Multiple sequence alignment - TraesCS6A01G308300

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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 TraesCS6A01G308300 chr6A 100.000 6126 0 0 1 6126 543211786 543205661 0.000000e+00 11313.0
1 TraesCS6A01G308300 chr6A 100.000 297 0 0 6449 6745 543205338 543205042 3.560000e-152 549.0
2 TraesCS6A01G308300 chr6B 91.617 5499 328 57 685 6125 593359158 593353735 0.000000e+00 7478.0
3 TraesCS6A01G308300 chr6B 84.902 457 46 11 198 649 593359602 593359164 2.230000e-119 440.0
4 TraesCS6A01G308300 chr6B 88.776 294 20 7 6452 6745 593353654 593353374 1.390000e-91 348.0
5 TraesCS6A01G308300 chr6B 94.737 76 4 0 139 214 593359697 593359622 1.190000e-22 119.0
6 TraesCS6A01G308300 chr6B 82.558 86 12 2 1 83 140420008 140419923 9.380000e-09 73.1
7 TraesCS6A01G308300 chr6B 82.558 86 12 2 1 83 140430527 140430442 9.380000e-09 73.1
8 TraesCS6A01G308300 chr6B 91.667 48 1 3 2012 2058 29561718 29561763 5.650000e-06 63.9
9 TraesCS6A01G308300 chr6D 96.947 3439 87 12 2691 6126 396842531 396839108 0.000000e+00 5753.0
10 TraesCS6A01G308300 chr6D 91.875 2043 130 18 685 2704 396846177 396844148 0.000000e+00 2820.0
11 TraesCS6A01G308300 chr6D 96.599 294 10 0 6452 6745 396839017 396838724 7.860000e-134 488.0
12 TraesCS6A01G308300 chr6D 82.573 241 28 6 407 647 396846411 396846185 4.130000e-47 200.0
13 TraesCS6A01G308300 chr6D 82.629 213 17 5 212 423 396846620 396846427 3.230000e-38 171.0
14 TraesCS6A01G308300 chr6D 93.421 76 5 0 139 214 396846737 396846662 5.530000e-21 113.0
15 TraesCS6A01G308300 chr6D 84.722 72 9 1 2 71 25764349 25764420 3.370000e-08 71.3
16 TraesCS6A01G308300 chr6D 82.143 84 13 2 2 83 137543889 137543806 3.370000e-08 71.3
17 TraesCS6A01G308300 chr2B 74.153 1033 186 52 3297 4267 57780954 57779941 2.990000e-93 353.0
18 TraesCS6A01G308300 chr2B 87.500 248 28 3 4651 4896 57779587 57779341 3.980000e-72 283.0
19 TraesCS6A01G308300 chr2B 89.437 142 12 1 991 1132 57781625 57781487 6.950000e-40 176.0
20 TraesCS6A01G308300 chr2B 88.028 142 14 2 991 1132 57682666 57682528 1.500000e-36 165.0
21 TraesCS6A01G308300 chr2B 79.091 220 44 2 5539 5757 57679795 57679577 4.210000e-32 150.0
22 TraesCS6A01G308300 chr2B 78.605 215 32 9 5549 5762 57778786 57778585 5.490000e-26 130.0
23 TraesCS6A01G308300 chr2B 96.078 51 2 0 4400 4450 57779798 57779748 4.330000e-12 84.2
24 TraesCS6A01G308300 chr2B 84.524 84 11 1 2 83 695721832 695721749 1.560000e-11 82.4
25 TraesCS6A01G308300 chr2B 90.323 62 5 1 4390 4450 57680813 57680752 5.610000e-11 80.5
26 TraesCS6A01G308300 chr5D 79.915 468 71 16 1595 2055 534016396 534016847 8.440000e-84 322.0
27 TraesCS6A01G308300 chr4D 79.443 467 73 16 1595 2055 380446176 380446625 6.570000e-80 309.0
28 TraesCS6A01G308300 chr2A 73.073 1025 202 47 3297 4273 38332071 38331073 5.110000e-76 296.0
29 TraesCS6A01G308300 chr2A 88.362 232 26 1 4651 4881 38330726 38330495 1.850000e-70 278.0
30 TraesCS6A01G308300 chr2A 78.475 446 64 23 991 1427 38324850 38324428 5.190000e-66 263.0
31 TraesCS6A01G308300 chr2A 88.732 142 13 1 991 1132 38332750 38332612 3.230000e-38 171.0
32 TraesCS6A01G308300 chr2A 79.812 213 29 9 5549 5760 38329925 38329726 7.050000e-30 143.0
33 TraesCS6A01G308300 chr2A 96.078 51 2 0 4400 4450 38330936 38330886 4.330000e-12 84.2
34 TraesCS6A01G308300 chr2A 90.476 63 5 1 4390 4451 38322900 38322838 1.560000e-11 82.4
35 TraesCS6A01G308300 chr7A 78.706 479 74 22 4656 5122 8750284 8749822 1.840000e-75 294.0
36 TraesCS6A01G308300 chr7A 72.840 810 154 44 3498 4264 8751380 8750594 4.100000e-52 217.0
37 TraesCS6A01G308300 chr7A 82.143 84 14 1 1 83 712811754 712811671 3.370000e-08 71.3
38 TraesCS6A01G308300 chr2D 88.793 232 25 1 4651 4881 35023661 35023430 3.980000e-72 283.0
39 TraesCS6A01G308300 chr2D 87.654 162 15 3 991 1152 35003279 35003123 4.150000e-42 183.0
40 TraesCS6A01G308300 chr2D 79.476 229 43 4 5537 5762 35000411 35000184 7.000000e-35 159.0
41 TraesCS6A01G308300 chr2D 86.765 136 15 2 997 1132 35025735 35025603 1.520000e-31 148.0
42 TraesCS6A01G308300 chr2D 73.306 487 90 23 3995 4450 35024300 35023823 7.050000e-30 143.0
43 TraesCS6A01G308300 chr2D 90.323 62 5 1 4390 4450 35001417 35001356 5.610000e-11 80.5
44 TraesCS6A01G308300 chr2D 81.818 88 13 2 2 86 86072102 86072189 3.370000e-08 71.3
45 TraesCS6A01G308300 chr7D 78.170 481 78 21 4651 5122 8292642 8292180 1.430000e-71 281.0
46 TraesCS6A01G308300 chr7D 73.350 803 149 43 3498 4258 8293728 8292949 3.140000e-58 237.0
47 TraesCS6A01G308300 chr7D 83.333 84 12 1 2 83 538377128 538377045 7.250000e-10 76.8
48 TraesCS6A01G308300 chr4A 86.087 230 32 0 4651 4880 731421446 731421675 1.450000e-61 248.0
49 TraesCS6A01G308300 chr4A 83.529 85 10 4 2 83 123797729 123797646 7.250000e-10 76.8
50 TraesCS6A01G308300 chr5B 76.744 129 27 3 1927 2054 369477661 369477787 1.210000e-07 69.4


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 TraesCS6A01G308300 chr6A 543205042 543211786 6744 True 5931.000000 11313 100.0000 1 6745 2 chr6A.!!$R1 6744
1 TraesCS6A01G308300 chr6B 593353374 593359697 6323 True 2096.250000 7478 90.0080 139 6745 4 chr6B.!!$R3 6606
2 TraesCS6A01G308300 chr6D 396838724 396846737 8013 True 1590.833333 5753 90.6740 139 6745 6 chr6D.!!$R2 6606
3 TraesCS6A01G308300 chr2B 57778585 57781625 3040 True 205.240000 353 85.1546 991 5762 5 chr2B.!!$R3 4771
4 TraesCS6A01G308300 chr7A 8749822 8751380 1558 True 255.500000 294 75.7730 3498 5122 2 chr7A.!!$R2 1624
5 TraesCS6A01G308300 chr7D 8292180 8293728 1548 True 259.000000 281 75.7600 3498 5122 2 chr7D.!!$R2 1624

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
674 752 0.029567 CGGAGACAGGAGTACATCGC 59.970 60.000 0.00 0.00 0.00 4.58 F
775 865 0.033796 AATGTGGCAGAGACCATGGG 60.034 55.000 18.09 0.00 43.01 4.00 F
1711 1836 0.168788 ACATGCAAAAGATCACGCCG 59.831 50.000 0.00 0.00 0.00 6.46 F
2338 2474 0.321671 TGCTAGAAAGGAGCTTGCGT 59.678 50.000 0.00 0.00 40.76 5.24 F
2967 4734 0.107897 GATGTGGTACCCATGACGCA 60.108 55.000 17.49 2.48 35.28 5.24 F
2970 4737 0.533491 GTGGTACCCATGACGCACTA 59.467 55.000 10.07 0.00 35.28 2.74 F
2971 4738 0.533491 TGGTACCCATGACGCACTAC 59.467 55.000 10.07 0.00 0.00 2.73 F
3560 5344 6.294899 GCAAATGGTGATAATGGTATGATGCT 60.295 38.462 0.00 0.00 0.00 3.79 F
4916 6846 2.223947 GGCACCAAATCAAACCGACTTT 60.224 45.455 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2200 0.178879 CCATGGCCTCCTATCCCTCT 60.179 60.000 3.32 0.00 0.00 3.69 R
2622 2758 0.374063 TAGCGAGAGAAGTCGAAGCG 59.626 55.000 0.00 0.00 42.85 4.68 R
2750 4516 0.734889 GCTCTTGCATGCACCGTTAT 59.265 50.000 22.58 0.00 39.41 1.89 R
4259 6139 2.487762 ACTTGCAACCATTGGTGATACG 59.512 45.455 9.62 1.37 35.34 3.06 R
4566 6486 3.806380 TGTAAAGGTTGGCGTACTTTGA 58.194 40.909 9.45 0.00 36.07 2.69 R
4882 6807 7.073457 TGATTTGGTGCCTAGTTAGCATATA 57.927 36.000 0.00 0.00 43.29 0.86 R
4903 6833 7.913821 GTCTTCAAAACTAAAAGTCGGTTTGAT 59.086 33.333 3.67 0.00 34.09 2.57 R
5233 7166 3.459232 TGAGAGACGATGGCATAAAGG 57.541 47.619 0.00 0.00 0.00 3.11 R
6486 8488 4.217767 ACCTTTATTTTGAAGCCTTCGTCC 59.782 41.667 0.00 0.00 0.00 4.79 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
63 64 8.764524 AGATGTTGTTTAGAGTGTAGATTCAC 57.235 34.615 0.00 0.00 38.46 3.18
76 77 8.467402 AGTGTAGATTCACTCATTTTACTTCG 57.533 34.615 0.00 0.00 44.07 3.79
77 78 8.088981 AGTGTAGATTCACTCATTTTACTTCGT 58.911 33.333 0.00 0.00 44.07 3.85
78 79 9.350357 GTGTAGATTCACTCATTTTACTTCGTA 57.650 33.333 0.00 0.00 35.68 3.43
112 113 7.750229 AAAGTATTACTATGGTCATGCATGG 57.250 36.000 25.97 11.47 0.00 3.66
113 114 6.439636 AGTATTACTATGGTCATGCATGGT 57.560 37.500 25.97 16.51 0.00 3.55
114 115 6.233434 AGTATTACTATGGTCATGCATGGTG 58.767 40.000 25.97 12.05 0.00 4.17
115 116 4.769345 TTACTATGGTCATGCATGGTGA 57.231 40.909 25.97 5.53 0.00 4.02
116 117 3.870538 ACTATGGTCATGCATGGTGAT 57.129 42.857 25.97 16.34 0.00 3.06
117 118 4.980339 ACTATGGTCATGCATGGTGATA 57.020 40.909 25.97 16.56 0.00 2.15
118 119 5.509832 ACTATGGTCATGCATGGTGATAT 57.490 39.130 25.97 15.05 0.00 1.63
119 120 6.625532 ACTATGGTCATGCATGGTGATATA 57.374 37.500 25.97 15.33 0.00 0.86
120 121 7.204243 ACTATGGTCATGCATGGTGATATAT 57.796 36.000 25.97 12.93 0.00 0.86
121 122 8.322905 ACTATGGTCATGCATGGTGATATATA 57.677 34.615 25.97 13.30 0.00 0.86
122 123 8.206867 ACTATGGTCATGCATGGTGATATATAC 58.793 37.037 25.97 13.03 0.00 1.47
123 124 6.625532 TGGTCATGCATGGTGATATATACT 57.374 37.500 25.97 0.00 0.00 2.12
124 125 6.643388 TGGTCATGCATGGTGATATATACTC 58.357 40.000 25.97 8.38 0.00 2.59
125 126 5.750547 GGTCATGCATGGTGATATATACTCG 59.249 44.000 25.97 0.00 0.00 4.18
126 127 5.750547 GTCATGCATGGTGATATATACTCGG 59.249 44.000 25.97 0.00 0.00 4.63
127 128 5.656416 TCATGCATGGTGATATATACTCGGA 59.344 40.000 25.97 0.00 0.00 4.55
128 129 5.993748 TGCATGGTGATATATACTCGGAA 57.006 39.130 0.00 0.00 0.00 4.30
129 130 6.544928 TGCATGGTGATATATACTCGGAAT 57.455 37.500 0.00 0.00 0.00 3.01
130 131 7.654022 TGCATGGTGATATATACTCGGAATA 57.346 36.000 0.00 0.00 0.00 1.75
131 132 8.250143 TGCATGGTGATATATACTCGGAATAT 57.750 34.615 0.00 0.00 0.00 1.28
132 133 9.362151 TGCATGGTGATATATACTCGGAATATA 57.638 33.333 0.00 0.00 0.00 0.86
178 179 2.422479 CGGTCCTCTCAAGTTGTCGATA 59.578 50.000 2.11 0.00 0.00 2.92
181 182 4.082136 GGTCCTCTCAAGTTGTCGATAGTT 60.082 45.833 2.11 0.00 37.40 2.24
195 196 3.129813 TCGATAGTTACAGCCACGTGAAT 59.870 43.478 19.30 1.15 37.40 2.57
299 345 0.179040 GACCCTTTCACGGACCACAA 60.179 55.000 0.00 0.00 0.00 3.33
301 347 0.889186 CCCTTTCACGGACCACAAGG 60.889 60.000 0.00 0.00 42.21 3.61
308 354 0.984230 ACGGACCACAAGGACATGAT 59.016 50.000 0.00 0.00 38.69 2.45
309 355 1.066143 ACGGACCACAAGGACATGATC 60.066 52.381 0.00 0.00 38.69 2.92
310 356 1.066215 CGGACCACAAGGACATGATCA 60.066 52.381 0.00 0.00 38.69 2.92
313 359 3.614092 GACCACAAGGACATGATCACAT 58.386 45.455 0.00 0.00 38.69 3.21
314 360 4.012374 GACCACAAGGACATGATCACATT 58.988 43.478 0.00 0.00 38.69 2.71
315 361 4.410099 ACCACAAGGACATGATCACATTT 58.590 39.130 0.00 0.00 38.69 2.32
342 388 1.572085 CCTGTGCGCACCTCTTTCTG 61.572 60.000 35.72 14.14 0.00 3.02
351 397 2.224646 GCACCTCTTTCTGGAACCTTCT 60.225 50.000 0.00 0.00 0.00 2.85
352 398 3.008049 GCACCTCTTTCTGGAACCTTCTA 59.992 47.826 0.00 0.00 0.00 2.10
387 433 4.373116 GCGTCAAGGCCCGTCTCA 62.373 66.667 0.00 0.00 0.00 3.27
400 446 0.109226 CGTCTCACCCTCGGAAGAAC 60.109 60.000 0.00 0.00 41.32 3.01
401 447 0.966920 GTCTCACCCTCGGAAGAACA 59.033 55.000 0.00 0.00 41.32 3.18
410 456 5.183140 CACCCTCGGAAGAACAAAATAATGT 59.817 40.000 0.00 0.00 41.32 2.71
431 509 3.068574 GGTAATGCTAACCGGCGAA 57.931 52.632 9.30 0.00 34.52 4.70
433 511 0.299597 GTAATGCTAACCGGCGAACG 59.700 55.000 9.30 0.00 43.80 3.95
485 563 3.726517 CAGGTCGCAGCCGTTTGG 61.727 66.667 0.00 0.00 38.77 3.28
511 589 0.469705 TCAAACAGTGGCATTGGGCT 60.470 50.000 14.80 0.00 44.01 5.19
550 628 2.483014 TCAAGGACAACCGGTAATGG 57.517 50.000 8.00 0.00 41.83 3.16
551 629 1.979308 TCAAGGACAACCGGTAATGGA 59.021 47.619 8.00 0.00 41.83 3.41
563 641 3.213506 CGGTAATGGATTGGATCAAGCA 58.786 45.455 0.00 0.00 30.75 3.91
581 659 0.320683 CATGACCGTGTGAGAAGGCA 60.321 55.000 0.00 0.00 0.00 4.75
588 666 0.108585 GTGTGAGAAGGCAAGGACCA 59.891 55.000 0.00 0.00 0.00 4.02
625 703 0.969894 ACGTGGAGAAGGAAGGACAG 59.030 55.000 0.00 0.00 0.00 3.51
633 711 4.070552 GGAAGGACAGGACGCGCT 62.071 66.667 5.73 0.00 0.00 5.92
668 746 2.439701 CGGCCGGAGACAGGAGTA 60.440 66.667 20.10 0.00 0.00 2.59
669 747 2.772691 CGGCCGGAGACAGGAGTAC 61.773 68.421 20.10 0.00 0.00 2.73
670 748 1.681327 GGCCGGAGACAGGAGTACA 60.681 63.158 5.05 0.00 0.00 2.90
671 749 1.043673 GGCCGGAGACAGGAGTACAT 61.044 60.000 5.05 0.00 0.00 2.29
672 750 0.386113 GCCGGAGACAGGAGTACATC 59.614 60.000 5.05 0.00 0.00 3.06
673 751 0.663688 CCGGAGACAGGAGTACATCG 59.336 60.000 0.00 0.00 0.00 3.84
674 752 0.029567 CGGAGACAGGAGTACATCGC 59.970 60.000 0.00 0.00 0.00 4.58
675 753 1.394618 GGAGACAGGAGTACATCGCT 58.605 55.000 0.00 0.00 0.00 4.93
676 754 1.066303 GGAGACAGGAGTACATCGCTG 59.934 57.143 0.00 3.22 34.31 5.18
677 755 2.017782 GAGACAGGAGTACATCGCTGA 58.982 52.381 0.00 0.00 33.13 4.26
678 756 1.746220 AGACAGGAGTACATCGCTGAC 59.254 52.381 0.00 1.77 33.13 3.51
679 757 0.452184 ACAGGAGTACATCGCTGACG 59.548 55.000 0.00 0.00 42.01 4.35
696 774 2.110226 GACGAAGGCGAAATCTCTACG 58.890 52.381 0.00 0.00 41.64 3.51
698 776 2.110226 CGAAGGCGAAATCTCTACGAC 58.890 52.381 0.00 0.00 40.82 4.34
728 809 4.947388 GCAACAGACAAAATCCCATAGGTA 59.053 41.667 0.00 0.00 0.00 3.08
757 847 1.537348 GGGCATAGCGTACATCGACAA 60.537 52.381 0.00 0.00 42.86 3.18
775 865 0.033796 AATGTGGCAGAGACCATGGG 60.034 55.000 18.09 0.00 43.01 4.00
856 948 8.975439 CCATTTTCTTCATCTTGTTTTCTTGAG 58.025 33.333 0.00 0.00 0.00 3.02
887 979 1.139853 GAGTGGACTTCCCCTATGCTG 59.860 57.143 0.00 0.00 34.29 4.41
918 1010 4.153655 TCGAGGACCATTATAAGTCGATCG 59.846 45.833 9.36 9.36 40.93 3.69
930 1022 2.993937 AGTCGATCGAGAACTTCTCCT 58.006 47.619 20.09 5.63 40.34 3.69
962 1054 3.924073 TGTTCATGTCGTTGAGGAATACG 59.076 43.478 0.00 0.00 39.03 3.06
1059 1161 1.944676 GACGCCGACATGGATCGTC 60.945 63.158 13.34 13.34 43.02 4.20
1153 1255 8.284435 AGGTATACATACGTACATACCCCATAT 58.716 37.037 25.13 13.09 35.25 1.78
1154 1256 8.917088 GGTATACATACGTACATACCCCATATT 58.083 37.037 21.51 0.00 31.21 1.28
1219 1321 5.523916 TCTGAACTGTTTCTCTGTTAACTGC 59.476 40.000 7.22 0.00 38.11 4.40
1338 1444 1.731160 GATTCATATCGCTGCTGCTCC 59.269 52.381 14.03 0.00 36.97 4.70
1455 1570 2.733218 CCGCGCACTTCGTTCTGA 60.733 61.111 8.75 0.00 41.07 3.27
1560 1675 3.372206 GCCATATCAGCCGTATGAATCAC 59.628 47.826 0.00 0.00 32.52 3.06
1569 1684 4.037565 AGCCGTATGAATCACGAGACATAA 59.962 41.667 0.00 0.00 41.91 1.90
1622 1737 6.894339 ATTGATTCATAATGCAGCATGAGA 57.106 33.333 9.18 4.62 39.69 3.27
1637 1752 8.316214 TGCAGCATGAGAGATACAATCATAATA 58.684 33.333 0.00 0.00 39.69 0.98
1667 1782 7.600375 ACACATCCGATATTTGCATAACTAGAG 59.400 37.037 0.00 0.00 0.00 2.43
1684 1809 0.884704 GAGTGCACAACCGACACCAT 60.885 55.000 21.04 0.00 34.83 3.55
1685 1810 0.465460 AGTGCACAACCGACACCATT 60.465 50.000 21.04 0.00 34.83 3.16
1694 1819 1.139256 ACCGACACCATTACACACACA 59.861 47.619 0.00 0.00 0.00 3.72
1695 1820 2.224426 ACCGACACCATTACACACACAT 60.224 45.455 0.00 0.00 0.00 3.21
1705 1830 5.574055 CCATTACACACACATGCAAAAGATC 59.426 40.000 0.00 0.00 0.00 2.75
1708 1833 2.975193 CACACACATGCAAAAGATCACG 59.025 45.455 0.00 0.00 0.00 4.35
1711 1836 0.168788 ACATGCAAAAGATCACGCCG 59.831 50.000 0.00 0.00 0.00 6.46
1712 1837 0.447406 CATGCAAAAGATCACGCCGA 59.553 50.000 0.00 0.00 0.00 5.54
1736 1861 6.000219 ACAAAGAGCAACATCATACAAGACT 59.000 36.000 0.00 0.00 0.00 3.24
1737 1862 6.072838 ACAAAGAGCAACATCATACAAGACTG 60.073 38.462 0.00 0.00 0.00 3.51
1738 1863 5.411831 AGAGCAACATCATACAAGACTGA 57.588 39.130 0.00 0.00 0.00 3.41
1739 1864 5.798132 AGAGCAACATCATACAAGACTGAA 58.202 37.500 0.00 0.00 0.00 3.02
1809 1944 2.347568 CGATATGCAACAACGACCATCG 60.348 50.000 0.00 0.00 46.93 3.84
1825 1960 2.564553 ATCGACGCCAACCAGCTCTC 62.565 60.000 0.00 0.00 0.00 3.20
1840 1975 1.784525 CTCTCGACAACACAAGGACC 58.215 55.000 0.00 0.00 0.00 4.46
1843 1978 0.528901 TCGACAACACAAGGACCACG 60.529 55.000 0.00 0.00 0.00 4.94
1871 2006 3.665745 TTCTTTGGAAGCAATGCCTTC 57.334 42.857 0.00 5.29 40.33 3.46
1877 2012 0.887933 GAAGCAATGCCTTCCCGAAA 59.112 50.000 0.00 0.00 36.15 3.46
1904 2039 2.357034 CACTAGTGCCGCCGTTGT 60.357 61.111 10.54 0.00 0.00 3.32
1907 2042 1.666553 CTAGTGCCGCCGTTGTCAA 60.667 57.895 0.00 0.00 0.00 3.18
1915 2050 1.801771 CCGCCGTTGTCAAATCTAACA 59.198 47.619 0.00 0.00 0.00 2.41
1922 2057 6.542852 CCGTTGTCAAATCTAACAATCGAAT 58.457 36.000 0.00 0.00 37.67 3.34
1959 2094 5.477607 TTTCACCCGAAAGATCAAGTCTA 57.522 39.130 0.00 0.00 36.19 2.59
1960 2095 4.720649 TCACCCGAAAGATCAAGTCTAG 57.279 45.455 0.00 0.00 35.67 2.43
1962 2097 3.195825 CACCCGAAAGATCAAGTCTAGGT 59.804 47.826 0.00 0.00 35.67 3.08
1969 2104 7.363094 CCGAAAGATCAAGTCTAGGTAAACTCT 60.363 40.741 0.00 0.00 35.67 3.24
1979 2114 6.070767 AGTCTAGGTAAACTCTAAGCAATGCA 60.071 38.462 8.35 0.00 0.00 3.96
1980 2115 6.763610 GTCTAGGTAAACTCTAAGCAATGCAT 59.236 38.462 8.35 0.00 0.00 3.96
1983 2118 5.945784 AGGTAAACTCTAAGCAATGCATTCA 59.054 36.000 9.53 0.00 0.00 2.57
2010 2145 4.107622 GCTAACAATCTAAAGACGCCGTA 58.892 43.478 0.00 0.00 0.00 4.02
2055 2190 4.018688 GGGTTAGACCTATGGTTTTCACCT 60.019 45.833 0.00 0.00 40.27 4.00
2065 2200 0.459489 GTTTTCACCTGGTGCAAGCA 59.541 50.000 22.02 1.12 45.41 3.91
2092 2227 2.386100 GGAGGCCATGGGGTGATGA 61.386 63.158 15.13 0.00 36.17 2.92
2134 2269 1.189524 CGAGGTTGGGGTGGTAGTCA 61.190 60.000 0.00 0.00 0.00 3.41
2140 2275 3.782443 GGGTGGTAGTCAGGGCCG 61.782 72.222 0.00 0.00 0.00 6.13
2141 2276 3.001406 GGTGGTAGTCAGGGCCGT 61.001 66.667 0.00 0.00 0.00 5.68
2157 2292 1.371183 CGTGCAGGGGAAGAGAACA 59.629 57.895 0.00 0.00 0.00 3.18
2228 2363 1.404391 CAGCATGCAAGATCTTCCACC 59.596 52.381 21.98 0.00 0.00 4.61
2338 2474 0.321671 TGCTAGAAAGGAGCTTGCGT 59.678 50.000 0.00 0.00 40.76 5.24
2505 2641 0.621082 GAGAAAGGGGAGTTGGGGAG 59.379 60.000 0.00 0.00 0.00 4.30
2622 2758 1.136305 TGCTCTTACGAGTGCCCATAC 59.864 52.381 0.00 0.00 40.73 2.39
2748 4514 9.705290 ATTAAACAAGTCTGTGTTTTTCTTTGT 57.295 25.926 8.45 0.00 46.97 2.83
2967 4734 0.107897 GATGTGGTACCCATGACGCA 60.108 55.000 17.49 2.48 35.28 5.24
2969 4736 1.295423 GTGGTACCCATGACGCACT 59.705 57.895 10.07 0.00 35.28 4.40
2970 4737 0.533491 GTGGTACCCATGACGCACTA 59.467 55.000 10.07 0.00 35.28 2.74
2971 4738 0.533491 TGGTACCCATGACGCACTAC 59.467 55.000 10.07 0.00 0.00 2.73
3150 4917 7.315142 CACTGCAAAAAGGCTTAGAAATATCA 58.685 34.615 0.00 0.00 34.04 2.15
3195 4962 7.012894 TCAGGAAATTTACCAACTACACAACAG 59.987 37.037 0.00 0.00 0.00 3.16
3222 4989 8.150945 TCAACTTCTGCATTTATCCTAGGTATC 58.849 37.037 9.08 0.00 0.00 2.24
3367 5134 6.546772 TGCACATATTTATCTTCATCTTGGCA 59.453 34.615 0.00 0.00 0.00 4.92
3560 5344 6.294899 GCAAATGGTGATAATGGTATGATGCT 60.295 38.462 0.00 0.00 0.00 3.79
3865 5668 9.465199 TCATTCTTCAAACAATTCTATGGATCA 57.535 29.630 0.00 0.00 0.00 2.92
4259 6139 6.329496 TCTTGTTGTTGAATGTTCAAGGTTC 58.671 36.000 8.34 0.00 46.80 3.62
4882 6807 6.976934 TTCTTTTGGCTCTTGGTAAGAATT 57.023 33.333 0.00 0.00 37.02 2.17
4903 6833 8.217799 AGAATTATATGCTAACTAGGCACCAAA 58.782 33.333 0.00 0.00 42.69 3.28
4910 6840 4.380550 GCTAACTAGGCACCAAATCAAACC 60.381 45.833 0.00 0.00 0.00 3.27
4916 6846 2.223947 GGCACCAAATCAAACCGACTTT 60.224 45.455 0.00 0.00 0.00 2.66
5095 7026 3.120060 GCATCATGGGAAATCGAGCATAC 60.120 47.826 0.00 0.00 0.00 2.39
5233 7166 3.706600 TGTTGTTACATCACCCTACCC 57.293 47.619 0.00 0.00 0.00 3.69
5302 7235 5.196695 GGATTGCCTCTTACCTTCTTTGAT 58.803 41.667 0.00 0.00 0.00 2.57
5324 7257 7.909267 TGATTATTTAGTGATTGCTCAACTCG 58.091 34.615 0.00 0.00 31.85 4.18
5623 7605 2.733956 TGTCAACTGGGCTGAAAAAGT 58.266 42.857 0.00 0.00 0.00 2.66
5658 7640 5.897250 ACAAGAATCCCAAGTAAAACACCTT 59.103 36.000 0.00 0.00 0.00 3.50
5659 7641 6.382859 ACAAGAATCCCAAGTAAAACACCTTT 59.617 34.615 0.00 0.00 0.00 3.11
6486 8488 2.744202 GGCAATATCCTAAGTCCGCATG 59.256 50.000 0.00 0.00 0.00 4.06
6553 8555 2.291089 TGTCATCCACCAAGCATGTCAT 60.291 45.455 0.00 0.00 0.00 3.06
6626 8628 1.697432 TCGGGCCCCATATTCACTAAG 59.303 52.381 18.66 0.00 0.00 2.18
6716 8718 3.554324 CGAGGAAGTTGAAAAGTCGAACA 59.446 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 9.856488 GTGAATCTACACTCTAAACAACATCTA 57.144 33.333 0.00 0.00 37.73 1.98
38 39 8.589338 AGTGAATCTACACTCTAAACAACATCT 58.411 33.333 0.00 0.00 46.36 2.90
39 40 8.764524 AGTGAATCTACACTCTAAACAACATC 57.235 34.615 0.00 0.00 46.36 3.06
52 53 8.240883 ACGAAGTAAAATGAGTGAATCTACAC 57.759 34.615 0.00 0.00 41.94 2.90
86 87 8.632679 CCATGCATGACCATAGTAATACTTTTT 58.367 33.333 28.31 0.00 0.00 1.94
87 88 7.779798 ACCATGCATGACCATAGTAATACTTTT 59.220 33.333 28.31 0.00 0.00 2.27
88 89 7.229306 CACCATGCATGACCATAGTAATACTTT 59.771 37.037 28.31 0.00 0.00 2.66
89 90 6.712095 CACCATGCATGACCATAGTAATACTT 59.288 38.462 28.31 0.00 0.00 2.24
90 91 6.043127 TCACCATGCATGACCATAGTAATACT 59.957 38.462 28.31 0.00 0.00 2.12
91 92 6.230472 TCACCATGCATGACCATAGTAATAC 58.770 40.000 28.31 0.00 0.00 1.89
92 93 6.432403 TCACCATGCATGACCATAGTAATA 57.568 37.500 28.31 2.87 0.00 0.98
93 94 5.308976 TCACCATGCATGACCATAGTAAT 57.691 39.130 28.31 0.00 0.00 1.89
94 95 4.769345 TCACCATGCATGACCATAGTAA 57.231 40.909 28.31 0.00 0.00 2.24
95 96 4.980339 ATCACCATGCATGACCATAGTA 57.020 40.909 28.31 4.77 0.00 1.82
96 97 3.870538 ATCACCATGCATGACCATAGT 57.129 42.857 28.31 12.93 0.00 2.12
97 98 8.427276 AGTATATATCACCATGCATGACCATAG 58.573 37.037 28.31 12.26 0.00 2.23
98 99 8.322905 AGTATATATCACCATGCATGACCATA 57.677 34.615 28.31 18.28 0.00 2.74
99 100 7.204243 AGTATATATCACCATGCATGACCAT 57.796 36.000 28.31 16.82 0.00 3.55
100 101 6.625532 AGTATATATCACCATGCATGACCA 57.374 37.500 28.31 10.83 0.00 4.02
101 102 5.750547 CGAGTATATATCACCATGCATGACC 59.249 44.000 28.31 7.74 0.00 4.02
102 103 5.750547 CCGAGTATATATCACCATGCATGAC 59.249 44.000 28.31 14.04 0.00 3.06
103 104 5.656416 TCCGAGTATATATCACCATGCATGA 59.344 40.000 28.31 9.85 0.00 3.07
104 105 5.906073 TCCGAGTATATATCACCATGCATG 58.094 41.667 20.19 20.19 0.00 4.06
105 106 6.544928 TTCCGAGTATATATCACCATGCAT 57.455 37.500 0.00 0.00 0.00 3.96
106 107 5.993748 TTCCGAGTATATATCACCATGCA 57.006 39.130 0.00 0.00 0.00 3.96
119 120 9.053840 CGGTGATACAGTATATATTCCGAGTAT 57.946 37.037 12.20 0.00 34.60 2.12
120 121 8.260114 TCGGTGATACAGTATATATTCCGAGTA 58.740 37.037 14.48 0.00 35.71 2.59
121 122 7.108194 TCGGTGATACAGTATATATTCCGAGT 58.892 38.462 14.48 0.00 35.71 4.18
122 123 7.549615 TCGGTGATACAGTATATATTCCGAG 57.450 40.000 14.48 0.00 35.71 4.63
123 124 7.926674 TTCGGTGATACAGTATATATTCCGA 57.073 36.000 14.48 14.48 37.21 4.55
124 125 9.020813 CATTTCGGTGATACAGTATATATTCCG 57.979 37.037 0.00 4.48 34.30 4.30
125 126 9.314321 CCATTTCGGTGATACAGTATATATTCC 57.686 37.037 0.00 0.00 0.00 3.01
126 127 8.818057 GCCATTTCGGTGATACAGTATATATTC 58.182 37.037 0.00 0.00 36.97 1.75
127 128 8.718102 GCCATTTCGGTGATACAGTATATATT 57.282 34.615 0.00 0.00 36.97 1.28
178 179 4.638304 AGTTAATTCACGTGGCTGTAACT 58.362 39.130 17.00 18.84 0.00 2.24
181 182 4.242475 CTGAGTTAATTCACGTGGCTGTA 58.758 43.478 17.00 0.40 0.00 2.74
195 196 1.289160 AGCTCATGGGGCTGAGTTAA 58.711 50.000 12.06 0.00 43.75 2.01
214 215 0.101040 CGTATCGCCCGTGTCCTTAA 59.899 55.000 0.00 0.00 0.00 1.85
320 366 3.772853 AAGAGGTGCGCACAGGCAA 62.773 57.895 38.60 0.00 45.93 4.52
324 370 1.572085 CCAGAAAGAGGTGCGCACAG 61.572 60.000 38.60 17.82 0.00 3.66
330 376 2.155279 GAAGGTTCCAGAAAGAGGTGC 58.845 52.381 0.00 0.00 0.00 5.01
342 388 3.481453 GGCATGGATTCTAGAAGGTTCC 58.519 50.000 14.34 14.34 0.00 3.62
351 397 2.280797 GCGGCGGCATGGATTCTA 60.281 61.111 9.78 0.00 39.62 2.10
352 398 4.181010 AGCGGCGGCATGGATTCT 62.181 61.111 19.21 0.00 43.41 2.40
387 433 5.321927 ACATTATTTTGTTCTTCCGAGGGT 58.678 37.500 0.00 0.00 0.00 4.34
400 446 8.776680 GGTTAGCATTACCGTACATTATTTTG 57.223 34.615 0.00 0.00 0.00 2.44
431 509 1.301479 GTTCCTTCCCAGCGAACGT 60.301 57.895 0.00 0.00 0.00 3.99
433 511 1.674651 GGGTTCCTTCCCAGCGAAC 60.675 63.158 0.00 0.00 46.30 3.95
441 519 2.902457 TTCGCTGGGGGTTCCTTCC 61.902 63.158 0.00 0.00 36.20 3.46
442 520 1.674651 GTTCGCTGGGGGTTCCTTC 60.675 63.158 0.00 0.00 36.20 3.46
467 545 4.389576 CAAACGGCTGCGACCTGC 62.390 66.667 0.00 0.00 46.70 4.85
468 546 3.726517 CCAAACGGCTGCGACCTG 61.727 66.667 0.00 0.00 0.00 4.00
469 547 4.250305 ACCAAACGGCTGCGACCT 62.250 61.111 0.00 0.00 0.00 3.85
470 548 3.723348 GACCAAACGGCTGCGACC 61.723 66.667 0.00 0.00 0.00 4.79
471 549 4.072088 CGACCAAACGGCTGCGAC 62.072 66.667 0.00 0.00 0.00 5.19
474 552 1.696832 GATCTCGACCAAACGGCTGC 61.697 60.000 0.00 0.00 0.00 5.25
483 561 1.608025 GCCACTGTTTGATCTCGACCA 60.608 52.381 0.00 0.00 0.00 4.02
485 563 1.795768 TGCCACTGTTTGATCTCGAC 58.204 50.000 0.00 0.00 0.00 4.20
498 576 1.422531 TTTTCAAGCCCAATGCCACT 58.577 45.000 0.00 0.00 42.71 4.00
499 577 2.477845 ATTTTCAAGCCCAATGCCAC 57.522 45.000 0.00 0.00 42.71 5.01
500 578 4.630644 TTTATTTTCAAGCCCAATGCCA 57.369 36.364 0.00 0.00 42.71 4.92
511 589 9.087871 TCCTTGATCATCTGGTTTTATTTTCAA 57.912 29.630 0.00 0.00 0.00 2.69
550 628 2.032550 CACGGTCATGCTTGATCCAATC 59.967 50.000 5.49 0.00 33.56 2.67
551 629 2.019249 CACGGTCATGCTTGATCCAAT 58.981 47.619 5.49 0.00 33.56 3.16
563 641 0.396435 TTGCCTTCTCACACGGTCAT 59.604 50.000 0.00 0.00 0.00 3.06
581 659 2.032071 CGGCGTTCCTTGGTCCTT 59.968 61.111 0.00 0.00 0.00 3.36
605 683 1.344763 CTGTCCTTCCTTCTCCACGTT 59.655 52.381 0.00 0.00 0.00 3.99
614 692 2.657237 CGCGTCCTGTCCTTCCTT 59.343 61.111 0.00 0.00 0.00 3.36
615 693 4.070552 GCGCGTCCTGTCCTTCCT 62.071 66.667 8.43 0.00 0.00 3.36
616 694 2.707849 TAGCGCGTCCTGTCCTTCC 61.708 63.158 8.43 0.00 0.00 3.46
617 695 1.516603 GTAGCGCGTCCTGTCCTTC 60.517 63.158 8.43 0.00 0.00 3.46
618 696 2.572284 GTAGCGCGTCCTGTCCTT 59.428 61.111 8.43 0.00 0.00 3.36
652 730 1.043673 ATGTACTCCTGTCTCCGGCC 61.044 60.000 0.00 0.00 0.00 6.13
653 731 0.386113 GATGTACTCCTGTCTCCGGC 59.614 60.000 0.00 0.00 0.00 6.13
654 732 0.663688 CGATGTACTCCTGTCTCCGG 59.336 60.000 0.00 0.00 0.00 5.14
655 733 0.029567 GCGATGTACTCCTGTCTCCG 59.970 60.000 0.00 0.00 0.00 4.63
656 734 1.066303 CAGCGATGTACTCCTGTCTCC 59.934 57.143 0.00 0.00 0.00 3.71
657 735 2.017782 TCAGCGATGTACTCCTGTCTC 58.982 52.381 0.00 0.00 0.00 3.36
658 736 1.746220 GTCAGCGATGTACTCCTGTCT 59.254 52.381 0.00 0.00 0.00 3.41
659 737 1.532090 CGTCAGCGATGTACTCCTGTC 60.532 57.143 0.00 0.00 41.33 3.51
660 738 0.452184 CGTCAGCGATGTACTCCTGT 59.548 55.000 0.00 0.00 41.33 4.00
661 739 0.733150 TCGTCAGCGATGTACTCCTG 59.267 55.000 0.00 0.00 42.81 3.86
662 740 3.170360 TCGTCAGCGATGTACTCCT 57.830 52.632 0.00 0.00 42.81 3.69
673 751 0.647925 GAGATTTCGCCTTCGTCAGC 59.352 55.000 0.00 0.00 36.96 4.26
674 752 2.285827 AGAGATTTCGCCTTCGTCAG 57.714 50.000 0.00 0.00 36.96 3.51
675 753 2.477357 CGTAGAGATTTCGCCTTCGTCA 60.477 50.000 0.00 0.00 36.96 4.35
676 754 2.110226 CGTAGAGATTTCGCCTTCGTC 58.890 52.381 0.00 0.00 36.96 4.20
677 755 1.741706 TCGTAGAGATTTCGCCTTCGT 59.258 47.619 0.00 0.00 36.96 3.85
678 756 2.110226 GTCGTAGAGATTTCGCCTTCG 58.890 52.381 0.00 0.00 36.95 3.79
679 757 3.146618 TGTCGTAGAGATTTCGCCTTC 57.853 47.619 0.00 0.00 36.95 3.46
680 758 3.802948 ATGTCGTAGAGATTTCGCCTT 57.197 42.857 0.00 0.00 37.12 4.35
728 809 1.754234 CGCTATGCCCCCAAGCTTT 60.754 57.895 0.00 0.00 34.03 3.51
757 847 1.611419 CCCATGGTCTCTGCCACAT 59.389 57.895 11.73 0.00 41.94 3.21
856 948 0.818040 AGTCCACTCCAAAACACGGC 60.818 55.000 0.00 0.00 0.00 5.68
887 979 0.179000 AATGGTCCTCGATGAGCACC 59.821 55.000 22.09 7.32 44.67 5.01
918 1010 3.145286 AGCAAGCAAAGGAGAAGTTCTC 58.855 45.455 22.47 22.47 42.66 2.87
930 1022 2.098934 ACGACATGAACAAGCAAGCAAA 59.901 40.909 0.00 0.00 0.00 3.68
962 1054 4.213482 CACTGCTAACCCTTGTTACTGTTC 59.787 45.833 0.00 0.00 35.87 3.18
1011 1113 1.257743 GCTTGGGTTTCCCTTCTTCC 58.742 55.000 6.38 0.00 45.70 3.46
1137 1239 4.224370 GGATGGAATATGGGGTATGTACGT 59.776 45.833 0.00 0.00 0.00 3.57
1153 1255 0.179084 GCTTCGTCGATGGGATGGAA 60.179 55.000 4.48 0.00 32.24 3.53
1154 1256 1.043116 AGCTTCGTCGATGGGATGGA 61.043 55.000 4.48 0.00 32.24 3.41
1233 1335 4.183865 CTCATCATCCTCTGCAAACGTAA 58.816 43.478 0.00 0.00 0.00 3.18
1234 1336 3.430790 CCTCATCATCCTCTGCAAACGTA 60.431 47.826 0.00 0.00 0.00 3.57
1338 1444 4.410400 GGCTCCCTGGAACACGGG 62.410 72.222 0.00 0.00 44.52 5.28
1637 1752 7.715249 AGTTATGCAAATATCGGATGTGTACTT 59.285 33.333 0.00 0.00 0.00 2.24
1646 1761 5.926542 GCACTCTAGTTATGCAAATATCGGA 59.073 40.000 0.00 0.00 39.23 4.55
1667 1782 1.069500 GTAATGGTGTCGGTTGTGCAC 60.069 52.381 10.75 10.75 0.00 4.57
1684 1809 5.518812 GTGATCTTTTGCATGTGTGTGTAA 58.481 37.500 0.00 0.00 0.00 2.41
1685 1810 4.319405 CGTGATCTTTTGCATGTGTGTGTA 60.319 41.667 0.00 0.00 0.00 2.90
1694 1819 0.447801 GTCGGCGTGATCTTTTGCAT 59.552 50.000 6.85 0.00 0.00 3.96
1695 1820 0.882484 TGTCGGCGTGATCTTTTGCA 60.882 50.000 6.85 0.00 0.00 4.08
1705 1830 1.082756 GTTGCTCTTTGTCGGCGTG 60.083 57.895 6.85 0.00 0.00 5.34
1708 1833 0.874390 TGATGTTGCTCTTTGTCGGC 59.126 50.000 0.00 0.00 0.00 5.54
1711 1836 6.148480 AGTCTTGTATGATGTTGCTCTTTGTC 59.852 38.462 0.00 0.00 0.00 3.18
1712 1837 6.000219 AGTCTTGTATGATGTTGCTCTTTGT 59.000 36.000 0.00 0.00 0.00 2.83
1736 1861 9.102757 CTTTTTGTCTATCTAAGCATAGCTTCA 57.897 33.333 7.62 0.00 46.77 3.02
1737 1862 9.319143 TCTTTTTGTCTATCTAAGCATAGCTTC 57.681 33.333 7.62 0.00 46.77 3.86
1739 1864 9.672673 TTTCTTTTTGTCTATCTAAGCATAGCT 57.327 29.630 0.00 0.00 42.56 3.32
1771 1906 2.941891 TCGTCAATCGCTTGTTTGAC 57.058 45.000 0.00 5.87 43.83 3.18
1809 1944 2.811317 CGAGAGCTGGTTGGCGTC 60.811 66.667 0.00 0.00 37.29 5.19
1825 1960 0.528901 TCGTGGTCCTTGTGTTGTCG 60.529 55.000 0.00 0.00 0.00 4.35
1840 1975 4.154737 TGCTTCCAAAGAATCTTGATCGTG 59.845 41.667 0.00 0.00 0.00 4.35
1843 1978 5.519206 GCATTGCTTCCAAAGAATCTTGATC 59.481 40.000 0.16 0.00 34.05 2.92
1871 2006 0.249741 AGTGTGTCGTTCCTTTCGGG 60.250 55.000 0.00 0.00 0.00 5.14
1877 2012 0.317479 GGCACTAGTGTGTCGTTCCT 59.683 55.000 23.44 0.00 45.44 3.36
1888 2023 2.048503 GACAACGGCGGCACTAGT 60.049 61.111 13.24 0.87 0.00 2.57
1898 2033 5.524511 TCGATTGTTAGATTTGACAACGG 57.475 39.130 12.19 3.06 38.46 4.44
1922 2057 5.600898 TCGGGTGAAAACCTATGATCTGATA 59.399 40.000 0.00 0.00 0.00 2.15
1959 2094 5.945784 TGAATGCATTGCTTAGAGTTTACCT 59.054 36.000 18.59 0.00 0.00 3.08
1960 2095 6.194796 TGAATGCATTGCTTAGAGTTTACC 57.805 37.500 18.59 0.00 0.00 2.85
1962 2097 7.213216 TGTTGAATGCATTGCTTAGAGTTTA 57.787 32.000 18.59 0.00 0.00 2.01
1969 2104 4.524316 AGCTTGTTGAATGCATTGCTTA 57.476 36.364 18.59 0.00 0.00 3.09
1979 2114 8.230486 CGTCTTTAGATTGTTAGCTTGTTGAAT 58.770 33.333 0.00 0.00 0.00 2.57
1980 2115 7.572759 CGTCTTTAGATTGTTAGCTTGTTGAA 58.427 34.615 0.00 0.00 0.00 2.69
1983 2118 5.106673 GGCGTCTTTAGATTGTTAGCTTGTT 60.107 40.000 0.00 0.00 0.00 2.83
2010 2145 5.445964 CCTAGTTGGTTATACCTGGCAATT 58.554 41.667 0.00 0.00 39.58 2.32
2055 2190 0.543277 CTATCCCTCTGCTTGCACCA 59.457 55.000 0.00 0.00 0.00 4.17
2065 2200 0.178879 CCATGGCCTCCTATCCCTCT 60.179 60.000 3.32 0.00 0.00 3.69
2092 2227 1.915769 GCTGGACTCACCACCCTCT 60.916 63.158 0.00 0.00 44.64 3.69
2140 2275 0.606673 GGTGTTCTCTTCCCCTGCAC 60.607 60.000 0.00 0.00 0.00 4.57
2141 2276 1.059584 TGGTGTTCTCTTCCCCTGCA 61.060 55.000 0.00 0.00 0.00 4.41
2157 2292 2.154462 GAGCAGCTTGTGTTGTATGGT 58.846 47.619 0.00 0.00 0.00 3.55
2228 2363 3.649986 GCGGGATTGCGGGATTCG 61.650 66.667 0.00 0.00 42.76 3.34
2423 2559 2.203252 CCGGGGATGATGGCAGTG 60.203 66.667 0.00 0.00 0.00 3.66
2505 2641 0.388907 TACCGTAGCGCCACAACTTC 60.389 55.000 2.29 0.00 0.00 3.01
2622 2758 0.374063 TAGCGAGAGAAGTCGAAGCG 59.626 55.000 0.00 0.00 42.85 4.68
2748 4514 2.354510 GCTCTTGCATGCACCGTTATTA 59.645 45.455 22.58 1.44 39.41 0.98
2749 4515 1.133025 GCTCTTGCATGCACCGTTATT 59.867 47.619 22.58 0.00 39.41 1.40
2750 4516 0.734889 GCTCTTGCATGCACCGTTAT 59.265 50.000 22.58 0.00 39.41 1.89
2967 4734 1.105759 GCGGATCCAGTACCCGTAGT 61.106 60.000 13.41 0.00 44.63 2.73
2969 4736 1.829533 GGCGGATCCAGTACCCGTA 60.830 63.158 13.41 0.00 44.63 4.02
2970 4737 3.152400 GGCGGATCCAGTACCCGT 61.152 66.667 13.41 0.00 44.63 5.28
2971 4738 3.925090 GGGCGGATCCAGTACCCG 61.925 72.222 13.41 3.43 45.51 5.28
2972 4739 2.147387 ATGGGCGGATCCAGTACCC 61.147 63.158 18.15 18.15 40.56 3.69
2973 4740 1.071471 CATGGGCGGATCCAGTACC 59.929 63.158 13.41 8.24 40.56 3.34
2974 4741 1.598130 GCATGGGCGGATCCAGTAC 60.598 63.158 13.41 0.00 40.56 2.73
3110 4877 4.502105 TGCAGTGGATATTTCTAAGCCA 57.498 40.909 0.00 0.00 0.00 4.75
3150 4917 7.645058 TCCTGAAATTTTCTGAAGTCTTTGT 57.355 32.000 15.29 0.00 0.00 2.83
3195 4962 6.116126 ACCTAGGATAAATGCAGAAGTTGAC 58.884 40.000 17.98 0.00 0.00 3.18
3276 5043 6.206395 ACATGCGGAATAACAAATCAATCA 57.794 33.333 0.00 0.00 0.00 2.57
3281 5048 4.556699 GCCCTACATGCGGAATAACAAATC 60.557 45.833 3.31 0.00 0.00 2.17
3287 5054 2.719531 TTGCCCTACATGCGGAATAA 57.280 45.000 3.31 0.00 0.00 1.40
3367 5134 4.274459 GCACTGAGAACAAAATGAGTGACT 59.726 41.667 0.00 0.00 0.00 3.41
3652 5439 4.577693 TGATCATTTCAGGAGCTGCATAAC 59.422 41.667 8.35 0.00 0.00 1.89
3723 5510 3.064820 CCAAATATCCTCCACCGTTTTCG 59.935 47.826 0.00 0.00 43.67 3.46
3865 5668 3.833732 TGTGTAGTCTTCCTCAGTGACT 58.166 45.455 0.00 0.00 42.74 3.41
4197 6077 3.709653 CCCAGAGGTACCAGCTACATAAA 59.290 47.826 15.94 0.00 0.00 1.40
4259 6139 2.487762 ACTTGCAACCATTGGTGATACG 59.512 45.455 9.62 1.37 35.34 3.06
4389 6293 9.747898 TCCAAATGTAGACATACAAACCTAAAT 57.252 29.630 0.00 0.00 44.85 1.40
4566 6486 3.806380 TGTAAAGGTTGGCGTACTTTGA 58.194 40.909 9.45 0.00 36.07 2.69
4882 6807 7.073457 TGATTTGGTGCCTAGTTAGCATATA 57.927 36.000 0.00 0.00 43.29 0.86
4903 6833 7.913821 GTCTTCAAAACTAAAAGTCGGTTTGAT 59.086 33.333 3.67 0.00 34.09 2.57
5233 7166 3.459232 TGAGAGACGATGGCATAAAGG 57.541 47.619 0.00 0.00 0.00 3.11
5302 7235 6.170506 ACCGAGTTGAGCAATCACTAAATAA 58.829 36.000 0.00 0.00 0.00 1.40
5324 7257 9.668497 AAGAATTAGTTACTCATAGACCAAACC 57.332 33.333 0.00 0.00 0.00 3.27
5544 7526 4.350816 TCTGAAAGAACTCCCCATCTTCAA 59.649 41.667 0.00 0.00 42.31 2.69
5623 7605 2.093658 GGGATTCTTGTGCGTCTCCTAA 60.094 50.000 0.00 0.00 0.00 2.69
5658 7640 3.319972 ACTTGTGAGTTGCCTACGTCTAA 59.680 43.478 0.00 0.00 29.87 2.10
5659 7641 2.889045 ACTTGTGAGTTGCCTACGTCTA 59.111 45.455 0.00 0.00 29.87 2.59
5688 7670 2.121291 TGAACTGCAACACCACTTGA 57.879 45.000 0.00 0.00 0.00 3.02
5826 7808 8.801299 TCCAAACATATGTGTCATGTAATTGTT 58.199 29.630 9.63 0.00 37.67 2.83
5995 7978 5.643777 CGATAGGAATATCCACAATTGGTCC 59.356 44.000 10.83 4.81 44.35 4.46
6450 8452 7.759607 AGGATATTGCCAACTATCTAAACCAT 58.240 34.615 0.00 0.00 0.00 3.55
6456 8458 7.093902 CGGACTTAGGATATTGCCAACTATCTA 60.094 40.741 0.00 0.00 0.00 1.98
6486 8488 4.217767 ACCTTTATTTTGAAGCCTTCGTCC 59.782 41.667 0.00 0.00 0.00 4.79
6716 8718 8.671987 AATAATGTCTAGGGCTGATGTACTAT 57.328 34.615 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.