Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398078.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1386.0, 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: 24132
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.27
Warning! 6791 characters in sequence are not A, C, G, or T
Found at i:1062 original size:170 final size:170
Alignment explanation
Indices: 3--1694 Score: 686
Period size: 171 Copynumber: 9.9 Consensus size: 170
1 CT
* * * **
3 TGAGAAACA-AGAAGAAAAAGATATTCATTGACAAGAAAAGTCCATTTATAGTAACCTATATCTT
1 TGAGAAACATA-AAGAAAAAGATA-TCGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTT
* * * * **********
67 TGAAAGCCTTCTTACTCGATTTAAATGCTTNNNNNNNNNNATAATTAGTTTTAAGTTGAACTTTT
64 CGAAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTT
* * *
132 TTAT-CTTTTTGTTAAAACATATTATAATTGAATGTCTTCCC
129 TTATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
*
173 TGACAAACATAAAGAAAAAGATATCAGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTC
1 TGAGAAACATAAAGAAAAAGATATC-GTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTC
*********
238 GAAAGCCTTNNNNNNNNNNTT-AAAT-ACTTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTT
65 GAAAGCCTT-GTTACTCGATTGAAATGA-TTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTT
* * * * * *
301 TTTACATTTTTTATTAAAATAGATTAAAATTGAATGTCTAGCT
128 TTTATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
* ** * * * **********
344 TAAGAAACATTGAGAGAAAGATATCCATTGGTAAGANNNNNNNNNNTATAGTCAA-CCATGCCTT
1 TGAGAAACATAAAGAAAAAGATAT-CGTTGGCAAGAAAAGTCCATTTATAGT-AACCCATGCCTT
** * * * * * *
408 CGAAAGTTTTATTACTCGCTTTAAAT-AGTTTTTT-A-CTCATACTTAATTTTTAA-TTGAACTT
64 CGAAAGCCTTGTTACTCGATTGAAATGA-TTTTTTAATCTTATAATT-AGTTTTAAGTTGAACTT
* ** *
469 TTTTATATTTATTATTAAAACGGATTATAATT-ATATGTTTA-CC
127 TTTTATATTTTTTATTAAAACATATTATAATTGA-ATGTCTACCC
* * * * * * *
512 TCAAGAAACGTGAAA-AAAAAGACATTCATTGGCAAGAAAAGTTCATTTATAGTCACCGATGCCT
1 T-GAGAAACAT-AAAGAAAAAGATA-TCGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCT
* * * ************ * *
576 TCAAAAGCCTTATTACTCGTTTTNNNNNNNNNNATAATCTCATAATT-GATTTTAATTTGAA-TT
63 TCGAAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAG-TTTTAAGTTGAACTT
* * * * *
639 GTTTTATATTTTTTATGAAAATAGATTATAATTGAATGTTTGGCTCC
127 -TTTTATATTTTTTATTAAAACATATTATAATTGAATGTCT-AC-CC
* * * * * * * * *
686 --AGAAACATGATGAAAAAGATATCCATTAGCAAGAAAAGTCTATTTATAGTCACCTAT-TCTTT
1 TGAGAAACATAAAGAAAAAGATAT-CGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTC
* * * * * * * ***********
748 GAAAAGCTTTATTACTCGCTCT-AAAGGATTTTATAACCTCATAATT-GATTNNNNNNNNNNTTT
65 G-AAAGCCTTGTTACTCGAT-TGAAATGATTTTTTAATCTTATAATTAG-TTTTAAGTTGAACTT
**
811 TTTTATATTTTTTATTAAAACATATTATAATTGAATGT-TTGCC
127 TTTTATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
* * * *
854 TCGAGAAATA-AGAAGAAAAAGATATTCATTGACAAGAAAAGTCCATTTATAGTAACCCATACCT
1 T-GAGAAACATA-AAGAAAAAGATA-TCGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCT
********** *
918 TCGAAAGCNNNNNNNNNNGATTGAAATGCTTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTT
63 TCGAAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTT
* *
983 TTTATA-TTTTTGTTAAAACAGATTATAATTGAATGTCTACCC
128 TTTATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
* *
1025 TGAGAAACATAAAGAAAAAGATATCCGTTGGCAAGAAAAGTCCATTTATAATAACCAATGCCTTC
1 TGAGAAACATAAAGAAAAAGATAT-CGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTC
* * **********
1090 GAAAGCCTTGTTACTCGCTTTAAATGATTTTTTAATCTTATANNNNNNNNNNAGTTGAACTTTTT
65 GAAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTT
* * *
1155 TATATTTTTTATTAAAATATATTAAAATTGAATGTCTACCT
130 TATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
* * * *
1196 TGAGAAACATAAAGAAAAAGATATCGAGTGGTAAGAAATGTCCATTTATAGTCACCCATGCCTTC
1 TGAGAAACATAAAGAAAAAGATATCG-TTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTC
* * * * * ******************* *
1261 GAAAGTCTTATTACTCGCTTTAAATGCTNNNNNNNNNNNNNNNNNNNTTTTAAGTTGAA-ATTTT
65 GAAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTT
* * * * * * *
1325 TATATGTTTTATTAAAATAGATTATAGTTAAATGTTTA-CT
130 TATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
* * * * * * ** *
1365 TCAGGAAACATGAAGAAAAAGATATTCATTGGCAA-AAGAAATTCATTTATTGTCGCCCACGCCT
1 TGA-GAAACATAAAGAAAAAGATA-TCGTTGGCAAGAA-AAGTCCATTTATAGTAACCCATGCCT
* * * * * * * * * * *
1429 TCAAAAGCCTTATTACTTGCTTTAAATGATTGTATAACCTCATAATTTGTTTTAAGTTGAATTTT
63 TCGAAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTT
* * * * * *
1494 TTTACAATTTTTATAAAAATAAATTATAATTGAATGTCTACCT
128 TTTATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
* * * * * * * **** *
1537 TAAGAAACCA-GAACAAAAAGATATCAATTGACAAAAAAAGTCCATTTGTAGTCTTTCACGCCTT
1 TGAGAAA-CATAAAGAAAAAGATATC-GTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTT
* ** * * * * * * * * *
1601 CAAAAGCCTCATCACTTGCATT-TAATGATTTTATAACCTTATAATTAATTTTAATTTTAATTTT
64 CGAAAGCCTTGTTACTCG-ATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTT
* *
1665 TTTATA-TTTTTATTAAAATAGATTATAATT
128 TTTATATTTTTTATTAAAACATATTATAATT
1695 NNNNNNNNNN
Statistics
Matches: 1142, Mismatches: 329, Indels: 102
0.73 0.21 0.06
Matches are distributed among these distances:
168 6 0.01
169 115 0.10
170 396 0.35
171 600 0.53
172 23 0.02
174 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.37
Consensus pattern (170 bp):
TGAGAAACATAAAGAAAAAGATATCGTTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCG
AAAGCCTTGTTACTCGATTGAAATGATTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTTT
ATATTTTTTATTAAAACATATTATAATTGAATGTCTACCC
Found at i:1774 original size:170 final size:171
Alignment explanation
Indices: 1308--1797 Score: 420
Period size: 171 Copynumber: 2.9 Consensus size: 171
1298 NNNNNNNNNN
* * * * * * * *
1308 TTTTAAGTTGAA-ATTTTTA-TATGTTTTATTAAAATAGATTATAGTTAAATGTTTA-CTTCAGG
1 TTTTAAGTTGAATTTTTTTACAAT-TTTTATAAAAATAAATTATAATTGAATGTCTACCTT-AAG
* * * *
1370 AAACATGAAGAAAAAGATATTCATTGGCAAAAGAAATT-CATTTATTGTCGCCCACGCCTTCAAA
64 AAACATGAAGAAAAAGATATCCATTGGCAAAA-AAATTCCATTTATAGTCACTCACGCCTTCAAA
* * **
1434 AGCCTTATTACTTGCTTTAAATGATTGTATAACCTCATAATTTG
128 AGCCTCATCACTTGCTTTAAATGATTGTATAACCTCATAATTAA
1478 TTTTAAGTTGAATTTTTTTACAATTTTTATAAAAATAAATTATAATTGAATGTCTACCTTAAGAA
1 TTTTAAGTTGAATTTTTTTACAATTTTTATAAAAATAAATTATAATTGAATGTCTACCTTAAGAA
* * * * * **
1543 ACCA-GAACAAAAAGATATCAATTGACAAAAAAAGTCCATTTGTAGTCTTTCACGCCTTCAAAAG
66 A-CATGAAGAAAAAGATATCCATTGGCAAAAAAATTCCATTTATAGTCACTCACGCCTTCAAAAG
* *
1607 CCTCATCACTTGCATTT-AATGATTTTATAACCTTATAATTAA
130 CCTCATCACTTGC-TTTAAATGATTGTATAACCTCATAATTAA
* * * * * **************
1649 TTTTAATTTTAATTTTTTTA-TATTTTTATTAAAATAGATTATAATTNNNNNNNNNNNNNGAGAA
1 TTTTAAGTTGAATTTTTTTACAATTTTTATAAAAATAAATTATAATTGAATGTCTACCTTAAGAA
* * *
1713 ACATGAAGAAAAAGATATCCATTGGCAAGAAAATTCCATTTATAGTCACTCATC-TCTTCAAAAT
66 ACATGAAGAAAAAGATATCCATTGGCAAAAAAATTCCATTTATAGTCACTCA-CGCCTTCAAAAG
* * *
1777 CCTTATTACTCGCTTTAAATG
130 CCTCATCACTTGCTTTAAATG
1798 CTTTTTTAAN
Statistics
Matches: 255, Mismatches: 56, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
169 5 0.02
170 106 0.42
171 134 0.53
172 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.38
Consensus pattern (171 bp):
TTTTAAGTTGAATTTTTTTACAATTTTTATAAAAATAAATTATAATTGAATGTCTACCTTAAGAA
ACATGAAGAAAAAGATATCCATTGGCAAAAAAATTCCATTTATAGTCACTCACGCCTTCAAAAGC
CTCATCACTTGCTTTAAATGATTGTATAACCTCATAATTAA
Found at i:5358 original size:171 final size:171
Alignment explanation
Indices: 5068--5397 Score: 450
Period size: 171 Copynumber: 1.9 Consensus size: 171
5058 ATAGTCACCC
* * * * * *
5068 ATGCCTTCGAAAGCCTTATTACTCGTTTTAAATAGTTTTTTACTCTCATACTTAATTTTTAGTTG
1 ATGCCTTCAAAAGCCTTATTACTCGATTTAAATAGTTTTATAATCTCATAATTAATTTTTAATTG
* * * *
5133 TACTTTTTTATACTTATTATTAAAACAGATTATAATTGTATGTTTACGTCAAGAAACGTGAAGAA
66 TAATTTTTTATACTTATTATGAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAAGAA
5198 AAAGACATCCATTGGCAAGAAAAGTCCATTTATAATCACTG
131 AAAGACATCCATTGGCAAGAAAAGTCCATTTATAATCACTG
* *
5239 ATGCCTTCAAAAGCCTTATTGCTCGATTTAAAT-GATTTTATAATCTCATAATT-GTTTTTAATT
1 ATGCCTTCAAAAGCCTTATTACTCGATTTAAATAG-TTTTATAATCTCATAATTAATTTTTAATT
* * * * *
5302 -TAAATTTTGTTATATTTTTTATGAAAAGAGATTATAATTGAATGTTTGCCTCAAGAAATGTGAA
65 GT-AATTTT-TTATACTTATTATGAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAA
*
5366 GAAAAAGATATCCATTGGCAAGAAAAGTCCAT
128 GAAAAAGACATCCATTGGCAAGAAAAGTCCAT
5398 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
169 1 0.01
170 14 0.10
171 123 0.89
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (171 bp):
ATGCCTTCAAAAGCCTTATTACTCGATTTAAATAGTTTTATAATCTCATAATTAATTTTTAATTG
TAATTTTTTATACTTATTATGAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAAGAA
AAAGACATCCATTGGCAAGAAAAGTCCATTTATAATCACTG
Found at i:10215 original size:171 final size:171
Alignment explanation
Indices: 9902--10220 Score: 395
Period size: 171 Copynumber: 1.9 Consensus size: 171
9892 NNGGGTTACT
* * * *
9902 ATAAATGGACTTTTTTTGCCAATGGATATATTTTTCTTCACGTTTCTCGAGGCAGACATTCAATT
1 ATAAATAGACTTTTCTTGCCAACGGATATATTTTTCTTCACGTTTCTCGAGGCAAACATTCAATT
* * ** **********
9967 ATAGTCTGTCTTAATAAAAAATATAAAAAAATTTAAATTAAAATCAATTATNNNNNNNNNNAATC
66 ATAATATGTCTTAATAAAAAATATAAAAAAATCCAAATTAAAATCAATTATGAGATTATAAAATC
* *
10032 CTTTAGAGCGAGTAATAAAGCTTTTGAAAGCATGGGTCACG
131 ATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTCACG
* * * *
10073 ATAAATAGACTTTTCTTGCCAACGGATATCTTTTTCTTCATGTTTTTTGAGGCAAACATTCAATT
1 ATAAATAGACTTTTCTTGCCAACGGATATATTTTTCTTCACGTTTCTCGAGGCAAACATTCAATT
* * *
10138 ATAATATGTTTTCATAAAAAATATAAAAAAATCCAAATTAATATCAATTATGAGATTATAAAATC
66 ATAATATGTCTTAATAAAAAATATAAAAAAATCCAAATTAAAATCAATTATGAGATTATAAAATC
10203 ATTTAAAGCGAGTAATAA
131 ATTTAAAGCGAGTAATAA
10221 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
171 121 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (171 bp):
ATAAATAGACTTTTCTTGCCAACGGATATATTTTTCTTCACGTTTCTCGAGGCAAACATTCAATT
ATAATATGTCTTAATAAAAAATATAAAAAAATCCAAATTAAAATCAATTATGAGATTATAAAATC
ATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTCACG
Found at i:12210 original size:171 final size:171
Alignment explanation
Indices: 11902--12242 Score: 452
Period size: 171 Copynumber: 2.0 Consensus size: 171
11892 NNNNNNNNNN
* *
11902 AAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTCTTGCCAATGGATATTATTTTCTTTA
1 AAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTCTTGCCAATGAATATTATTCTCTTTA
* * *************
11967 TGTTTCTCAGGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAANNNNNNNNNNNNN
66 TGTTTCTCAGAGCAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAACGTTCAACTTA
*
12032 NAACTAATTATAAGATTAAAAAAGCATTTAAA-TCGAGTAAG
131 AAACTAATTATAAGATTAAAAAAGCATTTAAAGT-GAGTAAG
*
12073 AAGGCTTTCGAAGGTATGGGTTACTATAAATGGACTTTTCTTGCCAATGAATATCT-TTCTCTTT
1 AAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTCTTGCCAATGAATAT-TATTCTCTTT
* * *
12137 ATGTTTCTCAGAGCAGACGTTCAATTATAATCTTTTTTAATAAAAAATATAAAAACGTTCAACTT
65 ATGTTTCTCAGAGCAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAACGTTCAACTT
12202 AAAACTAATTATAAGATTAAAAAAGCATTTAAAGTGAGTAA
130 AAAACTAATTATAAGATTAAAAAAGCATTTAAAGTGAGTAA
12243 TAAGNNNNNN
Statistics
Matches: 146, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
171 144 0.99
172 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
AAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTCTTGCCAATGAATATTATTCTCTTTA
TGTTTCTCAGAGCAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAACGTTCAACTTA
AAACTAATTATAAGATTAAAAAAGCATTTAAAGTGAGTAAG
Found at i:12757 original size:171 final size:171
Alignment explanation
Indices: 12471--12849 Score: 449
Period size: 171 Copynumber: 2.2 Consensus size: 171
12461 ATAAATGGAC
* * * *
12471 TTTTCTTGCTAATGGATATCTTTTTATTTACGTTTCTTAAGGTAAACATACAATTATAATTTGTT
1 TTTTCTTGCCAATGGATATCTTTTTATTCACGTTTCTTAAGGTAAACATACAATTATAATCTATT
12536 TTAATAACAAATAGAAAAAAGTTCAACAAAAAATTAAGTATGAGATTAAAAAACTATTTAAAACG
66 TTAATAACAAATAGAAAAAAGTTCAACAAAAAATTAAGTATGAGATTAAAAAACTATTTAAAACG
** * * *
12601 AGTATTAAGGCTTTTGAAGGCATTAGTAACTATAAATAA-AA
131 AGTAAAAAGGCTTTCGAAGACATGAGTAACTATAAA-AAGAA
* *
12642 TTTTCTTGCCAATGGATATCTTTTTATTCACGTTT-TTCGAGGTAAACATTCAATTATAATCTAT
1 TTTTCTTGCCAATGGATATCTTTTTATTCACGTTTCTT-AAGGTAAACATACAATTATAATCTAT
* ********** *
12706 TTTAATAATC-AATATAAAAAAGTTCAACAAAAAATNNNNNNNNNNATTAAAAAACTATTTAAAG
65 TTTAATAA-CAAATAGAAAAAAGTTCAACAAAAAATTAAGTATGAGATTAAAAAACTATTTAAAA
* * *
12770 CGAGTAAAAAGGCTTTCGAAGACATGGGTTACTATAAAAAGAT
129 CGAGTAAAAAGGCTTTCGAAGACATGAGTAACTATAAAAAGAA
* * *
12813 TTTTTTTGCCAATGGATATCTTTTTCTTCATGTTTCT
1 TTTTCTTGCCAATGGATATCTTTTTATTCACGTTTCT
12850 CANNNNNNNN
Statistics
Matches: 175, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
170 4 0.02
171 169 0.97
172 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.37
Consensus pattern (171 bp):
TTTTCTTGCCAATGGATATCTTTTTATTCACGTTTCTTAAGGTAAACATACAATTATAATCTATT
TTAATAACAAATAGAAAAAAGTTCAACAAAAAATTAAGTATGAGATTAAAAAACTATTTAAAACG
AGTAAAAAGGCTTTCGAAGACATGAGTAACTATAAAAAGAA
Found at i:14033 original size:170 final size:171
Alignment explanation
Indices: 13450--14529 Score: 825
Period size: 171 Copynumber: 6.3 Consensus size: 171
13440 NNNNNNNNNN
* * *
13450 GGCATGGGTTACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTA-TTTTCTC-AGG
1 GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGA-G
* * *
13513 GCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAGTTCAACTCAAAA-CTAATTA
65 GCAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATCAAAATC-AATTA
* * * * *
13577 TAAGATTAAAAAAGCATTTAAATCGAGTAAAAAGGCTTTTGAA
129 TGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAA
* * * * ** *
13620 GGTATGGGTTACTATAAATGGACTTCTCTTGCCAATGAATATCTTTTTCTTCTTGTTTCTCGAGA
1 GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGG
* * * * * *********
13685 CAGAGATTCAATTATAATCTATTTTAATAAAACATATAAAAAAATTCAAATTAAAANNNNNNNNN
66 CAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATCAAAATCAATTATG
* * * * * *
13750 NGGTTATAAAATCCTTTAGAGCGAGTAATAAAGCTTTTGAA
131 AGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAA
* * * * * * *
13791 AGAATGGGTGATTATAAATGGACTTTTCTTGCTAATGGATATCTTTTTATTCATGTTTCTGGAGG
1 GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGG
* * * * *
13856 CAAACATTTAATTATAATCTGTTTTCATAAAAAATATAAAAAAACTCAAATTAAAATCAATTACG
66 CAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATCAAAATCAATTATG
13921 AGATTAT-AAATCATTTAAAACGAGTAATAAGGCTTTTGAA
131 AGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAA
* * ** * * *
13961 GGCATCGGTGACTATAAATAGACTTTTCTTGTTAATGGATGTCTTTTTCTTCACGTTTTTTGAGG
1 GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGG
* * * *
14026 TAAACATTCAATTATAATCTGTTTTCATAAAAAACATAAAAAAAAATTCAAATCAAAATGAATTA
66 CAAACATTCAATTATAATCTGTTTTAAT-AAAAA-ATATAAAAAAATTCAAATCAAAATCAATTA
**********
14091 TGAGATTATAAAATCANNNNNNNNNNGTAATAAGGCTTTTGAA
129 TGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAA
* * * * *
14134 GGCATCGGT-AGCTATAAATGAACTTTTCTTGCGAATGGATATATTTTTCTTCACGTTTCTCGAT
1 GGCATGGGTGA-CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAG
* * * * * * * *
14198 GTAAACA-TAATATTATAATCTGTTTTAA-AAATAAGTATAAAAAAGTTCAACTAAAAATTAAGT
65 GCAAACATTCA-ATTATAATCTGTTTTAATAAA-AAATATAAAAAAATTCAAATCAAAATCAATT
* * ********** *
14261 ATGAGAGTA-AAAAACTATTTANNNNNNNNNNTAAGGCTTTCGAA
128 ATGAGATTATAAAATC-ATTTAAAACGAGTAATAAGGCTTTTGAA
* * * * * * * *
14305 GGCATGGGCGACTATAAATGGACTTTTCTTGCCAATGTATGTCTTTTTTTTTATGTTTATCAAGG
1 GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGG
* * ********** * * *
14370 TAGACATTCAATTATAATCTGTTTTNNNNNNNNNNAT--AAAAGTTCAACTTAAAA-CTAATTAT
66 CAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATCAAAATC-AATTAT
* * * * *
14432 AAGATTGA-AAAAGCATTTAAAGCAAGTAATAAGGCTTTCGAA
130 GAGATT-ATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAA
* * * *
14474 GACATGGGTTACTATAAATGGACTTTTTTTACCAATGGATATCTTTTTCTTCACGT
1 GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGT
14530 NNNNNNNNNN
Statistics
Matches: 725, Mismatches: 170, Indels: 31
0.78 0.18 0.03
Matches are distributed among these distances:
169 89 0.12
170 168 0.23
171 326 0.45
172 43 0.06
173 99 0.14
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
GGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGG
CAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATCAAAATCAATTATG
AGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAA
Found at i:17987 original size:171 final size:169
Alignment explanation
Indices: 17521--18227 Score: 583
Period size: 171 Copynumber: 4.1 Consensus size: 169
17511 NNNNNNNTTC
* * *
17521 ATAAAAAATATAAAAAAAATTCAAATTAAAATCAATTATGAGATTAAAAAATCATTT-AAGCGAG
1 ATAAAAAATAT-AAAAAAGTTCAAATTAAAATGAATTATAAGATTAAAAAATCATTTAAAGCGAG
** * * *
17585 TAATAAGGCTTTTAAAGGCATCGGTGT-CCATAAATGGAC-TTTTCTTGCTAATGGATATCTTTT
65 TAATAAGGCTTTCGAAGGCATGGGT-TACTATAAATGGACTTTTTC-TGCCAAT-GATATCTTTT
* * * * * *
17648 TATTCACGTTCCTCGAGCTAA-ACATAT-AATTATAATCTGTTTTA
127 TCTTTATGTTTCTCAAG-GAAGACAT-TCAA-TATAATCTGTTTTA
* * * ** * * *
17692 ATAATAAATATAAAAAAGTTCAACTAAAAATTCAGTATGAGATTAAAAAA-CTATTTAAAGCGTG
1 ATAAAAAATATAAAAAAGTTCAAATTAAAATGAATTATAAGATTAAAAAATC-ATTTAAAGCGAG
* * * ********** *
17756 TAATAAGGCTTTTGAAGGTATGGGTGANNNNNNNNNNAC-TTTTCTTACCAATGGATATCTTTTT
65 TAATAAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTTC-TGCCAAT-GATATCTTTTT
* *
17820 CTTTATATTTCTCAAGGAAGACATTTAAGTATAATCTGTTTTA
128 CTTTATGTTTCTCAAGGAAGACATTCAA-TATAATCTGTTTTA
* * * ******
17863 ATAAAGAATATAAAAAAGTTCGAGTTAAAACT-AATTATAAGATTAAAAAATCATTTANNNNNNN
1 ATAAAAAATATAAAAAAGTTCAAATTAAAA-TGAATTATAAGATTAAAAAATCATTTA-AAGCGA
***
17927 NNNA-AAGGCTTTCGAAGGCATGGGTTACTATAAATGGA-TTTTTCCTGCCAATGAATATCTTTT
64 GTAATAAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTT-CTGCCAATG-ATATCTTTT
* * * * *
17990 TCTTCT-TGTGTCTCGAGGCAA-ACAATCAATTATAATCTTTTTTC
127 TCTT-TATGTTTCTCAAGG-AAGACATTCAA-TATAATCTGTTTTA
* *
18034 ATAAAAAATATAAAAAAATTCAAATTAAAATGAATTATAAGATTATAAAATCATTTAAAGCGAGT
1 ATAAAAAATATAAAAAAGTTCAAATTAAAATGAATTATAAGATTAAAAAATCATTTAAAGCGAGT
* * *
18099 AATAAGGTTTTTGAAGGCATGGGTTACTATAAATGGACTTTTTTTGCCAACTGATATCTTTTTCT
66 AATAAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTTCTGCCAA-TGATATCTTTTTCT
* * *
18164 TTATGTTTATCAGGGCAGACATTCAATCATAATCTGTTTTA
130 TTATGTTTCTCAAGGAAGACATTCAAT-ATAATCTGTTTTA
18205 ATAAAAAATATAAAAAAGTTCAA
1 ATAAAAAATATAAAAAAGTTCAA
18228 CTTNNNNNNN
Statistics
Matches: 419, Mismatches: 97, Indels: 40
0.75 0.17 0.07
Matches are distributed among these distances:
169 1 0.00
170 46 0.11
171 358 0.85
172 14 0.03
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
ATAAAAAATATAAAAAAGTTCAAATTAAAATGAATTATAAGATTAAAAAATCATTTAAAGCGAGT
AATAAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTTCTGCCAATGATATCTTTTTCTT
TATGTTTCTCAAGGAAGACATTCAATATAATCTGTTTTA
Found at i:18924 original size:171 final size:170
Alignment explanation
Indices: 18615--19754 Score: 680
Period size: 171 Copynumber: 6.7 Consensus size: 170
18605 NNNNNNNNNN
* * * * * *
18615 TTTTAT-ATTTATTATTAAAACAGATTATAATTGTATGTTTACATCGAGAAACGTGAAGAAAAAT
1 TTTTATAATTT-TTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAAG
* *******
18679 ATATCCATTGACAAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGCCTTATTANNNNNNN
65 ATATCCATTGGCAAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGCCTTATTACTCGCTT
***
18744 NNNATGATTTTATAATCTCATAATTGATTTTAATTTGAATT
130 TAAATGATTTTATAATCTCATAATTGATTTTAATTTGAATT
* * * *
18785 TTTTAATAATTTTTATGAAAACAGATTATAATTGAATATTTGCCTTGAGAAACGTGAACAAAAAG
1 TTTT-ATAATTTTTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAAG
* * *
18850 ATATCCATTGGTAAGAAAAGTTCATTTATAGCCACTGATGCCTTCAAAAGCCTTATGACTCGCTT
65 ATATCCATTGGCAAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGCCTTATTACTCGCTT
**********
18915 TAAATGATTTTATAATCTCATAATTNNNNNNNNNNTGAATTT
130 TAAATGATTTTATAATCTCATAATTGATTTTAATTTGAA-TT
* * * *
18957 TTTTATATTTTTTATGAAAACAGATTATAATTGATTGTTTGCCTCGAAAAACAAGAAGAAAAAGA
1 TTTTATAATTTTTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAAGA
* * ** * * * *
19022 TATTCATTGGCAGGAAAAGTTCATTTATTA-TAACCCATGCCTTCGAAAGCCTTTTTACTCGATT
66 TATCCATTGGCAAGAAAAGTTCATTTA-TAGCCACCGATGCCTTCAAAAGCCTTATTACTCGCTT
* * ********** *
19086 TAAATGATTTTTTAATCTTANNNNNNNNNNTAACTTGAACTT
130 TAAATGATTTTATAATCTCATAATTGATTTTAATTTGAA-TT
* * * * * * *
19128 TTTTATATTTTTTATTAAAACAGATTATACTTAAATGTCTT-TCTTGAGAAACATAAAGAAAAAG
1 TTTTATAATTTTTATGAAAACAGATTATAATTGAATGT-TTGCCTCGAGAAACATGAAGAAAAAG
********** * *
19192 ATATCCATTGGCAAGANNNNNNNNNNTATAGTCACCCATGCCTTCAAAAGCCTTATTACAT-GCT
65 ATATCCATTGGCAAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGCCTTATTAC-TCGCT
* * * * *
19256 TTAAAT-AGTTTTTTGATCTCATAATTAATTTTTAGTTGAACTT
129 TTAAATGA-TTTTATAATCTCATAATTGATTTTAATTTGAA-TT
********* ** * * *
19299 TTTTAT-ATNNNNNNNNNNAACAGATTATAATTGTTTGTTTACCTCGACAAACATGAATAAAAAG
1 TTTTATAAT-TTTTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAAG
********** *
19363 ATATCCATTGGCNNNNNNNNNNCATTTATAGACACCGATGCCTTCAAAAGCCTTATTACTCGCTT
65 ATATCCATTGGCAAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGCCTTATTACTCGCTT
19428 TAAATGATTTT-TAATCTCATAATTGATTTTAATTTGAATT
130 TAAATGATTTTATAATCTCATAATTGATTTTAATTTGAATT
* * * **********
19468 TTTT-TATATTTATTATGAAAACATATTACAATTGAATGTTTGCCTCAAGANNNNNNNNNNAAAA
1 TTTTATA-ATTT-TTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAA
* ** * * * *
19532 GATATCCATTGGCAAGAAAAG-CCTATTTATAATCACCCATGCTTTCAAAAACTTTATTACTCGC
64 GATATCCATTGGCAAGAAAAGTTC-ATTTATAGCCACCGATGCCTTCAAAAGCCTTATTACTCGC
* * * **********
19596 TCTAAAGGATTTTATAAGCTCATAATTGATTNNNNNNNNNNTTT
128 TTTAAATGATTTTATAATCTCATAATTGATT-TTAATTTGAATT
* * ** * * * *
19640 TTTTATATTTTTTATTAAAATTGACTATAATTGAATGTCTGCCTTGAGAAACGTGAAGAAAAAGA
1 TTTTATAATTTTTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAAGA
* * ** * *
19705 TATCCATTGACGAA-AAAAGTCCATTTATAGTAACCCATGCCTTCGAAAGC
66 TATCCATTGGC-AAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGC
19755 NNNNNNNNNN
Statistics
Matches: 733, Mismatches: 216, Indels: 41
0.74 0.22 0.04
Matches are distributed among these distances:
168 1 0.00
169 7 0.01
170 122 0.17
171 572 0.78
172 29 0.04
173 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.36
Consensus pattern (170 bp):
TTTTATAATTTTTATGAAAACAGATTATAATTGAATGTTTGCCTCGAGAAACATGAAGAAAAAGA
TATCCATTGGCAAGAAAAGTTCATTTATAGCCACCGATGCCTTCAAAAGCCTTATTACTCGCTTT
AAATGATTTTATAATCTCATAATTGATTTTAATTTGAATT
Found at i:20274 original size:171 final size:161
Alignment explanation
Indices: 19969--20616 Score: 476
Period size: 171 Copynumber: 3.8 Consensus size: 161
19959 NNNNNNNNNN
19969 AAATGAACTTTTCTTGCCAATGGATATATTTTTCTTCACGTTTCTCGATGTAAACATACAATTAT
1 AAATGAACTTTTCTTGCCAATGGATATATTTTTCTTCACGTTTCTCGATGTAAACATACAATTAT
* * * *
20034 AATTTGTTTTAATAATAAATATAAAAAAGTTCAAATTAAAATCAATTATGAAATTATAAAATCAT
66 AATCTGTTTTAATAATAAATATAAAAAAGTTCAAATAAAAATCAAGTATGAAATTAAAAAATCAT
20099 TTAAAGCGAGTAATAAGNNNNNNNNNNGCATCGGTGGCTAT
131 TTAAAGCGAGTAATAAG----------GCATCGGTGGCTAT
* *
20140 AAATGAACTTTTCTTGCCAATGGATATATTTTTTTTCATGTTTCTCGATGTAAACATACAATTAT
1 AAATGAACTTTTCTTGCCAATGGATATATTTTTCTTCACGTTTCTCGATGTAAACATACAATTAT
********** * *
20205 AATCTGTTTTAATAATAAATATAAAANNNNNNNNNNAAAAATTAAGTATGAGATTAAAAAA-CTA
66 AATCTGTTTTAATAATAAATATAAAAAAGTTCAAATAAAAATCAAGTATGAAATTAAAAAATC-A
* *
20269 TTTAAAGCGTGTAATAAGGCTTTTGATGGCATGTGTGACTAT
130 TTTAAAGCGAGTAATAAGGC-----AT--C--G-GTGGCTAT
* * * * * * * *
20311 AAATGGACTTTTCTTG-CAATTGGATATCTTTTTCTTCACGTCTCTTGAGGCAAATATTCAATTA
1 AAATGAACTTTTCTTGCCAA-TGGATATATTTTTCTTCACGTTTCTCGATGTAAACATACAATTA
* * * * * * * ****
20375 TAATCTATTTTCATAAAAAATATAAAAAAAG-TCAAATTAAAATCAATTATGAGATTATAANNNN
65 TAATCTGTTTTAATAATAAATAT-AAAAAAGTTCAAATAAAAATCAAGTATGAAATTAAAAAATC
****** * *
20439 NNNNNNAGCGAGTAATAAGGCTTTTGAAGGCATCGATGGCTCT
129 ATTTAAAGCGAG---TAA------T-AAGGCATCGGTGGCTAT
* * *
20482 AAATGAACTTTTCTTACCAATAGATATATTTTTCTTCACGTTTCTCAATGTAAACATACAATTAT
1 AAATGAACTTTTCTTGCCAATGGATATATTTTTCTTCACGTTTCTCGATGTAAACATACAATTAT
* * * *
20547 AATCTGTTTTAATAATAAATATAAAATAA-TTCAAATTAAAATCAATTATGAGATTATAAAATCA
66 AATCTGTTTTAATAATAAATATAAAA-AAGTTCAAATAAAAATCAAGTATGAAATTAAAAAATCA
20611 TTTAAA
130 TTTAAA
20617 NNNNNNNNNN
Statistics
Matches: 367, Mismatches: 83, Indels: 54
0.73 0.16 0.11
Matches are distributed among these distances:
161 2 0.01
166 2 0.01
168 1 0.00
170 9 0.02
171 333 0.91
172 8 0.02
174 4 0.01
176 2 0.01
180 1 0.00
181 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.36
Consensus pattern (161 bp):
AAATGAACTTTTCTTGCCAATGGATATATTTTTCTTCACGTTTCTCGATGTAAACATACAATTAT
AATCTGTTTTAATAATAAATATAAAAAAGTTCAAATAAAAATCAAGTATGAAATTAAAAAATCAT
TTAAAGCGAGTAATAAGGCATCGGTGGCTAT
Found at i:23815 original size:171 final size:171
Alignment explanation
Indices: 23331--24121 Score: 537
Period size: 170 Copynumber: 4.6 Consensus size: 171
23321 NNNNNNNNNN
* * *
23331 TTTAAGTTGAACTTTTTTA-TATTTTTTATTAAAA-CAGATTATAATTTTGAATGTCTACCTTGA
1 TTTAAGTTGAA-TTTTTTACTA--TTTTAATAAAATCAGATTATAA--TTGAACGTCTACCTCGA
* * * * * * * *
23394 GAAACGTGAAGAAAAAGAGATTCATGGGCAA-AACAGGTCCATTTGTAGTCA-TCCATGCCTTCG
61 GAAACCTGAAGAAAAAGATATCCATTGGCAAGAA-AAGTCCATTTATAGTCACT-CATACCTTCA
* * * * * *
23457 AAAGCGTTC-TTACTTGCTTTAAAT-AGTTTTTTAATCC--CATAATTAGT
124 AAAGC-CTCATCACTCGCTTTAAATGA-TTGTATAA-CCTTCATAATTGGT
23504 TTTAAGTTGAACTTTTTTAC-ATTTTTAATGAAAAT-AGATTATAATTGAACGTCTACCT-GAGA
1 TTTAAGTTGAA-TTTTTTACTA-TTTTAAT-AAAATCAGATTATAATTGAACGTCTACCTCGAGA
* * ***********
23566 AACGTGAAGAAAAAGATATCCATTGGCAGGAAAAGTCCATTTATAGTCACNNNNNNNNNNGAAAG
63 AACCTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAG
* *
23631 CCTTATTACTCGCTTTAAATGATTGTAT-ACCTTCATAATTGGT
128 CCTCATCACTCGCTTTAAATGATTGTATAACCTTCATAATTGGT
* * * * *
23674 TGTAAGTTAAATTTTTTTACTATTTTGATAAAATCAAATTATAATTGAACGTCTACCTCAAGAAA
1 TTTAAGTTGAA-TTTTTTACTATTTTAATAAAATCAGATTATAATTGAACGTCTACCTCGAGAAA
* * * * *
23739 CCTGGACAAAAAGATATCCATTGGTAAGAAAAGTCCATTTATGGTCACTCATGCCTTCAAAAGCC
65 CCTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAGCC
* * * *
23804 TCATCACTCGCTTTTAATGATTTTATAACCTT-ATAGTTGAT
130 TCATCACTCGCTTTAAATGATTGTATAACCTTCATAATTGGT
* * * ** **
23845 TTTAATTTGAATTTTTTA-TATTTTTATTAAAA-CAGATTATAATTTAATAT-TTTCTCGAGAAA
1 TTTAAGTTGAATTTTTTACTA-TTTTAATAAAATCAGATTATAATTGAACGTCTACCTCGAGAAA
* * * *
23907 CTTGAAGAAAAA-AAATCCATGGGCAAGAAAAGTCCATTTATCGTCA-TCCATACCTTCAAAAG-
65 CCTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACT-CATACCTTCAAAAGC
* * ********* * *
23969 CTATATTACTCGCTNNNNNNNNNNT-TATAATC-TCATAATTGAT
129 CT-CATCACTCGCT-TTAAATGATTGTATAACCTTCATAATTGGT
* * * * * **
24012 TTTAATTTAAATATTTTTAAATATTTTATTAAAAT-AGACTATAATTGAATATCTACCTCGAGAA
1 TTTAAGTTGAAT-TTTTT-ACTATTTTAATAAAATCAGATTATAATTGAACGTCTACCTCGAGAA
* *
24076 ACCTGAAGAAAAACATATCCATTGCCAAGAAAAGTCCATTTATAGT
64 ACCTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGT
24122 AACCCATGCC
Statistics
Matches: 498, Mismatches: 96, Indels: 50
0.77 0.15 0.08
Matches are distributed among these distances:
166 4 0.01
167 77 0.15
168 26 0.05
169 50 0.10
170 161 0.32
171 135 0.27
172 12 0.02
173 33 0.07
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36
Consensus pattern (171 bp):
TTTAAGTTGAATTTTTTACTATTTTAATAAAATCAGATTATAATTGAACGTCTACCTCGAGAAAC
CTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAGCCT
CATCACTCGCTTTAAATGATTGTATAACCTTCATAATTGGT
Done.