Multiple sequence alignment - TraesCS5D01G412300

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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 TraesCS5D01G412300 chr5D 100.000 4217 0 0 1 4217 475512499 475508283 0.000000e+00 7788.0
1 TraesCS5D01G412300 chr5D 77.737 274 44 12 2162 2420 351006445 351006174 7.300000e-33 152.0
2 TraesCS5D01G412300 chr5D 88.608 79 9 0 997 1075 351007372 351007294 3.470000e-16 97.1
3 TraesCS5D01G412300 chr5D 95.455 44 1 1 4130 4172 120797299 120797342 7.570000e-08 69.4
4 TraesCS5D01G412300 chr5D 100.000 37 0 0 2621 2657 475509844 475509808 7.570000e-08 69.4
5 TraesCS5D01G412300 chr5D 100.000 37 0 0 2656 2692 475509879 475509843 7.570000e-08 69.4
6 TraesCS5D01G412300 chr5D 95.455 44 1 1 4130 4172 483806153 483806110 7.570000e-08 69.4
7 TraesCS5D01G412300 chr5D 95.455 44 1 1 4130 4172 503284731 503284774 7.570000e-08 69.4
8 TraesCS5D01G412300 chr5B 91.603 1846 101 30 74 1899 582892232 582890421 0.000000e+00 2501.0
9 TraesCS5D01G412300 chr5B 94.800 1000 22 13 2656 3641 582889652 582888669 0.000000e+00 1531.0
10 TraesCS5D01G412300 chr5B 93.497 815 47 5 1846 2655 582890432 582889619 0.000000e+00 1206.0
11 TraesCS5D01G412300 chr5B 88.952 353 23 2 3880 4217 582888443 582888092 5.040000e-114 422.0
12 TraesCS5D01G412300 chr5B 88.333 240 13 4 3632 3870 582888650 582888425 1.490000e-69 274.0
13 TraesCS5D01G412300 chr5B 74.102 529 103 26 1918 2419 411931341 411930820 2.000000e-43 187.0
14 TraesCS5D01G412300 chr5B 86.726 113 13 2 3880 3992 582888327 582888217 1.590000e-24 124.0
15 TraesCS5D01G412300 chr5B 87.342 79 10 0 997 1075 411932010 411931932 1.610000e-14 91.6
16 TraesCS5D01G412300 chr5A 92.938 1600 73 19 322 1901 594965024 594963445 0.000000e+00 2292.0
17 TraesCS5D01G412300 chr5A 90.085 1059 50 23 2671 3707 594962671 594961646 0.000000e+00 1323.0
18 TraesCS5D01G412300 chr5A 93.137 816 45 5 1846 2657 594963458 594962650 0.000000e+00 1186.0
19 TraesCS5D01G412300 chr5A 90.029 341 17 10 1 339 594966012 594965687 3.900000e-115 425.0
20 TraesCS5D01G412300 chr5A 87.006 354 28 9 3880 4217 594961492 594961141 2.380000e-102 383.0
21 TraesCS5D01G412300 chr5A 73.743 537 100 30 1918 2420 451480317 451479788 5.610000e-39 172.0
22 TraesCS5D01G412300 chr5A 88.000 100 2 2 3771 3870 594961563 594961474 4.460000e-20 110.0
23 TraesCS5D01G412300 chr5A 84.071 113 16 2 3880 3992 594961376 594961266 1.600000e-19 108.0
24 TraesCS5D01G412300 chr5A 88.608 79 9 0 997 1075 451480977 451480899 3.470000e-16 97.1
25 TraesCS5D01G412300 chr5A 95.455 44 1 1 4130 4172 426851670 426851713 7.570000e-08 69.4
26 TraesCS5D01G412300 chr3D 95.833 48 1 1 4130 4176 1113999 1114046 4.520000e-10 76.8
27 TraesCS5D01G412300 chr6D 95.455 44 1 1 4130 4172 45514139 45514096 7.570000e-08 69.4
28 TraesCS5D01G412300 chr1A 95.455 44 1 1 4130 4172 446250506 446250549 7.570000e-08 69.4


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 TraesCS5D01G412300 chr5D 475508283 475512499 4216 True 2642.266667 7788 100.000000 1 4217 3 chr5D.!!$R3 4216
1 TraesCS5D01G412300 chr5B 582888092 582892232 4140 True 1009.666667 2501 90.651833 74 4217 6 chr5B.!!$R2 4143
2 TraesCS5D01G412300 chr5A 594961141 594966012 4871 True 832.428571 2292 89.323714 1 4217 7 chr5A.!!$R2 4216

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
971 1672 1.226746 CGCCAAGACTCGACCTTTTT 58.773 50.0 0.00 0.0 0.0 1.94 F
1557 2267 0.741221 CGAAGTGGCTTCCCTGTAGC 60.741 60.0 3.63 0.0 37.2 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 3063 0.966875 TGTAGCCCAATGCCTGCAAG 60.967 55.000 0.0 0.0 42.71 4.01 R
3486 4267 1.002468 CAACTCTCCTTGTGCCAAACG 60.002 52.381 0.0 0.0 0.00 3.60 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
34 35 3.823304 ACAGCTTGGGATTCTCTGTTTTC 59.177 43.478 0.00 0.00 34.69 2.29
35 36 4.077822 CAGCTTGGGATTCTCTGTTTTCT 58.922 43.478 0.00 0.00 0.00 2.52
81 82 3.679824 TTTTGGGTTTTTGAACCGTGT 57.320 38.095 2.53 0.00 43.75 4.49
82 83 2.656560 TTGGGTTTTTGAACCGTGTG 57.343 45.000 2.53 0.00 43.75 3.82
85 86 1.273688 GGTTTTTGAACCGTGTGCAC 58.726 50.000 10.75 10.75 32.47 4.57
86 87 1.402984 GGTTTTTGAACCGTGTGCACA 60.403 47.619 17.42 17.42 32.47 4.57
87 88 1.917303 GTTTTTGAACCGTGTGCACAG 59.083 47.619 22.40 12.52 0.00 3.66
89 90 1.999071 TTTGAACCGTGTGCACAGGC 61.999 55.000 29.48 18.42 41.68 4.85
118 119 6.771267 AGTGGATCGTAGATGTGATTACTGTA 59.229 38.462 0.00 0.00 45.12 2.74
124 125 8.391075 TCGTAGATGTGATTACTGTATGATCA 57.609 34.615 0.00 0.00 31.11 2.92
125 126 8.507249 TCGTAGATGTGATTACTGTATGATCAG 58.493 37.037 0.09 0.00 34.17 2.90
126 127 8.507249 CGTAGATGTGATTACTGTATGATCAGA 58.493 37.037 0.09 0.00 34.17 3.27
162 163 8.664079 AGATAGATAGGGATAAAAGTTGCACAT 58.336 33.333 0.00 0.00 0.00 3.21
163 164 6.949352 AGATAGGGATAAAAGTTGCACATG 57.051 37.500 0.00 0.00 0.00 3.21
171 172 7.023575 GGATAAAAGTTGCACATGAACTGTAG 58.976 38.462 0.00 0.00 35.91 2.74
178 179 3.056536 TGCACATGAACTGTAGAGGAGTC 60.057 47.826 0.00 0.00 35.91 3.36
210 214 4.379918 GCAAACTCCCTCAAAATAGTGCTC 60.380 45.833 0.00 0.00 0.00 4.26
443 1132 1.626654 GAGTCACAATCGCACGTGGG 61.627 60.000 25.33 25.33 33.83 4.61
445 1134 4.101790 CACAATCGCACGTGGGGC 62.102 66.667 29.45 9.56 0.00 5.80
446 1135 4.634703 ACAATCGCACGTGGGGCA 62.635 61.111 29.45 14.11 0.00 5.36
472 1161 4.036616 ACAACCAAATACAACACGGGTAAC 59.963 41.667 0.00 0.00 0.00 2.50
509 1198 3.914426 ATAACAGGAGATTCACCGCTT 57.086 42.857 0.00 0.00 0.00 4.68
511 1200 1.270907 ACAGGAGATTCACCGCTTCT 58.729 50.000 0.00 0.00 0.00 2.85
514 1203 3.077359 CAGGAGATTCACCGCTTCTTTT 58.923 45.455 0.00 0.00 0.00 2.27
515 1204 3.126000 CAGGAGATTCACCGCTTCTTTTC 59.874 47.826 0.00 0.00 0.00 2.29
518 1207 4.023193 GGAGATTCACCGCTTCTTTTCAAA 60.023 41.667 0.00 0.00 0.00 2.69
521 1210 7.214467 AGATTCACCGCTTCTTTTCAAAATA 57.786 32.000 0.00 0.00 0.00 1.40
525 1214 8.655651 TTCACCGCTTCTTTTCAAAATATTTT 57.344 26.923 7.64 7.64 0.00 1.82
526 1215 8.293114 TCACCGCTTCTTTTCAAAATATTTTC 57.707 30.769 10.53 0.00 0.00 2.29
527 1216 7.114247 TCACCGCTTCTTTTCAAAATATTTTCG 59.886 33.333 10.53 7.91 0.00 3.46
528 1217 7.114247 CACCGCTTCTTTTCAAAATATTTTCGA 59.886 33.333 10.53 9.14 0.00 3.71
529 1218 7.650104 ACCGCTTCTTTTCAAAATATTTTCGAA 59.350 29.630 10.53 13.76 0.00 3.71
531 1220 9.289999 CGCTTCTTTTCAAAATATTTTCGAAAC 57.710 29.630 23.38 16.31 32.44 2.78
971 1672 1.226746 CGCCAAGACTCGACCTTTTT 58.773 50.000 0.00 0.00 0.00 1.94
1173 1874 3.077556 TGCCTCTTCGCCTCCTCC 61.078 66.667 0.00 0.00 0.00 4.30
1176 1877 2.440430 CTCTTCGCCTCCTCCCGA 60.440 66.667 0.00 0.00 0.00 5.14
1392 2099 2.361104 GCAAAGGCGGATGACCCA 60.361 61.111 0.00 0.00 34.14 4.51
1536 2246 2.437359 CTCCCCTTCTTGCAGGCG 60.437 66.667 0.00 0.00 31.69 5.52
1539 2249 3.121030 CCCTTCTTGCAGGCGACG 61.121 66.667 0.00 0.00 31.69 5.12
1557 2267 0.741221 CGAAGTGGCTTCCCTGTAGC 60.741 60.000 3.63 0.00 37.20 3.58
1572 2282 1.067846 TGTAGCGATATCATCACCGGC 60.068 52.381 0.00 0.00 0.00 6.13
1713 2426 2.126346 GTGATGGCGTTGCTTGGC 60.126 61.111 0.00 0.00 0.00 4.52
1716 2429 2.598394 ATGGCGTTGCTTGGCAGT 60.598 55.556 5.95 0.00 45.62 4.40
1725 2438 2.358615 CTTGGCAGTAGCGGTGCA 60.359 61.111 5.29 0.00 43.12 4.57
1770 2483 2.552315 CGTCAAGGCATTGTTTGGTAGT 59.448 45.455 11.36 0.00 37.68 2.73
1893 2648 4.099170 GCTGCTCTTGGTGCTGCG 62.099 66.667 7.44 0.00 43.24 5.18
1968 2723 1.936547 GATGATGCAAAGACCGTCCTC 59.063 52.381 0.00 0.00 0.00 3.71
1983 2738 2.025969 CCTCGCTGCTGTGACTGTG 61.026 63.158 2.33 0.00 0.00 3.66
2004 2759 2.158696 GCCACTGCTCCATAAATCCTCT 60.159 50.000 0.00 0.00 33.53 3.69
2010 2765 4.487804 TGCTCCATAAATCCTCTCTAGCT 58.512 43.478 0.00 0.00 0.00 3.32
2031 2786 2.367202 GCCGAGGTCCATCCCTTCA 61.367 63.158 0.00 0.00 34.03 3.02
2187 2942 4.715534 TTCATATATTTTCCGGGAGCCA 57.284 40.909 0.00 0.00 0.00 4.75
2242 2998 5.186797 CCTCTGGTCCTTCAGGTATGATATC 59.813 48.000 0.00 0.00 34.73 1.63
2249 3005 7.016268 GGTCCTTCAGGTATGATATCCAGTTTA 59.984 40.741 0.00 0.00 34.73 2.01
2266 3022 9.620259 ATCCAGTTTATCTTGTTATTTCTCTCC 57.380 33.333 0.00 0.00 0.00 3.71
2268 3024 7.011482 CCAGTTTATCTTGTTATTTCTCTCCGG 59.989 40.741 0.00 0.00 0.00 5.14
2279 3038 1.123077 TCTCTCCGGTTCATGATGGG 58.877 55.000 0.00 0.00 0.00 4.00
2282 3041 1.417517 TCTCCGGTTCATGATGGGATG 59.582 52.381 0.00 5.75 0.00 3.51
2304 3063 9.788960 GGATGTGTTATAATTTGGACTTCTTTC 57.211 33.333 0.00 0.00 0.00 2.62
2459 3219 4.150451 CGTTTTCTTGTTGGCATGAATTCC 59.850 41.667 2.27 0.00 38.18 3.01
2521 3281 9.754382 GATGGTCAATTATTAGTTAACGGAGTA 57.246 33.333 0.00 0.00 45.00 2.59
2545 3305 2.553904 CCAGGATGAGGACTTTGTGCTT 60.554 50.000 0.00 0.00 39.69 3.91
2549 3309 2.260844 TGAGGACTTTGTGCTTGAGG 57.739 50.000 0.00 0.00 33.56 3.86
2569 3329 3.157087 GGCACCCGATTATGAAATGGAT 58.843 45.455 0.00 0.00 0.00 3.41
2629 3389 8.454106 ACTAATGATCAAATGTTGTAGCTTGAC 58.546 33.333 0.00 0.00 31.00 3.18
2630 3390 6.822667 ATGATCAAATGTTGTAGCTTGACA 57.177 33.333 0.00 0.00 31.00 3.58
2631 3391 6.631971 TGATCAAATGTTGTAGCTTGACAA 57.368 33.333 0.00 0.00 36.98 3.18
2632 3392 7.036996 TGATCAAATGTTGTAGCTTGACAAA 57.963 32.000 3.64 0.00 40.88 2.83
2633 3393 7.487484 TGATCAAATGTTGTAGCTTGACAAAA 58.513 30.769 3.64 0.00 40.88 2.44
2634 3394 8.143193 TGATCAAATGTTGTAGCTTGACAAAAT 58.857 29.630 3.64 1.68 40.88 1.82
2635 3395 7.928908 TCAAATGTTGTAGCTTGACAAAATC 57.071 32.000 5.65 0.00 40.88 2.17
2636 3396 7.487484 TCAAATGTTGTAGCTTGACAAAATCA 58.513 30.769 5.65 0.78 40.88 2.57
2637 3397 7.434897 TCAAATGTTGTAGCTTGACAAAATCAC 59.565 33.333 5.65 0.00 40.88 3.06
2638 3398 5.826601 TGTTGTAGCTTGACAAAATCACA 57.173 34.783 3.64 0.00 40.88 3.58
2639 3399 6.201226 TGTTGTAGCTTGACAAAATCACAA 57.799 33.333 3.64 0.00 40.88 3.33
2640 3400 6.264832 TGTTGTAGCTTGACAAAATCACAAG 58.735 36.000 3.64 0.00 40.88 3.16
2641 3401 6.127758 TGTTGTAGCTTGACAAAATCACAAGT 60.128 34.615 3.64 0.00 40.88 3.16
2642 3402 6.449635 TGTAGCTTGACAAAATCACAAGTT 57.550 33.333 0.00 0.00 41.73 2.66
2643 3403 6.862209 TGTAGCTTGACAAAATCACAAGTTT 58.138 32.000 0.00 0.00 41.73 2.66
2644 3404 6.751425 TGTAGCTTGACAAAATCACAAGTTTG 59.249 34.615 0.00 0.00 44.06 2.93
2645 3405 5.964758 AGCTTGACAAAATCACAAGTTTGA 58.035 33.333 5.47 0.00 41.74 2.69
2646 3406 6.576185 AGCTTGACAAAATCACAAGTTTGAT 58.424 32.000 5.47 0.00 41.74 2.57
2647 3407 6.477688 AGCTTGACAAAATCACAAGTTTGATG 59.522 34.615 5.47 0.00 41.74 3.07
2648 3408 6.476380 GCTTGACAAAATCACAAGTTTGATGA 59.524 34.615 5.47 0.11 41.74 2.92
2649 3409 7.170320 GCTTGACAAAATCACAAGTTTGATGAT 59.830 33.333 5.47 2.31 41.74 2.45
2650 3410 9.681692 CTTGACAAAATCACAAGTTTGATGATA 57.318 29.630 5.47 0.00 41.74 2.15
2651 3411 9.462174 TTGACAAAATCACAAGTTTGATGATAC 57.538 29.630 5.47 0.00 41.74 2.24
2652 3412 8.081633 TGACAAAATCACAAGTTTGATGATACC 58.918 33.333 5.47 0.00 41.74 2.73
2653 3413 7.950512 ACAAAATCACAAGTTTGATGATACCA 58.049 30.769 5.47 0.00 41.74 3.25
2654 3414 8.420222 ACAAAATCACAAGTTTGATGATACCAA 58.580 29.630 5.47 0.00 41.74 3.67
2655 3415 8.918658 CAAAATCACAAGTTTGATGATACCAAG 58.081 33.333 0.00 0.00 41.74 3.61
2656 3416 7.765695 AATCACAAGTTTGATGATACCAAGT 57.234 32.000 0.00 0.00 36.31 3.16
2657 3417 8.862325 AATCACAAGTTTGATGATACCAAGTA 57.138 30.769 0.00 0.00 36.31 2.24
2658 3418 7.905604 TCACAAGTTTGATGATACCAAGTAG 57.094 36.000 0.00 0.00 0.00 2.57
2659 3419 6.371548 TCACAAGTTTGATGATACCAAGTAGC 59.628 38.462 0.00 0.00 0.00 3.58
2660 3420 6.372659 CACAAGTTTGATGATACCAAGTAGCT 59.627 38.462 0.00 0.00 0.00 3.32
2661 3421 6.942576 ACAAGTTTGATGATACCAAGTAGCTT 59.057 34.615 0.00 0.00 0.00 3.74
2662 3422 6.992063 AGTTTGATGATACCAAGTAGCTTG 57.008 37.500 0.00 2.16 40.75 4.01
2723 3490 8.729756 TCATTAAACTGTTGAACCTCATATGTG 58.270 33.333 1.90 0.00 0.00 3.21
2727 3494 5.248640 ACTGTTGAACCTCATATGTGAAGG 58.751 41.667 6.35 6.85 33.05 3.46
2743 3512 4.629634 TGTGAAGGTATTAATGTGCTGACG 59.370 41.667 0.00 0.00 0.00 4.35
2751 3520 7.011109 AGGTATTAATGTGCTGACGTATTTGTC 59.989 37.037 0.00 0.00 39.37 3.18
2839 3616 1.068741 GGTGGTCCATAAGAGCCTACG 59.931 57.143 0.00 0.00 42.62 3.51
3048 3828 7.754027 CCTGCTTGATTTCTTGAGACTAATTTG 59.246 37.037 0.00 0.00 0.00 2.32
3357 4138 0.247736 CGTAAGCCTGGCTGACTCTT 59.752 55.000 29.11 13.33 37.86 2.85
3479 4260 4.492895 GCAGCGCATGGAAATTTTGTTATG 60.493 41.667 11.47 0.00 0.00 1.90
3480 4261 4.626604 CAGCGCATGGAAATTTTGTTATGT 59.373 37.500 11.47 0.00 0.00 2.29
3481 4262 5.120519 CAGCGCATGGAAATTTTGTTATGTT 59.879 36.000 11.47 0.00 0.00 2.71
3482 4263 5.700373 AGCGCATGGAAATTTTGTTATGTTT 59.300 32.000 11.47 0.00 0.00 2.83
3483 4264 5.789512 GCGCATGGAAATTTTGTTATGTTTG 59.210 36.000 0.30 0.00 0.00 2.93
3484 4265 6.305639 CGCATGGAAATTTTGTTATGTTTGG 58.694 36.000 0.00 0.00 0.00 3.28
3485 4266 6.610456 GCATGGAAATTTTGTTATGTTTGGG 58.390 36.000 0.00 0.00 0.00 4.12
3486 4267 6.610456 CATGGAAATTTTGTTATGTTTGGGC 58.390 36.000 0.00 0.00 0.00 5.36
3576 4359 6.828273 CCATATTGTTCATCCTGTTCCTTGTA 59.172 38.462 0.00 0.00 0.00 2.41
3660 4472 3.291809 TGAAACGCGTCTTATCACAGA 57.708 42.857 14.44 0.00 0.00 3.41
3672 4484 4.462834 TCTTATCACAGACGATGTTCTGGT 59.537 41.667 5.83 0.00 46.38 4.00
3680 4492 3.131396 GACGATGTTCTGGTCTTGTGTT 58.869 45.455 0.00 0.00 30.49 3.32
3726 4539 5.457140 ACGTAGTTGTGGCATTTTGTAATG 58.543 37.500 0.00 0.00 37.78 1.90
3740 4553 8.216453 GCATTTTGTAATGATTGTGAGTTGTTC 58.784 33.333 2.25 0.00 43.12 3.18
3785 4616 6.447162 ACTTTTCAGCTTTTAGTATGTTGGC 58.553 36.000 0.00 0.00 0.00 4.52
3786 4617 5.385509 TTTCAGCTTTTAGTATGTTGGCC 57.614 39.130 0.00 0.00 0.00 5.36
3787 4618 3.006940 TCAGCTTTTAGTATGTTGGCCG 58.993 45.455 0.00 0.00 0.00 6.13
3788 4619 1.743394 AGCTTTTAGTATGTTGGCCGC 59.257 47.619 0.00 0.00 0.00 6.53
3789 4620 1.470890 GCTTTTAGTATGTTGGCCGCA 59.529 47.619 0.00 0.00 0.00 5.69
3790 4621 2.099098 GCTTTTAGTATGTTGGCCGCAT 59.901 45.455 15.54 15.54 0.00 4.73
3832 4663 2.743636 TAGCAGTACACTTGACAGCC 57.256 50.000 0.00 0.00 30.15 4.85
3867 4698 5.006552 GTGCAAAATATGTGCTTGTGTGTTT 59.993 36.000 11.71 0.00 42.69 2.83
3868 4699 5.583854 TGCAAAATATGTGCTTGTGTGTTTT 59.416 32.000 11.71 0.00 42.69 2.43
3869 4700 6.093219 TGCAAAATATGTGCTTGTGTGTTTTT 59.907 30.769 11.71 0.00 42.69 1.94
3887 4718 4.314740 TTTTTCAGCGGTTTATGTGCTT 57.685 36.364 0.00 0.00 36.69 3.91
3888 4719 2.987413 TTCAGCGGTTTATGTGCTTG 57.013 45.000 0.00 0.00 36.69 4.01
3889 4720 1.890876 TCAGCGGTTTATGTGCTTGT 58.109 45.000 0.00 0.00 36.69 3.16
3890 4721 1.535028 TCAGCGGTTTATGTGCTTGTG 59.465 47.619 0.00 0.00 36.69 3.33
3891 4722 1.266718 CAGCGGTTTATGTGCTTGTGT 59.733 47.619 0.00 0.00 36.69 3.72
3892 4723 1.266718 AGCGGTTTATGTGCTTGTGTG 59.733 47.619 0.00 0.00 34.80 3.82
3893 4724 1.001815 GCGGTTTATGTGCTTGTGTGT 60.002 47.619 0.00 0.00 0.00 3.72
3894 4725 2.542824 GCGGTTTATGTGCTTGTGTGTT 60.543 45.455 0.00 0.00 0.00 3.32
4031 4877 8.077991 TGTGCTGTATTCAAAGAATCTTTTCTG 58.922 33.333 5.36 0.00 41.42 3.02
4075 4921 9.461312 AAGGATTATTGTAGCTGTCAATTGTTA 57.539 29.630 18.96 4.29 36.92 2.41
4076 4922 9.113838 AGGATTATTGTAGCTGTCAATTGTTAG 57.886 33.333 18.96 6.36 36.92 2.34
4201 5048 1.667236 CTTGCATCCATTAGCCGTCA 58.333 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.077822 AGAAAACAGAGAATCCCAAGCTG 58.922 43.478 0.00 0.00 33.66 4.24
14 15 4.042684 AGAGAAAACAGAGAATCCCAAGCT 59.957 41.667 0.00 0.00 33.66 3.74
15 16 4.331108 AGAGAAAACAGAGAATCCCAAGC 58.669 43.478 0.00 0.00 33.66 4.01
16 17 6.890979 AAAGAGAAAACAGAGAATCCCAAG 57.109 37.500 0.00 0.00 33.66 3.61
17 18 6.040842 CCAAAAGAGAAAACAGAGAATCCCAA 59.959 38.462 0.00 0.00 33.66 4.12
81 82 0.391130 GATCCACTAACGCCTGTGCA 60.391 55.000 0.00 0.00 37.32 4.57
82 83 1.421410 CGATCCACTAACGCCTGTGC 61.421 60.000 0.00 0.00 33.26 4.57
85 86 1.674441 TCTACGATCCACTAACGCCTG 59.326 52.381 0.00 0.00 0.00 4.85
86 87 2.048444 TCTACGATCCACTAACGCCT 57.952 50.000 0.00 0.00 0.00 5.52
87 88 2.034305 ACATCTACGATCCACTAACGCC 59.966 50.000 0.00 0.00 0.00 5.68
89 90 4.547406 TCACATCTACGATCCACTAACG 57.453 45.455 0.00 0.00 0.00 3.18
162 163 2.074576 CGTCGACTCCTCTACAGTTCA 58.925 52.381 14.70 0.00 0.00 3.18
163 164 1.397692 CCGTCGACTCCTCTACAGTTC 59.602 57.143 14.70 0.00 0.00 3.01
171 172 3.519930 GCTCCCCGTCGACTCCTC 61.520 72.222 14.70 0.00 0.00 3.71
210 214 6.075046 CGTAACTGTTATATCCACACATCGTG 60.075 42.308 3.23 0.00 45.92 4.35
410 1096 7.232994 CGATTGTGACTCTTCTGATTCTTTTC 58.767 38.462 0.00 0.00 0.00 2.29
414 1100 4.180057 GCGATTGTGACTCTTCTGATTCT 58.820 43.478 0.00 0.00 0.00 2.40
443 1132 4.619336 CGTGTTGTATTTGGTTGTTATGCC 59.381 41.667 0.00 0.00 0.00 4.40
445 1134 5.157781 CCCGTGTTGTATTTGGTTGTTATG 58.842 41.667 0.00 0.00 0.00 1.90
446 1135 4.828387 ACCCGTGTTGTATTTGGTTGTTAT 59.172 37.500 0.00 0.00 0.00 1.89
472 1161 4.892433 TGTTATTTGGGCCATCTTGTTTG 58.108 39.130 7.26 0.00 0.00 2.93
514 1203 7.698970 GCCGGATAAGTTTCGAAAATATTTTGA 59.301 33.333 17.98 12.20 0.00 2.69
515 1204 7.043656 GGCCGGATAAGTTTCGAAAATATTTTG 60.044 37.037 17.98 10.28 0.00 2.44
518 1207 5.591067 TGGCCGGATAAGTTTCGAAAATATT 59.409 36.000 13.10 10.37 0.00 1.28
521 1210 3.349022 TGGCCGGATAAGTTTCGAAAAT 58.651 40.909 13.10 8.92 0.00 1.82
525 1214 1.537348 CGATGGCCGGATAAGTTTCGA 60.537 52.381 5.05 0.00 33.91 3.71
526 1215 0.859232 CGATGGCCGGATAAGTTTCG 59.141 55.000 5.05 0.00 33.91 3.46
527 1216 0.586802 GCGATGGCCGGATAAGTTTC 59.413 55.000 5.05 0.00 39.04 2.78
528 1217 0.107410 TGCGATGGCCGGATAAGTTT 60.107 50.000 5.05 0.00 38.85 2.66
529 1218 0.814010 GTGCGATGGCCGGATAAGTT 60.814 55.000 5.05 0.00 41.61 2.66
531 1220 0.946221 GAGTGCGATGGCCGGATAAG 60.946 60.000 5.05 0.00 41.61 1.73
532 1221 1.069090 GAGTGCGATGGCCGGATAA 59.931 57.895 5.05 0.00 41.61 1.75
631 1326 2.550978 GCGGCTTCTTTATGCTCTGTA 58.449 47.619 0.00 0.00 0.00 2.74
1176 1877 4.942481 TTGTGCTGCTCGACGCGT 62.942 61.111 13.85 13.85 43.27 6.01
1375 2082 2.361104 TGGGTCATCCGCCTTTGC 60.361 61.111 0.00 0.00 38.76 3.68
1524 2234 0.946221 ACTTCGTCGCCTGCAAGAAG 60.946 55.000 13.20 13.20 42.67 2.85
1536 2246 0.606604 TACAGGGAAGCCACTTCGTC 59.393 55.000 1.52 0.00 40.99 4.20
1539 2249 0.741221 CGCTACAGGGAAGCCACTTC 60.741 60.000 0.00 0.00 39.52 3.01
1551 2261 2.868662 CCGGTGATGATATCGCTACAG 58.131 52.381 0.00 0.00 39.66 2.74
1557 2267 0.737367 ATGCGCCGGTGATGATATCG 60.737 55.000 21.76 3.19 0.00 2.92
1572 2282 2.969238 GACCTGCGGGATGATGCG 60.969 66.667 21.41 0.00 36.25 4.73
1704 2417 1.966451 ACCGCTACTGCCAAGCAAC 60.966 57.895 3.38 0.00 40.08 4.17
1893 2648 3.066814 CTCTTGCTTGCCCCTGCC 61.067 66.667 0.00 0.00 36.33 4.85
1902 2657 1.627834 AGCCAGCTAGTTCTCTTGCTT 59.372 47.619 0.00 0.00 46.91 3.91
1968 2723 3.720193 GGCACAGTCACAGCAGCG 61.720 66.667 0.00 0.00 0.00 5.18
1983 2738 2.158696 AGAGGATTTATGGAGCAGTGGC 60.159 50.000 0.00 0.00 41.61 5.01
2004 2759 1.454111 GGACCTCGGCTCAGCTAGA 60.454 63.158 0.00 0.00 0.00 2.43
2010 2765 2.764128 GGGATGGACCTCGGCTCA 60.764 66.667 0.00 0.00 38.98 4.26
2187 2942 6.461509 GGAAGATCACAATGTCCAAAACTTGT 60.462 38.462 0.00 0.00 32.78 3.16
2242 2998 7.011482 CCGGAGAGAAATAACAAGATAAACTGG 59.989 40.741 0.00 0.00 0.00 4.00
2249 3005 6.049955 TGAACCGGAGAGAAATAACAAGAT 57.950 37.500 9.46 0.00 0.00 2.40
2254 3010 5.237344 CCATCATGAACCGGAGAGAAATAAC 59.763 44.000 9.46 0.00 0.00 1.89
2258 3014 2.092968 CCCATCATGAACCGGAGAGAAA 60.093 50.000 9.46 0.00 0.00 2.52
2261 3017 1.123077 TCCCATCATGAACCGGAGAG 58.877 55.000 9.46 0.00 0.00 3.20
2266 3022 2.042686 ACACATCCCATCATGAACCG 57.957 50.000 0.00 0.00 0.00 4.44
2268 3024 9.467258 CAAATTATAACACATCCCATCATGAAC 57.533 33.333 0.00 0.00 0.00 3.18
2282 3041 9.129209 GCAAGAAAGAAGTCCAAATTATAACAC 57.871 33.333 0.00 0.00 0.00 3.32
2304 3063 0.966875 TGTAGCCCAATGCCTGCAAG 60.967 55.000 0.00 0.00 42.71 4.01
2459 3219 7.282585 TCAGATAAGGAGGATACAAATGGTTG 58.717 38.462 0.00 0.00 40.84 3.77
2545 3305 3.213506 CATTTCATAATCGGGTGCCTCA 58.786 45.455 0.00 0.00 0.00 3.86
2549 3309 3.191371 GGATCCATTTCATAATCGGGTGC 59.809 47.826 6.95 0.00 0.00 5.01
2629 3389 8.815141 TTGGTATCATCAAACTTGTGATTTTG 57.185 30.769 10.62 0.00 36.04 2.44
2630 3390 8.641541 ACTTGGTATCATCAAACTTGTGATTTT 58.358 29.630 10.62 0.00 36.04 1.82
2631 3391 8.181904 ACTTGGTATCATCAAACTTGTGATTT 57.818 30.769 10.62 0.00 36.04 2.17
2632 3392 7.765695 ACTTGGTATCATCAAACTTGTGATT 57.234 32.000 10.62 1.10 36.04 2.57
2633 3393 7.066284 GCTACTTGGTATCATCAAACTTGTGAT 59.934 37.037 10.35 10.35 38.84 3.06
2634 3394 6.371548 GCTACTTGGTATCATCAAACTTGTGA 59.628 38.462 0.00 0.00 0.00 3.58
2635 3395 6.372659 AGCTACTTGGTATCATCAAACTTGTG 59.627 38.462 0.00 0.00 0.00 3.33
2636 3396 6.476378 AGCTACTTGGTATCATCAAACTTGT 58.524 36.000 0.00 0.00 0.00 3.16
2637 3397 6.992063 AGCTACTTGGTATCATCAAACTTG 57.008 37.500 0.00 0.00 0.00 3.16
2638 3398 7.119846 GTCAAGCTACTTGGTATCATCAAACTT 59.880 37.037 7.44 0.00 41.33 2.66
2639 3399 6.595716 GTCAAGCTACTTGGTATCATCAAACT 59.404 38.462 7.44 0.00 41.33 2.66
2640 3400 6.371548 TGTCAAGCTACTTGGTATCATCAAAC 59.628 38.462 7.44 0.00 41.33 2.93
2641 3401 6.472016 TGTCAAGCTACTTGGTATCATCAAA 58.528 36.000 7.44 0.00 41.33 2.69
2642 3402 6.048732 TGTCAAGCTACTTGGTATCATCAA 57.951 37.500 7.44 0.00 41.33 2.57
2643 3403 5.675684 TGTCAAGCTACTTGGTATCATCA 57.324 39.130 7.44 0.00 41.33 3.07
2644 3404 6.985188 TTTGTCAAGCTACTTGGTATCATC 57.015 37.500 7.44 0.00 41.33 2.92
2645 3405 7.611467 TGATTTTGTCAAGCTACTTGGTATCAT 59.389 33.333 7.44 0.00 41.33 2.45
2646 3406 6.939730 TGATTTTGTCAAGCTACTTGGTATCA 59.060 34.615 7.44 6.94 41.33 2.15
2647 3407 7.094805 TGTGATTTTGTCAAGCTACTTGGTATC 60.095 37.037 7.44 4.96 41.33 2.24
2648 3408 6.714810 TGTGATTTTGTCAAGCTACTTGGTAT 59.285 34.615 7.44 0.00 41.33 2.73
2649 3409 6.058833 TGTGATTTTGTCAAGCTACTTGGTA 58.941 36.000 7.44 0.00 41.33 3.25
2650 3410 4.887071 TGTGATTTTGTCAAGCTACTTGGT 59.113 37.500 7.44 0.00 41.33 3.67
2651 3411 5.437289 TGTGATTTTGTCAAGCTACTTGG 57.563 39.130 7.44 0.00 41.33 3.61
2652 3412 6.498304 ACTTGTGATTTTGTCAAGCTACTTG 58.502 36.000 0.81 0.81 42.25 3.16
2653 3413 6.699575 ACTTGTGATTTTGTCAAGCTACTT 57.300 33.333 0.00 0.00 41.22 2.24
2654 3414 6.699575 AACTTGTGATTTTGTCAAGCTACT 57.300 33.333 0.00 0.00 41.22 2.57
2655 3415 6.972328 TCAAACTTGTGATTTTGTCAAGCTAC 59.028 34.615 0.00 0.00 41.22 3.58
2656 3416 7.094508 TCAAACTTGTGATTTTGTCAAGCTA 57.905 32.000 0.00 0.00 41.22 3.32
2657 3417 5.964758 TCAAACTTGTGATTTTGTCAAGCT 58.035 33.333 0.00 0.00 41.22 3.74
2658 3418 6.476380 TCATCAAACTTGTGATTTTGTCAAGC 59.524 34.615 0.00 0.00 41.22 4.01
2659 3419 7.990541 TCATCAAACTTGTGATTTTGTCAAG 57.009 32.000 0.00 0.00 42.60 3.02
2660 3420 9.462174 GTATCATCAAACTTGTGATTTTGTCAA 57.538 29.630 10.62 0.00 38.90 3.18
2661 3421 8.081633 GGTATCATCAAACTTGTGATTTTGTCA 58.918 33.333 10.62 0.00 36.04 3.58
2662 3422 8.081633 TGGTATCATCAAACTTGTGATTTTGTC 58.918 33.333 10.62 0.00 36.04 3.18
2723 3490 7.478520 AATACGTCAGCACATTAATACCTTC 57.521 36.000 0.00 0.00 0.00 3.46
2727 3494 6.839301 CGACAAATACGTCAGCACATTAATAC 59.161 38.462 0.00 0.00 35.54 1.89
2801 3570 2.057922 ACCAATGGACCAGTGAGTTCT 58.942 47.619 23.20 0.00 30.53 3.01
2839 3616 6.481984 GCTACTTGCTTTATGATCAAGTCAC 58.518 40.000 9.72 1.66 44.87 3.67
3068 3848 6.184789 GGTCCCCTGTAATGACAAAAATAGA 58.815 40.000 0.00 0.00 34.35 1.98
3073 3853 2.785562 CGGTCCCCTGTAATGACAAAA 58.214 47.619 0.00 0.00 34.35 2.44
3268 4048 2.102084 GCAGCAGAGGTCATCAGTGATA 59.898 50.000 5.03 0.00 36.60 2.15
3316 4096 2.295629 TGCAAGGCGACATCAATCAAAA 59.704 40.909 0.00 0.00 0.00 2.44
3357 4138 1.074889 GTAGGGCAGGGGAAAAACTGA 59.925 52.381 0.00 0.00 36.86 3.41
3479 4260 1.151172 CTTGTGCCAAACGCCCAAAC 61.151 55.000 0.00 0.00 34.23 2.93
3480 4261 1.142748 CTTGTGCCAAACGCCCAAA 59.857 52.632 0.00 0.00 34.23 3.28
3481 4262 2.790791 CCTTGTGCCAAACGCCCAA 61.791 57.895 0.00 0.00 33.49 4.12
3482 4263 3.222855 CCTTGTGCCAAACGCCCA 61.223 61.111 0.00 0.00 36.24 5.36
3483 4264 2.909965 TCCTTGTGCCAAACGCCC 60.910 61.111 0.00 0.00 36.24 6.13
3484 4265 1.856265 CTCTCCTTGTGCCAAACGCC 61.856 60.000 0.00 0.00 36.24 5.68
3485 4266 1.166531 ACTCTCCTTGTGCCAAACGC 61.167 55.000 0.00 0.00 38.31 4.84
3486 4267 1.002468 CAACTCTCCTTGTGCCAAACG 60.002 52.381 0.00 0.00 0.00 3.60
3576 4359 5.825593 TCAGATGGTAACCAAAACTCTCT 57.174 39.130 0.00 0.00 36.95 3.10
3660 4472 2.910688 ACACAAGACCAGAACATCGT 57.089 45.000 0.00 0.00 0.00 3.73
3672 4484 4.873259 TCAACAACATCGAAGAACACAAGA 59.127 37.500 0.00 0.00 43.58 3.02
3680 4492 6.183360 CGTATCACAATCAACAACATCGAAGA 60.183 38.462 0.00 0.00 45.75 2.87
3726 4539 7.572759 TCATTTCTTACGAACAACTCACAATC 58.427 34.615 0.00 0.00 0.00 2.67
3740 4553 4.445718 AGTCGCAGCATATCATTTCTTACG 59.554 41.667 0.00 0.00 0.00 3.18
3756 4569 4.474226 ACTAAAAGCTGAAAAGTCGCAG 57.526 40.909 0.00 0.00 35.28 5.18
3757 4570 5.468746 ACATACTAAAAGCTGAAAAGTCGCA 59.531 36.000 0.00 0.00 0.00 5.10
3759 4572 6.797033 CCAACATACTAAAAGCTGAAAAGTCG 59.203 38.462 0.00 0.00 0.00 4.18
3787 4618 2.198287 ATCTTGCCCATGCGGATGC 61.198 57.895 11.99 1.38 41.78 3.91
3788 4619 1.105167 ACATCTTGCCCATGCGGATG 61.105 55.000 10.35 10.35 46.43 3.51
3789 4620 0.396139 AACATCTTGCCCATGCGGAT 60.396 50.000 4.56 0.00 41.78 4.18
3790 4621 0.611618 AAACATCTTGCCCATGCGGA 60.612 50.000 4.56 0.00 41.78 5.54
3832 4663 2.693797 ATTTTGCACTCGCTCAGTTG 57.306 45.000 0.00 0.00 39.64 3.16
3867 4698 3.067461 ACAAGCACATAAACCGCTGAAAA 59.933 39.130 0.00 0.00 35.79 2.29
3868 4699 2.621055 ACAAGCACATAAACCGCTGAAA 59.379 40.909 0.00 0.00 35.79 2.69
3869 4700 2.031245 CACAAGCACATAAACCGCTGAA 60.031 45.455 0.00 0.00 35.79 3.02
3870 4701 1.535028 CACAAGCACATAAACCGCTGA 59.465 47.619 0.00 0.00 35.79 4.26
3871 4702 1.266718 ACACAAGCACATAAACCGCTG 59.733 47.619 0.00 0.00 35.79 5.18
3872 4703 1.266718 CACACAAGCACATAAACCGCT 59.733 47.619 0.00 0.00 37.68 5.52
3873 4704 1.001815 ACACACAAGCACATAAACCGC 60.002 47.619 0.00 0.00 0.00 5.68
3874 4705 3.042189 CAACACACAAGCACATAAACCG 58.958 45.455 0.00 0.00 0.00 4.44
3875 4706 4.040445 ACAACACACAAGCACATAAACC 57.960 40.909 0.00 0.00 0.00 3.27
3876 4707 5.098893 TCAACAACACACAAGCACATAAAC 58.901 37.500 0.00 0.00 0.00 2.01
3877 4708 5.316327 TCAACAACACACAAGCACATAAA 57.684 34.783 0.00 0.00 0.00 1.40
3878 4709 4.972514 TCAACAACACACAAGCACATAA 57.027 36.364 0.00 0.00 0.00 1.90
3879 4710 5.512753 AATCAACAACACACAAGCACATA 57.487 34.783 0.00 0.00 0.00 2.29
3880 4711 4.389890 AATCAACAACACACAAGCACAT 57.610 36.364 0.00 0.00 0.00 3.21
3881 4712 3.865011 AATCAACAACACACAAGCACA 57.135 38.095 0.00 0.00 0.00 4.57
3882 4713 4.624882 TCAAAATCAACAACACACAAGCAC 59.375 37.500 0.00 0.00 0.00 4.40
3883 4714 4.814147 TCAAAATCAACAACACACAAGCA 58.186 34.783 0.00 0.00 0.00 3.91
3884 4715 5.750067 AGATCAAAATCAACAACACACAAGC 59.250 36.000 0.00 0.00 34.07 4.01
3885 4716 7.276218 ACAAGATCAAAATCAACAACACACAAG 59.724 33.333 0.00 0.00 34.07 3.16
3886 4717 7.095910 ACAAGATCAAAATCAACAACACACAA 58.904 30.769 0.00 0.00 34.07 3.33
3887 4718 6.629128 ACAAGATCAAAATCAACAACACACA 58.371 32.000 0.00 0.00 34.07 3.72
3888 4719 8.801715 ATACAAGATCAAAATCAACAACACAC 57.198 30.769 0.00 0.00 34.07 3.82
3889 4720 9.462174 GAATACAAGATCAAAATCAACAACACA 57.538 29.630 0.00 0.00 34.07 3.72
3890 4721 9.462174 TGAATACAAGATCAAAATCAACAACAC 57.538 29.630 0.00 0.00 34.07 3.32
3926 4757 8.514594 CCTTGACATACTTGCTCAAATAAAGAA 58.485 33.333 0.00 0.00 0.00 2.52
3932 4763 6.435277 ACAATCCTTGACATACTTGCTCAAAT 59.565 34.615 0.00 0.00 0.00 2.32
4031 4877 4.004982 TCCTTCGTATACTTGCCCAAAAC 58.995 43.478 0.56 0.00 0.00 2.43
4037 4883 7.148623 GCTACAATAATCCTTCGTATACTTGCC 60.149 40.741 0.56 0.00 0.00 4.52
4075 4921 8.804912 AAGCTCAGATGTTCATATTTCTTTCT 57.195 30.769 0.00 0.00 0.00 2.52
4126 4972 4.639171 TGACAGAAGCGCGCGACA 62.639 61.111 37.18 14.94 0.00 4.35


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

AutoCloner maintained by Alex Coulton.