Multiple sequence alignment - TraesCS2B01G255500

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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 TraesCS2B01G255500 chr2B 100.000 4314 0 0 1 4314 292866224 292870537 0.000000e+00 7967
1 TraesCS2B01G255500 chr2B 92.846 1887 90 9 666 2524 222490516 222488647 0.000000e+00 2695
2 TraesCS2B01G255500 chr2B 94.663 787 32 5 3535 4314 134453127 134453910 0.000000e+00 1212
3 TraesCS2B01G255500 chr2B 95.518 714 27 1 2826 3534 222487269 222486556 0.000000e+00 1136
4 TraesCS2B01G255500 chr2B 95.281 551 25 1 1 551 73208584 73209133 0.000000e+00 872
5 TraesCS2B01G255500 chr2B 91.137 519 43 2 552 1069 17629792 17630308 0.000000e+00 701
6 TraesCS2B01G255500 chr2B 96.203 316 9 3 2515 2828 222487636 222487322 8.270000e-142 514
7 TraesCS2B01G255500 chr1B 89.690 1290 80 21 551 1805 121889383 121890654 0.000000e+00 1596
8 TraesCS2B01G255500 chr1B 94.444 792 34 6 3530 4314 117069804 117070592 0.000000e+00 1210
9 TraesCS2B01G255500 chr1B 94.423 789 30 10 3535 4314 411249479 411248696 0.000000e+00 1201
10 TraesCS2B01G255500 chr1B 94.409 787 34 6 3535 4314 532820027 532820810 0.000000e+00 1201
11 TraesCS2B01G255500 chr1B 96.914 713 18 1 2826 3534 121891928 121892640 0.000000e+00 1192
12 TraesCS2B01G255500 chr1B 95.238 714 29 1 2826 3534 31371647 31370934 0.000000e+00 1125
13 TraesCS2B01G255500 chr1B 96.865 319 8 2 2511 2828 121891558 121891875 2.280000e-147 532
14 TraesCS2B01G255500 chr1B 96.508 315 9 2 2515 2828 14895795 14895482 1.780000e-143 520
15 TraesCS2B01G255500 chr1B 94.603 315 16 1 2515 2828 31372014 31371700 1.800000e-133 486
16 TraesCS2B01G255500 chr6B 91.530 1098 64 11 552 1621 39012124 39013220 0.000000e+00 1485
17 TraesCS2B01G255500 chr6B 94.430 790 32 7 3535 4314 383379966 383379179 0.000000e+00 1205
18 TraesCS2B01G255500 chr6B 94.409 787 36 5 3535 4314 643918557 643917772 0.000000e+00 1203
19 TraesCS2B01G255500 chr6B 95.910 709 27 1 2826 3534 39014287 39014993 0.000000e+00 1147
20 TraesCS2B01G255500 chr6B 94.918 551 28 0 1 551 621290476 621291026 0.000000e+00 863
21 TraesCS2B01G255500 chr6B 95.570 316 14 0 2513 2828 39013919 39014234 1.380000e-139 507
22 TraesCS2B01G255500 chr7B 94.325 793 37 4 3528 4314 497090124 497090914 0.000000e+00 1208
23 TraesCS2B01G255500 chr7B 95.245 715 27 2 2826 3534 615404858 615404145 0.000000e+00 1125
24 TraesCS2B01G255500 chr7B 95.281 551 25 1 1 551 49869517 49868968 0.000000e+00 872
25 TraesCS2B01G255500 chr7B 97.561 369 9 0 2156 2524 743565329 743565697 2.190000e-177 632
26 TraesCS2B01G255500 chr7B 97.019 369 11 0 2156 2524 591038519 591038151 4.740000e-174 621
27 TraesCS2B01G255500 chr7B 95.337 386 18 0 1720 2105 731916720 731917105 7.930000e-172 614
28 TraesCS2B01G255500 chr7B 94.118 204 8 2 2515 2717 743566548 743566748 1.510000e-79 307
29 TraesCS2B01G255500 chr7B 98.305 118 2 0 2711 2828 743586869 743586986 1.570000e-49 207
30 TraesCS2B01G255500 chr3B 94.529 786 35 4 3535 4313 542581401 542582185 0.000000e+00 1206
31 TraesCS2B01G255500 chr3B 94.289 788 38 3 3533 4314 682703641 682702855 0.000000e+00 1199
32 TraesCS2B01G255500 chr3B 95.944 715 23 2 2826 3534 228790702 228789988 0.000000e+00 1155
33 TraesCS2B01G255500 chr3B 94.972 716 29 1 2826 3534 550392962 550392247 0.000000e+00 1116
34 TraesCS2B01G255500 chr3B 94.398 714 34 2 2826 3534 185513150 185513862 0.000000e+00 1092
35 TraesCS2B01G255500 chr3B 95.644 551 24 0 1 551 630544803 630544253 0.000000e+00 885
36 TraesCS2B01G255500 chr3B 90.366 519 49 1 552 1069 753358069 753358587 0.000000e+00 680
37 TraesCS2B01G255500 chr3B 97.275 367 10 0 2158 2524 767810705 767810339 1.320000e-174 623
38 TraesCS2B01G255500 chr3B 93.674 411 21 3 1695 2105 194230174 194229769 1.030000e-170 610
39 TraesCS2B01G255500 chr3B 96.474 312 10 1 2515 2825 185512793 185513104 8.270000e-142 514
40 TraesCS2B01G255500 chr3B 95.238 315 14 1 2515 2828 767809328 767809014 8.330000e-137 497
41 TraesCS2B01G255500 chr3B 77.632 228 42 8 554 776 706563728 706563951 3.500000e-26 130
42 TraesCS2B01G255500 chr5B 95.798 714 25 1 2826 3534 506238805 506239518 0.000000e+00 1147
43 TraesCS2B01G255500 chr5B 97.019 369 11 0 2156 2524 506237059 506237427 4.740000e-174 621
44 TraesCS2B01G255500 chr5B 96.825 315 9 1 2515 2828 506238438 506238752 3.820000e-145 525
45 TraesCS2B01G255500 chr5A 96.007 551 22 0 1 551 433306407 433305857 0.000000e+00 896
46 TraesCS2B01G255500 chr5A 90.822 523 42 4 552 1072 687850677 687850159 0.000000e+00 695
47 TraesCS2B01G255500 chr1A 95.463 551 25 0 1 551 29275586 29275036 0.000000e+00 880
48 TraesCS2B01G255500 chr1A 95.281 551 26 0 1 551 29267721 29267171 0.000000e+00 874
49 TraesCS2B01G255500 chr1A 91.188 522 39 5 554 1069 320298227 320298747 0.000000e+00 702
50 TraesCS2B01G255500 chr4A 95.281 551 26 0 1 551 46528686 46529236 0.000000e+00 874
51 TraesCS2B01G255500 chr4A 95.281 551 26 0 1 551 46536009 46536559 0.000000e+00 874
52 TraesCS2B01G255500 chr6A 90.613 522 44 3 552 1072 173309616 173309099 0.000000e+00 688
53 TraesCS2B01G255500 chr6A 86.898 519 44 5 552 1069 57118027 57118522 1.050000e-155 560
54 TraesCS2B01G255500 chr6A 94.930 355 18 0 1751 2105 164496232 164496586 1.360000e-154 556
55 TraesCS2B01G255500 chr6A 91.176 170 11 2 1559 1728 164495176 164495341 1.210000e-55 228
56 TraesCS2B01G255500 chr3D 90.541 518 48 1 552 1068 500709636 500710153 0.000000e+00 684
57 TraesCS2B01G255500 chr3D 98.103 369 7 0 2156 2524 588084964 588084596 1.010000e-180 643
58 TraesCS2B01G255500 chr3D 85.714 392 23 14 1094 1461 581982509 581982891 2.430000e-102 383
59 TraesCS2B01G255500 chr3D 85.625 320 26 10 1257 1566 349056210 349056519 6.960000e-83 318
60 TraesCS2B01G255500 chr7D 97.832 369 8 0 2156 2524 504423282 504422914 4.700000e-179 638
61 TraesCS2B01G255500 chr7D 97.832 369 8 0 2156 2524 526509786 526510154 4.700000e-179 638
62 TraesCS2B01G255500 chr7D 86.250 320 23 11 1257 1566 34208618 34208926 1.160000e-85 327
63 TraesCS2B01G255500 chr7D 85.625 320 26 10 1257 1566 138842495 138842804 6.960000e-83 318
64 TraesCS2B01G255500 chr7D 84.688 320 29 13 1257 1566 107543703 107543394 7.010000e-78 302
65 TraesCS2B01G255500 chr5D 97.554 368 9 0 2157 2524 442382892 442382525 7.870000e-177 630
66 TraesCS2B01G255500 chr2D 85.625 320 26 12 1257 1566 77944606 77944297 6.960000e-83 318
67 TraesCS2B01G255500 chr2D 85.312 320 27 10 1257 1566 136901704 136902013 3.240000e-81 313
68 TraesCS2B01G255500 chr2D 85.312 320 27 9 1257 1566 475939605 475939296 3.240000e-81 313


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 TraesCS2B01G255500 chr2B 292866224 292870537 4313 False 7967.000000 7967 100.000000 1 4314 1 chr2B.!!$F4 4313
1 TraesCS2B01G255500 chr2B 222486556 222490516 3960 True 1448.333333 2695 94.855667 666 3534 3 chr2B.!!$R1 2868
2 TraesCS2B01G255500 chr2B 134453127 134453910 783 False 1212.000000 1212 94.663000 3535 4314 1 chr2B.!!$F3 779
3 TraesCS2B01G255500 chr2B 73208584 73209133 549 False 872.000000 872 95.281000 1 551 1 chr2B.!!$F2 550
4 TraesCS2B01G255500 chr2B 17629792 17630308 516 False 701.000000 701 91.137000 552 1069 1 chr2B.!!$F1 517
5 TraesCS2B01G255500 chr1B 117069804 117070592 788 False 1210.000000 1210 94.444000 3530 4314 1 chr1B.!!$F1 784
6 TraesCS2B01G255500 chr1B 411248696 411249479 783 True 1201.000000 1201 94.423000 3535 4314 1 chr1B.!!$R2 779
7 TraesCS2B01G255500 chr1B 532820027 532820810 783 False 1201.000000 1201 94.409000 3535 4314 1 chr1B.!!$F2 779
8 TraesCS2B01G255500 chr1B 121889383 121892640 3257 False 1106.666667 1596 94.489667 551 3534 3 chr1B.!!$F3 2983
9 TraesCS2B01G255500 chr1B 31370934 31372014 1080 True 805.500000 1125 94.920500 2515 3534 2 chr1B.!!$R3 1019
10 TraesCS2B01G255500 chr6B 383379179 383379966 787 True 1205.000000 1205 94.430000 3535 4314 1 chr6B.!!$R1 779
11 TraesCS2B01G255500 chr6B 643917772 643918557 785 True 1203.000000 1203 94.409000 3535 4314 1 chr6B.!!$R2 779
12 TraesCS2B01G255500 chr6B 39012124 39014993 2869 False 1046.333333 1485 94.336667 552 3534 3 chr6B.!!$F2 2982
13 TraesCS2B01G255500 chr6B 621290476 621291026 550 False 863.000000 863 94.918000 1 551 1 chr6B.!!$F1 550
14 TraesCS2B01G255500 chr7B 497090124 497090914 790 False 1208.000000 1208 94.325000 3528 4314 1 chr7B.!!$F1 786
15 TraesCS2B01G255500 chr7B 615404145 615404858 713 True 1125.000000 1125 95.245000 2826 3534 1 chr7B.!!$R3 708
16 TraesCS2B01G255500 chr7B 49868968 49869517 549 True 872.000000 872 95.281000 1 551 1 chr7B.!!$R1 550
17 TraesCS2B01G255500 chr7B 743565329 743566748 1419 False 469.500000 632 95.839500 2156 2717 2 chr7B.!!$F4 561
18 TraesCS2B01G255500 chr3B 542581401 542582185 784 False 1206.000000 1206 94.529000 3535 4313 1 chr3B.!!$F1 778
19 TraesCS2B01G255500 chr3B 682702855 682703641 786 True 1199.000000 1199 94.289000 3533 4314 1 chr3B.!!$R5 781
20 TraesCS2B01G255500 chr3B 228789988 228790702 714 True 1155.000000 1155 95.944000 2826 3534 1 chr3B.!!$R2 708
21 TraesCS2B01G255500 chr3B 550392247 550392962 715 True 1116.000000 1116 94.972000 2826 3534 1 chr3B.!!$R3 708
22 TraesCS2B01G255500 chr3B 630544253 630544803 550 True 885.000000 885 95.644000 1 551 1 chr3B.!!$R4 550
23 TraesCS2B01G255500 chr3B 185512793 185513862 1069 False 803.000000 1092 95.436000 2515 3534 2 chr3B.!!$F4 1019
24 TraesCS2B01G255500 chr3B 753358069 753358587 518 False 680.000000 680 90.366000 552 1069 1 chr3B.!!$F3 517
25 TraesCS2B01G255500 chr3B 767809014 767810705 1691 True 560.000000 623 96.256500 2158 2828 2 chr3B.!!$R6 670
26 TraesCS2B01G255500 chr5B 506237059 506239518 2459 False 764.333333 1147 96.547333 2156 3534 3 chr5B.!!$F1 1378
27 TraesCS2B01G255500 chr5A 433305857 433306407 550 True 896.000000 896 96.007000 1 551 1 chr5A.!!$R1 550
28 TraesCS2B01G255500 chr5A 687850159 687850677 518 True 695.000000 695 90.822000 552 1072 1 chr5A.!!$R2 520
29 TraesCS2B01G255500 chr1A 29275036 29275586 550 True 880.000000 880 95.463000 1 551 1 chr1A.!!$R2 550
30 TraesCS2B01G255500 chr1A 29267171 29267721 550 True 874.000000 874 95.281000 1 551 1 chr1A.!!$R1 550
31 TraesCS2B01G255500 chr1A 320298227 320298747 520 False 702.000000 702 91.188000 554 1069 1 chr1A.!!$F1 515
32 TraesCS2B01G255500 chr4A 46528686 46529236 550 False 874.000000 874 95.281000 1 551 1 chr4A.!!$F1 550
33 TraesCS2B01G255500 chr4A 46536009 46536559 550 False 874.000000 874 95.281000 1 551 1 chr4A.!!$F2 550
34 TraesCS2B01G255500 chr6A 173309099 173309616 517 True 688.000000 688 90.613000 552 1072 1 chr6A.!!$R1 520
35 TraesCS2B01G255500 chr6A 164495176 164496586 1410 False 392.000000 556 93.053000 1559 2105 2 chr6A.!!$F2 546
36 TraesCS2B01G255500 chr3D 500709636 500710153 517 False 684.000000 684 90.541000 552 1068 1 chr3D.!!$F2 516

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
731 732 0.542805 GACAATACCCGCCACCCTAA 59.457 55.0 0.0 0.0 0.00 2.69 F
2238 3167 0.105964 TGGTGGCTGCGTCCATATAC 59.894 55.0 9.7 0.0 38.57 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 4577 0.335019 TAGGGGTCTCAGTAGCAGCA 59.665 55.0 0.0 0.0 0.0 4.41 R
3905 5930 0.532573 GGATTGCTGAGTCCTCGTGA 59.467 55.0 0.0 0.0 0.0 4.35 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
17 18 3.052081 GTGGTGTCGTCTGGCTCT 58.948 61.111 0.00 0.00 0.00 4.09
116 117 5.621555 GTACTCATCCAAAGTACTCGCAAGA 60.622 44.000 0.00 0.00 43.68 3.02
201 202 6.347696 CAGAAATGCCAGAATAGAGAGAAGT 58.652 40.000 0.00 0.00 0.00 3.01
209 210 6.361433 CCAGAATAGAGAGAAGTCCTAGTCA 58.639 44.000 0.00 0.00 32.01 3.41
214 215 9.733556 GAATAGAGAGAAGTCCTAGTCATATCA 57.266 37.037 0.00 0.00 30.55 2.15
363 364 1.924731 TCCCAGAGCCATACTATCCG 58.075 55.000 0.00 0.00 0.00 4.18
373 374 3.921021 GCCATACTATCCGTTTCTCATCG 59.079 47.826 0.00 0.00 0.00 3.84
421 422 4.275196 CCAGTTCTAGTTGTATCGATCGGA 59.725 45.833 16.41 2.25 0.00 4.55
444 445 3.764237 ACAACTCCAAGTGTCCGTTAT 57.236 42.857 0.00 0.00 0.00 1.89
562 563 1.382695 ATGCCCGCACTACTAGGGT 60.383 57.895 1.46 0.00 46.69 4.34
659 660 2.875933 ACAAAACAAGCGCTACTGCTAA 59.124 40.909 12.05 0.00 46.60 3.09
661 662 4.201970 ACAAAACAAGCGCTACTGCTAAAA 60.202 37.500 12.05 0.00 46.60 1.52
707 708 3.754850 GGAACCACGCTACCACTAAAATT 59.245 43.478 0.00 0.00 0.00 1.82
731 732 0.542805 GACAATACCCGCCACCCTAA 59.457 55.000 0.00 0.00 0.00 2.69
746 747 4.189231 CACCCTAAATTTAGTAGCAGCGT 58.811 43.478 20.99 5.88 0.00 5.07
887 893 2.370189 CCCACCAAACTCTCTCTGTCTT 59.630 50.000 0.00 0.00 0.00 3.01
973 980 3.164269 CATCCCCTCCACCTCCCG 61.164 72.222 0.00 0.00 0.00 5.14
1010 1017 6.910259 TCTATATGCCCCTAGACTAGATCA 57.090 41.667 11.27 6.01 0.00 2.92
1025 1032 2.960957 GATCAAGCAGGCGAGCGCTA 62.961 60.000 11.50 0.00 37.54 4.26
1042 1049 1.135257 GCTATCAGATCGGGATCGGTG 60.135 57.143 6.24 1.24 42.48 4.94
1089 1096 2.684735 GAGGGGAGAGGAGGACGT 59.315 66.667 0.00 0.00 0.00 4.34
1299 1359 1.136828 CCCCGGATTGGATTGGACTA 58.863 55.000 0.73 0.00 42.00 2.59
1433 1493 2.555757 GCAGAGCAACAAGGTGAAATCT 59.444 45.455 0.00 0.00 0.00 2.40
1501 1562 1.285950 GGCCTGGAGCGTTTGTTTC 59.714 57.895 0.00 0.00 45.17 2.78
1514 1575 6.744112 AGCGTTTGTTTCCATTGAAGATTTA 58.256 32.000 0.00 0.00 0.00 1.40
1582 1643 0.312102 CACTCCGCGCATCATCTCTA 59.688 55.000 8.75 0.00 0.00 2.43
1591 1652 1.067669 GCATCATCTCTAGACACCGCA 59.932 52.381 0.00 0.00 0.00 5.69
1592 1653 2.288702 GCATCATCTCTAGACACCGCAT 60.289 50.000 0.00 0.00 0.00 4.73
1736 1797 5.819991 TCAATCTAACCTGATTCAGCCTTT 58.180 37.500 8.23 3.85 34.77 3.11
1783 2712 2.497675 GTTCCTGCTCACTCATCTACCA 59.502 50.000 0.00 0.00 0.00 3.25
1807 2736 6.017192 CAGCCAATCCGTACATATTTTCATGA 60.017 38.462 0.00 0.00 0.00 3.07
1852 2781 0.247460 TGGAACGAGCACTCCATCTG 59.753 55.000 0.00 0.00 36.79 2.90
1854 2783 1.476891 GGAACGAGCACTCCATCTGTA 59.523 52.381 0.00 0.00 0.00 2.74
1876 2805 7.611770 TGTAGCAGTAAAGAATTAGAGAAGCA 58.388 34.615 0.00 0.00 0.00 3.91
1925 2854 3.719871 AGAACTGGTTGGGGTTTTCTTT 58.280 40.909 0.00 0.00 0.00 2.52
2043 2972 7.032580 TGAACATTTTGTGTCTTTGTACCAAG 58.967 34.615 0.19 0.19 41.14 3.61
2066 2995 7.016361 AGAAATCGGTATAAGATTGTGCAAC 57.984 36.000 0.00 0.00 38.24 4.17
2151 3080 5.063060 GCTGAACCTGTAACCTGTAATAACG 59.937 44.000 0.00 0.00 0.00 3.18
2192 3121 5.359009 CCAAGTCGGTTAATAGGTGAGTCTA 59.641 44.000 0.00 0.00 0.00 2.59
2238 3167 0.105964 TGGTGGCTGCGTCCATATAC 59.894 55.000 9.70 0.00 38.57 1.47
2294 3223 7.291566 ACCTACACTAGCTCATTCACTACTAT 58.708 38.462 0.00 0.00 0.00 2.12
2370 3299 0.179468 GGCTCACCTATTAACCGGCA 59.821 55.000 0.00 0.00 0.00 5.69
2407 3336 8.828688 ACTAATCACCTAACTGAAACACTAAC 57.171 34.615 0.00 0.00 0.00 2.34
2545 4497 6.599638 AGATAAATTAGAGGCAGAACAACCAC 59.400 38.462 0.00 0.00 0.00 4.16
2643 4596 0.335019 TGCTGCTACTGAGACCCCTA 59.665 55.000 0.00 0.00 0.00 3.53
2782 4735 6.721318 TCTTTTTCTGGCTATGTATTCCAGT 58.279 36.000 7.31 0.00 45.67 4.00
2850 4858 1.167851 TTGGCCATTCTGCTTCTTCG 58.832 50.000 6.09 0.00 0.00 3.79
2865 4873 4.776743 CTTCTTCGTGTCCATTTCTTGTG 58.223 43.478 0.00 0.00 0.00 3.33
2894 4902 6.430000 GCAGTTTACCAAGTCTTCTCCAATAA 59.570 38.462 0.00 0.00 0.00 1.40
3114 5122 2.584791 GTAGCGCTGATTGGTGTTTTG 58.415 47.619 22.90 0.00 0.00 2.44
3131 5139 6.261826 GGTGTTTTGATGAAGAGATAGGATGG 59.738 42.308 0.00 0.00 0.00 3.51
3195 5203 2.028112 TGTTTGCACTAGCTGGGAGTAG 60.028 50.000 0.85 0.00 42.74 2.57
3268 5276 7.874528 CCATGACAATATGTATGCTCTTACAGA 59.125 37.037 0.00 0.00 35.65 3.41
3491 5507 0.447801 GGTTTGCATCCACGCTACTG 59.552 55.000 0.00 0.00 0.00 2.74
3707 5729 7.294473 CACACGAATACAACAACATCATACAA 58.706 34.615 0.00 0.00 0.00 2.41
3708 5730 7.478355 CACACGAATACAACAACATCATACAAG 59.522 37.037 0.00 0.00 0.00 3.16
3710 5732 7.688167 CACGAATACAACAACATCATACAAGAC 59.312 37.037 0.00 0.00 0.00 3.01
3720 5742 7.609146 ACAACATCATACAAGACATCAACATCT 59.391 33.333 0.00 0.00 0.00 2.90
3765 5787 0.762418 ACTCAAACGACATCCACCCA 59.238 50.000 0.00 0.00 0.00 4.51
3849 5874 1.882912 ACAAGCAAACATCGCTCTCA 58.117 45.000 0.00 0.00 39.29 3.27
3905 5930 6.817184 ACTGTTGTTGTAGTAATCTGTGAGT 58.183 36.000 0.00 0.00 0.00 3.41
3973 5999 2.993863 AGCTTAAAGGGAAAGGAAGGGA 59.006 45.455 0.00 0.00 0.00 4.20
3982 6008 3.024547 GGAAAGGAAGGGATAAAGTGGC 58.975 50.000 0.00 0.00 0.00 5.01
4032 6062 3.121544 GGTGGCTAACATACGCTAAGAC 58.878 50.000 0.00 0.00 0.00 3.01
4104 6135 5.394333 GGTGATCCTGAACTCCTACTTACAC 60.394 48.000 0.00 0.00 0.00 2.90
4108 6139 5.091552 TCCTGAACTCCTACTTACACCAAT 58.908 41.667 0.00 0.00 0.00 3.16
4161 6193 1.438651 CGCCGAAAAGAGACCATCAA 58.561 50.000 0.00 0.00 0.00 2.57
4256 6288 0.809636 CATCTGCCACATAACCGCGA 60.810 55.000 8.23 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 7.564793 TGTTGCATATGTAGTGTAGATCCTTT 58.435 34.615 4.29 0.00 0.00 3.11
209 210 7.609097 TCCAGAAGATGCTAGTCTTTGATAT 57.391 36.000 0.00 0.00 38.51 1.63
214 215 5.221925 TGGTTTCCAGAAGATGCTAGTCTTT 60.222 40.000 0.00 0.00 38.51 2.52
363 364 5.163723 TGAGAATTGGATTGCGATGAGAAAC 60.164 40.000 0.00 0.00 0.00 2.78
373 374 5.320549 ACTTGTGATGAGAATTGGATTGC 57.679 39.130 0.00 0.00 0.00 3.56
421 422 3.764237 ACGGACACTTGGAGTTGTATT 57.236 42.857 0.00 0.00 0.00 1.89
444 445 2.563261 ATCGATAGCCTGTCCTACGA 57.437 50.000 0.00 0.00 0.00 3.43
486 487 0.480690 TGGTGGGTAAGTTGGTGCAT 59.519 50.000 0.00 0.00 0.00 3.96
581 582 0.527113 TGTACCGCGCTGCTACTAAA 59.473 50.000 5.56 0.00 0.00 1.85
659 660 2.437413 GCTGCCCTACTGCTAACTTTT 58.563 47.619 0.00 0.00 39.94 2.27
661 662 0.253327 GGCTGCCCTACTGCTAACTT 59.747 55.000 7.66 0.00 42.51 2.66
674 675 4.284550 TGGTTCCACTGGGCTGCC 62.285 66.667 11.05 11.05 0.00 4.85
707 708 0.036765 GTGGCGGGTATTGTCTGTCA 60.037 55.000 0.00 0.00 0.00 3.58
776 777 6.072728 GGGTATCTCATCTCGCTATAGCTATG 60.073 46.154 21.98 19.85 39.32 2.23
791 792 2.383442 AGTAGCGTGGGGTATCTCAT 57.617 50.000 0.00 0.00 0.00 2.90
887 893 1.900351 CGGCTGTGGATGAGAGGAA 59.100 57.895 0.00 0.00 0.00 3.36
973 980 5.363939 GGCATATAGATGGATAGAAGGTGC 58.636 45.833 0.00 0.00 33.26 5.01
1010 1017 2.279784 GATAGCGCTCGCCTGCTT 60.280 61.111 16.34 0.00 42.48 3.91
1025 1032 1.547820 CATCACCGATCCCGATCTGAT 59.452 52.381 3.47 4.00 34.82 2.90
1248 1308 4.089239 TGCGGCGCCTTGGTGATA 62.089 61.111 30.82 3.60 0.00 2.15
1299 1359 1.077265 CAGCCACCCAACCCAATCT 59.923 57.895 0.00 0.00 0.00 2.40
1433 1493 5.646360 GCAAAGCTTAACCATACCTACAAGA 59.354 40.000 0.00 0.00 0.00 3.02
1501 1562 8.875803 CACAACCATTTGATAAATCTTCAATGG 58.124 33.333 18.15 18.15 40.94 3.16
1514 1575 4.840115 ACAATCCTTCCACAACCATTTGAT 59.160 37.500 0.00 0.00 36.48 2.57
1582 1643 1.580845 GCAGCAGAAATGCGGTGTCT 61.581 55.000 2.53 0.00 40.27 3.41
1736 1797 6.609212 AGTCAGATCAAACTAGCTAGGAATCA 59.391 38.462 24.35 5.06 0.00 2.57
1783 2712 6.061441 TCATGAAAATATGTACGGATTGGCT 58.939 36.000 0.00 0.00 0.00 4.75
1852 2781 7.762159 ACTGCTTCTCTAATTCTTTACTGCTAC 59.238 37.037 0.00 0.00 0.00 3.58
1854 2783 6.706295 ACTGCTTCTCTAATTCTTTACTGCT 58.294 36.000 0.00 0.00 0.00 4.24
1876 2805 8.725148 CAGAAGTCAGCACTAAATAAATCAACT 58.275 33.333 0.00 0.00 30.14 3.16
1925 2854 5.174761 GCATGCACACGAGTTGAAATTAAAA 59.825 36.000 14.21 0.00 0.00 1.52
1979 2908 5.419788 AGGATGTTGATGTGTTGCATAATGT 59.580 36.000 0.00 0.00 38.06 2.71
2043 2972 7.016361 AGTTGCACAATCTTATACCGATTTC 57.984 36.000 0.00 0.00 0.00 2.17
2129 3058 6.100404 ACGTTATTACAGGTTACAGGTTCA 57.900 37.500 0.00 0.00 0.00 3.18
2151 3080 4.652822 ACTTGGACTACAAATTCCTGGAC 58.347 43.478 0.00 0.00 38.91 4.02
2344 3273 4.381411 GGTTAATAGGTGAGCCATGACTC 58.619 47.826 1.44 1.44 37.19 3.36
2370 3299 2.694109 GGTGATTAGTCCTTCTACGGCT 59.306 50.000 0.00 0.00 0.00 5.52
2407 3336 8.417780 ACGAAGTTCAATCTATCTTCTGATTG 57.582 34.615 3.32 8.80 46.31 2.67
2545 4497 7.914537 AGAAGTTCAAAATGTCTAAAAAGCG 57.085 32.000 5.50 0.00 0.00 4.68
2624 4577 0.335019 TAGGGGTCTCAGTAGCAGCA 59.665 55.000 0.00 0.00 0.00 4.41
2782 4735 7.489757 GTGTACTTTGCAATACAAGTTGGAAAA 59.510 33.333 13.15 0.00 44.84 2.29
2850 4858 4.275936 ACTGCTTACACAAGAAATGGACAC 59.724 41.667 0.00 0.00 33.20 3.67
2865 4873 5.408909 GGAGAAGACTTGGTAAACTGCTTAC 59.591 44.000 0.00 0.00 39.45 2.34
2894 4902 7.161404 AGGAACATACATGACATACGCATTAT 58.839 34.615 0.00 0.00 0.00 1.28
2969 4977 3.953612 CCTGAGTGCCTGCCAAATTTATA 59.046 43.478 0.00 0.00 0.00 0.98
3114 5122 4.040217 ACAGTGCCATCCTATCTCTTCATC 59.960 45.833 0.00 0.00 0.00 2.92
3131 5139 3.868077 TGCATAAAAACACCAAACAGTGC 59.132 39.130 0.00 0.00 41.67 4.40
3195 5203 1.680338 ACACTTCTTGCCAAGTCACC 58.320 50.000 4.04 0.00 34.17 4.02
3268 5276 1.019673 CAGCGGCATTAGAGCACATT 58.980 50.000 1.45 0.00 35.83 2.71
3491 5507 6.868339 TCCCACGTTACTACTAAAAAGTTAGC 59.132 38.462 0.00 0.00 40.48 3.09
3648 5666 5.426833 GCCTCTTGTATGTATCCCCATCTAT 59.573 44.000 0.00 0.00 0.00 1.98
3707 5729 4.017126 TCCGTAGTCAGATGTTGATGTCT 58.983 43.478 0.00 0.00 38.29 3.41
3708 5730 4.371855 TCCGTAGTCAGATGTTGATGTC 57.628 45.455 0.00 0.00 38.29 3.06
3710 5732 4.053983 CCATCCGTAGTCAGATGTTGATG 58.946 47.826 0.00 0.00 38.57 3.07
3720 5742 3.181464 TGTTTGTGTTCCATCCGTAGTCA 60.181 43.478 0.00 0.00 0.00 3.41
3765 5787 4.101448 CGGCAACCTGGGCTAGCT 62.101 66.667 15.72 0.00 0.00 3.32
3849 5874 3.059884 GGTTATGCGATGATCATGACGT 58.940 45.455 14.30 8.59 33.02 4.34
3905 5930 0.532573 GGATTGCTGAGTCCTCGTGA 59.467 55.000 0.00 0.00 0.00 4.35
3973 5999 1.453155 CTGCAACCTCGCCACTTTAT 58.547 50.000 0.00 0.00 0.00 1.40
3982 6008 2.819117 TAGTCGCTGCTGCAACCTCG 62.819 60.000 16.29 5.43 39.64 4.63
4032 6062 3.370366 CGTTCCATTTGCTCTCTTCTCAG 59.630 47.826 0.00 0.00 0.00 3.35
4104 6135 3.257127 ACACGGTTTTGGGTTATGATTGG 59.743 43.478 0.00 0.00 0.00 3.16
4108 6139 3.315749 GTGAACACGGTTTTGGGTTATGA 59.684 43.478 0.00 0.00 0.00 2.15
4161 6193 2.167398 ATCAACCGCGTGTGTAGCCT 62.167 55.000 4.92 0.00 0.00 4.58
4256 6288 0.249911 AAACTTTCGAGAGCCGTGCT 60.250 50.000 2.28 0.00 43.88 4.40


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

AutoCloner maintained by Alex Coulton.