Multiple sequence alignment - TraesCS6D01G226000

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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 TraesCS6D01G226000 chr6D 100.000 5480 0 0 1 5480 317493787 317488308 0.000000e+00 10120
1 TraesCS6D01G226000 chr6A 93.684 2185 86 29 3307 5480 455048144 455046001 0.000000e+00 3223
2 TraesCS6D01G226000 chr6A 97.299 1296 30 2 1959 3250 455049455 455048161 0.000000e+00 2194
3 TraesCS6D01G226000 chr6A 92.403 724 34 13 574 1291 455050634 455049926 0.000000e+00 1013
4 TraesCS6D01G226000 chr6A 93.261 460 28 3 1473 1932 455049909 455049453 0.000000e+00 675
5 TraesCS6D01G226000 chr6B 91.811 2137 121 22 1155 3250 506702074 506704197 0.000000e+00 2928
6 TraesCS6D01G226000 chr6B 90.035 1144 72 20 1 1133 506700900 506702012 0.000000e+00 1443
7 TraesCS6D01G226000 chr6B 94.578 498 21 5 4153 4645 506706348 506706844 0.000000e+00 765
8 TraesCS6D01G226000 chr6B 92.432 370 22 5 4985 5349 506707290 506707658 1.750000e-144 523
9 TraesCS6D01G226000 chr6B 93.878 343 16 4 4640 4979 506706906 506707246 3.790000e-141 512
10 TraesCS6D01G226000 chr6B 95.484 310 11 3 3334 3641 506705556 506705864 4.930000e-135 492
11 TraesCS6D01G226000 chr6B 88.642 405 29 3 3637 4034 506705912 506706306 1.380000e-130 477
12 TraesCS6D01G226000 chr6B 87.313 134 7 3 5347 5480 506707819 506707942 1.590000e-30 145
13 TraesCS6D01G226000 chr5B 91.860 86 2 4 3246 3327 504177781 504177865 1.250000e-21 115
14 TraesCS6D01G226000 chr7D 91.463 82 6 1 3246 3326 622185086 622185167 1.610000e-20 111
15 TraesCS6D01G226000 chrUn 87.912 91 10 1 3246 3336 364537802 364537891 7.510000e-19 106
16 TraesCS6D01G226000 chr7A 87.912 91 10 1 3246 3336 31514441 31514352 7.510000e-19 106
17 TraesCS6D01G226000 chr7A 87.912 91 10 1 3246 3336 31532243 31532154 7.510000e-19 106
18 TraesCS6D01G226000 chr3A 87.912 91 10 1 3246 3336 39237373 39237284 7.510000e-19 106
19 TraesCS6D01G226000 chr3A 87.912 91 10 1 3246 3336 481865740 481865651 7.510000e-19 106
20 TraesCS6D01G226000 chr2A 87.912 91 10 1 3246 3336 510815357 510815446 7.510000e-19 106
21 TraesCS6D01G226000 chr1D 90.244 82 7 1 3227 3308 298577030 298577110 7.510000e-19 106


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 TraesCS6D01G226000 chr6D 317488308 317493787 5479 True 10120.000 10120 100.000000 1 5480 1 chr6D.!!$R1 5479
1 TraesCS6D01G226000 chr6A 455046001 455050634 4633 True 1776.250 3223 94.161750 574 5480 4 chr6A.!!$R1 4906
2 TraesCS6D01G226000 chr6B 506700900 506707942 7042 False 910.625 2928 91.771625 1 5480 8 chr6B.!!$F1 5479

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
154 155 0.037419 GTCATGGTTGCCGGCATTTT 60.037 50.000 33.25 13.08 0.00 1.82 F
1330 1420 0.033228 ATAGCAGGAGATGAGCACGC 59.967 55.000 0.00 0.00 0.00 5.34 F
1461 1553 1.001520 ACATGGTTCACACGGATTCGA 59.998 47.619 0.00 0.00 40.11 3.71 F
3071 3174 1.200020 GGGTTGATTCGACAAGCAAGG 59.800 52.381 16.67 0.00 46.00 3.61 F
3812 5285 1.899814 TCCCTGACTACACACCATGTC 59.100 52.381 0.00 0.00 42.09 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1650 0.335705 ATGTGTGGATGCATTGGGGA 59.664 50.0 0.0 0.0 0.00 4.81 R
2683 2779 0.107508 TCCAAGCACATAGAGGCAGC 60.108 55.0 0.0 0.0 0.00 5.25 R
3292 3395 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.0 0.0 0.0 0.00 4.37 R
4313 5796 0.321034 TATCAGAGCATGGATGGCGC 60.321 55.0 0.0 0.0 36.08 6.53 R
5436 7215 0.032130 GCTGGAATAGGCATCGTCGA 59.968 55.0 0.0 0.0 0.00 4.20 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 8.311836 TCTATCTTTGTCCGATGAAGTTTAGTT 58.688 33.333 0.00 0.00 0.00 2.24
36 37 6.258727 CCGATGAAGTTTAGTTGCATATGACT 59.741 38.462 6.97 4.56 0.00 3.41
37 38 7.340699 CGATGAAGTTTAGTTGCATATGACTC 58.659 38.462 6.97 0.00 0.00 3.36
38 39 6.647212 TGAAGTTTAGTTGCATATGACTCG 57.353 37.500 6.97 0.00 0.00 4.18
39 40 5.580691 TGAAGTTTAGTTGCATATGACTCGG 59.419 40.000 6.97 0.00 0.00 4.63
77 78 2.838637 TTGTGTCCCCTTTGGAGTTT 57.161 45.000 0.00 0.00 46.38 2.66
78 79 2.065899 TGTGTCCCCTTTGGAGTTTG 57.934 50.000 0.00 0.00 46.38 2.93
79 80 1.328279 GTGTCCCCTTTGGAGTTTGG 58.672 55.000 0.00 0.00 46.38 3.28
88 89 4.270008 CCTTTGGAGTTTGGGATTATCGT 58.730 43.478 0.00 0.00 0.00 3.73
92 93 3.118408 TGGAGTTTGGGATTATCGTCTGG 60.118 47.826 0.00 0.00 0.00 3.86
100 101 2.526432 GATTATCGTCTGGCCCTCCTA 58.474 52.381 0.00 0.00 0.00 2.94
114 115 3.238597 CCCTCCTAGATGCTAGCTTCTT 58.761 50.000 31.14 18.44 33.40 2.52
115 116 3.258123 CCCTCCTAGATGCTAGCTTCTTC 59.742 52.174 31.14 16.17 33.40 2.87
120 121 1.410882 AGATGCTAGCTTCTTCGGGAC 59.589 52.381 23.63 1.13 0.00 4.46
121 122 4.851860 TAGATGCTAGCTTCTTCGGGACG 61.852 52.174 31.14 0.00 41.01 4.79
138 139 3.637229 GGGACGATGATCTTCCTAAGTCA 59.363 47.826 16.32 0.00 35.37 3.41
139 140 4.282195 GGGACGATGATCTTCCTAAGTCAT 59.718 45.833 16.32 0.00 35.37 3.06
141 142 5.207110 ACGATGATCTTCCTAAGTCATGG 57.793 43.478 3.19 9.30 34.40 3.66
154 155 0.037419 GTCATGGTTGCCGGCATTTT 60.037 50.000 33.25 13.08 0.00 1.82
155 156 0.246086 TCATGGTTGCCGGCATTTTC 59.754 50.000 33.25 19.94 0.00 2.29
156 157 0.247185 CATGGTTGCCGGCATTTTCT 59.753 50.000 33.25 11.70 0.00 2.52
157 158 0.247185 ATGGTTGCCGGCATTTTCTG 59.753 50.000 33.25 0.00 0.00 3.02
158 159 1.079888 GGTTGCCGGCATTTTCTGG 60.080 57.895 33.25 0.00 35.57 3.86
166 167 2.614057 CCGGCATTTTCTGGTCTACATC 59.386 50.000 0.00 0.00 0.00 3.06
172 173 4.713824 TTTTCTGGTCTACATCGACGAT 57.286 40.909 4.05 4.05 34.75 3.73
177 178 2.288729 TGGTCTACATCGACGATAACCG 59.711 50.000 10.57 0.43 45.44 4.44
182 183 2.793933 ACATCGACGATAACCGAACTG 58.206 47.619 10.57 0.00 41.76 3.16
194 195 4.705337 AACCGAACTGTTGCTTTTACAA 57.295 36.364 0.00 0.00 0.00 2.41
196 197 4.606961 ACCGAACTGTTGCTTTTACAATG 58.393 39.130 0.00 0.00 0.00 2.82
201 202 6.075415 CGAACTGTTGCTTTTACAATGTCTTG 60.075 38.462 0.00 0.00 38.39 3.02
203 204 5.359576 ACTGTTGCTTTTACAATGTCTTGGA 59.640 36.000 0.00 0.00 36.64 3.53
229 230 2.842457 ACAAGGTTGTTCCGGTAAGAC 58.158 47.619 0.00 0.00 38.47 3.01
298 299 3.318839 TGGATGCAAAAGGAAGACAACAG 59.681 43.478 0.00 0.00 0.00 3.16
308 309 6.625873 AAGGAAGACAACAGTGATTTCTTC 57.374 37.500 16.80 16.80 40.93 2.87
311 312 5.236478 GGAAGACAACAGTGATTTCTTCGAA 59.764 40.000 17.86 0.00 42.05 3.71
315 316 5.360591 ACAACAGTGATTTCTTCGAAGACT 58.639 37.500 27.03 17.67 34.32 3.24
342 343 6.698766 GCCTGCAATTTCATATTCTTGTAAGG 59.301 38.462 0.00 0.00 32.39 2.69
345 346 5.985530 GCAATTTCATATTCTTGTAAGGGCC 59.014 40.000 0.00 0.00 0.00 5.80
468 470 9.926158 ATGATAATTGTGTGCTCAATTTTGTTA 57.074 25.926 14.62 1.36 42.88 2.41
469 471 9.926158 TGATAATTGTGTGCTCAATTTTGTTAT 57.074 25.926 14.62 5.17 42.88 1.89
471 473 9.926158 ATAATTGTGTGCTCAATTTTGTTATCA 57.074 25.926 14.62 0.00 42.88 2.15
472 474 8.836268 AATTGTGTGCTCAATTTTGTTATCAT 57.164 26.923 6.44 0.00 42.88 2.45
473 475 8.836268 ATTGTGTGCTCAATTTTGTTATCATT 57.164 26.923 0.00 0.00 34.86 2.57
474 476 8.659925 TTGTGTGCTCAATTTTGTTATCATTT 57.340 26.923 0.00 0.00 0.00 2.32
475 477 8.659925 TGTGTGCTCAATTTTGTTATCATTTT 57.340 26.923 0.00 0.00 0.00 1.82
476 478 9.107177 TGTGTGCTCAATTTTGTTATCATTTTT 57.893 25.926 0.00 0.00 0.00 1.94
502 504 7.088272 AGAACATTTTTATTGGGCGACTAAAC 58.912 34.615 0.00 0.00 33.13 2.01
543 545 5.874810 CGGGTAAATTTGAAGACAGATCAGA 59.125 40.000 0.00 0.00 0.00 3.27
544 546 6.371548 CGGGTAAATTTGAAGACAGATCAGAA 59.628 38.462 0.00 0.00 0.00 3.02
702 705 0.652592 CGTGTTCTGCCATTCGGATC 59.347 55.000 0.00 0.00 0.00 3.36
974 984 3.189473 TGCGTGCGTTCGTGTTGT 61.189 55.556 3.76 0.00 0.00 3.32
1167 1224 2.156917 TGTGCTCTGATTTGGCTTCAG 58.843 47.619 6.40 6.40 41.61 3.02
1184 1241 6.106003 GGCTTCAGTTTTCAGGAAAGAAAAA 58.894 36.000 3.71 0.00 45.81 1.94
1244 1320 1.530013 CGTAGGGACCTGTCGGTTGT 61.530 60.000 0.00 0.00 45.73 3.32
1315 1405 5.125417 TGCTTTGAATTCTGGTTGGTATAGC 59.875 40.000 7.05 0.00 0.00 2.97
1317 1407 6.678900 GCTTTGAATTCTGGTTGGTATAGCAG 60.679 42.308 7.05 0.00 43.29 4.24
1328 1418 2.630098 TGGTATAGCAGGAGATGAGCAC 59.370 50.000 0.00 0.00 0.00 4.40
1330 1420 0.033228 ATAGCAGGAGATGAGCACGC 59.967 55.000 0.00 0.00 0.00 5.34
1347 1437 4.012895 CGCGAGCGCCAAGTTTGT 62.013 61.111 2.29 0.00 37.98 2.83
1348 1438 2.663478 CGCGAGCGCCAAGTTTGTA 61.663 57.895 2.29 0.00 37.98 2.41
1349 1439 1.154469 GCGAGCGCCAAGTTTGTAC 60.154 57.895 2.29 0.00 34.56 2.90
1358 1448 5.032220 GCGCCAAGTTTGTACATATTTACC 58.968 41.667 0.00 0.00 0.00 2.85
1410 1502 9.531942 GATGACTTAGAATATCATGATAGCAGG 57.468 37.037 19.73 10.35 33.21 4.85
1414 1506 9.040259 ACTTAGAATATCATGATAGCAGGCTAA 57.960 33.333 19.73 17.56 31.73 3.09
1425 1517 3.939740 AGCAGGCTAAATTGAGATGGA 57.060 42.857 0.00 0.00 0.00 3.41
1427 1519 3.201708 AGCAGGCTAAATTGAGATGGAGT 59.798 43.478 0.00 0.00 0.00 3.85
1431 1523 6.528321 CAGGCTAAATTGAGATGGAGTATCA 58.472 40.000 0.00 0.00 38.31 2.15
1440 1532 4.652881 TGAGATGGAGTATCACTTCATGCT 59.347 41.667 4.81 2.87 44.24 3.79
1442 1534 6.095432 AGATGGAGTATCACTTCATGCTAC 57.905 41.667 4.81 0.00 44.24 3.58
1443 1535 5.600069 AGATGGAGTATCACTTCATGCTACA 59.400 40.000 4.81 0.00 44.24 2.74
1461 1553 1.001520 ACATGGTTCACACGGATTCGA 59.998 47.619 0.00 0.00 40.11 3.71
1462 1554 1.393539 CATGGTTCACACGGATTCGAC 59.606 52.381 0.00 0.00 40.11 4.20
1489 1582 3.637432 TGGCACTTTCAACAAATAAGCG 58.363 40.909 0.00 0.00 0.00 4.68
1498 1591 7.328493 ACTTTCAACAAATAAGCGAAATTAGGC 59.672 33.333 0.00 0.00 0.00 3.93
1550 1646 6.553524 ACTAGCTGATCTTAACACGTTACTC 58.446 40.000 0.00 0.00 0.00 2.59
1554 1650 6.929606 AGCTGATCTTAACACGTTACTCTTTT 59.070 34.615 0.00 0.00 0.00 2.27
1634 1730 2.430694 GGCATTTCCCCCTTGTATTGAC 59.569 50.000 0.00 0.00 0.00 3.18
1690 1786 4.957954 TGGAAATATGGAGCTGAGCAATTT 59.042 37.500 7.39 4.47 0.00 1.82
1699 1795 5.124457 TGGAGCTGAGCAATTTCATAAGTTC 59.876 40.000 7.39 0.00 0.00 3.01
1703 1799 6.317391 AGCTGAGCAATTTCATAAGTTCCTAC 59.683 38.462 7.39 0.00 0.00 3.18
1745 1841 5.677319 TTGTAAGGTCTACTCATTCCTGG 57.323 43.478 0.00 0.00 0.00 4.45
1754 1850 3.814504 ACTCATTCCTGGGTGTTCATT 57.185 42.857 0.00 0.00 33.75 2.57
1772 1868 6.095300 TGTTCATTGCCTATCTTATTGGTGTG 59.905 38.462 0.00 0.00 0.00 3.82
1780 1876 6.821665 GCCTATCTTATTGGTGTGAACTGTTA 59.178 38.462 0.00 0.00 0.00 2.41
1785 1881 9.787435 ATCTTATTGGTGTGAACTGTTAAAGTA 57.213 29.630 0.00 0.00 38.56 2.24
1830 1926 4.912187 CACGTAGATCACATAATCTCACCG 59.088 45.833 0.00 0.00 37.24 4.94
1881 1977 8.093927 CAGATAACAATAGATTTCCTCTCTCCC 58.906 40.741 0.00 0.00 35.28 4.30
1894 1990 3.133721 CCTCTCTCCCTGTACTTCCATTG 59.866 52.174 0.00 0.00 0.00 2.82
1911 2007 4.222366 TCCATTGTTGCAATTGAAGCCATA 59.778 37.500 10.34 0.00 0.00 2.74
1916 2012 4.280425 TGTTGCAATTGAAGCCATACAGAA 59.720 37.500 10.34 0.00 0.00 3.02
1953 2049 7.027874 ACAGTATGGAATTTCTTTCTGGGTA 57.972 36.000 9.98 0.00 43.62 3.69
1959 2055 7.227049 TGGAATTTCTTTCTGGGTAATGAAC 57.773 36.000 0.00 0.00 34.56 3.18
1969 2065 4.462483 TCTGGGTAATGAACATTTCCTTGC 59.538 41.667 17.83 6.92 38.05 4.01
1992 2088 5.178809 GCGGGTAGTCCAATGATATGTTAAC 59.821 44.000 0.00 0.00 34.36 2.01
2172 2268 6.211384 ACAAAAATCTAGCAAGCCAGGTTATT 59.789 34.615 0.00 0.00 0.00 1.40
2271 2367 5.808366 ATGCCATCGGAAGACTTTATAGA 57.192 39.130 0.00 0.00 46.97 1.98
2406 2502 4.390264 GTTCTAGAGGAAACAAGCAGGTT 58.610 43.478 0.00 0.00 35.51 3.50
2453 2549 5.983540 ACTGTATCCAGAACAGGAGAAATC 58.016 41.667 8.01 0.00 46.97 2.17
2651 2747 4.440525 GCAACTTATGGTGGATGATTGTGG 60.441 45.833 0.00 0.00 0.00 4.17
2683 2779 2.635714 TCATGTATGCTTGTCTGCCAG 58.364 47.619 0.00 0.00 0.00 4.85
2779 2875 2.847901 CAAGCATTTCAGCGAAGAGTG 58.152 47.619 0.00 0.00 40.15 3.51
2866 2962 4.682787 AGCTTTTTCTTGAGGTTTTTCCG 58.317 39.130 0.00 0.00 41.99 4.30
3041 3144 7.148590 GGCCATTTGTAACTTGATTTGATTGTC 60.149 37.037 0.00 0.00 0.00 3.18
3071 3174 1.200020 GGGTTGATTCGACAAGCAAGG 59.800 52.381 16.67 0.00 46.00 3.61
3188 3291 6.543465 TCTCGAAGGTATGCATCATGATTTTT 59.457 34.615 5.16 0.00 0.00 1.94
3221 3324 7.559590 AGGATTATGTTGTCTTTCACTATGC 57.440 36.000 0.00 0.00 0.00 3.14
3250 3353 9.052759 TGACTAGTTTCTTATGAACAAAAGGAC 57.947 33.333 0.00 0.00 31.02 3.85
3251 3354 8.084590 ACTAGTTTCTTATGAACAAAAGGACG 57.915 34.615 0.00 0.00 31.02 4.79
3252 3355 6.937436 AGTTTCTTATGAACAAAAGGACGT 57.063 33.333 0.00 0.00 31.02 4.34
3255 3358 8.248253 AGTTTCTTATGAACAAAAGGACGTTTT 58.752 29.630 0.05 0.05 39.03 2.43
3256 3359 8.865978 GTTTCTTATGAACAAAAGGACGTTTTT 58.134 29.630 3.17 0.00 36.11 1.94
3258 3361 7.763356 TCTTATGAACAAAAGGACGTTTTTGA 58.237 30.769 24.86 9.22 46.13 2.69
3259 3362 7.698970 TCTTATGAACAAAAGGACGTTTTTGAC 59.301 33.333 24.86 18.81 46.13 3.18
3261 3364 4.918583 TGAACAAAAGGACGTTTTTGACAC 59.081 37.500 24.86 16.86 46.13 3.67
3262 3365 4.776795 ACAAAAGGACGTTTTTGACACT 57.223 36.364 24.86 6.50 46.13 3.55
3263 3366 5.883503 ACAAAAGGACGTTTTTGACACTA 57.116 34.783 24.86 0.00 46.13 2.74
3264 3367 5.633927 ACAAAAGGACGTTTTTGACACTAC 58.366 37.500 24.86 0.00 46.13 2.73
3265 3368 5.181622 ACAAAAGGACGTTTTTGACACTACA 59.818 36.000 24.86 0.00 46.13 2.74
3266 3369 4.870221 AAGGACGTTTTTGACACTACAC 57.130 40.909 0.00 0.00 0.00 2.90
3267 3370 4.133013 AGGACGTTTTTGACACTACACT 57.867 40.909 0.00 0.00 0.00 3.55
3268 3371 5.266733 AGGACGTTTTTGACACTACACTA 57.733 39.130 0.00 0.00 0.00 2.74
3269 3372 5.287226 AGGACGTTTTTGACACTACACTAG 58.713 41.667 0.00 0.00 0.00 2.57
3270 3373 5.045872 GGACGTTTTTGACACTACACTAGT 58.954 41.667 0.00 0.00 40.28 2.57
3283 3386 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3284 3387 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3285 3388 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
3286 3389 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
3287 3390 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
3288 3391 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
3289 3392 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
3295 3398 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3296 3399 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3297 3400 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3298 3401 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3299 3402 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
3300 3403 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
3301 3404 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
3302 3405 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
3303 3406 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
3304 3407 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
3305 3408 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3359 4778 5.941788 AGTTGTGATTTGGACTTTCCTAGT 58.058 37.500 0.00 0.00 40.71 2.57
3430 4849 2.118228 TGCTGCATTTTCGTGTTGAC 57.882 45.000 0.00 0.00 0.00 3.18
3491 4910 6.128391 GGTTTCGAACATGACATAACTAAGCA 60.128 38.462 0.00 0.00 0.00 3.91
3812 5285 1.899814 TCCCTGACTACACACCATGTC 59.100 52.381 0.00 0.00 42.09 3.06
3878 5352 2.006888 CGGCAGATACGGTCACAAATT 58.993 47.619 0.00 0.00 0.00 1.82
3901 5375 5.304686 AGACCATGTTCAAGGACAGTTTA 57.695 39.130 1.00 0.00 32.19 2.01
4037 5520 9.974980 TTTTCTGTTGTGGGAAATATTTTCTAC 57.025 29.630 14.47 14.47 32.54 2.59
4079 5562 9.787435 AGTTTCCACAAATTGTCTAATGTACTA 57.213 29.630 0.00 0.00 0.00 1.82
4096 5579 8.970859 AATGTACTATCCAAGGAATCAGAAAG 57.029 34.615 0.00 0.00 0.00 2.62
4116 5599 8.177663 CAGAAAGTGCAAGTCGTATCATTATTT 58.822 33.333 0.00 0.00 0.00 1.40
4132 5615 8.743085 ATCATTATTTGACACATGCTCTTAGT 57.257 30.769 0.00 0.00 37.11 2.24
4136 5619 4.623932 TTGACACATGCTCTTAGTTCCT 57.376 40.909 0.00 0.00 0.00 3.36
4137 5620 5.738619 TTGACACATGCTCTTAGTTCCTA 57.261 39.130 0.00 0.00 0.00 2.94
4148 5631 6.491745 TGCTCTTAGTTCCTATATCAGTCCTG 59.508 42.308 0.00 0.00 0.00 3.86
4198 5681 4.385447 GCTTTGCGTGAAATATTGCAGAAA 59.615 37.500 0.00 0.00 38.75 2.52
4313 5796 2.028930 AGGTACGTCTTTGGCTCTCAAG 60.029 50.000 0.00 0.00 36.62 3.02
4375 5860 1.922369 ATGGTGCTGAGGCTGAGGT 60.922 57.895 2.44 0.00 39.59 3.85
4410 5895 1.813513 ACTGGAATTTCGAGCAGGTG 58.186 50.000 8.19 0.00 0.00 4.00
4446 5931 0.830444 ATAGCGAAGGGGCCGATGTA 60.830 55.000 0.00 0.00 0.00 2.29
4523 6008 5.399301 GGAAACAAAGATTGTGTTGTGATCG 59.601 40.000 0.00 0.00 44.59 3.69
4716 6273 1.288419 TATGTTGTGCGGTGTGAGCG 61.288 55.000 0.00 0.00 42.73 5.03
4732 6289 2.684374 TGAGCGTAGTATCGGCTTTGTA 59.316 45.455 0.00 0.00 0.00 2.41
4733 6290 3.317149 TGAGCGTAGTATCGGCTTTGTAT 59.683 43.478 0.00 0.00 0.00 2.29
4734 6291 4.516321 TGAGCGTAGTATCGGCTTTGTATA 59.484 41.667 0.00 0.00 0.00 1.47
4752 6309 7.675962 TTGTATACTTGTAAATGTCCACCAC 57.324 36.000 4.17 0.00 0.00 4.16
4783 6341 2.738904 TTGATACGTTGGCGCGCA 60.739 55.556 34.42 16.55 42.83 6.09
4785 6343 2.031044 TTGATACGTTGGCGCGCATC 62.031 55.000 34.42 24.61 42.83 3.91
4998 6597 2.738135 AGACCGGCAAAACAAAATTCG 58.262 42.857 0.00 0.00 0.00 3.34
5019 6618 8.779354 ATTCGAAACTGTTAGCTTAAGAATCT 57.221 30.769 6.67 0.00 0.00 2.40
5044 6643 7.307870 CTTCTGAAGAAAAGGAACTGATCACAG 60.308 40.741 12.01 0.00 40.86 3.66
5088 6687 7.329962 TGAATGCTTGCACATTTCATAGAAAAG 59.670 33.333 4.24 0.00 40.31 2.27
5284 6889 2.616510 GCACCAGTTAGCACATTCTCCT 60.617 50.000 0.00 0.00 0.00 3.69
5315 6920 9.130312 GCATCTTAGTTAGTACCTGATTAATCG 57.870 37.037 10.80 5.78 0.00 3.34
5383 7151 2.488545 ACGACGGGTCTATGATAGCATC 59.511 50.000 0.00 0.00 35.94 3.91
5436 7215 1.203052 CATCGCCAAGGCAAACATTCT 59.797 47.619 12.19 0.00 42.06 2.40
5437 7216 0.881118 TCGCCAAGGCAAACATTCTC 59.119 50.000 12.19 0.00 42.06 2.87
5438 7217 0.454957 CGCCAAGGCAAACATTCTCG 60.455 55.000 12.19 0.00 42.06 4.04
5439 7218 0.881118 GCCAAGGCAAACATTCTCGA 59.119 50.000 6.14 0.00 41.49 4.04
5440 7219 1.401539 GCCAAGGCAAACATTCTCGAC 60.402 52.381 6.14 0.00 41.49 4.20
5441 7220 1.135972 CCAAGGCAAACATTCTCGACG 60.136 52.381 0.00 0.00 0.00 5.12
5442 7221 1.798223 CAAGGCAAACATTCTCGACGA 59.202 47.619 0.00 0.00 0.00 4.20
5443 7222 2.386661 AGGCAAACATTCTCGACGAT 57.613 45.000 0.00 0.00 0.00 3.73
5444 7223 2.002586 AGGCAAACATTCTCGACGATG 58.997 47.619 0.00 0.00 0.00 3.84
5445 7224 1.529826 GGCAAACATTCTCGACGATGC 60.530 52.381 8.46 8.46 0.00 3.91
5458 7237 1.069204 GACGATGCCTATTCCAGCTCA 59.931 52.381 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.130857 TGCAACTAAACTTCATCGGACAA 58.869 39.130 0.00 0.00 0.00 3.18
12 13 7.239166 AGTCATATGCAACTAAACTTCATCG 57.761 36.000 0.00 0.00 0.00 3.84
20 21 4.109766 CGACCGAGTCATATGCAACTAAA 58.890 43.478 0.00 0.00 32.09 1.85
26 27 0.102300 CACCGACCGAGTCATATGCA 59.898 55.000 0.00 0.00 32.09 3.96
36 37 0.031585 CTCACAAGTTCACCGACCGA 59.968 55.000 0.00 0.00 0.00 4.69
37 38 0.249322 ACTCACAAGTTCACCGACCG 60.249 55.000 0.00 0.00 28.74 4.79
38 39 1.949465 AACTCACAAGTTCACCGACC 58.051 50.000 0.00 0.00 42.10 4.79
39 40 3.126343 ACAAAACTCACAAGTTCACCGAC 59.874 43.478 0.00 0.00 45.07 4.79
77 78 0.399949 AGGGCCAGACGATAATCCCA 60.400 55.000 6.18 0.00 36.24 4.37
78 79 0.321996 GAGGGCCAGACGATAATCCC 59.678 60.000 6.18 0.00 0.00 3.85
79 80 0.321996 GGAGGGCCAGACGATAATCC 59.678 60.000 6.18 0.00 0.00 3.01
88 89 0.860457 TAGCATCTAGGAGGGCCAGA 59.140 55.000 6.18 0.00 36.29 3.86
92 93 1.275010 GAAGCTAGCATCTAGGAGGGC 59.725 57.143 18.83 0.00 0.00 5.19
100 101 1.410882 GTCCCGAAGAAGCTAGCATCT 59.589 52.381 16.53 16.53 0.00 2.90
114 115 2.651382 TAGGAAGATCATCGTCCCGA 57.349 50.000 15.42 2.13 44.59 5.14
115 116 2.623889 ACTTAGGAAGATCATCGTCCCG 59.376 50.000 15.42 7.62 44.59 5.14
120 121 5.207110 ACCATGACTTAGGAAGATCATCG 57.793 43.478 0.00 0.00 31.48 3.84
121 122 5.238214 GCAACCATGACTTAGGAAGATCATC 59.762 44.000 0.00 0.00 31.48 2.92
132 133 0.034574 ATGCCGGCAACCATGACTTA 60.035 50.000 36.33 4.88 29.70 2.24
134 135 0.899717 AAATGCCGGCAACCATGACT 60.900 50.000 36.33 11.92 29.70 3.41
138 139 0.247185 CAGAAAATGCCGGCAACCAT 59.753 50.000 36.33 20.14 0.00 3.55
139 140 1.664873 CAGAAAATGCCGGCAACCA 59.335 52.632 36.33 10.72 0.00 3.67
141 142 0.388520 GACCAGAAAATGCCGGCAAC 60.389 55.000 36.33 23.53 0.00 4.17
154 155 3.562973 GGTTATCGTCGATGTAGACCAGA 59.437 47.826 17.98 0.00 37.85 3.86
155 156 3.606384 CGGTTATCGTCGATGTAGACCAG 60.606 52.174 17.98 11.50 37.85 4.00
156 157 2.288729 CGGTTATCGTCGATGTAGACCA 59.711 50.000 17.98 0.00 37.85 4.02
157 158 2.545526 TCGGTTATCGTCGATGTAGACC 59.454 50.000 17.98 16.68 37.85 3.85
158 159 3.867055 TCGGTTATCGTCGATGTAGAC 57.133 47.619 17.98 10.31 40.32 2.59
166 167 1.058695 GCAACAGTTCGGTTATCGTCG 59.941 52.381 0.00 0.00 40.32 5.12
172 173 5.814764 TTGTAAAAGCAACAGTTCGGTTA 57.185 34.783 0.00 0.00 0.00 2.85
177 178 6.198966 CCAAGACATTGTAAAAGCAACAGTTC 59.801 38.462 0.00 0.00 34.39 3.01
182 183 7.437862 TGAAATCCAAGACATTGTAAAAGCAAC 59.562 33.333 0.00 0.00 34.39 4.17
194 195 5.363580 ACAACCTTGTTGAAATCCAAGACAT 59.636 36.000 13.46 0.00 40.36 3.06
196 197 5.262588 ACAACCTTGTTGAAATCCAAGAC 57.737 39.130 13.46 0.00 40.36 3.01
229 230 2.796383 CGTTGCCGTCTCTAGGATTCTG 60.796 54.545 0.00 0.00 0.00 3.02
298 299 3.748568 AGGCAAGTCTTCGAAGAAATCAC 59.251 43.478 28.58 16.53 45.90 3.06
308 309 2.030893 TGAAATTGCAGGCAAGTCTTCG 60.031 45.455 12.66 0.00 39.47 3.79
311 312 5.655532 AGAATATGAAATTGCAGGCAAGTCT 59.344 36.000 12.66 0.00 39.47 3.24
315 316 6.040209 ACAAGAATATGAAATTGCAGGCAA 57.960 33.333 9.38 9.38 40.47 4.52
357 358 1.422531 AACCAGGCATTCCAGCAAAA 58.577 45.000 0.00 0.00 35.83 2.44
358 359 1.422531 AAACCAGGCATTCCAGCAAA 58.577 45.000 0.00 0.00 35.83 3.68
359 360 1.422531 AAAACCAGGCATTCCAGCAA 58.577 45.000 0.00 0.00 35.83 3.91
360 361 2.300956 TAAAACCAGGCATTCCAGCA 57.699 45.000 0.00 0.00 35.83 4.41
361 362 3.893326 AATAAAACCAGGCATTCCAGC 57.107 42.857 0.00 0.00 33.74 4.85
362 363 8.474025 TGTATTAAATAAAACCAGGCATTCCAG 58.526 33.333 0.00 0.00 33.74 3.86
363 364 8.367660 TGTATTAAATAAAACCAGGCATTCCA 57.632 30.769 0.00 0.00 33.74 3.53
374 375 7.709182 GTCCCAAGGCCATGTATTAAATAAAAC 59.291 37.037 5.01 0.00 0.00 2.43
445 447 9.926158 TGATAACAAAATTGAGCACACAATTAT 57.074 25.926 13.78 6.50 45.71 1.28
469 471 8.930760 CGCCCAATAAAAATGTTCTAAAAATGA 58.069 29.630 0.00 0.00 0.00 2.57
470 472 8.930760 TCGCCCAATAAAAATGTTCTAAAAATG 58.069 29.630 0.00 0.00 0.00 2.32
471 473 8.931775 GTCGCCCAATAAAAATGTTCTAAAAAT 58.068 29.630 0.00 0.00 0.00 1.82
472 474 8.145122 AGTCGCCCAATAAAAATGTTCTAAAAA 58.855 29.630 0.00 0.00 0.00 1.94
473 475 7.662897 AGTCGCCCAATAAAAATGTTCTAAAA 58.337 30.769 0.00 0.00 0.00 1.52
474 476 7.222000 AGTCGCCCAATAAAAATGTTCTAAA 57.778 32.000 0.00 0.00 0.00 1.85
475 477 6.827586 AGTCGCCCAATAAAAATGTTCTAA 57.172 33.333 0.00 0.00 0.00 2.10
476 478 7.925043 TTAGTCGCCCAATAAAAATGTTCTA 57.075 32.000 0.00 0.00 0.00 2.10
477 479 6.827586 TTAGTCGCCCAATAAAAATGTTCT 57.172 33.333 0.00 0.00 0.00 3.01
478 480 6.864165 TGTTTAGTCGCCCAATAAAAATGTTC 59.136 34.615 0.00 0.00 0.00 3.18
479 481 6.750148 TGTTTAGTCGCCCAATAAAAATGTT 58.250 32.000 0.00 0.00 0.00 2.71
480 482 6.334102 TGTTTAGTCGCCCAATAAAAATGT 57.666 33.333 0.00 0.00 0.00 2.71
502 504 7.932120 TTTACCCGTGAACATAAACAAATTG 57.068 32.000 0.00 0.00 0.00 2.32
549 551 7.685481 TCTTTTTCTTTTTGGGGAAGACTTTT 58.315 30.769 0.00 0.00 33.15 2.27
552 554 6.867519 TTCTTTTTCTTTTTGGGGAAGACT 57.132 33.333 0.00 0.00 33.15 3.24
902 912 2.876945 CGGATAGAGGGCAGGGCAG 61.877 68.421 0.00 0.00 0.00 4.85
903 913 2.844362 CGGATAGAGGGCAGGGCA 60.844 66.667 0.00 0.00 0.00 5.36
904 914 2.384653 GAACGGATAGAGGGCAGGGC 62.385 65.000 0.00 0.00 0.00 5.19
905 915 1.749033 GAACGGATAGAGGGCAGGG 59.251 63.158 0.00 0.00 0.00 4.45
906 916 1.749033 GGAACGGATAGAGGGCAGG 59.251 63.158 0.00 0.00 0.00 4.85
988 998 0.179067 TCGCCCATTTAACTAGCCGG 60.179 55.000 0.00 0.00 0.00 6.13
1093 1109 1.227263 CGATCCCGTGGACCATGAC 60.227 63.158 15.72 3.20 32.98 3.06
1167 1224 9.249457 CCAGATAACTTTTTCTTTCCTGAAAAC 57.751 33.333 2.44 0.00 43.09 2.43
1184 1241 3.950395 GCAATTCAGGAAGCCAGATAACT 59.050 43.478 0.00 0.00 0.00 2.24
1244 1320 4.803088 CACAAATCCGCAAAGTTTTCAAGA 59.197 37.500 0.00 0.00 0.00 3.02
1315 1405 3.260483 GCGCGTGCTCATCTCCTG 61.260 66.667 15.02 0.00 38.39 3.86
1317 1407 4.854784 TCGCGCGTGCTCATCTCC 62.855 66.667 30.98 0.00 39.65 3.71
1330 1420 2.663478 TACAAACTTGGCGCTCGCG 61.663 57.895 7.64 6.98 43.06 5.87
1337 1427 8.921670 CAAAAGGTAAATATGTACAAACTTGGC 58.078 33.333 0.00 0.00 0.00 4.52
1386 1476 7.179872 AGCCTGCTATCATGATATTCTAAGTCA 59.820 37.037 15.71 6.81 0.00 3.41
1403 1495 5.072872 ACTCCATCTCAATTTAGCCTGCTAT 59.927 40.000 0.00 0.00 0.00 2.97
1410 1502 7.712639 TGAAGTGATACTCCATCTCAATTTAGC 59.287 37.037 0.00 0.00 34.46 3.09
1414 1506 6.485984 GCATGAAGTGATACTCCATCTCAATT 59.514 38.462 0.00 0.00 34.46 2.32
1417 1509 4.652881 AGCATGAAGTGATACTCCATCTCA 59.347 41.667 0.00 0.00 34.46 3.27
1427 1519 5.817296 GTGAACCATGTAGCATGAAGTGATA 59.183 40.000 10.34 0.00 0.00 2.15
1431 1523 3.753272 GTGTGAACCATGTAGCATGAAGT 59.247 43.478 10.34 0.00 0.00 3.01
1440 1532 2.231721 TCGAATCCGTGTGAACCATGTA 59.768 45.455 0.00 0.00 37.05 2.29
1442 1534 1.393539 GTCGAATCCGTGTGAACCATG 59.606 52.381 0.00 0.00 37.05 3.66
1443 1535 1.275291 AGTCGAATCCGTGTGAACCAT 59.725 47.619 0.00 0.00 37.05 3.55
1461 1553 2.175202 TGTTGAAAGTGCCAAACCAGT 58.825 42.857 0.00 0.00 0.00 4.00
1462 1554 2.957491 TGTTGAAAGTGCCAAACCAG 57.043 45.000 0.00 0.00 0.00 4.00
1489 1582 5.612725 TCATTGAAATGGGGCCTAATTTC 57.387 39.130 25.53 25.53 41.25 2.17
1498 1591 5.657474 CACTCTGAATTCATTGAAATGGGG 58.343 41.667 8.96 0.00 37.03 4.96
1550 1646 1.901159 TGTGGATGCATTGGGGAAAAG 59.099 47.619 0.00 0.00 0.00 2.27
1554 1650 0.335705 ATGTGTGGATGCATTGGGGA 59.664 50.000 0.00 0.00 0.00 4.81
1575 1671 8.613060 ACCAGATTATTCATAGTTGCAGTATG 57.387 34.615 10.53 10.53 40.87 2.39
1579 1675 7.325660 ACAACCAGATTATTCATAGTTGCAG 57.674 36.000 0.00 0.00 34.41 4.41
1598 1694 4.556233 GAAATGCCAAAGTAGGAACAACC 58.444 43.478 0.00 0.00 39.35 3.77
1690 1786 6.719829 TGACTCTGTCTTGTAGGAACTTATGA 59.280 38.462 0.00 0.00 34.74 2.15
1699 1795 6.516739 TGAACTATGACTCTGTCTTGTAGG 57.483 41.667 0.00 0.00 33.15 3.18
1703 1799 8.763049 TTACAATGAACTATGACTCTGTCTTG 57.237 34.615 0.00 0.00 33.15 3.02
1745 1841 5.594317 ACCAATAAGATAGGCAATGAACACC 59.406 40.000 0.00 0.00 0.00 4.16
1754 1850 5.185454 CAGTTCACACCAATAAGATAGGCA 58.815 41.667 0.00 0.00 0.00 4.75
1780 1876 8.210946 TGGTAATGCAATAGCTCACTATACTTT 58.789 33.333 11.96 0.00 38.18 2.66
1785 1881 5.760253 GTGTGGTAATGCAATAGCTCACTAT 59.240 40.000 26.87 0.00 41.21 2.12
1881 1977 5.771469 TCAATTGCAACAATGGAAGTACAG 58.229 37.500 0.00 0.00 40.42 2.74
1894 1990 4.439305 TCTGTATGGCTTCAATTGCAAC 57.561 40.909 0.00 0.00 0.00 4.17
1911 2007 9.449719 CCATACTGTAAAAGAAATAGGTTCTGT 57.550 33.333 0.00 0.00 46.36 3.41
1940 2036 7.508977 AGGAAATGTTCATTACCCAGAAAGAAA 59.491 33.333 14.52 0.00 0.00 2.52
1969 2065 6.522054 AGTTAACATATCATTGGACTACCCG 58.478 40.000 8.61 0.00 37.93 5.28
1992 2088 5.386958 TGTTGCTGTTACTACCTACAGAG 57.613 43.478 6.43 0.00 43.45 3.35
2172 2268 6.376864 TCTGTGGTCTTTTGTTGATTTCTTCA 59.623 34.615 0.00 0.00 0.00 3.02
2271 2367 2.338809 TCAAGTGATTGTCCAGGAGGT 58.661 47.619 0.00 0.00 35.89 3.85
2437 2533 9.712305 AATATTATACGATTTCTCCTGTTCTGG 57.288 33.333 0.00 0.00 0.00 3.86
2683 2779 0.107508 TCCAAGCACATAGAGGCAGC 60.108 55.000 0.00 0.00 0.00 5.25
2842 2938 5.580691 CGGAAAAACCTCAAGAAAAAGCTTT 59.419 36.000 5.69 5.69 36.31 3.51
3041 3144 4.513692 TGTCGAATCAACCCACTACAAAAG 59.486 41.667 0.00 0.00 0.00 2.27
3071 3174 9.701098 TTCCTCGTATACAATATGTGGATAAAC 57.299 33.333 3.32 0.00 34.63 2.01
3221 3324 9.831737 CTTTTGTTCATAAGAAACTAGTCATGG 57.168 33.333 0.00 0.00 35.08 3.66
3261 3364 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3262 3365 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
3269 3372 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3270 3373 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3271 3374 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3272 3375 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3273 3376 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
3274 3377 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3275 3378 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3276 3379 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3277 3380 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3278 3381 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3279 3382 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3280 3383 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
3281 3384 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
3282 3385 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3283 3386 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3284 3387 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3285 3388 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3286 3389 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3287 3390 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
3288 3391 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3289 3392 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3290 3393 4.474303 TTAATACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
3291 3394 3.339713 TTAATACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
3292 3395 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3293 3396 4.020751 GGTATTTAATACTCCCTCCGTCCC 60.021 50.000 13.86 0.00 36.04 4.46
3294 3397 4.590222 TGGTATTTAATACTCCCTCCGTCC 59.410 45.833 13.86 0.00 36.04 4.79
3295 3398 5.303845 AGTGGTATTTAATACTCCCTCCGTC 59.696 44.000 13.86 0.00 36.04 4.79
3296 3399 5.214293 AGTGGTATTTAATACTCCCTCCGT 58.786 41.667 13.86 0.00 36.04 4.69
3297 3400 5.803237 AGTGGTATTTAATACTCCCTCCG 57.197 43.478 13.86 0.00 36.04 4.63
3430 4849 6.082338 GGACGCTTATTCTCAATATTGCATG 58.918 40.000 10.76 3.94 0.00 4.06
3491 4910 9.349713 TGTCAATAGTAATGTTTGTCCTTTTCT 57.650 29.630 0.00 0.00 0.00 2.52
3585 5005 8.744568 TTTTACATATAGTCCATGCAATGTCA 57.255 30.769 0.00 0.00 44.81 3.58
3621 5043 3.181469 GGCAGCATCCAAATCAACATGAT 60.181 43.478 0.00 0.00 39.09 2.45
3812 5285 0.103208 GAGTCATACGCACCCAGGAG 59.897 60.000 0.00 0.00 0.00 3.69
3878 5352 4.974645 AACTGTCCTTGAACATGGTCTA 57.025 40.909 12.94 3.09 0.00 2.59
3901 5375 8.147058 AGCAATGATTTATCTCGATTAGTCTGT 58.853 33.333 0.00 0.00 0.00 3.41
4037 5520 3.120649 GGAAACTCGTGATCAAAGGAACG 60.121 47.826 0.00 0.00 37.38 3.95
4079 5562 4.038271 TGCACTTTCTGATTCCTTGGAT 57.962 40.909 0.00 0.00 0.00 3.41
4096 5579 6.682863 GTGTCAAATAATGATACGACTTGCAC 59.317 38.462 0.00 0.00 39.85 4.57
4132 5615 4.556697 TGCTTCCAGGACTGATATAGGAA 58.443 43.478 0.00 0.00 34.30 3.36
4136 5619 5.069648 CACTTCTGCTTCCAGGACTGATATA 59.930 44.000 0.00 0.00 39.61 0.86
4137 5620 4.036518 ACTTCTGCTTCCAGGACTGATAT 58.963 43.478 0.00 0.00 39.61 1.63
4148 5631 0.687354 TCAGGTCCACTTCTGCTTCC 59.313 55.000 0.00 0.00 0.00 3.46
4198 5681 3.680490 GCTTAAGTCCTCTCAAAAGCCT 58.320 45.455 4.02 0.00 0.00 4.58
4284 5767 3.061697 GCCAAAGACGTACCTGAATTACG 59.938 47.826 0.00 0.55 46.25 3.18
4313 5796 0.321034 TATCAGAGCATGGATGGCGC 60.321 55.000 0.00 0.00 36.08 6.53
4359 5844 2.046507 CACCTCAGCCTCAGCACC 60.047 66.667 0.00 0.00 43.56 5.01
4375 5860 8.934023 AAATTCCAGTTTATAGGAAGACAACA 57.066 30.769 0.00 0.00 46.25 3.33
4410 5895 2.481952 GCTATGCATGACGGGATCTTTC 59.518 50.000 10.16 0.00 0.00 2.62
4523 6008 1.385743 CGCAGTTAGCAACTCGTGTAC 59.614 52.381 0.00 0.00 46.13 2.90
4645 6200 1.518572 CGACATGGCACGACCCTAC 60.519 63.158 0.00 0.00 37.83 3.18
4716 6273 9.520204 TTTACAAGTATACAAAGCCGATACTAC 57.480 33.333 5.50 0.00 35.76 2.73
4732 6289 5.876357 ACAGTGGTGGACATTTACAAGTAT 58.124 37.500 0.00 0.00 0.00 2.12
4733 6290 5.298989 ACAGTGGTGGACATTTACAAGTA 57.701 39.130 0.00 0.00 0.00 2.24
4734 6291 4.164843 ACAGTGGTGGACATTTACAAGT 57.835 40.909 0.00 0.00 0.00 3.16
4783 6341 2.745821 GCGACGTTTCCCCTTAAAAGAT 59.254 45.455 0.00 0.00 0.00 2.40
4785 6343 1.874872 TGCGACGTTTCCCCTTAAAAG 59.125 47.619 0.00 0.00 0.00 2.27
4961 6522 5.221048 GCCGGTCTAAATTAGAATGTGCATT 60.221 40.000 4.04 0.00 36.40 3.56
4979 6540 2.733517 TCGAATTTTGTTTTGCCGGTC 58.266 42.857 1.90 0.00 0.00 4.79
4998 6597 9.209175 TCAGAAGATTCTTAAGCTAACAGTTTC 57.791 33.333 0.00 0.00 34.74 2.78
5019 6618 6.356556 TGTGATCAGTTCCTTTTCTTCAGAA 58.643 36.000 0.00 0.00 0.00 3.02
5044 6643 6.369615 AGCATTCAAATTACAAACATTCCTGC 59.630 34.615 0.00 0.00 0.00 4.85
5088 6687 7.225734 GGAGCTGAGTTTGTTTTCTAGGATATC 59.774 40.741 0.00 0.00 0.00 1.63
5097 6696 2.218603 TCGGGAGCTGAGTTTGTTTTC 58.781 47.619 0.00 0.00 0.00 2.29
5284 6889 5.897250 TCAGGTACTAACTAAGATGCATCCA 59.103 40.000 23.06 10.54 36.02 3.41
5315 6920 3.058293 TGACAATGGTCTGTTCAATTCGC 60.058 43.478 1.02 0.00 44.61 4.70
5383 7151 4.498009 GCCTGGTAATGAAATTCCATGTCG 60.498 45.833 0.00 0.00 37.87 4.35
5436 7215 0.032130 GCTGGAATAGGCATCGTCGA 59.968 55.000 0.00 0.00 0.00 4.20
5437 7216 0.032678 AGCTGGAATAGGCATCGTCG 59.967 55.000 0.00 0.00 0.00 5.12
5438 7217 1.069204 TGAGCTGGAATAGGCATCGTC 59.931 52.381 0.00 0.00 0.00 4.20
5439 7218 1.123077 TGAGCTGGAATAGGCATCGT 58.877 50.000 0.00 0.00 0.00 3.73
5440 7219 2.469274 ATGAGCTGGAATAGGCATCG 57.531 50.000 0.00 0.00 0.00 3.84
5441 7220 6.830873 ATTAAATGAGCTGGAATAGGCATC 57.169 37.500 0.00 0.00 0.00 3.91
5442 7221 8.710749 TTTATTAAATGAGCTGGAATAGGCAT 57.289 30.769 0.00 0.00 0.00 4.40
5443 7222 8.532186 TTTTATTAAATGAGCTGGAATAGGCA 57.468 30.769 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.