Multiple sequence alignment - TraesCS3B01G147500

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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 TraesCS3B01G147500 chr3B 100.000 3552 0 0 2007 5558 138500972 138504523 0.000000e+00 6560.0
1 TraesCS3B01G147500 chr3B 100.000 1706 0 0 1 1706 138498966 138500671 0.000000e+00 3151.0
2 TraesCS3B01G147500 chr3B 92.091 1669 92 15 3026 4668 138375582 138377236 0.000000e+00 2314.0
3 TraesCS3B01G147500 chr3B 93.733 734 36 5 1 732 138373084 138373809 0.000000e+00 1092.0
4 TraesCS3B01G147500 chr3B 93.153 555 36 2 2007 2560 138374633 138375186 0.000000e+00 813.0
5 TraesCS3B01G147500 chr3B 97.971 345 6 1 1086 1429 138374068 138374412 1.030000e-166 597.0
6 TraesCS3B01G147500 chr3B 84.416 616 65 15 4968 5558 138377704 138378313 1.340000e-160 577.0
7 TraesCS3B01G147500 chr3B 92.195 205 10 4 854 1054 138373869 138374071 9.110000e-73 285.0
8 TraesCS3B01G147500 chr3B 87.243 243 12 3 2626 2865 138375188 138375414 5.520000e-65 259.0
9 TraesCS3B01G147500 chr3B 89.320 206 16 2 1456 1661 138374406 138374605 2.570000e-63 254.0
10 TraesCS3B01G147500 chr3B 85.043 234 27 4 4675 4902 138377299 138377530 1.200000e-56 231.0
11 TraesCS3B01G147500 chr3B 75.232 646 67 48 2 565 137851001 137851635 2.610000e-53 220.0
12 TraesCS3B01G147500 chr3B 97.917 96 2 0 743 838 138373790 138373885 3.440000e-37 167.0
13 TraesCS3B01G147500 chr3B 93.939 99 6 0 2900 2998 138375409 138375507 3.470000e-32 150.0
14 TraesCS3B01G147500 chr3B 96.296 81 3 0 3033 3113 138375509 138375589 3.490000e-27 134.0
15 TraesCS3B01G147500 chr3D 95.730 2693 84 14 2007 4674 89214399 89217085 0.000000e+00 4307.0
16 TraesCS3B01G147500 chr3D 90.773 1333 80 14 2149 3455 89052120 89053435 0.000000e+00 1740.0
17 TraesCS3B01G147500 chr3D 94.048 840 30 11 1 838 89212670 89213491 0.000000e+00 1256.0
18 TraesCS3B01G147500 chr3D 91.190 840 25 18 1 838 89050108 89050900 0.000000e+00 1096.0
19 TraesCS3B01G147500 chr3D 90.488 820 60 6 3863 4666 89054589 89055406 0.000000e+00 1066.0
20 TraesCS3B01G147500 chr3D 90.028 722 28 8 854 1570 89213475 89214157 0.000000e+00 894.0
21 TraesCS3B01G147500 chr3D 91.681 577 25 4 854 1429 89050884 89051438 0.000000e+00 778.0
22 TraesCS3B01G147500 chr3D 86.364 616 56 16 4968 5557 89055978 89056591 0.000000e+00 647.0
23 TraesCS3B01G147500 chr3D 91.860 430 29 3 5135 5558 89247124 89247553 3.710000e-166 595.0
24 TraesCS3B01G147500 chr3D 93.624 298 18 1 1 297 89211014 89211311 1.420000e-120 444.0
25 TraesCS3B01G147500 chr3D 87.018 285 27 7 5040 5318 89246826 89247106 4.180000e-81 313.0
26 TraesCS3B01G147500 chr3D 85.159 283 34 7 4675 4953 89217152 89217430 3.280000e-72 283.0
27 TraesCS3B01G147500 chr3D 91.748 206 11 2 1456 1661 89051432 89051631 1.180000e-71 281.0
28 TraesCS3B01G147500 chr3D 83.793 290 28 13 4675 4959 89055470 89055745 1.990000e-64 257.0
29 TraesCS3B01G147500 chr3D 92.105 114 8 1 2052 2164 89051988 89052101 5.760000e-35 159.0
30 TraesCS3B01G147500 chr3D 76.602 359 41 21 372 729 88432883 88433199 2.070000e-34 158.0
31 TraesCS3B01G147500 chr3D 95.161 62 1 1 4968 5029 89055804 89055863 4.580000e-16 97.1
32 TraesCS3B01G147500 chr3A 95.551 2697 83 15 2007 4674 105947367 105950055 0.000000e+00 4281.0
33 TraesCS3B01G147500 chr3A 89.602 1231 71 21 2349 3560 105720142 105721334 0.000000e+00 1511.0
34 TraesCS3B01G147500 chr3A 94.293 841 34 7 1 838 105944642 105945471 0.000000e+00 1275.0
35 TraesCS3B01G147500 chr3A 91.310 840 33 16 1 838 105713040 105713841 0.000000e+00 1110.0
36 TraesCS3B01G147500 chr3A 94.181 653 21 7 921 1570 105946382 105947020 0.000000e+00 979.0
37 TraesCS3B01G147500 chr3A 88.112 715 55 6 3966 4666 105726885 105727583 0.000000e+00 822.0
38 TraesCS3B01G147500 chr3A 95.977 348 13 1 1083 1429 105714009 105714356 1.050000e-156 564.0
39 TraesCS3B01G147500 chr3A 87.469 407 28 6 5126 5530 105950955 105951340 1.100000e-121 448.0
40 TraesCS3B01G147500 chr3A 88.782 312 32 3 3963 4273 105726864 105726555 4.060000e-101 379.0
41 TraesCS3B01G147500 chr3A 83.215 423 46 13 4968 5365 105728151 105728573 1.140000e-96 364.0
42 TraesCS3B01G147500 chr3A 88.552 297 16 1 1 297 105942976 105943254 1.480000e-90 344.0
43 TraesCS3B01G147500 chr3A 83.290 389 39 13 4955 5318 105950560 105950947 8.920000e-88 335.0
44 TraesCS3B01G147500 chr3A 86.195 297 19 5 1 297 105711268 105711542 9.050000e-78 302.0
45 TraesCS3B01G147500 chr3A 91.304 207 11 3 1456 1661 105714350 105714550 5.480000e-70 276.0
46 TraesCS3B01G147500 chr3A 87.215 219 25 2 4675 4892 105950122 105950338 4.300000e-61 246.0
47 TraesCS3B01G147500 chr3A 93.082 159 11 0 3559 3717 105721496 105721654 3.350000e-57 233.0
48 TraesCS3B01G147500 chr3A 77.725 422 38 23 2 373 105027391 105026976 2.030000e-49 207.0
49 TraesCS3B01G147500 chr3A 93.939 99 6 0 3812 3910 105726459 105726557 3.470000e-32 150.0
50 TraesCS3B01G147500 chr3A 75.278 360 45 23 375 732 105026938 105026621 1.260000e-26 132.0
51 TraesCS3B01G147500 chr7A 82.596 339 55 4 5182 5518 662827199 662826863 4.210000e-76 296.0
52 TraesCS3B01G147500 chr7A 93.939 99 3 3 4828 4926 49234363 49234458 4.490000e-31 147.0
53 TraesCS3B01G147500 chr7A 93.878 98 3 3 4828 4924 49270659 49270754 1.610000e-30 145.0
54 TraesCS3B01G147500 chrUn 94.898 98 3 2 4840 4935 368328764 368328667 9.640000e-33 152.0
55 TraesCS3B01G147500 chrUn 78.279 244 42 9 1101 1341 300649680 300649445 4.490000e-31 147.0
56 TraesCS3B01G147500 chrUn 78.279 244 42 9 1101 1341 359000581 359000346 4.490000e-31 147.0
57 TraesCS3B01G147500 chrUn 78.279 244 42 9 1101 1341 380415185 380415420 4.490000e-31 147.0
58 TraesCS3B01G147500 chr2B 94.898 98 3 2 4840 4935 6002007 6002104 9.640000e-33 152.0
59 TraesCS3B01G147500 chr2B 94.898 98 3 2 4840 4935 6011312 6011409 9.640000e-33 152.0
60 TraesCS3B01G147500 chr5B 78.367 245 40 11 1101 1341 42948544 42948779 4.490000e-31 147.0
61 TraesCS3B01G147500 chr1A 76.159 302 29 24 3405 3699 86567780 86568045 9.780000e-23 119.0
62 TraesCS3B01G147500 chr6B 72.388 536 81 40 3045 3548 710692555 710692055 2.120000e-19 108.0
63 TraesCS3B01G147500 chr5A 88.235 68 8 0 3465 3532 703664914 703664847 1.280000e-11 82.4


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 TraesCS3B01G147500 chr3B 138498966 138504523 5557 False 4855.500000 6560 100.000000 1 5558 2 chr3B.!!$F3 5557
1 TraesCS3B01G147500 chr3B 138373084 138378313 5229 False 572.750000 2314 91.943083 1 5558 12 chr3B.!!$F2 5557
2 TraesCS3B01G147500 chr3B 137851001 137851635 634 False 220.000000 220 75.232000 2 565 1 chr3B.!!$F1 563
3 TraesCS3B01G147500 chr3D 89211014 89217430 6416 False 1436.800000 4307 91.717800 1 4953 5 chr3D.!!$F3 4952
4 TraesCS3B01G147500 chr3D 89050108 89056591 6483 False 680.122222 1740 90.367000 1 5557 9 chr3D.!!$F2 5556
5 TraesCS3B01G147500 chr3D 89246826 89247553 727 False 454.000000 595 89.439000 5040 5558 2 chr3D.!!$F4 518
6 TraesCS3B01G147500 chr3A 105942976 105951340 8364 False 1129.714286 4281 90.078714 1 5530 7 chr3A.!!$F4 5529
7 TraesCS3B01G147500 chr3A 105720142 105721654 1512 False 872.000000 1511 91.342000 2349 3717 2 chr3A.!!$F2 1368
8 TraesCS3B01G147500 chr3A 105711268 105714550 3282 False 563.000000 1110 91.196500 1 1661 4 chr3A.!!$F1 1660
9 TraesCS3B01G147500 chr3A 105726459 105728573 2114 False 445.333333 822 88.422000 3812 5365 3 chr3A.!!$F3 1553

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
841 2803 0.392060 ATAAACCAGCGTCGTTCCCC 60.392 55.000 0.00 0.00 0.00 4.81 F
1164 4010 0.179048 CATGTCTAGCGATTGCCCCA 60.179 55.000 0.00 0.00 44.31 4.96 F
2189 5267 2.027745 TCAGCTACAGAAAGAGCCAAGG 60.028 50.000 0.00 0.00 39.65 3.61 F
2359 5455 1.134670 GCTTCTAGCCAACTGGTCGAT 60.135 52.381 0.00 0.00 34.48 3.59 F
3325 6512 3.565482 TCTGTGAAGAAAGTGCACATTCC 59.435 43.478 26.46 15.34 41.21 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 5343 0.627469 AGGGGGTGCCTCATGGTTAT 60.627 55.0 0.00 0.00 35.27 1.89 R
2359 5455 0.766131 TTACTTTCGGGAACTGGGCA 59.234 50.0 0.00 0.00 33.92 5.36 R
3586 6941 0.041684 TCTCCCCATGCTCTGAGACA 59.958 55.0 9.28 6.56 0.00 3.41 R
4064 8335 0.462047 CCATTTCTCCCCTTCGACGG 60.462 60.0 0.00 0.00 0.00 4.79 R
4958 9596 0.843309 TCAGCACTTCAACTTGGGGA 59.157 50.0 0.00 0.00 0.00 4.81 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
483 2435 1.767681 GCCCAGATGACTGAGGAGAAT 59.232 52.381 0.00 0.00 46.03 2.40
591 2549 0.923358 AGGAGGAGTGAGACCGATCT 59.077 55.000 0.00 0.00 38.15 2.75
592 2550 2.128535 AGGAGGAGTGAGACCGATCTA 58.871 52.381 0.00 0.00 34.34 1.98
593 2551 2.714250 AGGAGGAGTGAGACCGATCTAT 59.286 50.000 0.00 0.00 34.34 1.98
594 2552 3.078837 GGAGGAGTGAGACCGATCTATC 58.921 54.545 0.00 0.00 34.34 2.08
684 2644 4.501743 GCAACAAAATAAAAAGGGGACGGA 60.502 41.667 0.00 0.00 0.00 4.69
836 2798 2.855963 CGTATGAATAAACCAGCGTCGT 59.144 45.455 0.00 0.00 0.00 4.34
837 2799 3.305094 CGTATGAATAAACCAGCGTCGTT 59.695 43.478 0.00 0.00 0.00 3.85
838 2800 4.547587 CGTATGAATAAACCAGCGTCGTTC 60.548 45.833 0.00 0.00 0.00 3.95
839 2801 2.070783 TGAATAAACCAGCGTCGTTCC 58.929 47.619 0.00 0.00 0.00 3.62
840 2802 1.395954 GAATAAACCAGCGTCGTTCCC 59.604 52.381 0.00 0.00 0.00 3.97
841 2803 0.392060 ATAAACCAGCGTCGTTCCCC 60.392 55.000 0.00 0.00 0.00 4.81
842 2804 2.453379 TAAACCAGCGTCGTTCCCCC 62.453 60.000 0.00 0.00 0.00 5.40
848 2810 2.973600 CGTCGTTCCCCCGCAAAA 60.974 61.111 0.00 0.00 0.00 2.44
849 2811 2.544698 CGTCGTTCCCCCGCAAAAA 61.545 57.895 0.00 0.00 0.00 1.94
1002 3845 5.482908 CTCAATGGCTTACAGTACAGACTT 58.517 41.667 0.00 0.00 31.73 3.01
1141 3987 2.591429 CCGTGCTGGTGCTTGTGA 60.591 61.111 0.00 0.00 40.48 3.58
1164 4010 0.179048 CATGTCTAGCGATTGCCCCA 60.179 55.000 0.00 0.00 44.31 4.96
1430 4281 2.554032 GGTCAACAACCCATGAAGTCAG 59.446 50.000 0.00 0.00 42.85 3.51
1461 4312 4.677182 ACCCTGCCTATTGATTTGAAGTT 58.323 39.130 0.00 0.00 0.00 2.66
1644 4637 4.767409 AGAAAGGGGCAAGTCAATTCTAAC 59.233 41.667 0.00 0.00 0.00 2.34
1666 4659 9.741168 CTAACGAGAAAGTATTACAAATGTGTG 57.259 33.333 0.00 0.00 38.82 3.82
1667 4660 6.599437 ACGAGAAAGTATTACAAATGTGTGC 58.401 36.000 0.00 0.00 38.82 4.57
1692 4735 2.533266 TTCAGTTGAGAGACAGCCAC 57.467 50.000 0.00 0.00 0.00 5.01
2122 5166 4.385825 TGATCACACAGTTTACCTTGTCC 58.614 43.478 0.00 0.00 0.00 4.02
2189 5267 2.027745 TCAGCTACAGAAAGAGCCAAGG 60.028 50.000 0.00 0.00 39.65 3.61
2359 5455 1.134670 GCTTCTAGCCAACTGGTCGAT 60.135 52.381 0.00 0.00 34.48 3.59
2432 5528 8.800332 GGAAGATATTAATGTGCAATCCAATCT 58.200 33.333 0.00 0.00 0.00 2.40
2462 5558 6.889722 CCTTTTCAGGTTTGGTCTGGATATTA 59.110 38.462 0.00 0.00 35.06 0.98
2598 5694 7.336931 GTCACCTCATTATGATGTGTACCTTTT 59.663 37.037 23.03 0.00 41.64 2.27
2624 5725 4.605968 CTGGACGATAGACAACATCTCAG 58.394 47.826 0.00 0.00 39.04 3.35
2768 5876 3.774066 TGTGTATGTTCTCAGATGCTCG 58.226 45.455 0.00 0.00 0.00 5.03
2780 5888 6.573434 TCTCAGATGCTCGCTTCTTTTTATA 58.427 36.000 4.74 0.00 0.00 0.98
2877 5985 9.871175 TGTGACCACTTAGTATCTATGGTAATA 57.129 33.333 1.62 0.00 43.73 0.98
3063 6177 7.670979 ACAATATTGATGCAGGCCTCATATTTA 59.329 33.333 22.16 3.16 0.00 1.40
3193 6377 8.581253 ACAAACCTTGAATCCCTCTATTTAAG 57.419 34.615 0.00 0.00 34.11 1.85
3194 6378 8.170730 ACAAACCTTGAATCCCTCTATTTAAGT 58.829 33.333 0.00 0.00 33.06 2.24
3254 6441 6.366315 TGTGTGTTACCTGTGAATAAACAC 57.634 37.500 9.15 9.15 46.32 3.32
3276 6463 8.718102 ACACATATGTAACTAAATGAGGTCAC 57.282 34.615 8.32 0.00 37.26 3.67
3325 6512 3.565482 TCTGTGAAGAAAGTGCACATTCC 59.435 43.478 26.46 15.34 41.21 3.01
3586 6941 4.757149 GTCTGGCTGTTGACATTCTTAGTT 59.243 41.667 0.00 0.00 33.75 2.24
3772 7129 8.147058 AGATCTGAGGTAATGACATTATCACAC 58.853 37.037 18.48 10.73 41.24 3.82
3773 7130 7.181569 TCTGAGGTAATGACATTATCACACA 57.818 36.000 18.48 13.82 41.24 3.72
3799 7733 6.422400 GTCTTACTTGTGAGAAGAAGTCCTTG 59.578 42.308 0.00 0.00 34.68 3.61
4064 8335 1.540267 TCAGTACGAGTTCTGTCCTGC 59.460 52.381 9.17 0.00 33.89 4.85
4290 8561 3.429085 CCATGCGTGCTAGATGTTTTTC 58.571 45.455 0.00 0.00 0.00 2.29
4525 8803 0.039798 CCTGCATGCATAATCGCACC 60.040 55.000 22.97 0.00 46.56 5.01
4535 8813 3.392882 CATAATCGCACCTGTCTGCATA 58.607 45.455 0.00 0.00 36.94 3.14
4573 8851 7.284489 GCAACTTTCTGGGTACATGGATAATTA 59.716 37.037 0.00 0.00 0.00 1.40
4575 8853 9.574516 AACTTTCTGGGTACATGGATAATTATC 57.425 33.333 15.88 15.88 0.00 1.75
4585 8875 9.899226 GTACATGGATAATTATCTTTTGGCTTC 57.101 33.333 21.80 5.73 33.28 3.86
4594 8884 8.552083 AATTATCTTTTGGCTTCAACATTTCC 57.448 30.769 0.00 0.00 0.00 3.13
4690 9048 0.249031 AACAACTTTGGCTCTTGCGC 60.249 50.000 0.00 0.00 40.82 6.09
4730 9093 4.646492 GGAAGTATGGTTGCAGGAATCATT 59.354 41.667 5.64 0.00 36.70 2.57
4738 9101 5.113502 GTTGCAGGAATCATTATGCTACC 57.886 43.478 9.25 0.00 38.09 3.18
4739 9102 4.712051 TGCAGGAATCATTATGCTACCT 57.288 40.909 8.20 0.00 39.42 3.08
4786 9150 8.467402 CTGGAGTAAATTCTACAGTACTGTTG 57.533 38.462 32.15 28.59 41.83 3.33
4787 9151 6.872020 TGGAGTAAATTCTACAGTACTGTTGC 59.128 38.462 32.15 16.91 41.83 4.17
4788 9152 7.097834 GGAGTAAATTCTACAGTACTGTTGCT 58.902 38.462 32.15 21.06 41.83 3.91
4789 9153 8.248945 GGAGTAAATTCTACAGTACTGTTGCTA 58.751 37.037 32.15 20.36 41.83 3.49
4790 9154 8.983307 AGTAAATTCTACAGTACTGTTGCTAC 57.017 34.615 32.15 23.64 41.83 3.58
4793 9157 8.983307 AAATTCTACAGTACTGTTGCTACTAC 57.017 34.615 32.15 0.00 41.83 2.73
4794 9158 5.791367 TCTACAGTACTGTTGCTACTACG 57.209 43.478 32.15 10.59 41.83 3.51
4795 9159 5.240891 TCTACAGTACTGTTGCTACTACGT 58.759 41.667 32.15 6.64 41.83 3.57
4796 9160 6.398095 TCTACAGTACTGTTGCTACTACGTA 58.602 40.000 32.15 9.90 41.83 3.57
4797 9161 5.947228 ACAGTACTGTTGCTACTACGTAA 57.053 39.130 22.95 0.00 41.83 3.18
4838 9202 9.988350 AAACTAAATTATATCTTTGCACGTCAG 57.012 29.630 0.00 0.00 0.00 3.51
4924 9454 2.219903 GCAACGGCGCACTTTTTATTTT 59.780 40.909 10.83 0.00 0.00 1.82
4925 9455 3.660646 GCAACGGCGCACTTTTTATTTTC 60.661 43.478 10.83 0.00 0.00 2.29
4936 9466 4.216902 ACTTTTTATTTTCGACCCCCTTCG 59.783 41.667 0.00 0.00 40.53 3.79
4939 9469 1.817357 ATTTTCGACCCCCTTCGTTC 58.183 50.000 0.00 0.00 40.07 3.95
4954 9484 5.001232 CCTTCGTTCTATTCCTTTGGTCAA 58.999 41.667 0.00 0.00 0.00 3.18
4958 9596 6.414732 TCGTTCTATTCCTTTGGTCAATGAT 58.585 36.000 0.00 0.00 0.00 2.45
4961 9599 5.694995 TCTATTCCTTTGGTCAATGATCCC 58.305 41.667 0.00 0.00 0.00 3.85
4963 9601 1.999295 TCCTTTGGTCAATGATCCCCA 59.001 47.619 0.00 0.00 0.00 4.96
4974 9711 1.909700 TGATCCCCAAGTTGAAGTGC 58.090 50.000 3.87 0.00 0.00 4.40
5034 9790 1.363744 CTTCTAAAGCTGGCCACGAG 58.636 55.000 0.00 0.00 0.00 4.18
5035 9791 0.036388 TTCTAAAGCTGGCCACGAGG 60.036 55.000 0.00 0.00 38.23 4.63
5036 9792 1.192146 TCTAAAGCTGGCCACGAGGT 61.192 55.000 0.00 0.00 37.19 3.85
5038 9794 0.605319 TAAAGCTGGCCACGAGGTTG 60.605 55.000 0.00 0.00 37.19 3.77
5056 9812 2.378445 TGGAGCAAACGAATCGATCA 57.622 45.000 10.55 0.00 0.00 2.92
5102 9858 5.192923 TGGTATGCCTACATCTTTTTAGGGT 59.807 40.000 0.16 0.00 37.74 4.34
5103 9859 6.387513 TGGTATGCCTACATCTTTTTAGGGTA 59.612 38.462 0.16 0.00 37.74 3.69
5104 9860 6.935208 GGTATGCCTACATCTTTTTAGGGTAG 59.065 42.308 1.45 0.00 37.74 3.18
5144 9906 7.708998 ACAAGTTCAACAAACCGTTACAATAT 58.291 30.769 0.00 0.00 38.76 1.28
5146 9908 6.595794 AGTTCAACAAACCGTTACAATATCG 58.404 36.000 0.00 0.00 38.76 2.92
5150 9912 8.923609 TCAACAAACCGTTACAATATCGTATA 57.076 30.769 0.00 0.00 35.52 1.47
5164 9926 9.314321 ACAATATCGTATAGTTGAAAGAACCAG 57.686 33.333 0.00 0.00 0.00 4.00
5197 9959 1.752683 AGCCTATACTATCGGCCTCG 58.247 55.000 0.00 0.00 44.84 4.63
5248 10210 6.635030 AATTTACACTCCAAAACTCTCCAC 57.365 37.500 0.00 0.00 0.00 4.02
5307 10269 2.548493 CCCACCTTGGTTTGCTTCAATG 60.548 50.000 0.00 0.00 35.17 2.82
5326 10469 4.308458 CCTTGACCACCGTGGCGA 62.308 66.667 17.99 9.24 42.67 5.54
5369 10512 5.586243 CCCGAGTGATATTCAAATCAAGTGT 59.414 40.000 0.00 0.00 37.61 3.55
5388 10531 1.810151 GTTAATGCCAAAGCCTCACGA 59.190 47.619 0.00 0.00 38.69 4.35
5393 10536 1.017387 GCCAAAGCCTCACGATAAGG 58.983 55.000 0.00 0.00 36.95 2.69
5463 10610 0.771127 AAGAGCCCAAGCAGTTACCA 59.229 50.000 0.00 0.00 43.56 3.25
5474 10621 2.846206 AGCAGTTACCAAGATGATCCCA 59.154 45.455 0.00 0.00 0.00 4.37
5486 10633 5.909621 AGATGATCCCAACAAATCACAAG 57.090 39.130 0.00 0.00 34.88 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 2055 2.668550 GTGCCCGTGTCCCTGAAC 60.669 66.667 0.00 0.00 0.00 3.18
199 2082 3.842925 GAAGGCGCACTTGTCCCCA 62.843 63.158 10.83 0.00 40.21 4.96
349 2265 2.221299 CCTTCTGGTCCCCGGTGAA 61.221 63.158 0.00 0.00 0.00 3.18
458 2410 1.129917 CTCAGTCATCTGGGCAGGAT 58.870 55.000 0.00 0.00 41.59 3.24
522 2474 1.666234 GATCCCGCTGATCTTCCGC 60.666 63.158 5.99 0.00 45.46 5.54
562 2517 1.001503 ACTCCTCCTGCCTCTCCTG 59.998 63.158 0.00 0.00 0.00 3.86
564 2519 1.000993 TCACTCCTCCTGCCTCTCC 59.999 63.158 0.00 0.00 0.00 3.71
565 2520 0.033601 TCTCACTCCTCCTGCCTCTC 60.034 60.000 0.00 0.00 0.00 3.20
566 2521 0.324275 GTCTCACTCCTCCTGCCTCT 60.324 60.000 0.00 0.00 0.00 3.69
567 2522 1.326951 GGTCTCACTCCTCCTGCCTC 61.327 65.000 0.00 0.00 0.00 4.70
568 2523 1.305718 GGTCTCACTCCTCCTGCCT 60.306 63.158 0.00 0.00 0.00 4.75
569 2524 2.716017 CGGTCTCACTCCTCCTGCC 61.716 68.421 0.00 0.00 0.00 4.85
595 2553 1.327690 TGGGTGGACGGCTGATAGTC 61.328 60.000 0.00 0.00 36.70 2.59
596 2554 1.305802 TGGGTGGACGGCTGATAGT 60.306 57.895 0.00 0.00 0.00 2.12
597 2555 1.144057 GTGGGTGGACGGCTGATAG 59.856 63.158 0.00 0.00 0.00 2.08
598 2556 2.363975 GGTGGGTGGACGGCTGATA 61.364 63.158 0.00 0.00 0.00 2.15
670 2630 4.855298 AGATCAATCCGTCCCCTTTTTA 57.145 40.909 0.00 0.00 0.00 1.52
684 2644 9.512588 AGTTATTCACTTTCAGACAAGATCAAT 57.487 29.630 0.00 0.00 27.32 2.57
739 2701 7.070696 ACACAGATAAATACCACCATGCTACTA 59.929 37.037 0.00 0.00 0.00 1.82
854 2816 2.255316 CAAACAACGACGCTGGTTTTT 58.745 42.857 0.00 0.00 31.57 1.94
855 2817 1.200484 ACAAACAACGACGCTGGTTTT 59.800 42.857 0.00 0.00 31.57 2.43
856 2818 0.806241 ACAAACAACGACGCTGGTTT 59.194 45.000 0.00 2.79 34.03 3.27
857 2819 0.806241 AACAAACAACGACGCTGGTT 59.194 45.000 2.97 0.00 0.00 3.67
858 2820 0.806241 AAACAAACAACGACGCTGGT 59.194 45.000 2.97 0.00 0.00 4.00
859 2821 2.741122 TAAACAAACAACGACGCTGG 57.259 45.000 2.97 0.00 0.00 4.85
860 2822 4.128554 AGATAAACAAACAACGACGCTG 57.871 40.909 0.00 0.00 0.00 5.18
861 2823 5.063060 GGATAGATAAACAAACAACGACGCT 59.937 40.000 0.00 0.00 0.00 5.07
862 2824 5.253335 GGATAGATAAACAAACAACGACGC 58.747 41.667 0.00 0.00 0.00 5.19
863 2825 5.220529 GGGGATAGATAAACAAACAACGACG 60.221 44.000 0.00 0.00 0.00 5.12
864 2826 5.644636 TGGGGATAGATAAACAAACAACGAC 59.355 40.000 0.00 0.00 0.00 4.34
865 2827 5.806818 TGGGGATAGATAAACAAACAACGA 58.193 37.500 0.00 0.00 0.00 3.85
866 2828 6.693315 ATGGGGATAGATAAACAAACAACG 57.307 37.500 0.00 0.00 0.00 4.10
1141 3987 1.293924 GCAATCGCTAGACATGCTGT 58.706 50.000 0.00 0.00 38.66 4.40
1164 4010 4.400961 GAAGCCAGAGCGCAGGGT 62.401 66.667 11.47 11.61 46.67 4.34
1461 4312 1.490490 AGAGGCAAGACTGTGACCAAA 59.510 47.619 0.00 0.00 0.00 3.28
1644 4637 6.021596 GGCACACATTTGTAATACTTTCTCG 58.978 40.000 0.00 0.00 33.30 4.04
2122 5166 7.988737 TCAGTGGCAATTGATAAGACTAAATG 58.011 34.615 10.34 0.00 0.00 2.32
2189 5267 9.989869 GGTAATTTACTTTCTCACTAGAATTGC 57.010 33.333 6.52 0.00 41.36 3.56
2265 5343 0.627469 AGGGGGTGCCTCATGGTTAT 60.627 55.000 0.00 0.00 35.27 1.89
2359 5455 0.766131 TTACTTTCGGGAACTGGGCA 59.234 50.000 0.00 0.00 33.92 5.36
2395 5491 9.135189 CACATTAATATCTTCCATGAAGGGAAA 57.865 33.333 0.00 0.00 45.87 3.13
2432 5528 4.647399 CAGACCAAACCTGAAAAGGGTAAA 59.353 41.667 0.00 0.00 35.83 2.01
2462 5558 4.261447 GGAGTTCAGTAATTTTGGTTGCGT 60.261 41.667 0.00 0.00 0.00 5.24
2598 5694 3.394674 TGTTGTCTATCGTCCAGCAAA 57.605 42.857 0.00 0.00 0.00 3.68
2608 5704 9.160496 AGAAAATCAACTGAGATGTTGTCTATC 57.840 33.333 7.17 3.76 45.26 2.08
2612 5712 7.802251 CAGAAGAAAATCAACTGAGATGTTGTC 59.198 37.037 7.17 0.00 45.26 3.18
2624 5725 5.239525 ACTGCCAGTACAGAAGAAAATCAAC 59.760 40.000 0.00 0.00 40.25 3.18
2756 5864 3.325293 AAAAGAAGCGAGCATCTGAGA 57.675 42.857 3.49 0.00 0.00 3.27
2768 5876 7.781056 TGGGATTTGTCCATATAAAAAGAAGC 58.219 34.615 0.00 0.00 0.00 3.86
2780 5888 5.480422 GGTAAGAAACTTGGGATTTGTCCAT 59.520 40.000 0.00 0.00 33.82 3.41
2877 5985 3.557898 GCTGTGATACGGATGATGGGAAT 60.558 47.826 0.00 0.00 0.00 3.01
2930 6044 5.220557 TCAATAACATGATGCAAGTCGTG 57.779 39.130 0.00 7.79 40.23 4.35
3063 6177 1.530771 CCTTGCTATCAGCCAGGCT 59.469 57.895 8.70 8.70 45.52 4.58
3254 6441 8.948631 ACTGTGACCTCATTTAGTTACATATG 57.051 34.615 0.00 0.00 32.79 1.78
3586 6941 0.041684 TCTCCCCATGCTCTGAGACA 59.958 55.000 9.28 6.56 0.00 3.41
3772 7129 5.923684 GGACTTCTTCTCACAAGTAAGACTG 59.076 44.000 0.00 0.00 32.83 3.51
3773 7130 5.836358 AGGACTTCTTCTCACAAGTAAGACT 59.164 40.000 0.00 0.00 32.83 3.24
3844 7827 8.391106 GTCAAGGAAACTACATATCAATGTCAC 58.609 37.037 0.00 0.00 45.28 3.67
4064 8335 0.462047 CCATTTCTCCCCTTCGACGG 60.462 60.000 0.00 0.00 0.00 4.79
4209 8480 6.211184 TGCCAATCATAAACACAGGATTCTTT 59.789 34.615 0.00 0.00 26.90 2.52
4290 8561 1.139163 GGGCAATGCACGAAAACAAG 58.861 50.000 7.79 0.00 0.00 3.16
4573 8851 5.549742 TGGAAATGTTGAAGCCAAAAGAT 57.450 34.783 0.00 0.00 33.49 2.40
4575 8853 4.025813 CGTTGGAAATGTTGAAGCCAAAAG 60.026 41.667 0.00 0.00 40.02 2.27
4585 8875 2.098280 TCCACACACGTTGGAAATGTTG 59.902 45.455 4.96 0.00 45.42 3.33
4594 8884 3.649073 TCATAAGAGTCCACACACGTTG 58.351 45.455 0.00 0.00 0.00 4.10
4769 9133 7.094463 ACGTAGTAGCAACAGTACTGTAGAATT 60.094 37.037 28.13 10.13 41.21 2.17
4778 9142 8.728088 TTAAACTTACGTAGTAGCAACAGTAC 57.272 34.615 0.00 0.00 46.93 2.73
4779 9143 8.023128 CCTTAAACTTACGTAGTAGCAACAGTA 58.977 37.037 0.00 0.00 46.93 2.74
4780 9144 6.865205 CCTTAAACTTACGTAGTAGCAACAGT 59.135 38.462 0.00 0.00 46.93 3.55
4781 9145 6.865205 ACCTTAAACTTACGTAGTAGCAACAG 59.135 38.462 0.00 0.00 46.93 3.16
4813 9177 9.378551 TCTGACGTGCAAAGATATAATTTAGTT 57.621 29.630 0.00 0.00 0.00 2.24
4815 9179 9.035607 ACTCTGACGTGCAAAGATATAATTTAG 57.964 33.333 0.00 0.00 0.00 1.85
4822 9186 3.119459 ACGACTCTGACGTGCAAAGATAT 60.119 43.478 0.00 0.00 42.37 1.63
4826 9190 1.071239 CAACGACTCTGACGTGCAAAG 60.071 52.381 0.00 0.00 43.16 2.77
4831 9195 2.682952 ACTACAACGACTCTGACGTG 57.317 50.000 0.00 0.00 43.16 4.49
4833 9197 5.491092 CACTATACTACAACGACTCTGACG 58.509 45.833 0.00 0.00 0.00 4.35
4835 9199 5.494724 ACCACTATACTACAACGACTCTGA 58.505 41.667 0.00 0.00 0.00 3.27
4838 9202 7.313951 ACTTACCACTATACTACAACGACTC 57.686 40.000 0.00 0.00 0.00 3.36
4912 9362 5.462530 AAGGGGGTCGAAAATAAAAAGTG 57.537 39.130 0.00 0.00 0.00 3.16
4924 9454 1.753073 GAATAGAACGAAGGGGGTCGA 59.247 52.381 1.02 0.00 43.86 4.20
4925 9455 1.202498 GGAATAGAACGAAGGGGGTCG 60.202 57.143 0.00 0.00 46.54 4.79
4936 9466 6.039829 GGGATCATTGACCAAAGGAATAGAAC 59.960 42.308 0.00 0.00 31.22 3.01
4939 9469 4.829492 GGGGATCATTGACCAAAGGAATAG 59.171 45.833 0.00 0.00 31.22 1.73
4954 9484 2.042162 AGCACTTCAACTTGGGGATCAT 59.958 45.455 0.00 0.00 0.00 2.45
4958 9596 0.843309 TCAGCACTTCAACTTGGGGA 59.157 50.000 0.00 0.00 0.00 4.81
4961 9599 2.301346 AGGTTCAGCACTTCAACTTGG 58.699 47.619 0.00 0.00 0.00 3.61
4963 9601 3.891049 AGAAGGTTCAGCACTTCAACTT 58.109 40.909 7.12 0.00 44.20 2.66
4995 9733 1.607148 GGTTCAACACTTTTCCCCTCG 59.393 52.381 0.00 0.00 0.00 4.63
5034 9790 1.153353 TCGATTCGTTTGCTCCAACC 58.847 50.000 5.89 0.00 0.00 3.77
5035 9791 2.415168 TGATCGATTCGTTTGCTCCAAC 59.585 45.455 5.89 0.00 0.00 3.77
5036 9792 2.694213 TGATCGATTCGTTTGCTCCAA 58.306 42.857 5.89 0.00 0.00 3.53
5038 9794 3.546815 CCAATGATCGATTCGTTTGCTCC 60.547 47.826 5.89 0.00 30.93 4.70
5056 9812 2.003548 GGGGGCTGACTCTCCCAAT 61.004 63.158 0.00 0.00 44.43 3.16
5078 9834 5.192923 ACCCTAAAAAGATGTAGGCATACCA 59.807 40.000 6.00 0.00 39.06 3.25
5080 9836 6.935208 CCTACCCTAAAAAGATGTAGGCATAC 59.065 42.308 0.53 0.53 41.35 2.39
5115 9875 6.700520 TGTAACGGTTTGTTGAACTTGTTTTT 59.299 30.769 0.00 0.00 42.01 1.94
5116 9876 6.214399 TGTAACGGTTTGTTGAACTTGTTTT 58.786 32.000 0.00 0.00 42.01 2.43
5119 9879 5.373981 TTGTAACGGTTTGTTGAACTTGT 57.626 34.783 0.00 0.00 42.01 3.16
5133 9894 9.454585 TCTTTCAACTATACGATATTGTAACGG 57.545 33.333 6.91 3.56 0.00 4.44
5144 9906 6.335471 TGTCTGGTTCTTTCAACTATACGA 57.665 37.500 0.00 0.00 0.00 3.43
5146 9908 6.183360 GGCATGTCTGGTTCTTTCAACTATAC 60.183 42.308 0.00 0.00 0.00 1.47
5150 9912 2.887152 GGCATGTCTGGTTCTTTCAACT 59.113 45.455 0.00 0.00 0.00 3.16
5197 9959 5.048573 ACACGAGAGAAGGTCTAGAAACTTC 60.049 44.000 22.03 22.03 40.59 3.01
5276 10238 1.269012 CCAAGGTGGGAAACATGCAT 58.731 50.000 0.00 0.00 32.67 3.96
5307 10269 2.668550 GCCACGGTGGTCAAGGAC 60.669 66.667 26.86 6.02 40.46 3.85
5326 10469 5.989477 TCGGGTGATTATTTCTTCAGACAT 58.011 37.500 0.00 0.00 0.00 3.06
5369 10512 2.192664 TCGTGAGGCTTTGGCATTAA 57.807 45.000 0.00 0.00 40.87 1.40
5388 10531 5.560724 TCAACTTTAGAAGCACTGCCTTAT 58.439 37.500 0.00 0.00 0.00 1.73
5393 10536 5.862924 TGTATCAACTTTAGAAGCACTGC 57.137 39.130 0.00 0.00 0.00 4.40
5463 10610 5.337009 GCTTGTGATTTGTTGGGATCATCTT 60.337 40.000 0.00 0.00 35.01 2.40
5474 10621 0.670162 AGCAGCGCTTGTGATTTGTT 59.330 45.000 7.50 0.00 33.89 2.83
5486 10633 1.288752 GGAGATAGAGGAGCAGCGC 59.711 63.158 0.00 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.