Multiple sequence alignment - TraesCS5B01G027400

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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 TraesCS5B01G027400 chr5B 100.000 701 0 0 1 701 26610994 26610294 0.000000e+00 1295.0
1 TraesCS5B01G027400 chr5B 100.000 696 0 0 996 1691 26609999 26609304 0.000000e+00 1286.0
2 TraesCS5B01G027400 chr5B 100.000 446 0 0 1999 2444 26608996 26608551 0.000000e+00 824.0
3 TraesCS5B01G027400 chr5B 95.041 121 6 0 1552 1672 379309494 379309614 8.920000e-45 191.0
4 TraesCS5B01G027400 chr5B 95.082 122 5 1 1550 1671 525451722 525451602 8.920000e-45 191.0
5 TraesCS5B01G027400 chr5D 92.639 557 35 5 996 1551 35553700 35554251 0.000000e+00 797.0
6 TraesCS5B01G027400 chr5D 84.929 564 51 18 1008 1551 35286341 35285792 7.690000e-150 540.0
7 TraesCS5B01G027400 chr5D 90.358 363 23 6 341 701 35553235 35553587 1.320000e-127 466.0
8 TraesCS5B01G027400 chr5D 83.146 445 52 15 265 701 35286874 35286445 3.810000e-103 385.0
9 TraesCS5B01G027400 chr5D 93.889 180 9 2 164 343 35552625 35552802 1.110000e-68 270.0
10 TraesCS5B01G027400 chr5D 82.946 258 25 11 443 695 35329668 35329911 5.290000e-52 215.0
11 TraesCS5B01G027400 chr5D 88.750 80 4 1 2027 2106 35554289 35554363 2.590000e-15 93.5
12 TraesCS5B01G027400 chr5D 75.897 195 33 11 996 1186 35531709 35531893 1.200000e-13 87.9
13 TraesCS5B01G027400 chr5D 82.022 89 12 4 1100 1186 35326718 35326632 3.370000e-09 73.1
14 TraesCS5B01G027400 chr5A 93.047 489 27 4 182 668 24184069 24184552 0.000000e+00 708.0
15 TraesCS5B01G027400 chr5A 87.766 564 43 15 996 1551 24185057 24185602 9.530000e-179 636.0
16 TraesCS5B01G027400 chr5A 90.487 431 26 4 2026 2441 24185647 24186077 2.750000e-154 555.0
17 TraesCS5B01G027400 chr5A 84.109 516 52 18 1008 1509 24149727 24149228 2.840000e-129 472.0
18 TraesCS5B01G027400 chr5A 82.759 522 56 21 1008 1507 23919203 23918694 3.730000e-118 435.0
19 TraesCS5B01G027400 chr5A 82.271 502 53 14 205 697 23921641 23921167 3.790000e-108 401.0
20 TraesCS5B01G027400 chr5A 81.038 501 71 16 204 695 24150322 24149837 6.380000e-101 377.0
21 TraesCS5B01G027400 chr5A 94.397 232 12 1 182 413 23921135 23920905 2.990000e-94 355.0
22 TraesCS5B01G027400 chr5A 90.728 151 14 0 2026 2176 23942261 23942411 4.120000e-48 202.0
23 TraesCS5B01G027400 chr5A 88.028 142 17 0 1246 1387 23915286 23915145 4.180000e-38 169.0
24 TraesCS5B01G027400 chr5A 87.324 142 18 0 1246 1387 24189076 24189217 1.940000e-36 163.0
25 TraesCS5B01G027400 chr5A 88.136 118 9 4 2291 2405 23942429 23942544 4.240000e-28 135.0
26 TraesCS5B01G027400 chr5A 91.935 62 4 1 1128 1188 24177279 24177340 4.330000e-13 86.1
27 TraesCS5B01G027400 chr5A 91.228 57 4 1 1131 1186 23938549 23938493 2.610000e-10 76.8
28 TraesCS5B01G027400 chr5A 90.909 55 2 2 1008 1062 23942054 23942105 1.210000e-08 71.3
29 TraesCS5B01G027400 chrUn 83.019 530 53 10 179 697 268031249 268031752 1.720000e-121 446.0
30 TraesCS5B01G027400 chrUn 83.112 527 52 10 182 697 324441207 324440707 1.720000e-121 446.0
31 TraesCS5B01G027400 chrUn 81.836 501 52 18 204 693 268030745 268031217 3.810000e-103 385.0
32 TraesCS5B01G027400 chrUn 83.032 442 54 13 262 695 266220286 266219858 4.930000e-102 381.0
33 TraesCS5B01G027400 chrUn 83.032 442 54 13 262 695 266247081 266246653 4.930000e-102 381.0
34 TraesCS5B01G027400 chrUn 81.424 323 30 14 1008 1309 440671126 440670813 1.130000e-58 237.0
35 TraesCS5B01G027400 chrUn 87.324 142 18 0 1246 1387 313467613 313467754 1.940000e-36 163.0
36 TraesCS5B01G027400 chr7B 92.013 313 18 4 371 681 205198304 205197997 1.340000e-117 433.0
37 TraesCS5B01G027400 chr7A 87.259 259 24 5 1100 1349 3945541 3945799 1.110000e-73 287.0
38 TraesCS5B01G027400 chr2B 94.161 137 5 3 1551 1687 557988068 557987935 3.190000e-49 206.0
39 TraesCS5B01G027400 chr2B 96.694 121 4 0 1551 1671 17575875 17575755 4.120000e-48 202.0
40 TraesCS5B01G027400 chr2B 96.667 120 4 0 1552 1671 72863172 72863291 1.480000e-47 200.0
41 TraesCS5B01G027400 chr4B 94.488 127 6 1 1546 1671 588198501 588198627 6.900000e-46 195.0
42 TraesCS5B01G027400 chr6B 95.763 118 5 0 1554 1671 92916456 92916339 8.920000e-45 191.0
43 TraesCS5B01G027400 chr3B 95.726 117 5 0 1555 1671 727743047 727742931 3.210000e-44 189.0
44 TraesCS5B01G027400 chr1B 95.041 121 5 1 1551 1671 381935856 381935737 3.210000e-44 189.0


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 TraesCS5B01G027400 chr5B 26608551 26610994 2443 True 1135.000 1295 100.00000 1 2444 3 chr5B.!!$R2 2443
1 TraesCS5B01G027400 chr5D 35285792 35286874 1082 True 462.500 540 84.03750 265 1551 2 chr5D.!!$R2 1286
2 TraesCS5B01G027400 chr5D 35552625 35554363 1738 False 406.625 797 91.40900 164 2106 4 chr5D.!!$F3 1942
3 TraesCS5B01G027400 chr5A 24184069 24189217 5148 False 515.500 708 89.65600 182 2441 4 chr5A.!!$F3 2259
4 TraesCS5B01G027400 chr5A 24149228 24150322 1094 True 424.500 472 82.57350 204 1509 2 chr5A.!!$R3 1305
5 TraesCS5B01G027400 chr5A 23915145 23921641 6496 True 340.000 435 86.86375 182 1507 4 chr5A.!!$R2 1325
6 TraesCS5B01G027400 chrUn 324440707 324441207 500 True 446.000 446 83.11200 182 697 1 chrUn.!!$R3 515
7 TraesCS5B01G027400 chrUn 268030745 268031752 1007 False 415.500 446 82.42750 179 697 2 chrUn.!!$F2 518

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
40 41 0.402504 TGCTACGGGTGAAAATGGGT 59.597 50.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 3989 0.731417 CGCCACTGTAGCTACGTACT 59.269 55.0 18.74 0.0 0.0 2.73 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
33 34 1.448985 GCATTCTTGCTACGGGTGAA 58.551 50.000 0.00 0.00 45.77 3.18
34 35 1.810151 GCATTCTTGCTACGGGTGAAA 59.190 47.619 0.00 0.00 45.77 2.69
38 39 2.432444 TCTTGCTACGGGTGAAAATGG 58.568 47.619 0.00 0.00 0.00 3.16
39 40 1.472480 CTTGCTACGGGTGAAAATGGG 59.528 52.381 0.00 0.00 0.00 4.00
40 41 0.402504 TGCTACGGGTGAAAATGGGT 59.597 50.000 0.00 0.00 0.00 4.51
42 43 2.011947 GCTACGGGTGAAAATGGGTAC 58.988 52.381 0.00 0.00 0.00 3.34
113 114 9.498176 TTTACTTCAACTAAATGAACTACTCCC 57.502 33.333 0.00 0.00 35.55 4.30
117 118 5.105473 TCAACTAAATGAACTACTCCCTCCG 60.105 44.000 0.00 0.00 0.00 4.63
118 119 4.607239 ACTAAATGAACTACTCCCTCCGA 58.393 43.478 0.00 0.00 0.00 4.55
119 120 5.209659 ACTAAATGAACTACTCCCTCCGAT 58.790 41.667 0.00 0.00 0.00 4.18
121 122 2.068834 TGAACTACTCCCTCCGATCC 57.931 55.000 0.00 0.00 0.00 3.36
122 123 1.286849 TGAACTACTCCCTCCGATCCA 59.713 52.381 0.00 0.00 0.00 3.41
123 124 2.291996 TGAACTACTCCCTCCGATCCAA 60.292 50.000 0.00 0.00 0.00 3.53
129 130 4.152284 ACTCCCTCCGATCCAAATTAAC 57.848 45.455 0.00 0.00 0.00 2.01
130 131 3.118000 ACTCCCTCCGATCCAAATTAACC 60.118 47.826 0.00 0.00 0.00 2.85
133 134 3.821033 CCCTCCGATCCAAATTAACCATC 59.179 47.826 0.00 0.00 0.00 3.51
137 138 5.294356 TCCGATCCAAATTAACCATCGTAG 58.706 41.667 0.00 0.00 35.62 3.51
138 139 4.084013 CCGATCCAAATTAACCATCGTAGC 60.084 45.833 0.00 0.00 35.62 3.58
142 143 7.042321 CGATCCAAATTAACCATCGTAGCTTTA 60.042 37.037 0.00 0.00 33.29 1.85
143 144 7.548196 TCCAAATTAACCATCGTAGCTTTAG 57.452 36.000 0.00 0.00 0.00 1.85
146 147 8.548721 CCAAATTAACCATCGTAGCTTTAGTAG 58.451 37.037 0.00 0.00 0.00 2.57
159 160 4.147219 CTTTAGTAGCACAACCTTGCAC 57.853 45.455 0.00 0.00 45.62 4.57
161 162 1.597742 AGTAGCACAACCTTGCACAG 58.402 50.000 0.00 0.00 45.62 3.66
162 163 1.134098 AGTAGCACAACCTTGCACAGT 60.134 47.619 0.00 0.00 45.62 3.55
199 526 6.614906 TGGGTCATAAAATTGCATCCCTAATT 59.385 34.615 0.00 0.00 35.20 1.40
200 527 7.786943 TGGGTCATAAAATTGCATCCCTAATTA 59.213 33.333 0.00 0.00 35.20 1.40
368 1136 3.424703 ACTATCAGCAGGCACACATTTT 58.575 40.909 0.00 0.00 0.00 1.82
421 1189 0.606604 GCCACGACACCCTCTTCTTA 59.393 55.000 0.00 0.00 0.00 2.10
422 1190 1.001633 GCCACGACACCCTCTTCTTAA 59.998 52.381 0.00 0.00 0.00 1.85
445 1213 9.547753 TTAATTTACTGGTTAAAATTTGCAGCA 57.452 25.926 0.00 0.00 36.80 4.41
455 1223 8.344831 GGTTAAAATTTGCAGCATCTTTTTCTT 58.655 29.630 16.41 1.12 0.00 2.52
619 2703 1.080093 TAGAACGCGAGGCTTGGTG 60.080 57.895 15.93 1.14 0.00 4.17
655 2739 2.517402 TTTGTGGTGGACGGTGGC 60.517 61.111 0.00 0.00 0.00 5.01
1234 3536 1.040646 TGAGCGGACAGTGAAAGAGT 58.959 50.000 0.00 0.00 0.00 3.24
1345 3647 2.125512 GCGTCGACCAATGGCTCT 60.126 61.111 10.58 0.00 0.00 4.09
1427 3732 1.344942 GCTAACCGTCACAGCGTCAG 61.345 60.000 0.00 0.00 0.00 3.51
1450 3759 0.179076 CATGCCGATGTAGCCTGTCA 60.179 55.000 0.00 0.00 0.00 3.58
1452 3761 0.970427 TGCCGATGTAGCCTGTCAGA 60.970 55.000 0.00 0.00 0.00 3.27
1454 3763 1.405526 GCCGATGTAGCCTGTCAGAAA 60.406 52.381 0.00 0.00 0.00 2.52
1466 3783 1.071071 TGTCAGAAATCGGGACCGTTT 59.929 47.619 10.90 10.24 40.74 3.60
1467 3784 2.148768 GTCAGAAATCGGGACCGTTTT 58.851 47.619 16.95 16.95 41.90 2.43
1490 3807 1.441729 CCGGATAGCGGCAAGAAGA 59.558 57.895 0.00 0.00 0.00 2.87
1495 3812 0.528684 ATAGCGGCAAGAAGAGTCGC 60.529 55.000 3.78 3.78 45.72 5.19
1533 3851 3.153919 GGAGCAATTTGTGACCACCTAA 58.846 45.455 0.00 0.00 0.00 2.69
1551 3869 4.838986 ACCTAAGTGCCGGAAGATGTATAT 59.161 41.667 5.05 0.00 0.00 0.86
1553 3871 6.153000 ACCTAAGTGCCGGAAGATGTATATAG 59.847 42.308 5.05 0.00 0.00 1.31
1555 3873 7.338703 CCTAAGTGCCGGAAGATGTATATAGTA 59.661 40.741 5.05 0.00 0.00 1.82
1557 3875 6.246919 AGTGCCGGAAGATGTATATAGTACT 58.753 40.000 5.05 0.00 0.00 2.73
1558 3876 6.374894 AGTGCCGGAAGATGTATATAGTACTC 59.625 42.308 5.05 0.00 0.00 2.59
1559 3877 5.651139 TGCCGGAAGATGTATATAGTACTCC 59.349 44.000 5.05 0.00 0.00 3.85
1560 3878 5.067544 GCCGGAAGATGTATATAGTACTCCC 59.932 48.000 5.05 0.00 0.00 4.30
1561 3879 6.424883 CCGGAAGATGTATATAGTACTCCCT 58.575 44.000 0.00 0.00 0.00 4.20
1564 3882 7.411808 GGAAGATGTATATAGTACTCCCTCCA 58.588 42.308 0.00 0.00 0.00 3.86
1565 3883 8.062536 GGAAGATGTATATAGTACTCCCTCCAT 58.937 40.741 0.00 0.00 0.00 3.41
1568 3886 5.752650 TGTATATAGTACTCCCTCCATCCG 58.247 45.833 0.00 0.00 0.00 4.18
1570 3888 1.526315 TAGTACTCCCTCCATCCGGA 58.474 55.000 6.61 6.61 39.79 5.14
1574 3892 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
1575 3893 2.047830 ACTCCCTCCATCCGGAAATAC 58.952 52.381 9.01 0.00 42.21 1.89
1576 3894 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
1577 3895 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
1579 3897 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
1581 3899 3.123804 CTCCATCCGGAAATACTTGTCG 58.876 50.000 9.01 0.00 42.21 4.35
1584 3902 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
1585 3903 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
1586 3904 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
1589 3907 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
1592 3910 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
1593 3911 6.238484 GGAAATACTTGTCGGAGAAATGGATG 60.238 42.308 0.00 0.00 39.69 3.51
1595 3913 4.286297 ACTTGTCGGAGAAATGGATGAA 57.714 40.909 0.00 0.00 39.69 2.57
1596 3914 4.651778 ACTTGTCGGAGAAATGGATGAAA 58.348 39.130 0.00 0.00 39.69 2.69
1597 3915 5.070001 ACTTGTCGGAGAAATGGATGAAAA 58.930 37.500 0.00 0.00 39.69 2.29
1598 3916 5.711976 ACTTGTCGGAGAAATGGATGAAAAT 59.288 36.000 0.00 0.00 39.69 1.82
1599 3917 5.565592 TGTCGGAGAAATGGATGAAAATG 57.434 39.130 0.00 0.00 39.69 2.32
1600 3918 4.398988 TGTCGGAGAAATGGATGAAAATGG 59.601 41.667 0.00 0.00 39.69 3.16
1601 3919 4.640201 GTCGGAGAAATGGATGAAAATGGA 59.360 41.667 0.00 0.00 39.69 3.41
1602 3920 5.300286 GTCGGAGAAATGGATGAAAATGGAT 59.700 40.000 0.00 0.00 39.69 3.41
1603 3921 5.300034 TCGGAGAAATGGATGAAAATGGATG 59.700 40.000 0.00 0.00 0.00 3.51
1604 3922 5.068198 CGGAGAAATGGATGAAAATGGATGT 59.932 40.000 0.00 0.00 0.00 3.06
1605 3923 6.262944 CGGAGAAATGGATGAAAATGGATGTA 59.737 38.462 0.00 0.00 0.00 2.29
1606 3924 7.040201 CGGAGAAATGGATGAAAATGGATGTAT 60.040 37.037 0.00 0.00 0.00 2.29
1607 3925 8.302438 GGAGAAATGGATGAAAATGGATGTATC 58.698 37.037 0.00 0.00 0.00 2.24
1608 3926 9.075678 GAGAAATGGATGAAAATGGATGTATCT 57.924 33.333 0.00 0.00 0.00 1.98
1614 3932 9.699410 TGGATGAAAATGGATGTATCTAAAACT 57.301 29.630 0.00 0.00 0.00 2.66
1643 3961 7.652524 TGCATCTAGATACATCTATTCCTCC 57.347 40.000 4.54 0.00 38.60 4.30
1644 3962 6.319911 TGCATCTAGATACATCTATTCCTCCG 59.680 42.308 4.54 0.00 38.60 4.63
1645 3963 6.544197 GCATCTAGATACATCTATTCCTCCGA 59.456 42.308 4.54 0.00 38.60 4.55
1646 3964 7.468084 GCATCTAGATACATCTATTCCTCCGAC 60.468 44.444 4.54 0.00 38.60 4.79
1647 3965 7.017319 TCTAGATACATCTATTCCTCCGACA 57.983 40.000 0.00 0.00 38.60 4.35
1648 3966 7.459234 TCTAGATACATCTATTCCTCCGACAA 58.541 38.462 0.00 0.00 38.60 3.18
1649 3967 6.582677 AGATACATCTATTCCTCCGACAAG 57.417 41.667 0.00 0.00 34.85 3.16
1650 3968 6.071984 AGATACATCTATTCCTCCGACAAGT 58.928 40.000 0.00 0.00 34.85 3.16
1651 3969 7.232188 AGATACATCTATTCCTCCGACAAGTA 58.768 38.462 0.00 0.00 34.85 2.24
1652 3970 7.891183 AGATACATCTATTCCTCCGACAAGTAT 59.109 37.037 0.00 0.00 34.85 2.12
1653 3971 6.732896 ACATCTATTCCTCCGACAAGTATT 57.267 37.500 0.00 0.00 0.00 1.89
1654 3972 7.125792 ACATCTATTCCTCCGACAAGTATTT 57.874 36.000 0.00 0.00 0.00 1.40
1655 3973 7.565680 ACATCTATTCCTCCGACAAGTATTTT 58.434 34.615 0.00 0.00 0.00 1.82
1656 3974 8.047310 ACATCTATTCCTCCGACAAGTATTTTT 58.953 33.333 0.00 0.00 0.00 1.94
1657 3975 7.843490 TCTATTCCTCCGACAAGTATTTTTG 57.157 36.000 0.00 0.00 0.00 2.44
1658 3976 5.897377 ATTCCTCCGACAAGTATTTTTGG 57.103 39.130 0.00 0.00 32.32 3.28
1659 3977 4.627284 TCCTCCGACAAGTATTTTTGGA 57.373 40.909 0.00 0.00 32.32 3.53
1660 3978 4.320870 TCCTCCGACAAGTATTTTTGGAC 58.679 43.478 0.00 0.00 32.32 4.02
1661 3979 3.124636 CCTCCGACAAGTATTTTTGGACG 59.875 47.826 0.00 0.00 34.41 4.79
1662 3980 3.068560 TCCGACAAGTATTTTTGGACGG 58.931 45.455 15.12 15.12 44.84 4.79
1663 3981 3.068560 CCGACAAGTATTTTTGGACGGA 58.931 45.455 15.77 0.00 45.53 4.69
1664 3982 3.124636 CCGACAAGTATTTTTGGACGGAG 59.875 47.826 15.77 0.00 45.53 4.63
1665 3983 3.124636 CGACAAGTATTTTTGGACGGAGG 59.875 47.826 0.00 0.00 32.62 4.30
1666 3984 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
1667 3985 3.073356 ACAAGTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 32.32 4.20
1668 3986 3.629142 AGTATTTTTGGACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1669 3987 2.910977 AGTATTTTTGGACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1670 3988 4.098894 AGTATTTTTGGACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1671 3989 4.533311 AGTATTTTTGGACGGAGGGAGTAA 59.467 41.667 0.00 0.00 0.00 2.24
1672 3990 3.412237 TTTTTGGACGGAGGGAGTAAG 57.588 47.619 0.00 0.00 0.00 2.34
1673 3991 2.019807 TTTGGACGGAGGGAGTAAGT 57.980 50.000 0.00 0.00 0.00 2.24
1674 3992 2.905415 TTGGACGGAGGGAGTAAGTA 57.095 50.000 0.00 0.00 0.00 2.24
1675 3993 2.134789 TGGACGGAGGGAGTAAGTAC 57.865 55.000 0.00 0.00 0.00 2.73
1676 3994 1.020437 GGACGGAGGGAGTAAGTACG 58.980 60.000 0.00 0.00 0.00 3.67
1677 3995 1.680249 GGACGGAGGGAGTAAGTACGT 60.680 57.143 0.00 0.00 35.64 3.57
1678 3996 2.420129 GGACGGAGGGAGTAAGTACGTA 60.420 54.545 0.00 0.00 32.84 3.57
1679 3997 2.869192 GACGGAGGGAGTAAGTACGTAG 59.131 54.545 0.00 0.00 32.84 3.51
1680 3998 1.601430 CGGAGGGAGTAAGTACGTAGC 59.399 57.143 0.00 0.00 0.00 3.58
1681 3999 2.744494 CGGAGGGAGTAAGTACGTAGCT 60.744 54.545 0.00 0.00 0.00 3.32
1682 4000 3.493350 CGGAGGGAGTAAGTACGTAGCTA 60.493 52.174 0.00 0.00 0.00 3.32
1683 4001 3.812609 GGAGGGAGTAAGTACGTAGCTAC 59.187 52.174 14.19 14.19 0.00 3.58
1684 4002 4.446371 GAGGGAGTAAGTACGTAGCTACA 58.554 47.826 23.21 2.04 0.00 2.74
1685 4003 4.450053 AGGGAGTAAGTACGTAGCTACAG 58.550 47.826 23.21 17.17 0.00 2.74
1686 4004 4.080638 AGGGAGTAAGTACGTAGCTACAGT 60.081 45.833 23.21 21.31 0.00 3.55
1687 4005 4.034975 GGGAGTAAGTACGTAGCTACAGTG 59.965 50.000 23.21 9.92 0.00 3.66
1688 4006 4.034975 GGAGTAAGTACGTAGCTACAGTGG 59.965 50.000 23.21 9.56 0.00 4.00
1689 4007 2.935481 AAGTACGTAGCTACAGTGGC 57.065 50.000 23.21 16.51 0.00 5.01
1690 4008 0.731417 AGTACGTAGCTACAGTGGCG 59.269 55.000 23.21 10.81 34.52 5.69
2015 4333 4.599036 GTTGACCCCCACAAAGCT 57.401 55.556 0.00 0.00 0.00 3.74
2016 4334 2.341452 GTTGACCCCCACAAAGCTC 58.659 57.895 0.00 0.00 0.00 4.09
2017 4335 1.152830 TTGACCCCCACAAAGCTCC 59.847 57.895 0.00 0.00 0.00 4.70
2018 4336 2.359975 GACCCCCACAAAGCTCCG 60.360 66.667 0.00 0.00 0.00 4.63
2019 4337 4.660938 ACCCCCACAAAGCTCCGC 62.661 66.667 0.00 0.00 0.00 5.54
2021 4339 4.659172 CCCCACAAAGCTCCGCCA 62.659 66.667 0.00 0.00 0.00 5.69
2022 4340 3.365265 CCCACAAAGCTCCGCCAC 61.365 66.667 0.00 0.00 0.00 5.01
2023 4341 2.281761 CCACAAAGCTCCGCCACT 60.282 61.111 0.00 0.00 0.00 4.00
2024 4342 2.620112 CCACAAAGCTCCGCCACTG 61.620 63.158 0.00 0.00 0.00 3.66
2061 4388 0.464373 GGTCGTCATGGCCATGTGAT 60.464 55.000 38.18 7.92 39.72 3.06
2062 4389 0.659427 GTCGTCATGGCCATGTGATG 59.341 55.000 38.18 28.30 39.72 3.07
2063 4390 0.252761 TCGTCATGGCCATGTGATGT 59.747 50.000 38.18 6.25 39.72 3.06
2064 4391 0.379316 CGTCATGGCCATGTGATGTG 59.621 55.000 38.18 18.73 39.72 3.21
2065 4392 1.753930 GTCATGGCCATGTGATGTGA 58.246 50.000 38.18 20.72 39.72 3.58
2088 4415 4.225267 ACCATGACTCGTTCCCTCTAAAAT 59.775 41.667 0.00 0.00 0.00 1.82
2108 4435 3.138884 TGACACAGCTGCTAAATTGGA 57.861 42.857 15.27 0.00 0.00 3.53
2118 4445 4.732938 GCTGCTAAATTGGAAAGCTAGCTG 60.733 45.833 20.16 2.23 39.42 4.24
2161 4488 2.691409 TGCTAACCGCAGAAGCTATT 57.309 45.000 0.00 0.00 45.47 1.73
2185 4518 4.272748 AGAGTTTGGTACGTCAAAAGCTTC 59.727 41.667 0.00 1.98 38.21 3.86
2224 4557 4.333926 GCAATCCAGTCCAGAAATGTACTC 59.666 45.833 0.00 0.00 0.00 2.59
2242 4578 5.711506 TGTACTCGACTAAGGGAATGTACAA 59.288 40.000 0.00 0.00 36.93 2.41
2257 4593 9.744468 GGGAATGTACAATGGTGTTATTTTATC 57.256 33.333 0.00 0.00 39.30 1.75
2262 4598 9.290988 TGTACAATGGTGTTATTTTATCAGTGT 57.709 29.630 0.00 0.00 39.30 3.55
2305 4641 3.938963 CTCGGCAGGCAAAAGATTAACTA 59.061 43.478 0.00 0.00 0.00 2.24
2357 4750 4.631813 AGTGCCAAATAGAATCGTCAGAAC 59.368 41.667 0.00 0.00 0.00 3.01
2361 4754 6.016693 TGCCAAATAGAATCGTCAGAACAAAA 60.017 34.615 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.414852 CATTTTCACCCGTAGCAAGAATG 58.585 43.478 0.00 0.00 0.00 2.67
16 17 3.443681 CCATTTTCACCCGTAGCAAGAAT 59.556 43.478 0.00 0.00 0.00 2.40
19 20 1.472480 CCCATTTTCACCCGTAGCAAG 59.528 52.381 0.00 0.00 0.00 4.01
20 21 1.202952 ACCCATTTTCACCCGTAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
21 22 0.402504 ACCCATTTTCACCCGTAGCA 59.597 50.000 0.00 0.00 0.00 3.49
23 24 2.027007 TGGTACCCATTTTCACCCGTAG 60.027 50.000 10.07 0.00 0.00 3.51
25 26 0.772384 TGGTACCCATTTTCACCCGT 59.228 50.000 10.07 0.00 0.00 5.28
91 92 6.819146 GGAGGGAGTAGTTCATTTAGTTGAAG 59.181 42.308 0.00 0.00 36.34 3.02
95 96 5.021458 TCGGAGGGAGTAGTTCATTTAGTT 58.979 41.667 0.00 0.00 0.00 2.24
96 97 4.607239 TCGGAGGGAGTAGTTCATTTAGT 58.393 43.478 0.00 0.00 0.00 2.24
98 99 4.587684 GGATCGGAGGGAGTAGTTCATTTA 59.412 45.833 0.00 0.00 0.00 1.40
100 101 2.966516 GGATCGGAGGGAGTAGTTCATT 59.033 50.000 0.00 0.00 0.00 2.57
101 102 2.091278 TGGATCGGAGGGAGTAGTTCAT 60.091 50.000 0.00 0.00 0.00 2.57
103 104 2.068834 TGGATCGGAGGGAGTAGTTC 57.931 55.000 0.00 0.00 0.00 3.01
105 106 2.544844 TTTGGATCGGAGGGAGTAGT 57.455 50.000 0.00 0.00 0.00 2.73
107 108 4.102054 GGTTAATTTGGATCGGAGGGAGTA 59.898 45.833 0.00 0.00 0.00 2.59
110 111 2.847449 TGGTTAATTTGGATCGGAGGGA 59.153 45.455 0.00 0.00 0.00 4.20
111 112 3.290948 TGGTTAATTTGGATCGGAGGG 57.709 47.619 0.00 0.00 0.00 4.30
112 113 3.498397 CGATGGTTAATTTGGATCGGAGG 59.502 47.826 0.00 0.00 33.82 4.30
113 114 4.127171 ACGATGGTTAATTTGGATCGGAG 58.873 43.478 0.00 0.00 40.13 4.63
117 118 6.619801 AAGCTACGATGGTTAATTTGGATC 57.380 37.500 0.00 0.00 0.00 3.36
118 119 7.773690 ACTAAAGCTACGATGGTTAATTTGGAT 59.226 33.333 0.00 0.00 0.00 3.41
119 120 7.107542 ACTAAAGCTACGATGGTTAATTTGGA 58.892 34.615 0.00 0.00 0.00 3.53
138 139 3.563808 TGTGCAAGGTTGTGCTACTAAAG 59.436 43.478 0.00 0.00 45.17 1.85
142 143 1.134098 ACTGTGCAAGGTTGTGCTACT 60.134 47.619 0.00 0.00 45.17 2.57
143 144 1.308998 ACTGTGCAAGGTTGTGCTAC 58.691 50.000 0.00 0.00 45.17 3.58
146 147 1.308998 ACTACTGTGCAAGGTTGTGC 58.691 50.000 6.60 0.00 45.15 4.57
147 148 5.932303 AGTAATACTACTGTGCAAGGTTGTG 59.068 40.000 14.15 3.38 36.98 3.33
149 150 7.435068 AAAGTAATACTACTGTGCAAGGTTG 57.565 36.000 0.00 0.00 38.43 3.77
151 152 6.430000 CCAAAAGTAATACTACTGTGCAAGGT 59.570 38.462 0.00 0.00 38.43 3.50
152 153 6.128007 CCCAAAAGTAATACTACTGTGCAAGG 60.128 42.308 0.00 0.00 38.43 3.61
153 154 6.430000 ACCCAAAAGTAATACTACTGTGCAAG 59.570 38.462 0.00 0.00 38.43 4.01
155 156 5.871834 ACCCAAAAGTAATACTACTGTGCA 58.128 37.500 0.00 0.00 38.43 4.57
199 526 2.224185 ACCGCAGTTTGATGTGACAGTA 60.224 45.455 0.00 0.00 32.27 2.74
200 527 1.229428 CCGCAGTTTGATGTGACAGT 58.771 50.000 0.00 0.00 32.27 3.55
368 1136 2.539274 GCAAATGCGACAGCTTGAAAAA 59.461 40.909 0.00 0.00 45.42 1.94
421 1189 8.620116 ATGCTGCAAATTTTAACCAGTAAATT 57.380 26.923 6.36 0.00 35.95 1.82
422 1190 8.096414 AGATGCTGCAAATTTTAACCAGTAAAT 58.904 29.630 6.36 0.00 31.69 1.40
476 1244 7.555965 TCTCTCAATTTTTCATGACTATCGGA 58.444 34.615 0.00 0.00 0.00 4.55
587 2663 4.148696 TCGCGTTCTACTTTTACCTTTTCG 59.851 41.667 5.77 0.00 0.00 3.46
619 2703 6.250819 CACAAAGACAATGGTAATGACGATC 58.749 40.000 0.00 0.00 0.00 3.69
655 2739 3.558829 CACCTCATGGTCAGATCAAATCG 59.441 47.826 0.00 0.00 46.60 3.34
998 3270 2.372690 ACGACGAGCACGAACATGC 61.373 57.895 11.40 0.00 46.50 4.06
1427 3732 2.635899 GCTACATCGGCATGCTGC 59.364 61.111 22.21 2.40 44.08 5.25
1452 3761 2.547026 CGGAAAACGGTCCCGATTT 58.453 52.632 13.54 13.18 45.58 2.17
1475 3792 1.482278 CGACTCTTCTTGCCGCTATC 58.518 55.000 0.00 0.00 0.00 2.08
1533 3851 6.246919 AGTACTATATACATCTTCCGGCACT 58.753 40.000 0.00 0.00 0.00 4.40
1551 3869 1.526315 TCCGGATGGAGGGAGTACTA 58.474 55.000 0.00 0.00 40.17 1.82
1561 3879 2.159014 CCGACAAGTATTTCCGGATGGA 60.159 50.000 4.15 0.00 44.61 3.41
1564 3882 3.028850 TCTCCGACAAGTATTTCCGGAT 58.971 45.455 4.15 0.00 46.53 4.18
1565 3883 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
1568 3886 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
1570 3888 6.414732 TCATCCATTTCTCCGACAAGTATTT 58.585 36.000 0.00 0.00 0.00 1.40
1574 3892 3.981071 TCATCCATTTCTCCGACAAGT 57.019 42.857 0.00 0.00 0.00 3.16
1575 3893 5.627499 TTTTCATCCATTTCTCCGACAAG 57.373 39.130 0.00 0.00 0.00 3.16
1576 3894 5.105797 CCATTTTCATCCATTTCTCCGACAA 60.106 40.000 0.00 0.00 0.00 3.18
1577 3895 4.398988 CCATTTTCATCCATTTCTCCGACA 59.601 41.667 0.00 0.00 0.00 4.35
1579 3897 4.854173 TCCATTTTCATCCATTTCTCCGA 58.146 39.130 0.00 0.00 0.00 4.55
1581 3899 6.475596 ACATCCATTTTCATCCATTTCTCC 57.524 37.500 0.00 0.00 0.00 3.71
1617 3935 8.703743 GGAGGAATAGATGTATCTAGATGCAAT 58.296 37.037 24.65 18.54 42.20 3.56
1618 3936 7.148000 CGGAGGAATAGATGTATCTAGATGCAA 60.148 40.741 24.65 11.20 42.20 4.08
1619 3937 6.319911 CGGAGGAATAGATGTATCTAGATGCA 59.680 42.308 23.38 23.38 42.20 3.96
1620 3938 6.544197 TCGGAGGAATAGATGTATCTAGATGC 59.456 42.308 15.79 14.54 42.20 3.91
1621 3939 7.554476 TGTCGGAGGAATAGATGTATCTAGATG 59.446 40.741 15.79 0.00 42.20 2.90
1622 3940 7.634718 TGTCGGAGGAATAGATGTATCTAGAT 58.365 38.462 10.73 10.73 42.20 1.98
1623 3941 7.017319 TGTCGGAGGAATAGATGTATCTAGA 57.983 40.000 7.57 0.00 42.20 2.43
1624 3942 7.392113 ACTTGTCGGAGGAATAGATGTATCTAG 59.608 40.741 7.57 0.00 42.20 2.43
1625 3943 7.232188 ACTTGTCGGAGGAATAGATGTATCTA 58.768 38.462 4.22 4.22 43.00 1.98
1626 3944 6.071984 ACTTGTCGGAGGAATAGATGTATCT 58.928 40.000 0.00 0.00 40.86 1.98
1627 3945 6.334102 ACTTGTCGGAGGAATAGATGTATC 57.666 41.667 0.00 0.00 0.00 2.24
1628 3946 8.423906 AATACTTGTCGGAGGAATAGATGTAT 57.576 34.615 0.00 0.00 0.00 2.29
1629 3947 7.834881 AATACTTGTCGGAGGAATAGATGTA 57.165 36.000 0.00 0.00 0.00 2.29
1630 3948 6.732896 AATACTTGTCGGAGGAATAGATGT 57.267 37.500 0.00 0.00 0.00 3.06
1631 3949 8.338259 CAAAAATACTTGTCGGAGGAATAGATG 58.662 37.037 0.00 0.00 0.00 2.90
1632 3950 7.499232 CCAAAAATACTTGTCGGAGGAATAGAT 59.501 37.037 0.00 0.00 0.00 1.98
1633 3951 6.821665 CCAAAAATACTTGTCGGAGGAATAGA 59.178 38.462 0.00 0.00 0.00 1.98
1634 3952 6.821665 TCCAAAAATACTTGTCGGAGGAATAG 59.178 38.462 0.00 0.00 0.00 1.73
1635 3953 6.596497 GTCCAAAAATACTTGTCGGAGGAATA 59.404 38.462 0.00 0.00 0.00 1.75
1636 3954 5.414765 GTCCAAAAATACTTGTCGGAGGAAT 59.585 40.000 0.00 0.00 0.00 3.01
1637 3955 4.758165 GTCCAAAAATACTTGTCGGAGGAA 59.242 41.667 0.00 0.00 0.00 3.36
1638 3956 4.320870 GTCCAAAAATACTTGTCGGAGGA 58.679 43.478 0.00 0.00 0.00 3.71
1639 3957 3.124636 CGTCCAAAAATACTTGTCGGAGG 59.875 47.826 0.00 0.00 0.00 4.30
1640 3958 3.124636 CCGTCCAAAAATACTTGTCGGAG 59.875 47.826 9.84 0.00 40.80 4.63
1641 3959 3.068560 CCGTCCAAAAATACTTGTCGGA 58.931 45.455 9.84 0.00 40.80 4.55
1642 3960 3.068560 TCCGTCCAAAAATACTTGTCGG 58.931 45.455 0.00 0.00 40.25 4.79
1643 3961 3.124636 CCTCCGTCCAAAAATACTTGTCG 59.875 47.826 0.00 0.00 0.00 4.35
1644 3962 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
1645 3963 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
1646 3964 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
1647 3965 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
1648 3966 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
1649 3967 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
1650 3968 4.533311 ACTTACTCCCTCCGTCCAAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
1651 3969 3.329814 ACTTACTCCCTCCGTCCAAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
1652 3970 2.707257 ACTTACTCCCTCCGTCCAAAAA 59.293 45.455 0.00 0.00 0.00 1.94
1653 3971 2.332117 ACTTACTCCCTCCGTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1654 3972 2.019807 ACTTACTCCCTCCGTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1655 3973 2.450476 GTACTTACTCCCTCCGTCCAA 58.550 52.381 0.00 0.00 0.00 3.53
1656 3974 1.679944 CGTACTTACTCCCTCCGTCCA 60.680 57.143 0.00 0.00 0.00 4.02
1657 3975 1.020437 CGTACTTACTCCCTCCGTCC 58.980 60.000 0.00 0.00 0.00 4.79
1658 3976 1.743996 ACGTACTTACTCCCTCCGTC 58.256 55.000 0.00 0.00 0.00 4.79
1659 3977 2.911484 CTACGTACTTACTCCCTCCGT 58.089 52.381 0.00 0.00 0.00 4.69
1660 3978 1.601430 GCTACGTACTTACTCCCTCCG 59.399 57.143 0.00 0.00 0.00 4.63
1661 3979 2.929641 AGCTACGTACTTACTCCCTCC 58.070 52.381 0.00 0.00 0.00 4.30
1662 3980 4.446371 TGTAGCTACGTACTTACTCCCTC 58.554 47.826 18.74 0.00 0.00 4.30
1663 3981 4.080638 ACTGTAGCTACGTACTTACTCCCT 60.081 45.833 18.74 0.00 0.00 4.20
1664 3982 4.034975 CACTGTAGCTACGTACTTACTCCC 59.965 50.000 18.74 0.00 0.00 4.30
1665 3983 4.034975 CCACTGTAGCTACGTACTTACTCC 59.965 50.000 18.74 0.00 0.00 3.85
1666 3984 4.495514 GCCACTGTAGCTACGTACTTACTC 60.496 50.000 18.74 0.00 0.00 2.59
1667 3985 3.376546 GCCACTGTAGCTACGTACTTACT 59.623 47.826 18.74 2.09 0.00 2.24
1668 3986 3.689346 GCCACTGTAGCTACGTACTTAC 58.311 50.000 18.74 0.00 0.00 2.34
1669 3987 2.352651 CGCCACTGTAGCTACGTACTTA 59.647 50.000 18.74 0.00 0.00 2.24
1670 3988 1.131883 CGCCACTGTAGCTACGTACTT 59.868 52.381 18.74 0.00 0.00 2.24
1671 3989 0.731417 CGCCACTGTAGCTACGTACT 59.269 55.000 18.74 0.00 0.00 2.73
1672 3990 3.231222 CGCCACTGTAGCTACGTAC 57.769 57.895 18.74 12.84 0.00 3.67
1998 4316 1.179174 GGAGCTTTGTGGGGGTCAAC 61.179 60.000 0.00 0.00 0.00 3.18
1999 4317 1.152830 GGAGCTTTGTGGGGGTCAA 59.847 57.895 0.00 0.00 0.00 3.18
2000 4318 2.843545 GGAGCTTTGTGGGGGTCA 59.156 61.111 0.00 0.00 0.00 4.02
2001 4319 2.359975 CGGAGCTTTGTGGGGGTC 60.360 66.667 0.00 0.00 0.00 4.46
2019 4337 1.269309 CCTAGCTTAGCTACGCAGTGG 60.269 57.143 22.65 16.44 45.73 4.00
2020 4338 1.405821 ACCTAGCTTAGCTACGCAGTG 59.594 52.381 22.65 12.66 45.73 3.66
2022 4340 2.226912 CCTACCTAGCTTAGCTACGCAG 59.773 54.545 22.65 16.54 40.44 5.18
2023 4341 2.228059 CCTACCTAGCTTAGCTACGCA 58.772 52.381 22.65 9.06 40.44 5.24
2024 4342 2.226200 GACCTACCTAGCTTAGCTACGC 59.774 54.545 14.06 14.06 40.44 4.42
2061 4388 0.320374 GGGAACGAGTCATGGTCACA 59.680 55.000 0.00 0.00 0.00 3.58
2062 4389 0.608640 AGGGAACGAGTCATGGTCAC 59.391 55.000 0.00 0.00 0.00 3.67
2063 4390 0.895530 GAGGGAACGAGTCATGGTCA 59.104 55.000 0.00 0.00 0.00 4.02
2064 4391 1.187087 AGAGGGAACGAGTCATGGTC 58.813 55.000 0.00 0.00 0.00 4.02
2065 4392 2.526888 TAGAGGGAACGAGTCATGGT 57.473 50.000 0.00 0.00 0.00 3.55
2088 4415 3.138884 TCCAATTTAGCAGCTGTGTCA 57.861 42.857 16.64 0.00 0.00 3.58
2108 4435 3.659183 ATGAATGTCCCAGCTAGCTTT 57.341 42.857 16.46 5.53 0.00 3.51
2118 4445 3.019564 CCACTCCAAGAATGAATGTCCC 58.980 50.000 0.00 0.00 0.00 4.46
2161 4488 4.952460 AGCTTTTGACGTACCAAACTCTA 58.048 39.130 2.18 0.00 35.95 2.43
2185 4518 0.671163 TTGCTAACCGGTAACCGCAG 60.671 55.000 8.00 0.00 46.86 5.18
2224 4557 4.570772 CACCATTGTACATTCCCTTAGTCG 59.429 45.833 0.00 0.00 0.00 4.18
2257 4593 4.115516 CGGGATGACTCTATTTGACACTG 58.884 47.826 0.00 0.00 0.00 3.66
2349 4685 9.884465 AATTAAGAGAAGAATTTTGTTCTGACG 57.116 29.630 7.36 0.00 40.41 4.35


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

AutoCloner maintained by Alex Coulton.