Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000776.1 Hibiscus syriacus cultivar Beakdansim tig00001509_pilon, 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: 304350
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:171812 original size:200 final size:200
Alignment explanation
Indices: 171111--172441 Score: 1909
Period size: 200 Copynumber: 6.7 Consensus size: 200
171101 ATTTAACAAT
* * * * * * **
171111 TGTCGATACTTTATG-ATGA-CTATTTTCTCATAAAACCGGTATATTTATACCAGTTACATTGGA
1 TGTCGATACATTATGTA-GACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACA
* * * * * *
171174 AATTTATCTATTACATTATAATTATCGGTTTCGATGTTATTGGGATCGACACATTTTAAAAATGT
65 AAATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGT
* *
171239 ATCGACACTTTATGC-TTGCA--ACTTTTGG-ATTTTC-TTCTGGACAAAAAGTATCGACACAAA
130 ATCGACACTTTATTCGTT-CATCATTTTTGGCA--TTCATTCTGGACAAAAAGTATCGACACAAA
* ** *
171299 TTCCACAAG
192 ATAAAAAAG
* * * **
171308 TGTTGATACATGT-TGTAGACCTATTCTCTCATAAAATCGGTAT-TGTTATACCGGTTACATTGT
1 TGTCGATACAT-TATGTAGACCTATTCTCACATAAAATCGGTATAT-TTATACCGGTTATATTAC
* * * ** * * *
171371 AAATTTACCTGTTACATTATATTTATGGGTTTCAATGTTTTTGGTATCGACACTTCTTATAAATG
64 AAAATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATG
* *
171436 TATCGACACTTTATTCGTTCATCATTTTTTGCATTCATTCTGGACAAAAAGTTTCGACACAAAAT
129 TATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAAT
171501 AAAAAAAG
194 -AAAAAAG
* * * *
171509 TATCGATATATTATGTAGACCTATTCTTACATAAAATAGGTATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAA
* *
171574 AATTATCTATTACATTATAATTATTTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
66 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
*
171639 TCGACACTTTATTCGTTCATCATTTTTAGCATTCATTCTGGACAAAAAGTATCGACACAAAATAA
131 TCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAA
171704 AAAAG
196 AAAAG
* * *
171709 TGTCGATACATTATGTAGACCTATTCTTACATAAAACCGGTATATTTATACCGTTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAA
171774 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
66 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
* * * *
171839 TCGACACTTTATTCGTTCATTATTTTTGGCATTCATTATGGACAAAAAGTATC-ACACAACATTA
131 TCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAA
171903 AAAA-
196 AAAAG
* *
171907 -GTCGATACATTATGTAGACCTATTCTCACAAAAAATCGGTATATTTATACCTGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAA
* * *
171971 AATTACCTATTACATTATATTTAT-GGATTTCGATGTTTCTGGGATCGACACTTTTTA-AAACTG
66 AATTACCTATTACATTATAATTATCTG-TTTCGATGTTTTTGGGATCGACACTTTTTATAAA-TG
172034 TATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAAT
129 TATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAAT
172099 AAAAAAG
194 AAAAAAG
*
172106 TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGATATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAA
* * * *
172171 AATTACCTATTACATTATAATTATATGTTTGGATGTTTTTGGGATCGACACTTTTTATATATGCA
66 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
172236 TCGACACTTTATTCGTTCATCATTTTTGGCATT-ATTCTGGACAAAAAGTATCGACACAAAATAA
131 TCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAAT-A
172300 AAAAAG
195 AAAAAG
*
172306 TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAA
* *
172371 AATTACCTATTACATTATAATTATCTGTTTTGATGTTTTTGGGATCGACACGTTTTATAAATGTA
66 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
172436 TCGACA
131 TCGACA
172442 TATATGCTTA
Statistics
Matches: 1030, Mismatches: 84, Indels: 37
0.89 0.07 0.03
Matches are distributed among these distances:
196 4 0.00
197 180 0.17
198 124 0.12
199 47 0.05
200 497 0.48
201 177 0.17
202 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (200 bp):
TGTCGATACATTATGTAGACCTATTCTCACATAAAATCGGTATATTTATACCGGTTATATTACAA
AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
TCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAA
AAAAG
Found at i:172085 original size:397 final size:399
Alignment explanation
Indices: 171112--172441 Score: 1898
Period size: 397 Copynumber: 3.3 Consensus size: 399
171102 TTTAACAATT
* * * * * **
171112 GTCGATACTTTATG-ATGA-CTATTTTCTCATAAAACCGGTATATTTATACCAGTTACATTGGAA
1 GTCGATACATTATGTA-GACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
* * * * *
171175 ATTTATCTATTACATTATAATTATCGGTTTCGATGTTATTGGGATCGACACATTTTAAAAATGTA
65 AATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
* * *
171240 TCGACACTTTATGC-TTGCA--ACTTTTGG-ATTTTC-TTCTGGACAAAAAGTATCGACACAAAT
130 TCGACACTTTATTCGTT-CATCATTTTTGGCA--TTCATTCTGGACAAAAAGTATCGACACAAAA
** * *
171300 TCCACAAGTGTTGATACATGT-TGTAGACCTATTCTCT-CATAAAATCGGTAT-TGTTATACCGG
192 TAAAAAAGTGTCGATACAT-TATGTAGACCTATTCT-TACATAAAATCGGTATAT-TTATACCGG
* ** * * * ** * * *
171362 TTACATTGTAAATTTACCTGTTACATTATATTTATGGGTTTCAATGTTTTTGGTATCGACACTTC
254 TTATATTACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGACACTTT
* *
171427 TTATAAATGTATCGACACTTTATTCGTTCATCATTTTTTGCATTCATTCTGGACAAAAAGTTTCG
319 TTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCG
171492 ACACAAAATAAAAAAA
384 ACACAAAATAAAAAAA
* * **
171508 GTATCGATATATTATGTAGACCTATTCTTACATAAAATAGGTATATTTATACCGGTTATATTACA
1 G--TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACA
* **
171573 AAATTATCTATTACATTATAATTATTTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGT
64 AAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGT
*
171638 ATCGACACTTTATTCGTTCATCATTTTTAGCATTCATTCTGGACAAAAAGTATCGACACAAAATA
129 ATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATA
* *
171703 AAAAAGTGTCGATACATTATGTAGACCTATTCTTACATAAAACCGGTATATTTATACCGTTTATA
194 AAAAAGTGTCGATACATTATGTAGACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATA
*
171768 TTACAAAATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATA
259 TTACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGACACTTTTTATA
* *
171833 AATGTATCGACACTTTATTCGTTCATTATTTTTGGCATTCATTATGGACAAAAAGTATC-ACACA
324 AATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACA
* *
171897 ACAT-TAAAAA
389 AAATAAAAAAA
* * *
171907 GTCGATACATTATGTAGACCTATTCTCACAAAAAATCGGTATATTTATACCTGTTATATTACAAA
1 GTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAAA
* *
171972 ATTACCTATTACATTATATTTAT-GGATTTCGATGTTTCTGGGATCGACACTTTTTA-AAACTGT
66 ATTACCTATTACATTATAATTATCGG-TTTCGATGTTTTTGGGATCGACACTTTTTATAAA-TGT
172035 ATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATA
129 ATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATA
* *
172100 AAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAATCGATATATTTATACCGGTTATA
194 AAAAAGTGTCGATACATTATGTAGACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATA
*
172165 TTACAAAATTACCTATTACATTATAATTATATGTTTGGATGTTTTTGGGATCGACACTTTTTATA
259 TTACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGACACTTTTTATA
* *
172230 TATGCATCGACACTTTATTCGTTCATCATTTTTGGCATT-ATTCTGGACAAAAAGTATCGACACA
324 AATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACA
172294 AAATAAAAAAA
389 AAATAAAAAAA
172305 GTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACA
1 --GTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACA
* * *
172370 AAATTACCTATTACATTATAATTATCTGTTTTGATGTTTTTGGGATCGACACGTTTTATAAATGT
64 AAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGT
172435 ATCGACA
129 ATCGACA
172442 TATATGCTTA
Statistics
Matches: 840, Mismatches: 74, Indels: 36
0.88 0.08 0.04
Matches are distributed among these distances:
396 23 0.03
397 344 0.41
398 18 0.02
399 117 0.14
400 136 0.16
401 200 0.24
402 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (399 bp):
GTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAAA
ATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTAT
CGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAAA
AAAGTGTCGATACATTATGTAGACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATATT
ACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGACACTTTTTATAAA
TGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAA
ATAAAAAAA
Found at i:172306 original size:597 final size:596
Alignment explanation
Indices: 171111--172450 Score: 2013
Period size: 597 Copynumber: 2.2 Consensus size: 596
171101 ATTTAACAAT
* * * * **
171111 TGTCGATACTTTATG-ATGA-CTATTTTCTCATAAAACCGGTATATTTATACCAGTTACATTGGA
1 TGTCGATACATTATGTA-GACCTATTCTCACATAAAACCGGTATATTTATACC-GTTATATTACA
* * * * *
171174 AATTTATCTATTACATTATAATTATCGGTTTCGATGTTATTGGGATCGACACATTTTAAAAATGT
64 AAATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACATTTTATAAATGT
*
171239 ATCGACACTTTATGCTTGCAACTTTTGGATTTTCTTCTGGACAAAAAGTATCGACACAAATTCCA
129 ATCGACACTTTATGCTTGCAACTTTTGGA-TTTCTTATGGACAAAAAGTATCGACACAAATT-CA
** * * *
171304 CAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATTGTTATACCGGTTACATT
192 CAAAAGTCGATACATGTTGTAGACCTATTCTCACAAAAAATCGGTATTGTTATACCGGTTACATT
** * * * * *
171369 GTAAATTTACCTGTTACATTATATTTATGGGTTTCAATGTTTTTGGTATCGACACTTCTTATAAA
257 ACAAAATTACCTATTACATTATATTTATGGATTTCAATGTTTCTGGGATCGACACTTCTTATAAA
* *
171434 TGTATCGACACTTTATTCGTTCATCATTTTTTGCATTCATTCTGGACAAAAAGTTTCGACACAAA
322 TGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAA
* * *
171499 ATAAAAAAAGTATCGATATATTATGTAGACCTATTCTTACATAAAATAGGTATATTTATACCGGT
387 ATAAAAAAAGTATCGATACATTATGTAGACCTATTCTCACATAAAATAGATATATTTATACCGGT
* *
171564 TATATTACAAAATTATCTATTACATTATAATTATTTGTTTCGATGTTTTTGGGATCGACACTTTT
452 TATATTACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGACACTTTT
*
171629 TATAAATGTATCGACACTTTATTCGTTCATCATTTTTAGCATTCATTCTGGACAAAAAGTATCGA
517 TATAAATGCATCGACACTTTATTCGTTCATCATTTTTAGCATTCATTCTGGACAAAAAGTATCGA
171694 CACAAAATAAAAAAG
582 CACAAAATAAAAAAG
*
171709 TGTCGATACATTATGTAGACCTATTCTTACATAAAACCGGTATATTTATACCGTTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCG-TTATATTACAA
*
171774 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTA
65 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACATTTTATAAATGTA
* *
171839 TCGACACTTTATTCGTT-CATTATTTTTGGCA-TTCATTATGGACAAAAAGTATC-ACACAACAT
130 TCGACACTTTATGC-TTGCA--ACTTTTGG-ATTTC-TTATGGACAAAAAGTATCGACACAA-AT
*
171901 T-A-AAAAGTCGATACAT-TATGTAGACCTATTCTCACAAAAAATCGGTATAT-TTATACCTGTT
189 TCACAAAAGTCGATACATGT-TGTAGACCTATTCTCACAAAAAATCGGTAT-TGTTATACCGGTT
* * *
171962 ATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTCTGGGATCGACACTTTTT
252 ACATTACAAAATTACCTATTACATTATATTTATGGATTTCAATGTTTCTGGGATCGACACTTCTT
172027 A-AAACTGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGA
317 ATAAA-TGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGA
* *
172091 CACAAAAT-AAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAATCGATATATTTAT
381 CACAAAATAAAAAAAGTATCGATACATTATGTAGACCTATTCTCACATAAAATAGATATATTTAT
*
172155 ACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTTTGGATGTTTTTGGGATCGAC
446 ACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGAC
* *
172220 ACTTTTTATATATGCATCGACACTTTATTCGTTCATCATTTTTGGCATT-ATTCTGGACAAAAAG
511 ACTTTTTATAAATGCATCGACACTTTATTCGTTCATCATTTTTAGCATTCATTCTGGACAAAAAG
172284 TATCGACACAAAATAAAAAAAG
576 TATCGACACAAAAT-AAAAAAG
172306 TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACC-GTTATATTACAA
* *
172371 AATTACCTATTACATTATAATTATCTGTTTTGATGTTTTTGGGATCGACACGTTTTATAAATGTA
65 AATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACATTTTATAAATGTA
*
172436 TCGACA-TATATGCTT
130 TCGACACTTTATGCTT
172451 ACCTATTTTT
Statistics
Matches: 678, Mismatches: 50, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
595 2 0.00
596 34 0.05
597 301 0.44
598 188 0.28
599 114 0.17
600 11 0.02
601 27 0.04
602 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (596 bp):
TGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGTTATATTACAAA
ATTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGACACATTTTATAAATGTAT
CGACACTTTATGCTTGCAACTTTTGGATTTCTTATGGACAAAAAGTATCGACACAAATTCACAAA
AGTCGATACATGTTGTAGACCTATTCTCACAAAAAATCGGTATTGTTATACCGGTTACATTACAA
AATTACCTATTACATTATATTTATGGATTTCAATGTTTCTGGGATCGACACTTCTTATAAATGTA
TCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAA
AAAAAGTATCGATACATTATGTAGACCTATTCTCACATAAAATAGATATATTTATACCGGTTATA
TTACAAAATTACCTATTACATTATAATTATATGTTTCGATGTTTTTGGGATCGACACTTTTTATA
AATGCATCGACACTTTATTCGTTCATCATTTTTAGCATTCATTCTGGACAAAAAGTATCGACACA
AAATAAAAAAG
Found at i:172728 original size:19 final size:19
Alignment explanation
Indices: 172704--172752 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
172694 TTACATCCAC
172704 ATACAAAATTATAAAT-TGT
1 ATACAAAATTATAAATCT-T
172723 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
172742 ATACAAAATTA
1 ATACAAAATTA
172753 ACTCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:174341 original size:18 final size:18
Alignment explanation
Indices: 174320--174358 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
174310 TCTTCCTCAT
*
174320 TTCCTCTATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
174338 TTCCTCCCTCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
174356 TTC
1 TTC
174359 ATATTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:174524 original size:20 final size:20
Alignment explanation
Indices: 174501--174566 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 20
174491 CACAACCTCC
174501 TTCACCACTCCATCAATTTT
1 TTCACCACTCCATCAATTTT
* *
174521 TTCACCCCTCAACACCTCAACTTCT
1 TTCACCACTC--CA--TCAA-TTTT
*
174546 TTCACCACTCCATCTATTTT
1 TTCACCACTCCATCAATTTT
174566 T
1 T
174567 CCTTCCACTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
22 2 0.06
23 2 0.06
24 4 0.11
25 12 0.33
ACGTcount: A:0.23, C:0.39, G:0.00, T:0.38
Consensus pattern (20 bp):
TTCACCACTCCATCAATTTT
Found at i:174617 original size:21 final size:21
Alignment explanation
Indices: 174591--174631 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
174581 ATTATGCCTA
174591 TCAAGTGTCTCTTCGACTCTC
1 TCAAGTGTCTCTTCGACTCTC
*
174612 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTCTCTTCGACTCT
174632 TGATTGTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.32, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTCTCTTCGACTCTC
Found at i:174734 original size:15 final size:15
Alignment explanation
Indices: 174714--174743 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
174704 ACTCTGTTTT
174714 CCCTCACCATCATCC
1 CCCTCACCATCATCC
*
174729 CCCTCACCGTCATCC
1 CCCTCACCATCATCC
174744 TCCAATACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.60, G:0.03, T:0.20
Consensus pattern (15 bp):
CCCTCACCATCATCC
Found at i:177583 original size:181 final size:181
Alignment explanation
Indices: 177013--177684 Score: 945
Period size: 183 Copynumber: 3.7 Consensus size: 181
177003 TACGCGTACT
* * * * ***
177013 TATTAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCGATTTTTTCATTTAGAGACCG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
* * * *
177078 GTTTTGTCATATTTTTACTTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* * *
177143 CTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 -TATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* ** * * *
177195 TATTAAATTATCGACACTTTAAATATATCCGGTAGCGCTTTACCAGTTTTGTCTTTTCCTGACTG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
*
177260 GTTTTGTCATATTTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
66 GTTTTGTCATA-TTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
* *
177325 TTTATAAGCGCTAAAACTGATTCTCCTTTAAATTCACAATGTGTCGATACTTA
130 -TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
177378 TATTAAAGTATCGACACTTGCAATATATTCAGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
* * *
177443 GTTTTGTCTTATTTTTACCTATTATATTGTTGTGGATCGATACATATTTATAAAGAATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* *
177508 TATAGGTGCTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTA
131 TATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
177559 TATTAAAGTATCGATACGTGCAATATA-TCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACC
1 TATTAAAGTATCGACACTTGCAATATATTC-GGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACC
* * * *
177623 GG-TTTGTCATATTTTT-CCTGTTATATTGATGTGGATCGATACATTTTTATAAAGTATCGACA
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACA
177685 TAAACCGACA
Statistics
Matches: 439, Mismatches: 48, Indels: 9
0.89 0.10 0.02
Matches are distributed among these distances:
179 42 0.10
180 15 0.03
181 105 0.24
182 115 0.26
183 161 0.37
184 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTGCAATATATTCGGTAGCGCTTTACCGGTTTTGTCTTTTCCTGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:178479 original size:6 final size:6
Alignment explanation
Indices: 178468--178510 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
178458 TTTTAATATT
* * *
178468 CATTTA CATTTA CA-TTA CATATA CATATA CATATA CATTTA CA
1 CATTTA CATTTA CATTTA CATTTA CATTTA CATTTA CATTTA CA
178511 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (6 bp):
CATTTA
Found at i:178483 original size:12 final size:12
Alignment explanation
Indices: 178459--178510 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
178449 CATGCAAAAT
*
178459 TTTA-ATATTCA
1 TTTACATATACA
*
178470 TTTACATTTACA
1 TTTACATATACA
178482 -TTACATATACA
1 TTTACATATACA
*
178493 TATACATATACA
1 TTTACATATACA
178505 TTTACA
1 TTTACA
178511 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 14 0.41
12 20 0.59
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTACATATACA
Found at i:178498 original size:23 final size:23
Alignment explanation
Indices: 178463--178506 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
178453 CAAAATTTTA
* * *
178463 ATATTCATTTACATTTACATTAC
1 ATATACATATACATATACATTAC
178486 ATATACATATACATATACATT
1 ATATACATATACATATACATT
178507 TACAAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATACATATACATATACATTAC
Found at i:179442 original size:42 final size:42
Alignment explanation
Indices: 179216--179483 Score: 182
Period size: 43 Copynumber: 6.3 Consensus size: 42
179206 ATAGCGGCGT
* * * **
179216 CAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTGCAGA
1 CAAACGCCGCAGAAGATGTTGATATTTAGCGGCGTTTT-CCTA
* * * * * * **
179259 AAAACACCGCA-ATAGGTGTTGATATTTAACGGCATTTGGCAGA
1 CAAACGCCGCAGA-AGATGTTGATATTTAGCGGCGTTT-TCCTA
** * *
179302 CAAA-GCCGCA-ATAGGCGTTGATGTTTAGCGGCGTTTTCTTCA
1 CAAACGCCGCAGA-AGATGTTGATATTTAGCGGCGTTTTCCT-A
* * * *
179344 CAAACGCCGCAGTAGATGTTTATTTTTACCGGCGTTTTTCCTA
1 CAAACGCCGCAGAAGATGTTGATATTTAGCGGCG-TTTTCCTA
* *
179387 CAAACGCCACAGAAGATGTTGATATTTAGCGGTGTTTTCCTA
1 CAAACGCCGCAGAAGATGTTGATATTTAGCGGCGTTTTCCTA
* * * * *
179429 CAAACGCCGCAGAATATGTCTTGAGATTTAGCGGCATTTTCGTT
1 CAAACGCCGCAGAAGATG--TTGATATTTAGCGGCGTTTTCCTA
*
179473 GAAACGCCGCA
1 CAAACGCCGCA
179484 ATATGTCTTG
Statistics
Matches: 181, Mismatches: 36, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 57 0.31
43 88 0.49
44 35 0.19
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (42 bp):
CAAACGCCGCAGAAGATGTTGATATTTAGCGGCGTTTTCCTA
Found at i:179947 original size:21 final size:21
Alignment explanation
Indices: 179864--179941 Score: 86
Period size: 21 Copynumber: 3.6 Consensus size: 21
179854 ATATATTACT
*
179864 TCTCTCTG-TTCTGCTGCTGCC
1 TCTCTCTGCTTCCGCTGCTG-C
* * *
179885 TCTCTCTGTGCTGCCACTGCTTC
1 TCTCTC--TGCTTCCGCTGCTGC
179908 TCTCTCTGCTTCCGCTGCTGC
1 TCTCTCTGCTTCCGCTGCTGC
179929 TCTCTCTGCTTCC
1 TCTCTCTGCTTCC
179942 CTTGCTTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 31 0.66
23 9 0.19
24 7 0.15
ACGTcount: A:0.01, C:0.41, G:0.17, T:0.41
Consensus pattern (21 bp):
TCTCTCTGCTTCCGCTGCTGC
Found at i:188772 original size:41 final size:41
Alignment explanation
Indices: 188727--188876 Score: 144
Period size: 41 Copynumber: 3.7 Consensus size: 41
188717 TTAAAATTAA
188727 TTGCGGCGTTTAC-AGAAAAACGCCACTAATGTACGACCCAT
1 TTGCGGCGTTT-CTAGAAAAACGCCACTAATGTACGACCCAT
* * * ** * *
188768 TTGCGACGTTTCTTGTAAAACGCCACT-ATAAACAACTC-T
1 TTGCGGCGTTTCTAGAAAAACGCCACTAATGTACGACCCAT
* * *
188807 ATTGCGGCGTTTATATAAAAATGCCACTAATGTACGACCCAT
1 -TTGCGGCGTTTCTAGAAAAACGCCACTAATGTACGACCCAT
* * *
188849 TTACGGCGTTTCTTGTAAAACGCCACTA
1 TTGCGGCGTTTCTAGAAAAACGCCACTA
188877 TAAACAACTC
Statistics
Matches: 82, Mismatches: 23, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
39 1 0.01
40 29 0.35
41 51 0.62
42 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (41 bp):
TTGCGGCGTTTCTAGAAAAACGCCACTAATGTACGACCCAT
Found at i:188818 original size:81 final size:81
Alignment explanation
Indices: 188726--189040 Score: 388
Period size: 81 Copynumber: 3.9 Consensus size: 81
188716 GTTAAAATTA
* * *
188726 ATTGCGGCGTTTACAGAAAAACGCCACTAATGTACGACCCATTTGCGACGTTTCTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGCGTTTCTTGTAAAACGC
188791 CACTATAAACAACTCT
66 CACTATAAACAACTCT
* *
188807 ATTGCGGCGTTTATATAAAAATGCCACTAATGTACGACCCATTTACGGCGTTTCTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGCGTTTCTTGTAAAACGC
188872 CACTATAAACAACTCT
66 CACTATAAACAACTCT
* * * * *
188888 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACTACTC-TATTGCGGTGTTT-TTTTAGAAA
1 ATTGCGGCGTTTATATAAAAACGCCACT-AATGTACGACCCAT-TTGCGGCGTTTCTTGT--AAA
*
188950 ACACCACTATAAACAACTCT
62 ACGCCACTATAAACAACTCT
** * * *
188970 ATTGCGGCGTTTATATAAAAACGCTGCTAAAT-TACCACCC-TATTGCGGCGTTTGTTGAAAAAA
1 ATTGCGGCGTTTATATAAAAACGCCACT-AATGTACGACCCAT-TTGCGGCGTTTCTTG-TAAAA
189033 CGCCACTA
63 CGCCACTA
189041 AAGTTTCATT
Statistics
Matches: 208, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
80 4 0.02
81 117 0.56
82 85 0.41
83 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (81 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGCGTTTCTTGTAAAACGC
CACTATAAACAACTCT
Found at i:188969 original size:41 final size:40
Alignment explanation
Indices: 188784--188993 Score: 219
Period size: 41 Copynumber: 5.2 Consensus size: 40
188774 CGTTTCTTGT
188784 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
* ** * * * * *
188824 AAAATGCCACTAATGTACGAC-CCATTTACGGCGTTTCT-TGT
1 AAAACGCCACT-ATAAACAACTCTA-TTGCGGCGTTTATAT-A
188865 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
* * * * *
188905 AAAACGCCGCTA-AATTACTACTCTATTGCGGTGTTTTTTTA
1 AAAACGCCACTATAA--ACAACTCTATTGCGGCGTTTATATA
*
188946 GAAAACACCACTATAAACAACTCTATTGCGGCGTTTATATA
1 -AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
188987 AAAACGC
1 AAAACGC
188994 TGCTAAATTA
Statistics
Matches: 133, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
39 2 0.02
40 47 0.35
41 72 0.54
42 10 0.08
43 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (40 bp):
AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
Found at i:189031 original size:41 final size:41
Alignment explanation
Indices: 188799--189022 Score: 192
Period size: 41 Copynumber: 5.5 Consensus size: 41
188789 GCCACTATAA
* *
188799 ACAACTCTATTGCGGCGTTTATATAAAAATGCCACT-AATGT
1 ACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAAT-T
* * * * * *
188840 ACGAC-CCATTTACGGCGTTTCT-TGTAAAACGCCACTATAA--
1 ACAACTCTA-TTGCGGCGTTTATAT-AAAAACGCCGCTA-AATT
188880 ACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATT
1 ACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATT
* * * * * *
188921 ACTACTCTATTGCGGTGTTTTTTTAGAAAACACCACTATAA--
1 ACAACTCTATTGCGGCGTTTATATA-AAAACGCCGCTA-AATT
*
188962 ACAACTCTATTGCGGCGTTTATATAAAAACGCTGCTAAATT
1 ACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATT
* *
189003 ACCACCCTATTGCGGCGTTT
1 ACAACTCTATTGCGGCGTTT
189023 GTTGAAAAAA
Statistics
Matches: 144, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
39 4 0.03
40 38 0.26
41 88 0.61
42 10 0.07
43 4 0.03
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (41 bp):
ACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATT
Found at i:195082 original size:2 final size:2
Alignment explanation
Indices: 195075--195106 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
195065 GATGTGTAAG
*
195075 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195107 TTGGCCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199627 original size:44 final size:44
Alignment explanation
Indices: 199578--199678 Score: 202
Period size: 44 Copynumber: 2.3 Consensus size: 44
199568 GCACTCCTTA
199578 TGCATCGATGCACTAATTGCATTCGATGTTCATTTATTTGAGAG
1 TGCATCGATGCACTAATTGCATTCGATGTTCATTTATTTGAGAG
199622 TGCATCGATGCACTAATTGCATTCGATGTTCATTTATTTGAGAG
1 TGCATCGATGCACTAATTGCATTCGATGTTCATTTATTTGAGAG
199666 TGCATCGATGCAC
1 TGCATCGATGCAC
199679 ATTGAAGATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (44 bp):
TGCATCGATGCACTAATTGCATTCGATGTTCATTTATTTGAGAG
Found at i:202598 original size:24 final size:24
Alignment explanation
Indices: 202546--202603 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
202536 AATTAAGCCT
202546 AAATATT-ATTTAAAGAAAAAATA
1 AAATATTAATTTAAAGAAAAAATA
**
202569 TTATATTAATTTAAA-AATAAAATA
1 AAATATTAATTTAAAGAA-AAAATA
*
202593 AAATATAAATT
1 AAATATTAATT
202604 AATCTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATATTAATTTAAAGAAAAAATA
Found at i:208839 original size:21 final size:22
Alignment explanation
Indices: 208796--208842 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
208786 AACCTAACCT
208796 ATTTTAATTTTGAATATTGATAA
1 ATTTTAATTTTG-ATATTGATAA
* *
208819 ATTTTACTTTTG-TATTTATAA
1 ATTTTAATTTTGATATTGATAA
208840 ATT
1 ATT
208843 GTTTTATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
23 11 0.50
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTTAATTTTGATATTGATAA
Found at i:209845 original size:60 final size:60
Alignment explanation
Indices: 209781--209910 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
209771 TTAGAAAGAT
* * * * *
209781 ATCATAGTTTAGGGATGAAATT-AGTATGTTCAAAAGTTTAAGGATTATTTTAAA-ATGAGA
1 ATCATAGTTTAGGGATGAAATTGA-AATATTCAAAAGCTTAAGGACTAATTTAAAGA-GAGA
* *
209841 ATCATAGTTTAGGGGTGAAGTTGAAATATTCAAAAGCTTAAGGACTAATTTAAAGAGAGA
1 ATCATAGTTTAGGGATGAAATTGAAATATTCAAAAGCTTAAGGACTAATTTAAAGAGAGA
*
209901 ATTATAGTTT
1 ATCATAGTTT
209911 GAGGACATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 58 0.97
61 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (60 bp):
ATCATAGTTTAGGGATGAAATTGAAATATTCAAAAGCTTAAGGACTAATTTAAAGAGAGA
Found at i:224467 original size:24 final size:24
Alignment explanation
Indices: 224438--224491 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
224428 CAGATTCCTG
224438 CCAGCAGTAGTAGCCAAGATGCTA
1 CCAGCAGTAGTAGCCAAGATGCTA
*
224462 CTAGCAGTAGTAGCCAAGATGCTA
1 CCAGCAGTAGTAGCCAAGATGCTA
224486 CCAGCA
1 CCAGCA
224492 AGAACAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (24 bp):
CCAGCAGTAGTAGCCAAGATGCTA
Found at i:230624 original size:21 final size:21
Alignment explanation
Indices: 230598--230640 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
230588 TTGTTGACTT
*
230598 TGACTGAGTAAACCCTTTGAC
1 TGACTGAGTAAACCCGTTGAC
230619 TGACTGAGTAAACCCGTTGAC
1 TGACTGAGTAAACCCGTTGAC
230640 T
1 T
230641 TTGACCGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
TGACTGAGTAAACCCGTTGAC
Found at i:232726 original size:97 final size:96
Alignment explanation
Indices: 232584--232777 Score: 228
Period size: 97 Copynumber: 2.0 Consensus size: 96
232574 GATTTACTAG
* * * *
232584 TTTATGAACTATGGTTACTTGAAACATGTTCTCTAGTTACATGTTTTCACTATAAAATATGATCG
1 TTTATGAACTATGGTTACCTGAAACATGTTATCGAGTTACATGTTTTCACTAGAAAATATGATCG
* * *
232649 TTCCTTATTTATGGATCTTGGAACCTACTGGT
66 TTCCTGA-TTATGGATCATGAAACCTACTGGT
* * * * * * *
232681 TTTATGAACTATGGTTACCTGAAATGA-GTTATCGGGTTTCCTGTTTTCACTGGAAAATATTATT
1 TTTATGAACTATGGTTACCTGAAA-CATGTTATCGAGTTACATGTTTTCACTAGAAAATATGATC
*
232745 GTTCCTGATTATGGATCATGAAATCTACTGGT
65 GTTCCTGATTATGGATCATGAAACCTACTGGT
232777 T
1 T
232778 ACTACTAGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
96 22 0.27
97 58 0.72
98 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (96 bp):
TTTATGAACTATGGTTACCTGAAACATGTTATCGAGTTACATGTTTTCACTAGAAAATATGATCG
TTCCTGATTATGGATCATGAAACCTACTGGT
Found at i:232866 original size:18 final size:18
Alignment explanation
Indices: 232843--232883 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
232833 CAGCTCTGAT
232843 CAAGCTGGTAAATCCTTA
1 CAAGCTGGTAAATCCTTA
232861 CAAGCTGGTAAATCCTTA
1 CAAGCTGGTAAATCCTTA
232879 CAAGC
1 CAAGC
232884 CTAAGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (18 bp):
CAAGCTGGTAAATCCTTA
Found at i:239430 original size:23 final size:22
Alignment explanation
Indices: 239403--239481 Score: 79
Period size: 23 Copynumber: 3.6 Consensus size: 22
239393 GCATGACCCT
239403 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
239425 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* * *
239447 GTGTATCAATGCTCATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
239469 ATGCATCGATGCA
1 GTGCATCGATGCA
239482 TTGTTAGGTG
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
21 13 0.31
22 13 0.31
23 16 0.38
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:245011 original size:10 final size:11
Alignment explanation
Indices: 244996--245051 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 11
244986 GATTGATGTT
244996 TTCTCT-TTGA
1 TTCTCTCTTGA
245006 TTCTCTCTTGA
1 TTCTCTCTTGA
*
245017 TTCT-TGTTGA
1 TTCTCTCTTGA
245027 TTCTCTCTTGA
1 TTCTCTCTTGA
*
245038 TTCT-TGTTGA
1 TTCTCTCTTGA
245048 TTCT
1 TTCT
245052 TGTTTCTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
10 24 0.59
11 17 0.41
ACGTcount: A:0.09, C:0.20, G:0.12, T:0.59
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:245020 original size:21 final size:21
Alignment explanation
Indices: 245002--245051 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
244992 TGTTTTCTCT
245002 TTGATTCTCTCTTGATTCTTG
1 TTGATTCTCTCTTGATTCTTG
245023 TTGATTCTCTCTTGATTCTTG
1 TTGATTCTCTCTTGATTCTTG
245044 TTGATTCT
1 TTGATTCT
245052 TGTTTCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (21 bp):
TTGATTCTCTCTTGATTCTTG
Found at i:245048 original size:31 final size:31
Alignment explanation
Indices: 244996--245055 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
244986 GATTGATGTT
244996 TTCTCTTTGATTCTCTCTTGATTCTTGTTGA
1 TTCTCTTTGATTCTCTCTTGATTCTTGTTGA
*
245027 TTCTCTCTTGATTCT-TGTTGATTCTTGTT
1 TTCTCT-TTGATTCTCTCTTGATTCTTGTT
245056 TCTTGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.08, C:0.18, G:0.13, T:0.60
Consensus pattern (31 bp):
TTCTCTTTGATTCTCTCTTGATTCTTGTTGA
Found at i:245353 original size:20 final size:20
Alignment explanation
Indices: 245328--245407 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
245318 AAAAGCCTGA
*
245328 GTGCATCGATGCATGGTCTT
1 GTGCATCAATGCATGGTCTT
* *
245348 GTGCATCAATGCATCAAATGCTCTGA
1 GTGCATCAATG---C--ATGGTCT-T
*
245374 GTGCATCGATGCATGGTCTT
1 GTGCATCAATGCATGGTCTT
245394 GTGCATCAATGCAT
1 GTGCATCAATGCAT
245408 CAAATGCTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 23 0.49
21 6 0.13
23 2 0.04
25 6 0.13
26 10 0.21
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
GTGCATCAATGCATGGTCTT
Found at i:245379 original size:26 final size:26
Alignment explanation
Indices: 245348--245433 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
245338 GCATGGTCTT
245348 GTGCATCAATGCATCAAATGCTCTGA
1 GTGCATCAATGCATCAAATGCTCTGA
* * *
245374 GTGCATCGATG---C--ATGGTCT-T
1 GTGCATCAATGCATCAAATGCTCTGA
245394 GTGCATCAATGCATCAAATGCTCTGA
1 GTGCATCAATGCATCAAATGCTCTGA
*
245420 GTGCATCGATGCAT
1 GTGCATCAATGCAT
245434 GGTATGTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 10 0.21
21 6 0.13
23 2 0.04
25 6 0.13
26 23 0.49
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (26 bp):
GTGCATCAATGCATCAAATGCTCTGA
Found at i:245383 original size:46 final size:46
Alignment explanation
Indices: 245324--245459 Score: 229
Period size: 46 Copynumber: 3.0 Consensus size: 46
245314 TTGAAAAAGC
245324 CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCT
1 CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCT
245370 CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCT
1 CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCT
* ** *
245416 CTGAGTGCATCGATGCATGGT-ATGTGCATTGATGCATAAAATGC
1 CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGC
245460 ATTCGATGTT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 19 0.22
46 67 0.78
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCT
Found at i:253094 original size:20 final size:21
Alignment explanation
Indices: 253064--253102 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
253054 CAGAACCCCA
253064 GGGGGGTATCGATTCCCTCAT
1 GGGGGGTATCGATTCCCTCAT
253085 GGGGGG-ATCGATTCCCTC
1 GGGGGGTATCGATTCCCTC
253103 TGCACCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.13, C:0.26, G:0.36, T:0.26
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCTCAT
Found at i:262362 original size:85 final size:85
Alignment explanation
Indices: 262213--262378 Score: 199
Period size: 85 Copynumber: 2.0 Consensus size: 85
262203 ATACAATCAC
* * * * * * **
262213 GACACACGAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGCAATGTATGTCATA
1 GACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGAACATCATA
* **
262278 CATGCGTGTCATAAATTTAT
66 AATGCGCATCATAAATTTAT
* *
262298 GACACACAAATGTGTGTTATCTTAATTT-ATGACGGGGGCTTCAATGACACTCAATGAACATCAT
1 GACACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGAACATCAT
262362 AAATGCGCATCATAAAT
65 AAATGCGCATCATAAAT
262379 GTGTGTCATA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
85 64 0.96
86 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGAACATCATA
AATGCGCATCATAAATTTAT
Found at i:262397 original size:13 final size:13
Alignment explanation
Indices: 262358--262401 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
262348 TCAATGAACA
**
262358 TCATAAATGCGCA
1 TCATAAATGCGTG
*
262371 TCATAAATGTGTG
1 TCATAAATGCGTG
262384 TCATAAATGCGTG
1 TCATAAATGCGTG
262397 TCATA
1 TCATA
262402 GATTTATGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:262813 original size:25 final size:25
Alignment explanation
Indices: 262785--262832 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
262775 ATAAGCATGT
* *
262785 CATTTCATTTATTTCATTTACATTG
1 CATTCCATTTATTTCAGTTACATTG
*
262810 CATTCCATTTATTTTAGTTACAT
1 CATTCCATTTATTTCAGTTACAT
262833 ATTATATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (25 bp):
CATTCCATTTATTTCAGTTACATTG
Found at i:263263 original size:48 final size:47
Alignment explanation
Indices: 263202--263364 Score: 186
Period size: 48 Copynumber: 3.4 Consensus size: 47
263192 ATGGTCATCA
* *
263202 TTAAAGGACATGACTTTTCATACAACATGAAGGGATATAACTCAAAGC
1 TTAAA-GAGATGACTTTTCATACAACATGAAGGGACATAACTCAAAGC
* * * *
263250 TATAAATAGATGACTTTTAATACAACATGAAGAGACATAACTC-TAGCC
1 T-TAAAGAGATGACTTTTCATACAACATGAAGGGACATAACTCAAAG-C
* *
263298 TTAAAAGAGATGACTTTTCATA-ACACATGAAGGGACACAACTCAAACC
1 TT-AAAGAGATGACTTTTCATACA-ACATGAAGGGACATAACTCAAAGC
*
263346 TTAAAGACATGACTTTTCA
1 TTAAAGAGATGACTTTTCA
263365 AGAAGGAATG
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
47 20 0.21
48 72 0.74
49 5 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (47 bp):
TTAAAGAGATGACTTTTCATACAACATGAAGGGACATAACTCAAAGC
Found at i:264133 original size:15 final size:16
Alignment explanation
Indices: 264113--264143 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
264103 AATTGTGCCA
264113 AAAAAAAAG-AAAAAG
1 AAAAAAAAGTAAAAAG
264128 AAAAAAAAGTAAAAAG
1 AAAAAAAAGTAAAAAG
264144 CAAGGCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGTAAAAAG
Found at i:266313 original size:25 final size:25
Alignment explanation
Indices: 266248--266314 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 25
266238 TTTGATTTAC
*
266248 TAAAATATTAATAAATTTGAATAGT
1 TAAAATATTAATATATTTGAATAGT
* **
266273 TAAAATTATTTTATATATTT-AATCTT
1 TAAAA-TA-TTAATATATTTGAATAGT
266299 TAAAATATTAA-ATATT
1 TAAAATATTAATATATT
266315 AATAATTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 5 0.14
24 3 0.09
25 7 0.20
26 11 0.31
27 9 0.26
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (25 bp):
TAAAATATTAATATATTTGAATAGT
Found at i:271491 original size:15 final size:15
Alignment explanation
Indices: 271471--271558 Score: 63
Period size: 15 Copynumber: 5.8 Consensus size: 15
271461 CATTTTACTT
271471 AAATTATTATTATTA
1 AAATTATTATTATTA
271486 AAATTATTATTATTA
1 AAATTATTATTATTA
** * *
271501 TTATTATAAATATTA
1 AAATTATTATTATTA
**
271516 TTATTA-TATTATATA
1 AAATTATTATTAT-TA
* *
271531 TATTATATTATTATT-
1 AAAT-TATTATTATTA
271546 AAATATATTATTA
1 AAAT-TATTATTA
271559 CAAGCCCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
14 4 0.07
15 47 0.78
16 3 0.05
17 6 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:271493 original size:12 final size:12
Alignment explanation
Indices: 271476--271558 Score: 64
Period size: 12 Copynumber: 6.8 Consensus size: 12
271466 TACTTAAATT
271476 ATTATTATTAAA
1 ATTATTATTAAA
**
271488 ATTATTATTATT
1 ATTATTATTAAA
271500 ATTATTA-TAAA
1 ATTATTATTAAA
*
271511 TATTATTATT-AT
1 -ATTATTATTAAA
* *
271523 ATTATATATATTAT
1 ATTAT-TAT-TAAA
271537 ATTATTATT-AA
1 ATTATTATTAAA
271548 ATATATTATTA
1 AT-TATTATTA
271559 CAAGCCCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
11 10 0.17
12 36 0.62
13 5 0.09
14 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:271558 original size:3 final size:3
Alignment explanation
Indices: 271473--271546 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
271463 TTTTACTTAA
** * *
271473 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
271521 A-T ATT A-T ATAT ATT A-T ATT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
271547 AATATATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 6 0.10
3 50 0.85
4 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:271996 original size:5 final size:5
Alignment explanation
Indices: 271988--272044 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
271978 AACAAAAGAA
* *
271988 AAAAG AAAAG AAAA- AAAA- AACAG AAAGAG AGAAG AAAA- AAAACG -AAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG AAAA-G AAAAG
272036 AAAAG AAAA
1 AAAAG AAAA
272045 ACTACCAACG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 12 0.28
5 27 0.63
6 4 0.09
ACGTcount: A:0.79, C:0.04, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:271996 original size:12 final size:12
Alignment explanation
Indices: 271975--272027 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
271965 GAGAGCAGAG
*
271975 AAAAACAAAAGA
1 AAAAAGAAAAGA
271987 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
271999 AAAAA-AAAACA
1 AAAAAGAAAAGA
* *
272010 GAAAGAGAGAAGA
1 -AAAAAGAAAAGA
272023 AAAAA
1 AAAAA
272028 AACGAAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 5 0.15
12 24 0.73
13 4 0.12
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:272014 original size:29 final size:27
Alignment explanation
Indices: 271975--272029 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
271965 GAGAGCAGAG
271975 AAAAACAAAAGAAAAAAGAAAAGAAAAA
1 AAAAACAAAAGAAAAAAGAAAA-AAAAA
* *
272003 AAAAACAGAAAGAGAGAAGAAAAAAAA
1 AAAAACA-AAAGAAAAAAGAAAAAAAA
272030 CGAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.82, C:0.04, G:0.15, T:0.00
Consensus pattern (27 bp):
AAAAACAAAAGAAAAAAGAAAAAAAAA
Found at i:272022 original size:24 final size:24
Alignment explanation
Indices: 271958--272041 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 24
271948 ACCAAGATAC
* *
271958 AGAAACAGAGAGCAGAGAAAAACAAA
1 AGAAA-AGAGAGAAGA-AAAAAAAAA
* *
271984 AGAAAAAAGAAAAGAAAAAAAAAA
1 AGAAAAGAGAGAAGAAAAAAAAAA
272008 CAG-AAAGAGAGAAGAAAAAAAACGAA
1 -AGAAAAGAGAGAAGAAAAAAAA--AA
272034 AGAAAAGA
1 AGAAAAGA
272042 AAAACTACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 25 0.52
25 11 0.23
26 12 0.25
ACGTcount: A:0.74, C:0.06, G:0.20, T:0.00
Consensus pattern (24 bp):
AGAAAAGAGAGAAGAAAAAAAAAA
Found at i:272920 original size:22 final size:21
Alignment explanation
Indices: 272895--272947 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
272885 TTTTATTACT
* *
272895 TTTTATATTTAGTTTTAATTTA
1 TTTTA-ATTTAGTTTAAATATA
272917 TTTTAATTATAGTTTAAATATA
1 TTTTAATT-TAGTTTAAATATA
272939 TTTTAATTT
1 TTTTAATTT
272948 TATATGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTAATTTAGTTTAAATATA
Found at i:272932 original size:11 final size:11
Alignment explanation
Indices: 272907--272992 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
272897 TTATATTTAG
272907 TTTTAATT-TA
1 TTTTAATTATA
272917 TTTTAATTATA
1 TTTTAATTATA
* *
272928 GTTTAAATATA
1 TTTTAATTATA
272939 TTTTAATTTTATA
1 TTTTAA--TTATA
272952 TGTTT-A--ATA
1 T-TTTAATTATA
272961 TTTTAATTAGTA
1 TTTTAATTA-TA
*
272973 TTATT-ATTTTA
1 TT-TTAATTATA
*
272984 TTTTTATTA
1 TTTTAATTA
272993 ATATATATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
10 10 0.17
11 24 0.40
12 7 0.12
13 8 0.13
14 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
TTTTAATTATA
Found at i:272992 original size:23 final size:24
Alignment explanation
Indices: 272959--273004 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
272949 ATATGTTTAA
*
272959 TATTTTAATTAGTAT-TATTATTT
1 TATTTTAATTAATATATATTATTT
*
272982 TATTTTTATTAATATATATTATT
1 TATTTTAATTAATATATATTATT
273005 GATTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTTTAATTAATATATATTATTT
Found at i:273013 original size:27 final size:25
Alignment explanation
Indices: 272941--273025 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 25
272931 TAAATATATT
*
272941 TTAATTTTA-TATGTTTAATATTTTAA
1 TTAATATTATTAT-TTTAAT-TTTTAA
*
272967 TTAGTATTATTATTTT-ATTTTT-A
1 TTAATATTATTATTTTAATTTTTAA
272990 TTAATATATATTATTGATTAATTTTATAAA
1 TTAATAT-TATTATT--TTAATTTT-T-AA
273020 TTAATA
1 TTAATA
273026 ATGTTTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 7 0.15
24 11 0.23
25 2 0.04
26 12 0.25
27 8 0.17
28 1 0.02
30 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TTAATATTATTATTTTAATTTTTAA
Found at i:273400 original size:125 final size:124
Alignment explanation
Indices: 273162--273388 Score: 357
Period size: 125 Copynumber: 1.8 Consensus size: 124
273152 ACATTTTTAG
* *
273162 TTATTTATTTATCAATATCAAAGAAAAGAGTTGTCTTAAGGCACCTAGAAGCCATTTCTGATATT
1 TTATTTATTTATCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTCTGATATT
**
273227 TTTAAATAAATAAATATCTTATTAAAATAAATTTTTATTTTAAGAAAATCTTTTGGTTAT
66 TTTAAATAAATAAATATCTTATT-AAATAAATTAATATTTTAAGAAAATCTTTTGGTTAT
*
273287 TTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTTCTGATAT
1 TTATTTATTTATCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCA-TTTCTGATAT
* * *
273352 TTTTAAATAAGTAAATATCTTATT-TATATATTAATAT
65 TTTTAAATAAATAAATATCTTATTAAATAAATTAATAT
273389 ATTTCTTAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
124 9 0.10
125 51 0.55
126 33 0.35
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (124 bp):
TTATTTATTTATCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTCTGATATT
TTTAAATAAATAAATATCTTATTAAATAAATTAATATTTTAAGAAAATCTTTTGGTTAT
Found at i:289871 original size:16 final size:16
Alignment explanation
Indices: 289845--289882 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
289835 TCTACTAAAG
289845 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
289862 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
289878 CATGT
1 CATGT
289883 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:299551 original size:7 final size:7
Alignment explanation
Indices: 299497--299543 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
299487 AAAATGAGTG
299497 AAAATGA
1 AAAATGA
299504 AAAATGAA
1 AAAATG-A
**
299512 AAAAAAA
1 AAAATGA
*
299519 AAAAAGA
1 AAAATGA
299526 AAAATGA
1 AAAATGA
299533 AAAATGA
1 AAAATGA
299540 AAAA
1 AAAA
299544 ATGGAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.09
Consensus pattern (7 bp):
AAAATGA
Found at i:299551 original size:22 final size:22
Alignment explanation
Indices: 299497--299552 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
299487 AAAATGAGTG
299497 AAAATGAAAAATGAAAAAAAAA
1 AAAATGAAAAATGAAAAAAAAA
* **
299519 AAAAAGAAAAATGAAAAATGAA
1 AAAATGAAAAATGAAAAAAAAA
299541 AAAATGGAAAAA
1 AAAAT-GAAAAA
299553 AAGAAGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (22 bp):
AAAATGAAAAATGAAAAAAAAA
Found at i:300641 original size:55 final size:55
Alignment explanation
Indices: 300467--300698 Score: 303
Period size: 55 Copynumber: 4.3 Consensus size: 55
300457 CCCAACATTA
*
300467 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACGCAATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG
* * * * *
300522 ATGAAGATTG-T-GGGTCTTATACTCTCTGAAG-AATAGGGGGCAGAC-TAATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG
* * * * *
300573 TTGAAGATCGTTCGAGTCTTATACTCTCTGGAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG
* *
300628 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG
*
300683 TTGAAGA-TATTCGAGT
1 TTGAAGATTGTTCGAGT
300699 TCTATTCTCC
Statistics
Matches: 155, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
51 13 0.08
52 13 0.08
53 36 0.23
54 23 0.15
55 70 0.45
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG
Found at i:300723 original size:54 final size:54
Alignment explanation
Indices: 300467--300930 Score: 321
Period size: 54 Copynumber: 8.6 Consensus size: 54
300457 CCCAACATTA
* * * * * *
300467 TTGAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAAACGCAATTG
1 TTGAAGA-TATTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTG
* * * **
300522 ATGAAGAT-TGT-G-GGTCTTATACTCTCTGAAGAATAG-GGG-GCAGA-CTAATTG
1 TTGAAGATAT-TCGAGTTC-TATACTCCCTGAAGAA-AGAGGGAGCAGACCCGATTG
* * * * * *
300573 TTGAAGATCGTTCGAG-TCTTATACTCTCTGGAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGAT-ATTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTG
* * * *
300628 TTGAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGA-TATTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTG
* * *
300683 TTGAAGATATTCGAGTTCTATTCTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTG
1 TTGAAGATATTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAGACCCGATTG
** * *
300737 AAGAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGC-GAACCCGTTTG
1 TTGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAG-ACCCGATTG
** *
300791 AAGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GAACC-AGTTAG
1 TTGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGA-TT-G
** * * *
300845 CAGAAGAT-TCTTGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGGACCCG-TTAG
1 TTGAAGATAT-TCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCAGACCCGATT-G
**
300899 CAGAAGATTATTCGAGTTCTATACTCCCTGAA
1 TTGAAGA-TATTCGAGTTCTATACTCCCTGAA
300931 ACAATAGGGA
Statistics
Matches: 352, Mismatches: 32, Indels: 50
0.81 0.07 0.12
Matches are distributed among these distances:
51 12 0.03
52 7 0.02
53 53 0.15
54 184 0.52
55 94 0.27
56 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (54 bp):
TTGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTG
Found at i:300933 original size:55 final size:54
Alignment explanation
Indices: 300630--301004 Score: 368
Period size: 54 Copynumber: 6.9 Consensus size: 54
300620 CGCGATTGTT
* * * **
300630 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATT-GTT
1 GAAGATTATTCGAGTTCT-ATACTCCCTGAA-AAATAGGGAGCGA-ACCCG-TTAGCA
* * * * * *
300685 GAAGA-TATTCGAGTTCTATTCTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAA
1 GAAGATTATTCGAGTTCTATACTCCCT-GAAAAATAGGGAGCGAACCCGTTAGCA
* * * *
300739 GAAGA-TATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGATTATTCGAGTTCTATACTCCCTGAA-AAATAGGGAGCGAACCCGTTAGCA
* *
300793 GAAGA-TATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAA-AAATAGGGAGCGAACCCGTTAGCA
* *
300847 GAAGATTCTT-GAGTTCTATACTCCCTGAAACAATAGGGAGCGGACCCGTTAGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAA-AATAGGGAGCGAACCCGTTAGCA
***
300901 GAAGATTATTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCGTCCCCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAA-AATAGGGAGCGAACCCGTTAGCA
* * ** *
300956 GAAGATTCTTCAAGTTCTATGTTCCCTGAAACGATAGGGAGCGAACCCG
1 GAAGATTATTCGAGTTCTATACTCCCTGAAA-AATAGGGAGCGAACCCG
301005 ATTTTGAAGA
Statistics
Matches: 284, Mismatches: 28, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
53 5 0.02
54 181 0.64
55 98 0.35
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (54 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAAAAATAGGGAGCGAACCCGTTAGCA
Found at i:301287 original size:8 final size:8
Alignment explanation
Indices: 301271--301304 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
301261 TACGGATAAG
301271 TAATTAAA
1 TAATTAAA
*
301279 TAGTTAAA
1 TAATTAAA
301287 TAATTAAA
1 TAATTAAA
301295 TAATTAAA
1 TAATTAAA
301303 TA
1 TA
301305 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Done.