Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 61 of 120
Found at i:18010066 original size:11 final size:11
Alignment explanation
Indices: 18010022--18010074 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
18010012 CAAGTCAAAT
*
18010022 CGTTGACCGAT
1 CGTTGACCGAC
*
18010033 CGTTGATCGAC
1 CGTTGACCGAC
*
18010044 TGTTGACCGAC
1 CGTTGACCGAC
*
18010055 CGTTGACTGAC
1 CGTTGACCGAC
*
18010066 CTTTGACCG
1 CGTTGACCG
18010075 TTGATAGTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:18015808 original size:87 final size:87
Alignment explanation
Indices: 18015716--18015890 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
18015706 AATATATATA
18015716 TATATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAA
1 TATATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAA
*
18015781 CATATTTGATGAGTTTCTCCAT
66 CATATTTAATGAGTTTCTCCAT
18015803 TATATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAA
1 TATATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAA
18015868 CATATTTAATGAGTTTCTCCAT
66 CATATTTAATGAGTTTCTCCAT
18015890 T
1 T
18015891 GTAATCTATT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (87 bp):
TATATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAA
CATATTTAATGAGTTTCTCCAT
Found at i:18016988 original size:22 final size:22
Alignment explanation
Indices: 18016960--18017003 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
18016950 TTAAGATAAA
18016960 AAATTATTTCTAAAATTACACC
1 AAATTATTTCTAAAATTACACC
18016982 AAATTATTTCTAAAATTACACC
1 AAATTATTTCTAAAATTACACC
18017004 CCTATACCGC
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:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTATTTCTAAAATTACACC
Found at i:18017473 original size:11 final size:12
Alignment explanation
Indices: 18017452--18017477 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18017442 TTTTATGCAA
18017452 TTGTTATTTTTT
1 TTGTTATTTTTT
18017464 TTGTTATTTTTT
1 TTGTTATTTTTT
18017476 TT
1 TT
18017478 TTGAATGCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTGTTATTTTTT
Found at i:18022694 original size:838 final size:837
Alignment explanation
Indices: 18020774--18023122 Score: 2603
Period size: 838 Copynumber: 2.8 Consensus size: 837
18020764 TAGTAAAATT
* * *
18020774 AGGTTGGTAGGAGAAGATGGATTGTAAATTCAATGTTGTGTCCCATTAGAATGGACAAACTCACT
1 AGGTTGGTAGGAGAAGATGGATCGTAAATTCAATGTTGTGGCCCATTACAATGGACAAACTCACT
* *
18020839 ATATAAAAGACACCAATTTGAATGCTAGTAAATAAAAGTAGAGGGACCAAATACGCACAACTCAA
66 ATATCAAAGACACCAATTTGAATGCTAGTAAATAAAAGTAGAGGGACCAAATACGCACAAATCAA
** * * *
18020904 TAAGTACAAGGAAAATTCTTAGAATTTAACCAAAAATAATATTTGTTTCACTCAACTCTGCCACG
131 TAAGTACAAGGACTATTCTTAGAATTTAACCAAAAATAATATTTGTTTCACTCGACTATGACACG
* *
18020969 TGAGGTTC-TGAATATAAAATAATAATAATTTTTTTTATTTTAAAACTGCCATCTTATG-TGAAG
196 TGAGGTTCTTG-ATATAAAA-AATAATAATTTTTTTTATTTTAAAA-TTCCATCTTACGCT---G
**** * * ** * * *
18021032 ATTTCAAGATATAAAA-AA-AAAATATTTTGAAAATGTCTTTTTACGCGGC-GACTCCAAGA-AG
255 -TTTCAAGATATAAAATAATTTTTTATTTTGAAAGTGTCTCTTTACATGACAG-TTTCAAGATA-
* * ** *
18021093 TA-AAAAATGTTATTTCTAAAAATGCCCTTTTATATCGCGGTTTCAAATTAATAAAAATATTGTT
317 TACAAAAAAGTTATTTCTAAAAGTGCCCCCTTATACCGCGGTTTCAAATTAATAAAAATATT-TT
** ** *
18021157 TTTTAAAATAATTGGGTTAGGGGGAGGTCAGACCCTTA-CTCAGCTTTCAATTGAAACATCCATT
381 TTTTCTAA-AA-T-GACT-GGGGGAGGTCAGACCCTTACCT-AGCTGTCAATTGAAACATCCATT
* * *
18021221 GCGCAAAAAAAAATTCAAATTTTTATTTTTTTTATTCAATCTACTCTCTTCTTTCCTTCAAACAC
441 GCGC-AAAAAAAATTCAAATTTTAATTTTTTTTATTCAATCTACTCCCTTCTTTCC-TCAAACCC
* * * *
18021286 CTGTCCCAAACAACAGCATGTCACATGA-ATCTTTAATGAATTATTTTTTTTTTGAAATTGACAT
504 CTG-CCCCAACAACATCACGTCACATGACA-CTTTAATGAATTA--TTTTTTTTAAAATTGACAT
* * * *
18021350 GTCAGGTGGCAGTTATAAACTCCAAGATTCTAAAATTGAAAATATAATTACGAAATTATCCAATG
565 GTCAGGTGGCAGTTACAAACTCCAAGATTCTAAAATT-AAAA-AAAATTAC-AAAATACCCAATG
* * *
18021415 TAATTTATATGATT-TCCACCTCCATTTTTCTCACAAAAATATTCTCACAATTTCTTCTCTATTT
627 TAAATTATATGATTGT-CACCTCCATTTCTCCCACAAAAATATTCTCACAATTTCTTCTCTATTT
*
18021479 AAACTACTCTCCATTTTGTTGAAGTAAATTTGCTTTTTTAGTTTTTTTAAATTAATTTTTTAATT
691 AAACTACTCTCCATTTTGTTGAAGTAAATTTGCTTTTTTAGTTTTTTTAAAATAATTTTTTAATT
* * ** * *
18021544 TAGTAAATTTTCACTATAAAAGGCGATAACATTATTTGTATACTTGTTTTATTTTTATTTTTTTG
756 TAGTAAATTTTCACAATAAAAGGCGATAACATTAATTGTATACTAATTGTA--TATATTTTTTTG
18021609 TTATTTGTTCTGAATCTGC
819 TTATTTGTTCTGAATCTGC
** * * * * * * *
18021628 AGGTTATTAAGATAAGATGGATCATAAATGCAATATTGTGGCCCATTACAATGGACAAATTCACC
1 AGGTTGGTAGGAGAAGATGGATCGTAAATTCAATGTTGTGGCCCATTACAATGGACAAACTCACT
* * * *
18021693 ATATCAAAGACACTGAA-TCGAATGCTAGTAAATAAAAGTAGAGGGATCAAATATGCACAAATCA
66 ATATCAAAGACAC-CAATTTGAATGCTAGTAAATAAAAGTAGAGGGACCAAATACGCACAAATCA
* * * * *
18021757 ATAAGTACATGGACTATTCTTAGAATTCAACCAAAAATCATATTTGTTTCACTCGACAATGACAT
130 ATAAGTACAAGGACTATTCTTAGAATTTAACCAAAAATAATATTTGTTTCACTCGACTATGACAC
** *** *
18021822 ACGACACTCTTGATATAAAAAATAGTAA--TTTTTTATTTTAAAATTACCATCTTACGCTGTTTC
195 GTGAGGTTCTTGATATAAAAAATAATAATTTTTTTTATTTTAAAATT-CCATCTTACGCTGTTTC
*
18021885 AAGATATAAAATAATTTTTTATTTTGAAAGTGTCTCTTTATATGACAGTTTCAAGATATACAAAA
259 AAGATATAAAATAATTTTTTATTTTGAAAGTGTCTCTTTACATGACAGTTTCAAGATATACAAAA
* ***
18021950 AAGTTATTTTTAAAAGTGCCCCCTTATACCGCAAATTCAAATTAATAAAAATATTTTTTTTCTAA
324 AAGTTATTTCTAAAAGTGCCCCCTTATACCGCGGTTTCAAATTAATAAAAATATTTTTTTTCTAA
* * *
18022015 AATGACT-GGGGTGGTTAGACCCTTACCTAGCTGTCAATTGAAACATTCATTGCGCAAAAAAAAT
389 AATGACTGGGGGAGGTCAGACCCTTACCTAGCTGTCAATTGAAACATCCATTGCGCAAAAAAAAT
* * * * * * *
18022079 TCAAATATTAATATTTCTTATCCGATCTATTCCCTTCTTTCCATCAAACCCCTGCCGCCAACAAA
454 TCAAATTTTAATTTTTTTTATTCAATCTACTCCCTTCTTTCC-TCAAACCCCTGCC-CCAACAAC
* * * * *
18022144 ATCACGTCACATGACACTTTAATAAATTACTTTTTTT-AATTTGACATCTCAGGTGGCGGTTACA
517 ATCACGTCACATGACACTTTAATGAATTATTTTTTTTAAAATTGACATGTCAGGTGGCAGTTACA
*
18022208 AACTCCAAGATTCTAAAATT-AAAAAAATTACAAAAGTACCCAATGTAAATTATATAATTGTCAC
582 AACTCCAAGATTCTAAAATTAAAAAAAATTACAAAA-TACCCAATGTAAATTATATGATTGTCAC
* * * *
18022272 CTCCGTTTCTCCCACAAAAATATTCTCACAATTTTTTTTCTATTTAAACTACTCTTCATTTTGTT
646 CTCCATTTCTCCCACAAAAATATTCTCACAATTTCTTCTCTATTTAAACTACTCTCCATTTTGTT
* * **
18022337 GAAGTAAGTTTGCTTTTATTAGTTTTTTTAAAAT-ATTTTTTAATTTAGTTAATTTTCACAATCT
711 GAAGTAAATTTGCTTTT-TTAGTTTTTTTAAAATAATTTTTTAATTTAGTAAATTTTCACAATAA
** * * *
18022401 AAGGC-ATAATGTTAATTGTATGC-AATTGTA-ATATTTTTTTGTTATTT-TTTTGGAATGTGC
775 AAGGCGATAACATTAATTGTATACTAATTGTATATATTTTTTTGTTATTTGTTCT-GAATCTGC
*
18022461 AGGTTGGTAGGAGAAGATGGATCGTAAATTCAATGTTGTGGCCCATTACAATGTACAAACTCACT
1 AGGTTGGTAGGAGAAGATGGATCGTAAATTCAATGTTGTGGCCCATTACAATGGACAAACTCACT
* * * *
18022526 ATATCAAAGACACCAATTTGAATGCTACCAATAAATAAAAATAGAGGGACCAAATCCGCGCAAAT
66 ATATCAAAGACACCAATTTGAATGCT---AGTAAATAAAAGTAGAGGGACCAAATACGCACAAAT
* * * *
18022591 CAACAAATACAAGGACTATTCTTAGAATTTAA-CATAAGATAATATTTGTTTCACTCGACTTTGA
128 CAATAAGTACAAGGACTATTCTTAGAATTTAACCA-AAAATAATATTTGTTTCACTCGACTATGA
* * *
18022655 CACGTGAGGTTCTTGATATAAAAATTAATAATTTTTTTTA----AAACTGT-CATCATACGCGAC
192 CACGTGAGGTTCTTGATATAAAAAATAATAATTTTTTTTATTTTAAAAT-TCCATCTTA--CG-C
* * * *
18022715 AGTTTCAAGATATAAAATAATTTTTTTAGTTTGAAAGTGTTTCTTTACATGACAGTATCAAGATA
253 TGTTTCAAGATATAAAATAA-TTTTTTATTTTGAAAGTGTCTCTTTACATGACAGTTTCAAGATA
* * * *
18022780 TACATAAAAAGTTATTTCTAGAAGTGTCTCCTTATACCGCGGTTTCAAATTAATAGAAATATTTT
317 TACA-AAAAAGTTATTTCTAAAAGTGCCCCCTTATACCGCGGTTTCAAATTAATAAAAATATTTT
** * * * * *
18022845 TTTTCTAAAACAACTGGGTTAGGGGGCGATCAAACCCTTACCCAGCTGTCAATTGAAGCATCCAC
381 TTTTCTAAAATGACT-GG---GGGAG-G-TCAGACCCTTACCTAGCTGTCAATTGAAACATCCAT
* ** * * *
18022910 TGTGCAAAAAATTTTCAAATTTTAATTTTTTTTATTCAATCTACTCCCTTCATTTTCTTAAATCC
440 TGCGCAAAAAAAATTCAAATTTTAATTTTTTTTATTCAATCTACTCCCTTC-TTTCCTCAAACCC
** * * *
18022975 CTATCCCAACATCATCACGTCACATGACACTTTAATGATTTATTTTTTTCTAAAATTGACATGTA
504 CTGCCCCAACAACATCACGTCACATGACACTTTAATGAATTATTTTTTT-TAAAATTGACATGTC
* * *
18023040 AGGTGGCAGTTTCAAACTTCGAA-ATTCAAAAATTAAAAATAAAATTACGAAAATACCCAATGTA
568 AGGTGGCAGTTACAAAC-TCCAAGATTCTAAAATT-AAAA-AAAATTAC-AAAATACCCAATGTA
18023104 ATATATATATGATTGTCAC
629 A-AT-TATATGATTGTCAC
18023123 TTTCATTTTA
Statistics
Matches: 1252, Mismatches: 197, Indels: 95
0.81 0.13 0.06
Matches are distributed among these distances:
832 5 0.00
833 105 0.08
834 4 0.00
835 5 0.00
836 130 0.10
837 61 0.05
838 208 0.17
839 19 0.02
840 1 0.00
841 43 0.03
842 7 0.01
843 6 0.00
844 123 0.10
845 124 0.10
846 41 0.03
847 6 0.00
848 19 0.02
849 25 0.02
850 44 0.04
851 89 0.07
852 1 0.00
853 7 0.01
854 175 0.14
855 4 0.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (837 bp):
AGGTTGGTAGGAGAAGATGGATCGTAAATTCAATGTTGTGGCCCATTACAATGGACAAACTCACT
ATATCAAAGACACCAATTTGAATGCTAGTAAATAAAAGTAGAGGGACCAAATACGCACAAATCAA
TAAGTACAAGGACTATTCTTAGAATTTAACCAAAAATAATATTTGTTTCACTCGACTATGACACG
TGAGGTTCTTGATATAAAAAATAATAATTTTTTTTATTTTAAAATTCCATCTTACGCTGTTTCAA
GATATAAAATAATTTTTTATTTTGAAAGTGTCTCTTTACATGACAGTTTCAAGATATACAAAAAA
GTTATTTCTAAAAGTGCCCCCTTATACCGCGGTTTCAAATTAATAAAAATATTTTTTTTCTAAAA
TGACTGGGGGAGGTCAGACCCTTACCTAGCTGTCAATTGAAACATCCATTGCGCAAAAAAAATTC
AAATTTTAATTTTTTTTATTCAATCTACTCCCTTCTTTCCTCAAACCCCTGCCCCAACAACATCA
CGTCACATGACACTTTAATGAATTATTTTTTTTAAAATTGACATGTCAGGTGGCAGTTACAAACT
CCAAGATTCTAAAATTAAAAAAAATTACAAAATACCCAATGTAAATTATATGATTGTCACCTCCA
TTTCTCCCACAAAAATATTCTCACAATTTCTTCTCTATTTAAACTACTCTCCATTTTGTTGAAGT
AAATTTGCTTTTTTAGTTTTTTTAAAATAATTTTTTAATTTAGTAAATTTTCACAATAAAAGGCG
ATAACATTAATTGTATACTAATTGTATATATTTTTTTGTTATTTGTTCTGAATCTGC
Found at i:18023865 original size:54 final size:54
Alignment explanation
Indices: 18023801--18023915 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
18023791 GCGAGGTTCT
* *
18023801 AGATAGAAAATAATTTTTTTTATTTTAAAACTACCATC-TTACGTGGCGATTTCA
1 AGATATAAAATAATTTTTTTTATTTTAAAACTACC-TCTTTACGCGGCGATTTCA
* * * ** *
18023855 AGATATAAAATATTTTTTTTTATTTTGAAAGTGTCTCTTTACGCGGCGGTTTCA
1 AGATATAAAATAATTTTTTTTATTTTAAAACTACCTCTTTACGCGGCGATTTCA
18023909 AGATATA
1 AGATATA
18023916 CAAAAAAGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.04
54 50 0.96
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (54 bp):
AGATATAAAATAATTTTTTTTATTTTAAAACTACCTCTTTACGCGGCGATTTCA
Found at i:18027193 original size:94 final size:100
Alignment explanation
Indices: 18027083--18027267 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 100
18027073 TCTCTAATAT
* * * *
18027083 AATTATTTTTTGGTTAAAATT-TCATTCACAATAGTTTCACGAT-A-AA-AGTAATAATATTTTT
1 AATTATTTTTTGGTTAAAATTGTC-TCCACAACAATTTCACGATAATAATAATAATAATATTTTT
*
18027144 -TAACAAGATGATACAATGGGTGAAACCGTTGTATC
65 ATAACAAGATGACACAATGGGTGAAACCGTTGTATC
*
18027179 AATT-TTTTTT-GTTAAAATTGTCTCCACAACAATTTCATGATAATAATAATAATAATATTTTTA
1 AATTATTTTTTGGTTAAAATTGTCTCCACAACAATTTCACGATAATAATAATAATAATATTTTTA
*
18027242 TAACAAGATTACACAATGGGTGAAAC
66 TAACAAGATGACACAATGGGTGAAAC
18027268 TGTCATATCA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
94 24 0.31
95 9 0.12
96 6 0.08
97 14 0.18
98 24 0.31
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (100 bp):
AATTATTTTTTGGTTAAAATTGTCTCCACAACAATTTCACGATAATAATAATAATAATATTTTTA
TAACAAGATGACACAATGGGTGAAACCGTTGTATC
Found at i:18030265 original size:24 final size:24
Alignment explanation
Indices: 18030214--18030265 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
18030204 TTCGTAAGTC
* *
18030214 AAATACATTATGCTAATAAATGCA
1 AAATACATTATACTAATAAATACA
* *
18030238 AAATATATTATACTAATAAATACT
1 AAATACATTATACTAATAAATACA
18030262 AAAT
1 AAAT
18030266 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATACATTATACTAATAAATACA
Found at i:18031872 original size:27 final size:28
Alignment explanation
Indices: 18031841--18031894 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
18031831 ACTTCATAAA
18031841 TTTT-AAATTTAGTCTCC-CTACTTTTAT
1 TTTTAAAATTTAGTC-CCTCTACTTTTAT
18031868 TTTTAAAAATTTAGTCCCTCTACTTTT
1 TTTT-AAAATTTAGTCCCTCTACTTTT
18031895 CAAATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.17
28 2 0.08
29 18 0.75
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTTAAAATTTAGTCCCTCTACTTTTAT
Found at i:18031907 original size:30 final size:29
Alignment explanation
Indices: 18031845--18031907 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
18031835 CATAAATTTT
** *
18031845 AAATTTAGTCTCCCTACTTTTATTTTTAA
1 AAATTTAGTCTCCCTACTTTTAAATCTAA
18031874 AAATTTAGTC-CCTCTACTTTTCAAATCTAA
1 AAATTTAGTCTCC-CTACTTTT-AAATCTAA
18031904 AAAT
1 AAAT
18031908 CCAAGTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.07
29 18 0.62
30 9 0.31
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTAGTCTCCCTACTTTTAAATCTAA
Found at i:18034322 original size:19 final size:19
Alignment explanation
Indices: 18034295--18034332 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18034285 CCATTTTCAC
* *
18034295 CCATTGTAATCAAATTTAT
1 CCATCGTAATCAAAATTAT
18034314 CCATCGTAATCAAAATTAT
1 CCATCGTAATCAAAATTAT
18034333 TATTAACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (19 bp):
CCATCGTAATCAAAATTAT
Found at i:18034590 original size:18 final size:20
Alignment explanation
Indices: 18034549--18034591 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
18034539 CATCATTAAT
*
18034549 AATTCAATTTTAATATAAAC
1 AATTCAATTATAATATAAAC
18034569 -ATTCAA-TATAAT-TAAAC
1 AATTCAATTATAATATAAAC
18034586 AATTCA
1 AATTCA
18034592 CTAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTCAATTATAATATAAAC
Found at i:18036157 original size:16 final size:17
Alignment explanation
Indices: 18036136--18036174 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18036126 AATAATTTTT
18036136 TAAAAA-TA-AAAATATA
1 TAAAAATTAGAAAATA-A
18036152 TAAAAATTAGAAAATAA
1 TAAAAATTAGAAAATAA
18036169 TAAAAA
1 TAAAAA
18036175 ATCATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 9 0.43
18 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAAATTAGAAAATAA
Found at i:18036171 original size:41 final size:40
Alignment explanation
Indices: 18036091--18036171 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 40
18036081 CATTAATATA
*
18036091 TTTTAAAAAATAAAAATATTGAAACAAATTATAAAAATAAT
1 TTTTAAAAAATAAAAATATT-AAACAAATTAAAAAAATAAT
*
18036132 TTTTTAAAAATAAAAATA-TATAA-AAATTAGAAAATAATAA
1 TTTTAAAAAATAAAAATATTA-AACAAATTA-AAAA-AATAA
18036172 AAAATCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 7 0.20
40 6 0.17
41 22 0.63
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (40 bp):
TTTTAAAAAATAAAAATATTAAACAAATTAAAAAAATAAT
Found at i:18040475 original size:2 final size:2
Alignment explanation
Indices: 18040470--18040508 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18040460 TATATATATA
18040470 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
18040509 AATATTAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:18040750 original size:65 final size:66
Alignment explanation
Indices: 18040638--18040780 Score: 184
Period size: 65 Copynumber: 2.2 Consensus size: 66
18040628 AGTAGAATTC
18040638 GATTTGAGTTAATAGAATTTGAATTATTTGAATAAATTTAAATATGTAATTTGAATTTTTAAGTT
1 GATTTGAGTTAATAGAATTTGAATTATTTGAATAAATTTAAATATGTAATTTGAATTTTTAAGTT
18040703 T
66 T
* * * * * *
18040704 GATTTGGGTTAATTG-ATTTGAGTTATTTGAGGT-AATTTGAAA-ATGTAATTTGATTTTTTGAG
1 GATTTGAGTTAATAGAATTTGAATTATTTGA-ATAAATTT-AAATATGTAATTTGAATTTTTAAG
18040766 TTT
64 TTT
*
18040769 GAGTTGAGTTAA
1 GATTTGAGTTAA
18040781 ATTTTACAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
65 50 0.75
66 17 0.25
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (66 bp):
GATTTGAGTTAATAGAATTTGAATTATTTGAATAAATTTAAATATGTAATTTGAATTTTTAAGTT
T
Found at i:18040953 original size:2 final size:2
Alignment explanation
Indices: 18040946--18040978 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
18040936 GTTCCAAAAC
*
18040946 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18040979 TAAACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18046163 original size:17 final size:17
Alignment explanation
Indices: 18046145--18046176 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18046135 AAAAATATAT
18046145 TTTAAAA-AATAATAAA
1 TTTAAAATAATAATAAA
18046161 TTTAAAATAATAATAA
1 TTTAAAATAATAATAA
18046177 TAAGGGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTTAAAATAATAATAAA
Found at i:18049203 original size:26 final size:28
Alignment explanation
Indices: 18049153--18049204 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
18049143 ATATATAGAT
*
18049153 ATATAATAATTATTTTATAATATAATTA
1 ATATAATAATTATTTTATAACATAATTA
18049181 ATATAAT-ATT-TTTTATAACATAAT
1 ATATAATAATTATTTTATAACATAAT
18049205 ATATTCGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 3 0.13
28 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATAATAATTATTTTATAACATAATTA
Found at i:18052975 original size:18 final size:18
Alignment explanation
Indices: 18052952--18052986 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18052942 AATGTTTTAA
*
18052952 TTTTTTTAATTTTAAATG
1 TTTTTTTAAGTTTAAATG
18052970 TTTTTTTAAGTTTAAAT
1 TTTTTTTAAGTTTAAAT
18052987 TCATTTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTTTTAAGTTTAAATG
Found at i:18056250 original size:17 final size:17
Alignment explanation
Indices: 18056217--18056251 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18056207 TATTAAACTA
*
18056217 TTAAAATAATATTATTT
1 TTAAAATAATATAATTT
*
18056234 TTAAAATAATCTAATTT
1 TTAAAATAATATAATTT
18056251 T
1 T
18056252 CAAGTTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAATAATATAATTT
Found at i:18074481 original size:17 final size:17
Alignment explanation
Indices: 18074459--18074497 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18074449 AGGTGGAGAA
* *
18074459 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
18074476 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
18074493 CTTGT
1 CTTGT
18074498 CCAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:18077652 original size:20 final size:19
Alignment explanation
Indices: 18077629--18077669 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
18077619 ATAAATATGT
*
18077629 AATAAATAATTATAATATTA
1 AATAAATAATT-TAATAATA
18077649 AATAAATAATTTAATAATA
1 AATAAATAATTTAATAATA
18077668 AA
1 AA
18077670 AAGAAACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAATAATTTAATAATA
Found at i:18078687 original size:29 final size:29
Alignment explanation
Indices: 18078655--18078954 Score: 250
Period size: 29 Copynumber: 10.1 Consensus size: 29
18078645 GAATTTCTTA
** *
18078655 AAAATCACATTTTGTCCCCTAAACTTTCTA
1 AAAATCACATTTTAACCCCTAAACTTTC-C
*
18078685 AAAATCACATTTTAAGCCCTAAACTTTCC
1 AAAATCACATTTTAACCCCTAAACTTTCC
18078714 AAAATTCACATTTTAA-CCCTAAACTTTTCC
1 AAAA-TCACATTTTAACCCCTAAAC-TTTCC
* * *
18078744 AAAATTTACATGTTAAACCCTAAACTTTTCC
1 AAAA-TCACATTTTAACCCCTAAAC-TTTCC
* * *
18078775 AAAATTACATTTTAACCACTAAACTTCTCT
1 AAAATCACATTTTAACCCCTAAACTT-TCC
* *
18078805 AAAATTACATTTTAACCCC-AAACTTCTCT
1 AAAATCACATTTTAACCCCTAAACTT-TCC
* *
18078834 AAAATCACATTTTGACTCC-AAACTTCTCC
1 AAAATCACATTTTAACCCCTAAACTT-TCC
* * *
18078863 AAAATTACATTTTGA-CCCTAAACTTCTCT
1 AAAATCACATTTTAACCCCTAAACTT-TCC
* * * *
18078892 AAAATCTCATTTTGACCTC-AAGCTTTCCC
1 AAAATCACATTTTAACCCCTAAACTTT-CC
* *
18078921 AAAATTACATTTTTACACCCTAAACTTTTCC
1 AAAATCACATTTTAAC-CCCTAAAC-TTTCC
18078952 AAA
1 AAA
18078955 TTTACGTTTT
Statistics
Matches: 232, Mismatches: 28, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.01
29 104 0.45
30 96 0.41
31 26 0.11
32 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATCACATTTTAACCCCTAAACTTTCC
Found at i:18078689 original size:30 final size:30
Alignment explanation
Indices: 18078648--18078948 Score: 217
Period size: 30 Copynumber: 10.1 Consensus size: 30
18078638 GGTCCCTGAA
**
18078648 TTTCTTAAAAATCACATTTTGTCCCCTAAAC
1 TTTC-TAAAAATCACATTTTAACCCCTAAAC
*
18078679 TTTCTAAAAATCACATTTTAAGCCCTAAAC
1 TTTCTAAAAATCACATTTTAACCCCTAAAC
* *
18078709 TTTCCAAAATTCACATTTTAA-CCCTAAAC
1 TTTCTAAAAATCACATTTTAACCCCTAAAC
* * * * *
18078738 TTTTCCAAAATTTACATGTTAAACCCTAAAC
1 -TTTCTAAAAATCACATTTTAACCCCTAAAC
* * *
18078769 TTT-TCCAAAATTACATTTTAACCACTAAAC
1 TTTCT-AAAAATCACATTTTAACCCCTAAAC
*
18078799 TTCTCT-AAAATTACATTTTAACCCC-AAAC
1 TT-TCTAAAAATCACATTTTAACCCCTAAAC
* *
18078828 TTCTCT-AAAATCACATTTTGACTCC-AAAC
1 TT-TCTAAAAATCACATTTTAACCCCTAAAC
* * *
18078857 -TTCTCCAAAATTACATTTTGA-CCCTAAAC
1 TTTCT-AAAAATCACATTTTAACCCCTAAAC
* * * *
18078886 TTCTCT-AAAATCTCATTTTGACCTC-AAGC
1 TT-TCTAAAAATCACATTTTAACCCCTAAAC
** * *
18078915 TTTCCCAAAATTACATTTTTACACCCTAAAC
1 TTTCTAAAAATCACATTTTAAC-CCCTAAAC
18078946 TTT
1 TTT
18078949 TCCAAATTTA
Statistics
Matches: 227, Mismatches: 29, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 87 0.38
30 109 0.48
31 22 0.10
32 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTCTAAAAATCACATTTTAACCCCTAAAC
Found at i:18078965 original size:60 final size:59
Alignment explanation
Indices: 18078661--18078966 Score: 266
Period size: 60 Copynumber: 5.2 Consensus size: 59
18078651 CTTAAAAATC
* * * * *
18078661 ACATTTTGTCCCCTAAACTT-TCTAAAAATCACATTTTAAGCCCTAAAC-TTTCCAAAATTC
1 ACATTTTGACCTCTAAACTTCTC-CAAAATTACATTTTAA-CCCTAAACTTTTCC-AAATTT
* * * *
18078721 ACATTTTAACC-CTAAACTTTTCCAAAATTTACATGTTAAACCCTAAACTTTTCCAAAATT
1 ACATTTTGACCTCTAAACTTCTCCAAAA-TTACAT-TTTAACCCTAAACTTTTCCAAATTT
* * * * * * * *
18078781 ACATTTTAACCACTAAACTTCTCTAAAATTACATTTTAACCCCAAACTTCTCTAAAATC
1 ACATTTTGACCTCTAAACTTCTCCAAAATTACATTTTAACCCTAAACTTTTCCAAATTT
* * * * *
18078840 ACATTTTGA-CTCCAAACTTCTCCAAAATTACATTTTGACCCTAAACTTCTCTAAAATCT
1 ACATTTTGACCTCTAAACTTCTCCAAAATTACATTTTAACCCTAAACTTTTC-CAAATTT
*
18078899 -CATTTTGACCTC-AAGCTT-TCCCAAAATTACATTTTTACACCCTAAACTTTTCCAAATTT
1 ACATTTTGACCTCTAAACTTCT-CCAAAATTACA-TTTTA-ACCCTAAACTTTTCCAAATTT
*
18078958 ACGTTTTGA
1 ACATTTTGA
18078967 TCCCTTATTC
Statistics
Matches: 205, Mismatches: 30, Indels: 22
0.80 0.12 0.09
Matches are distributed among these distances:
57 1 0.00
58 61 0.30
59 55 0.27
60 65 0.32
61 23 0.11
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
ACATTTTGACCTCTAAACTTCTCCAAAATTACATTTTAACCCTAAACTTTTCCAAATTT
Found at i:18089641 original size:39 final size:39
Alignment explanation
Indices: 18089598--18089718 Score: 131
Period size: 39 Copynumber: 3.1 Consensus size: 39
18089588 TCACCTCGAC
18089598 CCTGGGGTAGATTGCAGCCATTTGATCTTTTACCCCAAG
1 CCTGGGGTAGATTGCAGCCATTTGATCTTTTACCCCAAG
* * * *
18089637 CCTGGGGTAGA-T-CA-CCATTAGCCAATCTCTTACCATCGAG
1 CCTGGGGTAGATTGCAGCCATTTG---ATCTTTTACC-CCAAG
* *
18089677 CCTGGGGCAGATTGCAGCCATCTGATCTTTTACCCCAAG
1 CCTGGGGTAGATTGCAGCCATTTGATCTTTTACCCCAAG
18089716 CCT
1 CCT
18089719 AAGGCAAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
36 6 0.09
37 2 0.03
38 1 0.02
39 26 0.40
40 22 0.34
41 1 0.02
42 2 0.03
43 5 0.08
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTGGGGTAGATTGCAGCCATTTGATCTTTTACCCCAAG
Found at i:18089689 original size:79 final size:78
Alignment explanation
Indices: 18089583--18089766 Score: 251
Period size: 79 Copynumber: 2.3 Consensus size: 78
18089573 GAAGATTCCG
* * * * ** * *
18089583 ATCTCTCACCTCGACCCTGGGGTAGATTGCAGCCATTTGATCTTTTACCCCAAGCCTGGGGTAGA
1 ATCTCTTACCTCGAGCCTGGGGCAGATTGCAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAAA
* *
18089648 TCACCATTAGCCA
66 TCACCATCAACCA
18089661 ATCTCTTACCATCGAGCCTGGGGCAGATTGCAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAA
1 ATCTCTTACC-TCGAGCCTGGGGCAGATTGCAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAA
18089726 ATCACCATCAACCA
65 ATCACCATCAACCA
* *
18089740 ATCTCTTACCCCGAGCTTGGGGCAGAT
1 ATCTCTTACCTCGAGCCTGGGGCAGAT
18089767 CACCATCAGC
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 24 0.26
79 69 0.74
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCTCGAGCCTGGGGCAGATTGCAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAAA
TCACCATCAACCA
Found at i:18089800 original size:39 final size:39
Alignment explanation
Indices: 18089622--18089945 Score: 248
Period size: 39 Copynumber: 8.3 Consensus size: 39
18089612 CAGCCATTTG
* * *
18089622 ATCTTTTACCCCAAGCCTGGGGTAGATCACCATTAGCCA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
* * *
18089661 ATCTCTTACCATCGAGCCTGGGGCAGATTGCAGCCATCTG---
1 ATCTCTTACC-CCAAGCCTGGGGCAGA-T-CA-CCATCAGCCA
* ** * *
18089701 ATCTTTTACCCCAAGCCTAAGGCAAATCACCATCAACCA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
* *
18089740 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
*
18089779 ATCTCTTACCCCAAGCCTGGGGCAGATTACAGCCATCTG---
1 ATCTCTTACCCCAAGCCTGGGGCAGA-T-CA-CCATCAGCCA
* * * *
18089818 ATCTTTTA-CCCTAGCTTGGGGCAGATTACCATCAGCCA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
* * ** * * **
18089856 ATCTCTTACCCTAAGCTTGGGGCAGATTGCAACCATTCA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
* * * * * *
18089895 ATCTTTTATCCCGAGCCTGGGGTAGATCACCATTAGGCA
1 ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
18089934 ATCTCTTACCCC
1 ATCTCTTACCCC
18089946 GCGACAGGGG
Statistics
Matches: 219, Mismatches: 52, Indels: 28
0.73 0.17 0.09
Matches are distributed among these distances:
35 6 0.03
36 6 0.03
37 3 0.01
38 23 0.11
39 142 0.65
40 23 0.11
41 3 0.01
42 8 0.04
43 5 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCAAGCCTGGGGCAGATCACCATCAGCCA
Found at i:18089849 original size:77 final size:78
Alignment explanation
Indices: 18089738--18089974 Score: 280
Period size: 77 Copynumber: 3.1 Consensus size: 78
18089728 CACCATCAAC
* *
18089738 CAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCA
1 CAATCTTTTATCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCA
*
18089803 GATTACAGCCA-T
66 GATTACAACCATT
* * * * *
18089815 CTGATCTTTTA-CCCTAGCTTGGGGCAGATTACCATCAGCCAATCTCTTACCCTAAGCTTGGGGC
1 C-AATCTTTTATCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGC
*
18089879 AGATTGCAACCATT
65 AGATTACAACCATT
* * * * ** * *
18089893 CAATCTTTTATCCCGAGCCTGGGGTAGATCACCATTAGGCAATCTCTTACCCCGCGACAGGGGCA
1 CAATCTTTTATCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCA
* *
18089958 GATTGCAACCATC
66 GATTACAACCATT
18089971 CAAT
1 CAAT
18089975 ATCTTACCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
77 68 0.50
78 67 0.50
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (78 bp):
CAATCTTTTATCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCA
GATTACAACCATT
Found at i:18089897 original size:116 final size:117
Alignment explanation
Indices: 18089622--18089921 Score: 341
Period size: 116 Copynumber: 2.6 Consensus size: 117
18089612 CAGCCATTTG
* * * * ** *
18089622 ATCTTTTACCCCAAGCCTGGGGTAGATCACCATTAGCCAATCTCTTACCATCGAGCCTGGGGCAG
1 ATCTCTTACCCCAAGCTTGGGGCAGATCACAACCAGCCAATCTCTTACC-CCGAGCCTGGGGCAG
*
18089687 ATTGCAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAAATCACCATCAACCA
65 ATTACAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAAATCACCATCAACCA
* * * *
18089740 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTGGGGCAGA
1 ATCTCTTACCCCAAGCTTGGGGCAGATCACAACCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
* * ** * * *
18089805 TTACAGCCATCTGATCTTTTA-CCCTAGCTTGGGGCAGATTACCATCAGCCA
66 TTACAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAAATCACCATCAACCA
* ** ** * * *
18089856 ATCTCTTACCCTAAGCTTGGGGCAGATTGCAACCATTCAATCTTTTATCCCGAGCCTGGGGTAGA
1 ATCTCTTACCCCAAGCTTGGGGCAGATCACAACCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
18089921 T
66 T
18089922 CACCATTAGG
Statistics
Matches: 155, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
116 77 0.50
117 34 0.22
118 44 0.28
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (117 bp):
ATCTCTTACCCCAAGCTTGGGGCAGATCACAACCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
TTACAGCCATCTGATCTTTTACCCCAAGCCTAAGGCAAATCACCATCAACCA
Found at i:18091080 original size:20 final size:19
Alignment explanation
Indices: 18091055--18091095 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
18091045 AAACATTTAT
*
18091055 AATAAATAATTATAATATTA
1 AATAAATAATT-TAATAATA
18091075 AATAAATAATTTAATAATA
1 AATAAATAATTTAATAATA
18091094 AA
1 AA
18091096 AAGAAACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAATAATTTAATAATA
Found at i:18091998 original size:31 final size:30
Alignment explanation
Indices: 18091818--18092190 Score: 256
Period size: 30 Copynumber: 12.5 Consensus size: 30
18091808 AAATTTCTTA
* * * **
18091818 AAAATCACATTTTAACCCCTGAGCTTTTTA
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* *
18091848 AAAATCACATTTTGA-CCCTCAAACTTTT-C
1 AAAATTACATTTTAACCCCT-AAACTTTTCC
* * *
18091877 AAAATTCATATTTTGACCCC-AAACTTTTTC
1 AAAATT-ACATTTTAACCCCTAAACTTTTCC
* * * * *
18091907 AAAATTACATTTTGACACTTAAATTTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCC
*
18091937 TAAATTACA-TTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* **
18091966 AAAACTACATTTTAACCCCTAATTTTTTTCC
1 AAAATTACATTTTAACCCCTAA-ACTTTTCC
*
18091997 AAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * * *
18092027 GAAATTTCATTTTAACCCTTAAACTTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
18092057 AAAATTACATTTTGACCCTTAAAC-CTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* ** * * * * *
18092086 TAAAATCATGTTTTGA-CCTTAAACATATCT
1 -AAAATTACATTTTAACCCCTAAACTTTTCC
* * * * *
18092116 AAAATCACATTTCAACCTC-AAGCTTTTCG
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* *
18092145 AAAATTACATTTTCACCTCCTAAATTTTTCC
1 AAAATTACATTTTAACC-CCTAAACTTTTCC
* *
18092176 AAATTTACGTTTTAA
1 AAAATTACATTTTAA
18092191 TCTCGTATTC
Statistics
Matches: 269, Mismatches: 62, Indels: 23
0.76 0.18 0.06
Matches are distributed among these distances:
29 91 0.34
30 130 0.48
31 48 0.18
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:18092061 original size:60 final size:60
Alignment explanation
Indices: 18091818--18092157 Score: 278
Period size: 59 Copynumber: 5.7 Consensus size: 60
18091808 AAATTTCTTA
* * * * ** * * *
18091818 AAAATCACATTTTAACCCCTGAGCTTTTTAAAAATCACATTTTGACCCTCAAACTTTTC-
1 AAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCT
* * * * *
18091877 AAAATTCATATTTTGACCCC-AAACTTTTTCAAAATTACATTTTGACACTTAAATTTTTCT
1 AAAATT-ACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCT
* * * * ** *
18091937 TAAATTACA-TTTAACCCCTAAACTTTTCCAAAACTACATTTTAACCCCTAATTTTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAA-ACTTTTCT
* *
18091997 AAAATTACATTTTGACCCCTAAACTTTTCCGAAATTTCATTTTAACCCTTAAACTTTTCT
1 AAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCT
* * * ** * * *
18092057 AAAATTACATTTTGACCCTTAAAC-CTTCCTAAAATCATGTTTTGA-CCTTAAACATATCT
1 AAAATTACATTTTGACCCCTAAACTTTTCC-AAAATTACATTTTAACCCTTAAACTTTTCT
* ** * * *
18092116 AAAATCACATTTCAACCTC-AAGCTTTTCGAAAATTACATTTT
1 AAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTT
18092158 CACCTCCTAA
Statistics
Matches: 224, Mismatches: 50, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
58 21 0.09
59 99 0.44
60 67 0.30
61 37 0.17
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCT
Found at i:18092133 original size:29 final size:28
Alignment explanation
Indices: 18092034--18092133 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
18092024 TCCGAAATTT
* *
18092034 CATTTTAACCCTTAAACTTTTCTAAAATTA
1 CATTTTAA-CCTTAAAC-ATTCTAAAATCA
* *
18092064 CATTTTGACCCTTAAACCTTCCTAAAATCA
1 CATTTT-AACCTTAAACATT-CTAAAATCA
** *
18092094 TGTTTTGACCTTAAACATATCTAAAATCA
1 CATTTTAACCTTAAACAT-TCTAAAATCA
*
18092123 CATTTCAACCT
1 CATTTTAACCT
18092134 CAAGCTTTTC
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
29 27 0.49
30 27 0.49
31 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (28 bp):
CATTTTAACCTTAAACATTCTAAAATCA
Found at i:18098443 original size:24 final size:24
Alignment explanation
Indices: 18098411--18098458 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
18098401 CACATTTAAT
18098411 CTTAGGTGTGAGAACCACTTACAC
1 CTTAGGTGTGAGAACCACTTACAC
18098435 CTTAGGTGTGAGAACCACTTACAC
1 CTTAGGTGTGAGAACCACTTACAC
18098459 TTGGAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
CTTAGGTGTGAGAACCACTTACAC
Found at i:18101348 original size:18 final size:17
Alignment explanation
Indices: 18101324--18101363 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18101314 AATATGCTCG
18101324 CTCTCTTTTGTTCTCTTA
1 CTCTCTTTTGTTCT-TTA
*
18101342 TTCTC-TTTGTTCTTTA
1 CTCTCTTTTGTTCTTTA
18101358 CTCTCT
1 CTCTCT
18101364 GTCCTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (17 bp):
CTCTCTTTTGTTCTTTA
Found at i:18103574 original size:17 final size:18
Alignment explanation
Indices: 18103552--18103585 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18103542 ATAACAATTA
*
18103552 TGAAGATTTTGG-ATATG
1 TGAAGATCTTGGCATATG
18103569 TGAAGATCTTGGCATAT
1 TGAAGATCTTGGCATAT
18103586 TCCCTAAAAT
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:0.29, C:0.06, G:0.26, T:0.38
Consensus pattern (18 bp):
TGAAGATCTTGGCATATG
Found at i:18113363 original size:40 final size:40
Alignment explanation
Indices: 18113298--18113459 Score: 209
Period size: 40 Copynumber: 4.0 Consensus size: 40
18113288 AAGTTATGTT
* *
18113298 TGATAAAGTTCAAGCTATGGCTTAGCAGGCTATGAGCCGG
1 TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* *
18113338 TGGTAGAGTTCAAGCTACGGTTTAGCAGGCTATGAGCCGG
1 TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* * *
18113378 TGATAGAGTTCAAGCTACAGCCTAGCAGGCTATGAGCCGA
1 TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
** * *
18113418 TGATA-AGAAACAAGCTATGGCTTAACAGGCTATGAGCCGG
1 TGATAGAG-TTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
18113458 TG
1 TG
18113460 TTAAAACTCA
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 2 0.02
40 103 0.98
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (40 bp):
TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
Found at i:18143165 original size:13 final size:13
Alignment explanation
Indices: 18143120--18143166 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
18143110 CTATGTAAAC
18143120 ATTTCATATAATT
1 ATTTCATATAATT
*
18143133 ACTTTCATATATTT
1 A-TTTCATATAATT
18143147 GA-TTCATATAATT
1 -ATTTCATATAATT
18143160 ATTTCAT
1 ATTTCAT
18143167 TTATCTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 1 0.03
13 16 0.55
14 11 0.38
15 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (13 bp):
ATTTCATATAATT
Found at i:18148672 original size:45 final size:45
Alignment explanation
Indices: 18148621--18148745 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
18148611 GTTTGAAGCG
* * * **
18148621 TGATGCCGTAATGCCTTTCAGCTATGGTCTTACTTGTCTGAATCA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAATCA
* *
18148666 TGATGCCATAACATCTTTCAGCTATTGTCTTACTCATCTGAATCA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAATCA
**
18148711 TGATGCCATAACGTCTTTCAATTATGGTCTTACTC
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTC
18148746 GTTTCCGGTA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAATCA
Found at i:18166674 original size:110 final size:110
Alignment explanation
Indices: 18166544--18166769 Score: 409
Period size: 110 Copynumber: 2.1 Consensus size: 110
18166534 GAAAATTGAG
* *
18166544 AATTGAGAATTGAGTTGAAAAGAATAAGATTGGAAGGCTTTATATAAA-AAAAAATATATATGGT
1 AATTGTGAATTGAGTTGAAAAGAATAAGATTGGAAGGCTTTATATAAAGAAAAAA-AAATATGGT
18166608 TGTTGGAGTCCCATAGCCATTGGGACTCCATAGATGGGACTCCAAT
65 TGTTGGAGTCCCATAGCCATTGGGACTCCATAGATGGGACTCCAAT
18166654 AATTGTGAATTGAGTTGAAAAGAATAAGATTGGAAGGCTTTATATAAAGAAAAAAAAATATGGTT
1 AATTGTGAATTGAGTTGAAAAGAATAAGATTGGAAGGCTTTATATAAAGAAAAAAAAATATGGTT
18166719 GTTGGAGTCCCATAGCCATTGGGACTCCATAGATGGGACTCCAAT
66 GTTGGAGTCCCATAGCCATTGGGACTCCATAGATGGGACTCCAAT
*
18166764 AGTTGT
1 AATTGT
18166770 TAAAATTTTT
Statistics
Matches: 112, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
110 106 0.95
111 6 0.05
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (110 bp):
AATTGTGAATTGAGTTGAAAAGAATAAGATTGGAAGGCTTTATATAAAGAAAAAAAAATATGGTT
GTTGGAGTCCCATAGCCATTGGGACTCCATAGATGGGACTCCAAT
Found at i:18169574 original size:27 final size:27
Alignment explanation
Indices: 18169544--18169601 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
18169534 CTAAAAATGG
18169544 TTATGTAGTTAAATGTGCTTTATTAAC
1 TTATGTAGTTAAATGTGCTTTATTAAC
*
18169571 TTATGTAGTTAAATGTGCTTTATTAAT
1 TTATGTAGTTAAATGTGCTTTATTAAC
18169598 TTAT
1 TTAT
18169602 TTCAACAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (27 bp):
TTATGTAGTTAAATGTGCTTTATTAAC
Found at i:18175932 original size:21 final size:21
Alignment explanation
Indices: 18175907--18175963 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
18175897 TGGAGTTTTT
*
18175907 AGTATCGGTAGAAGTTACACT
1 AGTATCGGTAGAAGTTACACA
* * * * *
18175928 TGTATCGATAGAACTTTCCCA
1 AGTATCGGTAGAAGTTACACA
18175949 AGTATCGGTAGAAGT
1 AGTATCGGTAGAAGT
18175964 CTGCACTATT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (21 bp):
AGTATCGGTAGAAGTTACACA
Found at i:18183739 original size:18 final size:17
Alignment explanation
Indices: 18183715--18183761 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
18183705 AACATTTTCC
18183715 ATTAATTAATTTAGAAAA
1 ATTAATTAATTTA-AAAA
*
18183733 TTTAATTAA-TTAAAAA
1 ATTAATTAATTTAAAAA
*
18183749 ATCAATTAATTTA
1 ATTAATTAATTTA
18183762 TTTGGTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 11 0.44
17 6 0.24
18 8 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTAATTAATTTAAAAA
Found at i:18184394 original size:21 final size:21
Alignment explanation
Indices: 18184351--18184394 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18184341 TTTAGAGTTG
* *
18184351 TAAAAGATTAAATATTTATGA
1 TAAAAAATTAAAAATTTATGA
18184372 TAAAAAATTAAAAATATTA-GA
1 TAAAAAATTAAAAAT-TTATGA
18184393 TA
1 TA
18184395 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAAAAATTAAAAATTTATGA
Found at i:18187424 original size:21 final size:20
Alignment explanation
Indices: 18187399--18187441 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
18187389 TAATGGGGAT
*
18187399 ATGTGAAATATTTTTAATTAG
1 ATGTGAAAT-TTATTAATTAG
* *
18187420 ATGTGTAATTTATTATTTAG
1 ATGTGAAATTTATTAATTAG
18187440 AT
1 AT
18187442 AATCTAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (20 bp):
ATGTGAAATTTATTAATTAG
Found at i:18189498 original size:30 final size:30
Alignment explanation
Indices: 18189464--18189520 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
18189454 ATTTTATACA
* *
18189464 TAATTTTGTTATTATTTTAGAGGCATTTGT
1 TAATTTTGTTACTATTTTACAGGCATTTGT
*
18189494 TAATTTTTTTACTATTTTACAGGCATT
1 TAATTTTGTTACTATTTTACAGGCATT
18189521 GCCTTCTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTACTATTTTACAGGCATTTGT
Found at i:18195984 original size:21 final size:18
Alignment explanation
Indices: 18195942--18195976 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18195932 GACACTTCCG
*
18195942 GTAAGGCCTTCACCTCCC
1 GTAAAGCCTTCACCTCCC
18195960 GTAAAGCCTTCACCTCC
1 GTAAAGCCTTCACCTCC
18195977 TCTTGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.14, T:0.23
Consensus pattern (18 bp):
GTAAAGCCTTCACCTCCC
Found at i:18197999 original size:62 final size:62
Alignment explanation
Indices: 18197902--18198025 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
18197892 ATGTCGTCAC
* * *
18197902 ATAGTGATCAACTTCATACTTATTTGTCTTCTAAAGGTTTCCTGTACACTCACAAAGTTCGT
1 ATAGTGATCAACTTCATAATTATTTATCTTCTAAAGGTTTCCTGCACACTCACAAAGTTCGT
**
18197964 ATAGTGATCAGGTTCATAATTATTTATCTTCTAAAGGTTTCCTGCACACTCACAAAGTTCGT
1 ATAGTGATCAACTTCATAATTATTTATCTTCTAAAGGTTTCCTGCACACTCACAAAGTTCGT
18198026 TAGCTAACCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (62 bp):
ATAGTGATCAACTTCATAATTATTTATCTTCTAAAGGTTTCCTGCACACTCACAAAGTTCGT
Found at i:18201547 original size:5 final size:5
Alignment explanation
Indices: 18201533--18201563 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
18201523 TTTGGTAGAT
*
18201533 GGGGA TGGGA GGGGA GGGGA GGGGA GGGGA G
1 GGGGA GGGGA GGGGA GGGGA GGGGA GGGGA G
18201564 AAAAAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.77, T:0.03
Consensus pattern (5 bp):
GGGGA
Found at i:18201602 original size:20 final size:21
Alignment explanation
Indices: 18201564--18201602 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18201554 GGGAGGGGAG
* *
18201564 AAAAAGTTTTGGGGGTAAAGT
1 AAAAAGGTTTGGGGATAAAGT
18201585 AAAAAGGTTT-GGGATAAA
1 AAAAAGGTTTGGGGATAAA
18201603 ATTGTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (21 bp):
AAAAAGGTTTGGGGATAAAGT
Found at i:18221434 original size:21 final size:21
Alignment explanation
Indices: 18221390--18221439 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
18221380 CCTATGACAG
* *
18221390 TTCTACCGAAACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
18221411 TTCTACCGAAACAAATCATA-C
1 TTCTACCGAAACAAATCA-AGC
18221432 TTCTACCG
1 TTCTACCG
18221440 GTACTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:18222193 original size:28 final size:28
Alignment explanation
Indices: 18222151--18222243 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
18222141 CGATATCTGA
*
18222151 TTTACTCCTTATTGACCCAAAGGTCATG
1 TTTACTCCCTATTGACCCAAAGGTCATG
*
18222179 TTTACTCCCTGTTGACCCAAAGGTCATGATG
1 TTTACTCCCTATTGACCCAAAGGTC---ATG
18222210 TTCATTTTACTCCCTATTGACCCAAAGGTCATG
1 -----TTTACTCCCTATTGACCCAAAGGTCATG
18222243 T
1 T
18222244 CTGTTACCAG
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
28 24 0.44
31 3 0.06
33 3 0.06
36 24 0.44
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (28 bp):
TTTACTCCCTATTGACCCAAAGGTCATG
Found at i:18222749 original size:3 final size:3
Alignment explanation
Indices: 18222741--18222791 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
18222731 ATTCGGCCTT
18222741 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
18222789 GAA
1 GAA
18222792 AGGATGAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:18222891 original size:10 final size:9
Alignment explanation
Indices: 18222869--18222904 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
18222859 TGATATTTTA
18222869 TAATTAACT
1 TAATTAACT
18222878 TAATTAACCT
1 TAATTAA-CT
18222888 TAATTAAGCT
1 TAATTAA-CT
18222898 TAATTAA
1 TAATTAA
18222905 ATTCACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (9 bp):
TAATTAACT
Found at i:18225504 original size:28 final size:28
Alignment explanation
Indices: 18225462--18225544 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
18225452 AAGTTACCAA
* *
18225462 AATATGAAAGACTTTGTGGTTGTTCTCT
1 AATATGGAAGCCTTTGTGGTTGTTCTCT
18225490 AATATGGAAGCCTTTGTGGTTGTTCTCT
1 AATATGGAAGCCTTTGTGGTTGTTCTCT
* *
18225518 AATATGTG-ATCCTTT-TAGTTGTTCTCT
1 AATATG-GAAGCCTTTGTGGTTGTTCTCT
18225545 GTTATATGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 11 0.22
28 38 0.76
29 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.46
Consensus pattern (28 bp):
AATATGGAAGCCTTTGTGGTTGTTCTCT
Found at i:18226948 original size:28 final size:27
Alignment explanation
Indices: 18226785--18226951 Score: 121
Period size: 28 Copynumber: 6.0 Consensus size: 27
18226775 TTGTTACAGA
* *
18226785 AATATAGCTCATTCGAGCCCAGAA-CAG
1 AATATCGCTCTTTCGAG-CCAGAATCAG
*
18226812 AGCA-AT-GCTCTTATCGAGCCAAAAAT-AG
1 A--ATATCGCTCTT-TCGAGCC-AGAATCAG
18226840 AATCAT-GCTTCTTTCGAGCCA-AAGTCTAG
1 AAT-ATCGC-TCTTTCGAGCCAGAA-TC-AG
* *
18226869 AATATTGCTCTTTCGAGCCTAGAGTCAG
1 AATATCGCTCTTTCGAGCC-AGAATCAG
*
18226897 AATATCGCTCTTTCCGAGCTAGAATCAG
1 AATATCGCTCTTT-CGAGCCAGAATCAG
*
18226925 AATATCACTCATTTCGAGCCAGAATCA
1 AATATCGCTC-TTTCGAGCCAGAATCA
18226952 ATTTTAACCG
Statistics
Matches: 116, Mismatches: 8, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
26 3 0.03
27 10 0.09
28 79 0.68
29 23 0.20
30 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (27 bp):
AATATCGCTCTTTCGAGCCAGAATCAG
Found at i:18229650 original size:30 final size:30
Alignment explanation
Indices: 18229583--18229653 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
18229573 TCTGATAAGT
* * * * *
18229583 GAGCCTTGGTCGCTTTTCACTGTTATATGT
1 GAGCCTTTGTGGCTATTCACTGTTAAATGG
18229613 GAGCCTTTGTGGCTATTCACTGTTAAATGG
1 GAGCCTTTGTGGCTATTCACTGTTAAATGG
18229643 GAGCCTTTGTG
1 GAGCCTTTGTG
18229654 ACTGTTTCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.39
Consensus pattern (30 bp):
GAGCCTTTGTGGCTATTCACTGTTAAATGG
Found at i:18233556 original size:14 final size:13
Alignment explanation
Indices: 18233523--18233560 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
18233513 ACCAAGTACG
18233523 GAAAAATAAATGA
1 GAAAAATAAATGA
*
18233536 -TAAAATAAATGCA
1 GAAAAATAAATG-A
18233549 GAAAAATAAATG
1 GAAAAATAAATG
18233561 GTAAATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 10 0.48
13 1 0.05
14 10 0.48
ACGTcount: A:0.66, C:0.03, G:0.13, T:0.18
Consensus pattern (13 bp):
GAAAAATAAATGA
Found at i:18235038 original size:27 final size:28
Alignment explanation
Indices: 18234992--18235077 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 28
18234982 AGATCTGTCA
* ** *
18234992 AATAACGAATAATGTTATAAAGATCGCT
1 AATAACAAATAATGCGATAAAGATCGCC
*
18235020 AATATC-AATAATGCGATAAAGATCGCC
1 AATAACAAATAATGCGATAAAGATCGCC
*
18235047 AATAACAAATAATGCGATAGAGATCGCC
1 AATAACAAATAATGCGATAAAGATCGCC
18235075 AAT
1 AAT
18235078 CCCCTTGGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 23 0.45
28 28 0.55
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (28 bp):
AATAACAAATAATGCGATAAAGATCGCC
Found at i:18239689 original size:18 final size:18
Alignment explanation
Indices: 18239666--18239704 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
18239656 CTTAAGCTTA
18239666 CTTCTAGAAAAACACTTG
1 CTTCTAGAAAAACACTTG
*
18239684 CTTCTAGAAAAAGACTTG
1 CTTCTAGAAAAACACTTG
18239702 CTT
1 CTT
18239705 TACTTAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (18 bp):
CTTCTAGAAAAACACTTG
Found at i:18247826 original size:45 final size:45
Alignment explanation
Indices: 18247777--18247902 Score: 182
Period size: 45 Copynumber: 2.8 Consensus size: 45
18247767 TAAGAATAGA
*
18247777 ATTTACAATATCATGCATATCATATAGCATAATCAATCCAAA-AAT
1 ATTTACAATATCATGCATATCGTATAGCATAATCAAT-CAAATAAT
* * *
18247822 ATTTACCATGTCATGCATATCGTGTAGCATAATCAATCAAATAAT
1 ATTTACAATATCATGCATATCGTATAGCATAATCAATCAAATAAT
* *
18247867 ATTTACAATATCTTACATATCGTATAGCATAATCAA
1 ATTTACAATATCATGCATATCGTATAGCATAATCAA
18247903 ACTTGGTTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.06
45 67 0.94
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (45 bp):
ATTTACAATATCATGCATATCGTATAGCATAATCAATCAAATAAT
Found at i:18248471 original size:21 final size:22
Alignment explanation
Indices: 18248436--18248476 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18248426 GTTTTTGAAG
18248436 TTTTAATTTTATTTTTCAATAC
1 TTTTAATTTTATTTTTCAATAC
18248458 TTTTAATTTT-TTTTTCAAT
1 TTTTAATTTTATTTTTCAAT
18248477 GATTACAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTAATTTTATTTTTCAATAC
Found at i:18254679 original size:13 final size:13
Alignment explanation
Indices: 18254661--18254691 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
18254651 GAGTGGTTGG
18254661 ACAAGTAAACTGC
1 ACAAGTAAACTGC
18254674 ACAAGTAAACTGC
1 ACAAGTAAACTGC
18254687 ACAAG
1 ACAAG
18254692 GAACAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.13
Consensus pattern (13 bp):
ACAAGTAAACTGC
Found at i:18262640 original size:8 final size:8
Alignment explanation
Indices: 18262627--18262652 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
18262617 TTTATACTTT
18262627 AAATTTTA
1 AAATTTTA
18262635 AAATTTTA
1 AAATTTTA
18262643 AAATTTTA
1 AAATTTTA
18262651 AA
1 AA
18262653 CCTCATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:18267214 original size:15 final size:14
Alignment explanation
Indices: 18267189--18267224 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
18267179 AAAGTTTTCA
18267189 TTTATTTATTTATT
1 TTTATTTATTTATT
18267203 TTTATGTTATTTATT
1 TTTAT-TTATTTATT
18267218 TTTATTT
1 TTTATTT
18267225 TTCAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:18268000 original size:8 final size:7
Alignment explanation
Indices: 18267982--18268032 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 7
18267972 GGTGGTAAGG
18267982 AATTTTT
1 AATTTTT
18267989 -ATTTTCT
1 AATTTT-T
18267996 AATTTTT
1 AATTTTT
18268003 AATTTATTT
1 AA-TT-TTT
18268012 AATTTATT
1 AATTT-TT
18268020 AACTTTTT
1 AA-TTTTT
18268028 AATTT
1 AATTT
18268033 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.13
7 8 0.21
8 17 0.45
9 8 0.21
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:18268012 original size:9 final size:9
Alignment explanation
Indices: 18268000--18268036 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
18267990 TTTTCTAATT
18268000 TTTAATTTA
1 TTTAATTTA
18268009 TTTAATTTA
1 TTTAATTTA
*
18268018 -TTAACTT-
1 TTTAATTTA
18268025 TTTAATTTA
1 TTTAATTTA
18268034 TTT
1 TTT
18268037 TAAATTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:18268016 original size:16 final size:15
Alignment explanation
Indices: 18267982--18268032 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
18267972 GGTGGTAAGG
*
18267982 AATTTTT-ATTTTCT
1 AATTTTTAATTTTTT
18267996 AATTTTTAATTTATTT
1 AATTTTTAATTT-TTT
*
18268012 AATTTATTAACTTTTT
1 AATTT-TTAATTTTTT
18268028 AATTT
1 AATTT
18268033 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 15 0.47
17 6 0.19
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTAATTTTTT
Found at i:18268047 original size:26 final size:25
Alignment explanation
Indices: 18267998--18268047 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18267988 TATTTTCTAA
*
18267998 TTTTTAATTTATTTAATTTATTAAC
1 TTTTTAATTTATTTAAATTATTAAC
*
18268023 TTTTTAATTTATTTTAAATTGTTAA
1 TTTTTAATTTA-TTTAAATTATTAA
18268048 TATTTTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTAATTTATTTAAATTATTAAC
Found at i:18268053 original size:26 final size:24
Alignment explanation
Indices: 18267995--18268054 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
18267985 TTTTATTTTC
*
18267995 TAATTTTTAATTTATTTAATTTAT
1 TAATTTTTAATTTATTTAAATTAT
*
18268019 TAACTTTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAATTTA-TTTAAATTAT
18268045 TAATATTTTA
1 TAAT-TTTTA
18268055 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.10
25 12 0.39
26 16 0.52
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:18268945 original size:18 final size:18
Alignment explanation
Indices: 18268924--18268958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18268914 AACAGTAAGC
*
18268924 TGAAGAAGAACAAGATCT
1 TGAAAAAGAACAAGATCT
*
18268942 TGAAAAAGAAGAAGATC
1 TGAAAAAGAACAAGATC
18268959 CTGTGGAAAT
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:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (18 bp):
TGAAAAAGAACAAGATCT
Found at i:18274008 original size:18 final size:18
Alignment explanation
Indices: 18273985--18274026 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
18273975 CCTTTTCATC
18273985 TCTTCATCTTCATCCAC-T
1 TCTTCA-CTTCATCCACTT
* *
18274003 TCTTCACTTGATTCACTT
1 TCTTCACTTCATCCACTT
18274021 TCTTCA
1 TCTTCA
18274027 ATGGTGGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.17, C:0.33, G:0.02, T:0.48
Consensus pattern (18 bp):
TCTTCACTTCATCCACTT
Found at i:18281496 original size:12 final size:12
Alignment explanation
Indices: 18281479--18281526 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
18281469 GTTCACGAAC
*
18281479 AAGCTCGTTTAA
1 AAGCTCGTTTAT
18281491 AAGCTCGTTTAT
1 AAGCTCGTTTAT
** *
18281503 TGGATCGTTTAT
1 AAGCTCGTTTAT
18281515 AAGCTCGTTTAT
1 AAGCTCGTTTAT
18281527 TGACTCGTTT
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:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:18281518 original size:24 final size:24
Alignment explanation
Indices: 18281482--18281538 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
18281472 CACGAACAAG
*
18281482 CTCGTTTAAAAGCTCGTTTATTGGA
1 CTCGTTTATAAGCTCGTTTATT-GA
18281507 -TCGTTTATAAGCTCGTTTATTGA
1 CTCGTTTATAAGCTCGTTTATTGA
18281530 CTCGTTTAT
1 CTCGTTTAT
18281539 TTATTAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.46
Consensus pattern (24 bp):
CTCGTTTATAAGCTCGTTTATTGA
Found at i:18281533 original size:12 final size:12
Alignment explanation
Indices: 18281494--18281539 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
18281484 CGTTTAAAAG
18281494 CTCGTTTATTGGA
1 CTCGTTTATT-GA
*
18281507 -TCGTTTA-TAA
1 CTCGTTTATTGA
18281517 GCTCGTTTATTGA
1 -CTCGTTTATTGA
18281530 CTCGTTTATT
1 CTCGTTTATT
18281540 TATTAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
10 1 0.04
11 1 0.04
12 24 0.86
13 2 0.07
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:18281693 original size:23 final size:23
Alignment explanation
Indices: 18281624--18281693 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
18281614 TCATTAACAT
* *
18281624 TGTTCGTAAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* * *
18281648 TGTTCATGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
18281671 TGTTCGTGAATATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
18281694 ATAAACAAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:18282084 original size:242 final size:242
Alignment explanation
Indices: 18281659--18282144 Score: 954
Period size: 242 Copynumber: 2.0 Consensus size: 242
18281649 GTTCATGAAC
18281659 ATGTTTGTTTAATGTTCGTGAATATGTTCGATTAAATAAACAAACATGTTCGTGAATATTAAATA
1 ATGTTTGTTTAATGTTCGTGAATATGTTCGATTAAATAAACAAACATGTTCGTGAATATTAAATA
* *
18281724 AACGAACATGAACATACATAATTTTAAATAAACGAACATAAACAAAAAAATTTGAAATCCTTAAC
66 AACGAACATGAACATACATAATTTTAAATAAACGAACATAAACAAAAAAAATTGAAATCCTTAAA
18281789 GAACATGAACCGAACATGAACAGCTTAAAAAATAAATAAACGAACATGAACAGAGATTTGTTCAT
131 GAACATGAACCGAACATGAACAGCTTAAAAAATAAATAAACGAACATGAACAGAGATTTGTTCAT
18281854 TCAAGCTCAGTTCATTTATAGCCCTAATGATTAGTATAAAAGAGTTT
196 TCAAGCTCAGTTCATTTATAGCCCTAATGATTAGTATAAAAGAGTTT
18281901 ATGTTTGTTTAATGTTCGTGAATATGTTCGATTAAATAAACAAACATGTTCGTGAATATTAAATA
1 ATGTTTGTTTAATGTTCGTGAATATGTTCGATTAAATAAACAAACATGTTCGTGAATATTAAATA
18281966 AACGAACATGAACATACATAATTTTAAATAAACGAACATAAACAAAAAAAATTGAAATCCTTAAA
66 AACGAACATGAACATACATAATTTTAAATAAACGAACATAAACAAAAAAAATTGAAATCCTTAAA
18282031 GAACATGAACCGAACATGAACAGCTTAAAAAATAAATAAACGAACATGAACAGAGATTTGTTCAT
131 GAACATGAACCGAACATGAACAGCTTAAAAAATAAATAAACGAACATGAACAGAGATTTGTTCAT
18282096 TCAAGCTCAGTTCATTTATAGCCCTAATGATTAGTATAAAAGAGTTT
196 TCAAGCTCAGTTCATTTATAGCCCTAATGATTAGTATAAAAGAGTTT
18282143 AT
1 AT
18282145 ATTTTATACA
Statistics
Matches: 242, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
242 242 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (242 bp):
ATGTTTGTTTAATGTTCGTGAATATGTTCGATTAAATAAACAAACATGTTCGTGAATATTAAATA
AACGAACATGAACATACATAATTTTAAATAAACGAACATAAACAAAAAAAATTGAAATCCTTAAA
GAACATGAACCGAACATGAACAGCTTAAAAAATAAATAAACGAACATGAACAGAGATTTGTTCAT
TCAAGCTCAGTTCATTTATAGCCCTAATGATTAGTATAAAAGAGTTT
Found at i:18282174 original size:21 final size:22
Alignment explanation
Indices: 18282149--18282192 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18282139 GTTTATATTT
18282149 TATACATCAATAA-TATATAAA
1 TATACATCAATAATTATATAAA
* *
18282170 TATACATCATTAATTATCTAAA
1 TATACATCAATAATTATATAAA
18282192 T
1 T
18282193 TTAAAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TATACATCAATAATTATATAAA
Found at i:18282453 original size:22 final size:22
Alignment explanation
Indices: 18282425--18282498 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
18282415 CTTAAGCCTC
18282425 AAGCCGCCTTTACTGCCCCTAG
1 AAGCCGCCTTTACTGCCCCTAG
18282447 AAGCCGCCTTTACTGCCCCTAG
1 AAGCCGCCTTTACTGCCCCTAG
* *
18282469 AAGCCACCTTTGCTGCCCCTCA-
1 AAGCCGCCTTTACTGCCCCT-AG
18282491 AAGCCGCC
1 AAGCCGCC
18282499 GCTGCTGCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 47 0.98
23 1 0.02
ACGTcount: A:0.19, C:0.43, G:0.18, T:0.20
Consensus pattern (22 bp):
AAGCCGCCTTTACTGCCCCTAG
Found at i:18283553 original size:11 final size:11
Alignment explanation
Indices: 18283531--18283612 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
18283521 TTTATTTAAA
*
18283531 ATTTAATTTTT
1 ATTTATTTTTT
18283542 ATTT-TTTATTT
1 ATTTATTT-TTT
* *
18283553 ACTTATTATTT
1 ATTTATTTTTT
* *
18283564 ATTTATTTGTG
1 ATTTATTTTTT
18283575 ATTTA-TTTTT
1 ATTTATTTTTT
* *
18283585 ACTTTATATTTA
1 A-TTTATTTTTT
*
18283597 ATTTTATTTATT
1 A-TTTATTTTTT
18283609 ATTT
1 ATTT
18283613 TTTATAGGAA
Statistics
Matches: 52, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
10 6 0.12
11 32 0.62
12 14 0.27
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTTATTTTTT
Found at i:18283564 original size:15 final size:15
Alignment explanation
Indices: 18283540--18283582 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
18283530 AATTTAATTT
*
18283540 TTATTTTTTATTTAC
1 TTATTATTTATTTAC
*
18283555 TTATTATTTATTTAT
1 TTATTATTTATTTAC
* *
18283570 TTGTGATTTATTT
1 TTATTATTTATTT
18283583 TTACTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (15 bp):
TTATTATTTATTTAC
Found at i:18283595 original size:17 final size:17
Alignment explanation
Indices: 18283550--18283612 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
18283540 TTATTTTTTA
*
18283550 TTTACTTATTATTT-A-
1 TTTATTTATTATTTAAT
* * *
18283565 TTTATTTGTGATTTATT
1 TTTATTTATTATTTAAT
18283582 TTTACTTTA-TATTTAAT
1 TTTA-TTTATTATTTAAT
18283599 TTTATTTATTATTT
1 TTTATTTATTATTT
18283613 TTTATAGGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 11 0.30
16 4 0.11
17 19 0.51
18 3 0.08
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTTATTATTTAAT
Found at i:18283600 original size:22 final size:21
Alignment explanation
Indices: 18283517--18283612 Score: 63
Period size: 22 Copynumber: 4.3 Consensus size: 21
18283507 ATTATTTGCA
18283517 TTATTT-TATTTAAAATTTAATTT
1 TTATTTATATTT--AATTT-ATTT
* *
18283540 TTATTTTTTATTT-ACTTATTAT
1 TTA-TTTATATTTAATTTATT-T
*
18283562 TTATTTAT-TTGTGATTTATTT
1 TTATTTATATT-TAATTTATTT
18283583 TTACTTTATATTTAATTTTATTT
1 TTA-TTTATATTTAA-TTTATTT
18283606 ATTATTT
1 -TTATTT
18283613 TTTATAGGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
20 2 0.03
21 12 0.20
22 20 0.33
23 15 0.25
24 6 0.10
25 5 0.08
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTTATATTTAATTTATTT
Found at i:18283866 original size:29 final size:28
Alignment explanation
Indices: 18283830--18283894 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
18283820 TAATTAAATA
*
18283830 ATATTAT-TGTCA-TTATTAGT-ATGATT
1 ATATTATATTTCATTTATTA-TCATGATT
*
18283856 ATATTACTATTTTATTTATTATCATGATT
1 ATATTA-TATTTCATTTATTATCATGATT
18283885 ATATTATATT
1 ATATTATATT
18283895 ATTTTATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 6 0.18
27 1 0.03
28 8 0.24
29 18 0.55
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (28 bp):
ATATTATATTTCATTTATTATCATGATT
Found at i:18286556 original size:21 final size:21
Alignment explanation
Indices: 18286532--18286571 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18286522 TTTTATATGG
18286532 AATT-TTGAATTGAAAAGTTTT
1 AATTATTGAATT-AAAAGTTTT
18286553 AATTATTGAATTAAAAGTT
1 AATTATTGAATTAAAAGTT
18286572 AATATAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (21 bp):
AATTATTGAATTAAAAGTTTT
Found at i:18288777 original size:52 final size:52
Alignment explanation
Indices: 18288588--18288876 Score: 368
Period size: 52 Copynumber: 5.6 Consensus size: 52
18288578 TAAACGAAAA
* *
18288588 AGGTCAGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
18288640 CGATCCAATG-CTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * ** *
18288691 AGGTCCGATAACT-TTTGTCATCGTGAATATATGAATTATTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
18288742 AGGTCTGATGACTATTTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
18288794 AGGTCCGATGACTATGTGTCATCGTGAGCATATGATTCCTTTTATGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
* *
18288846 AGCTCCGATGACTTTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
18288877 TAAATGGGAA
Statistics
Matches: 203, Mismatches: 31, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
51 90 0.44
52 104 0.51
53 9 0.04
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:18288785 original size:103 final size:103
Alignment explanation
Indices: 18288588--18288820 Score: 326
Period size: 103 Copynumber: 2.3 Consensus size: 103
18288578 TAAACGAAAA
* * * * *
18288588 AGGTCAGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGCGATCCAATGCTA
1 AGGTCCGATAACTATGTGTCATCGTGAATATATGAATCTTTTACAGATTATGAGATCCAATGCTA
*
18288653 TGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
66 TGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* * **
18288691 AGGTCCGATAACT-TTTGTCATCGTGAATATATGAAT-TATTTACAGATTATGAGGTCTGATGAC
1 AGGTCCGATAACTATGTGTCATCGTGAATATATGAATCT-TTTACAGATTATGAGATCCAATG-C
*
18288754 TATTTGTCATCATGAGTATATGAATCCTTTACGGATTATG
64 TATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
*
18288794 AGGTCCGATGACTATGTGTCATCGTGA
1 AGGTCCGATAACTATGTGTCATCGTGA
18288821 GCATATGATT
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
101 1 0.01
102 39 0.34
103 62 0.54
104 12 0.11
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (103 bp):
AGGTCCGATAACTATGTGTCATCGTGAATATATGAATCTTTTACAGATTATGAGATCCAATGCTA
TGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
Found at i:18298876 original size:15 final size:16
Alignment explanation
Indices: 18298856--18298895 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
18298846 GCCAAAGTTT
18298856 AGAGAAAAAAA-AATG
1 AGAGAAAAAAAGAATG
18298871 AGAGAATAAAAAAGAATG
1 AGAG-A-AAAAAAGAATG
18298889 AGAGAAA
1 AGAGAAA
18298896 CTCTCATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 3 0.14
17 7 0.32
18 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (16 bp):
AGAGAAAAAAAGAATG
Found at i:18298883 original size:18 final size:18
Alignment explanation
Indices: 18298860--18298894 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18298850 AAGTTTAGAG
18298860 AAAAAAAAATGAGAGAAT
1 AAAAAAAAATGAGAGAAT
*
18298878 AAAAAAGAATGAGAGAA
1 AAAAAAAAATGAGAGAA
18298895 ACTCTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAAAAAATGAGAGAAT
Found at i:18299015 original size:28 final size:28
Alignment explanation
Indices: 18298979--18299067 Score: 106
Period size: 28 Copynumber: 3.2 Consensus size: 28
18298969 TCCAAAAATT
*
18298979 CAACGGTCATATTGTAAAGATCAGATTC
1 CAACGGTCATATTGTAAAGGTCAGATTC
* *
18299007 CAACGGTCATATTGTAATGGTCAAATTC
1 CAACGGTCATATTGTAAAGGTCAGATTC
* * * * *
18299035 CAATGGCCATATTGCAACGGTTAGATTC
1 CAACGGTCATATTGTAAAGGTCAGATTC
18299063 CAACG
1 CAACG
18299068 ACCATATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (28 bp):
CAACGGTCATATTGTAAAGGTCAGATTC
Found at i:18309965 original size:21 final size:21
Alignment explanation
Indices: 18309941--18310009 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
18309931 TTAAAATTAT
18309941 TAAAATTATTTTTTTGAAATA
1 TAAAATTATTTTTTTGAAATA
*
18309962 TAAAATTA-----TTAAAATTA
1 TAAAATTATTTTTTTGAAA-TA
* *
18309979 TTATATTATTTTTTTGAAATA
1 TAAAATTATTTTTTTGAAATA
18310000 TAAAATTATT
1 TAAAATTATT
18310010 ATATGATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
21 18 0.50
22 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TAAAATTATTTTTTTGAAATA
Found at i:18309996 original size:38 final size:39
Alignment explanation
Indices: 18309931--18310010 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
18309921 ATAAATGATT
18309931 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
*
18309970 TTAAAATTATT-ATATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
18310008 TTA
1 TTA
18310011 TATGATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 29 0.73
39 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (39 bp):
TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
Found at i:18311120 original size:37 final size:39
Alignment explanation
Indices: 18311078--18311156 Score: 135
Period size: 37 Copynumber: 2.1 Consensus size: 39
18311068 TAAAATCATA
18311078 TAATAATTTTATAT-TCAAAAAAATAA-TATAATAATTT
1 TAATAATTTTATATATCAAAAAAATAATTATAATAATTT
*
18311115 TAATAATTTTATATATCAAAAAAATAATTTTAATAATTT
1 TAATAATTTTATATATCAAAAAAATAATTATAATAATTT
18311154 TAA
1 TAA
18311157 AATCATTTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 14 0.36
38 12 0.31
39 13 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (39 bp):
TAATAATTTTATATATCAAAAAAATAATTATAATAATTT
Found at i:18311130 original size:39 final size:37
Alignment explanation
Indices: 18311078--18311156 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 37
18311068 TAAAATCATA
18311078 TAATAATTTTATATTCAAAAAAATAA-TATAATAATTT
1 TAATAATTTTATA-TCAAAAAAATAATTATAATAATTT
*
18311115 TAATAATTTTATATATCAAAAAAATAATTTTAATAATTT
1 TAATAA-TTT-TATATCAAAAAAATAATTATAATAATTT
18311154 TAA
1 TAA
18311157 AATCATTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
37 6 0.16
38 15 0.39
39 17 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATAATTTTATATCAAAAAAATAATTATAATAATTT
Found at i:18324481 original size:33 final size:33
Alignment explanation
Indices: 18324444--18324567 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 33
18324434 ACACTTTACC
*
18324444 ACAACTCACACATGCTACAGCTTGCATATTGCA
1 ACAACTCACACATGCTACAGCTCGCATATTGCA
* ** *
18324477 ACAAC-CTGCACATGCTACATATCGCATATTTCA
1 ACAACTC-ACACATGCTACAGCTCGCATATTGCA
* * * * * *
18324510 ACAGCTCACACTTTACCACAACTCGTATATTG-A
1 ACAACTCACAC-ATGCTACAGCTCGCATATTGCA
*
18324543 ACAGCTCACACATGCTACAGCTCGC
1 ACAACTCACACATGCTACAGCTCGC
18324568 GCTGAATACT
Statistics
Matches: 69, Mismatches: 19, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
32 10 0.14
33 45 0.65
34 14 0.20
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.24
Consensus pattern (33 bp):
ACAACTCACACATGCTACAGCTCGCATATTGCA
Found at i:18324771 original size:53 final size:53
Alignment explanation
Indices: 18324684--18324801 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
18324674 GCACAATTAC
*
18324684 AGTTCACACATTCAATGAAATGACAATACGCATATCCAATACTTTGCAAAGAT
1 AGTTCACACATTCAATGAAATGACAATACACATATCCAATACTTTGCAAAGAT
* * **
18324737 AGTTCACACATTCAATGAAATGATAGTACACATATCTGATACTTTGCAAAGAT
1 AGTTCACACATTCAATGAAATGACAATACACATATCCAATACTTTGCAAAGAT
18324790 AGTTCACACATT
1 AGTTCACACATT
18324802 ATGACTGATC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (53 bp):
AGTTCACACATTCAATGAAATGACAATACACATATCCAATACTTTGCAAAGAT
Found at i:18326838 original size:51 final size:51
Alignment explanation
Indices: 18326742--18326839 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
18326732 ATCTATAAAA
* * * *
18326742 TCACGATGACACTTAGTCATCGGAACTTTAATCCATACAGGATTCATTTAC
1 TCACGATGACACTTAGTCATCAGAACATTAATCCATAAAAGATTCATTTAC
* * *
18326793 TCACGGTGACACTTAGTCATCAGACCATTAATCCATAAAATATTCAT
1 TCACGATGACACTTAGTCATCAGAACATTAATCCATAAAAGATTCAT
18326840 CATTAATCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (51 bp):
TCACGATGACACTTAGTCATCAGAACATTAATCCATAAAAGATTCATTTAC
Found at i:18326859 original size:22 final size:22
Alignment explanation
Indices: 18326818--18326861 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18326808 GTCATCAGAC
*
18326818 CATTAATCCATAAAATATTCAT
1 CATTAATCCATAAAAGATTCAT
* *
18326840 CATTAATCTATAAAGGATTCAT
1 CATTAATCCATAAAAGATTCAT
18326862 TTACTCACGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (22 bp):
CATTAATCCATAAAAGATTCAT
Found at i:18327225 original size:51 final size:51
Alignment explanation
Indices: 18327169--18327273 Score: 176
Period size: 52 Copynumber: 2.1 Consensus size: 51
18327159 CAATAAATTA
18327169 TTTAACATAATCAAAT-CCTTTTTGGTAAAATTACAATTTTACCCCTAATAC
1 TTTAACATAATCAAATCCCTTTTTGGTAAAATTACAATTTTACCCCT-ATAC
**
18327220 TTTAACATAATCAAATCCCTTTTTGGTAAAATTATTATTTTACCCCTATAC
1 TTTAACATAATCAAATCCCTTTTTGGTAAAATTACAATTTTACCCCTATAC
18327271 TTT
1 TTT
18327274 CTTTTTATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 23 0.45
52 28 0.55
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (51 bp):
TTTAACATAATCAAATCCCTTTTTGGTAAAATTACAATTTTACCCCTATAC
Found at i:18333987 original size:51 final size:51
Alignment explanation
Indices: 18333924--18334053 Score: 242
Period size: 51 Copynumber: 2.5 Consensus size: 51
18333914 GAATCTATAA
*
18333924 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTAATTT
*
18333975 ACTCACGATGACACTAAGTCATCGGACCATTAATCCATAAAGGATTAATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTAATTT
18334026 ACTCACGATGACACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
18334054 CTTTCGTTTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.27
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTAATTT
Found at i:18337392 original size:23 final size:23
Alignment explanation
Indices: 18337325--18337455 Score: 68
Period size: 23 Copynumber: 5.7 Consensus size: 23
18337315 ATTAACATTA
* * **
18337325 TTCGTGAACATGTTCGATTTTACA
1 TTCGTGAACATGTTC-AATTAATG
* * **
18337349 TTCATGAGCATGTTCGTTTAATG
1 TTCGTGAACATGTTCAATTAATG
*
18337372 TTCGTAAACATGTTCAATTAA-G
1 TTCGTGAACATGTTCAATTAATG
** * * *
18337394 TTAAATGAGCATGTCCATTTAATG
1 TT-CGTGAACATGTTCAATTAATG
*
18337418 TTCGTGAACATGTTCGATTAA-G
1 TTCGTGAACATGTTCAATTAATG
**
18337440 TTAAATGAACATGTTC
1 TT-CGTGAACATGTTC
18337456 GTTAACATTA
Statistics
Matches: 79, Mismatches: 25, Indels: 7
0.71 0.23 0.06
Matches are distributed among these distances:
22 6 0.08
23 57 0.72
24 16 0.20
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (23 bp):
TTCGTGAACATGTTCAATTAATG
Found at i:18337415 original size:46 final size:46
Alignment explanation
Indices: 18337352--18337453 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
18337342 TTTTACATTC
* *
18337352 ATGAGCATGTTCGTTTAATGTTCGTAAACATGTTCAATTAAGTTAA
1 ATGAGCATGTCCATTTAATGTTCGTAAACATGTTCAATTAAGTTAA
* *
18337398 ATGAGCATGTCCATTTAATGTTCGTGAACATGTTCGATTAAGTTAA
1 ATGAGCATGTCCATTTAATGTTCGTAAACATGTTCAATTAAGTTAA
*
18337444 ATGAACATGT
1 ATGAGCATGT
18337454 TCGTTAACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (46 bp):
ATGAGCATGTCCATTTAATGTTCGTAAACATGTTCAATTAAGTTAA
Found at i:18337456 original size:23 final size:23
Alignment explanation
Indices: 18337378--18337460 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
18337368 AATGTTCGTA
*
18337378 AACATGTTCAATTAAGTTAAATG
1 AACATGTTCGATTAAGTTAAATG
* * **
18337401 AGCATG-TCCATTTAATGTT-CGTG
1 AACATGTTCGA-TTAA-GTTAAATG
18337424 AACATGTTCGATTAAGTTAAATG
1 AACATGTTCGATTAAGTTAAATG
18337447 AACATGTTCG-TTAA
1 AACATGTTCGATTAA
18337461 CATTAAACAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
22 10 0.21
23 32 0.67
24 6 0.12
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (23 bp):
AACATGTTCGATTAAGTTAAATG
Found at i:18340030 original size:94 final size:94
Alignment explanation
Indices: 18339866--18340093 Score: 330
Period size: 94 Copynumber: 2.4 Consensus size: 94
18339856 ATGTCATTTT
* *
18339866 TGTTACTAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGTAACATATGTGATACCTCA
1 TGTTACTAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGCGATACCTCA
* * *
18339931 ACCATCGATGCAGTATCTGTACATATAAA
66 ACCATCAATACAGTATCTGTACATACAAA
* * * *
18339960 TGTTACCAATATACGATGCTCCTCACACTAAGCTGACGAGGACTCGCAACATATGCGGTACCTCA
1 TGTTACTAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGCGATACCTCA
* * * *
18340025 GCCATCAATACGGTATTTGTACATACAAC
66 ACCATCAATACAGTATCTGTACATACAAA
*
18340054 TGTTACTAGTATACGATGCTGCTCACACTAAGCTAACGAG
1 TGTTACTAGTATACGATGCTGCTCACACTAAGCTGACGAG
18340094 AATATACAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 117 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (94 bp):
TGTTACTAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGCGATACCTCA
ACCATCAATACAGTATCTGTACATACAAA
Found at i:18347977 original size:15 final size:16
Alignment explanation
Indices: 18347949--18348011 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 16
18347939 AGATGGTGAA
18347949 AAATAATAATAATTTT
1 AAATAATAATAATTTT
*
18347965 AAA-AATTATAATTAATT
1 AAATAATAATAATT--TT
18347982 AAATAATAATAATTTAAT
1 AAATAATAATAATTT--T
*
18348000 AAATAAAAATAA
1 AAATAATAATAA
18348012 GCTAGAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 9 0.23
16 4 0.10
17 5 0.13
18 21 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATAATAATTTT
Found at i:18351484 original size:15 final size:15
Alignment explanation
Indices: 18351450--18351520 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
18351440 TGTTGTTGAA
18351450 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
18351463 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
18351478 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
18351497 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
18351512 AAATGTTTT
1 AAATATTTT
18351521 TTAGTATAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 18 0.40
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:18355074 original size:15 final size:15
Alignment explanation
Indices: 18355054--18355099 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
18355044 ATAATAAATT
18355054 AACGTAAATTATTAA
1 AACGTAAATTATTAA
18355069 AACGTAACATT-TTAA
1 AACGTAA-ATTATTAA
18355084 ATA--TAAATTATTAA
1 A-ACGTAAATTATTAA
18355098 AA
1 AA
18355100 TGTACCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 12 0.43
16 4 0.14
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (15 bp):
AACGTAAATTATTAA
Found at i:18357348 original size:90 final size:90
Alignment explanation
Indices: 18357238--18357428 Score: 364
Period size: 90 Copynumber: 2.1 Consensus size: 90
18357228 TTTGGACAGG
*
18357238 TCAACATCAGATGCTGCCCCCCAGAAACCAACCTCTAATTCAAGCAAGATTGGCTCTAATGTCAT
1 TCAACATCAGATGCTGCCCCCCAGAAACCAACCTCTAATTCAAGCAAGACTGGCTCTAATGTCAT
18357303 GGAGAATCCTTTTCATGTCTTTGAA
66 GGAGAATCCTTTTCATGTCTTTGAA
*
18357328 TCAACATCAGATGCTGCCCCCCAGAAACCAGCCTCTAATTCAAGCAAGACTGGCTCTAATGTCAT
1 TCAACATCAGATGCTGCCCCCCAGAAACCAACCTCTAATTCAAGCAAGACTGGCTCTAATGTCAT
18357393 GGAGAATCCTTTTCATGTCTTTGAA
66 GGAGAATCCTTTTCATGTCTTTGAA
18357418 TCAACATCAGA
1 TCAACATCAGA
18357429 GACAGCAGAT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 99 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (90 bp):
TCAACATCAGATGCTGCCCCCCAGAAACCAACCTCTAATTCAAGCAAGACTGGCTCTAATGTCAT
GGAGAATCCTTTTCATGTCTTTGAA
Found at i:18357971 original size:15 final size:15
Alignment explanation
Indices: 18357943--18357977 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18357933 TACTAGTGCC
* *
18357943 CCACCCCCTTCAAGA
1 CCACCACCTCCAAGA
18357958 CCACCACCTCCAAGA
1 CCACCACCTCCAAGA
18357973 CCACC
1 CCACC
18357978 GCGAGTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.57, G:0.06, T:0.09
Consensus pattern (15 bp):
CCACCACCTCCAAGA
Found at i:18367239 original size:15 final size:16
Alignment explanation
Indices: 18367214--18367247 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18367204 AAGCTCACTA
18367214 AAAATACTATTCCCTT
1 AAAATACTATTCCCTT
*
18367230 AAAA-ACTATTCGCTT
1 AAAATACTATTCCCTT
18367245 AAA
1 AAA
18367248 TAAATATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAATACTATTCCCTT
Found at i:18378581 original size:45 final size:45
Alignment explanation
Indices: 18378532--18378622 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
18378522 AAGATCAAAA
*
18378532 TAAGTTTGGATGAACTTTAAATTCTAGTAGTCATCAGAATTAAAG
1 TAAGTTTGGATAAACTTTAAATTCTAGTAGTCATCAGAATTAAAG
*
18378577 TAAGTTTGGATAAACTTTAAATTCTAGTAGTTATCAGAATTAAAG
1 TAAGTTTGGATAAACTTTAAATTCTAGTAGTCATCAGAATTAAAG
18378622 T
1 T
18378623 TCTATTTCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (45 bp):
TAAGTTTGGATAAACTTTAAATTCTAGTAGTCATCAGAATTAAAG
Found at i:18378996 original size:15 final size:14
Alignment explanation
Indices: 18378976--18379009 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
18378966 TCGGGTTTTT
18378976 TTTAGATTTAGATTC
1 TTTAGATTTA-ATTC
*
18378991 TTTAGATTTAATTT
1 TTTAGATTTAATTC
18379005 TTTAG
1 TTTAG
18379010 CTCTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (14 bp):
TTTAGATTTAATTC
Found at i:18383004 original size:23 final size:23
Alignment explanation
Indices: 18382974--18383032 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
18382964 ACCAAACTTT
18382974 AATATTATACTAATGACCTCGTA
1 AATATTATACTAATGACCTCGTA
18382997 AATATTATACTAATGACCTCGTA
1 AATATTATACTAATGACCTCGTA
18383020 AATATTATA-TAAT
1 AATATTATACTAAT
18383033 TAATATTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (23 bp):
AATATTATACTAATGACCTCGTA
Found at i:18383842 original size:20 final size:20
Alignment explanation
Indices: 18383809--18383847 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18383799 TTAAATTGGT
*
18383809 TTAATTAAAGTTAAAAATGG
1 TTAATTAAACTTAAAAATGG
* *
18383829 TTAATTAGACTTAATAATG
1 TTAATTAAACTTAAAAATG
18383848 AAAGTCATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (20 bp):
TTAATTAAACTTAAAAATGG
Found at i:18388343 original size:46 final size:46
Alignment explanation
Indices: 18388282--18388377 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
18388272 GATTAAACTA
*
18388282 ATGATTGGTAAAAGTGAGTTAAGTTTGTTTTTGGATTTTGTTAAAC
1 ATGATTGGTAAAAGTGAGTTAAGTTTGTTATTGGATTTTGTTAAAC
18388328 ATGATTGGTAAAAGTGAGTTAAGTTTGTTATTGGATTTTGTTAAAC
1 ATGATTGGTAAAAGTGAGTTAAGTTTGTTATTGGATTTTGTTAAAC
18388374 ATGA
1 ATGA
18388378 ACAAAAGTGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (46 bp):
ATGATTGGTAAAAGTGAGTTAAGTTTGTTATTGGATTTTGTTAAAC
Found at i:18393861 original size:21 final size:22
Alignment explanation
Indices: 18393830--18393871 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
18393820 TAAAATAATA
18393830 AAATCAATTATAATATTTTTTG
1 AAATCAATTATAATATTTTTTG
*
18393852 AAAT-AATTATAATTTTTTTT
1 AAATCAATTATAATATTTTTT
18393872 TTTGAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
AAATCAATTATAATATTTTTTG
Found at i:18395210 original size:3 final size:3
Alignment explanation
Indices: 18395202--18395232 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
18395192 TGAAAAGAAT
18395202 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18395233 ATTTTTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18405079 original size:28 final size:28
Alignment explanation
Indices: 18405035--18405090 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
18405025 TAGATCTTGG
*
18405035 GATCTTCAATTAGCTAGGTATGGTTTTC
1 GATCTTCAATTAACTAGGTATGGTTTTC
18405063 GATCTTCAATTAACTAGGTATGGTTTTC
1 GATCTTCAATTAACTAGGTATGGTTTTC
18405091 CTTTAGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (28 bp):
GATCTTCAATTAACTAGGTATGGTTTTC
Done.