Multiple sequence alignment - TraesCS1A01G333400

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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 TraesCS1A01G333400 chr1A 100.000 2174 0 0 1 2174 521322088 521324261 0.000000e+00 4015
1 TraesCS1A01G333400 chr1D 88.316 873 69 13 1316 2173 426181245 426182099 0.000000e+00 1016
2 TraesCS1A01G333400 chr1D 89.043 721 51 11 1 706 426179895 426180602 0.000000e+00 869
3 TraesCS1A01G333400 chr1D 88.030 401 38 6 854 1250 426180819 426181213 1.180000e-127 466
4 TraesCS1A01G333400 chr1B 87.701 870 77 11 1316 2173 575867901 575868752 0.000000e+00 987
5 TraesCS1A01G333400 chr1B 82.391 937 91 33 1 887 575866557 575867469 0.000000e+00 749
6 TraesCS1A01G333400 chr1B 87.750 400 40 5 854 1250 575867476 575867869 1.970000e-125 459


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 TraesCS1A01G333400 chr1A 521322088 521324261 2173 False 4015.000000 4015 100.000000 1 2174 1 chr1A.!!$F1 2173
1 TraesCS1A01G333400 chr1D 426179895 426182099 2204 False 783.666667 1016 88.463000 1 2173 3 chr1D.!!$F1 2172
2 TraesCS1A01G333400 chr1B 575866557 575868752 2195 False 731.666667 987 85.947333 1 2173 3 chr1B.!!$F1 2172

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
909 1013 1.242076 CTCCTTGTGTCTGCCTTTGG 58.758 55.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1940 0.31836 TTTCACGCGTCTGACGACAT 60.318 50.0 32.07 14.1 46.05 3.06 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
31 33 1.778591 GTTGCACATTCGGTTCGTTTG 59.221 47.619 0.00 0.00 0.00 2.93
94 96 2.660206 AGGCAACCGCGTGACATA 59.340 55.556 4.92 0.00 39.92 2.29
95 97 1.740296 AGGCAACCGCGTGACATAC 60.740 57.895 4.92 0.00 39.92 2.39
110 112 6.405176 GCGTGACATACTAGTAAACCCTACTT 60.405 42.308 6.70 0.00 0.00 2.24
156 164 1.781555 CACTACGGCACAAGCTTCG 59.218 57.895 0.00 0.00 41.70 3.79
168 176 4.555511 GCACAAGCTTCGTCTTCTTCATTT 60.556 41.667 0.00 0.00 37.91 2.32
191 199 4.899239 CCCTGCGCTCGTGGGATC 62.899 72.222 18.70 0.00 43.47 3.36
192 200 3.842923 CCTGCGCTCGTGGGATCT 61.843 66.667 9.73 0.00 0.00 2.75
224 232 1.405121 GGCGTTCCACGGTAAATCTCT 60.405 52.381 0.00 0.00 42.82 3.10
289 297 4.161565 TGTTGTAGCCTTGTAGATCCGAAT 59.838 41.667 0.00 0.00 0.00 3.34
303 311 3.040655 TCCGAATCAGGGATCCTTGTA 57.959 47.619 22.17 10.51 0.00 2.41
313 321 2.835156 GGGATCCTTGTATAGAGAGCCC 59.165 54.545 12.58 0.00 40.32 5.19
407 419 3.822735 CCAGCTTTCTTTGTGGATTCTGA 59.177 43.478 0.00 0.00 31.04 3.27
429 441 4.432712 AGAAGTTTGATTGTTGTTGTGGC 58.567 39.130 0.00 0.00 0.00 5.01
453 465 2.105477 GCAATCTTCCTGGGAGCAGATA 59.895 50.000 0.00 0.00 0.00 1.98
454 466 3.244840 GCAATCTTCCTGGGAGCAGATAT 60.245 47.826 0.00 0.00 0.00 1.63
506 518 3.685550 GCAGTACAGCTAATGGGTCCATT 60.686 47.826 17.97 17.97 46.85 3.16
530 543 6.852420 AGGAGTAGACACAACTGCTTATTA 57.148 37.500 0.00 0.00 42.24 0.98
537 550 7.145932 AGACACAACTGCTTATTAACCATTC 57.854 36.000 0.00 0.00 0.00 2.67
538 551 5.938322 ACACAACTGCTTATTAACCATTCG 58.062 37.500 0.00 0.00 0.00 3.34
570 583 7.415229 TCAAGGCGTAGTATATCATATAAGCG 58.585 38.462 0.00 0.00 0.00 4.68
573 586 8.442632 AGGCGTAGTATATCATATAAGCGTTA 57.557 34.615 0.00 0.00 0.00 3.18
575 588 9.674824 GGCGTAGTATATCATATAAGCGTTAAT 57.325 33.333 0.00 0.00 0.00 1.40
592 605 5.560148 CGTTAATTGCATCAGTACTGGTTC 58.440 41.667 22.48 11.06 0.00 3.62
599 612 5.255687 TGCATCAGTACTGGTTCATTCAAT 58.744 37.500 22.48 2.68 0.00 2.57
604 617 6.640518 TCAGTACTGGTTCATTCAATCTACC 58.359 40.000 22.48 0.00 0.00 3.18
610 623 7.504403 ACTGGTTCATTCAATCTACCTATGAG 58.496 38.462 0.00 0.00 0.00 2.90
612 625 6.126796 TGGTTCATTCAATCTACCTATGAGCA 60.127 38.462 0.00 0.00 30.86 4.26
630 643 5.559770 TGAGCACTGAATGACCAATCTAAA 58.440 37.500 0.00 0.00 0.00 1.85
634 655 8.162878 AGCACTGAATGACCAATCTAAATATG 57.837 34.615 0.00 0.00 0.00 1.78
656 680 5.898174 TGTGTATGTAAGGATCAAGGTACG 58.102 41.667 0.00 0.00 0.00 3.67
669 693 9.970553 AGGATCAAGGTACGATATAATGTACTA 57.029 33.333 14.11 3.36 40.56 1.82
676 700 9.175312 AGGTACGATATAATGTACTACTGGATG 57.825 37.037 14.11 0.00 40.56 3.51
678 702 8.954350 GTACGATATAATGTACTACTGGATGGT 58.046 37.037 9.47 0.00 38.30 3.55
684 708 4.730949 TGTACTACTGGATGGTAGTTGC 57.269 45.455 11.64 7.14 46.88 4.17
698 722 1.832883 AGTTGCGTTATCATGCCCAA 58.167 45.000 0.00 0.00 33.44 4.12
701 725 1.539157 TGCGTTATCATGCCCAAACA 58.461 45.000 0.00 0.00 33.44 2.83
714 770 4.865905 TGCCCAAACAAGGTGATATGTAT 58.134 39.130 0.00 0.00 0.00 2.29
715 771 4.644234 TGCCCAAACAAGGTGATATGTATG 59.356 41.667 0.00 0.00 0.00 2.39
720 776 7.939039 CCCAAACAAGGTGATATGTATGTAGAT 59.061 37.037 0.00 0.00 0.00 1.98
740 796 8.692710 TGTAGATATGTCCAAAACTGTAGTAGG 58.307 37.037 0.00 0.00 0.00 3.18
755 811 6.950041 ACTGTAGTAGGTGTATCAGGTAACAA 59.050 38.462 0.00 0.00 41.41 2.83
764 820 6.202954 GGTGTATCAGGTAACAAGTGATATGC 59.797 42.308 0.00 0.00 34.81 3.14
765 821 6.761242 GTGTATCAGGTAACAAGTGATATGCA 59.239 38.462 0.00 0.00 34.81 3.96
766 822 7.279981 GTGTATCAGGTAACAAGTGATATGCAA 59.720 37.037 0.00 0.00 34.81 4.08
767 823 6.683974 ATCAGGTAACAAGTGATATGCAAC 57.316 37.500 0.00 0.00 41.41 4.17
768 824 5.804639 TCAGGTAACAAGTGATATGCAACT 58.195 37.500 0.00 0.00 41.41 3.16
769 825 6.237901 TCAGGTAACAAGTGATATGCAACTT 58.762 36.000 0.00 0.00 41.41 2.66
770 826 6.149308 TCAGGTAACAAGTGATATGCAACTTG 59.851 38.462 21.79 21.79 39.44 3.16
771 827 5.415701 AGGTAACAAGTGATATGCAACTTGG 59.584 40.000 25.23 12.58 38.65 3.61
841 899 3.632333 TCTATTCACCCGATGTGTCTCT 58.368 45.455 5.19 0.00 45.61 3.10
842 900 4.023980 TCTATTCACCCGATGTGTCTCTT 58.976 43.478 5.19 0.00 45.61 2.85
843 901 3.703001 ATTCACCCGATGTGTCTCTTT 57.297 42.857 5.19 0.00 45.61 2.52
844 902 2.743636 TCACCCGATGTGTCTCTTTC 57.256 50.000 5.19 0.00 45.61 2.62
846 904 2.632996 TCACCCGATGTGTCTCTTTCTT 59.367 45.455 5.19 0.00 45.61 2.52
847 905 3.830178 TCACCCGATGTGTCTCTTTCTTA 59.170 43.478 5.19 0.00 45.61 2.10
848 906 4.282449 TCACCCGATGTGTCTCTTTCTTAA 59.718 41.667 5.19 0.00 45.61 1.85
849 907 4.389077 CACCCGATGTGTCTCTTTCTTAAC 59.611 45.833 0.00 0.00 40.26 2.01
850 908 4.283722 ACCCGATGTGTCTCTTTCTTAACT 59.716 41.667 0.00 0.00 0.00 2.24
851 909 4.865365 CCCGATGTGTCTCTTTCTTAACTC 59.135 45.833 0.00 0.00 0.00 3.01
852 910 5.336849 CCCGATGTGTCTCTTTCTTAACTCT 60.337 44.000 0.00 0.00 0.00 3.24
873 977 7.041107 ACTCTTGTATGAGATTTCTCTTGCTC 58.959 38.462 8.91 0.00 43.25 4.26
876 980 6.535963 TGTATGAGATTTCTCTTGCTCTGA 57.464 37.500 8.91 0.00 43.25 3.27
880 984 9.709495 GTATGAGATTTCTCTTGCTCTGATATT 57.291 33.333 8.91 0.00 43.25 1.28
884 988 8.253867 AGATTTCTCTTGCTCTGATATTCTCT 57.746 34.615 0.00 0.00 0.00 3.10
909 1013 1.242076 CTCCTTGTGTCTGCCTTTGG 58.758 55.000 0.00 0.00 0.00 3.28
932 1036 4.752224 CGTCGCAGAAGCTTGAATATTAC 58.248 43.478 2.10 0.00 39.69 1.89
933 1037 4.318121 CGTCGCAGAAGCTTGAATATTACC 60.318 45.833 2.10 0.00 39.69 2.85
939 1043 6.238320 GCAGAAGCTTGAATATTACCACTCTG 60.238 42.308 2.10 0.24 37.91 3.35
945 1049 7.281774 AGCTTGAATATTACCACTCTGATGTTG 59.718 37.037 0.00 0.00 0.00 3.33
952 1056 3.620488 ACCACTCTGATGTTGTGTTTGT 58.380 40.909 0.00 0.00 0.00 2.83
954 1058 3.627123 CCACTCTGATGTTGTGTTTGTCA 59.373 43.478 0.00 0.00 0.00 3.58
958 1062 1.680735 TGATGTTGTGTTTGTCAGCCC 59.319 47.619 0.00 0.00 0.00 5.19
974 1078 2.232208 CAGCCCCATTTTCAGTTTCCTC 59.768 50.000 0.00 0.00 0.00 3.71
978 1082 3.160269 CCCATTTTCAGTTTCCTCTGCT 58.840 45.455 0.00 0.00 35.63 4.24
981 1085 4.543692 CATTTTCAGTTTCCTCTGCTGTG 58.456 43.478 0.00 0.00 35.63 3.66
982 1086 1.597742 TTCAGTTTCCTCTGCTGTGC 58.402 50.000 0.00 0.00 35.63 4.57
1041 1146 6.254589 GTGCATCTATATTTATCAGGCTCGTC 59.745 42.308 0.00 0.00 0.00 4.20
1059 1164 2.922503 TCAGCAGCCGGAACTGGA 60.923 61.111 5.05 0.00 38.16 3.86
1128 1233 4.655762 TGAGTTCAGGAAGTATGATCCG 57.344 45.455 0.00 0.00 42.03 4.18
1177 1282 2.376808 AGCCAAGATGAAGTGAGACG 57.623 50.000 0.00 0.00 0.00 4.18
1178 1283 0.723981 GCCAAGATGAAGTGAGACGC 59.276 55.000 0.00 0.00 0.00 5.19
1183 1288 1.001293 AGATGAAGTGAGACGCTGCAA 59.999 47.619 0.00 0.00 32.85 4.08
1189 1294 0.235926 GTGAGACGCTGCAACCTTTC 59.764 55.000 0.00 0.00 0.00 2.62
1196 1304 3.211045 ACGCTGCAACCTTTCTTTCTTA 58.789 40.909 0.00 0.00 0.00 2.10
1197 1305 3.003378 ACGCTGCAACCTTTCTTTCTTAC 59.997 43.478 0.00 0.00 0.00 2.34
1212 1320 7.657023 TCTTTCTTACCATAAGACCTCTACC 57.343 40.000 0.00 0.00 0.00 3.18
1222 1330 6.037172 CCATAAGACCTCTACCGTTCATTTTG 59.963 42.308 0.00 0.00 0.00 2.44
1225 1333 3.671716 ACCTCTACCGTTCATTTTGGTC 58.328 45.455 0.00 0.00 37.20 4.02
1250 1358 6.201044 CGAAGACGATGATGCTACCTTTATTT 59.799 38.462 0.00 0.00 42.66 1.40
1251 1359 7.254455 CGAAGACGATGATGCTACCTTTATTTT 60.254 37.037 0.00 0.00 42.66 1.82
1255 1363 6.073765 ACGATGATGCTACCTTTATTTTAGCG 60.074 38.462 0.00 0.00 41.02 4.26
1256 1364 6.560253 ATGATGCTACCTTTATTTTAGCGG 57.440 37.500 0.00 0.00 41.02 5.52
1258 1366 2.946990 TGCTACCTTTATTTTAGCGGGC 59.053 45.455 0.00 0.00 41.02 6.13
1261 1369 3.646736 ACCTTTATTTTAGCGGGCTCT 57.353 42.857 0.00 0.00 0.00 4.09
1266 1374 6.269307 ACCTTTATTTTAGCGGGCTCTAGATA 59.731 38.462 0.00 0.00 0.00 1.98
1267 1375 7.159372 CCTTTATTTTAGCGGGCTCTAGATAA 58.841 38.462 0.00 0.00 0.00 1.75
1268 1376 7.824779 CCTTTATTTTAGCGGGCTCTAGATAAT 59.175 37.037 0.00 0.00 0.00 1.28
1269 1377 9.220767 CTTTATTTTAGCGGGCTCTAGATAATT 57.779 33.333 0.00 0.00 0.00 1.40
1270 1378 9.569122 TTTATTTTAGCGGGCTCTAGATAATTT 57.431 29.630 0.00 0.00 0.00 1.82
1281 1389 9.998106 GGGCTCTAGATAATTTAGTTTCATGTA 57.002 33.333 0.00 0.00 0.00 2.29
1297 1405 8.660968 GTTTCATGTAAACAACTCTAATGAGC 57.339 34.615 12.84 0.00 45.72 4.26
1298 1406 7.977789 TTCATGTAAACAACTCTAATGAGCA 57.022 32.000 0.00 0.00 43.85 4.26
1299 1407 7.364522 TCATGTAAACAACTCTAATGAGCAC 57.635 36.000 0.00 0.00 43.85 4.40
1300 1408 5.839262 TGTAAACAACTCTAATGAGCACG 57.161 39.130 0.00 0.00 43.85 5.34
1301 1409 5.294356 TGTAAACAACTCTAATGAGCACGT 58.706 37.500 0.00 0.00 43.85 4.49
1302 1410 5.756347 TGTAAACAACTCTAATGAGCACGTT 59.244 36.000 0.00 0.00 43.85 3.99
1303 1411 5.751243 AAACAACTCTAATGAGCACGTTT 57.249 34.783 0.00 0.00 43.85 3.60
1304 1412 5.751243 AACAACTCTAATGAGCACGTTTT 57.249 34.783 0.00 0.00 43.85 2.43
1305 1413 5.095691 ACAACTCTAATGAGCACGTTTTG 57.904 39.130 0.00 0.00 43.85 2.44
1306 1414 4.814234 ACAACTCTAATGAGCACGTTTTGA 59.186 37.500 5.57 0.35 43.85 2.69
1307 1415 5.470098 ACAACTCTAATGAGCACGTTTTGAT 59.530 36.000 5.57 0.00 43.85 2.57
1308 1416 5.786401 ACTCTAATGAGCACGTTTTGATC 57.214 39.130 0.00 0.00 43.85 2.92
1309 1417 5.482908 ACTCTAATGAGCACGTTTTGATCT 58.517 37.500 0.00 0.00 41.56 2.75
1310 1418 5.578727 ACTCTAATGAGCACGTTTTGATCTC 59.421 40.000 0.00 0.00 41.56 2.75
1311 1419 3.729526 AATGAGCACGTTTTGATCTCG 57.270 42.857 0.00 0.00 41.56 4.04
1312 1420 2.148916 TGAGCACGTTTTGATCTCGT 57.851 45.000 0.00 0.00 41.56 4.18
1313 1421 2.058798 TGAGCACGTTTTGATCTCGTC 58.941 47.619 0.00 0.00 41.56 4.20
1314 1422 2.058798 GAGCACGTTTTGATCTCGTCA 58.941 47.619 0.00 0.00 37.67 4.35
1320 1428 1.126846 GTTTTGATCTCGTCAGCACCG 59.873 52.381 0.00 0.00 38.29 4.94
1334 1442 1.027357 GCACCGAATCAGCATGGATT 58.973 50.000 0.00 0.00 40.10 3.01
1335 1443 1.406539 GCACCGAATCAGCATGGATTT 59.593 47.619 0.00 0.00 37.61 2.17
1336 1444 2.159198 GCACCGAATCAGCATGGATTTT 60.159 45.455 0.00 0.00 37.61 1.82
1337 1445 3.699067 CACCGAATCAGCATGGATTTTC 58.301 45.455 0.00 0.00 37.61 2.29
1338 1446 3.129113 CACCGAATCAGCATGGATTTTCA 59.871 43.478 0.00 0.00 37.61 2.69
1350 1458 2.165998 GGATTTTCACTTGCTCTGCCT 58.834 47.619 0.00 0.00 0.00 4.75
1357 1465 2.987547 TTGCTCTGCCTTGCCTGC 60.988 61.111 0.00 0.00 0.00 4.85
1408 1524 0.811281 GCCTGCAAATGTACTGTCCC 59.189 55.000 0.00 0.00 0.00 4.46
1409 1525 1.886222 GCCTGCAAATGTACTGTCCCA 60.886 52.381 0.00 0.00 0.00 4.37
1410 1526 2.726821 CCTGCAAATGTACTGTCCCAT 58.273 47.619 0.00 0.00 0.00 4.00
1412 1528 3.511146 CCTGCAAATGTACTGTCCCATTT 59.489 43.478 10.73 10.73 40.85 2.32
1413 1529 4.021192 CCTGCAAATGTACTGTCCCATTTT 60.021 41.667 12.84 1.39 38.79 1.82
1414 1530 4.880759 TGCAAATGTACTGTCCCATTTTG 58.119 39.130 12.84 10.57 38.79 2.44
1425 1541 3.708631 TGTCCCATTTTGGTGTTGTGATT 59.291 39.130 0.00 0.00 35.17 2.57
1426 1542 4.163078 TGTCCCATTTTGGTGTTGTGATTT 59.837 37.500 0.00 0.00 35.17 2.17
1429 1545 5.587844 TCCCATTTTGGTGTTGTGATTTTTG 59.412 36.000 0.00 0.00 35.17 2.44
1436 1553 4.460731 TGGTGTTGTGATTTTTGTCAGTGA 59.539 37.500 0.00 0.00 0.00 3.41
1441 1558 4.619973 TGTGATTTTTGTCAGTGAATGCC 58.380 39.130 0.00 0.00 0.00 4.40
1444 1561 2.798976 TTTTGTCAGTGAATGCCTGC 57.201 45.000 0.00 0.00 0.00 4.85
1457 1574 4.216257 TGAATGCCTGCTTCTGAAACTTAC 59.784 41.667 0.00 0.00 0.00 2.34
1462 1579 3.058639 CCTGCTTCTGAAACTTACAGCAC 60.059 47.826 0.00 0.00 35.61 4.40
1474 1591 2.768253 TACAGCACCCACAGATGAAG 57.232 50.000 0.00 0.00 0.00 3.02
1559 1676 5.358725 TCCTTTCCTGTTTAACACCTGAAAC 59.641 40.000 0.00 0.00 36.33 2.78
1562 1679 7.013846 CCTTTCCTGTTTAACACCTGAAACATA 59.986 37.037 0.00 0.00 42.86 2.29
1583 1700 2.125512 GCTGTCTCCGCAACCGAT 60.126 61.111 0.00 0.00 36.29 4.18
1587 1704 2.545113 GCTGTCTCCGCAACCGATTATA 60.545 50.000 0.00 0.00 36.29 0.98
1607 1724 7.544804 TTATAAGATAGCTGAGAGGCATGAA 57.455 36.000 0.00 0.00 34.17 2.57
1641 1758 8.044060 ACTGATTATGTTTCGTGATTCATGTT 57.956 30.769 5.80 0.00 0.00 2.71
1661 1778 6.757897 TGTTTGAACTCTGAACAATGTTCT 57.242 33.333 24.30 6.13 39.38 3.01
1662 1779 7.156876 TGTTTGAACTCTGAACAATGTTCTT 57.843 32.000 24.30 12.00 39.38 2.52
1663 1780 7.601856 TGTTTGAACTCTGAACAATGTTCTTT 58.398 30.769 24.30 13.20 39.38 2.52
1664 1781 8.087750 TGTTTGAACTCTGAACAATGTTCTTTT 58.912 29.630 24.30 12.89 39.38 2.27
1665 1782 8.375465 GTTTGAACTCTGAACAATGTTCTTTTG 58.625 33.333 24.30 14.70 39.38 2.44
1666 1783 7.156876 TGAACTCTGAACAATGTTCTTTTGT 57.843 32.000 24.30 15.23 39.38 2.83
1667 1784 7.601856 TGAACTCTGAACAATGTTCTTTTGTT 58.398 30.769 24.30 20.89 46.89 2.83
1668 1785 8.087750 TGAACTCTGAACAATGTTCTTTTGTTT 58.912 29.630 24.30 11.39 44.90 2.83
1669 1786 7.816945 ACTCTGAACAATGTTCTTTTGTTTG 57.183 32.000 24.30 10.00 44.90 2.93
1679 1796 5.742446 TGTTCTTTTGTTTGTTTTGTGTGC 58.258 33.333 0.00 0.00 0.00 4.57
1694 1811 8.468399 TGTTTTGTGTGCATGACATCATATATT 58.532 29.630 0.00 0.00 36.78 1.28
1698 1815 8.907222 TGTGTGCATGACATCATATATTAACT 57.093 30.769 0.00 0.00 36.78 2.24
1752 1872 0.391661 GCAGGCTGTCGATCCTTGAA 60.392 55.000 17.16 0.00 0.00 2.69
1756 1876 2.026822 AGGCTGTCGATCCTTGAACATT 60.027 45.455 0.00 0.00 0.00 2.71
1792 1912 4.451629 TGGCAAGTAGCTAACTGTCTAC 57.548 45.455 0.00 0.00 44.79 2.59
1793 1913 3.830178 TGGCAAGTAGCTAACTGTCTACA 59.170 43.478 0.00 0.00 44.79 2.74
1794 1914 4.282449 TGGCAAGTAGCTAACTGTCTACAA 59.718 41.667 0.00 0.00 44.79 2.41
1795 1915 5.046591 TGGCAAGTAGCTAACTGTCTACAAT 60.047 40.000 0.00 0.00 44.79 2.71
1817 1940 7.016858 ACAATAAGGTCAGGTACTAACTTTCCA 59.983 37.037 0.00 0.00 36.02 3.53
1822 1945 4.863131 GTCAGGTACTAACTTTCCATGTCG 59.137 45.833 0.00 0.00 36.02 4.35
1847 1970 2.664851 CGTGAAACTGCTCGGCCA 60.665 61.111 2.24 0.00 31.75 5.36
1895 2018 3.545724 CTCTGCAAGCACATCCTGA 57.454 52.632 0.00 0.00 0.00 3.86
1899 2022 1.246056 TGCAAGCACATCCTGAAGCC 61.246 55.000 0.00 0.00 0.00 4.35
1918 2041 1.071385 CCAGGATCATAGTCCCACAGC 59.929 57.143 0.00 0.00 39.17 4.40
1925 2048 0.694444 ATAGTCCCACAGCCCGGATT 60.694 55.000 0.73 0.00 0.00 3.01
1990 2113 0.392863 TGTGGATGATGAAGCACCCG 60.393 55.000 0.00 0.00 0.00 5.28
1993 2116 1.162800 GGATGATGAAGCACCCGAGC 61.163 60.000 0.00 0.00 0.00 5.03
2013 2136 1.239296 TTCTTGCAAGCTGAGCGCAT 61.239 50.000 21.99 0.00 42.61 4.73
2014 2137 1.514228 CTTGCAAGCTGAGCGCATG 60.514 57.895 14.65 6.80 42.61 4.06
2017 2140 2.683859 GCAAGCTGAGCGCATGTCA 61.684 57.895 11.47 3.47 39.43 3.58
2029 2152 2.803203 CATGTCATGCCTTCCCCAG 58.197 57.895 0.00 0.00 0.00 4.45
2032 2155 1.452833 GTCATGCCTTCCCCAGAGC 60.453 63.158 0.00 0.00 0.00 4.09
2058 2181 0.766131 TAAGCTCCGTTGGGGAACAA 59.234 50.000 0.00 0.00 46.61 2.83
2059 2182 0.106419 AAGCTCCGTTGGGGAACAAA 60.106 50.000 0.00 0.00 46.61 2.83
2071 2194 0.326927 GGAACAAATCCCGGTCCAGA 59.673 55.000 0.00 0.00 43.00 3.86
2173 2296 1.556451 TCATAGAAGCTTGGCTGCTCA 59.444 47.619 2.10 0.00 41.37 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 94 9.199645 GGAAGAGAAAGTAGGGTTTACTAGTAT 57.800 37.037 2.79 0.00 0.00 2.12
93 95 7.617329 GGGAAGAGAAAGTAGGGTTTACTAGTA 59.383 40.741 0.00 0.00 0.00 1.82
94 96 6.440010 GGGAAGAGAAAGTAGGGTTTACTAGT 59.560 42.308 0.00 0.00 0.00 2.57
95 97 6.405619 CGGGAAGAGAAAGTAGGGTTTACTAG 60.406 46.154 0.00 0.00 0.00 2.57
110 112 1.916777 GGTGGGACCGGGAAGAGAA 60.917 63.158 6.32 0.00 0.00 2.87
156 164 2.027100 AGGGGACGGAAATGAAGAAGAC 60.027 50.000 0.00 0.00 0.00 3.01
207 215 2.629051 CCCAGAGATTTACCGTGGAAC 58.371 52.381 0.00 0.00 0.00 3.62
224 232 1.208706 TATTCAACGGATCCTGCCCA 58.791 50.000 10.75 0.00 0.00 5.36
289 297 4.411927 GCTCTCTATACAAGGATCCCTGA 58.588 47.826 17.55 1.41 32.13 3.86
303 311 1.820090 GCGTGGACTAGGGCTCTCTAT 60.820 57.143 0.00 0.00 0.00 1.98
346 354 2.724174 CGCAAAGAAATTTCGGTTCCAC 59.276 45.455 12.42 3.22 0.00 4.02
407 419 4.432712 GCCACAACAACAATCAAACTTCT 58.567 39.130 0.00 0.00 0.00 2.85
429 441 1.153086 CTCCCAGGAAGATTGCCCG 60.153 63.158 0.00 0.00 0.00 6.13
453 465 4.149922 CGATACAAACCGCATCAACGATAT 59.850 41.667 0.00 0.00 34.06 1.63
454 466 3.487942 CGATACAAACCGCATCAACGATA 59.512 43.478 0.00 0.00 34.06 2.92
506 518 6.852420 AATAAGCAGTTGTGTCTACTCCTA 57.148 37.500 0.00 0.00 0.00 2.94
537 550 2.358939 ACTACGCCTTGAGTAAACCG 57.641 50.000 0.00 0.00 0.00 4.44
538 551 6.742109 TGATATACTACGCCTTGAGTAAACC 58.258 40.000 0.00 0.00 32.11 3.27
568 581 3.374058 ACCAGTACTGATGCAATTAACGC 59.626 43.478 24.68 0.00 0.00 4.84
570 583 6.494893 TGAACCAGTACTGATGCAATTAAC 57.505 37.500 24.68 4.31 0.00 2.01
573 586 5.711506 TGAATGAACCAGTACTGATGCAATT 59.288 36.000 24.68 15.37 0.00 2.32
575 588 4.650734 TGAATGAACCAGTACTGATGCAA 58.349 39.130 24.68 6.11 0.00 4.08
581 594 6.644347 AGGTAGATTGAATGAACCAGTACTG 58.356 40.000 16.34 16.34 32.43 2.74
582 595 6.875972 AGGTAGATTGAATGAACCAGTACT 57.124 37.500 7.91 0.00 32.43 2.73
583 596 8.421784 TCATAGGTAGATTGAATGAACCAGTAC 58.578 37.037 7.91 0.00 32.43 2.73
592 605 6.519382 TCAGTGCTCATAGGTAGATTGAATG 58.481 40.000 0.00 0.00 0.00 2.67
599 612 4.342378 GGTCATTCAGTGCTCATAGGTAGA 59.658 45.833 0.00 0.00 0.00 2.59
604 617 5.366460 AGATTGGTCATTCAGTGCTCATAG 58.634 41.667 0.00 0.00 0.00 2.23
610 623 7.859377 CACATATTTAGATTGGTCATTCAGTGC 59.141 37.037 0.00 0.00 0.00 4.40
630 643 8.304596 CGTACCTTGATCCTTACATACACATAT 58.695 37.037 0.00 0.00 0.00 1.78
634 655 6.140303 TCGTACCTTGATCCTTACATACAC 57.860 41.667 0.00 0.00 0.00 2.90
669 693 3.196901 TGATAACGCAACTACCATCCAGT 59.803 43.478 0.00 0.00 0.00 4.00
670 694 3.792401 TGATAACGCAACTACCATCCAG 58.208 45.455 0.00 0.00 0.00 3.86
671 695 3.897141 TGATAACGCAACTACCATCCA 57.103 42.857 0.00 0.00 0.00 3.41
676 700 1.602377 GGGCATGATAACGCAACTACC 59.398 52.381 0.00 0.00 0.00 3.18
678 702 2.700722 TGGGCATGATAACGCAACTA 57.299 45.000 0.00 0.00 0.00 2.24
684 708 2.491693 ACCTTGTTTGGGCATGATAACG 59.508 45.455 0.00 0.00 0.00 3.18
701 725 9.547279 TGGACATATCTACATACATATCACCTT 57.453 33.333 0.00 0.00 0.00 3.50
714 770 8.692710 CCTACTACAGTTTTGGACATATCTACA 58.307 37.037 0.00 0.00 0.00 2.74
715 771 8.693625 ACCTACTACAGTTTTGGACATATCTAC 58.306 37.037 0.00 0.00 0.00 2.59
720 776 6.675413 ACACCTACTACAGTTTTGGACATA 57.325 37.500 0.00 0.00 0.00 2.29
722 778 6.268158 TGATACACCTACTACAGTTTTGGACA 59.732 38.462 0.00 0.00 0.00 4.02
723 779 6.694447 TGATACACCTACTACAGTTTTGGAC 58.306 40.000 0.00 0.00 0.00 4.02
740 796 6.761242 TGCATATCACTTGTTACCTGATACAC 59.239 38.462 0.00 0.00 31.31 2.90
755 811 5.126067 GGTCATACCAAGTTGCATATCACT 58.874 41.667 0.00 0.00 38.42 3.41
770 826 3.366052 AGGGTTCACATTGGTCATACC 57.634 47.619 0.00 0.00 39.22 2.73
771 827 5.722021 AAAAGGGTTCACATTGGTCATAC 57.278 39.130 0.00 0.00 0.00 2.39
827 885 4.283722 AGTTAAGAAAGAGACACATCGGGT 59.716 41.667 0.00 0.00 0.00 5.28
830 888 6.642950 ACAAGAGTTAAGAAAGAGACACATCG 59.357 38.462 0.00 0.00 0.00 3.84
846 904 8.535335 AGCAAGAGAAATCTCATACAAGAGTTA 58.465 33.333 12.65 0.00 45.21 2.24
847 905 7.393216 AGCAAGAGAAATCTCATACAAGAGTT 58.607 34.615 12.65 0.00 45.21 3.01
848 906 6.945218 AGCAAGAGAAATCTCATACAAGAGT 58.055 36.000 12.65 0.00 45.21 3.24
849 907 7.223193 CAGAGCAAGAGAAATCTCATACAAGAG 59.777 40.741 12.65 0.00 45.21 2.85
850 908 7.040494 CAGAGCAAGAGAAATCTCATACAAGA 58.960 38.462 12.65 0.00 45.21 3.02
851 909 7.040494 TCAGAGCAAGAGAAATCTCATACAAG 58.960 38.462 12.65 0.00 45.21 3.16
852 910 6.939622 TCAGAGCAAGAGAAATCTCATACAA 58.060 36.000 12.65 0.00 45.21 2.41
873 977 7.714377 ACACAAGGAGCATAAAGAGAATATCAG 59.286 37.037 0.00 0.00 0.00 2.90
876 980 7.714377 CAGACACAAGGAGCATAAAGAGAATAT 59.286 37.037 0.00 0.00 0.00 1.28
880 984 4.825422 CAGACACAAGGAGCATAAAGAGA 58.175 43.478 0.00 0.00 0.00 3.10
884 988 2.040278 AGGCAGACACAAGGAGCATAAA 59.960 45.455 0.00 0.00 0.00 1.40
887 991 0.403271 AAGGCAGACACAAGGAGCAT 59.597 50.000 0.00 0.00 0.00 3.79
909 1013 0.999406 TATTCAAGCTTCTGCGACGC 59.001 50.000 14.19 14.19 45.42 5.19
911 1015 4.570772 TGGTAATATTCAAGCTTCTGCGAC 59.429 41.667 0.00 0.00 45.42 5.19
913 1017 4.572389 AGTGGTAATATTCAAGCTTCTGCG 59.428 41.667 0.00 0.00 45.42 5.18
927 1031 6.995686 ACAAACACAACATCAGAGTGGTAATA 59.004 34.615 0.00 0.00 37.58 0.98
928 1032 5.827797 ACAAACACAACATCAGAGTGGTAAT 59.172 36.000 0.00 0.00 37.58 1.89
931 1035 3.620488 ACAAACACAACATCAGAGTGGT 58.380 40.909 0.00 0.00 37.58 4.16
932 1036 3.627123 TGACAAACACAACATCAGAGTGG 59.373 43.478 0.00 0.00 37.58 4.00
933 1037 4.787563 GCTGACAAACACAACATCAGAGTG 60.788 45.833 3.80 0.00 39.33 3.51
939 1043 1.000274 GGGGCTGACAAACACAACATC 60.000 52.381 0.00 0.00 0.00 3.06
945 1049 2.102252 TGAAAATGGGGCTGACAAACAC 59.898 45.455 0.00 0.00 0.00 3.32
952 1056 2.158325 AGGAAACTGAAAATGGGGCTGA 60.158 45.455 0.00 0.00 41.13 4.26
954 1058 2.110721 AGAGGAAACTGAAAATGGGGCT 59.889 45.455 0.00 0.00 44.43 5.19
958 1062 3.571401 ACAGCAGAGGAAACTGAAAATGG 59.429 43.478 0.00 0.00 44.43 3.16
974 1078 1.470098 GGGTATGAACTTGCACAGCAG 59.530 52.381 0.00 0.00 40.61 4.24
978 1082 2.949177 AGTGGGTATGAACTTGCACA 57.051 45.000 0.00 0.00 0.00 4.57
981 1085 4.130118 CCATCTAGTGGGTATGAACTTGC 58.870 47.826 4.04 0.00 44.79 4.01
1023 1128 5.476945 TGCTGAGACGAGCCTGATAAATATA 59.523 40.000 0.00 0.00 38.28 0.86
1041 1146 2.249413 ATCCAGTTCCGGCTGCTGAG 62.249 60.000 10.70 0.04 35.28 3.35
1050 1155 3.991773 TCACGTAGAAAAATCCAGTTCCG 59.008 43.478 0.00 0.00 0.00 4.30
1059 1164 3.496884 TCTTGCGCTTCACGTAGAAAAAT 59.503 39.130 9.73 0.00 46.11 1.82
1095 1200 3.065655 CCTGAACTCAAGCTTCTCTGTG 58.934 50.000 0.00 0.00 0.00 3.66
1128 1233 3.268013 AGAACATGCTTGTTTACACGC 57.732 42.857 17.99 4.57 46.01 5.34
1177 1282 3.317993 TGGTAAGAAAGAAAGGTTGCAGC 59.682 43.478 0.00 0.00 0.00 5.25
1178 1283 5.712152 ATGGTAAGAAAGAAAGGTTGCAG 57.288 39.130 0.00 0.00 0.00 4.41
1183 1288 7.237887 AGAGGTCTTATGGTAAGAAAGAAAGGT 59.762 37.037 1.29 0.00 31.41 3.50
1189 1294 6.096564 ACGGTAGAGGTCTTATGGTAAGAAAG 59.903 42.308 1.29 0.00 0.00 2.62
1196 1304 3.705051 TGAACGGTAGAGGTCTTATGGT 58.295 45.455 0.00 0.00 0.00 3.55
1197 1305 4.939052 ATGAACGGTAGAGGTCTTATGG 57.061 45.455 0.00 0.00 0.00 2.74
1212 1320 2.473609 TCGTCTTCGACCAAAATGAACG 59.526 45.455 0.00 0.00 41.35 3.95
1225 1333 2.783828 AGGTAGCATCATCGTCTTCG 57.216 50.000 0.00 0.00 38.55 3.79
1232 1340 6.348540 CCCGCTAAAATAAAGGTAGCATCATC 60.349 42.308 0.00 0.00 40.23 2.92
1233 1341 5.473504 CCCGCTAAAATAAAGGTAGCATCAT 59.526 40.000 0.00 0.00 40.23 2.45
1234 1342 4.819630 CCCGCTAAAATAAAGGTAGCATCA 59.180 41.667 0.00 0.00 40.23 3.07
1235 1343 4.320275 GCCCGCTAAAATAAAGGTAGCATC 60.320 45.833 0.00 0.00 40.23 3.91
1250 1358 6.912951 ACTAAATTATCTAGAGCCCGCTAA 57.087 37.500 0.00 0.00 0.00 3.09
1251 1359 6.912951 AACTAAATTATCTAGAGCCCGCTA 57.087 37.500 0.00 0.00 0.00 4.26
1255 1363 8.910351 ACATGAAACTAAATTATCTAGAGCCC 57.090 34.615 0.00 0.00 0.00 5.19
1281 1389 5.751243 AAACGTGCTCATTAGAGTTGTTT 57.249 34.783 0.00 0.00 44.00 2.83
1282 1390 5.295787 TCAAAACGTGCTCATTAGAGTTGTT 59.704 36.000 0.00 0.00 44.00 2.83
1283 1391 4.814234 TCAAAACGTGCTCATTAGAGTTGT 59.186 37.500 0.00 0.00 44.00 3.32
1284 1392 5.342806 TCAAAACGTGCTCATTAGAGTTG 57.657 39.130 0.00 0.00 44.00 3.16
1285 1393 5.934625 AGATCAAAACGTGCTCATTAGAGTT 59.065 36.000 0.00 0.00 44.00 3.01
1286 1394 5.482908 AGATCAAAACGTGCTCATTAGAGT 58.517 37.500 0.00 0.00 44.00 3.24
1287 1395 5.276114 CGAGATCAAAACGTGCTCATTAGAG 60.276 44.000 0.00 0.00 44.96 2.43
1288 1396 4.562789 CGAGATCAAAACGTGCTCATTAGA 59.437 41.667 0.00 0.00 0.00 2.10
1289 1397 4.327357 ACGAGATCAAAACGTGCTCATTAG 59.673 41.667 0.00 0.00 38.79 1.73
1290 1398 4.242475 ACGAGATCAAAACGTGCTCATTA 58.758 39.130 0.00 0.00 38.79 1.90
1291 1399 3.067106 ACGAGATCAAAACGTGCTCATT 58.933 40.909 0.00 0.00 38.79 2.57
1292 1400 2.668457 GACGAGATCAAAACGTGCTCAT 59.332 45.455 10.76 0.00 40.29 2.90
1293 1401 2.058798 GACGAGATCAAAACGTGCTCA 58.941 47.619 10.76 0.00 40.29 4.26
1294 1402 2.058798 TGACGAGATCAAAACGTGCTC 58.941 47.619 10.76 0.00 40.29 4.26
1295 1403 2.061773 CTGACGAGATCAAAACGTGCT 58.938 47.619 10.76 0.00 40.29 4.40
1296 1404 1.462541 GCTGACGAGATCAAAACGTGC 60.463 52.381 10.76 6.64 40.29 5.34
1297 1405 1.792367 TGCTGACGAGATCAAAACGTG 59.208 47.619 10.76 1.71 40.29 4.49
1298 1406 1.792949 GTGCTGACGAGATCAAAACGT 59.207 47.619 0.00 1.10 42.84 3.99
1299 1407 1.126846 GGTGCTGACGAGATCAAAACG 59.873 52.381 0.00 0.00 36.69 3.60
1300 1408 1.126846 CGGTGCTGACGAGATCAAAAC 59.873 52.381 0.00 0.00 36.69 2.43
1301 1409 1.000394 TCGGTGCTGACGAGATCAAAA 60.000 47.619 0.00 0.00 36.69 2.44
1302 1410 0.601057 TCGGTGCTGACGAGATCAAA 59.399 50.000 0.00 0.00 36.69 2.69
1303 1411 0.601057 TTCGGTGCTGACGAGATCAA 59.399 50.000 0.00 0.00 41.81 2.57
1304 1412 0.817654 ATTCGGTGCTGACGAGATCA 59.182 50.000 0.00 0.00 41.81 2.92
1305 1413 1.202302 TGATTCGGTGCTGACGAGATC 60.202 52.381 0.00 0.00 41.81 2.75
1306 1414 0.817654 TGATTCGGTGCTGACGAGAT 59.182 50.000 0.00 0.00 41.81 2.75
1307 1415 0.171231 CTGATTCGGTGCTGACGAGA 59.829 55.000 0.00 0.00 41.81 4.04
1308 1416 1.416813 GCTGATTCGGTGCTGACGAG 61.417 60.000 0.00 0.00 41.81 4.18
1309 1417 1.446099 GCTGATTCGGTGCTGACGA 60.446 57.895 0.00 0.00 38.78 4.20
1310 1418 1.086067 ATGCTGATTCGGTGCTGACG 61.086 55.000 0.00 0.00 0.00 4.35
1311 1419 0.376152 CATGCTGATTCGGTGCTGAC 59.624 55.000 0.00 0.00 0.00 3.51
1312 1420 0.745486 CCATGCTGATTCGGTGCTGA 60.745 55.000 0.00 0.00 0.00 4.26
1313 1421 0.745486 TCCATGCTGATTCGGTGCTG 60.745 55.000 0.00 0.00 0.00 4.41
1314 1422 0.182061 ATCCATGCTGATTCGGTGCT 59.818 50.000 0.00 0.00 0.00 4.40
1320 1428 4.565564 GCAAGTGAAAATCCATGCTGATTC 59.434 41.667 0.00 0.00 33.91 2.52
1334 1442 0.670162 GCAAGGCAGAGCAAGTGAAA 59.330 50.000 0.00 0.00 0.00 2.69
1335 1443 1.174712 GGCAAGGCAGAGCAAGTGAA 61.175 55.000 0.00 0.00 0.00 3.18
1336 1444 1.601759 GGCAAGGCAGAGCAAGTGA 60.602 57.895 0.00 0.00 0.00 3.41
1337 1445 1.602888 AGGCAAGGCAGAGCAAGTG 60.603 57.895 0.00 0.00 0.00 3.16
1338 1446 1.602888 CAGGCAAGGCAGAGCAAGT 60.603 57.895 0.00 0.00 0.00 3.16
1350 1458 7.175816 TCAGTTACAATACAAATAAGCAGGCAA 59.824 33.333 0.00 0.00 0.00 4.52
1405 1521 5.365021 AAAATCACAACACCAAAATGGGA 57.635 34.783 0.87 0.00 43.37 4.37
1408 1524 7.069852 TGACAAAAATCACAACACCAAAATG 57.930 32.000 0.00 0.00 0.00 2.32
1409 1525 6.878389 ACTGACAAAAATCACAACACCAAAAT 59.122 30.769 0.00 0.00 0.00 1.82
1410 1526 6.146837 CACTGACAAAAATCACAACACCAAAA 59.853 34.615 0.00 0.00 0.00 2.44
1412 1528 5.047731 TCACTGACAAAAATCACAACACCAA 60.048 36.000 0.00 0.00 0.00 3.67
1413 1529 4.460731 TCACTGACAAAAATCACAACACCA 59.539 37.500 0.00 0.00 0.00 4.17
1414 1530 4.992688 TCACTGACAAAAATCACAACACC 58.007 39.130 0.00 0.00 0.00 4.16
1425 1541 2.309613 AGCAGGCATTCACTGACAAAA 58.690 42.857 0.00 0.00 38.20 2.44
1426 1542 1.985473 AGCAGGCATTCACTGACAAA 58.015 45.000 0.00 0.00 38.20 2.83
1429 1545 1.467734 CAGAAGCAGGCATTCACTGAC 59.532 52.381 0.00 0.00 38.20 3.51
1436 1553 4.144297 TGTAAGTTTCAGAAGCAGGCATT 58.856 39.130 0.00 0.00 0.00 3.56
1441 1558 3.058639 GGTGCTGTAAGTTTCAGAAGCAG 60.059 47.826 13.18 0.00 41.01 4.24
1444 1561 3.251004 GTGGGTGCTGTAAGTTTCAGAAG 59.749 47.826 13.18 0.00 35.30 2.85
1457 1574 0.679002 CCCTTCATCTGTGGGTGCTG 60.679 60.000 0.00 0.00 36.32 4.41
1462 1579 1.765314 CTCTACCCCTTCATCTGTGGG 59.235 57.143 0.00 0.00 44.03 4.61
1474 1591 0.252558 TGGTTCAGACCCTCTACCCC 60.253 60.000 0.00 0.00 45.92 4.95
1519 1636 8.210946 ACAGGAAAGGAAAAGAAAATAAAAGGG 58.789 33.333 0.00 0.00 0.00 3.95
1528 1645 7.179516 AGGTGTTAAACAGGAAAGGAAAAGAAA 59.820 33.333 0.00 0.00 0.00 2.52
1550 1667 5.468072 GGAGACAGCATATATGTTTCAGGTG 59.532 44.000 14.14 5.52 34.39 4.00
1559 1676 2.738846 GGTTGCGGAGACAGCATATATG 59.261 50.000 8.45 8.45 44.74 1.78
1562 1679 0.530650 CGGTTGCGGAGACAGCATAT 60.531 55.000 0.00 0.00 44.74 1.78
1583 1700 7.544804 TTCATGCCTCTCAGCTATCTTATAA 57.455 36.000 0.00 0.00 0.00 0.98
1587 1704 4.978438 ATTCATGCCTCTCAGCTATCTT 57.022 40.909 0.00 0.00 0.00 2.40
1607 1724 9.325198 TCACGAAACATAATCAGTAATAGCAAT 57.675 29.630 0.00 0.00 0.00 3.56
1620 1737 9.128107 GTTCAAACATGAATCACGAAACATAAT 57.872 29.630 0.00 0.00 0.00 1.28
1638 1755 6.757897 AGAACATTGTTCAGAGTTCAAACA 57.242 33.333 26.73 0.00 42.01 2.83
1641 1758 7.601856 ACAAAAGAACATTGTTCAGAGTTCAA 58.398 30.769 26.73 0.00 42.01 2.69
1661 1778 5.237127 TGTCATGCACACAAAACAAACAAAA 59.763 32.000 0.00 0.00 0.00 2.44
1662 1779 4.751600 TGTCATGCACACAAAACAAACAAA 59.248 33.333 0.00 0.00 0.00 2.83
1663 1780 4.309933 TGTCATGCACACAAAACAAACAA 58.690 34.783 0.00 0.00 0.00 2.83
1664 1781 3.917988 TGTCATGCACACAAAACAAACA 58.082 36.364 0.00 0.00 0.00 2.83
1665 1782 4.565962 TGATGTCATGCACACAAAACAAAC 59.434 37.500 4.48 0.00 38.04 2.93
1666 1783 4.752146 TGATGTCATGCACACAAAACAAA 58.248 34.783 4.48 0.00 38.04 2.83
1667 1784 4.382345 TGATGTCATGCACACAAAACAA 57.618 36.364 4.48 0.00 38.04 2.83
1668 1785 4.587584 ATGATGTCATGCACACAAAACA 57.412 36.364 4.48 6.30 38.04 2.83
1669 1786 8.861033 AATATATGATGTCATGCACACAAAAC 57.139 30.769 5.78 1.54 38.04 2.43
1720 1840 2.233431 ACAGCCTGCTTGTTTTGACAAA 59.767 40.909 0.00 0.00 0.00 2.83
1725 1845 0.662619 TCGACAGCCTGCTTGTTTTG 59.337 50.000 0.00 0.00 0.00 2.44
1730 1850 0.392193 AAGGATCGACAGCCTGCTTG 60.392 55.000 4.28 0.00 34.00 4.01
1752 1872 6.040209 TGCCAATGCTAATTCTGAAAATGT 57.960 33.333 0.00 0.00 38.71 2.71
1756 1876 5.726980 ACTTGCCAATGCTAATTCTGAAA 57.273 34.783 0.00 0.00 38.71 2.69
1792 1912 7.391620 TGGAAAGTTAGTACCTGACCTTATTG 58.608 38.462 0.00 0.00 0.00 1.90
1793 1913 7.563724 TGGAAAGTTAGTACCTGACCTTATT 57.436 36.000 0.00 0.00 0.00 1.40
1794 1914 7.182206 ACATGGAAAGTTAGTACCTGACCTTAT 59.818 37.037 0.00 0.00 0.00 1.73
1795 1915 6.499350 ACATGGAAAGTTAGTACCTGACCTTA 59.501 38.462 0.00 0.00 0.00 2.69
1817 1940 0.318360 TTTCACGCGTCTGACGACAT 60.318 50.000 32.07 14.10 46.05 3.06
1822 1945 1.201825 GCAGTTTCACGCGTCTGAC 59.798 57.895 24.73 16.19 0.00 3.51
1831 1954 1.598130 AGTGGCCGAGCAGTTTCAC 60.598 57.895 0.00 0.00 0.00 3.18
1895 2018 1.771255 GTGGGACTATGATCCTGGCTT 59.229 52.381 0.00 0.00 38.95 4.35
1899 2022 1.071385 GGCTGTGGGACTATGATCCTG 59.929 57.143 0.00 0.00 38.95 3.86
1993 2116 1.154263 GCGCTCAGCTTGCAAGAAG 60.154 57.895 30.39 21.73 44.04 2.85
2013 2136 1.993653 CTCTGGGGAAGGCATGACA 59.006 57.895 0.00 0.00 0.00 3.58
2014 2137 1.452833 GCTCTGGGGAAGGCATGAC 60.453 63.158 0.00 0.00 0.00 3.06
2017 2140 3.424105 GGGCTCTGGGGAAGGCAT 61.424 66.667 0.00 0.00 0.00 4.40
2023 2146 0.914417 CTTACAAGGGGCTCTGGGGA 60.914 60.000 0.00 0.00 0.00 4.81
2024 2147 1.609783 CTTACAAGGGGCTCTGGGG 59.390 63.158 0.00 0.00 0.00 4.96
2032 2155 0.676782 CCAACGGAGCTTACAAGGGG 60.677 60.000 0.00 0.00 0.00 4.79
2058 2181 0.321298 CGTGTTTCTGGACCGGGATT 60.321 55.000 6.32 0.00 0.00 3.01
2059 2182 1.189524 TCGTGTTTCTGGACCGGGAT 61.190 55.000 6.32 0.00 0.00 3.85
2071 2194 1.011333 CAAACCTCACCGTCGTGTTT 58.989 50.000 0.00 0.00 41.09 2.83


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

AutoCloner maintained by Alex Coulton.