Multiple sequence alignment - TraesCS3B01G057300

Loading Multiple Alignment...

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 TraesCS3B01G057300 chr3B 100.000 7476 0 0 1 7476 29885128 29892603 0.000000e+00 13806
1 TraesCS3B01G057300 chr3B 97.161 2818 61 5 395 3211 30270523 30273322 0.000000e+00 4743
2 TraesCS3B01G057300 chr3B 95.240 2584 91 13 4916 7476 30276352 30278926 0.000000e+00 4061
3 TraesCS3B01G057300 chr3B 96.193 1681 50 5 3205 4873 30274694 30276372 0.000000e+00 2737
4 TraesCS3B01G057300 chr3B 86.772 2336 241 37 5026 7318 29951490 29953800 0.000000e+00 2540
5 TraesCS3B01G057300 chr3B 90.137 1967 172 18 5115 7064 29717868 29719829 0.000000e+00 2538
6 TraesCS3B01G057300 chr3B 89.706 1428 135 7 5164 6587 30438315 30439734 0.000000e+00 1812
7 TraesCS3B01G057300 chr3B 84.424 642 85 9 833 1472 29576758 29576130 1.070000e-172 617
8 TraesCS3B01G057300 chr3B 84.112 642 86 9 833 1472 30081648 30081021 2.310000e-169 606
9 TraesCS3B01G057300 chr3B 80.179 671 108 17 1080 1741 27516801 27517455 5.250000e-131 479
10 TraesCS3B01G057300 chr3B 79.701 468 87 5 2287 2750 143169535 143169072 1.550000e-86 331
11 TraesCS3B01G057300 chr3B 88.506 174 19 1 7062 7235 29720031 29720203 7.600000e-50 209
12 TraesCS3B01G057300 chr3B 76.259 417 80 14 4584 4983 29717313 29717727 3.540000e-48 204
13 TraesCS3B01G057300 chr3B 85.714 154 21 1 1562 1714 29576102 29575949 2.160000e-35 161
14 TraesCS3B01G057300 chr3B 86.000 150 21 0 1562 1711 30080993 30080844 2.160000e-35 161
15 TraesCS3B01G057300 chr3D 92.491 2011 126 12 5484 7476 18694124 18696127 0.000000e+00 2854
16 TraesCS3B01G057300 chr3D 88.642 1532 145 18 5115 6620 18730442 18731970 0.000000e+00 1838
17 TraesCS3B01G057300 chr3D 86.571 1117 142 8 5193 6305 18952667 18953779 0.000000e+00 1225
18 TraesCS3B01G057300 chr3D 80.484 661 114 9 1082 1741 17516697 17516051 6.740000e-135 492
19 TraesCS3B01G057300 chr3D 75.434 1095 203 40 2287 3340 613928501 613929570 8.780000e-129 472
20 TraesCS3B01G057300 chr3D 79.472 682 110 20 1082 1741 17645284 17644611 2.460000e-124 457
21 TraesCS3B01G057300 chr3D 79.421 656 117 12 1082 1734 17374462 17375102 1.480000e-121 448
22 TraesCS3B01G057300 chr3D 80.321 498 85 7 2258 2752 582893117 582892630 1.530000e-96 364
23 TraesCS3B01G057300 chr3D 76.393 682 102 29 1082 1741 11352378 11353022 5.630000e-81 313
24 TraesCS3B01G057300 chr3D 86.029 136 19 0 1598 1733 18906364 18906499 6.040000e-31 147
25 TraesCS3B01G057300 chr3D 82.301 113 20 0 1560 1672 18682366 18682478 1.720000e-16 99
26 TraesCS3B01G057300 chr3A 84.251 1289 171 20 5193 6477 26427636 26428896 0.000000e+00 1227
27 TraesCS3B01G057300 chr3A 83.929 1288 192 13 5193 6477 26261548 26262823 0.000000e+00 1218
28 TraesCS3B01G057300 chr3A 86.320 731 64 22 1 717 26238209 26238917 0.000000e+00 763
29 TraesCS3B01G057300 chr3A 80.150 665 115 13 1082 1741 19371400 19372052 1.460000e-131 481
30 TraesCS3B01G057300 chr3A 79.542 655 116 12 1082 1733 26469248 26469887 1.140000e-122 451
31 TraesCS3B01G057300 chr3A 89.385 179 17 2 799 976 26239007 26239184 2.710000e-54 224
32 TraesCS3B01G057300 chr4B 77.330 1116 181 36 2283 3351 368415830 368414740 1.800000e-165 593
33 TraesCS3B01G057300 chr4B 77.990 627 100 22 2754 3351 513055314 513055931 7.130000e-95 359
34 TraesCS3B01G057300 chr2D 75.735 1088 220 26 2298 3351 205588598 205587521 2.410000e-139 507
35 TraesCS3B01G057300 chrUn 79.265 680 118 17 1076 1741 37955885 37956555 3.180000e-123 453
36 TraesCS3B01G057300 chrUn 80.033 606 101 16 1147 1741 392408908 392408312 1.490000e-116 431
37 TraesCS3B01G057300 chr7D 75.315 1033 187 26 2334 3315 108983178 108982163 4.140000e-117 433
38 TraesCS3B01G057300 chr7D 80.682 352 67 1 2751 3102 503088510 503088860 9.560000e-69 272
39 TraesCS3B01G057300 chr7B 79.147 633 98 19 2753 3355 366042801 366042173 2.510000e-109 407
40 TraesCS3B01G057300 chr7B 76.019 638 108 25 2753 3351 71089885 71090516 9.490000e-74 289
41 TraesCS3B01G057300 chr2B 81.798 456 76 4 2300 2752 707608774 707608323 7.080000e-100 375
42 TraesCS3B01G057300 chr7A 79.570 558 87 11 2754 3286 409256291 409255736 2.550000e-99 374
43 TraesCS3B01G057300 chr7A 80.361 499 89 8 2258 2752 42800242 42799749 3.290000e-98 370
44 TraesCS3B01G057300 chr5D 80.873 481 75 9 2275 2752 429051596 429052062 5.510000e-96 363
45 TraesCS3B01G057300 chr5B 77.508 618 105 21 2750 3351 450768339 450768938 2.580000e-89 340
46 TraesCS3B01G057300 chr5B 76.741 632 110 23 2755 3358 571705878 571706500 1.210000e-82 318
47 TraesCS3B01G057300 chr5B 81.156 398 70 4 2339 2734 290810515 290810121 1.570000e-81 315


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 TraesCS3B01G057300 chr3B 29885128 29892603 7475 False 13806.000000 13806 100.000000 1 7476 1 chr3B.!!$F2 7475
1 TraesCS3B01G057300 chr3B 30270523 30278926 8403 False 3847.000000 4743 96.198000 395 7476 3 chr3B.!!$F6 7081
2 TraesCS3B01G057300 chr3B 29951490 29953800 2310 False 2540.000000 2540 86.772000 5026 7318 1 chr3B.!!$F3 2292
3 TraesCS3B01G057300 chr3B 30438315 30439734 1419 False 1812.000000 1812 89.706000 5164 6587 1 chr3B.!!$F4 1423
4 TraesCS3B01G057300 chr3B 29717313 29720203 2890 False 983.666667 2538 84.967333 4584 7235 3 chr3B.!!$F5 2651
5 TraesCS3B01G057300 chr3B 27516801 27517455 654 False 479.000000 479 80.179000 1080 1741 1 chr3B.!!$F1 661
6 TraesCS3B01G057300 chr3B 29575949 29576758 809 True 389.000000 617 85.069000 833 1714 2 chr3B.!!$R2 881
7 TraesCS3B01G057300 chr3B 30080844 30081648 804 True 383.500000 606 85.056000 833 1711 2 chr3B.!!$R3 878
8 TraesCS3B01G057300 chr3D 18694124 18696127 2003 False 2854.000000 2854 92.491000 5484 7476 1 chr3D.!!$F4 1992
9 TraesCS3B01G057300 chr3D 18730442 18731970 1528 False 1838.000000 1838 88.642000 5115 6620 1 chr3D.!!$F5 1505
10 TraesCS3B01G057300 chr3D 18952667 18953779 1112 False 1225.000000 1225 86.571000 5193 6305 1 chr3D.!!$F7 1112
11 TraesCS3B01G057300 chr3D 17516051 17516697 646 True 492.000000 492 80.484000 1082 1741 1 chr3D.!!$R1 659
12 TraesCS3B01G057300 chr3D 613928501 613929570 1069 False 472.000000 472 75.434000 2287 3340 1 chr3D.!!$F8 1053
13 TraesCS3B01G057300 chr3D 17644611 17645284 673 True 457.000000 457 79.472000 1082 1741 1 chr3D.!!$R2 659
14 TraesCS3B01G057300 chr3D 17374462 17375102 640 False 448.000000 448 79.421000 1082 1734 1 chr3D.!!$F2 652
15 TraesCS3B01G057300 chr3D 11352378 11353022 644 False 313.000000 313 76.393000 1082 1741 1 chr3D.!!$F1 659
16 TraesCS3B01G057300 chr3A 26427636 26428896 1260 False 1227.000000 1227 84.251000 5193 6477 1 chr3A.!!$F3 1284
17 TraesCS3B01G057300 chr3A 26261548 26262823 1275 False 1218.000000 1218 83.929000 5193 6477 1 chr3A.!!$F2 1284
18 TraesCS3B01G057300 chr3A 26238209 26239184 975 False 493.500000 763 87.852500 1 976 2 chr3A.!!$F5 975
19 TraesCS3B01G057300 chr3A 19371400 19372052 652 False 481.000000 481 80.150000 1082 1741 1 chr3A.!!$F1 659
20 TraesCS3B01G057300 chr3A 26469248 26469887 639 False 451.000000 451 79.542000 1082 1733 1 chr3A.!!$F4 651
21 TraesCS3B01G057300 chr4B 368414740 368415830 1090 True 593.000000 593 77.330000 2283 3351 1 chr4B.!!$R1 1068
22 TraesCS3B01G057300 chr4B 513055314 513055931 617 False 359.000000 359 77.990000 2754 3351 1 chr4B.!!$F1 597
23 TraesCS3B01G057300 chr2D 205587521 205588598 1077 True 507.000000 507 75.735000 2298 3351 1 chr2D.!!$R1 1053
24 TraesCS3B01G057300 chrUn 37955885 37956555 670 False 453.000000 453 79.265000 1076 1741 1 chrUn.!!$F1 665
25 TraesCS3B01G057300 chrUn 392408312 392408908 596 True 431.000000 431 80.033000 1147 1741 1 chrUn.!!$R1 594
26 TraesCS3B01G057300 chr7D 108982163 108983178 1015 True 433.000000 433 75.315000 2334 3315 1 chr7D.!!$R1 981
27 TraesCS3B01G057300 chr7B 366042173 366042801 628 True 407.000000 407 79.147000 2753 3355 1 chr7B.!!$R1 602
28 TraesCS3B01G057300 chr7B 71089885 71090516 631 False 289.000000 289 76.019000 2753 3351 1 chr7B.!!$F1 598
29 TraesCS3B01G057300 chr7A 409255736 409256291 555 True 374.000000 374 79.570000 2754 3286 1 chr7A.!!$R2 532
30 TraesCS3B01G057300 chr5B 450768339 450768938 599 False 340.000000 340 77.508000 2750 3351 1 chr5B.!!$F1 601
31 TraesCS3B01G057300 chr5B 571705878 571706500 622 False 318.000000 318 76.741000 2755 3358 1 chr5B.!!$F2 603

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
384 386 1.447489 CTGAGCGAGCAAGGAGTGG 60.447 63.158 0.00 0.00 0.00 4.00 F
721 770 2.108700 CACATTATTTAGCGCGCCAAC 58.891 47.619 30.33 0.00 0.00 3.77 F
1616 1715 0.393077 CTTCTCGAGTGGTTGGTGGT 59.607 55.000 13.13 0.00 0.00 4.16 F
2654 2758 0.745845 AGCGCATGCCTCCTACAAAG 60.746 55.000 13.15 0.00 44.31 2.77 F
3411 5005 1.399744 TAGGCACCCGGTATGAGCAG 61.400 60.000 0.00 0.00 0.00 4.24 F
3894 5489 1.214175 TGGTGGGTCATCAGTTTGTGT 59.786 47.619 0.00 0.00 0.00 3.72 F
5725 7382 1.286260 CTACCGGGATAGCTCGTGC 59.714 63.158 6.32 0.07 35.85 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1715 1.228094 TTGGTGCAATCGCCTGACA 60.228 52.632 0.00 0.00 43.26 3.58 R
2633 2737 0.104855 TTGTAGGAGGCATGCGCTAG 59.895 55.000 12.44 1.38 38.60 3.42 R
3509 5103 0.322816 TGGCCAAGTGCTCCTGATTC 60.323 55.000 0.61 0.00 40.92 2.52 R
3516 5110 0.595095 CTTCAAGTGGCCAAGTGCTC 59.405 55.000 7.24 0.00 40.92 4.26 R
4557 6153 1.372087 CCGCAATGAGGAGCTTCACC 61.372 60.000 0.00 0.00 0.00 4.02 R
5850 7508 0.615850 AGCTTGCTCTCCTTGGTACC 59.384 55.000 4.43 4.43 0.00 3.34 R
7137 9026 0.902531 TTAGGGGCCTGTCGAAGAAG 59.097 55.000 0.84 0.00 39.69 2.85 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
34 35 4.016444 TGGGATATTGCTCAAGTTTCCAC 58.984 43.478 9.16 0.00 0.00 4.02
41 43 2.171659 TGCTCAAGTTTCCACTGGTACA 59.828 45.455 0.00 0.00 31.60 2.90
46 48 5.063204 TCAAGTTTCCACTGGTACAATCAG 58.937 41.667 0.00 0.00 38.70 2.90
51 53 2.375174 TCCACTGGTACAATCAGCCTTT 59.625 45.455 0.00 0.00 38.70 3.11
54 56 4.336433 CCACTGGTACAATCAGCCTTTATG 59.664 45.833 0.00 0.00 38.70 1.90
64 66 4.811969 TCAGCCTTTATGTTCCTCGTAA 57.188 40.909 0.00 0.00 0.00 3.18
73 75 2.343101 TGTTCCTCGTAAAGCCAATCG 58.657 47.619 0.00 0.00 0.00 3.34
95 97 3.004419 GCTTCGTTTGTAGGCTTCCTTTT 59.996 43.478 0.00 0.00 34.61 2.27
108 110 6.759272 AGGCTTCCTTTTTAGGATTTGTTTC 58.241 36.000 0.00 0.00 37.87 2.78
121 123 7.771927 AGGATTTGTTTCTTGAGAACATCAT 57.228 32.000 0.00 0.00 37.89 2.45
132 134 3.074390 TGAGAACATCATGGAGGGTTTGT 59.926 43.478 0.00 0.00 31.12 2.83
139 141 3.909732 TCATGGAGGGTTTGTTGTCTTT 58.090 40.909 0.00 0.00 0.00 2.52
140 142 3.888930 TCATGGAGGGTTTGTTGTCTTTC 59.111 43.478 0.00 0.00 0.00 2.62
144 146 4.080243 TGGAGGGTTTGTTGTCTTTCAGTA 60.080 41.667 0.00 0.00 0.00 2.74
158 160 9.921637 TTGTCTTTCAGTACTTTTGAACATTTT 57.078 25.926 0.00 0.00 34.50 1.82
161 163 9.921637 TCTTTCAGTACTTTTGAACATTTTTGT 57.078 25.926 0.00 0.00 34.50 2.83
163 165 9.921637 TTTCAGTACTTTTGAACATTTTTGTCT 57.078 25.926 0.00 0.00 34.50 3.41
164 166 9.567848 TTCAGTACTTTTGAACATTTTTGTCTC 57.432 29.630 0.00 0.00 30.03 3.36
165 167 7.908082 TCAGTACTTTTGAACATTTTTGTCTCG 59.092 33.333 0.00 0.00 0.00 4.04
172 174 6.633500 TGAACATTTTTGTCTCGAGGAAAT 57.367 33.333 13.56 11.00 0.00 2.17
173 175 7.038154 TGAACATTTTTGTCTCGAGGAAATT 57.962 32.000 13.56 3.78 0.00 1.82
174 176 7.138736 TGAACATTTTTGTCTCGAGGAAATTC 58.861 34.615 13.56 12.00 0.00 2.17
184 186 4.040461 TCTCGAGGAAATTCTTCAACCTGT 59.960 41.667 13.56 0.00 32.75 4.00
196 198 8.868522 ATTCTTCAACCTGTCATTCTTATTCA 57.131 30.769 0.00 0.00 0.00 2.57
197 199 8.690203 TTCTTCAACCTGTCATTCTTATTCAA 57.310 30.769 0.00 0.00 0.00 2.69
251 253 5.805728 AGTAACCAGAGTACCATTTGAAGG 58.194 41.667 0.00 0.00 0.00 3.46
282 284 9.160496 GAGATAGTAATATCAGAAGCATTTGGG 57.840 37.037 12.40 0.00 0.00 4.12
286 288 6.944862 AGTAATATCAGAAGCATTTGGGGATC 59.055 38.462 0.00 0.00 0.00 3.36
289 291 2.029623 CAGAAGCATTTGGGGATCCAG 58.970 52.381 15.23 0.00 45.04 3.86
301 303 5.668135 TGGGGATCCAGACAATGAATTAT 57.332 39.130 15.23 0.00 38.32 1.28
304 306 6.183361 TGGGGATCCAGACAATGAATTATCAT 60.183 38.462 15.23 0.00 42.29 2.45
305 307 7.643155 TGGGGATCCAGACAATGAATTATCATT 60.643 37.037 15.23 0.00 45.98 2.57
331 333 2.046313 GTTCAATGCACTTTGAGCACG 58.954 47.619 10.84 0.00 45.95 5.34
332 334 1.592064 TCAATGCACTTTGAGCACGA 58.408 45.000 0.00 0.00 45.95 4.35
344 346 3.896648 TGAGCACGAAGGAACAAATTC 57.103 42.857 0.00 0.00 0.00 2.17
367 369 6.705302 TCATCTTGAGAGACACTAATTTGCT 58.295 36.000 0.00 0.00 33.99 3.91
384 386 1.447489 CTGAGCGAGCAAGGAGTGG 60.447 63.158 0.00 0.00 0.00 4.00
393 395 3.368427 CGAGCAAGGAGTGGTTCTCAATA 60.368 47.826 0.00 0.00 44.40 1.90
394 396 4.579869 GAGCAAGGAGTGGTTCTCAATAA 58.420 43.478 0.00 0.00 44.40 1.40
399 401 7.121315 AGCAAGGAGTGGTTCTCAATAATTAAC 59.879 37.037 0.00 0.00 44.40 2.01
400 402 7.094377 GCAAGGAGTGGTTCTCAATAATTAACA 60.094 37.037 0.00 0.00 44.40 2.41
721 770 2.108700 CACATTATTTAGCGCGCCAAC 58.891 47.619 30.33 0.00 0.00 3.77
939 989 2.928334 CATCTTCTTAGCACTGGCCAT 58.072 47.619 5.51 0.00 42.56 4.40
1616 1715 0.393077 CTTCTCGAGTGGTTGGTGGT 59.607 55.000 13.13 0.00 0.00 4.16
1735 1834 2.285220 CCAATAGATTGCGGTGAGTTCG 59.715 50.000 0.00 0.00 36.48 3.95
1978 2077 6.716934 TCATCCAGATTACTCCACTTAGAC 57.283 41.667 0.00 0.00 0.00 2.59
1980 2079 6.667848 TCATCCAGATTACTCCACTTAGACAA 59.332 38.462 0.00 0.00 0.00 3.18
2017 2117 9.305925 GTTTGTGAAGAAGTCAAATCAAAGAAT 57.694 29.630 0.00 0.00 38.23 2.40
2020 2120 7.068593 TGTGAAGAAGTCAAATCAAAGAATGGT 59.931 33.333 0.00 0.00 38.23 3.55
2135 2235 3.754965 GGTCCATTGCATTCTAGGCATA 58.245 45.455 0.00 0.00 41.58 3.14
2136 2236 4.338879 GGTCCATTGCATTCTAGGCATAT 58.661 43.478 0.00 0.00 41.58 1.78
2205 2305 4.645535 TCTCTTTGAGTCAAGTCAATGGG 58.354 43.478 5.56 9.25 36.34 4.00
2289 2389 1.672145 GGATTATTACCGCGGCCTCTC 60.672 57.143 28.58 14.42 0.00 3.20
2293 2393 0.830444 ATTACCGCGGCCTCTCCATA 60.830 55.000 28.58 4.04 34.01 2.74
2424 2527 1.524621 GATGATGTGCCCTGACCGG 60.525 63.158 0.00 0.00 0.00 5.28
2546 2649 1.064296 CGCTGTAGAATCCGTCGCT 59.936 57.895 0.00 0.00 0.00 4.93
2561 2664 2.616330 CGCTGCCTTCTTCCGCAAA 61.616 57.895 0.00 0.00 33.87 3.68
2585 2688 7.213178 ACCCATCTTCAGGAGTAATTAATGT 57.787 36.000 0.00 0.00 0.00 2.71
2601 2705 9.155975 GTAATTAATGTATCGATCTTGGCAGAT 57.844 33.333 0.00 0.00 43.03 2.90
2621 2725 1.651240 CCTTCTGCCATTGACGCCAG 61.651 60.000 0.00 0.00 0.00 4.85
2624 2728 3.047718 CTGCCATTGACGCCAGCAG 62.048 63.158 0.00 0.00 44.31 4.24
2654 2758 0.745845 AGCGCATGCCTCCTACAAAG 60.746 55.000 13.15 0.00 44.31 2.77
2670 2774 2.235402 ACAAAGACCCATCGAACGGTAT 59.765 45.455 6.76 1.40 30.56 2.73
2671 2775 3.448301 ACAAAGACCCATCGAACGGTATA 59.552 43.478 6.76 0.00 30.56 1.47
2689 2793 1.951923 TATCCACCGCCTAGACCCCA 61.952 60.000 0.00 0.00 0.00 4.96
2850 3010 1.442526 GCAGGAACCTCGCCATCATG 61.443 60.000 0.00 0.00 0.00 3.07
3008 3170 2.159585 CGCTGGCAAATTCACGTTCATA 60.160 45.455 0.00 0.00 0.00 2.15
3387 4981 6.379988 TCAGTGGCATTGACTAGTAGACATTA 59.620 38.462 8.78 0.00 0.00 1.90
3399 4993 7.897864 ACTAGTAGACATTATTCATAGGCACC 58.102 38.462 3.59 0.00 0.00 5.01
3406 5000 2.859165 ATTCATAGGCACCCGGTATG 57.141 50.000 0.00 1.29 0.00 2.39
3411 5005 1.399744 TAGGCACCCGGTATGAGCAG 61.400 60.000 0.00 0.00 0.00 4.24
3516 5110 9.197694 CATCGGTAAATAAAGTCTAGAATCAGG 57.802 37.037 0.00 0.00 0.00 3.86
3685 5279 2.734079 GTGACAGAACAAGTAGCTCAGC 59.266 50.000 0.00 0.00 0.00 4.26
3827 5422 5.687770 TGTGTTGTTGGTACATGATCTTG 57.312 39.130 0.00 7.04 39.30 3.02
3829 5424 4.078537 TGTTGTTGGTACATGATCTTGGG 58.921 43.478 12.76 0.00 39.30 4.12
3894 5489 1.214175 TGGTGGGTCATCAGTTTGTGT 59.786 47.619 0.00 0.00 0.00 3.72
3915 5510 5.928839 GTGTTGTTAGATCAGTCTGTGACAT 59.071 40.000 0.00 0.00 38.28 3.06
3958 5554 4.910458 ATACTCCACTTAGTTTGCCAGT 57.090 40.909 0.00 0.00 0.00 4.00
4105 5701 3.879295 CGAAGTGGGATATGCAGTCAATT 59.121 43.478 0.00 0.00 0.00 2.32
4125 5721 8.108782 GTCAATTCTCTTTACAGTATTGCGTAC 58.891 37.037 0.00 0.00 0.00 3.67
4254 5850 5.069781 GTGATATTCCAGGTAGCAAGAGAGT 59.930 44.000 0.00 0.00 0.00 3.24
4295 5891 8.890893 TCCTAATAGGTATGCTAGCAGTTGCAT 61.891 40.741 23.89 10.98 42.30 3.96
4478 6074 9.482627 CTAGGATCAATAACCTACATCTTCAAC 57.517 37.037 0.00 0.00 37.68 3.18
4550 6146 4.324267 CCATTCCTATAACCCGTTGGATC 58.676 47.826 0.00 0.00 34.81 3.36
4557 6153 2.272146 CCCGTTGGATCCTGGGTG 59.728 66.667 22.31 8.80 36.86 4.61
4873 6485 4.202101 CCGTACAGAAGATGAGAAGAGCAT 60.202 45.833 0.00 0.00 0.00 3.79
4874 6486 5.009110 CCGTACAGAAGATGAGAAGAGCATA 59.991 44.000 0.00 0.00 0.00 3.14
4875 6487 6.142139 CGTACAGAAGATGAGAAGAGCATAG 58.858 44.000 0.00 0.00 0.00 2.23
4876 6488 6.238621 CGTACAGAAGATGAGAAGAGCATAGT 60.239 42.308 0.00 0.00 0.00 2.12
4877 6489 5.904941 ACAGAAGATGAGAAGAGCATAGTG 58.095 41.667 0.00 0.00 0.00 2.74
4888 6500 3.624777 AGAGCATAGTGTCCCAAATTGG 58.375 45.455 4.74 4.74 37.25 3.16
4925 6544 2.838637 AGGGACAAGGTAGAGAGAGG 57.161 55.000 0.00 0.00 0.00 3.69
4926 6545 2.289467 AGGGACAAGGTAGAGAGAGGA 58.711 52.381 0.00 0.00 0.00 3.71
4927 6546 2.655407 AGGGACAAGGTAGAGAGAGGAA 59.345 50.000 0.00 0.00 0.00 3.36
4930 6549 4.345854 GGACAAGGTAGAGAGAGGAAAGA 58.654 47.826 0.00 0.00 0.00 2.52
5108 6734 4.462483 GTGGTCATGTGAAACCATAACCAT 59.538 41.667 7.22 0.00 46.69 3.55
5639 7296 4.019792 TGAGTACATGTGCAATGGTTCT 57.980 40.909 16.62 3.60 0.00 3.01
5725 7382 1.286260 CTACCGGGATAGCTCGTGC 59.714 63.158 6.32 0.07 35.85 5.34
5850 7508 1.225855 TGGTCTTGCTAAACTGTGCG 58.774 50.000 0.00 0.00 0.00 5.34
5990 7649 8.216423 AGTTATGGAATGATGTTGCTAGAGATT 58.784 33.333 0.00 0.00 0.00 2.40
6023 7682 5.867330 AGGAAAAATGTGAAATCATTGGCA 58.133 33.333 0.00 0.00 37.96 4.92
6666 8336 5.495926 AGATTATAGAGAAGGGCCATGTG 57.504 43.478 6.18 0.00 0.00 3.21
6785 8455 4.578105 GGCTCTATCTGTAAAGCATGCTTT 59.422 41.667 39.21 39.21 46.56 3.51
6841 8514 5.543714 TGTTGAGCTAAAGTTCCATTACGA 58.456 37.500 0.00 0.00 0.00 3.43
6881 8554 5.841957 AAGGAAATAATCACTGCATCACC 57.158 39.130 0.00 0.00 0.00 4.02
6938 8621 1.668826 TCAGGCTGGTAGTTGGGAAT 58.331 50.000 15.73 0.00 0.00 3.01
7033 8718 5.682943 TGCATAGCCGGTTATCATAAAAC 57.317 39.130 8.00 0.00 0.00 2.43
7035 8720 4.760204 GCATAGCCGGTTATCATAAAACCT 59.240 41.667 8.00 0.00 43.55 3.50
7069 8754 1.208358 CACAGCAATGTCACAGGCG 59.792 57.895 0.00 0.00 0.00 5.52
7093 8982 5.283717 GTGCATTATAGTTCTGCAACAAACG 59.716 40.000 0.00 0.00 46.51 3.60
7133 9022 3.703052 GGAGATGTCAAGGCCAATCATTT 59.297 43.478 5.01 0.00 0.00 2.32
7204 9097 5.124776 GCATACCAAGGTTATACAACTTGCA 59.875 40.000 0.00 0.00 34.88 4.08
7211 9104 5.560724 AGGTTATACAACTTGCATGTCACT 58.439 37.500 5.61 0.00 34.88 3.41
7254 9150 6.778069 TCCTATCACTGTATTCCAGGAAGTAG 59.222 42.308 8.20 8.11 46.06 2.57
7257 9153 6.770746 TCACTGTATTCCAGGAAGTAGTAC 57.229 41.667 8.20 5.93 46.06 2.73
7287 9192 4.755411 TCAGCCTTACAAGTTCGAATAGG 58.245 43.478 0.00 3.39 0.00 2.57
7403 9312 3.003897 TGCATAGAACGTGAAACCAAACC 59.996 43.478 0.00 0.00 0.00 3.27
7414 9323 4.889807 CCAAACCGGTCTGTCCAA 57.110 55.556 8.04 0.00 35.57 3.53
7445 9354 9.374838 GTTACAGATCTTCCGGAGTAAAATTTA 57.625 33.333 3.34 0.00 0.00 1.40
7457 9366 8.579006 CCGGAGTAAAATTTACCCTAAAAACTT 58.421 33.333 11.83 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.066505 GGAACATAAAGGCTGATTGTACCAG 59.933 44.000 0.00 0.00 34.88 4.00
41 43 4.222124 ACGAGGAACATAAAGGCTGATT 57.778 40.909 0.00 0.00 0.00 2.57
46 48 4.274421 GCTTTACGAGGAACATAAAGGC 57.726 45.455 0.00 0.00 36.72 4.35
51 53 4.116961 CGATTGGCTTTACGAGGAACATA 58.883 43.478 0.00 0.00 0.00 2.29
54 56 1.062148 GCGATTGGCTTTACGAGGAAC 59.938 52.381 0.00 0.00 39.11 3.62
73 75 1.809684 AGGAAGCCTACAAACGAAGC 58.190 50.000 0.00 0.00 28.47 3.86
78 80 6.835819 ATCCTAAAAAGGAAGCCTACAAAC 57.164 37.500 0.00 0.00 41.90 2.93
80 82 6.780522 ACAAATCCTAAAAAGGAAGCCTACAA 59.219 34.615 0.00 0.00 41.90 2.41
81 83 6.311735 ACAAATCCTAAAAAGGAAGCCTACA 58.688 36.000 0.00 0.00 41.90 2.74
95 97 8.690203 TGATGTTCTCAAGAAACAAATCCTAA 57.310 30.769 0.00 0.00 35.58 2.69
108 110 3.641434 ACCCTCCATGATGTTCTCAAG 57.359 47.619 0.00 0.00 37.44 3.02
121 123 3.287222 CTGAAAGACAACAAACCCTCCA 58.713 45.455 0.00 0.00 34.07 3.86
132 134 9.921637 AAAATGTTCAAAAGTACTGAAAGACAA 57.078 25.926 0.00 0.00 37.43 3.18
139 141 7.908082 CGAGACAAAAATGTTCAAAAGTACTGA 59.092 33.333 0.00 0.00 0.00 3.41
140 142 7.908082 TCGAGACAAAAATGTTCAAAAGTACTG 59.092 33.333 0.00 0.00 0.00 2.74
144 146 6.094881 TCCTCGAGACAAAAATGTTCAAAAGT 59.905 34.615 15.71 0.00 0.00 2.66
158 160 4.755123 GGTTGAAGAATTTCCTCGAGACAA 59.245 41.667 15.71 6.35 32.09 3.18
161 163 4.040461 ACAGGTTGAAGAATTTCCTCGAGA 59.960 41.667 15.71 0.00 32.09 4.04
162 164 4.319177 ACAGGTTGAAGAATTTCCTCGAG 58.681 43.478 5.13 5.13 32.09 4.04
163 165 4.202315 TGACAGGTTGAAGAATTTCCTCGA 60.202 41.667 0.00 0.00 32.09 4.04
164 166 4.065088 TGACAGGTTGAAGAATTTCCTCG 58.935 43.478 0.00 0.00 32.09 4.63
165 167 6.432472 AGAATGACAGGTTGAAGAATTTCCTC 59.568 38.462 0.00 0.00 32.09 3.71
172 174 8.690203 TTGAATAAGAATGACAGGTTGAAGAA 57.310 30.769 0.00 0.00 0.00 2.52
173 175 8.156820 TCTTGAATAAGAATGACAGGTTGAAGA 58.843 33.333 0.00 0.00 39.89 2.87
174 176 8.327941 TCTTGAATAAGAATGACAGGTTGAAG 57.672 34.615 0.00 0.00 39.89 3.02
196 198 5.948742 TCCAAGGAAACCACAAATTTCTT 57.051 34.783 0.00 0.00 36.49 2.52
197 199 5.602145 TCATCCAAGGAAACCACAAATTTCT 59.398 36.000 0.00 0.00 36.49 2.52
207 209 0.704664 ACCCCTCATCCAAGGAAACC 59.295 55.000 0.00 0.00 38.87 3.27
208 210 2.604912 AACCCCTCATCCAAGGAAAC 57.395 50.000 0.00 0.00 38.87 2.78
241 243 8.970859 ATTACTATCTCAAGTCCTTCAAATGG 57.029 34.615 0.00 0.00 0.00 3.16
301 303 6.985059 TCAAAGTGCATTGAACATGAAAATGA 59.015 30.769 17.80 6.15 36.42 2.57
304 306 5.234757 GCTCAAAGTGCATTGAACATGAAAA 59.765 36.000 0.00 0.00 38.75 2.29
305 307 4.746115 GCTCAAAGTGCATTGAACATGAAA 59.254 37.500 0.00 0.00 38.75 2.69
310 312 2.541383 CGTGCTCAAAGTGCATTGAACA 60.541 45.455 4.41 3.53 42.69 3.18
317 319 0.179059 TCCTTCGTGCTCAAAGTGCA 60.179 50.000 0.00 0.00 38.19 4.57
331 333 7.173907 TGTCTCTCAAGATGAATTTGTTCCTTC 59.826 37.037 0.00 0.00 33.08 3.46
332 334 7.000472 TGTCTCTCAAGATGAATTTGTTCCTT 59.000 34.615 0.00 0.00 33.08 3.36
344 346 6.592994 TCAGCAAATTAGTGTCTCTCAAGATG 59.407 38.462 0.00 0.00 33.08 2.90
367 369 1.758440 AACCACTCCTTGCTCGCTCA 61.758 55.000 0.00 0.00 0.00 4.26
375 377 8.237267 GTGTTAATTATTGAGAACCACTCCTTG 58.763 37.037 0.00 0.00 44.34 3.61
394 396 9.407380 TGCCTTATGAAGTTATGATGTGTTAAT 57.593 29.630 0.00 0.00 0.00 1.40
399 401 6.932356 ACTGCCTTATGAAGTTATGATGTG 57.068 37.500 0.00 0.00 0.00 3.21
400 402 6.992715 GGTACTGCCTTATGAAGTTATGATGT 59.007 38.462 0.00 0.00 0.00 3.06
721 770 5.844004 AGCATCCTCACTAAATTACTACCG 58.156 41.667 0.00 0.00 0.00 4.02
939 989 3.493129 GCATGGCGTGAAGATTATACGAA 59.507 43.478 11.71 0.00 40.01 3.85
1616 1715 1.228094 TTGGTGCAATCGCCTGACA 60.228 52.632 0.00 0.00 43.26 3.58
1735 1834 2.089349 GTGCAGAGTCGAGTTCGGC 61.089 63.158 12.89 12.89 45.56 5.54
1938 2037 2.656947 TGAAAAGCTGCTAAGTGGGT 57.343 45.000 0.90 0.00 0.00 4.51
2017 2117 2.324330 CGGCTGCGATGTTTGACCA 61.324 57.895 0.00 0.00 0.00 4.02
2020 2120 2.031919 ACCGGCTGCGATGTTTGA 59.968 55.556 0.00 0.00 0.00 2.69
2136 2236 1.818060 GGTGTAGTTCAATGCCATGCA 59.182 47.619 0.00 0.00 44.86 3.96
2205 2305 5.668558 AACACCGACTCTTAAATTGTGAC 57.331 39.130 0.00 0.00 0.00 3.67
2264 2364 2.481568 GGCCGCGGTAATAATCCTTTAC 59.518 50.000 28.70 3.83 0.00 2.01
2265 2365 2.369532 AGGCCGCGGTAATAATCCTTTA 59.630 45.455 28.70 0.00 0.00 1.85
2289 2389 1.797046 GATGTGTGCATCGCTCTATGG 59.203 52.381 0.00 0.00 41.60 2.74
2546 2649 1.901464 GGGTTTGCGGAAGAAGGCA 60.901 57.895 0.00 0.00 37.39 4.75
2561 2664 7.213178 ACATTAATTACTCCTGAAGATGGGT 57.787 36.000 0.00 0.00 0.00 4.51
2601 2705 1.377202 GGCGTCAATGGCAGAAGGA 60.377 57.895 0.00 0.00 0.00 3.36
2633 2737 0.104855 TTGTAGGAGGCATGCGCTAG 59.895 55.000 12.44 1.38 38.60 3.42
2654 2758 2.559668 TGGATATACCGTTCGATGGGTC 59.440 50.000 10.83 2.96 42.61 4.46
2670 2774 1.152398 GGGGTCTAGGCGGTGGATA 60.152 63.158 0.00 0.00 0.00 2.59
2671 2775 2.446036 GGGGTCTAGGCGGTGGAT 60.446 66.667 0.00 0.00 0.00 3.41
2689 2793 1.377725 CTTGGCGGCAAGATGGAGT 60.378 57.895 39.97 0.00 34.26 3.85
2850 3010 4.481463 GAGATTTAGGCTCTCAGTATCGC 58.519 47.826 0.00 0.00 39.18 4.58
2957 3118 3.706373 GCCCTCGGCCAGAACTGA 61.706 66.667 2.24 0.00 44.06 3.41
3239 4821 2.803029 AAGCCCAGACACGGGATGATT 61.803 52.381 0.00 0.00 46.85 2.57
3361 4955 4.711846 TGTCTACTAGTCAATGCCACTGAT 59.288 41.667 0.00 0.00 0.00 2.90
3364 4958 5.683876 AATGTCTACTAGTCAATGCCACT 57.316 39.130 0.00 0.00 0.00 4.00
3387 4981 2.303022 CTCATACCGGGTGCCTATGAAT 59.697 50.000 10.66 0.00 0.00 2.57
3399 4993 1.443407 CTCCCACTGCTCATACCGG 59.557 63.158 0.00 0.00 0.00 5.28
3504 5098 3.791245 CCAAGTGCTCCTGATTCTAGAC 58.209 50.000 0.00 0.00 0.00 2.59
3509 5103 0.322816 TGGCCAAGTGCTCCTGATTC 60.323 55.000 0.61 0.00 40.92 2.52
3516 5110 0.595095 CTTCAAGTGGCCAAGTGCTC 59.405 55.000 7.24 0.00 40.92 4.26
3780 5374 4.857871 TGTCGAAAATCTGGAAATAGCG 57.142 40.909 0.00 0.00 0.00 4.26
3797 5391 2.911819 ACCAACAACACAACTTGTCG 57.088 45.000 0.00 0.00 37.51 4.35
3862 5457 2.249139 GACCCACCAAGACACTAGAGT 58.751 52.381 0.00 0.00 0.00 3.24
3894 5489 9.554395 TTTTAATGTCACAGACTGATCTAACAA 57.446 29.630 10.08 0.00 32.25 2.83
4079 5675 3.270877 ACTGCATATCCCACTTCGTTTC 58.729 45.455 0.00 0.00 0.00 2.78
4105 5701 6.448852 TGTTGTACGCAATACTGTAAAGAGA 58.551 36.000 0.00 0.00 36.92 3.10
4136 5732 9.674068 TTAACAGGCTCAATACATAAACACATA 57.326 29.630 0.00 0.00 0.00 2.29
4254 5850 6.122277 CCTATTAGGAGAATCTTTGTGCCAA 58.878 40.000 3.41 0.00 37.67 4.52
4271 5867 5.541845 TGCAACTGCTAGCATACCTATTAG 58.458 41.667 19.72 5.53 42.66 1.73
4392 5988 9.530633 GTTCCAGTCGAATTATATAGTCAAACT 57.469 33.333 0.00 0.00 31.67 2.66
4401 5997 9.832445 AGTGTATTTGTTCCAGTCGAATTATAT 57.168 29.630 0.00 0.00 31.67 0.86
4483 6079 2.897326 AGGCGGCAAAAGTAGGATTTTT 59.103 40.909 13.08 0.00 30.01 1.94
4484 6080 2.525368 AGGCGGCAAAAGTAGGATTTT 58.475 42.857 13.08 0.00 32.65 1.82
4550 6146 2.190488 GAGGAGCTTCACCACCCAGG 62.190 65.000 0.00 0.00 45.67 4.45
4557 6153 1.372087 CCGCAATGAGGAGCTTCACC 61.372 60.000 0.00 0.00 0.00 4.02
4888 6500 7.120923 TGTCCCTATTTCTACATACAACTCC 57.879 40.000 0.00 0.00 0.00 3.85
4892 6504 7.504926 ACCTTGTCCCTATTTCTACATACAA 57.495 36.000 0.00 0.00 0.00 2.41
4896 6508 7.363031 TCTCTACCTTGTCCCTATTTCTACAT 58.637 38.462 0.00 0.00 0.00 2.29
4900 6512 6.093617 TCTCTCTACCTTGTCCCTATTTCT 57.906 41.667 0.00 0.00 0.00 2.52
4901 6513 5.303333 CCTCTCTCTACCTTGTCCCTATTTC 59.697 48.000 0.00 0.00 0.00 2.17
4903 6515 4.482772 TCCTCTCTCTACCTTGTCCCTATT 59.517 45.833 0.00 0.00 0.00 1.73
4983 6602 2.704596 CCTACTTAGGTTCCTAAGGGGC 59.295 54.545 30.15 0.00 45.73 5.80
5001 6620 2.648304 ACAGTCAGTACCAGACCTCCTA 59.352 50.000 11.29 0.00 36.68 2.94
5003 6622 1.819903 GACAGTCAGTACCAGACCTCC 59.180 57.143 11.29 0.03 36.68 4.30
5004 6623 2.490115 CAGACAGTCAGTACCAGACCTC 59.510 54.545 2.66 7.50 36.68 3.85
5006 6625 1.546476 CCAGACAGTCAGTACCAGACC 59.454 57.143 2.66 0.00 36.68 3.85
5007 6626 2.240279 ACCAGACAGTCAGTACCAGAC 58.760 52.381 2.66 7.75 36.26 3.51
5008 6627 2.677542 ACCAGACAGTCAGTACCAGA 57.322 50.000 2.66 0.00 0.00 3.86
5010 6629 3.418995 GTCTACCAGACAGTCAGTACCA 58.581 50.000 2.66 0.00 44.45 3.25
5072 6691 3.829948 CATGACCACATGCTTTCAACTC 58.170 45.455 0.00 0.00 45.51 3.01
5133 6771 5.843673 AGAGCTCTAAGAACATCGAATGA 57.156 39.130 16.50 0.00 0.00 2.57
5191 6847 5.335426 GCTGATGTCAAAGCTGAGATTGAAA 60.335 40.000 0.18 0.00 35.76 2.69
5639 7296 9.868160 TTCTCTGAGTAAATGTATCTATCCAGA 57.132 33.333 4.32 0.00 34.56 3.86
5725 7382 4.581824 AGCTATGGTGCAAATATTCCAGTG 59.418 41.667 0.00 0.00 33.33 3.66
5850 7508 0.615850 AGCTTGCTCTCCTTGGTACC 59.384 55.000 4.43 4.43 0.00 3.34
5990 7649 4.541705 TCACATTTTTCCTTCCTCCAACA 58.458 39.130 0.00 0.00 0.00 3.33
6023 7682 7.090808 GGAAATACTTTTCGCTGGATTTTTCT 58.909 34.615 0.00 0.00 41.84 2.52
6259 7918 6.607600 TGTAGAAGCATCTTACAGTAGTCCAT 59.392 38.462 0.00 0.00 37.10 3.41
6335 8002 6.403878 GGATAAGCAAGTAGGTCAAGTTACA 58.596 40.000 0.00 0.00 0.00 2.41
6666 8336 4.142609 TCACCACAGCTAGATTTCCATC 57.857 45.455 0.00 0.00 0.00 3.51
6726 8396 4.818534 GTCATTCAGACACAACACATGT 57.181 40.909 0.00 0.00 46.77 3.21
6806 8479 8.045176 ACTTTAGCTCAACAAGACATTTATCC 57.955 34.615 0.00 0.00 0.00 2.59
6881 8554 6.710744 GTGTTAGTCAATATAACCCCCATCTG 59.289 42.308 0.00 0.00 33.13 2.90
6938 8621 2.422597 CCTCTTATGTTTGACACGCCA 58.577 47.619 0.00 0.00 0.00 5.69
7033 8718 4.319766 GCTGTGAGTGTTATCAACAACAGG 60.320 45.833 17.50 8.73 43.19 4.00
7035 8720 4.195416 TGCTGTGAGTGTTATCAACAACA 58.805 39.130 0.00 0.00 44.16 3.33
7093 8982 7.655490 ACATCTCCATATGCAAGCTAATTTTC 58.345 34.615 0.00 0.00 0.00 2.29
7133 9022 1.544759 GGGGCCTGTCGAAGAAGAAAA 60.545 52.381 0.84 0.00 39.69 2.29
7137 9026 0.902531 TTAGGGGCCTGTCGAAGAAG 59.097 55.000 0.84 0.00 39.69 2.85
7151 9040 8.506168 AGTACAAATATGACACACATTTAGGG 57.494 34.615 0.00 0.00 40.07 3.53
7204 9097 4.441634 GCTTCGGTTATCACCTAGTGACAT 60.442 45.833 0.00 0.00 45.65 3.06
7211 9104 2.037144 GGAGGCTTCGGTTATCACCTA 58.963 52.381 0.00 0.00 41.64 3.08
7254 9150 5.296035 ACTTGTAAGGCTGAACACAAAGTAC 59.704 40.000 2.65 0.00 31.00 2.73
7257 9153 4.900635 ACTTGTAAGGCTGAACACAAAG 57.099 40.909 2.65 1.75 31.00 2.77
7307 9212 4.040461 TCTTGGTAAGTCTCTGTCTTTGGG 59.960 45.833 0.00 0.00 0.00 4.12
7314 9219 3.579151 GGAAGGTCTTGGTAAGTCTCTGT 59.421 47.826 0.00 0.00 0.00 3.41
7403 9312 3.659786 TGTAACTTGATTGGACAGACCG 58.340 45.455 0.00 0.00 42.61 4.79
7414 9323 4.712337 ACTCCGGAAGATCTGTAACTTGAT 59.288 41.667 5.23 0.00 0.00 2.57
7445 9354 5.694231 ATCGCGTTTAAAGTTTTTAGGGT 57.306 34.783 5.77 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.