Multiple sequence alignment - TraesCS3B01G141000

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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 TraesCS3B01G141000 chr3B 100.000 4733 0 0 1 4733 127301545 127296813 0.000000e+00 8741
1 TraesCS3B01G141000 chr3D 90.314 2168 147 37 2592 4714 81372935 81370786 0.000000e+00 2782
2 TraesCS3B01G141000 chr3D 83.276 1453 126 58 1351 2732 81382340 81380934 0.000000e+00 1229
3 TraesCS3B01G141000 chr3D 90.734 572 35 8 2166 2732 81373494 81372936 0.000000e+00 747
4 TraesCS3B01G141000 chr3D 93.418 471 26 4 970 1435 81374952 81374482 0.000000e+00 693
5 TraesCS3B01G141000 chr3D 83.112 752 57 30 1463 2157 81374481 81373743 5.200000e-174 621
6 TraesCS3B01G141000 chr3D 90.402 323 24 4 996 1318 81382645 81382330 7.330000e-113 418
7 TraesCS3B01G141000 chr3D 89.573 211 10 4 1 201 81375173 81374965 1.690000e-64 257
8 TraesCS3B01G141000 chr3D 86.792 212 15 10 1 202 81382894 81382686 1.710000e-54 224
9 TraesCS3B01G141000 chr3A 87.010 1886 133 51 2897 4714 95536233 95534392 0.000000e+00 2023
10 TraesCS3B01G141000 chr3A 93.003 586 36 4 2237 2819 95536824 95536241 0.000000e+00 850
11 TraesCS3B01G141000 chr3A 82.368 760 68 29 1413 2134 95537546 95536815 6.780000e-168 601
12 TraesCS3B01G141000 chr3A 91.117 349 29 1 996 1342 95537917 95537569 5.540000e-129 472
13 TraesCS3B01G141000 chr5B 95.109 777 25 5 203 968 590455652 590456426 0.000000e+00 1212
14 TraesCS3B01G141000 chr2B 87.147 778 62 20 203 970 643482346 643483095 0.000000e+00 848
15 TraesCS3B01G141000 chr2B 86.761 778 65 19 203 970 643435086 643435835 0.000000e+00 832
16 TraesCS3B01G141000 chr2B 85.751 779 72 20 203 970 643388549 643389299 0.000000e+00 787
17 TraesCS3B01G141000 chr2B 90.805 87 6 1 203 289 643435833 643435749 1.080000e-21 115
18 TraesCS3B01G141000 chr4D 87.030 771 57 21 201 969 327735516 327734787 0.000000e+00 830
19 TraesCS3B01G141000 chr4D 96.552 87 3 0 882 968 327735428 327735514 1.370000e-30 145
20 TraesCS3B01G141000 chr4A 84.286 700 57 23 301 965 641613619 641612938 6.680000e-178 634
21 TraesCS3B01G141000 chr4A 94.231 104 5 1 202 305 686388118 686388220 1.760000e-34 158
22 TraesCS3B01G141000 chr4A 96.552 87 2 1 882 968 686388204 686388119 4.940000e-30 143
23 TraesCS3B01G141000 chr6B 83.824 476 43 15 509 969 153878964 153878508 5.660000e-114 422
24 TraesCS3B01G141000 chr6B 87.379 309 30 5 203 502 153879251 153878943 3.510000e-91 346
25 TraesCS3B01G141000 chr6B 95.062 81 2 2 203 283 153878509 153878587 4.970000e-25 126


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 TraesCS3B01G141000 chr3B 127296813 127301545 4732 True 8741.000000 8741 100.000000 1 4733 1 chr3B.!!$R1 4732
1 TraesCS3B01G141000 chr3D 81370786 81375173 4387 True 1020.000000 2782 89.430200 1 4714 5 chr3D.!!$R1 4713
2 TraesCS3B01G141000 chr3D 81380934 81382894 1960 True 623.666667 1229 86.823333 1 2732 3 chr3D.!!$R2 2731
3 TraesCS3B01G141000 chr3A 95534392 95537917 3525 True 986.500000 2023 88.374500 996 4714 4 chr3A.!!$R1 3718
4 TraesCS3B01G141000 chr5B 590455652 590456426 774 False 1212.000000 1212 95.109000 203 968 1 chr5B.!!$F1 765
5 TraesCS3B01G141000 chr2B 643482346 643483095 749 False 848.000000 848 87.147000 203 970 1 chr2B.!!$F3 767
6 TraesCS3B01G141000 chr2B 643435086 643435835 749 False 832.000000 832 86.761000 203 970 1 chr2B.!!$F2 767
7 TraesCS3B01G141000 chr2B 643388549 643389299 750 False 787.000000 787 85.751000 203 970 1 chr2B.!!$F1 767
8 TraesCS3B01G141000 chr4D 327734787 327735516 729 True 830.000000 830 87.030000 201 969 1 chr4D.!!$R1 768
9 TraesCS3B01G141000 chr4A 641612938 641613619 681 True 634.000000 634 84.286000 301 965 1 chr4A.!!$R1 664
10 TraesCS3B01G141000 chr6B 153878508 153879251 743 True 384.000000 422 85.601500 203 969 2 chr6B.!!$R1 766

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
152 170 0.106015 ACCTGCCTTGGTTCTTTGCT 60.106 50.0 0.0 0.0 36.89 3.91 F
721 774 0.251165 CCGTCCCCTTGTGGAAACAT 60.251 55.0 0.0 0.0 46.14 2.71 F
1652 1781 0.948678 TTAAGAACCCACAGCAACGC 59.051 50.0 0.0 0.0 0.00 4.84 F
2223 2652 0.106419 TTTCCCTTTTCTGTGGCCGT 60.106 50.0 0.0 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1593 0.032130 GGAGAACGCAGACTCACACA 59.968 55.0 0.00 0.0 36.61 3.72 R
2205 2634 0.106419 AACGGCCACAGAAAAGGGAA 60.106 50.0 2.24 0.0 0.00 3.97 R
3566 4152 0.027194 CGCCTGAAAGACATCGCATG 59.973 55.0 0.00 0.0 34.07 4.06 R
3819 4407 0.040425 CGCCTCCGTTTCAAAAGGTG 60.040 55.0 1.72 0.0 33.45 4.00 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
42 43 3.963374 TGTCACTGCTCTCTTGGCTATAT 59.037 43.478 0.00 0.00 0.00 0.86
107 125 2.743928 CTCAGTGCCACCCGCTTC 60.744 66.667 0.00 0.00 38.78 3.86
152 170 0.106015 ACCTGCCTTGGTTCTTTGCT 60.106 50.000 0.00 0.00 36.89 3.91
191 209 0.467290 CGCCTCCTCTAGAGCTTCCT 60.467 60.000 14.73 0.00 41.74 3.36
193 211 2.235891 GCCTCCTCTAGAGCTTCCTAC 58.764 57.143 14.73 0.00 41.74 3.18
372 392 2.980246 TCTCTCAGAGTTCTCACCCA 57.020 50.000 0.36 0.00 0.00 4.51
426 446 2.201022 AACCTCCGTGCAGTCGTCT 61.201 57.895 0.00 0.00 0.00 4.18
635 672 1.454663 GGCTTCTCCCTCCAATGCC 60.455 63.158 0.00 0.00 0.00 4.40
704 743 2.890474 CGCCCGACTTGAATCCCG 60.890 66.667 0.00 0.00 0.00 5.14
721 774 0.251165 CCGTCCCCTTGTGGAAACAT 60.251 55.000 0.00 0.00 46.14 2.71
748 801 2.158755 AGGATCTACAAGCCAAATCCCG 60.159 50.000 0.00 0.00 37.24 5.14
786 849 9.981460 ATAAGGGAGAATAATTCAGTCTTTTGT 57.019 29.630 0.00 0.00 29.94 2.83
787 850 8.712228 AAGGGAGAATAATTCAGTCTTTTGTT 57.288 30.769 0.00 0.00 29.94 2.83
788 851 8.341892 AGGGAGAATAATTCAGTCTTTTGTTC 57.658 34.615 0.00 0.00 29.94 3.18
789 852 7.944554 AGGGAGAATAATTCAGTCTTTTGTTCA 59.055 33.333 0.00 0.00 29.94 3.18
790 853 8.023706 GGGAGAATAATTCAGTCTTTTGTTCAC 58.976 37.037 0.00 0.00 29.94 3.18
791 854 8.787852 GGAGAATAATTCAGTCTTTTGTTCACT 58.212 33.333 0.00 0.00 29.94 3.41
1297 1394 4.586001 ACAGCTCAAATCAAATCACCAAGT 59.414 37.500 0.00 0.00 0.00 3.16
1310 1407 1.045407 ACCAAGTCCAGCACTCGTTA 58.955 50.000 0.00 0.00 32.30 3.18
1329 1426 4.689345 CGTTACTAGTTTCAAAGTCTGGGG 59.311 45.833 0.00 0.00 0.00 4.96
1335 1432 4.663334 AGTTTCAAAGTCTGGGGAATACC 58.337 43.478 0.00 0.00 39.11 2.73
1336 1433 4.354087 AGTTTCAAAGTCTGGGGAATACCT 59.646 41.667 0.00 0.00 40.03 3.08
1338 1435 3.526899 TCAAAGTCTGGGGAATACCTCA 58.473 45.455 0.00 0.00 45.51 3.86
1339 1436 4.111577 TCAAAGTCTGGGGAATACCTCAT 58.888 43.478 0.00 0.00 46.58 2.90
1345 1447 4.822350 GTCTGGGGAATACCTCATTTTAGC 59.178 45.833 0.00 0.00 46.58 3.09
1366 1492 4.750598 AGCAGTCGTTCTTAGTTTTCTTCC 59.249 41.667 0.00 0.00 0.00 3.46
1429 1555 4.320023 TCGCAAAGGAAATAGCTGTGTTA 58.680 39.130 0.00 0.00 0.00 2.41
1445 1571 3.692101 TGTGTTACCTTGTCAAACAGTGG 59.308 43.478 0.00 0.00 34.01 4.00
1454 1580 7.231467 ACCTTGTCAAACAGTGGTCTTATTAT 58.769 34.615 0.00 0.00 33.61 1.28
1455 1581 7.724061 ACCTTGTCAAACAGTGGTCTTATTATT 59.276 33.333 0.00 0.00 33.61 1.40
1459 1585 9.733556 TGTCAAACAGTGGTCTTATTATTACAT 57.266 29.630 0.00 0.00 0.00 2.29
1480 1606 4.466567 TTACATTTTGTGTGAGTCTGCG 57.533 40.909 0.00 0.00 42.24 5.18
1519 1645 5.193663 GCATATGCTGTTCTAGTCTCTGA 57.806 43.478 20.64 0.00 38.21 3.27
1533 1660 3.514706 AGTCTCTGAATGTGCAGATGTCT 59.485 43.478 0.00 0.00 43.43 3.41
1552 1680 2.029020 TCTGTTGGTTGTCTGATCCTCG 60.029 50.000 0.00 0.00 0.00 4.63
1566 1694 6.581542 GTCTGATCCTCGTTGTATATTAACCG 59.418 42.308 0.00 0.00 0.00 4.44
1573 1701 5.108517 TCGTTGTATATTAACCGGTTCCAC 58.891 41.667 26.16 15.24 0.00 4.02
1652 1781 0.948678 TTAAGAACCCACAGCAACGC 59.051 50.000 0.00 0.00 0.00 4.84
1751 1880 1.972075 GAAGAGATAGCCCCAGGTACC 59.028 57.143 2.73 2.73 0.00 3.34
1768 1900 6.766467 CCAGGTACCAAGGTTAGTTCATATTC 59.234 42.308 15.94 0.00 0.00 1.75
1789 1921 5.968528 TCTCTGTCTCAAGGTTCTAGTTC 57.031 43.478 0.00 0.00 0.00 3.01
1791 1923 6.780901 TCTCTGTCTCAAGGTTCTAGTTCTA 58.219 40.000 0.00 0.00 0.00 2.10
1792 1924 6.882140 TCTCTGTCTCAAGGTTCTAGTTCTAG 59.118 42.308 0.83 0.83 0.00 2.43
1793 1925 6.544650 TCTGTCTCAAGGTTCTAGTTCTAGT 58.455 40.000 6.73 0.00 0.00 2.57
1794 1926 7.005296 TCTGTCTCAAGGTTCTAGTTCTAGTT 58.995 38.462 6.73 0.00 0.00 2.24
1795 1927 7.506261 TCTGTCTCAAGGTTCTAGTTCTAGTTT 59.494 37.037 6.73 0.00 0.00 2.66
1796 1928 8.019656 TGTCTCAAGGTTCTAGTTCTAGTTTT 57.980 34.615 6.73 0.00 0.00 2.43
1799 1931 5.995897 TCAAGGTTCTAGTTCTAGTTTTGCC 59.004 40.000 6.73 4.28 0.00 4.52
1800 1932 4.907809 AGGTTCTAGTTCTAGTTTTGCCC 58.092 43.478 6.73 0.00 0.00 5.36
1801 1933 4.008330 GGTTCTAGTTCTAGTTTTGCCCC 58.992 47.826 6.73 0.00 0.00 5.80
1802 1934 4.506095 GGTTCTAGTTCTAGTTTTGCCCCA 60.506 45.833 6.73 0.00 0.00 4.96
1803 1935 4.553330 TCTAGTTCTAGTTTTGCCCCAG 57.447 45.455 6.73 0.00 0.00 4.45
1804 1936 2.586648 AGTTCTAGTTTTGCCCCAGG 57.413 50.000 0.00 0.00 0.00 4.45
1839 1996 7.489160 CAATATGCAGTCACTGTACCTAGTTA 58.511 38.462 6.68 0.00 33.43 2.24
1879 2036 4.630894 CTGTCCTAGACTGCTAGTTCAG 57.369 50.000 0.00 0.00 42.11 3.02
1888 2045 4.513318 AGACTGCTAGTTCAGTTTTGCTTC 59.487 41.667 4.73 0.00 46.40 3.86
1926 2086 2.237534 GAGACTGGAGAGCCTGGCAC 62.238 65.000 22.65 15.46 43.29 5.01
1944 2115 2.420022 GCACATACACTTACCAAGCAGG 59.580 50.000 0.00 0.00 45.67 4.85
1966 2152 5.604231 AGGATGCTCAGTTATTCCACTCATA 59.396 40.000 0.00 0.00 0.00 2.15
1993 2181 8.905103 AGTATGAAAATTACATAACCAAACGC 57.095 30.769 6.78 0.00 33.04 4.84
2021 2209 4.235939 ACAAGATACTGCTCTATGCGAG 57.764 45.455 0.00 0.00 46.63 5.03
2022 2210 3.634448 ACAAGATACTGCTCTATGCGAGT 59.366 43.478 0.00 0.00 46.63 4.18
2076 2264 1.135199 GTGCAGCATGAGATTGGGTTG 60.135 52.381 0.00 0.00 39.69 3.77
2093 2281 7.941053 TTGGGTTGGGATGTAGTATTACTAT 57.059 36.000 6.82 0.00 32.65 2.12
2096 2284 8.783903 TGGGTTGGGATGTAGTATTACTATTTT 58.216 33.333 6.82 0.00 32.65 1.82
2097 2285 9.281371 GGGTTGGGATGTAGTATTACTATTTTC 57.719 37.037 6.82 4.97 32.65 2.29
2136 2324 4.380867 CCACAGTCTGTTCAAGTTTGCTTT 60.381 41.667 1.67 0.00 31.49 3.51
2137 2325 4.560035 CACAGTCTGTTCAAGTTTGCTTTG 59.440 41.667 1.67 0.00 31.49 2.77
2223 2652 0.106419 TTTCCCTTTTCTGTGGCCGT 60.106 50.000 0.00 0.00 0.00 5.68
2225 2654 0.106419 TCCCTTTTCTGTGGCCGTTT 60.106 50.000 0.00 0.00 0.00 3.60
2242 2671 8.931775 GTGGCCGTTTATTTATTTTCTCAAATT 58.068 29.630 0.00 0.00 34.29 1.82
2311 2740 7.987268 TCTCTATGTGTTGAATATTGACGTC 57.013 36.000 9.11 9.11 0.00 4.34
2361 2794 7.285629 TCCACTATAGATTCGTCTTGAGAACAT 59.714 37.037 6.78 0.00 0.00 2.71
2384 2817 6.882610 TGATTCCAGTAAATCATGGCATAC 57.117 37.500 0.00 0.00 39.98 2.39
2452 2885 6.830324 TCCAATCTTTGTATGAGGAATGGAAG 59.170 38.462 0.00 0.00 30.77 3.46
2470 2903 5.879763 TGGAAGATGAACCAGAAATTCTCA 58.120 37.500 0.00 0.00 0.00 3.27
2583 3016 2.158623 ACAGGACATTCCAGTTGCAAGA 60.159 45.455 0.00 0.00 39.61 3.02
2630 3063 6.610741 TCTTCTCTTTCTGTTTCTTCTTGC 57.389 37.500 0.00 0.00 0.00 4.01
2711 3145 6.663734 AGCTTGGCATCTTAAGTAAATAGGT 58.336 36.000 1.63 0.00 0.00 3.08
2786 3360 8.648557 TTATGATGTTCTGAACTATTTCCTCG 57.351 34.615 20.18 0.00 0.00 4.63
2788 3362 6.878317 TGATGTTCTGAACTATTTCCTCGAT 58.122 36.000 20.18 2.70 0.00 3.59
2792 3366 8.703604 TGTTCTGAACTATTTCCTCGATAAAG 57.296 34.615 20.18 0.00 0.00 1.85
2835 3409 6.212235 CGTGAGCATCTTTGTAGATCTACAT 58.788 40.000 31.03 17.41 40.00 2.29
2848 3422 8.662781 TGTAGATCTACATAGTTGCCATTTTC 57.337 34.615 27.96 0.39 40.77 2.29
2849 3423 8.486210 TGTAGATCTACATAGTTGCCATTTTCT 58.514 33.333 27.96 0.00 40.77 2.52
2861 3437 5.226194 TGCCATTTTCTAATTTGCTGGTT 57.774 34.783 0.00 0.00 0.00 3.67
2877 3453 6.135290 TGCTGGTTCTGCATATAAAATGAC 57.865 37.500 0.00 0.00 33.63 3.06
2894 3470 4.114997 CCCGGGCGACAATTGCAC 62.115 66.667 8.08 0.00 0.00 4.57
2940 3516 1.523758 CTGTAACTTGTGAGCCACCC 58.476 55.000 3.33 0.00 32.73 4.61
2941 3517 1.072331 CTGTAACTTGTGAGCCACCCT 59.928 52.381 3.33 0.00 32.73 4.34
2956 3532 4.346418 AGCCACCCTCTGACTTATATCTTG 59.654 45.833 0.00 0.00 0.00 3.02
2989 3565 2.087646 CCAGAAGGCTAGAAACTTGGC 58.912 52.381 0.00 0.00 32.76 4.52
3146 3722 0.902984 GGCCCCCAAAACCCTAGTTG 60.903 60.000 0.00 0.00 35.97 3.16
3150 3726 1.824852 CCCCAAAACCCTAGTTGCATC 59.175 52.381 0.00 0.00 35.97 3.91
3178 3754 9.100197 TGTCTAAATCTACTGGGCATGATATTA 57.900 33.333 0.00 0.00 0.00 0.98
3357 3936 2.363297 GACTCCGGTCTTCACCCTT 58.637 57.895 0.00 0.00 40.01 3.95
3450 4029 0.468226 ACGAGGAACTGGCAAGACAA 59.532 50.000 0.00 0.00 41.55 3.18
3505 4084 3.734293 CGTTAGTTTCGACTCCCATCTCC 60.734 52.174 0.00 0.00 0.00 3.71
3510 4089 2.588464 TCGACTCCCATCTCCTATCC 57.412 55.000 0.00 0.00 0.00 2.59
3566 4152 8.769891 CCGGAAATATTGTTTTATTAAATGGCC 58.230 33.333 0.00 0.00 0.00 5.36
3734 4320 2.509964 GAGGGAGGGGAAGATTTTAGCA 59.490 50.000 0.00 0.00 0.00 3.49
3747 4333 7.042725 GGAAGATTTTAGCACAGTTTCAAAACC 60.043 37.037 2.08 0.00 39.71 3.27
3875 4463 6.169094 TGGTCATCTTAAAAGCTTCTCTCTG 58.831 40.000 0.00 0.00 0.00 3.35
3881 4469 9.296400 CATCTTAAAAGCTTCTCTCTGTAGTAC 57.704 37.037 0.00 0.00 0.00 2.73
3889 4492 6.544564 AGCTTCTCTCTGTAGTACCTTATGAC 59.455 42.308 0.00 0.00 0.00 3.06
3962 4571 1.001641 AGTTGCCTCACCTGATGCC 60.002 57.895 0.77 0.00 35.27 4.40
3995 4604 3.963129 TGTCAAGGGTTCAGAAACAAGT 58.037 40.909 0.00 0.00 37.10 3.16
3999 4608 4.640201 TCAAGGGTTCAGAAACAAGTCAAG 59.360 41.667 0.00 0.00 37.10 3.02
4022 4632 5.104374 GCAACATGTGTATTTCCATGGAAG 58.896 41.667 25.69 14.67 42.15 3.46
4023 4633 5.105797 GCAACATGTGTATTTCCATGGAAGA 60.106 40.000 25.69 17.31 42.15 2.87
4038 4648 7.761409 TCCATGGAAGATTTTGATTTTACTCG 58.239 34.615 13.46 0.00 0.00 4.18
4053 4663 6.642707 TTTTACTCGTGGATTTGTGGAATT 57.357 33.333 0.00 0.00 0.00 2.17
4054 4664 5.621197 TTACTCGTGGATTTGTGGAATTG 57.379 39.130 0.00 0.00 0.00 2.32
4086 4696 5.938322 TCTGAACTTCAAACTGTTGACAAC 58.062 37.500 11.54 11.54 43.52 3.32
4102 4712 6.090088 TGTTGACAACGAATCAAACTTTTTGG 59.910 34.615 13.46 0.00 37.80 3.28
4104 4714 6.159988 TGACAACGAATCAAACTTTTTGGTT 58.840 32.000 0.00 0.00 0.00 3.67
4126 4736 9.233649 TGGTTACTTGTTTCTTCTTCTGTTTTA 57.766 29.630 0.00 0.00 0.00 1.52
4237 4886 5.325239 GCCCTTGCTAGAAAATATGGGTAT 58.675 41.667 7.23 0.00 36.00 2.73
4255 4904 3.937079 GGTATTGGGTTACAACTCGGAAG 59.063 47.826 0.00 0.00 42.94 3.46
4365 5029 1.962822 CGAGAGCCAGTGCAGCAAA 60.963 57.895 0.00 0.00 41.13 3.68
4442 5106 1.168714 GCTCGAGAAGGCAATTTGGT 58.831 50.000 18.75 0.00 0.00 3.67
4471 5135 4.085204 AATCGGCGGCGGGTTGTA 62.085 61.111 31.73 11.47 0.00 2.41
4606 5280 2.355481 GTCGACTTCACCGCCGTT 60.355 61.111 8.70 0.00 0.00 4.44
4707 5384 1.215647 CCTTCTCCGTTGGACTCCG 59.784 63.158 0.00 0.00 0.00 4.63
4714 5391 1.442184 CGTTGGACTCCGTCGTGAG 60.442 63.158 8.60 8.60 38.37 3.51
4719 5396 2.944429 ACTCCGTCGTGAGTCGTG 59.056 61.111 9.68 0.00 41.75 4.35
4720 5397 1.596203 ACTCCGTCGTGAGTCGTGA 60.596 57.895 9.68 0.00 41.75 4.35
4721 5398 1.154450 CTCCGTCGTGAGTCGTGAC 60.154 63.158 4.85 4.85 40.95 3.67
4724 5401 2.126965 GTCGTGAGTCGTGACGGG 60.127 66.667 4.70 0.00 40.80 5.28
4725 5402 3.359523 TCGTGAGTCGTGACGGGG 61.360 66.667 4.70 0.00 40.80 5.73
4726 5403 3.359523 CGTGAGTCGTGACGGGGA 61.360 66.667 4.70 0.00 36.20 4.81
4727 5404 2.697761 CGTGAGTCGTGACGGGGAT 61.698 63.158 4.70 0.00 36.20 3.85
4728 5405 1.139095 GTGAGTCGTGACGGGGATC 59.861 63.158 4.70 0.00 36.20 3.36
4729 5406 1.001269 TGAGTCGTGACGGGGATCT 60.001 57.895 4.70 0.00 36.20 2.75
4730 5407 1.030488 TGAGTCGTGACGGGGATCTC 61.030 60.000 4.70 6.62 36.20 2.75
4731 5408 2.049475 GAGTCGTGACGGGGATCTCG 62.049 65.000 4.70 7.30 37.03 4.04
4732 5409 2.045634 TCGTGACGGGGATCTCGT 60.046 61.111 4.70 12.85 44.03 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 8.967552 TTTTCTAAAACGAAACAGCAAAGTTA 57.032 26.923 0.00 0.00 32.99 2.24
74 85 4.273480 GCACTGAGAGAGCTAAACAACAAA 59.727 41.667 0.00 0.00 0.00 2.83
107 125 0.675522 AATCCGTAACCGCACAAGGG 60.676 55.000 0.00 0.00 35.02 3.95
191 209 2.173356 TCGATTCTCCCGGTAGGAAGTA 59.827 50.000 0.00 0.00 46.94 2.24
193 211 1.688772 TCGATTCTCCCGGTAGGAAG 58.311 55.000 0.00 0.00 46.94 3.46
372 392 0.321564 TGGCAGCAGTTTACGCAGAT 60.322 50.000 0.00 0.00 0.00 2.90
426 446 3.896133 GCGCGACCGAGGTATGGA 61.896 66.667 12.10 0.00 36.29 3.41
531 567 0.895100 GCTTCACAGGAATGGCACCA 60.895 55.000 0.00 0.00 31.34 4.17
583 620 1.602237 GCGTCAAGGGGAGGATTCA 59.398 57.895 0.00 0.00 33.18 2.57
585 622 1.616628 AGGCGTCAAGGGGAGGATT 60.617 57.895 0.00 0.00 33.18 3.01
696 735 1.682849 CACAAGGGGACGGGATTCA 59.317 57.895 0.00 0.00 0.00 2.57
704 743 2.224917 TGGTATGTTTCCACAAGGGGAC 60.225 50.000 0.00 0.00 36.46 4.46
721 774 3.398318 TGGCTTGTAGATCCTCTGGTA 57.602 47.619 0.00 0.00 0.00 3.25
748 801 5.941555 TTCTCCCTTATCTTCTCTTCACC 57.058 43.478 0.00 0.00 0.00 4.02
793 856 9.860898 CCGAATCAGTTGATATATAGATGAACA 57.139 33.333 11.45 0.00 33.73 3.18
1227 1322 1.064458 GTAGGAGAGCCGCTTCGTC 59.936 63.158 0.00 0.00 39.96 4.20
1297 1394 3.570975 TGAAACTAGTAACGAGTGCTGGA 59.429 43.478 0.00 0.00 0.00 3.86
1310 1407 5.584551 ATTCCCCAGACTTTGAAACTAGT 57.415 39.130 0.00 0.00 0.00 2.57
1329 1426 6.535508 AGAACGACTGCTAAAATGAGGTATTC 59.464 38.462 0.00 0.00 0.00 1.75
1335 1432 6.952935 ACTAAGAACGACTGCTAAAATGAG 57.047 37.500 0.00 0.00 0.00 2.90
1336 1433 7.724305 AAACTAAGAACGACTGCTAAAATGA 57.276 32.000 0.00 0.00 0.00 2.57
1338 1435 8.379457 AGAAAACTAAGAACGACTGCTAAAAT 57.621 30.769 0.00 0.00 0.00 1.82
1339 1436 7.781548 AGAAAACTAAGAACGACTGCTAAAA 57.218 32.000 0.00 0.00 0.00 1.52
1345 1447 5.054477 TGGGAAGAAAACTAAGAACGACTG 58.946 41.667 0.00 0.00 0.00 3.51
1366 1492 5.732633 TGGAATTCCAAGCAACATAATTGG 58.267 37.500 25.13 0.00 44.35 3.16
1429 1555 3.366052 AAGACCACTGTTTGACAAGGT 57.634 42.857 5.00 5.00 38.70 3.50
1454 1580 7.359595 GCAGACTCACACAAAATGTAATGTAA 58.640 34.615 0.00 0.00 40.64 2.41
1455 1581 6.347321 CGCAGACTCACACAAAATGTAATGTA 60.347 38.462 0.00 0.00 40.64 2.29
1457 1583 4.847757 CGCAGACTCACACAAAATGTAATG 59.152 41.667 0.00 0.00 40.64 1.90
1459 1585 3.874543 ACGCAGACTCACACAAAATGTAA 59.125 39.130 0.00 0.00 40.64 2.41
1460 1586 3.462982 ACGCAGACTCACACAAAATGTA 58.537 40.909 0.00 0.00 40.64 2.29
1461 1587 2.288666 ACGCAGACTCACACAAAATGT 58.711 42.857 0.00 0.00 44.81 2.71
1462 1588 3.002656 AGAACGCAGACTCACACAAAATG 59.997 43.478 0.00 0.00 0.00 2.32
1463 1589 3.206150 AGAACGCAGACTCACACAAAAT 58.794 40.909 0.00 0.00 0.00 1.82
1465 1591 2.201732 GAGAACGCAGACTCACACAAA 58.798 47.619 0.00 0.00 35.54 2.83
1466 1592 1.538204 GGAGAACGCAGACTCACACAA 60.538 52.381 0.00 0.00 36.61 3.33
1467 1593 0.032130 GGAGAACGCAGACTCACACA 59.968 55.000 0.00 0.00 36.61 3.72
1468 1594 0.315568 AGGAGAACGCAGACTCACAC 59.684 55.000 0.00 0.00 36.61 3.82
1470 1596 1.813786 ACTAGGAGAACGCAGACTCAC 59.186 52.381 0.00 0.00 36.61 3.51
1480 1606 5.007136 GCATATGCTCAAACACTAGGAGAAC 59.993 44.000 20.64 0.00 38.21 3.01
1511 1637 3.514706 AGACATCTGCACATTCAGAGACT 59.485 43.478 0.00 0.00 45.22 3.24
1533 1660 1.691976 ACGAGGATCAGACAACCAACA 59.308 47.619 0.00 0.00 33.17 3.33
1573 1701 5.354234 ACAGAAACTACCTGCATAAAATCGG 59.646 40.000 0.00 0.00 35.14 4.18
1631 1760 2.223618 GCGTTGCTGTGGGTTCTTAAAA 60.224 45.455 0.00 0.00 0.00 1.52
1751 1880 8.253810 TGAGACAGAGAATATGAACTAACCTTG 58.746 37.037 0.00 0.00 0.00 3.61
1768 1900 5.975693 AGAACTAGAACCTTGAGACAGAG 57.024 43.478 0.00 0.00 0.00 3.35
1789 1921 1.353022 TGGTACCTGGGGCAAAACTAG 59.647 52.381 14.36 0.00 0.00 2.57
1791 1923 0.112412 CTGGTACCTGGGGCAAAACT 59.888 55.000 14.36 0.00 0.00 2.66
1792 1924 0.111639 TCTGGTACCTGGGGCAAAAC 59.888 55.000 17.82 0.00 0.00 2.43
1793 1925 0.404040 CTCTGGTACCTGGGGCAAAA 59.596 55.000 17.82 0.00 0.00 2.44
1794 1926 1.497309 CCTCTGGTACCTGGGGCAAA 61.497 60.000 23.52 0.36 0.00 3.68
1795 1927 1.923395 CCTCTGGTACCTGGGGCAA 60.923 63.158 23.52 1.07 0.00 4.52
1796 1928 2.285368 CCTCTGGTACCTGGGGCA 60.285 66.667 23.52 1.44 0.00 5.36
1799 1931 1.507140 TATTGCCTCTGGTACCTGGG 58.493 55.000 17.82 14.88 0.00 4.45
1800 1932 2.811873 GCATATTGCCTCTGGTACCTGG 60.812 54.545 17.82 15.02 37.42 4.45
1801 1933 2.158769 TGCATATTGCCTCTGGTACCTG 60.159 50.000 14.36 13.33 44.23 4.00
1802 1934 2.105477 CTGCATATTGCCTCTGGTACCT 59.895 50.000 14.36 0.00 44.23 3.08
1803 1935 2.158755 ACTGCATATTGCCTCTGGTACC 60.159 50.000 4.43 4.43 44.23 3.34
1804 1936 3.134458 GACTGCATATTGCCTCTGGTAC 58.866 50.000 0.00 0.00 44.23 3.34
1823 1974 7.008992 CACGCTTATTTAACTAGGTACAGTGAC 59.991 40.741 0.00 0.00 0.00 3.67
1824 1975 7.031372 CACGCTTATTTAACTAGGTACAGTGA 58.969 38.462 0.00 0.00 0.00 3.41
1825 1976 6.810182 ACACGCTTATTTAACTAGGTACAGTG 59.190 38.462 0.00 0.00 0.00 3.66
1826 1977 6.928520 ACACGCTTATTTAACTAGGTACAGT 58.071 36.000 0.00 0.00 0.00 3.55
1831 1982 9.472361 CACATATACACGCTTATTTAACTAGGT 57.528 33.333 0.00 0.00 0.00 3.08
1839 1996 5.236478 GGACAGCACATATACACGCTTATTT 59.764 40.000 0.00 0.00 30.72 1.40
1879 2036 6.042143 TCCAAGTTGAATTGAGAAGCAAAAC 58.958 36.000 3.87 0.00 40.48 2.43
1888 2045 7.065563 CCAGTCTCTAATCCAAGTTGAATTGAG 59.934 40.741 3.87 6.24 31.55 3.02
1926 2086 3.313526 GCATCCTGCTTGGTAAGTGTATG 59.686 47.826 0.00 0.00 40.96 2.39
1944 2115 8.310382 ACTATATGAGTGGAATAACTGAGCATC 58.690 37.037 0.00 0.00 36.87 3.91
1990 2178 2.484264 GCAGTATCTTGTTTTCCAGCGT 59.516 45.455 0.00 0.00 0.00 5.07
1993 2181 6.238320 GCATAGAGCAGTATCTTGTTTTCCAG 60.238 42.308 0.00 0.00 44.79 3.86
2043 2231 2.512705 TGCTGCACCACACATCATTTA 58.487 42.857 0.00 0.00 0.00 1.40
2093 2281 3.117322 TGGGACAGAGAACCAATGGAAAA 60.117 43.478 6.16 0.00 0.00 2.29
2096 2284 1.351017 GTGGGACAGAGAACCAATGGA 59.649 52.381 6.16 0.00 41.80 3.41
2097 2285 1.073763 TGTGGGACAGAGAACCAATGG 59.926 52.381 0.00 0.00 41.80 3.16
2205 2634 0.106419 AACGGCCACAGAAAAGGGAA 60.106 50.000 2.24 0.00 0.00 3.97
2206 2635 0.106419 AAACGGCCACAGAAAAGGGA 60.106 50.000 2.24 0.00 0.00 4.20
2207 2636 1.611519 TAAACGGCCACAGAAAAGGG 58.388 50.000 2.24 0.00 0.00 3.95
2208 2637 3.934457 AATAAACGGCCACAGAAAAGG 57.066 42.857 2.24 0.00 0.00 3.11
2209 2638 7.883229 AAATAAATAAACGGCCACAGAAAAG 57.117 32.000 2.24 0.00 0.00 2.27
2210 2639 8.145122 AGAAAATAAATAAACGGCCACAGAAAA 58.855 29.630 2.24 0.00 0.00 2.29
2211 2640 7.662897 AGAAAATAAATAAACGGCCACAGAAA 58.337 30.769 2.24 0.00 0.00 2.52
2212 2641 7.040340 TGAGAAAATAAATAAACGGCCACAGAA 60.040 33.333 2.24 0.00 0.00 3.02
2214 2643 6.616947 TGAGAAAATAAATAAACGGCCACAG 58.383 36.000 2.24 0.00 0.00 3.66
2215 2644 6.576662 TGAGAAAATAAATAAACGGCCACA 57.423 33.333 2.24 0.00 0.00 4.17
2216 2645 7.876896 TTTGAGAAAATAAATAAACGGCCAC 57.123 32.000 2.24 0.00 0.00 5.01
2217 2646 9.495572 AAATTTGAGAAAATAAATAAACGGCCA 57.504 25.926 2.24 0.00 0.00 5.36
2293 2722 6.183360 GCATACTGACGTCAATATTCAACACA 60.183 38.462 20.49 0.00 0.00 3.72
2299 2728 8.338259 AGAAAATGCATACTGACGTCAATATTC 58.662 33.333 20.49 14.31 0.00 1.75
2311 2740 8.490355 GGAAAGAAAAACAGAAAATGCATACTG 58.510 33.333 19.70 19.70 36.58 2.74
2361 2794 6.487668 CAGTATGCCATGATTTACTGGAATCA 59.512 38.462 15.50 9.96 46.64 2.57
2414 2847 0.392595 GATTGGACAGTTCCCCCGAC 60.393 60.000 0.00 0.00 42.01 4.79
2452 2885 4.268359 AGCCTGAGAATTTCTGGTTCATC 58.732 43.478 3.03 0.00 44.48 2.92
2583 3016 8.002459 AGAAATATGAAACATTACCGGGGTATT 58.998 33.333 6.32 0.00 0.00 1.89
2630 3063 9.726232 CCTAATGACATCATTTTAGTGAACATG 57.274 33.333 12.16 0.00 43.48 3.21
2692 3126 9.726438 ATCATACACCTATTTACTTAAGATGCC 57.274 33.333 10.09 0.00 0.00 4.40
2751 3324 6.932356 TCAGAACATCATAATCTTCCAAGC 57.068 37.500 0.00 0.00 0.00 4.01
2792 3366 5.833082 TCACGGCTAACATAGAGAAATCTC 58.167 41.667 2.10 2.10 43.17 2.75
2835 3409 6.014669 ACCAGCAAATTAGAAAATGGCAACTA 60.015 34.615 0.00 0.00 31.78 2.24
2841 3415 5.349543 GCAGAACCAGCAAATTAGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
2848 3422 9.754382 ATTTTATATGCAGAACCAGCAAATTAG 57.246 29.630 0.00 0.00 46.27 1.73
2849 3423 9.531942 CATTTTATATGCAGAACCAGCAAATTA 57.468 29.630 0.00 0.00 46.27 1.40
2861 3437 3.750371 CCCGGGTCATTTTATATGCAGA 58.250 45.455 14.18 0.00 0.00 4.26
2877 3453 4.114997 GTGCAATTGTCGCCCGGG 62.115 66.667 19.09 19.09 0.00 5.73
2894 3470 2.996621 TCACCAAAGGTTTTGCAAAACG 59.003 40.909 36.05 27.41 47.00 3.60
2940 3516 6.853872 GCTACGACACAAGATATAAGTCAGAG 59.146 42.308 0.00 0.00 0.00 3.35
2941 3517 6.317893 TGCTACGACACAAGATATAAGTCAGA 59.682 38.462 0.00 0.00 0.00 3.27
2956 3532 1.402984 CCTTCTGGTCTGCTACGACAC 60.403 57.143 0.00 0.00 35.63 3.67
2989 3565 1.080501 ACGTGGTCATGAGCGACTG 60.081 57.895 19.36 15.06 36.12 3.51
3087 3663 2.839486 TCTGCAGTAGACTGTTTGGG 57.161 50.000 14.67 0.00 45.45 4.12
3146 3722 4.513318 GCCCAGTAGATTTAGACAAGATGC 59.487 45.833 0.00 0.00 0.00 3.91
3150 3726 5.674525 TCATGCCCAGTAGATTTAGACAAG 58.325 41.667 0.00 0.00 0.00 3.16
3178 3754 9.338622 AGTAAGTTTTAAGTTCTAACTGTGCAT 57.661 29.630 0.00 0.00 39.66 3.96
3215 3794 1.363744 GACAGCTTCGCTTACTGCAT 58.636 50.000 0.00 0.00 43.06 3.96
3357 3936 4.627255 GCTTTTCTCCTCTCCCATTCATCA 60.627 45.833 0.00 0.00 0.00 3.07
3450 4029 7.891183 TCTTCTAGATCTAGTTGTTCTTGGAGT 59.109 37.037 25.54 0.00 34.84 3.85
3528 4109 0.991920 ATTTCCGGACCAGTGGATGT 59.008 50.000 18.40 0.00 33.42 3.06
3566 4152 0.027194 CGCCTGAAAGACATCGCATG 59.973 55.000 0.00 0.00 34.07 4.06
3639 4225 0.251742 CACCCATTTCTTCAGGGCCA 60.252 55.000 6.18 0.00 46.88 5.36
3717 4303 3.956744 ACTGTGCTAAAATCTTCCCCTC 58.043 45.455 0.00 0.00 0.00 4.30
3768 4355 1.674962 GCCACCATCTCTGAAGATTGC 59.325 52.381 0.00 0.00 40.38 3.56
3818 4406 1.314730 GCCTCCGTTTCAAAAGGTGA 58.685 50.000 5.81 0.00 0.00 4.02
3819 4407 0.040425 CGCCTCCGTTTCAAAAGGTG 60.040 55.000 1.72 0.00 33.45 4.00
3820 4408 1.170290 CCGCCTCCGTTTCAAAAGGT 61.170 55.000 1.72 0.00 0.00 3.50
3831 4419 1.226974 CATGACACTACCGCCTCCG 60.227 63.158 0.00 0.00 0.00 4.63
3875 4463 7.751348 GTCATCATCATCGTCATAAGGTACTAC 59.249 40.741 0.00 0.00 38.49 2.73
3881 4469 5.144692 AGGTCATCATCATCGTCATAAGG 57.855 43.478 0.00 0.00 0.00 2.69
3889 4492 7.545362 AAGAGTTAAAAGGTCATCATCATCG 57.455 36.000 0.00 0.00 0.00 3.84
3924 4530 4.755411 ACTCAACTCAGAGTGAAACGAAA 58.245 39.130 3.05 0.00 46.58 3.46
3962 4571 2.821969 ACCCTTGACATTTTGCTAGCTG 59.178 45.455 17.23 8.25 0.00 4.24
3995 4604 5.336610 CCATGGAAATACACATGTTGCTTGA 60.337 40.000 5.56 0.00 42.15 3.02
3999 4608 4.717233 TCCATGGAAATACACATGTTGC 57.283 40.909 13.46 0.00 42.15 4.17
4022 4632 8.638565 CACAAATCCACGAGTAAAATCAAAATC 58.361 33.333 0.00 0.00 0.00 2.17
4023 4633 7.598493 CCACAAATCCACGAGTAAAATCAAAAT 59.402 33.333 0.00 0.00 0.00 1.82
4038 4648 2.562298 TCTGCCAATTCCACAAATCCAC 59.438 45.455 0.00 0.00 0.00 4.02
4053 4663 3.490439 TGAAGTTCAGAACATCTGCCA 57.510 42.857 17.27 3.53 43.95 4.92
4054 4664 4.276926 AGTTTGAAGTTCAGAACATCTGCC 59.723 41.667 21.97 6.85 43.95 4.85
4086 4696 7.749539 ACAAGTAACCAAAAAGTTTGATTCG 57.250 32.000 2.30 0.00 0.00 3.34
4223 4872 8.119891 AGTTGTAACCCAATACCCATATTTTCT 58.880 33.333 0.00 0.00 35.02 2.52
4224 4873 8.301252 AGTTGTAACCCAATACCCATATTTTC 57.699 34.615 0.00 0.00 35.02 2.29
4237 4886 3.469739 GTTCTTCCGAGTTGTAACCCAA 58.530 45.455 0.00 0.00 0.00 4.12
4442 5106 1.831286 GCCGATTCCCCGACTCCTA 60.831 63.158 0.00 0.00 0.00 2.94
4465 5129 1.146263 CCCTGCGGATCCTACAACC 59.854 63.158 10.75 0.00 0.00 3.77
4648 5322 2.496817 GCGCCCTCTCACCTGTAG 59.503 66.667 0.00 0.00 0.00 2.74
4669 5343 6.214412 AGAAGGAAGAAGATCTCCAAGCTAAA 59.786 38.462 0.00 0.00 0.00 1.85
4707 5384 2.126965 CCCGTCACGACTCACGAC 60.127 66.667 0.00 0.00 45.77 4.34
4714 5391 2.404995 ACGAGATCCCCGTCACGAC 61.405 63.158 0.00 0.00 34.97 4.34
4715 5392 2.045634 ACGAGATCCCCGTCACGA 60.046 61.111 0.00 0.00 34.97 4.35


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

AutoCloner maintained by Alex Coulton.