Multiple sequence alignment - TraesCS2B01G305900

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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 TraesCS2B01G305900 chr2B 100.000 5092 0 0 1 5092 436242147 436237056 0.000000e+00 9404
1 TraesCS2B01G305900 chr2B 84.240 717 96 9 4390 5091 184799846 184799132 0.000000e+00 682
2 TraesCS2B01G305900 chr2B 77.122 966 187 19 2756 3718 436960280 436961214 3.490000e-146 529
3 TraesCS2B01G305900 chr2D 93.811 3862 132 44 580 4364 367506112 367502281 0.000000e+00 5709
4 TraesCS2B01G305900 chr2D 76.580 965 194 18 2756 3718 367921944 367922878 7.610000e-138 501
5 TraesCS2B01G305900 chr2D 96.259 294 8 3 1 294 367506782 367506492 3.570000e-131 479
6 TraesCS2B01G305900 chr2D 93.293 164 7 2 287 447 367506401 367506239 6.590000e-59 239
7 TraesCS2B01G305900 chr2D 95.495 111 5 0 471 581 367506253 367506143 1.460000e-40 178
8 TraesCS2B01G305900 chr2A 93.530 3864 152 44 580 4364 497656065 497652221 0.000000e+00 5661
9 TraesCS2B01G305900 chr2A 76.708 966 191 19 2756 3718 498042668 498043602 1.640000e-139 507
10 TraesCS2B01G305900 chr2A 94.366 142 4 3 1 140 497656596 497656457 1.110000e-51 215
11 TraesCS2B01G305900 chr2A 90.647 139 8 2 231 367 497656465 497656330 4.050000e-41 180
12 TraesCS2B01G305900 chr2A 92.793 111 8 0 471 581 497656206 497656096 1.470000e-35 161
13 TraesCS2B01G305900 chr2A 93.902 82 2 1 365 443 497656276 497656195 2.490000e-23 121
14 TraesCS2B01G305900 chr4B 80.222 1896 264 72 1870 3728 600657049 600655228 0.000000e+00 1321
15 TraesCS2B01G305900 chr4B 94.828 232 12 0 1208 1439 600657761 600657530 3.750000e-96 363
16 TraesCS2B01G305900 chr4B 89.231 260 28 0 1530 1789 600657434 600657175 4.920000e-85 326
17 TraesCS2B01G305900 chr4B 83.861 316 39 5 3784 4096 600655139 600654833 1.790000e-74 291
18 TraesCS2B01G305900 chr4D 85.181 992 121 17 2756 3728 476304561 476303577 0.000000e+00 994
19 TraesCS2B01G305900 chr4D 77.251 822 125 41 1870 2650 476305457 476304657 4.710000e-115 425
20 TraesCS2B01G305900 chr4D 94.068 236 14 0 1208 1443 476306171 476305936 4.850000e-95 359
21 TraesCS2B01G305900 chr4D 85.443 316 34 5 3784 4096 476303488 476303182 8.230000e-83 318
22 TraesCS2B01G305900 chr7D 86.389 720 77 9 4389 5091 71120547 71119832 0.000000e+00 767
23 TraesCS2B01G305900 chr4A 88.800 625 68 2 3105 3728 683486144 683485521 0.000000e+00 765
24 TraesCS2B01G305900 chr4A 84.605 708 74 13 4390 5091 376722956 376723634 0.000000e+00 671
25 TraesCS2B01G305900 chr4A 85.921 554 68 7 4547 5091 605010891 605010339 2.640000e-162 582
26 TraesCS2B01G305900 chr4A 78.372 823 119 40 1870 2650 683487392 683486587 3.570000e-131 479
27 TraesCS2B01G305900 chr4A 94.828 232 12 0 1208 1439 683488120 683487889 3.750000e-96 363
28 TraesCS2B01G305900 chr4A 90.977 266 24 0 2756 3021 683486505 683486240 4.850000e-95 359
29 TraesCS2B01G305900 chr4A 89.098 266 28 1 1525 1789 683487773 683487508 3.800000e-86 329
30 TraesCS2B01G305900 chr4A 83.861 316 39 5 3784 4096 683485432 683485126 1.790000e-74 291
31 TraesCS2B01G305900 chr5D 86.541 691 74 7 4402 5082 484157693 484158374 0.000000e+00 743
32 TraesCS2B01G305900 chr5D 84.124 548 68 10 4392 4930 410536018 410535481 3.520000e-141 512
33 TraesCS2B01G305900 chr6D 85.734 708 70 13 4395 5091 464667704 464668391 0.000000e+00 719
34 TraesCS2B01G305900 chr6A 85.269 706 93 9 4389 5091 531467443 531468140 0.000000e+00 717
35 TraesCS2B01G305900 chr6A 84.388 237 34 2 1204 1437 33542563 33542327 3.970000e-56 230
36 TraesCS2B01G305900 chrUn 85.216 717 77 12 4389 5091 55810013 55810714 0.000000e+00 710
37 TraesCS2B01G305900 chr3D 85.299 585 61 17 4391 4955 10026042 10025463 9.500000e-162 580
38 TraesCS2B01G305900 chr7A 80.712 337 51 7 4389 4722 660917321 660916996 3.040000e-62 250


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 TraesCS2B01G305900 chr2B 436237056 436242147 5091 True 9404.00 9404 100.00000 1 5092 1 chr2B.!!$R2 5091
1 TraesCS2B01G305900 chr2B 184799132 184799846 714 True 682.00 682 84.24000 4390 5091 1 chr2B.!!$R1 701
2 TraesCS2B01G305900 chr2B 436960280 436961214 934 False 529.00 529 77.12200 2756 3718 1 chr2B.!!$F1 962
3 TraesCS2B01G305900 chr2D 367502281 367506782 4501 True 1651.25 5709 94.71450 1 4364 4 chr2D.!!$R1 4363
4 TraesCS2B01G305900 chr2D 367921944 367922878 934 False 501.00 501 76.58000 2756 3718 1 chr2D.!!$F1 962
5 TraesCS2B01G305900 chr2A 497652221 497656596 4375 True 1267.60 5661 93.04760 1 4364 5 chr2A.!!$R1 4363
6 TraesCS2B01G305900 chr2A 498042668 498043602 934 False 507.00 507 76.70800 2756 3718 1 chr2A.!!$F1 962
7 TraesCS2B01G305900 chr4B 600654833 600657761 2928 True 575.25 1321 87.03550 1208 4096 4 chr4B.!!$R1 2888
8 TraesCS2B01G305900 chr4D 476303182 476306171 2989 True 524.00 994 85.48575 1208 4096 4 chr4D.!!$R1 2888
9 TraesCS2B01G305900 chr7D 71119832 71120547 715 True 767.00 767 86.38900 4389 5091 1 chr7D.!!$R1 702
10 TraesCS2B01G305900 chr4A 376722956 376723634 678 False 671.00 671 84.60500 4390 5091 1 chr4A.!!$F1 701
11 TraesCS2B01G305900 chr4A 605010339 605010891 552 True 582.00 582 85.92100 4547 5091 1 chr4A.!!$R1 544
12 TraesCS2B01G305900 chr4A 683485126 683488120 2994 True 431.00 765 87.65600 1208 4096 6 chr4A.!!$R2 2888
13 TraesCS2B01G305900 chr5D 484157693 484158374 681 False 743.00 743 86.54100 4402 5082 1 chr5D.!!$F1 680
14 TraesCS2B01G305900 chr5D 410535481 410536018 537 True 512.00 512 84.12400 4392 4930 1 chr5D.!!$R1 538
15 TraesCS2B01G305900 chr6D 464667704 464668391 687 False 719.00 719 85.73400 4395 5091 1 chr6D.!!$F1 696
16 TraesCS2B01G305900 chr6A 531467443 531468140 697 False 717.00 717 85.26900 4389 5091 1 chr6A.!!$F1 702
17 TraesCS2B01G305900 chrUn 55810013 55810714 701 False 710.00 710 85.21600 4389 5091 1 chrUn.!!$F1 702
18 TraesCS2B01G305900 chr3D 10025463 10026042 579 True 580.00 580 85.29900 4391 4955 1 chr3D.!!$R1 564

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
983 1178 1.136984 GAACATCAGCAGCAGCAGC 59.863 57.895 3.17 0.46 45.49 5.25 F
2174 2534 0.593008 TTCACGACGTCGGTGTTCTG 60.593 55.000 37.89 26.22 44.95 3.02 F
3187 3617 1.262683 GCTCATATGGAAGAAGCACGC 59.737 52.381 2.13 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 2867 0.329596 ATGAGGTCCTTCTGTTGGGC 59.670 55.0 0.00 0.0 0.00 5.36 R
3378 3808 0.248825 AGCATCGTCATCTCGCTGAC 60.249 55.0 0.00 3.4 41.73 3.51 R
4383 4863 0.108472 GTAGGGTTAGGAGCGCGTTT 60.108 55.0 8.43 0.0 0.00 3.60 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
93 96 3.021695 TCATGCCACGCTAGTACTAGTT 58.978 45.455 26.76 14.29 35.65 2.24
158 161 3.263425 TCTCCCTGGTTTGAAGGTCATAC 59.737 47.826 0.00 0.00 32.45 2.39
161 164 3.009033 CCCTGGTTTGAAGGTCATACTCA 59.991 47.826 0.00 0.00 30.62 3.41
167 170 5.277828 GGTTTGAAGGTCATACTCAACACAC 60.278 44.000 0.06 0.00 30.62 3.82
171 174 5.758296 TGAAGGTCATACTCAACACACTTTC 59.242 40.000 0.00 0.00 0.00 2.62
297 400 8.880750 CATGACAGCAATAGATACTATTCATGG 58.119 37.037 15.33 3.90 33.52 3.66
333 436 4.716794 ACCGGAACAAAGTGGTAATTACA 58.283 39.130 17.16 1.24 31.60 2.41
364 467 9.298250 AGTGTACACTAACTCTTCTTCAATAGA 57.702 33.333 26.91 0.00 40.43 1.98
430 592 7.472334 AAATGAGGTCACTTATGCTTCAATT 57.528 32.000 0.00 0.00 0.00 2.32
431 593 8.579850 AAATGAGGTCACTTATGCTTCAATTA 57.420 30.769 0.00 0.00 0.00 1.40
432 594 8.757982 AATGAGGTCACTTATGCTTCAATTAT 57.242 30.769 0.00 0.00 0.00 1.28
433 595 9.851686 AATGAGGTCACTTATGCTTCAATTATA 57.148 29.630 0.00 0.00 0.00 0.98
435 597 9.276590 TGAGGTCACTTATGCTTCAATTATATG 57.723 33.333 0.00 0.00 0.00 1.78
436 598 8.627208 AGGTCACTTATGCTTCAATTATATGG 57.373 34.615 0.00 0.00 0.00 2.74
437 599 8.439971 AGGTCACTTATGCTTCAATTATATGGA 58.560 33.333 0.00 0.00 0.00 3.41
438 600 8.725148 GGTCACTTATGCTTCAATTATATGGAG 58.275 37.037 0.00 0.00 0.00 3.86
439 601 8.725148 GTCACTTATGCTTCAATTATATGGAGG 58.275 37.037 0.00 0.00 0.00 4.30
440 602 8.439971 TCACTTATGCTTCAATTATATGGAGGT 58.560 33.333 0.00 0.00 0.00 3.85
441 603 9.071276 CACTTATGCTTCAATTATATGGAGGTT 57.929 33.333 0.00 0.00 0.00 3.50
442 604 9.646522 ACTTATGCTTCAATTATATGGAGGTTT 57.353 29.630 0.00 0.00 0.00 3.27
443 605 9.903682 CTTATGCTTCAATTATATGGAGGTTTG 57.096 33.333 0.00 0.00 0.00 2.93
444 606 7.902920 ATGCTTCAATTATATGGAGGTTTGT 57.097 32.000 0.00 0.00 0.00 2.83
445 607 7.716799 TGCTTCAATTATATGGAGGTTTGTT 57.283 32.000 0.00 0.00 0.00 2.83
446 608 8.133024 TGCTTCAATTATATGGAGGTTTGTTT 57.867 30.769 0.00 0.00 0.00 2.83
447 609 8.250332 TGCTTCAATTATATGGAGGTTTGTTTC 58.750 33.333 0.00 0.00 0.00 2.78
448 610 7.706607 GCTTCAATTATATGGAGGTTTGTTTCC 59.293 37.037 0.00 0.00 0.00 3.13
449 611 8.893563 TTCAATTATATGGAGGTTTGTTTCCT 57.106 30.769 0.00 0.00 38.09 3.36
456 618 3.430333 GAGGTTTGTTTCCTCGCAAAA 57.570 42.857 0.00 0.00 41.36 2.44
457 619 3.776340 GAGGTTTGTTTCCTCGCAAAAA 58.224 40.909 0.00 0.00 41.36 1.94
540 702 6.698008 TGATTCTTTATCGGTGCAATTCAT 57.302 33.333 0.00 0.00 35.94 2.57
691 886 2.237751 GCATCGCACCGCTCGTTAT 61.238 57.895 0.00 0.00 0.00 1.89
700 895 5.090757 CGCACCGCTCGTTATATTTATAGA 58.909 41.667 0.00 0.00 0.00 1.98
742 937 2.756760 CTGCACTTGCTACCCAATGAAT 59.243 45.455 2.33 0.00 42.66 2.57
744 939 2.223340 GCACTTGCTACCCAATGAATCG 60.223 50.000 0.00 0.00 38.21 3.34
747 942 2.036958 TGCTACCCAATGAATCGTGG 57.963 50.000 0.00 0.00 34.44 4.94
874 1069 1.956297 TGGTTTTCACACCACTACCG 58.044 50.000 0.00 0.00 42.27 4.02
911 1106 2.426024 GCCATTGATGCAGGCCATATAG 59.574 50.000 5.01 0.00 42.58 1.31
983 1178 1.136984 GAACATCAGCAGCAGCAGC 59.863 57.895 3.17 0.46 45.49 5.25
984 1179 1.583495 GAACATCAGCAGCAGCAGCA 61.583 55.000 12.92 0.00 45.49 4.41
985 1180 1.587043 AACATCAGCAGCAGCAGCAG 61.587 55.000 12.92 3.97 45.49 4.24
986 1181 2.438614 ATCAGCAGCAGCAGCAGG 60.439 61.111 12.92 3.88 45.49 4.85
1163 1358 3.265737 AGCCTGGTGACCATGTAATGTTA 59.734 43.478 4.03 0.00 44.81 2.41
1167 1362 5.487433 CTGGTGACCATGTAATGTTACAGA 58.513 41.667 4.03 0.00 45.80 3.41
1168 1363 5.242434 TGGTGACCATGTAATGTTACAGAC 58.758 41.667 0.00 0.00 45.80 3.51
1170 1365 5.351465 GGTGACCATGTAATGTTACAGACAG 59.649 44.000 10.90 3.33 45.80 3.51
1171 1366 6.163476 GTGACCATGTAATGTTACAGACAGA 58.837 40.000 10.90 0.00 45.80 3.41
1172 1367 6.311445 GTGACCATGTAATGTTACAGACAGAG 59.689 42.308 10.90 5.36 45.80 3.35
1174 1369 5.178061 CCATGTAATGTTACAGACAGAGCA 58.822 41.667 10.90 0.00 45.80 4.26
1175 1370 5.643348 CCATGTAATGTTACAGACAGAGCAA 59.357 40.000 10.90 0.00 45.80 3.91
1176 1371 6.183360 CCATGTAATGTTACAGACAGAGCAAG 60.183 42.308 10.90 0.00 45.80 4.01
1178 1373 6.288294 TGTAATGTTACAGACAGAGCAAGTT 58.712 36.000 1.62 0.00 42.62 2.66
1192 1410 5.050499 CAGAGCAAGTTAAACTGACTGACTG 60.050 44.000 0.00 0.00 0.00 3.51
1193 1411 5.023533 AGCAAGTTAAACTGACTGACTGA 57.976 39.130 0.00 0.00 0.00 3.41
1494 1723 4.212425 TGCTGTCATACCAGTTTTTGTACG 59.788 41.667 0.00 0.00 34.84 3.67
1495 1724 4.708601 CTGTCATACCAGTTTTTGTACGC 58.291 43.478 0.00 0.00 0.00 4.42
1504 1733 4.986659 CCAGTTTTTGTACGCTACACTAGT 59.013 41.667 0.00 0.00 38.63 2.57
1651 1911 2.076100 CACATAGAAGCGCCAAACTCA 58.924 47.619 2.29 0.00 0.00 3.41
1823 2136 5.615289 AGAGCTTCAGTTGTGTTGTCTATT 58.385 37.500 0.00 0.00 0.00 1.73
1826 2139 7.386299 AGAGCTTCAGTTGTGTTGTCTATTAAG 59.614 37.037 0.00 0.00 0.00 1.85
1984 2333 1.066929 TGTGTCCATCAGTCCATCACG 60.067 52.381 0.00 0.00 0.00 4.35
1990 2339 3.960755 TCCATCAGTCCATCACGTCTAAT 59.039 43.478 0.00 0.00 0.00 1.73
1991 2340 4.053983 CCATCAGTCCATCACGTCTAATG 58.946 47.826 0.00 0.00 0.00 1.90
1993 2342 4.801330 TCAGTCCATCACGTCTAATGTT 57.199 40.909 0.00 0.00 0.00 2.71
1995 2344 3.865745 CAGTCCATCACGTCTAATGTTCC 59.134 47.826 0.00 0.00 0.00 3.62
2129 2489 1.541588 GTGTGGTTCCTTCTGATTGCC 59.458 52.381 0.00 0.00 0.00 4.52
2174 2534 0.593008 TTCACGACGTCGGTGTTCTG 60.593 55.000 37.89 26.22 44.95 3.02
2414 2797 4.574674 TGCTGACCTAGGACATTTCAAT 57.425 40.909 17.98 0.00 0.00 2.57
2481 2867 9.191995 AGCTTTCGGAAGTATAAACAAATTTTG 57.808 29.630 5.12 7.59 35.25 2.44
2505 2904 3.594134 CAACAGAAGGACCTCATCTGAC 58.406 50.000 24.18 0.10 42.48 3.51
3044 3462 3.366577 GCTAGCTAGCGAAGGATAAGTCC 60.367 52.174 28.89 0.00 41.22 3.85
3059 3480 7.256756 GGATAAGTCCTTTGTGATGATTCAG 57.743 40.000 0.00 0.00 41.60 3.02
3078 3503 2.158449 CAGTGAGGTTTTCATCTGACGC 59.842 50.000 0.00 0.00 38.29 5.19
3187 3617 1.262683 GCTCATATGGAAGAAGCACGC 59.737 52.381 2.13 0.00 0.00 5.34
3245 3675 4.016444 CCATAGAGCTGATCTACCTCTCC 58.984 52.174 4.56 0.00 43.35 3.71
3362 3792 2.041251 AGAGGTACTGGTACGAGCTC 57.959 55.000 2.73 2.73 41.55 4.09
3713 4143 3.614092 GCTCAAGATGTTCATCCAGGAA 58.386 45.455 8.89 0.00 0.00 3.36
3911 4380 3.775654 GACAGGGAGGTGGAGCGG 61.776 72.222 0.00 0.00 0.00 5.52
4079 4548 0.389817 TGCTCAAAGTCGGGATCACG 60.390 55.000 12.22 12.22 0.00 4.35
4099 4568 5.344396 TCACGTACGAGATATAGTGATCGAC 59.656 44.000 24.41 0.00 38.50 4.20
4129 4598 0.249398 AGTTCACCCCGAGTATGTGC 59.751 55.000 0.00 0.00 0.00 4.57
4137 4606 0.875908 CCGAGTATGTGCGGTGATGG 60.876 60.000 0.00 0.00 42.49 3.51
4148 4617 1.577328 CGGTGATGGTTCTGGTGCAC 61.577 60.000 8.80 8.80 0.00 4.57
4154 4623 2.639327 GGTTCTGGTGCACCATGGC 61.639 63.158 37.66 26.99 46.46 4.40
4155 4624 2.672651 TTCTGGTGCACCATGGCG 60.673 61.111 37.66 25.67 46.46 5.69
4156 4625 3.490031 TTCTGGTGCACCATGGCGT 62.490 57.895 37.66 0.00 46.46 5.68
4157 4626 2.974692 TTCTGGTGCACCATGGCGTT 62.975 55.000 37.66 0.00 46.46 4.84
4158 4627 3.271706 CTGGTGCACCATGGCGTTG 62.272 63.158 37.66 20.83 46.46 4.10
4159 4628 4.054825 GGTGCACCATGGCGTTGG 62.055 66.667 31.23 4.85 42.82 3.77
4160 4629 4.722855 GTGCACCATGGCGTTGGC 62.723 66.667 13.04 8.77 40.68 4.52
4195 4664 1.571460 CAAAGTGCCGACAGCTGTC 59.429 57.895 32.73 32.73 44.23 3.51
4213 4682 4.260538 GCTGTCGATTCAATAAGGAAGCAG 60.261 45.833 0.00 0.00 32.92 4.24
4233 4712 3.300962 AGGTGGGGGATGGGAGGA 61.301 66.667 0.00 0.00 0.00 3.71
4234 4713 2.774351 GGTGGGGGATGGGAGGAG 60.774 72.222 0.00 0.00 0.00 3.69
4331 4811 3.019564 AGGGTGATATTGCAACTGAAGC 58.980 45.455 0.00 0.00 0.00 3.86
4338 4818 6.471519 GTGATATTGCAACTGAAGCTTGAATC 59.528 38.462 2.10 0.00 0.00 2.52
4356 4836 5.359756 TGAATCTGTTGAATGTATCCTCCG 58.640 41.667 0.00 0.00 0.00 4.63
4364 4844 3.258372 TGAATGTATCCTCCGAGGCATAC 59.742 47.826 19.85 19.85 34.61 2.39
4365 4845 1.244816 TGTATCCTCCGAGGCATACG 58.755 55.000 20.55 0.00 34.22 3.06
4369 4849 3.616721 CTCCGAGGCATACGGGGG 61.617 72.222 15.25 7.32 46.21 5.40
4372 4852 4.609018 CGAGGCATACGGGGGCAG 62.609 72.222 0.00 0.00 0.00 4.85
4373 4853 3.480133 GAGGCATACGGGGGCAGT 61.480 66.667 0.00 0.00 0.00 4.40
4374 4854 3.462199 GAGGCATACGGGGGCAGTC 62.462 68.421 0.00 0.00 0.00 3.51
4375 4855 4.564110 GGCATACGGGGGCAGTCC 62.564 72.222 0.00 0.00 0.00 3.85
4376 4856 3.480133 GCATACGGGGGCAGTCCT 61.480 66.667 0.00 0.00 35.33 3.85
4377 4857 3.043999 GCATACGGGGGCAGTCCTT 62.044 63.158 0.00 0.00 35.33 3.36
4378 4858 1.607612 CATACGGGGGCAGTCCTTT 59.392 57.895 0.00 0.00 35.33 3.11
4379 4859 0.034477 CATACGGGGGCAGTCCTTTT 60.034 55.000 0.00 0.00 35.33 2.27
4380 4860 1.210967 CATACGGGGGCAGTCCTTTTA 59.789 52.381 0.00 0.00 35.33 1.52
4381 4861 1.587066 TACGGGGGCAGTCCTTTTAT 58.413 50.000 0.00 0.00 35.33 1.40
4382 4862 0.255033 ACGGGGGCAGTCCTTTTATC 59.745 55.000 0.00 0.00 35.33 1.75
4383 4863 0.254747 CGGGGGCAGTCCTTTTATCA 59.745 55.000 0.00 0.00 35.33 2.15
4384 4864 1.340600 CGGGGGCAGTCCTTTTATCAA 60.341 52.381 0.00 0.00 35.33 2.57
4385 4865 2.815158 GGGGGCAGTCCTTTTATCAAA 58.185 47.619 0.00 0.00 35.33 2.69
4386 4866 2.496070 GGGGGCAGTCCTTTTATCAAAC 59.504 50.000 0.00 0.00 35.33 2.93
4387 4867 2.163613 GGGGCAGTCCTTTTATCAAACG 59.836 50.000 0.00 0.00 35.33 3.60
4408 4891 0.468771 GCTCCTAACCCTACCCGCTA 60.469 60.000 0.00 0.00 0.00 4.26
4415 4898 3.454573 CCTACCCGCTACCGTGCA 61.455 66.667 0.00 0.00 0.00 4.57
4478 4962 1.630126 ATTCACTCCAGCGCATCCCT 61.630 55.000 11.47 0.00 0.00 4.20
4511 4998 2.264480 CGTTGGGGATGTCGCAGA 59.736 61.111 0.00 0.00 39.53 4.26
4606 5093 1.373497 GATGGCCGGATCTACAGCG 60.373 63.158 5.05 0.00 0.00 5.18
4609 5096 2.027751 GCCGGATCTACAGCGGAC 59.972 66.667 5.05 0.10 0.00 4.79
4692 5197 1.997311 TCTGGGTCCAGATGGCCTG 60.997 63.158 15.14 0.00 46.80 4.85
4834 5339 1.301401 CTTCGCCGGAGTTGGTCAA 60.301 57.895 5.05 0.00 0.00 3.18
4849 5356 1.770110 TCAACCTGAGGCTGGGTGT 60.770 57.895 8.61 0.00 40.38 4.16
4890 5397 0.179124 CTAGTCCTGGCTGCGAGTTC 60.179 60.000 10.78 3.51 0.00 3.01
5040 5580 0.827507 TCCAGATCGGATGATGGCGA 60.828 55.000 12.08 0.00 39.64 5.54
5087 5631 1.855213 GCATCGTTTGTGGAGCAGCA 61.855 55.000 0.00 0.00 0.00 4.41
5091 5635 1.159713 CGTTTGTGGAGCAGCACTGA 61.160 55.000 0.81 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 96 5.961272 TGAACTCATGCACGAAGATTAGTA 58.039 37.500 0.00 0.00 0.00 1.82
129 132 4.508662 CTTCAAACCAGGGAGAGATACAC 58.491 47.826 0.00 0.00 0.00 2.90
294 397 1.899142 CGGTCCCCAAATTGTTTCCAT 59.101 47.619 0.00 0.00 0.00 3.41
297 400 1.623163 TCCGGTCCCCAAATTGTTTC 58.377 50.000 0.00 0.00 0.00 2.78
340 443 9.909644 GTTCTATTGAAGAAGAGTTAGTGTACA 57.090 33.333 0.00 0.00 44.94 2.90
364 467 7.981225 ACAACAATTGAAGCAAATTACTCTGTT 59.019 29.630 13.59 0.00 0.00 3.16
437 599 3.878160 TTTTTGCGAGGAAACAAACCT 57.122 38.095 0.00 0.00 40.80 3.50
500 662 0.459078 TCAGCAGGCTTCTCATCTCG 59.541 55.000 0.00 0.00 0.00 4.04
700 895 2.787625 GGCCCCTAATAAACCCCTAGTT 59.212 50.000 0.00 0.00 41.81 2.24
742 937 1.001633 GTTCCTAAGCAAGACCCACGA 59.998 52.381 0.00 0.00 0.00 4.35
744 939 2.561478 TGTTCCTAAGCAAGACCCAC 57.439 50.000 0.00 0.00 0.00 4.61
747 942 3.751518 TCCTTTGTTCCTAAGCAAGACC 58.248 45.455 0.00 0.00 0.00 3.85
871 1066 1.270358 GCTCCAAGACTTTGAGACGGT 60.270 52.381 18.09 0.00 36.36 4.83
874 1069 2.550830 TGGCTCCAAGACTTTGAGAC 57.449 50.000 18.09 16.09 36.36 3.36
983 1178 1.079127 ATTTCTGGTCGGTCGCCTG 60.079 57.895 5.70 5.38 0.00 4.85
984 1179 1.079127 CATTTCTGGTCGGTCGCCT 60.079 57.895 5.70 0.00 0.00 5.52
985 1180 1.359459 GACATTTCTGGTCGGTCGCC 61.359 60.000 0.00 0.00 0.00 5.54
986 1181 2.079049 GACATTTCTGGTCGGTCGC 58.921 57.895 0.00 0.00 0.00 5.19
1056 1251 2.254350 CCGAACAGCGAGTCGTGA 59.746 61.111 15.08 0.00 44.57 4.35
1163 1358 4.811557 GTCAGTTTAACTTGCTCTGTCTGT 59.188 41.667 0.00 0.00 0.00 3.41
1167 1362 4.811557 GTCAGTCAGTTTAACTTGCTCTGT 59.188 41.667 0.00 0.00 0.00 3.41
1168 1363 5.050499 CAGTCAGTCAGTTTAACTTGCTCTG 60.050 44.000 0.00 2.64 0.00 3.35
1170 1365 5.050490 TCAGTCAGTCAGTTTAACTTGCTC 58.950 41.667 0.00 0.00 0.00 4.26
1171 1366 4.811557 GTCAGTCAGTCAGTTTAACTTGCT 59.188 41.667 0.00 0.00 0.00 3.91
1172 1367 4.811557 AGTCAGTCAGTCAGTTTAACTTGC 59.188 41.667 0.00 0.00 0.00 4.01
1174 1369 5.364157 AGGAGTCAGTCAGTCAGTTTAACTT 59.636 40.000 0.00 0.00 0.00 2.66
1175 1370 4.896482 AGGAGTCAGTCAGTCAGTTTAACT 59.104 41.667 0.00 0.00 0.00 2.24
1176 1371 4.985409 CAGGAGTCAGTCAGTCAGTTTAAC 59.015 45.833 0.00 0.00 0.00 2.01
1178 1373 3.574396 CCAGGAGTCAGTCAGTCAGTTTA 59.426 47.826 0.00 0.00 0.00 2.01
1192 1410 0.543277 TGCATCCATCACCAGGAGTC 59.457 55.000 0.00 0.00 38.83 3.36
1193 1411 0.545171 CTGCATCCATCACCAGGAGT 59.455 55.000 0.00 0.00 38.83 3.85
1494 1723 9.635520 TTCTTGTTACTTCAATACTAGTGTAGC 57.364 33.333 5.39 0.91 31.51 3.58
1504 1733 7.990886 ACACCAGAGTTTCTTGTTACTTCAATA 59.009 33.333 0.00 0.00 0.00 1.90
1651 1911 2.475371 ATTGCGCCCTCTTGAGCTGT 62.475 55.000 4.18 0.00 0.00 4.40
1809 2069 9.694137 AGTACTCTTCTTAATAGACAACACAAC 57.306 33.333 0.00 0.00 0.00 3.32
1841 2166 4.992319 CAGCACATCCATGAACAAAACATT 59.008 37.500 0.00 0.00 0.00 2.71
1984 2333 5.689383 TGCACAAAGAAGGAACATTAGAC 57.311 39.130 0.00 0.00 0.00 2.59
1990 2339 1.405105 GTGCTGCACAAAGAAGGAACA 59.595 47.619 26.70 0.00 34.08 3.18
1991 2340 1.405105 TGTGCTGCACAAAGAAGGAAC 59.595 47.619 31.31 2.22 41.69 3.62
1993 2342 3.493028 TGTGCTGCACAAAGAAGGA 57.507 47.368 31.31 7.04 41.69 3.36
2129 2489 1.157870 GGTTGTACATCCCGATGCCG 61.158 60.000 11.37 0.00 42.39 5.69
2414 2797 2.504175 GGTTACCTGAACAGCCCTGATA 59.496 50.000 1.69 0.00 40.09 2.15
2476 2862 1.970640 GGTCCTTCTGTTGGGCAAAAT 59.029 47.619 0.00 0.00 0.00 1.82
2481 2867 0.329596 ATGAGGTCCTTCTGTTGGGC 59.670 55.000 0.00 0.00 0.00 5.36
2505 2904 6.142817 GCAAGTGTAAGTACAAGAACCATTG 58.857 40.000 0.00 0.00 38.04 2.82
2686 3090 3.423539 TGCATGCATATTCTACTCCCC 57.576 47.619 18.46 0.00 0.00 4.81
3044 3462 5.954296 AACCTCACTGAATCATCACAAAG 57.046 39.130 0.00 0.00 0.00 2.77
3050 3468 6.596888 TCAGATGAAAACCTCACTGAATCATC 59.403 38.462 0.00 0.00 38.32 2.92
3051 3469 6.373774 GTCAGATGAAAACCTCACTGAATCAT 59.626 38.462 0.00 0.00 40.61 2.45
3054 3475 4.692625 CGTCAGATGAAAACCTCACTGAAT 59.307 41.667 0.00 0.00 40.61 2.57
3059 3480 2.413453 GAGCGTCAGATGAAAACCTCAC 59.587 50.000 0.00 0.00 36.69 3.51
3078 3503 2.238144 ACCAACATCAGATGGGTCAGAG 59.762 50.000 15.13 0.00 41.68 3.35
3187 3617 4.685165 CGTAGAAGAGCATGATGAAGATGG 59.315 45.833 0.00 0.00 0.00 3.51
3245 3675 5.410924 TCGATGAACTTTGACAGTATGGAG 58.589 41.667 0.00 0.00 43.62 3.86
3378 3808 0.248825 AGCATCGTCATCTCGCTGAC 60.249 55.000 0.00 3.40 41.73 3.51
3483 3913 1.967066 CGGTATCTTCTGGATCAGCCT 59.033 52.381 0.00 0.00 37.63 4.58
3738 4168 1.080705 CGTCCGAAACCTCTTCGCT 60.081 57.895 1.43 0.00 40.30 4.93
3739 4169 2.727684 GCGTCCGAAACCTCTTCGC 61.728 63.158 1.43 0.00 40.30 4.70
3779 4239 4.357947 TCCTCGCTGTGCACCGTC 62.358 66.667 15.69 3.58 0.00 4.79
3911 4380 1.352352 CCCATCAGATACACCATCCCC 59.648 57.143 0.00 0.00 33.75 4.81
4079 4548 4.861462 TCGGTCGATCACTATATCTCGTAC 59.139 45.833 0.00 0.00 33.10 3.67
4099 4568 0.801067 GGGTGAACTCGTTCGATCGG 60.801 60.000 16.41 8.96 42.28 4.18
4107 4576 0.815734 CATACTCGGGGTGAACTCGT 59.184 55.000 0.00 0.00 0.00 4.18
4129 4598 1.302431 TGCACCAGAACCATCACCG 60.302 57.895 0.00 0.00 0.00 4.94
4155 4624 0.249280 CTTCCAAACCAACGGCCAAC 60.249 55.000 2.24 0.00 0.00 3.77
4156 4625 1.395826 CCTTCCAAACCAACGGCCAA 61.396 55.000 2.24 0.00 0.00 4.52
4157 4626 1.830408 CCTTCCAAACCAACGGCCA 60.830 57.895 2.24 0.00 0.00 5.36
4158 4627 2.570284 CCCTTCCAAACCAACGGCC 61.570 63.158 0.00 0.00 0.00 6.13
4159 4628 3.047735 CCCTTCCAAACCAACGGC 58.952 61.111 0.00 0.00 0.00 5.68
4160 4629 1.395826 TTGCCCTTCCAAACCAACGG 61.396 55.000 0.00 0.00 0.00 4.44
4195 4664 2.945008 TGCCTGCTTCCTTATTGAATCG 59.055 45.455 0.00 0.00 0.00 3.34
4225 4703 5.305386 CCAAAAGAAAGAAAACTCCTCCCAT 59.695 40.000 0.00 0.00 0.00 4.00
4226 4704 4.649218 CCAAAAGAAAGAAAACTCCTCCCA 59.351 41.667 0.00 0.00 0.00 4.37
4233 4712 5.994668 TGTTGCAACCAAAAGAAAGAAAACT 59.005 32.000 26.14 0.00 31.68 2.66
4234 4713 6.234723 TGTTGCAACCAAAAGAAAGAAAAC 57.765 33.333 26.14 0.00 31.68 2.43
4307 4787 5.300286 GCTTCAGTTGCAATATCACCCTTAT 59.700 40.000 0.59 0.00 0.00 1.73
4331 4811 6.018425 CGGAGGATACATTCAACAGATTCAAG 60.018 42.308 0.00 0.00 41.41 3.02
4338 4818 3.722147 CCTCGGAGGATACATTCAACAG 58.278 50.000 19.57 0.00 37.67 3.16
4356 4836 3.462199 GACTGCCCCCGTATGCCTC 62.462 68.421 0.00 0.00 0.00 4.70
4364 4844 0.254747 TGATAAAAGGACTGCCCCCG 59.745 55.000 0.00 0.00 34.66 5.73
4365 4845 2.496070 GTTTGATAAAAGGACTGCCCCC 59.504 50.000 0.00 0.00 34.66 5.40
4366 4846 2.163613 CGTTTGATAAAAGGACTGCCCC 59.836 50.000 0.00 0.00 34.66 5.80
4367 4847 2.415491 GCGTTTGATAAAAGGACTGCCC 60.415 50.000 0.00 0.00 33.31 5.36
4368 4848 2.727916 CGCGTTTGATAAAAGGACTGCC 60.728 50.000 0.00 0.00 0.00 4.85
4369 4849 2.505866 CGCGTTTGATAAAAGGACTGC 58.494 47.619 0.00 0.00 0.00 4.40
4370 4850 2.159627 AGCGCGTTTGATAAAAGGACTG 59.840 45.455 8.43 0.00 0.00 3.51
4371 4851 2.415512 GAGCGCGTTTGATAAAAGGACT 59.584 45.455 8.43 0.00 0.00 3.85
4372 4852 2.475685 GGAGCGCGTTTGATAAAAGGAC 60.476 50.000 8.43 0.00 0.00 3.85
4373 4853 1.735571 GGAGCGCGTTTGATAAAAGGA 59.264 47.619 8.43 0.00 0.00 3.36
4374 4854 1.737793 AGGAGCGCGTTTGATAAAAGG 59.262 47.619 8.43 0.00 0.00 3.11
4375 4855 4.331962 GTTAGGAGCGCGTTTGATAAAAG 58.668 43.478 8.43 0.00 0.00 2.27
4376 4856 3.125658 GGTTAGGAGCGCGTTTGATAAAA 59.874 43.478 8.43 0.00 0.00 1.52
4377 4857 2.674357 GGTTAGGAGCGCGTTTGATAAA 59.326 45.455 8.43 0.00 0.00 1.40
4378 4858 2.273557 GGTTAGGAGCGCGTTTGATAA 58.726 47.619 8.43 0.00 0.00 1.75
4379 4859 1.472026 GGGTTAGGAGCGCGTTTGATA 60.472 52.381 8.43 0.00 0.00 2.15
4380 4860 0.743345 GGGTTAGGAGCGCGTTTGAT 60.743 55.000 8.43 0.00 0.00 2.57
4381 4861 1.375013 GGGTTAGGAGCGCGTTTGA 60.375 57.895 8.43 0.00 0.00 2.69
4382 4862 0.108520 TAGGGTTAGGAGCGCGTTTG 60.109 55.000 8.43 0.00 0.00 2.93
4383 4863 0.108472 GTAGGGTTAGGAGCGCGTTT 60.108 55.000 8.43 0.00 0.00 3.60
4384 4864 1.514553 GTAGGGTTAGGAGCGCGTT 59.485 57.895 8.43 0.00 0.00 4.84
4385 4865 2.421399 GGTAGGGTTAGGAGCGCGT 61.421 63.158 8.43 0.00 0.00 6.01
4386 4866 2.416260 GGTAGGGTTAGGAGCGCG 59.584 66.667 0.00 0.00 0.00 6.86
4387 4867 2.820261 GGGTAGGGTTAGGAGCGC 59.180 66.667 0.00 0.00 0.00 5.92
4444 4928 3.329542 GAATGGGAGACGGCTGGCA 62.330 63.158 0.00 0.00 0.00 4.92
4502 4989 1.597742 ACAAGCTTTGTCTGCGACAT 58.402 45.000 11.23 0.00 42.40 3.06
4503 4990 2.232756 TACAAGCTTTGTCTGCGACA 57.767 45.000 0.00 7.20 44.12 4.35
4511 4998 3.403239 GCTGCGGCATACAAGCTTTGT 62.403 52.381 14.08 1.20 41.89 2.83
4542 5029 1.301479 GTTGGCCGAGGAGAAACGT 60.301 57.895 0.00 0.00 0.00 3.99
4827 5332 1.455849 CCAGCCTCAGGTTGACCAA 59.544 57.895 9.60 0.00 35.94 3.67
4834 5339 2.883828 CGAACACCCAGCCTCAGGT 61.884 63.158 0.00 0.00 36.58 4.00
4890 5397 2.125912 CGGCAACTCTGTCTCCCG 60.126 66.667 0.00 0.00 0.00 5.14
4957 5488 3.679502 TCGACAGAAGTTACACGACGATA 59.320 43.478 0.00 0.00 0.00 2.92
5032 5564 0.536724 ACACTGCAGTATCGCCATCA 59.463 50.000 21.20 0.00 0.00 3.07
5040 5580 4.011023 AGAGAGTAACGACACTGCAGTAT 58.989 43.478 21.20 8.75 0.00 2.12


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

AutoCloner maintained by Alex Coulton.