Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 162 of 213
Found at i:48490936 original size:17 final size:17
Alignment explanation
Indices: 48490914--48490953 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
48490904 TAGAGGAAAA
* *
48490914 GAAAATTTATTAATGTT
1 GAAAATGTACTAATGTT
48490931 GAAAATGTACTAATGTT
1 GAAAATGTACTAATGTT
48490948 GAAAAT
1 GAAAAT
48490954 CGAATGATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (17 bp):
GAAAATGTACTAATGTT
Found at i:48492485 original size:56 final size:56
Alignment explanation
Indices: 48492396--48492509 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
48492386 CATGCTTAAC
*
48492396 AATGTTCAAAATACTTCCATGACAACTCGATCTTTCATGAGTTTAGAAACAAAATT
1 AATGTTCAAAATACTTCCATGACAACTCAATCTTTCATGAGTTTAGAAACAAAATT
*
48492452 AATGTTCAAAATACTTCCATGACAACTCAATCTTTCATGAGTTTGGAAACAAAATT
1 AATGTTCAAAATACTTCCATGACAACTCAATCTTTCATGAGTTTAGAAACAAAATT
48492508 AA
1 AA
48492510 GTCCTTTCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (56 bp):
AATGTTCAAAATACTTCCATGACAACTCAATCTTTCATGAGTTTAGAAACAAAATT
Found at i:48495077 original size:41 final size:41
Alignment explanation
Indices: 48495025--48495113 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
48495015 AAATCATGCT
*
48495025 TGCATTTGAACAAACTTATGAACAAAAATTATTTTTGAATA
1 TGCATTTGAACAAACTTATGAACAAAAATTATTTTTGAACA
48495066 TGCATTTGAACAAACTTATGAACAAAAATTATTTTTGAACA
1 TGCATTTGAACAAACTTATGAACAAAAATTATTTTTGAACA
*
48495107 TTCATTT
1 TGCATTT
48495114 ATTTTAGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (41 bp):
TGCATTTGAACAAACTTATGAACAAAAATTATTTTTGAACA
Found at i:48502182 original size:47 final size:47
Alignment explanation
Indices: 48502116--48502636 Score: 862
Period size: 47 Copynumber: 11.1 Consensus size: 47
48502106 GAAATGATAG
48502116 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
48502163 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
48502210 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATACATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
48502257 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
48502304 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
48502351 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
48502398 TAAGGCCTAATAGCCGATGTAATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
48502445 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
48502492 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGGGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
48502539 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
48502586 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
48502633 TAAG
1 TAAG
48502637 TCCCGAAGGG
Statistics
Matches: 445, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 445 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:48502811 original size:37 final size:37
Alignment explanation
Indices: 48502755--48502833 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
48502745 CCGAGCTCTA
* *
48502755 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
48502792 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
48502829 AAGAC
1 AAGAC
48502834 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:48504374 original size:7 final size:7
Alignment explanation
Indices: 48504356--48504385 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
48504346 TATTGAACAT
48504356 AAAATT-
1 AAAATTA
48504362 AAAATTA
1 AAAATTA
48504369 AAAATTA
1 AAAATTA
48504376 AAAATTA
1 AAAATTA
48504383 AAA
1 AAA
48504386 TGGAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:48513469 original size:223 final size:223
Alignment explanation
Indices: 48513074--48513518 Score: 773
Period size: 223 Copynumber: 2.0 Consensus size: 223
48513064 CAGTACTCCA
* *
48513074 GGTGCACTGCACTGATTACAAATAAATGTGGACTTAATATGCTGTTCATACTCCACGAAACTCCT
1 GGTGCACTGCACTGATTACAAATAAATGTGGACTTAATATACTGTTCATACACCACGAAACTCCT
* *
48513139 TCGTCAACCACAATGATAACCCACCCCAATGCACATGCAATATGTCATACAATCTCATACATAGT
66 CCGTCAACCACAATGATAACCCACCCCAATGCACATGCAACATGTCATACAATCTCATACATAGT
*
48513204 CATAATTCAATACTTTCTTAATTTATTGACAAGTTCAACATGCCCTCGAATTATCAAATACTTTC
131 CATAATTCAATACTTTCTCAATTTATTGACAAGTTCAACATGCCCTCGAATTATCAAATACTTTC
*
48513269 AGTGAACAGGATCGTGGATCCCAATTTT
196 AGTGAACAGGATCATGGATCCCAATTTT
* * * *
48513297 GGTGCAGTGCACTGATTACAAATAAATGTGGACTTAATATACTGTTCTTACACTACGGAACTCCT
1 GGTGCACTGCACTGATTACAAATAAATGTGGACTTAATATACTGTTCATACACCACGAAACTCCT
*
48513362 CCGTCAACCACAATGATAACCCACCCCAATGCACATGCAACATGTCATATAATCTCATACATAGT
66 CCGTCAACCACAATGATAACCCACCCCAATGCACATGCAACATGTCATACAATCTCATACATAGT
* *
48513427 CATAATTCAATACTTTCTCAATTTATTGACATGTTCAACATGCGCTCGAATTATCAAATACTTTC
131 CATAATTCAATACTTTCTCAATTTATTGACAAGTTCAACATGCCCTCGAATTATCAAATACTTTC
48513492 AGTGAACAGGATCATGGATCCCAATTT
196 AGTGAACAGGATCATGGATCCCAATTT
48513519 CGATTTACCA
Statistics
Matches: 209, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
223 209 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (223 bp):
GGTGCACTGCACTGATTACAAATAAATGTGGACTTAATATACTGTTCATACACCACGAAACTCCT
CCGTCAACCACAATGATAACCCACCCCAATGCACATGCAACATGTCATACAATCTCATACATAGT
CATAATTCAATACTTTCTCAATTTATTGACAAGTTCAACATGCCCTCGAATTATCAAATACTTTC
AGTGAACAGGATCATGGATCCCAATTTT
Found at i:48515776 original size:18 final size:18
Alignment explanation
Indices: 48515731--48515778 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
48515721 AAACTAAAAA
* *
48515731 TAATAAAATAAAATATTT
1 TAATTAAATTAAATATTT
*
48515749 TTA-T-AATTAAATATTT
1 TAATTAAATTAAATATTT
48515765 TAATTAAATTAAAT
1 TAATTAAATTAAAT
48515779 CTAATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 13 0.54
17 1 0.04
18 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTAAATTAAATATTT
Found at i:48515944 original size:30 final size:27
Alignment explanation
Indices: 48515908--48515974 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
48515898 ATATTAGGAG
48515908 TTATTATTATTATTTGATGTGTAT-AGT
1 TTATTATTATTATTTGATGTGT-TCAGT
48515935 TTATTATTATTATTTGATGTGTTCAGT
1 TTATTATTATTATTTGATGTGTTCAGT
*
48515962 TTTTTATTATTAT
1 TTATTATTATTAT
48515975 CTAATACTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.24, C:0.01, G:0.12, T:0.63
Consensus pattern (27 bp):
TTATTATTATTATTTGATGTGTTCAGT
Found at i:48516398 original size:47 final size:47
Alignment explanation
Indices: 48516347--48516444 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
48516337 ATGAGTATGT
48516347 TTAAGAAAAAACCCACCTCAACATTTTAAATGAAATTATTAACCACG
1 TTAAGAAAAAACCCACCTCAACATTTTAAATGAAATTATTAACCACG
48516394 TTAAGAAAAAACCCACCTCAACATTTTAAATGAAATTATTAACCACG
1 TTAAGAAAAAACCCACCTCAACATTTTAAATGAAATTATTAACCACG
48516441 TTAA
1 TTAA
48516445 TTATTTGGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (47 bp):
TTAAGAAAAAACCCACCTCAACATTTTAAATGAAATTATTAACCACG
Found at i:48518105 original size:40 final size:40
Alignment explanation
Indices: 48518021--48518200 Score: 209
Period size: 41 Copynumber: 4.5 Consensus size: 40
48518011 TTTGAATACT
* * * * *
48518021 TGAAAATGTTGAAAAGGAAGTTACCCGAAAGGGATAACACA
1 TGAAAAGGTTGAAAAGGAA-TTATCCGAAAAGGATATCAAA
* *
48518062 TGAAAAGGTTGAAAAAGAAATATCCGAAAAGGATATCAAA
1 TGAAAAGGTTGAAAAGGAATTATCCGAAAAGGATATCAAA
* * * *
48518102 TGAAAATGTTGAAGAGGACGTTATTCGAAAAGGATATCAAA
1 TGAAAAGGTTGAAAAGGA-ATTATCCGAAAAGGATATCAAA
* *
48518143 TGAAAAGGTTGAAAAGGACGTAATCCGAAAAGGATATC-AA
1 TGAAAAGGTTGAAAAGGA-ATTATCCGAAAAGGATATCAAA
48518183 TGAAAAGGTTGAAAAGGA
1 TGAAAAGGTTGAAAAGGA
48518201 TAGCAATGAA
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
40 51 0.42
41 70 0.58
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.19
Consensus pattern (40 bp):
TGAAAAGGTTGAAAAGGAATTATCCGAAAAGGATATCAAA
Found at i:48518137 original size:81 final size:81
Alignment explanation
Indices: 48518021--48518200 Score: 245
Period size: 81 Copynumber: 2.2 Consensus size: 81
48518011 TTTGAATACT
* *
48518021 TGAAAATGTTGAAAAGGAAGTTACCCGAAAGGGATAACACATGAAAAGGTTGAAAAAGAAAT-AT
1 TGAAAATGTTGAAAAGGAAGTTACCCGAAAAGGATAACAAATGAAAAGGTTGAAAAAGAAATAAT
48518085 CCGAAAAGGATATCAAA
66 CCGAAAAGGATATC-AA
* * ** * * **
48518102 TGAAAATGTTGAAGAGGACGTTATTCGAAAAGGATATCAAATGAAAAGGTTGAAAAGGACGTAAT
1 TGAAAATGTTGAAAAGGAAGTTACCCGAAAAGGATAACAAATGAAAAGGTTGAAAAAGAAATAAT
48518167 CCGAAAAGGATATCAA
66 CCGAAAAGGATATCAA
*
48518183 TGAAAAGGTTGAAAAGGA
1 TGAAAATGTTGAAAAGGA
48518201 TAGCAATGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 70 0.81
82 16 0.19
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.19
Consensus pattern (81 bp):
TGAAAATGTTGAAAAGGAAGTTACCCGAAAAGGATAACAAATGAAAAGGTTGAAAAAGAAATAAT
CCGAAAAGGATATCAA
Found at i:48535261 original size:596 final size:597
Alignment explanation
Indices: 48534141--48535883 Score: 2318
Period size: 596 Copynumber: 2.8 Consensus size: 597
48534131 TTTTTTTTTT
* * **
48534141 TGTAAAAAGATGTATGAAACATTTAGGTTGGGTTGAAATTTATTGAATTGGAACCAAATGGGATT
1 TGTAAAAAGATGAATGAAACATTTAGGTT-GGTTGAAAATTATTGAATTGGAATGAAATGGGATT
* *
48534206 TTTTTCCAAAAACAAGGGCCACATCGCAACTACCAAATTCTAACGTTGCAACATGGTGCG-ACAA
65 TTTTTCCAAAAACAAGGGCCACATC-CAACAACCAAATTCTAACGTTGCAACATGGAGCGAAC-A
* * * * * * * ** *
48534270 TGAGTGACGTCGCGACGTGGAAACCAGGAAGTTGTGACGTCAACCTGAAGTTTTGTAAACTTTAG
128 TGAGTGACGTTGCGACGTGGAAACCAAGAAGCTGTAATGTCGACCTGAAATTTTAAAAACTTTAC
* * * * * * * ** *
48534335 TATTTGGTCCTAA-TCACCCTCAGGTTAGCAAAATAGCTTTCATAAGCTCGGATAGGTAACCTAA
193 AATTTGGTTCTAATTCACCCTCAAGTTAGCAAAAGAGCTTTCGTAAGCTCGGACAAGTAATTTGA
** *
48534399 TACATATATA-TATTCACATAATGCATGT-CCGAAGGATGTGGTTTTGGAAATTTTTGTGTTTGC
258 TTTATATATATTGTTCACATAATGCATGTACC-AAGGATGTGGTTTTGGAAATTTTTGTGTTTGC
48534462 ACTTGCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGTTTTGGATGTTAAGTTTGATGAATGACT
322 ACTTGCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGTTTTGGATGTTAAGTTTGATGAATGACT
*
48534527 TAATTGATGCATGTTTAGTTATGTTTGATGCTATTAAAGATAGCGATCAAGAACTTGTATGAATT
387 TAATTGATGCATGTTTAGTTATGTTTGATGCTATTAAAGATAGCGATCAAGAACTTGCATGAATT
48534592 GTTAGGTTAAGGATTGAAAGGTGAGGTAGTTTACGTATAATAAGTTGATATATAAGTTAGAATTG
452 GTTAGGTTAAGGATTGAAAGGTGAGGTAGTTTACGTATAATAAGTTGATATATAAGTTAGAATTG
*
48534657 ATATGTTTAAACGTAAATATGAATTTGAACTCAAATGACAATATTTTGGCATTTGACATATTAAG
517 ATATGTTTAAACGTAAAGATGAATTTGAACTCAAATGACAATATTTTGGCATTTGACATATTAA-
*
48534722 AGGT-TT-TT-T-TTGCG
581 A-GTCTTGTTATATTACG
*
48534736 TGTAAAAAGATGCATGAAACATTTAGGTTGGTTGAAAATTATTGAATTGGAATGAAATGGGATTT
1 TGTAAAAAGATGAATGAAACATTTAGGTTGGTTGAAAATTATTGAATTGGAATGAAATGGGATTT
* * *
48534801 TTTTCCAAAAACAAGGGCCACATCACAACCACCAACTTCTGACGTTGCAACATGGAGCGAACATG
66 TTTTCCAAAAACAAGGGCCACATC-CAACAACCAAATTCTAACGTTGCAACATGGAGCGAACATG
* * *
48534866 AGTGACGTTGCGACGTGGAAACCAAGAAGCTATAATGCCGACCTAAAATTTTAAAAACTTTACAA
130 AGTGACGTTGCGACGTGGAAACCAAGAAGCTGTAATGTCGACCTGAAATTTTAAAAACTTTACAA
* * *
48534931 TTTGGTTCTAATTCACCCTCAAGTTAGGAAAAGAGCTTTTGTAAGCTCAGACAAGTAATTTGATT
195 TTTGGTTCTAATTCACCCTCAAGTTAGCAAAAGAGCTTTCGTAAGCTCGGACAAGTAATTTGATT
48534996 TATATATATTGTTCACATAATGCATGTACCAAGGATGTGGTTTTGGAAATTTTTGTGTTTGCACT
260 TATATATATTGTTCACATAATGCATGTACCAAGGATGTGGTTTTGGAAATTTTTGTGTTTGCACT
*
48535061 TGCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGTTTTAGATGTTAAGTTTGATGAATGACTTAA
325 TGCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGTTTTGGATGTTAAGTTTGATGAATGACTTAA
* *
48535126 TTGATGCATGTTTAGTTATGTTTGATGCTATTAAAAATAGCGATCAAGAACTTGCATGAATTTTT
390 TTGATGCATGTTTAGTTATGTTTGATGCTATTAAAGATAGCGATCAAGAACTTGCATGAATTGTT
48535191 AGGTTAAGGATTGAAAGGTGAGGTAGTTTACGTATAATAAGTTGATATATAAGTTAGAATTGATA
455 AGGTTAAGGATTGAAAGGTGAGGTAGTTTACGTATAATAAGTTGATATATAAGTTAGAATTGATA
* * * *
48535256 TGTTTAAATGTAAAGATGAATTTGAACTCAAATGATAATCTTTTGGTATTTGACATATTAAATTC
520 TGTTTAAACGTAAAGATGAATTTGAACTCAAATGACAATATTTTGGCATTTGACATATTAAA---
*
48535321 TTGGTTGAAATAGTTATGTGATCATATTAGCATGAAATTAAGATG
582 ------G---T--CT-TGT--T-ATATTA-C-------------G
* *
48535366 TTTTTTTTTTTTGTAAAAAGATGTATGAAACATTTAGGTTGGGCTGAAAATTATTGAATTGGAAT
1 -----------TGTAAAAAGATGAATGAAACATTTAGGTT-GGTTGAAAATTATTGAATTGGAAT
* * * * *
48535431 GAAATGGGA-TTATTTCCAAAAACAAGGGCCACATCACAACCACCAACTTCTGACATTGCAACAT
54 GAAATGGGATTTTTTTCCAAAAACAAGGGCCACATC-CAACAACCAAATTCTAACGTTGCAACAT
48535495 GGAGCGAACATGAGTGACGTTGCGACGTGGAAACCAAGAAGCTGTAATGTCGACCTGAAATTTTA
118 GGAGCGAACATGAGTGACGTTGCGACGTGGAAACCAAGAAGCTGTAATGTCGACCTGAAATTTTA
48535560 AAAACTTTACAATTTGGTTCTAATTCACCCTCAAGTTAGCAAAAGAGCTTTCGTAAGCTCGGACA
183 AAAACTTTACAATTTGGTTCTAATTCACCCTCAAGTTAGCAAAAGAGCTTTCGTAAGCTCGGACA
* *
48535625 AGTAATTTGATTCATATATATATTGTTCACATGATGCATGTACCAAGGATATGGTTTTGGAAATT
248 AGTAATTTGATT--TATATATATTGTTCACATAATGCATGTACCAAGGATGTGGTTTTGGAAATT
*
48535690 TTTGTGTTTGCACTTGCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGGTTTGGATGTTAAGTTT
311 TTTGTGTTTGCACTTGCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGTTTTGGATGTTAAGTTT
* * * * *
48535755 GATGAATTACTTAATTGATGCATGTTTAGTTATGTTTGATTCTATTACAGATAGTGATAAAGAAC
376 GATGAATGACTTAATTGATGCATGTTTAGTTATGTTTGATGCTATTAAAGATAGCGATCAAGAAC
* * *
48535820 TTGCATGAATTGTTAGGTTAA-GATTAAAAAGTGAGGTAGTTTATGTATAATAAGTTGATATATA
441 TTGCATGAATTGTTAGGTTAAGGATTGAAAGGTGAGGTAGTTTACGTATAATAAGTTGATATATA
48535884 TATGTAAAGA
Statistics
Matches: 1022, Mismatches: 73, Indels: 59
0.89 0.06 0.05
Matches are distributed among these distances:
594 151 0.15
595 79 0.08
596 299 0.29
597 2 0.00
603 1 0.00
606 1 0.00
609 1 0.00
610 1 0.00
611 1 0.00
613 1 0.00
615 1 0.00
616 2 0.00
617 1 0.00
630 1 0.00
641 217 0.21
642 72 0.07
643 191 0.19
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (597 bp):
TGTAAAAAGATGAATGAAACATTTAGGTTGGTTGAAAATTATTGAATTGGAATGAAATGGGATTT
TTTTCCAAAAACAAGGGCCACATCCAACAACCAAATTCTAACGTTGCAACATGGAGCGAACATGA
GTGACGTTGCGACGTGGAAACCAAGAAGCTGTAATGTCGACCTGAAATTTTAAAAACTTTACAAT
TTGGTTCTAATTCACCCTCAAGTTAGCAAAAGAGCTTTCGTAAGCTCGGACAAGTAATTTGATTT
ATATATATTGTTCACATAATGCATGTACCAAGGATGTGGTTTTGGAAATTTTTGTGTTTGCACTT
GCTAGTTTGTCATTTGGCTAAGTTGATGCTTGGTTTTGGATGTTAAGTTTGATGAATGACTTAAT
TGATGCATGTTTAGTTATGTTTGATGCTATTAAAGATAGCGATCAAGAACTTGCATGAATTGTTA
GGTTAAGGATTGAAAGGTGAGGTAGTTTACGTATAATAAGTTGATATATAAGTTAGAATTGATAT
GTTTAAACGTAAAGATGAATTTGAACTCAAATGACAATATTTTGGCATTTGACATATTAAAGTCT
TGTTATATTACG
Found at i:48541381 original size:78 final size:78
Alignment explanation
Indices: 48541297--48541454 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
48541287 CACTCTAAAA
* *
48541297 CATCCTTAAACACCATTAAACCATAACTCATGGTTCCAAATCATTTAAAAAATTTCTAATTTATG
1 CATCCTTAAACAACATTAAACCATAACTCATGGTTCCAAATCATTTAAAAAATTTCTAAATTATG
48541362 TTTAATCATAATT
66 TTTAATCATAATT
48541375 CATCCTTAAACAACATTAAACCATAACTCATGGTTCCAAATCATTTAAAAAATTTCTAAATTATG
1 CATCCTTAAACAACATTAAACCATAACTCATGGTTCCAAATCATTTAAAAAATTTCTAAATTATG
48541440 TTTAATCATAATT
66 TTTAATCATAATT
48541453 CA
1 CA
48541455 AAGTCATAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (78 bp):
CATCCTTAAACAACATTAAACCATAACTCATGGTTCCAAATCATTTAAAAAATTTCTAAATTATG
TTTAATCATAATT
Found at i:48545568 original size:21 final size:23
Alignment explanation
Indices: 48545542--48545584 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
48545532 ATTTTATTGA
48545542 TGAATTGA-AT-ATGGTAAATTT
1 TGAATTGATATAATGGTAAATTT
*
48545563 TGAATTGATATAATTGTAAATT
1 TGAATTGATATAATGGTAAATT
48545585 AAATGGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (23 bp):
TGAATTGATATAATGGTAAATTT
Found at i:48548088 original size:20 final size:20
Alignment explanation
Indices: 48548059--48548098 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48548049 ATACTTTGTA
*
48548059 AATGATAAAATTACCATTTT
1 AATGAAAAAATTACCATTTT
*
48548079 AATGAAAAAATTACTATTTT
1 AATGAAAAAATTACCATTTT
48548099 TCCCTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (20 bp):
AATGAAAAAATTACCATTTT
Found at i:48548871 original size:107 final size:108
Alignment explanation
Indices: 48548673--48548878 Score: 281
Period size: 107 Copynumber: 1.9 Consensus size: 108
48548663 TACCGTCGTA
* *
48548673 ATAATATAAATTATTTAAAATAATAAGGTTATTTTACTAATTTTCTTAACCAAGCTGGTGTTGAG
1 ATAATATAAATTATTTAAAATAATAAGGTTATTTTACTAATTTCCTTAACCAAGCTGGTGTCGAG
* *
48548738 TTGACTTGTGACACTAACTCAATCACACACTTAAGCAATAGAT
66 TTGACTCGTGACACCAACTCAATCACACACTTAAGCAATAGAT
* * * * * *
48548781 ATAATATAACTTATTTAAAAT-ATGAATGTTA-TTTAGTAATTTCCTTGATCAAGTTGGTGTCGA
1 ATAATATAAATTATTTAAAATAAT-AAGGTTATTTTACTAATTTCCTTAACCAAGCTGGTGTCGA
* *
48548844 GTTGACTCGTGACACCAACTTAGTCACACACTTAA
65 GTTGACTCGTGACACCAACTCAATCACACACTTAA
48548879 ATAATAGTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
107 59 0.69
108 26 0.31
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (108 bp):
ATAATATAAATTATTTAAAATAATAAGGTTATTTTACTAATTTCCTTAACCAAGCTGGTGTCGAG
TTGACTCGTGACACCAACTCAATCACACACTTAAGCAATAGAT
Found at i:48550759 original size:17 final size:17
Alignment explanation
Indices: 48550737--48550769 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
48550727 ATATTTAATA
48550737 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
48550754 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
48550770 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:48550775 original size:17 final size:17
Alignment explanation
Indices: 48550733--48550775 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
48550723 GTATATATTT
48550733 AATATATATTTGATTAAA
1 AATA-ATATTTGATTAAA
48550751 AAGT-ATATTTGATTAAA
1 AA-TAATATTTGATTAAA
48550768 AATAATAT
1 AATAATAT
48550776 ATATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 19 0.83
18 2 0.09
19 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (17 bp):
AATAATATTTGATTAAA
Found at i:48550791 original size:21 final size:21
Alignment explanation
Indices: 48550732--48550791 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 21
48550722 AGTATATATT
*
48550732 TAATATATATTTGAT-TAAAA
1 TAATATATATTTAATATAAAA
* * *
48550752 -AGTATAT-TTGATTA-AAAA
1 TAATATATATTTAATATAAAA
48550770 TAATATATATTTAATATAAAA
1 TAATATATATTTAATATAAAA
48550791 T
1 T
48550792 TTGGGCCTGG
Statistics
Matches: 29, Mismatches: 7, Indels: 7
0.67 0.16 0.16
Matches are distributed among these distances:
18 7 0.24
19 12 0.41
20 5 0.17
21 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TAATATATATTTAATATAAAA
Found at i:48558149 original size:37 final size:37
Alignment explanation
Indices: 48558108--48558283 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
48558098 TTTGAGTACT
48558108 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
48558145 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
48558182 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
48558219 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
48558256 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
48558284 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:48558355 original size:45 final size:46
Alignment explanation
Indices: 48558246--48558369 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
48558236 GTGATAAGTG
* *
48558246 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
48558292 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
48558337 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
48558370 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:48574851 original size:17 final size:17
Alignment explanation
Indices: 48574831--48574864 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48574821 AATATATAAT
48574831 TTTAGAAAAAGGACTAA
1 TTTAGAAAAAGGACTAA
* *
48574848 TTTATAAAAAGGTCTAA
1 TTTAGAAAAAGGACTAA
48574865 GGTTTGAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (17 bp):
TTTAGAAAAAGGACTAA
Found at i:48595705 original size:18 final size:20
Alignment explanation
Indices: 48595684--48595733 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
48595674 AAAGAAAGAC
48595684 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
48595702 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
48595722 AGAAAAAAGAGA
1 AG-AAAAAGAGA
48595734 TTGAGAGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:48597923 original size:40 final size:40
Alignment explanation
Indices: 48597839--48598022 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
48597829 TTGAATGCTG
* * * *
48597839 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
48597878 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
48597919 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
48597959 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
48597999 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
48598023 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:48597976 original size:80 final size:81
Alignment explanation
Indices: 48597839--48598019 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
48597829 TTGAATGCTG
* *
48597839 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
48597903 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
48597919 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
48597980 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
48597999 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
48598020 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:48602712 original size:13 final size:13
Alignment explanation
Indices: 48602694--48602719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48602684 CCCGGATAAT
48602694 TGAATTATTGAAG
1 TGAATTATTGAAG
48602707 TGAATTATTGAAG
1 TGAATTATTGAAG
48602720 ATGTGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TGAATTATTGAAG
Found at i:48607097 original size:21 final size:21
Alignment explanation
Indices: 48607068--48607108 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48607058 TTATATATTT
*
48607068 TTTAGAATTTTTTTTGAAATC
1 TTTACAATTTTTTTTGAAATC
*
48607089 TTTACAATTTTTTTTTAAAT
1 TTTACAATTTTTTTTGAAAT
48607109 ATAAATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTACAATTTTTTTTGAAATC
Found at i:48608156 original size:38 final size:38
Alignment explanation
Indices: 48608105--48608180 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
48608095 TATTACCCTC
*
48608105 AATAACTCCATTAAAGAAGAAACCACTCAAAACACCAT
1 AATAACTCCATTAAAGAAGAAACAACTCAAAACACCAT
48608143 AATAACTCCATTAAAGAAGAAACAACTCAAAACACCAT
1 AATAACTCCATTAAAGAAGAAACAACTCAAAACACCAT
48608181 CAATCGGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.54, C:0.25, G:0.05, T:0.16
Consensus pattern (38 bp):
AATAACTCCATTAAAGAAGAAACAACTCAAAACACCAT
Found at i:48609235 original size:10 final size:10
Alignment explanation
Indices: 48609220--48609247 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
48609210 GTGTATTAAT
48609220 TTTTATATTA
1 TTTTATATTA
48609230 TTTTATATTA
1 TTTTATATTA
48609240 TTTTATAT
1 TTTTATAT
48609248 AGGCGGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATATTA
Found at i:48609441 original size:158 final size:159
Alignment explanation
Indices: 48609259--48610123 Score: 1305
Period size: 158 Copynumber: 5.4 Consensus size: 159
48609249 GGCGGCACCC
*
48609259 CCCTTTGTTCCTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
* *
48609324 TTTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTG-TTTTTTAT
66 TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTGTTTTTTTAT
*
48609388 ATAAATTTAGTAAAAAACCCTCATTTTGG
131 ATAAATTTAGTAAAAAACCCTTATTTTGG
* * * * * * *
48609417 CCATTTGTTCGTATTTTCCTTATTTTCGGATTTTATTAGTTTCAAAATATATATTATTTTCATAT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
*
48609482 TTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTAT
66 TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTGTTTTTTTAT
* *
48609547 GTAAATTTAGTTAAAAAAACCCTTACTTTGG
131 ATAAATTTAG-T-AAAAAACCCTTATTTTGG
* *
48609578 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTATTTTCAAAAAATATATTATTTTCGTAT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
* *
48609643 TTTATTATTTTATATTATTTTAGTACATAAATTTTGAAATGTATTATTTTTGTGTGTTTTTTTTA
66 TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTG-TTTTTTTA
48609708 TATAAATTTAGTAAAAAA-CCTTATTTTGG
130 TATAAATTTAGTAAAAAACCCTTATTTTGG
* *
48609737 CCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTATTACTTTC-AAAAATATACTATTTTCGTAT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
* *
48609801 TTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTG-TTTTTTAT
66 TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTGTTTTTTTAT
*
48609865 ATAAATTTAGTAAAAAAACCCTTATTTTGA
131 ATAAATTTAGT-AAAAAACCCTTATTTTGG
** * *
48609895 CTATTTGTTCGTATTTTTCTTATTTT-TGAATTTTATTACTTTCAAAAAATATACTATTTTTGTA
1 CCCTTTGTTCGTATTTTTCTTATTTTCAG-ATTTTATTACTTTCAAAAAATATACTATTTTCGTA
48609959 TTTTATTATTTTATATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTGTGTTTTTTT
65 TTTTATTATTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTATTTTAGTGTGTTTTTTT
* *
48610023 ATATAAATTTAGT-GAAAACCCTTATTTTAG
129 ATATAAATTTAGTAAAAAACCCTTATTTTGG
* * ** *
48610053 CCCTTTGTTCGTATTTTTATTTTTTTC-GAATTTTATTACTTTCAGTAAATATACTATTTTCGTT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAG-ATTTTATTACTTTCAAAAAATATACTATTTTCGTA
48610117 TTTTATT
65 TTTTATT
48610124 TCTTTTCGTA
Statistics
Matches: 644, Mismatches: 52, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
156 19 0.03
157 7 0.01
158 305 0.47
159 140 0.22
160 26 0.04
161 129 0.20
162 18 0.03
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (159 bp):
CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTGTTTTTTTAT
ATAAATTTAGTAAAAAACCCTTATTTTGG
Found at i:48609489 original size:16 final size:16
Alignment explanation
Indices: 48609436--48609497 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
48609426 CGTATTTTCC
**
48609436 TTATTTTCGGATTTTA
1 TTATTTTCATATTTTA
* * *
48609452 TTAGTTTCAAAATATATA
1 TTATTTTC-ATAT-TTTA
48609470 TTATTTTCATATTTTA
1 TTATTTTCATATTTTA
48609486 TTATTTT-ATATT
1 TTATTTTCATATT
48609498 ATTTTAGTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 5 0.14
16 17 0.46
17 5 0.14
18 10 0.27
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (16 bp):
TTATTTTCATATTTTA
Found at i:48609612 original size:319 final size:316
Alignment explanation
Indices: 48609259--48610123 Score: 1378
Period size: 319 Copynumber: 2.7 Consensus size: 316
48609249 GGCGGCACCC
*
48609259 CCCTTTGTTCCTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
* *
48609324 TTTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTG-TTTTTTAT
66 TTTATTATTTTATATTATTTTAGTACATAAA-TTTGAAATGTATTATTTTAGTGTGTTTTTTTAT
* * * *
48609388 ATAAATTTAGTAAAAAACCCTCATTTTGGCCATTTGTTCGTATTTTCCTTATTTTCGGATTTTAT
130 ATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTAT
* * *
48609453 TAGTTTCAAAATATATATTATTTTCATATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
195 TACTTTCAAAA-ATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
* * *
48609518 AAATGTATTATTTTAGTGTGTTTTTTTATGTAAATTTAGTTAAAAAAACCCTTACTTTGG
259 AAATGTATTAATTTAGTGTG-TTTTTTATATAAATTTAG-TAAAAAAACCCTTACTTTGA
* *
48609578 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTATTTTCAAAAAATATATTATTTTCGTAT
1 CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
*
48609643 TTTATTATTTTATATTATTTTAGTACATAAATTTTGAAATGTATTATTTTTGTGTGTTTTTTTTA
66 TTTATTATTTTATATTATTTTAGTACATAAA-TTTGAAATGTATTATTTTAGTGTG-TTTTTTTA
48609708 TATAAATTTAGTAAAAAA-CCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTA
129 TATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTA
48609772 TTACTTTCAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
194 TTACTTTCAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
*
48609837 AAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGA
259 AAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAAACCCTTACTTTGA
** * *
48609895 CTATTTGTTCGTATTTTTCTTATTTT-TGAATTTTATTACTTTCAAAAAATATACTATTTTTGTA
1 CCCTTTGTTCGTATTTTTCTTATTTTCAG-ATTTTATTACTTTCAAAAAATATACTATTTTCGTA
48609959 TTTTATTATTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTTTA
65 TTTTATTATTTTATATTATTTTAGTACATAA-ATTTGAAATGTATTATTTTAGTGTGTTTTTTTA
* * * *
48610024 TATAAATTTAGT-GAAAACCCTTATTTTAGCCCTTTGTTCGTATTTTTATTTTTTTCGAATTTTA
129 TATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTA
* *
48610088 TTACTTTCAGTAAATATACTATTTTCGTTTTTTATT
194 TTACTTTCA-AAAATATACTATTTTCGTATTTTATT
48610124 TCTTTTCGTA
Statistics
Matches: 509, Mismatches: 31, Indels: 14
0.92 0.06 0.03
Matches are distributed among these distances:
315 4 0.01
316 73 0.14
317 152 0.30
318 18 0.04
319 184 0.36
320 53 0.10
321 25 0.05
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (316 bp):
CCCTTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
TTTATTATTTTATATTATTTTAGTACATAAATTTGAAATGTATTATTTTAGTGTGTTTTTTTATA
TAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCGGATTTTATT
ACTTTCAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
ATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAAACCCTTACTTTGA
Found at i:48609616 original size:16 final size:16
Alignment explanation
Indices: 48609592--48609653 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
48609582 TTGTTCGTAT
*
48609592 TTTTCTTATTTTCAGA
1 TTTTATTATTTTCAGA
*
48609608 TTTTATTATTTTCAAAAA
1 TTTTATTATTTTC--AGA
* *
48609626 ATATATTATTTTC-GTA
1 TTTTATTATTTTCAG-A
48609642 TTTTATTATTTT
1 TTTTATTATTTT
48609654 ATATTATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
16 23 0.64
18 13 0.36
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTATTATTTTCAGA
Found at i:48610131 original size:17 final size:17
Alignment explanation
Indices: 48610109--48610141 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48610099 AAATATACTA
*
48610109 TTTTCGTTTTTTATTTC
1 TTTTCGTATTTTATTTC
48610126 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
48610142 TTTCATAAAC
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:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCGTATTTTATTTC
Found at i:48611243 original size:29 final size:28
Alignment explanation
Indices: 48611176--48611243 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
48611166 CGATTTCGCG
*
48611176 AAAAATGGCACATTCCGGTAAATAATAA
1 AAAAATGGCTCATTCCGGTAAATAATAA
* **
48611204 AAAAATCGGCTCATTTCGGTAAATTTTGAA
1 AAAAAT-GGCTCATTCCGGTAAATAAT-AA
48611234 AAAAATGGCT
1 AAAAATGGCT
48611244 TTTATTGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.18
29 20 0.59
30 8 0.24
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAAATGGCTCATTCCGGTAAATAATAA
Found at i:48611317 original size:27 final size:27
Alignment explanation
Indices: 48611270--48611333 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
48611260 CCTAAAGGGG
* * *
48611270 GGTGCCGCCTATGGCAGTGGCACCTTT
1 GGTGCCGCCTATGCCACTGGCACCATT
*
48611297 GGTGCCGCCTCTGCCACTGGCACCATT
1 GGTGCCGCCTATGCCACTGGCACCATT
*
48611324 GGTGTCGCCT
1 GGTGCCGCCT
48611334 GTAGCAATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.09, C:0.34, G:0.31, T:0.25
Consensus pattern (27 bp):
GGTGCCGCCTATGCCACTGGCACCATT
Found at i:48611490 original size:17 final size:17
Alignment explanation
Indices: 48611468--48611502 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48611458 ATAATTAAGT
48611468 TTTAAATAATAAACATA
1 TTTAAATAATAAACATA
* *
48611485 TTTAAATATTATACATA
1 TTTAAATAATAAACATA
48611502 T
1 T
48611503 GTGTATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATAATAAACATA
Found at i:48615737 original size:15 final size:16
Alignment explanation
Indices: 48615709--48615738 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48615699 TAAATTCATA
48615709 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
48615725 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
48615739 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:48615763 original size:15 final size:16
Alignment explanation
Indices: 48615730--48615790 Score: 57
Period size: 15 Copynumber: 4.2 Consensus size: 16
48615720 ATTATTAAGA
48615730 ATTTTATTAAATTATAT
1 ATTTTATTAAA-TATAT
48615747 ATTTTATTAAA-ATAT
1 ATTTTATTAAATATAT
48615762 A---T-TT-AATATAT
1 ATTTTATTAAATATAT
48615773 -TTTTATTAAAT-TAT
1 ATTTTATTAAATATAT
48615787 ATTT
1 ATTT
48615791 AATAATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
10 2 0.05
11 6 0.16
12 1 0.03
13 1 0.03
14 5 0.14
15 11 0.30
17 11 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATTAAATATAT
Found at i:48615814 original size:42 final size:42
Alignment explanation
Indices: 48615731--48615891 Score: 117
Period size: 41 Copynumber: 3.9 Consensus size: 42
48615721 TTATTAAGAA
*
48615731 TTTTATTAAATTATATATTTTATTAA-AA-TATATTT-AA-TATAT
1 TTTTATTAAA-T-TATA-TTTAATAATAATTAT-TTTAAATTATAT
48615773 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATA-
1 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATAT
* * **
48615814 TTTTA-TAGTATTATATATT-ATGAT--TT-TAGTAAATTCATAT
1 TTTTATTA-AATTATAT-TTAATAATAATTATTTTAAATT-ATAT
*
48615854 ATTTTAATTAAATTATATTTAATAATAATTATGTTAAA
1 -TTTT-ATTAAATTATATTTAATAATAATTATTTTAAA
48615892 ATATGATTAA
Statistics
Matches: 95, Mismatches: 9, Indels: 27
0.73 0.07 0.21
Matches are distributed among these distances:
38 7 0.07
39 12 0.13
40 11 0.12
41 28 0.29
42 28 0.29
43 2 0.02
44 2 0.02
45 5 0.05
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (42 bp):
TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATAT
Found at i:48616062 original size:39 final size:41
Alignment explanation
Indices: 48616011--48616116 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
48616001 TTTCCTTATG
* *
48616011 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
*
48616051 C-ATTATGCCTCTATTCCATTTCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
48616096 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
48616117 ACGCATCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 12 0.22
40 2 0.04
41 4 0.07
44 19 0.35
45 5 0.09
46 13 0.24
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:48616077 original size:44 final size:46
Alignment explanation
Indices: 48616028--48616116 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
48616018 ACCTCTATTC
* *
48616028 CATTCAACCAAACACAAGAA-TACC-ATTATGCCTCTATTCCATTT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTT
48616072 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
48616117 ACGCATCTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.46
45 4 0.10
46 18 0.44
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.29
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTT
Found at i:48616119 original size:16 final size:16
Alignment explanation
Indices: 48616098--48616150 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
48616088 AGAATTACCT
48616098 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
48616114 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
48616130 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
48616146 ATTAC
1 ATTAC
48616151 AACGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:48617672 original size:18 final size:18
Alignment explanation
Indices: 48617634--48617669 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48617624 TTATTATTTT
*
48617634 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
48617652 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
48617670 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:48618210 original size:29 final size:27
Alignment explanation
Indices: 48618144--48618210 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
48618134 GAGTTTCACT
* *
48618144 TGTATAATTGCACCAAATTAAATTTTA
1 TGTATAATTGCACCAAATTAAAGTTCA
*
48618171 TGTATACAATTGCACATTAAATTAAAGTTCA
1 TGTAT--AATTGCAC--CAAATTAAAGTTCA
48618202 TGTATAATT
1 TGTATAATT
48618211 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.36
31 16 0.48
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (27 bp):
TGTATAATTGCACCAAATTAAAGTTCA
Found at i:48622896 original size:19 final size:21
Alignment explanation
Indices: 48622841--48622899 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
48622831 ATTGGGTGGA
* *
48622841 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTTACAAGCTTCTGT
48622862 TCAGCTCTTACAAGCTTCTGT
1 TCAGCTCTTACAAGCTTCTGT
*
48622883 TTAGCT-TT-CAAGCTTCT
1 TCAGCTCTTACAAGCTTCT
48622900 TTTGGTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 24 0.69
ACGTcount: A:0.17, C:0.29, G:0.15, T:0.39
Consensus pattern (21 bp):
TCAGCTCTTACAAGCTTCTGT
Found at i:48629118 original size:29 final size:29
Alignment explanation
Indices: 48629074--48629131 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
48629064 GACAAAGTAC
*
48629074 GCAGTTATGGTGAGACACTTGTGAAACTA
1 GCAGTTATGGTAAGACACTTGTGAAACTA
48629103 GCAGTTATGGTAAGACACTTGTGAAACTA
1 GCAGTTATGGTAAGACACTTGTGAAACTA
48629132 CCAAAGCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (29 bp):
GCAGTTATGGTAAGACACTTGTGAAACTA
Found at i:48632718 original size:51 final size:49
Alignment explanation
Indices: 48632603--48632883 Score: 221
Period size: 51 Copynumber: 5.6 Consensus size: 49
48632593 GATGGTCACG
* * * * * * * *
48632603 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGGTCTTA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA-GTTCGATC-AA
48632653 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCAA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TTCGATCAA
* * * * *
48632703 GTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGAATGATAGGTCG-T--A
1 -TGTGTAGTACTATGTGCAGGCTACTATGCGTA-CCG---GATAGTTCGATCAA
*
48632754 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TTCGATCA-A
* * * * * *
48632805 TGTGTAGTACTATGTGCAGGCTATTACGTGTATCAGATAGTGAT-GGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT--TCGATCA-A
*
48632856 TGTGTAGTACTATGTGCATGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
48632884 TGAATCCGTA
Statistics
Matches: 188, Mismatches: 29, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
46 5 0.03
47 3 0.02
48 1 0.01
49 2 0.01
50 65 0.35
51 100 0.53
52 3 0.02
53 1 0.01
54 3 0.02
55 5 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTCGATCAA
Found at i:48632724 original size:101 final size:101
Alignment explanation
Indices: 48632602--48632883 Score: 467
Period size: 101 Copynumber: 2.8 Consensus size: 101
48632592 TGATGGTCAC
* *
48632602 GTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCTTATGTGTAGTACTATG
1 GTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGAATGATAGGTCATATGTGTAGTACTATG
48632667 TGCAGGCTACTATGCGTACCGGATAGCTTCGATCAA
66 TGCAGGCTACTATGCGTACCGGATAGCTTCGATCAA
*
48632703 GTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGAATGATAGGTCGTATGTGTAGTACTATG
1 GTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGAATGATAGGTCATATGTGTAGTACTATG
*
48632768 TGCAGGCTACTATGCGTACCGGATAGCTTCGATCAC
66 TGCAGGCTACTATGCGTACCGGATAGCTTCGATCAA
* * *
48632804 GTGTGTAGTACTATGTGCAGGCTATTACGTGTATCAGATAGTGAT-GGTCACATGTGTAGTACTA
1 GTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGA-A-TGATAGGTCATATGTGTAGTACTA
*
48632868 TGTGCATGCTACTATG
64 TGTGCAGGCTACTATG
48632884 TGAATCCGTA
Statistics
Matches: 171, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
101 134 0.78
102 33 0.19
103 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGAATGATAGGTCATATGTGTAGTACTATG
TGCAGGCTACTATGCGTACCGGATAGCTTCGATCAA
Found at i:48632885 original size:26 final size:26
Alignment explanation
Indices: 48632805--48632885 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
48632795 TTCGATCACG
* *
48632805 TGTGTAGTACTATGTGCAGGCTATTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
48632831 CGTGTA-T-CAGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
48632856 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
48632882 TGTG
1 TGTG
48632886 AATCCGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 21 0.52
27 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:48632971 original size:43 final size:42
Alignment explanation
Indices: 48632889--48633019 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 42
48632879 CTATGTGAAT
*
48632889 CCGTATCATTGAATATAAAGGTGGTTTCTAAGTGCTGATTCC
1 CCGTATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
* * * *
48632931 ACCGTATCATTGACTGTGAAAGG-GGTTGCTATGTGTTGATTCC
1 -CCGTATCATTGAATAT-AAAGGTGGTTGCTAAGTGCTGATTCC
* * * *
48632974 CCGTATTATTGATTAT-AAGGTGGTTGTTAACTGCTGATTCC
1 CCGTATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
48633015 ACCGT
1 -CCGT
48633020 GTAACGGTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.05
41 16 0.22
42 17 0.23
43 31 0.42
44 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
CCGTATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
Found at i:48638042 original size:6 final size:6
Alignment explanation
Indices: 48638031--48638059 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
48638021 AAGAGCTCAT
48638031 GCATTA GCATTA GCATTA GCATTA GCATT
1 GCATTA GCATTA GCATTA GCATTA GCATT
48638060 CACATTGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
GCATTA
Found at i:48640431 original size:13 final size:13
Alignment explanation
Indices: 48640415--48640439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48640405 TAGAATTAAT
48640415 TAATAATAATAAA
1 TAATAATAATAAA
48640428 TAATAATAATAA
1 TAATAATAATAA
48640440 CTAAATTGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:48642248 original size:133 final size:132
Alignment explanation
Indices: 48642022--48642313 Score: 458
Period size: 133 Copynumber: 2.2 Consensus size: 132
48642012 TTTTAATCCG
* *
48642022 CTCCATTGCAACTTCAAGGAGATAGGATTATCGGCTTAATCTACTCCACTGCAACTTCAGGGAAA
1 CTCCACTGCAACTTCAAGGAGATAAGATTATCGGCTTAATCTACTCCACTGCAACTTCAGGGAAA
* **
48642087 TAAGATTTGCTATCTTCAGTCTGTCTCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTC
66 TAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTC
48642152 TA
131 TA
** *
48642154 CTCCACTGCAACTTCAAGGAGATAAGATTATCGGCTCTAATCTGGTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAAGGAGATAAGATTATCGGCT-TAATCTACTCCACTGCAACTTCAGGGAA
* * *
48642219 ATAAGATTTTCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGCTTGCTTAGT
65 ATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGT
*
48642284 CTG
130 CTA
*
48642287 CTCCACTGCAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAAGGAGATAAGA
48642314 CTAGATGCGA
Statistics
Matches: 146, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
132 34 0.23
133 112 0.77
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTATCGGCTTAATCTACTCCACTGCAACTTCAGGGAAA
TAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTC
TA
Found at i:48642353 original size:217 final size:215
Alignment explanation
Indices: 48642118--48642618 Score: 691
Period size: 217 Copynumber: 2.3 Consensus size: 215
48642108 TGTCTCACTG
* * * * * *
48642118 CAACTTCAG-GAGGATAAGACTTACTTACTTAGTCTACTCCACTGCAACTTCAAGGAGATAAGAT
1 CAACTTCAGAGA-GATAAGACTAAATT--TTAATCCACTCCACTGCAACTTCAGGGAGATAGGAT
* * * *
48642182 TATCGGCTCTAATCTGGTCCACTGCAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCTACCTC
63 TATCGGCTCTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTC
*
48642247 ACTGCAACTTCAGGAGGATAAGACTTGCTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
128 ACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
48642312 GACTAGATGCG-ATCTGCTCTCTA
193 GACTAGATG-GAATCTGCTCTCTA
* * *
48642335 CAACTTCAGAGAGATAAGATCCAAAGTTTTAATCCGCTCCACTGCAACCTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGA-CTAAA-TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATT
* * * *
48642400 ATCGGCTTTAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCAATCTTCAGTCTGCCTCA
64 ATCGGCTCTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTCA
* * *
48642465 TTGTAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAT
129 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
*
48642530 ACTAGATGGAATCTGCTCTCTG
194 ACTAGATGGAATCTGCTCTCTA
* * *
48642552 TAACTTCAGAGAGATAAGATCCAATGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGA-CTAA-ATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATT
48642617 AT
64 AT
48642619 TGGCCATGGA
Statistics
Matches: 253, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
216 1 0.00
217 246 0.97
218 4 0.02
219 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (215 bp):
CAACTTCAGAGAGATAAGACTAAATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTAT
CGGCTCTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTCACT
GCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
TAGATGGAATCTGCTCTCTA
Found at i:48642517 original size:44 final size:43
Alignment explanation
Indices: 48642021--48642528 Score: 283
Period size: 44 Copynumber: 11.6 Consensus size: 43
48642011 GTTTTAATCC
* * * * ** *
48642021 GCTCCATTGCAACTTCAAGGAGATAGGA-TTATCGGCTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTACTTAGTCT
* * *
48642064 ACTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA-CTT-AGTCT
*
48642109 G-TCTCACTGCAACTTCA-GGAGGATAAGACTTACTTACTTAGTCT
1 GCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAGTCT
* * * *
48642153 ACTCCACTGCAACTTCAAGGAGATAAGATTATCGGCT-C-TAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTACTTAGTCT
* * * *
48642197 GGTCCACTGCAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA-CTT-AGTCT
* *
48642242 AC-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTGCTTAGTCT
1 GCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAGTCT
* * * *
48642286 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC-GA-TCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAGTCT
* * * * * * * *
48642327 GCT-CTCTACAACTTCAGAGAGATAAGA--TCCAAAGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGC-TA--CTTAGTCT
* * * **
48642370 GCTCCACTGCAACCTCAGGGAGATAGGATTATCGGCT--TTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTACTTAGTCT
* ** *
48642414 GCTCCACTGCAACTTTAGGGAGATAAGGTTTGCAATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA-CTT-AGTCT
* *
48642459 GC-CTCATTGTAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCT
1 GCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAGTCT
48642503 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCCACTGCAACTTCAGGGAGATAA
48642529 TACTAGATGG
Statistics
Matches: 357, Mismatches: 68, Indels: 79
0.71 0.13 0.16
Matches are distributed among these distances:
40 21 0.06
41 9 0.03
42 2 0.01
43 35 0.10
44 181 0.51
45 102 0.29
46 4 0.01
47 2 0.01
49 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAGTCT
Found at i:48657278 original size:11 final size:11
Alignment explanation
Indices: 48657247--48657271 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48657237 GCAGATATTT
48657247 CCTTCCCTTCC
1 CCTTCCCTTCC
48657258 CCTTCCCTTCC
1 CCTTCCCTTCC
48657269 CCT
1 CCT
48657272 CTCCTTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (11 bp):
CCTTCCCTTCC
Found at i:48657449 original size:3 final size:3
Alignment explanation
Indices: 48657441--48657467 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48657431 TTTCAATTCG
48657441 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
48657468 AAACTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48659185 original size:25 final size:25
Alignment explanation
Indices: 48659145--48659194 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
48659135 TCTTTTCCAA
48659145 TCATTTACGATAATTACTATTTGTT
1 TCATTTACGATAATTACTATTTGTT
* *
48659170 TCATTTACTATTATTACTATTTGTT
1 TCATTTACGATAATTACTATTTGTT
48659195 ATTTTCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (25 bp):
TCATTTACGATAATTACTATTTGTT
Found at i:48668854 original size:9 final size:10
Alignment explanation
Indices: 48668837--48668869 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
48668827 TACTCTTAAG
48668837 AATTTTTTTA
1 AATTTTTTTA
48668847 AATTTTTTTA
1 AATTTTTTTA
*
48668857 AATTTTTTAA
1 AATTTTTTTA
48668867 AAT
1 AAT
48668870 ATAAATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:48668892 original size:18 final size:18
Alignment explanation
Indices: 48668872--48668935 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
48668862 TTTAAAATAT
48668872 AAATTTTGGAATTTTTATA
1 AAATTTT-GAATTTTTATA
48668891 AAATTTTGAATTTTTGA-A
1 AAATTTTGAATTTTT-ATA
*
48668909 AATTATTTTGAATTTTTTTA
1 AA--ATTTTGAATTTTTATA
48668929 AAATTTT
1 AAATTTT
48668936 TGTTGAGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 16 0.40
19 8 0.20
20 16 0.40
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (18 bp):
AAATTTTGAATTTTTATA
Found at i:48668918 original size:20 final size:20
Alignment explanation
Indices: 48668836--48668933 Score: 85
Period size: 20 Copynumber: 4.8 Consensus size: 20
48668826 ATACTCTTAA
* *
48668836 GAATTTTTTTAAATTTTTTT
1 GAATTTTTTAAAATTATTTT
*
48668856 AAATTTTTTAAAATATAAATTTT
1 GAATTTTTTAAAAT-T--ATTTT
48668879 GGAA-TTTTTATAAA--ATTTT
1 -GAATTTTTTA-AAATTATTTT
*
48668898 GAATTTTTGAAAATTATTTT
1 GAATTTTTTAAAATTATTTT
48668918 GAATTTTTTTAAAATT
1 GAA-TTTTTTAAAATT
48668934 TTTGTTGAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
18 6 0.10
19 10 0.16
20 20 0.32
21 12 0.19
23 10 0.16
24 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
GAATTTTTTAAAATTATTTT
Found at i:48669018 original size:9 final size:9
Alignment explanation
Indices: 48669004--48669032 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
48668994 CATTAATTTG
48669004 TTATTCGAA
1 TTATTCGAA
48669013 TTATTCGAA
1 TTATTCGAA
48669022 TTATTCGAA
1 TTATTCGAA
48669031 TT
1 TT
48669033 GTAAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:48670193 original size:34 final size:34
Alignment explanation
Indices: 48670131--48670195 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
48670121 CATGTTCAAA
* * *
48670131 ACAGATCAATACAGTAGCATTTAATATGCTTTTG
1 ACAGAACAATACAGTAGCAATCAATATGCTTTTG
*
48670165 ACAGAACAATACAGTAGCAATCATTATGCTT
1 ACAGAACAATACAGTAGCAATCAATATGCTT
48670196 ATAACAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (34 bp):
ACAGAACAATACAGTAGCAATCAATATGCTTTTG
Found at i:48686441 original size:19 final size:21
Alignment explanation
Indices: 48686419--48686457 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
48686409 TGCAAAGTTG
48686419 ATAATAAT-TAA-TATATATT
1 ATAATAATATAATTATATATT
48686438 ATAATAATATAATTATATAT
1 ATAATAATATAATTATATAT
48686458 CAATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAATAATATAATTATATATT
Found at i:48696012 original size:9 final size:10
Alignment explanation
Indices: 48695997--48696025 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
48695987 AATTTGTGGG
48695997 AAAATTAATT
1 AAAATTAATT
48696007 -AAATTAATT
1 AAAATTAATT
48696016 AAAATTAATT
1 AAAATTAATT
48696026 TAATACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATTAATT
Found at i:48696072 original size:20 final size:20
Alignment explanation
Indices: 48696047--48696100 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
48696037 TTAATAGTAT
48696047 TTTATTAATTTAATATTAAA
1 TTTATTAATTTAATATTAAA
48696067 TTTATT-ATCTTAATATTAAA
1 TTTATTAAT-TTAATATTAAA
48696087 -TTA--AATTTAATATT
1 TTTATTAATTTAATATT
48696101 TATCTTGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.25
18 2 0.06
19 5 0.16
20 17 0.53
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTAATTTAATATTAAA
Found at i:48696072 original size:25 final size:25
Alignment explanation
Indices: 48696044--48696095 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
48696034 ATCTTAATAG
*
48696044 TATTTTATTAAT-TTAATATTAAATT
1 TATTATATTAATATTAA-ATTAAATT
*
48696069 TATTATCTTAATATTAAATTAAATT
1 TATTATATTAATATTAAATTAAATT
48696094 TA
1 TA
48696096 ATATTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATATTAATATTAAATTAAATT
Found at i:48696141 original size:61 final size:58
Alignment explanation
Indices: 48696076--48696191 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 58
48696066 ATTTATTATC
* *
48696076 TTAATATTAAATTAAATT-TAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATAGAT
1 TTAATATTAAATT-AATTATAATATTTATC-T-T-GATAAGTATTATATTAATCTAATAGAT
*
48696137 TTAATATTAAATTTATTATAATATTTATCTTGATAAGTATTATATTAATCTAATA
1 TTAATATTAAATTAATTATAATATTTATCTTGATAAGTATTATATTAATCTAATA
48696192 TTAAAGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
58 22 0.43
59 1 0.02
60 4 0.08
61 24 0.47
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (58 bp):
TTAATATTAAATTAATTATAATATTTATCTTGATAAGTATTATATTAATCTAATAGAT
Found at i:48696204 original size:58 final size:60
Alignment explanation
Indices: 48696081--48696210 Score: 135
Period size: 58 Copynumber: 2.2 Consensus size: 60
48696071 TTATCTTAAT
* * * *
48696081 ATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATAGATTTAAT
1 ATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTATATTAATCTAATA-ATTAAAA
*
48696142 ATTAAATT-TATTATAATATTTATC-T-T-GATAAGTATTATATTAATCTAAT-ATTAAAGAA
1 ATTAAATTAAATT-TAATATTTATCTTGTAGATAAGTATTATATTAATCTAATAATT-AA-AA
48696200 ATTAAACTTAA
1 ATTAAA-TTAA
48696211 TCATAGTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
56 3 0.05
57 1 0.02
58 28 0.48
59 3 0.05
60 4 0.07
61 19 0.33
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (60 bp):
ATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTATATTAATCTAATAATTAAAA
Found at i:48698784 original size:55 final size:51
Alignment explanation
Indices: 48698719--48698959 Score: 179
Period size: 50 Copynumber: 4.7 Consensus size: 51
48698709 GGGAATGAGA
* * ** *
48698719 TCCCATGTAAGACCATGTCTGGGACATGACATTGGCATTATTGGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGAG--ATGAGAGG
*
48698774 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGC-ACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGG
* * * * **
48698824 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGC-ACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGG
** * * * * * **
48698874 TCCCGTGTAATACCATATCTGGGATATGGCATTGGTAGTA-C-AG--GAAACA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGAGATGAGAGG
* *
48698923 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
48698960 TGTTATTATC
Statistics
Matches: 152, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
49 34 0.22
50 79 0.52
51 1 0.01
52 4 0.03
53 1 0.01
55 33 0.22
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (51 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGG
Found at i:48698825 original size:50 final size:50
Alignment explanation
Indices: 48698766--48698959 Score: 185
Period size: 50 Copynumber: 3.9 Consensus size: 50
48698756 TTATTGGGTT
* *
48698766 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * * *
48698816 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** ** * * * *
48698866 ATGAGAACTCCCGTGTAATACCATATCTGGGATATGGCATTGGTA--GTAC
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** * *
48698915 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
48698960 TGTTATTATC
Statistics
Matches: 117, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
48 1 0.01
49 36 0.31
50 80 0.68
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:48699186 original size:20 final size:20
Alignment explanation
Indices: 48699161--48699209 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
48699151 TGAGTTATTT
*
48699161 AAGTAAGCAAGTAAGTGAAC
1 AAGTAAGCAAGTAAGTAAAC
*
48699181 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
48699201 AAG-AAGCAA
1 AAGTAAGCAA
48699210 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:48700651 original size:12 final size:12
Alignment explanation
Indices: 48700636--48700661 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48700626 TACTTATTCT
48700636 CTTACTTGCTTA
1 CTTACTTGCTTA
48700648 CTTACTTGCTTA
1 CTTACTTGCTTA
48700660 CT
1 CT
48700662 CTCTTACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.27, G:0.08, T:0.50
Consensus pattern (12 bp):
CTTACTTGCTTA
Found at i:48700664 original size:28 final size:28
Alignment explanation
Indices: 48700628--48700682 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
48700618 TTCTTCTTTA
*
48700628 CTTATTCTCTTACTTGCTTACTTACTTG
1 CTTACTCTCTTACTTGCTTACTTACTTG
*
48700656 CTTACTCTCTTACTTGTTTACTTACTT
1 CTTACTCTCTTACTTGCTTACTTACTT
48700683 TCTTTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.05, T:0.55
Consensus pattern (28 bp):
CTTACTCTCTTACTTGCTTACTTACTTG
Found at i:48701034 original size:50 final size:50
Alignment explanation
Indices: 48700962--48701086 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
48700952 TATCTTGGAT
* * ** * *
48700962 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCC-AGAC
1 ATGGCCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAG-C
*
48701012 ATGGCCTTAC-GGAGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAGC
1 ATGGCCTTACAGG-GGACCTCTCATATCGGTGCCAACGCCATGTCCCAAGC
* *
48701062 ATGGTCTTACATGGGACCTCTCATA
1 ATGGCCTTACAGGGGACCTCTCATA
48701087 ACCTCAATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.02
50 58 0.94
51 3 0.05
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
ATGGCCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAGC
Found at i:48711698 original size:10 final size:9
Alignment explanation
Indices: 48711683--48711721 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
48711673 TATCAAAATT
48711683 ATAATATAA
1 ATAATATAA
48711692 CATAATATAA
1 -ATAATATAA
*
48711702 ATATTATAA
1 ATAATATAA
48711711 ATAATTATAA
1 ATAA-TATAA
48711721 A
1 A
48711722 ACATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 11 0.42
10 15 0.58
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAATATAA
Found at i:48711720 original size:24 final size:24
Alignment explanation
Indices: 48711665--48711714 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
48711655 GATCATCTCA
48711665 AACATATATATCAAAATTATAATAT
1 AACATA-ATATCAAAATTATAATAT
48711690 AACATAATAT-AAATATTATAA-AT
1 AACATAATATCAAA-ATTATAATAT
48711713 AA
1 AA
48711715 TTATAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
AACATAATATCAAAATTATAATAT
Found at i:48715512 original size:24 final size:22
Alignment explanation
Indices: 48715464--48715512 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
48715454 ATTTTGAGGG
* * *
48715464 AATATAAAAAAGAATATTAAGA
1 AATAAAAAAAAGAATACTAAAA
48715486 AATAAAAAAAAGAGTATACTAAAA
1 AATAAAAAAAAGA--ATACTAAAA
48715510 AAT
1 AAT
48715513 TTGAAGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 12 0.55
24 10 0.45
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.20
Consensus pattern (22 bp):
AATAAAAAAAAGAATACTAAAA
Found at i:48718174 original size:15 final size:16
Alignment explanation
Indices: 48718149--48718178 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48718139 TTATATATAT
48718149 AATATATATTTGATAG
1 AATATATATTTGATAG
48718165 AATA-ATATTTGATA
1 AATATATATTTGATA
48718179 CACCATTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (16 bp):
AATATATATTTGATAG
Found at i:48720349 original size:41 final size:40
Alignment explanation
Indices: 48720303--48720576 Score: 251
Period size: 41 Copynumber: 6.6 Consensus size: 40
48720293 CTTTAAATGT
* * *
48720303 AAGGGGTTGCTAAGTGCAGATTCCCTGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCTGTATCATTGAT-TAA
* * ** *
48720344 AAGGGGTTGTTATGTGCTGATTCCCCATATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCTGTATCATTGATTAA
** * * *
48720384 AAGGTGGTTTTTAAGTGCTGATTCCATTGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CTGTATCATTGA-T-TAA
* * *
48720428 AAGGGGTTGCTATGTACTGATTCCCTGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCTGTATCATTGATTAA
* *
48720468 AAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTAA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CTGTATCATTGA-T-TAA
* * * *
48720512 AAGGGGTTACTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCTGTATCATTGATTAA
*
48720552 AAGGTGGTTGCTAAGTGTTGATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
48720577 ACCGGGATCC
Statistics
Matches: 186, Mismatches: 38, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
40 16 0.09
41 85 0.46
42 39 0.21
43 35 0.19
44 11 0.06
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCCTGTATCATTGATTAA
Found at i:48720442 original size:84 final size:84
Alignment explanation
Indices: 48720302--48720578 Score: 389
Period size: 84 Copynumber: 3.3 Consensus size: 84
48720292 TCTTTAAATG
** * * ** *
48720302 TAAGG-GGTTGCTAAGTGCAGATTCC-CTGAATCATTGA-TCAAAAAGGGGTTGTTATGTGCTGA
1 TAAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
*
48720364 TTCCCCATATCATTGATTA
66 TTCCCCGTATCATTGATTA
** * * * *
48720383 TAAGGTGGTTTTTAAGTGCTGATTCCATTGTATCCTTGATTGTGAAAGGGGTTGCTATGTACTGA
1 TAAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
*
48720448 TTCCCTGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
*
48720467 TAAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTAAAAGGGGTTACTATGTGCTGA
1 TAAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
48720532 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
48720551 TAAGGTGGTTGCTAAGTGTTGATTCCAC
1 TAAGGTGGTTGCTAAGTGTTGATTCCAC
48720579 CGGGATCCTT
Statistics
Matches: 172, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
81 5 0.03
82 17 0.10
83 9 0.05
84 141 0.82
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (84 bp):
TAAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTAAAAGGGGTTGCTATGTGCTGA
TTCCCCGTATCATTGATTA
Found at i:48722473 original size:12 final size:12
Alignment explanation
Indices: 48722456--48722480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48722446 ATTTGAAGAG
48722456 TTTAAATTTGAA
1 TTTAAATTTGAA
48722468 TTTAAATTTGAA
1 TTTAAATTTGAA
48722480 T
1 T
48722481 GAAATTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTAAATTTGAA
Found at i:48727921 original size:38 final size:38
Alignment explanation
Indices: 48727837--48727924 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
48727827 TTTTTTTGTT
* *
48727837 TTTCAGAATATTTTCGATTGAAGAAAATCCTATGACTA
1 TTTCAGAATATTTTCAATTGAAGAAAATCCTATCACTA
* * * *
48727875 TTGT-AGAATATTTTCAATTGAGGAAAATTCTCTCACTG
1 TT-TCAGAATATTTTCAATTGAAGAAAATCCTATCACTA
48727913 TTTCAGAATATT
1 TTTCAGAATATT
48727925 AATCATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
37 1 0.02
38 40 0.95
39 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (38 bp):
TTTCAGAATATTTTCAATTGAAGAAAATCCTATCACTA
Found at i:48737737 original size:37 final size:37
Alignment explanation
Indices: 48737687--48737761 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
48737677 CGTCTGTCCC
* *
48737687 TAATTTGATTGTTACACGGCCTGGCCACACGGTAGTG
1 TAATTTGATTGTTACACGGCCTAGCCACACGGCAGTG
48737724 TAATTTGATTGTTACACGGCCTAGCCACACGGCAGTG
1 TAATTTGATTGTTACACGGCCTAGCCACACGGCAGTG
48737761 T
1 T
48737762 GACCTCTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (37 bp):
TAATTTGATTGTTACACGGCCTAGCCACACGGCAGTG
Found at i:48738700 original size:25 final size:25
Alignment explanation
Indices: 48738672--48738723 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
48738662 GTGAGATTGA
48738672 TTTACCTTTCTTTTCAAGCCAACTT
1 TTTACCTTTCTTTTCAAGCCAACTT
48738697 TTTACCTTTCTTTTCAAGCCAACTT
1 TTTACCTTTCTTTTCAAGCCAACTT
48738722 TT
1 TT
48738724 AAACTTGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.27, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTACCTTTCTTTTCAAGCCAACTT
Found at i:48742985 original size:15 final size:15
Alignment explanation
Indices: 48742965--48742994 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48742955 ATTTCCTATA
48742965 TCAACCACTTATCTC
1 TCAACCACTTATCTC
48742980 TCAACCACTTATCTC
1 TCAACCACTTATCTC
48742995 AAACATTAGA
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:0.27, C:0.40, G:0.00, T:0.33
Consensus pattern (15 bp):
TCAACCACTTATCTC
Found at i:48761308 original size:21 final size:22
Alignment explanation
Indices: 48761283--48761326 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
48761273 CACTCTTCTT
48761283 TTTCTTCATCGATTATTGCAGG
1 TTTCTTCATCGATTATTGCAGG
48761305 TTCTTCTTCATCGATTATTGCA
1 -T-TTCTTCATCGATTATTGCA
48761327 CTGTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTCTTCATCGATTATTGCAGG
Found at i:48761341 original size:24 final size:24
Alignment explanation
Indices: 48761290--48761344 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
48761280 CTTTTTCTTC
* *
48761290 ATCGATTATTGCAGGTTCTTCTTC
1 ATCGATTATTGCAGGTTCTACTTA
*
48761314 ATCGATTATTGCACTGTTC-ACTTA
1 ATCGATTATTGCA-GGTTCTACTTA
48761338 ATCGATT
1 ATCGATT
48761345 TCCCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (24 bp):
ATCGATTATTGCAGGTTCTACTTA
Found at i:48762136 original size:27 final size:27
Alignment explanation
Indices: 48762096--48762150 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
48762086 GGTGAGAAAA
48762096 AGACTTCCCCTGCTCTATTTCATCTTT
1 AGACTTCCCCTGCTCTATTTCATCTTT
*
48762123 AGACTTCCCTTGCTCTATTTCATCTTT
1 AGACTTCCCCTGCTCTATTTCATCTTT
48762150 A
1 A
48762151 CTTCCATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.31, G:0.07, T:0.45
Consensus pattern (27 bp):
AGACTTCCCCTGCTCTATTTCATCTTT
Found at i:48762673 original size:23 final size:23
Alignment explanation
Indices: 48762596--48762674 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 23
48762586 ATACAGTGAG
*
48762596 CAATGGAAATTGTCTGCTGTTTT
1 CAATGGAAATTGTTTGCTGTTTT
* * * * *
48762619 CAATTCAGACAGTTTTTTGATATTGTT
1 CAA-T-GGA-AATTGTTTGCTGTT-TT
48762646 GCAATGGAAATTGTTTGCTGTTTT
1 -CAATGGAAATTGTTTGCTGTTTT
48762670 CAATG
1 CAATG
48762675 AAACTGGAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 8 0.20
24 3 0.08
25 12 0.30
26 11 0.28
27 3 0.08
28 3 0.08
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (23 bp):
CAATGGAAATTGTTTGCTGTTTT
Found at i:48762722 original size:23 final size:23
Alignment explanation
Indices: 48762694--48762755 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
48762684 ATTGTTGCAT
48762694 TTGTTTTGATATTGTTCTGGAAA
1 TTGTTTTGATATTGTTCTGGAAA
* * *
48762717 TTGTTTTGATAGTCTGCTGGAAA
1 TTGTTTTGATATTGTTCTGGAAA
48762740 TTGTTCTTGAT-TTGTT
1 TTGTT-TTGATATTGTT
48762756 AGTGAGTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 27 0.84
24 5 0.16
ACGTcount: A:0.18, C:0.06, G:0.23, T:0.53
Consensus pattern (23 bp):
TTGTTTTGATATTGTTCTGGAAA
Found at i:48762815 original size:22 final size:22
Alignment explanation
Indices: 48762776--48762862 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 22
48762766 AGATGAAACA
*
48762776 GGAAATTGTTGT-ATTTGTT-T
1 GGAAATTGTTTTGATTTGTTCT
* *
48762796 TGATATTGTTCTTGATTTGTTCT
1 GGAAATTGTT-TTGATTTGTTCT
*
48762819 GGAAATTGTTTTGA-TAGTCTGCT
1 GGAAATTGTTTTGATTTGT-T-CT
48762842 GGAAATTGTTCTTGATTTGTT
1 GGAAATTGTT-TTGATTTGTT
48762863 AGTGAGTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.15
21 4 0.08
22 12 0.23
23 21 0.40
24 5 0.09
25 3 0.06
ACGTcount: A:0.18, C:0.06, G:0.23, T:0.53
Consensus pattern (22 bp):
GGAAATTGTTTTGATTTGTTCT
Found at i:48762817 original size:107 final size:107
Alignment explanation
Indices: 48762694--48762890 Score: 369
Period size: 107 Copynumber: 1.8 Consensus size: 107
48762684 ATTGTTGCAT
48762694 TTGTTTTGATATTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGT
1 TTGTTTTGATATTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGT
48762759 GAGTAGAAGATGAAACAGGAAATTGTTGTATTTGTTTTGATA
66 GAGTAGAAGATGAAACAGGAAATTGTTGTATTTGTTTTGATA
48762801 TTGTTCTTGAT-TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAG
1 TTGTT-TTGATATTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAG
*
48762865 TGAGTAGAAGATGAAACTGGAAATTG
65 TGAGTAGAAGATGAAACAGGAAATTG
48762891 CAAGTATAGT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
107 83 0.94
108 5 0.06
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.45
Consensus pattern (107 bp):
TTGTTTTGATATTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGT
GAGTAGAAGATGAAACAGGAAATTGTTGTATTTGTTTTGATA
Found at i:48773732 original size:47 final size:46
Alignment explanation
Indices: 48773673--48773845 Score: 146
Period size: 47 Copynumber: 3.8 Consensus size: 46
48773663 TCATATAAGA
* *
48773673 ATATTTATTATTAAGAATTTTATGCAATTATATATGATTATTAAATT
1 ATATTTAATATTAAGAATTTTATG-AATTATATATAATTATTAAATT
* **
48773720 ATATTCAATATTAATTATTTTA--AATTATATA-AATTCATATAAGA--
1 ATATTTAATATTAAGAATTTTATGAATTATATATAATT-AT-TAA-ATT
* * * *
48773764 AAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTAATATTAAGAATTTTATG-AATTATATATAATTATTAAATT
**
48773811 ATATTTAATATTAATTATTTTA--AATTATATA-AATT
1 ATATTTAATATTAAGAATTTTATGAATTATATATAATT
48773846 CATATAAGAA
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
43 6 0.06
44 36 0.36
45 4 0.04
46 4 0.04
47 46 0.46
48 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (46 bp):
ATATTTAATATTAAGAATTTTATGAATTATATATAATTATTAAATT
Found at i:48773770 original size:91 final size:90
Alignment explanation
Indices: 48773658--48773951 Score: 396
Period size: 91 Copynumber: 3.4 Consensus size: 90
48773648 ATGATTTTAG
* *
48773658 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGCAATTATATATGATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATG-AATTATATATCATTATTAAATTATA
*
48773723 TTCAATATTAATTATTTTAAATTATA
65 TTTAATATTAATTATTTTAAATTATA
*
48773749 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATG-AATTATATATCATTATTAAATTATA
48773814 TTTAATATTAATTATTTTAAATTATA
65 TTTAATATTAATTATTTTAAATTATA
*
48773840 TAAATTCATATAAGAAAATTT-TTA-T--G------A--AATTATATATTATTATTAAATTATAT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAATTATATATCATTATTAAATTATAT
* *
48773893 TTAATAATAATTATATTAAATTATA
66 TTAATATTAATTATTTTAAATTATA
* * *
48773918 CAAATTCATATAAGAAAATTTATTACTAATAATT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATT
48773952 ATTTTAAATT
Statistics
Matches: 184, Mismatches: 11, Indels: 21
0.85 0.05 0.10
Matches are distributed among these distances:
78 68 0.37
79 3 0.02
80 1 0.01
81 1 0.01
87 1 0.01
90 3 0.02
91 107 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (90 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAATTATATATCATTATTAAATTATAT
TTAATATTAATTATTTTAAATTATA
Found at i:48773875 original size:78 final size:78
Alignment explanation
Indices: 48773781--48773938 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 78
48773771 TTATCAAGAA
* * *
48773781 TTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATT
1 TTTTATGAAATTATATATCATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
48773846 CATATAAGAAAAT
66 CATATAAGAAAAT
*
48773859 TTTTATGAAATTATATATTATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
1 TTTTATGAAATTATATATCATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
48773924 CATATAAGAAAAT
66 CATATAAGAAAAT
48773937 TT
1 TT
48773939 ATTACTAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (78 bp):
TTTTATGAAATTATATATCATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
CATATAAGAAAAT
Found at i:48774346 original size:18 final size:17
Alignment explanation
Indices: 48774318--48774352 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48774308 ATTACTAAGA
*
48774318 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48774335 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48774353 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48774372 original size:119 final size:120
Alignment explanation
Indices: 48773958--48774366 Score: 741
Period size: 120 Copynumber: 3.4 Consensus size: 120
48773948 AATTATTTTA
48773958 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
48774023 ATACTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
48774078 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
48774143 ATAGTATCATATATTATGATTTTAGTACATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
48774198 AATTTTATTAAATCTTATATTTTAATTAAAATATATTTAATAATAATTATCTT-AAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
* *
48774262 TATAGTATCAT-TATTATGATTTGAGTAAATTCATATAAGAATATTGATTACTAAG
65 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
48774317 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
48774367 GTTAAAATAT
Statistics
Matches: 280, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
119 89 0.32
120 189 0.68
121 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:48775888 original size:2 final size:2
Alignment explanation
Indices: 48775883--48775922 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
48775873 GTGTGTGTGT
48775883 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
48775923 CCTGTTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48779924 original size:13 final size:13
Alignment explanation
Indices: 48779906--48779930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48779896 GAAACTTATC
48779906 TGTAAATAATTTG
1 TGTAAATAATTTG
48779919 TGTAAATAATTT
1 TGTAAATAATTT
48779931 TACTAATATC
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TGTAAATAATTTG
Found at i:48788019 original size:26 final size:26
Alignment explanation
Indices: 48787963--48788011 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
48787953 ATTGATATTT
* *
48787963 AGAT-TTTGAGGACTCAGAAGAGGCA
1 AGATATTTGAGAACTCAAAAGAGGCA
48787988 AGATATTTGAGAACTCAAAAGAGG
1 AGATATTTGAGAACTCAAAAGAGG
48788012 GTAAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.20
Consensus pattern (26 bp):
AGATATTTGAGAACTCAAAAGAGGCA
Found at i:48799321 original size:41 final size:41
Alignment explanation
Indices: 48799243--48799350 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
48799233 ATCAGAGTGT
* * * * * * * *
48799243 AAACAGGGGCACATATATGTAATTTAGAGGTATCGAAGTCC
1 AAACAAGGGCACGTATGTGAAATTCAGCGGTACCGAAGTAC
* *
48799284 CAACAAGGGCATGTATGTGAAATTCAGCGGTACCGAAGTAC
1 AAACAAGGGCACGTATGTGAAATTCAGCGGTACCGAAGTAC
* *
48799325 AAACAGGGGCACGTATGTGCAATTCA
1 AAACAAGGGCACGTATGTGAAATTCA
48799351 TAAAATAATT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (41 bp):
AAACAAGGGCACGTATGTGAAATTCAGCGGTACCGAAGTAC
Found at i:48800380 original size:3 final size:3
Alignment explanation
Indices: 48800372--48800417 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
48800362 GATTTTCTAA
*
48800372 AAT AAT AAT AA- AAT AAT AA- AAT AAT AA- AAT AAT AAAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
48800415 AAT
1 AAT
48800418 TTACTTGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 6 0.16
3 28 0.76
4 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:48800388 original size:8 final size:8
Alignment explanation
Indices: 48800375--48800407 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
48800365 TTTCTAAAAT
48800375 AATAATAA
1 AATAATAA
48800383 AATAATAA
1 AATAATAA
48800391 AATAATAA
1 AATAATAA
48800399 AATAATAA
1 AATAATAA
48800407 A
1 A
48800408 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:48810647 original size:95 final size:95
Alignment explanation
Indices: 48810484--48810673 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 95
48810474 ATTGGACCAG
* *
48810484 ATATGAAAGAGGTCTAATAGCCTCTTATTTAATAAGGGGGACGACAAACCCTAGTAAAATTAACT
1 ATATGAAAGAAGTCCAATAGCCTCTTATTTAATAAGGGGGACGACAAACCCTAGTAAAATTAACT
48810549 AGGGTTGTCACCTCCTACAACCTAGTTGAA
66 AGGGTTGTCACCTCCTACAACCTAGTTGAA
* * *
48810579 ATATGGAAGAAGTCCAATAG-CTCCTTATTTAATAAGGGGGATGACAAACCCTAGTATAATTAAC
1 ATATGAAAGAAGTCCAATAGCCT-CTTATTTAATAAGGGGGACGACAAACCCTAGTAAAATTAAC
**
48810643 TAGGGTTGTCACCTTTTACAACCTAGTTGAA
65 TAGGGTTGTCACCTCCTACAACCTAGTTGAA
48810674 CTAGGATTTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 2 0.02
95 85 0.98
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (95 bp):
ATATGAAAGAAGTCCAATAGCCTCTTATTTAATAAGGGGGACGACAAACCCTAGTAAAATTAACT
AGGGTTGTCACCTCCTACAACCTAGTTGAA
Found at i:48811463 original size:47 final size:47
Alignment explanation
Indices: 48811402--48811547 Score: 249
Period size: 47 Copynumber: 3.1 Consensus size: 47
48811392 GTTTTGTGGA
*
48811402 CATCAACA-TCGCAGGTCAGAGAATGAGTGATCTTGTTGATATGGGAG
1 CATCAACAGT-GCAGGCCAGAGAATGAGTGATCTTGTTGATATGGGAG
48811449 CATCAACAGTGCAGGCCAGAGAATGAGTGATCTTGTTGATATGGGAG
1 CATCAACAGTGCAGGCCAGAGAATGAGTGATCTTGTTGATATGGGAG
* *
48811496 CATCAACAGCGTAGGCCAGAGAATGAGTGATCTTGTTGATATGGGAG
1 CATCAACAGTGCAGGCCAGAGAATGAGTGATCTTGTTGATATGGGAG
48811543 CATCA
1 CATCA
48811548 GACTTGTTCA
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
47 94 0.99
48 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (47 bp):
CATCAACAGTGCAGGCCAGAGAATGAGTGATCTTGTTGATATGGGAG
Found at i:48814101 original size:3 final size:3
Alignment explanation
Indices: 48814093--48814129 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
48814083 AGAGAGAGAG
48814093 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
48814130 TAGAGCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:48818516 original size:15 final size:16
Alignment explanation
Indices: 48818498--48818530 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
48818488 AAGTGTAAAC
48818498 AAATTTAAAAAT-AAT
1 AAATTTAAAAATGAAT
*
48818513 AAATTTGAAAATGAAT
1 AAATTTAAAAATGAAT
48818529 AA
1 AA
48818531 TAAGGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AAATTTAAAAATGAAT
Found at i:48819413 original size:22 final size:21
Alignment explanation
Indices: 48819386--48819448 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 21
48819376 AGGTTACAAA
48819386 ATCATATATTCTAAGATTGCAT
1 ATCATATA-TCTAAGATTGCAT
48819408 ATC--ATATCTAAGATTGCAT
1 ATCATATATCTAAGATTGCAT
* *
48819427 ATC--ATACCTAATATTGCAT
1 ATCATATATCTAAGATTGCAT
48819446 ATC
1 ATC
48819449 CTTGAGGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 33 0.85
20 3 0.08
22 3 0.08
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (21 bp):
ATCATATATCTAAGATTGCAT
Found at i:48819419 original size:19 final size:19
Alignment explanation
Indices: 48819395--48819448 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
48819385 AATCATATAT
48819395 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
48819414 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
48819433 CCTAATATTGCATATC
1 TCTAAGATTGCATATC
48819449 CTTGAGGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:48820111 original size:131 final size:132
Alignment explanation
Indices: 48819875--48820285 Score: 605
Period size: 131 Copynumber: 3.1 Consensus size: 132
48819865 AATTGGTAAT
** * * *
48819875 TTCAACCTGCTCCACTACAACTTTAGGGAGATAAGG-CTGGTGGCTTAAACCTGCTTCCCTACTA
1 TTCAACCTAATCCACTACATC-TCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCCTACTA
* * * *
48819939 CCTTGAGAAGATAAGACTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATAC
64 CCTTGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAC
48820004 AATC
129 AATC
* *
48820008 TTCAACCTATTCCACTAC-TGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTT-CCTACTAT
1 TTCAACCTAATCCACTACAT-CTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTAC
* *
48820071 CTCGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACA
65 CTTGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACA
*
48820136 GTC
130 ATC
* *
48820139 TTCAACCTACTCCACTACATCTCA-GGAGATAGGACTGGTGGCTTAAATCCGCTTCCCTACTACC
1 TTCAACCTAATCCACTACATCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
* *
48820203 TTGGGAAGATAAGATTCACCGTCTTTGATCTGCTCCACTACTGCTTAGAGAGACAGGATCTACAA
66 TTGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
48820268 TC
131 TC
48820270 TTCAACCTAATCCACT
1 TTCAACCTAATCCACT
48820286 GAAAACTCAG
Statistics
Matches: 252, Mismatches: 22, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
130 29 0.12
131 177 0.70
132 29 0.12
133 17 0.07
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (132 bp):
TTCAACCTAATCCACTACATCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
TTGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
TC
Found at i:48820140 original size:44 final size:44
Alignment explanation
Indices: 48819968--48820274 Score: 141
Period size: 44 Copynumber: 7.0 Consensus size: 44
48819958 GCCATCTTTG
* * *
48819968 ATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAGTCTTCA
* ** * *** * *
48820012 ACCTATTCCACTACTGCTCAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAGTCTTCA
* * * * *
48820055 ATCTGCTTCCTACTA-T-C-TCGGGAAGATAAGAT-TCGCCGTCTTCG
1 ATCTGC-TCC-ACTACTGCTTAGGG-AGATAGGATCT-ACAGTCTTCA
*
48820099 ATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAGTCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAGTCTTCA
* * * *** * *
48820143 ACCTACTCCACTACAT-CTCA-GGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTAC-TGCTTAGGGAGATAGGATCTACAGTCTTCA
* * * * **
48820185 ATCCGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACCGTCTTTG
1 ATCTGC-TCCACTACT-GCTTAGGG-AGATAGGATCT-ACAGTCTTCA
* * *
48820230 ATCTGCTCCACTACTGCTTAGAGAGACAGGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAGTCTTCA
48820274 A
1 A
48820275 CCTAATCCAC
Statistics
Matches: 185, Mismatches: 58, Indels: 40
0.65 0.20 0.14
Matches are distributed among these distances:
41 1 0.01
42 21 0.11
43 37 0.20
44 99 0.54
45 27 0.15
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAGTCTTCA
Found at i:48820384 original size:89 final size:89
Alignment explanation
Indices: 48820253--48820485 Score: 295
Period size: 89 Copynumber: 2.6 Consensus size: 89
48820243 CTGCTTAGAG
* * * * * * * * *
48820253 AGACAGGATCTACAATCTTCAACCTAATCCACTGAAAACTCAGAGAGGCAAGACTGGTGTTTTCG
1 AGACAAGATCTACTATCTTCACCCTACTCCGCTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCA
* *
48820318 ATCTGCTTCACTGCCAGTACAGGA
66 ATCTACTTCACTGCCAATACAGGA
* * ** * *
48820342 AGACAAGATCTACTATTTTTAGTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCA
1 AGACAAGATCTACTATCTTCACCCTACTCCGCTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCA
*
48820407 ATCTACTTCGCTGCCAATACAGGA
66 ATCTACTTCACTGCCAATACAGGA
*
48820431 AGACAAGATCTACTATCTTCACCCTACTCCGCTGTAAACTCAGGGAGGCAAGACT
1 AGACAAGATCTACTATCTTCACCCTACTCCGCTGCAAACTCAGGGAGGCAAGACT
48820486 TGTAGCTTCC
Statistics
Matches: 120, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
89 120 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (89 bp):
AGACAAGATCTACTATCTTCACCCTACTCCGCTGCAAACTCAGGGAGGCAAGACTGGTGTCTTCA
ATCTACTTCACTGCCAATACAGGA
Found at i:48820451 original size:45 final size:45
Alignment explanation
Indices: 48820318--48820451 Score: 119
Period size: 45 Copynumber: 3.0 Consensus size: 45
48820308 GGTGTTTTCG
* * * *
48820318 ATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACTATTTTTA
1 ATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTACTATCTTCA
* * * * * * ** *
48820363 GTCTGCTCCGCTGCAAACT-CAGGGAGGCAAG-GCTGGTGTCTTCA
1 ATCTGCTTCGCTGCCAA-TACAGGAAGACAAGATCTACTATCTTCA
*
48820407 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATCTTCA
1 ATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTACTATCTTCA
48820452 CCCTACTCCG
Statistics
Matches: 63, Mismatches: 23, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
43 1 0.02
44 30 0.48
45 31 0.49
46 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (45 bp):
ATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTACTATCTTCA
Found at i:48820483 original size:45 final size:45
Alignment explanation
Indices: 48820345--48820483 Score: 120
Period size: 45 Copynumber: 3.1 Consensus size: 45
48820335 TACAGGAAGA
* * * *
48820345 CAAGATCTACTATTTTTAGTCTGCTCCGCTGCAAACTCAGGGAGG
1 CAAGATCTACTATCTTCAATCTACTCCGCTGCAAACTCAGGGAGG
* ** * * * * *
48820390 CAAG-GCTGGTGTCTTCAATCTACTTCGCTGCCAA-TACAGGAAGA
1 CAAGATCTACTATCTTCAATCTACTCCGCTGCAAACT-CAGGGAGG
** *
48820434 CAAGATCTACTATCTTCACCCTACTCCGCTGTAAACTCAGGGAGG
1 CAAGATCTACTATCTTCAATCTACTCCGCTGCAAACTCAGGGAGG
48820479 CAAGA
1 CAAGA
48820484 CTTGTAGCTT
Statistics
Matches: 68, Mismatches: 23, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
43 1 0.01
44 30 0.44
45 36 0.53
46 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (45 bp):
CAAGATCTACTATCTTCAATCTACTCCGCTGCAAACTCAGGGAGG
Found at i:48820628 original size:44 final size:44
Alignment explanation
Indices: 48820580--48820743 Score: 145
Period size: 44 Copynumber: 3.7 Consensus size: 44
48820570 CCATCATTTT
* * * * *
48820580 AATCTGCTCTACTATAACTTTAAGGAGATAGGATTGGTTTCTTC
1 AATCTGCTCCACTACAACTTCAAGGAGATAAGATTGGTTTATTC
* *
48820624 AATCTGCTCCACTGCAACTTCACGGAGATAAGATTGGTTTATTC
1 AATCTGCTCCACTACAACTTCAAGGAGATAAGATTGGTTTATTC
* * * *
48820668 AGTCTGCTCCACTGCAACTTC-AGAGAGATAAGACTT-G-TAACTTG
1 AATCTGCTCCACTACAACTTCAAG-GAGATAAGA-TTGGTTTA-TTC
* * * *
48820712 AACCTGCTCCACTGCAATTTCAGGGAGATAAG
1 AATCTGCTCCACTACAACTTCAAGGAGATAAG
48820744 TTGTACTATG
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
43 3 0.03
44 95 0.94
45 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTACAACTTCAAGGAGATAAGATTGGTTTATTC
Found at i:48828157 original size:22 final size:22
Alignment explanation
Indices: 48828132--48828188 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
48828122 TACAAATTAA
48828132 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTACAAAATCAT
* *
48828154 ATCTTCTAAGATTGC-ATATCAT
1 ATC-TCTAAGATTACAAAATCAT
48828176 A--TCTAAGATTACA
1 ATCTCTAAGATTACA
48828189 TATCTTGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.33
22 10 0.33
23 10 0.33
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (22 bp):
ATCTCTAAGATTACAAAATCAT
Found at i:48828165 original size:23 final size:22
Alignment explanation
Indices: 48828122--48828179 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
48828112 AAAGGGTATC
* *
48828122 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
48828143 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
48828166 TGCATATCATATCT
1 TACAAATCATATCT
48828180 AAGATTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Done.