Multiple sequence alignment - TraesCS5D01G112500

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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 TraesCS5D01G112500 chr5D 100.000 3058 0 0 1 3058 128566475 128563418 0.000000e+00 5648
1 TraesCS5D01G112500 chr5D 87.524 513 64 0 2546 3058 35322139 35322651 7.300000e-166 593
2 TraesCS5D01G112500 chr5A 92.854 2533 109 26 1 2506 143553932 143551445 0.000000e+00 3609
3 TraesCS5D01G112500 chr5A 88.889 513 54 3 2546 3057 457837531 457838041 2.000000e-176 628
4 TraesCS5D01G112500 chr3D 90.927 507 46 0 2546 3052 70247623 70248129 0.000000e+00 682
5 TraesCS5D01G112500 chr3D 83.140 516 81 5 2546 3058 338583757 338583245 1.660000e-127 466
6 TraesCS5D01G112500 chr2A 89.648 512 52 1 2546 3057 655743429 655742919 0.000000e+00 651
7 TraesCS5D01G112500 chr2A 86.620 568 73 2 1048 1612 622853692 622853125 2.590000e-175 625
8 TraesCS5D01G112500 chr2A 86.444 568 74 2 1048 1612 622748004 622747437 1.200000e-173 619
9 TraesCS5D01G112500 chr2A 81.437 167 26 4 1675 1838 622746955 622746791 6.880000e-27 132
10 TraesCS5D01G112500 chr2D 86.796 568 72 3 1048 1612 480181621 480181054 5.560000e-177 630
11 TraesCS5D01G112500 chr2D 86.292 569 73 4 1048 1612 480325483 480324916 5.600000e-172 614
12 TraesCS5D01G112500 chr2D 84.912 570 79 7 1048 1612 159573864 159574431 1.230000e-158 569
13 TraesCS5D01G112500 chr2D 82.490 514 88 2 2546 3058 414408560 414408048 1.670000e-122 449
14 TraesCS5D01G112500 chr2D 81.765 510 87 5 2546 3052 88121904 88122410 3.650000e-114 422
15 TraesCS5D01G112500 chr2D 85.075 134 20 0 1693 1826 480324457 480324324 1.480000e-28 137
16 TraesCS5D01G112500 chr2D 83.582 134 22 0 1693 1826 480180549 480180416 3.200000e-25 126
17 TraesCS5D01G112500 chr2B 86.316 570 71 6 1048 1612 563046391 563045824 5.600000e-172 614
18 TraesCS5D01G112500 chr2B 86.092 568 74 4 1048 1611 563184907 563184341 9.380000e-170 606
19 TraesCS5D01G112500 chr2B 84.912 570 79 7 1048 1612 216708511 216709078 1.230000e-158 569
20 TraesCS5D01G112500 chr2B 83.108 148 22 2 1682 1826 563045296 563045149 6.880000e-27 132
21 TraesCS5D01G112500 chr3B 84.507 497 74 3 2544 3038 527378086 527377591 3.540000e-134 488
22 TraesCS5D01G112500 chr7D 82.745 510 82 5 2546 3052 607078559 607079065 1.670000e-122 449
23 TraesCS5D01G112500 chr4A 84.173 139 20 2 1690 1827 591862594 591862731 1.910000e-27 134


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 TraesCS5D01G112500 chr5D 128563418 128566475 3057 True 5648.0 5648 100.0000 1 3058 1 chr5D.!!$R1 3057
1 TraesCS5D01G112500 chr5D 35322139 35322651 512 False 593.0 593 87.5240 2546 3058 1 chr5D.!!$F1 512
2 TraesCS5D01G112500 chr5A 143551445 143553932 2487 True 3609.0 3609 92.8540 1 2506 1 chr5A.!!$R1 2505
3 TraesCS5D01G112500 chr5A 457837531 457838041 510 False 628.0 628 88.8890 2546 3057 1 chr5A.!!$F1 511
4 TraesCS5D01G112500 chr3D 70247623 70248129 506 False 682.0 682 90.9270 2546 3052 1 chr3D.!!$F1 506
5 TraesCS5D01G112500 chr3D 338583245 338583757 512 True 466.0 466 83.1400 2546 3058 1 chr3D.!!$R1 512
6 TraesCS5D01G112500 chr2A 655742919 655743429 510 True 651.0 651 89.6480 2546 3057 1 chr2A.!!$R2 511
7 TraesCS5D01G112500 chr2A 622853125 622853692 567 True 625.0 625 86.6200 1048 1612 1 chr2A.!!$R1 564
8 TraesCS5D01G112500 chr2A 622746791 622748004 1213 True 375.5 619 83.9405 1048 1838 2 chr2A.!!$R3 790
9 TraesCS5D01G112500 chr2D 159573864 159574431 567 False 569.0 569 84.9120 1048 1612 1 chr2D.!!$F2 564
10 TraesCS5D01G112500 chr2D 414408048 414408560 512 True 449.0 449 82.4900 2546 3058 1 chr2D.!!$R1 512
11 TraesCS5D01G112500 chr2D 88121904 88122410 506 False 422.0 422 81.7650 2546 3052 1 chr2D.!!$F1 506
12 TraesCS5D01G112500 chr2D 480180416 480181621 1205 True 378.0 630 85.1890 1048 1826 2 chr2D.!!$R2 778
13 TraesCS5D01G112500 chr2D 480324324 480325483 1159 True 375.5 614 85.6835 1048 1826 2 chr2D.!!$R3 778
14 TraesCS5D01G112500 chr2B 563184341 563184907 566 True 606.0 606 86.0920 1048 1611 1 chr2B.!!$R1 563
15 TraesCS5D01G112500 chr2B 216708511 216709078 567 False 569.0 569 84.9120 1048 1612 1 chr2B.!!$F1 564
16 TraesCS5D01G112500 chr2B 563045149 563046391 1242 True 373.0 614 84.7120 1048 1826 2 chr2B.!!$R2 778
17 TraesCS5D01G112500 chr7D 607078559 607079065 506 False 449.0 449 82.7450 2546 3052 1 chr7D.!!$F1 506

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
697 710 0.259065 TGACTAGACGATGCCCCTCT 59.741 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 3071 0.322366 TGCACCGAGGCAATCAATCA 60.322 50.0 0.0 0.0 41.65 2.57 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
20 21 3.624326 TCTAGCAAACACATTGTGCAC 57.376 42.857 16.62 10.75 41.32 4.57
22 23 2.669300 AGCAAACACATTGTGCACAA 57.331 40.000 32.78 32.78 41.32 3.33
85 86 4.336433 TGGTATTCTTAGTAGCGCGTAAGT 59.664 41.667 19.89 1.26 41.68 2.24
94 95 4.675510 AGTAGCGCGTAAGTAAATTAGCA 58.324 39.130 8.43 0.00 41.68 3.49
100 101 4.493545 CGCGTAAGTAAATTAGCAAGGGTG 60.494 45.833 0.00 0.00 41.68 4.61
102 103 5.446875 GCGTAAGTAAATTAGCAAGGGTGTC 60.447 44.000 0.00 0.00 41.68 3.67
129 130 2.230508 CGGCCTTATAGCGAAGGTGATA 59.769 50.000 14.24 0.00 46.73 2.15
131 132 3.258622 GGCCTTATAGCGAAGGTGATAGT 59.741 47.826 14.24 0.00 46.73 2.12
142 143 5.005779 GCGAAGGTGATAGTACATTCAACAG 59.994 44.000 13.58 7.14 40.34 3.16
154 155 3.627577 ACATTCAACAGGAGTGACACAAC 59.372 43.478 8.59 0.00 36.77 3.32
158 159 3.319689 TCAACAGGAGTGACACAACGATA 59.680 43.478 8.59 0.00 0.00 2.92
164 165 5.236478 CAGGAGTGACACAACGATACTTTTT 59.764 40.000 8.59 0.00 0.00 1.94
195 196 1.007336 GTCGTTTCGATGGAGCACGT 61.007 55.000 10.08 0.00 38.42 4.49
242 243 2.773487 TCAACCCGTTGTGTAAGGATG 58.227 47.619 7.42 0.00 41.16 3.51
252 253 6.086222 CGTTGTGTAAGGATGGATTTTCTTG 58.914 40.000 0.00 0.00 0.00 3.02
257 258 6.015434 GTGTAAGGATGGATTTTCTTGGTTGT 60.015 38.462 0.00 0.00 0.00 3.32
258 259 6.553100 TGTAAGGATGGATTTTCTTGGTTGTT 59.447 34.615 0.00 0.00 0.00 2.83
259 260 5.473066 AGGATGGATTTTCTTGGTTGTTG 57.527 39.130 0.00 0.00 0.00 3.33
260 261 4.284234 AGGATGGATTTTCTTGGTTGTTGG 59.716 41.667 0.00 0.00 0.00 3.77
261 262 4.563374 GGATGGATTTTCTTGGTTGTTGGG 60.563 45.833 0.00 0.00 0.00 4.12
262 263 2.103941 TGGATTTTCTTGGTTGTTGGGC 59.896 45.455 0.00 0.00 0.00 5.36
263 264 2.549992 GGATTTTCTTGGTTGTTGGGCC 60.550 50.000 0.00 0.00 0.00 5.80
323 324 6.920758 TGTTTGAGTTTTGGGTTATCGATTTG 59.079 34.615 1.71 0.00 0.00 2.32
340 341 7.797038 TCGATTTGATCATCAACATTCTGAT 57.203 32.000 0.00 0.00 35.89 2.90
396 397 3.805066 TGACAATCAATGGGGAACTGA 57.195 42.857 0.00 0.00 0.00 3.41
419 420 3.506067 GGATATCCAATGGGTTTTAGGCG 59.494 47.826 17.34 0.00 35.64 5.52
451 452 8.831550 GGAAAGTAGATGATTGGTCATAAGTTC 58.168 37.037 0.00 0.00 44.96 3.01
486 487 2.425578 ATTTAACGTTTGGTTGGCGG 57.574 45.000 5.91 0.00 39.75 6.13
500 501 0.393808 TGGCGGCTACAAGAAATCCC 60.394 55.000 11.43 0.00 0.00 3.85
505 506 3.881220 CGGCTACAAGAAATCCCCTAAA 58.119 45.455 0.00 0.00 0.00 1.85
508 509 5.163652 CGGCTACAAGAAATCCCCTAAAAAG 60.164 44.000 0.00 0.00 0.00 2.27
510 511 6.436218 GGCTACAAGAAATCCCCTAAAAAGAA 59.564 38.462 0.00 0.00 0.00 2.52
511 512 7.039293 GGCTACAAGAAATCCCCTAAAAAGAAA 60.039 37.037 0.00 0.00 0.00 2.52
512 513 8.364894 GCTACAAGAAATCCCCTAAAAAGAAAA 58.635 33.333 0.00 0.00 0.00 2.29
544 545 6.993902 AGGCATCATGAGAAAACACAAAAATT 59.006 30.769 0.09 0.00 0.00 1.82
545 546 7.499895 AGGCATCATGAGAAAACACAAAAATTT 59.500 29.630 0.09 0.00 0.00 1.82
558 559 2.385013 AAAATTTGGCGGCCAGAATC 57.615 45.000 22.59 0.00 33.81 2.52
564 565 4.508128 GCGGCCAGAATCGTCCGA 62.508 66.667 2.24 0.00 44.23 4.55
574 575 4.681942 CCAGAATCGTCCGAGATATGAAAC 59.318 45.833 0.00 0.00 0.00 2.78
577 578 5.299531 AGAATCGTCCGAGATATGAAACTGA 59.700 40.000 0.00 0.00 0.00 3.41
579 580 4.921547 TCGTCCGAGATATGAAACTGAAG 58.078 43.478 0.00 0.00 0.00 3.02
582 583 3.134458 CCGAGATATGAAACTGAAGGGC 58.866 50.000 0.00 0.00 0.00 5.19
584 585 4.039245 CCGAGATATGAAACTGAAGGGCTA 59.961 45.833 0.00 0.00 0.00 3.93
595 596 1.002251 TGAAGGGCTAAAAACGTTGCG 60.002 47.619 0.00 0.00 0.00 4.85
596 597 1.264826 GAAGGGCTAAAAACGTTGCGA 59.735 47.619 0.00 0.00 0.00 5.10
597 598 0.872388 AGGGCTAAAAACGTTGCGAG 59.128 50.000 0.00 0.00 0.00 5.03
599 600 1.662026 GGGCTAAAAACGTTGCGAGTG 60.662 52.381 0.00 0.00 0.00 3.51
600 601 1.662026 GGCTAAAAACGTTGCGAGTGG 60.662 52.381 0.00 0.00 0.00 4.00
605 618 2.228138 AAACGTTGCGAGTGGACTTA 57.772 45.000 0.00 0.00 0.00 2.24
618 631 4.844884 AGTGGACTTAAAAGGATGCCTAC 58.155 43.478 0.00 0.00 31.13 3.18
629 642 4.439253 AGGATGCCTACCTGTAAATTCC 57.561 45.455 0.00 0.00 36.30 3.01
676 689 9.781834 TTATTCAGCGTAAATAAATGTTGGAAG 57.218 29.630 0.00 0.00 0.00 3.46
683 696 8.231837 GCGTAAATAAATGTTGGAAGTTGACTA 58.768 33.333 0.00 0.00 0.00 2.59
688 701 4.866508 ATGTTGGAAGTTGACTAGACGA 57.133 40.909 0.00 0.00 0.00 4.20
689 702 4.866508 TGTTGGAAGTTGACTAGACGAT 57.133 40.909 0.00 0.00 0.00 3.73
690 703 4.556233 TGTTGGAAGTTGACTAGACGATG 58.444 43.478 0.00 0.00 0.00 3.84
691 704 3.232213 TGGAAGTTGACTAGACGATGC 57.768 47.619 0.00 0.00 0.00 3.91
692 705 2.094182 TGGAAGTTGACTAGACGATGCC 60.094 50.000 0.00 0.00 0.00 4.40
693 706 2.541556 GAAGTTGACTAGACGATGCCC 58.458 52.381 0.00 0.00 0.00 5.36
694 707 0.824759 AGTTGACTAGACGATGCCCC 59.175 55.000 0.00 0.00 0.00 5.80
695 708 0.824759 GTTGACTAGACGATGCCCCT 59.175 55.000 0.00 0.00 0.00 4.79
696 709 1.112113 TTGACTAGACGATGCCCCTC 58.888 55.000 0.00 0.00 0.00 4.30
697 710 0.259065 TGACTAGACGATGCCCCTCT 59.741 55.000 0.00 0.00 0.00 3.69
698 711 1.493446 TGACTAGACGATGCCCCTCTA 59.507 52.381 0.00 0.00 0.00 2.43
699 712 2.156098 GACTAGACGATGCCCCTCTAG 58.844 57.143 0.00 0.00 39.57 2.43
700 713 1.775459 ACTAGACGATGCCCCTCTAGA 59.225 52.381 10.06 0.00 37.84 2.43
701 714 2.377193 ACTAGACGATGCCCCTCTAGAT 59.623 50.000 10.06 0.00 37.84 1.98
702 715 1.917872 AGACGATGCCCCTCTAGATC 58.082 55.000 0.00 0.00 0.00 2.75
703 716 1.427368 AGACGATGCCCCTCTAGATCT 59.573 52.381 0.00 0.00 0.00 2.75
704 717 2.645297 AGACGATGCCCCTCTAGATCTA 59.355 50.000 1.69 1.69 0.00 1.98
705 718 3.013921 GACGATGCCCCTCTAGATCTAG 58.986 54.545 21.81 21.81 34.56 2.43
706 719 1.748493 CGATGCCCCTCTAGATCTAGC 59.252 57.143 22.81 13.34 33.32 3.42
707 720 2.620367 CGATGCCCCTCTAGATCTAGCT 60.620 54.545 22.81 0.00 33.32 3.32
708 721 3.371059 CGATGCCCCTCTAGATCTAGCTA 60.371 52.174 22.81 7.80 33.32 3.32
748 761 1.057636 AGTATGAACACGCGTCAACG 58.942 50.000 9.86 0.00 43.27 4.10
770 783 3.497942 GCCAGAAAAGGAAACACCCTCTA 60.498 47.826 0.00 0.00 40.05 2.43
788 801 4.636648 CCTCTATGTATACAGGCTAGGTCG 59.363 50.000 11.91 2.14 0.00 4.79
875 888 5.125367 ACCAACTTAAACCTTCCTCTTGT 57.875 39.130 0.00 0.00 0.00 3.16
882 895 1.760405 ACCTTCCTCTTGTCCCCAAT 58.240 50.000 0.00 0.00 0.00 3.16
895 908 2.243994 GTCCCCAATAGGCTTAAACCCT 59.756 50.000 0.00 0.00 36.47 4.34
908 921 7.645002 AGGCTTAAACCCTTATAAATACCACA 58.355 34.615 0.00 0.00 0.00 4.17
910 923 7.013942 GGCTTAAACCCTTATAAATACCACAGG 59.986 40.741 0.00 0.00 0.00 4.00
958 979 4.699925 AACACAAGGTCAAGTAGCCTTA 57.300 40.909 0.00 0.00 42.68 2.69
969 990 4.406003 TCAAGTAGCCTTACTTCCATCCTC 59.594 45.833 0.00 0.00 44.83 3.71
991 1012 3.815401 CGAGTTCCAAGAAAACCACAGAT 59.185 43.478 0.00 0.00 0.00 2.90
1323 1347 3.797353 ATCTCCGGCGGGCACATT 61.797 61.111 27.98 2.35 0.00 2.71
1510 1534 3.818787 CCGGGTACTCGGTCGGTG 61.819 72.222 26.56 0.00 44.60 4.94
1629 1658 1.045407 TACCGCACAAACCTGTCTCT 58.955 50.000 0.00 0.00 31.64 3.10
1656 1872 2.572104 ACCCTTTCTTCTATCGCCTTGT 59.428 45.455 0.00 0.00 0.00 3.16
1680 1896 6.863126 GTCACACTCCTTTTGATAAATGTTGG 59.137 38.462 0.00 0.00 0.00 3.77
1898 2428 5.163893 GGCAAGAATTTTAGTGTCGATCGAA 60.164 40.000 21.31 7.64 0.00 3.71
1915 2445 1.939934 CGAACTTGCCTGAACTGACAA 59.060 47.619 0.00 0.00 0.00 3.18
1916 2446 2.032549 CGAACTTGCCTGAACTGACAAG 60.033 50.000 0.00 0.00 43.99 3.16
1917 2447 2.717639 ACTTGCCTGAACTGACAAGT 57.282 45.000 7.34 7.34 45.86 3.16
1919 2449 1.002033 CTTGCCTGAACTGACAAGTGC 60.002 52.381 0.00 0.00 36.51 4.40
1920 2450 0.107263 TGCCTGAACTGACAAGTGCA 60.107 50.000 0.00 0.00 39.88 4.57
1929 2459 2.287970 ACTGACAAGTGCATGCATTGTG 60.288 45.455 33.47 27.49 37.29 3.33
1935 2465 1.897133 AGTGCATGCATTGTGGTTCAT 59.103 42.857 25.64 0.00 0.00 2.57
1942 2472 2.553602 TGCATTGTGGTTCATCTGTGAC 59.446 45.455 0.00 0.00 33.11 3.67
2006 2536 2.202623 GCGCTCTACCACCAGACG 60.203 66.667 0.00 0.00 0.00 4.18
2018 2548 4.193334 CAGACGATCCTCCGCGCA 62.193 66.667 8.75 0.00 0.00 6.09
2045 2575 2.427753 GGCTATGGCTCCTTCCGG 59.572 66.667 0.00 0.00 38.73 5.14
2068 2598 3.596743 CGCCTAGCTAGCTCGCCA 61.597 66.667 23.26 1.96 0.00 5.69
2070 2600 1.300542 GCCTAGCTAGCTCGCCAAG 60.301 63.158 23.26 12.63 0.00 3.61
2078 2608 3.885521 GCTCGCCAAGCCATCAGC 61.886 66.667 0.00 0.00 45.92 4.26
2104 2634 6.101997 CCAAAATTGGCATCTTTCTCCTTAC 58.898 40.000 0.00 0.00 42.21 2.34
2105 2635 6.071165 CCAAAATTGGCATCTTTCTCCTTACT 60.071 38.462 0.00 0.00 42.21 2.24
2170 2700 2.906354 AGTGAAGTGTCCTTGTGTGTC 58.094 47.619 0.00 0.00 0.00 3.67
2237 2768 4.042311 TGGTTCAGGGTAGCAGTCAATAAA 59.958 41.667 0.00 0.00 0.00 1.40
2297 2828 9.654417 CAAATTCACTTGTTTGATTGATTTTCC 57.346 29.630 0.00 0.00 37.48 3.13
2298 2829 9.617523 AAATTCACTTGTTTGATTGATTTTCCT 57.382 25.926 0.00 0.00 0.00 3.36
2299 2830 9.617523 AATTCACTTGTTTGATTGATTTTCCTT 57.382 25.926 0.00 0.00 0.00 3.36
2426 2957 2.569404 ACTGACTGTTTTGGGCCAAAAA 59.431 40.909 38.22 27.26 43.50 1.94
2493 3025 3.976701 AATTGGGGCGACGCTGGAG 62.977 63.158 20.77 0.00 45.02 3.86
2514 3046 4.324991 GGCCGACCGGTCCAACTT 62.325 66.667 28.52 0.00 37.65 2.66
2515 3047 2.281276 GCCGACCGGTCCAACTTT 60.281 61.111 28.52 0.00 37.65 2.66
2516 3048 2.322830 GCCGACCGGTCCAACTTTC 61.323 63.158 28.52 1.93 37.65 2.62
2517 3049 2.025418 CCGACCGGTCCAACTTTCG 61.025 63.158 28.52 14.70 0.00 3.46
2518 3050 2.025418 CGACCGGTCCAACTTTCGG 61.025 63.158 28.52 7.48 46.95 4.30
2520 3052 3.961729 CCGGTCCAACTTTCGGTC 58.038 61.111 0.00 0.00 37.92 4.79
2521 3053 1.070105 CCGGTCCAACTTTCGGTCA 59.930 57.895 0.00 0.00 37.92 4.02
2522 3054 0.949105 CCGGTCCAACTTTCGGTCAG 60.949 60.000 0.00 0.00 37.92 3.51
2523 3055 0.249741 CGGTCCAACTTTCGGTCAGT 60.250 55.000 0.00 0.00 0.00 3.41
2524 3056 1.509703 GGTCCAACTTTCGGTCAGTC 58.490 55.000 0.00 0.00 0.00 3.51
2525 3057 1.202604 GGTCCAACTTTCGGTCAGTCA 60.203 52.381 0.00 0.00 0.00 3.41
2526 3058 1.865340 GTCCAACTTTCGGTCAGTCAC 59.135 52.381 0.00 0.00 0.00 3.67
2527 3059 1.202604 TCCAACTTTCGGTCAGTCACC 60.203 52.381 0.00 0.00 42.69 4.02
2528 3060 1.202651 CCAACTTTCGGTCAGTCACCT 60.203 52.381 0.00 0.00 44.21 4.00
2529 3061 2.036733 CCAACTTTCGGTCAGTCACCTA 59.963 50.000 0.00 0.00 44.21 3.08
2530 3062 3.318017 CAACTTTCGGTCAGTCACCTAG 58.682 50.000 0.00 0.00 44.21 3.02
2531 3063 1.272769 ACTTTCGGTCAGTCACCTAGC 59.727 52.381 0.00 0.00 44.21 3.42
2532 3064 1.272490 CTTTCGGTCAGTCACCTAGCA 59.728 52.381 0.00 0.00 44.21 3.49
2533 3065 1.557099 TTCGGTCAGTCACCTAGCAT 58.443 50.000 0.00 0.00 44.21 3.79
2534 3066 1.103803 TCGGTCAGTCACCTAGCATC 58.896 55.000 0.00 0.00 44.21 3.91
2535 3067 0.103208 CGGTCAGTCACCTAGCATCC 59.897 60.000 0.00 0.00 44.21 3.51
2536 3068 1.195115 GGTCAGTCACCTAGCATCCA 58.805 55.000 0.00 0.00 42.84 3.41
2537 3069 1.134670 GGTCAGTCACCTAGCATCCAC 60.135 57.143 0.00 0.00 42.84 4.02
2538 3070 1.134670 GTCAGTCACCTAGCATCCACC 60.135 57.143 0.00 0.00 0.00 4.61
2539 3071 1.198713 CAGTCACCTAGCATCCACCT 58.801 55.000 0.00 0.00 0.00 4.00
2540 3072 1.134580 CAGTCACCTAGCATCCACCTG 60.135 57.143 0.00 0.00 0.00 4.00
2541 3073 1.195115 GTCACCTAGCATCCACCTGA 58.805 55.000 0.00 0.00 0.00 3.86
2542 3074 1.765314 GTCACCTAGCATCCACCTGAT 59.235 52.381 0.00 0.00 0.00 2.90
2543 3075 2.171448 GTCACCTAGCATCCACCTGATT 59.829 50.000 0.00 0.00 0.00 2.57
2544 3076 2.171237 TCACCTAGCATCCACCTGATTG 59.829 50.000 0.00 0.00 0.00 2.67
2618 3150 1.202417 CGCGTCCTCCATGACATACTT 60.202 52.381 0.00 0.00 34.88 2.24
2620 3152 2.159099 GCGTCCTCCATGACATACTTGA 60.159 50.000 0.00 0.00 34.88 3.02
2622 3154 3.131223 CGTCCTCCATGACATACTTGACT 59.869 47.826 0.00 0.00 34.88 3.41
2653 3185 1.485066 ACACTCGTCTTTGTGAGGGTT 59.515 47.619 0.00 0.00 46.37 4.11
2660 3192 0.310854 CTTTGTGAGGGTTTGCCGAC 59.689 55.000 0.00 0.00 34.97 4.79
2720 3252 3.512724 CCCCTCAAATGCAAGATCTTTGT 59.487 43.478 4.86 0.00 32.89 2.83
2753 3285 1.070786 AACATCGCTTGTGGACGGT 59.929 52.632 0.00 0.00 38.99 4.83
2787 3319 3.346315 TCGTCATGGTTTGCAAGATCAT 58.654 40.909 0.00 2.45 0.00 2.45
2793 3325 3.620488 TGGTTTGCAAGATCATACCTCC 58.380 45.455 14.99 1.97 38.41 4.30
2888 3420 2.577606 TGGATGGGTTGTTTCGACAT 57.422 45.000 0.00 0.00 0.00 3.06
2895 3427 2.567067 GGTTGTTTCGACATGTTACGC 58.433 47.619 0.00 0.00 0.00 4.42
3007 3540 1.875963 GACACCCTGGTCATTTGCG 59.124 57.895 0.00 0.00 37.73 4.85
3052 3585 0.240945 GAATGCCAGGGTGTTCAACG 59.759 55.000 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 6.046593 CGTCATAGACACCCTTGCTAATTTA 58.953 40.000 0.00 0.00 32.09 1.40
94 95 0.617820 AGGCCGTCATAGACACCCTT 60.618 55.000 0.00 0.00 31.61 3.95
100 101 2.486982 TCGCTATAAGGCCGTCATAGAC 59.513 50.000 19.52 12.22 0.00 2.59
102 103 3.502920 CTTCGCTATAAGGCCGTCATAG 58.497 50.000 13.84 13.84 0.00 2.23
129 130 4.100963 TGTGTCACTCCTGTTGAATGTACT 59.899 41.667 4.27 0.00 0.00 2.73
131 132 4.681074 TGTGTCACTCCTGTTGAATGTA 57.319 40.909 4.27 0.00 0.00 2.29
142 143 5.668558 AAAAAGTATCGTTGTGTCACTCC 57.331 39.130 4.27 0.00 0.00 3.85
154 155 8.866956 ACGACTTGACCTATTTAAAAAGTATCG 58.133 33.333 0.00 0.74 0.00 2.92
158 159 8.066000 CGAAACGACTTGACCTATTTAAAAAGT 58.934 33.333 1.31 1.31 0.00 2.66
164 165 5.808540 CCATCGAAACGACTTGACCTATTTA 59.191 40.000 0.00 0.00 39.18 1.40
183 184 1.921243 TCATTACACGTGCTCCATCG 58.079 50.000 17.22 0.00 0.00 3.84
229 230 6.015434 ACCAAGAAAATCCATCCTTACACAAC 60.015 38.462 0.00 0.00 0.00 3.32
242 243 2.549992 GGCCCAACAACCAAGAAAATCC 60.550 50.000 0.00 0.00 0.00 3.01
252 253 1.594021 CTTTTGCGGCCCAACAACC 60.594 57.895 6.19 0.00 31.97 3.77
274 275 5.822132 AGCTAATGATCATAGTTGGCTCT 57.178 39.130 9.04 0.00 35.15 4.09
323 324 9.330063 TGGTACTTAATCAGAATGTTGATGATC 57.670 33.333 0.00 0.00 37.83 2.92
340 341 7.201702 TGAACCCACATATCATGGTACTTAA 57.798 36.000 0.00 0.00 35.23 1.85
388 389 3.245052 CCCATTGGATATCCTCAGTTCCC 60.245 52.174 22.35 0.00 36.82 3.97
396 397 4.740902 GCCTAAAACCCATTGGATATCCT 58.259 43.478 22.35 0.00 36.82 3.24
419 420 5.501156 ACCAATCATCTACTTTCCCTTGTC 58.499 41.667 0.00 0.00 0.00 3.18
451 452 9.763465 AAACGTTAAATTTGATACAACTATCGG 57.237 29.630 0.00 0.00 32.58 4.18
486 487 7.462571 TTCTTTTTAGGGGATTTCTTGTAGC 57.537 36.000 0.00 0.00 0.00 3.58
512 513 6.647895 GTGTTTTCTCATGATGCCTCATTTTT 59.352 34.615 1.22 0.00 40.20 1.94
513 514 6.161381 GTGTTTTCTCATGATGCCTCATTTT 58.839 36.000 1.22 0.00 40.20 1.82
514 515 5.244402 TGTGTTTTCTCATGATGCCTCATTT 59.756 36.000 1.22 0.00 40.20 2.32
515 516 4.768448 TGTGTTTTCTCATGATGCCTCATT 59.232 37.500 1.22 0.00 40.20 2.57
516 517 4.338012 TGTGTTTTCTCATGATGCCTCAT 58.662 39.130 0.00 0.00 43.02 2.90
521 522 7.588488 CCAAATTTTTGTGTTTTCTCATGATGC 59.412 33.333 0.00 0.00 36.45 3.91
530 531 3.358775 GCCGCCAAATTTTTGTGTTTTC 58.641 40.909 2.63 0.00 36.45 2.29
544 545 2.435938 GACGATTCTGGCCGCCAA 60.436 61.111 14.45 0.00 30.80 4.52
545 546 4.467084 GGACGATTCTGGCCGCCA 62.467 66.667 12.67 12.67 0.00 5.69
558 559 4.045104 CCTTCAGTTTCATATCTCGGACG 58.955 47.826 0.00 0.00 0.00 4.79
564 565 7.148239 CGTTTTTAGCCCTTCAGTTTCATATCT 60.148 37.037 0.00 0.00 0.00 1.98
574 575 2.661594 GCAACGTTTTTAGCCCTTCAG 58.338 47.619 0.00 0.00 0.00 3.02
577 578 1.265905 CTCGCAACGTTTTTAGCCCTT 59.734 47.619 0.00 0.00 0.00 3.95
579 580 0.589708 ACTCGCAACGTTTTTAGCCC 59.410 50.000 0.00 0.00 0.00 5.19
582 583 2.542595 AGTCCACTCGCAACGTTTTTAG 59.457 45.455 0.00 0.00 0.00 1.85
584 585 1.375551 AGTCCACTCGCAACGTTTTT 58.624 45.000 0.00 0.00 0.00 1.94
595 596 3.956744 AGGCATCCTTTTAAGTCCACTC 58.043 45.455 0.00 0.00 0.00 3.51
596 597 4.324331 GGTAGGCATCCTTTTAAGTCCACT 60.324 45.833 0.00 0.00 34.61 4.00
597 598 3.945921 GGTAGGCATCCTTTTAAGTCCAC 59.054 47.826 0.00 0.00 34.61 4.02
599 600 4.200092 CAGGTAGGCATCCTTTTAAGTCC 58.800 47.826 0.00 0.00 34.61 3.85
600 601 4.844884 ACAGGTAGGCATCCTTTTAAGTC 58.155 43.478 0.00 0.00 34.61 3.01
605 618 5.656859 GGAATTTACAGGTAGGCATCCTTTT 59.343 40.000 0.00 0.00 34.61 2.27
676 689 0.824759 AGGGGCATCGTCTAGTCAAC 59.175 55.000 0.00 0.00 0.00 3.18
683 696 1.427368 AGATCTAGAGGGGCATCGTCT 59.573 52.381 0.00 6.71 42.53 4.18
688 701 4.571792 CCTTAGCTAGATCTAGAGGGGCAT 60.572 50.000 30.06 10.49 35.21 4.40
689 702 3.245443 CCTTAGCTAGATCTAGAGGGGCA 60.245 52.174 30.06 8.63 35.21 5.36
690 703 3.361786 CCTTAGCTAGATCTAGAGGGGC 58.638 54.545 30.06 16.71 35.21 5.80
691 704 3.361786 GCCTTAGCTAGATCTAGAGGGG 58.638 54.545 30.06 23.32 35.21 4.79
692 705 3.245443 TGGCCTTAGCTAGATCTAGAGGG 60.245 52.174 30.06 23.04 39.73 4.30
693 706 4.040936 TGGCCTTAGCTAGATCTAGAGG 57.959 50.000 30.06 26.09 39.73 3.69
703 716 6.099701 TCAATATTCTGTTCTGGCCTTAGCTA 59.900 38.462 3.32 0.00 39.73 3.32
704 717 5.104360 TCAATATTCTGTTCTGGCCTTAGCT 60.104 40.000 3.32 0.00 39.73 3.32
705 718 5.126067 TCAATATTCTGTTCTGGCCTTAGC 58.874 41.667 3.32 0.00 38.76 3.09
706 719 6.825721 ACTTCAATATTCTGTTCTGGCCTTAG 59.174 38.462 3.32 0.00 0.00 2.18
707 720 6.721318 ACTTCAATATTCTGTTCTGGCCTTA 58.279 36.000 3.32 0.00 0.00 2.69
708 721 5.574188 ACTTCAATATTCTGTTCTGGCCTT 58.426 37.500 3.32 0.00 0.00 4.35
748 761 1.613925 GAGGGTGTTTCCTTTTCTGGC 59.386 52.381 0.00 0.00 37.25 4.85
770 783 1.540267 CGCGACCTAGCCTGTATACAT 59.460 52.381 5.91 0.00 0.00 2.29
788 801 4.742659 TGCTTAATTTTGGAAAGTTGACGC 59.257 37.500 0.00 0.00 0.00 5.19
837 850 4.406456 AGTTGGTATGTGCATTTCCTTGA 58.594 39.130 0.00 0.00 0.00 3.02
838 851 4.789012 AGTTGGTATGTGCATTTCCTTG 57.211 40.909 0.00 0.00 0.00 3.61
848 861 6.238648 AGAGGAAGGTTTAAGTTGGTATGTG 58.761 40.000 0.00 0.00 0.00 3.21
849 862 6.449830 AGAGGAAGGTTTAAGTTGGTATGT 57.550 37.500 0.00 0.00 0.00 2.29
850 863 6.715264 ACAAGAGGAAGGTTTAAGTTGGTATG 59.285 38.462 0.00 0.00 0.00 2.39
875 888 2.580232 AGGGTTTAAGCCTATTGGGGA 58.420 47.619 14.62 0.00 45.76 4.81
895 908 8.549731 TGTGGTTATGACCTGTGGTATTTATAA 58.450 33.333 8.31 0.00 46.66 0.98
906 919 4.534500 TGGTCTATTGTGGTTATGACCTGT 59.466 41.667 8.31 0.00 46.66 4.00
908 921 4.534500 TGTGGTCTATTGTGGTTATGACCT 59.466 41.667 8.31 0.00 46.66 3.85
910 923 5.703592 TGTTGTGGTCTATTGTGGTTATGAC 59.296 40.000 0.00 0.00 0.00 3.06
922 935 4.338118 CCTTGTGTTTGTGTTGTGGTCTAT 59.662 41.667 0.00 0.00 0.00 1.98
923 936 3.692101 CCTTGTGTTTGTGTTGTGGTCTA 59.308 43.478 0.00 0.00 0.00 2.59
958 979 1.938585 TGGAACTCGAGGATGGAAGT 58.061 50.000 18.41 0.00 0.00 3.01
969 990 3.202906 TCTGTGGTTTTCTTGGAACTCG 58.797 45.455 0.00 0.00 0.00 4.18
991 1012 5.005628 ACCTCTTTGCCCATTTAACCTAA 57.994 39.130 0.00 0.00 0.00 2.69
1323 1347 3.572196 GAACGTCACGGCCGGGTTA 62.572 63.158 29.71 5.81 0.00 2.85
1497 1521 4.487412 CCCGCACCGACCGAGTAC 62.487 72.222 0.00 0.00 0.00 2.73
1629 1658 4.442706 GCGATAGAAGAAAGGGTTCATCA 58.557 43.478 0.00 0.00 34.57 3.07
1656 1872 6.549364 ACCAACATTTATCAAAAGGAGTGTGA 59.451 34.615 0.00 0.00 30.99 3.58
1680 1896 3.578688 GCCAACACCTTCATTCATCAAC 58.421 45.455 0.00 0.00 0.00 3.18
1705 2235 4.179579 GCGAACCCGATTGGCAGC 62.180 66.667 0.00 0.00 41.42 5.25
1804 2334 2.168054 GGCTTTGTCGCCGTTGTAT 58.832 52.632 0.00 0.00 40.79 2.29
1898 2428 2.717639 ACTTGTCAGTTCAGGCAAGT 57.282 45.000 8.01 8.01 44.36 3.16
1915 2445 1.330234 TGAACCACAATGCATGCACT 58.670 45.000 25.37 10.02 0.00 4.40
1916 2446 2.094390 AGATGAACCACAATGCATGCAC 60.094 45.455 25.37 8.21 0.00 4.57
1917 2447 2.094442 CAGATGAACCACAATGCATGCA 60.094 45.455 25.04 25.04 0.00 3.96
1918 2448 2.094390 ACAGATGAACCACAATGCATGC 60.094 45.455 11.82 11.82 0.00 4.06
1919 2449 3.191791 TCACAGATGAACCACAATGCATG 59.808 43.478 0.00 0.00 0.00 4.06
1920 2450 3.192001 GTCACAGATGAACCACAATGCAT 59.808 43.478 0.00 0.00 36.31 3.96
1942 2472 0.742281 CACCCAGAAGATCCACTGCG 60.742 60.000 10.18 5.80 33.40 5.18
2045 2575 0.596341 GAGCTAGCTAGGCGTTGCTC 60.596 60.000 19.38 17.02 40.25 4.26
2068 2598 2.289819 CCAATTTTGGTGCTGATGGCTT 60.290 45.455 0.95 0.00 43.43 4.35
2070 2600 1.729284 CCAATTTTGGTGCTGATGGC 58.271 50.000 0.95 0.00 43.43 4.40
2170 2700 1.291184 TGCTTCAATCGGACGCACAG 61.291 55.000 0.00 0.00 44.82 3.66
2237 2768 4.476113 TCACTTGGATTCTCCCATCTGAAT 59.524 41.667 0.00 0.00 35.03 2.57
2262 2793 7.382110 TCAAACAAGTGAATTTGTCTTTTCCA 58.618 30.769 0.00 0.00 40.24 3.53
2263 2794 7.826260 TCAAACAAGTGAATTTGTCTTTTCC 57.174 32.000 0.00 0.00 40.24 3.13
2299 2830 5.499139 AAAGCGTGACATTCTCTCAAAAA 57.501 34.783 0.00 0.00 0.00 1.94
2380 2911 5.622770 AACACAAAACGATCTAATGGGAC 57.377 39.130 0.00 0.00 0.00 4.46
2384 2915 7.740346 GTCAGTGTAACACAAAACGATCTAATG 59.260 37.037 0.00 0.00 41.43 1.90
2426 2957 7.565323 TTTTGGCACTTTCATTTTAGCATTT 57.435 28.000 0.00 0.00 0.00 2.32
2462 2994 3.997681 CGCCCCAATTTAAAACCGATTTT 59.002 39.130 0.00 0.00 41.07 1.82
2506 3038 1.865340 GTGACTGACCGAAAGTTGGAC 59.135 52.381 0.00 0.00 0.00 4.02
2507 3039 1.202604 GGTGACTGACCGAAAGTTGGA 60.203 52.381 0.00 0.00 34.02 3.53
2508 3040 1.226746 GGTGACTGACCGAAAGTTGG 58.773 55.000 0.00 0.00 34.02 3.77
2517 3049 1.134670 GTGGATGCTAGGTGACTGACC 60.135 57.143 0.00 0.00 46.58 4.02
2518 3050 1.134670 GGTGGATGCTAGGTGACTGAC 60.135 57.143 0.00 0.00 43.88 3.51
2519 3051 1.195115 GGTGGATGCTAGGTGACTGA 58.805 55.000 0.00 0.00 43.88 3.41
2520 3052 1.134580 CAGGTGGATGCTAGGTGACTG 60.135 57.143 0.00 0.00 43.88 3.51
2521 3053 2.628021 ATCAGGTGGATGCTAGGTGACT 60.628 50.000 0.00 0.00 38.72 3.41
2522 3054 1.195115 TCAGGTGGATGCTAGGTGAC 58.805 55.000 0.00 0.00 0.00 3.67
2523 3055 2.171237 CAATCAGGTGGATGCTAGGTGA 59.829 50.000 0.00 0.00 36.02 4.02
2524 3056 2.171237 TCAATCAGGTGGATGCTAGGTG 59.829 50.000 0.00 0.00 36.02 4.00
2525 3057 2.481441 TCAATCAGGTGGATGCTAGGT 58.519 47.619 0.00 0.00 36.02 3.08
2526 3058 3.784511 ATCAATCAGGTGGATGCTAGG 57.215 47.619 0.00 0.00 36.02 3.02
2527 3059 3.252701 GCAATCAATCAGGTGGATGCTAG 59.747 47.826 0.00 0.00 36.02 3.42
2528 3060 3.216800 GCAATCAATCAGGTGGATGCTA 58.783 45.455 0.00 0.00 36.02 3.49
2529 3061 2.029623 GCAATCAATCAGGTGGATGCT 58.970 47.619 0.00 0.00 36.02 3.79
2530 3062 1.068127 GGCAATCAATCAGGTGGATGC 59.932 52.381 0.00 0.00 36.02 3.91
2531 3063 2.621998 GAGGCAATCAATCAGGTGGATG 59.378 50.000 0.00 0.00 36.02 3.51
2532 3064 2.747467 CGAGGCAATCAATCAGGTGGAT 60.747 50.000 0.00 0.00 38.05 3.41
2533 3065 1.407299 CGAGGCAATCAATCAGGTGGA 60.407 52.381 0.00 0.00 0.00 4.02
2534 3066 1.019673 CGAGGCAATCAATCAGGTGG 58.980 55.000 0.00 0.00 0.00 4.61
2535 3067 1.019673 CCGAGGCAATCAATCAGGTG 58.980 55.000 0.00 0.00 0.00 4.00
2536 3068 0.620556 ACCGAGGCAATCAATCAGGT 59.379 50.000 0.00 0.00 0.00 4.00
2537 3069 1.019673 CACCGAGGCAATCAATCAGG 58.980 55.000 0.00 0.00 0.00 3.86
2538 3070 0.379669 GCACCGAGGCAATCAATCAG 59.620 55.000 0.00 0.00 0.00 2.90
2539 3071 0.322366 TGCACCGAGGCAATCAATCA 60.322 50.000 0.00 0.00 41.65 2.57
2540 3072 0.379669 CTGCACCGAGGCAATCAATC 59.620 55.000 2.69 0.00 44.40 2.67
2541 3073 1.660560 GCTGCACCGAGGCAATCAAT 61.661 55.000 0.00 0.00 44.40 2.57
2542 3074 2.334946 GCTGCACCGAGGCAATCAA 61.335 57.895 0.00 0.00 44.40 2.57
2543 3075 2.747460 GCTGCACCGAGGCAATCA 60.747 61.111 0.00 0.00 44.40 2.57
2544 3076 3.869272 CGCTGCACCGAGGCAATC 61.869 66.667 0.00 0.00 44.40 2.67
2618 3150 4.084287 ACGAGTGTAGGTGGATTTAGTCA 58.916 43.478 0.00 0.00 0.00 3.41
2620 3152 4.342359 AGACGAGTGTAGGTGGATTTAGT 58.658 43.478 0.00 0.00 0.00 2.24
2622 3154 5.011329 ACAAAGACGAGTGTAGGTGGATTTA 59.989 40.000 0.00 0.00 0.00 1.40
2653 3185 1.669760 CGTAAGGGCAAGTCGGCAA 60.670 57.895 0.00 0.00 43.60 4.52
2660 3192 3.499737 CTGCGGCGTAAGGGCAAG 61.500 66.667 9.37 0.00 42.43 4.01
2688 3220 1.815003 CATTTGAGGGGTGCAAGACTC 59.185 52.381 0.00 0.00 0.00 3.36
2720 3252 0.471591 ATGTTGGGAAGCCAGCCAAA 60.472 50.000 0.00 0.00 0.00 3.28
2775 3307 2.288666 GCGGAGGTATGATCTTGCAAA 58.711 47.619 0.00 0.00 0.00 3.68
2787 3319 1.961394 CAAGTATAGCAGGCGGAGGTA 59.039 52.381 0.00 0.00 0.00 3.08
2793 3325 2.797156 CTGTAAGCAAGTATAGCAGGCG 59.203 50.000 0.00 0.00 0.00 5.52
2888 3420 3.618594 GCAAGAGATCTGAATGCGTAACA 59.381 43.478 0.00 0.00 0.00 2.41
2895 3427 1.134280 ACGGGGCAAGAGATCTGAATG 60.134 52.381 0.00 0.00 0.00 2.67
2955 3488 0.948678 CTTCCTTCGCGAAACCCAAA 59.051 50.000 23.54 11.10 0.00 3.28
3007 3540 2.803155 TTCCAGAGTGACCATGCCGC 62.803 60.000 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.