Multiple sequence alignment - TraesCS4A01G493200

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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 TraesCS4A01G493200 chr4A 100.000 3623 0 0 1 3623 741815130 741811508 0.000000e+00 6691.0
1 TraesCS4A01G493200 chr4A 88.260 2828 273 26 1 2785 739652547 739655358 0.000000e+00 3328.0
2 TraesCS4A01G493200 chr4A 88.008 2827 275 25 1 2785 742057826 742060630 0.000000e+00 3284.0
3 TraesCS4A01G493200 chr4A 87.435 2881 273 37 2 2841 739868093 739870925 0.000000e+00 3232.0
4 TraesCS4A01G493200 chr4A 87.460 2847 254 48 44 2826 741483721 741480914 0.000000e+00 3184.0
5 TraesCS4A01G493200 chr4A 89.198 1546 145 8 1 1527 741590899 741592441 0.000000e+00 1910.0
6 TraesCS4A01G493200 chr4A 89.090 1549 145 9 1 1527 740018614 740017068 0.000000e+00 1903.0
7 TraesCS4A01G493200 chr4A 88.918 1552 146 12 1 1530 740579546 740581093 0.000000e+00 1890.0
8 TraesCS4A01G493200 chr4A 86.694 1210 124 16 1584 2773 742132887 742134079 0.000000e+00 1308.0
9 TraesCS4A01G493200 chr4A 86.667 1110 116 19 1757 2852 740939959 740941050 0.000000e+00 1201.0
10 TraesCS4A01G493200 chr4A 86.482 1117 120 12 1757 2852 740453193 740452087 0.000000e+00 1197.0
11 TraesCS4A01G493200 chr4A 86.597 1052 110 10 1792 2825 740016764 740015726 0.000000e+00 1133.0
12 TraesCS4A01G493200 chr4A 86.155 1069 117 14 1792 2841 740581393 740582449 0.000000e+00 1125.0
13 TraesCS4A01G493200 chr4A 84.986 1079 120 27 1792 2841 741592696 741593761 0.000000e+00 1057.0
14 TraesCS4A01G493200 chr4A 82.960 669 69 32 2968 3601 739870947 739871605 2.440000e-156 562.0
15 TraesCS4A01G493200 chr4A 84.096 415 35 13 1190 1601 742132398 742132784 4.420000e-99 372.0
16 TraesCS4A01G493200 chr4A 83.373 415 38 13 1190 1601 739735904 739736290 4.450000e-94 355.0
17 TraesCS4A01G493200 chr4A 83.249 197 19 7 2926 3108 740941147 740941343 6.220000e-38 169.0
18 TraesCS4A01G493200 chr4A 95.714 70 3 0 2988 3057 740015024 740014955 2.960000e-21 113.0
19 TraesCS4A01G493200 chr4A 85.526 76 8 2 1612 1687 740453336 740453264 3.880000e-10 76.8
20 TraesCS4A01G493200 chr7A 87.941 2894 272 34 1 2852 3207527 3204669 0.000000e+00 3339.0
21 TraesCS4A01G493200 chr7A 84.833 2901 318 49 1 2827 2117065 2114213 0.000000e+00 2808.0
22 TraesCS4A01G493200 chr7A 84.158 2891 334 52 1 2841 1995999 1993183 0.000000e+00 2687.0
23 TraesCS4A01G493200 chr7D 85.128 2703 251 78 550 3201 2563032 2560430 0.000000e+00 2625.0
24 TraesCS4A01G493200 chr7D 90.427 1546 124 9 1 1524 3632692 3631149 0.000000e+00 2013.0
25 TraesCS4A01G493200 chr7D 90.097 1545 131 7 1 1524 2357198 2355655 0.000000e+00 1986.0
26 TraesCS4A01G493200 chr7D 85.226 1550 197 17 1 1527 2609429 2607889 0.000000e+00 1565.0
27 TraesCS4A01G493200 chr7D 86.805 1061 101 19 1792 2827 3784670 3783624 0.000000e+00 1147.0
28 TraesCS4A01G493200 chr7D 86.181 1071 115 18 1792 2845 2607595 2606541 0.000000e+00 1127.0
29 TraesCS4A01G493200 chr7D 85.877 1055 98 25 1792 2827 2355378 2354356 0.000000e+00 1075.0
30 TraesCS4A01G493200 chr7D 92.469 478 34 2 3124 3601 2606260 2605785 0.000000e+00 682.0
31 TraesCS4A01G493200 chr7D 90.414 459 36 5 3145 3601 3237037 3236585 6.700000e-167 597.0
32 TraesCS4A01G493200 chr7D 90.196 459 37 5 3145 3601 3221828 3221376 3.120000e-165 592.0
33 TraesCS4A01G493200 chr7D 92.384 302 21 2 3302 3601 2560388 2560087 2.580000e-116 429.0
34 TraesCS4A01G493200 chr7D 89.333 225 19 5 2903 3123 3228229 3228006 9.910000e-71 278.0
35 TraesCS4A01G493200 chr7D 89.333 225 19 4 2903 3123 3243439 3243216 9.910000e-71 278.0
36 TraesCS4A01G493200 chrUn 90.591 457 35 5 3147 3601 325095615 325095165 1.860000e-167 599.0
37 TraesCS4A01G493200 chrUn 90.570 456 35 5 3145 3598 340806355 340806804 6.700000e-167 597.0
38 TraesCS4A01G493200 chrUn 89.778 225 18 5 2903 3123 328675037 328674814 2.130000e-72 283.0
39 TraesCS4A01G493200 chr5A 92.883 281 15 4 3212 3491 410810938 410810662 1.570000e-108 403.0
40 TraesCS4A01G493200 chr5A 92.883 281 15 4 3212 3491 464230997 464230721 1.570000e-108 403.0


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 TraesCS4A01G493200 chr4A 741811508 741815130 3622 True 6691.000000 6691 100.000000 1 3623 1 chr4A.!!$R2 3622
1 TraesCS4A01G493200 chr4A 739652547 739655358 2811 False 3328.000000 3328 88.260000 1 2785 1 chr4A.!!$F1 2784
2 TraesCS4A01G493200 chr4A 742057826 742060630 2804 False 3284.000000 3284 88.008000 1 2785 1 chr4A.!!$F3 2784
3 TraesCS4A01G493200 chr4A 741480914 741483721 2807 True 3184.000000 3184 87.460000 44 2826 1 chr4A.!!$R1 2782
4 TraesCS4A01G493200 chr4A 739868093 739871605 3512 False 1897.000000 3232 85.197500 2 3601 2 chr4A.!!$F4 3599
5 TraesCS4A01G493200 chr4A 740579546 740582449 2903 False 1507.500000 1890 87.536500 1 2841 2 chr4A.!!$F5 2840
6 TraesCS4A01G493200 chr4A 741590899 741593761 2862 False 1483.500000 1910 87.092000 1 2841 2 chr4A.!!$F7 2840
7 TraesCS4A01G493200 chr4A 740014955 740018614 3659 True 1049.666667 1903 90.467000 1 3057 3 chr4A.!!$R3 3056
8 TraesCS4A01G493200 chr4A 742132398 742134079 1681 False 840.000000 1308 85.395000 1190 2773 2 chr4A.!!$F8 1583
9 TraesCS4A01G493200 chr4A 740939959 740941343 1384 False 685.000000 1201 84.958000 1757 3108 2 chr4A.!!$F6 1351
10 TraesCS4A01G493200 chr4A 740452087 740453336 1249 True 636.900000 1197 86.004000 1612 2852 2 chr4A.!!$R4 1240
11 TraesCS4A01G493200 chr7A 3204669 3207527 2858 True 3339.000000 3339 87.941000 1 2852 1 chr7A.!!$R3 2851
12 TraesCS4A01G493200 chr7A 2114213 2117065 2852 True 2808.000000 2808 84.833000 1 2827 1 chr7A.!!$R2 2826
13 TraesCS4A01G493200 chr7A 1993183 1995999 2816 True 2687.000000 2687 84.158000 1 2841 1 chr7A.!!$R1 2840
14 TraesCS4A01G493200 chr7D 3631149 3632692 1543 True 2013.000000 2013 90.427000 1 1524 1 chr7D.!!$R5 1523
15 TraesCS4A01G493200 chr7D 2354356 2357198 2842 True 1530.500000 1986 87.987000 1 2827 2 chr7D.!!$R7 2826
16 TraesCS4A01G493200 chr7D 2560087 2563032 2945 True 1527.000000 2625 88.756000 550 3601 2 chr7D.!!$R8 3051
17 TraesCS4A01G493200 chr7D 3783624 3784670 1046 True 1147.000000 1147 86.805000 1792 2827 1 chr7D.!!$R6 1035
18 TraesCS4A01G493200 chr7D 2605785 2609429 3644 True 1124.666667 1565 87.958667 1 3601 3 chr7D.!!$R9 3600

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
324 326 1.277842 TGGCGCTTTCTCATAAGGTCA 59.722 47.619 7.64 0.0 0.00 4.02 F
1417 1467 0.179034 TGCAAAATTTGGGGGTGCAC 60.179 50.000 8.80 8.8 40.14 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2307 0.181350 GGGTCATAAGCCTCCCACTG 59.819 60.0 0.00 0.0 40.09 3.66 R
2818 3779 0.320771 ATTCCGTGGACACTCAGCAC 60.321 55.0 0.56 0.0 0.00 4.40 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
60 61 5.195940 CAGAGGGCTCCATAATCTTCAAAA 58.804 41.667 0.00 0.00 0.00 2.44
308 310 8.969267 GTAGATTATAATCGAAGGAATATGGCG 58.031 37.037 17.69 0.00 40.35 5.69
324 326 1.277842 TGGCGCTTTCTCATAAGGTCA 59.722 47.619 7.64 0.00 0.00 4.02
325 327 2.092968 TGGCGCTTTCTCATAAGGTCAT 60.093 45.455 7.64 0.00 0.00 3.06
326 328 2.545946 GGCGCTTTCTCATAAGGTCATC 59.454 50.000 7.64 0.00 0.00 2.92
327 329 3.198068 GCGCTTTCTCATAAGGTCATCA 58.802 45.455 0.00 0.00 0.00 3.07
330 332 5.111989 CGCTTTCTCATAAGGTCATCAGAA 58.888 41.667 0.00 0.00 0.00 3.02
343 363 7.649533 AGGTCATCAGAAATGCAAAATATGA 57.350 32.000 0.00 0.00 0.00 2.15
578 598 2.986479 CTGCATAAAACTTCCAAACCGC 59.014 45.455 0.00 0.00 0.00 5.68
650 670 2.311542 AGGCACTTATGTTCCATGGGAA 59.688 45.455 13.02 1.99 35.00 3.97
759 779 3.050275 GACCGAACCACCTGCAGC 61.050 66.667 8.66 0.00 0.00 5.25
905 925 2.365617 CCTCGGTTAGCTATGGTGATGT 59.634 50.000 0.00 0.00 0.00 3.06
909 929 3.560068 CGGTTAGCTATGGTGATGTTTCC 59.440 47.826 0.00 0.00 0.00 3.13
939 959 6.994421 AGATTTAAGTGGGTTTTGGACAAT 57.006 33.333 0.00 0.00 0.00 2.71
956 976 2.288666 CAATCTTACCCACCATGTCCG 58.711 52.381 0.00 0.00 0.00 4.79
1014 1046 7.599630 ATTTTGTGATATGCATTTGTGGAAC 57.400 32.000 3.54 0.00 37.35 3.62
1093 1125 7.992754 AATGATGTTGATATTCTTAGAGGGC 57.007 36.000 0.00 0.00 0.00 5.19
1126 1158 2.296190 ACTGCTCTGTCGTTGTATGTGA 59.704 45.455 0.00 0.00 0.00 3.58
1320 1370 6.072673 ACCAACGACTTGATCTTTATTTGGAC 60.073 38.462 15.17 0.00 35.54 4.02
1368 1418 5.009310 ACATGGTACTGCATTAATCAGCATG 59.991 40.000 12.51 12.51 40.42 4.06
1417 1467 0.179034 TGCAAAATTTGGGGGTGCAC 60.179 50.000 8.80 8.80 40.14 4.57
1431 1481 1.415659 GGTGCACCTGCTGATCTAGAT 59.584 52.381 29.12 4.47 42.66 1.98
1471 1521 4.149617 CGTAGTTAGTAATCATCCGAGCG 58.850 47.826 0.00 0.00 0.00 5.03
1507 1560 1.702401 TGCAACTGGTGGATTCTGGTA 59.298 47.619 0.00 0.00 0.00 3.25
1554 1625 0.727398 GCCGAGCTACATGGTTGTTC 59.273 55.000 0.00 0.00 37.28 3.18
1555 1626 1.943968 GCCGAGCTACATGGTTGTTCA 60.944 52.381 0.00 0.00 37.28 3.18
1556 1627 2.632377 CCGAGCTACATGGTTGTTCAT 58.368 47.619 0.00 0.00 37.28 2.57
1589 1780 7.880059 ACGTACTGAACCTAAATTAACTGTC 57.120 36.000 0.00 0.00 0.00 3.51
1640 1831 6.017605 GGTTGTTGTAATCTGCAGGATATCAG 60.018 42.308 15.13 0.00 33.71 2.90
1865 2173 3.775654 CCACCGCCTCTCCAGGTC 61.776 72.222 0.00 0.00 42.74 3.85
1866 2174 3.775654 CACCGCCTCTCCAGGTCC 61.776 72.222 0.00 0.00 42.74 4.46
1872 2180 0.389757 GCCTCTCCAGGTCCGAATAC 59.610 60.000 0.00 0.00 42.74 1.89
1905 2213 1.202604 TCCCTGAACCGTGACTTCAAC 60.203 52.381 0.00 0.00 0.00 3.18
1929 2237 1.078988 GGTTCGCAACGGGGACATA 60.079 57.895 0.00 0.00 35.48 2.29
1932 2240 2.549349 GGTTCGCAACGGGGACATATAT 60.549 50.000 0.00 0.00 35.48 0.86
1938 2246 1.183549 ACGGGGACATATATCGCCTC 58.816 55.000 14.51 0.25 46.89 4.70
1994 2305 2.246849 ACCTCTATTTCGGTAGTCCCCT 59.753 50.000 0.00 0.00 0.00 4.79
1996 2307 2.036089 CTCTATTTCGGTAGTCCCCTGC 59.964 54.545 0.00 0.00 0.00 4.85
2095 2421 2.571757 CGCTCGCTGTAGGAACCA 59.428 61.111 0.00 0.00 0.00 3.67
2100 2426 1.476891 CTCGCTGTAGGAACCAAGCTA 59.523 52.381 0.00 1.55 0.00 3.32
2168 2497 1.411246 CAATTCATGGACATGGCTGGG 59.589 52.381 11.98 0.00 39.24 4.45
2169 2498 0.632835 ATTCATGGACATGGCTGGGT 59.367 50.000 11.98 0.00 39.24 4.51
2170 2499 0.034186 TTCATGGACATGGCTGGGTC 60.034 55.000 11.98 0.00 39.24 4.46
2171 2500 1.206811 TCATGGACATGGCTGGGTCA 61.207 55.000 11.98 0.00 39.24 4.02
2172 2501 0.106369 CATGGACATGGCTGGGTCAT 60.106 55.000 0.00 0.00 35.74 3.06
2260 2598 1.065854 CGGGAGGCACTGATTCTTCTT 60.066 52.381 0.00 0.00 41.55 2.52
2265 2606 5.305644 GGGAGGCACTGATTCTTCTTATAGA 59.694 44.000 0.00 0.00 41.55 1.98
2292 2633 1.612950 AGCTCCGCAGAGATGTATGAG 59.387 52.381 0.00 0.00 43.39 2.90
2311 2652 1.825474 AGTCCGAGACACATACTTGGG 59.175 52.381 0.00 0.00 38.91 4.12
2335 2676 1.496429 CCCTTCCCAGCATGAATAGGT 59.504 52.381 0.00 0.00 39.69 3.08
2422 2766 1.808799 CGCGAGCTCTTGACATGCT 60.809 57.895 12.85 0.00 40.02 3.79
2463 2807 1.407656 GGCGGTCATGGAGGGTCATA 61.408 60.000 0.00 0.00 0.00 2.15
2466 2810 2.251818 CGGTCATGGAGGGTCATAGAT 58.748 52.381 0.00 0.00 0.00 1.98
2573 2932 8.551205 TGATTACAGCGAGAATAATGAATTGAC 58.449 33.333 0.00 0.00 0.00 3.18
2583 2953 6.318144 AGAATAATGAATTGACAGCTGGACAG 59.682 38.462 19.93 0.00 0.00 3.51
2617 2987 5.047802 CACTCTTGGAAAATTGCCTGTACAT 60.048 40.000 0.00 0.00 0.00 2.29
2634 3007 6.540189 CCTGTACATTCTAAGGACAAAGATGG 59.460 42.308 0.00 0.00 30.92 3.51
2635 3008 5.880332 TGTACATTCTAAGGACAAAGATGGC 59.120 40.000 0.00 0.00 0.00 4.40
2636 3009 5.184892 ACATTCTAAGGACAAAGATGGCT 57.815 39.130 0.00 0.00 33.84 4.75
2712 3085 7.468357 GCCTCCAATCATTTCTACTGATGAAAG 60.468 40.741 0.00 0.00 36.94 2.62
2818 3779 3.129502 CTGTGCGCAGTGATGGGG 61.130 66.667 19.30 0.00 37.92 4.96
2827 3788 0.675837 CAGTGATGGGGTGCTGAGTG 60.676 60.000 0.00 0.00 0.00 3.51
2828 3789 1.130054 AGTGATGGGGTGCTGAGTGT 61.130 55.000 0.00 0.00 0.00 3.55
2829 3790 0.674895 GTGATGGGGTGCTGAGTGTC 60.675 60.000 0.00 0.00 0.00 3.67
2852 3813 5.298276 TCCACGGAATAAAATACTGAATGCC 59.702 40.000 0.00 0.00 0.00 4.40
2868 3863 0.321298 TGCCGGTTTCAGACCTTAGC 60.321 55.000 1.90 0.00 46.92 3.09
2900 3896 7.667575 AACTGGACATCTATCTATCTGTTGT 57.332 36.000 0.00 0.00 0.00 3.32
2901 3897 8.768501 AACTGGACATCTATCTATCTGTTGTA 57.231 34.615 0.00 0.00 0.00 2.41
2905 3901 8.633561 TGGACATCTATCTATCTGTTGTACTTG 58.366 37.037 0.00 0.00 0.00 3.16
2906 3902 8.634444 GGACATCTATCTATCTGTTGTACTTGT 58.366 37.037 0.00 0.00 0.00 3.16
2908 3904 8.972127 ACATCTATCTATCTGTTGTACTTGTGT 58.028 33.333 0.00 0.00 0.00 3.72
2909 3905 9.809096 CATCTATCTATCTGTTGTACTTGTGTT 57.191 33.333 0.00 0.00 0.00 3.32
2913 3909 7.724305 TCTATCTGTTGTACTTGTGTTTTCC 57.276 36.000 0.00 0.00 0.00 3.13
2914 3910 7.506114 TCTATCTGTTGTACTTGTGTTTTCCT 58.494 34.615 0.00 0.00 0.00 3.36
2917 3913 7.311364 TCTGTTGTACTTGTGTTTTCCTTAC 57.689 36.000 0.00 0.00 0.00 2.34
2920 3916 6.433404 TGTTGTACTTGTGTTTTCCTTACCAA 59.567 34.615 0.00 0.00 0.00 3.67
2921 3917 7.122948 TGTTGTACTTGTGTTTTCCTTACCAAT 59.877 33.333 0.00 0.00 0.00 3.16
2923 3919 5.784578 ACTTGTGTTTTCCTTACCAATCC 57.215 39.130 0.00 0.00 0.00 3.01
2930 3926 7.726291 TGTGTTTTCCTTACCAATCCATTTCTA 59.274 33.333 0.00 0.00 0.00 2.10
2941 3943 7.043565 ACCAATCCATTTCTACATTTGCATTC 58.956 34.615 0.00 0.00 0.00 2.67
2942 3944 7.042950 CCAATCCATTTCTACATTTGCATTCA 58.957 34.615 0.00 0.00 0.00 2.57
3089 4206 2.360165 CCAGTTTGCTCCTTGATATGCC 59.640 50.000 0.00 0.00 0.00 4.40
3093 4210 5.357878 CAGTTTGCTCCTTGATATGCCTTTA 59.642 40.000 0.00 0.00 0.00 1.85
3117 4234 4.641396 TCAGTTGTGTTATCACCTTCTGG 58.359 43.478 14.32 0.00 43.26 3.86
3143 4300 4.634443 GGTACTGACACTGTGTTTCTGTTT 59.366 41.667 15.54 0.00 29.86 2.83
3156 4313 7.026562 TGTGTTTCTGTTTATATTTCCATGCG 58.973 34.615 0.00 0.00 0.00 4.73
3177 4334 2.358003 GCTGCTGGAACGTCTGCT 60.358 61.111 7.47 0.00 33.58 4.24
3184 4341 2.617274 GGAACGTCTGCTTGTGCCC 61.617 63.158 0.00 0.00 38.71 5.36
3258 4422 6.638610 AGAAGACATGTATGAGTTTGGAGAG 58.361 40.000 0.00 0.00 0.00 3.20
3259 4423 6.438741 AGAAGACATGTATGAGTTTGGAGAGA 59.561 38.462 0.00 0.00 0.00 3.10
3260 4424 6.219417 AGACATGTATGAGTTTGGAGAGAG 57.781 41.667 0.00 0.00 0.00 3.20
3331 4495 8.646004 TGTTTCAATTTGGATTCCAGAAATGTA 58.354 29.630 16.45 5.02 33.81 2.29
3339 4503 6.173339 TGGATTCCAGAAATGTAACTGTCTC 58.827 40.000 0.00 0.00 0.00 3.36
3380 4544 2.879026 TCTCTACCGTAGCATGCTACTG 59.121 50.000 40.41 37.37 44.80 2.74
3395 4560 6.744537 GCATGCTACTGTCAGTTATTTTTGAG 59.255 38.462 11.54 0.72 0.00 3.02
3614 4780 5.663795 CATGCAATGTGACACTACTATCC 57.336 43.478 7.20 0.00 40.20 2.59
3615 4781 4.137116 TGCAATGTGACACTACTATCCC 57.863 45.455 7.20 0.00 0.00 3.85
3616 4782 3.517500 TGCAATGTGACACTACTATCCCA 59.482 43.478 7.20 0.00 0.00 4.37
3617 4783 4.019771 TGCAATGTGACACTACTATCCCAA 60.020 41.667 7.20 0.00 0.00 4.12
3618 4784 4.332819 GCAATGTGACACTACTATCCCAAC 59.667 45.833 7.20 0.00 0.00 3.77
3619 4785 5.734720 CAATGTGACACTACTATCCCAACT 58.265 41.667 7.20 0.00 0.00 3.16
3620 4786 6.629515 GCAATGTGACACTACTATCCCAACTA 60.630 42.308 7.20 0.00 0.00 2.24
3621 4787 5.909621 TGTGACACTACTATCCCAACTAC 57.090 43.478 7.20 0.00 0.00 2.73
3622 4788 5.577100 TGTGACACTACTATCCCAACTACT 58.423 41.667 7.20 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 292 3.678056 AGCGCCATATTCCTTCGATTA 57.322 42.857 2.29 0.00 0.00 1.75
298 300 4.154918 CCTTATGAGAAAGCGCCATATTCC 59.845 45.833 2.29 0.00 0.00 3.01
308 310 6.992063 TTTCTGATGACCTTATGAGAAAGC 57.008 37.500 0.00 0.00 36.04 3.51
326 328 9.241317 GGTATCTTGTCATATTTTGCATTTCTG 57.759 33.333 0.00 0.00 0.00 3.02
327 329 8.970020 TGGTATCTTGTCATATTTTGCATTTCT 58.030 29.630 0.00 0.00 0.00 2.52
330 332 7.147863 TGCTGGTATCTTGTCATATTTTGCATT 60.148 33.333 0.00 0.00 0.00 3.56
343 363 4.910195 TCTGATGTTTGCTGGTATCTTGT 58.090 39.130 0.00 0.00 0.00 3.16
578 598 1.471119 AACATTGCAGCCCTCTCATG 58.529 50.000 0.00 0.00 0.00 3.07
609 629 5.368230 TGCCTCTTGGTGTATCCATAACATA 59.632 40.000 0.00 0.00 46.60 2.29
650 670 7.576236 GCAACAAGCGTGTGAGATATATAATT 58.424 34.615 5.91 0.00 38.27 1.40
759 779 3.127548 AGCGGTGTAGAAATGCAAAGATG 59.872 43.478 0.00 0.00 0.00 2.90
830 850 6.150976 CAGGCTGTCATGTTCATACCTTAAAA 59.849 38.462 6.28 0.00 0.00 1.52
905 925 4.217550 CCCACTTAAATCTTGCTTCGGAAA 59.782 41.667 0.00 0.00 0.00 3.13
909 929 4.766404 AACCCACTTAAATCTTGCTTCG 57.234 40.909 0.00 0.00 0.00 3.79
939 959 0.252330 TCCGGACATGGTGGGTAAGA 60.252 55.000 0.00 0.00 0.00 2.10
1014 1046 2.223340 GCATAGGTTGCCAAGTTCGATG 60.223 50.000 0.00 0.00 46.15 3.84
1093 1125 3.972971 GAGCAGTGAGGGCAGGCAG 62.973 68.421 0.00 0.00 0.00 4.85
1320 1370 1.238439 ATTGTTTCCACTGCTCACGG 58.762 50.000 0.00 0.00 0.00 4.94
1368 1418 1.152368 AAGGCCTGCCATATGCTCC 59.848 57.895 5.69 0.00 42.00 4.70
1417 1467 5.414144 TCGAGACATAATCTAGATCAGCAGG 59.586 44.000 5.51 0.00 38.00 4.85
1431 1481 1.754803 ACGCCAATCCTCGAGACATAA 59.245 47.619 15.71 0.00 0.00 1.90
1471 1521 5.050091 CCAGTTGCACGTCAATTATAGGATC 60.050 44.000 0.00 0.00 36.99 3.36
1507 1560 4.855340 CACTACCTTTTATCACCATGGGT 58.145 43.478 18.09 4.15 35.62 4.51
1554 1625 5.710984 AGGTTCAGTACGTAGAAGAACATG 58.289 41.667 24.27 0.00 40.11 3.21
1555 1626 5.979288 AGGTTCAGTACGTAGAAGAACAT 57.021 39.130 24.27 19.07 40.11 2.71
1556 1627 6.882610 TTAGGTTCAGTACGTAGAAGAACA 57.117 37.500 24.27 11.16 40.11 3.18
1557 1628 8.754230 AATTTAGGTTCAGTACGTAGAAGAAC 57.246 34.615 18.96 18.96 38.22 3.01
1589 1780 2.402305 GATAGCTTCGTCAGAGCATGG 58.598 52.381 0.00 0.00 0.00 3.66
1640 1831 2.047179 GGACTCCGGTGACCTTGC 60.047 66.667 16.29 0.00 0.00 4.01
1841 2149 3.672295 GAGAGGCGGTGGAGGCAAG 62.672 68.421 0.00 0.00 39.37 4.01
1866 2174 2.052237 GCAATGGCGCCGTATTCG 60.052 61.111 24.18 12.06 0.00 3.34
1905 2213 3.411351 CCGTTGCGAACCACCGAG 61.411 66.667 0.00 0.00 29.99 4.63
1929 2237 1.007271 CTTGCGACGGAGGCGATAT 60.007 57.895 0.00 0.00 0.00 1.63
1932 2240 3.001902 ATTCTTGCGACGGAGGCGA 62.002 57.895 0.00 0.00 0.00 5.54
1938 2246 2.046314 ACCCCATTCTTGCGACGG 60.046 61.111 0.00 0.00 0.00 4.79
1994 2305 0.253044 GTCATAAGCCTCCCACTGCA 59.747 55.000 0.00 0.00 0.00 4.41
1996 2307 0.181350 GGGTCATAAGCCTCCCACTG 59.819 60.000 0.00 0.00 40.09 3.66
2067 2381 4.537433 GCGAGCGCCTCCCAGATT 62.537 66.667 2.29 0.00 34.56 2.40
2095 2421 1.602377 GTTCGCAAACACCAGTAGCTT 59.398 47.619 0.00 0.00 35.36 3.74
2100 2426 0.745128 TTCGGTTCGCAAACACCAGT 60.745 50.000 0.00 0.00 37.10 4.00
2170 2499 1.268386 GGTGTTCATCGCATCAGCATG 60.268 52.381 0.00 0.00 42.27 4.06
2171 2500 1.019673 GGTGTTCATCGCATCAGCAT 58.980 50.000 0.00 0.00 42.27 3.79
2172 2501 1.026182 GGGTGTTCATCGCATCAGCA 61.026 55.000 0.00 0.00 42.27 4.41
2173 2502 1.718757 GGGGTGTTCATCGCATCAGC 61.719 60.000 0.00 0.00 37.42 4.26
2292 2633 1.739371 GCCCAAGTATGTGTCTCGGAC 60.739 57.143 0.00 0.00 0.00 4.79
2311 2652 2.757099 CATGCTGGGAAGGGGTGC 60.757 66.667 0.00 0.00 0.00 5.01
2335 2676 2.159099 CGCCAGAGCATTTGTACCTAGA 60.159 50.000 0.00 0.00 39.83 2.43
2422 2766 2.832129 GGTTCAGGTCATACTCCTCACA 59.168 50.000 0.00 0.00 32.37 3.58
2463 2807 2.703007 GAGCCCCTGAGACATGTTATCT 59.297 50.000 0.00 0.00 0.00 1.98
2466 2810 1.951209 TGAGCCCCTGAGACATGTTA 58.049 50.000 0.00 0.00 0.00 2.41
2583 2953 2.479566 TCCAAGAGTGATCCACTTGC 57.520 50.000 14.15 0.00 45.44 4.01
2617 2987 3.009473 AGCAGCCATCTTTGTCCTTAGAA 59.991 43.478 0.00 0.00 0.00 2.10
2634 3007 1.598701 GAAACCCATGTCCCAGCAGC 61.599 60.000 0.00 0.00 0.00 5.25
2635 3008 0.967380 GGAAACCCATGTCCCAGCAG 60.967 60.000 0.00 0.00 0.00 4.24
2636 3009 1.076549 GGAAACCCATGTCCCAGCA 59.923 57.895 0.00 0.00 0.00 4.41
2697 3070 4.993705 ACCACCCTTTCATCAGTAGAAA 57.006 40.909 0.00 0.00 34.16 2.52
2712 3085 1.909700 TGAATGAAGCTCAACCACCC 58.090 50.000 0.00 0.00 0.00 4.61
2809 3770 1.130054 ACACTCAGCACCCCATCACT 61.130 55.000 0.00 0.00 0.00 3.41
2818 3779 0.320771 ATTCCGTGGACACTCAGCAC 60.321 55.000 0.56 0.00 0.00 4.40
2827 3788 6.199393 GCATTCAGTATTTTATTCCGTGGAC 58.801 40.000 0.00 0.00 0.00 4.02
2828 3789 5.298276 GGCATTCAGTATTTTATTCCGTGGA 59.702 40.000 0.00 0.00 0.00 4.02
2829 3790 5.519722 GGCATTCAGTATTTTATTCCGTGG 58.480 41.667 0.00 0.00 0.00 4.94
2897 3893 7.201839 GGATTGGTAAGGAAAACACAAGTACAA 60.202 37.037 0.00 0.00 0.00 2.41
2900 3896 6.366340 TGGATTGGTAAGGAAAACACAAGTA 58.634 36.000 0.00 0.00 0.00 2.24
2901 3897 5.205056 TGGATTGGTAAGGAAAACACAAGT 58.795 37.500 0.00 0.00 0.00 3.16
2905 3901 6.993079 AGAAATGGATTGGTAAGGAAAACAC 58.007 36.000 0.00 0.00 0.00 3.32
2906 3902 7.726291 TGTAGAAATGGATTGGTAAGGAAAACA 59.274 33.333 0.00 0.00 0.00 2.83
2908 3904 8.893563 ATGTAGAAATGGATTGGTAAGGAAAA 57.106 30.769 0.00 0.00 0.00 2.29
2909 3905 8.893563 AATGTAGAAATGGATTGGTAAGGAAA 57.106 30.769 0.00 0.00 0.00 3.13
2913 3909 7.546358 TGCAAATGTAGAAATGGATTGGTAAG 58.454 34.615 0.00 0.00 0.00 2.34
2914 3910 7.473735 TGCAAATGTAGAAATGGATTGGTAA 57.526 32.000 0.00 0.00 0.00 2.85
2917 3913 7.042950 TGAATGCAAATGTAGAAATGGATTGG 58.957 34.615 0.00 0.00 34.57 3.16
2920 3916 7.649533 TCTGAATGCAAATGTAGAAATGGAT 57.350 32.000 0.00 0.00 0.00 3.41
2921 3917 7.339976 TGATCTGAATGCAAATGTAGAAATGGA 59.660 33.333 0.00 0.00 0.00 3.41
2923 3919 8.804743 GTTGATCTGAATGCAAATGTAGAAATG 58.195 33.333 0.00 0.00 0.00 2.32
2930 3926 4.219944 AGCTGTTGATCTGAATGCAAATGT 59.780 37.500 0.00 0.00 0.00 2.71
2941 3943 2.665537 GAGAACACGAGCTGTTGATCTG 59.334 50.000 8.27 0.00 43.60 2.90
2942 3944 2.353208 GGAGAACACGAGCTGTTGATCT 60.353 50.000 0.00 0.00 43.60 2.75
3080 4192 7.701539 ACACAACTGAATAAAGGCATATCAA 57.298 32.000 0.00 0.00 0.00 2.57
3117 4234 4.449068 CAGAAACACAGTGTCAGTACCATC 59.551 45.833 6.67 0.00 0.00 3.51
3156 4313 3.050275 GACGTTCCAGCAGCCACC 61.050 66.667 0.00 0.00 0.00 4.61
3177 4334 1.425066 AGACTTGAGAATGGGGCACAA 59.575 47.619 0.00 0.00 0.00 3.33
3184 4341 2.027377 ACTCCAGCAGACTTGAGAATGG 60.027 50.000 1.58 0.00 37.79 3.16
3331 4495 5.780793 AGTTGGGTCATAGTAAGAGACAGTT 59.219 40.000 0.00 0.00 34.04 3.16
3339 4503 9.968870 GTAGAGATAAAGTTGGGTCATAGTAAG 57.031 37.037 0.00 0.00 0.00 2.34
3395 4560 7.972277 ACACAAGATACAGATTGAATTTGATGC 59.028 33.333 2.46 0.00 0.00 3.91
3531 4697 5.248870 GATGAAATCCACGCTACCATTTT 57.751 39.130 0.00 0.00 37.38 1.82
3570 4736 3.059325 GCTTGTGAGTCTTGTGACACATC 60.059 47.826 9.55 4.53 43.49 3.06


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

AutoCloner maintained by Alex Coulton.