Multiple sequence alignment - TraesCS5B01G536400

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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 TraesCS5B01G536400 chr5B 100.000 4574 0 0 1 4574 692512687 692508114 0.000000e+00 8447.0
1 TraesCS5B01G536400 chr5B 88.446 1705 165 14 1909 3587 693204459 693206157 0.000000e+00 2028.0
2 TraesCS5B01G536400 chr5B 86.641 1789 203 16 1868 3626 540741542 540739760 0.000000e+00 1947.0
3 TraesCS5B01G536400 chr5B 86.381 536 60 11 127 660 411383864 411383340 1.430000e-159 573.0
4 TraesCS5B01G536400 chr5B 82.589 672 71 19 127 764 411382070 411381411 6.690000e-153 551.0
5 TraesCS5B01G536400 chr5B 77.612 737 119 35 1012 1716 693202843 693203565 5.510000e-109 405.0
6 TraesCS5B01G536400 chr5B 76.446 726 106 44 1029 1732 540742821 540742139 2.640000e-87 333.0
7 TraesCS5B01G536400 chr5D 94.274 2742 102 11 1866 4570 548322753 548320030 0.000000e+00 4143.0
8 TraesCS5B01G536400 chr5D 89.097 1706 155 13 1908 3587 559107529 559109229 0.000000e+00 2091.0
9 TraesCS5B01G536400 chr5D 86.755 1744 202 14 1868 3585 444080757 444079017 0.000000e+00 1914.0
10 TraesCS5B01G536400 chr5D 84.816 461 48 15 1293 1748 548323535 548323092 1.170000e-120 444.0
11 TraesCS5B01G536400 chr5D 85.503 338 38 3 3374 3706 548313607 548313276 4.380000e-90 342.0
12 TraesCS5B01G536400 chr5D 84.659 176 25 2 1557 1732 444081524 444081351 1.690000e-39 174.0
13 TraesCS5B01G536400 chr4A 93.630 2025 80 15 2571 4570 619148065 619146065 0.000000e+00 2979.0
14 TraesCS5B01G536400 chr4A 88.674 1704 163 12 1908 3587 612112063 612113760 0.000000e+00 2050.0
15 TraesCS5B01G536400 chr4A 87.354 1455 58 38 1 1387 619161978 619160582 0.000000e+00 1552.0
16 TraesCS5B01G536400 chr4A 95.426 634 15 7 1867 2489 619160322 619159692 0.000000e+00 998.0
17 TraesCS5B01G536400 chr4A 77.762 715 106 39 1029 1716 612110496 612111184 1.540000e-104 390.0
18 TraesCS5B01G536400 chr4A 98.824 85 1 0 2486 2570 619155805 619155721 7.930000e-33 152.0
19 TraesCS5B01G536400 chr5A 87.076 1741 195 14 1871 3585 561110720 561108984 0.000000e+00 1941.0
20 TraesCS5B01G536400 chr5A 85.795 176 23 2 1557 1732 561111496 561111323 7.810000e-43 185.0
21 TraesCS5B01G536400 chr3B 91.324 438 30 4 1917 2347 678830738 678830302 3.940000e-165 592.0
22 TraesCS5B01G536400 chr3B 83.510 661 74 13 3924 4564 2987015 2987660 6.590000e-163 584.0
23 TraesCS5B01G536400 chr1A 91.324 438 30 4 1917 2347 394425365 394424929 3.940000e-165 592.0
24 TraesCS5B01G536400 chr1A 85.795 176 25 0 1557 1732 394426193 394426018 2.170000e-43 187.0
25 TraesCS5B01G536400 chr1A 85.795 176 25 0 1557 1732 394514554 394514379 2.170000e-43 187.0
26 TraesCS5B01G536400 chr4B 81.804 621 66 20 211 795 533793371 533793980 1.150000e-130 477.0
27 TraesCS5B01G536400 chr4B 85.227 176 26 0 1557 1732 77596998 77597173 1.010000e-41 182.0
28 TraesCS5B01G536400 chr2B 85.632 174 25 0 1557 1730 238558667 238558494 2.810000e-42 183.0
29 TraesCS5B01G536400 chr2D 94.118 68 4 0 3825 3892 327614894 327614827 2.250000e-18 104.0
30 TraesCS5B01G536400 chr2D 94.118 68 3 1 3825 3891 8495971 8495904 8.100000e-18 102.0
31 TraesCS5B01G536400 chr2D 90.411 73 6 1 3825 3896 376701193 376701265 1.350000e-15 95.3
32 TraesCS5B01G536400 chr6D 91.026 78 4 3 3822 3896 469492412 469492335 8.100000e-18 102.0
33 TraesCS5B01G536400 chr6D 91.026 78 4 3 3822 3896 469511220 469511143 8.100000e-18 102.0
34 TraesCS5B01G536400 chr2A 94.118 68 3 1 3825 3891 754039018 754039085 8.100000e-18 102.0
35 TraesCS5B01G536400 chr6B 90.909 77 4 3 3822 3895 262114451 262114375 2.910000e-17 100.0
36 TraesCS5B01G536400 chr3A 85.000 60 7 2 820 877 33212688 33212629 4.940000e-05 60.2


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 TraesCS5B01G536400 chr5B 692508114 692512687 4573 True 8447.000000 8447 100.0000 1 4574 1 chr5B.!!$R1 4573
1 TraesCS5B01G536400 chr5B 693202843 693206157 3314 False 1216.500000 2028 83.0290 1012 3587 2 chr5B.!!$F1 2575
2 TraesCS5B01G536400 chr5B 540739760 540742821 3061 True 1140.000000 1947 81.5435 1029 3626 2 chr5B.!!$R3 2597
3 TraesCS5B01G536400 chr5B 411381411 411383864 2453 True 562.000000 573 84.4850 127 764 2 chr5B.!!$R2 637
4 TraesCS5B01G536400 chr5D 548320030 548323535 3505 True 2293.500000 4143 89.5450 1293 4570 2 chr5D.!!$R3 3277
5 TraesCS5B01G536400 chr5D 559107529 559109229 1700 False 2091.000000 2091 89.0970 1908 3587 1 chr5D.!!$F1 1679
6 TraesCS5B01G536400 chr5D 444079017 444081524 2507 True 1044.000000 1914 85.7070 1557 3585 2 chr5D.!!$R2 2028
7 TraesCS5B01G536400 chr4A 619146065 619148065 2000 True 2979.000000 2979 93.6300 2571 4570 1 chr4A.!!$R1 1999
8 TraesCS5B01G536400 chr4A 612110496 612113760 3264 False 1220.000000 2050 83.2180 1029 3587 2 chr4A.!!$F1 2558
9 TraesCS5B01G536400 chr4A 619155721 619161978 6257 True 900.666667 1552 93.8680 1 2570 3 chr4A.!!$R2 2569
10 TraesCS5B01G536400 chr5A 561108984 561111496 2512 True 1063.000000 1941 86.4355 1557 3585 2 chr5A.!!$R1 2028
11 TraesCS5B01G536400 chr3B 2987015 2987660 645 False 584.000000 584 83.5100 3924 4564 1 chr3B.!!$F1 640
12 TraesCS5B01G536400 chr1A 394424929 394426193 1264 True 389.500000 592 88.5595 1557 2347 2 chr1A.!!$R2 790
13 TraesCS5B01G536400 chr4B 533793371 533793980 609 False 477.000000 477 81.8040 211 795 1 chr4B.!!$F2 584

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
899 1046 0.326264 AAATCGCTGAGTCAAGGCCT 59.674 50.0 0.00 0.00 0.00 5.19 F
1635 1903 0.179100 GCTGCTGCTCTCCGATTACA 60.179 55.0 8.53 0.00 36.03 2.41 F
1836 2698 0.179111 TCCTTTCATCGCCTAGCACG 60.179 55.0 0.00 0.00 0.00 5.34 F
1837 2699 0.179111 CCTTTCATCGCCTAGCACGA 60.179 55.0 8.31 8.31 44.75 4.35 F
2700 8366 0.390998 GGCTCACTGCTCCTCTCAAC 60.391 60.0 0.00 0.00 42.39 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2477 0.179111 CGTGCTAGGCGATGAAAGGA 60.179 55.000 0.00 0.00 0.00 3.36 R
2976 8642 0.107263 TCACAAGCAAGCCACTGACA 60.107 50.000 0.00 0.00 0.00 3.58 R
3166 8832 1.453155 ATCAGTGTTGGAACATCGGC 58.547 50.000 0.00 0.00 41.59 5.54 R
3495 9200 1.524482 GATCCTCCCTTTCAGCGCT 59.476 57.895 2.64 2.64 0.00 5.92 R
4023 9881 0.034380 AGCAGCAGCATGACCAAGAT 60.034 50.000 3.17 0.00 45.49 2.40 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.822192 CGACGCCCGGACTCATCA 61.822 66.667 0.73 0.00 33.91 3.07
63 64 1.300931 GCGGTGACTCAAGTGCTGA 60.301 57.895 0.00 0.00 0.00 4.26
68 69 2.610479 GGTGACTCAAGTGCTGATTCGA 60.610 50.000 0.00 0.00 36.70 3.71
133 136 1.202510 ACTACGTTACGGTGCAAACCA 60.203 47.619 10.20 0.00 0.00 3.67
180 184 2.618709 CGGCCATGTATCTCCCTTTTTC 59.381 50.000 2.24 0.00 0.00 2.29
184 188 4.141251 GCCATGTATCTCCCTTTTTCCCTA 60.141 45.833 0.00 0.00 0.00 3.53
278 285 1.531149 CCATAACGCCATCGATCAACC 59.469 52.381 0.00 0.00 39.41 3.77
427 434 6.476380 ACGGTTTTATTCGGGTTTTCTTTTTC 59.524 34.615 0.00 0.00 0.00 2.29
525 536 8.944212 ACGTATTTTCTTTCTTTTGTATTCCG 57.056 30.769 0.00 0.00 0.00 4.30
883 1011 0.536006 GGCCATCTGAGCGCCTAAAT 60.536 55.000 2.29 0.00 39.70 1.40
894 1022 1.640428 CGCCTAAATCGCTGAGTCAA 58.360 50.000 0.00 0.00 0.00 3.18
895 1023 1.590238 CGCCTAAATCGCTGAGTCAAG 59.410 52.381 0.00 0.00 0.00 3.02
899 1046 0.326264 AAATCGCTGAGTCAAGGCCT 59.674 50.000 0.00 0.00 0.00 5.19
961 1123 3.882025 CGCAGCTTCCTGGAAGAC 58.118 61.111 34.70 25.35 41.71 3.01
962 1124 2.097038 CGCAGCTTCCTGGAAGACG 61.097 63.158 34.70 28.17 41.71 4.18
963 1125 1.743252 GCAGCTTCCTGGAAGACGG 60.743 63.158 34.70 25.59 41.71 4.79
964 1126 1.743252 CAGCTTCCTGGAAGACGGC 60.743 63.158 34.70 22.20 41.71 5.68
965 1127 2.815647 GCTTCCTGGAAGACGGCG 60.816 66.667 34.70 12.91 41.71 6.46
966 1128 2.125512 CTTCCTGGAAGACGGCGG 60.126 66.667 28.57 2.93 41.71 6.13
967 1129 4.388499 TTCCTGGAAGACGGCGGC 62.388 66.667 13.24 8.92 34.07 6.53
1007 1169 1.067582 GACGACCCCCGATGACATC 59.932 63.158 5.28 5.28 41.76 3.06
1008 1170 2.365095 GACGACCCCCGATGACATCC 62.365 65.000 9.87 0.00 41.76 3.51
1009 1171 2.829592 GACCCCCGATGACATCCC 59.170 66.667 9.87 0.00 0.00 3.85
1010 1172 1.766461 GACCCCCGATGACATCCCT 60.766 63.158 9.87 0.00 0.00 4.20
1015 1177 2.796193 CCGATGACATCCCTGGCGA 61.796 63.158 9.87 0.00 30.50 5.54
1342 1529 1.268845 CGCAGTAACCAACCAACCAAC 60.269 52.381 0.00 0.00 0.00 3.77
1343 1530 1.751924 GCAGTAACCAACCAACCAACA 59.248 47.619 0.00 0.00 0.00 3.33
1344 1531 2.166664 GCAGTAACCAACCAACCAACAA 59.833 45.455 0.00 0.00 0.00 2.83
1345 1532 3.368531 GCAGTAACCAACCAACCAACAAA 60.369 43.478 0.00 0.00 0.00 2.83
1346 1533 4.682050 GCAGTAACCAACCAACCAACAAAT 60.682 41.667 0.00 0.00 0.00 2.32
1347 1534 5.047188 CAGTAACCAACCAACCAACAAATC 58.953 41.667 0.00 0.00 0.00 2.17
1348 1535 4.959839 AGTAACCAACCAACCAACAAATCT 59.040 37.500 0.00 0.00 0.00 2.40
1349 1536 4.400529 AACCAACCAACCAACAAATCTC 57.599 40.909 0.00 0.00 0.00 2.75
1350 1537 2.360801 ACCAACCAACCAACAAATCTCG 59.639 45.455 0.00 0.00 0.00 4.04
1351 1538 2.393764 CAACCAACCAACAAATCTCGC 58.606 47.619 0.00 0.00 0.00 5.03
1352 1539 0.958822 ACCAACCAACAAATCTCGCC 59.041 50.000 0.00 0.00 0.00 5.54
1353 1540 0.243636 CCAACCAACAAATCTCGCCC 59.756 55.000 0.00 0.00 0.00 6.13
1354 1541 1.247567 CAACCAACAAATCTCGCCCT 58.752 50.000 0.00 0.00 0.00 5.19
1374 1565 2.812619 CCTCTCTTGATCCCCGCCC 61.813 68.421 0.00 0.00 0.00 6.13
1414 1642 3.276857 TGCTCATTCTGCCTTGAATCTC 58.723 45.455 0.00 0.00 34.77 2.75
1502 1737 0.742281 TCTGCTCGCTTGCTGGATTC 60.742 55.000 5.24 0.00 33.58 2.52
1512 1747 4.036027 CGCTTGCTGGATTCAGATTGTAAT 59.964 41.667 4.75 0.00 43.49 1.89
1516 1751 4.201940 TGCTGGATTCAGATTGTAATTGCG 60.202 41.667 4.75 0.00 43.49 4.85
1519 1754 3.882888 GGATTCAGATTGTAATTGCGGGA 59.117 43.478 0.00 0.00 0.00 5.14
1547 1800 4.022935 ACGCACATGTTTCATGTCTGAATT 60.023 37.500 11.68 0.00 40.95 2.17
1549 1802 5.403166 CGCACATGTTTCATGTCTGAATTTT 59.597 36.000 11.68 0.00 40.95 1.82
1583 1851 3.119096 GCGTTCAAGGGCCGAGTC 61.119 66.667 0.00 0.00 0.00 3.36
1635 1903 0.179100 GCTGCTGCTCTCCGATTACA 60.179 55.000 8.53 0.00 36.03 2.41
1640 1908 3.198068 GCTGCTCTCCGATTACATCAAA 58.802 45.455 0.00 0.00 0.00 2.69
1658 1926 3.050275 GTCAGCAAGGTGTCCGCC 61.050 66.667 0.00 0.00 0.00 6.13
1662 1930 4.373116 GCAAGGTGTCCGCCGAGA 62.373 66.667 0.00 0.00 0.00 4.04
1689 1957 3.242543 GCTGTTTGACGAGCAGGATATTG 60.243 47.826 8.47 0.00 37.11 1.90
1697 1965 3.465742 GAGCAGGATATTGTCAGCTCA 57.534 47.619 16.63 0.00 46.86 4.26
1746 2215 6.638468 CCTTCTTTTCGGCAGATATAAAATGC 59.362 38.462 0.00 0.00 39.25 3.56
1747 2216 6.691754 TCTTTTCGGCAGATATAAAATGCA 57.308 33.333 8.78 0.00 41.78 3.96
1749 2218 4.488126 TTCGGCAGATATAAAATGCAGC 57.512 40.909 0.00 0.00 41.78 5.25
1750 2219 2.480037 TCGGCAGATATAAAATGCAGCG 59.520 45.455 0.00 5.13 41.78 5.18
1751 2220 2.480037 CGGCAGATATAAAATGCAGCGA 59.520 45.455 0.00 0.00 41.78 4.93
1752 2221 3.125829 CGGCAGATATAAAATGCAGCGAT 59.874 43.478 0.00 0.00 41.78 4.58
1754 2223 3.850273 GCAGATATAAAATGCAGCGATGC 59.150 43.478 20.73 20.73 39.75 3.91
1767 2400 3.181507 GCAGCGATGCATGTTCTTTAAGA 60.182 43.478 22.72 0.00 34.41 2.10
1768 2401 4.672542 GCAGCGATGCATGTTCTTTAAGAA 60.673 41.667 22.72 2.94 34.41 2.52
1769 2402 5.026462 CAGCGATGCATGTTCTTTAAGAAG 58.974 41.667 2.46 0.00 34.42 2.85
1785 2418 8.303876 TCTTTAAGAAGCAAGTTTGAGTTGTTT 58.696 29.630 0.00 0.00 35.19 2.83
1805 2465 6.905736 TGTTTCCTATATGCCTGGTTGATAA 58.094 36.000 0.00 0.00 0.00 1.75
1808 2468 8.515414 GTTTCCTATATGCCTGGTTGATAATTC 58.485 37.037 0.00 0.00 0.00 2.17
1811 2471 7.884877 TCCTATATGCCTGGTTGATAATTCAAG 59.115 37.037 0.00 0.00 42.41 3.02
1812 2472 7.667219 CCTATATGCCTGGTTGATAATTCAAGT 59.333 37.037 0.00 0.00 42.41 3.16
1813 2473 5.587388 ATGCCTGGTTGATAATTCAAGTG 57.413 39.130 0.00 0.00 42.41 3.16
1814 2474 4.406456 TGCCTGGTTGATAATTCAAGTGT 58.594 39.130 0.00 0.00 42.41 3.55
1815 2475 4.832266 TGCCTGGTTGATAATTCAAGTGTT 59.168 37.500 0.00 0.00 42.41 3.32
1816 2476 5.304101 TGCCTGGTTGATAATTCAAGTGTTT 59.696 36.000 0.00 0.00 42.41 2.83
1817 2477 6.183360 TGCCTGGTTGATAATTCAAGTGTTTT 60.183 34.615 0.00 0.00 42.41 2.43
1819 2479 6.868339 CCTGGTTGATAATTCAAGTGTTTTCC 59.132 38.462 0.00 0.00 42.41 3.13
1820 2480 7.255942 CCTGGTTGATAATTCAAGTGTTTTCCT 60.256 37.037 0.00 0.00 42.41 3.36
1821 2481 8.017418 TGGTTGATAATTCAAGTGTTTTCCTT 57.983 30.769 0.00 0.00 42.41 3.36
1823 2483 8.978539 GGTTGATAATTCAAGTGTTTTCCTTTC 58.021 33.333 0.00 0.00 42.41 2.62
1836 2698 0.179111 TCCTTTCATCGCCTAGCACG 60.179 55.000 0.00 0.00 0.00 5.34
1837 2699 0.179111 CCTTTCATCGCCTAGCACGA 60.179 55.000 8.31 8.31 44.75 4.35
1863 3121 3.537580 TGTCACTGGACTGTTGGTTAAC 58.462 45.455 0.00 0.00 44.61 2.01
1937 3704 0.612229 CAGGAGGATGCACACTGTCT 59.388 55.000 0.00 0.00 0.00 3.41
2231 4005 2.097036 CACTGATGCCATCCACAACAT 58.903 47.619 1.49 0.00 0.00 2.71
2480 4255 5.902613 TTCAAGCATATTGACCCTTTGAG 57.097 39.130 0.00 0.00 0.00 3.02
2700 8366 0.390998 GGCTCACTGCTCCTCTCAAC 60.391 60.000 0.00 0.00 42.39 3.18
2775 8441 2.994995 TTCCTGGGCGAGCTTCGA 60.995 61.111 9.32 0.00 43.74 3.71
2787 8453 0.674895 AGCTTCGACCAGCCAACATC 60.675 55.000 5.48 0.00 41.12 3.06
2970 8636 0.469892 AAAAGGTGCCAGAAGTGGGG 60.470 55.000 0.00 0.00 45.17 4.96
2976 8642 0.846427 TGCCAGAAGTGGGGGATTCT 60.846 55.000 0.00 0.00 45.17 2.40
3072 8738 5.057149 CAGCTATCTACCACCAACATTACC 58.943 45.833 0.00 0.00 0.00 2.85
3095 8761 1.883084 GGCTCGCTGTCCCGTATTG 60.883 63.158 0.00 0.00 0.00 1.90
3166 8832 2.348666 GTGGAATCATCAACCGACGAAG 59.651 50.000 0.00 0.00 0.00 3.79
3288 8957 1.296715 GTCTGATTCCGTGGTGGCT 59.703 57.895 0.00 0.00 37.80 4.75
3330 8999 2.114411 GGACCAAAGGCCGTTCCA 59.886 61.111 0.00 0.00 37.29 3.53
3413 9118 3.411351 CGACGTTCAAGTGGCGGG 61.411 66.667 0.00 0.00 0.00 6.13
3444 9149 4.526970 AGCTTGTTATAACTGTGGATGGG 58.473 43.478 16.33 0.00 0.00 4.00
3477 9182 2.501610 GATGGGAGGAGCGGTGAC 59.498 66.667 0.00 0.00 0.00 3.67
3506 9211 2.174349 GAACGCAGCGCTGAAAGG 59.826 61.111 40.21 25.45 0.00 3.11
3527 9232 2.488355 GATCGAGACCGCGTTCCA 59.512 61.111 4.92 0.00 35.37 3.53
3653 9359 0.108138 GGCAGCAGGTCGTGTTAGAT 60.108 55.000 0.00 0.00 0.00 1.98
3654 9360 1.676014 GGCAGCAGGTCGTGTTAGATT 60.676 52.381 0.00 0.00 0.00 2.40
3655 9361 2.076863 GCAGCAGGTCGTGTTAGATTT 58.923 47.619 0.00 0.00 0.00 2.17
3656 9362 3.259064 GCAGCAGGTCGTGTTAGATTTA 58.741 45.455 0.00 0.00 0.00 1.40
3657 9363 3.307242 GCAGCAGGTCGTGTTAGATTTAG 59.693 47.826 0.00 0.00 0.00 1.85
3658 9364 4.744570 CAGCAGGTCGTGTTAGATTTAGA 58.255 43.478 0.00 0.00 0.00 2.10
3819 9525 4.517285 TCTCATCAGTTTCTGGTATTGGC 58.483 43.478 0.00 0.00 31.51 4.52
3848 9554 7.857404 TCCCTCTGTAAAGGAATATAAGAGG 57.143 40.000 8.54 8.54 38.87 3.69
4016 9874 9.715121 TTCCTCGGTATATGGTTATTACAATTC 57.285 33.333 0.00 0.00 0.00 2.17
4023 9881 9.787435 GTATATGGTTATTACAATTCTGGGTGA 57.213 33.333 0.00 0.00 0.00 4.02
4142 10991 0.675633 CTGGTTGTTGGCAAGGGAAG 59.324 55.000 0.00 0.00 34.94 3.46
4151 11030 3.806949 TGGCAAGGGAAGAACTAACAT 57.193 42.857 0.00 0.00 0.00 2.71
4152 11031 4.112634 TGGCAAGGGAAGAACTAACATT 57.887 40.909 0.00 0.00 0.00 2.71
4356 11273 1.450312 CCTGGGGCAACGATCACTC 60.450 63.158 0.00 0.00 37.60 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.663188 GCGATGATGAGTCCGGGC 60.663 66.667 0.00 0.00 0.00 6.13
22 23 3.032609 CGCCGCGATGATGAGTCC 61.033 66.667 8.23 0.00 0.00 3.85
68 69 1.144057 GTCTTGGCGATCCGTCCAT 59.856 57.895 0.00 0.00 34.40 3.41
208 214 0.463295 ACTAGTTCGATCTCCCGCGA 60.463 55.000 8.23 0.00 34.32 5.87
278 285 5.929697 TGAAAACTACTCAGCAATCACTG 57.070 39.130 0.00 0.00 39.12 3.66
399 406 1.900245 AACCCGAATAAAACCGTGCT 58.100 45.000 0.00 0.00 0.00 4.40
450 461 8.563289 AATCACGCATTTAGTAAAACGAAAAA 57.437 26.923 21.39 8.96 0.00 1.94
553 564 5.226194 TGGAAAAAGTTCATCCCATTTGG 57.774 39.130 4.84 0.00 35.25 3.28
865 993 0.871057 GATTTAGGCGCTCAGATGGC 59.129 55.000 7.64 0.00 0.00 4.40
883 1011 2.659016 CAGGCCTTGACTCAGCGA 59.341 61.111 0.00 0.00 0.00 4.93
887 1015 2.530151 AGCCCAGGCCTTGACTCA 60.530 61.111 0.00 0.00 43.17 3.41
891 1019 2.853542 TCACAGCCCAGGCCTTGA 60.854 61.111 0.00 0.00 43.17 3.02
899 1046 4.641645 CCGTTGCCTCACAGCCCA 62.642 66.667 0.00 0.00 0.00 5.36
952 1114 4.821589 GAGCCGCCGTCTTCCAGG 62.822 72.222 0.00 0.00 0.00 4.45
953 1115 3.708220 GAGAGCCGCCGTCTTCCAG 62.708 68.421 0.00 0.00 0.00 3.86
954 1116 3.760035 GAGAGCCGCCGTCTTCCA 61.760 66.667 0.00 0.00 0.00 3.53
955 1117 4.516195 GGAGAGCCGCCGTCTTCC 62.516 72.222 0.00 0.00 0.00 3.46
956 1118 3.418744 GAGGAGAGCCGCCGTCTTC 62.419 68.421 0.00 0.00 39.96 2.87
957 1119 3.453679 GAGGAGAGCCGCCGTCTT 61.454 66.667 0.00 0.00 39.96 3.01
958 1120 4.434354 AGAGGAGAGCCGCCGTCT 62.434 66.667 0.00 0.00 39.96 4.18
959 1121 3.894947 GAGAGGAGAGCCGCCGTC 61.895 72.222 0.00 0.00 39.96 4.79
960 1122 4.434354 AGAGAGGAGAGCCGCCGT 62.434 66.667 0.00 0.00 39.96 5.68
961 1123 3.591835 GAGAGAGGAGAGCCGCCG 61.592 72.222 0.00 0.00 39.96 6.46
962 1124 2.441164 TGAGAGAGGAGAGCCGCC 60.441 66.667 0.00 0.00 39.96 6.13
963 1125 1.391157 ATGTGAGAGAGGAGAGCCGC 61.391 60.000 0.00 0.00 39.96 6.53
964 1126 1.110442 AATGTGAGAGAGGAGAGCCG 58.890 55.000 0.00 0.00 39.96 5.52
965 1127 2.158971 GGAAATGTGAGAGAGGAGAGCC 60.159 54.545 0.00 0.00 0.00 4.70
966 1128 2.158971 GGGAAATGTGAGAGAGGAGAGC 60.159 54.545 0.00 0.00 0.00 4.09
967 1129 2.433970 GGGGAAATGTGAGAGAGGAGAG 59.566 54.545 0.00 0.00 0.00 3.20
1342 1529 0.105778 GAGAGGGAGGGCGAGATTTG 59.894 60.000 0.00 0.00 0.00 2.32
1343 1530 0.031616 AGAGAGGGAGGGCGAGATTT 60.032 55.000 0.00 0.00 0.00 2.17
1344 1531 0.031616 AAGAGAGGGAGGGCGAGATT 60.032 55.000 0.00 0.00 0.00 2.40
1345 1532 0.758685 CAAGAGAGGGAGGGCGAGAT 60.759 60.000 0.00 0.00 0.00 2.75
1346 1533 1.380515 CAAGAGAGGGAGGGCGAGA 60.381 63.158 0.00 0.00 0.00 4.04
1347 1534 0.758685 ATCAAGAGAGGGAGGGCGAG 60.759 60.000 0.00 0.00 0.00 5.03
1348 1535 0.757188 GATCAAGAGAGGGAGGGCGA 60.757 60.000 0.00 0.00 0.00 5.54
1349 1536 1.745264 GATCAAGAGAGGGAGGGCG 59.255 63.158 0.00 0.00 0.00 6.13
1350 1537 1.414866 GGGATCAAGAGAGGGAGGGC 61.415 65.000 0.00 0.00 0.00 5.19
1351 1538 0.766288 GGGGATCAAGAGAGGGAGGG 60.766 65.000 0.00 0.00 0.00 4.30
1352 1539 1.118356 CGGGGATCAAGAGAGGGAGG 61.118 65.000 0.00 0.00 0.00 4.30
1353 1540 1.753368 GCGGGGATCAAGAGAGGGAG 61.753 65.000 0.00 0.00 0.00 4.30
1354 1541 1.762460 GCGGGGATCAAGAGAGGGA 60.762 63.158 0.00 0.00 0.00 4.20
1374 1565 1.137872 CAGGATGGAGAAGGAAGGACG 59.862 57.143 0.00 0.00 0.00 4.79
1449 1677 2.182842 CCAGGAAGTATGGCAGCGC 61.183 63.158 0.00 0.00 0.00 5.92
1493 1728 4.201940 CGCAATTACAATCTGAATCCAGCA 60.202 41.667 0.00 0.00 40.20 4.41
1494 1729 4.285292 CGCAATTACAATCTGAATCCAGC 58.715 43.478 0.00 0.00 40.20 4.85
1495 1730 4.261322 CCCGCAATTACAATCTGAATCCAG 60.261 45.833 0.00 0.00 41.74 3.86
1496 1731 3.631686 CCCGCAATTACAATCTGAATCCA 59.368 43.478 0.00 0.00 0.00 3.41
1497 1732 3.882888 TCCCGCAATTACAATCTGAATCC 59.117 43.478 0.00 0.00 0.00 3.01
1502 1737 1.334869 GCCTCCCGCAATTACAATCTG 59.665 52.381 0.00 0.00 37.47 2.90
1516 1751 4.760047 ACATGTGCGTCGCCTCCC 62.760 66.667 15.88 0.46 0.00 4.30
1519 1754 0.955428 ATGAAACATGTGCGTCGCCT 60.955 50.000 15.88 0.00 0.00 5.52
1566 1834 3.119096 GACTCGGCCCTTGAACGC 61.119 66.667 0.00 0.00 0.00 4.84
1583 1851 2.040544 GGTGGCGTGGGTCATGAAG 61.041 63.158 0.00 0.00 0.00 3.02
1635 1903 2.508526 GGACACCTTGCTGACTTTGAT 58.491 47.619 0.00 0.00 0.00 2.57
1640 1908 2.031163 GCGGACACCTTGCTGACT 59.969 61.111 0.00 0.00 0.00 3.41
1716 1984 2.650322 TCTGCCGAAAAGAAGGTGTTT 58.350 42.857 0.00 0.00 0.00 2.83
1718 1986 2.568623 ATCTGCCGAAAAGAAGGTGT 57.431 45.000 0.00 0.00 0.00 4.16
1719 1987 6.677781 TTTATATCTGCCGAAAAGAAGGTG 57.322 37.500 0.00 0.00 0.00 4.00
1746 2215 4.604843 TCTTAAAGAACATGCATCGCTG 57.395 40.909 0.00 0.00 0.00 5.18
1747 2216 4.437930 GCTTCTTAAAGAACATGCATCGCT 60.438 41.667 0.00 0.00 34.14 4.93
1749 2218 4.973396 TGCTTCTTAAAGAACATGCATCG 58.027 39.130 0.00 0.00 30.96 3.84
1750 2219 6.385033 ACTTGCTTCTTAAAGAACATGCATC 58.615 36.000 0.00 0.00 34.38 3.91
1751 2220 6.336842 ACTTGCTTCTTAAAGAACATGCAT 57.663 33.333 0.00 0.00 34.38 3.96
1752 2221 5.772825 ACTTGCTTCTTAAAGAACATGCA 57.227 34.783 0.00 0.00 33.10 3.96
1754 2223 7.917505 ACTCAAACTTGCTTCTTAAAGAACATG 59.082 33.333 0.00 0.00 34.14 3.21
1755 2224 8.000780 ACTCAAACTTGCTTCTTAAAGAACAT 57.999 30.769 0.00 0.00 34.14 2.71
1767 2400 6.715347 ATAGGAAACAACTCAAACTTGCTT 57.285 33.333 0.00 0.00 0.00 3.91
1768 2401 7.575720 GCATATAGGAAACAACTCAAACTTGCT 60.576 37.037 0.00 0.00 0.00 3.91
1769 2402 6.528072 GCATATAGGAAACAACTCAAACTTGC 59.472 38.462 0.00 0.00 0.00 4.01
1785 2418 7.328404 TGAATTATCAACCAGGCATATAGGA 57.672 36.000 0.00 0.00 30.99 2.94
1805 2465 5.222631 GCGATGAAAGGAAAACACTTGAAT 58.777 37.500 0.00 0.00 0.00 2.57
1808 2468 3.004734 AGGCGATGAAAGGAAAACACTTG 59.995 43.478 0.00 0.00 0.00 3.16
1811 2471 3.426292 GCTAGGCGATGAAAGGAAAACAC 60.426 47.826 0.00 0.00 0.00 3.32
1812 2472 2.747446 GCTAGGCGATGAAAGGAAAACA 59.253 45.455 0.00 0.00 0.00 2.83
1813 2473 2.747446 TGCTAGGCGATGAAAGGAAAAC 59.253 45.455 0.00 0.00 0.00 2.43
1814 2474 2.747446 GTGCTAGGCGATGAAAGGAAAA 59.253 45.455 0.00 0.00 0.00 2.29
1815 2475 2.356135 GTGCTAGGCGATGAAAGGAAA 58.644 47.619 0.00 0.00 0.00 3.13
1816 2476 1.739035 CGTGCTAGGCGATGAAAGGAA 60.739 52.381 0.00 0.00 0.00 3.36
1817 2477 0.179111 CGTGCTAGGCGATGAAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
1819 2479 1.858091 ATCGTGCTAGGCGATGAAAG 58.142 50.000 0.00 0.00 45.79 2.62
1820 2480 3.446310 TTATCGTGCTAGGCGATGAAA 57.554 42.857 9.98 0.00 46.74 2.69
1821 2481 3.446310 TTTATCGTGCTAGGCGATGAA 57.554 42.857 9.98 5.77 46.74 2.57
1823 2483 3.059884 ACATTTATCGTGCTAGGCGATG 58.940 45.455 9.98 0.00 46.74 3.84
1836 2698 5.003804 ACCAACAGTCCAGTGACATTTATC 58.996 41.667 0.00 0.00 44.33 1.75
1837 2699 4.985538 ACCAACAGTCCAGTGACATTTAT 58.014 39.130 0.00 0.00 44.33 1.40
1863 3121 5.856986 GCAGAATCATGCATTAGCTGTAATG 59.143 40.000 0.00 0.00 45.88 1.90
2231 4005 1.228429 CGGCCCCCTTGAGAAACAA 60.228 57.895 0.00 0.00 36.97 2.83
2480 4255 6.051717 ACATCATGGAAGTTGTCTATGCTAC 58.948 40.000 0.00 0.00 43.23 3.58
2775 8441 2.880443 ACAAGAATGATGTTGGCTGGT 58.120 42.857 0.00 0.00 34.26 4.00
2787 8453 1.737793 GCTTCCCCGTGTACAAGAATG 59.262 52.381 10.61 0.00 0.00 2.67
2919 8585 2.018542 CAATTGCCTTGGCCATCTTG 57.981 50.000 6.09 0.60 0.00 3.02
2970 8636 0.807496 GCAAGCCACTGACAGAATCC 59.193 55.000 10.08 0.00 0.00 3.01
2976 8642 0.107263 TCACAAGCAAGCCACTGACA 60.107 50.000 0.00 0.00 0.00 3.58
3095 8761 6.136541 ACTTGATGACTTCAAAAGAACCAC 57.863 37.500 10.47 0.00 43.64 4.16
3166 8832 1.453155 ATCAGTGTTGGAACATCGGC 58.547 50.000 0.00 0.00 41.59 5.54
3288 8957 4.343814 TCACGCCCTATGTTCAAGATCATA 59.656 41.667 0.00 2.03 0.00 2.15
3330 8999 4.290722 ACCATCTCTGTTTCCTCTTCCATT 59.709 41.667 0.00 0.00 0.00 3.16
3413 9118 4.640647 CAGTTATAACAAGCTTCCCTTCCC 59.359 45.833 17.65 0.00 0.00 3.97
3444 9149 1.815421 ATCCAAGTGCGCGACATCC 60.815 57.895 12.10 0.00 0.00 3.51
3495 9200 1.524482 GATCCTCCCTTTCAGCGCT 59.476 57.895 2.64 2.64 0.00 5.92
3506 9211 2.665172 GAACGCGGTCTCGATCCTCC 62.665 65.000 18.88 0.00 39.00 4.30
3653 9359 9.448438 ACAATGCTATACAACTCATGTTCTAAA 57.552 29.630 0.00 0.00 43.63 1.85
3655 9361 9.750125 CTACAATGCTATACAACTCATGTTCTA 57.250 33.333 0.00 0.00 43.63 2.10
3656 9362 7.712639 CCTACAATGCTATACAACTCATGTTCT 59.287 37.037 0.00 0.00 43.63 3.01
3657 9363 7.519008 GCCTACAATGCTATACAACTCATGTTC 60.519 40.741 0.00 0.00 43.63 3.18
3658 9364 6.260936 GCCTACAATGCTATACAACTCATGTT 59.739 38.462 0.00 0.00 43.63 2.71
3819 9525 9.640963 CTTATATTCCTTTACAGAGGGATAACG 57.359 37.037 0.00 0.00 40.01 3.18
3863 9569 6.921857 TCCTTCCGTAAAGAAATATAAGAGCG 59.078 38.462 0.00 0.00 37.12 5.03
4016 9874 1.064906 AGCATGACCAAGATCACCCAG 60.065 52.381 0.00 0.00 0.00 4.45
4023 9881 0.034380 AGCAGCAGCATGACCAAGAT 60.034 50.000 3.17 0.00 45.49 2.40
4356 11273 2.163818 TCACTTGGTCGTTAAGCAGG 57.836 50.000 0.00 0.00 38.35 4.85
4496 11416 9.777297 ACAATTGTAAATTTTCAAGTAATGGCT 57.223 25.926 9.97 0.00 0.00 4.75
4539 11459 9.558396 AAAATGGCATAACAAGAATCTTTTTGA 57.442 25.926 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.