Multiple sequence alignment - TraesCS5D01G100200

Loading Multiple Alignment...

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 TraesCS5D01G100200 chr5D 100.000 4200 0 0 1 4200 112701013 112696814 0.000000e+00 7757.0
1 TraesCS5D01G100200 chr5D 97.297 37 0 1 2421 2456 112697644 112697608 1.260000e-05 62.1
2 TraesCS5D01G100200 chr5D 97.297 37 0 1 3370 3406 112698593 112698558 1.260000e-05 62.1
3 TraesCS5D01G100200 chr5D 97.143 35 0 1 1472 1505 537950343 537950377 1.630000e-04 58.4
4 TraesCS5D01G100200 chr5D 92.308 39 3 0 1528 1566 308353379 308353341 5.870000e-04 56.5
5 TraesCS5D01G100200 chr5B 95.996 2173 64 11 645 2810 121557223 121555067 0.000000e+00 3509.0
6 TraesCS5D01G100200 chr5B 98.407 565 7 2 2806 3370 121554967 121554405 0.000000e+00 992.0
7 TraesCS5D01G100200 chr5B 98.171 492 5 2 3418 3906 121554394 121553904 0.000000e+00 856.0
8 TraesCS5D01G100200 chr5B 89.969 638 54 8 3 631 434927624 434928260 0.000000e+00 815.0
9 TraesCS5D01G100200 chr5B 95.971 273 11 0 3907 4179 121553645 121553373 1.070000e-120 444.0
10 TraesCS5D01G100200 chr5B 89.394 132 13 1 2188 2318 490727680 490727811 9.340000e-37 165.0
11 TraesCS5D01G100200 chr5B 97.297 37 0 1 3370 3406 121555456 121555421 1.260000e-05 62.1
12 TraesCS5D01G100200 chr5B 100.000 33 0 0 1525 1557 641041063 641041095 1.260000e-05 62.1
13 TraesCS5D01G100200 chr5B 97.143 35 1 0 1522 1556 121556357 121556391 4.530000e-05 60.2
14 TraesCS5D01G100200 chr5A 92.687 1258 55 18 1553 2801 115619154 115617925 0.000000e+00 1779.0
15 TraesCS5D01G100200 chr5A 91.678 721 41 6 669 1372 115619872 115619154 0.000000e+00 981.0
16 TraesCS5D01G100200 chr5A 93.274 565 33 3 2806 3370 115617046 115616487 0.000000e+00 828.0
17 TraesCS5D01G100200 chr5A 86.224 813 47 19 3419 4200 115616475 115615697 0.000000e+00 821.0
18 TraesCS5D01G100200 chr5A 89.368 649 57 9 3 640 582124962 582124315 0.000000e+00 806.0
19 TraesCS5D01G100200 chr5A 79.714 419 69 9 2404 2810 706085120 706085534 5.310000e-74 289.0
20 TraesCS5D01G100200 chr5A 94.253 87 4 1 2031 2116 705839144 705839058 9.470000e-27 132.0
21 TraesCS5D01G100200 chr5A 78.409 176 30 6 2639 2810 705567572 705567743 1.600000e-19 108.0
22 TraesCS5D01G100200 chr5A 100.000 28 0 0 4157 4184 115615983 115615956 8.000000e-03 52.8
23 TraesCS5D01G100200 chr7A 90.980 643 53 5 2 640 203010438 203009797 0.000000e+00 861.0
24 TraesCS5D01G100200 chr7A 89.394 132 13 1 2188 2318 183660411 183660280 9.340000e-37 165.0
25 TraesCS5D01G100200 chr7A 100.000 33 0 0 1525 1557 17475473 17475505 1.260000e-05 62.1
26 TraesCS5D01G100200 chrUn 90.394 635 56 5 3 633 222298696 222298063 0.000000e+00 830.0
27 TraesCS5D01G100200 chrUn 90.394 635 56 5 3 633 282749259 282748626 0.000000e+00 830.0
28 TraesCS5D01G100200 chrUn 78.998 419 71 10 2404 2810 134251876 134251463 1.920000e-68 270.0
29 TraesCS5D01G100200 chrUn 81.646 316 33 10 2031 2340 108421852 108421556 5.430000e-59 239.0
30 TraesCS5D01G100200 chrUn 87.166 187 21 2 1798 1984 134250354 134250171 4.260000e-50 209.0
31 TraesCS5D01G100200 chrUn 76.651 424 69 14 2397 2810 108324547 108324950 1.530000e-49 207.0
32 TraesCS5D01G100200 chrUn 79.630 270 32 10 2188 2450 134270540 134270793 5.580000e-39 172.0
33 TraesCS5D01G100200 chrUn 88.889 126 14 0 2188 2313 108324387 108324512 5.620000e-34 156.0
34 TraesCS5D01G100200 chrUn 82.443 131 20 3 2675 2802 134275850 134275980 1.230000e-20 111.0
35 TraesCS5D01G100200 chrUn 84.746 59 7 2 3419 3476 134249265 134249208 1.630000e-04 58.4
36 TraesCS5D01G100200 chr3A 89.441 644 62 4 2 640 722442640 722441998 0.000000e+00 808.0
37 TraesCS5D01G100200 chr1B 89.335 647 63 4 2 643 58793787 58793142 0.000000e+00 808.0
38 TraesCS5D01G100200 chr7B 89.441 644 58 8 3 637 677230922 677230280 0.000000e+00 804.0
39 TraesCS5D01G100200 chr7B 97.222 36 0 1 1525 1560 697608972 697609006 4.530000e-05 60.2
40 TraesCS5D01G100200 chr1A 89.302 645 61 6 2 640 552353039 552352397 0.000000e+00 802.0
41 TraesCS5D01G100200 chr6B 77.243 602 85 21 2188 2775 88216885 88216322 5.280000e-79 305.0
42 TraesCS5D01G100200 chr6B 77.158 556 96 19 2266 2808 88182806 88182269 1.140000e-75 294.0
43 TraesCS5D01G100200 chr6B 86.667 135 16 1 668 800 643265971 643266105 9.410000e-32 148.0
44 TraesCS5D01G100200 chr6B 100.000 33 0 0 1525 1557 30734437 30734405 1.260000e-05 62.1
45 TraesCS5D01G100200 chr6B 100.000 33 0 0 1525 1557 30876418 30876386 1.260000e-05 62.1
46 TraesCS5D01G100200 chr4B 82.034 295 32 9 2031 2324 665565309 665565583 9.080000e-57 231.0
47 TraesCS5D01G100200 chr4B 89.394 132 13 1 2188 2318 195446136 195446267 9.340000e-37 165.0
48 TraesCS5D01G100200 chr4B 94.253 87 4 1 2031 2116 665872158 665872072 9.470000e-27 132.0
49 TraesCS5D01G100200 chr4B 83.871 93 14 1 2905 2996 625998224 625998316 2.080000e-13 87.9
50 TraesCS5D01G100200 chr1D 77.064 327 66 6 2311 2636 409313347 409313029 3.340000e-41 180.0
51 TraesCS5D01G100200 chr6D 89.394 132 13 1 2188 2318 417348409 417348278 9.340000e-37 165.0
52 TraesCS5D01G100200 chr6D 94.286 35 2 0 1470 1504 379336061 379336027 2.000000e-03 54.7
53 TraesCS5D01G100200 chr2A 86.087 115 14 2 2205 2318 735256929 735256816 5.700000e-24 122.0
54 TraesCS5D01G100200 chr2A 97.222 36 1 0 1180 1215 14991330 14991295 1.260000e-05 62.1
55 TraesCS5D01G100200 chr3B 75.655 267 48 14 2558 2810 68293407 68293670 2.650000e-22 117.0
56 TraesCS5D01G100200 chr3B 100.000 28 0 0 1470 1497 507008979 507009006 8.000000e-03 52.8
57 TraesCS5D01G100200 chr6A 95.918 49 2 0 668 716 572138798 572138846 3.480000e-11 80.5
58 TraesCS5D01G100200 chr4D 100.000 33 0 0 1525 1557 13244555 13244587 1.260000e-05 62.1
59 TraesCS5D01G100200 chr7D 92.105 38 3 0 1460 1497 386719180 386719217 2.000000e-03 54.7


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 TraesCS5D01G100200 chr5D 112696814 112701013 4199 True 2627.066667 7757 98.1980 1 4200 3 chr5D.!!$R2 4199
1 TraesCS5D01G100200 chr5B 121553373 121557223 3850 True 1172.620000 3509 97.1684 645 4179 5 chr5B.!!$R1 3534
2 TraesCS5D01G100200 chr5B 434927624 434928260 636 False 815.000000 815 89.9690 3 631 1 chr5B.!!$F2 628
3 TraesCS5D01G100200 chr5A 115615697 115619872 4175 True 892.360000 1779 92.7726 669 4200 5 chr5A.!!$R3 3531
4 TraesCS5D01G100200 chr5A 582124315 582124962 647 True 806.000000 806 89.3680 3 640 1 chr5A.!!$R1 637
5 TraesCS5D01G100200 chr7A 203009797 203010438 641 True 861.000000 861 90.9800 2 640 1 chr7A.!!$R2 638
6 TraesCS5D01G100200 chrUn 222298063 222298696 633 True 830.000000 830 90.3940 3 633 1 chrUn.!!$R2 630
7 TraesCS5D01G100200 chrUn 282748626 282749259 633 True 830.000000 830 90.3940 3 633 1 chrUn.!!$R3 630
8 TraesCS5D01G100200 chr3A 722441998 722442640 642 True 808.000000 808 89.4410 2 640 1 chr3A.!!$R1 638
9 TraesCS5D01G100200 chr1B 58793142 58793787 645 True 808.000000 808 89.3350 2 643 1 chr1B.!!$R1 641
10 TraesCS5D01G100200 chr7B 677230280 677230922 642 True 804.000000 804 89.4410 3 637 1 chr7B.!!$R1 634
11 TraesCS5D01G100200 chr1A 552352397 552353039 642 True 802.000000 802 89.3020 2 640 1 chr1A.!!$R1 638
12 TraesCS5D01G100200 chr6B 88216322 88216885 563 True 305.000000 305 77.2430 2188 2775 1 chr6B.!!$R4 587
13 TraesCS5D01G100200 chr6B 88182269 88182806 537 True 294.000000 294 77.1580 2266 2808 1 chr6B.!!$R3 542

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
702 717 0.535335 TCATCGTGTAGGGCCTTCAC 59.465 55.0 27.81 27.81 0.0 3.18 F
1239 1271 0.034186 AATTCATTCCCCTCGCAGCA 60.034 50.0 0.00 0.00 0.0 4.41 F
1522 1554 0.105964 ATCCATTTCCGATTCCGCGA 59.894 50.0 8.23 0.00 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1555 0.921347 CGGAATTACTTGTCGCGGAG 59.079 55.000 6.13 4.8 0.0 4.63 R
3154 4101 0.179215 CGACGACAAAATGCAGCTCC 60.179 55.000 0.00 0.0 0.0 4.70 R
3415 4362 2.037121 TCCGTGCTGAACAAGAAGATCA 59.963 45.455 0.00 0.0 0.0 2.92 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
27 28 2.781923 TGTAAAGGCTTCGGGTTTACC 58.218 47.619 0.00 0.00 36.31 2.85
326 332 8.104566 AGGAGCTAGATCGTACAGTTAGATTAT 58.895 37.037 0.46 0.00 0.00 1.28
421 427 3.135895 CCAGGGACATAACGGGTAGAATT 59.864 47.826 0.00 0.00 0.00 2.17
426 433 4.872124 GGACATAACGGGTAGAATTCGTTT 59.128 41.667 7.11 0.00 43.32 3.60
428 435 6.703165 GGACATAACGGGTAGAATTCGTTTAT 59.297 38.462 7.11 0.64 43.32 1.40
444 451 6.246925 TCGTTTATAGACAAATACGTTCGC 57.753 37.500 0.00 0.00 0.00 4.70
543 554 9.924650 GTAGACTCTTTGGAAAGACAGTATAAA 57.075 33.333 0.00 0.00 39.95 1.40
550 561 8.990163 TTTGGAAAGACAGTATAAAAAGGTCT 57.010 30.769 0.00 0.00 40.33 3.85
558 569 8.117312 AGACAGTATAAAAAGGTCTCTACTCCT 58.883 37.037 0.00 0.00 33.84 3.69
559 570 9.406113 GACAGTATAAAAAGGTCTCTACTCCTA 57.594 37.037 0.00 0.00 33.27 2.94
567 579 5.987019 AGGTCTCTACTCCTAATCTCAGT 57.013 43.478 0.00 0.00 31.66 3.41
569 581 6.126409 AGGTCTCTACTCCTAATCTCAGTTG 58.874 44.000 0.00 0.00 31.66 3.16
575 587 3.449018 ACTCCTAATCTCAGTTGTGCGAT 59.551 43.478 0.00 0.00 28.89 4.58
607 619 1.409427 ACCACAGATAAGCGTAGAGGC 59.591 52.381 0.00 0.00 0.00 4.70
624 639 1.061346 AGGCATAGGGGTAGACCACAT 60.061 52.381 3.26 0.00 43.57 3.21
640 655 7.184067 AGACCACATACCCTAAACTTCTAAG 57.816 40.000 0.00 0.00 0.00 2.18
643 658 6.040878 CCACATACCCTAAACTTCTAAGACG 58.959 44.000 0.00 0.00 0.00 4.18
649 664 4.174762 CCTAAACTTCTAAGACGCTGGTC 58.825 47.826 0.00 0.00 43.76 4.02
702 717 0.535335 TCATCGTGTAGGGCCTTCAC 59.465 55.000 27.81 27.81 0.00 3.18
843 858 5.188434 TCTGGCCACAAGAAATATCAGAAG 58.812 41.667 0.00 0.00 0.00 2.85
853 869 5.537188 AGAAATATCAGAAGCTAAGAGGCG 58.463 41.667 0.00 0.00 37.29 5.52
920 936 2.647297 GTGCCCTTGCTTGCAGAC 59.353 61.111 0.00 0.00 38.34 3.51
949 979 3.627237 GCTCCACCCCAGAATCCATAAAA 60.627 47.826 0.00 0.00 0.00 1.52
963 993 1.406539 CATAAAAGCCTCCGCAGCAAT 59.593 47.619 0.00 0.00 37.52 3.56
999 1029 2.009774 TCCGAGCTAAGCAATTTCAGC 58.990 47.619 0.00 0.00 0.00 4.26
1003 1033 3.181503 CGAGCTAAGCAATTTCAGCATGT 60.182 43.478 0.00 0.00 36.47 3.21
1026 1056 0.966179 TGCCGTTTCTAGCTCAGACA 59.034 50.000 0.00 0.00 31.12 3.41
1041 1071 4.799678 CTCAGACATCTCAAACTACACGT 58.200 43.478 0.00 0.00 0.00 4.49
1066 1096 0.749818 TGCGAGTTGTTTTGGGCTGA 60.750 50.000 0.00 0.00 0.00 4.26
1072 1102 1.000274 GTTGTTTTGGGCTGAATCGCT 60.000 47.619 0.00 0.00 0.00 4.93
1146 1178 8.931385 TGCTTTATCTTTATGATTTTCCAAGC 57.069 30.769 0.00 0.00 36.65 4.01
1163 1195 5.639139 TCCAAGCATATGCATATACCCAAA 58.361 37.500 28.62 1.94 45.16 3.28
1239 1271 0.034186 AATTCATTCCCCTCGCAGCA 60.034 50.000 0.00 0.00 0.00 4.41
1247 1279 1.174712 CCCCTCGCAGCATATTTGGG 61.175 60.000 0.00 0.00 0.00 4.12
1497 1529 2.564062 TCTCCGTCCGGAATTACTTGTT 59.436 45.455 5.23 0.00 44.66 2.83
1501 1533 2.070783 GTCCGGAATTACTTGTTGCGA 58.929 47.619 5.23 0.00 41.99 5.10
1510 1542 6.589907 GGAATTACTTGTTGCGAAATCCATTT 59.410 34.615 0.00 0.00 0.00 2.32
1511 1543 7.201435 GGAATTACTTGTTGCGAAATCCATTTC 60.201 37.037 2.39 2.39 42.00 2.17
1512 1544 3.913089 ACTTGTTGCGAAATCCATTTCC 58.087 40.909 6.48 1.46 42.34 3.13
1513 1545 2.627863 TGTTGCGAAATCCATTTCCG 57.372 45.000 6.48 3.85 42.34 4.30
1514 1546 2.155279 TGTTGCGAAATCCATTTCCGA 58.845 42.857 6.48 0.00 42.34 4.55
1515 1547 2.752354 TGTTGCGAAATCCATTTCCGAT 59.248 40.909 6.48 0.00 42.34 4.18
1516 1548 3.192422 TGTTGCGAAATCCATTTCCGATT 59.808 39.130 6.48 0.00 42.34 3.34
1517 1549 3.691049 TGCGAAATCCATTTCCGATTC 57.309 42.857 6.48 0.00 42.34 2.52
1518 1550 2.357637 TGCGAAATCCATTTCCGATTCC 59.642 45.455 6.48 0.00 42.34 3.01
1519 1551 2.602217 GCGAAATCCATTTCCGATTCCG 60.602 50.000 6.48 0.00 42.34 4.30
1520 1552 2.602217 CGAAATCCATTTCCGATTCCGC 60.602 50.000 6.48 0.00 42.34 5.54
1521 1553 0.944386 AATCCATTTCCGATTCCGCG 59.056 50.000 0.00 0.00 0.00 6.46
1522 1554 0.105964 ATCCATTTCCGATTCCGCGA 59.894 50.000 8.23 0.00 0.00 5.87
1523 1555 0.808453 TCCATTTCCGATTCCGCGAC 60.808 55.000 8.23 0.00 0.00 5.19
1666 1698 6.917533 AGAAAAGGACATGCTTGATTACTTG 58.082 36.000 6.60 0.00 0.00 3.16
2060 2095 5.335976 GGGCTTGGTTTCTGTAGATTTTGAG 60.336 44.000 0.00 0.00 0.00 3.02
2144 2179 1.090052 GCTGGCACGGACAGTTATCC 61.090 60.000 8.31 0.00 41.48 2.59
2159 2194 5.044105 ACAGTTATCCCCCTCTTTTGCTTAT 60.044 40.000 0.00 0.00 0.00 1.73
2162 2197 7.559897 CAGTTATCCCCCTCTTTTGCTTATTAA 59.440 37.037 0.00 0.00 0.00 1.40
2180 2217 9.390795 GCTTATTAACATTGCATCTGAACATAG 57.609 33.333 3.97 0.00 0.00 2.23
2378 2417 3.751175 CCTTTTTCTTGTGCCGTCAGATA 59.249 43.478 0.00 0.00 0.00 1.98
2476 2531 4.216687 CACAAACTTTCCCCTGCGTAATTA 59.783 41.667 0.00 0.00 0.00 1.40
2566 2621 3.128938 GGATAGTCTGTACAGTCACGCTT 59.871 47.826 21.99 3.69 0.00 4.68
2601 2657 4.826274 TCCATCAAGTAAGTTCTCCCTG 57.174 45.455 0.00 0.00 0.00 4.45
2805 3624 8.080417 CGATAGGAATTTGAGAGTCGGTAAATA 58.920 37.037 3.75 0.00 0.00 1.40
2976 3923 2.972625 TGCCTAAAATCAGGAGACACG 58.027 47.619 0.00 0.00 38.00 4.49
3142 4089 5.261216 ACATCCAAATTTCATCCGGTTACT 58.739 37.500 0.00 0.00 0.00 2.24
3154 4101 3.017442 TCCGGTTACTGAGAGATGTCTG 58.983 50.000 0.00 0.00 30.97 3.51
3178 4125 1.131826 GCATTTTGTCGTCGACCCG 59.868 57.895 22.05 7.44 0.00 5.28
3370 4317 2.191802 CAGTGACTGATGAGCGATGTC 58.808 52.381 6.79 0.00 32.44 3.06
3371 4318 2.098614 AGTGACTGATGAGCGATGTCT 58.901 47.619 0.00 0.00 0.00 3.41
3372 4319 3.065925 CAGTGACTGATGAGCGATGTCTA 59.934 47.826 6.79 0.00 32.44 2.59
3373 4320 3.888323 AGTGACTGATGAGCGATGTCTAT 59.112 43.478 0.00 0.00 0.00 1.98
3374 4321 4.023279 AGTGACTGATGAGCGATGTCTATC 60.023 45.833 0.00 0.00 0.00 2.08
3375 4322 4.023279 GTGACTGATGAGCGATGTCTATCT 60.023 45.833 0.00 0.00 0.00 1.98
3376 4323 4.582240 TGACTGATGAGCGATGTCTATCTT 59.418 41.667 0.00 0.00 0.00 2.40
3377 4324 4.869215 ACTGATGAGCGATGTCTATCTTG 58.131 43.478 0.00 0.00 0.00 3.02
3378 4325 4.582240 ACTGATGAGCGATGTCTATCTTGA 59.418 41.667 0.00 0.00 0.00 3.02
3380 4327 5.707931 TGATGAGCGATGTCTATCTTGATC 58.292 41.667 0.00 0.00 0.00 2.92
3381 4328 5.476254 TGATGAGCGATGTCTATCTTGATCT 59.524 40.000 0.00 0.00 0.00 2.75
3382 4329 5.118642 TGAGCGATGTCTATCTTGATCTG 57.881 43.478 0.00 0.00 0.00 2.90
3383 4330 3.911868 AGCGATGTCTATCTTGATCTGC 58.088 45.455 0.00 0.00 0.00 4.26
3384 4331 3.573538 AGCGATGTCTATCTTGATCTGCT 59.426 43.478 0.00 0.00 0.00 4.24
3385 4332 4.039004 AGCGATGTCTATCTTGATCTGCTT 59.961 41.667 0.00 0.00 0.00 3.91
3386 4333 4.150274 GCGATGTCTATCTTGATCTGCTTG 59.850 45.833 0.00 0.00 0.00 4.01
3387 4334 5.527033 CGATGTCTATCTTGATCTGCTTGA 58.473 41.667 0.00 0.00 0.00 3.02
3388 4335 5.981915 CGATGTCTATCTTGATCTGCTTGAA 59.018 40.000 0.00 0.00 0.00 2.69
3389 4336 6.478016 CGATGTCTATCTTGATCTGCTTGAAA 59.522 38.462 0.00 0.00 0.00 2.69
3390 4337 7.010830 CGATGTCTATCTTGATCTGCTTGAAAA 59.989 37.037 0.00 0.00 0.00 2.29
3391 4338 7.984422 TGTCTATCTTGATCTGCTTGAAAAA 57.016 32.000 0.00 0.00 0.00 1.94
3392 4339 8.571461 TGTCTATCTTGATCTGCTTGAAAAAT 57.429 30.769 0.00 0.00 0.00 1.82
3393 4340 9.017509 TGTCTATCTTGATCTGCTTGAAAAATT 57.982 29.630 0.00 0.00 0.00 1.82
3394 4341 9.500864 GTCTATCTTGATCTGCTTGAAAAATTC 57.499 33.333 0.00 0.00 0.00 2.17
3395 4342 9.458727 TCTATCTTGATCTGCTTGAAAAATTCT 57.541 29.630 0.00 0.00 0.00 2.40
3402 4349 9.850628 TGATCTGCTTGAAAAATTCTAATTCTG 57.149 29.630 0.00 0.00 0.00 3.02
3403 4350 8.699283 ATCTGCTTGAAAAATTCTAATTCTGC 57.301 30.769 0.00 0.00 0.00 4.26
3404 4351 7.660112 TCTGCTTGAAAAATTCTAATTCTGCA 58.340 30.769 0.00 0.00 34.65 4.41
3405 4352 7.596248 TCTGCTTGAAAAATTCTAATTCTGCAC 59.404 33.333 0.00 0.00 33.44 4.57
3406 4353 6.646240 TGCTTGAAAAATTCTAATTCTGCACC 59.354 34.615 0.00 0.00 32.70 5.01
3407 4354 6.870439 GCTTGAAAAATTCTAATTCTGCACCT 59.130 34.615 0.00 0.00 0.00 4.00
3408 4355 7.386025 GCTTGAAAAATTCTAATTCTGCACCTT 59.614 33.333 0.00 0.00 0.00 3.50
3409 4356 8.816640 TTGAAAAATTCTAATTCTGCACCTTC 57.183 30.769 0.00 0.00 0.00 3.46
3410 4357 8.181904 TGAAAAATTCTAATTCTGCACCTTCT 57.818 30.769 0.00 0.00 0.00 2.85
3411 4358 9.295825 TGAAAAATTCTAATTCTGCACCTTCTA 57.704 29.630 0.00 0.00 0.00 2.10
3414 4361 9.692325 AAAATTCTAATTCTGCACCTTCTATCT 57.308 29.630 0.00 0.00 0.00 1.98
3415 4362 9.692325 AAATTCTAATTCTGCACCTTCTATCTT 57.308 29.630 0.00 0.00 0.00 2.40
3416 4363 8.674263 ATTCTAATTCTGCACCTTCTATCTTG 57.326 34.615 0.00 0.00 0.00 3.02
3734 4684 3.402628 ACACTATTGTTCTGGTTCGCT 57.597 42.857 0.00 0.00 28.43 4.93
4119 5359 9.262472 CATTTAATCGCAGTACTGTTTTCTAAC 57.738 33.333 23.44 3.95 34.75 2.34
4193 5433 5.227569 TCCTCGTATATAGGGTTACGTGA 57.772 43.478 0.00 0.00 41.38 4.35
4197 5437 6.259608 CCTCGTATATAGGGTTACGTGATAGG 59.740 46.154 0.00 2.64 41.38 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.368311 TTGGTAAACCCGAAGCCTTT 57.632 45.000 0.00 0.00 35.15 3.11
17 18 7.889873 ATCATTCAAATATTGGTAAACCCGA 57.110 32.000 0.00 0.00 35.15 5.14
27 28 8.686397 TGTCCGAAACAATCATTCAAATATTG 57.314 30.769 0.00 0.00 34.03 1.90
47 48 2.029020 TCCAACATCTCTCACTTGTCCG 60.029 50.000 0.00 0.00 0.00 4.79
224 230 5.160607 TCCACTGATAATCGACCAACTTT 57.839 39.130 0.00 0.00 0.00 2.66
228 234 6.228616 TGTATTCCACTGATAATCGACCAA 57.771 37.500 0.00 0.00 0.00 3.67
393 399 0.249120 CGTTATGTCCCTGGAGCACA 59.751 55.000 0.00 0.00 0.00 4.57
401 407 3.069158 CGAATTCTACCCGTTATGTCCCT 59.931 47.826 3.52 0.00 0.00 4.20
421 427 5.053091 CGCGAACGTATTTGTCTATAAACGA 60.053 40.000 0.00 0.00 33.53 3.85
426 433 4.291540 ACCGCGAACGTATTTGTCTATA 57.708 40.909 8.23 0.00 37.70 1.31
428 435 2.634982 ACCGCGAACGTATTTGTCTA 57.365 45.000 8.23 0.00 37.70 2.59
438 445 1.194997 TCAAATTACCAACCGCGAACG 59.805 47.619 8.23 0.00 39.67 3.95
440 447 3.126171 CAGATCAAATTACCAACCGCGAA 59.874 43.478 8.23 0.00 0.00 4.70
444 451 4.261801 AGTCCAGATCAAATTACCAACCG 58.738 43.478 0.00 0.00 0.00 4.44
474 481 7.941795 TCCTAGTCTTTTCAACTAGTTTTCG 57.058 36.000 5.07 0.00 43.04 3.46
514 525 3.640029 TGTCTTTCCAAAGAGTCTACCGT 59.360 43.478 1.83 0.00 45.01 4.83
515 526 4.238514 CTGTCTTTCCAAAGAGTCTACCG 58.761 47.826 1.83 0.00 45.01 4.02
519 530 9.847224 TTTTTATACTGTCTTTCCAAAGAGTCT 57.153 29.630 1.83 0.00 45.01 3.24
543 554 6.737608 ACTGAGATTAGGAGTAGAGACCTTT 58.262 40.000 0.00 0.00 37.68 3.11
550 561 4.096532 CGCACAACTGAGATTAGGAGTAGA 59.903 45.833 0.00 0.00 0.00 2.59
555 566 4.471904 AATCGCACAACTGAGATTAGGA 57.528 40.909 0.00 0.00 43.00 2.94
558 569 4.994217 TCACAAATCGCACAACTGAGATTA 59.006 37.500 0.88 0.00 43.74 1.75
559 570 3.814842 TCACAAATCGCACAACTGAGATT 59.185 39.130 0.00 0.00 45.71 2.40
567 579 1.573932 CCGCTCACAAATCGCACAA 59.426 52.632 0.00 0.00 0.00 3.33
569 581 2.202349 GCCGCTCACAAATCGCAC 60.202 61.111 0.00 0.00 0.00 5.34
624 639 4.159135 CCAGCGTCTTAGAAGTTTAGGGTA 59.841 45.833 0.00 0.00 0.00 3.69
633 648 2.654939 GCGACCAGCGTCTTAGAAG 58.345 57.895 0.00 0.00 43.41 2.85
649 664 3.917760 GGATCGGGAGGACCAGCG 61.918 72.222 0.00 0.00 40.22 5.18
653 668 2.758737 ACACGGATCGGGAGGACC 60.759 66.667 5.18 0.00 32.98 4.46
702 717 4.455606 ACCTTGACTTTCTTTCCAGACTG 58.544 43.478 0.00 0.00 0.00 3.51
783 798 3.181510 GCGTATGGCTCTAAACAAACCAG 60.182 47.826 0.00 0.00 39.11 4.00
843 858 2.038387 TTTCCATTCCGCCTCTTAGC 57.962 50.000 0.00 0.00 0.00 3.09
853 869 1.546029 GGCACTGTCCTTTTCCATTCC 59.454 52.381 0.00 0.00 0.00 3.01
904 920 2.195411 TGTCTGCAAGCAAGGGCA 59.805 55.556 0.00 0.00 44.61 5.36
920 936 3.557903 CTGGGGTGGAGCTGTGGTG 62.558 68.421 0.00 0.00 0.00 4.17
949 979 0.820891 CCATTATTGCTGCGGAGGCT 60.821 55.000 5.93 0.00 40.82 4.58
963 993 2.365617 CTCGGAAGCTTAGCTCCCATTA 59.634 50.000 10.71 0.00 30.34 1.90
999 1029 2.679837 AGCTAGAAACGGCATCAACATG 59.320 45.455 0.00 0.00 0.00 3.21
1003 1033 2.233676 TCTGAGCTAGAAACGGCATCAA 59.766 45.455 0.00 0.00 30.84 2.57
1026 1056 4.307432 CAACAGGACGTGTAGTTTGAGAT 58.693 43.478 0.39 0.00 39.03 2.75
1041 1071 1.403679 CCAAAACAACTCGCAACAGGA 59.596 47.619 0.00 0.00 0.00 3.86
1136 1166 6.725369 TGGGTATATGCATATGCTTGGAAAAT 59.275 34.615 27.17 13.43 42.66 1.82
1163 1195 7.615365 TCTGCACCAGGAATATTTAGTTCAAAT 59.385 33.333 0.00 0.00 35.18 2.32
1176 1208 4.458397 CATCTACAATCTGCACCAGGAAT 58.542 43.478 0.00 0.00 31.51 3.01
1239 1271 2.608623 GCCATTAGTGGGCCCAAATAT 58.391 47.619 30.64 17.01 46.14 1.28
1247 1279 2.902343 GGAGCGCCATTAGTGGGC 60.902 66.667 2.29 7.87 46.14 5.36
1468 1500 3.784511 TTCCGGACGGAGAGAGTATAT 57.215 47.619 13.64 0.00 46.06 0.86
1476 1508 2.173519 ACAAGTAATTCCGGACGGAGA 58.826 47.619 13.64 5.90 46.06 3.71
1497 1529 2.357637 GGAATCGGAAATGGATTTCGCA 59.642 45.455 6.12 0.00 45.37 5.10
1501 1533 1.333619 CGCGGAATCGGAAATGGATTT 59.666 47.619 0.00 0.00 34.41 2.17
1510 1542 3.884350 CGGAGTCGCGGAATCGGA 61.884 66.667 6.13 0.00 36.79 4.55
1520 1552 1.582502 GAATTACTTGTCGCGGAGTCG 59.417 52.381 6.13 0.00 39.81 4.18
1521 1553 1.925185 GGAATTACTTGTCGCGGAGTC 59.075 52.381 6.13 0.00 0.00 3.36
1522 1554 1.734707 CGGAATTACTTGTCGCGGAGT 60.735 52.381 6.13 10.98 0.00 3.85
1523 1555 0.921347 CGGAATTACTTGTCGCGGAG 59.079 55.000 6.13 4.80 0.00 4.63
1666 1698 8.892723 CCTCTCATCTGATACTGAGATGTATAC 58.107 40.741 9.26 0.00 45.01 1.47
1967 2002 2.299297 GGTCGAAGAACTGGAAAGGAGA 59.701 50.000 0.00 0.00 43.75 3.71
2060 2095 3.902881 ATGTCATCTTCCACCTCAGAC 57.097 47.619 0.00 0.00 0.00 3.51
2137 2172 5.734031 ATAAGCAAAAGAGGGGGATAACT 57.266 39.130 0.00 0.00 0.00 2.24
2144 2179 5.812127 GCAATGTTAATAAGCAAAAGAGGGG 59.188 40.000 0.00 0.00 0.00 4.79
2162 2197 8.340618 AGTAAAACTATGTTCAGATGCAATGT 57.659 30.769 0.00 0.00 0.00 2.71
2180 2217 4.600692 ATCCTGTTGGGCAAAGTAAAAC 57.399 40.909 0.00 0.00 34.39 2.43
2185 2223 2.676748 TGAAATCCTGTTGGGCAAAGT 58.323 42.857 0.00 0.00 34.39 2.66
2378 2417 7.709182 CACTGCAAATTCATTGTCATATTGGAT 59.291 33.333 0.00 0.00 41.32 3.41
2476 2531 4.581309 TGGCTCTTTCAGATCAAGGAAT 57.419 40.909 0.00 0.00 0.00 3.01
2566 2621 5.556915 ACTTGATGGAAAACGGATAACTGA 58.443 37.500 0.00 0.00 0.00 3.41
2601 2657 6.093357 TCTGAAAGGGAACAAAAACAAAATGC 59.907 34.615 0.00 0.00 0.00 3.56
2805 3624 7.379750 GTTCTAGGTTCTGAATGTTCTACAGT 58.620 38.462 0.00 0.00 33.93 3.55
2849 3793 4.523083 TGCAACAGTTACTTGGTTCTTCT 58.477 39.130 0.00 0.00 0.00 2.85
2850 3794 4.335594 ACTGCAACAGTTACTTGGTTCTTC 59.664 41.667 0.00 0.00 42.59 2.87
2851 3795 4.270008 ACTGCAACAGTTACTTGGTTCTT 58.730 39.130 0.00 0.00 42.59 2.52
3142 4089 0.822811 GCAGCTCCAGACATCTCTCA 59.177 55.000 0.00 0.00 0.00 3.27
3154 4101 0.179215 CGACGACAAAATGCAGCTCC 60.179 55.000 0.00 0.00 0.00 4.70
3376 4323 9.850628 CAGAATTAGAATTTTTCAAGCAGATCA 57.149 29.630 0.00 0.00 0.00 2.92
3377 4324 8.805688 GCAGAATTAGAATTTTTCAAGCAGATC 58.194 33.333 0.00 0.00 0.00 2.75
3378 4325 8.308931 TGCAGAATTAGAATTTTTCAAGCAGAT 58.691 29.630 0.00 0.00 32.59 2.90
3380 4327 7.148689 GGTGCAGAATTAGAATTTTTCAAGCAG 60.149 37.037 0.00 0.00 35.12 4.24
3381 4328 6.646240 GGTGCAGAATTAGAATTTTTCAAGCA 59.354 34.615 0.00 0.00 33.36 3.91
3382 4329 6.870439 AGGTGCAGAATTAGAATTTTTCAAGC 59.130 34.615 0.00 0.00 0.00 4.01
3383 4330 8.822652 AAGGTGCAGAATTAGAATTTTTCAAG 57.177 30.769 0.00 0.00 0.00 3.02
3384 4331 8.641541 AGAAGGTGCAGAATTAGAATTTTTCAA 58.358 29.630 0.00 0.00 0.00 2.69
3385 4332 8.181904 AGAAGGTGCAGAATTAGAATTTTTCA 57.818 30.769 0.00 0.00 0.00 2.69
3388 4335 9.692325 AGATAGAAGGTGCAGAATTAGAATTTT 57.308 29.630 0.00 0.00 0.00 1.82
3389 4336 9.692325 AAGATAGAAGGTGCAGAATTAGAATTT 57.308 29.630 0.00 0.00 0.00 1.82
3390 4337 9.118300 CAAGATAGAAGGTGCAGAATTAGAATT 57.882 33.333 0.00 0.00 0.00 2.17
3391 4338 8.489489 TCAAGATAGAAGGTGCAGAATTAGAAT 58.511 33.333 0.00 0.00 0.00 2.40
3392 4339 7.851228 TCAAGATAGAAGGTGCAGAATTAGAA 58.149 34.615 0.00 0.00 0.00 2.10
3393 4340 7.423844 TCAAGATAGAAGGTGCAGAATTAGA 57.576 36.000 0.00 0.00 0.00 2.10
3394 4341 8.149647 AGATCAAGATAGAAGGTGCAGAATTAG 58.850 37.037 0.00 0.00 0.00 1.73
3395 4342 8.027524 AGATCAAGATAGAAGGTGCAGAATTA 57.972 34.615 0.00 0.00 0.00 1.40
3396 4343 6.897986 AGATCAAGATAGAAGGTGCAGAATT 58.102 36.000 0.00 0.00 0.00 2.17
3397 4344 6.497624 AGATCAAGATAGAAGGTGCAGAAT 57.502 37.500 0.00 0.00 0.00 2.40
3398 4345 5.946942 AGATCAAGATAGAAGGTGCAGAA 57.053 39.130 0.00 0.00 0.00 3.02
3399 4346 5.660417 AGAAGATCAAGATAGAAGGTGCAGA 59.340 40.000 0.00 0.00 0.00 4.26
3400 4347 5.916318 AGAAGATCAAGATAGAAGGTGCAG 58.084 41.667 0.00 0.00 0.00 4.41
3401 4348 5.946942 AGAAGATCAAGATAGAAGGTGCA 57.053 39.130 0.00 0.00 0.00 4.57
3402 4349 6.112058 ACAAGAAGATCAAGATAGAAGGTGC 58.888 40.000 0.00 0.00 0.00 5.01
3403 4350 7.821359 TGAACAAGAAGATCAAGATAGAAGGTG 59.179 37.037 0.00 0.00 0.00 4.00
3404 4351 7.911651 TGAACAAGAAGATCAAGATAGAAGGT 58.088 34.615 0.00 0.00 0.00 3.50
3405 4352 7.011295 GCTGAACAAGAAGATCAAGATAGAAGG 59.989 40.741 0.00 0.00 0.00 3.46
3406 4353 7.548427 TGCTGAACAAGAAGATCAAGATAGAAG 59.452 37.037 0.00 0.00 0.00 2.85
3407 4354 7.332926 GTGCTGAACAAGAAGATCAAGATAGAA 59.667 37.037 0.00 0.00 0.00 2.10
3408 4355 6.815641 GTGCTGAACAAGAAGATCAAGATAGA 59.184 38.462 0.00 0.00 0.00 1.98
3409 4356 6.237781 CGTGCTGAACAAGAAGATCAAGATAG 60.238 42.308 0.00 0.00 0.00 2.08
3410 4357 5.578336 CGTGCTGAACAAGAAGATCAAGATA 59.422 40.000 0.00 0.00 0.00 1.98
3411 4358 4.391216 CGTGCTGAACAAGAAGATCAAGAT 59.609 41.667 0.00 0.00 0.00 2.40
3412 4359 3.742882 CGTGCTGAACAAGAAGATCAAGA 59.257 43.478 0.00 0.00 0.00 3.02
3413 4360 3.120408 CCGTGCTGAACAAGAAGATCAAG 60.120 47.826 0.00 0.00 0.00 3.02
3414 4361 2.807967 CCGTGCTGAACAAGAAGATCAA 59.192 45.455 0.00 0.00 0.00 2.57
3415 4362 2.037121 TCCGTGCTGAACAAGAAGATCA 59.963 45.455 0.00 0.00 0.00 2.92
3416 4363 2.688507 TCCGTGCTGAACAAGAAGATC 58.311 47.619 0.00 0.00 0.00 2.75
3783 4733 3.450904 TGTATTGGAGGGAGTAGCAACT 58.549 45.455 0.00 0.00 39.21 3.16
4119 5359 9.559958 CACTACTTAGTTTTTGGAGCAATATTG 57.440 33.333 11.27 11.27 33.46 1.90


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

AutoCloner maintained by Alex Coulton.