:9312 original size:171 final size:170
Alignment explanation
Indices: 9016--9380 Score: 453
Period size: 171 Copynumber: 2.1 Consensus size: 170
9006 NNNNNNNNNN
* * * * * *
9016 CTTTTTCTTCACGTTTCCTAAGGCAGATATTCAATTATTATCAATTTTAACCAATAATGAAAAAA
1 CTTTTTCTTCATGTTTCCTGAGGTAGATATTCAATTATTATCAATTTCAACAAAAAATGAAAAAA
* * ***
9081 ATTTAACTTAAAATCAATTATGAGACTATAAAAATATTTAAAGCAAGTAGTGAGGCTTTTGAAGG
66 ATTCAACTTAAAATCAATTATGAGACTATAAAAACATTTAAAGCAAGTAAAAAGGCTTTTGAAGG
* * * ** * **
9146 CGTGGGCGACAATAGATGGTCTTTTCTTGCCAATGTATAT
131 CGTCGACGACAATAAATGAACTTTTCTTACCAATAAATAT
* * **
9186 CTTTTTCTTCATGTTTCTTGAGGTAGATATTCAATTTTTATCTGTTTCAACAAAAAATGAAAAAA
1 CTTTTTCTTCATGTTTCCTGAGGTAGATATTCAATTATTATCAATTTCAACAAAAAATG-AAAAA
* * * *
9251 AATTCAACTTCAAATCTATTATGAGAGTATAAAAACATTTAAAGCGAGTAAAAAGGCTTTTGAAG
65 AATTCAACTTAAAATCAATTATGAGACTATAAAAACATTTAAAGCAAGTAAAAAGGCTTTTGAAG
* *
9316 GCGTCGATGACTATAAATGAACTTTTCTTACCAATAAATAT
130 GCGTCGACGACAATAAATGAACTTTTCTTACCAATAAATAT
9357 CTTTTT-TTCATGTTTCCTGAGGTA
1 CTTTTTCTTCATGTTTCCTGAGGTA
9381 AACGTTCAAT
Statistics
Matches: 164, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
170 66 0.40
171 98 0.60
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (170 bp):
CTTTTTCTTCATGTTTCCTGAGGTAGATATTCAATTATTATCAATTTCAACAAAAAATGAAAAAA
ATTCAACTTAAAATCAATTATGAGACTATAAAAACATTTAAAGCAAGTAAAAAGGCTTTTGAAGG
CGTCGACGACAATAAATGAACTTTTCTTACCAATAAATAT
Found at i:11306 original size:171 final size:170
Alignment explanation
Indices: 10176--12775 Score: 2026
Period size: 171 Copynumber: 15.2 Consensus size: 170
10166 NNNNNNNNNN
* * * *
10176 TAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGGTTAT-AAAATATTT-AAGTTG
1 TAATAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAG-CG
* * * *
10239 AGTAATAAGGCTTTCGAAGGCATGGGTTACTATGAATGGACTTCTCTTTCCAATGGATATCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * * * *
10304 TCTTTACGTTTTTTGAA-GCAAAC-TTGCAATTATAATCTG-TT
129 TCTTCATGTTTCTT-AAGGTAGACATT-CAATTATAATCTGTTT
* * * *
10345 TAATAAAAAATATCAAAAAGTTTAATTTAAAACCAATTATGAGATTA-AAAAACTATTTAAAGCG
1 TAATAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAAC-ATTTAAAGCG
** * *
10409 AGTAATAAGGCTTTCGAAGATATGGGTGACTATAAATGGACTTTTCTTGCAAATGAAT-TCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * * * *
10473 TCTTCATGGTTCCTAAGATAGACATTAAATTATTATCTGTTT
129 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
*** * * * * * **
10515 TACGCAAAAATGTGAAACAATTCAACTTAAAATCATTTA-GAAGAATATAAAACCATTTAAAATG
1 TAATAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATG-AGATTATAAAAACATTTAAAGCG
* ** * * * * * **
10579 AGTAATAAGGGTTTTAAAGGCATGAGTGACTATAAGTAGACTTTTTTTGCCAATGCATGGCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * * ** * * * * *
10644 TCTTCAGGTTCCCT-CTGCAAACATTCAGTTATTATTTGTTT
129 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* * * * * * * * *
10685 GAATTAATAATGTAAAAAAATTCAGCTTGAAATCAATTATTAGATTATAAAAACATTGAAAGCAA
1 TAATAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA
* * * * * *
10750 GTAATAAGGCTTTCAAAGGCATCGGTGACTACAAATGGGCTTTTCTTACCAATGAATATCTTTTT
65 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTT
* * * *
10815 CTTCATGTTTCTCAAGGCAGACATTCAATAATTATCTGTTT
130 CTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
** * * *
10856 TAACT-GTAAATGTAAAAAAATT-AACTTAAAATCAACTT-TGAGATTATAAAAACGTTTAAGGC
1 TAA-TAAAAAATAT-AAAAAATTCAACTTAAAATCAA-TTATGAGATTATAAAAACATTTAAAGC
* * * * * * *
10918 CAGTAATAAGGCTTTTGAAAG-AGTGGGTGACTATAAATAGACTGTTATTGCCAATGAATATCTT
63 GAGTAATAAGGCTTTCGAAGGCA-TGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTT
** *
10982 TTTCTTCATGTTTCCCAGGGTAGACATTCAATTATAATCTG-TT
127 TTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* *
11025 TAATAAAAAATATAAGCAAATTCAACCTAAAATCAATTATGAGATTATAAAAACA-TTAAGAGCG
1 TAATAAAAAATATAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAA-AGCG
* * * * * * * *
11089 AATAATAAGACTTTCAAAGGGATGGGTAACTATAAGTGGACTTTTCTTACCAATGGACATCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * *
11154 TCTTCATGTTTCTTGAGGTAGACGTTCAATTGTAATCTGTTT
129 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* * * * * *
11196 TATTAAAAAAATATAAAAAAATAAACTTAAAATCAATTACGAGGTTATAAAATCATTTAAAGCGA
1 TAAT-AAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA
* * *
11261 GTAATAAAGTTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGGATATCTTTTT
65 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTT
* * * * *
11326 CTTCACGTTTCTCAAGATAGACATTCAATTACAATATGTTT
130 CTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* * * * *
11367 TAATAAAAAATATAAAACAATTTAACTTAAAATCAATTATAAGGTTATAAAAATATTT-AAGTTG
1 TAATAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAG-CG
* * * *
11431 AGTAATAAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTCTCTTTCCAACGGATATCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * * * * *
11496 TCTTTACGTTTTTTGAA-GCAAACATGT-AATTATAATCT-ATT
129 TCTTCATGTTTCTT-AAGGTAGACAT-TCAATTATAATCTGTTT
* * *
11537 TAATAAAAAATATTAAAAAGTTCAAGTTAAAACCAATTATGAGATTA-AAAAACCATTTAAAGCG
1 TAATAAAAAATA-TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAA-CATTTAAAGCG
* * * * *
11601 AGTAATAAGGCTTTCGAAAGTATGAGTGACTATAAATAGACTTTTCTTGCCAATGGATATCTCTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * * *
11666 TCTTCATCG-TTCCTAAGGTAAACATTCAATTATTATCTGCTT
129 TCTTCAT-GTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
*** * * * * *
11708 TACCCAAAAATGTGAAAGAATTCAACTTAAAATCATTTATGAGATTATAAAACCATTTAAAACGA
1 TAATAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA
* * * * * *
11773 GTAATAAGGGTTTTGAAGGCATGGGTGAATATAAGTAGACTTTTCTTGCCAATGAATGA-CTTTT
65 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGAT-ATCTTTT
* * * * * * * *
11837 TCTTCAGGTTTTCCT-CGGCAAACACTCAATTATTATTTGTTT
129 TCTTCATG-TTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* * * ** * * * **********
11879 GAATTAATAATGCAAAACAATTCAGCTTGAAATCAATTATGAGATTATCAAAANNNNNNNNNNGA
1 TAATAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA
** ** * * * * * *
11944 GTAATAAGGCTTTTAAAGGCATCAGTGACTACAAATGGGCTTTTCTTACGAATGAATACCTTTTT
65 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTT
* * *
12009 CTTCAAGTTT-TTCAAGGCAGACATTCAATTATTATCTGTTT
130 CTTCATGTTTCTT-AAGGTAGACATTCAATTATAATCTGTTT
* * * *
12050 TAACT-GAAAATGTAAAAAAATTTAACTTAAAATCAACTATGAGATTATAAAAACATTTAAAGCG
1 TAA-TAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCG
* * * * * * *
12114 AGTAATAAAGCTTTCGAAAGCGTGAGCGACTATAAATGGACTGTTCTTGCCAATGAATATCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
*
12179 TCTTCATGTTTCTCATA-GTAGACATTCAATTATAATCTGTTT
129 TCTTCATGTTTCTTA-AGGTAGACATTCAATTATAATCTGTTT
* * * * * * *
12221 TAATAAAAAATACAAACAAATACAACTTAAAACCAATTATGAGATTGT-AAAACTATCTCAAGTG
1 TAATAAAAAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAAAC-ATTTAAAGCG
* * * *
12285 AGTAATAAGGCTTTCTAAGGCATGGGTGACTATAAATGAACTTTCCTTGCCAATGAATATCTTTT
64 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* * * * * * *
12350 TCTTCAAGTTTTCCT-AGGAAGGCATTTAATTTTAATATGTTT
129 TCTTCATG-TTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* ********** * *
12392 TAATAAAAAATGTAAAAGNNNNNNNNNNAAAGTCAATTATGAGATTATAAAAATATTTAAAGCGA
1 TAATAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA
* * * * * * **
12457 GTAATAAGGTTTTTGAAGGCGTGGGTGACTATAAATTGA-TTATTCTTGCCCATGAATATCTTAA
65 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTT-TTCTTGCCAATGGATATCTTTT
* ********** *
12521 TCTTCATGTTTCTTGAGGTAGACATNNNNNNNNNNTATGTTT
129 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
* * * * *
12563 TAAT-AAAAATATAAAAAGATTCAATTTAAAATAAATTATGAGAATATAAAATCATTTAAAGTGA
1 TAATAAAAAATATAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGA
********* * * * *
12627 GTAATANNNNNNNNNNAA-GTATGGGTGACTATAAATGAACCTTTCTTGTCAATGGATATC-TTT
65 GTAATA-AGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTT
* ** ** * *
12690 TCTTCAAGTTTCACAAGGTAGGTATTCAATTATAAACTATTT
129 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
*
12732 TAATAAAAAAATATAAAAAAATTTAACTTAAAAT-AGATTATGAG
1 TAAT-AAAAAATAT-AAAAAATTCAACTTAAAATCA-ATTATGAG
12776 GTTANNNNNN
Statistics
Matches: 1906, Mismatches: 462, Indels: 124
0.76 0.19 0.05
Matches are distributed among these distances:
168 5 0.00
169 133 0.07
170 751 0.39
171 968 0.51
172 49 0.03
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
TAATAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAG
TAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTC
TTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT
Found at i:14239 original size:40 final size:40
Alignment explanation
Indices: 14195--14284 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
14185 GGTTCCTGAG
14195 ATAGACATTCAATTATTATCTAATTTACCCAAAAATGTAA
1 ATAGACATTCAATTATTATCTAATTTACCCAAAAATGTAA
14235 ATAGACATTCAATTATTATCTAATTTACCCAAAAATGTAA
1 ATAGACATTCAATTATTATCTAATTTACCCAAAAATGTAA
14275 A-AGA-ATTCAA
1 ATAGACATTCAA
14285 CTTAAAATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 6 0.12
39 3 0.06
40 41 0.82
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (40 bp):
ATAGACATTCAATTATTATCTAATTTACCCAAAAATGTAA
Found at i:15612 original size:171 final size:171
Alignment explanation
Indices: 15346--15710 Score: 389
Period size: 171 Copynumber: 2.1 Consensus size: 171
15336 NNNATCATTT
* *
15346 ATGAGATTAT-AAAACTATTTAAA-CGAGTAACAAGGGTTTTAAAGACATGAGTGACTATAAGTA
1 ATGAGATTATAAAAAC-ATTTAAAGCGAGTAACAAGGCTTTTAAAGACATGAGTGACTATAAATA
* * * * ** ** * *
15409 GACTTTTCTTGCCAATGAATGACTTTTTCTTCAGGTTTCCCTCGGCAAACATTCCGTTATTATTT
65 GACTATTATTGCCAATGAATGACTTATTCTTCAGATTTCCCGAGGCAAACATTCAATTATGATAT
* * *
15474 GTTTGAATTAATAA-TGTAAAAAAATTCAACTTAAAGTCAATC
130 GTTTGAA-TAAAAACTGTAAAAAAATTCAACTTAAAATAAATC
* * * * *
15516 ATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCGTG-GCTGACTATAAATT
1 ATGAGATTATAAAAACATTTAAAGCGAGTAACAAGGCTTTTAAAGACATGAG-TGACTATAAATA
* * * * *
15580 GACTATTATTGCCAATGAAT-ATCTTATTCTTCATATTTCTCGAGGTAGAGATTCAATTATGATA
65 GACTATTATTGCCAATGAATGA-CTTATTCTTCAGATTTCCCGAGGCAAACATTCAATTATGATA
* * *
15644 TGTTTTAATAAAAACTGTAAAAAGATTCAACTTAAAATAAATT
129 TGTTTGAATAAAAACTGTAAAAAAATTCAACTTAAAATAAATC
* *
15687 ATGAGAATATAAAATCATTTAAAG
1 ATGAGATTATAAAAACATTTAAAG
15711 TGNNNNNNNN
Statistics
Matches: 160, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
170 24 0.15
171 136 0.85
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (171 bp):
ATGAGATTATAAAAACATTTAAAGCGAGTAACAAGGCTTTTAAAGACATGAGTGACTATAAATAG
ACTATTATTGCCAATGAATGACTTATTCTTCAGATTTCCCGAGGCAAACATTCAATTATGATATG
TTTGAATAAAAACTGTAAAAAAATTCAACTTAAAATAAATC
Found at i:16998 original size:171 final size:161
Alignment explanation
Indices: 16806--17301 Score: 335
Period size: 171 Copynumber: 3.0 Consensus size: 161
16796 TTTTAGGCGC
** *
16806 GTAAAAAGGCTTTTGAAGGCAT-GAGTGACTATAAATAGACTTCTCTTACCAATGAATGGCTTTT
1 GTAAAAAGGCTTTCAAAGGCATCG-GTGACTATAAATAGACTTCTCTTACCAATGAATAGCTTTT
* * * * * *
16870 TCTTCA-AGTTT-TCCTAGGCGAACATTCAGTTATTATTTTTTTTAAATAAAAATGTAAAAAAAT
65 TCTTCACA-TTTCT-CAAGGCAAACATTCAATTATTATCTGTTTTAAATAAAAATATAAAAAAAT
* * *
16933 AGAGCTTGAAATCAATTATGAGATTATAAAAANNNNNNNNNNAA
128 AGAACTTAAAATCAACTATGAGATTATAAAAA----------AA
* * * * *
16977 GTAATAAGGCTTTCAAAGGCATCGGTGACTATAAATGGACTTTTCTTACCCATGAATATCTTTTT
1 GTAAAAAGGCTTTCAAAGGCATCGGTGACTATAAATAGACTTCTCTTACCAATGAATAGCTTTTT
* * * * * **
17042 CTTTACATTTCTCAATGTAAACATTCAATTATTATCTGTTTTAACTAAAAATATAAAACAATTTA
66 CTTCACATTTCTCAAGGCAAACATTCAATTATTATCTGTTTTAAATAAAAATATAAAAAAATAGA
17107 ACTTAAAATCAACTATGAGATTATAAAAATATTTAAGGCAA
131 ACTTAAAATCAACTATGAGATTAT---AA-A---AA---AA
* * * * * ** * *
17148 GTAACAAA-GCTTTCGAAGGC-GCGAGTGACTATAAATGGACTACTTTTGTCAATTAATATC-TT
1 GTAA-AAAGGCTTTCAAAGGCATCG-GTGACTATAAATAGACTTCTCTTACCAATGAATAGCTTT
** * * * *
17210 TT-TTCATGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTT-AA-AAAAATATAAAAAAATA
64 TTCTTCACATTTCTCAAGGCAAACATTCAATTATTATCTGTTTTAAATAAAAATATAAAAAAATA
* *
17272 CAACTTAAAATCAATTATGAGATTATAAAA
129 GAACTTAAAATCAACTATGAGATTATAAAA
17302 CTATTTNNNN
Statistics
Matches: 264, Mismatches: 49, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
160 1 0.00
163 1 0.00
164 2 0.01
167 39 0.15
168 1 0.00
169 34 0.13
170 6 0.02
171 170 0.64
172 5 0.02
174 2 0.01
175 1 0.00
178 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34
Consensus pattern (161 bp):
GTAAAAAGGCTTTCAAAGGCATCGGTGACTATAAATAGACTTCTCTTACCAATGAATAGCTTTTT
CTTCACATTTCTCAAGGCAAACATTCAATTATTATCTGTTTTAAATAAAAATATAAAAAAATAGA
ACTTAAAATCAACTATGAGATTATAAAAAAA
Done.