Multiple sequence alignment - TraesCS6D01G216000

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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 TraesCS6D01G216000 chr6D 100.000 5444 0 0 1 5444 306056603 306051160 0.000000e+00 10054
1 TraesCS6D01G216000 chr6D 100.000 475 0 0 5596 6070 306051008 306050534 0.000000e+00 878
2 TraesCS6D01G216000 chr6D 97.163 141 3 1 1665 1804 452949799 452949659 2.830000e-58 237
3 TraesCS6D01G216000 chr6A 94.428 1992 67 20 3487 5444 440536911 440534930 0.000000e+00 3024
4 TraesCS6D01G216000 chr6A 97.788 1085 24 0 2194 3278 440539480 440538396 0.000000e+00 1871
5 TraesCS6D01G216000 chr6A 90.223 1483 50 14 1 1415 440541678 440540223 0.000000e+00 1847
6 TraesCS6D01G216000 chr6A 92.857 476 23 5 5606 6070 440534923 440534448 0.000000e+00 680
7 TraesCS6D01G216000 chr6A 95.455 330 13 2 1821 2148 440539813 440539484 5.390000e-145 525
8 TraesCS6D01G216000 chr6A 94.355 248 7 2 3270 3511 440537460 440537214 2.070000e-99 374
9 TraesCS6D01G216000 chr6A 90.217 276 14 8 1401 1671 440540079 440539812 1.250000e-91 348
10 TraesCS6D01G216000 chr6B 93.591 1654 79 11 1821 3462 470791951 470793589 0.000000e+00 2442
11 TraesCS6D01G216000 chr6B 93.814 1067 43 12 4394 5444 470794642 470795701 0.000000e+00 1583
12 TraesCS6D01G216000 chr6B 91.889 900 31 14 553 1415 470785519 470786413 0.000000e+00 1219
13 TraesCS6D01G216000 chr6B 88.958 969 62 14 3454 4394 470793611 470794562 0.000000e+00 1155
14 TraesCS6D01G216000 chr6B 91.288 264 13 6 1411 1671 470791696 470791952 9.680000e-93 351
15 TraesCS6D01G216000 chr6B 86.879 282 21 9 5605 5885 470795717 470795983 9.890000e-78 302
16 TraesCS6D01G216000 chr6B 90.850 153 12 2 5918 6070 470797544 470797694 2.870000e-48 204
17 TraesCS6D01G216000 chr4D 92.220 437 34 0 1 437 448148159 448147723 2.400000e-173 619
18 TraesCS6D01G216000 chr4D 97.857 140 2 1 1666 1804 94769701 94769562 2.190000e-59 241
19 TraesCS6D01G216000 chr4D 97.857 140 2 1 1666 1804 94771882 94771743 2.190000e-59 241
20 TraesCS6D01G216000 chrUn 89.977 439 40 3 1 436 306601274 306600837 1.140000e-156 564
21 TraesCS6D01G216000 chrUn 89.977 439 40 3 1 436 339990139 339989702 1.140000e-156 564
22 TraesCS6D01G216000 chrUn 89.977 439 40 3 1 436 356659125 356658688 1.140000e-156 564
23 TraesCS6D01G216000 chrUn 82.353 153 21 6 5729 5879 19194626 19194774 1.780000e-25 128
24 TraesCS6D01G216000 chr1A 89.977 439 40 3 1 436 516083932 516084369 1.140000e-156 564
25 TraesCS6D01G216000 chr1A 88.889 180 15 4 3288 3466 218527004 218526829 3.680000e-52 217
26 TraesCS6D01G216000 chr5D 89.116 441 43 3 1 437 549796267 549796706 1.490000e-150 544
27 TraesCS6D01G216000 chr5D 95.918 147 5 1 1659 1804 74461456 74461310 2.830000e-58 237
28 TraesCS6D01G216000 chr2A 81.481 621 108 7 2417 3033 185275182 185275799 2.530000e-138 503
29 TraesCS6D01G216000 chr2A 79.406 471 79 8 3796 4258 185276922 185277382 3.530000e-82 316
30 TraesCS6D01G216000 chr2D 81.220 623 102 12 2416 3033 165478340 165477728 7.070000e-134 488
31 TraesCS6D01G216000 chr2D 96.528 144 3 2 1662 1804 647970264 647970122 2.830000e-58 237
32 TraesCS6D01G216000 chr2D 82.317 164 24 5 5716 5878 627930493 627930652 2.950000e-28 137
33 TraesCS6D01G216000 chr2B 80.578 623 111 10 2417 3033 232270371 232270989 7.120000e-129 472
34 TraesCS6D01G216000 chr2B 79.406 471 88 4 3796 4258 232272166 232272635 2.110000e-84 324
35 TraesCS6D01G216000 chr7D 97.842 139 2 1 1667 1804 459391921 459392059 7.860000e-59 239
36 TraesCS6D01G216000 chr7D 90.000 170 17 0 3288 3457 494749947 494749778 2.850000e-53 220
37 TraesCS6D01G216000 chr7D 80.702 171 25 7 5741 5906 366547178 366547011 6.390000e-25 126
38 TraesCS6D01G216000 chr7A 97.842 139 1 2 1667 1804 431989279 431989142 7.860000e-59 239
39 TraesCS6D01G216000 chr7A 86.432 199 21 5 3287 3483 426576226 426576420 4.770000e-51 213
40 TraesCS6D01G216000 chr7A 78.261 184 33 5 5721 5903 634399694 634399517 1.790000e-20 111
41 TraesCS6D01G216000 chr7A 78.846 156 27 6 5753 5907 721109722 721109572 3.870000e-17 100
42 TraesCS6D01G216000 chr5A 97.842 139 2 1 1667 1804 382566635 382566773 7.860000e-59 239
43 TraesCS6D01G216000 chr5A 79.787 188 35 3 5716 5902 435697877 435698062 3.820000e-27 134
44 TraesCS6D01G216000 chr5A 79.275 193 28 9 5716 5906 285396878 285396696 2.300000e-24 124
45 TraesCS6D01G216000 chr3B 92.593 162 11 1 3288 3448 42630981 42630820 1.320000e-56 231
46 TraesCS6D01G216000 chr3A 90.751 173 15 1 3288 3459 83748184 83748012 4.730000e-56 230
47 TraesCS6D01G216000 chr3D 90.698 172 14 2 3291 3460 426452019 426451848 1.700000e-55 228
48 TraesCS6D01G216000 chr3D 89.437 142 15 0 1 142 337521985 337522126 4.830000e-41 180
49 TraesCS6D01G216000 chr1B 93.506 154 8 2 1652 1804 31742117 31742269 1.700000e-55 228
50 TraesCS6D01G216000 chr1B 86.735 98 4 6 1 97 13466148 13466059 3.870000e-17 100
51 TraesCS6D01G216000 chr1D 88.889 180 15 4 3288 3466 175819999 175819824 3.680000e-52 217


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 TraesCS6D01G216000 chr6D 306050534 306056603 6069 True 5466.000000 10054 100.000000 1 6070 2 chr6D.!!$R2 6069
1 TraesCS6D01G216000 chr6A 440534448 440541678 7230 True 1238.428571 3024 93.617571 1 6070 7 chr6A.!!$R1 6069
2 TraesCS6D01G216000 chr6B 470785519 470786413 894 False 1219.000000 1219 91.889000 553 1415 1 chr6B.!!$F1 862
3 TraesCS6D01G216000 chr6B 470791696 470797694 5998 False 1006.166667 2442 90.896667 1411 6070 6 chr6B.!!$F2 4659
4 TraesCS6D01G216000 chr4D 94769562 94771882 2320 True 241.000000 241 97.857000 1666 1804 2 chr4D.!!$R2 138
5 TraesCS6D01G216000 chr2A 185275182 185277382 2200 False 409.500000 503 80.443500 2417 4258 2 chr2A.!!$F1 1841
6 TraesCS6D01G216000 chr2D 165477728 165478340 612 True 488.000000 488 81.220000 2416 3033 1 chr2D.!!$R1 617
7 TraesCS6D01G216000 chr2B 232270371 232272635 2264 False 398.000000 472 79.992000 2417 4258 2 chr2B.!!$F1 1841

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
183 184 0.099436 GCAAGCAATCACGCCCTTAG 59.901 55.000 0.00 0.0 0.00 2.18 F
195 196 0.179936 GCCCTTAGATGCAGAGCAGT 59.820 55.000 0.00 0.0 43.65 4.40 F
1419 1488 0.466124 CGTCCCCTCTCCTTTGGATC 59.534 60.000 0.00 0.0 0.00 3.36 F
1490 1722 1.213094 CCGTTCGGTGATATCGTGCC 61.213 60.000 2.82 0.0 0.00 5.01 F
2698 2954 1.137825 GGTCGCAGAAGAGGACTCG 59.862 63.158 0.00 0.0 39.69 4.18 F
3349 5620 1.056660 AGTGGTCTTGGGTTCGATGT 58.943 50.000 0.00 0.0 0.00 3.06 F
4267 7106 0.672091 TTGCAGTTTCCTCGCGCATA 60.672 50.000 8.75 0.0 31.67 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1787 0.318614 CCCAAAATCCGCACACACAC 60.319 55.000 0.00 0.00 0.00 3.82 R
1809 2045 1.176527 TGCAAATTACTCCCAGCTGC 58.823 50.000 8.66 0.00 0.00 5.25 R
2638 2882 1.340017 TGGTGTAGCTCTTCCAATGGC 60.340 52.381 0.00 0.00 0.00 4.40 R
3349 5620 1.676635 GTGCAATGCAGAGAGGCCA 60.677 57.895 8.73 0.00 40.08 5.36 R
4025 6848 0.618680 TCAGCAGACATGGGCCTAGT 60.619 55.000 4.53 2.52 0.00 2.57 R
4824 7754 0.741221 CCTGGCCTAGCAAACGAGAC 60.741 60.000 3.32 0.00 0.00 3.36 R
5595 8536 0.042188 CGACGACTGCAACCTTTGTG 60.042 55.000 0.00 0.00 0.00 3.33 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
100 101 1.134250 GGAGCAGTTCAGGGAAGATCC 60.134 57.143 0.00 0.00 35.23 3.36
101 102 0.539051 AGCAGTTCAGGGAAGATCCG 59.461 55.000 0.00 0.00 37.43 4.18
102 103 0.537188 GCAGTTCAGGGAAGATCCGA 59.463 55.000 0.00 0.00 37.43 4.55
136 137 6.756299 TTACATCAAGCATGCAGACATAAA 57.244 33.333 21.98 3.68 35.65 1.40
137 138 5.847111 ACATCAAGCATGCAGACATAAAT 57.153 34.783 21.98 0.00 35.65 1.40
138 139 5.828747 ACATCAAGCATGCAGACATAAATC 58.171 37.500 21.98 0.00 35.65 2.17
139 140 4.541085 TCAAGCATGCAGACATAAATCG 57.459 40.909 21.98 0.00 33.67 3.34
140 141 4.190772 TCAAGCATGCAGACATAAATCGA 58.809 39.130 21.98 0.00 33.67 3.59
141 142 4.034394 TCAAGCATGCAGACATAAATCGAC 59.966 41.667 21.98 0.00 33.67 4.20
180 181 3.434319 CGCAAGCAATCACGCCCT 61.434 61.111 0.00 0.00 0.00 5.19
181 182 2.964978 GCAAGCAATCACGCCCTT 59.035 55.556 0.00 0.00 0.00 3.95
182 183 1.643868 CGCAAGCAATCACGCCCTTA 61.644 55.000 0.00 0.00 0.00 2.69
183 184 0.099436 GCAAGCAATCACGCCCTTAG 59.901 55.000 0.00 0.00 0.00 2.18
184 185 1.737838 CAAGCAATCACGCCCTTAGA 58.262 50.000 0.00 0.00 0.00 2.10
185 186 2.292267 CAAGCAATCACGCCCTTAGAT 58.708 47.619 0.00 0.00 0.00 1.98
186 187 1.959042 AGCAATCACGCCCTTAGATG 58.041 50.000 0.00 0.00 0.00 2.90
187 188 0.308993 GCAATCACGCCCTTAGATGC 59.691 55.000 0.00 0.00 0.00 3.91
188 189 1.667236 CAATCACGCCCTTAGATGCA 58.333 50.000 0.00 0.00 0.00 3.96
189 190 1.600957 CAATCACGCCCTTAGATGCAG 59.399 52.381 0.00 0.00 0.00 4.41
190 191 1.123077 ATCACGCCCTTAGATGCAGA 58.877 50.000 0.00 0.00 0.00 4.26
191 192 0.461548 TCACGCCCTTAGATGCAGAG 59.538 55.000 0.00 0.00 0.00 3.35
192 193 1.144936 ACGCCCTTAGATGCAGAGC 59.855 57.895 0.00 0.00 0.00 4.09
193 194 1.144716 CGCCCTTAGATGCAGAGCA 59.855 57.895 0.00 0.00 44.86 4.26
194 195 0.879400 CGCCCTTAGATGCAGAGCAG 60.879 60.000 0.00 0.00 43.65 4.24
195 196 0.179936 GCCCTTAGATGCAGAGCAGT 59.820 55.000 0.00 0.00 43.65 4.40
198 199 2.559440 CCTTAGATGCAGAGCAGTTCC 58.441 52.381 0.00 0.00 43.65 3.62
221 222 1.512926 GAGGCTTTGCGAGACTTCAA 58.487 50.000 0.00 0.00 46.50 2.69
232 233 4.572571 ACTTCAACGGGGGCGCAA 62.573 61.111 10.83 0.00 0.00 4.85
293 294 1.666888 CGGGCTTGAGAATGTTGTTGC 60.667 52.381 0.00 0.00 0.00 4.17
497 498 8.644374 ATGCCCTAAACTAGTTTTTGTTATGA 57.356 30.769 25.07 4.73 34.23 2.15
542 543 4.517285 CTTAGGCAGCAAAAGAGATACCA 58.483 43.478 0.00 0.00 0.00 3.25
699 717 4.095610 GCGAATTCCAGAAATTACAACCG 58.904 43.478 0.00 0.00 37.70 4.44
864 882 8.152246 AGTAGTAGAGATATCAGTAGGACACAC 58.848 40.741 5.32 0.00 0.00 3.82
875 917 6.340522 TCAGTAGGACACACACAATCATATG 58.659 40.000 0.00 0.00 0.00 1.78
939 988 2.029844 GGAAGTGGTGCAGACTCGC 61.030 63.158 0.00 0.00 0.00 5.03
1173 1223 2.756283 CTCTCCCGCCTCTCCGTT 60.756 66.667 0.00 0.00 0.00 4.44
1201 1251 3.691342 CTCGCCAACCTCCGGACA 61.691 66.667 0.00 0.00 0.00 4.02
1204 1254 1.219664 CGCCAACCTCCGGACAATA 59.780 57.895 0.00 0.00 0.00 1.90
1212 1262 2.112998 CCTCCGGACAATACTAACCCA 58.887 52.381 0.00 0.00 0.00 4.51
1214 1264 3.528532 CTCCGGACAATACTAACCCAAC 58.471 50.000 0.00 0.00 0.00 3.77
1274 1343 2.905996 TTCTTGGACAGGGCGGCAT 61.906 57.895 12.47 0.00 0.00 4.40
1415 1484 0.977395 AACTCGTCCCCTCTCCTTTG 59.023 55.000 0.00 0.00 0.00 2.77
1416 1485 0.905337 ACTCGTCCCCTCTCCTTTGG 60.905 60.000 0.00 0.00 0.00 3.28
1417 1486 0.614979 CTCGTCCCCTCTCCTTTGGA 60.615 60.000 0.00 0.00 0.00 3.53
1419 1488 0.466124 CGTCCCCTCTCCTTTGGATC 59.534 60.000 0.00 0.00 0.00 3.36
1490 1722 1.213094 CCGTTCGGTGATATCGTGCC 61.213 60.000 2.82 0.00 0.00 5.01
1497 1729 2.743938 GGTGATATCGTGCCACTGTAG 58.256 52.381 0.00 0.00 0.00 2.74
1498 1730 2.100916 GGTGATATCGTGCCACTGTAGT 59.899 50.000 0.00 0.00 0.00 2.73
1501 1733 3.949113 TGATATCGTGCCACTGTAGTGTA 59.051 43.478 10.80 0.00 44.21 2.90
1503 1735 2.647529 TCGTGCCACTGTAGTGTATG 57.352 50.000 10.80 5.60 44.21 2.39
1504 1736 1.890489 TCGTGCCACTGTAGTGTATGT 59.110 47.619 10.80 0.00 44.21 2.29
1505 1737 3.083293 TCGTGCCACTGTAGTGTATGTA 58.917 45.455 10.80 0.00 44.21 2.29
1544 1779 5.073144 TGGTCCTTTGGTAAAGTCAGATTCT 59.927 40.000 0.00 0.00 36.77 2.40
1549 1784 4.365514 TGGTAAAGTCAGATTCTGGCAA 57.634 40.909 19.81 2.79 38.73 4.52
1552 1787 4.096984 GGTAAAGTCAGATTCTGGCAATGG 59.903 45.833 19.81 0.00 38.73 3.16
1791 2027 3.119602 TGCTCCGTATGTAGTCACTTGTC 60.120 47.826 0.00 0.00 0.00 3.18
1804 2040 6.189677 AGTCACTTGTCGAAATCTCTAGAG 57.810 41.667 13.98 13.98 0.00 2.43
1805 2041 4.796312 GTCACTTGTCGAAATCTCTAGAGC 59.204 45.833 15.35 0.00 0.00 4.09
1807 2043 4.797868 CACTTGTCGAAATCTCTAGAGCTG 59.202 45.833 15.35 2.93 0.00 4.24
1808 2044 4.702612 ACTTGTCGAAATCTCTAGAGCTGA 59.297 41.667 15.35 5.19 0.00 4.26
1809 2045 4.891627 TGTCGAAATCTCTAGAGCTGAG 57.108 45.455 15.35 5.46 0.00 3.35
1810 2046 3.066064 TGTCGAAATCTCTAGAGCTGAGC 59.934 47.826 15.35 0.00 0.00 4.26
1812 2048 3.314913 TCGAAATCTCTAGAGCTGAGCAG 59.685 47.826 15.35 0.00 0.00 4.24
2007 2243 5.527951 CAGGATGTAGTCTGCTCAGTATTC 58.472 45.833 0.00 0.00 0.00 1.75
2103 2339 4.763793 GGATAGGTCATAGTGCATTGCAAT 59.236 41.667 16.48 16.48 41.47 3.56
2161 2403 8.529476 GTCTAGAACAAGAATTAACCTACAGGA 58.471 37.037 1.29 0.00 38.94 3.86
2588 2832 9.471702 AATTCATAATTCACTTCCTCAGTTCAT 57.528 29.630 0.00 0.00 30.92 2.57
2638 2882 2.105306 TGATGCCACCTCTACCATGATG 59.895 50.000 0.00 0.00 0.00 3.07
2656 2912 2.113860 TGCCATTGGAAGAGCTACAC 57.886 50.000 6.95 0.00 0.00 2.90
2659 2915 2.636830 CCATTGGAAGAGCTACACCAG 58.363 52.381 0.00 0.00 33.85 4.00
2683 2939 1.996798 TCCCATCGATACCTCTGGTC 58.003 55.000 0.00 0.00 37.09 4.02
2698 2954 1.137825 GGTCGCAGAAGAGGACTCG 59.862 63.158 0.00 0.00 39.69 4.18
3255 4231 1.806542 ACATTCGTGTTGACCATGCTC 59.193 47.619 0.00 0.00 0.00 4.26
3349 5620 1.056660 AGTGGTCTTGGGTTCGATGT 58.943 50.000 0.00 0.00 0.00 3.06
3710 6478 6.878923 ACTCATCGTTCAGTATCAAAATCCAA 59.121 34.615 0.00 0.00 0.00 3.53
3716 6488 6.797033 CGTTCAGTATCAAAATCCAACAGTTC 59.203 38.462 0.00 0.00 0.00 3.01
3731 6503 5.356190 CCAACAGTTCTGCATGTCTGAATAT 59.644 40.000 15.58 3.74 35.54 1.28
4025 6848 2.018355 TGTAGGCTGTGGTACTTGGA 57.982 50.000 0.00 0.00 0.00 3.53
4067 6896 2.746904 CAATTGACAACAGCACCGGATA 59.253 45.455 9.46 0.00 0.00 2.59
4234 7063 9.671279 AACAAAATTCTTCTCCAAAATTCTTGT 57.329 25.926 0.00 0.00 0.00 3.16
4267 7106 0.672091 TTGCAGTTTCCTCGCGCATA 60.672 50.000 8.75 0.00 31.67 3.14
4318 7157 2.840038 TGGTCCTAGTGAATCAGCACAT 59.160 45.455 0.00 0.00 41.19 3.21
4352 7191 3.684103 TTGGCAACTATTTTATCGCCG 57.316 42.857 0.00 0.00 42.57 6.46
4411 7335 8.080417 TGTTTACTAGTACTAGTTTGTGAGCAG 58.920 37.037 34.30 9.75 43.35 4.24
4444 7368 4.281688 TGGAGCCATCCTTTTTCTTTCTTG 59.718 41.667 0.00 0.00 46.80 3.02
4450 7374 5.452356 CCATCCTTTTTCTTTCTTGTGCTGT 60.452 40.000 0.00 0.00 0.00 4.40
4475 7399 7.551617 GTCCTGCTACCTTATTGCTTTTAGTTA 59.448 37.037 0.00 0.00 0.00 2.24
4671 7601 6.742559 AAAACTACTCAAGGTGACCTCTTA 57.257 37.500 3.76 0.00 30.89 2.10
4684 7614 5.768164 GGTGACCTCTTACTTGAATTTTCCA 59.232 40.000 0.00 0.00 0.00 3.53
4693 7623 8.296713 TCTTACTTGAATTTTCCATTGTACTGC 58.703 33.333 0.00 0.00 0.00 4.40
4694 7624 6.403866 ACTTGAATTTTCCATTGTACTGCA 57.596 33.333 0.00 0.00 0.00 4.41
4702 7632 2.749076 TCCATTGTACTGCATGACAAGC 59.251 45.455 16.08 0.00 38.86 4.01
4704 7634 3.427098 CCATTGTACTGCATGACAAGCTG 60.427 47.826 16.08 7.85 38.86 4.24
4705 7635 2.837532 TGTACTGCATGACAAGCTGA 57.162 45.000 15.24 0.00 35.29 4.26
4728 7658 0.730494 GCTTGCTGGCTTAGTTTGCG 60.730 55.000 0.00 0.00 0.00 4.85
4731 7661 1.135523 GCTGGCTTAGTTTGCGCTC 59.864 57.895 9.73 0.00 0.00 5.03
4822 7752 4.865865 GCTGGAGGTCAGGTATGC 57.134 61.111 0.00 0.00 43.54 3.14
4823 7753 1.147153 GCTGGAGGTCAGGTATGCC 59.853 63.158 0.00 0.00 43.54 4.40
4824 7754 1.443407 CTGGAGGTCAGGTATGCCG 59.557 63.158 0.00 0.00 39.76 5.69
4827 7757 1.043673 GGAGGTCAGGTATGCCGTCT 61.044 60.000 0.00 0.00 40.50 4.18
4856 7786 4.689983 GCTAGGCCAGGGATACAAGAAATT 60.690 45.833 5.01 0.00 39.74 1.82
4865 7795 6.536224 CAGGGATACAAGAAATTTCCATTTGC 59.464 38.462 14.61 2.28 32.68 3.68
4875 7805 9.813446 AAGAAATTTCCATTTGCTCTATTGATC 57.187 29.630 14.61 0.00 32.35 2.92
5070 8002 8.579850 AATGGTCTCAGCAAATTACAAATAGA 57.420 30.769 0.00 0.00 0.00 1.98
5117 8049 7.789027 TGAAACACGGTTTCTTTTTCTTTTTC 58.211 30.769 21.90 0.00 0.00 2.29
5162 8097 3.995705 GTGATCTGGCTGAGCATTAGATC 59.004 47.826 25.42 25.42 43.41 2.75
5310 8250 2.176889 AGCAATGCCATTCAGAAGCTT 58.823 42.857 0.00 0.00 29.46 3.74
5362 8302 1.676006 CCGTCTTGGTATCCAATTGGC 59.324 52.381 20.33 6.24 43.07 4.52
5364 8304 3.433031 CCGTCTTGGTATCCAATTGGCTA 60.433 47.826 20.33 11.99 43.07 3.93
5406 8346 3.055819 GCCTCCAATCTGACAGTAGACAA 60.056 47.826 1.59 0.00 0.00 3.18
5422 8362 6.256539 CAGTAGACAATAGTGCACCATACAAG 59.743 42.308 14.63 0.00 0.00 3.16
5637 8578 1.072331 CCAGCGCAGGGTAAGGATAAT 59.928 52.381 11.68 0.00 0.00 1.28
5700 8647 5.357032 GCCAAAAGGTTAGCACATGTACTAT 59.643 40.000 6.63 0.00 0.00 2.12
5706 8653 7.841282 AGGTTAGCACATGTACTATGATACT 57.159 36.000 6.63 0.00 0.00 2.12
5725 8672 7.583625 TGATACTATCTTAGTTGAGGTGGAGA 58.416 38.462 0.00 0.00 40.14 3.71
5750 8697 7.579761 AAAGAGAAATCAGCAGAAAAGACTT 57.420 32.000 0.00 0.00 0.00 3.01
5903 8962 7.667557 AGACTATATGGCACGCTTAAGATAAA 58.332 34.615 6.67 0.00 0.00 1.40
5950 10425 6.893759 TGTTGTAATCCATGTTGACTTTACG 58.106 36.000 0.00 0.00 0.00 3.18
5965 10440 0.249447 TTACGAGGCATCATCGGCTG 60.249 55.000 0.00 0.00 44.36 4.85
5985 10460 2.102757 TGCTGGTGCATGAATTTGTTGT 59.897 40.909 0.00 0.00 45.31 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.285743 GGAACTGGGGAGGAGCCT 60.286 66.667 0.00 0.00 36.66 4.58
12 13 1.213296 TAATGGAACTGGGGAGGAGC 58.787 55.000 0.00 0.00 0.00 4.70
13 14 4.846367 TCATATAATGGAACTGGGGAGGAG 59.154 45.833 0.00 0.00 0.00 3.69
14 15 4.838403 TCATATAATGGAACTGGGGAGGA 58.162 43.478 0.00 0.00 0.00 3.71
16 17 6.782986 TCATTCATATAATGGAACTGGGGAG 58.217 40.000 0.00 0.00 0.00 4.30
21 22 8.685427 TGTGGTTTCATTCATATAATGGAACTG 58.315 33.333 17.18 4.33 42.80 3.16
22 23 8.821686 TGTGGTTTCATTCATATAATGGAACT 57.178 30.769 17.18 0.00 42.80 3.01
100 101 5.582269 TGCTTGATGTAATTTCCTTCTCTCG 59.418 40.000 0.00 0.00 0.00 4.04
101 102 6.992063 TGCTTGATGTAATTTCCTTCTCTC 57.008 37.500 0.00 0.00 0.00 3.20
102 103 6.183360 GCATGCTTGATGTAATTTCCTTCTCT 60.183 38.462 11.37 0.00 34.14 3.10
136 137 1.806542 GCATGTTGTGTTCCTGTCGAT 59.193 47.619 0.00 0.00 0.00 3.59
137 138 1.225855 GCATGTTGTGTTCCTGTCGA 58.774 50.000 0.00 0.00 0.00 4.20
138 139 0.943673 TGCATGTTGTGTTCCTGTCG 59.056 50.000 0.00 0.00 0.00 4.35
139 140 1.675483 TGTGCATGTTGTGTTCCTGTC 59.325 47.619 0.00 0.00 0.00 3.51
140 141 1.761449 TGTGCATGTTGTGTTCCTGT 58.239 45.000 0.00 0.00 0.00 4.00
141 142 3.671433 GCTATGTGCATGTTGTGTTCCTG 60.671 47.826 0.00 0.00 42.31 3.86
173 174 1.156645 GCTCTGCATCTAAGGGCGTG 61.157 60.000 0.00 0.00 29.94 5.34
174 175 1.144936 GCTCTGCATCTAAGGGCGT 59.855 57.895 0.00 0.00 29.94 5.68
175 176 0.879400 CTGCTCTGCATCTAAGGGCG 60.879 60.000 0.00 0.00 44.56 6.13
176 177 0.179936 ACTGCTCTGCATCTAAGGGC 59.820 55.000 0.00 0.00 41.81 5.19
177 178 2.559440 GAACTGCTCTGCATCTAAGGG 58.441 52.381 0.00 0.00 38.13 3.95
178 179 2.170187 AGGAACTGCTCTGCATCTAAGG 59.830 50.000 0.00 0.00 38.13 2.69
179 180 3.540314 AGGAACTGCTCTGCATCTAAG 57.460 47.619 0.00 0.00 38.13 2.18
193 194 1.075659 GCAAAGCCTCCCAGGAACT 59.924 57.895 0.00 0.00 37.67 3.01
194 195 2.335712 CGCAAAGCCTCCCAGGAAC 61.336 63.158 0.00 0.00 37.67 3.62
195 196 2.034066 CGCAAAGCCTCCCAGGAA 59.966 61.111 0.00 0.00 37.67 3.36
198 199 1.743252 GTCTCGCAAAGCCTCCCAG 60.743 63.158 0.00 0.00 0.00 4.45
232 233 2.031163 GTCGCCTCAAGCTGTGGT 59.969 61.111 0.00 0.00 40.39 4.16
293 294 1.135141 CCAAGAAGCGAGAGACTGGAG 60.135 57.143 0.00 0.00 0.00 3.86
333 334 0.454452 TGAAGATCACAGACGACGCG 60.454 55.000 3.53 3.53 0.00 6.01
336 337 2.645730 AGCTGAAGATCACAGACGAC 57.354 50.000 19.33 5.91 37.54 4.34
371 372 4.332543 ACCCCGAAGCCCCTCTGA 62.333 66.667 0.00 0.00 0.00 3.27
427 428 1.068264 GCAAGCTACCAGCAAACTTCC 60.068 52.381 0.38 0.00 45.56 3.46
485 486 1.403647 GGGCGGCCTCATAACAAAAAC 60.404 52.381 22.87 0.00 0.00 2.43
497 498 1.635817 ATGTACAATGAGGGCGGCCT 61.636 55.000 33.40 33.40 0.00 5.19
699 717 1.336755 AGCAAACACAACCGATCCAAC 59.663 47.619 0.00 0.00 0.00 3.77
864 882 5.012046 TCCAGCTAGGTACCATATGATTGTG 59.988 44.000 15.94 0.00 39.02 3.33
875 917 0.465824 TCTCGCTCCAGCTAGGTACC 60.466 60.000 2.73 2.73 39.32 3.34
939 988 0.896940 AGATGTTGGGCCTGCTTGTG 60.897 55.000 4.53 0.00 0.00 3.33
1157 1207 1.453379 CTAACGGAGAGGCGGGAGA 60.453 63.158 0.00 0.00 0.00 3.71
1201 1251 4.286032 TGCTGTCAGAGTTGGGTTAGTATT 59.714 41.667 3.32 0.00 0.00 1.89
1204 1254 2.047061 TGCTGTCAGAGTTGGGTTAGT 58.953 47.619 3.32 0.00 0.00 2.24
1212 1262 1.963338 GCGGCTTGCTGTCAGAGTT 60.963 57.895 3.32 0.00 41.73 3.01
1214 1264 3.123620 GGCGGCTTGCTGTCAGAG 61.124 66.667 3.32 0.00 45.43 3.35
1274 1343 4.794439 CACCTCATGCGCGACCGA 62.794 66.667 12.10 0.00 36.29 4.69
1415 1484 3.433615 CAGTTTCTCAAACGGACAGATCC 59.566 47.826 0.00 0.00 45.88 3.36
1416 1485 3.433615 CCAGTTTCTCAAACGGACAGATC 59.566 47.826 1.41 0.00 45.88 2.75
1417 1486 3.071023 TCCAGTTTCTCAAACGGACAGAT 59.929 43.478 1.41 0.00 45.88 2.90
1419 1488 2.802816 CTCCAGTTTCTCAAACGGACAG 59.197 50.000 1.41 0.00 45.88 3.51
1505 1737 9.936329 ACCAAAGGACCATATCAGTTTATTATT 57.064 29.630 0.00 0.00 0.00 1.40
1544 1779 2.843352 CGCACACACACCATTGCCA 61.843 57.895 0.00 0.00 0.00 4.92
1549 1784 1.000385 CAAAATCCGCACACACACCAT 60.000 47.619 0.00 0.00 0.00 3.55
1552 1787 0.318614 CCCAAAATCCGCACACACAC 60.319 55.000 0.00 0.00 0.00 3.82
1791 2027 3.631144 CTGCTCAGCTCTAGAGATTTCG 58.369 50.000 24.24 5.70 35.09 3.46
1805 2041 2.681848 CAAATTACTCCCAGCTGCTCAG 59.318 50.000 8.66 5.72 0.00 3.35
1807 2043 1.403323 GCAAATTACTCCCAGCTGCTC 59.597 52.381 8.66 0.00 0.00 4.26
1808 2044 1.272092 TGCAAATTACTCCCAGCTGCT 60.272 47.619 8.66 0.00 0.00 4.24
1809 2045 1.176527 TGCAAATTACTCCCAGCTGC 58.823 50.000 8.66 0.00 0.00 5.25
1810 2046 4.460948 AAATGCAAATTACTCCCAGCTG 57.539 40.909 6.78 6.78 0.00 4.24
1812 2048 6.818142 ACATAAAAATGCAAATTACTCCCAGC 59.182 34.615 0.00 0.00 0.00 4.85
1813 2049 7.278424 CCACATAAAAATGCAAATTACTCCCAG 59.722 37.037 0.00 0.00 0.00 4.45
1815 2051 7.327214 TCCACATAAAAATGCAAATTACTCCC 58.673 34.615 0.00 0.00 0.00 4.30
1816 2052 7.010460 GCTCCACATAAAAATGCAAATTACTCC 59.990 37.037 0.00 0.00 0.00 3.85
1817 2053 7.545265 TGCTCCACATAAAAATGCAAATTACTC 59.455 33.333 0.00 0.00 0.00 2.59
1818 2054 7.331687 GTGCTCCACATAAAAATGCAAATTACT 59.668 33.333 0.00 0.00 34.08 2.24
1819 2055 7.412891 GGTGCTCCACATAAAAATGCAAATTAC 60.413 37.037 0.00 0.00 35.86 1.89
2030 2266 1.792949 GTGGTGCTCTAGACACGTTTG 59.207 52.381 14.97 0.00 38.98 2.93
2103 2339 6.210584 TCAGTTTCCTGTCACAGACATACATA 59.789 38.462 6.30 0.00 41.94 2.29
2106 2342 4.883083 TCAGTTTCCTGTCACAGACATAC 58.117 43.478 6.30 0.00 41.94 2.39
2261 2503 4.235360 CTCTGGTGTTAGTAAACCTGACG 58.765 47.826 14.23 9.96 38.89 4.35
2311 2553 5.828299 ACTCAAAAAGTTCAACATTCGGA 57.172 34.783 0.00 0.00 33.03 4.55
2410 2652 3.057315 GCAAAATAAGCTCAGGTTGCTCA 60.057 43.478 14.49 0.00 40.22 4.26
2638 2882 1.340017 TGGTGTAGCTCTTCCAATGGC 60.340 52.381 0.00 0.00 0.00 4.40
2659 2915 6.195141 ACCAGAGGTATCGATGGGAACAAC 62.195 50.000 8.54 0.00 37.98 3.32
2683 2939 2.202676 GCCGAGTCCTCTTCTGCG 60.203 66.667 0.00 0.00 0.00 5.18
2698 2954 4.392138 GCATTAGAGGACCGTATAAATGCC 59.608 45.833 15.98 0.00 40.98 4.40
3255 4231 8.184192 GTCAATACAGATAATCCCACAAAAGTG 58.816 37.037 0.00 0.00 0.00 3.16
3349 5620 1.676635 GTGCAATGCAGAGAGGCCA 60.677 57.895 8.73 0.00 40.08 5.36
3665 6433 3.571401 AGTCAAAAGGAAATGTGCCTCAG 59.429 43.478 0.00 0.00 33.76 3.35
3710 6478 5.737860 TCATATTCAGACATGCAGAACTGT 58.262 37.500 13.65 3.87 0.00 3.55
3716 6488 7.725818 ACATACTTCATATTCAGACATGCAG 57.274 36.000 0.00 0.00 0.00 4.41
3731 6503 5.964477 ACCAGATAGGAGGAAACATACTTCA 59.036 40.000 0.00 0.00 41.22 3.02
4025 6848 0.618680 TCAGCAGACATGGGCCTAGT 60.619 55.000 4.53 2.52 0.00 2.57
4234 7063 1.110442 CTGCAACAAACCTTCCACCA 58.890 50.000 0.00 0.00 0.00 4.17
4318 7157 1.714541 TGCCAATCCTTGAAAAGCCA 58.285 45.000 0.00 0.00 44.44 4.75
4338 7177 5.266733 TGTTAGGACGGCGATAAAATAGT 57.733 39.130 16.62 0.00 0.00 2.12
4339 7178 5.751990 ACTTGTTAGGACGGCGATAAAATAG 59.248 40.000 16.62 9.58 0.00 1.73
4352 7191 9.581099 TTTTGAAATTTGAGAACTTGTTAGGAC 57.419 29.630 0.00 0.00 0.00 3.85
4394 7238 6.390721 TCAGATTCTGCTCACAAACTAGTAC 58.609 40.000 8.89 0.00 0.00 2.73
4396 7240 5.474578 TCAGATTCTGCTCACAAACTAGT 57.525 39.130 8.89 0.00 0.00 2.57
4398 7242 6.149973 CCATTTCAGATTCTGCTCACAAACTA 59.850 38.462 8.89 0.00 0.00 2.24
4399 7243 5.048224 CCATTTCAGATTCTGCTCACAAACT 60.048 40.000 8.89 0.00 0.00 2.66
4400 7244 5.048504 TCCATTTCAGATTCTGCTCACAAAC 60.049 40.000 8.89 0.00 0.00 2.93
4401 7245 5.072055 TCCATTTCAGATTCTGCTCACAAA 58.928 37.500 8.89 4.61 0.00 2.83
4411 7335 3.830121 AGGATGGCTCCATTTCAGATTC 58.170 45.455 2.53 0.00 44.79 2.52
4444 7368 2.939103 CAATAAGGTAGCAGGACAGCAC 59.061 50.000 0.00 0.00 36.85 4.40
4450 7374 6.062258 ACTAAAAGCAATAAGGTAGCAGGA 57.938 37.500 0.00 0.00 0.00 3.86
4475 7399 9.453830 ACCAACCTAAGATAGATTTTCTAGGAT 57.546 33.333 0.00 0.00 31.67 3.24
4549 7479 6.376299 AGCAGCAACAATAAGATCAGAATCAA 59.624 34.615 0.00 0.00 34.07 2.57
4553 7483 6.579666 AAAGCAGCAACAATAAGATCAGAA 57.420 33.333 0.00 0.00 0.00 3.02
4671 7601 6.403866 TGCAGTACAATGGAAAATTCAAGT 57.596 33.333 0.00 0.00 0.00 3.16
4684 7614 3.678289 TCAGCTTGTCATGCAGTACAAT 58.322 40.909 14.86 1.77 35.21 2.71
4702 7632 1.467734 CTAAGCCAGCAAGCTGTTCAG 59.532 52.381 19.60 6.51 44.11 3.02
4704 7634 1.528129 ACTAAGCCAGCAAGCTGTTC 58.472 50.000 19.60 11.40 44.11 3.18
4705 7635 1.986882 AACTAAGCCAGCAAGCTGTT 58.013 45.000 19.60 11.34 44.11 3.16
4728 7658 4.261280 GGAGTAGAAAGGATCAGTACGAGC 60.261 50.000 0.00 0.00 0.00 5.03
4731 7661 3.003482 CCGGAGTAGAAAGGATCAGTACG 59.997 52.174 0.00 0.00 0.00 3.67
4822 7752 1.810030 GGCCTAGCAAACGAGACGG 60.810 63.158 0.00 0.00 0.00 4.79
4823 7753 1.078759 CTGGCCTAGCAAACGAGACG 61.079 60.000 3.32 0.00 0.00 4.18
4824 7754 0.741221 CCTGGCCTAGCAAACGAGAC 60.741 60.000 3.32 0.00 0.00 3.36
4827 7757 1.271840 ATCCCTGGCCTAGCAAACGA 61.272 55.000 3.32 0.00 0.00 3.85
4856 7786 7.833682 TGTTAAGGATCAATAGAGCAAATGGAA 59.166 33.333 0.00 0.00 0.00 3.53
4921 7851 2.418609 CCGCTCCAATCACATGTCTGTA 60.419 50.000 0.00 0.00 33.14 2.74
5070 8002 7.962964 TCAGTTCTGAATCTATTCAACGTTT 57.037 32.000 0.00 0.00 45.26 3.60
5139 8074 3.036819 TCTAATGCTCAGCCAGATCACT 58.963 45.455 0.00 0.00 0.00 3.41
5310 8250 4.227300 AGGACCATCATGTTTAGCCTGTAA 59.773 41.667 0.00 0.00 0.00 2.41
5362 8302 6.434340 AGGCAAAAGGTTCTAGAATTTGGTAG 59.566 38.462 22.44 8.76 32.91 3.18
5364 8304 5.147767 AGGCAAAAGGTTCTAGAATTTGGT 58.852 37.500 22.44 7.35 32.91 3.67
5406 8346 5.163519 GCCAAAATCTTGTATGGTGCACTAT 60.164 40.000 20.20 20.20 35.34 2.12
5595 8536 0.042188 CGACGACTGCAACCTTTGTG 60.042 55.000 0.00 0.00 0.00 3.33
5596 8537 1.772063 GCGACGACTGCAACCTTTGT 61.772 55.000 0.00 0.00 0.00 2.83
5597 8538 1.082756 GCGACGACTGCAACCTTTG 60.083 57.895 0.00 0.00 0.00 2.77
5598 8539 1.222115 GAGCGACGACTGCAACCTTT 61.222 55.000 0.00 0.00 33.85 3.11
5599 8540 1.664965 GAGCGACGACTGCAACCTT 60.665 57.895 0.00 0.00 33.85 3.50
5600 8541 2.049063 GAGCGACGACTGCAACCT 60.049 61.111 0.00 0.00 33.85 3.50
5601 8542 3.112709 GGAGCGACGACTGCAACC 61.113 66.667 0.00 0.00 33.85 3.77
5602 8543 2.355837 TGGAGCGACGACTGCAAC 60.356 61.111 10.11 0.00 34.81 4.17
5603 8544 2.049156 CTGGAGCGACGACTGCAA 60.049 61.111 12.68 1.16 37.57 4.08
5637 8578 5.783360 TGAAGACCCATAGAAAGGTAAGTCA 59.217 40.000 0.00 0.00 36.17 3.41
5700 8647 7.583625 TCTCCACCTCAACTAAGATAGTATCA 58.416 38.462 12.66 0.00 38.26 2.15
5706 8653 7.674348 TCTCTTTTCTCCACCTCAACTAAGATA 59.326 37.037 0.00 0.00 0.00 1.98
5725 8672 7.579761 AGTCTTTTCTGCTGATTTCTCTTTT 57.420 32.000 0.00 0.00 0.00 2.27
5789 8736 7.126421 ACACTCCTAAAAGTATGATGAGACCAT 59.874 37.037 0.00 0.00 35.29 3.55
5891 8950 4.558860 GCAAAGCCTGTTTTATCTTAAGCG 59.441 41.667 0.00 0.00 0.00 4.68
5965 10440 2.477375 CACAACAAATTCATGCACCAGC 59.523 45.455 0.00 0.00 42.57 4.85


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

AutoCloner maintained by Alex Coulton.