Multiple sequence alignment - TraesCS6B01G039100

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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 TraesCS6B01G039100 chr6B 100.000 2996 0 0 1 2996 23529606 23526611 0.000000e+00 5533
1 TraesCS6B01G039100 chr6B 95.317 1025 45 1 1060 2084 24818055 24819076 0.000000e+00 1624
2 TraesCS6B01G039100 chr6B 82.075 993 134 15 110 1076 24799786 24800760 0.000000e+00 808
3 TraesCS6B01G039100 chr6D 95.490 1020 39 4 1079 2092 13197446 13198464 0.000000e+00 1622
4 TraesCS6B01G039100 chr7B 83.813 834 114 16 2162 2987 73480372 73481192 0.000000e+00 773
5 TraesCS6B01G039100 chr7B 81.210 777 117 18 110 873 615323987 615324747 1.540000e-167 599
6 TraesCS6B01G039100 chr4B 83.632 837 110 23 2162 2987 15704711 15703891 0.000000e+00 761
7 TraesCS6B01G039100 chr4B 83.310 725 103 13 2272 2987 15688162 15687447 0.000000e+00 652
8 TraesCS6B01G039100 chr2B 83.532 838 114 19 2162 2987 89177868 89178693 0.000000e+00 761
9 TraesCS6B01G039100 chr2B 88.235 102 12 0 1 102 150140033 150139932 4.060000e-24 122
10 TraesCS6B01G039100 chrUn 83.493 836 116 17 2162 2987 220732295 220733118 0.000000e+00 760
11 TraesCS6B01G039100 chrUn 87.255 102 13 0 1 102 62406730 62406629 1.890000e-22 117
12 TraesCS6B01G039100 chrUn 86.275 102 14 0 1 102 21234561 21234662 8.780000e-21 111
13 TraesCS6B01G039100 chr5A 83.153 831 119 17 2167 2987 520528918 520528099 0.000000e+00 739
14 TraesCS6B01G039100 chr5A 86.275 102 14 0 1 102 557116369 557116268 8.780000e-21 111
15 TraesCS6B01G039100 chr6A 84.021 776 102 16 2156 2923 69203421 69204182 0.000000e+00 726
16 TraesCS6B01G039100 chr1A 82.297 836 106 25 2161 2987 38371226 38370424 0.000000e+00 686
17 TraesCS6B01G039100 chr1A 85.050 602 72 15 2395 2987 474427258 474426666 5.530000e-167 597
18 TraesCS6B01G039100 chr1D 84.539 608 80 8 169 763 228825663 228825057 9.250000e-165 590
19 TraesCS6B01G039100 chr1D 83.439 628 89 7 169 785 437274697 437274074 1.210000e-158 569
20 TraesCS6B01G039100 chr5D 84.396 596 73 10 166 747 84314185 84314774 4.330000e-158 568
21 TraesCS6B01G039100 chr5D 83.387 620 84 7 166 772 10985805 10986418 9.380000e-155 556
22 TraesCS6B01G039100 chr5D 83.642 593 86 5 166 747 29876902 29877494 5.650000e-152 547
23 TraesCS6B01G039100 chr3D 81.199 734 97 22 171 887 8383110 8383819 1.210000e-153 553
24 TraesCS6B01G039100 chr7A 90.777 412 33 5 2157 2565 650935092 650934683 2.030000e-151 545
25 TraesCS6B01G039100 chr7A 90.709 409 35 3 2159 2565 13181541 13181134 2.630000e-150 542
26 TraesCS6B01G039100 chr4D 83.276 586 85 4 169 742 475957316 475956732 7.360000e-146 527
27 TraesCS6B01G039100 chr4D 86.869 99 13 0 4 102 417415197 417415099 8.780000e-21 111
28 TraesCS6B01G039100 chr2D 91.176 102 9 0 1 102 590164881 590164780 4.030000e-29 139
29 TraesCS6B01G039100 chr3B 90.099 101 10 0 1 101 524443270 524443370 6.740000e-27 132
30 TraesCS6B01G039100 chr1B 91.209 91 8 0 12 102 667913249 667913339 1.130000e-24 124
31 TraesCS6B01G039100 chr7D 87.255 102 13 0 1 102 16419856 16419957 1.890000e-22 117


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 TraesCS6B01G039100 chr6B 23526611 23529606 2995 True 5533 5533 100.000 1 2996 1 chr6B.!!$R1 2995
1 TraesCS6B01G039100 chr6B 24818055 24819076 1021 False 1624 1624 95.317 1060 2084 1 chr6B.!!$F2 1024
2 TraesCS6B01G039100 chr6B 24799786 24800760 974 False 808 808 82.075 110 1076 1 chr6B.!!$F1 966
3 TraesCS6B01G039100 chr6D 13197446 13198464 1018 False 1622 1622 95.490 1079 2092 1 chr6D.!!$F1 1013
4 TraesCS6B01G039100 chr7B 73480372 73481192 820 False 773 773 83.813 2162 2987 1 chr7B.!!$F1 825
5 TraesCS6B01G039100 chr7B 615323987 615324747 760 False 599 599 81.210 110 873 1 chr7B.!!$F2 763
6 TraesCS6B01G039100 chr4B 15703891 15704711 820 True 761 761 83.632 2162 2987 1 chr4B.!!$R2 825
7 TraesCS6B01G039100 chr4B 15687447 15688162 715 True 652 652 83.310 2272 2987 1 chr4B.!!$R1 715
8 TraesCS6B01G039100 chr2B 89177868 89178693 825 False 761 761 83.532 2162 2987 1 chr2B.!!$F1 825
9 TraesCS6B01G039100 chrUn 220732295 220733118 823 False 760 760 83.493 2162 2987 1 chrUn.!!$F2 825
10 TraesCS6B01G039100 chr5A 520528099 520528918 819 True 739 739 83.153 2167 2987 1 chr5A.!!$R1 820
11 TraesCS6B01G039100 chr6A 69203421 69204182 761 False 726 726 84.021 2156 2923 1 chr6A.!!$F1 767
12 TraesCS6B01G039100 chr1A 38370424 38371226 802 True 686 686 82.297 2161 2987 1 chr1A.!!$R1 826
13 TraesCS6B01G039100 chr1A 474426666 474427258 592 True 597 597 85.050 2395 2987 1 chr1A.!!$R2 592
14 TraesCS6B01G039100 chr1D 228825057 228825663 606 True 590 590 84.539 169 763 1 chr1D.!!$R1 594
15 TraesCS6B01G039100 chr1D 437274074 437274697 623 True 569 569 83.439 169 785 1 chr1D.!!$R2 616
16 TraesCS6B01G039100 chr5D 84314185 84314774 589 False 568 568 84.396 166 747 1 chr5D.!!$F3 581
17 TraesCS6B01G039100 chr5D 10985805 10986418 613 False 556 556 83.387 166 772 1 chr5D.!!$F1 606
18 TraesCS6B01G039100 chr5D 29876902 29877494 592 False 547 547 83.642 166 747 1 chr5D.!!$F2 581
19 TraesCS6B01G039100 chr3D 8383110 8383819 709 False 553 553 81.199 171 887 1 chr3D.!!$F1 716
20 TraesCS6B01G039100 chr4D 475956732 475957316 584 True 527 527 83.276 169 742 1 chr4D.!!$R2 573

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
141 142 0.033796 ACTTCCCGGTCCTCGATGTA 60.034 55.0 0.0 0.0 42.43 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2131 0.245539 GTCTTACGTGCTAGGCCACA 59.754 55.0 5.01 0.0 35.47 4.17 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
19 20 2.051334 TGCTGTTTTACTGTGCTGGT 57.949 45.000 0.00 0.00 0.00 4.00
20 21 3.201353 TGCTGTTTTACTGTGCTGGTA 57.799 42.857 0.00 0.00 0.00 3.25
21 22 2.875933 TGCTGTTTTACTGTGCTGGTAC 59.124 45.455 0.00 0.00 0.00 3.34
22 23 3.139077 GCTGTTTTACTGTGCTGGTACT 58.861 45.455 0.00 0.00 0.00 2.73
23 24 4.202274 TGCTGTTTTACTGTGCTGGTACTA 60.202 41.667 0.00 0.00 0.00 1.82
24 25 4.935808 GCTGTTTTACTGTGCTGGTACTAT 59.064 41.667 0.00 0.00 0.00 2.12
25 26 5.163854 GCTGTTTTACTGTGCTGGTACTATG 60.164 44.000 0.00 0.00 0.00 2.23
26 27 5.242434 TGTTTTACTGTGCTGGTACTATGG 58.758 41.667 0.00 0.00 0.00 2.74
27 28 4.481368 TTTACTGTGCTGGTACTATGGG 57.519 45.455 0.00 0.00 0.00 4.00
28 29 1.204146 ACTGTGCTGGTACTATGGGG 58.796 55.000 0.00 0.00 0.00 4.96
29 30 0.179045 CTGTGCTGGTACTATGGGGC 60.179 60.000 0.00 0.00 0.00 5.80
30 31 1.148498 GTGCTGGTACTATGGGGCC 59.852 63.158 0.00 0.00 0.00 5.80
31 32 1.004230 TGCTGGTACTATGGGGCCT 59.996 57.895 0.84 0.00 0.00 5.19
32 33 0.623324 TGCTGGTACTATGGGGCCTT 60.623 55.000 0.84 0.00 0.00 4.35
33 34 1.344598 TGCTGGTACTATGGGGCCTTA 60.345 52.381 0.84 0.00 0.00 2.69
34 35 1.348036 GCTGGTACTATGGGGCCTTAG 59.652 57.143 0.84 7.98 0.00 2.18
35 36 1.348036 CTGGTACTATGGGGCCTTAGC 59.652 57.143 0.84 0.00 38.76 3.09
36 37 1.344598 TGGTACTATGGGGCCTTAGCA 60.345 52.381 0.84 0.69 42.56 3.49
37 38 1.071857 GGTACTATGGGGCCTTAGCAC 59.928 57.143 0.84 6.21 43.97 4.40
38 39 1.045407 TACTATGGGGCCTTAGCACG 58.955 55.000 0.84 0.00 46.55 5.34
39 40 0.689745 ACTATGGGGCCTTAGCACGA 60.690 55.000 0.84 0.00 46.55 4.35
40 41 0.249911 CTATGGGGCCTTAGCACGAC 60.250 60.000 0.84 0.00 46.55 4.34
41 42 1.692173 TATGGGGCCTTAGCACGACC 61.692 60.000 0.84 0.00 46.55 4.79
42 43 4.832608 GGGGCCTTAGCACGACCG 62.833 72.222 0.84 0.00 46.55 4.79
44 45 4.452733 GGCCTTAGCACGACCGCT 62.453 66.667 0.00 0.00 46.26 5.52
45 46 2.434359 GCCTTAGCACGACCGCTT 60.434 61.111 4.24 0.00 43.56 4.68
46 47 2.033194 GCCTTAGCACGACCGCTTT 61.033 57.895 4.24 0.00 43.56 3.51
47 48 1.574702 GCCTTAGCACGACCGCTTTT 61.575 55.000 4.24 0.00 43.56 2.27
48 49 0.442699 CCTTAGCACGACCGCTTTTC 59.557 55.000 4.24 0.00 43.56 2.29
49 50 0.093026 CTTAGCACGACCGCTTTTCG 59.907 55.000 4.24 0.00 43.56 3.46
50 51 0.318869 TTAGCACGACCGCTTTTCGA 60.319 50.000 5.60 0.00 43.56 3.71
51 52 1.005294 TAGCACGACCGCTTTTCGAC 61.005 55.000 5.60 0.00 43.56 4.20
52 53 2.308039 GCACGACCGCTTTTCGACT 61.308 57.895 5.60 0.00 41.67 4.18
53 54 1.487231 CACGACCGCTTTTCGACTG 59.513 57.895 5.60 0.00 41.67 3.51
54 55 1.066918 ACGACCGCTTTTCGACTGT 59.933 52.632 5.60 0.00 41.67 3.55
55 56 0.938168 ACGACCGCTTTTCGACTGTC 60.938 55.000 0.00 0.00 41.67 3.51
56 57 0.663568 CGACCGCTTTTCGACTGTCT 60.664 55.000 6.21 0.00 41.67 3.41
57 58 1.400629 CGACCGCTTTTCGACTGTCTA 60.401 52.381 6.21 0.00 41.67 2.59
58 59 1.984297 GACCGCTTTTCGACTGTCTAC 59.016 52.381 6.21 0.00 41.67 2.59
59 60 1.612463 ACCGCTTTTCGACTGTCTACT 59.388 47.619 6.21 0.00 41.67 2.57
60 61 2.816087 ACCGCTTTTCGACTGTCTACTA 59.184 45.455 6.21 0.00 41.67 1.82
61 62 3.169733 CCGCTTTTCGACTGTCTACTAC 58.830 50.000 6.21 0.00 41.67 2.73
62 63 3.365666 CCGCTTTTCGACTGTCTACTACA 60.366 47.826 6.21 0.00 41.67 2.74
63 64 4.224433 CGCTTTTCGACTGTCTACTACAA 58.776 43.478 6.21 0.00 41.67 2.41
64 65 4.088213 CGCTTTTCGACTGTCTACTACAAC 59.912 45.833 6.21 0.00 41.67 3.32
65 66 4.980434 GCTTTTCGACTGTCTACTACAACA 59.020 41.667 6.21 0.00 37.74 3.33
66 67 5.461078 GCTTTTCGACTGTCTACTACAACAA 59.539 40.000 6.21 0.00 37.74 2.83
67 68 6.345882 GCTTTTCGACTGTCTACTACAACAAG 60.346 42.308 6.21 0.00 37.74 3.16
68 69 5.762825 TTCGACTGTCTACTACAACAAGT 57.237 39.130 6.21 0.00 37.74 3.16
69 70 5.762825 TCGACTGTCTACTACAACAAGTT 57.237 39.130 6.21 0.00 37.74 2.66
70 71 6.140303 TCGACTGTCTACTACAACAAGTTT 57.860 37.500 6.21 0.00 37.74 2.66
71 72 6.567050 TCGACTGTCTACTACAACAAGTTTT 58.433 36.000 6.21 0.00 37.74 2.43
72 73 7.037438 TCGACTGTCTACTACAACAAGTTTTT 58.963 34.615 6.21 0.00 37.74 1.94
73 74 7.221452 TCGACTGTCTACTACAACAAGTTTTTC 59.779 37.037 6.21 0.00 37.74 2.29
74 75 7.516312 CGACTGTCTACTACAACAAGTTTTTCC 60.516 40.741 6.21 0.00 37.74 3.13
75 76 6.541278 ACTGTCTACTACAACAAGTTTTTCCC 59.459 38.462 0.00 0.00 37.74 3.97
76 77 5.524646 TGTCTACTACAACAAGTTTTTCCCG 59.475 40.000 0.00 0.00 34.29 5.14
77 78 5.049886 GTCTACTACAACAAGTTTTTCCCGG 60.050 44.000 0.00 0.00 0.00 5.73
78 79 2.359848 ACTACAACAAGTTTTTCCCGGC 59.640 45.455 0.00 0.00 0.00 6.13
79 80 1.480789 ACAACAAGTTTTTCCCGGCT 58.519 45.000 0.00 0.00 0.00 5.52
80 81 1.407618 ACAACAAGTTTTTCCCGGCTC 59.592 47.619 0.00 0.00 0.00 4.70
81 82 1.037493 AACAAGTTTTTCCCGGCTCC 58.963 50.000 0.00 0.00 0.00 4.70
82 83 1.170290 ACAAGTTTTTCCCGGCTCCG 61.170 55.000 0.00 0.48 39.44 4.63
99 100 4.883354 GGCGAGGGAGGGGCAATG 62.883 72.222 0.00 0.00 0.00 2.82
100 101 3.797353 GCGAGGGAGGGGCAATGA 61.797 66.667 0.00 0.00 0.00 2.57
101 102 2.190578 CGAGGGAGGGGCAATGAC 59.809 66.667 0.00 0.00 0.00 3.06
102 103 2.370445 CGAGGGAGGGGCAATGACT 61.370 63.158 0.00 0.00 0.00 3.41
103 104 1.915078 CGAGGGAGGGGCAATGACTT 61.915 60.000 0.00 0.00 0.00 3.01
104 105 0.394899 GAGGGAGGGGCAATGACTTG 60.395 60.000 0.00 0.00 35.36 3.16
126 127 1.134965 CGGTCTGGGTCATGAGACTTC 60.135 57.143 11.35 0.00 44.36 3.01
128 129 1.208293 GTCTGGGTCATGAGACTTCCC 59.792 57.143 10.72 10.72 44.36 3.97
140 141 1.305046 ACTTCCCGGTCCTCGATGT 60.305 57.895 0.00 0.00 42.43 3.06
141 142 0.033796 ACTTCCCGGTCCTCGATGTA 60.034 55.000 0.00 0.00 42.43 2.29
149 150 2.485124 CGGTCCTCGATGTAGTAGGAGT 60.485 54.545 0.00 0.00 40.06 3.85
172 173 2.125106 GTGGGATGACGGGTCTGC 60.125 66.667 0.00 0.00 0.00 4.26
216 217 2.842496 TCTGCTGGAGATCTTCATTGGT 59.158 45.455 3.55 0.00 0.00 3.67
223 224 3.129988 GGAGATCTTCATTGGTTGCTTGG 59.870 47.826 0.00 0.00 0.00 3.61
224 225 3.094572 AGATCTTCATTGGTTGCTTGGG 58.905 45.455 0.00 0.00 0.00 4.12
225 226 2.380064 TCTTCATTGGTTGCTTGGGT 57.620 45.000 0.00 0.00 0.00 4.51
250 251 4.858850 TGTAGATTGCTGGATCAAATGGT 58.141 39.130 0.00 0.00 0.00 3.55
260 261 3.133183 TGGATCAAATGGTATTCGGTCGA 59.867 43.478 0.00 0.00 0.00 4.20
350 351 1.078988 GGGACACGCCGGTATTTCA 60.079 57.895 1.90 0.00 37.63 2.69
373 374 6.998074 TCAATTTTCATAGTGAAGACAGTGGT 59.002 34.615 0.00 0.00 37.70 4.16
381 382 3.392616 AGTGAAGACAGTGGTGGAGAATT 59.607 43.478 0.00 0.00 0.00 2.17
382 383 3.748568 GTGAAGACAGTGGTGGAGAATTC 59.251 47.826 0.00 0.00 0.00 2.17
403 404 3.386237 GGCGGCTGAGGTCTGAGT 61.386 66.667 0.00 0.00 0.00 3.41
414 415 3.055819 TGAGGTCTGAGTCCTTGTAATGC 60.056 47.826 0.00 0.00 35.20 3.56
489 490 3.818787 CGGCATCAGCAAGTGGGC 61.819 66.667 0.00 0.00 44.61 5.36
490 491 3.455469 GGCATCAGCAAGTGGGCC 61.455 66.667 0.00 0.00 44.61 5.80
564 565 1.342819 GTGGCCTTAATTGGTTGTGCA 59.657 47.619 3.32 0.00 0.00 4.57
688 702 1.068610 CGGCGCTTTTGGAGAATTTGA 60.069 47.619 7.64 0.00 0.00 2.69
695 709 5.519722 GCTTTTGGAGAATTTGAACTTCGA 58.480 37.500 0.00 0.00 0.00 3.71
710 725 3.220110 ACTTCGAGTGTTGTCTAGGTGA 58.780 45.455 0.00 0.00 0.00 4.02
718 733 3.307242 GTGTTGTCTAGGTGATGATTCGC 59.693 47.826 0.00 0.00 0.00 4.70
720 735 2.021457 TGTCTAGGTGATGATTCGCGA 58.979 47.619 3.71 3.71 32.95 5.87
737 752 1.262683 GCGATGCAGCTACAAGGAATC 59.737 52.381 0.00 0.00 0.00 2.52
752 767 2.131183 GGAATCGATCACTGTAGCAGC 58.869 52.381 0.00 0.00 34.37 5.25
755 770 4.550422 GAATCGATCACTGTAGCAGCATA 58.450 43.478 0.00 0.00 34.37 3.14
767 782 9.229784 CACTGTAGCAGCATATTTCTTTATTTG 57.770 33.333 0.00 0.00 34.37 2.32
773 788 8.863049 AGCAGCATATTTCTTTATTTGTTTTCG 58.137 29.630 0.00 0.00 0.00 3.46
820 835 3.023119 TGTCTTTTGGTTGTGTGCATCT 58.977 40.909 0.00 0.00 0.00 2.90
824 839 4.275689 TCTTTTGGTTGTGTGCATCTGTAG 59.724 41.667 0.00 0.00 0.00 2.74
829 844 2.455674 TGTGTGCATCTGTAGTGTCC 57.544 50.000 0.00 0.00 0.00 4.02
854 869 5.804692 ACGACATTGTGTTGTTGTAAAGA 57.195 34.783 0.00 0.00 42.03 2.52
873 891 4.252971 AGATCGGGTGTAATTGGTATCG 57.747 45.455 0.00 0.00 0.00 2.92
893 911 8.857098 GGTATCGTGATATTAATATAGCTCCCA 58.143 37.037 7.97 0.00 0.00 4.37
911 929 5.622770 TCCCATTTAAAGAAAGAGTTCGC 57.377 39.130 0.00 0.00 38.90 4.70
932 959 4.966970 CGCGAGCAAGCAGAGTATATATAG 59.033 45.833 0.00 0.00 36.85 1.31
933 960 5.220681 CGCGAGCAAGCAGAGTATATATAGA 60.221 44.000 0.00 0.00 36.85 1.98
968 995 2.613691 CAACCAGCATCCAATCAAAGC 58.386 47.619 0.00 0.00 0.00 3.51
969 996 1.927487 ACCAGCATCCAATCAAAGCA 58.073 45.000 0.00 0.00 0.00 3.91
970 997 1.547372 ACCAGCATCCAATCAAAGCAC 59.453 47.619 0.00 0.00 0.00 4.40
971 998 1.822990 CCAGCATCCAATCAAAGCACT 59.177 47.619 0.00 0.00 0.00 4.40
972 999 2.159282 CCAGCATCCAATCAAAGCACTC 60.159 50.000 0.00 0.00 0.00 3.51
973 1000 2.753452 CAGCATCCAATCAAAGCACTCT 59.247 45.455 0.00 0.00 0.00 3.24
974 1001 3.015327 AGCATCCAATCAAAGCACTCTC 58.985 45.455 0.00 0.00 0.00 3.20
975 1002 3.015327 GCATCCAATCAAAGCACTCTCT 58.985 45.455 0.00 0.00 0.00 3.10
976 1003 3.065095 GCATCCAATCAAAGCACTCTCTC 59.935 47.826 0.00 0.00 0.00 3.20
1015 1042 1.726791 GAGACATGTACCGTTGTGCTG 59.273 52.381 0.00 0.00 0.00 4.41
1121 1148 2.401766 CCATCGCAGACCTTGTGCC 61.402 63.158 0.00 0.00 42.51 5.01
1148 1175 6.276832 AGGTACGTCACTTTTGCTTAGATA 57.723 37.500 0.00 0.00 0.00 1.98
1149 1176 6.875076 AGGTACGTCACTTTTGCTTAGATAT 58.125 36.000 0.00 0.00 0.00 1.63
1150 1177 8.004087 AGGTACGTCACTTTTGCTTAGATATA 57.996 34.615 0.00 0.00 0.00 0.86
1226 1258 4.348857 CATCGATGATGCGCCTCA 57.651 55.556 21.02 17.82 33.17 3.86
1232 1264 0.462581 GATGATGCGCCTCAAGTGGA 60.463 55.000 19.32 0.00 0.00 4.02
1287 1319 2.672996 GCTTGGACCGGCATGTGT 60.673 61.111 0.00 0.00 0.00 3.72
1410 1442 4.778415 CTCCCACACGACCTCGCG 62.778 72.222 0.00 0.00 44.43 5.87
1433 1465 3.053896 GGTCCCCTTCGCAAACCG 61.054 66.667 0.00 0.00 38.61 4.44
1457 1489 1.293498 CCGTCCTCACCACCTTCAG 59.707 63.158 0.00 0.00 0.00 3.02
1594 1626 0.585357 GAGCGCCATGAACATGCTAG 59.415 55.000 2.29 4.29 37.49 3.42
1595 1627 0.816825 AGCGCCATGAACATGCTAGG 60.817 55.000 2.29 0.00 37.49 3.02
1632 1664 1.408266 GGTGACCATGGTATGTGGACC 60.408 57.143 19.80 12.85 39.12 4.46
1681 1713 1.006220 CTGCCACGTCAGCTGTACA 60.006 57.895 14.67 0.00 0.00 2.90
1706 1738 4.021925 GGCGGTCACCAAGCTCCT 62.022 66.667 0.00 0.00 0.00 3.69
1755 1787 2.587889 CCATTCCCCTACCGCGTT 59.412 61.111 4.92 0.00 0.00 4.84
1794 1826 3.637273 GGGCTCACGGACAAGGGT 61.637 66.667 0.00 0.00 0.00 4.34
1797 1829 0.252197 GGCTCACGGACAAGGGTTAT 59.748 55.000 0.00 0.00 0.00 1.89
2014 2046 1.955080 AGTAGGCTGCTACGATGTACC 59.045 52.381 2.25 0.00 35.16 3.34
2022 2058 3.527533 TGCTACGATGTACCAACAATCC 58.472 45.455 0.00 0.00 39.58 3.01
2029 2065 2.166829 TGTACCAACAATCCATGCCAC 58.833 47.619 0.00 0.00 30.91 5.01
2061 2097 5.644188 AGTACCATGGCCAATAATTAGCAT 58.356 37.500 10.96 0.00 0.00 3.79
2084 2120 4.070552 AGGGAGCGCGAGGTTCAC 62.071 66.667 12.10 1.86 45.11 3.18
2087 2123 2.049063 GAGCGCGAGGTTCACACT 60.049 61.111 12.10 0.00 45.11 3.55
2088 2124 2.356313 AGCGCGAGGTTCACACTG 60.356 61.111 12.10 0.00 40.01 3.66
2090 2126 1.954146 GCGCGAGGTTCACACTGAA 60.954 57.895 12.10 0.00 33.32 3.02
2091 2127 1.891060 GCGCGAGGTTCACACTGAAG 61.891 60.000 12.10 0.00 37.00 3.02
2092 2128 0.597637 CGCGAGGTTCACACTGAAGT 60.598 55.000 0.00 0.00 37.00 3.01
2102 2138 3.100545 CACTGAAGTGTTGTGGCCT 57.899 52.632 3.32 0.00 40.96 5.19
2103 2139 2.254546 CACTGAAGTGTTGTGGCCTA 57.745 50.000 3.32 0.00 40.96 3.93
2104 2140 2.146342 CACTGAAGTGTTGTGGCCTAG 58.854 52.381 3.32 0.00 40.96 3.02
2105 2141 1.160137 CTGAAGTGTTGTGGCCTAGC 58.840 55.000 3.32 0.00 0.00 3.42
2106 2142 0.472044 TGAAGTGTTGTGGCCTAGCA 59.528 50.000 3.32 0.00 0.00 3.49
2107 2143 0.875059 GAAGTGTTGTGGCCTAGCAC 59.125 55.000 15.97 15.97 0.00 4.40
2108 2144 0.884704 AAGTGTTGTGGCCTAGCACG 60.885 55.000 17.09 0.00 35.46 5.34
2109 2145 1.597027 GTGTTGTGGCCTAGCACGT 60.597 57.895 3.32 0.00 0.00 4.49
2110 2146 0.320073 GTGTTGTGGCCTAGCACGTA 60.320 55.000 3.32 0.00 0.00 3.57
2111 2147 0.393448 TGTTGTGGCCTAGCACGTAA 59.607 50.000 3.32 0.00 0.00 3.18
2113 2149 0.970640 TTGTGGCCTAGCACGTAAGA 59.029 50.000 3.32 0.00 43.62 2.10
2114 2150 0.245539 TGTGGCCTAGCACGTAAGAC 59.754 55.000 3.32 0.00 43.62 3.01
2115 2151 0.245539 GTGGCCTAGCACGTAAGACA 59.754 55.000 3.32 0.00 43.62 3.41
2116 2152 1.134788 GTGGCCTAGCACGTAAGACAT 60.135 52.381 3.32 0.00 43.62 3.06
2117 2153 1.553248 TGGCCTAGCACGTAAGACATT 59.447 47.619 3.32 0.00 43.62 2.71
2118 2154 2.027561 TGGCCTAGCACGTAAGACATTT 60.028 45.455 3.32 0.00 43.62 2.32
2119 2155 3.007635 GGCCTAGCACGTAAGACATTTT 58.992 45.455 0.00 0.00 43.62 1.82
2120 2156 3.181510 GGCCTAGCACGTAAGACATTTTG 60.182 47.826 0.00 0.00 43.62 2.44
2121 2157 3.435671 GCCTAGCACGTAAGACATTTTGT 59.564 43.478 0.00 0.00 43.62 2.83
2122 2158 4.628333 GCCTAGCACGTAAGACATTTTGTA 59.372 41.667 0.00 0.00 43.62 2.41
2123 2159 5.293569 GCCTAGCACGTAAGACATTTTGTAT 59.706 40.000 0.00 0.00 43.62 2.29
2124 2160 6.509677 GCCTAGCACGTAAGACATTTTGTATC 60.510 42.308 0.00 0.00 43.62 2.24
2125 2161 6.533723 CCTAGCACGTAAGACATTTTGTATCA 59.466 38.462 0.00 0.00 43.62 2.15
2126 2162 6.408858 AGCACGTAAGACATTTTGTATCAG 57.591 37.500 0.00 0.00 43.62 2.90
2127 2163 5.022021 GCACGTAAGACATTTTGTATCAGC 58.978 41.667 0.00 0.00 43.62 4.26
2128 2164 5.163854 GCACGTAAGACATTTTGTATCAGCT 60.164 40.000 0.00 0.00 43.62 4.24
2129 2165 6.243551 CACGTAAGACATTTTGTATCAGCTG 58.756 40.000 7.63 7.63 43.62 4.24
2130 2166 5.932303 ACGTAAGACATTTTGTATCAGCTGT 59.068 36.000 14.67 3.75 43.62 4.40
2131 2167 6.090898 ACGTAAGACATTTTGTATCAGCTGTC 59.909 38.462 14.67 6.49 43.62 3.51
2132 2168 6.090763 CGTAAGACATTTTGTATCAGCTGTCA 59.909 38.462 14.67 9.07 43.02 3.58
2133 2169 6.492007 AAGACATTTTGTATCAGCTGTCAG 57.508 37.500 14.67 0.00 36.37 3.51
2134 2170 4.394300 AGACATTTTGTATCAGCTGTCAGC 59.606 41.667 17.48 17.48 42.84 4.26
2145 2181 1.867615 CTGTCAGCTCAGCTTGTGC 59.132 57.895 0.00 0.00 36.40 4.57
2146 2182 1.575576 CTGTCAGCTCAGCTTGTGCC 61.576 60.000 0.00 0.00 36.40 5.01
2147 2183 1.598962 GTCAGCTCAGCTTGTGCCA 60.599 57.895 0.00 0.00 36.40 4.92
2148 2184 0.959372 GTCAGCTCAGCTTGTGCCAT 60.959 55.000 0.00 0.00 36.40 4.40
2149 2185 0.614812 TCAGCTCAGCTTGTGCCATA 59.385 50.000 0.00 0.00 36.40 2.74
2150 2186 1.003464 TCAGCTCAGCTTGTGCCATAA 59.997 47.619 0.00 0.00 36.40 1.90
2151 2187 1.400846 CAGCTCAGCTTGTGCCATAAG 59.599 52.381 0.00 0.00 36.40 1.73
2152 2188 0.737219 GCTCAGCTTGTGCCATAAGG 59.263 55.000 3.27 0.00 40.80 2.69
2153 2189 1.679944 GCTCAGCTTGTGCCATAAGGA 60.680 52.381 3.27 0.00 40.80 3.36
2154 2190 2.928334 CTCAGCTTGTGCCATAAGGAT 58.072 47.619 3.27 0.00 40.80 3.24
2192 2228 0.817634 CCACCGGTGCTTGAACTTGA 60.818 55.000 29.75 0.00 0.00 3.02
2253 2290 6.676950 ACATTAAATCGATGCAACAACTTGA 58.323 32.000 0.00 0.00 0.00 3.02
2257 2294 3.607422 TCGATGCAACAACTTGACTTG 57.393 42.857 0.00 0.00 0.00 3.16
2295 2332 3.501828 TGCAAATCACAGTTGAATACGCT 59.498 39.130 0.00 0.00 34.61 5.07
2296 2333 3.848019 GCAAATCACAGTTGAATACGCTG 59.152 43.478 0.00 0.00 34.61 5.18
2299 2337 2.488952 TCACAGTTGAATACGCTGCAA 58.511 42.857 0.00 0.00 33.87 4.08
2306 2344 0.654683 GAATACGCTGCAAGGCTGAG 59.345 55.000 0.00 0.00 34.12 3.35
2319 2357 2.185494 GCTGAGTAGGCATGCCAGC 61.185 63.158 37.18 30.56 42.52 4.85
2346 2384 4.329545 GGCCCGCTGTCAGGACAA 62.330 66.667 1.14 0.00 41.33 3.18
2357 2395 2.106338 TGTCAGGACAAAAGATGCAGGA 59.894 45.455 0.00 0.00 38.56 3.86
2364 2402 1.069022 CAAAAGATGCAGGACGTGTGG 60.069 52.381 0.00 0.00 0.00 4.17
2368 2406 2.238847 GATGCAGGACGTGTGGCCTA 62.239 60.000 3.32 0.00 32.03 3.93
2370 2408 0.973496 TGCAGGACGTGTGGCCTATA 60.973 55.000 3.32 0.00 32.03 1.31
2385 2423 7.651704 GTGTGGCCTATAAATTTGCGAAAATAT 59.348 33.333 3.32 0.00 0.00 1.28
2399 2437 9.712305 TTTGCGAAAATATCCTTGGAAATTTTA 57.288 25.926 0.00 0.00 33.03 1.52
2424 2462 1.003355 CGAGAAAGCCCCAGCAAGA 60.003 57.895 0.00 0.00 43.56 3.02
2425 2463 1.301677 CGAGAAAGCCCCAGCAAGAC 61.302 60.000 0.00 0.00 43.56 3.01
2453 2494 4.321750 CCCGTCTGTCAGTACAAAGTGTAT 60.322 45.833 0.00 0.00 35.05 2.29
2489 2531 3.229276 AGTCATGCTCTCTCTTGAACG 57.771 47.619 0.00 0.00 0.00 3.95
2502 2544 0.529773 TTGAACGCGAGAACTGCAGT 60.530 50.000 15.25 15.25 0.00 4.40
2526 2568 1.137086 CACGCTGAAGGTACTAGCCAT 59.863 52.381 0.00 0.00 38.49 4.40
2527 2569 1.137086 ACGCTGAAGGTACTAGCCATG 59.863 52.381 0.00 0.00 38.49 3.66
2528 2570 1.137086 CGCTGAAGGTACTAGCCATGT 59.863 52.381 0.00 0.00 38.49 3.21
2543 2585 2.455557 CCATGTCAGCCCCAACATTTA 58.544 47.619 0.00 0.00 33.92 1.40
2547 2589 2.225242 TGTCAGCCCCAACATTTACCAT 60.225 45.455 0.00 0.00 0.00 3.55
2548 2590 2.831526 GTCAGCCCCAACATTTACCATT 59.168 45.455 0.00 0.00 0.00 3.16
2550 2592 2.566724 CAGCCCCAACATTTACCATTGT 59.433 45.455 0.00 0.00 0.00 2.71
2555 2597 5.681179 GCCCCAACATTTACCATTGTCATAC 60.681 44.000 0.00 0.00 0.00 2.39
2558 2600 6.035843 CCAACATTTACCATTGTCATACTGC 58.964 40.000 0.00 0.00 0.00 4.40
2599 2641 5.416639 TCTTATAACAAGTACGCTCACTGGA 59.583 40.000 0.00 0.00 0.00 3.86
2607 2649 1.293179 CGCTCACTGGACATGGACA 59.707 57.895 0.00 0.00 0.00 4.02
2625 2667 3.169198 GCAGTTAGTGCGGCTCAC 58.831 61.111 0.00 0.00 43.99 3.51
2886 2937 7.716799 AATTTTCACTTGTGGCCTATATTCA 57.283 32.000 3.32 0.00 0.00 2.57
2887 2938 7.716799 ATTTTCACTTGTGGCCTATATTCAA 57.283 32.000 3.32 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.051334 ACCAGCACAGTAAAACAGCA 57.949 45.000 0.00 0.00 0.00 4.41
1 2 3.139077 AGTACCAGCACAGTAAAACAGC 58.861 45.455 0.00 0.00 0.00 4.40
2 3 5.351465 CCATAGTACCAGCACAGTAAAACAG 59.649 44.000 0.00 0.00 0.00 3.16
3 4 5.242434 CCATAGTACCAGCACAGTAAAACA 58.758 41.667 0.00 0.00 0.00 2.83
4 5 4.634443 CCCATAGTACCAGCACAGTAAAAC 59.366 45.833 0.00 0.00 0.00 2.43
5 6 4.323945 CCCCATAGTACCAGCACAGTAAAA 60.324 45.833 0.00 0.00 0.00 1.52
6 7 3.199071 CCCCATAGTACCAGCACAGTAAA 59.801 47.826 0.00 0.00 0.00 2.01
7 8 2.769663 CCCCATAGTACCAGCACAGTAA 59.230 50.000 0.00 0.00 0.00 2.24
8 9 2.394632 CCCCATAGTACCAGCACAGTA 58.605 52.381 0.00 0.00 0.00 2.74
9 10 1.204146 CCCCATAGTACCAGCACAGT 58.796 55.000 0.00 0.00 0.00 3.55
10 11 0.179045 GCCCCATAGTACCAGCACAG 60.179 60.000 0.00 0.00 0.00 3.66
11 12 1.632018 GGCCCCATAGTACCAGCACA 61.632 60.000 0.00 0.00 0.00 4.57
12 13 1.148498 GGCCCCATAGTACCAGCAC 59.852 63.158 0.00 0.00 0.00 4.40
13 14 0.623324 AAGGCCCCATAGTACCAGCA 60.623 55.000 0.00 0.00 0.00 4.41
14 15 1.348036 CTAAGGCCCCATAGTACCAGC 59.652 57.143 0.00 0.00 0.00 4.85
15 16 1.348036 GCTAAGGCCCCATAGTACCAG 59.652 57.143 0.00 0.00 0.00 4.00
16 17 1.344598 TGCTAAGGCCCCATAGTACCA 60.345 52.381 0.00 0.00 37.74 3.25
17 18 1.071857 GTGCTAAGGCCCCATAGTACC 59.928 57.143 14.33 2.29 37.74 3.34
18 19 1.270147 CGTGCTAAGGCCCCATAGTAC 60.270 57.143 14.94 14.94 37.74 2.73
19 20 1.045407 CGTGCTAAGGCCCCATAGTA 58.955 55.000 0.00 0.00 37.74 1.82
20 21 0.689745 TCGTGCTAAGGCCCCATAGT 60.690 55.000 0.00 0.00 37.74 2.12
21 22 0.249911 GTCGTGCTAAGGCCCCATAG 60.250 60.000 0.00 0.67 37.74 2.23
22 23 1.692173 GGTCGTGCTAAGGCCCCATA 61.692 60.000 0.00 0.00 37.74 2.74
23 24 2.590092 GTCGTGCTAAGGCCCCAT 59.410 61.111 0.00 0.00 37.74 4.00
24 25 3.712907 GGTCGTGCTAAGGCCCCA 61.713 66.667 0.00 0.00 37.74 4.96
25 26 4.832608 CGGTCGTGCTAAGGCCCC 62.833 72.222 0.00 0.00 37.74 5.80
27 28 3.952628 AAGCGGTCGTGCTAAGGCC 62.953 63.158 0.00 0.00 46.60 5.19
28 29 1.574702 AAAAGCGGTCGTGCTAAGGC 61.575 55.000 0.00 0.00 46.60 4.35
29 30 0.442699 GAAAAGCGGTCGTGCTAAGG 59.557 55.000 0.00 0.00 46.60 2.69
30 31 0.093026 CGAAAAGCGGTCGTGCTAAG 59.907 55.000 0.00 0.00 46.60 2.18
31 32 0.318869 TCGAAAAGCGGTCGTGCTAA 60.319 50.000 6.62 0.00 46.60 3.09
32 33 1.005294 GTCGAAAAGCGGTCGTGCTA 61.005 55.000 6.62 0.00 46.60 3.49
34 35 2.170273 GTCGAAAAGCGGTCGTGC 59.830 61.111 6.62 0.00 41.33 5.34
35 36 1.213094 ACAGTCGAAAAGCGGTCGTG 61.213 55.000 6.62 2.42 41.33 4.35
36 37 0.938168 GACAGTCGAAAAGCGGTCGT 60.938 55.000 6.62 0.00 41.33 4.34
37 38 0.663568 AGACAGTCGAAAAGCGGTCG 60.664 55.000 0.00 0.94 41.33 4.79
38 39 1.984297 GTAGACAGTCGAAAAGCGGTC 59.016 52.381 0.00 0.00 41.33 4.79
39 40 1.612463 AGTAGACAGTCGAAAAGCGGT 59.388 47.619 0.00 0.00 41.33 5.68
40 41 2.349297 AGTAGACAGTCGAAAAGCGG 57.651 50.000 0.00 0.00 41.33 5.52
41 42 3.818387 TGTAGTAGACAGTCGAAAAGCG 58.182 45.455 0.00 0.00 35.85 4.68
42 43 4.980434 TGTTGTAGTAGACAGTCGAAAAGC 59.020 41.667 0.00 0.00 39.88 3.51
43 44 6.696148 ACTTGTTGTAGTAGACAGTCGAAAAG 59.304 38.462 0.00 0.00 39.88 2.27
44 45 6.567050 ACTTGTTGTAGTAGACAGTCGAAAA 58.433 36.000 0.00 0.00 39.88 2.29
45 46 6.140303 ACTTGTTGTAGTAGACAGTCGAAA 57.860 37.500 0.00 0.00 39.88 3.46
46 47 5.762825 ACTTGTTGTAGTAGACAGTCGAA 57.237 39.130 0.00 0.00 39.88 3.71
47 48 5.762825 AACTTGTTGTAGTAGACAGTCGA 57.237 39.130 0.00 0.00 39.88 4.20
48 49 6.823678 AAAACTTGTTGTAGTAGACAGTCG 57.176 37.500 0.00 0.00 39.88 4.18
49 50 7.254692 GGGAAAAACTTGTTGTAGTAGACAGTC 60.255 40.741 0.00 0.00 39.88 3.51
50 51 6.541278 GGGAAAAACTTGTTGTAGTAGACAGT 59.459 38.462 0.00 0.00 39.88 3.55
51 52 6.292703 CGGGAAAAACTTGTTGTAGTAGACAG 60.293 42.308 0.00 0.00 39.88 3.51
52 53 5.524646 CGGGAAAAACTTGTTGTAGTAGACA 59.475 40.000 0.00 0.00 35.78 3.41
53 54 5.049886 CCGGGAAAAACTTGTTGTAGTAGAC 60.050 44.000 0.00 0.00 0.00 2.59
54 55 5.058490 CCGGGAAAAACTTGTTGTAGTAGA 58.942 41.667 0.00 0.00 0.00 2.59
55 56 4.319984 GCCGGGAAAAACTTGTTGTAGTAG 60.320 45.833 2.18 0.00 0.00 2.57
56 57 3.565063 GCCGGGAAAAACTTGTTGTAGTA 59.435 43.478 2.18 0.00 0.00 1.82
57 58 2.359848 GCCGGGAAAAACTTGTTGTAGT 59.640 45.455 2.18 0.00 0.00 2.73
58 59 2.621526 AGCCGGGAAAAACTTGTTGTAG 59.378 45.455 2.18 0.00 0.00 2.74
59 60 2.619646 GAGCCGGGAAAAACTTGTTGTA 59.380 45.455 2.18 0.00 0.00 2.41
60 61 1.407618 GAGCCGGGAAAAACTTGTTGT 59.592 47.619 2.18 0.00 0.00 3.32
61 62 1.269569 GGAGCCGGGAAAAACTTGTTG 60.270 52.381 2.18 0.00 0.00 3.33
62 63 1.037493 GGAGCCGGGAAAAACTTGTT 58.963 50.000 2.18 0.00 0.00 2.83
63 64 1.170290 CGGAGCCGGGAAAAACTTGT 61.170 55.000 2.18 0.00 35.56 3.16
64 65 1.579429 CGGAGCCGGGAAAAACTTG 59.421 57.895 2.18 0.00 35.56 3.16
65 66 4.074647 CGGAGCCGGGAAAAACTT 57.925 55.556 2.18 0.00 35.56 2.66
82 83 4.883354 CATTGCCCCTCCCTCGCC 62.883 72.222 0.00 0.00 0.00 5.54
83 84 3.797353 TCATTGCCCCTCCCTCGC 61.797 66.667 0.00 0.00 0.00 5.03
84 85 1.915078 AAGTCATTGCCCCTCCCTCG 61.915 60.000 0.00 0.00 0.00 4.63
85 86 0.394899 CAAGTCATTGCCCCTCCCTC 60.395 60.000 0.00 0.00 0.00 4.30
86 87 1.693640 CAAGTCATTGCCCCTCCCT 59.306 57.895 0.00 0.00 0.00 4.20
87 88 4.344237 CAAGTCATTGCCCCTCCC 57.656 61.111 0.00 0.00 0.00 4.30
95 96 1.308069 CCCAGACCGGCAAGTCATTG 61.308 60.000 0.00 0.00 39.34 2.82
96 97 1.002134 CCCAGACCGGCAAGTCATT 60.002 57.895 0.00 0.00 39.34 2.57
97 98 2.185310 GACCCAGACCGGCAAGTCAT 62.185 60.000 0.00 0.00 39.34 3.06
98 99 2.847234 ACCCAGACCGGCAAGTCA 60.847 61.111 0.00 0.00 39.34 3.41
99 100 2.047179 GACCCAGACCGGCAAGTC 60.047 66.667 0.00 0.00 37.01 3.01
100 101 2.224159 ATGACCCAGACCGGCAAGT 61.224 57.895 0.00 0.00 0.00 3.16
101 102 1.746615 CATGACCCAGACCGGCAAG 60.747 63.158 0.00 0.00 0.00 4.01
102 103 2.184020 CTCATGACCCAGACCGGCAA 62.184 60.000 0.00 0.00 0.00 4.52
103 104 2.606213 TCATGACCCAGACCGGCA 60.606 61.111 0.00 0.00 0.00 5.69
104 105 2.187946 CTCATGACCCAGACCGGC 59.812 66.667 0.00 0.00 0.00 6.13
105 106 0.972983 AGTCTCATGACCCAGACCGG 60.973 60.000 0.00 0.00 43.91 5.28
106 107 0.898320 AAGTCTCATGACCCAGACCG 59.102 55.000 8.72 0.00 43.91 4.79
107 108 1.208293 GGAAGTCTCATGACCCAGACC 59.792 57.143 8.72 0.00 43.91 3.85
108 109 1.208293 GGGAAGTCTCATGACCCAGAC 59.792 57.143 12.40 8.72 43.91 3.51
126 127 1.236628 CTACTACATCGAGGACCGGG 58.763 60.000 6.32 0.00 39.14 5.73
128 129 2.144730 CTCCTACTACATCGAGGACCG 58.855 57.143 3.06 0.00 34.36 4.79
140 141 4.730392 TCATCCCACCTCTAACTCCTACTA 59.270 45.833 0.00 0.00 0.00 1.82
141 142 3.532232 TCATCCCACCTCTAACTCCTACT 59.468 47.826 0.00 0.00 0.00 2.57
149 150 0.042131 ACCCGTCATCCCACCTCTAA 59.958 55.000 0.00 0.00 0.00 2.10
216 217 2.819608 GCAATCTACAAGACCCAAGCAA 59.180 45.455 0.00 0.00 0.00 3.91
223 224 4.142609 TGATCCAGCAATCTACAAGACC 57.857 45.455 0.00 0.00 0.00 3.85
224 225 6.459298 CCATTTGATCCAGCAATCTACAAGAC 60.459 42.308 0.00 0.00 0.00 3.01
225 226 5.591472 CCATTTGATCCAGCAATCTACAAGA 59.409 40.000 0.00 0.00 0.00 3.02
250 251 1.514087 GGGCACACTCGACCGAATA 59.486 57.895 0.00 0.00 0.00 1.75
260 261 2.976490 GCTGAGATGGGGGCACACT 61.976 63.158 0.00 0.00 0.00 3.55
340 341 8.673711 TCTTCACTATGAAAATTGAAATACCGG 58.326 33.333 0.00 0.00 35.73 5.28
350 351 6.207417 CCACCACTGTCTTCACTATGAAAATT 59.793 38.462 0.00 0.00 35.73 1.82
381 382 3.785859 GACCTCAGCCGCCATGGA 61.786 66.667 18.40 0.00 42.00 3.41
382 383 3.790437 AGACCTCAGCCGCCATGG 61.790 66.667 7.63 7.63 42.50 3.66
403 404 1.068588 CTCGATCCGGCATTACAAGGA 59.931 52.381 0.00 0.00 37.17 3.36
414 415 0.246635 ACCACAAAGACTCGATCCGG 59.753 55.000 0.00 0.00 0.00 5.14
507 508 3.181485 CCCTCAAAGCTAAGACTCGGTAG 60.181 52.174 0.00 0.00 0.00 3.18
511 512 2.231478 TCACCCTCAAAGCTAAGACTCG 59.769 50.000 0.00 0.00 0.00 4.18
544 545 1.342819 TGCACAACCAATTAAGGCCAC 59.657 47.619 5.01 0.00 0.00 5.01
564 565 2.233271 CTTCAACAAGGTCACTGCCAT 58.767 47.619 0.00 0.00 0.00 4.40
658 671 3.628646 AAAGCGCCGCCTCCAAGAT 62.629 57.895 4.98 0.00 0.00 2.40
688 702 3.635373 TCACCTAGACAACACTCGAAGTT 59.365 43.478 0.00 0.00 0.00 2.66
695 709 4.748892 CGAATCATCACCTAGACAACACT 58.251 43.478 0.00 0.00 0.00 3.55
710 725 1.143305 GTAGCTGCATCGCGAATCAT 58.857 50.000 15.24 2.61 34.40 2.45
718 733 1.524355 CGATTCCTTGTAGCTGCATCG 59.476 52.381 4.98 7.86 0.00 3.84
720 735 2.988010 TCGATTCCTTGTAGCTGCAT 57.012 45.000 4.98 0.00 0.00 3.96
737 752 4.987285 AGAAATATGCTGCTACAGTGATCG 59.013 41.667 0.00 0.00 33.43 3.69
789 804 7.170658 CACACAACCAAAAGACAAAAAGAAGAA 59.829 33.333 0.00 0.00 0.00 2.52
829 844 7.403421 TCTTTACAACAACACAATGTCGTAAG 58.597 34.615 0.00 0.00 31.81 2.34
841 856 3.811083 ACACCCGATCTTTACAACAACA 58.189 40.909 0.00 0.00 0.00 3.33
854 869 3.385433 TCACGATACCAATTACACCCGAT 59.615 43.478 0.00 0.00 0.00 4.18
887 905 5.631992 CGAACTCTTTCTTTAAATGGGAGC 58.368 41.667 0.00 0.00 0.00 4.70
888 906 5.631992 GCGAACTCTTTCTTTAAATGGGAG 58.368 41.667 0.00 0.00 0.00 4.30
890 908 4.153475 TCGCGAACTCTTTCTTTAAATGGG 59.847 41.667 6.20 0.00 0.00 4.00
893 911 4.451096 TGCTCGCGAACTCTTTCTTTAAAT 59.549 37.500 11.33 0.00 0.00 1.40
895 913 3.386486 TGCTCGCGAACTCTTTCTTTAA 58.614 40.909 11.33 0.00 0.00 1.52
900 918 0.179238 GCTTGCTCGCGAACTCTTTC 60.179 55.000 11.33 0.00 0.00 2.62
904 922 1.681945 CTCTGCTTGCTCGCGAACTC 61.682 60.000 11.33 2.75 0.00 3.01
905 923 1.735920 CTCTGCTTGCTCGCGAACT 60.736 57.895 11.33 0.00 0.00 3.01
911 929 6.238621 CCCTCTATATATACTCTGCTTGCTCG 60.239 46.154 0.00 0.00 0.00 5.03
954 981 3.015327 AGAGAGTGCTTTGATTGGATGC 58.985 45.455 0.00 0.00 0.00 3.91
957 984 2.639347 TGGAGAGAGTGCTTTGATTGGA 59.361 45.455 0.00 0.00 0.00 3.53
963 990 0.324285 AGCCTGGAGAGAGTGCTTTG 59.676 55.000 0.00 0.00 0.00 2.77
968 995 1.202330 ATTGGAGCCTGGAGAGAGTG 58.798 55.000 0.00 0.00 0.00 3.51
969 996 2.856760 TATTGGAGCCTGGAGAGAGT 57.143 50.000 0.00 0.00 0.00 3.24
970 997 4.005487 CAATATTGGAGCCTGGAGAGAG 57.995 50.000 7.62 0.00 0.00 3.20
992 1019 1.983605 CACAACGGTACATGTCTCGAC 59.016 52.381 22.09 7.69 0.00 4.20
1015 1042 2.069273 CACCACGATCAGAAAGACCAC 58.931 52.381 0.00 0.00 0.00 4.16
1042 1069 4.783621 GCTCATGGCCGGAGTGCA 62.784 66.667 21.34 0.00 34.83 4.57
1050 1077 1.217244 CCAAAAGCTGCTCATGGCC 59.783 57.895 17.37 0.00 40.92 5.36
1121 1148 2.542595 AGCAAAAGTGACGTACCTTTCG 59.457 45.455 11.15 3.43 0.00 3.46
1226 1258 2.982130 CAGGGTAGCGCTCCACTT 59.018 61.111 16.34 0.00 0.00 3.16
1232 1264 2.190578 GGAATGCAGGGTAGCGCT 59.809 61.111 17.26 17.26 37.31 5.92
1433 1465 4.373116 TGGTGAGGACGGCGCTTC 62.373 66.667 6.90 6.65 0.00 3.86
1457 1489 2.825836 CGGAGCCTGTTGGGATGC 60.826 66.667 0.00 0.00 38.50 3.91
1537 1569 0.669625 GACGTGGTGCAGACCCTAAC 60.670 60.000 0.00 0.00 42.34 2.34
1681 1713 3.637273 GGTGACCGCCTGGACCTT 61.637 66.667 0.00 0.00 39.21 3.50
1755 1787 1.606994 GCCGTCATGTGACACTGGTAA 60.607 52.381 13.07 0.00 44.99 2.85
1794 1826 1.672854 CCCGGAGCGAGACCACATAA 61.673 60.000 0.73 0.00 0.00 1.90
1827 1859 1.071471 CAACTTGGCTGTCGGTCCT 59.929 57.895 0.00 0.00 0.00 3.85
1830 1862 1.878953 CTAACAACTTGGCTGTCGGT 58.121 50.000 0.00 0.00 0.00 4.69
1983 2015 1.609841 GCAGCCTACTACGGTTTGGTT 60.610 52.381 0.00 0.00 0.00 3.67
2009 2041 2.166829 GTGGCATGGATTGTTGGTACA 58.833 47.619 0.00 0.00 0.00 2.90
2014 2046 0.819582 GGGAGTGGCATGGATTGTTG 59.180 55.000 0.00 0.00 0.00 3.33
2029 2065 0.674534 GCCATGGTACTAGACGGGAG 59.325 60.000 14.67 0.00 0.00 4.30
2087 2123 0.472044 TGCTAGGCCACAACACTTCA 59.528 50.000 5.01 0.00 0.00 3.02
2088 2124 0.875059 GTGCTAGGCCACAACACTTC 59.125 55.000 5.01 0.00 35.80 3.01
2090 2126 1.301716 CGTGCTAGGCCACAACACT 60.302 57.895 5.01 0.00 35.47 3.55
2091 2127 0.320073 TACGTGCTAGGCCACAACAC 60.320 55.000 5.01 6.84 35.47 3.32
2092 2128 0.393448 TTACGTGCTAGGCCACAACA 59.607 50.000 5.01 0.00 35.47 3.33
2093 2129 1.076332 CTTACGTGCTAGGCCACAAC 58.924 55.000 5.01 0.00 35.47 3.32
2094 2130 0.970640 TCTTACGTGCTAGGCCACAA 59.029 50.000 5.01 0.00 35.47 3.33
2095 2131 0.245539 GTCTTACGTGCTAGGCCACA 59.754 55.000 5.01 0.00 35.47 4.17
2096 2132 0.245539 TGTCTTACGTGCTAGGCCAC 59.754 55.000 5.01 0.00 0.00 5.01
2097 2133 1.191535 ATGTCTTACGTGCTAGGCCA 58.808 50.000 5.01 0.00 0.00 5.36
2098 2134 2.311124 AATGTCTTACGTGCTAGGCC 57.689 50.000 0.00 0.00 0.00 5.19
2099 2135 3.435671 ACAAAATGTCTTACGTGCTAGGC 59.564 43.478 0.00 0.00 0.00 3.93
2100 2136 6.533723 TGATACAAAATGTCTTACGTGCTAGG 59.466 38.462 0.00 0.00 0.00 3.02
2101 2137 7.520119 TGATACAAAATGTCTTACGTGCTAG 57.480 36.000 0.00 0.00 0.00 3.42
2102 2138 6.035650 GCTGATACAAAATGTCTTACGTGCTA 59.964 38.462 0.00 0.00 0.00 3.49
2103 2139 5.163854 GCTGATACAAAATGTCTTACGTGCT 60.164 40.000 0.00 0.00 0.00 4.40
2104 2140 5.022021 GCTGATACAAAATGTCTTACGTGC 58.978 41.667 0.00 0.00 0.00 5.34
2105 2141 6.128553 ACAGCTGATACAAAATGTCTTACGTG 60.129 38.462 23.35 0.00 0.00 4.49
2106 2142 5.932303 ACAGCTGATACAAAATGTCTTACGT 59.068 36.000 23.35 0.00 0.00 3.57
2107 2143 6.090763 TGACAGCTGATACAAAATGTCTTACG 59.909 38.462 23.35 0.00 38.26 3.18
2108 2144 7.364522 TGACAGCTGATACAAAATGTCTTAC 57.635 36.000 23.35 0.00 38.26 2.34
2109 2145 6.092670 GCTGACAGCTGATACAAAATGTCTTA 59.907 38.462 23.35 0.00 38.45 2.10
2110 2146 5.106396 GCTGACAGCTGATACAAAATGTCTT 60.106 40.000 23.35 0.00 38.45 3.01
2111 2147 4.394300 GCTGACAGCTGATACAAAATGTCT 59.606 41.667 23.35 0.00 38.45 3.41
2112 2148 4.656041 GCTGACAGCTGATACAAAATGTC 58.344 43.478 23.35 4.48 38.45 3.06
2113 2149 4.691860 GCTGACAGCTGATACAAAATGT 57.308 40.909 23.35 0.00 38.45 2.71
2127 2163 1.575576 GGCACAAGCTGAGCTGACAG 61.576 60.000 8.16 0.96 39.62 3.51
2128 2164 1.598962 GGCACAAGCTGAGCTGACA 60.599 57.895 8.16 0.00 39.62 3.58
2129 2165 1.598962 TGGCACAAGCTGAGCTGAC 60.599 57.895 8.16 0.00 39.62 3.51
2130 2166 2.831043 TGGCACAAGCTGAGCTGA 59.169 55.556 8.16 0.00 39.62 4.26
2142 2178 5.880332 TGACTCTTTGTTATCCTTATGGCAC 59.120 40.000 0.00 0.00 0.00 5.01
2143 2179 6.061022 TGACTCTTTGTTATCCTTATGGCA 57.939 37.500 0.00 0.00 0.00 4.92
2144 2180 7.573968 ATTGACTCTTTGTTATCCTTATGGC 57.426 36.000 0.00 0.00 0.00 4.40
2148 2184 9.444600 GGTGTAATTGACTCTTTGTTATCCTTA 57.555 33.333 0.00 0.00 0.00 2.69
2149 2185 7.942341 TGGTGTAATTGACTCTTTGTTATCCTT 59.058 33.333 0.00 0.00 0.00 3.36
2150 2186 7.390718 GTGGTGTAATTGACTCTTTGTTATCCT 59.609 37.037 0.00 0.00 0.00 3.24
2151 2187 7.361799 GGTGGTGTAATTGACTCTTTGTTATCC 60.362 40.741 0.00 0.00 0.00 2.59
2152 2188 7.527457 GGTGGTGTAATTGACTCTTTGTTATC 58.473 38.462 0.00 0.00 0.00 1.75
2153 2189 6.148811 CGGTGGTGTAATTGACTCTTTGTTAT 59.851 38.462 0.00 0.00 0.00 1.89
2154 2190 5.467399 CGGTGGTGTAATTGACTCTTTGTTA 59.533 40.000 0.00 0.00 0.00 2.41
2223 2260 9.158364 GTTGTTGCATCGATTTAATGTATACAG 57.842 33.333 11.91 0.00 0.00 2.74
2224 2261 8.888716 AGTTGTTGCATCGATTTAATGTATACA 58.111 29.630 8.27 8.27 0.00 2.29
2227 2264 8.458052 TCAAGTTGTTGCATCGATTTAATGTAT 58.542 29.630 2.11 0.00 33.23 2.29
2253 2290 4.022762 TGCACCGTATTTGCATAAACAAGT 60.023 37.500 0.00 0.00 45.06 3.16
2279 2316 2.162319 TGCAGCGTATTCAACTGTGA 57.838 45.000 0.00 0.00 33.87 3.58
2280 2317 2.413239 CCTTGCAGCGTATTCAACTGTG 60.413 50.000 0.00 0.00 33.87 3.66
2281 2318 1.806542 CCTTGCAGCGTATTCAACTGT 59.193 47.619 0.00 0.00 33.87 3.55
2284 2321 0.804989 AGCCTTGCAGCGTATTCAAC 59.195 50.000 0.00 0.00 38.01 3.18
2295 2332 0.393402 CATGCCTACTCAGCCTTGCA 60.393 55.000 0.00 0.00 0.00 4.08
2296 2333 1.722636 GCATGCCTACTCAGCCTTGC 61.723 60.000 6.36 0.00 33.21 4.01
2299 2337 1.980784 CTGGCATGCCTACTCAGCCT 61.981 60.000 35.53 0.00 45.42 4.58
2306 2344 3.204827 CCACGCTGGCATGCCTAC 61.205 66.667 35.53 25.53 36.94 3.18
2330 2368 1.856265 CTTTTGTCCTGACAGCGGGC 61.856 60.000 0.00 0.00 42.94 6.13
2333 2371 1.135859 GCATCTTTTGTCCTGACAGCG 60.136 52.381 0.00 0.00 42.94 5.18
2334 2372 1.881973 TGCATCTTTTGTCCTGACAGC 59.118 47.619 0.00 0.63 42.94 4.40
2345 2383 1.238439 CCACACGTCCTGCATCTTTT 58.762 50.000 0.00 0.00 0.00 2.27
2346 2384 1.237285 GCCACACGTCCTGCATCTTT 61.237 55.000 0.00 0.00 0.00 2.52
2357 2395 2.096819 CGCAAATTTATAGGCCACACGT 59.903 45.455 5.01 0.00 0.00 4.49
2364 2402 8.915654 CAAGGATATTTTCGCAAATTTATAGGC 58.084 33.333 0.00 0.00 34.29 3.93
2368 2406 9.883142 TTTCCAAGGATATTTTCGCAAATTTAT 57.117 25.926 0.00 0.00 34.29 1.40
2370 2408 8.791327 ATTTCCAAGGATATTTTCGCAAATTT 57.209 26.923 0.00 0.00 34.29 1.82
2385 2423 9.456147 TTCTCGTGATAATAAAATTTCCAAGGA 57.544 29.630 0.00 0.00 0.00 3.36
2399 2437 2.746472 GCTGGGGCTTTCTCGTGATAAT 60.746 50.000 0.00 0.00 35.22 1.28
2402 2440 1.078143 GCTGGGGCTTTCTCGTGAT 60.078 57.895 0.00 0.00 35.22 3.06
2407 2445 1.301677 CGTCTTGCTGGGGCTTTCTC 61.302 60.000 0.00 0.00 39.59 2.87
2473 2515 0.528017 TCGCGTTCAAGAGAGAGCAT 59.472 50.000 5.77 0.00 0.00 3.79
2489 2531 2.553268 GCACACTGCAGTTCTCGC 59.447 61.111 18.94 13.41 44.26 5.03
2502 2544 0.963225 TAGTACCTTCAGCGTGCACA 59.037 50.000 18.64 0.00 0.00 4.57
2509 2551 2.168521 TGACATGGCTAGTACCTTCAGC 59.831 50.000 0.00 0.00 34.48 4.26
2526 2568 1.145945 TGGTAAATGTTGGGGCTGACA 59.854 47.619 0.00 0.00 0.00 3.58
2527 2569 1.917872 TGGTAAATGTTGGGGCTGAC 58.082 50.000 0.00 0.00 0.00 3.51
2528 2570 2.830923 CAATGGTAAATGTTGGGGCTGA 59.169 45.455 0.00 0.00 0.00 4.26
2543 2585 4.428294 AGCTATGCAGTATGACAATGGT 57.572 40.909 0.00 0.00 39.69 3.55
2547 2589 3.643320 AGGCTAGCTATGCAGTATGACAA 59.357 43.478 15.72 0.00 39.69 3.18
2548 2590 3.234353 AGGCTAGCTATGCAGTATGACA 58.766 45.455 15.72 0.00 39.69 3.58
2550 2592 6.611613 ATTTAGGCTAGCTATGCAGTATGA 57.388 37.500 15.72 0.00 39.69 2.15
2586 2628 0.530744 TCCATGTCCAGTGAGCGTAC 59.469 55.000 0.00 0.00 0.00 3.67
2587 2629 0.530744 GTCCATGTCCAGTGAGCGTA 59.469 55.000 0.00 0.00 0.00 4.42
2599 2641 1.813513 GCACTAACTGCTGTCCATGT 58.186 50.000 0.00 0.00 43.33 3.21
2607 2649 1.374758 GTGAGCCGCACTAACTGCT 60.375 57.895 0.00 0.00 44.64 4.24
2856 2904 6.267496 AGGCCACAAGTGAAAATTATACAC 57.733 37.500 5.01 0.00 35.15 2.90


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

AutoCloner maintained by Alex Coulton.