Multiple sequence alignment - TraesCS7B01G061000

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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 TraesCS7B01G061000 chr7B 100.000 2393 0 0 1 2393 63624010 63621618 0.000000e+00 4420.0
1 TraesCS7B01G061000 chr7B 83.074 514 67 11 294 803 63742120 63741623 1.300000e-122 449.0
2 TraesCS7B01G061000 chr7B 83.200 500 73 11 309 803 63643633 63643140 4.690000e-122 448.0
3 TraesCS7B01G061000 chr7B 82.565 499 79 7 309 803 63642467 63641973 1.310000e-117 433.0
4 TraesCS7B01G061000 chr7B 100.000 31 0 0 2018 2048 63621902 63621872 9.240000e-05 58.4
5 TraesCS7B01G061000 chr7B 100.000 31 0 0 2109 2139 63621993 63621963 9.240000e-05 58.4
6 TraesCS7B01G061000 chr7A 92.345 1633 100 8 13 1623 109362843 109361214 0.000000e+00 2300.0
7 TraesCS7B01G061000 chr7A 83.795 469 70 4 309 774 109761214 109760749 7.850000e-120 440.0
8 TraesCS7B01G061000 chr7A 87.056 394 28 10 1633 2014 109359093 109358711 7.910000e-115 424.0
9 TraesCS7B01G061000 chr7A 93.488 215 11 3 2137 2349 109358590 109358377 1.380000e-82 316.0
10 TraesCS7B01G061000 chr7D 88.025 1762 159 21 13 1752 104939145 104937414 0.000000e+00 2037.0
11 TraesCS7B01G061000 chr7D 85.000 500 67 6 307 801 104940311 104939815 3.550000e-138 501.0
12 TraesCS7B01G061000 chr7D 83.936 498 75 4 309 804 104963241 104962747 2.780000e-129 472.0
13 TraesCS7B01G061000 chr7D 83.301 509 79 5 294 798 104945104 104944598 4.660000e-127 464.0
14 TraesCS7B01G061000 chr7D 90.566 159 13 2 2192 2349 104921228 104921071 2.410000e-50 209.0
15 TraesCS7B01G061000 chr3D 82.367 811 115 16 1061 1849 608856072 608856876 0.000000e+00 680.0
16 TraesCS7B01G061000 chr5D 76.238 101 22 2 1454 1553 448600860 448600761 4.000000e-03 52.8


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 TraesCS7B01G061000 chr7B 63621618 63624010 2392 True 1512.266667 4420 100.0000 1 2393 3 chr7B.!!$R2 2392
1 TraesCS7B01G061000 chr7B 63641973 63643633 1660 True 440.500000 448 82.8825 309 803 2 chr7B.!!$R3 494
2 TraesCS7B01G061000 chr7A 109358377 109362843 4466 True 1013.333333 2300 90.9630 13 2349 3 chr7A.!!$R2 2336
3 TraesCS7B01G061000 chr7D 104937414 104940311 2897 True 1269.000000 2037 86.5125 13 1752 2 chr7D.!!$R4 1739
4 TraesCS7B01G061000 chr7D 104944598 104945104 506 True 464.000000 464 83.3010 294 798 1 chr7D.!!$R2 504
5 TraesCS7B01G061000 chr3D 608856072 608856876 804 False 680.000000 680 82.3670 1061 1849 1 chr3D.!!$F1 788

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
855 3206 0.98423 ACCTCACATATATGGCCGGG 59.016 55.0 16.96 13.95 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 6615 0.027979 CCGCGAACTGCCAATACATG 59.972 55.0 8.23 0.0 42.08 3.21 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
20 1175 3.895232 ACTTCTCGGTAGTCGGTACTA 57.105 47.619 0.00 0.00 39.77 1.82
140 1298 5.439721 TCCACAAGGATCTGGATGTATTTG 58.560 41.667 0.00 0.00 39.61 2.32
154 1312 8.684386 TGGATGTATTTGTCACTTTCTGTAAA 57.316 30.769 0.00 0.00 0.00 2.01
173 1331 4.984146 AAAGGTGCTTTAGAAGAGTCCT 57.016 40.909 0.00 0.00 31.35 3.85
205 1363 3.426787 TTATGGTCTTCGGCCTTTTCA 57.573 42.857 0.00 0.00 0.00 2.69
268 1441 7.646548 ATTATGGGAGCCTCTTTTAGAAAAC 57.353 36.000 0.00 0.00 0.00 2.43
304 1477 3.587061 ACCAATCCTGACATGTTAGGACA 59.413 43.478 34.53 18.79 46.30 4.02
389 1565 3.133003 TCTCTTCTTTCATCGGGTGGATC 59.867 47.826 0.00 0.00 31.28 3.36
455 1631 6.205464 CCAAGTGTGATCTTTGTGACTACATT 59.795 38.462 0.00 0.00 36.53 2.71
503 1679 4.520492 CCTTTCTCTCTGCTCTCCTATCTC 59.480 50.000 0.00 0.00 0.00 2.75
590 2933 4.290985 TCATGAAACCTCCCATTCCTAACA 59.709 41.667 0.00 0.00 0.00 2.41
804 3155 5.044179 ACATGAGATTTGAGATTACCCCCAA 60.044 40.000 0.00 0.00 0.00 4.12
807 3158 7.219601 TGAGATTTGAGATTACCCCCAATAA 57.780 36.000 0.00 0.00 0.00 1.40
848 3199 3.177228 GCTCCCCAGACCTCACATATAT 58.823 50.000 0.00 0.00 0.00 0.86
850 3201 3.517100 CTCCCCAGACCTCACATATATGG 59.483 52.174 16.96 6.31 0.00 2.74
853 3204 2.354103 CCAGACCTCACATATATGGCCG 60.354 54.545 16.96 5.36 0.00 6.13
854 3205 1.902508 AGACCTCACATATATGGCCGG 59.097 52.381 16.96 14.26 0.00 6.13
855 3206 0.984230 ACCTCACATATATGGCCGGG 59.016 55.000 16.96 13.95 0.00 5.73
966 3317 3.418995 CCTCATATCCAGCCCAAATCTG 58.581 50.000 0.00 0.00 0.00 2.90
1018 3369 3.697439 ATGTCGGATTGGGCCCACG 62.697 63.158 28.70 25.68 0.00 4.94
1105 3456 5.016051 ACATATGATCGCAACAAGAGAGT 57.984 39.130 10.38 0.00 0.00 3.24
1116 3467 3.179443 ACAAGAGAGTTGAGTGCGAAA 57.821 42.857 0.00 0.00 0.00 3.46
1187 3538 5.578157 AGATTGGTAGTTACTTTGTGGGT 57.422 39.130 0.00 0.00 0.00 4.51
1211 3564 7.106239 GTCATTTGGACTATGAGAAGGAAAGA 58.894 38.462 0.00 0.00 43.46 2.52
1226 3579 8.446599 AGAAGGAAAGAAATACACGAAGAAAA 57.553 30.769 0.00 0.00 0.00 2.29
1297 3650 5.508200 TGAGTTGGAAAGCATTAAACGTT 57.492 34.783 0.00 0.00 0.00 3.99
1302 3655 4.717991 TGGAAAGCATTAAACGTTCATCG 58.282 39.130 0.00 0.00 46.00 3.84
1309 3662 1.149987 TAAACGTTCATCGGGTGTGC 58.850 50.000 0.00 0.00 44.69 4.57
1313 3666 0.172578 CGTTCATCGGGTGTGCTAGA 59.827 55.000 0.00 0.00 35.71 2.43
1407 3769 3.203086 TTGATGGAGGGTTGGCGCA 62.203 57.895 10.83 0.00 0.00 6.09
1452 3819 5.862678 TGTCTGTCGTAATCATATGGGAA 57.137 39.130 2.13 0.00 0.00 3.97
1498 3866 6.914665 TGGTTTTCCCAGATATCAATGATCT 58.085 36.000 5.32 0.00 38.72 2.75
1511 3879 3.380320 TCAATGATCTTGCATGCCTTGAG 59.620 43.478 16.68 8.11 0.00 3.02
1530 3898 1.153086 GCCCTGGCATGTCGAGAAT 60.153 57.895 2.58 0.00 41.49 2.40
1541 3909 3.283259 TGTCGAGAATCTCTAGCTCCA 57.717 47.619 8.77 0.00 0.00 3.86
1542 3910 3.621558 TGTCGAGAATCTCTAGCTCCAA 58.378 45.455 8.77 0.00 0.00 3.53
1608 3976 0.529992 GCCGGTAGTGGAGGAAATCG 60.530 60.000 1.90 0.00 0.00 3.34
1614 3982 4.277672 CGGTAGTGGAGGAAATCGAGAATA 59.722 45.833 0.00 0.00 0.00 1.75
1631 6110 5.505985 CGAGAATAGAACTAGTGGCAGGTAC 60.506 48.000 0.00 0.00 0.00 3.34
1661 6140 8.088981 TCTATTATTCGTGAAATCTAAGAGGGC 58.911 37.037 0.00 0.00 0.00 5.19
1756 6241 1.074889 TGGCTTTTTAGACCAGGGTCC 59.925 52.381 14.67 0.00 45.59 4.46
1778 6263 0.764890 ACTTGTGGCTAAGTGCTCCA 59.235 50.000 6.87 0.00 39.33 3.86
1798 6283 2.158841 CACACGACCCTTTTTGTATCCG 59.841 50.000 0.00 0.00 0.00 4.18
1807 6292 4.944930 CCCTTTTTGTATCCGTATGAACCA 59.055 41.667 0.00 0.00 0.00 3.67
1863 6354 4.404185 AAAAATGCTCCCCTAAGGAAGT 57.596 40.909 0.00 0.00 46.94 3.01
1886 6377 1.391157 TTGCTCTGGTTGGTTGCCAC 61.391 55.000 0.00 0.00 30.78 5.01
1887 6378 1.827789 GCTCTGGTTGGTTGCCACA 60.828 57.895 0.00 0.00 30.78 4.17
1896 6387 3.068873 GGTTGGTTGCCACATTCAAAGTA 59.931 43.478 0.00 0.00 30.78 2.24
1921 6412 3.188460 TGGCAACACGAAAGATTTCTAGC 59.812 43.478 3.98 1.32 46.17 3.42
1925 6416 2.028385 ACACGAAAGATTTCTAGCCCGT 60.028 45.455 3.98 0.00 35.07 5.28
1944 6435 7.578169 GCCCGTAGCTTAAATGTTACTATAG 57.422 40.000 0.00 0.00 38.99 1.31
2016 6507 8.316640 ACAACAAAAATTGCTTAGTTTTCACA 57.683 26.923 0.00 0.00 32.13 3.58
2019 6510 9.986833 AACAAAAATTGCTTAGTTTTCACATTC 57.013 25.926 0.00 0.00 32.13 2.67
2020 6511 8.327429 ACAAAAATTGCTTAGTTTTCACATTCG 58.673 29.630 0.00 0.00 32.13 3.34
2021 6512 6.452244 AAATTGCTTAGTTTTCACATTCGC 57.548 33.333 0.00 0.00 0.00 4.70
2022 6513 3.181826 TGCTTAGTTTTCACATTCGCG 57.818 42.857 0.00 0.00 0.00 5.87
2024 6515 2.158841 GCTTAGTTTTCACATTCGCGGA 59.841 45.455 6.13 0.00 0.00 5.54
2025 6516 3.725010 GCTTAGTTTTCACATTCGCGGAG 60.725 47.826 6.13 0.00 0.00 4.63
2026 6517 1.878953 AGTTTTCACATTCGCGGAGT 58.121 45.000 6.13 0.00 0.00 3.85
2027 6518 2.218603 AGTTTTCACATTCGCGGAGTT 58.781 42.857 6.13 0.00 0.00 3.01
2028 6519 2.223377 AGTTTTCACATTCGCGGAGTTC 59.777 45.455 6.13 0.00 0.00 3.01
2031 6551 2.561733 TCACATTCGCGGAGTTCTAG 57.438 50.000 6.13 0.00 0.00 2.43
2042 6562 3.556365 GCGGAGTTCTAGGCAGAAATAAC 59.444 47.826 1.78 0.00 42.41 1.89
2055 6575 6.017192 AGGCAGAAATAACCAAATTTGCAAAC 60.017 34.615 15.41 0.00 0.00 2.93
2065 6585 6.784176 ACCAAATTTGCAAACATTTCTTCAC 58.216 32.000 15.41 0.00 0.00 3.18
2077 6597 4.744631 ACATTTCTTCACGGAAATTTGCAC 59.255 37.500 10.49 0.00 42.02 4.57
2095 6615 4.292327 GCACGTGCATAAAACAATCAAC 57.708 40.909 34.52 0.00 41.59 3.18
2096 6616 3.733224 GCACGTGCATAAAACAATCAACA 59.267 39.130 34.52 0.00 41.59 3.33
2097 6617 4.385447 GCACGTGCATAAAACAATCAACAT 59.615 37.500 34.52 0.00 41.59 2.71
2098 6618 5.665943 GCACGTGCATAAAACAATCAACATG 60.666 40.000 34.52 0.00 41.59 3.21
2100 6620 6.580416 CACGTGCATAAAACAATCAACATGTA 59.420 34.615 0.82 0.00 0.00 2.29
2101 6621 7.273164 CACGTGCATAAAACAATCAACATGTAT 59.727 33.333 0.82 0.00 0.00 2.29
2102 6622 7.812191 ACGTGCATAAAACAATCAACATGTATT 59.188 29.630 0.00 0.00 0.00 1.89
2103 6623 8.103320 CGTGCATAAAACAATCAACATGTATTG 58.897 33.333 16.43 16.43 38.71 1.90
2104 6624 8.382130 GTGCATAAAACAATCAACATGTATTGG 58.618 33.333 20.30 7.21 37.40 3.16
2105 6625 7.064371 TGCATAAAACAATCAACATGTATTGGC 59.936 33.333 20.30 14.48 37.40 4.52
2106 6626 7.064371 GCATAAAACAATCAACATGTATTGGCA 59.936 33.333 20.30 7.28 37.40 4.92
2107 6627 8.597227 CATAAAACAATCAACATGTATTGGCAG 58.403 33.333 20.30 4.99 37.40 4.85
2108 6628 5.726980 AACAATCAACATGTATTGGCAGT 57.273 34.783 20.30 5.49 37.40 4.40
2109 6629 5.726980 ACAATCAACATGTATTGGCAGTT 57.273 34.783 20.30 2.27 37.40 3.16
2110 6630 5.713025 ACAATCAACATGTATTGGCAGTTC 58.287 37.500 20.30 0.00 37.40 3.01
2111 6631 4.621068 ATCAACATGTATTGGCAGTTCG 57.379 40.909 0.00 0.00 0.00 3.95
2112 6632 2.161410 TCAACATGTATTGGCAGTTCGC 59.839 45.455 0.00 0.00 41.28 4.70
2113 6633 0.726827 ACATGTATTGGCAGTTCGCG 59.273 50.000 0.00 0.00 43.84 5.87
2114 6634 0.027979 CATGTATTGGCAGTTCGCGG 59.972 55.000 6.13 0.00 43.84 6.46
2115 6635 0.107897 ATGTATTGGCAGTTCGCGGA 60.108 50.000 6.13 0.00 43.84 5.54
2116 6636 0.739462 TGTATTGGCAGTTCGCGGAG 60.739 55.000 6.13 0.00 43.84 4.63
2117 6637 0.739813 GTATTGGCAGTTCGCGGAGT 60.740 55.000 6.13 0.00 43.84 3.85
2118 6638 0.036765 TATTGGCAGTTCGCGGAGTT 60.037 50.000 6.13 0.00 43.84 3.01
2119 6639 1.298859 ATTGGCAGTTCGCGGAGTTC 61.299 55.000 6.13 0.00 43.84 3.01
2120 6640 2.048127 GGCAGTTCGCGGAGTTCT 60.048 61.111 6.13 0.00 43.84 3.01
2121 6641 1.214589 GGCAGTTCGCGGAGTTCTA 59.785 57.895 6.13 0.00 43.84 2.10
2122 6642 0.802607 GGCAGTTCGCGGAGTTCTAG 60.803 60.000 6.13 0.00 43.84 2.43
2123 6643 0.802607 GCAGTTCGCGGAGTTCTAGG 60.803 60.000 6.13 0.00 0.00 3.02
2124 6644 0.802607 CAGTTCGCGGAGTTCTAGGC 60.803 60.000 6.13 0.00 0.00 3.93
2125 6645 1.214589 GTTCGCGGAGTTCTAGGCA 59.785 57.895 6.13 0.00 0.00 4.75
2126 6646 0.802607 GTTCGCGGAGTTCTAGGCAG 60.803 60.000 6.13 0.00 0.00 4.85
2127 6647 0.963856 TTCGCGGAGTTCTAGGCAGA 60.964 55.000 6.13 0.00 0.00 4.26
2128 6648 0.963856 TCGCGGAGTTCTAGGCAGAA 60.964 55.000 6.13 0.00 38.49 3.02
2129 6649 0.108804 CGCGGAGTTCTAGGCAGAAA 60.109 55.000 0.00 0.00 42.41 2.52
2130 6650 1.471676 CGCGGAGTTCTAGGCAGAAAT 60.472 52.381 0.00 1.14 42.41 2.17
2131 6651 2.223735 CGCGGAGTTCTAGGCAGAAATA 60.224 50.000 0.00 0.00 42.41 1.40
2132 6652 3.737047 CGCGGAGTTCTAGGCAGAAATAA 60.737 47.826 0.00 0.00 42.41 1.40
2133 6653 3.556365 GCGGAGTTCTAGGCAGAAATAAC 59.444 47.826 1.78 0.00 42.41 1.89
2134 6654 4.120589 CGGAGTTCTAGGCAGAAATAACC 58.879 47.826 1.78 0.00 42.41 2.85
2135 6655 4.382685 CGGAGTTCTAGGCAGAAATAACCA 60.383 45.833 1.78 0.00 42.41 3.67
2139 6659 7.396540 AGTTCTAGGCAGAAATAACCAAATG 57.603 36.000 1.78 0.00 42.41 2.32
2243 6764 2.534298 CATCACGGCACTAAGACTCTG 58.466 52.381 0.00 0.00 0.00 3.35
2272 6794 6.588348 TGAGAGCAACATTAACATACATCG 57.412 37.500 0.00 0.00 0.00 3.84
2280 6802 8.172484 GCAACATTAACATACATCGAAGTAACA 58.828 33.333 4.40 0.00 0.00 2.41
2315 6837 5.658468 TCAAACAACTCAAATGTTCATGCA 58.342 33.333 0.00 0.00 39.98 3.96
2340 6862 6.366340 AGAGAAGAAAATGGCATCATCATCT 58.634 36.000 15.65 15.65 32.83 2.90
2349 6871 4.980573 TGGCATCATCATCTTCATCATCA 58.019 39.130 0.00 0.00 0.00 3.07
2350 6872 5.570320 TGGCATCATCATCTTCATCATCAT 58.430 37.500 0.00 0.00 0.00 2.45
2351 6873 5.648092 TGGCATCATCATCTTCATCATCATC 59.352 40.000 0.00 0.00 0.00 2.92
2352 6874 5.648092 GGCATCATCATCTTCATCATCATCA 59.352 40.000 0.00 0.00 0.00 3.07
2353 6875 6.319911 GGCATCATCATCTTCATCATCATCAT 59.680 38.462 0.00 0.00 0.00 2.45
2354 6876 7.413644 GCATCATCATCTTCATCATCATCATC 58.586 38.462 0.00 0.00 0.00 2.92
2355 6877 7.066284 GCATCATCATCTTCATCATCATCATCA 59.934 37.037 0.00 0.00 0.00 3.07
2356 6878 9.118300 CATCATCATCTTCATCATCATCATCAT 57.882 33.333 0.00 0.00 0.00 2.45
2357 6879 8.723942 TCATCATCTTCATCATCATCATCATC 57.276 34.615 0.00 0.00 0.00 2.92
2358 6880 8.321353 TCATCATCTTCATCATCATCATCATCA 58.679 33.333 0.00 0.00 0.00 3.07
2359 6881 9.118300 CATCATCTTCATCATCATCATCATCAT 57.882 33.333 0.00 0.00 0.00 2.45
2360 6882 8.723942 TCATCTTCATCATCATCATCATCATC 57.276 34.615 0.00 0.00 0.00 2.92
2361 6883 8.321353 TCATCTTCATCATCATCATCATCATCA 58.679 33.333 0.00 0.00 0.00 3.07
2362 6884 9.118300 CATCTTCATCATCATCATCATCATCAT 57.882 33.333 0.00 0.00 0.00 2.45
2363 6885 8.723942 TCTTCATCATCATCATCATCATCATC 57.276 34.615 0.00 0.00 0.00 2.92
2364 6886 8.321353 TCTTCATCATCATCATCATCATCATCA 58.679 33.333 0.00 0.00 0.00 3.07
2365 6887 9.118300 CTTCATCATCATCATCATCATCATCAT 57.882 33.333 0.00 0.00 0.00 2.45
2366 6888 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2367 6889 7.716998 TCATCATCATCATCATCATCATCATCC 59.283 37.037 0.00 0.00 0.00 3.51
2368 6890 7.200434 TCATCATCATCATCATCATCATCCT 57.800 36.000 0.00 0.00 0.00 3.24
2369 6891 7.633789 TCATCATCATCATCATCATCATCCTT 58.366 34.615 0.00 0.00 0.00 3.36
2370 6892 7.770897 TCATCATCATCATCATCATCATCCTTC 59.229 37.037 0.00 0.00 0.00 3.46
2371 6893 6.415573 TCATCATCATCATCATCATCCTTCC 58.584 40.000 0.00 0.00 0.00 3.46
2372 6894 6.215636 TCATCATCATCATCATCATCCTTCCT 59.784 38.462 0.00 0.00 0.00 3.36
2373 6895 6.449830 TCATCATCATCATCATCCTTCCTT 57.550 37.500 0.00 0.00 0.00 3.36
2374 6896 6.473758 TCATCATCATCATCATCCTTCCTTC 58.526 40.000 0.00 0.00 0.00 3.46
2375 6897 5.238624 TCATCATCATCATCCTTCCTTCC 57.761 43.478 0.00 0.00 0.00 3.46
2376 6898 4.661709 TCATCATCATCATCCTTCCTTCCA 59.338 41.667 0.00 0.00 0.00 3.53
2377 6899 5.312443 TCATCATCATCATCCTTCCTTCCAT 59.688 40.000 0.00 0.00 0.00 3.41
2378 6900 5.658198 TCATCATCATCCTTCCTTCCATT 57.342 39.130 0.00 0.00 0.00 3.16
2379 6901 6.022107 TCATCATCATCCTTCCTTCCATTT 57.978 37.500 0.00 0.00 0.00 2.32
2380 6902 6.437755 TCATCATCATCCTTCCTTCCATTTT 58.562 36.000 0.00 0.00 0.00 1.82
2381 6903 6.322969 TCATCATCATCCTTCCTTCCATTTTG 59.677 38.462 0.00 0.00 0.00 2.44
2382 6904 5.829986 TCATCATCCTTCCTTCCATTTTGA 58.170 37.500 0.00 0.00 0.00 2.69
2383 6905 5.653769 TCATCATCCTTCCTTCCATTTTGAC 59.346 40.000 0.00 0.00 0.00 3.18
2384 6906 4.996793 TCATCCTTCCTTCCATTTTGACA 58.003 39.130 0.00 0.00 0.00 3.58
2385 6907 5.582953 TCATCCTTCCTTCCATTTTGACAT 58.417 37.500 0.00 0.00 0.00 3.06
2386 6908 6.018469 TCATCCTTCCTTCCATTTTGACATT 58.982 36.000 0.00 0.00 0.00 2.71
2387 6909 6.497954 TCATCCTTCCTTCCATTTTGACATTT 59.502 34.615 0.00 0.00 0.00 2.32
2388 6910 6.345096 TCCTTCCTTCCATTTTGACATTTC 57.655 37.500 0.00 0.00 0.00 2.17
2389 6911 5.837979 TCCTTCCTTCCATTTTGACATTTCA 59.162 36.000 0.00 0.00 0.00 2.69
2390 6912 6.326064 TCCTTCCTTCCATTTTGACATTTCAA 59.674 34.615 0.00 0.00 40.14 2.69
2391 6913 7.016465 TCCTTCCTTCCATTTTGACATTTCAAT 59.984 33.333 0.00 0.00 41.50 2.57
2392 6914 8.313292 CCTTCCTTCCATTTTGACATTTCAATA 58.687 33.333 0.00 0.00 41.50 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.777832 AGTACCGACTACCGAGAAGT 57.222 50.000 0.00 0.00 41.76 3.01
10 11 4.916183 ACCTTGTAGAAGTAGTACCGACT 58.084 43.478 0.00 0.00 39.92 4.18
11 12 4.095632 GGACCTTGTAGAAGTAGTACCGAC 59.904 50.000 0.00 0.00 0.00 4.79
20 1175 5.152934 TGAAACCTAGGACCTTGTAGAAGT 58.847 41.667 17.98 0.00 0.00 3.01
31 1186 4.338400 AGCAAACTTGTTGAAACCTAGGAC 59.662 41.667 17.98 2.78 0.00 3.85
140 1298 5.500645 AAAGCACCTTTACAGAAAGTGAC 57.499 39.130 0.00 0.00 40.53 3.67
154 1312 3.558109 GCAAGGACTCTTCTAAAGCACCT 60.558 47.826 0.00 0.00 0.00 4.00
173 1331 6.037830 GCCGAAGACCATAAATTAAGTAGCAA 59.962 38.462 0.00 0.00 0.00 3.91
249 1407 6.002082 TGTTAGTTTTCTAAAAGAGGCTCCC 58.998 40.000 11.71 0.00 42.99 4.30
268 1441 8.739039 TGTCAGGATTGGTAATTCAAATGTTAG 58.261 33.333 0.00 0.00 0.00 2.34
389 1565 1.702886 GCATCGTCGTAGGATCATGG 58.297 55.000 0.00 0.00 0.00 3.66
406 1582 1.033574 CTGTTTACCAAAACCCCGCA 58.966 50.000 0.00 0.00 43.66 5.69
503 1679 0.252012 AGGAGTGGGAGTGGAGACAG 60.252 60.000 0.00 0.00 44.46 3.51
590 2933 6.032956 TGATGAGTTACGTCCAAGTGTATT 57.967 37.500 0.00 0.00 33.92 1.89
757 3108 8.791327 TGTGATGTGATGTGTATGTTCTATTT 57.209 30.769 0.00 0.00 0.00 1.40
762 3113 6.536224 TCTCATGTGATGTGATGTGTATGTTC 59.464 38.462 0.00 0.00 0.00 3.18
765 3116 7.492352 AATCTCATGTGATGTGATGTGTATG 57.508 36.000 10.87 0.00 41.21 2.39
804 3155 4.307432 CCGACCGTAAATGCTCTCATTAT 58.693 43.478 0.00 0.00 41.77 1.28
807 3158 1.202533 CCCGACCGTAAATGCTCTCAT 60.203 52.381 0.00 0.00 33.53 2.90
835 3186 1.066143 CCCGGCCATATATGTGAGGTC 60.066 57.143 11.73 0.00 0.00 3.85
899 3250 1.802880 GCATGTATGAAGCGTCCGTCT 60.803 52.381 0.00 0.00 0.00 4.18
937 3288 1.542108 GCTGGATATGAGGGTGTCAGC 60.542 57.143 0.00 0.00 39.07 4.26
966 3317 1.349357 GGGGCTCACCATATCTTCTCC 59.651 57.143 0.00 0.00 42.91 3.71
970 3321 1.418908 CCCGGGGCTCACCATATCTT 61.419 60.000 14.71 0.00 42.91 2.40
1026 3377 0.810031 AATGTATGTGGAGTCGCGGC 60.810 55.000 0.21 0.21 0.00 6.53
1029 3380 1.852895 GACGAATGTATGTGGAGTCGC 59.147 52.381 0.00 0.00 31.89 5.19
1105 3456 2.797792 GCAACCATTGTTTCGCACTCAA 60.798 45.455 0.00 0.00 30.42 3.02
1113 3464 6.843069 AACATTGTAAGCAACCATTGTTTC 57.157 33.333 0.00 0.00 37.44 2.78
1116 3467 5.911752 TCAAACATTGTAAGCAACCATTGT 58.088 33.333 0.00 0.00 37.44 2.71
1187 3538 7.257790 TCTTTCCTTCTCATAGTCCAAATGA 57.742 36.000 0.00 0.00 32.56 2.57
1211 3564 9.673454 GAGTTTGGTAATTTTCTTCGTGTATTT 57.327 29.630 0.00 0.00 0.00 1.40
1244 3597 4.819769 TCGATCAATGAACTGATGTGTCA 58.180 39.130 0.00 0.00 36.15 3.58
1297 3650 1.775385 TGATCTAGCACACCCGATGA 58.225 50.000 0.00 0.00 0.00 2.92
1302 3655 3.786656 TGCATGATCTAGCACACCC 57.213 52.632 8.30 0.00 35.51 4.61
1309 3662 2.876550 CACATGGTGGTGCATGATCTAG 59.123 50.000 0.00 0.00 33.38 2.43
1313 3666 1.272037 TGACACATGGTGGTGCATGAT 60.272 47.619 0.00 0.00 42.55 2.45
1407 3769 5.280654 ACAAAAGATGCTCCAACAATTGT 57.719 34.783 4.92 4.92 0.00 2.71
1452 3819 2.551270 TGCTGAGGAACCTAGGAACAT 58.449 47.619 17.98 6.29 0.00 2.71
1511 3879 2.615227 ATTCTCGACATGCCAGGGCC 62.615 60.000 8.02 0.00 41.09 5.80
1530 3898 4.802307 AGATCATGAGTTGGAGCTAGAGA 58.198 43.478 0.09 0.00 0.00 3.10
1541 3909 7.667219 ACTTTGTCCAACATAAGATCATGAGTT 59.333 33.333 0.09 0.00 0.00 3.01
1542 3910 7.120285 CACTTTGTCCAACATAAGATCATGAGT 59.880 37.037 0.09 0.00 0.00 3.41
1608 3976 5.505985 CGTACCTGCCACTAGTTCTATTCTC 60.506 48.000 0.00 0.00 0.00 2.87
1614 3982 1.183549 CCGTACCTGCCACTAGTTCT 58.816 55.000 0.00 0.00 0.00 3.01
1631 6110 9.459640 TCTTAGATTTCACGAATAATAGAACCG 57.540 33.333 0.00 0.00 0.00 4.44
1661 6140 2.653890 CAACTTGCAAACTGATGTCGG 58.346 47.619 0.00 0.00 0.00 4.79
1778 6263 2.224354 ACGGATACAAAAAGGGTCGTGT 60.224 45.455 0.00 0.00 0.00 4.49
1782 6267 5.065602 GGTTCATACGGATACAAAAAGGGTC 59.934 44.000 0.00 0.00 0.00 4.46
1863 6354 1.108727 CAACCAACCAGAGCAAGGCA 61.109 55.000 0.00 0.00 0.00 4.75
1886 6377 4.154015 TCGTGTTGCCATCTACTTTGAATG 59.846 41.667 0.00 0.00 0.00 2.67
1887 6378 4.323417 TCGTGTTGCCATCTACTTTGAAT 58.677 39.130 0.00 0.00 0.00 2.57
1896 6387 4.074970 AGAAATCTTTCGTGTTGCCATCT 58.925 39.130 0.00 0.00 41.92 2.90
1906 6397 3.737355 GCTACGGGCTAGAAATCTTTCGT 60.737 47.826 0.00 0.00 38.86 3.85
2014 6505 0.179108 GCCTAGAACTCCGCGAATGT 60.179 55.000 8.23 0.00 0.00 2.71
2015 6506 0.179111 TGCCTAGAACTCCGCGAATG 60.179 55.000 8.23 0.00 0.00 2.67
2016 6507 0.103208 CTGCCTAGAACTCCGCGAAT 59.897 55.000 8.23 0.00 0.00 3.34
2019 6510 0.108804 TTTCTGCCTAGAACTCCGCG 60.109 55.000 0.00 0.00 42.41 6.46
2020 6511 2.317530 ATTTCTGCCTAGAACTCCGC 57.682 50.000 0.00 0.00 42.41 5.54
2021 6512 4.120589 GGTTATTTCTGCCTAGAACTCCG 58.879 47.826 0.00 0.00 42.41 4.63
2022 6513 5.099042 TGGTTATTTCTGCCTAGAACTCC 57.901 43.478 0.00 0.00 42.41 3.85
2024 6515 8.306761 CAAATTTGGTTATTTCTGCCTAGAACT 58.693 33.333 10.49 0.00 42.41 3.01
2025 6516 7.063426 GCAAATTTGGTTATTTCTGCCTAGAAC 59.937 37.037 19.47 0.00 42.41 3.01
2026 6517 7.096551 GCAAATTTGGTTATTTCTGCCTAGAA 58.903 34.615 19.47 0.00 41.06 2.10
2027 6518 6.210385 TGCAAATTTGGTTATTTCTGCCTAGA 59.790 34.615 19.47 0.00 0.00 2.43
2028 6519 6.397272 TGCAAATTTGGTTATTTCTGCCTAG 58.603 36.000 19.47 0.00 0.00 3.02
2031 6551 5.938438 TTGCAAATTTGGTTATTTCTGCC 57.062 34.783 19.47 0.00 0.00 4.85
2042 6562 5.902981 CGTGAAGAAATGTTTGCAAATTTGG 59.097 36.000 16.21 2.11 0.00 3.28
2055 6575 4.143556 CGTGCAAATTTCCGTGAAGAAATG 60.144 41.667 0.00 0.00 43.90 2.32
2077 6597 7.739022 ATACATGTTGATTGTTTTATGCACG 57.261 32.000 2.30 0.00 0.00 5.34
2090 6610 3.181497 GCGAACTGCCAATACATGTTGAT 60.181 43.478 2.30 0.00 37.76 2.57
2092 6612 2.518949 GCGAACTGCCAATACATGTTG 58.481 47.619 2.30 0.00 37.76 3.33
2094 6614 0.726827 CGCGAACTGCCAATACATGT 59.273 50.000 0.00 2.69 42.08 3.21
2095 6615 0.027979 CCGCGAACTGCCAATACATG 59.972 55.000 8.23 0.00 42.08 3.21
2096 6616 0.107897 TCCGCGAACTGCCAATACAT 60.108 50.000 8.23 0.00 42.08 2.29
2097 6617 0.739462 CTCCGCGAACTGCCAATACA 60.739 55.000 8.23 0.00 42.08 2.29
2098 6618 0.739813 ACTCCGCGAACTGCCAATAC 60.740 55.000 8.23 0.00 42.08 1.89
2100 6620 1.298859 GAACTCCGCGAACTGCCAAT 61.299 55.000 8.23 0.00 42.08 3.16
2101 6621 1.959226 GAACTCCGCGAACTGCCAA 60.959 57.895 8.23 0.00 42.08 4.52
2102 6622 1.529152 TAGAACTCCGCGAACTGCCA 61.529 55.000 8.23 0.00 42.08 4.92
2103 6623 0.802607 CTAGAACTCCGCGAACTGCC 60.803 60.000 8.23 0.00 42.08 4.85
2104 6624 0.802607 CCTAGAACTCCGCGAACTGC 60.803 60.000 8.23 0.00 41.47 4.40
2105 6625 0.802607 GCCTAGAACTCCGCGAACTG 60.803 60.000 8.23 0.00 0.00 3.16
2106 6626 1.248785 TGCCTAGAACTCCGCGAACT 61.249 55.000 8.23 1.54 0.00 3.01
2107 6627 0.802607 CTGCCTAGAACTCCGCGAAC 60.803 60.000 8.23 0.00 0.00 3.95
2108 6628 0.963856 TCTGCCTAGAACTCCGCGAA 60.964 55.000 8.23 0.00 0.00 4.70
2109 6629 0.963856 TTCTGCCTAGAACTCCGCGA 60.964 55.000 8.23 0.00 37.99 5.87
2110 6630 0.108804 TTTCTGCCTAGAACTCCGCG 60.109 55.000 0.00 0.00 42.41 6.46
2111 6631 2.317530 ATTTCTGCCTAGAACTCCGC 57.682 50.000 0.00 0.00 42.41 5.54
2112 6632 4.120589 GGTTATTTCTGCCTAGAACTCCG 58.879 47.826 0.00 0.00 42.41 4.63
2113 6633 5.099042 TGGTTATTTCTGCCTAGAACTCC 57.901 43.478 0.00 0.00 42.41 3.85
2114 6634 7.121315 ACATTTGGTTATTTCTGCCTAGAACTC 59.879 37.037 0.00 0.00 42.41 3.01
2115 6635 6.948309 ACATTTGGTTATTTCTGCCTAGAACT 59.052 34.615 0.00 0.00 42.41 3.01
2116 6636 7.158099 ACATTTGGTTATTTCTGCCTAGAAC 57.842 36.000 0.00 0.00 42.41 3.01
2117 6637 7.775053 AACATTTGGTTATTTCTGCCTAGAA 57.225 32.000 0.00 0.00 38.37 2.10
2118 6638 7.775053 AAACATTTGGTTATTTCTGCCTAGA 57.225 32.000 0.00 0.00 39.29 2.43
2120 6640 9.868277 CAATAAACATTTGGTTATTTCTGCCTA 57.132 29.630 10.20 0.00 43.25 3.93
2121 6641 7.334171 GCAATAAACATTTGGTTATTTCTGCCT 59.666 33.333 10.20 0.00 43.25 4.75
2122 6642 7.413988 GGCAATAAACATTTGGTTATTTCTGCC 60.414 37.037 19.24 19.24 44.74 4.85
2123 6643 7.118971 TGGCAATAAACATTTGGTTATTTCTGC 59.881 33.333 10.20 11.28 43.25 4.26
2124 6644 8.442384 GTGGCAATAAACATTTGGTTATTTCTG 58.558 33.333 10.20 3.34 43.25 3.02
2125 6645 8.153550 TGTGGCAATAAACATTTGGTTATTTCT 58.846 29.630 10.20 0.00 43.25 2.52
2126 6646 8.316640 TGTGGCAATAAACATTTGGTTATTTC 57.683 30.769 10.20 6.54 43.25 2.17
2127 6647 8.682936 TTGTGGCAATAAACATTTGGTTATTT 57.317 26.923 10.20 0.00 43.25 1.40
2128 6648 8.682936 TTTGTGGCAATAAACATTTGGTTATT 57.317 26.923 7.60 7.60 45.77 1.40
2129 6649 8.682936 TTTTGTGGCAATAAACATTTGGTTAT 57.317 26.923 0.00 0.00 39.44 1.89
2130 6650 8.506168 TTTTTGTGGCAATAAACATTTGGTTA 57.494 26.923 0.00 0.00 39.29 2.85
2131 6651 7.396540 TTTTTGTGGCAATAAACATTTGGTT 57.603 28.000 0.00 0.00 42.98 3.67
2243 6764 5.801350 TGTTAATGTTGCTCTCATGCTAC 57.199 39.130 0.00 0.00 38.72 3.58
2272 6794 6.925610 TTGATGCATCACCTATGTTACTTC 57.074 37.500 28.72 0.00 37.93 3.01
2280 6802 5.255687 TGAGTTGTTTGATGCATCACCTAT 58.744 37.500 28.72 12.73 36.36 2.57
2283 6805 3.921119 TGAGTTGTTTGATGCATCACC 57.079 42.857 28.72 21.14 36.36 4.02
2285 6807 5.845103 ACATTTGAGTTGTTTGATGCATCA 58.155 33.333 25.42 25.42 34.44 3.07
2315 6837 6.834451 AGATGATGATGCCATTTTCTTCTCTT 59.166 34.615 2.38 0.00 32.09 2.85
2340 6862 9.113838 GATGATGATGATGATGATGATGATGAA 57.886 33.333 0.00 0.00 0.00 2.57
2349 6871 6.644308 AGGAAGGATGATGATGATGATGAT 57.356 37.500 0.00 0.00 0.00 2.45
2350 6872 6.449830 AAGGAAGGATGATGATGATGATGA 57.550 37.500 0.00 0.00 0.00 2.92
2351 6873 5.648526 GGAAGGAAGGATGATGATGATGATG 59.351 44.000 0.00 0.00 0.00 3.07
2352 6874 5.312443 TGGAAGGAAGGATGATGATGATGAT 59.688 40.000 0.00 0.00 0.00 2.45
2353 6875 4.661709 TGGAAGGAAGGATGATGATGATGA 59.338 41.667 0.00 0.00 0.00 2.92
2354 6876 4.981812 TGGAAGGAAGGATGATGATGATG 58.018 43.478 0.00 0.00 0.00 3.07
2355 6877 5.862422 ATGGAAGGAAGGATGATGATGAT 57.138 39.130 0.00 0.00 0.00 2.45
2356 6878 5.658198 AATGGAAGGAAGGATGATGATGA 57.342 39.130 0.00 0.00 0.00 2.92
2357 6879 6.322969 TCAAAATGGAAGGAAGGATGATGATG 59.677 38.462 0.00 0.00 0.00 3.07
2358 6880 6.323225 GTCAAAATGGAAGGAAGGATGATGAT 59.677 38.462 0.00 0.00 0.00 2.45
2359 6881 5.653769 GTCAAAATGGAAGGAAGGATGATGA 59.346 40.000 0.00 0.00 0.00 2.92
2360 6882 5.419788 TGTCAAAATGGAAGGAAGGATGATG 59.580 40.000 0.00 0.00 0.00 3.07
2361 6883 5.582953 TGTCAAAATGGAAGGAAGGATGAT 58.417 37.500 0.00 0.00 0.00 2.45
2362 6884 4.996793 TGTCAAAATGGAAGGAAGGATGA 58.003 39.130 0.00 0.00 0.00 2.92
2363 6885 5.927281 ATGTCAAAATGGAAGGAAGGATG 57.073 39.130 0.00 0.00 0.00 3.51
2364 6886 6.497954 TGAAATGTCAAAATGGAAGGAAGGAT 59.502 34.615 0.00 0.00 0.00 3.24
2365 6887 5.837979 TGAAATGTCAAAATGGAAGGAAGGA 59.162 36.000 0.00 0.00 0.00 3.36
2366 6888 6.100404 TGAAATGTCAAAATGGAAGGAAGG 57.900 37.500 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.