Multiple sequence alignment - TraesCS3A01G068900

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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 TraesCS3A01G068900 chr3A 100.000 3056 0 0 1 3056 41177317 41180372 0.000000e+00 5644
1 TraesCS3A01G068900 chr3A 88.224 1019 120 0 995 2013 40947303 40948321 0.000000e+00 1218
2 TraesCS3A01G068900 chr3A 88.126 1019 121 0 995 2013 41048105 41049123 0.000000e+00 1212
3 TraesCS3A01G068900 chr3A 87.795 1016 118 5 1001 2013 41355087 41356099 0.000000e+00 1184
4 TraesCS3A01G068900 chr3A 86.297 956 120 8 2107 3055 41538226 41539177 0.000000e+00 1029
5 TraesCS3A01G068900 chr3A 85.640 961 122 13 2107 3055 41610427 41611383 0.000000e+00 996
6 TraesCS3A01G068900 chr3A 84.874 952 140 4 2107 3055 41150966 41151916 0.000000e+00 957
7 TraesCS3A01G068900 chr3A 85.455 330 36 4 1 325 41047117 41047439 1.760000e-87 333
8 TraesCS3A01G068900 chr3A 81.463 410 54 12 356 761 41047436 41047827 1.770000e-82 316
9 TraesCS3A01G068900 chr3B 87.771 1014 122 2 1001 2013 52777751 52776739 0.000000e+00 1184
10 TraesCS3A01G068900 chr3B 87.475 1014 124 3 1001 2013 52853713 52852702 0.000000e+00 1166
11 TraesCS3A01G068900 chr3B 87.267 1021 128 2 994 2013 51947781 51948800 0.000000e+00 1164
12 TraesCS3A01G068900 chr3B 87.563 997 124 0 994 1990 51925134 51926130 0.000000e+00 1155
13 TraesCS3A01G068900 chr3B 86.765 1020 132 3 995 2013 51243337 51244354 0.000000e+00 1133
14 TraesCS3A01G068900 chr3B 86.680 1021 133 3 994 2013 51228526 51229544 0.000000e+00 1129
15 TraesCS3A01G068900 chr3B 85.879 956 125 10 2107 3056 52776752 52775801 0.000000e+00 1009
16 TraesCS3A01G068900 chr3B 86.281 933 119 7 2129 3055 51959841 51960770 0.000000e+00 1005
17 TraesCS3A01G068900 chr3B 85.729 953 130 6 2107 3055 52427329 52428279 0.000000e+00 1002
18 TraesCS3A01G068900 chr3B 85.356 956 131 6 2107 3055 52852715 52851762 0.000000e+00 981
19 TraesCS3A01G068900 chr3B 79.654 752 104 25 1 747 51957608 51958315 2.120000e-136 496
20 TraesCS3A01G068900 chr3B 85.385 130 18 1 356 485 51924253 51924381 1.910000e-27 134
21 TraesCS3A01G068900 chr3D 86.752 936 121 3 2107 3040 29971831 29972765 0.000000e+00 1038
22 TraesCS3A01G068900 chr3D 85.624 953 131 6 2107 3055 30007706 30008656 0.000000e+00 996
23 TraesCS3A01G068900 chr4A 100.000 109 0 0 2010 2118 343784181 343784073 5.170000e-48 202
24 TraesCS3A01G068900 chr4A 98.148 108 2 0 2009 2116 347308433 347308326 4.020000e-44 189
25 TraesCS3A01G068900 chr7A 98.148 108 2 0 2009 2116 25411003 25411110 4.020000e-44 189
26 TraesCS3A01G068900 chr5A 98.148 108 2 0 2010 2117 505508839 505508732 4.020000e-44 189
27 TraesCS3A01G068900 chr5A 96.460 113 4 0 2007 2119 397146004 397145892 1.450000e-43 187
28 TraesCS3A01G068900 chr5A 95.652 115 4 1 2002 2116 383832242 383832129 1.870000e-42 183
29 TraesCS3A01G068900 chr2A 98.148 108 2 0 2009 2116 763687462 763687569 4.020000e-44 189
30 TraesCS3A01G068900 chr2A 96.429 112 3 1 2010 2121 111501251 111501141 1.870000e-42 183
31 TraesCS3A01G068900 chr2A 92.063 126 8 2 2008 2131 683541945 683541820 3.130000e-40 176


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 TraesCS3A01G068900 chr3A 41177317 41180372 3055 False 5644.000000 5644 100.000000 1 3056 1 chr3A.!!$F3 3055
1 TraesCS3A01G068900 chr3A 40947303 40948321 1018 False 1218.000000 1218 88.224000 995 2013 1 chr3A.!!$F1 1018
2 TraesCS3A01G068900 chr3A 41355087 41356099 1012 False 1184.000000 1184 87.795000 1001 2013 1 chr3A.!!$F4 1012
3 TraesCS3A01G068900 chr3A 41538226 41539177 951 False 1029.000000 1029 86.297000 2107 3055 1 chr3A.!!$F5 948
4 TraesCS3A01G068900 chr3A 41610427 41611383 956 False 996.000000 996 85.640000 2107 3055 1 chr3A.!!$F6 948
5 TraesCS3A01G068900 chr3A 41150966 41151916 950 False 957.000000 957 84.874000 2107 3055 1 chr3A.!!$F2 948
6 TraesCS3A01G068900 chr3A 41047117 41049123 2006 False 620.333333 1212 85.014667 1 2013 3 chr3A.!!$F7 2012
7 TraesCS3A01G068900 chr3B 51947781 51948800 1019 False 1164.000000 1164 87.267000 994 2013 1 chr3B.!!$F3 1019
8 TraesCS3A01G068900 chr3B 51243337 51244354 1017 False 1133.000000 1133 86.765000 995 2013 1 chr3B.!!$F2 1018
9 TraesCS3A01G068900 chr3B 51228526 51229544 1018 False 1129.000000 1129 86.680000 994 2013 1 chr3B.!!$F1 1019
10 TraesCS3A01G068900 chr3B 52775801 52777751 1950 True 1096.500000 1184 86.825000 1001 3056 2 chr3B.!!$R1 2055
11 TraesCS3A01G068900 chr3B 52851762 52853713 1951 True 1073.500000 1166 86.415500 1001 3055 2 chr3B.!!$R2 2054
12 TraesCS3A01G068900 chr3B 52427329 52428279 950 False 1002.000000 1002 85.729000 2107 3055 1 chr3B.!!$F4 948
13 TraesCS3A01G068900 chr3B 51957608 51960770 3162 False 750.500000 1005 82.967500 1 3055 2 chr3B.!!$F6 3054
14 TraesCS3A01G068900 chr3B 51924253 51926130 1877 False 644.500000 1155 86.474000 356 1990 2 chr3B.!!$F5 1634
15 TraesCS3A01G068900 chr3D 29971831 29972765 934 False 1038.000000 1038 86.752000 2107 3040 1 chr3D.!!$F1 933
16 TraesCS3A01G068900 chr3D 30007706 30008656 950 False 996.000000 996 85.624000 2107 3055 1 chr3D.!!$F2 948

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
382 396 1.001633 ACCATCAGAGTAAACCGCGTT 59.998 47.619 4.92 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2629 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.0 0.0 0.0 0.0 4.3 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
26 27 1.872653 GCAGGGAAAGTTTCGTCTCGT 60.873 52.381 9.46 0.00 0.00 4.18
52 55 4.515191 GCTTGTGTTAGTCATTCCTGTTGA 59.485 41.667 0.00 0.00 0.00 3.18
76 79 2.756760 CACAGGCCACTTATGCTTGAAT 59.243 45.455 5.01 0.00 37.98 2.57
131 134 3.119173 ACTCTCAGCAGTGTCTTATCAGC 60.119 47.826 0.00 0.00 0.00 4.26
141 144 6.039493 GCAGTGTCTTATCAGCCTAGTTACTA 59.961 42.308 0.00 0.00 0.00 1.82
173 179 6.553953 TCAGGTATACATTGGCTTTCAGTA 57.446 37.500 5.01 0.00 0.00 2.74
176 182 8.052748 TCAGGTATACATTGGCTTTCAGTATTT 58.947 33.333 5.01 0.00 0.00 1.40
202 208 5.064452 GCACTTCTGGATCTCTAACACAATG 59.936 44.000 0.00 0.00 0.00 2.82
205 219 7.819415 CACTTCTGGATCTCTAACACAATGTTA 59.181 37.037 1.72 1.72 41.45 2.41
217 231 6.377327 AACACAATGTTAGTCCTTCTGTTG 57.623 37.500 0.00 0.00 39.09 3.33
255 269 9.617975 GATAATCTTCTATTTTGTATTGCAGGC 57.382 33.333 0.00 0.00 0.00 4.85
256 270 7.408756 AATCTTCTATTTTGTATTGCAGGCA 57.591 32.000 0.00 0.00 0.00 4.75
259 273 7.930217 TCTTCTATTTTGTATTGCAGGCATAC 58.070 34.615 0.00 0.84 0.00 2.39
260 274 7.555914 TCTTCTATTTTGTATTGCAGGCATACA 59.444 33.333 5.75 5.75 0.00 2.29
326 340 5.321102 TCTATTTTTGTTCTAGCTTGGGCA 58.679 37.500 0.00 0.00 41.70 5.36
345 359 5.105106 TGGGCACAATCTTACGAGATCTTAA 60.105 40.000 0.00 0.00 41.78 1.85
346 360 5.463724 GGGCACAATCTTACGAGATCTTAAG 59.536 44.000 0.00 2.12 41.78 1.85
349 363 6.975772 GCACAATCTTACGAGATCTTAAGAGT 59.024 38.462 17.66 14.04 41.78 3.24
351 365 6.975772 ACAATCTTACGAGATCTTAAGAGTGC 59.024 38.462 28.19 3.25 46.90 4.40
352 366 5.502153 TCTTACGAGATCTTAAGAGTGCC 57.498 43.478 11.53 0.65 33.53 5.01
353 367 4.948004 TCTTACGAGATCTTAAGAGTGCCA 59.052 41.667 11.53 0.00 33.53 4.92
354 368 5.417894 TCTTACGAGATCTTAAGAGTGCCAA 59.582 40.000 11.53 0.57 33.53 4.52
380 394 1.278238 GACCATCAGAGTAAACCGCG 58.722 55.000 0.00 0.00 0.00 6.46
382 396 1.001633 ACCATCAGAGTAAACCGCGTT 59.998 47.619 4.92 0.00 0.00 4.84
419 433 9.489084 TCACTATTGATTCTTATTATTGACGGG 57.511 33.333 0.00 0.00 0.00 5.28
456 470 6.043938 TGGAAGACTGGTTTGTAAGGTAAGAT 59.956 38.462 0.00 0.00 0.00 2.40
486 500 3.809832 TGTACTTCAGAGCTTGCAACTTC 59.190 43.478 0.00 0.00 0.00 3.01
543 557 4.382345 TTCTAGGCTAGAAACCGCTTAC 57.618 45.455 29.75 0.00 41.53 2.34
587 601 8.553459 AGATCTGACAAACAAAACTATACAGG 57.447 34.615 0.00 0.00 0.00 4.00
607 621 6.000219 ACAGGTGGATGATTAATCTGTATGC 59.000 40.000 16.24 7.72 35.43 3.14
610 624 7.230108 CAGGTGGATGATTAATCTGTATGCTTT 59.770 37.037 16.24 0.00 35.43 3.51
633 647 2.615447 ACTCAGTGCAACATTCAGTGTG 59.385 45.455 0.00 0.00 41.14 3.82
637 651 2.549754 AGTGCAACATTCAGTGTGTAGC 59.450 45.455 0.00 0.00 41.14 3.58
685 705 7.278875 TGGCCATTTAACTGAGAAAAACAAAT 58.721 30.769 0.00 0.00 0.00 2.32
724 744 9.043079 TCGACATACAAAACTAAAACACATGTA 57.957 29.630 0.00 0.00 0.00 2.29
747 1113 9.897744 TGTAAATTTTCAAGCACAAAGAGATAG 57.102 29.630 0.00 0.00 0.00 2.08
764 1130 5.033589 AGATAGAAGGACAGAATGCCAAG 57.966 43.478 0.00 0.00 42.53 3.61
775 1141 4.590222 ACAGAATGCCAAGTCAGGAATTTT 59.410 37.500 0.00 0.00 42.53 1.82
781 1147 3.321968 GCCAAGTCAGGAATTTTGACCTT 59.678 43.478 16.11 9.78 44.68 3.50
782 1148 4.797275 GCCAAGTCAGGAATTTTGACCTTG 60.797 45.833 16.11 16.88 44.68 3.61
783 1149 4.301628 CAAGTCAGGAATTTTGACCTTGC 58.698 43.478 16.11 0.00 44.68 4.01
790 1156 5.010012 CAGGAATTTTGACCTTGCTACTTGT 59.990 40.000 0.00 0.00 33.91 3.16
798 1164 3.248888 ACCTTGCTACTTGTCCCTACTT 58.751 45.455 0.00 0.00 0.00 2.24
799 1165 4.422984 ACCTTGCTACTTGTCCCTACTTA 58.577 43.478 0.00 0.00 0.00 2.24
800 1166 5.030820 ACCTTGCTACTTGTCCCTACTTAT 58.969 41.667 0.00 0.00 0.00 1.73
805 1171 6.817184 TGCTACTTGTCCCTACTTATGAATC 58.183 40.000 0.00 0.00 0.00 2.52
808 1174 5.675538 ACTTGTCCCTACTTATGAATCTGC 58.324 41.667 0.00 0.00 0.00 4.26
810 1176 5.023533 TGTCCCTACTTATGAATCTGCAC 57.976 43.478 0.00 0.00 0.00 4.57
829 1195 1.739466 ACGTTGCACAGCTCCATTATG 59.261 47.619 0.00 0.00 0.00 1.90
837 1203 5.827267 TGCACAGCTCCATTATGCTAAATTA 59.173 36.000 0.00 0.00 37.81 1.40
838 1204 6.491062 TGCACAGCTCCATTATGCTAAATTAT 59.509 34.615 0.00 0.00 37.81 1.28
839 1205 7.014518 TGCACAGCTCCATTATGCTAAATTATT 59.985 33.333 0.00 0.00 37.81 1.40
840 1206 7.540055 GCACAGCTCCATTATGCTAAATTATTC 59.460 37.037 0.00 0.00 37.81 1.75
841 1207 8.570488 CACAGCTCCATTATGCTAAATTATTCA 58.430 33.333 0.00 0.00 37.81 2.57
842 1208 9.135189 ACAGCTCCATTATGCTAAATTATTCAA 57.865 29.630 0.00 0.00 37.81 2.69
843 1209 9.970395 CAGCTCCATTATGCTAAATTATTCAAA 57.030 29.630 0.00 0.00 37.81 2.69
845 1211 9.971922 GCTCCATTATGCTAAATTATTCAAAGT 57.028 29.630 0.00 0.00 0.00 2.66
864 1230 9.677567 TTCAAAGTGTAAATAGAAACTCATTGC 57.322 29.630 0.00 0.00 0.00 3.56
865 1231 9.066892 TCAAAGTGTAAATAGAAACTCATTGCT 57.933 29.630 0.00 0.00 0.00 3.91
866 1232 9.334693 CAAAGTGTAAATAGAAACTCATTGCTC 57.665 33.333 0.00 0.00 0.00 4.26
867 1233 8.854614 AAGTGTAAATAGAAACTCATTGCTCT 57.145 30.769 0.00 0.00 0.00 4.09
868 1234 8.854614 AGTGTAAATAGAAACTCATTGCTCTT 57.145 30.769 0.00 0.00 0.00 2.85
869 1235 9.289782 AGTGTAAATAGAAACTCATTGCTCTTT 57.710 29.630 0.00 0.00 0.00 2.52
876 1242 7.440523 AGAAACTCATTGCTCTTTATCGTTT 57.559 32.000 0.00 0.00 0.00 3.60
927 1295 4.032703 ACTTGTGTCATTGTGAAAGCAC 57.967 40.909 0.00 0.00 45.35 4.40
1098 1511 3.508952 ATCCTAGGGGTGGAAGAAGAA 57.491 47.619 9.46 0.00 37.13 2.52
1108 1521 4.202367 GGGTGGAAGAAGAACTCAGAGAAA 60.202 45.833 3.79 0.00 0.00 2.52
1111 1524 6.226787 GTGGAAGAAGAACTCAGAGAAATGA 58.773 40.000 3.79 0.00 0.00 2.57
1116 1529 3.529533 AGAACTCAGAGAAATGATGCGG 58.470 45.455 3.79 0.00 0.00 5.69
1119 1532 0.811219 TCAGAGAAATGATGCGGCGG 60.811 55.000 9.78 0.00 0.00 6.13
1159 1573 6.962686 TGTTGCATATATGATGCTGAGAAAC 58.037 36.000 17.10 4.83 44.79 2.78
1274 1688 1.028868 GGAAGCAAGCTACTGCCTGG 61.029 60.000 6.77 0.00 43.73 4.45
1309 1723 2.094906 TCATCAAGCAAATCAGCTGCAC 60.095 45.455 9.47 0.00 45.89 4.57
1310 1724 1.612676 TCAAGCAAATCAGCTGCACT 58.387 45.000 9.47 0.00 45.89 4.40
1315 1729 4.796038 AGCAAATCAGCTGCACTTAAAT 57.204 36.364 9.47 0.00 44.66 1.40
1334 1748 7.724061 ACTTAAATGCCTTTCAGTTTCCTCTTA 59.276 33.333 0.00 0.00 34.50 2.10
1342 1756 7.418408 CCTTTCAGTTTCCTCTTACTTTTGTC 58.582 38.462 0.00 0.00 0.00 3.18
1373 1787 2.223845 CACGTCATGATGTTGCTGTTCA 59.776 45.455 18.05 0.00 0.00 3.18
1388 1802 3.870419 GCTGTTCAGATTAGAAGCCTCAG 59.130 47.826 3.84 0.00 0.00 3.35
1417 1831 8.797438 AGAAGATAGAAAACATTTCAAAGGACC 58.203 33.333 5.71 0.00 0.00 4.46
1482 2013 7.201582 GGAAATGCTCCAACATCAAAAATGATC 60.202 37.037 0.00 0.00 44.67 2.92
1497 2028 7.723616 TCAAAAATGATCAGAAGTTCCAACCTA 59.276 33.333 0.09 0.00 0.00 3.08
1524 2055 0.409484 CCAACCTTGTGGGGAAGGAT 59.591 55.000 6.31 0.00 44.87 3.24
1679 2210 8.352942 TCAGAAAATAAAAGGAAGCTTCAAGAC 58.647 33.333 27.02 10.34 0.00 3.01
1773 2304 2.675056 GCACAGTGAGCAAGGCGAG 61.675 63.158 4.15 0.00 0.00 5.03
1803 2334 1.154263 GCTGCAGAGAAAGCTTGCG 60.154 57.895 20.43 0.00 36.47 4.85
1819 2350 3.802139 GCTTGCGGAAATAATTAAAGGCC 59.198 43.478 0.00 0.00 0.00 5.19
1890 2421 6.037610 GGACAGATTTACTAAGACCTGCATTG 59.962 42.308 0.00 0.00 0.00 2.82
1891 2422 5.882557 ACAGATTTACTAAGACCTGCATTGG 59.117 40.000 0.00 0.00 0.00 3.16
1939 2470 2.679837 GCAACCACACGAGATGATCAAT 59.320 45.455 0.00 0.00 0.00 2.57
1947 2478 5.060077 CACACGAGATGATCAATTTGCAAAC 59.940 40.000 15.41 1.57 0.00 2.93
1986 2517 8.470002 CAATATACCCATCGAGTTGATCTCATA 58.530 37.037 0.00 0.00 42.88 2.15
1992 2523 5.862860 CCATCGAGTTGATCTCATATCAGTG 59.137 44.000 0.00 0.00 42.88 3.66
2009 2540 2.367512 GGAGGTGGGATGGGAGCT 60.368 66.667 0.00 0.00 0.00 4.09
2010 2541 1.074471 GGAGGTGGGATGGGAGCTA 60.074 63.158 0.00 0.00 0.00 3.32
2011 2542 1.411651 GGAGGTGGGATGGGAGCTAC 61.412 65.000 0.00 0.00 0.00 3.58
2012 2543 0.399233 GAGGTGGGATGGGAGCTACT 60.399 60.000 0.00 0.00 0.00 2.57
2013 2544 0.399233 AGGTGGGATGGGAGCTACTC 60.399 60.000 0.00 0.00 0.00 2.59
2021 2552 4.358810 GGAGCTACTCCCTCCGTT 57.641 61.111 1.98 0.00 44.36 4.44
2022 2553 2.117257 GGAGCTACTCCCTCCGTTC 58.883 63.158 1.98 0.00 44.36 3.95
2023 2554 1.393487 GGAGCTACTCCCTCCGTTCC 61.393 65.000 1.98 0.00 44.36 3.62
2024 2555 0.683504 GAGCTACTCCCTCCGTTCCA 60.684 60.000 0.00 0.00 0.00 3.53
2025 2556 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2026 2557 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2027 2558 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
2028 2559 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
2029 2560 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
2030 2561 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2031 2562 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2032 2563 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2033 2564 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2034 2565 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2035 2566 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2036 2567 3.368116 CCTCCGTTCCAAATTACTCGTCT 60.368 47.826 0.00 0.00 0.00 4.18
2037 2568 3.841643 TCCGTTCCAAATTACTCGTCTC 58.158 45.455 0.00 0.00 0.00 3.36
2038 2569 3.256383 TCCGTTCCAAATTACTCGTCTCA 59.744 43.478 0.00 0.00 0.00 3.27
2039 2570 3.612860 CCGTTCCAAATTACTCGTCTCAG 59.387 47.826 0.00 0.00 0.00 3.35
2040 2571 4.482386 CGTTCCAAATTACTCGTCTCAGA 58.518 43.478 0.00 0.00 0.00 3.27
2041 2572 4.921515 CGTTCCAAATTACTCGTCTCAGAA 59.078 41.667 0.00 0.00 0.00 3.02
2042 2573 5.404366 CGTTCCAAATTACTCGTCTCAGAAA 59.596 40.000 0.00 0.00 0.00 2.52
2043 2574 6.090898 CGTTCCAAATTACTCGTCTCAGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
2044 2575 6.968131 TCCAAATTACTCGTCTCAGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
2045 2576 5.874810 TCCAAATTACTCGTCTCAGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
2046 2577 5.874810 CCAAATTACTCGTCTCAGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
2047 2578 6.540189 CCAAATTACTCGTCTCAGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
2048 2579 7.404985 CAAATTACTCGTCTCAGAAATGGATG 58.595 38.462 0.00 0.00 0.00 3.51
2049 2580 5.661056 TTACTCGTCTCAGAAATGGATGT 57.339 39.130 0.00 0.00 0.00 3.06
2050 2581 6.769134 TTACTCGTCTCAGAAATGGATGTA 57.231 37.500 0.00 0.00 0.00 2.29
2051 2582 5.860941 ACTCGTCTCAGAAATGGATGTAT 57.139 39.130 0.00 0.00 0.00 2.29
2052 2583 6.227298 ACTCGTCTCAGAAATGGATGTATT 57.773 37.500 0.00 0.00 0.00 1.89
2053 2584 6.644347 ACTCGTCTCAGAAATGGATGTATTT 58.356 36.000 0.00 0.00 33.19 1.40
2054 2585 7.782049 ACTCGTCTCAGAAATGGATGTATTTA 58.218 34.615 0.00 0.00 30.78 1.40
2055 2586 7.923344 ACTCGTCTCAGAAATGGATGTATTTAG 59.077 37.037 0.00 0.00 30.78 1.85
2056 2587 8.007405 TCGTCTCAGAAATGGATGTATTTAGA 57.993 34.615 0.00 0.00 30.78 2.10
2057 2588 8.474831 TCGTCTCAGAAATGGATGTATTTAGAA 58.525 33.333 0.00 0.00 30.78 2.10
2058 2589 8.543774 CGTCTCAGAAATGGATGTATTTAGAAC 58.456 37.037 0.00 0.00 30.78 3.01
2059 2590 9.606631 GTCTCAGAAATGGATGTATTTAGAACT 57.393 33.333 0.00 0.00 30.78 3.01
2088 2619 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
2089 2620 6.162079 ACATCTAGATACATCCATTTCTGCG 58.838 40.000 4.54 0.00 0.00 5.18
2090 2621 6.015095 ACATCTAGATACATCCATTTCTGCGA 60.015 38.462 4.54 0.00 0.00 5.10
2091 2622 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2092 2623 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
2093 2624 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
2094 2625 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
2095 2626 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
2096 2627 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
2097 2628 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
2098 2629 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
2099 2630 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
2100 2631 3.863424 TCCATTTCTGCGACGAGTAATTC 59.137 43.478 0.00 0.00 0.00 2.17
2131 2662 2.237392 GGAGTACTTTGGAGGAGCATGT 59.763 50.000 0.00 0.00 0.00 3.21
2164 2882 7.865707 TGAAGAGAAAGAAGTGCAGAATTTAC 58.134 34.615 0.00 0.00 0.00 2.01
2214 2932 2.361737 GGTTGCCTCCCTCTTGCC 60.362 66.667 0.00 0.00 0.00 4.52
2264 2982 4.947645 AGCAGAGATCTAACAGAGAATGC 58.052 43.478 0.00 0.00 37.85 3.56
2282 3000 2.003301 TGCGTGGAAAAAGTTTTTGGC 58.997 42.857 18.07 14.66 0.00 4.52
2291 3009 8.841300 GTGGAAAAAGTTTTTGGCCAAATATAA 58.159 29.630 30.78 19.50 37.25 0.98
2337 3055 5.755861 GGATGAAATACAAGGAGCTCTGTAC 59.244 44.000 15.77 6.62 0.00 2.90
2358 3076 7.067421 TGTACCTAAGCTATGATGAGTTACCT 58.933 38.462 0.00 0.00 0.00 3.08
2417 3135 7.387122 TCTGTATGCTGAAGATTCTATCATTGC 59.613 37.037 0.00 0.00 0.00 3.56
2420 3138 5.434408 TGCTGAAGATTCTATCATTGCACT 58.566 37.500 0.00 0.00 0.00 4.40
2462 3180 2.012673 GATTGCTGAAGGCTTCATCGT 58.987 47.619 28.67 17.37 39.30 3.73
2508 3226 9.502091 CTAGAAGACATAGCAGAAGAGTACTAT 57.498 37.037 0.00 0.00 0.00 2.12
2543 3261 0.905357 CGGAATCTCCTCCAACCAGT 59.095 55.000 0.00 0.00 34.91 4.00
2547 3265 4.564821 CGGAATCTCCTCCAACCAGTTAAA 60.565 45.833 0.00 0.00 34.91 1.52
2550 3268 6.437477 GGAATCTCCTCCAACCAGTTAAAAAT 59.563 38.462 0.00 0.00 35.36 1.82
2602 3320 1.270732 ACCTCTTGAGACAGCTTGCTG 60.271 52.381 19.62 19.62 0.00 4.41
2619 3337 9.661187 CAGCTTGCTGTAAATATATCAAAAGAG 57.339 33.333 13.89 0.00 0.00 2.85
2634 3352 3.391506 AAAGAGGAATGCTTTGTTGGC 57.608 42.857 0.00 0.00 34.50 4.52
2743 3464 5.044846 AGCATGGATAAGGTGGAAGTTAAGT 60.045 40.000 0.00 0.00 0.00 2.24
2751 3472 3.714798 AGGTGGAAGTTAAGTTGAGGACA 59.285 43.478 0.00 0.00 0.00 4.02
2788 3509 5.039920 TGGTCCACAGATAATTGAGGATG 57.960 43.478 0.00 0.00 39.49 3.51
2807 3528 5.126707 AGGATGCATTGTTCAAGAGATTTCC 59.873 40.000 0.00 0.00 0.00 3.13
2814 3538 3.997021 TGTTCAAGAGATTTCCGCTTCTC 59.003 43.478 0.00 0.00 38.93 2.87
2827 3551 1.868498 CGCTTCTCCGTGTTTTGGTAA 59.132 47.619 0.00 0.00 0.00 2.85
2829 3553 3.058501 CGCTTCTCCGTGTTTTGGTAATT 60.059 43.478 0.00 0.00 0.00 1.40
2857 3581 3.734463 TCACTTGTACAAAGCATTCCGA 58.266 40.909 10.03 0.00 0.00 4.55
2861 3585 5.569059 CACTTGTACAAAGCATTCCGAATTC 59.431 40.000 10.03 0.00 0.00 2.17
2865 3589 4.806640 ACAAAGCATTCCGAATTCCATT 57.193 36.364 0.00 0.00 0.00 3.16
2955 3679 2.305927 TGGCTCCCTAAAGAACCTTCAG 59.694 50.000 0.00 0.00 0.00 3.02
2971 3695 0.469494 TCAGGTGCTGAGCTTGACAA 59.531 50.000 5.83 0.00 35.39 3.18
2981 3705 0.740737 AGCTTGACAAGGTGTGTTGC 59.259 50.000 18.73 1.48 41.96 4.17
3006 3732 0.750850 GCAGTCTACCTCCGGCAATA 59.249 55.000 0.00 0.00 0.00 1.90
3011 3737 0.834612 CTACCTCCGGCAATAACCCA 59.165 55.000 0.00 0.00 0.00 4.51
3033 3759 6.150976 CCCAATTGTGCAGTTTAAGATGTCTA 59.849 38.462 4.43 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.182775 ACGAAACTTTCCCTGCCTGT 59.817 50.000 0.00 0.00 0.00 4.00
5 6 1.157585 GAGACGAAACTTTCCCTGCC 58.842 55.000 0.00 0.00 0.00 4.85
26 27 4.887071 ACAGGAATGACTAACACAAGCAAA 59.113 37.500 0.00 0.00 0.00 3.68
52 55 0.921896 AGCATAAGTGGCCTGTGGAT 59.078 50.000 3.32 0.00 0.00 3.41
61 64 5.735354 GCAGGATCAATTCAAGCATAAGTGG 60.735 44.000 0.00 0.00 0.00 4.00
76 79 3.723235 GAGAGCGGCGCAGGATCAA 62.723 63.158 35.02 0.00 0.00 2.57
131 134 7.291411 ACCTGAATACATGCTAGTAACTAGG 57.709 40.000 0.00 0.00 34.88 3.02
158 164 4.990426 GTGCAAAATACTGAAAGCCAATGT 59.010 37.500 0.00 0.00 37.60 2.71
173 179 6.150140 GTGTTAGAGATCCAGAAGTGCAAAAT 59.850 38.462 0.00 0.00 0.00 1.82
176 182 4.040339 TGTGTTAGAGATCCAGAAGTGCAA 59.960 41.667 0.00 0.00 0.00 4.08
202 208 5.815740 TCAACAAGTCAACAGAAGGACTAAC 59.184 40.000 0.00 0.00 43.26 2.34
205 219 4.487714 TCAACAAGTCAACAGAAGGACT 57.512 40.909 0.00 0.00 45.85 3.85
206 220 4.084328 CGATCAACAAGTCAACAGAAGGAC 60.084 45.833 0.00 0.00 0.00 3.85
207 221 4.058124 CGATCAACAAGTCAACAGAAGGA 58.942 43.478 0.00 0.00 0.00 3.36
208 222 4.058124 TCGATCAACAAGTCAACAGAAGG 58.942 43.478 0.00 0.00 0.00 3.46
209 223 5.852738 ATCGATCAACAAGTCAACAGAAG 57.147 39.130 0.00 0.00 0.00 2.85
210 224 7.819415 AGATTATCGATCAACAAGTCAACAGAA 59.181 33.333 0.00 0.00 37.22 3.02
211 225 7.323420 AGATTATCGATCAACAAGTCAACAGA 58.677 34.615 0.00 0.00 37.22 3.41
212 226 7.531280 AGATTATCGATCAACAAGTCAACAG 57.469 36.000 0.00 0.00 37.22 3.16
255 269 5.047802 ACCAAGAGAAAACCATGCTTGTATG 60.048 40.000 0.00 0.00 35.41 2.39
256 270 5.047802 CACCAAGAGAAAACCATGCTTGTAT 60.048 40.000 0.00 0.00 35.41 2.29
259 273 3.318839 TCACCAAGAGAAAACCATGCTTG 59.681 43.478 0.00 0.00 36.58 4.01
260 274 3.565307 TCACCAAGAGAAAACCATGCTT 58.435 40.909 0.00 0.00 0.00 3.91
312 326 2.716217 AGATTGTGCCCAAGCTAGAAC 58.284 47.619 0.00 0.00 45.09 3.01
377 391 2.607187 AGTGATCCTTCTGTAAACGCG 58.393 47.619 3.53 3.53 0.00 6.01
380 394 9.606631 AGAATCAATAGTGATCCTTCTGTAAAC 57.393 33.333 6.07 0.00 44.02 2.01
456 470 5.106555 GCAAGCTCTGAAGTACAATAGCAAA 60.107 40.000 0.00 0.00 38.94 3.68
543 557 8.630917 TCAGATCTATCTTAAGTTCTTAACCCG 58.369 37.037 1.63 0.00 34.22 5.28
584 598 6.236409 AGCATACAGATTAATCATCCACCTG 58.764 40.000 17.56 7.51 31.20 4.00
587 601 9.884465 GTTAAAGCATACAGATTAATCATCCAC 57.116 33.333 17.56 2.80 31.20 4.02
605 619 4.337836 TGAATGTTGCACTGAGTTAAAGCA 59.662 37.500 0.00 0.00 0.00 3.91
607 621 5.911280 CACTGAATGTTGCACTGAGTTAAAG 59.089 40.000 0.00 0.00 0.00 1.85
610 624 4.273235 CACACTGAATGTTGCACTGAGTTA 59.727 41.667 0.00 0.00 40.64 2.24
699 719 9.653067 TTACATGTGTTTTAGTTTTGTATGTCG 57.347 29.630 9.11 0.00 0.00 4.35
724 744 9.688592 CTTCTATCTCTTTGTGCTTGAAAATTT 57.311 29.630 0.00 0.00 0.00 1.82
730 750 5.012046 TGTCCTTCTATCTCTTTGTGCTTGA 59.988 40.000 0.00 0.00 0.00 3.02
747 1113 2.746362 CTGACTTGGCATTCTGTCCTTC 59.254 50.000 0.00 0.00 0.00 3.46
764 1130 4.762251 AGTAGCAAGGTCAAAATTCCTGAC 59.238 41.667 10.71 10.71 42.08 3.51
775 1141 1.729586 AGGGACAAGTAGCAAGGTCA 58.270 50.000 0.00 0.00 32.00 4.02
781 1147 6.611642 AGATTCATAAGTAGGGACAAGTAGCA 59.388 38.462 0.00 0.00 0.00 3.49
782 1148 6.926272 CAGATTCATAAGTAGGGACAAGTAGC 59.074 42.308 0.00 0.00 0.00 3.58
783 1149 6.926272 GCAGATTCATAAGTAGGGACAAGTAG 59.074 42.308 0.00 0.00 0.00 2.57
790 1156 3.704566 ACGTGCAGATTCATAAGTAGGGA 59.295 43.478 0.00 0.00 0.00 4.20
808 1174 1.155889 TAATGGAGCTGTGCAACGTG 58.844 50.000 0.00 0.00 42.39 4.49
810 1176 1.532505 GCATAATGGAGCTGTGCAACG 60.533 52.381 0.00 0.00 42.39 4.10
817 1183 9.970395 TTTGAATAATTTAGCATAATGGAGCTG 57.030 29.630 0.00 0.00 41.97 4.24
838 1204 9.677567 GCAATGAGTTTCTATTTACACTTTGAA 57.322 29.630 0.00 0.00 0.00 2.69
839 1205 9.066892 AGCAATGAGTTTCTATTTACACTTTGA 57.933 29.630 0.00 0.00 0.00 2.69
840 1206 9.334693 GAGCAATGAGTTTCTATTTACACTTTG 57.665 33.333 0.00 0.00 0.00 2.77
841 1207 9.289782 AGAGCAATGAGTTTCTATTTACACTTT 57.710 29.630 0.00 0.00 0.00 2.66
842 1208 8.854614 AGAGCAATGAGTTTCTATTTACACTT 57.145 30.769 0.00 0.00 0.00 3.16
843 1209 8.854614 AAGAGCAATGAGTTTCTATTTACACT 57.145 30.769 0.00 0.00 0.00 3.55
848 1214 9.167311 ACGATAAAGAGCAATGAGTTTCTATTT 57.833 29.630 0.00 0.00 0.00 1.40
849 1215 8.723942 ACGATAAAGAGCAATGAGTTTCTATT 57.276 30.769 0.00 0.00 0.00 1.73
850 1216 8.723942 AACGATAAAGAGCAATGAGTTTCTAT 57.276 30.769 0.00 0.00 0.00 1.98
851 1217 8.547967 AAACGATAAAGAGCAATGAGTTTCTA 57.452 30.769 0.00 0.00 0.00 2.10
852 1218 7.440523 AAACGATAAAGAGCAATGAGTTTCT 57.559 32.000 0.00 0.00 0.00 2.52
853 1219 9.774742 ATTAAACGATAAAGAGCAATGAGTTTC 57.225 29.630 0.00 0.00 32.54 2.78
856 1222 9.774742 GAAATTAAACGATAAAGAGCAATGAGT 57.225 29.630 0.00 0.00 0.00 3.41
857 1223 9.994432 AGAAATTAAACGATAAAGAGCAATGAG 57.006 29.630 0.00 0.00 0.00 2.90
900 1268 7.443879 TGCTTTCACAATGACACAAGTCTATAA 59.556 33.333 0.00 0.00 45.20 0.98
903 1271 5.007626 GTGCTTTCACAATGACACAAGTCTA 59.992 40.000 0.00 0.00 42.69 2.59
1066 1479 3.115922 ACCCCTAGGATTAGTATGGCCTT 60.116 47.826 11.48 0.00 36.73 4.35
1098 1511 1.661341 GCCGCATCATTTCTCTGAGT 58.339 50.000 4.32 0.00 0.00 3.41
1108 1521 1.227556 GTTCTACCCGCCGCATCAT 60.228 57.895 0.00 0.00 0.00 2.45
1111 1524 1.686325 ATCAGTTCTACCCGCCGCAT 61.686 55.000 0.00 0.00 0.00 4.73
1116 1529 3.793559 ACATTGTATCAGTTCTACCCGC 58.206 45.455 0.00 0.00 0.00 6.13
1119 1532 6.683974 ATGCAACATTGTATCAGTTCTACC 57.316 37.500 0.00 0.00 0.00 3.18
1159 1573 1.866853 GCTTGCTCTTTTGTCCCCCG 61.867 60.000 0.00 0.00 0.00 5.73
1274 1688 4.880120 TGCTTGATGATGAAGAAGGATCAC 59.120 41.667 0.00 0.00 31.47 3.06
1309 1723 6.581171 AGAGGAAACTGAAAGGCATTTAAG 57.419 37.500 6.66 6.66 44.43 1.85
1310 1724 6.976934 AAGAGGAAACTGAAAGGCATTTAA 57.023 33.333 0.00 0.00 44.43 1.52
1315 1729 4.706842 AGTAAGAGGAAACTGAAAGGCA 57.293 40.909 0.00 0.00 44.43 4.75
1334 1748 2.357637 CGTGACCCAATGTGACAAAAGT 59.642 45.455 0.00 0.00 29.33 2.66
1342 1756 1.807139 TCATGACGTGACCCAATGTG 58.193 50.000 0.00 0.00 0.00 3.21
1373 1787 4.469227 TCTTCTTGCTGAGGCTTCTAATCT 59.531 41.667 0.00 0.00 39.59 2.40
1388 1802 8.919661 CCTTTGAAATGTTTTCTATCTTCTTGC 58.080 33.333 2.08 0.00 0.00 4.01
1473 1990 6.983906 AGGTTGGAACTTCTGATCATTTTT 57.016 33.333 0.00 0.00 0.00 1.94
1482 2013 3.748568 GCTCAACTAGGTTGGAACTTCTG 59.251 47.826 9.98 0.00 42.99 3.02
1524 2055 8.934697 ACCAACTTCCTGCTAGAATGTATAATA 58.065 33.333 0.00 0.00 0.00 0.98
1679 2210 4.150980 GTGAAACACAAATCCATGCATGTG 59.849 41.667 24.58 18.48 46.52 3.21
1743 2274 3.057315 GCTCACTGTGCACACCAATATTT 60.057 43.478 17.42 0.00 0.00 1.40
1773 2304 2.159128 TCTCTGCAGCTCTGTTATGCTC 60.159 50.000 9.47 0.00 40.62 4.26
1803 2334 8.067751 AGAAACTCTGGCCTTTAATTATTTCC 57.932 34.615 3.32 0.00 0.00 3.13
1819 2350 4.621991 TCCAGAACGAGAAAGAAACTCTG 58.378 43.478 0.00 0.00 32.87 3.35
1890 2421 1.002624 TCCGGCAGTTGTTCCATCC 60.003 57.895 0.00 0.00 0.00 3.51
1891 2422 0.321653 ACTCCGGCAGTTGTTCCATC 60.322 55.000 0.00 0.00 26.56 3.51
1939 2470 6.701145 TTGTACACCTATTCTGTTTGCAAA 57.299 33.333 8.05 8.05 0.00 3.68
1947 2478 7.759886 CGATGGGTATATTGTACACCTATTCTG 59.240 40.741 0.00 0.00 34.07 3.02
1986 2517 0.990282 CCCATCCCACCTCCACTGAT 60.990 60.000 0.00 0.00 0.00 2.90
1992 2523 1.074471 TAGCTCCCATCCCACCTCC 60.074 63.158 0.00 0.00 0.00 4.30
2009 2540 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2010 2541 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2011 2542 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2012 2543 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2013 2544 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2014 2545 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2015 2546 3.846360 AGACGAGTAATTTGGAACGGAG 58.154 45.455 0.00 0.00 0.00 4.63
2016 2547 3.256383 TGAGACGAGTAATTTGGAACGGA 59.744 43.478 0.00 0.00 0.00 4.69
2017 2548 3.581755 TGAGACGAGTAATTTGGAACGG 58.418 45.455 0.00 0.00 0.00 4.44
2018 2549 4.482386 TCTGAGACGAGTAATTTGGAACG 58.518 43.478 0.00 0.00 0.00 3.95
2019 2550 6.780706 TTTCTGAGACGAGTAATTTGGAAC 57.219 37.500 0.00 0.00 0.00 3.62
2020 2551 6.371548 CCATTTCTGAGACGAGTAATTTGGAA 59.628 38.462 0.00 0.00 0.00 3.53
2021 2552 5.874810 CCATTTCTGAGACGAGTAATTTGGA 59.125 40.000 0.00 0.00 0.00 3.53
2022 2553 5.874810 TCCATTTCTGAGACGAGTAATTTGG 59.125 40.000 0.00 0.00 0.00 3.28
2023 2554 6.968131 TCCATTTCTGAGACGAGTAATTTG 57.032 37.500 0.00 0.00 0.00 2.32
2024 2555 7.106239 ACATCCATTTCTGAGACGAGTAATTT 58.894 34.615 0.00 0.00 0.00 1.82
2025 2556 6.644347 ACATCCATTTCTGAGACGAGTAATT 58.356 36.000 0.00 0.00 0.00 1.40
2026 2557 6.227298 ACATCCATTTCTGAGACGAGTAAT 57.773 37.500 0.00 0.00 0.00 1.89
2027 2558 5.661056 ACATCCATTTCTGAGACGAGTAA 57.339 39.130 0.00 0.00 0.00 2.24
2028 2559 6.961360 ATACATCCATTTCTGAGACGAGTA 57.039 37.500 0.00 0.00 0.00 2.59
2029 2560 5.860941 ATACATCCATTTCTGAGACGAGT 57.139 39.130 0.00 0.00 0.00 4.18
2030 2561 8.138074 TCTAAATACATCCATTTCTGAGACGAG 58.862 37.037 0.00 0.00 30.84 4.18
2031 2562 8.007405 TCTAAATACATCCATTTCTGAGACGA 57.993 34.615 0.00 0.00 30.84 4.20
2032 2563 8.543774 GTTCTAAATACATCCATTTCTGAGACG 58.456 37.037 0.00 0.00 30.84 4.18
2033 2564 9.606631 AGTTCTAAATACATCCATTTCTGAGAC 57.393 33.333 0.00 0.00 30.84 3.36
2062 2593 9.664332 GCAGAAATGGATGTATCTAGATGTATT 57.336 33.333 15.79 4.32 0.00 1.89
2063 2594 7.978414 CGCAGAAATGGATGTATCTAGATGTAT 59.022 37.037 15.79 9.11 0.00 2.29
2064 2595 7.176690 TCGCAGAAATGGATGTATCTAGATGTA 59.823 37.037 15.79 4.44 0.00 2.29
2065 2596 6.015095 TCGCAGAAATGGATGTATCTAGATGT 60.015 38.462 15.79 1.25 0.00 3.06
2066 2597 6.309980 GTCGCAGAAATGGATGTATCTAGATG 59.690 42.308 15.79 0.00 39.69 2.90
2067 2598 6.393990 GTCGCAGAAATGGATGTATCTAGAT 58.606 40.000 10.73 10.73 39.69 1.98
2068 2599 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
2069 2600 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
2070 2601 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
2071 2602 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
2072 2603 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
2073 2604 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
2074 2605 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
2075 2606 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
2076 2607 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
2077 2608 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
2078 2609 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
2079 2610 3.301835 CGAATTACTCGTCGCAGAAATGG 60.302 47.826 0.00 0.00 42.89 3.16
2080 2611 3.301835 CCGAATTACTCGTCGCAGAAATG 60.302 47.826 0.00 0.00 46.65 2.32
2081 2612 2.858344 CCGAATTACTCGTCGCAGAAAT 59.142 45.455 0.00 0.00 46.65 2.17
2082 2613 2.095110 TCCGAATTACTCGTCGCAGAAA 60.095 45.455 0.00 0.00 46.65 2.52
2083 2614 1.469703 TCCGAATTACTCGTCGCAGAA 59.530 47.619 0.00 0.00 46.65 3.02
2084 2615 1.089112 TCCGAATTACTCGTCGCAGA 58.911 50.000 0.00 0.00 46.65 4.26
2085 2616 1.582502 GTTCCGAATTACTCGTCGCAG 59.417 52.381 0.00 0.00 46.65 5.18
2086 2617 1.621107 GTTCCGAATTACTCGTCGCA 58.379 50.000 0.00 0.00 46.65 5.10
2087 2618 0.564767 CGTTCCGAATTACTCGTCGC 59.435 55.000 0.00 0.00 46.65 5.19
2088 2619 1.186030 CCGTTCCGAATTACTCGTCG 58.814 55.000 0.00 0.00 46.65 5.12
2089 2620 2.448219 CTCCGTTCCGAATTACTCGTC 58.552 52.381 0.00 0.00 46.65 4.20
2090 2621 1.133790 CCTCCGTTCCGAATTACTCGT 59.866 52.381 0.00 0.00 46.65 4.18
2092 2623 1.753073 TCCCTCCGTTCCGAATTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2093 2624 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2094 2625 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2095 2626 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2096 2627 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2097 2628 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2098 2629 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
2099 2630 0.038744 AAGTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
2100 2631 0.893447 AAAGTACTCCCTCCGTTCCG 59.107 55.000 0.00 0.00 0.00 4.30
2101 2632 1.066358 CCAAAGTACTCCCTCCGTTCC 60.066 57.143 0.00 0.00 0.00 3.62
2102 2633 1.897802 TCCAAAGTACTCCCTCCGTTC 59.102 52.381 0.00 0.00 0.00 3.95
2103 2634 1.900486 CTCCAAAGTACTCCCTCCGTT 59.100 52.381 0.00 0.00 0.00 4.44
2104 2635 1.558233 CTCCAAAGTACTCCCTCCGT 58.442 55.000 0.00 0.00 0.00 4.69
2105 2636 0.824759 CCTCCAAAGTACTCCCTCCG 59.175 60.000 0.00 0.00 0.00 4.63
2106 2637 2.112190 CTCCTCCAAAGTACTCCCTCC 58.888 57.143 0.00 0.00 0.00 4.30
2107 2638 1.483004 GCTCCTCCAAAGTACTCCCTC 59.517 57.143 0.00 0.00 0.00 4.30
2108 2639 1.203313 TGCTCCTCCAAAGTACTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
2109 2640 1.276622 TGCTCCTCCAAAGTACTCCC 58.723 55.000 0.00 0.00 0.00 4.30
2110 2641 2.237392 ACATGCTCCTCCAAAGTACTCC 59.763 50.000 0.00 0.00 0.00 3.85
2111 2642 3.618690 ACATGCTCCTCCAAAGTACTC 57.381 47.619 0.00 0.00 0.00 2.59
2112 2643 3.838317 TGTACATGCTCCTCCAAAGTACT 59.162 43.478 0.00 0.00 34.31 2.73
2113 2644 4.202245 TGTACATGCTCCTCCAAAGTAC 57.798 45.455 0.00 0.00 34.05 2.73
2131 2662 6.936335 TGCACTTCTTTCTCTTCATCAATGTA 59.064 34.615 0.00 0.00 0.00 2.29
2164 2882 9.840427 ACTAACAATTTCAATTCCTATGTTTCG 57.160 29.630 0.00 0.00 0.00 3.46
2181 2899 6.295067 GGAGGCAACCACATTTACTAACAATT 60.295 38.462 0.00 0.00 37.17 2.32
2188 2906 1.710809 AGGGAGGCAACCACATTTACT 59.289 47.619 0.28 0.00 37.17 2.24
2214 2932 4.207891 AGCACTACCAGTAACCTTGATG 57.792 45.455 0.00 0.00 0.00 3.07
2264 2982 2.622436 TGGCCAAAAACTTTTTCCACG 58.378 42.857 0.61 0.00 30.16 4.94
2310 3028 5.065731 CAGAGCTCCTTGTATTTCATCCAAC 59.934 44.000 10.93 0.00 0.00 3.77
2358 3076 2.820059 AACACTGCTTCAGACGATGA 57.180 45.000 0.29 0.00 35.18 2.92
2462 3180 1.778017 TAGTTGGCCTTGCTGCTCCA 61.778 55.000 3.32 0.33 0.00 3.86
2508 3226 6.351371 GGAGATTCCGATGGATTAGCTCATAA 60.351 42.308 0.00 0.00 0.00 1.90
2547 3265 9.398170 CGACATGAAGACTTGTCAAAAATATTT 57.602 29.630 0.00 0.00 45.40 1.40
2550 3268 7.722795 TCGACATGAAGACTTGTCAAAAATA 57.277 32.000 0.00 0.00 45.40 1.40
2567 3285 2.558378 AGAGGTCATGCATTCGACATG 58.442 47.619 16.47 7.91 45.08 3.21
2571 3289 2.497273 TCTCAAGAGGTCATGCATTCGA 59.503 45.455 0.00 0.00 0.00 3.71
2572 3290 2.606725 GTCTCAAGAGGTCATGCATTCG 59.393 50.000 0.00 0.00 0.00 3.34
2619 3337 1.067635 ACATCGCCAACAAAGCATTCC 60.068 47.619 0.00 0.00 0.00 3.01
2660 3378 5.652744 AACACGTCTCAGTTTTGACATAC 57.347 39.130 0.00 0.00 33.18 2.39
2751 3472 3.321968 GTGGACCAGAAAAAGCAAGGAAT 59.678 43.478 0.00 0.00 0.00 3.01
2765 3486 4.760530 TCCTCAATTATCTGTGGACCAG 57.239 45.455 0.00 0.00 42.97 4.00
2777 3498 6.885918 TCTCTTGAACAATGCATCCTCAATTA 59.114 34.615 14.78 8.40 0.00 1.40
2788 3509 3.119708 AGCGGAAATCTCTTGAACAATGC 60.120 43.478 0.00 0.00 0.00 3.56
2807 3528 1.504359 TACCAAAACACGGAGAAGCG 58.496 50.000 0.00 0.00 0.00 4.68
2814 3538 8.508875 AGTGAGTAATTAATTACCAAAACACGG 58.491 33.333 27.21 0.00 42.71 4.94
2829 3553 8.726988 GGAATGCTTTGTACAAGTGAGTAATTA 58.273 33.333 8.56 0.00 0.00 1.40
2861 3585 7.816031 GGCATAGATGTATCAATTTTCCAATGG 59.184 37.037 0.00 0.00 0.00 3.16
2865 3589 8.439971 AGTAGGCATAGATGTATCAATTTTCCA 58.560 33.333 0.00 0.00 0.00 3.53
2884 3608 9.720769 GCCAGTATTATCTAAATTAAGTAGGCA 57.279 33.333 0.00 0.00 33.86 4.75
2896 3620 8.150827 AGCCAAGATATGCCAGTATTATCTAA 57.849 34.615 0.00 0.00 0.00 2.10
2902 3626 4.401925 GGAAGCCAAGATATGCCAGTATT 58.598 43.478 0.00 0.00 0.00 1.89
2919 3643 1.066152 GAGCCAATGGATTTCGGAAGC 59.934 52.381 2.05 0.00 0.00 3.86
2926 3650 4.608170 TCTTTAGGGAGCCAATGGATTT 57.392 40.909 2.05 0.00 0.00 2.17
2955 3679 0.536006 ACCTTGTCAAGCTCAGCACC 60.536 55.000 7.09 0.00 0.00 5.01
2958 3682 0.590195 CACACCTTGTCAAGCTCAGC 59.410 55.000 7.09 0.00 0.00 4.26
2981 3705 1.435515 GGAGGTAGACTGCGCAGAG 59.564 63.158 42.03 20.13 0.00 3.35
3006 3732 5.070313 ACATCTTAAACTGCACAATTGGGTT 59.930 36.000 9.94 6.12 0.00 4.11
3011 3737 9.846248 GATTTAGACATCTTAAACTGCACAATT 57.154 29.630 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.