Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403006.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_673.0, 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: 32088
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.24
Warning! 11221 characters in sequence are not A, C, G, or T
Found at i:1032 original size:172 final size:172
Alignment explanation
Indices: 673--1094 Score: 445
Period size: 172 Copynumber: 2.5 Consensus size: 172
663 NNNNNNNNNC
* * * * * * **
673 CATAATCGATTTTAAGTTGAATT-TTTTTACATTTTTAGTTAAAATAGACTACAATTGAATGTGG
1 CATAATCGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCA
** * *
737 ACCTCAAGAAACATAAGAAAAAAGGCATTCATTGGCAAGAAAAGTCCAATTATATTCACCCATTC
66 ACCTCAAGAAACATAAGAAAAAACACATTCATTGGCAAGAAAACTCCAATTATAGTCACCCATTC
* * * * * *
802 TTTCGAAAGCCTTATTACTCACTTTAAATGGTTTTATAATTT
131 TTTCAAAAGCCTCATTACTCACGTTAAATAGTTTCATAATCT
********** * * *
844 NNNNNNNNNNTTAAATTTGAATTCTTTGTGCATTTTTAGTTAAAACATATTATAATTGAATGTTA
1 CATAATCGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCA
** *
909 ACCTCAAGAAAGGTGAA-AAAAAACACTTTCATTGGCAAGAAAACT-CAATTTATAGTCACCCAT
66 ACCTCAAGAAACAT-AAGAAAAAACACATTCATTGGCAAGAAAACTCCAA-TTATAGTCACCCAT
972 TCTTTCAAAAGCCTCATTACTCACGTTAAATAGTTTCATAATCT
129 TCTTTCAAAAGCCTCATTACTCACGTTAAATAGTTTCATAATCT
* * * * *
1016 CATAATTGATTTAAATTTCAATTCTTTGTATATTTTTAGTTAAAACAGATTATAATAGAATGCCA
1 CATAATCGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCA
*
1081 AACTCAAGAAACAT
66 ACCTCAAGAAACAT
1095 GANNNNNNNN
Statistics
Matches: 195, Mismatches: 53, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
171 14 0.07
172 179 0.92
173 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.36
Consensus pattern (172 bp):
CATAATCGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCA
ACCTCAAGAAACATAAGAAAAAACACATTCATTGGCAAGAAAACTCCAATTATAGTCACCCATTC
TTTCAAAAGCCTCATTACTCACGTTAAATAGTTTCATAATCT
Found at i:3893 original size:13 final size:13
Alignment explanation
Indices: 3875--3901 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3865 ATTGGCAAGA
3875 AAAGCTCATTTAT
1 AAAGCTCATTTAT
3888 AAAGCTCATTTAT
1 AAAGCTCATTTAT
3901 A
1 A
3902 GTCGCTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
AAAGCTCATTTAT
Found at i:12555 original size:171 final size:169
Alignment explanation
Indices: 12168--13034 Score: 659
Period size: 171 Copynumber: 5.1 Consensus size: 169
12158 NATTTGAACA
* * * * * * * **
12168 TAAAATTAATTATGAGATTATAAACCAATTTAAATTGACTAATACGGCTTTTGAAGGAATAAGTG
1 TAAAATCAATTATTAGGTTATAAACC-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTG
* * * * ** * **
12233 ACTATAAATAGACTTTTCTTGCCAATG-ATGCCTTTTTCTTTACATTTCTCTAGATAGACATTCA
65 ACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGCAGACATTCA
* * ** * *
12297 ATTATAGTTTGTTTTAATGAAAAATGC-ATAAACATTCAACT
130 ATTATAGTCTATTTTAACCAAAAAT-CTA-AAAAATTAAACT
*
12338 TAAAATCAATTA-T-GGCATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTTG-AGGTATGG
1 TAAAATCAATTATTAGG--TTAT-AAACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGGTATGG
* * * **
12400 GTTACTATAAATGGACTTTTCTTGTCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGATGT
62 GTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGCAGACAT
* *
12465 TCAATTCTAGTCTATTTGAACCAAAAATCTAAAACAATTAAACT
127 TCAATTATAGTCTATTTTAACCAAAAATCTAAAA-AATTAAACT
* * * * * **
12509 TAAAATCAATTATTA-GTTCATAAGACGATTTAGAGTAAGCAATAAGGCTTTCGAAGGCT-TAAG
1 TAAAATCAATTATTAGGTT-ATAA-ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG-TATGGG
* * * * * * *
12572 TGGCTATAAATGGACTTTT-TGTGCCAATCG-TTGGC-TTTTGCTTCATATTTCTTAAAGCAGAC
63 TGACTATAAATGGACTTTTCT-TGCCAAT-GAAT-ACTTTTTTCTTCATGTTTCTCAAGGCAGAC
* * * * *
12634 ATTCAATTATAGCCTTTTTTAACAAAAAATGTAAAAAAATTCAACT
125 ATTCAATTATAGTCTATTTTAACCAAAAATCT-AAAAAATTAAACT
* **
12680 TAAAATCAATT-TTATGATTATAAAGCCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGT
1 TAAAATCAATTATTA-GGTTATAAA-CCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGT
* ** * *
12744 GACTATAAATGGACTTTTCTTGCCAATGAATGCCCTTTTCTTCAAGTTT-TCGAAGGCAGTCATT
64 GACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTC-AAGGCAGACATT
* ** * * * *
12808 CAATTATAATCTGGTTTCACCAGAAAGGTC-AAAAAATTTAACC
128 CAATTATAGTCTATTTTAACCA-AAA-ATCTAAAAAATTAAACT
* * * * **
12851 TAAAATCAATTATGAGGTTATAAAACCATTGAAAGTGAGTAAGAAGGCTTTTTAAAGGTACCGGT
1 TAAAATCAATTATTAGGTTAT-AAACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGGTATGGGT
* * * *
12916 GACTATAAATGCACTTTTCTTCCCAATTAA-AGCTTTTTTCTTCATGTTTCTCAAGGTAGACATT
64 GACTATAAATGGACTTTTCTTGCCAATGAATA-CTTTTTTCTTCATGTTTCTCAAGGCAGACATT
* * *
12980 CAATTCTAGTC-AGTTTTAATCAAAAATGTACAAAGAATTCAAA-T
128 CAATTATAGTCTA-TTTTAACCAAAAATCTA-AAA-AATT-AAACT
*
13024 TTAAATCAATT
1 TAAAATCAATT
13035 TTAAGATTNN
Statistics
Matches: 545, Mismatches: 115, Indels: 71
0.75 0.16 0.10
Matches are distributed among these distances:
168 1 0.00
170 86 0.16
171 339 0.62
172 100 0.18
173 17 0.03
174 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (169 bp):
TAAAATCAATTATTAGGTTATAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGA
CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGCAGACATTCAA
TTATAGTCTATTTTAACCAAAAATCTAAAAAATTAAACT
Found at i:13486 original size:171 final size:168
Alignment explanation
Indices: 13143--14392 Score: 1016
Period size: 171 Copynumber: 7.4 Consensus size: 168
13133 NNNNNNNNNN
*
13143 TTTGAAGGAATAGG-TGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTTCTTACA--T
1 TTTGAAGGAAT-GGATGACTATAAATGGACTTTTCTTGCCAATGAATGCC-TTTTTCTT-CATGT
* * * * * *
13205 TTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAATGTTCAAAGAATTCAAATTTAA
63 TTCTCAAGGTAGACATTCAATTATAGT-TTTTTTAAC-AAAAATG-T-AAAAAATTCAACTTAAA
* *
13270 ATCAATTTTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCT
124 ATCAATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCT
* * * * *
13315 TCTGAAGGAATGGATGACTATAAATGAACTTTTCATT-TCAATGAATGCCTTTTTCTTTAGGTTT
1 TTTGAAGGAATGGATGACTATAAATGGACTTTTC-TTGCCAATGAATGCCTTTTTCTTCATGTTT
* * *
13379 CTCGAGGTAGACATTCAATTATAGTCTTTTTTACCAAAAAAAGTGAAAAAATGT-AACTTAAAAT
65 CTCAAGGTAGACATTCAATTATAGT-TTTTTTAAC-AAAAATGT-AAAAAAT-TCAACTTAAAAT
*
13443 CAATTATGACATTATAAAACCATTAAAAGTGA-TATATAAGGCT
126 CAATTATGACATTATAAAACCATTTAAAGTGAGTA-ATAAGGCT
* * * * * *
13486 TTTGAAGGTATGGGTAACTATAAATAGACTTTTCTTGCCAATGAATG-CTTTTGCTTCATGCTTC
1 TTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
* * * * *
13550 TCAAGGTAGACATTCAATTCTAGTTAGTTTTAACAAACAATGTTCAAAGAATTCAAATTTAAATC
66 TCAAGGTAGACATTCAATTATAGTT-TTTTTAACAAA-AATG-T-AAAAAATTCAACTTAAAATC
* * *
13615 AATTTTGAAATTACAAAACCATTTAAAGTGAGTAATAAGGCT
127 AATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCT
* * * * ** *
13657 TTTAAAGAAATGGACGACTATAAATGTACTTTTCTTGCCAATGAATGTATTTTTCTCCATGTTTC
1 TTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
** * * * * * * *
13722 TTGAGCTAGACATTTAATTATAATATGTTTAAACCAAAAATGTAGAAAAATTTGAACTTAAAATT
66 TCAAGGTAGACATTCAATTATAGT-TTTTTTAA-CAAAAATGTA-AAAAA-TTCAACTTAAAATC
* * *
13787 AATTATGAGAATAT-AAA-C---T-AA-T--TTAATAAGGCT
127 AATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCT
* * * * * *
13820 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCGATG-ATGTC-TTTTCTTTATGTTAC
1 TTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
* * * * * * **
13883 TCTATGTTGACATTCAATTATAGTTTGTTTTAACGAAAATGTATAAACATTCAGCTTAAAATTGA
66 TCAAGGTAGACATTCAATTATAGTTT-TTTTAACAAAAATGTA-AAAAATTCAACTTAAAATCAA
* ** ** *
13948 TTATGGCATTATAAAATTATTTAAAACGACTAATAAGGCT
129 TTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCT
* * * *
13988 CTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTT
1 -TTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTT
* * * * * * *
14053 CTCAAGGAAGATATTCAAATCTAGTTTGTTTTAAGTAAAAATCTAAAAAGATTTAACTTAAAATC
65 CTCAAGGTAGACATTCAATTATAGTTT-TTTTAA-CAAAAATGTAAAAA-ATTCAACTTAAAATC
* * * * **
14118 AATTATTA-GTTCATAAGACTATTTAAAGCAAGTAATAAGGCT
127 AATTATGACATT-ATAAAACCATTTAAAGTGAGTAATAAGGCT
* * * ** * * *
14160 TTCGAAGG-CTTGAGTGACTATAAATGGACTTTT-TGTGCCAATGGTTGGCTTTTGCTTCACG-T
1 TTTGAAGGAATGGA-TGACTATAAATGGACTTTTCT-TGCCAATGAATGCCTTTTTCTTCATGTT
* * * * * *
14222 TCCCTAAAGCAGACATTCAATTATAGTCTATTTAACCAAAAATGTGAAAACATTCAACTTAAAAT
64 TCTC-AAGGTAGACATTCAATTATAGTTTTTTTAA-CAAAAATGT-AAAAAATTCAACTTAAAAT
* * * *
14287 CAATTATGGCATTATAAAACCATTTCAAG-CAGGTAATGAGGCT
126 CAATTATGACATTATAAAACCATTTAAAGTGA-GTAATAAGGCT
* * * * * * *
14330 TTTAAATGCATGGGTGACCATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
1 TTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTT
14393 NNNNNNNNNN
Statistics
Matches: 857, Mismatches: 179, Indels: 85
0.76 0.16 0.08
Matches are distributed among these distances:
159 22 0.03
160 17 0.02
161 34 0.04
162 4 0.00
163 46 0.05
164 1 0.00
165 3 0.00
166 2 0.00
167 1 0.00
168 10 0.01
169 44 0.05
170 159 0.19
171 314 0.37
172 193 0.23
173 7 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (168 bp):
TTTGAAGGAATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
TCAAGGTAGACATTCAATTATAGTTTTTTTAACAAAAATGTAAAAAATTCAACTTAAAATCAATT
ATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCT
Found at i:14295 original size:342 final size:335
Alignment explanation
Indices: 13155--14392 Score: 1118
Period size: 342 Copynumber: 3.7 Consensus size: 335
13145 TGAAGGAATA
* ** * * * *
13155 GGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTTCTTACAT-TTCTC-GAGGTAAA
1 GGTGACTATAAATGGACTTTTCTTGCCAATGGATGGC-TTTTGCTT-CATGTTCTCTAAAGTAGA
* * *
13218 CATTCAATTATAGTCTGTTTTAACTAAAAATGTTCAAAGAATTCAAATTTAAATCAATTTTGAAA
64 CATTCAATTATAGTCTGATTTAAC-AAAAATGTTCAAAGAATTCAAATTAAAATCAATTATGAAA
* * * *
13283 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTCTGAAGGAATGGATGACTATAAATGAACTTTT
128 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGGACTTTT
* * * *
13348 CATT-TCAATGAATGCCTTTTTCTTTAGGTTTCTCGAGGTAGACATTCAATTATAGTCTT-TTTT
193 C-TTGCCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGT-TTGTTTT
* * * * * *
13411 ACCAAAAAAAGTGAAAAAATGTAACTTAAAATCAATTATGACATTATAAAACCATTAAAAGTGAT
256 AACAAAAAATGT-AAAAAATTTAACTTAAAATCAATTATGA-GTTAT-AAACTATTTAAA--GAT
13476 ATATAAGGCTTTTGAAGGTATG
316 A-ATAAGGCTTTTGAAGGT-TG
* * * *
13498 GGTAACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTTGCTTCATGCTTCTC-AAGGTAGAC
1 GGTGACTATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCATG-TTCTCTAAAGTAGAC
* * * *
13561 ATTCAATTCTAGT-TAGTTTTAACAAACAATGTTCAAAGAATTCAAATTTAAATCAATTTTGAAA
65 ATTCAATTATAGTCT-GATTTAACAAA-AATGTTCAAAGAATTCAAATTAAAATCAATTATGAAA
* * * * *
13625 TTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGAAATGGACGACTATAAATGTACTTTT
128 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGGACTTTT
* * * * * * *
13690 CTTGCCAATGAATG-TATTTTTCTCCATGTTTCTTGAGCTAGACATTTAATTATAATATGTTTAA
193 CTTGCCAATGAATGCT-TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTTTGTTTTA
* * * *
13754 ACCAAAAATGTAGAAAAATTTGAACTTAAAATTAATTATGAGAATATAAACTAATT-----TAAT
257 ACAAAAAATGTA-AAAAATTT-AACTTAAAATCAATTATGAG-TTATAAACTATTTAAAGATAAT
*
13814 AAGGCTTTTGAAGGAATG
319 AAGGCTTTTGAAGG-TTG
* * * * * *
13832 GGTGACTATAAATGGACTTTTCTTACCGAT-GATGTCTTTT-CTTTATGTTACTCT-ATGTTGAC
1 GGTGACTATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCATGTT-CTCTAAAGTAGAC
* * * * ** ** **
13894 ATTCAATTATAGTTTGTTTTAACGAAAATGTAT-AAA-CATTCAGCTTAAAATTGATTATGGCAT
65 ATTCAATTATAGTCTGATTTAACAAAAATGT-TCAAAGAATTCAAATTAAAATCAATTATGAAAT
** * * * * *
13957 TATAAAATTATTTAAAACGACTAATAAGGCTCTTTGAAGGTATGGGTGACTATAAATGGACTTTT
129 TATAAAACCATTTAAAGCGAGTAATAAGGCT-TTTAAAGGAATGGATGACTATAAATGGACTTTT
* * * * * *
14022 CTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGAAGATATTCAAATCTAGTTTGTTTTAA
193 CTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTTTGTTTTAA
** * *
14087 GTAAAAATCTAAAAAGATTTAACTTAAAATCAATTATTAGTTCATAAGACTATTTAAAGCAAGTA
258 CAAAAAATGTAAAAA-ATTTAACTTAAAATCAATTATGAGTT-ATAA-ACTATTTAAAG--A-TA
*
14152 ATAAGGCTTTCGAAGGCTTG
317 ATAAGGCTTTTGAAGG-TTG
* * * * *
14172 AGTGACTATAAATGGACTTTT-TGTGCCAATGGTTGGCTTTTGCTTCACGTTCCCTAAAGCAGAC
1 GGTGACTATAAATGGACTTTTCT-TGCCAATGGATGGCTTTTGCTTCATGTTCTCTAAAGTAGAC
* * **
14236 ATTCAATTATAGTCT-ATTTAACCAAAAATG-TGAAA-ACATTCAACTTAAAATCAATTATGGCA
65 ATTCAATTATAGTCTGATTTAA-CAAAAATGTTCAAAGA-ATTCAAATTAAAATCAATTATGAAA
* * * * * *
14298 TTATAAAACCATTTCAAGC-AGGTAATGAGGCTTTTAAATGCATGGGTGACCATAAATGGACTTT
128 TTATAAAACCATTTAAAGCGA-GTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGGACTTT
*
14362 TCTTGCCAATGAATACTTTTTTCTTCATGTT
192 TCTTGCCAATGAATGCTTTTTTCTTCATGTT
14393 NNNNNNNNNN
Statistics
Matches: 738, Mismatches: 120, Indels: 76
0.79 0.13 0.08
Matches are distributed among these distances:
330 1 0.00
331 69 0.09
332 105 0.14
333 41 0.06
334 50 0.07
335 2 0.00
339 1 0.00
340 48 0.07
341 92 0.12
342 276 0.37
343 53 0.07
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (335 bp):
GGTGACTATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCATGTTCTCTAAAGTAGACA
TTCAATTATAGTCTGATTTAACAAAAATGTTCAAAGAATTCAAATTAAAATCAATTATGAAATTA
TAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGGACTTTTCTT
GCCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTTTGTTTTAACAA
AAAATGTAAAAAATTTAACTTAAAATCAATTATGAGTTATAAACTATTTAAAGATAATAAGGCTT
TTGAAGGTTG
Found at i:17840 original size:21 final size:21
Alignment explanation
Indices: 17787--17832 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
17777 GGTGACTATA
17787 AATGGACTTTTCTTGCCAATG
1 AATGGACTTTTCTTGCCAATG
17808 AATGGACTTTTCTTGCCAATG
1 AATGGACTTTTCTTGCCAATG
17829 AATG
1 AATG
17833 CTATTTTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (21 bp):
AATGGACTTTTCTTGCCAATG
Found at i:18401 original size:171 final size:171
Alignment explanation
Indices: 17852--18428 Score: 606
Period size: 171 Copynumber: 3.4 Consensus size: 171
17842 TTACGTTTCA
* * * *
17852 CAAGGTCAAA-ATTCAATTCTAGTTTGTTTTAAGCAAAAATAT-AAAAAATTTAACTAAAAATCA
1 CAAGGT-AAACATTCAATTATAGCTTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCA
* *
17915 ATTATTAGTTCATAAGACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAA
65 ATTATTAGTTCATAAGACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAA
* * * * * *
17980 TGAACTTTTGTGT-CAATGGTTGGCGTTTGCTTCACGTTCCC
130 TGGACTTTTCTGTCCAATAGATGGCTTTTACTTCACGTTCCC
* * * * *
18021 CAACGTAGACATTCAATTATAG-TCT-ATTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCA
1 CAAGGTAAACATTCAATTATAGCT-TGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCA
* * * * * * * *
18084 ATTA-TGGCATT-ATAAAACCATTTAAAACGAGTAATGAGGCTTTTGATGG-TATGGGTGACCAT
65 ATTATTAG--TTCATAAGACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCT-TGAGTGACTAT
* * * * * *
18146 AAATAGACTTTTCT-TGCCAATAAAT-GCTTTTTTCTTCATGTTTCT
127 AAATGGACTTTTCTGT-CCAATAGATGGC-TTTTACTTCACGTTCCC
* ** * * * *
18191 CAATGTTGACATGT-AATTCTAGTTTGTTTTAATCAAAAATATAAAAAAATTTAAATTAAAATCA
1 CAAGGTAAACAT-TCAATTATAGCTTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCA
18255 ATTATTAGTTCATAAGACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAA
65 ATTATTAGTTCATAAGACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAA
18320 TGGACTTTT-TGTACCAATAGATGGCTTTTACTTCACGTTCCC
130 TGGACTTTTCTGT-CCAATAGATGGCTTTTACTTCACGTTCCC
*
18362 CAAGGTAAACATTCAATTATAGCCTT-TTTTAACCAAAAATCTAAAAAAATTCT-ACTTAAAATC
1 CAAGGTAAACATTCAATTATAG-CTTGTTTTAACCAAAAATATAAAAAAATT-TAACTTAAAATC
18425 AATT
64 AATT
18429 TTGAGATTAT
Statistics
Matches: 328, Mismatches: 60, Indels: 38
0.77 0.14 0.09
Matches are distributed among these distances:
168 20 0.06
169 93 0.28
170 41 0.12
171 166 0.51
172 8 0.02
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (171 bp):
CAAGGTAAACATTCAATTATAGCTTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAA
TTATTAGTTCATAAGACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAAT
GGACTTTTCTGTCCAATAGATGGCTTTTACTTCACGTTCCC
Found at i:18451 original size:171 final size:170
Alignment explanation
Indices: 17862--18499 Score: 554
Period size: 171 Copynumber: 3.7 Consensus size: 170
17852 CAAGGTCAAA
* * * *
17862 ATTCAATTCTAGTTTGTTTTAAGCAAAAATAT-AAAAAATT-TAACTAAAAATCAATTATT-AG-
1 ATTCAATTATAGCTT-TTTTAACCAAAAATATAAAAAAATTCT-ACTTAAAATCAATT-TTGAGA
* * *
17923 TTCAT-AAGACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAATGAACTT
63 TT-ATAAAG-CCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTT
* * * * *
17987 TTGTGT-CAATGGTTGGCGTTTGCTTCACGTTCCCCAACGTAGAC
126 TTCTGTCCAATAGATGGCTTTTACTTCACGTTCCCCAACGTAGAC
* * * *
18031 ATTCAATTATAG-TCTATTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG-GCAT
1 ATTCAATTATAGCT-TTTTTAACCAAAAATATAAAAAAATTCTACTTAAAATCAATTTTGAG-AT
* * * * * * * *
18094 TATAAAACCATTTAAAACGAGTAATGAGGCTTTTGATGG-TATGGGTGACCATAAATAGACTTTT
64 TATAAAGCCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCT-TGAGTGACTATAAATGGACTTTT
* * * * * * *
18158 CT-TGCCAATAAAT-GCTTTTTTCTTCATGTTTCTCAATGTTGAC
128 CTGT-CCAATAGATGGC-TTTTACTTCACGTTCCCCAACGTAGAC
* * * *
18201 ATGT-AATTCTAGTTTGTTTTAATCAAAAATATAAAAAAATT-TAAATTAAAATCAATTATT-AG
1 AT-TCAATTATAGCTT-TTTTAACCAAAAATATAAAAAAATTCT-ACTTAAAATCAATT-TTGAG
18263 -TTCAT-AAGACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACT
62 ATT-ATAAAG-CCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACT
* *
18326 TTT-TGTACCAATAGATGGCTTTTACTTCACGTTCCCCAAGGTAAAC
125 TTTCTGT-CCAATAGATGGCTTTTACTTCACGTTCCCCAACGTAGAC
*
18372 ATTCAATTATAGCCTTTTTTAACCAAAAATCTAAAAAAATTCTACTTAAAATCAATTTTGAGATT
1 ATTCAATTATAG-CTTTTTTAACCAAAAATATAAAAAAATTCTACTTAAAATCAATTTTGAGATT
** *** * *** * *
18437 ATAAAGGTATTTAAATTGAGTAATAAGGTTTTTGAAGAAATGGGTGACTATAAACGGACTTTT
65 ATAAAGCCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTT
18500 TTTGCTAGTG
Statistics
Matches: 372, Mismatches: 69, Indels: 54
0.75 0.14 0.11
Matches are distributed among these distances:
168 18 0.05
169 83 0.22
170 47 0.13
171 211 0.57
172 13 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (170 bp):
ATTCAATTATAGCTTTTTTAACCAAAAATATAAAAAAATTCTACTTAAAATCAATTTTGAGATTA
TAAAGCCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTTCTG
TCCAATAGATGGCTTTTACTTCACGTTCCCCAACGTAGAC
Found at i:18522 original size:342 final size:339
Alignment explanation
Indices: 17866--18525 Score: 937
Period size: 342 Copynumber: 1.9 Consensus size: 339
17856 GTCAAAATTC
*
17866 AATTCTAGTTTGTTTTAAGCAAAAATATAAAAAATTTAACTAAAAATCAATTATTAGTTCATAAG
1 AATTCTAGTTTGTTTTAAGCAAAAATATAAAAAATTTAAATAAAAATCAATTATTAGTTCATAAG
*
17931 ACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAATGAACTTTTGTGTCAA
66 ACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGAACTTTTGTGTCAA
* * * * * *
17996 TGGTTGGCGTTTGCTTCACGTTCCCCAACGTAGACATTCAATTATAGTCTATTTAACCAAAAATG
131 TAGATGGCGTTTACTTCACGTTCCCCAACGTAAACATTCAATTATAGCCTATTTAACCAAAAATC
*
18061 TAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAACGAGTAATGAGGCTT
196 TAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAACGAGTAATAAGGCTT
* ** * * *
18126 TTGATGGTATGGGTGACCATAAATAGACTTTTCTTGCCAATAAATGCTTTTTTCTTCATGTTTCT
261 TTGAAGAAATGGGTGACCATAAACAGACTTTTCTTGCCAATAAATACCTTTTTCTTCATGTTTCT
18191 CAATGTTGACATGT
326 CAATGTTGACATGT
* *
18205 AATTCTAGTTTGTTTTAATCAAAAATATAAAAAAATTTAAATTAAAATCAATTATTAGTTCATAA
1 AATTCTAGTTTGTTTTAAGCAAAAATAT-AAAAAATTTAAATAAAAATCAATTATTAGTTCATAA
* *
18270 GACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTT-TGTAC
65 GACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGAACTTTTGTGT--
* * *
18334 CAATAGATGGCTTTTACTTCACGTTCCCCAAGGTAAACATTCAATTATAGCCTTTTTTAACCAAA
128 CAATAGATGGCGTTTACTTCACGTTCCCCAACGTAAACATTCAATTATAGCC-TATTTAACCAAA
* * *** **
18399 AATCTAAAAAAATTCTACTTAAAATCAATTTTGAG-ATTATAAAGGTATTTAAATTGAGTAATAA
192 AATCTAAAAAAATTCAACTTAAAATCAATTATG-GCATTATAAAACCATTTAAAACGAGTAATAA
* * * * * * *
18463 GGTTTTTGAAGAAATGGGTGACTATAAACGGACTTTTTTTGCTAGTGAATACCTTTTTCTTCA
256 GGCTTTTGAAGAAATGGGTGACCATAAACAGACTTTTCTTGCCAATAAATACCTTTTTCTTCA
18526 CATTTTTGAA
Statistics
Matches: 280, Mismatches: 36, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
339 30 0.11
340 90 0.32
341 45 0.16
342 114 0.41
343 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (339 bp):
AATTCTAGTTTGTTTTAAGCAAAAATATAAAAAATTTAAATAAAAATCAATTATTAGTTCATAAG
ACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGAACTTTTGTGTCAA
TAGATGGCGTTTACTTCACGTTCCCCAACGTAAACATTCAATTATAGCCTATTTAACCAAAAATC
TAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAACGAGTAATAAGGCTT
TTGAAGAAATGGGTGACCATAAACAGACTTTTCTTGCCAATAAATACCTTTTTCTTCATGTTTCT
CAATGTTGACATGT
Found at i:18598 original size:342 final size:340
Alignment explanation
Indices: 17812--18640 Score: 841
Period size: 342 Copynumber: 2.4 Consensus size: 340
17802 CCAATGAATG
* * * * *
17812 GACTTTTCTTGCCAATGAAT-GCTATTTTCGTT-ACGTTTCACAAGGTCAAA-AT-TCAATTCTA
1 GACTTTTCTTGCCAATAAATACCT-TTTTC-TTCACATTTCTCAAGG-CAAACATGT-AATTATA
* * * * * *
17873 GTTTGTTTTAAGCAAAAATAT-AAAAAATT-TAACTAAAAATCAATTATTAGTTCATAAGACCAT
62 ATTTGCTCTAACCAAAAAGATAAAAAAATTCAAACT-AAAATCAATTATTAGTTCATAAGACCAT
* * * *
17936 TTAAAGCAAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAATGAACTTTTGTGTCAATGGTT
126 TTAAAGCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGAACTTTTGTGTCAATAGAT
* * * *
18001 GGCGTTTGCTTCACGTTCCCCAACGTAGACATTCAATTATAGTCTATTTAACCAAAAATGTAAAA
191 GGCGTTTACTTCACGTTCCCCAACGTAAACATTCAATTATAGCCTATTTAACCAAAAATCTAAAA
* *
18066 AAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTGAT
256 AAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAA
** *
18131 GGTATGGGTGACCATAAATA
321 GAAATGGGTGACCATAAACA
* * ** * *** * *
18151 GACTTTTCTTGCCAATAAATGCTTTTTTCTTCATGTTTCTCAATGTTGACATGTAATTCTAGTTT
1 GACTTTTCTTGCCAATAAATACCTTTTTCTTCACATTTCTCAAGGCAAACATGTAATTATAATTT
* * * * * *
18216 GTTTTAATCAAAAATATAAAAAAATTTAAATTAAAATCAATTATTAGTTCATAAGACCATTTAAA
66 GCTCTAACCAAAAAGATAAAAAAATTCAAACTAAAATCAATTATTAGTTCATAAGACCATTTAAA
*
18281 GCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGACTTTT-TGTACCAATAGATGGC
131 GCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGAACTTTTGTGT--CAATAGATGGC
* * *
18345 TTTTACTTCACGTTCCCCAAGGTAAACATTCAATTATAGCCTTTTTTAACCAAAAATCTAAAAAA
194 GTTTACTTCACGTTCCCCAACGTAAACATTCAATTATAGCC-TATTTAACCAAAAATCTAAAAAA
* * *** ** *
18410 ATTCTACTTAAAATCAATTTTGAG-ATTATAAAGGTATTTAAATTGAGTAATAAGGTTTTTGAAG
258 ATTCAACTTAAAATCAATTATG-GCATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAG
* *
18474 AAATGGGTGACTATAAACG
322 AAATGGGTGACCATAAACA
* * * * * *
18493 GACTTTTTTTGCTAGTGAATACCTTTTTCTTCACATTTTTGAAGGCAAACAT-TCAATTATAATT
1 GACTTTTCTTGCCAATAAATACCTTTTTCTTCACATTTCTCAAGGCAAACATGT-AATTATAATT
* * * ** * * * * *
18557 TGCTCTAACCAGAAAGGTCAAAGTATTCAACCTATAATCAATTATAAGGTT-GTAAAACCATTTA
65 TGCTCTAACCAAAAAGATAAAAAAATTCAAACTAAAATCAATTATTA-GTTCATAAGACCATTTA
**
18621 AAGTGAGTAATAAGGCTTTT
129 AAGCAAGTAATAAGGCTTTT
18641 TCTTCATATT
Statistics
Matches: 405, Mismatches: 73, Indels: 21
0.81 0.15 0.04
Matches are distributed among these distances:
338 3 0.01
339 66 0.16
340 88 0.22
341 49 0.12
342 195 0.48
343 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (340 bp):
GACTTTTCTTGCCAATAAATACCTTTTTCTTCACATTTCTCAAGGCAAACATGTAATTATAATTT
GCTCTAACCAAAAAGATAAAAAAATTCAAACTAAAATCAATTATTAGTTCATAAGACCATTTAAA
GCAAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGAACTTTTGTGTCAATAGATGGCGT
TTACTTCACGTTCCCCAACGTAAACATTCAATTATAGCCTATTTAACCAAAAATCTAAAAAAATT
CAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGAAAT
GGGTGACCATAAACA
Found at i:18844 original size:171 final size:172
Alignment explanation
Indices: 18636--19168 Score: 613
Period size: 172 Copynumber: 3.1 Consensus size: 172
18626 AGTAATAAGG
* * *
18636 CTTTTTCTTCATATTTCTTGAGGTAGACATTCAATTATATTCTATTTTAACTTAAAATGTACAAA
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTACAAA
* *
18701 GAATTCAAATTTAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTT-AA
66 GAATTCAAATTTAAATTAATTTTGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAA
** *
18765 AGGAATGGGCAATTAT-AATGGACTTTTCTTGCCAATGAACGC
131 A-GAATGGGTGATTATAAATGGACTTTTCTTGCCAATGAATGC
* * * * * * * * * *
18807 TTTTTTCTTTATGTTTCTTGAGCTAAACATGCAATTATAATATCTTTTAACCAAAAATGAAAAAA
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTACAAA
* * * * ** * *
18872 TATTTGAACTCAAAATTAATTATGAGATTATAAATA-AATTTAAATTGAGTAATAAGGCTTTTGA
66 GAATTCAAATTTAAATTAATTTTGAGATTATAAA-ACAATTTAAAGTGAGTAATAAGGCTTTTGA
* **
18936 AAGAATGGGTGATTATAAATAGACTTTTCTTGTTAATGAATGC
130 AAGAATGGGTGATTATAAATGGACTTTTCTTGCCAATGAATGC
* * ** * * * *
18979 CTTTTTCTTTACGTTTCTCAAGGTTGACATTCAATTATAAACTGTTTTAACTAAAAATATACAAA
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTACAAA
* * * *
19044 GAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAGAGTAAGTAATAAGGCTTTTGAA
66 GAATTCAAATTTAAATTAATTTTGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAA
* * * *
19109 AGAATGGGTGACTATAAATGAAGTTTTCTTGCCAATGGATGC
131 AGAATGGGTGATTATAAATGGACTTTTCTTGCCAATGAATGC
*
19151 CTTTTTCTTCAAGTTTCT
1 CTTTTTCTTCATGTTTCT
19169 CNNNNNNNNN
Statistics
Matches: 293, Mismatches: 65, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
171 115 0.39
172 178 0.61
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (172 bp):
CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTACAAA
GAATTCAAATTTAAATTAATTTTGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAA
AGAATGGGTGATTATAAATGGACTTTTCTTGCCAATGAATGC
Found at i:26014 original size:173 final size:172
Alignment explanation
Indices: 25358--26104 Score: 680
Period size: 171 Copynumber: 4.4 Consensus size: 172
25348 NNNNTATGAA
* * * *
25358 AAAAATTCAACTCAAAATCAATTATGGCATTATAAAATCATTTAAAGCGAG-ATATGAGGC-TTT
1 AAAAATTCAACTTAAAATCAATTATGGTATTATAAAACCATTTAAAGCGAGTA-ATAAGGCTTTT
* * *
25421 TGAAGGTAT-GAGTGACTATAAATGGACTTTTCTGGCCAATGAATGC-TTTTTCTTCATGTTTCT
65 TGAAGGAATAG-GTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCT
* * * * **
25484 TAAAGTAGACATTCAACTCTAGTCAGTTTTAACCAAAAATGTAT
129 CAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAT
* * * * * * * *
25528 AAAGAATTTGAA-TTTAAATCAATTTTGAGAATGA-AAAACCATTTAAAGAGAATAATAAGG-GT
1 AAA-AA-TTCAACTTAAAATCAATTATG-GTATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * ** * * *
25590 TTTAAAGAAATAGGCGACTATAAATATACTTTTCTTGCCAATGAATGTTTTTTTCTTCATGTTTA
63 TTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTC
** * * * * *
25655 TTGAGCTAGACATCCAATTATAATATGTTTTAACCAAAAATGTAG
128 TCAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAT
* * ** * *
25700 AAAAATTTGAACTT-AAATCATTTATGAG-A-TAT-AAACCAATTTAAATTGACTAATAA-GCCT
1 AAAAA-TTCAACTTAAAATCAATTATG-GTATTATAAAACC-ATTTAAAGCGAGTAATAAGGCTT
* * * * * *
25760 TTTGAATGAATGGGTGACTATAAATGCACTTTTCTTGCCAAT-CATGCCTTTTTCTTTACGTTTC
63 TTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTC
* * **
25824 TCTAGGTAGACATTCAATTATAGTTTTTTTTAATGAAAAATGTAT
128 TCAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAT
* *
25869 AAACATTCAACTTAAAATCGATTATGGTATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTT
1 AAAAATTCAACTTAAAATCAATTATGGTATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTT
* *
25934 GAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCACATGAATGCTTTTTTCTTCACATTT-TG
66 GAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCA-ATGAATGCTTTTTTCTTCACGTTTCT-
* * * * *
25998 CAAGGTAGATATTCAATTCTAGTTTGTTTTAAGCAAAAATCTAA
129 CAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAT
* * * **
26042 AAAAATTCAGCTTAAAATCAATTAT--TAGTTCATAAGACTATTTAAAGTAAGTAATAAGGCTTT
1 AAAAATTCAACTTAAAATCAATTATGGTA-TT-ATAAAACCATTTAAAGCGAGTAATAAGGCTTT
26105 CGAAAGCTTG
Statistics
Matches: 466, Mismatches: 90, Indels: 39
0.78 0.15 0.07
Matches are distributed among these distances:
168 8 0.02
169 73 0.16
170 73 0.16
171 139 0.30
172 70 0.15
173 103 0.22
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (172 bp):
AAAAATTCAACTTAAAATCAATTATGGTATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTT
GAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCA
AGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAT
Found at i:27329 original size:172 final size:161
Alignment explanation
Indices: 27069--27396 Score: 342
Period size: 172 Copynumber: 2.0 Consensus size: 161
27059 ATATTTCTCG
*
27069 AGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTGAAAAAATTCAACTTAAAACCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTGAAAAAATTCAACTTAAAACCAATT
* * * *
27134 GTGGCATTATAAAACCGTTTAAAGCG-AGTAATAAGGCTTTTTGAA-GATATGAGTGACTATAAA
66 GTAGCATCATAAAACCATTTAAAG-GAAGTAATAAGGC-TTTTAAAGGAT-TGAGTGACTATAAA
27197 T-AGACTTTTCTTGCCAATGAATGCTTTTTTCATC
128 TGA-ACTTTTCTTGCCAATGAATGCTTTTTTCATC
* * *
27231 ANNNNNNNNNNGGTAGATATTCAATTCTAGTCTGTTTTAACCAAAAATGT-AAAAATATTCAATT
1 A----------GGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTGAAAAA-ATTCAACT
* * * * * *
27295 TAAAATCAATTATTAGC-TCGTAATACCATTTAAAGGAAGTAATAATGCTTTTAAAGGCTTGAGT
55 TAAAACCAATT-GTAGCATCATAAAACCATTTAAAGGAAGTAATAAGGCTTTTAAAGGATTGAGT
*
27359 GACTATAAATGAACTTTTCTTGCCTATGAATGCTTTTT
119 GACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTT
27397 CTTCATGTTT
Statistics
Matches: 136, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
162 1 0.01
171 52 0.38
172 80 0.59
173 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (161 bp):
AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTGAAAAAATTCAACTTAAAACCAATT
GTAGCATCATAAAACCATTTAAAGGAAGTAATAAGGCTTTTAAAGGATTGAGTGACTATAAATGA
ACTTTTCTTGCCAATGAATGCTTTTTTCATC
Found at i:31143 original size:160 final size:159
Alignment explanation
Indices: 30835--31323 Score: 443
Period size: 160 Copynumber: 3.0 Consensus size: 159
30825 CTTCAAATGT
* *
30835 CTTATTACTCCCTTTAAATGG-CTTTATAATCTCAAAATTGATTTTAAGTTGAATTTGTTTACAT
1 CTTATTACTCACTTTAAATGGTC-TTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTACAT
* * * * * *
30899 TTTTAGTTCAAAA-ATATATAATTGAATGTTTG-CCTTGGGGAACGTGAAGCAAAAGCCA-ACTA
65 TTTT-GTTCAAAATATATATAATTGAATG-TCGACCTTGAGAAACGTGAAGAAAAAGGCATTC-A
* * * *
30961 TTAGCACAAAGAGTCCATTTATAGTCACTCAAGC
127 TTGGCA-AAAAACTCTATTTATAGTCACTCAAGC
**
30995 CTTATTACTTGCTTTAAATGGTCTTATGAA-CT-AATAATTGATTTTAAGTTGAATTTTTTTACA
1 CTTATTACTCACTTTAAATGGTCTTAT-AATCTCAA-AATTGATTTTAAGTTGAATTTTTTTACA
* * * *
31058 TTTTTGGTCAAAATAGACTATAATTGAATGTCGACCTTGAGAAACATAAAG-AAAAGGCATTCAT
64 TTTTTGTTCAAAATATA-TATAATTGAATGTCGACCTTGAGAAACGTGAAGAAAAAGGCATTCAT
31122 TGGCAAGAAAACTCTATTTATAGTCACCTATTATTCTGAAAGC
128 TGGCAA-AAAACTCTATTTATAGTCA-C------TC---AAGC
* * * * **
31165 CTTATTACTCACTTTAAATGGTTTTATAATCTCAAATTTGATTTAAATTTGAATTCTTTGCACAT
1 CTTATTACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTTAAGTTGAATT-TTTTTACAT
* * * * * *
31230 TTTTCTTTAAAATATATTACAATTGAATGTCAACCTCGAGCAACGTGAAGAAAAAGGCATTCATT
65 TTTTGTTCAAAATATA-TATAATTGAATGTCGACCTTGAGAAACGTGAAGAAAAAGGCATTCATT
* *
31295 GGCAATAAAACTATATTTCTAGTCACTCA
129 GGCAA-AAAACTCTATTTATAGTCACTCA
31324 TTCTTTCAAA
Statistics
Matches: 269, Mismatches: 38, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
159 10 0.04
160 90 0.33
161 30 0.11
162 1 0.00
165 2 0.01
167 2 0.01
169 2 0.01
170 47 0.17
171 49 0.18
172 36 0.13
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (159 bp):
CTTATTACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATT
TTTGTTCAAAATATATATAATTGAATGTCGACCTTGAGAAACGTGAAGAAAAAGGCATTCATTGG
CAAAAAACTCTATTTATAGTCACTCAAGC
Found at i:31219 original size:170 final size:171
Alignment explanation
Indices: 30991--31399 Score: 479
Period size: 172 Copynumber: 2.4 Consensus size: 171
30981 ATAGTCACTC
** * *
30991 AAGCCTTATTACTTGCTTTAAATGGTCTTATGAA-CT-AATAATTGATTTTAAGTTGAATT-TTT
1 AAGCCTTATTACTCACTTTAAATGGTTTTAT-AATCTCAA-AATTGA-TTTAAATTGAATTCTTT
* * * * *
31053 TTACATTTTTGGTCAAAATAGACTATAATTGAATGTCGACCTTGAGAAACATAAAG-AAAAGGCA
63 GTACATTTTTCGTCAAAATAGACTACAATTGAATGTCAACCTCGAGAAACATAAAGAAAAAGGCA
* *
31117 TTCATTGGCAAGAAAACTCTATTTATAGTCAC-CTATTA-TTCTGA
128 TTCATTGGCAAGAAAACTATATTTATAGTCACTC-ATTATTTC-AA
* *
31161 AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAATTTGATTTAAATTTGAATTCTTTGC
1 AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAA-TTGAATTCTTTGT
* * * * * * *
31226 ACATTTTTCTTTAAAATATATTACAATTGAATGTCAACCTCGAGCAACGTGAAGAAAAAGGCATT
65 ACATTTTTCGTCAAAATAGACTACAATTGAATGTCAACCTCGAGAAACATAAAGAAAAAGGCATT
* * *
31291 CATTGGCAATAAAACTATATTTCTAGTCACTCATTCTTTCAA
130 CATTGGCAAGAAAACTATATTTATAGTCACTCATTATTTCAA
* * * *
31333 AATCCTTATTACTCACCTTAAATAGTTTTATAATCTCAAAATTCATTTAAATTGAATTCTTTGTA
1 AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTGAATTCTTTGTA
31398 CA
66 CA
31400 NNNNNNNNNN
Statistics
Matches: 203, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
169 7 0.03
170 42 0.21
171 63 0.31
172 87 0.43
173 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (171 bp):
AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTGAATTCTTTGTA
CATTTTTCGTCAAAATAGACTACAATTGAATGTCAACCTCGAGAAACATAAAGAAAAAGGCATTC
ATTGGCAAGAAAACTATATTTATAGTCACTCATTATTTCAA
Found at i:31929 original size:171 final size:170
Alignment explanation
Indices: 31582--32084 Score: 482
Period size: 171 Copynumber: 2.9 Consensus size: 170
31572 NNNNNNATTA
* * * *
31582 GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATAACT-AATTTAAATTAG-T
1 GCAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAA-TGGTT
* * * ** * *
31645 TTATAATCTCATAATTAGTTTTAAGTTCAAATATTTTTATATTTTTCGTTAAAACAT-ATTATAA
65 TTATAATCTCAAAATT-GATTTAAATTTGAAT-TTTTTATATTTTTAGTTAAAAC-TGACTATAA
** ** * * *
31709 TTGAATGTTTTGCTTGAGAAACGTGAAGAAAAAGGAGTTCATTG
127 TCAAATGTTTACCTTGAGAAACATGAAGAAAAAGCAGTTCATAG
* **
31753 GCAAGAAAAGTCCATTTATAATTGCTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
1 GCAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
**
31818 TATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTGCATTTTTAGTTAAAACTGACTA-AAGT
66 TATAATCTCAAAATTGATTTAAATTTGAATT-TTT-TATATTTTTAGTTAAAACTGACTATAA-T
31882 CAAATGTTTACCTTGAGAAACATGAAGAAAAAGCA-TTCATAG
128 CAAATGTTTACCTTGAGAAACATGAAGAAAAAGCAGTTCATAG
** * * *
31924 GCAAGAAAAGTCCATTTATAGTCACTCAAGCCTTCAAAAGCATTATTACTTC-CTTGAAATGGTA
1 GCAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTAC-TCACTTTAAATGGTT
* * * * *
31988 TTATGAGCT-AATAATTAATTTTAAA-TTGAATTTTTTTTATATTTTTAGTTAAAACAGACTAGA
65 TTATAATCTCAA-AATTGA-TTTAAATTTGAA--TTTTTTATATTTTTAGTTAAAACTGACTATA
** * * * * *
32051 ATTGAATATCTACCATAAGAAACATGATGAAAAA
126 ATCAAATGTTTACCTTGAGAAACATGAAGAAAAA
32085 AGCA
Statistics
Matches: 276, Mismatches: 44, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
170 3 0.01
171 187 0.68
172 84 0.30
173 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (170 bp):
GCAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
TATAATCTCAAAATTGATTTAAATTTGAATTTTTTATATTTTTAGTTAAAACTGACTATAATCAA
ATGTTTACCTTGAGAAACATGAAGAAAAAGCAGTTCATAG
Done.