Multiple sequence alignment - TraesCS5B01G266600

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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 TraesCS5B01G266600 chr5B 100.000 4883 0 0 1 4883 450846854 450841972 0.000000e+00 9018
1 TraesCS5B01G266600 chr5B 88.991 218 13 6 4667 4883 516605667 516605460 4.850000e-65 259
2 TraesCS5B01G266600 chr5D 92.121 3300 136 40 1 3286 377539225 377536036 0.000000e+00 4540
3 TraesCS5B01G266600 chr5D 89.859 1351 63 33 3565 4883 377535755 377534447 0.000000e+00 1668
4 TraesCS5B01G266600 chr5A 93.129 2474 109 31 1 2431 478326993 478324538 0.000000e+00 3570
5 TraesCS5B01G266600 chr5A 92.244 851 42 13 2498 3335 478324545 478323706 0.000000e+00 1184
6 TraesCS5B01G266600 chr5A 90.620 693 29 12 3565 4232 478323388 478322707 0.000000e+00 887
7 TraesCS5B01G266600 chr5A 91.506 518 23 10 4380 4883 478322531 478322021 0.000000e+00 693
8 TraesCS5B01G266600 chr7A 93.878 147 9 0 4737 4883 229143261 229143115 6.360000e-54 222
9 TraesCS5B01G266600 chr7D 91.772 158 13 0 4726 4883 216082343 216082186 2.290000e-53 220
10 TraesCS5B01G266600 chr7B 91.772 158 13 0 4726 4883 184299349 184299506 2.290000e-53 220
11 TraesCS5B01G266600 chr3A 92.086 139 9 2 4745 4883 17533080 17532944 1.390000e-45 195
12 TraesCS5B01G266600 chr2A 92.537 134 7 3 4745 4877 576659286 576659155 6.450000e-44 189
13 TraesCS5B01G266600 chrUn 91.803 122 8 2 4756 4877 176722652 176722533 8.410000e-38 169


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 TraesCS5B01G266600 chr5B 450841972 450846854 4882 True 9018.0 9018 100.00000 1 4883 1 chr5B.!!$R1 4882
1 TraesCS5B01G266600 chr5D 377534447 377539225 4778 True 3104.0 4540 90.99000 1 4883 2 chr5D.!!$R1 4882
2 TraesCS5B01G266600 chr5A 478322021 478326993 4972 True 1583.5 3570 91.87475 1 4883 4 chr5A.!!$R1 4882

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
594 620 0.741915 TGCTTTTGTGTTTCCCGACC 59.258 50.000 0.0 0.0 0.0 4.79 F
811 849 2.018515 TGCTCCCGTTTTCTTTTCGTT 58.981 42.857 0.0 0.0 0.0 3.85 F
2441 2523 1.670295 TCGATGAAATGGTGATTGCCG 59.330 47.619 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2326 1.153706 GCCACATCCTGCAATGCAC 60.154 57.895 2.72 0.0 33.79 4.57 R
2501 2583 1.608590 CAAAGCCGTCCACAGTGATTT 59.391 47.619 0.62 0.0 0.00 2.17 R
4327 4644 0.176910 GGAAGACTAGGAGCAGCACC 59.823 60.000 0.00 0.0 0.00 5.01 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
75 76 1.689582 GTGGTGGTAGGGAGGGGAG 60.690 68.421 0.00 0.00 0.00 4.30
76 77 2.040779 GGTGGTAGGGAGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
77 78 2.040779 GTGGTAGGGAGGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
78 79 3.373846 TGGTAGGGAGGGGAGGGG 61.374 72.222 0.00 0.00 0.00 4.79
79 80 4.188511 GGTAGGGAGGGGAGGGGG 62.189 77.778 0.00 0.00 0.00 5.40
80 81 3.040814 GTAGGGAGGGGAGGGGGA 61.041 72.222 0.00 0.00 0.00 4.81
131 133 5.404968 CAGTGAAAAACAGACAACAGCAAAA 59.595 36.000 0.00 0.00 0.00 2.44
135 140 6.365789 TGAAAAACAGACAACAGCAAAAGAAG 59.634 34.615 0.00 0.00 0.00 2.85
152 157 7.545615 GCAAAAGAAGAAAAATATACACAGGGG 59.454 37.037 0.00 0.00 0.00 4.79
305 317 6.348132 CGGCAAACCAAATTTAATCCCTTTTC 60.348 38.462 0.00 0.00 34.57 2.29
457 469 2.760650 AGCGAAATCCCCAAATTTCTCC 59.239 45.455 7.52 0.52 41.45 3.71
487 499 4.675029 CCCCGTCCGCAGTCGTTT 62.675 66.667 0.00 0.00 0.00 3.60
590 616 1.856802 CTGCTGCTTTTGTGTTTCCC 58.143 50.000 0.00 0.00 0.00 3.97
594 620 0.741915 TGCTTTTGTGTTTCCCGACC 59.258 50.000 0.00 0.00 0.00 4.79
650 677 3.502211 GGTATTATCCTGATTTGCGGTGG 59.498 47.826 0.00 0.00 0.00 4.61
672 699 2.666862 TCGGTGATTTTGCCGCGT 60.667 55.556 4.92 0.00 46.79 6.01
675 702 2.202298 GTGATTTTGCCGCGTCCG 60.202 61.111 4.92 0.00 0.00 4.79
805 843 2.032924 CGTTTCTTGCTCCCGTTTTCTT 59.967 45.455 0.00 0.00 0.00 2.52
806 844 3.488553 CGTTTCTTGCTCCCGTTTTCTTT 60.489 43.478 0.00 0.00 0.00 2.52
809 847 2.289547 TCTTGCTCCCGTTTTCTTTTCG 59.710 45.455 0.00 0.00 0.00 3.46
811 849 2.018515 TGCTCCCGTTTTCTTTTCGTT 58.981 42.857 0.00 0.00 0.00 3.85
812 850 2.424246 TGCTCCCGTTTTCTTTTCGTTT 59.576 40.909 0.00 0.00 0.00 3.60
813 851 3.119424 TGCTCCCGTTTTCTTTTCGTTTT 60.119 39.130 0.00 0.00 0.00 2.43
814 852 3.861113 GCTCCCGTTTTCTTTTCGTTTTT 59.139 39.130 0.00 0.00 0.00 1.94
844 882 3.508840 CCGTCATTTGCGGCCTCC 61.509 66.667 0.00 0.00 42.82 4.30
1033 1075 4.426112 CGTCGCAGGAGCAGCAGA 62.426 66.667 0.00 0.00 42.27 4.26
1294 1336 2.370445 AACATGGAGGAGGAGGCCG 61.370 63.158 0.00 0.00 0.00 6.13
1295 1337 4.247380 CATGGAGGAGGAGGCCGC 62.247 72.222 0.00 0.00 0.00 6.53
1299 1341 4.168291 GAGGAGGAGGCCGCCAAG 62.168 72.222 28.68 0.00 46.18 3.61
1300 1342 4.722535 AGGAGGAGGCCGCCAAGA 62.723 66.667 28.68 0.00 46.18 3.02
1301 1343 3.717294 GGAGGAGGCCGCCAAGAA 61.717 66.667 28.68 0.00 43.17 2.52
1302 1344 2.124942 GAGGAGGCCGCCAAGAAG 60.125 66.667 28.68 0.00 0.00 2.85
1303 1345 4.416738 AGGAGGCCGCCAAGAAGC 62.417 66.667 28.68 0.00 0.00 3.86
1386 1444 2.759973 CCCGAGGAGCCTACTGCA 60.760 66.667 0.00 0.00 44.83 4.41
1595 1653 6.431198 TCTCCATTTTTCTGTTATTACGGC 57.569 37.500 0.00 0.00 0.00 5.68
1614 1672 9.968870 ATTACGGCTTTAATTACTTTTGTGAAA 57.031 25.926 0.00 0.00 0.00 2.69
1772 1834 3.014623 GTGGAAATTACTGCTGTACCCC 58.985 50.000 2.52 3.56 0.00 4.95
1940 2009 3.786635 ACTGAAGTCTTGTGTGTCTGTC 58.213 45.455 0.00 0.00 0.00 3.51
1989 2058 6.294675 CCCTGCTTCTTCTGAGATCTATACAG 60.295 46.154 0.00 0.00 0.00 2.74
1998 2071 7.718334 TCTGAGATCTATACAGGTGTTTGAA 57.282 36.000 9.39 0.00 33.19 2.69
2015 2089 5.866633 TGTTTGAACATGTTCTTGGTGAAAC 59.133 36.000 32.57 29.30 40.14 2.78
2059 2134 2.571653 AGCTGGCTTTACTCCACATGTA 59.428 45.455 0.00 0.00 0.00 2.29
2118 2193 6.264771 TCCTCAATCCCATATTCACATTGA 57.735 37.500 0.00 0.00 33.48 2.57
2183 2258 3.916761 CACATACCAAAAAGCTGTGCAT 58.083 40.909 0.00 0.00 31.81 3.96
2184 2259 4.309099 CACATACCAAAAAGCTGTGCATT 58.691 39.130 0.00 0.00 31.81 3.56
2185 2260 4.751098 CACATACCAAAAAGCTGTGCATTT 59.249 37.500 0.00 0.00 30.66 2.32
2186 2261 5.236911 CACATACCAAAAAGCTGTGCATTTT 59.763 36.000 0.00 0.55 39.47 1.82
2187 2262 5.466393 ACATACCAAAAAGCTGTGCATTTTC 59.534 36.000 0.00 0.00 37.34 2.29
2188 2263 4.141233 ACCAAAAAGCTGTGCATTTTCT 57.859 36.364 0.00 0.00 37.34 2.52
2189 2264 3.872771 ACCAAAAAGCTGTGCATTTTCTG 59.127 39.130 0.00 1.69 37.34 3.02
2190 2265 4.121317 CCAAAAAGCTGTGCATTTTCTGA 58.879 39.130 0.00 0.00 37.34 3.27
2199 2274 5.234757 GCTGTGCATTTTCTGATTTTCACAA 59.765 36.000 0.00 0.00 33.55 3.33
2214 2296 9.190858 TGATTTTCACAATGTAACTACAAATGC 57.809 29.630 0.00 0.00 39.99 3.56
2244 2326 4.466828 CACTTGCGAATAACTTTGAGTGG 58.533 43.478 0.00 0.00 0.00 4.00
2348 2430 2.554893 GCCATTTCAAACGTGACCCTTA 59.445 45.455 0.00 0.00 31.90 2.69
2404 2486 5.339008 ACGAGGTATGCACTTCTTATTCA 57.661 39.130 0.00 0.00 0.00 2.57
2433 2515 9.784531 ATAATACATCTCTTTCGATGAAATGGT 57.215 29.630 7.69 0.00 42.63 3.55
2434 2516 5.808042 ACATCTCTTTCGATGAAATGGTG 57.192 39.130 7.69 0.55 42.63 4.17
2441 2523 1.670295 TCGATGAAATGGTGATTGCCG 59.330 47.619 0.00 0.00 0.00 5.69
2456 2538 5.901884 GTGATTGCCGATATACAAAAGTTCG 59.098 40.000 0.00 0.00 0.00 3.95
2457 2539 5.813157 TGATTGCCGATATACAAAAGTTCGA 59.187 36.000 0.00 0.00 31.74 3.71
2458 2540 5.712217 TTGCCGATATACAAAAGTTCGAG 57.288 39.130 0.00 0.00 31.74 4.04
2459 2541 5.001237 TGCCGATATACAAAAGTTCGAGA 57.999 39.130 0.00 0.00 31.74 4.04
2460 2542 5.412640 TGCCGATATACAAAAGTTCGAGAA 58.587 37.500 0.00 0.00 31.74 2.87
2461 2543 5.870433 TGCCGATATACAAAAGTTCGAGAAA 59.130 36.000 0.00 0.00 31.74 2.52
2462 2544 6.369340 TGCCGATATACAAAAGTTCGAGAAAA 59.631 34.615 0.00 0.00 31.74 2.29
2463 2545 7.095144 TGCCGATATACAAAAGTTCGAGAAAAA 60.095 33.333 0.00 0.00 31.74 1.94
2464 2546 7.908601 GCCGATATACAAAAGTTCGAGAAAAAT 59.091 33.333 0.00 0.00 31.74 1.82
2465 2547 9.210426 CCGATATACAAAAGTTCGAGAAAAATG 57.790 33.333 0.00 0.00 31.74 2.32
2466 2548 9.967245 CGATATACAAAAGTTCGAGAAAAATGA 57.033 29.630 0.00 0.00 31.74 2.57
2469 2551 5.281727 ACAAAAGTTCGAGAAAAATGAGGC 58.718 37.500 0.00 0.00 0.00 4.70
2470 2552 4.505313 AAAGTTCGAGAAAAATGAGGCC 57.495 40.909 0.00 0.00 0.00 5.19
2471 2553 3.425162 AGTTCGAGAAAAATGAGGCCT 57.575 42.857 3.86 3.86 0.00 5.19
2472 2554 3.077359 AGTTCGAGAAAAATGAGGCCTG 58.923 45.455 12.00 0.00 0.00 4.85
2473 2555 3.074412 GTTCGAGAAAAATGAGGCCTGA 58.926 45.455 12.00 0.00 0.00 3.86
2474 2556 3.634397 TCGAGAAAAATGAGGCCTGAT 57.366 42.857 12.00 3.35 0.00 2.90
2475 2557 3.535561 TCGAGAAAAATGAGGCCTGATC 58.464 45.455 12.00 0.00 0.00 2.92
2488 2570 6.009589 TGAGGCCTGATCAAAAACTGAAATA 58.990 36.000 12.00 0.00 37.67 1.40
2490 2572 5.105063 GGCCTGATCAAAAACTGAAATAGC 58.895 41.667 0.00 0.00 37.67 2.97
2518 2600 0.396435 TGAAATCACTGTGGACGGCT 59.604 50.000 8.11 0.00 0.00 5.52
2577 2663 4.413928 CCACAGGGCCGATTTGAA 57.586 55.556 0.00 0.00 0.00 2.69
2758 2844 1.980765 TCACACCAGCCTCAAATCTCT 59.019 47.619 0.00 0.00 0.00 3.10
2796 2882 5.123820 GTGCAGCCATAGTTTCACTTTCATA 59.876 40.000 0.00 0.00 0.00 2.15
2797 2883 5.123820 TGCAGCCATAGTTTCACTTTCATAC 59.876 40.000 0.00 0.00 0.00 2.39
2798 2884 5.355350 GCAGCCATAGTTTCACTTTCATACT 59.645 40.000 0.00 0.00 0.00 2.12
2799 2885 6.676456 GCAGCCATAGTTTCACTTTCATACTG 60.676 42.308 0.00 0.00 0.00 2.74
2800 2886 6.372659 CAGCCATAGTTTCACTTTCATACTGT 59.627 38.462 0.00 0.00 0.00 3.55
2814 2900 7.712639 ACTTTCATACTGTACATAGCATTCCTG 59.287 37.037 0.00 0.00 0.00 3.86
2826 2912 6.888632 ACATAGCATTCCTGATGAAACTTTCT 59.111 34.615 3.22 0.00 38.03 2.52
2827 2913 8.049117 ACATAGCATTCCTGATGAAACTTTCTA 58.951 33.333 3.22 0.00 38.03 2.10
2828 2914 6.998968 AGCATTCCTGATGAAACTTTCTAG 57.001 37.500 3.22 0.00 38.03 2.43
2866 2952 7.172361 TGCCAAAATACAGCCAAAAGTAAAATC 59.828 33.333 0.00 0.00 0.00 2.17
2889 2975 2.121291 TGCATATTTTCGTCCCAGCA 57.879 45.000 0.00 0.00 0.00 4.41
3017 3103 7.975866 AGCGAAAAGTAAAATTCTATGCATG 57.024 32.000 10.16 0.00 0.00 4.06
3048 3134 4.550422 TCAGCGTATTAGCATTCTAGCAG 58.450 43.478 0.00 0.00 40.15 4.24
3116 3204 3.511540 CCATGCCTCTCTGACGGATATTA 59.488 47.826 0.00 0.00 0.00 0.98
3134 3222 3.624326 TTATGTGCACACTGCTGAAAC 57.376 42.857 24.37 0.00 45.31 2.78
3141 3229 3.130869 TGCACACTGCTGAAACTTGAATT 59.869 39.130 0.00 0.00 45.31 2.17
3199 3287 8.688151 ACTGCTATTTACAGTTAGTTCTCTAGG 58.312 37.037 0.00 0.00 46.01 3.02
3208 3296 4.220163 AGTTAGTTCTCTAGGGTTTCCACG 59.780 45.833 0.00 0.00 34.83 4.94
3213 3301 3.972133 TCTCTAGGGTTTCCACGTCATA 58.028 45.455 0.00 0.00 34.83 2.15
3229 3317 3.572682 CGTCATAGGCATCCACCTACTAA 59.427 47.826 0.00 0.00 45.03 2.24
3281 3369 9.696917 ATTCTTTTCATAATTTCGCTTTTGAGT 57.303 25.926 0.00 0.00 0.00 3.41
3282 3370 8.506140 TCTTTTCATAATTTCGCTTTTGAGTG 57.494 30.769 0.00 0.00 0.00 3.51
3286 3374 8.673626 TTCATAATTTCGCTTTTGAGTGATTC 57.326 30.769 0.00 0.00 0.00 2.52
3287 3375 7.250569 TCATAATTTCGCTTTTGAGTGATTCC 58.749 34.615 0.00 0.00 0.00 3.01
3288 3376 5.712152 AATTTCGCTTTTGAGTGATTCCT 57.288 34.783 0.00 0.00 0.00 3.36
3289 3377 4.749245 TTTCGCTTTTGAGTGATTCCTC 57.251 40.909 0.00 0.00 0.00 3.71
3291 3379 3.329386 TCGCTTTTGAGTGATTCCTCTG 58.671 45.455 0.00 0.00 32.50 3.35
3318 3415 5.641636 TCTTTACTGCAGCAATCGTTTGATA 59.358 36.000 15.27 0.00 34.60 2.15
3319 3416 6.316140 TCTTTACTGCAGCAATCGTTTGATAT 59.684 34.615 15.27 0.00 34.60 1.63
3326 3423 6.427853 TGCAGCAATCGTTTGATATATAGCTT 59.572 34.615 10.37 0.00 34.60 3.74
3327 3424 6.958193 GCAGCAATCGTTTGATATATAGCTTC 59.042 38.462 10.37 0.00 34.60 3.86
3348 3454 3.581163 ATGTGCATCATGACTGCCA 57.419 47.368 20.32 17.91 38.89 4.92
3355 3461 3.512329 TGCATCATGACTGCCAATCTTTT 59.488 39.130 20.32 0.00 38.89 2.27
3361 3467 3.002791 TGACTGCCAATCTTTTCTAGCG 58.997 45.455 0.00 0.00 0.00 4.26
3362 3468 3.262420 GACTGCCAATCTTTTCTAGCGA 58.738 45.455 0.00 0.00 0.00 4.93
3413 3578 7.308450 AGCATTCTTCAGTATATTGCTCCTA 57.692 36.000 0.00 0.00 34.02 2.94
3414 3579 7.915930 AGCATTCTTCAGTATATTGCTCCTAT 58.084 34.615 0.00 0.00 34.02 2.57
3432 3660 6.038271 GCTCCTATATTTTGGATTCACGTTGT 59.962 38.462 0.00 0.00 0.00 3.32
3437 3665 9.277565 CTATATTTTGGATTCACGTTGTTTCAG 57.722 33.333 0.00 0.00 0.00 3.02
3458 3686 7.200434 TCAGGATTTTATTTCTCACTAGCCT 57.800 36.000 0.00 0.00 0.00 4.58
3460 3688 5.825151 AGGATTTTATTTCTCACTAGCCTGC 59.175 40.000 0.00 0.00 0.00 4.85
3462 3690 4.568072 TTTATTTCTCACTAGCCTGCCA 57.432 40.909 0.00 0.00 0.00 4.92
3463 3691 4.778213 TTATTTCTCACTAGCCTGCCAT 57.222 40.909 0.00 0.00 0.00 4.40
3470 3702 4.080356 TCTCACTAGCCTGCCATTTACAAT 60.080 41.667 0.00 0.00 0.00 2.71
3497 3729 5.860941 TTCCTAGACTCTCCACATCATTC 57.139 43.478 0.00 0.00 0.00 2.67
3498 3730 4.871822 TCCTAGACTCTCCACATCATTCA 58.128 43.478 0.00 0.00 0.00 2.57
3499 3731 5.462240 TCCTAGACTCTCCACATCATTCAT 58.538 41.667 0.00 0.00 0.00 2.57
3500 3732 5.901853 TCCTAGACTCTCCACATCATTCATT 59.098 40.000 0.00 0.00 0.00 2.57
3501 3733 5.990386 CCTAGACTCTCCACATCATTCATTG 59.010 44.000 0.00 0.00 0.00 2.82
3502 3734 4.778579 AGACTCTCCACATCATTCATTGG 58.221 43.478 0.00 0.00 0.00 3.16
3505 3737 3.889538 CTCTCCACATCATTCATTGGCAT 59.110 43.478 0.00 0.00 0.00 4.40
3506 3738 3.887110 TCTCCACATCATTCATTGGCATC 59.113 43.478 0.00 0.00 0.00 3.91
3507 3739 2.960384 TCCACATCATTCATTGGCATCC 59.040 45.455 0.00 0.00 0.00 3.51
3508 3740 2.696187 CCACATCATTCATTGGCATCCA 59.304 45.455 0.00 0.00 0.00 3.41
3509 3741 3.491964 CCACATCATTCATTGGCATCCAC 60.492 47.826 0.00 0.00 30.78 4.02
3510 3742 3.131400 CACATCATTCATTGGCATCCACA 59.869 43.478 0.00 0.00 30.78 4.17
3511 3743 3.964688 ACATCATTCATTGGCATCCACAT 59.035 39.130 0.00 0.00 30.78 3.21
3512 3744 5.010213 CACATCATTCATTGGCATCCACATA 59.990 40.000 0.00 0.00 30.78 2.29
3513 3745 5.778241 ACATCATTCATTGGCATCCACATAT 59.222 36.000 0.00 0.00 30.78 1.78
3514 3746 6.269077 ACATCATTCATTGGCATCCACATATT 59.731 34.615 0.00 0.00 30.78 1.28
3515 3747 7.452189 ACATCATTCATTGGCATCCACATATTA 59.548 33.333 0.00 0.00 30.78 0.98
3516 3748 7.457024 TCATTCATTGGCATCCACATATTAG 57.543 36.000 0.00 0.00 30.78 1.73
3517 3749 7.232910 TCATTCATTGGCATCCACATATTAGA 58.767 34.615 0.00 0.00 30.78 2.10
3518 3750 7.891712 TCATTCATTGGCATCCACATATTAGAT 59.108 33.333 0.00 0.00 30.78 1.98
3519 3751 7.692460 TTCATTGGCATCCACATATTAGATC 57.308 36.000 0.00 0.00 30.78 2.75
3520 3752 6.781943 TCATTGGCATCCACATATTAGATCA 58.218 36.000 0.00 0.00 30.78 2.92
3521 3753 6.882678 TCATTGGCATCCACATATTAGATCAG 59.117 38.462 0.00 0.00 30.78 2.90
3522 3754 5.830799 TGGCATCCACATATTAGATCAGT 57.169 39.130 0.00 0.00 0.00 3.41
3523 3755 6.933514 TGGCATCCACATATTAGATCAGTA 57.066 37.500 0.00 0.00 0.00 2.74
3524 3756 6.701340 TGGCATCCACATATTAGATCAGTAC 58.299 40.000 0.00 0.00 0.00 2.73
3586 3818 3.838317 TGACTAACCAGTGCTATCCTTGT 59.162 43.478 0.00 0.00 34.21 3.16
3698 3941 3.066190 ACCGAGGATGACGCCGAA 61.066 61.111 0.00 0.00 0.00 4.30
3828 4071 2.819595 CCGATGAACCAGGGCGTG 60.820 66.667 0.00 0.00 0.00 5.34
3893 4136 1.617850 CTGGAAGTGAGCTCAGTGTCT 59.382 52.381 24.53 11.70 0.00 3.41
3935 4178 2.563179 AGTGACCAGCTTGACGTAGAAT 59.437 45.455 0.00 0.00 0.00 2.40
3936 4179 2.924290 GTGACCAGCTTGACGTAGAATC 59.076 50.000 0.00 0.00 0.00 2.52
3950 4193 4.142271 ACGTAGAATCCTGAAGCAGAAGAG 60.142 45.833 0.00 0.00 32.44 2.85
3951 4194 4.097135 CGTAGAATCCTGAAGCAGAAGAGA 59.903 45.833 0.00 0.00 32.44 3.10
3952 4195 4.741321 AGAATCCTGAAGCAGAAGAGAG 57.259 45.455 0.00 0.00 32.44 3.20
3953 4196 3.451902 AGAATCCTGAAGCAGAAGAGAGG 59.548 47.826 0.00 0.00 32.44 3.69
4052 4298 2.136728 TGTTTAATGTGTCGTCGTGGG 58.863 47.619 0.00 0.00 0.00 4.61
4195 4452 1.281577 TGGCTGTGATGCTGATGGTTA 59.718 47.619 0.00 0.00 0.00 2.85
4200 4457 4.337555 GCTGTGATGCTGATGGTTATTCTT 59.662 41.667 0.00 0.00 0.00 2.52
4201 4458 5.163581 GCTGTGATGCTGATGGTTATTCTTT 60.164 40.000 0.00 0.00 0.00 2.52
4202 4459 6.626623 GCTGTGATGCTGATGGTTATTCTTTT 60.627 38.462 0.00 0.00 0.00 2.27
4203 4460 7.230849 TGTGATGCTGATGGTTATTCTTTTT 57.769 32.000 0.00 0.00 0.00 1.94
4204 4461 7.092079 TGTGATGCTGATGGTTATTCTTTTTG 58.908 34.615 0.00 0.00 0.00 2.44
4205 4462 6.532657 GTGATGCTGATGGTTATTCTTTTTGG 59.467 38.462 0.00 0.00 0.00 3.28
4216 4473 8.515414 TGGTTATTCTTTTTGGTTTTGGTTTTG 58.485 29.630 0.00 0.00 0.00 2.44
4234 4544 4.670227 TTTGGTTTTTGCAAGTTTTCCG 57.330 36.364 0.00 0.00 0.00 4.30
4260 4577 4.578105 GGTATTGCTAATCTTTCTGCTGCT 59.422 41.667 0.00 0.00 0.00 4.24
4289 4606 4.202151 GCTGATGGTTTTTCTGTTTGGACT 60.202 41.667 0.00 0.00 0.00 3.85
4290 4607 5.682212 GCTGATGGTTTTTCTGTTTGGACTT 60.682 40.000 0.00 0.00 0.00 3.01
4291 4608 5.901552 TGATGGTTTTTCTGTTTGGACTTC 58.098 37.500 0.00 0.00 0.00 3.01
4292 4609 5.656416 TGATGGTTTTTCTGTTTGGACTTCT 59.344 36.000 0.00 0.00 0.00 2.85
4293 4610 5.993748 TGGTTTTTCTGTTTGGACTTCTT 57.006 34.783 0.00 0.00 0.00 2.52
4294 4611 6.353404 TGGTTTTTCTGTTTGGACTTCTTT 57.647 33.333 0.00 0.00 0.00 2.52
4295 4612 6.394809 TGGTTTTTCTGTTTGGACTTCTTTC 58.605 36.000 0.00 0.00 0.00 2.62
4296 4613 6.210584 TGGTTTTTCTGTTTGGACTTCTTTCT 59.789 34.615 0.00 0.00 0.00 2.52
4297 4614 6.752351 GGTTTTTCTGTTTGGACTTCTTTCTC 59.248 38.462 0.00 0.00 0.00 2.87
4298 4615 7.363007 GGTTTTTCTGTTTGGACTTCTTTCTCT 60.363 37.037 0.00 0.00 0.00 3.10
4299 4616 6.927294 TTTCTGTTTGGACTTCTTTCTCTC 57.073 37.500 0.00 0.00 0.00 3.20
4301 4618 5.848406 TCTGTTTGGACTTCTTTCTCTCTC 58.152 41.667 0.00 0.00 0.00 3.20
4303 4620 5.848406 TGTTTGGACTTCTTTCTCTCTCTC 58.152 41.667 0.00 0.00 0.00 3.20
4305 4622 5.975693 TTGGACTTCTTTCTCTCTCTCTC 57.024 43.478 0.00 0.00 0.00 3.20
4345 4662 0.179124 CGGTGCTGCTCCTAGTCTTC 60.179 60.000 17.64 0.00 0.00 2.87
4350 4667 2.107366 GCTGCTCCTAGTCTTCCTCTT 58.893 52.381 0.00 0.00 0.00 2.85
4352 4669 3.430236 GCTGCTCCTAGTCTTCCTCTTTC 60.430 52.174 0.00 0.00 0.00 2.62
4355 4672 3.430236 GCTCCTAGTCTTCCTCTTTCTGC 60.430 52.174 0.00 0.00 0.00 4.26
4358 4675 2.470983 AGTCTTCCTCTTTCTGCTGC 57.529 50.000 0.00 0.00 0.00 5.25
4359 4676 1.003003 AGTCTTCCTCTTTCTGCTGCC 59.997 52.381 0.00 0.00 0.00 4.85
4363 4680 0.603707 TCCTCTTTCTGCTGCCGTTG 60.604 55.000 0.00 0.00 0.00 4.10
4366 4683 1.208614 CTTTCTGCTGCCGTTGCTC 59.791 57.895 0.00 0.00 38.71 4.26
4377 4694 1.370414 CGTTGCTCGGTTTTGCCAG 60.370 57.895 0.00 0.00 36.97 4.85
4396 4713 1.211449 CGAGTGCGTCTTCAGCTCT 59.789 57.895 0.00 0.00 40.57 4.09
4410 4727 2.029290 TCAGCTCTGGTTTACGGTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
4443 4760 2.603776 AGGAGGAGGCGACGGTTT 60.604 61.111 0.00 0.00 0.00 3.27
4464 4781 1.305297 AGATCACAGGAGGCGTCCA 60.305 57.895 26.40 6.94 46.80 4.02
4485 4802 4.803426 GCTGGGTCGTCTCGCTGG 62.803 72.222 0.00 0.00 0.00 4.85
4622 4945 4.530857 CGGAACCCTAGCCAGCCG 62.531 72.222 0.00 0.00 0.00 5.52
4623 4946 4.858680 GGAACCCTAGCCAGCCGC 62.859 72.222 0.00 0.00 37.98 6.53
4665 5000 2.818274 GCCAGTAGCGGGAAACGG 60.818 66.667 0.00 0.00 44.51 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 2.429235 TAACCCAAAGCCGTTCCCCC 62.429 60.000 0.00 0.00 0.00 5.40
76 77 0.963856 CTAACCCAAAGCCGTTCCCC 60.964 60.000 0.00 0.00 0.00 4.81
77 78 0.963856 CCTAACCCAAAGCCGTTCCC 60.964 60.000 0.00 0.00 0.00 3.97
78 79 0.251033 ACCTAACCCAAAGCCGTTCC 60.251 55.000 0.00 0.00 0.00 3.62
79 80 1.162698 GACCTAACCCAAAGCCGTTC 58.837 55.000 0.00 0.00 0.00 3.95
80 81 0.251033 GGACCTAACCCAAAGCCGTT 60.251 55.000 0.00 0.00 0.00 4.44
131 133 4.881850 CGCCCCTGTGTATATTTTTCTTCT 59.118 41.667 0.00 0.00 0.00 2.85
135 140 3.547746 TCCGCCCCTGTGTATATTTTTC 58.452 45.455 0.00 0.00 0.00 2.29
152 157 1.472480 TCTGCTTTTGGCTTTATCCGC 59.528 47.619 0.00 0.00 42.39 5.54
287 299 9.219603 GAGAAAAGGAAAAGGGATTAAATTTGG 57.780 33.333 0.00 0.00 0.00 3.28
288 300 9.777297 TGAGAAAAGGAAAAGGGATTAAATTTG 57.223 29.630 0.00 0.00 0.00 2.32
305 317 7.421530 TCTCACGTAATCTTTTGAGAAAAGG 57.578 36.000 8.55 0.00 46.11 3.11
517 537 4.821589 GCGGGGAAGACGGAGCTG 62.822 72.222 0.00 0.00 0.00 4.24
571 597 1.856802 GGGAAACACAAAAGCAGCAG 58.143 50.000 0.00 0.00 0.00 4.24
590 616 7.075741 ACAAAAGACAAGAAAATAATCGGTCG 58.924 34.615 0.00 0.00 35.24 4.79
594 620 7.075741 ACGGACAAAAGACAAGAAAATAATCG 58.924 34.615 0.00 0.00 0.00 3.34
811 849 5.799827 ATGACGGGAAAAATGAGGAAAAA 57.200 34.783 0.00 0.00 0.00 1.94
812 850 5.799827 AATGACGGGAAAAATGAGGAAAA 57.200 34.783 0.00 0.00 0.00 2.29
813 851 5.537188 CAAATGACGGGAAAAATGAGGAAA 58.463 37.500 0.00 0.00 0.00 3.13
814 852 4.560513 GCAAATGACGGGAAAAATGAGGAA 60.561 41.667 0.00 0.00 0.00 3.36
815 853 3.056891 GCAAATGACGGGAAAAATGAGGA 60.057 43.478 0.00 0.00 0.00 3.71
816 854 3.253230 GCAAATGACGGGAAAAATGAGG 58.747 45.455 0.00 0.00 0.00 3.86
817 855 2.916716 CGCAAATGACGGGAAAAATGAG 59.083 45.455 0.00 0.00 0.00 2.90
818 856 2.940147 CGCAAATGACGGGAAAAATGA 58.060 42.857 0.00 0.00 0.00 2.57
844 882 1.409427 GTATCTTGGGACGAGTGGGAG 59.591 57.143 0.00 0.00 0.00 4.30
1033 1075 4.888325 CCTCCCGGCCATCCCTCT 62.888 72.222 2.24 0.00 0.00 3.69
1263 1305 1.016130 CCATGTTGAGCTCGAACGCT 61.016 55.000 4.86 0.00 44.33 5.07
1305 1347 3.192230 TACTTCATTGCGCGGCCG 61.192 61.111 24.05 24.05 37.57 6.13
1306 1348 2.403586 GTACTTCATTGCGCGGCC 59.596 61.111 8.83 0.00 0.00 6.13
1307 1349 2.021380 CGTACTTCATTGCGCGGC 59.979 61.111 8.83 0.00 0.00 6.53
1308 1350 2.701006 CCGTACTTCATTGCGCGG 59.299 61.111 8.83 0.00 0.00 6.46
1309 1351 2.021380 GCCGTACTTCATTGCGCG 59.979 61.111 0.00 0.00 0.00 6.86
1386 1444 4.778143 GAATCACCGGGCGCCACT 62.778 66.667 30.85 6.31 0.00 4.00
1614 1672 7.505923 GGGCAGGTAAATAATTCCTCTAATTGT 59.494 37.037 0.00 0.00 38.29 2.71
1668 1730 5.925509 AGGCTAGGCAGTAAATTTCGAATA 58.074 37.500 19.70 0.00 0.00 1.75
1772 1834 4.276926 AGGCTACAGTTTGAAAAGCAAGAG 59.723 41.667 2.27 0.00 37.87 2.85
1912 1981 6.879458 AGACACACAAGACTTCAGTTAAAAGT 59.121 34.615 0.00 0.00 39.61 2.66
1913 1982 7.148407 ACAGACACACAAGACTTCAGTTAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
1940 2009 5.621228 GCGACACATTTTAAACTTCAGTCAG 59.379 40.000 0.00 0.00 0.00 3.51
1989 2058 4.111916 CACCAAGAACATGTTCAAACACC 58.888 43.478 33.92 11.57 42.51 4.16
1998 2071 6.959639 AATACAGTTTCACCAAGAACATGT 57.040 33.333 0.00 0.00 38.23 3.21
2188 2263 9.190858 GCATTTGTAGTTACATTGTGAAAATCA 57.809 29.630 0.00 0.00 35.89 2.57
2189 2264 9.410556 AGCATTTGTAGTTACATTGTGAAAATC 57.589 29.630 0.00 0.00 35.89 2.17
2190 2265 9.410556 GAGCATTTGTAGTTACATTGTGAAAAT 57.589 29.630 0.00 0.00 35.89 1.82
2199 2274 4.396166 GCTGTGGAGCATTTGTAGTTACAT 59.604 41.667 0.00 0.00 45.46 2.29
2213 2295 1.580845 ATTCGCAAGTGCTGTGGAGC 61.581 55.000 1.21 0.00 46.44 4.70
2214 2296 1.725641 TATTCGCAAGTGCTGTGGAG 58.274 50.000 1.21 0.00 39.32 3.86
2228 2310 4.685169 ATGCACCACTCAAAGTTATTCG 57.315 40.909 0.00 0.00 0.00 3.34
2244 2326 1.153706 GCCACATCCTGCAATGCAC 60.154 57.895 2.72 0.00 33.79 4.57
2433 2515 5.813157 TCGAACTTTTGTATATCGGCAATCA 59.187 36.000 0.00 0.00 32.78 2.57
2434 2516 6.200286 TCTCGAACTTTTGTATATCGGCAATC 59.800 38.462 0.00 0.00 32.78 2.67
2456 2538 5.649782 TTTGATCAGGCCTCATTTTTCTC 57.350 39.130 0.00 0.00 0.00 2.87
2457 2539 6.042437 AGTTTTTGATCAGGCCTCATTTTTCT 59.958 34.615 0.00 0.00 0.00 2.52
2458 2540 6.146673 CAGTTTTTGATCAGGCCTCATTTTTC 59.853 38.462 0.00 0.00 0.00 2.29
2459 2541 5.993441 CAGTTTTTGATCAGGCCTCATTTTT 59.007 36.000 0.00 0.00 0.00 1.94
2460 2542 5.305128 TCAGTTTTTGATCAGGCCTCATTTT 59.695 36.000 0.00 0.00 0.00 1.82
2461 2543 4.834496 TCAGTTTTTGATCAGGCCTCATTT 59.166 37.500 0.00 0.00 0.00 2.32
2462 2544 4.410099 TCAGTTTTTGATCAGGCCTCATT 58.590 39.130 0.00 0.00 0.00 2.57
2463 2545 4.038271 TCAGTTTTTGATCAGGCCTCAT 57.962 40.909 0.00 0.00 0.00 2.90
2464 2546 3.507162 TCAGTTTTTGATCAGGCCTCA 57.493 42.857 0.00 0.00 0.00 3.86
2465 2547 4.853924 TTTCAGTTTTTGATCAGGCCTC 57.146 40.909 0.00 0.00 35.27 4.70
2466 2548 5.105595 GCTATTTCAGTTTTTGATCAGGCCT 60.106 40.000 0.00 0.00 35.27 5.19
2467 2549 5.105063 GCTATTTCAGTTTTTGATCAGGCC 58.895 41.667 0.00 0.00 35.27 5.19
2468 2550 5.713025 TGCTATTTCAGTTTTTGATCAGGC 58.287 37.500 0.00 0.00 35.27 4.85
2469 2551 6.917533 ACTGCTATTTCAGTTTTTGATCAGG 58.082 36.000 0.00 0.00 44.26 3.86
2488 2570 3.696051 ACAGTGATTTCAACACAACTGCT 59.304 39.130 0.00 0.00 40.25 4.24
2490 2572 4.096231 TCCACAGTGATTTCAACACAACTG 59.904 41.667 0.62 0.00 40.25 3.16
2501 2583 1.608590 CAAAGCCGTCCACAGTGATTT 59.391 47.619 0.62 0.00 0.00 2.17
2577 2663 3.764434 ACGATCCAGACAGTGACAGTATT 59.236 43.478 0.00 0.00 0.00 1.89
2634 2720 2.676163 AAACACTCAGCCCACCGGTC 62.676 60.000 2.59 0.00 0.00 4.79
2658 2744 3.197790 CGGCCATCAGGACTTGCG 61.198 66.667 2.24 0.00 42.67 4.85
2735 2821 3.565307 AGATTTGAGGCTGGTGTGAAAA 58.435 40.909 0.00 0.00 0.00 2.29
2758 2844 8.102676 ACTATGGCTGCACATATATGATTTACA 58.897 33.333 19.63 10.53 33.22 2.41
2796 2882 5.876651 TCATCAGGAATGCTATGTACAGT 57.123 39.130 0.33 0.00 35.17 3.55
2797 2883 6.765036 AGTTTCATCAGGAATGCTATGTACAG 59.235 38.462 0.33 0.00 34.91 2.74
2798 2884 6.653020 AGTTTCATCAGGAATGCTATGTACA 58.347 36.000 0.00 0.00 34.91 2.90
2799 2885 7.559590 AAGTTTCATCAGGAATGCTATGTAC 57.440 36.000 0.00 0.00 34.91 2.90
2800 2886 8.049117 AGAAAGTTTCATCAGGAATGCTATGTA 58.951 33.333 17.65 0.00 34.91 2.29
2826 2912 8.457238 TGTATTTTGGCATATGCAATGTACTA 57.543 30.769 28.07 8.44 44.36 1.82
2827 2913 7.345422 TGTATTTTGGCATATGCAATGTACT 57.655 32.000 28.07 9.35 44.36 2.73
2828 2914 6.144402 GCTGTATTTTGGCATATGCAATGTAC 59.856 38.462 28.07 20.88 44.36 2.90
2866 2952 3.734902 GCTGGGACGAAAATATGCAAAGG 60.735 47.826 0.00 0.00 0.00 3.11
2889 2975 9.289782 AGTAAAGAAACTGAAGAATGCTAACAT 57.710 29.630 0.00 0.00 38.49 2.71
3011 3097 1.064505 CGCTGAAACCGAATCATGCAT 59.935 47.619 0.00 0.00 0.00 3.96
3017 3103 3.554324 TGCTAATACGCTGAAACCGAATC 59.446 43.478 0.00 0.00 0.00 2.52
3048 3134 1.343069 ACCCAGGAGACAGACAGTTC 58.657 55.000 0.00 0.00 0.00 3.01
3134 3222 9.666626 GAATAGAATCATGAAGCAGAATTCAAG 57.333 33.333 8.44 0.69 42.21 3.02
3141 3229 6.490241 TGAGGAATAGAATCATGAAGCAGA 57.510 37.500 0.00 0.00 0.00 4.26
3194 3282 3.028850 CCTATGACGTGGAAACCCTAGA 58.971 50.000 0.00 0.00 0.00 2.43
3199 3287 1.940613 GATGCCTATGACGTGGAAACC 59.059 52.381 0.00 0.00 0.00 3.27
3208 3296 4.833380 TCTTAGTAGGTGGATGCCTATGAC 59.167 45.833 0.00 0.00 42.46 3.06
3213 3301 3.900601 CTGATCTTAGTAGGTGGATGCCT 59.099 47.826 0.00 0.00 42.43 4.75
3229 3317 9.950496 TTTTTCTTGCTAATAGAGAACTGATCT 57.050 29.630 0.00 0.00 42.61 2.75
3262 3350 7.121168 AGGAATCACTCAAAAGCGAAATTATGA 59.879 33.333 0.00 0.00 0.00 2.15
3277 3365 4.630644 AAAGAAGCAGAGGAATCACTCA 57.369 40.909 0.00 0.00 39.97 3.41
3278 3366 5.580297 CAGTAAAGAAGCAGAGGAATCACTC 59.420 44.000 0.00 0.00 37.77 3.51
3279 3367 5.486526 CAGTAAAGAAGCAGAGGAATCACT 58.513 41.667 0.00 0.00 0.00 3.41
3280 3368 4.094146 GCAGTAAAGAAGCAGAGGAATCAC 59.906 45.833 0.00 0.00 0.00 3.06
3281 3369 4.256920 GCAGTAAAGAAGCAGAGGAATCA 58.743 43.478 0.00 0.00 0.00 2.57
3282 3370 4.256920 TGCAGTAAAGAAGCAGAGGAATC 58.743 43.478 0.00 0.00 33.75 2.52
3291 3379 2.160417 ACGATTGCTGCAGTAAAGAAGC 59.840 45.455 21.35 2.03 40.79 3.86
3341 3447 3.262420 TCGCTAGAAAAGATTGGCAGTC 58.738 45.455 1.12 1.12 0.00 3.51
3343 3449 4.685169 TTTCGCTAGAAAAGATTGGCAG 57.315 40.909 0.00 0.00 42.78 4.85
3376 3482 8.396272 ACTGAAGAATGCTAATACACTGTTTT 57.604 30.769 0.00 0.00 0.00 2.43
3377 3483 7.986085 ACTGAAGAATGCTAATACACTGTTT 57.014 32.000 0.00 0.00 0.00 2.83
3385 3491 9.658799 GGAGCAATATACTGAAGAATGCTAATA 57.341 33.333 0.00 0.00 42.24 0.98
3386 3492 8.381636 AGGAGCAATATACTGAAGAATGCTAAT 58.618 33.333 0.00 0.00 42.24 1.73
3387 3493 7.739825 AGGAGCAATATACTGAAGAATGCTAA 58.260 34.615 0.00 0.00 42.24 3.09
3388 3494 7.308450 AGGAGCAATATACTGAAGAATGCTA 57.692 36.000 0.00 0.00 42.24 3.49
3389 3495 6.185114 AGGAGCAATATACTGAAGAATGCT 57.815 37.500 0.00 0.00 44.61 3.79
3390 3496 9.829507 ATATAGGAGCAATATACTGAAGAATGC 57.170 33.333 0.00 0.00 0.00 3.56
3407 3513 6.038271 ACAACGTGAATCCAAAATATAGGAGC 59.962 38.462 0.00 0.00 37.34 4.70
3413 3578 7.040062 TCCTGAAACAACGTGAATCCAAAATAT 60.040 33.333 0.00 0.00 0.00 1.28
3414 3579 6.263392 TCCTGAAACAACGTGAATCCAAAATA 59.737 34.615 0.00 0.00 0.00 1.40
3420 3585 4.766404 AATCCTGAAACAACGTGAATCC 57.234 40.909 0.00 0.00 0.00 3.01
3422 3587 9.191995 GAAATAAAATCCTGAAACAACGTGAAT 57.808 29.630 0.00 0.00 0.00 2.57
3427 3592 8.076178 AGTGAGAAATAAAATCCTGAAACAACG 58.924 33.333 0.00 0.00 0.00 4.10
3432 3660 8.109634 AGGCTAGTGAGAAATAAAATCCTGAAA 58.890 33.333 0.00 0.00 0.00 2.69
3437 3665 5.009110 GGCAGGCTAGTGAGAAATAAAATCC 59.991 44.000 0.00 0.00 0.00 3.01
3458 3686 8.107095 AGTCTAGGAAAGTAATTGTAAATGGCA 58.893 33.333 0.00 0.00 0.00 4.92
3460 3688 9.892130 AGAGTCTAGGAAAGTAATTGTAAATGG 57.108 33.333 0.00 0.00 0.00 3.16
3463 3691 9.096823 TGGAGAGTCTAGGAAAGTAATTGTAAA 57.903 33.333 0.00 0.00 0.00 2.01
3470 3702 6.253758 TGATGTGGAGAGTCTAGGAAAGTAA 58.746 40.000 0.00 0.00 0.00 2.24
3497 3729 6.657966 ACTGATCTAATATGTGGATGCCAATG 59.342 38.462 0.00 0.00 34.18 2.82
3498 3730 6.787170 ACTGATCTAATATGTGGATGCCAAT 58.213 36.000 0.00 0.00 34.18 3.16
3499 3731 6.191657 ACTGATCTAATATGTGGATGCCAA 57.808 37.500 0.00 0.00 34.18 4.52
3500 3732 5.830799 ACTGATCTAATATGTGGATGCCA 57.169 39.130 0.00 0.00 0.00 4.92
3501 3733 6.815641 CAGTACTGATCTAATATGTGGATGCC 59.184 42.308 18.45 0.00 0.00 4.40
3502 3734 7.382110 ACAGTACTGATCTAATATGTGGATGC 58.618 38.462 29.30 0.00 0.00 3.91
3542 3774 8.421784 AGTCACTGACTCATTTCTTTAGTGTAA 58.578 33.333 5.82 0.00 38.71 2.41
3550 3782 6.174720 TGGTTAGTCACTGACTCATTTCTT 57.825 37.500 15.20 0.00 42.40 2.52
3556 3788 2.035961 GCACTGGTTAGTCACTGACTCA 59.964 50.000 15.20 6.89 42.40 3.41
3557 3789 2.297597 AGCACTGGTTAGTCACTGACTC 59.702 50.000 15.20 2.32 42.40 3.36
3558 3790 2.320781 AGCACTGGTTAGTCACTGACT 58.679 47.619 16.00 16.00 45.54 3.41
3559 3791 2.821991 AGCACTGGTTAGTCACTGAC 57.178 50.000 0.38 0.38 34.07 3.51
3560 3792 3.447586 GGATAGCACTGGTTAGTCACTGA 59.552 47.826 0.00 0.00 34.07 3.41
3561 3793 3.449018 AGGATAGCACTGGTTAGTCACTG 59.551 47.826 0.00 0.00 34.07 3.66
3562 3794 3.714144 AGGATAGCACTGGTTAGTCACT 58.286 45.455 0.00 0.00 34.07 3.41
3563 3795 4.184629 CAAGGATAGCACTGGTTAGTCAC 58.815 47.826 0.00 0.00 34.07 3.67
3618 3852 2.509561 GCCTTCTTCTCGGCGACC 60.510 66.667 4.99 0.00 36.45 4.79
3893 4136 1.810853 CGACGATGGCATGCAGACA 60.811 57.895 21.36 8.94 41.62 3.41
3935 4178 1.077828 TCCCTCTCTTCTGCTTCAGGA 59.922 52.381 0.00 0.00 31.51 3.86
3936 4179 1.566211 TCCCTCTCTTCTGCTTCAGG 58.434 55.000 0.00 0.00 31.51 3.86
4052 4298 1.467342 GACATCCGGGCTAACAACAAC 59.533 52.381 0.00 0.00 0.00 3.32
4150 4406 2.375174 ACCCAGCAGAGAACACCAATTA 59.625 45.455 0.00 0.00 0.00 1.40
4152 4408 0.773644 ACCCAGCAGAGAACACCAAT 59.226 50.000 0.00 0.00 0.00 3.16
4195 4452 7.531857 AACCAAAACCAAAACCAAAAAGAAT 57.468 28.000 0.00 0.00 0.00 2.40
4200 4457 5.753438 GCAAAAACCAAAACCAAAACCAAAA 59.247 32.000 0.00 0.00 0.00 2.44
4201 4458 5.163457 TGCAAAAACCAAAACCAAAACCAAA 60.163 32.000 0.00 0.00 0.00 3.28
4202 4459 4.340950 TGCAAAAACCAAAACCAAAACCAA 59.659 33.333 0.00 0.00 0.00 3.67
4203 4460 3.888930 TGCAAAAACCAAAACCAAAACCA 59.111 34.783 0.00 0.00 0.00 3.67
4204 4461 4.505313 TGCAAAAACCAAAACCAAAACC 57.495 36.364 0.00 0.00 0.00 3.27
4205 4462 5.524284 ACTTGCAAAAACCAAAACCAAAAC 58.476 33.333 0.00 0.00 0.00 2.43
4216 4473 2.350192 CACCGGAAAACTTGCAAAAACC 59.650 45.455 9.46 0.00 0.00 3.27
4234 4544 4.884164 AGCAGAAAGATTAGCAATACCACC 59.116 41.667 0.00 0.00 0.00 4.61
4260 4577 3.890756 ACAGAAAAACCATCAGCATCACA 59.109 39.130 0.00 0.00 0.00 3.58
4320 4637 0.618458 TAGGAGCAGCACCGGAAAAT 59.382 50.000 9.46 0.00 0.00 1.82
4327 4644 0.176910 GGAAGACTAGGAGCAGCACC 59.823 60.000 0.00 0.00 0.00 5.01
4345 4662 1.871772 CAACGGCAGCAGAAAGAGG 59.128 57.895 0.00 0.00 0.00 3.69
4350 4667 3.043713 CGAGCAACGGCAGCAGAA 61.044 61.111 0.00 0.00 44.61 3.02
4359 4676 1.370414 CTGGCAAAACCGAGCAACG 60.370 57.895 0.00 0.00 43.94 4.10
4363 4680 3.314388 CTCGCTGGCAAAACCGAGC 62.314 63.158 11.63 0.00 43.94 5.03
4366 4683 2.252260 CACTCGCTGGCAAAACCG 59.748 61.111 0.00 0.00 43.94 4.44
4377 4694 2.431601 AGCTGAAGACGCACTCGC 60.432 61.111 0.00 0.00 39.84 5.03
4412 4729 4.462133 CCTCCTCCTGAAGACGTATTCTA 58.538 47.826 22.26 9.17 32.51 2.10
4431 4748 1.404391 TGATCTCTAAACCGTCGCCTC 59.596 52.381 0.00 0.00 0.00 4.70
4443 4760 1.681538 GACGCCTCCTGTGATCTCTA 58.318 55.000 0.00 0.00 0.00 2.43
4464 4781 3.069980 GCGAGACGACCCAGCATCT 62.070 63.158 0.00 0.00 0.00 2.90
4485 4802 0.678048 GAAGATGTGGGACCCAGCAC 60.678 60.000 15.52 8.06 32.34 4.40
4623 4946 3.238497 TCCGGCGATACCCATGGG 61.238 66.667 30.23 30.23 42.03 4.00
4661 4996 2.231540 CTCCTCCTCCTCCTCCCGTT 62.232 65.000 0.00 0.00 0.00 4.44
4665 5000 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
4705 5043 0.314302 CCCTCCTAATCTACACCGCG 59.686 60.000 0.00 0.00 0.00 6.46
4706 5044 0.680061 CCCCTCCTAATCTACACCGC 59.320 60.000 0.00 0.00 0.00 5.68
4707 5045 2.240279 CTCCCCTCCTAATCTACACCG 58.760 57.143 0.00 0.00 0.00 4.94
4708 5046 2.179424 TCCTCCCCTCCTAATCTACACC 59.821 54.545 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.