Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403001.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_668.0, 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: 20392
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.23
Warning! 7338 characters in sequence are not A, C, G, or T
Found at i:1164 original size:172 final size:171
Alignment explanation
Indices: 871--1340 Score: 559
Period size: 172 Copynumber: 2.7 Consensus size: 171
861 TTTGCTTTTC
* * * * * * * *
871 TAGTTAAAACATATTATAATTGAACGTGTACCCTGAGAAACAT-AAGGAAGAGAACT-TTCATTG
1 TAGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAA-GAA-AAAAGTATTCATTG
* * * * * *
934 GCAAGAGAAGTCCATTTATAGTCAGCAATTCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTT
64 GCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * *
999 CATAATCTCAAAATTGATTTAAATTTGGATTCTTTGTACATTTT
129 CATAATCTCAAAATTGACTTAAATTT-AATTCTTTGTACAGTTT
* *
1043 TAGTTAAAATAGACTAGAATTGAATGTCTACCTTGAGAACCATGAAGAAAAAAGTATTCATTGGC
1 TAGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGC
* *
1108 AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
66 AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTCA
1173 TAATCTCAAAATTGACTTAAATTTAATTCTTTGTACAGTTT
131 TAATCTCAAAATTGACTTAAATTTAATTCTTTGTACAGTTT
* **********
1214 TAGTTTAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAANNNNNNNNNNG-
1 TAGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGC
** * * *
1278 AAGAAAAGTGTATGTATAGTCACCCATACCTTCAAAAGCCTTATTACTTGCGTTAAATGGTTT
66 AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
1341 TGTAATGCCA
Statistics
Matches: 256, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
170 57 0.22
171 70 0.27
172 127 0.50
173 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.33
Consensus pattern (171 bp):
TAGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGC
AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTCA
TAATCTCAAAATTGACTTAAATTTAATTCTTTGTACAGTTT
Found at i:1407 original size:170 final size:160
Alignment explanation
Indices: 936--1435 Score: 373
Period size: 170 Copynumber: 3.0 Consensus size: 160
926 TTTCATTGGC
* * * * * * * * * *
936 AAGAGAAGTCCATTTATAGTCAGCAATTCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTTCA
1 AAGAAAAGTCCATGTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAATGATTTTA
* ** * * *
1001 TAATCTCAAAATTGATTTAAATTTGGATTCTTTGTACATTTTTA-GTTAAA-ATAGACTAGAATT
66 TAATCTCAAAATTGACTTAAA-TTAAATTCTTTCTACAGTTTTAGGATAAACA-A-ACTAGAATT
* *
1064 GAATGTCTACCTTGAGAACCATGAAGAAAAAAGTATTCATTGG
128 GAATGTCTACCTTGAGAAACAT-AA-AGAAAA--A---A---G
* *
1107 CAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTT
1 -AAGAAAAGTCCATGTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAATGATTTT
* * ** *
1172 ATAATCTCAAAATTGACTTAAATTTAATTCTTTGTACAGTTTTAGTTTAAACAGACTAGAATTGA
65 ATAATCTCAAAATTGACTTAAATTAAATTCTTTCTACAGTTTTAGGATAAACAAACTAGAATTGA
*
1237 ATGTCTACCTTGAGAAACATGAAGAAAAAANNNNNNNNNNG
130 ATGTCTACCTTGAGAAACATAAAGAAAAAA----------G
** * * *
1278 AAGAAAAGTGTATGTATAGTCACCCATACCTTCAAAAGCCTTATTACTTGCGTTAAATGGTTTTG
1 AAGAAAAGTCCATGTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAATGATTTTA
* * * * **
1343 TAATGC-CATAAA-TGATTTTAAGTTAAATGT-TTTCTA-TGTTTTTGGATAAACAAACTCTAAT
66 TAAT-CTCA-AAATTGA-CTTAAATTAAAT-TCTTTCTACAGTTTTAGGATAAACAAACTAGAAT
1404 TGAATGTCTACCTTGAGAAACATAAAGAAAAA
127 TGAATGTCTACCTTGAGAAACATAAAGAAAAA
1436 GGCATTCNNN
Statistics
Matches: 276, Mismatches: 39, Indels: 28
0.80 0.11 0.08
Matches are distributed among these distances:
164 1 0.00
167 1 0.00
169 5 0.02
170 117 0.42
171 68 0.25
172 83 0.30
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.34
Consensus pattern (160 bp):
AAGAAAAGTCCATGTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAATGATTTTA
TAATCTCAAAATTGACTTAAATTAAATTCTTTCTACAGTTTTAGGATAAACAAACTAGAATTGAA
TGTCTACCTTGAGAAACATAAAGAAAAAAG
Found at i:2350 original size:171 final size:170
Alignment explanation
Indices: 1752--2637 Score: 903
Period size: 172 Copynumber: 5.2 Consensus size: 170
1742 NNNNNNNNNN
* *
1752 ACCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCAAACTTGATTTTAA
1 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
* * * * * *
1817 GTCCAAATTTTT-TTTCTTTTCT-GATTAAAACATATTATAATTGAATGTCTA-CTCTGAGAAAC
66 GT-TAAATTTTTGTATATTTT-TAG-TT-AAACAGACTAGAATTGAATGTCTACCT-TGAGAAAC
* * * * *
1879 ATAAAGAAGAGAA-CTTTCATTGGTAAGAGAAGTCCATTTATAGCC
126 ATGAAGAA-AAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* *
1924 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTCATAATCTCAAAATTGATTTAAA
1 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
* * * * * *
1989 TTTGAATTCTTTGTACATCTTTAGTTCAAACAGGCTAGAATTGAATGTCTACCTTGAGAAACTTG
66 GTTAAATT-TTTGTATATTTTTAGTT-AAACAGACTAGAATTGAATGTCTACCTTGAGAAACATG
** * *
2054 AAGAAGCAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTC
129 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* * **
2096 ACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGA-CCTAA
1 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
* ** *
2160 ATTTGATTCTTTGTATATTTTTAGTTAAAGCAGACTAGAATTCAATGTCTACCTTGAGAAACATG
66 GTTAAATT-TTTGTATATTTTTAGTTAAA-CAGACTAGAATTGAATGTCTACCTTGAGAAACATG
**
2225 AAGAAAAAAGCATTCATTGG-AAGAAAAGTGTATTTATAGTC
129 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* * * * * *
2266 ACCCATACCCTCAAAAGCCTTATTACTCGA-GTTAAATGGTTTTGTAATCCCATAATTGATTTTA
1 ACCCATTCCTTCAAAAGCCTTATTACTC-ACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
* * * * * *
2330 AGTTAAATGTTTTCTATATTTTTGGATAAACAAACTCA-AATTGAATGCCTACCTTGAGAAATAT
65 AGTTAAAT-TTTTGTATATTTTTAGTTAAACAGACT-AGAATTGAATGTCTACCTTGAGAAACAT
* * * * *
2394 -AAGAAAAAGGCATTCATTGGTAAGAAAAGTCCATTCACAATT
128 GAAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* * * * *
2436 ACCCACTT-CTTCAAGAGCCTTATTACGCACATTAAATGGTTTTATAATCTAAAAATTGATTTAA
1 ACCCA-TTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
* * ** * * * * * *
2500 ATTTGAATGTTTTGTGCATTTTTGGTTAAAATAGACGAGAATTGAATCTATACCATGAGAAACAT
65 AGTTAAAT-TTTTGTATATTTTTAGTT-AAACAGACTAGAATTGAATGTCTACCTTGAGAAACAT
* * *
2565 GAAGAAAAAA-TATTCATTGGTAAAAAAAGTCTATTTATAGTC
128 GAAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* *
2607 ACCCATTCCTTCAAAAACCTTATTAATCACT
1 ACCCATTCCTTCAAAAGCCTTATTACTCACT
2638 GGTAAAAAAA
Statistics
Matches: 591, Mismatches: 106, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
169 20 0.03
170 191 0.32
171 179 0.30
172 194 0.33
173 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (170 bp):
ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
GTTAAATTTTTGTATATTTTTAGTTAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAA
GAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
Found at i:2384 original size:170 final size:170
Alignment explanation
Indices: 1752--2637 Score: 887
Period size: 170 Copynumber: 5.2 Consensus size: 170
1742 NNNNNNNNNN
* *
1752 ACCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCAAACTTGATTTTAA
1 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
* * * * * *
1817 GTCCAAATTTTT-TTTCTTTTCT-GATTAAAACATATTATAATTGAATGTCTA-CTCTGAGAAAC
66 GT-TAAATTTTTGTATATTTT-TAG-TT-AAACAAACTAGAATTGAATGTCTACCT-TGAGAAAC
* * * * *
1879 ATAAAGAAGAGAA-CTTTCATTGGTAAGAGAAGTCCATTTATAGCC
126 ATGAAGAA-AAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* *
1924 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTCATAATCTCAAAATTGATTTAAA
1 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
* * * * ** *
1989 TTTGAATTCTTTGTACATCTTTAGTTCAAACAGGCTAGAATTGAATGTCTACCTTGAGAAACTTG
66 GTTAAATT-TTTGTATATTTTTAGTT-AAACAAACTAGAATTGAATGTCTACCTTGAGAAACATG
** * *
2054 AAGAAGCAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTC
129 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* * **
2096 ACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGA-CCTAA
1 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
* ** * *
2160 ATTTGATTCTTTGTATATTTTTAGTTAAAGCAGACTAGAATTCAATGTCTACCTTGAGAAACATG
66 GTTAAATT-TTTGTATATTTTTAGTTAAA-CAAACTAGAATTGAATGTCTACCTTGAGAAACATG
**
2225 AAGAAAAAAGCATTCATTGG-AAGAAAAGTGTATTTATAGTC
129 AAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* * * * * *
2266 ACCCATACCCTCAAAAGCCTTATTACTCGA-GTTAAATGGTTTTGTAATCCCATAATTGATTTTA
1 ACCCATTCCTTCAAAAGCCTTATTACTC-ACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
* * * * *
2330 AGTTAAATGTTTTCTATATTTTTGGATAAACAAACTCA-AATTGAATGCCTACCTTGAGAAATAT
65 AGTTAAAT-TTTTGTATATTTTTAGTTAAACAAACT-AGAATTGAATGTCTACCTTGAGAAACAT
* * * * *
2394 -AAGAAAAAGGCATTCATTGGTAAGAAAAGTCCATTCACAATT
128 GAAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* * * * *
2436 ACCCACTT-CTTCAAGAGCCTTATTACGCACATTAAATGGTTTTATAATCTAAAAATTGATTTAA
1 ACCCA-TTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
* * ** * * * * *
2500 ATTTGAATGTTTTGTGCATTTTTGGTTAAA-ATAGACGAGAATTGAATCTATACCATGAGAAACA
65 AGTTAAAT-TTTTGTATATTTTTAGTTAAACA-A-ACTAGAATTGAATGTCTACCTTGAGAAACA
* * *
2564 TGAAGAAAAAA-TATTCATTGGTAAAAAAAGTCTATTTATAGTC
127 TGAAGAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
* *
2607 ACCCATTCCTTCAAAAACCTTATTAATCACT
1 ACCCATTCCTTCAAAAGCCTTATTACTCACT
2638 GGTAAAAAAA
Statistics
Matches: 592, Mismatches: 104, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
169 21 0.04
170 195 0.33
171 175 0.30
172 194 0.33
173 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (170 bp):
ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA
GTTAAATTTTTGTATATTTTTAGTTAAACAAACTAGAATTGAATGTCTACCTTGAGAAACATGAA
GAAAAAAGCATTCATTGGTAAGAAAAGTCCATTTATAGTC
Found at i:2643 original size:55 final size:55
Alignment explanation
Indices: 2582--2692 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
2572 AAATATTCAT
2582 TGGTAAAAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAACCTTATTAATCAC
1 TGGTAAAAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAACCTTATTAATCAC
* *
2637 TGGTAAAAAAAGTCTATTTATAGTCACCCATTCCTTTAAAAGCCTTATTAATCAC
1 TGGTAAAAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAACCTTATTAATCAC
2692 T
1 T
2693 TTAAANNNNN
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (55 bp):
TGGTAAAAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAACCTTATTAATCAC
Found at i:12127 original size:172 final size:171
Alignment explanation
Indices: 11183--12127 Score: 997
Period size: 172 Copynumber: 5.5 Consensus size: 171
11173 NNNNNNNNNN
* * * *
11183 AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAAACTTTTCTTGCAAAAGAATAGT
1 AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACT
* * * * *
11248 TCTTTCTTCATGTTTCTTATGGTAGACATTGAATTCTAGTCTGTTTTAACAAAAAATGTACAAAG
66 TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTGTTTTAACAAAAAATGTACAAAG
*
11313 AATTCAGATTTAAATAAATTTTGAGATTATAAAACCATTTAA
131 AATTCA-ATTTAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * *
11355 AGTGATTAATAAGGCTTTTGAAGGAGTGGGTAACTATAAATGGACTTCTT-TTGCCAATGAATGC
1 AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTT-TTCTTGCCAATGAATAC
* * * * * * * * * * *
11419 CTTTTTATTTATGTTTCTTAGGGTGAAAAATTCAATTATAATATGTTTTAACCAGAAAAA--CAA
65 TTTTTTCTTCATGTTTCTCAAGGT-AGACATTCAATTCTAATCTGTTTTAA-CA-AAAAATGTAC
* ** *
11482 AAAAAATAGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAA
127 AAAGAATTCAA-TTTAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * * * * * * * *
11528 AGTTATTGATAAGCCTTTTGGAGCAATGAGTGACTATAAATAAACTTTTCTTGCTAAAGAACAAT
1 AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACT
* * * * *
11593 TTTTTCTTCATGTTTCTTAAAGTAGACATTCAATCCTAATCTGTTTTGACAAAAAAGGTACAAAG
66 TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTGTTTTAACAAAAAATGTACAAAG
* * *
11658 AATCCAGATTTAAATCAATTATG-GCATTACAAAACCATTTAA
131 AATTCA-ATTTAAATCAATTTTGAG-ATTATAAAACCATTTAA
* * * * *
11700 AGCGAGTAATAAGGCTTTCGAAGGT-ATGGGAGACTATAAATAGACTTTTCTTGCCAATGAATGC
1 AGTGATTAATAAGGCTTTTGAA-GTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATAC
**
11764 TTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTTGTCTGTTTTAACAAAAAATGTACAAA
65 TTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTGTTTTAACAAAAAATGTACAAA
*
11829 GAATTCAAATTTAAATCAATTTTGAGATTATGAAACCATTTAA
130 GAATTC-AATTTAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * *
11872 AGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTCTCTTGCCAATGAA-A-T
1 AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACT
* * * * * * *
11935 TTCTCTTCTTTATATTTCTCACGGTAGACATTCAATTATAATATGTTTTAACAAGAAAA-GCAAA
66 TT-T-TTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTGTTTTAACAA-AAAATGTACA
* * * * *
11999 AATATTTGAACTTAAAATCAATTTTGAGATTATAAAACCCTTTAA
128 AAGAATTCAA-TTTAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * *
12044 AGTAATTAATAAGGCTTTTGAATTAATGGGTGGCTATAAATAGACTTTTTTTGCTAATGAATACT
1 AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACT
12109 TTTTTCTTCATGTTTCTCA
66 TTTTTCTTCATGTTTCTCA
12128 TGGNNNNNNN
Statistics
Matches: 630, Mismatches: 123, Indels: 40
0.79 0.16 0.05
Matches are distributed among these distances:
170 8 0.01
171 7 0.01
172 468 0.74
173 137 0.22
174 5 0.01
175 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (171 bp):
AGTGATTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACT
TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTGTTTTAACAAAAAATGTACAAAG
AATTCAATTTAAATCAATTTTGAGATTATAAAACCATTTAA
Found at i:13097 original size:172 final size:172
Alignment explanation
Indices: 12699--13352 Score: 504
Period size: 172 Copynumber: 3.8 Consensus size: 172
12689 GTACAAAACA
* * * * * *
12699 TTCAAATTTAAATCAATTGTAAGATTATAAAACCATTTAAAGTGTGTAATAAGGCTCTTAAAGGA
1 TTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA-GA
* * * * * * ******
12764 GTAGG-TGACTATAAATGGACTTCTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTNNNNNNN
65 AT-GGATGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCT-CAAGGT
***** * * * * * * *
12828 NNNNNTT-AATT-AGAGT-T-TCTTTAACCAAAAATATAAAAACAG
128 AGACATTCAATTCATAATATGT-TTTAACAAAAAAAACAAAAATAT
* * ** * *
12870 TTCAACTTAAAATCAATTATG-GCATTCCAAAACCATTTAAAGCGGGTAATAAGGCTTTTGAAGA
1 TTCAAATTAAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGA
* * * *
12934 TATAGATGACTATAAATAGACTTTTCTTACCAATGATTGCTTTTTTCTTCCTGTTTCTCAAGGTA
65 -ATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTA
* * *
12999 GACATTCAATTC-TAGTCTGTTTTAATAAAAAATATACAAAAA-A-
129 GACATTCAATTCATAATATGTTTTAACAAAAAA-A-ACAAAAATAT
* * * *
13042 TTCAAATTTAAATCCATTTTGAGATTATGAAACCATTTAAAGTGAGTATTAAGGCTTTTGAAGGA
1 TTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA-GA
* * * * * * * *
13107 ATGGGTGACTATCAATGGACTTCTCTTGTCAATGAATGCTCTCTTC-TCTATGTTTCTCTAGGTA
65 ATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTC-ATGTTTCTCAAGGTA
* * * *
13171 GACATTCAA-ACATAATATGTTTTAACCAGAAAAGCAAAAATAT
129 GACATTCAATTCATAATATGTTTTAACAAAAAAAACAAAAATAT
* * * * *
13214 TTGAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGATTAATAAAGCTTTTGAAGCA
1 TTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG-A
** * *
13279 ATGGATGACTATAAATAGACTTTT-TTGCCAATGAATATTTTTTTCTTCATGTTTCTCATGGTAT
65 ATGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAG
*
13343 AGATTCAATT
130 ACATTCAATT
13353 NNNNNNNNNN
Statistics
Matches: 377, Mismatches: 88, Indels: 35
0.75 0.18 0.07
Matches are distributed among these distances:
170 12 0.03
171 144 0.38
172 210 0.56
173 5 0.01
174 6 0.02
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.37
Consensus pattern (172 bp):
TTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAA
TGGATGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGA
CATTCAATTCATAATATGTTTTAACAAAAAAAACAAAAATAT
Found at i:14224 original size:171 final size:171
Alignment explanation
Indices: 13728--14224 Score: 452
Period size: 168 Copynumber: 2.9 Consensus size: 171
13718 TTATTACTCG
* * *
13728 CTTTAAATGGTTTTGTAATGC-CATAATTGATTTAAATCTGAATTCTTTGTACATTTTTTGTCAA
1 CTTTAAATGGTTTTATAAT-CTCAAAATTGATTTAAATCTGAATTCTTTGTACATTTTTT-TTAA
* * * * * * *
13792 AACTGATTAGGATTGAGTGTCTACCTTAAGAAACATGAAGAAAAAAATGTTCTTCAGCAAGAAAA
64 AACAGATTAGGATTAAATGTCTACCCTAAGAAACATGAAGAAAAAAGTATTCTTTAGCAAGAAAA
*
13857 GTTTATTTATAGTCACCCATTGCTTCAAAATGCTTATCAATAA
129 GTTTATTTATAGTCACCCATTACTTCAAAATGCTTATCAATAA
* * * * *
13900 CTTTAAATGGTTTTATAATGTCCAAATTGATTTGAAGT-TCAATT-TTT-T---TTTTCTGGTTA
1 CTTTAAATGGTTTTATAATCTCAAAATTGATTT-AAATCTGAATTCTTTGTACATTTT-T-TTTA
* ** * * * * * * *
13959 AAACATATTATAATTAAATGTCTACCCTAAGAAACATAAATAAAAAGGCATTCATTGGCAAGAGA
63 AAACAGATTAGGATTAAATGTCTACCCTAAGAAACATGAAGAAAAAAGTATTCTTTAGCAAGAAA
** * * * * * *
14024 AGTCCATTCATAGTTACCCACTCCTTCAAAA-GCCTTATTAATCA
128 AGTTTATTTATAGTCACCCATTACTTCAAAATG-CTTATCAATAA
**********
14068 CTTTAAANNNNNNNNNNATCTCAAAATTGATTTAAATCTGAATTCTTTGTACATTTTTTTTAAAA
1 CTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATCTGAATTCTTTGTACATTTTTTTTAAAA
* * *
14133 CAGACTAGGATTCAATGTCTACCGTAAGAAACATGAAGAAAAAAGTATTCTTTAGCAAGAAAAGT
66 CAGATTAGGATTAAATGTCTACCCTAAGAAACATGAAGAAAAAAGTATTCTTTAGCAAGAAAAGT
*
14198 TTATTTATAGTCACTCATTACTTCAAA
131 TTATTTATAGTCACCCATTACTTCAAA
14225 NNNNNNNNNN
Statistics
Matches: 246, Mismatches: 68, Indels: 23
0.73 0.20 0.07
Matches are distributed among these distances:
167 8 0.03
168 111 0.45
169 3 0.01
170 2 0.01
171 81 0.33
172 34 0.14
173 7 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.36
Consensus pattern (171 bp):
CTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATCTGAATTCTTTGTACATTTTTTTTAAAA
CAGATTAGGATTAAATGTCTACCCTAAGAAACATGAAGAAAAAAGTATTCTTTAGCAAGAAAAGT
TTATTTATAGTCACCCATTACTTCAAAATGCTTATCAATAA
Found at i:16299 original size:171 final size:171
Alignment explanation
Indices: 15984--17447 Score: 1430
Period size: 171 Copynumber: 8.5 Consensus size: 171
15974 TTTGAACTTA
** * *
15984 AAATCAATTTTGAGACGATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGCAATAGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * *
16049 TATAAATAGAATTTTCTTGCTAATGAATACTTTTTTCTTCATGTTTCTGATGGTAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* *
16114 CCTAGTCCGTTTTAA-AAATAATATACAAAGAATTCAAATTT
131 CCTAGTCTGTTTTAACAAA-AATATACAAAAAATTCAAATTT
* *
16155 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAAAGGGTAAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGAC
** * * ** * ** **
16220 TATAAATGGGGTTTTCTTACCAATCAATA-TTCTCGTCTTTATGTTTCTCTGGGTAGATGTTCAA
66 TATAAATGGACTTTTCTTGCCAATGAATACTT-TTTTCTTCATGTTTCTCAAGGTAGACATTCAA
** * * * * * *
16284 TTATAATATGTTTTAACCAGAAAAGTA-A-AAAAATTTGAACTTA
130 TCCTAGTCTGTTTTAA-CA-AAAA-TATACAAAAAATTCAAATTT
* * *
16327 AAATCAATTTTTAGATTATAAAACCATTTAAAGTGATTAATAAGGATTTTGAAGCAATGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGAC
** * * * * * *
16392 TATAAAAAGACTTTTTTTTCCAATGAATACTTTTTTCTTCATGTTTCTCACGGCACAAATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * ** *
16457 TCTAGTCTATTTTAACTAAAAACGTACAAAACATTCAAATTT
131 CCTAGTCTGTTTTAAC-AAAAATATACAAAAAATTCAAATTT
* * * * * * *
16499 AAATCAATTTTGATATTATAACACCATTTAAACTGAATAATAAGGCTCTTGAAGGAATGGATGAA
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGAC
* * *
16564 TATAAATGGACTGTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCGAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * *
16629 CCCAGTCTGTTTTAACCAAAAATGTACAAAGAATTCAAATTT
131 CCTAGTCTGTTTTAA-CAAAAATATACAAAAAATTCAAATTT
* *
16671 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGCA-TAATAAGGCTTTT-ATGGAATGTGTGA
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTG-ATTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * * *
16734 CTATAAATGGACTTCTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAAGTAGGCATTCAA
65 CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
** * * *
16799 T--TAGAGTTTCTTTAACCAAAAATATA-AAAACAATTCAACTTA
130 TCCTAGTCTGT-TTTAA-CAAAAATATACAAAA-AATTCAAATTT
* * * * * * *
16841 AAATCAATTATG-GCATTACAAAACAATTTAAAGCGAGTAATAAGACTTTTGAAGGTATGGGTGA
1 AAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGA
* * *
16905 CTATAAATAGACTTTTCTTGCCAACGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAA
65 CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
*
16970 TCCTAGTCTGTTTTAACTAAAATATACAAAAAATTCAAATTT
130 TCCTAGTCTGTTTTAACAAAAATATACAAAAAATTCAAATTT
* * * ** *
17012 AAATCAATTTTGAGATTATAAAACGATTTAATGCGCGTAATAAGGCTTTTGAAGGAGTGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * *
17077 TATAAATGGACTTCTCTTGCCAATGAATGCCTTTTTATTTATGTTTCTCAAGGTAGGCATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
*** * * * * *
17142 TAGAGTTTG-TTTAACCAGAAATATAAAAAAAATTCAACTTA
131 CCTAGTCTGTTTTAA-CAAAAATATACAAAAAATTCAAATTT
* * * * * ** *
17183 AAATCAATTAGTG-CATTACAAAACCATTTAAAG-GTAGTAATAAGACTTTTGAAGGTGTGGGTA
1 AAATCAATT-TTGAGATTATAAAACCATTTAAAGTG-ATTAATAAGGCTTTTGAAGGAATGGGTG
* * *
17246 ACTATAAAAT-GACTTTTCTTGCCAATGAATATTTTTTTCTTCATGTTTCTTAAGGTAGACATTT
64 ACTAT-AAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * *
17310 AA-CTCTAGTGTGTTTTAACGAAAAATGTATAAAAAATTCAAATTT
128 AATC-CTAGTCTGTTTTAAC-AAAAATATACAAAAAATTCAAATTT
* ********** * *
17355 AAATAAATTTTGNNNNNNNNNNACCATTTAAAGTGAATAATAAGG-TTTTGAAAAGAATGGGTGA
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTG-AAGGAATGGGTGA
* *
17419 CTATAAATAGACTTCTCTTGCCAATGAAT
65 CTATAAATGGACTTTTCTTGCCAATGAAT
17448 GCTCTCTTNN
Statistics
Matches: 1052, Mismatches: 210, Indels: 61
0.80 0.16 0.05
Matches are distributed among these distances:
169 9 0.01
170 73 0.07
171 527 0.50
172 425 0.40
173 14 0.01
174 4 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (171 bp):
AAATCAATTTTGAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGAC
TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
CCTAGTCTGTTTTAACAAAAATATACAAAAAATTCAAATTT
Found at i:19088 original size:172 final size:172
Alignment explanation
Indices: 18865--19215 Score: 454
Period size: 172 Copynumber: 2.0 Consensus size: 172
18855 NNNNNNNATG
* *
18865 GTTTTATAATCTCAAAATTGATTTAAATTTGAATTCATTGTACATTTTTGGTTAAAACAGACTGG
1 GTTTTATAATCTCAAAATTGATTTAAATTTAAATTCATTGTACATTTTTGGTTAAAACAGACTAG
* * * **** *
18930 GATTGAATGTCTACTTTCAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAACAA-TCCATTTA
66 AATTGAATCTATACCAAAAGAAACATGAAGAAAAAAGTATTCATTGGCAA-AAAAAGTCCATTTA
* * * * *
18994 TATTCACCCATTCCTTCAAGAGCCTTATTATTCAGTTGAAATA
130 TAGTAACCCATTCCTTCAAAAGCCTTATTAATCACTTGAAATA
* * *
19037 GTTTTATAATCTCAAAATTGATTTAAATTTAAATGT-TTTGTACGTTTTTGGTTAAAATAGACTA
1 GTTTTATAATCTCAAAATTGATTTAAATTTAAAT-TCATTGTACATTTTTGGTTAAAACAGACTA
* **
19101 GAATTGAATCTATGCCAAAAGAAACATGAAGAAAAAAGTATTCATTGGCAAAAAAAGTCTTTTTA
65 GAATTGAATCTATACCAAAAGAAACATGAAGAAAAAAGTATTCATTGGCAAAAAAAGTCCATTTA
* * *
19166 TAGTAACCCATTGCTTCAAAAGCCTTATTAATCACTTTAAATG
130 TAGTAACCCATTCCTTCAAAAGCCTTATTAATCACTTGAAATA
19209 GTTTTAT
1 GTTTTAT
19216 NNNNNNNNNN
Statistics
Matches: 153, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
171 4 0.03
172 148 0.97
173 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (172 bp):
GTTTTATAATCTCAAAATTGATTTAAATTTAAATTCATTGTACATTTTTGGTTAAAACAGACTAG
AATTGAATCTATACCAAAAGAAACATGAAGAAAAAAGTATTCATTGGCAAAAAAAGTCCATTTAT
AGTAACCCATTCCTTCAAAAGCCTTATTAATCACTTGAAATA
Done.