Multiple sequence alignment - TraesCS4D01G223500

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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 TraesCS4D01G223500 chr4D 100.000 5222 0 0 1 5222 380335593 380340814 0.000000e+00 9644.0
1 TraesCS4D01G223500 chr4D 82.509 566 94 4 1896 2460 325366476 325367037 4.700000e-135 492.0
2 TraesCS4D01G223500 chr4D 90.566 53 4 1 1897 1949 404122178 404122127 9.380000e-08 69.4
3 TraesCS4D01G223500 chr4A 95.507 1647 58 8 2654 4287 83405366 83403723 0.000000e+00 2617.0
4 TraesCS4D01G223500 chr4A 92.781 1773 90 11 108 1848 83407153 83405387 0.000000e+00 2531.0
5 TraesCS4D01G223500 chr4A 96.875 32 1 0 439 470 672290003 672289972 3.000000e-03 54.7
6 TraesCS4D01G223500 chr4B 93.716 1655 74 15 2654 4287 467797492 467799137 0.000000e+00 2453.0
7 TraesCS4D01G223500 chr4B 92.830 1311 65 14 604 1892 467796187 467797490 0.000000e+00 1873.0
8 TraesCS4D01G223500 chr4B 92.276 479 37 0 108 586 467790329 467790807 0.000000e+00 680.0
9 TraesCS4D01G223500 chr4B 83.883 546 40 14 4286 4788 663904751 663905291 1.320000e-130 477.0
10 TraesCS4D01G223500 chr6D 93.111 929 52 1 4306 5222 289511266 289510338 0.000000e+00 1351.0
11 TraesCS4D01G223500 chr6D 92.080 947 56 7 4289 5222 47178817 47179757 0.000000e+00 1315.0
12 TraesCS4D01G223500 chr6D 91.034 948 70 4 4287 5222 461651440 461650496 0.000000e+00 1266.0
13 TraesCS4D01G223500 chr6D 87.791 516 49 3 4287 4789 116858277 116858791 4.500000e-165 592.0
14 TraesCS4D01G223500 chr6D 90.310 258 13 2 4288 4533 151960603 151960346 1.400000e-85 327.0
15 TraesCS4D01G223500 chr5B 92.105 950 61 3 4285 5222 693954322 693953375 0.000000e+00 1327.0
16 TraesCS4D01G223500 chr5B 91.561 948 65 4 4285 5220 693953063 693952119 0.000000e+00 1293.0
17 TraesCS4D01G223500 chr5B 91.204 955 68 9 4281 5222 693949452 693948501 0.000000e+00 1284.0
18 TraesCS4D01G223500 chr5B 79.557 768 132 20 1897 2654 49542093 49541341 4.630000e-145 525.0
19 TraesCS4D01G223500 chr5B 92.453 53 3 1 3907 3958 299680039 299680091 2.020000e-09 75.0
20 TraesCS4D01G223500 chr5D 92.741 923 54 5 4312 5222 544489527 544488606 0.000000e+00 1321.0
21 TraesCS4D01G223500 chr5D 97.976 593 12 0 1895 2487 505936651 505937243 0.000000e+00 1029.0
22 TraesCS4D01G223500 chr5D 86.747 747 93 5 1900 2643 466388958 466388215 0.000000e+00 826.0
23 TraesCS4D01G223500 chr5D 88.372 215 20 3 3749 3958 20094388 20094602 2.410000e-63 254.0
24 TraesCS4D01G223500 chr3D 91.081 953 69 4 4286 5222 598603826 598602874 0.000000e+00 1275.0
25 TraesCS4D01G223500 chr1A 90.957 940 67 13 4297 5222 10499603 10498668 0.000000e+00 1249.0
26 TraesCS4D01G223500 chr7B 95.703 768 31 2 1888 2654 179550277 179551043 0.000000e+00 1234.0
27 TraesCS4D01G223500 chr2A 86.202 761 101 3 1896 2653 194164558 194163799 0.000000e+00 821.0
28 TraesCS4D01G223500 chr6A 85.658 767 106 4 1889 2653 140543864 140544628 0.000000e+00 804.0
29 TraesCS4D01G223500 chr6A 96.800 125 4 0 4287 4411 185045503 185045627 5.300000e-50 209.0
30 TraesCS4D01G223500 chr1B 85.618 744 106 1 1895 2638 646226061 646225319 0.000000e+00 780.0
31 TraesCS4D01G223500 chr7D 88.337 523 42 6 4281 4788 1221075 1221593 1.240000e-170 610.0
32 TraesCS4D01G223500 chr7A 88.912 487 41 2 4284 4757 434754143 434753657 5.830000e-164 588.0
33 TraesCS4D01G223500 chr7A 88.538 253 12 6 4257 4497 490123836 490124083 1.840000e-74 291.0
34 TraesCS4D01G223500 chr1D 90.411 438 26 6 4280 4704 409013038 409013472 3.530000e-156 562.0
35 TraesCS4D01G223500 chr1D 79.190 716 130 13 1889 2592 119286058 119286766 3.660000e-131 479.0
36 TraesCS4D01G223500 chr6B 78.656 759 151 10 1897 2652 476419218 476418468 1.310000e-135 494.0
37 TraesCS4D01G223500 chr3B 86.111 216 24 4 3748 3958 542403938 542403724 1.460000e-55 228.0
38 TraesCS4D01G223500 chr3B 92.453 53 3 1 3907 3958 303333698 303333646 2.020000e-09 75.0
39 TraesCS4D01G223500 chr3B 93.878 49 3 0 3907 3955 554900672 554900720 2.020000e-09 75.0
40 TraesCS4D01G223500 chr2B 94.776 134 7 0 4278 4411 207620198 207620331 5.300000e-50 209.0


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 TraesCS4D01G223500 chr4D 380335593 380340814 5221 False 9644.000000 9644 100.000000 1 5222 1 chr4D.!!$F2 5221
1 TraesCS4D01G223500 chr4D 325366476 325367037 561 False 492.000000 492 82.509000 1896 2460 1 chr4D.!!$F1 564
2 TraesCS4D01G223500 chr4A 83403723 83407153 3430 True 2574.000000 2617 94.144000 108 4287 2 chr4A.!!$R2 4179
3 TraesCS4D01G223500 chr4B 467796187 467799137 2950 False 2163.000000 2453 93.273000 604 4287 2 chr4B.!!$F3 3683
4 TraesCS4D01G223500 chr4B 663904751 663905291 540 False 477.000000 477 83.883000 4286 4788 1 chr4B.!!$F2 502
5 TraesCS4D01G223500 chr6D 289510338 289511266 928 True 1351.000000 1351 93.111000 4306 5222 1 chr6D.!!$R2 916
6 TraesCS4D01G223500 chr6D 47178817 47179757 940 False 1315.000000 1315 92.080000 4289 5222 1 chr6D.!!$F1 933
7 TraesCS4D01G223500 chr6D 461650496 461651440 944 True 1266.000000 1266 91.034000 4287 5222 1 chr6D.!!$R3 935
8 TraesCS4D01G223500 chr6D 116858277 116858791 514 False 592.000000 592 87.791000 4287 4789 1 chr6D.!!$F2 502
9 TraesCS4D01G223500 chr5B 693948501 693954322 5821 True 1301.333333 1327 91.623333 4281 5222 3 chr5B.!!$R2 941
10 TraesCS4D01G223500 chr5B 49541341 49542093 752 True 525.000000 525 79.557000 1897 2654 1 chr5B.!!$R1 757
11 TraesCS4D01G223500 chr5D 544488606 544489527 921 True 1321.000000 1321 92.741000 4312 5222 1 chr5D.!!$R2 910
12 TraesCS4D01G223500 chr5D 505936651 505937243 592 False 1029.000000 1029 97.976000 1895 2487 1 chr5D.!!$F2 592
13 TraesCS4D01G223500 chr5D 466388215 466388958 743 True 826.000000 826 86.747000 1900 2643 1 chr5D.!!$R1 743
14 TraesCS4D01G223500 chr3D 598602874 598603826 952 True 1275.000000 1275 91.081000 4286 5222 1 chr3D.!!$R1 936
15 TraesCS4D01G223500 chr1A 10498668 10499603 935 True 1249.000000 1249 90.957000 4297 5222 1 chr1A.!!$R1 925
16 TraesCS4D01G223500 chr7B 179550277 179551043 766 False 1234.000000 1234 95.703000 1888 2654 1 chr7B.!!$F1 766
17 TraesCS4D01G223500 chr2A 194163799 194164558 759 True 821.000000 821 86.202000 1896 2653 1 chr2A.!!$R1 757
18 TraesCS4D01G223500 chr6A 140543864 140544628 764 False 804.000000 804 85.658000 1889 2653 1 chr6A.!!$F1 764
19 TraesCS4D01G223500 chr1B 646225319 646226061 742 True 780.000000 780 85.618000 1895 2638 1 chr1B.!!$R1 743
20 TraesCS4D01G223500 chr7D 1221075 1221593 518 False 610.000000 610 88.337000 4281 4788 1 chr7D.!!$F1 507
21 TraesCS4D01G223500 chr1D 119286058 119286766 708 False 479.000000 479 79.190000 1889 2592 1 chr1D.!!$F1 703
22 TraesCS4D01G223500 chr6B 476418468 476419218 750 True 494.000000 494 78.656000 1897 2652 1 chr6B.!!$R1 755

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
85 86 0.106708 CCAAGGCCGCTAGCTAATCA 59.893 55.0 13.93 0.00 43.05 2.57 F
495 496 0.108520 CCCATCACCAATTGTGCAGC 60.109 55.0 4.43 0.00 45.03 5.25 F
610 611 0.535335 CATCTGGCCTGCATTGCTTT 59.465 50.0 10.49 0.00 0.00 3.51 F
675 676 0.550914 TTGGGGTGCAAACTGAGTCT 59.449 50.0 0.00 0.00 0.00 3.24 F
2115 2165 0.596082 CCTTTGCCCAAAGTGTACCG 59.404 55.0 16.87 0.54 44.66 4.02 F
3022 3083 0.751643 ATGTGGCAATAGAACCGGGC 60.752 55.0 6.32 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1578 0.393944 GCAGGGGTACAGTTTAGGCC 60.394 60.000 0.00 0.00 0.00 5.19 R
2115 2165 0.179181 TCCAACGCATACGAGACGAC 60.179 55.000 0.00 0.00 43.93 4.34 R
2344 2394 2.240612 GATTGTGTCTTCGCACGGCC 62.241 60.000 0.00 0.00 41.94 6.13 R
2687 2738 2.169352 AGACCTAGATGCAACGCTCAAT 59.831 45.455 0.00 0.00 0.00 2.57 R
3849 3914 0.031994 AATGTCGCAACTTGGCCAAC 59.968 50.000 16.05 3.97 0.00 3.77 R
4890 9877 0.400213 TGTTCCTCTGTTTGGGCGAT 59.600 50.000 0.00 0.00 0.00 4.58 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
25 26 8.095452 GATACAATATATTCAGGTGGGGATCT 57.905 38.462 0.00 0.00 0.00 2.75
26 27 9.213777 GATACAATATATTCAGGTGGGGATCTA 57.786 37.037 0.00 0.00 0.00 1.98
27 28 7.259088 ACAATATATTCAGGTGGGGATCTAC 57.741 40.000 0.00 0.00 0.00 2.59
28 29 6.215636 ACAATATATTCAGGTGGGGATCTACC 59.784 42.308 0.00 6.31 43.94 3.18
38 39 3.754766 GGATCTACCCACGGTTGAC 57.245 57.895 0.00 0.00 39.88 3.18
39 40 0.177373 GGATCTACCCACGGTTGACC 59.823 60.000 0.00 0.00 39.88 4.02
40 41 0.899720 GATCTACCCACGGTTGACCA 59.100 55.000 0.51 0.00 39.88 4.02
41 42 1.485066 GATCTACCCACGGTTGACCAT 59.515 52.381 0.51 0.00 39.88 3.55
42 43 1.354101 TCTACCCACGGTTGACCATT 58.646 50.000 0.51 0.00 37.09 3.16
43 44 1.276989 TCTACCCACGGTTGACCATTC 59.723 52.381 0.51 0.00 37.09 2.67
44 45 1.002659 CTACCCACGGTTGACCATTCA 59.997 52.381 0.51 0.00 37.09 2.57
45 46 0.183971 ACCCACGGTTGACCATTCAA 59.816 50.000 0.51 0.00 39.55 2.69
46 47 1.323412 CCCACGGTTGACCATTCAAA 58.677 50.000 0.51 0.00 43.52 2.69
47 48 1.683917 CCCACGGTTGACCATTCAAAA 59.316 47.619 0.51 0.00 43.52 2.44
48 49 2.101582 CCCACGGTTGACCATTCAAAAA 59.898 45.455 0.51 0.00 43.52 1.94
66 67 3.801114 AAAAAGACCACTCACTTTGGC 57.199 42.857 0.00 0.00 37.69 4.52
67 68 1.692411 AAAGACCACTCACTTTGGCC 58.308 50.000 0.00 0.00 37.69 5.36
68 69 0.550914 AAGACCACTCACTTTGGCCA 59.449 50.000 0.00 0.00 37.69 5.36
69 70 0.550914 AGACCACTCACTTTGGCCAA 59.449 50.000 16.05 16.05 37.69 4.52
70 71 0.954452 GACCACTCACTTTGGCCAAG 59.046 55.000 19.48 15.02 37.69 3.61
71 72 0.468029 ACCACTCACTTTGGCCAAGG 60.468 55.000 24.95 24.95 37.69 3.61
72 73 1.662044 CACTCACTTTGGCCAAGGC 59.338 57.895 26.31 1.52 36.72 4.35
82 83 2.189521 GCCAAGGCCGCTAGCTAA 59.810 61.111 13.93 0.00 43.05 3.09
83 84 1.227973 GCCAAGGCCGCTAGCTAAT 60.228 57.895 13.93 0.00 43.05 1.73
84 85 1.231296 GCCAAGGCCGCTAGCTAATC 61.231 60.000 13.93 0.00 43.05 1.75
85 86 0.106708 CCAAGGCCGCTAGCTAATCA 59.893 55.000 13.93 0.00 43.05 2.57
86 87 1.475034 CCAAGGCCGCTAGCTAATCAA 60.475 52.381 13.93 0.00 43.05 2.57
87 88 2.498167 CAAGGCCGCTAGCTAATCAAT 58.502 47.619 13.93 0.00 43.05 2.57
88 89 3.557054 CCAAGGCCGCTAGCTAATCAATA 60.557 47.826 13.93 0.00 43.05 1.90
89 90 4.256920 CAAGGCCGCTAGCTAATCAATAT 58.743 43.478 13.93 0.00 43.05 1.28
90 91 3.866651 AGGCCGCTAGCTAATCAATATG 58.133 45.455 13.93 0.00 43.05 1.78
91 92 2.939103 GGCCGCTAGCTAATCAATATGG 59.061 50.000 13.93 3.34 43.05 2.74
92 93 3.369471 GGCCGCTAGCTAATCAATATGGA 60.369 47.826 13.93 0.00 43.05 3.41
93 94 3.619038 GCCGCTAGCTAATCAATATGGAC 59.381 47.826 13.93 0.00 38.99 4.02
94 95 4.621747 GCCGCTAGCTAATCAATATGGACT 60.622 45.833 13.93 0.00 38.99 3.85
95 96 5.105752 CCGCTAGCTAATCAATATGGACTC 58.894 45.833 13.93 0.00 0.00 3.36
96 97 5.105752 CGCTAGCTAATCAATATGGACTCC 58.894 45.833 13.93 0.00 0.00 3.85
97 98 5.336770 CGCTAGCTAATCAATATGGACTCCA 60.337 44.000 13.93 0.00 38.19 3.86
98 99 6.629068 CGCTAGCTAATCAATATGGACTCCAT 60.629 42.308 15.18 15.18 46.99 3.41
99 100 7.108847 GCTAGCTAATCAATATGGACTCCATT 58.891 38.462 16.03 0.41 42.23 3.16
100 101 7.609532 GCTAGCTAATCAATATGGACTCCATTT 59.390 37.037 16.03 5.54 42.23 2.32
101 102 9.512588 CTAGCTAATCAATATGGACTCCATTTT 57.487 33.333 16.03 11.44 42.23 1.82
102 103 8.174733 AGCTAATCAATATGGACTCCATTTTG 57.825 34.615 24.80 24.80 46.67 2.44
111 112 6.645790 ATGGACTCCATTTTGAATAGCATC 57.354 37.500 4.55 0.00 42.23 3.91
117 118 6.122850 TCCATTTTGAATAGCATCGAAGTG 57.877 37.500 0.00 0.00 32.85 3.16
147 148 1.423584 TCTCCAAGTGAACTCAGCCA 58.576 50.000 0.00 0.00 0.00 4.75
151 152 1.081892 CAAGTGAACTCAGCCATCGG 58.918 55.000 0.00 0.00 0.00 4.18
170 171 4.416738 GCCACCTCTCTGCCCCAC 62.417 72.222 0.00 0.00 0.00 4.61
176 177 0.622665 CCTCTCTGCCCCACAATCTT 59.377 55.000 0.00 0.00 0.00 2.40
194 195 2.093500 TCTTGCTGCGTATGATGTCCTT 60.093 45.455 0.00 0.00 0.00 3.36
227 228 4.561155 TCCTTCTCCCAGGACCAC 57.439 61.111 0.00 0.00 38.11 4.16
230 231 2.525629 TTCTCCCAGGACCACGCA 60.526 61.111 0.00 0.00 0.00 5.24
248 249 1.209128 CAATGGAGTCGCGTACATCC 58.791 55.000 5.77 10.18 0.00 3.51
254 255 1.875364 GTCGCGTACATCCGGGTTC 60.875 63.158 5.77 0.00 41.07 3.62
293 294 5.221382 TGTCTCAGTCCACAAGTTTAGGTAC 60.221 44.000 0.00 0.00 0.00 3.34
322 323 0.331278 ATTGGGGCTGTCAATTCCGA 59.669 50.000 0.00 0.00 31.49 4.55
337 338 2.263540 CGACCCAACACCGGTAGG 59.736 66.667 6.87 10.09 45.13 3.18
339 340 3.617143 GACCCAACACCGGTAGGCC 62.617 68.421 6.87 0.00 42.76 5.19
341 342 2.432563 CCAACACCGGTAGGCCAA 59.567 61.111 6.87 0.00 42.76 4.52
359 360 3.585990 CCGCCGTCCATCAATGCC 61.586 66.667 0.00 0.00 0.00 4.40
398 399 2.269562 CGCACCCGGGATTTGGTA 59.730 61.111 32.02 0.00 32.32 3.25
399 400 2.110352 CGCACCCGGGATTTGGTAC 61.110 63.158 32.02 5.63 32.32 3.34
445 446 0.693622 TGTACCCTTCGGCCATTCAA 59.306 50.000 2.24 0.00 0.00 2.69
478 479 3.117888 TCCCAGAATAGAGCATTGTTCCC 60.118 47.826 0.00 0.00 0.00 3.97
495 496 0.108520 CCCATCACCAATTGTGCAGC 60.109 55.000 4.43 0.00 45.03 5.25
529 530 5.928264 CCCTAAAAAGTTGCTTTGATTCCTG 59.072 40.000 0.00 0.00 33.64 3.86
545 546 1.071542 TCCTGAGGCACGTTGATTTGA 59.928 47.619 0.00 0.00 0.00 2.69
547 548 2.489329 CCTGAGGCACGTTGATTTGAAT 59.511 45.455 0.00 0.00 0.00 2.57
569 570 2.123726 GCCCATGGCCTTGTAGGG 60.124 66.667 16.81 14.40 44.06 3.53
609 610 1.327690 CCATCTGGCCTGCATTGCTT 61.328 55.000 10.49 0.00 0.00 3.91
610 611 0.535335 CATCTGGCCTGCATTGCTTT 59.465 50.000 10.49 0.00 0.00 3.51
614 615 2.428171 TCTGGCCTGCATTGCTTTTATC 59.572 45.455 10.49 0.00 0.00 1.75
639 640 1.879380 CACTTCAAGTTCGGAATGCCA 59.121 47.619 0.00 0.00 0.00 4.92
649 650 2.353610 GGAATGCCAAGGCCACCTG 61.354 63.158 5.01 0.00 41.09 4.00
675 676 0.550914 TTGGGGTGCAAACTGAGTCT 59.449 50.000 0.00 0.00 0.00 3.24
769 770 2.653726 TGCCCCAATTATACAGCTGTG 58.346 47.619 29.57 11.16 0.00 3.66
770 771 1.338020 GCCCCAATTATACAGCTGTGC 59.662 52.381 29.57 16.29 0.00 4.57
796 813 8.871862 CATTGATCTTTCTGTTGTTTGTCAAAA 58.128 29.630 0.00 0.00 37.81 2.44
864 889 1.420138 ACTCTTCACCGTTGGATGGTT 59.580 47.619 0.00 0.00 34.66 3.67
936 961 3.115390 CCTCCAATCCAAGGGTAGAGAA 58.885 50.000 1.87 0.00 0.00 2.87
1122 1150 4.094646 ACGCGTCCATGGCCATGA 62.095 61.111 41.32 26.15 41.20 3.07
1309 1337 4.681978 ACGCCCGTTCTGTGGAGC 62.682 66.667 0.00 0.00 0.00 4.70
1481 1511 5.649782 AAGCAAGAATGGTATTTGGACAG 57.350 39.130 0.00 0.00 35.91 3.51
1518 1548 9.383519 TGAAGTAAGATTAGGAGTAGCATTTTG 57.616 33.333 0.00 0.00 0.00 2.44
1544 1578 5.505173 ACATGTTGACTGAAACTGAAAGG 57.495 39.130 0.00 0.00 39.30 3.11
1556 1590 4.717279 AACTGAAAGGGCCTAAACTGTA 57.283 40.909 6.41 0.00 39.30 2.74
1691 1726 5.506317 CCCTTCGATTGATGTCCTAATTTGC 60.506 44.000 0.00 0.00 0.00 3.68
1736 1771 1.149987 TCGTTTCAATGGCACGGTAC 58.850 50.000 0.00 0.00 34.61 3.34
1766 1801 5.283060 ACATGTAAAATGAGACGAACTGC 57.717 39.130 0.00 0.00 0.00 4.40
1771 1806 0.976641 AATGAGACGAACTGCTGGGA 59.023 50.000 0.00 0.00 0.00 4.37
1851 1887 5.634859 CCAGTTAGTTTAGCTTGCATTTTGG 59.365 40.000 0.00 0.00 0.00 3.28
1887 1923 5.381174 TGCATTATATTTGCTCTCCATGC 57.619 39.130 10.56 0.00 40.77 4.06
1890 1926 6.041182 TGCATTATATTTGCTCTCCATGCTTT 59.959 34.615 10.56 0.00 40.77 3.51
1892 1928 7.431249 CATTATATTTGCTCTCCATGCTTTGT 58.569 34.615 0.00 0.00 0.00 2.83
1893 1929 8.570488 CATTATATTTGCTCTCCATGCTTTGTA 58.430 33.333 0.00 0.00 0.00 2.41
2115 2165 0.596082 CCTTTGCCCAAAGTGTACCG 59.404 55.000 16.87 0.54 44.66 4.02
2344 2394 2.664185 CGATGGCTGCCCAGATCG 60.664 66.667 20.69 20.69 46.24 3.69
2487 2537 2.359107 CTCAGCGCCAGCCAAGAA 60.359 61.111 2.29 0.00 46.67 2.52
2492 2542 1.211190 GCGCCAGCCAAGAAAAGAG 59.789 57.895 0.00 0.00 37.42 2.85
2687 2738 9.747898 TTTTAGCTGGAATGACCTTTTTAGATA 57.252 29.630 0.00 0.00 39.86 1.98
2691 2742 8.055181 AGCTGGAATGACCTTTTTAGATATTGA 58.945 33.333 0.00 0.00 39.86 2.57
2743 2794 9.491675 TTGTAAGGTCGATGTTAACTGAATAAA 57.508 29.630 7.22 0.00 0.00 1.40
2744 2795 9.491675 TGTAAGGTCGATGTTAACTGAATAAAA 57.508 29.630 7.22 0.00 0.00 1.52
2803 2859 7.810658 ACTGATGTATTCATTGTTTCACTCAC 58.189 34.615 0.00 0.00 34.06 3.51
2819 2875 4.081406 CACTCACTGAAATGGAATTGGGA 58.919 43.478 0.00 0.00 36.10 4.37
3022 3083 0.751643 ATGTGGCAATAGAACCGGGC 60.752 55.000 6.32 0.00 0.00 6.13
3108 3173 7.339598 TGTTTGAACAAGGCGTTAAGCAACT 62.340 40.000 0.00 0.00 41.31 3.16
3120 3185 5.447818 GCGTTAAGCAACTAAGCTGATGATT 60.448 40.000 0.00 0.00 45.89 2.57
3347 3412 6.180472 TCTTTTCCTTTTTCTCTGTGTCAGT 58.820 36.000 0.00 0.00 32.61 3.41
3441 3506 5.783875 AGGGACTGTTACTGTAGTAATTGGT 59.216 40.000 7.66 7.17 41.85 3.67
3557 3622 0.947244 CTTGATCGCAGGTAATGGGC 59.053 55.000 0.00 0.00 41.51 5.36
3647 3712 6.802608 TCAGAGTGGTACTATTGAATTACCG 58.197 40.000 2.58 0.00 38.53 4.02
3849 3914 3.510719 CCGTTTCTTATGCCCAAACATG 58.489 45.455 0.00 0.00 31.51 3.21
3860 3926 1.140652 CCCAAACATGTTGGCCAAGTT 59.859 47.619 21.21 16.99 36.59 2.66
3881 3947 2.616376 TGCGACATTCCGAATAAATGGG 59.384 45.455 0.00 0.00 38.23 4.00
4072 4141 9.622004 CATCAGGAAGATATGATTATTTTGTGC 57.378 33.333 0.00 0.00 33.91 4.57
4144 4213 5.210715 GCACACTCTTTTGATGTCTGAAAG 58.789 41.667 0.00 0.00 0.00 2.62
4158 4227 3.007398 GTCTGAAAGTGACTGTCCCTCAT 59.993 47.826 5.17 0.00 33.76 2.90
4223 4292 3.123621 GTCACATAGCGTGTTCTTTCCAG 59.876 47.826 0.00 0.00 46.44 3.86
4236 4308 6.311690 GTGTTCTTTCCAGTGTAGAAGATAGC 59.688 42.308 0.00 0.00 0.00 2.97
4420 5764 2.906354 CCACCATGTTGCTACTCCTAC 58.094 52.381 0.00 0.00 0.00 3.18
4475 7077 4.816385 CCTAATACCAAACAGACATCGCAT 59.184 41.667 0.00 0.00 0.00 4.73
4505 7107 2.269940 ACATCTAAAGCCAGGTGTCCT 58.730 47.619 0.00 0.00 34.77 3.85
4522 7151 3.052414 TGTCCTATCCAAGCCACTACCTA 60.052 47.826 0.00 0.00 0.00 3.08
4621 7250 0.820226 TCCATCCTCAGAGCAGAACG 59.180 55.000 0.00 0.00 0.00 3.95
4673 8408 1.606025 AATGCCACCATGACGCCAA 60.606 52.632 0.00 0.00 0.00 4.52
4766 9753 2.431771 CCACCGTCGACGATGCAA 60.432 61.111 37.65 0.00 43.02 4.08
4768 9755 1.631072 CACCGTCGACGATGCAATC 59.369 57.895 37.65 0.00 43.02 2.67
4933 9920 3.604129 TTTCGCCTGCGCTCATGGA 62.604 57.895 9.73 0.00 39.59 3.41
4940 9927 1.078918 TGCGCTCATGGAAGAGGTG 60.079 57.895 9.73 0.00 36.15 4.00
4961 9950 0.757935 GGGGCGTAGGATCCACACTA 60.758 60.000 15.82 0.00 0.00 2.74
4982 9971 0.253347 AGCCTCCAGGAAGGGAATCA 60.253 55.000 0.00 0.00 36.27 2.57
5064 10057 4.838152 CCACCCGCCAGATCCGTG 62.838 72.222 0.00 0.00 0.00 4.94
5077 10070 0.541392 ATCCGTGCAGGCAGTATTGA 59.459 50.000 0.00 0.00 40.77 2.57
5183 10176 3.450115 GAGGAGCCGCCGTAGTGT 61.450 66.667 0.00 0.00 43.43 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.095452 AGATCCCCACCTGAATATATTGTATC 57.905 38.462 1.78 0.00 0.00 2.24
3 4 6.215636 GGTAGATCCCCACCTGAATATATTGT 59.784 42.308 1.78 0.00 0.00 2.71
4 5 6.653989 GGTAGATCCCCACCTGAATATATTG 58.346 44.000 1.78 0.00 0.00 1.90
20 21 0.177373 GGTCAACCGTGGGTAGATCC 59.823 60.000 0.00 0.00 33.12 3.36
21 22 0.899720 TGGTCAACCGTGGGTAGATC 59.100 55.000 0.00 0.00 39.43 2.75
22 23 1.580059 ATGGTCAACCGTGGGTAGAT 58.420 50.000 0.00 0.00 39.43 1.98
23 24 1.276989 GAATGGTCAACCGTGGGTAGA 59.723 52.381 0.00 0.00 39.43 2.59
24 25 1.002659 TGAATGGTCAACCGTGGGTAG 59.997 52.381 0.00 0.00 39.43 3.18
25 26 1.057471 TGAATGGTCAACCGTGGGTA 58.943 50.000 0.00 0.00 39.43 3.69
26 27 0.183971 TTGAATGGTCAACCGTGGGT 59.816 50.000 0.00 0.00 38.88 4.51
27 28 1.323412 TTTGAATGGTCAACCGTGGG 58.677 50.000 0.00 0.00 43.52 4.61
28 29 3.444703 TTTTTGAATGGTCAACCGTGG 57.555 42.857 0.00 0.00 43.52 4.94
46 47 2.430694 GGCCAAAGTGAGTGGTCTTTTT 59.569 45.455 0.00 0.00 37.79 1.94
47 48 2.031870 GGCCAAAGTGAGTGGTCTTTT 58.968 47.619 0.00 0.00 37.79 2.27
48 49 1.064017 TGGCCAAAGTGAGTGGTCTTT 60.064 47.619 0.61 0.00 41.59 2.52
49 50 0.550914 TGGCCAAAGTGAGTGGTCTT 59.449 50.000 0.61 0.00 41.59 3.01
50 51 0.550914 TTGGCCAAAGTGAGTGGTCT 59.449 50.000 17.98 0.00 41.59 3.85
51 52 0.954452 CTTGGCCAAAGTGAGTGGTC 59.046 55.000 20.91 0.00 41.40 4.02
52 53 0.468029 CCTTGGCCAAAGTGAGTGGT 60.468 55.000 20.91 0.00 38.50 4.16
53 54 1.809567 GCCTTGGCCAAAGTGAGTGG 61.810 60.000 20.91 15.99 39.33 4.00
54 55 1.662044 GCCTTGGCCAAAGTGAGTG 59.338 57.895 20.91 5.60 33.66 3.51
55 56 1.531602 GGCCTTGGCCAAAGTGAGT 60.532 57.895 24.50 0.00 33.66 3.41
56 57 2.629656 CGGCCTTGGCCAAAGTGAG 61.630 63.158 27.80 7.05 33.66 3.51
57 58 2.597217 CGGCCTTGGCCAAAGTGA 60.597 61.111 27.80 0.00 33.66 3.41
58 59 4.362476 GCGGCCTTGGCCAAAGTG 62.362 66.667 27.80 12.02 33.66 3.16
59 60 3.204467 TAGCGGCCTTGGCCAAAGT 62.204 57.895 27.80 12.61 33.66 2.66
60 61 2.361104 TAGCGGCCTTGGCCAAAG 60.361 61.111 27.80 15.33 35.47 2.77
61 62 2.361104 CTAGCGGCCTTGGCCAAA 60.361 61.111 27.80 12.77 0.00 3.28
64 65 2.682582 ATTAGCTAGCGGCCTTGGCC 62.683 60.000 20.15 20.15 43.05 5.36
65 66 1.227973 ATTAGCTAGCGGCCTTGGC 60.228 57.895 9.55 2.49 43.05 4.52
66 67 0.106708 TGATTAGCTAGCGGCCTTGG 59.893 55.000 9.55 0.00 43.05 3.61
67 68 1.953559 TTGATTAGCTAGCGGCCTTG 58.046 50.000 9.55 0.00 43.05 3.61
68 69 2.938956 ATTGATTAGCTAGCGGCCTT 57.061 45.000 9.55 0.00 43.05 4.35
69 70 3.369892 CCATATTGATTAGCTAGCGGCCT 60.370 47.826 9.55 0.00 43.05 5.19
70 71 2.939103 CCATATTGATTAGCTAGCGGCC 59.061 50.000 9.55 0.00 43.05 6.13
71 72 3.619038 GTCCATATTGATTAGCTAGCGGC 59.381 47.826 9.55 0.00 42.19 6.53
72 73 5.078411 AGTCCATATTGATTAGCTAGCGG 57.922 43.478 9.55 0.01 0.00 5.52
73 74 5.105752 GGAGTCCATATTGATTAGCTAGCG 58.894 45.833 9.55 0.00 0.00 4.26
74 75 6.042638 TGGAGTCCATATTGATTAGCTAGC 57.957 41.667 8.12 6.62 0.00 3.42
75 76 9.512588 AAAATGGAGTCCATATTGATTAGCTAG 57.487 33.333 25.09 0.00 44.40 3.42
76 77 9.288576 CAAAATGGAGTCCATATTGATTAGCTA 57.711 33.333 25.09 0.00 44.40 3.32
77 78 8.000709 TCAAAATGGAGTCCATATTGATTAGCT 58.999 33.333 25.09 2.36 44.40 3.32
78 79 8.169977 TCAAAATGGAGTCCATATTGATTAGC 57.830 34.615 25.09 0.00 44.40 3.09
82 83 8.800332 GCTATTCAAAATGGAGTCCATATTGAT 58.200 33.333 25.09 16.33 44.40 2.57
83 84 7.779326 TGCTATTCAAAATGGAGTCCATATTGA 59.221 33.333 25.09 15.77 44.40 2.57
84 85 7.944061 TGCTATTCAAAATGGAGTCCATATTG 58.056 34.615 25.09 15.16 44.40 1.90
85 86 8.716674 ATGCTATTCAAAATGGAGTCCATATT 57.283 30.769 25.09 17.10 44.40 1.28
86 87 7.120285 CGATGCTATTCAAAATGGAGTCCATAT 59.880 37.037 25.09 16.05 44.40 1.78
87 88 6.427853 CGATGCTATTCAAAATGGAGTCCATA 59.572 38.462 25.09 9.57 44.40 2.74
89 90 4.576053 CGATGCTATTCAAAATGGAGTCCA 59.424 41.667 15.88 15.88 38.19 4.02
90 91 4.816385 TCGATGCTATTCAAAATGGAGTCC 59.184 41.667 0.73 0.73 0.00 3.85
91 92 5.991328 TCGATGCTATTCAAAATGGAGTC 57.009 39.130 0.00 0.00 0.00 3.36
92 93 5.882557 ACTTCGATGCTATTCAAAATGGAGT 59.117 36.000 0.00 0.00 0.00 3.85
93 94 6.197276 CACTTCGATGCTATTCAAAATGGAG 58.803 40.000 0.00 0.00 0.00 3.86
94 95 5.066375 CCACTTCGATGCTATTCAAAATGGA 59.934 40.000 0.00 0.00 0.00 3.41
95 96 5.276270 CCACTTCGATGCTATTCAAAATGG 58.724 41.667 0.00 0.00 0.00 3.16
96 97 5.276270 CCCACTTCGATGCTATTCAAAATG 58.724 41.667 0.00 0.00 0.00 2.32
97 98 4.339247 CCCCACTTCGATGCTATTCAAAAT 59.661 41.667 0.00 0.00 0.00 1.82
98 99 3.694072 CCCCACTTCGATGCTATTCAAAA 59.306 43.478 0.00 0.00 0.00 2.44
99 100 3.278574 CCCCACTTCGATGCTATTCAAA 58.721 45.455 0.00 0.00 0.00 2.69
100 101 2.917933 CCCCACTTCGATGCTATTCAA 58.082 47.619 0.00 0.00 0.00 2.69
101 102 1.475034 GCCCCACTTCGATGCTATTCA 60.475 52.381 0.00 0.00 0.00 2.57
102 103 1.230324 GCCCCACTTCGATGCTATTC 58.770 55.000 0.00 0.00 0.00 1.75
103 104 0.179018 GGCCCCACTTCGATGCTATT 60.179 55.000 0.00 0.00 0.00 1.73
104 105 1.056700 AGGCCCCACTTCGATGCTAT 61.057 55.000 0.00 0.00 0.00 2.97
105 106 1.271840 AAGGCCCCACTTCGATGCTA 61.272 55.000 0.00 0.00 0.00 3.49
106 107 2.606587 AAGGCCCCACTTCGATGCT 61.607 57.895 0.00 0.00 0.00 3.79
111 112 1.452108 GATCCAAGGCCCCACTTCG 60.452 63.158 0.00 0.00 0.00 3.79
147 148 2.765807 CAGAGAGGTGGCCCCGAT 60.766 66.667 0.00 0.00 38.74 4.18
170 171 3.303593 GGACATCATACGCAGCAAGATTG 60.304 47.826 0.00 0.00 0.00 2.67
176 177 1.066215 ACAAGGACATCATACGCAGCA 60.066 47.619 0.00 0.00 0.00 4.41
194 195 1.070786 GGACGGGTGCTTCTTGACA 59.929 57.895 0.00 0.00 0.00 3.58
230 231 0.248907 CGGATGTACGCGACTCCATT 60.249 55.000 15.93 0.00 0.00 3.16
254 255 2.896801 GACAACGTGGGTGCAGCTG 61.897 63.158 16.65 10.11 0.00 4.24
265 266 1.480954 ACTTGTGGACTGAGACAACGT 59.519 47.619 0.00 0.00 0.00 3.99
293 294 1.304713 AGCCCCAATGTTGCAGGAG 60.305 57.895 4.73 0.00 0.00 3.69
322 323 3.643554 GGCCTACCGGTGTTGGGT 61.644 66.667 19.93 0.00 37.78 4.51
339 340 1.429021 CATTGATGGACGGCGGTTG 59.571 57.895 13.24 0.00 0.00 3.77
341 342 2.824041 GCATTGATGGACGGCGGT 60.824 61.111 13.24 0.00 0.00 5.68
351 352 2.372264 CACTGTTAGCCAGGCATTGAT 58.628 47.619 15.80 0.00 46.06 2.57
396 397 1.997606 GCCGAACATATATGCCCGTAC 59.002 52.381 12.79 7.11 0.00 3.67
398 399 0.669318 CGCCGAACATATATGCCCGT 60.669 55.000 12.79 0.00 0.00 5.28
399 400 1.966493 GCGCCGAACATATATGCCCG 61.966 60.000 12.79 14.75 0.00 6.13
445 446 2.277008 ATTCTGGGAGGACAGATGGT 57.723 50.000 0.00 0.00 46.07 3.55
529 530 3.181506 GGAGATTCAAATCAACGTGCCTC 60.182 47.826 5.59 0.00 37.89 4.70
569 570 1.067199 CGTGGCTACAACGTACCGAC 61.067 60.000 0.00 0.00 0.00 4.79
605 606 3.052455 TGAAGTGGCTCGATAAAAGCA 57.948 42.857 0.00 0.00 41.66 3.91
609 610 3.678072 CGAACTTGAAGTGGCTCGATAAA 59.322 43.478 11.32 0.00 30.04 1.40
610 611 3.250744 CGAACTTGAAGTGGCTCGATAA 58.749 45.455 11.32 0.00 30.04 1.75
614 615 0.319555 TCCGAACTTGAAGTGGCTCG 60.320 55.000 10.11 10.11 0.00 5.03
722 723 2.301009 CTGGTAGTACGTGGGTTCCTTT 59.699 50.000 0.00 0.00 0.00 3.11
769 770 5.978919 TGACAAACAACAGAAAGATCAATGC 59.021 36.000 0.00 0.00 0.00 3.56
770 771 7.990541 TTGACAAACAACAGAAAGATCAATG 57.009 32.000 0.00 0.00 33.18 2.82
796 813 2.622436 GCCAGCTCGATTAGTTTCAGT 58.378 47.619 0.00 0.00 0.00 3.41
936 961 1.537202 GAAGTTTGCGAGCCTCACAAT 59.463 47.619 0.00 0.00 0.00 2.71
1081 1109 1.963338 GTTGGACGCTGCTGCTTCT 60.963 57.895 19.06 0.08 37.57 2.85
1112 1140 2.053865 GGTGGTGGTCATGGCCATG 61.054 63.158 35.76 35.76 41.08 3.66
1122 1150 3.923645 TCGGGAGGAGGTGGTGGT 61.924 66.667 0.00 0.00 0.00 4.16
1309 1337 2.420022 CGGCAGGAAATCAAGTGGTAAG 59.580 50.000 0.00 0.00 0.00 2.34
1481 1511 9.216117 TCCTAATCTTACTTCAGCAAACTTAAC 57.784 33.333 0.00 0.00 0.00 2.01
1518 1548 5.499139 TCAGTTTCAGTCAACATGTTTCC 57.501 39.130 8.77 2.07 0.00 3.13
1544 1578 0.393944 GCAGGGGTACAGTTTAGGCC 60.394 60.000 0.00 0.00 0.00 5.19
1586 1620 3.194116 TCTTTGCCTGCATTGGAGAAATC 59.806 43.478 6.77 0.00 0.00 2.17
1736 1771 6.364976 TCGTCTCATTTTACATGTAGTGTGTG 59.635 38.462 5.56 7.25 42.24 3.82
1766 1801 4.022329 ACTTTAACGCTTCCAAATTCCCAG 60.022 41.667 0.00 0.00 0.00 4.45
1771 1806 6.569780 ACTCAAACTTTAACGCTTCCAAATT 58.430 32.000 0.00 0.00 0.00 1.82
1818 1853 7.118680 GCAAGCTAAACTAACTGGTTGTACATA 59.881 37.037 0.00 0.00 39.28 2.29
1829 1865 6.405278 ACCAAAATGCAAGCTAAACTAACT 57.595 33.333 0.00 0.00 0.00 2.24
1851 1887 8.434661 CAAATATAATGCAAGTGTGAAACCAAC 58.565 33.333 0.00 0.00 34.36 3.77
2115 2165 0.179181 TCCAACGCATACGAGACGAC 60.179 55.000 0.00 0.00 43.93 4.34
2166 2216 2.350772 GCAGAGGAACGATGTGGTTTTG 60.351 50.000 0.00 0.00 0.00 2.44
2344 2394 2.240612 GATTGTGTCTTCGCACGGCC 62.241 60.000 0.00 0.00 41.94 6.13
2687 2738 2.169352 AGACCTAGATGCAACGCTCAAT 59.831 45.455 0.00 0.00 0.00 2.57
2691 2742 2.622436 GAAAGACCTAGATGCAACGCT 58.378 47.619 0.00 0.00 0.00 5.07
2803 2859 2.223876 CCGCATCCCAATTCCATTTCAG 60.224 50.000 0.00 0.00 0.00 3.02
2819 2875 1.327303 TTTCAAGAAACAGGCCGCAT 58.673 45.000 0.00 0.00 0.00 4.73
3022 3083 0.673644 ACTGAATTCTCCCAACGCCG 60.674 55.000 7.05 0.00 0.00 6.46
3441 3506 9.166173 CACTTTGATACTTCAGATTCACCATTA 57.834 33.333 0.00 0.00 32.27 1.90
3647 3712 6.956299 ATGTGTTAAGCATGCTTTCATTTC 57.044 33.333 35.99 21.60 37.47 2.17
3676 3741 7.559335 TCCACATTATGATGGCTTCTAGTAT 57.441 36.000 0.00 0.00 37.60 2.12
3681 3746 5.579753 AGATCCACATTATGATGGCTTCT 57.420 39.130 0.00 6.33 37.60 2.85
3849 3914 0.031994 AATGTCGCAACTTGGCCAAC 59.968 50.000 16.05 3.97 0.00 3.77
3860 3926 2.616376 CCCATTTATTCGGAATGTCGCA 59.384 45.455 13.37 0.00 33.65 5.10
3881 3947 4.757149 ACATCTCCTTTGTTCAAGCTACAC 59.243 41.667 0.00 0.00 0.00 2.90
4118 4187 5.550290 TCAGACATCAAAAGAGTGTGCATA 58.450 37.500 0.00 0.00 0.00 3.14
4158 4227 8.566260 CAACAAGAAAATATCATTTTTGCCCAA 58.434 29.630 0.00 0.00 0.00 4.12
4223 4292 4.338118 AGAGTCAGCTGCTATCTTCTACAC 59.662 45.833 9.47 0.00 0.00 2.90
4236 4308 1.296755 ACGCAATGCAGAGTCAGCTG 61.297 55.000 7.63 7.63 38.91 4.24
4475 7077 4.917385 TGGCTTTAGATGTTAGGCTTTGA 58.083 39.130 0.00 0.00 35.66 2.69
4505 7107 4.593206 CCAATCTAGGTAGTGGCTTGGATA 59.407 45.833 0.00 0.00 34.88 2.59
4522 7151 2.602676 CCGGTGTGGGACCCAATCT 61.603 63.158 16.98 0.00 42.62 2.40
4621 7250 3.134127 GGCAAGGTCGGTGCATCC 61.134 66.667 0.00 0.00 44.07 3.51
4673 8408 1.682257 GCAGGAGGAGGAAGCTGTT 59.318 57.895 0.00 0.00 0.00 3.16
4766 9753 2.202932 GAGCGGTGTGGCATCGAT 60.203 61.111 5.94 0.00 40.00 3.59
4768 9755 4.758251 TGGAGCGGTGTGGCATCG 62.758 66.667 0.00 0.00 41.32 3.84
4890 9877 0.400213 TGTTCCTCTGTTTGGGCGAT 59.600 50.000 0.00 0.00 0.00 4.58
4961 9950 1.286257 GATTCCCTTCCTGGAGGCTTT 59.714 52.381 0.00 0.00 38.35 3.51
5064 10057 0.457853 TCGACGTCAATACTGCCTGC 60.458 55.000 17.16 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.