Multiple sequence alignment - TraesCS6D01G044000

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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 TraesCS6D01G044000 chr6D 100.000 3990 0 0 1 3990 18777724 18773735 0.000000e+00 7369.0
1 TraesCS6D01G044000 chr6D 82.401 2199 283 55 1199 3316 5589527 5591702 0.000000e+00 1821.0
2 TraesCS6D01G044000 chr6D 82.263 1900 275 32 678 2527 13820911 13822798 0.000000e+00 1585.0
3 TraesCS6D01G044000 chr6D 86.425 442 51 5 542 977 5568786 5568348 3.610000e-130 475.0
4 TraesCS6D01G044000 chr6D 80.567 247 27 10 209 446 5588807 5589041 1.910000e-38 171.0
5 TraesCS6D01G044000 chr6A 81.374 3318 428 91 209 3382 5071295 5074566 0.000000e+00 2529.0
6 TraesCS6D01G044000 chr6A 95.505 1535 65 3 1091 2621 18891074 18889540 0.000000e+00 2449.0
7 TraesCS6D01G044000 chr6A 95.255 1096 36 9 2907 3990 18889210 18888119 0.000000e+00 1722.0
8 TraesCS6D01G044000 chr6A 80.854 2131 309 56 678 2738 4412989 4410888 0.000000e+00 1583.0
9 TraesCS6D01G044000 chr6A 80.469 2130 320 48 678 2738 4354661 4352559 0.000000e+00 1541.0
10 TraesCS6D01G044000 chr6A 82.770 1538 240 16 678 2196 4234266 4232735 0.000000e+00 1349.0
11 TraesCS6D01G044000 chr6A 90.476 945 35 5 155 1095 18902145 18901252 0.000000e+00 1195.0
12 TraesCS6D01G044000 chr6A 84.266 286 32 8 3156 3431 4282883 4282601 2.360000e-67 267.0
13 TraesCS6D01G044000 chr6A 84.727 275 33 5 3267 3535 4358049 4358320 2.360000e-67 267.0
14 TraesCS6D01G044000 chr6A 84.266 286 32 8 3156 3431 4410546 4410264 2.360000e-67 267.0
15 TraesCS6D01G044000 chr6A 84.364 275 34 5 3267 3535 4287450 4287721 1.100000e-65 261.0
16 TraesCS6D01G044000 chr6A 97.959 98 2 0 13 110 18902241 18902144 1.910000e-38 171.0
17 TraesCS6D01G044000 chr6B 78.851 2785 392 107 22 2712 9458166 9460847 0.000000e+00 1698.0
18 TraesCS6D01G044000 chr6B 82.915 597 81 11 678 1254 10852967 10852372 5.910000e-143 518.0
19 TraesCS6D01G044000 chrUn 80.932 2103 305 46 678 2711 62593114 62595189 0.000000e+00 1574.0
20 TraesCS6D01G044000 chrUn 80.789 2103 308 46 678 2711 62536699 62538774 0.000000e+00 1557.0
21 TraesCS6D01G044000 chrUn 80.573 2095 311 46 678 2703 62464689 62466756 0.000000e+00 1526.0
22 TraesCS6D01G044000 chrUn 80.171 2103 321 46 678 2711 62408834 62410909 0.000000e+00 1485.0
23 TraesCS6D01G044000 chrUn 80.674 1573 221 39 1197 2711 62348142 62349689 0.000000e+00 1144.0
24 TraesCS6D01G044000 chrUn 84.615 286 31 8 3156 3431 62467133 62467415 5.080000e-69 272.0
25 TraesCS6D01G044000 chrUn 84.615 286 31 8 3156 3431 62595558 62595840 5.080000e-69 272.0
26 TraesCS6D01G044000 chrUn 84.266 286 32 8 3156 3431 62350058 62350340 2.360000e-67 267.0
27 TraesCS6D01G044000 chrUn 84.321 287 30 10 3156 3431 62411278 62411560 2.360000e-67 267.0
28 TraesCS6D01G044000 chrUn 84.727 275 33 5 3267 3535 62533313 62533042 2.360000e-67 267.0
29 TraesCS6D01G044000 chrUn 84.266 286 32 8 3156 3431 62539143 62539425 2.360000e-67 267.0
30 TraesCS6D01G044000 chrUn 84.727 275 33 5 3267 3535 62589725 62589454 2.360000e-67 267.0
31 TraesCS6D01G044000 chrUn 84.727 275 33 5 3267 3535 247224086 247223815 2.360000e-67 267.0
32 TraesCS6D01G044000 chrUn 84.727 275 33 5 3267 3535 439030349 439030078 2.360000e-67 267.0
33 TraesCS6D01G044000 chrUn 83.916 286 33 8 3156 3431 62296127 62296409 1.100000e-65 261.0
34 TraesCS6D01G044000 chrUn 84.364 275 34 5 3267 3535 62344260 62343989 1.100000e-65 261.0
35 TraesCS6D01G044000 chrUn 84.000 275 35 5 3267 3535 62405601 62405330 5.120000e-64 255.0
36 TraesCS6D01G044000 chrUn 77.090 323 42 15 2958 3268 62344611 62344309 1.480000e-34 158.0
37 TraesCS6D01G044000 chrUn 77.564 312 34 17 2958 3263 247224421 247224140 5.340000e-34 156.0
38 TraesCS6D01G044000 chrUn 77.044 318 41 15 2958 3263 62461654 62461357 1.920000e-33 154.0
39 TraesCS6D01G044000 chrUn 77.044 318 41 15 2958 3263 62533664 62533367 1.920000e-33 154.0
40 TraesCS6D01G044000 chrUn 76.730 318 42 15 2958 3263 62405952 62405655 8.930000e-32 148.0
41 TraesCS6D01G044000 chrUn 89.189 74 6 2 3772 3844 44239792 44239864 1.530000e-14 91.6
42 TraesCS6D01G044000 chr2A 93.233 798 46 5 1989 2779 6378047 6378843 0.000000e+00 1168.0
43 TraesCS6D01G044000 chr2A 92.500 800 46 8 1989 2782 374195804 374195013 0.000000e+00 1133.0
44 TraesCS6D01G044000 chr7A 92.974 797 47 7 1989 2779 119835776 119836569 0.000000e+00 1153.0
45 TraesCS6D01G044000 chr1A 92.732 798 50 6 1989 2779 374715588 374716384 0.000000e+00 1146.0
46 TraesCS6D01G044000 chr1A 92.625 800 52 5 1989 2782 262339231 262338433 0.000000e+00 1144.0
47 TraesCS6D01G044000 chr5A 93.253 667 39 4 2119 2779 131075412 131076078 0.000000e+00 977.0
48 TraesCS6D01G044000 chr5A 89.017 173 12 1 2943 3115 470944360 470944195 1.450000e-49 207.0
49 TraesCS6D01G044000 chr3A 92.045 264 19 2 2521 2782 515065723 515065460 1.750000e-98 370.0
50 TraesCS6D01G044000 chr3A 89.017 173 12 4 2943 3115 662570900 662571065 1.450000e-49 207.0
51 TraesCS6D01G044000 chr3B 87.059 170 15 2 2946 3115 775655743 775655905 6.810000e-43 185.0
52 TraesCS6D01G044000 chr3B 90.000 70 7 0 3775 3844 49145635 49145704 1.530000e-14 91.6
53 TraesCS6D01G044000 chr7D 90.141 71 7 0 3774 3844 561665173 561665103 4.250000e-15 93.5
54 TraesCS6D01G044000 chr1D 90.141 71 7 0 3774 3844 35867261 35867331 4.250000e-15 93.5
55 TraesCS6D01G044000 chr1D 89.041 73 8 0 3772 3844 443550274 443550346 1.530000e-14 91.6
56 TraesCS6D01G044000 chr3D 89.189 74 6 2 3771 3844 386736092 386736163 1.530000e-14 91.6
57 TraesCS6D01G044000 chr4A 90.000 70 6 1 3775 3844 376724150 376724082 5.490000e-14 89.8
58 TraesCS6D01G044000 chr1B 85.542 83 9 3 3773 3854 470424823 470424903 2.560000e-12 84.2


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 TraesCS6D01G044000 chr6D 18773735 18777724 3989 True 7369.0 7369 100.0000 1 3990 1 chr6D.!!$R2 3989
1 TraesCS6D01G044000 chr6D 13820911 13822798 1887 False 1585.0 1585 82.2630 678 2527 1 chr6D.!!$F1 1849
2 TraesCS6D01G044000 chr6D 5588807 5591702 2895 False 996.0 1821 81.4840 209 3316 2 chr6D.!!$F2 3107
3 TraesCS6D01G044000 chr6A 5071295 5074566 3271 False 2529.0 2529 81.3740 209 3382 1 chr6A.!!$F3 3173
4 TraesCS6D01G044000 chr6A 18888119 18891074 2955 True 2085.5 2449 95.3800 1091 3990 2 chr6A.!!$R5 2899
5 TraesCS6D01G044000 chr6A 4352559 4354661 2102 True 1541.0 1541 80.4690 678 2738 1 chr6A.!!$R3 2060
6 TraesCS6D01G044000 chr6A 4232735 4234266 1531 True 1349.0 1349 82.7700 678 2196 1 chr6A.!!$R1 1518
7 TraesCS6D01G044000 chr6A 4410264 4412989 2725 True 925.0 1583 82.5600 678 3431 2 chr6A.!!$R4 2753
8 TraesCS6D01G044000 chr6A 18901252 18902241 989 True 683.0 1195 94.2175 13 1095 2 chr6A.!!$R6 1082
9 TraesCS6D01G044000 chr6B 9458166 9460847 2681 False 1698.0 1698 78.8510 22 2712 1 chr6B.!!$F1 2690
10 TraesCS6D01G044000 chr6B 10852372 10852967 595 True 518.0 518 82.9150 678 1254 1 chr6B.!!$R1 576
11 TraesCS6D01G044000 chrUn 62593114 62595840 2726 False 923.0 1574 82.7735 678 3431 2 chrUn.!!$F7 2753
12 TraesCS6D01G044000 chrUn 62536699 62539425 2726 False 912.0 1557 82.5275 678 3431 2 chrUn.!!$F6 2753
13 TraesCS6D01G044000 chrUn 62464689 62467415 2726 False 899.0 1526 82.5940 678 3431 2 chrUn.!!$F5 2753
14 TraesCS6D01G044000 chrUn 62408834 62411560 2726 False 876.0 1485 82.2460 678 3431 2 chrUn.!!$F4 2753
15 TraesCS6D01G044000 chrUn 62348142 62350340 2198 False 705.5 1144 82.4700 1197 3431 2 chrUn.!!$F3 2234
16 TraesCS6D01G044000 chrUn 247223815 247224421 606 True 211.5 267 81.1455 2958 3535 2 chrUn.!!$R7 577
17 TraesCS6D01G044000 chrUn 62533042 62533664 622 True 210.5 267 80.8855 2958 3535 2 chrUn.!!$R6 577
18 TraesCS6D01G044000 chrUn 62343989 62344611 622 True 209.5 261 80.7270 2958 3535 2 chrUn.!!$R4 577
19 TraesCS6D01G044000 chrUn 62405330 62405952 622 True 201.5 255 80.3650 2958 3535 2 chrUn.!!$R5 577
20 TraesCS6D01G044000 chr2A 6378047 6378843 796 False 1168.0 1168 93.2330 1989 2779 1 chr2A.!!$F1 790
21 TraesCS6D01G044000 chr2A 374195013 374195804 791 True 1133.0 1133 92.5000 1989 2782 1 chr2A.!!$R1 793
22 TraesCS6D01G044000 chr7A 119835776 119836569 793 False 1153.0 1153 92.9740 1989 2779 1 chr7A.!!$F1 790
23 TraesCS6D01G044000 chr1A 374715588 374716384 796 False 1146.0 1146 92.7320 1989 2779 1 chr1A.!!$F1 790
24 TraesCS6D01G044000 chr1A 262338433 262339231 798 True 1144.0 1144 92.6250 1989 2782 1 chr1A.!!$R1 793
25 TraesCS6D01G044000 chr5A 131075412 131076078 666 False 977.0 977 93.2530 2119 2779 1 chr5A.!!$F1 660

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
563 643 0.233332 GTGCGCTCTCTTTGTGTGTC 59.767 55.0 9.73 0.0 0.00 3.67 F
1009 1112 0.179171 CTTTGGCTCGATGCTGCTTG 60.179 55.0 0.00 0.0 42.39 4.01 F
1587 1714 0.326264 AGCTGCCACAAGGAGTTAGG 59.674 55.0 0.00 0.0 36.89 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1867 1.135139 GCACTATGCTCGTCCTCAAGA 59.865 52.381 0.00 0.0 40.96 3.02 R
1836 1963 1.620819 ACTGCCTTTCTCATGACGTCT 59.379 47.619 17.92 0.0 0.00 4.18 R
3155 3720 0.530288 TCGGTCGCAATCAGTCATGA 59.470 50.000 0.00 0.0 40.50 3.07 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
110 119 0.954452 GCCTGAACTGTTTGGACCTG 59.046 55.000 14.79 0.00 0.00 4.00
113 122 2.158755 CCTGAACTGTTTGGACCTGACT 60.159 50.000 7.47 0.00 0.00 3.41
115 124 2.503765 TGAACTGTTTGGACCTGACTGA 59.496 45.455 0.00 0.00 0.00 3.41
116 125 3.136443 TGAACTGTTTGGACCTGACTGAT 59.864 43.478 0.00 1.26 0.00 2.90
118 127 4.974645 ACTGTTTGGACCTGACTGATTA 57.025 40.909 10.21 0.00 0.00 1.75
119 128 4.642429 ACTGTTTGGACCTGACTGATTAC 58.358 43.478 10.21 0.00 0.00 1.89
120 129 4.348168 ACTGTTTGGACCTGACTGATTACT 59.652 41.667 10.21 0.00 0.00 2.24
121 130 5.542635 ACTGTTTGGACCTGACTGATTACTA 59.457 40.000 10.21 0.00 0.00 1.82
123 132 7.399191 ACTGTTTGGACCTGACTGATTACTATA 59.601 37.037 10.21 0.00 0.00 1.31
124 133 8.319057 TGTTTGGACCTGACTGATTACTATAT 57.681 34.615 0.00 0.00 0.00 0.86
125 134 8.204160 TGTTTGGACCTGACTGATTACTATATG 58.796 37.037 0.00 0.00 0.00 1.78
126 135 6.918067 TGGACCTGACTGATTACTATATGG 57.082 41.667 0.00 0.00 0.00 2.74
127 136 6.382087 TGGACCTGACTGATTACTATATGGT 58.618 40.000 0.00 0.00 0.00 3.55
128 137 6.267699 TGGACCTGACTGATTACTATATGGTG 59.732 42.308 1.31 0.00 0.00 4.17
129 138 6.295349 GGACCTGACTGATTACTATATGGTGG 60.295 46.154 1.31 0.00 0.00 4.61
137 146 0.387929 ACTATATGGTGGCACCGACG 59.612 55.000 30.14 18.39 42.58 5.12
145 154 4.500116 GGCACCGACGCTCCTCTC 62.500 72.222 0.00 0.00 0.00 3.20
147 156 3.827898 CACCGACGCTCCTCTCCC 61.828 72.222 0.00 0.00 0.00 4.30
152 173 1.813192 GACGCTCCTCTCCCTTCTG 59.187 63.158 0.00 0.00 0.00 3.02
156 177 1.567357 GCTCCTCTCCCTTCTGACTT 58.433 55.000 0.00 0.00 0.00 3.01
207 228 2.890311 CACTCACTTCACTCACTCTCCT 59.110 50.000 0.00 0.00 0.00 3.69
308 331 1.337387 CCGGATCCGAGGTTAGTCTTC 59.663 57.143 35.42 0.00 42.83 2.87
330 358 3.259625 CCTCCTTCCCCGATCTATTCTTC 59.740 52.174 0.00 0.00 0.00 2.87
331 359 4.156477 CTCCTTCCCCGATCTATTCTTCT 58.844 47.826 0.00 0.00 0.00 2.85
332 360 4.557705 TCCTTCCCCGATCTATTCTTCTT 58.442 43.478 0.00 0.00 0.00 2.52
333 361 4.969359 TCCTTCCCCGATCTATTCTTCTTT 59.031 41.667 0.00 0.00 0.00 2.52
334 362 5.428783 TCCTTCCCCGATCTATTCTTCTTTT 59.571 40.000 0.00 0.00 0.00 2.27
335 363 5.760743 CCTTCCCCGATCTATTCTTCTTTTC 59.239 44.000 0.00 0.00 0.00 2.29
336 364 5.291905 TCCCCGATCTATTCTTCTTTTCC 57.708 43.478 0.00 0.00 0.00 3.13
337 365 4.102681 TCCCCGATCTATTCTTCTTTTCCC 59.897 45.833 0.00 0.00 0.00 3.97
338 366 4.103311 CCCCGATCTATTCTTCTTTTCCCT 59.897 45.833 0.00 0.00 0.00 4.20
339 367 5.301555 CCCGATCTATTCTTCTTTTCCCTC 58.698 45.833 0.00 0.00 0.00 4.30
340 368 5.071115 CCCGATCTATTCTTCTTTTCCCTCT 59.929 44.000 0.00 0.00 0.00 3.69
341 369 6.220201 CCGATCTATTCTTCTTTTCCCTCTC 58.780 44.000 0.00 0.00 0.00 3.20
342 370 6.041523 CCGATCTATTCTTCTTTTCCCTCTCT 59.958 42.308 0.00 0.00 0.00 3.10
343 371 7.418483 CCGATCTATTCTTCTTTTCCCTCTCTT 60.418 40.741 0.00 0.00 0.00 2.85
344 372 7.984617 CGATCTATTCTTCTTTTCCCTCTCTTT 59.015 37.037 0.00 0.00 0.00 2.52
345 373 9.679661 GATCTATTCTTCTTTTCCCTCTCTTTT 57.320 33.333 0.00 0.00 0.00 2.27
346 374 9.679661 ATCTATTCTTCTTTTCCCTCTCTTTTC 57.320 33.333 0.00 0.00 0.00 2.29
347 375 8.885346 TCTATTCTTCTTTTCCCTCTCTTTTCT 58.115 33.333 0.00 0.00 0.00 2.52
348 376 9.513906 CTATTCTTCTTTTCCCTCTCTTTTCTT 57.486 33.333 0.00 0.00 0.00 2.52
455 527 3.373439 CAGTGTTCAGCTGGAAAGATAGC 59.627 47.826 15.13 0.00 37.23 2.97
553 633 3.414700 CACGGTTGGTGCGCTCTC 61.415 66.667 9.73 0.00 40.33 3.20
563 643 0.233332 GTGCGCTCTCTTTGTGTGTC 59.767 55.000 9.73 0.00 0.00 3.67
619 699 2.741517 TGGACGAATGCTGTTGTATGTG 59.258 45.455 0.00 0.00 0.00 3.21
630 710 2.210116 GTTGTATGTGCACTATCGGGG 58.790 52.381 19.41 0.00 0.00 5.73
661 757 2.945447 GCAGCAGCATTATTGGTTCA 57.055 45.000 0.00 0.00 41.58 3.18
662 758 3.235157 GCAGCAGCATTATTGGTTCAA 57.765 42.857 0.00 0.00 41.58 2.69
663 759 2.925563 GCAGCAGCATTATTGGTTCAAC 59.074 45.455 0.00 0.00 41.58 3.18
664 760 3.614630 GCAGCAGCATTATTGGTTCAACA 60.615 43.478 0.00 0.00 41.58 3.33
665 761 4.558178 CAGCAGCATTATTGGTTCAACAA 58.442 39.130 0.00 0.00 34.41 2.83
666 762 4.386652 CAGCAGCATTATTGGTTCAACAAC 59.613 41.667 0.00 0.00 32.39 3.32
667 763 4.281688 AGCAGCATTATTGGTTCAACAACT 59.718 37.500 0.00 0.00 32.39 3.16
668 764 4.990426 GCAGCATTATTGGTTCAACAACTT 59.010 37.500 0.00 0.00 32.39 2.66
669 765 5.107375 GCAGCATTATTGGTTCAACAACTTG 60.107 40.000 0.00 0.00 32.39 3.16
670 766 5.406175 CAGCATTATTGGTTCAACAACTTGG 59.594 40.000 0.00 0.00 32.39 3.61
671 767 4.690280 GCATTATTGGTTCAACAACTTGGG 59.310 41.667 0.00 0.00 32.39 4.12
672 768 5.741673 GCATTATTGGTTCAACAACTTGGGT 60.742 40.000 0.00 0.00 32.39 4.51
673 769 5.523438 TTATTGGTTCAACAACTTGGGTC 57.477 39.130 0.00 0.00 32.39 4.46
674 770 1.770294 TGGTTCAACAACTTGGGTCC 58.230 50.000 0.00 0.00 32.50 4.46
675 771 0.666374 GGTTCAACAACTTGGGTCCG 59.334 55.000 0.00 0.00 32.50 4.79
711 807 2.758736 TTTGTTTTTGTGGCTGCTGT 57.241 40.000 0.00 0.00 0.00 4.40
731 833 0.962356 CCATTTTGCAGGGTCGAGCT 60.962 55.000 15.18 0.00 0.00 4.09
952 1054 4.993028 CCTCTTAGGCTACTACATCTCCT 58.007 47.826 0.00 0.00 0.00 3.69
980 1082 2.259818 CGAGTCGGAGCAGCAAGT 59.740 61.111 4.10 0.00 0.00 3.16
1009 1112 0.179171 CTTTGGCTCGATGCTGCTTG 60.179 55.000 0.00 0.00 42.39 4.01
1050 1172 1.227823 CGACACCTGCCACCTTTCA 60.228 57.895 0.00 0.00 0.00 2.69
1147 1269 0.677731 CGGTGACCATGATGGCAGTT 60.678 55.000 12.25 0.00 42.67 3.16
1268 1391 2.285069 TATGCCCACCGTCCCACT 60.285 61.111 0.00 0.00 0.00 4.00
1483 1609 1.761449 TGAACCAAAAGCTGTGCTCA 58.239 45.000 0.00 0.00 38.25 4.26
1485 1611 2.294233 TGAACCAAAAGCTGTGCTCATC 59.706 45.455 0.00 0.00 38.25 2.92
1486 1612 1.251251 ACCAAAAGCTGTGCTCATCC 58.749 50.000 0.00 0.00 38.25 3.51
1491 1617 1.985473 AAGCTGTGCTCATCCACAAA 58.015 45.000 0.00 0.00 44.37 2.83
1548 1675 7.272244 ACATTATTGTCTTGGATATGACGACA 58.728 34.615 0.00 0.00 34.61 4.35
1553 1680 5.917462 TGTCTTGGATATGACGACATCAAT 58.083 37.500 3.03 0.00 41.93 2.57
1587 1714 0.326264 AGCTGCCACAAGGAGTTAGG 59.674 55.000 0.00 0.00 36.89 2.69
1629 1756 0.906775 TGTCTCCAGCTGATGATGCA 59.093 50.000 17.39 5.33 0.00 3.96
1644 1771 4.890158 TGATGCATCCGGTGTATATCTT 57.110 40.909 23.67 0.00 32.93 2.40
1670 1797 9.022884 TGTCCATATCAATGAATTTCAACTTCA 57.977 29.630 2.68 0.00 37.06 3.02
1740 1867 6.114187 TGTTTGAGGATGTTAGATCACACT 57.886 37.500 0.00 0.00 0.00 3.55
1803 1930 4.036027 GTGGGAGACAATGCTGAATATGTG 59.964 45.833 0.00 0.00 0.00 3.21
1822 1949 2.808543 GTGTTCTTGTGGATGACTGGAC 59.191 50.000 0.00 0.00 0.00 4.02
1836 1963 2.943690 GACTGGACGCACACTCTATCTA 59.056 50.000 0.00 0.00 0.00 1.98
1844 1971 3.248841 CGCACACTCTATCTAGACGTCAT 59.751 47.826 19.50 5.15 0.00 3.06
1848 1975 5.755861 CACACTCTATCTAGACGTCATGAGA 59.244 44.000 19.50 16.67 0.00 3.27
1855 1982 2.376808 AGACGTCATGAGAAAGGCAG 57.623 50.000 19.50 0.00 0.00 4.85
2075 2226 3.006537 GGTAACAGTGGTAGTCTGCTTGA 59.993 47.826 0.00 0.00 36.50 3.02
2109 2260 7.456253 CACTTCTCCGTGTATGATTAGTTTTG 58.544 38.462 0.00 0.00 0.00 2.44
2629 2833 1.672363 TGCGCTGATCCATGATTTGTC 59.328 47.619 9.73 0.00 0.00 3.18
2693 2903 4.831107 AGTTTGAGTTTGTGTGGCATTTT 58.169 34.783 0.00 0.00 0.00 1.82
2871 3083 9.236006 AGCACAGAAGAAACAATATTGACTATT 57.764 29.630 22.16 11.00 0.00 1.73
3028 3593 3.149196 GAGCTTTTGGATGGTCAGTGAA 58.851 45.455 0.00 0.00 0.00 3.18
3085 3650 6.072452 GCATTTCCTTACTTGCAGTTCTAGTT 60.072 38.462 0.00 0.00 35.22 2.24
3150 3715 5.298347 GGATACTATGTACCTTGCAGTTCC 58.702 45.833 0.00 0.00 0.00 3.62
3152 3717 4.207891 ACTATGTACCTTGCAGTTCCAG 57.792 45.455 0.00 0.00 0.00 3.86
3153 3718 3.583086 ACTATGTACCTTGCAGTTCCAGT 59.417 43.478 0.00 0.00 0.00 4.00
3154 3719 4.775780 ACTATGTACCTTGCAGTTCCAGTA 59.224 41.667 0.00 0.00 0.00 2.74
3155 3720 4.844349 ATGTACCTTGCAGTTCCAGTAT 57.156 40.909 0.00 0.00 0.00 2.12
3308 4034 5.242838 GGAATTGGTCTTGTTGTTCACCATA 59.757 40.000 0.00 0.00 0.00 2.74
3310 4036 3.750371 TGGTCTTGTTGTTCACCATAGG 58.250 45.455 0.00 0.00 0.00 2.57
3340 4069 7.435068 TTCTGCTTTGGTTAGCTTTACTTAG 57.565 36.000 0.00 0.00 41.76 2.18
3445 4182 2.561419 GGACAGCACTCTAGTTGTGGTA 59.439 50.000 17.67 0.00 43.14 3.25
3466 4203 5.531287 GGTAGTTGATTCAGGAGTGTTTTGT 59.469 40.000 0.00 0.00 0.00 2.83
3537 4276 7.140522 TGAAGTATTGATGGATGATGAAGGA 57.859 36.000 0.00 0.00 0.00 3.36
3538 4277 7.222161 TGAAGTATTGATGGATGATGAAGGAG 58.778 38.462 0.00 0.00 0.00 3.69
3539 4278 7.071572 TGAAGTATTGATGGATGATGAAGGAGA 59.928 37.037 0.00 0.00 0.00 3.71
3560 4299 2.307098 AGGTAAGCTCTGGTTGCTGAAT 59.693 45.455 0.00 0.00 41.03 2.57
3777 4516 5.924475 ATTGATCCGATGGTCGTTATTTC 57.076 39.130 0.00 0.00 38.40 2.17
3787 4526 8.231837 CCGATGGTCGTTATTTCTTTAGAAAAA 58.768 33.333 8.82 3.34 41.58 1.94
3837 4576 8.501580 CATCAATCGATGCATACAACTATCTTT 58.498 33.333 0.00 0.00 42.54 2.52
3865 4604 1.063027 CGTCTACATCTACGAACGGCA 59.937 52.381 0.00 0.00 41.55 5.69
3870 4609 1.006086 CATCTACGAACGGCATGCAA 58.994 50.000 21.36 0.00 0.00 4.08
3923 4662 1.226831 GAAGAGGGAAGAGAGCGCG 60.227 63.158 0.00 0.00 0.00 6.86
3977 4716 1.376942 GTCGACGGAGGAGGAGACA 60.377 63.158 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.525355 GGCTATTTTTCGCTTTTGCTAAAAG 58.475 36.000 13.66 13.66 46.03 2.27
4 5 5.117897 CGGCTATTTTTCGCTTTTGCTAAAA 59.882 36.000 0.00 0.00 44.62 1.52
5 6 4.619336 CGGCTATTTTTCGCTTTTGCTAAA 59.381 37.500 0.00 0.00 44.80 1.85
6 7 4.083217 TCGGCTATTTTTCGCTTTTGCTAA 60.083 37.500 0.00 0.00 44.80 3.09
8 9 2.227865 TCGGCTATTTTTCGCTTTTGCT 59.772 40.909 0.00 0.00 44.80 3.91
9 10 2.341464 GTCGGCTATTTTTCGCTTTTGC 59.659 45.455 0.00 0.00 43.23 3.68
10 11 3.821841 AGTCGGCTATTTTTCGCTTTTG 58.178 40.909 0.00 0.00 0.00 2.44
11 12 5.813080 ATAGTCGGCTATTTTTCGCTTTT 57.187 34.783 3.03 0.00 34.43 2.27
68 77 1.179174 TGTACAGTGGAGAGCAGCGT 61.179 55.000 0.00 0.00 0.00 5.07
69 78 0.174389 ATGTACAGTGGAGAGCAGCG 59.826 55.000 0.33 0.00 0.00 5.18
110 119 5.238583 GGTGCCACCATATAGTAATCAGTC 58.761 45.833 9.55 0.00 38.42 3.51
113 122 3.898741 TCGGTGCCACCATATAGTAATCA 59.101 43.478 15.45 0.00 38.47 2.57
115 124 3.305813 CGTCGGTGCCACCATATAGTAAT 60.306 47.826 15.45 0.00 38.47 1.89
116 125 2.034939 CGTCGGTGCCACCATATAGTAA 59.965 50.000 15.45 0.00 38.47 2.24
118 127 0.387929 CGTCGGTGCCACCATATAGT 59.612 55.000 15.45 0.00 38.47 2.12
119 128 0.944311 GCGTCGGTGCCACCATATAG 60.944 60.000 15.45 1.17 38.47 1.31
120 129 1.068417 GCGTCGGTGCCACCATATA 59.932 57.895 15.45 0.00 38.47 0.86
121 130 2.203015 GCGTCGGTGCCACCATAT 60.203 61.111 15.45 0.00 38.47 1.78
123 132 4.760047 GAGCGTCGGTGCCACCAT 62.760 66.667 15.45 0.00 38.47 3.55
128 137 4.500116 GAGAGGAGCGTCGGTGCC 62.500 72.222 12.54 8.36 34.65 5.01
129 138 4.500116 GGAGAGGAGCGTCGGTGC 62.500 72.222 7.97 7.97 0.00 5.01
137 146 1.480545 GAAGTCAGAAGGGAGAGGAGC 59.519 57.143 0.00 0.00 0.00 4.70
142 151 2.163509 CGAGTGAAGTCAGAAGGGAGA 58.836 52.381 0.00 0.00 0.00 3.71
145 154 0.605589 AGCGAGTGAAGTCAGAAGGG 59.394 55.000 0.00 0.00 0.00 3.95
147 156 1.270826 TGGAGCGAGTGAAGTCAGAAG 59.729 52.381 0.00 0.00 0.00 2.85
152 173 1.446966 GGCTGGAGCGAGTGAAGTC 60.447 63.158 0.00 0.00 43.26 3.01
156 177 3.071206 GGAGGCTGGAGCGAGTGA 61.071 66.667 0.00 0.00 43.26 3.41
308 331 2.896039 AGAATAGATCGGGGAAGGAGG 58.104 52.381 0.00 0.00 0.00 4.30
330 358 8.253810 ACAAAAAGAAGAAAAGAGAGGGAAAAG 58.746 33.333 0.00 0.00 0.00 2.27
331 359 8.034804 CACAAAAAGAAGAAAAGAGAGGGAAAA 58.965 33.333 0.00 0.00 0.00 2.29
332 360 7.363793 CCACAAAAAGAAGAAAAGAGAGGGAAA 60.364 37.037 0.00 0.00 0.00 3.13
333 361 6.096846 CCACAAAAAGAAGAAAAGAGAGGGAA 59.903 38.462 0.00 0.00 0.00 3.97
334 362 5.594317 CCACAAAAAGAAGAAAAGAGAGGGA 59.406 40.000 0.00 0.00 0.00 4.20
335 363 5.221322 CCCACAAAAAGAAGAAAAGAGAGGG 60.221 44.000 0.00 0.00 0.00 4.30
336 364 5.221322 CCCCACAAAAAGAAGAAAAGAGAGG 60.221 44.000 0.00 0.00 0.00 3.69
337 365 5.594317 TCCCCACAAAAAGAAGAAAAGAGAG 59.406 40.000 0.00 0.00 0.00 3.20
338 366 5.515106 TCCCCACAAAAAGAAGAAAAGAGA 58.485 37.500 0.00 0.00 0.00 3.10
339 367 5.852282 TCCCCACAAAAAGAAGAAAAGAG 57.148 39.130 0.00 0.00 0.00 2.85
340 368 5.896678 TGATCCCCACAAAAAGAAGAAAAGA 59.103 36.000 0.00 0.00 0.00 2.52
341 369 6.160576 TGATCCCCACAAAAAGAAGAAAAG 57.839 37.500 0.00 0.00 0.00 2.27
342 370 6.552445 TTGATCCCCACAAAAAGAAGAAAA 57.448 33.333 0.00 0.00 0.00 2.29
343 371 6.345298 GTTTGATCCCCACAAAAAGAAGAAA 58.655 36.000 0.00 0.00 38.63 2.52
344 372 5.163353 GGTTTGATCCCCACAAAAAGAAGAA 60.163 40.000 0.00 0.00 38.63 2.52
345 373 4.343814 GGTTTGATCCCCACAAAAAGAAGA 59.656 41.667 0.00 0.00 38.63 2.87
346 374 4.503123 GGGTTTGATCCCCACAAAAAGAAG 60.503 45.833 0.88 0.00 42.15 2.85
347 375 3.389656 GGGTTTGATCCCCACAAAAAGAA 59.610 43.478 0.88 0.00 42.15 2.52
348 376 2.969262 GGGTTTGATCCCCACAAAAAGA 59.031 45.455 0.88 0.00 42.15 2.52
455 527 2.025719 CAGCAGCAGCATCCATCTG 58.974 57.895 3.17 0.00 45.49 2.90
553 633 0.309922 CAGCAGCCAGACACACAAAG 59.690 55.000 0.00 0.00 0.00 2.77
563 643 2.643272 CACAAGCACAGCAGCCAG 59.357 61.111 0.00 0.00 34.23 4.85
619 699 0.811616 CAAGCTGACCCCGATAGTGC 60.812 60.000 0.00 0.00 0.00 4.40
630 710 0.938168 GCTGCTGCAAACAAGCTGAC 60.938 55.000 11.11 0.00 39.41 3.51
661 757 2.436417 CATCATCGGACCCAAGTTGTT 58.564 47.619 1.45 0.00 0.00 2.83
662 758 1.950484 GCATCATCGGACCCAAGTTGT 60.950 52.381 1.45 0.00 0.00 3.32
663 759 0.734889 GCATCATCGGACCCAAGTTG 59.265 55.000 0.00 0.00 0.00 3.16
664 760 0.394352 GGCATCATCGGACCCAAGTT 60.394 55.000 0.00 0.00 0.00 2.66
665 761 1.224592 GGCATCATCGGACCCAAGT 59.775 57.895 0.00 0.00 0.00 3.16
666 762 1.526917 GGGCATCATCGGACCCAAG 60.527 63.158 0.00 0.00 42.33 3.61
667 763 2.595095 GGGCATCATCGGACCCAA 59.405 61.111 0.00 0.00 42.33 4.12
669 765 1.302832 GATGGGCATCATCGGACCC 60.303 63.158 3.98 0.00 42.29 4.46
670 766 4.386413 GATGGGCATCATCGGACC 57.614 61.111 3.98 0.00 42.29 4.46
711 807 0.960364 GCTCGACCCTGCAAAATGGA 60.960 55.000 0.00 0.00 0.00 3.41
731 833 1.138883 GTCTCGCCATCTACGCACA 59.861 57.895 0.00 0.00 0.00 4.57
952 1054 3.129502 CGACTCGGCCGACCACTA 61.130 66.667 27.28 1.86 34.57 2.74
1009 1112 1.751927 CAGAATGCTCTGGGGGCAC 60.752 63.158 0.00 0.00 44.72 5.01
1147 1269 1.536766 CTGGAAGCGTTTGATCTGCAA 59.463 47.619 0.00 0.00 33.88 4.08
1548 1675 5.357314 CAGCTGAATTGTGGAGAAGATTGAT 59.643 40.000 8.42 0.00 0.00 2.57
1553 1680 2.430465 GCAGCTGAATTGTGGAGAAGA 58.570 47.619 20.43 0.00 0.00 2.87
1587 1714 8.205131 ACAACATGGTCCGAAAATAGTTATAC 57.795 34.615 0.00 0.00 0.00 1.47
1629 1756 6.667848 TGATATGGACAAGATATACACCGGAT 59.332 38.462 9.46 0.00 0.00 4.18
1644 1771 9.022884 TGAAGTTGAAATTCATTGATATGGACA 57.977 29.630 3.72 0.00 31.86 4.02
1670 1797 1.143813 CCCCTTGGAGAGCCATATGT 58.856 55.000 1.24 0.00 45.46 2.29
1740 1867 1.135139 GCACTATGCTCGTCCTCAAGA 59.865 52.381 0.00 0.00 40.96 3.02
1803 1930 2.069273 CGTCCAGTCATCCACAAGAAC 58.931 52.381 0.00 0.00 0.00 3.01
1822 1949 2.608090 TGACGTCTAGATAGAGTGTGCG 59.392 50.000 17.92 0.00 32.01 5.34
1836 1963 1.620819 ACTGCCTTTCTCATGACGTCT 59.379 47.619 17.92 0.00 0.00 4.18
1844 1971 3.503363 CACTTTATGCACTGCCTTTCTCA 59.497 43.478 0.00 0.00 0.00 3.27
2006 2146 3.750371 AGGAATTGTTCATGGTCACGAA 58.250 40.909 0.00 0.00 0.00 3.85
2125 2277 9.696917 AAACTCAATTGTTTCCATTTCATAGTC 57.303 29.630 5.13 0.00 35.50 2.59
2629 2833 9.926158 GGATAGCCACTATGATATATCAGAATG 57.074 37.037 19.73 15.27 40.64 2.67
2693 2903 4.973168 ACAAACTCTGACCATAGAAGCAA 58.027 39.130 0.00 0.00 0.00 3.91
2811 3023 6.683974 AATAATGAATCCGGTTGAGAACTG 57.316 37.500 0.00 0.00 37.52 3.16
2818 3030 9.669353 CAGAAATCTAAATAATGAATCCGGTTG 57.331 33.333 0.00 0.00 0.00 3.77
3028 3593 3.297620 CCTTGCTGGCGCCTTTGT 61.298 61.111 29.70 0.00 34.43 2.83
3120 3685 8.257602 TGCAAGGTACATAGTATCCTATTTCA 57.742 34.615 0.00 0.00 31.29 2.69
3121 3686 8.368668 ACTGCAAGGTACATAGTATCCTATTTC 58.631 37.037 0.00 0.00 39.30 2.17
3124 3689 7.038941 GGAACTGCAAGGTACATAGTATCCTAT 60.039 40.741 0.00 0.00 31.38 2.57
3139 3704 3.624861 GTCATGATACTGGAACTGCAAGG 59.375 47.826 0.00 0.00 39.30 3.61
3141 3706 4.020307 TCAGTCATGATACTGGAACTGCAA 60.020 41.667 13.06 0.00 45.69 4.08
3142 3707 3.515104 TCAGTCATGATACTGGAACTGCA 59.485 43.478 13.06 0.00 45.69 4.41
3143 3708 4.128925 TCAGTCATGATACTGGAACTGC 57.871 45.455 13.06 0.00 45.69 4.40
3144 3709 5.007430 GCAATCAGTCATGATACTGGAACTG 59.993 44.000 13.06 7.46 45.67 3.16
3145 3710 5.121811 GCAATCAGTCATGATACTGGAACT 58.878 41.667 13.06 0.00 45.67 3.01
3146 3711 4.025396 CGCAATCAGTCATGATACTGGAAC 60.025 45.833 13.06 2.69 45.67 3.62
3147 3712 4.122046 CGCAATCAGTCATGATACTGGAA 58.878 43.478 13.06 0.00 45.67 3.53
3149 3714 3.492383 GTCGCAATCAGTCATGATACTGG 59.508 47.826 13.06 1.24 45.67 4.00
3150 3715 3.492383 GGTCGCAATCAGTCATGATACTG 59.508 47.826 7.99 7.99 45.67 2.74
3152 3717 2.472861 CGGTCGCAATCAGTCATGATAC 59.527 50.000 0.00 0.00 45.67 2.24
3153 3718 2.360801 TCGGTCGCAATCAGTCATGATA 59.639 45.455 0.00 0.00 45.67 2.15
3155 3720 0.530288 TCGGTCGCAATCAGTCATGA 59.470 50.000 0.00 0.00 40.50 3.07
3308 4034 4.021981 GCTAACCAAAGCAGAATTTCACCT 60.022 41.667 0.00 0.00 42.30 4.00
3310 4036 5.126396 AGCTAACCAAAGCAGAATTTCAC 57.874 39.130 0.00 0.00 45.30 3.18
3321 4047 7.104290 AGCTACCTAAGTAAAGCTAACCAAAG 58.896 38.462 0.00 0.00 30.46 2.77
3340 4069 8.443937 CAGTTTTACAGTTGAAATAGAGCTACC 58.556 37.037 0.00 0.00 0.00 3.18
3445 4182 6.530019 AAACAAAACACTCCTGAATCAACT 57.470 33.333 0.00 0.00 0.00 3.16
3466 4203 4.141041 TCCTGAATCAACCTCCCTGAAAAA 60.141 41.667 0.00 0.00 0.00 1.94
3538 4277 1.276421 TCAGCAACCAGAGCTTACCTC 59.724 52.381 0.00 0.00 41.14 3.85
3539 4278 1.352083 TCAGCAACCAGAGCTTACCT 58.648 50.000 0.00 0.00 41.14 3.08
3560 4299 6.072508 CCAATTAGTTTAGTTGCTGCTTGAGA 60.073 38.462 0.00 0.00 0.00 3.27
3777 4516 8.021396 CGGTGGTTTTATCCTCTTTTTCTAAAG 58.979 37.037 0.00 0.00 41.74 1.85
3787 4526 0.255033 GGCCGGTGGTTTTATCCTCT 59.745 55.000 1.90 0.00 0.00 3.69
3837 4576 8.435430 CCGTTCGTAGATGTAGACGTATTAATA 58.565 37.037 0.00 0.00 40.00 0.98
3879 4618 2.042435 CTCTTCTCCCCTCGCCCT 60.042 66.667 0.00 0.00 0.00 5.19
3923 4662 1.219393 CCTCTCCTCTTCCCAACGC 59.781 63.158 0.00 0.00 0.00 4.84
3926 4665 0.614979 CCGTCCTCTCCTCTTCCCAA 60.615 60.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.