Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007910.1 Hibiscus syriacus cultivar Beakdansim tig00110306_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: 704475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:397280 original size:17 final size:15
Alignment explanation
Indices: 397258--397310 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
397248 TACTTCTCCT
397258 GAAAAAAATGTAAAAAA
1 GAAAAAAA-GT-AAAAA
397275 GAAAAAAAG-AAAAA
1 GAAAAAAAGTAAAAA
*
397289 GAAAGAAAAAATAAAAA
1 G-AA-AAAAAGTAAAAA
397306 GAAAA
1 GAAAA
397311 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 6 0.19
15 4 0.12
16 8 0.25
17 14 0.44
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (15 bp):
GAAAAAAAGTAAAAA
Found at i:397287 original size:14 final size:15
Alignment explanation
Indices: 397270--397315 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
397260 AAAAAATGTA
397270 AAAAAGAAA-AAAAG
1 AAAAAGAAAGAAAAG
397284 AAAAAGAAAGAAAA-
1 AAAAAGAAAGAAAAG
* *
397298 AATAA-AAAGAAAAT
1 AAAAAGAAAGAAAAG
397312 AAAA
1 AAAA
397316 TAAATAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 8 0.29
14 16 0.57
15 4 0.14
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:397315 original size:17 final size:17
Alignment explanation
Indices: 397272--397319 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
397262 AAAATGTAAA
*
397272 AAAGAAAAAAAGAAAAAG
1 AAAG-AAAAAATAAAAAG
397290 AAAGAAAAAATAAAAAG
1 AAAGAAAAAATAAAAAG
*
397307 AAA-ATAAAATAAA
1 AAAGAAAAAATAAA
397320 TAAAAGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 15 0.54
18 4 0.14
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.06
Consensus pattern (17 bp):
AAAGAAAAAATAAAAAG
Found at i:398867 original size:135 final size:133
Alignment explanation
Indices: 398631--398876 Score: 336
Period size: 135 Copynumber: 1.8 Consensus size: 133
398621 GATTCAATCG
* * *
398631 GATCTGATTTACCCTGAAGAAGCAGCAGAGAAGATTCCCTTTTCCATATTTGATATTCCCTAAAG
1 GATCTGATCTACCCTGAAGAAGCAGCAGAGAACATTCCCTTTTCCAAATTTGATATTCCCTAAAG
398696 AAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACATTAGAATAAAGCAACATTT
66 AAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACATTAGAATAAAGCAACATTT
398761 CCA
131 CCA
*
398764 GATCTGATCTACCCTGAAGAAGCAGC-G-GAACATATCCCTCTTTTCTCTAAATTTGATCTTCCC
1 GATCTGATCTACCCTGAAGAAGCAGCAGAGAACAT-T-CC-CTTTTC-C-AAATTTGATATTCCC
* * * * * *
398827 TGAGGAA-CATTGGAACAAATCTACCTTGATTCAATTTTCCCTGAAGAACA
61 TAAAGAAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACA
398877 GTGGATTGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
131 5 0.05
132 2 0.02
133 27 0.28
134 6 0.06
135 40 0.41
136 18 0.18
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (133 bp):
GATCTGATCTACCCTGAAGAAGCAGCAGAGAACATTCCCTTTTCCAAATTTGATATTCCCTAAAG
AAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACATTAGAATAAAGCAACATTT
CCA
Found at i:398912 original size:135 final size:132
Alignment explanation
Indices: 398631--398935 Score: 319
Period size: 135 Copynumber: 2.3 Consensus size: 132
398621 GATTCAATCG
* *
398631 GATCTGATTTACCCTGAAGAAGCAGCAGAGAAGAT-T-CCCTTTTCCATATTTGATATTCCCTAA
1 GATCTGA-TTACCCTGAAGAAGCAGC-G-GAACATATCCCCTTTTCCAAATTTGATATTCCCTAA
*
398694 AGAAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACATTAGAATAAAGCAACAT
63 AGAAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACAGTAGAATAAAGCAACAT
*
398759 TTCCA
128 TCCCA
* *
398764 GATCTGATCTACCCTGAAGAAGCAGCGGAACATATCCCTCTTTTCTCTAAATTTGATCTTCCCTG
1 GATCTGAT-TACCCTGAAGAAGCAGCGGAACATATCCC-CTTTTC-C-AAATTTGATATTCCCTA
* * * * * * * * * *
398829 AGGAA-CATTGGAACAAATCTACCTTGATTCAATTTTCCCTGAAGAACAGTGGATTGAATCAATA
62 AAGAAGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACAGTAGAATAAAGCAACA
*
398893 TTCCCT
127 TTCCCA
* * * * *
398899 TATCTGACTTACCCTAAAAAAGCAGTGGAGCATATCC
1 GATCTGA-TTACCCTGAAGAAGCAGCGGAACATATCC
398936 TTTTTCAGAT
Statistics
Matches: 143, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
131 5 0.03
132 3 0.02
133 26 0.18
134 6 0.04
135 84 0.59
136 19 0.13
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (132 bp):
GATCTGATTACCCTGAAGAAGCAGCGGAACATATCCCCTTTTCCAAATTTGATATTCCCTAAAGA
AGCAGTGGAACAAATCTACCTAGATTCAATCTTCCCAGAAGAACAGTAGAATAAAGCAACATTCC
CA
Found at i:399137 original size:3 final size:3
Alignment explanation
Indices: 399129--399250 Score: 165
Period size: 3 Copynumber: 40.3 Consensus size: 3
399119 TCCGGATAAC
399129 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
399177 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATC ATT ATT AAT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
399225 ATT ATT ATT ATTT ATTT ATT -TT ATT A
1 ATT ATT ATT A-TT A-TT ATT ATT ATT A
399251 ATTTATTTTC
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
2 2 0.02
3 103 0.92
4 7 0.06
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:399248 original size:13 final size:13
Alignment explanation
Indices: 399226--399259 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
399216 ATTAATAGTA
*
399226 TTATTATTATTTAT
1 TTATT-TTATTAAT
399240 TTATTTTATTAAT
1 TTATTTTATTAAT
399253 TTATTTT
1 TTATTTT
399260 CAGGTTACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATTAAT
Found at i:401709 original size:131 final size:131
Alignment explanation
Indices: 401452--401700 Score: 329
Period size: 131 Copynumber: 1.9 Consensus size: 131
401442 AATTACACTT
* * * *
401452 GGATTAATATTTAATTTTAGGATGAAATAGTAATATCACTTCATTTCGATTGGAGTAATAAAAGA
1 GGATTAATATTTAATTTTAGAAGGAAATAGTAATATCACTTCATTTCGATTGAAGTAAGAAAAGA
* * * * *
401517 TTGCTTTAGGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCT
66 CTGCTTTAAGGAATGAGAGGTCATTTATTCTCGATTAGAAATAATTAAATATTATCGTTTTCTCT
401582 C
131 C
** * * *
401583 GGATTAATATTTAATTTTAGAAGGAAATAGTAATATTTCTTTATTTTGATTGAAGTAAGAAATGA
1 GGATTAATATTTAATTTTAGAAGGAAATAGTAATATCACTTCATTTCGATTGAAGTAAGAAAAGA
** *
401648 CTGCTTTAAGGAATGAGAGGTTGTTTCTTCTCGA-TAGAAGATAATTAAATATT
66 CTGCTTTAAGGAATGAGAGGTCATTTATTCTCGATTAGAA-ATAATTAAATATT
401701 TCCTTTTTCC
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
130 4 0.04
131 96 0.96
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (131 bp):
GGATTAATATTTAATTTTAGAAGGAAATAGTAATATCACTTCATTTCGATTGAAGTAAGAAAAGA
CTGCTTTAAGGAATGAGAGGTCATTTATTCTCGATTAGAAATAATTAAATATTATCGTTTTCTCT
C
Found at i:406221 original size:819 final size:815
Alignment explanation
Indices: 404376--406821 Score: 3423
Period size: 819 Copynumber: 3.0 Consensus size: 815
404366 TGAACATTGT
* * * *
404376 AGAAAA-GACAAAAACAACCTAATTGAGATGAAAATTGTAGAAACTCAAGTAACAATATA-AAAA
1 AGAAAAGGACAAAAACAACCTAATTGATATGAACATTGTACAAACTCAAGTAACAACA-AGAAAA
* * * *
404439 CATATACAATTTTGTTAGTATCTTGATAGAGTAGGCGTTGAATGACGTCTTTCATCTCTTTTCTT
65 CATATACAA-TTT-TTAGTATCTTGATAGAGGAGGAGTTGAACGACGTCTTTCACCTCTTTTCTT
* * * * * * * *
404504 ATTTCCCGGCTGCTTTTTACCTCATGAAAAGTATCTTGAAAGAGGAGGTATTGAACGGCGTTGTT
128 CTTTCCCCGTTGCTTTTTACCTCATGAAAAGTATCTTGATAGAGAAGGCATTGAACGGTGTCGTT
** * * * * *
404569 ACGACCCATATTACAGTCTCTAAGGACGGTGAAGATCTCTCAGTCCATTCAGCTATTATTAAAAA
193 ACGGTCCATATTACAGTCTCTAAGGACGGCGAAGATCTCTCAGTCCGTGCAACTATTATTAACAA
* * * * * * * * *
404634 TCTCTTCAAGATTCA-CTAAAGACTGTAATATGGACCTTAGAGACGCCATTCAACGCCTCCTCAC
258 TCTCTTTAAGGTTCATCT-AAGACTGTAATATGGACCCTAGCGACACCTTTCTACGCTTCCTCTC
* * * *
404698 TCAAGATACTTTTCAAGAGGT------AAA-AA-AAAGACTCAAAGAATAAAATAGATGAAAAGA
322 CCAAGATACTTTTCAAGAGGTAAAAAGAAACAAGAAAGACTCAAAGAAGAAAAGAAATGAAAAGA
* * * * *
404755 AAAGGAACTAAAGTA-CTTTTTTATTGAACAAATTA-CTTTAATAAATTAGAAGCAAACTTGGGT
387 AAAGGAACTAATGTATTTTTTTTATTGAACAACTTACCTTTAATGAATTACAAGCAAACTTGGGT
* *
404818 ATTTTATATCCCAAATATAATTACCCAAAACATAAATAACTAGAGATATTTTTTAACTTGAATGT
452 ATTTTATAGCCCAAATATAATTACCCAAAACATAAATAATTAGAGATATTTTTTAACTT-AATGT
* * * *
404883 GATTGATTAAAACATAAACGATGTACATCAAATCTCATATGGCACATCTCTTGCACTCCCACTTT
516 GATTGATTAAAACATAAACGATGTACATCAAATCCCATATGCCACATCTCTAGCACTCCAACTTT
* * * * *
404948 TATCTTTCTAATTTACCTTTCTAACTTCTCTTAGCCA-ATTTTAATCCTTATTCAAATTTCAAAT
581 CATCTTTCTAATTTAGCTTTCAAACTTTTTTTAG-CATATTTTAATCCTTATTCAAATTTCAAA-
* ** * *
405012 CAGAACATATTCGATTAAAACTAGTTTTTTTTACGATATTCATTTTCATAATTTAATCCTTCAAA
644 CAGAACATATTCGATTCAAACTAGTTCCTTTTAAGAAATTCATTTTCATAATTTAATCCTTC-AA
*
405077 AAATTAATTTTTGATCATCATACGTCACAAAAATTCTAAACCAAATTTCTGAGTGTTAAAAAAAG
708 AAATTATTTTTTGATCATCATACGTCACAAAAATTCTAAACCAAATTTCTGAGTGTTAAAAAAAG
* *
405142 GTCATCTTACATCAACTATGATTCCATCTTATATGGATATAAA
773 ATCATCTTACATCAACTAGGATTCCATCTTATATGGATATAAA
405185 AGAAAAGGA-AAAAACAACCTAATTGATATGAACATTGTACAAACTCAAGTAACAACAAGAAAAC
1 AGAAAAGGACAAAAACAACCTAATTGATATGAACATTGTACAAACTCAAGTAACAACAAGAAAAC
* *
405249 ATATACAATTGTGTTAGTATCTTGATAGAGGAGGCA-TTGAACGGCGTATTTCACCTCTTTTCTT
66 ATATACAATT-T-TTAGTATCTTGATAGAGGAGG-AGTTGAACGACGTCTTTCACCTCTTTTCTT
* * * * * *
405313 CATT-CCCGCTTGGTTTTTACCACATGAAAAGTTTCTTGATAGA-AGAGGCATTGAATGGTTTCG
128 CTTTCCCCG-TTGCTTTTTACCTCATGAAAAGTATCTTGATAGAGA-AGGCATTGAACGGTGTCG
* *
405376 CTACGGTCCATATTACAGTCTCTAAGGACAAG-GAAGATCTCTCAGTCCGTGCAACTATTATTAA
191 TTACGGTCCATATTACAGTCTCTAAGGAC-GGCGAAGATCTCTCAGTCCGTGCAACTATTATTAA
405440 CAATCTCTTTAAGGTTCATCTAAGACTGTAATATGGACCCTAGCGACACCTTTCTACGCTTCCTC
255 CAATCTCTTTAAGGTTCATCTAAGACTGTAATATGGACCCTAGCGACACCTTTCTACGCTTCCTC
*
405505 TCCCAAGATATTTTTCAAGAGGTAAAAAGCAAACAAGAAAGACTCAAAGAAGAAAAGAAATGAAA
320 TCCCAAGATACTTTTCAAGAGGTAAAAAG-AAACAAGAAAGACTCAAAGAAGAAAAGAAATGAAA
*
405570 AGAAAAGGAACTAATGTATTTTTTTTATTGAACAACTTACCTTTAATGAATTACAAACAAACTTG
384 AGAAAAGGAACTAATGTATTTTTTTTATTGAACAACTTACCTTTAATGAATTACAAGCAAACTTG
* * * *
405635 TGTATTTTATAGCTCAGATACAATTACCCAAAACATAAATAATTAGAGATATTTTTTAACATTAA
449 GGTATTTTATAGCCCAAATATAATTACCCAAAACATAAATAATTAGAGATATTTTTTAAC-TTAA
405700 TGTGATTGATTAAAACATAAACGATGTACATCAAATCCCATATGCCACATCTCTAGCACTCCAAC
513 TGTGATTGATTAAAACATAAACGATGTACATCAAATCCCATATGCCACATCTCTAGCACTCCAAC
* * * *
405765 TTTCATCTTTCTAGTTTAGCTTACAAACTTTTTTTAGCATATTTTAATCCTTACTCAAATATT-G
578 TTTCATCTTTCTAATTTAGCTTTCAAACTTTTTTTAGCATATTTTAATCCTTATTCAAAT-TTCA
* * * * *
405829 AACAATAACATATTGGACTCAAACTAGATTCCTTTTAAGAGATTCATTTGCATAATTTAATCCTT
642 AAC-AGAACATATTCGATTCAAACTAG-TTCCTTTTAAGAAATTCATTTTCATAATTTAATCCTT
* * * ** *
405894 CAAAAATTATTTTTTGATCATCATACATAAGAAAAATTCTAAACCAAATTTCAAAGTCTT-AAAA
705 CAAAAATTATTTTTTGATCATCATACGTCACAAAAATTCTAAACCAAATTTCTGAGTGTTAAAAA
* *
405958 AAGATCATCTTACATCAACTAGGATTCCCTCTTATATGGATATAAC
770 AAGATCATCTTACATCAACTAGGATTCCATCTTATATGGATATAAA
*
406004 A-AAAGGGACAAAAACAACCTAATTGATATGAACATTGTACAAACTCAAGTAACAACAAGAAAAC
1 AGAAAAGGACAAAAACAACCTAATTGATATGAACATTGTACAAACTCAAGTAACAACAAGAAAAC
406068 ATATACAATATTTCTAGTATCTTGATAGAGGAGGAGTTGAACGACGTCTTTCACCTCTTTTCTTC
66 ATATACAAT-TTT-TAGTATCTTGATAGAGGAGGAGTTGAACGACGTCTTTCACCTCTTTTCTTC
*
406133 TTTCCCCGTTGCTTTTAACCTCAAT-AAAAGTATCTTGATAGAGAAGGCATTGAACGGTGTCGTT
129 TTTCCCCGTTGCTTTTTACCTC-ATGAAAAGTATCTTGATAGAGAAGGCATTGAACGGTGTCGTT
*
406197 ACGGTCAATATTACAGTCTCTAAGGACGGCGAAGATCTCTCAGTCCGTGCAACTATTATTAACAA
193 ACGGTCCATATTACAGTCTCTAAGGACGGCGAAGATCTCTCAGTCCGTGCAACTATTATTAACAA
*
406262 TCTC-TTAAGGTTCATCTAAGACTGTAATATGGACCCTAGCGGCACCTTTCTACGCTTCCTCTCC
258 TCTCTTTAAGGTTCATCTAAGACTGTAATATGGACCCTAGCGACACCTTTCTACGCTTCCTCTCC
* *
406326 CAAGATACTTTTCAAGAGGTAAAAAGAAAACAAGAAAGACTCAAGGAAGAAAAGAAATGAAAATA
323 CAAGATACTTTTCAAGAGGTAAAAAG-AAACAAGAAAGACTCAAAGAAGAAAAGAAATGAAAAGA
406391 AAAGGAACTAATGTATTTTTTTTATTGAACAACTTACCTTTAATGAATTACAAGCAAACTTGGGT
387 AAAGGAACTAATGTATTTTTTTTATTGAACAACTTACCTTTAATGAATTACAAGCAAACTTGGGT
*
406456 ATTTTATAGCCCAAATATAATTACCCAAAACATAAATAATTAGAAATATTTTTTTAACTTTAATG
452 ATTTTATAGCCCAAATATAATTACCCAAAACATAAATAATTAGAGATA-TTTTTTAAC-TTAATG
* * * * *
406521 TAATTGATTAAAACATAAATGATGTACATCAAATCCCATAGGCCACATCTCGAGGACTCCAACTT
515 TGATTGATTAAAACATAAACGATGTACATCAAATCCCATATGCCACATCTCTAGCACTCCAACTT
* * *
406586 TCATCTTTCTAATATAGCTTTCAAAC-CTTTTTAGCCTATTTTAATCCTTATTCAAATTTCAAAT
580 TCATCTTTCTAATTTAGCTTTCAAACTTTTTTTAGCATATTTTAATCCTTATTCAAATTTCAAA-
* *
406650 CAGAACATATTCGATTCAAACAAGTTTCGTTTTACA-AAATTCATTTTCATAATTTAATCCTTCA
644 CAGAACATATTCGATTCAAACTAG-TTCCTTTTA-AGAAATTCATTTTCATAATTTAATCCTTCA
* * *
406714 AAATTTTATTTTATGATCATCATACGTCACAAAAATTCTAAACGAAATTTCTGAGTGTTAAAAAA
707 AAA-ATTATTTTTTGATCATCATACGTCACAAAAATTCTAAACCAAATTTCTGAGTGTT-AAAAA
406779 AAGATCATCTTACATCAACTAGGATTCCATCTTATATGGATAT
770 AAGATCATCTTACATCAACTAGGATTCCATCTTATATGGATAT
406822 TTGTGTTAGT
Statistics
Matches: 1452, Mismatches: 146, Indels: 66
0.87 0.09 0.04
Matches are distributed among these distances:
808 6 0.00
809 281 0.19
810 5 0.00
816 3 0.00
817 4 0.00
818 364 0.25
819 437 0.30
820 269 0.19
821 83 0.06
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (815 bp):
AGAAAAGGACAAAAACAACCTAATTGATATGAACATTGTACAAACTCAAGTAACAACAAGAAAAC
ATATACAATTTTTAGTATCTTGATAGAGGAGGAGTTGAACGACGTCTTTCACCTCTTTTCTTCTT
TCCCCGTTGCTTTTTACCTCATGAAAAGTATCTTGATAGAGAAGGCATTGAACGGTGTCGTTACG
GTCCATATTACAGTCTCTAAGGACGGCGAAGATCTCTCAGTCCGTGCAACTATTATTAACAATCT
CTTTAAGGTTCATCTAAGACTGTAATATGGACCCTAGCGACACCTTTCTACGCTTCCTCTCCCAA
GATACTTTTCAAGAGGTAAAAAGAAACAAGAAAGACTCAAAGAAGAAAAGAAATGAAAAGAAAAG
GAACTAATGTATTTTTTTTATTGAACAACTTACCTTTAATGAATTACAAGCAAACTTGGGTATTT
TATAGCCCAAATATAATTACCCAAAACATAAATAATTAGAGATATTTTTTAACTTAATGTGATTG
ATTAAAACATAAACGATGTACATCAAATCCCATATGCCACATCTCTAGCACTCCAACTTTCATCT
TTCTAATTTAGCTTTCAAACTTTTTTTAGCATATTTTAATCCTTATTCAAATTTCAAACAGAACA
TATTCGATTCAAACTAGTTCCTTTTAAGAAATTCATTTTCATAATTTAATCCTTCAAAAATTATT
TTTTGATCATCATACGTCACAAAAATTCTAAACCAAATTTCTGAGTGTTAAAAAAAGATCATCTT
ACATCAACTAGGATTCCATCTTATATGGATATAAA
Found at i:410322 original size:817 final size:809
Alignment explanation
Indices: 408484--411227 Score: 3352
Period size: 817 Copynumber: 3.4 Consensus size: 809
408474 AAAAAAGAAA
* * *
408484 ACGAGATTCATTTTCATAATTTAATCCTTCAAAAATTATTTTATGATCATCAAACTTCAGAAAAA
1 ACGAGATTCATTTTCATAATTTAATCCTTCAAAAATTATTTTTTGATCATCAGACGTCAGAAAAA
* * * *
408549 TTCT-AATCAAATTTTGGAGTGTTAATAAAAGACCATCTTACATCAACCAGGATTATCTCTTATA
66 TTCTAAACCAAATTTTGGAGTGTTAA-AAAAGATCATCTTACATCAACTAGGATTACCTCTTATA
*
408613 TGGATAT-AAAGAAAAGAAAAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACA
130 TGGATATAAAAGAAAAG-ACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACA
* *
408677 ACAAGAAAACATATACAATTTTGTTAATATCTTGATAGAGGAGGCATTGAACGGTGTCTTTCATT
194 ACAAGAAAACATATACAATTTTGTTAATATCTTGATAGAGGAGGCATTGAACGGCGTCTTTCATC
* * * *
408742 TCTTTTATTCTTTCCTGCTTTC-CTTTTACCTCATGAAAAGTATCTTAATAGAGAAGGCGTTGAA
259 TCTTTTATTCTTTCCCGC--TCGCTTTTACCTCATGAAAAGTATCTTGATAGAGGAGGTGTTGAA
* * * *
408806 CGGCGTCGTTACGATCCATATTACAGTCTCTAAGGACAGAAAAGATCTCTCAGTTCGTGCAACTA
322 CAGCGTCGTTACGGTCCATATTACAGTCTCTAAGGACAGAGAAGATCTCTCAGTTCGTACAACTA
* *
408871 TTATTAACAATCTCTTTAAAATTCATTAAAAACTGTAATAT-GAACCCTGGCGACGCCGTTCAAT
387 TTATTAACAATCTCTTTAAGATTCATT-AAAACTGTAATATGGAA-CCTGGCGACGCCGTTCAAC
* * * * *
408935 GCCTCCTCTCTCAAGATAGTTTTCAAGAGCTAAAAATCAAACAGGAAAGACTCAAAGAAGAAAAG
450 GCCTCCTCTCTCAAGATACTTTTCAAGAGGTAAAAAGCAAACGGGAAAGACTAAAAGAAGAAAAG
* *
409000 AGATGAAAAGAAAAGGAACTAATGTATTGTTTTATTGAAC-TACTGACTTTAATGAATTACAAAC
515 AGATGAAAAGAAAAGGAACTAATGTATT-TTTTTTTTAACTTACTGACTTTAATGAATTACAAAC
* * *
409064 AAACTTGGGTATTTTATAGCCCAAATATAAATACCCAAAACATAAATAATTAGAGATATTTTTTA
579 AAACTTGGGTATTTTATAGCCCAAATAT-AATAACTAAAACGTAAAT-ATTAGAGATATTTTTTA
* *
409129 ACTTGAATGTGATTGATTAAAACATAAATGATGTACATCAAATCTCATATGCCACATCTCTAGTA
642 ACTT-AATGTGATTGATTAAAACATAAACGATGTACATCAAATCTCATATGCCA-ATCTCTAGCA
* * * * * ** *
409194 CTCCAACTTTCATCTTTCTAATTTAGCTTTCAAACATTTTTTTTTCATATTTTAATCCTTATTCC
705 TTTCAACTTTAATTTTTCTTATTTAGCTTTCAAA-A--TTTTTAGCATATTTTAATCCTTATTCA
* * * *
409259 AATTTCGAACCAGAACATATTCT-TTTCAAATTAGTTTCATTTT
767 AATTTCGAATCAGAACATATT-TGATTCAAACTAGTTTCTTTTT
* * * *
409302 AGGAGATTCA-TTTCATAATTTAATCCTTGAAAAATTAATTTTTTGATCATCATATGTCAGAAAA
1 ACGAGATTCATTTTCATAATTTAATCCTTCAAAAATT-ATTTTTTGATCATCAGACGTCAGAAAA
* * * *
409366 ATTCTAAACTAAATTTCGGAGTATT-AAAAAGATCATCTTACATCAACTAGTATTACCTCTTATA
65 ATTCTAAACCAAATTTTGGAGTGTTAAAAAAGATCATCTTACATCAACTAGGATTACCTCTTATA
*
409430 TAGATATAAAAGAAAAGACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACAA
130 TGGATATAAAAGAAAAGACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACAA
* * * * *
409495 CAACAAAACATGTACAATTTTGTTAGTATCTTGATAGAGGAGTCATTGAACGGCATCTTTCATCT
195 CAAGAAAACATATACAATTTTGTTAATATCTTGATAGAGGAGGCATTGAACGGCGTCTTTCATCT
* * * *
409560 CTTTTCTTCTTTCTCC-CTCGCTTTTTACCTTATGAAAAGTACCTTGATAGAGGAGGTGCTGAAC
260 CTTTTATTCTTTC-CCGCTCGC-TTTTACCTCATGAAAAGTATCTTGATAGAGGAGGTGTTGAAC
* * * * * *
409624 AGCGTCGTTACGGTCCATATTACAGCCTCCAAGGACAGTGAAGATCTCTCGGTCCATACAACTAT
323 AGCGTCGTTACGGTCCATATTACAGTCTCTAAGGACAGAGAAGATCTCTCAGTTCGTACAACTAT
* * * * * *
409689 TATTAACAATCTCTTTAAGATTAATTAAAGACTGAAATATGGAACCTAGCAACGTCATTCAACGC
388 TATTAACAATCTCTTTAAGATTCATTAAA-ACTGTAATATGGAACCTGGCGACGCCGTTCAACGC
*
409754 CTCCTCTCTCAAGGTACTTTTCAAGAGGTAAAAAGCAAACGGGAAAGACTAAAAGAAGAAAAGAG
452 CTCCTCTCTCAAGATACTTTTCAAGAGGTAAAAAGCAAACGGGAAAGACTAAAAGAAGAAAAGAG
* * * * *
409819 ATGAAAAGTATAGGAACTAATGTATTTTTTTTTTTACTTAATGACCTTAATGAATTACAAACAAA
517 ATGAAAAGAAAAGGAACTAATGTATTTTTTTTTTAACTTACTGACTTTAATGAATTACAAACAAA
409884 CTTGGGTATTTTATAGCCCAAATATAATAATCTAAAACGTAAATATTTAGAGATATTTTTTAACT
582 CTTGGGTATTTTATAGCCCAAATATAATAA-CTAAAACGTAAATA-TTAGAGATATTTTTTAAC-
*
409949 TTAATGTGATTGATTAAAACATAAACGATGTACATCAAATCTCATATGTCATATCTCTAGCATTT
644 TTAATGTGATTGATTAAAACATAAACGATGTACATCAAATCTCATATGCCA-ATCTCTAGCATTT
* *
410014 CAACTTTAATTTTTCTTATTTAGCTTTCAAAATTTTTAAGAATATTTTAATTCTTATTCAAATTT
708 CAACTTTAATTTTTCTTATTTAGCTTTCAAAATTTTT-AGCATATTTTAATCCTTATTCAAATTT
* *
410079 CTAATCAGAGCATATTTGATTCAAACTAGTTTCTTTTT
772 CGAATCAGAACATATTTGATTCAAACTAGTTTCTTTTT
* * * * *
410117 ACGAGACTCATTTTCATAATTTAATCCTTCAGAAATTATTTTCTAATCATCAGACATCAGAAAAA
1 ACGAGATTCATTTTCATAATTTAATCCTTCAAAAATTATTTTTTGATCATCAGACGTCAGAAAAA
* *
410182 TTCTAAACCAAATTTTGGAGTGTTAAAAAAGATCATCTTATATCAACTAGGATTCCCTCTTATAT
66 TTCTAAACCAAATTTTGGAGTGTTAAAAAAGATCATCTTACATCAACTAGGATTACCTCTTATAT
*
410247 GGATATAAAAGAAAAGACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACTAC
131 GGATATAAAAGAAAAGACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACAAC
** *
410312 AAGAAAAACATATACAATTTTGTTAGCATCTTGATAGAGGAGGCGTTGAACGGCGTCTTTCATCT
196 AAG-AAAACATATACAATTTTGTTAATATCTTGATAGAGGAGGCATTGAACGGCGTCTTTCATCT
* * * * * *
410377 CTTTTGTTCTTTCCCGTTTGCATTTTACCTGATGAAAAGTATCTTGATAGAGTAGGCT-TTGAGC
260 CTTTTATTCTTTCCCGCTCGC-TTTTACCTCATGAAAAGTATCTTGATAGAGGAGG-TGTTGAAC
* * * * * *
410441 GGCGCCATTACGGTCCATATTACAGTCTCTAAGGAC-GACGAAGGTCTCTCACTTCGTCCAACTA
323 AGCGTCGTTACGGTCCATATTACAGTCTCTAAGGACAGA-GAAGATCTCTCAGTTCGTACAACTA
* * * * *
410505 TTATTAAAAATCTCTTTATGATTCATTAAAAATGGTAATACGGATCCTGGCGACGCCGTTCAACG
387 TTATTAACAATCTCTTTAAGATTCATTAAAACT-GTAATATGGAACCTGGCGACGCCGTTCAACG
* *
410570 CCTCCTCTCTCTAGATACTTTTCAAGATGTAAAAAGCAAACGGGAAAGACTAAAAGAAGAAAAGA
451 CCTCCTCTCTCAAGATACTTTTCAAGAGGTAAAAAGCAAACGGGAAAGACTAAAAGAAGAAAAGA
*
410635 GATGAAACA-AAAAGGAA-TAATGTATTTTTTTATTGAA-TTACTGACTTTAATGAATTACAAAC
516 GATGAAA-AGAAAAGGAACTAATGTATTTTTTT-TTTAACTTACTGACTTTAATGAATTACAAAC
* **** * * * * ** ** * * * * *
410697 AAACATAAACA-ATTAGAG---ATATTTTTTAACTTTAATGTGATTGATTA-A-A-A--CTTAAA
579 AAACTTGGGTATTTTATAGCCCAAATATAATAACTAAAACGTAAAT-ATTAGAGATATTTTTTAA
* * * * * * * * * *
410753 C--GATGT-A--CATCAAATC-T---C-ATATGC--CACATCTC---TGGC-A-CTCCAAC-TTT
643 CTTAATGTGATTGATTAAAACATAAACGATGTACATCAAATCTCATATGCCAATCTCTAGCATTT
* * * ** * *
410800 CATCTTTCTTATTTTGCTT-TCAAACTTT----ATATTTAGCATATTTTAATCCTTATTCAAATT
708 CAAC-TT-TAATTTTTCTTATTTAGCTTTCAAAATTTTTAGCATATTTTAATCCTTATTCAAATT
*
410860 TCGAATCAGAACATATTCGATTCAAACTAGTTTCTTTTT
771 TCGAATCAGAACATATTTGATTCAAACTAGTTTCTTTTT
* *
410899 AAGAGATTCGTTTTCATAATTTAATCCTTCAAAAATTATTTTTTGATCATCAGACGTCAGAAAAA
1 ACGAGATTCATTTTCATAATTTAATCCTTCAAAAATTATTTTTTGATCATCAGACGTCAGAAAAA
* * *
410964 TTCTAAACCAAATTTTGGAGTCTTAAAAAAATATCATCTTACATCAACTAGGATTCCCTCTTATA
66 TTCTAAACCAAATTTTGGAGTGTT-AAAAAAGATCATCTTACATCAACTAGGATTACCTCTTATA
* *
411029 TGGATATAAAAGAAAATA-AAAAACAACCTAATTGATATGAACATTGTAGAAACTCATGTAACAA
130 TGGATATAAAAGAAAAGACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACAA
* * *
411093 CAAGAAAACATATACAATTTTGTTAATATCTTGATAGACGAGGCATTGAACAGCGTCTTTCATTT
195 CAAGAAAACATATACAATTTTGTTAATATCTTGATAGAGGAGGCATTGAACGGCGTCTTTCATCT
*
411158 CTTTTATTCTTTCCCGCTTTC-CTTTTACCTCATGAAAAGTATCTTGATAGAGGAGATGTTGAAC
260 CTTTTATTCTTTCCCGC--TCGCTTTTACCTCATGAAAAGTATCTTGATAGAGGAGGTGTTGAAC
411222 AGCGTC
323 AGCGTC
411228 TTTCATCTCC
Statistics
Matches: 1679, Mismatches: 217, Indels: 97
0.84 0.11 0.05
Matches are distributed among these distances:
780 1 0.00
781 110 0.07
782 190 0.11
783 61 0.04
786 6 0.00
787 13 0.01
788 10 0.01
790 3 0.00
793 7 0.00
795 4 0.00
796 1 0.00
799 1 0.00
800 6 0.00
802 1 0.00
803 4 0.00
806 5 0.00
808 1 0.00
809 1 0.00
810 1 0.00
811 11 0.01
812 8 0.00
814 6 0.00
815 111 0.07
816 192 0.11
817 855 0.51
818 55 0.03
819 15 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (809 bp):
ACGAGATTCATTTTCATAATTTAATCCTTCAAAAATTATTTTTTGATCATCAGACGTCAGAAAAA
TTCTAAACCAAATTTTGGAGTGTTAAAAAAGATCATCTTACATCAACTAGGATTACCTCTTATAT
GGATATAAAAGAAAAGACAAAAACAACCTAATTGATATGAACATTGTAGAAACTCAAGTAACAAC
AAGAAAACATATACAATTTTGTTAATATCTTGATAGAGGAGGCATTGAACGGCGTCTTTCATCTC
TTTTATTCTTTCCCGCTCGCTTTTACCTCATGAAAAGTATCTTGATAGAGGAGGTGTTGAACAGC
GTCGTTACGGTCCATATTACAGTCTCTAAGGACAGAGAAGATCTCTCAGTTCGTACAACTATTAT
TAACAATCTCTTTAAGATTCATTAAAACTGTAATATGGAACCTGGCGACGCCGTTCAACGCCTCC
TCTCTCAAGATACTTTTCAAGAGGTAAAAAGCAAACGGGAAAGACTAAAAGAAGAAAAGAGATGA
AAAGAAAAGGAACTAATGTATTTTTTTTTTAACTTACTGACTTTAATGAATTACAAACAAACTTG
GGTATTTTATAGCCCAAATATAATAACTAAAACGTAAATATTAGAGATATTTTTTAACTTAATGT
GATTGATTAAAACATAAACGATGTACATCAAATCTCATATGCCAATCTCTAGCATTTCAACTTTA
ATTTTTCTTATTTAGCTTTCAAAATTTTTAGCATATTTTAATCCTTATTCAAATTTCGAATCAGA
ACATATTTGATTCAAACTAGTTTCTTTTT
Found at i:411248 original size:78 final size:78
Alignment explanation
Indices: 411119--411451 Score: 531
Period size: 78 Copynumber: 4.3 Consensus size: 78
411109 ATTTTGTTAA
* ** * * * * * *
411119 TATCTTGATAGACGAGGCATTGAACAGCGTCTTTCATTTCTTTTATTCTTTCCCGCTTTCCTTTT
1 TATCTTGATAGAGGAGGTGTTGAACAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
*
411184 ACCTCATGAAAAG
66 ACCTAATGAAAAG
*
411197 TATCTTGATAGAGGAGATGTTGAACAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
1 TATCTTGATAGAGGAGGTGTTGAACAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
411262 ACCTAATGAAAAG
66 ACCTAATGAAAAG
*
411275 TATCTTGATAGAGGAGGTGTTGAACAGCGTCTTTCATCTCCTTTCTTATTTCACGCTTGCTTTTT
1 TATCTTGATAGAGGAGGTGTTGAACAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
*
411340 ACCTAATGAAAAA
66 ACCTAATGAAAAG
* *
411353 TATCTTGATAGAGGAGGTATTGAATAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
1 TATCTTGATAGAGGAGGTGTTGAACAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
411418 ACCTAATGAAAAG
66 ACCTAATGAAAAG
411431 TATCTTGATAGAGGAGGTGTT
1 TATCTTGATAGAGGAGGTGTT
411452 TAACGGCGGC
Statistics
Matches: 236, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 236 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (78 bp):
TATCTTGATAGAGGAGGTGTTGAACAGCGTCTTTCATCTCCTTTCTTCTTTCACGCTTGCTTTTT
ACCTAATGAAAAG
Found at i:414038 original size:20 final size:21
Alignment explanation
Indices: 413991--414038 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
413981 CATTCGATCC
*
413991 TTTATTTATCTTTTTTAATTTA
1 TTTA-TTATCTTTTTTAAATTA
**
414013 GCTATTAT-TTTTTTAAATTA
1 TTTATTATCTTTTTTAAATTA
414033 TTTATT
1 TTTATT
414039 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 15 0.71
21 4 0.19
22 2 0.10
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTATTATCTTTTTTAAATTA
Found at i:415947 original size:29 final size:30
Alignment explanation
Indices: 415907--415966 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
415897 TGAATAATCA
* *
415907 TTTTAACTAACTTGA-TTCTTTTTGTCTTG
1 TTTTAACTAACTTGATTTCCTTTTGCCTTG
*
415936 TTTTTACTAACTTGATTTCCTTTTGCCTTG
1 TTTTAACTAACTTGATTTCCTTTTGCCTTG
415966 T
1 T
415967 CTTGTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58
Consensus pattern (30 bp):
TTTTAACTAACTTGATTTCCTTTTGCCTTG
Found at i:425924 original size:29 final size:29
Alignment explanation
Indices: 425882--425939 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
425872 CATTCCTAGT
425882 TTCAACATTCTATCAACTATTTTTATCTC
1 TTCAACATTCTATCAACTATTTTTATCTC
425911 TTCAACATTCTATCAACTATTTTTATCTC
1 TTCAACATTCTATCAACTATTTTTATCTC
425940 CTTGAATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (29 bp):
TTCAACATTCTATCAACTATTTTTATCTC
Found at i:434553 original size:8 final size:8
Alignment explanation
Indices: 434540--434564 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
434530 TGCCACATGT
434540 TAAAATAA
1 TAAAATAA
434548 TAAAATAA
1 TAAAATAA
434556 TAAAATAA
1 TAAAATAA
434564 T
1 T
434565 TTATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAAATAA
Found at i:439920 original size:39 final size:39
Alignment explanation
Indices: 439877--439954 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
439867 GCAGTGAAAT
* *
439877 TTGTCTCGAAGGACCATTATGTCCCGTAGGACCACTGTA
1 TTGTCCCGAAGGACCACTATGTCCCGTAGGACCACTGTA
439916 TTGTCCCGAAGGACCACTATGTCCCGTAGGACCACTGTA
1 TTGTCCCGAAGGACCACTATGTCCCGTAGGACCACTGTA
439955 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
TTGTCCCGAAGGACCACTATGTCCCGTAGGACCACTGTA
Found at i:439922 original size:21 final size:20
Alignment explanation
Indices: 439886--439954 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 20
439876 TTTGTCTCGA
439886 AGGACCA-T-TATGTCCCGT
1 AGGACCACTGTATGTCCCGT
*
439904 AGGACCACTGTATTGTCCCGA
1 AGGACCACTGTA-TGTCCCGT
439925 AGGACCAC--TATGTCCCGT
1 AGGACCACTGTATGTCCCGT
439943 AGGACCACTGTA
1 AGGACCACTGTA
439955 ACCCTCGACT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 22 0.50
19 3 0.07
20 4 0.09
21 15 0.34
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (20 bp):
AGGACCACTGTATGTCCCGT
Found at i:440347 original size:15 final size:17
Alignment explanation
Indices: 440312--440348 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
440302 TACCTATTCT
440312 CATATATCTAATTTCATA
1 CATATATC-AATTTCATA
440330 CATATATC-ATTT-ATA
1 CATATATCAATTTCATA
440345 CATA
1 CATA
440349 CCTTTACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 4 0.21
18 8 0.42
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (17 bp):
CATATATCAATTTCATA
Found at i:457917 original size:47 final size:46
Alignment explanation
Indices: 457820--457944 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 46
457810 GTAACCATGC
* *
457820 AAATAAGCTTATGAGCTTACGGAAT-AATGG-AAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAAGTATATAGGAA
* * *
457864 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAA-TATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAAGTATATAGGAA
*
457911 AAATAAGCTTACGAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
457945 GAGATTTTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 1 0.01
47 35 0.49
48 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAAGTATATAGGAA
Found at i:459436 original size:22 final size:22
Alignment explanation
Indices: 459396--459441 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
459386 AACATAATTC
* * *
459396 AATCAAAATACAATAATTTGAA
1 AATCAAAAAAAAATAATTTCAA
*
459418 AATCAAAAAAAAATTATTTCAA
1 AATCAAAAAAAAATAATTTCAA
459440 AA
1 AA
459442 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (22 bp):
AATCAAAAAAAAATAATTTCAA
Found at i:459898 original size:21 final size:23
Alignment explanation
Indices: 459850--459908 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
459840 TTCCCCTGTG
459850 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
459873 GGGGGAATTGGTT-CCC-TCATA
1 GGGGGAATCGGTTCCCCTTCAAA
*
459894 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
459909 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.16
21 11 0.35
22 3 0.10
23 12 0.39
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:463758 original size:22 final size:21
Alignment explanation
Indices: 463716--463755 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
463706 GAGCTTCTTT
*
463716 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
463737 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
463756 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:467335 original size:18 final size:18
Alignment explanation
Indices: 467312--467346 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
467302 TAAAAAAGTC
467312 TTTAAAA-TAATTATTATT
1 TTTAAAATTAA-TATTATT
467330 TTTAAAATTAATATTAT
1 TTTAAAATTAATATTAT
467347 ATTAATGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAAATTAATATTATT
Found at i:471418 original size:14 final size:14
Alignment explanation
Indices: 471399--471429 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
471389 ATTTCCAACG
471399 TGGTTTTATAGTAT
1 TGGTTTTATAGTAT
471413 TGGTTTTATAGTAT
1 TGGTTTTATAGTAT
471427 TGG
1 TGG
471430 ACGCTGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (14 bp):
TGGTTTTATAGTAT
Found at i:472503 original size:29 final size:29
Alignment explanation
Indices: 472468--472549 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
472458 AAACTAAATT
*
472468 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
472497 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
472526 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
472550 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:476516 original size:28 final size:29
Alignment explanation
Indices: 476455--476536 Score: 130
Period size: 28 Copynumber: 2.8 Consensus size: 29
476445 CAAACTAAAT
*
476455 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
476484 AGATGTCATTGCTTACATCA-TTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
476512 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
476537 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
28 26 0.54
29 19 0.40
30 3 0.06
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:478116 original size:18 final size:19
Alignment explanation
Indices: 478084--478119 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
478074 ATTAAAAGTT
*
478084 TTAATTTTTTATAAATAAA
1 TTAAGTTTTTATAAATAAA
478103 TTAAGTTTTT-TAAATAA
1 TTAAGTTTTTATAAATAA
478120 TATTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAGTTTTTATAAATAAA
Found at i:479702 original size:15 final size:15
Alignment explanation
Indices: 479682--479721 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
479672 ATTGGGTATC
*
479682 CGGGTATCCGACATA
1 CGGGTACCCGACATA
479697 CGGGTACCCGACATA
1 CGGGTACCCGACATA
*
479712 CAGGTACCCG
1 CGGGTACCCG
479722 GAACATCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (15 bp):
CGGGTACCCGACATA
Found at i:480087 original size:21 final size:21
Alignment explanation
Indices: 480043--480094 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
480033 GGTAGAGCGA
* **
480043 TACCTAAAATGTTATTTTTTC
1 TACCTAAAATGTTAATTTCGC
*
480064 TACCGAAAATGTTAATTTCGC
1 TACCTAAAATGTTAATTTCGC
480085 TACCTAAAAT
1 TACCTAAAAT
480095 AAATATTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (21 bp):
TACCTAAAATGTTAATTTCGC
Found at i:482595 original size:14 final size:14
Alignment explanation
Indices: 482576--482606 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
482566 ATTTCCAACG
482576 TGGTTTTATAGTAT
1 TGGTTTTATAGTAT
482590 TGGTTTTATAGTAT
1 TGGTTTTATAGTAT
482604 TGG
1 TGG
482607 ACGCTGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (14 bp):
TGGTTTTATAGTAT
Found at i:486467 original size:15 final size:15
Alignment explanation
Indices: 486447--486486 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
486437 ATTGGGTATC
*
486447 CGGGTATCCGACATA
1 CGGGTACCCGACATA
486462 CGGGTACCCGACATA
1 CGGGTACCCGACATA
*
486477 CAGGTACCCG
1 CGGGTACCCG
486487 GAACATCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (15 bp):
CGGGTACCCGACATA
Found at i:486854 original size:21 final size:21
Alignment explanation
Indices: 486810--486861 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
486800 GGTAGAGCGA
* **
486810 TACCTAAAATGTTATTTTTTC
1 TACCTAAAATGTTAATTTCGC
*
486831 TACCGAAAATGTTAATTTCGC
1 TACCTAAAATGTTAATTTCGC
486852 TACCTAAAAT
1 TACCTAAAAT
486862 AAATATTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (21 bp):
TACCTAAAATGTTAATTTCGC
Found at i:489352 original size:14 final size:14
Alignment explanation
Indices: 489333--489363 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
489323 ATTTCCAACG
489333 TGGTTTTATAGTAT
1 TGGTTTTATAGTAT
489347 TGGTTTTATAGTAT
1 TGGTTTTATAGTAT
489361 TGG
1 TGG
489364 ACGCTGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (14 bp):
TGGTTTTATAGTAT
Found at i:491690 original size:27 final size:27
Alignment explanation
Indices: 491647--491704 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
491637 TTAAAAGTTT
**
491647 TAATTTTTTATAAATTAAGTTTTTAAA
1 TAATTTTTTATAAATTAAAATTTTAAA
*
491674 TAATATTTTTAT-TATTAAAATTTTAAA
1 TAAT-TTTTTATAAATTAAAATTTTAAA
491701 -AATT
1 TAATT
491705 AAAAGATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.04
26 3 0.11
27 16 0.59
28 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TAATTTTTTATAAATTAAAATTTTAAA
Found at i:493250 original size:15 final size:15
Alignment explanation
Indices: 493230--493269 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
493220 ATTGGGTATC
*
493230 CGGGTATCCGACATA
1 CGGGTACCCGACATA
493245 CGGGTACCCGACATA
1 CGGGTACCCGACATA
*
493260 CAGGTACCCG
1 CGGGTACCCG
493270 GAACATCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (15 bp):
CGGGTACCCGACATA
Found at i:493636 original size:21 final size:21
Alignment explanation
Indices: 493592--493643 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
493582 GGTAGAGCGA
* **
493592 TACCTAAAATGTTATTTTTTC
1 TACCTAAAATGTTAATTTCGC
*
493613 TACCGAAAATGTTAATTTCGC
1 TACCTAAAATGTTAATTTCGC
493634 TACCTAAAAT
1 TACCTAAAAT
493644 AAATATTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (21 bp):
TACCTAAAATGTTAATTTCGC
Found at i:495166 original size:13 final size:13
Alignment explanation
Indices: 495148--495177 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
495138 ATCACATTTC
495148 CATAATCATAAAA
1 CATAATCATAAAA
495161 CATAATCATAAAA
1 CATAATCATAAAA
495174 CATA
1 CATA
495178 GCTTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (13 bp):
CATAATCATAAAA
Found at i:497299 original size:26 final size:26
Alignment explanation
Indices: 497263--497315 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
497253 ATTAATTCAC
*
497263 AAAATCTTAATATAATACATTAATGG
1 AAAATCATAATATAATACATTAATGG
* *
497289 AAAATCATAATATCATGCATTAATGG
1 AAAATCATAATATAATACATTAATGG
497315 A
1 A
497316 TGAGAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (26 bp):
AAAATCATAATATAATACATTAATGG
Found at i:509125 original size:40 final size:40
Alignment explanation
Indices: 509031--509126 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
509021 GTGACGCGAC
* * *
509031 TCCTACGTGATGAGAAGATTTGGTCGGTAGATGACACGGT
1 TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACGGT
* *
509071 TCCTACGTGATGAGGAGATCTAGTCGGTGGATTACACGGT
1 TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACGGT
509111 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
509127 TGATTGGACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACGGT
Found at i:509243 original size:177 final size:174
Alignment explanation
Indices: 508897--509263 Score: 504
Period size: 177 Copynumber: 2.1 Consensus size: 174
508887 GTGACGTTGC
* *
508897 TCCTACGTGATGAGGAGATCTGGTCGGTAGATGACACGGTTCCTACGTGATGAGGATGGCTGGAT
1 TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACGGTTCCTACGTGATGAGGATGACTGGAT
* * * * *
508962 CTTTAGGGATAATGAAGATAACCAGTTACTACATGATGAGGAAGTCTAGCTATCTAAGGGTGACG
66 CGTTAGGAATAATAAAGATAACCAGTTACTACACGATGAGGAAGTCTAGCTATCTAAGGATGACG
*
509027 CGACTCCTACGTGATGAGAAGATTTGGTCGGTAGATGACACGGT
131 CGACTCCTACATGATGAGAAGATTTGGTCGGTAGATGACACGGT
* * *
509071 TCCTACGTGATGAGGAGATCTAGTCGGTGGATTACACGGTTCCTACGTGATGAGGATGATTGGAC
1 TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACGGTTCCTACGTGATGAGGATGACTGG--
* * ** *
509136 ATCGTTAGGAATAATAAAGATAGTA-CGGTTCCTATGCGATGAGGAAGTCTGGCTATCTAAGGAT
64 ATCGTTAGGAATAATAAAGATA--ACCAGTTACTACACGATGAGGAAGTCTAGCTATCTAAGGAT
* *
509200 GACGCAGA-TCCTACATGATGAGGAGATTTGGTCGGTGGATGACACGGT
127 GACGC-GACTCCTACATGATGAGAAGATTTGGTCGGTAGATGACACGGT
*
509248 TCCTACATGATGAGGA
1 TCCTACGTGATGAGGA
509264 TGACTGGCCA
Statistics
Matches: 169, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
174 58 0.34
176 19 0.11
177 89 0.53
178 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (174 bp):
TCCTACGTGATGAGGAGATCTAGTCGGTAGATGACACGGTTCCTACGTGATGAGGATGACTGGAT
CGTTAGGAATAATAAAGATAACCAGTTACTACACGATGAGGAAGTCTAGCTATCTAAGGATGACG
CGACTCCTACATGATGAGAAGATTTGGTCGGTAGATGACACGGT
Found at i:509306 original size:137 final size:137
Alignment explanation
Indices: 509071--509555 Score: 516
Period size: 137 Copynumber: 3.6 Consensus size: 137
509061 ATGACACGGT
* * * * *
509071 TCCTACGTGATGAGGAGATCTAGTCGGTGGATTACACGGTTCCTACGTGATGAGGATGATTGGAC
1 TCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACATGATGAGGATGATTGGCC
* * * * * *
509136 ATCGTTAGGAATAATAAAGATAGTACGGTTCCTATGCGATGAGGAAGTCTGGCTATCTAAGGATG
66 ATCTTTAGGGATAATGAAGATAATACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATG
*
509201 ACGCAGA
131 AAGCAGA
* * *
509208 TCCTACATGATGAGGAGATTTGGTCGGTGGATGACACGGTTCCTACATGATGAGGATGACTGGCC
1 TCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACATGATGAGGATGATTGGCC
* * * *
509273 ATTTTTAGGGATAATGAAGATAATACAGTTCCTACGTGATGAGGAAGTCTGGCTACCTAAGGGTG
66 ATCTTTAGGGATAATGAAGATAATACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATG
* *
509338 AAGCGGC
131 AAGCAGA
* * * * * * *
509345 TCCTACGTAATGATGAGATATGGTTGGTGGATGACATGGTTCCTACTTGATGAGGACGTTTGGCC
1 TCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACATGATGAGGATGATTGGCC
* * * * * *
509410 ATCTTTAGGGATAATGGAGATAACATGGTTCCTACGTGATGAGGAAGTCTAGCTATCTAACG-CG
66 ATCTTTAGGGATAATGAAGATAATACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATG
509474 -A-C---
131 AAGCAGA
* * * * * * * * * *
509476 TCTTACGTGGTGAGGAGATCTAGTCGGTGGATGATATGGTTCCTACGTGATAAGGACG-TCTAGC
1 TCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACATGATGAGGATGAT-TGGC
509540 CATCTTTAGGGATAAT
65 CATCTTTAGGGATAAT
509556 TTGTTTCAAG
Statistics
Matches: 297, Mismatches: 50, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
130 1 0.00
131 67 0.23
134 1 0.00
135 1 0.00
136 1 0.00
137 226 0.76
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (137 bp):
TCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACATGATGAGGATGATTGGCC
ATCTTTAGGGATAATGAAGATAATACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATG
AAGCAGA
Found at i:509677 original size:65 final size:65
Alignment explanation
Indices: 509557--509877 Score: 417
Period size: 65 Copynumber: 4.9 Consensus size: 65
509547 AGGGATAATT
* * * *
509557 TGTTTCAAGAGAAATTGTCTCAATAGAGACAAAACTTGTTTCAAGGGAAGCAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
** * * * * * *
509622 CATTTTAAGAGAAATTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * * ** *
509687 TGTTTTAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * * *
509752 TGTTTCAAGTGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAATTTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * *
509817 TGTTTCAAGGGATACTGTCTCAAGAGAGGCAAAATTTGTTTCAAGGGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG
509878 ATTTATCAAT
Statistics
Matches: 224, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 224 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:510031 original size:168 final size:168
Alignment explanation
Indices: 509853--510188 Score: 382
Period size: 168 Copynumber: 2.0 Consensus size: 168
509843 AGGCAAAATT
* * * *
509853 TGTTTCAAGGGAAACAATCTCAAAGAT-TTATC-AATTTTG-TTTCAAGT-GAAACAATTTCCAA
1 TGTTTCAAGGGAAACAATCTC-AAG-TGATA-CAAAATTTGCTTT-AAGTAAAAACAATAT-CAA
* * * * *
509914 AT-TTTGTGTTTTGAGAGAAAATTATCTCAAGCGAGACGAA-TCTGTTTTGAA-AAAAATAATCT
61 ATGTTTGTGTCTTAAG-GAAAACTATCTCAAGCGAGACAAAGTCTGTTTT-AAGAAAAACAATCT
* * *
509976 CAAGTGAGATTAATTTTGTTTCAAGT-AATACAACTTTGAAATTTG
124 CAAGTGAGATCAACTTTGTTTCAAGTGAA-ACAAATTTGAAATTTG
*
510021 TGTTTCAAGGGAAACTATCTCAAGTGATACAAAATTTGCTTTAAGTAAAAACAATATCAAATGTT
1 TGTTTCAAGGGAAACAATCTCAAGTGATACAAAATTTGCTTTAAGTAAAAACAATATCAAATGTT
** * * *
510086 TGTGTCTTAAGGAGGACTGTCTCAAGTGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGA
66 TGTGTCTTAAGGAAAACTATCTCAAGCGAGACAAAGTCTGTTTTAAGAAAAACAATCTCAAGTGA
510151 GATCAACTTTGTTTCAAGTGAAACAAATTTGAAATTTG
131 GATCAACTTTGTTTCAAGTGAAACAAATTTGAAATTTG
510189 CATCTCAAAG
Statistics
Matches: 142, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
166 2 0.01
167 40 0.28
168 98 0.69
169 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (168 bp):
TGTTTCAAGGGAAACAATCTCAAGTGATACAAAATTTGCTTTAAGTAAAAACAATATCAAATGTT
TGTGTCTTAAGGAAAACTATCTCAAGCGAGACAAAGTCTGTTTTAAGAAAAACAATCTCAAGTGA
GATCAACTTTGTTTCAAGTGAAACAAATTTGAAATTTG
Found at i:510247 original size:33 final size:35
Alignment explanation
Indices: 510199--510279 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 35
510189 CATCTCAAAG
* *
510199 GAAAAATT-TCTTAAGCGAGAC-GATT-TTTTTTA
1 GAAAAATTATCTTAAGCGAGACAAATTGTTTTTAA
510231 GAAAAATTATCTTAAGCGAGACAAAATTGGTTTTTAA
1 GAAAAATTATCTTAAGCGAGAC-AAATT-GTTTTTAA
510268 GAAAAATTATCT
1 GAAAAATTATCT
510280 CTAGTGAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 8 0.19
33 13 0.31
35 3 0.07
37 18 0.43
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (35 bp):
GAAAAATTATCTTAAGCGAGACAAATTGTTTTTAA
Found at i:512734 original size:8 final size:7
Alignment explanation
Indices: 512698--512739 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
512688 CTTAAAAAAT
512698 AAAATGC
1 AAAATGC
*
512705 -AGATGC
1 AAAATGC
512711 AAAATGC
1 AAAATGC
512718 AAAATGC
1 AAAATGC
512725 AAAGATGC
1 AAA-ATGC
512733 -AAATGC
1 AAAATGC
512739 A
1 A
512740 GATGTGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 9 0.30
7 17 0.57
8 4 0.13
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (7 bp):
AAAATGC
Found at i:517871 original size:44 final size:46
Alignment explanation
Indices: 517808--517917 Score: 134
Period size: 44 Copynumber: 2.4 Consensus size: 46
517798 AATATTTCTC
* *
517808 TTAGGGTGAAAACCCAAAAGAGCGCTCTAAATT-CTAAAA-AAAAG
1 TTAGGGTGAAAACCCAAAAGAGCACTCTAAATTGCAAAAAGAAAAG
* * * * *
517852 TTAGGGTGAAAACCTAAAAGGGCACTCTAAGTTGGAAAAAGAAAAT
1 TTAGGGTGAAAACCCAAAAGAGCACTCTAAATTGCAAAAAGAAAAG
*
517898 TTAGAGTGAAAACCCAAAAG
1 TTAGGGTGAAAACCCAAAAG
517918 GGAACTTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 29 0.53
45 4 0.07
46 22 0.40
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18
Consensus pattern (46 bp):
TTAGGGTGAAAACCCAAAAGAGCACTCTAAATTGCAAAAAGAAAAG
Found at i:517917 original size:46 final size:44
Alignment explanation
Indices: 517808--517929 Score: 136
Period size: 46 Copynumber: 2.7 Consensus size: 44
517798 AATATTTCTC
* * *
517808 TTAGGGTGAAAACCCAAAAGAGCGCTCTAAATTCTAAAAAAAAG
1 TTAGGGTGAAAACCCAAAAGGGCACTCTAAATTCAAAAAAAAAG
* * * *
517852 TTAGGGTGAAAACCTAAAAGGGCACTCTAAGTTGGAAAAAGAAAAT
1 TTAGGGTGAAAACCCAAAAGGGCACTCTAAATT-CAAAAA-AAAAG
* * *
517898 TTAGAGTGAAAACCCAAAAGGGAACTTTAAAT
1 TTAGGGTGAAAACCCAAAAGGGCACTCTAAAT
517930 AAAAATGAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 29 0.45
45 4 0.06
46 31 0.48
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (44 bp):
TTAGGGTGAAAACCCAAAAGGGCACTCTAAATTCAAAAAAAAAG
Found at i:521226 original size:13 final size:13
Alignment explanation
Indices: 521210--521236 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
521200 ATAATATAAT
521210 ATATTTTTTGAAA
1 ATATTTTTTGAAA
521223 ATATTTTTTGAAA
1 ATATTTTTTGAAA
521236 A
1 A
521237 CATATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATATTTTTTGAAA
Found at i:521270 original size:38 final size:37
Alignment explanation
Indices: 521203--521444 Score: 202
Period size: 38 Copynumber: 6.6 Consensus size: 37
521193 TATATATATA
***
521203 ATATAATATAT--TTTTTGAAAATATTTTTTGAAAAC
1 ATATAATATATAGTTTTTGAAAACGGTTTTTGAAAAC
* *
521238 ATATAATATATAGTTTTTAGAAAACGGGTTTTGAAAGC
1 ATATAATATATAGTTTTT-GAAAACGGTTTTTGAAAAC
* *
521276 ATATAATATGTAGTTTTTTAAAATCGGTTTTTG-AAA-
1 ATATAATATATAGTTTTTGAAAA-CGGTTTTTGAAAAC
* *
521312 ATATACATA-ATATGGTTTTGAAAACACGTTTTTGAAAAC
1 ATATA-ATATATA-GTTTTTGAAAAC-GGTTTTTGAAAAC
*
521351 ATAT-A-ATATAGTTTTTGAAAAC-CTTTTTGGAAAA-
1 ATATAATATATAGTTTTTGAAAACGGTTTTT-GAAAAC
* * * *
521385 ATATAATATATAG-TTATAAAAATGATTTTTGAAAAC
1 ATATAATATATAGTTTTTGAAAACGGTTTTTGAAAAC
521421 GTATATAATATA-A-TTTTTGAAAAC
1 --ATATAATATATAGTTTTTGAAAAC
521445 ATATTTTGAA
Statistics
Matches: 167, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
34 9 0.05
35 29 0.17
36 31 0.19
37 42 0.25
38 52 0.31
39 4 0.02
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (37 bp):
ATATAATATATAGTTTTTGAAAACGGTTTTTGAAAAC
Found at i:521573 original size:14 final size:13
Alignment explanation
Indices: 521542--521610 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 13
521532 TTTCAAAACG
521542 TATTATATAATTT
1 TATTATATAATTT
*
521555 T-TTATATAGTTTT
1 TATTATATA-ATTT
521568 TATTATAT-ATTAT
1 TATTATATAATT-T
521581 TA-TATATTAA-TT
1 TATTATA-TAATTT
521593 TA-TAT-TAATTT
1 TATTATATAATTT
521604 ATATTAT
1 -TATTAT
521611 TTATATTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
10 3 0.07
11 2 0.04
12 21 0.46
13 13 0.28
14 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (13 bp):
TATTATATAATTT
Found at i:521580 original size:10 final size:9
Alignment explanation
Indices: 521567--521631 Score: 87
Period size: 10 Copynumber: 6.9 Consensus size: 9
521557 TATATAGTTT
521567 TTATTATATA
1 TTATT-TATA
521577 TTATTATATA
1 TTATT-TATA
521587 TTAATTTATA
1 TT-ATTTATA
521597 TTAATTTATA
1 TT-ATTTATA
521607 TTATTTATA
1 TTATTTATA
521616 TTATTTAT-
1 TTATTTATA
521624 TTATTTAT
1 TTATTTAT
521632 TTTTATTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.15
9 15 0.28
10 28 0.52
11 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATTTATA
Found at i:521595 original size:36 final size:35
Alignment explanation
Indices: 521542--521631 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
521532 TTTCAAAACG
* * *
521542 TATTATATAATTTTTTATA-TAGTTTTTATTATATA
1 TATTATAT-ATTATTTATATTAATTTATATTATATA
*
521577 TTATTATATATTAATTTATATTAATTTATATTATTTA
1 -TATTATATATT-ATTTATATTAATTTATATTATATA
*
521614 TATTATTTATTTATTTAT
1 TATTATATA-TTATTTAT
521632 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
35 3 0.07
36 28 0.61
37 15 0.33
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (35 bp):
TATTATATATTATTTATATTAATTTATATTATATA
Found at i:521623 original size:4 final size:4
Alignment explanation
Indices: 521566--521633 Score: 57
Period size: 4 Copynumber: 15.8 Consensus size: 4
521556 TTATATAGTT
* *
521566 TTTA TTATA TATTA -TTA TATA TTAA TTTA TATTAA TTTA TATTA TTTA
1 TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA T-TT-A TTTA T-TTA TTTA
521614 TATTA TTTA TTTA TTTA TTT
1 T-TTA TTTA TTTA TTTA TTT
521634 TTATTTTTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 3 0.06
4 30 0.57
5 17 0.32
6 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:534512 original size:27 final size:25
Alignment explanation
Indices: 534472--534552 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
534462 GTATTTGGTT
534472 AGATAAAA-GAAGTGTGTTGTGTAAA
1 AGATAAAATG-AGTGTGTTGTGTAAA
*
534497 AGATCAAATATGAGTGTGTTGTGTAAG
1 AGAT-AAA-ATGAGTGTGTTGTGTAAA
* *
534524 AGATGAAATGAGTGTGTTATGTAAA
1 AGATAAAATGAGTGTGTTGTGTAAA
534549 AGAT
1 AGAT
534553 TGAAGATGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 24 0.49
26 5 0.10
27 19 0.39
28 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.28, T:0.31
Consensus pattern (25 bp):
AGATAAAATGAGTGTGTTGTGTAAA
Found at i:534561 original size:27 final size:26
Alignment explanation
Indices: 534482--534561 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 26
534472 AGATAAAAGA
**
534482 AGTGTGTTGTGTAAAAGATCAAATATG
1 AGTGTGTTGTGTAAAAGATTGAA-ATG
*
534509 AGTGTGTTGTGTAAGAGA-TGAAATG
1 AGTGTGTTGTGTAAAAGATTGAAATG
*
534534 AGTGTGTTATGTAAAAGATTGAAGATG
1 AGTGTGTTGTGTAAAAGATTGAA-ATG
534561 A
1 A
534562 TGTATACTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
25 19 0.41
26 6 0.13
27 21 0.46
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.33
Consensus pattern (26 bp):
AGTGTGTTGTGTAAAAGATTGAAATG
Found at i:537920 original size:44 final size:44
Alignment explanation
Indices: 537821--538352 Score: 663
Period size: 44 Copynumber: 12.0 Consensus size: 44
537811 AAACCAGGAG
* * **
537821 TGGCACCTTTTTGCCAA-AATGCACCATTATGCATTTAATTTTCATTGG
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGC-----ATTTTCATTTA
*
537869 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
537913 TGGCACCTGTCAGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
537957 TGGCACATTTCTGCTAATAATGCAACATTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
538001 TGGAACCTTTCTGCCAATAATACACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
538045 TGACACCTTTCTGCCAATAATGAAACGTTATGCATTTTCATTT-
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
538088 TTGAACCTTTCTGCCAATAATGCACTGTTATGCATTTTCTTTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
538132 TGACACATTTCTTCCAATAATGCCCCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
538176 TGACACCTTTCTGCCAATAATGCAACGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
538220 TGACACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
538264 TGGCACCTTTCTGCCAATAACGTAACATTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
538308 TGGCATCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
538352 T
1 T
538353 TCATTCATTT
Statistics
Matches: 425, Mismatches: 57, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
43 36 0.08
44 358 0.84
48 16 0.04
49 15 0.04
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:538252 original size:219 final size:220
Alignment explanation
Indices: 537858--538352 Score: 697
Period size: 219 Copynumber: 2.3 Consensus size: 220
537848 TATGCATTTA
** * * * *
537858 ATTTTCATTGGTGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTATGGCACCTGT
1 ATTTTCATTTATGGAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACATGT
* *
537923 CAGCCAATAATGCACCATTATGCATTTTCATTTATGGCACATTTCTGCTAATAATGCAACATTAT
66 CAGCCAATAATGCACCATTATGCATTTTCATTTATGACACATTTCTGCCAATAATGCAACATTAT
* *
537988 GCATTTTTATTTATGGAACCTTTCTGCCAATAATACACTGTTATGCATTTTCATTTATGACACCT
131 GCATTTTCATTTATGGAACCTTTCTGCCAATAATACACCGTTATGCATTTTCATTTATGACACCT
* * *
538053 TTCTGCCAATAATGAAACGTTATGC
196 TTCTGCCAATAACGAAACATTATAC
* * * *
538078 ATTTTCATTT-TTGAACCTTTCTGCCAATAATGCACTGTTATGCATTTTCTTTTATGACACATTT
1 ATTTTCATTTATGGAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACATGT
** * * * *
538142 CTTCCAATAATGCCCCGTTATGCATTTTCATTTATGACACCTTTCTGCCAATAATGCAACGTTAT
66 CAGCCAATAATGCACCATTATGCATTTTCATTTATGACACATTTCTGCCAATAATGCAACATTAT
* *
538207 GCATTTTCATTTAT-GACACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
131 GCATTTTCATTTATGGA-ACCTTTCTGCCAATAATACACCGTTATGCATTTTCATTTATGACACC
*
538271 TTTCTGCCAATAACGTAACATTATAC
195 TTTCTGCCAATAACGAAACATTATAC
* * * *
538297 ATTTTCATTTATGGCATCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTAT
1 ATTTTCATTTATGGAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
538353 TCATTCATTT
Statistics
Matches: 241, Mismatches: 32, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
218 2 0.01
219 192 0.80
220 47 0.20
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (220 bp):
ATTTTCATTTATGGAACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACATGT
CAGCCAATAATGCACCATTATGCATTTTCATTTATGACACATTTCTGCCAATAATGCAACATTAT
GCATTTTCATTTATGGAACCTTTCTGCCAATAATACACCGTTATGCATTTTCATTTATGACACCT
TTCTGCCAATAACGAAACATTATAC
Found at i:547703 original size:21 final size:21
Alignment explanation
Indices: 547655--547716 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
547645 TCGTCCCCAT
*
547655 GGGGAACCGATTCCCCCTTTGAA
1 GGGGAACCGATTCCCCC--TCAA
547678 GGGGAACCGATTCCCCC-CACA
1 GGGGAACCGATTCCCCCTCA-A
* *
547699 GGGGAATCGATACCCCCT
1 GGGGAACCGATTCCCCCT
547717 GGGGTTCTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.47
23 17 0.50
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (21 bp):
GGGGAACCGATTCCCCCTCAA
Found at i:549835 original size:13 final size:13
Alignment explanation
Indices: 549817--549841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
549807 GCCATGTCAC
549817 ATTAATTATGAAT
1 ATTAATTATGAAT
549830 ATTAATTATGAA
1 ATTAATTATGAA
549842 ACTAATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTAATTATGAAT
Found at i:556803 original size:74 final size:74
Alignment explanation
Indices: 556716--556872 Score: 287
Period size: 74 Copynumber: 2.1 Consensus size: 74
556706 TCCTTCTTCA
556716 TCATGTAGCGTTTAAGACATCTTTCTATAAGGTTTTGAGCCTGAATTCAGACATAAAAGTAAAAA
1 TCATGTAGCGTTTAAGACATCTTTCTATAAGGTTTTGAGCCTGAATTCAGACATAAAAGTAAAAA
556781 CAACATTAG
66 CAACATTAG
*
556790 TCATGTAGCGTTTAAGACATCTTTCTATAAGGTTTTGAGCCTTAATTCAGACATAAAAGTAAAAA
1 TCATGTAGCGTTTAAGACATCTTTCTATAAGGTTTTGAGCCTGAATTCAGACATAAAAGTAAAAA
556855 CAACATTAG
66 CAACATTAG
*
556864 CCATCGTAG
1 TCAT-GTAG
556873 ACAACATACC
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
74 76 0.95
75 4 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (74 bp):
TCATGTAGCGTTTAAGACATCTTTCTATAAGGTTTTGAGCCTGAATTCAGACATAAAAGTAAAAA
CAACATTAG
Found at i:560065 original size:5 final size:5
Alignment explanation
Indices: 560055--560079 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
560045 AATGATGATG
560055 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
560080 ATAGTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:560219 original size:24 final size:24
Alignment explanation
Indices: 560193--560240 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
560183 TTTTAATTTT
*
560193 AAATAATTATTAAATTATCAAATTA
1 AAAT-ATTAATAAATTATCAAATTA
560218 AAATATTAATAAATTATCAAATT
1 AAATATTAATAAATTATCAAATT
560241 GTGGCCAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATATTAATAAATTATCAAATTA
Found at i:561231 original size:5 final size:5
Alignment explanation
Indices: 561221--561247 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
561211 TAAGACGATC
561221 GTTTT GTTTT GTTTT GTTTT GTTTT GT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GT
561248 GCTTACGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (5 bp):
GTTTT
Found at i:563480 original size:3 final size:3
Alignment explanation
Indices: 563472--563529 Score: 62
Period size: 3 Copynumber: 17.3 Consensus size: 3
563462 CTGCACAAAT
563472 ATA ATA ATA ATA ATTA ATTA ATA ATA AGTA ATA ATA ATAA ATAA ATA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA AT-A AT-A ATA
563519 ATA ATA TATA A
1 ATA ATA -ATA A
563530 AATGTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 31 0.61
4 20 0.39
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:563495 original size:17 final size:18
Alignment explanation
Indices: 563473--563526 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
563463 TGCACAAATA
563473 TAATAATAATAAT-TAAT
1 TAATAATAATAATATAAT
563490 TAATAATAAGTAATAATAAT
1 TAATAATAA-TAAT-ATAAT
*
563510 AAATAAATAATAATATA
1 TAAT-AATAATAATATA
563527 TAAAATGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.28
18 4 0.12
19 3 0.09
20 11 0.34
21 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATATAAT
Found at i:563505 original size:27 final size:27
Alignment explanation
Indices: 563473--563524 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
563463 TGCACAAATA
* *
563473 TAATAATAATAATTAATTAATAATAAG
1 TAATAATAATAAATAAATAATAATAAG
563500 TAATAATAATAAATAAATAATAATA
1 TAATAATAATAAATAAATAATAATA
563525 TATAAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
TAATAATAATAAATAAATAATAATAAG
Found at i:563530 original size:14 final size:13
Alignment explanation
Indices: 563472--563529 Score: 71
Period size: 14 Copynumber: 4.3 Consensus size: 13
563462 CTGCACAAAT
563472 ATAATAATAATAA
1 ATAATAATAATAA
*
563485 TTAATTAATAATAA
1 ATAA-TAATAATAA
*
563499 GTAATAATAATAA
1 ATAATAATAATAA
*
563512 ATAAATAATAATAT
1 AT-AATAATAATAA
563526 ATAA
1 ATAA
563530 AATGTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 15 0.38
14 24 0.62
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:564221 original size:84 final size:84
Alignment explanation
Indices: 564069--564316 Score: 273
Period size: 84 Copynumber: 2.9 Consensus size: 84
564059 AATTTATTGA
* * * * * * ** *
564069 CAGATAGCCCTTCTTGCCTTGAA-CTATGTTGTAAATTTGATTTGCCTCTGAGTTGAATGTAATC
1 CAGATAGCCCTTCTAGCCTT-AAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGCGTAGTC
* *
564133 GAACTCGAGGGTCTTTGGTTGG
63 GAACTCAAAGGTCTTTGGTTGG
* *
564155 CAGATAGCCCTTCTCGCCTTAAGCTATGCTGCAAAAGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
564220 CTCTAAGGTCTTTGGTTGG
66 CTCAAAGGTCTTTGGTTGG
* * * * * * *
564239 TAGATAACCCTTCTAGCCTTGAGTTATGCTGCAACTGATGTGCCTTGGAGCTAAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
564304 CTCAAAGGTCTTT
66 CTCAAAGGTCTTT
564317 TGTTTCAAGA
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
84 108 0.78
85 2 0.01
86 29 0.21
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (84 bp):
CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTTGG
Found at i:564367 original size:36 final size:35
Alignment explanation
Indices: 564315--564420 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 35
564305 TCAAAGGTCT
* *
564315 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA
564351 TTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAA
*
564387 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAA
564421 TGGTGAACAC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 64 0.98
37 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (35 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAA
Found at i:564722 original size:43 final size:43
Alignment explanation
Indices: 564661--564910 Score: 149
Period size: 43 Copynumber: 5.4 Consensus size: 43
564651 ACCAGCGGTC
*
564661 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
* * * * ** ***
564704 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TATGGA-GTCCA-ATAT
*
564754 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
* * * * ** ***
564798 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TATGGA-GTCCA-ATAT
* *
564848 CCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
*
564892 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
564911 ATTGGCTCTG
Statistics
Matches: 148, Mismatches: 43, Indels: 32
0.66 0.19 0.14
Matches are distributed among these distances:
43 61 0.41
44 2 0.01
45 6 0.04
46 14 0.09
48 14 0.09
49 6 0.04
50 2 0.01
51 43 0.29
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
Found at i:564789 original size:94 final size:94
Alignment explanation
Indices: 564625--565127 Score: 754
Period size: 106 Copynumber: 5.1 Consensus size: 94
564615 AAATTGGCTC
*
564625 TGAAATCGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
564690 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
564719 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
564784 TTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
*
564813 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
564878 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
564907 TGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAA-------T----T-GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
564972 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
565013 TGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAA-------T----T-GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
565078 AACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
565119 TGAAATTGG
1 TGAAATTGG
565128 CTCTGAAATC
Statistics
Matches: 391, Mismatches: 6, Indels: 24
0.93 0.01 0.06
Matches are distributed among these distances:
94 191 0.49
95 1 0.00
99 1 0.00
101 1 0.00
105 1 0.00
106 196 0.50
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:570078 original size:3 final size:3
Alignment explanation
Indices: 570070--570131 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
570060 CTGCACAAAT
570070 ATA ATA ATA ATA ATTA ATTA ATA ATA AGTA ATA ATA ATA ATAA ATAA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA ATA AT-A AT-A
570117 ATA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA A
570132 AATGTTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.04
3 36 0.65
4 17 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:570103 original size:27 final size:26
Alignment explanation
Indices: 570070--570131 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
570060 CTGCACAAAT
* *
570070 ATAATAATAATAATTAATTAATAATA
1 ATAATAATAATAATAAATAAATAATA
570096 AGTAATAATAATAATAAATAAATAATA
1 A-TAATAATAATAATAAATAAATAATA
570123 AT-ATAATAA
1 ATAATAATAA
570132 AATGTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 7 0.21
26 2 0.06
27 24 0.73
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATAATAATAATAATAAATAAATAATA
Found at i:570823 original size:84 final size:84
Alignment explanation
Indices: 570671--570918 Score: 264
Period size: 84 Copynumber: 2.9 Consensus size: 84
570661 AATTTATTGA
* * * * * * ** *
570671 CAGATAGCCCTTCTTGCCTTGAA-CTATGTTGTAAATCTGATTTGCCTCTGAGTTGAATGTAATC
1 CAGATAGCCCTTCTAGCCTT-AAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGCGTAGTC
* *
570735 GAACTCGAGGGTCTTTGGTTGG
63 GAACTCAAAGGTCTTTGGTTGG
* *
570757 CAGATAGCCCTTCTCGCCTTAAGCTATGCTGCAAAAGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
570822 CTCTAAGGTCTTTGGTTGG
66 CTCAAAGGTCTTTGGTTGG
* * * * * * * *
570841 TAGATAACCCTTCTATCCTTGAGTTATGCTGCAACTGATGTGCCTTGGAGCTAAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
570906 CTCAAAGGTCTTT
66 CTCAAAGGTCTTT
570919 TGTTTCAAGA
Statistics
Matches: 138, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
84 107 0.78
85 2 0.01
86 29 0.21
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (84 bp):
CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTTGG
Found at i:570958 original size:36 final size:35
Alignment explanation
Indices: 570917--571022 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 35
570907 TCAAAGGTCT
* * *
570917 TTTGTTTCAAGAGAAACTGTCTTAAGGGAGTCAAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA
570953 TTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAA
*
570989 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAA
571023 TGGTGAGCAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 63 0.98
37 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (35 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAA
Found at i:571332 original size:106 final size:106
Alignment explanation
Indices: 571147--571822 Score: 1062
Period size: 106 Copynumber: 6.6 Consensus size: 106
571137 TATTGTTCCA
** * *
571147 AGTCCAATATCC-TCTGCCGTGAAGTTGAAATTGACTCTGGAA-CTGGGAAATTGTTTATTGACA
1 AGTCCAATATCCTTC-GTTGTGAAGTTGAAATTGGCTCTGAAATC-GGGAAATTGTTTATTGACA
*
571210 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
571253 AGTCCAATATCCTTCGTTGTGGAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
571318 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
571359 AGTCCAATATCCTTCGTTGTGAAGTTGAAA-------T----T-GGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
*
571412 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
571453 AGTCCAATATCCTTCGTTGTGAAGTTGAAA-------T----T-GGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
571506 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
571547 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
571612 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
571653 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
*
571718 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
571759 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATGTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAAT-TGTTTATTGACA
571823 GACAACTTTT
Statistics
Matches: 544, Mismatches: 11, Indels: 29
0.93 0.02 0.05
Matches are distributed among these distances:
94 184 0.34
95 1 0.00
99 1 0.00
101 1 0.00
105 1 0.00
106 342 0.63
107 14 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:571387 original size:43 final size:43
Alignment explanation
Indices: 571326--571575 Score: 158
Period size: 43 Copynumber: 5.4 Consensus size: 43
571316 ACCAGCGGTC
*
571326 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
* * * * ** ***
571369 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TATGGA-GTCCA-ATAT
*
571419 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
* * * * ** ***
571463 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TATGGA-GTCCA-ATAT
*
571513 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
*
571557 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
571576 ATTGGCTCTG
Statistics
Matches: 150, Mismatches: 41, Indels: 32
0.67 0.18 0.14
Matches are distributed among these distances:
43 62 0.41
44 2 0.01
45 6 0.04
46 14 0.09
48 14 0.09
49 6 0.04
50 2 0.01
51 44 0.29
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATAT
Found at i:574717 original size:16 final size:17
Alignment explanation
Indices: 574680--574719 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
574670 AAATGAAAAG
574680 TCCTACCCCACATGATA
1 TCCTACCCCACATGATA
*
574697 T-CTACCCCACATTAT-
1 TCCTACCCCACATGATA
574712 TCCTACCC
1 TCCTACCC
574720 GGACATGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.25, C:0.45, G:0.03, T:0.28
Consensus pattern (17 bp):
TCCTACCCCACATGATA
Found at i:577055 original size:3 final size:3
Alignment explanation
Indices: 577047--577108 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
577037 CTGCACAAAT
577047 ATA ATA ATA ATA ATTA ATTA ATA ATA AGTA ATA ATA ATA ATAA ATAA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA ATA AT-A AT-A
577094 ATA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA A
577109 AATGTTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.04
3 36 0.65
4 17 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:577080 original size:27 final size:26
Alignment explanation
Indices: 577047--577108 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
577037 CTGCACAAAT
* *
577047 ATAATAATAATAATTAATTAATAATA
1 ATAATAATAATAATAAATAAATAATA
577073 AGTAATAATAATAATAAATAAATAATA
1 A-TAATAATAATAATAAATAAATAATA
577100 AT-ATAATAA
1 ATAATAATAA
577109 AATGTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 7 0.21
26 2 0.06
27 24 0.73
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATAATAATAATAATAAATAAATAATA
Found at i:579041 original size:2 final size:2
Alignment explanation
Indices: 579034--579063 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
579024 TGTGAAAAGA
579034 AT AT AT AT 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
579064 GGTTAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:581689 original size:24 final size:24
Alignment explanation
Indices: 581634--581690 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
581624 CAAGCCAATG
* *
581634 AATTAGGATGAAGCTAGTGAAAAG
1 AATTAGGGTGAAGCTAGTGAAAAA
581658 AATTAGGGTGAAGCTAGTGAAAAA
1 AATTAGGGTGAAGCTAGTGAAAAA
581682 AATTAGGGT
1 AATTAGGGT
581691 AAACTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.04, G:0.30, T:0.23
Consensus pattern (24 bp):
AATTAGGGTGAAGCTAGTGAAAAA
Found at i:581775 original size:24 final size:23
Alignment explanation
Indices: 581734--581780 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
581724 TACGAGGGAG
* **
581734 TAAGTTATTTAACTTTGAAATAAA
1 TAAGGTATTTAAAATTG-AATAAA
581758 TAAGGTATTTAAAATTGAATAAA
1 TAAGGTATTTAAAATTGAATAAA
581781 CCATAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (23 bp):
TAAGGTATTTAAAATTGAATAAA
Found at i:583705 original size:31 final size:31
Alignment explanation
Indices: 583661--583720 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
583651 TCATGTTCTT
* *
583661 AAAATTGTCAAGCTCGACTTAAACTCGAAATAA
1 AAAATTG-CAAGCTCAAATT-AACTCGAAATAA
583694 AAAATTG-AAGCTCAAATTAACTCGAAA
1 AAAATTGCAAGCTCAAATTAACTCGAAA
583721 GCTCACGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 9 0.36
33 7 0.28
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (31 bp):
AAAATTGCAAGCTCAAATTAACTCGAAATAA
Found at i:584054 original size:17 final size:17
Alignment explanation
Indices: 584011--584055 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
584001 ATCGAATGGA
584011 CTCGACTCGAACTCGAG
1 CTCGACTCGAACTCGAG
*
584028 CTCAACTCGAACTCGAG
1 CTCGACTCGAACTCGAG
*
584045 CTCGATTCGAA
1 CTCGACTCGAA
584056 TTCTTAACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (17 bp):
CTCGACTCGAACTCGAG
Found at i:587715 original size:26 final size:27
Alignment explanation
Indices: 587652--587722 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
587642 AGTTTTAATT
* * * * *
587652 AATATTAAAAAATAAAATTAGAGTATA
1 AATAATAAAAATTCAAATTAAAGTACA
587679 AATAATAAAAATTCAAATTAAAGTACA
1 AATAATAAAAATTCAAATTAAAGTACA
*
587706 ATTAAT-AAAATTCAAAT
1 AATAATAAAAATTCAAAT
587723 GGTGCAGCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 11 0.29
27 27 0.71
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (27 bp):
AATAATAAAAATTCAAATTAAAGTACA
Found at i:595013 original size:88 final size:88
Alignment explanation
Indices: 594864--595038 Score: 242
Period size: 88 Copynumber: 2.0 Consensus size: 88
594854 TTTGATTGAC
* *
594864 AAGCACCTTTTTATATGTATTCTTTCCTCATTACTACTCAATCCTTTGGATGATAGTTAATCATT
1 AAGCACCTTTTTATATGTATTCTTTCCTCATTACTACTCAATCCATTGGATGATAATTAATCATT
* *
594929 TTTTCTTTTAGTTATATCATGTT
66 TTTTCTTTTAGCTAGATCATGTT
* * * ** **
594952 AAGCATCTTTTTGTTTGTATTCTTTCCTCATTACTGTTCGGTCCATTGGATGATAATTAATCATT
1 AAGCACCTTTTTATATGTATTCTTTCCTCATTACTACTCAATCCATTGGATGATAATTAATCATT
*
595017 TTTTGTTTTAGCTAGATCATGT
66 TTTTCTTTTAGCTAGATCATGT
595039 GGAATAGAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (88 bp):
AAGCACCTTTTTATATGTATTCTTTCCTCATTACTACTCAATCCATTGGATGATAATTAATCATT
TTTTCTTTTAGCTAGATCATGTT
Found at i:599526 original size:17 final size:17
Alignment explanation
Indices: 599506--599539 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
599496 TAATAATATT
*
599506 AATAATAATTAAATAAA
1 AATAATAATAAAATAAA
599523 AATAATAATAAAATAAA
1 AATAATAATAAAATAAA
599540 GACAGTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAATAATAAAATAAA
Found at i:599923 original size:134 final size:134
Alignment explanation
Indices: 599733--600333 Score: 753
Period size: 134 Copynumber: 4.5 Consensus size: 134
599723 ATTCCATTAT
* * * * * * * *
599733 TCTTTAGGAAAGATTGAATCGGAATCGATTTGCTTTATTACT-TATCAGGAAAACCAAATCTGAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCT-TCAAGAAGACCAAATCTGAA
* * *
599797 AGAGGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTTATCCACTTT
65 AGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTC
* *
599862 ACTAC
130 ATTGC
*
599867 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGATA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAA
* * * *
599932 GAAGAAGAATCTGCTCCACTACTCTTTATGGGAGATCAGACTCGAGGAAATTTTGATCCACTTCG
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
*
599997 TTTC
131 TTGC
* * * *
600001 TCTTCAGGGAAGATTGAATCAGAATCGATTTACTTCAATGCTCTTCAGGAAGACCAAATCTAAAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAA
* * * * * ** *
600066 TAAGAAGAATATGCTCTACTACTCTTTAGGGGATATCAGACTCGAGATAACTTTGATATACTTCG
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
600131 TTGC
131 TTGC
* *
600135 TCTTCAGGGAAGATTAAATCAGAATCGATTTGCTTCACTGCTCTT-AAGGAATACCAAATCTGAA
1 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAA-GAAGACCAAATCTGAA
* * *
600199 AGAAGAAGAATCTACT-CATCTACTCTTTAGGAGAGATCAGACTCGAGTAAACTTTGATCCACTT
65 AGAAGAAGAATCTGCTCCA-CTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTT
*
600263 CAGTGC
129 CATTGC
* * * *
600269 TCTTCAGGGAAGATTGAAT-TGAATTTGGTTTGCTTCTCTTG-TCTTCAAGAAGACCAAATCTGA
1 TCTTCAGGGAAGATTGAATCAGAA-TCGATTTGCTTCAC-TGCTCTTCAAGAAGACCAAATCTGA
600332 AA
64 AA
600334 ATCAAACATT
Statistics
Matches: 403, Mismatches: 58, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
133 5 0.01
134 393 0.98
135 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (134 bp):
TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAA
GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
TTGC
Found at i:601015 original size:50 final size:49
Alignment explanation
Indices: 600891--601071 Score: 203
Period size: 50 Copynumber: 3.8 Consensus size: 49
600881 AATACTACTG
* *
600891 AAAA-GTTGACTCCTCTCCGCGAGAAAGTCAAGTTGAGAATGACATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGTTGA-AATGACATCACT
* * ***
600940 AAAAGCTTGACTTCTCTTTGTGAGAAAGTCAAGTTGAAAATGACATCACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGTTG-AAATGACATCACT
*
600990 AAAAGGTTGACTCCTCTTCACGAGAAAATCAA---G-AATGACAAT-ACT
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGTTGAAATGAC-ATCACT
* *
601035 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGTTGA
1 AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGTTGA
601072 CAATATTGAA
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
45 38 0.34
46 2 0.02
47 1 0.01
48 1 0.01
49 4 0.04
50 64 0.58
51 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (49 bp):
AAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGTTGAAATGACATCACT
Found at i:601060 original size:95 final size:89
Alignment explanation
Indices: 600926--601156 Score: 239
Period size: 89 Copynumber: 2.5 Consensus size: 89
600916 AGTCAAGTTG
* * **
600926 AGAATGAC-ATCACTAAAAGCTTGACTTCTCTTTGTGAGAAAGTCAAGTTGAAAATGACATCACT
1 AGAATGACAAT-ACTAAAAGATTGACTCCTCTTTACGAGAAAGTCAAGTTGAAAAT---AT---T
*
600990 AAAAGGTTGACTCCTCTTCACGAGAAAATCA
59 AAAAGATTGACTCCTCTTCACGAGAAAATCA
* * * *
601021 AGAATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGTTGACAATATTGAAAGAT
1 AGAATGACAATACTAAAAGATTGACTCCTCTTTACGAGAAAGTCAAGTTGAAAATATTAAAAGAT
* * *
601086 TGACTGCTCTTCGCGAGAAAGTCA
66 TGACTCCTCTTCACGAGAAAATCA
* * * * *
601110 AGAAGGACAACACTAAAATATTAACTCCTCTTTACGAGAAAATCAAG
1 AGAATGACAATACTAAAAGATTGACTCCTCTTTACGAGAAAGTCAAG
601157 AATGACAATA
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
89 67 0.58
92 2 0.02
95 45 0.39
96 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (89 bp):
AGAATGACAATACTAAAAGATTGACTCCTCTTTACGAGAAAGTCAAGTTGAAAATATTAAAAGAT
TGACTCCTCTTCACGAGAAAATCA
Found at i:601088 original size:44 final size:45
Alignment explanation
Indices: 600978--601244 Score: 260
Period size: 45 Copynumber: 6.1 Consensus size: 45
600968 TCAAGTTGAA
* * *
600978 AATGAC-ATCACTAAAAGGTTGACTCCTCTTCACGAGAAAATCAAG
1 AATGACAAT-ACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
601023 AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
1 AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
* * * *
601068 -TTGACAATATTGAAAGATTGACTGCTCTTCGCGAGAAAGTCAAG
1 AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
* * * * * * *
601112 AAGGACAACACTAAAATATTAACTCCTCTTTACGAGAAAATCAAG
1 AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
* ** * *
601157 AATGACAATAC--AGAGATTGACTTATCATCACGAGAAAGTCTAG
1 AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
* * * * *
601200 --T-ATAACACTGAAAGATTGACTTCTCTTCACAAGAAATTCAAG
1 AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
601242 AAT
1 AAT
601245 AACAGATATT
Statistics
Matches: 179, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
40 5 0.03
41 1 0.01
42 26 0.15
43 23 0.13
44 41 0.23
45 81 0.45
46 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (45 bp):
AATGACAATACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
Found at i:601119 original size:89 final size:90
Alignment explanation
Indices: 600991--601256 Score: 238
Period size: 89 Copynumber: 3.0 Consensus size: 90
600981 GACATCACTA
* * * * *
600991 AAAGGTTGACTCCTCTTCACGAGAAAATCAAGAATGACAATACTGAAAGATTGACTCCTCTTCAC
1 AAAGATTGACTCCTCTTCACGAGAAAATCAAGAAGGACAACACTAAAAGATTAACTCCTCTTCAC
* *
601056 GAGAAAGTCAAG-TTGACAATATTG
66 GAGAAAATCAAGAATGACAATATTG
* * * * *
601080 AAAGATTGACTGCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAATATTAACTCCTCTTTAC
1 AAAGATTGACTCCTCTTCACGAGAAAATCAAGAAGGACAACACTAAAAGATTAACTCCTCTTCAC
*
601145 GAGAAAATCAAGAATGACAATA--C
66 GAGAAAATCAAGAATGACAATATTG
* ** * * * * * * * *
601168 AGAGATTGACTTATCATCACGAGAAAGTC---TAGTATAACACTGAAAGATTGACTTCTCTTCAC
1 AAAGATTGACTCCTCTTCACGAGAAAATCAAGAAGGACAACACTAAAAGATTAACTCCTCTTCAC
* * *
601230 AAGAAATTCAAGAATAACAGATATTG
66 GAGAAAATCAAGAATGACA-ATATTG
601256 A
1 A
601257 CTTCTCTTCT
Statistics
Matches: 143, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
85 41 0.29
86 3 0.02
88 25 0.17
89 66 0.46
90 8 0.06
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (90 bp):
AAAGATTGACTCCTCTTCACGAGAAAATCAAGAAGGACAACACTAAAAGATTAACTCCTCTTCAC
GAGAAAATCAAGAATGACAATATTG
Found at i:601263 original size:38 final size:38
Alignment explanation
Indices: 601210--601941 Score: 808
Period size: 38 Copynumber: 19.2 Consensus size: 38
601200 TATAACACTG
* * *
601210 AAAGATTGACTTCTCTTCACAAGAAATTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601248 AGATATTGACTTCTCTTCTCGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
601286 AAAGAATGACTTCTCTCCACGAGGGAA-TC-AGTAATGAT
1 AAAGATTGACTTCTCTTCACGA-GGAAGTCAAG-AATAAC
* ** *
601324 AAAGATTGACTCCTCTTCATAAGGAAGTCAAGAATGAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * * * * *
601362 ATTGGGCGATTGACTCCTCTTCGCAAGGGAGTCAGGAATAAC
1 A----AAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
601404 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATGAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
601442 AAAGATT-AGCTTCTCTTCACGGGGAAGTCAAGAATAAC
1 AAAGATTGA-CTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
601480 AAACATTAACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601518 AAAGATCGACTTATCTTCACGAGGAAGTCAAGAATAGC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
601556 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601594 AAAGATCGACTTATCTTCACGAGGAAGTCAATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
601632 AAAGATCT-ACTTCTCTTCATGAGGAAGTCAAGAATAAC
1 AAAGAT-TGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601670 AAAGATCGATTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
601708 AAAGATCGATTTTTCTTAATGAGGAAGTCAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601746 AAAGATCGACTTCTCTAT-ACGAGGAAGTCAATAATAAA
1 AAAGATTGACTTCTCT-TCACGAGGAAGTCAAGAATAAC
* *
601784 AAAGATTGCCTTCTCTTCACTAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601822 AAATATTGACTTCTCTTCATGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
601860 AAAGATTGAATTCTCTTCGCGAGGGAGTTAGGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
601898 AAAGATTGACTTCTCTTCATGGGGAAGCCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
601936 AAAGAT
1 AAAGAT
601942 AGAATGAGTT
Statistics
Matches: 587, Mismatches: 93, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
37 8 0.01
38 540 0.92
39 8 0.01
42 31 0.05
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:602835 original size:25 final size:22
Alignment explanation
Indices: 602800--602864 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 22
602790 TTTTATTTCC
602800 AAAAA-TTGAAAAATATTAATTA
1 AAAAATTTGAAAAATATTAA-TA
* *
602822 AAAGAATTTTGAAAAATGTTTAATG
1 AAA-AA-TTTGAAAAAT-ATTAATA
602847 AAAAATTTGAAAAATATT
1 AAAAATTTGAAAAATATT
602865 CCCCTTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 5 0.14
23 12 0.33
24 2 0.06
25 13 0.36
26 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (22 bp):
AAAAATTTGAAAAATATTAATA
Found at i:603807 original size:7 final size:7
Alignment explanation
Indices: 603797--603897 Score: 51
Period size: 8 Copynumber: 13.1 Consensus size: 7
603787 TTTTCTATTT
603797 TTTTCTC
1 TTTTCTC
603804 TTTTTCTTC
1 -TTTTC-TC
*
603813 TTTTTTC
1 TTTTCTC
603820 TTCTTCTTC
1 TT-TTC-TC
* *
603829 TTTACTAT
1 TTTTCT-C
603837 TTTTCTC
1 TTTTCTC
603844 TTTTCT-
1 TTTTCTC
603850 TTTTCTACC
1 TTTTCT--C
*
603859 TTTTCCC
1 TTTTCTC
603866 TTTTTCCTC
1 -TTTT-CTC
*
603875 TTGTCATC
1 TTTTC-TC
*
603883 TTTTTTC
1 TTTTCTC
603890 TTTTCTC
1 TTTTCTC
603897 T
1 T
603898 CATCTTTATC
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
6 6 0.08
7 22 0.31
8 30 0.42
9 13 0.18
ACGTcount: A:0.04, C:0.26, G:0.01, T:0.69
Consensus pattern (7 bp):
TTTTCTC
Found at i:603807 original size:18 final size:18
Alignment explanation
Indices: 603786--603847 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
603776 TTTGATTACT
603786 TTTTTCTAT-TTTTTTCTC
1 TTTTTCT-TCTTTTTTCTC
603804 TTTTTCTTCTTTTTTCTTC
1 TTTTTCTTCTTTTTTC-TC
*
603823 TTCTTCTTTACTATTTTTCTC
1 TTTTTC-TT-CT-TTTTTCTC
603844 TTTT
1 TTTT
603848 CTTTTTCTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.38
19 7 0.19
20 2 0.05
21 7 0.19
22 6 0.16
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTCTTCTTTTTTCTC
Found at i:603818 original size:21 final size:20
Alignment explanation
Indices: 603785--603847 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
603775 ATTTGATTAC
*
603785 TTTTTTCTATTTTTTTCTCT
1 TTTTTTCTATTTTCTTCTCT
*
603805 TTTTCTTCTTTTTTCTTCTTCT
1 TTTT-TTCTATTTTCTTC-TCT
* *
603827 TCTTTACTA-TTT-TTCTCT
1 TTTTTTCTATTTTCTTCTCT
603845 TTT
1 TTT
603848 CTTTTTCTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.14
19 3 0.09
20 7 0.20
21 14 0.40
22 6 0.17
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTCTATTTTCTTCTCT
Found at i:603821 original size:16 final size:17
Alignment explanation
Indices: 603786--603876 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 17
603776 TTTGATTACT
*
603786 TTTTTCTATTTTTTTCTC
1 TTTTTCT-TCTTTTTCTC
603804 TTTTTCTTCTTTTT-TC
1 TTTTTCTTCTTTTTCTC
* * *
603820 TTCTTCTTC-TTTACTA
1 TTTTTCTTCTTTTTCTC
603836 TTTTTC-TC--TTT-TC
1 TTTTTCTTCTTTTTCTC
* * *
603849 TTTTTCTACCTTTTCCC
1 TTTTTCTTCTTTTTCTC
*
603866 TTTTTCCTCTT
1 TTTTTCTTCTT
603877 GTCATCTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
13 7 0.12
14 3 0.05
15 5 0.09
16 19 0.34
17 15 0.27
18 7 0.12
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTCTTCTTTTTCTC
Found at i:603862 original size:22 final size:21
Alignment explanation
Indices: 603786--603869 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 21
603776 TTTGATTACT
*
603786 TTTTTCTA-TTTT-T-TTCTC
1 TTTTTCTACTTTTCTCTTTTC
* *
603804 TTTTTCTTCTTTTTTCTTCTTC
1 TTTTTCTACTTTTCTCTT-TTC
*
603826 TTCTTTACTATTTTTCTCTTTTC
1 TT-TTT-CTACTTTTCTCTTTTC
*
603849 TTTTTCTACCTTTTCCCTTTT
1 TTTTTCTA-CTTTTCTCTTTT
603870 TCCTCTTGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
18 7 0.13
19 4 0.08
20 1 0.02
21 5 0.10
22 17 0.33
23 8 0.15
24 10 0.19
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTCTACTTTTCTCTTTTC
Found at i:609066 original size:16 final size:17
Alignment explanation
Indices: 609030--609067 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
609020 TATTTCTAAA
*
609030 AAATAAGACTACAACTG
1 AAATAAGACTACAAATG
*
609047 AAATGAGACTA-AAATG
1 AAATAAGACTACAAATG
609063 AAATA
1 AAATA
609068 CAAATAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (17 bp):
AAATAAGACTACAAATG
Found at i:610726 original size:3 final size:3
Alignment explanation
Indices: 610718--610759 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
610708 CTAAAAACAA
* *
610718 AAT AAT AAT ATT AAT TA- AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
610760 AGACAGGTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:610739 original size:17 final size:17
Alignment explanation
Indices: 610717--610749 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
610707 CCTAAAAACA
*
610717 AAATAATAATATTAATT
1 AAATAATAATAATAATT
610734 AAATAATAATAATAAT
1 AAATAATAATAATAAT
610750 AATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAATAATAATAATT
Found at i:610743 original size:20 final size:20
Alignment explanation
Indices: 610718--610759 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
610708 CTAAAAACAA
* *
610718 AATAATAATATTAATTAAAT
1 AATAATAATAATAATAAAAT
610738 AATAATAATAATAATAAAAT
1 AATAATAATAATAATAAAAT
610758 AA
1 AA
610760 AGACAGGTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAATAATAATAAAAT
Found at i:611203 original size:200 final size:200
Alignment explanation
Indices: 610860--611236 Score: 601
Period size: 200 Copynumber: 1.9 Consensus size: 200
610850 GGTACCGATA
* *
610860 CCCAATTTTGATCGAGCCTCCCTAACCCTTTCAGTGTTGAGATGAACCTAAGTTTCACTAAACGA
1 CCCAATTTTGATCGAGCCTCCCTAACCCTTTCAATGTTGAGATGAACCTAAGTTTCACTAAACAA
* * * * *
610925 TTGGCATAGACTTAGTGCAATTTACATTGTAAACTTCAATTGAATAAAACAAAAGAAATTAACAA
66 TTGGCATAGACTTAGTGAAATTTACATTATAAACTTAAATTGAATAAAAAAAAAGAAATAAACAA
* *
610990 GTAACAAATTAAAAATCATCCTTAAACATGAAAGAAATCATCCAAGTAATCCCAAGTTCAAATTA
131 GTAACAAATTAAAAAACATCCCTAAACATGAAAGAAATCATCCAAGTAATCCCAAGTTCAAATTA
611055 AAAAT
196 AAAAT
*
611060 CCCAATTTTGATTGAGCCTCCCTAACCCTTTCAATGTTGAGATGAACCTAAGTTTCACTAAACAA
1 CCCAATTTTGATCGAGCCTCCCTAACCCTTTCAATGTTGAGATGAACCTAAGTTTCACTAAACAA
* * ** *
611125 TTGTCATTGACTTAGTGAAATTTGTATTATAAACTTAAATTGAGTAAAAAAAAAGAAATAAACAA
66 TTGGCATAGACTTAGTGAAATTTACATTATAAACTTAAATTGAATAAAAAAAAAGAAATAAACAA
* *
611190 GTAACAAATTAAAAAACATCCCTAAACATTAAAGAAGTCATCCAAGT
131 GTAACAAATTAAAAAACATCCCTAAACATGAAAGAAATCATCCAAGT
611237 TCACTAAGAA
Statistics
Matches: 160, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
200 160 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.28
Consensus pattern (200 bp):
CCCAATTTTGATCGAGCCTCCCTAACCCTTTCAATGTTGAGATGAACCTAAGTTTCACTAAACAA
TTGGCATAGACTTAGTGAAATTTACATTATAAACTTAAATTGAATAAAAAAAAAGAAATAAACAA
GTAACAAATTAAAAAACATCCCTAAACATGAAAGAAATCATCCAAGTAATCCCAAGTTCAAATTA
AAAAT
Found at i:614882 original size:228 final size:227
Alignment explanation
Indices: 614458--614964 Score: 687
Period size: 228 Copynumber: 2.2 Consensus size: 227
614448 TATTTCCACT
* * *
614458 AGAAATGTTGATCTCTCGAGTGAGGCATTACTGATTCGAAA-TGTCGTGAATCGAGCAATAGGAA
1 AGAAATGTTAATCCCTCAAGTG-GGCATTACTGATTC-AAAGTGTCGTGAATCGAGCAATAGGAA
* * *
614522 ATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGCCTTATCATCTTGCTCGAAAG
64 ATGTGAAAAAATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCAACTTGCTCGAAAG
* * * *
614587 ACTTATAGATGACTCGAAGGATTTAAGCATCATCCTCGAAAGAATTACTGATGGCCTAAAAGACT
129 ACTTATAGATGACCCGAAGGATTTAAGCATCATCCTCGAAAGAATTACTAATAGCCCAAAAGACT
* * *
614652 TTT-TCTTATTCAAAATGCCGTGAATCGAGCAATA
194 TTTGT-TGATTCAAAAGGCCATGAATCGAGCAATA
* *
614686 AGAAATGTTAATCCCTCAAGTAGGGCATTATTGATTCAAAGTGTCGTTAATCGAGCAATAGGAAA
1 AGAAATGTTAATCCCTCAAGT-GGGCATTACTGATTCAAAGTGTCGTGAATCGAGCAATAGGAAA
*
614751 TGTGAAAAAATCCTGCCCGAAGGTCTTATGGATGG-TCCGAATGACTTATCAACTTGCTCGAAAG
65 TGTGAAAAAATCCTGCCCGAAGGTCTTATGGATGGCT-CGAAGGACTTATCAACTTGCTCGAAAG
* * * * * * *
614815 ACTTATAGATGACCCGAAGGATTTAAGCTTCATGCTCGGAAGACTTACTAATATCCCGAAGGACT
129 ACTTATAGATGACCCGAAGGATTTAAGCATCATCCTCGAAAGAATTACTAATAGCCCAAAAGACT
*
614880 TTTGTTGATTTAAAAGGCCATGAATCGAGCAATA
194 TTTGTTGATTCAAAAGGCCATGAATCGAGCAATA
* * * *
614914 GGAAATGTTAATCCCTCAAGTGGGGCGTTACTGATTCGAAGTGTTGTGAAT
1 AGAAATGTTAATCCCTCAAGT-GGGCATTACTGATTCAAAGTGTCGTGAAT
614965 TAAGAAAAGG
Statistics
Matches: 244, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
227 4 0.02
228 238 0.98
229 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (227 bp):
AGAAATGTTAATCCCTCAAGTGGGCATTACTGATTCAAAGTGTCGTGAATCGAGCAATAGGAAAT
GTGAAAAAATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCAACTTGCTCGAAAGAC
TTATAGATGACCCGAAGGATTTAAGCATCATCCTCGAAAGAATTACTAATAGCCCAAAAGACTTT
TGTTGATTCAAAAGGCCATGAATCGAGCAATA
Found at i:615042 original size:59 final size:58
Alignment explanation
Indices: 614900--615042 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 58
614890 TAAAAGGCCA
* * * **
614900 TGAATCGAGCAATAGGAAATGTTAATCCCTCAAGTGGGGCGTTACTGATTCGAAGTGTTG
1 TGAATCGAG-AATAGGAAAT-TTGATCCCTCAAGTGAGGCGTTACTGATTCGAAATACTG
** * * *
614960 TGAATTAAGAAAAGGAAATTTTGATCCCTCACGTGAGGCGTTGCTGATTCGAAATACTG
1 TGAATCGAGAATAGGAAA-TTTGATCCCTCAAGTGAGGCGTTACTGATTCGAAATACTG
615019 TGAATCGAGTAATAGGAAATTTGA
1 TGAATCGAG-AATAGGAAATTTGA
615043 AAACATCTTG
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
59 52 0.76
60 16 0.24
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (58 bp):
TGAATCGAGAATAGGAAATTTGATCCCTCAAGTGAGGCGTTACTGATTCGAAATACTG
Found at i:617377 original size:15 final size:15
Alignment explanation
Indices: 617357--617386 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
617347 ATAAATCTCA
617357 GTTTAATGATTTAAT
1 GTTTAATGATTTAAT
617372 GTTTAATGATTTAAT
1 GTTTAATGATTTAAT
617387 AAGTAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
GTTTAATGATTTAAT
Found at i:617378 original size:7 final size:8
Alignment explanation
Indices: 617358--617386 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
617348 TAAATCTCAG
617358 TTTAATGA
1 TTTAATGA
617366 TTTAATG-
1 TTTAATGA
617373 TTTAATGA
1 TTTAATGA
617381 TTTAAT
1 TTTAAT
617387 AAGTAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TTTAATGA
Found at i:634756 original size:44 final size:44
Alignment explanation
Indices: 634662--634756 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 44
634652 ATTTTTAATT
* *
634662 AATTTTAATTATACTTACTTTAAAACTCCTTAAAATTAAATAAT
1 AATTTTAATTATACTTACTTTAAAACACCTTAAAATTAAATAAA
* *
634706 AA-TTTAATTATTATTTA-TTTAAAACACTTTTAAAA-TAAATAAA
1 AATTTTAATTA-TACTTACTTTAAAACAC-CTTAAAATTAAATAAA
634749 AATTTTAA
1 AATTTTAA
634757 ACATGTTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
43 26 0.59
44 18 0.41
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (44 bp):
AATTTTAATTATACTTACTTTAAAACACCTTAAAATTAAATAAA
Found at i:636044 original size:17 final size:18
Alignment explanation
Indices: 636012--636045 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
636002 CGTCTTTTCA
636012 TGGCTTCTTGAAGTTTAT
1 TGGCTTCTTGAAGTTTAT
*
636030 TGGCTT-TTGAGGTTTA
1 TGGCTTCTTGAAGTTTA
636046 ATCTTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (18 bp):
TGGCTTCTTGAAGTTTAT
Found at i:638139 original size:16 final size:16
Alignment explanation
Indices: 638120--638154 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
638110 TTCTTTTCCA
*
638120 AAATTTTTCTTTGTTT
1 AAATTTTTATTTGTTT
*
638136 AAATTTTTATTTTTTT
1 AAATTTTTATTTGTTT
638152 AAA
1 AAA
638155 ACTGCTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
AAATTTTTATTTGTTT
Found at i:651765 original size:19 final size:19
Alignment explanation
Indices: 651743--651781 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
651733 ATTTTTAAGG
651743 ATGCTCACGAGTTTTGCAA
1 ATGCTCACGAGTTTTGCAA
*
651762 ATGCTCATGAGTTTTGCAA
1 ATGCTCACGAGTTTTGCAA
651781 A
1 A
651782 GCATACGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (19 bp):
ATGCTCACGAGTTTTGCAA
Found at i:662262 original size:21 final size:21
Alignment explanation
Indices: 662220--662263 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
662210 ACTCCTAGAG
* *
662220 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
662241 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
662262 CT
1 CT
662264 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:663386 original size:19 final size:19
Alignment explanation
Indices: 663359--663397 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
663349 ACATCGAATG
* *
663359 CATTTCATGCATCGATGCA
1 CATTCCATGCACCGATGCA
663378 CATTCCATGCACCGATGCA
1 CATTCCATGCACCGATGCA
663397 C
1 C
663398 TGAGGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (19 bp):
CATTCCATGCACCGATGCA
Found at i:663460 original size:19 final size:19
Alignment explanation
Indices: 663434--663483 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
663424 TGCATTTGAT
663434 GCATCGATGCACCAGCCAA
1 GCATCGATGCACCAGCCAA
* *
663453 GTATCGATGCACCAGCCAT
1 GCATCGATGCACCAGCCAA
663472 GCATCGATGCAC
1 GCATCGATGCAC
663484 TCTGGCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (19 bp):
GCATCGATGCACCAGCCAA
Found at i:663480 original size:86 final size:83
Alignment explanation
Indices: 663369--663528 Score: 214
Period size: 83 Copynumber: 1.9 Consensus size: 83
663359 CATTTCATGC
* * * * *
663369 ATCGATGCACATTCCATGCACCGATGCACTGAGGATTTTTTATGAAAACATCGAATGCATTTGAT
1 ATCGATGCACATGCCATGCACCGATGCACTCAGG-CTATTT-TG-AAACATCGAATGCACTTGAT
663434 GCATCGATGCACCAGCCAAGT
63 GCATCGATGCACCAGCCAAGT
* *
663455 ATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGC
1 ATCGATGCA-CATGCCATGCACCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTGATGC
663519 ATCGATGCAC
65 ATCGATGCAC
663529 TCTTAGTGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
83 31 0.47
84 2 0.03
85 4 0.06
86 27 0.41
87 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
ATCGATGCACATGCCATGCACCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTGATGCA
TCGATGCACCAGCCAAGT
Found at i:663528 original size:17 final size:19
Alignment explanation
Indices: 663500--663548 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
663490 TATTTTGAAA
663500 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
663518 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
663537 CACCGATGCACT
1 CATCGATGCACT
663549 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:666373 original size:16 final size:16
Alignment explanation
Indices: 666352--666382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
666342 TGTATGTTCT
*
666352 TTATTTTATTATTTCA
1 TTATTTTACTATTTCA
666368 TTATTTTACTATTTC
1 TTATTTTACTATTTC
666383 TGTCATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTACTATTTCA
Found at i:666462 original size:16 final size:16
Alignment explanation
Indices: 666421--666462 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
666411 GAAAAAAATG
666421 TTTATGTTTATGTTTT
1 TTTATGTTTATGTTTT
* *
666437 TATATGTTTATTTTTAT
1 TTTATGTTTATGTTT-T
666454 TTTAT-TTTA
1 TTTATGTTTA
666463 AGAAGATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTATGTTTATGTTTT
Done.