Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 14 of 168
Found at i:3873825 original size:2 final size:2
Alignment explanation
Indices: 3873818--3873849 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3873808 TCCTTTATTA
3873818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3873850 TAAAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3879722 original size:43 final size:44
Alignment explanation
Indices: 3879636--3879901 Score: 180
Period size: 43 Copynumber: 6.0 Consensus size: 44
3879626 CGAAGAAAAT
* *
3879636 ATATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGC
1 ATATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGC
* *
3879680 ATATCTTGTCTTCATGTA-TGGCATGAAGTAGATCAGATATAGC
1 ATATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGC
* *** *** * **
3879723 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAA-AAAAA
1 ATATCTTGTCTTCATGTACTGG-CATGAAGTAGATCAAAGATAGC
* *
3879767 ATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAC
1 AT--ATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGC
* * *** ** * * **
3879812 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGAT-AGAAGAAAAT
1 ATATCTTGTCTTCATGTACTGG-CATGAAGTAGATCA-AAGATAGC
* * * *
3879857 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAATATAGC
1 ATATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGC
3879901 A
1 A
3879902 GGTCATGTCT
Statistics
Matches: 172, Mismatches: 41, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
43 53 0.31
44 52 0.30
45 49 0.28
46 18 0.10
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (44 bp):
ATATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGC
Found at i:3879815 original size:89 final size:90
Alignment explanation
Indices: 3879682--3879995 Score: 343
Period size: 89 Copynumber: 3.5 Consensus size: 90
3879672 AAGATAGCAT
* * * *
3879682 ATCTTGTCTTCATGTA-TGGCATGAAGTAGATCAGATATAGCAGATCTTGTCTTCCCATACTGGT
1 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
*
3879746 GGCGAAGTAGATCAAAAAAAAATAG
66 GGCGAAGTAGATCAAAAGAAAATAG
*
3879771 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCATACTGGT
1 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
* * *
3879835 GGTGGAGTAGAT-AGAAGAAAATAG
66 GGCGAAGTAGATCAAAAGAAAATAG
* * * * * *
3879859 ATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAATATAGCAGGTCATGTCTTCCTATA-TCGG
1 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT-GG
* * * *
3879923 TAGCGAAGTGGATC-AAAGATAACAG
65 TGGCGAAGTAGATCAAAAGAAAATAG
** * * *
3879948 ATCTTGTCTTCCCGTACTGGTGGCGAAGTAGATCGAAGA-AAGCAGATC
1 ATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAA-CAGATC
3879996 GAAGATGGCG
Statistics
Matches: 187, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
88 47 0.25
89 103 0.55
90 37 0.20
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (90 bp):
ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
GGCGAAGTAGATCAAAAGAAAATAG
Found at i:3879974 original size:45 final size:45
Alignment explanation
Indices: 3879607--3879995 Score: 276
Period size: 45 Copynumber: 8.8 Consensus size: 45
3879597 TATCTCCCCA
* * * * * * *
3879607 TACTGGTGGTGGAA-TAGATCGAAGAAAATATATCTTATCTTCATG
1 TACTGGTCGT-GAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
* * *
3879652 TACTGG-CGTGAAGTAGATCAAAGATAGCATATCTTGTCTTCATG
1 TACTGGTCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
* * * * **
3879696 TA-TGG-CATGAAGTAGATCAGATATAGCAGATCTTGTCTTCCCA
1 TACTGGTCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
* * * * * *
3879739 TACTGGTGGCGAAGTAGATCAAAAAAAAATAGATCTTGTCTTCATG
1 TACTGGTCGTGAAGTAGATC-AAAGATAACAGATCTTGTCTTCCTG
* **
3879785 TACTGG-CGTGAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCA
1 TACTGGTCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
* * * * * *
3879828 TACTGGTGGTGGAGTAGAT-AGAAGAAAATAGATCTTATCTTCATG
1 TACTGGTCGTGAAGTAGATCA-AAGATAACAGATCTTGTCTTCCTG
* * * * *
3879873 TACTGG-CGTGAAGTAGATCAAATATAGCAGGTCATGTCTTCCTA
1 TACTGGTCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
* * * *
3879917 TA-TCGGTAGCGAAGTGGATCAAAGATAACAGATCTTGTCTTCCCG
1 TACT-GGTCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
* * *
3879962 TACTGGTGGCGAAGTAGATCGAAGA-AAGCAGATC
1 TACTGGTCGTGAAGTAGATCAAAGATAA-CAGATC
3879996 GAAGATGGCG
Statistics
Matches: 269, Mismatches: 63, Indels: 24
0.76 0.18 0.07
Matches are distributed among these distances:
43 61 0.23
44 82 0.30
45 102 0.38
46 24 0.09
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (45 bp):
TACTGGTCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTG
Found at i:3881520 original size:3 final size:3
Alignment explanation
Indices: 3881492--3881544 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
3881482 TGCTATACCC
*
3881492 TTA TT- TTA TT- TTA TT- GTA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
3881535 TTA TTA TTA T
1 TTA TTA TTA T
3881545 ACTTATACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 5 0.11
3 36 0.82
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3881847 original size:15 final size:15
Alignment explanation
Indices: 3881827--3881857 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3881817 TTATTTTTTA
3881827 TACTTTATCTTTATT
1 TACTTTATCTTTATT
*
3881842 TACTTTATTTTTATT
1 TACTTTATCTTTATT
3881857 T
1 T
3881858 TGTAAATATA
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:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TACTTTATCTTTATT
Found at i:3883037 original size:13 final size:13
Alignment explanation
Indices: 3883008--3883058 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
3882998 AATGGCATGG
3883008 AAATAATATAAAC-
1 AAATAA-ATAAACA
3883021 AAATAAATAAACA
1 AAATAAATAAACA
* *
3883034 AAATTAATATACA
1 AAATAAATAAACA
3883047 AAA-AAA-AAACA
1 AAATAAATAAACA
3883058 A
1 A
3883059 TAATCCATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.15
12 8 0.24
13 20 0.61
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (13 bp):
AAATAAATAAACA
Found at i:3883644 original size:17 final size:17
Alignment explanation
Indices: 3883624--3883667 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3883614 ATTTTTTAAA
3883624 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
3883641 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
3883658 -ATATGTATAT
1 AAAATGTATAT
3883668 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:3883650 original size:27 final size:27
Alignment explanation
Indices: 3883620--3883671 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3883610 ATGTATTTTT
*
3883620 TAAAAAAATGTATATGTATATAAAATG
1 TAAAAAAATATATATGTATATAAAATG
***
3883647 TAAATGTATATATATGTATATAAAA
1 TAAAAAAATATATATGTATATAAAA
3883672 GTTATGCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (27 bp):
TAAAAAAATATATATGTATATAAAATG
Found at i:3883813 original size:3 final size:3
Alignment explanation
Indices: 3883798--3883857 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
3883788 ATATATATAG
*
3883798 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3883846 TAA TAA TAA TAA
1 TAA TAA TAA TAA
3883858 CAACTTAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3885524 original size:44 final size:44
Alignment explanation
Indices: 3885472--3885576 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
3885462 TACTCTACTG
* *
3885472 CAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCCGCTCCACTA
1 CAACTTCAGGGAGATAAGAT-TAGTGGCTTTAATCCGCTCCACTA
* * * * *
3885516 CAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCATTG
1 CAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCGCTCCACTA
3885560 CAACTTCAGGGAGATAA
1 CAACTTCAGGGAGATAA
3885577 TATTCGCCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCGCTCCACTA
Found at i:3885771 original size:100 final size:100
Alignment explanation
Indices: 3885587--3885795 Score: 265
Period size: 100 Copynumber: 2.1 Consensus size: 100
3885577 TATTCGCCAT
* * * *
3885587 CTTCAGTCTTTTAAATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAACTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCATAACTTCAATCTATTCCA
** * *
3885652 CTACACTGCCAGAGAAGTAAGATTCATCGTTGCGG
66 CTACACCACCAGAGAAGTAAGATTCACCGTCGCGG
* * * *
3885687 CTTCAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTCGTCGTCATAGCTTCAATCTATTTCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCATAACTTCAATCTATTCCA
* * * *
3885752 CTACACCACCAGGGGAGTAAGGTTCACCGTCGTGG
66 CTACACCACCAGAGAAGTAAGATTCACCGTCGCGG
*
3885787 TTTCAATCT
1 CTTCAATCT
3885796 GCTCCACTGT
Statistics
Matches: 92, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCATAACTTCAATCTATTCCA
CTACACCACCAGAGAAGTAAGATTCACCGTCGCGG
Found at i:3886164 original size:44 final size:44
Alignment explanation
Indices: 3886069--3886165 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
3886059 TGTTACTCAT
*
3886069 GGAGATAAGATTCACAATCTTCAACCTATTCCACTACTGACCAG
1 GGAGATAGGATTCACAATCTTCAACCTATTCCACTACTGACCAG
* *
3886113 GGAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGTCCAG
1 GGAGATAGGA-TTCACAATCTTCAACCTATTCCACTACTGACCAG
3886157 GGAGATAGG
1 GGAGATAGG
3886166 GCTGGGGTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 47 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (44 bp):
GGAGATAGGATTCACAATCTTCAACCTATTCCACTACTGACCAG
Found at i:3886285 original size:88 final size:88
Alignment explanation
Indices: 3886179--3886917 Score: 1068
Period size: 88 Copynumber: 8.4 Consensus size: 88
3886169 GGGGTCATTA
* * * * **
3886179 ATCTGCATCACTGCCGGTGCAGGCAGGCAAGATCTGCTATTTTTAACCTGCTTTGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
3886244 GGGAAGCAAGGCTGGTGTCTTTG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * * * *
3886267 ATCTGCTTCGCTTTCGGTGCAAGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCGACCTA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
3886332 GAGAAGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * **
3886355 ATCTTCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTATCCTGCTCCGCTATAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
3886420 GGGAGGCAATGG-TGGTGTCTTCG
66 GGGAGGCAA-GGCTGGTGTCTTCG
*
3886443 ATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
*
3886508 GGGAGGCAAGGCTAGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * * *
3886531 ATCTGCTTCACTGTCGGTGCAGGAAGGTAAGATCTGCTGTTTTTAACCTGCTCCGCTACAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
3886596 GGGTGGTAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
*
3886619 ATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
*
3886684 GGGAGGCAAGGCTAGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * * *
3886707 ATCTGCTTCACTGTCGGTGCAGGAAGGTAAGATCTGCTGTTTTTAACCTGCTCCGCTACAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
3886772 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
** * * * * *
3886795 ATCTTTTTCGCTGTCGGTGCAAGAAGGTAAAATATGCTA-TTTTAACCTACTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
3886859 GGGAGGCAAGGTTGGTATCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
*
3886882 ATCTGCTTCGCTGTCGGTGCAGGAATGCAAGATCTG
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
3886918 TTATCTTCAC
Statistics
Matches: 579, Mismatches: 70, Indels: 5
0.89 0.11 0.01
Matches are distributed among these distances:
87 75 0.13
88 502 0.87
89 2 0.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
GGGAGGCAAGGCTGGTGTCTTCG
Found at i:3888156 original size:2 final size:2
Alignment explanation
Indices: 3888149--3888173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3888139 TTCTTCTTCT
3888149 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3888174 TTTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3889158 original size:21 final size:22
Alignment explanation
Indices: 3889118--3889158 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3889108 AAGAAAATCC
*
3889118 AAAAGAATGAAAGAATTATTCA
1 AAAAGAATGAAAGAAATATTCA
3889140 AAAAGAATGAAA-AAATATT
1 AAAAGAATGAAAGAAATATT
3889159 GGCTCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (22 bp):
AAAAGAATGAAAGAAATATTCA
Found at i:3892695 original size:17 final size:17
Alignment explanation
Indices: 3892675--3892718 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3892665 ATTTTTAAAA
3892675 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
3892692 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
3892709 -ATATGTATAT
1 AAAATGTATAT
3892719 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:3892859 original size:3 final size:3
Alignment explanation
Indices: 3892853--3892906 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
3892843 GTAGTAGTAG
3892853 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3892901 TAA TAA
1 TAA TAA
3892907 CTTAATAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3898103 original size:12 final size:10
Alignment explanation
Indices: 3898082--3898116 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
3898072 AAATATGAAA
3898082 ATATGTATAT
1 ATATGTATAT
3898092 ATATAAGTATAT
1 ATAT--GTATAT
3898104 ATATGTATAT
1 ATATGTATAT
3898114 ATA
1 ATA
3898117 AAAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (10 bp):
ATATGTATAT
Found at i:3901177 original size:88 final size:88
Alignment explanation
Indices: 3901039--3901557 Score: 586
Period size: 88 Copynumber: 5.9 Consensus size: 88
3901029 CCATAAATCC
* *
3901039 TATCTCCCT-AGGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGC
1 TATCTCCCTGA-GCAGCAGTGGAGTAGGTTGAAAATAGAAGATCTTGTCTTCCTGTATTGGCAGC
* * * *
3901103 AAAGAAGATCGAAGA-CCTCAGCCT
65 GAAGTAGATCGAAGATAC-CAACCT
* * *
3901127 TATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGAAGATCTTATCTTCCTATATTGGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGAAGATCTTGTCTTCCTGTATTGGCAGCG
*
3901192 AAGTAGATCGAAGATACCAACTT
66 AAGTAGATCGAAGATACCAACCT
* * *
3901215 TATCTCCCTGAGCAGCTGTGGAGTAGGTTAAAAATA-ACAGATCTTGTCTTCCTGTATTAGCAGC
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGA-AGATCTTGTCTTCCTGTATTGGCAGC
* *
3901279 GAAGTAGATCGAAGA-CCTCAGCCT
65 GAAGTAGATCGAAGATAC-CAACCT
* * * *
3901303 TGTCTCCCTGAGCAGTAGTGGGGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGAAGATCTTGTCTTCCTGTATTGGCAGCG
*
3901368 AAGTAGATCAAAGATACCAACCT
66 AAGTAGATCGAAGATACCAACCT
* * * * *
3901391 TATCTCCCTGAGCAGCAGTGGAGTATGTTAAAAAAAGTAGATCTTGTCTTCCTGTATTGGCAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGAAGATCTTGTCTTCCTGTATTGGCAGCG
* * * **
3901456 AAGTAGATCAAAAACACCAGTCT
66 AAGTAGATCGAAGATACCAACCT
* * * * **
3901479 GACCTCTCTGGGTTACAGCA-T--AGTAGACTGAAAATA-ACAGATCTTGTCTTCCTGTATTGGC
1 TATCTCCCTGAG---CAGCAGTGGAGTAGGTTGAAAATAGA-AGATCTTGTCTTCCTGTATTGGC
3901540 AGCGAAGTAGATCGAAGA
62 AGCGAAGTAGATCGAAGA
3901558 CTCCAGTCTT
Statistics
Matches: 367, Mismatches: 54, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
87 2 0.01
88 356 0.97
89 3 0.01
90 1 0.00
91 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGAAGATCTTGTCTTCCTGTATTGGCAGCG
AAGTAGATCGAAGATACCAACCT
Found at i:3901333 original size:176 final size:176
Alignment explanation
Indices: 3901039--3901557 Score: 650
Period size: 176 Copynumber: 2.9 Consensus size: 176
3901029 CCATAAATCC
* * *
3901039 TATCTCCCT-AGGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGC
1 TATCTCCCTGA-GCAGCAGTGGAGTAGGTTAAAAATAACAGATCTTGTCTTCCTGTATTGGCAGC
* *
3901103 AAAGAAGATCGAAGACCTCAGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGAAGA
65 GAAGTAGATCGAAGACCTCAGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGAAGA
* *
3901168 TCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATACCAACTT
130 TCTTATCTTCCTATATTGGCAGCGAAGTAGATCAAAGATACCAACCT
* *
3901215 TATCTCCCTGAGCAGCTGTGGAGTAGGTTAAAAATAACAGATCTTGTCTTCCTGTATTAGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAACAGATCTTGTCTTCCTGTATTGGCAGCG
* ** * *
3901280 AAGTAGATCGAAGACCTCAGCCTTGTCTCCCTGAGCAGTAGTGGGGTAGGTTGAAAATAGCAGAT
66 AAGTAGATCGAAGACCTCAGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGAAGAT
* *
3901345 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATACCAACCT
131 CTTATCTTCCTATATTGGCAGCGAAGTAGATCAAAGATACCAACCT
* * *
3901391 TATCTCCCTGAGCAGCAGTGGAGTATGTTAAAAA-AAGTAGATCTTGTCTTCCTGTATTGGCAGT
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAA-CAGATCTTGTCTTCCTGTATTGGCAGC
* * * * * * * ** *** **
3901455 GAAGTAGATCAAAAACAC-CAGTCTGACCTCTCTGGGTTACAGCATAGTAGACTGAAAATA-ACA
65 GAAGTAGATCGAAGAC-CTCAGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGA-A
* * *
3901518 GATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
128 GATCTTATCTTCCTATATTGGCAGCGAAGTAGATCAAAGA
3901558 CTCCAGTCTT
Statistics
Matches: 298, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
175 2 0.01
176 294 0.99
177 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (176 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAACAGATCTTGTCTTCCTGTATTGGCAGCG
AAGTAGATCGAAGACCTCAGCCTTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGAAGAT
CTTATCTTCCTATATTGGCAGCGAAGTAGATCAAAGATACCAACCT
Found at i:3901515 original size:264 final size:263
Alignment explanation
Indices: 3901061--3901558 Score: 680
Period size: 264 Copynumber: 1.9 Consensus size: 263
3901051 CAGCAATGGA
* * *
3901061 GTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGAAGATCGAAGACCTCAGCC
1 GTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGAAGATCAAAGAACTCAACC
* *
3901126 TTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGAAGATCTTATCTTCCTATATTGGCAGC
66 TTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAAAAAGAAGATCTTATCTTCCTATATTGGCAGC
* * * * * * **
3901191 GAAGTAGATCGAAGATACCAACTTTATCTCCCTGAGCAGCTGTGGAGTAGGTTAAAAATAACAGA
131 GAAGTAGATCAAAAACACCAACTTGACCTCCCTGAGCAGCTAT-GAGTAGACTAAAAATAACAGA
3901256 TCTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGACCTCAGCCTTGTCTCCCTGAGCAGTAG
195 TCTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGACCTCAGCCTTGTCTCCCTGAGCAGTAG
3901321 TGGG
260 TGGG
* *
3901325 GTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAC-CAAC
1 GTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGAAGATCAAAGA-ACTCAAC
* * * * *
3901389 CTTATCTCCCTGAGCAGCAGTGGAGTATGTTAAAAAAAGTAGATCTTGTCTTCCTGTATTGGCAG
65 CTTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAAAAAGAAGATCTTATCTTCCTATATTGGCAG
* * * * *
3901454 TGAAGTAGATCAAAAACACC-AGTCTGACCTCTCTGGGTTACAGC-AT-AGTAGACTGAAAATAA
130 CGAAGTAGATCAAAAACACCAACT-TGACCTCCCTGAG---CAGCTATGAGTAGACTAAAAATAA
*
3901516 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAC
191 CAGATCTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGAC
3901559 TCCAGTCTTA
Statistics
Matches: 203, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
263 2 0.01
264 195 0.96
265 1 0.00
266 1 0.00
267 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (263 bp):
GTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGAAGATCAAAGAACTCAACC
TTATCTCCCTGAGCAACAGTGGAGTAGGTTAAAAAAAGAAGATCTTATCTTCCTATATTGGCAGC
GAAGTAGATCAAAAACACCAACTTGACCTCCCTGAGCAGCTATGAGTAGACTAAAAATAACAGAT
CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGACCTCAGCCTTGTCTCCCTGAGCAGTAGT
GGG
Found at i:3901666 original size:51 final size:51
Alignment explanation
Indices: 3901564--3901684 Score: 127
Period size: 51 Copynumber: 2.4 Consensus size: 51
3901554 AAGACTCCAG
* * * * *
3901564 TCTTATCGCCTTGGCATTGCAGTGGGACAGATTAAAGCTGAAGATAGCGAA
1 TCTTATCTCCCTGGCATTACAGTGGGACAGATTAAAGCTGAAGACAACGAA
* * * * * *
3901615 TCTTGTGTTCCTGGCATTACAGT-GGAGCAGATTAAAGTTGAGGGCAACGAA
1 TCTTATCTCCCTGGCATTACAGTGGGA-CAGATTAAAGCTGAAGACAACGAA
3901666 TCTTATCTCCCTGGCATTA
1 TCTTATCTCCCTGGCATTA
3901685 AGACTTAGAA
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
50 3 0.05
51 52 0.95
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (51 bp):
TCTTATCTCCCTGGCATTACAGTGGGACAGATTAAAGCTGAAGACAACGAA
Found at i:3901811 original size:50 final size:50
Alignment explanation
Indices: 3901757--3901943 Score: 207
Period size: 50 Copynumber: 3.7 Consensus size: 50
3901747 CATTACAGTG
* *
3901757 GAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGCGGTGTAGTA
1 GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGAAGTA
* * * * ** *
3901807 GAACAGATTGAAGCTACAACAGCTAATCTTGCTTCCCCGACATTGCAATTA
1 GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTG-AAGTA
* * * * *
3901858 -AATAGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTG
1 GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGAAGTA
*
3901907 GAACAAATTGAAGCTACAAC-GACGAATCTTACTTCCC
1 GAACAGATTGAAGCTACAACAG-CGAATCTTACTTCCC
3901944 CGATATTGCA
Statistics
Matches: 111, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
49 3 0.03
50 105 0.95
51 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (50 bp):
GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGAAGTA
Found at i:3901935 original size:100 final size:100
Alignment explanation
Indices: 3901761--3901959 Score: 292
Period size: 100 Copynumber: 2.0 Consensus size: 100
3901751 ACAGTGGAAC
* * * * *
3901761 AGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGCGGTGTAGTAGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTAGAACAAATTGAAGCTACAA
* *
3901826 CAGCTAATCTTGCTTCCCCGACATTGCAATTAAAT
66 CAGCGAATCTTACTTCCCCGACATTGCAATTAAAT
*
3901861 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTGGAACAAATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTAGAACAAATTGAAGCTACAA
* *
3901926 C-GACGAATCTTACTTCCCCGATATTGCAGTTAAA
66 CAG-CGAATCTTACTTCCCCGACATTGCAATTAAA
3901960 CGGACTGAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 1 0.01
100 87 0.99
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (100 bp):
AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAGCGGTGCAGTAGAACAAATTGAAGCTACAA
CAGCGAATCTTACTTCCCCGACATTGCAATTAAAT
Found at i:3902031 original size:44 final size:43
Alignment explanation
Indices: 3901976--3902097 Score: 154
Period size: 44 Copynumber: 2.8 Consensus size: 43
3901966 GAAGATGGCA
* *
3901976 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ACAAT
* * * *
3902020 AATCCTATCTCCCTGAAATTGCAGTGGAGCGGATTAAAATAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACAAT
* *
3902063 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
3902098 CGCATCAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 4 0.06
44 62 0.94
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACAAT
Found at i:3903475 original size:3 final size:3
Alignment explanation
Indices: 3903467--3903507 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
3903457 ATTTATGTAA
* * *
3903467 TAT TAT TAT TTT TAT TTT TAT TAT AAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3903508 CCACGTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3912792 original size:12 final size:11
Alignment explanation
Indices: 3912754--3912795 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
3912744 ATTTTTAAAA
3912754 TATTTTATGTT
1 TATTTTATGTT
*
3912765 GTA-TTTATTTT
1 -TATTTTATGTT
3912776 TATTTTATGTGT
1 TATTTTATGT-T
3912788 TATTTTAT
1 TATTTTAT
3912796 AATTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 2 0.08
11 13 0.50
12 11 0.42
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (11 bp):
TATTTTATGTT
Found at i:3923087 original size:31 final size:31
Alignment explanation
Indices: 3923026--3923107 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
3923016 ACTTAATAGC
3923026 TAATGACTTAAAT-AAAACTTTCAAATAATT
1 TAATGACTTAAATGAAAACTTTCAAATAATT
* **
3923056 TAATGACTTAAATGAAAATTTTTGAATAATT
1 TAATGACTTAAATGAAAACTTTCAAATAATT
* *
3923087 TAATGACTAAAATGTAAACTT
1 TAATGACTTAAATGAAAACTT
3923108 AATAATAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 13 0.29
31 32 0.71
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (31 bp):
TAATGACTTAAATGAAAACTTTCAAATAATT
Found at i:3923115 original size:31 final size:31
Alignment explanation
Indices: 3923049--3923119 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3923039 AAAACTTTCA
* **
3923049 AATAATTTAATGACTTAAATGAAAATTTTTG
1 AATAATTTAATGACTAAAATGAAAATTAATG
*
3923080 AATAATTTAATGACTAAAATGTAAACTTAAT-
1 AATAATTTAATGACTAAAATG-AAAATTAATG
3923111 AATAATTTA
1 AATAATTTA
3923120 GTATCTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 29 0.83
32 6 0.17
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.39
Consensus pattern (31 bp):
AATAATTTAATGACTAAAATGAAAATTAATG
Found at i:3925478 original size:22 final size:23
Alignment explanation
Indices: 3925435--3925480 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3925425 CACTTTTTAG
*
3925435 AATAATGCAATCAAGCTTCCAGA
1 AATAATGCAATCAAGCTGCCAGA
* *
3925458 AATAATGCGAT-AATCTGCCAGA
1 AATAATGCAATCAAGCTGCCAGA
3925480 A
1 A
3925481 TCAATAAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (23 bp):
AATAATGCAATCAAGCTGCCAGA
Found at i:3935263 original size:17 final size:17
Alignment explanation
Indices: 3935237--3935269 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3935227 CGTCGTCGCT
*
3935237 ATGGTGACCCGATCCGA
1 ATGGTAACCCGATCCGA
3935254 ATGGTAACCCGATCCG
1 ATGGTAACCCGATCCG
3935270 GGAAGGATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.18
Consensus pattern (17 bp):
ATGGTAACCCGATCCGA
Found at i:3935980 original size:19 final size:20
Alignment explanation
Indices: 3935952--3935991 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3935942 TTCTAAATTA
*
3935952 TTATCCACATGA-TTTAAAT
1 TTATCAACATGATTTTAAAT
*
3935971 TTATCAACATTATTTTAAAT
1 TTATCAACATGATTTTAAAT
3935991 T
1 T
3935992 CTTTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATCAACATGATTTTAAAT
Found at i:3937448 original size:24 final size:25
Alignment explanation
Indices: 3937421--3937474 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3937411 TGCCACTCAG
*
3937421 ATAATA-TGCAGCTGTGCTGCCAAA
1 ATAATATTGCAGCTGTACTGCCAAA
* * *
3937445 ATAATATTGCTGGTTTACTGCCAAA
1 ATAATATTGCAGCTGTACTGCCAAA
3937470 ATAAT
1 ATAAT
3937475 GTAGTATCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (25 bp):
ATAATATTGCAGCTGTACTGCCAAA
Found at i:3938591 original size:353 final size:354
Alignment explanation
Indices: 3937939--3938630 Score: 1341
Period size: 353 Copynumber: 2.0 Consensus size: 354
3937929 AAATTTCTAG
3937939 ATTTTCGTGACTGTTTTCAGTATTTTTGGGTTAGAACATACACCTTAATGCCTCTGGAATATCAG
1 ATTTTCGTGACTGTTTTCAGTATTTTTGGGTTAGAACATACACCTTAATGCCTCTGGAATATCAG
*
3938004 TACTACAACAGCGCACTCTGTACTTACACACGATATCAAATCGCACCAATTGATAAACACTCATA
66 TACTACAACAACGCACTCTGTACTTACACACGATATCAAATCGCACCAATTGATAAACACTCATA
*
3938069 CTAAAACAACCAAAACAATCAATCCTTGTAACTAAGGAAAACTAGCCCTTGATTTGAGTATCCGA
131 CTAAAAAAACCAAAACAATCAATCCTTGTAACTAAGGAAAACTAGCCCTTGATTTGAGTATCCGA
3938134 CCACTTACCCTTAATAAAAGGGAAACCTTTAACATCACTTAACTCGCCGAAGAATTTTTTGTTCC
196 CCACTTACCCTTAATAAAAGGGAAACCTTTAACATCACTTAACTCGCCGAAGAATTTTTTGTTCC
*
3938199 ACGATGATCACCTAACAAGATCGCAAATAATTTATCAAAATCGATTTCACCCAAAACATTCTACA
261 ACGATGATCACCTAACAAGACCGCAAATAATTTATCAAAATCGATTTCACCCAAAACATTCTACA
3938264 CAAACACTTACCTCTAGAATTTTCATGAA
326 CAAACACTTACCTCTAGAATTTTCATGAA
3938293 ATTTT-GTGACTGTTTTCAGTATTTTTGGGTTAGAACATACACCTTAATGCCTCTGGAATATCAG
1 ATTTTCGTGACTGTTTTCAGTATTTTTGGGTTAGAACATACACCTTAATGCCTCTGGAATATCAG
*
3938357 TACTACAACAACGCACTCTGTACTTACACACGATATCAAATTGCACCAATTGATAAACACTCATA
66 TACTACAACAACGCACTCTGTACTTACACACGATATCAAATCGCACCAATTGATAAACACTCATA
3938422 CTAAAAAAACCAAAACAATCAATCCTTGTAACTAAGGAAAACTAGCCCTTGATTTGAGTATCCGA
131 CTAAAAAAACCAAAACAATCAATCCTTGTAACTAAGGAAAACTAGCCCTTGATTTGAGTATCCGA
3938487 CCACTTACCCTTAATAAAAGGGAAACCTTTAACATCACTTAACTCGCCGAAGAATTTTTTGTTCC
196 CCACTTACCCTTAATAAAAGGGAAACCTTTAACATCACTTAACTCGCCGAAGAATTTTTTGTTCC
3938552 ACGATGATCACCTAACAAGACCGCAAATAATTTATCAAAATCGATTTCACCCAAAACATTCTACA
261 ACGATGATCACCTAACAAGACCGCAAATAATTTATCAAAATCGATTTCACCCAAAACATTCTACA
3938617 CAAACACTTACCTC
326 CAAACACTTACCTC
3938631 CACAAGAAAA
Statistics
Matches: 334, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
353 329 0.99
354 5 0.01
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.28
Consensus pattern (354 bp):
ATTTTCGTGACTGTTTTCAGTATTTTTGGGTTAGAACATACACCTTAATGCCTCTGGAATATCAG
TACTACAACAACGCACTCTGTACTTACACACGATATCAAATCGCACCAATTGATAAACACTCATA
CTAAAAAAACCAAAACAATCAATCCTTGTAACTAAGGAAAACTAGCCCTTGATTTGAGTATCCGA
CCACTTACCCTTAATAAAAGGGAAACCTTTAACATCACTTAACTCGCCGAAGAATTTTTTGTTCC
ACGATGATCACCTAACAAGACCGCAAATAATTTATCAAAATCGATTTCACCCAAAACATTCTACA
CAAACACTTACCTCTAGAATTTTCATGAA
Found at i:3940202 original size:18 final size:18
Alignment explanation
Indices: 3940179--3940225 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
3940169 TGAGATGGCC
3940179 TAATACAATCAAAGTTTA
1 TAATACAATCAAAGTTTA
3940197 TAATACAATCAAAGTTTA
1 TAATACAATCAAAGTTTA
*
3940215 TAAAACAATCA
1 TAATACAATCA
3940226 TTTAAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (18 bp):
TAATACAATCAAAGTTTA
Found at i:3951698 original size:30 final size:30
Alignment explanation
Indices: 3951662--3951809 Score: 255
Period size: 30 Copynumber: 5.0 Consensus size: 30
3951652 TTTTGTATAC
*
3951662 TGCCGAATTGATTTGTATATGAATATACAT
1 TGCCGAATTGATTTGTATATGGATATACAT
3951692 TGCCGAATTGATTTGTATATGGATATACAT
1 TGCCGAATTGATTTGTATATGGATATACAT
*
3951722 TGCCAAATTGATTTGTATATGGATATACAT
1 TGCCGAATTGATTTGTATATGGATATACAT
3951752 TGCCGAATTGATTTGTATATGGATATACAT
1 TGCCGAATTGATTTGTATATGGATATACAT
*
3951782 TACCGAATTGATTTGTATAT-G-TATACAT
1 TGCCGAATTGATTTGTATATGGATATACAT
3951810 ATATATTGTC
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
28 7 0.06
29 1 0.01
30 106 0.93
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (30 bp):
TGCCGAATTGATTTGTATATGGATATACAT
Found at i:3958812 original size:30 final size:30
Alignment explanation
Indices: 3958765--3958891 Score: 173
Period size: 30 Copynumber: 4.2 Consensus size: 30
3958755 GTATATGTTT
* *
3958765 TATATATTGCTGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * *
3958795 TATACATTACCGAATTGATTTTTATATTGA
1 TATACATTGCCGAATTGATTTGTATATGGA
3958825 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * * *
3958855 CATACATTGCCAAATTAATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
3958885 TATACAT
1 TATACAT
3958892 ATATATTGCC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:3965839 original size:18 final size:18
Alignment explanation
Indices: 3965816--3965850 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3965806 GTTTTCGAAA
3965816 AATGAAAATGGAAATGAG
1 AATGAAAATGGAAATGAG
3965834 AATGAAAATGGAAATGA
1 AATGAAAATGGAAATGA
3965851 TCCATTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (18 bp):
AATGAAAATGGAAATGAG
Found at i:3966795 original size:22 final size:21
Alignment explanation
Indices: 3966770--3966810 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3966760 CCAACTGTAA
3966770 TGGGGGTCGCAACACCAAAACT
1 TGGGGGTCGCAACA-CAAAACT
* *
3966792 TGGGTGTTGCAACACAAAA
1 TGGGGGTCGCAACACAAAA
3966811 GGCTAATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (21 bp):
TGGGGGTCGCAACACAAAACT
Found at i:3969321 original size:58 final size:59
Alignment explanation
Indices: 3969202--3969336 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 59
3969192 GATACATGGC
* * * ***
3969202 GTAAGGCCATAGATGAAA-TATGCCATGGTAGCATGGTATGAGGTAAAAGGTATATGGT
1 GTAAGACCATAGATGAAAGTATGCCATGGTAGCATGGTATAAGGTAAAAGGTAAACAAT
* * *
3969260 GTAAGACCATGGATGAAAGT-TGCCATGGTGGCATGGTATAAGGTATAAGGTAAACAAT
1 GTAAGACCATAGATGAAAGTATGCCATGGTAGCATGGTATAAGGTAAAAGGTAAACAAT
*
3969318 GTAAGACCATAAATGAAAG
1 GTAAGACCATAGATGAAAG
3969337 ACGCTATGGC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 64 0.98
59 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (59 bp):
GTAAGACCATAGATGAAAGTATGCCATGGTAGCATGGTATAAGGTAAAAGGTAAACAAT
Found at i:3977044 original size:21 final size:21
Alignment explanation
Indices: 3977010--3977049 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3977000 TAATTTCCTC
*
3977010 GTCCTTTCTCTTCTTCATTTT
1 GTCCTTTCTCTTCTCCATTTT
* *
3977031 GTCCTTTTTTTTCTCCATT
1 GTCCTTTCTCTTCTCCATT
3977050 GTCTACTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (21 bp):
GTCCTTTCTCTTCTCCATTTT
Found at i:3980288 original size:168 final size:168
Alignment explanation
Indices: 3980010--3980350 Score: 655
Period size: 168 Copynumber: 2.0 Consensus size: 168
3980000 TTTGGCAGTT
3980010 TTATTGCAATTCTAACGGTATACCCTCAATATATATATGGTAGCAACATAGCTGCAAATTTTTTG
1 TTATTGCAATTCTAACGGTATACCCTCAATATATATATGGTAGCAACATAGCTGCAAATTTTTTG
3980075 AATGGCATATGACCATATTCTGGTGTAATGGATGGATGGGTTCTTGTAATCCGAATTGATGTGAT
66 AATGGCATATGACCATATTCTGGTGTAATGGATGGATGGGTTCTTGTAATCCGAATTGATGTGAT
3980140 TGGTTGGATGGAGTGGTGTGTAGCAGATAGGGGTAGGA
131 TGGTTGGATGGAGTGGTGTGTAGCAGATAGGGGTAGGA
* *
3980178 TTATTGCCATTCTAATGGTATACCCTCAATATATATATGGTAGCAACATAGCTGCAAATTTTTTG
1 TTATTGCAATTCTAACGGTATACCCTCAATATATATATGGTAGCAACATAGCTGCAAATTTTTTG
*
3980243 AATGGCATATGACCATATTCTGGTGTAATGGATGGATGGGTTCTTGTAATCCTAATTGATGTGAT
66 AATGGCATATGACCATATTCTGGTGTAATGGATGGATGGGTTCTTGTAATCCGAATTGATGTGAT
3980308 TGGTTGGATGGAGTGGTGTGTAGCAGATAGGGGTAGGA
131 TGGTTGGATGGAGTGGTGTGTAGCAGATAGGGGTAGGA
3980346 TTATT
1 TTATT
3980351 CTTTTTATGA
Statistics
Matches: 170, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 170 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (168 bp):
TTATTGCAATTCTAACGGTATACCCTCAATATATATATGGTAGCAACATAGCTGCAAATTTTTTG
AATGGCATATGACCATATTCTGGTGTAATGGATGGATGGGTTCTTGTAATCCGAATTGATGTGAT
TGGTTGGATGGAGTGGTGTGTAGCAGATAGGGGTAGGA
Found at i:3995864 original size:35 final size:35
Alignment explanation
Indices: 3995822--3995891 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3995812 CTAAAGAGTA
3995822 TGAGAAGAAACAACAATCACAATAAGTTCTTAGAG
1 TGAGAAGAAACAACAATCACAATAAGTTCTTAGAG
3995857 TGAGAAGAAACAACAATCACAATAAGTTCTTAGAG
1 TGAGAAGAAACAACAATCACAATAAGTTCTTAGAG
3995892 AGGGGATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (35 bp):
TGAGAAGAAACAACAATCACAATAAGTTCTTAGAG
Found at i:4000617 original size:20 final size:22
Alignment explanation
Indices: 4000589--4000628 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
4000579 TTTATTTAAC
*
4000589 AATTTAAAT-ATAA-TAAAAAA
1 AATTCAAATCATAATTAAAAAA
4000609 AATTCAAATCATAATTAAAA
1 AATTCAAATCATAATTAAAA
4000629 CATTTATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTCAAATCATAATTAAAAAA
Found at i:4006060 original size:24 final size:24
Alignment explanation
Indices: 4006021--4006084 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
4006011 AAGCAAGCCA
*
4006021 ATTTTATTTTTA-TTTTGTTATAT
1 ATTTTATTTTTATTTTTATTATAT
* *
4006044 ATTTTATTTTTATTTTTATTTTCT
1 ATTTTATTTTTATTTTTATTATAT
4006068 ATTTTATTCTTTATTTT
1 ATTTTATT-TTTATTTT
4006085 CTTGCTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 12 0.33
24 16 0.44
25 8 0.22
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.77
Consensus pattern (24 bp):
ATTTTATTTTTATTTTTATTATAT
Found at i:4006070 original size:7 final size:6
Alignment explanation
Indices: 4006022--4006084 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
4006012 AGCAAGCCAA
* *
4006022 TTTTAT TTTTA- TTTT-G TTATAT ATTTTAT TTTTAT TTTTAT TTTCTA-
1 TTTTAT TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTT-TAT
4006069 TTTTAT TCTTTAT TTT
1 TTTTAT T-TTTAT TTT
4006085 CTTGCTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
5 9 0.19
6 26 0.54
7 13 0.27
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:4006072 original size:19 final size:19
Alignment explanation
Indices: 4006025--4006086 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
4006015 AAGCCAATTT
*
4006025 TATTTTTATTTTGTTATATATTT
1 TATTTTTA-TTT-TTAT-T-TTC
4006048 TATTTTTATTTTTATTTTC
1 TATTTTTATTTTTATTTTC
4006067 TA-TTTTATTCTTTATTTTC
1 TATTTTTATT-TTTATTTTC
4006086 T
1 T
4006087 TGCTTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 7 0.19
19 14 0.38
20 1 0.03
21 4 0.11
22 3 0.08
23 8 0.22
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.76
Consensus pattern (19 bp):
TATTTTTATTTTTATTTTC
Found at i:4006714 original size:5 final size:5
Alignment explanation
Indices: 4006704--4006758 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
4006694 GTTTCATTAA
4006704 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
4006754 AAAAT
1 AAAAT
4006759 CTAATGATTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:4007097 original size:105 final size:105
Alignment explanation
Indices: 4006906--4007097 Score: 255
Period size: 105 Copynumber: 1.8 Consensus size: 105
4006896 ACAAAAAAAA
* *
4006906 AGTGTGTTAGGCTGAATAACCTGGGTAGGGTGCTTGGGTTGTTATCCCACTTTCCGTCAAAAGGG
1 AGTGTGTTAGGCTGAATAACCTGGGTAGGGTGCTTGAGTTGTCATCCCACTTTCCGTCAAAAGGG
*
4006971 CCAAAACATTCTTAACCAAAAATTATAATAATAAAATAGG
66 CCAAAACATTCTTAACAAAAAATTATAATAATAAAATAGG
* * * *
4007011 AGTGTGTTGGGCTGAGTAA-CTGAGGT-GTGGTGTTTGAGTTGTCATCCCTC-TTCGCGTCAAAA
1 AGTGTGTTAGGCTGAATAACCTG-GGTAG-GGTGCTTGAGTTGTCATCCCACTTTC-CGTCAAAA
* *
4007073 GGGCCAATACATTCTTAAGAAAAAA
63 GGGCCAAAACATTCTTAACAAAAAA
4007098 AAACAAAAAC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
104 7 0.09
105 68 0.91
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (105 bp):
AGTGTGTTAGGCTGAATAACCTGGGTAGGGTGCTTGAGTTGTCATCCCACTTTCCGTCAAAAGGG
CCAAAACATTCTTAACAAAAAATTATAATAATAAAATAGG
Found at i:4008700 original size:19 final size:19
Alignment explanation
Indices: 4008673--4008710 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4008663 TTTCTTATGG
*
4008673 ATAGCTTATTTTTTGTGCT
1 ATAGCTTATTTTTGGTGCT
*
4008692 ATAGGTTATTTTTGGTGCT
1 ATAGCTTATTTTTGGTGCT
4008711 TTCAATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.08, G:0.21, T:0.55
Consensus pattern (19 bp):
ATAGCTTATTTTTGGTGCT
Found at i:4009135 original size:17 final size:16
Alignment explanation
Indices: 4009115--4009153 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
4009105 AATGATAGGC
4009115 AAAAAAGAAAATAAAG
1 AAAAAAGAAAATAAAG
*
4009131 TAAAATAGAAAATAAAG
1 -AAAAAAGAAAATAAAG
4009148 AAAAAA
1 AAAAAA
4009154 ACCAATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAGAAAATAAAG
Found at i:4012273 original size:16 final size:17
Alignment explanation
Indices: 4012253--4012611 Score: 120
Period size: 18 Copynumber: 21.0 Consensus size: 17
4012243 ACGAAAGTTT
*
4012253 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
4012270 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
4012288 TTTGT-AAACACGAAAA
1 TTTTTAAAACACGAAAA
*
4012304 -TTTTAGAAACGCGAAAA
1 TTTTTA-AAACACGAAAA
4012321 TTTTTAGAAGA-ACGAAAA
1 TTTTTA-AA-ACACGAAAA
**
4012339 TTTTTAAAACACGACATTT
1 TTTTTAAAACACGA-A-AA
*
4012358 TTTTTGAAACACG---A
1 TTTTTAAAACACGAAAA
*
4012372 --TTTAAAAAAC-AAAA
1 TTTTTAAAACACGAAAA
** * ** *
4012386 --AATGAAATGCGAGAA
1 TTTTTAAAACACGAAAA
* **
4012401 TATTTTGAAACACGAATT
1 T-TTTTAAAACACGAAAA
* * *
4012419 TTTTTTAAACGCGAGAA
1 TTTTTAAAACACGAAAA
*
4012436 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAAAA
* * * *
4012454 -CTTTGAAACACCG-GAG
1 TTTTTAAAACA-CGAAAA
*
4012470 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
* *
4012488 TTTGTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
* **
4012505 TTTGTGAAAACACGTAATTTT
1 TTT-TTAAAACACG-AA--AA
4012526 TTTTTAAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* * *
4012544 TTTTTGAAACGCCG-GAA
1 TTTTTAAAAC-ACGAAAA
*
4012561 TTTTTGAAAACAC--AGA
1 TTTTT-AAAACACGAAAA
*
4012577 TTTTTAAAACACGAAAC
1 TTTTTAAAACACGAAAA
4012594 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
4012612 CACAAAATTT
Statistics
Matches: 250, Mismatches: 62, Indels: 59
0.67 0.17 0.16
Matches are distributed among these distances:
12 8 0.03
14 6 0.02
15 13 0.05
16 23 0.09
17 77 0.31
18 94 0.38
19 15 0.06
20 3 0.01
21 11 0.04
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:4012447 original size:35 final size:34
Alignment explanation
Indices: 4012395--4012608 Score: 134
Period size: 35 Copynumber: 6.1 Consensus size: 34
4012385 AAATGAAATG
* * *
4012395 CGAGAATATTTTG-AAACACGAATTTTTTTTAAACG
1 CGAGAAT-TTTTGAAAACACGAA-ATTTTTGAAACA
* **
4012430 CGAGAATTTTTGAAAACATGAAAACTTTGAAACA
1 CGAGAATTTTTGAAAACACGAAATTTTTGAAACA
* *
4012464 CCG-GAGTTTTTGAAAACACGAGAATTTGTGAAACA
1 -CGAGAATTTTTGAAAACACGA-AATTTTTGAAACA
* * * *
4012499 CGAAAATTTGTGAAAACACGTAATTTTTTTTTAAAAACA
1 CGAGAATTTTTGAAAACACG-AA---ATTTTT-GAAACA
* * *
4012538 CGAAAATTTTTG-AAACGCCGGAATTTTTGAAAACA
1 CGAGAATTTTTGAAAAC-ACGAAATTTTTG-AAACA
4012573 C-AG-ATTTTT-AAAACACGAAACTTTTTGAAAACA
1 CGAGAATTTTTGAAAACACGAAA-TTTTTG-AAACA
4012606 CGA
1 CGA
4012609 AAACACAAAA
Statistics
Matches: 140, Mismatches: 25, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
32 4 0.03
33 23 0.16
34 32 0.23
35 53 0.38
36 1 0.01
38 9 0.06
39 18 0.13
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (34 bp):
CGAGAATTTTTGAAAACACGAAATTTTTGAAACA
Found at i:4012784 original size:17 final size:17
Alignment explanation
Indices: 4012762--4012800 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4012752 TATTATTATT
4012762 ATTTTGAA-ACACGAGAA
1 ATTTTGAAGACACGA-AA
*
4012779 ATTTTGAAGACATGAAA
1 ATTTTGAAGACACGAAA
4012796 ATTTT
1 ATTTT
4012801 TTAAAAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTTTGAAGACACGAAA
Found at i:4013443 original size:28 final size:32
Alignment explanation
Indices: 4013411--4013480 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
4013401 GTTTTTATAT
4013411 TTTTTTCTTT-AT-TTTATCTTT-TTCTC-TC
1 TTTTTTCTTTCATCTTTATCTTTCTTCTCTTC
* * *
4013439 TTTTTCCTTTCATCTTTCTGTTTCTTCTCTTC
1 TTTTTTCTTTCATCTTTATCTTTCTTCTCTTC
4013471 TTTTTTCTTT
1 TTTTTTCTTT
4013481 TCAGTTACCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 9 0.26
29 2 0.06
30 7 0.21
31 5 0.15
32 11 0.32
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.73
Consensus pattern (32 bp):
TTTTTTCTTTCATCTTTATCTTTCTTCTCTTC
Found at i:4014139 original size:29 final size:30
Alignment explanation
Indices: 4014052--4014188 Score: 124
Period size: 29 Copynumber: 4.7 Consensus size: 30
4014042 AAATATGGGC
* * *
4014052 CAAAATGTAATTTCTTA-AGAGTTTAGGGGT
1 CAAAATGTAAATT-TTAGAAAGTTTAAGGGT
* * *
4014082 CAAAGTG-CAATTTTGAGAAAGTCTAAGGGT
1 CAAAATGTAAATTTT-AGAAAGTTTAAGGGT
** *
4014112 TGAAATGT-AATTTTAGAAAGTTTTAGGGT
1 CAAAATGTAAATTTTAGAAAGTTTAAGGGT
4014141 CAAAATGTAAATTTTAGAAAAGTTT--GGGT
1 CAAAATGTAAATTTTAG-AAAGTTTAAGGGT
4014170 CAAAATGTAAATTTT-GAAA
1 CAAAATGTAAATTTTAGAAA
4014189 AGTACAGGGG
Statistics
Matches: 89, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
27 3 0.03
28 3 0.03
29 42 0.47
30 34 0.38
31 7 0.08
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (30 bp):
CAAAATGTAAATTTTAGAAAGTTTAAGGGT
Found at i:4014575 original size:74 final size:76
Alignment explanation
Indices: 4014403--4014714 Score: 334
Period size: 77 Copynumber: 4.1 Consensus size: 76
4014393 CTCGGCGTGC
* * * * ** * * *
4014403 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCCTCGAAAAACAAAAATCT---A-AA
1 GACCCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
*
4014464 ATACCTCGACATGT
65 ATACCTCGGCA--T
* * *
4014478 GCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATG-AA-TT-GAA-A
1 GACCCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACA-GAAATTTAAAAGA
**
4014539 AATACCTCGGTGT
64 AATACCTCGGCAT
*
4014552 GACCCGAGGCTCAACTCATCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
4014617 ATACCTCGGCAT
65 ATACCTCGGCAT
** *
4014629 GGTCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
4014694 ATACCTCGGCAT
65 ATACCTCGGCAT
4014706 GACCCGAGG
1 GACCCGAGG
4014715 TATTTTCTTT
Statistics
Matches: 201, Mismatches: 28, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
73 1 0.00
74 51 0.25
75 46 0.23
76 14 0.07
77 89 0.44
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (76 bp):
GACCCGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAA
TACCTCGGCAT
Found at i:4014678 original size:151 final size:152
Alignment explanation
Indices: 4014403--4014714 Score: 384
Period size: 149 Copynumber: 2.1 Consensus size: 152
4014393 CTCGGCGTGC
* * *
4014403 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCCTCGAAAAACAAAAATCTAAAATAC
1 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATCCTCGAAAAACAAAAATCTAAAATAC
*
4014468 CTCGACATGTGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATG-A
66 CTCGACATGTGCCCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACA-GAA
* **
4014532 A-TT-GAA-AAATACCTCGGTGT
130 ATTTAAAAGAAATACCTCGGCAT
* ** * * *
4014552 GACCCGAGGCTCAACTCATCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATCCTCGAAAAACAAAAATCT---A-AA
* * * *
4014617 ATACCTCGGCATG-G-TCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACA
62 ATACCTCGACATGTGCCCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACA
4014680 GAAATTTAAAAGAAATACCTCGGCAT
127 GAAATTTAAAAGAAATACCTCGGCAT
4014706 GACCCGAGG
1 GACCCGAGG
4014715 TATTTTCTTT
Statistics
Matches: 138, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
149 49 0.36
150 1 0.01
151 47 0.34
152 4 0.03
153 16 0.12
154 21 0.15
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (152 bp):
GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATCCTCGAAAAACAAAAATCTAAAATAC
CTCGACATGTGCCCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAGAAA
TTTAAAAGAAATACCTCGGCAT
Found at i:4015691 original size:1 final size:1
Alignment explanation
Indices: 4015680--4015762 Score: 58
Period size: 1 Copynumber: 83.0 Consensus size: 1
4015670 TTCATCTTGA
* * ** * * * * * *
4015680 TTTTTTCTTTTTTTTTGTTTTTTCCTTTTTTGTTTTGTTTTTTTCTATTTTTTTTGTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
4015745 TATTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTT
4015763 AAGCATAATA
Statistics
Matches: 60, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:4015702 original size:19 final size:19
Alignment explanation
Indices: 4015680--4015762 Score: 107
Period size: 20 Copynumber: 4.3 Consensus size: 19
4015670 TTCATCTTGA
4015680 TTTTTTCTTTTTTTTTG-T
1 TTTTTTCTTTTTTTTTGTT
*
4015698 TTTTTCCTTTTTTGTTT-TGT
1 TTTTTTCTTTTTT-TTTGT-T
4015718 TTTTTTCTATTTTTTTTGTT
1 TTTTTTCT-TTTTTTTTGTT
*
4015738 TTTTTTCTATTTTTTTGTT
1 TTTTTTCTTTTTTTTTGTT
4015757 TTTTTT
1 TTTTTT
4015763 AAGCATAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
18 12 0.21
19 19 0.33
20 20 0.35
21 6 0.11
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.86
Consensus pattern (19 bp):
TTTTTTCTTTTTTTTTGTT
Found at i:4015710 original size:20 final size:19
Alignment explanation
Indices: 4015687--4015760 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
4015677 TGATTTTTTC
4015687 TTTTTTTTTGTTTTTTCCTT
1 TTTTTTTTTGTTTTTT-CTT
*
4015707 TTTTGTTTTGTTTTTT-TCT
1 TTTTTTTTTGTTTTTTCT-T
*
4015726 ATTTTTTTTGTTTTTT-TT
1 TTTTTTTTTGTTTTTTCTT
*
4015744 CTATTTTTTTGTTTTTT
1 -TTTTTTTTTGTTTTTT
4015761 TTAAGCATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.04
19 30 0.64
20 15 0.32
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTCTT
Found at i:4022032 original size:90 final size:89
Alignment explanation
Indices: 4021902--4022074 Score: 240
Period size: 90 Copynumber: 1.9 Consensus size: 89
4021892 AACGCGAGAA
* * * * *
4021902 TTTTTGAAAACATGAAAACTTTGAAACACCGGAGTTTTTGAAAACACG-AGAATTTGTGAAACAC
1 TTTTTAAAAACACGAAAACTTTGAAACACCGGAATATTTGAAAACACGAAG-ATTTGTAAAACAC
4021966 GAAAATTTGTGAAAACACGTAATTT
65 GAAAATTTGTGAAAACACGTAATTT
* * *
4021991 TTTTTAAAAACACGAAAATTTTTGAAACGCCGGAATATTTGAAAACACGAAGATTTTTAAAACAC
1 TTTTTAAAAACACGAAAA-CTTTGAAACACCGGAATATTTGAAAACACGAAGATTTGTAAAACAC
*
4022056 GAAAATTTTTGAAAACACG
65 GAAAATTTGTGAAAACACG
4022075 AAAACACAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
89 16 0.22
90 55 0.75
91 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (89 bp):
TTTTTAAAAACACGAAAACTTTGAAACACCGGAATATTTGAAAACACGAAGATTTGTAAAACACG
AAAATTTGTGAAAACACGTAATTT
Found at i:4022076 original size:35 final size:35
Alignment explanation
Indices: 4021718--4022078 Score: 141
Period size: 35 Copynumber: 10.5 Consensus size: 35
4021708 AACGAAAGTT
* * * *
4021718 TTTTTTAAAACACGAGAATTTTTGAAAACATGAGAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAAA
* *
4021754 --TTTGTAAACACGAAAA-TTTTAGAAACGCGAAAA
1 TTTTTGAAAACACGAAAATTTTTA-AAACACGAAAA
* **
4021787 TTTTTAGAAGA-ACGAAAATTTTTAAAACACGACATTT
1 TTTTT-GAAAACACGAAAATTTTTAAAACACGA-A-AA
*
4021824 TTTTTG-AAACACG---A--TTTAAAAAAC-AAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
** ** * * *
4021852 -AATT--AAATGCGAGAATATTTTGAAACACG-AAT
1 TTTTTGAAAACACGAAAAT-TTTTAAAACACGAAAA
** * * *
4021884 TTTTTTTAAACGCGAGAATTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAAA
* * * *
4021920 -CTTTG-AAACACCG-GAGTTTTTGAAAACACGAGAA
1 TTTTTGAAAACA-CGAAAATTTTT-AAAACACGAAAA
* * **
4021954 TTTGTG-AAACACGAAAATTTGTGAAAACACGTAATTT
1 TTTTTGAAAACACGAAAATTT-TTAAAACACG-AA-AA
* * * *
4021991 TTTTTAAAAACACGAAAATTTTTGAAACGCCG-GAA
1 TTTTTGAAAACACGAAAATTTTTAAAAC-ACGAAAA
* *
4022026 TATTTGAAAACACGAAGATTTTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
4022061 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
4022079 CACAAAATTT
Statistics
Matches: 238, Mismatches: 58, Indels: 59
0.67 0.16 0.17
Matches are distributed among these distances:
26 5 0.02
27 2 0.01
29 2 0.01
30 1 0.00
31 9 0.04
32 11 0.05
33 15 0.06
34 43 0.18
35 103 0.43
36 17 0.07
37 14 0.06
38 16 0.07
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
Found at i:4022078 original size:18 final size:18
Alignment explanation
Indices: 4021718--4022078 Score: 160
Period size: 18 Copynumber: 21.0 Consensus size: 18
4021708 AACGAAAGTT
* *
4021718 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
4021736 TTTTTGAAAACATGAGAA
1 TTTTTGAAAACACGAAAA
*
4021754 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
4021770 TTTTAG-AAACGCGAAAA
1 TTTTTGAAAACACGAAAA
*
4021787 TTTTTAGAAGA-ACGAAAA
1 TTTTT-GAAAACACGAAAA
**
4021805 TTTTT-AAAACACGACATTT
1 TTTTTGAAAACACGA-A-AA
4021824 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
4021838 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
** ** *
4021852 -AATT--AAATGCGAGAA
1 TTTTTGAAAACACGAAAA
*
4021867 TATTTTG-AAACACG-AAT
1 T-TTTTGAAAACACGAAAA
** * *
4021884 TTTTTTTAAACGCGAGAA
1 TTTTTGAAAACACGAAAA
*
4021902 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
4021920 -CTTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
4021936 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
4021954 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
4021971 TTTGTGAAAACACGTAATTT
1 TTTTTGAAAACACG-AA-AA
*
4021991 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
4022009 TTTTTG-AAACGCCG-GAA
1 TTTTTGAAAAC-ACGAAAA
* *
4022026 TATTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
4022044 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
4022061 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
4022079 CACAAAATTT
Statistics
Matches: 256, Mismatches: 57, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
12 8 0.03
14 5 0.02
15 5 0.02
16 26 0.10
17 84 0.33
18 98 0.38
19 18 0.07
20 12 0.05
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:4022174 original size:18 final size:19
Alignment explanation
Indices: 4022151--4022186 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4022141 AGAATTTTTT
4022151 ATTTTTTTG-AAACACGAG
1 ATTTTTTTGAAAACACGAG
4022169 ATTTTTTTGAAAACACGA
1 ATTTTTTTGAAAACACGA
4022187 AAACACGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (19 bp):
ATTTTTTTGAAAACACGAG
Found at i:4022251 original size:17 final size:17
Alignment explanation
Indices: 4022231--4022269 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4022221 TATTATTATT
4022231 ATTTTGAA-ACACGAGAA
1 ATTTTGAAGACACGA-AA
*
4022248 ATTTTGAAGACATGAAA
1 ATTTTGAAGACACGAAA
4022265 ATTTT
1 ATTTT
4022270 TTAAAAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTTTGAAGACACGAAA
Found at i:4022912 original size:28 final size:32
Alignment explanation
Indices: 4022880--4022949 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
4022870 GTTTTTATAT
4022880 TTTTTTCTTT-AT-TTTATCTTT-TTCTC-TC
1 TTTTTTCTTTCATCTTTATCTTTCTTCTCTTC
* * *
4022908 TTTTTCCTTTCATCTTTCTGTTTCTTCTCTTC
1 TTTTTTCTTTCATCTTTATCTTTCTTCTCTTC
4022940 TTTTTTCTTT
1 TTTTTTCTTT
4022950 TCAGTTACCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 9 0.26
29 2 0.06
30 7 0.21
31 5 0.15
32 11 0.32
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.73
Consensus pattern (32 bp):
TTTTTTCTTTCATCTTTATCTTTCTTCTCTTC
Found at i:4023622 original size:30 final size:30
Alignment explanation
Indices: 4023582--4023660 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
4023572 CTAAGGGTTG
**
4023582 AAATGT-AATTTTAGAAATTTTTGGGGTCA
1 AAATGTAAATTTTAGAAAAGTTTGGGGTCA
4023611 AAATGTAAATTTTAGAAAAGTTTGGGGTCA
1 AAATGTAAATTTTAGAAAAGTTTGGGGTCA
4023641 AAATGTAAATTTT-GAAAAGT
1 AAATGTAAATTTTAGAAAAGT
4023661 ACAGGGGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 13 0.28
30 34 0.72
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.37
Consensus pattern (30 bp):
AAATGTAAATTTTAGAAAAGTTTGGGGTCA
Found at i:4023668 original size:30 final size:30
Alignment explanation
Indices: 4023582--4023675 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
4023572 CTAAGGGTTG
** **
4023582 AAATGT-AATTTTAGAAATTTTTGGGGTCA
1 AAATGTAAATTTTAGAAAAGTCAGGGGTCA
**
4023611 AAATGTAAATTTTAGAAAAGTTTGGGGTCA
1 AAATGTAAATTTTAGAAAAGTCAGGGGTCA
*
4023641 AAATGTAAATTTT-GAAAAGTACAGGGGTTA
1 AAATGTAAATTTTAGAAAAGT-CAGGGGTCA
4023671 AAATG
1 AAATG
4023676 CAAAAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
29 13 0.22
30 45 0.78
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
AAATGTAAATTTTAGAAAAGTCAGGGGTCA
Found at i:4024982 original size:48 final size:50
Alignment explanation
Indices: 4024886--4025044 Score: 125
Period size: 48 Copynumber: 3.2 Consensus size: 50
4024876 ATTTGGGCTG
* * ** * * *
4024886 TATAACGGGAAGCTCAC-AAGAGCCATATTCAGGAAGCTCC-AGATAGCCA
1 TATATCGGGAAGCTAACAAAGAGCTTTAATCGGGAAGCTCCGA-AGAGCCA
*
4024935 TATATCGGGAAG-T-TCAAACGAG--TTATATCGGGAAGCTCCGAAGAGCCA
1 TATATCGGGAAGCTAACAAA-GAGCTTTA-ATCGGGAAGCTCCGAAGAGCCA
**
4024983 T-TAATTAGGAAGCTAACAAAGAGCCTTTAATCGGGAAGCTCACGAAGAGCCA
1 TAT-ATCGGGAAGCTAACAAAGAG-CTTTAATCGGGAAGCTC-CGAAGAGCCA
4025035 TATATCGGGA
1 TATATCGGGA
4025045 CGCTCATAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
47 4 0.05
48 28 0.32
49 19 0.22
50 4 0.05
51 12 0.14
52 19 0.22
53 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (50 bp):
TATATCGGGAAGCTAACAAAGAGCTTTAATCGGGAAGCTCCGAAGAGCCA
Found at i:4025041 original size:26 final size:25
Alignment explanation
Indices: 4024886--4025057 Score: 126
Period size: 26 Copynumber: 6.9 Consensus size: 25
4024876 ATTTGGGCTG
*
4024886 TATAACGGGAAGCTCACAAGAGCCA
1 TATATCGGGAAGCTCACAAGAGCCA
* *
4024911 TAT-TCAGGAAGCTC-CAGATAGCCA
1 TATATCGGGAAGCTCACA-AGAGCCA
* *
4024935 TATATCGGGAAGTTCA-AACGAG--T
1 TATATCGGGAAGCTCACAA-GAGCCA
4024958 TATATCGGGAAGCTC-CGAAGAGCCA
1 TATATCGGGAAGCTCAC-AAGAGCCA
** *
4024983 T-TAATTAGGAAGCTAACAAAGAGCC-
1 TAT-ATCGGGAAGCTCAC-AAGAGCCA
*
4025008 TTTAATCGGGAAGCTCACGAAGAGCCA
1 TAT-ATCGGGAAGCTCAC-AAGAGCCA
* *
4025035 TATATCGGGACGCTCATAAGAGC
1 TATATCGGGAAGCTCACAAGAGC
4025058 TGCAGTGTGT
Statistics
Matches: 115, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
23 19 0.17
24 22 0.19
25 32 0.28
26 40 0.35
27 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
TATATCGGGAAGCTCACAAGAGCCA
Found at i:4031983 original size:63 final size:62
Alignment explanation
Indices: 4031897--4032016 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 62
4031887 CACAGCTTGG
* * *
4031897 ACACACGCCAGTGTCTCTGGCCCATGTGAAC-CTAATTCTAGAACAATGAGTTACAAGGCCTAT
1 ACACACGCCAGGGTCTCTGGCCCATGT-AACTCTAATTCCAAAACAATGAGTTA-AAGGCCTAT
* * * *
4031960 ACACACGCCTGGGTCTTTGGCCCATGTTACTCTAATTCCAAAACAGTGAGTTAAAGG
1 ACACACGCCAGGGTCTCTGGCCCATGTAACTCTAATTCCAAAACAATGAGTTAAAGG
4032017 GTTGCCACAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 6 0.12
63 43 0.88
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (62 bp):
ACACACGCCAGGGTCTCTGGCCCATGTAACTCTAATTCCAAAACAATGAGTTAAAGGCCTAT
Found at i:4049029 original size:45 final size:46
Alignment explanation
Indices: 4048954--4049076 Score: 140
Period size: 46 Copynumber: 2.7 Consensus size: 46
4048944 GATTGGAGGG
* * *
4048954 TGCCATGGTGTCTTTCAAACATGGTCTTATTTATTCT-TGACTTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCTGACATGA
* * * * * *
4048999 TGTCATAGTGTCTTTCAACCATGGTTTTATTCATTTTCTGTCATGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCTGACATGA
* *
4049045 TGCCCTAGTGTCTTTCAACTATGGTCTTATTT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTT
4049077 GTTTGATTCG
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
45 31 0.49
46 32 0.51
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCTGACATGA
Found at i:4049142 original size:45 final size:45
Alignment explanation
Indices: 4049054--4049211 Score: 172
Period size: 45 Copynumber: 3.5 Consensus size: 45
4049044 TTGCCCTAGT
* * * * * * *
4049054 GTCTTTCAACTATGGTCTTATTTGTTTGATTCGTTATGCCATAAC
1 GTCTTTCAAATATGGTCTTACTCGATAGAATCGTGATGCCATAAC
** * * *
4049099 GTCTACCAACTATGGTCTTGCTCGATAGAATCGTGATGTCATAAC
1 GTCTTTCAAATATGGTCTTACTCGATAGAATCGTGATGCCATAAC
** * *
4049144 GTCTTTCAGTTATGGTCTTACTCGATGGAATCATGATGCCATAAC
1 GTCTTTCAAATATGGTCTTACTCGATAGAATCGTGATGCCATAAC
4049189 GTCTTTCAAATATGGTCTTACTC
1 GTCTTTCAAATATGGTCTTACTC
4049212 ATTTCTGGTA
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (45 bp):
GTCTTTCAAATATGGTCTTACTCGATAGAATCGTGATGCCATAAC
Found at i:4049238 original size:45 final size:45
Alignment explanation
Indices: 4049189--4049298 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
4049179 ATGCCATAAC
* * * *
4049189 GTCTTTCAAATATGGTCTTACTCATTTCTGGTATGGTGTTATAGT
1 GTCTTTCAACTATGGTCTTACTCATTTCTGGTATAGTGTCATACT
* *
4049234 GTCTTTCAACTATGGTCTTATTTATTTCTGGTATAGTGTCATACT
1 GTCTTTCAACTATGGTCTTACTCATTTCTGGTATAGTGTCATACT
*
4049279 GTTTTTCAACTATGGTCTTA
1 GTCTTTCAACTATGGTCTTA
4049299 ATCAATTCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTACTCATTTCTGGTATAGTGTCATACT
Found at i:4050326 original size:11 final size:11
Alignment explanation
Indices: 4050310--4050341 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
4050300 ATAAAAAATT
4050310 TATTTTAAAAG
1 TATTTTAAAAG
4050321 TATTTTAAAAG
1 TATTTTAAAAG
4050332 TATTTTAAAA
1 TATTTTAAAA
4050342 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAG
Found at i:4053955 original size:16 final size:15
Alignment explanation
Indices: 4053934--4053963 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4053924 TGACTAGCTA
4053934 CTTTTTCTTTATTTTT
1 CTTTTTCTTT-TTTTT
4053950 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
4053964 GGGTTGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:4055670 original size:3 final size:3
Alignment explanation
Indices: 4055664--4055694 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4055654 AATAATACCC
*
4055664 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4055695 CAGCAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:4062439 original size:124 final size:124
Alignment explanation
Indices: 4062219--4062444 Score: 391
Period size: 124 Copynumber: 1.8 Consensus size: 124
4062209 TTATTTTGAG
*
4062219 TTGACGTTTCTGGTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTATG
1 TTGACGTTTCTGGTCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTATG
4062284 AAATCGCGCCCTCATGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCATGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* *
4062343 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTGTACCAAGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTAT
* *
4062407 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
65 GAAATCGCGCCCTCATGGACACGATTTTGCTACAGTAG
4062445 CAAGTTTGGG
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
124 95 0.99
125 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (124 bp):
TTGACGTTTCTGGTCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTATG
AAATCGCGCCCTCATGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:4065568 original size:10 final size:10
Alignment explanation
Indices: 4065553--4065577 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4065543 CAAATCTAAC
4065553 ATTATGTAAA
1 ATTATGTAAA
4065563 ATTATGTAAA
1 ATTATGTAAA
4065573 ATTAT
1 ATTAT
4065578 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:4065655 original size:55 final size:55
Alignment explanation
Indices: 4065561--4065852 Score: 514
Period size: 55 Copynumber: 5.3 Consensus size: 55
4065551 ACATTATGTA
* *
4065561 AAATTATGTAAAATTATTAAG-CCAAAAAAATTTTGTTAATGGTTAGTAAATTTATC
1 AAATTATGTAAAATTATTAAGTCC--AAAAATTGTGTTAATGGTTAGTAAAATTATC
*
4065617 AAATTATGTAAATTTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
4065672 AAATTATGTAAAATTATTAAGTCCGAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
4065727 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAATTTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
4065782 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
4065837 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
4065853 GGTTAGGGTT
Statistics
Matches: 227, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
55 205 0.90
56 20 0.09
57 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:4065897 original size:35 final size:29
Alignment explanation
Indices: 4065847--4065941 Score: 190
Period size: 29 Copynumber: 3.3 Consensus size: 29
4065837 AAATTATGTA
4065847 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
4065876 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
4065905 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
4065934 AAATTAGG
1 AAATTAGG
4065942 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:4066166 original size:71 final size:70
Alignment explanation
Indices: 4066042--4066190 Score: 253
Period size: 71 Copynumber: 2.1 Consensus size: 70
4066032 NNNNNNNNNN
* *
4066042 AAATAATATCAAAATAACTCGAAAACATTCTATGCCTATTATATCAAATAAACTTCTATTTTATT
1 AAATAATATCAAAATAACTCGAAAAAATTCTATGCCTATTACATCAAATAAACTTCTATTTTATT
*
4066107 ACATT
66 ACATC
*
4066112 AAATAATATCAAAATAACTCGAAAAAATTTCTATGCGTATTACATCAAATAAACTTCTATTTTAT
1 AAATAATATCAAAATAACTCGAAAAAA-TTCTATGCCTATTACATCAAATAAACTTCTATTTTAT
4066177 TACATC
65 TACATC
4066183 AAATAATA
1 AAATAATA
4066191 AATTTAAATA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
70 26 0.35
71 48 0.65
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (70 bp):
AAATAATATCAAAATAACTCGAAAAAATTCTATGCCTATTACATCAAATAAACTTCTATTTTATT
ACATC
Found at i:4066619 original size:18 final size:18
Alignment explanation
Indices: 4066592--4066626 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4066582 CGGAAAAGGA
* *
4066592 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
4066610 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
4066627 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:4069931 original size:32 final size:33
Alignment explanation
Indices: 4069894--4069962 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
4069884 GGCCATTGAT
*
4069894 AAAAATAT-AAAAAAATTTAAAATTATTTTAAA
1 AAAAATATAAAAAAAATTAAAAATTATTTTAAA
4069926 AAAAATATAAAAAAAATTAAAAATTATTTTAAA
1 AAAAATATAAAAAAAATTAAAAATTATTTTAAA
4069959 AAAA
1 AAAA
4069963 TGAAATTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (33 bp):
AAAAATATAAAAAAAATTAAAAATTATTTTAAA
Found at i:4070019 original size:51 final size:51
Alignment explanation
Indices: 4069964--4070076 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
4069954 TTAAAAAAAT
* *
4069964 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAA
*
4070015 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAA
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAA
*
4070066 AAAATTGAGAG
1 GAAATTGAGAG
4070077 AATTTTGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAA
Found at i:4070073 original size:22 final size:22
Alignment explanation
Indices: 4070048--4070098 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
4070038 AAATATGGGT
4070048 TTGAGAGAATTTTGGAAA-AAAA
1 TTGAGAGAATTTT-GAAAGAAAA
*
4070070 TTGAGAGAATTTTGAAAGGAAA
1 TTGAGAGAATTTTGAAAGAAAA
4070092 TTGAGAG
1 TTGAGAG
4070099 GATTAGAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGAAAGAAAA
Found at i:4070112 original size:21 final size:22
Alignment explanation
Indices: 4070048--4070113 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
4070038 AAATATGGGT
* *
4070048 TTGAGAGAATTTTGGAAA-AAAA
1 TTGAGAGAA-TTTAGAAAGGAAA
*
4070070 TTGAGAGAATTTTGAAAGGAAA
1 TTGAGAGAATTTAGAAAGGAAA
* *
4070092 TTGAGAGGA-TTAGAGAGGAAA
1 TTGAGAGAATTTAGAAAGGAAA
4070113 T
1 T
4070114 ATTAGATAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (22 bp):
TTGAGAGAATTTAGAAAGGAAA
Found at i:4070499 original size:14 final size:15
Alignment explanation
Indices: 4070480--4070514 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4070470 ATTAAAGTTC
*
4070480 AATTTTTT-TTGTTA
1 AATTTTTTATTGTGA
4070494 AATTTTTTATTGTGA
1 AATTTTTTATTGTGA
4070509 AATTTT
1 AATTTT
4070515 GAAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (15 bp):
AATTTTTTATTGTGA
Found at i:4071598 original size:13 final size:13
Alignment explanation
Indices: 4071582--4071614 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4071572 TCTCAAAAGT
4071582 ACTTTTCCACGTC
1 ACTTTTCCACGTC
4071595 ACTTTTCCACGTC
1 ACTTTTCCACGTC
*
4071608 ATTTTTC
1 ACTTTTC
4071615 AAAAGCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.33, G:0.06, T:0.45
Consensus pattern (13 bp):
ACTTTTCCACGTC
Found at i:4071881 original size:13 final size:13
Alignment explanation
Indices: 4071862--4071933 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
4071852 AAATACTGTG
4071862 GAAAAGTGCTTTT
1 GAAAAGTGCTTTT
* *
4071875 GAGAAGTG-TTGT
1 GAAAAGTGCTTTT
* *
4071887 GAAAAAATACTTTT
1 G-AAAAGTGCTTTT
*
4071901 GAAAAGTGTTTTT
1 GAAAAGTGCTTTT
*
4071914 GAGAAGTGCTTTT
1 GAAAAGTGCTTTT
*
4071927 AAAAAGT
1 GAAAAGT
4071934 TTAGTTTAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (13 bp):
GAAAAGTGCTTTT
Found at i:4071887 original size:26 final size:26
Alignment explanation
Indices: 4071858--4071933 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
4071848 TAAAAAATAC
*
4071858 TGTGGAAAAGTGCTTTTGAGAAGTGT
1 TGTGGAAAAGTGCTTTTGAAAAGTGT
* * *
4071884 TGTGAAAAAATACTTTTGAAAAGTGT
1 TGTGGAAAAGTGCTTTTGAAAAGTGT
* * * *
4071910 TTTTGAGAAGTGCTTTTAAAAAGT
1 TGTGGAAAAGTGCTTTTGAAAAGT
4071934 TTAGTTTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGTGGAAAAGTGCTTTTGAAAAGTGT
Found at i:4071931 original size:39 final size:38
Alignment explanation
Indices: 4071845--4071931 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 38
4071835 ATGATTGTGA
4071845 TTTTAAAAAATACTGTGGAAAAGTGCTTTTGAGAAGTG
1 TTTTAAAAAATACTGTGGAAAAGTGCTTTTGAGAAGTG
* * * *
4071883 TTGTGAAAAAATACTTTTGAAAAGTGTTTTTGAGAAGTG
1 TT-TTAAAAAATACTGTGGAAAAGTGCTTTTGAGAAGTG
4071922 CTTTTAAAAA
1 -TTTTAAAAA
4071932 GTTTAGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.05
39 38 0.90
40 2 0.05
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (38 bp):
TTTTAAAAAATACTGTGGAAAAGTGCTTTTGAGAAGTG
Found at i:4076641 original size:3 final size:3
Alignment explanation
Indices: 4076627--4076661 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4076617 CCCCATTTCT
*
4076627 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4076662 TTCTTCTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4091144 original size:69 final size:68
Alignment explanation
Indices: 4091052--4091348 Score: 217
Period size: 69 Copynumber: 4.4 Consensus size: 68
4091042 TCTATAAGCA
* *
4091052 AAAATATAATGGTATGAATTGTATAAAAATGTTAGCCGAATGTATATATATGTTTTGAATTTTAT
1 AAAATAAAAT-GTATGAATTGTATAAATATGTTAGCCG-ATGTATATATATGTTTTGAATTTTAT
4091117 AAGTT
64 AAGTT
* * * * *
4091122 AAAATAAAATGTATGAATTGTATATATATATGTGT-G-TGTTAGTCA-ATGTAT-ATTTGAGTTT
1 AAAATAAAATGTATGAATTGTATA-A-ATATGT-TAGCCGAT-GT-ATATATATGTTTTGAATTT
4091183 TATAAGTT
61 TATAAGTT
* * * * * ** *
4091191 AAAATAAATTGCA-GAAATTCTATATATAT-TTAGCCGA---ATATATATG--CTGGGTTTTGTA
1 AAAATAAAATGTATG-AATTGTATAAATATGTTAGCCGATGTATATATATGTTTTGAATTTTATA
4091249 AGTT
65 AGTT
* * * * *
4091253 -GAATGAAATTTAATGAA-T-TACATATATGTTAGCCGGATGTATATATATGTTTTGAATTTTAT
1 AAAATAAAATGT-ATGAATTGTATAAATATGTTAGCC-GATGTATATATATGTTTTGAATTTTAT
4091315 AAGTT
64 AAGTT
*
4091320 AAAATAAAATGTATGAATTGTATATATAT
1 AAAATAAAATGTATGAATTGTATAAATAT
4091349 ATATATATAT
Statistics
Matches: 174, Mismatches: 31, Indels: 45
0.70 0.12 0.18
Matches are distributed among these distances:
60 8 0.05
61 13 0.07
62 19 0.11
63 6 0.03
65 10 0.06
66 2 0.01
67 22 0.13
68 10 0.06
69 58 0.33
70 18 0.10
71 7 0.04
72 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.42
Consensus pattern (68 bp):
AAAATAAAATGTATGAATTGTATAAATATGTTAGCCGATGTATATATATGTTTTGAATTTTATAA
GTT
Found at i:4091363 original size:2 final size:2
Alignment explanation
Indices: 4091358--4091386 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4091348 TATATATATA
4091358 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4091387 TAGTCAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4091628 original size:2 final size:2
Alignment explanation
Indices: 4091623--4091649 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4091613 TAAAAAAAAA
4091623 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4091650 ATAATCGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4091918 original size:41 final size:41
Alignment explanation
Indices: 4091873--4092017 Score: 204
Period size: 41 Copynumber: 3.5 Consensus size: 41
4091863 GGCTCGATGC
*
4091873 CTAGCAGGTTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
4091914 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
* * * *
4091955 CTAGCAGGCTTAAGGCCGGTGAAATGA-TTCGGACTTTAAGT
1 CTAGCAGGCTTAATGCCGGTG-AATTATTTCAGACTTTATGT
*
4091996 CCAGCAGGC-TAAGTGCCGGTGA
1 CTAGCAGGCTTAA-TGCCGGTGA
4092018 TCTGAATCAG
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
40 4 0.04
41 87 0.92
42 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
Found at i:4092043 original size:41 final size:41
Alignment explanation
Indices: 4091998--4092099 Score: 186
Period size: 41 Copynumber: 2.5 Consensus size: 41
4091988 CTTTAAGTCC
*
4091998 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCT
*
4092039 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCT
4092080 AGCAGGCTAAGTGCCGGTGA
1 AGCAGGCTAAGTGCCGGTGA
4092100 ATATGTTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (41 bp):
AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCT
Found at i:4098066 original size:101 final size:101
Alignment explanation
Indices: 4097947--4098333 Score: 643
Period size: 101 Copynumber: 3.8 Consensus size: 101
4097937 AAAGTGATGG
*
4097947 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATGGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGTAC
*
4098012 TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACTGAATAGCTTCGA
* *
4098048 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGTAC
*
4098113 TATGTGCAGGCTACTATGCGTACTAAATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACTGAATAGCTTCGA
*
4098149 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGCAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGTAC
4098214 TATGTGCAGGCTACTATGCGTACTGAATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACTGAATAGCTTCGA
* * *
4098250 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGAAAT-GGTCACATGAGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G--ATGGGTCGCATGTGTAG
*
4098313 TACTATGTGTAGGCTACTATG
63 TACTATGTGCAGGCTACTATG
4098334 TGAACCGAGT
Statistics
Matches: 269, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
100 2 0.01
101 234 0.87
102 31 0.12
103 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACTGAATAGCTTCGA
Found at i:4098076 original size:51 final size:49
Alignment explanation
Indices: 4097941--4098341 Score: 392
Period size: 51 Copynumber: 8.0 Consensus size: 49
4097931 AAAGTGAAAG
*
4097941 TGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCTGAA
1 TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA
* * * *
4097990 TGATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAA
1 TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
* * *
4098039 TAGCTTCGATCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAA
1 T-G-ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA
* * * * **
4098091 TGATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACTAAA
1 TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
* * *
4098140 TAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
1 T-G-ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA
* * * * * *
4098192 TGATGGGTCGCATGTGTAGCACTATGTGCAGGCTACTATGCGTACTGAA
1 TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
* * * * *
4098241 TAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGA
1 T-G-ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
* * * *
4098292 TGGAAAT-GGTCACATGAGTAGTACTATGTGTAGGCTACTATGTGAACCGA
1 T-G--ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA
4098342 GTATCATTGA
Statistics
Matches: 282, Mismatches: 60, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
49 15 0.05
50 111 0.39
51 148 0.52
52 8 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (49 bp):
TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
Found at i:4098413 original size:43 final size:42
Alignment explanation
Indices: 4098342--4098423 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
4098332 TGTGAACCGA
* *
4098342 GTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACC
1 GTATCATTGAATATAAGGGGGTTGCTAAGTGCTGATTCCACC
*
4098384 GTATCTTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCC
1 GTATCATTGAATAT-AAGGGGGTTGCTAAGTGCTGATTCC
4098424 CCCAAGGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 12 0.33
43 24 0.67
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (42 bp):
GTATCATTGAATATAAGGGGGTTGCTAAGTGCTGATTCCACC
Found at i:4108647 original size:21 final size:22
Alignment explanation
Indices: 4108618--4108669 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
4108608 GTCTAACTAA
*
4108618 GGTTTTTTTGTTCCA-TATAAG
1 GGTTCTTTTGTTCCATTATAAG
*
4108639 GGTTCTTTTGTTCCATTATGAG
1 GGTTCTTTTGTTCCATTATAAG
*
4108661 GTTTCTTTT
1 GGTTCTTTT
4108670 CTTATTTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.13, C:0.12, G:0.19, T:0.56
Consensus pattern (22 bp):
GGTTCTTTTGTTCCATTATAAG
Found at i:4108666 original size:22 final size:21
Alignment explanation
Indices: 4108615--4108669 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
4108605 CTAGTCTAAC
4108615 TAAGGTTT-TTTTGTTCCATA
1 TAAGGTTTCTTTTGTTCCATA
*
4108635 TAAGGGTTCTTTTGTTCCATTA
1 TAAGGTTTCTTTTGTTCCA-TA
*
4108657 TGAGGTTTCTTTT
1 TAAGGTTTCTTTT
4108670 CTTATTTCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 7 0.23
21 10 0.33
22 13 0.43
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (21 bp):
TAAGGTTTCTTTTGTTCCATA
Found at i:4109281 original size:30 final size:30
Alignment explanation
Indices: 4109246--4109305 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4109236 GTTATGTTTT
**
4109246 ATTTTAATTCTGTTTGAATAGATATTTAAA
1 ATTTTAATTAGGTTTGAATAGATATTTAAA
* *
4109276 ATTTTAATTAGGTTTGAATTGCTATTTAAA
1 ATTTTAATTAGGTTTGAATAGATATTTAAA
4109306 TCGAATTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (30 bp):
ATTTTAATTAGGTTTGAATAGATATTTAAA
Found at i:4113825 original size:3 final size:3
Alignment explanation
Indices: 4113810--4113884 Score: 69
Period size: 3 Copynumber: 24.7 Consensus size: 3
4113800 AAAAGGTATT
* * ** * **
4113810 TAA TAA TAT TAA TAA TGA TGC TAA TAA TAA TAA TAA TAA TAA TAG TTT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4113858 TAA TAA TATA TAA TAA TAA AAA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TA
4113885 GCACATATTA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4122684 original size:25 final size:24
Alignment explanation
Indices: 4122656--4122743 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 24
4122646 ACGAGCATGT
4122656 TAACGAGAAGCTCTT-TCGAGCCATA
1 TAACGAGAAGCTCTTGT-GAGCCA-A
* *
4122681 TAAC-AGGAAGCTCTTGTTAGCTGAA
1 TAACGA-GAAGCTCTTGTGAGC-CAA
*
4122706 TAACGAGAAACTCTTGTGAGCCAAA
1 TAACGAGAAGCTCTTGTGAGCC-AA
*
4122731 TATCGAGAAGCTC
1 TAACGAGAAGCTC
4122744 AAACGAGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.02
25 47 0.92
26 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
TAACGAGAAGCTCTTGTGAGCCAA
Found at i:4122788 original size:25 final size:24
Alignment explanation
Indices: 4122756--4122829 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 24
4122746 ACGAGTTGTA
*
4122756 TAATGGGAAGCTCAAGAGAGCCAT
1 TAATGGGAAGCTCATGAGAGCCAT
*
4122780 TAATCGGGAAGCTCATGAGAGCCAAA
1 TAAT-GGGAAGCTCATGAGAGCC-AT
* *
4122806 TATTGGGAAGCTCGTGAGAGCCAT
1 TAATGGGAAGCTCATGAGAGCCAT
4122830 GGTGTGTCCG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
24 5 0.12
25 34 0.79
26 4 0.09
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.19
Consensus pattern (24 bp):
TAATGGGAAGCTCATGAGAGCCAT
Found at i:4123567 original size:22 final size:22
Alignment explanation
Indices: 4123534--4123589 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
4123524 TTTTCACAAA
4123534 CAAATATTCTCTCAATTTCCTTC
1 CAAA-ATTCTCTCAATTTCCTTC
*
4123557 TAAAATTCTCTCAATTTCCTTC
1 CAAAATTCTCTCAATTTCCTTC
4123579 CAAAATTCTCT
1 CAAAATTCTCT
4123590 TAAACTCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
CAAAATTCTCTCAATTTCCTTC
Found at i:4123600 original size:52 final size:52
Alignment explanation
Indices: 4123542--4123641 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
4123532 AACAAATATT
* * * * *
4123542 CTCTCAATTTCCTTCTAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
4123594 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
4123642 CAAATCCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.39
Consensus pattern (52 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
Found at i:4123633 original size:21 final size:22
Alignment explanation
Indices: 4123594--4123646 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
4123584 TTCTCTTAAA
4123594 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
4123616 CTCTCAATTTCCTTCAAAAAAT-
1 CTCTCAAATTCCTTC-CAAAATC
4123638 CTCTCAAAT
1 CTCTCAAAT
4123647 CCATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:4123714 original size:30 final size:28
Alignment explanation
Indices: 4123678--4123736 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 28
4123668 ATTCAATTTC
4123678 ATTTTTTTAAAGA-AAGTTTTAAATATTTTT
1 ATTTTTTTAAA-ATAA-TTTTAAA-ATTTTT
4123708 ATTTTTTTAAAATAATTTTAAAATTTTT
1 ATTTTTTTAAAATAATTTTAAAATTTTT
4123736 A
1 A
4123737 ATATTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 7 0.25
29 8 0.29
30 13 0.46
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATTTTTTTAAAATAATTTTAAAATTTTT
Found at i:4123743 original size:29 final size:30
Alignment explanation
Indices: 4123681--4123743 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
4123671 CAATTTCATT
*
4123681 TTTTTAAAGAAAGTTTTAAATATTTTTATT
1 TTTTTAAAGAAAGTTTTAAATATTTTTATA
4123711 TTTTTAAA-ATAA-TTTTAAA-ATTTTTAATA
1 TTTTTAAAGA-AAGTTTTAAATATTTTT-ATA
4123740 TTTT
1 TTTT
4123744 CAACAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.20
29 14 0.47
30 10 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTTTAAAGAAAGTTTTAAATATTTTTATA
Found at i:4125725 original size:24 final size:24
Alignment explanation
Indices: 4125698--4125753 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
4125688 GCATGGCTTT
* *
4125698 CAAACTCCGTCGCCGTTCATGATG
1 CAAACACCGTCGCCGTTCACGATG
4125722 CAAACACCGTCGCCGTTCACGATG
1 CAAACACCGTCGCCGTTCACGATG
4125746 CAAACACC
1 CAAACACC
4125754 TCCACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.38, G:0.18, T:0.18
Consensus pattern (24 bp):
CAAACACCGTCGCCGTTCACGATG
Found at i:4126083 original size:29 final size:29
Alignment explanation
Indices: 4126039--4126490 Score: 591
Period size: 29 Copynumber: 15.4 Consensus size: 29
4126029 TATAATTTGT
** *
4126039 TTAAAAACCC-AACCCTAACCTAATTAAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
4126067 TTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
** *
4126096 TTAAAAACCCTAAACCCTAACCTAATTAAA
1 TTAAAAACCCT-AACCCTAATTTAATTTAA
4126126 TTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
**
4126155 TTAAAAACCCTAAACCCTAACCTAATTTAA
1 TTAAAAACCCT-AACCCTAATTTAATTTAA
* ** *
4126185 TTAAAAACCCTAAACCATAACCTAATTAAA
1 TTAAAAACCCT-AACCCTAATTTAATTTAA
*
4126215 TTAAAAACCCTAACCCTAATTTAATTTTA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
4126244 TTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
** *
4126273 TTAAAAACCCTAAACCCTAACCTAATTAAA
1 TTAAAAACCCT-AACCCTAATTTAATTTAA
* *
4126303 TTAAAAAACCTAACCCTAATTTAATTTTA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
4126332 TTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
** *
4126361 TTAAAAACCCTAAACCCTAACCTAATTTTA
1 TTAAAAACCCT-AACCCTAATTTAATTTAA
*
4126391 TTAAAAACCCTAACCCTAATTTAATTTTA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
**
4126420 TTAAAAACTTTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
* *** *
4126449 TTAAAAGCCCTAACCCTAACCCATTTTAA
1 TTAAAAACCCTAACCCTAATTTAATTTAA
4126478 TTAAAAACCCTAA
1 TTAAAAACCCTAA
4126491 TCATTAACAA
Statistics
Matches: 374, Mismatches: 45, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
28 10 0.03
29 232 0.62
30 132 0.35
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (29 bp):
TTAAAAACCCTAACCCTAATTTAATTTAA
Found at i:4126125 original size:59 final size:58
Alignment explanation
Indices: 4126039--4126490 Score: 627
Period size: 59 Copynumber: 7.7 Consensus size: 58
4126029 TATAATTTGT
*
4126039 TTAAAAACCC-AACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAA
*
4126096 TTAAAAACCCTAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAA
* ** *
4126155 TTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCATAACCTAATTAAA
1 TTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAATTTAATTTAA
** *
4126215 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAA
* * *
4126273 TTAAAAACCCTAAACCCTAACCTAATTAAATTAAAAAACCTAACCCTAATTTAATTTTA
1 TTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAA
** ** *
4126332 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTTA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAATTTAATTTAA
** * **
4126391 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACTTTAACCCTAATTTAATTTAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAA
* * *
4126449 TTAAAAGCCCTAACCCTAACCCATTTTAATTAAAAACCCTAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
4126491 TCATTAACAA
Statistics
Matches: 352, Mismatches: 38, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
57 10 0.03
58 99 0.28
59 218 0.62
60 25 0.07
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (58 bp):
TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAA
Found at i:4126316 original size:88 final size:88
Alignment explanation
Indices: 4126039--4126490 Score: 728
Period size: 88 Copynumber: 5.1 Consensus size: 88
4126029 TATAATTTGT
** **
4126039 TTAAAAACCC-AACCCTAACCTAATTAAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
1 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
4126103 CCCTAAACCCTAACCTAATTAAA
66 CCCTAAACCCTAACCTAATTAAA
* **
4126126 TTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAA
1 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCT-AACCCTAATTTAATTTAATTAAAA
*
4126191 ACCCTAAACCATAACCTAATTAAA
65 ACCCTAAACCCTAACCTAATTAAA
4126215 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
1 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
4126280 CCCTAAACCCTAACCTAATTAAA
66 CCCTAAACCCTAACCTAATTAAA
*
4126303 TTAAAAAACCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
1 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
**
4126368 CCCTAAACCCTAACCTAATTTTA
66 CCCTAAACCCTAACCTAATTAAA
** *
4126391 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACTTTAACCCTAATTTAATTTAATTAAAAG
1 TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
* * *
4126456 CCCT-AACCCTAACCCATTTTAA
66 CCCTAAACCCTAACCTAATTAAA
4126478 TTAAAAACCCTAA
1 TTAAAAACCCTAA
4126491 TCATTAACAA
Statistics
Matches: 343, Mismatches: 20, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
87 38 0.11
88 221 0.64
89 84 0.24
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (88 bp):
TTAAAAACCCTAACCCTAATTTAATTTTATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA
CCCTAAACCCTAACCTAATTAAA
Found at i:4126594 original size:21 final size:22
Alignment explanation
Indices: 4126568--4126612 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
4126558 ATGTTTTGAC
4126568 TGGTACTAACA-TTTAAGAAAT
1 TGGTACTAACATTTTAAGAAAT
*
4126589 TGGTACTAACATTTTACGAAAT
1 TGGTACTAACATTTTAAGAAAT
4126611 TG
1 TG
4126613 TAGTAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTACTAACATTTTAAGAAAT
Found at i:4128297 original size:125 final size:125
Alignment explanation
Indices: 4128075--4128356 Score: 408
Period size: 125 Copynumber: 2.3 Consensus size: 125
4128065 CCACGAGGGC
* * * * **
4128075 GCGATTTGACACTATTTGCTCAGAAACATCAAAAAATAATTATTTCCTACATGACCAACTGTAGC
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAAATATGACCTACATGACCAACTGTAGC
* **
4128140 GAAATCGCGTCCACCAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCA
66 GAAATCGCGTCCACCAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAA
* *
4128200 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAA-AAATGTGACTTACATGACCAACTGTAG
1 GCGATTTTATACTATTTGCTCAG-AAACGTCAAAAAATAAATATGACCTACATGACCAACTGTAG
*
4128264 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAA
65 CGAAATCGCGTCCACCAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAA
4128325 GCGATTTTATACTATTTGAC-CAGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
4128357 CTCGAAATAA
Statistics
Matches: 142, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
124 10 0.07
125 119 0.84
126 13 0.09
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (125 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAAATATGACCTACATGACCAACTGTAGC
GAAATCGCGTCCACCAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAA
Done.