Multiple sequence alignment - TraesCS3A01G315500

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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 TraesCS3A01G315500 chr3A 100.000 4691 0 0 1 4691 556463394 556458704 0.000000e+00 8663.0
1 TraesCS3A01G315500 chr3D 93.766 3946 159 27 787 4686 429595430 429599334 0.000000e+00 5843.0
2 TraesCS3A01G315500 chr3D 91.049 391 29 4 27 416 429594332 429594717 1.500000e-144 523.0
3 TraesCS3A01G315500 chr3D 90.675 311 17 2 401 701 429595137 429595445 2.030000e-108 403.0
4 TraesCS3A01G315500 chr3D 94.737 76 3 1 706 781 307914827 307914901 2.970000e-22 117.0
5 TraesCS3A01G315500 chr3B 93.470 2741 134 19 1975 4686 561538761 561541485 0.000000e+00 4028.0
6 TraesCS3A01G315500 chr3B 91.660 1175 39 17 784 1919 561537610 561538764 0.000000e+00 1572.0
7 TraesCS3A01G315500 chr3B 83.230 483 51 10 123 593 561513264 561513728 2.610000e-112 416.0
8 TraesCS3A01G315500 chr3B 94.667 75 3 1 707 781 620657793 620657720 1.070000e-21 115.0
9 TraesCS3A01G315500 chr7D 87.156 218 23 4 324 538 155280182 155280397 4.690000e-60 243.0
10 TraesCS3A01G315500 chr7D 89.720 107 10 1 535 640 155285899 155286005 8.190000e-28 135.0
11 TraesCS3A01G315500 chr7D 97.368 76 1 1 706 781 158755235 158755161 1.370000e-25 128.0
12 TraesCS3A01G315500 chr5B 88.281 128 13 1 574 701 421285961 421285836 8.130000e-33 152.0
13 TraesCS3A01G315500 chr5B 96.053 76 2 1 706 781 371389031 371389105 6.370000e-24 122.0
14 TraesCS3A01G315500 chr5B 93.103 58 3 1 787 844 421285851 421285795 3.010000e-12 84.2
15 TraesCS3A01G315500 chr6A 95.890 73 3 0 704 776 578956715 578956643 8.250000e-23 119.0
16 TraesCS3A01G315500 chr6A 94.667 75 3 1 707 781 328382508 328382435 1.070000e-21 115.0
17 TraesCS3A01G315500 chr4A 93.506 77 5 0 705 781 105225835 105225759 1.070000e-21 115.0
18 TraesCS3A01G315500 chr4D 93.506 77 3 2 705 781 359677872 359677946 3.840000e-21 113.0
19 TraesCS3A01G315500 chr7A 90.361 83 7 1 699 781 10259353 10259434 1.780000e-19 108.0


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 TraesCS3A01G315500 chr3A 556458704 556463394 4690 True 8663.000000 8663 100.000 1 4691 1 chr3A.!!$R1 4690
1 TraesCS3A01G315500 chr3D 429594332 429599334 5002 False 2256.333333 5843 91.830 27 4686 3 chr3D.!!$F2 4659
2 TraesCS3A01G315500 chr3B 561537610 561541485 3875 False 2800.000000 4028 92.565 784 4686 2 chr3B.!!$F2 3902

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
634 1080 0.191064 AGGCTGATTCCCCTCGGATA 59.809 55.0 0.00 0.00 38.24 2.59 F
1893 2382 0.035152 ATCCTTGTTCATGCTCGGCA 60.035 50.0 1.01 1.01 44.86 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2911 0.611618 TTGGGGTTCGCTGCAATGAT 60.612 50.0 0.00 0.0 0.00 2.45 R
3828 4336 0.104120 AGGCAACGCATACGAGCATA 59.896 50.0 9.11 0.0 43.93 3.14 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
21 22 4.078639 GTTCTGGTGGGATAATCAGGAG 57.921 50.000 0.00 0.00 0.00 3.69
22 23 2.694397 TCTGGTGGGATAATCAGGAGG 58.306 52.381 0.00 0.00 0.00 4.30
23 24 2.250008 TCTGGTGGGATAATCAGGAGGA 59.750 50.000 0.00 0.00 0.00 3.71
24 25 3.116199 TCTGGTGGGATAATCAGGAGGAT 60.116 47.826 0.00 0.00 38.05 3.24
25 26 2.981784 TGGTGGGATAATCAGGAGGATG 59.018 50.000 0.00 0.00 36.02 3.51
49 50 5.385198 AGAAAATTGTTAAGGTGGCAGAGA 58.615 37.500 0.00 0.00 0.00 3.10
55 56 1.468506 TAAGGTGGCAGAGACACGCA 61.469 55.000 0.00 0.00 43.55 5.24
130 131 5.466728 CCTATTGCGTTGCACTAAGATGTAT 59.533 40.000 0.00 0.00 38.71 2.29
132 133 3.595173 TGCGTTGCACTAAGATGTATGT 58.405 40.909 0.00 0.00 31.71 2.29
144 145 3.282021 AGATGTATGTTGTGCACCATCC 58.718 45.455 20.84 9.03 38.53 3.51
162 163 4.645535 CATCCGATGGAACTTGGATATGT 58.354 43.478 0.00 0.00 39.16 2.29
214 215 3.901222 TGATGGACCGGCTGATTCTAATA 59.099 43.478 0.00 0.00 0.00 0.98
217 218 4.894784 TGGACCGGCTGATTCTAATAATC 58.105 43.478 0.00 0.00 0.00 1.75
218 219 4.346709 TGGACCGGCTGATTCTAATAATCA 59.653 41.667 0.00 0.91 35.56 2.57
219 220 5.013079 TGGACCGGCTGATTCTAATAATCAT 59.987 40.000 0.00 0.00 36.23 2.45
220 221 5.940470 GGACCGGCTGATTCTAATAATCATT 59.060 40.000 0.00 0.00 36.23 2.57
222 223 5.940470 ACCGGCTGATTCTAATAATCATTCC 59.060 40.000 0.00 5.39 36.23 3.01
223 224 5.355350 CCGGCTGATTCTAATAATCATTCCC 59.645 44.000 0.00 2.78 36.23 3.97
224 225 6.176183 CGGCTGATTCTAATAATCATTCCCT 58.824 40.000 1.20 0.00 36.23 4.20
241 242 7.504403 TCATTCCCTAATGAAAAAGTTGCAAA 58.496 30.769 0.00 0.00 46.64 3.68
246 247 6.293027 CCCTAATGAAAAAGTTGCAAAAGCTG 60.293 38.462 0.00 0.00 0.00 4.24
275 276 3.782523 AGGGCTTGTTATGATCTTCTCCA 59.217 43.478 0.00 0.00 0.00 3.86
277 278 4.949856 GGGCTTGTTATGATCTTCTCCAAA 59.050 41.667 0.00 0.00 0.00 3.28
279 280 6.460676 GGGCTTGTTATGATCTTCTCCAAATG 60.461 42.308 0.00 0.00 0.00 2.32
289 290 5.186996 TCTTCTCCAAATGCAAACTTCAC 57.813 39.130 0.00 0.00 0.00 3.18
307 308 1.153842 CCAATTTTCGGCCCGAAGC 60.154 57.895 19.18 0.00 46.43 3.86
328 329 4.715983 GCCCGAACGCGATAACTA 57.284 55.556 15.93 0.00 40.82 2.24
331 332 1.866880 GCCCGAACGCGATAACTACAT 60.867 52.381 15.93 0.00 40.82 2.29
341 342 4.267690 CGCGATAACTACATGAAGCTGAAA 59.732 41.667 0.00 0.00 0.00 2.69
344 345 6.564873 GCGATAACTACATGAAGCTGAAATCC 60.565 42.308 0.00 0.00 0.00 3.01
345 346 6.479990 CGATAACTACATGAAGCTGAAATCCA 59.520 38.462 0.00 0.00 0.00 3.41
346 347 7.307042 CGATAACTACATGAAGCTGAAATCCAG 60.307 40.741 0.00 0.00 45.67 3.86
356 357 1.863454 CTGAAATCCAGGAAGCGATCG 59.137 52.381 11.69 11.69 39.23 3.69
369 370 0.595310 GCGATCGTGGGCTCTAGTTC 60.595 60.000 17.81 0.00 0.00 3.01
381 382 5.196695 GGGCTCTAGTTCATTTTTCTGGAT 58.803 41.667 0.00 0.00 0.00 3.41
465 901 2.539476 CACTGCCAAGAAAAACGCTTT 58.461 42.857 0.00 0.00 0.00 3.51
502 948 4.473520 CCCGCTCGCCCACATCTT 62.474 66.667 0.00 0.00 0.00 2.40
510 956 1.032114 CGCCCACATCTTCCCTTTCC 61.032 60.000 0.00 0.00 0.00 3.13
519 965 3.179902 TCTTCCCTTTCCCTCGTCTTA 57.820 47.619 0.00 0.00 0.00 2.10
538 984 6.107343 GTCTTATCCTCTCAAACCCTAACAC 58.893 44.000 0.00 0.00 0.00 3.32
627 1073 1.152368 CATCCCAGGCTGATTCCCC 59.848 63.158 17.94 0.00 0.00 4.81
628 1074 1.006631 ATCCCAGGCTGATTCCCCT 59.993 57.895 17.94 0.00 0.00 4.79
634 1080 0.191064 AGGCTGATTCCCCTCGGATA 59.809 55.000 0.00 0.00 38.24 2.59
640 1086 2.257207 GATTCCCCTCGGATACCATCA 58.743 52.381 0.00 0.00 38.24 3.07
643 1089 1.149077 TCCCCTCGGATACCATCATCA 59.851 52.381 0.00 0.00 31.13 3.07
645 1091 2.251818 CCCTCGGATACCATCATCAGT 58.748 52.381 0.00 0.00 0.00 3.41
648 1094 2.298446 CTCGGATACCATCATCAGTGCT 59.702 50.000 0.00 0.00 0.00 4.40
683 1129 4.020617 CAAGGAGCTGCGACCCCA 62.021 66.667 13.44 0.00 0.00 4.96
684 1130 3.011517 AAGGAGCTGCGACCCCAT 61.012 61.111 13.44 1.06 0.00 4.00
685 1131 1.689233 AAGGAGCTGCGACCCCATA 60.689 57.895 13.44 0.00 0.00 2.74
686 1132 1.056700 AAGGAGCTGCGACCCCATAT 61.057 55.000 13.44 0.00 0.00 1.78
687 1133 1.302033 GGAGCTGCGACCCCATATG 60.302 63.158 0.00 0.00 0.00 1.78
688 1134 1.963338 GAGCTGCGACCCCATATGC 60.963 63.158 0.00 0.00 0.00 3.14
689 1135 2.980233 GCTGCGACCCCATATGCC 60.980 66.667 0.00 0.00 0.00 4.40
690 1136 2.831770 CTGCGACCCCATATGCCT 59.168 61.111 0.00 0.00 0.00 4.75
691 1137 1.302033 CTGCGACCCCATATGCCTC 60.302 63.158 0.00 0.00 0.00 4.70
692 1138 2.357517 GCGACCCCATATGCCTCG 60.358 66.667 0.00 4.08 0.00 4.63
693 1139 2.343758 CGACCCCATATGCCTCGG 59.656 66.667 0.00 0.00 0.00 4.63
694 1140 2.207229 CGACCCCATATGCCTCGGA 61.207 63.158 0.00 0.00 0.00 4.55
695 1141 1.674057 GACCCCATATGCCTCGGAG 59.326 63.158 0.00 0.00 0.00 4.63
696 1142 1.831652 GACCCCATATGCCTCGGAGG 61.832 65.000 19.95 19.95 38.80 4.30
697 1143 1.536418 CCCCATATGCCTCGGAGGA 60.536 63.158 27.95 12.87 37.67 3.71
698 1144 1.548357 CCCCATATGCCTCGGAGGAG 61.548 65.000 27.95 10.44 37.67 3.69
699 1145 1.294780 CCATATGCCTCGGAGGAGC 59.705 63.158 27.95 13.38 37.67 4.70
700 1146 1.190833 CCATATGCCTCGGAGGAGCT 61.191 60.000 27.95 12.68 37.67 4.09
701 1147 0.683973 CATATGCCTCGGAGGAGCTT 59.316 55.000 27.95 12.98 37.67 3.74
702 1148 1.071385 CATATGCCTCGGAGGAGCTTT 59.929 52.381 27.95 8.74 37.67 3.51
703 1149 1.204146 TATGCCTCGGAGGAGCTTTT 58.796 50.000 27.95 7.07 37.67 2.27
704 1150 0.329596 ATGCCTCGGAGGAGCTTTTT 59.670 50.000 27.95 0.53 37.67 1.94
727 1173 3.611025 TTTTTGAGGGATCCCACACTT 57.389 42.857 32.69 11.80 36.46 3.16
728 1174 3.611025 TTTTGAGGGATCCCACACTTT 57.389 42.857 32.69 10.96 36.46 2.66
729 1175 4.733077 TTTTGAGGGATCCCACACTTTA 57.267 40.909 32.69 14.57 36.46 1.85
730 1176 4.946160 TTTGAGGGATCCCACACTTTAT 57.054 40.909 32.69 9.28 36.46 1.40
731 1177 4.946160 TTGAGGGATCCCACACTTTATT 57.054 40.909 32.69 8.46 36.46 1.40
732 1178 6.395780 TTTGAGGGATCCCACACTTTATTA 57.604 37.500 32.69 12.69 36.46 0.98
733 1179 6.395780 TTGAGGGATCCCACACTTTATTAA 57.604 37.500 32.69 11.94 36.46 1.40
734 1180 6.590656 TGAGGGATCCCACACTTTATTAAT 57.409 37.500 32.69 6.81 38.92 1.40
735 1181 6.980577 TGAGGGATCCCACACTTTATTAATT 58.019 36.000 32.69 6.32 38.92 1.40
736 1182 8.108378 TGAGGGATCCCACACTTTATTAATTA 57.892 34.615 32.69 2.71 38.92 1.40
737 1183 8.217799 TGAGGGATCCCACACTTTATTAATTAG 58.782 37.037 32.69 0.00 38.92 1.73
738 1184 8.344939 AGGGATCCCACACTTTATTAATTAGA 57.655 34.615 32.69 0.00 38.92 2.10
739 1185 8.787818 AGGGATCCCACACTTTATTAATTAGAA 58.212 33.333 32.69 0.00 38.92 2.10
740 1186 9.416284 GGGATCCCACACTTTATTAATTAGAAA 57.584 33.333 26.95 0.00 35.81 2.52
762 1208 9.838339 AGAAACTATGTTCATAGGGATACAAAG 57.162 33.333 19.63 0.00 39.74 2.77
763 1209 8.980481 AAACTATGTTCATAGGGATACAAAGG 57.020 34.615 19.63 0.00 39.74 3.11
764 1210 7.079451 ACTATGTTCATAGGGATACAAAGGG 57.921 40.000 19.63 0.00 39.74 3.95
765 1211 4.788925 TGTTCATAGGGATACAAAGGGG 57.211 45.455 0.00 0.00 39.74 4.79
766 1212 3.461831 TGTTCATAGGGATACAAAGGGGG 59.538 47.826 0.00 0.00 39.74 5.40
767 1213 3.448277 TCATAGGGATACAAAGGGGGT 57.552 47.619 0.00 0.00 39.74 4.95
768 1214 3.323775 TCATAGGGATACAAAGGGGGTC 58.676 50.000 0.00 0.00 39.74 4.46
769 1215 2.974285 TAGGGATACAAAGGGGGTCA 57.026 50.000 0.00 0.00 39.74 4.02
770 1216 2.303660 AGGGATACAAAGGGGGTCAT 57.696 50.000 0.00 0.00 39.74 3.06
771 1217 1.852965 AGGGATACAAAGGGGGTCATG 59.147 52.381 0.00 0.00 39.74 3.07
772 1218 1.850345 GGGATACAAAGGGGGTCATGA 59.150 52.381 0.00 0.00 39.74 3.07
773 1219 2.158608 GGGATACAAAGGGGGTCATGAG 60.159 54.545 0.00 0.00 39.74 2.90
774 1220 2.158608 GGATACAAAGGGGGTCATGAGG 60.159 54.545 0.00 0.00 0.00 3.86
775 1221 1.295020 TACAAAGGGGGTCATGAGGG 58.705 55.000 0.00 0.00 0.00 4.30
776 1222 1.307647 CAAAGGGGGTCATGAGGGG 59.692 63.158 0.00 0.00 0.00 4.79
777 1223 1.935931 AAAGGGGGTCATGAGGGGG 60.936 63.158 0.00 0.00 0.00 5.40
778 1224 2.747514 AAAGGGGGTCATGAGGGGGT 62.748 60.000 0.00 0.00 0.00 4.95
779 1225 1.844296 AAGGGGGTCATGAGGGGGTA 61.844 60.000 0.00 0.00 0.00 3.69
780 1226 1.770518 GGGGGTCATGAGGGGGTAG 60.771 68.421 0.00 0.00 0.00 3.18
781 1227 2.452937 GGGGTCATGAGGGGGTAGC 61.453 68.421 0.00 0.00 0.00 3.58
782 1228 2.452937 GGGTCATGAGGGGGTAGCC 61.453 68.421 1.07 1.07 0.00 3.93
804 1250 0.896019 TATGCCTCGGAGGAGCTAGC 60.896 60.000 27.95 6.62 37.67 3.42
880 1326 3.160585 CCTGGCCTGTTGGAGTCA 58.839 61.111 3.32 0.00 34.57 3.41
918 1365 7.324388 TCTTACTTCTAGATCCAACCCAAAA 57.676 36.000 0.00 0.00 0.00 2.44
969 1418 2.235016 GGTCCACGACACACACACG 61.235 63.158 0.00 0.00 33.68 4.49
1114 1563 1.461268 TCCACTTCTGCCTCCCACA 60.461 57.895 0.00 0.00 0.00 4.17
1254 1703 1.099689 CGGTGGACCACAAGTTTGTT 58.900 50.000 25.75 0.00 39.91 2.83
1296 1745 0.860203 TCGCGTTCGTATCTTCAGCG 60.860 55.000 5.77 0.20 46.29 5.18
1369 1846 0.397535 TACTCCGGCCCCGAAATAGT 60.398 55.000 8.54 8.40 42.83 2.12
1387 1864 8.064222 CGAAATAGTAGTAGTCAAATTGGCATG 58.936 37.037 0.00 0.00 0.00 4.06
1416 1893 2.322830 CCGGCGCATGATCTGATGG 61.323 63.158 10.83 0.00 0.00 3.51
1432 1910 3.445008 TGATGGTCTCTCTGCTACCTTT 58.555 45.455 0.00 0.00 34.23 3.11
1433 1911 3.840666 TGATGGTCTCTCTGCTACCTTTT 59.159 43.478 0.00 0.00 34.23 2.27
1434 1912 3.963428 TGGTCTCTCTGCTACCTTTTC 57.037 47.619 0.00 0.00 34.23 2.29
1452 1930 6.761242 ACCTTTTCTTTTATGTTCTTGCCAAC 59.239 34.615 0.00 0.00 0.00 3.77
1453 1931 6.760770 CCTTTTCTTTTATGTTCTTGCCAACA 59.239 34.615 0.00 0.00 40.54 3.33
1454 1932 7.442062 CCTTTTCTTTTATGTTCTTGCCAACAT 59.558 33.333 9.85 9.85 46.54 2.71
1455 1933 7.712264 TTTCTTTTATGTTCTTGCCAACATG 57.288 32.000 13.39 0.00 44.92 3.21
1457 1935 4.870123 TTTATGTTCTTGCCAACATGCT 57.130 36.364 13.39 0.00 44.92 3.79
1458 1936 4.870123 TTATGTTCTTGCCAACATGCTT 57.130 36.364 13.39 0.00 44.92 3.91
1459 1937 5.973899 TTATGTTCTTGCCAACATGCTTA 57.026 34.783 13.39 0.00 44.92 3.09
1511 1994 5.418676 TCGAACAACATATGAAGCTCATCA 58.581 37.500 10.38 0.00 38.26 3.07
1575 2061 4.850680 TCTATTTACAATCCCGCCAAGTT 58.149 39.130 0.00 0.00 0.00 2.66
1660 2146 0.548031 TGCTCCCCTCTAGCATTTGG 59.452 55.000 0.00 0.00 44.78 3.28
1850 2337 2.347114 CCTCACATGGCCGTGTCA 59.653 61.111 28.08 15.52 38.12 3.58
1851 2338 1.078214 CCTCACATGGCCGTGTCAT 60.078 57.895 28.08 3.88 38.12 3.06
1859 2346 1.307355 TGGCCGTGTCATTGAGCATG 61.307 55.000 0.00 0.00 0.00 4.06
1860 2347 1.430632 GCCGTGTCATTGAGCATGG 59.569 57.895 16.72 16.72 42.91 3.66
1893 2382 0.035152 ATCCTTGTTCATGCTCGGCA 60.035 50.000 1.01 1.01 44.86 5.69
1996 2485 1.306568 AGGGAACTGGAGGAGGCTC 60.307 63.158 5.78 5.78 41.13 4.70
2212 2702 6.566141 TCTATTCCGTTTCACGTATTGATCA 58.434 36.000 0.00 0.00 40.58 2.92
2302 2792 8.918658 CACAAAATCTCCAACATAACATTTCTG 58.081 33.333 0.00 0.00 0.00 3.02
2421 2911 5.534278 TCTTGTGATTTTGTGACATTGCCTA 59.466 36.000 0.00 0.00 0.00 3.93
2799 3294 4.503714 TGAGGTAATGGATTCCCTTGAC 57.496 45.455 0.00 0.00 0.00 3.18
3044 3543 5.452078 TTGTTTTCTCCATTTCGCTGAAT 57.548 34.783 0.00 0.00 0.00 2.57
3276 3775 6.145534 TGCTATTATGTTACGCTGATACTTGC 59.854 38.462 0.00 0.00 0.00 4.01
3383 3888 6.240894 CCATATGGGCTTTATGCTTTCTAGA 58.759 40.000 14.52 0.00 42.39 2.43
3388 3893 4.279420 GGGCTTTATGCTTTCTAGAATGGG 59.721 45.833 17.41 7.98 42.39 4.00
3393 3898 8.633561 GCTTTATGCTTTCTAGAATGGGTTTAT 58.366 33.333 17.41 4.92 38.95 1.40
3410 3915 5.337733 GGGTTTATATTTTCCCCAACGCTTT 60.338 40.000 0.00 0.00 35.32 3.51
3416 3921 5.738619 ATTTTCCCCAACGCTTTATTTCT 57.261 34.783 0.00 0.00 0.00 2.52
3418 3923 4.776795 TTCCCCAACGCTTTATTTCTTC 57.223 40.909 0.00 0.00 0.00 2.87
3430 3935 7.093771 ACGCTTTATTTCTTCAAAAGATCCCAT 60.094 33.333 0.00 0.00 37.38 4.00
3453 3958 7.255173 CCATTCTTAAAAGATCCTGCTCAGATG 60.255 40.741 0.00 0.00 34.49 2.90
3498 4003 3.181465 ACTGTCCATTACCCATAAGCTCG 60.181 47.826 0.00 0.00 0.00 5.03
3508 4013 3.197766 ACCCATAAGCTCGTCAATCTTGA 59.802 43.478 0.00 0.00 34.20 3.02
3517 4022 4.864806 GCTCGTCAATCTTGATCTGTTACA 59.135 41.667 0.00 0.00 39.73 2.41
3636 4141 3.181475 GGACTGGAGTAAATCTCATGCGA 60.181 47.826 0.00 0.00 44.40 5.10
3720 4225 4.884164 AGGAAAATGCCACATAGCTAAGTC 59.116 41.667 0.00 0.00 0.00 3.01
3721 4226 4.036852 GGAAAATGCCACATAGCTAAGTCC 59.963 45.833 0.00 0.00 0.00 3.85
3722 4227 3.931907 AATGCCACATAGCTAAGTCCA 57.068 42.857 0.00 0.00 0.00 4.02
3724 4229 3.931907 TGCCACATAGCTAAGTCCAAT 57.068 42.857 0.00 0.00 0.00 3.16
3731 4236 0.929244 AGCTAAGTCCAATGGGGCAT 59.071 50.000 0.00 0.00 43.06 4.40
3742 4247 3.446799 CAATGGGGCATACAACATTTCG 58.553 45.455 0.00 0.00 31.67 3.46
3743 4248 2.498644 TGGGGCATACAACATTTCGA 57.501 45.000 0.00 0.00 0.00 3.71
3746 4251 1.676006 GGGCATACAACATTTCGAGGG 59.324 52.381 0.00 0.00 0.00 4.30
3761 4268 3.552875 TCGAGGGAGTAAACGAGATGAT 58.447 45.455 0.00 0.00 0.00 2.45
3762 4269 3.315470 TCGAGGGAGTAAACGAGATGATG 59.685 47.826 0.00 0.00 0.00 3.07
3768 4276 5.520649 GGGAGTAAACGAGATGATGTCTTTC 59.479 44.000 0.00 0.00 37.29 2.62
3780 4288 8.659925 AGATGATGTCTTTCAGTATGTTGATC 57.340 34.615 0.00 0.00 32.37 2.92
3784 4292 4.937620 TGTCTTTCAGTATGTTGATCCTGC 59.062 41.667 0.00 0.00 37.40 4.85
3790 4298 3.376234 CAGTATGTTGATCCTGCCAAGTG 59.624 47.826 0.00 0.00 0.00 3.16
3797 4305 1.541588 GATCCTGCCAAGTGAACCAAC 59.458 52.381 0.00 0.00 0.00 3.77
3798 4306 0.257328 TCCTGCCAAGTGAACCAACA 59.743 50.000 0.00 0.00 0.00 3.33
3854 4362 4.295870 CTCGTATGCGTTGCCTAATAAGA 58.704 43.478 2.37 0.00 39.49 2.10
3855 4363 4.295870 TCGTATGCGTTGCCTAATAAGAG 58.704 43.478 2.37 0.00 39.49 2.85
3862 4370 3.118738 CGTTGCCTAATAAGAGGTCTGGT 60.119 47.826 0.00 0.00 39.02 4.00
3873 4381 3.087031 AGAGGTCTGGTTTTCGTCGATA 58.913 45.455 0.00 0.00 0.00 2.92
3936 4444 0.587768 TTTGCGTGCTGTGATCTGTG 59.412 50.000 0.00 0.00 0.00 3.66
3971 4479 5.178438 GTGTTGTCCAAAAATTGTGTGTTGT 59.822 36.000 0.00 0.00 0.00 3.32
4004 4515 6.219417 AGCATGATCAGCCATACTAGTATC 57.781 41.667 12.62 3.11 0.00 2.24
4171 4682 2.011046 GCTGAGCCTGACCATGAGAAC 61.011 57.143 0.00 0.00 0.00 3.01
4181 4692 1.620819 ACCATGAGAACGCAGAACTCT 59.379 47.619 0.00 0.00 35.37 3.24
4421 4932 1.733399 GTCGAACTGCACCGAGGTC 60.733 63.158 0.00 0.00 35.31 3.85
4464 4975 4.867599 GCCCGATCCACGTCGACC 62.868 72.222 10.58 0.00 44.06 4.79
4483 4994 0.867753 CGCGAAGAACGGAGGATCAG 60.868 60.000 0.00 0.00 42.83 2.90
4485 4996 0.103208 CGAAGAACGGAGGATCAGGG 59.897 60.000 0.00 0.00 36.25 4.45
4489 5000 0.461961 GAACGGAGGATCAGGGACAG 59.538 60.000 0.00 0.00 36.25 3.51
4550 5071 2.043953 GGAGAATGGTGGGTGGGC 60.044 66.667 0.00 0.00 0.00 5.36
4647 5168 2.666272 TGGATGCCAACCAAAGTACA 57.334 45.000 0.00 0.00 34.25 2.90
4648 5169 2.513753 TGGATGCCAACCAAAGTACAG 58.486 47.619 0.00 0.00 34.25 2.74
4649 5170 1.818674 GGATGCCAACCAAAGTACAGG 59.181 52.381 0.00 0.00 0.00 4.00
4650 5171 1.202348 GATGCCAACCAAAGTACAGGC 59.798 52.381 0.00 0.00 38.41 4.85
4651 5172 0.106469 TGCCAACCAAAGTACAGGCA 60.106 50.000 0.00 0.00 42.69 4.75
4655 5176 1.000274 CAACCAAAGTACAGGCAAGGC 60.000 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181450 CCTCCTGATTATCCCACCAGAAC 60.181 52.174 0.00 0.00 0.00 3.01
1 2 3.048600 CCTCCTGATTATCCCACCAGAA 58.951 50.000 0.00 0.00 0.00 3.02
2 3 2.250008 TCCTCCTGATTATCCCACCAGA 59.750 50.000 0.00 0.00 0.00 3.86
3 4 2.694397 TCCTCCTGATTATCCCACCAG 58.306 52.381 0.00 0.00 0.00 4.00
4 5 2.887454 TCCTCCTGATTATCCCACCA 57.113 50.000 0.00 0.00 0.00 4.17
5 6 3.251484 TCATCCTCCTGATTATCCCACC 58.749 50.000 0.00 0.00 0.00 4.61
6 7 4.163427 TCTCATCCTCCTGATTATCCCAC 58.837 47.826 0.00 0.00 0.00 4.61
7 8 4.492182 TCTCATCCTCCTGATTATCCCA 57.508 45.455 0.00 0.00 0.00 4.37
8 9 5.832539 TTTCTCATCCTCCTGATTATCCC 57.167 43.478 0.00 0.00 0.00 3.85
9 10 7.723172 ACAATTTTCTCATCCTCCTGATTATCC 59.277 37.037 0.00 0.00 0.00 2.59
10 11 8.688747 ACAATTTTCTCATCCTCCTGATTATC 57.311 34.615 0.00 0.00 0.00 1.75
12 13 9.973661 TTAACAATTTTCTCATCCTCCTGATTA 57.026 29.630 0.00 0.00 0.00 1.75
13 14 8.884124 TTAACAATTTTCTCATCCTCCTGATT 57.116 30.769 0.00 0.00 0.00 2.57
14 15 7.559170 CCTTAACAATTTTCTCATCCTCCTGAT 59.441 37.037 0.00 0.00 0.00 2.90
15 16 6.886459 CCTTAACAATTTTCTCATCCTCCTGA 59.114 38.462 0.00 0.00 0.00 3.86
16 17 6.660949 ACCTTAACAATTTTCTCATCCTCCTG 59.339 38.462 0.00 0.00 0.00 3.86
17 18 6.660949 CACCTTAACAATTTTCTCATCCTCCT 59.339 38.462 0.00 0.00 0.00 3.69
18 19 6.127619 CCACCTTAACAATTTTCTCATCCTCC 60.128 42.308 0.00 0.00 0.00 4.30
19 20 6.625960 GCCACCTTAACAATTTTCTCATCCTC 60.626 42.308 0.00 0.00 0.00 3.71
20 21 5.185828 GCCACCTTAACAATTTTCTCATCCT 59.814 40.000 0.00 0.00 0.00 3.24
21 22 5.047377 TGCCACCTTAACAATTTTCTCATCC 60.047 40.000 0.00 0.00 0.00 3.51
22 23 6.024552 TGCCACCTTAACAATTTTCTCATC 57.975 37.500 0.00 0.00 0.00 2.92
23 24 5.774690 TCTGCCACCTTAACAATTTTCTCAT 59.225 36.000 0.00 0.00 0.00 2.90
24 25 5.136828 TCTGCCACCTTAACAATTTTCTCA 58.863 37.500 0.00 0.00 0.00 3.27
25 26 5.473504 TCTCTGCCACCTTAACAATTTTCTC 59.526 40.000 0.00 0.00 0.00 2.87
49 50 0.108520 AATTCGTACGGGATGCGTGT 60.109 50.000 16.52 0.00 37.71 4.49
55 56 1.066605 CCGACTCAATTCGTACGGGAT 59.933 52.381 16.52 7.32 37.29 3.85
62 63 2.007049 GCACCATCCGACTCAATTCGT 61.007 52.381 0.00 0.00 37.29 3.85
113 114 5.315982 CACAACATACATCTTAGTGCAACG 58.684 41.667 0.00 0.00 45.86 4.10
130 131 0.959867 CCATCGGATGGTGCACAACA 60.960 55.000 25.70 8.86 45.54 3.33
132 133 4.317359 CCATCGGATGGTGCACAA 57.683 55.556 25.70 8.12 45.54 3.33
144 145 3.059884 CCGACATATCCAAGTTCCATCG 58.940 50.000 0.00 0.00 0.00 3.84
159 160 2.573869 CACTCGTCCAGCCGACAT 59.426 61.111 2.76 0.00 42.07 3.06
184 185 2.279517 CGGTCCATCACGCCTAGC 60.280 66.667 0.00 0.00 0.00 3.42
196 197 4.894784 TGATTATTAGAATCAGCCGGTCC 58.105 43.478 1.90 0.00 33.20 4.46
217 218 7.727331 TTTGCAACTTTTTCATTAGGGAATG 57.273 32.000 0.00 0.00 43.39 2.67
218 219 7.041167 GCTTTTGCAACTTTTTCATTAGGGAAT 60.041 33.333 0.00 0.00 46.58 3.01
219 220 6.259829 GCTTTTGCAACTTTTTCATTAGGGAA 59.740 34.615 0.00 0.00 46.58 3.97
220 221 5.757808 GCTTTTGCAACTTTTTCATTAGGGA 59.242 36.000 0.00 0.00 46.58 4.20
263 264 6.209986 TGAAGTTTGCATTTGGAGAAGATCAT 59.790 34.615 0.00 0.00 0.00 2.45
270 271 3.295093 TGGTGAAGTTTGCATTTGGAGA 58.705 40.909 0.00 0.00 0.00 3.71
275 276 5.007528 CCGAAAATTGGTGAAGTTTGCATTT 59.992 36.000 0.00 0.00 29.72 2.32
277 278 4.057432 CCGAAAATTGGTGAAGTTTGCAT 58.943 39.130 0.00 0.00 29.72 3.96
279 280 2.220824 GCCGAAAATTGGTGAAGTTTGC 59.779 45.455 0.00 0.00 29.72 3.68
289 290 1.153842 GCTTCGGGCCGAAAATTGG 60.154 57.895 37.48 27.14 45.23 3.16
321 322 7.041508 CCTGGATTTCAGCTTCATGTAGTTATC 60.042 40.741 1.02 0.00 42.05 1.75
328 329 3.726557 TCCTGGATTTCAGCTTCATGT 57.273 42.857 0.00 0.00 42.05 3.21
331 332 2.440409 GCTTCCTGGATTTCAGCTTCA 58.560 47.619 10.20 0.00 42.05 3.02
341 342 1.443407 CCACGATCGCTTCCTGGAT 59.557 57.895 16.60 0.00 33.64 3.41
344 345 2.892425 GCCCACGATCGCTTCCTG 60.892 66.667 16.60 5.28 0.00 3.86
345 346 3.077556 AGCCCACGATCGCTTCCT 61.078 61.111 16.60 4.01 28.56 3.36
346 347 1.735376 TAGAGCCCACGATCGCTTCC 61.735 60.000 16.60 1.44 34.84 3.46
356 357 4.156739 CCAGAAAAATGAACTAGAGCCCAC 59.843 45.833 0.00 0.00 0.00 4.61
369 370 4.276926 GGAATCCCTCGATCCAGAAAAATG 59.723 45.833 0.00 0.00 0.00 2.32
381 382 1.762460 GGAGCTGGGAATCCCTCGA 60.762 63.158 20.55 0.00 45.70 4.04
436 872 2.284754 TCTTGGCAGTGGCATAACAA 57.715 45.000 21.29 3.87 43.71 2.83
448 884 2.949451 TCAAAGCGTTTTTCTTGGCA 57.051 40.000 0.00 0.00 0.00 4.92
465 901 2.178273 CGTGCGAGGACGTGATCA 59.822 61.111 8.95 0.00 41.98 2.92
502 948 2.023307 AGGATAAGACGAGGGAAAGGGA 60.023 50.000 0.00 0.00 0.00 4.20
510 956 3.181474 GGGTTTGAGAGGATAAGACGAGG 60.181 52.174 0.00 0.00 0.00 4.63
519 965 2.236395 CGGTGTTAGGGTTTGAGAGGAT 59.764 50.000 0.00 0.00 0.00 3.24
627 1073 2.298446 AGCACTGATGATGGTATCCGAG 59.702 50.000 0.00 0.00 0.00 4.63
628 1074 2.036346 CAGCACTGATGATGGTATCCGA 59.964 50.000 0.00 0.00 38.63 4.55
640 1086 2.202987 GCGGCTAGCAGCACTGAT 60.203 61.111 31.15 0.00 44.75 2.90
683 1129 1.428869 AAAGCTCCTCCGAGGCATAT 58.571 50.000 9.87 0.00 36.55 1.78
684 1130 1.204146 AAAAGCTCCTCCGAGGCATA 58.796 50.000 9.87 0.00 36.55 3.14
685 1131 0.329596 AAAAAGCTCCTCCGAGGCAT 59.670 50.000 9.87 0.00 36.55 4.40
686 1132 1.761174 AAAAAGCTCCTCCGAGGCA 59.239 52.632 9.87 0.00 36.55 4.75
687 1133 4.724262 AAAAAGCTCCTCCGAGGC 57.276 55.556 9.87 0.00 36.55 4.70
707 1153 3.611025 AAGTGTGGGATCCCTCAAAAA 57.389 42.857 32.11 9.65 40.65 1.94
708 1154 3.611025 AAAGTGTGGGATCCCTCAAAA 57.389 42.857 32.11 10.42 40.65 2.44
709 1155 4.946160 ATAAAGTGTGGGATCCCTCAAA 57.054 40.909 32.11 19.74 40.65 2.69
710 1156 4.946160 AATAAAGTGTGGGATCCCTCAA 57.054 40.909 32.11 19.68 40.65 3.02
711 1157 6.590656 ATTAATAAAGTGTGGGATCCCTCA 57.409 37.500 31.05 29.47 37.27 3.86
712 1158 8.437575 TCTAATTAATAAAGTGTGGGATCCCTC 58.562 37.037 31.05 27.17 36.94 4.30
713 1159 8.344939 TCTAATTAATAAAGTGTGGGATCCCT 57.655 34.615 31.05 12.72 36.94 4.20
714 1160 8.990163 TTCTAATTAATAAAGTGTGGGATCCC 57.010 34.615 25.22 25.22 0.00 3.85
736 1182 9.838339 CTTTGTATCCCTATGAACATAGTTTCT 57.162 33.333 17.07 5.42 39.23 2.52
737 1183 9.057089 CCTTTGTATCCCTATGAACATAGTTTC 57.943 37.037 17.07 6.82 39.23 2.78
738 1184 7.998964 CCCTTTGTATCCCTATGAACATAGTTT 59.001 37.037 17.07 7.13 39.23 2.66
739 1185 7.421382 CCCCTTTGTATCCCTATGAACATAGTT 60.421 40.741 17.07 7.39 39.23 2.24
740 1186 6.044404 CCCCTTTGTATCCCTATGAACATAGT 59.956 42.308 17.07 5.32 39.23 2.12
741 1187 6.476378 CCCCTTTGTATCCCTATGAACATAG 58.524 44.000 13.08 13.08 40.28 2.23
742 1188 5.312178 CCCCCTTTGTATCCCTATGAACATA 59.688 44.000 0.00 0.00 0.00 2.29
743 1189 4.106341 CCCCCTTTGTATCCCTATGAACAT 59.894 45.833 0.00 0.00 0.00 2.71
744 1190 3.461831 CCCCCTTTGTATCCCTATGAACA 59.538 47.826 0.00 0.00 0.00 3.18
745 1191 3.462205 ACCCCCTTTGTATCCCTATGAAC 59.538 47.826 0.00 0.00 0.00 3.18
746 1192 3.720002 GACCCCCTTTGTATCCCTATGAA 59.280 47.826 0.00 0.00 0.00 2.57
747 1193 3.311778 TGACCCCCTTTGTATCCCTATGA 60.312 47.826 0.00 0.00 0.00 2.15
748 1194 3.053077 TGACCCCCTTTGTATCCCTATG 58.947 50.000 0.00 0.00 0.00 2.23
749 1195 3.448277 TGACCCCCTTTGTATCCCTAT 57.552 47.619 0.00 0.00 0.00 2.57
750 1196 2.974285 TGACCCCCTTTGTATCCCTA 57.026 50.000 0.00 0.00 0.00 3.53
751 1197 1.852965 CATGACCCCCTTTGTATCCCT 59.147 52.381 0.00 0.00 0.00 4.20
752 1198 1.850345 TCATGACCCCCTTTGTATCCC 59.150 52.381 0.00 0.00 0.00 3.85
753 1199 2.158608 CCTCATGACCCCCTTTGTATCC 60.159 54.545 0.00 0.00 0.00 2.59
754 1200 2.158608 CCCTCATGACCCCCTTTGTATC 60.159 54.545 0.00 0.00 0.00 2.24
755 1201 1.852965 CCCTCATGACCCCCTTTGTAT 59.147 52.381 0.00 0.00 0.00 2.29
756 1202 1.295020 CCCTCATGACCCCCTTTGTA 58.705 55.000 0.00 0.00 0.00 2.41
757 1203 1.509548 CCCCTCATGACCCCCTTTGT 61.510 60.000 0.00 0.00 0.00 2.83
758 1204 1.307647 CCCCTCATGACCCCCTTTG 59.692 63.158 0.00 0.00 0.00 2.77
759 1205 1.935931 CCCCCTCATGACCCCCTTT 60.936 63.158 0.00 0.00 0.00 3.11
760 1206 1.844296 TACCCCCTCATGACCCCCTT 61.844 60.000 0.00 0.00 0.00 3.95
761 1207 2.269040 TACCCCCTCATGACCCCCT 61.269 63.158 0.00 0.00 0.00 4.79
762 1208 1.770518 CTACCCCCTCATGACCCCC 60.771 68.421 0.00 0.00 0.00 5.40
763 1209 2.452937 GCTACCCCCTCATGACCCC 61.453 68.421 0.00 0.00 0.00 4.95
764 1210 2.452937 GGCTACCCCCTCATGACCC 61.453 68.421 0.00 0.00 0.00 4.46
765 1211 3.241520 GGCTACCCCCTCATGACC 58.758 66.667 0.00 0.00 0.00 4.02
780 1226 2.177594 CTCCTCCGAGGCATATGGGC 62.178 65.000 9.87 0.00 43.80 5.36
781 1227 1.978473 CTCCTCCGAGGCATATGGG 59.022 63.158 9.87 0.00 34.61 4.00
782 1228 1.190833 AGCTCCTCCGAGGCATATGG 61.191 60.000 9.87 0.00 36.55 2.74
804 1250 2.438434 GGTCAATGGCGTCAGGGG 60.438 66.667 0.00 0.00 0.00 4.79
880 1326 3.926058 AGTAAGATGGGCCGTATTTGT 57.074 42.857 11.42 0.00 0.00 2.83
963 1412 2.092323 TCGATGGAGAAGATCGTGTGT 58.908 47.619 0.00 0.00 42.68 3.72
967 1416 0.663688 CCGTCGATGGAGAAGATCGT 59.336 55.000 19.48 0.00 42.68 3.73
969 1418 0.661780 CGCCGTCGATGGAGAAGATC 60.662 60.000 28.06 6.49 38.10 2.75
1021 1470 3.474486 TTGCTGCTGTGAGGCCGAA 62.474 57.895 0.00 0.00 0.00 4.30
1135 1584 4.873129 CGGCGATCCACCTGACGG 62.873 72.222 0.00 0.00 0.00 4.79
1136 1585 4.129737 ACGGCGATCCACCTGACG 62.130 66.667 16.62 0.00 0.00 4.35
1137 1586 2.509336 CACGGCGATCCACCTGAC 60.509 66.667 16.62 0.00 0.00 3.51
1138 1587 3.770040 CCACGGCGATCCACCTGA 61.770 66.667 16.62 0.00 0.00 3.86
1139 1588 4.838152 CCCACGGCGATCCACCTG 62.838 72.222 16.62 0.00 0.00 4.00
1254 1703 5.941788 ACAAGGAGCTTTAAAGAAGGAGAA 58.058 37.500 19.48 0.00 0.00 2.87
1296 1745 5.928153 AGCAGAAACTATAGAAACGCAAAC 58.072 37.500 6.78 0.00 0.00 2.93
1369 1846 5.643348 CACAGACATGCCAATTTGACTACTA 59.357 40.000 0.00 0.00 0.00 1.82
1387 1864 4.166011 GCGCCGGCAATCACAGAC 62.166 66.667 28.98 0.68 39.62 3.51
1416 1893 7.604545 ACATAAAAGAAAAGGTAGCAGAGAGAC 59.395 37.037 0.00 0.00 0.00 3.36
1432 1910 5.695816 GCATGTTGGCAAGAACATAAAAGAA 59.304 36.000 0.00 0.00 43.29 2.52
1433 1911 5.010922 AGCATGTTGGCAAGAACATAAAAGA 59.989 36.000 0.00 0.00 43.29 2.52
1434 1912 5.232463 AGCATGTTGGCAAGAACATAAAAG 58.768 37.500 0.00 0.00 43.29 2.27
1452 1930 8.021955 TCTGCGTTTTGATAGATATAAGCATG 57.978 34.615 0.00 0.00 0.00 4.06
1453 1931 7.875041 ACTCTGCGTTTTGATAGATATAAGCAT 59.125 33.333 0.00 0.00 0.00 3.79
1454 1932 7.210174 ACTCTGCGTTTTGATAGATATAAGCA 58.790 34.615 0.00 0.00 0.00 3.91
1455 1933 7.644986 ACTCTGCGTTTTGATAGATATAAGC 57.355 36.000 0.00 0.00 0.00 3.09
1457 1935 8.132995 TCGAACTCTGCGTTTTGATAGATATAA 58.867 33.333 0.00 0.00 35.56 0.98
1458 1936 7.645402 TCGAACTCTGCGTTTTGATAGATATA 58.355 34.615 0.00 0.00 35.56 0.86
1459 1937 6.504398 TCGAACTCTGCGTTTTGATAGATAT 58.496 36.000 0.00 0.00 35.56 1.63
1511 1994 3.252215 TGTTCGGATTTCACGCTTCAATT 59.748 39.130 0.00 0.00 0.00 2.32
1575 2061 1.152777 CAACCCAGTGGAGTTGGCA 60.153 57.895 24.76 0.00 39.73 4.92
1850 2337 3.563223 CTTCCTCAATCCCATGCTCAAT 58.437 45.455 0.00 0.00 0.00 2.57
1851 2338 2.357465 CCTTCCTCAATCCCATGCTCAA 60.357 50.000 0.00 0.00 0.00 3.02
1859 2346 3.428687 GGATGCCTTCCTCAATCCC 57.571 57.895 0.00 0.00 41.78 3.85
1893 2382 3.641437 GCTCGATGCTATGTTCTCTCT 57.359 47.619 0.00 0.00 38.95 3.10
1996 2485 8.933807 CATATATTGAGCACCTAATTGACTCAG 58.066 37.037 0.00 0.00 38.51 3.35
2032 2521 9.188588 AGGTTATTTCGTAATCGTATACACATG 57.811 33.333 3.32 0.00 38.33 3.21
2412 2902 1.335810 CGCTGCAATGATAGGCAATGT 59.664 47.619 0.00 0.00 39.93 2.71
2421 2911 0.611618 TTGGGGTTCGCTGCAATGAT 60.612 50.000 0.00 0.00 0.00 2.45
2484 2974 3.392616 ACTATAGCTAAGCCCATGCAACT 59.607 43.478 0.00 0.00 41.13 3.16
2521 3012 2.758423 TCAGCCACTACAATCGCTTCTA 59.242 45.455 0.00 0.00 0.00 2.10
3276 3775 3.197766 TGATGCCAGTAAACTGTCCTAGG 59.802 47.826 0.82 0.82 42.27 3.02
3388 3893 8.936070 AATAAAGCGTTGGGGAAAATATAAAC 57.064 30.769 0.00 0.00 0.00 2.01
3393 3898 6.844097 AGAAATAAAGCGTTGGGGAAAATA 57.156 33.333 0.00 0.00 0.00 1.40
3418 3923 8.975295 AGGATCTTTTAAGAATGGGATCTTTTG 58.025 33.333 0.00 0.00 40.13 2.44
3430 3935 6.715280 ACATCTGAGCAGGATCTTTTAAGAA 58.285 36.000 0.00 0.00 38.77 2.52
3498 4003 8.032952 TCAACATGTAACAGATCAAGATTGAC 57.967 34.615 0.00 0.00 40.49 3.18
3517 4022 6.604795 CACCCCTTTCAGATAAGAATCAACAT 59.395 38.462 0.00 0.00 34.28 2.71
3573 4078 1.547372 GTTGCTGCATCCCAGTCAAAT 59.453 47.619 1.84 0.00 43.71 2.32
3604 4109 5.881923 TTTACTCCAGTCCGCCTATAAAT 57.118 39.130 0.00 0.00 0.00 1.40
3720 4225 3.737663 CGAAATGTTGTATGCCCCATTGG 60.738 47.826 0.00 0.00 37.09 3.16
3721 4226 3.130164 TCGAAATGTTGTATGCCCCATTG 59.870 43.478 0.00 0.00 0.00 2.82
3722 4227 3.360867 TCGAAATGTTGTATGCCCCATT 58.639 40.909 0.00 0.00 0.00 3.16
3724 4229 2.364632 CTCGAAATGTTGTATGCCCCA 58.635 47.619 0.00 0.00 0.00 4.96
3731 4236 4.925054 CGTTTACTCCCTCGAAATGTTGTA 59.075 41.667 0.00 0.00 0.00 2.41
3742 4247 4.339814 AGACATCATCTCGTTTACTCCCTC 59.660 45.833 0.00 0.00 28.16 4.30
3743 4248 4.282496 AGACATCATCTCGTTTACTCCCT 58.718 43.478 0.00 0.00 28.16 4.20
3746 4251 6.809196 ACTGAAAGACATCATCTCGTTTACTC 59.191 38.462 0.00 0.00 36.27 2.59
3761 4268 4.937620 GCAGGATCAACATACTGAAAGACA 59.062 41.667 0.00 0.00 43.20 3.41
3762 4269 4.333926 GGCAGGATCAACATACTGAAAGAC 59.666 45.833 0.00 0.00 43.20 3.01
3768 4276 3.376234 CACTTGGCAGGATCAACATACTG 59.624 47.826 2.65 0.00 43.37 2.74
3780 4288 0.670162 CTGTTGGTTCACTTGGCAGG 59.330 55.000 0.00 0.00 0.00 4.85
3784 4292 3.016736 ACAACTCTGTTGGTTCACTTGG 58.983 45.455 13.86 0.00 28.57 3.61
3797 4305 4.818534 AATGTGCAGTACAACAACTCTG 57.181 40.909 0.00 0.00 43.77 3.35
3798 4306 5.835113 AAAATGTGCAGTACAACAACTCT 57.165 34.783 0.00 0.00 43.77 3.24
3826 4334 1.136252 GGCAACGCATACGAGCATATG 60.136 52.381 0.00 0.00 43.93 1.78
3828 4336 0.104120 AGGCAACGCATACGAGCATA 59.896 50.000 9.11 0.00 43.93 3.14
3835 4343 4.377897 ACCTCTTATTAGGCAACGCATAC 58.622 43.478 0.00 0.00 40.62 2.39
3836 4344 4.344102 AGACCTCTTATTAGGCAACGCATA 59.656 41.667 0.00 0.00 40.62 3.14
3840 4348 3.118738 ACCAGACCTCTTATTAGGCAACG 60.119 47.826 0.00 0.00 40.62 4.10
3854 4362 2.416972 GCTATCGACGAAAACCAGACCT 60.417 50.000 0.00 0.00 0.00 3.85
3855 4363 1.925185 GCTATCGACGAAAACCAGACC 59.075 52.381 0.00 0.00 0.00 3.85
3862 4370 0.527113 TGTCCCGCTATCGACGAAAA 59.473 50.000 0.00 0.00 38.10 2.29
3873 4381 2.365635 ACAGGCCTATGTCCCGCT 60.366 61.111 3.98 0.00 0.00 5.52
3936 4444 7.452630 TTTTTGGACAACACGCTTATAAAAC 57.547 32.000 0.00 0.00 0.00 2.43
3971 4479 7.770366 ATGGCTGATCATGCTATTGAAATAA 57.230 32.000 14.20 0.00 0.00 1.40
4004 4515 4.256920 CACTCCCTTCCTACTGAAACATG 58.743 47.826 0.00 0.00 31.06 3.21
4154 4665 1.086634 GCGTTCTCATGGTCAGGCTC 61.087 60.000 0.00 0.00 0.00 4.70
4181 4692 3.785859 GGCGCCCTGGATCAGACA 61.786 66.667 18.11 0.00 32.44 3.41
4406 4917 1.079750 GAGGACCTCGGTGCAGTTC 60.080 63.158 5.55 0.00 38.98 3.01
4464 4975 0.867753 CTGATCCTCCGTTCTTCGCG 60.868 60.000 0.00 0.00 38.35 5.87
4518 5033 5.193325 ACCATTCTCCTCTCATTCTCCATTT 59.807 40.000 0.00 0.00 0.00 2.32
4550 5071 1.792118 GCCGCCCCCTTATTTAAGCG 61.792 60.000 0.00 0.00 42.99 4.68
4650 5171 1.444895 GACGCCTGCAATTGCCTTG 60.445 57.895 26.94 15.89 41.18 3.61
4651 5172 2.964978 GACGCCTGCAATTGCCTT 59.035 55.556 26.94 5.93 41.18 4.35
4655 5176 2.176546 CCACGACGCCTGCAATTG 59.823 61.111 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.