Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 89 of 362
Found at i:28410698 original size:46 final size:47
Alignment explanation
Indices: 28410475--28410828 Score: 252
Period size: 46 Copynumber: 7.5 Consensus size: 47
28410465 ATACCAATGC
* * * **
28410475 CATGTCCCAAACATGGTCTTACACTGGCT-TATC-CATC-AAGTTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTA-CATATCGTAGCCGATG
28410521 CCATGTCCCAGACATAGTCTTACACTGGCTCTCACATATCTGT-GCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCT-ACATATC-GTAGCCGATG
* * * * **
28410571 CCATGTTCCAGACATGGTCTTACGCTGACAACTTTATA-CGT-GCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGC-TCTACATATCGTAGCCGATG
* *
28410619 CTATGTCCCAGACATGGTCTTACACT-G-AC-ACATCTCGTAGCCGATG
1 C-ATGTCCCAGACAT-GTCTTACACTGGCTCTACATATCGTAGCCGATG
* * *
28410665 CATGTCCTAGACATATCTTACACTGGCT-TACATCTCG-AGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTACATATCGTA-GCCGATG
* * * *
28410711 CATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTC-AATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTACATATCGTA-GCCGATG
* *
28410757 CTATGTCCCAGACGTGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATG
1 C-ATGTCCCAGACAT-GTCTTACACTGGCTCTACAT-ATCGTAGCCGATG
*
28410805 CATGTCCCAAACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
28410829 AGCACACAAA
Statistics
Matches: 253, Mismatches: 35, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
44 11 0.04
45 19 0.08
46 72 0.28
47 52 0.21
48 58 0.23
49 6 0.02
50 33 0.13
51 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTACATATCGTAGCCGATG
Found at i:28410801 original size:94 final size:93
Alignment explanation
Indices: 28410475--28410831 Score: 281
Period size: 94 Copynumber: 3.8 Consensus size: 93
28410465 ATACCAATGC
* * *
28410475 CATGTCCCAAACATGGTCTTACACTGGCTTATCCATCAA-GT---TGATGCCATGTCCCAGACAT
1 CATGTCCCAGACATGGTCTTACACTGGC-TCT-CAT-AATGTGGCCGATG-CATGTCCCAGACAT
* *
28410536 AGTCTTACACTGGCTCTCACATATCTGTGCCGATG
62 AGTCTTACACTAGCTCT--CATCTC-GTGCCGATG
* * * * * *
28410571 CCATGTTCCAGACATGGTCTTACGCTGACAACT-TTATACGT-GCCGATGCTATGTCCCAGACAT
1 -CATGTCCCAGACATGGTCTTACACTGGC-TCTCATA-ATGTGGCCGATGC-ATGTCCCAGACAT
* * *
28410634 GGTCTTACACT-G-ACACATCTCGTAGCCGATG
62 AGTCTTACACTAGCTCTCATCTCGT-GCCGATG
* * * *
28410665 CATGTCCTAGACAT-ATCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAGACAT-G
1 CATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGACATAG
* *
28410726 TCTTACACTAGCTCTCGTCTCAATGCCGATG
64 TCTTACACTAGCTCTCATCTC-GTGCCGATG
* *
28410757 CTATGTCCCAGACGTGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAAACAT-GT
1 C-ATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATAGT
28410821 CTTACACTAGC
65 CTTACACTAGC
28410832 ACACAAATAA
Statistics
Matches: 210, Mismatches: 33, Indels: 37
0.75 0.12 0.13
Matches are distributed among these distances:
90 11 0.05
91 15 0.07
92 33 0.16
93 26 0.12
94 64 0.30
95 4 0.02
96 3 0.01
97 27 0.13
98 27 0.13
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (93 bp):
CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATAGTC
TTACACTAGCTCTCATCTCGTGCCGATG
Found at i:28414852 original size:27 final size:27
Alignment explanation
Indices: 28414809--28414869 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28414799 AATTTCTTTC
*
28414809 ATTTACTT-TATTTTAACTATTA-TATT
1 ATTTA-TTATATTTTAACAATTATTATT
28414835 ATTATATTATATTTTAACAATTATTATT
1 ATT-TATTATATTTTAACAATTATTATT
28414863 ATTTATT
1 ATTTATT
28414870 TAAATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 5 0.16
27 19 0.61
28 7 0.23
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTATTATATTTTAACAATTATTATT
Found at i:28415239 original size:32 final size:32
Alignment explanation
Indices: 28415193--28415259 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
28415183 CGGTTCCCAT
28415193 TATATCTTCTGGTTCCCATGTTGCTTCTTCAA
1 TATATCTTCTGGTTCCCATGTTGCTTCTTCAA
28415225 TATATCTT-TCGGTTCCCATGTTGCTTCTTCAA
1 TATATCTTCT-GGTTCCCATGTTGCTTCTTCAA
28415257 TAT
1 TAT
28415260 TGTGACTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.16, C:0.24, G:0.12, T:0.48
Consensus pattern (32 bp):
TATATCTTCTGGTTCCCATGTTGCTTCTTCAA
Found at i:28419808 original size:47 final size:45
Alignment explanation
Indices: 28419583--28419798 Score: 153
Period size: 46 Copynumber: 4.7 Consensus size: 45
28419573 TGTGTGAGCT
* * *
28419583 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-TCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGAGACATGGCATCGGCTC-GA-GATGA-AG-C
* * * *
28419629 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGGAC
1 AGTGTAAGACCATGTCTGAGACATGGCATCGGC-TCGAGATGAAG-C
* *
28419676 TAGTGTAAGA-CATGTCT-AGGACGT-GCATCGGCCTCGAGACAGAAGCC
1 -AGTGTAAGACCATGTCTGA-GACATGGCATCGG-CTCGAGA-TGAAG-C
28419723 AGTGTAAGA-CATGTCTG-GAACAT-GCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGAG-ACATGGCATCGGCT-CGAGATGA-AG-C
28419769 AGTGTAAGACCATGTCTGAGACATGGCATC
1 AGTGTAAGACCATGTCTGAGACATGGCATC
28419799 AACTTGAGAT
Statistics
Matches: 140, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
45 5 0.04
46 64 0.46
47 44 0.31
48 25 0.18
49 1 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACCATGTCTGAGACATGGCATCGGCTCGAGATGAAGC
Found at i:28419820 original size:47 final size:47
Alignment explanation
Indices: 28419577--28419845 Score: 181
Period size: 47 Copynumber: 5.8 Consensus size: 47
28419567 CATTCGTGTG
* *
28419577 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-TC-ACATTA
1 TGAGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCTCGAGA-TA
* * * *
28419621 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 T--GAGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGC-TCGAGA-TA
* * *
28419672 GGA-CTAGTGTAAGA-CATGTCT-AGGACGT-GCATCGGCCTCGAGACA
1 TGAGCTAGTGTAAGACCATGTCTGA-GACATGGCATCGG-CTCGAGATA
*
28419717 -GAAGCCAGTGTAAGA-CATGTCTG-GAACAT-GCATCGGCTACGAGATGA
1 TG-AGCTAGTGTAAGACCATGTCTGAG-ACATGGCATCGGCT-CGAGAT-A
** *
28419764 T-AG-TCAGTGTAAGACCATGTCTGAGACATGGCATCAACTTGAGATA
1 TGAGCT-AGTGTAAGACCATGTCTGAGACATGGCATCGGCTCGAGATA
**
28419810 TGAGCTAGTGTAAGACTGTGTCT-AGGACATGGCATC
1 TGAGCTAGTGTAAGACCATGTCTGA-GACATGGCATC
28419846 AGCACCTTAC
Statistics
Matches: 182, Mismatches: 20, Indels: 43
0.74 0.08 0.18
Matches are distributed among these distances:
44 2 0.01
45 5 0.03
46 71 0.39
47 72 0.40
48 26 0.14
49 2 0.01
50 1 0.01
51 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
TGAGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCTCGAGATA
Found at i:28419835 original size:140 final size:140
Alignment explanation
Indices: 28419583--28419837 Score: 356
Period size: 140 Copynumber: 1.8 Consensus size: 140
28419573 TGTGTGAGCT
* * *
28419583 AGTGTAAGACATGTCTGGGACATGCATCGGTCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGAACATGCATCGGTCACATGATGAGAGCCAGTGTAAGACCATGTCTGA
**
28419648 GACATGGCATCGGCATTGAGACGAGGACTAGTGTAAGACATGTCTAGGACGTGCATCGGCCTCGA
66 GACATGGCATCAACATTGAGACGAGGACTAGTGTAAGACATGTCTAGGACGTGCATCGGCCTCGA
28419713 GACAGAAGCC
131 GACAGAAGCC
* *
28419723 AGTGTAAGACATGTCTGGAACATGCATCGG-CTACGA-GATGATAGTCAGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGAACATGCATCGGTC-AC-ATGATGAGAGCCAGTGTAAGACCATGTCT
* * *
28419786 GAGACATGGCATCAAC-TTGAGA-TATGAGCTAGTGTAAGACTGTGTCTAGGAC
64 GAGACATGGCATCAACATTGAGACGAGGA-CTAGTGTAAGAC-ATGTCTAGGAC
28419838 ATGGCATCAG
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
138 3 0.03
139 19 0.19
140 78 0.77
141 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGAACATGCATCGGTCACATGATGAGAGCCAGTGTAAGACCATGTCTGA
GACATGGCATCAACATTGAGACGAGGACTAGTGTAAGACATGTCTAGGACGTGCATCGGCCTCGA
GACAGAAGCC
Found at i:28422570 original size:49 final size:51
Alignment explanation
Indices: 28422491--28422633 Score: 195
Period size: 49 Copynumber: 2.8 Consensus size: 51
28422481 TGTAGACAAG
* *
28422491 GTTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGAAC-AA
1 GTTATCGGGTACGCGTAGTAGCCTGCACTTAGTACTACACATGTGAACGAA
* *
28422541 -TTATTC-GGTACAG-GTAGTAGCCTGCACTTAGTACTACACACGTGACCGAA
1 GTTA-TCGGGTAC-GCGTAGTAGCCTGCACTTAGTACTACACATGTGAACGAA
*
28422591 GTTATCGGGTACGCGTAGTAGCTTGCACTTAGTACTACACATG
1 GTTATCGGGTACGCGTAGTAGCCTGCACTTAGTACTACACATG
28422634 CAACCTCACA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
49 39 0.48
50 8 0.10
51 35 0.43
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (51 bp):
GTTATCGGGTACGCGTAGTAGCCTGCACTTAGTACTACACATGTGAACGAA
Found at i:28422915 original size:27 final size:27
Alignment explanation
Indices: 28422885--28422938 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28422875 TCATACAACC
*
28422885 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
**
28422912 CATGTAATAATAATTTTCCATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
28422939 TCACATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (27 bp):
CATGTAATAATAATTTAACATTCAATT
Found at i:28426444 original size:30 final size:30
Alignment explanation
Indices: 28426399--28426457 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28426389 TCCTGAGCCC
28426399 AGGGGAAAAAGTGTAATTATGCAAAAGTTT
1 AGGGGAAAAAGTGTAATTATGCAAAAGTTT
* *
28426429 AGGGGCAAAAA-TGTAATTTTGCCAAAGTT
1 AGGGG-AAAAAGTGTAATTATGCAAAAGTT
28426458 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (30 bp):
AGGGGAAAAAGTGTAATTATGCAAAAGTTT
Found at i:28433973 original size:30 final size:30
Alignment explanation
Indices: 28433937--28433996 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28433927 TTCCCGAGCC
*
28433937 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
28433967 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
28433997 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:28437250 original size:18 final size:18
Alignment explanation
Indices: 28437227--28437263 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28437217 CATAACCAAA
28437227 ATATGCATACTCCATTCT
1 ATATGCATACTCCATTCT
* *
28437245 ATATGCGTACTCTATTCT
1 ATATGCATACTCCATTCT
28437263 A
1 A
28437264 ACTTTAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATGCATACTCCATTCT
Found at i:28438696 original size:12 final size:12
Alignment explanation
Indices: 28438656--28438689 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28438646 CAAAACCCTA
*
28438656 TTTTTCCTT-TC
1 TTTTTCTTTCTC
28438667 TTTTTCTTTCTC
1 TTTTTCTTTCTC
28438679 TTTTTCTTTCT
1 TTTTTCTTTCT
28438690 TTCTTTCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:28439844 original size:22 final size:22
Alignment explanation
Indices: 28439803--28439844 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28439793 AACAACATAG
*
28439803 AGGCCCAAAATTATTTCATTGA
1 AGGCCCAAAATTATTCCATTGA
*
28439825 AGGCCCAAAATTGTTCCATT
1 AGGCCCAAAATTATTCCATT
28439845 TACCGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGCCCAAAATTATTCCATTGA
Found at i:28444643 original size:179 final size:178
Alignment explanation
Indices: 28444338--28444697 Score: 553
Period size: 179 Copynumber: 2.0 Consensus size: 178
28444328 TCAATTTGTG
* * *
28444338 TTAAAGAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGTTGATTCTAACTAGGATGGT
1 TTAAAAAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGCTGATTCTAACTAGGATAGT
*
28444403 TAAGGTTGAAGGATTTGTATTGACTATTGTAAGTTATATAAGGCAACTCAGAAAGATCATTTTTC
66 TAAGGTTGAAGGATTTGTATTGACTATCGTAAGTTATATAAGGCAACTCAGAAAGATCATTTTTC
* * *
28444468 GTTGCCATTTTTGGATCAAATTTTAGATAGACTTTTAGGACACAATTA
131 GTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
* *
28444516 TTAAAAAAGGGAGGTGTTACAGTTGTAATGAATGAGAATAATGAGCTGATTAC-AACTAGGATAG
1 TTAAAAAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGCTGATT-CTAACTAGGATAG
* * *
28444580 TTACATGTTGAAGGATTTGTATTTATTATCGTAAGTTATATAAGGCAACTCA-AAATGATCATTT
65 TTA-AGGTTGAAGGATTTGTATTGACTATCGTAAGTTATATAAGGCAACTCAGAAA-GATCATTT
* *
28444644 TTTGTTTCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
128 TTCGTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
28444695 TTA
1 TTA
28444698 CTATTTCCTA
Statistics
Matches: 165, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
178 63 0.38
179 102 0.62
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (178 bp):
TTAAAAAAGGGAGGTGTTACAGTTGCAAAGAATGAGAATAATGAGCTGATTCTAACTAGGATAGT
TAAGGTTGAAGGATTTGTATTGACTATCGTAAGTTATATAAGGCAACTCAGAAAGATCATTTTTC
GTTGCCATTTTTGGATCAAATGTTAGATAGACTTGTAGAACACAATTA
Found at i:28449915 original size:28 final size:27
Alignment explanation
Indices: 28449848--28449917 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
28449838 GGAATATGAT
* *
28449848 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTAACCATGCA
* *
28449875 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TAACCATGCA
*
28449903 GCACTAAGGGTGCGA
1 GCACTAAGTGTGCGA
28449918 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAACCATGCA
Found at i:28449933 original size:55 final size:53
Alignment explanation
Indices: 28449793--28449944 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 53
28449783 TAAATTGTAC
* * *
28449793 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAGGAATATG
1 AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAATATG
* ** * * *
28449846 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAA-TATG
* *
28449901 TAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGA
28449945 GTTGAGTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.48
55 40 0.49
56 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAACGAATATG
Found at i:28449949 original size:27 final size:27
Alignment explanation
Indices: 28449794--28449949 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
28449784 AAATTGTACA
* *
28449794 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
28449821 GCACTAAGTGTGCGAAAGGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
28449848 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
28449875 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * * *
28449903 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
28449930 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
28449950 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:28456061 original size:17 final size:18
Alignment explanation
Indices: 28456039--28456073 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28456029 ATGTGGGCTG
*
28456039 TGTGGG-CCACATGGGCA
1 TGTGGGCCCACAAGGGCA
28456056 TGTGGGCCCACAAGGGCA
1 TGTGGGCCCACAAGGGCA
28456074 GGCCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.20, C:0.26, G:0.40, T:0.14
Consensus pattern (18 bp):
TGTGGGCCCACAAGGGCA
Found at i:28464830 original size:46 final size:48
Alignment explanation
Indices: 28464728--28465045 Score: 297
Period size: 46 Copynumber: 6.8 Consensus size: 48
28464718 ACATTATGAG
* * *
28464728 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGATG-A
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGAGATGTA
* * *
28464775 GAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGATGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGAGATGTA
* *
28464822 AGCCAGTGTAAGA-CATGTTTGGGACAT-GCATC-GACTATGAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTA-GAGATGTA
* *
28464867 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-C-TAGAGATGTA
* *
28464915 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-AGATATGTGA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTAGAGATGT-A
* * * *
28464963 GAGCCAGTGTAAGACGATGTCTGGGACATGGCATC-GACT--TGATGTCC
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGAGATGT-A
* *
28465010 A-TCAGTGTAAGACCATGTTTGGGACATGGCATCGGC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
28465046 ATTACACCTT
Statistics
Matches: 232, Mismatches: 25, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
44 11 0.05
45 45 0.19
46 65 0.28
47 19 0.08
48 58 0.25
49 3 0.01
50 31 0.13
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGAGATGTA
Found at i:28465038 original size:143 final size:139
Alignment explanation
Indices: 28464731--28465046 Score: 396
Period size: 143 Copynumber: 2.3 Consensus size: 139
28464721 TTATGAGAGC
28464731 CAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACATTGAGATGAGAGCTAGTGTAAGACATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTGAGATGAGAGCTAGTGTAAGACATGT
* * *
28464794 TTGGGACATGCATCGGCCTCGAGATGTAAGCCAGTGTAAGACATGTTTGGGACATGCATCGACTA
66 CTGGGACATGCATCGGCCTAGAGATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACTA
*
28464859 TGAGATGTGT
131 T-AGATGTAT
* * *
28464869 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-AGATGTG-TC-AGTGTAAGACCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAT-TGAGATGAGAGCTAGTGTAAGA-CAT
*
28464931 GTCTGGGACATGGCATCGGCAC-AGATATGTGAGAGCCAGTGTAAGACGATGTCTGGGACATGGC
64 GTCTGGGACAT-GCATCGGC-CTAGAGATGT-A-AGCCAGTGTAAGAC-ATGTCTGGGACAT-GC
28464995 ATCGACT-T-GATGTCCAT
123 ATCGACTATAGATGT--AT
*
28465012 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
28465047 TTACACCTTA
Statistics
Matches: 157, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
138 40 0.25
139 15 0.10
140 23 0.15
141 8 0.05
142 14 0.09
143 48 0.31
144 9 0.06
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (139 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTGAGATGAGAGCTAGTGTAAGACATGT
CTGGGACATGCATCGGCCTAGAGATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACTA
TAGATGTAT
Found at i:28466065 original size:28 final size:28
Alignment explanation
Indices: 28466030--28466085 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28466020 CACGGGTTGA
28466030 GACACGGGCG-TGTCGAGGCCGTGTGAGG
1 GACACGGGCGATGTCGA-GCCGTGTGAGG
*
28466058 GACACGGGCGTATGTCTAGCCGTGTGAG
1 GACACGGGCG-ATGTCGAGCCGTGTGAG
28466086 AACCCCTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 10 0.40
30 5 0.20
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (28 bp):
GACACGGGCGATGTCGAGCCGTGTGAGG
Found at i:28471423 original size:40 final size:39
Alignment explanation
Indices: 28471379--28471508 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
28471369 GCGTTTGGAT
* *
28471379 AAAAAAGCCGCTATTGATCGAGCATTAGTAGCGCTTTTTG
1 AAAAAAGCCGCTATAGATCGAACATTAGT-GCGCTTTTTG
* * * *
28471419 AAAAACGCCACTGTAGATCGAACATTAGCGACGCTTTTT-
1 AAAAAAGCCGCTATAGATCGAACATTAGTG-CGCTTTTTG
* *
28471458 AAAAAATGCCGCTATAGGTCGATCATTAGCTGCGCTTTTTG
1 AAAAAA-GCCGCTATAGATCGAACATTAG-TGCGCTTTTTG
*
28471499 AAAAATGCCG
1 AAAAAAGCCG
28471509 AAAAAATTAA
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
39 6 0.08
40 61 0.84
41 6 0.08
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (39 bp):
AAAAAAGCCGCTATAGATCGAACATTAGTGCGCTTTTTG
Found at i:28471608 original size:40 final size:40
Alignment explanation
Indices: 28471553--28471696 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 40
28471543 AGCTTTAGTG
* *
28471553 GCATTAGCGACGCTTTTTGAAAAACGCCACTATAGATTGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
*
28471593 GCATTAGCAGCGCTTTTTG-AAAACGCCACTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* * ** *
28471632 GCGTTAGCGGCGCTTTTTTAAAAAAACCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* * *
28471672 GCTTTAGCGGCGCTTTATCAAAAAC
1 GCATTAGCGGCGCTTTTTGAAAAAC
28471697 ACCGCAATAA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 35 0.39
40 55 0.61
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
Found at i:28472024 original size:7 final size:7
Alignment explanation
Indices: 28472008--28472163 Score: 53
Period size: 7 Copynumber: 22.1 Consensus size: 7
28471998 TATCATTTTA
*
28472008 GTTTAGG
1 GTTTATG
28472015 GTTTATG
1 GTTTATG
*
28472022 GTTTAGG
1 GTTTATG
*
28472029 GTATATG
1 GTTTATG
*
28472036 GTTTAAG
1 GTTTATG
**
28472043 GTTTAAA
1 GTTTATG
*
28472050 GTTTAAG
1 GTTTATG
* *
28472057 AGTTAATA
1 -GTTTATG
* *
28472065 TTTTAAG
1 GTTTATG
*
28472072 GTTTAGG
1 GTTTATG
*
28472079 GATTATG
1 GTTTATG
*
28472086 GTTTATA
1 GTTTATG
* *
28472093 TTTTAAG
1 GTTTATG
* **
28472100 GGTTGGG
1 GTTTATG
*
28472107 GTTTAAG
1 GTTTATG
28472114 GTTTA-G
1 GTTTATG
* *
28472120 GAGTTAGG
1 G-TTTATG
*
28472128 GTTTAGG
1 GTTTATG
28472135 GTTTATG
1 GTTTATG
*
28472142 TTTTATG
1 GTTTATG
* *
28472149 ATTTACG
1 GTTTATG
28472156 GTTTATG
1 GTTTATG
28472163 G
1 G
28472164 GGATAAGGGT
Statistics
Matches: 107, Mismatches: 39, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
6 2 0.02
7 99 0.93
8 6 0.06
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (7 bp):
GTTTATG
Found at i:28472027 original size:14 final size:14
Alignment explanation
Indices: 28472008--28472163 Score: 64
Period size: 14 Copynumber: 11.1 Consensus size: 14
28471998 TATCATTTTA
28472008 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
*
28472022 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* **
28472036 GTTTAAGGTTTAAA
1 GTTTAGGGTTTATG
* * *
28472050 GTTTAAGAGTTAATA
1 GTTT-AGGGTTTATG
* * *
28472065 TTTTAAGGTTTAGG
1 GTTTAGGGTTTATG
* * *
28472079 GATTATGGTTTATA
1 GTTTAGGGTTTATG
* **
28472093 TTTTAAGGG-TTGGG
1 GTTT-AGGGTTTATG
*
28472107 GTTTAAGGTTTA-G
1 GTTTAGGGTTTATG
* *
28472120 GAGTTAGGGTTTAGG
1 G-TTTAGGGTTTATG
* *
28472135 GTTTATGTTTTATG
1 GTTTAGGGTTTATG
* *
28472149 ATTTACGGTTTATG
1 GTTTAGGGTTTATG
28472163 G
1 G
28472164 GGATAAGGGT
Statistics
Matches: 98, Mismatches: 39, Indels: 10
0.67 0.27 0.07
Matches are distributed among these distances:
13 5 0.05
14 79 0.81
15 14 0.14
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:28472100 original size:28 final size:28
Alignment explanation
Indices: 28472052--28472118 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
28472042 GGTTTAAAGT
* *
28472052 TTAAGAGTTAATATTTTAAGGTTTAGGGA
1 TTAAG-GTTTATATTTTAAGGGTTAGGGA
* * *
28472081 TTATGGTTTATATTTTAAGGGTTGGGGT
1 TTAAGGTTTATATTTTAAGGGTTAGGGA
28472109 TTAAGGTTTA
1 TTAAGGTTTA
28472119 GGAGTTAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (28 bp):
TTAAGGTTTATATTTTAAGGGTTAGGGA
Found at i:28472118 original size:21 final size:22
Alignment explanation
Indices: 28472066--28472139 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
28472056 GAGTTAATAT
* *
28472066 TTTAAGGTTTAGGGA-TTATGG
1 TTTAAGGTTTAAGGAGTTAGGG
* *
28472087 TTTATA-TTTTAAGG-GTTGGGG
1 TTTA-AGGTTTAAGGAGTTAGGG
28472108 TTTAAGGTTT-AGGAGTTAGGG
1 TTTAAGGTTTAAGGAGTTAGGG
*
28472129 TTTAGGGTTTA
1 TTTAAGGTTTA
28472140 TGTTTTATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 4 0.10
21 36 0.88
22 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.45
Consensus pattern (22 bp):
TTTAAGGTTTAAGGAGTTAGGG
Found at i:28478766 original size:43 final size:43
Alignment explanation
Indices: 28478687--28478829 Score: 143
Period size: 43 Copynumber: 3.4 Consensus size: 43
28478677 TTAATTTTTT
* *
28478687 TAAAGGTCA--TTCTTTAGCGGCATTTG-AGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAACGACATTTGCA-GGAAAAGCGCCGC
* * *
28478728 TAAAGGTCATGTTCTTTAACGACGTTTG-TGAGAGAAGCGCCGC
1 TAAAGGTCATGTTCTTTAACGACATTTGCAG-GAAAAGCGCCGC
* * * *
28478771 TAAAGGTCATGGTT-TTTAGCGGCATTTGCAGGAAAAGTGCTGC
1 TAAAGGTCAT-GTTCTTTAACGACATTTGCAGGAAAAGCGCCGC
28478814 TAAAGGTCATGTTCTT
1 TAAAGGTCATGTTCTT
28478830 GCGGGAAAAG
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
41 9 0.11
42 4 0.05
43 67 0.80
44 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAACGACATTTGCAGGAAAAGCGCCGC
Found at i:28480231 original size:46 final size:45
Alignment explanation
Indices: 28480086--28480297 Score: 171
Period size: 46 Copynumber: 4.6 Consensus size: 45
28480076 TGTGCGCTAA
* * *
28480086 TGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAATAT-A-AGCCAG
** * * * * *
28480132 TGTAAGACCATGTCTGGGACATGGCATCAACATTGAGACGA-GAGCTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA-A-TATAAGCCAG
28480180 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCGA-ATATAAGCCAG
* ** *
28480226 TGTAAGACATGTTTGGGACATGCATCGG-CTACGAA-ATGTGTCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGAATATAAGCCAG
*
28480270 TGTAAGACCATGTCTGGGGCATGGCATC
1 TGTAAGA-CATGTCTGGGACAT-GCATC
28480298 TGTAATAGTC
Statistics
Matches: 134, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
44 13 0.10
45 16 0.12
46 58 0.43
47 28 0.21
48 17 0.13
49 1 0.01
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTCGAATATAAGCCAG
Found at i:28482192 original size:46 final size:45
Alignment explanation
Indices: 28482139--28482275 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 45
28482129 TATATATACA
* * *
28482139 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACAT-TCGCATTAGCCATTCGGCTTTACCACATATC
* *
28482185 CATCTCATACACGATTCGCATTACCCATTCGGCTTTACCTCATATC
1 CATCTCATACAC-ATTCGCATTAGCCATTCGGCTTTACCACATATC
* *
28482231 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACA-TTCGCATTAGCCATTCGGCTTTACCACATAT
28482276 ATACATGTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.01
46 77 0.96
47 2 0.03
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.34
Consensus pattern (45 bp):
CATCTCATACACATTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:28482310 original size:47 final size:47
Alignment explanation
Indices: 28482249--28482537 Score: 416
Period size: 47 Copynumber: 6.1 Consensus size: 47
28482239 ACACATTTCG
* * * **
28482249 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
28482296 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
28482343 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
28482390 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * ** *
28482437 CATTGGCCATTCGGCTTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ACATACGCATGTTCACATTCATCA
28482488 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
28482535 CAT
1 CAT
28482538 AAAATCCTAA
Statistics
Matches: 219, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
47 176 0.80
49 2 0.01
51 41 0.19
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:28482569 original size:145 final size:141
Alignment explanation
Indices: 28482279--28482539 Score: 378
Period size: 145 Copynumber: 1.8 Consensus size: 141
28482269 CACATATATA
* * *
28482279 CATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCAC
1 CATGTTCACATTCATCACATTGGCCATTCGGCCTTATCGCATATATACAGGTTCACATTCATCAC
** * ****
28482344 ATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
66 ATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATAAGCCAATCGAAAATA
28482409 TCACACATACG
131 TCACACATACG
*
28482420 CATGTTCACATTCATCACATTGGCCATTCGGCTTTATCACGCATATATATACAGGTTCACATTCA
1 CATGTTCACATTCATCACATTGGCCATTCGGCCTTAT--CGC--ATATATACAGGTTCACATTCA
*
28482485 TCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATAA
62 TCACATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATAA
28482540 AATCCTAAAT
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
141 36 0.33
143 2 0.02
145 71 0.65
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.32
Consensus pattern (141 bp):
CATGTTCACATTCATCACATTGGCCATTCGGCCTTATCGCATATATACAGGTTCACATTCATCAC
ATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATTCATCACATAAGCCAATCGAAAATA
TCACACATACG
Found at i:28485896 original size:42 final size:43
Alignment explanation
Indices: 28485836--28485946 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 43
28485826 GATTTACGTA
* ***
28485836 TAAGA-CTATGTCTAGGACATCGGCATC-ATATCTG-ATTTTGTG
1 TAAGACCT-TGTCTGGGACATCGGCATCAATAT-TGAATTACATG
**
28485878 TAAGACCTTGTCTGGGACAGAGGCATCAATATTGAATTACATG
1 TAAGACCTTGTCTGGGACATCGGCATCAATATTGAATTACATG
** *
28485921 TAAGACCACGTCCGGGACATCGGCAT
1 TAAGACCTTGTCTGGGACATCGGCAT
28485947 TGTACTTGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
42 23 0.42
43 32 0.58
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
TAAGACCTTGTCTGGGACATCGGCATCAATATTGAATTACATG
Found at i:28495446 original size:49 final size:49
Alignment explanation
Indices: 28495264--28495438 Score: 269
Period size: 49 Copynumber: 3.5 Consensus size: 49
28495254 TGAGGTCACG
*
28495264 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * *
28495313 TGTGTAGTATTAAGTGCAGGCTATTATGTGTACCCGATAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
28495364 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
28495413 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
28495439 TGCGTACCAG
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 67 0.60
50 4 0.04
51 40 0.36
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
Found at i:28495446 original size:100 final size:100
Alignment explanation
Indices: 28495259--28495451 Score: 332
Period size: 100 Copynumber: 1.9 Consensus size: 100
28495249 TATTGTGAGG
* * *
28495259 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGTATGTGTAGTATT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
* * *
28495324 AAGTGCAGGCTATTATGTGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCAGATAACTTCGA
28495359 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
28495424 AAGTGCAGGCTACTATGCGTACCAGATA
66 AAGTGCAGGCTACTATGCGTACCAGATA
28495452 GTTTTGGCTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCAGATAACTTCGA
Found at i:28497527 original size:21 final size:21
Alignment explanation
Indices: 28497503--28497561 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
28497493 AATAGCGGTG
**
28497503 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGAAACTGTA
28497524 GCGGTGAGATTAGAAACTGTA
1 GCGGTGAGATTAGAAACTGTA
28497545 GCGGTGAGATTAGAAAC
1 GCGGTGAGATTAGAAAC
28497562 AATGGTGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.34, T:0.25
Consensus pattern (21 bp):
GCGGTGAGATTAGAAACTGTA
Found at i:28497840 original size:19 final size:19
Alignment explanation
Indices: 28497818--28497856 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28497808 TAAAATGATA
28497818 ATTATTTTAAATTTTTTAT
1 ATTATTTTAAATTTTTTAT
28497837 ATTATTTTAAATTTTTTAT
1 ATTATTTTAAATTTTTTAT
28497856 A
1 A
28497857 GTTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATTTTAAATTTTTTAT
Found at i:28497853 original size:9 final size:10
Alignment explanation
Indices: 28497817--28497854 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
28497807 ATAAAATGAT
28497817 AATTATTTTA
1 AATTATTTTA
28497827 AATT-TTTTA
1 AATTATTTTA
*
28497836 TATTATTTTA
1 AATTATTTTA
28497846 AATT-TTTTA
1 AATTATTTTA
28497855 TAGTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTATTTTA
Found at i:28504075 original size:41 final size:41
Alignment explanation
Indices: 28503959--28504083 Score: 143
Period size: 41 Copynumber: 3.1 Consensus size: 41
28503949 AAATCACGTA
* * **
28503959 CCTTC-GGAATTTAA-CCGGATATAGCT-ACTCGTTCAAATG
1 CCTTCGGGAACTTAACCCGGATTTAG-TAACTCGCACAAATG
* *
28503998 CCTTCGGG-ACATAGCCC-GATTATAGTAACTCGCACAAATG
1 CCTTCGGGAACTTAACCCGGATT-TAGTAACTCGCACAAATG
28504038 CCTTCGGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
28504079 CCTTC
1 CCTTC
28504084 AGATCTTAGT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
39 12 0.17
40 26 0.36
41 30 0.42
42 4 0.06
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (41 bp):
CCTTCGGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
Found at i:28504132 original size:40 final size:40
Alignment explanation
Indices: 28503992--28504138 Score: 156
Period size: 40 Copynumber: 3.6 Consensus size: 40
28503982 GCTACTCGTT
* *
28503992 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TATAGTAACTAGCA
* * *
28504032 CAAATGCCTTCGGGAACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-ACTTAGCCCGGATATAGTAACTAGCA
* * * *
28504073 CAAATGCCTTC-AGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
28504114 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28504139 CATCATTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 46 0.51
41 41 0.46
42 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:28506669 original size:50 final size:50
Alignment explanation
Indices: 28506615--28506711 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
28506605 GGTACAGGTA
*
28506615 TGTATGTAAAACCCATGAGTATGAACTTTGGTATGAGATGAATTCTTACC
1 TGTATGTAAAACCCATGAGTATGAACTTTGGTATGAGATGAACTCTTACC
28506665 TGTATGTAAAACCCATGAGTATGAACTTTGGTATGAGATGAACTCTT
1 TGTATGTAAAACCCATGAGTATGAACTTTGGTATGAGATGAACTCTT
28506712 TGTAATAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (50 bp):
TGTATGTAAAACCCATGAGTATGAACTTTGGTATGAGATGAACTCTTACC
Found at i:28521932 original size:342 final size:343
Alignment explanation
Indices: 28520988--28522017 Score: 1882
Period size: 343 Copynumber: 3.0 Consensus size: 343
28520978 TGAAACCCAG
* *
28520988 AAATGTGACAATGATTTGTAAGCCAAGAGAACTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
1 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
28521053 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
66 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
* *
28521118 TTCAGAAAATTCTTCATGAAGCATATAATGGTTATTTATCTATACATCCGGGTAGTACAAAAATG
131 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTATACATCCGGGTAGTACAAAAATG
* *
28521183 TATAATGACTTGAAGAAAATGTATTGGTAGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTT
196 TATAATGACTTGAAGAAAATGTATTGGTGGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
* *
28521248 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTAACTTTGGGTTTACTTCAGCCAG
261 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
28521313 TGATGGTACCCGAGTGGA
326 TGATGGTACCCGAGTGGA
*
28521331 AAATTTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
1 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
28521396 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
66 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
28521461 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTATACATCCGGGTAGTACAAAAATG
131 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTATACATCCGGGTAGTACAAAAATG
28521526 TATAATGACTTGAAGAAAATGTATTGGTGGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
196 TATAATGACTTGAAGAAAATGTATTGGTGGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
* *
28521591 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCGAGTACCTTCGGGTTTACTTCAGCTAG
261 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
*
28521656 TGATGGTACCCGAGTAGA
326 TGATGGTACCCGAGTGGA
28521674 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
1 AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
* *
28521739 TGTCGGATCCGATAATTGTTTGAT-ATTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
66 TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
* *
28521803 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTGTACATTCGGGTAGTACAAAAATG
131 TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTATACATCCGGGTAGTACAAAAATG
* * *
28521868 TATAATGACTTGAAGAAAATGTATTGGTGGTCAGGCATGAAAAAAGATATCTCTGAGTTTGTTTC
196 TATAATGACTTGAAGAAAATGTATTGGTGGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
28521933 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
261 GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
28521998 TGATGGTACCCGAGTGGA
326 TGATGGTACCCGAGTGGA
28522016 AA
1 AA
28522018 TGGGATAGGA
Statistics
Matches: 664, Mismatches: 23, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
342 246 0.37
343 418 0.63
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (343 bp):
AAATGTGACAATGATTTGCAAGCCAAGAGAGCTTATTGTGAATCGGTTAGTGATTCAGATTTTCA
TGTCGGATCCGATGATTGTTTGATGTTTTGAGGTAGAATTTGTGTACCAAAAAATGATGAACTCA
TTCAGAAAATTCTTCATGAAGCACATAATGGTTGTTTATCTATACATCCGGGTAGTACAAAAATG
TATAATGACTTGAAGAAAATGTATTGGTGGTCGGGCATGAAAAGAGATATCTCCGAGTTTGTTTC
GAGATGTCTAATTTGTCAATAAGTGAAAGCTGAACACCAAGTACCTTCGGGTTTACTTCAGCCAG
TGATGGTACCCGAGTGGA
Found at i:28527495 original size:42 final size:42
Alignment explanation
Indices: 28527433--28527554 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 42
28527423 TAGGGTTAGT
* *
28527433 TGAGATTACC-TGTAACACCATATTTGGGATATGGCATCGATA
1 TGAGATT-CCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * **
28527475 TGAGACTT-CGTGTAAGACCATAGCTGGGCTATTTACATCGATA
1 TGAGA-TTCCGTGTAAGACCATATCTGGGATA-TGGCATCGATA
28527518 TGAGATTCCGTGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTCCGTGTAAGACCATATCTGGGATATGGCAT
28527555 TGGTATGGTA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
41 1 0.02
42 28 0.42
43 37 0.56
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (42 bp):
TGAGATTCCGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:28527665 original size:20 final size:20
Alignment explanation
Indices: 28527637--28527683 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28527627 TGGCAATGTT
28527637 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
28527657 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
28527677 TAAGTTG
1 TAAGTTG
28527684 CAAGTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:28533070 original size:24 final size:25
Alignment explanation
Indices: 28533036--28533168 Score: 109
Period size: 24 Copynumber: 5.5 Consensus size: 25
28533026 TCCCAGCTAT
*
28533036 ATAAT-GGGAAGCTCA-TAAGAGCC
1 ATAATCGGGAAGCTCACAAAGAGCC
* *
28533059 ATAATCGGGAAGTTCACAAAGAACC
1 ATAATCGGGAAGCTCACAAAGAGCC
* *
28533084 AT-ATCGGGAAGGTCACAAAAAGCC
1 ATAATCGGGAAGCTCACAAAGAGCC
*
28533108 -T-ATCAGGAAGCTCACAAAGAGCC
1 ATAATCGGGAAGCTCACAAAGAGCC
* * *
28533131 ATGTAA-AGGGAAGCTC-CGAATAGCC
1 A--TAATCGGGAAGCTCACAAAGAGCC
28533156 ATATATCGGGAAG
1 ATA-ATCGGGAAG
28533169 TTCAAGCGAG
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
23 27 0.31
24 29 0.33
25 22 0.25
26 9 0.10
27 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (25 bp):
ATAATCGGGAAGCTCACAAAGAGCC
Found at i:28533913 original size:20 final size:20
Alignment explanation
Indices: 28533888--28533932 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28533878 AGGGACTAAA
* *
28533888 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
28533908 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
28533928 ATGAA
1 ATGAA
28533933 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:28537266 original size:25 final size:25
Alignment explanation
Indices: 28537238--28537287 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28537228 ATAAACAAGA
28537238 TTGGTAAGTTTAGTTTCTGTTATAC
1 TTGGTAAGTTTAGTTTCTGTTATAC
28537263 TTGGTAAGTTTAGTTTCTGTTATAC
1 TTGGTAAGTTTAGTTTCTGTTATAC
28537288 GAACTTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (25 bp):
TTGGTAAGTTTAGTTTCTGTTATAC
Found at i:28541813 original size:48 final size:48
Alignment explanation
Indices: 28541751--28541943 Score: 323
Period size: 48 Copynumber: 4.0 Consensus size: 48
28541741 TATATATGTG
*
28541751 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
** *
28541799 TGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGATATATATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
28541847 TGTGGTAAATCTGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
28541895 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATGTGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
28541943 T
1 T
28541944 ATTGTGGCCG
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 133 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:28542131 original size:37 final size:37
Alignment explanation
Indices: 28542076--28542185 Score: 193
Period size: 37 Copynumber: 3.0 Consensus size: 37
28542066 GGAAATATAT
28542076 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
28542113 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28542150 TCCGGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
28542186 TCGAGCTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28543931 original size:43 final size:43
Alignment explanation
Indices: 28543882--28544183 Score: 527
Period size: 43 Copynumber: 7.1 Consensus size: 43
28543872 GAAACTCGGG
*
28543882 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGCCGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
* *
28543925 GATATGTATTCAGGCTTTCGTGCCTAGCAGGCTTCGTGCCGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
28543968 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
28544011 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTG-CGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
28544053 GATATGTATTCGGG-CTTCGTGCCTAGCAGGCTTCGTGCCGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
*
28544095 GATATGTATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
* **
28544138 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTAATGCCGGT
1 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
28544181 GAT
1 GAT
28544184 TCGAGCAAGG
Statistics
Matches: 247, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
41 23 0.09
42 36 0.15
43 188 0.76
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (43 bp):
GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
Found at i:28544098 original size:127 final size:129
Alignment explanation
Indices: 28543882--28544183 Score: 545
Period size: 127 Copynumber: 2.4 Consensus size: 129
28543872 GAAACTCGGG
28543882 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATGTATTCAGGCTTTCGTG
1 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATGTATTCAGGCTTTCGTG
*
28543947 CCTAGCAGGCTTCGTGCCGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGT
66 CCTAGCAGGCTTCGTGCCGGTGATATGTATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGT
* *
28544011 GATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTG-CGGTGATATGTATTCGGGC-TTCGTG
1 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATGTATTCAGGCTTTCGTG
28544074 CCTAGCAGGCTTCGTGCCGGTGATATGTATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGT
66 CCTAGCAGGCTTCGTGCCGGTGATATGTATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGT
**
28544138 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTAATGCCGGTGAT
1 GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGCCGGTGAT
28544184 TCGAGCAAGG
Statistics
Matches: 166, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
127 104 0.63
128 25 0.15
129 37 0.22
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (129 bp):
GATATGTATTCGGGTCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATGTATTCAGGCTTTCGTG
CCTAGCAGGCTTCGTGCCGGTGATATGTATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGT
Found at i:28544440 original size:29 final size:29
Alignment explanation
Indices: 28544340--28544441 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
28544330 ATGATTAGAG
* * *
28544340 GCACTGTGTGTGCAAATTCCGTTAACCGA
1 GCACTATGTGTGCGAATTCCATTAACCGA
* **
28544369 GCACTATGTGTGCGAGA-T-CAGTAATTGA
1 GCACTATGTGTGCGA-ATTCCATTAACCGA
* *
28544397 GGCACTGTGTGTGCGAATTCCTTTAACCGA
1 -GCACTATGTGTGCGAATTCCATTAACCGA
*
28544427 GCATTATGTGTGCGA
1 GCACTATGTGTGCGA
28544442 GATTGGTAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 7 0.12
29 42 0.75
30 7 0.12
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (29 bp):
GCACTATGTGTGCGAATTCCATTAACCGA
Found at i:28544465 original size:29 final size:28
Alignment explanation
Indices: 28544362--28544501 Score: 104
Period size: 29 Copynumber: 4.9 Consensus size: 28
28544352 CAAATTCCGT
* *
28544362 TAACCGAGCACTATGTGTGCGAGATCAG
1 TAACTGAGCACTATGTGTGCGAGATTAG
* * **
28544390 TAATTGAGGCACTGTGTGTGCGA-ATTCCTT
1 TAACTGA-GCACTATGTGTGCGAGATT--AG
* * *
28544420 TAACCGAGCATTATGTGTGCGAGATTGG
1 TAACTGAGCACTATGTGTGCGAGATTAG
* * **
28544448 TAATTGAGGCACTGTGTGTGCGAG-TTCT
1 TAACTGA-GCACTATGTGTGCGAGATTAG
28544476 TCAACTGAGCACTATGTGTGCGAGAT
1 T-AACTGAGCACTATGTGTGCGAGAT
28544502 CGGTCAGTGG
Statistics
Matches: 85, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
28 30 0.35
29 47 0.55
30 8 0.09
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TAACTGAGCACTATGTGTGCGAGATTAG
Found at i:28544515 original size:28 final size:28
Alignment explanation
Indices: 28544369--28544523 Score: 80
Period size: 29 Copynumber: 5.4 Consensus size: 28
28544359 CGTTAACCGA
* * *
28544369 GCACTATGTGTGCGAGATCAGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* ** * * *
28544398 GCACTGTGTGTGCGA-ATTCCTTTAACCGA
1 GCACTATGTGTGCGAGA-T-CGGTCACTGG
* * * *
28544427 GCATTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* * * *
28544456 GCACTGTGTGTGCGAGTTC-TTCAACTGA
1 GCACTATGTGTGCGAGATCGGTC-ACTGG
*
28544484 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCACTGG
*
28544512 GCACTAAGTGTG
1 GCACTATGTGTG
28544524 TGAAATGAGA
Statistics
Matches: 92, Mismatches: 28, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
28 37 0.40
29 49 0.53
30 6 0.07
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCACTGG
Found at i:28544525 original size:58 final size:58
Alignment explanation
Indices: 28544337--28544505 Score: 252
Period size: 58 Copynumber: 2.9 Consensus size: 58
28544327 CGAATGATTA
* *
28544337 GAGGCACTGTGTGTGCAAATTCCGTT-AACCGAGCACTATGTGTGCGAGATCAGTAATT
1 GAGGCACTGTGTGTGCGAATTCC-TTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
* * *
28544395 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCATTATGTGTGCGAGATTGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
* *
28544453 GAGGCACTGTGTGTGCGAGTT-CTTCAACTGAGCACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGT
28544506 CAGTGGGCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
57 30 0.30
58 71 0.70
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
Found at i:28547968 original size:48 final size:48
Alignment explanation
Indices: 28547897--28548100 Score: 318
Period size: 48 Copynumber: 4.2 Consensus size: 48
28547887 CAAGATAAAT
* * *
28547897 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
**
28547945 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
28547993 ATAAATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 AT--ATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
28548043 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
28548091 ATGTGTATAT
1 ATATGTATAT
28548101 ATTGTGGCCG
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
48 98 0.69
50 44 0.31
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:28548102 original size:98 final size:98
Alignment explanation
Indices: 28547899--28548092 Score: 343
Period size: 98 Copynumber: 2.0 Consensus size: 98
28547889 AGATAAATAT
* *
28547899 ATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAG
1 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
28547964 CCGAATGGCTAACATGAAATATGTATGAGATAA
66 CCGAATGGCTAACATGAAATATGTATGAGATAA
*
28547997 ATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
1 ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
**
28548062 CCGAATGGCTAATGTGAAATATGTATGAGAT
66 CCGAATGGCTAACATGAAATATGTATGAGAT
28548093 GTGTATATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.31
Consensus pattern (98 bp):
ATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
CCGAATGGCTAACATGAAATATGTATGAGATAA
Found at i:28548325 original size:36 final size:37
Alignment explanation
Indices: 28548233--28548341 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
28548223 GGAAATATAT
28548233 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
28548270 TCCGAGTAAGACCTGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28548307 TCCGGGT-AGACCCGATGACTACGTGTGGGGATTAT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
28548342 TCGAGCTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 25 0.38
37 40 0.62
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28555627 original size:40 final size:40
Alignment explanation
Indices: 28555481--28555613 Score: 232
Period size: 40 Copynumber: 3.3 Consensus size: 40
28555471 GGACTAAGAT
28555481 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
28555521 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
28555561 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
28555601 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28555614 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 88 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:28558503 original size:15 final size:15
Alignment explanation
Indices: 28558483--28558512 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28558473 ATTTATTTGC
28558483 ATTATTATTACTATT
1 ATTATTATTACTATT
*
28558498 ATTATTATTTCTATT
1 ATTATTATTACTATT
28558513 TTTTTAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTACTATT
Found at i:28559090 original size:27 final size:26
Alignment explanation
Indices: 28559048--28559118 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 26
28559038 TACTTTGTGA
28559048 ATTATTTATCTT-AATTT-ATTTAACAT
1 ATTATTTAT-TTAAATTTGATTT-ACAT
* *
28559074 ATTATTTATTTGAAATTTGCTTTATAT
1 ATTATTTATTT-AAATTTGATTTACAT
28559101 ATTATGTTATTTCAAATT
1 ATTAT-TTATTT-AAATT
28559119 GTTTTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
26 9 0.24
27 13 0.34
28 14 0.37
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTATTTATTTAAATTTGATTTACAT
Found at i:28559124 original size:27 final size:27
Alignment explanation
Indices: 28559072--28559133 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28559062 TTTATTTAAC
*
28559072 ATATTATTTATTTGAAATTTGCTTTAT
1 ATATTATTTATTTCAAATTTGCTTTAT
*
28559099 ATATTATGTTATTTCAAA-TTGTTTTAT
1 ATATTAT-TTATTTCAAATTTGCTTTAT
*
28559126 ATTTTATT
1 ATATTATT
28559134 CATGTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (27 bp):
ATATTATTTATTTCAAATTTGCTTTAT
Found at i:28560499 original size:20 final size:20
Alignment explanation
Indices: 28560474--28560518 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28560464 AGGGACTAAA
* *
28560474 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
28560494 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
28560514 ATGAA
1 ATGAA
28560519 TACAAGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:28567766 original size:3 final size:3
Alignment explanation
Indices: 28567723--28567748 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28567713 ACTATTTTCG
28567723 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
28567749 ACGTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28568035 original size:3 final size:3
Alignment explanation
Indices: 28567990--28568021 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28567980 TATACATTTA
28567990 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28568022 GTTTTGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28568580 original size:3 final size:3
Alignment explanation
Indices: 28568572--28568612 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28568562 CATTGTTTGC
28568572 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28568613 ATATACTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28580791 original size:43 final size:44
Alignment explanation
Indices: 28580727--28580821 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
28580717 GCCTCAGCGA
* * *
28580727 AGCAGATTGAAGTCACTAGTCTTATCTCCCTGAAGT-GCAGTGG
1 AGCAGACTGAAGTCACAAGTCTCATCTCCCTGAAGTCGCAGTGG
* * *
28580770 AGTAGACTGAAGTTACAAGTCTCATCTCCTTGAAGTCGCAGTGG
1 AGCAGACTGAAGTCACAAGTCTCATCTCCCTGAAGTCGCAGTGG
28580814 AGCAGACT
1 AGCAGACT
28580822 AAATGTACAG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 30 0.68
44 14 0.32
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
AGCAGACTGAAGTCACAAGTCTCATCTCCCTGAAGTCGCAGTGG
Found at i:28581390 original size:41 final size:42
Alignment explanation
Indices: 28581345--28581462 Score: 186
Period size: 41 Copynumber: 2.9 Consensus size: 42
28581335 AAAGCCATAG
28581345 CAGATCTCCTTGAAGTTTCA-TGGAATTGATCGAAGCTACAA
1 CAGATCTCCTTGAAGTTTCAGTGGAATTGATCGAAGCTACAA
* * *
28581386 CAGATCTCCTTGAAGTTTCAGTGG-ATTAAGCGAAGCTACAG
1 CAGATCTCCTTGAAGTTTCAGTGGAATTGATCGAAGCTACAA
*
28581427 CAGATCTCCTTGAAGTTTCAGTGGAATTGATTGAAG
1 CAGATCTCCTTGAAGTTTCAGTGGAATTGATCGAAG
28581463 TCACGTGTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 58 0.84
42 11 0.16
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
CAGATCTCCTTGAAGTTTCAGTGGAATTGATCGAAGCTACAA
Found at i:28583073 original size:14 final size:14
Alignment explanation
Indices: 28583054--28583082 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28583044 TACATTTTAT
28583054 TATTATTATTATTA
1 TATTATTATTATTA
28583068 TATTATTATTATTA
1 TATTATTATTATTA
28583082 T
1 T
28583083 TAGTTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:28583073 original size:17 final size:17
Alignment explanation
Indices: 28583051--28583084 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28583041 GTATACATTT
28583051 TATTATTATTATTATTA
1 TATTATTATTATTATTA
28583068 TATTATTATTATTATTA
1 TATTATTATTATTATTA
28583085 GTTTTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:28583098 original size:3 final size:3
Alignment explanation
Indices: 28583050--28583084 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
28583040 CGTATACATT
28583050 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28583085 GTTTTGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28585500 original size:5 final size:5
Alignment explanation
Indices: 28585490--28585517 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28585480 TTTTTTACAA
28585490 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
28585518 GGGTATACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:28588075 original size:2 final size:2
Alignment explanation
Indices: 28588068--28588097 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28588058 AACGCCTTAA
28588068 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28588098 TCCCCCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28595163 original size:23 final size:23
Alignment explanation
Indices: 28595129--28595183 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
28595119 ATTTGATTTT
* *
28595129 TAAT-TTTTGAATTACTTAGTGA
1 TAATATTTAGAATTACTTAATGA
*
28595151 TAATATTTAGAATTATTTAATGA
1 TAATATTTAGAATTACTTAATGA
28595174 TAATATTTAG
1 TAATATTTAG
28595184 GAAAAATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (23 bp):
TAATATTTAGAATTACTTAATGA
Found at i:28597889 original size:34 final size:34
Alignment explanation
Indices: 28597845--28597919 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
28597835 ATAAATGTAT
* *
28597845 ATATATATTCA-TCTTCGGTTATATCAAACCATAC
1 ATATATATTCACT-TTCGATTATACCAAACCATAC
* * *
28597879 ATATGTATTCACTTTCTATTATACCAAACTATAC
1 ATATATATTCACTTTCGATTATACCAAACCATAC
28597913 ATATATA
1 ATATATA
28597920 ATTATGTACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (34 bp):
ATATATATTCACTTTCGATTATACCAAACCATAC
Found at i:28612455 original size:26 final size:26
Alignment explanation
Indices: 28612422--28612474 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28612412 CCGAAGGTAT
28612422 CAGGGTAGATCCAAGTAAAATCTCAG
1 CAGGGTAGATCCAAGTAAAATCTCAG
28612448 CAGGGTAGATCCAAGTAAAATCTCAG
1 CAGGGTAGATCCAAGTAAAATCTCAG
28612474 C
1 C
28612475 TATTGTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (26 bp):
CAGGGTAGATCCAAGTAAAATCTCAG
Found at i:28616373 original size:41 final size:41
Alignment explanation
Indices: 28616274--28616366 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
28616264 TTATAGCTAA
*
28616274 CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAGCGCCG
1 CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAACGCCG
* *
28616315 CTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAACGTCG
1 CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAACGCCG
*
28616356 CTATTGCTCTG
1 CTAATGCTCTG
28616367 TATTTTATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (41 bp):
CTAATGCTCTGGTTTTTAACGGCGTTTTACCAAAAACGCCG
Found at i:28617055 original size:6 final size:6
Alignment explanation
Indices: 28617044--28617073 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
28617034 ACTGCATTTG
28617044 AAAATA AAAATA AAAATA AAAATA ATAAAT
1 AAAATA AAAATA AAAATA AAAATA A-AAAT
28617074 TGATAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:28625336 original size:53 final size:55
Alignment explanation
Indices: 28625273--28625412 Score: 171
Period size: 53 Copynumber: 2.6 Consensus size: 55
28625263 TTTTGAACAT
* *
28625273 ACCATTGCCATGTCTTGACATGGTCTTA-AGTGGTATCC-TTGCCTTAT-G-AACTC
1 ACCAATGCCATGTCTTGACATGGTCTTACA-TGGGA-CCATTGCCTTATAGTAACTC
* *
28625326 ACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCATTGCCTTATAGTAACTC
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGACCATTGCCTTATAGTAACTC
* * *
28625381 ATCAATGCCATGTCTTGAAATGGTCTTTCATG
1 ACCAATGCCATGTCTTGACATGGTCTTACATG
28625413 ATTTCCTTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
52 2 0.03
53 38 0.51
54 2 0.03
55 32 0.43
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (55 bp):
ACCAATGCCATGTCTTGACATGGTCTTACATGGGACCATTGCCTTATAGTAACTC
Found at i:28625458 original size:54 final size:55
Alignment explanation
Indices: 28625278--28625474 Score: 206
Period size: 55 Copynumber: 3.6 Consensus size: 55
28625268 AACATACCAT
* * * *
28625278 TGCCATGTCTTGACATGGTCTTA-AGTGGTATCCTTGCCTTAT-G-AACTCACCAA
1 TGCCATGCCTTGGCATGGTCTTACA-TGATATCCTTGCCTTATAGTAACTCATCAA
**
28625331 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCATTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCC-TTGCCTTATAGTAACTCATCAA
* ** * * * * *
28625386 TGCCATGTCTTGAAATGGTCTTTCATGATTTCCTTTCCTTTTAG-AACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGTAACTCATCAA
*
28625440 TTCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
28625475 ATCTTACCGA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 40 0.34
55 41 0.34
56 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (55 bp):
TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGTAACTCATCAA
Found at i:28626614 original size:66 final size:69
Alignment explanation
Indices: 28626485--28626614 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 69
28626475 GGGATGTATC
* *
28626485 CCATATAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATATAGACAAGAGAGCTACG-GAGAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
28626550 AGGACA
64 AGGACA
* * *
28626556 CCATGTAGACAAGAGAGCTAC-GAGA-A-AAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATATAGACAAGAGAGCTACGGAGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
28626615 TTCACCATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
66 23 0.43
67 4 0.08
68 2 0.04
69 4 0.08
71 20 0.38
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (69 bp):
CCATATAGACAAGAGAGCTACGGAGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAG
GACA
Found at i:28627966 original size:44 final size:44
Alignment explanation
Indices: 28627899--28627985 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
28627889 GTTACATTAA
* *
28627899 CCGTCAATTCTTCCTTAAATGCCATGTTATGAA-CATGGACTTTT
1 CCGTCAATTCTTCCTTAAATGCCATGGTA-CAACCATGGACTTTT
*
28627943 CCGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CCGTCAATTCTTCCTTAAATGCCATGGTACAACCATGGACTTT
28627986 GAGATATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 2 0.05
44 37 0.95
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (44 bp):
CCGTCAATTCTTCCTTAAATGCCATGGTACAACCATGGACTTTT
Found at i:28631055 original size:489 final size:489
Alignment explanation
Indices: 28630137--28631113 Score: 1918
Period size: 489 Copynumber: 2.0 Consensus size: 489
28630127 ATACTAACTA
28630137 TAATAGCTTCTGAGATACTTGAAAATCAACTTTAACTCTCTAAAAGTTTAGGTATCGGATTCAAA
1 TAATAGCTTCTGAGATACTTGAAAATCAACTTTAACTCTCTAAAAGTTTAGGTATCGGATTCAAA
28630202 GTCTGGTACATAACATTTCACACTCTTACTAGTATAACTAAATCAAGTTATCATCCATCTCCGTA
66 GTCTGGTACATAACATTTCACACTCTTACTAGTATAACTAAATCAAGTTATCATCCATCTCCGTA
28630267 CTTCTTAAATAATCAAATAATTATCATTGTGCTAGGCATCATAACTGTTGCAAAATCTCTTGATT
131 CTTCTTAAATAATCAAATAATTATCATTGTGCTAGGCATCATAACTGTTGCAAAATCTCTTGATT
28630332 TCTCATTAACACATTTCTACAAACCATAAACTCTTTATTCAAACCAAGCTGAATCATAATGGATA
196 TCTCATTAACACATTTCTACAAACCATAAACTCTTTATTCAAACCAAGCTGAATCATAATGGATA
28630397 CTTCAATTATCAATATCTTCAAATGTTTATACTTTATTAGCATGAATTTAAGCCAAACTAAACTT
261 CTTCAATTATCAATATCTTCAAATGTTTATACTTTATTAGCATGAATTTAAGCCAAACTAAACTT
28630462 CATACAATGAGAACTTTAACAATCAGACTTGGATTTGCAAAAATATACCTCTGATGCAACCATTC
326 CATACAATGAGAACTTTAACAATCAGACTTGGATTTGCAAAAATATACCTCTGATGCAACCATTC
28630527 TTATATGCGTGTACAACTCAGTATCATAACCTCTAGAATATGTACTATTTACTCAGGTCATTTAT
391 TTATATGCGTGTACAACTCAGTATCATAACCTCTAGAATATGTACTATTTACTCAGGTCATTTAT
28630592 CTATTTATACATGAACAATCAGCATTTAACTCTC
456 CTATTTATACATGAACAATCAGCATTTAACTCTC
28630626 TAATAGCTTCTGAGATACTTGAAAATCAACTTTAACTCTCTAAAAGTTTAGGTATCGGATTCAAA
1 TAATAGCTTCTGAGATACTTGAAAATCAACTTTAACTCTCTAAAAGTTTAGGTATCGGATTCAAA
*
28630691 TTCTGGTACATAACATTTCACACTCTTACTAGTATAACTAAATCAAGTTATCATCCATCTCCGTA
66 GTCTGGTACATAACATTTCACACTCTTACTAGTATAACTAAATCAAGTTATCATCCATCTCCGTA
28630756 CTTCTTAAATAATCAAATAATTATCATTGTGCTAGGCATCATAACTGTTGCAAAATCTCTTGATT
131 CTTCTTAAATAATCAAATAATTATCATTGTGCTAGGCATCATAACTGTTGCAAAATCTCTTGATT
28630821 TCTCATTAACACATTTCTACAAACCATAAACTCTTTATTCAAACCAAGCTGAATCATAATGGATA
196 TCTCATTAACACATTTCTACAAACCATAAACTCTTTATTCAAACCAAGCTGAATCATAATGGATA
*
28630886 CTTCAATTGTCAATATCTTCAAATGTTTATACTTTATTAGCATGAATTTAAGCCAAACTAAACTT
261 CTTCAATTATCAATATCTTCAAATGTTTATACTTTATTAGCATGAATTTAAGCCAAACTAAACTT
28630951 CATACAATGAGAACTTTAACAATCAGACTTGGATTTGCAAAAATATACCTCTGATGCAACCATTC
326 CATACAATGAGAACTTTAACAATCAGACTTGGATTTGCAAAAATATACCTCTGATGCAACCATTC
28631016 TTATATGCGTGTACAACTCAGTATCATAACCTCTAGAATATGTACTATTTACTCAGGTCATTTAT
391 TTATATGCGTGTACAACTCAGTATCATAACCTCTAGAATATGTACTATTTACTCAGGTCATTTAT
* *
28631081 TTATTTATACATGAACAATCAGCATTTATCTCT
456 CTATTTATACATGAACAATCAGCATTTAACTCT
28631114 GAAGCCATGA
Statistics
Matches: 484, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
489 484 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (489 bp):
TAATAGCTTCTGAGATACTTGAAAATCAACTTTAACTCTCTAAAAGTTTAGGTATCGGATTCAAA
GTCTGGTACATAACATTTCACACTCTTACTAGTATAACTAAATCAAGTTATCATCCATCTCCGTA
CTTCTTAAATAATCAAATAATTATCATTGTGCTAGGCATCATAACTGTTGCAAAATCTCTTGATT
TCTCATTAACACATTTCTACAAACCATAAACTCTTTATTCAAACCAAGCTGAATCATAATGGATA
CTTCAATTATCAATATCTTCAAATGTTTATACTTTATTAGCATGAATTTAAGCCAAACTAAACTT
CATACAATGAGAACTTTAACAATCAGACTTGGATTTGCAAAAATATACCTCTGATGCAACCATTC
TTATATGCGTGTACAACTCAGTATCATAACCTCTAGAATATGTACTATTTACTCAGGTCATTTAT
CTATTTATACATGAACAATCAGCATTTAACTCTC
Found at i:28634838 original size:54 final size:54
Alignment explanation
Indices: 28634687--28634855 Score: 193
Period size: 55 Copynumber: 3.1 Consensus size: 54
28634677 GGTCTCGTGG
* * *
28634687 TATCCTTGCCTTAT-GAACTCA-CTAATTCCATGCCTTGGCATGCTCTTACATGG
1 TATCCTTGCCTTATAGAACTCATC-AATTCCATGCCTTTGCATGGTCTTACATGA
* * * *
28634740 GA-CCTTTACCTTATAGTAAGTCATCAATTCCATGTC-TTGACATGGTCTTACATGA
1 TATCC-TTGCCTTATAG-AACTCATCAATTCCATGCCTTTG-CATGGTCTTACATGA
* *
28634795 TTTCCTTGCCTTATAGAACTTATCAATTCCATGCCTTTGCATGGTCTTACATGA
1 TATCCTTGCCTTATAGAACTCATCAATTCCATGCCTTTGCATGGTCTTACATGA
28634849 TATCCTT
1 TATCCTT
28634856 ATCTTACCAA
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
52 2 0.02
53 9 0.09
54 40 0.42
55 41 0.43
56 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (54 bp):
TATCCTTGCCTTATAGAACTCATCAATTCCATGCCTTTGCATGGTCTTACATGA
Found at i:28635095 original size:44 final size:44
Alignment explanation
Indices: 28635044--28635130 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
28635034 GTATCCTTAA
* *
28635044 CCGTCAATTCCTCCTGAAATGCCATGTTATGAA-CATGGACTTTT
1 CCGTCAATTCCTCCTGAAATGCCATGGTA-CAACCATGGACTTTT
* * *
28635088 CCGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CCGTCAATTCCTCCTGAAATGCCATGGTACAACCATGGACTTT
28635131 GAGATATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.34
Consensus pattern (44 bp):
CCGTCAATTCCTCCTGAAATGCCATGGTACAACCATGGACTTTT
Found at i:28640584 original size:55 final size:55
Alignment explanation
Indices: 28640518--28640628 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
28640508 AACCCTAATC
* *
28640518 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAGAGTTATGGTT
1 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAAAGCTATGGTT
28640573 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAAAGCTATGGTT
1 TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAAAGCTATGGTT
28640628 T
1 T
28640629 AGTCAGTTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (55 bp):
TGGTGTTGGATATGGGTTAGGGGTGTTACATTTAGTTAGTATCAAAGCTATGGTT
Found at i:28648379 original size:40 final size:40
Alignment explanation
Indices: 28648344--28648495 Score: 261
Period size: 40 Copynumber: 3.8 Consensus size: 40
28648334 GGATATAGCC
*
28648344 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
28648384 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28648424 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28648464 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
28648496 TTATCATCTG
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
40 106 0.98
41 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:28654855 original size:12 final size:12
Alignment explanation
Indices: 28654838--28654862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28654828 TTATTATAGT
28654838 AAATGATAATTA
1 AAATGATAATTA
28654850 AAATGATAATTA
1 AAATGATAATTA
28654862 A
1 A
28654863 CTGAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AAATGATAATTA
Found at i:28655157 original size:20 final size:20
Alignment explanation
Indices: 28655108--28655157 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28655098 ATGTGTATTT
*
28655108 TGAAGTTTCTTGATAGATTA
1 TGAAGTTTGTTGATAGATTA
*
28655128 TGAATATTTGTTGATAG-TTA
1 TGAA-GTTTGTTGATAGATTA
28655148 TGTAAGTTTG
1 TG-AAGTTTG
28655158 GTAAAGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (20 bp):
TGAAGTTTGTTGATAGATTA
Found at i:28659768 original size:25 final size:26
Alignment explanation
Indices: 28659710--28659769 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 26
28659700 TAGAGCGTAT
28659710 TTAGA-TAGATTTGTTGTTGTGTTTA
1 TTAGACTAGATTTGTTGTTGTGTTTA
28659735 TTGACGACTAGATTTGTTGTTGTGTTTA
1 TT-A-GACTAGATTTGTTGTTGTGTTTA
28659763 TT-GACTA
1 TTAGACTA
28659770 CATTCTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 7 0.22
26 1 0.03
27 2 0.06
28 22 0.69
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.52
Consensus pattern (26 bp):
TTAGACTAGATTTGTTGTTGTGTTTA
Found at i:28665739 original size:14 final size:14
Alignment explanation
Indices: 28665722--28665760 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
28665712 TCAAAACAAG
28665722 AATTTAGAACACAT
1 AATTTAGAACACAT
28665736 AATTTAGAACACAT
1 AATTTAGAACACAT
*
28665750 AATTAAGAACA
1 AATTTAGAACA
28665761 AATCAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.26
Consensus pattern (14 bp):
AATTTAGAACACAT
Found at i:28668035 original size:44 final size:42
Alignment explanation
Indices: 28667963--28668069 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 42
28667953 TGTGTTTTCA
* * **
28667963 TGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTATGATTTATG
1 TGTAAGACCATGTCTGGGACATCAGCATCGTA-TT-TGATTT-TG
*
28668007 TGTAAGACCATGTCTGGGATATCAGCATCGTATTTGATTTTG
1 TGTAAGACCATGTCTGGGACATCAGCATCGTATTTGATTTTG
*
28668049 TGTAAGACCCTGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
28668070 GTGGCATCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 21 0.38
43 6 0.11
44 27 0.49
45 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATCAGCATCGTATTTGATTTTG
Found at i:28668077 original size:42 final size:43
Alignment explanation
Indices: 28667963--28668088 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 43
28667953 TGTGTTTTCA
28667963 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCG-ACTTATGATTTATG
1 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGTA-TT-TGATTTATG
* * *
28668007 TGTAAGACCATGTCTGGGATA-TCAGCATCGTATTTGATTT-TG
1 TGTAAGACCCTGTCTGGGACAGT-GGCATCGTATTTGATTTATG
*
28668049 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATATGATT
1 TGTAAGACCCTGTCTGGGACAGTGGCATCG-TATTTGATT
28668089 ACATGTAAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
42 27 0.39
43 16 0.23
44 25 0.36
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTAAGACCCTGTCTGGGACAGTGGCATCGTATTTGATTTATG
Found at i:28668110 original size:43 final size:43
Alignment explanation
Indices: 28667961--28668119 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
28667951 TATGTGTTTT
28667961 CATGTAAGACCACGTCTGGGACGTTGGCATCGACT-TATGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGA-TATATGA-TTA
** * ** ** * *
28668005 TGTGTAAGACCATGTCTGGGATATCAGCATCG-TATTTGATTT
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
**
28668047 TGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATATGATTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATATGATTA
*
28668090 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
28668120 TGTATGAGCG
Statistics
Matches: 90, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
42 29 0.32
43 35 0.39
44 26 0.29
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
Found at i:28669644 original size:12 final size:12
Alignment explanation
Indices: 28669627--28669664 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28669617 TTATTATAGT
28669627 AAATGATAATTA
1 AAATGATAATTA
28669639 AAATGATAATT-
1 AAATGATAATTA
*
28669650 AAATGA-AAATA
1 AAATGATAATTA
28669661 AAAT
1 AAAT
28669665 ACAAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 10 0.42
12 11 0.46
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (12 bp):
AAATGATAATTA
Found at i:28676376 original size:18 final size:21
Alignment explanation
Indices: 28676338--28676376 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
28676328 AGTATGTCAG
28676338 TTGTGGAATATGAACGTAAGT
1 TTGTGGAATATGAACGTAAGT
28676359 TTGT-GAATAT-AA-GTAAGT
1 TTGTGGAATATGAACGTAAGT
28676377 ATGCTCGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 6 0.33
21 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGTGGAATATGAACGTAAGT
Found at i:28685526 original size:55 final size:54
Alignment explanation
Indices: 28685384--28685577 Score: 237
Period size: 55 Copynumber: 3.6 Consensus size: 54
28685374 TTACCATTAC
* * *
28685384 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCATTGT
1 CATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTTACCAATGT
* * ** *
28685437 CATGCCTTGGCATGGTCTTACATGGTATCTTTGCCTTATAGTAGTTTATCAATGT
1 CATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG-AACTTACCAATGT
* * * * *
28685492 CATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAAAACTTACCAATGC
1 CATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTTACCAATGT
* *
28685546 CATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 CATGCCTTGACATGGTCTTACATGGTATCCTT
28685578 AAACCCTAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
53 36 0.31
54 37 0.32
55 43 0.37
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (54 bp):
CATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTTACCAATGT
Found at i:28687465 original size:5 final size:5
Alignment explanation
Indices: 28687455--28687530 Score: 62
Period size: 5 Copynumber: 13.6 Consensus size: 5
28687445 TCACCCCCAT
* *
28687455 TTTTA TTTTA TTTTA TTTTA TTTATTA TTTGTT TTATTA TTTATT TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TT-TTA TTT-TA TT-TTA TTT-TA TTTTA
28687505 TTTTA CTAATTTA TTTTA TTTTA TTT
1 TTTTA -T--TTTA TTTTA TTTTA TTT
28687531 ATTATTCTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
5 35 0.59
6 15 0.25
7 5 0.08
8 4 0.07
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:28687605 original size:18 final size:18
Alignment explanation
Indices: 28687565--28687604 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
28687555 ATTAATTTTA
28687565 ATTTTAATTTTTTTAGCT
1 ATTTTAATTTTTTTAGCT
28687583 ATTTTAATTTTTTTAG-T
1 ATTTTAATTTTTTTAGCT
28687600 ATTTT
1 ATTTT
28687605 TTTACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (18 bp):
ATTTTAATTTTTTTAGCT
Found at i:28689426 original size:55 final size:55
Alignment explanation
Indices: 28689236--28689490 Score: 235
Period size: 55 Copynumber: 4.8 Consensus size: 55
28689226 ACACGGGTAC
* * * * *
28689236 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA----T-CCTT-TCGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAGAAA
* * * * *
28689285 CTTACCATTGCCATGTCTCGACAAGGTCTTACATGGTATCTTTGCCTTAT-G-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAGAAA
* * *
28689338 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAGAAA
** * *
28689393 CTTATTAATGCCATGTCTTGACATGGTCTTACATGATATCC-TTGCC-T-TAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTTGCCTTATAGAAA
*
28689446 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
28689491 AAATCCTAAT
Statistics
Matches: 169, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
49 33 0.20
53 51 0.30
54 13 0.08
55 69 0.41
56 3 0.02
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (55 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTTGCCTTATAGAAA
Found at i:28692889 original size:47 final size:47
Alignment explanation
Indices: 28692825--28692987 Score: 158
Period size: 47 Copynumber: 3.5 Consensus size: 47
28692815 ATTCATAGGT
*
28692825 GAACTCGAACCCAACTCAACGAGCTTGGATGCCTAGTTACATCTCAC
1 GAACTCGAACTCAACTCAACGAGCTTGGATGCCTAGTTACATCTCAC
* * * * *
28692872 GAACTCGGACTCAACTCAACAAG-TTCGGATGTTCGC-AG--CCA--TAAGT
1 GAACTCGAACTCAACTCAACGAGCTT-GGATG--C-CTAGTTACATCTCA-C
* *
28692918 GAACTCGAACTCAACTCAACGAGCTCGAATGCCTAGTTACATCTCAC
1 GAACTCGAACTCAACTCAACGAGCTTGGATGCCTAGTTACATCTCAC
*
28692965 GAACTCGGACTCAACTCAACGAG
1 GAACTCGAACTCAACTCAACGAG
28692988 TTCAGACGTT
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 29 0.32
47 50 0.55
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.20
Consensus pattern (47 bp):
GAACTCGAACTCAACTCAACGAGCTTGGATGCCTAGTTACATCTCAC
Found at i:28692932 original size:46 final size:45
Alignment explanation
Indices: 28692872--28693041 Score: 139
Period size: 46 Copynumber: 3.7 Consensus size: 45
28692862 TACATCTCAC
*
28692872 GAACTCGGACTCAACTCAACAAGTTCGGATGTTCGCAGCCATAAGT
1 GAACTCGAACTCAACTCAACAAGTTCGGATGTTCGCAGCCATAA-T
* * * * * *
28692918 GAACTCGAACTCAACTCAACGAGCTCGAATG--C-CTAGTTACATCTCAC
1 GAACTCGAACTCAACTCAACAAGTTCGGATGTTCGC-AG--CCA--TAAT
* * * * * *
28692965 GAACTCGGACTCAACTCAACGAGTTCAGACGTTTGCATCCATAAAT
1 GAACTCGAACTCAACTCAACAAGTTCGGATGTTCGCAGCCAT-AAT
28693011 GAACTCGAACTCAACTCAACAAGTTCGGATG
1 GAACTCGAACTCAACTCAACAAGTTCGGATG
28693042 CCCAAATATC
Statistics
Matches: 94, Mismatches: 21, Indels: 18
0.71 0.16 0.14
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 57 0.61
47 28 0.30
48 2 0.02
49 1 0.01
50 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (45 bp):
GAACTCGAACTCAACTCAACAAGTTCGGATGTTCGCAGCCATAAT
Found at i:28692938 original size:93 final size:93
Alignment explanation
Indices: 28692779--28693043 Score: 370
Period size: 93 Copynumber: 2.8 Consensus size: 93
28692769 GCCCATAAGT
* * * * * * *
28692779 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCACATTCATAGGTGAACTCGAACCCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
28692844 CGAGCTTGGATGCCTAGTTACATCTCAC
66 CGAGCTTGGATGCCTAGTTACATCTCAC
* * *
28692872 GAACTCGGACTCAACTCAACAAGTTCGGATGTTCGCAGCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
* *
28692937 CGAGCTCGAATGCCTAGTTACATCTCAC
66 CGAGCTTGGATGCCTAGTTACATCTCAC
* * *
28692965 GAACTCGGACTCAACTCAACGAGTTCAGACGTTTGCATCCATAAATGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
28693030 CAAG-TTCGGATGCC
66 CGAGCTT-GGATGCC
28693044 CAAATATCCG
Statistics
Matches: 150, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
92 1 0.01
93 149 0.99
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTTGGATGCCTAGTTACATCTCAC
Found at i:28700512 original size:27 final size:29
Alignment explanation
Indices: 28700444--28700514 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
28700434 TAGATCAAGT
* *
28700444 ATAACACATATAAAACGTTGAATCAAATA
1 ATAACACACATAAAGCGTTGAATCAAATA
28700473 ATAACACACATAAAGCGTTGAATC-AAT-
1 ATAACACACATAAAGCGTTGAATCAAATA
* *
28700500 GTAACACGCATAAAG
1 ATAACACACATAAAG
28700515 TGCAGGATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 13 0.34
28 3 0.08
29 22 0.58
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (29 bp):
ATAACACACATAAAGCGTTGAATCAAATA
Found at i:28704659 original size:37 final size:37
Alignment explanation
Indices: 28704602--28704746 Score: 166
Period size: 37 Copynumber: 3.9 Consensus size: 37
28704592 ATCCAACCGA
28704602 AACACGCCAATCGC-CTATAAGAGCTAATCCACCCAAT
1 AACACGCCAATCGCTC-ATAAGAGCTAATCCACCCAAT
* * * *
28704639 AACATGCCAATTGCTCATAAGATCTAATCCACCCGAT
1 AACACGCCAATCGCTCATAAGAGCTAATCCACCCAAT
* * * *
28704676 AACCCACTAATCGGTCATAAGAGCTAATCCACCCAAT
1 AACACGCCAATCGCTCATAAGAGCTAATCCACCCAAT
* * * *
28704713 AACACGACAATCGCTCACAAAAGCCAATCCACCC
1 AACACGCCAATCGCTCATAAGAGCTAATCCACCC
28704747 GGTAACACAC
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
37 86 0.99
38 1 0.01
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.17
Consensus pattern (37 bp):
AACACGCCAATCGCTCATAAGAGCTAATCCACCCAAT
Found at i:28705652 original size:36 final size:36
Alignment explanation
Indices: 28705605--28705674 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
28705595 GTGTATTCGG
28705605 TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTTAT
1 TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTTAT
* *
28705641 TTATGAAGAAGAGAAATGAAGACGAAAGTAGCTT
1 TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTT
28705675 TTACTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.21
Consensus pattern (36 bp):
TTATGAAGAAGAGAAATGAAAAAGAAAGTAGCTTAT
Found at i:28711164 original size:29 final size:29
Alignment explanation
Indices: 28711132--28711215 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
28711122 TACACACAGC
* *
28711132 CATGTCACATGTCGTGTGTGGCACATGGA
1 CATGTCACAGGTCGTGTGTGGCACACGGA
*
28711161 CATGTCGCAGGTCGTGTGTGGCACACGGA
1 CATGTCACAGGTCGTGTGTGGCACACGGA
*
28711190 CATGTTACAGGTCGTGTGTGGCACAC
1 CATGTCACAGGTCGTGTGTGGCACAC
28711216 AGCCAAGTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (29 bp):
CATGTCACAGGTCGTGTGTGGCACACGGA
Found at i:28711231 original size:31 final size:29
Alignment explanation
Indices: 28711124--28711231 Score: 99
Period size: 29 Copynumber: 3.7 Consensus size: 29
28711114 TGACTTAATA
* * *
28711124 CACACAGCCATGTCACATGTCGTGTGTGG
1 CACACAGACATGGCACAGGTCGTGTGTGG
** * *
28711153 CACATGGACATGTCGCAGGTCGTGTGTGG
1 CACACAGACATGGCACAGGTCGTGTGTGG
* **
28711182 CACACGGACATGTTACAGGTCGTGTGTGG
1 CACACAGACATGGCACAGGTCGTGTGTGG
*
28711211 CACACAGCCAAGTGGCACAGG
1 CACACAGAC-A-TGGCACAGG
28711232 CCTGTCCCAG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 57 0.88
30 1 0.02
31 7 0.11
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.20
Consensus pattern (29 bp):
CACACAGACATGGCACAGGTCGTGTGTGG
Found at i:28712216 original size:37 final size:37
Alignment explanation
Indices: 28712113--28712233 Score: 113
Period size: 37 Copynumber: 3.3 Consensus size: 37
28712103 ATCCAACCGA
** * * *
28712113 AACACGCCAATCATTCATAAGAGCGAATCCACTCGAT
1 AACACGCCAATCGCTCCTAAAAGAGAATCCACTCGAT
*
28712150 AACATGCCAAAT-GCT-C-AAAAGAGCTAATCCACTCGAT
1 AACACGCC-AATCGCTCCTAAAAGAG--AATCCACTCGAT
* * *
28712187 AACACGCCAATCGCTCCTAAAAGTGAATCCTCTTGAT
1 AACACGCCAATCGCTCCTAAAAGAGAATCCACTCGAT
28712224 AACACGCCAA
1 AACACGCCAA
28712234 AACAGGGAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
35 5 0.07
36 3 0.04
37 50 0.74
38 4 0.06
39 6 0.09
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (37 bp):
AACACGCCAATCGCTCCTAAAAGAGAATCCACTCGAT
Found at i:28713561 original size:16 final size:16
Alignment explanation
Indices: 28713542--28713576 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28713532 GCTGATACAA
28713542 AAACATAAGTTTAATG
1 AAACATAAGTTTAATG
* *
28713558 AAACATAATTTTATTG
1 AAACATAAGTTTAATG
28713574 AAA
1 AAA
28713577 AGGAAAAGAA
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:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (16 bp):
AAACATAAGTTTAATG
Found at i:28714297 original size:39 final size:39
Alignment explanation
Indices: 28714202--28714299 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
28714192 TTCACTTTTG
* * *
28714202 AGCATGTATCACATTACACATATAATCACATAACATTTA
1 AGCATATATCACAATACTCATATAATCACATAACATTTA
* *
28714241 GGCATACATCACAATACTCATATAATCACATAACATTTA
1 AGCATATATCACAATACTCATATAATCACATAACATTTA
28714280 AGCATATATCACAATACTCA
1 AGCATATATCACAATACTCA
28714300 AAATCATGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (39 bp):
AGCATATATCACAATACTCATATAATCACATAACATTTA
Found at i:28718156 original size:46 final size:46
Alignment explanation
Indices: 28718089--28718236 Score: 224
Period size: 46 Copynumber: 3.2 Consensus size: 46
28718079 CAGATCAATT
** *
28718089 GATTGAAGAAGCCACAAATCCTATACCCCTGAGCTGCAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
*
28718135 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTAGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * * *
28718181 GATTAAAGATGATACAAATCCTATACCCTTGAGTTGTAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
28718227 GATTGAAGAA
1 GATTGAAGAA
28718237 ACCAAATTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (46 bp):
GATTGAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
Found at i:28718691 original size:44 final size:45
Alignment explanation
Indices: 28718588--28718825 Score: 158
Period size: 44 Copynumber: 5.2 Consensus size: 45
28718578 TGAATCCATA
* * * * * **
28718588 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCA-CC
1 AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGTG
** *
28718632 AGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGTG
1 AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGTG
* * * * * * *
28718677 AATCTCA-CTTCCTGAAGTTGTAGTGGAACAGATTAAAGCTACAAATTATGG
1 AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAG--AC--A--GT-G
* * * *
28718728 CAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-TC
1 -A-ATCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGTG
* * *
28718774 AGTCTTATCTTCCTGAAGTTACAGCAGAGCAGACTGAAGACAGTG
1 AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGTG
28718819 AATCTTA
1 AATCTTA
28718826 CTTTCCTAAC
Statistics
Matches: 150, Mismatches: 32, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
44 96 0.64
45 12 0.08
46 2 0.01
47 1 0.01
48 1 0.01
50 2 0.01
51 1 0.01
52 2 0.01
53 5 0.03
54 28 0.19
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGTG
Found at i:28718971 original size:44 final size:44
Alignment explanation
Indices: 28718871--28719283 Score: 163
Period size: 44 Copynumber: 9.0 Consensus size: 44
28718861 CAAATTATGG
* * *
28718871 CGAATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGCAA
* ** * * *
28718915 CCAGCCTCATCTCCCTGAAGTTGCAGTGGAGCA-ACTGAAGATAA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAG-CAA
* * *
28718959 CGAATCTTATCTCCCTGAAGTTGCAGTGAAATAGATTGAAGCTACAAATTA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAG---C--A--A
* * * ** * *
28719010 TGGCAAATCTTATCTTCCTGATGTTGCAGTGGAGGAGATTGAAGCCA
1 ---CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGCAA
* ** * * ** *
28719057 CCAGCCTCATCTCCCTGAATTTGCAGCAGAACAGACTGAAGACAG
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAG-CAA
* *
28719102 CGAATCTTATCTTCCTGAAGTT---GTGGAACAGATTGAAGCTACAAATTA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAG---C--A--A
* * * * * *
28719150 TGGCAAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTTAAGCAA
1 ---CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGCAA
* * *
28719197 C-TAGCTTTATCTCCCTGAAGTTGCAGTGGAGA-AGACTGAAGACAG
1 CGAATC-TTATCTCCCTGAAGTTGCAGTGGA-ACAGACTGAAG-CAA
* * * * * *
28719242 CGAATCCTATTTCCCTGAAGTTACAGCGGAATAGATTGAAGC
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGC
28719284 TACAAGTCGC
Statistics
Matches: 272, Mismatches: 68, Indels: 58
0.68 0.17 0.15
Matches are distributed among these distances:
42 13 0.05
43 8 0.03
44 117 0.43
45 54 0.20
46 3 0.01
47 3 0.01
49 2 0.01
51 24 0.09
54 48 0.18
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
CGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGCAA
Found at i:28719027 original size:142 final size:143
Alignment explanation
Indices: 28718587--28719332 Score: 956
Period size: 142 Copynumber: 5.3 Consensus size: 143
28718577 ATGAATCCAT
* *
28718587 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * *
28718652 GCAGCGGAGCAGACTGAAGACAGTGAATCTCA-CTTCCTGAAGTTGTAGTGGAACAGATTAAAGC
66 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATCTTCCTGAAGTTGCAGTGGAATAGATTGAAGC
28718716 TACAAATTATGGC
131 TACAAATTATGGC
* * * *
28718729 AGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAGTCTTATCTTCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * * *
28718794 ACAGCAGAGCAGACTGAAGACAGTGAATCTTA-CTTTCCT-AACATTGCAGTGGAATAAATTAAA
66 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATC-TTCCTGAA-GTTGCAGTGGAATAGATTGAA
28718857 GCTACAAATTATGGC
129 GCTACAAATTATGGC
* * *
28718872 GAATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTCATCTCCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * *
28718937 GCAGTGGAGCA-ACTGAAGATAACGAATCTTATCTCCCTGAAGTTGCAGTGAAATAGATTGAAGC
66 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATCTTCCTGAAGTTGCAGTGGAATAGATTGAAGC
28719001 TACAAATTATGGC
131 TACAAATTATGGC
* * * *
28719014 AAATCTTATCTTCCTGATGTTGCAGTGGAGGAGATTGAAGCCACCAGCCTCATCTCCCTGAATTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * *
28719079 GCAGCAGAACAGACTGAAGACAGCGAATCTTATCTTCCTGAAGTT---GTGGAACAGATTGAAGC
66 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATCTTCCTGAAGTTGCAGTGGAATAGATTGAAGC
28719141 TACAAATTATGGC
131 TACAAATTATGGC
* * * * *
28719154 AAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTTAAGCAACTAGCTTTATCTCCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * *
28719219 GCAGTGGAGAAGACTGAAGACAGCGAATCCTAT-TTCCCTGAAGTTACAGCGGAATAGATTGAAG
66 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATCTT-CCTGAAGTTGCAGTGGAATAGATTGAAG
* *
28719283 CTAC-AA--GTCGC
130 CTACAAATTATGGC
* * * *
28719294 AAACCTTATCTCCCTGAAGTTGAAGTGGAGCAGGTTGAA
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAA
28719333 ATTACCAATT
Statistics
Matches: 527, Mismatches: 68, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
139 2 0.00
140 157 0.30
142 214 0.41
143 154 0.29
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (143 bp):
AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
GCAGCGGAGCAGACTGAAGACAGCGAATCTTATCTTCCTGAAGTTGCAGTGGAATAGATTGAAGC
TACAAATTATGGC
Found at i:28719098 original size:285 final size:283
Alignment explanation
Indices: 28718587--28719332 Score: 984
Period size: 285 Copynumber: 2.6 Consensus size: 283
28718577 ATGAATCCAT
* *
28718587 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * * * *
28718652 GCAGCGGAGCAGACTGAAGACAGTGAATCTCA-CTTCCTGAAGTTGTAGTGGAACAGATTAAAGC
66 GCAGTGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGC
* * * *
28718716 TACAAATTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCAGTCTTA
131 TACAAATTATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTCA
* * *
28718781 TCTTCCTGAAGTTACAGCAGAGCAGACTGAAGACAGTGAATCTTA-CTTTCCT-AACATTGCAGT
196 TCTCCCTGAAGTTACAGCAGAACAGACTGAAGACAGCGAATCTTATC-TTCCTGAA-ATT---GT
*
28718844 GGAATAAATTAAAGCTACAAATTATGGC
256 GGAACAAATTAAAGCTACAAATTATGGC
* * *
28718872 GAATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTCATCTCCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * *
28718937 GCAGTGGAGCA-ACTGAAGATAACGAATCTTATCTCCCTGAAGTTGCAGTGAAATAGATTGAAGC
66 GCAGTGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGC
* *
28719001 TACAAATTATGGCAAATCTTATCTTCCTGATGTTGCAGTGGAGGAGATTGAAGCCACCAGCCTCA
131 TACAAATTATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTCA
* * *
28719066 TCTCCCTGAATTTGCAGCAGAACAGACTGAAGACAGCGAATCTTATCTTCCTGAAGTTGTGGAAC
196 TCTCCCTGAAGTTACAGCAGAACAGACTGAAGACAGCGAATCTTATCTTCCTGAAATTGTGGAAC
* *
28719131 AGATTGAAGCTACAAATTATGGC
261 AAATTAAAGCTACAAATTATGGC
* * * * *
28719154 AAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTTAAGCAACTAGCTTTATCTCCCTGAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * *
28719219 GCAGTGGAGAAGACTGAAGACAGCGAATCCTATTTCCCTGAAGTTACAGCGGAATAGATTGAAGC
66 GCAGTGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGC
* * * * * *
28719284 TAC-AA--GTCGCAAACCTTATCTCCCTGAAGTTGAAGTGGAGCAGGTTGAA
131 TACAAATTATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAA
28719333 ATTACCAATT
Statistics
Matches: 403, Mismatches: 54, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
280 36 0.09
282 96 0.24
283 49 0.12
284 16 0.04
285 203 0.50
286 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (283 bp):
AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
GCAGTGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGC
TACAAATTATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTCA
TCTCCCTGAAGTTACAGCAGAACAGACTGAAGACAGCGAATCTTATCTTCCTGAAATTGTGGAAC
AAATTAAAGCTACAAATTATGGC
Found at i:28720206 original size:27 final size:28
Alignment explanation
Indices: 28720153--28720208 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
28720143 CAAAGGTTGC
*
28720153 ATTTTTATTATGTTTTTATTTTCATTTT
1 ATTTTTATTATGTTTTTAGTTTCATTTT
* * *
28720181 ATTTTT-TTATTTTTTTGGTTTGATTTT
1 ATTTTTATTATGTTTTTAGTTTCATTTT
28720208 A
1 A
28720209 CTCCTAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (28 bp):
ATTTTTATTATGTTTTTAGTTTCATTTT
Found at i:28722864 original size:10 final size:10
Alignment explanation
Indices: 28722846--28722915 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 10
28722836 TTTACATACA
28722846 TATTATATAT
1 TATTATATAT
*
28722856 TATTCTATAT
1 TATTATATAT
28722866 TATTATATCAT
1 TATTATAT-AT
* *
28722877 T-TTTTATAC
1 TATTATATAT
28722886 TATCATATATATT
1 TAT--TATATA-T
*
28722899 TATCTATATGT
1 TAT-TATATAT
28722910 TATTAT
1 TATTAT
28722916 CACTAAAGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
9 2 0.04
10 25 0.53
11 7 0.15
12 10 0.21
13 3 0.06
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (10 bp):
TATTATATAT
Found at i:28722871 original size:20 final size:19
Alignment explanation
Indices: 28722841--28722906 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
28722831 TTATTTTTAC
28722841 ATACATATTATATATTATTCT
1 ATAC-TATTATATATT-TTCT
* *
28722862 ATATTATTATATCATTTTTT
1 ATACTATTATAT-ATTTTCT
28722882 ATACTATCATATATATTTATCT
1 ATACTAT--TATATATTT-TCT
28722904 ATA
1 ATA
28722907 TGTTATTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 17 0.46
21 10 0.27
22 10 0.27
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (19 bp):
ATACTATTATATATTTTCT
Done.