Multiple sequence alignment - TraesCS4A01G228100

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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 TraesCS4A01G228100 chr4A 100.000 4066 0 0 1 4066 536773767 536769702 0.000000e+00 7509.0
1 TraesCS4A01G228100 chr4B 92.972 1366 66 14 181 1536 89054584 89055929 0.000000e+00 1964.0
2 TraesCS4A01G228100 chr4B 90.702 1054 42 14 2496 3500 89057395 89058441 0.000000e+00 1352.0
3 TraesCS4A01G228100 chr4B 95.936 566 23 0 3501 4066 454996098 454995533 0.000000e+00 918.0
4 TraesCS4A01G228100 chr4B 88.190 525 20 19 1582 2072 89055935 89056451 4.530000e-164 588.0
5 TraesCS4A01G228100 chr4B 90.881 329 16 14 2159 2482 89057093 89057412 2.900000e-116 429.0
6 TraesCS4A01G228100 chr4B 95.161 186 8 1 1 186 89052257 89052441 3.980000e-75 292.0
7 TraesCS4A01G228100 chr4B 96.429 56 1 1 2099 2153 89056985 89057040 1.560000e-14 91.6
8 TraesCS4A01G228100 chr4D 93.476 1027 41 6 2496 3501 59645133 59646154 0.000000e+00 1502.0
9 TraesCS4A01G228100 chr4D 93.396 530 24 3 1 528 59641894 59642414 0.000000e+00 774.0
10 TraesCS4A01G228100 chr4D 89.769 606 29 9 928 1526 59642960 59643539 0.000000e+00 745.0
11 TraesCS4A01G228100 chr4D 96.183 393 11 2 511 901 59642573 59642963 1.230000e-179 640.0
12 TraesCS4A01G228100 chr4D 94.161 411 12 4 1685 2088 59643678 59644083 2.080000e-172 616.0
13 TraesCS4A01G228100 chr4D 92.642 299 12 7 2188 2482 59644858 59645150 4.860000e-114 422.0
14 TraesCS4A01G228100 chr4D 93.651 63 1 3 2101 2160 59644302 59644364 1.560000e-14 91.6
15 TraesCS4A01G228100 chr3A 96.837 569 18 0 3498 4066 235445843 235446411 0.000000e+00 952.0
16 TraesCS4A01G228100 chr3B 95.782 569 24 0 3498 4066 574345130 574345698 0.000000e+00 918.0
17 TraesCS4A01G228100 chr5B 94.876 566 29 0 3501 4066 270872859 270872294 0.000000e+00 885.0
18 TraesCS4A01G228100 chr5B 94.876 566 26 2 3501 4066 377211730 377211168 0.000000e+00 881.0
19 TraesCS4A01G228100 chr2A 93.827 567 34 1 3498 4064 60719445 60720010 0.000000e+00 852.0
20 TraesCS4A01G228100 chr2A 91.135 564 50 0 3501 4064 605019891 605019328 0.000000e+00 765.0
21 TraesCS4A01G228100 chrUn 93.794 564 35 0 3501 4064 231018042 231017479 0.000000e+00 848.0
22 TraesCS4A01G228100 chrUn 93.085 564 39 0 3501 4064 204481695 204481132 0.000000e+00 826.0


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 TraesCS4A01G228100 chr4A 536769702 536773767 4065 True 7509.000000 7509 100.000000 1 4066 1 chr4A.!!$R1 4065
1 TraesCS4A01G228100 chr4B 454995533 454996098 565 True 918.000000 918 95.936000 3501 4066 1 chr4B.!!$R1 565
2 TraesCS4A01G228100 chr4B 89052257 89058441 6184 False 786.100000 1964 92.389167 1 3500 6 chr4B.!!$F1 3499
3 TraesCS4A01G228100 chr4D 59641894 59646154 4260 False 684.371429 1502 93.325429 1 3501 7 chr4D.!!$F1 3500
4 TraesCS4A01G228100 chr3A 235445843 235446411 568 False 952.000000 952 96.837000 3498 4066 1 chr3A.!!$F1 568
5 TraesCS4A01G228100 chr3B 574345130 574345698 568 False 918.000000 918 95.782000 3498 4066 1 chr3B.!!$F1 568
6 TraesCS4A01G228100 chr5B 270872294 270872859 565 True 885.000000 885 94.876000 3501 4066 1 chr5B.!!$R1 565
7 TraesCS4A01G228100 chr5B 377211168 377211730 562 True 881.000000 881 94.876000 3501 4066 1 chr5B.!!$R2 565
8 TraesCS4A01G228100 chr2A 60719445 60720010 565 False 852.000000 852 93.827000 3498 4064 1 chr2A.!!$F1 566
9 TraesCS4A01G228100 chr2A 605019328 605019891 563 True 765.000000 765 91.135000 3501 4064 1 chr2A.!!$R1 563
10 TraesCS4A01G228100 chrUn 231017479 231018042 563 True 848.000000 848 93.794000 3501 4064 1 chrUn.!!$R2 563
11 TraesCS4A01G228100 chrUn 204481132 204481695 563 True 826.000000 826 93.085000 3501 4064 1 chrUn.!!$R1 563

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
914 3244 0.606096 TTCATCGACCAGAAAGCCGA 59.394 50.0 0.00 0.0 35.43 5.54 F
1877 4252 0.032815 TAGCTAGCGTTGCACACACA 59.967 50.0 9.55 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 5600 0.460811 GTGCCATGATCAGCGAGTGA 60.461 55.0 0.09 0.0 40.38 3.41 R
3083 6498 0.454620 GACACTGCTGGTAGACGTCG 60.455 60.0 10.46 0.0 0.00 5.12 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
46 49 1.614413 AGTTGAGAGAAGGGTCACGAC 59.386 52.381 0.00 0.00 0.00 4.34
85 88 4.632153 ACGTGGCATATATTCACTTCCTC 58.368 43.478 11.81 0.00 0.00 3.71
193 2344 2.035632 AGCAATCCTCTAACCTCTCCG 58.964 52.381 0.00 0.00 0.00 4.63
194 2345 1.539280 GCAATCCTCTAACCTCTCCGC 60.539 57.143 0.00 0.00 0.00 5.54
203 2354 2.295253 AACCTCTCCGCTTATTCACG 57.705 50.000 0.00 0.00 0.00 4.35
377 2528 7.084268 AGGAAAAGCATATATCCTTACTGCT 57.916 36.000 0.00 0.00 44.62 4.24
385 2536 6.628398 GCATATATCCTTACTGCTACCACCTC 60.628 46.154 0.00 0.00 0.00 3.85
411 2562 2.472695 TTGCACTGCACTAGGGTTAG 57.527 50.000 2.26 0.00 38.71 2.34
422 2573 6.101332 TGCACTAGGGTTAGTTAAATACACG 58.899 40.000 0.00 0.00 38.05 4.49
441 2592 1.531677 CGGCATGCAACCACTAAATCG 60.532 52.381 21.36 5.06 0.00 3.34
460 2611 1.069227 CGCCTTACAAACAACTCTGGC 60.069 52.381 0.00 0.00 36.14 4.85
493 2644 8.918202 AGGTCTTCTTTTTGACATTGTATGTA 57.082 30.769 0.00 0.00 45.03 2.29
494 2645 9.003658 AGGTCTTCTTTTTGACATTGTATGTAG 57.996 33.333 0.00 0.00 45.03 2.74
495 2646 8.237267 GGTCTTCTTTTTGACATTGTATGTAGG 58.763 37.037 0.00 0.00 45.03 3.18
496 2647 8.999431 GTCTTCTTTTTGACATTGTATGTAGGA 58.001 33.333 0.00 0.00 45.03 2.94
497 2648 9.219603 TCTTCTTTTTGACATTGTATGTAGGAG 57.780 33.333 0.00 0.00 45.03 3.69
604 2931 6.157994 TCCTAGGTAGCAGAACAAATACCATT 59.842 38.462 9.08 0.00 40.16 3.16
607 2934 9.561069 CTAGGTAGCAGAACAAATACCATTATT 57.439 33.333 3.31 0.00 40.16 1.40
608 2935 8.823220 AGGTAGCAGAACAAATACCATTATTT 57.177 30.769 3.31 0.00 40.16 1.40
627 2957 7.672983 TTATTTGGAGAGCAAAGTACAGAAG 57.327 36.000 0.00 0.00 0.00 2.85
770 3100 2.124983 CATGTGGCTCCACCTCCG 60.125 66.667 15.76 0.00 45.63 4.63
785 3115 1.477295 CCTCCGTTTCCTACTCACTCC 59.523 57.143 0.00 0.00 0.00 3.85
912 3242 2.098117 CCATTTCATCGACCAGAAAGCC 59.902 50.000 12.94 0.00 37.19 4.35
913 3243 1.438651 TTTCATCGACCAGAAAGCCG 58.561 50.000 5.67 0.00 30.80 5.52
914 3244 0.606096 TTCATCGACCAGAAAGCCGA 59.394 50.000 0.00 0.00 35.43 5.54
915 3245 0.606096 TCATCGACCAGAAAGCCGAA 59.394 50.000 0.00 0.00 34.59 4.30
946 3276 2.781757 TCCATCCATTTCTCTGCCTCAT 59.218 45.455 0.00 0.00 0.00 2.90
947 3277 3.147629 CCATCCATTTCTCTGCCTCATC 58.852 50.000 0.00 0.00 0.00 2.92
951 3281 3.134262 TCCATTTCTCTGCCTCATCTCAG 59.866 47.826 0.00 0.00 0.00 3.35
1015 3345 1.956629 AAGCATGAGCAATGGCAGCC 61.957 55.000 3.66 3.66 45.49 4.85
1053 3383 1.303398 TTCGGTCTGCTCGAGGTCT 60.303 57.895 15.58 0.00 37.93 3.85
1084 3414 6.489675 GTGATTGCTAACCAGTTGACATATG 58.510 40.000 0.00 0.00 0.00 1.78
1085 3415 6.094048 GTGATTGCTAACCAGTTGACATATGT 59.906 38.462 8.43 8.43 0.00 2.29
1129 3472 4.569966 GTCAGCCTGTATTGTGATCTTCAG 59.430 45.833 0.00 0.00 0.00 3.02
1130 3473 4.223700 TCAGCCTGTATTGTGATCTTCAGT 59.776 41.667 0.00 0.00 0.00 3.41
1139 3482 7.879677 TGTATTGTGATCTTCAGTTCTTCACAT 59.120 33.333 5.04 0.15 44.25 3.21
1171 3514 3.424829 GCCTGATCGTGTTTGTGTATGTG 60.425 47.826 0.00 0.00 0.00 3.21
1172 3515 3.424829 CCTGATCGTGTTTGTGTATGTGC 60.425 47.826 0.00 0.00 0.00 4.57
1178 3521 1.068679 TGTTTGTGTATGTGCGCCATG 60.069 47.619 18.08 0.00 34.86 3.66
1181 3524 1.748879 GTGTATGTGCGCCATGGGT 60.749 57.895 15.13 0.00 34.86 4.51
1548 3891 9.678941 TTCTATAGTACTACATTCATTTCTGCG 57.321 33.333 4.31 0.00 0.00 5.18
1549 3892 9.063615 TCTATAGTACTACATTCATTTCTGCGA 57.936 33.333 4.31 0.00 0.00 5.10
1550 3893 7.932120 ATAGTACTACATTCATTTCTGCGAC 57.068 36.000 4.31 0.00 0.00 5.19
1551 3894 5.720202 AGTACTACATTCATTTCTGCGACA 58.280 37.500 0.00 0.00 0.00 4.35
1552 3895 6.163476 AGTACTACATTCATTTCTGCGACAA 58.837 36.000 0.00 0.00 0.00 3.18
1553 3896 5.940192 ACTACATTCATTTCTGCGACAAA 57.060 34.783 0.00 0.00 0.00 2.83
1554 3897 6.500684 ACTACATTCATTTCTGCGACAAAT 57.499 33.333 0.00 0.00 0.00 2.32
1555 3898 7.609760 ACTACATTCATTTCTGCGACAAATA 57.390 32.000 0.00 0.00 0.00 1.40
1556 3899 8.039603 ACTACATTCATTTCTGCGACAAATAA 57.960 30.769 0.00 0.00 0.00 1.40
1557 3900 8.677300 ACTACATTCATTTCTGCGACAAATAAT 58.323 29.630 0.00 0.00 0.00 1.28
1558 3901 9.507280 CTACATTCATTTCTGCGACAAATAATT 57.493 29.630 0.00 0.00 0.00 1.40
1559 3902 8.398491 ACATTCATTTCTGCGACAAATAATTC 57.602 30.769 0.00 0.00 0.00 2.17
1560 3903 7.218773 ACATTCATTTCTGCGACAAATAATTCG 59.781 33.333 0.00 0.00 38.31 3.34
1561 3904 6.415798 TCATTTCTGCGACAAATAATTCGA 57.584 33.333 0.00 0.00 37.43 3.71
1562 3905 6.477742 TCATTTCTGCGACAAATAATTCGAG 58.522 36.000 0.00 0.00 37.43 4.04
1563 3906 3.925688 TCTGCGACAAATAATTCGAGC 57.074 42.857 0.00 0.00 37.43 5.03
1564 3907 2.607635 TCTGCGACAAATAATTCGAGCC 59.392 45.455 0.00 0.00 37.43 4.70
1565 3908 1.326245 TGCGACAAATAATTCGAGCCG 59.674 47.619 0.00 0.00 37.43 5.52
1566 3909 1.332904 GCGACAAATAATTCGAGCCGG 60.333 52.381 0.00 0.00 37.43 6.13
1567 3910 2.198406 CGACAAATAATTCGAGCCGGA 58.802 47.619 5.05 0.00 37.43 5.14
1568 3911 2.605818 CGACAAATAATTCGAGCCGGAA 59.394 45.455 5.05 0.00 37.43 4.30
1569 3912 3.302480 CGACAAATAATTCGAGCCGGAAG 60.302 47.826 5.05 0.00 37.43 3.46
1570 3913 6.300369 CGACAAATAATTCGAGCCGGAAGG 62.300 50.000 5.05 0.00 46.15 3.46
1619 3962 2.839486 TTTGCTGTAGAGGTGTCTGG 57.161 50.000 0.00 0.00 33.84 3.86
1642 3985 0.521735 GTGATTTGGGCTCACGAACC 59.478 55.000 0.00 0.00 34.24 3.62
1652 3997 2.329379 GCTCACGAACCAGAAGTGTAG 58.671 52.381 0.00 0.00 37.20 2.74
1803 4178 1.007502 CCAACCCAACACATGTGCG 60.008 57.895 25.68 16.44 0.00 5.34
1874 4249 1.696832 GCCTAGCTAGCGTTGCACAC 61.697 60.000 15.74 0.00 0.00 3.82
1875 4250 0.389817 CCTAGCTAGCGTTGCACACA 60.390 55.000 15.74 0.00 0.00 3.72
1876 4251 0.716108 CTAGCTAGCGTTGCACACAC 59.284 55.000 8.05 0.00 0.00 3.82
1877 4252 0.032815 TAGCTAGCGTTGCACACACA 59.967 50.000 9.55 0.00 0.00 3.72
1919 4294 3.696051 CAGTAATTGATTCTGTGGGTGGG 59.304 47.826 0.00 0.00 0.00 4.61
1920 4295 2.999185 AATTGATTCTGTGGGTGGGT 57.001 45.000 0.00 0.00 0.00 4.51
1921 4296 4.538490 AGTAATTGATTCTGTGGGTGGGTA 59.462 41.667 0.00 0.00 0.00 3.69
1938 4316 5.353400 GGTGGGTAGTACTGCACTTATTTTC 59.647 44.000 14.65 0.00 38.80 2.29
1956 4334 0.179702 TCATCTGACATGGAGCAGCC 59.820 55.000 0.00 0.00 32.27 4.85
2036 4422 1.739049 CACCTCGAGATCCCAGAGC 59.261 63.158 15.71 0.00 0.00 4.09
2045 4431 2.086251 GATCCCAGAGCGAGCAGAGG 62.086 65.000 0.00 0.00 0.00 3.69
2088 4799 1.944709 GCTAGATGCATGCATGTGTGA 59.055 47.619 36.73 17.33 42.31 3.58
2090 4801 3.004419 GCTAGATGCATGCATGTGTGATT 59.996 43.478 36.73 12.27 42.31 2.57
2092 4803 5.278120 GCTAGATGCATGCATGTGTGATTAA 60.278 40.000 36.73 15.16 42.31 1.40
2094 4805 5.769367 AGATGCATGCATGTGTGATTAATC 58.231 37.500 36.73 18.46 36.70 1.75
2095 4806 4.310357 TGCATGCATGTGTGATTAATCC 57.690 40.909 26.79 7.03 0.00 3.01
2097 4808 3.068448 GCATGCATGTGTGATTAATCCCA 59.932 43.478 26.79 4.69 0.00 4.37
2098 4809 4.262292 GCATGCATGTGTGATTAATCCCAT 60.262 41.667 26.79 9.22 0.00 4.00
2149 5070 2.292016 ACCGTGAATTTGATGCGACAAA 59.708 40.909 9.79 9.79 42.58 2.83
2220 5607 4.745649 ACCTCTTTAAGTACATCACTCGC 58.254 43.478 0.00 0.00 36.04 5.03
2324 5712 3.370978 CCGTTTTGGATGTAGCTACTGTG 59.629 47.826 23.84 4.66 42.00 3.66
2349 5737 7.148188 TGCTAATATTCCTCACAAGAAAAGCTG 60.148 37.037 0.00 0.00 0.00 4.24
2361 5749 3.477530 AGAAAAGCTGGTCCACTAACAC 58.522 45.455 0.00 0.00 0.00 3.32
2377 5768 6.112734 CACTAACACTGCATTATAACCCTGA 58.887 40.000 0.00 0.00 0.00 3.86
2427 5821 3.603158 AGTTCACTACACACACACACA 57.397 42.857 0.00 0.00 0.00 3.72
2428 5822 3.259064 AGTTCACTACACACACACACAC 58.741 45.455 0.00 0.00 0.00 3.82
2429 5823 2.997303 GTTCACTACACACACACACACA 59.003 45.455 0.00 0.00 0.00 3.72
2430 5824 2.612604 TCACTACACACACACACACAC 58.387 47.619 0.00 0.00 0.00 3.82
2435 5829 3.932545 ACACACACACACACACAAAAT 57.067 38.095 0.00 0.00 0.00 1.82
2436 5830 5.644206 ACTACACACACACACACACAAAATA 59.356 36.000 0.00 0.00 0.00 1.40
2445 5839 8.629158 ACACACACACACAAAATAATATCAACT 58.371 29.630 0.00 0.00 0.00 3.16
2482 5876 6.513806 TGATCAATGTGTTTACCCTTCATG 57.486 37.500 0.00 0.00 0.00 3.07
2483 5877 6.009589 TGATCAATGTGTTTACCCTTCATGT 58.990 36.000 0.00 0.00 0.00 3.21
2486 5880 6.068010 TCAATGTGTTTACCCTTCATGTTCT 58.932 36.000 0.00 0.00 0.00 3.01
2487 5881 6.206634 TCAATGTGTTTACCCTTCATGTTCTC 59.793 38.462 0.00 0.00 0.00 2.87
2488 5882 5.042463 TGTGTTTACCCTTCATGTTCTCA 57.958 39.130 0.00 0.00 0.00 3.27
2489 5883 5.441500 TGTGTTTACCCTTCATGTTCTCAA 58.558 37.500 0.00 0.00 0.00 3.02
2490 5884 5.888724 TGTGTTTACCCTTCATGTTCTCAAA 59.111 36.000 0.00 0.00 0.00 2.69
2491 5885 6.378564 TGTGTTTACCCTTCATGTTCTCAAAA 59.621 34.615 0.00 0.00 0.00 2.44
2492 5886 7.093727 TGTGTTTACCCTTCATGTTCTCAAAAA 60.094 33.333 0.00 0.00 0.00 1.94
2588 5989 1.190833 AGCAGTGGGAGTCTGACCTG 61.191 60.000 3.76 5.50 35.20 4.00
3026 6427 3.299977 ACTACGTGCCCGTCAGCA 61.300 61.111 0.00 0.00 46.28 4.41
3070 6485 4.065321 ACTCCGAGGAGAATTAAGCATG 57.935 45.455 24.53 0.00 44.53 4.06
3083 6498 4.864916 TTAAGCATGTGAATTCTCTCGC 57.135 40.909 7.05 9.75 0.00 5.03
3089 6504 0.908505 GTGAATTCTCTCGCGACGTC 59.091 55.000 3.71 5.18 0.00 4.34
3098 6517 2.577112 CGCGACGTCTACCAGCAG 60.577 66.667 14.70 2.43 0.00 4.24
3116 6535 2.933492 GCAGTGTCACCATTAGGCGTAA 60.933 50.000 0.64 0.64 39.06 3.18
3173 6592 0.674581 TTGAGAGTTGCCTGCATCCG 60.675 55.000 0.00 0.00 0.00 4.18
3174 6593 1.078848 GAGAGTTGCCTGCATCCGT 60.079 57.895 0.00 0.00 0.00 4.69
3175 6594 0.175760 GAGAGTTGCCTGCATCCGTA 59.824 55.000 0.00 0.00 0.00 4.02
3176 6595 0.108138 AGAGTTGCCTGCATCCGTAC 60.108 55.000 0.00 0.00 0.00 3.67
3177 6596 0.108138 GAGTTGCCTGCATCCGTACT 60.108 55.000 0.00 0.00 0.00 2.73
3178 6597 1.136305 GAGTTGCCTGCATCCGTACTA 59.864 52.381 0.00 0.00 0.00 1.82
3264 6689 4.383948 GCATGCTTCTAAGTGCTCAAAAAC 59.616 41.667 11.37 0.00 34.85 2.43
3274 6702 1.066002 TGCTCAAAAACAGCTGCAGTC 59.934 47.619 15.27 7.83 37.79 3.51
3347 6786 3.068873 GTGTCTCCAGTGTTTCAGAGTCT 59.931 47.826 0.00 0.00 0.00 3.24
3359 6798 4.585955 TTCAGAGTCTAGTCACCAACAC 57.414 45.455 0.00 0.00 0.00 3.32
3378 6817 6.151648 CCAACACAGTTCATTAATCCTGACAT 59.848 38.462 11.39 0.00 0.00 3.06
3408 6847 5.242393 ACAAAATGCAGCAATAACTCAGAGT 59.758 36.000 0.00 0.00 0.00 3.24
3409 6848 5.557891 AAATGCAGCAATAACTCAGAGTC 57.442 39.130 2.72 0.00 0.00 3.36
3410 6849 3.969287 TGCAGCAATAACTCAGAGTCT 57.031 42.857 2.72 0.00 0.00 3.24
3412 6851 5.003692 TGCAGCAATAACTCAGAGTCTAG 57.996 43.478 2.72 0.00 0.00 2.43
3413 6852 4.464244 TGCAGCAATAACTCAGAGTCTAGT 59.536 41.667 2.72 0.00 0.00 2.57
3414 6853 5.040635 GCAGCAATAACTCAGAGTCTAGTC 58.959 45.833 2.72 0.00 0.00 2.59
3415 6854 5.393569 GCAGCAATAACTCAGAGTCTAGTCA 60.394 44.000 2.72 0.00 0.00 3.41
3416 6855 6.033341 CAGCAATAACTCAGAGTCTAGTCAC 58.967 44.000 2.72 0.00 0.00 3.67
3441 6887 5.627182 ACAGATCAGTGCAAGGATAGAAT 57.373 39.130 0.00 0.00 0.00 2.40
3465 6911 9.566331 AATACATATTTATCAGGGATCAGGAGA 57.434 33.333 0.00 0.00 0.00 3.71
3475 6921 2.738812 ATCAGGAGATGATCGCCGT 58.261 52.632 9.58 0.00 46.01 5.68
3834 7280 0.393267 GTGGGCTAACCGTTATGCCA 60.393 55.000 22.51 12.56 46.53 4.92
3974 7420 1.270041 GGCCGCAAAAGGAAATGTTCA 60.270 47.619 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.370166 CCTTCTCTCAACTAGAATTGGTTGTC 59.630 42.308 0.00 0.00 42.15 3.18
46 49 0.388649 CGTCAGAACCAAGAGGACCG 60.389 60.000 0.00 0.00 38.69 4.79
85 88 2.353610 GCCAACCAAGCTCCATGGG 61.354 63.158 13.02 3.69 42.48 4.00
193 2344 7.527084 AGTGAGATTAAAGTCGTGAATAAGC 57.473 36.000 0.00 0.00 0.00 3.09
295 2446 1.764854 GATGCCGGGGGAAGGTCTA 60.765 63.158 2.18 0.00 0.00 2.59
297 2448 1.764854 TAGATGCCGGGGGAAGGTC 60.765 63.158 2.18 0.00 0.00 3.85
375 2526 1.098050 CAAATGCCAGAGGTGGTAGC 58.902 55.000 0.00 0.00 46.96 3.58
376 2527 1.098050 GCAAATGCCAGAGGTGGTAG 58.902 55.000 0.00 0.00 46.96 3.18
377 2528 0.403655 TGCAAATGCCAGAGGTGGTA 59.596 50.000 2.46 0.00 46.96 3.25
411 2562 3.175929 GGTTGCATGCCGTGTATTTAAC 58.824 45.455 16.68 9.12 0.00 2.01
422 2573 1.798813 GCGATTTAGTGGTTGCATGCC 60.799 52.381 16.68 0.00 0.00 4.40
441 2592 1.069227 CGCCAGAGTTGTTTGTAAGGC 60.069 52.381 0.00 0.00 37.54 4.35
460 2611 6.205784 TGTCAAAAAGAAGACCTAATTTGCG 58.794 36.000 0.00 0.00 34.45 4.85
493 2644 8.722177 GCCTAGTGCAATATATGGAGTACTCCT 61.722 44.444 35.83 25.01 44.52 3.69
494 2645 6.628398 GCCTAGTGCAATATATGGAGTACTCC 60.628 46.154 31.61 31.61 44.49 3.85
495 2646 6.334202 GCCTAGTGCAATATATGGAGTACTC 58.666 44.000 14.87 14.87 40.77 2.59
496 2647 5.105716 CGCCTAGTGCAATATATGGAGTACT 60.106 44.000 0.00 0.00 41.33 2.73
497 2648 5.103000 CGCCTAGTGCAATATATGGAGTAC 58.897 45.833 2.42 0.00 41.33 2.73
528 2855 6.878389 TGATGAAGAGTTGTTGCATGTACATA 59.122 34.615 8.32 0.00 0.00 2.29
604 2931 6.769512 ACTTCTGTACTTTGCTCTCCAAATA 58.230 36.000 0.00 0.00 42.22 1.40
607 2934 4.689612 ACTTCTGTACTTTGCTCTCCAA 57.310 40.909 0.00 0.00 0.00 3.53
608 2935 6.360370 AATACTTCTGTACTTTGCTCTCCA 57.640 37.500 0.00 0.00 0.00 3.86
609 2936 6.402658 GCAAATACTTCTGTACTTTGCTCTCC 60.403 42.308 15.38 0.00 42.11 3.71
627 2957 5.965922 AGGGCACTAGAAAAATGCAAATAC 58.034 37.500 0.00 0.00 41.27 1.89
770 3100 3.697542 GAGAGGAGGAGTGAGTAGGAAAC 59.302 52.174 0.00 0.00 0.00 2.78
785 3115 3.489398 CGAGGTTTTATGACGGAGAGGAG 60.489 52.174 0.00 0.00 0.00 3.69
912 3242 8.783833 AGAAATGGATGGATATCTATTGTTCG 57.216 34.615 2.77 0.00 41.81 3.95
913 3243 9.956640 AGAGAAATGGATGGATATCTATTGTTC 57.043 33.333 2.77 5.32 41.81 3.18
914 3244 9.736414 CAGAGAAATGGATGGATATCTATTGTT 57.264 33.333 2.77 0.00 41.81 2.83
915 3245 7.828223 GCAGAGAAATGGATGGATATCTATTGT 59.172 37.037 2.77 0.00 41.81 2.71
946 3276 4.282957 GCCTAGGATGATGATGTTCTGAGA 59.717 45.833 14.75 0.00 0.00 3.27
947 3277 4.040095 TGCCTAGGATGATGATGTTCTGAG 59.960 45.833 14.75 0.00 0.00 3.35
951 3281 4.077300 TGTGCCTAGGATGATGATGTTC 57.923 45.455 14.75 0.00 0.00 3.18
1053 3383 0.878416 GGTTAGCAATCACGCACCAA 59.122 50.000 0.00 0.00 30.30 3.67
1084 3414 6.928492 TGACAAATTAAGAAGCAAAATGGGAC 59.072 34.615 0.00 0.00 0.00 4.46
1085 3415 7.060383 TGACAAATTAAGAAGCAAAATGGGA 57.940 32.000 0.00 0.00 0.00 4.37
1171 3514 1.999024 CAAATTACAAACCCATGGCGC 59.001 47.619 6.09 0.00 0.00 6.53
1172 3515 3.311486 ACAAATTACAAACCCATGGCG 57.689 42.857 6.09 2.02 0.00 5.69
1178 3521 6.183360 TGGACCTACAAACAAATTACAAACCC 60.183 38.462 0.00 0.00 0.00 4.11
1397 3740 3.036429 GCTCCGGAACATCTGCCCT 62.036 63.158 5.23 0.00 0.00 5.19
1526 3869 7.489160 TGTCGCAGAAATGAATGTAGTACTAT 58.511 34.615 5.75 0.00 39.69 2.12
1527 3870 6.859017 TGTCGCAGAAATGAATGTAGTACTA 58.141 36.000 0.00 0.00 39.69 1.82
1528 3871 5.720202 TGTCGCAGAAATGAATGTAGTACT 58.280 37.500 0.00 0.00 39.69 2.73
1536 3879 7.471721 TCGAATTATTTGTCGCAGAAATGAAT 58.528 30.769 0.00 0.00 39.69 2.57
1537 3880 6.836953 TCGAATTATTTGTCGCAGAAATGAA 58.163 32.000 0.00 0.00 39.69 2.57
1539 3882 5.170270 GCTCGAATTATTTGTCGCAGAAATG 59.830 40.000 0.00 0.00 39.69 2.32
1541 3884 4.436852 GGCTCGAATTATTTGTCGCAGAAA 60.437 41.667 9.84 0.00 39.69 2.52
1543 3886 2.607635 GGCTCGAATTATTTGTCGCAGA 59.392 45.455 9.84 0.00 37.19 4.26
1544 3887 2.597505 CGGCTCGAATTATTTGTCGCAG 60.598 50.000 9.84 4.35 37.19 5.18
1546 3889 1.332904 CCGGCTCGAATTATTTGTCGC 60.333 52.381 0.00 0.00 37.19 5.19
1547 3890 2.198406 TCCGGCTCGAATTATTTGTCG 58.802 47.619 0.00 0.00 38.62 4.35
1548 3891 3.002348 CCTTCCGGCTCGAATTATTTGTC 59.998 47.826 0.00 0.00 0.00 3.18
1549 3892 2.943033 CCTTCCGGCTCGAATTATTTGT 59.057 45.455 0.00 0.00 0.00 2.83
1550 3893 3.202906 TCCTTCCGGCTCGAATTATTTG 58.797 45.455 0.00 0.00 0.00 2.32
1551 3894 3.118371 ACTCCTTCCGGCTCGAATTATTT 60.118 43.478 0.00 0.00 0.00 1.40
1552 3895 2.434702 ACTCCTTCCGGCTCGAATTATT 59.565 45.455 0.00 0.00 0.00 1.40
1553 3896 2.040178 ACTCCTTCCGGCTCGAATTAT 58.960 47.619 0.00 0.00 0.00 1.28
1554 3897 1.481871 ACTCCTTCCGGCTCGAATTA 58.518 50.000 0.00 0.00 0.00 1.40
1555 3898 1.136500 GTACTCCTTCCGGCTCGAATT 59.864 52.381 0.00 0.00 0.00 2.17
1556 3899 0.745468 GTACTCCTTCCGGCTCGAAT 59.255 55.000 0.00 0.00 0.00 3.34
1557 3900 0.323178 AGTACTCCTTCCGGCTCGAA 60.323 55.000 0.00 0.00 0.00 3.71
1558 3901 0.543277 TAGTACTCCTTCCGGCTCGA 59.457 55.000 0.00 0.00 0.00 4.04
1559 3902 1.606903 ATAGTACTCCTTCCGGCTCG 58.393 55.000 0.00 0.00 0.00 5.03
1560 3903 8.404765 GTTATATTATAGTACTCCTTCCGGCTC 58.595 40.741 0.00 0.00 0.00 4.70
1561 3904 8.114743 AGTTATATTATAGTACTCCTTCCGGCT 58.885 37.037 0.00 0.00 0.00 5.52
1562 3905 8.189460 CAGTTATATTATAGTACTCCTTCCGGC 58.811 40.741 0.00 0.00 0.00 6.13
1563 3906 9.240734 ACAGTTATATTATAGTACTCCTTCCGG 57.759 37.037 0.00 0.00 0.00 5.14
1619 3962 1.586154 CGTGAGCCCAAATCACCCAC 61.586 60.000 0.82 0.00 43.36 4.61
1642 3985 9.823647 AATCATACTCCAATAACTACACTTCTG 57.176 33.333 0.00 0.00 0.00 3.02
1803 4178 2.264794 CCCAGGCACGGTAGACAC 59.735 66.667 0.00 0.00 0.00 3.67
1874 4249 2.260869 CCTTCACGGTTGGCCTGTG 61.261 63.158 3.32 7.98 39.16 3.66
1875 4250 2.113139 CCTTCACGGTTGGCCTGT 59.887 61.111 3.32 0.00 0.00 4.00
1876 4251 2.672996 CCCTTCACGGTTGGCCTG 60.673 66.667 3.32 0.00 0.00 4.85
1877 4252 3.966543 CCCCTTCACGGTTGGCCT 61.967 66.667 3.32 0.00 0.00 5.19
1919 4294 8.596380 GTCAGATGAAAATAAGTGCAGTACTAC 58.404 37.037 0.00 0.00 39.18 2.73
1920 4295 8.311109 TGTCAGATGAAAATAAGTGCAGTACTA 58.689 33.333 0.00 0.00 39.18 1.82
1921 4296 7.161404 TGTCAGATGAAAATAAGTGCAGTACT 58.839 34.615 0.00 0.00 42.89 2.73
1938 4316 1.158484 CGGCTGCTCCATGTCAGATG 61.158 60.000 0.00 0.00 32.26 2.90
2011 4390 1.112113 GGATCTCGAGGTGCCAACTA 58.888 55.000 13.56 0.00 0.00 2.24
2045 4431 1.956170 CATCCTCGTATGGCGTGCC 60.956 63.158 3.30 3.30 42.13 5.01
2052 4438 5.976534 GCATCTAGCTAATCATCCTCGTATG 59.023 44.000 0.00 0.00 41.15 2.39
2068 4454 1.944709 TCACACATGCATGCATCTAGC 59.055 47.619 30.07 0.00 45.96 3.42
2088 4799 9.728100 TTCCTTCTGGAATAAAATGGGATTAAT 57.272 29.630 0.00 0.00 46.57 1.40
2213 5600 0.460811 GTGCCATGATCAGCGAGTGA 60.461 55.000 0.09 0.00 40.38 3.41
2304 5692 4.003648 AGCACAGTAGCTACATCCAAAAC 58.996 43.478 25.28 6.64 44.50 2.43
2324 5712 7.192232 CAGCTTTTCTTGTGAGGAATATTAGC 58.808 38.462 0.00 0.00 0.00 3.09
2349 5737 5.296035 GGTTATAATGCAGTGTTAGTGGACC 59.704 44.000 0.00 0.00 0.00 4.46
2361 5749 6.349300 ACTAGTTGTCAGGGTTATAATGCAG 58.651 40.000 0.00 0.00 0.00 4.41
2377 5768 5.677319 TCCAGCTAAGCATAACTAGTTGT 57.323 39.130 18.56 8.87 0.00 3.32
2445 5839 9.453572 AACACATTGATCAGCTTAAATAGAGAA 57.546 29.630 0.00 0.00 0.00 2.87
2493 5887 8.721133 AGGATAATGAAGGGTAAACACTTTTT 57.279 30.769 0.00 0.16 40.21 1.94
2494 5888 7.396339 GGAGGATAATGAAGGGTAAACACTTTT 59.604 37.037 0.00 0.00 40.21 2.27
2495 5889 6.890268 GGAGGATAATGAAGGGTAAACACTTT 59.110 38.462 0.00 0.00 40.21 2.66
2496 5890 6.424032 GGAGGATAATGAAGGGTAAACACTT 58.576 40.000 0.00 0.00 43.39 3.16
2497 5891 5.396436 CGGAGGATAATGAAGGGTAAACACT 60.396 44.000 0.00 0.00 0.00 3.55
2498 5892 4.814771 CGGAGGATAATGAAGGGTAAACAC 59.185 45.833 0.00 0.00 0.00 3.32
2499 5893 5.031066 CGGAGGATAATGAAGGGTAAACA 57.969 43.478 0.00 0.00 0.00 2.83
2840 6241 3.338126 CTTCTCGACGACCCACCCG 62.338 68.421 0.00 0.00 0.00 5.28
3070 6485 0.908505 GACGTCGCGAGAGAATTCAC 59.091 55.000 10.24 0.74 43.49 3.18
3083 6498 0.454620 GACACTGCTGGTAGACGTCG 60.455 60.000 10.46 0.00 0.00 5.12
3116 6535 7.654116 CCATTTTCCACAAAACCGTATTTACTT 59.346 33.333 0.00 0.00 34.24 2.24
3173 6592 4.272018 TCTCGCTCGACCAAATACTAGTAC 59.728 45.833 4.31 0.00 0.00 2.73
3174 6593 4.445453 TCTCGCTCGACCAAATACTAGTA 58.555 43.478 4.77 4.77 0.00 1.82
3175 6594 3.276857 TCTCGCTCGACCAAATACTAGT 58.723 45.455 0.00 0.00 0.00 2.57
3176 6595 3.965292 TCTCGCTCGACCAAATACTAG 57.035 47.619 0.00 0.00 0.00 2.57
3177 6596 4.097437 ACATTCTCGCTCGACCAAATACTA 59.903 41.667 0.00 0.00 0.00 1.82
3178 6597 3.119101 ACATTCTCGCTCGACCAAATACT 60.119 43.478 0.00 0.00 0.00 2.12
3264 6689 9.004717 TCTTTATACTATAGTAGACTGCAGCTG 57.995 37.037 15.27 10.11 33.52 4.24
3347 6786 6.653320 GGATTAATGAACTGTGTTGGTGACTA 59.347 38.462 0.00 0.00 0.00 2.59
3359 6798 4.885907 AGCCATGTCAGGATTAATGAACTG 59.114 41.667 0.00 0.00 0.00 3.16
3378 6817 0.751452 TTGCTGCATTTTGTGAGCCA 59.249 45.000 1.84 0.00 33.07 4.75
3408 6847 3.056536 GCACTGATCTGTTGGTGACTAGA 60.057 47.826 1.95 0.00 32.12 2.43
3409 6848 3.257393 GCACTGATCTGTTGGTGACTAG 58.743 50.000 1.95 0.00 32.12 2.57
3410 6849 2.632512 TGCACTGATCTGTTGGTGACTA 59.367 45.455 1.95 0.00 32.12 2.59
3412 6851 1.882912 TGCACTGATCTGTTGGTGAC 58.117 50.000 1.95 0.00 32.12 3.67
3413 6852 2.497138 CTTGCACTGATCTGTTGGTGA 58.503 47.619 1.95 0.00 32.12 4.02
3414 6853 1.538512 CCTTGCACTGATCTGTTGGTG 59.461 52.381 1.95 1.54 0.00 4.17
3415 6854 1.421268 TCCTTGCACTGATCTGTTGGT 59.579 47.619 1.95 0.00 0.00 3.67
3416 6855 2.189594 TCCTTGCACTGATCTGTTGG 57.810 50.000 1.95 3.99 0.00 3.77
3441 6887 8.985922 CATCTCCTGATCCCTGATAAATATGTA 58.014 37.037 0.00 0.00 0.00 2.29
3465 6911 0.465705 ATCTTCACCACGGCGATCAT 59.534 50.000 16.62 0.00 0.00 2.45
3471 6917 2.369870 CGTGTATCTTCACCACGGC 58.630 57.895 3.66 0.00 45.97 5.68
3475 6921 2.139917 GCACAACGTGTATCTTCACCA 58.860 47.619 0.00 0.00 35.75 4.17
3611 7057 1.296715 CCTAGCTTGCTCCCAACGT 59.703 57.895 0.00 0.00 0.00 3.99
3834 7280 1.474077 GGCCAGCACTTGATTTTCGAT 59.526 47.619 0.00 0.00 0.00 3.59
3974 7420 3.629398 GGTCCGATTGCAATCTCAGAATT 59.371 43.478 31.12 0.19 33.24 2.17


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

AutoCloner maintained by Alex Coulton.