Multiple sequence alignment - TraesCS2D01G021500

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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 TraesCS2D01G021500 chr2D 100.000 3774 0 0 1 3774 9885620 9881847 0.000000e+00 6970.0
1 TraesCS2D01G021500 chr2D 88.623 167 18 1 2799 2965 362930815 362930980 6.390000e-48 202.0
2 TraesCS2D01G021500 chr2A 91.550 1858 132 11 960 2793 21275651 21273795 0.000000e+00 2538.0
3 TraesCS2D01G021500 chr2A 92.842 936 57 4 1867 2793 9388549 9389483 0.000000e+00 1349.0
4 TraesCS2D01G021500 chr2A 92.283 933 59 6 1874 2793 9841327 9842259 0.000000e+00 1312.0
5 TraesCS2D01G021500 chr2A 93.266 698 47 0 1137 1834 9838779 9839476 0.000000e+00 1029.0
6 TraesCS2D01G021500 chr2A 89.263 801 66 14 2983 3772 9389544 9390335 0.000000e+00 985.0
7 TraesCS2D01G021500 chr2A 92.507 694 37 10 2952 3636 21273796 21273109 0.000000e+00 979.0
8 TraesCS2D01G021500 chr2A 88.889 801 69 14 2983 3772 9842320 9843111 0.000000e+00 968.0
9 TraesCS2D01G021500 chr2A 83.745 972 88 33 156 1096 9138990 9138058 0.000000e+00 856.0
10 TraesCS2D01G021500 chr2A 82.265 998 147 18 992 1980 682635637 682634661 0.000000e+00 835.0
11 TraesCS2D01G021500 chr2A 83.257 651 86 9 2136 2776 682634554 682633917 9.090000e-161 577.0
12 TraesCS2D01G021500 chr2A 81.930 653 36 34 1 611 9837821 9838433 9.480000e-131 477.0
13 TraesCS2D01G021500 chr2A 77.083 864 156 30 1093 1947 5927740 5928570 9.550000e-126 460.0
14 TraesCS2D01G021500 chr2A 82.278 316 45 10 306 611 21276208 21275894 2.890000e-66 263.0
15 TraesCS2D01G021500 chr2A 96.262 107 4 0 1093 1199 9137633 9137527 3.870000e-40 176.0
16 TraesCS2D01G021500 chr7D 80.711 928 173 3 1032 1953 177876599 177877526 0.000000e+00 717.0
17 TraesCS2D01G021500 chr7D 86.842 266 24 6 3506 3763 485106459 485106721 1.720000e-73 287.0
18 TraesCS2D01G021500 chr7D 86.792 265 24 6 3506 3762 199607137 199606876 6.170000e-73 285.0
19 TraesCS2D01G021500 chr7D 89.130 46 5 0 2465 2510 613717192 613717237 1.460000e-04 58.4
20 TraesCS2D01G021500 chr7A 79.721 932 172 11 1032 1953 181695885 181696809 0.000000e+00 658.0
21 TraesCS2D01G021500 chr7B 84.518 633 96 2 2136 2767 143811062 143811693 3.200000e-175 625.0
22 TraesCS2D01G021500 chr7B 83.651 367 60 0 1032 1398 143808268 143808634 2.790000e-91 346.0
23 TraesCS2D01G021500 chr7B 87.454 271 22 6 3500 3762 540063193 540063459 6.130000e-78 302.0
24 TraesCS2D01G021500 chr7B 87.719 57 7 0 403 459 242957324 242957380 2.430000e-07 67.6
25 TraesCS2D01G021500 chr3A 80.676 828 127 22 993 1802 46584135 46583323 2.490000e-171 612.0
26 TraesCS2D01G021500 chr3A 77.953 635 101 19 2136 2764 46583111 46582510 9.970000e-96 361.0
27 TraesCS2D01G021500 chr4A 87.023 262 27 5 3502 3762 352482009 352481754 4.770000e-74 289.0
28 TraesCS2D01G021500 chr2B 86.842 266 24 6 3508 3765 438744180 438743918 1.720000e-73 287.0
29 TraesCS2D01G021500 chr5B 85.556 270 26 7 3507 3767 527760621 527760356 1.730000e-68 270.0
30 TraesCS2D01G021500 chr5B 91.613 155 13 0 2799 2953 612672830 612672984 8.210000e-52 215.0
31 TraesCS2D01G021500 chr5B 90.446 157 15 0 2799 2955 46768871 46769027 1.370000e-49 207.0
32 TraesCS2D01G021500 chr3B 86.275 255 28 6 3520 3772 80104427 80104676 1.730000e-68 270.0
33 TraesCS2D01G021500 chr1D 85.771 253 26 3 3518 3762 338927406 338927156 3.740000e-65 259.0
34 TraesCS2D01G021500 chr1D 97.059 34 0 1 421 454 355428974 355429006 5.270000e-04 56.5
35 TraesCS2D01G021500 chr3D 85.271 258 27 11 3518 3772 50537805 50538054 4.840000e-64 255.0
36 TraesCS2D01G021500 chr1A 91.613 155 13 0 2799 2953 181769434 181769588 8.210000e-52 215.0
37 TraesCS2D01G021500 chr1A 79.828 233 39 8 378 608 343611205 343610979 3.020000e-36 163.0
38 TraesCS2D01G021500 chr1A 85.616 146 9 7 650 783 168443372 168443517 3.930000e-30 143.0
39 TraesCS2D01G021500 chrUn 90.506 158 15 0 2797 2954 96464816 96464973 3.820000e-50 209.0
40 TraesCS2D01G021500 chrUn 85.616 146 9 7 650 783 93417096 93417241 3.930000e-30 143.0
41 TraesCS2D01G021500 chrUn 85.616 146 9 7 650 783 278886248 278886393 3.930000e-30 143.0
42 TraesCS2D01G021500 chrUn 85.616 146 9 7 650 783 327660628 327660773 3.930000e-30 143.0
43 TraesCS2D01G021500 chr1B 89.024 164 18 0 2792 2955 49836448 49836285 1.780000e-48 204.0
44 TraesCS2D01G021500 chr1B 89.024 164 18 0 2792 2955 49838679 49838516 1.780000e-48 204.0
45 TraesCS2D01G021500 chr1B 89.024 164 18 0 2792 2955 49839423 49839260 1.780000e-48 204.0
46 TraesCS2D01G021500 chr4B 85.075 201 18 11 2772 2964 97894861 97895057 1.070000e-45 195.0
47 TraesCS2D01G021500 chr4B 85.616 146 9 7 650 783 642713950 642714095 3.930000e-30 143.0
48 TraesCS2D01G021500 chr4B 87.719 57 7 0 403 459 195383723 195383779 2.430000e-07 67.6
49 TraesCS2D01G021500 chr4B 85.965 57 8 0 403 459 160479313 160479369 1.130000e-05 62.1
50 TraesCS2D01G021500 chr5D 86.014 143 8 7 653 783 503213151 503213009 3.930000e-30 143.0
51 TraesCS2D01G021500 chr5D 81.053 95 18 0 1342 1436 522761316 522761222 4.040000e-10 76.8
52 TraesCS2D01G021500 chr4D 85.315 143 9 5 653 783 468230 468088 1.830000e-28 137.0
53 TraesCS2D01G021500 chr4D 85.315 143 9 7 653 783 19923712 19923570 1.830000e-28 137.0
54 TraesCS2D01G021500 chr5A 89.796 49 5 0 378 426 534988103 534988055 3.150000e-06 63.9


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 TraesCS2D01G021500 chr2D 9881847 9885620 3773 True 6970.0 6970 100.000000 1 3774 1 chr2D.!!$R1 3773
1 TraesCS2D01G021500 chr2A 21273109 21276208 3099 True 1260.0 2538 88.778333 306 3636 3 chr2A.!!$R2 3330
2 TraesCS2D01G021500 chr2A 9388549 9390335 1786 False 1167.0 1349 91.052500 1867 3772 2 chr2A.!!$F2 1905
3 TraesCS2D01G021500 chr2A 9837821 9843111 5290 False 946.5 1312 89.092000 1 3772 4 chr2A.!!$F3 3771
4 TraesCS2D01G021500 chr2A 682633917 682635637 1720 True 706.0 835 82.761000 992 2776 2 chr2A.!!$R3 1784
5 TraesCS2D01G021500 chr2A 9137527 9138990 1463 True 516.0 856 90.003500 156 1199 2 chr2A.!!$R1 1043
6 TraesCS2D01G021500 chr2A 5927740 5928570 830 False 460.0 460 77.083000 1093 1947 1 chr2A.!!$F1 854
7 TraesCS2D01G021500 chr7D 177876599 177877526 927 False 717.0 717 80.711000 1032 1953 1 chr7D.!!$F1 921
8 TraesCS2D01G021500 chr7A 181695885 181696809 924 False 658.0 658 79.721000 1032 1953 1 chr7A.!!$F1 921
9 TraesCS2D01G021500 chr7B 143808268 143811693 3425 False 485.5 625 84.084500 1032 2767 2 chr7B.!!$F3 1735
10 TraesCS2D01G021500 chr3A 46582510 46584135 1625 True 486.5 612 79.314500 993 2764 2 chr3A.!!$R1 1771
11 TraesCS2D01G021500 chr1B 49836285 49839423 3138 True 204.0 204 89.024000 2792 2955 3 chr1B.!!$R1 163

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
986 1124 0.606673 GTTGGACTGGAGACCAAGCC 60.607 60.000 10.34 0.0 46.98 4.35 F
1482 3912 1.651240 CCATCAAGCAAGCCGAGGTG 61.651 60.000 0.00 0.0 0.00 4.00 F
1895 6145 1.001633 GCACGAGGAAGACACCCTTAA 59.998 52.381 0.00 0.0 34.68 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 4296 0.679505 CCAACAGGTCTTCGTCCTCA 59.320 55.000 0.0 0.0 32.37 3.86 R
2639 6921 1.404986 CGGAATCGCCCAGTCAAAGTA 60.405 52.381 0.0 0.0 0.00 2.24 R
2943 7976 1.807142 GCTTGCACAACTACTTCCTCC 59.193 52.381 0.0 0.0 0.00 4.30 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.739300 CCCAACTGTACACTTGTAAGACG 59.261 47.826 12.44 0.00 31.52 4.18
37 38 5.008619 TGTACACTTGTAAGACGTGGAAA 57.991 39.130 0.00 0.00 33.13 3.13
41 42 6.445357 ACACTTGTAAGACGTGGAAATTTT 57.555 33.333 0.00 0.00 33.13 1.82
42 43 6.262601 ACACTTGTAAGACGTGGAAATTTTG 58.737 36.000 0.00 0.00 33.13 2.44
43 44 5.173131 CACTTGTAAGACGTGGAAATTTTGC 59.827 40.000 0.00 0.00 0.00 3.68
45 46 5.250235 TGTAAGACGTGGAAATTTTGCAA 57.750 34.783 4.81 0.00 30.97 4.08
46 47 5.277825 TGTAAGACGTGGAAATTTTGCAAG 58.722 37.500 13.36 13.36 36.62 4.01
47 48 4.385358 AAGACGTGGAAATTTTGCAAGT 57.615 36.364 18.83 18.83 45.10 3.16
51 52 3.632145 ACGTGGAAATTTTGCAAGTCTCT 59.368 39.130 14.50 0.00 39.18 3.10
52 53 4.222114 CGTGGAAATTTTGCAAGTCTCTC 58.778 43.478 4.81 0.00 30.97 3.20
53 54 4.261155 CGTGGAAATTTTGCAAGTCTCTCA 60.261 41.667 4.81 0.00 30.97 3.27
54 55 5.591099 GTGGAAATTTTGCAAGTCTCTCAA 58.409 37.500 4.81 0.00 30.97 3.02
55 56 5.689068 GTGGAAATTTTGCAAGTCTCTCAAG 59.311 40.000 4.81 0.00 30.97 3.02
56 57 5.221303 TGGAAATTTTGCAAGTCTCTCAAGG 60.221 40.000 0.00 0.00 0.00 3.61
57 58 4.861102 AATTTTGCAAGTCTCTCAAGGG 57.139 40.909 0.00 0.00 0.00 3.95
59 60 4.431416 TTTTGCAAGTCTCTCAAGGGTA 57.569 40.909 0.00 0.00 0.00 3.69
62 63 2.284190 GCAAGTCTCTCAAGGGTATGC 58.716 52.381 0.00 0.00 0.00 3.14
63 64 2.544685 CAAGTCTCTCAAGGGTATGCG 58.455 52.381 0.00 0.00 0.00 4.73
64 65 1.853963 AGTCTCTCAAGGGTATGCGT 58.146 50.000 0.00 0.00 0.00 5.24
65 66 1.478510 AGTCTCTCAAGGGTATGCGTG 59.521 52.381 0.00 0.00 0.00 5.34
66 67 0.824109 TCTCTCAAGGGTATGCGTGG 59.176 55.000 0.00 0.00 0.00 4.94
67 68 0.811616 CTCTCAAGGGTATGCGTGGC 60.812 60.000 0.00 0.00 0.00 5.01
68 69 2.125310 TCAAGGGTATGCGTGGCG 60.125 61.111 0.00 0.00 0.00 5.69
69 70 2.125310 CAAGGGTATGCGTGGCGA 60.125 61.111 0.00 0.00 0.00 5.54
70 71 2.125269 AAGGGTATGCGTGGCGAC 60.125 61.111 0.00 0.00 0.00 5.19
124 142 4.511454 GTCAATAGCGTGCATGGAATAAGA 59.489 41.667 8.27 0.00 0.00 2.10
129 147 2.286294 GCGTGCATGGAATAAGAGTGAG 59.714 50.000 8.27 0.00 0.00 3.51
143 161 4.647564 AGAGTGAGATTTCATGGTTGGT 57.352 40.909 0.00 0.00 35.39 3.67
163 181 3.562973 GGTGTGCAATAGATGTGATGGAG 59.437 47.826 0.00 0.00 0.00 3.86
172 190 2.915604 AGATGTGATGGAGTTTGGAGGT 59.084 45.455 0.00 0.00 0.00 3.85
194 212 3.626028 GTTGATTCCAACGTCTTGCTT 57.374 42.857 0.00 0.00 42.60 3.91
195 213 3.300009 GTTGATTCCAACGTCTTGCTTG 58.700 45.455 0.00 0.00 42.60 4.01
216 236 2.581216 AGAAGACGTGTACTCCCTCA 57.419 50.000 0.00 0.00 0.00 3.86
217 237 3.088789 AGAAGACGTGTACTCCCTCAT 57.911 47.619 0.00 0.00 0.00 2.90
218 238 4.232188 AGAAGACGTGTACTCCCTCATA 57.768 45.455 0.00 0.00 0.00 2.15
219 239 4.794334 AGAAGACGTGTACTCCCTCATAT 58.206 43.478 0.00 0.00 0.00 1.78
220 240 4.580995 AGAAGACGTGTACTCCCTCATATG 59.419 45.833 0.00 0.00 0.00 1.78
221 241 4.166246 AGACGTGTACTCCCTCATATGA 57.834 45.455 5.07 5.07 0.00 2.15
222 242 4.533815 AGACGTGTACTCCCTCATATGAA 58.466 43.478 6.90 0.00 0.00 2.57
223 243 4.338682 AGACGTGTACTCCCTCATATGAAC 59.661 45.833 6.90 1.54 0.00 3.18
338 359 2.285083 GGTGTGTTAGTGTGTGCTTGA 58.715 47.619 0.00 0.00 0.00 3.02
376 397 2.362077 GGCCTGCAGGGTGTATTTATTG 59.638 50.000 33.46 4.10 37.43 1.90
484 506 6.976934 AAATCCACAACAGTAATCCAGTTT 57.023 33.333 0.00 0.00 0.00 2.66
618 667 7.269316 GGACAAACCTAAAACCTGAATTTGAA 58.731 34.615 0.00 0.00 35.41 2.69
620 669 9.325198 GACAAACCTAAAACCTGAATTTGAAAT 57.675 29.630 0.00 0.00 31.59 2.17
621 670 9.108284 ACAAACCTAAAACCTGAATTTGAAATG 57.892 29.630 0.00 0.00 31.59 2.32
622 671 9.323985 CAAACCTAAAACCTGAATTTGAAATGA 57.676 29.630 0.00 0.00 0.00 2.57
655 745 9.692749 TTACAACTTACAGTTAAGTCATCTCTG 57.307 33.333 0.00 0.00 46.10 3.35
663 753 5.997746 CAGTTAAGTCATCTCTGGGTTTCAA 59.002 40.000 0.00 0.00 0.00 2.69
668 758 4.823989 AGTCATCTCTGGGTTTCAACTTTG 59.176 41.667 0.00 0.00 0.00 2.77
675 765 3.215151 TGGGTTTCAACTTTGCGACATA 58.785 40.909 0.00 0.00 0.00 2.29
728 830 2.806608 TAAAGCGTATCATCCGACCC 57.193 50.000 0.00 0.00 0.00 4.46
783 885 6.584185 TTCCTAAAGTTTTGGGTAGAATGC 57.416 37.500 14.91 0.00 39.55 3.56
799 901 7.224297 GGTAGAATGCTGGTATGAGGAAAATA 58.776 38.462 0.00 0.00 0.00 1.40
804 906 8.627208 AATGCTGGTATGAGGAAAATATACAG 57.373 34.615 0.00 0.00 0.00 2.74
842 944 2.544686 TCCCATACGTTGTTGTCGTTTG 59.455 45.455 0.00 0.00 41.72 2.93
875 977 0.817634 CTTTCGGTGGTGTGGCAGAA 60.818 55.000 0.00 0.00 0.00 3.02
919 1025 0.973632 TCTTGCATGACCTACGGTGT 59.026 50.000 0.00 0.00 35.25 4.16
932 1038 1.267121 ACGGTGTAGCAACTCCATCT 58.733 50.000 0.00 0.00 38.88 2.90
974 1112 5.997384 AAATAAGAGTACCGAGTTGGACT 57.003 39.130 2.42 2.28 42.00 3.85
986 1124 0.606673 GTTGGACTGGAGACCAAGCC 60.607 60.000 10.34 0.00 46.98 4.35
1087 1265 2.259917 TGATTCTGAGGCAGGTTCTGA 58.740 47.619 0.00 0.00 32.44 3.27
1231 1840 3.695606 ACGGTCCGCTCATGCTGT 61.696 61.111 12.28 0.00 36.97 4.40
1287 1896 4.161295 CCCGAGGCAGCGATGGAA 62.161 66.667 1.46 0.00 0.00 3.53
1348 1957 4.028490 GCCCCACGGTGGACATCA 62.028 66.667 28.36 0.00 40.96 3.07
1482 3912 1.651240 CCATCAAGCAAGCCGAGGTG 61.651 60.000 0.00 0.00 0.00 4.00
1622 4061 4.008933 GTGTCGGCAGCAGGAGGT 62.009 66.667 0.00 0.00 0.00 3.85
1804 4243 2.485814 GAGCGCAAGGAGAAGAAACAAT 59.514 45.455 11.47 0.00 38.28 2.71
1839 4296 1.139853 GCTGCCACTGCTACTCCTAAT 59.860 52.381 0.00 0.00 38.71 1.73
1859 4316 4.695560 GGACGAAGACCTGTTGGG 57.304 61.111 0.00 0.00 39.76 4.12
1893 6143 1.371558 GCACGAGGAAGACACCCTT 59.628 57.895 0.00 0.00 37.93 3.95
1895 6145 1.001633 GCACGAGGAAGACACCCTTAA 59.998 52.381 0.00 0.00 34.68 1.85
1900 6150 4.286291 ACGAGGAAGACACCCTTAATTTCT 59.714 41.667 0.00 0.00 34.68 2.52
1910 6160 5.826208 ACACCCTTAATTTCTCTTTGACGTT 59.174 36.000 0.00 0.00 0.00 3.99
1918 6168 1.069432 TCTCTTTGACGTTCGAGACCG 60.069 52.381 0.00 0.47 37.07 4.79
1980 6230 1.967319 ATCACTCGTTTGCAACCAGT 58.033 45.000 0.00 0.00 32.90 4.00
1982 6232 2.088423 TCACTCGTTTGCAACCAGTTT 58.912 42.857 0.00 0.00 30.12 2.66
1996 6246 8.036273 TGCAACCAGTTTTATTTAGCTACTAC 57.964 34.615 0.00 0.00 0.00 2.73
2002 6252 9.028185 CCAGTTTTATTTAGCTACTACTAACCG 57.972 37.037 0.00 0.00 31.94 4.44
2056 6313 2.762535 TCCCCATCAGTTCGAACTTC 57.237 50.000 27.79 1.65 37.08 3.01
2065 6322 4.519213 TCAGTTCGAACTTCTTTTTCCCA 58.481 39.130 27.79 0.00 37.08 4.37
2075 6332 7.201705 CGAACTTCTTTTTCCCAGACTTTTAGT 60.202 37.037 0.00 0.00 0.00 2.24
2230 6506 1.074072 ACACGTAATGGCAAGGGCA 59.926 52.632 0.00 0.00 43.71 5.36
2293 6572 2.740055 GTCACCAGCGCAGACCTG 60.740 66.667 11.47 0.00 0.00 4.00
2300 6579 4.479993 GCGCAGACCTGGATGGCT 62.480 66.667 0.30 0.00 40.22 4.75
2302 6581 1.522092 CGCAGACCTGGATGGCTTA 59.478 57.895 0.00 0.00 40.22 3.09
2639 6921 0.036875 GCTGGCAAACCTCCTGTACT 59.963 55.000 0.00 0.00 36.63 2.73
2704 6986 1.603455 CATGGGCGAGGTGTTTGGT 60.603 57.895 0.00 0.00 0.00 3.67
2791 7080 1.972872 AGTGCACTGCAAGCTTTACT 58.027 45.000 20.97 4.80 41.47 2.24
2792 7081 3.126001 AGTGCACTGCAAGCTTTACTA 57.874 42.857 20.97 0.00 41.47 1.82
2793 7082 2.808543 AGTGCACTGCAAGCTTTACTAC 59.191 45.455 20.97 1.51 41.47 2.73
2794 7083 2.095718 GTGCACTGCAAGCTTTACTACC 60.096 50.000 10.32 0.00 41.47 3.18
2795 7084 2.224523 TGCACTGCAAGCTTTACTACCT 60.225 45.455 0.00 0.00 37.60 3.08
2796 7085 2.416893 GCACTGCAAGCTTTACTACCTC 59.583 50.000 0.00 0.00 37.60 3.85
2797 7086 3.664107 CACTGCAAGCTTTACTACCTCA 58.336 45.455 0.00 0.00 37.60 3.86
2801 7090 2.866762 GCAAGCTTTACTACCTCATCCG 59.133 50.000 0.00 0.00 0.00 4.18
2867 7900 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2891 7924 9.920133 TCTACACTCGAAAGTACGTCTATATAT 57.080 33.333 0.00 0.00 33.25 0.86
2948 7981 7.427989 AACACTTATATTTAGGAACGGAGGA 57.572 36.000 0.00 0.00 0.00 3.71
3020 8472 2.686816 CGGCCATCACCAAACCGTC 61.687 63.158 2.24 0.00 39.05 4.79
3038 8490 9.061610 CAAACCGTCATTAAGTCAACATAAATC 57.938 33.333 0.00 0.00 0.00 2.17
3052 8603 4.717877 ACATAAATCTCCGGATTGCATGA 58.282 39.130 3.57 0.00 40.86 3.07
3057 8608 3.565764 TCTCCGGATTGCATGATTTCT 57.434 42.857 3.57 0.00 0.00 2.52
3063 8614 5.652014 TCCGGATTGCATGATTTCTTTTACT 59.348 36.000 0.00 0.00 0.00 2.24
3075 8626 4.411256 TTCTTTTACTGTGGACGAACCT 57.589 40.909 0.00 0.00 39.86 3.50
3221 8773 6.364945 GCCTACTGCTTAATAAAGTTCTGG 57.635 41.667 0.00 0.00 36.87 3.86
3226 8778 9.431887 CTACTGCTTAATAAAGTTCTGGTTACA 57.568 33.333 0.00 0.00 34.99 2.41
3440 9767 5.516044 TGCTCTGACCCTAGTTATTACAGA 58.484 41.667 0.00 0.00 0.00 3.41
3460 9787 5.044105 ACAGAGAGCAAATATTAAGGGGGTT 60.044 40.000 0.00 0.00 0.00 4.11
3466 9793 6.826668 AGCAAATATTAAGGGGGTTTTATGC 58.173 36.000 0.00 0.00 0.00 3.14
3664 10318 3.064820 GCGGTATTGACTTGGTATTGTGG 59.935 47.826 0.00 0.00 0.00 4.17
3671 10325 7.630242 ATTGACTTGGTATTGTGGATGTTAG 57.370 36.000 0.00 0.00 0.00 2.34
3672 10326 6.367374 TGACTTGGTATTGTGGATGTTAGA 57.633 37.500 0.00 0.00 0.00 2.10
3673 10327 6.774673 TGACTTGGTATTGTGGATGTTAGAA 58.225 36.000 0.00 0.00 0.00 2.10
3675 10329 8.544622 TGACTTGGTATTGTGGATGTTAGAATA 58.455 33.333 0.00 0.00 0.00 1.75
3677 10331 9.920946 ACTTGGTATTGTGGATGTTAGAATATT 57.079 29.630 0.00 0.00 0.00 1.28
3716 10370 8.854117 ACTTGATCAAAGCTTAGAAAGTTTGAT 58.146 29.630 9.88 18.95 43.55 2.57
3719 10373 6.241207 TCAAAGCTTAGAAAGTTTGATCCG 57.759 37.500 0.00 0.00 35.56 4.18
3720 10374 5.995282 TCAAAGCTTAGAAAGTTTGATCCGA 59.005 36.000 0.00 0.00 35.56 4.55
3721 10375 6.147821 TCAAAGCTTAGAAAGTTTGATCCGAG 59.852 38.462 0.00 0.00 35.56 4.63
3727 10381 7.519970 GCTTAGAAAGTTTGATCCGAGACAAAA 60.520 37.037 0.00 0.00 37.66 2.44
3740 10394 5.518847 TCCGAGACAAAACTAATATGCGAAG 59.481 40.000 0.00 0.00 0.00 3.79
3772 10426 5.878406 ATGGAGGGAGTACATAAGACTTG 57.122 43.478 0.00 0.00 0.00 3.16
3773 10427 4.942944 TGGAGGGAGTACATAAGACTTGA 58.057 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.763035 AGTGTACAGTTGGGTGGACC 59.237 55.000 0.00 0.00 40.81 4.46
12 13 4.098349 TCCACGTCTTACAAGTGTACAGTT 59.902 41.667 10.24 10.24 34.34 3.16
14 15 4.233123 TCCACGTCTTACAAGTGTACAG 57.767 45.455 0.00 0.00 34.34 2.74
31 32 5.186996 TGAGAGACTTGCAAAATTTCCAC 57.813 39.130 0.00 0.00 0.00 4.02
37 38 3.837355 ACCCTTGAGAGACTTGCAAAAT 58.163 40.909 0.00 0.00 0.00 1.82
41 42 2.355108 GCATACCCTTGAGAGACTTGCA 60.355 50.000 0.00 0.00 0.00 4.08
42 43 2.284190 GCATACCCTTGAGAGACTTGC 58.716 52.381 0.00 0.00 0.00 4.01
43 44 2.093973 ACGCATACCCTTGAGAGACTTG 60.094 50.000 0.00 0.00 0.00 3.16
45 46 1.478510 CACGCATACCCTTGAGAGACT 59.521 52.381 0.00 0.00 0.00 3.24
46 47 1.471676 CCACGCATACCCTTGAGAGAC 60.472 57.143 0.00 0.00 0.00 3.36
47 48 0.824109 CCACGCATACCCTTGAGAGA 59.176 55.000 0.00 0.00 0.00 3.10
48 49 0.811616 GCCACGCATACCCTTGAGAG 60.812 60.000 0.00 0.00 0.00 3.20
49 50 1.220749 GCCACGCATACCCTTGAGA 59.779 57.895 0.00 0.00 0.00 3.27
51 52 2.125310 CGCCACGCATACCCTTGA 60.125 61.111 0.00 0.00 0.00 3.02
52 53 2.125310 TCGCCACGCATACCCTTG 60.125 61.111 0.00 0.00 0.00 3.61
53 54 2.125269 GTCGCCACGCATACCCTT 60.125 61.111 0.00 0.00 0.00 3.95
54 55 3.075005 AGTCGCCACGCATACCCT 61.075 61.111 0.00 0.00 0.00 4.34
55 56 2.890474 CAGTCGCCACGCATACCC 60.890 66.667 0.00 0.00 0.00 3.69
56 57 2.890474 CCAGTCGCCACGCATACC 60.890 66.667 0.00 0.00 0.00 2.73
57 58 3.564027 GCCAGTCGCCACGCATAC 61.564 66.667 0.00 0.00 0.00 2.39
66 67 1.933853 CTATTACAAGTGGCCAGTCGC 59.066 52.381 15.03 0.00 0.00 5.19
67 68 3.247006 ACTATTACAAGTGGCCAGTCG 57.753 47.619 15.03 4.91 0.00 4.18
68 69 4.575885 TCAACTATTACAAGTGGCCAGTC 58.424 43.478 15.03 0.00 0.00 3.51
69 70 4.634012 TCAACTATTACAAGTGGCCAGT 57.366 40.909 5.11 6.41 0.00 4.00
70 71 5.957842 TTTCAACTATTACAAGTGGCCAG 57.042 39.130 5.11 0.00 0.00 4.85
106 107 3.132111 TCACTCTTATTCCATGCACGCTA 59.868 43.478 0.00 0.00 0.00 4.26
108 109 2.279741 TCACTCTTATTCCATGCACGC 58.720 47.619 0.00 0.00 0.00 5.34
124 142 3.822735 CACACCAACCATGAAATCTCACT 59.177 43.478 0.00 0.00 33.30 3.41
129 147 3.383620 TTGCACACCAACCATGAAATC 57.616 42.857 0.00 0.00 0.00 2.17
143 161 4.492494 ACTCCATCACATCTATTGCACA 57.508 40.909 0.00 0.00 0.00 4.57
163 181 4.083484 CGTTGGAATCAACTACCTCCAAAC 60.083 45.833 4.04 0.00 46.68 2.93
172 190 9.108230 CTTCAAGCAAGACGTTGGAATCAACTA 62.108 40.741 7.51 0.00 41.52 2.24
186 204 2.866762 ACACGTCTTCTTCAAGCAAGAC 59.133 45.455 14.83 14.83 41.13 3.01
194 212 2.818432 GAGGGAGTACACGTCTTCTTCA 59.182 50.000 0.00 0.00 0.00 3.02
195 213 2.818432 TGAGGGAGTACACGTCTTCTTC 59.182 50.000 0.00 0.00 0.00 2.87
216 236 1.046472 TCCGGGCTGGACGTTCATAT 61.046 55.000 12.08 0.00 43.74 1.78
217 237 1.683025 TCCGGGCTGGACGTTCATA 60.683 57.895 12.08 0.00 43.74 2.15
218 238 3.000819 TCCGGGCTGGACGTTCAT 61.001 61.111 12.08 0.00 43.74 2.57
263 284 9.293404 CAAGATCCTTTATGTATCCACATCAAT 57.707 33.333 0.00 0.00 44.42 2.57
338 359 1.021390 GCCTGCACACATCGCTACTT 61.021 55.000 0.00 0.00 0.00 2.24
376 397 6.156519 ACTTCAAATATTTTGAAACGGAGGC 58.843 36.000 14.33 0.00 37.89 4.70
553 602 9.877178 CTCTAGTCTGACCAAGTTTGTAAATAT 57.123 33.333 3.76 0.00 0.00 1.28
555 604 7.016268 TCCTCTAGTCTGACCAAGTTTGTAAAT 59.984 37.037 3.76 0.00 0.00 1.40
572 621 6.208994 TGTCCTAAGTCAAACTTCCTCTAGTC 59.791 42.308 0.00 0.00 39.51 2.59
576 625 5.888982 TTGTCCTAAGTCAAACTTCCTCT 57.111 39.130 0.00 0.00 39.51 3.69
655 745 2.793278 ATGTCGCAAAGTTGAAACCC 57.207 45.000 0.00 0.00 0.00 4.11
697 787 9.562583 GGATGATACGCTTTAAAAATGTACAAA 57.437 29.630 0.00 0.00 0.00 2.83
698 788 7.906010 CGGATGATACGCTTTAAAAATGTACAA 59.094 33.333 0.00 0.00 0.00 2.41
699 789 7.278203 TCGGATGATACGCTTTAAAAATGTACA 59.722 33.333 0.00 0.00 0.00 2.90
700 790 7.581600 GTCGGATGATACGCTTTAAAAATGTAC 59.418 37.037 0.00 0.00 0.00 2.90
701 791 7.254522 GGTCGGATGATACGCTTTAAAAATGTA 60.255 37.037 0.00 0.00 0.00 2.29
702 792 6.457799 GGTCGGATGATACGCTTTAAAAATGT 60.458 38.462 0.00 0.00 0.00 2.71
703 793 5.907391 GGTCGGATGATACGCTTTAAAAATG 59.093 40.000 0.00 0.00 0.00 2.32
704 794 5.008316 GGGTCGGATGATACGCTTTAAAAAT 59.992 40.000 0.00 0.00 0.00 1.82
728 830 5.978934 AGTTGGTATAAATTCGTAAGCCG 57.021 39.130 0.00 0.00 38.13 5.52
764 866 5.390387 ACCAGCATTCTACCCAAAACTTTA 58.610 37.500 0.00 0.00 0.00 1.85
766 868 3.844640 ACCAGCATTCTACCCAAAACTT 58.155 40.909 0.00 0.00 0.00 2.66
768 870 4.947388 TCATACCAGCATTCTACCCAAAAC 59.053 41.667 0.00 0.00 0.00 2.43
777 879 8.439971 TGTATATTTTCCTCATACCAGCATTCT 58.560 33.333 0.00 0.00 0.00 2.40
783 885 9.613428 TCAAACTGTATATTTTCCTCATACCAG 57.387 33.333 0.00 0.00 0.00 4.00
819 921 1.342174 ACGACAACAACGTATGGGAGT 59.658 47.619 0.00 0.00 42.17 3.85
842 944 2.093447 ACCGAAAGTCCAGATCATGTCC 60.093 50.000 0.00 0.00 0.00 4.02
919 1025 5.010112 GTGTAGATGCTAGATGGAGTTGCTA 59.990 44.000 0.00 0.00 0.00 3.49
970 1108 1.599576 GAGGCTTGGTCTCCAGTCC 59.400 63.158 0.00 0.00 33.81 3.85
986 1124 2.060383 TCCATGGCGACTGGAGGAG 61.060 63.158 6.96 0.00 37.87 3.69
1087 1265 1.671742 CTCCGGTGTGCTTACCACT 59.328 57.895 0.00 0.00 44.92 4.00
1231 1840 2.048222 CACTTCGCCGAGCCTCAA 60.048 61.111 0.00 0.00 0.00 3.02
1253 1862 2.642254 GGGGTGGACACGATGACGA 61.642 63.158 0.00 0.00 42.66 4.20
1339 1948 1.434622 CCGCTGCTGATGATGTCCAC 61.435 60.000 0.00 0.00 0.00 4.02
1348 1957 4.365111 TTTGCCCCCGCTGCTGAT 62.365 61.111 0.00 0.00 35.36 2.90
1377 1986 2.687200 TGGTCACCATAGGGCGCT 60.687 61.111 7.64 8.86 37.90 5.92
1482 3912 0.108615 CCGACTCCATGAGGTGTGTC 60.109 60.000 0.00 0.00 41.49 3.67
1593 4032 1.303091 GCCGACACTTACCGCCAAAT 61.303 55.000 0.00 0.00 0.00 2.32
1602 4041 1.591703 CTCCTGCTGCCGACACTTA 59.408 57.895 0.00 0.00 0.00 2.24
1751 4190 2.766263 TCTGCCAGGATTCGTTGTATCT 59.234 45.455 0.00 0.00 0.00 1.98
1804 4243 1.450134 CAGCAGCCGAGGCATTACA 60.450 57.895 17.18 0.00 44.88 2.41
1839 4296 0.679505 CCAACAGGTCTTCGTCCTCA 59.320 55.000 0.00 0.00 32.37 3.86
1893 6143 5.632347 GGTCTCGAACGTCAAAGAGAAATTA 59.368 40.000 11.85 0.00 40.84 1.40
1895 6145 3.988517 GGTCTCGAACGTCAAAGAGAAAT 59.011 43.478 11.85 0.00 40.84 2.17
1900 6150 3.467043 CGGTCTCGAACGTCAAAGA 57.533 52.632 0.00 0.00 36.64 2.52
1910 6160 3.633609 ATGGTCCCGACGGTCTCGA 62.634 63.158 13.94 0.00 46.14 4.04
1918 6168 2.403252 ACAAAGATGATGGTCCCGAC 57.597 50.000 0.00 0.00 0.00 4.79
1927 6177 5.431765 AGCGGAATCACTTACAAAGATGAT 58.568 37.500 0.00 0.00 33.62 2.45
2056 6313 7.702348 CAGTTCAACTAAAAGTCTGGGAAAAAG 59.298 37.037 0.00 0.00 0.00 2.27
2065 6322 9.391006 TGTATCAAACAGTTCAACTAAAAGTCT 57.609 29.630 0.00 0.00 33.01 3.24
2075 6332 7.432059 TGAATTGCATGTATCAAACAGTTCAA 58.568 30.769 0.00 0.00 42.70 2.69
2179 6455 1.381599 TTCTGCCATGGCCCATTCC 60.382 57.895 33.44 5.22 41.09 3.01
2230 6506 2.548920 CCTCTGCTGGAGTTCGAGTTTT 60.549 50.000 0.00 0.00 40.30 2.43
2293 6572 3.321111 TCCGAAGATAGTGTAAGCCATCC 59.679 47.826 0.00 0.00 0.00 3.51
2295 6574 4.262635 CCATCCGAAGATAGTGTAAGCCAT 60.263 45.833 0.00 0.00 0.00 4.40
2296 6575 3.069586 CCATCCGAAGATAGTGTAAGCCA 59.930 47.826 0.00 0.00 0.00 4.75
2300 6579 5.596772 TGATGACCATCCGAAGATAGTGTAA 59.403 40.000 7.46 0.00 37.02 2.41
2302 6581 3.960755 TGATGACCATCCGAAGATAGTGT 59.039 43.478 7.46 0.00 37.02 3.55
2494 6773 3.768757 CACTCATCTCCTCAAACCTCTCT 59.231 47.826 0.00 0.00 0.00 3.10
2639 6921 1.404986 CGGAATCGCCCAGTCAAAGTA 60.405 52.381 0.00 0.00 0.00 2.24
2704 6986 2.159338 GGACCTAGTTTGCACGACGATA 60.159 50.000 0.00 0.00 0.00 2.92
2779 7068 3.678806 CGGATGAGGTAGTAAAGCTTGCA 60.679 47.826 0.00 0.00 35.60 4.08
2780 7069 2.866762 CGGATGAGGTAGTAAAGCTTGC 59.133 50.000 0.00 0.00 35.60 4.01
2791 7080 8.716674 ACTTATATTTAGGAACGGATGAGGTA 57.283 34.615 0.00 0.00 0.00 3.08
2792 7081 7.509659 AGACTTATATTTAGGAACGGATGAGGT 59.490 37.037 0.00 0.00 0.00 3.85
2793 7082 7.897864 AGACTTATATTTAGGAACGGATGAGG 58.102 38.462 0.00 0.00 0.00 3.86
2794 7083 9.765795 AAAGACTTATATTTAGGAACGGATGAG 57.234 33.333 0.00 0.00 0.00 2.90
2795 7084 9.760077 GAAAGACTTATATTTAGGAACGGATGA 57.240 33.333 0.00 0.00 0.00 2.92
2796 7085 9.765795 AGAAAGACTTATATTTAGGAACGGATG 57.234 33.333 0.00 0.00 0.00 3.51
2824 7113 9.085645 TCCGTATGTAATCTATAGTGGAATGTT 57.914 33.333 0.00 0.00 0.00 2.71
2826 7115 7.702772 GCTCCGTATGTAATCTATAGTGGAATG 59.297 40.741 0.00 0.00 0.00 2.67
2836 7125 7.438160 CACTCATTTTGCTCCGTATGTAATCTA 59.562 37.037 0.00 0.00 0.00 1.98
2837 7126 6.258727 CACTCATTTTGCTCCGTATGTAATCT 59.741 38.462 0.00 0.00 0.00 2.40
2926 7959 7.498443 ACTTCCTCCGTTCCTAAATATAAGTG 58.502 38.462 0.00 0.00 0.00 3.16
2943 7976 1.807142 GCTTGCACAACTACTTCCTCC 59.193 52.381 0.00 0.00 0.00 4.30
2948 7981 3.443681 ACAACTTGCTTGCACAACTACTT 59.556 39.130 0.00 0.00 32.41 2.24
3020 8472 7.786178 TCCGGAGATTTATGTTGACTTAATG 57.214 36.000 0.00 0.00 0.00 1.90
3038 8490 4.644103 AAAGAAATCATGCAATCCGGAG 57.356 40.909 11.34 0.00 0.00 4.63
3052 8603 5.374071 AGGTTCGTCCACAGTAAAAGAAAT 58.626 37.500 2.77 0.00 39.02 2.17
3057 8608 5.021033 TGTTAGGTTCGTCCACAGTAAAA 57.979 39.130 2.77 0.00 39.02 1.52
3063 8614 3.547054 AGTTTGTTAGGTTCGTCCACA 57.453 42.857 2.77 0.00 39.02 4.17
3198 8750 5.880887 ACCAGAACTTTATTAAGCAGTAGGC 59.119 40.000 0.00 0.00 45.30 3.93
3407 9652 4.112634 AGGGTCAGAGCAATTACCAAAA 57.887 40.909 1.20 0.00 33.46 2.44
3440 9767 7.202001 GCATAAAACCCCCTTAATATTTGCTCT 60.202 37.037 0.00 0.00 0.00 4.09
3460 9787 7.602265 TGCGATATAGATAAGTTGCTGCATAAA 59.398 33.333 1.84 0.00 0.00 1.40
3466 9793 6.199908 GGCTATGCGATATAGATAAGTTGCTG 59.800 42.308 10.29 0.00 0.00 4.41
3639 10293 5.234329 CACAATACCAAGTCAATACCGCTAG 59.766 44.000 0.00 0.00 0.00 3.42
3642 10296 3.064820 CCACAATACCAAGTCAATACCGC 59.935 47.826 0.00 0.00 0.00 5.68
3643 10297 4.509616 TCCACAATACCAAGTCAATACCG 58.490 43.478 0.00 0.00 0.00 4.02
3695 10349 6.655003 TCGGATCAAACTTTCTAAGCTTTGAT 59.345 34.615 11.41 18.69 43.55 2.57
3702 10356 7.421530 TTTGTCTCGGATCAAACTTTCTAAG 57.578 36.000 0.00 0.00 0.00 2.18
3706 10360 6.061231 AGTTTTGTCTCGGATCAAACTTTC 57.939 37.500 0.00 2.31 34.05 2.62
3716 10370 5.001237 TCGCATATTAGTTTTGTCTCGGA 57.999 39.130 0.00 0.00 0.00 4.55
3746 10400 7.272144 AGTCTTATGTACTCCCTCCATTTTT 57.728 36.000 0.00 0.00 0.00 1.94
3750 10404 5.529289 TCAAGTCTTATGTACTCCCTCCAT 58.471 41.667 0.00 0.00 0.00 3.41
3751 10405 4.942944 TCAAGTCTTATGTACTCCCTCCA 58.057 43.478 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.