Multiple sequence alignment - TraesCS5B01G478200

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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 TraesCS5B01G478200 chr5B 100.000 2502 0 0 1 2502 650054644 650052143 0.000000e+00 4621.0
1 TraesCS5B01G478200 chr5B 85.851 629 53 11 1228 1821 650124336 650123709 9.760000e-179 636.0
2 TraesCS5B01G478200 chr5B 83.282 646 73 12 1 621 650047229 650046594 1.680000e-156 562.0
3 TraesCS5B01G478200 chr5B 85.043 575 45 19 632 1181 650046613 650046055 4.710000e-152 547.0
4 TraesCS5B01G478200 chr5B 88.544 419 36 7 2086 2502 650062456 650062048 4.810000e-137 497.0
5 TraesCS5B01G478200 chr5B 84.099 283 26 12 2166 2445 417800109 417800375 3.190000e-64 255.0
6 TraesCS5B01G478200 chr5B 87.562 201 24 1 2088 2287 650127311 650127111 5.380000e-57 231.0
7 TraesCS5B01G478200 chr5B 81.553 309 29 12 1235 1528 650132542 650132247 1.940000e-56 230.0
8 TraesCS5B01G478200 chr5B 89.189 74 3 2 1905 1978 650052622 650052554 1.230000e-13 87.9
9 TraesCS5B01G478200 chr5B 89.189 74 3 2 2023 2091 650052740 650052667 1.230000e-13 87.9
10 TraesCS5B01G478200 chr5B 82.667 75 11 2 2382 2455 417863530 417863457 5.780000e-07 65.8
11 TraesCS5B01G478200 chr5D 85.529 850 62 23 1219 2015 517590920 517590079 0.000000e+00 832.0
12 TraesCS5B01G478200 chr5D 84.169 638 74 12 1 621 517522736 517522109 5.960000e-166 593.0
13 TraesCS5B01G478200 chr5D 85.635 543 49 15 632 1160 517522128 517521601 6.090000e-151 544.0
14 TraesCS5B01G478200 chr5D 91.089 303 18 5 2203 2502 517589435 517589139 3.880000e-108 401.0
15 TraesCS5B01G478200 chr5D 87.037 216 20 7 1184 1398 517600227 517600019 1.160000e-58 237.0
16 TraesCS5B01G478200 chr5D 79.791 287 33 16 885 1160 517600564 517600292 4.250000e-43 185.0
17 TraesCS5B01G478200 chr5D 88.525 61 5 2 2385 2445 243313099 243313157 3.450000e-09 73.1
18 TraesCS5B01G478200 chr5D 83.824 68 9 2 2382 2448 353759480 353759414 2.080000e-06 63.9
19 TraesCS5B01G478200 chr5D 94.286 35 2 0 264 298 517600558 517600524 1.000000e-03 54.7
20 TraesCS5B01G478200 chr5A 85.340 839 76 19 1219 2014 644920149 644919315 0.000000e+00 824.0
21 TraesCS5B01G478200 chr5A 87.738 367 32 7 795 1160 644911317 644910963 1.380000e-112 416.0
22 TraesCS5B01G478200 chr5A 81.466 491 55 20 1 472 644917791 644917318 1.090000e-98 370.0
23 TraesCS5B01G478200 chr5A 78.479 618 70 37 1221 1797 644910793 644910198 1.840000e-91 346.0
24 TraesCS5B01G478200 chr5A 86.164 318 36 5 2088 2403 644939177 644938866 1.110000e-88 337.0
25 TraesCS5B01G478200 chr5A 90.533 169 10 2 1235 1398 644923037 644922870 4.190000e-53 219.0
26 TraesCS5B01G478200 chr5A 79.878 328 41 15 1606 1914 644922368 644922047 1.510000e-52 217.0
27 TraesCS5B01G478200 chr5A 89.655 87 8 1 1928 2014 644939272 644939187 2.630000e-20 110.0
28 TraesCS5B01G478200 chr5A 97.297 37 1 0 264 300 644920667 644920631 2.080000e-06 63.9
29 TraesCS5B01G478200 chr5A 89.362 47 5 0 2045 2091 644939269 644939223 2.690000e-05 60.2
30 TraesCS5B01G478200 chr6D 81.588 277 42 6 2088 2361 430272565 430272295 1.160000e-53 220.0
31 TraesCS5B01G478200 chr7B 76.382 398 63 12 2086 2459 140852951 140852561 4.250000e-43 185.0
32 TraesCS5B01G478200 chr2D 76.923 325 58 11 2143 2458 80221694 80221378 4.280000e-38 169.0
33 TraesCS5B01G478200 chr4A 79.268 164 19 7 2103 2263 511918164 511918013 1.580000e-17 100.0
34 TraesCS5B01G478200 chr4A 87.879 66 7 1 2377 2441 511917908 511917843 2.670000e-10 76.8
35 TraesCS5B01G478200 chr2A 82.500 80 11 3 2380 2457 591754882 591754804 1.610000e-07 67.6


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 TraesCS5B01G478200 chr5B 650052143 650054644 2501 True 1598.933333 4621 92.792667 1 2502 3 chr5B.!!$R5 2501
1 TraesCS5B01G478200 chr5B 650046055 650047229 1174 True 554.500000 562 84.162500 1 1181 2 chr5B.!!$R4 1180
2 TraesCS5B01G478200 chr5B 650123709 650127311 3602 True 433.500000 636 86.706500 1228 2287 2 chr5B.!!$R6 1059
3 TraesCS5B01G478200 chr5D 517589139 517590920 1781 True 616.500000 832 88.309000 1219 2502 2 chr5D.!!$R3 1283
4 TraesCS5B01G478200 chr5D 517521601 517522736 1135 True 568.500000 593 84.902000 1 1160 2 chr5D.!!$R2 1159
5 TraesCS5B01G478200 chr5A 644910198 644911317 1119 True 381.000000 416 83.108500 795 1797 2 chr5A.!!$R1 1002
6 TraesCS5B01G478200 chr5A 644917318 644923037 5719 True 338.780000 824 86.902800 1 2014 5 chr5A.!!$R2 2013

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
998 3171 0.319297 GAGTTGCTTGCAGCTTTGGG 60.319 55.0 12.84 0.0 42.97 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 4579 0.037975 GCTTCAAACACATGCAGGGG 60.038 55.0 0.0 0.0 0.0 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 692 8.506168 TTGTATTCTGGTTCATTGGTCTATTC 57.494 34.615 0.00 0.00 0.00 1.75
111 1811 4.111916 GACACTGACAAACACAAAATGGG 58.888 43.478 0.00 0.00 0.00 4.00
114 1814 1.833630 TGACAAACACAAAATGGGGCA 59.166 42.857 0.00 0.00 0.00 5.36
137 1837 4.036852 AGCAAAGCACACTTTCCTTCTAAC 59.963 41.667 0.00 0.00 44.41 2.34
196 1896 1.987807 ATGGACGGGGCATGGAAGAG 61.988 60.000 0.00 0.00 0.00 2.85
203 1903 0.692419 GGGCATGGAAGAGGGAGAGA 60.692 60.000 0.00 0.00 0.00 3.10
211 1911 3.729524 TGGAAGAGGGAGAGATGGAGATA 59.270 47.826 0.00 0.00 0.00 1.98
232 2368 1.331214 ATGCCCAACAAGTCCAAGTG 58.669 50.000 0.00 0.00 0.00 3.16
234 2370 0.668535 GCCCAACAAGTCCAAGTGAC 59.331 55.000 0.00 0.00 44.82 3.67
253 2389 2.544267 GACGGAAAAGACACAAGACCAG 59.456 50.000 0.00 0.00 0.00 4.00
255 2391 2.484770 CGGAAAAGACACAAGACCAGGA 60.485 50.000 0.00 0.00 0.00 3.86
260 2396 5.505181 AAAGACACAAGACCAGGATATGT 57.495 39.130 0.00 0.00 0.00 2.29
316 2469 1.742880 CAGGACCTACCGACGACGA 60.743 63.158 9.28 0.00 44.74 4.20
344 2497 0.322008 CTGTTTGGGAGAGCAGGTCC 60.322 60.000 0.00 0.00 0.00 4.46
385 2538 0.832135 TCCTGCGTGGGAAGAAGAGT 60.832 55.000 0.00 0.00 36.20 3.24
395 2548 5.105473 CGTGGGAAGAAGAGTGATAAGGTTA 60.105 44.000 0.00 0.00 0.00 2.85
403 2556 4.695606 AGAGTGATAAGGTTACTGGGGAA 58.304 43.478 0.00 0.00 0.00 3.97
404 2557 5.289510 AGAGTGATAAGGTTACTGGGGAAT 58.710 41.667 0.00 0.00 0.00 3.01
410 2563 1.831736 AGGTTACTGGGGAATGTCTCG 59.168 52.381 0.00 0.00 0.00 4.04
411 2564 1.134491 GGTTACTGGGGAATGTCTCGG 60.134 57.143 0.00 0.00 0.00 4.63
412 2565 0.539986 TTACTGGGGAATGTCTCGGC 59.460 55.000 0.00 0.00 0.00 5.54
414 2567 4.467084 TGGGGAATGTCTCGGCGC 62.467 66.667 0.00 0.00 0.00 6.53
456 2609 1.174078 TGCCTACGTCCACGACTTCA 61.174 55.000 6.03 0.00 43.02 3.02
466 2619 2.298163 TCCACGACTTCAACTACTTCCC 59.702 50.000 0.00 0.00 0.00 3.97
469 2622 1.403780 CGACTTCAACTACTTCCCCGG 60.404 57.143 0.00 0.00 0.00 5.73
498 2651 1.134936 CCGACGATATGGGTGACAACA 60.135 52.381 0.00 0.00 0.00 3.33
499 2652 2.612604 CGACGATATGGGTGACAACAA 58.387 47.619 0.00 0.00 0.00 2.83
500 2653 3.194861 CGACGATATGGGTGACAACAAT 58.805 45.455 0.00 0.00 0.00 2.71
544 2697 3.272364 TTGAAGCCTCTGCCGCCAT 62.272 57.895 0.00 0.00 38.69 4.40
546 2699 1.596477 GAAGCCTCTGCCGCCATAG 60.596 63.158 0.00 0.00 38.69 2.23
547 2700 2.317149 GAAGCCTCTGCCGCCATAGT 62.317 60.000 0.00 0.00 38.69 2.12
553 2706 2.627945 CTCTGCCGCCATAGTTTTGTA 58.372 47.619 0.00 0.00 0.00 2.41
558 2711 3.189702 TGCCGCCATAGTTTTGTACTTTC 59.810 43.478 0.00 0.00 38.33 2.62
559 2712 3.726782 GCCGCCATAGTTTTGTACTTTCG 60.727 47.826 0.00 0.00 38.33 3.46
580 2738 9.451002 CTTTCGAACTAGAGGGTATGATCTATA 57.549 37.037 0.00 0.00 0.00 1.31
618 2776 4.394920 CCGTTCATGTGTTAGCCATACTTT 59.605 41.667 0.00 0.00 0.00 2.66
619 2777 5.106317 CCGTTCATGTGTTAGCCATACTTTT 60.106 40.000 0.00 0.00 0.00 2.27
620 2778 6.378582 CGTTCATGTGTTAGCCATACTTTTT 58.621 36.000 0.00 0.00 0.00 1.94
640 2798 4.314740 TTTTTGGTGGTGATGTGTTAGC 57.685 40.909 0.00 0.00 0.00 3.09
641 2799 1.904287 TTGGTGGTGATGTGTTAGCC 58.096 50.000 0.00 0.00 0.00 3.93
642 2800 0.767998 TGGTGGTGATGTGTTAGCCA 59.232 50.000 0.00 0.00 0.00 4.75
643 2801 1.354031 TGGTGGTGATGTGTTAGCCAT 59.646 47.619 0.00 0.00 0.00 4.40
644 2802 2.573915 TGGTGGTGATGTGTTAGCCATA 59.426 45.455 0.00 0.00 0.00 2.74
645 2803 2.943033 GGTGGTGATGTGTTAGCCATAC 59.057 50.000 0.00 0.00 0.00 2.39
646 2804 3.370527 GGTGGTGATGTGTTAGCCATACT 60.371 47.826 0.00 0.00 0.00 2.12
647 2805 4.261801 GTGGTGATGTGTTAGCCATACTT 58.738 43.478 0.00 0.00 0.00 2.24
648 2806 4.094887 GTGGTGATGTGTTAGCCATACTTG 59.905 45.833 0.00 0.00 0.00 3.16
649 2807 4.261801 GGTGATGTGTTAGCCATACTTGT 58.738 43.478 0.00 0.00 0.00 3.16
650 2808 4.700213 GGTGATGTGTTAGCCATACTTGTT 59.300 41.667 0.00 0.00 0.00 2.83
710 2868 4.220602 TGCTCACATGTTTAGCTCTCAGTA 59.779 41.667 23.61 5.89 37.16 2.74
713 2871 5.111989 TCACATGTTTAGCTCTCAGTATGC 58.888 41.667 0.00 0.00 34.76 3.14
730 2888 9.358872 CTCAGTATGCGATTAATATTCTTAGCA 57.641 33.333 9.82 9.82 37.77 3.49
748 2906 8.907222 TCTTAGCAATGTCATCATGCTTTATA 57.093 30.769 15.44 0.00 38.41 0.98
756 2914 6.834876 TGTCATCATGCTTTATATGCGAATC 58.165 36.000 0.00 0.00 0.00 2.52
757 2915 6.427547 TGTCATCATGCTTTATATGCGAATCA 59.572 34.615 0.00 0.00 0.00 2.57
856 3020 6.126507 TGGAGAATTGGAGATGTATGCCTAAA 60.127 38.462 0.00 0.00 0.00 1.85
857 3021 6.429385 GGAGAATTGGAGATGTATGCCTAAAG 59.571 42.308 0.00 0.00 0.00 1.85
859 3023 5.912149 ATTGGAGATGTATGCCTAAAGGA 57.088 39.130 0.00 0.00 37.39 3.36
897 3061 0.959372 CAAGCCAAGCCAGGAGTCAG 60.959 60.000 0.00 0.00 0.00 3.51
963 3127 2.634982 TGACGCAGAAAATTGGCATC 57.365 45.000 0.00 0.00 0.00 3.91
971 3135 4.676196 GCAGAAAATTGGCATCGAACATCT 60.676 41.667 0.00 0.00 0.00 2.90
989 3162 7.412346 CGAACATCTATATATGGAGTTGCTTGC 60.412 40.741 14.23 0.00 0.00 4.01
998 3171 0.319297 GAGTTGCTTGCAGCTTTGGG 60.319 55.000 12.84 0.00 42.97 4.12
1025 3198 4.081198 ACACAACCACAACAAAACCATCAT 60.081 37.500 0.00 0.00 0.00 2.45
1028 3201 5.114780 CAACCACAACAAAACCATCATTCA 58.885 37.500 0.00 0.00 0.00 2.57
1034 3207 5.163561 ACAACAAAACCATCATTCAACGAGT 60.164 36.000 0.00 0.00 0.00 4.18
1036 3209 6.241207 ACAAAACCATCATTCAACGAGTAG 57.759 37.500 0.00 0.00 0.00 2.57
1038 3211 6.655003 ACAAAACCATCATTCAACGAGTAGAT 59.345 34.615 0.00 0.00 0.00 1.98
1039 3212 6.910536 AAACCATCATTCAACGAGTAGATC 57.089 37.500 0.00 0.00 0.00 2.75
1078 3251 1.967319 TTGCTCCACAAGTTCAGGAC 58.033 50.000 0.00 0.00 33.24 3.85
1079 3252 0.108585 TGCTCCACAAGTTCAGGACC 59.891 55.000 0.00 0.00 0.00 4.46
1080 3253 0.108585 GCTCCACAAGTTCAGGACCA 59.891 55.000 0.00 0.00 0.00 4.02
1082 3255 2.222027 CTCCACAAGTTCAGGACCAAC 58.778 52.381 0.00 0.00 0.00 3.77
1083 3256 1.133915 TCCACAAGTTCAGGACCAACC 60.134 52.381 0.00 0.00 39.35 3.77
1085 3258 2.374184 CACAAGTTCAGGACCAACCAA 58.626 47.619 0.00 0.00 42.04 3.67
1087 3260 1.333619 CAAGTTCAGGACCAACCAACG 59.666 52.381 0.00 0.00 42.04 4.10
1089 3262 1.420138 AGTTCAGGACCAACCAACGAT 59.580 47.619 0.00 0.00 42.04 3.73
1090 3263 1.535462 GTTCAGGACCAACCAACGATG 59.465 52.381 0.00 0.00 42.04 3.84
1093 3266 1.806542 CAGGACCAACCAACGATGAAG 59.193 52.381 0.00 0.00 42.04 3.02
1094 3267 1.697432 AGGACCAACCAACGATGAAGA 59.303 47.619 0.00 0.00 42.04 2.87
1096 3269 2.225727 GGACCAACCAACGATGAAGAAC 59.774 50.000 0.00 0.00 38.79 3.01
1097 3270 2.875933 GACCAACCAACGATGAAGAACA 59.124 45.455 0.00 0.00 0.00 3.18
1099 3272 2.350772 CCAACCAACGATGAAGAACAGC 60.351 50.000 0.00 0.00 0.00 4.40
1100 3273 2.254546 ACCAACGATGAAGAACAGCA 57.745 45.000 0.00 0.00 34.21 4.41
1101 3274 1.873591 ACCAACGATGAAGAACAGCAC 59.126 47.619 0.00 0.00 34.21 4.40
1102 3275 1.136252 CCAACGATGAAGAACAGCACG 60.136 52.381 0.00 0.00 34.21 5.34
1103 3276 0.512952 AACGATGAAGAACAGCACGC 59.487 50.000 0.00 0.00 34.21 5.34
1104 3277 0.319900 ACGATGAAGAACAGCACGCT 60.320 50.000 0.00 0.00 34.21 5.07
1105 3278 0.792640 CGATGAAGAACAGCACGCTT 59.207 50.000 0.00 0.00 34.21 4.68
1107 3280 1.532868 GATGAAGAACAGCACGCTTGT 59.467 47.619 0.00 0.00 34.76 3.16
1108 3281 0.657312 TGAAGAACAGCACGCTTGTG 59.343 50.000 0.00 0.00 46.67 3.33
1119 3292 2.045926 GCTTGTGGCGATCCTGGT 60.046 61.111 0.00 0.00 0.00 4.00
1120 3293 2.109126 GCTTGTGGCGATCCTGGTC 61.109 63.158 0.00 0.00 0.00 4.02
1121 3294 1.811266 CTTGTGGCGATCCTGGTCG 60.811 63.158 12.35 12.35 44.14 4.79
1122 3295 2.507110 CTTGTGGCGATCCTGGTCGT 62.507 60.000 16.20 0.00 43.27 4.34
1123 3296 2.202756 GTGGCGATCCTGGTCGTC 60.203 66.667 13.75 13.75 45.83 4.20
1124 3297 3.458163 TGGCGATCCTGGTCGTCC 61.458 66.667 16.59 16.67 45.08 4.79
1125 3298 3.148279 GGCGATCCTGGTCGTCCT 61.148 66.667 16.20 0.00 43.27 3.85
1127 3300 3.121019 CGATCCTGGTCGTCCTCC 58.879 66.667 0.00 0.00 36.88 4.30
1133 3306 4.631740 TGGTCGTCCTCCAGGCCA 62.632 66.667 5.01 0.00 34.44 5.36
1134 3307 3.083997 GGTCGTCCTCCAGGCCAT 61.084 66.667 5.01 0.00 34.44 4.40
1137 3310 1.383109 TCGTCCTCCAGGCCATCAT 60.383 57.895 5.01 0.00 34.44 2.45
1139 3312 1.150081 GTCCTCCAGGCCATCATGG 59.850 63.158 5.01 3.38 41.55 3.66
1140 3313 1.308128 TCCTCCAGGCCATCATGGT 60.308 57.895 5.01 0.00 40.46 3.55
1141 3314 1.150081 CCTCCAGGCCATCATGGTC 59.850 63.158 5.01 0.00 44.07 4.02
1142 3315 1.638679 CCTCCAGGCCATCATGGTCA 61.639 60.000 11.91 0.00 46.77 4.02
1143 3316 0.477204 CTCCAGGCCATCATGGTCAT 59.523 55.000 11.91 0.00 46.77 3.06
1145 3318 1.701292 TCCAGGCCATCATGGTCATAG 59.299 52.381 11.91 0.00 46.77 2.23
1147 3320 1.701292 CAGGCCATCATGGTCATAGGA 59.299 52.381 11.91 0.00 46.77 2.94
1148 3321 2.107031 CAGGCCATCATGGTCATAGGAA 59.893 50.000 11.91 0.00 46.77 3.36
1149 3322 2.991713 AGGCCATCATGGTCATAGGAAT 59.008 45.455 11.91 0.00 46.77 3.01
1150 3323 3.009916 AGGCCATCATGGTCATAGGAATC 59.990 47.826 11.91 0.00 46.77 2.52
1151 3324 3.350833 GCCATCATGGTCATAGGAATCC 58.649 50.000 5.31 0.00 40.46 3.01
1152 3325 3.009916 GCCATCATGGTCATAGGAATCCT 59.990 47.826 7.13 7.13 40.46 3.24
1153 3326 4.508047 GCCATCATGGTCATAGGAATCCTT 60.508 45.833 7.30 0.00 40.46 3.36
1154 3327 5.638133 CCATCATGGTCATAGGAATCCTTT 58.362 41.667 7.30 0.00 31.46 3.11
1155 3328 5.709164 CCATCATGGTCATAGGAATCCTTTC 59.291 44.000 7.30 0.00 31.46 2.62
1158 3331 5.191522 TCATGGTCATAGGAATCCTTTCACA 59.808 40.000 7.30 1.43 34.61 3.58
1160 3333 3.871594 GGTCATAGGAATCCTTTCACACG 59.128 47.826 7.30 0.00 34.61 4.49
1162 3335 2.396590 TAGGAATCCTTTCACACGCC 57.603 50.000 7.30 0.00 34.61 5.68
1163 3336 0.673644 AGGAATCCTTTCACACGCCG 60.674 55.000 0.00 0.00 33.23 6.46
1164 3337 1.134694 GAATCCTTTCACACGCCGC 59.865 57.895 0.00 0.00 0.00 6.53
1169 3342 3.367051 CTTTCACACGCCGCCGATG 62.367 63.158 0.00 0.00 38.29 3.84
1173 3346 3.845259 ACACGCCGCCGATGGTAT 61.845 61.111 0.00 0.00 38.29 2.73
1175 3348 3.845259 ACGCCGCCGATGGTATGT 61.845 61.111 0.00 0.00 38.29 2.29
1176 3349 2.337170 CGCCGCCGATGGTATGTA 59.663 61.111 0.00 0.00 36.29 2.29
1177 3350 2.019951 CGCCGCCGATGGTATGTAC 61.020 63.158 0.00 0.00 36.29 2.90
1178 3351 2.019951 GCCGCCGATGGTATGTACG 61.020 63.158 0.00 0.00 0.00 3.67
1180 3353 0.249155 CCGCCGATGGTATGTACGTT 60.249 55.000 0.00 0.00 0.00 3.99
1181 3354 1.126079 CGCCGATGGTATGTACGTTC 58.874 55.000 0.00 0.00 0.00 3.95
1183 3356 1.202440 GCCGATGGTATGTACGTTCCA 60.202 52.381 14.98 14.98 0.00 3.53
1184 3357 2.466846 CCGATGGTATGTACGTTCCAC 58.533 52.381 14.94 8.78 32.60 4.02
1186 3359 3.429822 CCGATGGTATGTACGTTCCACTT 60.430 47.826 14.94 1.34 32.60 3.16
1187 3360 4.202040 CCGATGGTATGTACGTTCCACTTA 60.202 45.833 14.94 0.00 32.60 2.24
1188 3361 5.508489 CCGATGGTATGTACGTTCCACTTAT 60.508 44.000 14.94 0.28 32.60 1.73
1189 3362 5.628193 CGATGGTATGTACGTTCCACTTATC 59.372 44.000 14.94 8.39 32.60 1.75
1190 3363 6.514541 CGATGGTATGTACGTTCCACTTATCT 60.515 42.308 14.94 0.00 32.60 1.98
1191 3364 5.898174 TGGTATGTACGTTCCACTTATCTG 58.102 41.667 9.22 0.00 0.00 2.90
1192 3365 5.419788 TGGTATGTACGTTCCACTTATCTGT 59.580 40.000 9.22 0.00 0.00 3.41
1193 3366 5.975939 GGTATGTACGTTCCACTTATCTGTC 59.024 44.000 5.90 0.00 0.00 3.51
1194 3367 4.445452 TGTACGTTCCACTTATCTGTCC 57.555 45.455 0.00 0.00 0.00 4.02
1197 3370 1.470979 CGTTCCACTTATCTGTCCCGG 60.471 57.143 0.00 0.00 0.00 5.73
1198 3371 0.539986 TTCCACTTATCTGTCCCGGC 59.460 55.000 0.00 0.00 0.00 6.13
1199 3372 0.325296 TCCACTTATCTGTCCCGGCT 60.325 55.000 0.00 0.00 0.00 5.52
1200 3373 0.179073 CCACTTATCTGTCCCGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
1201 3374 0.811616 CACTTATCTGTCCCGGCTGC 60.812 60.000 0.00 0.00 0.00 5.25
1202 3375 1.264749 ACTTATCTGTCCCGGCTGCA 61.265 55.000 0.50 0.00 0.00 4.41
1203 3376 0.107703 CTTATCTGTCCCGGCTGCAA 60.108 55.000 0.50 0.00 0.00 4.08
1206 3379 2.410322 ATCTGTCCCGGCTGCAACAA 62.410 55.000 0.50 0.00 0.00 2.83
1208 3381 2.904866 GTCCCGGCTGCAACAACA 60.905 61.111 0.50 0.00 0.00 3.33
1211 3384 1.973281 CCCGGCTGCAACAACATCT 60.973 57.895 0.50 0.00 0.00 2.90
1212 3385 1.210931 CCGGCTGCAACAACATCTG 59.789 57.895 0.50 0.00 0.00 2.90
1213 3386 1.443194 CGGCTGCAACAACATCTGC 60.443 57.895 0.50 0.00 39.09 4.26
1214 3387 1.859427 CGGCTGCAACAACATCTGCT 61.859 55.000 0.50 0.00 39.38 4.24
1215 3388 0.316204 GGCTGCAACAACATCTGCTT 59.684 50.000 0.50 0.00 39.38 3.91
1216 3389 1.415374 GCTGCAACAACATCTGCTTG 58.585 50.000 0.00 0.00 39.38 4.01
1218 3391 1.338973 CTGCAACAACATCTGCTTGGT 59.661 47.619 0.00 0.00 39.38 3.67
1220 3393 2.168106 TGCAACAACATCTGCTTGGTTT 59.832 40.909 0.00 0.00 39.38 3.27
1221 3394 2.540931 GCAACAACATCTGCTTGGTTTG 59.459 45.455 0.00 0.00 35.62 2.93
1222 3395 3.737663 GCAACAACATCTGCTTGGTTTGA 60.738 43.478 0.00 0.00 35.62 2.69
1223 3396 4.624015 CAACAACATCTGCTTGGTTTGAT 58.376 39.130 0.00 0.00 0.00 2.57
1225 3398 4.624015 ACAACATCTGCTTGGTTTGATTG 58.376 39.130 0.00 0.00 0.00 2.67
1226 3399 3.308438 ACATCTGCTTGGTTTGATTGC 57.692 42.857 0.00 0.00 0.00 3.56
1227 3400 2.629137 ACATCTGCTTGGTTTGATTGCA 59.371 40.909 0.00 0.00 0.00 4.08
1230 3403 1.730064 CTGCTTGGTTTGATTGCATGC 59.270 47.619 11.82 11.82 33.02 4.06
1231 3404 0.717224 GCTTGGTTTGATTGCATGCG 59.283 50.000 14.09 0.00 0.00 4.73
1486 3937 0.807667 GTGAGATCGATGTTGCGCCT 60.808 55.000 0.54 0.00 0.00 5.52
1530 4015 1.413445 GATGAGATGAGCAGAGCCACT 59.587 52.381 0.00 0.00 0.00 4.00
1604 4103 9.849166 AAATAAATAAACACGGGTATCAGTTTG 57.151 29.630 0.00 0.00 35.90 2.93
1675 4175 3.755526 TTGTGCTGTCCAGTGCGCT 62.756 57.895 9.73 0.00 40.02 5.92
1677 4177 4.240103 TGCTGTCCAGTGCGCTGT 62.240 61.111 24.85 0.00 41.02 4.40
1693 4193 1.675552 CTGTGGTGAACGGAACCTTT 58.324 50.000 5.23 0.00 37.33 3.11
1745 4249 4.277239 TCGGTGCGAGTTGAATGG 57.723 55.556 0.00 0.00 0.00 3.16
1817 4332 1.602165 CCGCTGACGTTTGTACTGTCT 60.602 52.381 0.00 0.00 37.70 3.41
1833 4348 1.546029 TGTCTAGTGCAGCGATGAACT 59.454 47.619 19.96 19.96 0.00 3.01
1883 4415 2.604382 GCAAGGGTGGGCCACATT 60.604 61.111 35.69 26.21 35.86 2.71
1890 4422 1.319614 GGTGGGCCACATTATTGCGT 61.320 55.000 35.69 0.00 35.86 5.24
1898 4431 2.032894 CCACATTATTGCGTCGTGATCC 60.033 50.000 0.00 0.00 0.00 3.36
1963 4496 4.479158 TGTGTTTGAAGCTTAATCCCCTT 58.521 39.130 0.00 0.00 0.00 3.95
1964 4497 4.522789 TGTGTTTGAAGCTTAATCCCCTTC 59.477 41.667 0.00 0.00 36.42 3.46
2016 4549 0.321210 TAGCACGGTTCACCCACATG 60.321 55.000 0.00 0.00 0.00 3.21
2018 4551 0.960364 GCACGGTTCACCCACATGAT 60.960 55.000 0.00 0.00 0.00 2.45
2019 4552 1.533625 CACGGTTCACCCACATGATT 58.466 50.000 0.00 0.00 0.00 2.57
2020 4553 1.199789 CACGGTTCACCCACATGATTG 59.800 52.381 0.00 0.00 0.00 2.67
2021 4554 0.810648 CGGTTCACCCACATGATTGG 59.189 55.000 0.00 0.00 36.26 3.16
2031 4564 2.459644 CACATGATTGGGTGGATTGGT 58.540 47.619 0.00 0.00 0.00 3.67
2032 4565 2.428171 CACATGATTGGGTGGATTGGTC 59.572 50.000 0.00 0.00 0.00 4.02
2033 4566 2.042842 ACATGATTGGGTGGATTGGTCA 59.957 45.455 0.00 0.00 0.00 4.02
2034 4567 2.214376 TGATTGGGTGGATTGGTCAC 57.786 50.000 0.00 0.00 34.61 3.67
2035 4568 1.426983 TGATTGGGTGGATTGGTCACA 59.573 47.619 0.00 0.00 36.90 3.58
2036 4569 2.042842 TGATTGGGTGGATTGGTCACAT 59.957 45.455 0.00 0.00 36.90 3.21
2037 4570 1.921982 TTGGGTGGATTGGTCACATG 58.078 50.000 0.00 0.00 36.90 3.21
2038 4571 1.071434 TGGGTGGATTGGTCACATGA 58.929 50.000 0.00 0.00 36.90 3.07
2039 4572 1.426983 TGGGTGGATTGGTCACATGAA 59.573 47.619 0.00 0.00 36.90 2.57
2040 4573 2.042842 TGGGTGGATTGGTCACATGAAT 59.957 45.455 0.00 0.00 36.90 2.57
2041 4574 2.428171 GGGTGGATTGGTCACATGAATG 59.572 50.000 0.00 0.00 36.90 2.67
2042 4575 3.091545 GGTGGATTGGTCACATGAATGT 58.908 45.455 0.00 0.00 42.84 2.71
2051 4584 3.985410 ACATGAATGTGGACCCCTG 57.015 52.632 0.00 0.00 40.03 4.45
2052 4585 0.323725 ACATGAATGTGGACCCCTGC 60.324 55.000 0.00 0.00 40.03 4.85
2053 4586 0.323633 CATGAATGTGGACCCCTGCA 60.324 55.000 0.00 0.00 0.00 4.41
2054 4587 0.632835 ATGAATGTGGACCCCTGCAT 59.367 50.000 0.00 0.00 0.00 3.96
2055 4588 0.323633 TGAATGTGGACCCCTGCATG 60.324 55.000 0.00 0.00 0.00 4.06
2056 4589 0.323725 GAATGTGGACCCCTGCATGT 60.324 55.000 0.00 0.00 0.00 3.21
2057 4590 0.612732 AATGTGGACCCCTGCATGTG 60.613 55.000 0.00 0.00 0.00 3.21
2058 4591 1.792757 ATGTGGACCCCTGCATGTGT 61.793 55.000 0.00 0.00 0.00 3.72
2059 4592 1.228552 GTGGACCCCTGCATGTGTT 60.229 57.895 0.00 0.00 0.00 3.32
2060 4593 0.827507 GTGGACCCCTGCATGTGTTT 60.828 55.000 0.00 0.00 0.00 2.83
2061 4594 0.827089 TGGACCCCTGCATGTGTTTG 60.827 55.000 0.00 0.00 0.00 2.93
2062 4595 0.539438 GGACCCCTGCATGTGTTTGA 60.539 55.000 0.00 0.00 0.00 2.69
2063 4596 1.327303 GACCCCTGCATGTGTTTGAA 58.673 50.000 0.00 0.00 0.00 2.69
2064 4597 1.270550 GACCCCTGCATGTGTTTGAAG 59.729 52.381 0.00 0.00 0.00 3.02
2065 4598 0.037975 CCCCTGCATGTGTTTGAAGC 60.038 55.000 0.00 0.00 0.00 3.86
2066 4599 0.963962 CCCTGCATGTGTTTGAAGCT 59.036 50.000 0.00 0.00 0.00 3.74
2067 4600 1.342174 CCCTGCATGTGTTTGAAGCTT 59.658 47.619 0.00 0.00 0.00 3.74
2068 4601 2.557924 CCCTGCATGTGTTTGAAGCTTA 59.442 45.455 0.00 0.00 0.00 3.09
2069 4602 3.005684 CCCTGCATGTGTTTGAAGCTTAA 59.994 43.478 0.00 0.00 0.00 1.85
2070 4603 4.322198 CCCTGCATGTGTTTGAAGCTTAAT 60.322 41.667 0.00 0.00 0.00 1.40
2071 4604 4.860907 CCTGCATGTGTTTGAAGCTTAATC 59.139 41.667 0.00 0.00 0.00 1.75
2072 4605 4.808558 TGCATGTGTTTGAAGCTTAATCC 58.191 39.130 0.00 0.00 0.00 3.01
2073 4606 4.176271 GCATGTGTTTGAAGCTTAATCCC 58.824 43.478 0.00 0.00 0.00 3.85
2074 4607 4.747810 CATGTGTTTGAAGCTTAATCCCC 58.252 43.478 0.00 0.00 0.00 4.81
2075 4608 4.112634 TGTGTTTGAAGCTTAATCCCCT 57.887 40.909 0.00 0.00 0.00 4.79
2076 4609 4.479158 TGTGTTTGAAGCTTAATCCCCTT 58.521 39.130 0.00 0.00 0.00 3.95
2077 4610 4.522789 TGTGTTTGAAGCTTAATCCCCTTC 59.477 41.667 0.00 0.00 36.42 3.46
2078 4611 3.756434 TGTTTGAAGCTTAATCCCCTTCG 59.244 43.478 0.00 0.00 38.19 3.79
2079 4612 3.992943 TTGAAGCTTAATCCCCTTCGA 57.007 42.857 0.00 0.00 38.19 3.71
2080 4613 3.992943 TGAAGCTTAATCCCCTTCGAA 57.007 42.857 0.00 0.00 38.19 3.71
2081 4614 4.503714 TGAAGCTTAATCCCCTTCGAAT 57.496 40.909 0.00 0.00 38.19 3.34
2082 4615 4.855340 TGAAGCTTAATCCCCTTCGAATT 58.145 39.130 0.00 0.00 38.19 2.17
2083 4616 4.881850 TGAAGCTTAATCCCCTTCGAATTC 59.118 41.667 0.00 0.00 38.19 2.17
2084 4617 3.821748 AGCTTAATCCCCTTCGAATTCC 58.178 45.455 0.00 0.00 0.00 3.01
2092 4625 0.106519 CCTTCGAATTCCCCCATGCT 60.107 55.000 0.00 0.00 0.00 3.79
2124 4657 8.482128 TCTTGACTTCAAATTTTAACCCATTGT 58.518 29.630 0.00 0.00 35.15 2.71
2164 4697 9.482627 AAAATCCAATTAGTATTTCGTTTGCAA 57.517 25.926 0.00 0.00 0.00 4.08
2183 4716 5.743467 TGCAAATTAGTGTTAGTTGTGACG 58.257 37.500 0.00 0.00 0.00 4.35
2219 5272 4.623932 AGACCACTCTTGAGCATGTTTA 57.376 40.909 0.00 0.00 0.00 2.01
2273 5326 4.809426 ACTACTGAAACTTGACAAGAACGG 59.191 41.667 21.95 16.81 0.00 4.44
2276 5329 5.607477 ACTGAAACTTGACAAGAACGGATA 58.393 37.500 21.95 1.10 0.00 2.59
2426 5480 6.590234 AACCTAGAACCCTAAAAGCAAATG 57.410 37.500 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 692 8.929827 TTGTTAATAATGTCATCTTGCCATTG 57.070 30.769 0.00 0.00 31.63 2.82
89 848 4.111916 CCCATTTTGTGTTTGTCAGTGTC 58.888 43.478 0.00 0.00 0.00 3.67
111 1811 0.598419 GGAAAGTGTGCTTTGCTGCC 60.598 55.000 0.00 0.00 45.66 4.85
196 1896 3.645687 GGGCATATATCTCCATCTCTCCC 59.354 52.174 3.65 0.00 0.00 4.30
203 1903 5.515534 GGACTTGTTGGGCATATATCTCCAT 60.516 44.000 4.83 0.00 0.00 3.41
211 1911 3.091545 CACTTGGACTTGTTGGGCATAT 58.908 45.455 0.00 0.00 0.00 1.78
232 2368 2.544267 CTGGTCTTGTGTCTTTTCCGTC 59.456 50.000 0.00 0.00 0.00 4.79
234 2370 1.873591 CCTGGTCTTGTGTCTTTTCCG 59.126 52.381 0.00 0.00 0.00 4.30
253 2389 7.396540 AACTTGTTTGATTCCTCACATATCC 57.603 36.000 0.00 0.00 0.00 2.59
260 2396 6.310941 TGGGATAAACTTGTTTGATTCCTCA 58.689 36.000 8.79 9.04 0.00 3.86
305 2441 1.135939 CATGCACTCGTCGTCGGTA 59.864 57.895 1.55 0.00 37.69 4.02
306 2442 2.126463 CATGCACTCGTCGTCGGT 60.126 61.111 1.55 0.00 37.69 4.69
316 2469 1.421268 TCTCCCAAACAGTCATGCACT 59.579 47.619 0.00 0.00 34.67 4.40
344 2497 0.179001 ACAAAGGGTGGAGTTTCGGG 60.179 55.000 0.00 0.00 0.00 5.14
385 2538 5.036916 AGACATTCCCCAGTAACCTTATCA 58.963 41.667 0.00 0.00 0.00 2.15
395 2548 2.990479 GCCGAGACATTCCCCAGT 59.010 61.111 0.00 0.00 0.00 4.00
432 2585 0.104487 TCGTGGACGTAGGCAAACAA 59.896 50.000 0.00 0.00 40.80 2.83
456 2609 1.993948 GGAGGCCGGGGAAGTAGTT 60.994 63.158 2.18 0.00 0.00 2.24
469 2622 2.207924 ATATCGTCGGTGGGGAGGC 61.208 63.158 0.00 0.00 0.00 4.70
498 2651 7.395489 AGCCTTCTTGTTTGAGATGTTGATATT 59.605 33.333 0.00 0.00 0.00 1.28
499 2652 6.888632 AGCCTTCTTGTTTGAGATGTTGATAT 59.111 34.615 0.00 0.00 0.00 1.63
500 2653 6.149973 CAGCCTTCTTGTTTGAGATGTTGATA 59.850 38.462 0.00 0.00 0.00 2.15
544 2697 7.014615 ACCCTCTAGTTCGAAAGTACAAAACTA 59.985 37.037 0.00 0.00 37.50 2.24
546 2699 5.987953 ACCCTCTAGTTCGAAAGTACAAAAC 59.012 40.000 0.00 0.00 33.41 2.43
547 2700 6.165700 ACCCTCTAGTTCGAAAGTACAAAA 57.834 37.500 0.00 0.00 33.41 2.44
553 2706 6.130569 AGATCATACCCTCTAGTTCGAAAGT 58.869 40.000 0.00 0.00 0.00 2.66
558 2711 8.740123 ATGTATAGATCATACCCTCTAGTTCG 57.260 38.462 0.00 0.00 39.08 3.95
559 2712 9.127277 GGATGTATAGATCATACCCTCTAGTTC 57.873 40.741 11.64 0.00 39.08 3.01
580 2738 3.643237 TGAACGGATAAGAGAGGGATGT 58.357 45.455 0.00 0.00 0.00 3.06
619 2777 3.068873 GGCTAACACATCACCACCAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
620 2778 2.625790 GGCTAACACATCACCACCAAAA 59.374 45.455 0.00 0.00 0.00 2.44
621 2779 2.235016 GGCTAACACATCACCACCAAA 58.765 47.619 0.00 0.00 0.00 3.28
622 2780 1.143889 TGGCTAACACATCACCACCAA 59.856 47.619 0.00 0.00 0.00 3.67
623 2781 0.767998 TGGCTAACACATCACCACCA 59.232 50.000 0.00 0.00 0.00 4.17
624 2782 2.128771 ATGGCTAACACATCACCACC 57.871 50.000 0.00 0.00 32.13 4.61
625 2783 3.873910 AGTATGGCTAACACATCACCAC 58.126 45.455 0.00 0.00 32.13 4.16
626 2784 4.260985 CAAGTATGGCTAACACATCACCA 58.739 43.478 0.00 0.00 34.28 4.17
627 2785 4.261801 ACAAGTATGGCTAACACATCACC 58.738 43.478 0.00 0.00 0.00 4.02
628 2786 5.181245 ACAACAAGTATGGCTAACACATCAC 59.819 40.000 0.00 0.00 0.00 3.06
629 2787 5.312895 ACAACAAGTATGGCTAACACATCA 58.687 37.500 0.00 0.00 0.00 3.07
630 2788 5.880054 ACAACAAGTATGGCTAACACATC 57.120 39.130 0.00 0.00 0.00 3.06
631 2789 7.609918 TGATAACAACAAGTATGGCTAACACAT 59.390 33.333 0.00 0.00 0.00 3.21
632 2790 6.937465 TGATAACAACAAGTATGGCTAACACA 59.063 34.615 0.00 0.00 0.00 3.72
633 2791 7.372451 TGATAACAACAAGTATGGCTAACAC 57.628 36.000 0.00 0.00 0.00 3.32
634 2792 9.325198 CTATGATAACAACAAGTATGGCTAACA 57.675 33.333 0.00 0.00 0.00 2.41
635 2793 9.542462 TCTATGATAACAACAAGTATGGCTAAC 57.458 33.333 0.00 0.00 0.00 2.34
637 2795 9.710900 CATCTATGATAACAACAAGTATGGCTA 57.289 33.333 0.00 0.00 0.00 3.93
638 2796 8.213679 ACATCTATGATAACAACAAGTATGGCT 58.786 33.333 0.00 0.00 0.00 4.75
639 2797 8.383318 ACATCTATGATAACAACAAGTATGGC 57.617 34.615 0.00 0.00 0.00 4.40
667 2825 7.636359 GTGAGCACGTAATAAGCATAGAAAAAG 59.364 37.037 0.00 0.00 0.00 2.27
669 2827 6.592220 TGTGAGCACGTAATAAGCATAGAAAA 59.408 34.615 0.00 0.00 0.00 2.29
670 2828 6.103330 TGTGAGCACGTAATAAGCATAGAAA 58.897 36.000 0.00 0.00 0.00 2.52
682 2840 3.659786 AGCTAAACATGTGAGCACGTAA 58.340 40.909 26.44 0.00 38.73 3.18
710 2868 9.002600 TGACATTGCTAAGAATATTAATCGCAT 57.997 29.630 0.00 0.00 0.00 4.73
730 2888 6.806388 TCGCATATAAAGCATGATGACATT 57.194 33.333 0.00 0.00 34.15 2.71
793 2954 5.973565 GTGCATGCACCTATTTTCTCATAAC 59.026 40.000 35.69 8.32 40.79 1.89
818 2982 0.530744 TTCTCCATCTTCCACGTCCG 59.469 55.000 0.00 0.00 0.00 4.79
856 3020 0.627986 CTTTCCCTGGCTTGGATCCT 59.372 55.000 14.23 0.00 0.00 3.24
857 3021 0.396278 CCTTTCCCTGGCTTGGATCC 60.396 60.000 4.20 4.20 0.00 3.36
859 3023 1.000866 GCCTTTCCCTGGCTTGGAT 59.999 57.895 0.00 0.00 46.38 3.41
883 3047 1.079543 CCGTCTGACTCCTGGCTTG 60.080 63.158 6.21 0.00 0.00 4.01
963 3127 7.412346 GCAAGCAACTCCATATATAGATGTTCG 60.412 40.741 6.60 0.00 0.00 3.95
989 3162 0.031178 GTTGTGTCTGCCCAAAGCTG 59.969 55.000 0.00 0.00 44.23 4.24
998 3171 2.645730 TTTGTTGTGGTTGTGTCTGC 57.354 45.000 0.00 0.00 0.00 4.26
1034 3207 2.241430 TCTTCCCAGTCCTGTCGATCTA 59.759 50.000 0.00 0.00 0.00 1.98
1036 3209 1.407258 CTCTTCCCAGTCCTGTCGATC 59.593 57.143 0.00 0.00 0.00 3.69
1038 3211 0.404426 TCTCTTCCCAGTCCTGTCGA 59.596 55.000 0.00 0.00 0.00 4.20
1039 3212 1.479709 ATCTCTTCCCAGTCCTGTCG 58.520 55.000 0.00 0.00 0.00 4.35
1078 3251 2.350772 GCTGTTCTTCATCGTTGGTTGG 60.351 50.000 0.00 0.00 0.00 3.77
1079 3252 2.290367 TGCTGTTCTTCATCGTTGGTTG 59.710 45.455 0.00 0.00 0.00 3.77
1080 3253 2.290641 GTGCTGTTCTTCATCGTTGGTT 59.709 45.455 0.00 0.00 0.00 3.67
1082 3255 1.136252 CGTGCTGTTCTTCATCGTTGG 60.136 52.381 0.00 0.00 0.00 3.77
1083 3256 1.722751 GCGTGCTGTTCTTCATCGTTG 60.723 52.381 0.00 0.00 0.00 4.10
1085 3258 0.319900 AGCGTGCTGTTCTTCATCGT 60.320 50.000 0.00 0.00 0.00 3.73
1087 3260 1.532868 ACAAGCGTGCTGTTCTTCATC 59.467 47.619 0.00 0.00 0.00 2.92
1089 3262 0.657312 CACAAGCGTGCTGTTCTTCA 59.343 50.000 0.00 0.00 36.06 3.02
1090 3263 0.040958 CCACAAGCGTGCTGTTCTTC 60.041 55.000 0.00 0.00 42.17 2.87
1093 3266 2.050985 GCCACAAGCGTGCTGTTC 60.051 61.111 0.00 0.00 42.17 3.18
1102 3275 2.045926 ACCAGGATCGCCACAAGC 60.046 61.111 0.00 0.00 36.29 4.01
1103 3276 1.811266 CGACCAGGATCGCCACAAG 60.811 63.158 0.00 0.00 34.90 3.16
1104 3277 2.264480 CGACCAGGATCGCCACAA 59.736 61.111 0.00 0.00 34.90 3.33
1105 3278 2.994995 ACGACCAGGATCGCCACA 60.995 61.111 10.34 0.00 46.22 4.17
1107 3280 3.458163 GGACGACCAGGATCGCCA 61.458 66.667 10.34 0.00 46.22 5.69
1108 3281 3.140225 GAGGACGACCAGGATCGCC 62.140 68.421 6.71 11.63 46.22 5.54
1121 3294 1.150081 CCATGATGGCCTGGAGGAC 59.850 63.158 3.32 0.00 45.93 3.85
1122 3295 1.308128 ACCATGATGGCCTGGAGGA 60.308 57.895 15.38 0.00 42.67 3.71
1123 3296 1.150081 GACCATGATGGCCTGGAGG 59.850 63.158 15.38 7.88 42.67 4.30
1124 3297 0.477204 ATGACCATGATGGCCTGGAG 59.523 55.000 15.38 0.00 42.67 3.86
1125 3298 1.701292 CTATGACCATGATGGCCTGGA 59.299 52.381 15.38 0.00 42.67 3.86
1127 3300 1.701292 TCCTATGACCATGATGGCCTG 59.299 52.381 12.25 0.00 42.67 4.85
1130 3303 3.009916 AGGATTCCTATGACCATGATGGC 59.990 47.826 12.25 5.15 34.13 4.40
1133 3306 6.126390 TGTGAAAGGATTCCTATGACCATGAT 60.126 38.462 5.43 0.00 34.49 2.45
1134 3307 5.191522 TGTGAAAGGATTCCTATGACCATGA 59.808 40.000 5.43 0.00 34.49 3.07
1137 3310 4.622933 CGTGTGAAAGGATTCCTATGACCA 60.623 45.833 5.43 0.00 34.49 4.02
1139 3312 3.309954 GCGTGTGAAAGGATTCCTATGAC 59.690 47.826 5.43 3.54 34.49 3.06
1140 3313 3.531538 GCGTGTGAAAGGATTCCTATGA 58.468 45.455 5.43 0.00 34.49 2.15
1141 3314 2.614057 GGCGTGTGAAAGGATTCCTATG 59.386 50.000 5.43 0.00 34.49 2.23
1142 3315 2.741878 CGGCGTGTGAAAGGATTCCTAT 60.742 50.000 5.43 0.00 34.49 2.57
1143 3316 1.404986 CGGCGTGTGAAAGGATTCCTA 60.405 52.381 5.43 0.00 34.49 2.94
1145 3318 1.794222 CGGCGTGTGAAAGGATTCC 59.206 57.895 0.00 0.00 34.49 3.01
1147 3320 2.332654 GGCGGCGTGTGAAAGGATT 61.333 57.895 9.37 0.00 0.00 3.01
1148 3321 2.746277 GGCGGCGTGTGAAAGGAT 60.746 61.111 9.37 0.00 0.00 3.24
1151 3324 3.118454 ATCGGCGGCGTGTGAAAG 61.118 61.111 31.06 0.00 0.00 2.62
1152 3325 3.418913 CATCGGCGGCGTGTGAAA 61.419 61.111 31.06 11.28 0.00 2.69
1155 3328 4.805231 TACCATCGGCGGCGTGTG 62.805 66.667 31.06 27.02 0.00 3.82
1158 3331 2.491897 TACATACCATCGGCGGCGT 61.492 57.895 31.06 15.68 0.00 5.68
1160 3333 2.019951 CGTACATACCATCGGCGGC 61.020 63.158 7.21 0.00 0.00 6.53
1162 3335 1.126079 GAACGTACATACCATCGGCG 58.874 55.000 0.00 0.00 0.00 6.46
1163 3336 1.202440 TGGAACGTACATACCATCGGC 60.202 52.381 0.00 0.00 0.00 5.54
1164 3337 2.100252 AGTGGAACGTACATACCATCGG 59.900 50.000 0.00 0.00 45.86 4.18
1166 3339 6.641314 CAGATAAGTGGAACGTACATACCATC 59.359 42.308 0.00 0.00 45.86 3.51
1167 3340 6.097839 ACAGATAAGTGGAACGTACATACCAT 59.902 38.462 0.00 0.00 45.86 3.55
1169 3342 5.899299 ACAGATAAGTGGAACGTACATACC 58.101 41.667 0.00 0.00 45.86 2.73
1170 3343 5.975939 GGACAGATAAGTGGAACGTACATAC 59.024 44.000 0.00 0.00 45.86 2.39
1171 3344 5.068198 GGGACAGATAAGTGGAACGTACATA 59.932 44.000 0.00 0.00 45.86 2.29
1173 3346 3.194116 GGGACAGATAAGTGGAACGTACA 59.806 47.826 0.00 0.00 45.86 2.90
1175 3348 2.424601 CGGGACAGATAAGTGGAACGTA 59.575 50.000 0.00 0.00 45.86 3.57
1176 3349 1.203994 CGGGACAGATAAGTGGAACGT 59.796 52.381 0.00 0.00 45.86 3.99
1177 3350 1.470979 CCGGGACAGATAAGTGGAACG 60.471 57.143 0.00 0.00 45.86 3.95
1178 3351 1.742750 GCCGGGACAGATAAGTGGAAC 60.743 57.143 2.18 0.00 0.00 3.62
1180 3353 0.325296 AGCCGGGACAGATAAGTGGA 60.325 55.000 2.18 0.00 0.00 4.02
1181 3354 0.179073 CAGCCGGGACAGATAAGTGG 60.179 60.000 2.18 0.00 0.00 4.00
1183 3356 1.264749 TGCAGCCGGGACAGATAAGT 61.265 55.000 2.18 0.00 0.00 2.24
1184 3357 0.107703 TTGCAGCCGGGACAGATAAG 60.108 55.000 2.18 0.00 0.00 1.73
1186 3359 1.220749 GTTGCAGCCGGGACAGATA 59.779 57.895 2.18 0.00 0.00 1.98
1187 3360 2.045926 GTTGCAGCCGGGACAGAT 60.046 61.111 2.18 0.00 0.00 2.90
1188 3361 3.113514 TTGTTGCAGCCGGGACAGA 62.114 57.895 2.18 0.00 0.00 3.41
1189 3362 2.594303 TTGTTGCAGCCGGGACAG 60.594 61.111 2.18 0.00 0.00 3.51
1190 3363 2.904866 GTTGTTGCAGCCGGGACA 60.905 61.111 2.18 0.00 0.00 4.02
1191 3364 2.200170 GATGTTGTTGCAGCCGGGAC 62.200 60.000 2.18 0.00 0.00 4.46
1192 3365 1.971167 GATGTTGTTGCAGCCGGGA 60.971 57.895 2.18 0.00 0.00 5.14
1193 3366 1.973281 AGATGTTGTTGCAGCCGGG 60.973 57.895 2.18 0.00 0.00 5.73
1194 3367 1.210931 CAGATGTTGTTGCAGCCGG 59.789 57.895 0.00 0.00 0.00 6.13
1197 3370 1.415374 CAAGCAGATGTTGTTGCAGC 58.585 50.000 0.00 0.00 42.67 5.25
1198 3371 1.338973 ACCAAGCAGATGTTGTTGCAG 59.661 47.619 0.00 0.00 42.67 4.41
1199 3372 1.401761 ACCAAGCAGATGTTGTTGCA 58.598 45.000 0.00 0.00 42.67 4.08
1200 3373 2.514205 AACCAAGCAGATGTTGTTGC 57.486 45.000 0.00 0.00 40.57 4.17
1201 3374 4.044336 TCAAACCAAGCAGATGTTGTTG 57.956 40.909 0.00 0.00 0.00 3.33
1202 3375 4.942761 ATCAAACCAAGCAGATGTTGTT 57.057 36.364 0.00 0.00 0.00 2.83
1203 3376 4.624015 CAATCAAACCAAGCAGATGTTGT 58.376 39.130 0.00 0.00 0.00 3.32
1206 3379 2.629137 TGCAATCAAACCAAGCAGATGT 59.371 40.909 0.00 0.00 0.00 3.06
1208 3381 3.857052 CATGCAATCAAACCAAGCAGAT 58.143 40.909 0.00 0.00 38.75 2.90
1211 3384 1.798283 GCATGCAATCAAACCAAGCA 58.202 45.000 14.21 0.00 39.79 3.91
1212 3385 0.717224 CGCATGCAATCAAACCAAGC 59.283 50.000 19.57 0.00 0.00 4.01
1213 3386 2.068837 ACGCATGCAATCAAACCAAG 57.931 45.000 19.57 0.00 0.00 3.61
1214 3387 2.402305 GAACGCATGCAATCAAACCAA 58.598 42.857 19.57 0.00 0.00 3.67
1215 3388 1.665448 CGAACGCATGCAATCAAACCA 60.665 47.619 19.57 0.00 0.00 3.67
1216 3389 0.984109 CGAACGCATGCAATCAAACC 59.016 50.000 19.57 0.00 0.00 3.27
1218 3391 1.684142 CACGAACGCATGCAATCAAA 58.316 45.000 19.57 0.00 0.00 2.69
1220 3393 1.154244 GCACGAACGCATGCAATCA 60.154 52.632 19.57 0.00 41.65 2.57
1221 3394 3.666730 GCACGAACGCATGCAATC 58.333 55.556 19.57 13.69 41.65 2.67
1225 3398 2.202222 GTCTGCACGAACGCATGC 60.202 61.111 7.91 7.91 42.06 4.06
1226 3399 0.166597 ATTGTCTGCACGAACGCATG 59.833 50.000 0.00 0.00 42.06 4.06
1227 3400 0.874390 AATTGTCTGCACGAACGCAT 59.126 45.000 0.00 0.00 42.06 4.73
1230 3403 1.399727 GGGAAATTGTCTGCACGAACG 60.400 52.381 0.00 0.00 0.00 3.95
1231 3404 1.068541 GGGGAAATTGTCTGCACGAAC 60.069 52.381 0.00 0.00 0.00 3.95
1455 3887 2.016318 CGATCTCACTGTCTGAGCTCT 58.984 52.381 16.19 0.00 45.64 4.09
1530 4015 1.056660 AAGGAAAGAGAACGCTGGGA 58.943 50.000 0.00 0.00 0.00 4.37
1675 4175 2.018515 GAAAAGGTTCCGTTCACCACA 58.981 47.619 0.00 0.00 36.67 4.17
1677 4177 1.301423 CGAAAAGGTTCCGTTCACCA 58.699 50.000 8.31 0.00 36.67 4.17
1711 4215 1.825474 CCGAGTGTGACAACCCTAGAT 59.175 52.381 0.00 0.00 0.00 1.98
1712 4216 1.254026 CCGAGTGTGACAACCCTAGA 58.746 55.000 0.00 0.00 0.00 2.43
1713 4217 0.966920 ACCGAGTGTGACAACCCTAG 59.033 55.000 0.00 0.00 0.00 3.02
1776 4290 3.313526 GGTGTATCTTTCGATGCAATGCT 59.686 43.478 6.82 0.00 42.61 3.79
1779 4293 2.287915 GCGGTGTATCTTTCGATGCAAT 59.712 45.455 0.00 0.00 42.61 3.56
1798 4312 1.767289 AGACAGTACAAACGTCAGCG 58.233 50.000 0.00 0.00 44.93 5.18
1817 4332 2.481969 GGATCAGTTCATCGCTGCACTA 60.482 50.000 0.00 0.00 34.21 2.74
1833 4348 0.323087 TCGTCCACCGAGAAGGATCA 60.323 55.000 0.00 0.00 45.00 2.92
1898 4431 3.426159 GCATGTGACCAATCCACTTTACG 60.426 47.826 0.00 0.00 35.66 3.18
1963 4496 3.200483 CATGTCTCATGCAGGAATTCGA 58.800 45.455 1.37 0.00 0.00 3.71
1964 4497 2.941064 ACATGTCTCATGCAGGAATTCG 59.059 45.455 1.37 0.00 0.00 3.34
2016 4549 2.214376 TGTGACCAATCCACCCAATC 57.786 50.000 0.00 0.00 33.80 2.67
2018 4551 1.426983 TCATGTGACCAATCCACCCAA 59.573 47.619 0.00 0.00 33.80 4.12
2019 4552 1.071434 TCATGTGACCAATCCACCCA 58.929 50.000 0.00 0.00 33.80 4.51
2020 4553 2.214376 TTCATGTGACCAATCCACCC 57.786 50.000 0.00 0.00 33.80 4.61
2021 4554 3.091545 ACATTCATGTGACCAATCCACC 58.908 45.455 0.00 0.00 40.03 4.61
2033 4566 0.323725 GCAGGGGTCCACATTCATGT 60.324 55.000 0.00 0.00 42.84 3.21
2034 4567 0.323633 TGCAGGGGTCCACATTCATG 60.324 55.000 0.00 0.00 0.00 3.07
2035 4568 0.632835 ATGCAGGGGTCCACATTCAT 59.367 50.000 0.00 0.00 0.00 2.57
2036 4569 0.323633 CATGCAGGGGTCCACATTCA 60.324 55.000 0.00 0.00 0.00 2.57
2037 4570 0.323725 ACATGCAGGGGTCCACATTC 60.324 55.000 2.31 0.00 0.00 2.67
2038 4571 0.612732 CACATGCAGGGGTCCACATT 60.613 55.000 2.31 0.00 0.00 2.71
2039 4572 1.000521 CACATGCAGGGGTCCACAT 60.001 57.895 2.31 0.00 0.00 3.21
2040 4573 2.005606 AACACATGCAGGGGTCCACA 62.006 55.000 6.76 0.00 0.00 4.17
2041 4574 0.827507 AAACACATGCAGGGGTCCAC 60.828 55.000 6.76 0.00 0.00 4.02
2042 4575 0.827089 CAAACACATGCAGGGGTCCA 60.827 55.000 6.76 0.00 0.00 4.02
2043 4576 0.539438 TCAAACACATGCAGGGGTCC 60.539 55.000 6.76 0.00 0.00 4.46
2044 4577 1.270550 CTTCAAACACATGCAGGGGTC 59.729 52.381 6.76 0.00 0.00 4.46
2045 4578 1.331214 CTTCAAACACATGCAGGGGT 58.669 50.000 0.00 0.00 0.00 4.95
2046 4579 0.037975 GCTTCAAACACATGCAGGGG 60.038 55.000 0.00 0.00 0.00 4.79
2047 4580 0.963962 AGCTTCAAACACATGCAGGG 59.036 50.000 2.31 0.00 0.00 4.45
2048 4581 2.806608 AAGCTTCAAACACATGCAGG 57.193 45.000 0.00 0.00 0.00 4.85
2049 4582 4.860907 GGATTAAGCTTCAAACACATGCAG 59.139 41.667 0.00 0.00 0.00 4.41
2050 4583 4.321899 GGGATTAAGCTTCAAACACATGCA 60.322 41.667 0.00 0.00 0.00 3.96
2051 4584 4.176271 GGGATTAAGCTTCAAACACATGC 58.824 43.478 0.00 0.00 0.00 4.06
2052 4585 4.463891 AGGGGATTAAGCTTCAAACACATG 59.536 41.667 0.00 0.00 0.00 3.21
2053 4586 4.677182 AGGGGATTAAGCTTCAAACACAT 58.323 39.130 0.00 0.00 0.00 3.21
2054 4587 4.112634 AGGGGATTAAGCTTCAAACACA 57.887 40.909 0.00 0.00 0.00 3.72
2055 4588 4.379499 CGAAGGGGATTAAGCTTCAAACAC 60.379 45.833 0.00 0.00 0.00 3.32
2056 4589 3.756434 CGAAGGGGATTAAGCTTCAAACA 59.244 43.478 0.00 0.00 0.00 2.83
2057 4590 4.007659 TCGAAGGGGATTAAGCTTCAAAC 58.992 43.478 0.00 0.00 0.00 2.93
2058 4591 4.295141 TCGAAGGGGATTAAGCTTCAAA 57.705 40.909 0.00 0.00 0.00 2.69
2059 4592 3.992943 TCGAAGGGGATTAAGCTTCAA 57.007 42.857 0.00 0.00 0.00 2.69
2060 4593 3.992943 TTCGAAGGGGATTAAGCTTCA 57.007 42.857 0.00 0.00 0.00 3.02
2061 4594 4.276183 GGAATTCGAAGGGGATTAAGCTTC 59.724 45.833 0.00 0.00 0.00 3.86
2062 4595 4.207955 GGAATTCGAAGGGGATTAAGCTT 58.792 43.478 3.48 3.48 0.00 3.74
2063 4596 3.435169 GGGAATTCGAAGGGGATTAAGCT 60.435 47.826 3.35 0.00 0.00 3.74
2064 4597 2.885266 GGGAATTCGAAGGGGATTAAGC 59.115 50.000 3.35 0.00 0.00 3.09
2065 4598 3.487372 GGGGAATTCGAAGGGGATTAAG 58.513 50.000 3.35 0.00 0.00 1.85
2066 4599 2.176148 GGGGGAATTCGAAGGGGATTAA 59.824 50.000 3.35 0.00 0.00 1.40
2067 4600 1.778484 GGGGGAATTCGAAGGGGATTA 59.222 52.381 3.35 0.00 0.00 1.75
2068 4601 0.556258 GGGGGAATTCGAAGGGGATT 59.444 55.000 3.35 0.00 0.00 3.01
2069 4602 0.626277 TGGGGGAATTCGAAGGGGAT 60.626 55.000 3.35 0.00 0.00 3.85
2070 4603 0.626277 ATGGGGGAATTCGAAGGGGA 60.626 55.000 3.35 0.00 0.00 4.81
2071 4604 0.468029 CATGGGGGAATTCGAAGGGG 60.468 60.000 3.35 0.00 0.00 4.79
2072 4605 1.109323 GCATGGGGGAATTCGAAGGG 61.109 60.000 3.35 0.00 0.00 3.95
2073 4606 0.106519 AGCATGGGGGAATTCGAAGG 60.107 55.000 3.35 0.00 0.00 3.46
2074 4607 1.767759 AAGCATGGGGGAATTCGAAG 58.232 50.000 3.35 0.00 0.00 3.79
2075 4608 2.230130 AAAGCATGGGGGAATTCGAA 57.770 45.000 0.00 0.00 0.00 3.71
2076 4609 2.230130 AAAAGCATGGGGGAATTCGA 57.770 45.000 0.00 0.00 0.00 3.71
2077 4610 2.497273 AGAAAAAGCATGGGGGAATTCG 59.503 45.455 0.00 0.00 0.00 3.34
2078 4611 3.771479 AGAGAAAAAGCATGGGGGAATTC 59.229 43.478 0.00 0.00 0.00 2.17
2079 4612 3.794911 AGAGAAAAAGCATGGGGGAATT 58.205 40.909 0.00 0.00 0.00 2.17
2080 4613 3.479866 AGAGAAAAAGCATGGGGGAAT 57.520 42.857 0.00 0.00 0.00 3.01
2081 4614 2.899256 CAAGAGAAAAAGCATGGGGGAA 59.101 45.455 0.00 0.00 0.00 3.97
2082 4615 2.109834 TCAAGAGAAAAAGCATGGGGGA 59.890 45.455 0.00 0.00 0.00 4.81
2083 4616 2.232208 GTCAAGAGAAAAAGCATGGGGG 59.768 50.000 0.00 0.00 0.00 5.40
2084 4617 3.160269 AGTCAAGAGAAAAAGCATGGGG 58.840 45.455 0.00 0.00 0.00 4.96
2149 4682 9.607285 CTAACACTAATTTGCAAACGAAATACT 57.393 29.630 15.41 0.00 0.00 2.12
2164 4697 5.011329 TCCCTCGTCACAACTAACACTAATT 59.989 40.000 0.00 0.00 0.00 1.40
2183 4716 2.820197 GTGGTCTTGTTCCAAATCCCTC 59.180 50.000 0.00 0.00 36.68 4.30
2211 5264 6.751888 AGTTTCAAACACTTGTCTAAACATGC 59.248 34.615 2.41 0.00 34.73 4.06
2219 5272 4.764823 TGGTGAAGTTTCAAACACTTGTCT 59.235 37.500 2.41 0.00 39.21 3.41
2265 5318 8.458843 ACTTGGTGAATTTATTATCCGTTCTTG 58.541 33.333 0.00 0.00 0.00 3.02
2307 5360 9.270707 AGGGTTTAGGGTTTTAGTTTTAGTTTT 57.729 29.630 0.00 0.00 0.00 2.43
2308 5361 8.843308 AGGGTTTAGGGTTTTAGTTTTAGTTT 57.157 30.769 0.00 0.00 0.00 2.66
2309 5362 9.934784 TTAGGGTTTAGGGTTTTAGTTTTAGTT 57.065 29.630 0.00 0.00 0.00 2.24
2310 5363 9.578576 CTTAGGGTTTAGGGTTTTAGTTTTAGT 57.421 33.333 0.00 0.00 0.00 2.24
2311 5364 9.578576 ACTTAGGGTTTAGGGTTTTAGTTTTAG 57.421 33.333 0.00 0.00 0.00 1.85
2312 5365 9.934784 AACTTAGGGTTTAGGGTTTTAGTTTTA 57.065 29.630 0.00 0.00 33.90 1.52
2313 5366 8.843308 AACTTAGGGTTTAGGGTTTTAGTTTT 57.157 30.769 0.00 0.00 33.90 2.43
2319 5372 9.491406 TTTTAGAAACTTAGGGTTTAGGGTTTT 57.509 29.630 0.00 0.00 46.77 2.43
2360 5413 0.756903 GGGCTTAGGGCTACGAATCA 59.243 55.000 0.00 0.00 41.46 2.57
2361 5414 1.049402 AGGGCTTAGGGCTACGAATC 58.951 55.000 0.00 0.00 41.46 2.52
2363 5416 2.163810 TTAGGGCTTAGGGCTACGAA 57.836 50.000 0.00 0.00 41.46 3.85
2365 5418 1.202615 GGTTTAGGGCTTAGGGCTACG 60.203 57.143 0.00 0.00 41.46 3.51


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

AutoCloner maintained by Alex Coulton.