Multiple sequence alignment - TraesCS7A01G317400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G317400 chr7A 100.000 4299 0 0 1 4299 457567738 457572036 0.000000e+00 7939.0
1 TraesCS7A01G317400 chr7A 99.275 138 1 0 1 138 708293287 708293150 2.570000e-62 250.0
2 TraesCS7A01G317400 chrUn 95.280 2246 66 19 134 2349 92483214 92480979 0.000000e+00 3524.0
3 TraesCS7A01G317400 chrUn 95.903 1074 44 0 2345 3418 92480945 92479872 0.000000e+00 1740.0
4 TraesCS7A01G317400 chr7B 96.707 1397 36 5 957 2349 408567007 408568397 0.000000e+00 2316.0
5 TraesCS7A01G317400 chr7B 96.122 954 35 2 2345 3296 408568431 408569384 0.000000e+00 1555.0
6 TraesCS7A01G317400 chr7B 89.937 795 50 18 134 922 408565929 408566699 0.000000e+00 998.0
7 TraesCS7A01G317400 chr7B 86.580 693 77 14 3616 4298 440237163 440237849 0.000000e+00 750.0
8 TraesCS7A01G317400 chr7B 91.139 158 9 1 3242 3399 408569397 408569549 4.360000e-50 209.0
9 TraesCS7A01G317400 chr7B 90.566 53 5 0 1844 1896 534059643 534059695 2.140000e-08 71.3
10 TraesCS7A01G317400 chr1A 88.679 689 64 9 3616 4298 524115524 524114844 0.000000e+00 828.0
11 TraesCS7A01G317400 chr2A 88.438 666 64 9 3640 4299 14238600 14237942 0.000000e+00 791.0
12 TraesCS7A01G317400 chr2A 92.982 171 12 0 3435 3605 673284459 673284629 2.570000e-62 250.0
13 TraesCS7A01G317400 chr2D 86.880 686 79 9 3621 4299 28622437 28623118 0.000000e+00 758.0
14 TraesCS7A01G317400 chr6D 86.561 692 75 12 3616 4299 364230472 364229791 0.000000e+00 747.0
15 TraesCS7A01G317400 chr6D 86.316 665 81 9 3640 4299 7039324 7038665 0.000000e+00 715.0
16 TraesCS7A01G317400 chr6D 92.442 172 13 0 3437 3608 158111828 158111999 3.320000e-61 246.0
17 TraesCS7A01G317400 chr3A 86.795 674 81 6 3632 4299 588740973 588741644 0.000000e+00 745.0
18 TraesCS7A01G317400 chr3A 91.329 173 14 1 3437 3608 485901919 485901747 7.190000e-58 235.0
19 TraesCS7A01G317400 chr3A 90.116 172 15 2 3435 3605 40825587 40825757 5.600000e-54 222.0
20 TraesCS7A01G317400 chr3A 83.621 116 19 0 1822 1937 73513095 73513210 4.550000e-20 110.0
21 TraesCS7A01G317400 chr1D 86.807 667 74 10 3640 4299 10210915 10211574 0.000000e+00 732.0
22 TraesCS7A01G317400 chr5B 85.341 689 95 4 3616 4299 176568542 176567855 0.000000e+00 708.0
23 TraesCS7A01G317400 chr5B 99.275 138 1 0 1 138 158896980 158897117 2.570000e-62 250.0
24 TraesCS7A01G317400 chr5B 91.429 175 15 0 3435 3609 233445111 233445285 1.540000e-59 241.0
25 TraesCS7A01G317400 chr3B 98.621 145 1 1 1 145 542900748 542900605 5.520000e-64 255.0
26 TraesCS7A01G317400 chr3B 99.275 138 1 0 1 138 193963582 193963445 2.570000e-62 250.0
27 TraesCS7A01G317400 chr3B 95.946 148 5 1 1 148 642090039 642090185 5.560000e-59 239.0
28 TraesCS7A01G317400 chr3B 83.621 116 19 0 1822 1937 104971056 104971171 4.550000e-20 110.0
29 TraesCS7A01G317400 chr6B 99.281 139 1 0 2 140 69707002 69707140 7.140000e-63 252.0
30 TraesCS7A01G317400 chr5A 99.281 139 1 0 1 139 687716979 687716841 7.140000e-63 252.0
31 TraesCS7A01G317400 chr5A 98.571 140 2 0 1 140 521678100 521678239 9.230000e-62 248.0
32 TraesCS7A01G317400 chr6A 99.275 138 1 0 1 138 90770661 90770798 2.570000e-62 250.0
33 TraesCS7A01G317400 chr7D 89.888 178 18 0 3435 3612 70039354 70039531 3.340000e-56 230.0
34 TraesCS7A01G317400 chr4B 89.326 178 18 1 3437 3614 8037675 8037499 5.600000e-54 222.0
35 TraesCS7A01G317400 chr4B 88.235 187 21 1 3429 3615 362138085 362137900 5.600000e-54 222.0
36 TraesCS7A01G317400 chr1B 87.831 189 22 1 3428 3616 454924987 454924800 2.010000e-53 220.0
37 TraesCS7A01G317400 chr3D 81.897 116 21 0 1822 1937 63779625 63779740 9.840000e-17 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G317400 chr7A 457567738 457572036 4298 False 7939.0 7939 100.00000 1 4299 1 chr7A.!!$F1 4298
1 TraesCS7A01G317400 chrUn 92479872 92483214 3342 True 2632.0 3524 95.59150 134 3418 2 chrUn.!!$R1 3284
2 TraesCS7A01G317400 chr7B 408565929 408569549 3620 False 1269.5 2316 93.47625 134 3399 4 chr7B.!!$F3 3265
3 TraesCS7A01G317400 chr7B 440237163 440237849 686 False 750.0 750 86.58000 3616 4298 1 chr7B.!!$F1 682
4 TraesCS7A01G317400 chr1A 524114844 524115524 680 True 828.0 828 88.67900 3616 4298 1 chr1A.!!$R1 682
5 TraesCS7A01G317400 chr2A 14237942 14238600 658 True 791.0 791 88.43800 3640 4299 1 chr2A.!!$R1 659
6 TraesCS7A01G317400 chr2D 28622437 28623118 681 False 758.0 758 86.88000 3621 4299 1 chr2D.!!$F1 678
7 TraesCS7A01G317400 chr6D 364229791 364230472 681 True 747.0 747 86.56100 3616 4299 1 chr6D.!!$R2 683
8 TraesCS7A01G317400 chr6D 7038665 7039324 659 True 715.0 715 86.31600 3640 4299 1 chr6D.!!$R1 659
9 TraesCS7A01G317400 chr3A 588740973 588741644 671 False 745.0 745 86.79500 3632 4299 1 chr3A.!!$F3 667
10 TraesCS7A01G317400 chr1D 10210915 10211574 659 False 732.0 732 86.80700 3640 4299 1 chr1D.!!$F1 659
11 TraesCS7A01G317400 chr5B 176567855 176568542 687 True 708.0 708 85.34100 3616 4299 1 chr5B.!!$R1 683

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
135 136 0.035820 TGTGGCAGTTATTCGGACCC 60.036 55.0 0.00 0.0 0.00 4.46 F
529 547 0.249363 GTACCTGGCTAGCTAACGGC 60.249 60.0 15.72 0.0 42.19 5.68 F
695 742 0.592500 CGTCCGTCCACTCATCATCG 60.593 60.0 0.00 0.0 0.00 3.84 F
1791 2142 0.788391 CTCGAGGTGTTTGCCGTAAC 59.212 55.0 3.91 0.0 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 2092 0.176680 AATGAGATCGACGGCAAGCT 59.823 50.0 0.00 0.0 0.00 3.74 R
1749 2093 0.579156 GAATGAGATCGACGGCAAGC 59.421 55.0 0.00 0.0 0.00 4.01 R
2106 2457 1.086067 CGACAGATGCGAATGCTGGT 61.086 55.0 7.48 0.0 43.34 4.00 R
3421 3874 0.104304 ATCTCCCGTTGTATCCACGC 59.896 55.0 0.00 0.0 0.00 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.645975 GTTGCCACACACCGGACG 61.646 66.667 9.46 0.00 0.00 4.79
18 19 4.164087 TTGCCACACACCGGACGT 62.164 61.111 9.46 0.78 0.00 4.34
32 33 4.903010 ACGTGCGGGTCGTGCTTT 62.903 61.111 0.00 0.00 40.07 3.51
33 34 3.645975 CGTGCGGGTCGTGCTTTT 61.646 61.111 0.00 0.00 0.00 2.27
34 35 2.051345 GTGCGGGTCGTGCTTTTG 60.051 61.111 0.00 0.00 0.00 2.44
35 36 2.515057 TGCGGGTCGTGCTTTTGT 60.515 55.556 0.00 0.00 0.00 2.83
36 37 2.051345 GCGGGTCGTGCTTTTGTG 60.051 61.111 0.00 0.00 0.00 3.33
37 38 2.051345 CGGGTCGTGCTTTTGTGC 60.051 61.111 0.00 0.00 0.00 4.57
38 39 2.051345 GGGTCGTGCTTTTGTGCG 60.051 61.111 0.00 0.00 35.36 5.34
39 40 2.725815 GGTCGTGCTTTTGTGCGC 60.726 61.111 0.00 0.00 39.78 6.09
40 41 2.327940 GTCGTGCTTTTGTGCGCT 59.672 55.556 9.73 0.00 40.87 5.92
41 42 1.722507 GTCGTGCTTTTGTGCGCTC 60.723 57.895 9.73 5.51 40.87 5.03
42 43 2.792543 CGTGCTTTTGTGCGCTCG 60.793 61.111 9.73 0.00 40.87 5.03
43 44 2.427410 GTGCTTTTGTGCGCTCGG 60.427 61.111 9.73 0.00 40.01 4.63
44 45 2.590291 TGCTTTTGTGCGCTCGGA 60.590 55.556 9.73 0.00 35.36 4.55
45 46 2.127232 GCTTTTGTGCGCTCGGAC 60.127 61.111 9.73 6.98 36.97 4.79
46 47 2.170985 CTTTTGTGCGCTCGGACG 59.829 61.111 9.73 0.00 39.39 4.79
47 48 2.586635 TTTTGTGCGCTCGGACGT 60.587 55.556 9.73 0.00 39.39 4.34
48 49 2.748546 CTTTTGTGCGCTCGGACGTG 62.749 60.000 9.73 0.00 39.39 4.49
74 75 2.657237 GGCCGATCCCCGTCTATG 59.343 66.667 0.00 0.00 36.31 2.23
75 76 2.048127 GCCGATCCCCGTCTATGC 60.048 66.667 0.00 0.00 36.31 3.14
76 77 2.657237 CCGATCCCCGTCTATGCC 59.343 66.667 0.00 0.00 36.31 4.40
77 78 2.258591 CGATCCCCGTCTATGCCG 59.741 66.667 0.00 0.00 0.00 5.69
78 79 2.048127 GATCCCCGTCTATGCCGC 60.048 66.667 0.00 0.00 0.00 6.53
79 80 2.842462 ATCCCCGTCTATGCCGCA 60.842 61.111 0.00 0.00 0.00 5.69
80 81 3.165160 ATCCCCGTCTATGCCGCAC 62.165 63.158 0.00 0.00 0.00 5.34
82 83 4.201679 CCCGTCTATGCCGCACGA 62.202 66.667 0.00 0.00 35.49 4.35
83 84 2.655364 CCGTCTATGCCGCACGAG 60.655 66.667 0.00 0.00 35.49 4.18
84 85 2.655364 CGTCTATGCCGCACGAGG 60.655 66.667 0.00 0.00 35.49 4.63
103 104 4.171103 GTGCGGGCGGGTTCCTAT 62.171 66.667 0.00 0.00 0.00 2.57
104 105 3.857038 TGCGGGCGGGTTCCTATC 61.857 66.667 0.00 0.00 0.00 2.08
105 106 4.963428 GCGGGCGGGTTCCTATCG 62.963 72.222 0.00 0.00 0.00 2.92
106 107 3.221389 CGGGCGGGTTCCTATCGA 61.221 66.667 0.00 0.00 0.00 3.59
107 108 2.420466 GGGCGGGTTCCTATCGAC 59.580 66.667 0.00 0.00 0.00 4.20
108 109 2.027169 GGCGGGTTCCTATCGACG 59.973 66.667 0.00 0.00 0.00 5.12
109 110 2.657620 GCGGGTTCCTATCGACGC 60.658 66.667 0.00 0.00 40.19 5.19
110 111 2.027169 CGGGTTCCTATCGACGCC 59.973 66.667 0.00 0.00 0.00 5.68
111 112 2.777972 CGGGTTCCTATCGACGCCA 61.778 63.158 0.00 0.00 0.00 5.69
112 113 1.227176 GGGTTCCTATCGACGCCAC 60.227 63.158 0.00 0.00 0.00 5.01
113 114 1.514087 GGTTCCTATCGACGCCACA 59.486 57.895 0.00 0.00 0.00 4.17
114 115 0.804933 GGTTCCTATCGACGCCACAC 60.805 60.000 0.00 0.00 0.00 3.82
129 130 2.594529 CACACGTGTGGCAGTTATTC 57.405 50.000 35.65 0.00 42.10 1.75
130 131 1.136363 CACACGTGTGGCAGTTATTCG 60.136 52.381 35.65 10.09 42.10 3.34
131 132 0.442310 CACGTGTGGCAGTTATTCGG 59.558 55.000 7.58 0.00 0.00 4.30
132 133 0.319083 ACGTGTGGCAGTTATTCGGA 59.681 50.000 0.00 0.00 0.00 4.55
133 134 0.719465 CGTGTGGCAGTTATTCGGAC 59.281 55.000 0.00 0.00 0.00 4.79
134 135 1.084289 GTGTGGCAGTTATTCGGACC 58.916 55.000 0.00 0.00 0.00 4.46
135 136 0.035820 TGTGGCAGTTATTCGGACCC 60.036 55.000 0.00 0.00 0.00 4.46
136 137 0.252197 GTGGCAGTTATTCGGACCCT 59.748 55.000 0.00 0.00 0.00 4.34
137 138 0.988832 TGGCAGTTATTCGGACCCTT 59.011 50.000 0.00 0.00 0.00 3.95
185 186 9.771915 AAAACATTCAATTTTTGCAAGTACTTG 57.228 25.926 27.85 27.85 43.14 3.16
211 212 2.438254 TGCGTATGGGCAGCCAAG 60.438 61.111 15.19 0.00 38.17 3.61
321 322 2.278596 CACCGTATCTGCGTCCCG 60.279 66.667 0.00 0.00 0.00 5.14
368 369 0.596083 GATCGGTCCATCTCAGCACG 60.596 60.000 0.00 0.00 0.00 5.34
435 436 6.636850 GTGCCGACAAATTACATAAATCCATC 59.363 38.462 0.00 0.00 0.00 3.51
516 534 2.494471 TGGTTACATGGAGTCGTACCTG 59.506 50.000 0.00 0.00 31.31 4.00
529 547 0.249363 GTACCTGGCTAGCTAACGGC 60.249 60.000 15.72 0.00 42.19 5.68
546 564 2.901042 CGCCAACTCCCCCTCTAC 59.099 66.667 0.00 0.00 0.00 2.59
557 575 2.637872 TCCCCCTCTACACACTTTCTTG 59.362 50.000 0.00 0.00 0.00 3.02
613 657 9.151471 ACGTATACATATACTCCAAAATGATGC 57.849 33.333 3.32 0.00 37.10 3.91
614 658 9.371136 CGTATACATATACTCCAAAATGATGCT 57.629 33.333 3.32 0.00 37.10 3.79
695 742 0.592500 CGTCCGTCCACTCATCATCG 60.593 60.000 0.00 0.00 0.00 3.84
738 785 1.877576 GCTCAAAAGGCTTTCCCCCG 61.878 60.000 13.76 2.08 0.00 5.73
807 854 1.518774 CACAGCATGGGGAAATGGC 59.481 57.895 0.00 0.00 43.62 4.40
921 969 2.810887 CTGCGCGTCTGCTGCTAA 60.811 61.111 8.43 0.00 39.97 3.09
948 1282 2.499197 TGCTCCACATAAAAGACGCAA 58.501 42.857 0.00 0.00 0.00 4.85
1087 1427 4.554363 CGTAGCCGTGCGAGGGAG 62.554 72.222 0.00 0.00 32.81 4.30
1088 1428 4.208686 GTAGCCGTGCGAGGGAGG 62.209 72.222 0.00 0.00 0.00 4.30
1150 1490 4.681978 GCGAGCCGGTGGTGTTCT 62.682 66.667 1.90 0.00 0.00 3.01
1359 1700 4.178861 TCGGCGTTCGATTCTTGG 57.821 55.556 6.85 0.00 43.74 3.61
1366 1707 2.347755 GCGTTCGATTCTTGGTTAGTCC 59.652 50.000 0.00 0.00 0.00 3.85
1694 2038 4.840288 TACGCGGCCATCGTCGTG 62.840 66.667 21.27 6.56 45.45 4.35
1709 2053 4.681978 GTGCAGACCGCCTTCCGT 62.682 66.667 0.00 0.00 41.33 4.69
1791 2142 0.788391 CTCGAGGTGTTTGCCGTAAC 59.212 55.000 3.91 0.00 0.00 2.50
2075 2426 2.288961 AGTACACCCAAGAATACGCG 57.711 50.000 3.53 3.53 0.00 6.01
2106 2457 1.616865 CTGTGGTCCGTCTCTACCAAA 59.383 52.381 0.00 0.00 46.97 3.28
2138 2489 4.492160 TGTCGATCTCGTGGCGCC 62.492 66.667 22.73 22.73 40.80 6.53
2327 2678 3.462021 GCTCTCATACGCCTTTTCTCAT 58.538 45.455 0.00 0.00 0.00 2.90
2365 2754 6.648310 TCAGTGCATTTGAAGTTTTGACAAAA 59.352 30.769 9.30 9.30 37.14 2.44
2366 2755 7.172190 TCAGTGCATTTGAAGTTTTGACAAAAA 59.828 29.630 14.75 0.00 37.14 1.94
2396 2786 9.594478 TTATAGCTGTTCGATCTTATTGTTTGA 57.406 29.630 0.00 0.00 0.00 2.69
2815 3205 1.987855 TGGAGGGGGAAGCTACACG 60.988 63.158 0.00 0.00 0.00 4.49
3179 3569 1.152631 TCGTCCACCACTGACCTCA 60.153 57.895 0.00 0.00 0.00 3.86
3317 3770 3.030291 TGCCTTTTGGTGTCATTCTGTT 58.970 40.909 0.00 0.00 42.99 3.16
3318 3771 4.211125 TGCCTTTTGGTGTCATTCTGTTA 58.789 39.130 0.00 0.00 42.99 2.41
3444 3897 2.622064 GGATACAACGGGAGATGCTT 57.378 50.000 0.00 0.00 35.89 3.91
3445 3898 3.746045 GGATACAACGGGAGATGCTTA 57.254 47.619 0.00 0.00 35.89 3.09
3446 3899 3.654414 GGATACAACGGGAGATGCTTAG 58.346 50.000 0.00 0.00 35.89 2.18
3447 3900 3.321111 GGATACAACGGGAGATGCTTAGA 59.679 47.826 0.00 0.00 35.89 2.10
3448 3901 4.202223 GGATACAACGGGAGATGCTTAGAA 60.202 45.833 0.00 0.00 35.89 2.10
3449 3902 3.695830 ACAACGGGAGATGCTTAGAAA 57.304 42.857 0.00 0.00 35.89 2.52
3450 3903 4.015872 ACAACGGGAGATGCTTAGAAAA 57.984 40.909 0.00 0.00 35.89 2.29
3451 3904 4.394729 ACAACGGGAGATGCTTAGAAAAA 58.605 39.130 0.00 0.00 35.89 1.94
3452 3905 5.010282 ACAACGGGAGATGCTTAGAAAAAT 58.990 37.500 0.00 0.00 35.89 1.82
3453 3906 6.177610 ACAACGGGAGATGCTTAGAAAAATA 58.822 36.000 0.00 0.00 35.89 1.40
3454 3907 6.657541 ACAACGGGAGATGCTTAGAAAAATAA 59.342 34.615 0.00 0.00 35.89 1.40
3455 3908 7.175990 ACAACGGGAGATGCTTAGAAAAATAAA 59.824 33.333 0.00 0.00 35.89 1.40
3456 3909 7.085052 ACGGGAGATGCTTAGAAAAATAAAC 57.915 36.000 0.00 0.00 0.00 2.01
3457 3910 6.657541 ACGGGAGATGCTTAGAAAAATAAACA 59.342 34.615 0.00 0.00 0.00 2.83
3458 3911 7.148239 ACGGGAGATGCTTAGAAAAATAAACAG 60.148 37.037 0.00 0.00 0.00 3.16
3459 3912 7.065803 CGGGAGATGCTTAGAAAAATAAACAGA 59.934 37.037 0.00 0.00 0.00 3.41
3460 3913 8.739972 GGGAGATGCTTAGAAAAATAAACAGAA 58.260 33.333 0.00 0.00 0.00 3.02
3495 3948 7.623268 GCACCGATGCCTATTTTTATAAAAG 57.377 36.000 10.40 0.20 46.97 2.27
3496 3949 7.422399 GCACCGATGCCTATTTTTATAAAAGA 58.578 34.615 10.40 3.25 46.97 2.52
3497 3950 7.591426 GCACCGATGCCTATTTTTATAAAAGAG 59.409 37.037 10.40 11.36 46.97 2.85
3498 3951 8.836413 CACCGATGCCTATTTTTATAAAAGAGA 58.164 33.333 17.36 4.12 0.00 3.10
3499 3952 8.837389 ACCGATGCCTATTTTTATAAAAGAGAC 58.163 33.333 17.36 10.42 0.00 3.36
3500 3953 8.009974 CCGATGCCTATTTTTATAAAAGAGACG 58.990 37.037 17.36 15.60 0.00 4.18
3501 3954 7.530861 CGATGCCTATTTTTATAAAAGAGACGC 59.469 37.037 17.36 14.37 0.00 5.19
3502 3955 7.859325 TGCCTATTTTTATAAAAGAGACGCT 57.141 32.000 17.36 0.00 0.00 5.07
3503 3956 8.276252 TGCCTATTTTTATAAAAGAGACGCTT 57.724 30.769 17.36 0.00 38.88 4.68
3504 3957 9.386010 TGCCTATTTTTATAAAAGAGACGCTTA 57.614 29.630 17.36 1.22 35.24 3.09
3505 3958 9.865484 GCCTATTTTTATAAAAGAGACGCTTAG 57.135 33.333 17.36 8.54 35.24 2.18
3532 3985 9.763465 TTAAGCGTTTATCTTGTACAAATAAGC 57.237 29.630 10.03 15.00 0.00 3.09
3533 3986 7.372451 AGCGTTTATCTTGTACAAATAAGCA 57.628 32.000 21.92 10.89 0.00 3.91
3534 3987 7.241376 AGCGTTTATCTTGTACAAATAAGCAC 58.759 34.615 21.92 17.24 0.00 4.40
3535 3988 6.468000 GCGTTTATCTTGTACAAATAAGCACC 59.532 38.462 21.92 14.91 0.00 5.01
3536 3989 7.523219 CGTTTATCTTGTACAAATAAGCACCA 58.477 34.615 21.92 10.05 0.00 4.17
3537 3990 7.692291 CGTTTATCTTGTACAAATAAGCACCAG 59.308 37.037 21.92 7.44 0.00 4.00
3538 3991 8.512138 GTTTATCTTGTACAAATAAGCACCAGT 58.488 33.333 10.03 0.00 0.00 4.00
3539 3992 5.940192 TCTTGTACAAATAAGCACCAGTG 57.060 39.130 10.03 0.00 0.00 3.66
3554 4007 5.100751 CACCAGTGCTTAAGAAAAGTCTG 57.899 43.478 6.67 0.00 33.05 3.51
3555 4008 4.023707 CACCAGTGCTTAAGAAAAGTCTGG 60.024 45.833 13.86 13.86 41.89 3.86
3556 4009 4.137543 CCAGTGCTTAAGAAAAGTCTGGT 58.862 43.478 6.67 0.00 37.08 4.00
3557 4010 4.580580 CCAGTGCTTAAGAAAAGTCTGGTT 59.419 41.667 6.67 0.00 37.08 3.67
3558 4011 5.067805 CCAGTGCTTAAGAAAAGTCTGGTTT 59.932 40.000 6.67 0.00 37.08 3.27
3559 4012 6.262273 CCAGTGCTTAAGAAAAGTCTGGTTTA 59.738 38.462 6.67 0.00 37.08 2.01
3560 4013 7.040409 CCAGTGCTTAAGAAAAGTCTGGTTTAT 60.040 37.037 6.67 0.00 37.08 1.40
3561 4014 8.352942 CAGTGCTTAAGAAAAGTCTGGTTTATT 58.647 33.333 6.67 0.00 33.05 1.40
3562 4015 8.914011 AGTGCTTAAGAAAAGTCTGGTTTATTT 58.086 29.630 6.67 0.00 33.05 1.40
3563 4016 9.181805 GTGCTTAAGAAAAGTCTGGTTTATTTC 57.818 33.333 6.67 0.00 33.05 2.17
3564 4017 9.131791 TGCTTAAGAAAAGTCTGGTTTATTTCT 57.868 29.630 6.67 0.00 40.90 2.52
3565 4018 9.613957 GCTTAAGAAAAGTCTGGTTTATTTCTC 57.386 33.333 6.67 0.00 38.89 2.87
3570 4023 9.004717 AGAAAAGTCTGGTTTATTTCTCTAAGC 57.995 33.333 0.00 0.00 35.96 3.09
3571 4024 8.691661 AAAAGTCTGGTTTATTTCTCTAAGCA 57.308 30.769 0.00 0.00 0.00 3.91
3572 4025 7.674471 AAGTCTGGTTTATTTCTCTAAGCAC 57.326 36.000 0.00 0.00 0.00 4.40
3573 4026 6.174049 AGTCTGGTTTATTTCTCTAAGCACC 58.826 40.000 0.00 0.00 0.00 5.01
3574 4027 6.013293 AGTCTGGTTTATTTCTCTAAGCACCT 60.013 38.462 0.00 0.00 0.00 4.00
3575 4028 6.314152 GTCTGGTTTATTTCTCTAAGCACCTC 59.686 42.308 0.00 0.00 0.00 3.85
3576 4029 6.213600 TCTGGTTTATTTCTCTAAGCACCTCT 59.786 38.462 0.00 0.00 0.00 3.69
3577 4030 6.407202 TGGTTTATTTCTCTAAGCACCTCTC 58.593 40.000 0.00 0.00 0.00 3.20
3578 4031 6.213600 TGGTTTATTTCTCTAAGCACCTCTCT 59.786 38.462 0.00 0.00 0.00 3.10
3579 4032 7.106890 GGTTTATTTCTCTAAGCACCTCTCTT 58.893 38.462 0.00 0.00 0.00 2.85
3580 4033 8.258708 GGTTTATTTCTCTAAGCACCTCTCTTA 58.741 37.037 0.00 0.00 0.00 2.10
3581 4034 9.654663 GTTTATTTCTCTAAGCACCTCTCTTAA 57.345 33.333 0.00 0.00 0.00 1.85
3582 4035 9.877178 TTTATTTCTCTAAGCACCTCTCTTAAG 57.123 33.333 0.00 0.00 0.00 1.85
3583 4036 4.993029 TCTCTAAGCACCTCTCTTAAGC 57.007 45.455 0.00 0.00 0.00 3.09
3584 4037 4.344978 TCTCTAAGCACCTCTCTTAAGCA 58.655 43.478 0.00 0.00 0.00 3.91
3585 4038 4.158764 TCTCTAAGCACCTCTCTTAAGCAC 59.841 45.833 0.00 0.00 0.00 4.40
3586 4039 2.481289 AAGCACCTCTCTTAAGCACC 57.519 50.000 0.00 0.00 0.00 5.01
3587 4040 1.650528 AGCACCTCTCTTAAGCACCT 58.349 50.000 0.00 0.00 0.00 4.00
3588 4041 1.981495 AGCACCTCTCTTAAGCACCTT 59.019 47.619 0.00 0.00 0.00 3.50
3589 4042 2.373502 AGCACCTCTCTTAAGCACCTTT 59.626 45.455 0.00 0.00 0.00 3.11
3590 4043 2.744741 GCACCTCTCTTAAGCACCTTTC 59.255 50.000 0.00 0.00 0.00 2.62
3591 4044 3.807209 GCACCTCTCTTAAGCACCTTTCA 60.807 47.826 0.00 0.00 0.00 2.69
3592 4045 4.583871 CACCTCTCTTAAGCACCTTTCAT 58.416 43.478 0.00 0.00 0.00 2.57
3593 4046 5.006386 CACCTCTCTTAAGCACCTTTCATT 58.994 41.667 0.00 0.00 0.00 2.57
3594 4047 5.006386 ACCTCTCTTAAGCACCTTTCATTG 58.994 41.667 0.00 0.00 0.00 2.82
3595 4048 5.006386 CCTCTCTTAAGCACCTTTCATTGT 58.994 41.667 0.00 0.00 0.00 2.71
3596 4049 6.173339 CCTCTCTTAAGCACCTTTCATTGTA 58.827 40.000 0.00 0.00 0.00 2.41
3597 4050 6.092807 CCTCTCTTAAGCACCTTTCATTGTAC 59.907 42.308 0.00 0.00 0.00 2.90
3598 4051 6.530120 TCTCTTAAGCACCTTTCATTGTACA 58.470 36.000 0.00 0.00 0.00 2.90
3599 4052 6.995686 TCTCTTAAGCACCTTTCATTGTACAA 59.004 34.615 11.41 11.41 0.00 2.41
3600 4053 7.173218 TCTCTTAAGCACCTTTCATTGTACAAG 59.827 37.037 14.65 6.58 0.00 3.16
3601 4054 4.853924 AAGCACCTTTCATTGTACAAGG 57.146 40.909 13.96 13.96 42.59 3.61
3602 4055 2.558359 AGCACCTTTCATTGTACAAGGC 59.442 45.455 15.24 7.55 40.85 4.35
3603 4056 2.352715 GCACCTTTCATTGTACAAGGCC 60.353 50.000 15.24 0.00 40.85 5.19
3604 4057 3.157087 CACCTTTCATTGTACAAGGCCT 58.843 45.455 15.24 0.00 40.85 5.19
3605 4058 3.573967 CACCTTTCATTGTACAAGGCCTT 59.426 43.478 13.78 13.78 40.85 4.35
3606 4059 4.764823 CACCTTTCATTGTACAAGGCCTTA 59.235 41.667 20.00 1.64 40.85 2.69
3607 4060 5.010282 ACCTTTCATTGTACAAGGCCTTAG 58.990 41.667 20.00 15.05 40.85 2.18
3608 4061 5.222048 ACCTTTCATTGTACAAGGCCTTAGA 60.222 40.000 20.00 5.98 40.85 2.10
3609 4062 5.355350 CCTTTCATTGTACAAGGCCTTAGAG 59.645 44.000 20.00 8.91 30.94 2.43
3610 4063 3.873910 TCATTGTACAAGGCCTTAGAGC 58.126 45.455 20.00 9.48 0.00 4.09
3611 4064 3.263170 TCATTGTACAAGGCCTTAGAGCA 59.737 43.478 20.00 12.05 0.00 4.26
3612 4065 3.780804 TTGTACAAGGCCTTAGAGCAA 57.219 42.857 20.00 17.08 0.00 3.91
3613 4066 3.053831 TGTACAAGGCCTTAGAGCAAC 57.946 47.619 20.00 10.42 0.00 4.17
3614 4067 2.637872 TGTACAAGGCCTTAGAGCAACT 59.362 45.455 20.00 0.00 0.00 3.16
3619 4072 0.909623 GGCCTTAGAGCAACTACCCA 59.090 55.000 0.00 0.00 0.00 4.51
3624 4077 3.370953 CCTTAGAGCAACTACCCAGCAAT 60.371 47.826 0.00 0.00 0.00 3.56
3630 4083 3.016736 GCAACTACCCAGCAATACATGT 58.983 45.455 2.69 2.69 0.00 3.21
3635 4088 4.962995 ACTACCCAGCAATACATGTAGACT 59.037 41.667 11.91 5.57 32.19 3.24
3685 4138 3.438781 CGGTCCAATTTTCCGATCAGAAA 59.561 43.478 0.00 0.00 46.05 2.52
3703 4156 1.961180 AAAGAGCCCGCATACTCGCT 61.961 55.000 0.00 0.00 37.99 4.93
3784 4238 3.556625 CCGTGATTCGTTTGCGGA 58.443 55.556 0.00 0.00 44.57 5.54
3805 4260 0.918983 CCAAACCCTATCTCCTGCCA 59.081 55.000 0.00 0.00 0.00 4.92
3808 4263 0.253160 AACCCTATCTCCTGCCACCA 60.253 55.000 0.00 0.00 0.00 4.17
3814 4270 3.314331 CTCCTGCCACCACCGAGT 61.314 66.667 0.00 0.00 0.00 4.18
3886 4343 2.675242 CCCACCTCCAACCGCCATA 61.675 63.158 0.00 0.00 0.00 2.74
4012 4470 2.359975 GCCCGGAAGTGGACCAAG 60.360 66.667 0.73 0.00 0.00 3.61
4205 4673 1.741770 GCGCATTCACCTTCGTCCT 60.742 57.895 0.30 0.00 0.00 3.85
4254 4722 3.770040 CATGGAGTCGTCGGGCCA 61.770 66.667 4.39 4.54 34.45 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.645975 CGTCCGGTGTGTGGCAAC 61.646 66.667 0.00 0.00 0.00 4.17
1 2 4.164087 ACGTCCGGTGTGTGGCAA 62.164 61.111 0.00 0.00 0.00 4.52
2 3 4.901123 CACGTCCGGTGTGTGGCA 62.901 66.667 17.74 0.00 41.89 4.92
15 16 4.903010 AAAGCACGACCCGCACGT 62.903 61.111 0.00 0.00 44.83 4.49
16 17 3.645975 AAAAGCACGACCCGCACG 61.646 61.111 0.00 0.00 0.00 5.34
17 18 2.051345 CAAAAGCACGACCCGCAC 60.051 61.111 0.00 0.00 0.00 5.34
18 19 2.515057 ACAAAAGCACGACCCGCA 60.515 55.556 0.00 0.00 0.00 5.69
19 20 2.051345 CACAAAAGCACGACCCGC 60.051 61.111 0.00 0.00 0.00 6.13
20 21 2.051345 GCACAAAAGCACGACCCG 60.051 61.111 0.00 0.00 0.00 5.28
21 22 2.051345 CGCACAAAAGCACGACCC 60.051 61.111 0.00 0.00 0.00 4.46
22 23 2.725815 GCGCACAAAAGCACGACC 60.726 61.111 0.30 0.00 0.00 4.79
23 24 1.722507 GAGCGCACAAAAGCACGAC 60.723 57.895 11.47 0.00 35.48 4.34
24 25 2.631428 GAGCGCACAAAAGCACGA 59.369 55.556 11.47 0.00 35.48 4.35
25 26 2.792543 CGAGCGCACAAAAGCACG 60.793 61.111 11.47 0.00 40.48 5.34
26 27 2.427410 CCGAGCGCACAAAAGCAC 60.427 61.111 11.47 0.00 35.48 4.40
27 28 2.590291 TCCGAGCGCACAAAAGCA 60.590 55.556 11.47 0.00 35.48 3.91
28 29 2.127232 GTCCGAGCGCACAAAAGC 60.127 61.111 11.47 0.00 0.00 3.51
29 30 2.170985 CGTCCGAGCGCACAAAAG 59.829 61.111 11.47 0.00 0.00 2.27
30 31 2.586635 ACGTCCGAGCGCACAAAA 60.587 55.556 11.47 0.00 34.88 2.44
31 32 3.334751 CACGTCCGAGCGCACAAA 61.335 61.111 11.47 0.00 34.88 2.83
59 60 2.657237 GGCATAGACGGGGATCGG 59.343 66.667 0.00 0.00 44.45 4.18
60 61 2.258591 CGGCATAGACGGGGATCG 59.741 66.667 0.00 0.00 45.88 3.69
61 62 2.048127 GCGGCATAGACGGGGATC 60.048 66.667 0.00 0.00 32.98 3.36
62 63 2.842462 TGCGGCATAGACGGGGAT 60.842 61.111 0.00 0.00 32.98 3.85
63 64 3.845259 GTGCGGCATAGACGGGGA 61.845 66.667 5.72 0.00 32.98 4.81
65 66 4.201679 TCGTGCGGCATAGACGGG 62.202 66.667 5.72 0.00 32.98 5.28
66 67 2.655364 CTCGTGCGGCATAGACGG 60.655 66.667 5.72 0.00 32.98 4.79
67 68 2.655364 CCTCGTGCGGCATAGACG 60.655 66.667 5.72 5.03 36.98 4.18
86 87 4.171103 ATAGGAACCCGCCCGCAC 62.171 66.667 0.00 0.00 0.00 5.34
87 88 3.857038 GATAGGAACCCGCCCGCA 61.857 66.667 0.00 0.00 0.00 5.69
88 89 4.963428 CGATAGGAACCCGCCCGC 62.963 72.222 0.00 0.00 0.00 6.13
89 90 3.221389 TCGATAGGAACCCGCCCG 61.221 66.667 0.00 0.00 0.00 6.13
90 91 2.420466 GTCGATAGGAACCCGCCC 59.580 66.667 0.00 0.00 0.00 6.13
91 92 2.027169 CGTCGATAGGAACCCGCC 59.973 66.667 0.00 0.00 0.00 6.13
92 93 2.657620 GCGTCGATAGGAACCCGC 60.658 66.667 0.00 0.00 0.00 6.13
93 94 2.027169 GGCGTCGATAGGAACCCG 59.973 66.667 0.00 0.00 0.00 5.28
94 95 1.227176 GTGGCGTCGATAGGAACCC 60.227 63.158 0.00 0.00 0.00 4.11
95 96 0.804933 GTGTGGCGTCGATAGGAACC 60.805 60.000 0.00 0.00 0.00 3.62
96 97 1.138047 CGTGTGGCGTCGATAGGAAC 61.138 60.000 0.00 0.00 35.54 3.62
97 98 1.138036 CGTGTGGCGTCGATAGGAA 59.862 57.895 0.00 0.00 35.54 3.36
98 99 2.795973 CGTGTGGCGTCGATAGGA 59.204 61.111 0.00 0.00 35.54 2.94
110 111 1.136363 CGAATAACTGCCACACGTGTG 60.136 52.381 36.13 36.13 45.23 3.82
111 112 1.144969 CGAATAACTGCCACACGTGT 58.855 50.000 17.22 17.22 0.00 4.49
112 113 0.442310 CCGAATAACTGCCACACGTG 59.558 55.000 15.48 15.48 0.00 4.49
113 114 0.319083 TCCGAATAACTGCCACACGT 59.681 50.000 0.00 0.00 0.00 4.49
114 115 0.719465 GTCCGAATAACTGCCACACG 59.281 55.000 0.00 0.00 0.00 4.49
115 116 1.084289 GGTCCGAATAACTGCCACAC 58.916 55.000 0.00 0.00 0.00 3.82
116 117 0.035820 GGGTCCGAATAACTGCCACA 60.036 55.000 0.00 0.00 0.00 4.17
117 118 0.252197 AGGGTCCGAATAACTGCCAC 59.748 55.000 0.00 0.00 0.00 5.01
118 119 0.988832 AAGGGTCCGAATAACTGCCA 59.011 50.000 0.00 0.00 0.00 4.92
119 120 2.941064 GTTAAGGGTCCGAATAACTGCC 59.059 50.000 0.00 0.00 0.00 4.85
120 121 3.870274 AGTTAAGGGTCCGAATAACTGC 58.130 45.455 10.25 0.00 37.25 4.40
121 122 7.015001 AGGTATAGTTAAGGGTCCGAATAACTG 59.985 40.741 16.79 0.00 38.61 3.16
122 123 7.015001 CAGGTATAGTTAAGGGTCCGAATAACT 59.985 40.741 13.78 13.78 40.59 2.24
123 124 7.150640 CAGGTATAGTTAAGGGTCCGAATAAC 58.849 42.308 0.00 3.19 0.00 1.89
124 125 6.268387 CCAGGTATAGTTAAGGGTCCGAATAA 59.732 42.308 0.00 0.00 0.00 1.40
125 126 5.776716 CCAGGTATAGTTAAGGGTCCGAATA 59.223 44.000 0.00 0.00 0.00 1.75
126 127 4.591924 CCAGGTATAGTTAAGGGTCCGAAT 59.408 45.833 0.00 0.00 0.00 3.34
127 128 3.962718 CCAGGTATAGTTAAGGGTCCGAA 59.037 47.826 0.00 0.00 0.00 4.30
128 129 3.569491 CCAGGTATAGTTAAGGGTCCGA 58.431 50.000 0.00 0.00 0.00 4.55
129 130 2.036862 GCCAGGTATAGTTAAGGGTCCG 59.963 54.545 0.00 0.00 0.00 4.79
130 131 2.371179 GGCCAGGTATAGTTAAGGGTCC 59.629 54.545 0.00 0.00 0.00 4.46
131 132 2.371179 GGGCCAGGTATAGTTAAGGGTC 59.629 54.545 4.39 0.00 0.00 4.46
132 133 2.293991 TGGGCCAGGTATAGTTAAGGGT 60.294 50.000 0.00 0.00 0.00 4.34
133 134 2.414612 TGGGCCAGGTATAGTTAAGGG 58.585 52.381 0.00 0.00 0.00 3.95
134 135 3.650942 TGATGGGCCAGGTATAGTTAAGG 59.349 47.826 13.78 0.00 0.00 2.69
135 136 4.974645 TGATGGGCCAGGTATAGTTAAG 57.025 45.455 13.78 0.00 0.00 1.85
136 137 4.475381 TGTTGATGGGCCAGGTATAGTTAA 59.525 41.667 13.78 0.00 0.00 2.01
137 138 4.041464 TGTTGATGGGCCAGGTATAGTTA 58.959 43.478 13.78 0.00 0.00 2.24
185 186 1.654023 GCCCATACGCACCCAGTTTC 61.654 60.000 0.00 0.00 0.00 2.78
321 322 0.036875 ACTGCCTCAACCCAAGTAGC 59.963 55.000 0.00 0.00 0.00 3.58
368 369 6.198966 AGACGAATCATTTTCTGTTTTTGTGC 59.801 34.615 0.00 0.00 0.00 4.57
435 436 5.525012 TGAGCATGATTGTTTCTTATCCTCG 59.475 40.000 0.00 0.00 0.00 4.63
516 534 4.524318 TGGCGCCGTTAGCTAGCC 62.524 66.667 23.90 12.80 45.44 3.93
529 547 1.987855 TGTAGAGGGGGAGTTGGCG 60.988 63.158 0.00 0.00 0.00 5.69
546 564 9.552114 GAATTGATAATGACTCAAGAAAGTGTG 57.448 33.333 0.00 0.00 36.16 3.82
695 742 0.108520 TGTCTAATCCGTTCGGGTGC 60.109 55.000 11.37 0.00 37.00 5.01
807 854 3.557903 CTGACAGGTGGGGCCAGTG 62.558 68.421 4.39 0.00 37.09 3.66
1011 1345 4.821589 CAGGAGGCGGCCGAGTTC 62.822 72.222 33.48 21.51 0.00 3.01
1044 1384 0.238817 GCTACTCGATCCTAGCGTGG 59.761 60.000 0.00 0.00 0.00 4.94
1085 1425 2.365768 GACCCACCTCCCTCCCTC 60.366 72.222 0.00 0.00 0.00 4.30
1086 1426 4.400251 CGACCCACCTCCCTCCCT 62.400 72.222 0.00 0.00 0.00 4.20
1087 1427 3.698263 ATCGACCCACCTCCCTCCC 62.698 68.421 0.00 0.00 0.00 4.30
1088 1428 2.041819 ATCGACCCACCTCCCTCC 60.042 66.667 0.00 0.00 0.00 4.30
1150 1490 1.499007 GCCCTTCTTATTCCCCATGGA 59.501 52.381 15.22 0.00 39.54 3.41
1359 1700 6.755141 TCATGCATTAACTCGTAAGGACTAAC 59.245 38.462 0.00 0.00 38.47 2.34
1366 1707 5.275927 CGTCAGTCATGCATTAACTCGTAAG 60.276 44.000 8.25 0.00 0.00 2.34
1682 2026 3.188786 GTCTGCACGACGATGGCC 61.189 66.667 0.00 0.00 32.04 5.36
1748 2092 0.176680 AATGAGATCGACGGCAAGCT 59.823 50.000 0.00 0.00 0.00 3.74
1749 2093 0.579156 GAATGAGATCGACGGCAAGC 59.421 55.000 0.00 0.00 0.00 4.01
2075 2426 4.681978 ACCACAGAGCGGCGTTCC 62.682 66.667 20.21 3.67 0.00 3.62
2106 2457 1.086067 CGACAGATGCGAATGCTGGT 61.086 55.000 7.48 0.00 43.34 4.00
2327 2678 6.542005 TCAAATGCACTGAGTTTCTTACTTGA 59.458 34.615 0.00 0.00 37.17 3.02
2366 2755 9.547753 ACAATAAGATCGAACAGCTATAACATT 57.452 29.630 0.00 0.00 0.00 2.71
2367 2756 9.547753 AACAATAAGATCGAACAGCTATAACAT 57.452 29.630 0.00 0.00 0.00 2.71
2369 2758 9.638300 CAAACAATAAGATCGAACAGCTATAAC 57.362 33.333 0.00 0.00 0.00 1.89
2396 2786 5.789643 ATCTTTAAGCCAACACACAACAT 57.210 34.783 0.00 0.00 0.00 2.71
2792 3182 2.547123 TAGCTTCCCCCTCCACCTCC 62.547 65.000 0.00 0.00 0.00 4.30
2794 3184 1.307084 GTAGCTTCCCCCTCCACCT 60.307 63.158 0.00 0.00 0.00 4.00
2815 3205 4.704833 TGGGAGTGCAAGCTCGGC 62.705 66.667 3.50 3.50 36.41 5.54
2860 3250 2.895372 GCCGCCATGTAGTTCGGG 60.895 66.667 0.00 0.00 41.96 5.14
2962 3352 4.324991 CCGGCGGGGTTATAGGCC 62.325 72.222 20.56 0.00 42.14 5.19
3103 3493 0.674534 ACAGAGAAGACACGGTGGAC 59.325 55.000 13.48 6.30 0.00 4.02
3115 3505 3.039134 TCTGCGCACGACAGAGAA 58.961 55.556 5.66 0.00 39.21 2.87
3317 3770 0.472925 TGACACTCAAGCCCCACCTA 60.473 55.000 0.00 0.00 0.00 3.08
3318 3771 1.770110 TGACACTCAAGCCCCACCT 60.770 57.895 0.00 0.00 0.00 4.00
3419 3872 0.390603 CTCCCGTTGTATCCACGCAA 60.391 55.000 0.00 0.00 0.00 4.85
3420 3873 1.216977 CTCCCGTTGTATCCACGCA 59.783 57.895 0.00 0.00 0.00 5.24
3421 3874 0.104304 ATCTCCCGTTGTATCCACGC 59.896 55.000 0.00 0.00 0.00 5.34
3422 3875 1.852942 CATCTCCCGTTGTATCCACG 58.147 55.000 0.00 0.00 0.00 4.94
3423 3876 1.139058 AGCATCTCCCGTTGTATCCAC 59.861 52.381 0.00 0.00 0.00 4.02
3424 3877 1.496060 AGCATCTCCCGTTGTATCCA 58.504 50.000 0.00 0.00 0.00 3.41
3425 3878 2.622064 AAGCATCTCCCGTTGTATCC 57.378 50.000 0.00 0.00 0.00 2.59
3426 3879 4.585955 TCTAAGCATCTCCCGTTGTATC 57.414 45.455 0.00 0.00 0.00 2.24
3427 3880 5.353394 TTTCTAAGCATCTCCCGTTGTAT 57.647 39.130 0.00 0.00 0.00 2.29
3428 3881 4.811969 TTTCTAAGCATCTCCCGTTGTA 57.188 40.909 0.00 0.00 0.00 2.41
3429 3882 3.695830 TTTCTAAGCATCTCCCGTTGT 57.304 42.857 0.00 0.00 0.00 3.32
3430 3883 5.567138 ATTTTTCTAAGCATCTCCCGTTG 57.433 39.130 0.00 0.00 0.00 4.10
3431 3884 7.175990 TGTTTATTTTTCTAAGCATCTCCCGTT 59.824 33.333 0.00 0.00 0.00 4.44
3432 3885 6.657541 TGTTTATTTTTCTAAGCATCTCCCGT 59.342 34.615 0.00 0.00 0.00 5.28
3433 3886 7.065803 TCTGTTTATTTTTCTAAGCATCTCCCG 59.934 37.037 0.00 0.00 0.00 5.14
3434 3887 8.281212 TCTGTTTATTTTTCTAAGCATCTCCC 57.719 34.615 0.00 0.00 0.00 4.30
3472 3925 8.836413 TCTCTTTTATAAAAATAGGCATCGGTG 58.164 33.333 11.62 0.00 0.00 4.94
3473 3926 8.837389 GTCTCTTTTATAAAAATAGGCATCGGT 58.163 33.333 11.62 0.00 0.00 4.69
3474 3927 8.009974 CGTCTCTTTTATAAAAATAGGCATCGG 58.990 37.037 17.86 3.93 0.00 4.18
3475 3928 7.530861 GCGTCTCTTTTATAAAAATAGGCATCG 59.469 37.037 17.86 15.77 0.00 3.84
3476 3929 8.560374 AGCGTCTCTTTTATAAAAATAGGCATC 58.440 33.333 21.20 13.90 0.00 3.91
3477 3930 8.451908 AGCGTCTCTTTTATAAAAATAGGCAT 57.548 30.769 21.20 10.80 0.00 4.40
3478 3931 7.859325 AGCGTCTCTTTTATAAAAATAGGCA 57.141 32.000 21.20 6.10 0.00 4.75
3479 3932 9.865484 CTAAGCGTCTCTTTTATAAAAATAGGC 57.135 33.333 11.62 14.43 36.25 3.93
3506 3959 9.763465 GCTTATTTGTACAAGATAAACGCTTAA 57.237 29.630 8.56 0.00 0.00 1.85
3507 3960 8.937884 TGCTTATTTGTACAAGATAAACGCTTA 58.062 29.630 8.56 0.00 0.00 3.09
3508 3961 7.749126 GTGCTTATTTGTACAAGATAAACGCTT 59.251 33.333 8.56 0.00 0.00 4.68
3509 3962 7.241376 GTGCTTATTTGTACAAGATAAACGCT 58.759 34.615 8.56 0.00 0.00 5.07
3510 3963 6.468000 GGTGCTTATTTGTACAAGATAAACGC 59.532 38.462 8.56 14.83 0.00 4.84
3511 3964 7.523219 TGGTGCTTATTTGTACAAGATAAACG 58.477 34.615 8.56 6.82 0.00 3.60
3512 3965 8.512138 ACTGGTGCTTATTTGTACAAGATAAAC 58.488 33.333 8.56 11.03 29.87 2.01
3513 3966 8.511321 CACTGGTGCTTATTTGTACAAGATAAA 58.489 33.333 8.56 1.80 29.87 1.40
3514 3967 8.039603 CACTGGTGCTTATTTGTACAAGATAA 57.960 34.615 8.56 13.40 29.87 1.75
3515 3968 7.609760 CACTGGTGCTTATTTGTACAAGATA 57.390 36.000 8.56 7.27 29.87 1.98
3516 3969 6.500684 CACTGGTGCTTATTTGTACAAGAT 57.499 37.500 8.56 8.17 29.87 2.40
3517 3970 5.940192 CACTGGTGCTTATTTGTACAAGA 57.060 39.130 8.56 0.90 29.87 3.02
3532 3985 4.023707 CCAGACTTTTCTTAAGCACTGGTG 60.024 45.833 16.25 0.00 38.78 4.17
3533 3986 4.137543 CCAGACTTTTCTTAAGCACTGGT 58.862 43.478 16.25 0.00 38.78 4.00
3534 3987 4.137543 ACCAGACTTTTCTTAAGCACTGG 58.862 43.478 19.84 19.84 43.78 4.00
3535 3988 5.757850 AACCAGACTTTTCTTAAGCACTG 57.242 39.130 0.00 0.00 0.00 3.66
3536 3989 8.465273 AATAAACCAGACTTTTCTTAAGCACT 57.535 30.769 0.00 0.00 0.00 4.40
3537 3990 9.181805 GAAATAAACCAGACTTTTCTTAAGCAC 57.818 33.333 0.00 0.00 0.00 4.40
3538 3991 9.131791 AGAAATAAACCAGACTTTTCTTAAGCA 57.868 29.630 0.00 0.00 33.97 3.91
3539 3992 9.613957 GAGAAATAAACCAGACTTTTCTTAAGC 57.386 33.333 0.00 0.00 36.91 3.09
3544 3997 9.004717 GCTTAGAGAAATAAACCAGACTTTTCT 57.995 33.333 0.00 0.00 38.86 2.52
3545 3998 8.784043 TGCTTAGAGAAATAAACCAGACTTTTC 58.216 33.333 0.00 0.00 0.00 2.29
3546 3999 8.568794 GTGCTTAGAGAAATAAACCAGACTTTT 58.431 33.333 0.00 0.00 0.00 2.27
3547 4000 7.175119 GGTGCTTAGAGAAATAAACCAGACTTT 59.825 37.037 0.00 0.00 0.00 2.66
3548 4001 6.655425 GGTGCTTAGAGAAATAAACCAGACTT 59.345 38.462 0.00 0.00 0.00 3.01
3549 4002 6.013293 AGGTGCTTAGAGAAATAAACCAGACT 60.013 38.462 0.00 0.00 0.00 3.24
3550 4003 6.174049 AGGTGCTTAGAGAAATAAACCAGAC 58.826 40.000 0.00 0.00 0.00 3.51
3551 4004 6.213600 AGAGGTGCTTAGAGAAATAAACCAGA 59.786 38.462 0.00 0.00 0.00 3.86
3552 4005 6.410540 AGAGGTGCTTAGAGAAATAAACCAG 58.589 40.000 0.00 0.00 0.00 4.00
3553 4006 6.213600 AGAGAGGTGCTTAGAGAAATAAACCA 59.786 38.462 0.00 0.00 0.00 3.67
3554 4007 6.645306 AGAGAGGTGCTTAGAGAAATAAACC 58.355 40.000 0.00 0.00 0.00 3.27
3555 4008 9.654663 TTAAGAGAGGTGCTTAGAGAAATAAAC 57.345 33.333 0.00 0.00 0.00 2.01
3556 4009 9.877178 CTTAAGAGAGGTGCTTAGAGAAATAAA 57.123 33.333 0.00 0.00 0.00 1.40
3557 4010 7.982354 GCTTAAGAGAGGTGCTTAGAGAAATAA 59.018 37.037 6.67 0.00 0.00 1.40
3558 4011 7.124298 TGCTTAAGAGAGGTGCTTAGAGAAATA 59.876 37.037 6.67 0.00 0.00 1.40
3559 4012 6.070538 TGCTTAAGAGAGGTGCTTAGAGAAAT 60.071 38.462 6.67 0.00 0.00 2.17
3560 4013 5.246203 TGCTTAAGAGAGGTGCTTAGAGAAA 59.754 40.000 6.67 0.00 0.00 2.52
3561 4014 4.772624 TGCTTAAGAGAGGTGCTTAGAGAA 59.227 41.667 6.67 0.00 0.00 2.87
3562 4015 4.158764 GTGCTTAAGAGAGGTGCTTAGAGA 59.841 45.833 6.67 0.00 0.00 3.10
3563 4016 4.429108 GTGCTTAAGAGAGGTGCTTAGAG 58.571 47.826 6.67 0.00 0.00 2.43
3564 4017 3.195825 GGTGCTTAAGAGAGGTGCTTAGA 59.804 47.826 6.67 0.00 0.00 2.10
3565 4018 3.196685 AGGTGCTTAAGAGAGGTGCTTAG 59.803 47.826 6.67 0.00 0.00 2.18
3566 4019 3.173965 AGGTGCTTAAGAGAGGTGCTTA 58.826 45.455 6.67 0.00 0.00 3.09
3567 4020 1.981495 AGGTGCTTAAGAGAGGTGCTT 59.019 47.619 6.67 0.00 0.00 3.91
3568 4021 1.650528 AGGTGCTTAAGAGAGGTGCT 58.349 50.000 6.67 0.00 0.00 4.40
3569 4022 2.481289 AAGGTGCTTAAGAGAGGTGC 57.519 50.000 6.67 0.00 0.00 5.01
3570 4023 4.008074 TGAAAGGTGCTTAAGAGAGGTG 57.992 45.455 6.67 0.00 0.00 4.00
3571 4024 4.917906 ATGAAAGGTGCTTAAGAGAGGT 57.082 40.909 6.67 0.00 0.00 3.85
3572 4025 5.006386 ACAATGAAAGGTGCTTAAGAGAGG 58.994 41.667 6.67 0.00 0.00 3.69
3573 4026 6.650807 TGTACAATGAAAGGTGCTTAAGAGAG 59.349 38.462 6.67 0.00 0.00 3.20
3574 4027 6.530120 TGTACAATGAAAGGTGCTTAAGAGA 58.470 36.000 6.67 0.00 0.00 3.10
3575 4028 6.801539 TGTACAATGAAAGGTGCTTAAGAG 57.198 37.500 6.67 0.00 0.00 2.85
3576 4029 6.206634 CCTTGTACAATGAAAGGTGCTTAAGA 59.793 38.462 9.13 0.00 36.50 2.10
3577 4030 6.381801 CCTTGTACAATGAAAGGTGCTTAAG 58.618 40.000 9.13 0.00 36.50 1.85
3578 4031 5.278758 GCCTTGTACAATGAAAGGTGCTTAA 60.279 40.000 14.26 0.00 42.13 1.85
3579 4032 4.217550 GCCTTGTACAATGAAAGGTGCTTA 59.782 41.667 14.26 0.00 42.13 3.09
3580 4033 3.005791 GCCTTGTACAATGAAAGGTGCTT 59.994 43.478 14.26 0.00 42.13 3.91
3581 4034 2.558359 GCCTTGTACAATGAAAGGTGCT 59.442 45.455 14.26 0.00 42.13 4.40
3582 4035 2.352715 GGCCTTGTACAATGAAAGGTGC 60.353 50.000 14.26 5.47 42.13 5.01
3583 4036 3.157087 AGGCCTTGTACAATGAAAGGTG 58.843 45.455 14.26 0.00 42.13 4.00
3584 4037 3.525800 AGGCCTTGTACAATGAAAGGT 57.474 42.857 14.26 0.00 42.13 3.50
3585 4038 5.253330 TCTAAGGCCTTGTACAATGAAAGG 58.747 41.667 28.77 10.22 42.86 3.11
3586 4039 5.163713 GCTCTAAGGCCTTGTACAATGAAAG 60.164 44.000 28.77 12.95 0.00 2.62
3587 4040 4.700213 GCTCTAAGGCCTTGTACAATGAAA 59.300 41.667 28.77 2.40 0.00 2.69
3588 4041 4.261801 GCTCTAAGGCCTTGTACAATGAA 58.738 43.478 28.77 3.22 0.00 2.57
3589 4042 3.263170 TGCTCTAAGGCCTTGTACAATGA 59.737 43.478 28.77 12.34 0.00 2.57
3590 4043 3.609853 TGCTCTAAGGCCTTGTACAATG 58.390 45.455 28.77 7.68 0.00 2.82
3591 4044 4.010349 GTTGCTCTAAGGCCTTGTACAAT 58.990 43.478 28.77 1.45 0.00 2.71
3592 4045 3.072476 AGTTGCTCTAAGGCCTTGTACAA 59.928 43.478 28.77 21.40 0.00 2.41
3593 4046 2.637872 AGTTGCTCTAAGGCCTTGTACA 59.362 45.455 28.77 17.00 0.00 2.90
3594 4047 3.336138 AGTTGCTCTAAGGCCTTGTAC 57.664 47.619 28.77 14.60 0.00 2.90
3595 4048 3.197116 GGTAGTTGCTCTAAGGCCTTGTA 59.803 47.826 28.77 14.41 0.00 2.41
3596 4049 2.027100 GGTAGTTGCTCTAAGGCCTTGT 60.027 50.000 28.77 4.97 0.00 3.16
3597 4050 2.633488 GGTAGTTGCTCTAAGGCCTTG 58.367 52.381 28.77 17.30 0.00 3.61
3598 4051 1.560146 GGGTAGTTGCTCTAAGGCCTT 59.440 52.381 24.18 24.18 0.00 4.35
3599 4052 1.205055 GGGTAGTTGCTCTAAGGCCT 58.795 55.000 0.00 0.00 0.00 5.19
3600 4053 0.909623 TGGGTAGTTGCTCTAAGGCC 59.090 55.000 0.00 0.00 0.00 5.19
3601 4054 1.744114 GCTGGGTAGTTGCTCTAAGGC 60.744 57.143 0.00 0.00 0.00 4.35
3602 4055 1.555075 TGCTGGGTAGTTGCTCTAAGG 59.445 52.381 0.00 0.00 0.00 2.69
3603 4056 3.334583 TTGCTGGGTAGTTGCTCTAAG 57.665 47.619 0.00 0.00 0.00 2.18
3604 4057 4.224147 TGTATTGCTGGGTAGTTGCTCTAA 59.776 41.667 0.00 0.00 0.00 2.10
3605 4058 3.772572 TGTATTGCTGGGTAGTTGCTCTA 59.227 43.478 0.00 0.00 0.00 2.43
3606 4059 2.571653 TGTATTGCTGGGTAGTTGCTCT 59.428 45.455 0.00 0.00 0.00 4.09
3607 4060 2.985896 TGTATTGCTGGGTAGTTGCTC 58.014 47.619 0.00 0.00 0.00 4.26
3608 4061 3.282021 CATGTATTGCTGGGTAGTTGCT 58.718 45.455 0.00 0.00 0.00 3.91
3609 4062 3.016736 ACATGTATTGCTGGGTAGTTGC 58.983 45.455 0.00 0.00 0.00 4.17
3610 4063 5.523916 GTCTACATGTATTGCTGGGTAGTTG 59.476 44.000 5.91 0.00 32.26 3.16
3611 4064 5.425539 AGTCTACATGTATTGCTGGGTAGTT 59.574 40.000 5.91 0.00 32.26 2.24
3612 4065 4.962995 AGTCTACATGTATTGCTGGGTAGT 59.037 41.667 5.91 0.00 32.26 2.73
3613 4066 5.533482 GAGTCTACATGTATTGCTGGGTAG 58.467 45.833 5.91 0.00 0.00 3.18
3614 4067 4.037565 CGAGTCTACATGTATTGCTGGGTA 59.962 45.833 5.91 0.00 0.00 3.69
3619 4072 8.718102 AATTTTACGAGTCTACATGTATTGCT 57.282 30.769 5.91 4.97 0.00 3.91
3624 4077 6.267817 CCGGAATTTTACGAGTCTACATGTA 58.732 40.000 5.25 5.25 36.35 2.29
3630 4083 2.423185 TCGCCGGAATTTTACGAGTCTA 59.577 45.455 5.05 0.00 36.35 2.59
3635 4088 2.937469 TACTCGCCGGAATTTTACGA 57.063 45.000 5.05 0.85 36.35 3.43
3685 4138 2.107141 GCGAGTATGCGGGCTCTT 59.893 61.111 0.00 0.00 0.00 2.85
3784 4238 1.777272 GGCAGGAGATAGGGTTTGGAT 59.223 52.381 0.00 0.00 0.00 3.41
3805 4260 2.814183 GAATCGCGTGACTCGGTGGT 62.814 60.000 5.77 0.00 40.26 4.16
3808 4263 2.181021 GGAATCGCGTGACTCGGT 59.819 61.111 5.77 0.00 40.26 4.69
3814 4270 1.078708 GGGAAAGGGAATCGCGTGA 60.079 57.895 5.77 0.00 0.00 4.35
3886 4343 2.597340 CTCCACATTCGGCCCCAT 59.403 61.111 0.00 0.00 0.00 4.00
4048 4507 0.731417 CGGTCGTACTCATCGGTCTT 59.269 55.000 0.00 0.00 0.00 3.01
4076 4535 1.824329 GATCTCGCGGAGGAGGACA 60.824 63.158 6.13 0.00 34.74 4.02
4141 4609 0.041238 TCCGACCACTCCCTCTTCAT 59.959 55.000 0.00 0.00 0.00 2.57
4187 4655 1.696832 GAGGACGAAGGTGAATGCGC 61.697 60.000 0.00 0.00 0.00 6.09
4191 4659 1.254026 TCACGAGGACGAAGGTGAAT 58.746 50.000 0.00 0.00 42.66 2.57
4205 4673 2.939261 GCGGGTTCCTCCTTCACGA 61.939 63.158 0.00 0.00 36.25 4.35
4238 4706 3.461773 CTGGCCCGACGACTCCAT 61.462 66.667 0.00 0.00 0.00 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.