Multiple sequence alignment - TraesCS5B01G237900

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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 TraesCS5B01G237900 chr5B 100.000 5381 0 0 1 5381 418815836 418810456 0.000000e+00 9937.0
1 TraesCS5B01G237900 chr5B 88.851 592 46 9 4785 5366 418810471 418811052 0.000000e+00 710.0
2 TraesCS5B01G237900 chr5B 88.863 422 23 7 4663 5066 116672651 116672236 1.040000e-136 497.0
3 TraesCS5B01G237900 chr5B 94.389 303 15 2 5072 5373 116672217 116672518 1.060000e-126 464.0
4 TraesCS5B01G237900 chr5B 100.000 176 0 0 3513 3688 215888250 215888075 5.200000e-85 326.0
5 TraesCS5B01G237900 chr5B 100.000 175 0 0 3513 3687 291789119 291789293 1.870000e-84 324.0
6 TraesCS5B01G237900 chr5A 96.364 2640 69 9 1 2626 455468379 455465753 0.000000e+00 4318.0
7 TraesCS5B01G237900 chr5A 92.350 902 44 16 3688 4570 455464603 455463708 0.000000e+00 1260.0
8 TraesCS5B01G237900 chr5A 97.125 313 8 1 3207 3518 455464902 455464590 1.330000e-145 527.0
9 TraesCS5B01G237900 chr5A 96.939 294 9 0 2915 3208 455465250 455464957 1.350000e-135 494.0
10 TraesCS5B01G237900 chr5A 98.347 242 4 0 2647 2888 455465490 455465249 4.980000e-115 425.0
11 TraesCS5B01G237900 chr5A 99.438 178 1 0 3514 3691 177619418 177619241 1.870000e-84 324.0
12 TraesCS5B01G237900 chr5A 95.588 68 3 0 4596 4663 455463707 455463640 5.700000e-20 110.0
13 TraesCS5B01G237900 chr5D 98.318 1605 20 2 1612 3209 354503661 354502057 0.000000e+00 2808.0
14 TraesCS5B01G237900 chr5D 97.390 1571 32 2 1 1570 354505219 354503657 0.000000e+00 2665.0
15 TraesCS5B01G237900 chr5D 93.379 876 35 10 3688 4544 354501704 354500833 0.000000e+00 1275.0
16 TraesCS5B01G237900 chr5D 98.722 313 3 1 3207 3518 354502003 354501691 6.090000e-154 555.0
17 TraesCS5B01G237900 chr5D 87.097 186 15 5 4661 4842 396918046 396917866 9.140000e-48 202.0
18 TraesCS5B01G237900 chr5D 95.238 84 4 0 4578 4661 354500832 354500749 3.380000e-27 134.0
19 TraesCS5B01G237900 chrUn 87.129 1212 102 20 993 2165 104870522 104869326 0.000000e+00 1325.0
20 TraesCS5B01G237900 chrUn 88.857 1050 75 19 2176 3208 104868374 104867350 0.000000e+00 1253.0
21 TraesCS5B01G237900 chrUn 87.854 848 60 22 3685 4496 104866995 104866155 0.000000e+00 955.0
22 TraesCS5B01G237900 chr6A 89.289 1055 79 12 2167 3208 42924611 42925644 0.000000e+00 1291.0
23 TraesCS5B01G237900 chr6A 85.087 1207 121 17 993 2165 42922690 42923871 0.000000e+00 1177.0
24 TraesCS5B01G237900 chr6A 84.859 568 48 17 3685 4247 42926002 42926536 6.130000e-149 538.0
25 TraesCS5B01G237900 chr6A 92.484 306 18 4 5072 5373 510971774 510972078 2.980000e-117 433.0
26 TraesCS5B01G237900 chr6A 86.190 420 32 13 4664 5065 510972205 510971794 1.070000e-116 431.0
27 TraesCS5B01G237900 chr6A 100.000 174 0 0 3514 3687 168007205 168007032 6.720000e-84 322.0
28 TraesCS5B01G237900 chr6A 83.668 349 24 15 4177 4496 42926542 42926886 1.130000e-76 298.0
29 TraesCS5B01G237900 chr6A 91.892 148 6 3 3355 3502 42925852 42925993 9.140000e-48 202.0
30 TraesCS5B01G237900 chr6B 89.110 1056 77 17 2170 3208 76858810 76859844 0.000000e+00 1279.0
31 TraesCS5B01G237900 chr6B 85.797 1211 117 21 993 2165 76856579 76857772 0.000000e+00 1232.0
32 TraesCS5B01G237900 chr6B 86.541 847 73 21 3685 4496 76860210 76861050 0.000000e+00 894.0
33 TraesCS5B01G237900 chr6B 89.027 401 24 4 4682 5065 697045478 697045081 3.770000e-131 479.0
34 TraesCS5B01G237900 chr6B 95.318 299 13 1 5076 5373 697136568 697136270 1.750000e-129 473.0
35 TraesCS5B01G237900 chr6B 87.707 423 29 13 4662 5066 697136136 697136553 6.310000e-129 472.0
36 TraesCS5B01G237900 chr6B 88.264 409 28 6 4674 5065 697276541 697276136 6.310000e-129 472.0
37 TraesCS5B01G237900 chr6B 87.828 419 26 13 4662 5062 697044221 697044632 8.160000e-128 468.0
38 TraesCS5B01G237900 chr6B 87.775 409 30 4 4674 5065 697137414 697137009 1.370000e-125 460.0
39 TraesCS5B01G237900 chr6B 94.295 298 16 1 5076 5373 697044651 697044355 6.350000e-124 455.0
40 TraesCS5B01G237900 chr6B 93.092 304 15 2 5072 5373 451934854 451934555 1.780000e-119 440.0
41 TraesCS5B01G237900 chr6B 91.935 62 5 0 4073 4134 645555966 645556027 2.670000e-13 87.9
42 TraesCS5B01G237900 chr4B 89.362 423 19 8 4664 5066 618649410 618648994 4.810000e-140 508.0
43 TraesCS5B01G237900 chr4B 92.881 295 19 2 5081 5373 618648984 618649278 1.390000e-115 427.0
44 TraesCS5B01G237900 chr4B 91.776 304 23 1 5072 5373 180991382 180991685 6.440000e-114 422.0
45 TraesCS5B01G237900 chr7B 93.399 303 17 2 5072 5373 323844983 323844683 3.820000e-121 446.0
46 TraesCS5B01G237900 chr7B 100.000 174 0 0 3514 3687 672656197 672656370 6.720000e-84 322.0
47 TraesCS5B01G237900 chr2B 91.475 305 23 2 5072 5373 708046406 708046102 3.000000e-112 416.0
48 TraesCS5B01G237900 chr7D 85.112 403 49 8 48 447 11676438 11676044 8.390000e-108 401.0
49 TraesCS5B01G237900 chr7D 94.872 39 1 1 3209 3246 58171320 58171358 5.820000e-05 60.2
50 TraesCS5B01G237900 chr4A 98.396 187 3 0 3504 3690 733434349 733434535 4.020000e-86 329.0
51 TraesCS5B01G237900 chr1A 100.000 176 0 0 3512 3687 99155045 99154870 5.200000e-85 326.0
52 TraesCS5B01G237900 chr1A 100.000 174 0 0 3514 3687 259052829 259053002 6.720000e-84 322.0
53 TraesCS5B01G237900 chr1A 76.190 252 45 13 686 927 515838235 515838481 9.470000e-23 119.0
54 TraesCS5B01G237900 chr7A 98.895 181 1 1 3508 3687 605175528 605175708 6.720000e-84 322.0
55 TraesCS5B01G237900 chr7A 83.333 264 40 1 42 301 11104831 11104568 1.940000e-59 241.0


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 TraesCS5B01G237900 chr5B 418810456 418815836 5380 True 9937.000000 9937 100.000000 1 5381 1 chr5B.!!$R3 5380
1 TraesCS5B01G237900 chr5B 418810471 418811052 581 False 710.000000 710 88.851000 4785 5366 1 chr5B.!!$F3 581
2 TraesCS5B01G237900 chr5A 455463640 455468379 4739 True 1189.000000 4318 96.118833 1 4663 6 chr5A.!!$R2 4662
3 TraesCS5B01G237900 chr5D 354500749 354505219 4470 True 1487.400000 2808 96.609400 1 4661 5 chr5D.!!$R2 4660
4 TraesCS5B01G237900 chrUn 104866155 104870522 4367 True 1177.666667 1325 87.946667 993 4496 3 chrUn.!!$R1 3503
5 TraesCS5B01G237900 chr6A 42922690 42926886 4196 False 701.200000 1291 86.959000 993 4496 5 chr6A.!!$F2 3503
6 TraesCS5B01G237900 chr6B 76856579 76861050 4471 False 1135.000000 1279 87.149333 993 4496 3 chr6B.!!$F4 3503
7 TraesCS5B01G237900 chr6B 697044355 697045478 1123 True 467.000000 479 91.661000 4682 5373 2 chr6B.!!$R3 691
8 TraesCS5B01G237900 chr6B 697136270 697137414 1144 True 466.500000 473 91.546500 4674 5373 2 chr6B.!!$R4 699

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
765 771 0.109723 ACTTAGGCAAGGGTTCGCAA 59.890 50.000 0.00 0.0 35.97 4.85 F
1117 1123 0.310854 GTTCTTGTTCTTGCACCCCG 59.689 55.000 0.00 0.0 0.00 5.73 F
2048 2150 0.540133 TGGCTCCAGCAAATGAAGCA 60.540 50.000 0.03 0.0 44.36 3.91 F
2683 4105 1.129624 TGCACGTTCCGATAATTGCAC 59.870 47.619 0.00 0.0 35.13 4.57 F
3625 5212 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.0 30.80 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1724 0.683504 TCGTAGAAGGAGGGGCAGTC 60.684 60.0 0.0 0.0 0.00 3.51 R
2787 4209 0.385473 GACAACCACGCAATGTTCCG 60.385 55.0 0.0 0.0 0.00 4.30 R
3606 5193 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.0 0.0 0.0 44.64 4.12 R
4206 5877 0.038343 CTGCGAAAACCACAATGGGG 60.038 55.0 0.0 0.0 43.37 4.96 R
4556 6257 0.184451 CATGGAGGGTGGGATTCCAG 59.816 60.0 4.8 0.0 45.05 3.86 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
25 26 4.329545 GGGCTTGGACCACTCGCA 62.330 66.667 10.69 0.00 0.00 5.10
26 27 2.045926 GGCTTGGACCACTCGCAT 60.046 61.111 10.69 0.00 0.00 4.73
54 55 0.532573 AGGTACAGTCTGTGATGCCG 59.467 55.000 16.03 0.00 0.00 5.69
94 95 5.632347 GTGGAAAGAGCTGAATGAATTGTTG 59.368 40.000 0.00 0.00 0.00 3.33
145 146 3.875727 CAGTAGCAGATGTCAATTCAGGG 59.124 47.826 0.00 0.00 0.00 4.45
428 434 2.422597 TGGTCCGAGTAAATGCAAGTG 58.577 47.619 0.00 0.00 0.00 3.16
502 508 6.101997 TCTATCTAGGCGATACATTGCATTG 58.898 40.000 7.04 7.04 38.98 2.82
765 771 0.109723 ACTTAGGCAAGGGTTCGCAA 59.890 50.000 0.00 0.00 35.97 4.85
1117 1123 0.310854 GTTCTTGTTCTTGCACCCCG 59.689 55.000 0.00 0.00 0.00 5.73
1258 1265 6.071051 GGTTTTAGAAACTATGGATTTGGGCA 60.071 38.462 3.85 0.00 0.00 5.36
1396 1405 3.234353 TGCTGCTATGTGCTATCTACCT 58.766 45.455 0.00 0.00 43.37 3.08
1578 1594 0.732571 TGCTAAATAACGGCAGCTGC 59.267 50.000 30.88 30.88 41.14 5.25
1662 1724 4.623167 GTGCCGATAGATGTATGTGCTAAG 59.377 45.833 0.00 0.00 39.76 2.18
2048 2150 0.540133 TGGCTCCAGCAAATGAAGCA 60.540 50.000 0.03 0.00 44.36 3.91
2243 3397 9.148104 GCTCTTTGATTGAAAATTTAGCTTCAT 57.852 29.630 0.00 0.00 31.85 2.57
2683 4105 1.129624 TGCACGTTCCGATAATTGCAC 59.870 47.619 0.00 0.00 35.13 4.57
2787 4209 1.140816 GAACTGGAAGAGCACGTCAC 58.859 55.000 0.00 0.00 37.43 3.67
2843 4265 5.762218 CCTATCTTGACATTCCTCCATTCAC 59.238 44.000 0.00 0.00 0.00 3.18
2993 4415 3.807622 TCAAGTTGCAGAAGAAAGTACGG 59.192 43.478 0.00 0.00 0.00 4.02
3088 4510 5.344743 TGTGTATCTTCCTGGATGTTCTC 57.655 43.478 9.18 4.07 0.00 2.87
3492 5071 4.588951 TCTGACTGCCTTGTCTTCTTAGAA 59.411 41.667 0.00 0.00 37.79 2.10
3511 5098 9.910267 TCTTAGAAGGTTTACTTTTAGGTTGTT 57.090 29.630 0.00 0.00 40.21 2.83
3512 5099 9.946165 CTTAGAAGGTTTACTTTTAGGTTGTTG 57.054 33.333 0.00 0.00 40.21 3.33
3513 5100 6.802608 AGAAGGTTTACTTTTAGGTTGTTGC 58.197 36.000 0.00 0.00 40.21 4.17
3514 5101 6.605995 AGAAGGTTTACTTTTAGGTTGTTGCT 59.394 34.615 0.00 0.00 40.21 3.91
3515 5102 7.776500 AGAAGGTTTACTTTTAGGTTGTTGCTA 59.224 33.333 0.00 0.00 40.21 3.49
3516 5103 8.473358 AAGGTTTACTTTTAGGTTGTTGCTAT 57.527 30.769 0.00 0.00 35.35 2.97
3517 5104 7.882179 AGGTTTACTTTTAGGTTGTTGCTATG 58.118 34.615 0.00 0.00 0.00 2.23
3518 5105 7.504574 AGGTTTACTTTTAGGTTGTTGCTATGT 59.495 33.333 0.00 0.00 0.00 2.29
3519 5106 8.139350 GGTTTACTTTTAGGTTGTTGCTATGTT 58.861 33.333 0.00 0.00 0.00 2.71
3520 5107 9.524106 GTTTACTTTTAGGTTGTTGCTATGTTT 57.476 29.630 0.00 0.00 0.00 2.83
3526 5113 9.535878 TTTTAGGTTGTTGCTATGTTTTTAAGG 57.464 29.630 0.00 0.00 0.00 2.69
3527 5114 5.538118 AGGTTGTTGCTATGTTTTTAAGGC 58.462 37.500 0.00 0.00 0.00 4.35
3528 5115 4.384547 GGTTGTTGCTATGTTTTTAAGGCG 59.615 41.667 0.00 0.00 0.00 5.52
3529 5116 5.216648 GTTGTTGCTATGTTTTTAAGGCGA 58.783 37.500 0.00 0.00 0.00 5.54
3530 5117 4.789784 TGTTGCTATGTTTTTAAGGCGAC 58.210 39.130 0.00 0.00 35.42 5.19
3531 5118 3.733024 TGCTATGTTTTTAAGGCGACG 57.267 42.857 0.00 0.00 0.00 5.12
3532 5119 2.159626 TGCTATGTTTTTAAGGCGACGC 60.160 45.455 12.43 12.43 0.00 5.19
3544 5131 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
3545 5132 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
3546 5133 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
3547 5134 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
3548 5135 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
3549 5136 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
3595 5182 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
3596 5183 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
3604 5191 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
3622 5209 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
3623 5210 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
3624 5211 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
3625 5212 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
3626 5213 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
3627 5214 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
3628 5215 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
3629 5216 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
3630 5217 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
3631 5218 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
3632 5219 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
3633 5220 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
3640 5227 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
3641 5228 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
3649 5236 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
3675 5262 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
3676 5263 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
3677 5264 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.00 0.00 44.82 1.85
3678 5265 0.896923 TCGCCTTAGGGACGCTTTAA 59.103 50.000 0.00 0.00 34.09 1.52
3679 5266 1.275856 TCGCCTTAGGGACGCTTTAAA 59.724 47.619 0.00 0.00 34.09 1.52
3680 5267 2.078392 CGCCTTAGGGACGCTTTAAAA 58.922 47.619 0.00 0.00 33.58 1.52
3681 5268 2.485038 CGCCTTAGGGACGCTTTAAAAA 59.515 45.455 0.00 0.00 33.58 1.94
3682 5269 3.668757 CGCCTTAGGGACGCTTTAAAAAC 60.669 47.826 0.00 0.00 33.58 2.43
3683 5270 3.253921 GCCTTAGGGACGCTTTAAAAACA 59.746 43.478 0.00 0.00 33.58 2.83
3684 5271 4.082408 GCCTTAGGGACGCTTTAAAAACAT 60.082 41.667 0.00 0.00 33.58 2.71
3685 5272 5.124297 GCCTTAGGGACGCTTTAAAAACATA 59.876 40.000 0.00 0.00 33.58 2.29
3686 5273 6.677187 GCCTTAGGGACGCTTTAAAAACATAG 60.677 42.308 0.00 0.00 33.58 2.23
3687 5274 6.183360 CCTTAGGGACGCTTTAAAAACATAGG 60.183 42.308 0.00 0.00 33.58 2.57
3688 5275 4.014406 AGGGACGCTTTAAAAACATAGGG 58.986 43.478 0.00 0.00 0.00 3.53
3689 5276 3.760151 GGGACGCTTTAAAAACATAGGGT 59.240 43.478 0.00 0.00 36.63 4.34
3690 5277 4.219070 GGGACGCTTTAAAAACATAGGGTT 59.781 41.667 0.00 0.00 42.98 4.11
3691 5278 5.158494 GGACGCTTTAAAAACATAGGGTTG 58.842 41.667 0.00 0.00 40.35 3.77
3692 5279 5.278610 GGACGCTTTAAAAACATAGGGTTGT 60.279 40.000 0.00 0.00 40.35 3.32
3732 5319 6.009589 ACATTGAGATGGTATTGTTTCCACA 58.990 36.000 0.00 0.00 37.60 4.17
3741 5328 2.869233 TTGTTTCCACAGCTTCTTGC 57.131 45.000 0.00 0.00 43.29 4.01
3773 5360 7.976135 AAAGCTATTGAAATCTATCGAGCAT 57.024 32.000 0.00 0.00 0.00 3.79
3914 5505 1.037493 TATTCATGAGTCGGTCCGGG 58.963 55.000 12.29 0.00 0.00 5.73
3948 5539 6.876789 TCTGAAACCATTCTTCGCAGTAAATA 59.123 34.615 0.00 0.00 36.48 1.40
3977 5570 6.978343 TGCATGTATAGTTTACTTGACCAC 57.022 37.500 9.76 0.00 0.00 4.16
3978 5571 6.468543 TGCATGTATAGTTTACTTGACCACA 58.531 36.000 9.76 0.00 0.00 4.17
4105 5698 1.227674 GGTGGATGGAGGCGACATC 60.228 63.158 13.72 13.72 43.04 3.06
4177 5770 4.866508 TCCTTCGATTGTAAGTGTCTGT 57.133 40.909 0.00 0.00 0.00 3.41
4178 5771 5.970317 TCCTTCGATTGTAAGTGTCTGTA 57.030 39.130 0.00 0.00 0.00 2.74
4179 5772 5.706916 TCCTTCGATTGTAAGTGTCTGTAC 58.293 41.667 0.00 0.00 0.00 2.90
4190 5785 1.153745 GTCTGTACCTCAGCGGCTG 60.154 63.158 23.72 23.72 43.32 4.85
4195 5866 0.737715 GTACCTCAGCGGCTGAACAG 60.738 60.000 30.38 23.38 40.18 3.16
4206 5877 0.233332 GCTGAACAGTGACGAACAGC 59.767 55.000 0.00 0.00 42.44 4.40
4263 5934 4.436584 CGAGAAGATTGTGCTGATGTTTCC 60.437 45.833 0.00 0.00 0.00 3.13
4302 5973 3.726607 CCTCAATGTCTACAGCATCCTC 58.273 50.000 0.00 0.00 0.00 3.71
4314 5985 0.393402 GCATCCTCCAGCATGACACA 60.393 55.000 0.00 0.00 39.69 3.72
4382 6053 4.632974 CCCCATCAGCCGCTAGCC 62.633 72.222 9.66 0.00 45.47 3.93
4383 6054 4.976925 CCCATCAGCCGCTAGCCG 62.977 72.222 9.66 3.53 45.47 5.52
4384 6055 4.227134 CCATCAGCCGCTAGCCGT 62.227 66.667 9.66 0.00 45.47 5.68
4385 6056 2.659897 CATCAGCCGCTAGCCGTC 60.660 66.667 9.66 0.00 45.47 4.79
4386 6057 3.147595 ATCAGCCGCTAGCCGTCA 61.148 61.111 9.66 0.00 45.47 4.35
4388 6059 2.907897 ATCAGCCGCTAGCCGTCAAC 62.908 60.000 9.66 0.00 45.47 3.18
4548 6249 0.106708 TATGGAGAACCTGCGGATGC 59.893 55.000 0.00 0.00 43.20 3.91
4570 6271 2.287194 CCCCTGGAATCCCACCCT 60.287 66.667 0.00 0.00 37.58 4.34
4571 6272 2.386935 CCCCTGGAATCCCACCCTC 61.387 68.421 0.00 0.00 37.58 4.30
4572 6273 2.386935 CCCTGGAATCCCACCCTCC 61.387 68.421 0.00 0.00 37.58 4.30
4573 6274 1.619363 CCTGGAATCCCACCCTCCA 60.619 63.158 0.00 0.00 37.58 3.86
4574 6275 0.995675 CCTGGAATCCCACCCTCCAT 60.996 60.000 0.00 0.00 38.55 3.41
4575 6276 0.184451 CTGGAATCCCACCCTCCATG 59.816 60.000 0.00 0.00 38.55 3.66
4576 6277 0.253583 TGGAATCCCACCCTCCATGA 60.254 55.000 0.00 0.00 37.58 3.07
4592 6293 2.133553 CATGATCCATCAGCAGTCGTC 58.866 52.381 0.00 0.00 40.64 4.20
4632 6333 6.209788 CCCCTTCATAATACACTAGAGGACTC 59.790 46.154 0.00 0.00 0.00 3.36
4663 6364 4.445545 GCGCCGTTCTTCGCTTGG 62.446 66.667 0.00 0.00 46.92 3.61
4664 6365 4.445545 CGCCGTTCTTCGCTTGGC 62.446 66.667 0.00 0.00 42.29 4.52
4665 6366 3.050275 GCCGTTCTTCGCTTGGCT 61.050 61.111 0.00 0.00 42.44 4.75
4666 6367 1.740296 GCCGTTCTTCGCTTGGCTA 60.740 57.895 0.00 0.00 42.44 3.93
4667 6368 1.296056 GCCGTTCTTCGCTTGGCTAA 61.296 55.000 0.00 0.00 42.44 3.09
4668 6369 1.369625 CCGTTCTTCGCTTGGCTAAT 58.630 50.000 0.00 0.00 38.35 1.73
4669 6370 1.737793 CCGTTCTTCGCTTGGCTAATT 59.262 47.619 0.00 0.00 38.35 1.40
4670 6371 2.161609 CCGTTCTTCGCTTGGCTAATTT 59.838 45.455 0.00 0.00 38.35 1.82
4671 6372 3.365969 CCGTTCTTCGCTTGGCTAATTTT 60.366 43.478 0.00 0.00 38.35 1.82
4672 6373 4.226761 CGTTCTTCGCTTGGCTAATTTTT 58.773 39.130 0.00 0.00 0.00 1.94
4764 6469 3.826754 CTCGCTGCAGGCCGACTA 61.827 66.667 17.12 0.00 37.74 2.59
4846 6564 1.474077 CAGCAAGCCAATTAGTCCCAC 59.526 52.381 0.00 0.00 0.00 4.61
4847 6565 0.817654 GCAAGCCAATTAGTCCCACC 59.182 55.000 0.00 0.00 0.00 4.61
4848 6566 1.890573 GCAAGCCAATTAGTCCCACCA 60.891 52.381 0.00 0.00 0.00 4.17
4860 6578 2.662596 CCACCAGTCGGCTTGCTA 59.337 61.111 0.00 0.00 34.57 3.49
4862 6580 1.005037 CACCAGTCGGCTTGCTACA 60.005 57.895 0.00 0.00 34.57 2.74
4997 6715 9.442047 AAATGAATTTGGTTTGTGTTGAAACTA 57.558 25.926 0.00 0.00 36.30 2.24
5005 6723 6.820656 TGGTTTGTGTTGAAACTATTTGCATT 59.179 30.769 0.00 0.00 36.30 3.56
5277 7430 2.350895 CCACCACAGGCCGATTGA 59.649 61.111 0.00 0.00 0.00 2.57
5323 7480 4.764823 CCTACTGGACTAATTGGTTTGCAA 59.235 41.667 0.00 0.00 34.57 4.08
5350 7507 0.541863 ATTAGTCCCAGTCGGCTTGG 59.458 55.000 0.00 0.00 0.00 3.61
5368 7525 4.373116 TGCGGGTCGACTGGAAGC 62.373 66.667 16.46 13.64 37.60 3.86
5373 7530 1.026718 GGGTCGACTGGAAGCCAATG 61.027 60.000 16.46 0.00 37.60 2.82
5374 7531 0.036388 GGTCGACTGGAAGCCAATGA 60.036 55.000 16.46 0.00 37.60 2.57
5375 7532 1.363744 GTCGACTGGAAGCCAATGAG 58.636 55.000 8.70 0.00 37.60 2.90
5376 7533 1.066858 GTCGACTGGAAGCCAATGAGA 60.067 52.381 8.70 0.00 37.60 3.27
5377 7534 1.623311 TCGACTGGAAGCCAATGAGAA 59.377 47.619 0.00 0.00 37.60 2.87
5378 7535 2.038426 TCGACTGGAAGCCAATGAGAAA 59.962 45.455 0.00 0.00 37.60 2.52
5379 7536 3.012518 CGACTGGAAGCCAATGAGAAAT 58.987 45.455 0.00 0.00 37.60 2.17
5380 7537 3.181503 CGACTGGAAGCCAATGAGAAATG 60.182 47.826 0.00 0.00 37.60 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.831736 AGACTGTACCTAAAGGCGCAT 59.168 47.619 10.83 0.00 39.32 4.73
26 27 1.067142 CAGACTGTACCTAAAGGCGCA 60.067 52.381 10.83 0.00 39.32 6.09
94 95 1.869767 GAGCTGCACACATATAGCACC 59.130 52.381 1.02 0.00 38.59 5.01
145 146 1.078426 CCCTTCCATGACACGGACC 60.078 63.158 0.00 0.00 30.29 4.46
286 287 2.439701 CAGCACATCAGCCAGGGG 60.440 66.667 0.00 0.00 34.23 4.79
428 434 7.655490 AGCATTCTGGTTTGATTATCTAATGC 58.345 34.615 0.00 0.00 44.24 3.56
765 771 6.042777 CGTATGGATGTCAGATTACAGTGTT 58.957 40.000 0.00 0.00 31.70 3.32
1099 1105 0.106918 ACGGGGTGCAAGAACAAGAA 60.107 50.000 0.00 0.00 0.00 2.52
1117 1123 0.250513 GTGACAGACATGGGGAGGAC 59.749 60.000 0.00 0.00 0.00 3.85
1258 1265 2.845659 TGGTACCATCCCAACAGAGAT 58.154 47.619 11.60 0.00 0.00 2.75
1570 1586 2.266627 GCCATATCCAGCAGCTGCC 61.267 63.158 34.39 17.05 43.38 4.85
1662 1724 0.683504 TCGTAGAAGGAGGGGCAGTC 60.684 60.000 0.00 0.00 0.00 3.51
2048 2150 1.978580 AGAAGTTCCGGTGGAATCAGT 59.021 47.619 0.00 0.00 44.04 3.41
2205 3355 3.106242 TCAAAGAGCGCAGAGTTAACA 57.894 42.857 11.47 0.00 0.00 2.41
2243 3397 8.869109 AGTCCCATTATGAAAAATCTTGTTCAA 58.131 29.630 0.00 0.00 37.31 2.69
2787 4209 0.385473 GACAACCACGCAATGTTCCG 60.385 55.000 0.00 0.00 0.00 4.30
2843 4265 6.094048 CCGGAGCCTATTCAATACCATTTATG 59.906 42.308 0.00 0.00 0.00 1.90
2993 4415 2.546162 GGCTATCTTAAGTCCCAGACGC 60.546 54.545 1.63 0.00 37.67 5.19
3088 4510 3.018149 AGGAAGGAGCTAACTCTACACG 58.982 50.000 0.00 0.00 42.98 4.49
3139 4562 7.765360 GGGTTCATGATTTAATGCAGAATTCAA 59.235 33.333 8.44 0.00 0.00 2.69
3492 5071 7.504574 ACATAGCAACAACCTAAAAGTAAACCT 59.495 33.333 0.00 0.00 0.00 3.50
3511 5098 2.159626 GCGTCGCCTTAAAAACATAGCA 60.160 45.455 5.75 0.00 0.00 3.49
3512 5099 2.437626 GCGTCGCCTTAAAAACATAGC 58.562 47.619 5.75 0.00 0.00 2.97
3513 5100 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
3532 5119 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
3533 5120 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
3534 5121 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
3535 5122 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
3536 5123 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
3578 5165 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
3579 5166 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
3587 5174 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
3605 5192 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
3606 5193 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
3607 5194 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
3608 5195 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
3609 5196 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
3610 5197 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
3611 5198 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
3612 5199 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
3613 5200 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
3614 5201 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
3624 5211 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
3632 5219 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
3658 5245 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.00 43.57 5.19
3659 5246 0.896923 TTAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
3660 5247 1.729284 TTTAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
3661 5248 3.253921 TGTTTTTAAAGCGTCCCTAAGGC 59.746 43.478 0.00 0.00 39.09 4.35
3662 5249 5.638596 ATGTTTTTAAAGCGTCCCTAAGG 57.361 39.130 0.00 0.00 0.00 2.69
3663 5250 6.183360 CCCTATGTTTTTAAAGCGTCCCTAAG 60.183 42.308 0.00 0.00 0.00 2.18
3664 5251 5.648960 CCCTATGTTTTTAAAGCGTCCCTAA 59.351 40.000 0.00 0.00 0.00 2.69
3665 5252 5.187687 CCCTATGTTTTTAAAGCGTCCCTA 58.812 41.667 0.00 0.00 0.00 3.53
3666 5253 4.014406 CCCTATGTTTTTAAAGCGTCCCT 58.986 43.478 0.00 0.00 0.00 4.20
3667 5254 3.760151 ACCCTATGTTTTTAAAGCGTCCC 59.240 43.478 0.00 0.00 0.00 4.46
3668 5255 5.158494 CAACCCTATGTTTTTAAAGCGTCC 58.842 41.667 0.00 0.00 34.00 4.79
3669 5256 5.765176 ACAACCCTATGTTTTTAAAGCGTC 58.235 37.500 0.00 0.00 34.00 5.19
3670 5257 5.777850 ACAACCCTATGTTTTTAAAGCGT 57.222 34.783 0.00 0.00 34.00 5.07
3671 5258 5.107645 GCAACAACCCTATGTTTTTAAAGCG 60.108 40.000 0.00 0.00 41.44 4.68
3672 5259 5.989168 AGCAACAACCCTATGTTTTTAAAGC 59.011 36.000 0.00 0.00 41.44 3.51
3673 5260 9.705290 ATAAGCAACAACCCTATGTTTTTAAAG 57.295 29.630 0.00 0.00 41.44 1.85
3674 5261 9.482627 CATAAGCAACAACCCTATGTTTTTAAA 57.517 29.630 0.00 0.00 41.44 1.52
3675 5262 8.861086 TCATAAGCAACAACCCTATGTTTTTAA 58.139 29.630 0.00 0.00 41.44 1.52
3676 5263 8.410673 TCATAAGCAACAACCCTATGTTTTTA 57.589 30.769 0.00 0.00 41.44 1.52
3677 5264 7.232534 TCTCATAAGCAACAACCCTATGTTTTT 59.767 33.333 0.00 0.00 41.44 1.94
3678 5265 6.719370 TCTCATAAGCAACAACCCTATGTTTT 59.281 34.615 0.00 0.00 41.44 2.43
3679 5266 6.245408 TCTCATAAGCAACAACCCTATGTTT 58.755 36.000 0.00 0.00 41.44 2.83
3680 5267 5.815581 TCTCATAAGCAACAACCCTATGTT 58.184 37.500 0.00 0.00 44.08 2.71
3681 5268 5.435686 TCTCATAAGCAACAACCCTATGT 57.564 39.130 0.00 0.00 34.24 2.29
3682 5269 5.824624 ACATCTCATAAGCAACAACCCTATG 59.175 40.000 0.00 0.00 0.00 2.23
3683 5270 6.006275 ACATCTCATAAGCAACAACCCTAT 57.994 37.500 0.00 0.00 0.00 2.57
3684 5271 5.435686 ACATCTCATAAGCAACAACCCTA 57.564 39.130 0.00 0.00 0.00 3.53
3685 5272 4.307032 ACATCTCATAAGCAACAACCCT 57.693 40.909 0.00 0.00 0.00 4.34
3686 5273 5.414454 TGTTACATCTCATAAGCAACAACCC 59.586 40.000 0.00 0.00 0.00 4.11
3687 5274 6.494893 TGTTACATCTCATAAGCAACAACC 57.505 37.500 0.00 0.00 0.00 3.77
3688 5275 8.236586 TCAATGTTACATCTCATAAGCAACAAC 58.763 33.333 0.00 0.00 0.00 3.32
3689 5276 8.334263 TCAATGTTACATCTCATAAGCAACAA 57.666 30.769 0.00 0.00 0.00 2.83
3690 5277 7.823799 TCTCAATGTTACATCTCATAAGCAACA 59.176 33.333 0.00 0.00 0.00 3.33
3691 5278 8.201554 TCTCAATGTTACATCTCATAAGCAAC 57.798 34.615 0.00 0.00 0.00 4.17
3692 5279 8.833493 CATCTCAATGTTACATCTCATAAGCAA 58.167 33.333 0.00 0.00 0.00 3.91
3732 5319 4.140536 AGCTTTTACTCTTGCAAGAAGCT 58.859 39.130 32.48 32.48 45.94 3.74
3898 5489 2.036731 ACCCGGACCGACTCATGA 59.963 61.111 17.49 0.00 0.00 3.07
3914 5505 5.096443 AGAATGGTTTCAGATGGAGAGAC 57.904 43.478 0.00 0.00 34.08 3.36
3948 5539 8.814235 GTCAAGTAAACTATACATGCATACGTT 58.186 33.333 0.00 0.00 0.00 3.99
3977 5570 7.024340 AGATGCAGAGCTACAATAAAACATG 57.976 36.000 0.00 0.00 0.00 3.21
3978 5571 7.636150 AAGATGCAGAGCTACAATAAAACAT 57.364 32.000 0.00 0.00 0.00 2.71
4105 5698 6.043411 AGTAGCCAGCTTTAACTTCTTATCG 58.957 40.000 0.00 0.00 0.00 2.92
4177 5770 1.185618 ACTGTTCAGCCGCTGAGGTA 61.186 55.000 21.87 11.95 41.75 3.08
4178 5771 2.345244 CTGTTCAGCCGCTGAGGT 59.655 61.111 21.87 0.00 41.75 3.85
4179 5772 2.031516 CACTGTTCAGCCGCTGAGG 61.032 63.158 21.87 17.52 41.75 3.86
4190 5785 1.228657 GGGGCTGTTCGTCACTGTTC 61.229 60.000 0.00 0.00 0.00 3.18
4195 5866 0.889186 ACAATGGGGCTGTTCGTCAC 60.889 55.000 0.00 0.00 0.00 3.67
4206 5877 0.038343 CTGCGAAAACCACAATGGGG 60.038 55.000 0.00 0.00 43.37 4.96
4263 5934 0.462789 GGCCCTGCATTTGAAGATGG 59.537 55.000 0.00 0.00 0.00 3.51
4302 5973 2.078849 TTACGAGTGTGTCATGCTGG 57.921 50.000 0.00 0.00 0.00 4.85
4314 5985 0.731417 CGTCCCGAGTCATTACGAGT 59.269 55.000 0.00 0.00 35.66 4.18
4382 6053 2.731976 GTCTAGCAAGGTTCTGTTGACG 59.268 50.000 0.00 0.00 0.00 4.35
4383 6054 3.728845 TGTCTAGCAAGGTTCTGTTGAC 58.271 45.455 0.00 0.00 0.00 3.18
4384 6055 4.284490 AGATGTCTAGCAAGGTTCTGTTGA 59.716 41.667 0.00 0.00 0.00 3.18
4385 6056 4.573900 AGATGTCTAGCAAGGTTCTGTTG 58.426 43.478 0.00 0.00 0.00 3.33
4386 6057 4.899352 AGATGTCTAGCAAGGTTCTGTT 57.101 40.909 0.00 0.00 0.00 3.16
4388 6059 7.011857 GGATAAAAGATGTCTAGCAAGGTTCTG 59.988 40.741 0.00 0.00 0.00 3.02
4553 6254 2.287194 AGGGTGGGATTCCAGGGG 60.287 66.667 4.80 0.00 45.05 4.79
4555 6256 0.995675 ATGGAGGGTGGGATTCCAGG 60.996 60.000 4.80 0.00 45.05 4.45
4556 6257 0.184451 CATGGAGGGTGGGATTCCAG 59.816 60.000 4.80 0.00 45.05 3.86
4570 6271 1.069668 CGACTGCTGATGGATCATGGA 59.930 52.381 0.00 0.00 36.02 3.41
4571 6272 1.202615 ACGACTGCTGATGGATCATGG 60.203 52.381 0.00 0.00 36.02 3.66
4572 6273 2.133553 GACGACTGCTGATGGATCATG 58.866 52.381 0.00 0.00 36.02 3.07
4573 6274 1.069823 GGACGACTGCTGATGGATCAT 59.930 52.381 0.00 0.00 36.02 2.45
4574 6275 0.461548 GGACGACTGCTGATGGATCA 59.538 55.000 0.00 0.00 35.16 2.92
4575 6276 0.596083 CGGACGACTGCTGATGGATC 60.596 60.000 0.00 0.00 0.00 3.36
4576 6277 1.439228 CGGACGACTGCTGATGGAT 59.561 57.895 0.00 0.00 0.00 3.41
4592 6293 0.546598 AGGGGATGTAGGAAAAGCGG 59.453 55.000 0.00 0.00 0.00 5.52
4726 6427 6.512091 GCGAGCCGATGGTGTATTATTTAAAA 60.512 38.462 0.00 0.00 0.00 1.52
4748 6453 3.356639 CTTAGTCGGCCTGCAGCGA 62.357 63.158 8.66 10.47 45.17 4.93
4846 6564 1.448540 CCTGTAGCAAGCCGACTGG 60.449 63.158 6.33 6.33 38.77 4.00
4847 6565 2.103042 GCCTGTAGCAAGCCGACTG 61.103 63.158 0.00 0.00 42.97 3.51
4848 6566 2.266055 GCCTGTAGCAAGCCGACT 59.734 61.111 0.00 0.00 42.97 4.18
4860 6578 2.032681 GGCTTTCAGTCGGCCTGT 59.967 61.111 0.00 0.00 42.19 4.00
4862 6580 0.678048 GATTGGCTTTCAGTCGGCCT 60.678 55.000 0.00 0.00 45.45 5.19
4979 6697 6.166279 TGCAAATAGTTTCAACACAAACCAA 58.834 32.000 0.00 0.00 37.01 3.67
5235 7386 1.272648 ACTAGGTGCATGTGGCCATTT 60.273 47.619 9.72 0.00 43.89 2.32
5291 7444 4.451150 TCCAGTAGGCTTGCCGCG 62.451 66.667 0.00 0.00 40.44 6.46
5294 7447 2.945668 CAATTAGTCCAGTAGGCTTGCC 59.054 50.000 2.97 2.97 33.74 4.52
5302 7455 5.699097 GTTGCAAACCAATTAGTCCAGTA 57.301 39.130 0.00 0.00 42.21 2.74
5323 7480 2.615493 CGACTGGGACTAATTGGCTTGT 60.615 50.000 0.00 0.00 0.00 3.16
5350 7507 2.432628 CTTCCAGTCGACCCGCAC 60.433 66.667 13.01 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.