Multiple sequence alignment - TraesCS3D01G350200

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 TraesCS3D01G350200 chr3D 100.000 2621 0 0 1 2621 461427797 461425177 0.000000e+00 4841.0
1 TraesCS3D01G350200 chr3D 93.387 1119 50 10 1514 2621 461371557 461370452 0.000000e+00 1635.0
2 TraesCS3D01G350200 chr3D 83.243 925 93 44 530 1427 461373514 461372625 0.000000e+00 793.0
3 TraesCS3D01G350200 chr3D 83.333 924 87 42 530 1427 461314173 461313291 0.000000e+00 791.0
4 TraesCS3D01G350200 chr3D 86.180 521 46 17 920 1417 461589620 461589103 8.250000e-150 540.0
5 TraesCS3D01G350200 chr3D 95.960 99 3 1 1423 1521 461372580 461372483 2.700000e-35 159.0
6 TraesCS3D01G350200 chr3D 97.297 37 1 0 718 754 461589850 461589814 2.180000e-06 63.9
7 TraesCS3D01G350200 chr3A 90.835 1222 62 13 1423 2621 603846852 603845658 0.000000e+00 1591.0
8 TraesCS3D01G350200 chr3A 82.513 995 102 50 471 1427 603814620 603813660 0.000000e+00 808.0
9 TraesCS3D01G350200 chr3A 88.226 603 26 18 850 1427 603847479 603846897 0.000000e+00 678.0
10 TraesCS3D01G350200 chr3A 85.000 520 51 11 914 1417 603895942 603895434 1.080000e-138 503.0
11 TraesCS3D01G350200 chr3A 87.812 320 21 11 194 510 603848060 603847756 2.480000e-95 359.0
12 TraesCS3D01G350200 chr3A 88.496 226 8 8 539 763 603847758 603847550 9.310000e-65 257.0
13 TraesCS3D01G350200 chr3A 84.871 271 24 10 1426 1690 603895368 603895109 9.310000e-65 257.0
14 TraesCS3D01G350200 chr3A 79.570 186 28 1 1729 1904 136035590 136035405 9.850000e-25 124.0
15 TraesCS3D01G350200 chr3A 97.500 40 1 0 718 757 603896163 603896124 4.680000e-08 69.4
16 TraesCS3D01G350200 chr3A 88.235 51 5 1 104 154 474961767 474961718 2.820000e-05 60.2
17 TraesCS3D01G350200 chr3B 82.799 1029 121 24 1559 2564 612293999 612293004 0.000000e+00 869.0
18 TraesCS3D01G350200 chr3B 82.684 924 82 47 530 1413 612104781 612103896 0.000000e+00 749.0
19 TraesCS3D01G350200 chr3B 89.185 601 32 17 843 1427 612296194 612295611 0.000000e+00 719.0
20 TraesCS3D01G350200 chr3B 85.255 529 49 12 914 1417 612360406 612359882 3.870000e-143 518.0
21 TraesCS3D01G350200 chr3B 85.234 535 32 18 148 668 612297291 612296790 8.370000e-140 507.0
22 TraesCS3D01G350200 chr3B 81.053 285 43 5 1429 1707 612359813 612359534 1.580000e-52 217.0
23 TraesCS3D01G350200 chr3B 90.435 115 3 3 1423 1529 612295566 612295452 7.560000e-31 145.0
24 TraesCS3D01G350200 chr3B 97.500 40 1 0 718 757 612360623 612360584 4.680000e-08 69.4
25 TraesCS3D01G350200 chr3B 87.273 55 7 0 104 158 809833080 809833134 2.180000e-06 63.9
26 TraesCS3D01G350200 chr2A 79.503 161 22 2 1720 1869 16018100 16018260 1.280000e-18 104.0
27 TraesCS3D01G350200 chr2B 81.679 131 14 5 1715 1835 756998972 756999102 1.660000e-17 100.0
28 TraesCS3D01G350200 chr2B 90.000 50 4 1 108 156 779647318 779647367 2.180000e-06 63.9
29 TraesCS3D01G350200 chr1B 84.810 79 12 0 1784 1862 99078869 99078791 2.160000e-11 80.5
30 TraesCS3D01G350200 chr7A 90.196 51 5 0 104 154 435725660 435725710 1.680000e-07 67.6
31 TraesCS3D01G350200 chr6B 86.154 65 6 2 93 154 504603096 504603160 1.680000e-07 67.6
32 TraesCS3D01G350200 chr6B 90.000 50 4 1 108 156 9570467 9570516 2.180000e-06 63.9
33 TraesCS3D01G350200 chr4D 91.304 46 4 0 104 149 11573331 11573376 2.180000e-06 63.9
34 TraesCS3D01G350200 chr6A 84.615 65 7 2 93 154 456599256 456599192 7.830000e-06 62.1
35 TraesCS3D01G350200 chr5B 89.583 48 5 0 104 151 107735584 107735537 7.830000e-06 62.1


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 TraesCS3D01G350200 chr3D 461425177 461427797 2620 True 4841.000000 4841 100.000000 1 2621 1 chr3D.!!$R2 2620
1 TraesCS3D01G350200 chr3D 461370452 461373514 3062 True 862.333333 1635 90.863333 530 2621 3 chr3D.!!$R3 2091
2 TraesCS3D01G350200 chr3D 461313291 461314173 882 True 791.000000 791 83.333000 530 1427 1 chr3D.!!$R1 897
3 TraesCS3D01G350200 chr3D 461589103 461589850 747 True 301.950000 540 91.738500 718 1417 2 chr3D.!!$R4 699
4 TraesCS3D01G350200 chr3A 603813660 603814620 960 True 808.000000 808 82.513000 471 1427 1 chr3A.!!$R3 956
5 TraesCS3D01G350200 chr3A 603845658 603848060 2402 True 721.250000 1591 88.842250 194 2621 4 chr3A.!!$R4 2427
6 TraesCS3D01G350200 chr3A 603895109 603896163 1054 True 276.466667 503 89.123667 718 1690 3 chr3A.!!$R5 972
7 TraesCS3D01G350200 chr3B 612103896 612104781 885 True 749.000000 749 82.684000 530 1413 1 chr3B.!!$R1 883
8 TraesCS3D01G350200 chr3B 612293004 612297291 4287 True 560.000000 869 86.913250 148 2564 4 chr3B.!!$R2 2416
9 TraesCS3D01G350200 chr3B 612359534 612360623 1089 True 268.133333 518 87.936000 718 1707 3 chr3B.!!$R3 989

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
213 214 0.251073 AATTCCACGGAGGTTACGGG 59.749 55.0 0.0 0.0 39.02 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 4988 1.055849 TCAGCCATATACGGTGCCAT 58.944 50.0 0.0 0.0 0.0 4.4 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.261180 TCTAAACAATCTTATAATGCTCCTTCG 57.739 33.333 0.00 0.00 0.00 3.79
43 44 9.261180 CTAAACAATCTTATAATGCTCCTTCGA 57.739 33.333 0.00 0.00 0.00 3.71
44 45 7.721286 AACAATCTTATAATGCTCCTTCGAG 57.279 36.000 0.00 0.00 39.33 4.04
45 46 6.821388 ACAATCTTATAATGCTCCTTCGAGT 58.179 36.000 0.00 0.00 38.49 4.18
46 47 7.275920 ACAATCTTATAATGCTCCTTCGAGTT 58.724 34.615 0.00 0.00 38.49 3.01
47 48 7.770897 ACAATCTTATAATGCTCCTTCGAGTTT 59.229 33.333 0.00 0.00 38.49 2.66
48 49 7.721286 ATCTTATAATGCTCCTTCGAGTTTG 57.279 36.000 0.00 0.00 38.49 2.93
49 50 5.523916 TCTTATAATGCTCCTTCGAGTTTGC 59.476 40.000 0.00 0.00 38.49 3.68
50 51 2.191128 AATGCTCCTTCGAGTTTGCT 57.809 45.000 0.00 0.00 38.49 3.91
51 52 3.334583 AATGCTCCTTCGAGTTTGCTA 57.665 42.857 0.00 0.00 38.49 3.49
52 53 3.550437 ATGCTCCTTCGAGTTTGCTAT 57.450 42.857 0.00 0.00 38.49 2.97
53 54 2.621338 TGCTCCTTCGAGTTTGCTATG 58.379 47.619 0.00 0.00 38.49 2.23
54 55 2.028112 TGCTCCTTCGAGTTTGCTATGT 60.028 45.455 0.00 0.00 38.49 2.29
55 56 3.003480 GCTCCTTCGAGTTTGCTATGTT 58.997 45.455 0.00 0.00 38.49 2.71
56 57 3.062774 GCTCCTTCGAGTTTGCTATGTTC 59.937 47.826 0.00 0.00 38.49 3.18
57 58 3.250744 TCCTTCGAGTTTGCTATGTTCG 58.749 45.455 0.00 0.00 0.00 3.95
58 59 2.993899 CCTTCGAGTTTGCTATGTTCGT 59.006 45.455 0.00 0.00 33.35 3.85
59 60 3.181530 CCTTCGAGTTTGCTATGTTCGTG 60.182 47.826 0.00 0.00 33.35 4.35
60 61 3.021269 TCGAGTTTGCTATGTTCGTGT 57.979 42.857 0.00 0.00 33.35 4.49
61 62 2.729360 TCGAGTTTGCTATGTTCGTGTG 59.271 45.455 0.00 0.00 33.35 3.82
62 63 2.475111 CGAGTTTGCTATGTTCGTGTGT 59.525 45.455 0.00 0.00 0.00 3.72
63 64 3.671459 CGAGTTTGCTATGTTCGTGTGTA 59.329 43.478 0.00 0.00 0.00 2.90
64 65 4.432503 CGAGTTTGCTATGTTCGTGTGTAC 60.433 45.833 0.00 0.00 0.00 2.90
65 66 4.628074 AGTTTGCTATGTTCGTGTGTACT 58.372 39.130 0.00 0.00 0.00 2.73
66 67 5.054477 AGTTTGCTATGTTCGTGTGTACTT 58.946 37.500 0.00 0.00 0.00 2.24
67 68 5.526111 AGTTTGCTATGTTCGTGTGTACTTT 59.474 36.000 0.00 0.00 0.00 2.66
68 69 6.702723 AGTTTGCTATGTTCGTGTGTACTTTA 59.297 34.615 0.00 0.00 0.00 1.85
69 70 7.225145 AGTTTGCTATGTTCGTGTGTACTTTAA 59.775 33.333 0.00 0.00 0.00 1.52
70 71 7.661127 TTGCTATGTTCGTGTGTACTTTAAT 57.339 32.000 0.00 0.00 0.00 1.40
71 72 7.056002 TGCTATGTTCGTGTGTACTTTAATG 57.944 36.000 0.00 0.00 0.00 1.90
72 73 6.869388 TGCTATGTTCGTGTGTACTTTAATGA 59.131 34.615 0.00 0.00 0.00 2.57
73 74 7.547722 TGCTATGTTCGTGTGTACTTTAATGAT 59.452 33.333 0.00 0.00 0.00 2.45
74 75 8.056571 GCTATGTTCGTGTGTACTTTAATGATC 58.943 37.037 0.00 0.00 0.00 2.92
75 76 9.302345 CTATGTTCGTGTGTACTTTAATGATCT 57.698 33.333 0.00 0.00 0.00 2.75
77 78 9.647797 ATGTTCGTGTGTACTTTAATGATCTAA 57.352 29.630 0.00 0.00 0.00 2.10
78 79 9.478768 TGTTCGTGTGTACTTTAATGATCTAAA 57.521 29.630 0.00 0.00 0.00 1.85
79 80 9.737025 GTTCGTGTGTACTTTAATGATCTAAAC 57.263 33.333 0.00 0.00 0.00 2.01
80 81 9.478768 TTCGTGTGTACTTTAATGATCTAAACA 57.521 29.630 0.00 0.00 0.00 2.83
81 82 9.478768 TCGTGTGTACTTTAATGATCTAAACAA 57.521 29.630 0.00 0.00 0.00 2.83
98 99 9.614792 ATCTAAACAATCTTATGTTGTACTCCC 57.385 33.333 0.00 0.00 42.49 4.30
99 100 8.822805 TCTAAACAATCTTATGTTGTACTCCCT 58.177 33.333 0.00 0.00 42.49 4.20
100 101 7.923414 AAACAATCTTATGTTGTACTCCCTC 57.077 36.000 0.00 0.00 42.49 4.30
101 102 5.990668 ACAATCTTATGTTGTACTCCCTCC 58.009 41.667 0.00 0.00 37.98 4.30
102 103 4.939052 ATCTTATGTTGTACTCCCTCCG 57.061 45.455 0.00 0.00 0.00 4.63
103 104 3.705051 TCTTATGTTGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
104 105 4.858850 TCTTATGTTGTACTCCCTCCGTA 58.141 43.478 0.00 0.00 0.00 4.02
105 106 5.263599 TCTTATGTTGTACTCCCTCCGTAA 58.736 41.667 0.00 0.00 0.00 3.18
106 107 5.359009 TCTTATGTTGTACTCCCTCCGTAAG 59.641 44.000 0.00 0.00 0.00 2.34
122 123 3.306818 CGTAAGGTAGGAATCTAAGCGC 58.693 50.000 0.00 0.00 0.00 5.92
123 124 3.004524 CGTAAGGTAGGAATCTAAGCGCT 59.995 47.826 2.64 2.64 0.00 5.92
124 125 3.737032 AAGGTAGGAATCTAAGCGCTC 57.263 47.619 12.06 0.00 0.00 5.03
125 126 1.964933 AGGTAGGAATCTAAGCGCTCC 59.035 52.381 12.06 6.71 0.00 4.70
126 127 1.964933 GGTAGGAATCTAAGCGCTCCT 59.035 52.381 12.06 15.02 41.29 3.69
127 128 3.155501 GGTAGGAATCTAAGCGCTCCTA 58.844 50.000 12.06 13.85 39.13 2.94
128 129 3.764972 GGTAGGAATCTAAGCGCTCCTAT 59.235 47.826 19.98 8.06 41.45 2.57
129 130 4.948621 GGTAGGAATCTAAGCGCTCCTATA 59.051 45.833 19.98 5.38 41.45 1.31
130 131 5.595133 GGTAGGAATCTAAGCGCTCCTATAT 59.405 44.000 19.98 3.35 41.45 0.86
131 132 6.097129 GGTAGGAATCTAAGCGCTCCTATATT 59.903 42.308 19.98 10.69 41.45 1.28
132 133 6.613153 AGGAATCTAAGCGCTCCTATATTT 57.387 37.500 12.06 0.00 36.51 1.40
133 134 6.635755 AGGAATCTAAGCGCTCCTATATTTC 58.364 40.000 12.06 3.91 36.51 2.17
134 135 6.439058 AGGAATCTAAGCGCTCCTATATTTCT 59.561 38.462 12.06 6.30 36.51 2.52
135 136 7.038658 AGGAATCTAAGCGCTCCTATATTTCTT 60.039 37.037 12.06 1.92 36.51 2.52
136 137 7.604545 GGAATCTAAGCGCTCCTATATTTCTTT 59.395 37.037 12.06 0.00 0.00 2.52
137 138 9.640963 GAATCTAAGCGCTCCTATATTTCTTTA 57.359 33.333 12.06 0.00 0.00 1.85
138 139 8.989653 ATCTAAGCGCTCCTATATTTCTTTAC 57.010 34.615 12.06 0.00 0.00 2.01
139 140 7.948357 TCTAAGCGCTCCTATATTTCTTTACA 58.052 34.615 12.06 0.00 0.00 2.41
140 141 8.082852 TCTAAGCGCTCCTATATTTCTTTACAG 58.917 37.037 12.06 0.00 0.00 2.74
141 142 6.406692 AGCGCTCCTATATTTCTTTACAGA 57.593 37.500 2.64 0.00 0.00 3.41
142 143 6.451393 AGCGCTCCTATATTTCTTTACAGAG 58.549 40.000 2.64 0.00 0.00 3.35
143 144 5.635700 GCGCTCCTATATTTCTTTACAGAGG 59.364 44.000 0.00 0.00 0.00 3.69
144 145 6.159988 CGCTCCTATATTTCTTTACAGAGGG 58.840 44.000 0.00 0.00 0.00 4.30
145 146 6.015350 CGCTCCTATATTTCTTTACAGAGGGA 60.015 42.308 0.00 0.00 34.72 4.20
146 147 7.382898 GCTCCTATATTTCTTTACAGAGGGAG 58.617 42.308 0.00 0.00 38.61 4.30
163 164 7.458170 ACAGAGGGAGTATTTCTTTAAAGAGGA 59.542 37.037 17.05 11.05 36.22 3.71
176 177 7.542025 TCTTTAAAGAGGAAGTACGTGGTATC 58.458 38.462 13.99 0.00 0.00 2.24
187 188 8.386606 GGAAGTACGTGGTATCTATAATACGAG 58.613 40.741 0.00 0.00 35.69 4.18
213 214 0.251073 AATTCCACGGAGGTTACGGG 59.749 55.000 0.00 0.00 39.02 5.28
224 229 0.612453 GGTTACGGGCCCCATTTTGA 60.612 55.000 18.66 0.00 0.00 2.69
353 359 0.317269 CGCAGCAACAAGACAAGGTG 60.317 55.000 0.00 0.00 0.00 4.00
428 440 1.138047 ATCGTCGCGCGGAAGTAAAG 61.138 55.000 31.69 11.88 41.72 1.85
431 443 2.095843 CGCGCGGAAGTAAAGCAC 59.904 61.111 24.84 0.00 0.00 4.40
432 444 2.095843 GCGCGGAAGTAAAGCACG 59.904 61.111 8.83 0.00 0.00 5.34
433 445 2.095843 CGCGGAAGTAAAGCACGC 59.904 61.111 0.00 0.00 46.04 5.34
436 448 1.129809 CGGAAGTAAAGCACGCACG 59.870 57.895 0.00 0.00 0.00 5.34
437 449 1.495951 GGAAGTAAAGCACGCACGG 59.504 57.895 0.00 0.00 0.00 4.94
438 450 1.154469 GAAGTAAAGCACGCACGGC 60.154 57.895 0.00 0.00 0.00 5.68
439 451 1.837538 GAAGTAAAGCACGCACGGCA 61.838 55.000 6.35 0.00 0.00 5.69
440 452 2.113131 AAGTAAAGCACGCACGGCAC 62.113 55.000 6.35 0.00 0.00 5.01
476 496 2.758327 ACGCTAGGCCACCATCGA 60.758 61.111 5.01 0.00 0.00 3.59
488 508 1.267574 ACCATCGAGCAGGTCCACAT 61.268 55.000 1.48 0.00 30.79 3.21
496 516 0.957395 GCAGGTCCACATGTGTCTGG 60.957 60.000 27.24 15.28 0.00 3.86
522 550 3.488090 GTTCTGTAGCCGGTGCGC 61.488 66.667 1.90 0.00 44.33 6.09
603 647 5.851808 AGATACTGCTATCTAGACTCCCA 57.148 43.478 0.00 0.00 37.87 4.37
604 648 6.401537 AGATACTGCTATCTAGACTCCCAT 57.598 41.667 0.00 0.00 37.87 4.00
605 649 6.186957 AGATACTGCTATCTAGACTCCCATG 58.813 44.000 0.00 0.00 37.87 3.66
606 650 4.461450 ACTGCTATCTAGACTCCCATGA 57.539 45.455 0.00 0.00 0.00 3.07
607 651 5.009436 ACTGCTATCTAGACTCCCATGAT 57.991 43.478 0.00 0.00 0.00 2.45
608 652 4.771577 ACTGCTATCTAGACTCCCATGATG 59.228 45.833 0.00 0.00 0.00 3.07
609 653 3.513119 TGCTATCTAGACTCCCATGATGC 59.487 47.826 0.00 0.00 0.00 3.91
646 691 1.325355 CAGATCCGTACGGGTGGTAT 58.675 55.000 32.80 19.11 37.00 2.73
647 692 2.507484 CAGATCCGTACGGGTGGTATA 58.493 52.381 32.80 13.28 37.00 1.47
648 693 2.227388 CAGATCCGTACGGGTGGTATAC 59.773 54.545 32.80 13.82 37.00 1.47
649 694 2.107204 AGATCCGTACGGGTGGTATACT 59.893 50.000 32.80 15.97 37.00 2.12
664 713 7.228308 GGGTGGTATACTTACTGTAGTAGACTG 59.772 44.444 2.25 0.00 40.77 3.51
668 1168 9.487790 GGTATACTTACTGTAGTAGACTGGTAG 57.512 40.741 2.25 0.69 40.77 3.18
675 1175 6.568869 ACTGTAGTAGACTGGTAGTACTACG 58.431 44.000 23.40 14.75 40.54 3.51
690 1191 8.977505 GGTAGTACTACGAGTAACTAATCTCTG 58.022 40.741 23.40 0.00 36.94 3.35
691 1192 8.977505 GTAGTACTACGAGTAACTAATCTCTGG 58.022 40.741 16.96 0.00 31.62 3.86
782 1319 1.067776 ACACTTGCGAGCCACTAGTAC 60.068 52.381 0.00 0.00 0.00 2.73
817 1360 2.474032 GCGCTCATTTGTTTCCTACGTC 60.474 50.000 0.00 0.00 0.00 4.34
823 1366 2.536761 TTGTTTCCTACGTCCACCAG 57.463 50.000 0.00 0.00 0.00 4.00
848 1400 0.378257 AACTCAAGTTGCGCACACTG 59.622 50.000 11.12 7.61 36.80 3.66
864 1421 3.195610 CACACTGTATAAGAGCCACCAGA 59.804 47.826 0.00 0.00 0.00 3.86
907 1469 0.723414 CATTACACAGTGCAGCCGAG 59.277 55.000 0.00 0.00 0.00 4.63
912 1474 4.383861 CAGTGCAGCCGAGAGCCA 62.384 66.667 0.00 0.00 45.47 4.75
1618 4727 7.610580 TGTTTGGATAAGTTGGGAAAAAGAT 57.389 32.000 0.00 0.00 0.00 2.40
1622 4731 9.990360 TTTGGATAAGTTGGGAAAAAGATAAAC 57.010 29.630 0.00 0.00 0.00 2.01
1629 4738 9.981114 AAGTTGGGAAAAAGATAAACATACTTG 57.019 29.630 0.00 0.00 0.00 3.16
1630 4739 8.088365 AGTTGGGAAAAAGATAAACATACTTGC 58.912 33.333 0.00 0.00 0.00 4.01
1631 4740 7.531857 TGGGAAAAAGATAAACATACTTGCA 57.468 32.000 0.00 0.00 0.00 4.08
1632 4741 8.133024 TGGGAAAAAGATAAACATACTTGCAT 57.867 30.769 0.00 0.00 0.00 3.96
1633 4742 8.592809 TGGGAAAAAGATAAACATACTTGCATT 58.407 29.630 0.00 0.00 0.00 3.56
1634 4743 9.087424 GGGAAAAAGATAAACATACTTGCATTC 57.913 33.333 0.00 0.00 0.00 2.67
1635 4744 9.860898 GGAAAAAGATAAACATACTTGCATTCT 57.139 29.630 0.00 0.00 0.00 2.40
1717 4832 7.936584 TGTTGATCGATGGTTTAAGAAAAGTT 58.063 30.769 0.54 0.00 0.00 2.66
1718 4833 9.058174 TGTTGATCGATGGTTTAAGAAAAGTTA 57.942 29.630 0.54 0.00 0.00 2.24
1766 4894 4.935808 GTCACGGATGTTTGATTTAGTCCT 59.064 41.667 0.00 0.00 0.00 3.85
1850 4988 2.831685 AGACATAAAGTGTGCCGACA 57.168 45.000 0.00 0.00 42.36 4.35
1982 5130 1.555477 GTGGAAACGCAAACACCAAG 58.445 50.000 0.00 0.00 41.67 3.61
1999 5147 2.501223 AAGTTCATCGCGGGCTCGAA 62.501 55.000 12.03 0.00 42.15 3.71
2084 5232 2.099263 GACCTTGTGCTCGTGCTCTATA 59.901 50.000 11.19 0.00 40.48 1.31
2119 5270 0.179176 CAGTTCTCGACGAGGAGCAG 60.179 60.000 23.92 5.12 33.98 4.24
2214 5366 1.380650 GTTCCCTCTCCTCGGCTCT 60.381 63.158 0.00 0.00 0.00 4.09
2229 5381 0.382515 GCTCTGGAGACGACGCTAAT 59.617 55.000 1.35 0.00 0.00 1.73
2260 5412 4.129737 GCGACTGCGGAGGTGCTA 62.130 66.667 9.36 0.00 38.16 3.49
2269 5421 4.971125 GAGGTGCTATCGGCGGGC 62.971 72.222 7.21 10.21 45.43 6.13
2292 5444 3.072476 GAGCTTCACCTGGCTCCA 58.928 61.111 3.87 0.00 46.32 3.86
2308 5460 2.611518 CTCCAAAGAAGCGGAGTACTG 58.388 52.381 0.00 0.00 43.32 2.74
2309 5461 1.968493 TCCAAAGAAGCGGAGTACTGT 59.032 47.619 0.00 0.00 0.00 3.55
2433 5585 4.008933 GCTGGAGCCTCACACCGT 62.009 66.667 0.00 0.00 34.31 4.83
2452 5604 2.107178 GTAATACTTCGACGACGGCAG 58.893 52.381 7.55 6.65 40.21 4.85
2467 5619 0.388134 GGCAGCTGCAACATGTTCAG 60.388 55.000 37.63 22.94 44.36 3.02
2510 5662 3.480133 GGTGCTCGGGGTAGGCAT 61.480 66.667 0.00 0.00 38.27 4.40
2609 5761 4.146156 TGGTCGGGGGAGGCGATA 62.146 66.667 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.261180 CGAAGGAGCATTATAAGATTGTTTAGA 57.739 33.333 0.00 0.00 0.00 2.10
17 18 9.261180 TCGAAGGAGCATTATAAGATTGTTTAG 57.739 33.333 0.00 0.00 0.00 1.85
18 19 9.261180 CTCGAAGGAGCATTATAAGATTGTTTA 57.739 33.333 0.00 0.00 32.61 2.01
19 20 7.770897 ACTCGAAGGAGCATTATAAGATTGTTT 59.229 33.333 0.00 0.00 44.48 2.83
20 21 7.275920 ACTCGAAGGAGCATTATAAGATTGTT 58.724 34.615 0.00 0.00 44.48 2.83
21 22 6.821388 ACTCGAAGGAGCATTATAAGATTGT 58.179 36.000 0.00 0.00 44.48 2.71
22 23 7.721286 AACTCGAAGGAGCATTATAAGATTG 57.279 36.000 0.00 0.00 44.48 2.67
23 24 7.254932 GCAAACTCGAAGGAGCATTATAAGATT 60.255 37.037 0.00 0.00 44.48 2.40
24 25 6.203723 GCAAACTCGAAGGAGCATTATAAGAT 59.796 38.462 0.00 0.00 44.48 2.40
25 26 5.523916 GCAAACTCGAAGGAGCATTATAAGA 59.476 40.000 0.00 0.00 44.48 2.10
26 27 5.525378 AGCAAACTCGAAGGAGCATTATAAG 59.475 40.000 0.00 0.00 44.48 1.73
27 28 5.428253 AGCAAACTCGAAGGAGCATTATAA 58.572 37.500 0.00 0.00 44.48 0.98
28 29 5.023533 AGCAAACTCGAAGGAGCATTATA 57.976 39.130 0.00 0.00 44.48 0.98
29 30 3.878778 AGCAAACTCGAAGGAGCATTAT 58.121 40.909 0.00 0.00 44.48 1.28
30 31 3.334583 AGCAAACTCGAAGGAGCATTA 57.665 42.857 0.00 0.00 44.48 1.90
31 32 2.191128 AGCAAACTCGAAGGAGCATT 57.809 45.000 0.00 0.00 44.48 3.56
32 33 3.201290 CATAGCAAACTCGAAGGAGCAT 58.799 45.455 0.00 0.00 44.48 3.79
33 34 2.028112 ACATAGCAAACTCGAAGGAGCA 60.028 45.455 0.00 0.00 44.48 4.26
34 35 2.622436 ACATAGCAAACTCGAAGGAGC 58.378 47.619 0.00 0.00 44.48 4.70
35 36 3.304559 CGAACATAGCAAACTCGAAGGAG 59.695 47.826 0.00 0.00 46.13 3.69
36 37 3.250744 CGAACATAGCAAACTCGAAGGA 58.749 45.455 0.00 0.00 0.00 3.36
37 38 2.993899 ACGAACATAGCAAACTCGAAGG 59.006 45.455 0.00 0.00 33.81 3.46
38 39 3.428870 ACACGAACATAGCAAACTCGAAG 59.571 43.478 0.00 0.00 33.81 3.79
39 40 3.183574 CACACGAACATAGCAAACTCGAA 59.816 43.478 0.00 0.00 33.81 3.71
40 41 2.729360 CACACGAACATAGCAAACTCGA 59.271 45.455 0.00 0.00 33.81 4.04
41 42 2.475111 ACACACGAACATAGCAAACTCG 59.525 45.455 0.00 0.00 35.68 4.18
42 43 4.684703 AGTACACACGAACATAGCAAACTC 59.315 41.667 0.00 0.00 0.00 3.01
43 44 4.628074 AGTACACACGAACATAGCAAACT 58.372 39.130 0.00 0.00 0.00 2.66
44 45 4.985044 AGTACACACGAACATAGCAAAC 57.015 40.909 0.00 0.00 0.00 2.93
45 46 5.994887 AAAGTACACACGAACATAGCAAA 57.005 34.783 0.00 0.00 0.00 3.68
46 47 7.385478 TCATTAAAGTACACACGAACATAGCAA 59.615 33.333 0.00 0.00 0.00 3.91
47 48 6.869388 TCATTAAAGTACACACGAACATAGCA 59.131 34.615 0.00 0.00 0.00 3.49
48 49 7.285783 TCATTAAAGTACACACGAACATAGC 57.714 36.000 0.00 0.00 0.00 2.97
49 50 9.302345 AGATCATTAAAGTACACACGAACATAG 57.698 33.333 0.00 0.00 0.00 2.23
51 52 9.647797 TTAGATCATTAAAGTACACACGAACAT 57.352 29.630 0.00 0.00 0.00 2.71
52 53 9.478768 TTTAGATCATTAAAGTACACACGAACA 57.521 29.630 0.00 0.00 0.00 3.18
53 54 9.737025 GTTTAGATCATTAAAGTACACACGAAC 57.263 33.333 0.00 0.00 0.00 3.95
54 55 9.478768 TGTTTAGATCATTAAAGTACACACGAA 57.521 29.630 0.00 0.00 0.00 3.85
55 56 9.478768 TTGTTTAGATCATTAAAGTACACACGA 57.521 29.630 0.00 0.00 0.00 4.35
72 73 9.614792 GGGAGTACAACATAAGATTGTTTAGAT 57.385 33.333 0.00 0.00 40.68 1.98
73 74 8.822805 AGGGAGTACAACATAAGATTGTTTAGA 58.177 33.333 0.00 0.00 40.68 2.10
74 75 9.099454 GAGGGAGTACAACATAAGATTGTTTAG 57.901 37.037 0.00 0.00 40.68 1.85
75 76 8.044908 GGAGGGAGTACAACATAAGATTGTTTA 58.955 37.037 0.00 0.00 40.68 2.01
76 77 6.884836 GGAGGGAGTACAACATAAGATTGTTT 59.115 38.462 0.00 0.00 40.68 2.83
77 78 6.415573 GGAGGGAGTACAACATAAGATTGTT 58.584 40.000 0.00 0.00 40.68 2.83
78 79 5.395324 CGGAGGGAGTACAACATAAGATTGT 60.395 44.000 0.00 0.00 42.78 2.71
79 80 5.050490 CGGAGGGAGTACAACATAAGATTG 58.950 45.833 0.00 0.00 0.00 2.67
80 81 4.715297 ACGGAGGGAGTACAACATAAGATT 59.285 41.667 0.00 0.00 0.00 2.40
81 82 4.287552 ACGGAGGGAGTACAACATAAGAT 58.712 43.478 0.00 0.00 0.00 2.40
82 83 3.705051 ACGGAGGGAGTACAACATAAGA 58.295 45.455 0.00 0.00 0.00 2.10
83 84 5.451520 CCTTACGGAGGGAGTACAACATAAG 60.452 48.000 0.00 0.00 42.26 1.73
84 85 4.403432 CCTTACGGAGGGAGTACAACATAA 59.597 45.833 0.00 0.00 42.26 1.90
85 86 3.956199 CCTTACGGAGGGAGTACAACATA 59.044 47.826 0.00 0.00 42.26 2.29
86 87 2.764572 CCTTACGGAGGGAGTACAACAT 59.235 50.000 0.00 0.00 42.26 2.71
87 88 2.173519 CCTTACGGAGGGAGTACAACA 58.826 52.381 0.00 0.00 42.26 3.33
88 89 2.955477 CCTTACGGAGGGAGTACAAC 57.045 55.000 0.00 0.00 42.26 3.32
98 99 4.320348 CGCTTAGATTCCTACCTTACGGAG 60.320 50.000 0.00 0.00 0.00 4.63
99 100 3.567164 CGCTTAGATTCCTACCTTACGGA 59.433 47.826 0.00 0.00 0.00 4.69
100 101 3.856267 GCGCTTAGATTCCTACCTTACGG 60.856 52.174 0.00 0.00 0.00 4.02
101 102 3.004524 AGCGCTTAGATTCCTACCTTACG 59.995 47.826 2.64 0.00 0.00 3.18
102 103 4.548494 GAGCGCTTAGATTCCTACCTTAC 58.452 47.826 13.26 0.00 0.00 2.34
103 104 3.573110 GGAGCGCTTAGATTCCTACCTTA 59.427 47.826 13.26 0.00 0.00 2.69
104 105 2.365941 GGAGCGCTTAGATTCCTACCTT 59.634 50.000 13.26 0.00 0.00 3.50
105 106 1.964933 GGAGCGCTTAGATTCCTACCT 59.035 52.381 13.26 0.00 0.00 3.08
106 107 1.964933 AGGAGCGCTTAGATTCCTACC 59.035 52.381 13.26 3.43 38.26 3.18
107 108 6.702716 ATATAGGAGCGCTTAGATTCCTAC 57.297 41.667 19.59 0.28 43.15 3.18
108 109 7.616150 AGAAATATAGGAGCGCTTAGATTCCTA 59.384 37.037 19.51 19.51 44.13 2.94
109 110 6.439058 AGAAATATAGGAGCGCTTAGATTCCT 59.561 38.462 13.26 15.43 42.50 3.36
110 111 6.635755 AGAAATATAGGAGCGCTTAGATTCC 58.364 40.000 13.26 7.28 0.00 3.01
111 112 8.541133 AAAGAAATATAGGAGCGCTTAGATTC 57.459 34.615 13.26 10.36 0.00 2.52
112 113 9.425577 GTAAAGAAATATAGGAGCGCTTAGATT 57.574 33.333 13.26 7.30 0.00 2.40
113 114 8.585881 TGTAAAGAAATATAGGAGCGCTTAGAT 58.414 33.333 13.26 7.77 0.00 1.98
114 115 7.948357 TGTAAAGAAATATAGGAGCGCTTAGA 58.052 34.615 13.26 0.00 0.00 2.10
115 116 8.082852 TCTGTAAAGAAATATAGGAGCGCTTAG 58.917 37.037 13.26 0.00 0.00 2.18
116 117 7.948357 TCTGTAAAGAAATATAGGAGCGCTTA 58.052 34.615 13.26 0.00 0.00 3.09
117 118 6.817184 TCTGTAAAGAAATATAGGAGCGCTT 58.183 36.000 13.26 0.00 0.00 4.68
118 119 6.406692 TCTGTAAAGAAATATAGGAGCGCT 57.593 37.500 11.27 11.27 0.00 5.92
119 120 5.635700 CCTCTGTAAAGAAATATAGGAGCGC 59.364 44.000 0.00 0.00 0.00 5.92
120 121 6.015350 TCCCTCTGTAAAGAAATATAGGAGCG 60.015 42.308 0.00 0.00 0.00 5.03
121 122 7.015779 ACTCCCTCTGTAAAGAAATATAGGAGC 59.984 40.741 0.00 0.00 0.00 4.70
122 123 8.485578 ACTCCCTCTGTAAAGAAATATAGGAG 57.514 38.462 0.00 0.00 0.00 3.69
136 137 8.759782 CCTCTTTAAAGAAATACTCCCTCTGTA 58.240 37.037 18.25 0.00 34.03 2.74
137 138 7.458170 TCCTCTTTAAAGAAATACTCCCTCTGT 59.542 37.037 18.25 0.00 34.03 3.41
138 139 7.852263 TCCTCTTTAAAGAAATACTCCCTCTG 58.148 38.462 18.25 2.90 34.03 3.35
139 140 8.450780 TTCCTCTTTAAAGAAATACTCCCTCT 57.549 34.615 18.25 0.00 34.03 3.69
140 141 8.322828 ACTTCCTCTTTAAAGAAATACTCCCTC 58.677 37.037 18.25 0.00 34.03 4.30
141 142 8.220898 ACTTCCTCTTTAAAGAAATACTCCCT 57.779 34.615 18.25 0.00 34.03 4.20
142 143 9.381033 GTACTTCCTCTTTAAAGAAATACTCCC 57.619 37.037 18.25 1.32 34.03 4.30
143 144 9.085250 CGTACTTCCTCTTTAAAGAAATACTCC 57.915 37.037 18.25 5.04 34.03 3.85
144 145 9.636879 ACGTACTTCCTCTTTAAAGAAATACTC 57.363 33.333 18.25 6.58 34.03 2.59
145 146 9.420551 CACGTACTTCCTCTTTAAAGAAATACT 57.579 33.333 18.25 4.85 34.03 2.12
146 147 8.654215 CCACGTACTTCCTCTTTAAAGAAATAC 58.346 37.037 18.25 13.69 34.03 1.89
157 158 8.937207 ATTATAGATACCACGTACTTCCTCTT 57.063 34.615 0.00 0.00 0.00 2.85
159 160 8.386606 CGTATTATAGATACCACGTACTTCCTC 58.613 40.741 0.00 0.00 0.00 3.71
163 164 8.839310 ACTCGTATTATAGATACCACGTACTT 57.161 34.615 0.00 0.00 0.00 2.24
187 188 5.163923 CGTAACCTCCGTGGAATTTAGAAAC 60.164 44.000 0.00 0.00 39.71 2.78
213 214 1.404047 CGTCCATGTTCAAAATGGGGC 60.404 52.381 6.76 0.00 44.10 5.80
224 229 2.736995 CGGCGTGACGTCCATGTT 60.737 61.111 14.12 0.00 34.28 2.71
316 322 3.906998 TGCGGTCACCAAATTTATTGTG 58.093 40.909 0.00 7.86 0.00 3.33
353 359 1.098712 TTTCACACTCCCGTTGGTGC 61.099 55.000 0.00 0.00 36.99 5.01
433 445 3.645975 GTGGTTCACCGTGCCGTG 61.646 66.667 0.00 0.00 39.43 4.94
434 446 4.922026 GGTGGTTCACCGTGCCGT 62.922 66.667 1.01 0.00 44.95 5.68
465 485 4.101448 ACCTGCTCGATGGTGGCC 62.101 66.667 0.00 0.00 34.90 5.36
476 496 0.035881 CAGACACATGTGGACCTGCT 59.964 55.000 28.64 12.89 34.19 4.24
488 508 2.168936 AGAACCGTAAACACCAGACACA 59.831 45.455 0.00 0.00 0.00 3.72
496 516 1.723003 CGGCTACAGAACCGTAAACAC 59.277 52.381 0.00 0.00 44.46 3.32
603 647 4.201980 CGTTCAATCTTGTCATGGCATCAT 60.202 41.667 0.00 0.00 0.00 2.45
604 648 3.127376 CGTTCAATCTTGTCATGGCATCA 59.873 43.478 0.00 0.00 0.00 3.07
605 649 3.688272 CGTTCAATCTTGTCATGGCATC 58.312 45.455 0.00 0.00 0.00 3.91
606 650 2.159338 GCGTTCAATCTTGTCATGGCAT 60.159 45.455 0.00 0.00 0.00 4.40
607 651 1.199789 GCGTTCAATCTTGTCATGGCA 59.800 47.619 0.00 0.00 0.00 4.92
608 652 1.199789 TGCGTTCAATCTTGTCATGGC 59.800 47.619 0.00 0.00 0.00 4.40
609 653 2.743664 TCTGCGTTCAATCTTGTCATGG 59.256 45.455 0.00 0.00 0.00 3.66
646 691 9.261035 AGTACTACCAGTCTACTACAGTAAGTA 57.739 37.037 0.00 0.00 0.00 2.24
647 692 8.144862 AGTACTACCAGTCTACTACAGTAAGT 57.855 38.462 0.00 0.00 0.00 2.24
648 693 9.528018 GTAGTACTACCAGTCTACTACAGTAAG 57.472 40.741 20.47 0.00 38.88 2.34
649 694 8.191446 CGTAGTACTACCAGTCTACTACAGTAA 58.809 40.741 24.06 0.00 38.93 2.24
664 713 8.977505 CAGAGATTAGTTACTCGTAGTACTACC 58.022 40.741 24.06 11.11 38.08 3.18
668 1168 6.259608 TGCCAGAGATTAGTTACTCGTAGTAC 59.740 42.308 0.00 0.00 38.08 2.73
675 1175 3.707793 CGGTGCCAGAGATTAGTTACTC 58.292 50.000 0.00 0.00 0.00 2.59
703 1208 5.243207 TCTACTTTTCGATGGGGAAGTTTC 58.757 41.667 0.00 0.00 34.46 2.78
800 1343 3.181453 TGGTGGACGTAGGAAACAAATGA 60.181 43.478 0.00 0.00 0.00 2.57
802 1345 3.071892 TCTGGTGGACGTAGGAAACAAAT 59.928 43.478 0.00 0.00 0.00 2.32
803 1346 2.435069 TCTGGTGGACGTAGGAAACAAA 59.565 45.455 0.00 0.00 0.00 2.83
804 1347 2.040939 TCTGGTGGACGTAGGAAACAA 58.959 47.619 0.00 0.00 0.00 2.83
805 1348 1.342174 GTCTGGTGGACGTAGGAAACA 59.658 52.381 0.00 0.00 35.07 2.83
817 1360 0.250901 CTTGAGTTGGGGTCTGGTGG 60.251 60.000 0.00 0.00 0.00 4.61
848 1400 4.547532 CGTATGTCTGGTGGCTCTTATAC 58.452 47.826 0.00 0.00 0.00 1.47
907 1469 2.608261 GCTACTGGATCGTGTATGGCTC 60.608 54.545 0.00 0.00 0.00 4.70
912 1474 2.223829 GCTGTGCTACTGGATCGTGTAT 60.224 50.000 0.00 0.00 0.00 2.29
1442 2187 2.032681 AAGGCGTCAGGTTCAGGC 59.967 61.111 0.00 0.00 0.00 4.85
1630 4739 6.072286 ACAACAAGGATCTAGTTGCAAGAATG 60.072 38.462 18.60 0.00 44.77 2.67
1631 4740 6.006449 ACAACAAGGATCTAGTTGCAAGAAT 58.994 36.000 18.60 0.00 44.77 2.40
1632 4741 5.239306 CACAACAAGGATCTAGTTGCAAGAA 59.761 40.000 18.60 0.00 44.77 2.52
1633 4742 4.756642 CACAACAAGGATCTAGTTGCAAGA 59.243 41.667 18.60 0.00 44.77 3.02
1634 4743 4.516698 ACACAACAAGGATCTAGTTGCAAG 59.483 41.667 18.60 13.60 44.77 4.01
1635 4744 4.460263 ACACAACAAGGATCTAGTTGCAA 58.540 39.130 18.60 0.00 44.77 4.08
1636 4745 4.085357 ACACAACAAGGATCTAGTTGCA 57.915 40.909 18.60 0.00 44.77 4.08
1717 4832 7.701539 AATTCAAGCACCACTGATGTATTTA 57.298 32.000 0.00 0.00 0.00 1.40
1718 4833 6.594788 AATTCAAGCACCACTGATGTATTT 57.405 33.333 0.00 0.00 0.00 1.40
1850 4988 1.055849 TCAGCCATATACGGTGCCAT 58.944 50.000 0.00 0.00 0.00 4.40
1982 5130 2.508439 TTCGAGCCCGCGATGAAC 60.508 61.111 8.23 0.00 40.35 3.18
1999 5147 1.064017 AGGAGATGTTCGAGGAGCTCT 60.064 52.381 14.64 0.00 0.00 4.09
2084 5232 3.509575 AGAACTGAGCATTCTTCGAGTCT 59.490 43.478 0.00 0.00 32.32 3.24
2119 5270 3.077556 TCTTCCTGGAGGAGCCGC 61.078 66.667 4.13 0.00 46.36 6.53
2214 5366 2.098607 CCTTGTATTAGCGTCGTCTCCA 59.901 50.000 0.00 0.00 0.00 3.86
2229 5381 0.036164 AGTCGCCATTGTGCCTTGTA 59.964 50.000 0.00 0.00 0.00 2.41
2258 5410 1.153449 TCAACTTGCCCGCCGATAG 60.153 57.895 0.00 0.00 0.00 2.08
2260 5412 2.436646 CTCAACTTGCCCGCCGAT 60.437 61.111 0.00 0.00 0.00 4.18
2269 5421 0.595095 GCCAGGTGAAGCTCAACTTG 59.405 55.000 1.50 3.05 42.87 3.16
2292 5444 3.589988 CATGACAGTACTCCGCTTCTTT 58.410 45.455 0.00 0.00 0.00 2.52
2307 5459 0.527600 GCATCTACGACGCCATGACA 60.528 55.000 0.00 0.00 0.00 3.58
2308 5460 0.527600 TGCATCTACGACGCCATGAC 60.528 55.000 0.00 0.00 0.00 3.06
2309 5461 0.389025 ATGCATCTACGACGCCATGA 59.611 50.000 0.00 0.00 0.00 3.07
2433 5585 1.532505 GCTGCCGTCGTCGAAGTATTA 60.533 52.381 2.98 0.00 39.71 0.98
2452 5604 1.135199 CATCCCTGAACATGTTGCAGC 60.135 52.381 17.58 1.54 0.00 5.25
2467 5619 1.227556 CGGATTCCGTCACCATCCC 60.228 63.158 17.08 0.00 42.73 3.85
2510 5662 2.759114 CCCTTGAGCTTCCAGCCA 59.241 61.111 0.00 0.00 43.77 4.75
2575 5727 1.073125 ACCACCATGTCGTTGAATCCA 59.927 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.