Multiple sequence alignment - TraesCS4A01G196800

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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 TraesCS4A01G196800 chr4A 100.000 3402 0 0 1 3402 478869300 478865899 0.000000e+00 6283
1 TraesCS4A01G196800 chr4A 86.154 130 12 2 2574 2697 478752331 478752202 5.920000e-28 135
2 TraesCS4A01G196800 chr4D 93.519 2407 110 22 142 2538 97375390 97377760 0.000000e+00 3539
3 TraesCS4A01G196800 chr4D 86.090 266 36 1 3122 3386 97379126 97379391 5.560000e-73 285
4 TraesCS4A01G196800 chr4D 99.174 121 1 0 1 121 97375283 97375403 5.720000e-53 219
5 TraesCS4A01G196800 chr4D 85.096 208 29 2 2719 2925 97378399 97378605 9.560000e-51 211
6 TraesCS4A01G196800 chr4D 91.791 134 4 2 2568 2694 97378275 97378408 2.700000e-41 180
7 TraesCS4A01G196800 chr4D 88.189 127 9 2 2574 2694 97383175 97383301 2.740000e-31 147
8 TraesCS4A01G196800 chr4B 91.406 2362 133 36 143 2480 139021569 139023884 0.000000e+00 3173
9 TraesCS4A01G196800 chr4B 90.706 269 24 1 3122 3389 139025346 139025614 1.160000e-94 357
10 TraesCS4A01G196800 chr4B 93.780 209 13 0 2719 2927 139024592 139024800 7.090000e-82 315
11 TraesCS4A01G196800 chr4B 96.241 133 5 0 2565 2697 139024472 139024604 5.720000e-53 219
12 TraesCS4A01G196800 chr4B 97.521 121 3 0 1 121 139021461 139021581 1.240000e-49 207
13 TraesCS4A01G196800 chr3D 91.935 186 14 1 2934 3118 613759275 613759090 3.370000e-65 259
14 TraesCS4A01G196800 chr7D 91.477 176 15 0 2936 3111 121796616 121796791 3.390000e-60 243
15 TraesCS4A01G196800 chr7D 90.503 179 17 0 2936 3114 121190766 121190588 1.580000e-58 237
16 TraesCS4A01G196800 chr7D 86.740 181 19 5 2934 3113 246406544 246406720 2.680000e-46 196
17 TraesCS4A01G196800 chr7D 85.792 183 19 5 2935 3115 549094029 549094206 1.610000e-43 187
18 TraesCS4A01G196800 chr3B 89.385 179 19 0 2937 3115 587547710 587547888 3.420000e-55 226
19 TraesCS4A01G196800 chr2A 85.027 187 24 3 2934 3118 2230689 2230505 1.610000e-43 187
20 TraesCS4A01G196800 chr2D 84.783 184 18 8 2936 3115 21427835 21428012 3.490000e-40 176
21 TraesCS4A01G196800 chr2D 85.165 182 16 9 2933 3109 471504391 471504566 3.490000e-40 176


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 TraesCS4A01G196800 chr4A 478865899 478869300 3401 True 6283.0 6283 100.000000 1 3402 1 chr4A.!!$R2 3401
1 TraesCS4A01G196800 chr4D 97375283 97383301 8018 False 763.5 3539 90.643167 1 3386 6 chr4D.!!$F1 3385
2 TraesCS4A01G196800 chr4B 139021461 139025614 4153 False 854.2 3173 93.930800 1 3389 5 chr4B.!!$F1 3388

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
197 199 0.751277 TGGTCACAAACTGCACAGGG 60.751 55.0 2.21 0.0 0.0 4.45 F
1886 1918 0.307760 GGCCCGCTGATGAATAAACG 59.692 55.0 0.00 0.0 0.0 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2074 0.258484 TCGAGGGTCCCGGTGTATAA 59.742 55.0 0.99 0.00 0.0 0.98 R
2974 3542 0.041839 GATGGTCGCATGCATCGTTC 60.042 55.0 19.57 4.87 0.0 3.95 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
123 124 5.594724 GCATACTGCAGAATCAAGATCTC 57.405 43.478 23.35 0.00 44.26 2.75
124 125 5.299148 GCATACTGCAGAATCAAGATCTCT 58.701 41.667 23.35 0.00 44.26 3.10
125 126 5.759273 GCATACTGCAGAATCAAGATCTCTT 59.241 40.000 23.35 0.00 44.26 2.85
126 127 6.260493 GCATACTGCAGAATCAAGATCTCTTT 59.740 38.462 23.35 0.00 44.26 2.52
127 128 7.201714 GCATACTGCAGAATCAAGATCTCTTTT 60.202 37.037 23.35 0.00 44.26 2.27
128 129 8.675504 CATACTGCAGAATCAAGATCTCTTTTT 58.324 33.333 23.35 0.00 33.11 1.94
147 148 4.408182 TTTTTCCCCGAAAATTGCAGAA 57.592 36.364 0.71 0.00 40.50 3.02
148 149 4.615588 TTTTCCCCGAAAATTGCAGAAT 57.384 36.364 0.00 0.00 36.73 2.40
149 150 3.866883 TTCCCCGAAAATTGCAGAATC 57.133 42.857 0.00 0.00 0.00 2.52
150 151 2.801483 TCCCCGAAAATTGCAGAATCA 58.199 42.857 0.00 0.00 0.00 2.57
151 152 3.161067 TCCCCGAAAATTGCAGAATCAA 58.839 40.909 0.00 0.00 0.00 2.57
152 153 3.576118 TCCCCGAAAATTGCAGAATCAAA 59.424 39.130 0.00 0.00 0.00 2.69
197 199 0.751277 TGGTCACAAACTGCACAGGG 60.751 55.000 2.21 0.00 0.00 4.45
216 218 3.537795 GGAACCTTAAGGGAAAAGGGT 57.462 47.619 25.31 0.00 46.90 4.34
217 219 3.162666 GGAACCTTAAGGGAAAAGGGTG 58.837 50.000 25.31 0.00 44.22 4.61
218 220 3.181426 GGAACCTTAAGGGAAAAGGGTGA 60.181 47.826 25.31 0.00 44.22 4.02
219 221 4.476297 GAACCTTAAGGGAAAAGGGTGAA 58.524 43.478 25.31 0.00 44.22 3.18
220 222 4.546224 ACCTTAAGGGAAAAGGGTGAAA 57.454 40.909 25.31 0.00 46.56 2.69
221 223 4.480115 ACCTTAAGGGAAAAGGGTGAAAG 58.520 43.478 25.31 0.00 46.56 2.62
222 224 4.169264 ACCTTAAGGGAAAAGGGTGAAAGA 59.831 41.667 25.31 0.00 46.56 2.52
225 227 6.270000 CCTTAAGGGAAAAGGGTGAAAGAAAT 59.730 38.462 14.25 0.00 39.94 2.17
240 242 7.328493 GGTGAAAGAAATATAACACTTTGGCAC 59.672 37.037 0.00 0.00 33.61 5.01
245 248 2.969821 ATAACACTTTGGCACCAGGA 57.030 45.000 0.00 0.00 0.00 3.86
246 249 2.738587 TAACACTTTGGCACCAGGAA 57.261 45.000 0.00 0.00 0.00 3.36
272 275 1.336795 ACGACTCGATTGTGTGCATCA 60.337 47.619 5.20 0.00 0.00 3.07
314 318 6.603237 GGTTTCAACCTCCATTTCAAAAAG 57.397 37.500 1.08 0.00 45.75 2.27
333 337 7.650504 TCAAAAAGAAAAATCATGACTGCTCTG 59.349 33.333 0.00 0.00 0.00 3.35
336 340 7.750229 AAGAAAAATCATGACTGCTCTGTTA 57.250 32.000 0.00 0.00 0.00 2.41
346 350 2.169352 ACTGCTCTGTTATGCCGAGATT 59.831 45.455 0.00 0.00 0.00 2.40
347 351 2.799412 CTGCTCTGTTATGCCGAGATTC 59.201 50.000 0.00 0.00 0.00 2.52
349 353 3.198068 GCTCTGTTATGCCGAGATTCAA 58.802 45.455 0.00 0.00 0.00 2.69
352 358 5.220931 GCTCTGTTATGCCGAGATTCAAAAT 60.221 40.000 0.00 0.00 0.00 1.82
359 365 5.155509 TGCCGAGATTCAAAATTACATCG 57.844 39.130 0.00 0.00 0.00 3.84
375 381 9.800433 AAATTACATCGAAATCAATTATGCACA 57.200 25.926 0.00 0.00 0.00 4.57
389 395 1.434555 TGCACATAGCTAAAACGCGT 58.565 45.000 5.58 5.58 45.94 6.01
391 397 2.224549 TGCACATAGCTAAAACGCGTTT 59.775 40.909 30.36 30.36 45.94 3.60
394 400 4.647964 CACATAGCTAAAACGCGTTTGAT 58.352 39.130 35.31 24.70 32.36 2.57
399 405 7.223193 ACATAGCTAAAACGCGTTTGATATACA 59.777 33.333 35.31 18.35 32.36 2.29
400 406 6.032722 AGCTAAAACGCGTTTGATATACAG 57.967 37.500 35.31 22.17 32.36 2.74
401 407 4.664851 GCTAAAACGCGTTTGATATACAGC 59.335 41.667 35.31 26.39 32.36 4.40
402 408 4.939509 AAAACGCGTTTGATATACAGCT 57.060 36.364 35.31 14.62 32.36 4.24
403 409 3.925688 AACGCGTTTGATATACAGCTG 57.074 42.857 20.79 13.48 0.00 4.24
404 410 2.888594 ACGCGTTTGATATACAGCTGT 58.111 42.857 25.12 25.12 0.00 4.40
406 412 2.033747 CGCGTTTGATATACAGCTGTGG 60.034 50.000 29.57 7.77 0.00 4.17
407 413 2.286418 GCGTTTGATATACAGCTGTGGC 60.286 50.000 29.57 15.08 39.06 5.01
436 442 3.841845 TGGTACATAGTAGTTGGCCTTGT 59.158 43.478 3.32 0.00 0.00 3.16
568 574 4.816925 GGTGGGGAATTAAAATCTCGAGAG 59.183 45.833 21.52 0.00 0.00 3.20
713 722 7.611467 AGCAACTACATTGATAAATTCCTCACA 59.389 33.333 0.00 0.00 41.23 3.58
839 852 1.302192 GTCGGCTAGCAACCACCAA 60.302 57.895 18.24 0.00 0.00 3.67
975 988 2.590575 CACCACGACCACCACCAC 60.591 66.667 0.00 0.00 0.00 4.16
976 989 3.868985 ACCACGACCACCACCACC 61.869 66.667 0.00 0.00 0.00 4.61
977 990 3.867783 CCACGACCACCACCACCA 61.868 66.667 0.00 0.00 0.00 4.17
981 994 2.843545 GACCACCACCACCACCAT 59.156 61.111 0.00 0.00 0.00 3.55
983 996 1.152567 ACCACCACCACCACCATTG 60.153 57.895 0.00 0.00 0.00 2.82
985 998 2.203625 ACCACCACCACCATTGCC 60.204 61.111 0.00 0.00 0.00 4.52
994 1013 0.890683 CCACCATTGCCAAGGAGAAC 59.109 55.000 0.00 0.00 0.00 3.01
1116 1135 1.153823 CTTCCTCAACGACGGCGAT 60.154 57.895 22.49 0.16 41.64 4.58
1143 1162 4.436998 GGTGACGGCCAGGACGAG 62.437 72.222 25.69 0.00 35.20 4.18
1182 1201 1.372582 GCGGATTGATCAAGCACAGA 58.627 50.000 23.99 0.00 33.92 3.41
1256 1275 4.736307 CCAATGTTGCATATCAATCGTGTG 59.264 41.667 0.00 0.00 36.99 3.82
1297 1323 2.236893 TGTGATGGAGCTCTGCATGTAA 59.763 45.455 14.64 0.00 41.80 2.41
1298 1324 2.871022 GTGATGGAGCTCTGCATGTAAG 59.129 50.000 14.64 0.00 41.80 2.34
1299 1325 1.872313 GATGGAGCTCTGCATGTAAGC 59.128 52.381 14.64 8.98 41.80 3.09
1523 1549 1.338107 TGGTCGGTGAGAATGACACT 58.662 50.000 0.00 0.00 34.32 3.55
1554 1580 5.752472 CACTCTCATGATTGACGCTTCTAAT 59.248 40.000 0.00 0.00 0.00 1.73
1590 1622 8.649810 AGTTTTAAAATGCGTAATCAGTAACG 57.350 30.769 3.52 0.00 41.92 3.18
1620 1652 9.856488 GGAAGTCATTACCCTAAATTTTCTTTC 57.144 33.333 0.00 0.00 0.00 2.62
1764 1796 2.363975 GGGAGCCCACACCGACATA 61.364 63.158 0.00 0.00 35.81 2.29
1833 1865 1.298667 GGTGAGCCGCCTTCCTTTA 59.701 57.895 0.00 0.00 0.00 1.85
1840 1872 1.379527 CCGCCTTCCTTTATGTCCAC 58.620 55.000 0.00 0.00 0.00 4.02
1886 1918 0.307760 GGCCCGCTGATGAATAAACG 59.692 55.000 0.00 0.00 0.00 3.60
2042 2074 0.620121 CTCCCTCTTCCTGGCCTTCT 60.620 60.000 3.32 0.00 0.00 2.85
2044 2076 1.080498 TCCCTCTTCCTGGCCTTCTTA 59.920 52.381 3.32 0.00 0.00 2.10
2196 2228 3.755526 TTGCGGCGATGGATCCTGG 62.756 63.158 12.98 3.07 0.00 4.45
2204 2236 0.109342 GATGGATCCTGGGAATGCGT 59.891 55.000 14.23 0.00 0.00 5.24
2425 2467 8.246871 TGAAGTGCACATGTATATAGCTAGATC 58.753 37.037 21.04 0.00 0.00 2.75
2426 2468 7.106439 AGTGCACATGTATATAGCTAGATCC 57.894 40.000 21.04 0.00 0.00 3.36
2427 2469 6.894654 AGTGCACATGTATATAGCTAGATCCT 59.105 38.462 21.04 0.00 0.00 3.24
2428 2470 8.055790 AGTGCACATGTATATAGCTAGATCCTA 58.944 37.037 21.04 0.00 0.00 2.94
2429 2471 8.349245 GTGCACATGTATATAGCTAGATCCTAG 58.651 40.741 13.17 0.00 0.00 3.02
2430 2472 8.275040 TGCACATGTATATAGCTAGATCCTAGA 58.725 37.037 3.65 0.00 0.00 2.43
2431 2473 9.295825 GCACATGTATATAGCTAGATCCTAGAT 57.704 37.037 3.65 1.40 0.00 1.98
2473 2516 3.038017 CACAGAAAAGTCGTTGCATGTG 58.962 45.455 0.00 0.00 0.00 3.21
2512 2572 1.936547 GCAAGAGTAATTCAGGCTCCG 59.063 52.381 0.00 0.00 0.00 4.63
2538 2598 4.621087 GGGCTGGGCAACTTGGGT 62.621 66.667 0.00 0.00 0.00 4.51
2541 2601 1.607467 GCTGGGCAACTTGGGTCAT 60.607 57.895 0.00 0.00 0.00 3.06
2542 2602 0.323360 GCTGGGCAACTTGGGTCATA 60.323 55.000 0.00 0.00 0.00 2.15
2543 2603 1.755179 CTGGGCAACTTGGGTCATAG 58.245 55.000 0.00 0.00 0.00 2.23
2544 2604 0.331278 TGGGCAACTTGGGTCATAGG 59.669 55.000 0.00 0.00 0.00 2.57
2545 2605 0.623723 GGGCAACTTGGGTCATAGGA 59.376 55.000 0.00 0.00 0.00 2.94
2546 2606 1.682087 GGGCAACTTGGGTCATAGGAC 60.682 57.143 0.00 0.00 43.55 3.85
2547 2607 1.004277 GGCAACTTGGGTCATAGGACA 59.996 52.381 10.08 0.00 46.17 4.02
2550 2610 3.622206 GCAACTTGGGTCATAGGACATCA 60.622 47.826 10.08 4.39 46.17 3.07
2551 2611 4.194640 CAACTTGGGTCATAGGACATCAG 58.805 47.826 10.08 3.95 46.17 2.90
2552 2612 2.171448 ACTTGGGTCATAGGACATCAGC 59.829 50.000 10.08 0.00 46.17 4.26
2553 2613 2.180946 TGGGTCATAGGACATCAGCT 57.819 50.000 10.08 0.00 46.17 4.24
2554 2614 3.328535 TGGGTCATAGGACATCAGCTA 57.671 47.619 10.08 0.00 46.17 3.32
2555 2615 3.861846 TGGGTCATAGGACATCAGCTAT 58.138 45.455 10.08 0.00 46.17 2.97
2556 2616 3.834813 TGGGTCATAGGACATCAGCTATC 59.165 47.826 10.08 0.00 46.17 2.08
2557 2617 4.093011 GGGTCATAGGACATCAGCTATCT 58.907 47.826 10.08 0.00 46.17 1.98
2558 2618 4.530161 GGGTCATAGGACATCAGCTATCTT 59.470 45.833 10.08 0.00 46.17 2.40
2560 2620 6.350612 GGGTCATAGGACATCAGCTATCTTAC 60.351 46.154 10.08 0.00 46.17 2.34
2561 2621 6.435904 GGTCATAGGACATCAGCTATCTTACT 59.564 42.308 10.08 0.00 46.17 2.24
2563 2623 8.364142 GTCATAGGACATCAGCTATCTTACTTT 58.636 37.037 1.92 0.00 43.73 2.66
2565 2625 9.853555 CATAGGACATCAGCTATCTTACTTTAG 57.146 37.037 0.00 0.00 0.00 1.85
2566 2626 9.815306 ATAGGACATCAGCTATCTTACTTTAGA 57.185 33.333 0.00 0.00 0.00 2.10
2568 2628 8.584157 AGGACATCAGCTATCTTACTTTAGATG 58.416 37.037 0.00 0.00 36.34 2.90
2569 2629 7.816995 GGACATCAGCTATCTTACTTTAGATGG 59.183 40.741 0.00 0.00 36.34 3.51
2685 3253 2.124983 CCACCATCCTCGTGGCTG 60.125 66.667 0.00 0.00 44.10 4.85
2686 3254 2.665000 CACCATCCTCGTGGCTGT 59.335 61.111 6.61 0.00 43.27 4.40
2687 3255 1.003355 CACCATCCTCGTGGCTGTT 60.003 57.895 6.61 0.00 43.27 3.16
2688 3256 0.249120 CACCATCCTCGTGGCTGTTA 59.751 55.000 6.61 0.00 43.27 2.41
2689 3257 0.537188 ACCATCCTCGTGGCTGTTAG 59.463 55.000 6.61 0.00 43.27 2.34
2690 3258 0.824109 CCATCCTCGTGGCTGTTAGA 59.176 55.000 6.61 0.00 31.43 2.10
2691 3259 1.414181 CCATCCTCGTGGCTGTTAGAT 59.586 52.381 6.61 0.00 31.43 1.98
2692 3260 2.477825 CATCCTCGTGGCTGTTAGATG 58.522 52.381 0.00 0.00 0.00 2.90
2693 3261 1.557099 TCCTCGTGGCTGTTAGATGT 58.443 50.000 0.00 0.00 0.00 3.06
2694 3262 2.730382 TCCTCGTGGCTGTTAGATGTA 58.270 47.619 0.00 0.00 0.00 2.29
2695 3263 3.296854 TCCTCGTGGCTGTTAGATGTAT 58.703 45.455 0.00 0.00 0.00 2.29
2696 3264 3.704566 TCCTCGTGGCTGTTAGATGTATT 59.295 43.478 0.00 0.00 0.00 1.89
2697 3265 4.161565 TCCTCGTGGCTGTTAGATGTATTT 59.838 41.667 0.00 0.00 0.00 1.40
2698 3266 4.876107 CCTCGTGGCTGTTAGATGTATTTT 59.124 41.667 0.00 0.00 0.00 1.82
2699 3267 5.354234 CCTCGTGGCTGTTAGATGTATTTTT 59.646 40.000 0.00 0.00 0.00 1.94
2734 3302 8.016301 AGAATGAGCTGTTAGATGTATTCTCA 57.984 34.615 0.00 0.00 35.79 3.27
2753 3321 3.808728 TCATCTAGTACAAGGCAATGGC 58.191 45.455 0.00 0.00 40.13 4.40
2756 3324 1.665679 CTAGTACAAGGCAATGGCACG 59.334 52.381 10.05 1.47 43.71 5.34
2758 3326 1.094785 GTACAAGGCAATGGCACGAT 58.905 50.000 10.05 0.00 43.71 3.73
2760 3328 1.832883 ACAAGGCAATGGCACGATAA 58.167 45.000 10.05 0.00 43.71 1.75
2806 3374 1.819632 GGGGACAGTGGCTAATGCG 60.820 63.158 0.00 0.00 40.82 4.73
2830 3398 2.232452 ACTAGATCCTATGATGCCGTGC 59.768 50.000 0.00 0.00 0.00 5.34
2927 3495 6.484308 TGTCGTGAGGTAATACATCGATCTTA 59.516 38.462 0.00 0.00 30.36 2.10
2928 3496 7.016466 GTCGTGAGGTAATACATCGATCTTAG 58.984 42.308 0.00 0.00 30.36 2.18
2931 3499 8.666573 CGTGAGGTAATACATCGATCTTAGTAT 58.333 37.037 0.00 0.00 30.36 2.12
2966 3534 2.529389 AGGTTGTCCTCCGGCCTT 60.529 61.111 0.00 0.00 40.58 4.35
2967 3535 2.046217 GGTTGTCCTCCGGCCTTC 60.046 66.667 0.00 0.00 0.00 3.46
2968 3536 2.434359 GTTGTCCTCCGGCCTTCG 60.434 66.667 0.00 0.00 38.88 3.79
2969 3537 4.388499 TTGTCCTCCGGCCTTCGC 62.388 66.667 0.00 0.00 37.59 4.70
2972 3540 3.849951 TCCTCCGGCCTTCGCATC 61.850 66.667 0.00 0.00 37.59 3.91
2973 3541 4.161295 CCTCCGGCCTTCGCATCA 62.161 66.667 0.00 0.00 37.59 3.07
2974 3542 2.587194 CTCCGGCCTTCGCATCAG 60.587 66.667 0.00 0.00 37.59 2.90
2976 3544 2.125147 CCGGCCTTCGCATCAGAA 60.125 61.111 0.00 0.00 37.59 3.02
2977 3545 2.464459 CCGGCCTTCGCATCAGAAC 61.464 63.158 0.00 0.00 37.59 3.01
2979 3547 1.447838 GGCCTTCGCATCAGAACGA 60.448 57.895 0.00 0.00 36.38 3.85
2987 3555 3.432759 CATCAGAACGATGCATGCG 57.567 52.632 14.09 10.48 44.95 4.73
2992 3644 0.462581 AGAACGATGCATGCGACCAT 60.463 50.000 20.36 0.00 0.00 3.55
2993 3645 0.041839 GAACGATGCATGCGACCATC 60.042 55.000 20.36 9.35 35.61 3.51
2995 3647 0.877649 ACGATGCATGCGACCATCTC 60.878 55.000 20.36 0.29 36.55 2.75
3001 3653 3.479489 TGCATGCGACCATCTCATTAAT 58.521 40.909 14.09 0.00 0.00 1.40
3003 3655 5.062528 TGCATGCGACCATCTCATTAATAA 58.937 37.500 14.09 0.00 0.00 1.40
3006 3658 4.702831 TGCGACCATCTCATTAATAAGCA 58.297 39.130 0.00 0.00 0.00 3.91
3010 3665 6.634436 GCGACCATCTCATTAATAAGCAAAAG 59.366 38.462 0.00 0.00 0.00 2.27
3025 3680 9.468532 AATAAGCAAAAGATTCAACAAAGTCTC 57.531 29.630 0.00 0.00 0.00 3.36
3030 3685 4.713792 AGATTCAACAAAGTCTCCAGGT 57.286 40.909 0.00 0.00 0.00 4.00
3031 3686 4.646572 AGATTCAACAAAGTCTCCAGGTC 58.353 43.478 0.00 0.00 0.00 3.85
3032 3687 4.349342 AGATTCAACAAAGTCTCCAGGTCT 59.651 41.667 0.00 0.00 0.00 3.85
3033 3688 3.753294 TCAACAAAGTCTCCAGGTCTC 57.247 47.619 0.00 0.00 0.00 3.36
3034 3689 3.038280 TCAACAAAGTCTCCAGGTCTCA 58.962 45.455 0.00 0.00 0.00 3.27
3035 3690 3.454447 TCAACAAAGTCTCCAGGTCTCAA 59.546 43.478 0.00 0.00 0.00 3.02
3037 3692 4.503714 ACAAAGTCTCCAGGTCTCAAAA 57.496 40.909 0.00 0.00 0.00 2.44
3038 3693 4.855340 ACAAAGTCTCCAGGTCTCAAAAA 58.145 39.130 0.00 0.00 0.00 1.94
3039 3694 4.884164 ACAAAGTCTCCAGGTCTCAAAAAG 59.116 41.667 0.00 0.00 0.00 2.27
3040 3695 3.778954 AGTCTCCAGGTCTCAAAAAGG 57.221 47.619 0.00 0.00 0.00 3.11
3041 3696 3.049344 AGTCTCCAGGTCTCAAAAAGGT 58.951 45.455 0.00 0.00 0.00 3.50
3043 3698 1.882623 CTCCAGGTCTCAAAAAGGTGC 59.117 52.381 0.00 0.00 0.00 5.01
3047 3702 3.491447 CCAGGTCTCAAAAAGGTGCAAAG 60.491 47.826 0.00 0.00 0.00 2.77
3049 3704 2.473816 GTCTCAAAAAGGTGCAAAGCC 58.526 47.619 0.00 0.00 0.00 4.35
3050 3705 2.101415 GTCTCAAAAAGGTGCAAAGCCT 59.899 45.455 0.00 0.00 38.11 4.58
3051 3706 2.362077 TCTCAAAAAGGTGCAAAGCCTC 59.638 45.455 0.00 0.00 34.81 4.70
3054 4044 1.484038 AAAAGGTGCAAAGCCTCACA 58.516 45.000 0.00 0.00 34.81 3.58
3060 4050 0.670162 TGCAAAGCCTCACAAAGAGC 59.330 50.000 0.00 0.00 43.31 4.09
3066 4056 2.936202 AGCCTCACAAAGAGCAAGAAA 58.064 42.857 0.00 0.00 43.31 2.52
3069 4059 3.798878 GCCTCACAAAGAGCAAGAAAAAC 59.201 43.478 0.00 0.00 43.31 2.43
3071 4061 5.594926 CCTCACAAAGAGCAAGAAAAACAT 58.405 37.500 0.00 0.00 43.31 2.71
3075 4065 7.095910 TCACAAAGAGCAAGAAAAACATGAAA 58.904 30.769 0.00 0.00 0.00 2.69
3076 4066 7.063308 TCACAAAGAGCAAGAAAAACATGAAAC 59.937 33.333 0.00 0.00 0.00 2.78
3077 4067 6.034898 ACAAAGAGCAAGAAAAACATGAAACG 59.965 34.615 0.00 0.00 0.00 3.60
3079 4069 3.716601 AGCAAGAAAAACATGAAACGGG 58.283 40.909 0.00 0.00 0.00 5.28
3081 4071 4.039124 AGCAAGAAAAACATGAAACGGGAT 59.961 37.500 0.00 0.00 0.00 3.85
3082 4072 5.242838 AGCAAGAAAAACATGAAACGGGATA 59.757 36.000 0.00 0.00 0.00 2.59
3083 4073 5.572896 GCAAGAAAAACATGAAACGGGATAG 59.427 40.000 0.00 0.00 0.00 2.08
3084 4074 5.310720 AGAAAAACATGAAACGGGATAGC 57.689 39.130 0.00 0.00 0.00 2.97
3085 4075 4.157840 AGAAAAACATGAAACGGGATAGCC 59.842 41.667 0.00 0.00 0.00 3.93
3087 4077 2.038387 ACATGAAACGGGATAGCCAC 57.962 50.000 0.00 0.00 35.15 5.01
3089 4079 2.290641 ACATGAAACGGGATAGCCACAA 60.291 45.455 0.00 0.00 35.15 3.33
3091 4081 1.092348 GAAACGGGATAGCCACAACC 58.908 55.000 0.00 0.00 35.15 3.77
3100 4090 2.437002 GCCACAACCGGCGGAATA 60.437 61.111 35.78 0.00 43.52 1.75
3104 4094 1.269998 CCACAACCGGCGGAATAAAAA 59.730 47.619 35.78 0.00 0.00 1.94
3105 4095 2.094442 CCACAACCGGCGGAATAAAAAT 60.094 45.455 35.78 3.72 0.00 1.82
3106 4096 3.128938 CCACAACCGGCGGAATAAAAATA 59.871 43.478 35.78 0.00 0.00 1.40
3108 4098 4.095185 CACAACCGGCGGAATAAAAATAGA 59.905 41.667 35.78 0.00 0.00 1.98
3109 4099 4.885325 ACAACCGGCGGAATAAAAATAGAT 59.115 37.500 35.78 0.96 0.00 1.98
3110 4100 6.017770 CACAACCGGCGGAATAAAAATAGATA 60.018 38.462 35.78 0.00 0.00 1.98
3112 4102 6.796705 ACCGGCGGAATAAAAATAGATAAG 57.203 37.500 35.78 0.00 0.00 1.73
3113 4103 6.527423 ACCGGCGGAATAAAAATAGATAAGA 58.473 36.000 35.78 0.00 0.00 2.10
3114 4104 6.993902 ACCGGCGGAATAAAAATAGATAAGAA 59.006 34.615 35.78 0.00 0.00 2.52
3115 4105 7.172703 ACCGGCGGAATAAAAATAGATAAGAAG 59.827 37.037 35.78 0.00 0.00 2.85
3119 4118 8.994170 GCGGAATAAAAATAGATAAGAAGCTCT 58.006 33.333 0.00 0.00 0.00 4.09
3187 4186 1.006571 GGCACGTCGACTTCCTTGA 60.007 57.895 14.70 0.00 0.00 3.02
3210 4209 2.307496 TCACCCCTACAACGAGGTTA 57.693 50.000 0.00 0.00 34.45 2.85
3224 4223 5.700722 ACGAGGTTATTTTCTTGGGTTTC 57.299 39.130 0.00 0.00 0.00 2.78
3259 4258 6.670695 AGTGGCTTATCATTTGAAAACCTT 57.329 33.333 0.00 0.00 0.00 3.50
3335 4334 5.914635 CACAAATGGCATGTACGGATTATTC 59.085 40.000 0.00 0.00 0.00 1.75
3337 4336 3.847671 TGGCATGTACGGATTATTCCA 57.152 42.857 4.60 0.00 42.74 3.53
3338 4337 4.365514 TGGCATGTACGGATTATTCCAT 57.634 40.909 4.60 0.00 42.74 3.41
3339 4338 5.491323 TGGCATGTACGGATTATTCCATA 57.509 39.130 4.60 0.00 42.74 2.74
3340 4339 5.242434 TGGCATGTACGGATTATTCCATAC 58.758 41.667 3.49 3.49 42.74 2.39
3346 4345 2.038033 ACGGATTATTCCATACACCCCG 59.962 50.000 4.60 0.00 42.74 5.73
3358 4358 1.378382 CACCCCGTGCATGATTGGA 60.378 57.895 7.72 0.00 0.00 3.53
3389 4389 1.160137 GCACGCTTCAAGGAGTCATT 58.840 50.000 0.00 0.00 0.00 2.57
3390 4390 1.537202 GCACGCTTCAAGGAGTCATTT 59.463 47.619 0.00 0.00 0.00 2.32
3392 4392 3.558505 CACGCTTCAAGGAGTCATTTTG 58.441 45.455 0.00 0.00 0.00 2.44
3393 4393 3.250762 CACGCTTCAAGGAGTCATTTTGA 59.749 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.611374 TGTTCTAAGAAGGAAGGACAACAG 58.389 41.667 0.00 0.00 0.00 3.16
126 127 4.408182 TTCTGCAATTTTCGGGGAAAAA 57.592 36.364 7.52 0.00 43.32 1.94
127 128 4.039730 TGATTCTGCAATTTTCGGGGAAAA 59.960 37.500 6.05 6.05 44.04 2.29
128 129 3.576118 TGATTCTGCAATTTTCGGGGAAA 59.424 39.130 0.00 0.00 0.00 3.13
129 130 3.161067 TGATTCTGCAATTTTCGGGGAA 58.839 40.909 0.00 0.00 0.00 3.97
130 131 2.801483 TGATTCTGCAATTTTCGGGGA 58.199 42.857 0.00 0.00 0.00 4.81
131 132 3.591196 TTGATTCTGCAATTTTCGGGG 57.409 42.857 0.00 0.00 0.00 5.73
132 133 6.484818 AATTTTGATTCTGCAATTTTCGGG 57.515 33.333 0.00 0.00 0.00 5.14
172 173 0.740737 GCAGTTTGTGACCAGCTGTT 59.259 50.000 13.81 0.00 31.87 3.16
180 181 1.065551 GTTCCCTGTGCAGTTTGTGAC 59.934 52.381 0.00 0.00 0.00 3.67
197 199 4.108501 TCACCCTTTTCCCTTAAGGTTC 57.891 45.455 20.22 0.00 40.47 3.62
211 213 8.585018 CCAAAGTGTTATATTTCTTTCACCCTT 58.415 33.333 0.00 0.00 0.00 3.95
212 214 7.309805 GCCAAAGTGTTATATTTCTTTCACCCT 60.310 37.037 0.00 0.00 0.00 4.34
213 215 6.811665 GCCAAAGTGTTATATTTCTTTCACCC 59.188 38.462 0.00 0.00 0.00 4.61
214 216 7.328493 GTGCCAAAGTGTTATATTTCTTTCACC 59.672 37.037 0.00 0.00 0.00 4.02
215 217 7.328493 GGTGCCAAAGTGTTATATTTCTTTCAC 59.672 37.037 0.00 0.00 30.76 3.18
216 218 7.014711 TGGTGCCAAAGTGTTATATTTCTTTCA 59.985 33.333 0.00 0.00 0.00 2.69
217 219 7.375053 TGGTGCCAAAGTGTTATATTTCTTTC 58.625 34.615 0.00 0.00 0.00 2.62
218 220 7.296628 TGGTGCCAAAGTGTTATATTTCTTT 57.703 32.000 0.00 0.00 0.00 2.52
219 221 6.071391 CCTGGTGCCAAAGTGTTATATTTCTT 60.071 38.462 0.00 0.00 0.00 2.52
220 222 5.418840 CCTGGTGCCAAAGTGTTATATTTCT 59.581 40.000 0.00 0.00 0.00 2.52
221 223 5.417580 TCCTGGTGCCAAAGTGTTATATTTC 59.582 40.000 0.00 0.00 0.00 2.17
222 224 5.329399 TCCTGGTGCCAAAGTGTTATATTT 58.671 37.500 0.00 0.00 0.00 1.40
225 227 4.374689 TTCCTGGTGCCAAAGTGTTATA 57.625 40.909 0.00 0.00 0.00 0.98
246 249 3.303132 GCACACAATCGAGTCGTCTTTTT 60.303 43.478 13.12 0.00 0.00 1.94
253 256 1.349234 TGATGCACACAATCGAGTCG 58.651 50.000 6.09 6.09 0.00 4.18
256 259 5.662211 TCATTATGATGCACACAATCGAG 57.338 39.130 0.00 0.00 33.14 4.04
257 260 5.992729 CATCATTATGATGCACACAATCGA 58.007 37.500 20.33 0.00 46.37 3.59
272 275 2.968574 ACCTCCGTCTCTGCATCATTAT 59.031 45.455 0.00 0.00 0.00 1.28
308 312 7.437267 ACAGAGCAGTCATGATTTTTCTTTTTG 59.563 33.333 0.00 0.00 0.00 2.44
309 313 7.495055 ACAGAGCAGTCATGATTTTTCTTTTT 58.505 30.769 0.00 0.00 0.00 1.94
314 318 6.471519 GCATAACAGAGCAGTCATGATTTTTC 59.528 38.462 0.00 0.00 0.00 2.29
319 323 3.474600 GGCATAACAGAGCAGTCATGAT 58.525 45.455 0.00 0.00 0.00 2.45
320 324 2.739609 CGGCATAACAGAGCAGTCATGA 60.740 50.000 0.00 0.00 0.00 3.07
321 325 1.596260 CGGCATAACAGAGCAGTCATG 59.404 52.381 0.00 0.00 0.00 3.07
333 337 7.321271 CGATGTAATTTTGAATCTCGGCATAAC 59.679 37.037 0.00 0.00 0.00 1.89
336 340 5.527214 TCGATGTAATTTTGAATCTCGGCAT 59.473 36.000 0.00 0.00 0.00 4.40
349 353 9.800433 TGTGCATAATTGATTTCGATGTAATTT 57.200 25.926 0.00 0.00 0.00 1.82
373 379 4.939509 ATCAAACGCGTTTTAGCTATGT 57.060 36.364 33.05 7.91 34.40 2.29
375 381 7.568861 GCTGTATATCAAACGCGTTTTAGCTAT 60.569 37.037 33.05 23.43 34.40 2.97
385 391 2.033747 CCACAGCTGTATATCAAACGCG 60.034 50.000 21.20 3.53 0.00 6.01
399 405 4.655021 TGTACCAAACACAGCCACAGCT 62.655 50.000 0.00 0.00 41.50 4.24
400 406 0.310854 GTACCAAACACAGCCACAGC 59.689 55.000 0.00 0.00 40.32 4.40
401 407 1.674359 TGTACCAAACACAGCCACAG 58.326 50.000 0.00 0.00 31.43 3.66
402 408 2.356665 ATGTACCAAACACAGCCACA 57.643 45.000 0.00 0.00 42.09 4.17
403 409 3.408634 ACTATGTACCAAACACAGCCAC 58.591 45.455 0.00 0.00 42.09 5.01
404 410 3.780804 ACTATGTACCAAACACAGCCA 57.219 42.857 0.00 0.00 42.09 4.75
406 412 5.121768 CCAACTACTATGTACCAAACACAGC 59.878 44.000 0.00 0.00 42.09 4.40
407 413 5.121768 GCCAACTACTATGTACCAAACACAG 59.878 44.000 0.00 0.00 42.09 3.66
590 596 6.645790 AAATGAGCAGGATAACCAATCATC 57.354 37.500 4.76 0.00 35.42 2.92
635 641 3.634283 CCATTTTCCAACACGGTAACAC 58.366 45.455 0.00 0.00 35.57 3.32
640 646 0.673437 CTGCCATTTTCCAACACGGT 59.327 50.000 0.00 0.00 35.57 4.83
713 722 7.063074 CGAATGTACTCCAAAAGATAAAGACGT 59.937 37.037 0.00 0.00 0.00 4.34
788 801 4.451096 CACAAGCAGTACGTGGAACTAATT 59.549 41.667 0.00 0.00 31.20 1.40
789 802 3.994392 CACAAGCAGTACGTGGAACTAAT 59.006 43.478 0.00 0.00 31.20 1.73
790 803 3.386486 CACAAGCAGTACGTGGAACTAA 58.614 45.455 0.00 0.00 31.20 2.24
791 804 3.021269 CACAAGCAGTACGTGGAACTA 57.979 47.619 0.00 0.00 31.20 2.24
872 885 0.773644 AGGAGGATGGTGTGTTGCTT 59.226 50.000 0.00 0.00 0.00 3.91
975 988 0.890683 GTTCTCCTTGGCAATGGTGG 59.109 55.000 0.00 0.00 0.00 4.61
976 989 0.523072 CGTTCTCCTTGGCAATGGTG 59.477 55.000 0.00 5.97 0.00 4.17
977 990 0.400213 TCGTTCTCCTTGGCAATGGT 59.600 50.000 0.00 0.00 0.00 3.55
981 994 0.179032 TGCTTCGTTCTCCTTGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
983 996 0.449388 CATGCTTCGTTCTCCTTGGC 59.551 55.000 0.00 0.00 0.00 4.52
985 998 1.734465 GTCCATGCTTCGTTCTCCTTG 59.266 52.381 0.00 0.00 0.00 3.61
1139 1158 3.923864 TCACCAAGCCACGCTCGT 61.924 61.111 0.00 0.00 38.25 4.18
1182 1201 1.708993 TTGCCTTGGTGGAGCTGTCT 61.709 55.000 0.00 0.00 38.35 3.41
1256 1275 4.296690 ACAGTTCGTGACAGCTTAAGTAC 58.703 43.478 4.02 0.00 0.00 2.73
1297 1323 4.836825 TCAGCTTAAGTATCTTGCTTGCT 58.163 39.130 4.02 0.00 0.00 3.91
1298 1324 5.065731 ACATCAGCTTAAGTATCTTGCTTGC 59.934 40.000 4.02 0.00 0.00 4.01
1299 1325 6.238320 GGACATCAGCTTAAGTATCTTGCTTG 60.238 42.308 4.02 0.00 0.00 4.01
1523 1549 2.028203 TCAATCATGAGAGTGGCGTCAA 60.028 45.455 0.09 0.00 40.13 3.18
1554 1580 8.690680 ACGCATTTTAAAACTTTAACTGAACA 57.309 26.923 1.97 0.00 32.77 3.18
1590 1622 1.125633 TAGGGTAATGACTTCCCGGC 58.874 55.000 0.00 0.00 45.27 6.13
1620 1652 2.029649 CCCCTGCTTCAACATCACAAAG 60.030 50.000 0.00 0.00 0.00 2.77
1707 1739 3.003173 CCCTGCTCGAGGAACCCA 61.003 66.667 15.58 1.81 46.33 4.51
1764 1796 2.504367 CCATTTCCTGGTTTGACGACT 58.496 47.619 0.00 0.00 40.49 4.18
1776 1808 3.774599 GATCGGCGGCCCATTTCCT 62.775 63.158 14.55 0.00 0.00 3.36
1833 1865 2.272146 GGCGGTGATGGTGGACAT 59.728 61.111 0.00 0.00 44.18 3.06
1872 1904 9.394477 GGGTTAATTATTCGTTTATTCATCAGC 57.606 33.333 0.00 0.00 0.00 4.26
1873 1905 9.893305 GGGGTTAATTATTCGTTTATTCATCAG 57.107 33.333 0.00 0.00 0.00 2.90
1886 1918 1.605232 CACGGCCGGGGTTAATTATTC 59.395 52.381 31.76 0.00 0.00 1.75
2008 2040 3.444805 GAGAGCTCGTCGTGGGCT 61.445 66.667 8.37 4.48 39.16 5.19
2042 2074 0.258484 TCGAGGGTCCCGGTGTATAA 59.742 55.000 0.99 0.00 0.00 0.98
2044 2076 1.755783 GTCGAGGGTCCCGGTGTAT 60.756 63.158 0.99 0.00 0.00 2.29
2128 2160 4.959446 GGCACGTCGTACTTGTCT 57.041 55.556 0.00 0.00 0.00 3.41
2178 2210 2.203056 CAGGATCCATCGCCGCAA 60.203 61.111 15.82 0.00 0.00 4.85
2179 2211 4.240103 CCAGGATCCATCGCCGCA 62.240 66.667 15.82 0.00 0.00 5.69
2204 2236 4.680237 CACCTCCAGCGTCCGCAA 62.680 66.667 14.70 0.00 44.88 4.85
2409 2441 9.519191 CTGCATCTAGGATCTAGCTATATACAT 57.481 37.037 4.30 0.00 0.00 2.29
2447 2490 1.164041 AACGACTTTTCTGTGCCCGG 61.164 55.000 0.00 0.00 0.00 5.73
2479 2522 1.470098 ACTCTTGCATTTGATCGCACC 59.530 47.619 0.00 0.00 38.00 5.01
2512 2572 2.360475 GCCCAGCCCTGAACTGAC 60.360 66.667 0.00 0.00 37.32 3.51
2538 2598 8.484214 AAAGTAAGATAGCTGATGTCCTATGA 57.516 34.615 0.00 0.00 0.00 2.15
2541 2601 9.815306 ATCTAAAGTAAGATAGCTGATGTCCTA 57.185 33.333 0.00 0.00 34.40 2.94
2542 2602 8.584157 CATCTAAAGTAAGATAGCTGATGTCCT 58.416 37.037 0.00 0.00 34.40 3.85
2543 2603 7.816995 CCATCTAAAGTAAGATAGCTGATGTCC 59.183 40.741 0.00 0.00 34.40 4.02
2544 2604 8.580720 TCCATCTAAAGTAAGATAGCTGATGTC 58.419 37.037 0.00 0.00 34.40 3.06
2545 2605 8.364142 GTCCATCTAAAGTAAGATAGCTGATGT 58.636 37.037 0.00 0.00 34.40 3.06
2546 2606 7.816995 GGTCCATCTAAAGTAAGATAGCTGATG 59.183 40.741 0.00 0.00 34.40 3.07
2547 2607 7.038658 GGGTCCATCTAAAGTAAGATAGCTGAT 60.039 40.741 0.00 0.00 34.40 2.90
2550 2610 6.143915 TGGGTCCATCTAAAGTAAGATAGCT 58.856 40.000 0.00 0.00 34.40 3.32
2551 2611 6.420913 TGGGTCCATCTAAAGTAAGATAGC 57.579 41.667 0.00 0.00 34.40 2.97
2552 2612 8.532819 GGTATGGGTCCATCTAAAGTAAGATAG 58.467 40.741 5.67 0.00 37.82 2.08
2553 2613 8.239478 AGGTATGGGTCCATCTAAAGTAAGATA 58.761 37.037 5.67 0.00 37.82 1.98
2554 2614 7.082972 AGGTATGGGTCCATCTAAAGTAAGAT 58.917 38.462 5.67 0.00 37.82 2.40
2555 2615 6.449956 AGGTATGGGTCCATCTAAAGTAAGA 58.550 40.000 5.67 0.00 37.82 2.10
2556 2616 6.749036 AGGTATGGGTCCATCTAAAGTAAG 57.251 41.667 5.67 0.00 37.82 2.34
2557 2617 6.445786 ACAAGGTATGGGTCCATCTAAAGTAA 59.554 38.462 5.67 0.00 37.82 2.24
2558 2618 5.968167 ACAAGGTATGGGTCCATCTAAAGTA 59.032 40.000 5.67 0.00 37.82 2.24
2560 2620 5.126067 CACAAGGTATGGGTCCATCTAAAG 58.874 45.833 5.67 0.00 37.82 1.85
2561 2621 4.538490 ACACAAGGTATGGGTCCATCTAAA 59.462 41.667 5.67 0.00 44.33 1.85
2563 2623 3.731431 ACACAAGGTATGGGTCCATCTA 58.269 45.455 5.67 0.00 44.33 1.98
2702 3270 6.650807 ACATCTAACAGCTCATTCTCGAAAAA 59.349 34.615 0.00 0.00 0.00 1.94
2703 3271 6.166279 ACATCTAACAGCTCATTCTCGAAAA 58.834 36.000 0.00 0.00 0.00 2.29
2704 3272 5.724328 ACATCTAACAGCTCATTCTCGAAA 58.276 37.500 0.00 0.00 0.00 3.46
2705 3273 5.330455 ACATCTAACAGCTCATTCTCGAA 57.670 39.130 0.00 0.00 0.00 3.71
2706 3274 4.991153 ACATCTAACAGCTCATTCTCGA 57.009 40.909 0.00 0.00 0.00 4.04
2707 3275 7.144661 AGAATACATCTAACAGCTCATTCTCG 58.855 38.462 0.00 0.00 36.32 4.04
2708 3276 8.140628 TGAGAATACATCTAACAGCTCATTCTC 58.859 37.037 12.00 12.00 43.60 2.87
2709 3277 8.016301 TGAGAATACATCTAACAGCTCATTCT 57.984 34.615 0.00 0.00 38.96 2.40
2710 3278 8.830201 ATGAGAATACATCTAACAGCTCATTC 57.170 34.615 0.00 0.00 38.33 2.67
2711 3279 8.830201 GATGAGAATACATCTAACAGCTCATT 57.170 34.615 0.00 0.00 40.69 2.57
2734 3302 3.545703 GTGCCATTGCCTTGTACTAGAT 58.454 45.455 5.85 0.00 36.33 1.98
2753 3321 2.603560 GGCGGAGAAAAGACTTATCGTG 59.396 50.000 0.00 0.00 0.00 4.35
2756 3324 3.623510 CCTTGGCGGAGAAAAGACTTATC 59.376 47.826 0.00 0.00 33.16 1.75
2758 3326 2.874457 GCCTTGGCGGAGAAAAGACTTA 60.874 50.000 0.00 0.00 33.16 2.24
2760 3328 0.606673 GCCTTGGCGGAGAAAAGACT 60.607 55.000 0.00 0.00 33.16 3.24
2785 3353 1.683943 CATTAGCCACTGTCCCCATG 58.316 55.000 0.00 0.00 0.00 3.66
2806 3374 2.478709 CGGCATCATAGGATCTAGTCGC 60.479 54.545 0.00 0.00 0.00 5.19
2830 3398 4.760047 CACCTTGGACCGCCCGAG 62.760 72.222 0.00 3.11 44.70 4.63
2848 3416 4.321008 CCTCGCCAATACACACTATATCGT 60.321 45.833 0.00 0.00 0.00 3.73
2957 3525 2.578163 TTCTGATGCGAAGGCCGGAG 62.578 60.000 5.05 0.00 43.19 4.63
2958 3526 2.655073 TTCTGATGCGAAGGCCGGA 61.655 57.895 5.05 0.00 44.31 5.14
2959 3527 2.125147 TTCTGATGCGAAGGCCGG 60.125 61.111 0.00 0.00 38.85 6.13
2960 3528 2.802667 CGTTCTGATGCGAAGGCCG 61.803 63.158 0.00 0.00 38.85 6.13
2962 3530 2.682893 ATCGTTCTGATGCGAAGGC 58.317 52.632 8.48 0.00 40.61 4.35
2970 3538 0.933097 GTCGCATGCATCGTTCTGAT 59.067 50.000 19.57 0.00 38.01 2.90
2972 3540 1.349627 GGTCGCATGCATCGTTCTG 59.650 57.895 19.57 0.00 0.00 3.02
2973 3541 0.462581 ATGGTCGCATGCATCGTTCT 60.463 50.000 19.57 0.00 0.00 3.01
2974 3542 0.041839 GATGGTCGCATGCATCGTTC 60.042 55.000 19.57 4.87 0.00 3.95
2976 3544 0.877649 GAGATGGTCGCATGCATCGT 60.878 55.000 19.57 6.66 0.00 3.73
2977 3545 0.877213 TGAGATGGTCGCATGCATCG 60.877 55.000 19.57 4.09 0.00 3.84
2979 3547 1.977056 AATGAGATGGTCGCATGCAT 58.023 45.000 19.57 2.77 37.00 3.96
2981 3549 5.611796 TTATTAATGAGATGGTCGCATGC 57.388 39.130 7.91 7.91 37.00 4.06
2983 3551 5.308014 TGCTTATTAATGAGATGGTCGCAT 58.692 37.500 11.23 0.00 38.55 4.73
2984 3552 4.702831 TGCTTATTAATGAGATGGTCGCA 58.297 39.130 11.23 0.00 0.00 5.10
2985 3553 5.673337 TTGCTTATTAATGAGATGGTCGC 57.327 39.130 11.23 0.00 0.00 5.19
2986 3554 7.919690 TCTTTTGCTTATTAATGAGATGGTCG 58.080 34.615 11.23 0.00 0.00 4.79
3001 3653 7.068103 TGGAGACTTTGTTGAATCTTTTGCTTA 59.932 33.333 0.00 0.00 0.00 3.09
3003 3655 5.360714 TGGAGACTTTGTTGAATCTTTTGCT 59.639 36.000 0.00 0.00 0.00 3.91
3006 3658 5.893824 ACCTGGAGACTTTGTTGAATCTTTT 59.106 36.000 0.00 0.00 0.00 2.27
3010 3665 4.646572 AGACCTGGAGACTTTGTTGAATC 58.353 43.478 0.00 0.00 0.00 2.52
3014 3669 3.475566 TGAGACCTGGAGACTTTGTTG 57.524 47.619 0.00 0.00 0.00 3.33
3015 3670 4.503714 TTTGAGACCTGGAGACTTTGTT 57.496 40.909 0.00 0.00 0.00 2.83
3017 3672 4.276926 CCTTTTTGAGACCTGGAGACTTTG 59.723 45.833 0.00 0.00 0.00 2.77
3024 3679 1.214175 TGCACCTTTTTGAGACCTGGA 59.786 47.619 0.00 0.00 0.00 3.86
3025 3680 1.691196 TGCACCTTTTTGAGACCTGG 58.309 50.000 0.00 0.00 0.00 4.45
3030 3685 2.362077 GAGGCTTTGCACCTTTTTGAGA 59.638 45.455 0.00 0.00 37.77 3.27
3031 3686 2.101249 TGAGGCTTTGCACCTTTTTGAG 59.899 45.455 0.00 0.00 37.77 3.02
3032 3687 2.106566 TGAGGCTTTGCACCTTTTTGA 58.893 42.857 0.00 0.00 37.77 2.69
3033 3688 2.204237 GTGAGGCTTTGCACCTTTTTG 58.796 47.619 0.00 0.00 37.77 2.44
3034 3689 1.830477 TGTGAGGCTTTGCACCTTTTT 59.170 42.857 2.76 0.00 37.77 1.94
3035 3690 1.484038 TGTGAGGCTTTGCACCTTTT 58.516 45.000 2.76 0.00 37.77 2.27
3037 3692 1.410153 CTTTGTGAGGCTTTGCACCTT 59.590 47.619 2.76 0.00 37.77 3.50
3038 3693 1.035139 CTTTGTGAGGCTTTGCACCT 58.965 50.000 0.00 0.00 41.41 4.00
3039 3694 1.000938 CTCTTTGTGAGGCTTTGCACC 60.001 52.381 2.76 0.00 39.08 5.01
3040 3695 1.601412 GCTCTTTGTGAGGCTTTGCAC 60.601 52.381 0.00 0.00 42.87 4.57
3041 3696 0.670162 GCTCTTTGTGAGGCTTTGCA 59.330 50.000 0.00 0.00 42.87 4.08
3043 3698 2.620115 TCTTGCTCTTTGTGAGGCTTTG 59.380 45.455 0.00 0.00 42.87 2.77
3047 3702 3.715628 TTTTCTTGCTCTTTGTGAGGC 57.284 42.857 0.00 0.00 42.87 4.70
3049 3704 6.267817 TCATGTTTTTCTTGCTCTTTGTGAG 58.732 36.000 0.00 0.00 45.33 3.51
3050 3705 6.206395 TCATGTTTTTCTTGCTCTTTGTGA 57.794 33.333 0.00 0.00 0.00 3.58
3051 3706 6.890663 TTCATGTTTTTCTTGCTCTTTGTG 57.109 33.333 0.00 0.00 0.00 3.33
3054 4044 5.519927 CCGTTTCATGTTTTTCTTGCTCTTT 59.480 36.000 0.00 0.00 0.00 2.52
3060 4050 5.572896 GCTATCCCGTTTCATGTTTTTCTTG 59.427 40.000 0.00 0.00 0.00 3.02
3066 4056 2.752903 GTGGCTATCCCGTTTCATGTTT 59.247 45.455 0.00 0.00 35.87 2.83
3069 4059 2.036958 TGTGGCTATCCCGTTTCATG 57.963 50.000 0.00 0.00 35.87 3.07
3071 4061 1.612199 GGTTGTGGCTATCCCGTTTCA 60.612 52.381 0.00 0.00 35.87 2.69
3075 4065 2.582436 CGGTTGTGGCTATCCCGT 59.418 61.111 0.00 0.00 35.87 5.28
3076 4066 2.203015 CCGGTTGTGGCTATCCCG 60.203 66.667 0.00 0.00 38.39 5.14
3084 4074 0.882474 TTTTATTCCGCCGGTTGTGG 59.118 50.000 1.63 0.00 46.66 4.17
3085 4075 2.708386 TTTTTATTCCGCCGGTTGTG 57.292 45.000 1.63 0.00 0.00 3.33
3087 4077 4.886247 TCTATTTTTATTCCGCCGGTTG 57.114 40.909 1.63 0.00 0.00 3.77
3089 4079 6.527423 TCTTATCTATTTTTATTCCGCCGGT 58.473 36.000 1.63 0.00 0.00 5.28
3091 4081 7.015877 GCTTCTTATCTATTTTTATTCCGCCG 58.984 38.462 0.00 0.00 0.00 6.46
3092 4082 8.100508 AGCTTCTTATCTATTTTTATTCCGCC 57.899 34.615 0.00 0.00 0.00 6.13
3112 4102 9.294030 CCAAAATGTTATCATTGTTAGAGCTTC 57.706 33.333 0.00 0.00 42.60 3.86
3113 4103 9.023962 TCCAAAATGTTATCATTGTTAGAGCTT 57.976 29.630 0.00 0.00 42.60 3.74
3114 4104 8.579850 TCCAAAATGTTATCATTGTTAGAGCT 57.420 30.769 0.00 0.00 42.60 4.09
3115 4105 9.455847 GATCCAAAATGTTATCATTGTTAGAGC 57.544 33.333 0.00 0.00 42.60 4.09
3131 4130 8.806146 CCCCTACCATATTTAAGATCCAAAATG 58.194 37.037 11.35 8.32 0.00 2.32
3132 4131 8.742437 TCCCCTACCATATTTAAGATCCAAAAT 58.258 33.333 7.72 7.72 0.00 1.82
3135 4134 6.274672 CCTCCCCTACCATATTTAAGATCCAA 59.725 42.308 0.00 0.00 0.00 3.53
3147 4146 2.889522 AAGAAGCCTCCCCTACCATA 57.110 50.000 0.00 0.00 0.00 2.74
3187 4186 1.346722 CCTCGTTGTAGGGGTGAAAGT 59.653 52.381 0.00 0.00 32.55 2.66
3259 4258 7.069578 GGATGTCACCTAGATACTGAACCTTTA 59.930 40.741 0.00 0.00 0.00 1.85
3279 4278 1.940613 GTAATCACTTGGGCGGATGTC 59.059 52.381 0.00 0.00 0.00 3.06
3337 4336 1.679139 CAATCATGCACGGGGTGTAT 58.321 50.000 0.00 0.00 39.29 2.29
3338 4337 0.393673 CCAATCATGCACGGGGTGTA 60.394 55.000 0.00 0.00 35.75 2.90
3339 4338 1.678635 CCAATCATGCACGGGGTGT 60.679 57.895 0.00 0.00 35.75 4.16
3340 4339 1.378382 TCCAATCATGCACGGGGTG 60.378 57.895 0.00 0.00 36.51 4.61
3341 4340 1.077501 CTCCAATCATGCACGGGGT 60.078 57.895 0.00 0.00 0.00 4.95
3342 4341 0.816825 CTCTCCAATCATGCACGGGG 60.817 60.000 0.00 0.00 0.00 5.73
3346 4345 1.329906 CGAAGCTCTCCAATCATGCAC 59.670 52.381 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.