Multiple sequence alignment - TraesCS7A01G171400

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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 TraesCS7A01G171400 chr7A 100.000 5934 0 0 1 5934 126916123 126910190 0.000000e+00 10959.0
1 TraesCS7A01G171400 chr2A 90.480 5641 433 57 3 5576 756212637 756207034 0.000000e+00 7347.0
2 TraesCS7A01G171400 chr2A 89.779 362 34 3 5573 5933 756206993 756206634 1.510000e-125 460.0
3 TraesCS7A01G171400 chr4A 92.092 4843 323 29 1 4794 544593447 544598278 0.000000e+00 6767.0
4 TraesCS7A01G171400 chr4A 90.104 576 49 6 5365 5934 544607109 544607682 0.000000e+00 741.0
5 TraesCS7A01G171400 chr6A 86.256 5639 631 73 396 5929 42323287 42317688 0.000000e+00 5987.0
6 TraesCS7A01G171400 chr6A 85.810 5652 640 80 11 5572 42645263 42639684 0.000000e+00 5845.0
7 TraesCS7A01G171400 chr6A 86.651 5259 586 70 396 5577 42523599 42518380 0.000000e+00 5716.0
8 TraesCS7A01G171400 chr6A 86.843 4872 534 63 765 5577 42357163 42352340 0.000000e+00 5347.0
9 TraesCS7A01G171400 chr6A 87.223 4602 496 51 765 5308 42611807 42607240 0.000000e+00 5156.0
10 TraesCS7A01G171400 chr6A 87.147 3011 311 36 396 3346 42545935 42542941 0.000000e+00 3347.0
11 TraesCS7A01G171400 chr6A 87.913 2333 241 19 765 3065 42576157 42573834 0.000000e+00 2708.0
12 TraesCS7A01G171400 chr6A 86.434 2462 280 36 2873 5308 42567410 42564977 0.000000e+00 2647.0
13 TraesCS7A01G171400 chr6A 86.635 2297 269 28 3294 5572 42688561 42686285 0.000000e+00 2507.0
14 TraesCS7A01G171400 chr6A 85.373 1087 124 28 4490 5572 42572529 42571474 0.000000e+00 1094.0
15 TraesCS7A01G171400 chr7D 97.143 35 0 1 430 464 616690939 616690906 2.310000e-04 58.4
16 TraesCS7A01G171400 chr5B 97.059 34 0 1 430 463 35249164 35249132 8.310000e-04 56.5


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 TraesCS7A01G171400 chr7A 126910190 126916123 5933 True 10959.0 10959 100.0000 1 5934 1 chr7A.!!$R1 5933
1 TraesCS7A01G171400 chr2A 756206634 756212637 6003 True 3903.5 7347 90.1295 3 5933 2 chr2A.!!$R1 5930
2 TraesCS7A01G171400 chr4A 544593447 544598278 4831 False 6767.0 6767 92.0920 1 4794 1 chr4A.!!$F1 4793
3 TraesCS7A01G171400 chr4A 544607109 544607682 573 False 741.0 741 90.1040 5365 5934 1 chr4A.!!$F2 569
4 TraesCS7A01G171400 chr6A 42317688 42323287 5599 True 5987.0 5987 86.2560 396 5929 1 chr6A.!!$R1 5533
5 TraesCS7A01G171400 chr6A 42639684 42645263 5579 True 5845.0 5845 85.8100 11 5572 1 chr6A.!!$R7 5561
6 TraesCS7A01G171400 chr6A 42518380 42523599 5219 True 5716.0 5716 86.6510 396 5577 1 chr6A.!!$R3 5181
7 TraesCS7A01G171400 chr6A 42352340 42357163 4823 True 5347.0 5347 86.8430 765 5577 1 chr6A.!!$R2 4812
8 TraesCS7A01G171400 chr6A 42607240 42611807 4567 True 5156.0 5156 87.2230 765 5308 1 chr6A.!!$R6 4543
9 TraesCS7A01G171400 chr6A 42542941 42545935 2994 True 3347.0 3347 87.1470 396 3346 1 chr6A.!!$R4 2950
10 TraesCS7A01G171400 chr6A 42564977 42567410 2433 True 2647.0 2647 86.4340 2873 5308 1 chr6A.!!$R5 2435
11 TraesCS7A01G171400 chr6A 42686285 42688561 2276 True 2507.0 2507 86.6350 3294 5572 1 chr6A.!!$R8 2278
12 TraesCS7A01G171400 chr6A 42571474 42576157 4683 True 1901.0 2708 86.6430 765 5572 2 chr6A.!!$R9 4807

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
131 132 0.326264 GTCCAGATGGTTCCAGCTGT 59.674 55.000 27.64 0.31 45.61 4.40 F
1849 1885 0.390866 AGCACCTTCTCGATGCAGTG 60.391 55.000 10.33 6.15 41.97 3.66 F
3682 3773 0.172803 GACTGATCTGCGTTACCGGT 59.827 55.000 13.98 13.98 33.68 5.28 F
4460 4555 1.218316 CCCCGTTGTAGCTGAGGAC 59.782 63.158 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2148 0.032678 CGATGGAAGGACTCGGGATG 59.967 60.000 0.00 0.0 0.00 3.51 R
3842 3933 0.698886 ATGGGGGCATCTAGGCAAGA 60.699 55.000 0.00 0.0 46.44 3.02 R
4855 4953 0.109597 CCTCATGCGCCAACTTTGAC 60.110 55.000 4.18 0.0 0.00 3.18 R
5741 5918 2.616842 TGCTCGAACTTTGAACTTTCCC 59.383 45.455 0.00 0.0 0.00 3.97 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
50 51 2.202388 CCAGATTGTTGCTGCGCG 60.202 61.111 0.00 0.00 32.06 6.86
87 88 2.442643 CCGGCTGGGCATGGATTT 60.443 61.111 2.57 0.00 0.00 2.17
131 132 0.326264 GTCCAGATGGTTCCAGCTGT 59.674 55.000 27.64 0.31 45.61 4.40
138 139 3.264193 AGATGGTTCCAGCTGTCATACAA 59.736 43.478 13.81 0.00 31.00 2.41
150 151 1.677300 CATACAACCCCAGGCGCAA 60.677 57.895 10.83 0.00 0.00 4.85
202 203 4.025858 AGGCTGCGATGCACCAGT 62.026 61.111 11.18 0.00 34.10 4.00
204 205 2.743538 GCTGCGATGCACCAGTCA 60.744 61.111 11.18 0.00 33.79 3.41
223 224 3.883462 CGCAGGCGGTCAACAATA 58.117 55.556 5.63 0.00 35.56 1.90
285 286 1.162698 CATCTGGTGCACAAGGACTG 58.837 55.000 21.25 12.23 36.20 3.51
296 297 3.120086 AAGGACTGGCCGCAGTTGT 62.120 57.895 0.00 0.00 43.43 3.32
310 311 0.608130 AGTTGTCGTGCTCATGGCTA 59.392 50.000 7.54 0.00 42.39 3.93
373 374 5.795441 GTGCTTGCTATGTACTTTGCTTAAC 59.205 40.000 14.37 6.14 0.00 2.01
641 661 8.859090 CCCTAGACCATAATGAATAAATTTGCA 58.141 33.333 0.00 0.00 0.00 4.08
655 675 7.849804 ATAAATTTGCACTACACGATCTCTT 57.150 32.000 0.00 0.00 0.00 2.85
656 676 5.536554 AATTTGCACTACACGATCTCTTG 57.463 39.130 0.00 0.00 0.00 3.02
657 677 2.654749 TGCACTACACGATCTCTTGG 57.345 50.000 0.00 0.00 0.00 3.61
658 678 1.893137 TGCACTACACGATCTCTTGGT 59.107 47.619 0.00 0.00 0.00 3.67
743 775 3.394313 GGGCGACCGTAATTTTTGTAG 57.606 47.619 0.00 0.00 43.64 2.74
763 795 4.451150 GACGAGCCGGCACATCCA 62.451 66.667 31.54 0.00 33.63 3.41
818 850 5.826643 ACTCTAATTATGAAGGGGCAAACA 58.173 37.500 0.00 0.00 0.00 2.83
819 851 5.652452 ACTCTAATTATGAAGGGGCAAACAC 59.348 40.000 0.00 0.00 0.00 3.32
831 863 1.601914 GGCAAACACGTCATTTCACCC 60.602 52.381 0.00 0.00 0.00 4.61
832 864 1.924191 GCAAACACGTCATTTCACCCG 60.924 52.381 0.00 0.00 0.00 5.28
891 927 2.351835 CCACGGATCCAGTCATATCGTC 60.352 54.545 13.41 0.00 0.00 4.20
908 944 1.067425 CGTCAACCATACCGACCAAGA 60.067 52.381 0.00 0.00 0.00 3.02
979 1015 0.326264 CCTCTTTGCCAGGCAGTACT 59.674 55.000 15.50 0.00 40.61 2.73
1006 1042 3.194755 TCGTACTCACAACAGCATGGTAT 59.805 43.478 0.00 0.00 43.62 2.73
1049 1085 9.990360 TGTTTTCTCTGTTCATGTTGTACTATA 57.010 29.630 0.00 0.00 0.00 1.31
1052 1088 9.856488 TTTCTCTGTTCATGTTGTACTATAGTC 57.144 33.333 9.12 2.17 0.00 2.59
1064 1100 6.451064 TGTACTATAGTCAGTGTGTCATGG 57.549 41.667 9.12 0.00 0.00 3.66
1071 1107 1.134995 TCAGTGTGTCATGGATCTCGC 60.135 52.381 0.00 0.00 0.00 5.03
1086 1122 0.463204 CTCGCCCAGATCTGACACAT 59.537 55.000 24.62 0.00 0.00 3.21
1141 1177 3.772025 CCCTGTAGGATGACCATAGATCC 59.228 52.174 0.00 0.00 38.83 3.36
1352 1388 7.178628 ACAAGAAGTGGTTAGTAGAGCAGATTA 59.821 37.037 0.00 0.00 0.00 1.75
1513 1549 6.437477 AGGATTTCTACAAGGTTTTTGGGATC 59.563 38.462 0.00 0.00 0.00 3.36
1788 1824 0.630673 TGGGGAGCCATAGCAAACAT 59.369 50.000 0.00 0.00 43.56 2.71
1849 1885 0.390866 AGCACCTTCTCGATGCAGTG 60.391 55.000 10.33 6.15 41.97 3.66
1883 1919 3.285484 AGAGACATGATGGCCAACAATC 58.715 45.455 20.58 18.99 0.00 2.67
1982 2026 6.427547 AGGTATGTTTCATTTTTGCAACCATG 59.572 34.615 0.00 4.57 0.00 3.66
2001 2045 3.579335 TGCATGAATTGACATGGTGTG 57.421 42.857 0.00 0.00 45.14 3.82
2014 2058 1.592131 GGTGTGTGCCAACGTCGTA 60.592 57.895 0.00 0.00 0.00 3.43
2102 2148 6.169800 GTGCTCCCTAGGATATCAGAATTTC 58.830 44.000 11.48 0.00 0.00 2.17
2104 2150 6.503217 TGCTCCCTAGGATATCAGAATTTCAT 59.497 38.462 11.48 0.00 0.00 2.57
2118 2164 1.651737 TTTCATCCCGAGTCCTTCCA 58.348 50.000 0.00 0.00 0.00 3.53
2228 2275 4.194640 TGCTTGAGTATGCAGGAAATCTC 58.805 43.478 0.00 0.00 33.57 2.75
2240 2287 3.303881 GGAAATCTCCTTTGCACCAAC 57.696 47.619 0.00 0.00 38.88 3.77
2242 2289 0.598065 AATCTCCTTTGCACCAACGC 59.402 50.000 0.00 0.00 0.00 4.84
2290 2337 7.029563 CAGCCAGTTATTGTCTCATTTTTACC 58.970 38.462 0.00 0.00 0.00 2.85
2292 2339 7.232534 AGCCAGTTATTGTCTCATTTTTACCAA 59.767 33.333 0.00 0.00 0.00 3.67
2322 2370 1.882167 GCGGATGCAGCTGAGAGAC 60.882 63.158 20.43 0.00 42.15 3.36
2337 2385 1.402259 AGAGACGCTTCGACAGTATGG 59.598 52.381 0.00 0.00 43.62 2.74
2407 2455 1.621814 ACAAGCTTACTAGGCGTTCCA 59.378 47.619 0.00 0.00 33.74 3.53
2417 2465 3.204827 GCGTTCCAGCATGCCGAT 61.205 61.111 15.66 0.00 37.05 4.18
2563 2629 8.547967 TCTAGTATGTGCTTCCTTTTTAAGTG 57.452 34.615 0.00 0.00 0.00 3.16
2625 2691 0.253820 ATCCCCAGGTCCTCACCATT 60.254 55.000 0.00 0.00 46.68 3.16
2731 2797 0.704076 ACAAAATCCAGCAGGCCCTA 59.296 50.000 0.00 0.00 33.74 3.53
2818 2884 1.742831 ACAAATCGTTGTGTGTGCTGT 59.257 42.857 0.00 0.00 46.40 4.40
2857 2924 1.480137 GAGTGTCCAGATCAGGTCAGG 59.520 57.143 4.37 0.00 34.93 3.86
2918 2988 3.191162 GCCTTCACATGCACAAGTCATTA 59.809 43.478 0.00 0.00 0.00 1.90
2931 3001 7.763528 TGCACAAGTCATTAATTTGTTTCTGTT 59.236 29.630 1.98 0.00 33.06 3.16
2932 3002 9.243637 GCACAAGTCATTAATTTGTTTCTGTTA 57.756 29.630 1.98 0.00 33.06 2.41
2951 3021 1.181098 ATTGCCGCCATCCATTAGCC 61.181 55.000 0.00 0.00 0.00 3.93
2978 3048 0.389948 CCACCTCCAAGTCTGTACGC 60.390 60.000 0.00 0.00 0.00 4.42
3017 3088 4.522789 GCAGGAAAAATACAGGGACAAAGA 59.477 41.667 0.00 0.00 0.00 2.52
3019 3090 5.048013 CAGGAAAAATACAGGGACAAAGACC 60.048 44.000 0.00 0.00 0.00 3.85
3044 3115 3.118629 AGCTATCTGATTGCGAAGGTCAA 60.119 43.478 16.27 0.00 36.14 3.18
3061 3132 5.452255 AGGTCAAATGACATCCTGCAATAT 58.548 37.500 14.93 0.00 46.47 1.28
3131 3208 6.406400 CCTCGTCCAGAAACATCTCTAATCTT 60.406 42.308 0.00 0.00 0.00 2.40
3222 3311 3.544684 TGCGCAGGATTCTACATCAAAT 58.455 40.909 5.66 0.00 0.00 2.32
3450 3539 1.300853 GCCACACATGCCAACAACC 60.301 57.895 0.00 0.00 0.00 3.77
3595 3685 5.750524 TGCTCATTATTTAGCACCCTTACA 58.249 37.500 0.00 0.00 43.56 2.41
3608 3699 3.687698 CACCCTTACATTCTAACCCGTTG 59.312 47.826 0.00 0.00 0.00 4.10
3624 3715 2.973224 CCGTTGTCTTTTGAATTCGCTG 59.027 45.455 0.04 0.00 0.00 5.18
3636 3727 9.941664 CTTTTGAATTCGCTGAATGAACTATAT 57.058 29.630 0.04 0.00 32.14 0.86
3664 3755 8.631480 ACTATATTATACATGACAGTCCACGA 57.369 34.615 0.00 0.00 0.00 4.35
3682 3773 0.172803 GACTGATCTGCGTTACCGGT 59.827 55.000 13.98 13.98 33.68 5.28
3770 3861 2.108970 GGAGGTATTCCCAGTTCGACT 58.891 52.381 0.00 0.00 40.37 4.18
3842 3933 4.079253 ACCTGAATTTGCGGTAATTCTGT 58.921 39.130 15.40 11.35 42.39 3.41
3885 3976 6.723298 TTTTTCATCTTGGTCCTTTGCTTA 57.277 33.333 0.00 0.00 0.00 3.09
3933 4024 3.439129 CCTCCAAGTTTATCGTTCAACCC 59.561 47.826 0.00 0.00 0.00 4.11
4155 4246 3.485378 CGTTTATTGTGCACCAACTTGTG 59.515 43.478 15.69 0.00 35.44 3.33
4172 4266 7.500892 CCAACTTGTGGCATACATATAAACCTA 59.499 37.037 0.00 0.00 41.72 3.08
4209 4304 3.607078 GCTAAACCTTTCGTTGTGCTCTG 60.607 47.826 0.00 0.00 33.93 3.35
4227 4322 2.158769 TCTGCTCAGTTCTTCTTGCCAA 60.159 45.455 0.00 0.00 0.00 4.52
4269 4364 5.369404 TGGATAATACTGATGTGGGACATGT 59.631 40.000 0.00 0.00 44.52 3.21
4386 4481 1.896220 TCACGCTCTTTTCCAATGCT 58.104 45.000 0.00 0.00 0.00 3.79
4460 4555 1.218316 CCCCGTTGTAGCTGAGGAC 59.782 63.158 0.00 0.00 0.00 3.85
4487 4583 4.383173 TCGATACGTATGTAGCCTTCTCA 58.617 43.478 13.97 0.00 33.40 3.27
4488 4584 4.212847 TCGATACGTATGTAGCCTTCTCAC 59.787 45.833 13.97 0.00 33.40 3.51
4516 4612 7.281100 CCCTAATTCTACAGGAACTTTCATCAC 59.719 40.741 0.00 0.00 34.60 3.06
4528 4624 6.208599 GGAACTTTCATCACTTTTCCCATACA 59.791 38.462 0.00 0.00 0.00 2.29
4648 4744 3.709141 AGAAGCTGAAGATCCCTCTAACC 59.291 47.826 0.00 0.00 0.00 2.85
4672 4768 5.695424 AGGTAGGTCCATTCTCTTAAACC 57.305 43.478 0.00 0.00 39.02 3.27
4693 4789 3.129988 CCCGTCTACTCTTACCGATGTTT 59.870 47.826 0.00 0.00 0.00 2.83
4694 4790 4.381292 CCCGTCTACTCTTACCGATGTTTT 60.381 45.833 0.00 0.00 0.00 2.43
4728 4824 4.081406 TGCAGAGTCATTACAAATGGCTT 58.919 39.130 8.07 0.00 33.60 4.35
4730 4826 5.355071 TGCAGAGTCATTACAAATGGCTTAG 59.645 40.000 8.07 5.63 33.60 2.18
4822 4920 1.221466 GCAAAACGAAAAGGCAGGCC 61.221 55.000 0.97 0.97 0.00 5.19
4855 4953 2.293122 TGTCAAACTTCAGGGCAATTCG 59.707 45.455 0.00 0.00 0.00 3.34
4897 5010 1.252904 TGTGGACGGTACTAGCACCC 61.253 60.000 6.55 0.00 34.90 4.61
4906 5019 0.330604 TACTAGCACCCACCGACTCT 59.669 55.000 0.00 0.00 0.00 3.24
4944 5057 2.050350 CCGGTTAGAGGGACAGCGA 61.050 63.158 0.00 0.00 33.26 4.93
4949 5062 1.272769 GTTAGAGGGACAGCGAGTTGT 59.727 52.381 0.00 0.00 0.00 3.32
4965 5078 0.468226 TTGTGGGAACTGCTTCGTCT 59.532 50.000 0.00 0.00 0.00 4.18
4982 5095 8.576442 TGCTTCGTCTGAATGAATATGTATCTA 58.424 33.333 0.00 0.00 32.61 1.98
5006 5119 5.523916 ACTGCTGATTTCGGTGTATCATAAC 59.476 40.000 0.00 0.00 30.91 1.89
5026 5139 2.054363 CGCATCGTTTATCGCTCAGAT 58.946 47.619 0.00 0.00 43.19 2.90
5031 5144 3.105937 TCGTTTATCGCTCAGATGTTCG 58.894 45.455 0.00 0.00 40.40 3.95
5032 5145 2.216488 CGTTTATCGCTCAGATGTTCGG 59.784 50.000 0.00 0.00 40.40 4.30
5033 5146 3.187700 GTTTATCGCTCAGATGTTCGGT 58.812 45.455 0.00 0.00 40.40 4.69
5035 5148 2.386661 ATCGCTCAGATGTTCGGTTT 57.613 45.000 0.00 0.00 38.36 3.27
5042 5155 4.610945 CTCAGATGTTCGGTTTGCTTTTT 58.389 39.130 0.00 0.00 0.00 1.94
5043 5156 5.757886 CTCAGATGTTCGGTTTGCTTTTTA 58.242 37.500 0.00 0.00 0.00 1.52
5048 5161 8.334632 CAGATGTTCGGTTTGCTTTTTATTTTT 58.665 29.630 0.00 0.00 0.00 1.94
5109 5222 1.400494 GTGTGAACCATGGTATTCGGC 59.600 52.381 20.12 10.42 0.00 5.54
5111 5224 1.670811 GTGAACCATGGTATTCGGCAG 59.329 52.381 20.12 0.00 0.00 4.85
5159 5273 9.787435 TTAAGAATGTAGTATGAACCACTTGTT 57.213 29.630 0.00 0.00 40.81 2.83
5217 5331 4.002906 TCGGAAATCGATCCCCTTTATG 57.997 45.455 0.00 0.00 43.74 1.90
5254 5368 7.971168 CAGAACTCATACTCACTAGGTAGTTTG 59.029 40.741 4.76 7.45 33.46 2.93
5257 5371 8.596781 ACTCATACTCACTAGGTAGTTTGAAT 57.403 34.615 15.54 7.75 34.64 2.57
5317 5450 6.707440 ATTATCCAACATAATTGCCGAACA 57.293 33.333 0.00 0.00 0.00 3.18
5328 5461 3.915437 TTGCCGAACAAAATCTCCTTC 57.085 42.857 0.00 0.00 34.56 3.46
5329 5462 1.804151 TGCCGAACAAAATCTCCTTCG 59.196 47.619 0.00 0.00 36.19 3.79
5333 5466 3.123621 CCGAACAAAATCTCCTTCGTCTG 59.876 47.826 0.00 0.00 34.93 3.51
5409 5542 5.764131 TCTCAAATCGGCGTTTGTAAATTT 58.236 33.333 23.78 12.53 39.50 1.82
5413 5546 2.386249 TCGGCGTTTGTAAATTTGTGC 58.614 42.857 6.85 0.00 0.00 4.57
5415 5548 2.097637 CGGCGTTTGTAAATTTGTGCAC 60.098 45.455 10.75 10.75 0.00 4.57
5452 5585 5.879777 TGTACAACAAGGTCCATATGACATG 59.120 40.000 3.65 6.55 46.38 3.21
5507 5640 4.126520 AGGGTTTGGGAAATAGCTTCAA 57.873 40.909 0.00 0.00 35.55 2.69
5535 5669 4.855388 CGAAAATGGAAGTTCTGCTCAATG 59.145 41.667 2.25 0.00 0.00 2.82
5613 5789 6.797454 TGTAAAATTTACAGTTTGACCGCTT 58.203 32.000 13.93 0.00 0.00 4.68
5626 5802 3.270027 TGACCGCTTAACCATGATCTTG 58.730 45.455 0.00 1.60 0.00 3.02
5680 5857 3.055385 ACAATCCAGTATGTAGCAACCGT 60.055 43.478 0.00 0.00 0.00 4.83
5715 5892 4.038402 CCCCAAATGAGGATGCATTTCTAC 59.962 45.833 0.00 0.00 44.30 2.59
5716 5893 4.891756 CCCAAATGAGGATGCATTTCTACT 59.108 41.667 0.00 0.00 44.30 2.57
5741 5918 0.597637 ACTGAGTGACTTTGTCGCCG 60.598 55.000 7.52 0.92 43.20 6.46
5743 5920 2.027625 GAGTGACTTTGTCGCCGGG 61.028 63.158 2.18 0.00 43.20 5.73
5776 5953 4.156556 AGTTCGAGCACCTACACGTATTTA 59.843 41.667 1.01 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.713248 TGAGTCATCCTCCTGCAATATGT 59.287 43.478 0.00 0.00 39.65 2.29
87 88 0.889994 GGTTGCCATGATGAACTGCA 59.110 50.000 0.00 0.00 0.00 4.41
131 132 2.130821 TTGCGCCTGGGGTTGTATGA 62.131 55.000 12.70 0.00 0.00 2.15
189 190 2.358615 GGTGACTGGTGCATCGCA 60.359 61.111 0.00 0.00 35.60 5.10
223 224 2.418197 GCATGATGGCTTCAGCAAACAT 60.418 45.455 9.09 0.00 40.39 2.71
310 311 2.498167 GGTGAGCAAGATGTTGACAGT 58.502 47.619 6.80 0.00 35.46 3.55
373 374 1.002468 ACGCAGCAGCAACACTTTAAG 60.002 47.619 0.82 0.00 42.27 1.85
632 652 6.092122 CCAAGAGATCGTGTAGTGCAAATTTA 59.908 38.462 0.00 0.00 0.00 1.40
639 659 2.531206 GACCAAGAGATCGTGTAGTGC 58.469 52.381 0.00 0.00 0.00 4.40
641 661 2.755655 CTGGACCAAGAGATCGTGTAGT 59.244 50.000 0.00 0.00 0.00 2.73
655 675 2.289819 GGTATCGAAAACCACTGGACCA 60.290 50.000 13.85 0.00 36.96 4.02
656 676 2.353323 GGTATCGAAAACCACTGGACC 58.647 52.381 13.85 0.00 36.96 4.46
657 677 1.997606 CGGTATCGAAAACCACTGGAC 59.002 52.381 17.60 0.00 36.78 4.02
658 678 1.673626 GCGGTATCGAAAACCACTGGA 60.674 52.381 17.60 0.00 36.78 3.86
741 773 1.391933 ATGTGCCGGCTCGTCATCTA 61.392 55.000 29.70 6.44 0.00 1.98
743 775 2.202932 ATGTGCCGGCTCGTCATC 60.203 61.111 29.70 9.44 0.00 2.92
818 850 1.736645 CGCTCGGGTGAAATGACGT 60.737 57.895 0.00 0.00 0.00 4.34
819 851 2.452813 CCGCTCGGGTGAAATGACG 61.453 63.158 0.00 0.00 0.00 4.35
891 927 1.355971 CGTCTTGGTCGGTATGGTTG 58.644 55.000 0.00 0.00 0.00 3.77
954 990 2.759114 CTGGCAAAGAGGAGGGCA 59.241 61.111 0.00 0.00 35.66 5.36
979 1015 4.776795 TGCTGTTGTGAGTACGAATAGA 57.223 40.909 0.00 0.00 0.00 1.98
1006 1042 5.134339 AGAAAACATAATATGGGAGGGAGCA 59.866 40.000 5.16 0.00 33.60 4.26
1049 1085 2.165234 CGAGATCCATGACACACTGACT 59.835 50.000 0.00 0.00 0.00 3.41
1052 1088 1.284657 GCGAGATCCATGACACACTG 58.715 55.000 0.00 0.00 0.00 3.66
1071 1107 2.422479 CAGCAAATGTGTCAGATCTGGG 59.578 50.000 22.42 0.00 0.00 4.45
1086 1122 4.810191 AAAAGGGTACACAAACAGCAAA 57.190 36.364 0.00 0.00 0.00 3.68
1165 1201 0.964860 CATTGCCACAACCATCCCGA 60.965 55.000 0.00 0.00 0.00 5.14
1352 1388 2.619074 GCTTCAGCATACCTCCAAACCT 60.619 50.000 0.00 0.00 41.59 3.50
1534 1570 0.251742 TGTTTGCATCCCTCCCCTTG 60.252 55.000 0.00 0.00 0.00 3.61
1632 1668 4.871993 ATGTCACGCATCAGAAAATCTC 57.128 40.909 0.00 0.00 30.67 2.75
1788 1824 8.739039 ACCAGTTAAATTGATCGATTGATTCAA 58.261 29.630 9.01 0.75 34.09 2.69
1849 1885 6.479660 CCATCATGTCTCTCTTAAGCTTCTTC 59.520 42.308 0.00 0.00 0.00 2.87
1982 2026 3.247442 CACACACCATGTCAATTCATGC 58.753 45.455 2.33 0.00 40.64 4.06
1987 2031 1.702182 TGGCACACACCATGTCAATT 58.298 45.000 0.00 0.00 40.64 2.32
2001 2045 0.877213 AACCACTACGACGTTGGCAC 60.877 55.000 16.78 0.00 0.00 5.01
2014 2058 3.860641 CAAAAAGACCTGCAAAACCACT 58.139 40.909 0.00 0.00 0.00 4.00
2102 2148 0.032678 CGATGGAAGGACTCGGGATG 59.967 60.000 0.00 0.00 0.00 3.51
2104 2150 0.323999 TTCGATGGAAGGACTCGGGA 60.324 55.000 0.00 0.00 33.38 5.14
2118 2164 0.754217 AGCCATGGCAAGCATTCGAT 60.754 50.000 37.18 10.88 44.88 3.59
2228 2275 1.299316 CACAGCGTTGGTGCAAAGG 60.299 57.895 3.74 0.00 37.31 3.11
2230 2277 1.138459 CACACAGCGTTGGTGCAAA 59.862 52.632 3.74 0.00 39.87 3.68
2240 2287 5.082059 GTGAATTCAGATAAACACACAGCG 58.918 41.667 8.80 0.00 0.00 5.18
2322 2370 2.182825 GTGTACCATACTGTCGAAGCG 58.817 52.381 0.00 0.00 0.00 4.68
2337 2385 1.003223 GGAAACTTGTGGCGTGTGTAC 60.003 52.381 0.00 0.00 0.00 2.90
2382 2430 2.000447 CGCCTAGTAAGCTTGTTGGTC 59.000 52.381 9.86 3.09 0.00 4.02
2390 2438 0.175989 GCTGGAACGCCTAGTAAGCT 59.824 55.000 0.00 0.00 33.62 3.74
2433 2481 4.022068 CCATGCATTACAGGAGTTGTGTTT 60.022 41.667 0.00 0.00 41.10 2.83
2731 2797 2.543635 AGCCCATTCTTTGCTTCCAAT 58.456 42.857 0.00 0.00 29.17 3.16
2802 2868 1.831389 GCGACAGCACACACAACGAT 61.831 55.000 0.00 0.00 44.35 3.73
2918 2988 3.993736 GGCGGCAATAACAGAAACAAATT 59.006 39.130 3.07 0.00 0.00 1.82
2931 3001 1.533625 GCTAATGGATGGCGGCAATA 58.466 50.000 18.31 5.61 0.00 1.90
2932 3002 1.181098 GGCTAATGGATGGCGGCAAT 61.181 55.000 18.31 1.34 0.00 3.56
2951 3021 2.935481 TTGGAGGTGGCAGGGAGG 60.935 66.667 0.00 0.00 0.00 4.30
2978 3048 1.471676 CCTGCTACAGGCGTCCTAAAG 60.472 57.143 0.00 1.37 45.13 1.85
3017 3088 2.034878 TCGCAATCAGATAGCTCAGGT 58.965 47.619 0.00 0.00 0.00 4.00
3019 3090 3.058450 CCTTCGCAATCAGATAGCTCAG 58.942 50.000 0.00 0.00 0.00 3.35
3044 3115 9.624373 GAGGATAATATATTGCAGGATGTCATT 57.376 33.333 8.28 0.00 39.31 2.57
3152 3229 2.478890 GGCAGAGGCGACGTAGCTA 61.479 63.158 20.15 0.00 42.47 3.32
3222 3311 1.202417 CGCGAGGAGGATTTCTTGCTA 60.202 52.381 0.00 0.00 38.05 3.49
3450 3539 1.821216 AGTGGGCAACAATAAGGTCG 58.179 50.000 0.00 0.00 39.74 4.79
3506 3595 7.704899 GGATAAAAATGAATAAGTTGAACGGGG 59.295 37.037 0.00 0.00 0.00 5.73
3595 3685 6.894339 ATTCAAAAGACAACGGGTTAGAAT 57.106 33.333 0.00 0.00 0.00 2.40
3608 3699 6.145535 AGTTCATTCAGCGAATTCAAAAGAC 58.854 36.000 6.22 0.00 28.87 3.01
3643 3734 6.954487 AGTCGTGGACTGTCATGTATAATA 57.046 37.500 10.38 0.00 41.76 0.98
3770 3861 4.000988 GGACACTTTGAATTCGCTTCCTA 58.999 43.478 0.04 0.00 32.49 2.94
3842 3933 0.698886 ATGGGGGCATCTAGGCAAGA 60.699 55.000 0.00 0.00 46.44 3.02
3870 3961 1.197721 CGCAGTAAGCAAAGGACCAAG 59.802 52.381 0.00 0.00 46.13 3.61
3881 3972 1.061570 GAGCATGCACGCAGTAAGC 59.938 57.895 21.98 0.00 41.61 3.09
3933 4024 3.209410 GGTGAATGCATAAGAGGTCAGG 58.791 50.000 0.00 0.00 0.00 3.86
4076 4167 6.883756 TGAGCATGGATGTAATTAAGTTCACA 59.116 34.615 0.00 0.00 0.00 3.58
4198 4292 0.510359 GAACTGAGCAGAGCACAACG 59.490 55.000 4.21 0.00 0.00 4.10
4209 4304 3.127721 GGTATTGGCAAGAAGAACTGAGC 59.872 47.826 5.96 0.00 0.00 4.26
4269 4364 0.468226 ACGTGGAGCTTCCTTGACAA 59.532 50.000 0.00 0.00 37.46 3.18
4386 4481 1.401931 GCCAGCGTAGTACTCGTTCAA 60.402 52.381 0.00 0.00 0.00 2.69
4460 4555 6.641314 AGAAGGCTACATACGTATCGAAATTG 59.359 38.462 4.74 0.00 0.00 2.32
4487 4583 4.090027 AGTTCCTGTAGAATTAGGGGGT 57.910 45.455 0.00 0.00 36.69 4.95
4488 4584 5.045140 TGAAAGTTCCTGTAGAATTAGGGGG 60.045 44.000 0.00 0.00 36.69 5.40
4648 4744 5.880887 GGTTTAAGAGAATGGACCTACCTTG 59.119 44.000 0.00 0.00 39.86 3.61
4672 4768 4.367386 AAACATCGGTAAGAGTAGACGG 57.633 45.455 0.00 0.00 0.00 4.79
4693 4789 3.149196 GACTCTGCATGACTTTGGGAAA 58.851 45.455 0.00 0.00 0.00 3.13
4694 4790 2.106338 TGACTCTGCATGACTTTGGGAA 59.894 45.455 0.00 0.00 0.00 3.97
4728 4824 5.836358 AGCCACAACAAGGGAAAAATAACTA 59.164 36.000 0.00 0.00 0.00 2.24
4730 4826 4.749598 CAGCCACAACAAGGGAAAAATAAC 59.250 41.667 0.00 0.00 0.00 1.89
4822 4920 2.224606 AGTTTGACACACTCATGCAGG 58.775 47.619 0.00 0.00 0.00 4.85
4855 4953 0.109597 CCTCATGCGCCAACTTTGAC 60.110 55.000 4.18 0.00 0.00 3.18
4897 5010 1.672356 CCCAAGCCAAGAGTCGGTG 60.672 63.158 0.00 0.00 0.00 4.94
4944 5057 0.180406 ACGAAGCAGTTCCCACAACT 59.820 50.000 0.00 0.00 0.00 3.16
4949 5062 0.756294 TTCAGACGAAGCAGTTCCCA 59.244 50.000 0.00 0.00 0.00 4.37
4982 5095 3.610040 TGATACACCGAAATCAGCAGT 57.390 42.857 0.00 0.00 0.00 4.40
5006 5119 1.477105 TCTGAGCGATAAACGATGCG 58.523 50.000 0.00 0.00 41.91 4.73
5133 5247 9.787435 AACAAGTGGTTCATACTACATTCTTAA 57.213 29.630 0.00 0.00 38.14 1.85
5136 5250 8.567948 CAAAACAAGTGGTTCATACTACATTCT 58.432 33.333 0.00 0.00 39.29 2.40
5154 5268 6.424683 GTTTCGGTAGGACTTACAAAACAAG 58.575 40.000 14.66 0.00 38.28 3.16
5159 5273 3.652274 CCGTTTCGGTAGGACTTACAAA 58.348 45.455 0.00 0.00 42.73 2.83
5180 5294 6.454186 CGATTTCCGATTGAAAAGCCATTTTC 60.454 38.462 6.53 6.53 45.67 2.29
5217 5331 7.115095 GTGAGTATGAGTTCTGTGTTTCAGTAC 59.885 40.741 0.00 0.00 43.97 2.73
5266 5389 7.429633 TGTAAAACAATGTTGTCCATGTAAGG 58.570 34.615 0.00 0.00 41.31 2.69
5317 5450 8.622948 AGAAAAATACAGACGAAGGAGATTTT 57.377 30.769 0.00 0.00 0.00 1.82
5362 5495 5.687166 AATCGGATCCTTAAGTTGGTACA 57.313 39.130 10.75 0.00 0.00 2.90
5409 5542 5.478332 TGTACATAAATTGATTGGGTGCACA 59.522 36.000 20.43 0.00 0.00 4.57
5413 5546 7.545265 CCTTGTTGTACATAAATTGATTGGGTG 59.455 37.037 0.00 0.00 0.00 4.61
5415 5548 7.610865 ACCTTGTTGTACATAAATTGATTGGG 58.389 34.615 0.00 0.00 0.00 4.12
5468 5601 4.770795 ACCCTTCGTCCATCTATCAAAAG 58.229 43.478 0.00 0.00 0.00 2.27
5486 5619 3.825908 TGAAGCTATTTCCCAAACCCT 57.174 42.857 0.00 0.00 34.77 4.34
5507 5640 3.303791 GCAGAACTTCCATTTTCGTTCGT 60.304 43.478 0.00 0.00 40.36 3.85
5535 5669 5.266242 CGTGATGCAGGAAGCTAAAAATAC 58.734 41.667 0.00 0.00 45.94 1.89
5613 5789 6.096987 GTGAGGAGTAGACAAGATCATGGTTA 59.903 42.308 2.59 0.00 0.00 2.85
5626 5802 7.113658 TGAGATTATTTGGTGAGGAGTAGAC 57.886 40.000 0.00 0.00 0.00 2.59
5680 5857 3.691575 TCATTTGGGGAAATGCTACGAA 58.308 40.909 0.00 0.00 39.39 3.85
5715 5892 5.388890 GCGACAAAGTCACTCAGTTATCAAG 60.389 44.000 0.00 0.00 32.09 3.02
5716 5893 4.447724 GCGACAAAGTCACTCAGTTATCAA 59.552 41.667 0.00 0.00 32.09 2.57
5741 5918 2.616842 TGCTCGAACTTTGAACTTTCCC 59.383 45.455 0.00 0.00 0.00 3.97
5743 5920 3.312697 AGGTGCTCGAACTTTGAACTTTC 59.687 43.478 0.00 0.00 0.00 2.62
5866 6045 7.817418 TTAGAAGCCAGAAAAACATAAGTGT 57.183 32.000 0.00 0.00 41.28 3.55
5867 6046 7.323656 CGTTTAGAAGCCAGAAAAACATAAGTG 59.676 37.037 0.00 0.00 31.85 3.16


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

AutoCloner maintained by Alex Coulton.