Multiple sequence alignment - TraesCS6A01G382700

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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 TraesCS6A01G382700 chr6A 100.000 2521 0 0 1 2521 601951448 601953968 0.000000e+00 4656.0
1 TraesCS6A01G382700 chr6A 83.730 252 16 12 1 239 601473664 601473903 5.460000e-52 215.0
2 TraesCS6A01G382700 chr6D 89.087 1063 88 17 1479 2521 455296711 455297765 0.000000e+00 1295.0
3 TraesCS6A01G382700 chr6D 92.453 530 18 8 1 514 455252425 455252948 0.000000e+00 737.0
4 TraesCS6A01G382700 chr6D 89.655 522 27 16 1 512 455295374 455295878 7.600000e-180 640.0
5 TraesCS6A01G382700 chr6D 79.444 827 82 45 1730 2521 455255796 455256569 2.890000e-139 505.0
6 TraesCS6A01G382700 chr6D 92.905 296 14 2 1085 1373 361286652 361286947 8.340000e-115 424.0
7 TraesCS6A01G382700 chr6D 79.928 558 54 26 564 1093 455254392 455254919 8.580000e-95 357.0
8 TraesCS6A01G382700 chr6D 86.047 258 32 2 1479 1733 455255225 455255481 8.880000e-70 274.0
9 TraesCS6A01G382700 chr6D 85.098 255 13 11 1 243 455100054 455100295 1.170000e-58 237.0
10 TraesCS6A01G382700 chr6D 89.796 98 9 1 1371 1467 455254915 455255012 9.470000e-25 124.0
11 TraesCS6A01G382700 chr6B 86.152 946 48 35 1 902 692429610 692430516 0.000000e+00 944.0
12 TraesCS6A01G382700 chr6B 88.676 521 29 13 2021 2521 692431412 692431922 2.140000e-170 608.0
13 TraesCS6A01G382700 chr6B 85.098 255 13 12 1 243 692235191 692235432 1.170000e-58 237.0
14 TraesCS6A01G382700 chr6B 79.412 102 16 4 1473 1572 648108041 648108139 1.620000e-07 67.6
15 TraesCS6A01G382700 chr3D 94.158 291 10 2 1089 1373 527633010 527633299 1.070000e-118 436.0
16 TraesCS6A01G382700 chr4D 93.243 296 13 2 1085 1373 83549308 83549013 1.790000e-116 429.0
17 TraesCS6A01G382700 chr4D 93.127 291 14 1 1089 1373 499689611 499689901 3.000000e-114 422.0
18 TraesCS6A01G382700 chr4D 92.230 296 16 3 1085 1373 291245590 291245295 1.800000e-111 412.0
19 TraesCS6A01G382700 chr2A 93.151 292 14 1 1088 1373 685744208 685744499 8.340000e-115 424.0
20 TraesCS6A01G382700 chr2D 92.491 293 12 4 1089 1373 410179212 410178922 6.490000e-111 411.0
21 TraesCS6A01G382700 chr3B 92.334 287 16 1 1091 1371 179634497 179634783 1.090000e-108 403.0
22 TraesCS6A01G382700 chr5D 91.089 303 18 4 1080 1373 171619331 171619633 3.910000e-108 401.0


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 TraesCS6A01G382700 chr6A 601951448 601953968 2520 False 4656.0 4656 100.0000 1 2521 1 chr6A.!!$F2 2520
1 TraesCS6A01G382700 chr6D 455295374 455297765 2391 False 967.5 1295 89.3710 1 2521 2 chr6D.!!$F4 2520
2 TraesCS6A01G382700 chr6D 455252425 455256569 4144 False 399.4 737 85.5336 1 2521 5 chr6D.!!$F3 2520
3 TraesCS6A01G382700 chr6B 692429610 692431922 2312 False 776.0 944 87.4140 1 2521 2 chr6B.!!$F3 2520

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
760 2390 0.606604 TTGACTACGGCAGGGAACTC 59.393 55.0 0.0 0.0 40.21 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 4461 1.063806 GCATACGAGCTAAGATGGCG 58.936 55.0 0.0 0.0 34.52 5.69 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
43 44 2.027625 GTCGGCAAGACGGACAAGG 61.028 63.158 0.00 0.00 45.42 3.61
547 608 9.912634 TTTTACCTCATTTAGCAAAATTCTCTG 57.087 29.630 0.00 0.00 32.87 3.35
618 2075 7.520451 ACCTACAAAACAAATTACCTCCTTC 57.480 36.000 0.00 0.00 0.00 3.46
741 2371 0.744281 CTGAACCCAAAAACGGTGCT 59.256 50.000 0.00 0.00 32.55 4.40
757 2387 1.295423 GCTTGACTACGGCAGGGAA 59.705 57.895 0.00 0.00 0.00 3.97
758 2388 1.019805 GCTTGACTACGGCAGGGAAC 61.020 60.000 0.00 0.00 0.00 3.62
759 2389 0.608640 CTTGACTACGGCAGGGAACT 59.391 55.000 0.00 0.00 46.44 3.01
760 2390 0.606604 TTGACTACGGCAGGGAACTC 59.393 55.000 0.00 0.00 40.21 3.01
761 2391 1.255667 TGACTACGGCAGGGAACTCC 61.256 60.000 0.00 0.00 40.21 3.85
861 2501 1.741770 GTTGTTGCTCGATCCGGCT 60.742 57.895 0.00 0.00 0.00 5.52
898 2538 1.302511 CACAAACACGGGAGGGGAG 60.303 63.158 0.00 0.00 37.82 4.30
940 2606 1.961277 CTTGAGGTCCGCGCAAACT 60.961 57.895 8.75 1.64 0.00 2.66
950 2616 2.949106 CGCAAACTGGTGAGGCAG 59.051 61.111 0.00 0.00 0.00 4.85
1083 2753 2.476519 CGAAGGAGTAGACGAGCTTGAC 60.477 54.545 8.31 0.65 0.00 3.18
1093 2763 1.469308 ACGAGCTTGACGAGGTTAGAG 59.531 52.381 8.31 0.00 35.91 2.43
1094 2764 1.795889 CGAGCTTGACGAGGTTAGAGC 60.796 57.143 0.00 0.00 35.91 4.09
1095 2765 1.202582 GAGCTTGACGAGGTTAGAGCA 59.797 52.381 0.00 0.00 35.91 4.26
1096 2766 1.827969 AGCTTGACGAGGTTAGAGCAT 59.172 47.619 0.00 0.00 30.17 3.79
1097 2767 1.929836 GCTTGACGAGGTTAGAGCATG 59.070 52.381 0.00 0.00 0.00 4.06
1098 2768 2.544685 CTTGACGAGGTTAGAGCATGG 58.455 52.381 0.00 0.00 0.00 3.66
1099 2769 1.557099 TGACGAGGTTAGAGCATGGT 58.443 50.000 0.00 0.00 0.00 3.55
1100 2770 1.899814 TGACGAGGTTAGAGCATGGTT 59.100 47.619 0.00 0.00 0.00 3.67
1101 2771 3.093814 TGACGAGGTTAGAGCATGGTTA 58.906 45.455 0.00 0.00 0.00 2.85
1102 2772 3.512329 TGACGAGGTTAGAGCATGGTTAA 59.488 43.478 0.00 0.00 0.00 2.01
1103 2773 4.161565 TGACGAGGTTAGAGCATGGTTAAT 59.838 41.667 0.00 0.00 0.00 1.40
1104 2774 4.442706 ACGAGGTTAGAGCATGGTTAATG 58.557 43.478 0.00 0.00 39.49 1.90
1105 2775 3.809832 CGAGGTTAGAGCATGGTTAATGG 59.190 47.826 0.00 0.00 36.71 3.16
1107 2777 5.452776 CGAGGTTAGAGCATGGTTAATGGTA 60.453 44.000 0.00 0.00 46.95 3.25
1108 2778 6.515512 AGGTTAGAGCATGGTTAATGGTAT 57.484 37.500 0.00 0.00 46.95 2.73
1109 2779 7.524863 CGAGGTTAGAGCATGGTTAATGGTATA 60.525 40.741 0.00 0.00 46.95 1.47
1110 2780 7.680730 AGGTTAGAGCATGGTTAATGGTATAG 58.319 38.462 0.00 0.00 46.95 1.31
1111 2781 6.371825 GGTTAGAGCATGGTTAATGGTATAGC 59.628 42.308 0.00 0.00 46.95 2.97
1112 2782 4.911390 AGAGCATGGTTAATGGTATAGCC 58.089 43.478 0.00 0.00 46.95 3.93
1144 2814 6.917217 GCTATAAGCCATTGTCCTATCATC 57.083 41.667 0.00 0.00 34.48 2.92
1145 2815 6.648192 GCTATAAGCCATTGTCCTATCATCT 58.352 40.000 0.00 0.00 34.48 2.90
1146 2816 7.786030 GCTATAAGCCATTGTCCTATCATCTA 58.214 38.462 0.00 0.00 34.48 1.98
1147 2817 8.428063 GCTATAAGCCATTGTCCTATCATCTAT 58.572 37.037 0.00 0.00 34.48 1.98
1150 2820 6.232581 AGCCATTGTCCTATCATCTATAGC 57.767 41.667 0.00 0.00 36.92 2.97
1151 2821 5.130145 AGCCATTGTCCTATCATCTATAGCC 59.870 44.000 0.00 0.00 36.92 3.93
1152 2822 5.686124 GCCATTGTCCTATCATCTATAGCCC 60.686 48.000 0.00 0.00 36.92 5.19
1153 2823 5.426509 CCATTGTCCTATCATCTATAGCCCA 59.573 44.000 0.00 0.00 36.92 5.36
1154 2824 6.100859 CCATTGTCCTATCATCTATAGCCCAT 59.899 42.308 0.00 0.00 36.92 4.00
1155 2825 6.798427 TTGTCCTATCATCTATAGCCCATC 57.202 41.667 0.00 0.00 36.92 3.51
1156 2826 6.097439 TGTCCTATCATCTATAGCCCATCT 57.903 41.667 0.00 0.00 36.92 2.90
1157 2827 6.506661 TGTCCTATCATCTATAGCCCATCTT 58.493 40.000 0.00 0.00 36.92 2.40
1158 2828 7.652554 TGTCCTATCATCTATAGCCCATCTTA 58.347 38.462 0.00 0.00 36.92 2.10
1159 2829 8.292480 TGTCCTATCATCTATAGCCCATCTTAT 58.708 37.037 0.00 0.00 36.92 1.73
1160 2830 9.815306 GTCCTATCATCTATAGCCCATCTTATA 57.185 37.037 0.00 0.00 36.92 0.98
1162 2832 8.748412 CCTATCATCTATAGCCCATCTTATAGC 58.252 40.741 0.00 0.00 36.92 2.97
1163 2833 6.985653 TCATCTATAGCCCATCTTATAGCC 57.014 41.667 0.00 0.00 0.00 3.93
1164 2834 6.443832 TCATCTATAGCCCATCTTATAGCCA 58.556 40.000 0.00 0.00 0.00 4.75
1165 2835 6.902974 TCATCTATAGCCCATCTTATAGCCAA 59.097 38.462 0.00 0.00 0.00 4.52
1166 2836 7.570232 TCATCTATAGCCCATCTTATAGCCAAT 59.430 37.037 0.00 0.00 0.00 3.16
1167 2837 8.874156 CATCTATAGCCCATCTTATAGCCAATA 58.126 37.037 0.00 0.00 0.00 1.90
1168 2838 9.626840 ATCTATAGCCCATCTTATAGCCAATAT 57.373 33.333 0.00 0.00 0.00 1.28
1169 2839 8.874156 TCTATAGCCCATCTTATAGCCAATATG 58.126 37.037 0.00 0.00 0.00 1.78
1170 2840 5.786121 AGCCCATCTTATAGCCAATATGT 57.214 39.130 0.00 0.00 0.00 2.29
1171 2841 6.891306 AGCCCATCTTATAGCCAATATGTA 57.109 37.500 0.00 0.00 0.00 2.29
1172 2842 6.653989 AGCCCATCTTATAGCCAATATGTAC 58.346 40.000 0.00 0.00 0.00 2.90
1173 2843 6.215431 AGCCCATCTTATAGCCAATATGTACA 59.785 38.462 0.00 0.00 0.00 2.90
1174 2844 6.884295 GCCCATCTTATAGCCAATATGTACAA 59.116 38.462 0.00 0.00 0.00 2.41
1175 2845 7.557719 GCCCATCTTATAGCCAATATGTACAAT 59.442 37.037 0.00 0.00 0.00 2.71
1220 2890 9.762381 TTTTTATTATATGACCCACCTTTCACT 57.238 29.630 0.00 0.00 0.00 3.41
1221 2891 8.974060 TTTATTATATGACCCACCTTTCACTC 57.026 34.615 0.00 0.00 0.00 3.51
1222 2892 6.831664 ATTATATGACCCACCTTTCACTCT 57.168 37.500 0.00 0.00 0.00 3.24
1223 2893 4.762289 ATATGACCCACCTTTCACTCTC 57.238 45.455 0.00 0.00 0.00 3.20
1224 2894 1.801242 TGACCCACCTTTCACTCTCA 58.199 50.000 0.00 0.00 0.00 3.27
1225 2895 1.416401 TGACCCACCTTTCACTCTCAC 59.584 52.381 0.00 0.00 0.00 3.51
1226 2896 1.416401 GACCCACCTTTCACTCTCACA 59.584 52.381 0.00 0.00 0.00 3.58
1227 2897 1.843851 ACCCACCTTTCACTCTCACAA 59.156 47.619 0.00 0.00 0.00 3.33
1228 2898 2.241176 ACCCACCTTTCACTCTCACAAA 59.759 45.455 0.00 0.00 0.00 2.83
1229 2899 2.880890 CCCACCTTTCACTCTCACAAAG 59.119 50.000 0.00 0.00 0.00 2.77
1230 2900 3.545703 CCACCTTTCACTCTCACAAAGT 58.454 45.455 0.00 0.00 0.00 2.66
1231 2901 3.313526 CCACCTTTCACTCTCACAAAGTG 59.686 47.826 0.00 0.00 44.43 3.16
1232 2902 2.945668 ACCTTTCACTCTCACAAAGTGC 59.054 45.455 0.00 0.00 43.09 4.40
1233 2903 2.291741 CCTTTCACTCTCACAAAGTGCC 59.708 50.000 0.00 0.00 43.09 5.01
1234 2904 3.209410 CTTTCACTCTCACAAAGTGCCT 58.791 45.455 0.00 0.00 43.09 4.75
1235 2905 4.380531 CTTTCACTCTCACAAAGTGCCTA 58.619 43.478 0.00 0.00 43.09 3.93
1236 2906 3.667497 TCACTCTCACAAAGTGCCTAG 57.333 47.619 0.00 0.00 43.09 3.02
1237 2907 2.300152 TCACTCTCACAAAGTGCCTAGG 59.700 50.000 3.67 3.67 43.09 3.02
1238 2908 2.300152 CACTCTCACAAAGTGCCTAGGA 59.700 50.000 14.75 0.00 37.88 2.94
1239 2909 2.564947 ACTCTCACAAAGTGCCTAGGAG 59.435 50.000 14.75 0.00 32.98 3.69
1240 2910 1.276421 TCTCACAAAGTGCCTAGGAGC 59.724 52.381 14.75 3.68 32.98 4.70
1241 2911 1.002430 CTCACAAAGTGCCTAGGAGCA 59.998 52.381 14.75 0.22 41.46 4.26
1257 2927 2.575993 CACGTGCTAGAGCTGGCT 59.424 61.111 0.82 0.00 42.66 4.75
1258 2928 1.518133 CACGTGCTAGAGCTGGCTC 60.518 63.158 14.02 14.02 42.66 4.70
1268 2938 2.687700 GAGCTGGCTCTTCATCAAGA 57.312 50.000 14.51 0.00 39.80 3.02
1274 2944 4.941609 TCTTCATCAAGAGCCCGC 57.058 55.556 0.00 0.00 33.38 6.13
1275 2945 2.290847 TCTTCATCAAGAGCCCGCT 58.709 52.632 0.00 0.00 33.38 5.52
1276 2946 0.615331 TCTTCATCAAGAGCCCGCTT 59.385 50.000 0.00 0.00 33.38 4.68
1277 2947 1.831106 TCTTCATCAAGAGCCCGCTTA 59.169 47.619 0.00 0.00 33.38 3.09
1278 2948 1.936547 CTTCATCAAGAGCCCGCTTAC 59.063 52.381 0.00 0.00 0.00 2.34
1279 2949 0.178068 TCATCAAGAGCCCGCTTACC 59.822 55.000 0.00 0.00 0.00 2.85
1280 2950 0.179000 CATCAAGAGCCCGCTTACCT 59.821 55.000 0.00 0.00 0.00 3.08
1281 2951 0.912486 ATCAAGAGCCCGCTTACCTT 59.088 50.000 0.00 0.00 0.00 3.50
1282 2952 0.249398 TCAAGAGCCCGCTTACCTTC 59.751 55.000 0.00 0.00 0.00 3.46
1283 2953 0.250513 CAAGAGCCCGCTTACCTTCT 59.749 55.000 0.00 0.00 0.00 2.85
1284 2954 0.537653 AAGAGCCCGCTTACCTTCTC 59.462 55.000 0.00 0.00 0.00 2.87
1285 2955 0.324830 AGAGCCCGCTTACCTTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
1286 2956 0.103390 GAGCCCGCTTACCTTCTCTC 59.897 60.000 0.00 0.00 0.00 3.20
1287 2957 0.324830 AGCCCGCTTACCTTCTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
1288 2958 0.537653 GCCCGCTTACCTTCTCTCTT 59.462 55.000 0.00 0.00 0.00 2.85
1289 2959 1.471851 GCCCGCTTACCTTCTCTCTTC 60.472 57.143 0.00 0.00 0.00 2.87
1290 2960 2.104170 CCCGCTTACCTTCTCTCTTCT 58.896 52.381 0.00 0.00 0.00 2.85
1291 2961 2.100087 CCCGCTTACCTTCTCTCTTCTC 59.900 54.545 0.00 0.00 0.00 2.87
1292 2962 3.020984 CCGCTTACCTTCTCTCTTCTCT 58.979 50.000 0.00 0.00 0.00 3.10
1293 2963 3.445805 CCGCTTACCTTCTCTCTTCTCTT 59.554 47.826 0.00 0.00 0.00 2.85
1294 2964 4.081917 CCGCTTACCTTCTCTCTTCTCTTT 60.082 45.833 0.00 0.00 0.00 2.52
1295 2965 5.474825 CGCTTACCTTCTCTCTTCTCTTTT 58.525 41.667 0.00 0.00 0.00 2.27
1296 2966 5.575218 CGCTTACCTTCTCTCTTCTCTTTTC 59.425 44.000 0.00 0.00 0.00 2.29
1297 2967 6.571537 CGCTTACCTTCTCTCTTCTCTTTTCT 60.572 42.308 0.00 0.00 0.00 2.52
1298 2968 7.158697 GCTTACCTTCTCTCTTCTCTTTTCTT 58.841 38.462 0.00 0.00 0.00 2.52
1299 2969 7.659799 GCTTACCTTCTCTCTTCTCTTTTCTTT 59.340 37.037 0.00 0.00 0.00 2.52
1300 2970 9.203421 CTTACCTTCTCTCTTCTCTTTTCTTTC 57.797 37.037 0.00 0.00 0.00 2.62
1301 2971 6.530120 ACCTTCTCTCTTCTCTTTTCTTTCC 58.470 40.000 0.00 0.00 0.00 3.13
1302 2972 6.328934 ACCTTCTCTCTTCTCTTTTCTTTCCT 59.671 38.462 0.00 0.00 0.00 3.36
1303 2973 6.873605 CCTTCTCTCTTCTCTTTTCTTTCCTC 59.126 42.308 0.00 0.00 0.00 3.71
1304 2974 6.353404 TCTCTCTTCTCTTTTCTTTCCTCC 57.647 41.667 0.00 0.00 0.00 4.30
1305 2975 5.841237 TCTCTCTTCTCTTTTCTTTCCTCCA 59.159 40.000 0.00 0.00 0.00 3.86
1306 2976 6.327626 TCTCTCTTCTCTTTTCTTTCCTCCAA 59.672 38.462 0.00 0.00 0.00 3.53
1307 2977 6.292150 TCTCTTCTCTTTTCTTTCCTCCAAC 58.708 40.000 0.00 0.00 0.00 3.77
1308 2978 6.100424 TCTCTTCTCTTTTCTTTCCTCCAACT 59.900 38.462 0.00 0.00 0.00 3.16
1309 2979 7.290248 TCTCTTCTCTTTTCTTTCCTCCAACTA 59.710 37.037 0.00 0.00 0.00 2.24
1310 2980 7.802117 TCTTCTCTTTTCTTTCCTCCAACTAA 58.198 34.615 0.00 0.00 0.00 2.24
1311 2981 7.934120 TCTTCTCTTTTCTTTCCTCCAACTAAG 59.066 37.037 0.00 0.00 0.00 2.18
1312 2982 7.138054 TCTCTTTTCTTTCCTCCAACTAAGT 57.862 36.000 0.00 0.00 0.00 2.24
1313 2983 8.258850 TCTCTTTTCTTTCCTCCAACTAAGTA 57.741 34.615 0.00 0.00 0.00 2.24
1314 2984 8.711170 TCTCTTTTCTTTCCTCCAACTAAGTAA 58.289 33.333 0.00 0.00 0.00 2.24
1315 2985 8.904099 TCTTTTCTTTCCTCCAACTAAGTAAG 57.096 34.615 0.00 0.00 0.00 2.34
1316 2986 8.711170 TCTTTTCTTTCCTCCAACTAAGTAAGA 58.289 33.333 0.00 0.00 0.00 2.10
1317 2987 9.338622 CTTTTCTTTCCTCCAACTAAGTAAGAA 57.661 33.333 0.00 0.00 0.00 2.52
1318 2988 9.862149 TTTTCTTTCCTCCAACTAAGTAAGAAT 57.138 29.630 0.00 0.00 32.40 2.40
1346 3016 8.894768 ACTAGTTTATTTCTTATAGCCAGCTG 57.105 34.615 6.78 6.78 0.00 4.24
1347 3017 8.705594 ACTAGTTTATTTCTTATAGCCAGCTGA 58.294 33.333 17.39 0.00 0.00 4.26
1348 3018 7.793927 AGTTTATTTCTTATAGCCAGCTGAC 57.206 36.000 17.39 2.52 0.00 3.51
1349 3019 7.569240 AGTTTATTTCTTATAGCCAGCTGACT 58.431 34.615 17.39 12.46 0.00 3.41
1350 3020 7.713073 AGTTTATTTCTTATAGCCAGCTGACTC 59.287 37.037 17.39 3.75 0.00 3.36
1351 3021 5.885449 ATTTCTTATAGCCAGCTGACTCT 57.115 39.130 17.39 11.53 0.00 3.24
1352 3022 4.662468 TTCTTATAGCCAGCTGACTCTG 57.338 45.455 17.39 0.00 0.00 3.35
1353 3023 2.363680 TCTTATAGCCAGCTGACTCTGC 59.636 50.000 17.39 9.76 32.87 4.26
1354 3024 2.079170 TATAGCCAGCTGACTCTGCT 57.921 50.000 17.39 17.09 39.15 4.24
1355 3025 0.752054 ATAGCCAGCTGACTCTGCTC 59.248 55.000 17.39 0.00 36.55 4.26
1356 3026 0.324183 TAGCCAGCTGACTCTGCTCT 60.324 55.000 17.39 6.04 36.55 4.09
1357 3027 0.324183 AGCCAGCTGACTCTGCTCTA 60.324 55.000 17.39 0.00 36.55 2.43
1358 3028 0.752054 GCCAGCTGACTCTGCTCTAT 59.248 55.000 17.39 0.00 36.55 1.98
1359 3029 1.138661 GCCAGCTGACTCTGCTCTATT 59.861 52.381 17.39 0.00 36.55 1.73
1360 3030 2.823984 CCAGCTGACTCTGCTCTATTG 58.176 52.381 17.39 0.00 36.55 1.90
1361 3031 2.168106 CCAGCTGACTCTGCTCTATTGT 59.832 50.000 17.39 0.00 36.55 2.71
1362 3032 3.382865 CCAGCTGACTCTGCTCTATTGTA 59.617 47.826 17.39 0.00 36.55 2.41
1363 3033 4.358851 CAGCTGACTCTGCTCTATTGTAC 58.641 47.826 8.42 0.00 36.55 2.90
1364 3034 4.097741 CAGCTGACTCTGCTCTATTGTACT 59.902 45.833 8.42 0.00 36.55 2.73
1365 3035 4.709397 AGCTGACTCTGCTCTATTGTACTT 59.291 41.667 4.65 0.00 33.52 2.24
1366 3036 4.803088 GCTGACTCTGCTCTATTGTACTTG 59.197 45.833 0.80 0.00 0.00 3.16
1367 3037 4.748892 TGACTCTGCTCTATTGTACTTGC 58.251 43.478 0.00 0.00 0.00 4.01
1368 3038 4.464244 TGACTCTGCTCTATTGTACTTGCT 59.536 41.667 0.00 0.00 0.00 3.91
1369 3039 5.004922 ACTCTGCTCTATTGTACTTGCTC 57.995 43.478 0.00 0.00 0.00 4.26
1370 3040 4.709397 ACTCTGCTCTATTGTACTTGCTCT 59.291 41.667 0.00 0.00 0.00 4.09
1371 3041 5.186797 ACTCTGCTCTATTGTACTTGCTCTT 59.813 40.000 0.00 0.00 0.00 2.85
1372 3042 6.378564 ACTCTGCTCTATTGTACTTGCTCTTA 59.621 38.462 0.00 0.00 0.00 2.10
1373 3043 6.800543 TCTGCTCTATTGTACTTGCTCTTAG 58.199 40.000 0.00 0.00 0.00 2.18
1374 3044 6.603599 TCTGCTCTATTGTACTTGCTCTTAGA 59.396 38.462 0.00 0.00 0.00 2.10
1375 3045 7.286546 TCTGCTCTATTGTACTTGCTCTTAGAT 59.713 37.037 0.00 0.00 0.00 1.98
1376 3046 7.786030 TGCTCTATTGTACTTGCTCTTAGATT 58.214 34.615 0.00 0.00 0.00 2.40
1377 3047 7.708322 TGCTCTATTGTACTTGCTCTTAGATTG 59.292 37.037 0.00 0.00 0.00 2.67
1378 3048 7.170658 GCTCTATTGTACTTGCTCTTAGATTGG 59.829 40.741 0.00 0.00 0.00 3.16
1379 3049 8.306313 TCTATTGTACTTGCTCTTAGATTGGA 57.694 34.615 0.00 0.00 0.00 3.53
1380 3050 8.417106 TCTATTGTACTTGCTCTTAGATTGGAG 58.583 37.037 0.00 0.00 0.00 3.86
1397 3067 0.179936 GAGCTTGGGAGGATGTGGAG 59.820 60.000 0.00 0.00 0.00 3.86
1436 3106 0.905357 CCAAACTGGGAGAGGTCGAT 59.095 55.000 0.00 0.00 32.67 3.59
1440 3110 0.039764 ACTGGGAGAGGTCGATGTCA 59.960 55.000 0.00 0.00 0.00 3.58
1446 3116 3.356639 GAGGTCGATGTCAGGCGCA 62.357 63.158 10.83 0.00 0.00 6.09
1459 3129 2.894387 GCGCATCCTGTCTGAGGC 60.894 66.667 0.30 0.00 42.47 4.70
1471 3343 0.175760 TCTGAGGCGACTGGCAATAC 59.824 55.000 0.00 0.00 46.16 1.89
1476 3348 2.461110 GCGACTGGCAATACCACCG 61.461 63.158 0.00 0.00 46.36 4.94
1477 3349 1.079405 CGACTGGCAATACCACCGT 60.079 57.895 0.00 0.00 46.36 4.83
1496 3369 9.036671 ACCACCGTAAAGTTTGAAATAAATTTG 57.963 29.630 0.00 0.00 0.00 2.32
1530 3403 5.179452 AGCACAGGTGTAAATTGTAGGAT 57.821 39.130 0.91 0.00 0.00 3.24
1533 3406 7.172342 AGCACAGGTGTAAATTGTAGGATTTA 58.828 34.615 0.91 0.00 31.96 1.40
1572 3445 1.519408 CACCACAAGGAACCTAACCG 58.481 55.000 0.00 0.00 38.69 4.44
1583 3456 5.574188 AGGAACCTAACCGTCTAAGTTAGA 58.426 41.667 8.59 8.59 46.31 2.10
1598 3471 7.883217 TCTAAGTTAGACTCAGTTTGTGGTAG 58.117 38.462 8.59 0.00 0.00 3.18
1717 3595 5.335661 CGAAACTTACCTGGCAAGCTAAATT 60.336 40.000 6.58 0.00 0.00 1.82
1722 3600 2.965147 ACCTGGCAAGCTAAATTTGTGT 59.035 40.909 0.00 0.00 0.00 3.72
1723 3601 3.243839 ACCTGGCAAGCTAAATTTGTGTG 60.244 43.478 0.00 0.00 0.00 3.82
1757 3953 3.132289 ACTTGCTGCTAGGCTAAATCGTA 59.868 43.478 15.18 0.00 0.00 3.43
1802 3999 4.009675 GGTGGTTGCACATTGAGATTCTA 58.990 43.478 0.00 0.00 0.00 2.10
1811 4033 9.985730 TTGCACATTGAGATTCTATTTTCTTTT 57.014 25.926 0.00 0.00 0.00 2.27
1812 4034 9.630098 TGCACATTGAGATTCTATTTTCTTTTC 57.370 29.630 0.00 0.00 0.00 2.29
1813 4035 9.852091 GCACATTGAGATTCTATTTTCTTTTCT 57.148 29.630 0.00 0.00 0.00 2.52
1832 4054 9.927668 TCTTTTCTTCAATGGTCATAAAAATCC 57.072 29.630 0.00 0.00 0.00 3.01
1833 4055 9.933723 CTTTTCTTCAATGGTCATAAAAATCCT 57.066 29.630 0.00 0.00 0.00 3.24
1839 4061 8.519799 TCAATGGTCATAAAAATCCTTAGTCC 57.480 34.615 0.00 0.00 0.00 3.85
2106 4368 1.280998 CCATCGGGGGTCTACTTTTGT 59.719 52.381 0.00 0.00 0.00 2.83
2107 4369 2.502538 CCATCGGGGGTCTACTTTTGTA 59.497 50.000 0.00 0.00 0.00 2.41
2108 4370 3.528532 CATCGGGGGTCTACTTTTGTAC 58.471 50.000 0.00 0.00 0.00 2.90
2175 4441 0.585357 GCTGCATGATGTCATCGGAC 59.415 55.000 8.29 0.75 44.57 4.79
2176 4442 1.224075 CTGCATGATGTCATCGGACC 58.776 55.000 8.29 0.00 43.65 4.46
2195 4461 1.202348 CCGGATCAAAAGGGTTTCTGC 59.798 52.381 0.00 0.00 0.00 4.26
2196 4462 1.135689 CGGATCAAAAGGGTTTCTGCG 60.136 52.381 0.00 0.00 0.00 5.18
2249 4515 7.494211 ACGTGTATAGCATTAGTTCCATGTAA 58.506 34.615 0.00 0.00 0.00 2.41
2317 4585 4.256920 AGCCTGAGATTTGTGTACATGAC 58.743 43.478 0.00 0.00 0.00 3.06
2420 4702 1.518572 CTTAGGCGCCACCACGTAG 60.519 63.158 31.54 10.40 43.14 3.51
2421 4703 1.940883 CTTAGGCGCCACCACGTAGA 61.941 60.000 31.54 1.89 43.14 2.59
2422 4704 1.534336 TTAGGCGCCACCACGTAGAA 61.534 55.000 31.54 4.98 43.14 2.10
2484 4770 2.801699 GCTTTGTTTGCCCACCAAGTAC 60.802 50.000 0.00 0.00 34.34 2.73
2508 4794 1.860078 GTGGCGTCTTCAGTTTCCG 59.140 57.895 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 203 1.078285 TTGCTCGGCTCATGCATGA 60.078 52.632 27.10 27.10 41.91 3.07
624 2081 8.045507 TCTACAATCAGCAGAGAATGAGAAAAT 58.954 33.333 0.00 0.00 0.00 1.82
625 2082 7.389232 TCTACAATCAGCAGAGAATGAGAAAA 58.611 34.615 0.00 0.00 0.00 2.29
629 2086 5.177881 GCATCTACAATCAGCAGAGAATGAG 59.822 44.000 0.00 0.00 0.00 2.90
630 2087 5.055144 GCATCTACAATCAGCAGAGAATGA 58.945 41.667 0.00 0.00 0.00 2.57
631 2088 4.213694 GGCATCTACAATCAGCAGAGAATG 59.786 45.833 0.00 0.00 0.00 2.67
741 2371 0.606604 GAGTTCCCTGCCGTAGTCAA 59.393 55.000 0.00 0.00 0.00 3.18
765 2395 3.581687 GATCTGAGCCCGGCCGATC 62.582 68.421 30.73 21.44 0.00 3.69
811 2441 1.069358 CGAGGAGGGAATAGAACAGGC 59.931 57.143 0.00 0.00 0.00 4.85
861 2501 2.203788 AAGAGGAGCACCGGGTCA 60.204 61.111 6.32 0.00 43.32 4.02
898 2538 1.745087 TCAATTGATTTGAGCTCCGCC 59.255 47.619 12.15 0.00 39.44 6.13
994 2660 4.273318 GCTACTCCTCCATCCATGTTTTT 58.727 43.478 0.00 0.00 0.00 1.94
1000 2666 0.833834 CCCGCTACTCCTCCATCCAT 60.834 60.000 0.00 0.00 0.00 3.41
1013 2682 4.124351 CGTCGAGGTTGCCCGCTA 62.124 66.667 0.00 0.00 35.12 4.26
1031 2700 3.319198 GCCCTCCAACTCCACGGA 61.319 66.667 0.00 0.00 0.00 4.69
1052 2722 1.030488 TACTCCTTCGACCGCCTCAG 61.030 60.000 0.00 0.00 0.00 3.35
1083 2753 3.809832 CCATTAACCATGCTCTAACCTCG 59.190 47.826 0.00 0.00 0.00 4.63
1121 2791 6.648192 AGATGATAGGACAATGGCTTATAGC 58.352 40.000 0.00 0.00 41.46 2.97
1124 2794 8.428063 GCTATAGATGATAGGACAATGGCTTAT 58.572 37.037 3.21 0.00 38.43 1.73
1125 2795 7.147655 GGCTATAGATGATAGGACAATGGCTTA 60.148 40.741 3.21 0.00 38.43 3.09
1126 2796 6.352565 GGCTATAGATGATAGGACAATGGCTT 60.353 42.308 3.21 0.00 38.43 4.35
1127 2797 5.130145 GGCTATAGATGATAGGACAATGGCT 59.870 44.000 3.21 0.00 38.43 4.75
1128 2798 5.363939 GGCTATAGATGATAGGACAATGGC 58.636 45.833 3.21 0.00 38.43 4.40
1129 2799 5.426509 TGGGCTATAGATGATAGGACAATGG 59.573 44.000 3.21 0.00 38.43 3.16
1130 2800 6.550938 TGGGCTATAGATGATAGGACAATG 57.449 41.667 3.21 0.00 38.43 2.82
1131 2801 7.138250 AGATGGGCTATAGATGATAGGACAAT 58.862 38.462 3.21 0.00 38.43 2.71
1132 2802 6.506661 AGATGGGCTATAGATGATAGGACAA 58.493 40.000 3.21 0.00 38.43 3.18
1133 2803 6.097439 AGATGGGCTATAGATGATAGGACA 57.903 41.667 3.21 0.00 38.43 4.02
1134 2804 8.719645 ATAAGATGGGCTATAGATGATAGGAC 57.280 38.462 3.21 0.00 38.43 3.85
1136 2806 8.748412 GCTATAAGATGGGCTATAGATGATAGG 58.252 40.741 3.21 0.00 38.43 2.57
1137 2807 8.748412 GGCTATAAGATGGGCTATAGATGATAG 58.252 40.741 3.21 0.46 40.65 2.08
1138 2808 8.234525 TGGCTATAAGATGGGCTATAGATGATA 58.765 37.037 3.21 0.00 37.22 2.15
1139 2809 7.078396 TGGCTATAAGATGGGCTATAGATGAT 58.922 38.462 3.21 0.00 37.22 2.45
1140 2810 6.443832 TGGCTATAAGATGGGCTATAGATGA 58.556 40.000 3.21 0.00 37.22 2.92
1141 2811 6.737720 TGGCTATAAGATGGGCTATAGATG 57.262 41.667 3.21 0.00 37.22 2.90
1142 2812 7.944414 ATTGGCTATAAGATGGGCTATAGAT 57.056 36.000 3.21 0.00 37.22 1.98
1143 2813 8.874156 CATATTGGCTATAAGATGGGCTATAGA 58.126 37.037 3.21 0.00 37.41 1.98
1144 2814 8.654997 ACATATTGGCTATAAGATGGGCTATAG 58.345 37.037 0.00 0.00 37.41 1.31
1145 2815 8.567198 ACATATTGGCTATAAGATGGGCTATA 57.433 34.615 0.00 3.91 38.02 1.31
1146 2816 7.457380 ACATATTGGCTATAAGATGGGCTAT 57.543 36.000 0.00 0.00 34.46 2.97
1147 2817 6.891306 ACATATTGGCTATAAGATGGGCTA 57.109 37.500 0.00 0.00 34.46 3.93
1148 2818 5.786121 ACATATTGGCTATAAGATGGGCT 57.214 39.130 0.00 0.00 34.46 5.19
1149 2819 6.414732 TGTACATATTGGCTATAAGATGGGC 58.585 40.000 0.00 0.00 34.46 5.36
1194 2864 9.762381 AGTGAAAGGTGGGTCATATAATAAAAA 57.238 29.630 0.00 0.00 0.00 1.94
1195 2865 9.403583 GAGTGAAAGGTGGGTCATATAATAAAA 57.596 33.333 0.00 0.00 0.00 1.52
1196 2866 8.778059 AGAGTGAAAGGTGGGTCATATAATAAA 58.222 33.333 0.00 0.00 0.00 1.40
1197 2867 8.331931 AGAGTGAAAGGTGGGTCATATAATAA 57.668 34.615 0.00 0.00 0.00 1.40
1198 2868 7.567250 TGAGAGTGAAAGGTGGGTCATATAATA 59.433 37.037 0.00 0.00 0.00 0.98
1199 2869 6.386927 TGAGAGTGAAAGGTGGGTCATATAAT 59.613 38.462 0.00 0.00 0.00 1.28
1200 2870 5.724370 TGAGAGTGAAAGGTGGGTCATATAA 59.276 40.000 0.00 0.00 0.00 0.98
1201 2871 5.128827 GTGAGAGTGAAAGGTGGGTCATATA 59.871 44.000 0.00 0.00 0.00 0.86
1202 2872 4.080863 GTGAGAGTGAAAGGTGGGTCATAT 60.081 45.833 0.00 0.00 0.00 1.78
1203 2873 3.260884 GTGAGAGTGAAAGGTGGGTCATA 59.739 47.826 0.00 0.00 0.00 2.15
1204 2874 2.039084 GTGAGAGTGAAAGGTGGGTCAT 59.961 50.000 0.00 0.00 0.00 3.06
1205 2875 1.416401 GTGAGAGTGAAAGGTGGGTCA 59.584 52.381 0.00 0.00 0.00 4.02
1206 2876 1.416401 TGTGAGAGTGAAAGGTGGGTC 59.584 52.381 0.00 0.00 0.00 4.46
1207 2877 1.507140 TGTGAGAGTGAAAGGTGGGT 58.493 50.000 0.00 0.00 0.00 4.51
1208 2878 2.638480 TTGTGAGAGTGAAAGGTGGG 57.362 50.000 0.00 0.00 0.00 4.61
1209 2879 3.313526 CACTTTGTGAGAGTGAAAGGTGG 59.686 47.826 0.00 0.00 45.72 4.61
1210 2880 3.242870 GCACTTTGTGAGAGTGAAAGGTG 60.243 47.826 8.33 0.00 45.72 4.00
1211 2881 2.945668 GCACTTTGTGAGAGTGAAAGGT 59.054 45.455 8.33 0.00 45.72 3.50
1212 2882 2.291741 GGCACTTTGTGAGAGTGAAAGG 59.708 50.000 8.33 0.00 45.72 3.11
1213 2883 3.209410 AGGCACTTTGTGAGAGTGAAAG 58.791 45.455 8.33 0.00 45.72 2.62
1214 2884 3.281727 AGGCACTTTGTGAGAGTGAAA 57.718 42.857 8.33 0.00 45.72 2.69
1215 2885 3.244215 CCTAGGCACTTTGTGAGAGTGAA 60.244 47.826 8.33 0.00 45.72 3.18
1216 2886 2.300152 CCTAGGCACTTTGTGAGAGTGA 59.700 50.000 8.33 0.00 45.72 3.41
1217 2887 2.300152 TCCTAGGCACTTTGTGAGAGTG 59.700 50.000 2.96 0.10 45.64 3.51
1218 2888 2.564947 CTCCTAGGCACTTTGTGAGAGT 59.435 50.000 2.96 0.00 41.75 3.24
1219 2889 2.676463 GCTCCTAGGCACTTTGTGAGAG 60.676 54.545 2.96 0.00 41.75 3.20
1220 2890 1.276421 GCTCCTAGGCACTTTGTGAGA 59.724 52.381 2.96 0.00 41.75 3.27
1221 2891 1.002430 TGCTCCTAGGCACTTTGTGAG 59.998 52.381 2.96 0.00 41.75 3.51
1222 2892 1.055849 TGCTCCTAGGCACTTTGTGA 58.944 50.000 2.96 0.00 41.75 3.58
1223 2893 3.631453 TGCTCCTAGGCACTTTGTG 57.369 52.632 2.96 0.00 41.75 3.33
1239 2909 3.191539 GCCAGCTCTAGCACGTGC 61.192 66.667 32.79 32.79 45.16 5.34
1240 2910 1.518133 GAGCCAGCTCTAGCACGTG 60.518 63.158 12.28 12.28 45.16 4.49
1241 2911 2.888863 GAGCCAGCTCTAGCACGT 59.111 61.111 12.42 0.00 45.16 4.49
1257 2927 0.615331 AAGCGGGCTCTTGATGAAGA 59.385 50.000 0.00 0.00 36.72 2.87
1258 2928 1.936547 GTAAGCGGGCTCTTGATGAAG 59.063 52.381 0.00 0.00 0.00 3.02
1259 2929 1.406887 GGTAAGCGGGCTCTTGATGAA 60.407 52.381 0.00 0.00 0.00 2.57
1260 2930 0.178068 GGTAAGCGGGCTCTTGATGA 59.822 55.000 0.00 0.00 0.00 2.92
1261 2931 0.179000 AGGTAAGCGGGCTCTTGATG 59.821 55.000 0.00 0.00 0.00 3.07
1262 2932 0.912486 AAGGTAAGCGGGCTCTTGAT 59.088 50.000 0.00 0.00 0.00 2.57
1263 2933 0.249398 GAAGGTAAGCGGGCTCTTGA 59.751 55.000 0.00 0.00 0.00 3.02
1264 2934 0.250513 AGAAGGTAAGCGGGCTCTTG 59.749 55.000 0.00 0.00 0.00 3.02
1265 2935 0.537653 GAGAAGGTAAGCGGGCTCTT 59.462 55.000 0.00 0.00 0.00 2.85
1266 2936 0.324830 AGAGAAGGTAAGCGGGCTCT 60.325 55.000 0.00 0.00 0.00 4.09
1267 2937 0.103390 GAGAGAAGGTAAGCGGGCTC 59.897 60.000 0.00 0.00 0.00 4.70
1268 2938 0.324830 AGAGAGAAGGTAAGCGGGCT 60.325 55.000 0.00 0.00 0.00 5.19
1269 2939 0.537653 AAGAGAGAAGGTAAGCGGGC 59.462 55.000 0.00 0.00 0.00 6.13
1270 2940 2.100087 GAGAAGAGAGAAGGTAAGCGGG 59.900 54.545 0.00 0.00 0.00 6.13
1271 2941 3.020984 AGAGAAGAGAGAAGGTAAGCGG 58.979 50.000 0.00 0.00 0.00 5.52
1272 2942 4.712122 AAGAGAAGAGAGAAGGTAAGCG 57.288 45.455 0.00 0.00 0.00 4.68
1273 2943 6.697395 AGAAAAGAGAAGAGAGAAGGTAAGC 58.303 40.000 0.00 0.00 0.00 3.09
1274 2944 9.203421 GAAAGAAAAGAGAAGAGAGAAGGTAAG 57.797 37.037 0.00 0.00 0.00 2.34
1275 2945 8.151596 GGAAAGAAAAGAGAAGAGAGAAGGTAA 58.848 37.037 0.00 0.00 0.00 2.85
1276 2946 7.511028 AGGAAAGAAAAGAGAAGAGAGAAGGTA 59.489 37.037 0.00 0.00 0.00 3.08
1277 2947 6.328934 AGGAAAGAAAAGAGAAGAGAGAAGGT 59.671 38.462 0.00 0.00 0.00 3.50
1278 2948 6.768483 AGGAAAGAAAAGAGAAGAGAGAAGG 58.232 40.000 0.00 0.00 0.00 3.46
1279 2949 6.873605 GGAGGAAAGAAAAGAGAAGAGAGAAG 59.126 42.308 0.00 0.00 0.00 2.85
1280 2950 6.327626 TGGAGGAAAGAAAAGAGAAGAGAGAA 59.672 38.462 0.00 0.00 0.00 2.87
1281 2951 5.841237 TGGAGGAAAGAAAAGAGAAGAGAGA 59.159 40.000 0.00 0.00 0.00 3.10
1282 2952 6.107901 TGGAGGAAAGAAAAGAGAAGAGAG 57.892 41.667 0.00 0.00 0.00 3.20
1283 2953 6.100424 AGTTGGAGGAAAGAAAAGAGAAGAGA 59.900 38.462 0.00 0.00 0.00 3.10
1284 2954 6.295249 AGTTGGAGGAAAGAAAAGAGAAGAG 58.705 40.000 0.00 0.00 0.00 2.85
1285 2955 6.253946 AGTTGGAGGAAAGAAAAGAGAAGA 57.746 37.500 0.00 0.00 0.00 2.87
1286 2956 7.717436 ACTTAGTTGGAGGAAAGAAAAGAGAAG 59.283 37.037 0.00 0.00 0.00 2.85
1287 2957 7.574607 ACTTAGTTGGAGGAAAGAAAAGAGAA 58.425 34.615 0.00 0.00 0.00 2.87
1288 2958 7.138054 ACTTAGTTGGAGGAAAGAAAAGAGA 57.862 36.000 0.00 0.00 0.00 3.10
1289 2959 8.904099 TTACTTAGTTGGAGGAAAGAAAAGAG 57.096 34.615 0.00 0.00 0.00 2.85
1290 2960 8.711170 TCTTACTTAGTTGGAGGAAAGAAAAGA 58.289 33.333 0.00 0.00 0.00 2.52
1291 2961 8.904099 TCTTACTTAGTTGGAGGAAAGAAAAG 57.096 34.615 0.00 0.00 0.00 2.27
1292 2962 9.862149 ATTCTTACTTAGTTGGAGGAAAGAAAA 57.138 29.630 7.88 0.00 35.63 2.29
1320 2990 9.982651 CAGCTGGCTATAAGAAATAAACTAGTA 57.017 33.333 5.57 0.00 0.00 1.82
1321 2991 8.705594 TCAGCTGGCTATAAGAAATAAACTAGT 58.294 33.333 15.13 0.00 0.00 2.57
1322 2992 8.983724 GTCAGCTGGCTATAAGAAATAAACTAG 58.016 37.037 12.09 0.00 0.00 2.57
1323 2993 8.705594 AGTCAGCTGGCTATAAGAAATAAACTA 58.294 33.333 21.80 0.00 0.00 2.24
1324 2994 7.569240 AGTCAGCTGGCTATAAGAAATAAACT 58.431 34.615 21.80 3.19 0.00 2.66
1325 2995 7.713073 AGAGTCAGCTGGCTATAAGAAATAAAC 59.287 37.037 23.29 3.58 0.00 2.01
1326 2996 7.712639 CAGAGTCAGCTGGCTATAAGAAATAAA 59.287 37.037 23.29 0.00 32.26 1.40
1327 2997 7.212976 CAGAGTCAGCTGGCTATAAGAAATAA 58.787 38.462 23.29 0.00 32.26 1.40
1328 2998 6.739843 GCAGAGTCAGCTGGCTATAAGAAATA 60.740 42.308 23.29 0.00 36.41 1.40
1329 2999 5.609423 CAGAGTCAGCTGGCTATAAGAAAT 58.391 41.667 23.29 0.00 32.26 2.17
1330 3000 4.681781 GCAGAGTCAGCTGGCTATAAGAAA 60.682 45.833 23.29 0.00 36.41 2.52
1331 3001 3.181471 GCAGAGTCAGCTGGCTATAAGAA 60.181 47.826 23.29 0.00 36.41 2.52
1332 3002 2.363680 GCAGAGTCAGCTGGCTATAAGA 59.636 50.000 23.29 0.00 36.41 2.10
1333 3003 2.364970 AGCAGAGTCAGCTGGCTATAAG 59.635 50.000 23.29 8.48 41.61 1.73
1334 3004 2.363680 GAGCAGAGTCAGCTGGCTATAA 59.636 50.000 23.29 0.00 43.58 0.98
1335 3005 1.959985 GAGCAGAGTCAGCTGGCTATA 59.040 52.381 23.29 0.00 43.58 1.31
1336 3006 0.752054 GAGCAGAGTCAGCTGGCTAT 59.248 55.000 23.29 16.85 43.58 2.97
1337 3007 0.324183 AGAGCAGAGTCAGCTGGCTA 60.324 55.000 23.29 0.00 43.58 3.93
1338 3008 0.324183 TAGAGCAGAGTCAGCTGGCT 60.324 55.000 23.48 23.48 43.58 4.75
1339 3009 0.752054 ATAGAGCAGAGTCAGCTGGC 59.248 55.000 15.54 11.28 43.58 4.85
1340 3010 2.168106 ACAATAGAGCAGAGTCAGCTGG 59.832 50.000 15.54 0.00 43.58 4.85
1341 3011 3.523606 ACAATAGAGCAGAGTCAGCTG 57.476 47.619 15.54 7.63 43.58 4.24
1342 3012 4.277476 AGTACAATAGAGCAGAGTCAGCT 58.723 43.478 10.16 10.16 46.82 4.24
1343 3013 4.647424 AGTACAATAGAGCAGAGTCAGC 57.353 45.455 0.00 0.00 0.00 4.26
1344 3014 4.803088 GCAAGTACAATAGAGCAGAGTCAG 59.197 45.833 0.00 0.00 0.00 3.51
1345 3015 4.464244 AGCAAGTACAATAGAGCAGAGTCA 59.536 41.667 0.00 0.00 0.00 3.41
1346 3016 5.004922 AGCAAGTACAATAGAGCAGAGTC 57.995 43.478 0.00 0.00 0.00 3.36
1347 3017 4.709397 AGAGCAAGTACAATAGAGCAGAGT 59.291 41.667 0.00 0.00 0.00 3.24
1348 3018 5.261209 AGAGCAAGTACAATAGAGCAGAG 57.739 43.478 0.00 0.00 0.00 3.35
1349 3019 5.667539 AAGAGCAAGTACAATAGAGCAGA 57.332 39.130 0.00 0.00 0.00 4.26
1350 3020 6.800543 TCTAAGAGCAAGTACAATAGAGCAG 58.199 40.000 0.00 0.00 0.00 4.24
1351 3021 6.775594 TCTAAGAGCAAGTACAATAGAGCA 57.224 37.500 0.00 0.00 0.00 4.26
1352 3022 7.170658 CCAATCTAAGAGCAAGTACAATAGAGC 59.829 40.741 0.00 0.00 0.00 4.09
1353 3023 8.417106 TCCAATCTAAGAGCAAGTACAATAGAG 58.583 37.037 0.00 0.00 0.00 2.43
1354 3024 8.306313 TCCAATCTAAGAGCAAGTACAATAGA 57.694 34.615 0.00 0.00 0.00 1.98
1355 3025 8.586570 CTCCAATCTAAGAGCAAGTACAATAG 57.413 38.462 0.00 0.00 0.00 1.73
1367 3037 3.181456 CCTCCCAAGCTCCAATCTAAGAG 60.181 52.174 0.00 0.00 0.00 2.85
1368 3038 2.774234 CCTCCCAAGCTCCAATCTAAGA 59.226 50.000 0.00 0.00 0.00 2.10
1369 3039 2.774234 TCCTCCCAAGCTCCAATCTAAG 59.226 50.000 0.00 0.00 0.00 2.18
1370 3040 2.845659 TCCTCCCAAGCTCCAATCTAA 58.154 47.619 0.00 0.00 0.00 2.10
1371 3041 2.568546 TCCTCCCAAGCTCCAATCTA 57.431 50.000 0.00 0.00 0.00 1.98
1372 3042 1.493871 CATCCTCCCAAGCTCCAATCT 59.506 52.381 0.00 0.00 0.00 2.40
1373 3043 1.213926 ACATCCTCCCAAGCTCCAATC 59.786 52.381 0.00 0.00 0.00 2.67
1374 3044 1.064166 CACATCCTCCCAAGCTCCAAT 60.064 52.381 0.00 0.00 0.00 3.16
1375 3045 0.329261 CACATCCTCCCAAGCTCCAA 59.671 55.000 0.00 0.00 0.00 3.53
1376 3046 1.565390 CCACATCCTCCCAAGCTCCA 61.565 60.000 0.00 0.00 0.00 3.86
1377 3047 1.225704 CCACATCCTCCCAAGCTCC 59.774 63.158 0.00 0.00 0.00 4.70
1378 3048 0.179936 CTCCACATCCTCCCAAGCTC 59.820 60.000 0.00 0.00 0.00 4.09
1379 3049 1.919600 GCTCCACATCCTCCCAAGCT 61.920 60.000 0.00 0.00 0.00 3.74
1380 3050 1.452833 GCTCCACATCCTCCCAAGC 60.453 63.158 0.00 0.00 0.00 4.01
1381 3051 1.415659 CTAGCTCCACATCCTCCCAAG 59.584 57.143 0.00 0.00 0.00 3.61
1382 3052 1.500474 CTAGCTCCACATCCTCCCAA 58.500 55.000 0.00 0.00 0.00 4.12
1383 3053 0.399091 CCTAGCTCCACATCCTCCCA 60.399 60.000 0.00 0.00 0.00 4.37
1384 3054 0.399233 ACCTAGCTCCACATCCTCCC 60.399 60.000 0.00 0.00 0.00 4.30
1397 3067 1.138069 GCTTCTTCCTCTCCACCTAGC 59.862 57.143 0.00 0.00 0.00 3.42
1446 3116 1.326213 CCAGTCGCCTCAGACAGGAT 61.326 60.000 2.92 0.00 46.73 3.24
1471 3343 8.491950 CCAAATTTATTTCAAACTTTACGGTGG 58.508 33.333 0.00 0.00 0.00 4.61
1473 3345 9.819267 TTCCAAATTTATTTCAAACTTTACGGT 57.181 25.926 0.00 0.00 0.00 4.83
1495 3368 3.056678 CACCTGTGCTTGCATATTTTCCA 60.057 43.478 0.00 0.00 0.00 3.53
1496 3369 3.056607 ACACCTGTGCTTGCATATTTTCC 60.057 43.478 0.00 0.00 0.00 3.13
1530 3403 5.993748 GAACCAATCCATCCAGGTTTAAA 57.006 39.130 0.00 0.00 43.94 1.52
1583 3456 8.691661 ATGATAAAAACTACCACAAACTGAGT 57.308 30.769 0.00 0.00 0.00 3.41
1591 3464 7.611467 AGCTTCATGATGATAAAAACTACCACA 59.389 33.333 12.54 0.00 0.00 4.17
1686 3564 4.448210 TGCCAGGTAAGTTTCGGAATATC 58.552 43.478 0.00 0.00 0.00 1.63
1689 3567 2.871096 TGCCAGGTAAGTTTCGGAAT 57.129 45.000 0.00 0.00 0.00 3.01
1693 3571 1.523758 AGCTTGCCAGGTAAGTTTCG 58.476 50.000 17.80 0.00 0.00 3.46
1717 3595 7.639039 CAGCAAGTACTAAAAGAATCACACAA 58.361 34.615 0.00 0.00 0.00 3.33
1722 3600 6.818644 CCTAGCAGCAAGTACTAAAAGAATCA 59.181 38.462 0.00 0.00 0.00 2.57
1723 3601 6.238239 GCCTAGCAGCAAGTACTAAAAGAATC 60.238 42.308 0.00 0.00 0.00 2.52
1734 3930 3.132289 ACGATTTAGCCTAGCAGCAAGTA 59.868 43.478 0.00 0.00 34.23 2.24
1757 3953 4.695455 CGGTGTACAATCTTGTCAGGATTT 59.305 41.667 7.43 3.38 42.35 2.17
1811 4033 9.753674 ACTAAGGATTTTTATGACCATTGAAGA 57.246 29.630 0.00 0.00 0.00 2.87
1813 4035 8.966868 GGACTAAGGATTTTTATGACCATTGAA 58.033 33.333 0.00 0.00 0.00 2.69
1814 4036 8.336235 AGGACTAAGGATTTTTATGACCATTGA 58.664 33.333 0.00 0.00 0.00 2.57
1815 4037 8.525290 AGGACTAAGGATTTTTATGACCATTG 57.475 34.615 0.00 0.00 0.00 2.82
1818 4040 9.457436 GTTAAGGACTAAGGATTTTTATGACCA 57.543 33.333 0.00 0.00 0.00 4.02
1819 4041 8.900781 GGTTAAGGACTAAGGATTTTTATGACC 58.099 37.037 0.00 0.00 0.00 4.02
1820 4042 9.682465 AGGTTAAGGACTAAGGATTTTTATGAC 57.318 33.333 0.00 0.00 0.00 3.06
1821 4043 9.901172 GAGGTTAAGGACTAAGGATTTTTATGA 57.099 33.333 0.00 0.00 0.00 2.15
1822 4044 9.907229 AGAGGTTAAGGACTAAGGATTTTTATG 57.093 33.333 0.00 0.00 0.00 1.90
1825 4047 8.047911 GCTAGAGGTTAAGGACTAAGGATTTTT 58.952 37.037 0.00 0.00 0.00 1.94
1826 4048 7.365742 GGCTAGAGGTTAAGGACTAAGGATTTT 60.366 40.741 0.00 0.00 0.00 1.82
1827 4049 6.099990 GGCTAGAGGTTAAGGACTAAGGATTT 59.900 42.308 0.00 0.00 0.00 2.17
1828 4050 5.603395 GGCTAGAGGTTAAGGACTAAGGATT 59.397 44.000 0.00 0.00 0.00 3.01
1829 4051 5.149239 GGCTAGAGGTTAAGGACTAAGGAT 58.851 45.833 0.00 0.00 0.00 3.24
1830 4052 4.544683 GGCTAGAGGTTAAGGACTAAGGA 58.455 47.826 0.00 0.00 0.00 3.36
1831 4053 3.318557 CGGCTAGAGGTTAAGGACTAAGG 59.681 52.174 0.00 0.00 0.00 2.69
1832 4054 3.952967 ACGGCTAGAGGTTAAGGACTAAG 59.047 47.826 0.00 0.00 0.00 2.18
1833 4055 3.973425 ACGGCTAGAGGTTAAGGACTAA 58.027 45.455 0.00 0.00 0.00 2.24
1834 4056 3.659183 ACGGCTAGAGGTTAAGGACTA 57.341 47.619 0.00 0.00 0.00 2.59
1839 4061 1.553704 ACCCAACGGCTAGAGGTTAAG 59.446 52.381 0.00 0.00 0.00 1.85
2106 4368 5.909621 AAAAGTGGCGAGTAGATGTAGTA 57.090 39.130 0.00 0.00 0.00 1.82
2107 4369 4.803098 AAAAGTGGCGAGTAGATGTAGT 57.197 40.909 0.00 0.00 0.00 2.73
2108 4370 7.772332 AATTAAAAGTGGCGAGTAGATGTAG 57.228 36.000 0.00 0.00 0.00 2.74
2175 4441 1.202348 GCAGAAACCCTTTTGATCCGG 59.798 52.381 0.00 0.00 0.00 5.14
2176 4442 1.135689 CGCAGAAACCCTTTTGATCCG 60.136 52.381 0.00 0.00 0.00 4.18
2195 4461 1.063806 GCATACGAGCTAAGATGGCG 58.936 55.000 0.00 0.00 34.52 5.69
2196 4462 2.154854 TGCATACGAGCTAAGATGGC 57.845 50.000 0.00 0.00 34.99 4.40
2249 4515 1.970640 TGCTGGACCACGCATAGATAT 59.029 47.619 12.79 0.00 0.00 1.63
2399 4681 3.127533 GTGGTGGCGCCTAAGCTG 61.128 66.667 29.70 0.00 38.35 4.24
2400 4682 4.760047 CGTGGTGGCGCCTAAGCT 62.760 66.667 29.70 0.00 38.35 3.74
2420 4702 5.306532 TGAAGGTCTGTATACACGTCTTC 57.693 43.478 19.83 19.83 0.00 2.87
2421 4703 5.652891 AGATGAAGGTCTGTATACACGTCTT 59.347 40.000 0.08 5.62 0.00 3.01
2422 4704 5.194432 AGATGAAGGTCTGTATACACGTCT 58.806 41.667 0.08 4.80 0.00 4.18
2469 4755 1.899534 GGCGTACTTGGTGGGCAAA 60.900 57.895 0.00 0.00 0.00 3.68
2496 4782 1.374947 CCCCTGCGGAAACTGAAGA 59.625 57.895 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.