Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397407.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_858.0, 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: 23190
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.28
Warning! 5214 characters in sequence are not A, C, G, or T
Found at i:287 original size:172 final size:172
Alignment explanation
Indices: 1--1670 Score: 1354
Period size: 171 Copynumber: 9.8 Consensus size: 172
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTC-GAAAGGCATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCATG
* * * * *
65 GTTGACTATAAATAGACTTTTCTTG-CACTTGAATAGCTTTTTCTTCATATTTTTAGAAGGCAAA
66 GGTGACTACAAATGGACTTTTCTTGCCA-ATGAATAGCTTTTTCTTCATGTTTTT-GAAGGCAAA
* *
129 CATTCAACTATAATCTGTTTTAACTAAAAATATAAAAAAATTTC-
129 CATTCAATTATAATCTATTTTAACTAAAAATATAAAAAAA-TTCA
* * *
173 ACTTAAAATCAATTATG-GAATTATAAAACTATTTAAAGTAAGTAATAAGGCTTCT-AAAAGCAT
1 ACTTAAAATCAATTATGAG-ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCAT
* * * * * * * *
236 GGGTTACTACAAATAGACTTTTCTTGTCACTGAATAGCTTTTTCTTCATATTTCTCG-AGGTACA
65 GGGTGACTACAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTCATGTTT-TTGAAGGCAAA
* * *
300 CATT-AAATATTAATCTATTTTAACCAAAAATGTAAAAACAA-TCA
129 CATTCAATTA-TAATCTATTTTAACTAAAAATATAAAAA-AATTCA
* * * *******
344 ACTTGAAATCAA-TATTGAGATTATATAACCATTTAAAGCGAGTAATAAGGCTT-TGANNNNNNN
1 ACTTAAAATCAATTA-TGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCAT
*** * * * * *
407 NNNTGACTATAAATGGACATTTCTTGCCAATGAATGGCTTCTTT-TTCATGTTTCTGAAGGGAAA
65 GGGTGACTACAAATGGACTTTTCTTGCCAATGAATAGCTT-TTTCTTCATGTTTTTGAAGGCAAA
* * * *
471 CACTCTATTATAATCTGTTTTAACTAAAAATATAAAACAATTCA
129 CATTCAATTATAATCTATTTTAACTAAAAATATAAAAAAATTCA
* * * *********
515 ACTTAAAATC-AGTACTGAGATTAT-AAACCATTGAAAGCGAGTAATAAGGCTT-TNNNNNNNNN
1 ACTTAAAATCAATTA-TGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCAT
* * * * * *
577 NGGTGACTATAAATGGATTTTTCTTGCC-ATGAATGGCTTTTTCTTCATGTTTCCTG-AGGTAAA
65 GGGTGACTACAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTCATGTTT-TTGAAGGCAAA
* * * * * *
640 CACTCAATTATAATCTGTTTTGACCAAAAATACAAAAAAACTCA
129 CATTCAATTATAATCTATTTTAACTAAAAATATAAAAAAATTCA
* * ** * *
684 ACTTAAAATCAATTATGCGATTATAAAACTATTTAAAGGGAGTAATAAGACTT-TGAAAGGTATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCATG
* * * * * **
748 GATGACTATAAATGGACTTTTC-TGACCAATGACTAACTTTTTATTCATGTTTCTTG-AGATAAA
66 GGTGACTACAAATGGACTTTTCTTG-CCAATGAATAGCTTTTTCTTCATGTTT-TTGAAGGCAAA
* * * * * * *
811 TACTCAATTATAATATATTGTAACAAAAAATGTAAAAACAAGTCA
129 CATTCAATTATAATCTATTTTAACTAAAAATATAAAAA-AATTCA
* * * *
856 A-TGAAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTACTAAGGCTTC-GGAAGGCAT
1 ACTTAAAA-TCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCAT
* * * * *
919 GGGTGACT-CTAAATGCACTTTTCTTG-CACTTGAATAGC-TTTTCGCTCTTGTTTCT-AAGGCA
65 GGGTGACTAC-AAATGGACTTTTCTTGCCA-ATGAATAGCTTTTTC-TTCATGTTTTTGAAGGCA
* * * * * **
980 AACACTCAAATAT-ATCTATTTTAACCAACAATATAAAAACATTTG
127 AACATTCAATTATAATCTATTTTAACTAAAAATATAAAAAAATTCA
* * * * *
1025 ACTTAAAATCAAGTATGAGATTATAAAACTATTTAAAGCAAGAAATAAGG-TTTTCAAAAGGCAT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCT-GAAAGGCAT
* * * * *
1089 GGGTGACAACAAATGGACTTTTTCTTGTCAATGAATAGTTTTTTCTTCATGTTGCTTGCAGTGC-
65 GGGTGACTACAAATGGAC-TTTTCTTGCCAATGAATAGCTTTTTCTTCATGTT-TTTGAAG-GCA
* * * * **
1153 -ACATTGAA-TATTAATCTGTTTTAA-TCCAAAATGTAAAAGCATTCA
127 AACATTCAATTA-TAATCTATTTTAACT-AAAAATATAAAAAAATTCA
* * *
1198 ACTTAAAAGCAATAATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTT-TGAAAGGCATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCATG
* * * *
1262 GGTGACTATAACA--GACTTTTCTCGCCAATGAAT-GACTTTTT-TCTCATATTTCTTG-AGACA
66 GGTGACTACAA-ATGGACTTTTCTTGCCAATGAATAG-CTTTTTCT-TCATGTTT-TTGAAGGCA
* * *
1322 AACATTCAATTATAATATATTTTAATTAAAAATCTAAAAAAATTCA
127 AACATTCAATTATAATCTATTTTAACTAAAAATATAAAAAAATTCA
* * ** * *
1368 ACTTAAAATCAATTATAAGATCATAAAAATATTTAAAGCAAGTAATAAGGCTTCT-AAAGGCGTA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCATG
* * ** * * *
1432 GGTGACTACAAATGGACTTTTCTTGCCAAT-AGATAGCTTTTGCATCATGTTTTCAAAAGTAAGC
66 GGTGACTACAAATGGACTTTTCTTGCCAATGA-ATAGCTTTTTCTTCATGTTTTTGAAGGCAAAC
* *
1496 ATTCAATTATAATATATTTTAA-TAAAAAATATAAAAAACATTTA
130 ATTCAATTATAATCTATTTTAACT-AAAAATATAAAAAA-ATTCA
* * * * * * *
1540 ACTAAAAATTAATTATGAGATTATAAAATCATTTAAAGTACGTAATAAGGCTTCAG-AAGGCATA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCATG
* * * **
1604 GGTAACTACAAATGGACTTTTCTTG-CACTTGAATAGCTTTTTGTTCATGTTTCCGAAGGCAAAC
66 GGTGACTACAAATGGACTTTTCTTGCCA-ATGAATAGCTTTTTCTTCATGTTTTTGAAGGCAAAC
1668 ATT
130 ATT
1671 ACAAAATCAT
Statistics
Matches: 1214, Mismatches: 221, Indels: 126
0.78 0.14 0.08
Matches are distributed among these distances:
168 6 0.00
169 129 0.11
170 299 0.25
171 358 0.29
172 341 0.28
173 77 0.06
174 4 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (172 bp):
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGGCATG
GGTGACTACAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTCATGTTTTTGAAGGCAAACA
TTCAATTATAATCTATTTTAACTAAAAATATAAAAAAATTCA
Found at i:1222 original size:173 final size:169
Alignment explanation
Indices: 1--1629 Score: 881
Period size: 170 Copynumber: 9.5 Consensus size: 169
* * *
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCGAAAGGCATGG
1 ACTTAAAATCAA-TATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGTTTCAAAAGGCATGG
* * * * * *
66 TTGACTATAAATAGACTTTTCTTG-CACTTGAAT-AGC-TTTTTCTTCATATT-TTTAGAAGGCA
65 GTGACTACAAATGGACTTTTCTTGCCA-ATGAATGA-CTTTTTTC-TCATATTGCTT-G-AGAC-
* * * *
127 AACATTCAACTATAATCTGTTTTAA-CTAAAAATATAAAAAAATTTC-
124 AACATTCAATTATAATCTATTTTAATC-CAAAATATAAAAACA-TTCA
* *
173 ACTTAAAATCAATTATG-GAATTATAAAACTATTTAAAGTAAGTAATAAGGCTTCTAAAA-GCAT
1 ACTTAAAATCAA-TATGAG-ATTATAAAACTATTTAAAGCAAGTAATAAGGTTTC-AAAAGGCAT
* * * * * *
236 GGGTTACTACAAATAGACTTTTCTTGTCACTGAAT-AGC-TTTTTCTTCATATTTCTCGAGGTAC
63 GGGTGACTACAAATGGACTTTTCTTGCCAATGAATGA-CTTTTTTC-TCATATTGCTTGA-G-AC
* * *
299 -ACATT-AAATATTAATCTATTTTAA-CCAAAAATGTAAAAACAATCA
124 AACATTCAATTA-TAATCTATTTTAATCC-AAAATATAAAAACATTCA
* * * * * ********
344 ACTTGAAATCAATATTGAGATTATATAACCATTTAAAGCGAGTAATAAGGCTTT-GANNNNNNNN
1 ACTTAAAATCAATA-TGAGATTATAAAACTATTTAAAGCAAGTAATAAGG-TTTCAAAAGGCATG
** * * * * *
408 NNTGACTATAAATGGACATTTCTTGCCAATGAATGGCTTCTTTT-TCATGTTTC-TGAAGGGA-A
64 GGTGACTACAAATGGACTTTTCTTGCCAATGAATGACTT-TTTTCTCATATTGCTTG-A--GACA
* * * *
470 ACACTCTATTATAATCTGTTTTAA-CTAAAA-ATATAAAACAATTCA
125 ACATTCAATTATAATCTATTTTAATCCAAAATATA-AAAAC-ATTCA
* * * * **********
515 ACTTAAAATCAGTACTGAGATTAT-AAACCATTGAAAGCGAGTAATAAGGCTTT-NNNNNNNNNN
1 ACTTAAAATCAATA-TGAGATTATAAAACTATTTAAAGCAAGTAATAAGG-TTTCAAAAGGCATG
* * * * * *
578 GGTGACTATAAATGGATTTTTCTTGCC-ATGAATGGC-TTTTTCTTCATGTTTCCTGAGGTA-AA
64 GGTGACTACAAATGGACTTTTCTTGCCAATGAATGACTTTTTTC-TCATATTGCTTGA-G-ACAA
* * * * * *
640 CACTCAATTATAATCTGTTTTGA-CCAAAAATACAAAAAAACTCA
126 CATTCAATTATAATCTATTTTAATCC-AAAATATAAAAACATTCA
* ** * * *
684 ACTTAAAATCAATTATGCGATTATAAAACTATTTAAAGGGAGTAATAAGACTTT-GAAAGGTATG
1 ACTTAAAATCAA-TATGAGATTATAAAACTATTTAAAGCAAGTAATAAG-GTTTCAAAAGGCATG
* * * * * * *
748 GATGACTATAAATGGACTTTTC-TGACCAATGACTAACTTTTTAT-TCATGTTTCTTGAGATAA-
64 GGTGACTACAAATGGACTTTTCTTG-CCAATGAATGACTTTTT-TCTCATATTGCTTGAGACAAC
* * * * *
810 ATACTCAATTATAATATATTGTAA-CAAAAAATGTAAAAACAAGTCA
127 AT--TCAATTATAATCTATTTTAATC-CAAAATATAAAAAC-ATTCA
* * * * * **
856 A-TGAAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTACTAAGGCTTCGGAAGGCATG
1 ACTTAAAA-TCAA-TATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGTTTCAAAAGGCATG
* * ** * * * * *
920 GGTGACT-CTAAATGCACTTTTCTTG-CACTTGAAT-AGCTTTTCGCTCTTGTTTC-TAAGGCAA
64 GGTGACTAC-AAATGGACTTTTCTTGCCA-ATGAATGA-CTTTTTTCTCATATTGCTTGAGAC-A
* * **
981 ACACTCAAATAT-ATCTATTTTAA-CCAACAATATAAAAACATTTG
125 ACATTCAATTATAATCTATTTTAATCCAA-AATATAAAAACATTCA
*
1025 ACTTAAAATCAAGTATGAGATTATAAAACTATTTAAAGCAAGAAATAAGGTTTTCAAAAGGCATG
1 ACTTAAAATCAA-TATGAGATTATAAAACTATTTAAAGCAAGTAATAAGG-TTTCAAAAGGCATG
* * * * *
1090 GGTGACAACAAATGGACTTTTTCTTGTCAATGAAT-AGTTTTTTCTTCATGTTGCTTGCAGTGC-
64 GGTGACTACAAATGGAC-TTTTCTTGCCAATGAATGACTTTTTTC-TCATATTGCTTG-AG-ACA
* * * *
1153 ACATTGAA-TATTAATCTGTTTTAATCCAAAATGTAAAAGCATTCA
125 ACATTCAATTA-TAATCTATTTTAATCCAAAATATAAAAACATTCA
* * * *
1198 ACTTAAAAGCAATAATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT-GAAAGGCATG
1 ACTTAAAATCAAT-ATGAGATTATAAAACTATTTAAAGCAAGTAATAAGG-TTTCAAAAGGCATG
* * *
1262 GGTGACTATAACA--GACTTTTCTCGCCAATGAATGACTTTTTTCTCATATTTCTTGAGACAAAC
64 GGTGACTACAA-ATGGACTTTTCTTGCCAATGAATGACTTTTTTCTCATATTGCTTGAGAC-AAC
* ** * *
1325 ATTCAATTATAATATATTTTAATTAAAAATCTAAAAAAATTCA
127 ATTCAATTATAATCTATTTTAATCCAAAATATAAAAACATTCA
* * * * * * *
1368 ACTTAAAATCAATTATAAGATCATAAAAATATTTAAAGCAAGTAATAAGGCTTCTAAAGGCGTAG
1 ACTTAAAATCAA-TATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGTTTCAAAAGGCATGG
* * * * *
1433 GTGACTACAAATGGACTTTTCTTGCCAAT-AGAT-AGC-TTTTGCATCATGTT--TTCAAAAGTA
65 GTGACTACAAATGGACTTTTCTTGCCAATGA-ATGA-CTTTTTTC-TCATATTGCTT-GAGA-CA
* ** *
1493 AGCATTCAATTATAATATATTTTAATAAAAAATATAAAAAACATTTA
125 A-CATTCAATTATAATCTATTTTAATCCAAAATAT-AAAAACATTCA
* * * * * * *
1540 ACTAAAAATTAATTATGAGATTATAAAA-TCATTTAAAGTACGTAATAAGGCTTCAGAAGGCATA
1 ACTTAAAATCAA-TATGAGATTATAAAACT-ATTTAAAGCAAGTAATAAGGTTTCAAAAGGCATG
*
1604 GGTAACTACAAATGGACTTTTCTTGC
64 GGTGACTACAAATGGACTTTTCTTGC
1630 ACTTGAATAG
Statistics
Matches: 1173, Mismatches: 204, Indels: 160
0.76 0.13 0.10
Matches are distributed among these distances:
167 4 0.00
168 4 0.00
169 122 0.10
170 321 0.27
171 312 0.27
172 317 0.27
173 87 0.07
174 6 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.33
Consensus pattern (169 bp):
ACTTAAAATCAATATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGTTTCAAAAGGCATGGG
TGACTACAAATGGACTTTTCTTGCCAATGAATGACTTTTTTCTCATATTGCTTGAGACAACATTC
AATTATAATCTATTTTAATCCAAAATATAAAAACATTCA
Found at i:1901 original size:281 final size:280
Alignment explanation
Indices: 1393--1952 Score: 881
Period size: 281 Copynumber: 2.0 Consensus size: 280
1383 TAAGATCATA
* **
1393 AAAATATTTAAAGCAAGTAATAAGGCTTCTAAAGGCGTAGGTGACTACAAATGGACTTTTCTTGC
1 AAAATATTTAAAGCAAGTAATAAGGCTTCCAAAGGCGTAGGTGACTACAAATAAACTTTTCTTGC
* *
1458 CAATAGATAGCTTTTGCATCATGTTTTCAAAAGTAAGCATTCAATTATAATATATTTTAATAAAA
66 CAATAGATAGCTTTTGCATCACGTTTTCAAAAGCAAGCATTCAATTATAATATATTTTAATAAAA
* * *
1523 AATATAAAAAACATTTAACTAAAAATTAATTATGAGATTATAAAATCATTTAAAGTACGTAATAA
131 AATATAAAAAACATTTAACTAAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGTAATAA
* *
1588 GGCTTCAGAAGGCATAGGTAACTACAAATGGACTTTTCTTGCACTTGAATAGCTTTTTGTTCATG
196 GGCTTCAGAAGACATAGGTAACTACAAATGGACTTTTCTTGCACTTGAATAGCTTTTTGTTCACG
1653 TTTCCGAAGGCAAACATTAC
261 TTTCCGAAGGCAAACATTAC
* * * *
1673 AAAATCATTTAAAGTAAGTACTAAGGCTTCCGAAGGCGTAGGTGACTATAAATAAACTTTTCTTG
1 AAAAT-ATTTAAAGCAAGTAATAAGGCTTCCAAAGGCGTAGGTGACTACAAATAAACTTTTCTTG
*
1738 CCAATAGATAGCTTTTGCATCACGTTTTCTAAAGCAAGCATTCAATTATAATATATTTTAATAAA
65 CCAATAGATAGCTTTTGCATCACGTTTTCAAAAGCAAGCATTCAATTATAATATATTTTAATAAA
* *
1803 AAATATAAAACAA-ATTTAACTGAAAGTCAATTATGAGATTATAAAA-CTATTTAAAGCAAGTAA
130 AAATATAAAA-AACATTTAACTAAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCAAGTAA
* * * *
1866 TAAGGCTTCAGAAGATATGGGTGACTATAAATGGACTTTTCTTGCACTTGAATAGCTTTTTGTTC
193 TAAGGCTTCAGAAGACATAGGTAACTACAAATGGACTTTTCTTGCACTTGAATAGCTTTTTGTTC
*
1931 ACGTTTCCTAAGGCAAACATTA
258 ACGTTTCCGAAGGCAAACATTA
1953 GAATATAATC
Statistics
Matches: 255, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
280 6 0.02
281 247 0.97
282 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (280 bp):
AAAATATTTAAAGCAAGTAATAAGGCTTCCAAAGGCGTAGGTGACTACAAATAAACTTTTCTTGC
CAATAGATAGCTTTTGCATCACGTTTTCAAAAGCAAGCATTCAATTATAATATATTTTAATAAAA
AATATAAAAAACATTTAACTAAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGTAATAA
GGCTTCAGAAGACATAGGTAACTACAAATGGACTTTTCTTGCACTTGAATAGCTTTTTGTTCACG
TTTCCGAAGGCAAACATTAC
Found at i:2079 original size:171 final size:171
Alignment explanation
Indices: 1668--2095 Score: 474
Period size: 172 Copynumber: 2.5 Consensus size: 171
1658 GAAGGCAAAC
* * * *
1668 ATTACAAAATCATTTAAAGTAAGTACTAAGGCTTCCGAAGGCGTAGGTGACTATAAATAAACTTT
1 ATTATAAAATCATTTAAAGTAAGTA-TAAGGCTTCCAAAGGCAT-GGGGACTATAAATAAACTTT
* * * *
1733 TCTTGCCAATAG-ATAGC-TTTTGCATCACGTTTTCTAAAGCAAGCATTCAATTATAATATATTT
64 TCTTG-CAATTGAATAGCTTTTTGCATCACGTTTCCTAAAGCAAACATTCAAATATAATATATTT
*
1796 TAATAAAAAATATAAAACAAATTTAACTGAAAGTCAATTATGAG
128 TAATAAAAAATATAAAACAAATTTAACTGAAAATCAATTATGAG
* ** **
1840 ATTATAAAA-CTATTTAAAGCAAGTAATAAGGCTT-CAGAAGATATGGGTGACTATAAATGGACT
1 ATTATAAAATC-ATTTAAAGTAAGT-ATAAGGCTTCCA-AAGGCATGGG-GACTATAAATAAACT
* * * * *
1903 TTTCTTGCACTTGAATAGCTTTTTG-TTCACGTTTCCTAAGGCAAACATT-AGAATATAATCTGT
62 TTTCTTGCAATTGAATAGCTTTTTGCATCACGTTTCCTAAAGCAAACATTCA-AATATAATATAT
* * * * *
1966 TTTAATTAAAAATGTAAAA-ACATTTGACTTAAAATCAATTATGAG
126 TTTAATAAAAAATATAAAACAAATTTAACTGAAAATCAATTATGAG
* *
2011 ATTATAAAATCATTTAAAGTAAGTGATAAGGCTTCCAAAGGCATGGAGGACTACAAATAAATTTT
1 ATTATAAAATCATTTAAAGTAAGT-ATAAGGCTTCCAAAGGCATGG-GGACTATAAATAAACTTT
*
2076 TCTTGCAAATGAATAGCTTT
64 TCTTGCAATTGAATAGCTTT
2096 CTCTTAGTGT
Statistics
Matches: 212, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
171 99 0.47
172 107 0.50
173 6 0.03
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (171 bp):
ATTATAAAATCATTTAAAGTAAGTATAAGGCTTCCAAAGGCATGGGGACTATAAATAAACTTTTC
TTGCAATTGAATAGCTTTTTGCATCACGTTTCCTAAAGCAAACATTCAAATATAATATATTTTAA
TAAAAAATATAAAACAAATTTAACTGAAAATCAATTATGAG
Found at i:2140 original size:171 final size:166
Alignment explanation
Indices: 1668--2175 Score: 449
Period size: 171 Copynumber: 3.0 Consensus size: 166
1658 GAAGGCAAAC
* * * *
1668 ATTACAAAATCATTTAAAGTAAGTACTAAGGCTTCCGAAGGCGTAGGTGACTATAAATAAACTTT
1 ATTATAAAATCATTTAAAGTAAGTA-TAAGGCTTCCAAAGGCAT-GGGGACTATAAATAAACTTT
* * * * *
1733 TCTTGCCAAT-AGATAGCTTTTGCATCACGT-TTTCT-AAAGCAAGCATTCAAT-TATAATATAT
64 TCTTGCAAATGA-ATAGCTTTT-C-TTA-GTGTTTCTCAAGGCAA-CATTGAATAT-TAATATGT
* * * *
1794 TTTAATAAAAAATATAAAACAAATTTAACTGAAAGTCAATTATGAG
123 TTTAATTAAAAATGT-AAA-AAATTTAACTTAAAATCAATTATGAG
* ** **
1840 ATTATAAAA-CTATTTAAAGCAAGTAATAAGGCTT-CAGAAGATATGGGTGACTATAAATGGACT
1 ATTATAAAATC-ATTTAAAGTAAGT-ATAAGGCTTCCA-AAGGCATGGG-GACTATAAATAAACT
** * * *
1903 TTTCTTGCACTTGAATAGCTTTTTGTTCA-CGTTTC-CTAAGGCAAACATTAGAATA-TAATCTG
62 TTTCTTGCAAATGAATAGC-TTTTCTT-AGTGTTTCTC-AAGGC-AACATT-GAATATTAATATG
*
1965 TTTTAATTAAAAATGTAAAAACATTTGACTTAAAATCAATTATGAG
122 TTTTAATTAAAAATGTAAAAA-ATTTAACTTAAAATCAATTATGAG
* *
2011 ATTATAAAATCATTTAAAGTAAGTGATAAGGCTTCCAAAGGCATGGAGGACTACAAATAAATTTT
1 ATTATAAAATCATTTAAAGTAAGT-ATAAGGCTTCCAAAGGCATGG-GGACTATAAATAAACTTT
* *
2076 TCTTGCAAATGAATAGCTTTCTCTTAGTGTTTCTCGAGGTACACATTGAATATTAATATGTTTTA
64 TCTTGCAAATGAATAGCTTT-TCTTAGTGTTTCTCAAGGCA-ACATTGAATATTAATATGTTTTA
* * *
2141 ACTAAAAAAGTTAAAAAATTCAACTTAAAATCAAT
127 ATTAAAAATG-TAAAAAATTTAACTTAAAATCAAT
2176 ANNNNNNNNN
Statistics
Matches: 270, Mismatches: 43, Indels: 47
0.75 0.12 0.13
Matches are distributed among these distances:
170 12 0.04
171 149 0.55
172 98 0.36
173 11 0.04
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (166 bp):
ATTATAAAATCATTTAAAGTAAGTATAAGGCTTCCAAAGGCATGGGGACTATAAATAAACTTTTC
TTGCAAATGAATAGCTTTTCTTAGTGTTTCTCAAGGCAACATTGAATATTAATATGTTTTAATTA
AAAATGTAAAAAATTTAACTTAAAATCAATTATGAG
Found at i:2777 original size:165 final size:168
Alignment explanation
Indices: 1782--2951 Score: 453
Period size: 171 Copynumber: 6.9 Consensus size: 168
1772 CAAGCATTCA
* * * * * *
1782 ATTATAATATATTTTAA-TAAAAAATATAAAACAAATTTAACTGAAAGTCAATTATGAGATTATA
1 ATTATAATATATTTTAACTCAAACA-ATAAAA-AAATTTAACTTAAAATCAATTATAAGATTA-G
* * ** * * *
1846 AAACTATTTAAAGCAAGTAATAAGGCTT-CAGAAGATATGGGTGACTATAAATGGACTTTTCTTG
63 AAACCATTTAAGGCAAGTAATAAGGCTTCCA-AAGGCATGAGTGACTACAAATGGACTTTTTTTG
* * * * * * *
1910 C-ACTTGAATAGCTTTTTGTTCACGTTTCCT-AAGGCAAACATTAG
127 CTA-ATGAATGGCTTTTTCTTCACATTTCCTGAA-G-AGATA-TAC
* * * * * * * *
1954 AATATAATCTGTTTTAA-TTAAA-AATGTAAAAACATTTGACTTAAAATCAATTATGAGATTATA
1 ATTATAATATATTTTAACTCAAACAA--TAAAAAAATTTAACTTAAAATCAATTATAAGATTA-G
* * * * * *
2017 AAATCATTTAAAGTAAGTGATAAGGCTTCCAAAGGCATGGAG-GACTACAAAT-AAATTTTTCTT
63 AAACCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCAT-GAGTGACTACAAATGGACTTTTT-TT
* * * * * * * * **
2080 GCAAATGAATAGCTTTCTCTT-A-GTGTTTCTCGAGGTACACATTG
126 GCTAATGAATGGCTTTTTCTTCACAT-TTCCT-GAAG-AGATATAC
* * * * * *******
2124 AATATTAATATGTTTTAACT-AAAAAAGTTAAAAAATTCAACTTAAAATCAA-TANNNNNNNNNN
1 ATTA-TAATATATTTTAACTCAAACAA-TAAAAAAATTTAACTTAAAATCAATTA---TAAGATT
* * ** ** * ** * *
2187 A-AAACTATTTAAAGTGAGTAATAAGGCTTTGAAAGGCATGACTGAAAATAAATGGAC-TTTTCT
61 AGAAACCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCATGAGTGACTACAAATGGACTTTTTTT
* * * * * *
2250 -CATCAACGAATGACTTTTT-TGTCACTTTTCCTGAGACAGACATTC
126 GC-T-AATGAATGGCTTTTTCT-TCACATTTCCTGA-AGAGATATAC
* * *
2295 AATTATAAAATATTTT-AGT-AAA-AATTGTAAACAAAA-TTAACTTAAAATCAATTGTAAGATT
1 -ATTATAATATATTTTAACTCAAACAA---TAAA-AAAATTTAACTTAAAATCAATTATAAGATT
* * * * * *
2356 ATAAAACCATTTAAGGTAAGTAATAAGGCTTCTAAAAGCATAAGTGACTACAAATGGACTTTTCT
61 A-GAAACCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCATGAGTGACTACAAATGGACTTTTTT
* * * * * *
2421 TGCCAATGGATGGCTTTTGCATCATATTTCCTGAAGCAGATATTAT
125 TGCTAATGAATGGCTTTTTCTTCACATTTCCTGAAG-AGATA-TAC
* *********
2467 ATTATAATATATTTTAACTCAAATAATAAAAAAATTTAACTTAAAATCAATTATNNNNNNNNNNA
1 ATTATAATATATTTTAACTCAAACAATAAAAAAATTTAACTTAAAATCAATTAT-AAGATTAGAA
* * * *
2532 ACCATTTAAGGCGAGTAATAAGGCTTCGAAAGGCATGAGTGACTATAAATGGACTTTTTTT-ATA
65 ACCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCATGAGTGACTACAAATGGACTTTTTTTGCTA
* *
2596 CTTGAATAGG-TTTTTCTTTACA-TTCCTGAAG-GA-A-AC
130 -ATGAAT-GGCTTTTTCTTCACATTTCCTGAAGAGATATAC
* * **
2632 ATT-TAATGTATTTTAAC-CAAACAATATAAAATATTTGAACTTAAAATCAATTATGCGATTAGA
1 ATTATAATATATTTTAACTCAAACAATA-AAAAAATTT-AACTTAAAATCAATTATAAGATTAGA
* * * *
2695 AAGCCATTTAAAGCAATTAATAAGGCTTCCAAAGGTATGGGTGACTACAAATGGACTTTTTTTGC
64 AA-CCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCATGAGTGACTACAAATGGACTTTTTTTGC
** * *
2760 TAATGAATGGCTTTTTCTTCATGTTT-CTCAAGGTAGACATTGA-
128 TAATGAATGGCTTTTTCTTCACATTTCCTGAA-G-AGATA-T-AC
* * * * * * * * * *
2803 ATTTTAATCTGTTTTAAC-CAAA-ATATAAAAAAACTCAACTTGATATTAA-TATTGAGATTATA
1 ATTATAATATATTTTAACTCAAACA-ATAAAAAAATTTAACTTAAAATCAATTA-TAAGATTA-G
* * * ** * * * * *
2865 AAATCATTTAAAGCGAGTAATAAGGCTTCGGAAGGCATGGGTGACTATAAATGAACATTTATTGC
63 AAACCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCATGAGTGACTACAAATGGACTTTTTTTGC
**
2930 CCATGAATGGCTTTTTCTTCAC
128 TAATGAATGGCTTTTTCTTCAC
2952 TTTTTCTAAG
Statistics
Matches: 761, Mismatches: 178, Indels: 120
0.72 0.17 0.11
Matches are distributed among these distances:
163 8 0.01
164 25 0.03
165 92 0.12
166 5 0.01
167 1 0.00
168 4 0.01
169 9 0.01
170 131 0.17
171 403 0.53
172 75 0.10
173 6 0.01
174 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (168 bp):
ATTATAATATATTTTAACTCAAACAATAAAAAAATTTAACTTAAAATCAATTATAAGATTAGAAA
CCATTTAAGGCAAGTAATAAGGCTTCCAAAGGCATGAGTGACTACAAATGGACTTTTTTTGCTAA
TGAATGGCTTTTTCTTCACATTTCCTGAAGAGATATAC
Found at i:3738 original size:154 final size:155
Alignment explanation
Indices: 3473--3765 Score: 360
Period size: 154 Copynumber: 1.9 Consensus size: 155
3463 NNNNNNNNNT
* * * *
3473 ATTTAAAACGAGTAATAAGGCTTAAGAAAGTATGGATGACTATAAATAGACTTTTCTTGCACTTG
1 ATTTAAAACAAGTAATAAGGCTTAACAAAGTATGGATGAATATAAATAGACTTTTCTTGCACATG
* * *
3538 AATAGCTGTTTCTTTATGTTTTCTAAGGTAGACATTTCAATATAATCTATTTTAATCAAAAATAT
66 AATAGCTGTTTCTTCATGTTTTCTAAGGTAAACATTTCAATATAATCCATTTTAATCAAAAATAT
3603 AAAA-AATTAGACGATTATAAAATC
131 AAAAGAATTAGACGATTATAAAATC
** * * *
3627 ATTTAAAACAAGTAATAAGGCTTCCCAAGGTATGGGTGAATATAAATGGACTTTTCTTGC-CAAT
1 ATTTAAAACAAGTAATAAGGCTTAACAAAGTATGGATGAATATAAATAGACTTTTCTTGCAC-AT
* * * * * *
3691 GAATGGCTTTTTCTTCATG-TTTCTCAAGGTAAACA-TTGAATTTTAATCCGTTTTAATGAAAAA
65 GAATAGCTGTTTCTTCATGTTTTCT-AAGGTAAACATTTCAA-TATAATCCATTTTAATCAAAAA
*
3754 TGTAAAAGAATT
128 TATAAAAGAATT
3766 CAACTTGAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
153 10 0.09
154 102 0.88
155 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (155 bp):
ATTTAAAACAAGTAATAAGGCTTAACAAAGTATGGATGAATATAAATAGACTTTTCTTGCACATG
AATAGCTGTTTCTTCATGTTTTCTAAGGTAAACATTTCAATATAATCCATTTTAATCAAAAATAT
AAAAGAATTAGACGATTATAAAATC
Found at i:4193 original size:289 final size:279
Alignment explanation
Indices: 3676--4204 Score: 566
Period size: 289 Copynumber: 1.9 Consensus size: 279
3666 ATATAAATGG
* * ** * * *
3676 ACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCTCAAGGTAAACATTGAATTTTAATCCG
1 ACTTTTCTTACCAATGAATAGCTTTTTCTTCACATTTCTCAAGGTAAACATTCAATTATAAGCCG
** * * *
3741 TTTTAATGAAAAATGTAAAAGAATTCAACTTGAAATCAATATTGAGATTATAAAACCTTTTAAAG
66 TTTTAACAAAAAATATAAAAGAATTCAACTTAAAATCAATATTGAGATTATAAAACCGTTTAAAG
** * * **
3806 TGGGTAATAAAGCTTTGGAAGGCATGGCTGACCATAAATGGACATTTCTTGTCAATGAATGACTT
131 TAAGTAATAAAGCTTTGGAAGGAATGGCTGACCATAAATAGACATTTCTTACCAATGAATGACTT
*
3871 ATTCTTCATGTTTCTCAAGGCAAATACTCAATTACAATCTATTTTGGATTAAAATATAAATAAGG
196 ATTCTTCATGTTTCTCAAGGCAAACACTCAATTACAATCTATTTTGGATTAAAATATAAATAAGG
3936 CTTTTGAAGGAATGGGTNNNNNNNNNNGC
261 CTTTTGAAGGAATGGGT----------GC
** *
3965 ACTTTTCTTACCAATGAATATTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTAT-AGCCT
1 ACTTTTCTTACCAATGAATAGCTTTTTCTTCACATTTCTCAAGGTAAACATTCAATTATAAGCC-
4029 GTTTTAACAAAAAATATAAATA-AATTCAACTTAAAA-CTAAT-TATGAGATTATAAAACCGTTT
65 GTTTTAACAAAAAATATAAA-AGAATTCAACTTAAAATC-AATAT-TGAGATTATAAAACCGTTT
* * * * *
4091 AAAGTAAGTAAT-AAGACTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTTTACCAA-GATA
127 AAAGTAAGTAATAAAG-CTTTGGAAGGAATGGCTGACCATAAATAGACATTTCTTACCAATGA-A
* ** * * **
4154 TGACTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATTATCTATTTT
190 TGACTTATTCTTCATGTTTCTCAAGGCAAACACTCAATTACAATCTATTTT
4205 AACTAAAAAT
Statistics
Matches: 200, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
288 10 0.05
289 189 0.94
290 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (279 bp):
ACTTTTCTTACCAATGAATAGCTTTTTCTTCACATTTCTCAAGGTAAACATTCAATTATAAGCCG
TTTTAACAAAAAATATAAAAGAATTCAACTTAAAATCAATATTGAGATTATAAAACCGTTTAAAG
TAAGTAATAAAGCTTTGGAAGGAATGGCTGACCATAAATAGACATTTCTTACCAATGAATGACTT
ATTCTTCATGTTTCTCAAGGCAAACACTCAATTACAATCTATTTTGGATTAAAATATAAATAAGG
CTTTTGAAGGAATGGGTGC
Found at i:4228 original size:171 final size:171
Alignment explanation
Indices: 3965--7323 Score: 2209
Period size: 171 Copynumber: 19.6 Consensus size: 171
3955 NNNNNNNNGC
* * ** * *
3965 ACTTTTCTTACCAATGAAT-ATTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGCCT
1 ACTTTTCTTGCCAATGAATGA-CTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * * *
4029 GTTTTAACAAAAAATATAAATAAATTCAACTTAAAA-CTAATTATGAGATTATAAAACCGTTTAA
65 GTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATC-AATTATGAGATTATAAAACCATTTAA
** * *
4093 AGTAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATAG
129 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * *
4136 ACTTTTTTTACCAA-GATATGACTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATTA-TC
1 ACTTTTCTTGCCAATGA-ATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTA-TAGTC
* *
4199 TATTTTAACTAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
64 TGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * *
4264 AGTGAGTAATAAGACTTTTGAAGAAATGGTTGACTATAAATGG
129 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * * * *** * *
4307 ACTTTT-TTTCTCCATGAATGGCATTTTCTACAAGTTTCCCGAGGTAGACATTTAATTATAGTTT
1 ACTTTTCTTGC-CAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * * **********
4371 ATTTTAA-TGAAAAATATAAAAAAATTCAACTTTAAATCNNNNNNNNNNTTATAAAACCATTTAA
65 GTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * *
4435 AGCGAGTAATAATGCTTTTAAAAGAATGGGTGACTATAAATGA
129 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * * * *
4478 ATTTTTTTTGCCAATGAAAGCCTTTTTCTTCATATTTCTT-AGGATAGGCATTCAATTATAGCCT
1 ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGG-TAGACATTCAATTATAGTCT
** * * * *
4542 GTTTTAACTAAAAATAAAAAAAAAATCAGCTTAAAATTAATTATGAAATTATAAAACCATTTAAA
65 GTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * *
4607 GTGAGTAAAAAGACTTTCT-AAGGAATGGGTAACCATAAATGA
130 GCGAGTAATAAGGCTTT-TGAAGGAATGGGTGACTATAAATGG
* ** * * *
4649 AATTTTCTTGCCAATGGAA-G-CTTTCTTCTTCACATTTCTTAACGTAGACAATCAATTACAG-C
1 ACTTTTCTTGCCAAT-GAATGACTTT-TTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTC
* * * * * **
4711 TTTTTTTAACCAAAAATATAAAAAAAATT-AACTTGAAATCAATTATTAGATTATAAAACCATGA
64 -TGTTTTAACTAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* **********
4775 AAAGTGAGTAATAAGGCTTTTGAAGGAANNNNNNNNNNTAAATGG
127 AAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * ** ** * *
4820 ACTTTTCTTGCCAATAAATGATTTTTTCTTCACATTTCTTAATATATATATTTC-ATTACT-GTC
1 ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACA-TTCAATTA-TAGTC
* * *
4883 TGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAA
64 TGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* *
4948 AGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAG
129 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * *
4991 ACTTTTCTTACTAATGAATG-CTTTCTTTTTCATGTTTCTCAACGTAGACATTCAATTATAGTCT
1 ACTTTTCTTGCCAATGAATGACTTT-TTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCT
********** * *
5055 GTTTTAA-TCAAAAA-NNNNNNNNNNTCAACTTAAAATCAATTATTAGATTATAATACCATTTAA
65 GTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* **
5118 AGCGTGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTA
129 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * ** * * *
5161 ACTTTTCTTGCCAATAAATGATTTTTTCTTTACATTTCTTAAGCTAGACATTCAATTATTGTCTA
1 ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* * * * * *
5226 TTTTAACAAAAAATATAAAACAATTCAACTTAAAGTCAATTATGAGATTATAAAACCAATTAAAA
66 TTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* *
5291 CGAGTAATAAGGCTTTTGAAAGAATGGTTGACTATAAATGG
131 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * * * *
5332 ACTTTTCTTATCC-ATGAATGGCATTTT-TT-ATAGGTTCTCCAATGTA-AGCATTTAATTATAG
1 ACTTTTCTT-GCCAATGAATGACTTTTTCTTCAT-GTTTCT-TAAGGTAGA-CATTCAATTATAG
* * *
5393 TCTGTTTTAA-TGAAAAATGTAAAAAAAATCAACTTCAAATCAATTATAAGATTATAAAACCATT
62 TCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
**********
5457 TAAAGCGAGTNNNNNNNNNNTTGAAGGAATGGGTGACTATAAATGG
126 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * *
5503 ACTTTTTTTGCCAACGAATG-CTTTTTTCTTCATGTTTTTTAGGGTAGGCATTCAATTATAGTCT
1 ACTTTTCTTGCCAATGAATGAC-TTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCT
* * * * * *
5567 ATTCTAACTAAAAATATAAAAAAA-CCAACTTAAAATTAATTATGAGATTGTAAAACCATTTAAA
65 GTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * *
5631 GCGAGTAATAGGGCTTTTGAAGGAATAGGTGACCATAAATGG
130 GCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* ********* * *
5673 ACTTTTCTTGCCAATAAATGA-TTTNNNNNNNNNNTTTCTTGAGGTAGACATTTAATTAATTATT
1 ACTTTTCTTGCCAATGAATGACTTT-TTCTTCATGTTTCTTAAGGTAGACATTCAATT-A-TA--
* ** * * *****
5737 GTGTGTTTTAACCGAAAATGTAAAACAAA-TCAACTTAAAATCATTTATGAAATTATAAANNNNN
61 GTCTGTTTTAACTAAAAATGTAAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
***** * * * *
5801 NNNNNGCGAGTAATAAGGCTTTTGAAGGAATTGGTAACTATAAGTGA
125 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * * *
5848 ACTTTTCTT-CTCAATGAATGA-TATTTTCTTTATGTTTCCTAAGGCAGACATTTAGTTATAGTT
1 ACTTTTCTTGC-CAATGAATGACT-TTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTC
********** * * *
5911 TGTTTTAA-TGAAAAATGTAAAAAANNNNNNNNNNAAATCGATTATGAGATTATAAAATCATTCA
64 TGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * **********
5975 AAGTGAGTAATAAGACTTTTGAAGGAANNNNNNNNNNTAAATGG
128 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * ** ** ** *
6019 ACTTTTCTTGCCAATAAATAATTTTTTCTTTACATTTCTCGACTTAGACATTCAATTATTGTCTG
1 ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
********** * * * * * * *
6084 TTTNNNNNNNNNNTATAAAACAATTCAACTTAAAATTAACTATGAGATCATAAAACTATTTAAAA
66 TTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * ******
6149 CGAGTAATAAGGCCTTTGAAGGAATGAGTGACTATNNNNNN
131 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
**** * * * *
6190 NNNNTTCTT-CTCAATGAATGGCTTTTTCTATACA--TTTCCTAAGGCA-AGATTCAATTATAGT
1 ACTTTTCTTGC-CAATGAATGACTTTTTCT-T-CATGTTTCTTAAGGTAGACATTCAATTATAGT
* * * ** * * *
6251 TTATTTTAACCAAAAATGTAAAAAAGCTCAACCTAAAACCAATTATGAGATTATAAAACCATTTC
63 CTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * **
6316 AGGTGAGTAATAAGGCTTTTAAAGGATTGAGTGACTATAAAAAG
128 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
*** **
6360 ACTTTTCTT-CTCAATGAATTG-CTTTTTCTAT-ATGTTTCACCAGACA-AGCATTCAATTATAG
1 ACTTTTCTTGC-CAATGAA-TGACTTTTTCT-TCATGTTTCTTAAGGTAGA-CATTCAATTATAG
* ** **********
6421 TCTATTTTAA-TGAAAAATGTAAAAAAATAAAACTNNNNNNNNNNTATGAGATTATAAAACCATT
62 TCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
*
6485 TAAAGCCG-GTAATAAGGCTTTTGAA-GACATGAGTGACTATAAATGG
126 TAAAG-CGAGTAATAAGGCTTTTGAAGGA-ATGGGTGACTATAAATGG
* * * * * *
6531 ACTTTTTTTGCCAATGAATGTCTTTTTCTTCACG-TTC-CAAGGGTAGGCATTAAATTATCA-TC
1 ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAA-GGTAGACATTCAATTAT-AGTC
* * * * ** * **********
6593 TCTTTTAGCCAAAACTACAAAAAAATTCAACTTAAAATTAATTATGAGATTATANNNNNNNNNNA
64 TGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* *
6658 AGCGAGTAATAAGG-TTTTGAAGGTATGGGTGACTATAAGTGG
129 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * * *
6700 ACTTTTCTTACCAATGAATGCTTTCTTTTTTTTACA--TTTCTCAAAGTAGACATTCAATTATAG
1 ACTTTTCTTGCCAATGAATG---ACTTTTTCTT-CATGTTTCTTAAGGTAGACATTCAATTATAG
* * * * * * * *
6763 TCTGTTTTAACCAAAAATGCAAAGAAATTTAACCTAAAATTAATTATTAGATTATAAAATCATTT
62 TCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
*** * * * *
6828 AAAATAAGTAATAAGGCTTTTGAAGGAATGGGAGACAACAAATAG
127 AAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
*** * * * * *
6873 ACTTTTCTAATCAATGAATGCCTTTTTGTTCATGTTTCTCAACGTAGACATTCAATTATAATCTG
1 ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
* * * * * * *
6938 TTTTGACAAAAAATGTAAAAAAAATTGAACTCAAAATCAGTTTTGAGATTATAAAAGCATTTAAA
66 TTTTAACTAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * ** *
7003 GTGAGTAATAAGGCTTTTGGAGGAATAAGTGATTAT-AATGG
130 GCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
**
7044 ACTTTTCTTGCCAATGAATG-CATTTTTCTTCA-GCTTTCCCAAGGTAGACATTCAATTATTA-T
1 ACTTTTCTTGCCAATGAATGAC-TTTTTCTTCATG-TTTCTTAAGGTAGACATTCAATTA-TAGT
* *
7106 CTGTTTTAACTAAAAATGTAGAAAAAATTCAACTTAAAATCAATTATGGGATGATAAAACCATTT
63 CTGTTTTAACTAAAAATGTA-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
** * ** * *
7171 AAAGTTAGTAATAAGACTTTTGAAGGAATGCATGATTATAAATAG
127 AAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* ** * *
7216 ACTTTTCTT-CTCAATGAATGACTTTTTCTACGCGTTTGC-TGAGGTAAACATTCAATTATAGTC
1 ACTTTTCTTGC-CAATGAATGACTTTTTCTTCATGTTT-CTTAAGGTAGACATTCAATTATAGTC
* * * *
7279 TATTTTTTAA--AAAGATGTAAAAAAATTTAACTCAAAATCAATTAT
64 --TGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
7324 AAGACTATTT
Statistics
Matches: 2438, Mismatches: 652, Indels: 196
0.74 0.20 0.06
Matches are distributed among these distances:
168 1 0.00
169 51 0.02
170 482 0.20
171 1460 0.60
172 259 0.11
173 53 0.02
174 28 0.01
175 102 0.04
176 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
ACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTG
TTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
Found at i:5298 original size:512 final size:505
Alignment explanation
Indices: 3965--7284 Score: 1908
Period size: 512 Copynumber: 6.5 Consensus size: 505
3955 NNNNNNNNGC
* * ** ** * *
3965 ACTTTTCTTACCAATGAATATTTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGCCTG
1 ACTTTTTTTGCCAATGAATGCTTTTTT-TTCATGTTTCT-AAGGTAGGCATTCAATTATAGTCTG
* * *
4030 TTTTAAC-AAAAAATATAAATAAATTCAACTTAAAA-CTAATTATGAGATTATAAAACCGTTTAA
64 TTTTAACTAAAAAA-A-AAAAAAAATCAACTTAAAATC-AATTATGAGATTATAAAACCATTTAA
** * * * * *
4093 AGTAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAAT-AGACTTTTTTTACCAAGATATGA
126 AGCGAGTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGA-ACTTTTCTTGCCAATAAATGA
* ** * * * * * *
4157 CTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATTATCTATTTTAACTAAAAATGTAAAAC
190 TTTTTTCTTCACATTTCTTAAGCTAGACATTCAATTATTGTCTATTTTAACAAAAAATATAAAAC
* * *
4222 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAG
255 AATTCAACTT-AAATCAATTATGAGATTATAAAACCAATTAAAATGAGTAATAAGGCTTTTGAAG
* * *** * * * *
4287 AAATGGTTGACTATAAATGGACTTTTTTTCTCCATGAATGGCATTTTCTACAAGTTTCCCGAGGT
319 GAATGGTTGACTATAAATGGACTTTTCTT-TCCATGAATGATTTTTTCTTCAA-TTTCTCAATGT
* * * * ********
4352 AGACATTTAATTATAGTTTATTTTAATGAAAAATATAAAAAAATTCAACTTTAAATCNNNNNNNN
382 A-ACATTTAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAA
** * * *
4417 NNTTATAAAACCATTTAAAGCGAGTAATAATGCTTTTAAAAGAATGGGTGACTATAAATG
446 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* * * * * *
4477 AATTTTTTTTGCCAATGAAAGCCTTTTTCTTCATATTTCTTAGGATAGGCATTCAATTATAGCCT
1 -ACTTTTTTTGCCAATGAATG-CTTTTTTTTCATGTTTCTAAGG-TAGGCATTCAATTATAGTCT
* * *
4542 GTTTTAACTAAAAATAAAAAAAAAATCAGCTTAAAATTAATTATGAAATTATAAAACCATTTAAA
63 GTTTTAACTAAAAA-AAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * *
4607 GTGAGTAAAAAGACTTTCT-AAGGAATGGGTAACCATAAATGAAATTTTCTTGCCAATGGAA-GC
127 GCGAGTAATAAGACTTT-TGAAGGAATGGGTGACCATAAATGAACTTTTCTTGCCAAT-AAATGA
* * ** * *
4670 TTTCTTCTTCACATTTCTTAA-CGTAGACAATCAATTACAG-CTTTTTTTAACCAAAAATATAAA
190 TTTTTTCTTCACATTTCTTAAGC-TAGACATTCAATTATTGTC-TATTTTAACAAAAAATAT-AA
* * *
4733 AAAAATT-AACTTGAAATCAATTATTAGATTATAAAACC-ATGAAAAGTGAGTAATAAGGCTTTT
252 AACAATTCAACTT-AAATCAATTATGAGATTATAAAACCAATTAAAA-TGAGTAATAAGGCTTTT
********** * * *
4796 GAAGGAANNNNNNNNNNTAAATGGACTTTTCTTGCCAATAAATGATTTTTTCTTCACATTTCTTA
315 GAAGGAATGGTTGACTATAAATGGACTTTTCTTTCC-ATGAATGATTTTTTCTTCA-ATTTCTCA
* * * ** *
4861 ATATATATATTTCATTACT-GTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAAT
378 ATGTA-ACATTTAATTA-TAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAAT
* * *
4925 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATA
441 TATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-
4990 G
505 G
* * * * *
4991 ACTTTTCTTACTAATGAATGCTTTCTTTTTCATGTTTCTCAACGTAGACATTCAATTATAGTCTG
1 ACTTTTTTTGCCAATGAATGCTTT-TTTTTCATGTTTCT-AAGGTAGGCATTCAATTATAGTCTG
********** * *
5056 TTTTAA-TCAAAAANNNNNNNNNNTCAACTTAAAATCAATTATTAGATTATAATACCATTTAAAG
64 TTTTAACT-AAAAAAAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
5120 CGTGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTAACTTTTCTTGCCAATAAATGATTT
128 CGAGTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGAACTTTTCTTGCCAATAAATGATTT
*
5185 TTTCTTTACATTTCTTAAGCTAGACATTCAATTATTGTCTATTTTAACAAAAAATATAAAACAAT
193 TTTCTTCACATTTCTTAAGCTAGACATTCAATTATTGTCTATTTTAACAAAAAATATAAAACAAT
* *
5250 TCAACTTAAAGTCAATTATGAGATTATAAAACCAATTAAAACGAGTAATAAGGCTTTTGAAAGAA
258 TCAACTTAAA-TCAATTATGAGATTATAAAACCAATTAAAATGAGTAATAAGGCTTTTGAAGGAA
* **
5315 TGGTTGACTATAAATGGACTTTTCTTATCCATGAATGGCATTTTTT-AT-AGGTTCTCCAATGTA
322 TGGTTGACTATAAATGGACTTTTCTT-TCCATGAAT-G-ATTTTTTCTTCAATTTCT-CAATGTA
* *
5378 AGCATTTAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAAATCAACTTCAAATCAATTATAAG
383 A-CATTTAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAG
**********
5443 ATTATAAAACCATTTAAAGCGAGTNNNNNNNNNNTTGAAGGAATGGGTGACTATAAATGG
447 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-G
* * * *
5503 ACTTTTTTTGCCAACGAATGCTTTTTTCTTCATGTTTTTTAGGGTAGGCATTCAATTATAGTCTA
1 ACTTTTTTTGCCAATGAATGCTTTTTT-TTCATG-TTTCTAAGGTAGGCATTCAATTATAGTCTG
* * * * * *
5568 TTCTAACTAAAAATATAAAAAAACCAACTTAAAATTAATTATGAGATTGTAAAACCATTTAAAGC
64 TTTTAACTAAAAAAAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
* * * * *
5633 GAGTAATAGGGCTTTTGAAGGAATAGGTGACCATAAATGGACTTTTCTTGCCAATAAATGATTTN
129 GAGTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGAACTTTTCTTGCCAATAAATGATTTT
********* * * * * * ** *
5698 NNNNNNNNNTTTCTTGAGGTAGACATTTAATTAATTATTGTGTGTTTTAACCGAAAATGTAAAAC
194 TTCTTCACATTTCTTAAGCTAGACA--T--TCAATTATTGTCTATTTTAACAAAAAATATAAAAC
* * * ************
5763 AAATCAACTTAAAATCATTTATGAAATTATAAANNNNNNNNNNGCGAGTAATAAGGCTTTTGAAG
255 AATTCAACTT-AAATCAATTATGAGATTATAAAACCAATTAAAATGAGTAATAAGGCTTTTGAAG
* * * * * * * *
5828 GAATTGG-TAACTATAAGTGAACTTTTCTTCTCAATGAATGATATTTTCTTTATGTTTC-CTAAG
319 GAA-TGGTTGACTATAAATGGACTTTTCTT-TCCATGAATGATTTTTTCTTCA-ATTTCTC-AAT
* * * ********** *
5891 GCAGACATTTAGTTATAGTTTGTTTTAATGAAAAATGTAAAAAANNNNNNNNNNAAATCGATTAT
380 GTA-ACATTTAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
* * * * * **********
5956 GAGATTATAAAATCATTCAAAGTGAGTAATAAGACTTTTGAAGGAANNNNNNNNNNTAAATGG
444 AAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-G
* * ** * ** * ** * *
6019 ACTTTTCTTGCCAATAAATAATTTTTTCTTTACATTTCTCGACTTAGACATTCAATTATTGTCTG
1 ACTTTTTTTGCCAATGAATGCTTTTTT-TTCATGTTTCT-AAGGTAGGCATTCAATTATAGTCTG
********** * * * * * * * *
6084 TTTNNNNNNNNNNTATAAAACAATTCAACTTAAAATTAACTATGAGATCATAAAACTATTTAAAA
64 TTT-TAACTAAAAAAAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * ********** * **
6149 CGAGTAATAAGGCCTTTGAAGGAATGAGTGACTATNNNNNNNNNNTTCTT-CTCAATGAATGGCT
128 CGAGTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGAACTTTTCTTGC-CAATAAATGATT
* * * * * *
6213 TTTTCTAT-ACATTTCCTAAGGC-A-AGATTCAATTATAGTTTATTTTAACCAAAAATGTAAAA-
192 TTTTCT-TCACATTTCTTAA-GCTAGACATTCAATTATTGTCTATTTTAACAAAAAATATAAAAC
* * * * * ** *
6274 AAGCTCAACCTAAAACCAATTATGAGATTATAAAACCATTTCAGGTGAGTAATAAGGCTTTTAAA
255 AA-TTCAA-CTTAAATCAATTATGAGATTATAAAACCAATTAAAATGAGTAATAAGGCTTTTGAA
* ** * * * * *
6339 GGATTGAG-TGACTATAAAAAGACTTTTCTTCTCAATGAATTG-CTTTTTCTAT-ATGTTTCACC
318 GGAATG-GTTGACTATAAATGGACTTTTCTT-TCCATGAA-TGATTTTTTCT-TCA-ATTTCTCA
* * * ** **********
6401 A-GACAAGCATTCAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATAAAACTNNNNNNNNNN
378 ATG-TAA-CATTTAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAAT
* *
6465 TATGAGATTATAAAACCATTTAAAGCCG-GTAATAAGGCTTTTGAA-GACATGAGTGACTATAAA
441 TATAAGATTATAAAACCATTTAAAG-CGAGTAATAAGGCTTTTGAAGGA-ATGGGTGACTATAAA
6528 TGG
504 T-G
* * * *
6531 ACTTTTTTTGCCAATGAATGTCTTTTTCTTCACG-TTCCAAGGGTAGGCATTAAATTATCA-TCT
1 ACTTTTTTTGCCAATGAATG-CTTTTTTTTCATGTTTCTAA-GGTAGGCATTCAATTAT-AGTCT
* * * * * * * **********
6594 CTTTTAGCCAAAACTACAAAAAAATTCAACTTAAAATTAATTATGAGATTATANNNNNNNNNNAA
63 GTTTTAACTAAAA-AAAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * * * *
6659 GCGAGTAATAAG-GTTTTGAAGGTATGGGTGACTATAAGTGGACTTTTCTTACCAATGAATGCTT
127 GCGAGTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGAACTTTTCTTGCCAATAAATG-AT
* * * * * * **
6723 TCTTTTTTTTACATTTCTCAAAG-TAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAAG
191 T-TTTTCTTCACATTTCT-TAAGCTAGACATTCAATTATTGTCTATTTTAACAAAAAATATAAA-
* * * * * * *
6787 A-AATTTAACCTAAAATTAATTATTAGATTATAAAATCATTTAAAATAAGTAATAAGGCTTTTGA
253 ACAATTCAA-CTTAAATCAATTATGAGATTATAAAACCAATTAAAATGAGTAATAAGGCTTTTGA
** * * * * * ** * * *
6851 AGGAATGGGAGACAACAAATAGACTTTTCTAATCAATGAATGCCTTTTTGTTCATGTTTCTCAAC
317 AGGAATGGTTGACTATAAATGGACTTTTCT-TTCCATGAATGATTTTTTCTTCA-ATTTCTCAAT
* * * ** * * * *
6916 GTAGACATTCAATTATAATCTGTTTTGACAAAAAATGTAAAAAAAATTGAACTCAAAATCAGTTT
380 GTA-ACATTTAATTATAGTCTGTTTTAATGAAAAATGT-AAAAAAATTCAACTTAAAATCAATTA
* * * * ** *
6981 TGAGATTATAAAAGCATTTAAAGTGAGTAATAAGGCTTTTGGAGGAATAAGTGATTAT-AATGG
443 TAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-G
* * * *
7044 ACTTTTCTTGCCAATGAATGCATTTTTCTTCA-GCTTTCCCAAGGTAGACATTCAATTATTA-TC
1 ACTTTTTTTGCCAATGAATGC-TTTTTTTTCATG-TTT-CTAAGGTAGGCATTCAATTA-TAGTC
* * * * *
7107 TGTTTTAACTAAAAATGTAGAAAAAATTCAACTTAAAATCAATTATGGGATGATAAAACCATTTA
62 TGTTTTAACTAAAAA--AAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
** ** ** *
7172 AAGTTAGTAATAAGACTTTTGAAGGAATGCATGATTATAAAT-AGACTTTTCTT-CTCAATGAAT
125 AAGCGAGTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGA-ACTTTTCTTGC-CAATAAAT
* * * * * * * *
7235 GACTTTTTCTACGCGTTTGC-TGAGGTAAACATTCAATTATAGTCTATTTT
188 GATTTTTTCTTCACATTT-CTTAAGCTAGACATTCAATTATTGTCTATTTT
7285 TTAAAAAGAT
Statistics
Matches: 2137, Mismatches: 576, Indels: 187
0.74 0.20 0.06
Matches are distributed among these distances:
510 34 0.02
511 104 0.05
512 730 0.34
513 649 0.30
514 170 0.08
515 62 0.03
516 284 0.13
517 103 0.05
518 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (505 bp):
ACTTTTTTTGCCAATGAATGCTTTTTTTTCATGTTTCTAAGGTAGGCATTCAATTATAGTCTGTT
TTAACTAAAAAAAAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
GTAATAAGACTTTTGAAGGAATGGGTGACCATAAATGAACTTTTCTTGCCAATAAATGATTTTTT
CTTCACATTTCTTAAGCTAGACATTCAATTATTGTCTATTTTAACAAAAAATATAAAACAATTCA
ACTTAAATCAATTATGAGATTATAAAACCAATTAAAATGAGTAATAAGGCTTTTGAAGGAATGGT
TGACTATAAATGGACTTTTCTTTCCATGAATGATTTTTTCTTCAATTTCTCAATGTAACATTTAA
TTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAA
CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
Found at i:7299 original size:343 final size:343
Alignment explanation
Indices: 6661--7318 Score: 801
Period size: 343 Copynumber: 1.9 Consensus size: 343
6651 NNNNNNAAGC
* ** *
6661 GAGTAATAAGGTTTTGAAGGTATGGGTGACTATAAGTGGACTTTTCTTACCAATGAATGCTTTCT
1 GAGTAATAAGGTTTTGAAGGAATAAGTGACTATAAGTGGACTTTTCTTACCAATGAATGCTATCT
* * * *
6726 TTTTTTTACATTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAAGAAAT
66 TTTCTTCACATTTCCCAAAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAAAAAAT
* * * * * *
6791 TTAACCTAAAATTAATTATTAGATTATAAAATCATTTAAAATAAGTAATAAGGCTTTTGAAGGAA
131 TCAACCTAAAATCAATTATGAGATGATAAAACCATTTAAAATAAGTAATAAGACTTTTGAAGGAA
* * * * * *
6856 TGGGAGACAACAAATAGACTTTTCTAATCAATGAATGCCTTTTTGTTCATGTTTCTCAACGTAGA
196 TGGCAGACAACAAATAGACTTTTCTAATCAATGAATGACTTTTTCTACACGTTTCTCAACGTAAA
6921 CATTCAATTATAATCTGTTTTGACAAAAAATGTAAAAAAAATTGAACTCAAAATCAGTTTTGAGA
261 CATTCAATTATAATCTGTTTTGACAAAAAATGT-AAAAAAATTGAACTCAAAATCAGTTTTGAGA
6986 TTATAAAAGCATTTAAAGT
325 TTATAAAAGCATTTAAAGT
* * *
7005 GAGTAATAAGGCTTTTGGAGGAATAAGTGATTATAA-TGGACTTTTCTTGCCAATGAATGC-AT-
1 GAGTAATAAGG-TTTTGAAGGAATAAGTGACTATAAGTGGACTTTTCTTACCAATGAATGCTATC
* * *
7067 TTTTCTTCAGC-TTTCCCAAGGTAGACATTCAATTATTA-TCTGTTTTAACTAAAAATGTAGAAA
65 TTTTCTTCA-CATTTCCCAAAGTAGACATTCAATTA-TAGTCTGTTTTAACCAAAAATGCA-AAA
* * * *
7130 AAATTCAACTTAAAATCAATTATGGGATGATAAAACCATTTAAAGTTAGTAATAAGACTTTTGAA
127 AAATTCAACCTAAAATCAATTATGAGATGATAAAACCATTTAAAATAAGTAATAAGACTTTTGAA
** * ** * *
7195 GGAAT-GCATGATTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTCTACGCGTTTGCT-GA
192 GGAATGGCA-GACAACAAATAGACTTTTCTAATCAATGAATGACTTTTTCTACACGTTT-CTCAA
* * * * * *
7258 GGTAAACATTCAATTATAGTCTATTTTTTA-AAAAGATGTAAAAAAATTTAACTCAAAATCA
255 CGTAAACATTCAATTATAATCT-GTTTTGACAAAAAATGTAAAAAAATTGAACTCAAAATCA
7319 ATTATAAGAC
Statistics
Matches: 264, Mismatches: 43, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
342 71 0.27
343 133 0.50
344 41 0.16
345 19 0.07
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (343 bp):
GAGTAATAAGGTTTTGAAGGAATAAGTGACTATAAGTGGACTTTTCTTACCAATGAATGCTATCT
TTTCTTCACATTTCCCAAAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAAAAAAT
TCAACCTAAAATCAATTATGAGATGATAAAACCATTTAAAATAAGTAATAAGACTTTTGAAGGAA
TGGCAGACAACAAATAGACTTTTCTAATCAATGAATGACTTTTTCTACACGTTTCTCAACGTAAA
CATTCAATTATAATCTGTTTTGACAAAAAATGTAAAAAAATTGAACTCAAAATCAGTTTTGAGAT
TATAAAAGCATTTAAAGT
Found at i:8484 original size:171 final size:168
Alignment explanation
Indices: 8085--8787 Score: 423
Period size: 171 Copynumber: 4.1 Consensus size: 168
8075 NNNNNNNNNN
* * * * * * * * *
8085 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAACTGATTTTAGGTTCATTTTTTT
1 AAAAGCCTTATTACTCGCTTAAAAAGATTTTATAATCTCATAATTAATTTTAAGTTGA--ATTTT
* ********* * **
8150 TTTACATTTTTTATTAAAGCAGATTATAATTGAATGTCTACNNNNNNNNNNATGAAGAGAAAGGC
64 TTTACA-TTTTTATTAAAACAGATTATAATTGAATGTCTAC-TCTAGAAACATGAAGACAAAAAC
* * *
8215 ATTCATTGGCAAAAAAAGTCTATTTATTA-TCACCCATTCCTTC
127 ATTCATTGG-AAGAAAAGTCCATTTA-TAGTAACCCATTCCTTC
* * * * * ********* *
8258 AAAAGCCTTATTACTTGCTTTAAATGGTTTTATAGTCT-ANNNNNNNNNNTTAAGTTCAATTTTT
1 AAAAGCCTTATTACTCGCTTAAAAAGATTTTATAATCTCA-TAATTAATTTTAAGTTGAATTTTT
*
8322 TTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTAGCTCTAGAAACATGAAGACAAAAACA
65 TTACATTTTT-ATTAAAACAGATTATAATTGAATGTCTA-CTCTAGAAACATGAAGACAAAAACA
* *
8387 TTCATTGGCAAGAAAAGTCCACTTATAGTTACCCATTCCTTC
128 TTCATTGG-AAGAAAAGTCCATTTATAGTAACCCATTCCTTC
* **********
8429 AAAAGCCTTATTAGTCGCNNNNNNNNNNTTTATAATCTCATAATTAATTTTAAGTTGAATTGTTT
1 AAAAGCCTTATTACTCGCTTAAAAAGATTTTATAATCTCATAATTAATTTTAAGTTGAATT-TTT
* * * * * * * *
8494 GGTA-GTTTTTCTTACAACAGACTATAATTGAATGTTTACCCTAGAAAACATGAAGA-AAAAGGC
65 -TTACATTTTTATTAAAACAGATTATAATTGAATGTCTACTCTAG-AAACATGAAGACAAAA-AC
* * **
8557 ATTCACTGGTAA-AAAATTTTATTTACT-GTAACCCATTCCTTC
127 ATTCATTGG-AAGAAAAGTCCATTTA-TAGTAACCCATTCCTTC
** * *
8599 AAAAGCCTTATTACTTACTTAAAAAGATTTTATAATCTCATAATTGATTTTAAATTGAATTTTTT
1 AAAAGCCTTATTACTCGCTTAAAAAGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTT
* * * * * ** **
8664 TACATTTTACATTAAAACAAATTATAATTAAAT-ACTTCCCTCGGGAAACATGTAA-ACAAAGTC
66 TACATTTT-TATTAAAACAGATTATAATTGAATGTC-T-ACTCTAGAAACATG-AAGACAAAAAC
* * *
8727 ATTCATTGAGAAGAAAAGTCCATTTACAGTCACCTATTCCTTC
127 ATTCATTG-GAAGAAAAGTCCATTTATAGTAACCCATTCCTTC
8770 AAAAGCCTTATTACTCGC
1 AAAAGCCTTATTACTCGC
8788 NNNNNNNNNN
Statistics
Matches: 402, Mismatches: 109, Indels: 40
0.73 0.20 0.07
Matches are distributed among these distances:
168 2 0.00
169 7 0.02
170 122 0.30
171 214 0.53
172 11 0.03
173 46 0.11
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.36
Consensus pattern (168 bp):
AAAAGCCTTATTACTCGCTTAAAAAGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTT
TACATTTTTATTAAAACAGATTATAATTGAATGTCTACTCTAGAAACATGAAGACAAAAACATTC
ATTGGAAGAAAAGTCCATTTATAGTAACCCATTCCTTC
Found at i:8692 original size:170 final size:171
Alignment explanation
Indices: 8457--8784 Score: 371
Period size: 170 Copynumber: 1.9 Consensus size: 171
8447 NNNNNNNNNN
* * * * *
8457 TTTATAATCTCATAATTAATTTTAAGTTGAATTGTTTGGTAGTTTTTCTTACAACAGACTATAAT
1 TTTATAATCTCATAATTAATTTTAAATTGAATTGTTTGGTAATTTTACTTAAAACAAACTATAAT
* ** * **
8522 TGAATGTTTACCCT-AGAAAACATG-AAGAAAAAGGCATTCACTG-GTAA-AAAATTTTATTTAC
66 TAAATACTT-CCCTCAGAAAACATGTAA-AAAAAGGCATTCACTGAG-AAGAAAAGTCCATTTAC
*
8583 TGTAACCCATTCCTTCAAAAGCCTTATTACTTACTTAAAAAGAT
128 AGTAACCCATTCCTTCAAAAGCCTTATTACTTACTTAAAAAGAT
* * *
8627 TTTATAATCTCATAATTGATTTTAAATTGAATT-TTT-TTACATTTTACATTAAAACAAATTATA
1 TTTATAATCTCATAATTAATTTTAAATTGAATTGTTTGGTA-ATTTTAC-TTAAAACAAACTATA
* * * * *
8690 ATTAAATACTTCCCTCGGGAAACATGTAAACAAAGTCATTCATTGAGAAGAAAAGTCCATTTACA
64 ATTAAATACTTCCCTCAGAAAACATGTAAAAAAAGGCATTCACTGAGAAGAAAAGTCCATTTACA
* *
8755 GTCACCTATTCCTTCAAAAGCCTTATTACT
129 GTAACCCATTCCTTCAAAAGCCTTATTACT
8785 CGCNNNNNNN
Statistics
Matches: 130, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
168 2 0.02
169 12 0.09
170 74 0.57
171 42 0.32
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (171 bp):
TTTATAATCTCATAATTAATTTTAAATTGAATTGTTTGGTAATTTTACTTAAAACAAACTATAAT
TAAATACTTCCCTCAGAAAACATGTAAAAAAAGGCATTCACTGAGAAGAAAAGTCCATTTACAGT
AACCCATTCCTTCAAAAGCCTTATTACTTACTTAAAAAGAT
Found at i:9845 original size:9 final size:10
Alignment explanation
Indices: 9824--9850 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9814 TATTTTATTG
9824 AAAAATTTAA
1 AAAAATTTAA
9834 AAAAATTTAA
1 AAAAATTTAA
9844 AAAAATT
1 AAAAATT
9851 CAACTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:12961 original size:171 final size:172
Alignment explanation
Indices: 12657--13021 Score: 425
Period size: 171 Copynumber: 2.1 Consensus size: 172
12647 NNNNNNNNNN
*
12657 CGCTTTAAATGGTTTTATAATCAAAAAACTAATTTTATGTTCAATTTTTTTTACATGTTTTGCAA
1 CGCTTTAAATGGTTTTATAATCAAAAAACTAATTTTAAGTTCAATTTTTTTTACATGTTTTGCAA
* * *
12722 AAAGAGATTATAATTGAATGTCTACATTTAGAAACGTTAAGAAAAAGGCATTCATTGGCAAAAAA
66 AAAGAGACTATAATTGAATGTCTACATTTAGAAACGTGAAGAAAAAGGCATTCATTGACAAAAAA
* *** * *
12787 AGTCTATTTATTTTCATCCATTCTTTCAAAAGCCTTTTTACT
131 AGTCTACTTACAGTCACCCATTCTTTCAAAAGCCTTATTACT
* * * * * * *
12829 TGCTTTAAATAGTTTTATAGT-AGAATAATTAATTTTAAGTTGAA-TTTTTTTACAT-TTTTGGT
1 CGCTTTAAATGGTTTTATAATCA-AAAAACTAATTTTAAGTTCAATTTTTTTTACATGTTTT-GC
* * * * * * *
12891 TAAAATAGACTCTAATTGAATGT-T-TATTTCAAGAAATGTGAAGAAAAATGCATTCATTGACTA
64 AAAAAGAGACTATAATTGAATGTCTACATTT--AGAAACGTGAAGAAAAAGGCATTCATTGACAA
*
12954 GAAAAGTCTACTTACAGTCACCCATTCTTTCAAAAGCCTTATTACT
127 AAAAAGTCTACTTACAGTCACCCATTCTTTCAAAAGCCTTATTACT
*
13000 CGGTTTAAATGGTTTTATAATC
1 CGCTTTAAATGGTTTTATAATC
13022 TNNNNNNNNN
Statistics
Matches: 159, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
169 4 0.03
170 5 0.03
171 115 0.72
172 35 0.22
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (172 bp):
CGCTTTAAATGGTTTTATAATCAAAAAACTAATTTTAAGTTCAATTTTTTTTACATGTTTTGCAA
AAAGAGACTATAATTGAATGTCTACATTTAGAAACGTGAAGAAAAAGGCATTCATTGACAAAAAA
AGTCTACTTACAGTCACCCATTCTTTCAAAAGCCTTATTACT
Found at i:14230 original size:171 final size:167
Alignment explanation
Indices: 14053--14478 Score: 442
Period size: 171 Copynumber: 2.5 Consensus size: 167
14043 TGTTTGAATG
* * * * *
14053 AAAAATGTTAAAAAATTCAACTGAAAATCAAATATAAGATTATAATACCATTTAAAGTGACTAAT
1 AAAAATGTAAAAAAATTCAACTGAAAATCAATTATTAGATTATAA-ACCATTTAAAGCGAGTAAT
* * * * ** * *
14118 AAGGCTTTTTAAAGAATGAGTGACAGTAAGTGGACTTTTCTTATCAATGAAT-ACTTTTCTCTTC
65 AAGGCTTTTGAAGGAATGA-TGACAATAAATACACTTTTCTTACCAATGAATGACTTTT-TCTTA
* *
14182 ACATTTCTTGAA-ATAGACATTCAATTATAGTCTCTTTTAACC
128 ACATTTC-T-AATATAGACATTCAAGTATAATCTCTTTTAA-C
* * * * * * *
14224 AAAAATGTAAAAAAATTCAACTTAAAATTAATTATTATACTATACAACTATTTAAAGCAAGTAAA
1 AAAAATGTAAAAAAATTCAACTGAAAATCAATTATTAGATTATA-AACCATTTAAAGCGAGTAAT
* *
14289 AAGGCTTTTGAAGGAATCGATGACAATAAATACACTTTTCTTCCCAATGAATGCCTTTTTCTTAA
65 AAGGCTTTTGAAGGAAT-GATGACAATAAATACACTTTTCTTACCAATGAATGACTTTTTCTTAA
* * *
14354 CGTTTCTAATTGTAGACATTCAAGTATAATCTGTTTTAAC
129 CATTTCTAA-TATAGACATTCAAGTATAATCTCTTTTAAC
* * ** *
14394 AAAACATGTAAAAAAATTGAACCGAAAATCTGTTTTTAGATTATAAAACCATTTAAAGCGAGTAA
1 AAAA-ATGTAAAAAAATTCAACTGAAAATCAATTATTAGATTAT-AAACCATTTAAAGCGAGTAA
*
14459 TTAGGCTTTTGAAGGAATGA
64 TAAGGCTTTTGAAGGAATGA
14479 NNNNNNNNNN
Statistics
Matches: 208, Mismatches: 40, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
169 2 0.01
170 8 0.04
171 189 0.91
172 9 0.04
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (167 bp):
AAAAATGTAAAAAAATTCAACTGAAAATCAATTATTAGATTATAAACCATTTAAAGCGAGTAATA
AGGCTTTTGAAGGAATGATGACAATAAATACACTTTTCTTACCAATGAATGACTTTTTCTTAACA
TTTCTAATATAGACATTCAAGTATAATCTCTTTTAAC
Found at i:15530 original size:171 final size:168
Alignment explanation
Indices: 15068--15690 Score: 475
Period size: 171 Copynumber: 3.6 Consensus size: 168
15058 NNNNNNNNNN
* ** * *
15068 AAAAATTCAACTTAAAATCAACTATGAGATTATAAAACCATGTAAAGCGAGTAATAAGGCTTTTG
1 AAAAATTCAACCTAAAATCATTTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * ** *
15133 AAAGAATAGATGACAATAAATAGACTTTTCTTGC-CAATGAATGCCTTTTTCT-TAACATTT-CT
66 AAGGAATAG-TGACTATAAATAGACTTTTCTT-CTCAATGAATGCAATTTTCTAT-ACATTTCCC
* * * * *
15195 ACATG-TAGACATTCAATTATA-ATCTGTTTTATCAAAACATGAAAA
128 A-AAGCAAG-CATT-AATTATAGA-CTATTTTAT-AAAAAATG-TAA
* * * * * *
15240 AAAAATTGAACCTAAAATCAATTT-TTAGACTATAAAACCATTAAAAGTGAGTAATAAGGTTTTT
1 AAAAATTCAACCTAAAATC-ATTTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* **********
15304 CAAGGAATTAGTGACTATAAATAGACTTTTCTTCTCAATNNNNNNNNNNTTCTATACATTTCCCA
65 GAAGGAA-TAGTGACTATAAATAGACTTTTCTTCTCAATGAATGCAATTTTCTATACATTTCCCA
*
15369 AAGCAAGCATTAAGTTATAGACTATTTTATTGAAAAATGTAA
129 AAGCAAGCATTAA-TTATAGACTATTTTA-TAAAAAATGTAA
* *
15411 AAAAATTCAACCTAAAATCATTTATCAGATTATAAAACCATTTACAGCAAGTAATAAGGCTTTTG
1 AAAAATTCAACCTAAAATCATTTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * *
15476 AAGGAATGAGTGACTATAAATGGGCTTTTCTTCTCGATGAATGGAATTTTCTATACGTTTCTCGA
66 AAGGAAT-AGTGACTATAAATAGACTTTTCTTCTCAATGAATGCAATTTTCTATACATTTCCCAA
* * * *
15541 GGCAAGCATTTAATTCTAGTCTATTTTAATAAAAAATGTTA
130 AGCAAGCA-TTAATTATAGACTATTTT-ATAAAAAATGTAA
* **********
15582 AAAAATTCAACTTAAAATCANNNNNNNNNNTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
1 AAAAATTCAACCTAAAATCATTTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * **
15647 AAAGAATCGGCGACTATAAGTGGACTTTTCTAGTCAATGAATGC
66 AAGGAAT-AGTGACTATAAATAGACTTTTCTTCTCAATGAATGC
15691 TTTTTTCTTC
Statistics
Matches: 355, Mismatches: 83, Indels: 27
0.76 0.18 0.06
Matches are distributed among these distances:
170 5 0.01
171 218 0.61
172 120 0.34
173 12 0.03
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.32
Consensus pattern (168 bp):
AAAAATTCAACCTAAAATCATTTATCAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAATAGTGACTATAAATAGACTTTTCTTCTCAATGAATGCAATTTTCTATACATTTCCCAAA
GCAAGCATTAATTATAGACTATTTTATAAAAAATGTAA
Done.