Multiple sequence alignment - TraesCS3D01G013900

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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 TraesCS3D01G013900 chr3D 100.000 5058 0 0 1 5058 4970326 4965269 0.000000e+00 9341
1 TraesCS3D01G013900 chr3D 87.366 1306 151 11 2928 4225 5007053 5005754 0.000000e+00 1485
2 TraesCS3D01G013900 chr3D 90.062 161 9 2 4905 5058 5004611 5004451 8.590000e-48 202
3 TraesCS3D01G013900 chr3D 75.936 374 76 11 1236 1602 27881147 27881513 4.020000e-41 180
4 TraesCS3D01G013900 chrUn 93.259 2166 92 11 1 2156 238781281 238783402 0.000000e+00 3142
5 TraesCS3D01G013900 chrUn 93.259 2166 92 11 1 2156 240354993 240352872 0.000000e+00 3142
6 TraesCS3D01G013900 chrUn 92.686 2133 115 15 2170 4271 238783951 238786073 0.000000e+00 3037
7 TraesCS3D01G013900 chrUn 92.686 2133 115 15 2170 4271 240352323 240350201 0.000000e+00 3037
8 TraesCS3D01G013900 chrUn 87.237 1332 151 8 2928 4248 36344504 36345827 0.000000e+00 1500
9 TraesCS3D01G013900 chrUn 87.191 1335 152 8 2928 4251 214890501 214889175 0.000000e+00 1500
10 TraesCS3D01G013900 chrUn 86.012 1344 180 3 2928 4271 296501502 296500167 0.000000e+00 1434
11 TraesCS3D01G013900 chrUn 86.910 848 103 3 3415 4262 222639002 222639841 0.000000e+00 944
12 TraesCS3D01G013900 chrUn 89.242 660 51 11 4400 5058 39597160 39596520 0.000000e+00 808
13 TraesCS3D01G013900 chrUn 87.201 711 57 13 4351 5058 296499678 296498999 0.000000e+00 778
14 TraesCS3D01G013900 chrUn 84.908 709 87 10 3575 4271 250052725 250053425 0.000000e+00 699
15 TraesCS3D01G013900 chrUn 84.908 709 87 10 3575 4271 261089705 261090405 0.000000e+00 699
16 TraesCS3D01G013900 chrUn 86.444 450 49 8 4268 4716 250053801 250054239 2.740000e-132 483
17 TraesCS3D01G013900 chrUn 86.444 450 49 8 4268 4716 261090781 261091219 2.740000e-132 483
18 TraesCS3D01G013900 chrUn 86.435 317 32 6 4273 4588 238786453 238786759 2.260000e-88 337
19 TraesCS3D01G013900 chrUn 86.250 320 33 6 4273 4591 240349821 240349512 2.260000e-88 337
20 TraesCS3D01G013900 chrUn 85.625 320 35 6 4273 4591 260327178 260326869 4.880000e-85 326
21 TraesCS3D01G013900 chrUn 84.615 325 38 7 4268 4591 36346522 36346835 3.800000e-81 313
22 TraesCS3D01G013900 chrUn 84.615 325 38 7 4268 4591 214888483 214888170 3.800000e-81 313
23 TraesCS3D01G013900 chrUn 85.276 163 16 3 4884 5046 271416641 271416487 1.460000e-35 161
24 TraesCS3D01G013900 chr3A 87.335 1366 153 8 2919 4271 10952701 10951343 0.000000e+00 1546
25 TraesCS3D01G013900 chr3A 88.185 1295 145 6 2934 4225 11410052 11408763 0.000000e+00 1537
26 TraesCS3D01G013900 chr3A 84.853 713 82 16 4285 4981 11408184 11407482 0.000000e+00 695
27 TraesCS3D01G013900 chr3A 83.477 581 70 14 99 670 10955096 10954533 7.510000e-143 518
28 TraesCS3D01G013900 chr3A 91.553 367 25 3 4691 5057 10950329 10949969 7.560000e-138 501
29 TraesCS3D01G013900 chr3A 88.000 375 30 8 4273 4643 10950660 10950297 3.620000e-116 429
30 TraesCS3D01G013900 chr3A 83.784 148 19 5 932 1075 10954492 10954346 8.830000e-28 135
31 TraesCS3D01G013900 chr3B 86.513 1342 174 2 2930 4271 13966272 13967606 0.000000e+00 1469
32 TraesCS3D01G013900 chr3B 85.714 448 50 8 4273 4716 13967987 13968424 1.280000e-125 460
33 TraesCS3D01G013900 chr1D 78.963 328 60 7 237 558 7350538 7350862 1.100000e-51 215
34 TraesCS3D01G013900 chr1D 76.081 393 74 15 237 613 7207307 7207695 2.400000e-43 187
35 TraesCS3D01G013900 chr1A 78.107 169 33 4 2504 2671 9550738 9550573 2.490000e-18 104


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 TraesCS3D01G013900 chr3D 4965269 4970326 5057 True 9341.0 9341 100.000000 1 5058 1 chr3D.!!$R1 5057
1 TraesCS3D01G013900 chr3D 5004451 5007053 2602 True 843.5 1485 88.714000 2928 5058 2 chr3D.!!$R2 2130
2 TraesCS3D01G013900 chrUn 238781281 238786759 5478 False 2172.0 3142 90.793333 1 4588 3 chrUn.!!$F3 4587
3 TraesCS3D01G013900 chrUn 240349512 240354993 5481 True 2172.0 3142 90.731667 1 4591 3 chrUn.!!$R5 4590
4 TraesCS3D01G013900 chrUn 296498999 296501502 2503 True 1106.0 1434 86.606500 2928 5058 2 chrUn.!!$R6 2130
5 TraesCS3D01G013900 chrUn 222639002 222639841 839 False 944.0 944 86.910000 3415 4262 1 chrUn.!!$F1 847
6 TraesCS3D01G013900 chrUn 36344504 36346835 2331 False 906.5 1500 85.926000 2928 4591 2 chrUn.!!$F2 1663
7 TraesCS3D01G013900 chrUn 214888170 214890501 2331 True 906.5 1500 85.903000 2928 4591 2 chrUn.!!$R4 1663
8 TraesCS3D01G013900 chrUn 39596520 39597160 640 True 808.0 808 89.242000 4400 5058 1 chrUn.!!$R1 658
9 TraesCS3D01G013900 chrUn 250052725 250054239 1514 False 591.0 699 85.676000 3575 4716 2 chrUn.!!$F4 1141
10 TraesCS3D01G013900 chrUn 261089705 261091219 1514 False 591.0 699 85.676000 3575 4716 2 chrUn.!!$F5 1141
11 TraesCS3D01G013900 chr3A 11407482 11410052 2570 True 1116.0 1537 86.519000 2934 4981 2 chr3A.!!$R2 2047
12 TraesCS3D01G013900 chr3A 10949969 10955096 5127 True 625.8 1546 86.829800 99 5057 5 chr3A.!!$R1 4958
13 TraesCS3D01G013900 chr3B 13966272 13968424 2152 False 964.5 1469 86.113500 2930 4716 2 chr3B.!!$F1 1786

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
440 452 0.333993 ATCTCTGGGCCATGTTTGCT 59.666 50.0 6.72 0.0 0.00 3.91 F
1396 1476 0.033228 CCAAGTTTTTCATGCGGGCA 59.967 50.0 0.00 0.0 0.00 5.36 F
1801 1884 0.237235 CCCGACGATTGTGTGTTTGG 59.763 55.0 0.00 0.0 0.00 3.28 F
1967 2071 0.250124 TCAATGTGAACGGGAAGCGT 60.250 50.0 0.00 0.0 0.00 5.07 F
2128 2269 0.250124 CGTGACCTGTTAAGCCACCA 60.250 55.0 0.00 0.0 0.00 4.17 F
2141 2282 0.529378 GCCACCAGAGCTTCAAATGG 59.471 55.0 0.00 0.0 38.83 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1862 0.677288 AACACACAATCGTCGGGAGA 59.323 50.000 0.00 0.0 0.00 3.71 R
2562 3241 0.391661 AGTATCTGCAAGGCACACCG 60.392 55.000 0.00 0.0 42.76 4.94 R
3613 4471 0.033504 TGACACCAAAGCTCCGAGAC 59.966 55.000 0.00 0.0 0.00 3.36 R
3788 4649 0.392706 TGCATGTCGTCAACAGGAGT 59.607 50.000 0.00 0.0 42.26 3.85 R
4010 4880 1.202989 TGAGATCTCATCCTCCTCCGG 60.203 57.143 21.67 0.0 34.14 5.14 R
4120 4998 3.467803 ACAGTCAACCAGTTAAGCAGTC 58.532 45.455 0.00 0.0 0.00 3.51 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
40 41 6.475402 GTCCACCAAATACAAAAAGTGAGTTG 59.525 38.462 0.00 0.00 0.00 3.16
72 73 1.452833 GGAGACTGGCCCAGCAATC 60.453 63.158 11.63 6.27 34.37 2.67
74 75 2.440980 GACTGGCCCAGCAATCCC 60.441 66.667 11.63 0.00 34.37 3.85
75 76 2.943265 ACTGGCCCAGCAATCCCT 60.943 61.111 11.63 0.00 34.37 4.20
78 79 2.830370 GGCCCAGCAATCCCTTCG 60.830 66.667 0.00 0.00 0.00 3.79
86 87 0.819259 GCAATCCCTTCGGCAGCATA 60.819 55.000 0.00 0.00 0.00 3.14
250 254 5.306678 CAGGGAGATGAGGAGTATAAAAGCT 59.693 44.000 0.00 0.00 0.00 3.74
301 305 4.406648 TCTATGGCAGTGACCTTACATG 57.593 45.455 0.00 0.00 0.00 3.21
439 451 0.743097 GATCTCTGGGCCATGTTTGC 59.257 55.000 6.72 0.00 0.00 3.68
440 452 0.333993 ATCTCTGGGCCATGTTTGCT 59.666 50.000 6.72 0.00 0.00 3.91
441 453 0.609957 TCTCTGGGCCATGTTTGCTG 60.610 55.000 6.72 0.00 0.00 4.41
442 454 2.221906 CTCTGGGCCATGTTTGCTGC 62.222 60.000 6.72 0.00 0.00 5.25
443 455 2.523657 TGGGCCATGTTTGCTGCA 60.524 55.556 0.00 0.00 0.00 4.41
444 456 2.102109 CTGGGCCATGTTTGCTGCAA 62.102 55.000 11.69 11.69 0.00 4.08
686 711 1.972872 CAACCAGAGTTGTGCCTCTT 58.027 50.000 0.00 0.00 46.88 2.85
687 712 3.126001 CAACCAGAGTTGTGCCTCTTA 57.874 47.619 0.00 0.00 46.88 2.10
688 713 3.679389 CAACCAGAGTTGTGCCTCTTAT 58.321 45.455 0.00 0.00 46.88 1.73
689 714 4.832248 CAACCAGAGTTGTGCCTCTTATA 58.168 43.478 0.00 0.00 46.88 0.98
690 715 5.431765 CAACCAGAGTTGTGCCTCTTATAT 58.568 41.667 0.00 0.00 46.88 0.86
691 716 6.582636 CAACCAGAGTTGTGCCTCTTATATA 58.417 40.000 0.00 0.00 46.88 0.86
692 717 7.220030 CAACCAGAGTTGTGCCTCTTATATAT 58.780 38.462 0.00 0.00 46.88 0.86
693 718 8.367911 CAACCAGAGTTGTGCCTCTTATATATA 58.632 37.037 0.00 0.00 46.88 0.86
694 719 8.671987 ACCAGAGTTGTGCCTCTTATATATAT 57.328 34.615 0.00 0.00 39.81 0.86
695 720 9.769677 ACCAGAGTTGTGCCTCTTATATATATA 57.230 33.333 0.00 0.00 39.81 0.86
766 791 0.889994 TGTGAATGCAACCTCATGCC 59.110 50.000 0.00 0.00 45.83 4.40
778 803 1.002366 CTCATGCCGTGTTCTAGTGC 58.998 55.000 0.00 0.00 0.00 4.40
779 804 0.608130 TCATGCCGTGTTCTAGTGCT 59.392 50.000 0.00 0.00 0.00 4.40
807 832 3.978687 GTGACTGCACAGTAGTTGTAGT 58.021 45.455 2.68 0.00 44.51 2.73
824 849 6.497259 AGTTGTAGTCAAGGATTCTAGAACCA 59.503 38.462 19.72 0.00 38.11 3.67
828 853 5.738909 AGTCAAGGATTCTAGAACCATGTG 58.261 41.667 19.72 15.35 0.00 3.21
838 863 3.485463 AGAACCATGTGGAAACTCGAA 57.515 42.857 5.96 0.00 38.94 3.71
1050 1077 5.586155 TGAACCCTTACCAAGTAAATGGA 57.414 39.130 0.00 0.00 43.54 3.41
1057 1084 5.888161 CCTTACCAAGTAAATGGAGCAGAAT 59.112 40.000 0.00 0.00 43.54 2.40
1063 1090 7.226720 ACCAAGTAAATGGAGCAGAATATTACG 59.773 37.037 0.00 0.00 43.54 3.18
1067 1094 8.426489 AGTAAATGGAGCAGAATATTACGGTAA 58.574 33.333 2.62 2.62 0.00 2.85
1072 1099 5.221382 GGAGCAGAATATTACGGTAAGTCCA 60.221 44.000 6.74 0.00 35.57 4.02
1074 1101 6.827727 AGCAGAATATTACGGTAAGTCCAAT 58.172 36.000 6.74 0.00 35.57 3.16
1075 1102 7.959175 AGCAGAATATTACGGTAAGTCCAATA 58.041 34.615 6.74 0.00 35.57 1.90
1096 1123 7.431249 CAATATAAATTGGCAGCTCAGTCAAT 58.569 34.615 0.00 0.00 45.08 2.57
1098 1125 2.211250 ATTGGCAGCTCAGTCAATGT 57.789 45.000 3.27 0.00 41.87 2.71
1099 1126 1.985473 TTGGCAGCTCAGTCAATGTT 58.015 45.000 0.00 0.00 0.00 2.71
1100 1127 1.985473 TGGCAGCTCAGTCAATGTTT 58.015 45.000 0.00 0.00 0.00 2.83
1101 1128 2.309613 TGGCAGCTCAGTCAATGTTTT 58.690 42.857 0.00 0.00 0.00 2.43
1129 1156 4.866682 GCTCCAGCTATGTTCTTTGTAC 57.133 45.455 0.00 0.00 38.21 2.90
1130 1157 4.253685 GCTCCAGCTATGTTCTTTGTACA 58.746 43.478 0.00 0.00 38.21 2.90
1181 1209 6.386927 TCCAAAGTCAGTAGTATCCCAATCAT 59.613 38.462 0.00 0.00 0.00 2.45
1185 1213 4.993584 GTCAGTAGTATCCCAATCATGCTG 59.006 45.833 0.00 0.00 0.00 4.41
1266 1346 3.753272 GGAGTACTCAAGCATCTGCAAAA 59.247 43.478 23.91 0.00 45.16 2.44
1269 1349 4.823989 AGTACTCAAGCATCTGCAAAACTT 59.176 37.500 4.79 0.00 45.16 2.66
1367 1447 3.324246 GGAAGATGTCCAGGGAGGA 57.676 57.895 0.00 0.00 46.97 3.71
1396 1476 0.033228 CCAAGTTTTTCATGCGGGCA 59.967 50.000 0.00 0.00 0.00 5.36
1455 1535 2.281761 CACCTGGGTGTGGTGCTC 60.282 66.667 11.29 0.00 46.73 4.26
1587 1667 3.337358 GCCAATTTTAATGCCAACAGCT 58.663 40.909 0.00 0.00 44.23 4.24
1644 1724 4.333649 ACACATACGGCTTCATTGATTCAG 59.666 41.667 0.00 0.00 0.00 3.02
1666 1746 8.213518 TCAGATTACTATCTTGATTTGGCAAC 57.786 34.615 0.00 0.00 39.11 4.17
1668 1748 8.341173 CAGATTACTATCTTGATTTGGCAACTC 58.659 37.037 10.36 10.36 39.11 3.01
1669 1749 6.662414 TTACTATCTTGATTTGGCAACTCG 57.338 37.500 12.20 0.52 37.61 4.18
1777 1860 6.380846 AGCAATTCACATGTTTATGTATGGGT 59.619 34.615 0.00 0.00 45.53 4.51
1779 1862 7.546358 CAATTCACATGTTTATGTATGGGTGT 58.454 34.615 0.00 0.00 45.53 4.16
1800 1883 1.194547 CTCCCGACGATTGTGTGTTTG 59.805 52.381 0.00 0.00 0.00 2.93
1801 1884 0.237235 CCCGACGATTGTGTGTTTGG 59.763 55.000 0.00 0.00 0.00 3.28
1809 1892 4.452455 ACGATTGTGTGTTTGGAGATCTTC 59.548 41.667 0.00 0.00 0.00 2.87
1810 1893 4.434725 CGATTGTGTGTTTGGAGATCTTCG 60.435 45.833 0.00 0.00 0.00 3.79
1820 1903 4.052159 TGGAGATCTTCGATCTTCTTGC 57.948 45.455 12.13 0.00 0.00 4.01
1884 1988 4.521130 TCTGACAGCCAACAAGTAGTAG 57.479 45.455 0.00 0.00 0.00 2.57
1946 2050 3.028130 TGGGTTTTCTGTTCAGTTTCCC 58.972 45.455 13.20 13.20 0.00 3.97
1967 2071 0.250124 TCAATGTGAACGGGAAGCGT 60.250 50.000 0.00 0.00 0.00 5.07
2055 2165 1.748591 GCCATGTCACCCTCTCATTCC 60.749 57.143 0.00 0.00 0.00 3.01
2061 2171 3.588842 TGTCACCCTCTCATTCCATTTCT 59.411 43.478 0.00 0.00 0.00 2.52
2074 2184 5.743636 TTCCATTTCTTCCTGAATTTGGG 57.256 39.130 0.00 0.00 38.15 4.12
2128 2269 0.250124 CGTGACCTGTTAAGCCACCA 60.250 55.000 0.00 0.00 0.00 4.17
2141 2282 0.529378 GCCACCAGAGCTTCAAATGG 59.471 55.000 0.00 0.00 38.83 3.16
2147 2288 3.181434 ACCAGAGCTTCAAATGGGTACAA 60.181 43.478 0.00 0.00 37.13 2.41
2156 2297 4.580868 TCAAATGGGTACAATCACGCTAA 58.419 39.130 0.00 0.00 32.86 3.09
2157 2298 5.004448 TCAAATGGGTACAATCACGCTAAA 58.996 37.500 0.00 0.00 32.86 1.85
2158 2299 4.957759 AATGGGTACAATCACGCTAAAC 57.042 40.909 0.00 0.00 32.86 2.01
2159 2300 3.688694 TGGGTACAATCACGCTAAACT 57.311 42.857 0.00 0.00 32.86 2.66
2160 2301 4.804868 TGGGTACAATCACGCTAAACTA 57.195 40.909 0.00 0.00 32.86 2.24
2161 2302 5.149973 TGGGTACAATCACGCTAAACTAA 57.850 39.130 0.00 0.00 32.86 2.24
2163 2304 5.047164 TGGGTACAATCACGCTAAACTAAGA 60.047 40.000 0.00 0.00 32.86 2.10
2165 2306 6.537660 GGGTACAATCACGCTAAACTAAGATT 59.462 38.462 0.00 0.00 0.00 2.40
2167 2308 5.869350 ACAATCACGCTAAACTAAGATTGC 58.131 37.500 11.56 0.00 43.57 3.56
2168 2309 5.643777 ACAATCACGCTAAACTAAGATTGCT 59.356 36.000 11.56 0.00 43.57 3.91
2190 2866 8.116651 TGCTATTTGCTAATTTAGTTGGACAA 57.883 30.769 0.00 0.00 43.37 3.18
2220 2896 7.969536 AATTAGAAGGACACAATCATATCCG 57.030 36.000 0.00 0.00 36.28 4.18
2227 2903 3.141398 ACACAATCATATCCGACATGGC 58.859 45.455 0.00 0.00 37.80 4.40
2233 2909 6.014584 ACAATCATATCCGACATGGCTACTTA 60.015 38.462 0.00 0.00 37.80 2.24
2240 2916 4.222145 TCCGACATGGCTACTTAAACTCTT 59.778 41.667 0.00 0.00 37.80 2.85
2405 3084 5.885449 AAACCAAACATCCTCATTTTCCA 57.115 34.783 0.00 0.00 0.00 3.53
2433 3112 2.653766 CAAACACAACCCGCACGC 60.654 61.111 0.00 0.00 0.00 5.34
2445 3124 1.708193 CCGCACGCATCATCACACAT 61.708 55.000 0.00 0.00 0.00 3.21
2492 3171 2.973694 TACCAGCCGCTTAAACTAGG 57.026 50.000 0.00 0.00 0.00 3.02
2504 3183 4.506095 GCTTAAACTAGGTGGTGGAAGGAA 60.506 45.833 0.00 0.00 0.00 3.36
2505 3184 3.790089 AAACTAGGTGGTGGAAGGAAG 57.210 47.619 0.00 0.00 0.00 3.46
2562 3241 9.256477 CCCTTCTTAATTTCCTTTTTGTGTAAC 57.744 33.333 0.00 0.00 37.35 2.50
2833 3615 4.335315 CCTGTTGTGTAAGCTGTTCTTTGA 59.665 41.667 0.00 0.00 36.25 2.69
2841 3623 6.651225 GTGTAAGCTGTTCTTTGATAGGTTCT 59.349 38.462 0.00 0.00 36.25 3.01
2852 3660 9.444600 TTCTTTGATAGGTTCTTATTGTACCAC 57.555 33.333 0.00 0.00 38.41 4.16
2856 3664 7.207383 TGATAGGTTCTTATTGTACCACGATG 58.793 38.462 0.00 0.00 38.41 3.84
3005 3863 8.822805 TCTACAAGTACTGGAAAACAAGGATAT 58.177 33.333 3.64 0.00 0.00 1.63
3015 3873 8.365060 TGGAAAACAAGGATATCAATTGATGT 57.635 30.769 27.59 22.34 36.05 3.06
3349 4207 4.158764 CCTCGAGGTTCTCTTGACAAGTAT 59.841 45.833 24.04 0.00 32.64 2.12
3390 4248 1.661463 TTCTCCTGGGACAAGCTCAT 58.339 50.000 0.00 0.00 38.70 2.90
3493 4351 2.821969 GCCACACAACATCCTTCTTGAT 59.178 45.455 0.00 0.00 0.00 2.57
3613 4471 4.081752 GGGTACATAGCTCCTGAGATGATG 60.082 50.000 0.00 0.88 0.00 3.07
3664 4522 1.871039 TCTGACGTTTACAGCTTTGGC 59.129 47.619 0.00 0.00 35.61 4.52
3706 4564 2.026822 TGGAGGAAGAAGGAATGCTGAC 60.027 50.000 0.00 0.00 0.00 3.51
3798 4659 4.588951 AGTGTGTGAGATAACTCCTGTTGA 59.411 41.667 0.00 0.00 41.99 3.18
3799 4669 4.686554 GTGTGTGAGATAACTCCTGTTGAC 59.313 45.833 0.00 0.00 41.99 3.18
3911 4781 1.452833 GAGATGCTGGAAGGTGGCC 60.453 63.158 0.00 0.00 0.00 5.36
3976 4846 2.607892 GCACACTGCTGTTCCGGAC 61.608 63.158 1.83 0.00 40.96 4.79
4010 4880 1.175983 ATCCGAGCTGACCGAGATCC 61.176 60.000 0.00 0.00 33.11 3.36
4053 4923 3.791953 TTCTTATGTTTCCCGGGTCAA 57.208 42.857 22.86 12.31 0.00 3.18
4058 4928 0.768622 TGTTTCCCGGGTCAAGTGAT 59.231 50.000 22.86 0.00 0.00 3.06
4091 4965 9.104965 CGTGGAAACATGTAATAAAATCTAGGA 57.895 33.333 0.00 0.00 46.14 2.94
4120 4998 6.037098 CAGTTAAAGAGGATGTAGAACTCCG 58.963 44.000 0.00 0.00 36.62 4.63
4130 5008 4.170292 TGTAGAACTCCGACTGCTTAAC 57.830 45.455 0.00 0.00 0.00 2.01
4138 5027 1.798813 CCGACTGCTTAACTGGTTGAC 59.201 52.381 0.00 0.00 0.00 3.18
4217 5109 3.193479 GGAAGCTGAAGTGTTATTTGGGG 59.807 47.826 0.00 0.00 0.00 4.96
4257 5152 5.645929 TGTTAGCACGAATACATGGTTGAAT 59.354 36.000 0.00 0.00 0.00 2.57
4262 5157 6.035843 GCACGAATACATGGTTGAATGAATT 58.964 36.000 0.00 0.00 0.00 2.17
4271 5166 8.564509 ACATGGTTGAATGAATTTATTTTGGG 57.435 30.769 0.00 0.00 0.00 4.12
4361 6140 9.598517 AAATAACATCAAAGTTCAGCAGAAAAA 57.401 25.926 0.00 0.00 35.08 1.94
4371 6150 4.771590 TCAGCAGAAAAATACAAGCCAG 57.228 40.909 0.00 0.00 0.00 4.85
4378 6157 4.774200 AGAAAAATACAAGCCAGGAATGCT 59.226 37.500 0.00 0.00 41.89 3.79
4407 6186 1.066908 CCGTGTGTGTTCCTGCAATTT 59.933 47.619 0.00 0.00 0.00 1.82
4434 6214 0.179134 GATTGTAGACTCGCTGCCGT 60.179 55.000 0.00 0.00 35.54 5.68
4476 6256 0.036388 TAAACAGCCCCTGCGAGAAG 60.036 55.000 0.00 0.00 44.33 2.85
4511 6291 5.565509 TGGCTCATATGAACCACTACAAAA 58.434 37.500 21.47 0.00 35.54 2.44
4512 6292 5.647658 TGGCTCATATGAACCACTACAAAAG 59.352 40.000 21.47 0.16 35.54 2.27
4513 6293 5.648092 GGCTCATATGAACCACTACAAAAGT 59.352 40.000 18.46 0.00 39.81 2.66
4514 6294 6.821665 GGCTCATATGAACCACTACAAAAGTA 59.178 38.462 18.46 0.00 35.76 2.24
4515 6295 7.201617 GGCTCATATGAACCACTACAAAAGTAC 60.202 40.741 18.46 0.00 35.76 2.73
4516 6296 7.333423 GCTCATATGAACCACTACAAAAGTACA 59.667 37.037 6.90 0.00 35.76 2.90
4517 6297 9.214957 CTCATATGAACCACTACAAAAGTACAA 57.785 33.333 6.90 0.00 35.76 2.41
4518 6298 9.562408 TCATATGAACCACTACAAAAGTACAAA 57.438 29.630 1.98 0.00 35.76 2.83
4566 6352 1.342074 CCAGGACACCTCACTCTCAA 58.658 55.000 0.00 0.00 0.00 3.02
4567 6353 1.694150 CCAGGACACCTCACTCTCAAA 59.306 52.381 0.00 0.00 0.00 2.69
4568 6354 2.104792 CCAGGACACCTCACTCTCAAAA 59.895 50.000 0.00 0.00 0.00 2.44
4645 6432 7.349711 ACATGTAAACGTCAAATGACTTGTAC 58.650 34.615 11.45 11.47 42.66 2.90
4666 6453 2.030007 CACCGAGAACAAATTGCCACAT 60.030 45.455 0.00 0.00 0.00 3.21
4676 6464 6.778834 ACAAATTGCCACATCATTCTGATA 57.221 33.333 0.00 0.00 34.28 2.15
4851 6645 3.560481 CAGCAGAGAATGATGGATGTGAC 59.440 47.826 0.00 0.00 41.75 3.67
4933 6727 5.350365 CGAAAATGACGAGTCCTTCCATTAA 59.650 40.000 0.34 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.512515 GGTGGACGCATCTGAGCC 60.513 66.667 0.00 0.00 0.00 4.70
40 41 3.462021 CAGTCTCCTGCCTTAGTAATGC 58.538 50.000 3.42 3.42 0.00 3.56
57 58 2.440980 GGGATTGCTGGGCCAGTC 60.441 66.667 32.80 24.55 33.43 3.51
86 87 2.226330 TCACGCCAACAAGCAGTATTT 58.774 42.857 0.00 0.00 0.00 1.40
95 96 1.865865 GAGAGAGTTCACGCCAACAA 58.134 50.000 0.37 0.00 0.00 2.83
96 97 0.318699 CGAGAGAGTTCACGCCAACA 60.319 55.000 0.37 0.00 31.03 3.33
97 98 1.009389 CCGAGAGAGTTCACGCCAAC 61.009 60.000 0.00 0.00 36.30 3.77
250 254 2.158623 GGAGTGCCATGAATATCACCCA 60.159 50.000 0.00 0.00 0.00 4.51
301 305 2.840753 TTCACCCAGTCCTTGGCCC 61.841 63.158 0.00 0.00 46.32 5.80
439 451 0.249699 TGTCCACCGTACAGTTGCAG 60.250 55.000 0.00 0.00 0.00 4.41
440 452 0.249699 CTGTCCACCGTACAGTTGCA 60.250 55.000 0.00 0.00 39.61 4.08
441 453 2.528797 CTGTCCACCGTACAGTTGC 58.471 57.895 0.00 0.00 39.61 4.17
717 742 4.829064 TCAACCATGATAATTAAGGCGC 57.171 40.909 0.00 0.00 0.00 6.53
766 791 2.095668 ACTCTCGAAGCACTAGAACACG 60.096 50.000 0.00 0.00 0.00 4.49
778 803 1.000827 ACTGTGCAGTCACTCTCGAAG 60.001 52.381 0.00 0.00 43.49 3.79
779 804 1.032794 ACTGTGCAGTCACTCTCGAA 58.967 50.000 0.00 0.00 43.49 3.71
802 827 6.440647 ACATGGTTCTAGAATCCTTGACTACA 59.559 38.462 27.56 7.62 32.88 2.74
807 832 4.782691 TCCACATGGTTCTAGAATCCTTGA 59.217 41.667 27.56 12.96 36.34 3.02
838 863 4.333649 CACGCATGAAACTGATGGAAGTAT 59.666 41.667 0.00 0.00 0.00 2.12
1050 1077 5.864418 TGGACTTACCGTAATATTCTGCT 57.136 39.130 0.00 0.00 42.61 4.24
1072 1099 7.069085 ACATTGACTGAGCTGCCAATTTATATT 59.931 33.333 0.00 0.00 0.00 1.28
1074 1101 5.887598 ACATTGACTGAGCTGCCAATTTATA 59.112 36.000 0.00 0.00 0.00 0.98
1075 1102 4.708421 ACATTGACTGAGCTGCCAATTTAT 59.292 37.500 0.00 0.00 0.00 1.40
1096 1123 1.032014 GCTGGAGCTGGAACAAAACA 58.968 50.000 0.00 0.00 38.70 2.83
1117 1144 5.807520 CGCTATCTGACTGTACAAAGAACAT 59.192 40.000 0.00 0.00 0.00 2.71
1122 1149 6.893958 AAATCGCTATCTGACTGTACAAAG 57.106 37.500 0.00 0.00 0.00 2.77
1181 1209 4.601420 TGATTATATAAGGAAGGCCCAGCA 59.399 41.667 0.00 0.00 37.41 4.41
1185 1213 9.397280 GATTACTTGATTATATAAGGAAGGCCC 57.603 37.037 0.00 0.00 30.77 5.80
1367 1447 3.096092 TGAAAAACTTGGGCACTTGTCT 58.904 40.909 0.00 0.00 0.00 3.41
1455 1535 4.274459 GCTACAAACCAGCTCATATCCTTG 59.726 45.833 0.00 0.00 36.07 3.61
1587 1667 1.607756 ACCGAGGAAGAGAGCAGCA 60.608 57.895 0.00 0.00 0.00 4.41
1644 1724 7.224753 TCGAGTTGCCAAATCAAGATAGTAATC 59.775 37.037 5.67 0.00 0.00 1.75
1779 1862 0.677288 AACACACAATCGTCGGGAGA 59.323 50.000 0.00 0.00 0.00 3.71
1785 1868 3.997021 AGATCTCCAAACACACAATCGTC 59.003 43.478 0.00 0.00 0.00 4.20
1800 1883 3.049206 CGCAAGAAGATCGAAGATCTCC 58.951 50.000 12.31 0.71 41.29 3.71
1801 1884 3.049206 CCGCAAGAAGATCGAAGATCTC 58.951 50.000 12.31 7.05 41.29 2.75
1809 1892 1.590238 CAAGTAGCCGCAAGAAGATCG 59.410 52.381 0.00 0.00 43.02 3.69
1810 1893 1.936547 CCAAGTAGCCGCAAGAAGATC 59.063 52.381 0.00 0.00 43.02 2.75
1862 1945 3.838244 ACTACTTGTTGGCTGTCAGAA 57.162 42.857 3.32 0.00 0.00 3.02
1946 2050 1.202065 CGCTTCCCGTTCACATTGATG 60.202 52.381 0.00 0.00 0.00 3.07
2055 2165 5.244626 AGTGACCCAAATTCAGGAAGAAATG 59.755 40.000 0.87 0.00 40.22 2.32
2061 2171 3.140144 AGGAAGTGACCCAAATTCAGGAA 59.860 43.478 0.87 0.00 0.00 3.36
2096 2237 5.924475 ACAGGTCACGTTAATTCTTCTTG 57.076 39.130 0.00 0.00 0.00 3.02
2099 2240 6.304882 GCTTAACAGGTCACGTTAATTCTTC 58.695 40.000 0.00 0.00 37.97 2.87
2102 2243 4.453136 TGGCTTAACAGGTCACGTTAATTC 59.547 41.667 0.00 0.00 37.97 2.17
2128 2269 4.702131 GTGATTGTACCCATTTGAAGCTCT 59.298 41.667 0.00 0.00 0.00 4.09
2139 2280 3.688694 AGTTTAGCGTGATTGTACCCA 57.311 42.857 0.00 0.00 0.00 4.51
2141 2282 7.399523 CAATCTTAGTTTAGCGTGATTGTACC 58.600 38.462 0.00 0.00 37.23 3.34
2147 2288 8.338259 CAAATAGCAATCTTAGTTTAGCGTGAT 58.662 33.333 0.00 0.00 0.00 3.06
2195 2871 8.866093 TCGGATATGATTGTGTCCTTCTAATTA 58.134 33.333 0.00 0.00 0.00 1.40
2220 2896 8.950208 ATAGAAAGAGTTTAAGTAGCCATGTC 57.050 34.615 0.00 0.00 0.00 3.06
2240 2916 9.726438 GCTATGGGCTCTTAAATAGAAATAGAA 57.274 33.333 0.00 0.00 38.06 2.10
2255 2931 2.368221 GACAAGAGATGCTATGGGCTCT 59.632 50.000 0.00 0.00 42.39 4.09
2283 2959 4.115199 GGCCCCCGCAGATGTTCT 62.115 66.667 0.00 0.00 36.38 3.01
2405 3084 4.447290 GGGTTGTGTTTGTTGCCTAAAAT 58.553 39.130 0.00 0.00 0.00 1.82
2445 3124 5.527214 CCACCGATATTTTAGAAGATGCACA 59.473 40.000 0.00 0.00 0.00 4.57
2478 3157 1.084289 CACCACCTAGTTTAAGCGGC 58.916 55.000 0.00 0.00 0.00 6.53
2492 3171 1.303643 CTGCCCTTCCTTCCACCAC 60.304 63.158 0.00 0.00 0.00 4.16
2504 3183 7.400627 ACTTCTTAGATAAGAGTAAACTGCCCT 59.599 37.037 2.76 0.00 42.66 5.19
2505 3184 7.492994 CACTTCTTAGATAAGAGTAAACTGCCC 59.507 40.741 2.76 0.00 42.66 5.36
2562 3241 0.391661 AGTATCTGCAAGGCACACCG 60.392 55.000 0.00 0.00 42.76 4.94
2833 3615 7.120923 ACATCGTGGTACAATAAGAACCTAT 57.879 36.000 0.00 0.00 44.16 2.57
2852 3660 8.733510 CGGATTACGCAATATAAATTACATCG 57.266 34.615 0.00 0.00 34.82 3.84
3005 3863 6.071334 AGGAACTTCTCGACTACATCAATTGA 60.071 38.462 11.26 11.26 27.25 2.57
3015 3873 2.486472 ACGGAGGAACTTCTCGACTA 57.514 50.000 0.00 0.00 41.55 2.59
3214 4072 4.751767 AGAGACCTCACTGATGAAATCC 57.248 45.455 0.00 0.00 44.73 3.01
3541 4399 3.287222 CACAAAACTCTTGTCCCTTGGA 58.713 45.455 0.00 0.00 0.00 3.53
3613 4471 0.033504 TGACACCAAAGCTCCGAGAC 59.966 55.000 0.00 0.00 0.00 3.36
3664 4522 1.448119 CCATCTCCAGCAGCAGCATG 61.448 60.000 3.17 0.00 45.49 4.06
3706 4564 2.556287 GAGTTTGCTGCGTTCGGG 59.444 61.111 0.00 0.00 0.00 5.14
3788 4649 0.392706 TGCATGTCGTCAACAGGAGT 59.607 50.000 0.00 0.00 42.26 3.85
3798 4659 1.276138 TCTCCAACTCATGCATGTCGT 59.724 47.619 25.43 19.77 0.00 4.34
3799 4669 1.931841 CTCTCCAACTCATGCATGTCG 59.068 52.381 25.43 19.16 0.00 4.35
3911 4781 2.252346 GCATCTGCAGGCCATCGAG 61.252 63.158 15.13 0.00 41.59 4.04
3976 4846 4.120589 GCTCGGATAACAAAGGGTAAGAG 58.879 47.826 0.00 0.00 0.00 2.85
4010 4880 1.202989 TGAGATCTCATCCTCCTCCGG 60.203 57.143 21.67 0.00 34.14 5.14
4053 4923 4.330944 TGTTTCCACGTACAAGATCACT 57.669 40.909 0.00 0.00 0.00 3.41
4058 4928 8.604640 TTTATTACATGTTTCCACGTACAAGA 57.395 30.769 2.30 0.00 0.00 3.02
4065 4935 9.104965 TCCTAGATTTTATTACATGTTTCCACG 57.895 33.333 2.30 0.00 0.00 4.94
4087 4961 6.195700 ACATCCTCTTTAACTGCTACTCCTA 58.804 40.000 0.00 0.00 0.00 2.94
4088 4962 5.026790 ACATCCTCTTTAACTGCTACTCCT 58.973 41.667 0.00 0.00 0.00 3.69
4089 4963 5.346181 ACATCCTCTTTAACTGCTACTCC 57.654 43.478 0.00 0.00 0.00 3.85
4090 4964 7.336161 TCTACATCCTCTTTAACTGCTACTC 57.664 40.000 0.00 0.00 0.00 2.59
4091 4965 7.397761 AGTTCTACATCCTCTTTAACTGCTACT 59.602 37.037 0.00 0.00 0.00 2.57
4092 4966 7.548967 AGTTCTACATCCTCTTTAACTGCTAC 58.451 38.462 0.00 0.00 0.00 3.58
4120 4998 3.467803 ACAGTCAACCAGTTAAGCAGTC 58.532 45.455 0.00 0.00 0.00 3.51
4130 5008 6.093219 CCAGAAAGATGATTACAGTCAACCAG 59.907 42.308 0.00 0.00 0.00 4.00
4138 5027 7.102346 AGTGTCTTCCAGAAAGATGATTACAG 58.898 38.462 0.00 0.00 45.57 2.74
4175 5064 8.121167 GCTTCCACGAGCTATTATTCATATAC 57.879 38.462 0.00 0.00 39.57 1.47
4196 5088 3.826729 ACCCCAAATAACACTTCAGCTTC 59.173 43.478 0.00 0.00 0.00 3.86
4217 5109 7.429920 TCGTGCTAACAATGTTTTAACAGAAAC 59.570 33.333 3.17 0.00 43.04 2.78
4257 5152 9.651913 GATAGCAAGAAACCCAAAATAAATTCA 57.348 29.630 0.00 0.00 0.00 2.57
4262 5157 7.375053 GTGTGATAGCAAGAAACCCAAAATAA 58.625 34.615 0.00 0.00 0.00 1.40
4267 5162 2.811431 CGTGTGATAGCAAGAAACCCAA 59.189 45.455 0.00 0.00 0.00 4.12
4281 6053 5.095691 GATTAAATCGGAATGCGTGTGAT 57.904 39.130 0.00 0.00 0.00 3.06
4330 6102 9.844790 CTGCTGAACTTTGATGTTATTTGAATA 57.155 29.630 0.00 0.00 0.00 1.75
4339 6111 8.196771 TGTATTTTTCTGCTGAACTTTGATGTT 58.803 29.630 5.41 0.00 31.02 2.71
4361 6140 2.780010 AGGTAGCATTCCTGGCTTGTAT 59.220 45.455 0.00 0.00 42.62 2.29
4371 6150 1.227674 CGGCAGGAGGTAGCATTCC 60.228 63.158 0.00 0.00 0.00 3.01
4378 6157 1.404479 AACACACACGGCAGGAGGTA 61.404 55.000 0.00 0.00 0.00 3.08
4434 6214 0.250234 CTGAAGATGCGGGACTGGAA 59.750 55.000 0.00 0.00 0.00 3.53
4511 6291 3.619979 GCTGCTGTCCAGGTATTTGTACT 60.620 47.826 0.00 0.00 42.03 2.73
4512 6292 2.678336 GCTGCTGTCCAGGTATTTGTAC 59.322 50.000 0.00 0.00 42.03 2.90
4513 6293 2.304470 TGCTGCTGTCCAGGTATTTGTA 59.696 45.455 0.00 0.00 42.03 2.41
4514 6294 1.073763 TGCTGCTGTCCAGGTATTTGT 59.926 47.619 0.00 0.00 42.03 2.83
4515 6295 1.741706 CTGCTGCTGTCCAGGTATTTG 59.258 52.381 0.00 0.00 42.03 2.32
4516 6296 1.952367 GCTGCTGCTGTCCAGGTATTT 60.952 52.381 8.53 0.00 42.03 1.40
4517 6297 0.393537 GCTGCTGCTGTCCAGGTATT 60.394 55.000 8.53 0.00 42.03 1.89
4518 6298 1.222936 GCTGCTGCTGTCCAGGTAT 59.777 57.895 8.53 0.00 42.03 2.73
4521 6301 2.281970 TTGCTGCTGCTGTCCAGG 60.282 61.111 17.00 0.00 42.03 4.45
4545 6325 1.229336 AGAGTGAGGTGTCCTGGGG 60.229 63.158 0.00 0.00 31.76 4.96
4552 6338 3.209410 CTTGCTTTTGAGAGTGAGGTGT 58.791 45.455 0.00 0.00 0.00 4.16
4566 6352 3.137360 AGAGACAGGACTTTCCTTGCTTT 59.863 43.478 0.00 0.00 46.91 3.51
4567 6353 2.708325 AGAGACAGGACTTTCCTTGCTT 59.292 45.455 0.00 0.00 46.91 3.91
4568 6354 2.038295 CAGAGACAGGACTTTCCTTGCT 59.962 50.000 0.00 0.00 46.91 3.91
4645 6432 1.336440 TGTGGCAATTTGTTCTCGGTG 59.664 47.619 0.00 0.00 0.00 4.94
4840 6634 3.868077 GCAAGTCTACAGTCACATCCATC 59.132 47.826 0.00 0.00 0.00 3.51
4851 6645 1.795768 TTTCCGCAGCAAGTCTACAG 58.204 50.000 0.00 0.00 0.00 2.74
4933 6727 5.316167 TGCTACTGATGTCCACTGATTTTT 58.684 37.500 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.