Multiple sequence alignment - TraesCS6D01G189600

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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 TraesCS6D01G189600 chr6D 100.000 5251 0 0 1 5251 262431850 262426600 0.000000e+00 9697.0
1 TraesCS6D01G189600 chr6B 93.099 2391 84 23 2358 4678 348093821 348096200 0.000000e+00 3426.0
2 TraesCS6D01G189600 chr6B 86.906 2337 116 88 97 2320 348091424 348093683 0.000000e+00 2446.0
3 TraesCS6D01G189600 chr6B 90.741 270 25 0 4830 5099 348096370 348096639 1.390000e-95 361.0
4 TraesCS6D01G189600 chr6B 90.845 142 12 1 5111 5251 348097544 348097685 6.940000e-44 189.0
5 TraesCS6D01G189600 chr6B 85.294 170 18 7 4297 4460 348097104 348097272 9.040000e-38 169.0
6 TraesCS6D01G189600 chr6A 95.233 1993 76 10 2349 4328 322702292 322704278 0.000000e+00 3136.0
7 TraesCS6D01G189600 chr6A 94.763 802 28 5 1556 2350 322701387 322702181 0.000000e+00 1236.0
8 TraesCS6D01G189600 chr6A 84.476 496 25 21 473 960 322700470 322700921 4.830000e-120 442.0
9 TraesCS6D01G189600 chr6A 89.308 318 16 11 91 393 322700100 322700414 2.970000e-102 383.0
10 TraesCS6D01G189600 chr6A 90.236 297 11 10 1193 1486 322701067 322701348 6.420000e-99 372.0
11 TraesCS6D01G189600 chr6A 98.160 163 3 0 1011 1173 322700928 322701090 8.610000e-73 285.0
12 TraesCS6D01G189600 chr6A 95.035 141 7 0 5111 5251 322705426 322705566 6.840000e-54 222.0
13 TraesCS6D01G189600 chr6A 92.857 98 4 3 4379 4474 322704283 322704379 7.090000e-29 139.0
14 TraesCS6D01G189600 chr6A 89.320 103 8 3 4469 4570 322704409 322704509 5.520000e-25 126.0
15 TraesCS6D01G189600 chr6A 92.500 40 3 0 4414 4453 322705112 322705151 2.040000e-04 58.4
16 TraesCS6D01G189600 chr5D 96.471 85 2 1 1 84 136352096 136352180 7.090000e-29 139.0
17 TraesCS6D01G189600 chr5D 91.667 84 7 0 1 84 230029608 230029691 3.320000e-22 117.0
18 TraesCS6D01G189600 chr5A 92.857 84 6 0 1 84 425009563 425009480 7.140000e-24 122.0
19 TraesCS6D01G189600 chrUn 91.765 85 6 1 1 84 65963493 65963409 3.320000e-22 117.0
20 TraesCS6D01G189600 chr2A 90.588 85 7 1 1 84 745560710 745560794 1.550000e-20 111.0


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 TraesCS6D01G189600 chr6D 262426600 262431850 5250 True 9697.00 9697 100.0000 1 5251 1 chr6D.!!$R1 5250
1 TraesCS6D01G189600 chr6B 348091424 348097685 6261 False 1318.20 3426 89.3770 97 5251 5 chr6B.!!$F1 5154
2 TraesCS6D01G189600 chr6A 322700100 322705566 5466 False 639.94 3136 92.1888 91 5251 10 chr6A.!!$F1 5160

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
375 393 0.250338 GGGTCGGTGCTCTTTTCACT 60.250 55.0 0.00 0.00 34.97 3.41 F
1179 1237 0.104671 CCTTCTCCTCTGCAGCTAGC 59.895 60.0 9.47 6.62 45.96 3.42 F
1674 1790 0.183492 TTGCACTTTGCCTCCTCACT 59.817 50.0 0.00 0.00 44.23 3.41 F
2441 2716 0.320697 GTGCCCAGGGATATACCGAC 59.679 60.0 10.89 0.00 40.11 4.79 F
2868 3147 0.598065 GTGTGAAGGACATGGCAACC 59.402 55.0 0.00 0.00 36.78 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1258 0.037605 GGAACGGCGGAGAAGAGAAA 60.038 55.0 13.24 0.0 0.0 2.52 R
2424 2692 0.834687 TGGTCGGTATATCCCTGGGC 60.835 60.0 8.22 0.0 0.0 5.36 R
3580 3860 0.176910 TGACTTGCACTGTTGACCGA 59.823 50.0 0.00 0.0 0.0 4.69 R
4080 4360 0.468226 AAACTCAAGCCTCGGTCACA 59.532 50.0 0.00 0.0 0.0 3.58 R
4859 5281 0.108329 AGAAATGTCCGTACGCCCAG 60.108 55.0 10.49 0.0 0.0 4.45 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
44 45 8.451908 AGATTCCATAAGAAAAATTCCTACGG 57.548 34.615 0.00 0.00 38.21 4.02
45 46 7.502561 AGATTCCATAAGAAAAATTCCTACGGG 59.497 37.037 0.00 0.00 38.21 5.28
46 47 6.316280 TCCATAAGAAAAATTCCTACGGGA 57.684 37.500 0.00 0.00 40.36 5.14
47 48 6.906848 TCCATAAGAAAAATTCCTACGGGAT 58.093 36.000 0.00 0.00 41.87 3.85
48 49 6.996282 TCCATAAGAAAAATTCCTACGGGATC 59.004 38.462 0.00 0.00 41.87 3.36
49 50 6.206829 CCATAAGAAAAATTCCTACGGGATCC 59.793 42.308 1.92 1.92 41.87 3.36
50 51 4.855298 AGAAAAATTCCTACGGGATCCA 57.145 40.909 15.23 0.00 41.87 3.41
51 52 5.187621 AGAAAAATTCCTACGGGATCCAA 57.812 39.130 15.23 0.00 41.87 3.53
52 53 5.766590 AGAAAAATTCCTACGGGATCCAAT 58.233 37.500 15.23 2.83 41.87 3.16
53 54 5.828328 AGAAAAATTCCTACGGGATCCAATC 59.172 40.000 15.23 0.00 41.87 2.67
70 71 8.743714 GGATCCAATCCTATGAATTAAATGACC 58.256 37.037 6.95 0.00 46.19 4.02
71 72 9.300681 GATCCAATCCTATGAATTAAATGACCA 57.699 33.333 0.00 0.00 0.00 4.02
72 73 9.659135 ATCCAATCCTATGAATTAAATGACCAA 57.341 29.630 0.00 0.00 0.00 3.67
73 74 8.912988 TCCAATCCTATGAATTAAATGACCAAC 58.087 33.333 0.00 0.00 0.00 3.77
74 75 8.694540 CCAATCCTATGAATTAAATGACCAACA 58.305 33.333 0.00 0.00 0.00 3.33
111 112 1.742880 CATGTACTGCAGTGGCGCT 60.743 57.895 29.57 10.30 45.35 5.92
126 127 1.061411 CGCTGATCCACAATGCACG 59.939 57.895 0.00 0.00 0.00 5.34
127 128 1.226491 GCTGATCCACAATGCACGC 60.226 57.895 0.00 0.00 0.00 5.34
128 129 1.651240 GCTGATCCACAATGCACGCT 61.651 55.000 0.00 0.00 0.00 5.07
133 138 4.764336 CACAATGCACGCTGCCCG 62.764 66.667 7.38 0.00 44.23 6.13
152 157 1.666888 CGAAGGAAAGGCACATGCAAC 60.667 52.381 6.15 0.00 44.36 4.17
215 224 4.481368 TTACTTACACTGGCTACCCATG 57.519 45.455 0.00 0.00 41.21 3.66
217 226 1.837439 CTTACACTGGCTACCCATGGA 59.163 52.381 15.22 0.00 41.21 3.41
218 227 1.496060 TACACTGGCTACCCATGGAG 58.504 55.000 15.22 4.42 41.21 3.86
219 228 0.547712 ACACTGGCTACCCATGGAGT 60.548 55.000 15.22 12.19 41.21 3.85
242 251 1.313772 ATTAAACACACACCAGCGCA 58.686 45.000 11.47 0.00 0.00 6.09
292 304 1.471287 CAGTTGTCACATGCCATGGAG 59.529 52.381 18.40 6.84 33.60 3.86
341 353 1.654954 CTTCTGCATGCCAGCCAGAC 61.655 60.000 16.68 0.00 41.50 3.51
344 356 3.138798 GCATGCCAGCCAGACCAG 61.139 66.667 6.36 0.00 0.00 4.00
351 363 0.607489 CCAGCCAGACCAGACCAAAG 60.607 60.000 0.00 0.00 0.00 2.77
352 364 0.607489 CAGCCAGACCAGACCAAAGG 60.607 60.000 0.00 0.00 0.00 3.11
375 393 0.250338 GGGTCGGTGCTCTTTTCACT 60.250 55.000 0.00 0.00 34.97 3.41
394 412 0.540365 TGGGAAAAGGCAAGCAGGAG 60.540 55.000 0.00 0.00 0.00 3.69
396 414 1.181098 GGAAAAGGCAAGCAGGAGCA 61.181 55.000 0.00 0.00 45.49 4.26
442 462 2.924454 GCACACGTTTCTCTCTCTCTGG 60.924 54.545 0.00 0.00 0.00 3.86
445 465 3.082548 CACGTTTCTCTCTCTCTGGGTA 58.917 50.000 0.00 0.00 0.00 3.69
491 537 5.858381 AGAGATGCAAGTGTGACTCTTTTA 58.142 37.500 0.00 0.00 31.84 1.52
539 588 0.608130 CTCCATCCACCGTGAGTCAA 59.392 55.000 0.00 0.00 0.00 3.18
555 604 1.227383 CAATAGGGGCCCACTCCAC 59.773 63.158 27.72 4.38 0.00 4.02
594 643 4.500887 CGTTTCCTCCACTACTCAACTCAA 60.501 45.833 0.00 0.00 0.00 3.02
607 663 2.009051 CAACTCAATCTATGCACCGCA 58.991 47.619 0.00 0.00 44.86 5.69
647 703 6.964807 ATGGAATGGAATCGAATGATGAAA 57.035 33.333 0.00 0.00 34.24 2.69
649 705 5.067674 TGGAATGGAATCGAATGATGAAACC 59.932 40.000 0.00 0.00 34.24 3.27
650 706 4.818534 ATGGAATCGAATGATGAAACCG 57.181 40.909 0.00 0.00 34.24 4.44
732 788 2.416162 GGAAAGCAAACAAACACACGGA 60.416 45.455 0.00 0.00 0.00 4.69
740 796 1.451207 AAACACACGGACTGCTGCA 60.451 52.632 0.88 0.88 0.00 4.41
741 797 1.714899 AAACACACGGACTGCTGCAC 61.715 55.000 0.00 0.00 0.00 4.57
742 798 2.280389 CACACGGACTGCTGCACT 60.280 61.111 0.00 0.00 0.00 4.40
743 799 2.029666 ACACGGACTGCTGCACTC 59.970 61.111 0.00 0.00 0.00 3.51
744 800 2.740055 CACGGACTGCTGCACTCC 60.740 66.667 15.75 15.75 0.00 3.85
745 801 3.233980 ACGGACTGCTGCACTCCA 61.234 61.111 22.55 0.00 0.00 3.86
755 811 0.394899 CTGCACTCCATTCCCTTCCC 60.395 60.000 0.00 0.00 0.00 3.97
757 813 0.394899 GCACTCCATTCCCTTCCCTG 60.395 60.000 0.00 0.00 0.00 4.45
828 886 3.582120 CGCGGCGGCCATTATTGT 61.582 61.111 20.71 0.00 35.02 2.71
910 968 1.043116 TCCTCTCCGCGACCATCATT 61.043 55.000 8.23 0.00 0.00 2.57
1032 1090 0.795085 CAAGACGAGCAAGCAAGAGG 59.205 55.000 0.00 0.00 0.00 3.69
1171 1229 5.421693 TCTCTTCAATCTTCCTTCTCCTCTG 59.578 44.000 0.00 0.00 0.00 3.35
1172 1230 3.902881 TCAATCTTCCTTCTCCTCTGC 57.097 47.619 0.00 0.00 0.00 4.26
1173 1231 3.176411 TCAATCTTCCTTCTCCTCTGCA 58.824 45.455 0.00 0.00 0.00 4.41
1174 1232 3.197333 TCAATCTTCCTTCTCCTCTGCAG 59.803 47.826 7.63 7.63 0.00 4.41
1175 1233 0.901124 TCTTCCTTCTCCTCTGCAGC 59.099 55.000 9.47 0.00 0.00 5.25
1176 1234 0.903942 CTTCCTTCTCCTCTGCAGCT 59.096 55.000 9.47 0.00 0.00 4.24
1177 1235 2.106566 CTTCCTTCTCCTCTGCAGCTA 58.893 52.381 9.47 0.00 0.00 3.32
1178 1236 1.774110 TCCTTCTCCTCTGCAGCTAG 58.226 55.000 9.47 6.15 0.00 3.42
1179 1237 0.104671 CCTTCTCCTCTGCAGCTAGC 59.895 60.000 9.47 6.62 45.96 3.42
1180 1238 1.113788 CTTCTCCTCTGCAGCTAGCT 58.886 55.000 12.68 12.68 45.94 3.32
1181 1239 0.822811 TTCTCCTCTGCAGCTAGCTG 59.177 55.000 35.54 35.54 45.94 4.24
1189 1247 2.585524 CAGCTAGCTGCAGCCTCG 60.586 66.667 34.39 22.80 45.94 4.63
1190 1248 4.527583 AGCTAGCTGCAGCCTCGC 62.528 66.667 34.39 30.24 45.94 5.03
1191 1249 4.527583 GCTAGCTGCAGCCTCGCT 62.528 66.667 34.39 18.55 43.38 4.93
1192 1250 2.186384 CTAGCTGCAGCCTCGCTT 59.814 61.111 34.39 17.78 43.38 4.68
1193 1251 1.882167 CTAGCTGCAGCCTCGCTTC 60.882 63.158 34.39 5.26 43.38 3.86
1194 1252 2.295472 CTAGCTGCAGCCTCGCTTCT 62.295 60.000 34.39 16.24 43.38 2.85
1195 1253 1.892819 TAGCTGCAGCCTCGCTTCTT 61.893 55.000 34.39 15.49 43.38 2.52
1196 1254 2.748843 GCTGCAGCCTCGCTTCTTC 61.749 63.158 28.76 0.00 36.40 2.87
1197 1255 1.375140 CTGCAGCCTCGCTTCTTCA 60.375 57.895 0.00 0.00 36.40 3.02
1198 1256 1.360194 CTGCAGCCTCGCTTCTTCAG 61.360 60.000 0.00 0.00 36.40 3.02
1199 1257 1.079543 GCAGCCTCGCTTCTTCAGA 60.080 57.895 0.00 0.00 36.40 3.27
1200 1258 0.461693 GCAGCCTCGCTTCTTCAGAT 60.462 55.000 0.00 0.00 36.40 2.90
1201 1259 2.011046 GCAGCCTCGCTTCTTCAGATT 61.011 52.381 0.00 0.00 36.40 2.40
1202 1260 2.354259 CAGCCTCGCTTCTTCAGATTT 58.646 47.619 0.00 0.00 36.40 2.17
1203 1261 2.351111 CAGCCTCGCTTCTTCAGATTTC 59.649 50.000 0.00 0.00 36.40 2.17
1204 1262 2.235898 AGCCTCGCTTCTTCAGATTTCT 59.764 45.455 0.00 0.00 33.89 2.52
1205 1263 2.607180 GCCTCGCTTCTTCAGATTTCTC 59.393 50.000 0.00 0.00 0.00 2.87
1206 1264 3.678529 GCCTCGCTTCTTCAGATTTCTCT 60.679 47.826 0.00 0.00 0.00 3.10
1207 1265 4.502962 CCTCGCTTCTTCAGATTTCTCTT 58.497 43.478 0.00 0.00 0.00 2.85
1208 1266 4.566360 CCTCGCTTCTTCAGATTTCTCTTC 59.434 45.833 0.00 0.00 0.00 2.87
1209 1267 5.398603 TCGCTTCTTCAGATTTCTCTTCT 57.601 39.130 0.00 0.00 0.00 2.85
1210 1268 5.406649 TCGCTTCTTCAGATTTCTCTTCTC 58.593 41.667 0.00 0.00 0.00 2.87
1211 1269 4.566360 CGCTTCTTCAGATTTCTCTTCTCC 59.434 45.833 0.00 0.00 0.00 3.71
1341 1434 4.960938 CCAGGAGGTAATCGATCAATCAA 58.039 43.478 0.00 0.00 0.00 2.57
1391 1484 0.962356 CAAATCCCACGCCTCAGCTT 60.962 55.000 0.00 0.00 36.60 3.74
1392 1485 0.962356 AAATCCCACGCCTCAGCTTG 60.962 55.000 0.00 0.00 37.97 4.01
1505 1598 5.626955 CCGCACATTTTTCTTCTTCTTCTTC 59.373 40.000 0.00 0.00 0.00 2.87
1554 1670 0.996762 TTGGGGTGGGTGTTCCTCTT 60.997 55.000 0.00 0.00 36.20 2.85
1654 1770 4.748892 AGGTGACATGTAAGAACATCTCG 58.251 43.478 0.00 0.00 44.70 4.04
1672 1788 1.165907 CGTTGCACTTTGCCTCCTCA 61.166 55.000 0.00 0.00 44.23 3.86
1674 1790 0.183492 TTGCACTTTGCCTCCTCACT 59.817 50.000 0.00 0.00 44.23 3.41
1675 1791 0.535780 TGCACTTTGCCTCCTCACTG 60.536 55.000 0.00 0.00 44.23 3.66
1677 1793 1.270839 GCACTTTGCCTCCTCACTGTA 60.271 52.381 0.00 0.00 37.42 2.74
1678 1794 2.810400 GCACTTTGCCTCCTCACTGTAA 60.810 50.000 0.00 0.00 37.42 2.41
1679 1795 3.679389 CACTTTGCCTCCTCACTGTAAT 58.321 45.455 0.00 0.00 0.00 1.89
1680 1796 3.686726 CACTTTGCCTCCTCACTGTAATC 59.313 47.826 0.00 0.00 0.00 1.75
1681 1797 3.327757 ACTTTGCCTCCTCACTGTAATCA 59.672 43.478 0.00 0.00 0.00 2.57
1682 1798 4.202461 ACTTTGCCTCCTCACTGTAATCAA 60.202 41.667 0.00 0.00 0.00 2.57
1683 1799 3.616956 TGCCTCCTCACTGTAATCAAG 57.383 47.619 0.00 0.00 0.00 3.02
1686 1802 3.055819 GCCTCCTCACTGTAATCAAGTCA 60.056 47.826 0.00 0.00 0.00 3.41
1687 1803 4.499183 CCTCCTCACTGTAATCAAGTCAC 58.501 47.826 0.00 0.00 0.00 3.67
1835 1987 3.055530 ACTCCTACATGTTCAGGCTTCAG 60.056 47.826 2.30 1.69 0.00 3.02
1932 2084 1.301716 CTACCTGCACTGCAACCGT 60.302 57.895 4.99 4.46 38.41 4.83
2019 2171 6.140303 TCTAGTACAAGGTATTAGCGTTGG 57.860 41.667 0.00 0.00 38.22 3.77
2177 2330 8.893219 ATATCATGACGTGTGTATTCATTCTT 57.107 30.769 0.00 0.00 0.00 2.52
2239 2392 0.674534 GGATCTTGCCTCGTCGGTAT 59.325 55.000 0.00 0.00 34.25 2.73
2319 2472 5.702670 CAGTCATTCACAACCATCTGTTACT 59.297 40.000 0.00 0.00 34.69 2.24
2320 2473 6.205464 CAGTCATTCACAACCATCTGTTACTT 59.795 38.462 0.00 0.00 34.69 2.24
2321 2474 6.205464 AGTCATTCACAACCATCTGTTACTTG 59.795 38.462 0.00 0.00 34.69 3.16
2322 2475 6.017109 GTCATTCACAACCATCTGTTACTTGT 60.017 38.462 0.00 0.00 34.69 3.16
2323 2476 7.172532 GTCATTCACAACCATCTGTTACTTGTA 59.827 37.037 0.00 0.00 34.69 2.41
2324 2477 7.717436 TCATTCACAACCATCTGTTACTTGTAA 59.283 33.333 0.00 0.00 34.69 2.41
2325 2478 6.854496 TCACAACCATCTGTTACTTGTAAC 57.146 37.500 14.63 14.63 34.69 2.50
2353 2506 9.826574 TGTGTATAGTCCCAATTAAGTATTGAC 57.173 33.333 0.00 0.00 45.35 3.18
2354 2507 9.826574 GTGTATAGTCCCAATTAAGTATTGACA 57.173 33.333 0.00 0.00 45.35 3.58
2438 2713 1.614317 GCATGTGCCCAGGGATATACC 60.614 57.143 10.89 0.00 34.60 2.73
2441 2716 0.320697 GTGCCCAGGGATATACCGAC 59.679 60.000 10.89 0.00 40.11 4.79
2442 2717 0.834687 TGCCCAGGGATATACCGACC 60.835 60.000 10.89 0.00 40.11 4.79
2443 2718 0.834687 GCCCAGGGATATACCGACCA 60.835 60.000 10.89 0.00 40.11 4.02
2616 2893 1.270907 CTTGGTGAGCTCCCAGTACT 58.729 55.000 19.29 0.00 32.49 2.73
2620 2897 4.259933 TGGTGAGCTCCCAGTACTATTA 57.740 45.455 17.12 0.00 0.00 0.98
2621 2898 4.215908 TGGTGAGCTCCCAGTACTATTAG 58.784 47.826 17.12 0.00 0.00 1.73
2623 2900 4.650131 GGTGAGCTCCCAGTACTATTAGTT 59.350 45.833 12.15 0.00 0.00 2.24
2702 2979 9.573133 CTCAAAAAGCTTGTCTTTCTTCTTTTA 57.427 29.630 0.00 0.00 43.84 1.52
2723 3000 3.820557 ACTGTCAGGTTGCTGTATGTTT 58.179 40.909 4.53 0.00 0.00 2.83
2767 3044 5.304778 TGCATTCAAAGCTACAGTTAGTGA 58.695 37.500 0.00 0.00 0.00 3.41
2868 3147 0.598065 GTGTGAAGGACATGGCAACC 59.402 55.000 0.00 0.00 36.78 3.77
2976 3256 2.164422 TCTCAGTACTGCGGATCAACTG 59.836 50.000 18.45 7.58 39.10 3.16
3011 3291 6.409524 AATTGAGCATTCTTTCACAGGAAA 57.590 33.333 0.00 0.00 40.60 3.13
3333 3613 3.209429 CGAAGCATTACAAGCAGCG 57.791 52.632 0.00 0.00 0.00 5.18
3403 3683 4.422057 TCTATCAACTGTTGGTACCCAGA 58.578 43.478 21.06 9.85 33.81 3.86
3580 3860 1.304547 AGTCCAGTAGAGGCTGCGT 60.305 57.895 0.00 0.00 35.28 5.24
3585 3865 2.102553 GTAGAGGCTGCGTCGGTC 59.897 66.667 15.71 7.49 0.00 4.79
3673 3953 1.302832 GAGCACAGGAAGGGTGTGG 60.303 63.158 5.45 0.00 44.64 4.17
3726 4006 3.696051 GCATGGGTGATGTAGATGTTGTT 59.304 43.478 0.00 0.00 34.14 2.83
3729 4009 5.491323 TGGGTGATGTAGATGTTGTTACA 57.509 39.130 0.00 0.00 38.95 2.41
3909 4189 1.137513 CAGGTGTTCTTCGACCGTTC 58.862 55.000 0.00 0.00 37.32 3.95
3995 4275 2.042433 CAAAGTTTGGAGGGTCCCCATA 59.958 50.000 3.51 0.00 35.03 2.74
3999 4279 2.848071 GTTTGGAGGGTCCCCATAACTA 59.152 50.000 3.51 0.00 35.03 2.24
4010 4290 5.246429 GGTCCCCATAACTAATCTAGTGGAG 59.754 48.000 0.00 0.00 39.39 3.86
4038 4318 4.406648 TGAGAATCTTGTGTGTGAGTGT 57.593 40.909 0.00 0.00 34.92 3.55
4048 4328 2.112190 TGTGTGAGTGTGTGTTCCCTA 58.888 47.619 0.00 0.00 0.00 3.53
4052 4332 4.578928 GTGTGAGTGTGTGTTCCCTATTTT 59.421 41.667 0.00 0.00 0.00 1.82
4086 4366 6.803154 ATAGCTTCACTAAAGTTTGTGACC 57.197 37.500 15.80 11.74 41.33 4.02
4339 4629 4.779993 TTGGTTTTTGCCAAATAGGGTT 57.220 36.364 0.00 0.00 44.67 4.11
4377 4667 3.736530 GCAACATTCTGCTGACAGTAG 57.263 47.619 13.89 13.89 44.77 2.57
4463 4753 9.565090 TCATAGGAGTTCATGATTAGAAATTGG 57.435 33.333 0.00 0.00 0.00 3.16
4464 4754 9.347240 CATAGGAGTTCATGATTAGAAATTGGT 57.653 33.333 0.00 0.00 0.00 3.67
4466 4756 8.970859 AGGAGTTCATGATTAGAAATTGGTAG 57.029 34.615 0.00 0.00 0.00 3.18
4467 4757 8.552296 AGGAGTTCATGATTAGAAATTGGTAGT 58.448 33.333 0.00 0.00 0.00 2.73
4473 4808 8.271458 TCATGATTAGAAATTGGTAGTAGGCAA 58.729 33.333 0.00 0.00 0.00 4.52
4555 4891 6.322201 GTCACATTGAAATTCTGTATGGGGAT 59.678 38.462 0.00 0.00 0.00 3.85
4621 4981 2.845784 TGGAACAGGCATGCCAGT 59.154 55.556 37.18 32.41 37.43 4.00
4669 5029 0.729116 CGTCGCAATTCATTGGCTCT 59.271 50.000 1.77 0.00 38.21 4.09
4673 5033 2.615447 TCGCAATTCATTGGCTCTCATC 59.385 45.455 1.77 0.00 38.21 2.92
4695 5087 2.386660 GCTGAGCCGAAGTGCAGAC 61.387 63.158 0.00 0.00 0.00 3.51
4708 5100 2.158696 AGTGCAGACTTTTCTCTTGGCT 60.159 45.455 0.00 0.00 0.00 4.75
4711 5103 1.462670 CAGACTTTTCTCTTGGCTCGC 59.537 52.381 0.00 0.00 0.00 5.03
4713 5105 0.398318 ACTTTTCTCTTGGCTCGCCT 59.602 50.000 9.65 0.00 36.94 5.52
4715 5107 1.466558 CTTTTCTCTTGGCTCGCCTTC 59.533 52.381 9.65 0.00 36.94 3.46
4716 5108 0.396435 TTTCTCTTGGCTCGCCTTCA 59.604 50.000 9.65 0.00 36.94 3.02
4717 5109 0.320771 TTCTCTTGGCTCGCCTTCAC 60.321 55.000 9.65 0.00 36.94 3.18
4718 5110 1.004560 CTCTTGGCTCGCCTTCACA 60.005 57.895 9.65 0.00 36.94 3.58
4720 5112 0.884704 TCTTGGCTCGCCTTCACAAC 60.885 55.000 9.65 0.00 36.94 3.32
4721 5113 1.153066 TTGGCTCGCCTTCACAACA 60.153 52.632 9.65 0.00 36.94 3.33
4722 5114 1.165907 TTGGCTCGCCTTCACAACAG 61.166 55.000 9.65 0.00 36.94 3.16
4723 5115 1.301716 GGCTCGCCTTCACAACAGA 60.302 57.895 0.00 0.00 0.00 3.41
4724 5116 0.674895 GGCTCGCCTTCACAACAGAT 60.675 55.000 0.00 0.00 0.00 2.90
4744 5166 1.543065 CCTGTCTGTCAGCTCTGCCT 61.543 60.000 0.00 0.00 42.38 4.75
4772 5194 3.605895 GAGACCGTCTCCCACCTC 58.394 66.667 16.58 0.00 37.55 3.85
4773 5195 1.000646 GAGACCGTCTCCCACCTCT 60.001 63.158 16.58 0.00 37.55 3.69
4774 5196 1.304547 AGACCGTCTCCCACCTCTG 60.305 63.158 0.00 0.00 0.00 3.35
4780 5202 0.251832 GTCTCCCACCTCTGTCTGGA 60.252 60.000 0.00 0.00 0.00 3.86
4787 5209 1.915266 CCTCTGTCTGGACTGCCCA 60.915 63.158 2.38 0.00 44.25 5.36
4880 5302 1.143969 GGGCGTACGGACATTTCTCG 61.144 60.000 18.39 0.00 0.00 4.04
4909 5331 1.971505 GCATCCACCTCACCATCGGA 61.972 60.000 0.00 0.00 0.00 4.55
4935 5357 0.846427 ATGGTGGGAGGGATGTGTGT 60.846 55.000 0.00 0.00 0.00 3.72
4949 5371 1.612950 TGTGTGTGGCATTTGGATGAC 59.387 47.619 0.00 0.00 41.98 3.06
4987 5409 4.503296 CCTCAGCGGCTACCTAATTTACAT 60.503 45.833 0.26 0.00 0.00 2.29
4989 5411 5.433526 TCAGCGGCTACCTAATTTACATTT 58.566 37.500 0.26 0.00 0.00 2.32
5002 5424 7.278424 CCTAATTTACATTTTGTGGAATGCCTG 59.722 37.037 0.00 0.00 39.97 4.85
5017 5439 3.068881 CTGGAAGGAGCGGAACCA 58.931 61.111 0.00 0.00 0.00 3.67
5018 5440 1.376037 CTGGAAGGAGCGGAACCAC 60.376 63.158 0.00 0.00 0.00 4.16
5019 5441 2.046217 GGAAGGAGCGGAACCACC 60.046 66.667 0.00 0.00 0.00 4.61
5052 5474 1.122501 GCACGCGTATGATGTACATCG 59.877 52.381 26.56 18.12 40.63 3.84
5066 5488 0.749649 ACATCGAGGTGGCTCATCTC 59.250 55.000 0.00 5.62 38.17 2.75
5076 5498 2.027745 GTGGCTCATCTCACCTTCAAGA 60.028 50.000 0.00 0.00 0.00 3.02
5081 5503 4.699257 GCTCATCTCACCTTCAAGAACATT 59.301 41.667 0.00 0.00 0.00 2.71
5084 5506 6.409704 TCATCTCACCTTCAAGAACATTAGG 58.590 40.000 0.00 0.00 0.00 2.69
5099 5521 3.117169 ACATTAGGCATAGGGAATTGGCA 60.117 43.478 0.00 0.00 40.61 4.92
5100 5522 2.957402 TAGGCATAGGGAATTGGCAG 57.043 50.000 0.00 0.00 40.61 4.85
5101 5523 0.186873 AGGCATAGGGAATTGGCAGG 59.813 55.000 0.00 0.00 40.61 4.85
5102 5524 1.466851 GGCATAGGGAATTGGCAGGC 61.467 60.000 0.00 0.00 38.23 4.85
5103 5525 0.756442 GCATAGGGAATTGGCAGGCA 60.756 55.000 0.00 0.00 0.00 4.75
5105 5527 0.186873 ATAGGGAATTGGCAGGCAGG 59.813 55.000 0.00 0.00 0.00 4.85
5106 5528 1.936767 TAGGGAATTGGCAGGCAGGG 61.937 60.000 0.00 0.00 0.00 4.45
5107 5529 2.360191 GGAATTGGCAGGCAGGGA 59.640 61.111 0.00 0.00 0.00 4.20
5108 5530 1.755783 GGAATTGGCAGGCAGGGAG 60.756 63.158 0.00 0.00 0.00 4.30
5109 5531 2.363406 AATTGGCAGGCAGGGAGC 60.363 61.111 0.00 0.00 44.65 4.70
5138 6576 0.178998 CCATCATTCTCCAGGCAGGG 60.179 60.000 0.00 0.00 38.24 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.300681 TGGTCATTTAATTCATAGGATTGGATC 57.699 33.333 0.00 0.00 0.00 3.36
46 47 9.659135 TTGGTCATTTAATTCATAGGATTGGAT 57.341 29.630 0.00 0.00 0.00 3.41
47 48 8.912988 GTTGGTCATTTAATTCATAGGATTGGA 58.087 33.333 0.00 0.00 0.00 3.53
48 49 8.694540 TGTTGGTCATTTAATTCATAGGATTGG 58.305 33.333 0.00 0.00 0.00 3.16
79 80 3.498397 CAGTACATGTCACGGCTCTTTTT 59.502 43.478 0.00 0.00 0.00 1.94
80 81 3.067106 CAGTACATGTCACGGCTCTTTT 58.933 45.455 0.00 0.00 0.00 2.27
81 82 2.688507 CAGTACATGTCACGGCTCTTT 58.311 47.619 0.00 0.00 0.00 2.52
82 83 1.673033 GCAGTACATGTCACGGCTCTT 60.673 52.381 0.00 0.00 34.74 2.85
83 84 0.108615 GCAGTACATGTCACGGCTCT 60.109 55.000 0.00 0.00 34.74 4.09
84 85 0.389817 TGCAGTACATGTCACGGCTC 60.390 55.000 21.24 3.56 37.87 4.70
85 86 0.390340 CTGCAGTACATGTCACGGCT 60.390 55.000 21.24 6.57 37.87 5.52
86 87 0.670546 ACTGCAGTACATGTCACGGC 60.671 55.000 20.16 11.93 37.57 5.68
87 88 1.070821 CACTGCAGTACATGTCACGG 58.929 55.000 21.20 0.00 0.00 4.94
88 89 1.070821 CCACTGCAGTACATGTCACG 58.929 55.000 21.20 3.35 0.00 4.35
89 90 0.798776 GCCACTGCAGTACATGTCAC 59.201 55.000 21.20 0.00 37.47 3.67
94 95 1.742880 CAGCGCCACTGCAGTACAT 60.743 57.895 21.20 3.59 40.19 2.29
111 112 1.925415 GCAGCGTGCATTGTGGATCA 61.925 55.000 0.00 0.00 44.26 2.92
126 127 3.443925 GCCTTTCCTTCGGGCAGC 61.444 66.667 0.00 0.00 44.69 5.25
133 138 1.615392 AGTTGCATGTGCCTTTCCTTC 59.385 47.619 2.07 0.00 41.18 3.46
170 175 1.663161 GCGAGCAGTTTTACCTTGTGC 60.663 52.381 0.00 0.00 0.00 4.57
215 224 5.350640 GCTGGTGTGTGTTTAATACTACTCC 59.649 44.000 0.00 2.27 33.12 3.85
217 226 4.927425 CGCTGGTGTGTGTTTAATACTACT 59.073 41.667 0.00 0.00 0.00 2.57
218 227 4.435121 GCGCTGGTGTGTGTTTAATACTAC 60.435 45.833 0.00 0.00 0.00 2.73
219 228 3.680937 GCGCTGGTGTGTGTTTAATACTA 59.319 43.478 0.00 0.00 0.00 1.82
242 251 4.385405 GCTCCACTCCACTGCGCT 62.385 66.667 9.73 0.00 0.00 5.92
292 304 2.835027 AGGTTTCTCCGTTTCACACTC 58.165 47.619 0.00 0.00 41.99 3.51
341 353 1.882352 CGACCCTTTCCTTTGGTCTGG 60.882 57.143 6.37 0.00 45.13 3.86
344 356 0.109913 ACCGACCCTTTCCTTTGGTC 59.890 55.000 0.00 0.00 44.12 4.02
351 363 0.250770 AAAGAGCACCGACCCTTTCC 60.251 55.000 0.00 0.00 0.00 3.13
352 364 1.535896 GAAAAGAGCACCGACCCTTTC 59.464 52.381 0.00 0.00 0.00 2.62
375 393 0.540365 CTCCTGCTTGCCTTTTCCCA 60.540 55.000 0.00 0.00 0.00 4.37
428 446 6.498538 AGAAATCTACCCAGAGAGAGAGAAA 58.501 40.000 0.00 0.00 33.22 2.52
429 447 6.086011 AGAAATCTACCCAGAGAGAGAGAA 57.914 41.667 0.00 0.00 33.22 2.87
430 448 5.725551 AGAAATCTACCCAGAGAGAGAGA 57.274 43.478 0.00 0.00 33.22 3.10
431 449 6.607198 AGAAAGAAATCTACCCAGAGAGAGAG 59.393 42.308 0.00 0.00 33.22 3.20
432 450 6.498538 AGAAAGAAATCTACCCAGAGAGAGA 58.501 40.000 0.00 0.00 33.22 3.10
433 451 6.790232 AGAAAGAAATCTACCCAGAGAGAG 57.210 41.667 0.00 0.00 33.22 3.20
442 462 8.091449 TCTCAAGTCTGAAGAAAGAAATCTACC 58.909 37.037 0.00 0.00 0.00 3.18
445 465 7.961351 TCTCTCAAGTCTGAAGAAAGAAATCT 58.039 34.615 0.00 0.00 0.00 2.40
502 548 8.478877 TGGATGGAGTAGTATTTTCTCTTCTTC 58.521 37.037 0.00 0.00 0.00 2.87
505 554 6.987404 GGTGGATGGAGTAGTATTTTCTCTTC 59.013 42.308 0.00 0.00 0.00 2.87
506 555 6.407074 CGGTGGATGGAGTAGTATTTTCTCTT 60.407 42.308 0.00 0.00 0.00 2.85
539 588 2.368329 GGTGGAGTGGGCCCCTAT 60.368 66.667 22.27 4.35 0.00 2.57
594 643 2.588877 GCGGTGCGGTGCATAGAT 60.589 61.111 0.00 0.00 41.91 1.98
627 683 5.007626 TCGGTTTCATCATTCGATTCCATTC 59.992 40.000 0.00 0.00 0.00 2.67
649 705 4.085721 GCTCAACTAATTAATCCGTCGTCG 60.086 45.833 0.00 0.00 0.00 5.12
650 706 5.041940 AGCTCAACTAATTAATCCGTCGTC 58.958 41.667 0.00 0.00 0.00 4.20
718 774 1.132262 CAGCAGTCCGTGTGTTTGTTT 59.868 47.619 0.00 0.00 0.00 2.83
732 788 1.001641 GGGAATGGAGTGCAGCAGT 60.002 57.895 1.04 1.04 0.00 4.40
740 796 2.715295 CCAGGGAAGGGAATGGAGT 58.285 57.895 0.00 0.00 34.60 3.85
755 811 1.324005 GGAGGAAGACGGAGACCCAG 61.324 65.000 0.00 0.00 0.00 4.45
757 813 1.000612 AGGAGGAAGACGGAGACCC 59.999 63.158 0.00 0.00 0.00 4.46
815 873 1.226945 GTGGCACAATAATGGCCGC 60.227 57.895 13.86 7.72 44.16 6.53
828 886 4.539083 ACGCGTGTGGAAGTGGCA 62.539 61.111 12.93 0.00 0.00 4.92
880 938 1.528309 GGAGAGGAGAGGAGAGCGG 60.528 68.421 0.00 0.00 0.00 5.52
1007 1065 3.300667 CTTGCTCGTCTTGTGGCGC 62.301 63.158 0.00 0.00 0.00 6.53
1032 1090 2.224161 CCATCGGATTCCTCACCTCTTC 60.224 54.545 0.30 0.00 0.00 2.87
1172 1230 2.585524 CGAGGCTGCAGCTAGCTG 60.586 66.667 35.54 35.54 45.94 4.24
1173 1231 4.527583 GCGAGGCTGCAGCTAGCT 62.528 66.667 35.82 25.26 45.94 3.32
1174 1232 4.527583 AGCGAGGCTGCAGCTAGC 62.528 66.667 35.82 33.03 45.96 3.42
1175 1233 1.882167 GAAGCGAGGCTGCAGCTAG 60.882 63.158 35.82 26.43 39.62 3.42
1176 1234 1.892819 AAGAAGCGAGGCTGCAGCTA 61.893 55.000 35.82 0.00 39.62 3.32
1177 1235 3.251231 AAGAAGCGAGGCTGCAGCT 62.251 57.895 35.82 22.72 39.62 4.24
1178 1236 2.745492 AAGAAGCGAGGCTGCAGC 60.745 61.111 30.88 30.88 39.62 5.25
1179 1237 1.360194 CTGAAGAAGCGAGGCTGCAG 61.360 60.000 10.11 10.11 39.62 4.41
1180 1238 1.375140 CTGAAGAAGCGAGGCTGCA 60.375 57.895 0.50 0.00 39.62 4.41
1181 1239 0.461693 ATCTGAAGAAGCGAGGCTGC 60.462 55.000 0.00 0.00 39.62 5.25
1182 1240 2.021355 AATCTGAAGAAGCGAGGCTG 57.979 50.000 0.00 0.00 39.62 4.85
1183 1241 2.235898 AGAAATCTGAAGAAGCGAGGCT 59.764 45.455 0.00 0.00 42.56 4.58
1184 1242 2.607180 GAGAAATCTGAAGAAGCGAGGC 59.393 50.000 0.00 0.00 0.00 4.70
1185 1243 4.122143 AGAGAAATCTGAAGAAGCGAGG 57.878 45.455 0.00 0.00 0.00 4.63
1186 1244 5.410067 AGAAGAGAAATCTGAAGAAGCGAG 58.590 41.667 0.00 0.00 0.00 5.03
1187 1245 5.398603 AGAAGAGAAATCTGAAGAAGCGA 57.601 39.130 0.00 0.00 0.00 4.93
1188 1246 4.566360 GGAGAAGAGAAATCTGAAGAAGCG 59.434 45.833 0.00 0.00 0.00 4.68
1189 1247 4.566360 CGGAGAAGAGAAATCTGAAGAAGC 59.434 45.833 0.00 0.00 0.00 3.86
1190 1248 4.566360 GCGGAGAAGAGAAATCTGAAGAAG 59.434 45.833 0.00 0.00 0.00 2.85
1191 1249 4.499183 GCGGAGAAGAGAAATCTGAAGAA 58.501 43.478 0.00 0.00 0.00 2.52
1192 1250 3.118956 GGCGGAGAAGAGAAATCTGAAGA 60.119 47.826 0.00 0.00 0.00 2.87
1193 1251 3.194062 GGCGGAGAAGAGAAATCTGAAG 58.806 50.000 0.00 0.00 0.00 3.02
1194 1252 2.417379 CGGCGGAGAAGAGAAATCTGAA 60.417 50.000 0.00 0.00 0.00 3.02
1195 1253 1.135139 CGGCGGAGAAGAGAAATCTGA 59.865 52.381 0.00 0.00 0.00 3.27
1196 1254 1.134965 ACGGCGGAGAAGAGAAATCTG 60.135 52.381 13.24 0.00 0.00 2.90
1197 1255 1.187087 ACGGCGGAGAAGAGAAATCT 58.813 50.000 13.24 0.00 0.00 2.40
1198 1256 1.927838 GAACGGCGGAGAAGAGAAATC 59.072 52.381 13.24 0.00 0.00 2.17
1199 1257 1.405661 GGAACGGCGGAGAAGAGAAAT 60.406 52.381 13.24 0.00 0.00 2.17
1200 1258 0.037605 GGAACGGCGGAGAAGAGAAA 60.038 55.000 13.24 0.00 0.00 2.52
1201 1259 0.898789 AGGAACGGCGGAGAAGAGAA 60.899 55.000 13.24 0.00 0.00 2.87
1202 1260 0.898789 AAGGAACGGCGGAGAAGAGA 60.899 55.000 13.24 0.00 0.00 3.10
1203 1261 0.458716 GAAGGAACGGCGGAGAAGAG 60.459 60.000 13.24 0.00 0.00 2.85
1204 1262 1.590147 GAAGGAACGGCGGAGAAGA 59.410 57.895 13.24 0.00 0.00 2.87
1205 1263 1.448013 GGAAGGAACGGCGGAGAAG 60.448 63.158 13.24 0.00 0.00 2.85
1206 1264 2.660802 GGAAGGAACGGCGGAGAA 59.339 61.111 13.24 0.00 0.00 2.87
1207 1265 3.387947 GGGAAGGAACGGCGGAGA 61.388 66.667 13.24 0.00 0.00 3.71
1208 1266 4.468689 GGGGAAGGAACGGCGGAG 62.469 72.222 13.24 0.00 0.00 4.63
1210 1268 4.029809 AAGGGGAAGGAACGGCGG 62.030 66.667 13.24 0.00 0.00 6.13
1211 1269 2.741486 TTCAAGGGGAAGGAACGGCG 62.741 60.000 4.80 4.80 0.00 6.46
1332 1425 6.976925 GGTTTGAGGTGATTGATTGATTGATC 59.023 38.462 0.00 0.00 0.00 2.92
1333 1426 6.666546 AGGTTTGAGGTGATTGATTGATTGAT 59.333 34.615 0.00 0.00 0.00 2.57
1341 1434 8.749354 GGTTTATTAAGGTTTGAGGTGATTGAT 58.251 33.333 0.00 0.00 0.00 2.57
1391 1484 3.680786 CAGACGGACGGACTGCCA 61.681 66.667 7.83 0.00 0.00 4.92
1554 1670 0.249868 CAGTTCAGTCTTGGCCGACA 60.250 55.000 12.61 0.00 36.38 4.35
1605 1721 2.223144 GCAGTAACTTGTGACGATGCAA 59.777 45.455 0.00 0.00 32.79 4.08
1835 1987 6.313744 AGCACCAAACATACAGTAAGTTTC 57.686 37.500 10.36 1.57 33.54 2.78
1932 2084 2.842462 AGGTCACGGTGGAGCACA 60.842 61.111 8.50 0.00 37.74 4.57
1983 2135 8.511604 ACCTTGTACTAGAAATGAAATGATGG 57.488 34.615 5.85 0.00 0.00 3.51
2019 2171 3.191371 CAGGTGGTGAGGAAAATGTTAGC 59.809 47.826 0.00 0.00 0.00 3.09
2111 2263 8.100791 TGAAGTTGTGTAGTAATTTGAGCCTAT 58.899 33.333 0.00 0.00 0.00 2.57
2168 2321 5.771666 TCAGCTGTTTGGAGAAAGAATGAAT 59.228 36.000 14.67 0.00 0.00 2.57
2177 2330 2.813754 CCGAAATCAGCTGTTTGGAGAA 59.186 45.455 14.67 0.00 0.00 2.87
2239 2392 2.944129 AGTTAGCAAAAGGTTGAGGCA 58.056 42.857 0.00 0.00 36.83 4.75
2267 2420 5.995446 TGTCCTGCCAATAACATGTACATA 58.005 37.500 8.32 0.00 0.00 2.29
2278 2431 3.008923 TGACTGAACATGTCCTGCCAATA 59.991 43.478 0.00 0.00 33.83 1.90
2320 2473 9.661563 CTTAATTGGGACTATACACAAGTTACA 57.338 33.333 0.00 0.00 36.60 2.41
2321 2474 9.662947 ACTTAATTGGGACTATACACAAGTTAC 57.337 33.333 0.00 0.00 36.60 2.50
2350 2503 5.110598 TGCTTTCACGTTTAACTACTGTCA 58.889 37.500 0.00 0.00 0.00 3.58
2353 2506 7.483691 AGTTTTTGCTTTCACGTTTAACTACTG 59.516 33.333 0.00 0.00 0.00 2.74
2354 2507 7.483691 CAGTTTTTGCTTTCACGTTTAACTACT 59.516 33.333 0.00 0.00 0.00 2.57
2424 2692 0.834687 TGGTCGGTATATCCCTGGGC 60.835 60.000 8.22 0.00 0.00 5.36
2467 2744 1.704628 TGAGAAGTGGAATCTGGCCAA 59.295 47.619 7.01 0.00 37.12 4.52
2620 2897 9.535878 CAGAAGACTAGAGTTAACTTCAAAACT 57.464 33.333 10.02 3.60 39.22 2.66
2621 2898 9.315525 ACAGAAGACTAGAGTTAACTTCAAAAC 57.684 33.333 10.02 0.00 39.22 2.43
2623 2900 8.692710 TCACAGAAGACTAGAGTTAACTTCAAA 58.307 33.333 10.02 0.00 39.22 2.69
2702 2979 3.492102 AACATACAGCAACCTGACAGT 57.508 42.857 0.93 0.00 41.77 3.55
2787 3064 6.859112 AGAGAGAAACTGAAGCAGGTAATA 57.141 37.500 0.00 0.00 35.51 0.98
2868 3147 9.530129 GACGATCTGTTTATTTTGTTGACTAAG 57.470 33.333 0.00 0.00 0.00 2.18
2943 3222 6.199908 CCGCAGTACTGAGAGATCATTTAAAG 59.800 42.308 27.08 1.90 31.84 1.85
3011 3291 7.063593 TCCTCAGCATACTCTTAACTATCTGT 58.936 38.462 0.00 0.00 0.00 3.41
3279 3559 1.293498 GCCGACTCTCTTTCTGCCA 59.707 57.895 0.00 0.00 0.00 4.92
3333 3613 2.294233 TGTTTCTGATGTTTGCTCTGCC 59.706 45.455 0.00 0.00 0.00 4.85
3580 3860 0.176910 TGACTTGCACTGTTGACCGA 59.823 50.000 0.00 0.00 0.00 4.69
3585 3865 3.155093 AGCTTTTGACTTGCACTGTTG 57.845 42.857 0.00 0.00 0.00 3.33
3673 3953 3.572255 ACTCCTTGACAAGACTCTGTCTC 59.428 47.826 16.99 0.00 42.59 3.36
3726 4006 4.352893 TCACTGGTGATGATTCCTCTGTA 58.647 43.478 0.00 0.00 34.14 2.74
3729 4009 2.170187 GCTCACTGGTGATGATTCCTCT 59.830 50.000 3.80 0.00 39.13 3.69
3909 4189 2.811317 GACACAGCTCCTTCGCCG 60.811 66.667 0.00 0.00 0.00 6.46
3995 4275 9.261035 TCTCAAATTCTCTCCACTAGATTAGTT 57.739 33.333 0.00 0.00 36.76 2.24
3999 4279 8.991275 AGATTCTCAAATTCTCTCCACTAGATT 58.009 33.333 0.00 0.00 32.41 2.40
4010 4290 7.041508 ACTCACACACAAGATTCTCAAATTCTC 60.042 37.037 0.00 0.00 0.00 2.87
4038 4318 5.304686 ACACTCTCAAAATAGGGAACACA 57.695 39.130 0.00 0.00 0.00 3.72
4052 4332 9.409918 ACTTTAGTGAAGCTATATACACTCTCA 57.590 33.333 6.93 0.00 42.39 3.27
4080 4360 0.468226 AAACTCAAGCCTCGGTCACA 59.532 50.000 0.00 0.00 0.00 3.58
4081 4361 2.450609 TAAACTCAAGCCTCGGTCAC 57.549 50.000 0.00 0.00 0.00 3.67
4085 4365 6.538742 TCAAGATAAATAAACTCAAGCCTCGG 59.461 38.462 0.00 0.00 0.00 4.63
4086 4366 7.539712 TCAAGATAAATAAACTCAAGCCTCG 57.460 36.000 0.00 0.00 0.00 4.63
4275 4564 4.497300 GACATGTCCCCATTCACAAATTG 58.503 43.478 15.31 0.00 0.00 2.32
4377 4667 8.082334 GATAGAATCCAAGAGTAAACTGATGC 57.918 38.462 0.00 0.00 0.00 3.91
4457 4747 5.124036 TGCCTATTGCCTACTACCAATTT 57.876 39.130 0.00 0.00 40.16 1.82
4460 4750 4.788925 ATTGCCTATTGCCTACTACCAA 57.211 40.909 0.00 0.00 40.16 3.67
4462 4752 6.127451 ACAAAAATTGCCTATTGCCTACTACC 60.127 38.462 0.00 0.00 40.16 3.18
4463 4753 6.751888 CACAAAAATTGCCTATTGCCTACTAC 59.248 38.462 0.00 0.00 40.16 2.73
4464 4754 6.435904 ACACAAAAATTGCCTATTGCCTACTA 59.564 34.615 0.00 0.00 40.16 1.82
4466 4756 5.478407 ACACAAAAATTGCCTATTGCCTAC 58.522 37.500 0.00 0.00 40.16 3.18
4467 4757 5.337169 GGACACAAAAATTGCCTATTGCCTA 60.337 40.000 0.00 0.00 40.16 3.93
4473 4808 6.211184 TCAATGAGGACACAAAAATTGCCTAT 59.789 34.615 0.00 0.00 0.00 2.57
4555 4891 3.256383 CCATGGTTTCTGTGAAAGCATCA 59.744 43.478 25.20 8.34 43.83 3.07
4624 4984 3.057734 GGTGGAACTAGCCGAATATTCG 58.942 50.000 27.19 27.19 43.41 3.34
4630 4990 1.547372 GTGTAGGTGGAACTAGCCGAA 59.453 52.381 0.00 0.00 36.74 4.30
4669 5029 0.179065 CTTCGGCTCAGCATGGATGA 60.179 55.000 0.00 0.00 36.16 2.92
4673 5033 2.758089 GCACTTCGGCTCAGCATGG 61.758 63.158 0.00 0.00 36.16 3.66
4695 5087 1.466558 GAAGGCGAGCCAAGAGAAAAG 59.533 52.381 17.18 0.00 38.92 2.27
4708 5100 0.976641 AGGATCTGTTGTGAAGGCGA 59.023 50.000 0.00 0.00 0.00 5.54
4711 5103 3.692257 AGACAGGATCTGTTGTGAAGG 57.308 47.619 1.90 0.00 45.44 3.46
4721 5113 2.101783 CAGAGCTGACAGACAGGATCT 58.898 52.381 6.65 0.00 45.82 2.75
4722 5114 1.471327 GCAGAGCTGACAGACAGGATC 60.471 57.143 6.65 0.00 45.82 3.36
4723 5115 0.536260 GCAGAGCTGACAGACAGGAT 59.464 55.000 6.65 0.00 45.82 3.24
4724 5116 1.539560 GGCAGAGCTGACAGACAGGA 61.540 60.000 6.65 0.00 45.82 3.86
4762 5184 0.251832 GTCCAGACAGAGGTGGGAGA 60.252 60.000 0.00 0.00 34.27 3.71
4767 5189 1.294780 GGCAGTCCAGACAGAGGTG 59.705 63.158 0.00 0.00 0.00 4.00
4768 5190 1.915769 GGGCAGTCCAGACAGAGGT 60.916 63.158 0.00 0.00 35.00 3.85
4770 5192 3.797331 TGGGCAGTCCAGACAGAG 58.203 61.111 0.00 0.00 41.46 3.35
4780 5202 1.675641 GCCGAAGTGAATGGGCAGT 60.676 57.895 0.00 0.00 44.91 4.40
4838 5260 4.479993 AGCACCAGCAGGCGGATC 62.480 66.667 0.00 0.00 45.49 3.36
4839 5261 4.479993 GAGCACCAGCAGGCGGAT 62.480 66.667 0.00 0.00 45.49 4.18
4843 5265 3.715097 AGGAGAGCACCAGCAGGC 61.715 66.667 0.00 0.00 45.49 4.85
4844 5266 2.268280 CAGGAGAGCACCAGCAGG 59.732 66.667 0.00 0.00 45.49 4.85
4848 5270 4.463879 CGCCCAGGAGAGCACCAG 62.464 72.222 0.00 0.00 0.00 4.00
4859 5281 0.108329 AGAAATGTCCGTACGCCCAG 60.108 55.000 10.49 0.00 0.00 4.45
4866 5288 1.140161 CCGGCGAGAAATGTCCGTA 59.860 57.895 9.30 0.00 40.23 4.02
4909 5331 3.402681 CCTCCCACCATGCGTCCT 61.403 66.667 0.00 0.00 0.00 3.85
4914 5336 1.454479 CACATCCCTCCCACCATGC 60.454 63.158 0.00 0.00 0.00 4.06
4935 5357 0.037447 TGACCGTCATCCAAATGCCA 59.963 50.000 0.00 0.00 32.58 4.92
4949 5371 2.750350 AGGCACCTCCTTTGACCG 59.250 61.111 0.00 0.00 44.75 4.79
4982 5404 4.155709 TCCAGGCATTCCACAAAATGTAA 58.844 39.130 0.00 0.00 38.60 2.41
4987 5409 1.969923 CCTTCCAGGCATTCCACAAAA 59.030 47.619 0.00 0.00 33.74 2.44
4989 5411 0.776810 TCCTTCCAGGCATTCCACAA 59.223 50.000 0.00 0.00 34.61 3.33
5002 5424 2.046217 GGTGGTTCCGCTCCTTCC 60.046 66.667 2.41 0.00 0.00 3.46
5017 5439 1.300697 GTGCCGTTGAAGACTCGGT 60.301 57.895 0.00 0.00 45.11 4.69
5018 5440 2.372690 CGTGCCGTTGAAGACTCGG 61.373 63.158 0.00 0.00 45.94 4.63
5019 5441 3.000080 GCGTGCCGTTGAAGACTCG 62.000 63.158 0.00 0.00 0.00 4.18
5021 5443 3.036084 CGCGTGCCGTTGAAGACT 61.036 61.111 0.00 0.00 0.00 3.24
5041 5463 1.409064 GAGCCACCTCGATGTACATCA 59.591 52.381 30.15 18.31 37.69 3.07
5066 5488 5.297776 CCTATGCCTAATGTTCTTGAAGGTG 59.702 44.000 0.00 0.00 0.00 4.00
5073 5495 5.835280 CCAATTCCCTATGCCTAATGTTCTT 59.165 40.000 0.00 0.00 0.00 2.52
5076 5498 3.897505 GCCAATTCCCTATGCCTAATGTT 59.102 43.478 0.00 0.00 0.00 2.71
5081 5503 1.425066 CCTGCCAATTCCCTATGCCTA 59.575 52.381 0.00 0.00 0.00 3.93
5084 5506 0.756442 TGCCTGCCAATTCCCTATGC 60.756 55.000 0.00 0.00 0.00 3.14
5099 5521 1.000396 GTTGGATTGCTCCCTGCCT 60.000 57.895 0.00 0.00 41.29 4.75
5100 5522 2.054453 GGTTGGATTGCTCCCTGCC 61.054 63.158 0.00 0.00 41.29 4.85
5101 5523 2.054453 GGGTTGGATTGCTCCCTGC 61.054 63.158 0.00 0.00 41.29 4.85
5102 5524 1.380380 GGGGTTGGATTGCTCCCTG 60.380 63.158 8.32 0.00 41.29 4.45
5103 5525 1.224003 ATGGGGTTGGATTGCTCCCT 61.224 55.000 0.00 0.00 41.29 4.20
5105 5527 0.033208 TGATGGGGTTGGATTGCTCC 60.033 55.000 0.00 0.00 42.45 4.70
5106 5528 2.077687 ATGATGGGGTTGGATTGCTC 57.922 50.000 0.00 0.00 0.00 4.26
5107 5529 2.023695 AGAATGATGGGGTTGGATTGCT 60.024 45.455 0.00 0.00 0.00 3.91
5108 5530 2.363359 GAGAATGATGGGGTTGGATTGC 59.637 50.000 0.00 0.00 0.00 3.56
5109 5531 2.961062 GGAGAATGATGGGGTTGGATTG 59.039 50.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.