Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 181 of 318
Found at i:56727252 original size:51 final size:51
Alignment explanation
Indices: 56727111--56727288 Score: 254
Period size: 51 Copynumber: 3.5 Consensus size: 51
56727101 ACTAGTGACT
** *
56727111 CAAGTGTGGTACTATGTGAAGGTAACTTTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
*
56727160 AAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGTCA
*
56727212 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTC-A
* *
56727263 CAAGGGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
56727289 GGGGTATTCG
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
49 31 0.26
50 2 0.02
51 43 0.37
52 41 0.35
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
Found at i:56729116 original size:21 final size:25
Alignment explanation
Indices: 56729092--56729151 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 25
56729082 GTACGACCTG
56729092 TAGCCGTTCTGT-ATA-A-GGCTT-
1 TAGCCGTTCTGTGATATATGGCTTA
*
56729113 TAGCCTTTCTGTGATACTTATGGCTTA
1 TAGCCGTTCTGTGATA--TATGGCTTA
56729140 TAGCCGTTCTGT
1 TAGCCGTTCTGT
56729152 TAACTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 11 0.35
22 3 0.10
25 1 0.03
26 5 0.16
27 11 0.35
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.42
Consensus pattern (25 bp):
TAGCCGTTCTGTGATATATGGCTTA
Found at i:56734804 original size:63 final size:63
Alignment explanation
Indices: 56734724--56734849 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
56734714 TCTTGATAAG
*
56734724 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAATTCTCC
1 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
56734787 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
1 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
56734850 CTATATAAAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (63 bp):
TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
Found at i:56738847 original size:17 final size:17
Alignment explanation
Indices: 56738825--56738859 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
56738815 GATGGGCTGA
**
56738825 AATGGGCTTGTGGGCCC
1 AATGGGCTCATGGGCCC
56738842 AATGGGCTCATGGGCCC
1 AATGGGCTCATGGGCCC
56738859 A
1 A
56738860 TACGGACAAG
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:0.17, C:0.26, G:0.37, T:0.20
Consensus pattern (17 bp):
AATGGGCTCATGGGCCC
Found at i:56739112 original size:27 final size:27
Alignment explanation
Indices: 56739074--56739257 Score: 181
Period size: 27 Copynumber: 6.9 Consensus size: 27
56739064 AAGACCACCG
56739074 ATTTGTAAAATTACCAAAATACCCCTA
1 ATTTGTAAAATTACCAAAATACCCCTA
*
56739101 ATTTGTAAAATTACCAAAATACCCTTA
1 ATTTGTAAAATTACCAAAATACCCCTA
* * * *
56739128 ACTTGTAAAATTACTAAAATACCTCTT
1 ATTTGTAAAATTACCAAAATACCCCTA
* *
56739155 ATTTATAAAATTACCAAAATACTCCTA
1 ATTTGTAAAATTACCAAAATACCCCTA
* *** * *
56739182 ACTTGT-AAATTATTTAAATACACCTG
1 ATTTGTAAAATTACCAAAATACCCCTA
* * * *
56739208 ATTTATAAAATTACCGAAATACCCTTG
1 ATTTGTAAAATTACCAAAATACCCCTA
* * *
56739235 ATTTGTGAAATTATCGAAATACC
1 ATTTGTAAAATTACCAAAATACC
56739258 TCTATGAGGT
Statistics
Matches: 127, Mismatches: 29, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
26 19 0.15
27 108 0.85
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (27 bp):
ATTTGTAAAATTACCAAAATACCCCTA
Found at i:56739164 original size:54 final size:54
Alignment explanation
Indices: 56739076--56739261 Score: 209
Period size: 54 Copynumber: 3.5 Consensus size: 54
56739066 GACCACCGAT
* * *
56739076 TTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTAAC
1 TTGTAAAATTACTAAAATACCTCTAATTTATAAAATTACCAAAATACCCTTAAC
*
56739130 TTGTAAAATTACTAAAATACCTCTTATTTATAAAATTACCAAAATACTCC-TAAC
1 TTGTAAAATTACTAAAATACCTCTAATTTATAAAATTACCAAAATAC-CCTTAAC
* * * * * *
56739184 TTGT-AAATTATTTAAATACAC-CTGATTTATAAAATTACCGAAATACCCTTGAT
1 TTGTAAAATTACTAAAATAC-CTCTAATTTATAAAATTACCAAAATACCCTTAAC
* *
56739237 TTGTGAAATTA-TCGAAATACCTCTA
1 TTGTAAAATTACT-AAAATACCTCTA
56739262 TGAGGTAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
52 2 0.02
53 44 0.39
54 66 0.58
55 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (54 bp):
TTGTAAAATTACTAAAATACCTCTAATTTATAAAATTACCAAAATACCCTTAAC
Found at i:56739274 original size:27 final size:25
Alignment explanation
Indices: 56739244--56739365 Score: 113
Period size: 27 Copynumber: 4.6 Consensus size: 25
56739234 GATTTGTGAA
*
56739244 ATTATCGAAATACCTCTATGAGGTAGG
1 ATTA-CGAAATACC-CTGTGAGGTAGG
*
56739271 ATTACCGAAATACCCTTGTGGGGTAGG
1 ATTA-CGAAATACCC-TGTGAGGTAGG
56739298 ATTACTGAAATACCCTGT-AGGGTAGG
1 ATTAC-GAAATACCCTGTGA-GGTAGG
*
56739324 ATTACAAAAATACCCCTGT-AGGGTAGG
1 ATTAC-GAAATA-CCCTGTGA-GGTAGG
*
56739351 ATTACAAAATACCCT
1 ATTACGAAATACCCT
56739366 TGTAGGGTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.05
26 27 0.32
27 54 0.64
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (25 bp):
ATTACGAAATACCCTGTGAGGTAGG
Found at i:56739327 original size:26 final size:26
Alignment explanation
Indices: 56739265--56739374 Score: 150
Period size: 26 Copynumber: 4.2 Consensus size: 26
56739255 ACCTCTATGA
* *
56739265 GGTAGGATTACCGAAATACCCTTGTGG
1 GGTAGGATTA-CAAAATACCCTTGTAG
*
56739292 GGTAGGATTACTGAAATACCC-TGTAG
1 GGTAGGATTAC-AAAATACCCTTGTAG
*
56739318 GGTAGGATTACAAAAATACCCCTGTAG
1 GGTAGGATTAC-AAAATACCCTTGTAG
56739345 GGTAGGATTACAAAATACCCTTGTAG
1 GGTAGGATTACAAAATACCCTTGTAG
56739371 GGTA
1 GGTA
56739375 AAATGCCCGT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
26 42 0.55
27 35 0.45
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (26 bp):
GGTAGGATTACAAAATACCCTTGTAG
Found at i:56739348 original size:53 final size:53
Alignment explanation
Indices: 56739265--56739374 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 53
56739255 ACCTCTATGA
** * * *
56739265 GGTAGGATTACCGAAATACCCTTGTGGGGTAGGATTACTGAAATACCC-TGTAG
1 GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTAC-AAAATACCCTTGTAG
56739318 GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTACAAAATACCCTTGTAG
1 GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTACAAAATACCCTTGTAG
56739371 GGTA
1 GGTA
56739375 AAATGCCCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 8 0.16
53 43 0.84
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (53 bp):
GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTACAAAATACCCTTGTAG
Found at i:56743505 original size:27 final size:26
Alignment explanation
Indices: 56743473--56743712 Score: 134
Period size: 27 Copynumber: 8.9 Consensus size: 26
56743463 GACCCTTGAT
*
56743473 TTGTAAAATTATTGAAATA-CTCTCGA
1 TTGTAAAATTACTGAAATACCTCT-GA
** * *
56743499 TATGTAAAATTACCAAAATACCCCTAA
1 T-TGTAAAATTACTGAAATACCTCTGA
* * *
56743526 TTTGTAAAATTACTGAAATACCCCCGGG
1 -TTGTAAAATTACTGAAATA-CCTCTGA
* *
56743554 TTATAAAATTA-TCGAAATACCTCTAA
1 TTGTAAAATTACT-GAAATACCTCTGA
*
56743580 CTTGTAAAATTACTAAAATACC-CTTGA
1 -TTGTAAAATTACTGAAATACCTC-TGA
*
56743607 TTTGTAAAATTACCGAAATA-CTCCTGA
1 -TTGTAAAATTACTGAAATACCT-CTGA
* * *
56743634 CTTGTAAAATTATTAAAATACCCCTGA
1 -TTGTAAAATTACTGAAATACCTCTGA
*
56743661 TTTGTGAAATTACT-AGAATACCCTCT-A
1 -TTGTAAAATTACTGA-AATA-CCTCTGA
* *
56743688 TTTGTGAAATTA-TCAAAATACCTCT
1 -TTGTAAAATTACT-GAAATACCTCT
56743713 ATGGGGTAGG
Statistics
Matches: 169, Mismatches: 30, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
26 14 0.08
27 139 0.82
28 16 0.09
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (26 bp):
TTGTAAAATTACTGAAATACCTCTGA
Found at i:56743611 original size:81 final size:79
Alignment explanation
Indices: 56743476--56743709 Score: 245
Period size: 81 Copynumber: 2.9 Consensus size: 79
56743466 CCTTGATTTG
* * *
56743476 TAAAATTATTGAAATA-CTCTCGATATGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACT
1 TAAAATTATTGAAATACCTCT-GAT-TGTAAAATTACTAAAATA-CCCTTATTTGTAAAATTACC
**
56743540 GAAATACCCCCGGGTTA
63 GAAATACCCCCGACTTA
* *
56743557 TAAAATTATCGAAATACCTCTAACTTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCG
1 TAAAATTATTGAAATACCTCTGA-TTGTAAAATTACTAAAATACCCTT-ATTTGTAAAATTACCG
* * *
56743622 AAATACTCCTGACTTG
64 AAATACCCCCGACTTA
* * * * * * *
56743638 TAAAATTATTAAAATACCCCTGATTTGTGAAATTACTAGAATACCCTCTATTTGTGAAATTATCA
1 TAAAATTATTGAAATACCTCTGA-TTGTAAAATTACTAAAATACCCT-TATTTGTAAAATTACCG
56743703 AAATACC
64 AAATACC
56743710 TCTATGGGGT
Statistics
Matches: 128, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
80 4 0.03
81 118 0.92
82 6 0.05
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (79 bp):
TAAAATTATTGAAATACCTCTGATTGTAAAATTACTAAAATACCCTTATTTGTAAAATTACCGAA
ATACCCCCGACTTA
Found at i:56743662 original size:54 final size:53
Alignment explanation
Indices: 56743473--56743673 Score: 215
Period size: 54 Copynumber: 3.7 Consensus size: 53
56743463 GACCCTTGAT
* * * * * *
56743473 TTGTAAAATTATTGAAATA-CTCTCGATATGTAAAATTACCAAAATACCCCTAAT
1 TTGTAAAATTACTAAAATACCCCT-GATTTGTAAAATTACCGAAATA-CCCTAAC
* * ** * *
56743527 TTGTAAAATTACTGAAATACCCCCGGGTTATAAAATTATCGAAATACCTCTAAC
1 TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTACCGAAATACC-CTAAC
* *
56743581 TTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCGAAATACTCCTGAC
1 TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTACCGAAATAC-CCTAAC
* *
56743635 TTGTAAAATTATTAAAATACCCCTGATTTGTGAAATTAC
1 TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTAC
56743674 TAGAATACCC
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
53 2 0.02
54 118 0.96
55 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.33
Consensus pattern (53 bp):
TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTACCGAAATACCCTAAC
Found at i:56743681 original size:54 final size:54
Alignment explanation
Indices: 56743473--56743709 Score: 205
Period size: 54 Copynumber: 4.4 Consensus size: 54
56743463 GACCCTTGAT
* * * * *
56743473 TTGTAAAATTATTGAAATA-CTCTCGATATGTAAAATTACCA-AAATACCCCTAAT
1 TTGTAAAATTATTAAAATACCCCT-GATTTGTAAAATTACTAGAAATA-CCCTAAC
* * * ** * *
56743527 TTGTAAAATTACTGAAATACCCCCGGGTTATAAAATTA-TCGAAATACCTCTAAC
1 TTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTACTAGAAATACC-CTAAC
* * * *
56743581 TTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTAC-CGAAATACTCCTGAC
1 TTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTACTAGAAATAC-CCTAAC
* * *
56743635 TTGTAAAATTATTAAAATACCCCTGATTTGTGAAATTACTAG-AATACCCTCTAT
1 TTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTACTAGAAATACCCT-AAC
* *
56743689 TTGTGAAATTATCAAAATACC
1 TTGTAAAATTATTAAAATACC
56743710 TCTATGGGGT
Statistics
Matches: 151, Mismatches: 25, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
53 5 0.03
54 142 0.94
55 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (54 bp):
TTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTACTAGAAATACCCTAAC
Found at i:56743726 original size:27 final size:27
Alignment explanation
Indices: 56743696--56743787 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
56743686 TATTTGTGAA
* *
56743696 ATTATCAAAATACCTCTATGGGGTAGG
1 ATTATCGAAATACCTCTGTGGGGTAGG
*
56743723 ATTATCGAAATACCCCTGTGGGGTAGG
1 ATTATCGAAATACCTCTGTGGGGTAGG
* *
56743750 ATTATCGAAATACCTTTGTAGGGTAGG
1 ATTATCGAAATACCTCTGTGGGGTAGG
*
56743777 ATTATTGAAAT
1 ATTATCGAAAT
56743788 GTAGGGTAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (27 bp):
ATTATCGAAATACCTCTGTGGGGTAGG
Found at i:56743808 original size:21 final size:21
Alignment explanation
Indices: 56743766--56743808 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56743756 GAAATACCTT
***
56743766 TGTAGGGTAGGATTATTGAAA
1 TGTAGGGTAGGATTACAAAAA
56743787 TGTAGGGTAGGATTACAAAAA
1 TGTAGGGTAGGATTACAAAAA
56743808 T
1 T
56743809 ACCCCTATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTAGGGTAGGATTACAAAAA
Found at i:56743820 original size:27 final size:27
Alignment explanation
Indices: 56743789--56743849 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
56743779 TATTGAAATG
56743789 TAGGGTAGGATTACAAAAATACCCCTA
1 TAGGGTAGGATTACAAAAATACCCCTA
** * *
56743816 TAGGGTAGGATTACCGAAATACCCTTG
1 TAGGGTAGGATTACAAAAATACCCCTA
56743843 TAGGGTA
1 TAGGGTA
56743850 AAATGCCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
TAGGGTAGGATTACAAAAATACCCCTA
Found at i:56745304 original size:18 final size:18
Alignment explanation
Indices: 56745281--56745325 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
56745271 AAATAAGAAG
56745281 GGTTTTCAATGAAAACAT
1 GGTTTTCAATGAAAACAT
56745299 GGTTTTCAATGAAAACAT
1 GGTTTTCAATGAAAACAT
56745317 GGTTTTCAA
1 GGTTTTCAA
56745326 AAAACACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAT
Found at i:56745895 original size:43 final size:41
Alignment explanation
Indices: 56745843--56745984 Score: 167
Period size: 43 Copynumber: 3.4 Consensus size: 41
56745833 AAAGTGTGAT
56745843 TTCATGTAAGACCATGTCTGGGACATTGGCATCAGTATAAGA
1 TTCATGTAAGACCATGTCTGGGACATTGGCATC-GTATAAGA
*
56745885 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAAGA
1 TT-CATGTAAGACCATGTCTGGGACATTGGCATCGTATAAGA
* * * * * **
56745927 TTCATGTAAGACCCTATCTAGGACAGTGGTATCGATATGTGA
1 TTCATGTAAGACCATGTCTGGGACATTGGCATCG-TATAAGA
*
56745969 TAGCATGTAAGACCAT
1 T-TCATGTAAGACCAT
56745985 ATCCAGGATA
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 26 0.30
42 18 0.21
43 42 0.49
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (41 bp):
TTCATGTAAGACCATGTCTGGGACATTGGCATCGTATAAGA
Found at i:56751649 original size:65 final size:65
Alignment explanation
Indices: 56751568--56751704 Score: 274
Period size: 65 Copynumber: 2.1 Consensus size: 65
56751558 CAATAGGGAC
56751568 TAAATTGTAAAAATTGTAAATGTCAGGGGTAAAATGGTAATTTTTCCATTTATGTGTTTTTGGAT
1 TAAATTGTAAAAATTGTAAATGTCAGGGGTAAAATGGTAATTTTTCCATTTATGTGTTTTTGGAT
56751633 TAAATTGTAAAAATTGTAAATGTCAGGGGTAAAATGGTAATTTTTCCATTTATGTGTTTTTGGAT
1 TAAATTGTAAAAATTGTAAATGTCAGGGGTAAAATGGTAATTTTTCCATTTATGTGTTTTTGGAT
56751698 TAAATTG
1 TAAATTG
56751705 AATGAAAATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 72 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (65 bp):
TAAATTGTAAAAATTGTAAATGTCAGGGGTAAAATGGTAATTTTTCCATTTATGTGTTTTTGGAT
Found at i:56772101 original size:14 final size:14
Alignment explanation
Indices: 56772082--56772115 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
56772072 ACTTTTTCCA
56772082 CTCTTTTTATTTTG
1 CTCTTTTTATTTTG
* *
56772096 CTCTTTTTCTTTTT
1 CTCTTTTTATTTTG
56772110 CTCTTT
1 CTCTTT
56772116 CAATGGATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
CTCTTTTTATTTTG
Found at i:56774018 original size:14 final size:14
Alignment explanation
Indices: 56773996--56774040 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
56773986 TTAAAGAAGC
56773996 AACTCATTAAATTA
1 AACTCATTAAATTA
*
56774010 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
56774023 AACTCATTTAATTA
1 AACTCATTAAATTA
56774037 AACT
1 AACT
56774041 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:56774078 original size:22 final size:22
Alignment explanation
Indices: 56774052--56774121 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
56774042 AGATGAGTTG
56774052 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
56774074 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
56774093 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
56774116 TATTAA
1 TATTAA
56774122 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:56774084 original size:42 final size:42
Alignment explanation
Indices: 56774023--56774128 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
56774013 TCATTAAATA
56774023 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
56774066 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
56774108 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
56774129 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:56776297 original size:22 final size:24
Alignment explanation
Indices: 56776263--56776306 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
56776253 CTTGGACCAA
56776263 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
**
56776285 GATTTCCTTGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
56776307 GCTCCGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:56777505 original size:23 final size:22
Alignment explanation
Indices: 56777453--56777505 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
56777443 TCCACGTCTT
*
56777453 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
56777475 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
56777498 TTTCTTTT
1 TTTCTTTT
56777506 TCACTCTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:56778819 original size:9 final size:9
Alignment explanation
Indices: 56778804--56778838 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
56778794 TGAATTTCGT
56778804 CTTTTTTGA
1 CTTTTTTGA
*
56778813 TTTTTTTGA
1 CTTTTTTGA
56778822 CTTTTTTGA
1 CTTTTTTGA
56778831 CTTATTTT
1 CTT-TTTT
56778839 TTTGCGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (9 bp):
CTTTTTTGA
Found at i:56795373 original size:20 final size:20
Alignment explanation
Indices: 56795350--56795403 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
56795340 AGTTTTACCC
*
56795350 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
56795370 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
56795390 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
56795404 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:56795385 original size:30 final size:30
Alignment explanation
Indices: 56795350--56795423 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
56795340 AGTTTTACCC
56795350 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
56795380 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
56795410 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
56795424 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:56795413 original size:20 final size:20
Alignment explanation
Indices: 56795350--56795414 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
56795340 AGTTTTACCC
* * * *
56795350 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
56795370 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
56795389 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
56795410 AGCTC
1 AGCTC
56795415 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:56800774 original size:27 final size:28
Alignment explanation
Indices: 56800737--56800876 Score: 175
Period size: 27 Copynumber: 5.2 Consensus size: 28
56800727 AGCATGGCTG
* *
56800737 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
56800763 CCAGATACAGATA-ATCGCGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
56800791 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
56800818 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
56800845 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
56800872 CCAGA
1 CCAGA
56800877 ACGCTTCCTC
Statistics
Matches: 104, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
26 5 0.05
27 83 0.80
28 16 0.15
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:56802605 original size:26 final size:26
Alignment explanation
Indices: 56802496--56802597 Score: 177
Period size: 26 Copynumber: 3.9 Consensus size: 26
56802486 CATGAAATTC
56802496 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
56802522 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
56802548 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
56802574 TTATCATGGAACATTTACCTAACC
1 TTATCATGAAACATTTACCTAACC
56802598 TTTTATCAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:56804400 original size:10 final size:10
Alignment explanation
Indices: 56804385--56804411 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
56804375 TAAGTTGAAG
56804385 TTGAGCTGAT
1 TTGAGCTGAT
56804395 TTGAGCTGAT
1 TTGAGCTGAT
56804405 TTGAGCT
1 TTGAGCT
56804412 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:56805746 original size:18 final size:17
Alignment explanation
Indices: 56805714--56805747 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56805704 TTAATTGAGT
56805714 TCATATTAGTTAATAAC
1 TCATATTAGTTAATAAC
*
56805731 TCATCTTAGATTAATAA
1 TCATATTAG-TTAATAA
56805748 ATGAGTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
TCATATTAGTTAATAAC
Found at i:56807870 original size:20 final size:20
Alignment explanation
Indices: 56807823--56807870 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
56807813 AGTAAGCTCG
56807823 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
56807843 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
56807863 GTTGAGCT
1 GTTGAGCT
56807871 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:56812853 original size:14 final size:13
Alignment explanation
Indices: 56812831--56812884 Score: 90
Period size: 13 Copynumber: 4.0 Consensus size: 13
56812821 AAACCGTATG
56812831 CAATTTTTTTTTT
1 CAATTTTTTTTTT
56812844 CAATTTTTTTTTT
1 CAATTTTTTTTTT
56812857 CAATTTTTTTTTT
1 CAATTTTTTTTTT
56812870 CGAACTTTTTTTTTT
1 C-AA-TTTTTTTTTT
56812885 TACGCACCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 27 0.69
14 2 0.05
15 10 0.26
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:56816380 original size:21 final size:20
Alignment explanation
Indices: 56816332--56816392 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
56816322 AACTCCGACC
*
56816332 AGCTCAAAT-GAGCTCATTT
1 AGCTCAATTCGAGCTCATTT
56816351 CAGCTCAA-TCGAGCTCAATTT
1 -AGCTCAATTCGAGCTC-ATTT
56816372 AGCTACAATTC-AGCTCATTT
1 AGCT-CAATTCGAGCTCATTT
56816392 A
1 A
56816393 TTTTATTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 12 0.32
22 2 0.05
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (20 bp):
AGCTCAATTCGAGCTCATTT
Found at i:56816386 original size:11 final size:10
Alignment explanation
Indices: 56816331--56816388 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
56816321 CAACTCCGAC
*
56816331 CAGCTCAAAT
1 CAGCTCAATT
* *
56816341 GAGCTCATTT
1 CAGCTCAATT
56816351 CAGCTCAA-T
1 CAGCTCAATT
56816360 CGAGCTCAATT
1 C-AGCTCAATT
*
56816371 TAGCTACAATT
1 CAGCT-CAATT
56816382 CAGCTCA
1 CAGCTCA
56816389 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.68
11 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:56817572 original size:15 final size:16
Alignment explanation
Indices: 56817552--56817584 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56817542 CTCCATCAAT
56817552 TACCTT-TTTCTAATC
1 TACCTTGTTTCTAATC
*
56817567 TACCTTGTTTCTATTC
1 TACCTTGTTTCTAATC
56817583 TA
1 TA
56817585 AACCGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.55
Consensus pattern (16 bp):
TACCTTGTTTCTAATC
Found at i:56817910 original size:12 final size:12
Alignment explanation
Indices: 56817893--56817962 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
56817883 TTGGAGTAAC
56817893 AAAAAAAA-TC-
1 AAAAAAAATTCA
56817903 AAAAAAAATTCGA
1 AAAAAAAATTC-A
* *
56817916 AAAAAATTGATTGA
1 AAAAAA--AATTCA
56817930 AAAAAAAATTCA
1 AAAAAAAATTCA
* *
56817942 AAAAAAAAGTGA
1 AAAAAAAATTCA
56817954 AAAAAAAAT
1 AAAAAAAAT
56817963 CGAGCAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 8 0.17
11 2 0.04
12 22 0.46
13 6 0.12
14 7 0.15
15 3 0.06
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:56817959 original size:27 final size:27
Alignment explanation
Indices: 56817903--56817961 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
56817893 AAAAAAAATC
* * **
56817903 AAAAAAAATTCGAAAAAAATTGATTGA
1 AAAAAAAATTCAAAAAAAAGTGATAAA
56817930 AAAAAAAATTCAAAAAAAAAGTGA-AAA
1 AAAAAAAATTC-AAAAAAAAGTGATAAA
56817957 AAAAA
1 AAAAA
56817962 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAAAATTCAAAAAAAAGTGATAAA
Found at i:56817972 original size:28 final size:27
Alignment explanation
Indices: 56817941--56818012 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
56817931 AAAAAAATTC
*
56817941 AAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAG-A
* * *
56817969 AAAAAAAAGGTGACCAAAAAAATCAAGT
1 AAAAAAAAAGTGA-AAAAAAAATCAAGA
*
56817997 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
56818013 GTCTTGCGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 2 0.06
28 23 0.64
29 11 0.31
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (27 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGA
Found at i:56817973 original size:24 final size:24
Alignment explanation
Indices: 56817903--56817962 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
56817893 AAAAAAAATC
* *
56817903 AAAAAAAATTCGAAAAAAATTGATTGA
1 AAAAAAAATTC-AAAAAAA--AAGTGA
56817930 AAAAAAAATTCAAAAAAAAAGTGA
1 AAAAAAAATTCAAAAAAAAAGTGA
56817954 AAAAAAAAT
1 AAAAAAAAT
56817963 CGAGCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 13 0.42
26 7 0.23
27 11 0.35
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (24 bp):
AAAAAAAATTCAAAAAAAAAGTGA
Found at i:56817987 original size:29 final size:28
Alignment explanation
Indices: 56817940--56818012 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
56817930 AAAAAAAATT
*
56817940 CAAAAAAAAA-GTGAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAATCAAG
*
56817967 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAGGTGA-AAAAAAAATCAAG
**
56817996 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
56818013 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 12 0.31
28 8 0.21
29 19 0.49
ACGTcount: A:0.68, C:0.08, G:0.14, T:0.10
Consensus pattern (28 bp):
CAAAAAAAAAGGTGAAAAAAAAATCAAG
Found at i:56818895 original size:18 final size:18
Alignment explanation
Indices: 56818874--56818908 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56818864 AGAAAAGAAA
56818874 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
56818892 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
56818909 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:56821029 original size:21 final size:20
Alignment explanation
Indices: 56820981--56821041 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
56820971 AACTCCGACC
*
56820981 AGCTCAAAT-GAGCTCATTT
1 AGCTCAATTCGAGCTCATTT
56821000 CAGCTCAA-TCGAGCTCAATTT
1 -AGCTCAATTCGAGCTC-ATTT
56821021 AGCTACAATTC-AGCTCATTT
1 AGCT-CAATTCGAGCTCATTT
56821041 A
1 A
56821042 TTTTATTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 12 0.32
22 2 0.05
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (20 bp):
AGCTCAATTCGAGCTCATTT
Found at i:56821035 original size:11 final size:10
Alignment explanation
Indices: 56820980--56821037 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
56820970 CAACTCCGAC
*
56820980 CAGCTCAAAT
1 CAGCTCAATT
* *
56820990 GAGCTCATTT
1 CAGCTCAATT
56821000 CAGCTCAA-T
1 CAGCTCAATT
56821009 CGAGCTCAATT
1 C-AGCTCAATT
*
56821020 TAGCTACAATT
1 CAGCT-CAATT
56821031 CAGCTCA
1 CAGCTCA
56821038 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.68
11 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:56823199 original size:11 final size:10
Alignment explanation
Indices: 56823180--56823209 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
56823170 TCACATTCAC
56823180 GAATTTTTTT
1 GAATTTTTTT
56823190 GAATTTTTTT
1 GAATTTTTTT
56823200 GAATTTTTTT
1 GAATTTTTTT
56823210 CAAATACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (10 bp):
GAATTTTTTT
Found at i:56826741 original size:19 final size:19
Alignment explanation
Indices: 56826714--56826752 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
56826704 TTATTCCATC
*
56826714 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
56826733 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
56826752 A
1 A
56826753 GTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:56831664 original size:10 final size:10
Alignment explanation
Indices: 56831649--56831685 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
56831639 AAGAGAAAAT
56831649 AAAGAAA-AGA
1 AAAGAAATA-A
56831659 AAAGAAATAA
1 AAAGAAATAA
56831669 AAAGAAATAA
1 AAAGAAATAA
56831679 AAAGAAA
1 AAAGAAA
56831686 AGAGAGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 25 0.96
11 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAGAAATAA
Found at i:56831765 original size:12 final size:12
Alignment explanation
Indices: 56831757--56831781 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56831747 TTTGAAAAGA
56831757 AAAAAGAAAATG
1 AAAAAGAAAATG
56831769 AAAAAGAAAATG
1 AAAAAGAAAATG
56831781 A
1 A
56831782 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:56831791 original size:30 final size:31
Alignment explanation
Indices: 56831757--56831838 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
56831747 TTTGAAAAGA
*
56831757 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
56831787 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
56831817 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
56831839 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:56833987 original size:30 final size:31
Alignment explanation
Indices: 56833953--56834049 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
56833943 AGCTCACTCC
*
56833953 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
56833983 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
56834013 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
56834043 TAGCTCA
1 TAGCTCA
56834050 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:56834938 original size:22 final size:20
Alignment explanation
Indices: 56834906--56834954 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
56834896 GCCAAATTTA
56834906 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
56834929 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
56834949 TGAACA
1 TGAACA
56834955 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:56836064 original size:20 final size:20
Alignment explanation
Indices: 56836041--56836094 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
56836031 AGTTTTTCCC
*
56836041 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
56836061 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
56836081 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
56836095 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:56836076 original size:30 final size:30
Alignment explanation
Indices: 56836041--56836114 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
56836031 AGTTTTTCCC
56836041 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
56836071 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
56836101 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
56836115 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:56836104 original size:20 final size:20
Alignment explanation
Indices: 56836041--56836105 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
56836031 AGTTTTTCCC
* * * *
56836041 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
56836061 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
56836080 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
56836101 AGCTC
1 AGCTC
56836106 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:56837747 original size:12 final size:13
Alignment explanation
Indices: 56837723--56837748 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56837713 AAAAGAGAAG
56837723 AAATTCAAAAAAA
1 AAATTCAAAAAAA
56837736 AAATTCAAAAAAA
1 AAATTCAAAAAAA
56837749 TCGAAAAAAA
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:56839312 original size:20 final size:20
Alignment explanation
Indices: 56839289--56839335 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56839279 GGGTTAAGAT
*
56839289 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
56839309 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
56839329 TGAGCTG
1 TGAGCTG
56839336 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:56841059 original size:48 final size:48
Alignment explanation
Indices: 56841004--56841109 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
56840994 TTGTCTTTTC
*
56841004 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
56841052 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
56841100 TTTCTTTTTC
1 TTTCTTTTTC
56841110 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:56843743 original size:10 final size:10
Alignment explanation
Indices: 56843728--56843765 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
56843718 TTGGGTTAAG
56843728 ATTGAGCTGA
1 ATTGAGCTGA
56843738 ATTGAGCTTG-
1 ATTGAGC-TGA
*
56843748 AGTGAGCTGA
1 ATTGAGCTGA
56843758 ATTGAGCT
1 ATTGAGCT
56843766 CGAGTGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:56843753 original size:20 final size:20
Alignment explanation
Indices: 56843730--56843776 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
56843720 GGGTTAAGAT
*
56843730 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
56843750 TGAGCTGAATTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
56843770 TGAGCTG
1 TGAGCTG
56843777 GAAACGAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:56845522 original size:47 final size:47
Alignment explanation
Indices: 56845445--56845549 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
56845435 TTGTCTTTTC
* *
56845445 TTTCTTTTTCAATTTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTCTTT-CTCACATCCTTT-TTCAATCTCAA
* *
56845493 TTTCTTTTTCGATTTCTTTCTCTTT-TCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCTCTTTCTCACATCCTTTTTCAATCTCAA
56845540 TTTCTTTTTC
1 TTTCTTTTTC
56845550 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTTCTCTCTTTCTCACATCCTTTTTCAATCTCAA
Found at i:56848182 original size:20 final size:20
Alignment explanation
Indices: 56848159--56848205 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56848149 GGGTTAAGAT
*
56848159 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
56848179 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
56848199 TGAGCTG
1 TGAGCTG
56848206 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:56849205 original size:12 final size:12
Alignment explanation
Indices: 56849184--56849340 Score: 55
Period size: 12 Copynumber: 13.6 Consensus size: 12
56849174 AGAAAAGGAG
*
56849184 AAAGAGATTGAA
1 AAAGAAATTGAA
56849196 AAAGAAATTG--
1 AAAGAAATTGAA
**
56849206 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
56849217 AAAGAAAACGAA
1 AAAGAAATTGAA
**
56849229 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
56849241 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
56849253 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
56849265 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
56849277 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
56849291 AAAGAAAATTGAA
1 AAAG-AAATTGAA
56849304 AAAGAAATTG--
1 AAAGAAATTGAA
56849314 --AG-AA-TGAA
1 AAAGAAATTGAA
*
56849322 AAAAAAATTGAA
1 AAAGAAATTGAA
56849334 AAAGAAA
1 AAAGAAA
56849341 AAGCGAAAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 28
0.69 0.14 0.18
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 2 0.02
10 8 0.07
11 12 0.11
12 63 0.58
13 9 0.08
14 6 0.06
15 5 0.05
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:56849238 original size:6 final size:6
Alignment explanation
Indices: 56849206--56849343 Score: 73
Period size: 6 Copynumber: 22.7 Consensus size: 6
56849196 AAAGAAATTG
* * ** *
56849206 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
56849253 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
** * * *
56849304 AAAGAA ATTGAG AATGAA AAA-AA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAG
56849344 CGAAAAAAGA
Statistics
Matches: 95, Mismatches: 32, Indels: 11
0.69 0.23 0.08
Matches are distributed among these distances:
5 7 0.07
6 73 0.77
7 11 0.12
8 4 0.04
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:56849329 original size:30 final size:27
Alignment explanation
Indices: 56849274--56849360 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 27
56849264 AAAAGTGAGA
*
56849274 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAAAAAATT
*
56849301 GAAAAAGAAATTGAGAATGAAAAAAAAATT
1 GAAAAAGAAAAT--GAA-GAAAAAAAAATT
* *
56849331 GAAAAAGAAAAAG-CGAAAAAAGAAATT
1 GAAAAAGAAAATGAAGAAAAAA-AAATT
56849358 GAA
1 GAA
56849361 GGAGAGCTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.14
27 19 0.37
28 1 0.02
29 3 0.06
30 21 0.41
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAAAAAATT
Found at i:56849357 original size:57 final size:52
Alignment explanation
Indices: 56849184--56849360 Score: 169
Period size: 57 Copynumber: 3.2 Consensus size: 52
56849174 AGAAAAGGAG
* *
56849184 AAAGAGATTGAAAAAGAAATTGAAA-GAAAACAAAAAGAAAACGAAAAAG-AA
1 AAAGAAATTGAAAAAGAAATTGAAATGAAAA-AAAAAGAAAAAGAAAAAGAAA
* ** * * *
56849235 AAAGAAATTGCAAAAGAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGA
1 AAAGAAATTGAAAAAGAAATTGAAAT-GAAAAA--AAAAGAAAAAGAAAAAGAA-A
56849291 AAAGAAAATTGAAAAAGAAATTGAGAATGAAAAAAAAATTGAAAAAGAAAAAGCGAAA
1 AAAG-AAATTGAAAAAGAAATTGA-AATGAAAAAAAAA--GAAAAAGAAAAA--GAAA
56849349 AAAGAAATTGAA
1 AAAGAAATTGAA
56849361 GGAGAGCTTG
Statistics
Matches: 100, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
51 21 0.21
52 1 0.01
53 5 0.05
54 13 0.13
55 3 0.03
56 5 0.05
57 41 0.41
58 8 0.08
59 3 0.03
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.10
Consensus pattern (52 bp):
AAAGAAATTGAAAAAGAAATTGAAATGAAAAAAAAAGAAAAAGAAAAAGAAA
Found at i:56851220 original size:20 final size:20
Alignment explanation
Indices: 56851197--56851250 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
56851187 AGTTTTTCCC
*
56851197 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
56851217 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
56851237 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
56851251 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:56851232 original size:30 final size:30
Alignment explanation
Indices: 56851197--56851270 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
56851187 AGTTTTTCCC
56851197 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
56851227 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
56851257 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
56851271 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:56851260 original size:20 final size:20
Alignment explanation
Indices: 56851197--56851261 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
56851187 AGTTTTTCCC
* * * *
56851197 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
56851217 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
56851236 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
56851257 AGCTC
1 AGCTC
56851262 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:56856122 original size:30 final size:29
Alignment explanation
Indices: 56856088--56856184 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
56856078 TAAACTAAAA
56856088 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGT
* * * * * * *
56856118 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGTTTAGCTCGTGAGCTAAAGT
56856148 TGAGCTAAAGTTTAGCTCGTGAGCTAAA-T
1 TGAGCT-AAGTTTAGCTCGTGAGCTAAAGT
56856177 ATGAGCTA
1 -TGAGCTA
56856185 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
29 2 0.04
30 46 0.92
31 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (29 bp):
TGAGCTAAGTTTAGCTCGTGAGCTAAAGT
Found at i:56858380 original size:12 final size:12
Alignment explanation
Indices: 56858365--56858395 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
56858355 TTCTTTTTGC
56858365 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56858377 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56858389 TTTTCAA
1 TTTTCAA
56858396 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:56858453 original size:5 final size:5
Alignment explanation
Indices: 56858443--56858504 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
56858433 CTCTTGCCTC
* *
56858443 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTCTT GCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCT-TT TC-TTT TCTTT
56858490 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
56858505 GTTTTCTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.09
5 32 0.68
6 9 0.19
7 2 0.04
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:56858500 original size:15 final size:14
Alignment explanation
Indices: 56858443--56858511 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 14
56858433 CTCTTGCCTC
56858443 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
56858458 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
*
56858473 TCTCTTGCTTTTTCTTT
1 TCT-TTTC-TTTT-TTT
*
56858490 TCTTTTCTTTTCTT
1 TCTTTTCTTTTTTT
*
56858504 TGTTTTCT
1 TCTTTTCT
56858512 CTTTACAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.23
15 12 0.27
16 17 0.39
17 5 0.11
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:56858501 original size:36 final size:37
Alignment explanation
Indices: 56858445--56858514 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
56858435 CTTGCCTCTC
56858445 TTTTCTTTTTATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTCATTTTCTTTGTT-TTCTCTTGCT
56858482 TTTTCTTTTCT-TTTC-TTTTCTTTGTTTTCTCTT
1 TTTTCTTTT-TATTTCATTTTCTTTGTTTTCTCTT
56858515 TACAAGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
36 15 0.48
37 15 0.48
38 1 0.03
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTCATTTTCTTTGTTTTCTCTTGCT
Found at i:56859457 original size:22 final size:22
Alignment explanation
Indices: 56859429--56859472 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
56859419 TTTAACTCGA
56859429 TCTTTTTTGTC-ACTTTTTTTTT
1 TCTTTTTTGTCGA-TTTTTTTTT
*
56859451 TCTTTTTTTTCGATTTTTTTTT
1 TCTTTTTTGTCGATTTTTTTTT
56859473 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.80
Consensus pattern (22 bp):
TCTTTTTTGTCGATTTTTTTTT
Found at i:56859467 original size:11 final size:11
Alignment explanation
Indices: 56859444--56859484 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 11
56859434 TTTGTCACTT
56859444 TTTTTTTTC--
1 TTTTTTTTCGA
56859453 TTTTTTTTCGA
1 TTTTTTTTCGA
*
56859464 TTTTTTTTTGAA
1 TTTTTTTTCG-A
56859476 TTTTTTTTC
1 TTTTTTTTC
56859485 TGAATTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:56859480 original size:13 final size:13
Alignment explanation
Indices: 56859453--56859491 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
56859443 TTTTTTTTTC
56859453 TTTTTTTTC-G-A
1 TTTTTTTTCTGAA
56859464 TTTTTTTT-TGAA
1 TTTTTTTTCTGAA
56859476 TTTTTTTTCTGAA
1 TTTTTTTTCTGAA
56859489 TTT
1 TTT
56859492 CTTCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.36
12 9 0.36
13 7 0.28
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCTGAA
Found at i:56861253 original size:30 final size:29
Alignment explanation
Indices: 56861219--56861315 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
56861209 TAAACTAAAA
56861219 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGT
* * * * * * *
56861249 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGTTTAGCTCGTGAGCTAAAGT
56861279 TGAGCTAAAGTTTAGCTCGTGAGCTAAA-T
1 TGAGCT-AAGTTTAGCTCGTGAGCTAAAGT
56861308 ATGAGCTA
1 -TGAGCTA
56861316 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
29 2 0.04
30 46 0.92
31 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (29 bp):
TGAGCTAAGTTTAGCTCGTGAGCTAAAGT
Found at i:56863231 original size:30 final size:30
Alignment explanation
Indices: 56863197--56863293 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
56863187 TAAACTAAAA
*
56863197 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * *
56863227 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* * *
56863257 TGAGCTAAGGTTTCGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
56863287 TGAGCTA
1 TGAGCTA
56863294 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.83
31 7 0.13
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:56863717 original size:20 final size:20
Alignment explanation
Indices: 56863694--56863741 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
56863684 AGCTCCGTCC
56863694 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
56863714 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
56863734 AGCTCAAC
1 AGCTCAAC
56863742 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:56865908 original size:12 final size:12
Alignment explanation
Indices: 56865891--56865937 Score: 67
Period size: 13 Copynumber: 3.8 Consensus size: 12
56865881 TGTAGATTCA
*
56865891 AAAAAAAAATCG
1 AAAAAAAAATTG
56865903 AAAAAAAAATTG
1 AAAAAAAAATTG
56865915 AAAAAAAAAATTTG
1 -AAAAAAAAA-TTG
56865929 AAAAAAAAA
1 AAAAAAAAA
56865938 ATTTTGCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 11 0.34
13 18 0.56
14 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:56865941 original size:14 final size:13
Alignment explanation
Indices: 56865890--56865940 Score: 77
Period size: 14 Copynumber: 3.9 Consensus size: 13
56865880 TTGTAGATTC
*
56865890 AAAAAAAAAATCG
1 AAAAAAAAAATTG
56865903 -AAAAAAAAATTG
1 AAAAAAAAAATTG
56865915 AAAAAAAAAATTTG
1 AAAAAAAAAA-TTG
56865929 AAAAAAAAAATT
1 AAAAAAAAAATT
56865941 TTGCATACGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
12 11 0.31
13 11 0.31
14 13 0.37
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:56869432 original size:20 final size:20
Alignment explanation
Indices: 56869386--56869432 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56869376 AGCTCGTTTC
*
56869386 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
56869406 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
56869426 CAGCTCA
1 CAGCTCA
56869433 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:56879465 original size:13 final size:12
Alignment explanation
Indices: 56879447--56879503 Score: 62
Period size: 11 Copynumber: 4.6 Consensus size: 12
56879437 CCGTATGCAA
56879447 TTTTTTTTCAAAT
1 TTTTTTTTC-AAT
56879460 TTTTTTTTCAATTT
1 TTTTTTTTCAA--T
*
56879474 TTTTTTTTCGA-
1 TTTTTTTTCAAT
*
56879485 TTTTTTTTCGAT
1 TTTTTTTTCAAT
56879497 TTTTTTT
1 TTTTTTT
56879504 GAATCTACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 11 0.28
12 9 0.22
13 9 0.22
14 11 0.28
ACGTcount: A:0.12, C:0.07, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:56886420 original size:11 final size:11
Alignment explanation
Indices: 56886402--56886436 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
56886392 AAAATTTGAT
56886402 TGAAAAAAAAA
1 TGAAAAAAAAA
*
56886413 TTAAAAAAAAA
1 TGAAAAAAAAA
56886424 GTGAAAAAAAAA
1 -TGAAAAAAAAA
56886436 T
1 T
56886437 CGAGCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:56886477 original size:30 final size:28
Alignment explanation
Indices: 56886413--56886486 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
56886403 GAAAAAAAAA
*
56886413 TTAAAAAAAAAGTGAAAAAAAAATCGAG
1 TTAAAAAAAAAGTGAAAAAAAAATCAAG
** *
56886441 CAAAAAAAAAAGGTGACCAAAAAAATCAAG
1 TTAAAAAAAAA-GTGA-AAAAAAAATCAAG
56886471 TT--AAAAAAAGTGAAAA
1 TTAAAAAAAAAGTGAAAA
56886487 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 16 0.43
29 4 0.11
30 11 0.30
ACGTcount: A:0.68, C:0.07, G:0.14, T:0.12
Consensus pattern (28 bp):
TTAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:56887377 original size:18 final size:18
Alignment explanation
Indices: 56887356--56887390 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56887346 AGAAAAGAAA
56887356 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
56887374 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
56887391 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:56894095 original size:14 final size:14
Alignment explanation
Indices: 56894078--56894123 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
56894068 GAAAAGAGTG
56894078 AAAATGTAAAAAGA
1 AAAATGTAAAAAGA
56894092 AAAATG-AGAAAAGA
1 AAAATGTA-AAAAGA
56894106 AAAA-GATGAAAAAGA
1 AAAATG-T-AAAAAGA
56894121 AAA
1 AAA
56894124 GGAGTGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.07
14 16 0.57
15 9 0.32
16 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATGTAAAAAGA
Found at i:56894102 original size:22 final size:20
Alignment explanation
Indices: 56894061--56894111 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
56894051 GATCAATGAG
*
56894061 AGAAAAAGAAAAGAGTGAAA
1 AGAAAAAGAAAAGAGAGAAA
56894081 ATGTAAAAAGAAAA-ATGAGAAA
1 A-G-AAAAAGAAAAGA-GAGAAA
56894103 AGAAAAAGA
1 AGAAAAAGA
56894112 TGAAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 8 0.30
21 3 0.11
22 16 0.59
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.08
Consensus pattern (20 bp):
AGAAAAAGAAAAGAGAGAAA
Found at i:56894109 original size:15 final size:15
Alignment explanation
Indices: 56894085--56894123 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
56894075 GTGAAAATGT
56894085 AAAAAG-AAAA-ATG
1 AAAAAGAAAAAGATG
56894098 AGAAAAGAAAAAGATG
1 A-AAAAGAAAAAGATG
56894114 AAAAAGAAAA
1 AAAAAGAAAA
56894124 GGAGTGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 5 0.22
15 13 0.57
16 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (15 bp):
AAAAAGAAAAAGATG
Found at i:56894124 original size:14 final size:14
Alignment explanation
Indices: 56894085--56894124 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
56894075 GTGAAAATGT
56894085 AAAAAGAAAA-ATG
1 AAAAAGAAAAGATG
56894098 AGAAAAGAAAAAGATG
1 A-AAAAG-AAAAGATG
56894114 AAAAAGAAAAG
1 AAAAAGAAAAG
56894125 GAGTGTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 9 0.38
16 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (14 bp):
AAAAAGAAAAGATG
Found at i:56895051 original size:30 final size:30
Alignment explanation
Indices: 56895017--56895113 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
56895007 AGCTCACTCC
56895017 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
56895047 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
56895077 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
56895107 TAGCTCA
1 TAGCTCA
56895114 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:56898936 original size:82 final size:82
Alignment explanation
Indices: 56898780--56898942 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
56898770 TTTTACTTCC
** * ** *
56898780 CTTTAAATACCGTTCCATGCATGGGAACTTCTCCTTAATGCATGTTTCCTTTGCCATTAAGTAGC
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAATGCATGCCTCCTTAGCCATTAAGTAGC
56898845 CGAATTTCAATGACCTT
66 CGAATTTCAATGACCTT
* * **
56898862 CTTTAAATGCCGTTCCTTGCATGTTAACAGCACCTTAAATGCATGCCTCCTTAGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTT-AATGCATGCCTCCTTAGCCATTAAGTAG
56898927 CCGAA-TTCAATGACCT
65 CCGAATTTCAATGACCT
56898943 GCAGACACAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
82 40 0.57
83 30 0.43
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (82 bp):
CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAATGCATGCCTCCTTAGCCATTAAGTAGC
CGAATTTCAATGACCTT
Found at i:56900498 original size:12 final size:12
Alignment explanation
Indices: 56900483--56900545 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
56900473 TCAAGCTCTC
56900483 TTTCAATTTCTT
1 TTTCAATTTCTT
*
56900495 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
56900510 TTTC---TTCTT
1 TTTCAATTTCTT
56900519 TTTCAATTTCTT
1 TTTCAATTTCTT
*
56900531 TTTCAATCTCTT
1 TTTCAATTTCTT
56900543 TTT
1 TTT
56900546 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:56900620 original size:21 final size:21
Alignment explanation
Indices: 56900584--56900642 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
56900574 CTCATTTTCA
* *
56900584 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
56900605 TCTTTTTCTCTCATTTATTTT
1 TCTTTTTCTCTCATTTCTTTT
*
56900626 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
56900643 ATTCAAGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:56901574 original size:28 final size:28
Alignment explanation
Indices: 56901530--56901599 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
56901520 TTTCAATCAC
* * *
56901530 TCTTTTTTTTTTCAATTTCAATTTTTTT
1 TCTTTTTTTTTTTAATTCCAAATTTTTT
56901558 TCTTTTTTTTTTTAATTCCAAATTTTTT
1 TCTTTTTTTTTTTAATTCCAAATTTTTT
56901586 TCTTCTTTTTTTTT
1 TCTT-TTTTTTTTT
56901600 CTTCAATACT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 29 0.76
29 9 0.24
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (28 bp):
TCTTTTTTTTTTTAATTCCAAATTTTTT
Found at i:56901661 original size:12 final size:11
Alignment explanation
Indices: 56901644--56901698 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 11
56901634 GAATACAAAC
56901644 TTTTTTTTTGAA
1 TTTTTTTTT-AA
*
56901656 TTTTTTTTCAAA
1 TTTTTTTT-TAA
56901668 TTTTTTTTTCAA
1 TTTTTTTTT-AA
56901680 GTTTTTTTTT-A
1 -TTTTTTTTTAA
56901691 TTTTTTTT
1 TTTTTTTT
56901699 ACAATACCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 8 0.21
11 1 0.03
12 20 0.53
13 9 0.24
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:56901662 original size:13 final size:12
Alignment explanation
Indices: 56901644--56901703 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 12
56901634 GAATACAAAC
*
56901644 TTTTTTTTTGAA
1 TTTTTTTTTCAA
56901656 -TTTTTTTTCAAA
1 TTTTTTTTTC-AA
56901668 TTTTTTTTTCAA
1 TTTTTTTTTCAA
56901680 GTTTTTTTTT--A
1 -TTTTTTTTTCAA
*
56901691 TTTTTTTTACAA
1 TTTTTTTTTCAA
56901703 T
1 T
56901704 ACCGTAATAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 8 0.20
11 9 0.22
12 6 0.15
13 18 0.44
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:56902562 original size:82 final size:82
Alignment explanation
Indices: 56902411--56902573 Score: 213
Period size: 82 Copynumber: 2.0 Consensus size: 82
56902401 TTGTGTCTGC
* * **
56902411 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAAACATGCATTTAAGGAGAAGTTAACATGCAA
56902476 GGAACGACATTTAAAGA
66 GGAACGACATTTAAAGA
**
56902493 AGGTCATTGAAATTCGGCTACTTAATGGC-AGAGGAAACATGCA-TTAAGGAGAAGTTCCCATGC
1 AGGTCATTG-AATTCGGCTACTTAATGGCTA-AGGAAACATGCATTTAAGGAGAAGTTAACATGC
* **
56902556 ATGGAACGGTATTTAAAG
64 AAGGAACGACATTTAAAG
56902574 GGAAGTAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 40 0.57
83 30 0.43
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAAACATGCATTTAAGGAGAAGTTAACATGCAA
GGAACGACATTTAAAGA
Found at i:56904057 original size:13 final size:12
Alignment explanation
Indices: 56904031--56904082 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
56904021 ACGGTATTGT
56904031 AAAAAAA-T-AA
1 AAAAAAATTGAA
*
56904041 AAAAAACTTGAA
1 AAAAAAATTGAA
*
56904053 AAAAAATTTGAA
1 AAAAAAATTGAA
*
56904065 AAAAAAATTCAA
1 AAAAAAATTGAA
56904077 AAAAAA
1 AAAAAA
56904083 GTTTGTATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
10 6 0.17
11 1 0.03
12 29 0.81
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:56904167 original size:25 final size:28
Alignment explanation
Indices: 56904126--56904187 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 28
56904116 TAGTATTGAA
* *
56904126 GAAAAAAAAGAAGAAAAAATTCGGAATT
1 GAAAAAAAAGAAGAAAAAAATCGAAATT
56904154 -AAAAAAAAG-A-AAAAAAATCGAAATT
1 GAAAAAAAAGAAGAAAAAAATCGAAATT
56904179 GAAAAAAAA
1 GAAAAAAAA
56904188 AGAGTGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 13 0.42
26 9 0.29
27 9 0.29
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.11
Consensus pattern (28 bp):
GAAAAAAAAGAAGAAAAAAATCGAAATT
Found at i:56904190 original size:27 final size:27
Alignment explanation
Indices: 56904127--56904187 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
56904117 AGTATTGAAG
*
56904127 AAAAAAAAGAAGAAAAAATTCGGAATT
1 AAAAAAAAGAAGAAAAAATTCGAAATT
56904154 AAAAAAAAGAA-AAAAAA-TCGAAATT
1 AAAAAAAAGAAGAAAAAATTCGAAATT
56904179 GAAAAAAAA
1 -AAAAAAAA
56904188 AGAGTGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 7 0.22
26 14 0.44
27 11 0.34
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.11
Consensus pattern (27 bp):
AAAAAAAAGAAGAAAAAATTCGAAATT
Found at i:56905115 original size:21 final size:21
Alignment explanation
Indices: 56905076--56905133 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
56905066 AATCTTGAAT
56905076 GAAATTGAGAG-AAAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
56905096 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
56905117 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
56905134 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 20 0.59
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:56905189 original size:12 final size:12
Alignment explanation
Indices: 56905172--56905245 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
56905162 AGTGAAAAGC
56905172 AAAAAGAGATTG
1 AAAAAGAGATTG
*
56905184 AAAAAGAAATTG
1 AAAAAGAGATTG
56905196 AAAAAGA-A--G
1 AAAAAGAGATTG
*
56905205 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
56905220 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
56905232 AAAGAGAGCTTG
1 AAAAAGAGATTG
56905244 AA
1 AA
56905246 CAGAATTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 32 0.64
13 2 0.04
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:56907007 original size:17 final size:18
Alignment explanation
Indices: 56906977--56907010 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56906967 AGCAACTCAT
56906977 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
56906995 TTATTAA-CTAAGATGA
1 TTATTAATCTAAGATGA
56907011 ACTCAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:56907024 original size:19 final size:19
Alignment explanation
Indices: 56907000--56907048 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
56906990 ATGAGTTATT
56907000 AACTAAGATGAACTCAATA
1 AACTAAGATGAACTCAATA
* *
56907019 AACTAAAATGAACTCAATT
1 AACTAAGATGAACTCAATA
56907038 AACTAAGATGA
1 AACTAAGATGA
56907049 GTAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.22
Consensus pattern (19 bp):
AACTAAGATGAACTCAATA
Found at i:56909248 original size:21 final size:20
Alignment explanation
Indices: 56909219--56909257 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56909209 TCTTTTCAAA
56909219 CTCAATCTCATTTTGCTTTCT
1 CTCAATCTC-TTTTGCTTTCT
* *
56909240 CTCATTCTCTTTTTCTTT
1 CTCAATCTCTTTTGCTTT
56909258 ATCATTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.28, G:0.03, T:0.59
Consensus pattern (20 bp):
CTCAATCTCTTTTGCTTTCT
Found at i:56911472 original size:30 final size:30
Alignment explanation
Indices: 56911387--56911483 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
56911377 TAAACTAAAA
* *
56911387 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
56911417 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
56911447 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
56911476 ATGAGCTA
1 -TGAGCTA
56911484 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:56913785 original size:30 final size:29
Alignment explanation
Indices: 56913717--56913796 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 29
56913707 CTTTTGTTTC
*
56913717 AATTTCTTTTTC-TTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTTCTTTTTCAATCTCA
56913745 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TT-TCTTTTTCAATCTCA
*
56913774 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC--TTTCTTTTT
56913797 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
27 5 0.11
28 6 0.14
29 6 0.14
30 25 0.57
31 2 0.05
ACGTcount: A:0.12, C:0.21, G:0.01, T:0.65
Consensus pattern (29 bp):
AATTTCTTTTTCTTTCTTTTTCAATCTCA
Found at i:56913796 original size:18 final size:18
Alignment explanation
Indices: 56913747--56913802 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56913737 CACTCTCAAA
* *
56913747 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
56913764 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
56913782 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
56913801 TT
1 TT
56913803 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:56913803 original size:12 final size:12
Alignment explanation
Indices: 56913772--56913796 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56913762 TTTTTCAATC
56913772 TCATTTTCTTTT
1 TCATTTTCTTTT
56913784 TCATTTTCTTTT
1 TCATTTTCTTTT
56913796 T
1 T
56913797 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:56913887 original size:6 final size:5
Alignment explanation
Indices: 56913865--56913920 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
56913855 CTCTTGCCTC
56913865 TCTTT TCTTT T-TATT TCATTT TCTTT TC--T TCTTT TGCTATT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-CT-TT TCTTT
56913911 TCTTT TCTTT
1 TCTTT TCTTT
56913921 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 28 0.64
6 8 0.18
7 4 0.09
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:56913891 original size:21 final size:20
Alignment explanation
Indices: 56913865--56913916 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
56913855 CTCTTGCCTC
*
56913865 TCTTTTCTTTTTATTTC-ATTT
1 TCTTTTCTTTTT-TTGCTA-TT
*
56913886 TCTTTTCTTCTTTTGCTATT
1 TCTTTTCTTTTTTTGCTATT
56913906 TCTTTTCTTTT
1 TCTTTTCTTTT
56913917 CTTTATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (20 bp):
TCTTTTCTTTTTTTGCTATT
Found at i:56913917 original size:25 final size:24
Alignment explanation
Indices: 56913869--56913919 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
56913859 TGCCTCTCTT
56913869 TTCTTTTTATTTCATTTTCTTTTC
1 TTCTTTTTATTTCATTTTCTTTTC
56913893 TTCTTTTGCTATTTC-TTTTCTTTTC
1 TTCTTTT--TATTTCATTTTCTTTTC
56913918 TT
1 TT
56913920 TATTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (24 bp):
TTCTTTTTATTTCATTTTCTTTTC
Found at i:56913925 original size:26 final size:26
Alignment explanation
Indices: 56913876--56913925 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
56913866 CTTTTCTTTT
*
56913876 TATTTCATTTTCTTTTCTTCTTTTGC
1 TATTTCATTTTCTTTTCTTATTTTGC
56913902 TATTTC-TTTTCTTTTCTTTATTTT
1 TATTTCATTTTCTTTTC-TTATTTT
56913926 CTCTTTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.74
Consensus pattern (26 bp):
TATTTCATTTTCTTTTCTTATTTTGC
Found at i:56920469 original size:14 final size:15
Alignment explanation
Indices: 56920420--56920469 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
56920410 GTATCTTGGG
*
56920420 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
56920435 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
56920450 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
56920464 TTTCTT
1 TTTCTT
56920470 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:56922911 original size:46 final size:46
Alignment explanation
Indices: 56922858--56923033 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
56922848 TGGTTGAGCA
* *
56922858 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAAGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGAAGCAAACG
* * ** *
56922904 TCCGAACTCGTTGAGTTGAGTCTGAGTTCA-TGAGATGTAA-CTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACT--TATGGAAGC-AAACG
* * *
56922951 TCCGAACTTGTTGAGTTGAGTCTGAGTTCACTCATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGAAGCAAACG
* ** *
56922997 -CCCAAGCTCGTTGAGTTGAGTCAAAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCTGAGTTCACTTATGG
56923034 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
45 5 0.05
46 62 0.60
47 36 0.35
48 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGAAGCAAACG
Found at i:56923025 original size:93 final size:93
Alignment explanation
Indices: 56922855--56923025 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
56922845 GGATGGTTGA
* * *
56922855 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAAGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGAAGCAAACGTCCCAACTCGTTGAGT
**
56922920 TGAGTCTGAGTTCATGAGATGTAACTAG
66 TGAGTCAAAGTTCATGAGATGTAACTAG
* * *
56922948 GCATCCGAACTTGTTGAGTTGAGTCTGAGTTCACTCATGGATGCAAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGAAGCAAACGTCCCAA-CTCGTTGAG
56923012 TTGAGTCAAAGTTC
65 TTGAGTCAAAGTTC
56923026 GCTTATGGGC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 4 0.06
93 65 0.94
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGAAGCAAACGTCCCAACTCGTTGAGT
TGAGTCAAAGTTCATGAGATGTAACTAG
Found at i:56925172 original size:14 final size:14
Alignment explanation
Indices: 56925150--56925197 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
56925140 ACCTAAACCG
* *
56925150 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
56925164 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
56925178 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
56925192 ACCATT
1 ACCATT
56925198 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Done.