Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398410.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_171.0, 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: 38452
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.24
Warning! 13662 characters in sequence are not A, C, G, or T
Found at i:1113 original size:341 final size:333
Alignment explanation
Indices: 297--1395 Score: 940
Period size: 341 Copynumber: 3.2 Consensus size: 333
287 NNNNNNNNNN
* * * *
297 AAAAACAATTATGATATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCTTGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCATGGATGA
* * * * *
362 CTGTAAATGGGCTTTT-TCTACCAATGAATCACTTTTTCTTCACGTTTCCCAAGGTAGACATTCA
66 CTATAAATAGACTTTTCTC-ACCAATGAAT-ACTTTTTC-TCACGTTTCCTAAGGTAAACATTCA
* * * *
426 ATTATAATTTGTTTTAACCAAAAAATTAAAAAAATTTAACTTAAAATCAATAATGAGATTATAAA
128 ATTATAATATGTTTTAACC-AAAAATT-AAATAA-TGAACCTAAAATCAATAATGAGATTATAAA
* *
491 ACCATTT---GC-AGTCAATAATAAGACTTTTAATGGAATGAGCCACTATAAAT-AGACTTTTCT
190 ACTATTTAAAGCGAGTC-AT-A-AAG-CTTTTAAAGGAATGAG--ACTATAAATGA-ACTTTTCT
** * * * *
551 TATTAATGAATGCCTTTTCCTTCACATTTCTCAAGGTAGACAATCAATTATTATCTGTTTTAACC
248 T-CCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACC
**
616 GAAAA-AGTAAAAGAATTTGACCT
312 -AAAATA-TAAAAGAATTCAACCT
* ** * * *
639 AAAATCAATTATGAGATTATAAAACCAATTAAAGCGAGTAATAAGGCTTTTGAAGGCCT-GAGTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCATGGA-TG
* * * * * * * * ** *
703 ATTATAAATAGGCTTTCCTTACCAATAAATGGCTTTTCCTCATGTTTCCTAAGACAACCACTT-A
65 ACTATAAATAGACTTTTCTCACCAATGAAT-ACTTTTTCTCACGTTTCCTAAGGTAAACA-TTCA
* *
767 ATTATAATATGTTTTAACCCAAAATGTCAAATAATGCAACCTAAAATCAATGATGAGATTATAAA
128 ATTATAATATGTTTTAACCAAAAAT-T-AAATAATG-AACCTAAAATCAATAATGAGATTATAAA
* *
832 ACTATTTAAAGCGAGTCATAAAGCTTTCAAAGGAATGGATGAATATAAATGAACTTTTCTTGCCA
190 ACTATTTAAAGCGAGTCATAAAGCTTTTAAAGGAAT-GA-GACTATAAATGAACTTTTCTT-CCA
* * * *
897 ATGAATGCCTTTTTCTGCACGTTTTTCAAGGTATACATTCAATTATAATCCGTTTTAACCAAAAC
252 ATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAA-
962 TATAAAAGAATTCAACCT
316 TATAAAAGAATTCAACCT
* * * * * *
980 AAAATCAATTATCAGATTATAAAACTATTTAAAGTTAGTAATAAGGCTTTTG-AAGAATGGATGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCATGGATGA
* * * **
1044 CTATAAATTGACTTTTCTCATCAATGCATATCTTTTTCTACACGTTTTTTAAGGTAAACATTCAA
66 CTATAAATAGACTTTTCTCACCAATGAATA-CTTTTTCT-CACGTTTCCTAAGGTAAACATTCAA
* * *
1109 TTATAATATGTTTTAA-CTAAAA--AAAT-TTG-A-CTCAAAATCAATTATGA-AGTTATAAAAC
129 TTATAATATGTTTTAACCAAAAATTAAATAATGAACCT-AAAATCAATAATGAGA-TTATAAAAC
* * * * * ** *
1167 TATTGAAA-CTGAGTAATAAGGTTTTTGAACAAATAGACGACTATAAATGGACTTTTCTTCCTAA
192 TATTTAAAGC-GAGTCATAAAGCTTTTAAAGGAAT-GA-GACTATAAATGAACTTTTCTTCC-AA
* * * * * *
1231 TGAAAGCTTTTTTCTTCACGTTTCTAAAGGCAGGCATTCAATTATAATCTGTTTTTACCAAAAAT
253 TGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACC-AAAAT
* **
1296 GTCAAAA-AATTCAATGT
317 AT-AAAAGAATTCAACCT
* * * * * * ** *
1313 AAAATGAATTATGAGATCATAAAACTATTTAAAATAAGTATTAAGCCTTTCGAAAGTGTGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCATGGATGA
*
1378 CTATTAATAGACTTTTCT
66 CTATAAATAGACTTTTCT
1396 TGTCAATGAA
Statistics
Matches: 619, Mismatches: 113, Indels: 58
0.78 0.14 0.07
Matches are distributed among these distances:
332 6 0.01
333 173 0.28
334 33 0.05
335 2 0.00
336 4 0.01
340 51 0.08
341 249 0.40
342 90 0.15
343 3 0.00
344 4 0.01
345 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (333 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCATGGATGA
CTATAAATAGACTTTTCTCACCAATGAATACTTTTTCTCACGTTTCCTAAGGTAAACATTCAATT
ATAATATGTTTTAACCAAAAATTAAATAATGAACCTAAAATCAATAATGAGATTATAAAACTATT
TAAAGCGAGTCATAAAGCTTTTAAAGGAATGAGACTATAAATGAACTTTTCTTCCAATGAATGCC
TTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAATATAAAAGAA
TTCAACCT
Found at i:1273 original size:163 final size:162
Alignment explanation
Indices: 980--1294 Score: 384
Period size: 163 Copynumber: 1.9 Consensus size: 162
970 AATTCAACCT
* * * * * * *
980 AAAATCAATTATCAGATTATAAAACTATTTAAAGTTAGTAATAAGGCTTTTGAAGAATGGATGAC
1 AAAATCAATTATAAGATTATAAAACTATTGAAACTGAGTAATAAGGCTTTTGAAAAATAGACGAC
* * * * * *
1045 TATAAATTGACTTTTCTCATCAATGCATATCTTTTTCTACACGTTTTTTAAGGTAAACATTCAAT
66 TATAAATGGACTTTTCTCATCAATGCAAAGCTTTTTCTACACGTTTCTAAAGGCAAACATTCAAT
*
1110 TATAATATGTTTTAACTAAAAAAATTTGACTC
131 TATAATATGTTTTAACCAAAAAAATTTGACTC
*
1142 AAAATCAATTATGAAG-TTATAAAACTATTGAAACTGAGTAATAAGGTTTTTGAACAAATAGACG
1 AAAATCAATTAT-AAGATTATAAAACTATTGAAACTGAGTAATAAGGCTTTTGAA-AAATAGACG
* * **
1206 ACTATAAATGGACTTTTCTTCCT-AATG-AAAGCTTTTTTCTTCACGTTTCTAAAGGCAGGCATT
64 ACTATAAATGGACTTTTC-TCATCAATGCAAAGC-TTTTTCTACACGTTTCTAAAGGCAAACATT
* *
1269 CAATTATAATCTGTTTTTACCAAAAA
127 CAATTATAATATGTTTTAACCAAAAA
1295 TGTCAAAAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
162 49 0.38
163 76 0.59
164 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (162 bp):
AAAATCAATTATAAGATTATAAAACTATTGAAACTGAGTAATAAGGCTTTTGAAAAATAGACGAC
TATAAATGGACTTTTCTCATCAATGCAAAGCTTTTTCTACACGTTTCTAAAGGCAAACATTCAAT
TATAATATGTTTTAACCAAAAAAATTTGACTC
Found at i:1417 original size:171 final size:169
Alignment explanation
Indices: 297--1417 Score: 836
Period size: 171 Copynumber: 6.6 Consensus size: 169
287 NNNNNNNNNN
* * * * *
297 AAAAACAATTATGATATTATAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAAGCTTGGGTGA
1 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAG-GTGGGTGA
* * * *
362 CTGTAAATGGGCTTTT-TCTACCAATGAATCA-CTTTTTCTTCACGTTTCCCAAGGTAGACATTC
65 CTATAAATAGACTTTTCT-TACCAATGAAT-AGCTTTTTCTTCACGTTTCTCAAGGTAGACATTC
* * *
425 AATTATAATTTGTTTTAACCAAAAAAT-TAAAAAAATTTAACTT
128 AATTATAATCTGTTTTAACC-AAAAATGT-AAAAAATTCAACCT
* * ** * * * * * * **
468 AAAATCAATAATGAGATTATAAAACCATTTGCAGTCAATAATAAGACTTT-TAATGGAATGAGCC
1 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAGG--TGGGTG
** * * *
532 ACTATAAATAGACTTTTCTTATTAATGAAT-GCCTTTTCCTTCACATTTCTCAAGGTAGACAATC
64 ACTATAAATAGACTTTTCTTACCAATGAATAG-CTTTTTCTTCACGTTTCTCAAGGTAGACATTC
* **
596 AATTATTATCTGTTTTAACCGAAAAA-GTAAAAGAATTTGACCT
128 AATTATAATCTGTTTTAACC-AAAAATGTAAAA-AATTCAACCT
* * * * *
639 AAAATCAATTATGAGATTATAAAACCAATTAAAGCGAGTAATAAGGCTTTTG-AAGGCCTGAGTG
1 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAGG--TGGGTG
* * * * * * * **
703 ATTATAAATAGGCTTTCCTTACCAATAAATGGC-TTTTCCTCATGTTTC-CTAAGACA-ACCACT
64 ACTATAAATAGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTC-AAGGTAGA-CA-T
* * * *
765 T-AATTATAATATGTTTTAACCCAAAATGTCAAATAATGCAACCT
126 TCAATTATAATCTGTTTTAACCAAAAATGT-AAAAAATTCAACCT
* * * * *
809 AAAATCAATGATGAGATTATAAAACTATTTAAAGCGAGTCATAAAGCTTTC-AAAGGAATGGATG
1 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAGG--TGGGTG
* * * * *
873 AATATAAAT-GAACTTTTCTTGCCAATGAAT-GCCTTTTTCTGCACGTTTTTCAAGGTATACATT
64 ACTATAAATAG-ACTTTTCTTACCAATGAATAG-CTTTTTCTTCACGTTTCTCAAGGTAGACATT
* * *
936 CAATTATAATCCGTTTTAACCAAAACTATAAAAGAATTCAACCT
127 CAATTATAATCTGTTTTAACCAAAAATGTAAAA-AATTCAACCT
* * * * *
980 AAAATCAATTATCAGATTATAAAACTATTTAAAGTTAGTAATAAGGCTTTTG-AAGAATGGATGA
1 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAG-GTGGGTGA
* * * * * * * * *
1044 CTATAAATTGACTTTTCTCATCAATGCATATCTTTTTCTACACGTTTTTTAAGGTAAACATTCAA
65 CTATAAATAGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * **
1109 TTATAATATGTTTTAA-C-----T-AAAAAAATTTGA-CT
130 TTATAATCTGTTTTAACCAAAAATGTAAAAAATTCAACCT
* * * * ** * **
1141 CAAAATCAATTATGA-AGTTATAAAACTATTGAAACTGAGTAATAAGGTTTTTGAACAAATAGAC
1 -AAAATCAATTATGAGA-TTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAA-AGGTGGGT
* * * *
1205 GACTATAAATGGACTTTTCTT-CCTAATGAA-AGCTTTTTTCTTCACGTTTCTAAAGGCAGGCAT
63 GACTATAAATAGACTTTTCTTACC-AATGAATAGC-TTTTTCTTCACGTTTCTCAAGGTAGACAT
* **
1268 TCAATTATAATCTGTTTTTACCAAAAATGTCAAAAAATTCAATGT
126 TCAATTATAATCTGTTTTAACCAAAAATGT-AAAAAATTCAACCT
* * * * * *
1313 AAAATGAATTATGAGATCATAAAACTATTTAAAATAAGTATTAAGCCTTTCGAAAGTGTGGGTGA
1 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAG-GTGGGTGA
* ** *
1378 CTATTAATAGACTTTTCTTGTCAATGAATAGCATTTTCTT
65 CTATAAATAGACTTTTCTTACCAATGAATAGCTTTTTCTT
1418 TACAAGTCCC
Statistics
Matches: 749, Mismatches: 156, Indels: 90
0.75 0.16 0.09
Matches are distributed among these distances:
161 3 0.00
162 53 0.07
163 74 0.10
164 3 0.00
169 10 0.01
170 208 0.28
171 388 0.52
172 10 0.01
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (169 bp):
AAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAAGGTGGGTGAC
TATAAATAGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAAT
TATAATCTGTTTTAACCAAAAATGTAAAAAATTCAACCT
Found at i:2261 original size:171 final size:169
Alignment explanation
Indices: 2081--2495 Score: 408
Period size: 170 Copynumber: 2.4 Consensus size: 169
2071 NNNNNNTCTG
*
2081 ATAATTGATTTTAGGTTGAATTCTTTTACAATTTTGGTTAAAACATATTACAATTGAATGTCTAC
1 ATAATTGATTTTAGGTTGAATTCTTTTAC-ATTTTGGTTAAAACATATTATAATTGAATGTCTAC
* * **
2146 CTTGGAAAACATGTAGAAAAA-CGCATTCATTGGCAAGAAAAG-TTCATTTATAGTCA-TACATT
65 CTTGGAAAACATG-AGAAAAAGC-CATTCATTGGCAAGAAAAGCCT-ATTTATAATCAGT-CAGG
*
2208 CCTTCAAAAGCTTTATGACTCGCTTTAAATAGTTTTATAATCTC
126 CCTTCAAAAGCCTTATGACTCGCTTTAAATAGTTTTATAATCTC
* * * * * * * *
2252 ATCATTGATTTTAGATTGCATTATTTGACATTTTGGGTTAAAACAGATTATAATTAAATGGT-TN
1 ATAATTGATTTTAGGTTGAATTCTTTTACATTTT-GGTTAAAACATATTATAATTGAAT-GTCTA
********* * * * *
2316 NNNNNNNNNACATGAGGAAAAGCCATTTATTGGTAAGGAAAGCCTATTTATAATCAGTCAGGCCT
64 CCTTGGAAAACATGAGAAAAAGCCATTCATTGGCAAGAAAAGCCTATTTATAATCAGTCAGGCCT
* * * *
2381 TCAAAAGCCTTATTACTCGCTTTAATTAGTTTTATATTCTT
129 TCAAAAGCCTTATGACTCGCTTTAAATAGTTTTATAATCTC
* *
2422 ATAATTGATTTTAGGTTAAATTCTTTTAC-TATTTGGATTAAAACATATTATAATTGAACGTCTA
1 ATAATTGATTTTAGGTTGAATTCTTTTACAT-TTTGG-TTAAAACATATTATAATTGAATGTCTA
2486 CCTTGAGAAA
64 CCTTG-GAAA
2496 TGCGAAGGAA
Statistics
Matches: 185, Mismatches: 50, Indels: 18
0.73 0.20 0.07
Matches are distributed among these distances:
169 5 0.03
170 124 0.67
171 54 0.29
172 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.38
Consensus pattern (169 bp):
ATAATTGATTTTAGGTTGAATTCTTTTACATTTTGGTTAAAACATATTATAATTGAATGTCTACC
TTGGAAAACATGAGAAAAAGCCATTCATTGGCAAGAAAAGCCTATTTATAATCAGTCAGGCCTTC
AAAAGCCTTATGACTCGCTTTAAATAGTTTTATAATCTC
Found at i:5949 original size:169 final size:171
Alignment explanation
Indices: 5549--6481 Score: 921
Period size: 170 Copynumber: 5.5 Consensus size: 171
5539 AAAGCTAACA
* *
5549 CATTTATGGTCACTCAAGCCTTCGAAAA-CCTTATTACTCGCTTTAAATGGTTTTATAATCTCAT
1 CATTTATAGTCACTCAAGCCTTC-AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTAT
* * * * *
5613 AATTGATTTTAAGTTGGATTCTTTTACTTTTTTGGTTAAAACATATTATAATTGAATGTCTA-CC
65 AATTGATTTTAGGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTATCT
* ** *
5677 TAGAGAAACGTGAA-AAAAAGGCA-TCTATTAACAAGAAAAGTC
130 TAG-GAAACTTGAAGAAAAAACCATTC-ATTAGCAAGAAAAGTC
* ** * *
5719 TATTTATAGT-AGCTCATTCTTTCAAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTTAT
1 CATTTATAGTCA-CTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTAT
* * * * * * * *
5783 AGTTGACTTTAAGTTAAATTCTTTTACATTTTTGGTGAAAACAGATTATAATTAAATGTTTGTCT
65 AATTGATTTTAGGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTATCT
* * * *
5848 CAGGAAACATGAA-AAAAAACCATTCATTAGTAAGGAAAG-C
130 TAGGAAACTTGAAGAAAAAACCATTCATTAGCAAGAAAAGTC
*
5888 CATTTATAGTCAC-CTAAGCCTTCAAAAGCCTTACTACTCGCTTTAAATGGTTTTATAATCTTAT
1 CATTTATAGTCACTC-AAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTAT
* * ** * *
5952 ATTTGATTTTGGGTTGAATTCTTTTACATTTTTCATTAAAACATATTATAATTGAATGTCTATTT
65 AATTGATTTTAGGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTATCT
** * * * *
6017 TACAAAACTTCAAGAAAAAATCATTCATTGGCAAGAAAAGTA
130 TAGGAAACTTGAAGAAAAAACCATTCATTAGCAAGAAAAGTC
* ** * *
6059 AATTTATAGTCACTC-ATTCTGTCGAAAGCCTTATT-C-C-CTTTAAATGGTTTTAAAAT-TTCA
1 CATTTATAGTCACTCAAGCCT-TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTT-A
* * * *
6119 TAATTGATTTTAGGTTGAATTATTTTACATTTTTAGCTAAAACAGATTATAATTGAATGTCTGTC
64 TAATTGATTTTAGGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTATC
* * * *
6184 TTAGGAAACTTGAAGAAAAAGCCAATCATTGGTAA-AGAAAG-C
129 TTAGGAAACTTGAAGAAAAAACCATTCATTAGCAAGA-AAAGTC
*
6226 CATTTATAGTCACTCAAACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT-TTAAT
1 CATTTATAGTCACTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTT-AT
* * * * *
6290 AATTAATTTTAGGTTGAATTCTTTTACTTTTTTTGTTAAAACAGATTACAATTGATTGTCTA-CT
65 AATTGATTTTAGGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTATCT
* * * *
6354 TCAAGAAA-TGTGAAGACAAAAAGCATTTATTAGCAACAAAAGTC
130 T-AGGAAACT-TGAAGA-AAAAACCATTCATTAGCAAGAAAAGTC
** ** * ** * * * ** *
6398 TTTTTATAGTTGCCCATTCTTTCAAAAGCTTTATTACTCACTTTAAATGGTTCAATAATCTCATA
1 CATTTATAGTCACTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTATA
* *
6463 ATTGATTGTAAGTTGAATT
66 ATTGATTTTAGGTTGAATT
6482 NNNNNNNNNN
Statistics
Matches: 627, Mismatches: 114, Indels: 42
0.80 0.15 0.05
Matches are distributed among these distances:
167 30 0.05
168 112 0.18
169 126 0.20
170 243 0.39
171 46 0.07
172 69 0.11
173 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
CATTTATAGTCACTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTATA
ATTGATTTTAGGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTATCTT
AGGAAACTTGAAGAAAAAACCATTCATTAGCAAGAAAAGTC
Found at i:6307 original size:338 final size:337
Alignment explanation
Indices: 5549--6481 Score: 1062
Period size: 339 Copynumber: 2.7 Consensus size: 337
5539 AAAGCTAACA
* *
5549 CATTTATGGTCACTCAAGCCTTCGAAAA-CCTTATTACTCGCTTTAAATGGTTTTATAATCTCAT
1 CATTTATAGTCACTCAAGCCTTC-AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT-TTAT
* * *
5613 AATTGATTTTAAGTTGGATTCTTTTACTTTTTTGGTTAAAACATATTATAATTGAATGTCTACCT
64 AATTGATTTTAGGTTGAATTCTTTTACTTTTTTCGTTAAAACATATTATAATTGAATGTCTACCT
* * * ** *
5678 AGAGAAACGTGAAAAAAAGGCATCTATTAACAAGAAAAGTCTATTTATAGTAGCTCATTCTTTCA
129 ACAGAAACGTCAAAAAAAAGCATCTATTAACAAGAAAAGTAAATTTATAGTAGCTCATTCTGTCA
* * * *
5743 AAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTTATAGTTGACTTTAAGTTAAATTCTTTT
194 AAAGCCTTATTAC-TCCTTTAAATGGTTTTAAAATCTTATAATTGACTTTAAGTTAAATTATTTT
* * *
5808 ACATTTTTGGTGAAAACAGATTATAATTAAATGTTTGTCTCAGGAAACATGAAAAAAAACCATTC
258 ACATTTTTGCTGAAAACAGATTATAATTAAATGTCTGTCTCAGGAAACATGAAAAAAAACCAATC
*
5873 ATTAGTAAGGAAAGC
323 ATTAGTAAAGAAAGC
*
5888 CATTTATAGTCAC-CTAAGCCTTCAAAAGCCTTACTACTCGCTTTAAATGGTTTTATAATCTTAT
1 CATTTATAGTCACTC-AAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT-TTAT
* * * * **
5952 ATTTGATTTTGGGTTGAATTCTTTTACATTTTTCATTAAAACATATTATAATTGAATGTCTATTT
64 AATTGATTTTAGGTTGAATTCTTTTACTTTTTTCGTTAAAACATATTATAATTGAATGTCTA-CC
* * **
6017 TACA-AAACTTCAAGAAAAAATCAT-TCATTGGCAAGAAAAGTAAATTTATAGTCA-CTCATTCT
128 TACAGAAACGTCAA-AAAAAAGCATCT-ATTAACAAGAAAAGTAAATTTATAGT-AGCTCATTCT
* * * *
6079 GTCGAAAGCCTTATT-C-CCTTTAAATGGTTTTAAAAT-TTCATAATTGATTTTAGGTTGAATTA
190 GTCAAAAGCCTTATTACTCCTTTAAATGGTTTTAAAATCTT-ATAATTGACTTTAAGTTAAATTA
* * * *
6141 TTTTACATTTTTAGCT-AAAACAGATTATAATTGAATGTCTGTCTTAGGAAACTTGAAGAAAAAG
254 TTTTACATTTTT-GCTGAAAACAGATTATAATTAAATGTCTGTCTCAGGAAACATGAA-AAAAAA
*
6205 CCAATCATTGGTAAAGAAAGC
317 CCAATCATTAGTAAAGAAAGC
*
6226 CATTTATAGTCACTCAAACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTAATA
1 CATTTATAGTCACTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTT-ATA
* * * * * *
6291 ATTAATTTTAGGTTGAATTCTTTTACTTTTTTTGTTAAAACAGATTACAATTGATTGTCTA-CTT
65 ATTGATTTTAGGTTGAATTCTTTTACTTTTTTCGTTAAAACATATTATAATTGAATGTCTACCTA
* * * * * *** * * *
6355 CAAGAAATGTGAAGACAAAAAGCATTTATTAGCAACAAAAGTCTTTTTATAGTTGCCCATTCTTT
130 C-AGAAACGTCAA-A-AAAAAGCATCTATTAACAAGAAAAGTAAATTTATAGTAGCTCATTCTGT
* * * *
6420 CAAAAGCTTTATTACTCACTTTAAATGG-TTCAATAATCTCATAATTGA-TTGTAAGTTGAATT
192 CAAAAGCCTTATTACTC-CTTTAAATGGTTTTAA-AATCTTATAATTGACTT-TAAGTTAAATT
6482 NNNNNNNNNN
Statistics
Matches: 503, Mismatches: 69, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
336 4 0.01
337 88 0.17
338 148 0.29
339 167 0.33
340 56 0.11
341 8 0.02
342 31 0.06
343 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (337 bp):
CATTTATAGTCACTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTATAA
TTGATTTTAGGTTGAATTCTTTTACTTTTTTCGTTAAAACATATTATAATTGAATGTCTACCTAC
AGAAACGTCAAAAAAAAGCATCTATTAACAAGAAAAGTAAATTTATAGTAGCTCATTCTGTCAAA
AGCCTTATTACTCCTTTAAATGGTTTTAAAATCTTATAATTGACTTTAAGTTAAATTATTTTACA
TTTTTGCTGAAAACAGATTATAATTAAATGTCTGTCTCAGGAAACATGAAAAAAAACCAATCATT
AGTAAAGAAAGC
Found at i:8662 original size:170 final size:171
Alignment explanation
Indices: 8440--9216 Score: 528
Period size: 170 Copynumber: 4.6 Consensus size: 171
8430 AGGTAGACAA
* * ** *
8440 TCAATTATAATCTGTTTTAACCGAAAAAGTAAAAGAATTTGACCCAAAATCAATTATAAGATTAT
1 TCAATTATAATCTGTTTTAACCCAAAATGTAAAAGAATTCAACCTAAAATCAATTATAAGATTAT
* * * * ** * *
8505 AAAACCAATTAAAGCAAGTAAGAAGGCTTTTGAAGGCTTGAGTGATTATAAAT-AGGCTTTCCTT
66 AAAACTATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGAGTGAATATAAATGA-ACTTTCCTT
**
8569 ACCAATAAATGGCTTTTCCT-CATG-TTTCGTAAG-ACAACCACT
130 ACCAATAAATGGCTTTTCCTGCATGTTTTCCAAAGTA-AA-CA-T
* * * * * *
8611 T-AATTATAATATGTTTTAACCCAAAATGTCAAATAATGCAACCTAAAATCAATGATGAGATTAT
1 TCAATTATAATCTGTTTTAACCCAAAATGTAAAAGAATTCAACCTAAAATCAATTATAAGATTAT
* * * *
8675 AAAACTATTTAAAGTGAGTCATAAAGCTTTTGAAGGAATG-GATGAATATAAATGAACTTTTCTT
66 AAAACTATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGAG-TGAATATAAATGAACTTTCCTT
* * * * * *
8739 GCTAATGAATGTCTTTTTCTGCATGTTTTCCAAAGTAGACAT
130 ACCAATAAATGGCTTTTCCTGCATGTTTTCCAAAGTAAACAT
* * *
8781 TCAATTATAATCCGTTTTAA-CTAAAACTGTAAAAGAATTCAACCTAAAATCAATTATCAGATTA
1 TCAATTATAATCTGTTTTAACCCAAAA-TGTAAAAGAATTCAACCTAAAATCAATTATAAGATTA
* * * *
8845 TAAAACTATTTAAAGTTAGTAATAAGGTTTTTGAAGGAATGAGTGACTATAAATTG-ACTTTTCT
65 TAAAACTATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGAGTGAATATAAA-TGAACTTTCCT
* * ** ** * * * ** *
8909 CATCAATGGAT-ATTTTTTCTACACGCTTTT-TGAGGTAAACAT
129 TACCAATAAATGGCTTTTCCTGCATG-TTTTCCAAAGTAAACAT
* ** * ** *
8951 TCAATTATAATATGTTTTAACTAAAAATCTAACAA-AATTTGA-CTCAAAATCAATTATGACG-T
1 TCAATTATAATCTGTTTTAACCCAAAATGTAA-AAGAATTCAACCT-AAAATCAATTAT-AAGAT
* * * * ** * * * *
9013 TATAAAACTATTGAAACTGAGTAACAAGGCTTTTGAACAAAT-AGACGACTATAAATGGACTTTT
63 TATAAAACTATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGAG-TGAATATAAATGAACTTTC
* * * * * ****
9077 CTTACTAATGAAA--GCTTTCTTCTTCACG-TTTCTAAAGGTAGGTGT
127 CTTACCAAT-AAATGGCTTT-TCCTGCATGTTTTCCAAA-GTAAACAT
* * * * * *
9122 TCAATTATAATCTGTTTTTACCAAAAATGTAAAA-ACATTCAACTTAAAATGAATTATGAGATCA
1 TCAATTATAATCTGTTTTAACCCAAAATGTAAAAGA-ATTCAACCTAAAATCAATTATAAGATTA
* *
9186 TAAAACTATTTAAAGTAAGTATTAAGCCTTT
65 TAAAACTATTTAAAGTAAGTAATAAGGCTTT
9217 CGAAAGCGTG
Statistics
Matches: 478, Mismatches: 105, Indels: 46
0.76 0.17 0.07
Matches are distributed among these distances:
169 10 0.02
170 245 0.51
171 210 0.44
172 12 0.03
173 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
TCAATTATAATCTGTTTTAACCCAAAATGTAAAAGAATTCAACCTAAAATCAATTATAAGATTAT
AAAACTATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGAGTGAATATAAATGAACTTTCCTTA
CCAATAAATGGCTTTTCCTGCATGTTTTCCAAAGTAAACAT
Found at i:8833 original size:171 final size:167
Alignment explanation
Indices: 8352--9260 Score: 660
Period size: 171 Copynumber: 5.3 Consensus size: 167
8342 TTACAGTCAA
* * * * *
8352 TAATAAGACTTTTGAAGGAATGA-GCCACTATAAATAGAATTTTCTTATTAATGAATGCCTTTCT
1 TAATAAGGCTTTTGAAGGAATGATG--ACTATAAAT-GACTTTTCTT-CTAATGAATGTCTTTTT
* * * * *
8416 CTTCAC-ATTTCTCAAGGTAGACAATCAATTATAATCTGTTTTAACCGAAAAA-GTAAAAGAATT
62 CTACACGTTTTCT-AAAGTAGACATTCAATTATAATATGTTTTAACC-AAAAATGTAAAA-AATT
** * * * * **
8479 TGACCCAAAATCAATTATAAGATTATAAAACCAATTAAAGCAAG
124 CAACCTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
* ** * * * * * * *
8523 TAAGAAGGCTTTTGAAGGCTTGAGTGATTATAAATAGGCTTTCCTTACCAATAAATGGCTTTTCC
1 TAATAAGGCTTTTGAAGGAATGA-TGACTATAAAT-GACTTTTCTT-CTAATGAATGTCTTTTTC
* * * *
8588 T-CATG-TTTCGT-AAG-ACAACCACTT-AATTATAATATGTTTTAACCCAAAATGTCAAATAAT
63 TACACGTTTTC-TAAAGTA-GA-CA-TTCAATTATAATATGTTTTAACCAAAAATGT-AAAAAAT
* *
8648 GCAACCTAAAATCAATGATGAGATTATAAAACTATTTAAAGTGAG
123 TCAACCTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
* * *
8693 TCATAAAGCTTTTGAAGGAATGGATGAATATAAATGAACTTTTCTTGCTAATGAATGTCTTTTTC
1 TAATAAGGCTTTTGAAGGAAT-GATGACTATAAATG-ACTTTTCTT-CTAATGAATGTCTTTTTC
* * * ** * *
8758 TGCATGTTTTCCAAAGTAGACATTCAATTATAATCCGTTTTAACTAAAACTGTAAAAGAATTCAA
63 TACACGTTTTCTAAAGTAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAA-AATTCAA
* *
8823 CCTAAAATCAATTATCAGATTATAAAACTATTTAAAGTTAG
127 CCTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
* * *
8864 TAATAAGGTTTTTGAAGGAATGAGTGACTATAAATTGACTTTTC-TCATCAATGGATAT-TTTTT
1 TAATAAGGCTTTTGAAGGAATGA-TGACTATAAA-TGACTTTTCTTC-T-AATGAATGTCTTTTT
* * * * * *
8927 CTACACGCTTTT-TGAGGTAAACATTCAATTATAATATGTTTTAACTAAAAATCTAACAAAATTT
62 CTACACG-TTTTCTAAAGTAGACATTCAATTATAATATGTTTTAACCAAAAATGTAA-AAAATTC
* * *
8991 GA-CTCAAAATCAATTATGACG-TTATAAAACTATTGAAACTGAG
125 AACCT-AAAATCAATTATGA-GATTATAAAACTATTTAAAGTGAG
* ** * *
9034 TAACAAGGCTTTTGAACAAATAGACGACTATAAATGGACTTTTCTTACTAATGAAAG-CTTTCTT
1 TAATAAGGCTTTTGAAGGAAT-GATGACTATAAAT-GACTTTTCTT-CTAATGAATGTCTTT-TT
* *** * *
9098 CTTCACG-TTTCTAAAGGTAGGTGTTCAATTATAATCTGTTTTTACCAAAAATGTAAAAACATTC
62 CTACACGTTTTCTAAA-GTAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAA-ATTC
* * * *
9162 AACTTAAAATGAATTATGAGATCATAAAACTATTTAAAGTAAG
125 AACCTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
* * * * ** * *
9205 TATTAAGCCTTTCGAAAGCGTGAGTGACTATTAATAGACTTTTCTTGTCAATGAAT
1 TAATAAGGCTTTTGAAGGAATGA-TGACTATAAAT-GACTTTTCTTCT-AATGAAT
9261 AGCATTTTCT
Statistics
Matches: 582, Mismatches: 118, Indels: 76
0.75 0.15 0.10
Matches are distributed among these distances:
168 1 0.00
169 15 0.03
170 258 0.44
171 294 0.51
172 12 0.02
173 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (167 bp):
TAATAAGGCTTTTGAAGGAATGATGACTATAAATGACTTTTCTTCTAATGAATGTCTTTTTCTAC
ACGTTTTCTAAAGTAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAATTCAACCTA
AAATCAATTATGAGATTATAAAACTATTTAAAGTGAG
Found at i:9889 original size:171 final size:170
Alignment explanation
Indices: 9358--9949 Score: 674
Period size: 170 Copynumber: 3.5 Consensus size: 170
9348 AGGAAGATGC
* * * * * * *
9358 TCAATTATAATATG-TTTATACCAAAAATGAAAAAACAAACTCAACCAAAAATCAAT-TTAGACA
1 TCAATTATAATCTGTTTTA-ACAAAAAATG-TAAAA-AAATTCAA-CTAAAATCAATCAT-GAGA
* * *
9421 TTATATAACCATTTAAAGTGAGTAATAAGGCTTT-AAAGAAATGGGTAACTATAAATGGACTTTT
61 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATGGACTTTT
* * * *
9485 TTTGTCAATGAATACCTTTTTCTTCATGTTTCTTGATG-TAGACAT
126 ATTGTCAATGAATGCCTTTTTCTTCATGTTTCTCGA-GACAGACAT
* * ** *
9530 TCAATTATAATCTATTTTAACTAAAAATACAAAAAAAATTCAACCT-AAATCAATTATGAGATTA
1 TCAATTATAATCTGTTTTAACAAAAAAT-GTAAAAAAATTCAA-CTAAAATCAATCATGAGATTA
* *
9594 TAAAACAATTTAAAGTGAGTAATAAGGCTTTG-AAGGAATGGGTGACTATAAATGGACTTTTCTT
64 TAAAACCATTTAAAGTGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTATT
* * * *
9658 ATCAATGAATGTCTTTATCTTCATGTTTTTCGAGACAGACAT
129 GTCAATGAATGCCTTTTTCTTCATGTTTCTCGAGACAGACAT
* *
9700 TCAATTATAATATGTTTTAACAAAAAATGTAAAAAAATTCAATCTAAAATCACTCATGAGATTAT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAA-CTAAAATCAATCATGAGATTAT
* * * *
9765 AAAACCGTTTAAAGTGAGTAATAAGGCTTTGAAAGGAATGAGTGACTATAAATAGACTTTAATTG
65 AAAACCATTTAAAGTGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTATTG
*
9830 TCAATGAATGCCTTTTTCTTCATGGTTCTCGAGACAGACAT
130 TCAATGAATGCCTTTTTCTTCATGTTTCTCGAGACAGACAT
** * * * * * *
9871 TTTACTATAATCTGTTTTAATAAAAAATGTAAAAATATTCAACTTAAAATCGATGATGAGACTAT
1 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAAC-TAAAATCAATCATGAGATTAT
* *
9936 GAAACTATTTAAAG
65 AAAACCATTTAAAG
9950 CGAGCANNNN
Statistics
Matches: 360, Mismatches: 52, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
169 15 0.04
170 177 0.49
171 139 0.39
172 25 0.07
173 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
TCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTAAAATCAATCATGAGATTATA
AAACCATTTAAAGTGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTATTGT
CAATGAATGCCTTTTTCTTCATGTTTCTCGAGACAGACAT
Found at i:9948 original size:341 final size:341
Alignment explanation
Indices: 9299--9949 Score: 782
Period size: 341 Copynumber: 1.9 Consensus size: 341
9289 AACATTCAAA
* * * **
9299 TATAAATGTACTTTTCTTACCAATGAATGATTTTTTTTTACTTTTTTCGAGGAAGATGCTCAATT
1 TATAAATGGACTTTTCTTACCAATGAATGATTTTTCTTCACTTTTTTCGAGGAAGACACTCAATT
* * *
9364 ATAATATGTTTATACCAAAAATGAAAAAACAAACTCAACCAAAAATCAATTTAGACATTATATAA
66 ATAATATGTTTATACAAAAAATGAAAAAACAAACTCAACCAAAAATCAATATAGACATTATAAAA
* * **
9429 CCATTTAAAGTGAGTAATAAGGCTTTAAAGAAATGGGTAACTATAAATGGACTTTTTTTGTCAAT
131 CCATTTAAAGTGAGTAATAAGGCTTTAAAGAAATGAGTAACTATAAATAGACTTTAATTGTCAAT
* * * *
9494 GAATACCTTTTTCTTCATGTTTCTTGATGTAGACATTCAATTATAATCTATTTTAACTAAAAATA
196 GAATACCTTTTTCTTCATGGTTCTCGATGCAGACATTCAACTATAATCTATTTTAACTAAAAATA
* *
9559 CAAAAAAAATTCAACCTAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTT
261 CAAAAAAAATTCAACCTAAATCAATGATGAGACTATAAAACAATTTAAAGTGAGTAATAAGGCTT
9624 TGAAGGAATGGGTGAC
326 TGAAGGAATGGGTGAC
* *
9640 TATAAATGGACTTTTCTTATCAATGAATG-TCTTTATCTTCA-TGTTTTTCGA-GACAGACATTC
1 TATAAATGGACTTTTCTTACCAATGAATGAT-TTT-TCTTCACT-TTTTTCGAGGA-AGACACTC
* * * * * *
9702 AATTATAATATGTTT-TAACAAAAAATG-TAAAA-AAATTCAATCTAAAATCACTCAT-GAGATT
62 AATTATAATATGTTTAT-ACAAAAAATGAAAAAACAAACTCAACCAAAAATCAAT-ATAGACATT
* * *
9763 ATAAAACCGTTTAAAGTGAGTAATAAGGCTTTGAAAGGAATGAGTGACTATAAATAGACTTTAAT
125 ATAAAACCATTTAAAGTGAGTAATAAGGCTTT-AAAGAAATGAGTAACTATAAATAGACTTTAAT
* ** *
9828 TGTCAATGAATGCCTTTTTCTTCATGGTTCTCGA-GACAGACATTTTACTATAATCTGTTTTAA-
189 TGTCAATGAATACCTTTTTCTTCATGGTTCTCGATG-CAGACATTCAACTATAATCTATTTTAAC
** * * * * *
9891 TAAAAA-ATGTAAAAATATTCAACTTAAAATCGATGATGAGACTATGAAACTATTTAAAG
253 TAAAAATA-CAAAAAAAATTCAACCT-AAATCAATGATGAGACTATAAAACAATTTAAAG
9950 CGAGCANNNN
Statistics
Matches: 260, Mismatches: 40, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
339 1 0.00
340 72 0.28
341 146 0.56
342 41 0.16
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (341 bp):
TATAAATGGACTTTTCTTACCAATGAATGATTTTTCTTCACTTTTTTCGAGGAAGACACTCAATT
ATAATATGTTTATACAAAAAATGAAAAAACAAACTCAACCAAAAATCAATATAGACATTATAAAA
CCATTTAAAGTGAGTAATAAGGCTTTAAAGAAATGAGTAACTATAAATAGACTTTAATTGTCAAT
GAATACCTTTTTCTTCATGGTTCTCGATGCAGACATTCAACTATAATCTATTTTAACTAAAAATA
CAAAAAAAATTCAACCTAAATCAATGATGAGACTATAAAACAATTTAAAGTGAGTAATAAGGCTT
TGAAGGAATGGGTGAC
Found at i:17251 original size:171 final size:170
Alignment explanation
Indices: 16760--17761 Score: 950
Period size: 171 Copynumber: 5.9 Consensus size: 170
16750 NNNNNNNNNN
* ** * * * *
16760 TGAGTAATAAGGCTTTTGAAGAAATGAGCAACTATAAATAGACTTTTCTTGCCAGTGAATCCTTT
1 TGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGGCTTTTCCTACCAATGAATCC--T
** * *
16825 TTTTCTTCATGTTTCTTGAA-GTAGACAATCAATTATAATCTGTTTTAACCAAAAAAGTAAAAGA
64 TTTTCTTCATGTTTC-CCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGA
* *
16889 ATTCAACCTAAAAAT-AATTATTAGATTATAAAACTATTTAAAG
128 ATTCAACCT-AAAATCAATTATGAGATTATAAAACCATTTAAAG
** **
16932 TGAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAAT-GGC-TTTCCTTACCAATGAATAGTT
1 TGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGGCTTTTCC-TACCAATGAAT-CCT
** * *** * * *
16995 TTTTCTTCATGTTTCTTACGGCCTACGTTCAATTATAATCTGTTTTAACCAACAATGTAAAAAAA
64 TTTTCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGAA
** * *
17060 TTCAACCTAAAAAAAATTATGATATTATAAAACTATTTAAAG
129 TTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
17102 TGAGTAATAAGGCTTTCGACA-GATTGAGTGACTATAAATGGGCTTTTCCAACCAATGAATCACT
1 TGAGTAATAAGGCTTTTGA-AGGAATGAGTGACTATAAATAGGCTTTTCCTACCAATGAATC-CT
* * *
17166 TTTTCTTCATGTTTCCCAAGGTAGACATTCCATTATAATTTGTTTTAACCAAAAATGTAAAAAAA
64 TTTTCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGAA
* * *
17231 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTACAG
129 TTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * * ** *
17273 TCAATAATAAGACTTTTGAAGGAATGAGCCG-CTATAAATAGACTTTTCTTATTAATGACTGCCT
1 TGAGTAATAAGGCTTTTGAAGGAATGAG-TGACTATAAATAGGCTTTTCCTACCAATGAAT-CCT
* ** * *
17337 TTTCCTTCACATTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACCGAAAAA-GTAAAAGA
64 TTTTCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACC-AAAAATGTAAAAGA
* * *
17401 ATTTAACCTAAAATCATTTATGAGATTATAAAACCAATTAAAG
128 ATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* ** * * *
17444 CGAGTAATAAGGCTTTTGAAGGCCTGAGTGATTATAAATAGGC-TTTCCTTACCAATAAATGGC-
1 TGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGGCTTTTCC-TACCAATGAAT-CCT
* ** * * * * * *
17507 TTTTCCTCATGTTTCCCAAGACAGTCTTTTAATTATAATCTGTTTTAACCCAAAATGTTAAATAA
64 TTTTCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGAA
* *
17572 TACAACCTAAAATCAATGATGAGATTATAAAACCATTTAAAG
129 TTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAG
** * * * * ** *
17614 CAAGTCATAAAGCTTTTGAAGGAATG-GATGACTATAAAT-GAACTTTTCTTGTCAATGAATGCT
1 TGAGTAATAAGGCTTTTGAAGGAATGAG-TGACTATAAATAG-GCTTTTCCTACCAATGAAT-CC
* * * * * *
17677 TTTTTCTGCACGTTAT-CCAAGGTAGACAGTCAA-TATAATCTGTTTTAATCAAAATTGTAGAAG
63 TTTTTCTTCATGTT-TCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAG
*
17740 AATTCAACCTAATATCAATTAT
127 AATTCAACCTAAAATCAATTAT
17762 CANNNNNNNN
Statistics
Matches: 674, Mismatches: 136, Indels: 42
0.79 0.16 0.05
Matches are distributed among these distances:
169 12 0.02
170 299 0.44
171 316 0.47
172 47 0.07
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (170 bp):
TGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGGCTTTTCCTACCAATGAATCCTTT
TTCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGAATT
CAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAG
Found at i:17519 original size:341 final size:340
Alignment explanation
Indices: 16845--17761 Score: 1001
Period size: 341 Copynumber: 2.7 Consensus size: 340
16835 GTTTCTTGAA
* * * *
16845 GTAGACAATCAATTATAATCTGTTTTAACCAAAAAAGTAAAAGAATTCAACCTAAAAAT-AATTA
1 GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAA-CTTAAAATCAATTA
* * * * * ** *
16909 TTAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGC
65 TGAGATTATAAAACCATTTAAAGTCAATAATAAGACTTTTGAAGGAATGAGTGACTATAAATGAC
* * * * * *** *
16974 TTTCCTTACCAATGAATAG-TTTTTTCTTCATGTTTCTTACGGCCTACGTTCAATTATAATCTGT
130 TTTTCTTATCAATGAAT-GCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGT
* ** * * * *
17038 TTTAACCAACAATGTAAAAAAATTCAACCTAAAAAAAATTATGATATTATAAAACTATTTAAAGT
194 TTTAACCAA-AATGTAAAAGAATTCAACCTAAAATCAATTATGAGATTATAAAACCAATTAAAGC
* * *
17103 GAGTAATAAGGCTTTCGACAGATTGAGTGACTATAAATGGGCTTTTCCAACCAATGAATCACTTT
258 GAGTAATAAGGCTTTCGACAGACTGAGTGACTATAAATAGGCTTTTCCAACCAATAAATCACTTT
*
17168 TTCTTCATGTTTCCCAAG
323 TTCCTCATGTTTCCCAAG
* * *
17186 GTAGACATTCCATTATAATTTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTAT
1 GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
* *
17251 GAGATTATAAAACCATTTACAGTCAATAATAAGACTTTTGAAGGAATGAGCCG-CTATAAATAGA
66 GAGATTATAAAACCATTTAAAGTCAATAATAAGACTTTTGAAGGAATGAG-TGACTATAAAT-GA
* * * * * *
17315 CTTTTCTTATTAATGACTGCCTTTTCCTTCACATTTCTCAATGTAGACATTCAATTATAATCTGT
129 CTTTTCTTATCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGT
* * *
17380 TTTAACCGAAAAAGTAAAAGAATTTAACCTAAAATCATTTATGAGATTATAAAACCAATTAAAGC
194 TTTAACC-AAAATGTAAAAGAATTCAACCTAAAATCAATTATGAGATTATAAAACCAATTAAAGC
* * * * **
17445 GAGTAATAAGGCTTTTGA-AGGCCTGAGTGATTATAAATAGGC-TTTCCTTACCAATAAATGGC-
258 GAGTAATAAGGCTTTCGACA-GACTGAGTGACTATAAATAGGCTTTTCC-AACCAATAAATCACT
17507 TTTTCCTCATGTTTCCCAAG
321 TTTTCCTCATGTTTCCCAAG
** * * * * * * * * *
17527 ACAGTCTTTTAATTATAATCTGTTTTAACCCAAAATGTTAAATAATACAACCTAAAATCAATGAT
1 GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
*
17592 GAGATTATAAAACCATTTAAAG-CAAGTCATAA-AGCTTTTGAAGGAATG-GATGACTATAAATG
66 GAGATTATAAAACCATTTAAAGTCAA-TAATAAGA-CTTTTGAAGGAATGAG-TGACTATAAATG
* * *
17654 AACTTTTCTTGTCAATGAATGCTTTTTTCTGCACGTTATC-CAAGGTAGACAGTCAA-TATAATC
128 -ACTTTTCTTATCAATGAATGCTTTTTTCTTCACGTT-TCTCAAGGTAGACATTCAATTATAATC
* * *
17717 TGTTTTAATCAAAATTGTAGAAGAATTCAACCTAATATCAATTAT
191 TGTTTTAACCAAAA-TGTAAAAGAATTCAACCTAAAATCAATTAT
17762 CANNNNNNNN
Statistics
Matches: 478, Mismatches: 85, Indels: 27
0.81 0.14 0.05
Matches are distributed among these distances:
339 4 0.01
340 55 0.12
341 268 0.56
342 149 0.31
343 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (340 bp):
GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
GAGATTATAAAACCATTTAAAGTCAATAATAAGACTTTTGAAGGAATGAGTGACTATAAATGACT
TTTCTTATCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTGTTT
TAACCAAAATGTAAAAGAATTCAACCTAAAATCAATTATGAGATTATAAAACCAATTAAAGCGAG
TAATAAGGCTTTCGACAGACTGAGTGACTATAAATAGGCTTTTCCAACCAATAAATCACTTTTTC
CTCATGTTTCCCAAG
Found at i:19705 original size:171 final size:169
Alignment explanation
Indices: 19415--20003 Score: 514
Period size: 171 Copynumber: 3.4 Consensus size: 169
19405 NNNNNNNNNN
* * * * ** * * * *
19415 AACGTGAAGAAAAAGCTATTCATTGGCAAGAAAAGTCCATTTATAGCCACCCATA-CTTTTGAAA
1 AACGTGAAAAAAAAGCCATTTATTGACCTGAAAAGTCTATTTATAGTCACTCA-AGCCTTTGAAA
* * * * * *
19479 GCCTTATTACTCATTTTAAAAAGTTTTATTATCACATAATTGATTTTAGGTTGAAT-TGTTTAAC
65 GCCTTATTACTC-GTTTAAATAGTTTTATAATC-CATAATTGATTTTAAGTTGAATAT-TTTTAT
* *
19543 ATTTTTTACTAAAACAGATTATAATTGAATGCTTGCCTTAAGA
127 ATTTTTTATTAAAACAAATTATAATTGAATGCTTGCCTTAAGA
* *
19586 AACGTGAACAAAAAGTCATTTATTGACCTGAAAAGTCTATTTATAGTCACGT-AAGCCTTTGAAA
1 AACGTGAAAAAAAAGCCATTTATTGACCTGAAAAGTCTATTTATAGTCAC-TCAAGCCTTTGAAA
*
19650 GCCTTATTACTCGCTTTCAATAGTTTTATAATCCGATAATTGATTTTAAGTTGAATATTTTTATA
65 GCCTTATTACTCG-TTTAAATAGTTTTATAATCC-ATAATTGATTTTAAGTTGAATATTTTTATA
* * * * *
19715 TTTTTTATTGAAAGATATTATAATTTGATAT-C-TACCTT-CGAA
128 TTTTTTATTAAAACAAATTATAA-TTGA-ATGCTTGCCTTAAG-A
** * *
19757 AACGT-AAAAGAAAAGCCATGCATTAGGA-C-GAAAAGTCTATTTATAGTCTCTCAAGCCTTCGA
1 AACGTGAAAA-AAAAGCCATTTATT--GACCTGAAAAGTCTATTTATAGTCACTCAAGCCTTTGA
* * * * *
19819 AAGCCTTATTGCTCGTTGTAAATAGTTTCAGAATATCATAATCGATTTTAAGTTGAATATTTTTA
63 AAGCCTTATTACTCGTT-TAAATAGTTTTATAAT-CCATAATTGATTTTAAGTTGAATATTTTTA
* * * * *
19884 TAGTTTTTATTAAAACAAATTATAACTAAATGTTTGCATTAAGA
126 TATTTTTTATTAAAACAAATTATAATTGAATGCTTGCCTTAAGA
* * * * * * ** * *
19928 AATGTGAAGAAAAAGGCATTTATTAACAAT-TAAAGTCTATTTATAGTCACTCATTCTTTTCAAA
1 AACGTGAAAAAAAAGCCATTTATTGAC-CTGAAAAGTCTATTTATAGTCACTCAAGCCTTTGAAA
19992 GCCTTATTACTC
65 GCCTTATTACTC
20004 ACTNNNNNNN
Statistics
Matches: 336, Mismatches: 61, Indels: 42
0.77 0.14 0.10
Matches are distributed among these distances:
169 3 0.01
170 11 0.03
171 306 0.91
172 12 0.04
173 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (169 bp):
AACGTGAAAAAAAAGCCATTTATTGACCTGAAAAGTCTATTTATAGTCACTCAAGCCTTTGAAAG
CCTTATTACTCGTTTAAATAGTTTTATAATCCATAATTGATTTTAAGTTGAATATTTTTATATTT
TTTATTAAAACAAATTATAATTGAATGCTTGCCTTAAGA
Found at i:28570 original size:158 final size:149
Alignment explanation
Indices: 28309--28615 Score: 386
Period size: 158 Copynumber: 2.0 Consensus size: 149
28299 ATCAACTATG
* *
28309 AGATTATAAAACCATTAACGCGAGTAATAAGGTTTTTCAAGGCTTGGGTGACTATAAATGCACTT
1 AGATTATAAAACCATTAACGCGAGTAATAAGCTTTTTCAAGGCTTGGGGGACTATAAATGCACTT
* * ** *
28374 TCCTTACAAATGAATGGCTTTTTCTTCGTGTTTCTTGAGACAGATATTTAATTTAA-CAAAAA-A
66 TCCTTACAAATAAATGGCTTTTCCTTCACGTTTCTTGAGACAGACATTTAATTTAATCAAAAATA
28437 TAAAAGAATTCAATATAAA
131 TAAAAGAATTCAATATAAA
28456 NNNNNNNNNNAGATTATAAAACCATTTAACGCGAGTAATAAAGCTTTTT-AAGGCTTGGGGGACT
1 ----------AGATTATAAAACCA-TTAACGCGAGTAAT-AAGCTTTTTCAAGGCTTGGGGGACT
* * *
28520 ATAAATGCACTTTCCTTACCAATAAATGGCTTTTCCTTCACGTTTTTTGAGACGGACATTTAATT
54 ATAAATGCACTTTCCTTACAAATAAATGGCTTTTCCTTCACGTTTCTTGAGACAGACATTTAATT
*
28585 TAATCAAAAATATAAAAGAATTCAATCTAAA
119 TAATCAAAAATATAAAAGAATTCAATATAAA
28616 GTCAATTATN
Statistics
Matches: 135, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
157 14 0.10
158 88 0.65
159 14 0.10
160 19 0.14
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.33
Consensus pattern (149 bp):
AGATTATAAAACCATTAACGCGAGTAATAAGCTTTTTCAAGGCTTGGGGGACTATAAATGCACTT
TCCTTACAAATAAATGGCTTTTCCTTCACGTTTCTTGAGACAGACATTTAATTTAATCAAAAATA
TAAAAGAATTCAATATAAA
Found at i:30716 original size:170 final size:170
Alignment explanation
Indices: 30322--30866 Score: 386
Period size: 171 Copynumber: 3.2 Consensus size: 170
30312 NNNNNNNNNN
* * *
30322 AAAATCAATTATGAAATTATAAAACCATTTAAAG-AGAGTAATAAGGCTTTTGACAGAATGAGTA
1 AAAATCAAATATGAGATTATAAAACCATTTAAAGCA-AGCAATAAGGCTTTTGA-AGAATGAGTA
* * * * ** * *
30386 TCTATAAGTGGACTTTTCTTGCCAATGAATGATTTTTTCTTGAAGTTTTGTAATACAGACATTCA
64 TCTATAAATGGACTTTCCTTACCAATGAATGATTTTTTCTTCAAGTTTCCTAAGACAAACATTCA
*
30451 ATTATAATCTGTTTTAACAAAAAATGTACAAGAATTCAACCT
129 ATTATAATCTATTTTAACAAAAAATGTACAAGAATTCAACCT
* * ********** ** *
30493 AAAATCAAATATAAGATTATAAAACCATTTAAAGCGANNNNNNNNNNTTTTGAAGGCTTGGGTGA
1 AAAATCAAATATGAGATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAA-GAATGAGT-A
* * *
30558 -CTATAAATGG-CTTTCCTTACTAATGAATAGA-TTTTTCTTCAAGTTTCCTAAGGCAAACATTT
64 TCTATAAATGGACTTTCCTTACCAATGAAT-GATTTTTTCTTCAAGTTTCCTAAGACAAACATTC
* * * * *
30620 AATTATAATCTATTTTAACTAAACATTTA-AAGGAATTTAACTT
128 AATTATAATCTATTTTAACAAAAAATGTACAA-GAATTCAACCT
* * *
30663 AAAGTCAACTATGAGATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAAGAATGGGCTA
1 AAAATCAAATATGAGATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTG-AAGAATGAG-TA
* * *** * ********** * *
30728 -CTATAAATAGACTTTTCTTGTTAATGGATNNNNNNNNNNTCATGTTT-CTCGAGACAAACATTC
64 TCTATAAATGGACTTTCCTTACCAATGAATGATTTTTTCTTCAAGTTTCCT-AAGACAAACATTC
* * * * *
30791 AATTATAATTTGTTTTAACTAAAAAA-GTAAAAGAATACAACTT
128 AATTATAATCTATTTTAAC-AAAAAATGTACAAGAATTCAACCT
*
30834 AAAATCAATTATGAGATTATAAAACCATTTAAA
1 AAAATCAAATATGAGATTATAAAACCATTTAAA
30867 ANNNNNNNNN
Statistics
Matches: 285, Mismatches: 77, Indels: 24
0.74 0.20 0.06
Matches are distributed among these distances:
169 2 0.01
170 129 0.45
171 147 0.52
172 7 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.33
Consensus pattern (170 bp):
AAAATCAAATATGAGATTATAAAACCATTTAAAGCAAGCAATAAGGCTTTTGAAGAATGAGTATC
TATAAATGGACTTTCCTTACCAATGAATGATTTTTTCTTCAAGTTTCCTAAGACAAACATTCAAT
TATAATCTATTTTAACAAAAAATGTACAAGAATTCAACCT
Found at i:33828 original size:170 final size:171
Alignment explanation
Indices: 33523--34971 Score: 1433
Period size: 170 Copynumber: 8.5 Consensus size: 171
33513 NNNNNNNNNN
* * * *
33523 CATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAAT-GAACTTGTCTTGCTAA
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-ACTTTTCTTACCAA
* * * * *
33587 TGAATGCCTTTTTCTTCATGTTT-CTAAGACAAACATTCAATTATAATATGTTTTCACCAATAAT
65 TGAATGGCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAAT
* *
33651 GTAAAAAAAATCAACTTAAAGTCAACTATGAGATTATAAAAC
130 GTAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAAC
* ** * *
33693 CATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGGCAACTAAAAATAGATTTTTCTTACCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAAT
* * * **
33758 GAATGGCTTTTGC-TCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTTACCACAAACA
66 GAATGGCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATG
**
33822 TAAAAAAATTCAA-TGTAAAGCCAACTATGAGATTATAAAAC
131 TAAAAAAATTCAACT-TAAAATCAACTATGAGATTATAAAAC
* * *
33863 CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGGCTTTTCTTGA-CAA
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-ACCAA
* * * * * * *
33927 TAAATGACTTTTTCTTCACGTTTCCCT-TGGCAAGCATTCAATTATAATTTGTTTTTACCAAAAA
65 TGAATGGCTTTTTCTTCATGTTT-CCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAA
*
33991 TGTAAAAAAATTCAACTTAAAGTCAACTATGAGATTATAAAAC
129 TGTAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAAC
* * ** * * *
34034 CATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGGGTGTCTATAAATAGACTTTCCTTGA-TAA
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-ACCAA
* * * ** *
34098 TCAATGGC-TTTTCTTCATATTTCTTGTGGTCAAA-ATTCAATTATAATCTGTTTTAACTAAAAA
65 TGAATGGCTTTTTCTTCATGTTTCCTAAGG-CAAACATTCAATTATAATCTGTTTTAACCAAAAA
* * * * *
34161 TGTAGAAGAATTCAATTTAAAATCAATTATGAGATTATACAAC
129 TGTAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAAC
* * * * * *
34204 CATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTAATTATAAATGGACTTTTCTTACCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAAT
* ** * * * *
34269 GAGTACCTTTTTCTTCATATTTTCTGAGGTAAACATTCAATTATAATCTGTTTTAACCAAAAATG
66 GAATGGCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATG
* * * **
34334 TAAAAAAAATCAACTTACAATCAA-TCAGGAGATTATTGAAC
131 TAAAAAAATTCAACTTAAAATCAACT-ATGAGATTATAAAAC
* ** *
34375 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGCAACTATAAATAGACTTTTCTTGCCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAAT
* ** * * * * *
34440 GAAT-GCTTTTTTTCTTTACATTTCTTGAA-GTAGACAATCAATTGTAATCTGTTTTAACCAAAA
66 GAATGGC--TTTTTCTTCATGTTTCCT-AAGGCAAACATTCAATTATAATCTGTTTTAACCAAAA
* * * *
34503 A---AAAAAGGAATTCAACCTAAAATTAATTATTAGATTATAAAAC
128 ATGTAAAAA--AATTCAACTTAAAATCAACTATGAGATTATAAAAC
* ** * * *
34546 CATTTAAAACGAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAAT-GGCTTTCCTTACCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAAT
* * * * *
34610 GAATGGATTTTTCTTCAAGTTTCCTAAGACAAACATTTAATTATAATCTGTTTTAACCAAAAATA
66 GAATGGCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATG
* ** * *
34675 TAAAAAAACTCAACCCAAAATCAATTATGAAATTATAAAAC
131 TAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAAC
* ** * * * * *
34716 CATGTAAAGAAAGAAATAAGGCTTTCGACA-GAATGAGTGACTATAAATGGACTTTTCTTCCCAA
1 CATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGGGTGACTATAAATAGACTTTTCTTACCAA
** * * ** * * * ***
34780 TG-ATGATTTTTTCTTGAAGTTTTGTAAGACAAATATTCAATTATAATCTATTTTATTGAAAAAT
65 TGAATGGCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAAT
* * * * *
34844 GTAAAAGAATTCAACCTAAAATCAAATATAAGATTAGAAAAC
130 GTAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAAC
* ** * * * *
34886 CATTTAAAACGAGTAATAAGGCTTTTGAAGGCTTAGGTGACTATAAAT-GGCTTTCCTTACTAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAAT
*
34950 GAATGGCTTTTTCTTCAAGTTT
66 GAATGGCTTTTTCTTCATGTTT
34972 NNNNNNNNNN
Statistics
Matches: 1062, Mismatches: 189, Indels: 56
0.81 0.14 0.04
Matches are distributed among these distances:
168 2 0.00
169 74 0.07
170 563 0.53
171 366 0.34
172 56 0.05
173 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (171 bp):
CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAAT
GAATGGCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATG
TAAAAAAATTCAACTTAAAATCAACTATGAGATTATAAAAC
Found at i:34145 original size:341 final size:341
Alignment explanation
Indices: 33523--34971 Score: 1493
Period size: 341 Copynumber: 4.3 Consensus size: 341
33513 NNNNNNNNNN
* ** * *
33523 CATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGAACTTGTCTTGCTAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTCTTAC-AAT
* * * * *
33588 GAATGCCTTTTTCTTCATGTTT-CTAAGACAAACATTCAATTATAATATGTTTTCACCAATAATG
65 GAATGACTTTTTCTTCAAGTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAACCAAAAATG
*
33652 TAAAAAAAATCAACTTAAAGTCAACTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTA
130 TAAAAAAAATCAACTTAAAGTCAACTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT-
* * *
33717 TT-GAAGGAATGGGCAACTAAAAATAGATTTTTCTT-ACCAATGAATGGCTTTTGC-TCATGTTT
194 TTCGAAGGAATGGGCAACTATAAATAGACTTTTCTTGA-CAATGAATGGCTTTT-CTTCATATTT
* * * * * ** **
33779 CCT-AAGGCAAACATTCAATTATAATCTGTTTTTACCACAAACATAAAAAAATTCAATGTAAAGC
257 CTTGAAGTCAAACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAAT
*
33843 CAACTATGAGATTATAAAAC
322 CAATTATGAGATTATAAAAC
*
33863 CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGGCTTTTCTTGACAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTCTT-ACAAT
* * * * * * *
33928 AAATGACTTTTTCTTCACGTTTCCCT-TGGCAAGCATTCAATTATAATTTGTTTTTACCAAAAAT
65 GAATGACTTTTTCTTCAAGTTT-CCTAAGACAAACATTCAATTATAATCTGTTTTAACCAAAAAT
*
33992 GTAAAAAAATTCAACTTAAAGTCAACTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT
129 GTAAAAAAAATCAACTTAAAGTCAACTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT
** *** * * *
34057 TTCGAAGGCTTGGGTGTCTATAAATAGACTTTCCTTGATAATCAATGGCTTTTCTTCATATTTCT
194 TTCGAAGGAATGGGCAACTATAAATAGACTTTTCTTGACAATGAATGGCTTTTCTTCATATTTCT
** * * * * **
34122 TGTGGTCAAA-ATTCAATTATAATCTGTTTTAACTAAAAATGTAGAAGAATTCAATTTAAAATCA
259 TGAAGTCAAACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAATCA
*
34186 ATTATGAGATTATACAAC
324 ATTATGAGATTATAAAAC
* * * * * *
34204 CATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGAGTAATTATAAATGGACTTTTCTTACCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTCTTA-CAAT
* * * **
34269 GAGT-ACCTTTTTCTTCATA-TTTTCTGAGGTAAACATTCAATTATAATCTGTTTTAACCAAAAA
65 GAATGA-CTTTTTCTTCA-AGTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAACCAAAAA
* **
34332 TGTAAAAAAAATCAACTTACAA-TCAA-TCAGGAGATTATTGAACCATTTAAAGTGAGTAATAAG
128 TGTAAAAAAAATCAACTTA-AAGTCAACT-ATGAGATTATAAAACCATTTAAAGTGAGTAATAAG
* * * *
34395 GCTTTTGAAGGAATGGGCAACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTTTTTCTTTAC
191 GCTTTCGAAGGAATGGGCAACTATAAATAGACTTTTCTTGACAATGAATGGC---TTTTCTTCAT
* * * *
34459 ATTTCTTGAAGT-AGACAATCAATTGTAATCTGTTTTAACCAAAAA-A-AAAAGGAATTCAACCT
253 ATTTCTTGAAGTCAAACATTCAATTATAATCTGTTTTAACCAAAAATATAAAA-AAATTCAACCT
* *
34521 AAAATTAATTATTAGATTATAAAAC
317 AAAATCAATTATGAGATTATAAAAC
* ** * *
34546 CATTTAAAACGAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAAT-GGCTTTCCTTACCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTCTTA-CAAT
*
34610 GAATGGA-TTTTTCTTCAAGTTTCCTAAGACAAACATTTAATTATAATCTGTTTTAACCAAAAAT
65 GAAT-GACTTTTTCTTCAAGTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAACCAAAAAT
* * ** * * * * ** *
34674 ATAAAAAAACTCAACCCAAAATCAATTATGAAATTATAAAACCATGTAAAGAAAGAAATAAGGCT
129 GTAAAAAAAATCAACTTAAAGTCAACTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT
* ** * ** ** * *
34739 TTCGACA-GAATGAGTGACTATAAATGGACTTTTCTTCCCAATG-ATGATTTTTTCTTGA-AGTT
194 TTCGA-AGGAATGGGCAACTATAAATAGACTTTTCTTGACAATGAATG-GCTTTTCTTCATATTT
* * * *** * *
34801 -TTGTAAGACAAATATTCAATTATAATCTATTTTATTGAAAAATGTAAAAGAATTCAACCTAAAA
257 CTTG-AAGTCAAACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAA
* * *
34865 TCAAATATAAGATTAGAAAAC
321 TCAATTATGAGATTATAAAAC
* ** * *
34886 CATTTAAAACGAGTAATAAGGCTTTTGAAGGCTTAGGTGACTATAAAT-GGCTTTCCTTACTAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTCTTAC-AAT
*
34950 GAATGGCTTTTTCTTCAAGTTT
65 GAATGACTTTTTCTTCAAGTTT
34972 NNNNNNNNNN
Statistics
Matches: 934, Mismatches: 143, Indels: 64
0.82 0.13 0.06
Matches are distributed among these distances:
337 3 0.00
338 6 0.01
339 35 0.04
340 202 0.22
341 557 0.60
342 86 0.09
343 45 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (341 bp):
CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCTTTTCTTACAATG
AATGACTTTTTCTTCAAGTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAACCAAAAATGT
AAAAAAAATCAACTTAAAGTCAACTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
CGAAGGAATGGGCAACTATAAATAGACTTTTCTTGACAATGAATGGCTTTTCTTCATATTTCTTG
AAGTCAAACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACCTAAAATCAAT
TATGAGATTATAAAAC
Found at i:36451 original size:170 final size:170
Alignment explanation
Indices: 36045--36457 Score: 429
Period size: 170 Copynumber: 2.4 Consensus size: 170
36035 AAAAATATAA
* * * * ** *
36045 AAAAATGTAAAACAATTCAA-TCAAAAATTAATTATGTGATAATAAAACCATTTATCGCGAGTAA
1 AAAAATGTAAAACAATTCAACTC-AAAATCAACTATGAGATTATAAAACCATTTAAAGCAAGTAA
** * * * *
36109 TAAGGCTTTCGGAAACATGAGTAGCTATAATAGACTTTTCTTGCCAATGAATGGCTTTTTCTTCA
65 TAAGGCTTTCGGAAACATGAACAGCTATAAAAGACTTTTCTTACCAATGAATGCCTTTTTCTCCA
36174 CGTTACTAGAGGTAGACATTGAATTATAATATGTTTTAACC
130 CGTTACTAGAGGTAGACATTGAATTATAATATGTTTTAACC
*********** * *
36215 AAAAATGTAAAACAATTCAACTTNNNNNNNNNNATGAGATTATAAAACTATATAAAGCAAGTAAT
1 AAAAATGTAAAACAATTCAACTCAAAATCAACTATGAGATTATAAAACCATTTAAAGCAAGTAAT
** * *
36280 AAGGCTTTC-GAGAGTATGAACGGCTATAAAAGGACTTTTCTTATCAATGAATGACCTTTTT-TC
66 AAGGCTTTCGGA-AACATGAACAGCTATAAAA-GACTTTTCTTACCAATGAATG-CCTTTTTCTC
* * * *
36343 CATGTTTCTAGAGGTTGACATTGAATTATAATCTGTTTTAACC
128 CACGTTACTAGAGGTAGACATTGAATTATAATATGTTTTAACC
* * *
36386 AAAAATGTAAAA-AATTTAACTCAAAATCGACTATGAGATTATAAAACCATTTAAAGCTAGTAAT
1 AAAAATGTAAAACAATTCAACTCAAAATCAACTATGAGATTATAAAACCATTTAAAGCAAGTAAT
36450 AAGGCTTT
66 AAGGCTTT
36458 TCAAGGCTTG
Statistics
Matches: 192, Mismatches: 47, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
169 2 0.01
170 112 0.58
171 72 0.38
172 6 0.03
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.32
Consensus pattern (170 bp):
AAAAATGTAAAACAATTCAACTCAAAATCAACTATGAGATTATAAAACCATTTAAAGCAAGTAAT
AAGGCTTTCGGAAACATGAACAGCTATAAAAGACTTTTCTTACCAATGAATGCCTTTTTCTCCAC
GTTACTAGAGGTAGACATTGAATTATAATATGTTTTAACC
Done.