Multiple sequence alignment - TraesCS7A01G145900

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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 TraesCS7A01G145900 chr7A 100.000 5312 0 0 1 5312 97579075 97573764 0.000000e+00 9810.0
1 TraesCS7A01G145900 chr7B 95.032 2959 100 21 1622 4555 48190811 48187875 0.000000e+00 4606.0
2 TraesCS7A01G145900 chr7B 95.197 1395 47 13 128 1506 48192450 48191060 0.000000e+00 2187.0
3 TraesCS7A01G145900 chr7B 88.706 425 38 5 4564 4986 48187692 48187276 1.320000e-140 510.0
4 TraesCS7A01G145900 chr7B 91.146 192 17 0 4988 5179 48187112 48186921 1.470000e-65 261.0
5 TraesCS7A01G145900 chr7B 94.783 115 6 0 1506 1620 48191015 48190901 4.230000e-41 180.0
6 TraesCS7A01G145900 chr7D 94.663 2998 108 26 1506 4471 94130392 94127415 0.000000e+00 4602.0
7 TraesCS7A01G145900 chr7D 94.657 1516 63 11 2 1506 94131945 94130437 0.000000e+00 2335.0
8 TraesCS7A01G145900 chr7D 93.617 47 3 0 4509 4555 94127414 94127368 2.650000e-08 71.3
9 TraesCS7A01G145900 chr7D 94.595 37 2 0 4516 4552 438070473 438070437 2.070000e-04 58.4
10 TraesCS7A01G145900 chr2D 84.288 751 107 9 4565 5312 527924256 527923514 0.000000e+00 723.0
11 TraesCS7A01G145900 chr3D 86.282 503 65 2 4565 5067 431620875 431620377 1.300000e-150 544.0
12 TraesCS7A01G145900 chr6A 79.518 747 122 22 4566 5307 187269473 187268753 2.210000e-138 503.0
13 TraesCS7A01G145900 chr6D 78.559 597 99 6 4710 5303 142135091 142134521 3.020000e-97 366.0
14 TraesCS7A01G145900 chr5D 74.140 727 154 21 4590 5298 558076153 558076863 2.440000e-68 270.0
15 TraesCS7A01G145900 chr1B 100.000 29 0 0 4510 4538 673917637 673917609 3.000000e-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 TraesCS7A01G145900 chr7A 97573764 97579075 5311 True 9810.0 9810 100.000000 1 5312 1 chr7A.!!$R1 5311
1 TraesCS7A01G145900 chr7B 48186921 48192450 5529 True 1548.8 4606 92.972800 128 5179 5 chr7B.!!$R1 5051
2 TraesCS7A01G145900 chr7D 94127368 94131945 4577 True 2336.1 4602 94.312333 2 4555 3 chr7D.!!$R2 4553
3 TraesCS7A01G145900 chr2D 527923514 527924256 742 True 723.0 723 84.288000 4565 5312 1 chr2D.!!$R1 747
4 TraesCS7A01G145900 chr6A 187268753 187269473 720 True 503.0 503 79.518000 4566 5307 1 chr6A.!!$R1 741
5 TraesCS7A01G145900 chr6D 142134521 142135091 570 True 366.0 366 78.559000 4710 5303 1 chr6D.!!$R1 593
6 TraesCS7A01G145900 chr5D 558076153 558076863 710 False 270.0 270 74.140000 4590 5298 1 chr5D.!!$F1 708

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
95 99 0.106894 CGCTCCAGTTCTTATCCCCC 59.893 60.000 0.00 0.00 0.00 5.40 F
124 128 0.732880 TTTCTCTTCTTCCTCGCGCG 60.733 55.000 26.76 26.76 0.00 6.86 F
273 284 1.295792 GTGTCTGCCAACAACTCGAA 58.704 50.000 0.00 0.00 0.00 3.71 F
746 758 1.702182 TGCCATTTTGGTGCTTCTCA 58.298 45.000 0.00 0.00 40.46 3.27 F
2394 2551 1.000955 GAGGTCACAGTCAACGATGGT 59.999 52.381 0.00 0.00 0.00 3.55 F
3779 3956 0.107703 TGGAGATGGAATGCACGGTC 60.108 55.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2028 4.678509 TGGCGATCACAAAAAGATACAC 57.321 40.909 0.00 0.0 0.00 2.90 R
1900 2057 6.072948 GCCCAGTTTAACACAAAAACAAGTTT 60.073 34.615 0.00 0.0 38.92 2.66 R
2192 2349 3.680490 TCGGAAGATGCCAACATAAACA 58.320 40.909 0.00 0.0 36.35 2.83 R
2630 2788 2.682893 GCATACAGCACTTCCTCCG 58.317 57.895 0.00 0.0 44.79 4.63 R
4020 4199 0.321996 ACGGAAGCTCCTTCAGGAAC 59.678 55.000 9.31 0.0 44.91 3.62 R
5179 5724 0.188342 ACCCTTTTGGCAGTGTGGAT 59.812 50.000 0.00 0.0 37.83 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
45 49 2.610232 CCGGGCCTGTCATTTCTTTTTG 60.610 50.000 11.58 0.00 0.00 2.44
51 55 6.223120 GGCCTGTCATTTCTTTTTGTTGTAT 58.777 36.000 0.00 0.00 0.00 2.29
52 56 7.375053 GGCCTGTCATTTCTTTTTGTTGTATA 58.625 34.615 0.00 0.00 0.00 1.47
53 57 7.542130 GGCCTGTCATTTCTTTTTGTTGTATAG 59.458 37.037 0.00 0.00 0.00 1.31
54 58 8.296713 GCCTGTCATTTCTTTTTGTTGTATAGA 58.703 33.333 0.00 0.00 0.00 1.98
82 86 0.818938 AAATGATGCAATGCGCTCCA 59.181 45.000 9.73 0.12 43.06 3.86
93 97 0.178068 TGCGCTCCAGTTCTTATCCC 59.822 55.000 9.73 0.00 0.00 3.85
95 99 0.106894 CGCTCCAGTTCTTATCCCCC 59.893 60.000 0.00 0.00 0.00 5.40
104 108 4.034410 AGTTCTTATCCCCCTCTCTGTTC 58.966 47.826 0.00 0.00 0.00 3.18
107 111 4.699994 TCTTATCCCCCTCTCTGTTCTTT 58.300 43.478 0.00 0.00 0.00 2.52
108 112 4.717280 TCTTATCCCCCTCTCTGTTCTTTC 59.283 45.833 0.00 0.00 0.00 2.62
109 113 2.723530 TCCCCCTCTCTGTTCTTTCT 57.276 50.000 0.00 0.00 0.00 2.52
110 114 2.541466 TCCCCCTCTCTGTTCTTTCTC 58.459 52.381 0.00 0.00 0.00 2.87
112 116 2.909662 CCCCCTCTCTGTTCTTTCTCTT 59.090 50.000 0.00 0.00 0.00 2.85
113 117 3.055458 CCCCCTCTCTGTTCTTTCTCTTC 60.055 52.174 0.00 0.00 0.00 2.87
116 120 5.478407 CCCTCTCTGTTCTTTCTCTTCTTC 58.522 45.833 0.00 0.00 0.00 2.87
117 121 5.478407 CCTCTCTGTTCTTTCTCTTCTTCC 58.522 45.833 0.00 0.00 0.00 3.46
118 122 5.245977 CCTCTCTGTTCTTTCTCTTCTTCCT 59.754 44.000 0.00 0.00 0.00 3.36
119 123 6.339587 TCTCTGTTCTTTCTCTTCTTCCTC 57.660 41.667 0.00 0.00 0.00 3.71
120 124 5.048364 TCTCTGTTCTTTCTCTTCTTCCTCG 60.048 44.000 0.00 0.00 0.00 4.63
122 126 2.638556 TCTTTCTCTTCTTCCTCGCG 57.361 50.000 0.00 0.00 0.00 5.87
123 127 0.995728 CTTTCTCTTCTTCCTCGCGC 59.004 55.000 0.00 0.00 0.00 6.86
124 128 0.732880 TTTCTCTTCTTCCTCGCGCG 60.733 55.000 26.76 26.76 0.00 6.86
125 129 3.251043 CTCTTCTTCCTCGCGCGC 61.251 66.667 27.95 23.91 0.00 6.86
257 268 3.504134 TGTTTGCGCCATTATTACTGTGT 59.496 39.130 4.18 0.00 0.00 3.72
273 284 1.295792 GTGTCTGCCAACAACTCGAA 58.704 50.000 0.00 0.00 0.00 3.71
283 294 8.609176 TCTGCCAACAACTCGAATATTAATTAC 58.391 33.333 0.00 0.00 0.00 1.89
419 430 6.035843 TCTTTTGAGTGTTGAGTCAATTTGC 58.964 36.000 9.18 0.00 40.50 3.68
468 479 7.001674 TGTTTGTACTCTTTAATCCATGTGGT 58.998 34.615 0.00 0.00 36.34 4.16
470 481 4.941263 TGTACTCTTTAATCCATGTGGTGC 59.059 41.667 0.00 0.00 36.34 5.01
492 503 2.094130 GCCCAGTTGGTCAGAGTAGTAC 60.094 54.545 0.00 0.00 36.04 2.73
497 508 4.094590 CAGTTGGTCAGAGTAGTACTACCG 59.905 50.000 25.97 16.35 36.75 4.02
531 542 2.899900 TGAGGCTACTTTCTTGCAGAGA 59.100 45.455 0.00 0.00 0.00 3.10
579 590 5.771469 TGCTTATTGTGTCAATTTGAGGTG 58.229 37.500 0.00 0.00 0.00 4.00
581 592 6.183360 TGCTTATTGTGTCAATTTGAGGTGTT 60.183 34.615 0.00 0.00 0.00 3.32
583 594 7.096065 GCTTATTGTGTCAATTTGAGGTGTTTC 60.096 37.037 0.00 0.00 0.00 2.78
592 604 7.759433 GTCAATTTGAGGTGTTTCTTTCAGAAA 59.241 33.333 0.00 0.00 41.51 2.52
672 684 7.982354 AGTGATCCAGTTACTAACTTATTGAGC 59.018 37.037 0.00 0.00 40.46 4.26
696 708 5.455326 CCCCTTAATGTGGATCCTTCACTAG 60.455 48.000 14.23 9.80 36.21 2.57
746 758 1.702182 TGCCATTTTGGTGCTTCTCA 58.298 45.000 0.00 0.00 40.46 3.27
889 902 5.006153 TCCATTCTTGGTACACTCATACG 57.994 43.478 0.00 0.00 44.06 3.06
959 972 6.026947 ACTCAATATATGGCGAGTCCTTAC 57.973 41.667 6.81 0.00 33.49 2.34
984 997 6.500684 AAGTGGTACTAAGATTGTGCATTG 57.499 37.500 0.00 0.00 0.00 2.82
1059 1072 4.452733 GCTACCGGTGAGCGGCTT 62.453 66.667 24.30 7.26 0.00 4.35
1224 1237 4.386049 CACTCCACACATCTCTTTCGTTAC 59.614 45.833 0.00 0.00 0.00 2.50
1281 1294 8.766000 AGTTAATGTATGTGTGTTCGTTATCA 57.234 30.769 0.00 0.00 0.00 2.15
1435 1456 8.447200 TGGTATCCAATTCTTGATGATCCATAA 58.553 33.333 0.00 0.00 0.00 1.90
1499 1520 8.358148 TCTTACTCGGTATACAGAAATGGATTC 58.642 37.037 7.15 0.00 38.39 2.52
1500 1521 5.529791 ACTCGGTATACAGAAATGGATTCG 58.470 41.667 7.15 0.00 43.15 3.34
1501 1522 5.301045 ACTCGGTATACAGAAATGGATTCGA 59.699 40.000 7.15 0.61 43.15 3.71
1503 1524 4.684703 CGGTATACAGAAATGGATTCGACC 59.315 45.833 5.01 0.00 43.15 4.79
1504 1525 5.607477 GGTATACAGAAATGGATTCGACCA 58.393 41.667 5.01 0.00 43.15 4.02
1608 1673 6.360370 TTCAAGTAGATGGAAGTAAGCTGT 57.640 37.500 0.00 0.00 0.00 4.40
1609 1674 5.724328 TCAAGTAGATGGAAGTAAGCTGTG 58.276 41.667 0.00 0.00 0.00 3.66
1610 1675 4.744795 AGTAGATGGAAGTAAGCTGTGG 57.255 45.455 0.00 0.00 0.00 4.17
1620 1768 5.122396 GGAAGTAAGCTGTGGAATGTTACTG 59.878 44.000 0.00 0.00 34.83 2.74
1686 1842 3.091545 TCTTGAAGGGGTGATTTGATGC 58.908 45.455 0.00 0.00 0.00 3.91
1709 1865 6.767902 TGCCACCTCATTATGTTCTTTCTATC 59.232 38.462 0.00 0.00 0.00 2.08
1754 1910 9.533831 AGAATATTTCTTTGTTCTGGTACCAAT 57.466 29.630 17.11 4.87 36.36 3.16
1771 1927 6.088883 GGTACCAATTCTAAACGCAACAATTG 59.911 38.462 7.15 3.24 35.22 2.32
1891 2048 4.678509 TGTGTATCTTTTTGTGATCGCC 57.321 40.909 3.31 0.00 0.00 5.54
1894 2051 5.009110 TGTGTATCTTTTTGTGATCGCCAAA 59.991 36.000 3.31 2.37 0.00 3.28
2264 2421 2.644299 TGCTTCCCAGAAATCTCCAGAA 59.356 45.455 0.00 0.00 0.00 3.02
2394 2551 1.000955 GAGGTCACAGTCAACGATGGT 59.999 52.381 0.00 0.00 0.00 3.55
2630 2788 0.737219 CCCTTCACTATGCAGCTTGC 59.263 55.000 0.00 1.70 45.29 4.01
2677 2835 6.011122 AGTATGCATTGAATTCTCCCTTCT 57.989 37.500 3.54 0.00 0.00 2.85
2683 2841 9.597681 ATGCATTGAATTCTCCCTTCTATAAAT 57.402 29.630 7.05 0.00 0.00 1.40
2775 2933 3.153369 TGGGAGCTGAAAATGCTAACA 57.847 42.857 0.00 0.00 41.30 2.41
2933 3091 0.667993 TCACGCTTCTTTTTGGGCTG 59.332 50.000 0.00 0.00 0.00 4.85
2953 3111 7.939039 TGGGCTGTATTATCAGAATTTCTAAGG 59.061 37.037 0.00 0.00 37.61 2.69
2995 3153 0.390472 GCTGTGACTAGTGTCTGCCC 60.390 60.000 0.00 0.00 43.29 5.36
3272 3430 6.381420 CAGAAGGGAGACTACTAATTCTTCCA 59.619 42.308 0.00 0.00 39.77 3.53
3352 3510 6.731292 AATACCAGACAGAGTATGTGCATA 57.269 37.500 0.00 0.00 44.17 3.14
3443 3602 9.504708 TGAAATTTGTCCAAAATATCAAGCATT 57.495 25.926 0.00 0.00 33.56 3.56
3463 3640 0.660488 TGTACTTGTGCACAAAGCCG 59.340 50.000 30.62 21.55 44.83 5.52
3484 3661 7.491682 AGCCGCAATCATTTACTTAATTGAAT 58.508 30.769 0.00 0.00 32.14 2.57
3487 3664 9.398170 CCGCAATCATTTACTTAATTGAATAGG 57.602 33.333 0.00 0.00 32.14 2.57
3510 3687 3.939592 GGAAGTAAGTAAGGTCACCATGC 59.060 47.826 0.00 0.00 0.00 4.06
3581 3758 7.467623 ACGCAGATTATTGAGAATGAGAAAAC 58.532 34.615 0.00 0.00 0.00 2.43
3591 3768 7.031226 TGAGAATGAGAAAACTTGGACTTTG 57.969 36.000 0.00 0.00 0.00 2.77
3639 3816 3.364964 CGAGGCACATTTCCAGTTAACAC 60.365 47.826 8.61 0.00 0.00 3.32
3640 3817 2.552315 AGGCACATTTCCAGTTAACACG 59.448 45.455 8.61 0.00 0.00 4.49
3667 3844 6.314917 ACAGAGAAACAATTCCCCATTTACT 58.685 36.000 0.00 0.00 36.12 2.24
3668 3845 7.466804 ACAGAGAAACAATTCCCCATTTACTA 58.533 34.615 0.00 0.00 36.12 1.82
3779 3956 0.107703 TGGAGATGGAATGCACGGTC 60.108 55.000 0.00 0.00 0.00 4.79
3794 3971 0.384309 CGGTCGCTGCAGAAGGTATA 59.616 55.000 20.43 0.00 0.00 1.47
3795 3972 1.854227 GGTCGCTGCAGAAGGTATAC 58.146 55.000 20.43 4.41 0.00 1.47
3796 3973 1.409427 GGTCGCTGCAGAAGGTATACT 59.591 52.381 20.43 0.00 0.00 2.12
3825 4002 7.384660 CAGACTAATCCTCATGCTGAATAGTTC 59.615 40.741 11.16 6.95 0.00 3.01
3831 4008 5.663106 TCCTCATGCTGAATAGTTCTACCTT 59.337 40.000 0.00 0.00 0.00 3.50
3835 4012 7.671302 TCATGCTGAATAGTTCTACCTTATCC 58.329 38.462 0.00 0.00 0.00 2.59
3850 4029 8.333984 TCTACCTTATCCTATCCATTCATACGA 58.666 37.037 0.00 0.00 0.00 3.43
3851 4030 7.979786 ACCTTATCCTATCCATTCATACGAT 57.020 36.000 0.00 0.00 0.00 3.73
4017 4196 4.787871 GTGAAGCTCACAGGCACT 57.212 55.556 10.30 0.00 46.22 4.40
4020 4199 0.038251 TGAAGCTCACAGGCACTACG 60.038 55.000 0.00 0.00 36.02 3.51
4046 4225 1.135333 GAAGGAGCTTCCGTGGACTAG 59.865 57.143 0.00 0.00 42.75 2.57
4143 4322 2.606519 TCCTCGGTTCACCTGGGG 60.607 66.667 0.00 0.00 33.39 4.96
4156 4335 0.991920 CCTGGGGTGCTCCTCTTTTA 59.008 55.000 6.20 0.00 34.72 1.52
4212 4391 0.966875 TGAATTGCGGCAGGCTTGAT 60.967 50.000 1.67 0.00 44.05 2.57
4417 4596 6.315642 CAGCATCTGTTCATGTCTATCTGTTT 59.684 38.462 0.00 0.00 0.00 2.83
4418 4597 7.493645 CAGCATCTGTTCATGTCTATCTGTTTA 59.506 37.037 0.00 0.00 0.00 2.01
4419 4598 8.209584 AGCATCTGTTCATGTCTATCTGTTTAT 58.790 33.333 0.00 0.00 0.00 1.40
4420 4599 8.834465 GCATCTGTTCATGTCTATCTGTTTATT 58.166 33.333 0.00 0.00 0.00 1.40
4423 4602 8.668353 TCTGTTCATGTCTATCTGTTTATTTGC 58.332 33.333 0.00 0.00 0.00 3.68
4424 4603 8.565896 TGTTCATGTCTATCTGTTTATTTGCT 57.434 30.769 0.00 0.00 0.00 3.91
4549 4733 5.344743 TCATTGATAGGTGGAGAGAACAC 57.655 43.478 0.00 0.00 38.10 3.32
4552 4736 2.492088 TGATAGGTGGAGAGAACACACG 59.508 50.000 0.00 0.00 40.54 4.49
4555 4739 0.320771 GGTGGAGAGAACACACGCAT 60.321 55.000 0.00 0.00 40.54 4.73
4556 4740 1.067142 GGTGGAGAGAACACACGCATA 60.067 52.381 0.00 0.00 40.54 3.14
4558 4742 1.893137 TGGAGAGAACACACGCATACT 59.107 47.619 0.00 0.00 0.00 2.12
4561 4745 3.429547 GGAGAGAACACACGCATACTCAT 60.430 47.826 0.00 0.00 0.00 2.90
4562 4746 3.515630 AGAGAACACACGCATACTCATG 58.484 45.455 0.00 0.00 35.07 3.07
4563 4747 2.604914 GAGAACACACGCATACTCATGG 59.395 50.000 0.00 0.00 32.36 3.66
4567 4751 1.131638 ACACGCATACTCATGGGGAT 58.868 50.000 0.00 0.00 46.58 3.85
4569 4753 0.250467 ACGCATACTCATGGGGATGC 60.250 55.000 30.07 30.07 46.58 3.91
4570 4754 0.250424 CGCATACTCATGGGGATGCA 60.250 55.000 36.14 0.00 43.94 3.96
4573 4930 2.295349 GCATACTCATGGGGATGCAAAG 59.705 50.000 33.79 2.62 43.36 2.77
4592 4949 0.474184 GGGGGTCATGTGGATGTAGG 59.526 60.000 0.00 0.00 0.00 3.18
4604 4961 1.555075 GGATGTAGGAGCCACAAGTGA 59.445 52.381 0.94 0.00 0.00 3.41
4613 4970 0.249398 GCCACAAGTGACGACCCTAT 59.751 55.000 0.94 0.00 0.00 2.57
4666 5023 1.302511 TGCCTTCTGGTTCGAAGCC 60.303 57.895 23.50 15.71 39.21 4.35
4753 5121 4.890158 TGTGATATGCGGACCTCATAAT 57.110 40.909 8.22 0.00 31.08 1.28
4756 5124 3.837731 TGATATGCGGACCTCATAATCCA 59.162 43.478 8.22 4.81 34.35 3.41
4774 5142 4.700268 TCCATTTTTGATGTCATCCACG 57.300 40.909 10.36 0.00 0.00 4.94
4813 5181 4.778534 AGCAATCACCAAATGACTCAAG 57.221 40.909 0.00 0.00 41.24 3.02
4846 5216 0.465097 CTAGTGCCAAGGCCTCATGG 60.465 60.000 17.97 17.97 41.09 3.66
4936 5309 6.543831 GGTAATTACCTTGTTCATCTCTGCAT 59.456 38.462 24.79 0.00 43.10 3.96
4937 5310 6.446781 AATTACCTTGTTCATCTCTGCATG 57.553 37.500 0.00 0.00 0.00 4.06
4986 5529 4.352893 TCATGAGACAGTCCACCATCTAA 58.647 43.478 0.00 0.00 0.00 2.10
5000 5543 6.260050 TCCACCATCTAAATAAATCTTCACGC 59.740 38.462 0.00 0.00 0.00 5.34
5053 5597 0.798159 TGTTGATCACATGAGTGCGC 59.202 50.000 0.00 0.00 45.49 6.09
5075 5620 2.749839 TTGGCATGGCGGTACTGC 60.750 61.111 18.83 18.83 35.16 4.40
5147 5692 1.067776 AGTCGACATCGGACTTTGGTC 60.068 52.381 19.50 0.00 41.43 4.02
5161 5706 0.605319 TTGGTCAATGGCCTCGTGTC 60.605 55.000 5.15 0.00 0.00 3.67
5174 5719 2.224314 CCTCGTGTCTTGCTTTTCTTCC 59.776 50.000 0.00 0.00 0.00 3.46
5179 5724 3.023119 TGTCTTGCTTTTCTTCCTGCAA 58.977 40.909 0.00 0.00 42.16 4.08
5204 5749 1.480137 CACTGCCAAAAGGGTCACAAA 59.520 47.619 0.00 0.00 39.65 2.83
5213 5758 5.221501 CCAAAAGGGTCACAAACATCTTCAT 60.222 40.000 0.00 0.00 0.00 2.57
5220 5765 5.471456 GGTCACAAACATCTTCATGAAGTCT 59.529 40.000 29.80 18.22 39.38 3.24
5226 5771 4.586884 ACATCTTCATGAAGTCTGCATGT 58.413 39.130 29.80 26.44 42.77 3.21
5282 5827 0.238289 GCATTGGGTTCGTGTGACTG 59.762 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.588146 ATTCCGCGACTACGACACCG 62.588 60.000 8.23 0.00 42.66 4.94
2 3 0.638746 CAATTCCGCGACTACGACAC 59.361 55.000 8.23 0.00 42.66 3.67
4 5 1.319669 GAACAATTCCGCGACTACGAC 59.680 52.381 8.23 0.00 42.66 4.34
5 6 1.621107 GAACAATTCCGCGACTACGA 58.379 50.000 8.23 0.00 42.66 3.43
6 7 0.643820 GGAACAATTCCGCGACTACG 59.356 55.000 8.23 0.00 40.59 3.51
15 16 1.304134 ACAGGCCCGGAACAATTCC 60.304 57.895 0.73 0.00 46.62 3.01
51 55 7.201453 CGCATTGCATCATTTTGACATTTTCTA 60.201 33.333 9.69 0.00 0.00 2.10
52 56 6.401688 CGCATTGCATCATTTTGACATTTTCT 60.402 34.615 9.69 0.00 0.00 2.52
53 57 5.730802 CGCATTGCATCATTTTGACATTTTC 59.269 36.000 9.69 0.00 0.00 2.29
54 58 5.623335 CGCATTGCATCATTTTGACATTTT 58.377 33.333 9.69 0.00 0.00 1.82
82 86 3.786213 ACAGAGAGGGGGATAAGAACT 57.214 47.619 0.00 0.00 0.00 3.01
93 97 5.478407 GAAGAAGAGAAAGAACAGAGAGGG 58.522 45.833 0.00 0.00 0.00 4.30
95 99 6.345096 AGGAAGAAGAGAAAGAACAGAGAG 57.655 41.667 0.00 0.00 0.00 3.20
104 108 0.995728 GCGCGAGGAAGAAGAGAAAG 59.004 55.000 12.10 0.00 0.00 2.62
107 111 2.485582 CGCGCGAGGAAGAAGAGA 59.514 61.111 28.94 0.00 0.00 3.10
108 112 3.251043 GCGCGCGAGGAAGAAGAG 61.251 66.667 37.18 0.00 0.00 2.85
109 113 3.567478 TTGCGCGCGAGGAAGAAGA 62.567 57.895 37.18 0.47 0.00 2.87
110 114 2.170260 TTTTGCGCGCGAGGAAGAAG 62.170 55.000 37.18 0.23 0.00 2.85
112 116 2.663520 TTTTGCGCGCGAGGAAGA 60.664 55.556 37.18 14.66 0.00 2.87
113 117 2.202222 CTTTTGCGCGCGAGGAAG 60.202 61.111 37.18 26.37 0.00 3.46
116 120 2.513065 ATTGACTTTTGCGCGCGAGG 62.513 55.000 37.18 21.95 0.00 4.63
117 121 1.122419 GATTGACTTTTGCGCGCGAG 61.122 55.000 37.18 24.31 0.00 5.03
118 122 1.154488 GATTGACTTTTGCGCGCGA 60.154 52.632 37.18 23.83 0.00 5.87
119 123 2.145905 GGATTGACTTTTGCGCGCG 61.146 57.895 28.44 28.44 0.00 6.86
120 124 2.145905 CGGATTGACTTTTGCGCGC 61.146 57.895 27.26 27.26 0.00 6.86
122 126 0.237235 TCACGGATTGACTTTTGCGC 59.763 50.000 0.00 0.00 0.00 6.09
123 127 1.725931 GCTCACGGATTGACTTTTGCG 60.726 52.381 0.00 0.00 0.00 4.85
124 128 1.537202 AGCTCACGGATTGACTTTTGC 59.463 47.619 0.00 0.00 0.00 3.68
125 129 2.807967 TGAGCTCACGGATTGACTTTTG 59.192 45.455 13.74 0.00 0.00 2.44
183 193 0.396811 CTTCTCAGGGACAACGGGTT 59.603 55.000 0.00 0.00 0.00 4.11
224 235 1.641577 GCGCAAACAGTACTAGGAGG 58.358 55.000 0.30 0.00 0.00 4.30
257 268 7.624360 AATTAATATTCGAGTTGTTGGCAGA 57.376 32.000 0.00 0.00 0.00 4.26
295 306 8.088981 ACGCCCTCTATCTTACTACAATTATTG 58.911 37.037 3.07 3.07 0.00 1.90
492 503 3.491619 CCTCAGATGATCCAACACGGTAG 60.492 52.174 0.00 0.00 35.57 3.18
497 508 2.706339 AGCCTCAGATGATCCAACAC 57.294 50.000 0.00 0.00 0.00 3.32
531 542 0.541863 CCTAAACCGAGGTGGCATCT 59.458 55.000 0.00 0.00 43.94 2.90
583 594 4.843220 ATGTTGGCTCACTTTCTGAAAG 57.157 40.909 24.58 24.58 44.10 2.62
592 604 1.530013 GGCAGCAATGTTGGCTCACT 61.530 55.000 15.80 0.00 40.23 3.41
672 684 3.203040 AGTGAAGGATCCACATTAAGGGG 59.797 47.826 15.82 0.00 44.73 4.79
696 708 5.497474 ACCCCAGACATTTGTACACTAATC 58.503 41.667 0.00 0.00 0.00 1.75
746 758 1.774856 ACTAAGCCACCTGTCCACTTT 59.225 47.619 0.00 0.00 0.00 2.66
889 902 4.439289 GGTCATACAATTCTGAAGCCAAGC 60.439 45.833 0.00 0.00 0.00 4.01
959 972 7.549134 TCAATGCACAATCTTAGTACCACTTAG 59.451 37.037 0.00 0.00 0.00 2.18
984 997 2.972713 TCCCATGGTGCTTCTACCTATC 59.027 50.000 11.73 0.00 41.43 2.08
1257 1270 9.982291 ATTGATAACGAACACACATACATTAAC 57.018 29.630 0.00 0.00 0.00 2.01
1499 1520 5.109210 TGTAAGATTGCAACTAGATGGTCG 58.891 41.667 0.00 0.00 0.00 4.79
1500 1521 6.595716 ACTTGTAAGATTGCAACTAGATGGTC 59.404 38.462 0.00 0.00 0.00 4.02
1501 1522 6.476378 ACTTGTAAGATTGCAACTAGATGGT 58.524 36.000 0.00 0.00 0.00 3.55
1582 1647 5.869888 AGCTTACTTCCATCTACTTGAAACG 59.130 40.000 0.00 0.00 0.00 3.60
1608 1673 7.062749 AGTCAACTAAGACAGTAACATTCCA 57.937 36.000 0.00 0.00 40.98 3.53
1609 1674 7.873505 AGAAGTCAACTAAGACAGTAACATTCC 59.126 37.037 0.00 0.00 40.98 3.01
1610 1675 8.819643 AGAAGTCAACTAAGACAGTAACATTC 57.180 34.615 0.00 0.00 40.98 2.67
1647 1800 9.007901 CCTTCAAGAATGTTCCAATAGGATATC 57.992 37.037 0.00 0.00 45.26 1.63
1686 1842 8.428063 AGAGATAGAAAGAACATAATGAGGTGG 58.572 37.037 0.00 0.00 0.00 4.61
1868 2024 5.088739 GGCGATCACAAAAAGATACACAAG 58.911 41.667 0.00 0.00 0.00 3.16
1871 2028 4.678509 TGGCGATCACAAAAAGATACAC 57.321 40.909 0.00 0.00 0.00 2.90
1899 2056 7.520776 GCCCAGTTTAACACAAAAACAAGTTTT 60.521 33.333 5.16 5.16 43.88 2.43
1900 2057 6.072948 GCCCAGTTTAACACAAAAACAAGTTT 60.073 34.615 0.00 0.00 38.92 2.66
2114 2271 9.211485 CATCAAAAGCTTCCTTATTTGTTTCAT 57.789 29.630 0.00 0.00 0.00 2.57
2192 2349 3.680490 TCGGAAGATGCCAACATAAACA 58.320 40.909 0.00 0.00 36.35 2.83
2264 2421 7.168219 TCCATCTGACTTTGCATTAACTAGTT 58.832 34.615 13.68 13.68 0.00 2.24
2497 2655 4.365723 TGTGAGAAGTAACGGTCAAACTC 58.634 43.478 0.00 0.00 0.00 3.01
2499 2657 4.748102 TGATGTGAGAAGTAACGGTCAAAC 59.252 41.667 0.00 0.00 0.00 2.93
2500 2658 4.951254 TGATGTGAGAAGTAACGGTCAAA 58.049 39.130 0.00 0.00 0.00 2.69
2630 2788 2.682893 GCATACAGCACTTCCTCCG 58.317 57.895 0.00 0.00 44.79 4.63
2683 2841 6.887545 ACGGGAATTGGACAATTACTTGATAA 59.112 34.615 17.02 0.00 40.60 1.75
2775 2933 3.074857 TGGAATTCCCTAGGCATACCT 57.925 47.619 21.90 0.00 42.30 3.08
2910 3068 3.572255 AGCCCAAAAAGAAGCGTGAAATA 59.428 39.130 0.00 0.00 0.00 1.40
2995 3153 7.035004 TCAGCGAAGGAAAATGGATTTATTTG 58.965 34.615 0.00 0.00 31.05 2.32
3116 3274 6.967199 GGAAATTGTTTTCTAACGAGGCATAG 59.033 38.462 0.00 0.00 40.91 2.23
3272 3430 7.244558 TCAGTGGAAGAGATAGATATGGTGAT 58.755 38.462 0.00 0.00 0.00 3.06
3352 3510 4.806330 AGACGTGACGAAATGATAACAGT 58.194 39.130 13.70 0.00 0.00 3.55
3443 3602 1.064803 CGGCTTTGTGCACAAGTACAA 59.935 47.619 29.50 15.55 46.44 2.41
3463 3640 9.696917 CCCCTATTCAATTAAGTAAATGATTGC 57.303 33.333 0.00 0.00 31.33 3.56
3484 3661 4.202814 TGGTGACCTTACTTACTTCCCCTA 60.203 45.833 2.11 0.00 0.00 3.53
3487 3664 4.514401 CATGGTGACCTTACTTACTTCCC 58.486 47.826 2.11 0.00 0.00 3.97
3491 3668 3.182152 AGGCATGGTGACCTTACTTACT 58.818 45.455 2.11 0.00 29.74 2.24
3510 3687 1.315690 TAGGCATCTACGTTCCGAGG 58.684 55.000 0.00 0.00 0.00 4.63
3542 3719 1.626654 CTGCGTCTGTTAAGGTGCGG 61.627 60.000 0.00 0.00 0.00 5.69
3543 3720 0.666274 TCTGCGTCTGTTAAGGTGCG 60.666 55.000 0.00 0.00 0.00 5.34
3581 3758 1.151668 CCAGCGAGACAAAGTCCAAG 58.848 55.000 0.00 0.00 32.18 3.61
3608 3785 3.511699 GAAATGTGCCTCGGGAAAAATC 58.488 45.455 0.00 0.00 0.00 2.17
3639 3816 2.488153 GGGGAATTGTTTCTCTGTTCCG 59.512 50.000 0.00 0.00 39.33 4.30
3640 3817 3.496331 TGGGGAATTGTTTCTCTGTTCC 58.504 45.455 0.00 0.00 38.05 3.62
3667 3844 7.918562 TGTGAACGATCAAATATGAGTCGATTA 59.081 33.333 0.00 2.01 39.39 1.75
3668 3845 6.756542 TGTGAACGATCAAATATGAGTCGATT 59.243 34.615 0.00 0.00 39.39 3.34
3779 3956 4.041740 TGTTAGTATACCTTCTGCAGCG 57.958 45.455 9.47 2.02 0.00 5.18
3794 3971 5.658634 TCAGCATGAGGATTAGTCTGTTAGT 59.341 40.000 0.00 0.00 42.56 2.24
3795 3972 6.154203 TCAGCATGAGGATTAGTCTGTTAG 57.846 41.667 0.00 0.00 42.56 2.34
3825 4002 8.521170 TCGTATGAATGGATAGGATAAGGTAG 57.479 38.462 0.00 0.00 0.00 3.18
3865 4044 3.356290 ACTCATGGCCACAACCTATTTC 58.644 45.455 8.16 0.00 0.00 2.17
3866 4045 3.456380 ACTCATGGCCACAACCTATTT 57.544 42.857 8.16 0.00 0.00 1.40
3957 4136 2.421952 GCACAGAGGGCAAGATATGGAA 60.422 50.000 0.00 0.00 0.00 3.53
4017 4196 1.549170 GGAAGCTCCTTCAGGAACGTA 59.451 52.381 7.22 0.00 44.91 3.57
4020 4199 0.321996 ACGGAAGCTCCTTCAGGAAC 59.678 55.000 9.31 0.00 44.91 3.62
4046 4225 1.863454 CACATAGAGCCAACGATGAGC 59.137 52.381 0.00 0.00 0.00 4.26
4117 4296 1.310933 TGAACCGAGGAGGAGCGTAC 61.311 60.000 0.00 0.00 45.00 3.67
4143 4322 3.536570 GGTGGATCTAAAAGAGGAGCAC 58.463 50.000 0.00 0.00 0.00 4.40
4318 4497 1.822371 ACAACGCCAACAAAAAGGAGT 59.178 42.857 0.00 0.00 39.73 3.85
4509 4692 8.585471 ATCAATGAAATGATACACAAGTCCTT 57.415 30.769 0.00 0.00 38.25 3.36
4511 4694 8.562892 CCTATCAATGAAATGATACACAAGTCC 58.437 37.037 0.00 0.00 40.44 3.85
4549 4733 1.516161 CATCCCCATGAGTATGCGTG 58.484 55.000 0.00 0.00 32.79 5.34
4552 4736 1.985473 TTGCATCCCCATGAGTATGC 58.015 50.000 15.17 15.17 43.92 3.14
4555 4739 1.215173 CCCTTTGCATCCCCATGAGTA 59.785 52.381 0.00 0.00 30.57 2.59
4556 4740 0.032813 CCCTTTGCATCCCCATGAGT 60.033 55.000 0.00 0.00 30.57 3.41
4558 4742 1.310715 CCCCTTTGCATCCCCATGA 59.689 57.895 0.00 0.00 30.57 3.07
4561 4745 2.868566 ACCCCCTTTGCATCCCCA 60.869 61.111 0.00 0.00 0.00 4.96
4562 4746 2.042944 GACCCCCTTTGCATCCCC 60.043 66.667 0.00 0.00 0.00 4.81
4563 4747 1.044790 CATGACCCCCTTTGCATCCC 61.045 60.000 0.00 0.00 0.00 3.85
4564 4748 0.324645 ACATGACCCCCTTTGCATCC 60.325 55.000 0.00 0.00 0.00 3.51
4567 4751 1.228831 CCACATGACCCCCTTTGCA 60.229 57.895 0.00 0.00 0.00 4.08
4569 4753 1.272648 ACATCCACATGACCCCCTTTG 60.273 52.381 0.00 0.00 33.72 2.77
4570 4754 1.084018 ACATCCACATGACCCCCTTT 58.916 50.000 0.00 0.00 33.72 3.11
4573 4930 0.474184 CCTACATCCACATGACCCCC 59.526 60.000 0.00 0.00 33.72 5.40
4592 4949 1.668151 GGGTCGTCACTTGTGGCTC 60.668 63.158 3.84 0.00 0.00 4.70
4604 4961 3.482436 TGTTTTGCTTTCATAGGGTCGT 58.518 40.909 0.00 0.00 0.00 4.34
4636 4993 3.181445 ACCAGAAGGCACACAATCTTGTA 60.181 43.478 0.00 0.00 37.66 2.41
4637 4994 2.233271 CCAGAAGGCACACAATCTTGT 58.767 47.619 0.00 0.00 43.36 3.16
4666 5023 4.963276 TGATTTTATGTTCGAAGGCCAG 57.037 40.909 5.01 0.00 0.00 4.85
4728 5085 4.890158 TGAGGTCCGCATATCACAATAT 57.110 40.909 0.00 0.00 0.00 1.28
4753 5121 4.331108 TCGTGGATGACATCAAAAATGGA 58.669 39.130 17.08 1.97 0.00 3.41
4756 5124 4.035558 CCGATCGTGGATGACATCAAAAAT 59.964 41.667 17.08 3.17 0.00 1.82
4813 5181 1.399791 GCACTAGCTGCTGATTTGTCC 59.600 52.381 13.43 0.00 43.33 4.02
4846 5216 2.295885 AGTCTTGAAGCCATAGCATGC 58.704 47.619 10.51 10.51 43.56 4.06
4958 5331 2.234661 GTGGACTGTCTCATGATGGTCA 59.765 50.000 7.85 0.00 32.41 4.02
4986 5529 1.745232 TGGCCGCGTGAAGATTTATT 58.255 45.000 4.92 0.00 0.00 1.40
5000 5543 2.203126 GCCTCCTCTGAATGGCCG 60.203 66.667 0.00 0.00 39.49 6.13
5147 5692 0.957395 AGCAAGACACGAGGCCATTG 60.957 55.000 5.01 0.19 0.00 2.82
5174 5719 0.675083 TTTGGCAGTGTGGATTGCAG 59.325 50.000 0.00 0.00 42.02 4.41
5179 5724 0.188342 ACCCTTTTGGCAGTGTGGAT 59.812 50.000 0.00 0.00 37.83 3.41
5204 5749 4.395231 CACATGCAGACTTCATGAAGATGT 59.605 41.667 36.15 29.16 42.84 3.06
5213 5758 4.186856 TCGTTATCACATGCAGACTTCA 57.813 40.909 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.