Multiple sequence alignment - TraesCS3B01G271500

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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 TraesCS3B01G271500 chr3B 100.000 3579 0 0 1 3579 436838204 436834626 0.000000e+00 6610
1 TraesCS3B01G271500 chr3B 94.501 1764 84 10 731 2486 744039244 744041002 0.000000e+00 2708
2 TraesCS3B01G271500 chr3B 94.501 1764 84 10 731 2486 744056176 744057934 0.000000e+00 2708
3 TraesCS3B01G271500 chr3B 91.384 1207 90 8 1828 3024 181707263 181706061 0.000000e+00 1640
4 TraesCS3B01G271500 chr3B 89.716 1128 68 21 724 1813 181708481 181707364 0.000000e+00 1397
5 TraesCS3B01G271500 chr3B 96.558 552 19 0 3027 3578 654443284 654443835 0.000000e+00 915
6 TraesCS3B01G271500 chr3B 96.196 552 21 0 3027 3578 373976559 373977110 0.000000e+00 904
7 TraesCS3B01G271500 chr2D 95.138 2098 88 11 728 2819 647863558 647865647 0.000000e+00 3297
8 TraesCS3B01G271500 chr2D 89.879 1482 101 29 1469 2909 181285846 181287319 0.000000e+00 1860
9 TraesCS3B01G271500 chr2D 96.196 552 21 0 3027 3578 466251489 466250938 0.000000e+00 904
10 TraesCS3B01G271500 chr6B 94.455 2110 102 7 731 2835 28739491 28737392 0.000000e+00 3234
11 TraesCS3B01G271500 chr6B 92.297 701 46 5 727 1423 90976473 90977169 0.000000e+00 989
12 TraesCS3B01G271500 chr6B 95.878 558 22 1 3021 3578 551110667 551111223 0.000000e+00 902
13 TraesCS3B01G271500 chr7B 93.934 2077 105 10 862 2922 641462303 641464374 0.000000e+00 3118
14 TraesCS3B01G271500 chr7B 91.312 2187 126 25 731 2876 394078188 394076025 0.000000e+00 2928
15 TraesCS3B01G271500 chr5B 94.571 2026 86 13 730 2736 610368938 610366918 0.000000e+00 3110
16 TraesCS3B01G271500 chr5B 96.022 553 22 0 3027 3579 650620872 650620320 0.000000e+00 900
17 TraesCS3B01G271500 chr2B 92.012 1928 98 25 731 2628 731577461 731575560 0.000000e+00 2656
18 TraesCS3B01G271500 chr2B 93.788 998 34 2 1781 2751 753116750 753117746 0.000000e+00 1474
19 TraesCS3B01G271500 chr1D 90.188 1600 105 33 1469 3024 69770810 69772401 0.000000e+00 2037
20 TraesCS3B01G271500 chr1D 89.779 1585 112 30 1483 3026 261726015 261727590 0.000000e+00 1984
21 TraesCS3B01G271500 chr1D 89.073 1510 107 34 1469 2932 11302966 11304463 0.000000e+00 1821
22 TraesCS3B01G271500 chr1D 93.767 738 40 6 1828 2563 21319396 21318663 0.000000e+00 1103
23 TraesCS3B01G271500 chr1D 92.697 712 34 6 728 1423 261725112 261725821 0.000000e+00 1011
24 TraesCS3B01G271500 chr1D 95.856 555 23 0 3023 3577 258762616 258762062 0.000000e+00 898
25 TraesCS3B01G271500 chr1D 88.131 337 31 8 2657 2988 69772082 69772414 3.350000e-105 392
26 TraesCS3B01G271500 chr1D 84.718 373 43 12 2657 3024 261727273 261727636 9.450000e-96 361
27 TraesCS3B01G271500 chr5D 89.601 1606 108 38 1469 3026 235203232 235204826 0.000000e+00 1986
28 TraesCS3B01G271500 chr5D 91.026 702 50 6 731 1423 379341695 379340998 0.000000e+00 935
29 TraesCS3B01G271500 chr5D 87.791 344 32 9 2660 2998 235204558 235204896 9.310000e-106 394
30 TraesCS3B01G271500 chr5D 85.255 373 43 11 2657 3024 235204507 235204872 1.210000e-99 374
31 TraesCS3B01G271500 chr6D 89.725 1489 104 31 1469 2919 17867487 17868964 0.000000e+00 1857
32 TraesCS3B01G271500 chr5A 91.357 1157 76 18 1828 2968 678335150 678334002 0.000000e+00 1561
33 TraesCS3B01G271500 chr5A 92.199 705 43 6 730 1423 439396381 439395678 0.000000e+00 987
34 TraesCS3B01G271500 chr5A 91.773 705 45 7 730 1423 439427906 439427204 0.000000e+00 968
35 TraesCS3B01G271500 chr1B 91.308 1139 74 15 1828 2950 661876112 661877241 0.000000e+00 1531
36 TraesCS3B01G271500 chr6A 94.537 842 44 2 1828 2669 67473687 67472848 0.000000e+00 1299
37 TraesCS3B01G271500 chr3D 92.752 745 37 1 3 730 338582103 338581359 0.000000e+00 1061
38 TraesCS3B01G271500 chr4D 96.377 552 19 1 3027 3578 401800068 401800618 0.000000e+00 907
39 TraesCS3B01G271500 chr4B 96.050 557 22 0 3023 3579 411916075 411915519 0.000000e+00 907
40 TraesCS3B01G271500 chr7D 96.196 552 21 0 3027 3578 238711703 238712254 0.000000e+00 904
41 TraesCS3B01G271500 chr7D 87.228 368 37 8 2660 3024 562225096 562224736 9.250000e-111 411
42 TraesCS3B01G271500 chr7D 85.561 374 39 12 2660 3026 94459990 94459625 9.380000e-101 377
43 TraesCS3B01G271500 chr7D 84.824 369 46 9 2657 3024 45627798 45628157 2.630000e-96 363
44 TraesCS3B01G271500 chr3A 91.667 492 29 4 3 482 456808231 456807740 0.000000e+00 671
45 TraesCS3B01G271500 chr3A 92.228 193 15 0 538 730 456807097 456806905 1.270000e-69 274
46 TraesCS3B01G271500 chrUn 77.212 452 96 6 1904 2353 84447985 84447539 1.270000e-64 257


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 TraesCS3B01G271500 chr3B 436834626 436838204 3578 True 6610.000000 6610 100.000000 1 3579 1 chr3B.!!$R1 3578
1 TraesCS3B01G271500 chr3B 744039244 744041002 1758 False 2708.000000 2708 94.501000 731 2486 1 chr3B.!!$F3 1755
2 TraesCS3B01G271500 chr3B 744056176 744057934 1758 False 2708.000000 2708 94.501000 731 2486 1 chr3B.!!$F4 1755
3 TraesCS3B01G271500 chr3B 181706061 181708481 2420 True 1518.500000 1640 90.550000 724 3024 2 chr3B.!!$R2 2300
4 TraesCS3B01G271500 chr3B 654443284 654443835 551 False 915.000000 915 96.558000 3027 3578 1 chr3B.!!$F2 551
5 TraesCS3B01G271500 chr3B 373976559 373977110 551 False 904.000000 904 96.196000 3027 3578 1 chr3B.!!$F1 551
6 TraesCS3B01G271500 chr2D 647863558 647865647 2089 False 3297.000000 3297 95.138000 728 2819 1 chr2D.!!$F2 2091
7 TraesCS3B01G271500 chr2D 181285846 181287319 1473 False 1860.000000 1860 89.879000 1469 2909 1 chr2D.!!$F1 1440
8 TraesCS3B01G271500 chr2D 466250938 466251489 551 True 904.000000 904 96.196000 3027 3578 1 chr2D.!!$R1 551
9 TraesCS3B01G271500 chr6B 28737392 28739491 2099 True 3234.000000 3234 94.455000 731 2835 1 chr6B.!!$R1 2104
10 TraesCS3B01G271500 chr6B 90976473 90977169 696 False 989.000000 989 92.297000 727 1423 1 chr6B.!!$F1 696
11 TraesCS3B01G271500 chr6B 551110667 551111223 556 False 902.000000 902 95.878000 3021 3578 1 chr6B.!!$F2 557
12 TraesCS3B01G271500 chr7B 641462303 641464374 2071 False 3118.000000 3118 93.934000 862 2922 1 chr7B.!!$F1 2060
13 TraesCS3B01G271500 chr7B 394076025 394078188 2163 True 2928.000000 2928 91.312000 731 2876 1 chr7B.!!$R1 2145
14 TraesCS3B01G271500 chr5B 610366918 610368938 2020 True 3110.000000 3110 94.571000 730 2736 1 chr5B.!!$R1 2006
15 TraesCS3B01G271500 chr5B 650620320 650620872 552 True 900.000000 900 96.022000 3027 3579 1 chr5B.!!$R2 552
16 TraesCS3B01G271500 chr2B 731575560 731577461 1901 True 2656.000000 2656 92.012000 731 2628 1 chr2B.!!$R1 1897
17 TraesCS3B01G271500 chr2B 753116750 753117746 996 False 1474.000000 1474 93.788000 1781 2751 1 chr2B.!!$F1 970
18 TraesCS3B01G271500 chr1D 11302966 11304463 1497 False 1821.000000 1821 89.073000 1469 2932 1 chr1D.!!$F1 1463
19 TraesCS3B01G271500 chr1D 69770810 69772414 1604 False 1214.500000 2037 89.159500 1469 3024 2 chr1D.!!$F2 1555
20 TraesCS3B01G271500 chr1D 261725112 261727636 2524 False 1118.666667 1984 89.064667 728 3026 3 chr1D.!!$F3 2298
21 TraesCS3B01G271500 chr1D 21318663 21319396 733 True 1103.000000 1103 93.767000 1828 2563 1 chr1D.!!$R1 735
22 TraesCS3B01G271500 chr1D 258762062 258762616 554 True 898.000000 898 95.856000 3023 3577 1 chr1D.!!$R2 554
23 TraesCS3B01G271500 chr5D 379340998 379341695 697 True 935.000000 935 91.026000 731 1423 1 chr5D.!!$R1 692
24 TraesCS3B01G271500 chr5D 235203232 235204896 1664 False 918.000000 1986 87.549000 1469 3026 3 chr5D.!!$F1 1557
25 TraesCS3B01G271500 chr6D 17867487 17868964 1477 False 1857.000000 1857 89.725000 1469 2919 1 chr6D.!!$F1 1450
26 TraesCS3B01G271500 chr5A 678334002 678335150 1148 True 1561.000000 1561 91.357000 1828 2968 1 chr5A.!!$R3 1140
27 TraesCS3B01G271500 chr5A 439395678 439396381 703 True 987.000000 987 92.199000 730 1423 1 chr5A.!!$R1 693
28 TraesCS3B01G271500 chr5A 439427204 439427906 702 True 968.000000 968 91.773000 730 1423 1 chr5A.!!$R2 693
29 TraesCS3B01G271500 chr1B 661876112 661877241 1129 False 1531.000000 1531 91.308000 1828 2950 1 chr1B.!!$F1 1122
30 TraesCS3B01G271500 chr6A 67472848 67473687 839 True 1299.000000 1299 94.537000 1828 2669 1 chr6A.!!$R1 841
31 TraesCS3B01G271500 chr3D 338581359 338582103 744 True 1061.000000 1061 92.752000 3 730 1 chr3D.!!$R1 727
32 TraesCS3B01G271500 chr4D 401800068 401800618 550 False 907.000000 907 96.377000 3027 3578 1 chr4D.!!$F1 551
33 TraesCS3B01G271500 chr4B 411915519 411916075 556 True 907.000000 907 96.050000 3023 3579 1 chr4B.!!$R1 556
34 TraesCS3B01G271500 chr7D 238711703 238712254 551 False 904.000000 904 96.196000 3027 3578 1 chr7D.!!$F2 551
35 TraesCS3B01G271500 chr3A 456806905 456808231 1326 True 472.500000 671 91.947500 3 730 2 chr3A.!!$R1 727

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
229 234 0.297820 GCATACAGAGCGCGTTGTAC 59.702 55.0 23.09 12.04 33.03 2.90 F
557 1157 0.462759 GCTGCTCCTTTATGCCGTCT 60.463 55.0 0.00 0.00 0.00 4.18 F
903 1506 0.603439 GGTCCCGTTTTTCGCCTACA 60.603 55.0 0.00 0.00 38.35 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 2052 0.480252 AACAAAGAAGCCTCCTGCCT 59.520 50.000 0.00 0.00 42.71 4.75 R
2212 3161 0.612229 ACAGTAGCATGAGCAGCTGT 59.388 50.000 16.64 1.59 45.99 4.40 R
2776 4275 2.195727 TGACCCTACATGATGCCTCAA 58.804 47.619 0.00 0.00 34.37 3.02 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
64 65 2.764944 GTGGACGACGAGCTCTCTA 58.235 57.895 12.85 0.00 0.00 2.43
80 81 2.515853 TCTCTAATCTCTGAGCTGGGGA 59.484 50.000 0.00 0.00 0.00 4.81
168 173 2.089980 GCATGAGGTGAAGATGCACTT 58.910 47.619 0.00 0.00 41.78 3.16
205 210 0.963856 ACTCCGGTATGTCGTGCAGA 60.964 55.000 0.00 0.00 0.00 4.26
229 234 0.297820 GCATACAGAGCGCGTTGTAC 59.702 55.000 23.09 12.04 33.03 2.90
239 244 2.307309 GCGTTGTACTCGTGCAGCA 61.307 57.895 0.00 0.00 0.00 4.41
240 245 1.827315 GCGTTGTACTCGTGCAGCAA 61.827 55.000 0.00 0.00 0.00 3.91
327 332 3.424703 CATGACTGGGAAAAGTGTGGAT 58.575 45.455 0.00 0.00 0.00 3.41
382 387 1.486310 TCGAGTTCATTGATCCCCCAG 59.514 52.381 0.00 0.00 0.00 4.45
408 413 4.440145 GGCCTTGGAAATGAGCCA 57.560 55.556 0.00 0.00 43.32 4.75
433 446 2.749682 CAGGCTGTGCTGTGGGTA 59.250 61.111 6.28 0.00 0.00 3.69
513 1096 1.348064 TTGACGGATCTGGACAAGGT 58.652 50.000 6.47 0.00 0.00 3.50
523 1106 4.120331 GACAAGGTGCGCATGGCC 62.120 66.667 15.91 11.00 42.61 5.36
557 1157 0.462759 GCTGCTCCTTTATGCCGTCT 60.463 55.000 0.00 0.00 0.00 4.18
584 1184 8.280084 AGTCTGTACAGTATATGAGTTCCCTTA 58.720 37.037 21.99 0.00 0.00 2.69
654 1254 0.681887 TATGTCGCCGACCCTCAAGA 60.682 55.000 15.60 0.00 0.00 3.02
671 1271 1.682684 GACGAGGGAAGGGAGCTCA 60.683 63.158 17.19 0.00 0.00 4.26
672 1272 1.002274 ACGAGGGAAGGGAGCTCAT 59.998 57.895 17.19 0.00 0.00 2.90
708 1308 1.464376 GCGACTGGATAGCAGCCCTA 61.464 60.000 0.00 0.00 0.00 3.53
842 1444 6.237861 GCGTAATTGTTTTGCAAAAACCACTA 60.238 34.615 25.40 11.65 40.91 2.74
847 1449 4.268884 TGTTTTGCAAAAACCACTAATCGC 59.731 37.500 25.40 9.56 0.00 4.58
886 1488 2.897969 AGTGAGTTTATGACAGGTCGGT 59.102 45.455 0.00 0.00 0.00 4.69
903 1506 0.603439 GGTCCCGTTTTTCGCCTACA 60.603 55.000 0.00 0.00 38.35 2.74
1100 1779 1.412710 GAGTGATGGGTCGGATAGCAA 59.587 52.381 0.00 0.00 0.00 3.91
1206 1885 7.233632 TGATATTTGGGGATTTCTCGAATGAT 58.766 34.615 0.00 0.00 0.00 2.45
1270 1949 0.835971 TCCAGGTTCCTGCTAGCACA 60.836 55.000 14.93 0.00 33.07 4.57
1372 2052 1.610624 GCCTTCGAAGGGATTCACACA 60.611 52.381 38.28 0.00 46.56 3.72
1382 2062 1.001641 ATTCACACAGGCAGGAGGC 60.002 57.895 0.00 0.00 43.74 4.70
1397 2077 1.408702 GGAGGCTTCTTTGTTGTGCAA 59.591 47.619 0.00 0.00 34.87 4.08
1408 2088 3.641437 TGTTGTGCAAAGAAGGTATGC 57.359 42.857 0.00 0.00 40.45 3.14
1449 2130 5.764686 ACAGATCTGTCATTTGTTTGCACTA 59.235 36.000 22.89 0.00 40.24 2.74
1570 2428 8.862325 ATTATATTGTGAAGTTTGGACAGTGA 57.138 30.769 0.00 0.00 0.00 3.41
1613 2471 3.005791 GCCAGCATTGTTTAGTCTGGTTT 59.994 43.478 8.19 0.00 44.53 3.27
1752 2615 9.719279 TTGTTTAGTTAGGTCATTTTGTTAACG 57.281 29.630 0.26 0.00 31.36 3.18
1872 2821 5.869753 ATCATTGTAAGCAAGTCACTGTC 57.130 39.130 0.00 0.00 38.10 3.51
1981 2930 3.314635 CCTTGAGAATGCACTATCCAAGC 59.685 47.826 14.71 0.00 0.00 4.01
2027 2976 7.817440 ACTAAGATAGACAGGACTGAGGAATA 58.183 38.462 6.29 0.00 0.00 1.75
2212 3161 8.367911 AGAAGTATGACACTGTGAAGAACATAA 58.632 33.333 15.86 0.00 38.39 1.90
2223 3172 4.394300 GTGAAGAACATAACAGCTGCTCAT 59.606 41.667 15.27 1.08 0.00 2.90
2493 3446 6.209589 TGAGTACTCCTGAACTATGGATATGC 59.790 42.308 20.11 0.00 0.00 3.14
2534 3487 5.710513 TGCATTTGAACTAGTGCTGAATT 57.289 34.783 1.64 0.00 38.37 2.17
2772 4271 3.703001 TGGGTTTTTGGCTTTTTGTCA 57.297 38.095 0.00 0.00 0.00 3.58
2776 4275 4.397730 GGGTTTTTGGCTTTTTGTCAATGT 59.602 37.500 0.00 0.00 40.27 2.71
2787 4286 5.471556 TTTTGTCAATGTTGAGGCATCAT 57.528 34.783 0.03 0.00 37.98 2.45
2804 4352 4.684214 GCATCATGTAGGGTCAAGTGATGA 60.684 45.833 15.10 0.00 43.30 2.92
2894 4542 1.136305 GCTGACGCATCAAGTAGGGTA 59.864 52.381 0.00 0.00 33.30 3.69
2899 4547 4.251268 GACGCATCAAGTAGGGTAAAGTT 58.749 43.478 0.00 0.00 0.00 2.66
2900 4548 4.648651 ACGCATCAAGTAGGGTAAAGTTT 58.351 39.130 0.00 0.00 0.00 2.66
2901 4549 4.454504 ACGCATCAAGTAGGGTAAAGTTTG 59.545 41.667 0.00 0.00 0.00 2.93
2904 4552 5.321927 CATCAAGTAGGGTAAAGTTTGGGT 58.678 41.667 0.00 0.00 0.00 4.51
2943 4641 0.824109 TGTCGAGGCATCAAGTAGGG 59.176 55.000 0.00 0.00 0.00 3.53
2944 4642 0.824759 GTCGAGGCATCAAGTAGGGT 59.175 55.000 0.00 0.00 0.00 4.34
2950 4648 2.026822 AGGCATCAAGTAGGGTCAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2952 4650 3.370953 GGCATCAAGTAGGGTCAAGTGAT 60.371 47.826 0.00 0.00 0.00 3.06
2999 4697 2.026822 AGGCATCAAGTAGGGTCAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3000 4698 2.359900 GCATCAAGTAGGGTCAAGTGG 58.640 52.381 0.00 0.00 0.00 4.00
3001 4699 2.290323 GCATCAAGTAGGGTCAAGTGGT 60.290 50.000 0.00 0.00 0.00 4.16
3002 4700 3.338249 CATCAAGTAGGGTCAAGTGGTG 58.662 50.000 0.00 0.00 0.00 4.17
3003 4701 1.697432 TCAAGTAGGGTCAAGTGGTGG 59.303 52.381 0.00 0.00 0.00 4.61
3004 4702 1.420138 CAAGTAGGGTCAAGTGGTGGT 59.580 52.381 0.00 0.00 0.00 4.16
3005 4703 1.815757 AGTAGGGTCAAGTGGTGGTT 58.184 50.000 0.00 0.00 0.00 3.67
3006 4704 2.132686 AGTAGGGTCAAGTGGTGGTTT 58.867 47.619 0.00 0.00 0.00 3.27
3007 4705 2.512476 AGTAGGGTCAAGTGGTGGTTTT 59.488 45.455 0.00 0.00 0.00 2.43
3008 4706 2.543037 AGGGTCAAGTGGTGGTTTTT 57.457 45.000 0.00 0.00 0.00 1.94
3009 4707 2.107366 AGGGTCAAGTGGTGGTTTTTG 58.893 47.619 0.00 0.00 0.00 2.44
3010 4708 1.138069 GGGTCAAGTGGTGGTTTTTGG 59.862 52.381 0.00 0.00 0.00 3.28
3011 4709 1.472552 GGTCAAGTGGTGGTTTTTGGC 60.473 52.381 0.00 0.00 0.00 4.52
3012 4710 1.480545 GTCAAGTGGTGGTTTTTGGCT 59.519 47.619 0.00 0.00 0.00 4.75
3013 4711 2.093711 GTCAAGTGGTGGTTTTTGGCTT 60.094 45.455 0.00 0.00 0.00 4.35
3014 4712 2.093764 TCAAGTGGTGGTTTTTGGCTTG 60.094 45.455 0.00 0.00 34.80 4.01
3015 4713 1.567357 AGTGGTGGTTTTTGGCTTGT 58.433 45.000 0.00 0.00 0.00 3.16
3016 4714 1.905894 AGTGGTGGTTTTTGGCTTGTT 59.094 42.857 0.00 0.00 0.00 2.83
3017 4715 2.006169 GTGGTGGTTTTTGGCTTGTTG 58.994 47.619 0.00 0.00 0.00 3.33
3018 4716 1.625818 TGGTGGTTTTTGGCTTGTTGT 59.374 42.857 0.00 0.00 0.00 3.32
3019 4717 2.276201 GGTGGTTTTTGGCTTGTTGTC 58.724 47.619 0.00 0.00 0.00 3.18
3020 4718 1.923864 GTGGTTTTTGGCTTGTTGTCG 59.076 47.619 0.00 0.00 0.00 4.35
3021 4719 1.819288 TGGTTTTTGGCTTGTTGTCGA 59.181 42.857 0.00 0.00 0.00 4.20
3199 4897 4.407296 ACCCTGCAACCAAATAACAAAGAA 59.593 37.500 0.00 0.00 0.00 2.52
3262 4960 1.153628 GGTGCACTAGTTCGGCGAT 60.154 57.895 17.98 0.00 0.00 4.58
3267 4965 1.469251 GCACTAGTTCGGCGATGAGAA 60.469 52.381 11.76 0.00 0.00 2.87
3303 5001 7.932491 AGTGCAATATGGATGATAGATATGAGC 59.068 37.037 0.00 0.00 0.00 4.26
3429 5127 4.811557 ACTAGTGCAAGTTCTCTCAACAAC 59.188 41.667 0.00 0.00 0.00 3.32
3489 5187 3.793465 GCAACAAAGAGTCACTCCAAAGC 60.793 47.826 0.00 0.00 0.00 3.51
3490 5188 3.281727 ACAAAGAGTCACTCCAAAGCA 57.718 42.857 0.00 0.00 0.00 3.91
3521 5219 5.409826 AGCGGAGAACAAACAAAGAGATTAG 59.590 40.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.534203 GGCACTTCCCAAACTCGACA 60.534 55.000 0.00 0.00 0.00 4.35
32 33 1.531149 CGTCCACGAGTGCAAATTCTT 59.469 47.619 0.00 0.00 43.02 2.52
64 65 1.767681 GATGTCCCCAGCTCAGAGATT 59.232 52.381 0.00 0.00 0.00 2.40
80 81 1.415672 AAGGTCGTGGTGGTGGATGT 61.416 55.000 0.00 0.00 0.00 3.06
116 120 1.304134 TGCTGCACCTCGACTCCTA 60.304 57.895 0.00 0.00 0.00 2.94
205 210 1.874019 CGCGCTCTGTATGCTCGTT 60.874 57.895 5.56 0.00 34.50 3.85
212 217 1.531264 CGAGTACAACGCGCTCTGTAT 60.531 52.381 17.92 9.69 34.21 2.29
215 220 1.442184 ACGAGTACAACGCGCTCTG 60.442 57.895 5.73 3.57 45.19 3.35
229 234 3.114616 CTCCCGTTGCTGCACGAG 61.115 66.667 20.55 11.42 43.15 4.18
239 244 3.553095 GAGGTTGCCTGCTCCCGTT 62.553 63.158 0.00 0.00 31.76 4.44
240 245 4.021925 GAGGTTGCCTGCTCCCGT 62.022 66.667 0.00 0.00 31.76 5.28
275 280 4.880426 TCCCCGCTCCTCATCCCC 62.880 72.222 0.00 0.00 0.00 4.81
310 315 3.312736 ACAATCCACACTTTTCCCAGT 57.687 42.857 0.00 0.00 0.00 4.00
327 332 2.361757 CCAACTCACTGGCATCAAACAA 59.638 45.455 0.00 0.00 0.00 2.83
382 387 2.279743 TCCAAGGCCATGGATGCC 59.720 61.111 25.76 9.95 44.52 4.40
408 413 3.677527 GCACAGCCTGCATGAACT 58.322 55.556 0.00 0.00 46.29 3.01
425 430 4.177026 CTCGAGTTCTTCATTACCCACAG 58.823 47.826 3.62 0.00 0.00 3.66
433 446 2.676463 GCTGAGGCTCGAGTTCTTCATT 60.676 50.000 15.13 0.00 35.22 2.57
557 1157 7.813331 AGGGAACTCATATACTGTACAGACTA 58.187 38.462 29.30 18.33 32.90 2.59
584 1184 5.397221 CCTCCTCCACAGTGACATTTATCAT 60.397 44.000 0.62 0.00 0.00 2.45
596 1196 0.618968 GATGGGTCCTCCTCCACAGT 60.619 60.000 0.00 0.00 35.67 3.55
654 1254 1.002274 ATGAGCTCCCTTCCCTCGT 59.998 57.895 12.15 0.00 0.00 4.18
661 1261 1.277580 CCTCCCACATGAGCTCCCTT 61.278 60.000 12.15 0.00 0.00 3.95
718 1318 0.606604 ATTTACTCACTCCCGCACGT 59.393 50.000 0.00 0.00 0.00 4.49
725 1325 6.806739 GTGGTTTTATGCAATTTACTCACTCC 59.193 38.462 0.00 0.00 0.00 3.85
886 1488 1.444836 CATGTAGGCGAAAAACGGGA 58.555 50.000 0.00 0.00 42.83 5.14
931 1534 1.288127 GCCGTCTAACACCGTCTGT 59.712 57.895 0.00 0.00 32.89 3.41
1075 1754 2.184322 CGACCCATCACTCCACGG 59.816 66.667 0.00 0.00 0.00 4.94
1100 1779 1.228769 TACTCCCTGGTGTGCTCGT 60.229 57.895 1.25 0.00 0.00 4.18
1206 1885 6.537453 TTGGTCCATTGTTTGAAAAGAAGA 57.463 33.333 0.00 0.00 0.00 2.87
1270 1949 2.167487 GCCCTCGAAATCTGAGTCTTCT 59.833 50.000 0.00 0.00 0.00 2.85
1372 2052 0.480252 AACAAAGAAGCCTCCTGCCT 59.520 50.000 0.00 0.00 42.71 4.75
1408 2088 8.037758 ACAGATCTGTCATAGTTAAGTTGGAAG 58.962 37.037 22.89 0.00 40.24 3.46
1449 2130 4.197559 TCCCCAAATATAAATGCCTGCT 57.802 40.909 0.00 0.00 0.00 4.24
1570 2428 7.761249 GCTGGCAGAGTAAACAATTAATGAATT 59.239 33.333 20.86 0.00 35.56 2.17
1613 2471 7.867305 TGACCTAACTAAACAATGTTGACAA 57.133 32.000 0.00 0.00 0.00 3.18
1752 2615 5.299279 TCCTAAAATAAGCTAACATGGCAGC 59.701 40.000 11.70 11.70 38.09 5.25
2027 2976 4.724074 ACAACAAATGAATGCATCGGAT 57.276 36.364 0.00 0.00 32.35 4.18
2133 3082 1.075970 TATCACCGCCCTCTGCTCT 60.076 57.895 0.00 0.00 38.05 4.09
2212 3161 0.612229 ACAGTAGCATGAGCAGCTGT 59.388 50.000 16.64 1.59 45.99 4.40
2223 3172 5.675684 TCATGTTCCTAATGACAGTAGCA 57.324 39.130 4.37 0.00 0.00 3.49
2534 3487 5.067273 CACCACTAGTTCAAATACCACCAA 58.933 41.667 0.00 0.00 0.00 3.67
2772 4271 3.053395 ACCCTACATGATGCCTCAACATT 60.053 43.478 0.00 0.00 34.37 2.71
2776 4275 2.195727 TGACCCTACATGATGCCTCAA 58.804 47.619 0.00 0.00 34.37 3.02
2787 4286 5.476599 CCAAAAATCATCACTTGACCCTACA 59.523 40.000 0.00 0.00 37.11 2.74
2804 4352 3.776340 ACGTCGACAAAAAGCCAAAAAT 58.224 36.364 17.16 0.00 0.00 1.82
2876 4524 3.259876 ACTTTACCCTACTTGATGCGTCA 59.740 43.478 3.97 3.97 0.00 4.35
2879 4527 4.142687 CCAAACTTTACCCTACTTGATGCG 60.143 45.833 0.00 0.00 0.00 4.73
2911 4609 2.069273 CCTCGACATCGACAAAAAGCT 58.931 47.619 0.00 0.00 44.22 3.74
2943 4641 3.733443 AGCCAAAAACCATCACTTGAC 57.267 42.857 0.00 0.00 0.00 3.18
2944 4642 4.751767 AAAGCCAAAAACCATCACTTGA 57.248 36.364 0.00 0.00 0.00 3.02
2950 4648 4.026062 GTCGACAAAAAGCCAAAAACCATC 60.026 41.667 11.55 0.00 0.00 3.51
2952 4650 3.254892 GTCGACAAAAAGCCAAAAACCA 58.745 40.909 11.55 0.00 0.00 3.67
2999 4697 2.276201 GACAACAAGCCAAAAACCACC 58.724 47.619 0.00 0.00 0.00 4.61
3000 4698 1.923864 CGACAACAAGCCAAAAACCAC 59.076 47.619 0.00 0.00 0.00 4.16
3001 4699 1.819288 TCGACAACAAGCCAAAAACCA 59.181 42.857 0.00 0.00 0.00 3.67
3002 4700 2.190161 GTCGACAACAAGCCAAAAACC 58.810 47.619 11.55 0.00 0.00 3.27
3003 4701 1.843753 CGTCGACAACAAGCCAAAAAC 59.156 47.619 17.16 0.00 0.00 2.43
3004 4702 1.469308 ACGTCGACAACAAGCCAAAAA 59.531 42.857 17.16 0.00 0.00 1.94
3005 4703 1.062880 GACGTCGACAACAAGCCAAAA 59.937 47.619 17.16 0.00 0.00 2.44
3006 4704 0.653636 GACGTCGACAACAAGCCAAA 59.346 50.000 17.16 0.00 0.00 3.28
3007 4705 0.179094 AGACGTCGACAACAAGCCAA 60.179 50.000 17.16 0.00 0.00 4.52
3008 4706 0.874175 CAGACGTCGACAACAAGCCA 60.874 55.000 17.16 0.00 0.00 4.75
3009 4707 0.596600 TCAGACGTCGACAACAAGCC 60.597 55.000 17.16 0.00 0.00 4.35
3010 4708 1.125021 CATCAGACGTCGACAACAAGC 59.875 52.381 17.16 0.00 0.00 4.01
3011 4709 2.394708 ACATCAGACGTCGACAACAAG 58.605 47.619 17.16 0.66 0.00 3.16
3012 4710 2.034179 AGACATCAGACGTCGACAACAA 59.966 45.455 17.16 1.95 38.46 2.83
3013 4711 1.607148 AGACATCAGACGTCGACAACA 59.393 47.619 17.16 0.00 38.46 3.33
3014 4712 2.333389 AGACATCAGACGTCGACAAC 57.667 50.000 17.16 8.58 38.46 3.32
3015 4713 3.072211 AGTAGACATCAGACGTCGACAA 58.928 45.455 17.16 0.00 40.29 3.18
3016 4714 2.696506 AGTAGACATCAGACGTCGACA 58.303 47.619 17.16 0.00 40.29 4.35
3017 4715 3.301707 CGTAGTAGACATCAGACGTCGAC 60.302 52.174 10.46 5.18 38.74 4.20
3018 4716 2.856557 CGTAGTAGACATCAGACGTCGA 59.143 50.000 10.46 11.04 38.46 4.20
3019 4717 2.597040 GCGTAGTAGACATCAGACGTCG 60.597 54.545 10.46 5.48 38.46 5.12
3020 4718 2.350804 TGCGTAGTAGACATCAGACGTC 59.649 50.000 7.70 7.70 33.05 4.34
3021 4719 2.353323 TGCGTAGTAGACATCAGACGT 58.647 47.619 0.00 0.00 33.05 4.34
3262 4960 4.350368 TTGCACTTGTATCACCTTCTCA 57.650 40.909 0.00 0.00 0.00 3.27
3267 4965 5.372343 TCCATATTGCACTTGTATCACCT 57.628 39.130 0.00 0.00 0.00 4.00
3451 5149 3.609853 TGTTGCATGTTGAGGGATAGTC 58.390 45.455 0.00 0.00 0.00 2.59
3489 5187 5.856126 TGTTTGTTCTCCGCTATTAGTTG 57.144 39.130 0.00 0.00 0.00 3.16
3490 5188 6.708949 TCTTTGTTTGTTCTCCGCTATTAGTT 59.291 34.615 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.