Multiple sequence alignment - TraesCS7D01G248300

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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 TraesCS7D01G248300 chr7D 100.000 4640 0 0 1 4640 219827082 219831721 0.000000e+00 8569.0
1 TraesCS7D01G248300 chr7D 79.933 299 48 10 131 421 460516451 460516157 4.700000e-50 209.0
2 TraesCS7D01G248300 chr7A 96.751 3355 82 10 762 4107 232374356 232377692 0.000000e+00 5566.0
3 TraesCS7D01G248300 chr7A 96.709 547 11 5 4100 4640 232377714 232378259 0.000000e+00 904.0
4 TraesCS7D01G248300 chr7A 90.476 441 32 8 136 573 232371589 232372022 1.450000e-159 573.0
5 TraesCS7D01G248300 chr7A 81.481 297 45 5 118 408 194793923 194793631 7.760000e-58 235.0
6 TraesCS7D01G248300 chr7A 97.059 102 3 0 666 767 232374206 232374307 6.170000e-39 172.0
7 TraesCS7D01G248300 chr7A 94.444 108 4 2 574 681 232373301 232373406 1.030000e-36 165.0
8 TraesCS7D01G248300 chr7B 96.510 3352 86 14 762 4105 179924626 179921298 0.000000e+00 5513.0
9 TraesCS7D01G248300 chr7B 95.941 542 17 3 4104 4640 179921269 179920728 0.000000e+00 874.0
10 TraesCS7D01G248300 chr7B 93.750 144 7 2 623 766 179924818 179924677 1.010000e-51 215.0
11 TraesCS7D01G248300 chr5A 89.524 1871 177 10 1894 3754 36373689 36371828 0.000000e+00 2351.0
12 TraesCS7D01G248300 chr5A 88.918 388 35 3 1559 1939 36374069 36373683 5.430000e-129 472.0
13 TraesCS7D01G248300 chr5B 90.044 1597 129 18 1993 3568 45823892 45822305 0.000000e+00 2041.0
14 TraesCS7D01G248300 chr5B 88.303 1214 89 26 2511 3715 45650531 45649362 0.000000e+00 1406.0
15 TraesCS7D01G248300 chr5B 88.483 903 87 9 1558 2458 45651412 45650525 0.000000e+00 1075.0
16 TraesCS7D01G248300 chr5B 88.342 386 31 3 1561 1946 45824268 45823897 7.080000e-123 451.0
17 TraesCS7D01G248300 chr5B 81.206 282 42 7 135 410 664884612 664884888 2.810000e-52 217.0
18 TraesCS7D01G248300 chr5B 80.000 300 48 8 130 422 447575411 447575705 1.310000e-50 211.0
19 TraesCS7D01G248300 chr5D 89.070 613 54 4 1558 2168 45601344 45600743 0.000000e+00 749.0
20 TraesCS7D01G248300 chr5D 92.623 488 28 4 2496 2976 45598901 45598415 0.000000e+00 695.0
21 TraesCS7D01G248300 chr5D 89.753 283 24 2 2164 2442 45599374 45599093 1.590000e-94 357.0
22 TraesCS7D01G248300 chr5D 80.328 305 45 10 126 421 96012898 96013196 2.810000e-52 217.0
23 TraesCS7D01G248300 chr5D 89.000 100 2 1 3010 3109 45598411 45598321 1.060000e-21 115.0
24 TraesCS7D01G248300 chr5D 93.151 73 5 0 1068 1140 45601415 45601343 1.770000e-19 108.0
25 TraesCS7D01G248300 chr4D 81.757 296 40 11 126 413 434065317 434065606 7.760000e-58 235.0
26 TraesCS7D01G248300 chr3D 79.868 303 48 8 126 419 255424391 255424689 4.700000e-50 209.0
27 TraesCS7D01G248300 chr3D 82.667 225 21 11 4379 4585 603590324 603590548 2.850000e-42 183.0
28 TraesCS7D01G248300 chr3B 79.868 303 47 9 126 419 377115119 377115416 4.700000e-50 209.0
29 TraesCS7D01G248300 chr3B 88.372 129 14 1 4458 4585 810282997 810282869 2.240000e-33 154.0
30 TraesCS7D01G248300 chr3A 82.667 225 21 12 4379 4585 732483538 732483314 2.850000e-42 183.0
31 TraesCS7D01G248300 chr6D 80.531 226 25 11 4379 4585 455720994 455720769 6.220000e-34 156.0
32 TraesCS7D01G248300 chr6A 80.444 225 26 10 4379 4585 590781026 590781250 6.220000e-34 156.0
33 TraesCS7D01G248300 chr2A 81.579 114 16 5 588 698 425909014 425908903 6.390000e-14 89.8


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 TraesCS7D01G248300 chr7D 219827082 219831721 4639 False 8569.000000 8569 100.000000 1 4640 1 chr7D.!!$F1 4639
1 TraesCS7D01G248300 chr7A 232371589 232378259 6670 False 1476.000000 5566 95.087800 136 4640 5 chr7A.!!$F1 4504
2 TraesCS7D01G248300 chr7B 179920728 179924818 4090 True 2200.666667 5513 95.400333 623 4640 3 chr7B.!!$R1 4017
3 TraesCS7D01G248300 chr5A 36371828 36374069 2241 True 1411.500000 2351 89.221000 1559 3754 2 chr5A.!!$R1 2195
4 TraesCS7D01G248300 chr5B 45822305 45824268 1963 True 1246.000000 2041 89.193000 1561 3568 2 chr5B.!!$R2 2007
5 TraesCS7D01G248300 chr5B 45649362 45651412 2050 True 1240.500000 1406 88.393000 1558 3715 2 chr5B.!!$R1 2157
6 TraesCS7D01G248300 chr5D 45598321 45601415 3094 True 404.800000 749 90.719400 1068 3109 5 chr5D.!!$R1 2041

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
37 38 0.984109 GCATCATTGCGTTTTCGGTG 59.016 50.0 0.00 0.00 44.29 4.94 F
1059 3216 0.322906 CCTGCCCTCAGTTTTCCCTC 60.323 60.0 0.00 0.00 38.66 4.30 F
1062 3219 0.391793 GCCCTCAGTTTTCCCTCGAG 60.392 60.0 5.13 5.13 0.00 4.04 F
2315 5893 0.482446 AGGCTTTGTTGGGATGGACA 59.518 50.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 3223 0.793617 AGGAGAGTGGGAGAGGGAAA 59.206 55.000 0.00 0.00 0.00 3.13 R
2673 6397 0.588252 CGATAAAATCAGGCTGCCCG 59.412 55.000 16.57 5.01 35.76 6.13 R
2700 6424 3.152341 GCAAAGGCCACTGATATATGCT 58.848 45.455 5.01 0.00 0.00 3.79 R
4107 7870 0.106708 TGTGTCACAGAGAACAGGGC 59.893 55.000 0.18 0.00 0.00 5.19 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
36 37 3.399879 GCATCATTGCGTTTTCGGT 57.600 47.368 0.00 0.00 44.29 4.69
37 38 0.984109 GCATCATTGCGTTTTCGGTG 59.016 50.000 0.00 0.00 44.29 4.94
38 39 1.665735 GCATCATTGCGTTTTCGGTGT 60.666 47.619 0.00 0.00 44.29 4.16
39 40 2.660490 CATCATTGCGTTTTCGGTGTT 58.340 42.857 0.00 0.00 44.29 3.32
40 41 3.816091 CATCATTGCGTTTTCGGTGTTA 58.184 40.909 0.00 0.00 44.29 2.41
41 42 3.529634 TCATTGCGTTTTCGGTGTTAG 57.470 42.857 0.00 0.00 44.29 2.34
42 43 3.132160 TCATTGCGTTTTCGGTGTTAGA 58.868 40.909 0.00 0.00 44.29 2.10
43 44 3.185594 TCATTGCGTTTTCGGTGTTAGAG 59.814 43.478 0.00 0.00 44.29 2.43
44 45 2.228138 TGCGTTTTCGGTGTTAGAGT 57.772 45.000 0.00 0.00 44.29 3.24
45 46 2.553086 TGCGTTTTCGGTGTTAGAGTT 58.447 42.857 0.00 0.00 44.29 3.01
46 47 2.937799 TGCGTTTTCGGTGTTAGAGTTT 59.062 40.909 0.00 0.00 44.29 2.66
47 48 3.374678 TGCGTTTTCGGTGTTAGAGTTTT 59.625 39.130 0.00 0.00 44.29 2.43
48 49 4.142643 TGCGTTTTCGGTGTTAGAGTTTTT 60.143 37.500 0.00 0.00 44.29 1.94
49 50 4.203563 GCGTTTTCGGTGTTAGAGTTTTTG 59.796 41.667 0.00 0.00 44.29 2.44
50 51 4.203563 CGTTTTCGGTGTTAGAGTTTTTGC 59.796 41.667 0.00 0.00 39.94 3.68
51 52 3.974871 TTCGGTGTTAGAGTTTTTGCC 57.025 42.857 0.00 0.00 0.00 4.52
52 53 1.868498 TCGGTGTTAGAGTTTTTGCCG 59.132 47.619 0.00 0.00 39.33 5.69
53 54 1.868498 CGGTGTTAGAGTTTTTGCCGA 59.132 47.619 0.00 0.00 40.27 5.54
54 55 2.482721 CGGTGTTAGAGTTTTTGCCGAT 59.517 45.455 0.00 0.00 40.27 4.18
55 56 3.058501 CGGTGTTAGAGTTTTTGCCGATT 60.059 43.478 0.00 0.00 40.27 3.34
56 57 4.473199 GGTGTTAGAGTTTTTGCCGATTC 58.527 43.478 0.00 0.00 0.00 2.52
57 58 4.023536 GGTGTTAGAGTTTTTGCCGATTCA 60.024 41.667 0.00 0.00 0.00 2.57
58 59 5.335661 GGTGTTAGAGTTTTTGCCGATTCAT 60.336 40.000 0.00 0.00 0.00 2.57
59 60 6.128117 GGTGTTAGAGTTTTTGCCGATTCATA 60.128 38.462 0.00 0.00 0.00 2.15
60 61 7.415206 GGTGTTAGAGTTTTTGCCGATTCATAT 60.415 37.037 0.00 0.00 0.00 1.78
61 62 7.429340 GTGTTAGAGTTTTTGCCGATTCATATG 59.571 37.037 0.00 0.00 0.00 1.78
62 63 7.120579 TGTTAGAGTTTTTGCCGATTCATATGT 59.879 33.333 1.90 0.00 0.00 2.29
63 64 5.883661 AGAGTTTTTGCCGATTCATATGTG 58.116 37.500 1.90 0.00 0.00 3.21
64 65 5.647658 AGAGTTTTTGCCGATTCATATGTGA 59.352 36.000 1.90 0.00 0.00 3.58
65 66 5.883661 AGTTTTTGCCGATTCATATGTGAG 58.116 37.500 1.90 0.00 35.39 3.51
66 67 4.898829 TTTTGCCGATTCATATGTGAGG 57.101 40.909 1.90 4.06 35.39 3.86
67 68 3.836365 TTGCCGATTCATATGTGAGGA 57.164 42.857 1.90 0.00 35.39 3.71
68 69 3.836365 TGCCGATTCATATGTGAGGAA 57.164 42.857 1.90 0.00 35.39 3.36
69 70 4.356405 TGCCGATTCATATGTGAGGAAT 57.644 40.909 1.90 0.00 41.20 3.01
70 71 4.067192 TGCCGATTCATATGTGAGGAATG 58.933 43.478 1.90 0.00 38.65 2.67
71 72 4.067896 GCCGATTCATATGTGAGGAATGT 58.932 43.478 1.90 0.00 38.65 2.71
72 73 4.516698 GCCGATTCATATGTGAGGAATGTT 59.483 41.667 1.90 0.00 38.65 2.71
73 74 5.334414 GCCGATTCATATGTGAGGAATGTTC 60.334 44.000 1.90 0.00 38.65 3.18
74 75 5.994054 CCGATTCATATGTGAGGAATGTTCT 59.006 40.000 1.90 0.00 38.65 3.01
75 76 6.146837 CCGATTCATATGTGAGGAATGTTCTC 59.853 42.308 1.90 0.00 38.65 2.87
76 77 6.927936 CGATTCATATGTGAGGAATGTTCTCT 59.072 38.462 1.90 0.00 38.65 3.10
77 78 7.440556 CGATTCATATGTGAGGAATGTTCTCTT 59.559 37.037 1.90 0.00 38.65 2.85
78 79 8.674263 ATTCATATGTGAGGAATGTTCTCTTC 57.326 34.615 1.90 0.00 37.19 2.87
79 80 6.586344 TCATATGTGAGGAATGTTCTCTTCC 58.414 40.000 1.90 0.00 42.13 3.46
91 92 9.061435 GGAATGTTCTCTTCCTTATTCTATTGG 57.939 37.037 0.00 0.00 39.30 3.16
92 93 8.457238 AATGTTCTCTTCCTTATTCTATTGGC 57.543 34.615 0.00 0.00 0.00 4.52
93 94 6.957631 TGTTCTCTTCCTTATTCTATTGGCA 58.042 36.000 0.00 0.00 0.00 4.92
94 95 7.577303 TGTTCTCTTCCTTATTCTATTGGCAT 58.423 34.615 0.00 0.00 0.00 4.40
95 96 8.055181 TGTTCTCTTCCTTATTCTATTGGCATT 58.945 33.333 0.00 0.00 0.00 3.56
96 97 8.907885 GTTCTCTTCCTTATTCTATTGGCATTT 58.092 33.333 0.00 0.00 0.00 2.32
97 98 9.479549 TTCTCTTCCTTATTCTATTGGCATTTT 57.520 29.630 0.00 0.00 0.00 1.82
98 99 9.479549 TCTCTTCCTTATTCTATTGGCATTTTT 57.520 29.630 0.00 0.00 0.00 1.94
122 123 9.840427 TTTTGCATTGCTAGTTCTAAGTATTTC 57.160 29.630 10.49 0.00 0.00 2.17
123 124 7.234187 TGCATTGCTAGTTCTAAGTATTTCG 57.766 36.000 10.49 0.00 0.00 3.46
124 125 7.039270 TGCATTGCTAGTTCTAAGTATTTCGA 58.961 34.615 10.49 0.00 0.00 3.71
125 126 7.710907 TGCATTGCTAGTTCTAAGTATTTCGAT 59.289 33.333 10.49 0.00 0.00 3.59
126 127 9.193133 GCATTGCTAGTTCTAAGTATTTCGATA 57.807 33.333 0.16 0.00 0.00 2.92
203 204 2.749621 CTCTTGGTCCAATCTTTTCCCG 59.250 50.000 4.34 0.00 0.00 5.14
290 291 8.362639 ACCAAATGTCTCATCAAAATATATGGC 58.637 33.333 0.00 0.00 0.00 4.40
297 298 8.671921 GTCTCATCAAAATATATGGCGAATCAT 58.328 33.333 0.00 0.00 0.00 2.45
299 300 7.764331 TCATCAAAATATATGGCGAATCATGG 58.236 34.615 0.00 0.00 0.00 3.66
381 382 9.924650 ACAAGCTAACTTACTATTTATATCCCG 57.075 33.333 0.00 0.00 33.74 5.14
389 390 3.994392 ACTATTTATATCCCGCTGCAACG 59.006 43.478 1.65 1.65 0.00 4.10
394 395 2.867793 TATCCCGCTGCAACGCACAT 62.868 55.000 3.43 0.00 33.79 3.21
406 407 4.749598 TGCAACGCACATACATTATCCTAG 59.250 41.667 0.00 0.00 31.71 3.02
413 414 8.585881 ACGCACATACATTATCCTAGTTAATCT 58.414 33.333 0.00 0.00 0.00 2.40
414 415 9.424319 CGCACATACATTATCCTAGTTAATCTT 57.576 33.333 0.00 0.00 0.00 2.40
474 475 3.621558 GAGGGGAAACGAATCCAATCTT 58.378 45.455 12.16 0.00 41.55 2.40
477 478 3.128764 GGGGAAACGAATCCAATCTTCAC 59.871 47.826 12.16 0.00 41.55 3.18
513 516 4.438562 TGCATGGCGGTTGCATGC 62.439 61.111 11.82 11.82 44.73 4.06
517 520 3.942377 ATGGCGGTTGCATGCAGGA 62.942 57.895 21.50 3.84 45.35 3.86
573 576 9.082313 CTCCCATGCTACCATTTATTTTAGAAT 57.918 33.333 0.00 0.00 0.00 2.40
683 2777 9.696917 ACATTGAGAAATAAAAGACAAATCCAC 57.303 29.630 0.00 0.00 0.00 4.02
699 2793 6.716628 ACAAATCCACATGTGAATAGTGTCTT 59.283 34.615 27.46 0.00 0.00 3.01
781 2929 3.391049 GTGTCTTTGTACACCCTCTGTC 58.609 50.000 0.00 0.00 43.23 3.51
787 2935 6.935208 GTCTTTGTACACCCTCTGTCTTTAAT 59.065 38.462 0.00 0.00 33.91 1.40
880 3029 4.789012 ATGTGCCAACCTACATCAAAAG 57.211 40.909 0.00 0.00 32.32 2.27
983 3132 3.395639 TCTTGAATCCAACGGTACACAC 58.604 45.455 0.00 0.00 0.00 3.82
1005 3154 2.495669 TGAGTGAGTCGGCATCATGTTA 59.504 45.455 0.00 0.00 0.00 2.41
1054 3211 2.282462 CCGCCTGCCCTCAGTTTT 60.282 61.111 0.00 0.00 38.66 2.43
1055 3212 2.335712 CCGCCTGCCCTCAGTTTTC 61.336 63.158 0.00 0.00 38.66 2.29
1056 3213 2.335712 CGCCTGCCCTCAGTTTTCC 61.336 63.158 0.00 0.00 38.66 3.13
1057 3214 1.979155 GCCTGCCCTCAGTTTTCCC 60.979 63.158 0.00 0.00 38.66 3.97
1058 3215 1.770324 CCTGCCCTCAGTTTTCCCT 59.230 57.895 0.00 0.00 38.66 4.20
1059 3216 0.322906 CCTGCCCTCAGTTTTCCCTC 60.323 60.000 0.00 0.00 38.66 4.30
1060 3217 0.674895 CTGCCCTCAGTTTTCCCTCG 60.675 60.000 0.00 0.00 35.61 4.63
1061 3218 1.125093 TGCCCTCAGTTTTCCCTCGA 61.125 55.000 0.00 0.00 0.00 4.04
1062 3219 0.391793 GCCCTCAGTTTTCCCTCGAG 60.392 60.000 5.13 5.13 0.00 4.04
1063 3220 1.267121 CCCTCAGTTTTCCCTCGAGA 58.733 55.000 15.71 0.00 0.00 4.04
1064 3221 1.205893 CCCTCAGTTTTCCCTCGAGAG 59.794 57.143 15.71 0.00 0.00 3.20
1065 3222 1.896465 CCTCAGTTTTCCCTCGAGAGT 59.104 52.381 15.71 0.00 0.00 3.24
1066 3223 2.300437 CCTCAGTTTTCCCTCGAGAGTT 59.700 50.000 15.71 0.00 0.00 3.01
1171 3328 4.486529 TCTTCTTCTCCTTATCCCCCTACT 59.513 45.833 0.00 0.00 0.00 2.57
1815 3979 4.503314 GCTGCGGGATTGCTTGGC 62.503 66.667 0.00 0.00 35.36 4.52
1941 4146 2.071778 AAATGCACAAGTCAGGGTGT 57.928 45.000 0.00 0.00 37.35 4.16
1965 4170 3.119245 AGCCGACTGTTGTGACGTATAAT 60.119 43.478 0.00 0.00 0.00 1.28
2315 5893 0.482446 AGGCTTTGTTGGGATGGACA 59.518 50.000 0.00 0.00 0.00 4.02
2673 6397 3.319122 GGGATGATATGGTGAAAGTTGGC 59.681 47.826 0.00 0.00 0.00 4.52
2700 6424 4.333649 CAGCCTGATTTTATCGCTTTCTCA 59.666 41.667 0.00 0.00 0.00 3.27
2760 6484 1.604278 GAGGCTTATCGGGCATTTGTC 59.396 52.381 0.00 0.00 0.00 3.18
3189 6939 2.999355 GAGAGTGCTGGATGAACTTGTC 59.001 50.000 0.00 0.00 33.85 3.18
3267 7024 2.540265 ATGATGTCCTTGATCGAGCC 57.460 50.000 4.21 0.00 0.00 4.70
3492 7250 3.898123 TCCAGGGTAGAGTTGCTGATATC 59.102 47.826 0.00 0.00 0.00 1.63
3501 7263 4.272018 AGAGTTGCTGATATCGACAAATGC 59.728 41.667 13.20 7.04 0.00 3.56
3510 7272 7.087409 TGATATCGACAAATGCATGTTTCTT 57.913 32.000 0.00 0.00 32.57 2.52
3656 7418 8.237811 ACTGGGTAATAGCCAAATTTCATAAG 57.762 34.615 12.62 0.00 46.28 1.73
3790 7553 0.546122 ATCAATTAGCCGGCCAGACA 59.454 50.000 26.15 2.94 0.00 3.41
3808 7571 5.013547 CAGACAAAAGAGAGTAGGAGGAGA 58.986 45.833 0.00 0.00 0.00 3.71
3829 7592 4.457949 AGAAGGAAGAAGAAGACGAGACTC 59.542 45.833 0.00 0.00 0.00 3.36
3832 7595 4.770010 AGGAAGAAGAAGACGAGACTCATT 59.230 41.667 2.82 0.00 0.00 2.57
3862 7625 2.036731 TGATCGACGGGGTCCTGT 59.963 61.111 0.31 0.31 38.41 4.00
3977 7740 4.155826 GTCTCTCATCTCCATCTACATCCG 59.844 50.000 0.00 0.00 0.00 4.18
4006 7769 9.933723 CTCCATTTTTATTCATCTTGTTTCCTT 57.066 29.630 0.00 0.00 0.00 3.36
4107 7870 7.470079 CCTCAATCTTCATCTTGTTATGTGTG 58.530 38.462 0.00 0.00 0.00 3.82
4108 7871 6.845302 TCAATCTTCATCTTGTTATGTGTGC 58.155 36.000 0.00 0.00 0.00 4.57
4172 7965 5.480073 AGAATAGTTGTGCTCTGTTCTCTCT 59.520 40.000 0.00 0.00 38.38 3.10
4173 7966 3.383620 AGTTGTGCTCTGTTCTCTCTG 57.616 47.619 0.00 0.00 0.00 3.35
4174 7967 1.797635 GTTGTGCTCTGTTCTCTCTGC 59.202 52.381 0.00 0.00 0.00 4.26
4175 7968 1.336131 TGTGCTCTGTTCTCTCTGCT 58.664 50.000 0.00 0.00 0.00 4.24
4176 7969 2.519013 TGTGCTCTGTTCTCTCTGCTA 58.481 47.619 0.00 0.00 0.00 3.49
4226 8020 3.942130 ATTTCTAGTGTTTTGGGCTGC 57.058 42.857 0.00 0.00 0.00 5.25
4230 8024 1.956477 CTAGTGTTTTGGGCTGCTGTT 59.044 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.330231 ACACCGAAAACGCAATGATG 57.670 45.000 0.00 0.00 0.00 3.07
20 21 3.749088 TCTAACACCGAAAACGCAATGAT 59.251 39.130 0.00 0.00 0.00 2.45
21 22 3.132160 TCTAACACCGAAAACGCAATGA 58.868 40.909 0.00 0.00 0.00 2.57
22 23 3.059188 ACTCTAACACCGAAAACGCAATG 60.059 43.478 0.00 0.00 0.00 2.82
23 24 3.135994 ACTCTAACACCGAAAACGCAAT 58.864 40.909 0.00 0.00 0.00 3.56
24 25 2.553086 ACTCTAACACCGAAAACGCAA 58.447 42.857 0.00 0.00 0.00 4.85
25 26 2.228138 ACTCTAACACCGAAAACGCA 57.772 45.000 0.00 0.00 0.00 5.24
26 27 3.597377 AAACTCTAACACCGAAAACGC 57.403 42.857 0.00 0.00 0.00 4.84
27 28 4.203563 GCAAAAACTCTAACACCGAAAACG 59.796 41.667 0.00 0.00 0.00 3.60
28 29 4.501559 GGCAAAAACTCTAACACCGAAAAC 59.498 41.667 0.00 0.00 0.00 2.43
29 30 4.674475 GGCAAAAACTCTAACACCGAAAA 58.326 39.130 0.00 0.00 0.00 2.29
30 31 3.242804 CGGCAAAAACTCTAACACCGAAA 60.243 43.478 0.00 0.00 41.86 3.46
31 32 2.288458 CGGCAAAAACTCTAACACCGAA 59.712 45.455 0.00 0.00 41.86 4.30
32 33 1.868498 CGGCAAAAACTCTAACACCGA 59.132 47.619 0.00 0.00 41.86 4.69
33 34 1.868498 TCGGCAAAAACTCTAACACCG 59.132 47.619 0.00 0.00 40.70 4.94
34 35 4.023536 TGAATCGGCAAAAACTCTAACACC 60.024 41.667 0.00 0.00 0.00 4.16
35 36 5.103290 TGAATCGGCAAAAACTCTAACAC 57.897 39.130 0.00 0.00 0.00 3.32
36 37 5.957842 ATGAATCGGCAAAAACTCTAACA 57.042 34.783 0.00 0.00 0.00 2.41
37 38 7.429340 CACATATGAATCGGCAAAAACTCTAAC 59.571 37.037 10.38 0.00 0.00 2.34
38 39 7.335673 TCACATATGAATCGGCAAAAACTCTAA 59.664 33.333 10.38 0.00 0.00 2.10
39 40 6.821160 TCACATATGAATCGGCAAAAACTCTA 59.179 34.615 10.38 0.00 0.00 2.43
40 41 5.647658 TCACATATGAATCGGCAAAAACTCT 59.352 36.000 10.38 0.00 0.00 3.24
41 42 5.879237 TCACATATGAATCGGCAAAAACTC 58.121 37.500 10.38 0.00 0.00 3.01
42 43 5.163622 CCTCACATATGAATCGGCAAAAACT 60.164 40.000 10.38 0.00 33.30 2.66
43 44 5.036737 CCTCACATATGAATCGGCAAAAAC 58.963 41.667 10.38 0.00 33.30 2.43
44 45 4.946772 TCCTCACATATGAATCGGCAAAAA 59.053 37.500 10.38 0.00 33.30 1.94
45 46 4.522114 TCCTCACATATGAATCGGCAAAA 58.478 39.130 10.38 0.00 33.30 2.44
46 47 4.149511 TCCTCACATATGAATCGGCAAA 57.850 40.909 10.38 0.00 33.30 3.68
47 48 3.836365 TCCTCACATATGAATCGGCAA 57.164 42.857 10.38 0.00 33.30 4.52
48 49 3.836365 TTCCTCACATATGAATCGGCA 57.164 42.857 10.38 0.00 33.30 5.69
49 50 4.067896 ACATTCCTCACATATGAATCGGC 58.932 43.478 10.38 0.00 33.30 5.54
50 51 5.994054 AGAACATTCCTCACATATGAATCGG 59.006 40.000 10.38 4.41 33.30 4.18
51 52 6.927936 AGAGAACATTCCTCACATATGAATCG 59.072 38.462 10.38 0.00 33.30 3.34
52 53 8.674263 AAGAGAACATTCCTCACATATGAATC 57.326 34.615 10.38 0.00 33.30 2.52
53 54 7.718753 GGAAGAGAACATTCCTCACATATGAAT 59.281 37.037 10.38 0.00 42.52 2.57
54 55 7.050377 GGAAGAGAACATTCCTCACATATGAA 58.950 38.462 10.38 0.00 42.52 2.57
55 56 6.586344 GGAAGAGAACATTCCTCACATATGA 58.414 40.000 10.38 0.00 42.52 2.15
56 57 6.857777 GGAAGAGAACATTCCTCACATATG 57.142 41.667 0.00 0.00 42.52 1.78
65 66 9.061435 CCAATAGAATAAGGAAGAGAACATTCC 57.939 37.037 0.00 0.00 45.56 3.01
66 67 8.563732 GCCAATAGAATAAGGAAGAGAACATTC 58.436 37.037 0.00 0.00 0.00 2.67
67 68 8.055181 TGCCAATAGAATAAGGAAGAGAACATT 58.945 33.333 0.00 0.00 0.00 2.71
68 69 7.577303 TGCCAATAGAATAAGGAAGAGAACAT 58.423 34.615 0.00 0.00 0.00 2.71
69 70 6.957631 TGCCAATAGAATAAGGAAGAGAACA 58.042 36.000 0.00 0.00 0.00 3.18
70 71 8.457238 AATGCCAATAGAATAAGGAAGAGAAC 57.543 34.615 0.00 0.00 0.00 3.01
71 72 9.479549 AAAATGCCAATAGAATAAGGAAGAGAA 57.520 29.630 0.00 0.00 0.00 2.87
72 73 9.479549 AAAAATGCCAATAGAATAAGGAAGAGA 57.520 29.630 0.00 0.00 0.00 3.10
96 97 9.840427 GAAATACTTAGAACTAGCAATGCAAAA 57.160 29.630 8.35 0.00 0.00 2.44
97 98 8.175069 CGAAATACTTAGAACTAGCAATGCAAA 58.825 33.333 8.35 0.00 0.00 3.68
98 99 7.547722 TCGAAATACTTAGAACTAGCAATGCAA 59.452 33.333 8.35 0.00 0.00 4.08
99 100 7.039270 TCGAAATACTTAGAACTAGCAATGCA 58.961 34.615 8.35 0.00 0.00 3.96
100 101 7.464830 TCGAAATACTTAGAACTAGCAATGC 57.535 36.000 0.00 0.00 0.00 3.56
132 133 8.475639 GGGACATTACATTCTTCTGAAGTAGTA 58.524 37.037 16.43 13.80 35.44 1.82
133 134 7.331791 GGGACATTACATTCTTCTGAAGTAGT 58.668 38.462 16.43 14.64 35.44 2.73
134 135 6.477033 CGGGACATTACATTCTTCTGAAGTAG 59.523 42.308 16.43 10.21 35.44 2.57
142 143 5.180492 TGAAACACGGGACATTACATTCTTC 59.820 40.000 0.00 0.00 0.00 2.87
147 148 4.015872 AGTGAAACACGGGACATTACAT 57.984 40.909 0.00 0.00 41.43 2.29
149 150 4.823790 AAAGTGAAACACGGGACATTAC 57.176 40.909 0.00 0.00 41.43 1.89
191 192 9.831737 GATTGATTATCATACGGGAAAAGATTG 57.168 33.333 0.00 0.00 33.21 2.67
196 197 7.287061 AGGTGATTGATTATCATACGGGAAAA 58.713 34.615 0.00 0.00 44.75 2.29
271 272 8.032952 TGATTCGCCATATATTTTGATGAGAC 57.967 34.615 0.00 0.00 0.00 3.36
278 279 5.104374 GCCCATGATTCGCCATATATTTTG 58.896 41.667 0.00 0.00 0.00 2.44
285 286 0.250858 CCTGCCCATGATTCGCCATA 60.251 55.000 0.00 0.00 0.00 2.74
290 291 1.520494 CAGATCCTGCCCATGATTCG 58.480 55.000 0.00 0.00 0.00 3.34
381 382 2.823196 TAATGTATGTGCGTTGCAGC 57.177 45.000 0.00 0.00 40.08 5.25
421 422 6.817765 AAAGAAGATTGGATTCGTTAAGCA 57.182 33.333 0.00 0.00 0.00 3.91
452 453 2.092375 AGATTGGATTCGTTTCCCCTCC 60.092 50.000 4.35 0.00 34.67 4.30
454 455 3.010138 TGAAGATTGGATTCGTTTCCCCT 59.990 43.478 4.35 0.00 34.67 4.79
457 458 5.181245 TCAAGTGAAGATTGGATTCGTTTCC 59.819 40.000 0.21 0.21 36.24 3.13
458 459 6.080406 GTCAAGTGAAGATTGGATTCGTTTC 58.920 40.000 0.00 0.00 0.00 2.78
474 475 5.412594 GCACATATCTCAAAAGGTCAAGTGA 59.587 40.000 0.00 0.00 0.00 3.41
477 478 5.885230 TGCACATATCTCAAAAGGTCAAG 57.115 39.130 0.00 0.00 0.00 3.02
513 516 2.684881 GGTATCACCATGTGCTTTCCTG 59.315 50.000 0.00 0.00 38.42 3.86
683 2777 5.122711 TGCACATGAAGACACTATTCACATG 59.877 40.000 0.00 0.00 39.36 3.21
699 2793 7.440198 TGTTTATTTTGAGGAAATGCACATGA 58.560 30.769 0.00 0.00 38.40 3.07
905 3054 1.268539 CGTCGCTTCAAGGCTTTTGTT 60.269 47.619 0.00 0.00 0.00 2.83
983 3132 1.134877 ACATGATGCCGACTCACTCAG 60.135 52.381 0.00 0.00 0.00 3.35
993 3142 4.816385 AGGTTGACTATTAACATGATGCCG 59.184 41.667 0.00 0.00 0.00 5.69
1005 3154 2.076863 GCGCACTTGAGGTTGACTATT 58.923 47.619 0.30 0.00 0.00 1.73
1053 3210 1.900486 GAGGGAAAACTCTCGAGGGAA 59.100 52.381 21.80 0.00 34.65 3.97
1054 3211 1.077334 AGAGGGAAAACTCTCGAGGGA 59.923 52.381 21.80 0.00 44.23 4.20
1055 3212 1.562783 AGAGGGAAAACTCTCGAGGG 58.437 55.000 11.78 11.78 44.23 4.30
1062 3219 2.235155 GAGAGTGGGAGAGGGAAAACTC 59.765 54.545 0.00 0.00 37.77 3.01
1063 3220 2.261729 GAGAGTGGGAGAGGGAAAACT 58.738 52.381 0.00 0.00 0.00 2.66
1064 3221 1.279558 GGAGAGTGGGAGAGGGAAAAC 59.720 57.143 0.00 0.00 0.00 2.43
1065 3222 1.152271 AGGAGAGTGGGAGAGGGAAAA 59.848 52.381 0.00 0.00 0.00 2.29
1066 3223 0.793617 AGGAGAGTGGGAGAGGGAAA 59.206 55.000 0.00 0.00 0.00 3.13
1171 3328 0.963962 GTCGTGGTGGAGAGTTGGTA 59.036 55.000 0.00 0.00 0.00 3.25
1941 4146 1.299850 CGTCACAACAGTCGGCTCA 60.300 57.895 0.00 0.00 0.00 4.26
1965 4170 3.440872 GGCACCGTACATTCACCAAAATA 59.559 43.478 0.00 0.00 0.00 1.40
2315 5893 1.076118 TGCCGGGCATCATCCAATT 60.076 52.632 19.77 0.00 31.71 2.32
2673 6397 0.588252 CGATAAAATCAGGCTGCCCG 59.412 55.000 16.57 5.01 35.76 6.13
2700 6424 3.152341 GCAAAGGCCACTGATATATGCT 58.848 45.455 5.01 0.00 0.00 3.79
2760 6484 4.448537 AAGACCTCTTCTTGTCATCTCG 57.551 45.455 0.00 0.00 43.45 4.04
3216 6966 4.095334 CCATCCATCAGTGTGTTGTATGTG 59.905 45.833 0.00 0.00 0.00 3.21
3492 7250 4.539870 ACTCAAGAAACATGCATTTGTCG 58.460 39.130 0.00 0.00 0.00 4.35
3501 7263 7.587629 TGAGCATTAAGAACTCAAGAAACATG 58.412 34.615 0.00 0.00 37.49 3.21
3510 7272 7.317390 TGTACGTTATGAGCATTAAGAACTCA 58.683 34.615 0.00 7.17 44.06 3.41
3617 7379 8.837389 GCTATTACCCAGTATCTAAAACTTTGG 58.163 37.037 0.00 0.00 0.00 3.28
3656 7418 6.524586 GCTAATGTTTTCAAGTAGTCATGTGC 59.475 38.462 0.00 0.00 0.00 4.57
3790 7553 5.278127 TCCTTCTCCTCCTACTCTCTTTT 57.722 43.478 0.00 0.00 0.00 2.27
3808 7571 4.145807 TGAGTCTCGTCTTCTTCTTCCTT 58.854 43.478 0.00 0.00 0.00 3.36
3829 7592 0.677731 ATCACACGCCCTGACCAATG 60.678 55.000 0.00 0.00 0.00 2.82
3832 7595 2.662596 GATCACACGCCCTGACCA 59.337 61.111 0.00 0.00 0.00 4.02
4006 7769 2.747460 GCAGCGGAACATCTGGCA 60.747 61.111 0.00 0.00 0.00 4.92
4107 7870 0.106708 TGTGTCACAGAGAACAGGGC 59.893 55.000 0.18 0.00 0.00 5.19
4172 7965 1.773653 TGACCATGGGCACATATAGCA 59.226 47.619 19.12 0.00 34.99 3.49
4173 7966 2.566833 TGACCATGGGCACATATAGC 57.433 50.000 19.12 0.00 34.99 2.97
4174 7967 4.290711 TGATGACCATGGGCACATATAG 57.709 45.455 26.45 0.00 34.99 1.31
4175 7968 4.654915 CTTGATGACCATGGGCACATATA 58.345 43.478 26.45 4.54 34.99 0.86
4176 7969 3.493334 CTTGATGACCATGGGCACATAT 58.507 45.455 26.45 6.83 34.99 1.78
4226 8020 5.571784 ATTTGCATCACAGACCATAACAG 57.428 39.130 0.00 0.00 0.00 3.16
4230 8024 8.785946 CATTGTATATTTGCATCACAGACCATA 58.214 33.333 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.