Multiple sequence alignment - TraesCS7A01G455200

Loading Multiple Alignment...

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 TraesCS7A01G455200 chr7A 100.000 7439 0 0 1 7439 650621627 650629065 0.000000e+00 13738.0
1 TraesCS7A01G455200 chr7A 95.373 778 28 4 5802 6575 650720256 650721029 0.000000e+00 1230.0
2 TraesCS7A01G455200 chr7A 87.295 976 94 16 5625 6573 650891117 650892089 0.000000e+00 1088.0
3 TraesCS7A01G455200 chr7A 87.295 976 94 16 5625 6573 650904294 650905266 0.000000e+00 1088.0
4 TraesCS7A01G455200 chr7A 89.486 428 42 3 5374 5800 650675032 650675457 8.490000e-149 538.0
5 TraesCS7A01G455200 chr7A 82.892 567 68 18 5721 6261 650865555 650866118 4.040000e-132 483.0
6 TraesCS7A01G455200 chr7A 83.040 454 54 15 4895 5329 650674592 650675041 2.520000e-104 390.0
7 TraesCS7A01G455200 chr7A 83.002 453 55 15 4895 5329 650688857 650689305 2.520000e-104 390.0
8 TraesCS7A01G455200 chr7A 92.000 250 19 1 4614 4863 650815946 650816194 4.270000e-92 350.0
9 TraesCS7A01G455200 chr7A 91.200 250 21 1 4614 4863 650674348 650674596 9.250000e-89 339.0
10 TraesCS7A01G455200 chr7A 90.763 249 22 1 4615 4863 650688614 650688861 1.550000e-86 331.0
11 TraesCS7A01G455200 chr7A 88.608 237 25 2 5374 5609 650816609 650816844 3.400000e-73 287.0
12 TraesCS7A01G455200 chr7A 85.664 286 23 9 7156 7439 475549668 475549937 1.220000e-72 285.0
13 TraesCS7A01G455200 chr7A 94.872 78 4 0 5723 5800 650819653 650819730 1.010000e-23 122.0
14 TraesCS7A01G455200 chr7A 82.759 116 15 4 6463 6575 650815744 650815857 1.710000e-16 99.0
15 TraesCS7A01G455200 chr7A 80.531 113 21 1 6464 6575 650688410 650688522 1.330000e-12 86.1
16 TraesCS7A01G455200 chr7D 93.902 6641 230 66 1 6575 564966924 564973455 0.000000e+00 9858.0
17 TraesCS7A01G455200 chr7D 87.162 148 19 0 5632 5779 565069476 565069623 1.280000e-37 169.0
18 TraesCS7A01G455200 chr7D 89.216 102 11 0 6474 6575 565016428 565016529 2.180000e-25 128.0
19 TraesCS7A01G455200 chr7B 97.626 3622 63 8 2966 6575 614870604 614874214 0.000000e+00 6191.0
20 TraesCS7A01G455200 chr7B 94.934 1066 36 4 1779 2835 614869553 614870609 0.000000e+00 1653.0
21 TraesCS7A01G455200 chr7B 87.660 1410 79 44 242 1622 614867921 614869264 0.000000e+00 1552.0
22 TraesCS7A01G455200 chr7B 95.556 900 33 4 5390 6287 614914038 614914932 0.000000e+00 1434.0
23 TraesCS7A01G455200 chr7B 91.821 379 28 3 4614 4992 614907870 614908245 6.610000e-145 525.0
24 TraesCS7A01G455200 chr7B 93.559 295 14 2 6285 6575 614915360 614915653 1.150000e-117 435.0
25 TraesCS7A01G455200 chr7B 94.056 286 7 5 7156 7439 723877252 723877529 6.900000e-115 425.0
26 TraesCS7A01G455200 chr7B 88.850 287 21 6 7156 7439 610330767 610330489 7.150000e-90 342.0
27 TraesCS7A01G455200 chr7B 91.096 146 9 2 6363 6505 614903027 614903171 2.120000e-45 195.0
28 TraesCS7A01G455200 chr7B 83.920 199 27 3 1 199 614867722 614867915 1.270000e-42 185.0
29 TraesCS7A01G455200 chr7B 89.655 58 2 3 6573 6627 700885862 700885806 3.720000e-08 71.3
30 TraesCS7A01G455200 chr1D 76.094 1188 230 39 5151 6303 465534707 465535875 8.370000e-159 571.0
31 TraesCS7A01G455200 chr1D 91.509 212 14 2 6572 6780 418204497 418204707 9.440000e-74 289.0
32 TraesCS7A01G455200 chr1D 96.324 136 5 0 6875 7010 418204905 418205040 2.700000e-54 224.0
33 TraesCS7A01G455200 chr1D 86.022 186 26 0 1075 1260 465531315 465531500 4.550000e-47 200.0
34 TraesCS7A01G455200 chr1D 94.949 99 5 0 6774 6872 418204754 418204852 9.990000e-34 156.0
35 TraesCS7A01G455200 chr1A 75.475 1158 229 42 5184 6303 557951251 557952391 1.430000e-141 514.0
36 TraesCS7A01G455200 chr1A 89.474 285 20 6 7156 7439 291678878 291678603 1.190000e-92 351.0
37 TraesCS7A01G455200 chr1A 86.010 193 21 4 1075 1264 557948096 557948285 1.270000e-47 202.0
38 TraesCS7A01G455200 chrUn 88.889 315 18 9 7126 7439 38662534 38662236 9.120000e-99 372.0
39 TraesCS7A01G455200 chr4A 87.850 321 22 12 7126 7439 690237437 690237747 1.970000e-95 361.0
40 TraesCS7A01G455200 chr4A 88.718 195 17 5 6586 6776 494629238 494629431 4.490000e-57 233.0
41 TraesCS7A01G455200 chr4A 82.437 279 36 2 3357 3635 31395398 31395663 1.610000e-56 231.0
42 TraesCS7A01G455200 chr3D 89.199 287 20 5 7156 7439 359953388 359953666 1.540000e-91 348.0
43 TraesCS7A01G455200 chr6B 89.123 285 21 6 7156 7439 471316328 471316053 5.530000e-91 346.0
44 TraesCS7A01G455200 chr6B 89.531 277 19 6 7164 7439 471315730 471315463 7.150000e-90 342.0
45 TraesCS7A01G455200 chr5D 91.855 221 13 3 6572 6789 51229489 51229707 3.370000e-78 303.0
46 TraesCS7A01G455200 chr5D 92.271 207 13 1 6572 6775 51305876 51306082 2.630000e-74 291.0
47 TraesCS7A01G455200 chr5D 93.382 136 9 0 6875 7010 51306284 51306419 1.270000e-47 202.0
48 TraesCS7A01G455200 chr5D 90.977 133 12 0 6875 7007 51229897 51230029 5.930000e-41 180.0
49 TraesCS7A01G455200 chr5D 95.000 100 5 0 6774 6873 51229746 51229845 2.780000e-34 158.0
50 TraesCS7A01G455200 chr5D 94.000 100 6 0 6774 6873 51306133 51306232 1.290000e-32 152.0
51 TraesCS7A01G455200 chr4D 90.950 221 15 3 6572 6789 314659610 314659392 7.300000e-75 292.0
52 TraesCS7A01G455200 chr4D 92.806 139 9 1 6875 7013 314659202 314659065 4.550000e-47 200.0
53 TraesCS7A01G455200 chr4D 94.059 101 6 0 6774 6874 314659353 314659253 3.590000e-33 154.0
54 TraesCS7A01G455200 chr6A 89.778 225 17 4 6568 6789 502711467 502711246 4.390000e-72 283.0
55 TraesCS7A01G455200 chr6A 95.683 139 6 0 6875 7013 502711056 502710918 2.700000e-54 224.0
56 TraesCS7A01G455200 chr6A 93.069 101 7 0 6774 6874 502711207 502711107 1.670000e-31 148.0
57 TraesCS7A01G455200 chr1B 84.615 221 26 6 1048 1264 642470796 642471012 5.850000e-51 213.0
58 TraesCS7A01G455200 chr2A 85.165 182 13 10 7124 7303 653873256 653873425 2.760000e-39 174.0
59 TraesCS7A01G455200 chr2B 81.667 180 26 4 6602 6774 450753653 450753474 7.780000e-30 143.0
60 TraesCS7A01G455200 chr2B 86.957 69 3 5 6572 6636 119627924 119627990 1.040000e-08 73.1
61 TraesCS7A01G455200 chr3B 89.394 66 3 4 6570 6633 418669017 418669080 6.190000e-11 80.5


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 TraesCS7A01G455200 chr7A 650621627 650629065 7438 False 13738.000000 13738 100.000000 1 7439 1 chr7A.!!$F2 7438
1 TraesCS7A01G455200 chr7A 650720256 650721029 773 False 1230.000000 1230 95.373000 5802 6575 1 chr7A.!!$F3 773
2 TraesCS7A01G455200 chr7A 650891117 650892089 972 False 1088.000000 1088 87.295000 5625 6573 1 chr7A.!!$F5 948
3 TraesCS7A01G455200 chr7A 650904294 650905266 972 False 1088.000000 1088 87.295000 5625 6573 1 chr7A.!!$F6 948
4 TraesCS7A01G455200 chr7A 650865555 650866118 563 False 483.000000 483 82.892000 5721 6261 1 chr7A.!!$F4 540
5 TraesCS7A01G455200 chr7A 650674348 650675457 1109 False 422.333333 538 87.908667 4614 5800 3 chr7A.!!$F7 1186
6 TraesCS7A01G455200 chr7A 650688410 650689305 895 False 269.033333 390 84.765333 4615 6575 3 chr7A.!!$F8 1960
7 TraesCS7A01G455200 chr7A 650815744 650819730 3986 False 214.500000 350 89.559750 4614 6575 4 chr7A.!!$F9 1961
8 TraesCS7A01G455200 chr7D 564966924 564973455 6531 False 9858.000000 9858 93.902000 1 6575 1 chr7D.!!$F1 6574
9 TraesCS7A01G455200 chr7B 614867722 614874214 6492 False 2395.250000 6191 91.035000 1 6575 4 chr7B.!!$F4 6574
10 TraesCS7A01G455200 chr7B 614914038 614915653 1615 False 934.500000 1434 94.557500 5390 6575 2 chr7B.!!$F5 1185
11 TraesCS7A01G455200 chr1D 465531315 465535875 4560 False 385.500000 571 81.058000 1075 6303 2 chr1D.!!$F2 5228
12 TraesCS7A01G455200 chr1D 418204497 418205040 543 False 223.000000 289 94.260667 6572 7010 3 chr1D.!!$F1 438
13 TraesCS7A01G455200 chr1A 557948096 557952391 4295 False 358.000000 514 80.742500 1075 6303 2 chr1A.!!$F1 5228
14 TraesCS7A01G455200 chr6B 471315463 471316328 865 True 344.000000 346 89.327000 7156 7439 2 chr6B.!!$R1 283
15 TraesCS7A01G455200 chr5D 51305876 51306419 543 False 215.000000 291 93.217667 6572 7010 3 chr5D.!!$F2 438
16 TraesCS7A01G455200 chr5D 51229489 51230029 540 False 213.666667 303 92.610667 6572 7007 3 chr5D.!!$F1 435
17 TraesCS7A01G455200 chr4D 314659065 314659610 545 True 215.333333 292 92.605000 6572 7013 3 chr4D.!!$R1 441
18 TraesCS7A01G455200 chr6A 502710918 502711467 549 True 218.333333 283 92.843333 6568 7013 3 chr6A.!!$R1 445

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
808 867 0.037326 TTCATCTGCGTCACCTCACC 60.037 55.000 0.00 0.00 0.00 4.02 F
828 887 0.108898 CCACTCTCTGAGCTGTTCCG 60.109 60.000 0.00 0.00 32.04 4.30 F
844 903 0.682852 TCCGTTCTTGATCCAACCGT 59.317 50.000 0.00 0.00 0.00 4.83 F
1570 1650 1.429463 AGTTTTTCTACTGCGAGCGG 58.571 50.000 1.84 1.84 0.00 5.52 F
2346 2583 2.770130 GGGTGGCCCATTCCTTGA 59.230 61.111 0.00 0.00 44.65 3.02 F
2941 3444 0.759436 CAGTACGGATAGCCACCCCT 60.759 60.000 0.00 0.00 0.00 4.79 F
2958 3461 2.785857 CCCCTCTTTTATGTCCCCATCT 59.214 50.000 0.00 0.00 32.29 2.90 F
3488 3998 3.441572 ACTACTTCCAAATGCATGCTGTC 59.558 43.478 20.33 0.00 0.00 3.51 F
5259 5832 6.104146 TGCACACAGTAAGTCCACTAAATA 57.896 37.500 0.00 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2931 1.134280 AGAAAGGGCACGATCCTCATG 60.134 52.381 0.00 0.00 32.59 3.07 R
2622 3097 5.893897 AAGTGAAGAATTGGATGCTCTTC 57.106 39.130 7.50 7.50 43.51 2.87 R
2849 3352 9.148104 GGTTTAATGACTAGTAATTGACGAACT 57.852 33.333 14.89 0.00 0.00 3.01 R
2876 3379 0.184451 CTAGGCCATGCAGGTCCATT 59.816 55.000 5.01 0.00 45.84 3.16 R
3398 3908 2.397549 GTTGGATCAGTTGCTGCAAAC 58.602 47.619 17.80 11.27 0.00 2.93 R
4112 4622 6.406177 GCAACTGATCACCACCATCAAATATT 60.406 38.462 0.00 0.00 29.74 1.28 R
5340 5915 0.974383 CTTACGGTGTTCTCCCCTGT 59.026 55.000 0.00 0.00 0.00 4.00 R
5690 6267 1.605710 CTGAAGTTGCAGTGGGTTGAG 59.394 52.381 0.00 0.00 0.00 3.02 R
6776 10587 0.482446 TCCCAACAGGAAAGCCATGT 59.518 50.000 0.00 0.00 43.78 3.21 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
50 52 1.376086 CCATCCACTCCACAGCACA 59.624 57.895 0.00 0.00 0.00 4.57
52 54 0.877071 CATCCACTCCACAGCACAAC 59.123 55.000 0.00 0.00 0.00 3.32
57 59 2.896801 CTCCACAGCACAACACCGC 61.897 63.158 0.00 0.00 0.00 5.68
65 67 1.287815 CACAACACCGCCGAGACTA 59.712 57.895 0.00 0.00 0.00 2.59
77 79 1.516603 GAGACTACCGCCAACGAGC 60.517 63.158 0.00 0.00 43.93 5.03
87 89 1.079127 CCAACGAGCGACATCCCTT 60.079 57.895 0.00 0.00 0.00 3.95
90 92 2.125552 CGAGCGACATCCCTTGCA 60.126 61.111 0.00 0.00 0.00 4.08
99 101 0.106569 CATCCCTTGCATGGCCTACA 60.107 55.000 13.15 0.00 0.00 2.74
139 142 3.562232 TTCCCCCGGAGCACGTTT 61.562 61.111 0.73 0.00 42.24 3.60
172 175 2.398036 GGTGCCAAATACGTCGCG 59.602 61.111 0.00 0.00 0.00 5.87
176 179 2.510691 CCAAATACGTCGCGCCCT 60.511 61.111 0.00 0.00 0.00 5.19
177 180 2.701006 CAAATACGTCGCGCCCTG 59.299 61.111 0.00 0.00 0.00 4.45
178 181 2.098233 CAAATACGTCGCGCCCTGT 61.098 57.895 0.00 0.00 0.00 4.00
211 214 3.515286 CGACGGCGCTCTTCCCTA 61.515 66.667 6.90 0.00 0.00 3.53
213 216 3.753070 GACGGCGCTCTTCCCTACG 62.753 68.421 6.90 0.55 0.00 3.51
219 222 3.823330 CTCTTCCCTACGCCGCGT 61.823 66.667 23.72 23.72 44.35 6.01
220 223 4.124351 TCTTCCCTACGCCGCGTG 62.124 66.667 28.10 16.86 41.39 5.34
221 224 4.124351 CTTCCCTACGCCGCGTGA 62.124 66.667 28.10 14.20 41.39 4.35
222 225 3.426117 CTTCCCTACGCCGCGTGAT 62.426 63.158 28.10 3.95 41.39 3.06
223 226 3.709880 TTCCCTACGCCGCGTGATG 62.710 63.158 28.10 16.68 41.39 3.07
254 257 3.372954 GCCGCCGTCATGTATATATCTC 58.627 50.000 0.00 0.00 0.00 2.75
391 395 1.597027 GTGGATAACCGCCCCGATG 60.597 63.158 0.00 0.00 40.47 3.84
404 408 1.063567 CCCCGATGACCCCCAAAAATA 60.064 52.381 0.00 0.00 0.00 1.40
405 409 2.425683 CCCCGATGACCCCCAAAAATAT 60.426 50.000 0.00 0.00 0.00 1.28
406 410 2.890945 CCCGATGACCCCCAAAAATATC 59.109 50.000 0.00 0.00 0.00 1.63
422 437 2.474410 TATCATCTCTAGCGGCGAGA 57.526 50.000 12.98 12.28 41.36 4.04
423 438 1.164411 ATCATCTCTAGCGGCGAGAG 58.836 55.000 27.72 27.72 40.53 3.20
424 439 0.886938 TCATCTCTAGCGGCGAGAGG 60.887 60.000 30.97 21.54 40.53 3.69
505 521 1.273606 TCCAACAGTAGCTGTCTGAGC 59.726 52.381 21.75 0.00 44.62 4.26
754 812 2.491693 CAGCTCGTCCTCTTCTTCTTCT 59.508 50.000 0.00 0.00 0.00 2.85
755 813 3.056891 CAGCTCGTCCTCTTCTTCTTCTT 60.057 47.826 0.00 0.00 0.00 2.52
759 817 2.093921 CGTCCTCTTCTTCTTCTTCCCC 60.094 54.545 0.00 0.00 0.00 4.81
791 850 0.729690 GCCTCAAAGCCATCGTCTTC 59.270 55.000 0.00 0.00 0.00 2.87
792 851 1.945819 GCCTCAAAGCCATCGTCTTCA 60.946 52.381 0.00 0.00 0.00 3.02
794 853 2.611292 CCTCAAAGCCATCGTCTTCATC 59.389 50.000 0.00 0.00 0.00 2.92
795 854 3.529533 CTCAAAGCCATCGTCTTCATCT 58.470 45.455 0.00 0.00 0.00 2.90
798 857 0.529337 AGCCATCGTCTTCATCTGCG 60.529 55.000 0.00 0.00 0.00 5.18
799 858 0.807667 GCCATCGTCTTCATCTGCGT 60.808 55.000 0.00 0.00 0.00 5.24
800 859 1.203928 CCATCGTCTTCATCTGCGTC 58.796 55.000 0.00 0.00 0.00 5.19
801 860 1.469767 CCATCGTCTTCATCTGCGTCA 60.470 52.381 0.00 0.00 0.00 4.35
802 861 1.585668 CATCGTCTTCATCTGCGTCAC 59.414 52.381 0.00 0.00 0.00 3.67
803 862 0.109272 TCGTCTTCATCTGCGTCACC 60.109 55.000 0.00 0.00 0.00 4.02
804 863 0.109086 CGTCTTCATCTGCGTCACCT 60.109 55.000 0.00 0.00 0.00 4.00
805 864 1.634702 GTCTTCATCTGCGTCACCTC 58.365 55.000 0.00 0.00 0.00 3.85
806 865 1.067565 GTCTTCATCTGCGTCACCTCA 60.068 52.381 0.00 0.00 0.00 3.86
807 866 1.067565 TCTTCATCTGCGTCACCTCAC 60.068 52.381 0.00 0.00 0.00 3.51
808 867 0.037326 TTCATCTGCGTCACCTCACC 60.037 55.000 0.00 0.00 0.00 4.02
809 868 1.448540 CATCTGCGTCACCTCACCC 60.449 63.158 0.00 0.00 0.00 4.61
810 869 2.660064 ATCTGCGTCACCTCACCCC 61.660 63.158 0.00 0.00 0.00 4.95
811 870 3.625897 CTGCGTCACCTCACCCCA 61.626 66.667 0.00 0.00 0.00 4.96
812 871 3.883744 CTGCGTCACCTCACCCCAC 62.884 68.421 0.00 0.00 0.00 4.61
813 872 3.626924 GCGTCACCTCACCCCACT 61.627 66.667 0.00 0.00 0.00 4.00
814 873 2.657237 CGTCACCTCACCCCACTC 59.343 66.667 0.00 0.00 0.00 3.51
815 874 1.908793 CGTCACCTCACCCCACTCT 60.909 63.158 0.00 0.00 0.00 3.24
816 875 1.878656 CGTCACCTCACCCCACTCTC 61.879 65.000 0.00 0.00 0.00 3.20
817 876 0.543174 GTCACCTCACCCCACTCTCT 60.543 60.000 0.00 0.00 0.00 3.10
818 877 0.542938 TCACCTCACCCCACTCTCTG 60.543 60.000 0.00 0.00 0.00 3.35
819 878 0.542938 CACCTCACCCCACTCTCTGA 60.543 60.000 0.00 0.00 0.00 3.27
820 879 0.252012 ACCTCACCCCACTCTCTGAG 60.252 60.000 0.00 0.00 35.52 3.35
821 880 1.612395 CCTCACCCCACTCTCTGAGC 61.612 65.000 0.00 0.00 32.04 4.26
822 881 0.614415 CTCACCCCACTCTCTGAGCT 60.614 60.000 0.00 0.00 32.04 4.09
823 882 0.902048 TCACCCCACTCTCTGAGCTG 60.902 60.000 0.00 0.00 32.04 4.24
824 883 1.157276 ACCCCACTCTCTGAGCTGT 59.843 57.895 0.00 0.00 32.04 4.40
825 884 0.472734 ACCCCACTCTCTGAGCTGTT 60.473 55.000 0.00 0.00 32.04 3.16
826 885 0.248843 CCCCACTCTCTGAGCTGTTC 59.751 60.000 0.00 0.00 32.04 3.18
827 886 0.248843 CCCACTCTCTGAGCTGTTCC 59.751 60.000 0.00 0.00 32.04 3.62
828 887 0.108898 CCACTCTCTGAGCTGTTCCG 60.109 60.000 0.00 0.00 32.04 4.30
844 903 0.682852 TCCGTTCTTGATCCAACCGT 59.317 50.000 0.00 0.00 0.00 4.83
848 907 2.347731 GTTCTTGATCCAACCGTCTCC 58.652 52.381 0.00 0.00 0.00 3.71
1291 1353 5.560724 TCCTTCACTTCTTTTATCACCCTG 58.439 41.667 0.00 0.00 0.00 4.45
1292 1354 5.073144 TCCTTCACTTCTTTTATCACCCTGT 59.927 40.000 0.00 0.00 0.00 4.00
1296 1358 7.272037 TCACTTCTTTTATCACCCTGTTTTC 57.728 36.000 0.00 0.00 0.00 2.29
1443 1507 2.074547 TTCGGCGACTTTTCCACTAG 57.925 50.000 10.16 0.00 0.00 2.57
1447 1511 1.679032 GGCGACTTTTCCACTAGCCAT 60.679 52.381 0.00 0.00 42.37 4.40
1448 1512 2.419574 GGCGACTTTTCCACTAGCCATA 60.420 50.000 0.00 0.00 42.37 2.74
1449 1513 3.467803 GCGACTTTTCCACTAGCCATAT 58.532 45.455 0.00 0.00 0.00 1.78
1451 1515 4.740934 GCGACTTTTCCACTAGCCATATCT 60.741 45.833 0.00 0.00 0.00 1.98
1452 1516 4.747108 CGACTTTTCCACTAGCCATATCTG 59.253 45.833 0.00 0.00 0.00 2.90
1455 1519 6.904626 ACTTTTCCACTAGCCATATCTGATT 58.095 36.000 0.00 0.00 0.00 2.57
1456 1520 6.769822 ACTTTTCCACTAGCCATATCTGATTG 59.230 38.462 0.00 0.00 0.00 2.67
1570 1650 1.429463 AGTTTTTCTACTGCGAGCGG 58.571 50.000 1.84 1.84 0.00 5.52
1707 1876 3.926821 TCGGCCCAGAAATAACAAAAC 57.073 42.857 0.00 0.00 0.00 2.43
1711 1880 3.506844 GGCCCAGAAATAACAAAACCGTA 59.493 43.478 0.00 0.00 0.00 4.02
1715 1884 6.647481 GCCCAGAAATAACAAAACCGTATTTT 59.353 34.615 0.00 0.00 0.00 1.82
1900 2114 3.019564 AGCATATCTGTTCAAAGTGCCC 58.980 45.455 0.00 0.00 0.00 5.36
2012 2235 4.926238 CGTCAGAGTTGATGAGTAGCTTTT 59.074 41.667 0.00 0.00 41.91 2.27
2067 2302 9.109393 TGCATATATGAAGAAACCTGTTACTTC 57.891 33.333 17.10 0.00 39.08 3.01
2138 2373 8.964420 TCATACTTTGTTTAGTTAATTGCTGC 57.036 30.769 0.00 0.00 0.00 5.25
2174 2409 8.691797 GTCTGAGATTCACTTCTTAGATTAGGT 58.308 37.037 0.17 0.00 39.62 3.08
2190 2425 6.741724 AGATTAGGTGTCATAAATTTGGGGT 58.258 36.000 0.00 0.00 0.00 4.95
2346 2583 2.770130 GGGTGGCCCATTCCTTGA 59.230 61.111 0.00 0.00 44.65 3.02
2390 2854 2.770164 AATTGCCTAGCTCGTGTTCT 57.230 45.000 0.00 0.00 0.00 3.01
2466 2931 6.862711 AAAGTACTGTTGCTCTAAACTTCC 57.137 37.500 0.00 0.00 0.00 3.46
2622 3097 6.808212 CCTTAAGGTGCAAGAAACATGTATTG 59.192 38.462 13.83 6.39 0.00 1.90
2876 3379 8.928733 GTTCGTCAATTACTAGTCATTAAACCA 58.071 33.333 0.00 0.00 0.00 3.67
2887 3390 3.509575 GTCATTAAACCAATGGACCTGCA 59.490 43.478 6.16 0.00 43.68 4.41
2899 3402 2.898840 CCTGCATGGCCTAGCGTG 60.899 66.667 3.32 5.16 0.00 5.34
2912 3415 3.554731 GCCTAGCGTGTACAGTATTTTCC 59.445 47.826 0.00 0.00 0.00 3.13
2927 3430 8.028938 ACAGTATTTTCCAAATGCATTCAGTAC 58.971 33.333 13.38 9.08 0.00 2.73
2939 3442 1.117150 TTCAGTACGGATAGCCACCC 58.883 55.000 0.00 0.00 0.00 4.61
2941 3444 0.759436 CAGTACGGATAGCCACCCCT 60.759 60.000 0.00 0.00 0.00 4.79
2958 3461 2.785857 CCCCTCTTTTATGTCCCCATCT 59.214 50.000 0.00 0.00 32.29 2.90
2961 3464 4.445448 CCCTCTTTTATGTCCCCATCTGAG 60.445 50.000 0.00 0.00 32.29 3.35
2962 3465 4.445448 CCTCTTTTATGTCCCCATCTGAGG 60.445 50.000 0.00 0.00 32.35 3.86
3102 3606 5.785940 CCTATTAAGGCCCTAGAACTGGTAT 59.214 44.000 0.00 0.00 35.64 2.73
3398 3908 4.938080 AGCTACATGTTCCACTTCTATCG 58.062 43.478 2.30 0.00 0.00 2.92
3488 3998 3.441572 ACTACTTCCAAATGCATGCTGTC 59.558 43.478 20.33 0.00 0.00 3.51
4112 4622 6.370593 CAGTTTGCGTCTATCAAAGCTTAAA 58.629 36.000 0.00 0.00 34.50 1.52
5259 5832 6.104146 TGCACACAGTAAGTCCACTAAATA 57.896 37.500 0.00 0.00 0.00 1.40
5312 5887 6.834168 TTTGTATTCTTTTCCCATCTGGAC 57.166 37.500 0.00 0.00 45.11 4.02
5690 6267 2.208431 CCATGCGTTGAGATCTTCCTC 58.792 52.381 0.00 0.00 0.00 3.71
6446 10246 9.388506 CTTGACACTTGTAGGATTCATAAATCT 57.611 33.333 0.00 0.00 40.99 2.40
6447 10247 9.739276 TTGACACTTGTAGGATTCATAAATCTT 57.261 29.630 0.00 0.00 40.99 2.40
6448 10248 9.739276 TGACACTTGTAGGATTCATAAATCTTT 57.261 29.630 0.00 0.00 40.99 2.52
6531 10339 9.503399 GTCCCAACTATTAATATTCCGAGAATT 57.497 33.333 4.76 0.00 0.00 2.17
6548 10356 6.037172 CCGAGAATTATTTTCTTGACCGACAT 59.963 38.462 4.50 0.00 32.85 3.06
6560 10368 3.466836 TGACCGACATGCCTTATGATTC 58.533 45.455 0.00 0.00 39.21 2.52
6561 10369 3.134623 TGACCGACATGCCTTATGATTCT 59.865 43.478 0.00 0.00 39.21 2.40
6671 10479 2.775384 ACAAAGTGGTGTTACTCTCCCA 59.225 45.455 0.00 0.00 0.00 4.37
6685 10493 7.946776 TGTTACTCTCCCAGTATTATAGTACCC 59.053 40.741 2.01 0.00 37.44 3.69
6714 10525 3.246112 CCCGGTGACCCAGGTGAA 61.246 66.667 0.00 0.00 0.00 3.18
6776 10587 1.952990 TGCTCTTGTTGCGGAAAATGA 59.047 42.857 0.00 0.00 0.00 2.57
6816 10679 0.592637 TGCACAAACTCGATTGGCTG 59.407 50.000 3.94 0.00 34.56 4.85
6829 10692 1.724148 TTGGCTGACCCACCAATCCA 61.724 55.000 0.00 0.00 45.34 3.41
6859 10722 1.131126 CATGAAGGTGCCATGTCGAAC 59.869 52.381 0.00 0.00 37.28 3.95
6914 10827 3.952628 GACTCCGGCTCCCGTTTGG 62.953 68.421 0.00 0.00 46.80 3.28
6958 10871 2.125326 CCATCCCCGACGTGCTAGA 61.125 63.158 0.00 0.00 0.00 2.43
6976 10889 3.703001 AGACGATCAGTGGTCCAAATT 57.297 42.857 0.00 0.00 33.99 1.82
7010 10923 1.334869 CAAGCCACGCAAAGAACTTCT 59.665 47.619 0.00 0.00 0.00 2.85
7013 10926 1.593196 CCACGCAAAGAACTTCTCCA 58.407 50.000 0.00 0.00 0.00 3.86
7014 10927 1.264288 CCACGCAAAGAACTTCTCCAC 59.736 52.381 0.00 0.00 0.00 4.02
7015 10928 1.939934 CACGCAAAGAACTTCTCCACA 59.060 47.619 0.00 0.00 0.00 4.17
7016 10929 1.940613 ACGCAAAGAACTTCTCCACAC 59.059 47.619 0.00 0.00 0.00 3.82
7017 10930 1.264288 CGCAAAGAACTTCTCCACACC 59.736 52.381 0.00 0.00 0.00 4.16
7018 10931 1.264288 GCAAAGAACTTCTCCACACCG 59.736 52.381 0.00 0.00 0.00 4.94
7019 10932 2.561569 CAAAGAACTTCTCCACACCGT 58.438 47.619 0.00 0.00 0.00 4.83
7020 10933 2.240493 AAGAACTTCTCCACACCGTG 57.760 50.000 0.00 0.00 0.00 4.94
7021 10934 1.120530 AGAACTTCTCCACACCGTGT 58.879 50.000 0.00 0.00 0.00 4.49
7036 10949 5.790593 ACACCGTGTGATCTAAAATGTACT 58.209 37.500 2.57 0.00 36.96 2.73
7037 10950 6.228258 ACACCGTGTGATCTAAAATGTACTT 58.772 36.000 2.57 0.00 36.96 2.24
7038 10951 6.708949 ACACCGTGTGATCTAAAATGTACTTT 59.291 34.615 2.57 0.00 36.96 2.66
7039 10952 7.227910 ACACCGTGTGATCTAAAATGTACTTTT 59.772 33.333 2.57 1.06 37.61 2.27
7040 10953 7.744715 CACCGTGTGATCTAAAATGTACTTTTC 59.255 37.037 7.15 0.00 35.71 2.29
7041 10954 7.442969 ACCGTGTGATCTAAAATGTACTTTTCA 59.557 33.333 7.15 0.00 38.09 2.69
7042 10955 8.450964 CCGTGTGATCTAAAATGTACTTTTCAT 58.549 33.333 7.15 1.38 38.09 2.57
7043 10956 9.478019 CGTGTGATCTAAAATGTACTTTTCATC 57.522 33.333 7.15 9.35 38.09 2.92
7052 10965 8.871686 AAAATGTACTTTTCATCACTGTTTCC 57.128 30.769 7.15 0.00 31.23 3.13
7053 10966 5.666969 TGTACTTTTCATCACTGTTTCCG 57.333 39.130 0.00 0.00 0.00 4.30
7054 10967 5.361427 TGTACTTTTCATCACTGTTTCCGA 58.639 37.500 0.00 0.00 0.00 4.55
7055 10968 5.818336 TGTACTTTTCATCACTGTTTCCGAA 59.182 36.000 0.00 0.00 0.00 4.30
7056 10969 5.424121 ACTTTTCATCACTGTTTCCGAAG 57.576 39.130 0.00 0.00 0.00 3.79
7057 10970 4.881850 ACTTTTCATCACTGTTTCCGAAGT 59.118 37.500 0.00 0.00 0.00 3.01
7058 10971 4.811555 TTTCATCACTGTTTCCGAAGTG 57.188 40.909 0.00 0.00 44.23 3.16
7062 10975 3.093717 TCACTGTTTCCGAAGTGAGTC 57.906 47.619 1.50 0.00 45.97 3.36
7063 10976 2.693591 TCACTGTTTCCGAAGTGAGTCT 59.306 45.455 1.50 0.00 45.97 3.24
7064 10977 3.887110 TCACTGTTTCCGAAGTGAGTCTA 59.113 43.478 1.50 0.00 45.97 2.59
7065 10978 4.523173 TCACTGTTTCCGAAGTGAGTCTAT 59.477 41.667 1.50 0.00 45.97 1.98
7066 10979 5.708697 TCACTGTTTCCGAAGTGAGTCTATA 59.291 40.000 1.50 0.00 45.97 1.31
7067 10980 6.030849 CACTGTTTCCGAAGTGAGTCTATAG 58.969 44.000 0.00 0.00 45.43 1.31
7068 10981 5.944599 ACTGTTTCCGAAGTGAGTCTATAGA 59.055 40.000 0.00 0.00 0.00 1.98
7069 10982 6.603997 ACTGTTTCCGAAGTGAGTCTATAGAT 59.396 38.462 5.57 0.00 0.00 1.98
7070 10983 6.796426 TGTTTCCGAAGTGAGTCTATAGATG 58.204 40.000 5.57 0.00 0.00 2.90
7071 10984 6.183360 TGTTTCCGAAGTGAGTCTATAGATGG 60.183 42.308 5.57 0.00 0.00 3.51
7072 10985 3.821600 TCCGAAGTGAGTCTATAGATGGC 59.178 47.826 5.57 0.00 0.00 4.40
7073 10986 3.823873 CCGAAGTGAGTCTATAGATGGCT 59.176 47.826 5.57 0.00 0.00 4.75
7074 10987 4.279671 CCGAAGTGAGTCTATAGATGGCTT 59.720 45.833 5.57 8.31 0.00 4.35
7075 10988 5.457140 CGAAGTGAGTCTATAGATGGCTTC 58.543 45.833 5.57 14.64 0.00 3.86
7076 10989 5.240623 CGAAGTGAGTCTATAGATGGCTTCT 59.759 44.000 22.30 8.09 38.57 2.85
7077 10990 6.238897 CGAAGTGAGTCTATAGATGGCTTCTT 60.239 42.308 22.30 15.86 35.79 2.52
7078 10991 7.430760 AAGTGAGTCTATAGATGGCTTCTTT 57.569 36.000 5.57 3.54 35.79 2.52
7079 10992 7.430760 AGTGAGTCTATAGATGGCTTCTTTT 57.569 36.000 5.57 0.17 35.79 2.27
7080 10993 7.856415 AGTGAGTCTATAGATGGCTTCTTTTT 58.144 34.615 5.57 0.00 35.79 1.94
7115 11028 8.421673 AGTACGATAGAAAAATAAACTCTGCC 57.578 34.615 0.00 0.00 41.38 4.85
7116 11029 8.038944 AGTACGATAGAAAAATAAACTCTGCCA 58.961 33.333 0.00 0.00 41.38 4.92
7117 11030 7.865706 ACGATAGAAAAATAAACTCTGCCAT 57.134 32.000 0.00 0.00 41.38 4.40
7118 11031 7.697691 ACGATAGAAAAATAAACTCTGCCATG 58.302 34.615 0.00 0.00 41.38 3.66
7119 11032 6.634436 CGATAGAAAAATAAACTCTGCCATGC 59.366 38.462 0.00 0.00 39.76 4.06
7120 11033 5.726980 AGAAAAATAAACTCTGCCATGCA 57.273 34.783 0.00 0.00 36.92 3.96
7121 11034 6.290294 AGAAAAATAAACTCTGCCATGCAT 57.710 33.333 0.00 0.00 38.13 3.96
7122 11035 6.704310 AGAAAAATAAACTCTGCCATGCATT 58.296 32.000 0.00 0.00 38.13 3.56
7123 11036 7.163441 AGAAAAATAAACTCTGCCATGCATTT 58.837 30.769 0.00 0.00 38.13 2.32
7124 11037 8.313292 AGAAAAATAAACTCTGCCATGCATTTA 58.687 29.630 0.00 0.00 38.13 1.40
7125 11038 8.845413 AAAAATAAACTCTGCCATGCATTTAA 57.155 26.923 0.00 0.00 38.13 1.52
7126 11039 9.452287 AAAAATAAACTCTGCCATGCATTTAAT 57.548 25.926 0.00 0.00 38.13 1.40
7127 11040 8.652810 AAATAAACTCTGCCATGCATTTAATC 57.347 30.769 0.00 0.00 38.13 1.75
7128 11041 5.927281 AAACTCTGCCATGCATTTAATCT 57.073 34.783 0.00 0.00 38.13 2.40
7129 11042 8.696043 ATAAACTCTGCCATGCATTTAATCTA 57.304 30.769 0.00 0.00 38.13 1.98
7130 11043 7.592885 AAACTCTGCCATGCATTTAATCTAT 57.407 32.000 0.00 0.00 38.13 1.98
7131 11044 8.696043 AAACTCTGCCATGCATTTAATCTATA 57.304 30.769 0.00 0.00 38.13 1.31
7132 11045 8.874744 AACTCTGCCATGCATTTAATCTATAT 57.125 30.769 0.00 0.00 38.13 0.86
7133 11046 8.503458 ACTCTGCCATGCATTTAATCTATATC 57.497 34.615 0.00 0.00 38.13 1.63
7134 11047 8.327271 ACTCTGCCATGCATTTAATCTATATCT 58.673 33.333 0.00 0.00 38.13 1.98
7135 11048 9.828039 CTCTGCCATGCATTTAATCTATATCTA 57.172 33.333 0.00 0.00 38.13 1.98
7195 11108 4.225267 AGGTGATATTCTTGGTTTCGTCCT 59.775 41.667 0.00 0.00 0.00 3.85
7197 11110 3.938963 TGATATTCTTGGTTTCGTCCTGC 59.061 43.478 0.00 0.00 0.00 4.85
7208 11711 4.501071 GTTTCGTCCTGCTTAGGTGATTA 58.499 43.478 0.00 0.00 0.00 1.75
7214 11717 9.470399 TTCGTCCTGCTTAGGTGATTATATATA 57.530 33.333 0.00 0.00 0.00 0.86
7271 11774 8.894409 TTTGCTACAAAACAGATTCATATTCG 57.106 30.769 0.00 0.00 0.00 3.34
7278 11781 8.956426 ACAAAACAGATTCATATTCGTTACCAT 58.044 29.630 0.00 0.00 0.00 3.55
7310 11813 2.270850 GGGGTCTATGCACGCCAA 59.729 61.111 3.56 0.00 46.40 4.52
7329 11832 2.694760 CGCTGCTCTGGGCCTTTTC 61.695 63.158 4.53 0.00 40.92 2.29
7335 11838 1.251251 CTCTGGGCCTTTTCTTGGTG 58.749 55.000 4.53 0.00 0.00 4.17
7338 11841 2.378547 TCTGGGCCTTTTCTTGGTGTAT 59.621 45.455 4.53 0.00 0.00 2.29
7375 11878 2.362120 ATGGGCCTGCTCTTGTGC 60.362 61.111 4.53 0.00 0.00 4.57
7382 11885 2.154462 GCCTGCTCTTGTGCTTAGAAA 58.846 47.619 0.00 0.00 0.00 2.52
7433 11937 3.432051 GATCGAGCCCACGACCTGG 62.432 68.421 0.00 0.00 44.84 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 2.968206 GGTAGTCTCGGCGGTGTT 59.032 61.111 7.21 0.00 0.00 3.32
52 54 4.849329 GCGGTAGTCTCGGCGGTG 62.849 72.222 7.21 0.00 0.00 4.94
57 59 2.202570 CGTTGGCGGTAGTCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
71 73 1.741770 GCAAGGGATGTCGCTCGTT 60.742 57.895 0.00 0.00 38.25 3.85
77 79 2.484062 GGCCATGCAAGGGATGTCG 61.484 63.158 10.51 0.00 43.46 4.35
87 89 1.284491 TGGAGATTTGTAGGCCATGCA 59.716 47.619 5.01 0.00 0.00 3.96
90 92 4.102524 TCGTTATGGAGATTTGTAGGCCAT 59.897 41.667 5.01 0.00 41.81 4.40
133 136 1.236616 TGCTGCCAGGATCAAACGTG 61.237 55.000 0.00 0.00 0.00 4.49
134 137 1.073025 TGCTGCCAGGATCAAACGT 59.927 52.632 0.00 0.00 0.00 3.99
139 142 4.100084 CCGGTGCTGCCAGGATCA 62.100 66.667 0.00 0.00 36.97 2.92
176 179 4.028490 GGCATCGGGGTGGTCACA 62.028 66.667 3.40 0.00 0.00 3.58
177 180 4.796495 GGGCATCGGGGTGGTCAC 62.796 72.222 0.00 0.00 0.00 3.67
230 233 3.734682 TATATACATGACGGCGGCGGC 62.735 57.143 35.05 33.93 38.90 6.53
231 234 0.171679 TATATACATGACGGCGGCGG 59.828 55.000 35.05 19.50 0.00 6.13
234 237 4.335594 TCTGAGATATATACATGACGGCGG 59.664 45.833 13.24 0.00 0.00 6.13
307 311 1.348064 AGGGTCGTGTCATGGAGAAA 58.652 50.000 0.00 0.00 0.00 2.52
391 395 5.707764 GCTAGAGATGATATTTTTGGGGGTC 59.292 44.000 0.00 0.00 0.00 4.46
399 403 4.218635 TCTCGCCGCTAGAGATGATATTTT 59.781 41.667 0.00 0.00 39.57 1.82
404 408 1.164411 CTCTCGCCGCTAGAGATGAT 58.836 55.000 15.23 0.00 42.63 2.45
405 409 0.886938 CCTCTCGCCGCTAGAGATGA 60.887 60.000 20.61 0.00 42.63 2.92
406 410 1.578926 CCTCTCGCCGCTAGAGATG 59.421 63.158 20.61 5.14 42.63 2.90
435 450 4.388499 TCTTTCCCGCGGGCACTC 62.388 66.667 39.89 0.00 34.68 3.51
436 451 4.394712 CTCTTTCCCGCGGGCACT 62.395 66.667 39.89 0.00 34.68 4.40
440 455 1.819632 CATTCCTCTTTCCCGCGGG 60.820 63.158 39.13 39.13 0.00 6.13
441 456 0.392461 TTCATTCCTCTTTCCCGCGG 60.392 55.000 21.04 21.04 0.00 6.46
442 457 1.668419 ATTCATTCCTCTTTCCCGCG 58.332 50.000 0.00 0.00 0.00 6.46
443 458 3.699779 GAATTCATTCCTCTTTCCCGC 57.300 47.619 0.00 0.00 0.00 6.13
582 616 4.605967 GTGGCGTGTTGTGCGGTG 62.606 66.667 0.00 0.00 0.00 4.94
584 618 4.312231 CTGTGGCGTGTTGTGCGG 62.312 66.667 0.00 0.00 0.00 5.69
585 619 3.506312 GACTGTGGCGTGTTGTGCG 62.506 63.158 0.00 0.00 0.00 5.34
586 620 2.327940 GACTGTGGCGTGTTGTGC 59.672 61.111 0.00 0.00 0.00 4.57
587 621 2.625906 CGACTGTGGCGTGTTGTG 59.374 61.111 0.00 0.00 0.00 3.33
588 622 3.269347 GCGACTGTGGCGTGTTGT 61.269 61.111 0.00 0.00 0.00 3.32
589 623 4.012895 GGCGACTGTGGCGTGTTG 62.013 66.667 8.69 0.00 0.00 3.33
609 667 1.014564 GTAGCAGCGAGTCCACCAAC 61.015 60.000 0.00 0.00 0.00 3.77
610 668 1.185618 AGTAGCAGCGAGTCCACCAA 61.186 55.000 0.00 0.00 0.00 3.67
611 669 1.595993 GAGTAGCAGCGAGTCCACCA 61.596 60.000 0.00 0.00 0.00 4.17
612 670 1.139947 GAGTAGCAGCGAGTCCACC 59.860 63.158 0.00 0.00 0.00 4.61
613 671 1.226435 CGAGTAGCAGCGAGTCCAC 60.226 63.158 4.88 0.00 0.00 4.02
621 679 0.595310 GGGAATCGTCGAGTAGCAGC 60.595 60.000 0.00 0.00 0.00 5.25
655 713 4.331108 CTGGGAGGGAGAAAGAAAGAAAG 58.669 47.826 0.00 0.00 0.00 2.62
656 714 3.498661 GCTGGGAGGGAGAAAGAAAGAAA 60.499 47.826 0.00 0.00 0.00 2.52
657 715 2.040412 GCTGGGAGGGAGAAAGAAAGAA 59.960 50.000 0.00 0.00 0.00 2.52
658 716 1.630878 GCTGGGAGGGAGAAAGAAAGA 59.369 52.381 0.00 0.00 0.00 2.52
691 749 2.517402 CTCCGTCTCCTCCTCCGG 60.517 72.222 0.00 0.00 41.75 5.14
700 758 3.507009 CGTCCCCGTCTCCGTCTC 61.507 72.222 0.00 0.00 0.00 3.36
784 843 0.109272 GGTGACGCAGATGAAGACGA 60.109 55.000 0.00 0.00 0.00 4.20
791 850 1.448540 GGGTGAGGTGACGCAGATG 60.449 63.158 0.00 0.00 42.29 2.90
792 851 2.660064 GGGGTGAGGTGACGCAGAT 61.660 63.158 0.00 0.00 42.29 2.90
794 853 3.625897 TGGGGTGAGGTGACGCAG 61.626 66.667 0.00 0.00 42.29 5.18
795 854 3.936203 GTGGGGTGAGGTGACGCA 61.936 66.667 0.00 0.00 38.03 5.24
798 857 0.543174 AGAGAGTGGGGTGAGGTGAC 60.543 60.000 0.00 0.00 0.00 3.67
799 858 0.542938 CAGAGAGTGGGGTGAGGTGA 60.543 60.000 0.00 0.00 0.00 4.02
800 859 0.542938 TCAGAGAGTGGGGTGAGGTG 60.543 60.000 0.00 0.00 0.00 4.00
801 860 0.252012 CTCAGAGAGTGGGGTGAGGT 60.252 60.000 0.00 0.00 34.06 3.85
802 861 1.612395 GCTCAGAGAGTGGGGTGAGG 61.612 65.000 0.00 0.00 37.49 3.86
803 862 0.614415 AGCTCAGAGAGTGGGGTGAG 60.614 60.000 0.00 0.00 35.42 3.51
804 863 1.466979 AGCTCAGAGAGTGGGGTGA 59.533 57.895 0.00 0.00 35.42 4.02
805 864 4.126908 AGCTCAGAGAGTGGGGTG 57.873 61.111 0.00 0.00 35.42 4.61
806 865 0.472734 AACAGCTCAGAGAGTGGGGT 60.473 55.000 0.00 0.00 38.14 4.95
807 866 0.248843 GAACAGCTCAGAGAGTGGGG 59.751 60.000 0.00 0.00 31.39 4.96
808 867 0.248843 GGAACAGCTCAGAGAGTGGG 59.751 60.000 0.00 0.00 31.39 4.61
809 868 0.108898 CGGAACAGCTCAGAGAGTGG 60.109 60.000 0.00 0.00 31.39 4.00
810 869 0.600557 ACGGAACAGCTCAGAGAGTG 59.399 55.000 0.00 0.00 31.39 3.51
811 870 1.271102 GAACGGAACAGCTCAGAGAGT 59.729 52.381 0.00 0.00 31.39 3.24
812 871 1.543802 AGAACGGAACAGCTCAGAGAG 59.456 52.381 0.00 0.00 0.00 3.20
813 872 1.621992 AGAACGGAACAGCTCAGAGA 58.378 50.000 0.00 0.00 0.00 3.10
814 873 2.064762 CAAGAACGGAACAGCTCAGAG 58.935 52.381 0.00 0.00 0.00 3.35
815 874 1.686587 TCAAGAACGGAACAGCTCAGA 59.313 47.619 0.00 0.00 0.00 3.27
816 875 2.154854 TCAAGAACGGAACAGCTCAG 57.845 50.000 0.00 0.00 0.00 3.35
817 876 2.612972 GGATCAAGAACGGAACAGCTCA 60.613 50.000 0.00 0.00 0.00 4.26
818 877 2.003301 GGATCAAGAACGGAACAGCTC 58.997 52.381 0.00 0.00 0.00 4.09
819 878 1.347707 TGGATCAAGAACGGAACAGCT 59.652 47.619 0.00 0.00 0.00 4.24
820 879 1.808411 TGGATCAAGAACGGAACAGC 58.192 50.000 0.00 0.00 0.00 4.40
821 880 2.484264 GGTTGGATCAAGAACGGAACAG 59.516 50.000 0.00 0.00 0.00 3.16
822 881 2.500229 GGTTGGATCAAGAACGGAACA 58.500 47.619 0.00 0.00 0.00 3.18
823 882 1.463444 CGGTTGGATCAAGAACGGAAC 59.537 52.381 0.00 0.00 0.00 3.62
824 883 1.071071 ACGGTTGGATCAAGAACGGAA 59.929 47.619 12.84 0.00 0.00 4.30
825 884 0.682852 ACGGTTGGATCAAGAACGGA 59.317 50.000 12.84 0.00 0.00 4.69
826 885 1.076332 GACGGTTGGATCAAGAACGG 58.924 55.000 0.00 1.71 0.00 4.44
827 886 1.993370 GAGACGGTTGGATCAAGAACG 59.007 52.381 0.00 0.00 0.00 3.95
828 887 2.028020 AGGAGACGGTTGGATCAAGAAC 60.028 50.000 0.00 0.00 0.00 3.01
844 903 1.454111 GCGGCAGAGTAGGAGGAGA 60.454 63.158 0.00 0.00 0.00 3.71
848 907 1.452145 GAGGAGCGGCAGAGTAGGAG 61.452 65.000 1.45 0.00 0.00 3.69
1429 1493 4.747108 CAGATATGGCTAGTGGAAAAGTCG 59.253 45.833 0.00 0.00 0.00 4.18
1443 1507 2.867624 TGCTTCCCAATCAGATATGGC 58.132 47.619 6.24 0.00 35.28 4.40
1447 1511 3.216800 GCACATGCTTCCCAATCAGATA 58.783 45.455 0.00 0.00 38.21 1.98
1448 1512 2.029623 GCACATGCTTCCCAATCAGAT 58.970 47.619 0.00 0.00 38.21 2.90
1449 1513 1.466856 GCACATGCTTCCCAATCAGA 58.533 50.000 0.00 0.00 38.21 3.27
1570 1650 4.244425 TCTTACTCAATGGAGCTATCGC 57.756 45.455 0.00 0.00 45.42 4.58
1707 1876 2.798834 ACGTGCGAATGAAAATACGG 57.201 45.000 0.00 0.00 36.01 4.02
1711 1880 3.374058 CCCTTCTACGTGCGAATGAAAAT 59.626 43.478 0.00 0.00 0.00 1.82
1715 1884 1.179152 TCCCTTCTACGTGCGAATGA 58.821 50.000 0.00 0.00 0.00 2.57
1900 2114 4.734398 TGCAATAATTTACAAGGCCCAG 57.266 40.909 0.00 0.00 0.00 4.45
2012 2235 4.289672 AGGCCTGGATCAAAGAAACTAAGA 59.710 41.667 3.11 0.00 0.00 2.10
2138 2373 5.782047 AGTGAATCTCAGACAGAAAGACAG 58.218 41.667 0.00 0.00 33.62 3.51
2211 2446 2.287188 ACACTGCAGCTCAATTGTTTCG 60.287 45.455 15.27 0.00 0.00 3.46
2379 2843 5.068329 TGAATCATCTCATAGAACACGAGCT 59.932 40.000 0.00 0.00 0.00 4.09
2390 2854 9.749340 ATCAAGCCATTATTGAATCATCTCATA 57.251 29.630 0.00 0.00 39.92 2.15
2466 2931 1.134280 AGAAAGGGCACGATCCTCATG 60.134 52.381 0.00 0.00 32.59 3.07
2622 3097 5.893897 AAGTGAAGAATTGGATGCTCTTC 57.106 39.130 7.50 7.50 43.51 2.87
2849 3352 9.148104 GGTTTAATGACTAGTAATTGACGAACT 57.852 33.333 14.89 0.00 0.00 3.01
2876 3379 0.184451 CTAGGCCATGCAGGTCCATT 59.816 55.000 5.01 0.00 45.84 3.16
2887 3390 1.771565 TACTGTACACGCTAGGCCAT 58.228 50.000 5.01 0.00 0.00 4.40
2899 3402 8.028938 ACTGAATGCATTTGGAAAATACTGTAC 58.971 33.333 14.33 0.00 0.00 2.90
2912 3415 4.319766 GGCTATCCGTACTGAATGCATTTG 60.320 45.833 14.33 12.05 0.00 2.32
2927 3430 0.546598 AAAAGAGGGGTGGCTATCCG 59.453 55.000 0.00 0.00 34.14 4.18
2958 3461 6.542821 ACTCTTCATCCAAAAACATACCTCA 58.457 36.000 0.00 0.00 0.00 3.86
2961 3464 9.974980 TTTAAACTCTTCATCCAAAAACATACC 57.025 29.630 0.00 0.00 0.00 2.73
3137 3641 4.369182 GGGAACAAGAGATGGTATGTACG 58.631 47.826 0.00 0.00 0.00 3.67
3192 3699 6.521527 ACTGGAGATTATAAGGCAAGGAAT 57.478 37.500 0.00 0.00 0.00 3.01
3208 3715 6.946583 ACTGTCTTACATACACTAACTGGAGA 59.053 38.462 0.00 0.00 0.00 3.71
3398 3908 2.397549 GTTGGATCAGTTGCTGCAAAC 58.602 47.619 17.80 11.27 0.00 2.93
4112 4622 6.406177 GCAACTGATCACCACCATCAAATATT 60.406 38.462 0.00 0.00 29.74 1.28
5340 5915 0.974383 CTTACGGTGTTCTCCCCTGT 59.026 55.000 0.00 0.00 0.00 4.00
5690 6267 1.605710 CTGAAGTTGCAGTGGGTTGAG 59.394 52.381 0.00 0.00 0.00 3.02
6000 9346 2.446982 AAAGGCCCCAGAAGCTTCCC 62.447 60.000 22.81 15.75 0.00 3.97
6153 9518 2.294074 GGCCGTATTTGAGCAATGGTA 58.706 47.619 0.00 0.00 0.00 3.25
6531 10339 3.950397 AGGCATGTCGGTCAAGAAAATA 58.050 40.909 0.00 0.00 0.00 1.40
6580 10388 4.454504 TGAGGTAAATCTTTTGCCTCGTTC 59.545 41.667 23.25 8.87 40.68 3.95
6582 10390 4.015872 TGAGGTAAATCTTTTGCCTCGT 57.984 40.909 23.25 1.26 40.68 4.18
6618 10426 5.169295 GGCTCGTGTAAACACTCTATTCTT 58.831 41.667 11.22 0.00 44.34 2.52
6629 10437 3.531262 ATTTGTTCGGCTCGTGTAAAC 57.469 42.857 0.00 0.00 0.00 2.01
6642 10450 7.927048 AGAGTAACACCACTTTGTATTTGTTC 58.073 34.615 0.00 0.00 0.00 3.18
6671 10479 8.124808 GCTAAGAAGCTGGGTACTATAATACT 57.875 38.462 0.00 0.00 45.85 2.12
6714 10525 2.157738 GCAACATCAAGAGTGAAGCCT 58.842 47.619 0.00 0.00 37.30 4.58
6776 10587 0.482446 TCCCAACAGGAAAGCCATGT 59.518 50.000 0.00 0.00 43.78 3.21
6816 10679 3.593442 TCCATTATGGATTGGTGGGTC 57.407 47.619 10.29 0.00 42.67 4.46
6829 10692 3.202818 TGGCACCTTCATGACTCCATTAT 59.797 43.478 0.00 0.00 0.00 1.28
6840 10703 1.003580 AGTTCGACATGGCACCTTCAT 59.996 47.619 0.00 0.00 0.00 2.57
6859 10722 1.581934 TCAAGCGACAACCTTGACAG 58.418 50.000 0.09 0.00 42.58 3.51
6914 10827 1.454663 GCCATCTTTGCCCCCTCTC 60.455 63.158 0.00 0.00 0.00 3.20
6958 10871 2.346803 CGAATTTGGACCACTGATCGT 58.653 47.619 0.00 0.00 0.00 3.73
6976 10889 2.989639 CTTGCCATCCAGGACCGA 59.010 61.111 0.00 0.00 41.22 4.69
7013 10926 5.790593 AGTACATTTTAGATCACACGGTGT 58.209 37.500 8.21 8.21 34.79 4.16
7014 10927 6.721571 AAGTACATTTTAGATCACACGGTG 57.278 37.500 6.58 6.58 34.45 4.94
7015 10928 7.442969 TGAAAAGTACATTTTAGATCACACGGT 59.557 33.333 0.00 0.00 41.24 4.83
7016 10929 7.802738 TGAAAAGTACATTTTAGATCACACGG 58.197 34.615 0.00 0.00 41.24 4.94
7017 10930 9.478019 GATGAAAAGTACATTTTAGATCACACG 57.522 33.333 0.00 0.00 41.24 4.49
7026 10939 9.959749 GGAAACAGTGATGAAAAGTACATTTTA 57.040 29.630 0.00 0.00 41.24 1.52
7027 10940 7.647715 CGGAAACAGTGATGAAAAGTACATTTT 59.352 33.333 0.00 0.72 43.88 1.82
7028 10941 7.012894 TCGGAAACAGTGATGAAAAGTACATTT 59.987 33.333 0.00 0.00 0.00 2.32
7029 10942 6.485313 TCGGAAACAGTGATGAAAAGTACATT 59.515 34.615 0.00 0.00 0.00 2.71
7030 10943 5.995282 TCGGAAACAGTGATGAAAAGTACAT 59.005 36.000 0.00 0.00 0.00 2.29
7031 10944 5.361427 TCGGAAACAGTGATGAAAAGTACA 58.639 37.500 0.00 0.00 0.00 2.90
7032 10945 5.917541 TCGGAAACAGTGATGAAAAGTAC 57.082 39.130 0.00 0.00 0.00 2.73
7033 10946 6.018262 CACTTCGGAAACAGTGATGAAAAGTA 60.018 38.462 0.00 0.00 34.50 2.24
7034 10947 4.881850 ACTTCGGAAACAGTGATGAAAAGT 59.118 37.500 0.00 0.00 0.00 2.66
7035 10948 5.007626 TCACTTCGGAAACAGTGATGAAAAG 59.992 40.000 6.87 0.00 36.51 2.27
7036 10949 4.878971 TCACTTCGGAAACAGTGATGAAAA 59.121 37.500 6.87 0.00 36.51 2.29
7037 10950 4.447290 TCACTTCGGAAACAGTGATGAAA 58.553 39.130 6.87 0.00 36.51 2.69
7038 10951 4.058124 CTCACTTCGGAAACAGTGATGAA 58.942 43.478 10.52 0.00 40.02 2.57
7039 10952 3.069586 ACTCACTTCGGAAACAGTGATGA 59.930 43.478 10.52 0.00 40.02 2.92
7040 10953 3.393800 ACTCACTTCGGAAACAGTGATG 58.606 45.455 10.52 8.14 40.02 3.07
7041 10954 3.322254 AGACTCACTTCGGAAACAGTGAT 59.678 43.478 10.52 3.40 40.02 3.06
7042 10955 2.693591 AGACTCACTTCGGAAACAGTGA 59.306 45.455 9.87 9.87 38.74 3.41
7043 10956 3.099267 AGACTCACTTCGGAAACAGTG 57.901 47.619 2.57 2.57 0.00 3.66
7044 10957 5.944599 TCTATAGACTCACTTCGGAAACAGT 59.055 40.000 0.00 0.00 0.00 3.55
7045 10958 6.438259 TCTATAGACTCACTTCGGAAACAG 57.562 41.667 0.00 0.00 0.00 3.16
7046 10959 6.183360 CCATCTATAGACTCACTTCGGAAACA 60.183 42.308 4.10 0.00 0.00 2.83
7047 10960 6.210078 CCATCTATAGACTCACTTCGGAAAC 58.790 44.000 4.10 0.00 0.00 2.78
7048 10961 5.221263 GCCATCTATAGACTCACTTCGGAAA 60.221 44.000 4.10 0.00 0.00 3.13
7049 10962 4.278669 GCCATCTATAGACTCACTTCGGAA 59.721 45.833 4.10 0.00 0.00 4.30
7050 10963 3.821600 GCCATCTATAGACTCACTTCGGA 59.178 47.826 4.10 0.00 0.00 4.55
7051 10964 3.823873 AGCCATCTATAGACTCACTTCGG 59.176 47.826 4.10 0.00 0.00 4.30
7052 10965 5.240623 AGAAGCCATCTATAGACTCACTTCG 59.759 44.000 20.11 0.00 36.32 3.79
7053 10966 6.648879 AGAAGCCATCTATAGACTCACTTC 57.351 41.667 19.37 19.37 36.32 3.01
7054 10967 7.430760 AAAGAAGCCATCTATAGACTCACTT 57.569 36.000 4.10 6.71 37.42 3.16
7055 10968 7.430760 AAAAGAAGCCATCTATAGACTCACT 57.569 36.000 4.10 0.00 37.42 3.41
7089 11002 9.525409 GGCAGAGTTTATTTTTCTATCGTACTA 57.475 33.333 0.00 0.00 0.00 1.82
7090 11003 8.038944 TGGCAGAGTTTATTTTTCTATCGTACT 58.961 33.333 0.00 0.00 0.00 2.73
7091 11004 8.193250 TGGCAGAGTTTATTTTTCTATCGTAC 57.807 34.615 0.00 0.00 0.00 3.67
7092 11005 8.826710 CATGGCAGAGTTTATTTTTCTATCGTA 58.173 33.333 0.00 0.00 0.00 3.43
7093 11006 7.679638 GCATGGCAGAGTTTATTTTTCTATCGT 60.680 37.037 0.00 0.00 0.00 3.73
7094 11007 6.634436 GCATGGCAGAGTTTATTTTTCTATCG 59.366 38.462 0.00 0.00 0.00 2.92
7095 11008 7.483307 TGCATGGCAGAGTTTATTTTTCTATC 58.517 34.615 0.00 0.00 33.32 2.08
7096 11009 7.408756 TGCATGGCAGAGTTTATTTTTCTAT 57.591 32.000 0.00 0.00 33.32 1.98
7097 11010 6.832520 TGCATGGCAGAGTTTATTTTTCTA 57.167 33.333 0.00 0.00 33.32 2.10
7098 11011 5.726980 TGCATGGCAGAGTTTATTTTTCT 57.273 34.783 0.00 0.00 33.32 2.52
7099 11012 6.973229 AATGCATGGCAGAGTTTATTTTTC 57.027 33.333 0.00 0.00 43.65 2.29
7100 11013 8.845413 TTAAATGCATGGCAGAGTTTATTTTT 57.155 26.923 0.00 0.00 43.65 1.94
7101 11014 9.101655 GATTAAATGCATGGCAGAGTTTATTTT 57.898 29.630 0.00 0.00 43.65 1.82
7102 11015 8.480501 AGATTAAATGCATGGCAGAGTTTATTT 58.519 29.630 0.00 0.00 43.65 1.40
7103 11016 8.015185 AGATTAAATGCATGGCAGAGTTTATT 57.985 30.769 0.00 0.00 43.65 1.40
7104 11017 7.592885 AGATTAAATGCATGGCAGAGTTTAT 57.407 32.000 0.00 0.00 43.65 1.40
7105 11018 8.696043 ATAGATTAAATGCATGGCAGAGTTTA 57.304 30.769 0.00 0.00 43.65 2.01
7106 11019 5.927281 AGATTAAATGCATGGCAGAGTTT 57.073 34.783 0.00 0.00 43.65 2.66
7107 11020 8.874744 ATATAGATTAAATGCATGGCAGAGTT 57.125 30.769 0.00 0.00 43.65 3.01
7108 11021 8.327271 AGATATAGATTAAATGCATGGCAGAGT 58.673 33.333 0.00 0.00 43.65 3.24
7109 11022 8.734218 AGATATAGATTAAATGCATGGCAGAG 57.266 34.615 0.00 0.00 43.65 3.35
7145 11058 9.031537 TGCTTTAATAGTAGGTAGCATAGCATA 57.968 33.333 0.00 0.00 42.67 3.14
7146 11059 7.907389 TGCTTTAATAGTAGGTAGCATAGCAT 58.093 34.615 0.00 0.00 42.67 3.79
7147 11060 7.297936 TGCTTTAATAGTAGGTAGCATAGCA 57.702 36.000 0.00 0.00 42.67 3.49
7148 11061 7.332182 CCTTGCTTTAATAGTAGGTAGCATAGC 59.668 40.741 0.00 0.00 38.30 2.97
7149 11062 8.368668 ACCTTGCTTTAATAGTAGGTAGCATAG 58.631 37.037 0.00 0.00 38.47 2.23
7150 11063 8.148351 CACCTTGCTTTAATAGTAGGTAGCATA 58.852 37.037 0.00 0.00 38.31 3.14
7151 11064 6.992715 CACCTTGCTTTAATAGTAGGTAGCAT 59.007 38.462 0.00 0.00 38.31 3.79
7152 11065 6.155565 TCACCTTGCTTTAATAGTAGGTAGCA 59.844 38.462 0.00 0.00 38.31 3.49
7153 11066 6.579865 TCACCTTGCTTTAATAGTAGGTAGC 58.420 40.000 0.00 0.00 38.31 3.58
7288 11791 0.885196 GCGTGCATAGACCCCAAAAA 59.115 50.000 0.00 0.00 0.00 1.94
7289 11792 0.963355 GGCGTGCATAGACCCCAAAA 60.963 55.000 0.00 0.00 0.00 2.44
7290 11793 1.377987 GGCGTGCATAGACCCCAAA 60.378 57.895 0.00 0.00 0.00 3.28
7291 11794 2.130821 TTGGCGTGCATAGACCCCAA 62.131 55.000 0.00 0.00 32.47 4.12
7292 11795 2.597818 TTGGCGTGCATAGACCCCA 61.598 57.895 0.00 0.00 0.00 4.96
7293 11796 2.112815 GTTGGCGTGCATAGACCCC 61.113 63.158 0.00 0.00 0.00 4.95
7294 11797 2.461110 CGTTGGCGTGCATAGACCC 61.461 63.158 0.00 0.00 0.00 4.46
7303 11806 4.081030 CAGAGCAGCGTTGGCGTG 62.081 66.667 0.16 0.00 46.35 5.34
7310 11813 3.497884 AAAAGGCCCAGAGCAGCGT 62.498 57.895 0.00 0.00 46.50 5.07
7335 11838 2.414138 GCCCAGTACGTTTGTGACATAC 59.586 50.000 0.00 0.00 0.00 2.39
7338 11841 0.533308 GGCCCAGTACGTTTGTGACA 60.533 55.000 0.00 0.00 0.00 3.58
7411 11915 1.389609 GGTCGTGGGCTCGATCCTTA 61.390 60.000 5.10 0.00 41.78 2.69


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

AutoCloner maintained by Alex Coulton.