Multiple sequence alignment - TraesCS7D01G036600

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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 TraesCS7D01G036600 chr7D 100.000 6161 0 0 1 6161 18678580 18684740 0.000000e+00 11378
1 TraesCS7D01G036600 chr7D 83.212 274 33 4 5630 5900 18689659 18689922 7.980000e-59 239
2 TraesCS7D01G036600 chr7D 81.503 173 23 5 5989 6161 18690000 18690163 3.870000e-27 134
3 TraesCS7D01G036600 chr7A 89.762 5978 376 102 3 5846 19002222 19008097 0.000000e+00 7432
4 TraesCS7D01G036600 chr7A 92.079 202 14 1 5844 6045 19008220 19008419 3.640000e-72 283
5 TraesCS7D01G036600 chr7A 94.845 97 4 1 6045 6140 19035509 19035605 3.850000e-32 150
6 TraesCS7D01G036600 chr4A 92.804 3335 199 20 2211 5522 714179196 714175880 0.000000e+00 4791
7 TraesCS7D01G036600 chr4A 85.044 1364 107 43 944 2225 714180583 714179235 0.000000e+00 1299
8 TraesCS7D01G036600 chr4A 84.746 531 27 17 170 686 714181172 714180682 3.340000e-132 483
9 TraesCS7D01G036600 chr4A 88.095 168 15 2 5525 5687 714175807 714175640 1.750000e-45 195
10 TraesCS7D01G036600 chr4A 87.629 97 5 4 6045 6140 714175399 714175309 8.450000e-19 106
11 TraesCS7D01G036600 chr1B 88.292 521 50 5 1004 1521 91810435 91809923 1.140000e-171 614
12 TraesCS7D01G036600 chr4B 92.000 300 19 3 1063 1359 391676759 391677056 3.440000e-112 416
13 TraesCS7D01G036600 chr2D 78.261 391 65 15 1739 2125 119070731 119070357 3.710000e-57 233
14 TraesCS7D01G036600 chr2A 77.635 389 63 18 1739 2125 121145167 121144801 1.350000e-51 215
15 TraesCS7D01G036600 chr2B 76.093 389 69 14 1739 2125 171034263 171033897 1.360000e-41 182


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 TraesCS7D01G036600 chr7D 18678580 18684740 6160 False 11378.0 11378 100.0000 1 6161 1 chr7D.!!$F1 6160
1 TraesCS7D01G036600 chr7A 19002222 19008419 6197 False 3857.5 7432 90.9205 3 6045 2 chr7A.!!$F2 6042
2 TraesCS7D01G036600 chr4A 714175309 714181172 5863 True 1374.8 4791 87.6636 170 6140 5 chr4A.!!$R1 5970
3 TraesCS7D01G036600 chr1B 91809923 91810435 512 True 614.0 614 88.2920 1004 1521 1 chr1B.!!$R1 517

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
887 944 0.029567 TTTGCGCCGTCGAATGTTTT 59.970 45.000 4.18 0.0 38.10 2.43 F
998 1060 0.248843 GCAGCAGACTAGGCTTGAGT 59.751 55.000 0.00 0.0 40.23 3.41 F
1571 1721 0.316204 AGCATCAAAACCAGCACTGC 59.684 50.000 0.00 0.0 0.00 4.40 F
1580 1730 0.675633 ACCAGCACTGCAATGTTTCC 59.324 50.000 3.30 0.0 0.00 3.13 F
2599 2825 1.003580 GAGCATTTGTCTGGTCTCCCA 59.996 52.381 0.00 0.0 39.86 4.37 F
3558 3791 1.299850 GGAAACCTTGTTGCGTGCC 60.300 57.895 0.00 0.0 0.00 5.01 F
4355 4598 1.095807 GTATGGCAAGAACCCTCGCC 61.096 60.000 0.00 0.0 45.11 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2676 2902 0.846693 AATACTCCAGGCCCCATGAC 59.153 55.0 0.00 0.00 0.00 3.06 R
2750 2978 1.692411 GCCAAGTTCTTGGAACCTGT 58.308 50.0 28.87 0.00 44.82 4.00 R
3221 3454 0.034767 TTGCATCAGGGAGAAGCCTG 60.035 55.0 0.00 0.00 40.14 4.85 R
3524 3757 0.387622 TTCCGTCGCTGTAGTTTCCG 60.388 55.0 0.00 0.00 0.00 4.30 R
3899 4142 1.113788 TCCATTAGGCCATGCAAAGC 58.886 50.0 5.01 2.80 33.74 3.51 R
5121 5365 0.037326 CCTCAACAGCTAGCGGAACA 60.037 55.0 22.16 3.31 0.00 3.18 R
5971 6447 0.838122 CAGAACCCTCACCCCTCAGT 60.838 60.0 0.00 0.00 0.00 3.41 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
44 45 4.417641 TCCTCGCGGAGAAGAAGT 57.582 55.556 6.13 0.00 33.30 3.01
58 64 0.036022 AGAAGTGCAAGGTGAGCTCC 59.964 55.000 12.15 2.19 0.00 4.70
62 68 1.842920 TGCAAGGTGAGCTCCTCCA 60.843 57.895 21.67 8.60 36.74 3.86
66 84 1.004044 CAAGGTGAGCTCCTCCACATT 59.996 52.381 21.67 11.42 36.74 2.71
93 111 3.181465 TGGAGTTCTTCTTTCTTCTGCGT 60.181 43.478 0.00 0.00 0.00 5.24
116 134 1.592081 GCTCTGCTATGCTCTGTTTCG 59.408 52.381 0.00 0.00 0.00 3.46
130 148 3.427598 TTTCGGTGTCGTCGGTGCA 62.428 57.895 0.00 0.00 37.69 4.57
144 162 0.538287 GGTGCAGCCTCCTCTGTTTT 60.538 55.000 4.03 0.00 36.49 2.43
151 169 1.683385 GCCTCCTCTGTTTTTGCTGTT 59.317 47.619 0.00 0.00 0.00 3.16
186 204 5.733226 AAAAATAAAGTGGTTTGCTGCAC 57.267 34.783 0.00 0.00 0.00 4.57
201 219 0.687757 TGCACTAGCCACTAGGGGAG 60.688 60.000 17.67 6.71 37.89 4.30
202 220 1.403687 GCACTAGCCACTAGGGGAGG 61.404 65.000 17.67 5.97 37.89 4.30
203 221 0.760945 CACTAGCCACTAGGGGAGGG 60.761 65.000 17.67 0.15 38.30 4.30
214 232 0.327000 AGGGGAGGGGACAGAAGATG 60.327 60.000 0.00 0.00 0.00 2.90
252 270 1.626356 CGGAGATGTGGTGGATGGGT 61.626 60.000 0.00 0.00 0.00 4.51
260 278 2.668632 GTGGATGGGTGCTTCCGA 59.331 61.111 0.00 0.00 37.00 4.55
301 319 4.674623 GCAAGTTGCCATCATTCTCTTCTG 60.675 45.833 17.36 0.00 37.42 3.02
303 321 5.426689 AGTTGCCATCATTCTCTTCTGTA 57.573 39.130 0.00 0.00 0.00 2.74
304 322 5.426504 AGTTGCCATCATTCTCTTCTGTAG 58.573 41.667 0.00 0.00 0.00 2.74
305 323 5.188555 AGTTGCCATCATTCTCTTCTGTAGA 59.811 40.000 0.00 0.00 0.00 2.59
336 354 1.040339 TTTCAGCACCAACCCACCAC 61.040 55.000 0.00 0.00 0.00 4.16
337 355 2.912025 CAGCACCAACCCACCACC 60.912 66.667 0.00 0.00 0.00 4.61
338 356 3.425014 AGCACCAACCCACCACCA 61.425 61.111 0.00 0.00 0.00 4.17
362 380 3.758554 GTGGATGCACCTTAGATGTTGTT 59.241 43.478 5.98 0.00 39.86 2.83
371 389 6.422400 GCACCTTAGATGTTGTTAGATCTAGC 59.578 42.308 9.50 9.50 37.77 3.42
378 396 5.830000 TGTTGTTAGATCTAGCGAGCTTA 57.170 39.130 11.44 0.00 37.12 3.09
396 416 3.386078 GCTTACTCACTCATGGATCCTCA 59.614 47.826 14.23 0.00 0.00 3.86
397 417 4.040217 GCTTACTCACTCATGGATCCTCAT 59.960 45.833 14.23 0.00 0.00 2.90
507 529 5.278660 GCCATGGTTAATTAGCTCCAGATTG 60.279 44.000 14.67 5.85 33.33 2.67
562 584 1.873591 CGCCTAATCACCACCATTAGC 59.126 52.381 0.00 0.00 33.92 3.09
625 658 2.346803 TGATCTCGTGCTTTACAAGGC 58.653 47.619 0.00 0.00 0.00 4.35
713 753 2.990967 CATGCAAACCCACCGGCT 60.991 61.111 0.00 0.00 0.00 5.52
728 768 0.802607 CGGCTTCTGTCGGCTACTTC 60.803 60.000 0.00 0.00 37.69 3.01
745 785 0.599204 TTCAACTTCTCGCCGGACAC 60.599 55.000 5.05 0.00 0.00 3.67
762 802 0.325296 CACCACCTGGGCTACCTCTA 60.325 60.000 0.00 0.00 42.05 2.43
763 803 0.416231 ACCACCTGGGCTACCTCTAA 59.584 55.000 0.00 0.00 42.05 2.10
822 879 2.287977 TCTCGGTCCTCTGTCTGAAA 57.712 50.000 0.00 0.00 0.00 2.69
886 943 0.659123 GTTTGCGCCGTCGAATGTTT 60.659 50.000 4.18 0.00 38.10 2.83
887 944 0.029567 TTTGCGCCGTCGAATGTTTT 59.970 45.000 4.18 0.00 38.10 2.43
888 945 0.866427 TTGCGCCGTCGAATGTTTTA 59.134 45.000 4.18 0.00 38.10 1.52
919 976 3.748048 TGGTCTTCTTCAAATCTTGCTCG 59.252 43.478 0.00 0.00 0.00 5.03
927 984 2.154462 CAAATCTTGCTCGGTTCCTGT 58.846 47.619 0.00 0.00 0.00 4.00
948 1005 5.485620 TGTTCATCTGTTGGATCTCTGAAG 58.514 41.667 0.00 0.00 31.27 3.02
950 1007 5.336150 TCATCTGTTGGATCTCTGAAGTC 57.664 43.478 0.00 0.00 31.27 3.01
957 1014 4.543590 TGGATCTCTGAAGTCAAGAACC 57.456 45.455 0.00 10.27 33.77 3.62
998 1060 0.248843 GCAGCAGACTAGGCTTGAGT 59.751 55.000 0.00 0.00 40.23 3.41
1146 1216 1.237285 CCTGCACTGCCACTGTTACC 61.237 60.000 0.00 0.00 0.00 2.85
1152 1227 3.705604 CACTGCCACTGTTACCTTTTTG 58.294 45.455 0.00 0.00 0.00 2.44
1171 1256 8.087750 CCTTTTTGTTGATAAGTTTATGCCAGA 58.912 33.333 0.00 0.00 0.00 3.86
1194 1279 6.944862 AGAATATAAATCTCTTGGTGATGGCC 59.055 38.462 0.00 0.00 0.00 5.36
1207 1294 5.575157 TGGTGATGGCCAGTATTAGAAAAA 58.425 37.500 13.05 0.00 33.97 1.94
1419 1563 7.458409 AGAATGATTGTATTCTGCACTTTGT 57.542 32.000 0.00 0.00 43.75 2.83
1528 1678 8.484575 ACATCTGACTGAACTGAATCTCATATT 58.515 33.333 0.00 0.00 0.00 1.28
1555 1705 5.762711 TCTGTCAAGTTTAGTAAATGCAGCA 59.237 36.000 0.00 0.00 0.00 4.41
1571 1721 0.316204 AGCATCAAAACCAGCACTGC 59.684 50.000 0.00 0.00 0.00 4.40
1580 1730 0.675633 ACCAGCACTGCAATGTTTCC 59.324 50.000 3.30 0.00 0.00 3.13
1583 1733 2.129607 CAGCACTGCAATGTTTCCAAC 58.870 47.619 3.30 0.00 0.00 3.77
1610 1760 7.972832 GGAATTCCAAATTCTTCTCTGAATGAC 59.027 37.037 20.04 0.00 35.07 3.06
1616 1766 3.599730 TCTTCTCTGAATGACGCATGT 57.400 42.857 0.00 0.00 0.00 3.21
1637 1787 4.662468 TTGTGCTAAACAATGGCTTCAA 57.338 36.364 0.00 0.00 43.96 2.69
1683 1833 8.597167 CAAATATATCTGGGTGGATCTTACTCA 58.403 37.037 3.74 3.74 0.00 3.41
1727 1877 1.160137 GGTGGATCTTATGCGGCATC 58.840 55.000 20.34 5.27 0.00 3.91
2047 2197 2.774234 CTGGGAGTATGTGAGGGTCAAT 59.226 50.000 0.00 0.00 0.00 2.57
2053 2203 3.840666 AGTATGTGAGGGTCAATGTGAGT 59.159 43.478 0.00 0.00 0.00 3.41
2253 2477 2.355010 AGGACTTTGTGCTTGAGCTT 57.645 45.000 4.44 0.00 42.66 3.74
2292 2516 2.687566 TCCTTCCCTCGCCCTTCC 60.688 66.667 0.00 0.00 0.00 3.46
2380 2604 1.207791 CAAGGAGAGCATGTACCCCT 58.792 55.000 0.00 0.00 0.00 4.79
2585 2811 1.977293 GAGGAAGGCCGAGGAGCATT 61.977 60.000 0.00 0.00 39.91 3.56
2599 2825 1.003580 GAGCATTTGTCTGGTCTCCCA 59.996 52.381 0.00 0.00 39.86 4.37
2676 2902 6.932400 TGTATTGTACGGAATTATTAGCCAGG 59.068 38.462 0.00 0.00 0.00 4.45
2678 2904 4.952460 TGTACGGAATTATTAGCCAGGTC 58.048 43.478 0.00 0.00 0.00 3.85
2740 2968 8.500773 TGAGATGTTATTAACGGTTCTTTTGAC 58.499 33.333 0.00 0.00 0.00 3.18
2750 2978 5.127491 ACGGTTCTTTTGACTGGACAAATA 58.873 37.500 0.00 0.00 39.09 1.40
2910 3138 3.569277 TGGTGTTCAATGTTGTCATCCTG 59.431 43.478 0.00 0.00 32.56 3.86
3003 3232 7.078249 TCCTGCATAGTTTATACATGGTCAT 57.922 36.000 0.00 0.00 0.00 3.06
3089 3318 2.094182 TCAAGTCCGTGCTATGGAGAAC 60.094 50.000 0.00 0.00 33.08 3.01
3155 3384 5.422970 ACCACGGATCCTTATTGTAAGTGTA 59.577 40.000 10.75 0.00 0.00 2.90
3157 3386 6.990349 CCACGGATCCTTATTGTAAGTGTAAT 59.010 38.462 10.75 0.00 0.00 1.89
3178 3408 9.810545 TGTAATATCTCGATGATACACAAAACA 57.189 29.630 13.07 0.00 40.12 2.83
3524 3757 2.502295 GCCAATCCTGACCTGATCATC 58.498 52.381 0.00 0.00 36.48 2.92
3539 3772 2.273370 TCATCGGAAACTACAGCGAC 57.727 50.000 0.00 0.00 0.00 5.19
3558 3791 1.299850 GGAAACCTTGTTGCGTGCC 60.300 57.895 0.00 0.00 0.00 5.01
3614 3847 4.154195 TGAATTCTAGCCGCTTTTCTGTTC 59.846 41.667 7.05 0.00 0.00 3.18
3670 3903 5.346181 TGATGTTACCATGATCGTTGGTA 57.654 39.130 18.61 18.61 45.62 3.25
3816 4049 3.275999 CCATGCTGACTTCATCATCACA 58.724 45.455 0.00 0.00 36.31 3.58
3880 4113 7.426929 ACAACTGAACTTTCACTGATCATAC 57.573 36.000 0.00 0.00 32.90 2.39
3883 4116 5.249393 ACTGAACTTTCACTGATCATACCCT 59.751 40.000 0.00 0.00 32.90 4.34
3897 4130 6.549364 TGATCATACCCTTCTGTTTTGTTGTT 59.451 34.615 0.00 0.00 0.00 2.83
3899 4142 3.885724 ACCCTTCTGTTTTGTTGTTGG 57.114 42.857 0.00 0.00 0.00 3.77
4019 4262 5.475220 TGTTGTCCATGGTATCGATGTTTTT 59.525 36.000 12.58 0.00 0.00 1.94
4154 4397 3.314913 ACAGCGATGTTGACAACAATGAA 59.685 39.130 24.00 1.32 45.86 2.57
4212 4455 1.926511 GCTGCACCGGTTTGATCCAG 61.927 60.000 2.97 6.08 0.00 3.86
4288 4531 3.064545 GGAACAAGCCAATCATCTTCTCG 59.935 47.826 0.00 0.00 0.00 4.04
4355 4598 1.095807 GTATGGCAAGAACCCTCGCC 61.096 60.000 0.00 0.00 45.11 5.54
4495 4738 1.825341 CCATGTCCGCTGGATCTCA 59.175 57.895 0.67 0.00 35.70 3.27
4594 4837 7.695480 AACTACATGTTGCATAAACCACATA 57.305 32.000 2.30 0.00 38.06 2.29
4597 4840 5.953183 ACATGTTGCATAAACCACATACTG 58.047 37.500 0.00 0.00 38.06 2.74
4602 4845 2.358898 GCATAAACCACATACTGGCCTG 59.641 50.000 8.29 8.29 45.32 4.85
4639 4882 3.660501 TCACATAACTCTTCTGCGTGT 57.339 42.857 0.00 0.00 0.00 4.49
4755 4998 2.093306 TCATCGTGAATGGTGTGTCC 57.907 50.000 0.00 0.00 35.94 4.02
4794 5037 2.352805 CAGGGTGACAAGGCCTCC 59.647 66.667 5.23 1.19 0.00 4.30
4795 5038 2.121963 AGGGTGACAAGGCCTCCA 60.122 61.111 5.23 1.29 0.00 3.86
4803 5046 1.377994 CAAGGCCTCCACTCTGCTT 59.622 57.895 5.23 0.00 0.00 3.91
4854 5097 3.658398 CAGCCACTGGACCAAGATT 57.342 52.632 0.00 0.00 0.00 2.40
4863 5106 1.177401 GGACCAAGATTTCACAGGGC 58.823 55.000 0.00 0.00 0.00 5.19
5004 5248 3.430236 GGAAGCTTTACTCTGAGAGGCTC 60.430 52.174 14.83 6.34 33.35 4.70
5016 5260 2.601664 GAGGCTCATGACCCTCACT 58.398 57.895 26.03 0.00 45.55 3.41
5079 5323 3.459063 GAGACCCGCCGCTACCTT 61.459 66.667 0.00 0.00 0.00 3.50
5145 5389 0.532573 CGCTAGCTGTTGAGGGAGAA 59.467 55.000 13.93 0.00 0.00 2.87
5148 5392 2.169352 GCTAGCTGTTGAGGGAGAATCA 59.831 50.000 7.70 0.00 36.25 2.57
5151 5395 1.339438 GCTGTTGAGGGAGAATCAGCA 60.339 52.381 9.56 0.00 44.80 4.41
5159 5403 1.471684 GGGAGAATCAGCAAGCAAGTG 59.528 52.381 0.00 0.00 36.25 3.16
5164 5408 3.940221 AGAATCAGCAAGCAAGTGATCTC 59.060 43.478 0.00 0.00 30.43 2.75
5174 5418 0.904865 AAGTGATCTCGCCACCTCCA 60.905 55.000 0.00 0.00 35.23 3.86
5175 5419 0.689080 AGTGATCTCGCCACCTCCAT 60.689 55.000 0.00 0.00 35.23 3.41
5221 5465 6.845758 TTCCTGCAAAGATTGAGATTTGAT 57.154 33.333 2.04 0.00 38.42 2.57
5300 5545 4.995487 AGTGTGCTAGTTTGGTTTAGTAGC 59.005 41.667 0.00 0.00 42.33 3.58
5379 5631 6.531240 GTCGTATTTCTTGGATGTTACCGTTA 59.469 38.462 0.00 0.00 0.00 3.18
5474 5726 1.015085 GTCACTGCTGCTGAGCTCTG 61.015 60.000 16.19 15.96 46.39 3.35
5486 5738 4.709886 TGCTGAGCTCTGTTACCTAATACA 59.290 41.667 20.24 4.65 0.00 2.29
5602 5938 6.405065 CCTGGTTTCTATGTGATTGTCAATGG 60.405 42.308 1.88 0.00 0.00 3.16
5636 5972 9.671279 TGCAATATATATGAATCCGACAAGATT 57.329 29.630 0.00 0.00 39.19 2.40
5687 6024 6.775629 AGTTAAAACTAGTGCCCAGAAATTCA 59.224 34.615 0.00 0.00 37.52 2.57
5706 6043 9.187455 GAAATTCAAGTTCGCTGGTAAAATTAA 57.813 29.630 0.00 0.00 0.00 1.40
5736 6087 2.092321 ACTCGCACCCTCTATGTAGTCT 60.092 50.000 0.00 0.00 0.00 3.24
5739 6090 2.292016 CGCACCCTCTATGTAGTCTGAG 59.708 54.545 0.00 0.00 0.00 3.35
5766 6117 2.563179 AGTCGAAGCTCAATAGGTGTGT 59.437 45.455 0.00 0.00 32.57 3.72
5794 6145 1.073397 CCTAGGAGGAGGGGCCATT 60.073 63.158 1.05 0.00 37.67 3.16
5834 6185 3.134623 TGAGAGAGCTCTGTGAACCAAAA 59.865 43.478 23.91 0.00 40.61 2.44
5836 6187 4.723309 AGAGAGCTCTGTGAACCAAAAAT 58.277 39.130 23.91 0.00 38.75 1.82
5890 6366 6.480524 TCGATTAAACACAATCAGAACTGG 57.519 37.500 1.93 0.00 35.09 4.00
5892 6368 6.147164 TCGATTAAACACAATCAGAACTGGAC 59.853 38.462 1.93 0.00 35.09 4.02
5955 6431 8.106247 TCCCTTTTTAGTAGCACATTTTACTG 57.894 34.615 0.00 0.00 32.64 2.74
5984 6460 1.127567 TGGTGAACTGAGGGGTGAGG 61.128 60.000 0.00 0.00 0.00 3.86
6019 6495 5.641636 ACCAAAACCAACAAAATCAACTGAC 59.358 36.000 0.00 0.00 0.00 3.51
6039 6515 2.288273 ACTGCTACACGAGTTCTTCCAC 60.288 50.000 0.00 0.00 0.00 4.02
6056 6532 2.991190 TCCACAAGAACGCGAACTAATC 59.009 45.455 15.93 0.67 0.00 1.75
6071 6547 5.570844 CGAACTAATCAGAAAAGGGGAGGAA 60.571 44.000 0.00 0.00 0.00 3.36
6100 6576 4.892198 AGACCTAATTAAGCAGGGGTAGA 58.108 43.478 9.36 0.00 36.15 2.59
6101 6577 4.902448 AGACCTAATTAAGCAGGGGTAGAG 59.098 45.833 9.36 0.00 36.15 2.43
6102 6578 3.391626 ACCTAATTAAGCAGGGGTAGAGC 59.608 47.826 9.36 0.00 36.15 4.09
6103 6579 3.391296 CCTAATTAAGCAGGGGTAGAGCA 59.609 47.826 0.00 0.00 0.00 4.26
6104 6580 3.567478 AATTAAGCAGGGGTAGAGCAG 57.433 47.619 0.00 0.00 0.00 4.24
6105 6581 1.204146 TTAAGCAGGGGTAGAGCAGG 58.796 55.000 0.00 0.00 0.00 4.85
6106 6582 0.338467 TAAGCAGGGGTAGAGCAGGA 59.662 55.000 0.00 0.00 0.00 3.86
6107 6583 0.980231 AAGCAGGGGTAGAGCAGGAG 60.980 60.000 0.00 0.00 0.00 3.69
6108 6584 1.687493 GCAGGGGTAGAGCAGGAGT 60.687 63.158 0.00 0.00 0.00 3.85
6109 6585 1.965754 GCAGGGGTAGAGCAGGAGTG 61.966 65.000 0.00 0.00 0.00 3.51
6110 6586 0.324738 CAGGGGTAGAGCAGGAGTGA 60.325 60.000 0.00 0.00 0.00 3.41
6134 6610 2.967397 CAGACCTTGCGACGGGTA 59.033 61.111 0.00 0.00 35.77 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.726351 CGAGGAGAGCCCCAGGAAC 61.726 68.421 0.00 0.00 34.66 3.62
41 42 0.036022 GAGGAGCTCACCTTGCACTT 59.964 55.000 17.19 0.00 40.73 3.16
44 45 1.842920 TGGAGGAGCTCACCTTGCA 60.843 57.895 23.23 12.03 40.73 4.08
62 68 6.310149 AGAAAGAAGAACTCCATTGGAATGT 58.690 36.000 6.88 0.00 34.60 2.71
66 84 6.000219 CAGAAGAAAGAAGAACTCCATTGGA 59.000 40.000 5.05 5.05 0.00 3.53
75 93 3.846383 GCACACGCAGAAGAAAGAAGAAC 60.846 47.826 0.00 0.00 38.36 3.01
93 111 0.900421 ACAGAGCATAGCAGAGCACA 59.100 50.000 0.00 0.00 0.00 4.57
130 148 1.133668 ACAGCAAAAACAGAGGAGGCT 60.134 47.619 0.00 0.00 0.00 4.58
184 202 0.760945 CCCTCCCCTAGTGGCTAGTG 60.761 65.000 2.96 0.00 32.62 2.74
186 204 1.152226 CCCCTCCCCTAGTGGCTAG 60.152 68.421 0.00 0.00 34.16 3.42
201 219 1.064463 TGATTGCCATCTTCTGTCCCC 60.064 52.381 0.00 0.00 0.00 4.81
202 220 2.295885 CTGATTGCCATCTTCTGTCCC 58.704 52.381 0.00 0.00 0.00 4.46
203 221 1.674962 GCTGATTGCCATCTTCTGTCC 59.325 52.381 0.00 0.00 35.15 4.02
204 222 2.362736 TGCTGATTGCCATCTTCTGTC 58.637 47.619 0.00 0.00 42.00 3.51
205 223 2.502142 TGCTGATTGCCATCTTCTGT 57.498 45.000 0.00 0.00 42.00 3.41
214 232 0.179119 GCAAGTGGATGCTGATTGCC 60.179 55.000 9.36 0.00 43.06 4.52
301 319 3.434641 GCTGAAACCTTAAACCCGTCTAC 59.565 47.826 0.00 0.00 0.00 2.59
303 321 2.158726 TGCTGAAACCTTAAACCCGTCT 60.159 45.455 0.00 0.00 0.00 4.18
304 322 2.031420 GTGCTGAAACCTTAAACCCGTC 60.031 50.000 0.00 0.00 0.00 4.79
305 323 1.951602 GTGCTGAAACCTTAAACCCGT 59.048 47.619 0.00 0.00 0.00 5.28
336 354 2.787473 TCTAAGGTGCATCCACTTGG 57.213 50.000 0.00 0.00 41.75 3.61
337 355 3.614092 ACATCTAAGGTGCATCCACTTG 58.386 45.455 0.00 0.00 41.75 3.16
338 356 4.012374 CAACATCTAAGGTGCATCCACTT 58.988 43.478 0.00 0.00 41.75 3.16
371 389 3.551863 GGATCCATGAGTGAGTAAGCTCG 60.552 52.174 6.95 0.00 44.48 5.03
378 396 2.971330 GGATGAGGATCCATGAGTGAGT 59.029 50.000 15.82 0.00 46.93 3.41
462 484 3.260740 CTGCTAGCACAAGAAAGGAGAG 58.739 50.000 14.93 0.00 29.71 3.20
507 529 3.816523 TGTTACCGGGAAATGACAGAAAC 59.183 43.478 0.00 0.00 0.00 2.78
514 536 2.835580 TTCGTGTTACCGGGAAATGA 57.164 45.000 0.00 0.00 0.00 2.57
562 584 1.185315 CCATGCCAAGGTGGTTAAGG 58.815 55.000 0.00 0.00 40.46 2.69
713 753 3.321111 AGAAGTTGAAGTAGCCGACAGAA 59.679 43.478 0.00 0.00 0.00 3.02
728 768 2.027625 GGTGTCCGGCGAGAAGTTG 61.028 63.158 9.30 0.00 0.00 3.16
745 785 1.209747 GTTTAGAGGTAGCCCAGGTGG 59.790 57.143 0.00 0.00 37.09 4.61
762 802 9.878599 GAGTGTGCGCATTTATAATTATAGTTT 57.121 29.630 15.91 0.00 0.00 2.66
763 803 8.504005 GGAGTGTGCGCATTTATAATTATAGTT 58.496 33.333 15.91 0.00 0.00 2.24
906 963 2.224523 ACAGGAACCGAGCAAGATTTGA 60.225 45.455 0.00 0.00 0.00 2.69
919 976 3.140325 TCCAACAGATGAACAGGAACC 57.860 47.619 0.00 0.00 0.00 3.62
927 984 5.246883 TGACTTCAGAGATCCAACAGATGAA 59.753 40.000 0.00 0.00 34.42 2.57
948 1005 2.568623 ATCAGTGGTGGGTTCTTGAC 57.431 50.000 0.00 0.00 0.00 3.18
950 1007 4.848357 AGATTATCAGTGGTGGGTTCTTG 58.152 43.478 0.00 0.00 0.00 3.02
957 1014 4.095483 GCAGAACAAGATTATCAGTGGTGG 59.905 45.833 0.00 0.00 0.00 4.61
1026 1088 4.463879 CTGTGGAGGCGGCTGAGG 62.464 72.222 19.63 0.00 0.00 3.86
1121 1188 2.203480 TGGCAGTGCAGGGGAAAC 60.203 61.111 18.61 0.00 0.00 2.78
1146 1216 9.474920 TTCTGGCATAAACTTATCAACAAAAAG 57.525 29.630 0.00 0.00 0.00 2.27
1171 1256 6.613699 TGGCCATCACCAAGAGATTTATATT 58.386 36.000 0.00 0.00 36.55 1.28
1419 1563 4.467795 AGCAAGTCTTGATTAGCACTAGGA 59.532 41.667 16.99 0.00 0.00 2.94
1474 1621 4.346127 CCACATAGATCCTGTCAGATCCAA 59.654 45.833 0.00 0.00 43.14 3.53
1528 1678 8.450964 GCTGCATTTACTAAACTTGACAGAATA 58.549 33.333 0.00 0.00 0.00 1.75
1532 1682 6.000891 TGCTGCATTTACTAAACTTGACAG 57.999 37.500 0.00 0.00 0.00 3.51
1553 1703 0.032403 TGCAGTGCTGGTTTTGATGC 59.968 50.000 17.60 0.00 0.00 3.91
1555 1705 2.366266 ACATTGCAGTGCTGGTTTTGAT 59.634 40.909 17.60 0.00 0.00 2.57
1580 1730 6.072508 TCAGAGAAGAATTTGGAATTCCGTTG 60.073 38.462 19.57 2.63 39.43 4.10
1583 1733 6.500684 TTCAGAGAAGAATTTGGAATTCCG 57.499 37.500 19.57 0.66 39.43 4.30
1890 2040 5.624281 GCTCAAGAAGTCTGCTGAGATAAGT 60.624 44.000 12.28 0.00 34.39 2.24
2047 2197 1.287191 GACAGCGAGCTCACTCACA 59.713 57.895 15.40 0.00 43.66 3.58
2179 2331 9.269453 TCGATAGAGTAAGAGAACGAAATCATA 57.731 33.333 0.00 0.00 42.67 2.15
2201 2353 7.931407 TGCCAAAACATAGAAGTACATATCGAT 59.069 33.333 2.16 2.16 0.00 3.59
2209 2361 5.154222 GTTGCTGCCAAAACATAGAAGTAC 58.846 41.667 0.00 0.00 31.68 2.73
2292 2516 1.450312 GCCGATGGACTTGGACAGG 60.450 63.158 0.00 0.00 0.00 4.00
2380 2604 1.667830 CGCGGAGGAAGTTGAGCAA 60.668 57.895 0.00 0.00 0.00 3.91
2599 2825 1.107114 CCGAGTATGGAGTGTCTGCT 58.893 55.000 0.00 0.00 0.00 4.24
2676 2902 0.846693 AATACTCCAGGCCCCATGAC 59.153 55.000 0.00 0.00 0.00 3.06
2678 2904 2.091665 AGAAAATACTCCAGGCCCCATG 60.092 50.000 0.00 0.00 0.00 3.66
2740 2968 4.651778 TCTTGGAACCTGTATTTGTCCAG 58.348 43.478 0.00 0.00 0.00 3.86
2750 2978 1.692411 GCCAAGTTCTTGGAACCTGT 58.308 50.000 28.87 0.00 44.82 4.00
2886 3114 4.834496 AGGATGACAACATTGAACACCATT 59.166 37.500 0.00 0.00 36.82 3.16
2910 3138 2.312436 AAAGTAACCGTGCGGCGAC 61.312 57.895 12.98 8.77 44.77 5.19
3003 3232 8.375506 AGATTAATCAGAACAGGTTTAGTCACA 58.624 33.333 17.56 0.00 0.00 3.58
3077 3306 2.034878 AGCATCTCGTTCTCCATAGCA 58.965 47.619 0.00 0.00 0.00 3.49
3089 3318 0.388294 TGATCCTCAGCAGCATCTCG 59.612 55.000 0.00 0.00 0.00 4.04
3221 3454 0.034767 TTGCATCAGGGAGAAGCCTG 60.035 55.000 0.00 0.00 40.14 4.85
3479 3712 0.456221 GCTCTCCGGAAATCTCGTGA 59.544 55.000 5.23 0.00 0.00 4.35
3524 3757 0.387622 TTCCGTCGCTGTAGTTTCCG 60.388 55.000 0.00 0.00 0.00 4.30
3539 3772 1.657181 GCACGCAACAAGGTTTCCG 60.657 57.895 0.00 0.00 0.00 4.30
3578 3811 7.148641 CGGCTAGAATTCATACATGAGTAACT 58.851 38.462 8.44 0.00 38.19 2.24
3614 3847 8.849168 TCAATATGTGGTAAATATGCTTCCAAG 58.151 33.333 0.00 0.00 0.00 3.61
3816 4049 2.165998 GCAATCTCTTGGAAGGTGCTT 58.834 47.619 0.00 0.00 32.72 3.91
3880 4113 2.168313 AGCCAACAACAAAACAGAAGGG 59.832 45.455 0.00 0.00 0.00 3.95
3883 4116 3.434984 GCAAAGCCAACAACAAAACAGAA 59.565 39.130 0.00 0.00 0.00 3.02
3899 4142 1.113788 TCCATTAGGCCATGCAAAGC 58.886 50.000 5.01 2.80 33.74 3.51
3986 4229 2.006888 CCATGGACAACACGGTACATC 58.993 52.381 5.56 0.00 40.36 3.06
4019 4262 5.308497 TGAGACTATGTTAAACTTGGGGTCA 59.692 40.000 0.00 0.00 0.00 4.02
4073 4316 2.422235 CCTCCTCTGTGACTCGGAGTAT 60.422 54.545 11.27 0.00 45.40 2.12
4136 4379 4.596097 TGTGTTCATTGTTGTCAACATCG 58.404 39.130 18.83 12.75 41.79 3.84
4137 4380 6.020440 CACTTGTGTTCATTGTTGTCAACATC 60.020 38.462 18.83 8.32 41.79 3.06
4154 4397 4.696479 ATTCTCCAGTTCTCACTTGTGT 57.304 40.909 0.46 0.00 0.00 3.72
4212 4455 8.723942 ATTCTAGTCAGATGAACACCAATAAC 57.276 34.615 0.00 0.00 0.00 1.89
4219 4462 7.704472 CAGAAGGTATTCTAGTCAGATGAACAC 59.296 40.741 0.00 0.00 44.15 3.32
4288 4531 1.375523 ACGGTCCAAACGAGCCATC 60.376 57.895 0.00 0.00 35.44 3.51
4355 4598 3.632145 ACAAGGTTAACAAGTTCCTGCAG 59.368 43.478 6.78 6.78 0.00 4.41
4495 4738 1.296715 GACACGGTTCATCTGGGCT 59.703 57.895 0.00 0.00 0.00 5.19
4610 4853 6.373779 CAGAAGAGTTATGTGAAAACGCAAT 58.626 36.000 0.00 0.00 32.00 3.56
4614 4857 4.084537 ACGCAGAAGAGTTATGTGAAAACG 60.085 41.667 2.09 0.00 36.01 3.60
4618 4861 3.990092 ACACGCAGAAGAGTTATGTGAA 58.010 40.909 2.09 0.00 36.01 3.18
4626 4869 0.244994 CAGGCTACACGCAGAAGAGT 59.755 55.000 0.00 0.00 41.67 3.24
4639 4882 2.918712 GCCTCATAGAAAGCAGGCTA 57.081 50.000 1.40 0.00 46.88 3.93
4755 4998 0.469917 AGGGATCAATGTGGTAGCCG 59.530 55.000 0.00 0.00 0.00 5.52
4794 5037 4.333649 TCAAAGAACTCAACAAGCAGAGTG 59.666 41.667 0.00 0.00 43.88 3.51
4795 5038 4.517285 TCAAAGAACTCAACAAGCAGAGT 58.483 39.130 0.00 0.00 46.45 3.24
4803 5046 3.627577 GGCACTTCTCAAAGAACTCAACA 59.372 43.478 0.00 0.00 36.30 3.33
4854 5097 3.551496 CTGAAGCCCGCCCTGTGAA 62.551 63.158 0.00 0.00 0.00 3.18
4863 5106 1.154205 CCTCAATACGCTGAAGCCCG 61.154 60.000 0.00 0.00 37.91 6.13
4920 5163 5.066634 TCGCAGAAACTAGTTATCCTCAGAG 59.933 44.000 8.92 2.02 0.00 3.35
5016 5260 0.178858 TCCAGAACCCATACACCCCA 60.179 55.000 0.00 0.00 0.00 4.96
5019 5263 3.677976 CGTACTTCCAGAACCCATACACC 60.678 52.174 0.00 0.00 0.00 4.16
5121 5365 0.037326 CCTCAACAGCTAGCGGAACA 60.037 55.000 22.16 3.31 0.00 3.18
5145 5389 2.277969 CGAGATCACTTGCTTGCTGAT 58.722 47.619 0.00 0.00 0.00 2.90
5148 5392 2.464682 GCGAGATCACTTGCTTGCT 58.535 52.632 0.00 0.00 46.70 3.91
5159 5403 1.596477 GCATGGAGGTGGCGAGATC 60.596 63.158 0.00 0.00 0.00 2.75
5174 5418 1.678970 GCCACCCTTCTTTCGGCAT 60.679 57.895 0.00 0.00 42.50 4.40
5175 5419 2.282180 GCCACCCTTCTTTCGGCA 60.282 61.111 0.00 0.00 42.50 5.69
5221 5465 7.414098 GCGTCTAGGAAGAAAATCAAAGCATTA 60.414 37.037 0.00 0.00 32.16 1.90
5231 5475 3.196685 AGAGCAGCGTCTAGGAAGAAAAT 59.803 43.478 0.00 0.00 32.16 1.82
5258 5503 4.523173 ACACTGACTCGACCTTGAATCTTA 59.477 41.667 0.00 0.00 0.00 2.10
5300 5545 2.675423 TGTCCCGACTCACTCCCG 60.675 66.667 0.00 0.00 0.00 5.14
5379 5631 3.951680 CACCAAGGCCGTTCCTATTATTT 59.048 43.478 0.00 0.00 46.94 1.40
5431 5683 6.265422 ACAAAGATTTTCTTGGAAACGAGGAT 59.735 34.615 0.00 0.00 42.59 3.24
5486 5738 7.348537 AGCTCTTTATCCCACCTTCTAGTAATT 59.651 37.037 0.00 0.00 0.00 1.40
5518 5780 5.437289 TGCTCATTTGGTTAACTGAAGTG 57.563 39.130 5.42 6.36 0.00 3.16
5672 6009 2.554032 CGAACTTGAATTTCTGGGCACT 59.446 45.455 0.00 0.00 0.00 4.40
5676 6013 2.095059 CCAGCGAACTTGAATTTCTGGG 60.095 50.000 0.00 0.00 36.78 4.45
5687 6024 7.360361 CAGAACTTAATTTTACCAGCGAACTT 58.640 34.615 0.00 0.00 0.00 2.66
5739 6090 4.811557 ACCTATTGAGCTTCGACTAATTGC 59.188 41.667 0.00 0.00 0.00 3.56
5766 6117 3.631087 CCCTCCTCCTAGGATGTTCTTGA 60.631 52.174 13.12 0.22 44.81 3.02
5794 6145 7.297936 TCTCTCAATCGGCTATAACCAATAA 57.702 36.000 0.00 0.00 0.00 1.40
5809 6160 3.056250 TGGTTCACAGAGCTCTCTCAATC 60.056 47.826 14.96 7.29 41.81 2.67
5868 6344 6.073276 TGTCCAGTTCTGATTGTGTTTAATCG 60.073 38.462 1.00 0.00 39.39 3.34
5890 6366 8.032952 TGACAGATTACAGACATCATTTTGTC 57.967 34.615 0.00 0.00 45.15 3.18
5892 6368 8.291740 TGTTGACAGATTACAGACATCATTTTG 58.708 33.333 0.00 0.00 0.00 2.44
5955 6431 1.737236 TCAGTTCACCAATGCGTATGC 59.263 47.619 0.00 0.00 43.20 3.14
5965 6441 1.127567 CCTCACCCCTCAGTTCACCA 61.128 60.000 0.00 0.00 0.00 4.17
5966 6442 1.679898 CCTCACCCCTCAGTTCACC 59.320 63.158 0.00 0.00 0.00 4.02
5971 6447 0.838122 CAGAACCCTCACCCCTCAGT 60.838 60.000 0.00 0.00 0.00 3.41
5984 6460 1.754226 TGGTTTTGGTGCTTCAGAACC 59.246 47.619 18.43 18.43 46.17 3.62
6019 6495 2.288213 TGTGGAAGAACTCGTGTAGCAG 60.288 50.000 0.00 0.00 0.00 4.24
6039 6515 4.903638 TTCTGATTAGTTCGCGTTCTTG 57.096 40.909 5.77 0.00 0.00 3.02
6056 6532 2.357569 CCCTCATTCCTCCCCTTTTCTG 60.358 54.545 0.00 0.00 0.00 3.02
6071 6547 4.349342 CCTGCTTAATTAGGTCTCCCTCAT 59.651 45.833 0.00 0.00 41.45 2.90
6100 6576 4.385405 GCACGGCTCACTCCTGCT 62.385 66.667 0.00 0.00 31.80 4.24
6101 6577 4.687215 TGCACGGCTCACTCCTGC 62.687 66.667 0.00 0.00 33.68 4.85
6102 6578 2.433838 CTGCACGGCTCACTCCTG 60.434 66.667 0.00 0.00 0.00 3.86
6103 6579 2.601666 TCTGCACGGCTCACTCCT 60.602 61.111 0.00 0.00 0.00 3.69
6104 6580 2.433318 GTCTGCACGGCTCACTCC 60.433 66.667 0.00 0.00 0.00 3.85
6105 6581 2.433318 GGTCTGCACGGCTCACTC 60.433 66.667 0.00 0.00 0.00 3.51
6106 6582 2.511452 AAGGTCTGCACGGCTCACT 61.511 57.895 0.00 0.00 0.00 3.41
6107 6583 2.031163 AAGGTCTGCACGGCTCAC 59.969 61.111 0.00 0.00 0.00 3.51
6108 6584 2.031012 CAAGGTCTGCACGGCTCA 59.969 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.