Multiple sequence alignment - TraesCS1A01G026100

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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 TraesCS1A01G026100 chr1A 100.000 2872 0 0 1 2872 12406320 12403449 0.000000e+00 5304.0
1 TraesCS1A01G026100 chr1A 76.459 1474 219 68 763 2193 12770526 12769138 0.000000e+00 682.0
2 TraesCS1A01G026100 chr1B 99.305 719 5 0 1 719 172386472 172387190 0.000000e+00 1301.0
3 TraesCS1A01G026100 chr1B 94.505 728 32 3 1 720 321676606 321675879 0.000000e+00 1116.0
4 TraesCS1A01G026100 chr1B 79.887 885 134 23 1118 1977 15896564 15895699 2.450000e-170 608.0
5 TraesCS1A01G026100 chr5A 99.164 718 6 0 1 718 271542746 271543463 0.000000e+00 1293.0
6 TraesCS1A01G026100 chr7A 98.189 718 12 1 1 718 269100577 269101293 0.000000e+00 1253.0
7 TraesCS1A01G026100 chr7A 91.248 697 41 8 2194 2872 686193977 686193283 0.000000e+00 931.0
8 TraesCS1A01G026100 chr7A 89.076 714 41 14 2191 2872 624074488 624073780 0.000000e+00 852.0
9 TraesCS1A01G026100 chr7A 74.860 358 79 9 718 1070 18996232 18996583 4.960000e-33 152.0
10 TraesCS1A01G026100 chr4B 98.164 708 13 0 1 708 142773804 142774511 0.000000e+00 1236.0
11 TraesCS1A01G026100 chr3A 97.354 718 18 1 1 718 111804220 111803504 0.000000e+00 1219.0
12 TraesCS1A01G026100 chr3A 92.722 687 42 7 2192 2872 746627050 746627734 0.000000e+00 985.0
13 TraesCS1A01G026100 chr3A 95.238 168 8 0 2194 2361 54469490 54469657 1.700000e-67 267.0
14 TraesCS1A01G026100 chr5D 95.041 726 27 4 1 718 43197272 43196548 0.000000e+00 1133.0
15 TraesCS1A01G026100 chr6D 94.650 729 31 3 1 721 313017541 313016813 0.000000e+00 1123.0
16 TraesCS1A01G026100 chr6D 77.844 167 29 5 895 1059 27101465 27101625 2.360000e-16 97.1
17 TraesCS1A01G026100 chr6B 94.650 729 31 3 1 721 560644133 560644861 0.000000e+00 1123.0
18 TraesCS1A01G026100 chr2A 94.628 726 31 3 1 718 424509555 424508830 0.000000e+00 1118.0
19 TraesCS1A01G026100 chr2A 91.210 694 42 7 2194 2872 612410815 612411504 0.000000e+00 926.0
20 TraesCS1A01G026100 chr2A 92.190 589 25 7 2194 2766 53435816 53435233 0.000000e+00 813.0
21 TraesCS1A01G026100 chr2A 87.679 560 34 11 2335 2872 30846458 30847004 1.130000e-173 619.0
22 TraesCS1A01G026100 chr2A 92.308 117 9 0 2756 2872 53434941 53434825 1.770000e-37 167.0
23 TraesCS1A01G026100 chrUn 92.132 699 34 12 2194 2872 1595921 1596618 0.000000e+00 966.0
24 TraesCS1A01G026100 chrUn 80.068 883 134 22 1118 1977 305995541 305994678 4.070000e-173 617.0
25 TraesCS1A01G026100 chr4A 89.799 696 49 8 2194 2872 138830335 138831025 0.000000e+00 872.0
26 TraesCS1A01G026100 chr4A 89.362 705 40 9 2193 2872 729838274 729837580 0.000000e+00 854.0
27 TraesCS1A01G026100 chr4A 79.693 586 98 14 1408 1979 714191884 714191306 1.240000e-108 403.0
28 TraesCS1A01G026100 chr4A 74.309 362 74 14 718 1070 714192540 714192189 4.990000e-28 135.0
29 TraesCS1A01G026100 chr7D 78.731 583 100 15 1390 1954 18632032 18632608 4.520000e-98 368.0
30 TraesCS1A01G026100 chr7D 77.826 230 50 1 757 986 18589181 18589409 1.070000e-29 141.0


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 TraesCS1A01G026100 chr1A 12403449 12406320 2871 True 5304 5304 100.000 1 2872 1 chr1A.!!$R1 2871
1 TraesCS1A01G026100 chr1A 12769138 12770526 1388 True 682 682 76.459 763 2193 1 chr1A.!!$R2 1430
2 TraesCS1A01G026100 chr1B 172386472 172387190 718 False 1301 1301 99.305 1 719 1 chr1B.!!$F1 718
3 TraesCS1A01G026100 chr1B 321675879 321676606 727 True 1116 1116 94.505 1 720 1 chr1B.!!$R2 719
4 TraesCS1A01G026100 chr1B 15895699 15896564 865 True 608 608 79.887 1118 1977 1 chr1B.!!$R1 859
5 TraesCS1A01G026100 chr5A 271542746 271543463 717 False 1293 1293 99.164 1 718 1 chr5A.!!$F1 717
6 TraesCS1A01G026100 chr7A 269100577 269101293 716 False 1253 1253 98.189 1 718 1 chr7A.!!$F2 717
7 TraesCS1A01G026100 chr7A 686193283 686193977 694 True 931 931 91.248 2194 2872 1 chr7A.!!$R2 678
8 TraesCS1A01G026100 chr7A 624073780 624074488 708 True 852 852 89.076 2191 2872 1 chr7A.!!$R1 681
9 TraesCS1A01G026100 chr4B 142773804 142774511 707 False 1236 1236 98.164 1 708 1 chr4B.!!$F1 707
10 TraesCS1A01G026100 chr3A 111803504 111804220 716 True 1219 1219 97.354 1 718 1 chr3A.!!$R1 717
11 TraesCS1A01G026100 chr3A 746627050 746627734 684 False 985 985 92.722 2192 2872 1 chr3A.!!$F2 680
12 TraesCS1A01G026100 chr5D 43196548 43197272 724 True 1133 1133 95.041 1 718 1 chr5D.!!$R1 717
13 TraesCS1A01G026100 chr6D 313016813 313017541 728 True 1123 1123 94.650 1 721 1 chr6D.!!$R1 720
14 TraesCS1A01G026100 chr6B 560644133 560644861 728 False 1123 1123 94.650 1 721 1 chr6B.!!$F1 720
15 TraesCS1A01G026100 chr2A 424508830 424509555 725 True 1118 1118 94.628 1 718 1 chr2A.!!$R1 717
16 TraesCS1A01G026100 chr2A 612410815 612411504 689 False 926 926 91.210 2194 2872 1 chr2A.!!$F2 678
17 TraesCS1A01G026100 chr2A 30846458 30847004 546 False 619 619 87.679 2335 2872 1 chr2A.!!$F1 537
18 TraesCS1A01G026100 chr2A 53434825 53435816 991 True 490 813 92.249 2194 2872 2 chr2A.!!$R2 678
19 TraesCS1A01G026100 chrUn 1595921 1596618 697 False 966 966 92.132 2194 2872 1 chrUn.!!$F1 678
20 TraesCS1A01G026100 chrUn 305994678 305995541 863 True 617 617 80.068 1118 1977 1 chrUn.!!$R1 859
21 TraesCS1A01G026100 chr4A 138830335 138831025 690 False 872 872 89.799 2194 2872 1 chr4A.!!$F1 678
22 TraesCS1A01G026100 chr4A 729837580 729838274 694 True 854 854 89.362 2193 2872 1 chr4A.!!$R1 679
23 TraesCS1A01G026100 chr4A 714191306 714192540 1234 True 269 403 77.001 718 1979 2 chr4A.!!$R2 1261
24 TraesCS1A01G026100 chr7D 18632032 18632608 576 False 368 368 78.731 1390 1954 1 chr7D.!!$F2 564

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
797 809 0.249447 GCAGGGAAAACACTGTTGGC 60.249 55.0 0.0 0.0 37.07 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2762 2897 0.319555 TGCACTGTAGCGTCCACTTC 60.32 55.0 0.0 0.0 37.31 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 9.476202 GTTCAAATATCACTTTTTGGCTAAAGT 57.524 29.630 11.00 11.00 46.42 2.66
700 709 2.884663 TATTAACCTGTTGCAACGCG 57.115 45.000 23.79 17.86 0.00 6.01
739 748 6.479654 GTCTAACTAAGACGCTCATAAACG 57.520 41.667 0.00 0.00 45.05 3.60
748 757 4.842139 ACGCTCATAAACGTCTTCATTC 57.158 40.909 0.00 0.00 38.28 2.67
749 758 3.303495 ACGCTCATAAACGTCTTCATTCG 59.697 43.478 0.00 0.00 38.28 3.34
756 765 1.779569 ACGTCTTCATTCGTGGTGAC 58.220 50.000 0.00 0.00 38.85 3.67
758 767 2.131972 CGTCTTCATTCGTGGTGACAA 58.868 47.619 0.00 0.00 46.06 3.18
759 768 2.736721 CGTCTTCATTCGTGGTGACAAT 59.263 45.455 0.00 0.00 46.06 2.71
783 795 1.280133 TCCATCAGAAAGACTGCAGGG 59.720 52.381 19.93 5.30 45.38 4.45
793 805 1.212935 AGACTGCAGGGAAAACACTGT 59.787 47.619 19.93 0.00 37.07 3.55
797 809 0.249447 GCAGGGAAAACACTGTTGGC 60.249 55.000 0.00 0.00 37.07 4.52
799 811 0.395173 AGGGAAAACACTGTTGGCGT 60.395 50.000 0.00 0.00 0.00 5.68
808 820 0.655733 ACTGTTGGCGTTGTTTCTCG 59.344 50.000 0.00 0.00 0.00 4.04
819 831 1.388547 TGTTTCTCGGCAGCAAAAGT 58.611 45.000 0.00 0.00 0.00 2.66
820 832 2.566913 TGTTTCTCGGCAGCAAAAGTA 58.433 42.857 0.00 0.00 0.00 2.24
821 833 2.289547 TGTTTCTCGGCAGCAAAAGTAC 59.710 45.455 0.00 0.00 0.00 2.73
822 834 2.543777 TTCTCGGCAGCAAAAGTACT 57.456 45.000 0.00 0.00 0.00 2.73
841 853 2.124996 CCACCCTCCTCCCCAAGA 59.875 66.667 0.00 0.00 0.00 3.02
843 855 1.140134 CCACCCTCCTCCCCAAGAAA 61.140 60.000 0.00 0.00 0.00 2.52
847 859 1.710809 CCCTCCTCCCCAAGAAAGAAA 59.289 52.381 0.00 0.00 0.00 2.52
849 861 3.157881 CCTCCTCCCCAAGAAAGAAAAC 58.842 50.000 0.00 0.00 0.00 2.43
854 866 3.821033 CTCCCCAAGAAAGAAAACGATGT 59.179 43.478 0.00 0.00 0.00 3.06
873 885 0.375454 TGTTTGTTGGTCAACTCGCG 59.625 50.000 13.96 0.00 41.67 5.87
876 888 0.934496 TTGTTGGTCAACTCGCGAAG 59.066 50.000 11.33 7.16 41.67 3.79
886 904 4.262510 GTCAACTCGCGAAGATACTTGTAC 59.737 45.833 11.33 0.00 0.00 2.90
887 905 4.083164 TCAACTCGCGAAGATACTTGTACA 60.083 41.667 11.33 0.00 0.00 2.90
895 913 4.142752 CGAAGATACTTGTACAGGACGACA 60.143 45.833 12.54 0.00 0.00 4.35
899 917 3.746045 ACTTGTACAGGACGACAACAT 57.254 42.857 12.54 0.00 32.31 2.71
911 929 5.415701 AGGACGACAACATATGCAGAAAAAT 59.584 36.000 1.58 0.00 0.00 1.82
940 958 5.277876 GCAGAAATTCTGGAGCATCTATGTG 60.278 44.000 22.73 0.00 44.43 3.21
948 966 6.283694 TCTGGAGCATCTATGTGTTCATTAC 58.716 40.000 0.00 0.00 35.70 1.89
949 967 5.988287 TGGAGCATCTATGTGTTCATTACA 58.012 37.500 0.00 0.00 35.70 2.41
963 981 5.985530 TGTTCATTACACTGAGAACACTGAG 59.014 40.000 0.00 0.00 43.66 3.35
964 982 5.139435 TCATTACACTGAGAACACTGAGG 57.861 43.478 0.00 0.00 0.00 3.86
967 985 6.663523 TCATTACACTGAGAACACTGAGGATA 59.336 38.462 0.00 0.00 0.00 2.59
968 986 6.911250 TTACACTGAGAACACTGAGGATAA 57.089 37.500 0.00 0.00 0.00 1.75
982 1000 7.068839 ACACTGAGGATAATAGTACACTCAAGG 59.931 40.741 0.00 5.26 34.90 3.61
984 1002 7.839705 ACTGAGGATAATAGTACACTCAAGGAA 59.160 37.037 0.00 0.00 34.90 3.36
985 1003 8.783660 TGAGGATAATAGTACACTCAAGGAAT 57.216 34.615 0.00 0.00 32.60 3.01
986 1004 9.877222 TGAGGATAATAGTACACTCAAGGAATA 57.123 33.333 0.00 0.00 32.60 1.75
1020 1038 9.534565 GATATTATGCCACAGGTACATACATAG 57.465 37.037 0.00 0.00 0.00 2.23
1022 1040 7.553504 TTATGCCACAGGTACATACATAGAT 57.446 36.000 0.00 0.00 0.00 1.98
1023 1041 8.658840 TTATGCCACAGGTACATACATAGATA 57.341 34.615 0.00 0.00 0.00 1.98
1024 1042 6.987403 TGCCACAGGTACATACATAGATAA 57.013 37.500 0.00 0.00 0.00 1.75
1026 1044 7.973402 TGCCACAGGTACATACATAGATAATT 58.027 34.615 0.00 0.00 0.00 1.40
1027 1045 7.877612 TGCCACAGGTACATACATAGATAATTG 59.122 37.037 0.00 0.00 0.00 2.32
1066 1084 8.519799 TGTCTGTTATTTCTTCCTTTTTGTCT 57.480 30.769 0.00 0.00 0.00 3.41
1067 1085 8.966868 TGTCTGTTATTTCTTCCTTTTTGTCTT 58.033 29.630 0.00 0.00 0.00 3.01
1078 1096 8.802267 TCTTCCTTTTTGTCTTTCTTTCTTCAA 58.198 29.630 0.00 0.00 0.00 2.69
1079 1097 8.986477 TTCCTTTTTGTCTTTCTTTCTTCAAG 57.014 30.769 0.00 0.00 0.00 3.02
1101 1119 3.005155 GCATGCAAGGTGAATATTCCTCC 59.995 47.826 14.21 14.11 33.09 4.30
1105 1123 3.686691 GCAAGGTGAATATTCCTCCAGCT 60.687 47.826 21.09 12.70 38.79 4.24
1108 1126 5.559148 AGGTGAATATTCCTCCAGCTAAG 57.441 43.478 21.09 0.00 35.85 2.18
1129 1158 3.453353 AGCCATTCATTCATTCCCCTTTG 59.547 43.478 0.00 0.00 0.00 2.77
1140 1169 3.959535 TTCCCCTTTGATGACAATTGC 57.040 42.857 5.05 0.00 35.85 3.56
1165 1194 5.853282 CACATTTCCTTCTTTGCGTTTCTAG 59.147 40.000 0.00 0.00 0.00 2.43
1173 1202 6.578919 CCTTCTTTGCGTTTCTAGAACATTTC 59.421 38.462 4.18 0.00 0.00 2.17
1177 1206 7.803189 TCTTTGCGTTTCTAGAACATTTCATTC 59.197 33.333 4.18 0.00 0.00 2.67
1180 1209 7.648142 TGCGTTTCTAGAACATTTCATTCTTT 58.352 30.769 4.18 0.00 37.57 2.52
1181 1210 8.134895 TGCGTTTCTAGAACATTTCATTCTTTT 58.865 29.630 4.18 0.00 37.57 2.27
1182 1211 8.630840 GCGTTTCTAGAACATTTCATTCTTTTC 58.369 33.333 4.18 0.00 37.57 2.29
1209 1240 8.656849 CAATTATAAAGTAGTCGCAACAACTCT 58.343 33.333 0.00 0.00 0.00 3.24
1210 1241 7.807687 TTATAAAGTAGTCGCAACAACTCTC 57.192 36.000 0.00 0.00 0.00 3.20
1214 1245 2.715737 AGTCGCAACAACTCTCTCTC 57.284 50.000 0.00 0.00 0.00 3.20
1216 1247 2.227865 AGTCGCAACAACTCTCTCTCTC 59.772 50.000 0.00 0.00 0.00 3.20
1218 1249 2.486203 TCGCAACAACTCTCTCTCTCTC 59.514 50.000 0.00 0.00 0.00 3.20
1220 1251 3.426159 CGCAACAACTCTCTCTCTCTCTC 60.426 52.174 0.00 0.00 0.00 3.20
1221 1252 3.758554 GCAACAACTCTCTCTCTCTCTCT 59.241 47.826 0.00 0.00 0.00 3.10
1222 1253 4.142600 GCAACAACTCTCTCTCTCTCTCTC 60.143 50.000 0.00 0.00 0.00 3.20
1223 1254 5.248640 CAACAACTCTCTCTCTCTCTCTCT 58.751 45.833 0.00 0.00 0.00 3.10
1224 1255 5.091261 ACAACTCTCTCTCTCTCTCTCTC 57.909 47.826 0.00 0.00 0.00 3.20
1226 1257 5.105146 ACAACTCTCTCTCTCTCTCTCTCTC 60.105 48.000 0.00 0.00 0.00 3.20
1229 1270 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1232 1273 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1234 1275 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1268 1309 6.401153 CGTTGTAGGTGCTCAAAGAAATACTC 60.401 42.308 0.00 0.00 0.00 2.59
1269 1310 6.360370 TGTAGGTGCTCAAAGAAATACTCT 57.640 37.500 0.00 0.00 35.13 3.24
1270 1311 7.476540 TGTAGGTGCTCAAAGAAATACTCTA 57.523 36.000 0.00 0.00 32.46 2.43
1272 1313 8.198109 TGTAGGTGCTCAAAGAAATACTCTATC 58.802 37.037 0.00 0.00 32.46 2.08
1273 1314 7.187824 AGGTGCTCAAAGAAATACTCTATCA 57.812 36.000 0.00 0.00 32.46 2.15
1279 1320 7.519649 GCTCAAAGAAATACTCTATCACCATGC 60.520 40.741 0.00 0.00 32.46 4.06
1285 1326 3.827008 ACTCTATCACCATGCGTCAAT 57.173 42.857 0.00 0.00 0.00 2.57
1302 1348 4.381411 GTCAATAGGAGAAGGAATTCCCG 58.619 47.826 21.22 0.00 40.87 5.14
1303 1350 3.391296 TCAATAGGAGAAGGAATTCCCGG 59.609 47.826 21.22 0.00 40.87 5.73
1312 1359 0.106419 GGAATTCCCGGGTATGCCAA 60.106 55.000 28.38 12.20 36.17 4.52
1315 1362 2.470057 ATTCCCGGGTATGCCAAATT 57.530 45.000 22.86 0.00 36.17 1.82
1345 1392 2.223711 ACGTCGAAAGCCAAAGCAAAAT 60.224 40.909 0.00 0.00 43.56 1.82
1355 1405 3.992427 GCCAAAGCAAAATGAAGAAGAGG 59.008 43.478 0.00 0.00 39.53 3.69
1357 1407 5.739935 GCCAAAGCAAAATGAAGAAGAGGAA 60.740 40.000 0.00 0.00 39.53 3.36
1373 1423 7.670364 AGAAGAGGAAGAAGAAGAAGAAGAAG 58.330 38.462 0.00 0.00 0.00 2.85
1374 1424 7.508977 AGAAGAGGAAGAAGAAGAAGAAGAAGA 59.491 37.037 0.00 0.00 0.00 2.87
1375 1425 6.993079 AGAGGAAGAAGAAGAAGAAGAAGAC 58.007 40.000 0.00 0.00 0.00 3.01
1376 1426 6.553100 AGAGGAAGAAGAAGAAGAAGAAGACA 59.447 38.462 0.00 0.00 0.00 3.41
1377 1427 7.070571 AGAGGAAGAAGAAGAAGAAGAAGACAA 59.929 37.037 0.00 0.00 0.00 3.18
1378 1428 6.989759 AGGAAGAAGAAGAAGAAGAAGACAAC 59.010 38.462 0.00 0.00 0.00 3.32
1379 1429 6.074034 GGAAGAAGAAGAAGAAGAAGACAACG 60.074 42.308 0.00 0.00 0.00 4.10
1380 1430 6.150396 AGAAGAAGAAGAAGAAGACAACGA 57.850 37.500 0.00 0.00 0.00 3.85
1381 1431 6.212955 AGAAGAAGAAGAAGAAGACAACGAG 58.787 40.000 0.00 0.00 0.00 4.18
1382 1432 4.303282 AGAAGAAGAAGAAGACAACGAGC 58.697 43.478 0.00 0.00 0.00 5.03
1383 1433 3.735237 AGAAGAAGAAGACAACGAGCA 57.265 42.857 0.00 0.00 0.00 4.26
1384 1434 4.060038 AGAAGAAGAAGACAACGAGCAA 57.940 40.909 0.00 0.00 0.00 3.91
1385 1435 4.054671 AGAAGAAGAAGACAACGAGCAAG 58.945 43.478 0.00 0.00 0.00 4.01
1386 1436 3.735237 AGAAGAAGACAACGAGCAAGA 57.265 42.857 0.00 0.00 0.00 3.02
1387 1437 4.060038 AGAAGAAGACAACGAGCAAGAA 57.940 40.909 0.00 0.00 0.00 2.52
1388 1438 4.054671 AGAAGAAGACAACGAGCAAGAAG 58.945 43.478 0.00 0.00 0.00 2.85
1406 1456 1.494960 AGACTTCATCCTCTCCTGGC 58.505 55.000 0.00 0.00 0.00 4.85
1418 1468 1.133199 TCTCCTGGCCAAAACCAACAT 60.133 47.619 7.01 0.00 39.86 2.71
1431 1481 3.648339 ACCAACATCACAAGTTGCATC 57.352 42.857 1.81 0.00 43.74 3.91
1432 1482 2.297033 ACCAACATCACAAGTTGCATCC 59.703 45.455 1.81 0.00 43.74 3.51
1464 1514 0.246360 CCTCTGTGTGACGGCATGTA 59.754 55.000 0.00 0.00 0.00 2.29
1471 1521 4.065789 TGTGTGACGGCATGTAACAAATA 58.934 39.130 0.00 0.00 43.76 1.40
1472 1522 4.697828 TGTGTGACGGCATGTAACAAATAT 59.302 37.500 0.00 0.00 43.76 1.28
1488 1538 5.977635 ACAAATATCACCTTGATCTCGACA 58.022 37.500 0.00 0.00 38.26 4.35
1497 1550 5.049474 CACCTTGATCTCGACACAATTTTGA 60.049 40.000 0.00 0.00 0.00 2.69
1502 1555 5.866092 TGATCTCGACACAATTTTGAGAGAG 59.134 40.000 20.23 14.66 38.91 3.20
1504 1557 4.039245 TCTCGACACAATTTTGAGAGAGGT 59.961 41.667 15.30 0.00 32.88 3.85
1511 1564 6.931840 ACACAATTTTGAGAGAGGTAAGAGAC 59.068 38.462 0.00 0.00 0.00 3.36
1528 1581 3.027412 GAGACCAAGCTACAGATCCAGA 58.973 50.000 0.00 0.00 0.00 3.86
1534 1587 5.663106 ACCAAGCTACAGATCCAGAAGAATA 59.337 40.000 0.00 0.00 0.00 1.75
1536 1589 7.510685 ACCAAGCTACAGATCCAGAAGAATATA 59.489 37.037 0.00 0.00 0.00 0.86
1537 1590 7.816995 CCAAGCTACAGATCCAGAAGAATATAC 59.183 40.741 0.00 0.00 0.00 1.47
1590 1643 4.538490 AGTTAAACAGGGGTATCATCACCA 59.462 41.667 0.00 0.00 40.65 4.17
1644 1697 3.484407 AGGATGGTGATAGCAGAAATGC 58.516 45.455 0.00 0.00 0.00 3.56
1737 1799 1.763655 ATGCTGGATCTCGAGGGCA 60.764 57.895 13.56 14.85 0.00 5.36
1760 1822 0.672401 TGGTTTTCGCCACCGAGATC 60.672 55.000 0.00 0.00 45.35 2.75
1767 1829 4.738198 CCACCGAGATCACGATGG 57.262 61.111 11.78 11.78 40.68 3.51
1770 1832 2.355126 CCGAGATCACGATGGCGG 60.355 66.667 14.43 2.00 43.17 6.13
1793 1855 4.643387 GCCACTGCCGACACCCTT 62.643 66.667 0.00 0.00 0.00 3.95
1808 1870 1.279271 ACCCTTGATTCCCTCGTGAAG 59.721 52.381 0.00 0.00 0.00 3.02
1809 1871 1.555075 CCCTTGATTCCCTCGTGAAGA 59.445 52.381 0.00 0.00 0.00 2.87
1827 1889 1.444119 GAAAGCACGGCAACTCCACA 61.444 55.000 0.00 0.00 34.01 4.17
1835 1897 1.466167 CGGCAACTCCACAGAGAAATG 59.534 52.381 0.00 0.00 43.39 2.32
1839 1901 3.365767 GCAACTCCACAGAGAAATGAAGC 60.366 47.826 0.00 0.00 43.39 3.86
1853 1915 2.827800 TGAAGCACCAAGACTCAGAG 57.172 50.000 0.00 0.00 0.00 3.35
1858 1920 3.974719 AGCACCAAGACTCAGAGATAGA 58.025 45.455 3.79 0.00 0.00 1.98
1864 1926 4.206375 CAAGACTCAGAGATAGAGCCAGA 58.794 47.826 3.79 0.00 36.58 3.86
1867 1929 6.199557 AGACTCAGAGATAGAGCCAGATAA 57.800 41.667 3.79 0.00 36.58 1.75
1904 1970 5.956171 GCAAACAAGCTAGATTATTTGCC 57.044 39.130 29.90 16.80 43.77 4.52
1962 2030 3.058293 GGATTTGCGTCTGTTCATTCACA 60.058 43.478 0.00 0.00 0.00 3.58
1983 2051 9.865321 TTCACATGTACTCTACTGTATTAAACC 57.135 33.333 0.00 0.00 0.00 3.27
1998 2066 8.550710 TGTATTAAACCACATTGTACTACCAC 57.449 34.615 0.00 0.00 0.00 4.16
2003 2071 4.060205 ACCACATTGTACTACCACGTTTC 58.940 43.478 0.00 0.00 0.00 2.78
2010 2078 2.234300 ACTACCACGTTTCCTGTGTG 57.766 50.000 0.00 0.00 35.56 3.82
2012 2080 1.864711 CTACCACGTTTCCTGTGTGTG 59.135 52.381 0.00 0.00 35.56 3.82
2015 2083 1.264020 CCACGTTTCCTGTGTGTGATG 59.736 52.381 0.00 0.00 35.56 3.07
2016 2084 1.939934 CACGTTTCCTGTGTGTGATGT 59.060 47.619 0.00 0.00 32.39 3.06
2017 2085 2.032894 CACGTTTCCTGTGTGTGATGTC 60.033 50.000 0.00 0.00 32.39 3.06
2018 2086 2.209273 CGTTTCCTGTGTGTGATGTCA 58.791 47.619 0.00 0.00 0.00 3.58
2019 2087 2.807967 CGTTTCCTGTGTGTGATGTCAT 59.192 45.455 0.00 0.00 0.00 3.06
2020 2088 3.120546 CGTTTCCTGTGTGTGATGTCATC 60.121 47.826 5.83 5.83 0.00 2.92
2021 2089 3.767902 TTCCTGTGTGTGATGTCATCA 57.232 42.857 11.62 11.62 36.84 3.07
2022 2090 3.986996 TCCTGTGTGTGATGTCATCAT 57.013 42.857 18.32 0.00 42.04 2.45
2023 2091 3.602483 TCCTGTGTGTGATGTCATCATG 58.398 45.455 18.32 5.63 42.04 3.07
2024 2092 3.008266 TCCTGTGTGTGATGTCATCATGT 59.992 43.478 18.32 0.00 42.04 3.21
2025 2093 3.126343 CCTGTGTGTGATGTCATCATGTG 59.874 47.826 18.32 6.53 42.04 3.21
2026 2094 2.485038 TGTGTGTGATGTCATCATGTGC 59.515 45.455 18.32 6.51 42.04 4.57
2027 2095 1.733360 TGTGTGATGTCATCATGTGCG 59.267 47.619 18.32 0.00 42.04 5.34
2028 2096 1.733912 GTGTGATGTCATCATGTGCGT 59.266 47.619 18.32 0.00 42.04 5.24
2029 2097 2.160219 GTGTGATGTCATCATGTGCGTT 59.840 45.455 18.32 0.00 42.04 4.84
2047 2115 4.468951 CGTTTGAGCGCATTAACATTTC 57.531 40.909 11.47 0.00 0.00 2.17
2054 2122 6.389091 TGAGCGCATTAACATTTCATTTCTT 58.611 32.000 11.47 0.00 0.00 2.52
2075 2143 8.647143 TTCTTTGATTTTCAAGTGATGGAAAC 57.353 30.769 0.00 0.00 39.34 2.78
2077 2145 7.922278 TCTTTGATTTTCAAGTGATGGAAACTG 59.078 33.333 0.00 0.00 39.34 3.16
2079 2147 5.302568 TGATTTTCAAGTGATGGAAACTGCT 59.697 36.000 0.00 0.00 39.34 4.24
2082 2150 4.890158 TCAAGTGATGGAAACTGCTCTA 57.110 40.909 0.00 0.00 0.00 2.43
2083 2151 5.227569 TCAAGTGATGGAAACTGCTCTAA 57.772 39.130 0.00 0.00 0.00 2.10
2088 2156 5.645497 AGTGATGGAAACTGCTCTAACAATC 59.355 40.000 0.00 0.00 0.00 2.67
2093 2162 6.115446 TGGAAACTGCTCTAACAATCCTATG 58.885 40.000 0.00 0.00 0.00 2.23
2099 2168 5.601662 TGCTCTAACAATCCTATGTGCTAC 58.398 41.667 0.00 0.00 32.81 3.58
2117 2186 7.102993 TGTGCTACACATATACTTGTCACAAT 58.897 34.615 0.00 0.00 39.62 2.71
2123 2192 7.083858 ACACATATACTTGTCACAATGTTTGC 58.916 34.615 0.00 0.00 0.00 3.68
2126 2195 1.133982 ACTTGTCACAATGTTTGCGCA 59.866 42.857 5.66 5.66 0.00 6.09
2146 2223 1.673993 CACAGTTGCGCCATACCCA 60.674 57.895 4.18 0.00 0.00 4.51
2149 2226 0.101040 CAGTTGCGCCATACCCAATG 59.899 55.000 4.18 0.00 35.15 2.82
2150 2227 1.226945 GTTGCGCCATACCCAATGC 60.227 57.895 4.18 0.00 33.92 3.56
2160 2237 4.685924 CCATACCCAATGCAAATGTCTTC 58.314 43.478 0.00 0.00 33.92 2.87
2176 2253 4.729868 TGTCTTCGATCAGATGATAGGGA 58.270 43.478 0.00 0.00 35.79 4.20
2211 2288 5.623956 TCTTGGGTGAATTCCGTATATGT 57.376 39.130 2.27 0.00 0.00 2.29
2256 2334 4.501915 CGCATATGCCATTGGAAATTTCCT 60.502 41.667 32.02 14.90 42.22 3.36
2359 2437 5.617252 AGTGGAAGGTGAAAAGACGATTTA 58.383 37.500 0.00 0.00 0.00 1.40
2397 2475 0.872881 GCACTGCAGCACCAACTTTG 60.873 55.000 15.27 1.87 0.00 2.77
2485 2582 9.151471 CAACTAGTGCACTGTAGTAACAATTAT 57.849 33.333 29.57 5.17 34.49 1.28
2679 2803 5.470845 CTACAGTAATTGTTGCTACAGCC 57.529 43.478 0.37 0.00 41.29 4.85
2681 2805 3.000041 CAGTAATTGTTGCTACAGCCGA 59.000 45.455 0.37 0.00 41.18 5.54
2797 3235 2.783275 CATCAGACGCTGCAGTGC 59.217 61.111 26.78 18.59 0.00 4.40
2843 3281 4.347583 TCAGGGGCAAAATTGTCTTTTCAT 59.652 37.500 0.00 0.00 32.28 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 5.221185 GGCACTACTACTCGTATCCAATCAA 60.221 44.000 0.00 0.00 0.00 2.57
700 709 2.361230 ACTAGCAAAAGGGCCCGC 60.361 61.111 18.44 14.38 0.00 6.13
728 737 3.303495 ACGAATGAAGACGTTTATGAGCG 59.697 43.478 0.00 0.00 39.75 5.03
733 742 4.387862 GTCACCACGAATGAAGACGTTTAT 59.612 41.667 0.00 0.00 40.76 1.40
737 746 1.067974 TGTCACCACGAATGAAGACGT 59.932 47.619 0.00 0.00 43.50 4.34
739 748 3.120199 CCATTGTCACCACGAATGAAGAC 60.120 47.826 0.00 0.00 32.93 3.01
745 754 1.453155 GAGCCATTGTCACCACGAAT 58.547 50.000 0.00 0.00 0.00 3.34
748 757 0.677731 ATGGAGCCATTGTCACCACG 60.678 55.000 0.00 0.00 31.82 4.94
749 758 1.098050 GATGGAGCCATTGTCACCAC 58.902 55.000 3.11 0.00 36.70 4.16
756 765 3.377485 CAGTCTTTCTGATGGAGCCATTG 59.623 47.826 3.11 0.84 46.27 2.82
758 767 2.683152 GCAGTCTTTCTGATGGAGCCAT 60.683 50.000 0.71 0.71 46.27 4.40
759 768 1.339438 GCAGTCTTTCTGATGGAGCCA 60.339 52.381 0.00 0.00 46.27 4.75
793 805 1.781025 CTGCCGAGAAACAACGCCAA 61.781 55.000 0.00 0.00 0.00 4.52
797 809 0.028770 TTTGCTGCCGAGAAACAACG 59.971 50.000 0.00 0.00 0.00 4.10
799 811 1.748493 ACTTTTGCTGCCGAGAAACAA 59.252 42.857 0.00 0.00 0.00 2.83
819 831 2.040606 GGGAGGAGGGTGGCAGTA 59.959 66.667 0.00 0.00 0.00 2.74
822 834 4.608514 TTGGGGAGGAGGGTGGCA 62.609 66.667 0.00 0.00 0.00 4.92
841 853 5.474825 ACCAACAAACACATCGTTTTCTTT 58.525 33.333 0.00 0.00 45.79 2.52
843 855 4.156922 TGACCAACAAACACATCGTTTTCT 59.843 37.500 0.00 0.00 45.79 2.52
847 859 3.442273 AGTTGACCAACAAACACATCGTT 59.558 39.130 14.42 0.00 43.47 3.85
849 861 3.617669 GAGTTGACCAACAAACACATCG 58.382 45.455 14.42 0.00 43.47 3.84
854 866 0.375454 CGCGAGTTGACCAACAAACA 59.625 50.000 14.42 0.00 43.47 2.83
865 877 4.163552 TGTACAAGTATCTTCGCGAGTTG 58.836 43.478 9.59 9.79 0.00 3.16
866 878 4.413087 CTGTACAAGTATCTTCGCGAGTT 58.587 43.478 9.59 0.35 0.00 3.01
867 879 3.181499 CCTGTACAAGTATCTTCGCGAGT 60.181 47.826 9.59 3.51 0.00 4.18
873 885 5.306532 TGTCGTCCTGTACAAGTATCTTC 57.693 43.478 0.00 0.00 0.00 2.87
876 888 4.801891 TGTTGTCGTCCTGTACAAGTATC 58.198 43.478 0.00 0.00 36.33 2.24
886 904 2.892374 TCTGCATATGTTGTCGTCCTG 58.108 47.619 4.29 0.00 0.00 3.86
887 905 3.610040 TTCTGCATATGTTGTCGTCCT 57.390 42.857 4.29 0.00 0.00 3.85
911 929 1.542915 GCTCCAGAATTTCTGCTGCAA 59.457 47.619 24.17 8.93 42.98 4.08
940 958 5.406780 CCTCAGTGTTCTCAGTGTAATGAAC 59.593 44.000 11.24 11.24 43.31 3.18
948 966 7.106439 ACTATTATCCTCAGTGTTCTCAGTG 57.894 40.000 0.00 0.00 43.96 3.66
949 967 7.834681 TGTACTATTATCCTCAGTGTTCTCAGT 59.165 37.037 0.00 0.00 0.00 3.41
957 975 7.285629 TCCTTGAGTGTACTATTATCCTCAGTG 59.714 40.741 0.00 0.00 31.28 3.66
958 976 7.355101 TCCTTGAGTGTACTATTATCCTCAGT 58.645 38.462 0.00 0.00 31.28 3.41
959 977 7.825331 TCCTTGAGTGTACTATTATCCTCAG 57.175 40.000 0.00 0.00 31.28 3.35
995 1013 9.267071 TCTATGTATGTACCTGTGGCATAATAT 57.733 33.333 0.00 0.00 0.00 1.28
997 1015 7.553504 TCTATGTATGTACCTGTGGCATAAT 57.446 36.000 0.00 0.00 0.00 1.28
999 1017 8.658840 TTATCTATGTATGTACCTGTGGCATA 57.341 34.615 0.00 0.00 0.00 3.14
1042 1060 9.803315 AAAGACAAAAAGGAAGAAATAACAGAC 57.197 29.630 0.00 0.00 0.00 3.51
1056 1074 6.813152 TGCTTGAAGAAAGAAAGACAAAAAGG 59.187 34.615 0.00 0.00 38.24 3.11
1061 1079 5.163530 TGCATGCTTGAAGAAAGAAAGACAA 60.164 36.000 20.33 0.00 38.24 3.18
1063 1081 4.863491 TGCATGCTTGAAGAAAGAAAGAC 58.137 39.130 20.33 0.00 38.24 3.01
1065 1083 4.684703 CCTTGCATGCTTGAAGAAAGAAAG 59.315 41.667 20.33 8.95 38.24 2.62
1066 1084 4.099881 ACCTTGCATGCTTGAAGAAAGAAA 59.900 37.500 20.33 0.00 38.24 2.52
1067 1085 3.638160 ACCTTGCATGCTTGAAGAAAGAA 59.362 39.130 20.33 0.00 38.24 2.52
1069 1087 3.005050 TCACCTTGCATGCTTGAAGAAAG 59.995 43.478 20.33 11.65 39.07 2.62
1070 1088 2.957680 TCACCTTGCATGCTTGAAGAAA 59.042 40.909 20.33 1.44 0.00 2.52
1071 1089 2.585330 TCACCTTGCATGCTTGAAGAA 58.415 42.857 20.33 2.23 0.00 2.52
1074 1092 5.394443 GGAATATTCACCTTGCATGCTTGAA 60.394 40.000 20.33 19.92 0.00 2.69
1075 1093 4.098349 GGAATATTCACCTTGCATGCTTGA 59.902 41.667 20.33 12.80 0.00 3.02
1078 1096 3.887716 GAGGAATATTCACCTTGCATGCT 59.112 43.478 20.33 0.00 36.57 3.79
1079 1097 3.005155 GGAGGAATATTCACCTTGCATGC 59.995 47.826 17.07 11.82 36.57 4.06
1101 1119 4.261909 GGGAATGAATGAATGGCTTAGCTG 60.262 45.833 3.59 0.00 0.00 4.24
1105 1123 4.541250 AGGGGAATGAATGAATGGCTTA 57.459 40.909 0.00 0.00 0.00 3.09
1108 1126 3.451902 TCAAAGGGGAATGAATGAATGGC 59.548 43.478 0.00 0.00 0.00 4.40
1129 1158 4.460948 AGGAAATGTGGCAATTGTCATC 57.539 40.909 17.07 9.37 29.66 2.92
1140 1169 3.369546 AACGCAAAGAAGGAAATGTGG 57.630 42.857 0.00 0.00 0.00 4.17
1177 1206 9.274065 GTTGCGACTACTTTATAATTGGAAAAG 57.726 33.333 0.00 7.19 36.51 2.27
1180 1209 7.908827 TGTTGCGACTACTTTATAATTGGAA 57.091 32.000 5.50 0.00 0.00 3.53
1181 1210 7.604927 AGTTGTTGCGACTACTTTATAATTGGA 59.395 33.333 14.56 0.00 38.43 3.53
1182 1211 7.748847 AGTTGTTGCGACTACTTTATAATTGG 58.251 34.615 14.56 0.00 38.43 3.16
1186 1215 7.600065 AGAGAGTTGTTGCGACTACTTTATAA 58.400 34.615 20.14 0.00 41.00 0.98
1188 1217 6.026947 AGAGAGTTGTTGCGACTACTTTAT 57.973 37.500 20.14 10.85 41.00 1.40
1190 1219 4.038162 AGAGAGAGTTGTTGCGACTACTTT 59.962 41.667 20.14 15.51 41.00 2.66
1209 1240 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1210 1241 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1214 1245 3.708631 ACCAGAGAGAGAGAGAGAGAGAG 59.291 52.174 0.00 0.00 0.00 3.20
1216 1247 4.494091 AACCAGAGAGAGAGAGAGAGAG 57.506 50.000 0.00 0.00 0.00 3.20
1218 1249 6.710744 GGTAATAACCAGAGAGAGAGAGAGAG 59.289 46.154 0.00 0.00 45.98 3.20
1220 1251 6.877611 GGTAATAACCAGAGAGAGAGAGAG 57.122 45.833 0.00 0.00 45.98 3.20
1234 1275 3.865446 AGCACCTACAACGGTAATAACC 58.135 45.455 0.00 0.00 42.95 2.85
1248 1289 8.198109 GTGATAGAGTATTTCTTTGAGCACCTA 58.802 37.037 0.00 0.00 37.36 3.08
1268 1309 4.021981 TCTCCTATTGACGCATGGTGATAG 60.022 45.833 0.00 2.16 0.00 2.08
1269 1310 3.895041 TCTCCTATTGACGCATGGTGATA 59.105 43.478 0.00 0.00 0.00 2.15
1270 1311 2.700371 TCTCCTATTGACGCATGGTGAT 59.300 45.455 0.00 0.00 0.00 3.06
1272 1313 2.602257 TCTCCTATTGACGCATGGTG 57.398 50.000 0.00 0.00 0.00 4.17
1273 1314 2.158900 CCTTCTCCTATTGACGCATGGT 60.159 50.000 0.00 0.00 0.00 3.55
1279 1320 4.381411 GGGAATTCCTTCTCCTATTGACG 58.619 47.826 23.63 0.00 35.95 4.35
1285 1326 1.009183 ACCCGGGAATTCCTTCTCCTA 59.991 52.381 32.02 0.00 35.95 2.94
1302 1348 5.408604 CGTCAGTATCTAATTTGGCATACCC 59.591 44.000 0.00 0.00 33.59 3.69
1303 1350 5.989777 ACGTCAGTATCTAATTTGGCATACC 59.010 40.000 0.00 0.00 0.00 2.73
1312 1359 5.041940 GGCTTTCGACGTCAGTATCTAATT 58.958 41.667 17.16 0.00 0.00 1.40
1315 1362 3.011818 TGGCTTTCGACGTCAGTATCTA 58.988 45.455 17.16 0.00 0.00 1.98
1345 1392 6.985653 TCTTCTTCTTCTTCCTCTTCTTCA 57.014 37.500 0.00 0.00 0.00 3.02
1355 1405 6.697892 TCGTTGTCTTCTTCTTCTTCTTCTTC 59.302 38.462 0.00 0.00 0.00 2.87
1357 1407 6.150396 TCGTTGTCTTCTTCTTCTTCTTCT 57.850 37.500 0.00 0.00 0.00 2.85
1373 1423 3.123804 TGAAGTCTTCTTGCTCGTTGTC 58.876 45.455 13.67 0.00 33.64 3.18
1374 1424 3.179443 TGAAGTCTTCTTGCTCGTTGT 57.821 42.857 13.67 0.00 33.64 3.32
1375 1425 3.124297 GGATGAAGTCTTCTTGCTCGTTG 59.876 47.826 13.67 0.00 33.64 4.10
1376 1426 3.007398 AGGATGAAGTCTTCTTGCTCGTT 59.993 43.478 14.43 0.00 31.44 3.85
1377 1427 2.564947 AGGATGAAGTCTTCTTGCTCGT 59.435 45.455 14.43 5.85 31.44 4.18
1378 1428 3.186119 GAGGATGAAGTCTTCTTGCTCG 58.814 50.000 24.56 0.00 40.52 5.03
1379 1429 4.432712 GAGAGGATGAAGTCTTCTTGCTC 58.567 47.826 28.33 28.33 42.75 4.26
1380 1430 3.197549 GGAGAGGATGAAGTCTTCTTGCT 59.802 47.826 18.60 18.60 42.75 3.91
1381 1431 3.197549 AGGAGAGGATGAAGTCTTCTTGC 59.802 47.826 13.67 12.14 42.75 4.01
1382 1432 4.382901 CCAGGAGAGGATGAAGTCTTCTTG 60.383 50.000 13.67 0.00 42.75 3.02
1383 1433 3.774216 CCAGGAGAGGATGAAGTCTTCTT 59.226 47.826 13.67 7.39 42.75 2.52
1384 1434 3.373830 CCAGGAGAGGATGAAGTCTTCT 58.626 50.000 13.67 0.00 45.10 2.85
1385 1435 2.158971 GCCAGGAGAGGATGAAGTCTTC 60.159 54.545 5.58 5.58 33.35 2.87
1386 1436 1.836802 GCCAGGAGAGGATGAAGTCTT 59.163 52.381 0.00 0.00 0.00 3.01
1387 1437 1.494960 GCCAGGAGAGGATGAAGTCT 58.505 55.000 0.00 0.00 0.00 3.24
1388 1438 0.467804 GGCCAGGAGAGGATGAAGTC 59.532 60.000 0.00 0.00 0.00 3.01
1406 1456 3.309410 GCAACTTGTGATGTTGGTTTTGG 59.691 43.478 8.39 0.00 43.37 3.28
1431 1481 1.461075 AGAGGGATAGCAGGGCAGG 60.461 63.158 0.00 0.00 0.00 4.85
1432 1482 1.053264 ACAGAGGGATAGCAGGGCAG 61.053 60.000 0.00 0.00 0.00 4.85
1464 1514 6.313905 GTGTCGAGATCAAGGTGATATTTGTT 59.686 38.462 0.00 0.00 37.20 2.83
1471 1521 3.961480 TTGTGTCGAGATCAAGGTGAT 57.039 42.857 0.00 0.00 40.34 3.06
1472 1522 3.961480 ATTGTGTCGAGATCAAGGTGA 57.039 42.857 0.00 0.00 0.00 4.02
1488 1538 6.468543 GGTCTCTTACCTCTCTCAAAATTGT 58.531 40.000 0.00 0.00 45.75 2.71
1504 1557 4.610333 TGGATCTGTAGCTTGGTCTCTTA 58.390 43.478 0.00 0.00 0.00 2.10
1511 1564 4.478206 TTCTTCTGGATCTGTAGCTTGG 57.522 45.455 0.00 0.00 0.00 3.61
1528 1581 5.300286 GCAAGGCTGAACATGGTATATTCTT 59.700 40.000 0.00 0.00 0.00 2.52
1534 1587 1.065491 TCGCAAGGCTGAACATGGTAT 60.065 47.619 0.00 0.00 38.47 2.73
1536 1589 1.073025 TCGCAAGGCTGAACATGGT 59.927 52.632 0.00 0.00 38.47 3.55
1537 1590 1.236616 TGTCGCAAGGCTGAACATGG 61.237 55.000 0.00 0.00 46.88 3.66
1590 1643 1.109920 ATCGCTGTCAGGCTATCGGT 61.110 55.000 1.14 0.00 0.00 4.69
1639 1692 1.260544 GCCCCTGAGTTTCTGCATTT 58.739 50.000 0.00 0.00 0.00 2.32
1644 1697 0.682209 CCATGGCCCCTGAGTTTCTG 60.682 60.000 0.00 0.00 0.00 3.02
1671 1733 4.021544 GTCCATGAGGCTCTCGAGATTAAT 60.022 45.833 17.03 2.28 32.35 1.40
1672 1734 3.319405 GTCCATGAGGCTCTCGAGATTAA 59.681 47.826 17.03 0.71 32.35 1.40
1706 1768 2.381109 CAGCATGGTCTCTGAAGCG 58.619 57.895 0.00 0.00 32.26 4.68
1737 1799 2.625823 CGGTGGCGAAAACCATGCT 61.626 57.895 0.00 0.00 43.01 3.79
1760 1822 2.890474 GCAGGTACCGCCATCGTG 60.890 66.667 15.22 4.38 40.61 4.35
1770 1832 2.434359 GTCGGCAGTGGCAGGTAC 60.434 66.667 17.80 5.21 43.71 3.34
1793 1855 2.038426 TGCTTTCTTCACGAGGGAATCA 59.962 45.455 0.00 0.00 0.00 2.57
1808 1870 1.282875 GTGGAGTTGCCGTGCTTTC 59.717 57.895 0.00 0.00 40.66 2.62
1809 1871 1.447317 CTGTGGAGTTGCCGTGCTTT 61.447 55.000 0.00 0.00 40.66 3.51
1827 1889 4.202398 TGAGTCTTGGTGCTTCATTTCTCT 60.202 41.667 0.00 0.00 0.00 3.10
1835 1897 3.608316 ATCTCTGAGTCTTGGTGCTTC 57.392 47.619 4.32 0.00 0.00 3.86
1839 1901 3.068024 GGCTCTATCTCTGAGTCTTGGTG 59.932 52.174 4.32 0.00 33.75 4.17
1864 1926 5.047021 TGTTTGCACTGAGAGAGCTAGTTAT 60.047 40.000 0.00 0.00 32.86 1.89
1867 1929 2.630098 TGTTTGCACTGAGAGAGCTAGT 59.370 45.455 0.00 0.00 32.86 2.57
1983 2051 4.151689 CAGGAAACGTGGTAGTACAATGTG 59.848 45.833 3.18 0.00 0.00 3.21
1988 2056 2.694628 ACACAGGAAACGTGGTAGTACA 59.305 45.455 2.06 0.00 38.56 2.90
1998 2066 2.209273 TGACATCACACACAGGAAACG 58.791 47.619 0.00 0.00 0.00 3.60
2003 2071 3.126343 CACATGATGACATCACACACAGG 59.874 47.826 20.21 1.66 43.01 4.00
2010 2078 3.120234 TCAAACGCACATGATGACATCAC 60.120 43.478 20.21 6.96 43.01 3.06
2012 2080 3.677601 CTCAAACGCACATGATGACATC 58.322 45.455 8.59 8.59 34.15 3.06
2015 2083 1.787989 CGCTCAAACGCACATGATGAC 60.788 52.381 0.00 0.00 0.00 3.06
2016 2084 0.443478 CGCTCAAACGCACATGATGA 59.557 50.000 0.00 0.00 0.00 2.92
2017 2085 2.920640 CGCTCAAACGCACATGATG 58.079 52.632 0.00 0.00 0.00 3.07
2026 2094 3.911365 TGAAATGTTAATGCGCTCAAACG 59.089 39.130 9.73 0.00 0.00 3.60
2027 2095 6.393720 AATGAAATGTTAATGCGCTCAAAC 57.606 33.333 9.73 10.49 0.00 2.93
2028 2096 6.867816 AGAAATGAAATGTTAATGCGCTCAAA 59.132 30.769 9.73 0.00 0.00 2.69
2029 2097 6.389091 AGAAATGAAATGTTAATGCGCTCAA 58.611 32.000 9.73 0.00 0.00 3.02
2047 2115 8.821147 TCCATCACTTGAAAATCAAAGAAATG 57.179 30.769 0.00 0.00 35.73 2.32
2054 2122 5.984926 GCAGTTTCCATCACTTGAAAATCAA 59.015 36.000 0.00 0.00 34.79 2.57
2062 2130 4.756642 TGTTAGAGCAGTTTCCATCACTTG 59.243 41.667 0.00 0.00 0.00 3.16
2075 2143 4.701765 AGCACATAGGATTGTTAGAGCAG 58.298 43.478 0.00 0.00 0.00 4.24
2077 2145 5.463724 GTGTAGCACATAGGATTGTTAGAGC 59.536 44.000 0.00 0.00 34.08 4.09
2079 2147 6.538945 TGTGTAGCACATAGGATTGTTAGA 57.461 37.500 0.00 0.00 39.62 2.10
2093 2162 6.961359 TTGTGACAAGTATATGTGTAGCAC 57.039 37.500 0.00 0.00 32.57 4.40
2099 2168 6.249050 CGCAAACATTGTGACAAGTATATGTG 59.751 38.462 3.74 2.63 43.66 3.21
2113 2182 0.595567 CTGTGCTGCGCAAACATTGT 60.596 50.000 21.81 0.00 41.47 2.71
2117 2186 1.226632 CAACTGTGCTGCGCAAACA 60.227 52.632 20.69 20.69 41.47 2.83
2136 2213 1.136695 ACATTTGCATTGGGTATGGCG 59.863 47.619 0.00 0.00 34.66 5.69
2138 2215 4.685924 GAAGACATTTGCATTGGGTATGG 58.314 43.478 0.00 0.00 34.66 2.74
2146 2223 5.587443 TCATCTGATCGAAGACATTTGCATT 59.413 36.000 0.00 0.00 42.51 3.56
2149 2226 5.670149 ATCATCTGATCGAAGACATTTGC 57.330 39.130 0.00 0.00 42.51 3.68
2150 2227 6.368243 CCCTATCATCTGATCGAAGACATTTG 59.632 42.308 0.00 0.00 42.51 2.32
2160 2237 4.078537 ACTCAGTCCCTATCATCTGATCG 58.921 47.826 0.00 0.00 36.55 3.69
2176 2253 9.178758 GAATTCACCCAAGATAATTAACTCAGT 57.821 33.333 0.00 0.00 0.00 3.41
2211 2288 2.623878 TACGGGCAAGTTTTGAGTGA 57.376 45.000 0.00 0.00 0.00 3.41
2270 2348 1.727535 CGCGGTGCAAATTTTCGATGA 60.728 47.619 0.00 0.00 0.00 2.92
2397 2475 1.669779 ACGCTACAGTACTGGATCGAC 59.330 52.381 32.07 11.82 34.19 4.20
2549 2652 6.140737 GTCGCAGTAATTGTTCACTTTCAAAG 59.859 38.462 0.00 0.00 0.00 2.77
2644 2754 6.128499 ACAATTACTGTAGCACGCGATTTTTA 60.128 34.615 15.93 0.00 36.10 1.52
2735 2867 4.689612 AATGTGAATATCTGTACCGCCT 57.310 40.909 0.00 0.00 0.00 5.52
2762 2897 0.319555 TGCACTGTAGCGTCCACTTC 60.320 55.000 0.00 0.00 37.31 3.01
2769 3207 0.456824 CGTCTGATGCACTGTAGCGT 60.457 55.000 0.00 0.00 37.31 5.07
2818 3256 3.967332 AAGACAATTTTGCCCCTGATG 57.033 42.857 0.00 0.00 0.00 3.07
2819 3257 4.347583 TGAAAAGACAATTTTGCCCCTGAT 59.652 37.500 0.00 0.00 0.00 2.90
2843 3281 1.760613 AGTTGACCGTCAAGTGGAAGA 59.239 47.619 18.84 0.00 38.51 2.87


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

AutoCloner maintained by Alex Coulton.