Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397827.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1129.0, 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: 15504
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.26
Warning! 4919 characters in sequence are not A, C, G, or T
Found at i:4795 original size:18 final size:17
Alignment explanation
Indices: 4774--4820 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
4764 CTTTAAATGG
4774 TTTTATAATCTTAAAATT
1 TTTTATAAT-TTAAAATT
* *
4792 TTTTTTAATTTCAAATT
1 TTTTATAATTTAAAATT
4809 TTTTATATATTT
1 TTTTATA-ATTT
4821 TTTTAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATAATTTAAAATT
Found at i:5624 original size:28 final size:28
Alignment explanation
Indices: 5592--5650 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
5582 CTGCCATGGG
5592 AAACATAAAGAAAAAGGTATTCATCGAT
1 AAACATAAAGAAAAAGGTATTCATCGAT
5620 AAACATAAAGAAAAAGGTATTCATCGAT
1 AAACATAAAGAAAAAGGTATTCATCGAT
5648 AAA
1 AAA
5651 AAAAGTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.14, T:0.20
Consensus pattern (28 bp):
AAACATAAAGAAAAAGGTATTCATCGAT
Found at i:7252 original size:170 final size:171
Alignment explanation
Indices: 7033--7500 Score: 514
Period size: 170 Copynumber: 2.7 Consensus size: 171
7023 TGTTCATTGG
* * **
7033 CAAGAAAAGTCCATTTATTGTTACGAATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTT
1 CAAGAAAAGTCCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTT
* *
7098 ATAATCTCATAATTGATTTTAGGTTGAATTTTTTTAGGTTTTTAGTTAGAACAGATTATAATGGA
66 ATAATCTCATAATTGATTTTAGGTTGAACTTTTTGAGGTTTTTAGTTAGAACAGATTATAATGGA
*
7163 ATGTTTGGAC-TGGGAAACA-CAAAGAAAAA-GCATTCATCGA
131 ATGTCT-GACTTGGGAAACATCAAA-AAAAATGCATTCATCGA
** * * * * * *
7203 CAAGAATGGTCCATTTATAGTTG-CTCATTTCTTGAAAGGCCTTATTACTCACTGTAAATGGTTT
1 CAAGAAAAGTCCATTTAT-GGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
* * ** * * *
7267 TATAGTCTCATAATTGATGTTAGGTTGAACTTTTTGATTTTTTTGGTTAGGACAGATTATAATTG
65 TATAATCTCATAATTGATTTTAGGTTGAACTTTTTGAGGTTTTTAGTTAGAACAGATTATAATGG
* * * * *
7332 AATGTCTGCCTTGGGAAACATGAAAAAAAATGTATTCATTGG
130 AATGTCTGACTTGGGAAACATCAAAAAAAATGCATTCATCGA
* * * ** *
7374 TAAGAAAAGTTCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCAATTTAAAAAGTTTC
1 CAAGAAAAGTCCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTT
* * ** * *
7439 ATATTCTCATAATTGATTTTAGGTTGAACCTTTTGACATTTTTTA-TTTGAACAAATTATAAT
66 ATAATCTCATAATTGATTTTAGGTTGAACTTTTTGA-GGTTTTTAGTTAGAACAGATTATAAT
7501 TAAACGTCTG
Statistics
Matches: 244, Mismatches: 48, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
169 2 0.01
170 130 0.53
171 106 0.43
172 6 0.02
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (171 bp):
CAAGAAAAGTCCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTT
ATAATCTCATAATTGATTTTAGGTTGAACTTTTTGAGGTTTTTAGTTAGAACAGATTATAATGGA
ATGTCTGACTTGGGAAACATCAAAAAAAATGCATTCATCGA
Found at i:7454 original size:171 final size:169
Alignment explanation
Indices: 6965--7522 Score: 559
Period size: 171 Copynumber: 3.3 Consensus size: 169
6955 TTGTTTTATA
* * ** * *
6965 TTTTTGTTTAAAACATATTATAATTGAATGTCTACGCC-GATAAACATGAAGAAAAAGGTGTTCA
1 TTTTTG-TTAGAACAGATTATAATTGAATGTCTA-GCCTGGGAAACATGAA-AAAAAAGTATTCA
* * **
7029 TTGGCAAGAAAAGTCCATTTATTGTTACGAATTCCTTCAAAAGCCTTATTACTCACTTTAAATGG
63 TTGGCAAGAAAAGTCCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGG
* * *
7094 TTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTAGGT
128 TTTTATAATCTCATAATTGATTTTAGGTTGAACTTTTTGA-AT
* * * * * * * *
7137 TTTTAGTTAGAACAGATTATAATGGAATGTTTGGACTGGGAAACA-CAAAGAAAAAGCATTCATC
1 TTTTTGTTAGAACAGATTATAATTGAATGTCTAGCCTGGGAAACATGAAA-AAAAAGTATTCATT
* ** * * * * * *
7201 GACAAGAATGGTCCATTTATAGTTG-CTCATTTCTTGAAAGGCCTTATTACTCACTGTAAATGGT
65 GGCAAGAAAAGTCCATTTAT-GGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGT
* * *
7265 TTTATAGTCTCATAATTGATGTTAGGTTGAACTTTTTGATT
129 TTTATAATCTCATAATTGATTTTAGGTTGAACTTTTTGAAT
*
7306 TTTTTGGTTAGGACAGATTATAATTGAATGTCT-GCCTTGGGAAACATGAAAAAAAATGTATTCA
1 TTTTT-GTTAGAACAGATTATAATTGAATGTCTAGCC-TGGGAAACATGAAAAAAAA-GTATTCA
* * * **
7370 TTGGTAAGAAAAGTTCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCAATTTAAAAAG
63 TTGGCAAGAAAAGTCCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGG
* * *
7435 TTTCATATTCTCATAATTGATTTTAGGTTGAACCTTTTGACAT
128 TTTTATAATCTCATAATTGATTTTAGGTTGAACTTTTTGA-AT
* * * * *
7478 TTTTTATTTGAACAAATTATAATTAAACGTCT-GCCATGGGAAACA
1 TTTTTGTTAGAACAGATTATAATTGAATGTCTAGCC-TGGGAAACA
7523 NNNNNNNNNN
Statistics
Matches: 312, Mismatches: 65, Indels: 19
0.79 0.16 0.05
Matches are distributed among these distances:
169 8 0.03
170 140 0.45
171 153 0.49
172 11 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (169 bp):
TTTTTGTTAGAACAGATTATAATTGAATGTCTAGCCTGGGAAACATGAAAAAAAAGTATTCATTG
GCAAGAAAAGTCCATTTATGGTGACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
TATAATCTCATAATTGATTTTAGGTTGAACTTTTTGAAT
Found at i:8749 original size:171 final size:170
Alignment explanation
Indices: 8439--8795 Score: 443
Period size: 171 Copynumber: 2.1 Consensus size: 170
8429 NNNNNNNNNN
* * * * * *
8439 ATTGATTTTAGGTTGAATTTTTTTACGTTTTTAGTTAGAATAGATTATAATTGAATGTTTGCCCT
1 ATTGATTTTAGGTTGAACTTTTTTACGTTTTTAGTTAGAACAAATTATAATTGAACGTCTGCCAT
* * ** **
8504 AGAAACGCGAAGAAAAAGGCATTCATCGATAAGAATGGTCCATTTATAGTCCCTCATTTCTTTGA
66 AGAAACACGAAGAAAAAGGCATTCATCGACAAGAAAAGTCCATTTATAGTCCCTCATTTCTTCAA
* *
8569 AGCCCTTATTACTCAC-TGTAAATAGTTTTATAGTCTTATA
131 AGCCCTTATTACTCACTTG-AAATAGTTTTATAATCTCATA
* *
8609 ATTGATTTTAGGTTGAGCTTTTTTACATTTTTTA-TTAGAACAAATTATAATTGAACGTCTGCCA
1 ATTGATTTTAGGTTGAACTTTTTTAC-GTTTTTAGTTAGAACAAATTATAATTGAACGTCTGCCA
* * * *
8673 TGGGAAACATGAAGAAAAAGGTATTCATCGACAAGAAAAGTCTATTTATAGTCACC-CA-TTCGT
65 T-AGAAACACGAAGAAAAAGGCATTCATCGACAAGAAAAGTCCATTTATAGTC-CCTCATTTC-T
* *
8736 TCAAAGGCCTTATTACTTACTTGAAATAGTTTTATAATCTCATA
127 TCAAAGCCCTTATTACTCACTTGAAATAGTTTTATAATCTCATA
8780 ATTGATTTTAGGTTGA
1 ATTGATTTTAGGTTGA
8796 NNNNNNNNNN
Statistics
Matches: 160, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
170 53 0.33
171 103 0.64
172 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (170 bp):
ATTGATTTTAGGTTGAACTTTTTTACGTTTTTAGTTAGAACAAATTATAATTGAACGTCTGCCAT
AGAAACACGAAGAAAAAGGCATTCATCGACAAGAAAAGTCCATTTATAGTCCCTCATTTCTTCAA
AGCCCTTATTACTCACTTGAAATAGTTTTATAATCTCATA
Found at i:9260 original size:172 final size:168
Alignment explanation
Indices: 8898--10649 Score: 1240
Period size: 171 Copynumber: 10.2 Consensus size: 168
8888 NNNNNNNNAC
* * * * * ** * *
8898 AGTGAGTAATAAGGCCTTTCAAGAAATGAGG-GACTATAAATGGACCATTCTTTTCGATGAATGC
1 AGTGAGTAATAAGGCTTTTGAAGGAATG-GGTGACTATAAAT-GAACTTTCTTGCCAATGAATAC
** * * * * *
8962 CTTTTTCTTCGCGTTTTCCAGGGCAAACATTCCATTATAATCTGTTCTAACTAAAAACGTAAAAG
64 CTTTTTCTTCATGTTTT-CAAGGCAGACATTCAATTATAATCTGTTTTAAC-AAAAACATAAAA-
* **
9027 AA-TTCAACCTAAAATCAATTATGAGATTATAAAAATATTTAA
126 AAGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * *
9069 AGTGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATGAACTCTTCTT-CGCAATGAACAC
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACT-TTCTTGC-CAATGAATAC
* * * * * *
9133 CTTTTTCTTCATGTTTGTCGACGTAGATATTCAATTATAATATGTTTTAAACAAAAAGATAAAAC
64 CTTTTTCTTCATGTTT-TCAAGGCAGACATTCAATTATAATCTGTTTT-AACAAAAACATAAAA-
* * *
9198 AATTTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAA
126 AAGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * * ***
9241 AGTGAGTAATAAAGCTTTTGAAGCAATGGGTGACTATAAATAGACCTTTCTTGTCAATTAATGTA
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GAACTTTCTTGCCAATGAATACC
* * * * * * *
9306 TTTTTCTTTATATTTCTCGAGGTAGACATTCAATTACAATCTGTTTTAAAAAAATATATAAACAA
65 TTTTTCTTCATGTTT-TCAAGGCAGACATTCAATTATAATCTGTTTTAACAAAA-ACATAAA-AA
* * ** * *
9371 ATTTGAAATTAAAATAAATTTTAAGATTATAAAACCATTTAA
127 AGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * ** *
9413 ATTGAGTAATAAGGCTTTTGAAAGAATATGTGACTATAAATTAACTTTTCTTGCCAATGAATACC
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAAC-TTTCTTGCCAATGAATACC
* * * *
9478 TTTTTCTTCATGTTTCGCAACAGCAAACATTCAATTATAATCTGTTTTAACAAAAA-ATGTCAAA
65 TTTTTCTTCATGTTT-TCAA-GGCAGACATTCAATTATAATCTGTTTTAACAAAAACA--TAAAA
* *
9542 AAGTTCAACCTAAAATAAATTTTGAGACTAT-AAACCATTTAA
126 AAGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * *
9584 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGATTATAAATAGACCTTTGTTGCCGATGAATACC
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GAACTTTCTTGCCAATGAATACC
* * *
9649 TTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACAGAAAAAA
65 TTTTTCTTCATGTTT-TCAAGGCAGACATTCAATTATAATCTGTTTTAAC-AAAAACATAAAAAA
9714 -TTCAACCTAAAATC-ATTTATGAGATTATAAAACCATTTAA
128 GTTCAACCTAAAATCAATTT-TGAGATTATAAAACCATTTAA
* * * * * *
9754 AGTGAGTAAGAAGGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTGCCCACGAATTCC
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAAC-TTTCTTGCCAATGAATACC
* * * * * * * * *
9819 TTTTTCTTCATGTTTCCCATGGCAGATATTTAATTATCATTTGTTCTAATAAAAA-ATGTCAAAA
65 TTTTTCTTCATGTTT-TCAAGGCAGACATTCAATTATAATCTGTTTTAACAAAAACA--TAAAAA
* * * * *
9883 AGCTCAACCTAAAATCAATTATGAGAATATGAAACTATTTAA
127 AGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * *
9925 AGTGAGTAATAAGGCTTATGAAGGAATGGGTCACTATAAATGAACCTTTGTTGCCAATGAATACC
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAA-CTTTCTTGCCAATGAATACC
* * *
9990 TTTTTCTTCATGTTTTCCAGGGCAGACATTCAATTATAATCTGTCTTAACCAAAAACATGAAAAA
65 TTTTTCTTCATGTTTT-CAAGGCAGACATTCAATTATAATCTGTTTTAA-CAAAAACATAAAAAA
* * *
10055 GTTCAACCTAAAATCAATTATGAGACTATAAAACCATTTAC
128 GTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * * ** * * * * *
10096 AGTAAGTAATAAGGCCTTTAAAAAAATAAGG-GACTATAAATGGACCATTCTTG-TAGATGAATG
1 AGTGAGTAATAAGGCTTTTGAAGGAAT-GGGTGACTATAAAT-GAACTTTCTTGCCA-ATGAATA
*** * * * * *
10159 CCTTTTTCTTTGCGTTTCCCAAGGCAAACATTCCATTATAATCTGTTCTAACTAAAAACGTAAAA
63 CCTTTTTCTTCATGTTT-TCAAGGCAGACATTCAATTATAATCTGTTTTAAC-AAAAACATAAAA
* *************************
10224 AAATTCAACCTAAAATCANNNNNNNNNNNNNNNNNNNNNNNNN
126 AAGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
**** * * * * ***
10267 NNNNAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTTCTAATGAATGTA
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAAC-TTTCTTGCCAATGAATACC
* * * * * * **
10332 TTTTTCTTCATATTTGTCGAGGTAGACAATCAATTATAATATGTTTTAAACAGAAATGTAAAAAA
65 TTTTTCTTCATGTTT-TCAAGGCAGACATTCAATTATAATCTGTTTT-AACAAAAACAT-AAAAA
* * * * *
10397 ATTTGAACTTAAAATCAATTTTGAGATTATAAAACTATTTAN
127 AGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
********* * * * * * ***
10439 NNNNNNNNNTAAGGCTTTTGAAGCAATAGGTGACTATAAATAGACCTTTCTTGTCAATTAATGTA
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GAACTTTCTTGCCAATGAATACC
* * * * * *
10504 TTTTTCTTTACAT-TTCTCGAGGTAGACATTCAATTATAATCTATTTTAAAAAAAATATAAAAAA
65 TTTTTC-TT-CATGTTTTCAAGGCAGACATTCAATTATAATCTGTTTTAACAAAAACAT-AAAAA
* * ** * * *
10568 ATTTGAAATTAAAATAAATTTTAAGATAATAAAACCATTTAA
127 AGTTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* *
10610 AGTGAGTAATAAGGCTTTCGAAAGAATGGGTGACTATAAA
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
10650 NNNNNNNNNN
Statistics
Matches: 1245, Mismatches: 295, Indels: 82
0.77 0.18 0.05
Matches are distributed among these distances:
168 5 0.00
169 28 0.02
170 153 0.12
171 624 0.50
172 388 0.31
173 44 0.04
174 3 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.34
Consensus pattern (168 bp):
AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTCTTGCCAATGAATACCT
TTTTCTTCATGTTTTCAAGGCAGACATTCAATTATAATCTGTTTTAACAAAAACATAAAAAAGTT
CAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
Found at i:9646 original size:171 final size:169
Alignment explanation
Indices: 8898--10241 Score: 1264
Period size: 171 Copynumber: 7.9 Consensus size: 169
8888 NNNNNNNNAC
* * * * ** * *
8898 AGTGAGTAATAAGGCCTTTCAAGAAATGAGG-GACTATAAATGGACCATTCTTTTCGATGAATGC
1 AGTGAGTAATAAGGCCTTTGAAGGAATG-GGTGACTATAAATAGACCTTTCTTGCCAATGAATAC
** * * * *
8962 CTTTTTCTTCGCGTTTTCCAGGGCAAACATTCCATTATAATCTGTTCTAACTAAAAACGTAAAAG
65 CTTTTTCTTCATG-TTTCCAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAAATGTAAAA-
* **
9027 AATTCAACCTAAAATCAATTATGAGATTATAAAAATATTTAA
128 AATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * *
9069 AGTGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAAT-GAACTCTTCTT-CGCAATGAACA
1 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATAGACCT-TTCTTGC-CAATGAATA
* * * * * * * *
9132 CCTTTTTCTTCATGTTTGTCGACGTAGATATTCAATTATAATATGTTTTAA-ACAAAAA-GATAA
64 CCTTTTTCTTCATGTTT-CCAAGGCAAACATTCAATTATAATCTGTTCTAACA-AAAAATG-TAA
* *
9195 AACAATTTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAA
126 AA-AA-TTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * * ***
9241 AGTGAGTAATAAAGCTTTTGAAGCAATGGGTGACTATAAATAGACCTTTCTTGTCAATTAATGTA
1 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTGCCAATGAATACC
* * * * * * * *
9306 TTTTTCTTTATATTTCTCGAGGTAGACATTCAATTACAATCTGTTTTAA-AAAAATATATAAACA
66 TTTTTCTTCATGTTTC-CAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAA-ATGTAAA-A
* ** * *
9370 AATTTGAAATTAAAATAAATTTTAAGATTATAAAACCATTTAA
128 AA-TTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * * ** *
9413 ATTGAGTAATAAGGCTTTTGAAAGAATATGTGACTATAAATTA-ACTTTTCTTGCCAATGAATAC
1 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAA-TAGACCTTTCTTGCCAATGAATAC
* *
9477 CTTTTTCTTCATGTTTCGCAACAGCAAACATTCAATTATAATCTGTTTTAACAAAAAATGTCAAA
65 CTTTTTCTTCATGTTTC-CAA-GGCAAACATTCAATTATAATCTGTTCTAACAAAAAATGT-AAA
* * *
9542 AAGTTCAACCTAAAATAAATTTTGAGACTAT-AAACCATTTAA
127 AAATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * *
9584 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGATTATAAATAGACCTTTGTTGCCGATGAATACC
1 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTGCCAATGAATACC
9649 TTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACA-G-AAAA
66 TTTTTCTTCATGTTTC-CAAGGCAAACATTCAATTATAATCTGTTCTAAC-AAAAA-ATGTAAAA
9712 AATTCAACCTAAAATC-ATTTATGAGATTATAAAACCATTTAA
128 AATTCAACCTAAAATCAATTT-TGAGATTATAAAACCATTTAA
* * * * * * * *
9754 AGTGAGTAAGAAGGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTGCCCACGAATTCC
1 AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTGCCAATGAATACC
* * * * * * *
9819 TTTTTCTTCATGTTTCCCATGGCAGATATTTAATTATCATTTGTTCTAATAAAAAATGTCAAAAA
66 TTTTTCTTCATGTTT-CCAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAAATGT-AAAAA
** * * * *
9884 GCTCAACCTAAAATCAATTATGAGAATATGAAACTATTTAA
129 ATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* *
9925 AGTGAGTAATAAGG-CTTATGAAGGAATGGGTCACTATAAAT-GAACCTTTGTTGCCAATGAATA
1 AGTGAGTAATAAGGCCTT-TGAAGGAATGGGTGACTATAAATAG-ACCTTTCTTGCCAATGAATA
* *
9988 CCTTTTTCTTCATGTTTTCCAGGGCAGACATTCAATTATAATCTG-TCTTAACCAAAAACATG-A
64 CCTTTTTCTTCATG-TTTCCAAGGCAAACATTCAATTATAATCTGTTC-TAA-CAAAAA-ATGTA
* * * *
10051 AAAAGTTCAACCTAAAATCAATTATGAGACTATAAAACCATTTAC
125 AAAAATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
* * ** * * * * *
10096 AGTAAGTAATAAGGCCTTTAAAAAAATAAGG-GACTATAAATGGACCATTCTTG-TAGATGAATG
1 AGTGAGTAATAAGGCCTTTGAAGGAAT-GGGTGACTATAAATAGACCTTTCTTGCCA-ATGAATA
*** * * *
10159 CCTTTTTCTTTGCGTTTCCCAAGGCAAACATTCCATTATAATCTGTTCTAACTAAAAACGTAAAA
64 CCTTTTTCTTCATGTTT-CCAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAAATGT-AAA
10224 AAATTCAACCTAAAATCA
127 AAATTCAACCTAAAATCA
10242 NNNNNNNNNN
Statistics
Matches: 977, Mismatches: 155, Indels: 82
0.80 0.13 0.07
Matches are distributed among these distances:
168 5 0.01
169 34 0.03
170 159 0.16
171 452 0.46
172 279 0.29
173 40 0.04
174 8 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (169 bp):
AGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTGCCAATGAATACC
TTTTTCTTCATGTTTCCAAGGCAAACATTCAATTATAATCTGTTCTAACAAAAAATGTAAAAAAT
TCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAA
Found at i:10107 original size:512 final size:510
Alignment explanation
Indices: 8930--10241 Score: 1446
Period size: 512 Copynumber: 2.6 Consensus size: 510
8920 GAAATGAGGG
* * ** * * ** *
8930 ACTATAAATGGACCATTCTTTTCGATGAATGCCTTTTTCTTCGCGTTTTCCAGGGCAAACATTCC
1 ACTATAAATGAACCTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTTCCAGGGCAAACATTCA
* * * *
8995 ATTATAATCTGTTCTAACTAAAAACGT-AAAAGAATTCAACCTAAAATCAATTATGAGATTATAA
66 ATTATAATCTGTT-TAACCAAAAACATGAAAA-AGTTCAACCTAAAATCAATTATGAGACTATAA
** * * * *
9059 AAATATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATGAACTCTTCTT-CG
129 AACCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGACCT-TTCTTGC-
* * * * * * * * * *
9123 CAATGAACACCTTTTTCTTCATGTTTGTCGACGTAGATATTCAATTATAATATGTTTTAAAC-AA
192 CGATGAATACCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCT-AACTAA
* * * * *
9187 AAAGATAAAACAATTTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATA
256 AAACAGAAAA-AA-TTCAACCTAAAATC-ATTTTGAGATTATAAAACCATTTAAAGTGAGTAAGA
* * ** *
9252 AAGCTTTTGAAGCAATGGGTGACTATAAATAGACCTTTCTTGTCAATTAATGTATTTTTCTTTAT
318 AAGCTTTTGAAGCAATGGGTAACTATAAATAGACCTTTCTTGCCAACGAATGTATTTTTCTTCAT
* * * ** * *
9317 ATTTCTCGAGGTAGACATTCAATTACAATCTGTTTTAAAAAAATATATAAACAAATTTGAAATTA
383 ATTTCTCCAGGCAGACATTCAATTACAATCTGTTCTAAAAAAATATATAAACAAAGCTCAAACTA
* * * * * *
9382 AAATAAATTTTAAGATTATAAAACCATTTAAATTGAGTAATAAGGCTTTTGAAAGAATATGTG
448 AAATAAATTATAAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTATGAAAGAATAGGTC
* * **
9445 ACTATAAATTAACTTTTCTTGCCAATGAATACCTTTTTCTTCATG-TTTCGCAACAGCAAACATT
1 ACTATAAATGAACCTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTTC-C-AGGGCAAACATT
* *
9509 CAATTATAATCTGTTTTAA-CAAAAA-ATGTCAAAAAGTTCAACCTAAAATAAATTTTGAGACTA
64 CAATTATAATCTG-TTTAACCAAAAACATG--AAAAAGTTCAACCTAAAATCAATTATGAGACTA
* *
9572 T-AAACCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGATTATAAATAGACCTTTGTT
126 TAAAACCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAAT-GACCTTTCTT
9636 GCCGATGAATACCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACTA
190 GCCGATGAATACCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACTA
9701 AAAACAGAAAAAATTCAACCTAAAATCATTTATGAGATTATAAAACCATTTAAAGTGAGTAAGAA
255 AAAACAGAAAAAATTCAACCTAAAATCATTT-TGAGATTATAAAACCATTTAAAGTGAGTAAGAA
* * * * * *
9766 GGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTGCCCACGAAT-TCCTTTTTCTTCAT
319 AGCTTTTGAAGCAATGGGTAACTATAAATAGACCTTTCTTGCCAACGAATGT-ATTTTTCTTCAT
* * * * * * *
9830 GTTTC-CCATGGCAGATATTTAATTATC-ATTTGTTCTAATAAAAA-ATGTCAA-AAAGCTCAAC
383 ATTTCTCCA-GGCAGACATTCAATTA-CAATCTGTTCTAA-AAAAATATATAAACAAAGCTCAAA
* * * * * *
9891 CTAAAATCAATTATGAGAATATGAAACTATTTAAAGTGAGTAATAAGGCTTATGAAGGAATGGGT
445 CTAAAATAAATTATAAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTATGAAAGAATAGGT
9956 C
510 C
* *
9957 ACTATAAATGAACCTTTGTTGCCAATGAATACCTTTTTCTTCATGTTTTCCAGGGCAGACATTCA
1 ACTATAAATGAACCTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTTCCAGGGCAAACATTCA
10022 ATTATAATCTGTCTTAACCAAAAACATGAAAAAGTTCAACCTAAAATCAATTATGAGACTATAAA
66 ATTATAATCTGT-TTAACCAAAAACATGAAAAAGTTCAACCTAAAATCAATTATGAGACTATAAA
* * * ** * * **
10087 ACCATTTACAGTAAGTAATAAGGCCTTTAAAAAAATAAGG-GACTATAAATGGACCATTCTTGTA
130 ACCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAAT-GGGTGACTATAAAT-GACCTTTCTTGCC
* *** * *
10151 GATGAATGCCTTTTTCTTTGCGTTTCCCAAGGCAAACATTCCATTATAATCTGTTCTAACTAAAA
193 GATGAATACCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAA
10216 AC-GTAAAAAAATTCAACCTAAAATCA
258 ACAG--AAAAAATTCAACCTAAAATCA
10242 NNNNNNNNNN
Statistics
Matches: 670, Mismatches: 105, Indels: 46
0.82 0.13 0.06
Matches are distributed among these distances:
510 1 0.00
511 59 0.09
512 227 0.34
513 156 0.23
514 16 0.02
515 149 0.22
516 56 0.08
517 6 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (510 bp):
ACTATAAATGAACCTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTTCCAGGGCAAACATTCA
ATTATAATCTGTTTAACCAAAAACATGAAAAAGTTCAACCTAAAATCAATTATGAGACTATAAAA
CCATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGACCTTTCTTGCCGAT
GAATACCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATCTGTTCTAACTAAAAACA
GAAAAAATTCAACCTAAAATCATTTTGAGATTATAAAACCATTTAAAGTGAGTAAGAAAGCTTTT
GAAGCAATGGGTAACTATAAATAGACCTTTCTTGCCAACGAATGTATTTTTCTTCATATTTCTCC
AGGCAGACATTCAATTACAATCTGTTCTAAAAAAATATATAAACAAAGCTCAAACTAAAATAAAT
TATAAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTATGAAAGAATAGGTC
Found at i:10586 original size:17 final size:17
Alignment explanation
Indices: 10556--10588 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10546 ATTTTAAAAA
10556 AAATATAAAAAAATTTG
1 AAATATAAAAAAATTTG
10573 AAAT-TAAAATAAATTT
1 AAATATAAAA-AAATTT
10589 TAAGATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATATAAAAAAATTTG
Found at i:12975 original size:170 final size:170
Alignment explanation
Indices: 12676--12987 Score: 448
Period size: 170 Copynumber: 1.8 Consensus size: 170
12666 TTATATATTT
* * * * *
12676 TTTTAGGTTGAACTTTTTGACATTTTTGGTTAGAACAGATTATAATTGAATGTTTGCCCTGGGAA
1 TTTTAGGTTGAACTTTTTGACATTTTTGATTAGAACAAATTATAATTGAACGTCTGCCATGGGAA
* ** * *
12741 ACGTGAAGAAAAGGCATTCATCGAAAAGAATGGTCCATTTATAGTCCCTCATTTCTTTAAAGGCC
66 ACATGAAGAAAAGGCATTCATCGAAAAGAAAAGTCCATTTATAGTCCCTCATTCCTTCAAAGGCC
12806 TTATTACTCACTGTAAATAGTTTTATAGTCTCGTAATTCA
131 TTATTACTCACTGTAAATAGTTTTATAGTCTCGTAATTCA
* *
12846 TTTTAGGTTGAGCTTTTTGACATTTTTTATTAGAACAAATTATAATTGAACGTCTGCCATGGG-A
1 TTTTAGGTTGAACTTTTTGACATTTTTGATTAGAACAAATTATAATTGAACGTCTGCCATGGGAA
* * * *
12910 ACATGAAGAAAAATGTATTCATCGACAAGAAAAGTCTATTTATAGTCACC-CATTCCTTCAAAGG
66 ACATGAAG-AAAAGGCATTCATCGAAAAGAAAAGTCCATTTATAGTC-CCTCATTCCTTCAAAGG
12974 CCTTATTACTCACT
129 CCTTATTACTCACT
12988 TNNNNNNNNN
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
169 8 0.06
170 114 0.92
171 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (170 bp):
TTTTAGGTTGAACTTTTTGACATTTTTGATTAGAACAAATTATAATTGAACGTCTGCCATGGGAA
ACATGAAGAAAAGGCATTCATCGAAAAGAAAAGTCCATTTATAGTCCCTCATTCCTTCAAAGGCC
TTATTACTCACTGTAAATAGTTTTATAGTCTCGTAATTCA
Done.