Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 197 of 226
Found at i:62661740 original size:33 final size:31
Alignment explanation
Indices: 62661702--62661795 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 31
62661692 TGCATTATTG
62661702 CATTGTACCGATACTGTATTGGGCTAAGGCCCA
1 CATTGTA-CG-TACTGTATTGGGCTAAGGCCCA
*
62661735 CATTGT---TACTGTATTGGGCTGAGGCCCA
1 CATTGTACGTACTGTATTGGGCTAAGGCCCA
* * *
62661763 CATTGTACTGTTACTGAATAGGGCTCAGGCCCA
1 CATTGTAC-G-TACTGTATTGGGCTAAGGCCCA
62661796 GACTGTCACT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
28 27 0.52
33 25 0.48
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (31 bp):
CATTGTACGTACTGTATTGGGCTAAGGCCCA
Found at i:62661753 original size:28 final size:27
Alignment explanation
Indices: 62661713--62661773 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 27
62661703 ATTGTACCGA
62661713 TACTGTATTGGGCTAAGGCCCACATTG
1 TACTGTATTGGGCTAAGGCCCACATTG
*
62661740 TTACTGTATTGGGCTGAGGCCCACATTG
1 -TACTGTATTGGGCTAAGGCCCACATTG
62661768 TACTGT
1 TACTGT
62661774 TACTGAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (27 bp):
TACTGTATTGGGCTAAGGCCCACATTG
Found at i:62668892 original size:56 final size:56
Alignment explanation
Indices: 62668771--62668958 Score: 211
Period size: 56 Copynumber: 3.3 Consensus size: 56
62668761 CAGTTTCATT
* * * *
62668771 TTTCATTT-T-CATTTTCATTTCCGTTTTAGAGAAAACCA-AGTTCATTTCCGAATGA
1 TTTCATTTCTCCATTTTCATTTTCATTTTGGAGAAAACCATA--TCATTTCCAAATGA
* *
62668826 TTCCATTTCTCCATTTTCATTTTCATTTTGGAGAAAACCATATCATTTTCAAATGA
1 TTTCATTTCTCCATTTTCATTTTCATTTTGGAGAAAACCATATCATTTCCAAATGA
* * * * *
62668882 TTTCATTTCTCTATTTTCATTTTTATTTTGCAGAAATCCATAATCATTTCCAAATGT
1 TTTCATTTCTCCATTTTCATTTTCATTTTGGAGAAAACCAT-ATCATTTCCAAATGA
*
62668939 TTCTCATTTCTACATTTTCA
1 TT-TCATTTCTCCATTTTCA
62668959 CCATTTTTAT
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
55 7 0.06
56 49 0.43
57 41 0.36
58 16 0.14
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (56 bp):
TTTCATTTCTCCATTTTCATTTTCATTTTGGAGAAAACCATATCATTTCCAAATGA
Found at i:62669096 original size:22 final size:23
Alignment explanation
Indices: 62669071--62669118 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
62669061 ATGATTTATA
*
62669071 ATTAAGTTCT-AACTTTTTGCCT
1 ATTAAGTTATAAACTTTTTGCCT
*
62669093 ATT-ATTTATAAACTTTTTGCCT
1 ATTAAGTTATAAACTTTTTGCCT
62669115 ATTA
1 ATTA
62669119 CCAAATTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTAAGTTATAAACTTTTTGCCT
Found at i:62680288 original size:19 final size:20
Alignment explanation
Indices: 62680264--62680307 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
62680254 TAAACTTGTT
62680264 AAATTTTTATATTTAG-GTC
1 AAATTTTTATATTTAGAGTC
62680283 AAATTTTTATATTTAGAGTC
1 AAATTTTTATATTTAGAGTC
62680303 AAATT
1 AAATT
62680308 AATAGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (20 bp):
AAATTTTTATATTTAGAGTC
Found at i:62683157 original size:25 final size:24
Alignment explanation
Indices: 62683111--62683156 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
62683101 ATTTTCAAAG
*
62683111 AAAATAAAATTATTTTCTAAAATA
1 AAAATAAAAATATTTTCTAAAATA
62683135 AAAATAAAAAATATTTT-TAAAA
1 AAAAT-AAAAATATTTTCTAAAA
62683157 AATATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAAAAATATTTTCTAAAATA
Found at i:62690108 original size:69 final size:69
Alignment explanation
Indices: 62689906--62690298 Score: 400
Period size: 69 Copynumber: 5.7 Consensus size: 69
62689896 AACATTTATA
* * * *
62689906 TCATCTTAAGGCTC-TCAGGATAAAAATTGTAACCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
1 TCATCTTAAGGCTCGT-AGGATAAAAACTGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
62689970 AACTG
65 AACTG
* * * * *
62689975 TCATATTAAGGCTCGTAGGATAAAAAACTGCAGCCTCTAACACAGTTAGCAAAAGTAAAGCTCCC
1 TCATCTTAAGGCTCGTAGGAT-AAAAACTGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCC
62690040 AACTG
65 AACTG
** * *
62690045 TCATCTTAAGGCTCGTAGGATAAAAACCACAGCCTCTAACATAGTTAGCGAGAGCAAAGCTCCCA
1 TCATCTTAAGGCTCGTAGGATAAAAACTGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCA
*
62690110 ACTA
66 ACTG
* * * * * **
62690114 TCATATTAAGGCTCGTAGGATAAAAACTACAGCTTCTAACACAATTAATGAGAGCAAAGCTCCCA
1 TCATCTTAAGGCTCGTAGGATAAAAACTGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCA
62690179 ACTG
66 ACTG
* * * * * * *
62690183 TCATAC-TAAGGCTCAG-AGGACAAGATC-GCCGCCTCCAACATAGTTAGCAAGAGCAAATCTCC
1 TCAT-CTTAAGGCTC-GTAGGATAAAAACTGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
* *
62690245 TACCTG
64 CAACTG
* * * *
62690251 TCATAC-TAAGGCTTGTAGGATAAATACTGCATCCTCCAACATAGTTAG
1 TCAT-CTTAAGGCTCGTAGGATAAAAACTGCAGCCTCCAACACAGTTAG
62690299 TAAAAGTTGA
Statistics
Matches: 270, Mismatches: 48, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
67 1 0.00
68 49 0.18
69 158 0.59
70 62 0.23
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (69 bp):
TCATCTTAAGGCTCGTAGGATAAAAACTGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCA
ACTG
Found at i:62690118 original size:139 final size:137
Alignment explanation
Indices: 62689906--62690305 Score: 448
Period size: 139 Copynumber: 2.9 Consensus size: 137
62689896 AACATTTATA
*** * * *
62689906 TCATCTTAAGGCTC-TCAGGATAAAAATTGTAACCTCCAACACAGTTAGTGAGAGCAAAGCTCCC
1 TCATCTTAAGGCTCGT-AGGATAAAAA-CCCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCC
*
62689970 AACTGTCATATTAAGGCTCGTAGGATAAAAAACTGCAGCCTCTAACACAGTTAGCAAAAGTAAAG
64 AACTGTCATATTAAGGCTCGTAGGAT-AAAAACTGCAGCCTCTAACACAGTTAGTAAAAGTAAAG
62690035 CTCCCAACTG
128 CTCCCAACTG
*
62690045 TCATCTTAAGGCTCGTAGGATAAAAACCACAGCCTCTAACATAGTTAGCGAGAGCAAAGCTCCCA
1 TCATCTTAAGGCTCGTAGGATAAAAACC-CAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCA
* * * * * * * *
62690110 ACTATCATATTAAGGCTCGTAGGATAAAAACTACAGCTTCTAACACAATTAATGAGAGCAAAGCT
65 ACTGTCATATTAAGGCTCGTAGGATAAAAACTGCAGCCTCTAACACAGTTAGTAAAAGTAAAGCT
62690175 CCCAACTG
130 CCCAACTG
* * * * *
62690183 TCATAC-TAAGGCTCAG-AGGACAAGATCGCC-GCCTCCAACATAGTTAGCAAGAGCAAATCTCC
1 TCAT-CTTAAGGCTC-GTAGGATAAAAAC-CCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCC
* * * * * * * *
62690245 TACCTGTCATACTAAGGCTTGTAGGATAAATACTGCATCCTCCAACATAGTTAGTAAAAGT
63 CAACTGTCATATTAAGGCTCGTAGGATAAAAACTGCAGCCTCTAACACAGTTAGTAAAAGT
62690306 TGAAAACTCC
Statistics
Matches: 218, Mismatches: 38, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
137 74 0.34
138 61 0.28
139 82 0.38
140 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (137 bp):
TCATCTTAAGGCTCGTAGGATAAAAACCCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
CTGTCATATTAAGGCTCGTAGGATAAAAACTGCAGCCTCTAACACAGTTAGTAAAAGTAAAGCTC
CCAACTG
Found at i:62690432 original size:58 final size:58
Alignment explanation
Indices: 62690323--62690478 Score: 156
Period size: 58 Copynumber: 2.7 Consensus size: 58
62690313 TCCTAATTGT
* * * * *
62690323 GTTATCTTTCAAAATTTTCTTAAGTATAAAATAGCTCGTAGATTCATATCCCCAGCTA
1 GTTATCTTTCAAAATTTTCTTAAGTATAAAACAACTCGCAGATCCACATCCCCAGCTA
* * ** *
62690381 GTTATC-TTCTAAAATTTTCTTAAGTCTAAAACAACTCGCGGATCCACATCCCCAATTG
1 GTTATCTTTC-AAAATTTTCTTAAGTATAAAACAACTCGCAGATCCACATCCCCAGCTA
* * **
62690439 GTTATTTTTC--AATTTTTTTAAGTATAAAATTACTCGCAGA
1 GTTATCTTTCAAAATTTTCTTAAGTATAAAACAACTCGCAGA
62690479 CTAATATTCC
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
56 25 0.31
57 3 0.04
58 49 0.61
59 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.38
Consensus pattern (58 bp):
GTTATCTTTCAAAATTTTCTTAAGTATAAAACAACTCGCAGATCCACATCCCCAGCTA
Found at i:62704879 original size:17 final size:18
Alignment explanation
Indices: 62704852--62704885 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
62704842 ACAAGATTAT
*
62704852 ACTTGCAAGAACGAAAAC
1 ACTTGCAAGAAAGAAAAC
62704870 ACTT-CAAGAAAGAAAA
1 ACTTGCAAGAAAGAAAA
62704886 GATTATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.12
Consensus pattern (18 bp):
ACTTGCAAGAAAGAAAAC
Found at i:62708742 original size:162 final size:162
Alignment explanation
Indices: 62708475--62708798 Score: 585
Period size: 162 Copynumber: 2.0 Consensus size: 162
62708465 AGGCATTTAG
*
62708475 AATCCTGAAAATCAACAAGACCAATCTAGCATCACTCATCTGTCAACTCAACATGACAACTACAT
1 AATCCTGAAAATCAACAAGACCAATCTAACATCACTCATCTGTCAACTCAACATGACAACTACAT
** *
62708540 TCATAATAAAGGATGAGTTATACATTCCACTACATAATGTATAAAGGCAGAGCTAAACAAGCTGA
66 TCATAATAAAGGACAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
* *
62708605 GCTTTGAAGCGATAAATCAAAAGTTAGCCACT
131 ACTTTGAAGCAATAAATCAAAAGTTAGCCACT
62708637 AATCCTGAAAATCAACAAGACCAATCTAACATCACTCATCTGTCAACTCAACATGACAACTACAT
1 AATCCTGAAAATCAACAAGACCAATCTAACATCACTCATCTGTCAACTCAACATGACAACTACAT
*
62708702 TCGTAATAAAGGACAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
66 TCATAATAAAGGACAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
62708767 ACTTTGAAGCAATAAATCAAAAGTTAGCCACT
131 ACTTTGAAGCAATAAATCAAAAGTTAGCCACT
62708799 CAAAAAATTT
Statistics
Matches: 155, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 155 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (162 bp):
AATCCTGAAAATCAACAAGACCAATCTAACATCACTCATCTGTCAACTCAACATGACAACTACAT
TCATAATAAAGGACAAGTTATACATTCCACTACATAATGTATAAAGGCAAAGCTAAACAAGCTGA
ACTTTGAAGCAATAAATCAAAAGTTAGCCACT
Found at i:62712168 original size:20 final size:21
Alignment explanation
Indices: 62712137--62712175 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
62712127 AAATATTGTA
*
62712137 AAAATATTTTTTTTGATAATC
1 AAAATATTTTTTATGATAATC
62712158 AAAAT-TTTTTTATGATAA
1 AAAATATTTTTTATGATAA
62712176 GATAAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (21 bp):
AAAATATTTTTTATGATAATC
Found at i:62712759 original size:24 final size:26
Alignment explanation
Indices: 62712726--62712774 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
62712716 AAGTAGGATA
62712726 TAAACAAATAACCAT-ATTTATATTC
1 TAAACAAATAACCATAATTTATATTC
**
62712751 TAAA-AAATATTCATAATTTATATT
1 TAAACAAATAACCATAATTTATATT
62712775 ATGAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAACAAATAACCATAATTTATATTC
Found at i:62712886 original size:20 final size:20
Alignment explanation
Indices: 62712851--62712893 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
62712841 TTTTTTCTAG
*
62712851 TAAAATATTAAGAATATTACT
1 TAAAATATTAAAAATATTA-T
62712872 TAAAAT-TTAAAAATATTAT
1 TAAAATATTAAAAATATTAT
62712891 TAA
1 TAA
62712894 TGTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATATTAAAAATATTAT
Found at i:62712907 original size:19 final size:18
Alignment explanation
Indices: 62712885--62712921 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
62712875 AATTTAAAAA
*
62712885 TATTATTAATGTTAAAATT
1 TATTATTAAAG-TAAAATT
62712904 TATTATTAAAGTAAAATT
1 TATTATTAAAGTAAAATT
62712922 GTAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TATTATTAAAGTAAAATT
Found at i:62721585 original size:20 final size:19
Alignment explanation
Indices: 62721550--62721608 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
62721540 TTTAAAGTTA
62721550 AAATATATAT-TGTAATATT
1 AAATATATATAT-TAATATT
62721569 AAATATTATATATTAATTATT
1 AAATA-TATATATTAA-TATT
*
62721590 AAGTATATATATT-ATATT
1 AAATATATATATTAATATT
62721608 A
1 A
62721609 TATTATAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 5 0.14
19 6 0.17
20 16 0.44
21 9 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAATATATATATTAATATT
Found at i:62722667 original size:40 final size:40
Alignment explanation
Indices: 62722543--62722682 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
62722533 GACTTCGAGT
* * *
62722543 CGATGAGACACTGGGTGTCAATTTACTACTTCAGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATT-ATC
* * * * *
62722584 CGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAAC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* * *
62722621 CAATGAGACATTGGGTGTCAAATTATTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* *
62722661 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
62722683 CTGGTGTGTT
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 15 0.20
38 12 0.16
39 2 0.03
40 31 0.41
41 16 0.21
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
Found at i:62725224 original size:18 final size:18
Alignment explanation
Indices: 62725198--62725235 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
62725188 TGTCTCCTTA
*
62725198 CCCATTGGTGATAGTAGT
1 CCCACTGGTGATAGTAGT
62725216 CCCACTGGTGATAGTAGT
1 CCCACTGGTGATAGTAGT
62725234 CC
1 CC
62725236 TGGTCCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (18 bp):
CCCACTGGTGATAGTAGT
Found at i:62735252 original size:47 final size:46
Alignment explanation
Indices: 62735136--62735258 Score: 138
Period size: 47 Copynumber: 2.6 Consensus size: 46
62735126 ATATATATAA
* *
62735136 ATATATTTGTTATGCATGAAAATGAATTAATCTATAGCTGAATGTAT
1 ATATATTTGTTATGCATG-AAATGAATTAAACTATAGCCGAATGTAT
* * * * *
62735183 ATGTAATTGTTATACAGAGAAATGAATTAAACTATGGCCGAATGTAT
1 ATATATTTGTTATGCA-TGAAATGAATTAAACTATAGCCGAATGTAT
* *
62735230 ATATATTTGTTGTGCATTGAAATAAATTA
1 ATATATTTGTTATGCA-TGAAATGAATTA
62735259 TTTGAAATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
47 60 0.98
48 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (46 bp):
ATATATTTGTTATGCATGAAATGAATTAAACTATAGCCGAATGTAT
Found at i:62735295 original size:2 final size:2
Alignment explanation
Indices: 62735288--62735338 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
62735278 TGGCCGAATG
62735288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62735330 TA TA TA TA T
1 TA TA TA TA T
62735339 TTGTTATACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62735402 original size:47 final size:49
Alignment explanation
Indices: 62735328--62735548 Score: 189
Period size: 47 Copynumber: 4.4 Consensus size: 49
62735318 TATATATATA
* ** * *
62735328 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGTTGAATG
1 TATATATATATTTGTTATGCAGAGAAATGAATTAAACTATAGCTGAATG
* * * * *
62735377 TATATGTA-A-TTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATATATATATA
1 TATATATATATTTGTTATGCAGAGAAATGAATTAAACTATAG-C-----T-GA-ATG
* ** *
62735432 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 TATATATATATTTGTTATGCAGAGAAATGAATTAAACTATAGCTGAATG
* * *
62735481 TATATGTA-A-TTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG
1 TATATATATATTTGTTATGCAGAGAAATGAATTAAACTATAGCTGAATG
62735528 TATATATATATTTGTTATGCA
1 TATATATATATTTGTTATGCA
62735549 TTGAAATAAA
Statistics
Matches: 133, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
47 64 0.48
48 3 0.02
49 26 0.20
50 1 0.01
51 1 0.01
53 1 0.01
54 1 0.01
55 9 0.07
56 2 0.02
57 25 0.19
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.40
Consensus pattern (49 bp):
TATATATATATTTGTTATGCAGAGAAATGAATTAAACTATAGCTGAATG
Found at i:62735447 original size:104 final size:104
Alignment explanation
Indices: 62735317--62735538 Score: 417
Period size: 104 Copynumber: 2.1 Consensus size: 104
62735307 ATATATATAT
*
62735317 ATATATATATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGTTGAATGTATAT
1 ATATATATATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATAT
62735382 GTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGA
66 GTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGA
62735421 ATATATATATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATAT
1 ATATATATATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATAT
*
62735486 GTAATTGTTATGCAGAGAAATGAATTAAACTATGGCCGA
66 GTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGA
*
62735525 ATGTATATATATAT
1 ATATATATATATAT
62735539 TTGTTATGCA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 115 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.40
Consensus pattern (104 bp):
ATATATATATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATAT
GTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGA
Found at i:62735859 original size:41 final size:41
Alignment explanation
Indices: 62735665--62735851 Score: 266
Period size: 41 Copynumber: 4.6 Consensus size: 41
62735655 TTTTGTAAGT
*
62735665 TCGGGCTTTATGCCTAGCAGGCTCTGTGCCGATGAAATGTA
1 TCGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
* * *
62735706 TTGGGCTTTATGCCTAGCAAGCTCTGTGTCGGTGAAATGTA
1 TCGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
* * * *
62735747 TTGGGCTTTATGCCTAGCAGGTTCTGTACTGGTGAAATGTA
1 TCGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
* *
62735788 TCAGGATTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
1 TCGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
* *
62735829 TCGGGCTTTGTGTCTAGCAGGCT
1 TCGGGCTTTATGCCTAGCAGGCT
62735852 TTATGCCGAT
Statistics
Matches: 127, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (41 bp):
TCGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
Found at i:62736958 original size:4 final size:4
Alignment explanation
Indices: 62736949--62736981 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
62736939 ATTTAAATAT
62736949 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
62736982 CTTACTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:62741071 original size:12 final size:13
Alignment explanation
Indices: 62741045--62741075 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
62741035 AATTAAATTA
62741045 AATTAATTATCTC
1 AATTAATTATCTC
62741058 AATTAATT-TCTC
1 AATTAATTATCTC
62741070 AATTAA
1 AATTAA
62741076 ATAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTAATTATCTC
Found at i:62749402 original size:12 final size:12
Alignment explanation
Indices: 62749385--62749416 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
62749375 TAAGTTTGTA
62749385 AGTTAATTTAAT
1 AGTTAATTTAAT
62749397 AGTTAATTTAAT
1 AGTTAATTTAAT
62749409 AGTTAATT
1 AGTTAATT
62749417 AATTGATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
AGTTAATTTAAT
Found at i:62749590 original size:45 final size:45
Alignment explanation
Indices: 62749482--62749648 Score: 164
Period size: 45 Copynumber: 3.7 Consensus size: 45
62749472 TTGGATTGAG
*
62749482 AAATGTGAAAGACCAT-GATTGAAAGATA-TCATGGCATTAACCCG-
1 AAATGTGAAAGACCATAG-TTGAAAGATACT-ATGGCATTAAACCGA
*
62749526 AAATGAT-AAAGACCATAGTTGAAAGATACTATGGCACTAAACCGA
1 AAATG-TGAAAGACCATAGTTGAAAGATACTATGGCATTAAACCGA
* * * * * *
62749571 AAATGTGTAAGGCCATAGTTGAAAGATATTATGACATTAAATCTA
1 AAATGTGAAAGACCATAGTTGAAAGATACTATGGCATTAAACCGA
* * *
62749616 ATACG-AATAAGACCATAGTTGAAAGATACTATG
1 AAATGTGA-AAGACCATAGTTGAAAGATACTATG
62749649 ACATCACATC
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
44 37 0.36
45 65 0.64
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.25
Consensus pattern (45 bp):
AAATGTGAAAGACCATAGTTGAAAGATACTATGGCATTAAACCGA
Found at i:62749649 original size:45 final size:43
Alignment explanation
Indices: 62749534--62749696 Score: 173
Period size: 45 Copynumber: 3.7 Consensus size: 43
62749524 CGAAATGATA
* * * * * *
62749534 AAGACCATAGTTGAAAGATACTATGGCACTAAACCGAAAATGTGT
1 AAGACCATAGTTGAAAGATACTATGACATTAAATC-AATACG-AT
* *
62749579 AAGGCCATAGTTGAAAGATATTATGACATTAAATCTAATACGAAT
1 AAGACCATAGTTGAAAGATACTATGACATTAAATC-AATACG-AT
* * *
62749624 AAGACCATAGTTGAAAGATACTATGACATCACATCAGTAACGAT
1 AAGACCATAGTTGAAAGATACTATGACATTAAATCAAT-ACGAT
62749668 CAAGACCATAGTTGAAAGATACTATGACA
1 -AAGACCATAGTTGAAAGATACTATGACA
62749697 CTACTTTGGG
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
44 4 0.04
45 97 0.96
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (43 bp):
AAGACCATAGTTGAAAGATACTATGACATTAAATCAATACGAT
Found at i:62760543 original size:184 final size:184
Alignment explanation
Indices: 62760234--62760600 Score: 725
Period size: 184 Copynumber: 2.0 Consensus size: 184
62760224 TAAATGCGAG
62760234 GCACACTCCCCACATGATAAATCCTAATTTATAGTTCTAAGTTTATATCAGAGTTTCACAGTTTT
1 GCACACTCCCCACATGATAAATCCTAATTTATAGTTCTAAGTTTATATCAGAGTTTCACAGTTTT
*
62760299 AACACAAACCTTTTCATCATCGAATGTTGTATCCTCTGCAAGTTTTTCCACCGCATAGTGTACCA
66 AACACAAACCTTTTCATCATCGAATGCTGTATCCTCTGCAAGTTTTTCCACCGCATAGTGTACCA
62760364 AATCAGTTTCTAGCTCCGCAAAAGCAGCCATAGAAACACACCTAGGAAATCTTC
131 AATCAGTTTCTAGCTCCGCAAAAGCAGCCATAGAAACACACCTAGGAAATCTTC
62760418 GCACACTCCCCACATGATAAATCCTAATTTATAGTTCTAAGTTTATATCAGAGTTTCACAGTTTT
1 GCACACTCCCCACATGATAAATCCTAATTTATAGTTCTAAGTTTATATCAGAGTTTCACAGTTTT
62760483 AACACAAACCTTTTCATCATCGAATGCTGTATCCTCTGCAAGTTTTTCCACCGCATAGTGTACCA
66 AACACAAACCTTTTCATCATCGAATGCTGTATCCTCTGCAAGTTTTTCCACCGCATAGTGTACCA
62760548 AATCAGTTTCTAGCTCCGCAAAAGCAGCCATAGAAACACACCTAGGAAATCTT
131 AATCAGTTTCTAGCTCCGCAAAAGCAGCCATAGAAACACACCTAGGAAATCTT
62760601 AAATGTAGAC
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 182 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (184 bp):
GCACACTCCCCACATGATAAATCCTAATTTATAGTTCTAAGTTTATATCAGAGTTTCACAGTTTT
AACACAAACCTTTTCATCATCGAATGCTGTATCCTCTGCAAGTTTTTCCACCGCATAGTGTACCA
AATCAGTTTCTAGCTCCGCAAAAGCAGCCATAGAAACACACCTAGGAAATCTTC
Found at i:62761012 original size:28 final size:28
Alignment explanation
Indices: 62760976--62761047 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
62760966 AATTAAGCTT
* *
62760976 AAAGATGATTAATTTAAAATTAACTAAG
1 AAAGTTGATTTATTTAAAATTAACTAAG
62761004 AAAGTTGATTTATTTAAAATTAACTAAG
1 AAAGTTGATTTATTTAAAATTAACTAAG
62761032 AAAGTTGATTTATTTA
1 AAAGTTGATTTATTTA
62761048 CAATAAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (28 bp):
AAAGTTGATTTATTTAAAATTAACTAAG
Found at i:62768003 original size:16 final size:16
Alignment explanation
Indices: 62767984--62768018 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
62767974 AATAATGAGT
62767984 AAAT-AAAATAACAATG
1 AAATAAAAATAA-AATG
62768000 AAATAAAAATAAAATG
1 AAATAAAAATAAAATG
62768016 AAA
1 AAA
62768019 ACAAGTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Found at i:62779216 original size:36 final size:36
Alignment explanation
Indices: 62779176--62779254 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
62779166 GCCAACATAC
62779176 GGCCCAAAATTGCGCCCAAAACCACGCACAAAAGAT
1 GGCCCAAAATTGCGCCCAAAACCACGCACAAAAGAT
* * * * * *
62779212 GGCCCAAAATTGTGCCCATAATCACGCCCAACAGCT
1 GGCCCAAAATTGCGCCCAAAACCACGCACAAAAGAT
62779248 GGCCCAA
1 GGCCCAA
62779255 GACCACTGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.35, G:0.18, T:0.11
Consensus pattern (36 bp):
GGCCCAAAATTGCGCCCAAAACCACGCACAAAAGAT
Found at i:62784327 original size:31 final size:30
Alignment explanation
Indices: 62784201--62784345 Score: 94
Period size: 31 Copynumber: 4.5 Consensus size: 30
62784191 TCCACGCATG
*
62784201 TATATATTATATATATAACAAGACCATTTTACACA
1 TATATA-T-TATATATAACAAGACCA---TAAACA
* * * *
62784236 TATTTATTATATAAAACATGACCTTCAAACGCA
1 TATATATTATATATAACAAGACCAT-AAA--CA
*** *
62784269 TATATATTATATATTTTATGACCCATAAACA
1 TATATATTATATATAACAAGA-CCATAAACA
*
62784300 TATATATTATATATAACAAGACGCATAAATA
1 TATATATTATATATAACAAGAC-CATAAACA
62784331 TAT-TATTTATATATA
1 TATATA-TTATATATA
62784346 TATATCTATT
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
30 4 0.05
31 40 0.45
33 35 0.40
34 4 0.05
35 5 0.06
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (30 bp):
TATATATTATATATAACAAGACCATAAACA
Found at i:62789761 original size:137 final size:136
Alignment explanation
Indices: 62789515--62789825 Score: 376
Period size: 137 Copynumber: 2.3 Consensus size: 136
62789505 TGGTATAGTC
** * ** * * *
62789515 TAAAGGTTTGTCTGTTTAAGATCGCAACCTCCAAAGCAGCTAGTGGACCTATGCTCCTAGCTGAC
1 TAAAGGTTTG-CAATTTAAGATCACAACCTCCAAAGCAGCTAACGGACCTATGCTCCCAACTAAC
* * * * *
62789580 ATTCTAAAAGCTGGCAGAGTTAAGCTTGTAGCTCTAACACAGCTAGCGGACCTACTCTCTCAACT
65 ATTATAAAAGCTGGCAGAGTTAAGCTTGCAGCTCCAACACAGCTAGCGGACCTACGCTCCCAACT
62789645 GATGTCA
130 GATGTCA
* *
62789652 TAAAGGTATAT-CGATTTAAGATCACAACCTCCAAAGTAGCTAACGGACCTACT-CTCCCAACTA
1 TAAAGGT-T-TGCAATTTAAGATCACAACCTCCAAAGCAGCTAACGGACCTA-TGCTCCCAACTA
* * * *
62789715 ATATTATAAGAGCTTGCAGAGTTAAG-TTCGCAGCTCCAACACAGCTAGTGGACCTACGCTCCCA
63 ACATTATAAAAGCTGGCAGAGTTAAGCTT-GCAGCTCCAACACAGCTAGCGGACCTACGCTCCCA
62789779 ACTGATGTCA
127 ACTGATGTCA
*
62789789 TAAAGGTTTGCAATTTAAGATCCCAACCTCCAAAGCA
1 TAAAGGTTTGCAATTTAAGATCACAACCTCCAAAGCA
62789826 ACTAGCAAAC
Statistics
Matches: 148, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
135 1 0.01
136 27 0.18
137 117 0.79
138 2 0.01
139 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (136 bp):
TAAAGGTTTGCAATTTAAGATCACAACCTCCAAAGCAGCTAACGGACCTATGCTCCCAACTAACA
TTATAAAAGCTGGCAGAGTTAAGCTTGCAGCTCCAACACAGCTAGCGGACCTACGCTCCCAACTG
ATGTCA
Found at i:62789800 original size:68 final size:68
Alignment explanation
Indices: 62789593--62789800 Score: 192
Period size: 68 Copynumber: 3.0 Consensus size: 68
62789583 CTAAAAGCTG
* * *
62789593 GCAGAGTTAAGCTT-GTAGCTCTAACACAGCTAGCGGACCTACTCTCTCAACTGATGTCATAAAG
1 GCAGAGTTAAG-TTCGCAGCTCCAACACAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAG
62789657 GTATAT
65 GT-T-T
* * * * * * * * *
62789663 -C-GATTTAAGATCACAACCTCCAA-AGTAGCTAACGGACCTACTCTCCCAACTAATATTAT-AA
1 GCAGAGTTAAGTTCGC-AGCTCCAACA-CAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAA
*
62789724 GAGCTT
64 G-GTTT
* *
62789730 GCAGAGTTAAGTTCGCAGCTCCAACACAGCTAGTGGACCTACGCTCCCAACTGATGTCATAAAGG
1 GCAGAGTTAAGTTCGCAGCTCCAACACAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAGG
62789795 TTT
66 TTT
62789798 GCA
1 GCA
62789801 ATTTAAGATC
Statistics
Matches: 105, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
67 2 0.02
68 53 0.50
69 50 0.48
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (68 bp):
GCAGAGTTAAGTTCGCAGCTCCAACACAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAGG
TTT
Found at i:62789838 original size:68 final size:68
Alignment explanation
Indices: 62789619--62789831 Score: 209
Period size: 68 Copynumber: 3.1 Consensus size: 68
62789609 AGCTCTAACA
* *
62789619 CAGCTAGCGGACCTACTCTCTCAACTGATGTCATAAAGGTATAT-CGATTTAAGATCACAACCTC
1 CAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAGGT-T-TGCAATTTAAGATCACAACCTC
62789683 CAAAG
64 CAAAG
* * * * * * * * * *
62789688 TAGCTAACGGACCTACTCTCCCAACTAATATTAT-AAGAGCTTGCAGAGTTAAGTTCGC-AGCTC
1 CAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAG-GTTTGCA-ATTTAAGATCACAACCTC
62789751 CAACA-
64 CAA-AG
* * *
62789756 CAGCTAGTGGACCTACGCTCCCAACTGATGTCATAAAGGTTTGCAATTTAAGATCCCAACCTCCA
1 CAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAGGTTTGCAATTTAAGATCACAACCTCCA
62789821 AAG
66 AAG
*
62789824 CAACTAGC
1 CAGCTAGC
62789832 AAACCTAAAT
Statistics
Matches: 111, Mismatches: 26, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
67 11 0.10
68 58 0.52
69 42 0.38
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (68 bp):
CAGCTAGCGGACCTACTCTCCCAACTGATGTCATAAAGGTTTGCAATTTAAGATCACAACCTCCA
AAG
Found at i:62789900 original size:136 final size:137
Alignment explanation
Indices: 62789529--62789900 Score: 331
Period size: 137 Copynumber: 2.7 Consensus size: 137
62789519 GGTTTGTCTG
* * **** * * * * * *
62789529 TTTAAGATCGCAACCTCCAAAGCAGCTAGTGGACCT-ATGCTCCTAGCTGACATTCTAAAAGCTG
1 TTTAAGATCACAACCTCCAAAGCAACTAACAAACCTAAT-CTCCAAACTAACATTATAAGAGCTT
* * * * * * * * *
62789593 GCAGAGTTAAGCTTGTAGCTCTAACACAGCTAGCGGACCTACTCTCTCAACTGATGTCATAAAGG
65 GCAGAATTAAGCTCGCAGATCCAACACAACTAGTGGACCTACGCTCCCAACTGATGTCATAAAGG
*
62789658 TATATCGA
130 TATATCAA
* * ** * * *
62789666 TTTAAGATCACAACCTCCAAAGTAGCTAACGGACCTACTCTCCCAACTAATATTATAAGAGCTTG
1 TTTAAGATCACAACCTCCAAAGCAACTAACAAACCTAATCTCCAAACTAACATTATAAGAGCTTG
* * * *
62789731 CAGAGTTAAGTTCGCAGCTCCAACACAGCTAGTGGACCTACGCTCCCAACTGATGTCATAAAGGT
66 CAGAATTAAGCTCGCAGATCCAACACAACTAGTGGACCTACGCTCCCAACTGATGTCATAAAGGT
62789796 -T-TGCAA
131 ATAT-CAA
* * *
62789802 TTTAAGATCCCAACCTCCAAAGCAACTAGCAAACCTAAAT-TCCAAACTGACATTATAAGAGCTC
1 TTTAAGATCACAACCTCCAAAGCAACTAACAAACCT-AATCTCCAAACTAACATTATAAGAGCT-
* *
62789866 T-CAGAATTAAGCTCGCAGATCCAATACAATTAGTG
64 TGCAGAATTAAGCTCGCAGATCCAACACAACTAGTG
62789901 AGACTACCTT
Statistics
Matches: 195, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
135 1 0.01
136 81 0.42
137 112 0.57
138 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (137 bp):
TTTAAGATCACAACCTCCAAAGCAACTAACAAACCTAATCTCCAAACTAACATTATAAGAGCTTG
CAGAATTAAGCTCGCAGATCCAACACAACTAGTGGACCTACGCTCCCAACTGATGTCATAAAGGT
ATATCAA
Found at i:62797856 original size:125 final size:125
Alignment explanation
Indices: 62797634--62798007 Score: 595
Period size: 125 Copynumber: 3.0 Consensus size: 125
62797624 TTAGGGTTTT
* * *
62797634 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCACTTCTAGT
1 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
62797699 AGAATGTTGTTTGATAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTCTGCTACAG
66 AGAATGTTGTTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
62797759 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATTGCTTCTAGC
1 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
62797824 AGTATGTTGTTTGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGCGCTTTTACTACAG
66 AGAATGTTGTTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
62797884 TAGGTCATGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * * * * * *
62797949 AGGATGCTATTTGAGAATAATTTGTGAAAGCGCGCCCTTGTGGACGCACTTTTGCTACA
66 AGAATGTTGTTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
62798008 ATAGCATGTT
Statistics
Matches: 229, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 229 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (125 bp):
TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGAATGTTGTTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:62799763 original size:22 final size:22
Alignment explanation
Indices: 62799732--62801246 Score: 1110
Period size: 23 Copynumber: 67.5 Consensus size: 22
62799722 CTAGTTTAAA
* *
62799732 GTTTTAAAGTTAAGGGTTAAGG
1 GTTTTTAAGTTAAGGGTTTAGG
*
62799754 GTTTTTAAGTTAAGGG-TTAAG
1 GTTTTTAAGTTAAGGGTTTAGG
*
62799775 GTTTTTAAGTTGAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
62799796 GTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
**
62799818 GTTTTTAA-TTAA-ATTAGTTAGG
1 GTTTTTAAGTTAAGGGT--TTAGG
*
62799840 GTTTTTAAGTTTAAGAGTTTAGG
1 GTTTTTAAG-TTAAGGGTTTAGG
**
62799863 GTTTTTAA-TTAATTTAGTTTAGG
1 GTTTTTAAGTTAA--GGGTTTAGG
*
62799886 GTTTTTAAGTTAAGGGCTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
*
62799908 GTTTTTAATTTTAAGGGTTTAGG
1 GTTTTTAA-GTTAAGGGTTTAGG
*
62799931 GTTTTTAATTTTAAGGGTTTAGG
1 GTTTTTAA-GTTAAGGGTTTAGG
* * *
62799954 GTTTTTAATTTGAGGG-TTATG
1 GTTTTTAAGTTAAGGGTTTAGG
*
62799975 GTTTTTAAGTTAAGCGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* * *
62799997 G-TTTTAAGTTAAGAGTCTACG
1 GTTTTTAAGTTAAGGGTTTAGG
* ** *
62800018 ATTTTTAA-TTAAATTAGTTTCGG
1 GTTTTTAAGTT-AA-GGGTTTAGG
62800041 GTTTTTAAGTTAAGGGTTAGGGTTTAGG
1 GTTTTTAAGTT-A-----AGGGTTTAGG
* *
62800069 GTTTTTAATTTAAGGGTTTATG
1 GTTTTTAAGTTAAGGGTTTAGG
* ** *
62800091 GTTTTTAAGTAAATTAGATTAGG
1 GTTTTTAAGTTAA-GGGTTTAGG
* *
62800114 GTTTTTAATTTAAGGATTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* **
62800136 GTTTTTAAGTAAATTAGTTTAGG
1 GTTTTTAAGTTAA-GGGTTTAGG
* *
62800159 GTTTTTAAGTTGAGGATTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* **
62800181 GTTTTTAA-TGAAATTAGTTTAGG
1 GTTTTTAAGT-TAA-GGGTTTAGG
62800204 GTTTTTAAGTTAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
**
62800225 GTTTTTAA-TTAAATTAGTTTAGG
1 GTTTTTAAGTT-AA-GGGTTTAGG
62800248 GTTTTTAAGTTAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
62800269 GTTTTTAGGTTTAAGGGTTTAAG
1 GTTTTTAAG-TTAAGGGTTTAGG
**
62800292 GTTTTTAA-TTAAATTAGTTTAGG
1 GTTTTTAAGTT-AA-GGGTTTAGG
62800315 GTTTTTAAGTTAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* * *
62800336 G--TTTAGGGTTTAGGGTTTAGA
1 GTTTTTA-AGTTAAGGGTTTAGG
**
62800357 GTTTTTATTTTTAAGGGTTTAGG
1 GTTTTTA-AGTTAAGGGTTTAGG
** *
62800380 GTTTTTAA-TTAAATTAGTTTAAG
1 GTTTTTAAGTT-AA-GGGTTTAGG
* *
62800403 ATTTTTAAGTTAAGGGTTTAGA
1 GTTTTTAAGTTAAGGGTTTAGG
* * *
62800425 GTTTTTAATTTTAAGAGTTTAAG
1 GTTTTTAA-GTTAAGGGTTTAGG
* *
62800448 GTTTTTAATTTACGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* **
62800469 GTTTTTAAGTTAAAGGCGTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
*
62800491 GTTTTTAATTTTAAGGG-TTAGG
1 GTTTTTAA-GTTAAGGGTTTAGG
* *
62800513 GTTTTTAAGTTAATGGTTTAAG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
62800535 GTTTTTAATTTTAAGGGTTTAGT
1 GTTTTTAA-GTTAAGGGTTTAGG
* *
62800558 G-TTTTAATTTAA-GG-CTA-G
1 GTTTTTAAGTTAAGGGTTTAGG
*
62800576 GTTTTTAAATTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* **
62800598 G-TTTTAAATTAAATTAGTTTAGG
1 GTTTTTAAGTT-AA-GGGTTTAGG
** *
62800621 GTTTTTAA-TTAAATTAGTTTAGA
1 GTTTTTAAGTT-AA-GGGTTTAGG
62800644 GTTTTTAAGTTAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
62800665 GTTTTTAAGTTTAAGGGTTTAGG
1 GTTTTTAAG-TTAAGGGTTTAGG
**
62800688 GTTTTTAA-TTAAATTAGTTTAGG
1 GTTTTTAAGTT-AA-GGGTTTAGG
*
62800711 GTTTTTAAGTTAAGAGTTCGGGTTTGGG
1 GTTTTTAAGTT-A-A----GGGTTTAGG
* * *
62800739 GTTTTTTAATTTAAGGGTTTAAG
1 GTTTTTAAGTT-AAGGGTTTAGG
** *
62800762 GTTTTTAA-TTGAATTAGTTTAAG
1 GTTTTTAAGTT-AA-GGGTTTAGG
62800785 GTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
**
62800807 GTTTTTAA-TTAAATTTGTTTAGG
1 GTTTTTAAGTT-AA-GGGTTTAGG
*
62800830 GTTTTTAAGTTAAGGG-TTAGA
1 GTTTTTAAGTTAAGGGTTTAGG
62800851 GTTTTTAAGTTTAAGGGTTTAGG
1 GTTTTTAAG-TTAAGGGTTTAGG
* **
62800874 G-TTTTAAATTAACTTAGTTTAGG
1 GTTTTTAAGTTAA--GGGTTTAGG
62800897 GTTTTTAAGTTAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
**
62800918 GTTTAGGGTTTTGTTTTTAAGGGTTTAGG
1 GTTT----TTAAG---TTAAGGGTTTAGG
* **
62800947 GTTTTTAATTTAATTAGTTTAGG
1 GTTTTTAAGTTAA-GGGTTTAGG
62800970 GTTTTTAATTAAGTTAAGGGTTTAGG
1 G--TTT--TTAAGTTAAGGGTTTAGG
*
62800996 GTTTTTAATTTTAAGGGTTTAGG
1 GTTTTTAA-GTTAAGGGTTTAGG
*
62801019 GTTTTTAATTTACA-GG-TTAGG
1 GTTTTTAAGTTA-AGGGTTTAGG
* *
62801040 ATTTTTAAGTTAAGGGTTCA-G
1 GTTTTTAAGTTAAGGGTTTAGG
*
62801061 GTTTTTAAGTTAAGAGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
*
62801083 G-TTTTAATTTAAGGG-TTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
62801103 GTTTTTAATTTAAGGG-TTAAG
1 GTTTTTAAGTTAAGGGTTTAGG
62801124 GTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
62801146 GTTTTAAATTTTAAGGGTTTAGG
1 GTTTTTAA-GTTAAGGGTTTAGG
* * **
62801169 TTTTTTAA-TGAAATTAGTTTAGG
1 GTTTTTAAGT-TAA-GGGTTTAGG
62801192 GTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGGTTTAGG
* *
62801214 GTTTTAAATTTTAAGGGTTTAGG
1 GTTTTTAA-GTTAAGGGTTTAGG
62801237 GTTTTTAAGT
1 GTTTTTAAGT
62801247 AATAACTCAA
Statistics
Matches: 1202, Mismatches: 193, Indels: 196
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.00
19 16 0.01
20 21 0.02
21 288 0.24
22 296 0.25
23 453 0.38
24 49 0.04
25 11 0.01
26 8 0.01
27 10 0.01
28 39 0.03
29 10 0.01
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.48
Consensus pattern (22 bp):
GTTTTTAAGTTAAGGGTTTAGG
Found at i:62799867 original size:45 final size:45
Alignment explanation
Indices: 62799743--62801246 Score: 1035
Period size: 45 Copynumber: 33.5 Consensus size: 45
62799733 TTTTAAAGTT
* *
62799743 AAGGGTTAAGGGTTTTTAAG-TTAAGGG-TTAAGGTTTTTAAGTT-
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
*
62799786 GAGGG-TTAGGGTTTTTAAG-TTAAGGGTTTAGGGTTTTTAATTA
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
** *
62799829 AATTAG-TTAGGGTTTTTAAGTTTAAGAGTTTAGGGTTTTTAATTA
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
*** * *
62799874 ATTTAGTTTAGGGTTTTTAAG-TTAAGGGCTTAGGGTTTTTAATTTT
1 A-AGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
* *
62799920 AAGGGTTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTT
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
* * *
62799965 GAGGG-TTATGGTTTTTAAG-TTAAGCGTTTAGGG-TTTTAAGTT-
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
* * * * * ** *
62800007 AAGAGTCTACGATTTTTAA-TTAAATTAGTTTCGGGTTTTTAAGTTA
1 AAGGGTTTAGGGTTTTTAAGTTTAA-GGGTTTAGGGTTTTTAA-TTA
* *
62800053 AGGGTTAGGGTTTAGGGTTTTTAA-TTTAAGGGTTTATGGTTTTTAAGTA
1 A-----AGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
** * * *
62800102 AATTAGATTAGGGTTTTTAA-TTTAAGGATTTAGGGTTTTTAAGTA
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
** * * *
62800147 AATTAGTTTAGGGTTTTTAAG-TTGAGGATTTAGGGTTTTTAATGA
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
**
62800192 AATTAGTTTAGGGTTTTTAAG-TTAAGGG-TTAGGGTTTTTAATTA
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
** * *
62800236 AATTAGTTTAGGGTTTTTAAG-TTAAGGG-TTAGGGTTTTTAGGTTT
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTA-ATTA
* * **
62800281 AAGGGTTTAAGGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAGTT-
1 AAGGGTTTAGGGTTTTTAAGTTTAA-GGGTTTAGGGTTTTTAA-TTA
* * * *
62800326 AAGGG-TTAGGG--TTTAGGGTTT-AGGGTTTAGAGTTTTTATTTTT
1 AAGGGTTTAGGGTTTTTA-AGTTTAAGGGTTTAGGGTTTTTA-ATTA
* ** * *
62800369 AAGGGTTTAGGGTTTTTAA-TTAAATTAGTTTAAGATTTTTAAGTT-
1 AAGGGTTTAGGGTTTTTAAGTTTAA-GGGTTTAGGGTTTTTAA-TTA
* * * * *
62800414 AAGGGTTTAGAGTTTTTAATTTTAAGAGTTTAAGGTTTTTAATTT
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
* * *
62800459 ACGGG-TTAGGGTTTTTAAGTTAAAGGCG--TAGGGTTTTTAATTTT
1 AAGGGTTTAGGGTTTTTAAGTTTAAGG-GTTTAGGGTTTTTAA-TTA
* * *
62800503 AAGGG-TTAGGGTTTTTAAG-TTAATGGTTTAAGGTTTTTAATTTT
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
* *
62800547 AAGGGTTTAGTG-TTTTAA-TTTAA-GG-CTA-GGTTTTTAAATT-
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTT-AATTA
* * **
62800587 AAGGGTTTAGGG-TTTTAAATTAAATTAGTTTAGGGTTTTTAATTA
1 AAGGGTTTAGGGTTTTTAAGTTTAA-GGGTTTAGGGTTTTTAATTA
** * *
62800632 AATTAGTTTAGAGTTTTTAAG-TTAAGGG-TTAGGGTTTTTAAGTTT
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
* **
62800677 AAGGGTTTAGGGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAGTTA
1 AAGGGTTTAGGGTTTTTAAGTTTAA-GGGTTTAGGGTTTTTAA-TTA
* *
62800723 AGAGTTCGGGTTTGGGGTTTTTTAA-TTTAAGGGTTTAAGGTTTTTAATTGA
1 A-A----GGGTTTAGGG-TTTTTAAGTTTAAGGGTTTAGGGTTTTTAATT-A
*** *
62800774 ATTAGTTTAAGGTTTTTAAG-TTAAGGGTTTAGGGTTTTTAATTA
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
** * *
62800818 AATTTGTTTAGGGTTTTTAAG-TTAAGGG-TTAGAGTTTTTAAGTTT
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
* **
62800863 AAGGGTTTAGGG-TTTTAA-ATTAACTTAGTTTAGGGTTTTTAAGTTA
1 AAGGGTTTAGGGTTTTTAAGTTTAA--GGGTTTAGGGTTTTTAA-TTA
*
62800909 AGGGTTAGGGTTTAGGGTTTTGT--TTTTAAGGGTTTAGGGTTTTTAATTTA
1 A-----AGGGTTTAGGGTTTT-TAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
*** * *
62800959 ATTAGTTTAGGGTTTTTAATTAAGTTAAGGGTTTAGGGTTTTTAATTTT
1 AAGGGTTTAGGGTTTTTAAGT---TTAAGGGTTTAGGGTTTTTAA-TTA
*
62801008 AAGGGTTTAGGGTTTTTAA-TTTACA-GG-TTAGGATTTTTAAGTT-
1 AAGGGTTTAGGGTTTTTAAGTTTA-AGGGTTTAGGGTTTTTAA-TTA
* * *
62801051 AAGGGTTCA-GGTTTTTAAG-TTAAGAGTTTAGGG-TTTTAATTT
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
*
62801093 AAGGG-TTAGGGTTTTTAA-TTTAAGGG-TTAAGGTTTTTAAGTT-
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
* * * *
62801135 AAGGGTTTAGGGTTTTAAATTTTAAGGGTTTAGGTTTTTTAATGA
1 AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
** * *
62801180 AATTAGTTTAGGGTTTTTAAG-TTAAGGGTTTAGGGTTTTAAATTTT
1 AA-GGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAA-TTA
62801226 AAGGGTTTAGGGTTTTTAAGT
1 AAGGGTTTAGGGTTTTTAAGT
62801247 AATAACTCAA
Statistics
Matches: 1196, Mismatches: 165, Indels: 197
0.77 0.11 0.13
Matches are distributed among these distances:
40 17 0.01
41 23 0.02
42 105 0.09
43 106 0.09
44 274 0.23
45 371 0.31
46 142 0.12
47 7 0.01
48 1 0.00
49 43 0.04
50 34 0.03
51 54 0.05
52 18 0.02
53 1 0.00
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.48
Consensus pattern (45 bp):
AAGGGTTTAGGGTTTTTAAGTTTAAGGGTTTAGGGTTTTTAATTA
Found at i:62800380 original size:7 final size:7
Alignment explanation
Indices: 62800327--62800360 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
62800317 TTTTAAGTTA
62800327 AGGG-TT
1 AGGGTTT
62800333 AGGGTTT
1 AGGGTTT
62800340 AGGGTTT
1 AGGGTTT
62800347 AGGGTTT
1 AGGGTTT
*
62800354 AGAGTTT
1 AGGGTTT
62800361 TTATTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:62800976 original size:18 final size:19
Alignment explanation
Indices: 62800955--62800992 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
62800945 GGGTTTTTAA
*
62800955 TTTAATT-AGTTTAGGGTT
1 TTTAATTAAGTTAAGGGTT
62800973 TTTAATTAAGTTAAGGGTT
1 TTTAATTAAGTTAAGGGTT
62800992 T
1 T
62800993 AGGGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
TTTAATTAAGTTAAGGGTT
Found at i:62801435 original size:20 final size:21
Alignment explanation
Indices: 62801412--62801451 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
62801402 TTGTCCAGCT
*
62801412 TCTGGCGGGG-TTGTGGTTCC
1 TCTGGCGGGGATTCTGGTTCC
*
62801432 TCTGGTGGGGATTCTGGTTC
1 TCTGGCGGGGATTCTGGTTC
62801452 TTCCGGTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.03, C:0.17, G:0.42, T:0.38
Consensus pattern (21 bp):
TCTGGCGGGGATTCTGGTTCC
Found at i:62801739 original size:18 final size:18
Alignment explanation
Indices: 62801713--62801755 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
62801703 GACTCGGAAA
* *
62801713 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
62801731 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
62801749 AGGAAAC
1 AGGAAAC
62801756 TCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:62802635 original size:20 final size:20
Alignment explanation
Indices: 62802598--62802635 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
62802588 TTTATTTTTA
*
62802598 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
62802618 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
62802636 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:62803635 original size:11 final size:11
Alignment explanation
Indices: 62803621--62803687 Score: 68
Period size: 11 Copynumber: 6.0 Consensus size: 11
62803611 ATTAAATATG
62803621 AATTTGAGAGA
1 AATTTGAGAGA
62803632 AATTTG-GAAGA
1 AATTTGAG-AGA
62803643 AATTTGAGAGCA
1 AATTTGAGAG-A
62803655 AA-TTGAGAGGA
1 AATTTGAGA-GA
*
62803666 AA-TTAAGAGGA
1 AATTTGAGA-GA
62803677 AATTTGAGAGA
1 AATTTGAGAGA
62803688 GGATTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
10 1 0.02
11 38 0.78
12 10 0.20
ACGTcount: A:0.46, C:0.01, G:0.28, T:0.24
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:62804372 original size:50 final size:50
Alignment explanation
Indices: 62804318--62804420 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
62804308 CAATTTATTA
* * * *
62804318 TTTATTATTTATATTAATTTTTTTATAAATGTATTTGTTATATAATTTGT
1 TTTATTATTTATATCAAATTTTTAATAAATGTATTTGTTACATAATTTGT
62804368 TTTATTATTTATATCAAATTTTTAATAAATGTATTTGTTACATAATTTGT
1 TTTATTATTTATATCAAATTTTTAATAAATGTATTTGTTACATAATTTGT
62804418 TTT
1 TTT
62804421 TCGCCCGCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (50 bp):
TTTATTATTTATATCAAATTTTTAATAAATGTATTTGTTACATAATTTGT
Found at i:62808742 original size:36 final size:37
Alignment explanation
Indices: 62808700--62808793 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 37
62808690 GTTTCTTTGT
*
62808700 TTTTCTTTTCTGCCGATTT-TCTCCCAGTTTATTTTC
1 TTTTCTTTTCTGCCGATTTCTCCCCCAGTTTATTTTC
* *
62808736 TTTTCTTTTCTGCCGATTTGCTCCCCCCGTTTCTTTTC
1 TTTTCTTTTCTGCCGATTT-CTCCCCCAGTTTATTTTC
*
62808774 TTTTCTTTTTCGGCCGATTT
1 TTTTC-TTTTCTGCCGATTT
62808794 GCTCAGTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 19 0.37
38 19 0.37
39 13 0.25
ACGTcount: A:0.05, C:0.28, G:0.11, T:0.56
Consensus pattern (37 bp):
TTTTCTTTTCTGCCGATTTCTCCCCCAGTTTATTTTC
Found at i:62810237 original size:69 final size:69
Alignment explanation
Indices: 62810153--62810292 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
62810143 TTTGTTGGTT
62810153 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
62810218 AAAC
66 AAAC
* * * * * * * *
62810222 TGTTCTGGCAGTTGTTTTGATTGTCTGCTGGAAATTGTTCTTGATTTGTTAGTTAGTAGAATATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
62810287 AAAC
66 AAAC
62810291 TG
1 TG
62810293 GAACTTGATT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (69 bp):
TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
AAAC
Found at i:62814852 original size:91 final size:91
Alignment explanation
Indices: 62814705--62814912 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
62814695 TTGATTTTAG
* *
62814705 TAAATTCATATAAGAACATTTTATTATTAAGAAATTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTAT
* * *
62814770 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * * *
62814797 TAAATTAATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTATA
62814862 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
62814888 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
62814913 GTTATAATTA
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 89 0.86
92 15 0.14
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:62814881 original size:26 final size:28
Alignment explanation
Indices: 62814726--62814887 Score: 84
Period size: 26 Copynumber: 5.6 Consensus size: 28
62814716 AAGAACATTT
** *
62814726 TATTATTAAGAAATT-TATGAAATTATA
1 TATTATTATTAAATTATATGAAATAATA
* ** *
62814753 TATCATTATTAAATTATATTTAATATTA
1 TATTATTATTAAATTATATGAAATAATA
*
62814781 -ATTATT-TTAAATTGTAT-AAATTAATA
1 TATTATTATTAAATTATATGAAA-TAATA
* * *
62814807 TAAGAAAATTTATTATCAATAATTTTATGAAATTATA
1 T------A-TTATTAT-TA-AATTATATGAAATAATA
*
62814844 TATTATTATTAAATTATATGTAATAATA
1 TATTATTATTAAATTATATGAAATAATA
62814872 -ATTATT-TTAAATTATA
1 TATTATTATTAAATTATA
62814888 CAAATTCATA
Statistics
Matches: 103, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
25 2 0.02
26 24 0.23
27 23 0.22
28 22 0.21
29 1 0.01
30 7 0.07
31 1 0.01
33 1 0.01
34 5 0.05
35 1 0.01
36 1 0.01
37 12 0.12
38 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (28 bp):
TATTATTATTAAATTATATGAAATAATA
Found at i:62815036 original size:66 final size:62
Alignment explanation
Indices: 62814966--62815283 Score: 224
Period size: 59 Copynumber: 5.2 Consensus size: 62
62814956 AAATATATTT
62814966 AATATTAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAA
1 AATATTAATTATTT--AA-TATATTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
62815031 G
62 G
* * * * * **
62815032 AATATTAATTA-TTAAGA-ATTTTATTA-AATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTAATATATTTTA-TAGTATCATATATTATGATTTAGTAAATTCATATAAG
*
62815086 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAA--TATATTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
62815151 G
62 G
* * * * * **
62815152 AATATTAATTA-TTAAGA-ATTTTATTA-AATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTAATATATTTTA-TAGTATCATATATTATGATTTAGTAAATTCATATAAG
*
62815206 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATAT-A
1 AATATTAATTAT-TTAA--TATATTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
62815270 G
62 G
*
62815271 AATATTGATTATT
1 AATATTAATTATT
62815284 AAGAATTTTA
Statistics
Matches: 192, Mismatches: 33, Indels: 56
0.68 0.12 0.20
Matches are distributed among these distances:
54 20 0.10
55 8 0.04
56 10 0.05
57 4 0.02
58 8 0.04
59 32 0.17
60 16 0.08
61 32 0.17
62 8 0.04
63 6 0.03
64 7 0.04
65 20 0.10
66 21 0.11
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (62 bp):
AATATTAATTATTTAATATATTTTATAGTATCATATATTATGATTTAGTAAATTCATATAAG
Found at i:62815052 original size:120 final size:120
Alignment explanation
Indices: 62814928--62815335 Score: 657
Period size: 120 Copynumber: 3.4 Consensus size: 120
62814918 AATTATTTTA
* * *
62814928 AATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAAATAAAATATATTTAATAATAATTATGTT-AATTTATATTT
*
62814992 TATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
62815048 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATAAAATATATTTAATAATAATTATGTTAATTTATATTTT
62815113 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
62815168 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
62815233 ATAGTATCATATATTATGATTTGAGTAAATTCATAT-AGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
62815287 AATTTTATTAAATTGTATA-TTTAAATTATATATATTT-AT-AT-ATTATGTT
1 AATTTTATTAAATTATATATTTTAAATAAAATATATTTAATAATAATTATGTT
62815336 TAATATGATT
Statistics
Matches: 275, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
115 8 0.03
116 2 0.01
117 2 0.01
118 14 0.05
119 35 0.13
120 212 0.77
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAAATAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:62815088 original size:15 final size:15
Alignment explanation
Indices: 62815053--62815104 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
62815043 TTAAGAATTT
*
62815053 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62815067 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62815081 TATTTAATAATAAT-
1 TATTTAATTATAATA
62815095 TATGTTAATT
1 TAT-TTAATT
62815105 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62815208 original size:15 final size:15
Alignment explanation
Indices: 62815173--62815224 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
62815163 TTAAGAATTT
*
62815173 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62815187 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62815201 TATTTAATAATAAT-
1 TATTTAATTATAATA
62815215 TATGTTAATT
1 TAT-TTAATT
62815225 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62815583 original size:45 final size:44
Alignment explanation
Indices: 62815502--62815591 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
62815492 ACCTCTATTC
*
62815502 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
62815546 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
62815591 C
1 C
62815592 GCCTCTATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:62815596 original size:16 final size:16
Alignment explanation
Indices: 62815571--62815608 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
62815561 TTGATTTGCT
62815571 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
62815587 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
62815603 AATACA
1 ATTACA
62815609 GCAAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:62816178 original size:23 final size:22
Alignment explanation
Indices: 62816138--62816181 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
62816128 AAATTATAAA
*
62816138 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
62816160 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
62816182 TGTGAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:62816904 original size:22 final size:22
Alignment explanation
Indices: 62816882--62816961 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
62816872 AAATTAAATC
* *
62816882 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
*
62816905 TCTAAGATTGCATATCACATCT
1 TCTAAGATTGCATATCATATCT
62816927 TCTAAGATTGCATATCATA---
1 TCTAAGATTGCATATCATATCT
62816946 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
62816962 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.30
22 27 0.51
23 10 0.19
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:62816951 original size:19 final size:20
Alignment explanation
Indices: 62816905--62816961 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 20
62816895 AATCATATCT
*
62816905 TCTAAGATTGCATATCACATCT
1 TCTAAGATTGCATAT--CATCA
62816927 TCTAAGATTGCATATCAT-A
1 TCTAAGATTGCATATCATCA
62816946 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
62816962 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 3 0.09
22 15 0.44
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
TCTAAGATTGCATATCATCA
Found at i:62817878 original size:11 final size:11
Alignment explanation
Indices: 62817838--62817887 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
62817828 ATAAACACCA
62817838 AAAAATTATTTT
1 AAAAA-TATTTT
*
62817850 AAAAATA---A
1 AAAAATATTTT
62817858 AAAAAGTATTTT
1 AAAAA-TATTTT
62817870 AAAAATATTTT
1 AAAAATATTTT
62817881 AAAAATA
1 AAAAATA
62817888 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
11 15 0.47
12 10 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:62817895 original size:19 final size:20
Alignment explanation
Indices: 62817837--62817876 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
62817827 AATAAACACC
*
62817837 AAAAAATTATTTTAAAAATA
1 AAAAAAGTATTTTAAAAATA
62817857 AAAAAAGTATTTTAAAAATA
1 AAAAAAGTATTTTAAAAATA
62817877 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAAAGTATTTTAAAAATA
Found at i:62817898 original size:7 final size:8
Alignment explanation
Indices: 62817881--62817905 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
62817871 AAAATATTTT
62817881 AAAAATAA
1 AAAAATAA
62817889 AAAAATAA
1 AAAAATAA
62817897 AAAAATAA
1 AAAAATAA
62817905 A
1 A
62817906 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:62817907 original size:31 final size:31
Alignment explanation
Indices: 62817837--62817910 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
62817827 AATAAACACC
* **
62817837 AAAAAATTATTTTAAAAATAAAAAAAGTATT
1 AAAAAAATATTTTAAAAATAAAAAAAGTAAA
**
62817868 TTAAAAATATTTTAAAAATAAAAAAA-TAAA
1 AAAAAAATATTTTAAAAATAAAAAAAGTAAA
62817898 AAAATAAATATTT
1 AAAA-AAATATTT
62817911 ATTATATATT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (31 bp):
AAAAAAATATTTTAAAAATAAAAAAAGTAAA
Found at i:62819026 original size:22 final size:22
Alignment explanation
Indices: 62818996--62819047 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
62818986 ATTTCCTCTC
*
62818996 AATTCCTCTCAATTTTCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
62819019 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
62819041 AATTCTC
1 AATTCTC
62819048 CCAAATCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:62819135 original size:51 final size:50
Alignment explanation
Indices: 62819021--62819135 Score: 194
Period size: 50 Copynumber: 2.3 Consensus size: 50
62819011 TCTTCCAAAA
62819021 TTCTCTCAATTTCCTTCCAAAATTCTCCCAAATCCATATTAATTTCAATT
1 TTCTCTCAATTTCCTTCCAAAATTCTCCCAAATCCATATTAATTTCAATT
* **
62819071 TCCTCTCAATTTCCTTCCAAAATTCTCTGAAATCCATATTTAATTTCAATT
1 TTCTCTCAATTTCCTTCCAAAATTCTCCCAAATCCATA-TTAATTTCAATT
62819122 TTCTCTCAATTTCC
1 TTCTCTCAATTTCC
62819136 CTTATTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 35 0.58
51 25 0.42
ACGTcount: A:0.28, C:0.28, G:0.01, T:0.43
Consensus pattern (50 bp):
TTCTCTCAATTTCCTTCCAAAATTCTCCCAAATCCATATTAATTTCAATT
Found at i:62820288 original size:7 final size:7
Alignment explanation
Indices: 62820278--62820302 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62820268 ATTCGATTGA
62820278 TATTTAG
1 TATTTAG
62820285 TATTTAG
1 TATTTAG
62820292 TATTTAG
1 TATTTAG
62820299 TATT
1 TATT
62820303 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:62820977 original size:18 final size:18
Alignment explanation
Indices: 62820951--62820985 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62820941 AGGTGCGTTT
* *
62820951 CCTAGCCCTTTTATGTAC
1 CCTAACCCTTATATGTAC
62820969 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
62820986 TCCTTTTCCA
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:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:62821495 original size:25 final size:25
Alignment explanation
Indices: 62821461--62821598 Score: 166
Period size: 25 Copynumber: 5.8 Consensus size: 25
62821451 TATTTTGATA
62821461 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
62821486 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
62821511 TTATTTTATGTAA-AAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
62821535 TT-TTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
62821553 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
62821579 TTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATA
62821599 AAAAAATTTC
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 8 0.08
21 2 0.02
22 2 0.02
23 5 0.05
24 15 0.16
25 58 0.61
26 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:62821525 original size:93 final size:93
Alignment explanation
Indices: 62821418--62821598 Score: 362
Period size: 93 Copynumber: 1.9 Consensus size: 93
62821408 TATTTTGATA
62821418 TTATTTTATGTAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGA
1 TTATTTTATGTAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGA
62821483 AGTTTATTTGATGTAATAAAATAGAAGT
66 AGTTTATTTGATGTAATAAAATAGAAGT
62821511 TTATTTTATGTAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGA
1 TTATTTTATGTAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGA
62821576 AGTTTATTTGATGTAATAAAATA
66 AGTTTATTTGATGTAATAAAATA
62821599 AAAAAATTTC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (93 bp):
TTATTTTATGTAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGA
AGTTTATTTGATGTAATAAAATAGAAGT
Found at i:62821635 original size:69 final size:69
Alignment explanation
Indices: 62821486--62821665 Score: 301
Period size: 69 Copynumber: 2.6 Consensus size: 69
62821476 AAATAGAAGT
* * * *
62821486 TTATTTGATGTAATAAAATAGAAGTTTATTTTATGTAA-AAAATAGAAATTTTTTGAGTTATTTT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAAAAAATTTCTGAGTTATTTT
62821550 GATA
66 GATA
62821554 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAAAAAAATTTCT-AGTTATTT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAT-AAAAAATTTCTGAGTTATTT
62821618 TGATA
65 TGATA
62821623 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
62821666 ACCCTAACCT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
68 37 0.35
69 61 0.58
70 8 0.08
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (69 bp):
TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAAAAAATTTCTGAGTTATTTT
GATA
Found at i:62821724 original size:29 final size:29
Alignment explanation
Indices: 62821681--62822037 Score: 308
Period size: 29 Copynumber: 12.7 Consensus size: 29
62821671 AACCTAATTT
*
62821681 AACCCTAAACCCTAACTTAAATTAATTAAA
1 AACCCT-AACCCTAACCTAAATTAATTAAA
*
62821711 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAAATTAATTAAA
*
62821740 AACCCTCACCCTAACCTAATTTAATTTAATTAAA
1 AACCCTAACCCTAACCT-A---AA-TTAATTAAA
*
62821774 AACCCTAACCCTAACCTAAATTAATTACA
1 AACCCTAACCCTAACCTAAATTAATTAAA
62821803 AACCCTAA-CCTAA--T---TTAATTAAA
1 AACCCTAACCCTAACCTAAATTAATTAAA
* *
62821826 AACCCTAACCCCTAGCCTAAATTAATTACA
1 AACCCTAA-CCCTAACCTAAATTAATTAAA
*
62821856 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAAATTAATTAAA
* *
62821885 AGCCCTAAACCCT----T--A--ACTTAAA
1 AACCCT-AACCCTAACCTAAATTAATTAAA
* *
62821907 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAAATTAATTAAA
*
62821936 AACCCTAAACCCT----T--A--ACTTAAA
1 AACCCT-AACCCTAACCTAAATTAATTAAA
** *
62821958 AACCCTAACATTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAAATTAATTAAA
*
62821987 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAAATTAATTAAA
*
62822016 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCC-TAACCTAAA
62822038 AACCCTAACC
Statistics
Matches: 265, Mismatches: 30, Indels: 63
0.74 0.08 0.18
Matches are distributed among these distances:
21 9 0.03
22 23 0.09
23 16 0.06
25 6 0.02
26 3 0.01
27 1 0.00
28 5 0.02
29 127 0.48
30 41 0.15
31 7 0.03
33 2 0.01
34 25 0.09
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAAATTAATTAAA
Found at i:62821743 original size:52 final size:52
Alignment explanation
Indices: 62821665--62822023 Score: 246
Period size: 51 Copynumber: 6.6 Consensus size: 52
62821655 ATGTAATAAA
* ** *
62821665 AACCCTAACCTAATTTAA-CCCTAAACCCTAACTTAAATTAATTAAAAACCCT
1 AACCCTAACCTAAATTAATTAC-AAACCCTAACTTAATTTAATTAAAAACCCT
* *
62821717 AACCCTAACCTAATTTAATTAAAAACCCTCACCCTAACCTAATTTAATTTAATTAAAAACCCT
1 AACCCTAACCTAAATTAATT-ACAA-----ACCCTAA-C----TTAATTTAATTAAAAACCCT
*
62821780 AACCCTAACCTAAATTAATTACAAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAAATTAATTACAAACCCTAACTTAATTTAATTAAAAACCCT
* *
62821832 AACCCCTAGCCTAAATTAATTACAAACCCTAACCCTAACCTAATTTAATTAAAAGCCCT
1 AA-CCCTAACCTAAATTAATTACAAACCCTAA--CT----TAATTTAATTAAAAACCCT
* ** * * *
62821891 AAACCCTTAACTTAAA--AA-CCCTAACCTTAACCTAATTTAATTAAAAACCCT
1 -AACCC-TAACCTAAATTAATTACAAACCCTAACTTAATTTAATTAAAAACCCT
* ** * ** *
62821942 AAACCCTTAACTTAAA--AA-CCCTAACATTAACCTAATTTAATTAAAAACCCT
1 -AACCC-TAACCTAAATTAATTACAAACCCTAACTTAATTTAATTAAAAACCCT
* *
62821993 AACCCTAACCTAATTTAATTAAAAACCCTAA
1 AACCCTAACCTAAATTAATTACAAACCCTAA
62822024 ACCCTTAACT
Statistics
Matches: 256, Mismatches: 27, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
49 7 0.03
50 5 0.02
51 70 0.27
52 45 0.18
53 30 0.12
55 2 0.01
56 1 0.00
57 15 0.06
58 9 0.04
59 22 0.09
60 9 0.04
62 3 0.01
63 38 0.15
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (52 bp):
AACCCTAACCTAAATTAATTACAAACCCTAACTTAATTTAATTAAAAACCCT
Found at i:62821745 original size:23 final size:23
Alignment explanation
Indices: 62821661--62821720 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
62821651 TTTGATGTAA
*
62821661 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAAATTAAC
*** * *
62821684 CCTAAACCCTAACTTAAATTAAT
1 TAAAAACCCTAACCTAAATTAAC
62821707 TAAAAACCCTAACC
1 TAAAAACCCTAACC
62821721 CTAACCTAAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAAAACCCTAACCTAAATTAAC
Found at i:62821758 original size:34 final size:34
Alignment explanation
Indices: 62821711--62821792 Score: 128
Period size: 34 Copynumber: 2.4 Consensus size: 34
62821701 ATTAATTAAA
62821711 AACCCTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAA-CCTAACCTAATTTAATTAAAAACCCT
* **
62821746 CACCCTAACCTAATTTAATTTAATTAAAAACCCT
1 AACCCTAACCTAACCTAATTTAATTAAAAACCCT
62821780 AACCCTAACCTAA
1 AACCCTAACCTAA
62821793 ATTAATTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 36 0.84
35 7 0.16
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (34 bp):
AACCCTAACCTAACCTAATTTAATTAAAAACCCT
Found at i:62821834 original size:23 final size:23
Alignment explanation
Indices: 62821780--62821835 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
62821770 TAAAAACCCT
*
62821780 AACCCTAACCTAAATTAATTACA
1 AACCCTAACCTAAATTAATTAAA
*
62821803 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
62821826 AACCCTAACC
1 AACCCTAACC
62821836 CCTAGCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:62821916 original size:21 final size:21
Alignment explanation
Indices: 62821876--62821921 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
62821866 CTAACCTAAT
*
62821876 TTAA-TTAAAAGCCCTAAACCC
1 TTAACTTAAAAACCCTAAA-CC
62821897 TTAACTTAAAAACCCT-AACC
1 TTAACTTAAAAACCCTAAACC
62821917 TTAAC
1 TTAAC
62821922 CTAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 10 0.43
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:62821922 original size:51 final size:51
Alignment explanation
Indices: 62821847--62821998 Score: 254
Period size: 51 Copynumber: 3.0 Consensus size: 51
62821837 CTAGCCTAAA
* * *
62821847 TTAA-TTACAAACCCTAACCCTAACCTAATTTAATTAAAAGCCCTAAACCC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCC
62821897 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCC
*
62821948 TTAACTTAAAAACCCTAACATTAACCTAATTTAATTAAAAACCCT-AACCC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCC
62821998 T
1 T
62821999 AACCTAATTT
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
50 10 0.10
51 87 0.90
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.28
Consensus pattern (51 bp):
TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCC
Found at i:62821986 original size:80 final size:81
Alignment explanation
Indices: 62821897--62822057 Score: 288
Period size: 80 Copynumber: 2.0 Consensus size: 81
62821887 CCCTAAACCC
*
62821897 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACC
1 TTAACTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACC
62821962 CTAACATTAACCTAAT
66 CTAACATTAACCTAAT
62821978 TTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACC
1 TTAACTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACC
* *
62822042 CTAACCTTAACGTAAT
66 CTAACATTAACCTAAT
62822058 GTTAGATTTG
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 73 0.95
81 4 0.05
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (81 bp):
TTAACTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACC
CTAACATTAACCTAAT
Found at i:62822012 original size:131 final size:131
Alignment explanation
Indices: 62821765--62822057 Score: 430
Period size: 131 Copynumber: 2.2 Consensus size: 131
62821755 CTAATTTAAT
* * * *
62821765 TTAA-TTAAAAACCCTAACCCTAACCTAAATTAATTACAAACCCTAACCTAATTTAATTAAAAAC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACC--ACTTAATTAAAAAC
* * * *
62821829 CCTAACCCCTAGCCTAAATTAATTACAAACCCTAACCCTAACCTAATTTAATTAAAAGCCCTAAA
64 CCTAACCACTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAA
62821894 CCC
129 CCC
62821897 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACC-CTTAACTTAAAAAC
1 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCT-AACCACTTAA-TTAAAAAC
* *
62821961 CCTAA-CATTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAA
64 CCTAACCACTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAA
62822025 CCC
129 CCC
*
62822028 TTAACTTAAAAACCCTAACCTTAACGTAAT
1 TTAACTTAAAAACCCTAACCTTAACCTAAT
62822058 GTTAGATTTG
Statistics
Matches: 147, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
131 89 0.61
132 17 0.12
133 37 0.25
134 4 0.03
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (131 bp):
TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCACTTAATTAAAAACCC
TAACCACTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
C
Found at i:62822039 original size:22 final size:20
Alignment explanation
Indices: 62822007--62822052 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
62821997 CTAACCTAAT
62822007 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AA-CC
62822028 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
62822048 TTAAC
1 TTAAC
62822053 GTAATGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:62822258 original size:116 final size:116
Alignment explanation
Indices: 62822054--62822271 Score: 400
Period size: 116 Copynumber: 1.9 Consensus size: 116
62822044 AACCTTAACG
62822054 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
*
62822119 ATTTTACTAACTATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* *
62822170 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAATAATTTTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
*
62822235 GTTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
62822272 CAATTTATCA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 98 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:62822288 original size:17 final size:18
Alignment explanation
Indices: 62822247--62822288 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
62822237 TTTACTAACC
* *
62822247 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
62822265 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
62822282 ATTAATA
1 ATTAATA
62822289 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:62840927 original size:45 final size:45
Alignment explanation
Indices: 62840863--62841080 Score: 287
Period size: 45 Copynumber: 4.9 Consensus size: 45
62840853 TACTGAGTAT
*
62840863 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
* *
62840908 CATTGATTATAAAGGTGGTTGCCATGTGCTGATTCCACCGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
* * * * *
62840953 CATTGATTATAAAGGTGGTTGCTATGTGTTGACTCCACTGGAAAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
** * * *
62840998 CATTGAAAATAAAGGTGGTTGCTATATGCTGATTCCACCGAATAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
* *
62841043 AATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
62841081 TGTAATGGTT
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 7 0.05
44 12 0.08
45 133 0.88
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
Found at i:62846833 original size:15 final size:16
Alignment explanation
Indices: 62846804--62846836 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62846794 ATAACTAACT
*
62846804 TAACTAACACTAAGAA
1 TAACTAAAACTAAGAA
62846820 TAACTAAAAC-AAGAA
1 TAACTAAAACTAAGAA
62846835 TA
1 TA
62846837 GTTACTGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (16 bp):
TAACTAAAACTAAGAA
Found at i:62850959 original size:29 final size:29
Alignment explanation
Indices: 62850926--62850991 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
62850916 ACCTTGTGAG
62850926 ACTTATGATGTGTATAGGCAATTAAATGA
1 ACTTATGATGTGTATAGGCAATTAAATGA
62850955 ACTTATGATGTGTATAGGCAATTAAATGA
1 ACTTATGATGTGTATAGGCAATTAAATGA
62850984 ACTTATGA
1 ACTTATGA
62850992 CCTTGATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.35
Consensus pattern (29 bp):
ACTTATGATGTGTATAGGCAATTAAATGA
Found at i:62856043 original size:21 final size:21
Alignment explanation
Indices: 62856001--62856076 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
62855991 GTTTGCCCAT
* *
62856001 AAGGTCGTATACCTCAGTCAC
1 AAGGTCGTGTACCTCAGCCAC
* * *
62856022 ACGGTTGTGTACCTTAGCCAC
1 AAGGTCGTGTACCTCAGCCAC
*
62856043 AAGGTCGTGTATCTCAGCCAC
1 AAGGTCGTGTACCTCAGCCAC
62856064 ATA-GTCGTGTACC
1 A-AGGTCGTGTACC
62856077 CCTGTAACAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 43 0.98
22 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (21 bp):
AAGGTCGTGTACCTCAGCCAC
Found at i:62866099 original size:25 final size:25
Alignment explanation
Indices: 62866050--62866130 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
62866040 ATACATGTAT
* *
62866050 GCTCATACAAGC-G-ATATACGATAA
1 GCTCATACGAGCTGAATA-ACGGTAA
* *
62866074 GCTCCTCCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
62866099 GCTCATACGAGCTGAGTATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
62866124 GCTCATA
1 GCTCATA
62866131 AAAGCTGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
24 9 0.19
25 35 0.74
26 3 0.06
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:62866136 original size:25 final size:25
Alignment explanation
Indices: 62866083--62866147 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
62866073 AGCTCCTCCG
* * **
62866083 AGCTGAATAACGGTAAGCTCATACG
1 AGCTGAGTATCGGTAAGCTCATAAA
62866108 AGCTGAGTATCGGTAAGCTCATAAA
1 AGCTGAGTATCGGTAAGCTCATAAA
*
62866133 AGCTG-GAATCGGTAA
1 AGCTGAGTATCGGTAA
62866148 CCCTAATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
24 9 0.26
25 26 0.74
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (25 bp):
AGCTGAGTATCGGTAAGCTCATAAA
Found at i:62868687 original size:18 final size:18
Alignment explanation
Indices: 62868641--62868684 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
62868631 TTGATTTTTT
62868641 TATAAAAAATTCAAAAAA
1 TATAAAAAATTCAAAAAA
* *
62868659 TATAAAAAATTCGAAAAG
1 TATAAAAAATTCAAAAAA
62868677 T-TAAAAAA
1 TATAAAAAA
62868685 ATTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (18 bp):
TATAAAAAATTCAAAAAA
Found at i:62868720 original size:9 final size:9
Alignment explanation
Indices: 62868641--62868722 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 9
62868631 TTGATTTTTT
62868641 TATAAAAAA
1 TATAAAAAA
62868650 T-TCAAAAAA
1 TAT-AAAAAA
62868659 TATAAAAAA
1 TATAAAAAA
* *
62868668 T-TCGAAAAG
1 TAT-AAAAAA
62868677 T-TAAAAAAA
1 TAT-AAAAAA
* *
62868686 TTATTAAAAT
1 -TATAAAAAA
62868696 TATTAAAAAA
1 TA-TAAAAAA
62868706 TCATAAAAAA
1 T-ATAAAAAA
62868716 TATAAAA
1 TATAAAA
62868723 TTTATTTAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
8 2 0.04
9 33 0.58
10 20 0.35
11 2 0.04
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (9 bp):
TATAAAAAA
Found at i:62870144 original size:15 final size:16
Alignment explanation
Indices: 62870124--62870166 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
62870114 ATGTAGGTGG
62870124 TTCGCATATAATCT-A
1 TTCGCATATAATCTAA
*
62870139 TTCGCATATCAT-TAA
1 TTCGCATATAATCTAA
*
62870154 TTCACATATAATC
1 TTCGCATATAATC
62870167 AATCTCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (16 bp):
TTCGCATATAATCTAA
Found at i:62870709 original size:74 final size:72
Alignment explanation
Indices: 62870605--62870746 Score: 162
Period size: 74 Copynumber: 1.9 Consensus size: 72
62870595 TGCAAAAGTG
* * * *
62870605 CATATATTATTTATAGTAAACCCACGCATGCA-TACATATAATAT-AAAACCATTTTTGATGCAA
1 CATATATTATTTATAATAAACCCACACATGCACT-CATATAAT-TCAAAACCACTTTTAATGCAA
62870668 AGATATGTT
64 AGATATGTT
** * *
62870677 CATATATTATTTATAATATAAACCTGCACATGCACTCATTTAATTCAAAACCCCTTTTAATGCAA
1 CATATATTATTTAT-A-ATAAACCCACACATGCACTCATATAATTCAAAACCACTTTTAATGCAA
62870742 AGATA
64 AGATA
62870747 CATGTATTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
72 14 0.24
73 2 0.03
74 41 0.71
75 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.35
Consensus pattern (72 bp):
CATATATTATTTATAATAAACCCACACATGCACTCATATAATTCAAAACCACTTTTAATGCAAAG
ATATGTT
Found at i:62870981 original size:23 final size:22
Alignment explanation
Indices: 62870921--62870983 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
62870911 TACATTTAAA
**
62870921 AGGTTCGCACAACACATAGAAG
1 AGGTTCGCACAATGCATAGAAG
* * *
62870943 AGGTTCCCACATTGCATGGAAG
1 AGGTTCGCACAATGCATAGAAG
*
62870965 AAGTTTCGCACAATGCATA
1 -AGGTTCGCACAATGCATA
62870984 TAATAAATAC
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (22 bp):
AGGTTCGCACAATGCATAGAAG
Found at i:62873025 original size:12 final size:12
Alignment explanation
Indices: 62873010--62873036 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62873000 TTTTTCTATA
62873010 AATTTTTTAATT
1 AATTTTTTAATT
62873022 AATTTTTTAATT
1 AATTTTTTAATT
62873034 AAT
1 AAT
62873037 AAGCATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AATTTTTTAATT
Found at i:62873444 original size:16 final size:14
Alignment explanation
Indices: 62873413--62873453 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
62873403 AAACACCAAC
62873413 TATTTTTTTTTATA
1 TATTTTTTTTTATA
*
62873427 TATTTTTCTTTATA
1 TATTTTTTTTTATA
**
62873441 TATAATTTTTTAT
1 TATTTTTTTTTAT
62873454 GTTATATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTTTTATA
Found at i:62873653 original size:109 final size:109
Alignment explanation
Indices: 62873440--62873647 Score: 242
Period size: 109 Copynumber: 1.9 Consensus size: 109
62873430 TTTTCTTTAT
* * * * * *
62873440 ATATAATTTTTTATGTTATATGTTTATTTTTTTTCACGTATATTGTGAGTATCGTAAATTCTAAT
1 ATATAATTTTTTATGTTAAATATTTATGTTTTTCCACCTACATTGTGAGTATCGTAAATTCTAAT
* * *
62873505 ATGAAAAATTAATTAATCATTTCAAATATTATTGATTTTAATAA
66 ATAAAAAATTAAATAATCATTTCAAATATAATTGATTTTAATAA
*
62873549 ATATAATTTTTATATG-TAAATATTTATGTTTTTCCACCTACATTGT-ACGTAT-GATAGATTCT
1 ATATAATTTTT-TATGTTAAATATTTATGTTTTTCCACCTACATTGTGA-GTATCG-TAAATTCT
* * *
62873611 AATATTAAAAAATTAAATGATTATTTCAATTATAATT
63 AATA-TAAAAAATTAAATAATCATTTCAAATATAATT
62873648 TTTTTATATG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
108 2 0.02
109 50 0.61
110 30 0.37
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.49
Consensus pattern (109 bp):
ATATAATTTTTTATGTTAAATATTTATGTTTTTCCACCTACATTGTGAGTATCGTAAATTCTAAT
ATAAAAAATTAAATAATCATTTCAAATATAATTGATTTTAATAA
Found at i:62873929 original size:13 final size:14
Alignment explanation
Indices: 62873911--62873943 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
62873901 TATTTGACTC
62873911 ATAAAAAT-TATAT
1 ATAAAAATATATAT
62873924 AT-AAAATATATAT
1 ATAAAAATATATAT
62873937 ATAAAAA
1 ATAAAAA
62873944 ATTAGTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 9 0.50
14 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATATATAT
Found at i:62884420 original size:31 final size:31
Alignment explanation
Indices: 62884385--62884477 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
62884375 AGGAAAATTA
62884385 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
*
62884416 CAAGAGTAATTGAATCCTATTAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
62884447 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
62884478 AAAATTATCT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:62890048 original size:18 final size:18
Alignment explanation
Indices: 62890027--62890088 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
62890017 TTTTTTGCGG
62890027 TTTTTTTGCGCTTTTTGC
1 TTTTTTTGCGCTTTTTGC
***
62890045 TTTTTCTT-TTTTTTTTGCC
1 TTTTT-TTGCGCTTTTTG-C
*
62890064 TTTTTTTGCGCCTTTTGC
1 TTTTTTTGCGCTTTTTGC
62890082 TTTTTTT
1 TTTTTTT
62890089 TTTAAAGAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (18 bp):
TTTTTTTGCGCTTTTTGC
Found at i:62890049 original size:19 final size:19
Alignment explanation
Indices: 62890027--62890089 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
62890017 TTTTTTGCGG
62890027 TTTTTTTGCGCTTTTTGCT
1 TTTTTTTGCGCTTTTTGCT
** *
62890046 TTTTCTTT--TTTTTTTGCC
1 TTTT-TTTGCGCTTTTTGCT
*
62890064 TTTTTTTGCGCCTTTTGCT
1 TTTTTTTGCGCTTTTTGCT
62890083 TTTTTTT
1 TTTTTTT
62890090 TTAAAGAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 17 0.50
20 3 0.09
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (19 bp):
TTTTTTTGCGCTTTTTGCT
Found at i:62890068 original size:37 final size:37
Alignment explanation
Indices: 62890012--62890091 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
62890002 GGTAGGCAAC
* *
62890012 TTTTTTTTTTTGCGGTTTTTTTGCGCTTTTTGCTTTT
1 TTTTTTTTTTTGCGCTTTTTTTGCGCCTTTTGCTTTT
62890049 TCTTTTTTTTTTGC-CTTTTTTTGCGCCTTTTGCTTTT
1 T-TTTTTTTTTTGCGCTTTTTTTGCGCCTTTTGCTTTT
62890086 TTTTTT
1 TTTTTT
62890092 AAAGAATAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 5 0.12
37 23 0.57
38 12 0.30
ACGTcount: A:0.00, C:0.14, G:0.12, T:0.74
Consensus pattern (37 bp):
TTTTTTTTTTTGCGCTTTTTTTGCGCCTTTTGCTTTT
Found at i:62890300 original size:3 final size:3
Alignment explanation
Indices: 62890292--62890323 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
62890282 AAATTAGTTA
62890292 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62890324 AAGGATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62892380 original size:22 final size:22
Alignment explanation
Indices: 62892355--62892397 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
62892345 CTCATGGCTA
62892355 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
62892377 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
62892398 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:62895977 original size:84 final size:83
Alignment explanation
Indices: 62895798--62896185 Score: 327
Period size: 84 Copynumber: 4.7 Consensus size: 83
62895788 TTATATCATT
* *
62895798 AAATCAAATTAAAATC-TGTTAAACGACGAGAATAAATCCCGAAACAGA-ATTATTTGA-TTACA
1 AAATCAAA-TAAAATCTTGTTAAACGACGAGAATAAATCCCGAAACAGATTTTATTTAATTTA-A
** *
62895860 TCTTTTTTTGGAAACAAAACA
64 T-TTAATTTGGAAACAAAATA
* * * *
62895881 ATATCGAATAAAATCTTGTTAAAC-AGCGAAAATTAATCCCGAAACAGATTTTATTTAATTTAAT
1 AAATCAAATAAAATCTTGTTAAACGA-CGAGAATAAATCCCGAAACAGATTTTATTTAATTTAAT
62895945 TTAAATTTGGAAACAAAATA
65 TT-AATTTGGAAACAAAATA
* * * *
62895965 AAATCAATTAAAATCTTGTTAAATGACTG-GAATAAATCGCGAAACATATTTTATTTAATTCT-A
1 AAATCAAATAAAATCTTGTTAAACGAC-GAGAATAAATCCCGAAACAGATTTTATTTAATT-TAA
62896028 TTCTAATTTGGAAACAAAAT-
64 TT-TAATTTGGAAACAAAATA
* *
62896048 --A--AAATAAAATCTTGTTAAACG-CCATGAATAAATCCCGAAACAGATTTTATTTTATTTAAT
1 AAATCAAATAAAATCTTGTTAAACGACGA-GAATAAATCCCGAAACAGATTTTATTTAATTTAA-
* *
62896108 TTCTCATTTTTGACAACAAAATCA
64 TT-T-AATTTGGA-AACAAAAT-A
** * * * * * *
62896132 AAAT-TTATTAAAT-TCGTTGAACGACGGGAATCAATCCCGAAAAAGATTTTATTT
1 AAATCAAATAAAATCTTGTTAAACGACGAGAATAAATCCCGAAACAGATTTTATTT
62896186 TACTCGTTTT
Statistics
Matches: 250, Mismatches: 34, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
78 2 0.01
79 47 0.19
80 4 0.02
81 7 0.03
82 16 0.06
83 36 0.14
84 90 0.36
85 7 0.03
86 34 0.14
87 7 0.03
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (83 bp):
AAATCAAATAAAATCTTGTTAAACGACGAGAATAAATCCCGAAACAGATTTTATTTAATTTAATT
TAATTTGGAAACAAAATA
Found at i:62896335 original size:79 final size:79
Alignment explanation
Indices: 62896145--62896422 Score: 373
Period size: 79 Copynumber: 3.5 Consensus size: 79
62896135 TTTATTAAAT
* * **
62896145 TCGTTGAACGACGGGAATCAATCCCGAAAAAGATTTTATTTTACTCGTTTTTGGAAAT-AAA-AA
1 TCGTTAAACGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAACAA
* *
62896208 AAT-TTGAATAAAA
66 AATATGGAAAAAAA
* *
62896221 TCGTTAAACGGCTGGAATCAATCCCGAAACTGATTTTATTTTACTCGTTTTTGGAAATAAAACAA
1 TCGTTAAACGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAACAA
62896286 AATATGGAAAAAAA
66 AATATGGAAAAAAA
*
62896300 TCGTTAAATGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAATCA
1 TCGTTAAACGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAA-CA
*
62896365 AAATAATGGAATAAAAT
65 AAAT-ATGGAA-AAAAA
* * * * *
62896382 TCATTGAACAGCGGGAATAAATCCCGAAATGGATTTTATTT
1 TCGTTAAACGGCGGGAATCAATCCCGAAACGGATTTTATTT
62896423 ACTTCTAATT
Statistics
Matches: 179, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
76 53 0.30
77 3 0.02
78 5 0.03
79 67 0.37
80 6 0.03
81 6 0.03
82 39 0.22
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (79 bp):
TCGTTAAACGGCGGGAATCAATCCCGAAACGGATTTTATTTTACTCGTTTTTGGAAATAAAACAA
AATATGGAAAAAAA
Found at i:62898755 original size:44 final size:43
Alignment explanation
Indices: 62898651--62898781 Score: 135
Period size: 43 Copynumber: 3.0 Consensus size: 43
62898641 AAAGCTCGTA
* * *
62898651 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATC-AAATAT
1 CAATGCCAACGTCCCAGACG-GGTCTTACACGAAATCTCAATAT
*
62898694 CGATGCC-ACTGTCCCAGACAGGGTCTTACACGAAAGTCTCAA-AT
1 CAATGCCAAC-GTCCCAGAC-GGGTCTTACACGAAA-TCTCAATAT
* *
62898738 CAATGCCAACGTCCCAGACTTGGTCTTACACCAAATCTC-ATAT
1 CAATGCCAACGTCCCAGAC-GGGTCTTACACGAAATCTCAATAT
62898781 C
1 C
62898782 GAAATCCTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
42 3 0.04
43 34 0.46
44 33 0.45
45 4 0.05
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGGGTCTTACACGAAATCTCAATAT
Found at i:62900052 original size:3 final size:3
Alignment explanation
Indices: 62900044--62900073 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
62900034 CCCCCAAAAT
62900044 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
62900074 GTGATCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:62903307 original size:50 final size:50
Alignment explanation
Indices: 62903250--62903348 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
62903240 TTTTTATGGA
62903250 AGATGTGCTTCTTAGCCGCTTGATTGGAATTGTTATGTATTGTGTTACTT
1 AGATGTGCTTCTTAGCCGCTTGATTGGAATTGTTATGTATTGTGTTACTT
*
62903300 AGATGTGCTTCTTAGCTGCTTGATTGGAATTGTTATGTATTGTGTTACT
1 AGATGTGCTTCTTAGCCGCTTGATTGGAATTGTTATGTATTGTGTTACT
62903349 ACCAGCTCTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.46
Consensus pattern (50 bp):
AGATGTGCTTCTTAGCCGCTTGATTGGAATTGTTATGTATTGTGTTACTT
Found at i:62909722 original size:14 final size:15
Alignment explanation
Indices: 62909694--62909730 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
62909684 GTTATTTTAC
*
62909694 TTAATTTCA-TTAGT
1 TTAATTTAACTTAGT
62909708 TT-ATTTAACTTAGT
1 TTAATTTAACTTAGT
62909722 TTAATTTAA
1 TTAATTTAA
62909731 TTTCTACAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (15 bp):
TTAATTTAACTTAGT
Found at i:62913234 original size:19 final size:20
Alignment explanation
Indices: 62913200--62913238 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
62913190 CACAGAAAGG
62913200 AATTGAAGTGGATAGAAAAA
1 AATTGAAGTGGATAGAAAAA
62913220 AATTGAAGT-GATAGAAAAA
1 AATTGAAGTGGATAGAAAAA
62913239 TTGCCATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (20 bp):
AATTGAAGTGGATAGAAAAA
Found at i:62913241 original size:17 final size:19
Alignment explanation
Indices: 62913200--62913238 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
62913190 CACAGAAAGG
62913200 AATTGAAGTGGATAGAAAAA
1 AATTGAAGTGGATAG-AAAA
62913220 AATTGAAGT-GATAGAAAA
1 AATTGAAGTGGATAGAAAA
62913238 A
1 A
62913239 TTGCCATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AATTGAAGTGGATAGAAAA
Found at i:62923487 original size:45 final size:45
Alignment explanation
Indices: 62923418--62923524 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
62923408 CTTTTAGCCG
* * * *
62923418 TGGTCTTACTCATTTCT-ATTATGATACTATATCATCTTTCAGCTA
1 TGGTCATACTCATTT-TAATGATGATACTATAGCATCATTCAGCTA
**
62923463 TGGTCATACTCATTTTAATGATGATGTTATAGCATCATTCAGCTA
1 TGGTCATACTCATTTTAATGATGATACTATAGCATCATTCAGCTA
*
62923508 TGGTCATACTCAATTTA
1 TGGTCATACTCATTTTA
62923525 GGTGTATAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 53 0.98
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (45 bp):
TGGTCATACTCATTTTAATGATGATACTATAGCATCATTCAGCTA
Found at i:62930089 original size:6 final size:6
Alignment explanation
Indices: 62930078--62930103 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
62930068 CGCTTCGCTC
62930078 TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TT
62930104 GTTTTCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:62933979 original size:8 final size:9
Alignment explanation
Indices: 62933952--62934025 Score: 73
Period size: 9 Copynumber: 8.0 Consensus size: 9
62933942 AAAAAAATAT
62933952 TTTAAAAATA
1 TTTAAAAA-A
*
62933962 TTT-TAAAA
1 TTTAAAAAA
62933970 -TTAAAAAA
1 TTTAAAAAA
62933978 TTTAAAAAGTA
1 TTTAAAAA--A
62933989 TTTTAAAAAA
1 -TTTAAAAAA
62933999 TTT-AAAAA
1 TTTAAAAAA
62934007 TTTAAAAAA
1 TTTAAAAAA
62934016 TTTTAAAAAA
1 -TTTAAAAAA
62934026 GTATTTTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
7 2 0.04
8 13 0.24
9 18 0.33
10 13 0.24
11 1 0.02
12 8 0.15
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:62934036 original size:11 final size:10
Alignment explanation
Indices: 62933945--62934048 Score: 69
Period size: 11 Copynumber: 10.5 Consensus size: 10
62933935 AAAAATTAAA
62933945 AAAATATTTT
1 AAAATATTTT
62933955 AAAAATATTTT
1 -AAAATATTTT
62933966 -AAA-A--TT
1 AAAATATTTT
* *
62933972 AAAAAATTTA
1 AAAATATTTT
62933982 AAAAGTATTTT
1 AAAA-TATTTT
*
62933993 AAAA-AATTT
1 AAAATATTTT
62934002 AAAA-A-TTT
1 AAAATATTTT
*
62934010 AAAAAATTTT
1 AAAATATTTT
62934020 AAAAAAGTATTTT
1 --AAAA-TATTTT
62934033 AAAAGTATTTT
1 AAAA-TATTTT
62934044 AAAAT
1 AAAAT
62934049 TAAAAAAATA
Statistics
Matches: 78, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 9 0.12
9 13 0.17
10 9 0.12
11 33 0.42
12 4 0.05
13 5 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
AAAATATTTT
Found at i:62934784 original size:30 final size:29
Alignment explanation
Indices: 62934752--62934806 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
62934742 AAGTCTAATT
*
62934752 TTTTTTA-AATTTACCGAAATGGGCCCGG
1 TTTTTTATTATTTACCGAAATGGGCCCGG
*
62934780 TTTTTTATTATTTACCGGAATGGGCCC
1 TTTTTTATTATTTACCGAAATGGGCCC
62934807 TTTTCCCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (29 bp):
TTTTTTATTATTTACCGAAATGGGCCCGG
Found at i:62934922 original size:40 final size:40
Alignment explanation
Indices: 62934847--62934924 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
62934837 GATGTCAAGG
* * * **
62934847 GACGTGTCAGCAAATCGCGTCCACGTCAGCGCGGTTTGCT
1 GACGTGGCAGCAAATCGCATCCACGTAAGAACGGTTTGCT
62934887 GACGTGGCAGCAAATCGCATCCACGTAAGAACGGTTTG
1 GACGTGGCAGCAAATCGCATCCACGTAAGAACGGTTTG
62934925 TGTCCACGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (40 bp):
GACGTGGCAGCAAATCGCATCCACGTAAGAACGGTTTGCT
Found at i:62936366 original size:7 final size:7
Alignment explanation
Indices: 62936354--62936379 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
62936344 TAGTCGATTG
62936354 GTATTTA
1 GTATTTA
62936361 GTATTTA
1 GTATTTA
62936368 GTATTTA
1 GTATTTA
62936375 GTATT
1 GTATT
62936380 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:62937057 original size:18 final size:18
Alignment explanation
Indices: 62937030--62937069 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
62937020 TAGGTGCGTT
* *
62937030 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
62937048 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
62937066 TCCT
1 TCCT
62937070 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Done.