Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 42 of 193
Found at i:12792943 original size:59 final size:59
Alignment explanation
Indices: 12792777--12792943 Score: 248
Period size: 59 Copynumber: 2.8 Consensus size: 59
12792767 AAACTTCCCT
* *
12792777 AAATCCCATTTTTAACCCCGATTTCACCAAAATTTACCA-TTTTACCCCGAATCTTTTAA
1 AAATTCCATTTTTAACCCCGATTTCACCAAAA-TTACCATTTTTCCCCCGAATCTTTTAA
*
12792836 AAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTT-A
1 AAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTTCCCCCGAATCTTTTAA
* *
12792895 AAATTCCATTTTTAACCTCGATTACACCAAAATTACCATTTTGTCCCCC
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTT-TCCCCC
12792944 AGGTATCCAT
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
58 14 0.14
59 65 0.66
60 20 0.20
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTTCCCCCGAATCTTTTAA
Found at i:12809070 original size:11 final size:11
Alignment explanation
Indices: 12809047--12809086 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
12809037 TTACAATCCA
12809047 ATTTTATTTTTT
1 ATTTTA-TTTTT
12809059 ATTTTATTTTT
1 ATTTTATTTTT
*
12809070 A-TTTATTATT
1 ATTTTATTTTT
12809080 ATTTTAT
1 ATTTTAT
12809087 AAACAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 11 0.42
12 6 0.23
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:12810414 original size:76 final size:76
Alignment explanation
Indices: 12810311--12810511 Score: 255
Period size: 76 Copynumber: 2.6 Consensus size: 76
12810301 TTATAATATA
* * ** *
12810311 TATATATATATATATTGCTT-ATTCTTTATATATAGTATGTATATATTTGCCATATACCTGCTGT
1 TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCGT
*
12810375 TTCTTTAAGTT
66 TTCCTTAAGTT
* * *
12810386 GTATATACATATATATAG-TTAATTCTTTATATATAGTATGCATATATTTGTCATATACCCACCG
1 -TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCG
12810450 TTTCCTTAAGTT
65 TTTCCTTAAGTT
* *
12810462 T-TATGTATATATATAGCTTATTTCTTTATATAGTATGTATGAATATATTT
1 TATATATATATATATAGCTTAATTCTTTATATA-TA-GTATGAATATATTT
12810512 TATTCTGTAT
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
74 13 0.12
75 17 0.16
76 66 0.61
77 13 0.12
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.50
Consensus pattern (76 bp):
TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCGT
TTCCTTAAGTT
Found at i:12822269 original size:50 final size:50
Alignment explanation
Indices: 12822161--12822269 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
12822151 GTGGAGGTGC
* * * * *
12822161 AGATTGAAACCATAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGT
1 AGATTGAAGCCATAATGGAAAATCTCATACACCTAAAGCTGTAAAGGAGA
* * *
12822211 AGAATGAAGCTATAATGGAAAATCTCATCCACCTAAAGCTGTAAAGGAGA
1 AGATTGAAGCCATAATGGAAAATCTCATACACCTAAAGCTGTAAAGGAGA
12822261 AGATTGAAG
1 AGATTGAAG
12822270 TCACAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (50 bp):
AGATTGAAGCCATAATGGAAAATCTCATACACCTAAAGCTGTAAAGGAGA
Found at i:12822391 original size:40 final size:40
Alignment explanation
Indices: 12822347--12822869 Score: 217
Period size: 40 Copynumber: 13.3 Consensus size: 40
12822337 CTAATCAGAA
*
12822347 GGCAGATTGAAAACCATCCGATCTCTTACCCCGATCATGG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCATGG
* * * * **
12822387 GGCAGATTG-AAGCAATCCAATCTTTTACCCTAACCA-GAG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCATG-G
* ** * * *
12822426 GGCATAATTGAAGGCCATCCAATCTCTTACCCCGATCATGA
1 GGCA-GATTGAAAACCATCCGATCTCTTACCCCGACCATGG
* * ** *
12822467 GGCAGATTGAAGAA--ATCCAATCTTTTACCCTAACTA-GAG
1 GGCAGATTGAA-AACCATCCGATCTCTTACCCCGACCATG-G
* * * *
12822506 GGCAGATTGAAGATCATCCGATCTTTTACCCTC-ATCATGG
1 GGCAGATTGAAAACCATCCGATCTCTTACCC-CGACCATGG
* * * * * * * *
12822546 GGCAGATTG-AAGCAATTCAATCTTTTA-CACTAGC-TAGAG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCAT-G-G
* * *
12822585 GGCAGATTGAAGACCATCCGATCTCTTACCTCGATCATGG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCATGG
* * * * * *
12822625 GGCAGATTG-AAGCAATCCAATCTTTTA-CCCTAGC-TAGAG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCAT-G-G
* *
12822664 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATAG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCATGG
** * * *
12822704 GGCAGATT-AAAGGTCATCTGATCTTTTACCTCGACCA-GAG
1 GGCAGATTGAAA-ACCATCCGATCTCTTACCCCGACCATG-G
* * * **
12822744 GACAGATT-AAAGATCATTCGATCTCTTACCCAAACCATGG
1 GGCAGATTGAAA-ACCATCCGATCTCTTACCCCGACCATGG
** * * ** * *
12822784 GATAGATTG-AAGCAAT-C---CT-TTACCCTAATCGA-AG
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGA-CCATGG
* * *
12822818 GGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGA
1 GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCATGG
12822858 GGCAGATTGAAA
1 GGCAGATTGAAA
12822870 CAATCTTTTA
Statistics
Matches: 355, Mismatches: 95, Indels: 66
0.69 0.18 0.13
Matches are distributed among these distances:
34 16 0.05
35 8 0.02
36 1 0.00
37 3 0.01
38 13 0.04
39 106 0.30
40 168 0.47
41 37 0.10
42 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (40 bp):
GGCAGATTGAAAACCATCCGATCTCTTACCCCGACCATGG
Found at i:12822567 original size:79 final size:79
Alignment explanation
Indices: 12822326--12822874 Score: 641
Period size: 79 Copynumber: 7.0 Consensus size: 79
12822316 TATAACCTCT
* *
12822326 AATCTTTTACCCTAA-TCAGAAGGCAGATTGAAAACCATCCGATCTCTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACT-AGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGC
12822390 AGATTGAAGCAATCC
65 AGATTGAAGCAATCC
* * * * *
12822405 AATCTTTTACCCTAACCAGAGGGCATAATTGAAGGCCATCCAATCTCTTACCCCGATCATGAGGC
1 AATCTTTTACCCTAACTAGAGGGCA-GATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGC
*
12822470 AGATTGAAGAAATCC
65 AGATTGAAGCAATCC
* *
12822485 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGATCATCCGATCTTTTACCCTC-ATCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCC-CGATCATGGGGC
*
12822549 AGATTGAAGCAATTC
65 AGATTGAAGCAATCC
* * *
12822564 AATCTTTTACACTAGCTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCTCGATCATGGGGCA
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGCA
12822629 GATTGAAGCAATCC
66 GATTGAAGCAATCC
* * *
12822643 AATCTTTTACCCTAGCTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATAGGGCA
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGCA
* *
12822708 GATTAAAGGTC-ATCT
66 GATTGAA-G-CAATCC
* * * * * * * ** * **
12822723 GATCTTTTA-CCTCGACCAGAGGACAGATTAAAGATCATTCGATCTCTTACCCAAACCATGGGAT
1 AATCTTTTACCCT-AACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGC
12822787 AGATTGAAGCAAT-C
65 AGATTGAAGCAATCC
* * * *
12822801 ---C-TTTACCCTAA-TCGAAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGAGGC
1 AATCTTTTACCCTAACTAG-AGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGC
*
12822861 AGATTGAAACAATC
65 AGATTGAAGCAATC
12822875 TTTTACCTTA
Statistics
Matches: 403, Mismatches: 56, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
73 1 0.00
74 54 0.13
75 4 0.01
78 2 0.00
79 210 0.52
80 131 0.33
81 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (79 bp):
AATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGCA
GATTGAAGCAATCC
Found at i:12822759 original size:238 final size:233
Alignment explanation
Indices: 12822326--12822874 Score: 676
Period size: 238 Copynumber: 2.3 Consensus size: 233
12822316 TATAACCTCT
* * *
12822326 AATCTTTTACCCTAATCAGAA-GGCAGATTGAAAACCATCCGATCTCTTACCCCGATCATGGGGC
1 AATCCTTTACACTAAT-AGAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGC
*
12822390 AGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATAATTGAAGGCCATCCAATCTCTTA
65 AGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATAATTGAAGACCATCCAATCTCTTA
* * * * *
12822455 CCCCGATCATGAGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGAT
130 CCCCGACCATGAGGCAGATTAAAGAAATCCAATCTTTTACCCTAACCAGAGGACAGATTAAAGAT
* ** * *
12822520 CATCCGATCTTTTACCCTCATCATGGGGCAGATTGAAGC
195 CATCCGATCTCTTACCCAAACCATGGGACAGATTGAAGC
* *
12822559 AATTCAATCTTTTACACTAGCTAG-AGGGCAGATTGAAGACCATCCGATCTCTTACCTCGATCAT
1 AA-TC---C-TTTACACTA-ATAGAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCAT
* * * *
12822623 GGGGCAGATTGAAGCAATCCAATCTTTTACCCTAGCTAGAGGGCA-GATTGAAGACCATCCGATC
60 GGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATAATTGAAGACCATCCAATC
** ** *
12822687 TCTTACCCCGACCAT-AGGGCAGATTAAAGGTCATCTGATCTTTTA-CCTCGACCAGAGGACAGA
125 TCTTACCCCGACCATGA-GGCAGATTAAA-GAAATCCAATCTTTTACCCT-AACCAGAGGACAGA
* *
12822750 TTAAAGATCATTCGATCTCTTACCCAAACCATGGGATAGATTGAAGC
187 TTAAAGATCATCCGATCTCTTACCCAAACCATGGGACAGATTGAAGC
* * * * *
12822797 AATCCTTTACCCTAATCGAAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGAGGCA
1 AATCCTTTACACTAATAGAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGCA
*
12822862 GATTGAAACAATC
66 GATTGAAGCAATC
12822875 TTTTACCTTA
Statistics
Matches: 270, Mismatches: 35, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
232 2 0.01
233 64 0.24
234 3 0.01
236 1 0.00
237 46 0.17
238 153 0.57
239 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (233 bp):
AATCCTTTACACTAATAGAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGCA
GATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATAATTGAAGACCATCCAATCTCTTAC
CCCGACCATGAGGCAGATTAAAGAAATCCAATCTTTTACCCTAACCAGAGGACAGATTAAAGATC
ATCCGATCTCTTACCCAAACCATGGGACAGATTGAAGC
Found at i:12823380 original size:11 final size:11
Alignment explanation
Indices: 12823364--12823396 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12823354 CAATTTTGTT
12823364 TTTTTATTTTA
1 TTTTTATTTTA
12823375 TTTTTA-TTTA
1 TTTTTATTTTA
*
12823385 TTATTATTTTA
1 TTTTTATTTTA
12823396 T
1 T
12823397 AAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:12823396 original size:15 final size:15
Alignment explanation
Indices: 12823362--12823394 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12823352 TCCAATTTTG
12823362 TTTT-TTTATTTTAT
1 TTTTATTTATTTTAT
12823376 TTTTATTTATTATTAT
1 TTTTATTTATT-TTAT
12823392 TTT
1 TTT
12823395 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTATTTTAT
Found at i:12824695 original size:69 final size:70
Alignment explanation
Indices: 12824622--12824828 Score: 292
Period size: 69 Copynumber: 2.9 Consensus size: 70
12824612 CCTTATATAA
12824622 TATATATATATATATATATTGCTTATTCTTTATATATAGTATGTATATATTTGCCATATACCTGC
1 TATATATATATATATATATTGCTTATTCTTTATATATAGTATGTATATATTTGCCATATACCTGC
12824687 TG-TT
66 TGTTT
12824691 TATATATATATATATATATTGCTTATTCTTTATATATAGTATGTATATATTTGCCATATACCTGC
1 TATATATATATATATATATTGCTTATTCTTTATATATAGTATGTATATATTTGCCATATACCTGC
12824756 TGTTTCTT
66 TG--T-TT
* * * * *
12824764 TAAGTTGTATATACATATATATAG-TTAATTCTTTATATATAGTATGCATATATTTGTCATATAC
1 T-A--TATATATATATATATATTGCTT-ATTCTTTATATATAGTATGTATATATTTGCCATATAC
12824828 C
62 C
12824829 CACCGTTTCC
Statistics
Matches: 125, Mismatches: 5, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
69 67 0.54
73 3 0.02
74 1 0.01
75 2 0.02
76 52 0.42
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (70 bp):
TATATATATATATATATATTGCTTATTCTTTATATATAGTATGTATATATTTGCCATATACCTGC
TGTTT
Found at i:12824802 original size:76 final size:76
Alignment explanation
Indices: 12824626--12824895 Score: 281
Period size: 76 Copynumber: 3.6 Consensus size: 76
12824616 ATATAATATA
* * **
12824626 TATATATATATATATTGCTT-ATTCTTTATATATAGTATGTATATATTTGCCATATA-CCTGC-T
1 TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCGT
* *
12824688 GT--TT-A-TA
66 TTCCTTAAGTT
* * ** *
12824695 TATATATATATATATTGCTT-ATTCTTTATATATAGTATGTATATATTTGCCATATACCTGCTGT
1 TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCGT
*
12824759 TTCTTTAAGTT
66 TTCCTTAAGTT
* * *
12824770 GTATATACATATATATAG-TTAATTCTTTATATATAGTATGCATATATTTGTCATATACCCACCG
1 -TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCG
12824834 TTTCCTTAAGTT
65 TTTCCTTAAGTT
* * *
12824846 T-TTTGTATATATATAGCTTATTTCTTTATATAGTATGTATGAATATATTT
1 TATATATATATATATAGCTTAATTCTTTATATA-TA-GTATGAATATATTT
12824896 TATTCTGTAT
Statistics
Matches: 171, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
69 56 0.33
70 1 0.01
71 2 0.01
73 2 0.01
74 13 0.08
75 18 0.11
76 66 0.39
77 13 0.08
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.50
Consensus pattern (76 bp):
TATATATATATATATAGCTTAATTCTTTATATATAGTATGAATATATTTGCCATATACCCACCGT
TTCCTTAAGTT
Found at i:12837424 original size:151 final size:151
Alignment explanation
Indices: 12837242--12837677 Score: 779
Period size: 148 Copynumber: 2.9 Consensus size: 151
12837232 CTCTTCTTCA
*
12837242 TCTTCATCTTCATCTTCTTCCCTTTTGATTCTAATATATTTAATTACAAATCTGTCTCAAAGCTT
1 TCTTCATCTTCATCTTCTTCCCTTTTGATTCTAATATATTTAGTTACAAATCTGTCTCAAAGCTT
12837307 GAATCTTTGAAACTCATTAACCTAAAAAAACTTAACGGGAAGAAGATATTGGATTCAAAGATATT
66 GAATCTTTGAAACTCATTAACCTAAAAAAACTTAACGGGAAGAAGATATTGGATTCAAAGATATT
12837372 GAATCTTCCACAGACCTCTCT
131 GAATCTTCCACAGACCTCTCT
*
12837393 TCTTCATATTCATCTTCTTCCCTTTTGATTCTAATATATTTAGTTACAAATCTGTCTCAAAGCTT
1 TCTTCATCTTCATCTTCTTCCCTTTTGATTCTAATATATTTAGTTACAAATCTGTCTCAAAGCTT
12837458 GAATCTTTGAAACTCATTAACCTAAAAAAACTTAACGGGAAGAAGATATTGGATTCAAAG---TT
66 GAATCTTTGAAACTCATTAACCTAAAAAAACTTAACGGGAAGAAGATATTGGATTCAAAGATATT
12837520 GAATCTTCCACAGACCTCTCT
131 GAATCTTCCACAGACCTCTCT
* *
12837541 TCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTT
1 TCTTCATCTTCATCTTCTTCCCTTTTGATTCTAATATATTTAGTTACAAATCTGTCTCAAAGCTT
* * * *
12837606 GAATCTTTGAAACCCATTAACCCAAAAAAACTTAATGGGAAGAAGATATTGGAATCAAAGATATT
66 GAATCTTTGAAACTCATTAACCTAAAAAAACTTAACGGGAAGAAGATATTGGATTCAAAGATATT
12837671 GAATCTT
131 GAATCTT
12837678 TGGGTTAATG
Statistics
Matches: 273, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
148 141 0.52
151 132 0.48
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (151 bp):
TCTTCATCTTCATCTTCTTCCCTTTTGATTCTAATATATTTAGTTACAAATCTGTCTCAAAGCTT
GAATCTTTGAAACTCATTAACCTAAAAAAACTTAACGGGAAGAAGATATTGGATTCAAAGATATT
GAATCTTCCACAGACCTCTCT
Found at i:12838733 original size:20 final size:20
Alignment explanation
Indices: 12838708--12838745 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12838698 CAAGTACTTA
12838708 TATCTAGTATTATTCATCCT
1 TATCTAGTATTATTCATCCT
*
12838728 TATCTATTATTATTCATC
1 TATCTAGTATTATTCATC
12838746 ATTTGTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (20 bp):
TATCTAGTATTATTCATCCT
Found at i:12838861 original size:8 final size:8
Alignment explanation
Indices: 12838848--12838875 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
12838838 ATATATACCA
12838848 CAAATATT
1 CAAATATT
12838856 CAAATATT
1 CAAATATT
12838864 CAAATATT
1 CAAATATT
12838872 CAAA
1 CAAA
12838876 GAAAATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (8 bp):
CAAATATT
Found at i:12845978 original size:30 final size:30
Alignment explanation
Indices: 12845938--12845998 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
12845928 CCAAGAAGAA
12845938 TTATTATGGTTACAAAAGTCTCGTAGTGAG
1 TTATTATGGTTACAAAAGTCTCGTAGTGAG
* *
12845968 TTATTCTGGTTACGAAAGTCTCGTAGTGAG
1 TTATTATGGTTACAAAAGTCTCGTAGTGAG
12845998 T
1 T
12845999 GGTTATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (30 bp):
TTATTATGGTTACAAAAGTCTCGTAGTGAG
Found at i:12853337 original size:22 final size:22
Alignment explanation
Indices: 12853312--12853355 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12853302 ATATTTTGAG
12853312 TTCAAATCATTTTAAGTTTTAT
1 TTCAAATCATTTTAAGTTTTAT
12853334 TTCAAATCATTTTAAGTTTTAT
1 TTCAAATCATTTTAAGTTTTAT
12853356 ATCATTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.55
Consensus pattern (22 bp):
TTCAAATCATTTTAAGTTTTAT
Found at i:12856844 original size:24 final size:24
Alignment explanation
Indices: 12856709--12856869 Score: 94
Period size: 24 Copynumber: 6.8 Consensus size: 24
12856699 TATCAAATAT
* **
12856709 ACGAGCATAAACGTATAGTGATTG
1 ACGAACATAAACGTATAGTGGCTG
* *
12856733 A-TAAGCATAAACGTATAATGGCT-
1 ACGAA-CATAAACGTATAGTGGCTG
* *
12856756 AGCTAGCATAAACGTATAGT-GCTG
1 A-CGAACATAAACGTATAGTGGCTG
* * ** * *
12856780 ACGGATATAAATATATAATGGTTG
1 ACGAACATAAACGTATAGTGGCTG
** ** *
12856804 ACGAGTATAAATATATAGTGACTG
1 ACGAACATAAACGTATAGTGGCTG
* *
12856828 ACAAACATAAACGTATAGAGGCTG
1 ACGAACATAAACGTATAGTGGCTG
*
12856852 ACGAATATAAACGTATAG
1 ACGAACATAAACGTATAG
12856870 CGAATAACAA
Statistics
Matches: 103, Mismatches: 29, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
23 16 0.16
24 85 0.83
25 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (24 bp):
ACGAACATAAACGTATAGTGGCTG
Found at i:12856869 original size:48 final size:48
Alignment explanation
Indices: 12856709--12856869 Score: 148
Period size: 48 Copynumber: 3.4 Consensus size: 48
12856699 TATCAAATAT
* * * *
12856709 ACGAGCATAAACGTATAGTGATTGATAAGCATAAACGTATAATGGCT-
1 ACGAGTATAAACGTATAGTGACTGACAAACATAAACGTATAATGGCTG
* * ** * ** *
12856756 AGCTAGCATAAACGTATAGTG-CTGACGGATATAAATATATAATGGTTG
1 A-CGAGTATAAACGTATAGTGACTGACAAACATAAACGTATAATGGCTG
**
12856804 ACGAGTATAAATATATAGTGACTGACAAACATAAACGTATAGA-GGCTG
1 ACGAGTATAAACGTATAGTGACTGACAAACATAAACGTATA-ATGGCTG
*
12856852 ACGAATATAAACGTATAG
1 ACGAGTATAAACGTATAG
12856870 CGAATAACAA
Statistics
Matches: 87, Mismatches: 23, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
47 33 0.38
48 53 0.61
49 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (48 bp):
ACGAGTATAAACGTATAGTGACTGACAAACATAAACGTATAATGGCTG
Found at i:12856882 original size:24 final size:24
Alignment explanation
Indices: 12856828--12856884 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
12856818 ATAGTGACTG
* ** *
12856828 ACAAACATAAACGTATAGAGGCTG
1 ACAAATATAAACGTATAGAGAATA
* *
12856852 ACGAATATAAACGTATAGCGAATA
1 ACAAATATAAACGTATAGAGAATA
12856876 ACAAATATA
1 ACAAATATA
12856885 TTATACGTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (24 bp):
ACAAATATAAACGTATAGAGAATA
Found at i:12859970 original size:6 final size:6
Alignment explanation
Indices: 12859959--12859986 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12859949 TATATTTATT
12859959 AAATTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAAT
12859987 GAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:12869152 original size:12 final size:12
Alignment explanation
Indices: 12869121--12869168 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
12869111 TTTATAAGTA
12869121 AAAAATATACAT
1 AAAAATATACAT
**
12869133 AATGATATACAT
1 AAAAATATACAT
*
12869145 AAAAATATCCAT
1 AAAAATATACAT
*
12869157 AAAAATGTACAT
1 AAAAATATACAT
12869169 TAAAGTACAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.27
Consensus pattern (12 bp):
AAAAATATACAT
Found at i:12877724 original size:11 final size:10
Alignment explanation
Indices: 12877707--12877753 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
12877697 TTATTAGTCG
12877707 ATTAAAATTT
1 ATTAAAATTT
*
12877717 ATTAAAAATT
1 ATTAAAATTT
*
12877727 ATTTAAATGTT
1 ATTAAAAT-TT
*
12877738 A-TAAAAGTT
1 ATTAAAATTT
12877747 ATTAAAA
1 ATTAAAA
12877754 AAAAAAAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 3 0.10
10 24 0.80
11 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (10 bp):
ATTAAAATTT
Found at i:12877978 original size:31 final size:32
Alignment explanation
Indices: 12877942--12878003 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
12877932 TGTTAAAAGT
* * *
12877942 ATTTTTA-CATTTTTTTACATTTAAAAAAATC
1 ATTTTTATAATTTTTTAACAATTAAAAAAATC
*
12877973 ATTTTTATAATTTTTTAACAATTATAAAAAT
1 ATTTTTATAATTTTTTAACAATTAAAAAAAT
12878004 TCTAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTTTATAATTTTTTAACAATTAAAAAAATC
Found at i:12878027 original size:25 final size:26
Alignment explanation
Indices: 12877980--12878028 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
12877970 ATCATTTTTA
*
12877980 TAATTTTTTAACAATTATAAAAATTC
1 TAATTTTTTAACAAATATAAAAATTC
*
12878006 TAATTTTTTAA-AAATATGAAAAT
1 TAATTTTTTAACAAATATAAAAAT
12878029 CATTAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (26 bp):
TAATTTTTTAACAAATATAAAAATTC
Found at i:12885535 original size:19 final size:19
Alignment explanation
Indices: 12885511--12885553 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
12885501 TAAACGCCTC
12885511 TAAATTA-TTGTTTAAATTT
1 TAAATTACTT-TTTAAATTT
12885530 TAAATTAGCTTTTTAAATTT
1 TAAATTA-CTTTTTAAATTT
12885550 TAAA
1 TAAA
12885554 AATTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 13 0.59
21 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
TAAATTACTTTTTAAATTT
Found at i:12888059 original size:24 final size:24
Alignment explanation
Indices: 12888032--12888077 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12888022 AATAAATCAA
* *
12888032 AATTTATTGTATTCTAATCCAACG
1 AATTTATTGAATACTAATCCAACG
*
12888056 AATTTGTTGAATACTAATCCAA
1 AATTTATTGAATACTAATCCAA
12888078 TTTGATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (24 bp):
AATTTATTGAATACTAATCCAACG
Found at i:12892244 original size:154 final size:153
Alignment explanation
Indices: 12892012--12892289 Score: 432
Period size: 154 Copynumber: 1.8 Consensus size: 153
12892002 TTTCATTTAA
* * * *
12892012 TACTCGCGATGACATATTGTCATCGGACCTTTAATTCGTCATGGATTCATTTACTCACGATGACA
1 TACTCACGATGACATATTGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACA
* * *
12892077 CCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGATATTTAGTCATCGGAC
66 CCTAGTCACCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGAC
12892142 CTTTAATCCGTAAAGGATTCATT
131 CTTTAATCCGTAAAGGATTCATT
*
12892165 TACTCACGATGACAT-TTAGTCATTGGACCTTTAATCCGTAAAGGAATTCATTTACTCACGATGA
1 TACTCACGATGACATATT-GTCATCGGACCTTTAATCCGTAAAGG-ATTCATTTACTCACGATGA
* * *
12892229 CACTTAGTCACCGGACCTTTAATCCGTAAAGGATTCATTTGCTCATGATGACACTTAGTCA
64 CACCTAGTCACCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCA
12892290 CTGGACCCTT
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
152 2 0.02
153 36 0.32
154 74 0.66
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (153 bp):
TACTCACGATGACATATTGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACA
CCTAGTCACCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGAC
CTTTAATCCGTAAAGGATTCATT
Found at i:12892290 original size:51 final size:51
Alignment explanation
Indices: 12892012--12892289 Score: 414
Period size: 51 Copynumber: 5.4 Consensus size: 51
12892002 TTTCATTTAA
* * * * *
12892012 TACTCGCGATGACA-TATTGTCATCGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
12892063 TACTCACGATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
12892114 TACTCACGATGATATTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
12892165 TACTCACGATGACATTTAGTCATTGGACCTTTAATCCGTAAAGGAATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG-ATTCATT
*
12892217 TACTCACGATGACACTTAGTCACCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
12892268 TGCTCATGATGACACTTAGTCA
1 TACTCACGATGACACTTAGTCA
12892290 CTGGACCCTT
Statistics
Matches: 209, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
51 161 0.77
52 48 0.23
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:12896352 original size:2 final size:2
Alignment explanation
Indices: 12896345--12896371 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12896335 AATTGTCATT
12896345 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12896372 GAAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12897274 original size:51 final size:51
Alignment explanation
Indices: 12897192--12897484 Score: 318
Period size: 51 Copynumber: 5.6 Consensus size: 51
12897182 GCTATAAACA
*
12897192 AAAGAGTCCGATGACTAACTGTCATCGTGAGTAAATGAATCCCTTACGAATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
* * *
12897244 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAAAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATG--AATCCCTTACGAATT
* * *
12897297 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
* * * * * * *
12897348 AAAGGTCCGATGACTAAGTTTCATCATAAGCAAATGAATTCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
* * * * **
12897399 AAAAGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAACAA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCT-TAC-GAA-TT
* *
12897453 AAAGGTCCAATGAATATA-TGTCATCGTGAGTA
1 AAAGGTCCGATGACTA-AGTGTCATCGTGAGTA
12897485 TTAAATGAAA
Statistics
Matches: 205, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
51 122 0.60
52 6 0.03
53 50 0.24
54 26 0.13
55 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATT
Found at i:12897329 original size:104 final size:102
Alignment explanation
Indices: 12897196--12897446 Score: 340
Period size: 104 Copynumber: 2.4 Consensus size: 102
12897186 TAAACAAAAG
*
12897196 AGTCCGATGACTAACTGTCATCGTGAGTAAATGAATCCCTTACGAATTAAAGGTCCGATGACTAA
1 AGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATTAAAGGTCCGATGACTAA
* * * * *
12897261 GTGTCATCATGAGTAAATGAAAATCCTTTACGGATTAAA
66 GTGTCATCATAAGCAAATG--AATCCATGACGAATTAAA
* * * *
12897300 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAA
1 AGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATTAAAGGTCCGATGACTAA
* *
12897365 GTTTCATCATAAGCAAATGAATTCATGACGAATTAAA
66 GTGTCATCATAAGCAAATGAATCCATGACGAATTAAA
* * *
12897402 AGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACG
1 AGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCT-TACG
12897447 GAACAAAAAG
Statistics
Matches: 128, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
102 48 0.38
103 4 0.03
104 76 0.59
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (102 bp):
AGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGAATTAAAGGTCCGATGACTAA
GTGTCATCATAAGCAAATGAATCCATGACGAATTAAA
Found at i:12902752 original size:45 final size:46
Alignment explanation
Indices: 12902703--12902794 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
12902693 TAAGAAATAC
12902703 AAATTTGATTAATTCTAACA-TTTTCAATAATTTTTATTATTAACA
1 AAATTTGATTAATTCTAACATTTTTCAATAATTTTTATTATTAACA
*
12902748 AAATTTGATTAATTCTAACATTTTTCAGTAATTTTTATTATTAACA
1 AAATTTGATTAATTCTAACATTTTTCAATAATTTTTATTATTAACA
12902794 A
1 A
12902795 TAGTTAGTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 20 0.44
46 25 0.56
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (46 bp):
AAATTTGATTAATTCTAACATTTTTCAATAATTTTTATTATTAACA
Found at i:12906980 original size:18 final size:18
Alignment explanation
Indices: 12906957--12906992 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12906947 AAGCTTAGGG
*
12906957 TTAATAACATAACATAAT
1 TTAATAACATAAAATAAT
*
12906975 TTAATAATATAAAATAAT
1 TTAATAACATAAAATAAT
12906993 AAAAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAATAACATAAAATAAT
Found at i:12907690 original size:74 final size:72
Alignment explanation
Indices: 12907597--12907733 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 72
12907587 CAAATTCCCC
* *
12907597 GACAAATCATCCATTATATGCTTCAATTGTCAATAAAAACATCGAAACCCTGTCAAGAAATAAAC
1 GACAAATCATCCATTATATGCTTCAATTGTCAACAAAAACATCGAAAACC--TCAAGAAATAAAC
12907662 ATTATTCAA
64 ATTATTCAA
* * * *
12907671 GACAAATTATCCATTATATGCTTCAATTGTCAACACAAACATTGAAAACCTCGAGAAATAAAC
1 GACAAATCATCCATTATATGCTTCAATTGTCAACAAAAACATCGAAAACCTCAAGAAATAAAC
12907734 TTGGAGCTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 12 0.21
74 45 0.79
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (72 bp):
GACAAATCATCCATTATATGCTTCAATTGTCAACAAAAACATCGAAAACCTCAAGAAATAAACAT
TATTCAA
Found at i:12910365 original size:12 final size:12
Alignment explanation
Indices: 12910348--12910390 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
12910338 TAAAATTATT
12910348 AAATATTAAAAA
1 AAATATTAAAAA
*
12910360 AAATATTTTAAAA
1 AAATA-TTAAAAA
12910373 AAA-ATTAAAAA
1 AAATATTAAAAA
12910384 ATAATAT
1 A-AATAT
12910391 GGACGGGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.27
12 8 0.31
13 11 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATTAAAAA
Found at i:12917803 original size:28 final size:26
Alignment explanation
Indices: 12917753--12917845 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
12917743 GAAAAAATGA
*
12917753 TAAAAAA-TATAAAAATCAATAAAATT
1 TAAAAAATTATAAAAAT-ATTAAAATT
*
12917779 GTAAAAAATTATAAAAATATTTAAATTT
1 -TAAAAAATTATAAAAATA-TTAAAATT
* * *
12917807 TATTAAAAATTACAAAATTATTAAAAGT
1 TA--AAAAATTATAAAAATATTAAAATT
*
12917835 TAGAAAATTAT
1 TAAAAAATTAT
12917846 TTAAAATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
26 7 0.13
27 10 0.19
28 23 0.43
29 14 0.26
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (26 bp):
TAAAAAATTATAAAAATATTAAAATT
Found at i:12917829 original size:18 final size:18
Alignment explanation
Indices: 12917806--12917854 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
12917796 TATTTAAATT
12917806 TTATTAAAAATTACAAAA
1 TTATTAAAAATTACAAAA
* *
12917824 TTATTAAAAGTTAGAAAA
1 TTATTAAAAATTACAAAA
*
12917842 TTATTTAAAATTA
1 TTATTAAAAATTA
12917855 TATAGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
TTATTAAAAATTACAAAA
Found at i:12917872 original size:21 final size:21
Alignment explanation
Indices: 12917835--12917894 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
12917825 TATTAAAAGT
12917835 TAGAAAATTATTTAAAATTATA
1 TAGAAAA-TATTTAAAATTATA
* *
12917857 TAGAAAATAATTAAAAATATA
1 TAGAAAATATTTAAAATTATA
12917878 TA-AAAATATTATAAAAT
1 TAGAAAATATT-TAAAAT
12917895 ATAAATATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 19 0.58
22 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAGAAAATATTTAAAATTATA
Found at i:12917882 original size:19 final size:19
Alignment explanation
Indices: 12917808--12917897 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 19
12917798 TTTAAATTTT
* *
12917808 ATTAAAAAT-TACAAAATT
1 ATTAAAAATATAGAAAATA
*
12917826 ATTAAAAGT-TAGAAAATTA
1 ATTAAAAATATAGAAAA-TA
*
12917845 TTTAAAATTATATAGAAAATA
1 ATTAAAA--ATATAGAAAATA
*
12917866 ATTAAAAATATATAAAA-A
1 ATTAAAAATATAGAAAATA
12917884 TATTATAAAATATA
1 -ATTA-AAAATATA
12917898 AATATAGAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.25
19 20 0.34
20 8 0.14
21 9 0.15
22 7 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTAAAAATATAGAAAATA
Found at i:12917890 original size:11 final size:10
Alignment explanation
Indices: 12917752--12917897 Score: 69
Period size: 10 Copynumber: 15.1 Consensus size: 10
12917742 AGAAAAAATG
12917752 ATAAAAA-AT
1 ATAAAAATAT
12917761 ATAAAAATCA-
1 ATAAAAAT-AT
* *
12917771 ATAAAATTGT
1 ATAAAAATAT
12917781 A-AAAAAT-T
1 ATAAAAATAT
12917789 ATAAAAATAT
1 ATAAAAATAT
* * *
12917799 -TTAAATTTT
1 ATAAAAATAT
12917808 ATTAAAAAT-T
1 A-TAAAAATAT
* *
12917818 ACAAAATTAT
1 ATAAAAATAT
*
12917828 -TAAAAGT-T
1 ATAAAAATAT
* *
12917836 AGAAAATTAT
1 ATAAAAATAT
* *
12917846 TTAAAATTAT
1 ATAAAAATAT
12917856 ATAGAAAATA-
1 ATA-AAAATAT
12917866 ATTAAAAATAT
1 A-TAAAAATAT
12917877 ATAAAAATAT
1 ATAAAAATAT
12917887 -TATAAAATAT
1 ATA-AAAATAT
12917897 A
1 A
12917898 AATATAGAGT
Statistics
Matches: 104, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
8 3 0.03
9 41 0.39
10 46 0.44
11 14 0.13
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:12918334 original size:10 final size:10
Alignment explanation
Indices: 12918319--12918446 Score: 56
Period size: 10 Copynumber: 13.1 Consensus size: 10
12918309 ATAAATATTC
12918319 TATATTTTTA
1 TATATTTTTA
12918329 TATATTTTTAA
1 TATATTTTT-A
* *
12918340 TAAATTTCTA
1 TATATTTTTA
12918350 TA-ATTTTTTA
1 TATA-TTTTTA
12918360 TATATATTTT-
1 TATAT-TTTTA
* ** *
12918370 TAAAAATTAA
1 TATATTTTTA
12918380 TA-ATTTTTA
1 TATATTTTTA
* *
12918389 AACATTTTTA
1 TATATTTTTA
*
12918399 TCTAATTTTTA
1 TAT-ATTTTTA
*
12918410 TAT-TTGTT-
1 TATATTTTTA
12918418 TATA-TTTTA
1 TATATTTTTA
*
12918427 TA-AATTTTA
1 TATATTTTTA
12918436 T-TGATTTTTA
1 TAT-ATTTTTA
12918446 T
1 T
12918447 CTTACGGGCT
Statistics
Matches: 88, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
8 7 0.08
9 20 0.23
10 39 0.44
11 22 0.25
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (10 bp):
TATATTTTTA
Found at i:12918337 original size:31 final size:30
Alignment explanation
Indices: 12918289--12918425 Score: 95
Period size: 29 Copynumber: 4.6 Consensus size: 30
12918279 TATATTTTAC
*
12918289 ATATTTTAATGAT-TTTTTTTATAAATATTCT
1 ATATTTTTAT-ATATTTTTTTATAAAT-TTCT
*
12918320 ATATTTTTATATA-TTTTTAATAAATTTCT
1 ATATTTTTATATATTTTTTTATAAATTTCT
* * **
12918349 ATAATTTTTTATATATATTTTTAAAAATTAAT
1 AT-A-TTTTTATATATTTTTTTATAAATTTCT
* * * * *
12918381 A-ATTTTTAAACATTTTTATCT-AATTTTT
1 ATATTTTTATATATTTTTTTATAAATTTCT
12918409 ATATTTGTT-TATATTTT
1 ATATTT-TTATATATTTT
12918426 ATAAATTTTA
Statistics
Matches: 83, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 6 0.07
29 29 0.35
30 17 0.20
31 19 0.23
32 12 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (30 bp):
ATATTTTTATATATTTTTTTATAAATTTCT
Found at i:12918788 original size:19 final size:19
Alignment explanation
Indices: 12918755--12918791 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
12918745 TTAGATAATA
12918755 AAAAAGTAATATTATTTAT
1 AAAAAGTAATATTATTTAT
12918774 AAAAA-TAATACTTATTTA
1 AAAAAGTAATA-TTATTTA
12918792 AATAGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAAGTAATATTATTTAT
Found at i:12918800 original size:19 final size:18
Alignment explanation
Indices: 12918755--12918804 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
12918745 TTAGATAATA
12918755 AAAAAGTAATATTATTTAT
1 AAAAA-TAATATTATTTAT
12918774 AAAAATAATACTTATTTA-
1 AAAAATAATA-TTATTTAT
*
12918792 AATAGATAATATT
1 AA-AAATAATATT
12918805 GAATTAGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
AAAAATAATATTATTTAT
Found at i:12918920 original size:23 final size:24
Alignment explanation
Indices: 12918875--12918927 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
12918865 TTAATATTAC
* *
12918875 ATTTATATACTAATTAAAACTAAT
1 ATTTATATAATAATAAAAACTAAT
12918899 ATTTATATAATAA-AAAAACTAAT
1 ATTTATATAATAATAAAAACTAAT
12918922 ATTTAT
1 ATTTAT
12918928 TATTTAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTATATAATAATAAAAACTAAT
Found at i:12921912 original size:19 final size:19
Alignment explanation
Indices: 12921890--12921972 Score: 66
Period size: 20 Copynumber: 4.4 Consensus size: 19
12921880 AAATTGATTG
12921890 ATTTTTATATTTTATAAT-A
1 ATTTTTATATTTT-TAATAA
12921909 ATTTTATATATTTTTAATAA
1 ATTTT-TATATTTTTAATAA
* *
12921929 ATTTCTATAATTTTTTA-AA
1 ATTTTTAT-ATTTTTAATAA
** *
12921948 ATTAATA-ATTTTTAA-AC
1 ATTTTTATATTTTTAATAA
12921965 ATTTTTAT
1 ATTTTTAT
12921973 CTAATTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
17 13 0.25
19 19 0.37
20 20 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTATATTTTTAATAA
Found at i:12921920 original size:20 final size:20
Alignment explanation
Indices: 12921890--12921943 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
12921880 AAATTGATTG
12921890 ATTTT-TATATTTTATAAT-A
1 ATTTTATATATTTT-TAATAA
12921909 ATTTTATATATTTTTAATAA
1 ATTTTATATATTTTTAATAA
12921929 ATTTCTATA-ATTTTT
1 ATTT-TATATATTTTT
12921944 TAAAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.28
20 19 0.59
21 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTATATATTTTTAATAA
Found at i:12922019 original size:47 final size:46
Alignment explanation
Indices: 12921891--12922021 Score: 122
Period size: 47 Copynumber: 2.7 Consensus size: 46
12921881 AATTGATTGA
*
12921891 TTTTTATATTTTATAATAATTTTATATATTTTTAAT-AAATTTCTATAAT
1 TTTTTATATTTTATAAT--TTTTAT-TATTTTT-ATCTAATTTCTATAAT
* * * ** *
12921940 TTTTTAAAATTAATAATTTTTAAACATTTTTATCTAATTTTTAT-AT
1 TTTTTATATTTTATAATTTTT-ATTATTTTTATCTAATTTCTATAAT
12921986 TTGTTTATATTTTATAATTTTTATTGATTTTTATCT
1 TT-TTTATATTTTATAATTTTTATT-ATTTTTATCT
12922022 TTTTAATATT
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
46 7 0.11
47 44 0.67
48 1 0.02
49 14 0.21
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (46 bp):
TTTTTATATTTTATAATTTTTATTATTTTTATCTAATTTCTATAAT
Found at i:12925082 original size:26 final size:24
Alignment explanation
Indices: 12925040--12925087 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
12925030 AAACTTGGCA
12925040 TTTTTTTTAATTAGGTACTTAATT
1 TTTTTTTTAATTAGGTACTTAATT
*
12925064 TTTTTTTTACATTTTGGTACTTAA
1 TTTTTTTTA-A-TTAGGTACTTAA
12925088 ACTTGTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 1 0.05
26 11 0.52
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.62
Consensus pattern (24 bp):
TTTTTTTTAATTAGGTACTTAATT
Found at i:12925488 original size:12 final size:12
Alignment explanation
Indices: 12925462--12925508 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
12925452 TGAAAATCTC
12925462 TTTTTTTTATAAA
1 TTTTTTTTAT-AA
*
12925475 TTTTTTTTCTAA
1 TTTTTTTTATAA
*
12925487 TTTTTATTTATGA
1 TTTTT-TTTATAA
12925500 TTTTTTTTA
1 TTTTTTTTA
12925509 ACCATTGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTTTTATAA
Found at i:12931264 original size:13 final size:13
Alignment explanation
Indices: 12931248--12931287 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
12931238 AATCATTGCA
12931248 ATATATGTAAAAT
1 ATATATGTAAAAT
12931261 ATATATGTAAAA-
1 ATATATGTAAAAT
*
12931273 ACA-ATGTAAAAT
1 ATATATGTAAAAT
12931285 ATA
1 ATA
12931288 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (13 bp):
ATATATGTAAAAT
Found at i:12931460 original size:20 final size:20
Alignment explanation
Indices: 12931411--12931461 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
12931401 AAATATTAAC
*
12931411 TTTTCCAAAAAAGTAATTCA
1 TTTTCCAGAAAAGTAATTCA
**
12931431 TTTTATAGAAAAGTAACTT-A
1 TTTTCCAGAAAAGTAA-TTCA
12931451 TTTTCCAGAAA
1 TTTTCCAGAAA
12931462 TCATTTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTTCCAGAAAAGTAATTCA
Found at i:12934972 original size:26 final size:25
Alignment explanation
Indices: 12934945--12935024 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 25
12934935 TGTTGGAACG
12934945 ATATACTGAACTTGCTCGTAAGAGC-
1 ATATACTGAAC-TGCTCGTAAGAGCA
*
12934970 -GATACTG----GCTCGTAAGAGCA
1 ATATACTGAACTGCTCGTAAGAGCA
*
12934990 ATATACTGTACTGGCTCGTAAGAGCA
1 ATATACTGAACT-GCTCGTAAGAGCA
*
12935016 ATTTACTGA
1 ATATACTGA
12935025 TTGGGCTCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
19 12 0.27
21 6 0.14
24 6 0.14
26 20 0.45
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
ATATACTGAACTGCTCGTAAGAGCA
Found at i:12935031 original size:26 final size:26
Alignment explanation
Indices: 12934972--12935040 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
12934962 GTAAGAGCGA
12934972 TACTGGCTCGTAAGAGCAATATACTG
1 TACTGGCTCGTAAGAGCAATATACTG
*
12934998 TACTGGCTCGTAAGAGCAATTTACTG
1 TACTGGCTCGTAAGAGCAATATACTG
* *
12935024 -ATTGGGCTCGTATGAGC
1 TACT-GGCTCGTAAGAGC
12935041 TAAAAATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
25 2 0.05
26 37 0.95
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (26 bp):
TACTGGCTCGTAAGAGCAATATACTG
Found at i:12946609 original size:15 final size:15
Alignment explanation
Indices: 12946584--12946641 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
12946574 TTTAAGTATT
12946584 AAAGAAGAAGAAGAGA
1 AAAG-AGAAGAAGAGA
12946600 AAAGAGAAGAAGA-A
1 AAAGAGAAGAAGAGA
*
12946614 TAAAGAGAAGAAAAGGA
1 -AAAGAGAAGAAGA-GA
12946631 AAA-AGAAGAAG
1 AAAGAGAAGAAG
12946642 TTGTTCCGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 1 0.03
15 28 0.76
16 7 0.19
17 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
AAAGAGAAGAAGAGA
Found at i:12946624 original size:30 final size:31
Alignment explanation
Indices: 12946583--12946641 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
12946573 TTTTAAGTAT
*
12946583 TAAAGAAGAAGAAGA-GAAAAGAGAAGAAGAA
1 TAAAGAAGAAGAAAAGGAAAA-AGAAGAAGAA
12946614 TAAAG-AGAAGAAAAGGAAAAAGAAGAAG
1 TAAAGAAGAAGAAAAGGAAAAAGAAGAAG
12946642 TTGTTCCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (31 bp):
TAAAGAAGAAGAAAAGGAAAAAGAAGAAGAA
Found at i:12947048 original size:17 final size:17
Alignment explanation
Indices: 12947026--12947066 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12947016 ACGTTTCATC
12947026 TAATTGTCATTACATTT
1 TAATTGTCATTACATTT
* *
12947043 TAATTGTCTTTGCATTT
1 TAATTGTCATTACATTT
*
12947060 TAGTTGT
1 TAATTGT
12947067 TCTCACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (17 bp):
TAATTGTCATTACATTT
Found at i:12947700 original size:2 final size:2
Alignment explanation
Indices: 12947693--12947720 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12947683 GATAAAAAGA
12947693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12947721 GACAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12948114 original size:32 final size:32
Alignment explanation
Indices: 12948075--12948139 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
12948065 ATACTTAGTA
** *
12948075 TTTGCATTTTCTAAATTTGTGTTGTATGGTCT
1 TTTGCATTTTCTAAATCAGTGTTGTACGGTCT
12948107 TTTGCATTTTCTAAATCAGTGTTGTACGGTCT
1 TTTGCATTTTCTAAATCAGTGTTGTACGGTCT
12948139 T
1 T
12948140 ACTTTCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.52
Consensus pattern (32 bp):
TTTGCATTTTCTAAATCAGTGTTGTACGGTCT
Found at i:12949292 original size:23 final size:24
Alignment explanation
Indices: 12949259--12949307 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
12949249 ACAATCAATT
* *
12949259 CATTTTCTATTA-AATTGCTCTGA
1 CATTTTATATTATAATTGCACTGA
*
12949282 CATTTTATATTATATTTGCACTGA
1 CATTTTATATTATAATTGCACTGA
12949306 CA
1 CA
12949308 GATTTAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (24 bp):
CATTTTATATTATAATTGCACTGA
Found at i:12954874 original size:19 final size:19
Alignment explanation
Indices: 12954850--12954889 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12954840 ACCAGACTCA
*
12954850 TTGACTTTGATCGCTGACT
1 TTGACTTTGACCGCTGACT
*
12954869 TTGACTTTGACCGTTGACT
1 TTGACTTTGACCGCTGACT
12954888 TT
1 TT
12954890 TTTGAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGACTTTGACCGCTGACT
Found at i:12957777 original size:40 final size:40
Alignment explanation
Indices: 12957722--12957797 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
12957712 TCAAACACTG
12957722 GTTTTAGTTTATTTTATAAATCTGAACTTGTTAGAATCTT
1 GTTTTAGTTTATTTTATAAATCTGAACTTGTTAGAATCTT
12957762 GTTTTAGTTTATTTTATAAATCTGAACTTGTTAGAA
1 GTTTTAGTTTATTTTATAAATCTGAACTTGTTAGAA
12957798 ATGGTGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (40 bp):
GTTTTAGTTTATTTTATAAATCTGAACTTGTTAGAATCTT
Found at i:12961427 original size:21 final size:22
Alignment explanation
Indices: 12961394--12961436 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
12961384 TTTTTAAAAG
**
12961394 ATAATAATTATTGATAA-GATA
1 ATAATAAAAATTGATAATGATA
*
12961415 ATAATAAAAATTGTTAATGATA
1 ATAATAAAAATTGATAATGATA
12961437 TTTTGATAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
ATAATAAAAATTGATAATGATA
Found at i:12961914 original size:40 final size:40
Alignment explanation
Indices: 12961859--12961941 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
12961849 GGTATAACAC
12961859 ATAATGGGAGTTGGTCGGTGGGGTTCCTATTTTCCCTCAT
1 ATAATGGGAGTTGGTCGGTGGGGTTCCTATTTTCCCTCAT
12961899 ATAATGGGAGTTGGTCGGTGGGGTTCCTATTTTCCCTCAT
1 ATAATGGGAGTTGGTCGGTGGGGTTCCTATTTTCCCTCAT
12961939 ATA
1 ATA
12961942 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (40 bp):
ATAATGGGAGTTGGTCGGTGGGGTTCCTATTTTCCCTCAT
Found at i:12961944 original size:2 final size:2
Alignment explanation
Indices: 12961937--12961963 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12961927 ATTTTCCCTC
12961937 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12961964 AACCAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12963742 original size:21 final size:21
Alignment explanation
Indices: 12963711--12963754 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
12963701 GTTAGAATTT
12963711 AATTAATTTTTA-AAATTTAA
1 AATTAATTTTTATAAATTTAA
*
12963731 AATTATATTTTTATAATTTTAA
1 AATTA-ATTTTTATAAATTTAA
12963753 AA
1 AA
12963755 ATCATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTAATTTTTATAAATTTAA
Found at i:12966663 original size:136 final size:132
Alignment explanation
Indices: 12966432--12966742 Score: 407
Period size: 136 Copynumber: 2.3 Consensus size: 132
12966422 AGTCTAGATC
* *
12966432 GTGAGAGAGAG-T--TACTTGGGTATTTATACCTAGCCTTGGGGGCATCAATGCTCTGGAGTGCT
1 GTGAGAGAGAGTTGGTACTTGGGTATTTATACCTAGCCTT-GGGGCATCAATGCTCCGGAATGCT
12966494 ATGTGATGCTTAAGTTAGCAAAGGAGAATGTGTAATGGATAAAAAAAGAGCTTAAGCTAGCAG-A
65 ATGTGATGCTTAAGTTAGCAAAGGAGAATGTGTAATGGATAAAAAAA-A-C-T-AGC-AG-AGAA
*
12966558 GAA-AAAGT
124 GAAGAAAGA
* *
12966566 GTGAGAGAGAGTTGGTACTTGGATATTTATACCTAGCCTTGGGGCATCAATGCTCCGGAATGCTC
1 GTGAGAGAGAGTTGGTACTTGGGTATTTATACCTAGCCTTGGGGCATCAATGCTCCGGAATGCTA
* * * ** *
12966631 TTTGATGCTTAAGTTAGCAAAGGAGATTGTGTAATGGGTAAAGCAAACTAGCAGAGAAGAAGTAA
66 TGTGATGCTTAAGTTAGCAAAGGAGAATGTGTAATGGATAAAAAAAACTAGCAGAGAAGAAGAAA
12966696 GA
131 GA
* *
12966698 GAGAGTGAGAGTTGGTACTTGGGTATTTATACCTAGCCTTGGGGC
1 GTGAGAGAGAGTTGGTACTTGGGTATTTATACCTAGCCTTGGGGC
12966743 TGCCCGTTGC
Statistics
Matches: 158, Mismatches: 14, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
130 2 0.01
131 6 0.04
132 48 0.30
133 1 0.01
134 12 0.08
135 2 0.01
136 63 0.40
137 24 0.15
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (132 bp):
GTGAGAGAGAGTTGGTACTTGGGTATTTATACCTAGCCTTGGGGCATCAATGCTCCGGAATGCTA
TGTGATGCTTAAGTTAGCAAAGGAGAATGTGTAATGGATAAAAAAAACTAGCAGAGAAGAAGAAA
GA
Found at i:12970680 original size:30 final size:30
Alignment explanation
Indices: 12970646--12970711 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
12970636 TGATAAAGGT
* * *
12970646 AAAATTTTACTTTGTCCTCTAAAAAGGATA
1 AAAATTCTACTTTGACCTCTAAAAAAGATA
12970676 AAAATTCTACTTTGACCTCTAAAAAAGATA
1 AAAATTCTACTTTGACCTCTAAAAAAGATA
12970706 AAAATT
1 AAAATT
12970712 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (30 bp):
AAAATTCTACTTTGACCTCTAAAAAAGATA
Found at i:12971332 original size:23 final size:23
Alignment explanation
Indices: 12971306--12971351 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12971296 AAATTCGAAT
** *
12971306 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCAAGTTA
*
12971329 TTCGAGTTAAACGAATCAAGTTA
1 TTCGAATTAAACGAATCAAGTTA
12971352 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (23 bp):
TTCGAATTAAACGAATCAAGTTA
Found at i:12971658 original size:42 final size:42
Alignment explanation
Indices: 12971584--12971666 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
12971574 AAATATTTTA
* * *
12971584 AAACTCAAATATAATTTCATTCTTCAAAAACACTTATAAACT
1 AAACCCAAATATAATTTCATTCCTCAAAAACACTCATAAACT
*
12971626 AAACCCAAATATAATTTTATTCCT-AAATAACACTCATAAAC
1 AAACCCAAATATAATTTCATTCCTCAAA-AACACTCATAAAC
12971667 AACTCATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 3 0.08
42 33 0.92
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (42 bp):
AAACCCAAATATAATTTCATTCCTCAAAAACACTCATAAACT
Found at i:12980699 original size:16 final size:16
Alignment explanation
Indices: 12980678--12980712 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12980668 TATCCGAGTG
*
12980678 AACTTGAAATGACTCA
1 AACTTGAAATGACCCA
*
12980694 AACTTGGAATGACCCA
1 AACTTGAAATGACCCA
12980710 AAC
1 AAC
12980713 AACAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (16 bp):
AACTTGAAATGACCCA
Found at i:12986814 original size:19 final size:20
Alignment explanation
Indices: 12986790--12986833 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
12986780 CTAATTTGAT
12986790 ATTTTAAAC-TATTTTTTAA
1 ATTTTAAACTTATTTTTTAA
* *
12986809 ATTTT-ATCTTATTTTTTTA
1 ATTTTAAACTTATTTTTTAA
12986828 ATTTTA
1 ATTTTA
12986834 TAATCACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTAAACTTATTTTTTAA
Found at i:12996942 original size:31 final size:31
Alignment explanation
Indices: 12996907--12996966 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12996897 AAGGTATCCA
* *
12996907 ACATCGGTACAAGGTACCTGGTACTTTTTAG
1 ACATCGATACAAAGTACCTGGTACTTTTTAG
* *
12996938 ACATCGATACAAAGTACCTGTTGCTTTTT
1 ACATCGATACAAAGTACCTGGTACTTTTT
12996967 GGACCTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (31 bp):
ACATCGATACAAAGTACCTGGTACTTTTTAG
Found at i:13000530 original size:2 final size:2
Alignment explanation
Indices: 13000523--13000548 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13000513 ATTTGTTACG
13000523 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13000549 GGGGAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13001153 original size:20 final size:21
Alignment explanation
Indices: 13001115--13001155 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13001105 TATTGTGAAA
13001115 TTCATTGACTTGTTCCGGTAG
1 TTCATTGACTTGTTCCGGTAG
13001136 TTCATT-ACTTGTAT-CGGTAG
1 TTCATTGACTTGT-TCCGGTAG
13001156 AACCTCTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (21 bp):
TTCATTGACTTGTTCCGGTAG
Found at i:13002410 original size:37 final size:36
Alignment explanation
Indices: 13002358--13002575 Score: 224
Period size: 37 Copynumber: 5.9 Consensus size: 36
13002348 TTCCTTTATG
* *
13002358 ATTCACCGACACAAAGCCTATTAGGCACAAATCCCAA
1 ATTCACCGACACAAAGCCTACTAGGCACAAAGCCC-A
* *
13002395 ATTCACCGACGCAAAGCCTACTAGGCACAAAGCCCG
1 ATTCACCGACACAAAGCCTACTAGGCACAAAGCCCA
* *
13002431 ATTACACCGGCACAAAGCCTACTAGGCACATAGCCCGA
1 ATT-CACCGACACAAAGCCTACTAGGCACAAAGCCC-A
* * * *
13002469 ATACACAGACACAAAGCCTACTAGGCACACAGCTCGA
1 ATTCACCGACACAAAGCCTACTAGGCACAAAGC-CCA
* * **
13002506 ATACACC-AGCACCAAA-CTTACTAGGCACAAAGTCTGA
1 ATTCACCGA-CA-CAAAGCCTACTAGGCACAAAG-CCCA
*
13002543 ATACACCGACACAAAGCCTACTAGGCACAAAGC
1 ATTCACCGACACAAAGCCTACTAGGCACAAAGC
13002576 TCGATTATTT
Statistics
Matches: 155, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
36 9 0.06
37 137 0.88
38 9 0.06
ACGTcount: A:0.39, C:0.33, G:0.16, T:0.13
Consensus pattern (36 bp):
ATTCACCGACACAAAGCCTACTAGGCACAAAGCCCA
Found at i:13002427 original size:16 final size:16
Alignment explanation
Indices: 13002406--13002497 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 16
13002396 TTCACCGACG
13002406 CAAAGCCTACTAGGCA
1 CAAAGCCTACTAGGCA
13002422 CAAAGCCCGATTAC-ACCGGCA
1 CAAAG-CC---TACTA--GGCA
13002443 CAAAGCCTACTAGGCA
1 CAAAGCCTACTAGGCA
* * *
13002459 CATAGCCCGAATACACAGACA
1 CAAAG-CC---TAC-TAGGCA
13002480 CAAAGCCTACTAGGCA
1 CAAAGCCTACTAGGCA
13002496 CA
1 CA
13002498 CAGCTCGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
16 19 0.33
17 10 0.17
18 1 0.02
19 1 0.02
20 10 0.17
21 17 0.29
ACGTcount: A:0.38, C:0.34, G:0.17, T:0.11
Consensus pattern (16 bp):
CAAAGCCTACTAGGCA
Found at i:13002484 original size:74 final size:74
Alignment explanation
Indices: 13002357--13002582 Score: 294
Period size: 74 Copynumber: 3.1 Consensus size: 74
13002347 ATTCCTTTAT
* * * * * *
13002357 GATT-CACCGACACAAAGCCTATTAGGCACAAATCCCAAATTCACCGACGCAAAGCCTACTAGGC
1 GATTACACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATACACCGACACAAAGCCTACTAGGC
*
13002421 ACAAAGCCC
66 ACAAAGCTC
* *
13002430 GATTACACCGGCACAAAGCCTACTAGGCACATAGCCCGAATACACAGACACAAAGCCTACTAGGC
1 GATTACACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATACACCGACACAAAGCCTACTAGGC
*
13002495 ACACAGCTC
66 ACAAAGCTC
* * * * *
13002504 GAATACACCAGCACCAAA-CTTACTAGGCACAAAGTCTGAATACACCGACACAAAGCCTACTAGG
1 GATTACACCGGCA-CAAAGCCTACTAGGCACAAAGCCCGAATACACCGACACAAAGCCTACTAGG
13002568 CACAAAGCTC
65 CACAAAGCTC
13002578 GATTA
1 GATTA
13002583 TTTAAATGCA
Statistics
Matches: 132, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
73 4 0.03
74 124 0.94
75 4 0.03
ACGTcount: A:0.38, C:0.32, G:0.16, T:0.14
Consensus pattern (74 bp):
GATTACACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATACACCGACACAAAGCCTACTAGGC
ACAAAGCTC
Found at i:13002559 original size:111 final size:111
Alignment explanation
Indices: 13002365--13002571 Score: 283
Period size: 111 Copynumber: 1.9 Consensus size: 111
13002355 ATGATTCACC
* * *
13002365 GACACAAAGCCTATTAGGCACAAATCCCAAATTCACCGACGCAAAGCCTACTAGGCACAAAGCCC
1 GACACAAAGCCTACTAGGCACAAAGCCCAAATACACCGACGCAAAGCCTACTAGGCACAAAGCCC
* *
13002430 GATTACACCGGCACAAAGCCTACTAGGCACATAGCCCGAATACACA
66 GAATACACCGACACAAAGCCTACTAGGCACATAGCCCGAATACACA
* * * * *
13002476 GACACAAAGCCTACTAGGCACACAGCTCGAATACACCAGCAC-CAAA-CTTACTAGGCACAAAGT
1 GACACAAAGCCTACTAGGCACAAAGCCCAAATACACC-G-ACGCAAAGCCTACTAGGCACAAAGC
*
13002539 CTGAATACACCGACACAAAGCCTACTAGGCACA
64 CCGAATACACCGACACAAAGCCTACTAGGCACA
13002572 AAGCTCGATT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 76 0.92
112 5 0.06
113 2 0.02
ACGTcount: A:0.39, C:0.33, G:0.16, T:0.13
Consensus pattern (111 bp):
GACACAAAGCCTACTAGGCACAAAGCCCAAATACACCGACGCAAAGCCTACTAGGCACAAAGCCC
GAATACACCGACACAAAGCCTACTAGGCACATAGCCCGAATACACA
Found at i:13004103 original size:15 final size:15
Alignment explanation
Indices: 13004080--13004118 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
13004070 AAATAATATT
13004080 AATAAATAATAAACA
1 AATAAATAATAAACA
* *
13004095 AATAGATAATAAATA
1 AATAAATAATAAACA
13004110 AATAAATAA
1 AATAAATAA
13004119 ATATATACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (15 bp):
AATAAATAATAAACA
Found at i:13004111 original size:4 final size:4
Alignment explanation
Indices: 13004070--13004121 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
13004060 ACATATTCAC
* * *
13004070 AAAT AATAT TAAT AAAT -AAT AAAC AAAT AGAT -AAT AAAT AAAT AAAT
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
13004117 AAAT A
1 AAAT A
13004122 TATACACACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 5 0.13
4 31 0.79
5 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:13004865 original size:21 final size:21
Alignment explanation
Indices: 13004789--13004872 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
13004779 TTCAAGAAAT
*
13004789 AGTGCAGACTTCTACCGATACCT
1 AGTG-AGACTTCTACCGATA-CA
* *
13004812 A-TGACAATTCTACCGATACA
1 AGTGAGACTTCTACCGATACA
*
13004832 AGTGAGACATCTACCGATACA
1 AGTGAGACTTCTACCGATACA
* *
13004853 AGTTATG-CTTCTATCGATAC
1 AGTGA-GACTTCTACCGATAC
13004873 TAAAAACTCC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.04
21 44 0.88
22 3 0.06
23 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (21 bp):
AGTGAGACTTCTACCGATACA
Found at i:13020857 original size:59 final size:59
Alignment explanation
Indices: 13020747--13020895 Score: 201
Period size: 59 Copynumber: 2.5 Consensus size: 59
13020737 ATTGAATCTT
* * * *
13020747 AAAAAAAGCTTAGGTACCAAATTA-AAAAAAATGCCAAGTTCAGGTATCAAATTGGGTC
1 AAAAAAAGTTTAGGTATCAAATTAGAAAAAAATGCCAAGTTCAGATACCAAATTGGGTC
* * * *
13020805 CAAAAAAGTTTAGGTATCAAATTAGAAAAAATTGTCAAGTTTAGATACCAAATTGGGTC
1 AAAAAAAGTTTAGGTATCAAATTAGAAAAAAATGCCAAGTTCAGATACCAAATTGGGTC
**
13020864 AAAAAAAGTTTAAATATCAAATTAGAAAAAAA
1 AAAAAAAGTTTAGGTATCAAATTAGAAAAAAA
13020896 AATGTCAAGT
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
58 21 0.27
59 57 0.73
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTATCAAATTAGAAAAAAATGCCAAGTTCAGATACCAAATTGGGTC
Found at i:13021577 original size:32 final size:32
Alignment explanation
Indices: 13021531--13021596 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
13021521 TACATATTTT
*
13021531 ATAAATTACCAATAAGCCAATGAAGTAAGTGA
1 ATAAATTACCAATAACCCAATGAAGTAAGTGA
*
13021563 ATAAGTTACCAATAACCCAATGAAGTAAGTGA
1 ATAAATTACCAATAACCCAATGAAGTAAGTGA
13021595 AT
1 AT
13021597 GAAGCTCTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (32 bp):
ATAAATTACCAATAACCCAATGAAGTAAGTGA
Found at i:13021787 original size:23 final size:23
Alignment explanation
Indices: 13021757--13021811 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
13021747 TTATCTGCCT
13021757 TTGTGGCACGCTTTTCCTTTGTC
1 TTGTGGCACGCTTTTCCTTTGTC
*
13021780 TTGTGGCACGCTTTTTCTTTGTC
1 TTGTGGCACGCTTTTCCTTTGTC
13021803 TTGTGGCAC
1 TTGTGGCAC
13021812 TCTTCTGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.05, C:0.24, G:0.24, T:0.47
Consensus pattern (23 bp):
TTGTGGCACGCTTTTCCTTTGTC
Found at i:13022879 original size:17 final size:19
Alignment explanation
Indices: 13022840--13022879 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
13022830 TTTTTTTTGT
*
13022840 TTTTTCATTATTTAATAAG
1 TTTTTCAGTATTTAATAAG
13022859 -TTTTCAGT-TTTAA-AAG
1 TTTTTCAGTATTTAATAAG
13022875 TTTTT
1 TTTTT
13022880 TTCTGTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTCAGTATTTAATAAG
Found at i:13029410 original size:58 final size:58
Alignment explanation
Indices: 13029346--13029462 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
13029336 AAAAAATGTG
*
13029346 AAATTATTGTAAGCATCATAGTCCATCTATTTATATGCACTTAATGGACACCTTTTGA
1 AAATTATTATAAGCATCATAGTCCATCTATTTATATGCACTTAATGGACACCTTTTGA
* * *
13029404 AAATTATTATGAGCATCATAGTTCATCTCTTTATATGCACTTAATGGACACCTTTTGA
1 AAATTATTATAAGCATCATAGTCCATCTATTTATATGCACTTAATGGACACCTTTTGA
13029462 A
1 A
13029463 GAGTCACAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (58 bp):
AAATTATTATAAGCATCATAGTCCATCTATTTATATGCACTTAATGGACACCTTTTGA
Found at i:13029501 original size:39 final size:40
Alignment explanation
Indices: 13029447--13029526 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
13029437 TATGCACTTA
13029447 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
*
13029486 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
13029526 A
1 A
13029527 CATACCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 28 0.72
40 11 0.28
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:13029542 original size:39 final size:38
Alignment explanation
Indices: 13029451--13029543 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
13029441 CACTTAATGG
* *
13029451 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
13029490 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
*
13029528 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
13029544 ACTTGTCCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 5 0.10
39 32 0.67
40 11 0.23
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:13035927 original size:17 final size:17
Alignment explanation
Indices: 13035874--13035952 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 17
13035864 TTTGGGATTG
*
13035874 AAATTATTTTCAATTC-
1 AAATTATTTTGAATTCA
*
13035890 GAATTAATTTTGAAATT--
1 AAATT-ATTTTG-AATTCA
*
13035907 AAATTATTTTGAGTTCA
1 AAATTATTTTGAATTCA
*
13035924 AAA-TATTTTGAATTCG
1 AAATTATTTTGAATTCA
13035940 AAATT-TTTT-AATT
1 AAATTATTTTGAATT
13035953 TGAGATTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.13
16 28 0.54
17 13 0.25
18 4 0.08
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (17 bp):
AAATTATTTTGAATTCA
Found at i:13035944 original size:33 final size:34
Alignment explanation
Indices: 13035861--13035952 Score: 86
Period size: 33 Copynumber: 2.8 Consensus size: 34
13035851 AATTTGGGTG
** * *
13035861 AATTTTGGGATTGAAATTATTTTCAATTCGAATT
1 AATTTTGAAATTGAAATTATTTTCAATTCAAAAT
* *
13035895 AATTTTGAAATT-AAATTATTTTGAGTTCAAAAT
1 AATTTTGAAATTGAAATTATTTTCAATTCAAAAT
13035928 -ATTTTG-AATTCGAAATT-TTTT-AATT
1 AATTTTGAAATT-GAAATTATTTTCAATT
13035953 TGAGATTCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
31 7 0.14
32 10 0.20
33 22 0.45
34 10 0.20
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (34 bp):
AATTTTGAAATTGAAATTATTTTCAATTCAAAAT
Found at i:13039899 original size:198 final size:198
Alignment explanation
Indices: 13039519--13039909 Score: 512
Period size: 198 Copynumber: 2.0 Consensus size: 198
13039509 TAAAAGTTGA
* * ** *
13039519 TCCATGTACGTCAGCATAAGGTGTACGTGGCATATCACATGTCACTATCTAGTTATTCCATCAAT
1 TCCATGCACGTCAACATAAGGTACACGTGGCATATCACATGTCACTATCTAGTTATTCCATCAAC
* * * * * *
13039584 TATATCAGTTTTTAATAGTACAAATAAATGAATTTTTTAAAAGAAATGACCAATTTGCTATTTAA
66 CACACCAGTTTTTAACAGTACAAATAAATGAAATTTTTAAAAGAAAGGACCAATTTGCTATTTAA
* * * *** *
13039649 TCTAATGTATAAGGACTAGTTTGCCCATTTTTTTAATAGCGGAGGCAAAATGCAATTCAACTAAT
131 TCTAATGTATAAGAACTAGTTTACCCATTTTTTGAATAGAAAAAGCAAAATGCAATTCAACTAAT
13039714 TGG
196 TGG
* * *
13039717 TCCATGCACGTCAACATAATGTACACGTGGCATGTCACATGTCACTGTCTAGTTATTCCATCAAC
1 TCCATGCACGTCAACATAAGGTACACGTGGCATATCACATGTCACTATCTAGTTATTCCATCAAC
* ** * *
13039782 CACGCCAGTTTTTAACAGTACAAATTGATGAAATTTTTAACAGAAAGGATCAATTTGCTATTTAA
66 CACACCAGTTTTTAACAGTACAAATAAATGAAATTTTTAAAAGAAAGGACCAATTTGCTATTTAA
* * * *
13039847 TCTAATGTATAAGAATTAGTTTATCCATTTTTTGAATAGAAAAAGTAAAATGCAATTCGACTA
131 TCTAATGTATAAGAACTAGTTTACCCATTTTTTGAATAGAAAAAGCAAAATGCAATTCAACTA
13039910 CTAGTATAAT
Statistics
Matches: 163, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
198 163 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (198 bp):
TCCATGCACGTCAACATAAGGTACACGTGGCATATCACATGTCACTATCTAGTTATTCCATCAAC
CACACCAGTTTTTAACAGTACAAATAAATGAAATTTTTAAAAGAAAGGACCAATTTGCTATTTAA
TCTAATGTATAAGAACTAGTTTACCCATTTTTTGAATAGAAAAAGCAAAATGCAATTCAACTAAT
TGG
Found at i:13041065 original size:55 final size:55
Alignment explanation
Indices: 13040980--13041119 Score: 190
Period size: 55 Copynumber: 2.5 Consensus size: 55
13040970 GTTATGTAAC
* * * *
13040980 AATCGATTTAAAAGAAGTAATATTCCAACATAACAATCAATTTAAACATATAAAT
1 AATCGATTTAAAAGAAGCAGTACTCCAACATAACAATCAATTTAAACATATAAAA
* * *
13041035 AATCGATTTAAAAAAAGCAGTACTCTAACATAACAATCGATTTAAACATATAAAA
1 AATCGATTTAAAAGAAGCAGTACTCCAACATAACAATCAATTTAAACATATAAAA
* * *
13041090 AATTGATTCAAAAGAAGCAGTATTCCAACA
1 AATCGATTTAAAAGAAGCAGTACTCCAACA
13041120 ATTAAGAAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.26
Consensus pattern (55 bp):
AATCGATTTAAAAGAAGCAGTACTCCAACATAACAATCAATTTAAACATATAAAA
Found at i:13041348 original size:17 final size:18
Alignment explanation
Indices: 13041328--13041365 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
13041318 CATTTCATTT
13041328 TCATTTCT-ATTTTCATA
1 TCATTTCTCATTTTCATA
*
13041345 TCA-TTCTCATTTTCATT
1 TCATTTCTCATTTTCATA
13041362 TCAT
1 TCAT
13041366 ATTCAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTTCTCATTTTCATA
Found at i:13042796 original size:45 final size:45
Alignment explanation
Indices: 13042742--13042944 Score: 203
Period size: 45 Copynumber: 4.5 Consensus size: 45
13042732 CTTATATGCT
* **
13042742 AACTCATACATGTGAACTCGTAAAAGAAGATTCATAGATATGGCG
1 AACTCATACATGTGAACTCATAGTAGAAGATTCATAGATATGGCG
* *** * *
13042787 AACTTATACATGTGGGTTCATGGTAGAAGATTCATGGATATGGCG
1 AACTCATACATGTGAACTCATAGTAGAAGATTCATAGATATGGCG
* * * *
13042832 AACTCGTATATGCTG-ATTCATAGTAGAATATTCATAGATATGGCG
1 AACTCATACATG-TGAACTCATAGTAGAAGATTCATAGATATGGCG
* * *
13042877 AACTCATATATG-CAGACTCATAGTAGAAGATTCATAGATATGACG
1 AACTCATACATGTGA-ACTCATAGTAGAAGATTCATAGATATGGCG
* * *
13042922 GACTCATACATGTGGATTCATAG
1 AACTCATACATGTGAACTCATAG
13042945 ATATAGAGGA
Statistics
Matches: 128, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
45 126 0.98
46 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
AACTCATACATGTGAACTCATAGTAGAAGATTCATAGATATGGCG
Found at i:13042873 original size:90 final size:90
Alignment explanation
Indices: 13042742--13042944 Score: 228
Period size: 90 Copynumber: 2.3 Consensus size: 90
13042732 CTTATATGCT
* * * ** * ** **
13042742 AACTCATACATGTGAACTCGTAAAAGAAGATTCATAGATATGGCGAACTTATACATGTGGGTTCA
1 AACTCATACATGTGGATTCATAGTAGAAGATTCATAGATATGGCGAACTCATACATGCAGACTCA
* * *
13042807 TGGTAGAAGATTCATGGATATGGCG
66 TAGTAGAAGATTCATAGATATGACG
* * * *
13042832 AACTCGTATATGCT-GATTCATAGTAGAATATTCATAGATATGGCGAACTCATATATGCAGACTC
1 AACTCATACATG-TGGATTCATAGTAGAAGATTCATAGATATGGCGAACTCATACATGCAGACTC
13042896 ATAGTAGAAGATTCATAGATATGACG
65 ATAGTAGAAGATTCATAGATATGACG
*
13042922 GACTCATACATGTGGATTCATAG
1 AACTCATACATGTGGATTCATAG
13042945 ATATAGAGGA
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
89 1 0.01
90 89 0.98
91 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (90 bp):
AACTCATACATGTGGATTCATAGTAGAAGATTCATAGATATGGCGAACTCATACATGCAGACTCA
TAGTAGAAGATTCATAGATATGACG
Found at i:13042926 original size:31 final size:30
Alignment explanation
Indices: 13042902--13043005 Score: 136
Period size: 31 Copynumber: 3.4 Consensus size: 30
13042892 ACTCATAGTA
13042902 GAAGATTCATAGATATGACGGACTCATACAT
1 GAAGATTCATAGATATGA-GGACTCATACAT
**
13042933 GTGGATTCATAGATATAGAGGACTCATACAT
1 GAAGATTCATAGATAT-GAGGACTCATACAT
* *
13042964 GCAGATTCATAGATATGATGGACTTATACAT
1 GAAGATTCATAGATATGA-GGACTCATACAT
*
13042995 GCAGATTCATA
1 GAAGATTCATA
13043006 TAAGAAGATT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
30 2 0.03
31 62 0.94
32 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (30 bp):
GAAGATTCATAGATATGAGGACTCATACAT
Found at i:13051631 original size:69 final size:70
Alignment explanation
Indices: 13051514--13051662 Score: 185
Period size: 69 Copynumber: 2.1 Consensus size: 70
13051504 TAAAATGATA
* * * *
13051514 AGAGAATCTTGTCAGAAAATCTCACTGTTCACGTAAAAGAATCACACTGTTCATTTTGTTTTTTC
1 AGAGAATATTATCAGAAAATCTCACTGTTCACGTAAAAGAATCACACTGTTCACTTTGTTTGTTC
*
13051579 -TTGG
66 TTTGC
* * * * *
13051583 AGAGAATATTATCAGAGAATCTCATTGTTCACGT-CAGGAAATCTCACTGTTCACTTTGTTTGTT
1 AGAGAATATTATCAGAAAATCTCACTGTTCACGTAAAAG-AATCACACTGTTCACTTTGTTTGTT
13051647 CTTTGC
65 CTTTGC
13051653 AGAGAATATT
1 AGAGAATATT
13051663 TCATGTTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 2 0.03
69 53 0.78
70 13 0.19
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (70 bp):
AGAGAATATTATCAGAAAATCTCACTGTTCACGTAAAAGAATCACACTGTTCACTTTGTTTGTTC
TTTGC
Found at i:13068428 original size:20 final size:20
Alignment explanation
Indices: 13068403--13068442 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13068393 AATTTTTTTT
13068403 TTAAGAATTGATTGCAAATC
1 TTAAGAATTGATTGCAAATC
13068423 TTAAGAATTGATTGCAAATC
1 TTAAGAATTGATTGCAAATC
13068443 AACAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
TTAAGAATTGATTGCAAATC
Found at i:13070178 original size:52 final size:52
Alignment explanation
Indices: 13070107--13070218 Score: 145
Period size: 52 Copynumber: 2.2 Consensus size: 52
13070097 TTCTTTGCAA
* * * * *
13070107 GAAAAAATAAAGTGAACAGTAAGATTC-CTTGATGTGGACAGTGAGATTCTCT
1 GAAAAAATAAAATGAACAGTAAGATTCTC-TAACGTGAACAGTGAGATTATCT
*
13070159 GAAAAAATAAAATGAACAGTGAGATTCTCTAACGTGAACAGTGAGATTATCT
1 GAAAAAATAAAATGAACAGTAAGATTCTCTAACGTGAACAGTGAGATTATCT
*
13070211 GACAAAAT
1 GAAAAAAT
13070219 TCTCTTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.25
Consensus pattern (52 bp):
GAAAAAATAAAATGAACAGTAAGATTCTCTAACGTGAACAGTGAGATTATCT
Found at i:13070438 original size:14 final size:14
Alignment explanation
Indices: 13070419--13070471 Score: 72
Period size: 13 Copynumber: 3.8 Consensus size: 14
13070409 GTTTCTCCAA
13070419 AAATTTTAATTTTC
1 AAATTTTAATTTTC
*
13070433 AAA-TTTAATTTTT
1 AAATTTTAATTTTC
*
13070446 AAAATTTAAGTTTTC
1 AAATTTTAA-TTTTC
13070461 AAATTTTAATT
1 AAATTTTAATT
13070472 ACATTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.35
14 10 0.29
15 12 0.35
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (14 bp):
AAATTTTAATTTTC
Found at i:13070441 original size:13 final size:14
Alignment explanation
Indices: 13070423--13070466 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
13070413 CTCCAAAAAT
13070423 TTTAA-TTTTCAAA
1 TTTAAGTTTTCAAA
* *
13070436 TTTAATTTTTAAAA
1 TTTAAGTTTTCAAA
13070450 TTTAAGTTTTCAAA
1 TTTAAGTTTTCAAA
13070464 TTT
1 TTT
13070467 TAATTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (14 bp):
TTTAAGTTTTCAAA
Found at i:13070481 original size:22 final size:22
Alignment explanation
Indices: 13070456--13070499 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13070446 AAAATTTAAG
*
13070456 TTTTCAAATTTTAATTACATTA
1 TTTTCAAATTTGAATTACATTA
*
13070478 TTTTGAAATTTGAATTACATTA
1 TTTTCAAATTTGAATTACATTA
13070500 GAACTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTCAAATTTGAATTACATTA
Found at i:13070549 original size:2 final size:2
Alignment explanation
Indices: 13070542--13070566 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13070532 GACGATTTGG
13070542 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13070567 TCTCCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13071720 original size:29 final size:27
Alignment explanation
Indices: 13071661--13071720 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
13071651 AATCTGTTGG
*
13071661 TGACAAAAAAAAATTTAAATAATTCAG
1 TGACAAAAAAAAATTTAAATAATTCAA
* *
13071688 TGACAAAAAAGAAATTTATATTAATTGAA
1 TGACAAAAAA-AAATTTA-AATAATTCAA
13071717 TGAC
1 TGAC
13071721 TATTAATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 7 0.25
29 11 0.39
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (27 bp):
TGACAAAAAAAAATTTAAATAATTCAA
Found at i:13074927 original size:30 final size:30
Alignment explanation
Indices: 13074891--13074954 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
13074881 ATTTACCTCA
*
13074891 TTCATTCTTTGACCATTACTTGTTACTTAT
1 TTCATTCTTTGACCATTACCTGTTACTTAT
13074921 TTCATTCTTTGACCATTACCTGTTACTTAT
1 TTCATTCTTTGACCATTACCTGTTACTTAT
13074951 TTCA
1 TTCA
13074955 AAAAATTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (30 bp):
TTCATTCTTTGACCATTACCTGTTACTTAT
Found at i:13076674 original size:28 final size:28
Alignment explanation
Indices: 13076634--13076703 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
13076624 ATTGATTTGT
13076634 TCACACAAGCTGTATAAA-ACGGGTCTGC
1 TCACACAAGCTGTA-AAATACGGGTCTGC
13076662 TCACACAAGCTGTAAAATACGGGTCTGC
1 TCACACAAGCTGTAAAATACGGGTCTGC
*
13076690 TCACACAAGTTGTA
1 TCACACAAGCTGTA
13076704 GGTTAGGATT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 3 0.08
28 37 0.93
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (28 bp):
TCACACAAGCTGTAAAATACGGGTCTGC
Found at i:13079202 original size:50 final size:49
Alignment explanation
Indices: 13079124--13079219 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 49
13079114 CTGACACGAT
* *
13079124 TCATTTTGATTCTGATCAGCTGAAGAGCTTAAACGTTCTGTCTGTCATAA
1 TCATTATGATCCTGATCAGCTGAAGAGCTTAAACGTTCTGT-TGTCATAA
*
13079174 TCATTATGATCCTGAAT-AGCTGATGAGCTTAAACGTTCTGTTGTCA
1 TCATTATGATCCTG-ATCAGCTGAAGAGCTTAAACGTTCTGTTGTCA
13079220 CGTTTGAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 5 0.12
50 35 0.83
51 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Consensus pattern (49 bp):
TCATTATGATCCTGATCAGCTGAAGAGCTTAAACGTTCTGTTGTCATAA
Found at i:13080934 original size:13 final size:11
Alignment explanation
Indices: 13080906--13080948 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
13080896 AGTTAAATAT
13080906 TATTTTATTAA
1 TATTTTATTAA
13080917 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
13080930 TA-TTTATTAT
1 TATTTTATTAA
13080940 TATTTTATT
1 TATTTTATT
13080949 TGGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:13083102 original size:24 final size:23
Alignment explanation
Indices: 13083065--13083110 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13083055 CAATGGTTTT
13083065 ATTCTTTTCTTTTCACTCTTGAAA
1 ATTCTTTTCTTTTCACT-TTGAAA
*
13083089 ATTC-TTTCTATTTCTCTTTGAA
1 ATTCTTTTCT-TTTCACTTTGAA
13083111 TTTTTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (23 bp):
ATTCTTTTCTTTTCACTTTGAAA
Found at i:13085000 original size:14 final size:14
Alignment explanation
Indices: 13084976--13085008 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13084966 TGGTTCTTTG
13084976 TTTAA-ATTTGTAA
1 TTTAATATTTGTAA
*
13084989 TTTAATATTTGTAT
1 TTTAATATTTGTAA
13085003 TTTAAT
1 TTTAAT
13085009 TTGACATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTTAATATTTGTAA
Found at i:13085034 original size:2 final size:2
Alignment explanation
Indices: 13085022--13085092 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
13085012 ACATAATTAG
13085022 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13085063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13085093 TAGTCCAAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13085367 original size:29 final size:29
Alignment explanation
Indices: 13085333--13085398 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
13085323 AAGTGGGTTA
*
13085333 AATATATTTATATTTTAATTATATTTTAT
1 AATATATTTATATTTTAAATATATTTTAT
* *
13085362 GATATA-TT-TATTTTAAATGTATTTTAT
1 AATATATTTATATTTTAAATATATTTTAT
*
13085389 AACATATTTA
1 AATATATTTA
13085399 AAATAAGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
27 21 0.70
28 4 0.13
29 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
AATATATTTATATTTTAAATATATTTTAT
Found at i:13088317 original size:7 final size:7
Alignment explanation
Indices: 13088294--13088357 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
13088284 TTGAAGGAAA
13088294 AAAGAAAG
1 AAAG-AAG
13088302 AAA-AA-
1 AAAGAAG
13088307 AAAGAAG
1 AAAGAAG
13088314 AAAGACAG
1 AAAGA-AG
*
13088322 ACAGATAG
1 AAAGA-AG
13088330 AAAGAAG
1 AAAGAAG
*
13088337 GAAGAAG
1 AAAGAAG
*
13088344 GAAGAAG
1 AAAGAAG
*
13088351 GAAGAAG
1 AAAGAAG
13088358 GAGAAGGAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
5 3 0.06
6 4 0.08
7 27 0.55
8 15 0.31
ACGTcount: A:0.66, C:0.03, G:0.30, T:0.02
Consensus pattern (7 bp):
AAAGAAG
Found at i:13088358 original size:7 final size:7
Alignment explanation
Indices: 13088331--13088371 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
13088321 GACAGATAGA
13088331 AAGAAGG
1 AAGAAGG
13088338 AAGAAGG
1 AAGAAGG
13088345 AAGAAGG
1 AAGAAGG
13088352 AAGAAGG
1 AAGAAGG
13088359 -AGAAGG
1 AAGAAGG
13088365 -AGAAGG
1 AAGAAGG
13088371 A
1 A
13088372 GAAAGAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:13088381 original size:6 final size:6
Alignment explanation
Indices: 13088332--13088380 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
13088322 ACAGATAGAA
*
13088332 AGAAGG AAGAAGG AAGAAGG AAGAAGG AGAAGG AGAAGG AGAAAG AGAA
1 AGAAGG -AGAAGG -AGAAGG -AGAAGG AGAAGG AGAAGG AGAAGG AGAA
13088381 AAATGTAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
6 21 0.51
7 20 0.49
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:13088558 original size:22 final size:18
Alignment explanation
Indices: 13088516--13088550 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13088506 GGAAAAAAAG
13088516 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
13088534 TAAGTTTGATTAATTTT
1 TAAGTTTGATTAATTTT
13088551 AAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:13089191 original size:24 final size:21
Alignment explanation
Indices: 13089164--13089216 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
13089154 TTTAAGCTAT
13089164 AATTAAAATTAATTATAAGTATGA
1 AATTAAAATTAATT-TAA-T-TGA
13089188 AATTAAAA--AATTTAATTGA
1 AATTAAAATTAATTTAATTGA
13089207 AA-TAAAATTA
1 AATTAAAATTA
13089217 GAGTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 2 0.07
21 3 0.11
22 4 0.15
24 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
AATTAAAATTAATTTAATTGA
Found at i:13089512 original size:16 final size:16
Alignment explanation
Indices: 13089467--13089516 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
13089457 TAAACCTAGC
*
13089467 TAATTAATTGCCAAAA
1 TAATTAATTACCAAAA
*
13089483 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
13089497 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
13089513 TAAT
1 TAAT
13089517 ATCCCATCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 13 0.48
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:13089582 original size:30 final size:30
Alignment explanation
Indices: 13089548--13089642 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
13089538 AAATGGTACA
*
13089548 AAATAAATATTTATTTTGTATCATTTTAGT
1 AAATAAATATATATTTTGTATCATTTTAGT
** * * *
13089578 AAAT-AAT-GGT-GTGTGTATACCATTTTGGT
1 AAATAAATATATATTTTGTAT--CATTTTAGT
*
13089607 ATATAAATATATATTTTGTA-CTATTTTAGT
1 AAATAAATATATATTTTGTATC-ATTTTAGT
13089637 AAATAA
1 AAATAA
13089643 CCCATTTTGA
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
27 6 0.13
28 1 0.02
29 15 0.32
30 19 0.40
31 1 0.02
32 5 0.11
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (30 bp):
AAATAAATATATATTTTGTATCATTTTAGT
Done.