Multiple sequence alignment - TraesCS3D01G321600

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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 TraesCS3D01G321600 chr3D 100.000 2339 0 0 1 2339 434893350 434891012 0.000000e+00 4320.0
1 TraesCS3D01G321600 chr3A 92.471 1315 94 5 54 1365 688910668 688909356 0.000000e+00 1875.0
2 TraesCS3D01G321600 chr2B 91.009 1368 109 10 1 1362 579987488 579986129 0.000000e+00 1832.0
3 TraesCS3D01G321600 chr2B 82.609 69 10 2 2048 2116 488083962 488083896 2.510000e-05 60.2
4 TraesCS3D01G321600 chr7B 89.451 1365 139 5 1 1362 81435097 81433735 0.000000e+00 1718.0
5 TraesCS3D01G321600 chr7B 83.333 624 89 11 1358 1975 568373744 568374358 1.570000e-156 562.0
6 TraesCS3D01G321600 chr7B 79.974 784 120 21 1356 2116 524890388 524889619 5.680000e-151 544.0
7 TraesCS3D01G321600 chr4B 89.231 1365 142 5 1 1361 245673014 245671651 0.000000e+00 1701.0
8 TraesCS3D01G321600 chr4B 75.258 291 53 16 1828 2115 606449567 606449293 1.140000e-23 121.0
9 TraesCS3D01G321600 chr6B 88.808 1367 146 7 1 1362 583184185 583185549 0.000000e+00 1670.0
10 TraesCS3D01G321600 chr2D 85.798 1366 188 6 1 1362 75164028 75165391 0.000000e+00 1443.0
11 TraesCS3D01G321600 chr2D 80.265 755 110 26 1357 2083 644675780 644675037 1.230000e-147 532.0
12 TraesCS3D01G321600 chr2D 79.692 778 115 28 1359 2100 395303600 395302830 2.660000e-144 521.0
13 TraesCS3D01G321600 chr2D 77.571 807 97 34 1355 2113 643654110 643654880 6.020000e-111 411.0
14 TraesCS3D01G321600 chr2D 87.958 191 19 4 2122 2310 470381762 470381950 3.030000e-54 222.0
15 TraesCS3D01G321600 chr4D 86.086 1344 182 5 1 1342 126638011 126639351 0.000000e+00 1441.0
16 TraesCS3D01G321600 chr1A 85.926 1350 187 3 1 1349 260841565 260842912 0.000000e+00 1437.0
17 TraesCS3D01G321600 chr5A 85.537 1369 188 10 1 1362 26539411 26538046 0.000000e+00 1423.0
18 TraesCS3D01G321600 chr6D 84.326 638 88 7 1358 1988 155260323 155260955 4.270000e-172 614.0
19 TraesCS3D01G321600 chr6D 83.444 151 25 0 1970 2120 393408715 393408565 8.710000e-30 141.0
20 TraesCS3D01G321600 chr6D 82.353 153 25 2 1971 2122 386523106 386523257 5.240000e-27 132.0
21 TraesCS3D01G321600 chr5B 80.357 784 115 29 1359 2117 692745674 692746443 2.030000e-155 558.0
22 TraesCS3D01G321600 chr5B 89.011 182 16 4 2131 2310 687881557 687881378 3.030000e-54 222.0
23 TraesCS3D01G321600 chr5B 86.058 208 24 4 2106 2312 271098564 271098767 3.910000e-53 219.0
24 TraesCS3D01G321600 chr5D 80.000 775 125 21 1355 2116 566065582 566066339 1.580000e-151 545.0
25 TraesCS3D01G321600 chr5D 89.000 200 18 4 2114 2312 532757613 532757417 6.460000e-61 244.0
26 TraesCS3D01G321600 chr5D 91.111 180 15 1 2131 2310 350759379 350759201 2.320000e-60 243.0
27 TraesCS3D01G321600 chr5D 87.000 200 22 4 2114 2312 443306435 443306631 3.030000e-54 222.0
28 TraesCS3D01G321600 chr5D 86.124 209 24 4 2106 2313 394834472 394834268 1.090000e-53 220.0
29 TraesCS3D01G321600 chr5D 84.564 149 23 0 1969 2117 263162640 263162788 5.210000e-32 148.0
30 TraesCS3D01G321600 chrUn 82.087 642 87 12 1364 1988 108409498 108408868 7.410000e-145 523.0
31 TraesCS3D01G321600 chr3B 81.633 588 91 11 1357 1939 790190529 790189954 2.720000e-129 472.0
32 TraesCS3D01G321600 chr6A 79.970 659 107 17 1466 2115 516419069 516418427 1.640000e-126 462.0
33 TraesCS3D01G321600 chr4A 80.112 357 43 18 1978 2313 284627224 284626875 8.350000e-60 241.0
34 TraesCS3D01G321600 chr4A 74.648 355 76 11 1972 2315 501889287 501888936 6.740000e-31 145.0
35 TraesCS3D01G321600 chr1D 90.110 182 18 0 2131 2312 204144174 204144355 1.080000e-58 237.0
36 TraesCS3D01G321600 chr2A 82.353 68 10 2 2049 2116 732203377 732203442 9.030000e-05 58.4


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 TraesCS3D01G321600 chr3D 434891012 434893350 2338 True 4320 4320 100.000 1 2339 1 chr3D.!!$R1 2338
1 TraesCS3D01G321600 chr3A 688909356 688910668 1312 True 1875 1875 92.471 54 1365 1 chr3A.!!$R1 1311
2 TraesCS3D01G321600 chr2B 579986129 579987488 1359 True 1832 1832 91.009 1 1362 1 chr2B.!!$R2 1361
3 TraesCS3D01G321600 chr7B 81433735 81435097 1362 True 1718 1718 89.451 1 1362 1 chr7B.!!$R1 1361
4 TraesCS3D01G321600 chr7B 568373744 568374358 614 False 562 562 83.333 1358 1975 1 chr7B.!!$F1 617
5 TraesCS3D01G321600 chr7B 524889619 524890388 769 True 544 544 79.974 1356 2116 1 chr7B.!!$R2 760
6 TraesCS3D01G321600 chr4B 245671651 245673014 1363 True 1701 1701 89.231 1 1361 1 chr4B.!!$R1 1360
7 TraesCS3D01G321600 chr6B 583184185 583185549 1364 False 1670 1670 88.808 1 1362 1 chr6B.!!$F1 1361
8 TraesCS3D01G321600 chr2D 75164028 75165391 1363 False 1443 1443 85.798 1 1362 1 chr2D.!!$F1 1361
9 TraesCS3D01G321600 chr2D 644675037 644675780 743 True 532 532 80.265 1357 2083 1 chr2D.!!$R2 726
10 TraesCS3D01G321600 chr2D 395302830 395303600 770 True 521 521 79.692 1359 2100 1 chr2D.!!$R1 741
11 TraesCS3D01G321600 chr2D 643654110 643654880 770 False 411 411 77.571 1355 2113 1 chr2D.!!$F3 758
12 TraesCS3D01G321600 chr4D 126638011 126639351 1340 False 1441 1441 86.086 1 1342 1 chr4D.!!$F1 1341
13 TraesCS3D01G321600 chr1A 260841565 260842912 1347 False 1437 1437 85.926 1 1349 1 chr1A.!!$F1 1348
14 TraesCS3D01G321600 chr5A 26538046 26539411 1365 True 1423 1423 85.537 1 1362 1 chr5A.!!$R1 1361
15 TraesCS3D01G321600 chr6D 155260323 155260955 632 False 614 614 84.326 1358 1988 1 chr6D.!!$F1 630
16 TraesCS3D01G321600 chr5B 692745674 692746443 769 False 558 558 80.357 1359 2117 1 chr5B.!!$F2 758
17 TraesCS3D01G321600 chr5D 566065582 566066339 757 False 545 545 80.000 1355 2116 1 chr5D.!!$F3 761
18 TraesCS3D01G321600 chrUn 108408868 108409498 630 True 523 523 82.087 1364 1988 1 chrUn.!!$R1 624
19 TraesCS3D01G321600 chr3B 790189954 790190529 575 True 472 472 81.633 1357 1939 1 chr3B.!!$R1 582
20 TraesCS3D01G321600 chr6A 516418427 516419069 642 True 462 462 79.970 1466 2115 1 chr6A.!!$R1 649

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
613 618 0.247736 GTTGATCGTGCTGGAGAGGT 59.752 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2356 0.040425 CCTCAAACGGGCTTCAAACG 60.04 55.0 0.0 0.0 0.0 3.6 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
46 47 1.071228 TGAGAAGATGCATGGATCCCG 59.929 52.381 22.14 1.00 0.00 5.14
50 52 2.486472 AGATGCATGGATCCCGAATC 57.514 50.000 22.14 10.08 0.00 2.52
95 99 4.134563 CCTAAGGGGGACAATTGTTATCG 58.865 47.826 13.36 0.00 0.00 2.92
168 172 4.227300 TGATTAGACAAACTATGTGGCCCT 59.773 41.667 0.00 0.00 44.12 5.19
292 296 6.543465 TCTGCTTATTATGTGGAGTGGAATTG 59.457 38.462 0.00 0.00 0.00 2.32
330 334 9.538508 GTAAACTAACATATTCTAACGGGATGT 57.461 33.333 0.00 0.00 32.18 3.06
338 342 4.545208 TTCTAACGGGATGTGATGAACA 57.455 40.909 0.00 0.00 44.79 3.18
352 356 3.264964 TGATGAACAACCCCTAACCCTAC 59.735 47.826 0.00 0.00 0.00 3.18
383 387 8.429641 TGTAAGATATGGAAGTTATCTTGTCCC 58.570 37.037 13.53 0.00 43.11 4.46
442 447 1.553248 CACCCTCCCATGTCGAGTAAA 59.447 52.381 6.36 0.00 0.00 2.01
517 522 5.479375 AGGGTCTAGAAGATACGAAACACAA 59.521 40.000 0.00 0.00 0.00 3.33
519 524 6.349944 GGGTCTAGAAGATACGAAACACAAGA 60.350 42.308 0.00 0.00 0.00 3.02
613 618 0.247736 GTTGATCGTGCTGGAGAGGT 59.752 55.000 0.00 0.00 0.00 3.85
694 699 8.826710 CCAAAATGTACGAGAAATGATAGCTAA 58.173 33.333 0.00 0.00 0.00 3.09
724 729 5.456763 GCTTGGTATCTATGGTGGGAAAGAT 60.457 44.000 0.00 0.00 33.42 2.40
757 762 8.271458 TGGTGCATAAGGAATTAACTCAGAATA 58.729 33.333 0.00 0.00 0.00 1.75
996 1004 7.148787 GGAAAGATCGAATATTGTACGGATGTC 60.149 40.741 0.00 0.00 0.00 3.06
1006 1014 1.134521 GTACGGATGTCCTGATGGCAA 60.135 52.381 0.00 0.00 0.00 4.52
1026 1034 5.478407 GCAAAAGCTTTAGCCCTGAAATTA 58.522 37.500 13.10 0.00 43.38 1.40
1068 1076 1.508632 CGGGATGTAACCGCCTAATG 58.491 55.000 0.00 0.00 45.34 1.90
1184 1194 3.978718 TGCATGTGATTTTGTCGTGAA 57.021 38.095 0.00 0.00 0.00 3.18
1196 1206 5.430220 TTTGTCGTGAATAGATTCGAACG 57.570 39.130 0.00 0.00 39.62 3.95
1211 1221 5.633830 TTCGAACGTTGTAATAGAGAGGT 57.366 39.130 5.00 0.00 0.00 3.85
1314 1325 7.864108 AATTGTAATGATCCTCACGAATGAA 57.136 32.000 0.00 0.00 33.30 2.57
1318 1329 7.203218 TGTAATGATCCTCACGAATGAAGTAG 58.797 38.462 0.00 0.00 33.30 2.57
1461 1476 3.939939 TGGCAGTTGCAGCTCCGA 61.940 61.111 0.00 0.00 44.36 4.55
1463 1478 2.666190 GCAGTTGCAGCTCCGACA 60.666 61.111 0.00 0.00 41.59 4.35
1506 1550 0.111446 TCCTCTGCCTCTATCTCCGG 59.889 60.000 0.00 0.00 0.00 5.14
1509 1553 0.261991 TCTGCCTCTATCTCCGGGTT 59.738 55.000 0.00 0.00 0.00 4.11
1614 1658 1.045911 AGACTCCGGGATTCTCTGCC 61.046 60.000 10.86 0.00 0.00 4.85
1673 1723 1.817099 CTCCGCCTGCTCCATGTTC 60.817 63.158 0.00 0.00 0.00 3.18
1679 1729 0.609957 CCTGCTCCATGTTCAAGCCA 60.610 55.000 0.00 0.00 35.12 4.75
1702 1779 4.834453 CTGCTGCTCCGGCTCCTG 62.834 72.222 0.00 0.00 39.59 3.86
1724 1801 1.679898 CTCCGCCTTCTCCACCTTT 59.320 57.895 0.00 0.00 0.00 3.11
1726 1803 0.611714 TCCGCCTTCTCCACCTTTAC 59.388 55.000 0.00 0.00 0.00 2.01
1753 1834 1.156322 ACCTCCTCCTCCTCTTCCCA 61.156 60.000 0.00 0.00 0.00 4.37
1777 1861 1.764054 CCTCCGCCTCTTCCTCCAT 60.764 63.158 0.00 0.00 0.00 3.41
1860 1949 0.602562 GATCTCCTGCTGGATCTCGG 59.397 60.000 13.33 1.07 42.29 4.63
1927 2016 1.448540 CCATGGCGGAGTGTCAGAC 60.449 63.158 0.00 0.00 36.56 3.51
1929 2018 0.817654 CATGGCGGAGTGTCAGACTA 59.182 55.000 1.31 0.00 33.83 2.59
1930 2019 1.410517 CATGGCGGAGTGTCAGACTAT 59.589 52.381 1.31 0.00 33.83 2.12
1931 2020 0.817654 TGGCGGAGTGTCAGACTATG 59.182 55.000 1.31 0.00 33.83 2.23
1932 2021 0.103208 GGCGGAGTGTCAGACTATGG 59.897 60.000 1.31 0.00 33.83 2.74
1933 2022 0.103208 GCGGAGTGTCAGACTATGGG 59.897 60.000 1.31 0.00 33.83 4.00
1934 2023 0.103208 CGGAGTGTCAGACTATGGGC 59.897 60.000 1.31 0.00 33.83 5.36
1935 2024 1.195115 GGAGTGTCAGACTATGGGCA 58.805 55.000 1.31 0.00 33.83 5.36
1936 2025 1.137872 GGAGTGTCAGACTATGGGCAG 59.862 57.143 1.31 0.00 33.83 4.85
1937 2026 2.103373 GAGTGTCAGACTATGGGCAGA 58.897 52.381 1.31 0.00 33.83 4.26
1938 2027 2.100584 GAGTGTCAGACTATGGGCAGAG 59.899 54.545 1.31 0.00 33.83 3.35
1939 2028 0.826715 TGTCAGACTATGGGCAGAGC 59.173 55.000 1.31 0.00 0.00 4.09
1940 2029 0.249238 GTCAGACTATGGGCAGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
1941 2030 0.684479 TCAGACTATGGGCAGAGCGT 60.684 55.000 0.00 0.00 0.00 5.07
1942 2031 0.249238 CAGACTATGGGCAGAGCGTC 60.249 60.000 0.00 0.00 0.00 5.19
1943 2032 1.299468 GACTATGGGCAGAGCGTCG 60.299 63.158 0.00 0.00 0.00 5.12
1944 2033 2.028190 CTATGGGCAGAGCGTCGG 59.972 66.667 0.00 0.00 0.00 4.79
1945 2034 2.441348 TATGGGCAGAGCGTCGGA 60.441 61.111 0.00 0.00 0.00 4.55
1946 2035 2.685387 CTATGGGCAGAGCGTCGGAC 62.685 65.000 0.00 0.00 0.00 4.79
1988 2107 1.383803 AGAGGGAGGAGGTGGATGC 60.384 63.158 0.00 0.00 0.00 3.91
1998 2159 2.576615 GAGGTGGATGCATTAGGGTTC 58.423 52.381 0.00 0.00 0.00 3.62
2023 2184 1.339342 ACGCCGCCCAACTTAAATAGT 60.339 47.619 0.00 0.00 39.32 2.12
2043 2204 1.299976 GGATTCCGTCTTGGGCAGT 59.700 57.895 0.00 0.00 38.76 4.40
2125 2286 3.508840 GGGTTTCCGAGCATGGCG 61.509 66.667 0.00 0.00 0.00 5.69
2132 2293 3.344215 CGAGCATGGCGGAGATGC 61.344 66.667 0.00 0.00 45.56 3.91
2153 2314 2.594592 GGCGTGCCCATATCCACC 60.595 66.667 0.00 0.00 0.00 4.61
2154 2315 2.594592 GCGTGCCCATATCCACCC 60.595 66.667 0.00 0.00 0.00 4.61
2155 2316 2.113139 CGTGCCCATATCCACCCC 59.887 66.667 0.00 0.00 0.00 4.95
2156 2317 2.751731 CGTGCCCATATCCACCCCA 61.752 63.158 0.00 0.00 0.00 4.96
2157 2318 1.853428 GTGCCCATATCCACCCCAT 59.147 57.895 0.00 0.00 0.00 4.00
2158 2319 1.072266 GTGCCCATATCCACCCCATA 58.928 55.000 0.00 0.00 0.00 2.74
2159 2320 1.640670 GTGCCCATATCCACCCCATAT 59.359 52.381 0.00 0.00 0.00 1.78
2160 2321 2.042979 GTGCCCATATCCACCCCATATT 59.957 50.000 0.00 0.00 0.00 1.28
2161 2322 2.726896 TGCCCATATCCACCCCATATTT 59.273 45.455 0.00 0.00 0.00 1.40
2162 2323 3.099141 GCCCATATCCACCCCATATTTG 58.901 50.000 0.00 0.00 0.00 2.32
2163 2324 3.711863 CCCATATCCACCCCATATTTGG 58.288 50.000 0.00 0.00 43.23 3.28
2177 2338 6.192970 CCATATTTGGGCTAGATATAGGGG 57.807 45.833 0.00 0.00 39.56 4.79
2178 2339 5.456763 CCATATTTGGGCTAGATATAGGGGC 60.457 48.000 0.00 0.00 39.56 5.80
2179 2340 3.291626 TTTGGGCTAGATATAGGGGCT 57.708 47.619 0.00 0.00 0.00 5.19
2180 2341 2.254152 TGGGCTAGATATAGGGGCTG 57.746 55.000 0.00 0.00 0.00 4.85
2181 2342 0.833949 GGGCTAGATATAGGGGCTGC 59.166 60.000 0.00 0.00 0.00 5.25
2182 2343 0.833949 GGCTAGATATAGGGGCTGCC 59.166 60.000 11.05 11.05 0.00 4.85
2183 2344 0.461961 GCTAGATATAGGGGCTGCCG 59.538 60.000 13.40 0.00 0.00 5.69
2184 2345 1.115467 CTAGATATAGGGGCTGCCGG 58.885 60.000 13.40 0.00 0.00 6.13
2185 2346 0.412244 TAGATATAGGGGCTGCCGGT 59.588 55.000 13.40 4.51 0.00 5.28
2186 2347 0.905337 AGATATAGGGGCTGCCGGTC 60.905 60.000 13.40 4.90 0.00 4.79
2187 2348 1.152118 ATATAGGGGCTGCCGGTCA 60.152 57.895 13.40 0.00 0.00 4.02
2188 2349 1.194781 ATATAGGGGCTGCCGGTCAG 61.195 60.000 13.40 18.16 45.62 3.51
2211 2372 3.916439 GCGTTTGAAGCCCGTTTG 58.084 55.556 0.00 0.00 0.00 2.93
2212 2373 1.357334 GCGTTTGAAGCCCGTTTGA 59.643 52.632 0.00 0.00 0.00 2.69
2213 2374 0.660300 GCGTTTGAAGCCCGTTTGAG 60.660 55.000 0.00 0.00 0.00 3.02
2214 2375 0.040425 CGTTTGAAGCCCGTTTGAGG 60.040 55.000 0.00 0.00 0.00 3.86
2221 2382 4.675029 CCCGTTTGAGGCGTCCGT 62.675 66.667 3.56 0.00 0.00 4.69
2222 2383 3.110178 CCGTTTGAGGCGTCCGTC 61.110 66.667 3.56 0.00 0.00 4.79
2223 2384 2.049433 CGTTTGAGGCGTCCGTCT 60.049 61.111 3.56 0.00 0.00 4.18
2224 2385 2.372690 CGTTTGAGGCGTCCGTCTG 61.373 63.158 0.00 0.00 0.00 3.51
2225 2386 2.027625 GTTTGAGGCGTCCGTCTGG 61.028 63.158 0.00 0.00 0.00 3.86
2226 2387 3.234630 TTTGAGGCGTCCGTCTGGG 62.235 63.158 0.00 0.00 35.24 4.45
2227 2388 4.988716 TGAGGCGTCCGTCTGGGT 62.989 66.667 0.00 0.00 37.00 4.51
2228 2389 4.131088 GAGGCGTCCGTCTGGGTC 62.131 72.222 0.00 0.00 37.00 4.46
2234 2395 3.294079 GTCCGTCTGGGTCGAAAAA 57.706 52.632 0.00 0.00 37.00 1.94
2251 2412 2.684001 AAAACGTGACTGGTCAGTGA 57.316 45.000 8.49 0.00 42.66 3.41
2252 2413 1.935933 AAACGTGACTGGTCAGTGAC 58.064 50.000 15.24 15.24 42.66 3.67
2260 2421 4.736896 GGTCAGTGACCGGACGGC 62.737 72.222 26.12 2.06 43.14 5.68
2261 2422 4.736896 GTCAGTGACCGGACGGCC 62.737 72.222 9.46 0.00 39.32 6.13
2262 2423 4.988716 TCAGTGACCGGACGGCCT 62.989 66.667 9.46 1.49 39.32 5.19
2263 2424 4.742201 CAGTGACCGGACGGCCTG 62.742 72.222 9.46 0.00 39.32 4.85
2277 2438 4.609018 CCTGCCCGGGCGTATGAG 62.609 72.222 39.00 29.12 45.51 2.90
2278 2439 4.609018 CTGCCCGGGCGTATGAGG 62.609 72.222 39.00 18.56 45.51 3.86
2284 2445 4.171103 GGGCGTATGAGGCGGGTT 62.171 66.667 0.00 0.00 37.59 4.11
2285 2446 2.124860 GGCGTATGAGGCGGGTTT 60.125 61.111 0.00 0.00 0.00 3.27
2286 2447 2.469516 GGCGTATGAGGCGGGTTTG 61.470 63.158 0.00 0.00 0.00 2.93
2287 2448 1.448893 GCGTATGAGGCGGGTTTGA 60.449 57.895 0.00 0.00 0.00 2.69
2288 2449 1.429148 GCGTATGAGGCGGGTTTGAG 61.429 60.000 0.00 0.00 0.00 3.02
2289 2450 0.810031 CGTATGAGGCGGGTTTGAGG 60.810 60.000 0.00 0.00 0.00 3.86
2290 2451 1.095807 GTATGAGGCGGGTTTGAGGC 61.096 60.000 0.00 0.00 0.00 4.70
2291 2452 2.587322 TATGAGGCGGGTTTGAGGCG 62.587 60.000 0.00 0.00 38.03 5.52
2298 2459 4.699522 GGTTTGAGGCGCCCGACT 62.700 66.667 26.15 3.43 35.26 4.18
2299 2460 3.423154 GTTTGAGGCGCCCGACTG 61.423 66.667 26.15 0.00 30.74 3.51
2300 2461 3.936203 TTTGAGGCGCCCGACTGT 61.936 61.111 26.15 1.92 30.74 3.55
2301 2462 2.575893 TTTGAGGCGCCCGACTGTA 61.576 57.895 26.15 0.00 30.74 2.74
2302 2463 2.501223 TTTGAGGCGCCCGACTGTAG 62.501 60.000 26.15 0.00 30.74 2.74
2303 2464 3.138798 GAGGCGCCCGACTGTAGA 61.139 66.667 26.15 0.00 30.74 2.59
2304 2465 2.442272 AGGCGCCCGACTGTAGAT 60.442 61.111 26.15 0.00 28.47 1.98
2305 2466 2.279517 GGCGCCCGACTGTAGATG 60.280 66.667 18.11 0.00 0.00 2.90
2306 2467 2.962253 GCGCCCGACTGTAGATGC 60.962 66.667 0.00 0.00 0.00 3.91
2307 2468 2.808315 CGCCCGACTGTAGATGCT 59.192 61.111 0.00 0.00 0.00 3.79
2308 2469 1.299468 CGCCCGACTGTAGATGCTC 60.299 63.158 0.00 0.00 0.00 4.26
2309 2470 1.729470 CGCCCGACTGTAGATGCTCT 61.729 60.000 0.00 0.00 0.00 4.09
2310 2471 1.319541 GCCCGACTGTAGATGCTCTA 58.680 55.000 0.00 0.00 0.00 2.43
2311 2472 1.681793 GCCCGACTGTAGATGCTCTAA 59.318 52.381 0.00 0.00 29.58 2.10
2312 2473 2.297597 GCCCGACTGTAGATGCTCTAAT 59.702 50.000 0.00 0.00 29.58 1.73
2313 2474 3.243907 GCCCGACTGTAGATGCTCTAATT 60.244 47.826 0.00 0.00 29.58 1.40
2314 2475 4.302455 CCCGACTGTAGATGCTCTAATTG 58.698 47.826 0.00 0.00 29.58 2.32
2315 2476 3.738282 CCGACTGTAGATGCTCTAATTGC 59.262 47.826 0.00 0.00 29.58 3.56
2316 2477 4.363138 CGACTGTAGATGCTCTAATTGCA 58.637 43.478 0.00 0.00 44.95 4.08
2317 2478 4.208047 CGACTGTAGATGCTCTAATTGCAC 59.792 45.833 0.00 0.00 43.59 4.57
2318 2479 4.115516 ACTGTAGATGCTCTAATTGCACG 58.884 43.478 0.00 0.00 43.59 5.34
2319 2480 2.866156 TGTAGATGCTCTAATTGCACGC 59.134 45.455 0.00 0.00 43.59 5.34
2320 2481 2.028420 AGATGCTCTAATTGCACGCA 57.972 45.000 0.00 0.00 43.59 5.24
2321 2482 2.358957 AGATGCTCTAATTGCACGCAA 58.641 42.857 6.95 6.95 43.59 4.85
2322 2483 2.353889 AGATGCTCTAATTGCACGCAAG 59.646 45.455 10.60 0.00 43.59 4.01
2323 2484 0.168788 TGCTCTAATTGCACGCAAGC 59.831 50.000 10.60 8.02 45.62 4.01
2324 2485 0.449388 GCTCTAATTGCACGCAAGCT 59.551 50.000 10.60 2.83 45.62 3.74
2325 2486 1.665679 GCTCTAATTGCACGCAAGCTA 59.334 47.619 10.60 3.82 45.62 3.32
2326 2487 2.537730 GCTCTAATTGCACGCAAGCTAC 60.538 50.000 10.60 0.00 45.62 3.58
2327 2488 2.672874 CTCTAATTGCACGCAAGCTACA 59.327 45.455 10.60 0.00 45.62 2.74
2328 2489 3.270027 TCTAATTGCACGCAAGCTACAT 58.730 40.909 10.60 0.00 45.62 2.29
2329 2490 3.689161 TCTAATTGCACGCAAGCTACATT 59.311 39.130 10.60 1.39 45.62 2.71
2330 2491 3.302365 AATTGCACGCAAGCTACATTT 57.698 38.095 10.60 0.00 45.62 2.32
2331 2492 4.433186 AATTGCACGCAAGCTACATTTA 57.567 36.364 10.60 0.00 45.62 1.40
2332 2493 3.906014 TTGCACGCAAGCTACATTTAA 57.094 38.095 0.00 0.00 45.62 1.52
2333 2494 3.196007 TGCACGCAAGCTACATTTAAC 57.804 42.857 0.00 0.00 45.62 2.01
2334 2495 2.550180 TGCACGCAAGCTACATTTAACA 59.450 40.909 0.00 0.00 45.62 2.41
2335 2496 3.190327 TGCACGCAAGCTACATTTAACAT 59.810 39.130 0.00 0.00 45.62 2.71
2336 2497 3.543494 GCACGCAAGCTACATTTAACATG 59.457 43.478 0.00 0.00 45.62 3.21
2337 2498 4.097714 CACGCAAGCTACATTTAACATGG 58.902 43.478 0.00 0.00 45.62 3.66
2338 2499 3.756434 ACGCAAGCTACATTTAACATGGT 59.244 39.130 0.00 0.00 45.62 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.329596 ACTTCCCTGGTGGCAGATTC 59.670 55.000 0.00 0.00 0.00 2.52
50 52 1.151450 ACAACTTCCCTGGTGGCAG 59.849 57.895 0.00 0.00 0.00 4.85
95 99 5.011023 AGGGTCAATCAAATCAACCACTTTC 59.989 40.000 0.00 0.00 0.00 2.62
168 172 4.809958 TGAAAGAATCCGTTGTACGTCAAA 59.190 37.500 0.00 0.00 40.58 2.69
250 254 4.079253 AGCAGACCATACCGAAAACAAAT 58.921 39.130 0.00 0.00 0.00 2.32
330 334 2.354328 AGGGTTAGGGGTTGTTCATCA 58.646 47.619 0.00 0.00 0.00 3.07
338 342 1.920351 CACCATGTAGGGTTAGGGGTT 59.080 52.381 0.00 0.00 43.89 4.11
352 356 9.784531 AAGATAACTTCCATATCTTACACCATG 57.215 33.333 6.94 0.00 44.35 3.66
442 447 6.476378 ACCTTCATGTGTCTATTAGCAAGTT 58.524 36.000 0.00 0.00 0.00 2.66
517 522 7.275920 CCTTGCTTTACTACATAGGAACATCT 58.724 38.462 0.00 0.00 0.00 2.90
519 524 6.157994 TCCCTTGCTTTACTACATAGGAACAT 59.842 38.462 0.00 0.00 0.00 2.71
694 699 5.190528 CCCACCATAGATACCAAGCTGATAT 59.809 44.000 0.00 0.00 0.00 1.63
724 729 9.474313 AGTTAATTCCTTATGCACCAATTTCTA 57.526 29.630 0.00 0.00 0.00 2.10
757 762 5.370584 TGATCCCCATTGATATCTGAGTTGT 59.629 40.000 3.98 0.00 0.00 3.32
867 875 7.219484 AGCAGCATTAACATTTAGTTTCACT 57.781 32.000 0.00 0.00 41.64 3.41
888 896 3.759618 TCAGCATGTCATGATCAAAAGCA 59.240 39.130 17.24 0.00 37.40 3.91
889 897 4.103357 GTCAGCATGTCATGATCAAAAGC 58.897 43.478 17.24 5.82 37.40 3.51
1006 1014 4.160439 GCCTAATTTCAGGGCTAAAGCTTT 59.840 41.667 17.30 17.30 42.31 3.51
1026 1034 2.365293 CCTTTGTGCCAAAGTTAAGCCT 59.635 45.455 19.68 0.00 0.00 4.58
1147 1157 8.785329 TCACATGCATAGTGAAAACAGTTATA 57.215 30.769 21.82 3.50 42.57 0.98
1184 1194 8.291032 CCTCTCTATTACAACGTTCGAATCTAT 58.709 37.037 0.00 0.00 0.00 1.98
1211 1221 6.486657 AGCAAGTTCATGAGCTACTTTGTTTA 59.513 34.615 12.88 0.00 35.19 2.01
1255 1266 4.739793 TCCTCAAACCAATCCAAAGTCAT 58.260 39.130 0.00 0.00 0.00 3.06
1361 1372 6.111768 TGATCGAAGTAGTACGTAGGTTTC 57.888 41.667 0.00 0.00 0.00 2.78
1377 1392 4.998033 ACGATGAGTAGCTAGATGATCGAA 59.002 41.667 24.72 0.00 36.11 3.71
1474 1515 3.771160 GAGGAGGCCGGAGCGAAA 61.771 66.667 5.05 0.00 41.24 3.46
1506 1550 1.627550 GCTCTTCGCCGAACTCAACC 61.628 60.000 0.00 0.00 0.00 3.77
1509 1553 1.372997 GTGCTCTTCGCCGAACTCA 60.373 57.895 0.00 0.00 38.05 3.41
1673 1723 3.749064 CAGCAGCTGCCTGGCTTG 61.749 66.667 34.39 21.00 41.00 4.01
1706 1783 0.902531 TAAAGGTGGAGAAGGCGGAG 59.097 55.000 0.00 0.00 0.00 4.63
1707 1784 0.611714 GTAAAGGTGGAGAAGGCGGA 59.388 55.000 0.00 0.00 0.00 5.54
1769 1850 1.825474 GACTCGTTGGAGATGGAGGAA 59.175 52.381 0.00 0.00 43.27 3.36
1927 2016 2.028190 CCGACGCTCTGCCCATAG 59.972 66.667 0.00 0.00 0.00 2.23
1929 2018 4.148825 GTCCGACGCTCTGCCCAT 62.149 66.667 0.00 0.00 0.00 4.00
1932 2021 4.148825 ATGGTCCGACGCTCTGCC 62.149 66.667 0.00 0.00 0.00 4.85
1933 2022 2.887568 CATGGTCCGACGCTCTGC 60.888 66.667 0.00 0.00 0.00 4.26
1934 2023 2.202797 CCATGGTCCGACGCTCTG 60.203 66.667 2.57 0.00 0.00 3.35
1935 2024 3.461773 CCCATGGTCCGACGCTCT 61.462 66.667 11.73 0.00 0.00 4.09
1939 2028 3.723235 CTCTGCCCATGGTCCGACG 62.723 68.421 11.73 0.00 0.00 5.12
1940 2029 2.187946 CTCTGCCCATGGTCCGAC 59.812 66.667 11.73 0.00 0.00 4.79
1941 2030 3.785859 GCTCTGCCCATGGTCCGA 61.786 66.667 11.73 0.00 0.00 4.55
1962 2070 0.998945 CCTCCTCCCTCTCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1988 2107 1.523032 GCGTCCCGGAACCCTAATG 60.523 63.158 0.73 0.00 0.00 1.90
2096 2257 1.664306 GAAACCCGACGGTCTGACT 59.336 57.895 13.94 0.00 43.71 3.41
2136 2297 2.594592 GGTGGATATGGGCACGCC 60.595 66.667 0.00 0.00 0.00 5.68
2137 2298 2.594592 GGGTGGATATGGGCACGC 60.595 66.667 0.00 0.00 0.00 5.34
2138 2299 2.067932 ATGGGGTGGATATGGGCACG 62.068 60.000 0.00 0.00 0.00 5.34
2139 2300 1.072266 TATGGGGTGGATATGGGCAC 58.928 55.000 0.00 0.00 0.00 5.01
2140 2301 2.073397 ATATGGGGTGGATATGGGCA 57.927 50.000 0.00 0.00 0.00 5.36
2141 2302 3.099141 CAAATATGGGGTGGATATGGGC 58.901 50.000 0.00 0.00 0.00 5.36
2142 2303 3.711863 CCAAATATGGGGTGGATATGGG 58.288 50.000 0.00 0.00 43.51 4.00
2155 2316 5.370880 AGCCCCTATATCTAGCCCAAATATG 59.629 44.000 0.00 0.00 0.00 1.78
2156 2317 5.370880 CAGCCCCTATATCTAGCCCAAATAT 59.629 44.000 0.00 0.00 0.00 1.28
2157 2318 4.721776 CAGCCCCTATATCTAGCCCAAATA 59.278 45.833 0.00 0.00 0.00 1.40
2158 2319 3.525199 CAGCCCCTATATCTAGCCCAAAT 59.475 47.826 0.00 0.00 0.00 2.32
2159 2320 2.912956 CAGCCCCTATATCTAGCCCAAA 59.087 50.000 0.00 0.00 0.00 3.28
2160 2321 2.551270 CAGCCCCTATATCTAGCCCAA 58.449 52.381 0.00 0.00 0.00 4.12
2161 2322 1.901689 GCAGCCCCTATATCTAGCCCA 60.902 57.143 0.00 0.00 0.00 5.36
2162 2323 0.833949 GCAGCCCCTATATCTAGCCC 59.166 60.000 0.00 0.00 0.00 5.19
2163 2324 0.833949 GGCAGCCCCTATATCTAGCC 59.166 60.000 0.00 0.00 0.00 3.93
2164 2325 0.461961 CGGCAGCCCCTATATCTAGC 59.538 60.000 5.63 0.00 0.00 3.42
2165 2326 1.115467 CCGGCAGCCCCTATATCTAG 58.885 60.000 5.63 0.00 0.00 2.43
2166 2327 0.412244 ACCGGCAGCCCCTATATCTA 59.588 55.000 5.63 0.00 0.00 1.98
2167 2328 0.905337 GACCGGCAGCCCCTATATCT 60.905 60.000 5.63 0.00 0.00 1.98
2168 2329 1.192146 TGACCGGCAGCCCCTATATC 61.192 60.000 5.63 0.00 0.00 1.63
2169 2330 1.152118 TGACCGGCAGCCCCTATAT 60.152 57.895 5.63 0.00 0.00 0.86
2170 2331 1.837051 CTGACCGGCAGCCCCTATA 60.837 63.158 5.63 0.00 37.90 1.31
2171 2332 3.164269 CTGACCGGCAGCCCCTAT 61.164 66.667 5.63 0.00 37.90 2.57
2185 2346 4.257654 TTCAAACGCCCGGGCTGA 62.258 61.111 41.01 33.71 39.32 4.26
2186 2347 3.737172 CTTCAAACGCCCGGGCTG 61.737 66.667 41.01 33.95 39.32 4.85
2193 2354 1.660264 CAAACGGGCTTCAAACGCC 60.660 57.895 0.00 0.00 46.83 5.68
2194 2355 0.660300 CTCAAACGGGCTTCAAACGC 60.660 55.000 0.00 0.00 0.00 4.84
2195 2356 0.040425 CCTCAAACGGGCTTCAAACG 60.040 55.000 0.00 0.00 0.00 3.60
2196 2357 0.318699 GCCTCAAACGGGCTTCAAAC 60.319 55.000 0.00 0.00 45.57 2.93
2197 2358 1.791103 CGCCTCAAACGGGCTTCAAA 61.791 55.000 3.25 0.00 46.73 2.69
2198 2359 2.258013 CGCCTCAAACGGGCTTCAA 61.258 57.895 3.25 0.00 46.73 2.69
2199 2360 2.668212 CGCCTCAAACGGGCTTCA 60.668 61.111 3.25 0.00 46.73 3.02
2200 2361 2.668550 ACGCCTCAAACGGGCTTC 60.669 61.111 3.25 0.00 46.73 3.86
2201 2362 2.668550 GACGCCTCAAACGGGCTT 60.669 61.111 3.25 0.00 46.73 4.35
2202 2363 4.699522 GGACGCCTCAAACGGGCT 62.700 66.667 3.25 0.00 46.73 5.19
2204 2365 4.675029 ACGGACGCCTCAAACGGG 62.675 66.667 0.00 0.00 34.00 5.28
2205 2366 3.110178 GACGGACGCCTCAAACGG 61.110 66.667 0.00 0.00 34.00 4.44
2206 2367 2.049433 AGACGGACGCCTCAAACG 60.049 61.111 0.00 0.00 0.00 3.60
2207 2368 2.027625 CCAGACGGACGCCTCAAAC 61.028 63.158 0.00 0.00 0.00 2.93
2208 2369 2.342279 CCAGACGGACGCCTCAAA 59.658 61.111 0.00 0.00 0.00 2.69
2209 2370 3.691342 CCCAGACGGACGCCTCAA 61.691 66.667 0.00 0.00 0.00 3.02
2210 2371 4.988716 ACCCAGACGGACGCCTCA 62.989 66.667 0.00 0.00 34.64 3.86
2211 2372 4.131088 GACCCAGACGGACGCCTC 62.131 72.222 0.00 0.00 34.64 4.70
2216 2377 3.294079 TTTTTCGACCCAGACGGAC 57.706 52.632 0.00 0.00 34.64 4.79
2231 2392 2.676342 GTCACTGACCAGTCACGTTTTT 59.324 45.455 0.00 0.00 40.20 1.94
2232 2393 2.277084 GTCACTGACCAGTCACGTTTT 58.723 47.619 0.00 0.00 40.20 2.43
2233 2394 1.935933 GTCACTGACCAGTCACGTTT 58.064 50.000 0.00 0.00 40.20 3.60
2234 2395 3.661745 GTCACTGACCAGTCACGTT 57.338 52.632 0.00 0.00 40.20 3.99
2244 2405 4.736896 GGCCGTCCGGTCACTGAC 62.737 72.222 5.28 0.00 40.19 3.51
2245 2406 4.988716 AGGCCGTCCGGTCACTGA 62.989 66.667 13.43 0.00 43.56 3.41
2246 2407 4.742201 CAGGCCGTCCGGTCACTG 62.742 72.222 13.43 11.92 43.56 3.66
2260 2421 4.609018 CTCATACGCCCGGGCAGG 62.609 72.222 42.78 30.38 42.06 4.85
2261 2422 4.609018 CCTCATACGCCCGGGCAG 62.609 72.222 42.78 34.78 42.06 4.85
2267 2428 3.692370 AAACCCGCCTCATACGCCC 62.692 63.158 0.00 0.00 0.00 6.13
2268 2429 2.124860 AAACCCGCCTCATACGCC 60.125 61.111 0.00 0.00 0.00 5.68
2269 2430 1.429148 CTCAAACCCGCCTCATACGC 61.429 60.000 0.00 0.00 0.00 4.42
2270 2431 0.810031 CCTCAAACCCGCCTCATACG 60.810 60.000 0.00 0.00 0.00 3.06
2271 2432 1.095807 GCCTCAAACCCGCCTCATAC 61.096 60.000 0.00 0.00 0.00 2.39
2272 2433 1.223487 GCCTCAAACCCGCCTCATA 59.777 57.895 0.00 0.00 0.00 2.15
2273 2434 2.044946 GCCTCAAACCCGCCTCAT 60.045 61.111 0.00 0.00 0.00 2.90
2274 2435 4.697756 CGCCTCAAACCCGCCTCA 62.698 66.667 0.00 0.00 0.00 3.86
2281 2442 4.699522 AGTCGGGCGCCTCAAACC 62.700 66.667 28.56 7.30 0.00 3.27
2282 2443 2.775032 TACAGTCGGGCGCCTCAAAC 62.775 60.000 28.56 18.35 0.00 2.93
2283 2444 2.501223 CTACAGTCGGGCGCCTCAAA 62.501 60.000 28.56 6.44 0.00 2.69
2284 2445 2.992689 TACAGTCGGGCGCCTCAA 60.993 61.111 28.56 9.30 0.00 3.02
2285 2446 3.449227 CTACAGTCGGGCGCCTCA 61.449 66.667 28.56 10.47 0.00 3.86
2286 2447 2.491022 ATCTACAGTCGGGCGCCTC 61.491 63.158 28.56 15.77 0.00 4.70
2287 2448 2.442272 ATCTACAGTCGGGCGCCT 60.442 61.111 28.56 7.78 0.00 5.52
2288 2449 2.279517 CATCTACAGTCGGGCGCC 60.280 66.667 21.18 21.18 0.00 6.53
2289 2450 2.962253 GCATCTACAGTCGGGCGC 60.962 66.667 0.00 0.00 0.00 6.53
2290 2451 1.299468 GAGCATCTACAGTCGGGCG 60.299 63.158 0.00 0.00 0.00 6.13
2291 2452 4.740235 GAGCATCTACAGTCGGGC 57.260 61.111 0.00 0.00 0.00 6.13
2300 2461 8.835440 TAGCTTGCGTGCAATTAGAGCATCTA 62.835 42.308 15.45 0.31 44.79 1.98
2301 2462 2.353889 CTTGCGTGCAATTAGAGCATCT 59.646 45.455 7.85 0.00 44.79 2.90
2302 2463 2.713011 CTTGCGTGCAATTAGAGCATC 58.287 47.619 7.85 0.00 44.79 3.91
2303 2464 1.202222 GCTTGCGTGCAATTAGAGCAT 60.202 47.619 7.85 0.00 44.79 3.79
2304 2465 0.168788 GCTTGCGTGCAATTAGAGCA 59.831 50.000 7.85 0.00 40.19 4.26
2305 2466 0.449388 AGCTTGCGTGCAATTAGAGC 59.551 50.000 7.85 7.51 35.20 4.09
2306 2467 2.672874 TGTAGCTTGCGTGCAATTAGAG 59.327 45.455 7.85 0.00 35.20 2.43
2307 2468 2.694213 TGTAGCTTGCGTGCAATTAGA 58.306 42.857 7.85 0.55 35.20 2.10
2308 2469 3.680642 ATGTAGCTTGCGTGCAATTAG 57.319 42.857 7.85 0.00 35.20 1.73
2309 2470 4.433186 AAATGTAGCTTGCGTGCAATTA 57.567 36.364 7.85 1.71 35.20 1.40
2310 2471 3.302365 AAATGTAGCTTGCGTGCAATT 57.698 38.095 7.85 2.66 35.20 2.32
2311 2472 4.165779 GTTAAATGTAGCTTGCGTGCAAT 58.834 39.130 7.85 0.00 35.20 3.56
2312 2473 3.003793 TGTTAAATGTAGCTTGCGTGCAA 59.996 39.130 7.12 7.12 34.99 4.08
2313 2474 2.550180 TGTTAAATGTAGCTTGCGTGCA 59.450 40.909 0.00 0.00 34.99 4.57
2314 2475 3.196007 TGTTAAATGTAGCTTGCGTGC 57.804 42.857 0.00 0.00 0.00 5.34
2315 2476 4.097714 CCATGTTAAATGTAGCTTGCGTG 58.902 43.478 0.00 0.00 0.00 5.34
2316 2477 3.756434 ACCATGTTAAATGTAGCTTGCGT 59.244 39.130 0.00 0.00 0.00 5.24
2317 2478 4.355543 ACCATGTTAAATGTAGCTTGCG 57.644 40.909 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.