Multiple sequence alignment - TraesCS4A01G298600

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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 TraesCS4A01G298600 chr4A 100.000 3169 0 0 1 3169 597670700 597673868 0.000000e+00 5853
1 TraesCS4A01G298600 chr4D 87.249 2337 151 76 1 2269 6044881 6042624 0.000000e+00 2529
2 TraesCS4A01G298600 chr4D 87.778 180 17 3 2336 2510 6042620 6042441 4.140000e-49 206
3 TraesCS4A01G298600 chr4B 87.483 2165 129 66 113 2183 10610471 10608355 0.000000e+00 2366
4 TraesCS4A01G298600 chr4B 87.765 425 34 6 2746 3169 10607924 10607517 6.150000e-132 481
5 TraesCS4A01G298600 chr4B 89.153 378 38 3 2307 2683 10608296 10607921 4.790000e-128 468
6 TraesCS4A01G298600 chr4B 80.899 178 34 0 2506 2683 467460679 467460502 1.190000e-29 141
7 TraesCS4A01G298600 chr4B 90.000 90 7 2 1 90 10610555 10610468 7.180000e-22 115
8 TraesCS4A01G298600 chr1A 94.326 141 8 0 1344 1484 442158053 442158193 1.910000e-52 217
9 TraesCS4A01G298600 chr2B 85.000 180 26 1 2506 2684 45729622 45729801 6.980000e-42 182
10 TraesCS4A01G298600 chr5B 84.916 179 26 1 2506 2684 527760537 527760360 2.510000e-41 180
11 TraesCS4A01G298600 chr7D 82.184 174 29 2 2506 2677 507424451 507424278 7.080000e-32 148
12 TraesCS4A01G298600 chr2A 81.522 184 27 5 2506 2684 194713220 194713401 9.160000e-31 145
13 TraesCS4A01G298600 chr5A 80.899 178 32 2 2506 2682 411991175 411990999 4.260000e-29 139
14 TraesCS4A01G298600 chr7B 81.034 174 28 2 2506 2677 13129958 13129788 1.980000e-27 134
15 TraesCS4A01G298600 chr7B 81.595 163 28 2 2521 2681 535826663 535826501 1.980000e-27 134


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 TraesCS4A01G298600 chr4A 597670700 597673868 3168 False 5853.0 5853 100.00000 1 3169 1 chr4A.!!$F1 3168
1 TraesCS4A01G298600 chr4D 6042441 6044881 2440 True 1367.5 2529 87.51350 1 2510 2 chr4D.!!$R1 2509
2 TraesCS4A01G298600 chr4B 10607517 10610555 3038 True 857.5 2366 88.60025 1 3169 4 chr4B.!!$R2 3168

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
758 780 0.99192 TACTTCCCTTGAGGCTTGGG 59.008 55.0 13.01 13.01 42.2 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2554 0.179161 CCTCGACGCGATCAAGAACT 60.179 55.0 15.93 0.0 34.61 3.01 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
26 27 2.202932 GTGCGTCCATCATCGGCT 60.203 61.111 0.00 0.00 0.00 5.52
64 65 7.337689 TCTCAGCAGTAATCTGTATGCATTTTT 59.662 33.333 3.54 0.00 43.05 1.94
83 84 8.175069 GCATTTTTACTGACGATTCATAGTTGA 58.825 33.333 0.00 0.00 0.00 3.18
111 112 1.028905 CGGGGTTTCTGACAAGCAAA 58.971 50.000 0.00 0.00 0.00 3.68
155 158 7.642586 GCGAACAATTTCACTGTACTAAAGTTT 59.357 33.333 0.00 0.00 0.00 2.66
171 174 1.899814 AGTTTGATGCTGAGTCGGGTA 59.100 47.619 0.05 0.00 0.00 3.69
196 203 3.753294 ACCTTGAGTCTACTTGTGGTG 57.247 47.619 0.00 0.00 0.00 4.17
197 204 3.305720 ACCTTGAGTCTACTTGTGGTGA 58.694 45.455 0.00 0.00 0.00 4.02
198 205 3.322254 ACCTTGAGTCTACTTGTGGTGAG 59.678 47.826 0.00 0.00 0.00 3.51
199 206 3.322254 CCTTGAGTCTACTTGTGGTGAGT 59.678 47.826 0.00 0.00 0.00 3.41
204 211 1.000607 TCTACTTGTGGTGAGTCGTGC 60.001 52.381 0.00 0.00 0.00 5.34
252 260 7.581011 AAAATTGTTTCAGTTGTGACACTTC 57.419 32.000 7.20 0.04 34.87 3.01
299 307 1.600957 GCTCGTTGATGCATATGCTGT 59.399 47.619 27.13 16.38 42.66 4.40
300 308 2.349249 GCTCGTTGATGCATATGCTGTC 60.349 50.000 27.13 23.07 42.66 3.51
301 309 3.129109 CTCGTTGATGCATATGCTGTCT 58.871 45.455 27.13 10.33 42.66 3.41
304 312 3.558829 CGTTGATGCATATGCTGTCTCTT 59.441 43.478 27.13 4.77 42.66 2.85
339 347 5.296531 TGAATCAGATAAAGCGCTTTATGCA 59.703 36.000 44.06 30.58 43.52 3.96
361 369 2.216046 CAGTGAAACAAGAGCAGCAGA 58.784 47.619 0.00 0.00 41.43 4.26
369 377 1.463831 CAAGAGCAGCAGACACACATC 59.536 52.381 0.00 0.00 0.00 3.06
417 428 7.408123 TCAAGCAAAAACTTTGTGCAAATATG 58.592 30.769 17.28 8.88 40.83 1.78
425 436 6.603940 ACTTTGTGCAAATATGGGTACATT 57.396 33.333 0.00 0.00 38.53 2.71
433 444 5.684552 GCAAATATGGGTACATTGCCATTGT 60.685 40.000 6.68 0.00 38.53 2.71
470 486 3.422993 CGCAATTCGACGAGATTCACAAA 60.423 43.478 0.00 0.00 41.67 2.83
501 517 2.158519 ACCTCAAGAACCCGACCAAATT 60.159 45.455 0.00 0.00 0.00 1.82
507 523 2.884639 AGAACCCGACCAAATTGACAAG 59.115 45.455 0.00 0.00 0.00 3.16
540 557 4.664688 AGAACCCAAAGATCACCTGAAT 57.335 40.909 0.00 0.00 0.00 2.57
568 585 3.693085 AGAAACCACTCATATGCAAGCAG 59.307 43.478 0.00 0.00 0.00 4.24
583 600 4.751098 TGCAAGCAGACATTTGAAAAATCC 59.249 37.500 0.00 0.00 0.00 3.01
605 622 2.694043 CGAATTCGCGGATTCAAAGAC 58.306 47.619 33.24 11.81 36.12 3.01
638 656 7.991736 TCAAAATTTGAAAAGTTCGAATAGCG 58.008 30.769 5.87 0.00 41.73 4.26
693 711 7.778185 ACCTACCCTATTATACACTCATGAC 57.222 40.000 0.00 0.00 0.00 3.06
694 712 7.536625 ACCTACCCTATTATACACTCATGACT 58.463 38.462 0.00 0.00 0.00 3.41
695 713 7.670559 ACCTACCCTATTATACACTCATGACTC 59.329 40.741 0.00 0.00 0.00 3.36
696 714 7.670140 CCTACCCTATTATACACTCATGACTCA 59.330 40.741 0.00 0.00 0.00 3.41
697 715 9.249053 CTACCCTATTATACACTCATGACTCAT 57.751 37.037 0.00 0.00 0.00 2.90
722 743 8.807667 TCAATCAATCAAGAAAGAAAAAGAGC 57.192 30.769 0.00 0.00 0.00 4.09
723 744 8.415553 TCAATCAATCAAGAAAGAAAAAGAGCA 58.584 29.630 0.00 0.00 0.00 4.26
740 762 3.270960 AGAGCAAAACCCCACCCAATATA 59.729 43.478 0.00 0.00 0.00 0.86
758 780 0.991920 TACTTCCCTTGAGGCTTGGG 59.008 55.000 13.01 13.01 42.20 4.12
798 820 4.676109 TCCACATGGACATGGATTTTCTT 58.324 39.130 15.94 0.00 40.17 2.52
799 821 4.706476 TCCACATGGACATGGATTTTCTTC 59.294 41.667 15.94 0.00 40.17 2.87
800 822 4.142093 CCACATGGACATGGATTTTCTTCC 60.142 45.833 15.94 0.00 42.91 3.46
801 823 4.026052 ACATGGACATGGATTTTCTTCCC 58.974 43.478 15.94 0.00 42.91 3.97
802 824 3.100207 TGGACATGGATTTTCTTCCCC 57.900 47.619 0.00 0.00 34.67 4.81
891 925 2.742372 CGCCGGGAGAAACACCAG 60.742 66.667 2.18 0.00 0.00 4.00
975 1013 3.143406 TCTATTCTTCCCCTCCTCCTCT 58.857 50.000 0.00 0.00 0.00 3.69
1002 1047 6.040729 CCTCTCATGGCTCCTGACTATATATG 59.959 46.154 0.00 0.00 0.00 1.78
1036 1081 4.148825 GGCGACCGGCATCACTCT 62.149 66.667 0.00 0.00 46.16 3.24
1055 1104 1.603455 CCACCACCACCACCATCAC 60.603 63.158 0.00 0.00 0.00 3.06
1057 1106 2.359850 CCACCACCACCATCACCG 60.360 66.667 0.00 0.00 0.00 4.94
1059 1108 3.565214 ACCACCACCATCACCGCA 61.565 61.111 0.00 0.00 0.00 5.69
1060 1109 2.282110 CCACCACCATCACCGCAA 60.282 61.111 0.00 0.00 0.00 4.85
1061 1110 2.334946 CCACCACCATCACCGCAAG 61.335 63.158 0.00 0.00 0.00 4.01
1062 1111 2.672996 ACCACCATCACCGCAAGC 60.673 61.111 0.00 0.00 0.00 4.01
1064 1113 2.048023 CCACCATCACCGCAAGCAT 61.048 57.895 0.00 0.00 0.00 3.79
1066 1115 1.750399 ACCATCACCGCAAGCATCC 60.750 57.895 0.00 0.00 0.00 3.51
1067 1116 2.711311 CATCACCGCAAGCATCCG 59.289 61.111 0.00 0.00 0.00 4.18
1096 1145 0.387565 CGGGTTTGTTGTTTGGGAGG 59.612 55.000 0.00 0.00 0.00 4.30
1223 1272 1.135094 AAGATCATCGTCCCAGGCAT 58.865 50.000 0.00 0.00 0.00 4.40
1240 1298 1.822581 CATGCATGCAACTCACATCG 58.177 50.000 26.68 1.00 0.00 3.84
1249 1307 4.180817 TGCAACTCACATCGTATGGTTAG 58.819 43.478 0.00 0.00 33.60 2.34
1251 1309 4.267928 GCAACTCACATCGTATGGTTAGTC 59.732 45.833 0.00 0.00 33.60 2.59
1256 1316 2.686405 ACATCGTATGGTTAGTCGAGCA 59.314 45.455 0.00 0.00 35.85 4.26
1275 1335 0.753479 AAACAATGGCGGGTGTGTGA 60.753 50.000 0.00 0.00 0.00 3.58
1276 1336 0.539438 AACAATGGCGGGTGTGTGAT 60.539 50.000 0.00 0.00 0.00 3.06
1277 1337 1.243342 ACAATGGCGGGTGTGTGATG 61.243 55.000 0.00 0.00 0.00 3.07
1278 1338 1.678635 AATGGCGGGTGTGTGATGG 60.679 57.895 0.00 0.00 0.00 3.51
1280 1340 4.344865 GGCGGGTGTGTGATGGGT 62.345 66.667 0.00 0.00 0.00 4.51
1282 1342 2.747022 CGGGTGTGTGATGGGTGA 59.253 61.111 0.00 0.00 0.00 4.02
1283 1343 1.299648 CGGGTGTGTGATGGGTGAT 59.700 57.895 0.00 0.00 0.00 3.06
1293 1368 1.005805 TGATGGGTGATGGGTTCTTGG 59.994 52.381 0.00 0.00 0.00 3.61
1294 1369 0.324645 ATGGGTGATGGGTTCTTGGC 60.325 55.000 0.00 0.00 0.00 4.52
1295 1370 1.384191 GGGTGATGGGTTCTTGGCT 59.616 57.895 0.00 0.00 0.00 4.75
1685 1763 1.614241 CCGTCGTCCCTTCCCAGAAT 61.614 60.000 0.00 0.00 0.00 2.40
2108 2216 2.356553 TACGTGTGGCGCAACCTC 60.357 61.111 13.54 4.77 46.11 3.85
2183 2294 2.278026 TGTGAACTGTGATCGATCGG 57.722 50.000 20.03 14.44 0.00 4.18
2184 2295 1.135112 TGTGAACTGTGATCGATCGGG 60.135 52.381 20.03 14.11 0.00 5.14
2185 2296 0.179111 TGAACTGTGATCGATCGGGC 60.179 55.000 20.03 13.00 0.00 6.13
2190 2304 1.953138 GTGATCGATCGGGCAGCAG 60.953 63.158 20.03 0.00 0.00 4.24
2192 2306 3.157217 GATCGATCGGGCAGCAGGT 62.157 63.158 16.41 0.00 0.00 4.00
2193 2307 3.451556 ATCGATCGGGCAGCAGGTG 62.452 63.158 16.41 0.00 0.00 4.00
2212 2326 1.090052 GCCAGGTGGTGCGAAGTATC 61.090 60.000 0.00 0.00 37.57 2.24
2216 2334 1.899814 AGGTGGTGCGAAGTATCTGAA 59.100 47.619 0.00 0.00 0.00 3.02
2225 2343 3.358775 CGAAGTATCTGAAGCGTGAGAG 58.641 50.000 0.00 0.00 0.00 3.20
2226 2344 3.181505 CGAAGTATCTGAAGCGTGAGAGT 60.182 47.826 0.00 0.00 0.00 3.24
2250 2376 3.070446 AGTGAAAGTTCATACGTGTGGGA 59.930 43.478 12.66 0.00 39.73 4.37
2258 2384 0.611714 ATACGTGTGGGAAGGTGGTC 59.388 55.000 0.00 0.00 0.00 4.02
2260 2386 2.668550 GTGTGGGAAGGTGGTCGC 60.669 66.667 0.00 0.00 0.00 5.19
2261 2387 4.308458 TGTGGGAAGGTGGTCGCG 62.308 66.667 0.00 0.00 33.32 5.87
2269 2395 2.511600 GGTGGTCGCGAATGGAGG 60.512 66.667 12.06 0.00 0.00 4.30
2271 2397 3.390521 TGGTCGCGAATGGAGGCT 61.391 61.111 12.06 0.00 0.00 4.58
2272 2398 2.586357 GGTCGCGAATGGAGGCTC 60.586 66.667 12.06 5.78 0.00 4.70
2273 2399 2.496817 GTCGCGAATGGAGGCTCT 59.503 61.111 12.06 0.00 0.00 4.09
2274 2400 1.880340 GTCGCGAATGGAGGCTCTG 60.880 63.158 12.06 0.99 0.00 3.35
2275 2401 2.052104 TCGCGAATGGAGGCTCTGA 61.052 57.895 15.23 1.57 0.00 3.27
2276 2402 1.153568 CGCGAATGGAGGCTCTGAA 60.154 57.895 15.23 0.82 0.00 3.02
2277 2403 1.150567 CGCGAATGGAGGCTCTGAAG 61.151 60.000 15.23 4.02 0.00 3.02
2278 2404 0.176680 GCGAATGGAGGCTCTGAAGA 59.823 55.000 15.23 0.00 0.00 2.87
2279 2405 1.406069 GCGAATGGAGGCTCTGAAGAA 60.406 52.381 15.23 0.00 0.00 2.52
2280 2406 2.936993 GCGAATGGAGGCTCTGAAGAAA 60.937 50.000 15.23 0.00 0.00 2.52
2281 2407 3.338249 CGAATGGAGGCTCTGAAGAAAA 58.662 45.455 15.23 0.00 0.00 2.29
2282 2408 3.753272 CGAATGGAGGCTCTGAAGAAAAA 59.247 43.478 15.23 0.00 0.00 1.94
2283 2409 4.397417 CGAATGGAGGCTCTGAAGAAAAAT 59.603 41.667 15.23 0.00 0.00 1.82
2284 2410 5.648572 GAATGGAGGCTCTGAAGAAAAATG 58.351 41.667 15.23 0.00 0.00 2.32
2285 2411 3.424703 TGGAGGCTCTGAAGAAAAATGG 58.575 45.455 15.23 0.00 0.00 3.16
2286 2412 3.074390 TGGAGGCTCTGAAGAAAAATGGA 59.926 43.478 15.23 0.00 0.00 3.41
2287 2413 4.082125 GGAGGCTCTGAAGAAAAATGGAA 58.918 43.478 15.23 0.00 0.00 3.53
2288 2414 4.157472 GGAGGCTCTGAAGAAAAATGGAAG 59.843 45.833 15.23 0.00 0.00 3.46
2289 2415 4.734266 AGGCTCTGAAGAAAAATGGAAGT 58.266 39.130 0.00 0.00 0.00 3.01
2290 2416 5.880901 AGGCTCTGAAGAAAAATGGAAGTA 58.119 37.500 0.00 0.00 0.00 2.24
2291 2417 6.488715 AGGCTCTGAAGAAAAATGGAAGTAT 58.511 36.000 0.00 0.00 0.00 2.12
2292 2418 7.633789 AGGCTCTGAAGAAAAATGGAAGTATA 58.366 34.615 0.00 0.00 0.00 1.47
2293 2419 8.277918 AGGCTCTGAAGAAAAATGGAAGTATAT 58.722 33.333 0.00 0.00 0.00 0.86
2294 2420 9.561069 GGCTCTGAAGAAAAATGGAAGTATATA 57.439 33.333 0.00 0.00 0.00 0.86
2301 2427 8.336801 AGAAAAATGGAAGTATATATTCCCGC 57.663 34.615 14.06 2.22 44.76 6.13
2302 2428 6.737254 AAAATGGAAGTATATATTCCCGCG 57.263 37.500 14.06 0.00 44.76 6.46
2303 2429 5.670792 AATGGAAGTATATATTCCCGCGA 57.329 39.130 8.23 0.00 44.76 5.87
2304 2430 5.670792 ATGGAAGTATATATTCCCGCGAA 57.329 39.130 8.23 0.00 44.76 4.70
2305 2431 5.471556 TGGAAGTATATATTCCCGCGAAA 57.528 39.130 8.23 1.06 44.76 3.46
2418 2548 5.689383 TGCACAAGCCTTTAACTTTCTAG 57.311 39.130 0.00 0.00 41.13 2.43
2423 2554 8.943002 GCACAAGCCTTTAACTTTCTAGTATAA 58.057 33.333 0.00 0.00 31.65 0.98
2477 2608 7.203218 TCTACAAGCATGTATGTGTATGACTC 58.797 38.462 13.63 0.00 41.09 3.36
2478 2609 5.733676 ACAAGCATGTATGTGTATGACTCA 58.266 37.500 0.00 0.00 38.24 3.41
2519 2650 6.870517 GCAGACTGCAAATTTAAACTTTCAG 58.129 36.000 22.62 7.37 44.26 3.02
2586 2717 9.821662 GTTCTAATGGTATTAATTCGGTAATGC 57.178 33.333 0.00 0.00 0.00 3.56
2587 2718 9.562408 TTCTAATGGTATTAATTCGGTAATGCA 57.438 29.630 0.00 0.00 30.24 3.96
2596 2727 7.804614 TTAATTCGGTAATGCAAATGTCAAC 57.195 32.000 0.00 0.00 0.00 3.18
2599 2730 5.384063 TCGGTAATGCAAATGTCAACAAT 57.616 34.783 0.00 0.00 0.00 2.71
2600 2731 5.398169 TCGGTAATGCAAATGTCAACAATC 58.602 37.500 0.00 0.00 0.00 2.67
2618 2750 7.437862 TCAACAATCTTTTGCATAAACTTGACC 59.562 33.333 14.04 0.00 36.22 4.02
2643 2775 7.323656 CCAAAGTTTACAAAGTTTAGCTCGATG 59.676 37.037 7.09 0.00 38.98 3.84
2658 2790 3.729684 CTCGATGCAAAGCTAATATGCG 58.270 45.455 0.00 0.00 42.91 4.73
2680 2812 9.994432 ATGCGAAGTAAATAAAAATGAAGAGAG 57.006 29.630 0.00 0.00 0.00 3.20
2681 2813 8.999431 TGCGAAGTAAATAAAAATGAAGAGAGT 58.001 29.630 0.00 0.00 0.00 3.24
2694 2826 8.827177 AAATGAAGAGAGTACGTTCAATAACA 57.173 30.769 0.00 0.00 34.02 2.41
2695 2827 7.813852 ATGAAGAGAGTACGTTCAATAACAC 57.186 36.000 0.00 0.00 34.02 3.32
2696 2828 6.978338 TGAAGAGAGTACGTTCAATAACACT 58.022 36.000 0.00 0.00 35.16 3.55
2697 2829 8.102800 TGAAGAGAGTACGTTCAATAACACTA 57.897 34.615 0.00 0.00 35.16 2.74
2698 2830 8.235226 TGAAGAGAGTACGTTCAATAACACTAG 58.765 37.037 0.00 0.00 35.16 2.57
2699 2831 6.553524 AGAGAGTACGTTCAATAACACTAGC 58.446 40.000 0.00 0.00 35.16 3.42
2700 2832 5.330295 AGAGTACGTTCAATAACACTAGCG 58.670 41.667 0.00 0.00 35.16 4.26
2701 2833 5.051891 AGTACGTTCAATAACACTAGCGT 57.948 39.130 0.00 0.00 35.16 5.07
2702 2834 5.464168 AGTACGTTCAATAACACTAGCGTT 58.536 37.500 0.00 1.16 35.16 4.84
2703 2835 5.922544 AGTACGTTCAATAACACTAGCGTTT 59.077 36.000 0.70 0.00 35.16 3.60
2704 2836 7.083858 AGTACGTTCAATAACACTAGCGTTTA 58.916 34.615 0.70 0.00 35.16 2.01
2705 2837 6.956299 ACGTTCAATAACACTAGCGTTTAT 57.044 33.333 0.70 0.00 35.16 1.40
2706 2838 6.758149 ACGTTCAATAACACTAGCGTTTATG 58.242 36.000 0.70 2.29 35.16 1.90
2707 2839 6.182634 CGTTCAATAACACTAGCGTTTATGG 58.817 40.000 0.70 0.00 35.16 2.74
2708 2840 6.483687 GTTCAATAACACTAGCGTTTATGGG 58.516 40.000 0.70 0.00 35.56 4.00
2709 2841 5.979993 TCAATAACACTAGCGTTTATGGGA 58.020 37.500 0.70 0.00 0.00 4.37
2710 2842 6.046593 TCAATAACACTAGCGTTTATGGGAG 58.953 40.000 0.70 0.00 0.00 4.30
2711 2843 5.864418 ATAACACTAGCGTTTATGGGAGA 57.136 39.130 0.70 0.00 0.00 3.71
2712 2844 4.546829 AACACTAGCGTTTATGGGAGAA 57.453 40.909 0.00 0.00 0.00 2.87
2713 2845 3.858247 ACACTAGCGTTTATGGGAGAAC 58.142 45.455 0.00 0.00 0.00 3.01
2714 2846 3.259876 ACACTAGCGTTTATGGGAGAACA 59.740 43.478 0.00 0.00 0.00 3.18
2715 2847 4.081087 ACACTAGCGTTTATGGGAGAACAT 60.081 41.667 0.00 0.00 34.90 2.71
2716 2848 4.876107 CACTAGCGTTTATGGGAGAACATT 59.124 41.667 0.00 0.00 32.39 2.71
2717 2849 5.354234 CACTAGCGTTTATGGGAGAACATTT 59.646 40.000 0.00 0.00 32.39 2.32
2718 2850 4.701956 AGCGTTTATGGGAGAACATTTG 57.298 40.909 0.00 0.00 32.39 2.32
2719 2851 3.119495 AGCGTTTATGGGAGAACATTTGC 60.119 43.478 0.00 0.00 32.39 3.68
2720 2852 3.425404 CGTTTATGGGAGAACATTTGCG 58.575 45.455 0.00 0.00 32.39 4.85
2721 2853 3.119990 CGTTTATGGGAGAACATTTGCGT 60.120 43.478 0.00 0.00 32.39 5.24
2722 2854 4.093703 CGTTTATGGGAGAACATTTGCGTA 59.906 41.667 0.00 0.00 32.39 4.42
2723 2855 5.329493 GTTTATGGGAGAACATTTGCGTAC 58.671 41.667 0.00 0.00 32.39 3.67
2724 2856 2.851263 TGGGAGAACATTTGCGTACT 57.149 45.000 0.00 0.00 0.00 2.73
2725 2857 3.134574 TGGGAGAACATTTGCGTACTT 57.865 42.857 0.00 0.00 0.00 2.24
2726 2858 2.811431 TGGGAGAACATTTGCGTACTTG 59.189 45.455 0.00 0.00 0.00 3.16
2727 2859 3.071479 GGGAGAACATTTGCGTACTTGA 58.929 45.455 0.00 0.00 0.00 3.02
2728 2860 3.689649 GGGAGAACATTTGCGTACTTGAT 59.310 43.478 0.00 0.00 0.00 2.57
2729 2861 4.156008 GGGAGAACATTTGCGTACTTGATT 59.844 41.667 0.00 0.00 0.00 2.57
2730 2862 5.353123 GGGAGAACATTTGCGTACTTGATTA 59.647 40.000 0.00 0.00 0.00 1.75
2731 2863 6.456988 GGGAGAACATTTGCGTACTTGATTAG 60.457 42.308 0.00 0.00 0.00 1.73
2732 2864 5.869350 AGAACATTTGCGTACTTGATTAGC 58.131 37.500 0.00 0.00 0.00 3.09
2733 2865 5.643777 AGAACATTTGCGTACTTGATTAGCT 59.356 36.000 0.00 0.00 0.00 3.32
2734 2866 5.880054 ACATTTGCGTACTTGATTAGCTT 57.120 34.783 0.00 0.00 0.00 3.74
2735 2867 6.254281 ACATTTGCGTACTTGATTAGCTTT 57.746 33.333 0.00 0.00 0.00 3.51
2736 2868 6.677913 ACATTTGCGTACTTGATTAGCTTTT 58.322 32.000 0.00 0.00 0.00 2.27
2737 2869 7.812648 ACATTTGCGTACTTGATTAGCTTTTA 58.187 30.769 0.00 0.00 0.00 1.52
2738 2870 7.749126 ACATTTGCGTACTTGATTAGCTTTTAC 59.251 33.333 0.00 0.00 0.00 2.01
2739 2871 7.429636 TTTGCGTACTTGATTAGCTTTTACT 57.570 32.000 0.00 0.00 0.00 2.24
2740 2872 6.403333 TGCGTACTTGATTAGCTTTTACTG 57.597 37.500 0.00 0.00 0.00 2.74
2741 2873 6.160684 TGCGTACTTGATTAGCTTTTACTGA 58.839 36.000 0.00 0.00 0.00 3.41
2742 2874 6.310467 TGCGTACTTGATTAGCTTTTACTGAG 59.690 38.462 0.00 0.00 0.00 3.35
2743 2875 6.530534 GCGTACTTGATTAGCTTTTACTGAGA 59.469 38.462 0.00 0.00 0.00 3.27
2744 2876 7.063074 GCGTACTTGATTAGCTTTTACTGAGAA 59.937 37.037 0.00 0.00 0.00 2.87
2750 2882 9.436957 TTGATTAGCTTTTACTGAGAAAGTAGG 57.563 33.333 0.00 0.00 42.38 3.18
2752 2884 8.779354 ATTAGCTTTTACTGAGAAAGTAGGTG 57.221 34.615 0.00 0.00 42.38 4.00
2756 2888 4.948341 TTACTGAGAAAGTAGGTGCACA 57.052 40.909 20.43 0.00 42.38 4.57
2768 2900 6.354794 AGTAGGTGCACATTAGACTTAACA 57.645 37.500 20.43 0.00 0.00 2.41
2776 2908 9.410556 GTGCACATTAGACTTAACATTGAAAAT 57.589 29.630 13.17 0.00 0.00 1.82
2786 2918 9.243637 GACTTAACATTGAAAATGCTTGTGTAA 57.756 29.630 0.00 0.00 0.00 2.41
2799 2931 4.819088 TGCTTGTGTAAGTTTGCATCTGTA 59.181 37.500 0.00 0.00 36.27 2.74
2824 2956 4.211374 AGCAAAAACTAGCAACGAGTAGTG 59.789 41.667 0.00 0.00 29.71 2.74
2883 3015 3.877508 GCGACTAACAAATAGGCAATCCT 59.122 43.478 0.00 0.00 39.93 3.24
2884 3016 4.260784 GCGACTAACAAATAGGCAATCCTG 60.261 45.833 0.00 0.00 44.08 3.86
2893 3025 8.133024 ACAAATAGGCAATCCTGTTATTTTCA 57.867 30.769 0.00 0.00 42.15 2.69
2899 3031 5.408299 GGCAATCCTGTTATTTTCACAAACC 59.592 40.000 0.00 0.00 0.00 3.27
2918 3050 9.438291 CACAAACCTTTGATGATAATCGTAATC 57.562 33.333 4.77 0.00 40.55 1.75
2921 3053 6.238648 ACCTTTGATGATAATCGTAATCCCC 58.761 40.000 0.00 0.00 0.00 4.81
2922 3054 6.183361 ACCTTTGATGATAATCGTAATCCCCA 60.183 38.462 0.00 0.00 0.00 4.96
2923 3055 6.886459 CCTTTGATGATAATCGTAATCCCCAT 59.114 38.462 0.00 0.00 0.00 4.00
2924 3056 7.066284 CCTTTGATGATAATCGTAATCCCCATC 59.934 40.741 0.00 0.00 0.00 3.51
2925 3057 6.619329 TGATGATAATCGTAATCCCCATCA 57.381 37.500 0.00 0.00 37.43 3.07
2926 3058 7.014988 TGATGATAATCGTAATCCCCATCAA 57.985 36.000 0.00 0.00 37.01 2.57
2927 3059 7.632861 TGATGATAATCGTAATCCCCATCAAT 58.367 34.615 0.00 0.00 37.01 2.57
2928 3060 8.108999 TGATGATAATCGTAATCCCCATCAATT 58.891 33.333 0.00 0.00 37.01 2.32
2929 3061 9.613428 GATGATAATCGTAATCCCCATCAATTA 57.387 33.333 0.00 0.00 32.01 1.40
2930 3062 9.618890 ATGATAATCGTAATCCCCATCAATTAG 57.381 33.333 0.00 0.00 0.00 1.73
2931 3063 8.821817 TGATAATCGTAATCCCCATCAATTAGA 58.178 33.333 0.00 0.00 0.00 2.10
2932 3064 9.667107 GATAATCGTAATCCCCATCAATTAGAA 57.333 33.333 0.00 0.00 0.00 2.10
2934 3066 7.928307 ATCGTAATCCCCATCAATTAGAATG 57.072 36.000 0.00 0.00 0.00 2.67
2935 3067 6.237901 TCGTAATCCCCATCAATTAGAATGG 58.762 40.000 6.68 6.68 0.00 3.16
2947 3079 9.123902 CATCAATTAGAATGGGATTCACACTAA 57.876 33.333 0.00 0.00 41.71 2.24
2959 3091 6.661805 GGGATTCACACTAATGTAAAAAGGGA 59.338 38.462 0.00 0.00 36.72 4.20
2967 3099 7.120726 ACACTAATGTAAAAAGGGAGGAATTCG 59.879 37.037 0.00 0.00 37.26 3.34
2976 3109 1.095228 GGAGGAATTCGCATCGCCAA 61.095 55.000 0.00 0.00 0.00 4.52
2992 3125 1.135689 GCCAAGAAACCTACATGTGCG 60.136 52.381 9.11 0.01 0.00 5.34
3024 3157 2.258591 GTCTCGCCGTTGCTCTCA 59.741 61.111 0.00 0.00 34.43 3.27
3029 3162 0.108186 TCGCCGTTGCTCTCATTGAT 60.108 50.000 0.00 0.00 34.43 2.57
3037 3170 2.304092 TGCTCTCATTGATTCCATGCC 58.696 47.619 0.00 0.00 0.00 4.40
3041 3174 3.548770 TCTCATTGATTCCATGCCTGAC 58.451 45.455 0.00 0.00 0.00 3.51
3053 3186 1.302033 GCCTGACTGTGGTGAGTGG 60.302 63.158 0.00 0.00 0.00 4.00
3066 3199 1.535462 GTGAGTGGTGGTTCAATTCGG 59.465 52.381 0.00 0.00 0.00 4.30
3078 3211 2.091541 TCAATTCGGCAGATTTGGGAC 58.908 47.619 17.48 0.00 37.95 4.46
3086 3219 3.686016 GGCAGATTTGGGACAGAAGTTA 58.314 45.455 0.00 0.00 42.39 2.24
3099 3232 1.205893 AGAAGTTAGAGGAGCAAGGCG 59.794 52.381 0.00 0.00 0.00 5.52
3135 3268 1.290134 GGGACAGAGGTTCCTCCATT 58.710 55.000 14.40 0.37 39.86 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.211212 CTGCTGAGATGATGGTTCCCA 59.789 52.381 0.00 0.00 38.19 4.37
39 40 6.615264 AAATGCATACAGATTACTGCTGAG 57.385 37.500 0.00 0.00 46.95 3.35
41 42 8.400947 AGTAAAAATGCATACAGATTACTGCTG 58.599 33.333 15.68 0.00 46.95 4.41
64 65 6.185852 TCGTTCAACTATGAATCGTCAGTA 57.814 37.500 10.77 0.00 46.67 2.74
83 84 0.321298 CAGAAACCCCGACCATCGTT 60.321 55.000 0.00 0.00 38.40 3.85
105 106 7.493743 CAGTATGCTCTGAATATCTTTGCTT 57.506 36.000 0.00 0.00 37.61 3.91
155 158 1.831106 ACAATACCCGACTCAGCATCA 59.169 47.619 0.00 0.00 0.00 3.07
171 174 5.307196 ACCACAAGTAGACTCAAGGTACAAT 59.693 40.000 0.00 0.00 0.00 2.71
196 203 2.298300 CAAAACAATGTCGCACGACTC 58.702 47.619 22.26 0.00 44.80 3.36
197 204 1.596954 GCAAAACAATGTCGCACGACT 60.597 47.619 22.26 6.98 44.80 4.18
198 205 0.770008 GCAAAACAATGTCGCACGAC 59.230 50.000 15.94 15.94 44.77 4.34
199 206 0.660488 AGCAAAACAATGTCGCACGA 59.340 45.000 0.00 0.00 0.00 4.35
204 211 6.746104 TGATACAAAAGCAAAACAATGTCG 57.254 33.333 0.00 0.00 0.00 4.35
252 260 3.213506 TGTCAAACAGTTGGGATCAGTG 58.786 45.455 0.00 0.00 35.29 3.66
308 316 4.858692 GCGCTTTATCTGATTCAGCAAAAA 59.141 37.500 8.89 7.91 0.00 1.94
339 347 2.357009 CTGCTGCTCTTGTTTCACTGTT 59.643 45.455 0.00 0.00 0.00 3.16
361 369 0.179009 AGCAAGCAGGTGATGTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
384 392 5.750067 ACAAAGTTTTTGCTTGATGCTACAG 59.250 36.000 1.68 0.00 43.37 2.74
393 404 6.633634 CCATATTTGCACAAAGTTTTTGCTTG 59.366 34.615 23.28 14.00 37.16 4.01
399 410 6.821388 TGTACCCATATTTGCACAAAGTTTT 58.179 32.000 1.92 0.00 33.32 2.43
417 428 3.118038 TCCTAGACAATGGCAATGTACCC 60.118 47.826 8.43 0.00 0.00 3.69
425 436 4.776435 TCATTCATCCTAGACAATGGCA 57.224 40.909 0.00 0.00 0.00 4.92
433 444 4.925646 CGAATTGCGATCATTCATCCTAGA 59.074 41.667 0.00 0.00 44.57 2.43
470 486 5.045869 TCGGGTTCTTGAGGTTGATTCTAAT 60.046 40.000 0.00 0.00 0.00 1.73
501 517 6.183361 TGGGTTCTTGAGATTCTAACTTGTCA 60.183 38.462 0.00 0.00 0.00 3.58
507 523 7.607991 TGATCTTTGGGTTCTTGAGATTCTAAC 59.392 37.037 0.00 0.00 0.00 2.34
540 557 6.048732 TGCATATGAGTGGTTTCTCTGTTA 57.951 37.500 6.97 0.00 35.68 2.41
560 577 4.751098 GGATTTTTCAAATGTCTGCTTGCA 59.249 37.500 0.00 0.00 0.00 4.08
568 585 5.496969 CGAATTCGCGGATTTTTCAAATGTC 60.497 40.000 15.11 0.00 0.00 3.06
594 611 6.455360 TTTGATATGCCTGTCTTTGAATCC 57.545 37.500 0.00 0.00 0.00 3.01
605 622 8.164153 CGAACTTTTCAAATTTTGATATGCCTG 58.836 33.333 12.39 3.04 39.84 4.85
638 656 3.406361 ATGCGCGCGATTCGATCC 61.406 61.111 37.18 13.89 41.67 3.36
650 668 4.324267 AGGTATTATTTAGGACCATGCGC 58.676 43.478 0.00 0.00 34.18 6.09
651 669 5.873164 GGTAGGTATTATTTAGGACCATGCG 59.127 44.000 0.00 0.00 34.18 4.73
691 709 9.903682 TTTTCTTTCTTGATTGATTGATGAGTC 57.096 29.630 0.00 0.00 0.00 3.36
696 714 9.420551 GCTCTTTTTCTTTCTTGATTGATTGAT 57.579 29.630 0.00 0.00 0.00 2.57
697 715 8.415553 TGCTCTTTTTCTTTCTTGATTGATTGA 58.584 29.630 0.00 0.00 0.00 2.57
722 743 4.404394 GGAAGTATATTGGGTGGGGTTTTG 59.596 45.833 0.00 0.00 0.00 2.44
723 744 4.573303 GGGAAGTATATTGGGTGGGGTTTT 60.573 45.833 0.00 0.00 0.00 2.43
740 762 1.770324 CCCAAGCCTCAAGGGAAGT 59.230 57.895 0.00 0.00 45.80 3.01
758 780 0.108945 GATTTGCAGCAGAGGTTGGC 60.109 55.000 0.00 0.00 0.00 4.52
806 828 4.958897 TGGTTTTCGGCCGGGGTG 62.959 66.667 27.83 0.00 0.00 4.61
891 925 5.049405 ACAAGTGATGTTTTTCTCCATCGAC 60.049 40.000 0.00 0.00 40.06 4.20
964 1002 0.633921 TGAGAGGAAGAGGAGGAGGG 59.366 60.000 0.00 0.00 0.00 4.30
975 1013 1.198713 GTCAGGAGCCATGAGAGGAA 58.801 55.000 0.00 0.00 0.00 3.36
1002 1047 1.508088 CCTTTTGCCGTGGAGATGC 59.492 57.895 0.00 0.00 0.00 3.91
1036 1081 1.772156 TGATGGTGGTGGTGGTGGA 60.772 57.895 0.00 0.00 0.00 4.02
1055 1104 2.563086 GAACGAACGGATGCTTGCGG 62.563 60.000 17.38 2.94 41.53 5.69
1057 1106 0.447801 ATGAACGAACGGATGCTTGC 59.552 50.000 0.00 0.00 0.00 4.01
1059 1108 0.999406 CGATGAACGAACGGATGCTT 59.001 50.000 0.00 0.00 45.77 3.91
1060 1109 2.665777 CGATGAACGAACGGATGCT 58.334 52.632 0.00 0.00 45.77 3.79
1066 1115 0.863144 ACAAACCCGATGAACGAACG 59.137 50.000 0.00 0.00 45.77 3.95
1067 1116 2.032426 ACAACAAACCCGATGAACGAAC 59.968 45.455 0.00 0.00 45.77 3.95
1096 1145 2.182030 CGGCACCTCCTTCTCGAC 59.818 66.667 0.00 0.00 0.00 4.20
1223 1272 2.091852 TACGATGTGAGTTGCATGCA 57.908 45.000 18.46 18.46 0.00 3.96
1230 1288 4.397103 TCGACTAACCATACGATGTGAGTT 59.603 41.667 0.00 0.00 0.00 3.01
1240 1298 5.447279 CCATTGTTTGCTCGACTAACCATAC 60.447 44.000 8.76 0.00 33.64 2.39
1249 1307 1.154225 CCGCCATTGTTTGCTCGAC 60.154 57.895 0.00 0.00 0.00 4.20
1251 1309 2.179018 CCCGCCATTGTTTGCTCG 59.821 61.111 0.00 0.00 0.00 5.03
1256 1316 0.753479 TCACACACCCGCCATTGTTT 60.753 50.000 0.00 0.00 0.00 2.83
1275 1335 0.324645 GCCAAGAACCCATCACCCAT 60.325 55.000 0.00 0.00 0.00 4.00
1276 1336 1.076549 GCCAAGAACCCATCACCCA 59.923 57.895 0.00 0.00 0.00 4.51
1277 1337 0.967380 CAGCCAAGAACCCATCACCC 60.967 60.000 0.00 0.00 0.00 4.61
1278 1338 1.598701 GCAGCCAAGAACCCATCACC 61.599 60.000 0.00 0.00 0.00 4.02
1280 1340 0.609957 CAGCAGCCAAGAACCCATCA 60.610 55.000 0.00 0.00 0.00 3.07
1282 1342 1.980772 GCAGCAGCCAAGAACCCAT 60.981 57.895 0.00 0.00 33.58 4.00
1283 1343 2.598394 GCAGCAGCCAAGAACCCA 60.598 61.111 0.00 0.00 33.58 4.51
1293 1368 1.584380 CTCTTGAACCCTGCAGCAGC 61.584 60.000 17.81 3.76 42.57 5.25
1294 1369 0.959372 CCTCTTGAACCCTGCAGCAG 60.959 60.000 16.23 16.23 0.00 4.24
1295 1370 1.073722 CCTCTTGAACCCTGCAGCA 59.926 57.895 8.66 0.00 0.00 4.41
1776 1866 2.747686 GTTGTGCCTCTTCGGGGA 59.252 61.111 0.00 0.00 0.00 4.81
1780 1870 2.383527 GCTCCGTTGTGCCTCTTCG 61.384 63.158 0.00 0.00 0.00 3.79
2185 2296 4.275508 ACCACCTGGCACCTGCTG 62.276 66.667 0.00 0.00 41.70 4.41
2190 2304 4.947147 TTCGCACCACCTGGCACC 62.947 66.667 0.00 0.00 39.32 5.01
2192 2306 1.836999 ATACTTCGCACCACCTGGCA 61.837 55.000 0.00 0.00 39.32 4.92
2193 2307 1.078426 ATACTTCGCACCACCTGGC 60.078 57.895 0.00 0.00 39.32 4.85
2194 2308 0.537188 AGATACTTCGCACCACCTGG 59.463 55.000 0.00 0.00 42.17 4.45
2198 2312 1.661112 GCTTCAGATACTTCGCACCAC 59.339 52.381 0.00 0.00 0.00 4.16
2212 2326 1.268079 TCACTCACTCTCACGCTTCAG 59.732 52.381 0.00 0.00 0.00 3.02
2216 2334 1.683917 ACTTTCACTCACTCTCACGCT 59.316 47.619 0.00 0.00 0.00 5.07
2225 2343 4.084537 CCACACGTATGAACTTTCACTCAC 60.085 45.833 0.00 0.00 40.49 3.51
2226 2344 4.055360 CCACACGTATGAACTTTCACTCA 58.945 43.478 0.00 0.00 40.49 3.41
2250 2376 1.079127 CTCCATTCGCGACCACCTT 60.079 57.895 9.15 0.00 0.00 3.50
2258 2384 1.150567 CTTCAGAGCCTCCATTCGCG 61.151 60.000 0.00 0.00 0.00 5.87
2260 2386 2.680312 TTCTTCAGAGCCTCCATTCG 57.320 50.000 0.00 0.00 0.00 3.34
2261 2387 5.393896 CCATTTTTCTTCAGAGCCTCCATTC 60.394 44.000 0.00 0.00 0.00 2.67
2275 2401 8.793592 GCGGGAATATATACTTCCATTTTTCTT 58.206 33.333 18.07 0.00 43.34 2.52
2276 2402 7.119262 CGCGGGAATATATACTTCCATTTTTCT 59.881 37.037 18.07 0.00 43.34 2.52
2277 2403 7.118680 TCGCGGGAATATATACTTCCATTTTTC 59.881 37.037 6.13 3.59 43.34 2.29
2278 2404 6.938030 TCGCGGGAATATATACTTCCATTTTT 59.062 34.615 6.13 0.00 43.34 1.94
2279 2405 6.469410 TCGCGGGAATATATACTTCCATTTT 58.531 36.000 6.13 0.00 43.34 1.82
2280 2406 6.045072 TCGCGGGAATATATACTTCCATTT 57.955 37.500 6.13 0.00 43.34 2.32
2281 2407 5.670792 TCGCGGGAATATATACTTCCATT 57.329 39.130 6.13 0.00 43.34 3.16
2282 2408 5.670792 TTCGCGGGAATATATACTTCCAT 57.329 39.130 11.32 0.00 43.34 3.41
2283 2409 5.471556 TTTCGCGGGAATATATACTTCCA 57.528 39.130 16.24 0.00 43.34 3.53
2284 2410 6.790285 TTTTTCGCGGGAATATATACTTCC 57.210 37.500 16.24 12.18 41.26 3.46
2323 2449 3.955771 AACAAACCACGATACACACAC 57.044 42.857 0.00 0.00 0.00 3.82
2327 2453 6.476243 AATCTGTAACAAACCACGATACAC 57.524 37.500 0.00 0.00 0.00 2.90
2333 2459 5.924254 TCTCTGTAATCTGTAACAAACCACG 59.076 40.000 0.00 0.00 0.00 4.94
2418 2548 4.277258 TCGACGCGATCAAGAACTTATAC 58.723 43.478 15.93 0.00 0.00 1.47
2423 2554 0.179161 CCTCGACGCGATCAAGAACT 60.179 55.000 15.93 0.00 34.61 3.01
2432 2563 2.068837 ACAAATTAACCTCGACGCGA 57.931 45.000 15.93 2.20 0.00 5.87
2555 2686 8.215050 ACCGAATTAATACCATTAGAACCATCA 58.785 33.333 0.00 0.00 0.00 3.07
2560 2691 9.821662 GCATTACCGAATTAATACCATTAGAAC 57.178 33.333 0.00 0.00 0.00 3.01
2574 2705 5.777802 TGTTGACATTTGCATTACCGAATT 58.222 33.333 0.00 0.00 0.00 2.17
2586 2717 9.372541 GTTTATGCAAAAGATTGTTGACATTTG 57.627 29.630 0.00 4.41 38.85 2.32
2587 2718 9.328845 AGTTTATGCAAAAGATTGTTGACATTT 57.671 25.926 0.00 0.00 38.85 2.32
2589 2720 8.767085 CAAGTTTATGCAAAAGATTGTTGACAT 58.233 29.630 0.00 0.00 38.85 3.06
2596 2727 7.712264 TTGGTCAAGTTTATGCAAAAGATTG 57.288 32.000 0.00 2.38 39.65 2.67
2599 2730 6.872920 ACTTTGGTCAAGTTTATGCAAAAGA 58.127 32.000 6.20 0.00 43.89 2.52
2618 2750 7.149128 GCATCGAGCTAAACTTTGTAAACTTTG 60.149 37.037 0.00 0.00 41.15 2.77
2623 2755 5.933187 TGCATCGAGCTAAACTTTGTAAA 57.067 34.783 8.07 0.00 45.94 2.01
2627 2759 3.605486 GCTTTGCATCGAGCTAAACTTTG 59.395 43.478 9.28 0.00 45.94 2.77
2643 2775 9.445786 TTTATTTACTTCGCATATTAGCTTTGC 57.554 29.630 0.00 0.00 0.00 3.68
2671 2803 7.603651 AGTGTTATTGAACGTACTCTCTTCAT 58.396 34.615 0.00 0.00 38.51 2.57
2672 2804 6.978338 AGTGTTATTGAACGTACTCTCTTCA 58.022 36.000 0.00 0.00 38.51 3.02
2675 2807 6.553524 GCTAGTGTTATTGAACGTACTCTCT 58.446 40.000 0.00 0.00 38.51 3.10
2677 2809 5.106396 ACGCTAGTGTTATTGAACGTACTCT 60.106 40.000 2.24 0.00 38.51 3.24
2678 2810 5.091431 ACGCTAGTGTTATTGAACGTACTC 58.909 41.667 2.24 0.00 38.51 2.59
2679 2811 5.051891 ACGCTAGTGTTATTGAACGTACT 57.948 39.130 2.24 0.00 38.51 2.73
2680 2812 5.752098 AACGCTAGTGTTATTGAACGTAC 57.248 39.130 19.88 0.00 38.51 3.67
2681 2813 7.009448 CCATAAACGCTAGTGTTATTGAACGTA 59.991 37.037 21.40 8.48 38.51 3.57
2682 2814 6.183360 CCATAAACGCTAGTGTTATTGAACGT 60.183 38.462 21.40 6.54 38.51 3.99
2683 2815 6.182634 CCATAAACGCTAGTGTTATTGAACG 58.817 40.000 21.40 6.83 38.51 3.95
2684 2816 6.314400 TCCCATAAACGCTAGTGTTATTGAAC 59.686 38.462 21.40 0.00 36.00 3.18
2685 2817 6.408035 TCCCATAAACGCTAGTGTTATTGAA 58.592 36.000 21.40 10.68 0.00 2.69
2686 2818 5.979993 TCCCATAAACGCTAGTGTTATTGA 58.020 37.500 21.40 11.22 0.00 2.57
2687 2819 6.046593 TCTCCCATAAACGCTAGTGTTATTG 58.953 40.000 21.40 19.29 0.00 1.90
2688 2820 6.229936 TCTCCCATAAACGCTAGTGTTATT 57.770 37.500 21.40 10.04 0.00 1.40
2689 2821 5.864418 TCTCCCATAAACGCTAGTGTTAT 57.136 39.130 21.40 13.76 0.00 1.89
2690 2822 5.047164 TGTTCTCCCATAAACGCTAGTGTTA 60.047 40.000 21.40 10.64 0.00 2.41
2691 2823 4.251268 GTTCTCCCATAAACGCTAGTGTT 58.749 43.478 15.91 15.91 0.00 3.32
2692 2824 3.259876 TGTTCTCCCATAAACGCTAGTGT 59.740 43.478 2.24 2.24 0.00 3.55
2693 2825 3.857052 TGTTCTCCCATAAACGCTAGTG 58.143 45.455 0.59 0.59 0.00 2.74
2694 2826 4.755266 ATGTTCTCCCATAAACGCTAGT 57.245 40.909 0.00 0.00 0.00 2.57
2695 2827 5.730568 GCAAATGTTCTCCCATAAACGCTAG 60.731 44.000 0.00 0.00 0.00 3.42
2696 2828 4.095782 GCAAATGTTCTCCCATAAACGCTA 59.904 41.667 0.00 0.00 0.00 4.26
2697 2829 3.119495 GCAAATGTTCTCCCATAAACGCT 60.119 43.478 0.00 0.00 0.00 5.07
2698 2830 3.179048 GCAAATGTTCTCCCATAAACGC 58.821 45.455 0.00 0.00 0.00 4.84
2699 2831 3.119990 ACGCAAATGTTCTCCCATAAACG 60.120 43.478 0.00 0.00 0.00 3.60
2700 2832 4.434713 ACGCAAATGTTCTCCCATAAAC 57.565 40.909 0.00 0.00 0.00 2.01
2701 2833 5.250200 AGTACGCAAATGTTCTCCCATAAA 58.750 37.500 0.00 0.00 0.00 1.40
2702 2834 4.839121 AGTACGCAAATGTTCTCCCATAA 58.161 39.130 0.00 0.00 0.00 1.90
2703 2835 4.481368 AGTACGCAAATGTTCTCCCATA 57.519 40.909 0.00 0.00 0.00 2.74
2704 2836 3.350219 AGTACGCAAATGTTCTCCCAT 57.650 42.857 0.00 0.00 0.00 4.00
2705 2837 2.811431 CAAGTACGCAAATGTTCTCCCA 59.189 45.455 0.00 0.00 0.00 4.37
2706 2838 3.071479 TCAAGTACGCAAATGTTCTCCC 58.929 45.455 0.00 0.00 0.00 4.30
2707 2839 4.946784 ATCAAGTACGCAAATGTTCTCC 57.053 40.909 0.00 0.00 0.00 3.71
2708 2840 5.960105 GCTAATCAAGTACGCAAATGTTCTC 59.040 40.000 0.00 0.00 0.00 2.87
2709 2841 5.643777 AGCTAATCAAGTACGCAAATGTTCT 59.356 36.000 0.00 0.00 0.00 3.01
2710 2842 5.869350 AGCTAATCAAGTACGCAAATGTTC 58.131 37.500 0.00 0.00 0.00 3.18
2711 2843 5.880054 AGCTAATCAAGTACGCAAATGTT 57.120 34.783 0.00 0.00 0.00 2.71
2712 2844 5.880054 AAGCTAATCAAGTACGCAAATGT 57.120 34.783 0.00 0.00 0.00 2.71
2713 2845 7.962918 AGTAAAAGCTAATCAAGTACGCAAATG 59.037 33.333 0.00 0.00 0.00 2.32
2714 2846 7.962918 CAGTAAAAGCTAATCAAGTACGCAAAT 59.037 33.333 0.00 0.00 0.00 2.32
2715 2847 7.171848 TCAGTAAAAGCTAATCAAGTACGCAAA 59.828 33.333 0.00 0.00 0.00 3.68
2716 2848 6.647481 TCAGTAAAAGCTAATCAAGTACGCAA 59.353 34.615 0.00 0.00 0.00 4.85
2717 2849 6.160684 TCAGTAAAAGCTAATCAAGTACGCA 58.839 36.000 0.00 0.00 0.00 5.24
2718 2850 6.530534 TCTCAGTAAAAGCTAATCAAGTACGC 59.469 38.462 0.00 0.00 0.00 4.42
2719 2851 8.462143 TTCTCAGTAAAAGCTAATCAAGTACG 57.538 34.615 0.00 0.00 0.00 3.67
2721 2853 9.998106 ACTTTCTCAGTAAAAGCTAATCAAGTA 57.002 29.630 0.00 0.00 37.26 2.24
2722 2854 8.910351 ACTTTCTCAGTAAAAGCTAATCAAGT 57.090 30.769 0.00 0.00 37.26 3.16
2724 2856 9.436957 CCTACTTTCTCAGTAAAAGCTAATCAA 57.563 33.333 0.00 0.00 37.54 2.57
2725 2857 8.594550 ACCTACTTTCTCAGTAAAAGCTAATCA 58.405 33.333 0.00 0.00 37.54 2.57
2726 2858 8.874816 CACCTACTTTCTCAGTAAAAGCTAATC 58.125 37.037 0.00 0.00 37.54 1.75
2727 2859 7.334671 GCACCTACTTTCTCAGTAAAAGCTAAT 59.665 37.037 0.00 0.00 37.54 1.73
2728 2860 6.649557 GCACCTACTTTCTCAGTAAAAGCTAA 59.350 38.462 0.00 0.00 37.54 3.09
2729 2861 6.164176 GCACCTACTTTCTCAGTAAAAGCTA 58.836 40.000 0.00 0.00 37.54 3.32
2730 2862 4.998033 GCACCTACTTTCTCAGTAAAAGCT 59.002 41.667 0.00 0.00 37.54 3.74
2731 2863 4.755123 TGCACCTACTTTCTCAGTAAAAGC 59.245 41.667 0.00 0.00 37.54 3.51
2732 2864 5.758296 TGTGCACCTACTTTCTCAGTAAAAG 59.242 40.000 15.69 0.00 37.54 2.27
2733 2865 5.676552 TGTGCACCTACTTTCTCAGTAAAA 58.323 37.500 15.69 0.00 37.54 1.52
2734 2866 5.284861 TGTGCACCTACTTTCTCAGTAAA 57.715 39.130 15.69 0.00 37.54 2.01
2735 2867 4.948341 TGTGCACCTACTTTCTCAGTAA 57.052 40.909 15.69 0.00 37.54 2.24
2736 2868 5.483685 AATGTGCACCTACTTTCTCAGTA 57.516 39.130 15.69 0.00 36.88 2.74
2737 2869 4.357918 AATGTGCACCTACTTTCTCAGT 57.642 40.909 15.69 0.00 39.87 3.41
2738 2870 5.578727 GTCTAATGTGCACCTACTTTCTCAG 59.421 44.000 15.69 0.00 0.00 3.35
2739 2871 5.246203 AGTCTAATGTGCACCTACTTTCTCA 59.754 40.000 15.69 0.00 0.00 3.27
2740 2872 5.725362 AGTCTAATGTGCACCTACTTTCTC 58.275 41.667 15.69 0.00 0.00 2.87
2741 2873 5.746990 AGTCTAATGTGCACCTACTTTCT 57.253 39.130 15.69 2.14 0.00 2.52
2742 2874 7.386848 TGTTAAGTCTAATGTGCACCTACTTTC 59.613 37.037 15.69 12.20 0.00 2.62
2743 2875 7.221450 TGTTAAGTCTAATGTGCACCTACTTT 58.779 34.615 15.69 3.06 0.00 2.66
2744 2876 6.765403 TGTTAAGTCTAATGTGCACCTACTT 58.235 36.000 15.69 16.95 0.00 2.24
2750 2882 8.795786 TTTTCAATGTTAAGTCTAATGTGCAC 57.204 30.769 10.75 10.75 0.00 4.57
2752 2884 8.375465 GCATTTTCAATGTTAAGTCTAATGTGC 58.625 33.333 0.00 0.00 0.00 4.57
2768 2900 6.538021 TGCAAACTTACACAAGCATTTTCAAT 59.462 30.769 0.00 0.00 34.94 2.57
2776 2908 3.631686 ACAGATGCAAACTTACACAAGCA 59.368 39.130 0.00 0.00 34.94 3.91
2799 2931 3.467803 ACTCGTTGCTAGTTTTTGCTCT 58.532 40.909 0.00 0.00 0.00 4.09
2851 2983 3.695830 TTGTTAGTCGCCTGGATTTCT 57.304 42.857 0.00 0.00 0.00 2.52
2852 2984 4.965119 ATTTGTTAGTCGCCTGGATTTC 57.035 40.909 0.00 0.00 0.00 2.17
2853 2985 4.881850 CCTATTTGTTAGTCGCCTGGATTT 59.118 41.667 0.00 0.00 0.00 2.17
2854 2986 4.451900 CCTATTTGTTAGTCGCCTGGATT 58.548 43.478 0.00 0.00 0.00 3.01
2893 3025 8.621286 GGATTACGATTATCATCAAAGGTTTGT 58.379 33.333 2.49 0.00 39.18 2.83
2899 3031 7.607607 TGATGGGGATTACGATTATCATCAAAG 59.392 37.037 0.00 0.00 37.42 2.77
2909 3041 7.394359 CCATTCTAATTGATGGGGATTACGATT 59.606 37.037 8.62 0.00 0.00 3.34
2921 3053 7.578310 AGTGTGAATCCCATTCTAATTGATG 57.422 36.000 0.00 0.00 39.96 3.07
2922 3054 9.872684 ATTAGTGTGAATCCCATTCTAATTGAT 57.127 29.630 0.00 0.00 39.96 2.57
2923 3055 9.123902 CATTAGTGTGAATCCCATTCTAATTGA 57.876 33.333 0.00 0.00 39.96 2.57
2924 3056 8.906867 ACATTAGTGTGAATCCCATTCTAATTG 58.093 33.333 0.00 0.00 39.96 2.32
2927 3059 9.967451 TTTACATTAGTGTGAATCCCATTCTAA 57.033 29.630 0.34 0.00 39.39 2.10
2928 3060 9.967451 TTTTACATTAGTGTGAATCCCATTCTA 57.033 29.630 0.34 0.00 39.39 2.10
2929 3061 8.877864 TTTTACATTAGTGTGAATCCCATTCT 57.122 30.769 0.34 0.00 39.39 2.40
2930 3062 9.573133 CTTTTTACATTAGTGTGAATCCCATTC 57.427 33.333 0.34 0.00 39.39 2.67
2931 3063 8.531146 CCTTTTTACATTAGTGTGAATCCCATT 58.469 33.333 0.34 0.00 39.39 3.16
2932 3064 7.124147 CCCTTTTTACATTAGTGTGAATCCCAT 59.876 37.037 0.34 0.00 39.39 4.00
2933 3065 6.435904 CCCTTTTTACATTAGTGTGAATCCCA 59.564 38.462 0.34 0.00 39.39 4.37
2934 3066 6.661805 TCCCTTTTTACATTAGTGTGAATCCC 59.338 38.462 0.34 0.00 39.39 3.85
2935 3067 7.148069 CCTCCCTTTTTACATTAGTGTGAATCC 60.148 40.741 0.34 0.00 39.39 3.01
2936 3068 7.610305 TCCTCCCTTTTTACATTAGTGTGAATC 59.390 37.037 0.34 0.00 39.39 2.52
2937 3069 7.466804 TCCTCCCTTTTTACATTAGTGTGAAT 58.533 34.615 0.34 0.00 39.39 2.57
2938 3070 6.843752 TCCTCCCTTTTTACATTAGTGTGAA 58.156 36.000 0.34 0.00 39.39 3.18
2947 3079 4.340617 TGCGAATTCCTCCCTTTTTACAT 58.659 39.130 0.00 0.00 0.00 2.29
2959 3091 0.107703 TCTTGGCGATGCGAATTCCT 60.108 50.000 0.00 0.00 0.00 3.36
2967 3099 1.448985 TGTAGGTTTCTTGGCGATGC 58.551 50.000 0.00 0.00 0.00 3.91
2976 3109 0.981183 TCCCGCACATGTAGGTTTCT 59.019 50.000 15.73 0.00 0.00 2.52
3013 3146 2.358957 TGGAATCAATGAGAGCAACGG 58.641 47.619 0.00 0.00 0.00 4.44
3024 3157 3.021695 CACAGTCAGGCATGGAATCAAT 58.978 45.455 0.00 0.00 0.00 2.57
3029 3162 0.250858 CACCACAGTCAGGCATGGAA 60.251 55.000 0.00 0.00 36.04 3.53
3037 3170 0.250038 CCACCACTCACCACAGTCAG 60.250 60.000 0.00 0.00 0.00 3.51
3041 3174 0.180171 TGAACCACCACTCACCACAG 59.820 55.000 0.00 0.00 0.00 3.66
3053 3186 3.244976 CAAATCTGCCGAATTGAACCAC 58.755 45.455 0.00 0.00 32.90 4.16
3066 3199 4.579869 TCTAACTTCTGTCCCAAATCTGC 58.420 43.478 0.00 0.00 0.00 4.26
3078 3211 2.626840 GCCTTGCTCCTCTAACTTCTG 58.373 52.381 0.00 0.00 0.00 3.02
3086 3219 1.908340 AATGCTCGCCTTGCTCCTCT 61.908 55.000 0.00 0.00 0.00 3.69
3135 3268 6.716628 AGGAAAGCACATGAACATAAGAAAGA 59.283 34.615 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.