Multiple sequence alignment - TraesCS3B01G403800

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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 TraesCS3B01G403800 chr3B 100.000 3188 0 0 1 3188 638285378 638288565 0.000000e+00 5888.0
1 TraesCS3B01G403800 chr3B 86.047 215 14 9 2966 3166 638288083 638288295 1.930000e-52 217.0
2 TraesCS3B01G403800 chr3B 86.047 215 14 9 2706 2918 638288343 638288543 1.930000e-52 217.0
3 TraesCS3B01G403800 chr3D 94.339 2367 74 24 610 2953 478528127 478530456 0.000000e+00 3574.0
4 TraesCS3B01G403800 chr3A 94.005 2202 70 27 619 2807 621832427 621834579 0.000000e+00 3278.0
5 TraesCS3B01G403800 chr3A 94.602 389 13 6 2804 3188 621834681 621835065 2.120000e-166 595.0
6 TraesCS3B01G403800 chr3A 83.932 529 68 9 6 524 621829116 621829637 1.030000e-134 490.0
7 TraesCS3B01G403800 chr3A 86.512 215 13 8 2706 2918 621834843 621835043 4.140000e-54 222.0
8 TraesCS3B01G403800 chr3A 93.827 81 3 2 2966 3044 621834477 621834557 1.550000e-23 121.0
9 TraesCS3B01G403800 chr1A 93.684 190 8 3 2999 3188 363927651 363927836 6.730000e-72 281.0
10 TraesCS3B01G403800 chr7B 86.939 245 24 3 1409 1649 463421186 463421426 5.240000e-68 268.0
11 TraesCS3B01G403800 chr7B 81.720 93 16 1 2545 2636 115195 115287 3.410000e-10 76.8
12 TraesCS3B01G403800 chr7D 94.444 72 1 3 2568 2636 446941279 446941208 1.210000e-19 108.0
13 TraesCS3B01G403800 chr7D 89.552 67 5 1 2576 2640 604296072 604296006 2.040000e-12 84.2
14 TraesCS3B01G403800 chr7D 89.552 67 5 1 2576 2640 604297627 604297561 2.040000e-12 84.2
15 TraesCS3B01G403800 chr6B 90.123 81 5 3 2570 2647 147708702 147708622 5.630000e-18 102.0
16 TraesCS3B01G403800 chr4B 91.667 72 2 2 2568 2639 526729073 526729140 2.620000e-16 97.1
17 TraesCS3B01G403800 chr5A 85.106 94 5 5 2543 2636 54748069 54747985 1.580000e-13 87.9
18 TraesCS3B01G403800 chr2D 93.220 59 3 1 2544 2602 61804622 61804679 5.670000e-13 86.1
19 TraesCS3B01G403800 chr5B 89.706 68 1 1 2569 2636 563122258 563122319 7.330000e-12 82.4
20 TraesCS3B01G403800 chr1B 91.228 57 5 0 2544 2600 661577899 661577955 9.480000e-11 78.7
21 TraesCS3B01G403800 chr2B 89.091 55 4 2 2547 2600 408191321 408191268 2.050000e-07 67.6


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 TraesCS3B01G403800 chr3B 638285378 638288565 3187 False 2107.333333 5888 90.6980 1 3188 3 chr3B.!!$F1 3187
1 TraesCS3B01G403800 chr3D 478528127 478530456 2329 False 3574.000000 3574 94.3390 610 2953 1 chr3D.!!$F1 2343
2 TraesCS3B01G403800 chr3A 621829116 621835065 5949 False 941.200000 3278 90.5756 6 3188 5 chr3A.!!$F1 3182

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
577 588 0.036388 CGCTTACTGGCCAGGAGAAA 60.036 55.0 35.42 21.45 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 5252 0.395586 AGTGGCAGCAAGGTTTCACA 60.396 50.0 0.0 0.0 0.0 3.58 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
18 19 1.076485 GTCCCTCAGCATGGGCAAT 60.076 57.895 0.00 0.00 44.23 3.56
33 34 2.475519 GGGCAATGTTGTATTGTCGTCG 60.476 50.000 0.00 0.00 34.68 5.12
58 59 4.357947 GCGACTGCTGGTGACCGA 62.358 66.667 0.00 0.00 38.39 4.69
60 61 2.920645 CGACTGCTGGTGACCGACT 61.921 63.158 0.00 0.00 0.00 4.18
66 67 1.442184 CTGGTGACCGACTTCGACG 60.442 63.158 0.00 0.00 43.02 5.12
72 73 1.873355 GACCGACTTCGACGTTGCAC 61.873 60.000 3.76 0.00 43.02 4.57
77 78 0.179121 ACTTCGACGTTGCACTGTCA 60.179 50.000 15.57 3.04 34.78 3.58
78 79 1.139989 CTTCGACGTTGCACTGTCAT 58.860 50.000 15.57 0.00 34.78 3.06
92 93 6.446318 TGCACTGTCATTTGTTATTTCTTCC 58.554 36.000 0.00 0.00 0.00 3.46
97 98 6.454795 TGTCATTTGTTATTTCTTCCCTTGC 58.545 36.000 0.00 0.00 0.00 4.01
98 99 6.267471 TGTCATTTGTTATTTCTTCCCTTGCT 59.733 34.615 0.00 0.00 0.00 3.91
102 103 4.724399 TGTTATTTCTTCCCTTGCTGTCA 58.276 39.130 0.00 0.00 0.00 3.58
105 106 0.843309 TTCTTCCCTTGCTGTCACCA 59.157 50.000 0.00 0.00 0.00 4.17
109 110 1.909700 TCCCTTGCTGTCACCATTTC 58.090 50.000 0.00 0.00 0.00 2.17
131 132 4.980805 GTGGCGCCACCGAGTTCA 62.981 66.667 43.24 11.17 43.94 3.18
138 139 3.499737 CACCGAGTTCATGGCCGC 61.500 66.667 0.00 0.00 0.00 6.53
152 153 2.738521 CCGCCGTTGTGTCTCCAG 60.739 66.667 0.00 0.00 0.00 3.86
155 156 2.029073 CCGTTGTGTCTCCAGCGT 59.971 61.111 0.00 0.00 37.35 5.07
159 160 1.007734 TTGTGTCTCCAGCGTCGAC 60.008 57.895 5.18 5.18 0.00 4.20
225 226 1.566231 GTCATTGAGGAAGGGGATGGT 59.434 52.381 0.00 0.00 0.00 3.55
228 229 1.753903 TTGAGGAAGGGGATGGTTGA 58.246 50.000 0.00 0.00 0.00 3.18
243 244 0.464452 GTTGACGGTGAGGATAGGGG 59.536 60.000 0.00 0.00 0.00 4.79
244 245 0.042131 TTGACGGTGAGGATAGGGGT 59.958 55.000 0.00 0.00 0.00 4.95
250 251 3.942439 GAGGATAGGGGTGGCGGC 61.942 72.222 0.00 0.00 0.00 6.53
287 297 4.680237 TTGTGTGCGAGCGGGAGG 62.680 66.667 0.00 0.00 0.00 4.30
303 313 0.733909 GAGGCAGCGTGGATTTTTGC 60.734 55.000 0.00 0.00 0.00 3.68
307 317 1.973138 CAGCGTGGATTTTTGCTCAG 58.027 50.000 0.00 0.00 34.99 3.35
311 321 1.798223 CGTGGATTTTTGCTCAGACGA 59.202 47.619 0.00 0.00 0.00 4.20
312 322 2.416547 CGTGGATTTTTGCTCAGACGAT 59.583 45.455 0.00 0.00 0.00 3.73
314 324 3.436704 GTGGATTTTTGCTCAGACGATCA 59.563 43.478 0.00 0.00 0.00 2.92
328 338 1.274167 ACGATCACGGCTGGACTAAAA 59.726 47.619 0.00 0.00 44.46 1.52
336 346 1.608283 GGCTGGACTAAAAGTGAGCGT 60.608 52.381 0.00 0.00 33.32 5.07
350 360 4.308265 AGTGAGCGTCTAGGAAAGTTTTC 58.692 43.478 0.00 0.00 36.46 2.29
367 377 9.244799 GAAAGTTTTCGGAGAAAACACATATTT 57.755 29.630 28.66 21.88 45.90 1.40
370 380 8.013378 AGTTTTCGGAGAAAACACATATTTACG 58.987 33.333 28.66 0.00 45.90 3.18
394 405 8.547894 ACGAAAAATTGGTTTTAGAAGATTTGC 58.452 29.630 0.00 0.00 39.60 3.68
395 406 8.009409 CGAAAAATTGGTTTTAGAAGATTTGCC 58.991 33.333 0.00 0.00 39.60 4.52
470 481 8.535335 TGATTATCAGGGATCTACTAGAAATGC 58.465 37.037 0.00 0.00 0.00 3.56
476 487 7.231722 TCAGGGATCTACTAGAAATGCTCTAAC 59.768 40.741 0.00 0.00 36.17 2.34
513 524 3.418684 TGGAGCTAAACCTCACCTTTC 57.581 47.619 0.00 0.00 33.47 2.62
517 528 1.464997 GCTAAACCTCACCTTTCGCTG 59.535 52.381 0.00 0.00 0.00 5.18
520 531 3.121030 CCTCACCTTTCGCTGCCG 61.121 66.667 0.00 0.00 0.00 5.69
524 535 3.626924 ACCTTTCGCTGCCGGACT 61.627 61.111 5.05 0.00 34.56 3.85
525 536 2.358737 CCTTTCGCTGCCGGACTT 60.359 61.111 5.05 0.00 34.56 3.01
528 539 1.901650 CTTTCGCTGCCGGACTTGAC 61.902 60.000 5.05 0.00 34.56 3.18
530 541 4.680237 CGCTGCCGGACTTGACCA 62.680 66.667 5.05 0.00 0.00 4.02
531 542 3.050275 GCTGCCGGACTTGACCAC 61.050 66.667 5.05 0.00 0.00 4.16
532 543 2.358737 CTGCCGGACTTGACCACC 60.359 66.667 5.05 0.00 0.00 4.61
533 544 2.847234 TGCCGGACTTGACCACCT 60.847 61.111 5.05 0.00 0.00 4.00
534 545 2.047179 GCCGGACTTGACCACCTC 60.047 66.667 5.05 0.00 0.00 3.85
535 546 2.879233 GCCGGACTTGACCACCTCA 61.879 63.158 5.05 0.00 0.00 3.86
536 547 1.983224 CCGGACTTGACCACCTCAT 59.017 57.895 0.00 0.00 0.00 2.90
537 548 0.324943 CCGGACTTGACCACCTCATT 59.675 55.000 0.00 0.00 0.00 2.57
555 566 0.242825 TTAGAGGTGCGAGACGTTGG 59.757 55.000 0.00 0.00 0.00 3.77
558 569 0.731855 GAGGTGCGAGACGTTGGTAC 60.732 60.000 0.00 0.00 0.00 3.34
568 579 2.075761 CGTTGGTACGCTTACTGGC 58.924 57.895 0.00 0.00 41.41 4.85
569 580 1.356527 CGTTGGTACGCTTACTGGCC 61.357 60.000 0.00 0.00 41.41 5.36
570 581 0.320946 GTTGGTACGCTTACTGGCCA 60.321 55.000 4.71 4.71 0.00 5.36
571 582 0.036765 TTGGTACGCTTACTGGCCAG 60.037 55.000 31.60 31.60 0.00 4.85
572 583 1.153429 GGTACGCTTACTGGCCAGG 60.153 63.158 35.42 19.99 0.00 4.45
573 584 1.610554 GGTACGCTTACTGGCCAGGA 61.611 60.000 35.42 27.38 0.00 3.86
574 585 0.179108 GTACGCTTACTGGCCAGGAG 60.179 60.000 35.42 30.00 0.00 3.69
575 586 0.323999 TACGCTTACTGGCCAGGAGA 60.324 55.000 35.42 18.26 0.00 3.71
576 587 1.192146 ACGCTTACTGGCCAGGAGAA 61.192 55.000 35.42 23.68 0.00 2.87
577 588 0.036388 CGCTTACTGGCCAGGAGAAA 60.036 55.000 35.42 21.45 0.00 2.52
578 589 1.407437 CGCTTACTGGCCAGGAGAAAT 60.407 52.381 35.42 16.75 0.00 2.17
579 590 2.158957 CGCTTACTGGCCAGGAGAAATA 60.159 50.000 35.42 15.66 0.00 1.40
580 591 3.206964 GCTTACTGGCCAGGAGAAATAC 58.793 50.000 35.42 15.36 0.00 1.89
581 592 3.370527 GCTTACTGGCCAGGAGAAATACA 60.371 47.826 35.42 10.53 0.00 2.29
582 593 4.687219 GCTTACTGGCCAGGAGAAATACAT 60.687 45.833 35.42 13.72 0.00 2.29
583 594 3.287867 ACTGGCCAGGAGAAATACATG 57.712 47.619 35.42 8.01 0.00 3.21
584 595 2.578021 ACTGGCCAGGAGAAATACATGT 59.422 45.455 35.42 8.72 0.00 3.21
585 596 2.947652 CTGGCCAGGAGAAATACATGTG 59.052 50.000 26.14 0.00 0.00 3.21
586 597 2.308570 TGGCCAGGAGAAATACATGTGT 59.691 45.455 9.11 0.00 0.00 3.72
588 599 2.684881 GCCAGGAGAAATACATGTGTGG 59.315 50.000 9.11 0.00 0.00 4.17
590 601 3.614092 CAGGAGAAATACATGTGTGGCT 58.386 45.455 9.11 2.77 0.00 4.75
591 602 3.624861 CAGGAGAAATACATGTGTGGCTC 59.375 47.826 9.11 11.81 0.00 4.70
592 603 3.264193 AGGAGAAATACATGTGTGGCTCA 59.736 43.478 19.48 0.00 0.00 4.26
594 605 4.274459 GGAGAAATACATGTGTGGCTCATC 59.726 45.833 19.48 6.46 0.00 2.92
595 606 3.873361 AGAAATACATGTGTGGCTCATCG 59.127 43.478 9.11 0.00 0.00 3.84
599 2134 0.391528 CATGTGTGGCTCATCGGTCA 60.392 55.000 0.00 0.00 0.00 4.02
613 2148 3.458163 GTCACCGGGCGAGATCCA 61.458 66.667 6.32 0.00 0.00 3.41
614 2149 2.682136 TCACCGGGCGAGATCCAA 60.682 61.111 6.32 0.00 0.00 3.53
646 3360 0.468214 TGCCAATTTCACCGGGACAA 60.468 50.000 6.32 0.00 0.00 3.18
876 3608 4.503314 CGCCGTACCCGAACCCTC 62.503 72.222 0.00 0.00 35.63 4.30
885 3617 4.143333 CGAACCCTCCCATCGCGT 62.143 66.667 5.77 0.00 0.00 6.01
1752 4495 4.175337 TACATCTGCCAGGCCGCC 62.175 66.667 9.64 0.00 0.00 6.13
1920 4663 2.572284 GTCGAGGACTGGAACGGG 59.428 66.667 0.00 0.00 40.47 5.28
1974 4717 4.270482 ATGCAGGCCATCATGGTG 57.730 55.556 5.01 0.00 40.46 4.17
1983 4726 3.014538 ATCATGGTGGCGGTGGGA 61.015 61.111 0.00 0.00 0.00 4.37
2231 4974 4.072913 CGTGCTCGACGTTATGCT 57.927 55.556 1.00 0.00 43.50 3.79
2232 4975 3.229652 CGTGCTCGACGTTATGCTA 57.770 52.632 1.00 0.00 43.50 3.49
2233 4976 0.838229 CGTGCTCGACGTTATGCTAC 59.162 55.000 1.00 0.00 43.50 3.58
2234 4977 0.838229 GTGCTCGACGTTATGCTACG 59.162 55.000 0.00 5.30 46.52 3.51
2235 4978 0.864377 TGCTCGACGTTATGCTACGC 60.864 55.000 0.00 0.00 45.06 4.42
2236 4979 1.852989 GCTCGACGTTATGCTACGCG 61.853 60.000 3.53 3.53 45.06 6.01
2237 4980 0.588233 CTCGACGTTATGCTACGCGT 60.588 55.000 19.17 19.17 45.06 6.01
2238 4981 0.858548 TCGACGTTATGCTACGCGTG 60.859 55.000 24.59 13.17 45.06 5.34
2239 4982 1.794455 CGACGTTATGCTACGCGTGG 61.794 60.000 24.59 21.81 45.06 4.94
2240 4983 0.799534 GACGTTATGCTACGCGTGGT 60.800 55.000 24.59 6.47 45.06 4.16
2241 4984 0.388907 ACGTTATGCTACGCGTGGTT 60.389 50.000 24.59 13.50 45.06 3.67
2242 4985 0.296642 CGTTATGCTACGCGTGGTTC 59.703 55.000 24.59 7.72 34.45 3.62
2243 4986 1.636988 GTTATGCTACGCGTGGTTCT 58.363 50.000 24.59 10.32 0.00 3.01
2267 5010 4.385358 TTTCTTTTTGGACCTGCTTGTC 57.615 40.909 0.00 0.00 34.42 3.18
2303 5046 1.264749 TGCTCTGCGAGGTGGGTTAT 61.265 55.000 7.50 0.00 0.00 1.89
2504 5247 8.433421 TTTCTTCCGAATCAAATGTATACCTC 57.567 34.615 0.00 0.00 0.00 3.85
2505 5248 6.522054 TCTTCCGAATCAAATGTATACCTCC 58.478 40.000 0.00 0.00 0.00 4.30
2507 5250 6.494666 TCCGAATCAAATGTATACCTCCTT 57.505 37.500 0.00 0.00 0.00 3.36
2508 5251 7.606135 TCCGAATCAAATGTATACCTCCTTA 57.394 36.000 0.00 0.00 0.00 2.69
2509 5252 8.202461 TCCGAATCAAATGTATACCTCCTTAT 57.798 34.615 0.00 0.00 0.00 1.73
2510 5253 8.094548 TCCGAATCAAATGTATACCTCCTTATG 58.905 37.037 0.00 0.00 0.00 1.90
2511 5254 7.878127 CCGAATCAAATGTATACCTCCTTATGT 59.122 37.037 0.00 0.00 0.00 2.29
2513 5256 9.778741 GAATCAAATGTATACCTCCTTATGTGA 57.221 33.333 0.00 0.00 0.00 3.58
2558 5301 5.073428 CAGCTGATATGTACTCCCTCTGTA 58.927 45.833 8.42 0.00 0.00 2.74
2560 5303 5.536916 AGCTGATATGTACTCCCTCTGTAAC 59.463 44.000 0.00 0.00 0.00 2.50
2561 5304 5.536916 GCTGATATGTACTCCCTCTGTAACT 59.463 44.000 0.00 0.00 0.00 2.24
2565 5308 8.910944 TGATATGTACTCCCTCTGTAACTAAAC 58.089 37.037 0.00 0.00 0.00 2.01
2566 5309 5.633830 TGTACTCCCTCTGTAACTAAACG 57.366 43.478 0.00 0.00 0.00 3.60
2570 5313 6.655078 ACTCCCTCTGTAACTAAACGTAAA 57.345 37.500 0.00 0.00 0.00 2.01
2571 5314 6.450545 ACTCCCTCTGTAACTAAACGTAAAC 58.549 40.000 0.00 0.00 0.00 2.01
2574 5317 4.919754 CCTCTGTAACTAAACGTAAACGCT 59.080 41.667 1.74 0.00 44.43 5.07
2575 5318 5.060200 CCTCTGTAACTAAACGTAAACGCTC 59.940 44.000 1.74 0.00 44.43 5.03
2579 5322 8.023128 TCTGTAACTAAACGTAAACGCTCTTAT 58.977 33.333 1.74 0.00 44.43 1.73
2590 5333 8.526681 ACGTAAACGCTCTTATATTTCTTTACG 58.473 33.333 14.48 14.48 45.27 3.18
2591 5334 7.994894 CGTAAACGCTCTTATATTTCTTTACGG 59.005 37.037 10.14 0.00 40.27 4.02
2592 5335 9.023967 GTAAACGCTCTTATATTTCTTTACGGA 57.976 33.333 0.00 0.00 0.00 4.69
2593 5336 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
2594 5337 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
2595 5338 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2599 5342 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
2609 5352 2.100418 ACGGAGGGAGTAATCTAAACGC 59.900 50.000 0.00 0.00 0.00 4.84
2742 5486 6.183360 GCTTGCTGATGTCTTCTTGATATGTT 60.183 38.462 0.00 0.00 0.00 2.71
2772 5517 9.379791 CTTTTTACCCTACTTATCATCGAACTT 57.620 33.333 0.00 0.00 0.00 2.66
2835 5690 0.109226 GCGTTTCGTCAGGAGTAGCT 60.109 55.000 0.00 0.00 0.00 3.32
2836 5691 1.131883 GCGTTTCGTCAGGAGTAGCTA 59.868 52.381 0.00 0.00 0.00 3.32
2837 5692 2.791849 GCGTTTCGTCAGGAGTAGCTAG 60.792 54.545 0.00 0.00 0.00 3.42
2838 5693 2.791849 CGTTTCGTCAGGAGTAGCTAGC 60.792 54.545 6.62 6.62 0.00 3.42
2839 5694 2.124277 TTCGTCAGGAGTAGCTAGCA 57.876 50.000 18.83 0.00 0.00 3.49
2841 5696 2.222886 TCGTCAGGAGTAGCTAGCATC 58.777 52.381 18.83 11.52 0.00 3.91
2842 5697 1.950216 CGTCAGGAGTAGCTAGCATCA 59.050 52.381 18.83 0.00 0.00 3.07
2843 5698 2.287308 CGTCAGGAGTAGCTAGCATCAC 60.287 54.545 18.83 11.52 0.00 3.06
2897 5753 3.724374 AGCTCGTGTGCTAAGTTTGTTA 58.276 40.909 0.00 0.00 42.10 2.41
2957 5813 7.949903 TGAACCATTTTCATCTTGTTTGATG 57.050 32.000 0.00 0.00 43.66 3.07
2995 5853 3.072944 ACTGCTTGCTGATGTCTTCTTC 58.927 45.455 6.50 0.00 0.00 2.87
3012 5870 9.567776 TGTCTTCTTCATATGTGTTCCTTTTTA 57.432 29.630 1.90 0.00 0.00 1.52
3117 5975 4.262592 GGTCCAACAAGATGAAAATGGCTT 60.263 41.667 0.00 0.00 0.00 4.35
3142 6000 2.823924 TAGCTCGTGTGCCAAGTTTA 57.176 45.000 0.00 0.00 0.00 2.01
3181 6039 3.443681 ACTGTCAACTTGTTGGACCAAAG 59.556 43.478 8.94 6.43 0.00 2.77
3184 6042 3.192633 GTCAACTTGTTGGACCAAAGTGT 59.807 43.478 8.94 5.02 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.892755 ACAACATTGCCCATGCTGAG 59.107 50.000 3.95 0.00 36.14 3.35
8 9 3.189285 GACAATACAACATTGCCCATGC 58.811 45.455 0.00 0.00 36.14 4.06
11 12 2.486203 GACGACAATACAACATTGCCCA 59.514 45.455 0.00 0.00 32.55 5.36
18 19 0.318869 ACCGCGACGACAATACAACA 60.319 50.000 8.23 0.00 0.00 3.33
45 46 1.734477 CGAAGTCGGTCACCAGCAG 60.734 63.158 0.00 0.00 35.37 4.24
56 57 1.206745 ACAGTGCAACGTCGAAGTCG 61.207 55.000 4.00 0.00 45.86 4.18
58 59 0.179121 TGACAGTGCAACGTCGAAGT 60.179 50.000 0.00 0.00 45.86 3.01
60 61 1.577468 AATGACAGTGCAACGTCGAA 58.423 45.000 0.00 0.00 45.86 3.71
66 67 7.096065 GGAAGAAATAACAAATGACAGTGCAAC 60.096 37.037 0.00 0.00 0.00 4.17
72 73 6.587608 GCAAGGGAAGAAATAACAAATGACAG 59.412 38.462 0.00 0.00 0.00 3.51
77 78 6.267471 TGACAGCAAGGGAAGAAATAACAAAT 59.733 34.615 0.00 0.00 0.00 2.32
78 79 5.596361 TGACAGCAAGGGAAGAAATAACAAA 59.404 36.000 0.00 0.00 0.00 2.83
102 103 3.055719 CGCCACCGCAGAAATGGT 61.056 61.111 0.00 0.00 39.66 3.55
131 132 4.329545 AGACACAACGGCGGCCAT 62.330 61.111 20.71 0.00 0.00 4.40
135 136 2.738521 CTGGAGACACAACGGCGG 60.739 66.667 13.24 0.00 35.60 6.13
138 139 2.022129 GACGCTGGAGACACAACGG 61.022 63.158 0.00 0.00 35.60 4.44
141 142 1.007734 GTCGACGCTGGAGACACAA 60.008 57.895 0.00 0.00 35.19 3.33
155 156 2.264480 CCTTGGCACCATCGTCGA 59.736 61.111 0.00 0.00 0.00 4.20
159 160 3.443045 GCACCCTTGGCACCATCG 61.443 66.667 0.00 0.00 0.00 3.84
179 180 3.127548 CAGAATGAAAATGTCGTCCCCTG 59.872 47.826 0.00 0.00 39.69 4.45
180 181 3.347216 CAGAATGAAAATGTCGTCCCCT 58.653 45.455 0.00 0.00 39.69 4.79
185 186 1.468520 CCGGCAGAATGAAAATGTCGT 59.531 47.619 0.00 0.00 40.28 4.34
187 188 2.487762 TGACCGGCAGAATGAAAATGTC 59.512 45.455 0.00 0.00 39.69 3.06
225 226 0.042131 ACCCCTATCCTCACCGTCAA 59.958 55.000 0.00 0.00 0.00 3.18
228 229 1.382695 CCACCCCTATCCTCACCGT 60.383 63.158 0.00 0.00 0.00 4.83
258 259 1.959226 CACACAACCTTCCCGTCCG 60.959 63.158 0.00 0.00 0.00 4.79
261 262 2.590575 CGCACACAACCTTCCCGT 60.591 61.111 0.00 0.00 0.00 5.28
262 263 2.280524 TCGCACACAACCTTCCCG 60.281 61.111 0.00 0.00 0.00 5.14
269 270 3.414700 CTCCCGCTCGCACACAAC 61.415 66.667 0.00 0.00 0.00 3.32
270 271 4.680237 CCTCCCGCTCGCACACAA 62.680 66.667 0.00 0.00 0.00 3.33
287 297 0.039256 TGAGCAAAAATCCACGCTGC 60.039 50.000 0.00 0.00 34.12 5.25
290 300 1.725931 CGTCTGAGCAAAAATCCACGC 60.726 52.381 0.00 0.00 0.00 5.34
291 301 1.798223 TCGTCTGAGCAAAAATCCACG 59.202 47.619 0.00 0.00 0.00 4.94
295 305 3.484229 CCGTGATCGTCTGAGCAAAAATC 60.484 47.826 0.00 0.00 43.13 2.17
303 313 1.226802 CCAGCCGTGATCGTCTGAG 60.227 63.158 0.41 0.00 44.28 3.35
307 317 0.454600 TTAGTCCAGCCGTGATCGTC 59.545 55.000 0.00 0.00 35.01 4.20
311 321 2.301870 TCACTTTTAGTCCAGCCGTGAT 59.698 45.455 0.00 0.00 0.00 3.06
312 322 1.689813 TCACTTTTAGTCCAGCCGTGA 59.310 47.619 0.00 0.00 0.00 4.35
314 324 1.608283 GCTCACTTTTAGTCCAGCCGT 60.608 52.381 0.00 0.00 29.09 5.68
328 338 4.308265 GAAAACTTTCCTAGACGCTCACT 58.692 43.478 0.00 0.00 0.00 3.41
336 346 6.259387 GTGTTTTCTCCGAAAACTTTCCTAGA 59.741 38.462 24.19 6.98 39.97 2.43
350 360 8.716619 TTTTTCGTAAATATGTGTTTTCTCCG 57.283 30.769 0.00 0.00 0.00 4.63
370 380 9.056005 AGGCAAATCTTCTAAAACCAATTTTTC 57.944 29.630 0.00 0.00 38.91 2.29
449 460 6.322126 AGAGCATTTCTAGTAGATCCCTGAT 58.678 40.000 0.00 0.00 33.23 2.90
451 462 7.014711 TGTTAGAGCATTTCTAGTAGATCCCTG 59.985 40.741 0.00 0.00 39.50 4.45
494 505 2.347731 CGAAAGGTGAGGTTTAGCTCC 58.652 52.381 6.50 0.00 0.00 4.70
513 524 4.680237 TGGTCAAGTCCGGCAGCG 62.680 66.667 0.00 0.00 0.00 5.18
517 528 2.047179 GAGGTGGTCAAGTCCGGC 60.047 66.667 0.00 0.00 0.00 6.13
520 531 4.130286 CTCTAATGAGGTGGTCAAGTCC 57.870 50.000 0.00 0.00 39.19 3.85
532 543 1.402259 ACGTCTCGCACCTCTAATGAG 59.598 52.381 0.00 0.00 39.92 2.90
533 544 1.460504 ACGTCTCGCACCTCTAATGA 58.539 50.000 0.00 0.00 0.00 2.57
534 545 1.920574 CAACGTCTCGCACCTCTAATG 59.079 52.381 0.00 0.00 0.00 1.90
535 546 1.135083 CCAACGTCTCGCACCTCTAAT 60.135 52.381 0.00 0.00 0.00 1.73
536 547 0.242825 CCAACGTCTCGCACCTCTAA 59.757 55.000 0.00 0.00 0.00 2.10
537 548 0.892358 ACCAACGTCTCGCACCTCTA 60.892 55.000 0.00 0.00 0.00 2.43
555 566 0.179108 CTCCTGGCCAGTAAGCGTAC 60.179 60.000 30.63 1.07 0.00 3.67
558 569 0.036388 TTTCTCCTGGCCAGTAAGCG 60.036 55.000 30.63 15.44 0.00 4.68
560 571 4.487714 TGTATTTCTCCTGGCCAGTAAG 57.512 45.455 30.63 25.30 0.00 2.34
562 573 3.780294 ACATGTATTTCTCCTGGCCAGTA 59.220 43.478 30.63 15.68 0.00 2.74
564 575 2.947652 CACATGTATTTCTCCTGGCCAG 59.052 50.000 26.87 26.87 0.00 4.85
565 576 2.308570 ACACATGTATTTCTCCTGGCCA 59.691 45.455 4.71 4.71 0.00 5.36
566 577 2.684881 CACACATGTATTTCTCCTGGCC 59.315 50.000 0.00 0.00 0.00 5.36
568 579 2.684881 GCCACACATGTATTTCTCCTGG 59.315 50.000 0.00 0.00 0.00 4.45
569 580 3.614092 AGCCACACATGTATTTCTCCTG 58.386 45.455 0.00 0.00 0.00 3.86
570 581 3.264193 TGAGCCACACATGTATTTCTCCT 59.736 43.478 0.00 0.00 0.00 3.69
571 582 3.609853 TGAGCCACACATGTATTTCTCC 58.390 45.455 0.00 0.00 0.00 3.71
572 583 4.025396 CGATGAGCCACACATGTATTTCTC 60.025 45.833 0.00 4.34 0.00 2.87
573 584 3.873361 CGATGAGCCACACATGTATTTCT 59.127 43.478 0.00 0.00 0.00 2.52
574 585 3.002656 CCGATGAGCCACACATGTATTTC 59.997 47.826 0.00 0.00 0.00 2.17
575 586 2.945008 CCGATGAGCCACACATGTATTT 59.055 45.455 0.00 0.00 0.00 1.40
576 587 2.092968 ACCGATGAGCCACACATGTATT 60.093 45.455 0.00 0.00 0.00 1.89
577 588 1.486310 ACCGATGAGCCACACATGTAT 59.514 47.619 0.00 0.00 0.00 2.29
578 589 0.901827 ACCGATGAGCCACACATGTA 59.098 50.000 0.00 0.00 0.00 2.29
579 590 0.391661 GACCGATGAGCCACACATGT 60.392 55.000 0.00 0.00 0.00 3.21
580 591 0.391528 TGACCGATGAGCCACACATG 60.392 55.000 0.00 0.00 0.00 3.21
581 592 0.391661 GTGACCGATGAGCCACACAT 60.392 55.000 0.00 0.00 0.00 3.21
582 593 1.005037 GTGACCGATGAGCCACACA 60.005 57.895 0.00 0.00 0.00 3.72
583 594 1.741770 GGTGACCGATGAGCCACAC 60.742 63.158 0.00 0.00 0.00 3.82
584 595 2.662596 GGTGACCGATGAGCCACA 59.337 61.111 0.00 0.00 0.00 4.17
595 606 4.222847 GGATCTCGCCCGGTGACC 62.223 72.222 0.00 0.00 0.00 4.02
599 2134 3.470888 CCTTGGATCTCGCCCGGT 61.471 66.667 0.00 0.00 0.00 5.28
610 2145 0.469144 GCACTTTTGTCCCCCTTGGA 60.469 55.000 0.00 0.00 42.41 3.53
613 2148 0.031616 TTGGCACTTTTGTCCCCCTT 60.032 50.000 0.00 0.00 25.89 3.95
614 2149 0.190815 ATTGGCACTTTTGTCCCCCT 59.809 50.000 0.00 0.00 25.89 4.79
646 3360 1.608717 TTGTTTGCGTGTTGGCCCTT 61.609 50.000 0.00 0.00 0.00 3.95
1752 4495 2.504244 GCGACGTCGAGGAAGTGG 60.504 66.667 39.74 9.55 43.02 4.00
1902 4645 2.572284 CCGTTCCAGTCCTCGACC 59.428 66.667 0.00 0.00 32.18 4.79
1983 4726 2.737180 CTCACCCTGTCGCACACT 59.263 61.111 0.00 0.00 0.00 3.55
2169 4912 2.547826 GCCTAATGGTAGAACACGACC 58.452 52.381 0.00 0.00 36.17 4.79
2230 4973 2.673833 AGAAAAGAGAACCACGCGTAG 58.326 47.619 13.44 7.50 0.00 3.51
2231 4974 2.806608 AGAAAAGAGAACCACGCGTA 57.193 45.000 13.44 0.00 0.00 4.42
2232 4975 1.949465 AAGAAAAGAGAACCACGCGT 58.051 45.000 5.58 5.58 0.00 6.01
2233 4976 3.334272 AAAAGAAAAGAGAACCACGCG 57.666 42.857 3.53 3.53 0.00 6.01
2234 4977 3.796717 CCAAAAAGAAAAGAGAACCACGC 59.203 43.478 0.00 0.00 0.00 5.34
2235 4978 5.034797 GTCCAAAAAGAAAAGAGAACCACG 58.965 41.667 0.00 0.00 0.00 4.94
2236 4979 5.127194 AGGTCCAAAAAGAAAAGAGAACCAC 59.873 40.000 0.00 0.00 0.00 4.16
2237 4980 5.127031 CAGGTCCAAAAAGAAAAGAGAACCA 59.873 40.000 0.00 0.00 0.00 3.67
2238 4981 5.592054 CAGGTCCAAAAAGAAAAGAGAACC 58.408 41.667 0.00 0.00 0.00 3.62
2239 4982 5.043903 GCAGGTCCAAAAAGAAAAGAGAAC 58.956 41.667 0.00 0.00 0.00 3.01
2240 4983 4.956075 AGCAGGTCCAAAAAGAAAAGAGAA 59.044 37.500 0.00 0.00 0.00 2.87
2241 4984 4.536765 AGCAGGTCCAAAAAGAAAAGAGA 58.463 39.130 0.00 0.00 0.00 3.10
2242 4985 4.926140 AGCAGGTCCAAAAAGAAAAGAG 57.074 40.909 0.00 0.00 0.00 2.85
2243 4986 4.466015 ACAAGCAGGTCCAAAAAGAAAAGA 59.534 37.500 0.00 0.00 0.00 2.52
2267 5010 3.750130 AGAGCACATTTTACACTGAGCAG 59.250 43.478 0.00 0.00 32.31 4.24
2504 5247 2.094545 GGCAGCAAGGTTTCACATAAGG 60.095 50.000 0.00 0.00 0.00 2.69
2505 5248 2.557924 TGGCAGCAAGGTTTCACATAAG 59.442 45.455 0.00 0.00 0.00 1.73
2507 5250 1.885887 GTGGCAGCAAGGTTTCACATA 59.114 47.619 0.00 0.00 0.00 2.29
2508 5251 0.675633 GTGGCAGCAAGGTTTCACAT 59.324 50.000 0.00 0.00 0.00 3.21
2509 5252 0.395586 AGTGGCAGCAAGGTTTCACA 60.396 50.000 0.00 0.00 0.00 3.58
2510 5253 1.604604 TAGTGGCAGCAAGGTTTCAC 58.395 50.000 0.00 0.00 0.00 3.18
2511 5254 2.161855 CATAGTGGCAGCAAGGTTTCA 58.838 47.619 0.00 0.00 0.00 2.69
2513 5256 2.584835 TCATAGTGGCAGCAAGGTTT 57.415 45.000 0.00 0.00 0.00 3.27
2514 5257 2.814805 ATCATAGTGGCAGCAAGGTT 57.185 45.000 0.00 0.00 0.00 3.50
2515 5258 2.025981 TGAATCATAGTGGCAGCAAGGT 60.026 45.455 0.00 0.00 0.00 3.50
2565 5308 7.994894 CCGTAAAGAAATATAAGAGCGTTTACG 59.005 37.037 14.08 14.08 45.42 3.18
2566 5309 9.023967 TCCGTAAAGAAATATAAGAGCGTTTAC 57.976 33.333 0.00 0.00 0.00 2.01
2570 5313 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2571 5314 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2574 5317 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2579 5322 7.909485 AGATTACTCCCTCCGTAAAGAAATA 57.091 36.000 0.00 0.00 31.36 1.40
2582 5325 7.550712 GTTTAGATTACTCCCTCCGTAAAGAA 58.449 38.462 0.00 0.00 31.36 2.52
2583 5326 6.183360 CGTTTAGATTACTCCCTCCGTAAAGA 60.183 42.308 0.00 0.00 31.36 2.52
2587 5330 3.316308 GCGTTTAGATTACTCCCTCCGTA 59.684 47.826 0.00 0.00 0.00 4.02
2588 5331 2.100418 GCGTTTAGATTACTCCCTCCGT 59.900 50.000 0.00 0.00 0.00 4.69
2589 5332 2.361438 AGCGTTTAGATTACTCCCTCCG 59.639 50.000 0.00 0.00 0.00 4.63
2590 5333 3.637694 AGAGCGTTTAGATTACTCCCTCC 59.362 47.826 0.00 0.00 0.00 4.30
2591 5334 4.922471 AGAGCGTTTAGATTACTCCCTC 57.078 45.455 0.00 0.00 0.00 4.30
2592 5335 6.980416 ATAAGAGCGTTTAGATTACTCCCT 57.020 37.500 0.00 0.00 0.00 4.20
2593 5336 9.708092 AAATATAAGAGCGTTTAGATTACTCCC 57.292 33.333 4.35 0.00 0.00 4.30
2626 5369 7.064229 CCTAAGAGAAACTACATACTCCCTCT 58.936 42.308 0.00 0.00 0.00 3.69
2742 5486 9.370930 TCGATGATAAGTAGGGTAAAAAGGATA 57.629 33.333 0.00 0.00 0.00 2.59
2772 5517 4.283467 ACACTGTTATCCTGTTAGCTCACA 59.717 41.667 0.00 0.00 0.00 3.58
2835 5690 3.072330 TCTTGTTGGACCAAGTGATGCTA 59.928 43.478 7.31 0.00 42.01 3.49
2836 5691 2.158623 TCTTGTTGGACCAAGTGATGCT 60.159 45.455 7.31 0.00 42.01 3.79
2837 5692 2.229792 TCTTGTTGGACCAAGTGATGC 58.770 47.619 7.31 0.00 42.01 3.91
2838 5693 4.074259 TCATCTTGTTGGACCAAGTGATG 58.926 43.478 24.11 24.11 42.01 3.07
2839 5694 4.371624 TCATCTTGTTGGACCAAGTGAT 57.628 40.909 7.31 8.71 42.01 3.06
2841 5696 4.916983 TTTCATCTTGTTGGACCAAGTG 57.083 40.909 7.31 0.92 42.01 3.16
2842 5697 5.221501 CCATTTTCATCTTGTTGGACCAAGT 60.222 40.000 7.31 0.00 42.01 3.16
2843 5698 5.221501 ACCATTTTCATCTTGTTGGACCAAG 60.222 40.000 7.31 0.00 42.57 3.61
2897 5753 5.360714 ACACTGACAATGGTTCAAACTCATT 59.639 36.000 0.00 4.68 33.24 2.57
2957 5813 5.629079 AGCAGTAAAATAAGGCTTCACAC 57.371 39.130 1.30 0.00 0.00 3.82
2995 5853 8.575649 AAGTAGGGTAAAAAGGAACACATATG 57.424 34.615 0.00 0.00 0.00 1.78
3012 5870 5.535406 CCACTAGTTCGATGATAAGTAGGGT 59.465 44.000 0.00 0.00 33.27 4.34
3072 5930 3.542712 AAGTGATGCTACGCAAACAAG 57.457 42.857 0.00 0.00 43.62 3.16
3074 5932 2.031245 CCAAAGTGATGCTACGCAAACA 60.031 45.455 0.00 0.00 43.62 2.83
3087 5945 4.163441 TCATCTTGTTGGACCAAAGTGA 57.837 40.909 8.94 7.56 0.00 3.41
3117 5975 2.177394 TGGCACACGAGCTAAATTCA 57.823 45.000 0.00 0.00 34.17 2.57
3142 6000 5.132502 TGACAGTGGTTCAAACTCATCAAT 58.867 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.