Multiple sequence alignment - TraesCS2A01G450300

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 TraesCS2A01G450300 chr2A 100.000 3499 0 0 1 3499 699870031 699866533 0.000000e+00 6462
1 TraesCS2A01G450300 chr2A 99.219 128 1 0 2725 2852 27345279 27345152 7.550000e-57 231
2 TraesCS2A01G450300 chr2B 90.072 2790 133 62 2 2720 668379380 668376664 0.000000e+00 3485
3 TraesCS2A01G450300 chr2B 91.743 545 37 6 2958 3499 731345112 731345651 0.000000e+00 750
4 TraesCS2A01G450300 chr2B 98.425 127 2 0 2725 2851 692126810 692126936 1.260000e-54 224
5 TraesCS2A01G450300 chr2B 94.964 139 5 2 2717 2855 171995532 171995396 2.110000e-52 217
6 TraesCS2A01G450300 chr2D 92.667 1732 65 29 681 2394 559312359 559310672 0.000000e+00 2438
7 TraesCS2A01G450300 chr2D 91.066 694 33 19 2 677 559313335 559312653 0.000000e+00 911
8 TraesCS2A01G450300 chr2D 91.973 299 11 7 2429 2724 559310597 559310309 1.170000e-109 407
9 TraesCS2A01G450300 chr2D 86.624 157 15 4 2960 3112 627309126 627308972 6.010000e-38 169
10 TraesCS2A01G450300 chr4A 94.669 544 24 4 2957 3499 598313743 598313204 0.000000e+00 839
11 TraesCS2A01G450300 chr7A 94.291 543 28 2 2957 3499 694501190 694501729 0.000000e+00 828
12 TraesCS2A01G450300 chr7A 97.692 130 3 0 2724 2853 351612884 351612755 1.260000e-54 224
13 TraesCS2A01G450300 chr1A 93.761 545 29 5 2958 3499 418594311 418593769 0.000000e+00 813
14 TraesCS2A01G450300 chr1A 97.710 131 3 0 2722 2852 505408405 505408535 3.510000e-55 226
15 TraesCS2A01G450300 chr1B 91.209 546 42 5 2958 3499 540363394 540362851 0.000000e+00 737
16 TraesCS2A01G450300 chr1B 94.406 143 7 1 2712 2853 3935985 3935843 5.880000e-53 219
17 TraesCS2A01G450300 chr7D 90.859 547 32 11 2959 3499 42907041 42906507 0.000000e+00 717
18 TraesCS2A01G450300 chr5A 93.627 408 24 1 3094 3499 531618551 531618144 2.990000e-170 608
19 TraesCS2A01G450300 chr6D 77.927 965 181 21 1419 2373 354992211 354991269 1.090000e-159 573
20 TraesCS2A01G450300 chr6D 86.056 251 31 4 1137 1385 354992544 354992296 2.070000e-67 267
21 TraesCS2A01G450300 chr6B 77.824 965 182 22 1419 2373 523065128 523066070 5.070000e-158 568
22 TraesCS2A01G450300 chr6B 89.548 354 31 5 2958 3307 703355973 703356324 8.910000e-121 444
23 TraesCS2A01G450300 chr6B 86.220 254 31 4 1134 1385 523064795 523065046 4.450000e-69 272
24 TraesCS2A01G450300 chr6B 96.842 95 3 0 3405 3499 703357246 703357340 3.610000e-35 159
25 TraesCS2A01G450300 chr6A 77.513 965 185 22 1419 2373 486841118 486842060 5.100000e-153 551
26 TraesCS2A01G450300 chr6A 86.694 248 29 4 1134 1379 486840788 486841033 4.450000e-69 272
27 TraesCS2A01G450300 chr4B 97.710 131 3 0 2725 2855 210282884 210282754 3.510000e-55 226
28 TraesCS2A01G450300 chr3A 97.692 130 3 0 2722 2851 17261541 17261670 1.260000e-54 224
29 TraesCS2A01G450300 chr3A 96.970 132 4 0 2722 2853 57867684 57867553 4.550000e-54 222
30 TraesCS2A01G450300 chr5D 91.946 149 12 0 3298 3446 548217450 548217598 3.540000e-50 209
31 TraesCS2A01G450300 chr3D 85.263 190 16 6 2957 3136 23955890 23956077 5.960000e-43 185
32 TraesCS2A01G450300 chrUn 86.585 164 18 2 3133 3292 33362720 33362883 9.980000e-41 178
33 TraesCS2A01G450300 chr3B 86.861 137 16 1 3310 3446 739510515 739510381 6.050000e-33 152


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 TraesCS2A01G450300 chr2A 699866533 699870031 3498 True 6462.0 6462 100.0000 1 3499 1 chr2A.!!$R2 3498
1 TraesCS2A01G450300 chr2B 668376664 668379380 2716 True 3485.0 3485 90.0720 2 2720 1 chr2B.!!$R2 2718
2 TraesCS2A01G450300 chr2B 731345112 731345651 539 False 750.0 750 91.7430 2958 3499 1 chr2B.!!$F2 541
3 TraesCS2A01G450300 chr2D 559310309 559313335 3026 True 1252.0 2438 91.9020 2 2724 3 chr2D.!!$R2 2722
4 TraesCS2A01G450300 chr4A 598313204 598313743 539 True 839.0 839 94.6690 2957 3499 1 chr4A.!!$R1 542
5 TraesCS2A01G450300 chr7A 694501190 694501729 539 False 828.0 828 94.2910 2957 3499 1 chr7A.!!$F1 542
6 TraesCS2A01G450300 chr1A 418593769 418594311 542 True 813.0 813 93.7610 2958 3499 1 chr1A.!!$R1 541
7 TraesCS2A01G450300 chr1B 540362851 540363394 543 True 737.0 737 91.2090 2958 3499 1 chr1B.!!$R2 541
8 TraesCS2A01G450300 chr7D 42906507 42907041 534 True 717.0 717 90.8590 2959 3499 1 chr7D.!!$R1 540
9 TraesCS2A01G450300 chr6D 354991269 354992544 1275 True 420.0 573 81.9915 1137 2373 2 chr6D.!!$R1 1236
10 TraesCS2A01G450300 chr6B 523064795 523066070 1275 False 420.0 568 82.0220 1134 2373 2 chr6B.!!$F1 1239
11 TraesCS2A01G450300 chr6B 703355973 703357340 1367 False 301.5 444 93.1950 2958 3499 2 chr6B.!!$F2 541
12 TraesCS2A01G450300 chr6A 486840788 486842060 1272 False 411.5 551 82.1035 1134 2373 2 chr6A.!!$F1 1239

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
849 1167 0.459585 AGTTTGTGACGACGCTGTGT 60.46 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2842 3281 0.036294 GTGCACCCAAGTACTCCCTC 60.036 60.0 5.22 0.0 0.0 4.3 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
25 26 5.980698 TTGAATTTTTCAAGAAATGCGCA 57.019 30.435 14.96 14.96 44.21 6.09
30 31 9.363763 TGAATTTTTCAAGAAATGCGCATTATA 57.636 25.926 34.05 15.75 36.59 0.98
57 59 1.771565 AGGTATGCAGTGTACCGCTA 58.228 50.000 8.92 0.00 45.01 4.26
203 205 5.358298 ACGGAGCAAACATAAGAAGAAAC 57.642 39.130 0.00 0.00 0.00 2.78
233 235 8.560374 GCTGGATCAGGAATAATTTAACACTAC 58.440 37.037 0.00 0.00 31.21 2.73
258 261 1.003355 CTGTTGTCATCACCGGCCT 60.003 57.895 0.00 0.00 0.00 5.19
296 299 1.980765 ACTCCAACCTGCATCTCAAGA 59.019 47.619 0.00 0.00 0.00 3.02
327 330 8.882736 CAACCCTAGAAAATAAAAATCAATGCC 58.117 33.333 0.00 0.00 0.00 4.40
329 332 7.402941 ACCCTAGAAAATAAAAATCAATGCCCT 59.597 33.333 0.00 0.00 0.00 5.19
367 377 7.822658 AGATAAGTAGCAGTAGTATTAGCAGC 58.177 38.462 0.00 0.00 0.00 5.25
368 378 5.854010 AAGTAGCAGTAGTATTAGCAGCA 57.146 39.130 0.00 0.00 0.00 4.41
369 379 5.446143 AGTAGCAGTAGTATTAGCAGCAG 57.554 43.478 0.00 0.00 0.00 4.24
409 419 2.575532 TCTTCCTCTTGTTTGTGGCAG 58.424 47.619 0.00 0.00 0.00 4.85
474 484 0.813184 ATTTCCGCTCTAACCGACGA 59.187 50.000 0.00 0.00 0.00 4.20
490 517 1.283793 CGAGCTGTTGGGTTGCTTG 59.716 57.895 0.00 0.00 37.16 4.01
504 531 2.456119 GCTTGAGTCGACGCCCATG 61.456 63.158 16.94 14.63 0.00 3.66
627 654 2.870411 GTCGCGCCACCTTTATCTTTAT 59.130 45.455 0.00 0.00 0.00 1.40
679 707 2.284754 TGCCAACCTTGCACTCAATA 57.715 45.000 0.00 0.00 32.85 1.90
735 1053 1.886037 TTATACGCGCATACGATCCG 58.114 50.000 5.73 0.00 43.93 4.18
791 1109 2.096013 GCTGCTCGGTTTATCCTGTTTC 59.904 50.000 0.00 0.00 0.00 2.78
805 1123 5.593679 TCCTGTTTCTCTATAGGGTTTCG 57.406 43.478 0.00 0.00 0.00 3.46
806 1124 4.120589 CCTGTTTCTCTATAGGGTTTCGC 58.879 47.826 0.00 0.00 0.00 4.70
808 1126 5.353394 TGTTTCTCTATAGGGTTTCGCAT 57.647 39.130 0.00 0.00 0.00 4.73
813 1131 4.593206 TCTCTATAGGGTTTCGCATGGATT 59.407 41.667 0.00 0.00 0.00 3.01
814 1132 5.071788 TCTCTATAGGGTTTCGCATGGATTT 59.928 40.000 0.00 0.00 0.00 2.17
815 1133 5.690865 TCTATAGGGTTTCGCATGGATTTT 58.309 37.500 0.00 0.00 0.00 1.82
816 1134 6.126409 TCTATAGGGTTTCGCATGGATTTTT 58.874 36.000 0.00 0.00 0.00 1.94
845 1163 7.585286 TTAAATATAAGTTTGTGACGACGCT 57.415 32.000 0.00 0.00 0.00 5.07
849 1167 0.459585 AGTTTGTGACGACGCTGTGT 60.460 50.000 0.00 0.00 0.00 3.72
900 1229 3.047115 AGAGTGGATGCCTCATTCAGAT 58.953 45.455 5.72 0.00 28.96 2.90
901 1230 3.458857 AGAGTGGATGCCTCATTCAGATT 59.541 43.478 5.72 0.00 28.96 2.40
902 1231 4.079901 AGAGTGGATGCCTCATTCAGATTT 60.080 41.667 5.72 0.00 28.96 2.17
903 1232 4.205587 AGTGGATGCCTCATTCAGATTTC 58.794 43.478 0.00 0.00 28.96 2.17
904 1233 3.949754 GTGGATGCCTCATTCAGATTTCA 59.050 43.478 0.00 0.00 28.96 2.69
905 1234 4.036498 GTGGATGCCTCATTCAGATTTCAG 59.964 45.833 0.00 0.00 28.96 3.02
906 1235 4.080186 TGGATGCCTCATTCAGATTTCAGA 60.080 41.667 0.00 0.00 0.00 3.27
948 1277 0.466189 TTCTACGGGCTACCTACGGG 60.466 60.000 0.00 0.00 38.88 5.28
949 1278 2.519302 TACGGGCTACCTACGGGC 60.519 66.667 0.00 0.00 35.63 6.13
950 1279 2.972892 CTACGGGCTACCTACGGGCT 62.973 65.000 0.00 0.00 35.63 5.19
951 1280 1.705002 TACGGGCTACCTACGGGCTA 61.705 60.000 0.00 0.00 35.63 3.93
970 1299 1.835494 AGCTTGCATGACTTCAGCAT 58.165 45.000 3.33 0.00 38.19 3.79
977 1306 2.789092 GCATGACTTCAGCATTACGCAC 60.789 50.000 0.00 0.00 46.13 5.34
980 1309 1.296145 CTTCAGCATTACGCACGCG 60.296 57.895 10.36 10.36 46.13 6.01
987 1316 1.446445 ATTACGCACGCGCAGGTTA 60.446 52.632 12.02 0.00 44.19 2.85
1000 1332 3.198068 CGCAGGTTACAGTTGCAGATAT 58.802 45.455 6.56 0.00 37.69 1.63
1019 1351 9.515226 GCAGATATTATAAAACCAACATCCCTA 57.485 33.333 0.00 0.00 0.00 3.53
1038 1370 3.758554 CCTATTGGTTCCCAGACAAACTG 59.241 47.826 0.00 0.00 45.36 3.16
1058 1390 4.021719 ACTGCATTTCATTTCAGGACAAGG 60.022 41.667 0.00 0.00 0.00 3.61
1060 1392 4.588106 TGCATTTCATTTCAGGACAAGGAA 59.412 37.500 0.00 0.00 0.00 3.36
1063 1395 6.312180 GCATTTCATTTCAGGACAAGGAATTC 59.688 38.462 0.00 0.00 0.00 2.17
1064 1396 6.975196 TTTCATTTCAGGACAAGGAATTCA 57.025 33.333 7.93 0.00 0.00 2.57
1066 1398 5.012239 TCATTTCAGGACAAGGAATTCAGG 58.988 41.667 7.93 0.00 0.00 3.86
1067 1399 2.496899 TCAGGACAAGGAATTCAGGC 57.503 50.000 7.93 0.00 0.00 4.85
1069 1401 0.035056 AGGACAAGGAATTCAGGCCG 60.035 55.000 7.93 0.00 0.00 6.13
1070 1402 1.657751 GGACAAGGAATTCAGGCCGC 61.658 60.000 7.93 0.00 0.00 6.53
1084 1416 2.796651 CCGCTTGATTGGCTGCTC 59.203 61.111 0.00 0.00 0.00 4.26
1085 1417 2.402388 CGCTTGATTGGCTGCTCG 59.598 61.111 0.00 0.00 0.00 5.03
1086 1418 2.101770 GCTTGATTGGCTGCTCGC 59.898 61.111 0.00 0.00 38.13 5.03
1111 1443 1.012234 GTGATTTGGCGCGTCGATC 60.012 57.895 16.93 16.93 0.00 3.69
1113 1445 2.202690 ATTTGGCGCGTCGATCGA 60.203 55.556 15.15 15.15 42.86 3.59
1115 1447 1.548973 ATTTGGCGCGTCGATCGATC 61.549 55.000 22.50 15.68 42.86 3.69
1538 1925 1.299976 GGAGGATTTCGTGGCCTGT 59.700 57.895 3.32 0.00 30.70 4.00
1847 2234 1.822990 GACGACATGGTCAAGTCCCTA 59.177 52.381 0.00 0.00 36.91 3.53
2405 2830 5.178438 TCTCAAGTGATCTATCAGTCGATCG 59.822 44.000 9.36 9.36 39.44 3.69
2421 2846 2.792890 CGATCGGCAAGTGTACAGAGAG 60.793 54.545 7.38 0.00 0.00 3.20
2433 2862 1.456518 CAGAGAGGCGGGAGGATGA 60.457 63.158 0.00 0.00 0.00 2.92
2437 2872 0.471617 AGAGGCGGGAGGATGAAATG 59.528 55.000 0.00 0.00 0.00 2.32
2445 2880 3.505680 CGGGAGGATGAAATGTTGTTTGA 59.494 43.478 0.00 0.00 0.00 2.69
2504 2939 4.092821 TGAGCATGCGTGTACAGATTAAAC 59.907 41.667 13.01 0.00 0.00 2.01
2507 2942 4.322934 CATGCGTGTACAGATTAAACGTG 58.677 43.478 0.00 0.00 36.65 4.49
2508 2943 2.156117 TGCGTGTACAGATTAAACGTGC 59.844 45.455 0.00 0.00 36.65 5.34
2509 2944 2.778641 GCGTGTACAGATTAAACGTGCG 60.779 50.000 0.00 0.00 36.65 5.34
2510 2945 2.754478 GTGTACAGATTAAACGTGCGC 58.246 47.619 0.00 0.00 0.00 6.09
2584 3020 1.102978 ATTCCAGTTTGGCGGCATAC 58.897 50.000 22.03 22.03 37.47 2.39
2594 3030 1.039856 GGCGGCATACCCATGATTTT 58.960 50.000 3.07 0.00 33.67 1.82
2595 3031 1.269726 GGCGGCATACCCATGATTTTG 60.270 52.381 3.07 0.00 33.67 2.44
2596 3032 1.408702 GCGGCATACCCATGATTTTGT 59.591 47.619 0.00 0.00 33.67 2.83
2597 3033 2.621055 GCGGCATACCCATGATTTTGTA 59.379 45.455 0.00 0.00 33.67 2.41
2603 3042 8.344831 CGGCATACCCATGATTTTGTATATATG 58.655 37.037 0.00 0.00 33.67 1.78
2701 3140 2.241176 GACATGGTTCTGTTCCCCCATA 59.759 50.000 0.00 0.00 35.95 2.74
2730 3169 8.431910 TCTTTGTTAGGGTGATATATACTCCC 57.568 38.462 9.90 9.90 40.22 4.30
2732 3171 8.431910 TTTGTTAGGGTGATATATACTCCCTC 57.568 38.462 19.04 10.76 44.80 4.30
2733 3172 6.500336 TGTTAGGGTGATATATACTCCCTCC 58.500 44.000 19.04 13.78 44.80 4.30
2734 3173 4.252570 AGGGTGATATATACTCCCTCCG 57.747 50.000 13.12 0.00 44.80 4.63
2735 3174 3.596956 AGGGTGATATATACTCCCTCCGT 59.403 47.826 13.12 0.00 44.80 4.69
2736 3175 4.045590 AGGGTGATATATACTCCCTCCGTT 59.954 45.833 13.12 0.00 44.80 4.44
2737 3176 4.401837 GGGTGATATATACTCCCTCCGTTC 59.598 50.000 10.39 0.00 37.86 3.95
2738 3177 4.401837 GGTGATATATACTCCCTCCGTTCC 59.598 50.000 0.00 0.00 0.00 3.62
2739 3178 4.096081 GTGATATATACTCCCTCCGTTCCG 59.904 50.000 0.00 0.00 0.00 4.30
2740 3179 2.965671 ATATACTCCCTCCGTTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
2741 3180 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
2742 3181 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
2743 3182 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
2744 3183 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2745 3184 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2746 3185 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2747 3186 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2748 3187 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2749 3188 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2750 3189 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2751 3190 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2752 3191 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2753 3192 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
2754 3193 3.991773 CCGTTCCGAATTACTTGTCTTGA 59.008 43.478 0.00 0.00 0.00 3.02
2755 3194 4.449743 CCGTTCCGAATTACTTGTCTTGAA 59.550 41.667 0.00 0.00 0.00 2.69
2756 3195 5.121768 CCGTTCCGAATTACTTGTCTTGAAT 59.878 40.000 0.00 0.00 0.00 2.57
2757 3196 6.348213 CCGTTCCGAATTACTTGTCTTGAATT 60.348 38.462 0.00 0.00 0.00 2.17
2758 3197 7.075741 CGTTCCGAATTACTTGTCTTGAATTT 58.924 34.615 0.00 0.00 0.00 1.82
2759 3198 7.059488 CGTTCCGAATTACTTGTCTTGAATTTG 59.941 37.037 0.00 0.00 0.00 2.32
2760 3199 7.504924 TCCGAATTACTTGTCTTGAATTTGT 57.495 32.000 0.00 0.00 0.00 2.83
2761 3200 7.581476 TCCGAATTACTTGTCTTGAATTTGTC 58.419 34.615 0.00 0.00 0.00 3.18
2762 3201 7.444183 TCCGAATTACTTGTCTTGAATTTGTCT 59.556 33.333 0.00 0.00 0.00 3.41
2763 3202 8.717821 CCGAATTACTTGTCTTGAATTTGTCTA 58.282 33.333 0.00 0.00 0.00 2.59
2764 3203 9.746711 CGAATTACTTGTCTTGAATTTGTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
2769 3208 8.467402 ACTTGTCTTGAATTTGTCTAGATACG 57.533 34.615 0.00 0.00 39.77 3.06
2770 3209 7.545965 ACTTGTCTTGAATTTGTCTAGATACGG 59.454 37.037 0.00 0.00 39.77 4.02
2771 3210 7.165460 TGTCTTGAATTTGTCTAGATACGGA 57.835 36.000 0.00 0.00 39.77 4.69
2772 3211 7.782049 TGTCTTGAATTTGTCTAGATACGGAT 58.218 34.615 0.00 0.00 39.77 4.18
2773 3212 7.706607 TGTCTTGAATTTGTCTAGATACGGATG 59.293 37.037 0.00 0.00 39.77 3.51
2774 3213 7.707035 GTCTTGAATTTGTCTAGATACGGATGT 59.293 37.037 0.00 0.00 39.77 3.06
2775 3214 8.909923 TCTTGAATTTGTCTAGATACGGATGTA 58.090 33.333 0.00 0.00 33.79 2.29
2776 3215 9.698309 CTTGAATTTGTCTAGATACGGATGTAT 57.302 33.333 0.00 0.00 43.97 2.29
2792 3231 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
2793 3232 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
2794 3233 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
2795 3234 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
2798 3237 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
2802 3241 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
2803 3242 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
2804 3243 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
2805 3244 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
2806 3245 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
2807 3246 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
2808 3247 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
2809 3248 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
2825 3264 8.302515 ACCTCCGTATCTAGACAAATTTAAGA 57.697 34.615 0.00 0.00 0.00 2.10
2826 3265 8.196103 ACCTCCGTATCTAGACAAATTTAAGAC 58.804 37.037 0.00 0.00 0.00 3.01
2827 3266 8.195436 CCTCCGTATCTAGACAAATTTAAGACA 58.805 37.037 0.00 0.00 0.00 3.41
2828 3267 9.582431 CTCCGTATCTAGACAAATTTAAGACAA 57.418 33.333 0.00 0.00 0.00 3.18
2829 3268 9.582431 TCCGTATCTAGACAAATTTAAGACAAG 57.418 33.333 0.00 0.00 0.00 3.16
2830 3269 9.367444 CCGTATCTAGACAAATTTAAGACAAGT 57.633 33.333 0.00 0.00 0.00 3.16
2838 3277 9.280174 AGACAAATTTAAGACAAGTAATTCGGA 57.720 29.630 0.00 0.00 0.00 4.55
2839 3278 9.887406 GACAAATTTAAGACAAGTAATTCGGAA 57.113 29.630 0.00 0.00 0.00 4.30
2842 3281 9.855021 AAATTTAAGACAAGTAATTCGGAATGG 57.145 29.630 3.59 0.00 0.00 3.16
2843 3282 8.801882 ATTTAAGACAAGTAATTCGGAATGGA 57.198 30.769 3.59 0.00 0.00 3.41
2844 3283 7.843490 TTAAGACAAGTAATTCGGAATGGAG 57.157 36.000 3.59 0.00 0.00 3.86
2845 3284 4.770795 AGACAAGTAATTCGGAATGGAGG 58.229 43.478 3.59 0.00 0.00 4.30
2846 3285 3.877508 GACAAGTAATTCGGAATGGAGGG 59.122 47.826 3.59 0.00 0.00 4.30
2847 3286 3.521937 ACAAGTAATTCGGAATGGAGGGA 59.478 43.478 3.59 0.00 0.00 4.20
2848 3287 4.130118 CAAGTAATTCGGAATGGAGGGAG 58.870 47.826 3.59 0.00 0.00 4.30
2849 3288 3.385115 AGTAATTCGGAATGGAGGGAGT 58.615 45.455 3.59 0.00 0.00 3.85
2850 3289 4.553678 AGTAATTCGGAATGGAGGGAGTA 58.446 43.478 3.59 0.00 0.00 2.59
2851 3290 3.840124 AATTCGGAATGGAGGGAGTAC 57.160 47.619 3.59 0.00 0.00 2.73
2852 3291 2.544844 TTCGGAATGGAGGGAGTACT 57.455 50.000 0.00 0.00 0.00 2.73
2853 3292 2.544844 TCGGAATGGAGGGAGTACTT 57.455 50.000 0.00 0.00 0.00 2.24
2854 3293 2.108168 TCGGAATGGAGGGAGTACTTG 58.892 52.381 0.00 0.00 0.00 3.16
2855 3294 1.139058 CGGAATGGAGGGAGTACTTGG 59.861 57.143 0.00 0.00 0.00 3.61
2856 3295 1.490910 GGAATGGAGGGAGTACTTGGG 59.509 57.143 0.00 0.00 0.00 4.12
2857 3296 2.197465 GAATGGAGGGAGTACTTGGGT 58.803 52.381 0.00 0.00 0.00 4.51
2858 3297 1.584724 ATGGAGGGAGTACTTGGGTG 58.415 55.000 0.00 0.00 0.00 4.61
2859 3298 1.198759 TGGAGGGAGTACTTGGGTGC 61.199 60.000 0.00 0.00 0.00 5.01
2860 3299 1.198759 GGAGGGAGTACTTGGGTGCA 61.199 60.000 0.00 0.00 0.00 4.57
2861 3300 0.036294 GAGGGAGTACTTGGGTGCAC 60.036 60.000 8.80 8.80 0.00 4.57
2862 3301 0.473886 AGGGAGTACTTGGGTGCACT 60.474 55.000 17.98 0.00 0.00 4.40
2863 3302 0.036294 GGGAGTACTTGGGTGCACTC 60.036 60.000 17.98 14.58 37.32 3.51
2864 3303 0.685097 GGAGTACTTGGGTGCACTCA 59.315 55.000 17.47 17.47 39.33 3.41
2865 3304 1.608283 GGAGTACTTGGGTGCACTCAC 60.608 57.143 21.68 8.08 39.33 3.51
2874 3313 2.533318 GTGCACTCACCTCTTTCGG 58.467 57.895 10.32 0.00 37.24 4.30
2875 3314 0.249911 GTGCACTCACCTCTTTCGGT 60.250 55.000 10.32 0.00 37.24 4.69
2876 3315 1.000506 GTGCACTCACCTCTTTCGGTA 59.999 52.381 10.32 0.00 37.24 4.02
2877 3316 1.689813 TGCACTCACCTCTTTCGGTAA 59.310 47.619 0.00 0.00 34.94 2.85
2878 3317 2.103432 TGCACTCACCTCTTTCGGTAAA 59.897 45.455 0.00 0.00 34.94 2.01
2879 3318 3.135994 GCACTCACCTCTTTCGGTAAAA 58.864 45.455 0.00 0.00 34.94 1.52
2880 3319 3.751698 GCACTCACCTCTTTCGGTAAAAT 59.248 43.478 0.00 0.00 34.94 1.82
2881 3320 4.142881 GCACTCACCTCTTTCGGTAAAATC 60.143 45.833 0.00 0.00 34.94 2.17
2882 3321 4.994852 CACTCACCTCTTTCGGTAAAATCA 59.005 41.667 0.00 0.00 34.94 2.57
2883 3322 5.120830 CACTCACCTCTTTCGGTAAAATCAG 59.879 44.000 0.00 0.00 34.94 2.90
2884 3323 5.221661 ACTCACCTCTTTCGGTAAAATCAGT 60.222 40.000 0.00 0.00 34.94 3.41
2885 3324 4.994852 TCACCTCTTTCGGTAAAATCAGTG 59.005 41.667 0.00 0.00 34.94 3.66
2886 3325 4.994852 CACCTCTTTCGGTAAAATCAGTGA 59.005 41.667 0.00 0.00 34.94 3.41
2887 3326 5.468746 CACCTCTTTCGGTAAAATCAGTGAA 59.531 40.000 0.00 0.00 34.94 3.18
2888 3327 6.017440 CACCTCTTTCGGTAAAATCAGTGAAA 60.017 38.462 0.00 0.00 34.94 2.69
2889 3328 6.017357 ACCTCTTTCGGTAAAATCAGTGAAAC 60.017 38.462 0.00 0.00 34.94 2.78
2890 3329 8.120084 ACCTCTTTCGGTAAAATCAGTGAAACT 61.120 37.037 0.00 0.00 42.06 2.66
2906 3345 6.570690 GTGAAACTATACACGATGGAAGTC 57.429 41.667 0.00 0.00 0.00 3.01
2907 3346 5.519206 GTGAAACTATACACGATGGAAGTCC 59.481 44.000 0.00 0.00 0.00 3.85
2942 3381 9.331282 AGTACATATCTAGAAAAATTCCACAGC 57.669 33.333 0.00 0.00 0.00 4.40
2943 3382 9.109393 GTACATATCTAGAAAAATTCCACAGCA 57.891 33.333 0.00 0.00 0.00 4.41
2944 3383 8.757982 ACATATCTAGAAAAATTCCACAGCAT 57.242 30.769 0.00 0.00 0.00 3.79
2945 3384 9.193806 ACATATCTAGAAAAATTCCACAGCATT 57.806 29.630 0.00 0.00 0.00 3.56
2949 3388 9.860898 ATCTAGAAAAATTCCACAGCATTTTAC 57.139 29.630 0.00 0.00 32.54 2.01
2950 3389 8.855110 TCTAGAAAAATTCCACAGCATTTTACA 58.145 29.630 0.00 0.00 32.54 2.41
2951 3390 7.713764 AGAAAAATTCCACAGCATTTTACAC 57.286 32.000 0.00 0.00 32.54 2.90
2952 3391 7.271511 AGAAAAATTCCACAGCATTTTACACA 58.728 30.769 0.00 0.00 32.54 3.72
2953 3392 7.768120 AGAAAAATTCCACAGCATTTTACACAA 59.232 29.630 0.00 0.00 32.54 3.33
2954 3393 7.481275 AAAATTCCACAGCATTTTACACAAG 57.519 32.000 0.00 0.00 32.05 3.16
2955 3394 6.403866 AATTCCACAGCATTTTACACAAGA 57.596 33.333 0.00 0.00 0.00 3.02
2964 3403 4.321156 GCATTTTACACAAGATCAGTGGCA 60.321 41.667 18.72 6.92 41.21 4.92
2991 3430 3.954258 CAGGAATTAAAGTTAGCTGGGGG 59.046 47.826 0.00 0.00 0.00 5.40
2992 3431 2.693591 GGAATTAAAGTTAGCTGGGGGC 59.306 50.000 0.00 0.00 42.19 5.80
2993 3432 3.361786 GAATTAAAGTTAGCTGGGGGCA 58.638 45.455 0.00 0.00 44.79 5.36
3169 3612 0.391130 CTGACCCGCAAATTCCTCGA 60.391 55.000 0.00 0.00 0.00 4.04
3190 3635 4.025563 CGAGTATGTCCGTTTTTGTGTTCA 60.026 41.667 0.00 0.00 0.00 3.18
3215 3660 2.094182 GTGGTCCGCGGATATGATATGT 60.094 50.000 33.58 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.688578 CGGTACACTGCATACCTTCTATAAT 58.311 40.000 12.11 0.00 40.10 1.28
31 32 6.080648 CGGTACACTGCATACCTTCTATAA 57.919 41.667 12.11 0.00 40.10 0.98
35 36 2.961526 CGGTACACTGCATACCTTCT 57.038 50.000 12.11 0.00 40.10 2.85
57 59 6.650120 TCTAAAGACGAATTCCTTAATGGCT 58.350 36.000 0.00 0.00 35.26 4.75
203 205 3.692257 ATTATTCCTGATCCAGCTCCG 57.308 47.619 0.00 0.00 0.00 4.63
233 235 2.287547 CGGTGATGACAACAGGGTTTTG 60.288 50.000 0.00 0.00 32.53 2.44
238 241 2.040544 GCCGGTGATGACAACAGGG 61.041 63.158 1.90 0.00 32.53 4.45
243 246 0.907704 AGGTAGGCCGGTGATGACAA 60.908 55.000 1.90 0.00 40.50 3.18
258 261 5.338632 TGGAGTTGTTAAGATGAGGAGGTA 58.661 41.667 0.00 0.00 0.00 3.08
324 327 7.110155 ACTTATCTTTATCTTTTCGAAGGGCA 58.890 34.615 0.00 0.00 0.00 5.36
327 330 9.314321 TGCTACTTATCTTTATCTTTTCGAAGG 57.686 33.333 0.00 0.00 0.00 3.46
329 332 9.871238 ACTGCTACTTATCTTTATCTTTTCGAA 57.129 29.630 0.00 0.00 0.00 3.71
368 378 9.225436 GGAAGATGAAATGTTTACTTCTTCTCT 57.775 33.333 3.64 0.00 40.89 3.10
369 379 9.225436 AGGAAGATGAAATGTTTACTTCTTCTC 57.775 33.333 3.64 0.00 40.89 2.87
474 484 0.106519 ACTCAAGCAACCCAACAGCT 60.107 50.000 0.00 0.00 41.03 4.24
483 501 2.668280 GGGCGTCGACTCAAGCAAC 61.668 63.158 14.70 2.99 0.00 4.17
490 517 0.876342 GATTCCATGGGCGTCGACTC 60.876 60.000 13.02 5.30 0.00 3.36
504 531 1.985473 TAGCCACATGCATGGATTCC 58.015 50.000 29.41 13.08 43.02 3.01
576 603 2.125552 TGCCACGATCTTCAGCCG 60.126 61.111 0.00 0.00 0.00 5.52
642 669 9.640952 AGGTTGGCAAATATGTTTGTATATACT 57.359 29.630 15.30 5.82 45.14 2.12
679 707 2.254152 TAGTCAGAGGGCCAGAATGT 57.746 50.000 6.18 0.00 0.00 2.71
735 1053 4.662145 CACCTTATCGGTTTGATTTCTGC 58.338 43.478 0.00 0.00 46.37 4.26
791 1109 4.543590 ATCCATGCGAAACCCTATAGAG 57.456 45.455 0.00 0.00 0.00 2.43
818 1136 9.269415 GCGTCGTCACAAACTTATATTTAAATT 57.731 29.630 5.91 0.00 0.00 1.82
819 1137 8.662141 AGCGTCGTCACAAACTTATATTTAAAT 58.338 29.630 5.89 5.89 0.00 1.40
827 1145 2.475111 CACAGCGTCGTCACAAACTTAT 59.525 45.455 0.00 0.00 0.00 1.73
833 1151 2.993449 TATACACAGCGTCGTCACAA 57.007 45.000 0.00 0.00 0.00 3.33
900 1229 3.192541 TGTGCAGCAGTAGTTCTGAAA 57.807 42.857 0.00 0.00 46.27 2.69
901 1230 2.908688 TGTGCAGCAGTAGTTCTGAA 57.091 45.000 0.00 0.00 46.27 3.02
902 1231 2.613725 CCATGTGCAGCAGTAGTTCTGA 60.614 50.000 0.00 0.00 46.27 3.27
903 1232 1.736126 CCATGTGCAGCAGTAGTTCTG 59.264 52.381 0.00 0.00 46.12 3.02
904 1233 1.625315 TCCATGTGCAGCAGTAGTTCT 59.375 47.619 0.00 0.00 0.00 3.01
905 1234 2.099141 TCCATGTGCAGCAGTAGTTC 57.901 50.000 0.00 0.00 0.00 3.01
906 1235 2.795231 ATCCATGTGCAGCAGTAGTT 57.205 45.000 0.00 0.00 0.00 2.24
948 1277 1.063764 GCTGAAGTCATGCAAGCTAGC 59.936 52.381 6.62 6.62 0.00 3.42
949 1278 2.353323 TGCTGAAGTCATGCAAGCTAG 58.647 47.619 5.93 0.00 33.48 3.42
950 1279 2.477845 TGCTGAAGTCATGCAAGCTA 57.522 45.000 5.93 0.00 33.48 3.32
951 1280 1.835494 ATGCTGAAGTCATGCAAGCT 58.165 45.000 5.93 0.00 40.24 3.74
977 1306 2.173382 GCAACTGTAACCTGCGCG 59.827 61.111 0.00 0.00 0.00 6.86
980 1309 6.867662 ATAATATCTGCAACTGTAACCTGC 57.132 37.500 0.00 0.00 36.60 4.85
987 1316 9.019656 TGTTGGTTTTATAATATCTGCAACTGT 57.980 29.630 0.00 0.00 0.00 3.55
1022 1354 9.989530 AAATGAAATGCAGTTTGTCTGGGAACC 62.990 40.741 0.00 0.00 43.78 3.62
1038 1370 4.789012 TCCTTGTCCTGAAATGAAATGC 57.211 40.909 0.00 0.00 0.00 3.56
1058 1390 1.202336 CCAATCAAGCGGCCTGAATTC 60.202 52.381 5.24 0.00 0.00 2.17
1060 1392 1.669999 GCCAATCAAGCGGCCTGAAT 61.670 55.000 5.24 0.00 42.82 2.57
1067 1399 2.796651 GAGCAGCCAATCAAGCGG 59.203 61.111 0.00 0.00 34.64 5.52
1069 1401 2.101770 GCGAGCAGCCAATCAAGC 59.898 61.111 0.00 0.00 40.81 4.01
1092 1424 2.665326 GATCGACGCGCCAAATCACG 62.665 60.000 5.73 0.00 0.00 4.35
1093 1425 1.012234 GATCGACGCGCCAAATCAC 60.012 57.895 5.73 0.00 0.00 3.06
1094 1426 2.513157 CGATCGACGCGCCAAATCA 61.513 57.895 10.26 0.00 34.51 2.57
1095 1427 1.548973 ATCGATCGACGCGCCAAATC 61.549 55.000 22.06 3.53 42.26 2.17
1096 1428 1.548973 GATCGATCGACGCGCCAAAT 61.549 55.000 22.06 0.00 42.26 2.32
1097 1429 2.202690 ATCGATCGACGCGCCAAA 60.203 55.556 22.06 0.00 42.26 3.28
1098 1430 2.654085 GATCGATCGACGCGCCAA 60.654 61.111 22.06 0.00 42.26 4.52
1107 1439 5.223225 TAGAATGGATCTTCGATCGATCG 57.777 43.478 35.91 35.91 44.23 3.69
1111 1443 4.142491 CCTCCTAGAATGGATCTTCGATCG 60.142 50.000 9.36 9.36 39.71 3.69
1113 1445 3.513515 GCCTCCTAGAATGGATCTTCGAT 59.486 47.826 0.00 0.00 39.71 3.59
1115 1447 2.028567 GGCCTCCTAGAATGGATCTTCG 60.029 54.545 0.00 0.00 39.71 3.79
1157 1490 3.368571 GGGCACAGGAACAGCTGC 61.369 66.667 15.27 0.00 0.00 5.25
1307 1640 2.029964 TTGGGCGTGAGGTCGAAC 59.970 61.111 0.00 0.00 0.00 3.95
1308 1641 2.029964 GTTGGGCGTGAGGTCGAA 59.970 61.111 0.00 0.00 0.00 3.71
1523 1910 1.635663 CGTCACAGGCCACGAAATCC 61.636 60.000 5.01 0.00 38.32 3.01
1526 1913 2.280524 CCGTCACAGGCCACGAAA 60.281 61.111 14.42 0.00 38.32 3.46
1613 2000 3.685214 CTCCTCGCACGTCCGGAAG 62.685 68.421 16.38 16.38 0.00 3.46
1664 2051 1.674980 GTCCACCGACTCCTCGTCT 60.675 63.158 0.00 0.00 40.59 4.18
1847 2234 2.041686 GTCGGAGAGCAGGTCGAGT 61.042 63.158 0.00 0.00 36.95 4.18
2405 2830 0.737715 CGCCTCTCTGTACACTTGCC 60.738 60.000 0.00 0.00 0.00 4.52
2421 2846 0.740737 CAACATTTCATCCTCCCGCC 59.259 55.000 0.00 0.00 0.00 6.13
2433 2862 8.421249 TCAATCTTCCCTATCAAACAACATTT 57.579 30.769 0.00 0.00 0.00 2.32
2437 2872 7.976175 GGATTTCAATCTTCCCTATCAAACAAC 59.024 37.037 0.00 0.00 35.73 3.32
2445 2880 5.310594 TGGATCGGATTTCAATCTTCCCTAT 59.689 40.000 0.00 0.00 35.73 2.57
2485 2920 4.322934 CACGTTTAATCTGTACACGCATG 58.677 43.478 0.00 0.00 34.14 4.06
2543 2979 4.639078 TGATGAGTGATTGAAACCTGGA 57.361 40.909 0.00 0.00 0.00 3.86
2549 2985 7.528996 AACTGGAATTGATGAGTGATTGAAA 57.471 32.000 0.00 0.00 0.00 2.69
2553 2989 5.337009 GCCAAACTGGAATTGATGAGTGATT 60.337 40.000 0.00 0.00 40.96 2.57
2734 3173 7.860872 ACAAATTCAAGACAAGTAATTCGGAAC 59.139 33.333 0.00 0.00 0.00 3.62
2735 3174 7.936584 ACAAATTCAAGACAAGTAATTCGGAA 58.063 30.769 0.00 0.00 0.00 4.30
2736 3175 7.444183 AGACAAATTCAAGACAAGTAATTCGGA 59.556 33.333 0.00 0.00 0.00 4.55
2737 3176 7.584987 AGACAAATTCAAGACAAGTAATTCGG 58.415 34.615 0.00 0.00 0.00 4.30
2738 3177 9.746711 CTAGACAAATTCAAGACAAGTAATTCG 57.253 33.333 0.00 0.00 0.00 3.34
2743 3182 9.569167 CGTATCTAGACAAATTCAAGACAAGTA 57.431 33.333 0.00 0.00 0.00 2.24
2744 3183 7.545965 CCGTATCTAGACAAATTCAAGACAAGT 59.454 37.037 0.00 0.00 0.00 3.16
2745 3184 7.759886 TCCGTATCTAGACAAATTCAAGACAAG 59.240 37.037 0.00 0.00 0.00 3.16
2746 3185 7.608153 TCCGTATCTAGACAAATTCAAGACAA 58.392 34.615 0.00 0.00 0.00 3.18
2747 3186 7.165460 TCCGTATCTAGACAAATTCAAGACA 57.835 36.000 0.00 0.00 0.00 3.41
2748 3187 7.707035 ACATCCGTATCTAGACAAATTCAAGAC 59.293 37.037 0.00 0.00 0.00 3.01
2749 3188 7.782049 ACATCCGTATCTAGACAAATTCAAGA 58.218 34.615 0.00 0.00 0.00 3.02
2750 3189 9.698309 ATACATCCGTATCTAGACAAATTCAAG 57.302 33.333 0.00 0.00 32.66 3.02
2766 3205 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
2767 3206 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
2768 3207 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
2769 3208 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
2772 3211 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
2776 3215 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
2777 3216 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
2778 3217 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
2779 3218 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
2780 3219 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
2781 3220 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
2782 3221 6.153067 CGGAGGTATCTAGCACTAAAATGAG 58.847 44.000 0.00 0.00 0.00 2.90
2783 3222 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
2784 3223 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
2785 3224 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
2799 3238 9.412460 TCTTAAATTTGTCTAGATACGGAGGTA 57.588 33.333 0.00 0.00 0.00 3.08
2800 3239 8.196103 GTCTTAAATTTGTCTAGATACGGAGGT 58.804 37.037 0.00 0.00 0.00 3.85
2801 3240 8.195436 TGTCTTAAATTTGTCTAGATACGGAGG 58.805 37.037 0.00 0.00 0.00 4.30
2802 3241 9.582431 TTGTCTTAAATTTGTCTAGATACGGAG 57.418 33.333 0.00 0.00 0.00 4.63
2803 3242 9.582431 CTTGTCTTAAATTTGTCTAGATACGGA 57.418 33.333 0.00 0.00 0.00 4.69
2804 3243 9.367444 ACTTGTCTTAAATTTGTCTAGATACGG 57.633 33.333 0.00 0.00 0.00 4.02
2812 3251 9.280174 TCCGAATTACTTGTCTTAAATTTGTCT 57.720 29.630 0.00 0.00 0.00 3.41
2813 3252 9.887406 TTCCGAATTACTTGTCTTAAATTTGTC 57.113 29.630 0.00 0.00 0.00 3.18
2816 3255 9.855021 CCATTCCGAATTACTTGTCTTAAATTT 57.145 29.630 0.00 0.00 0.00 1.82
2817 3256 9.238368 TCCATTCCGAATTACTTGTCTTAAATT 57.762 29.630 0.00 0.00 0.00 1.82
2818 3257 8.801882 TCCATTCCGAATTACTTGTCTTAAAT 57.198 30.769 0.00 0.00 0.00 1.40
2819 3258 7.335924 CCTCCATTCCGAATTACTTGTCTTAAA 59.664 37.037 0.00 0.00 0.00 1.52
2820 3259 6.821665 CCTCCATTCCGAATTACTTGTCTTAA 59.178 38.462 0.00 0.00 0.00 1.85
2821 3260 6.346096 CCTCCATTCCGAATTACTTGTCTTA 58.654 40.000 0.00 0.00 0.00 2.10
2822 3261 5.186198 CCTCCATTCCGAATTACTTGTCTT 58.814 41.667 0.00 0.00 0.00 3.01
2823 3262 4.384208 CCCTCCATTCCGAATTACTTGTCT 60.384 45.833 0.00 0.00 0.00 3.41
2824 3263 3.877508 CCCTCCATTCCGAATTACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
2825 3264 3.521937 TCCCTCCATTCCGAATTACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
2826 3265 4.130118 CTCCCTCCATTCCGAATTACTTG 58.870 47.826 0.00 0.00 0.00 3.16
2827 3266 3.780850 ACTCCCTCCATTCCGAATTACTT 59.219 43.478 0.00 0.00 0.00 2.24
2828 3267 3.385115 ACTCCCTCCATTCCGAATTACT 58.615 45.455 0.00 0.00 0.00 2.24
2829 3268 3.840124 ACTCCCTCCATTCCGAATTAC 57.160 47.619 0.00 0.00 0.00 1.89
2830 3269 4.553678 AGTACTCCCTCCATTCCGAATTA 58.446 43.478 0.00 0.00 0.00 1.40
2831 3270 3.385115 AGTACTCCCTCCATTCCGAATT 58.615 45.455 0.00 0.00 0.00 2.17
2832 3271 3.047695 AGTACTCCCTCCATTCCGAAT 57.952 47.619 0.00 0.00 0.00 3.34
2833 3272 2.500098 CAAGTACTCCCTCCATTCCGAA 59.500 50.000 0.00 0.00 0.00 4.30
2834 3273 2.108168 CAAGTACTCCCTCCATTCCGA 58.892 52.381 0.00 0.00 0.00 4.55
2835 3274 1.139058 CCAAGTACTCCCTCCATTCCG 59.861 57.143 0.00 0.00 0.00 4.30
2836 3275 1.490910 CCCAAGTACTCCCTCCATTCC 59.509 57.143 0.00 0.00 0.00 3.01
2837 3276 2.092914 CACCCAAGTACTCCCTCCATTC 60.093 54.545 0.00 0.00 0.00 2.67
2838 3277 1.916181 CACCCAAGTACTCCCTCCATT 59.084 52.381 0.00 0.00 0.00 3.16
2839 3278 1.584724 CACCCAAGTACTCCCTCCAT 58.415 55.000 0.00 0.00 0.00 3.41
2840 3279 1.198759 GCACCCAAGTACTCCCTCCA 61.199 60.000 0.00 0.00 0.00 3.86
2841 3280 1.198759 TGCACCCAAGTACTCCCTCC 61.199 60.000 0.00 0.00 0.00 4.30
2842 3281 0.036294 GTGCACCCAAGTACTCCCTC 60.036 60.000 5.22 0.00 0.00 4.30
2843 3282 0.473886 AGTGCACCCAAGTACTCCCT 60.474 55.000 14.63 0.00 27.57 4.20
2844 3283 0.036294 GAGTGCACCCAAGTACTCCC 60.036 60.000 14.63 0.00 42.96 4.30
2845 3284 0.685097 TGAGTGCACCCAAGTACTCC 59.315 55.000 14.63 0.00 46.56 3.85
2856 3295 0.249911 ACCGAAAGAGGTGAGTGCAC 60.250 55.000 9.40 9.40 44.07 4.57
2857 3296 1.334160 TACCGAAAGAGGTGAGTGCA 58.666 50.000 0.00 0.00 45.54 4.57
2858 3297 2.450609 TTACCGAAAGAGGTGAGTGC 57.549 50.000 0.00 0.00 45.54 4.40
2859 3298 4.994852 TGATTTTACCGAAAGAGGTGAGTG 59.005 41.667 0.00 0.00 45.54 3.51
2860 3299 5.221661 ACTGATTTTACCGAAAGAGGTGAGT 60.222 40.000 0.00 0.00 45.54 3.41
2861 3300 5.120830 CACTGATTTTACCGAAAGAGGTGAG 59.879 44.000 0.00 0.00 45.54 3.51
2862 3301 4.994852 CACTGATTTTACCGAAAGAGGTGA 59.005 41.667 0.00 0.00 45.54 4.02
2863 3302 4.994852 TCACTGATTTTACCGAAAGAGGTG 59.005 41.667 0.00 0.00 45.54 4.00
2865 3304 6.204882 AGTTTCACTGATTTTACCGAAAGAGG 59.795 38.462 0.00 0.00 37.30 3.69
2866 3305 7.190920 AGTTTCACTGATTTTACCGAAAGAG 57.809 36.000 0.00 0.00 0.00 2.85
2867 3306 8.842358 ATAGTTTCACTGATTTTACCGAAAGA 57.158 30.769 0.00 0.00 0.00 2.52
2868 3307 9.968743 GTATAGTTTCACTGATTTTACCGAAAG 57.031 33.333 0.00 0.00 0.00 2.62
2869 3308 9.491675 TGTATAGTTTCACTGATTTTACCGAAA 57.508 29.630 0.00 0.00 0.00 3.46
2870 3309 8.928733 GTGTATAGTTTCACTGATTTTACCGAA 58.071 33.333 0.00 0.00 0.00 4.30
2871 3310 7.274033 CGTGTATAGTTTCACTGATTTTACCGA 59.726 37.037 0.00 0.00 33.07 4.69
2872 3311 7.274033 TCGTGTATAGTTTCACTGATTTTACCG 59.726 37.037 0.00 0.00 33.07 4.02
2873 3312 8.470040 TCGTGTATAGTTTCACTGATTTTACC 57.530 34.615 0.00 0.00 33.07 2.85
2874 3313 9.901724 CATCGTGTATAGTTTCACTGATTTTAC 57.098 33.333 0.00 0.00 31.38 2.01
2875 3314 9.093970 CCATCGTGTATAGTTTCACTGATTTTA 57.906 33.333 0.00 0.00 31.38 1.52
2876 3315 7.822334 TCCATCGTGTATAGTTTCACTGATTTT 59.178 33.333 0.00 0.00 31.38 1.82
2877 3316 7.327975 TCCATCGTGTATAGTTTCACTGATTT 58.672 34.615 0.00 0.00 31.38 2.17
2878 3317 6.873997 TCCATCGTGTATAGTTTCACTGATT 58.126 36.000 0.00 0.00 31.38 2.57
2879 3318 6.465439 TCCATCGTGTATAGTTTCACTGAT 57.535 37.500 0.00 0.00 32.68 2.90
2880 3319 5.907866 TCCATCGTGTATAGTTTCACTGA 57.092 39.130 0.00 0.00 33.07 3.41
2881 3320 6.100004 ACTTCCATCGTGTATAGTTTCACTG 58.900 40.000 0.00 0.00 33.07 3.66
2882 3321 6.282199 ACTTCCATCGTGTATAGTTTCACT 57.718 37.500 0.00 0.00 33.07 3.41
2883 3322 5.519206 GGACTTCCATCGTGTATAGTTTCAC 59.481 44.000 0.00 0.00 35.64 3.18
2884 3323 5.186215 TGGACTTCCATCGTGTATAGTTTCA 59.814 40.000 0.00 0.00 42.01 2.69
2885 3324 5.657474 TGGACTTCCATCGTGTATAGTTTC 58.343 41.667 0.00 0.00 42.01 2.78
2886 3325 5.670792 TGGACTTCCATCGTGTATAGTTT 57.329 39.130 0.00 0.00 42.01 2.66
2887 3326 5.670792 TTGGACTTCCATCGTGTATAGTT 57.329 39.130 0.00 0.00 46.97 2.24
2888 3327 5.670792 TTTGGACTTCCATCGTGTATAGT 57.329 39.130 0.00 0.00 46.97 2.12
2889 3328 6.978343 TTTTTGGACTTCCATCGTGTATAG 57.022 37.500 0.00 0.00 46.97 1.31
2916 3355 9.331282 GCTGTGGAATTTTTCTAGATATGTACT 57.669 33.333 0.00 0.00 0.00 2.73
2917 3356 9.109393 TGCTGTGGAATTTTTCTAGATATGTAC 57.891 33.333 0.00 0.00 0.00 2.90
2918 3357 9.851686 ATGCTGTGGAATTTTTCTAGATATGTA 57.148 29.630 0.00 0.00 0.00 2.29
2919 3358 8.757982 ATGCTGTGGAATTTTTCTAGATATGT 57.242 30.769 0.00 0.00 0.00 2.29
2923 3362 9.860898 GTAAAATGCTGTGGAATTTTTCTAGAT 57.139 29.630 0.00 0.00 40.22 1.98
2924 3363 8.855110 TGTAAAATGCTGTGGAATTTTTCTAGA 58.145 29.630 0.81 0.00 40.22 2.43
2925 3364 8.915654 GTGTAAAATGCTGTGGAATTTTTCTAG 58.084 33.333 0.81 0.00 40.22 2.43
2926 3365 8.417106 TGTGTAAAATGCTGTGGAATTTTTCTA 58.583 29.630 0.81 0.00 40.22 2.10
2927 3366 7.271511 TGTGTAAAATGCTGTGGAATTTTTCT 58.728 30.769 0.81 0.00 40.22 2.52
2928 3367 7.475771 TGTGTAAAATGCTGTGGAATTTTTC 57.524 32.000 0.81 0.00 40.22 2.29
2929 3368 7.768120 TCTTGTGTAAAATGCTGTGGAATTTTT 59.232 29.630 0.81 0.00 40.22 1.94
2930 3369 7.271511 TCTTGTGTAAAATGCTGTGGAATTTT 58.728 30.769 0.00 0.00 41.87 1.82
2931 3370 6.815089 TCTTGTGTAAAATGCTGTGGAATTT 58.185 32.000 0.00 0.00 32.36 1.82
2932 3371 6.403866 TCTTGTGTAAAATGCTGTGGAATT 57.596 33.333 0.00 0.00 0.00 2.17
2933 3372 6.209192 TGATCTTGTGTAAAATGCTGTGGAAT 59.791 34.615 0.00 0.00 0.00 3.01
2934 3373 5.534278 TGATCTTGTGTAAAATGCTGTGGAA 59.466 36.000 0.00 0.00 0.00 3.53
2935 3374 5.069318 TGATCTTGTGTAAAATGCTGTGGA 58.931 37.500 0.00 0.00 0.00 4.02
2936 3375 5.048504 ACTGATCTTGTGTAAAATGCTGTGG 60.049 40.000 0.00 0.00 0.00 4.17
2937 3376 5.854866 CACTGATCTTGTGTAAAATGCTGTG 59.145 40.000 10.05 0.00 0.00 3.66
2938 3377 5.048504 CCACTGATCTTGTGTAAAATGCTGT 60.049 40.000 14.88 0.00 33.92 4.40
2939 3378 5.396484 CCACTGATCTTGTGTAAAATGCTG 58.604 41.667 14.88 0.00 33.92 4.41
2940 3379 4.082571 GCCACTGATCTTGTGTAAAATGCT 60.083 41.667 14.88 0.00 33.92 3.79
2941 3380 4.168760 GCCACTGATCTTGTGTAAAATGC 58.831 43.478 14.88 8.53 33.92 3.56
2942 3381 5.181811 TCTGCCACTGATCTTGTGTAAAATG 59.818 40.000 14.88 3.94 33.92 2.32
2943 3382 5.182001 GTCTGCCACTGATCTTGTGTAAAAT 59.818 40.000 14.88 0.00 33.92 1.82
2944 3383 4.515191 GTCTGCCACTGATCTTGTGTAAAA 59.485 41.667 14.88 0.82 33.92 1.52
2945 3384 4.065088 GTCTGCCACTGATCTTGTGTAAA 58.935 43.478 14.88 3.68 33.92 2.01
2946 3385 3.557054 GGTCTGCCACTGATCTTGTGTAA 60.557 47.826 14.88 5.46 33.92 2.41
2947 3386 2.028112 GGTCTGCCACTGATCTTGTGTA 60.028 50.000 14.88 6.25 33.92 2.90
2948 3387 1.271054 GGTCTGCCACTGATCTTGTGT 60.271 52.381 14.88 0.00 33.92 3.72
2949 3388 1.446907 GGTCTGCCACTGATCTTGTG 58.553 55.000 10.94 10.94 35.39 3.33
2950 3389 0.326264 GGGTCTGCCACTGATCTTGT 59.674 55.000 0.00 0.00 36.17 3.16
2951 3390 0.325933 TGGGTCTGCCACTGATCTTG 59.674 55.000 0.00 0.00 36.17 3.02
2952 3391 0.617413 CTGGGTCTGCCACTGATCTT 59.383 55.000 0.00 0.00 36.17 2.40
2953 3392 1.270414 CCTGGGTCTGCCACTGATCT 61.270 60.000 0.00 0.00 36.17 2.75
2954 3393 1.222936 CCTGGGTCTGCCACTGATC 59.777 63.158 0.00 0.00 36.17 2.92
2955 3394 0.842030 TTCCTGGGTCTGCCACTGAT 60.842 55.000 0.00 0.00 36.17 2.90
2964 3403 5.501156 CAGCTAACTTTAATTCCTGGGTCT 58.499 41.667 0.00 0.00 0.00 3.85
3092 3535 7.594015 CGATAATAGTCCACGTTAGCAGTTTAT 59.406 37.037 0.00 0.00 0.00 1.40
3169 3612 5.007332 GTCTGAACACAAAAACGGACATACT 59.993 40.000 0.00 0.00 38.19 2.12
3190 3635 1.826921 ATATCCGCGGACCACGTCT 60.827 57.895 33.75 15.89 46.52 4.18
3215 3660 1.668826 AGTGTTGGATGGCTCCCTTA 58.331 50.000 1.34 0.00 41.29 2.69
3337 4153 3.176708 CGGTGATTAGTTACTGTCGTGG 58.823 50.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.