Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold337
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: 762055
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:522891 original size:19 final size:18
Alignment explanation
Indices: 522866--522930 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
522856 ATTTCAACGA
522866 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
522884 TGTTGTATTGATAC---A-
1 T-TTGTATCGATACATAAG
522899 -TTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
522916 TTTTATATCGATACA
1 -TTTGTATCGATACA
522931 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
13 11 0.30
16 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:522908 original size:32 final size:32
Alignment explanation
Indices: 522867--522938 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
522857 TTTCAACGAT
* *
522867 TTGTATCGATACATAAGTGTTGTATTGATACA
1 TTGTATCGATACATAAGTGTTATATCGATACA
*
522899 TTGTATCGATACATAAGTTTTATATCGATACA
1 TTGTATCGATACATAAGTGTTATATCGATACA
*
522931 ATGTATCG
1 TTGTATCG
522939 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (32 bp):
TTGTATCGATACATAAGTGTTATATCGATACA
Found at i:523001 original size:13 final size:13
Alignment explanation
Indices: 522983--523007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522973 ATTACTCAAA
522983 TGTATCGATACAT
1 TGTATCGATACAT
522996 TGTATCGATACA
1 TGTATCGATACA
523008 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:530027 original size:42 final size:42
Alignment explanation
Indices: 529963--530048 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
529953 ACAATAACTA
*
529963 AGCTCTACCTTTTCAAAGGAATGCTCCTAAGTCTTATTAGGG
1 AGCTCTACCTTTTCAAAGGAATGCTCCTAAGTCCTATTAGGG
* *
530005 AGCTTTACCTTTTCAAAGGAATGTTCCTAAGTCCTATTAGGG
1 AGCTCTACCTTTTCAAAGGAATGCTCCTAAGTCCTATTAGGG
530047 AG
1 AG
530049 AGGCCATTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
AGCTCTACCTTTTCAAAGGAATGCTCCTAAGTCCTATTAGGG
Found at i:535139 original size:163 final size:161
Alignment explanation
Indices: 534921--535251 Score: 411
Period size: 163 Copynumber: 2.0 Consensus size: 161
534911 ATTGAAACTT
* *
534921 TTTTTTCGAAATACGAAATTTTCTACTCCGTAAATGTTTTCGAGGGGATTTTTCTTAGGT-TTTA
1 TTTTTTCGAAATACGAAATTTTCTACTCAGTAAA-GTTTTCGAGGGGATTTTTCTT-GGTCTTCA
* * * * *
534985 ATTTTTAAAATTCATCAAATATCATTA-TTGATTTTATATTAATTCAATTTTAAAAAATTAATTC
64 ATTTTCAAAATTCATCAAACATCATCATTTGA-TTCATATTAATT-AAGTTT-AAAAA--AATT-
**
535049 ATTTTCATGAATTTTTTATTTTTTCT-TTGAAATTCTCA
123 ATTTTCATGAATTTTGAATTTTTTCTGTTGAAATTCTCA
** *
535087 TTTTTTCGAAATACGGTATTTTTTACTCAGTAAA-TTTT-GAGGGGATTTTTCTTGGTCTTCAAT
1 TTTTTTCGAAATACGAAATTTTCTACTCAGTAAAGTTTTCGAGGGGATTTTTCTTGGTCTTCAAT
*
535150 TTTCAAAATTCATCAAACATCATCATTTGATTCATATTAATTTAGTTTAAAAAAATTATTTTCAT
66 TTTCAAAATTCATCAAACATCATCATTTGATTCATATTAATTAAGTTTAAAAAAATTATTTTCAT
* * *
535215 GAGTTTTGAATTTTTTTTGTTGAAATTCTCT
131 GAATTTTGAATTTTTTCTGTTGAAATTCTCA
535246 TTTTTT
1 TTTTTT
535252 TTTCGAGAAA
Statistics
Matches: 146, Mismatches: 16, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
158 22 0.15
159 21 0.14
161 5 0.03
162 7 0.05
163 53 0.36
164 8 0.05
166 30 0.21
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (161 bp):
TTTTTTCGAAATACGAAATTTTCTACTCAGTAAAGTTTTCGAGGGGATTTTTCTTGGTCTTCAAT
TTTCAAAATTCATCAAACATCATCATTTGATTCATATTAATTAAGTTTAAAAAAATTATTTTCAT
GAATTTTGAATTTTTTCTGTTGAAATTCTCA
Found at i:535862 original size:13 final size:13
Alignment explanation
Indices: 535837--535886 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
535827 ACTCACGGCA
535837 AGAA-GAAGAAAAG
1 AGAAGGAAG-AAAG
*
535850 AGAAGGGAGAAAG
1 AGAAGGAAGAAAG
535863 AGAAGGAAGAAA-
1 AGAAGGAAGAAAG
535875 AGAAGAGAAGAA
1 AGAAG-GAAGAA
535887 GAAATGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 5 0.15
13 25 0.76
14 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
AGAAGGAAGAAAG
Found at i:536069 original size:21 final size:21
Alignment explanation
Indices: 536043--536119 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
536033 AAGCAGCAAC
536043 AAGCAGCAACGGCAACGCCAT
1 AAGCAGCAACGGCAACGCCAT
* ** *
536064 AAGCAGCAAAACCAGCTGCAGCAAT
1 AAGCAGC--AA-CGGCAAC-GCCAT
*
536089 AAGAAGCAACGGCAACGCCAT
1 AAGCAGCAACGGCAACGCCAT
536110 AAGCAGCAAC
1 AAGCAGCAAC
536120 ACCAGCTGCA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
21 20 0.48
22 4 0.10
23 4 0.10
24 4 0.10
25 10 0.24
ACGTcount: A:0.43, C:0.30, G:0.22, T:0.05
Consensus pattern (21 bp):
AAGCAGCAACGGCAACGCCAT
Found at i:536087 original size:46 final size:46
Alignment explanation
Indices: 536035--536150 Score: 205
Period size: 46 Copynumber: 2.5 Consensus size: 46
536025 TGATGACAAA
* *
536035 GCAGCAACAAGCAGCAACGGCAACGCCATAAGCAGCAAAACCAGCT
1 GCAGCAATAAGAAGCAACGGCAACGCCATAAGCAGCAAAACCAGCT
*
536081 GCAGCAATAAGAAGCAACGGCAACGCCATAAGCAGCAACACCAGCT
1 GCAGCAATAAGAAGCAACGGCAACGCCATAAGCAGCAAAACCAGCT
536127 GCAGCAATAAGAAGCAACGGCAAC
1 GCAGCAATAAGAAGCAACGGCAAC
536151 AACAACAACA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.42, C:0.30, G:0.22, T:0.05
Consensus pattern (46 bp):
GCAGCAATAAGAAGCAACGGCAACGCCATAAGCAGCAAAACCAGCT
Found at i:536144 original size:25 final size:25
Alignment explanation
Indices: 536062--536144 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 25
536052 CGGCAACGCC
* *
536062 ATAAGCAGCAAAACCAGCTGCAGCA
1 ATAAGAAGCAACACCAGCTGCAGCA
** *
536087 ATAAGAAGCAACGGCAAC-GC--C-
1 ATAAGAAGCAACACCAGCTGCAGCA
*
536108 ATAAGCAGCAACACCAGCTGCAGCA
1 ATAAGAAGCAACACCAGCTGCAGCA
536133 ATAAGAAGCAAC
1 ATAAGAAGCAAC
536145 GGCAACAACA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
21 14 0.32
22 3 0.07
24 3 0.07
25 24 0.55
ACGTcount: A:0.45, C:0.28, G:0.20, T:0.07
Consensus pattern (25 bp):
ATAAGAAGCAACACCAGCTGCAGCA
Found at i:536708 original size:40 final size:40
Alignment explanation
Indices: 536621--536713 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
536611 GATGGTGGAG
* * *
536621 GAGCAACAGCAACTAATGGAGGAGGAAGCAGCAGCGTCAA
1 GAGCAACAGCAGCTAATGGAAGAGGAAACAGCAGCGTCAA
*
536661 GAACAACAGCAGCTAATGGAAGAGGAAACTA-CAGCAG-CAA
1 GAGCAACAGCAGCTAATGGAAGAGGAAAC-AGCAGC-GTCAA
*
536701 GAGCAACAACAGC
1 GAGCAACAGCAGC
536714 AGTAGGAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 43 0.96
41 2 0.04
ACGTcount: A:0.44, C:0.22, G:0.28, T:0.06
Consensus pattern (40 bp):
GAGCAACAGCAGCTAATGGAAGAGGAAACAGCAGCGTCAA
Found at i:536787 original size:22 final size:22
Alignment explanation
Indices: 536759--536822 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
536749 ACAGCATGAC
*
536759 GAAACAGCAAGTGAGGAAAGAA
1 GAAACAGCAAGTGAAGAAAGAA
**
536781 GAAACAGCAAGCAAAGAAAGAA
1 GAAACAGCAAGTGAAGAAAGAA
*
536803 GAAACAACAAGTGAAAGAAA
1 GAAACAGCAAGTG-AAGAAA
536823 AGAAAAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 29 0.83
23 6 0.17
ACGTcount: A:0.61, C:0.11, G:0.25, T:0.03
Consensus pattern (22 bp):
GAAACAGCAAGTGAAGAAAGAA
Found at i:547840 original size:20 final size:19
Alignment explanation
Indices: 547794--547871 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
547784 TTTTACCTTG
* *
547794 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATGA
* *
547814 ATATATCAATACATGTATGA
1 ATGTATCGATACAT-TATGA
*
547834 ATGTATCGATATATTCTAT-A
1 ATGTATCGATACA-T-TATGA
547854 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
547872 TCTTTTTACC
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 3 0.07
19 2 0.04
20 37 0.80
21 4 0.09
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:547866 original size:40 final size:39
Alignment explanation
Indices: 547794--547871 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
547784 TTTTACCTTG
*
547794 ATGTATCGATACATTTTTCAATATATCAATACATGTATGA
1 ATGTATCGATACATTTATCAATATATCAATACAT-TATGA
* * *
547834 ATGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TATCAATATATCAATACATTATG
547872 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.82
41 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTATCAATATATCAATACATTATGA
Found at i:557464 original size:21 final size:19
Alignment explanation
Indices: 557440--557487 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
557430 ATATGAATAC
557440 TTTTATTTGAAAATATAAAA
1 TTTTATTT-AAAATATAAAA
* * *
557460 TTTTTAATTAAATTATTAAA
1 -TTTTATTTAAAATATAAAA
557480 TTTTATTT
1 TTTTATTT
557488 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTATTTAAAATATAAAA
Found at i:558296 original size:19 final size:20
Alignment explanation
Indices: 558272--558313 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
558262 TATAAGTAAG
*
558272 AATTTTA-ATTTTATAAAAA
1 AATTTTATATTTGATAAAAA
*
558291 AATTTTATATTTGATAATAA
1 AATTTTATATTTGATAAAAA
558311 AAT
1 AAT
558314 AAAAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTTTATATTTGATAAAAA
Found at i:559770 original size:26 final size:26
Alignment explanation
Indices: 559733--559787 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
559723 ACTTATGTAG
*
559733 AATCCTAGATAAAGCTGAACTTTATC
1 AATCCTAAATAAAGCTGAACTTTATC
*
559759 AATCCTAAATAAAGTTGAACTTTATC
1 AATCCTAAATAAAGCTGAACTTTATC
559785 AAT
1 AAT
559788 TCTTCTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (26 bp):
AATCCTAAATAAAGCTGAACTTTATC
Found at i:563064 original size:20 final size:19
Alignment explanation
Indices: 563022--563091 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
563012 ACCCTAGAAA
* * *
563022 GTATCGATACATATCCAGAT
1 GTATCGATACATTTGCA-TT
*
563042 GTATCGATACATTATGCTTT
1 GTATCGATACATT-TGCATT
*
563062 GTATCGATACATTTTCATT
1 GTATCGATACATTTGCATT
563081 GTATCGATACA
1 GTATCGATACA
563092 CACTCAATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
19 15 0.35
20 26 0.60
21 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (19 bp):
GTATCGATACATTTGCATT
Found at i:563167 original size:20 final size:20
Alignment explanation
Indices: 563136--563194 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
563126 GCTACCCTAA
563136 GTGAAATGTATCGATACATG
1 GTGAAATGTATCGATACATG
*
563156 G-GACATTGTATCGATACATG
1 GTGA-AATGTATCGATACATG
*
563176 GTGAAAAGTATCGATACAT
1 GTGAAATGTATCGATACAT
563195 TGTGCCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGAAATGTATCGATACATG
Found at i:566570 original size:32 final size:33
Alignment explanation
Indices: 566515--566585 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 33
566505 TTTAACGATT
*
566515 TGTATCGATACATAAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
566548 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
566580 TGTATC
1 TGTATC
566586 AATATCGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 24 0.65
33 13 0.35
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:566661 original size:13 final size:13
Alignment explanation
Indices: 566643--566668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
566633 TACTCAAATA
566643 TATCGATACATTG
1 TATCGATACATTG
566656 TATCGATACATTG
1 TATCGATACATTG
566669 ATCTTTGTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:566716 original size:52 final size:52
Alignment explanation
Indices: 566676--566789 Score: 192
Period size: 52 Copynumber: 2.2 Consensus size: 52
566666 TTGATCTTTG
566676 TATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAATA
1 TATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAATA
* * * *
566728 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAATA
566780 TATCGATACA
1 TATCGATACA
566790 CTATGAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (52 bp):
TATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAATA
Found at i:566782 original size:20 final size:20
Alignment explanation
Indices: 566757--566809 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
566747 ATTTGCCCAG
566757 ATGTATCGATACACTATGAA
1 ATGTATCGATACACTATGAA
566777 ATGTATCGATACACTATGAA
1 ATGTATCGATACACTATGAA
566797 ATGTATCGATACA
1 ATGTATCGATACA
566810 TGCAAGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACACTATGAA
Found at i:575593 original size:20 final size:19
Alignment explanation
Indices: 575564--575615 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
575554 ACCCTAAAAA
*
575564 GTATCGATACATATCCTGAT
1 GTATCAATACATATCCT-AT
* *
575584 GTATCAATACATTATGCTTT
1 GTATCAATACA-TATCCTAT
575604 GTATCAATACAT
1 GTATCAATACAT
575616 TATATCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.79
21 5 0.18
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (19 bp):
GTATCAATACATATCCTAT
Found at i:575706 original size:20 final size:19
Alignment explanation
Indices: 575674--575712 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
575664 TACCCTAAGT
*
575674 GACATGTATCGATAGATGG
1 GACATGTAACGATAGATGG
*
575693 GACATTGTAACGATATATGG
1 GACA-TGTAACGATAGATGG
575713 TGAAAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (19 bp):
GACATGTAACGATAGATGG
Found at i:578823 original size:20 final size:20
Alignment explanation
Indices: 578798--578868 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
578788 TTTTACCCAG
*
578798 ATGTATCGATACTTTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
578818 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
578838 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
578858 ATGTATCGATA
1 ATGTATCGATA
578869 TATTCTATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:585852 original size:20 final size:20
Alignment explanation
Indices: 585829--585901 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
585819 ACAATTCAAA
585829 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
585849 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
*
585870 GTATCGATATATGTTGCAAT
1 GTATCGATACATGTTGCAAT
585890 GTATCGATACAT
1 GTATCGATACAT
585902 AAAAAAGTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:585873 original size:21 final size:21
Alignment explanation
Indices: 585847--585922 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
585837 ACATGTTGCA
585847 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
* ****
585868 ATGTATCGATATATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
585888 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
585909 TTGTATCGATACAT
1 ATGTATCGATACAT
585923 TTCTTGGCAG
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 28 0.67
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:585884 original size:41 final size:41
Alignment explanation
Indices: 585829--585922 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
585819 ACAATTCAAA
*
585829 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
* *
585870 GTATCGATATATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
585911 GTATCGATACAT
1 GTATCGATACAT
585923 TTCTTGGCAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:585979 original size:13 final size:13
Alignment explanation
Indices: 585961--585986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585951 TACAGCAAGT
585961 ATGTATCGATACA
1 ATGTATCGATACA
585974 ATGTATCGATACA
1 ATGTATCGATACA
585987 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:590068 original size:15 final size:15
Alignment explanation
Indices: 590048--590078 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
590038 TAAAAATGTC
*
590048 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
590063 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
590078 C
1 C
590079 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:592175 original size:13 final size:13
Alignment explanation
Indices: 592157--592195 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
592147 ACATTTTTCT
592157 TTGTATCGATACA
1 TTGTATCGATACA
592170 TTGTATCGATACA
1 TTGTATCGATACA
*
592183 CTGTATCGATACA
1 TTGTATCGATACA
592196 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:595488 original size:28 final size:28
Alignment explanation
Indices: 595407--595488 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
595397 TTTTGGAGAT
*
595407 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
595435 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
595463 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
595489 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:595631 original size:51 final size:51
Alignment explanation
Indices: 595471--595641 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
595461 GAAATAACGA
* * *
595471 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
595523 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
595576 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
595627 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
595642 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:595687 original size:27 final size:28
Alignment explanation
Indices: 595624--595699 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
595614 AAAATAAAGT
*
595624 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
595652 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
595679 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
595700 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:598182 original size:13 final size:13
Alignment explanation
Indices: 598164--598189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
598154 ACAAAGATCC
598164 ATGTATCGATACA
1 ATGTATCGATACA
598177 ATGTATCGATACA
1 ATGTATCGATACA
598190 CAGAAAAATG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:598185 original size:33 final size:33
Alignment explanation
Indices: 598143--598209 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
598133 AAAATTTCCA
***
598143 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
598176 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
598209 A
1 A
598210 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:598253 original size:19 final size:18
Alignment explanation
Indices: 598229--598296 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
598219 CAGTAGCTAA
598229 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
598248 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
598263 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
598280 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
598297 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:598269 original size:13 final size:13
Alignment explanation
Indices: 598251--598275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
598241 ACAATACTTA
598251 TGTATCGATACAT
1 TGTATCGATACAT
598264 TGTATCGATACA
1 TGTATCGATACA
598276 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:598273 original size:32 final size:32
Alignment explanation
Indices: 598232--598294 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
598222 TAGCTAATTA
*
598232 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
598264 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
598295 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:598376 original size:21 final size:21
Alignment explanation
Indices: 598352--598408 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
598342 CATTTGTAGG
598352 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
598373 ATGTATCGATACATTCGACAA
1 ATGTATCGATACATTCCACAA
598394 ATGTATCGATACATT
1 ATGTATCGATACATT
598409 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:598544 original size:13 final size:13
Alignment explanation
Indices: 598526--598553 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
598516 GTGTCTACAG
598526 CTACTAGCCAGGC
1 CTACTAGCCAGGC
598539 CTACTAGCCAGGC
1 CTACTAGCCAGGC
598552 CT
1 CT
598554 TAAATTGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.39, G:0.21, T:0.18
Consensus pattern (13 bp):
CTACTAGCCAGGC
Found at i:599087 original size:55 final size:54
Alignment explanation
Indices: 598998--599746 Score: 950
Period size: 55 Copynumber: 13.4 Consensus size: 54
598988 ATAAATTGTA
* * * * *
598998 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
599053 TCCTGCTCTTTGAGGACTGAAAGGTGCCATCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
599108 TCCTGCTCTTTGAGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTC--T---TTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
599168 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
599223 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
599278 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGGGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
599333 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
599388 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGATTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
599443 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * *
599504 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
599559 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
599614 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
599669 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
599724 TCCCGCTCTTTGAGGACTAAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
599747 GCGGAAGGAG
Statistics
Matches: 620, Mismatches: 47, Indels: 55
0.86 0.07 0.08
Matches are distributed among these distances:
54 23 0.04
55 482 0.78
56 16 0.03
57 1 0.00
58 1 0.00
60 47 0.08
61 47 0.08
62 3 0.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:599277 original size:29 final size:29
Alignment explanation
Indices: 599192--599277 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
599182 GACTAGAAAA
599192 TGCCACCAACTTGTGTGGGCTTTAAGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGG
** * *
599221 TGTCCTGC-TCTT-TG-GGGAC-TGAA-AGG
1 TG-CCACCAACTTGTGTGGG-CTTTAAGAGG
599247 TGCCACCAACTTGTGTGGGCTTTAAGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGG
599276 TG
1 TG
599278 TCCTGCTCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 9 0.21
28 9 0.21
29 10 0.24
30 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAGG
Found at i:599355 original size:27 final size:27
Alignment explanation
Indices: 599325--599468 Score: 73
Period size: 27 Copynumber: 5.3 Consensus size: 27
599315 GGTGGGCTTT
599325 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
599352 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
599380 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
599407 GAAA-ATG-CCACCAACTTGTGTGGGATTT
1 GAAAGGTGTCCTGC-TCTT-TG-AGGACTG
599435 GAAAGGTGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
599461 GAAAGGTG
1 GAAAGGTG
599469 CCACCAACTT
Statistics
Matches: 80, Mismatches: 27, Indels: 21
0.62 0.21 0.16
Matches are distributed among these distances:
25 6 0.08
26 18 0.22
27 20 0.25
28 20 0.25
29 10 0.12
30 6 0.08
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:600746 original size:12 final size:12
Alignment explanation
Indices: 600723--600780 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
600713 CTTTTCTCTC
*
600723 TTTTTCTTTGTT
1 TTTTTTTTTGTT
*
600735 TTGTTTTTTG-T
1 TTTTTTTTTGTT
** *
600746 TTTTTTCCTCTT
1 TTTTTTTTTGTT
600758 TTTTTTTTTGCTT
1 TTTTTTTTTG-TT
600771 TTTTTTTTTG
1 TTTTTTTTTG
600781 AAGAGAAGGC
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
11 7 0.20
12 16 0.46
13 12 0.34
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:600751 original size:15 final size:14
Alignment explanation
Indices: 600723--600779 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
600713 CTTTTCTCTC
*
600723 TTTTTCTTTGTTTTG
1 TTTTT-TTTTTTTTG
*
600738 TTTTTTGTTTTTTTCC
1 TTTTTT-TTTTTTT-G
*
600754 TCTTTTTTTTTTTG
1 TTTTTTTTTTTTTG
600768 CTTTTTTTTTTT
1 -TTTTTTTTTTT
600780 GAAGAGAAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.03
15 28 0.82
16 5 0.15
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:600778 original size:13 final size:13
Alignment explanation
Indices: 600755--600780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
600745 TTTTTTTCCT
600755 CTTTTTTTTTTTG
1 CTTTTTTTTTTTG
600768 CTTTTTTTTTTTG
1 CTTTTTTTTTTTG
600781 AAGAGAAGGC
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:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
CTTTTTTTTTTTG
Found at i:606798 original size:268 final size:268
Alignment explanation
Indices: 606321--607398 Score: 2129
Period size: 268 Copynumber: 4.0 Consensus size: 268
606311 TCTGCCAGAT
606321 CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
1 CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
606386 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
66 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
606451 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
131 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
*
606516 CCTCCCACAGAGCACCACTATATCTACAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
196 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
606581 ATGGTGAC
261 ATGGTGAC
606589 CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
1 CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
606654 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
66 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
606719 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
131 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
606784 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
196 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
606849 ATGGTGAC
261 ATGGTGAC
*
606857 CGTAATCATTGGTACTCTAAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
1 CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
606922 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
66 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
606987 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
131 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
607052 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
196 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
607117 ATGGTGAC
261 ATGGTGAC
*
607125 CATAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
1 CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
607190 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
66 ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
607255 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
131 GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
607320 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
196 CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
607385 ATGGTGAC
261 ATGGTGAC
607393 CGTAAT
1 CGTAAT
607399 GTGCCAATAA
Statistics
Matches: 805, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
268 805 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (268 bp):
CGTAATCATTGGTACTCTGAGTTCCTCGACATTCCTTACAATCTCACAGTCTTGTTCAGTGACGA
ACCTTTCTAACTCTGGATCTGCACGAGTTCGGGACGAACTAGCTCCCACATCGATTCTTGACTGT
GGCTTCCTTTCGACTTCGCCTTCCTTCTTACCTCTACCGGATTCCTTTTTTAGAGCTTCATCCAT
CCTCCCACAGAGCACCACTATATCTGCAAAACTCTTTGGAAATCTCCTTGCCACTTCATCATAAT
ATGGTGAC
Found at i:608363 original size:13 final size:13
Alignment explanation
Indices: 608345--608370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
608335 TACAGCAAGT
608345 ATGTATCGATACA
1 ATGTATCGATACA
608358 ATGTATCGATACA
1 ATGTATCGATACA
608371 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:609626 original size:18 final size:15
Alignment explanation
Indices: 609594--609636 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 15
609584 TATCAACATA
609594 AATATGATAAAAATTGCT
1 AATAT-ATAAAAATT--T
609612 AATATATAAATAATTT
1 AATATATAAA-AATTT
609628 AATATATAA
1 AATATATAA
609637 TTAAAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.42
17 5 0.21
18 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (15 bp):
AATATATAAAAATTT
Found at i:610719 original size:17 final size:17
Alignment explanation
Indices: 610691--610749 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
610681 TATATATTTA
610691 TATAGTATATAAATAATT
1 TATA-TATATAAATAATT
*
610709 T-TATATAATAATTAAATT
1 TATATAT-ATAAAT-AATT
*
610727 TA-ATATATAAATTATT
1 TATATATATAAATAATT
610743 TATATAT
1 TATATAT
610750 TTATATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 8 0.24
17 16 0.47
18 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATATAAATAATT
Found at i:610739 original size:18 final size:18
Alignment explanation
Indices: 610696--610740 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
610686 ATTTATATAG
*
610696 TATATAAA-T-AATTTTA
1 TATATAAATTAAATTTAA
610712 TATA-ATAATTAAATTTAA
1 TATATA-AATTAAATTTAA
610730 TATATAAATTA
1 TATATAAATTA
610741 TTTATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 6 0.25
17 1 0.04
18 15 0.62
19 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATAAATTAAATTTAA
Found at i:611048 original size:15 final size:14
Alignment explanation
Indices: 611030--611075 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
611020 TTTATTTATA
611030 ATATTTTAAATTATT
1 ATATTTTAAA-TATT
* *
611045 ATATGTTAAATAGT
1 ATATTTTAAATATT
611059 A-ATTTTAAATATT
1 ATATTTTAAATATT
611072 ATAT
1 ATAT
611076 AAAATTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 11 0.42
14 6 0.23
15 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
ATATTTTAAATATT
Found at i:611172 original size:13 final size:14
Alignment explanation
Indices: 611147--611178 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
611137 TTTATAATAT
611147 TATTATGATATAAA
1 TATTATGATATAAA
611161 TATTAT-ATATAAA
1 TATTATGATATAAA
611174 TATTA
1 TATTA
611179 CGAAACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TATTATGATATAAA
Found at i:611598 original size:2 final size:2
Alignment explanation
Indices: 611591--611616 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
611581 AAAATTTACA
611591 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
611617 GCATATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:613565 original size:79 final size:78
Alignment explanation
Indices: 613378--613760 Score: 297
Period size: 79 Copynumber: 4.9 Consensus size: 78
613368 AGATAACAAT
* * * * * * * * *
613378 GGGGCTGGAGTGTCCCCGATTATCG-AAATCAATGTTCTGGAAATAAAATCAGGGTTAGAGTATC
1 GGGGTTGGAGTAT-CCCGATTATGGAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
*
613442 CCCTCTAAAATAAC
65 CCCTCGAAAATAAC
* * * ** *
613456 AGGGTTGGAGCATCCCTGATTATAGG-AAATCGGTGTTTT-GAAAATAAAATTGGGGTTGAAGTA
1 GGGGTTGGAGTATCCC-GATTAT-GGAAAATCGATGTTTTAG-AAATAAAACCGGGGTTGGAGTA
*
613519 TCCCCTTGAAAATAAC
63 TCCCCTCGAAAATAAC
* * * ** ** *
613535 GGGGTTGGAGTATGCCCGATTGTGGAAAATCGAGGCTTTAGAAATAAGGCCAAGGTTGGAGTATT
1 GGGGTTGGAGTAT-CCCGATTATGGAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
* *
613600 CCCGCCAAAATAAC
65 CCCTCGAAAATAAC
* * * * * * *
613614 GGGGTTAGAGTATCCTCAATTGT-GAGAAATCAATATTTTAGAAATAAAGCTGGGGTTGGAGTAT
1 GGGGTTGGAGTATCC-CGATTATGGA-AAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
613678 CCCCTCGGAAATAAC
64 CCCCTCGAAAATAAC
* * * * * *
613693 GGGATTGGAGTGTCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAAACGGGGTTGGAGTATC
1 GGGGTTGGAGTAT-CCCGATTATGGAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
613758 CCC
65 CCC
613761 GAGATGAAAA
Statistics
Matches: 237, Mismatches: 58, Indels: 19
0.75 0.18 0.06
Matches are distributed among these distances:
77 3 0.01
78 22 0.09
79 205 0.86
80 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCGATTATGGAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCGAAAATAAC
Found at i:613750 original size:158 final size:157
Alignment explanation
Indices: 613383--613761 Score: 379
Period size: 158 Copynumber: 2.4 Consensus size: 157
613373 ACAATGGGGC
* * * * *
613383 TGGAGTGTCCCCGATTATCG-AAATCAATGTTCTGGAAATAAAATCAGGGTTAGAGTATCCCCTC
1 TGGAGTGTCCCCGATTAT-GAAAATCGATGTTTTGGAAATAAAAACAGGGTTGGAGTATCCCCGC
* * * ** * *
613447 TAAAATAACAGGGTTGGAGCATCCCTGATTATAGGAAATCGGTGTTTTGAAAATAAAATTGGGGT
65 CAAAATAACAGGGTTAGAGCATCCCTAATTATAGGAAATCAATATTTTGAAAATAAAACTGGGGT
* *
613512 TGAAGTATCCCCTTGAAAATAACGGGGT
130 TGAAGTATCCCCTCGAAAATAACGGGAT
* * * * * * *** * *
613540 TGGAGTATGCCCGATTGTGGAAAATCGAGGCTTTAGAAATAAGGCCAAGGTTGGAGTATTCCCGC
1 TGGAGTGTCCCCGATTAT-GAAAATCGATGTTTTGGAAATAAAAACAGGGTTGGAGTATCCCCGC
* * * *
613605 CAAAATAACGGGGTTAGAGTAT-CCTCAATTGT-GAGAAATCAATATTTT-AGAAATAAAGCTGG
65 CAAAATAACAGGGTTAGAGCATCCCT-AATTATAG-GAAATCAATATTTTGA-AAATAAAACTGG
* *
613667 GGTTGGAGTATCCCCTCGGAAATAACGGGAT
127 GGTTGAAGTATCCCCTCGAAAATAACGGGAT
* *
613698 TGGAGTGTCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAAACGGGGTTGGAGTATCCCCG
1 TGGAGTGTCCCCGATTATG-AAAATCGATGTTTTGGAAATAAAAACAGGGTTGGAGTATCCCCG
613762 AGATGAAAAA
Statistics
Matches: 173, Mismatches: 44, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
157 22 0.13
158 151 0.87
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (157 bp):
TGGAGTGTCCCCGATTATGAAAATCGATGTTTTGGAAATAAAAACAGGGTTGGAGTATCCCCGCC
AAAATAACAGGGTTAGAGCATCCCTAATTATAGGAAATCAATATTTTGAAAATAAAACTGGGGTT
GAAGTATCCCCTCGAAAATAACGGGAT
Found at i:613789 original size:50 final size:50
Alignment explanation
Indices: 613690--613808 Score: 132
Period size: 50 Copynumber: 2.4 Consensus size: 50
613680 CCTCGGAAAT
* * * ** * *
613690 AACGGGATTGGAGTGTCCCCGATTATGAAAAATTGATGTTTTGGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATGATGAAAAATCAATATTTTAGAAAT-AA
613741 AACGGGGTTGGAGTATCCCCGA-GATGAAAAATCAATATTTTAGAAATAA
1 AACGGGGTTGGAGTATCCCCGATGATGAAAAATCAATATTTTAGAAATAA
* *
613790 AGCTGGGGTTGAAGTATCC
1 AAC-GGGGTTGGAGTATCC
613809 TCTCGAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 4 0.07
50 34 0.59
51 20 0.34
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (50 bp):
AACGGGGTTGGAGTATCCCCGATGATGAAAAATCAATATTTTAGAAATAA
Found at i:613844 original size:208 final size:208
Alignment explanation
Indices: 613606--613981 Score: 461
Period size: 208 Copynumber: 1.8 Consensus size: 208
613596 TATTCCCGCC
* * *
613606 AAAATAACGGGGTTAGAGTATCCTCAATTGTGAGAAA-TCAATATTTTAGAAATAAAGCTGGGGT
1 AAAATAACGGGGTTAGAGTATCCTCAATTGTGAAAAATTCAA-ACTTTAGAAATAAAGCCGGGGT
* * ** * * * ** ** *
613670 TGGAGTATCCCCTCGGAAATAACGGGATTGGAGTGTCCCCGATTATGAAAAATTGATGTTTTGGA
65 TGGAATATCCCCGCCAAAATAACGGGATTAGAGTATCCCCAATTATGAAAAATCAACATTTTAGA
*
613735 AATAAAAACGGGGTTGGAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCTGGGGTT
130 AATAAAAACGGGGTTGGAGTATACCCGAGATGAAAAATCAATATTTTAGAAATAAAGCTGGGGTT
613800 GAAGTATCCTCTCG
195 GAAGTATCCTCTCG
* * * *
613814 AAAATAACGGGGTT-GAAGTAT-TTCCAATTGTGAAAAATTGAAGCTTTAGAAATAAGGCCGGGG
1 AAAATAACGGGGTTAG-AGTATCCT-CAATTGTGAAAAATTCAAACTTTAGAAATAAAGCCGGGG
* * * *
613877 TTGGAATATTCCCGCCAAAATAACGGGGTTAGAGTATCCCCAATTGTGAGAAATCAACATTTTAG
64 TTGGAATATCCCCGCCAAAATAACGGGATTAGAGTATCCCCAATTATGAAAAATCAACATTTTAG
** *
613942 AAATAAAGCCGGGGTTGGAGTATACCTGAGATGAAAAATC
129 AAATAAAAACGGGGTTGGAGTATACCCGAGATGAAAAATC
613982 TAGAAATTTA
Statistics
Matches: 138, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
207 2 0.01
208 133 0.96
209 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (208 bp):
AAAATAACGGGGTTAGAGTATCCTCAATTGTGAAAAATTCAAACTTTAGAAATAAAGCCGGGGTT
GGAATATCCCCGCCAAAATAACGGGATTAGAGTATCCCCAATTATGAAAAATCAACATTTTAGAA
ATAAAAACGGGGTTGGAGTATACCCGAGATGAAAAATCAATATTTTAGAAATAAAGCTGGGGTTG
AAGTATCCTCTCG
Found at i:613867 original size:79 final size:77
Alignment explanation
Indices: 613741--613964 Score: 224
Period size: 79 Copynumber: 2.9 Consensus size: 77
613731 TGGAAATAAA
* * * *
613741 AACGGGGTTGGAGTATCCCCGA--GATGAAAAATCAATATTTTAGAAATAAAGCTGGGGTTGAAG
1 AACGGGGTTAGAGTATCCCCAATTG-TGAAAAATCAACA-TTTAGAAATAAAGCCGGGGTTGAAG
* *
613804 TATCCTCTCGAAAAT
64 TATCC-CGCCAAAAT
** * *
613819 AACGGGGTT-GAAGTATTTCCAATTGTGAAAAATTGAAGC-TTTAGAAATAAGGCCGGGGTTGGA
1 AACGGGGTTAG-AGTATCCCCAATTGTGAAAAA-TCAA-CATTTAGAAATAAAGCCGGGGTT-GA
613882 A-TATTCCCGCCAAAAT
62 AGTA-TCCCGCCAAAAT
* *
613898 AACGGGGTTAGAGTATCCCCAATTGTGAGAAATCAACATTTTAGAAATAAAGCCGGGGTTGGAGT
1 AACGGGGTTAGAGTATCCCCAATTGTGAAAAATCAACA-TTTAGAAATAAAGCCGGGGTTGAAGT
613963 AT
65 AT
613965 ACCTGAGATG
Statistics
Matches: 120, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
77 2 0.02
78 23 0.19
79 84 0.70
80 11 0.09
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (77 bp):
AACGGGGTTAGAGTATCCCCAATTGTGAAAAATCAACATTTAGAAATAAAGCCGGGGTTGAAGTA
TCCCGCCAAAAT
Found at i:613876 original size:129 final size:129
Alignment explanation
Indices: 613640--613890 Score: 340
Period size: 129 Copynumber: 1.9 Consensus size: 129
613630 CAATTGTGAG
* * * *
613640 AAATCAATATTTTAGAAATAAAGCTGGGGTTGGAGTATCCCCTCGGAAATAACGGGATTGGAGTG
1 AAATCAATATTTTAGAAATAAAGCTGGGGTTGAAGTATCCCCTCGAAAATAACGGGATTGAAGTA
* * * * *
613705 TCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAAACGGGGTTGGAGTATCCCCGAGATGAA
66 TCCCCAATTATGAAAAATTGAAGCTTTAGAAATAAAAACGGGGTTGGAATATCCCCGAGATGAA
* *
613769 AAATCAATATTTTAGAAATAAAGCTGGGGTTGAAGTATCCTCTCGAAAATAACGGGGTTGAAGTA
1 AAATCAATATTTTAGAAATAAAGCTGGGGTTGAAGTATCCCCTCGAAAATAACGGGATTGAAGTA
** * *** *
613834 TTTCCAATTGTGAAAAATTGAAGCTTTAGAAATAAGGCCGGGGTTGGAATATTCCCG
66 TCCCCAATTATGAAAAATTGAAGCTTTAGAAATAAAAACGGGGTTGGAATATCCCCG
613891 CCAAAATAAC
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
129 104 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (129 bp):
AAATCAATATTTTAGAAATAAAGCTGGGGTTGAAGTATCCCCTCGAAAATAACGGGATTGAAGTA
TCCCCAATTATGAAAAATTGAAGCTTTAGAAATAAAAACGGGGTTGGAATATCCCCGAGATGAA
Found at i:616322 original size:29 final size:29
Alignment explanation
Indices: 616280--616388 Score: 103
Period size: 29 Copynumber: 3.6 Consensus size: 29
616270 GATACATTGA
616280 AAAATGTATCGATACATATGGGTAAACCC
1 AAAATGTATCGATACATATGGGTAAACCC
* * **
616309 AAAATGTATCGATACATTGTATCGATACAA-TG
1 AAAATGTATCGATACA---TATGGGTA-AACCC
*
616341 AACAATGTATCGATACATCTGGGTAAAAACCC
1 AA-AATGTATCGATACATATGGGT--AAACCC
616373 AAAATGTATCGATACA
1 AAAATGTATCGATACA
616389 ATGAACAATG
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
29 16 0.25
30 4 0.06
31 16 0.25
32 11 0.17
33 16 0.25
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (29 bp):
AAAATGTATCGATACATATGGGTAAACCC
Found at i:616331 original size:13 final size:13
Alignment explanation
Indices: 616313--616337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
616303 AAACCCAAAA
616313 TGTATCGATACAT
1 TGTATCGATACAT
616326 TGTATCGATACA
1 TGTATCGATACA
616338 ATGAACAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:616348 original size:62 final size:63
Alignment explanation
Indices: 616264--616388 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 63
616254 AATGCCTGAA
*
616264 TGTATCGATACATTGAAAAATGTATCGATACATATGGGT-AAACCCAAAATGTATCGATACAT
1 TGTATCGATACAATGAAAAATGTATCGATACATATGGGTAAAACCCAAAATGTATCGATACAT
* *
616326 TGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAAACCCAAAATGTATCGATACA
1 TGTATCGATACAATGAAAAATGTATCGATACATATGGGT-AAAACCCAAAATGTATCGATACA
616389 ATGAACAATG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 36 0.62
64 22 0.38
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (63 bp):
TGTATCGATACAATGAAAAATGTATCGATACATATGGGTAAAACCCAAAATGTATCGATACAT
Found at i:617120 original size:83 final size:83
Alignment explanation
Indices: 617017--617177 Score: 184
Period size: 83 Copynumber: 1.9 Consensus size: 83
617007 TTCGAGGATT
* *
617017 AAGGAAAAGGAGAATGAAATGGGTTC-TGCTCCTTGGGGACTAAGGAAAAAAG-GAAATAAAATG
1 AAGGAAAAGGAGAATGAAATGGG-TCATGCTCCTTGAGGACAAAGGAAAAAAGAG-AATAAAATG
*
617080 CATCTTGCCCTTTGAAGACA
64 CATCATGCCCTTTGAAGACA
* * ** *
617100 AAGGAAACAGGAG-ATTAAATGTGTCATGCTTTTTGAGGACAAAGGAAAAAAGAGAATAAAGTGC
1 AAGGAAA-AGGAGAATGAAATGGGTCATGCTCCTTGAGGACAAAGGAAAAAAGAGAATAAAATGC
* *
617164 GTCATGCTCTTTGA
65 ATCATGCCCTTTGA
617178 GAACTAGAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
82 2 0.03
83 57 0.88
84 6 0.09
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (83 bp):
AAGGAAAAGGAGAATGAAATGGGTCATGCTCCTTGAGGACAAAGGAAAAAAGAGAATAAAATGCA
TCATGCCCTTTGAAGACA
Found at i:617135 original size:41 final size:42
Alignment explanation
Indices: 617058--617177 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 42
617048 CTTGGGGACT
* * * *
617058 AAGGAAAAAAG-GAAATAAAATGCATCTTGCCCTTTGAAGACA
1 AAGGAAAAAAGAG-AATAAAGTGCGTCATGCTCTTTGAAGACA
* * * * * *
617100 AAGGAAACAGGAGATTAAA-TGTGTCATGCTTTTTGAGGACA
1 AAGGAAAAAAGAGAATAAAGTGCGTCATGCTCTTTGAAGACA
617141 AAGGAAAAAAGAGAATAAAGTGCGTCATGCTCTTTGA
1 AAGGAAAAAAGAGAATAAAGTGCGTCATGCTCTTTGA
617178 GAACTAGAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
41 32 0.52
42 29 0.47
43 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (42 bp):
AAGGAAAAAAGAGAATAAAGTGCGTCATGCTCTTTGAAGACA
Found at i:617178 original size:42 final size:41
Alignment explanation
Indices: 617017--617178 Score: 132
Period size: 42 Copynumber: 3.9 Consensus size: 41
617007 TTCGAGGATT
* * * * *
617017 AAGG-AAAAGGAGAATGAAATGGGTTC-TGCTCCTTGGGGACT
1 AAGGAAAAAAGAGAAT-AAATGCG-TCATGCTCTTTGAGGACA
* * * *
617058 AAGGAAAAAAG-GAAATAAAATGCATCTTGCCCTTTGAAGACA
1 AAGGAAAAAAGAG-AAT-AAATGCGTCATGCTCTTTGAGGACA
* * * * *
617100 AAGGAAACAGGAGATTAAATGTGTCATGCTTTTTGAGGACA
1 AAGGAAAAAAGAGAATAAATGCGTCATGCTCTTTGAGGACA
617141 AAGGAAAAAAGAGAATAAAGTGCGTCATGCTCTTTGAG
1 AAGGAAAAAAGAGAATAAA-TGCGTCATGCTCTTTGAG
617179 AACTAGAAGG
Statistics
Matches: 93, Mismatches: 23, Indels: 9
0.74 0.18 0.07
Matches are distributed among these distances:
41 42 0.45
42 50 0.54
43 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.22
Consensus pattern (41 bp):
AAGGAAAAAAGAGAATAAATGCGTCATGCTCTTTGAGGACA
Found at i:617441 original size:51 final size:51
Alignment explanation
Indices: 617301--617766 Score: 182
Period size: 51 Copynumber: 8.9 Consensus size: 51
617291 AATATCCTGG
* * *
617301 TTTTATGTCCAAAACATCAATTTTTCTTAATCGGGGATACTCTAACTCCGA
1 TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGA
* * * ** *
617352 TTTTATTTCTAAAGCATCGATTTACCATAATCGGGGATACTCCAACTCTGA
1 TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGA
* * * * *
617403 TTTTATTTCCAAAACACCAATTTTTCACAATTGAGGATACTCCAACCCCG-
1 TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGA
* * *
617453 --TTATTTCATCGAGGATAC-TCCAACCCCATTATTTC-CAA--GGGGATACTCCAAC-CCTA
1 TTTTATTTC--C-A--AAACAT-C-A----ATT-TTTCATAATCGGGGATACTCCAACTCCGA
* * * * * * *
617509 GCTTTATATCCAAAATATTGATTTTTTTCATAATCGGGGGTACTCCAACTCTGTTA
1 -TTTTATTTCCAAAACA-TCA-ATTTTTCATAATCGGGGATACTCCAACTCCG--A
* ***** * ** ** *
617565 TTTCATCGGGGATAC-TCCAATCCCGTT-ATTTTCGAGGGGATACTCCAACTCCAA
1 TTTTATTTCCAAAACAT-CAAT--TTTTCATAATC--GGGGATACTCCAACTCCGA
* * *
617619 TTTTATTTCTAAAATA-CTAATTTTTCAAAATCGGGGATACTCCAACTCCGA
1 TTTTATTTCCAAAACATC-AATTTTTCATAATCGGGGATACTCCAACTCCGA
* * * * * *
617670 TTTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCC-ATTCCCGG
1 TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACT-CCGA
** * * *
617721 CCTTATTTCTAAAGCATCGATTTTTCATAATCGGGGATACTCCAAC
1 TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
617767 CCTGTTATTT
Statistics
Matches: 297, Mismatches: 83, Indels: 69
0.66 0.18 0.15
Matches are distributed among these distances:
48 7 0.02
50 7 0.02
51 177 0.60
52 4 0.01
53 23 0.08
54 21 0.07
55 10 0.03
56 31 0.10
57 1 0.00
58 6 0.02
59 10 0.03
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGA
Found at i:617467 original size:28 final size:28
Alignment explanation
Indices: 617435--617506 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
617425 TTTCACAATT
* *
617435 GAGGATACTCCAACCCCGTTATTT-CATC
1 GAGGATACTCCAACCCCATTATTTCCA-A
617463 GAGGATACTCCAACCCCATTATTTCCAA
1 GAGGATACTCCAACCCCATTATTTCCAA
*
617491 GGGGATACTCCAACCC
1 GAGGATACTCCAACCC
617507 TAGCTTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (28 bp):
GAGGATACTCCAACCCCATTATTTCCAA
Found at i:617578 original size:109 final size:107
Alignment explanation
Indices: 617384--617668 Score: 320
Period size: 109 Copynumber: 2.6 Consensus size: 107
617374 TACCATAATC
** * * * * * * *
617384 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAATTGAGGATACTCCAAC
1 GGGGATACTCCAACTCCAACTTTATATCCAAAATACTAATTTTTCAAAATCGGGGATACTCCAAC
*
617449 CCCGTTATTTCATCGAGGATACTCCAACCCCATTATTTCCAA
66 TCCGTTATTTCATCGAGGATACTCCAACCCCATTATTTCCAA
* * * * *
617491 GGGGATACTCCAAC-CCTAGCTTTATATCCAAAATATTGATTTTTTTCATAATCGGGGGTACTCC
1 GGGGATACTCCAACTCC-AACTTTATATCCAAAATACT-A-ATTTTTCAAAATCGGGGATACTCC
* * * * * *
617555 AACTCTGTTATTTCATCGGGGATACTCCAATCCCGTTATTTTCGA
63 AACTCCGTTATTTCATCGAGGATACTCCAACCCCATTATTTCCAA
* * *
617600 GGGGATACTCCAACTCCAATTTTATTTCTAAAATACTAATTTTTCAAAATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCAACTTTATATCCAAAATACTAATTTTTCAAAATCGGGGATACTCCAAC
617665 TCCG
66 TCCG
617669 ATTTTATTTT
Statistics
Matches: 145, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
106 1 0.01
107 54 0.37
108 2 0.01
109 86 0.59
110 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
GGGGATACTCCAACTCCAACTTTATATCCAAAATACTAATTTTTCAAAATCGGGGATACTCCAAC
TCCGTTATTTCATCGAGGATACTCCAACCCCATTATTTCCAA
Found at i:617580 original size:28 final size:27
Alignment explanation
Indices: 617541--617616 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
617531 TTTTTTCATA
* *
617541 ATCGGGGGTACTCCAACTCTGTTATTT
1 ATCGGGGATACTCCAACTCCGTTATTT
617568 CATCGGGGATACTCCAA-TCCCGTTATTT
1 -ATCGGGGATACTCCAACT-CCGTTATTT
617596 -TCGAGGGGATACTCCAACTCC
1 ATC--GGGGATACTCCAACTCC
617617 AATTTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 38 0.90
29 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (27 bp):
ATCGGGGATACTCCAACTCCGTTATTT
Found at i:628589 original size:20 final size:20
Alignment explanation
Indices: 628564--628615 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
628554 AAATTCCCAG
628564 ATGTATCGATACAAAG-ATCA
1 ATGTATCGATACAAAGAAT-A
**
628584 ATGTATCGATACATTGAATA
1 ATGTATCGATACAAAGAATA
628604 ATGTATCGATAC
1 ATGTATCGATAC
628616 GTTTTCTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:633746 original size:61 final size:61
Alignment explanation
Indices: 633542--633976 Score: 523
Period size: 60 Copynumber: 7.3 Consensus size: 61
633532 CACTTTTCAA
* ** * * *
633542 TCCTCAAAGAGCAGGATGCCTTTTCCATTT-AAAGCCCACACAAGTTGGTGGTACTTTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTCGCC-TTTCAAAGCCCACACAAGTTGGTGGCA-TCTTCCAG
* ** * * *
633604 TCTTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAG
* *
633665 TCCTCAAAGAGCAGGA------CGCCTTTCAAAGCCCACACAAGTTTGTGGCATTTTCCAG
1 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAG
* * *
633720 TCCTCAAAGAGTAGGACACCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTCCAG
1 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAG
* * * * *
633780 TCCTGAAAGAGCAGGATGCCTTCGCCTTTCAAAGCCCACACATGTTGGTGGTACCTT-CAG
1 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAG
* * *
633840 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGCTAGTGGCACCTT-CAG
1 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAG
* *
633900 TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAG
1 TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCC-AG
633961 TCCTCAAAGAGCAGGA
1 TCCTCAAAGAGCAGGA
633977 TGCTCTCTCT
Statistics
Matches: 333, Mismatches: 30, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
55 49 0.15
59 3 0.01
60 159 0.48
61 76 0.23
62 46 0.14
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (61 bp):
TCCTCAAAGAGCAGGACGCCTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCATCTTCCAG
Found at i:634093 original size:62 final size:61
Alignment explanation
Indices: 634020--634318 Score: 301
Period size: 62 Copynumber: 5.0 Consensus size: 61
634010 GTAGGACACA
*
634020 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATACCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTC
* * * *
634081 ATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCTTTAAAAAGTAGGATAG-CTTTTCC
1 -TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGAT-GCCTTTT-C
* * * * * *
634144 TTTTAAAGCCCACACAAGTTGGTGGCA-TTTTTTAGTCCTCATAGAGAAAGACGCC-TTGC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTC
* * * * * *
634203 ----AAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAAAGCAGGACGTCTCTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTC
* * * * *
634259 TTTTCAAAGCCTACACGAGTTGGTGGCACTGTT-TAGTCCTCGAAGAGCAAGATGCCTTTT
1 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
634319 TCTTCTCTCC
Statistics
Matches: 192, Mismatches: 34, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
55 42 0.22
56 2 0.01
59 1 0.01
60 3 0.02
61 60 0.31
62 83 0.43
63 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (61 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTC
Found at i:634294 original size:116 final size:117
Alignment explanation
Indices: 634020--634316 Score: 296
Period size: 116 Copynumber: 2.5 Consensus size: 117
634010 GTAGGACACA
* * * * ** *
634020 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATACCTTTTCATTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTGTT-TAGTCCTCGAAGAGAAAGACGCC-TTGC----
* * * * * *
634085 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCTTTAAAAAGTAGGATAGCTTTTCC
60 -AAAGCCCACACAAGTTGGTGGCACTCTTCCAGTCCTCAAAAAGCAGGATAGCTCTTCC
* *
634144 TTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTC-ATAGAGAAAGACGCCTTGCAAAGC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTGTTTAGTCCTCGA-AGAGAAAGACGCCTTGCAAAGC
*
634208 CCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAAAGCAGGA-CGTCTCTT-C
65 CCACACAAGTTGGTGGCACTCTTCCAGTCCTCAAAAAGCAGGATAG-CTCTTCC
* * * *
634259 TTTTCAAAGCCTACACGAGTTGGTGGCACTGTTTAGTCCTCGAAGAGCAAGATGCCTT
1 TTTT-AAAGCCCACACAAGTTGGTGGCACTGTTTAGTCCTCGAAGAGAAAGACGCCTT
634317 TTTCTTCTCT
Statistics
Matches: 150, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
115 6 0.04
116 67 0.45
117 25 0.17
122 4 0.03
123 17 0.11
124 31 0.21
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (117 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTGTTTAGTCCTCGAAGAGAAAGACGCCTTGCAAAGCC
CACACAAGTTGGTGGCACTCTTCCAGTCCTCAAAAAGCAGGATAGCTCTTCC
Found at i:634431 original size:41 final size:40
Alignment explanation
Indices: 634329--634455 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 40
634319 TCTTCTCTCC
* * *
634329 TTTGTCCTCAAAGAGCAGGACACACTTCATTCCCTT-ATTTTCCCT
1 TTTGTCCTCAAAGAGCAGGACGCATTTCATT---TTCCTTTT---T
634374 TTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTCTTTT
1 TTTGTCCTCAAAGAGCAGGACGCA-TTTCATTTTCCT-TTTT
*
634415 TTTGTCCTCAAGGAGCAGGACGCATTTCATTTTCCTTTTT
1 TTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTTT
634455 T
1 T
634456 CCTTTGTCTT
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
40 8 0.11
41 32 0.43
42 2 0.03
43 1 0.01
44 3 0.04
45 26 0.35
46 2 0.03
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (40 bp):
TTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTTT
Found at i:634528 original size:41 final size:41
Alignment explanation
Indices: 634485--634608 Score: 196
Period size: 41 Copynumber: 3.0 Consensus size: 41
634475 GGACATACTC
634485 TTTTTCACTTTATCCTCAAGAAGCAAGACACTTTTCTTTTCT
1 TTTTTC-CTTTATCCTCAAGAAGCAAGACACTTTTCTTTTCT
*
634527 TTTTTCCTTTATCCTCAAGAAGCAGGACACTTTTCTTTTCT
1 TTTTTCCTTTATCCTCAAGAAGCAAGACACTTTTCTTTTCT
*
634568 TTTTTCCTTTATCCTCAAGGAGCAAGAC-CTATTTCGTTTTC
1 TTTTTCCTTTATCCTCAAGAAGCAAGACACT-TTTC-TTTTC
634609 CTTTGTCTTC
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
40 2 0.03
41 64 0.83
42 11 0.14
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (41 bp):
TTTTTCCTTTATCCTCAAGAAGCAAGACACTTTTCTTTTCT
Found at i:634566 original size:76 final size:78
Alignment explanation
Indices: 634419--634612 Score: 191
Period size: 82 Copynumber: 2.4 Consensus size: 78
634409 TCTTTTTTTG
* * * * *
634419 TCCTCAAGGAGCAGGACGCATTTCATTTTCCTTTTTTCCTTTGTCTTCGAAAAGCAGGACATACT
1 TCCTCAAGAAGCAAGACACATTTCATTTTCCTTTTTTCCTTTATCCTCGAAAAGCAGGACATACT
634484 CTTTTTCACTTTA
66 CTTTTTCACTTTA
*
634497 TCCTCAAGAAGCAAGACACTTTTC-TTTT-CTTTTTTCCTTTATCCTC-AAGAAGCAGGACACTT
1 TCCTCAAGAAGCAAGACACATTTCATTTTCCTTTTTTCCTTTATCCTCGAA-AAGCAGGACA---
*
634559 TTCTTTTCTTTTTTC-CTTTA
62 TAC---TC-TTTTTCACTTTA
* *
634579 TCCTCAAGGAGCAAGAC-CTATTTCGTTTTCCTTT
1 TCCTCAAGAAGCAAGACAC-ATTTCATTTTCCTTT
634613 GTCTTCAAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 16
0.79 0.07 0.13
Matches are distributed among these distances:
75 2 0.02
76 26 0.27
77 4 0.04
78 20 0.21
79 2 0.02
81 1 0.01
82 27 0.28
83 10 0.10
84 4 0.04
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (78 bp):
TCCTCAAGAAGCAAGACACATTTCATTTTCCTTTTTTCCTTTATCCTCGAAAAGCAGGACATACT
CTTTTTCACTTTA
Found at i:638475 original size:20 final size:19
Alignment explanation
Indices: 638442--638480 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
638432 TACCTTAAGT
638442 GACATGTATCGATAAATGG
1 GACATGTATCGATAAATGG
* *
638461 GACATTGTATTGATATATGG
1 GACA-TGTATCGATAAATGG
638481 TGAAAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (19 bp):
GACATGTATCGATAAATGG
Found at i:642403 original size:51 final size:51
Alignment explanation
Indices: 642348--642480 Score: 212
Period size: 51 Copynumber: 2.6 Consensus size: 51
642338 AATTTTTCTT
* *
642348 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGC
1 AATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATTTACCAC
* *
642399 AATCGAGGATACTCCAACTCTGATTTTATTTCTGAAGCATCGATTTACCAC
1 AATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATTTACCAC
* *
642450 AATCAGGGATACTCCAACTTTGATTTTATTT
1 AATCGGGGATACTCCAACTCTGATTTTATTT
642481 TCAAAACACC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATTTACCAC
Found at i:642502 original size:51 final size:50
Alignment explanation
Indices: 642330--642518 Score: 182
Period size: 51 Copynumber: 3.7 Consensus size: 50
642320 TTTCATGTCC
** ** *
642330 AAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCT
1 AAAACATCAATTTACCACAATC-GGGATACTCCAACTCTGATTTTATTTCT
* * *
642381 AAAGCATCGATTTACCGCAATCGAGGATACTCCAACTCTGATTTTATTTCT
1 AAAACATCAATTTACCACAATCG-GGATACTCCAACTCTGATTTTATTTCT
* * * *
642432 GAAGCATCGATTTACCACAATCAGGGATACTCCAACTTTGATTTTATTT-T
1 AAAACATCAATTTACCACAATC-GGGATACTCCAACTCTGATTTTATTTCT
* ** *
642482 CAAAACACCAATTTTTCACAATTGGAGATACTCCAAC
1 -AAAACATCAATTTACCACAATCGG-GATACTCCAAC
642519 CCCGTTATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
50 4 0.03
51 112 0.96
52 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.34
Consensus pattern (50 bp):
AAAACATCAATTTACCACAATCGGGATACTCCAACTCTGATTTTATTTCT
Found at i:642623 original size:28 final size:28
Alignment explanation
Indices: 642583--642636 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
642573 TTTTTTCTTA
*
642583 ATCGGGGGTACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCTAACCCCGTTATTTC
* *
642611 ATCGGGGATACTCTAATCCTGTTATT
1 ATCGGGGATACTCTAACCCCGTTATT
642637 CCTGAGGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (28 bp):
ATCGGGGATACTCTAACCCCGTTATTTC
Found at i:642769 original size:51 final size:50
Alignment explanation
Indices: 642642--642810 Score: 162
Period size: 51 Copynumber: 3.3 Consensus size: 50
642632 TTATTCCTGA
** * *
642642 GGGGATACTCCAAGCCC-GATTTTATTTCTAAAATACCAATTTTTCATAATT
1 GGGGATACTCCAA-CCCTGACCTTATTTCTAAAATACCAA-TTTTCACAATC
* ** *
642693 GGGGATACTCCAACTCTGATTTTATTT-TCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCCTGACCTTATTTCT-AAAATACCAATTT-TCACAATC
* * * *
642744 GGGGATACTCCAACCCTGGCCTTATTTCTAAAGTATCGATTTTCAACAATC
1 GGGGATACTCCAACCCTGACCTTATTTCTAAAATACCAATTTTC-ACAATC
*
642795 GGGGATACTCGAACCC
1 GGGGATACTCCAACCC
642811 CGTTATTTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
50 8 0.08
51 91 0.91
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACCCTGACCTTATTTCTAAAATACCAATTTTCACAATC
Found at i:643920 original size:42 final size:41
Alignment explanation
Indices: 643803--643929 Score: 130
Period size: 40 Copynumber: 3.0 Consensus size: 41
643793 ACGTAGCGAT
*
643803 AAAATGCGTCCTGCTCCTTGAGGACAAAGGAAAAAA-GAAA
1 AAAATGCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
* * * * *
643843 AAAAAGCATCTTGCTCTTCGAGGTCAAAAGGGGAAAAAAGGAAA
1 AAAATGCGTCCTGCTCTTTGAGGAC-AAA--GGAAAAAAGGAAA
* * *
643887 TGAAATGTGTCCTACTCTTTGAGGACAAAGGAAAAAAGGAAA
1 -AAAATGCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
643929 A
1 A
643930 GACGTCCTGC
Statistics
Matches: 67, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
40 19 0.28
41 3 0.04
42 13 0.19
43 8 0.12
44 7 0.10
45 17 0.25
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.17
Consensus pattern (41 bp):
AAAATGCGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
Found at i:644034 original size:61 final size:62
Alignment explanation
Indices: 643956--644321 Score: 432
Period size: 61 Copynumber: 6.1 Consensus size: 62
643946 GGGCAAATGA
* * *
643956 GAAAAGGAAAAGACGTCCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
644018 GAAAA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCCTT
1 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** * *
644079 GAAAAGAAAAAGATGTCCTACTCTTTGAGGACTAGAAAAGTGCCAACAACTTGTGTGGGCTTT
1 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
644142 -AAAAGGAAAAGGTGTCCTACTCTTTGAGGACT-AAAGGTGCCACCAGCTTGTGTGGGCTTT
1 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * **
644202 -AAAAGGAAAAGGCGTCTTGCTCTTTGAGGATTGGAAAGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
644263 -------AAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTGGTGTGGGCTTT
1 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTT
644318 GAAA
1 GAAA
644322 GGCGTCATGC
Statistics
Matches: 267, Mismatches: 29, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
55 45 0.17
56 4 0.01
60 53 0.20
61 82 0.31
62 59 0.22
63 24 0.09
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (62 bp):
GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:644197 original size:184 final size:177
Alignment explanation
Indices: 643957--644323 Score: 470
Period size: 184 Copynumber: 2.0 Consensus size: 177
643947 GGCAAATGAG
*
643957 AAAAGGAAAAGACGTCCTGCTCTTTAAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
1 AAAAGGAAAAGACGTCCTACTCTTTAAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT-AAA
644022 A-GAAAAGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCCTTGAAAAG
65 AGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAA-GTGCCACCAACTCGTGTGGG-CTTGAAAAG
*
644085 AAAAAGATGTCCTACTCTTTGAGGACTAGAAAAGTGCCAACAACTTGTGTGGGCTTT
128 -----G-TGTCCTACTCTTTGAGGACTAGAAAA-TGCCAACAACTGGTGTGGGCTTT
** * * * *
644142 AAAAGGAAAAGGTGTCCTACTCTTTGAGGACT-AAAGGTGCCACCAGCTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGACGTCCTACTCTTTAAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTAAAA
* * * * *
644206 GGAAAAGGCGTCTTGCTCTTTGAGGATTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
66 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTGAAAAGGTG
* * *
644271 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTT
131 TCCTACTCTTTGAGGACTAGAAAATGCCAACAACTGGTGTGGGCTTT
*
644318 GAAAGG
1 AAAAGG
644324 CGTCATGCAC
Statistics
Matches: 163, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
176 26 0.16
177 24 0.15
178 1 0.01
183 12 0.07
184 69 0.42
185 31 0.19
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (177 bp):
AAAAGGAAAAGACGTCCTACTCTTTAAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTAAAA
GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTGAAAAGGTG
TCCTACTCTTTGAGGACTAGAAAATGCCAACAACTGGTGTGGGCTTT
Found at i:644431 original size:61 final size:61
Alignment explanation
Indices: 644352--644540 Score: 290
Period size: 61 Copynumber: 3.1 Consensus size: 61
644342 CTAAAGGGTG
* *
644352 AAAGGAG-AGAGCGTCCTGCTCTTTGAGGGCTGGAAAGTGCCACCAACTTGTGTGAGCTTTA
1 AAAGGAGAAG-GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA
* *
644413 AAAGGAGAAGGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA
* * *
644474 AAAGGAAAAGGCGTCCTTCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTA
644536 AAAGG
1 AAAGG
644541 CGTCTTGCTT
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
61 82 0.70
62 35 0.30
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (61 bp):
AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA
Found at i:644609 original size:217 final size:210
Alignment explanation
Indices: 644155--644668 Score: 744
Period size: 217 Copynumber: 2.4 Consensus size: 210
644145 AGGAAAAGGT
* * *
644155 GTCCTACTCTTTGAGGACT--AAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
1 GTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTC
* * *
644218 TTGCTCTTTGAGGATTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTG
65 CTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTG
* *
644283 AGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCGTCATGCACTTTGAAGACTAAAG
130 AGGACTAGAAAATGCCACCAACTGGTGTGGGCTTTAAAAGGCGTCATGCACTTTGAAGACTAAAG
644348 GGTGAAAGGAGAGAGC
195 GGTGAAAGGAGAGAGC
* * *
644364 GTCCTGCTCTTTGAGGGCTGGAAAGTGCCACCAACTTGTGTGAGCTTTAAAAGGAGAAGGCATCC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
* *
644429 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTTCT
66 TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT------AAAAGGCGTCCTGCT
* * ** *
644494 CTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCTTGCTTTTTGAGGA
125 CTTTGAGGACTAGAAAA-TGCCACCAACTGGTGTGGGCTTTAAAAGGCGTCATGCACTTTGAAGA
644559 CTAAAGGGTGAAAGGAGAGAGC
189 CTAAAGGGTGAAAGGAGAGAGC
* *
644581 GTCCTGCTGTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
* *
644646 TGCTCTTTAAGGACTGAAAAGTG
66 TGCTCTTTGAGGACTGGAAAGTG
644669 AAAGGAGAAA
Statistics
Matches: 270, Mismatches: 26, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
209 17 0.06
210 78 0.29
211 3 0.01
216 29 0.11
217 143 0.53
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (210 bp):
GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGA
GGACTAGAAAATGCCACCAACTGGTGTGGGCTTTAAAAGGCGTCATGCACTTTGAAGACTAAAGG
GTGAAAGGAGAGAGC
Found at i:645588 original size:1 final size:1
Alignment explanation
Indices: 645582--645644 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
645572 CTTTTCTCTC
* * * * * * * *
645582 TTTTTTTGTTTTTTTGTTTTGTTTTTGTTTTATTTTTTTATTTTTTTATTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
645645 AAAGAAGGTG
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (1 bp):
T
Found at i:645595 original size:8 final size:8
Alignment explanation
Indices: 645582--645643 Score: 65
Period size: 8 Copynumber: 7.9 Consensus size: 8
645572 CTTTTCTCTC
645582 TTTTTTTG
1 TTTTTTTG
645590 TTTTTTTG
1 TTTTTTTG
645598 TTTTGTTT-
1 TTTT-TTTG
* *
645606 TTGTTTTA
1 TTTTTTTG
*
645614 TTTTTTTA
1 TTTTTTTG
645622 TTTTTTT-
1 TTTTTTTG
*
645629 ATTTTTTG
1 TTTTTTTG
645637 TTTTTTT
1 TTTTTTT
645644 TAAAGAAGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 9 0.19
8 35 0.74
9 3 0.06
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:645644 original size:16 final size:15
Alignment explanation
Indices: 645582--645645 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 15
645572 CTTTTCTCTC
*
645582 TTTTTTTGTTTTTTTG
1 TTTTTTT-TTTTTTTA
*
645598 TTTTGTTTTTGTTTTA
1 TTTT-TTTTTTTTTTA
645614 TTTTTTTATTTTTTTA
1 TTTTTTT-TTTTTTTA
645630 TTTTTTGTTTTTTTTA
1 TTTTTT-TTTTTTTTA
645646 AAGAAGGTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.07
16 35 0.83
17 4 0.10
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTTTA
Found at i:657895 original size:79 final size:78
Alignment explanation
Indices: 657791--658177 Score: 310
Period size: 79 Copynumber: 4.9 Consensus size: 78
657781 TGGAGATAAC
*
657791 AACGGGGCTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTGGAAATAAAATCGGTGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTGGAAATAAAATCGG-GTTGGAGT
657856 ATCCCCTCGAAAAT
65 ATCCCCTCGAAAAT
* * * * * *
657870 AACAGGGTTGGAGAATCCCTGATTAT-AGAAAATCAGTGTTTTGAAAATAAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATCGGTGCTTTGGAAATAAAATC-GGGTTGGAG
* * *
657934 TATCTCTTTGAAAAT
64 TATCCCCTCGAAAAT
* * ** * ** *
657949 AACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGAAGCTTTAGAAATAAGGTTAGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTGGAAATAA-AATCGGGTTGGAGT
* *
658014 ATCCCCGCCAAAAT
65 ATCCCCTCGAAAAT
* * ** ** * ** ***
658028 AACGGGGTTGGAGTATCCCCAATTGT-AAGAAATCAATATTTTAGAAATAAAGCCGAGGTCAAAG
1 AACGGGGTTGGAGTATCCCCGATTATGAA-AAATCGGTGCTTTGGAAATAAAATCG-GGTTGGAG
*
658092 TATCCCCTTGAAAAT
64 TATCCCCTCGAAAAT
* * * * * *** * *
658107 AACGGGATTTGAGTGTTCCCGATTATTAAAAATTTATGTTTTGGAAATAAAATCGGGGTTAGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTGGAAATAAAATC-GGGTTGGAGT
658172 ATCCCC
65 ATCCCC
658178 GAGATGAAAA
Statistics
Matches: 241, Mismatches: 59, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
78 4 0.02
79 230 0.95
80 7 0.03
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTGGAAATAAAATCGGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:657962 original size:28 final size:30
Alignment explanation
Indices: 657909--657965 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
657899 AAATCAGTGT
*
657909 TTTGAAAATAAAATCGGGGTTGGAGTATCTC
1 TTTGAAAAT-AAATCGGGGTTAGAGTATCTC
657940 TTTGAAAAT-AA-CGGGGTTAGAGTATC
1 TTTGAAAATAAATCGGGGTTAGAGTATC
657966 CCCGATTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
29 2 0.08
31 9 0.36
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (30 bp):
TTTGAAAATAAATCGGGGTTAGAGTATCTC
Found at i:658094 original size:158 final size:158
Alignment explanation
Indices: 657791--658178 Score: 377
Period size: 158 Copynumber: 2.5 Consensus size: 158
657781 TGGAGATAAC
* * ** * *
657791 AACGGGGCTGGAGTATCCCCGATTATGAAAAATCGGTGCTTTGGAAATAAAATCGGTGTTGGAGT
1 AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGAAGCTTTAGAAATAAAATAGGTGTTGGAGT
* * ** * *
657856 ATCCCCTCGAAAATAACAGGGTTGGAGAATCCCTGATTATAGAAAATCAGTGTTTTGAAAATAAA
66 ATCCCCGCCAAAATAACAGGGTTGGAGAATCCCCAATTATAGAAAATCAATATTTTGAAAATAAA
* * *** * *
657921 ATCGGGGTTGGAGTATCTCTTTGAAAAT
131 ACCGAGGTCAAAGTATCCCCTTGAAAAT
* **
657949 AACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGAAGCTTTAGAAATAAGGTTAGG-GTTGGAG
1 AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGAAGCTTTAGAAATAA-AATAGGTGTTGGAG
* * *
658013 TATCCCCGCCAAAATAACGGGGTTGGAGTATCCCCAATTGTA-AGAAATCAATATTTT-AGAAAT
65 TATCCCCGCCAAAATAACAGGGTTGGAGAATCCCCAATTATAGA-AAATCAATATTTTGA-AAAT
*
658076 AAAGCCGAGGTCAAAGTATCCCCTTGAAAAT
128 AAAACCGAGGTCAAAGTATCCCCTTGAAAAT
* * * * * ** * * * * * *
658107 AACGGGATTTGAGTGTTCCCGATTATTAAAAATTTATGTTTTGGAAATAAAATCGGGGTTAGAGT
1 AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGAAGCTTTAGAAATAAAATAGGTGTTGGAGT
658172 ATCCCCG
66 ATCCCCG
658179 AGATGAAAAA
Statistics
Matches: 185, Mismatches: 41, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
157 5 0.03
158 177 0.96
159 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (158 bp):
AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGAAGCTTTAGAAATAAAATAGGTGTTGGAGT
ATCCCCGCCAAAATAACAGGGTTGGAGAATCCCCAATTATAGAAAATCAATATTTTGAAAATAAA
ACCGAGGTCAAAGTATCCCCTTGAAAAT
Found at i:658293 original size:129 final size:131
Alignment explanation
Indices: 658030--658307 Score: 323
Period size: 129 Copynumber: 2.1 Consensus size: 131
658020 GCCAAAATAA
*
658030 CGGGGTTGGAGTATCCCC-AATTGTAAGAAATCAATATTTTAGAAATAAAGCCGAGGTCAAAGTA
1 CGGGGTTGGAGTATCCCCGAATTGTAAGAAATCAATATTTTAGAAATAAAACCGAGGTCAAAGTA
* * * * * * * * *
658094 TCCCCTTGAAAATAACGGGATTTGAGTGTTCCCGATTATTAAAAATTTATGTTTTGGAAATAAAA
66 TCCCCTCGAAAATAACGGGATTGGAGTATCCCCAATTATTAAAAATTGAAGCTTTAGAAATAAAA
*
658159 T
131 C
* * * **
658160 CGGGGTTAGAGTATCCCCGAGA-TG-AA-AAATCAGTATTTTAGAAATAAAACTGAGGTTGAAGT
1 CGGGGTTGGAGTATCCCCGA-ATTGTAAGAAATCAATATTTTAGAAATAAAACCGAGGTCAAAGT
* *
658222 ATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATT-TTGAAAACTTGAAGCTTTAGAAATAA
65 ATCCCCTCGAAAATAACGGGATTGGAGTATCCCCAATTATT-AAAAATTGAAGCTTTAGAAATAA
**
658286 GGC
129 AAC
658289 CGGGGTTGGAGTATCCCCG
1 CGGGGTTGGAGTATCCCCG
658308 CCAAAATAAC
Statistics
Matches: 124, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
128 2 0.02
129 99 0.80
130 19 0.15
131 3 0.02
132 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (131 bp):
CGGGGTTGGAGTATCCCCGAATTGTAAGAAATCAATATTTTAGAAATAAAACCGAGGTCAAAGTA
TCCCCTCGAAAATAACGGGATTGGAGTATCCCCAATTATTAAAAATTGAAGCTTTAGAAATAAAA
C
Found at i:658338 original size:208 final size:208
Alignment explanation
Indices: 657951--658398 Score: 474
Period size: 208 Copynumber: 2.1 Consensus size: 208
657941 TTGAAAATAA
** * *
657951 CGGGGTTAGAGTATCCCCGATTG-TGAAAAATCGAAGCTTTAGAAATAAGGTTAGGGTTGGAGTA
1 CGGGGTTAGAGTATCCCCGA--GATGAAAAATCGAAGCTTTAGAAATAAACTGAGGGTTGAAGTA
*
658015 TCCCCGCCAAAATAACGGGGTTGGAGTATCCCCAATTGTAAGAAATCAATATTTTAGAAATAAAG
64 TCCCCGCCAAAATAACGGGGTTGGAGTATCCCCAATTGTAAGAAATCAATACTTTAGAAATAAAG
*** * * * * ** *
658080 CCGAGGTCAAAGTATCCCCTTGAAAATAACGGGATTTGAGTGTTCCCGATTATTAAAAATTTATG
129 CCGAGGTCAAAGTATCCCCGCCAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATA
* *
658145 TTTTGGAAATAAAAT
194 TTTTAGAAATAAAAC
* *
658160 CGGGGTTAGAGTATCCCCGAGATGAAAAATCAGTA-TTTTAGAAATAAAACTGA-GGTTGAAGTA
1 CGGGGTTAGAGTATCCCCGAGATGAAAAATC-GAAGCTTTAGAAAT-AAACTGAGGGTTGAAGTA
* * * * * *
658223 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTTTGAA-AACTTGAA-GCTTTAGAAATAA
64 TCCCCGCCAAAATAACGGGGTTGGAGTATCCCCAATTGT-AAGAA-ATCAATACTTTAGAAATAA
* * *** * * *
658286 GGCCGGGGTTGGAGTATCCCCGCCAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAA
127 AGCCGAGGTCAAAGTATCCCCGCCAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAA
*
658351 TATTTTAGAAATAAAGC
192 TATTTTAGAAATAAAAC
* * *
658368 CGGGGTTGGAGTATCCTCGAGATAAAAAATC
1 CGGGGTTAGAGTATCCCCGAGATGAAAAATC
658399 TATAAATTTA
Statistics
Matches: 197, Mismatches: 37, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
207 1 0.01
208 165 0.84
209 31 0.16
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (208 bp):
CGGGGTTAGAGTATCCCCGAGATGAAAAATCGAAGCTTTAGAAATAAACTGAGGGTTGAAGTATC
CCCGCCAAAATAACGGGGTTGGAGTATCCCCAATTGTAAGAAATCAATACTTTAGAAATAAAGCC
GAGGTCAAAGTATCCCCGCCAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATATT
TTAGAAATAAAAC
Found at i:658358 original size:79 final size:78
Alignment explanation
Indices: 658160--658383 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
658150 GAAATAAAAT
* * * * * *
658160 CGGGGTTAGAGTATCCCCGA--GATGAAAAATCAGTATTTTAGAAATAAAACTGAGGTTGAAGTA
1 CGGGGTTGGAGTATCCCCGATTG-TG-AAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTA
* *
658223 TCCCCTCGAAAATAA
64 TCCCCGCCAAAATAA
* * * ** *
658238 CGGGGTTGGAGTATCCCCAATTTTGAAAACTTGAA-GCTTTAGAAATAAGGCCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAA--TCAATATTTTAGAAATAAAGCCGGGGTTGGAGTA
658302 TCCCCGCCAAAATAA
64 TCCCCGCCAAAATAA
658317 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGA-AAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
658382 CC
65 CC
658384 TCGAGATAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
78 25 0.21
79 90 0.75
80 5 0.04
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
CCCGCCAAAATAA
Found at i:668220 original size:20 final size:20
Alignment explanation
Indices: 668199--668258 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
668189 AAGTATTTTT
668199 AATTATTTTTATATATTATTA
1 AATTATTTTTATA-ATTATTA
*
668220 AATT-TTATTATAATT-TTA
1 AATTATTTTTATAATTATTA
*
668238 AAATATTTATTATAATTATTA
1 AATTATTT-TTATAATTATTA
668259 GGAGATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.18
19 5 0.15
20 15 0.45
21 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTATTTTTATAATTATTA
Found at i:669095 original size:19 final size:19
Alignment explanation
Indices: 669071--669107 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
669061 TTTTTTTTGT
669071 GTTGAGACTAAAAAAAAAA
1 GTTGAGACTAAAAAAAAAA
*
669090 GTTGAGATTAAAAAAAAA
1 GTTGAGACTAAAAAAAAA
669108 TTTTAAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (19 bp):
GTTGAGACTAAAAAAAAAA
Found at i:671462 original size:20 final size:20
Alignment explanation
Indices: 671420--671465 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
671410 GTTGAGCATA
*
671420 ATGTATTAATACAATTCTTC
1 ATGTATTAATACAATTCTCC
*
671440 ATGTATTGATACAATGTC-CC
1 ATGTATTAATACAAT-TCTCC
671460 ATGTAT
1 ATGTAT
671466 CGATGCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATTAATACAATTCTCC
Found at i:671527 original size:20 final size:19
Alignment explanation
Indices: 671502--671592 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 19
671492 TGCCAATTTC
671502 ATGTATCGATACAATTGAGT
1 ATGTATCGATACAA-TGAGT
**
671522 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAGT
* *
671541 ATGTATCAATACAAAGCA-T
1 ATGTATCGATACAATG-AGT
*
671560 AATGTATCGATACATCTG-GAT
1 -ATGTATCGATACA-ATGAG-T
671581 ATGTATCGATAC
1 ATGTATCGATAC
671593 TTTCTAGGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 17 0.29
20 39 0.67
21 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAGT
Found at i:673258 original size:78 final size:80
Alignment explanation
Indices: 673158--673329 Score: 226
Period size: 78 Copynumber: 2.2 Consensus size: 80
673148 TAATAATGGG
*
673158 GTTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTAT-CCCGGTTGTGAAAAATCGATG-ATTA
1 GTTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTATTA
673221 GGAAATAAAATCGG-
66 GGAAATAAAATCGGA
* * * * *
673235 GATTGGAGTATCCCCTCT-GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAATATTGGTGTTT
1 G-TTGGAGTATCCCCT-TAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTAT
* *
673299 TTGGAAATAAAATCGTA
64 TAGGAAATAAAATCGGA
673316 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
673330 GATTAAAGGA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
77 1 0.01
78 34 0.41
79 18 0.22
80 28 0.34
81 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (80 bp):
GTTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTATTA
GGAAATAAAATCGGA
Found at i:673322 original size:52 final size:49
Alignment explanation
Indices: 673258--673443 Score: 230
Period size: 52 Copynumber: 3.6 Consensus size: 49
673248 CCTCTGAAAT
673258 AACGGGGTTGGAGTATCCCCGATTGTGAAATATTGGTGTTTTTGGAAATAA
1 AACGGGGTTGGAGTATCCCCGATTGTGAAA-ATTGGTG-TTTTGGAAATAA
** *
673309 AATCGTAGTTGGAGTATCCCCGATTAAAG-GAAAATTGGTGTTTTGAAAATAA
1 AA-CGGGGTTGGAGTATCCCCGATT---GTGAAAATTGGTGTTTTGGAAATAA
* *
673361 AACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAA
1 AA-CGGGGTTGGAGTATCCCCGATTGT-GAAAATTGGTGTTTTGGAAATAA
*
673412 AACTGGGGTTGGAGTATCCCCGATTATGAAAA
1 AAC-GGGGTTGGAGTATCCCCGATTGTGAAAA
673444 ATTGAGAAAC
Statistics
Matches: 118, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
49 1 0.01
50 6 0.05
51 46 0.39
52 53 0.45
53 7 0.06
54 4 0.03
55 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (49 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAATTGGTGTTTTGGAAATAA
Found at i:673413 original size:51 final size:50
Alignment explanation
Indices: 673260--673447 Score: 234
Period size: 51 Copynumber: 3.7 Consensus size: 50
673250 TCTGAAATAA
* *
673260 CGGGGTTGGAGTATCCCCGATTGT-GAAATATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGGAAA-ATTGGTG-TTTT-GAAATAAAAC
** *
673312 CGTAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-ATGGAAAATTGGTGTTTTG-AAATAAAAC
* *
673364 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTT-GAAATAAAAC
* *
673415 TGGGGTTGGAGTATCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCCGATTATGGAAAATTG
673448 AGAAACTTAA
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
51 54 0.46
52 53 0.45
53 7 0.06
54 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAATAAAAC
Found at i:675870 original size:32 final size:34
Alignment explanation
Indices: 675811--675875 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
675801 AAGATCGATG
**
675811 TATCGATACATTACCTTAATGTATCGATACATTA
1 TATCGATACAGCACCTTAATGTATCGATACATTA
675845 TATCGATACAGCA-CTT-ATGTATCGATACATT
1 TATCGATACAGCACCTTAATGTATCGATACATT
675876 TACGGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 15 0.52
33 3 0.10
34 11 0.38
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (34 bp):
TATCGATACAGCACCTTAATGTATCGATACATTA
Found at i:676000 original size:4 final size:4
Alignment explanation
Indices: 675991--676024 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
675981 TTTTTTAAAA
675991 TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT T
676025 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:677120 original size:13 final size:13
Alignment explanation
Indices: 677102--677126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
677092 ACACACAGTA
677102 TGTATCGATACAT
1 TGTATCGATACAT
677115 TGTATCGATACA
1 TGTATCGATACA
677127 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:677123 original size:32 final size:33
Alignment explanation
Indices: 677082--677149 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
677072 GTAGCTAAAC
**
677082 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
677114 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
677147 TTG
1 TTG
677150 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:688098 original size:13 final size:13
Alignment explanation
Indices: 688080--688104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
688070 ATGTTGCATA
688080 GTATCGATACATT
1 GTATCGATACATT
688093 GTATCGATACAT
1 GTATCGATACAT
688105 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:688213 original size:13 final size:13
Alignment explanation
Indices: 688195--688219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
688185 ACACACAGTA
688195 TGTATCGATACAT
1 TGTATCGATACAT
688208 TGTATCGATACA
1 TGTATCGATACA
688220 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:688216 original size:32 final size:33
Alignment explanation
Indices: 688175--688241 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
688165 GTAGCTAAAC
**
688175 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
688207 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
688240 TT
1 TT
688242 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:690887 original size:100 final size:100
Alignment explanation
Indices: 690714--690912 Score: 371
Period size: 100 Copynumber: 2.0 Consensus size: 100
690704 TTCATAAAAA
690714 GAAAGGTAAAGACACTAAAAACACAAGTATGAGAGATATAAGAGAAGTAAAAACACTTGGTATAA
1 GAAAGGTAAAGACACTAAAAACACAAGTATGAGAGATATAAGAGAAGTAAAAACACTTGGTATAA
*
690779 ACATGAAATCAAGGCAGATTCTTAAGGCCAAGTTT
66 ACATGAAATCAAGGCAGATTCTTAAGACCAAGTTT
* *
690814 GAAAGGTAAAGACATTAAAAACATAAGTATGAGAGATATAAGAGAAGTAAAAACACTTGGTATAA
1 GAAAGGTAAAGACACTAAAAACACAAGTATGAGAGATATAAGAGAAGTAAAAACACTTGGTATAA
690879 ACATGAAATCAAGGCAGATTCTTAAGACCAAGTT
66 ACATGAAATCAAGGCAGATTCTTAAGACCAAGTT
690913 CTCTCCTAAG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.21
Consensus pattern (100 bp):
GAAAGGTAAAGACACTAAAAACACAAGTATGAGAGATATAAGAGAAGTAAAAACACTTGGTATAA
ACATGAAATCAAGGCAGATTCTTAAGACCAAGTTT
Found at i:691286 original size:20 final size:19
Alignment explanation
Indices: 691263--691335 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
691253 CACACCTAGA
* *
691263 TGTATCGATACCTGCTGCTT
1 TGTATCGATACATG-TGCAT
*
691283 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
691302 TGTATCGATACATG-GACAAT
1 TGTATCGATACATGTG-C-AT
691322 TGTATCGATACATG
1 TGTATCGATACATG
691336 AAACTGGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.62
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:691401 original size:13 final size:13
Alignment explanation
Indices: 691380--691410 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
691370 CGATACATGG
*
691380 TACAATGTATCGA
1 TACATTGTATCGA
691393 TACATTGTATCGA
1 TACATTGTATCGA
691406 TACAT
1 TACAT
691411 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:691401 original size:33 final size:32
Alignment explanation
Indices: 691364--691430 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
691354 CTATCACTAT
691364 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
691397 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
691430 T
1 T
691431 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:697974 original size:28 final size:28
Alignment explanation
Indices: 697893--697974 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
697883 TTTTGGAGAT
*
697893 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
697921 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
697949 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
697975 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:698119 original size:51 final size:51
Alignment explanation
Indices: 697959--698127 Score: 203
Period size: 51 Copynumber: 3.3 Consensus size: 51
697949 AATAACGAGG
* * * *
697959 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAA
1 TTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGGGA
* * * * * *
698011 TTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGGGA
* *
698064 TTGGAGTATCCCCGATTATGAAAAATTGATATTTTGAAAATAAAGTCGGGA
1 TTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGA
698115 TTGGAGTATCCCC
1 TTGGAGTATCCCC
698128 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGA
Found at i:698146 original size:28 final size:27
Alignment explanation
Indices: 698110--698182 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
698100 AAAATAAAGT
*
698110 CGGGATTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-CATG-AATAA
* *
698138 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCCATGAATAA
*
698165 CGGGGTTGGAGTGTCCCC
1 CGGGGTTGGAGTATCCCC
698183 GATTGTGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCCATGAATAA
Found at i:700667 original size:13 final size:13
Alignment explanation
Indices: 700649--700674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
700639 ACAAAGATCC
700649 ATGTATCGATACA
1 ATGTATCGATACA
700662 ATGTATCGATACA
1 ATGTATCGATACA
700675 CAGAAAAATG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:700670 original size:33 final size:33
Alignment explanation
Indices: 700628--700694 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
700618 AAAATTTCCA
***
700628 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
700661 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
700694 A
1 A
700695 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Done.