Multiple sequence alignment - TraesCS3A01G360000

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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 TraesCS3A01G360000 chr3A 100.000 3856 0 0 1 3856 608092403 608096258 0.000000e+00 7121.0
1 TraesCS3A01G360000 chr5A 91.935 3844 254 20 41 3854 234433145 234436962 0.000000e+00 5330.0
2 TraesCS3A01G360000 chr5A 86.869 1980 207 29 40 1981 524226215 524228179 0.000000e+00 2167.0
3 TraesCS3A01G360000 chr5D 81.073 1659 265 27 545 2169 520992967 520991324 0.000000e+00 1279.0
4 TraesCS3A01G360000 chr5D 76.428 2049 383 65 187 2177 288132007 288130001 0.000000e+00 1016.0
5 TraesCS3A01G360000 chr5D 76.834 1649 310 50 187 1786 504989815 504988190 0.000000e+00 863.0
6 TraesCS3A01G360000 chr5D 86.184 304 42 0 2261 2564 520991227 520990924 2.870000e-86 329.0
7 TraesCS3A01G360000 chr5D 81.590 239 44 0 2729 2967 288129481 288129243 8.450000e-47 198.0
8 TraesCS3A01G360000 chr5D 73.047 256 65 3 1913 2166 482848741 482848488 1.910000e-13 87.9
9 TraesCS3A01G360000 chr1D 81.039 1656 266 26 545 2166 404199341 404200982 0.000000e+00 1275.0
10 TraesCS3A01G360000 chr1D 80.841 856 135 13 1336 2169 33573639 33572791 0.000000e+00 645.0
11 TraesCS3A01G360000 chr1D 83.833 600 90 5 593 1187 33574661 33574064 7.230000e-157 564.0
12 TraesCS3A01G360000 chr1D 86.207 290 39 1 2272 2561 404201093 404201381 2.890000e-81 313.0
13 TraesCS3A01G360000 chr1D 84.868 304 46 0 2261 2564 33572694 33572391 1.350000e-79 307.0
14 TraesCS3A01G360000 chr3D 80.941 1658 269 28 545 2169 584756438 584754795 0.000000e+00 1267.0
15 TraesCS3A01G360000 chr3D 80.380 1264 193 30 1336 2561 520187535 520186289 0.000000e+00 909.0
16 TraesCS3A01G360000 chr3D 83.179 648 102 5 545 1187 520188550 520187905 1.540000e-163 586.0
17 TraesCS3A01G360000 chr3D 85.526 304 44 0 2261 2564 584754697 584754394 6.220000e-83 318.0
18 TraesCS3A01G360000 chr3D 78.750 240 32 10 2736 2974 18930964 18931185 4.020000e-30 143.0
19 TraesCS3A01G360000 chr2A 79.194 1663 291 37 542 2166 57900248 57901893 0.000000e+00 1103.0
20 TraesCS3A01G360000 chr2A 82.721 544 79 13 179 714 673994178 673993642 1.620000e-128 470.0
21 TraesCS3A01G360000 chrUn 79.146 1640 287 36 542 2143 313445476 313443854 0.000000e+00 1083.0
22 TraesCS3A01G360000 chrUn 80.439 501 80 15 2017 2505 344774552 344775046 2.190000e-97 366.0
23 TraesCS3A01G360000 chr7B 82.906 702 111 7 532 1228 653889159 653888462 1.180000e-174 623.0
24 TraesCS3A01G360000 chr7B 80.570 561 91 16 2017 2565 693680440 693679886 2.140000e-112 416.0
25 TraesCS3A01G360000 chr6D 77.396 960 148 39 2017 2964 15170695 15171597 1.240000e-139 507.0
26 TraesCS3A01G360000 chr7A 83.364 541 78 11 179 714 65571879 65571346 1.240000e-134 490.0
27 TraesCS3A01G360000 chr7A 80.776 541 78 13 179 714 549016844 549016325 2.160000e-107 399.0
28 TraesCS3A01G360000 chr7A 81.876 469 62 7 1338 1786 79120817 79120352 1.310000e-99 374.0
29 TraesCS3A01G360000 chr1A 82.625 541 82 11 179 714 535410207 535409674 5.830000e-128 468.0
30 TraesCS3A01G360000 chr1A 86.364 66 9 0 2884 2949 496152274 496152339 5.340000e-09 73.1
31 TraesCS3A01G360000 chr4B 81.296 540 83 12 179 714 428701546 428702071 4.610000e-114 422.0
32 TraesCS3A01G360000 chr4B 79.825 228 43 2 233 457 22986495 22986268 3.080000e-36 163.0
33 TraesCS3A01G360000 chr3B 82.942 469 61 8 1336 1786 761922163 761921696 4.640000e-109 405.0
34 TraesCS3A01G360000 chr4A 82.833 466 60 9 1339 1786 661031875 661031412 2.160000e-107 399.0
35 TraesCS3A01G360000 chr4A 78.947 247 45 5 1925 2166 706715836 706715592 1.110000e-35 161.0
36 TraesCS3A01G360000 chr2D 74.342 304 62 11 1873 2171 644714063 644713771 8.750000e-22 115.0
37 TraesCS3A01G360000 chr6A 83.333 114 17 2 345 457 12615815 12615703 1.890000e-18 104.0
38 TraesCS3A01G360000 chr7D 80.000 135 25 2 2825 2958 608342566 608342433 8.820000e-17 99.0


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 TraesCS3A01G360000 chr3A 608092403 608096258 3855 False 7121.000000 7121 100.000000 1 3856 1 chr3A.!!$F1 3855
1 TraesCS3A01G360000 chr5A 234433145 234436962 3817 False 5330.000000 5330 91.935000 41 3854 1 chr5A.!!$F1 3813
2 TraesCS3A01G360000 chr5A 524226215 524228179 1964 False 2167.000000 2167 86.869000 40 1981 1 chr5A.!!$F2 1941
3 TraesCS3A01G360000 chr5D 504988190 504989815 1625 True 863.000000 863 76.834000 187 1786 1 chr5D.!!$R2 1599
4 TraesCS3A01G360000 chr5D 520990924 520992967 2043 True 804.000000 1279 83.628500 545 2564 2 chr5D.!!$R4 2019
5 TraesCS3A01G360000 chr5D 288129243 288132007 2764 True 607.000000 1016 79.009000 187 2967 2 chr5D.!!$R3 2780
6 TraesCS3A01G360000 chr1D 404199341 404201381 2040 False 794.000000 1275 83.623000 545 2561 2 chr1D.!!$F1 2016
7 TraesCS3A01G360000 chr1D 33572391 33574661 2270 True 505.333333 645 83.180667 593 2564 3 chr1D.!!$R1 1971
8 TraesCS3A01G360000 chr3D 584754394 584756438 2044 True 792.500000 1267 83.233500 545 2564 2 chr3D.!!$R2 2019
9 TraesCS3A01G360000 chr3D 520186289 520188550 2261 True 747.500000 909 81.779500 545 2561 2 chr3D.!!$R1 2016
10 TraesCS3A01G360000 chr2A 57900248 57901893 1645 False 1103.000000 1103 79.194000 542 2166 1 chr2A.!!$F1 1624
11 TraesCS3A01G360000 chr2A 673993642 673994178 536 True 470.000000 470 82.721000 179 714 1 chr2A.!!$R1 535
12 TraesCS3A01G360000 chrUn 313443854 313445476 1622 True 1083.000000 1083 79.146000 542 2143 1 chrUn.!!$R1 1601
13 TraesCS3A01G360000 chr7B 653888462 653889159 697 True 623.000000 623 82.906000 532 1228 1 chr7B.!!$R1 696
14 TraesCS3A01G360000 chr7B 693679886 693680440 554 True 416.000000 416 80.570000 2017 2565 1 chr7B.!!$R2 548
15 TraesCS3A01G360000 chr6D 15170695 15171597 902 False 507.000000 507 77.396000 2017 2964 1 chr6D.!!$F1 947
16 TraesCS3A01G360000 chr7A 65571346 65571879 533 True 490.000000 490 83.364000 179 714 1 chr7A.!!$R1 535
17 TraesCS3A01G360000 chr7A 549016325 549016844 519 True 399.000000 399 80.776000 179 714 1 chr7A.!!$R3 535
18 TraesCS3A01G360000 chr1A 535409674 535410207 533 True 468.000000 468 82.625000 179 714 1 chr1A.!!$R1 535
19 TraesCS3A01G360000 chr4B 428701546 428702071 525 False 422.000000 422 81.296000 179 714 1 chr4B.!!$F1 535

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
203 212 0.249489 GACAGAGTGCGAGTTGGTGT 60.249 55.0 0.0 0.0 0.0 4.16 F
2093 2438 0.818040 AAGGTCACGGTGGTTGAAGC 60.818 55.0 8.5 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2464 0.322322 CCCATGTGTGCAAATTGCCT 59.678 50.0 15.98 0.0 44.23 4.75 R
3759 4180 0.038599 ATGCCCACATGCAGAGACAA 59.961 50.0 0.00 0.0 45.93 3.18 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
57 58 7.445402 AGCTTGTTATATTGGTAGGTTGCATAG 59.555 37.037 0.00 0.00 0.00 2.23
92 93 8.671921 GTGGATATATAATTTGACCTGCTGATG 58.328 37.037 0.00 0.00 0.00 3.07
116 118 9.631257 ATGGTTAAGATCACAATTGATGACATA 57.369 29.630 13.59 4.40 42.95 2.29
167 176 3.774066 TGCTAGACTCACATGTCATTCG 58.226 45.455 0.00 0.00 39.27 3.34
170 179 4.032217 GCTAGACTCACATGTCATTCGTTG 59.968 45.833 0.00 0.00 39.27 4.10
172 181 2.416547 GACTCACATGTCATTCGTTGGG 59.583 50.000 0.00 0.00 36.97 4.12
203 212 0.249489 GACAGAGTGCGAGTTGGTGT 60.249 55.000 0.00 0.00 0.00 4.16
261 270 1.202580 ACAGCGCTTGAGAAGACTGTT 60.203 47.619 7.50 0.00 41.65 3.16
464 473 1.129811 CGGATGTGCGGTAAGGAAAAC 59.870 52.381 0.00 0.00 0.00 2.43
489 498 7.767250 CATAGACTGGAAGATCTGTACCATA 57.233 40.000 14.19 7.27 37.43 2.74
563 603 2.893489 GTTTGATTTGTCAGGGGAAGCT 59.107 45.455 0.00 0.00 0.00 3.74
580 620 7.454694 AGGGGAAGCTAATTGTTGAAAATACTT 59.545 33.333 0.00 0.00 0.00 2.24
586 626 8.088365 AGCTAATTGTTGAAAATACTTGTTCCC 58.912 33.333 0.00 0.00 0.00 3.97
614 654 3.947196 TGTGAATGCCCATCACTCATAAC 59.053 43.478 12.86 0.00 45.81 1.89
904 945 3.257393 GAGCAATCAGAAGACGATGTGT 58.743 45.455 0.00 0.00 0.00 3.72
916 957 5.499139 AGACGATGTGTGAAAAACAATGT 57.501 34.783 0.00 0.00 37.78 2.71
931 972 9.696917 GAAAAACAATGTAAGTCTTCCATGATT 57.303 29.630 0.00 0.00 0.00 2.57
961 1002 6.469410 TCAAACGATCCACAGTTTACCTATT 58.531 36.000 0.00 0.00 38.37 1.73
985 1026 2.479566 TCAAGCAGACAATGAGGGTC 57.520 50.000 0.00 0.00 35.50 4.46
986 1027 1.699083 TCAAGCAGACAATGAGGGTCA 59.301 47.619 0.00 0.00 37.74 4.02
1058 1099 5.946377 ACTTCTTTGGGGATGTCATTACTTC 59.054 40.000 0.00 0.00 0.00 3.01
1094 1135 4.216042 CAGGACAAACTTGTATGACATGCA 59.784 41.667 1.64 1.64 42.43 3.96
1113 1154 2.805671 GCACTTTGGGTTATTTGTTGGC 59.194 45.455 0.00 0.00 0.00 4.52
1323 1648 4.102524 AGCCGGAAATACTAATGACCATCA 59.897 41.667 5.05 0.00 0.00 3.07
1445 1771 2.912956 AGGCAAAGGAGTCATTAGGTCA 59.087 45.455 0.00 0.00 0.00 4.02
1748 2093 7.723616 TGAGTTTGATTTTTGACAGGGAATCTA 59.276 33.333 8.19 0.99 31.48 1.98
1752 2097 7.466746 TGATTTTTGACAGGGAATCTAAAGG 57.533 36.000 8.19 0.00 31.48 3.11
1809 2154 8.532977 AGGGTTGAATGAAATACAAATTTTCG 57.467 30.769 0.00 0.00 35.41 3.46
1865 2210 8.622948 AGCTAACTAATTACTTATTGATGCCC 57.377 34.615 0.00 0.00 0.00 5.36
1983 2328 6.486253 CACATATTATATGAGTGTGGTGCC 57.514 41.667 17.95 0.00 37.20 5.01
2015 2360 4.380339 GGAAGAGATTGAGAAAGGCAAAGC 60.380 45.833 0.00 0.00 0.00 3.51
2093 2438 0.818040 AAGGTCACGGTGGTTGAAGC 60.818 55.000 8.50 0.00 0.00 3.86
2119 2464 3.141398 GAGGAGTTTGATTGTGAGTGCA 58.859 45.455 0.00 0.00 0.00 4.57
2185 2532 1.737838 AATGTACATGTCCTGGCACG 58.262 50.000 9.63 0.00 0.00 5.34
2194 2541 2.046023 CCTGGCACGGAGAATGCA 60.046 61.111 0.00 0.00 45.27 3.96
2200 2547 0.804364 GCACGGAGAATGCACATTGA 59.196 50.000 0.00 0.00 42.88 2.57
2217 2564 4.095932 ACATTGAGCTTGTATGCATGACAG 59.904 41.667 10.16 2.95 34.99 3.51
2307 2716 2.554032 ACAGAAATCCCAAAGAAGCACG 59.446 45.455 0.00 0.00 0.00 5.34
2318 2727 4.411327 CAAAGAAGCACGTTGTGAAAAGA 58.589 39.130 0.24 0.00 35.23 2.52
2507 2916 3.192001 CACTATTCAACCAATGTGCAGCT 59.808 43.478 0.00 0.00 0.00 4.24
2566 2975 0.823356 TTGGAAGACAGGTTGGCAGC 60.823 55.000 0.00 0.00 0.00 5.25
2575 2984 5.368989 AGACAGGTTGGCAGCTAATAATAC 58.631 41.667 0.24 0.00 0.00 1.89
2582 2991 3.389983 TGGCAGCTAATAATACGGTTCCT 59.610 43.478 0.00 0.00 0.00 3.36
2598 3007 3.008704 GGTTCCTAGTAGGGTTGAAGCAA 59.991 47.826 16.44 0.00 35.59 3.91
2601 3010 3.649023 TCCTAGTAGGGTTGAAGCAAACA 59.351 43.478 16.44 0.00 35.59 2.83
2602 3011 3.751698 CCTAGTAGGGTTGAAGCAAACAC 59.248 47.826 8.50 0.00 31.89 3.32
2604 3013 2.092103 AGTAGGGTTGAAGCAAACACCA 60.092 45.455 0.00 0.00 33.72 4.17
2616 3025 2.874457 GCAAACACCATTCCGAGTAGGT 60.874 50.000 0.00 0.00 41.99 3.08
2628 3049 2.482142 CCGAGTAGGTTTGAGGCAGATC 60.482 54.545 0.00 0.00 34.51 2.75
2633 3054 0.744771 GGTTTGAGGCAGATCCCGAC 60.745 60.000 0.00 0.00 34.51 4.79
2702 3123 5.027293 ACAGCATATCAGCTAATGTGTCA 57.973 39.130 0.00 0.00 44.54 3.58
2770 3191 1.214589 GAAGGCCGACGAGCAGTAA 59.785 57.895 0.00 0.00 0.00 2.24
2780 3201 0.179097 CGAGCAGTAAGGAGAAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
2855 3276 5.551233 CAAGGACATAAGAGAACAACCTGA 58.449 41.667 0.00 0.00 0.00 3.86
2953 3374 5.674525 CAGGAATAACTGTCATAAGGCAGA 58.325 41.667 6.57 0.00 36.62 4.26
2954 3375 6.294473 CAGGAATAACTGTCATAAGGCAGAT 58.706 40.000 6.57 0.00 36.62 2.90
2974 3395 4.993584 AGATGAACTTAGGCTGCGATAATG 59.006 41.667 0.00 0.00 0.00 1.90
2977 3398 5.289595 TGAACTTAGGCTGCGATAATGTAG 58.710 41.667 0.00 0.00 0.00 2.74
2978 3399 4.939052 ACTTAGGCTGCGATAATGTAGT 57.061 40.909 0.00 0.00 0.00 2.73
2980 3401 5.290386 ACTTAGGCTGCGATAATGTAGTTC 58.710 41.667 0.00 0.00 0.00 3.01
2981 3402 3.819564 AGGCTGCGATAATGTAGTTCA 57.180 42.857 0.00 0.00 0.00 3.18
2982 3403 4.342862 AGGCTGCGATAATGTAGTTCAT 57.657 40.909 0.00 0.00 38.57 2.57
2983 3404 4.310769 AGGCTGCGATAATGTAGTTCATC 58.689 43.478 0.00 0.00 35.48 2.92
2984 3405 3.433615 GGCTGCGATAATGTAGTTCATCC 59.566 47.826 0.00 0.00 35.48 3.51
2985 3406 4.310769 GCTGCGATAATGTAGTTCATCCT 58.689 43.478 0.00 0.00 35.48 3.24
2986 3407 5.470368 GCTGCGATAATGTAGTTCATCCTA 58.530 41.667 0.00 0.00 35.48 2.94
2987 3408 6.102663 GCTGCGATAATGTAGTTCATCCTAT 58.897 40.000 0.00 0.00 35.48 2.57
2988 3409 6.035435 GCTGCGATAATGTAGTTCATCCTATG 59.965 42.308 0.00 0.00 35.48 2.23
2989 3410 6.993079 TGCGATAATGTAGTTCATCCTATGT 58.007 36.000 0.00 0.00 35.48 2.29
2990 3411 6.868339 TGCGATAATGTAGTTCATCCTATGTG 59.132 38.462 0.00 0.00 35.48 3.21
2991 3412 6.868864 GCGATAATGTAGTTCATCCTATGTGT 59.131 38.462 0.00 0.00 35.48 3.72
2995 3416 7.615582 AATGTAGTTCATCCTATGTGTTGTG 57.384 36.000 0.00 0.00 35.48 3.33
2996 3417 6.353404 TGTAGTTCATCCTATGTGTTGTGA 57.647 37.500 0.00 0.00 0.00 3.58
2997 3418 6.946340 TGTAGTTCATCCTATGTGTTGTGAT 58.054 36.000 0.00 0.00 0.00 3.06
2998 3419 6.818142 TGTAGTTCATCCTATGTGTTGTGATG 59.182 38.462 0.00 0.00 35.32 3.07
2999 3420 6.053632 AGTTCATCCTATGTGTTGTGATGA 57.946 37.500 0.00 0.00 39.86 2.92
3000 3421 6.111382 AGTTCATCCTATGTGTTGTGATGAG 58.889 40.000 0.00 0.00 41.81 2.90
3001 3422 5.682234 TCATCCTATGTGTTGTGATGAGT 57.318 39.130 0.00 0.00 37.49 3.41
3002 3423 5.422145 TCATCCTATGTGTTGTGATGAGTG 58.578 41.667 0.00 0.00 37.49 3.51
3040 3461 9.856162 AGGAACTAAAAATAAACCAGTAGTTGA 57.144 29.630 0.00 0.00 35.90 3.18
3099 3520 6.531240 TGTCTCAAGTGCAAAAACTGAATTTC 59.469 34.615 0.00 0.00 0.00 2.17
3101 3522 5.976458 TCAAGTGCAAAAACTGAATTTCCT 58.024 33.333 0.00 0.00 0.00 3.36
3121 3542 2.924757 TGAATATGCAGCTGAGGAGG 57.075 50.000 20.43 0.00 0.00 4.30
3124 3545 3.054139 TGAATATGCAGCTGAGGAGGTTT 60.054 43.478 20.43 0.47 0.00 3.27
3130 3551 2.551071 GCAGCTGAGGAGGTTTAGTGTT 60.551 50.000 20.43 0.00 0.00 3.32
3146 3567 6.677781 TTAGTGTTTCTGTTGTTCCTTCAG 57.322 37.500 0.00 0.00 0.00 3.02
3150 3571 5.066505 GTGTTTCTGTTGTTCCTTCAGACAT 59.933 40.000 0.00 0.00 37.84 3.06
3198 3619 2.930826 ATGGTTGTTTGTCCGTCTCT 57.069 45.000 0.00 0.00 0.00 3.10
3202 3623 2.287103 GGTTGTTTGTCCGTCTCTGAAC 59.713 50.000 0.00 0.00 0.00 3.18
3216 3637 2.290367 CTCTGAACATGTTTGTGCGGAA 59.710 45.455 13.36 0.00 44.64 4.30
3236 3657 3.947910 AAAATGAGGTGGCATCAGTTG 57.052 42.857 0.00 0.00 35.36 3.16
3277 3698 1.047596 TTTGCTGCCAATGGGTGTGT 61.048 50.000 0.00 0.00 36.17 3.72
3280 3701 1.870055 GCTGCCAATGGGTGTGTCAG 61.870 60.000 0.00 0.00 36.17 3.51
3282 3703 0.822944 TGCCAATGGGTGTGTCAGTG 60.823 55.000 0.00 0.00 36.17 3.66
3299 3720 2.477375 CAGTGAAATTTGTGTGCATGGC 59.523 45.455 0.00 0.00 0.00 4.40
3333 3754 0.245539 CATCCCTTTGCTGCAACCTG 59.754 55.000 15.72 8.26 0.00 4.00
3368 3789 6.116711 TGTGTAAATGGAGTAGGCAAACTA 57.883 37.500 0.00 0.00 0.00 2.24
3388 3809 0.109597 GTGGAGTTGGCATTGAAGCG 60.110 55.000 0.00 0.00 34.64 4.68
3394 3815 1.266718 GTTGGCATTGAAGCGAACTGA 59.733 47.619 6.58 0.00 45.83 3.41
3396 3817 0.179179 GGCATTGAAGCGAACTGAGC 60.179 55.000 0.00 0.00 34.64 4.26
3420 3841 4.024133 GGGCTTGCGTTTCAAATTCAAAAT 60.024 37.500 0.00 0.00 33.65 1.82
3421 3842 4.905295 GGCTTGCGTTTCAAATTCAAAATG 59.095 37.500 0.00 2.02 33.65 2.32
3434 3855 2.709883 AAAATGCACGGGCGGGATG 61.710 57.895 4.58 0.00 45.35 3.51
3436 3857 4.552365 ATGCACGGGCGGGATGAG 62.552 66.667 4.58 0.00 45.35 2.90
3443 3864 4.996434 GGCGGGATGAGGCCGATG 62.996 72.222 0.00 0.00 39.93 3.84
3444 3865 3.928779 GCGGGATGAGGCCGATGA 61.929 66.667 0.00 0.00 0.00 2.92
3445 3866 2.029666 CGGGATGAGGCCGATGAC 59.970 66.667 0.00 0.00 0.00 3.06
3446 3867 2.502492 CGGGATGAGGCCGATGACT 61.502 63.158 0.00 0.00 0.00 3.41
3447 3868 1.070445 GGGATGAGGCCGATGACTG 59.930 63.158 0.00 0.00 0.00 3.51
3448 3869 1.690219 GGGATGAGGCCGATGACTGT 61.690 60.000 0.00 0.00 0.00 3.55
3449 3870 0.179000 GGATGAGGCCGATGACTGTT 59.821 55.000 0.00 0.00 0.00 3.16
3450 3871 1.407437 GGATGAGGCCGATGACTGTTT 60.407 52.381 0.00 0.00 0.00 2.83
3482 3903 2.597217 TTGCAACCTGAAGGGGCG 60.597 61.111 0.00 0.00 40.89 6.13
3517 3938 0.737219 GCTTAGGAGTTGCAGCATGG 59.263 55.000 2.55 0.00 35.86 3.66
3526 3947 2.195139 GCAGCATGGGAGCCTCAT 59.805 61.111 0.00 0.00 35.86 2.90
3538 3959 2.095461 GAGCCTCATTTCTTTCCCACC 58.905 52.381 0.00 0.00 0.00 4.61
3540 3961 2.158325 AGCCTCATTTCTTTCCCACCAA 60.158 45.455 0.00 0.00 0.00 3.67
3543 3964 4.151883 CCTCATTTCTTTCCCACCAAGAA 58.848 43.478 0.00 0.00 38.27 2.52
3554 3975 2.240667 CCCACCAAGAATCCTCAGTGAT 59.759 50.000 0.00 0.00 30.91 3.06
3558 3979 2.419159 CCAAGAATCCTCAGTGATCGCA 60.419 50.000 9.33 0.00 0.00 5.10
3582 4003 3.857549 GAGGAATTCTCAAAGGGTTGC 57.142 47.619 5.23 0.00 42.02 4.17
3585 4006 2.159382 GAATTCTCAAAGGGTTGCGGA 58.841 47.619 0.00 0.00 34.50 5.54
3595 4016 1.215647 GGTTGCGGACTCTCGATGT 59.784 57.895 0.00 0.00 0.00 3.06
3602 4023 1.003759 CGGACTCTCGATGTAGGTTCG 60.004 57.143 0.00 0.00 37.94 3.95
3617 4038 1.199327 GGTTCGTTGCCTTTCCTTAGC 59.801 52.381 0.00 0.00 0.00 3.09
3623 4044 3.181510 CGTTGCCTTTCCTTAGCATACAC 60.182 47.826 0.00 0.00 36.20 2.90
3639 4060 7.195374 AGCATACACCCAACTTAGAAATCTA 57.805 36.000 0.00 0.00 0.00 1.98
3645 4066 5.875359 CACCCAACTTAGAAATCTACTGACC 59.125 44.000 0.00 0.00 0.00 4.02
3646 4067 5.045797 ACCCAACTTAGAAATCTACTGACCC 60.046 44.000 0.00 0.00 0.00 4.46
3648 4069 6.109359 CCAACTTAGAAATCTACTGACCCTG 58.891 44.000 0.00 0.00 0.00 4.45
3661 4082 8.783660 TCTACTGACCCTGATTATTAGTTGAT 57.216 34.615 0.00 0.00 0.00 2.57
3663 4084 9.482627 CTACTGACCCTGATTATTAGTTGATTC 57.517 37.037 0.00 0.00 0.00 2.52
3667 4088 6.055588 ACCCTGATTATTAGTTGATTCACCG 58.944 40.000 0.00 0.00 0.00 4.94
3675 4096 3.559238 AGTTGATTCACCGTGAAATGC 57.441 42.857 17.64 10.69 40.12 3.56
3723 4144 3.519913 AGTTAACCAGGGAGATGAACCTC 59.480 47.826 0.88 0.00 34.05 3.85
3725 4146 3.491766 AACCAGGGAGATGAACCTCTA 57.508 47.619 0.00 0.00 34.05 2.43
3727 4148 2.316372 ACCAGGGAGATGAACCTCTAGT 59.684 50.000 0.00 0.00 34.05 2.57
3759 4180 3.369892 CGAGACTTCAGGGATTTCCACAT 60.370 47.826 0.00 0.00 38.24 3.21
3770 4191 3.698040 GGATTTCCACATTGTCTCTGCAT 59.302 43.478 0.00 0.00 35.64 3.96
3827 4248 4.149511 TGTAGCTTACATGCATGGCTAA 57.850 40.909 27.22 18.67 37.27 3.09
3829 4250 4.756642 TGTAGCTTACATGCATGGCTAATC 59.243 41.667 27.22 19.68 37.27 1.75
3842 4263 1.929836 GGCTAATCTGTTCGCAGTCAG 59.070 52.381 0.00 0.00 45.19 3.51
3854 4275 1.719600 GCAGTCAGAGCAGGTTAGTG 58.280 55.000 0.00 0.00 0.00 2.74
3855 4276 1.719600 CAGTCAGAGCAGGTTAGTGC 58.280 55.000 0.00 0.00 44.35 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.661847 GCAACCTACCAATATAACAAGCTATCT 59.338 37.037 0.00 0.00 0.00 1.98
28 29 7.444183 TGCAACCTACCAATATAACAAGCTATC 59.556 37.037 0.00 0.00 0.00 2.08
29 30 7.287061 TGCAACCTACCAATATAACAAGCTAT 58.713 34.615 0.00 0.00 0.00 2.97
30 31 6.654959 TGCAACCTACCAATATAACAAGCTA 58.345 36.000 0.00 0.00 0.00 3.32
31 32 5.505780 TGCAACCTACCAATATAACAAGCT 58.494 37.500 0.00 0.00 0.00 3.74
32 33 5.828299 TGCAACCTACCAATATAACAAGC 57.172 39.130 0.00 0.00 0.00 4.01
33 34 8.902540 TCTATGCAACCTACCAATATAACAAG 57.097 34.615 0.00 0.00 0.00 3.16
34 35 9.283768 CATCTATGCAACCTACCAATATAACAA 57.716 33.333 0.00 0.00 0.00 2.83
35 36 8.436778 ACATCTATGCAACCTACCAATATAACA 58.563 33.333 0.00 0.00 0.00 2.41
36 37 8.848474 ACATCTATGCAACCTACCAATATAAC 57.152 34.615 0.00 0.00 0.00 1.89
37 38 8.880244 AGACATCTATGCAACCTACCAATATAA 58.120 33.333 0.00 0.00 0.00 0.98
38 39 8.435931 AGACATCTATGCAACCTACCAATATA 57.564 34.615 0.00 0.00 0.00 0.86
141 143 5.205759 TGACATGTGAGTCTAGCATATGG 57.794 43.478 1.15 0.00 38.63 2.74
150 152 3.329386 CCAACGAATGACATGTGAGTCT 58.671 45.455 10.89 0.00 39.27 3.24
151 153 2.416547 CCCAACGAATGACATGTGAGTC 59.583 50.000 1.15 1.92 38.99 3.36
167 176 1.347707 TGTCCAGTCAGATCACCCAAC 59.652 52.381 0.00 0.00 0.00 3.77
170 179 1.480137 CTCTGTCCAGTCAGATCACCC 59.520 57.143 0.00 0.00 42.47 4.61
172 181 2.673610 GCACTCTGTCCAGTCAGATCAC 60.674 54.545 0.00 0.00 42.47 3.06
203 212 2.034687 GCCTTCCTGGAGCAGCAA 59.965 61.111 9.10 0.00 38.35 3.91
229 238 3.384789 TCAAGCGCTGTTATCCTGTCTAT 59.615 43.478 12.58 0.00 0.00 1.98
261 270 1.476833 GGATGCTCCGCAAATTCCCTA 60.477 52.381 0.00 0.00 43.62 3.53
285 294 2.897271 TTGGCACCATAACCACATCT 57.103 45.000 0.00 0.00 35.10 2.90
510 540 9.525826 AGTCAGAATTCATACTCAAGGATTTTT 57.474 29.630 8.44 0.00 0.00 1.94
563 603 6.864165 GCGGGAACAAGTATTTTCAACAATTA 59.136 34.615 0.00 0.00 0.00 1.40
580 620 1.024046 CATTCACATCGGCGGGAACA 61.024 55.000 7.21 0.00 0.00 3.18
586 626 2.121564 GATGGGCATTCACATCGGCG 62.122 60.000 0.00 0.00 34.77 6.46
614 654 5.391950 CCATTGTCCTTTGACCGAAGTAATG 60.392 44.000 0.00 0.00 41.01 1.90
904 945 8.231692 TCATGGAAGACTTACATTGTTTTTCA 57.768 30.769 10.40 0.00 0.00 2.69
916 957 5.559770 TGAGCACAAATCATGGAAGACTTA 58.440 37.500 0.00 0.00 0.00 2.24
931 972 1.872952 CTGTGGATCGTTTGAGCACAA 59.127 47.619 0.00 0.00 30.14 3.33
961 1002 2.507484 CTCATTGTCTGCTTGAACCCA 58.493 47.619 0.00 0.00 0.00 4.51
985 1026 2.094390 CCCACATCAGGTTGCTGATTTG 60.094 50.000 0.00 0.00 41.65 2.32
986 1027 2.173519 CCCACATCAGGTTGCTGATTT 58.826 47.619 0.00 0.00 41.65 2.17
1058 1099 3.364889 TTGTCCTGTAAGTCGTGTCAG 57.635 47.619 0.00 0.00 0.00 3.51
1094 1135 2.696187 ACGCCAACAAATAACCCAAAGT 59.304 40.909 0.00 0.00 0.00 2.66
1113 1154 2.350772 GCTCTGGAAATGGTTGTTGACG 60.351 50.000 0.00 0.00 0.00 4.35
1229 1548 5.487488 ACCATCTTACCAGTTAGGATTGTCA 59.513 40.000 0.00 0.00 41.22 3.58
1286 1605 2.792878 TCCGGCTATCTACCTTAGAGC 58.207 52.381 0.00 0.00 38.38 4.09
1323 1648 6.604396 TGTTCTGATCTGCAATCCATACAATT 59.396 34.615 0.00 0.00 0.00 2.32
1445 1771 2.635915 TGGAACTCTGGTCGGTACAAAT 59.364 45.455 0.00 0.00 0.00 2.32
1565 1909 5.811018 TTTGTGTCGTATCTCGTACAAAC 57.189 39.130 15.07 0.00 43.90 2.93
1748 2093 4.455606 CGCTTCTCCTCATAATTCCCTTT 58.544 43.478 0.00 0.00 0.00 3.11
1752 2097 3.181465 TGTCCGCTTCTCCTCATAATTCC 60.181 47.826 0.00 0.00 0.00 3.01
1865 2210 3.256281 GGCCTTCCCTGAGAAACAG 57.744 57.895 0.00 0.00 45.36 3.16
1884 2229 1.002033 GCCAGATTTGCTCGCATAAGG 60.002 52.381 0.00 0.00 30.37 2.69
1983 2328 6.477053 TTCTCAATCTCTTCCACCTGATAG 57.523 41.667 0.00 0.00 0.00 2.08
2015 2360 3.697982 TCTGTATGTATTGCCACGTACG 58.302 45.455 15.01 15.01 41.73 3.67
2093 2438 2.040278 TCACAATCAAACTCCTCCCCTG 59.960 50.000 0.00 0.00 0.00 4.45
2119 2464 0.322322 CCCATGTGTGCAAATTGCCT 59.678 50.000 15.98 0.00 44.23 4.75
2185 2532 2.490903 ACAAGCTCAATGTGCATTCTCC 59.509 45.455 10.02 0.00 0.00 3.71
2194 2541 4.011698 TGTCATGCATACAAGCTCAATGT 58.988 39.130 0.00 0.00 34.99 2.71
2200 2547 3.900966 TCTCTGTCATGCATACAAGCT 57.099 42.857 0.00 0.00 34.99 3.74
2307 2716 3.888930 TCCCTTGTCCATCTTTTCACAAC 59.111 43.478 0.00 0.00 0.00 3.32
2318 2727 1.949847 CTCTCGCGTCCCTTGTCCAT 61.950 60.000 5.77 0.00 0.00 3.41
2358 2767 3.365364 GCATTGTCTTTCTGGTACTGCAC 60.365 47.826 0.00 0.00 0.00 4.57
2507 2916 3.405831 CTCTGTGAGTGGCTTCATTTCA 58.594 45.455 0.00 0.00 0.00 2.69
2566 2975 8.302438 CAACCCTACTAGGAACCGTATTATTAG 58.698 40.741 3.36 0.00 37.67 1.73
2575 2984 2.418334 GCTTCAACCCTACTAGGAACCG 60.418 54.545 3.36 0.00 37.67 4.44
2582 2991 3.136809 TGGTGTTTGCTTCAACCCTACTA 59.863 43.478 0.00 0.00 0.00 1.82
2598 3007 3.071892 TCAAACCTACTCGGAATGGTGTT 59.928 43.478 0.00 0.00 36.31 3.32
2601 3010 2.236395 CCTCAAACCTACTCGGAATGGT 59.764 50.000 0.00 0.00 36.31 3.55
2602 3011 2.906354 CCTCAAACCTACTCGGAATGG 58.094 52.381 0.00 0.00 36.31 3.16
2604 3013 1.906574 TGCCTCAAACCTACTCGGAAT 59.093 47.619 0.00 0.00 36.31 3.01
2616 3025 1.218047 CGTCGGGATCTGCCTCAAA 59.782 57.895 0.00 0.00 36.66 2.69
2633 3054 1.203928 CTTCTACTGCCTCGAATGCG 58.796 55.000 0.00 0.00 39.35 4.73
2642 3063 4.575885 TCATTTGTGTACCTTCTACTGCC 58.424 43.478 0.00 0.00 0.00 4.85
2702 3123 3.034635 CAGGTTATCCAGCCTAGTCACT 58.965 50.000 0.00 0.00 32.77 3.41
2770 3191 1.739750 CTCATATGGGGCCTTCTCCT 58.260 55.000 0.84 0.00 0.00 3.69
2855 3276 1.558294 GGTAAATCCCCTCGTTCAGGT 59.442 52.381 0.00 0.00 41.51 4.00
2953 3374 4.708177 ACATTATCGCAGCCTAAGTTCAT 58.292 39.130 0.00 0.00 0.00 2.57
2954 3375 4.137116 ACATTATCGCAGCCTAAGTTCA 57.863 40.909 0.00 0.00 0.00 3.18
2974 3395 7.041721 TCATCACAACACATAGGATGAACTAC 58.958 38.462 0.00 0.00 40.80 2.73
2977 3398 5.877012 ACTCATCACAACACATAGGATGAAC 59.123 40.000 0.00 0.00 42.49 3.18
2978 3399 5.876460 CACTCATCACAACACATAGGATGAA 59.124 40.000 0.00 0.00 42.49 2.57
2980 3401 5.181009 ACACTCATCACAACACATAGGATG 58.819 41.667 0.00 0.00 37.33 3.51
2981 3402 5.426689 ACACTCATCACAACACATAGGAT 57.573 39.130 0.00 0.00 0.00 3.24
2982 3403 4.890158 ACACTCATCACAACACATAGGA 57.110 40.909 0.00 0.00 0.00 2.94
2983 3404 5.947228 AAACACTCATCACAACACATAGG 57.053 39.130 0.00 0.00 0.00 2.57
3070 3491 3.063997 AGTTTTTGCACTTGAGACAGACG 59.936 43.478 0.00 0.00 0.00 4.18
3073 3494 4.621068 TCAGTTTTTGCACTTGAGACAG 57.379 40.909 0.00 0.00 0.00 3.51
3099 3520 3.139850 CTCCTCAGCTGCATATTCAAGG 58.860 50.000 9.47 8.21 0.00 3.61
3101 3522 2.507058 ACCTCCTCAGCTGCATATTCAA 59.493 45.455 9.47 0.00 0.00 2.69
3121 3542 6.848451 TGAAGGAACAACAGAAACACTAAAC 58.152 36.000 0.00 0.00 0.00 2.01
3124 3545 5.815740 GTCTGAAGGAACAACAGAAACACTA 59.184 40.000 0.00 0.00 42.06 2.74
3130 3551 6.419484 TCTATGTCTGAAGGAACAACAGAA 57.581 37.500 0.00 0.00 42.06 3.02
3179 3600 2.104111 TCAGAGACGGACAAACAACCAT 59.896 45.455 0.00 0.00 0.00 3.55
3187 3608 3.469008 AACATGTTCAGAGACGGACAA 57.531 42.857 4.92 0.00 0.00 3.18
3198 3619 3.510388 TTTTCCGCACAAACATGTTCA 57.490 38.095 12.39 0.00 0.00 3.18
3202 3623 3.429543 CCTCATTTTTCCGCACAAACATG 59.570 43.478 0.00 0.00 0.00 3.21
3216 3637 3.499338 TCAACTGATGCCACCTCATTTT 58.501 40.909 0.00 0.00 0.00 1.82
3251 3672 4.992319 CACCCATTGGCAGCAAATATTATG 59.008 41.667 0.00 0.00 33.59 1.90
3270 3691 3.130340 ACACAAATTTCACTGACACACCC 59.870 43.478 0.00 0.00 0.00 4.61
3277 3698 3.799574 GCCATGCACACAAATTTCACTGA 60.800 43.478 0.00 0.00 0.00 3.41
3280 3701 2.481854 TGCCATGCACACAAATTTCAC 58.518 42.857 0.00 0.00 31.71 3.18
3299 3720 1.359848 GGATGGCTTCAGTACACGTG 58.640 55.000 15.48 15.48 0.00 4.49
3348 3769 5.585047 CCACTAGTTTGCCTACTCCATTTAC 59.415 44.000 0.00 0.00 0.00 2.01
3356 3777 3.008049 CCAACTCCACTAGTTTGCCTACT 59.992 47.826 0.00 0.00 46.61 2.57
3368 3789 1.251251 GCTTCAATGCCAACTCCACT 58.749 50.000 0.00 0.00 0.00 4.00
3376 3797 1.159285 CTCAGTTCGCTTCAATGCCA 58.841 50.000 0.00 0.00 0.00 4.92
3388 3809 3.793144 CGCAAGCCCGCTCAGTTC 61.793 66.667 0.00 0.00 0.00 3.01
3394 3815 1.805428 ATTTGAAACGCAAGCCCGCT 61.805 50.000 0.00 0.00 45.62 5.52
3396 3817 1.059942 GAATTTGAAACGCAAGCCCG 58.940 50.000 0.00 0.00 45.62 6.13
3434 3855 2.380084 TGTAAACAGTCATCGGCCTC 57.620 50.000 0.00 0.00 0.00 4.70
3436 3857 3.427503 CCATTTGTAAACAGTCATCGGCC 60.428 47.826 0.00 0.00 0.00 6.13
3437 3858 3.427503 CCCATTTGTAAACAGTCATCGGC 60.428 47.826 0.00 0.00 0.00 5.54
3439 3860 3.190327 TGCCCATTTGTAAACAGTCATCG 59.810 43.478 0.00 0.00 0.00 3.84
3440 3861 4.782019 TGCCCATTTGTAAACAGTCATC 57.218 40.909 0.00 0.00 0.00 2.92
3442 3863 4.343526 ACATTGCCCATTTGTAAACAGTCA 59.656 37.500 0.00 0.00 0.00 3.41
3443 3864 4.881920 ACATTGCCCATTTGTAAACAGTC 58.118 39.130 0.00 0.00 0.00 3.51
3444 3865 4.953940 ACATTGCCCATTTGTAAACAGT 57.046 36.364 0.00 0.00 0.00 3.55
3445 3866 5.594724 CAACATTGCCCATTTGTAAACAG 57.405 39.130 0.00 0.00 0.00 3.16
3469 3890 2.609610 TAGCCGCCCCTTCAGGTT 60.610 61.111 0.00 0.00 0.00 3.50
3502 3923 1.302285 CTCCCATGCTGCAACTCCT 59.698 57.895 6.36 0.00 0.00 3.69
3517 3938 2.095461 GTGGGAAAGAAATGAGGCTCC 58.905 52.381 12.86 0.00 0.00 4.70
3526 3947 4.141041 TGAGGATTCTTGGTGGGAAAGAAA 60.141 41.667 2.99 0.00 44.49 2.52
3538 3959 2.897436 TGCGATCACTGAGGATTCTTG 58.103 47.619 0.00 0.00 0.00 3.02
3540 3961 2.499289 ACTTGCGATCACTGAGGATTCT 59.501 45.455 0.00 0.00 0.00 2.40
3543 3964 1.827344 TCACTTGCGATCACTGAGGAT 59.173 47.619 0.00 0.00 0.00 3.24
3582 4003 1.003759 CGAACCTACATCGAGAGTCCG 60.004 57.143 0.00 0.00 42.76 4.79
3585 4006 2.415625 GCAACGAACCTACATCGAGAGT 60.416 50.000 2.65 0.00 42.76 3.24
3595 4016 2.943036 AAGGAAAGGCAACGAACCTA 57.057 45.000 0.00 0.00 46.39 3.08
3602 4023 3.128764 GGTGTATGCTAAGGAAAGGCAAC 59.871 47.826 0.00 0.00 39.46 4.17
3617 4038 8.258007 TCAGTAGATTTCTAAGTTGGGTGTATG 58.742 37.037 0.00 0.00 0.00 2.39
3623 4044 5.189934 AGGGTCAGTAGATTTCTAAGTTGGG 59.810 44.000 0.00 0.00 0.00 4.12
3639 4060 7.770897 GTGAATCAACTAATAATCAGGGTCAGT 59.229 37.037 0.00 0.00 0.00 3.41
3645 4066 6.761242 TCACGGTGAATCAACTAATAATCAGG 59.239 38.462 8.68 0.00 0.00 3.86
3646 4067 7.770801 TCACGGTGAATCAACTAATAATCAG 57.229 36.000 8.68 0.00 0.00 2.90
3648 4069 9.438291 CATTTCACGGTGAATCAACTAATAATC 57.562 33.333 22.97 0.00 36.11 1.75
3661 4082 0.821301 TGCCTGCATTTCACGGTGAA 60.821 50.000 19.07 19.07 34.03 3.18
3663 4084 1.210931 CTGCCTGCATTTCACGGTG 59.789 57.895 0.56 0.56 0.00 4.94
3667 4088 2.180017 CCGCTGCCTGCATTTCAC 59.820 61.111 0.00 0.00 43.06 3.18
3689 4110 3.826157 CCTGGTTAACTGATGCTTCCAAA 59.174 43.478 5.42 0.00 0.00 3.28
3691 4112 2.290896 CCCTGGTTAACTGATGCTTCCA 60.291 50.000 5.42 0.00 0.00 3.53
3723 4144 3.341857 AGTCTCGCTTATCGCAACTAG 57.658 47.619 0.00 0.00 39.08 2.57
3725 4146 2.094700 TGAAGTCTCGCTTATCGCAACT 60.095 45.455 0.00 0.00 37.59 3.16
3727 4148 2.530177 CTGAAGTCTCGCTTATCGCAA 58.470 47.619 0.00 0.00 37.59 4.85
3759 4180 0.038599 ATGCCCACATGCAGAGACAA 59.961 50.000 0.00 0.00 45.93 3.18
3770 4191 1.005805 AGCTGATTTACCATGCCCACA 59.994 47.619 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.