Multiple sequence alignment - TraesCS1A01G189300

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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 TraesCS1A01G189300 chr1A 100.000 3199 0 0 1 3199 342436083 342432885 0.000000e+00 5908.0
1 TraesCS1A01G189300 chr1A 79.551 401 72 8 1441 1839 342392828 342392436 8.740000e-71 278.0
2 TraesCS1A01G189300 chr1A 84.800 125 16 3 434 556 541472940 541472817 4.330000e-24 122.0
3 TraesCS1A01G189300 chr1A 90.789 76 5 2 2862 2935 397258588 397258513 2.030000e-17 100.0
4 TraesCS1A01G189300 chr1D 91.937 2344 95 34 640 2961 258552864 258555135 0.000000e+00 3195.0
5 TraesCS1A01G189300 chr1D 79.052 401 74 5 1441 1839 258576322 258576714 1.890000e-67 267.0
6 TraesCS1A01G189300 chr1D 89.474 95 8 2 3053 3145 328887039 328886945 5.610000e-23 119.0
7 TraesCS1A01G189300 chr1D 85.000 100 9 5 2862 2959 106848774 106848869 2.630000e-16 97.1
8 TraesCS1A01G189300 chr1B 90.467 2465 99 43 636 3055 354241023 354238650 0.000000e+00 3125.0
9 TraesCS1A01G189300 chr1B 86.939 245 20 4 401 633 640059451 640059695 6.800000e-67 265.0
10 TraesCS1A01G189300 chr1B 84.772 197 30 0 1441 1637 354234599 354234403 7.000000e-47 198.0
11 TraesCS1A01G189300 chr1B 80.567 247 28 16 189 432 461239949 461239720 4.240000e-39 172.0
12 TraesCS1A01G189300 chr1B 89.247 93 5 1 3053 3145 12831707 12831794 9.380000e-21 111.0
13 TraesCS1A01G189300 chr3B 96.220 291 11 0 1778 2068 612295120 612294830 8.030000e-131 477.0
14 TraesCS1A01G189300 chr3B 87.755 245 18 4 401 633 508714446 508714202 3.140000e-70 276.0
15 TraesCS1A01G189300 chr3B 94.350 177 9 1 1893 2068 51953127 51952951 1.460000e-68 270.0
16 TraesCS1A01G189300 chr3B 96.914 162 4 1 1622 1783 51953273 51953113 1.460000e-68 270.0
17 TraesCS1A01G189300 chr3B 97.059 68 1 1 1667 1733 612295182 612295115 2.610000e-21 113.0
18 TraesCS1A01G189300 chr3B 95.455 44 0 2 4 46 822814341 822814383 5.730000e-08 69.4
19 TraesCS1A01G189300 chr2B 94.565 276 15 0 1793 2068 672340153 672340428 8.200000e-116 427.0
20 TraesCS1A01G189300 chr2B 99.130 115 1 0 1617 1731 672340040 672340154 1.160000e-49 207.0
21 TraesCS1A01G189300 chr2B 97.170 106 3 0 1963 2068 107119095 107119200 2.540000e-41 180.0
22 TraesCS1A01G189300 chr2B 84.940 166 23 2 469 633 184405533 184405369 1.970000e-37 167.0
23 TraesCS1A01G189300 chr2B 87.129 101 8 2 3046 3146 745781619 745781714 3.370000e-20 110.0
24 TraesCS1A01G189300 chr2B 94.643 56 2 1 1728 1783 107119026 107119080 5.690000e-13 86.1
25 TraesCS1A01G189300 chr7B 90.574 244 22 1 1 244 602437857 602437615 3.980000e-84 322.0
26 TraesCS1A01G189300 chr7B 87.288 236 25 2 403 633 724343386 724343621 6.800000e-67 265.0
27 TraesCS1A01G189300 chr7B 83.525 261 15 9 401 633 602437464 602437204 5.370000e-53 219.0
28 TraesCS1A01G189300 chr7B 90.217 92 9 0 348 439 724343289 724343380 1.560000e-23 121.0
29 TraesCS1A01G189300 chr7B 86.916 107 12 2 3041 3145 474550482 474550588 5.610000e-23 119.0
30 TraesCS1A01G189300 chr7B 84.000 100 10 5 2862 2959 502910330 502910235 1.220000e-14 91.6
31 TraesCS1A01G189300 chr4D 89.912 228 21 2 404 630 361371408 361371182 3.120000e-75 292.0
32 TraesCS1A01G189300 chr4D 80.321 249 42 5 1069 1312 502749879 502749633 7.050000e-42 182.0
33 TraesCS1A01G189300 chr4D 80.663 181 31 4 1121 1299 502751469 502751291 1.550000e-28 137.0
34 TraesCS1A01G189300 chr4A 94.915 177 8 1 1893 2068 712882367 712882191 3.140000e-70 276.0
35 TraesCS1A01G189300 chr4A 94.611 167 8 1 1617 1783 712882518 712882353 1.140000e-64 257.0
36 TraesCS1A01G189300 chr4A 90.426 94 3 1 3053 3146 578107362 578107275 5.610000e-23 119.0
37 TraesCS1A01G189300 chr4A 84.694 98 10 2 2862 2959 571000235 571000143 3.400000e-15 93.5
38 TraesCS1A01G189300 chr4B 95.808 167 6 1 1617 1783 139108331 139108496 5.260000e-68 268.0
39 TraesCS1A01G189300 chr4B 93.220 177 11 1 1893 2068 139108482 139108658 3.170000e-65 259.0
40 TraesCS1A01G189300 chr4B 80.159 252 40 7 1069 1312 647637951 647637702 2.540000e-41 180.0
41 TraesCS1A01G189300 chr4B 80.000 180 34 2 1121 1299 647639525 647639347 7.200000e-27 132.0
42 TraesCS1A01G189300 chr3A 85.841 226 20 4 401 614 617256609 617256834 2.480000e-56 230.0
43 TraesCS1A01G189300 chr3A 91.919 99 4 1 3053 3151 23484971 23484877 5.570000e-28 135.0
44 TraesCS1A01G189300 chr5D 90.511 137 13 0 1 137 326123438 326123574 7.050000e-42 182.0
45 TraesCS1A01G189300 chr5A 80.159 252 40 7 1069 1312 687269167 687268918 2.540000e-41 180.0
46 TraesCS1A01G189300 chr5A 81.548 168 27 2 469 633 534902947 534902781 5.570000e-28 135.0
47 TraesCS1A01G189300 chr2A 82.738 168 25 2 469 633 723107516 723107682 2.570000e-31 147.0
48 TraesCS1A01G189300 chr6B 90.526 95 9 0 3052 3146 707934702 707934796 3.350000e-25 126.0
49 TraesCS1A01G189300 chr6B 82.692 104 12 3 2862 2959 103577943 103578046 1.580000e-13 87.9
50 TraesCS1A01G189300 chr5B 89.362 94 7 2 3053 3146 638836045 638836135 7.250000e-22 115.0
51 TraesCS1A01G189300 chr5B 89.362 94 5 4 3053 3145 638836134 638836045 2.610000e-21 113.0
52 TraesCS1A01G189300 chr5B 83.761 117 12 4 2862 2971 577662537 577662421 1.570000e-18 104.0
53 TraesCS1A01G189300 chr7A 90.909 77 4 3 2862 2935 120137549 120137473 2.030000e-17 100.0


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 TraesCS1A01G189300 chr1A 342432885 342436083 3198 True 5908.0 5908 100.0000 1 3199 1 chr1A.!!$R2 3198
1 TraesCS1A01G189300 chr1D 258552864 258555135 2271 False 3195.0 3195 91.9370 640 2961 1 chr1D.!!$F2 2321
2 TraesCS1A01G189300 chr1B 354238650 354241023 2373 True 3125.0 3125 90.4670 636 3055 1 chr1B.!!$R2 2419
3 TraesCS1A01G189300 chr7B 602437204 602437857 653 True 270.5 322 87.0495 1 633 2 chr7B.!!$R2 632

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
992 1096 0.107214 GGCCGTCTCATTCATTCCCA 60.107 55.0 0.00 0.0 0.00 4.37 F
1925 2034 0.399233 CCCTCCGGAAGAAGAGGGAT 60.399 60.0 17.41 0.0 38.82 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2064 0.389391 CGGCCATGTCCCTGTAGTAG 59.611 60.0 2.24 0.0 0.00 2.57 R
3018 3159 0.320247 CTACCATCAGCGGAGGCATC 60.320 60.0 0.00 0.0 43.41 3.91 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
63 64 2.520020 ACACGTCAGGGACACGGA 60.520 61.111 0.00 0.00 41.73 4.69
69 70 2.359975 CAGGGACACGGAAAGCCC 60.360 66.667 0.00 0.00 41.00 5.19
70 71 2.852075 AGGGACACGGAAAGCCCA 60.852 61.111 0.00 0.00 43.20 5.36
91 92 1.870055 TACAAGCCGACTCGTGACCC 61.870 60.000 0.00 0.00 0.00 4.46
100 101 0.320697 ACTCGTGACCCTAAACAGCC 59.679 55.000 0.00 0.00 0.00 4.85
104 105 0.960861 GTGACCCTAAACAGCCAGCC 60.961 60.000 0.00 0.00 0.00 4.85
116 117 2.743718 CCAGCCCACTCAGTTCGT 59.256 61.111 0.00 0.00 0.00 3.85
118 119 0.535102 CCAGCCCACTCAGTTCGTTT 60.535 55.000 0.00 0.00 0.00 3.60
138 139 2.247437 GGCGGCAGATTGGATCGAC 61.247 63.158 3.07 0.00 0.00 4.20
153 154 1.944676 CGACTATTCGCGGGTGAGC 60.945 63.158 6.13 0.00 38.71 4.26
187 188 2.098680 CTGGAGTCGCTCGTCGTC 59.901 66.667 0.00 0.00 39.67 4.20
217 218 2.811317 GGCTGAAGTCGCTCACCG 60.811 66.667 0.00 0.00 38.61 4.94
218 219 2.049063 GCTGAAGTCGCTCACCGT 60.049 61.111 0.00 0.00 38.35 4.83
222 223 1.796749 GAAGTCGCTCACCGTCGTC 60.797 63.158 0.00 0.00 38.35 4.20
238 239 2.283173 TCTGGACTCGCCTCTGCA 60.283 61.111 0.00 0.00 37.32 4.41
240 241 1.227205 CTGGACTCGCCTCTGCATC 60.227 63.158 0.00 0.00 37.32 3.91
241 242 2.107953 GGACTCGCCTCTGCATCC 59.892 66.667 0.00 0.00 37.32 3.51
242 243 2.279120 GACTCGCCTCTGCATCCG 60.279 66.667 0.00 0.00 37.32 4.18
243 244 4.521062 ACTCGCCTCTGCATCCGC 62.521 66.667 0.00 0.00 37.32 5.54
272 273 4.771356 CGTCGCCGTGACCGTGAT 62.771 66.667 6.50 0.00 45.23 3.06
273 274 3.179265 GTCGCCGTGACCGTGATG 61.179 66.667 0.19 0.00 42.04 3.07
313 314 2.008268 GCTGGCTGTGTGTGCTTGTT 62.008 55.000 0.00 0.00 0.00 2.83
314 315 1.308047 CTGGCTGTGTGTGCTTGTTA 58.692 50.000 0.00 0.00 0.00 2.41
315 316 1.265095 CTGGCTGTGTGTGCTTGTTAG 59.735 52.381 0.00 0.00 0.00 2.34
316 317 1.308998 GGCTGTGTGTGCTTGTTAGT 58.691 50.000 0.00 0.00 0.00 2.24
317 318 1.676006 GGCTGTGTGTGCTTGTTAGTT 59.324 47.619 0.00 0.00 0.00 2.24
318 319 2.541588 GGCTGTGTGTGCTTGTTAGTTG 60.542 50.000 0.00 0.00 0.00 3.16
319 320 2.097466 GCTGTGTGTGCTTGTTAGTTGT 59.903 45.455 0.00 0.00 0.00 3.32
320 321 3.427503 GCTGTGTGTGCTTGTTAGTTGTT 60.428 43.478 0.00 0.00 0.00 2.83
352 360 1.339134 CGTACGTATGTGTGCGTGC 59.661 57.895 7.22 0.00 46.18 5.34
360 368 4.988486 GTGTGCGTGCTTGCTGGC 62.988 66.667 2.56 0.00 35.36 4.85
407 415 3.812053 GCATGCAAGTACTAGGAGGATTG 59.188 47.826 14.21 0.00 0.00 2.67
426 476 6.825721 AGGATTGAGTAAAGTGATGGTCATTC 59.174 38.462 0.00 0.00 0.00 2.67
445 495 4.356405 TTCAGTCATTGAGAAAGAGGCA 57.644 40.909 0.00 0.00 37.07 4.75
467 517 0.458370 GATGCAACAAATGGGCGGTC 60.458 55.000 0.00 0.00 0.00 4.79
485 535 3.465871 GGTCTTTGATCTCATCTCAGGC 58.534 50.000 0.00 0.00 0.00 4.85
493 543 5.306394 TGATCTCATCTCAGGCATTCAATC 58.694 41.667 0.00 0.00 0.00 2.67
497 547 4.142038 TCATCTCAGGCATTCAATCCATG 58.858 43.478 0.00 0.00 0.00 3.66
513 563 7.758609 TCAATCCATGGTCTTCATAATATGGT 58.241 34.615 12.58 0.00 37.09 3.55
579 657 7.484035 TGCTGTTTTTAAAAATTGCCGTATT 57.516 28.000 24.63 0.00 32.18 1.89
580 658 7.920738 TGCTGTTTTTAAAAATTGCCGTATTT 58.079 26.923 24.63 0.00 32.18 1.40
581 659 8.398665 TGCTGTTTTTAAAAATTGCCGTATTTT 58.601 25.926 24.63 0.00 38.90 1.82
582 660 8.677635 GCTGTTTTTAAAAATTGCCGTATTTTG 58.322 29.630 16.02 0.00 37.67 2.44
603 681 1.318158 ATCCCCGTATCCGTATCGCC 61.318 60.000 0.00 0.00 0.00 5.54
608 686 1.131126 CCGTATCCGTATCGCCGTATT 59.869 52.381 0.00 0.00 0.00 1.89
634 712 2.605094 CCGTATCGGTGCTTCATGG 58.395 57.895 0.00 0.00 42.73 3.66
759 837 1.276622 ATCGTACCCAAGCTCACCTT 58.723 50.000 0.00 0.00 0.00 3.50
789 868 1.586154 CCGAAAGCAAAGCCCACGAT 61.586 55.000 0.00 0.00 0.00 3.73
803 882 2.390288 CGATCGCGTCCACAAACG 59.610 61.111 5.77 0.00 45.31 3.60
907 996 3.253955 CGTAGCACAGCACCAACC 58.746 61.111 0.00 0.00 0.00 3.77
908 997 1.596752 CGTAGCACAGCACCAACCA 60.597 57.895 0.00 0.00 0.00 3.67
909 998 1.568612 CGTAGCACAGCACCAACCAG 61.569 60.000 0.00 0.00 0.00 4.00
968 1072 0.739112 CCAGCTTTCAGACTCGAGGC 60.739 60.000 18.41 15.26 0.00 4.70
984 1088 4.162690 GCTCGGGGCCGTCTCATT 62.163 66.667 0.00 0.00 40.74 2.57
985 1089 2.107141 CTCGGGGCCGTCTCATTC 59.893 66.667 0.00 0.00 40.74 2.67
986 1090 2.682136 TCGGGGCCGTCTCATTCA 60.682 61.111 0.00 0.00 40.74 2.57
987 1091 2.032860 CTCGGGGCCGTCTCATTCAT 62.033 60.000 0.00 0.00 40.74 2.57
988 1092 1.153168 CGGGGCCGTCTCATTCATT 60.153 57.895 0.00 0.00 34.35 2.57
989 1093 1.160329 CGGGGCCGTCTCATTCATTC 61.160 60.000 0.00 0.00 34.35 2.67
990 1094 0.819666 GGGGCCGTCTCATTCATTCC 60.820 60.000 0.00 0.00 0.00 3.01
991 1095 0.819666 GGGCCGTCTCATTCATTCCC 60.820 60.000 0.00 0.00 0.00 3.97
992 1096 0.107214 GGCCGTCTCATTCATTCCCA 60.107 55.000 0.00 0.00 0.00 4.37
993 1097 1.477558 GGCCGTCTCATTCATTCCCAT 60.478 52.381 0.00 0.00 0.00 4.00
994 1098 1.876156 GCCGTCTCATTCATTCCCATC 59.124 52.381 0.00 0.00 0.00 3.51
995 1099 2.746142 GCCGTCTCATTCATTCCCATCA 60.746 50.000 0.00 0.00 0.00 3.07
996 1100 3.748083 CCGTCTCATTCATTCCCATCAT 58.252 45.455 0.00 0.00 0.00 2.45
997 1101 3.750130 CCGTCTCATTCATTCCCATCATC 59.250 47.826 0.00 0.00 0.00 2.92
1330 1434 0.815213 TGCTGCGCATACATTCTCCC 60.815 55.000 12.24 0.00 31.71 4.30
1868 1977 1.078426 CTACCTCCCCAACAAGCGG 60.078 63.158 0.00 0.00 0.00 5.52
1925 2034 0.399233 CCCTCCGGAAGAAGAGGGAT 60.399 60.000 17.41 0.00 38.82 3.85
1955 2064 2.447714 GCAGGGGATCCAGGAGTCC 61.448 68.421 15.23 0.00 34.83 3.85
2159 2268 3.234630 CTTCCTGTCCGCCGTTCCA 62.235 63.158 0.00 0.00 0.00 3.53
2200 2309 2.882137 TCCGGACACTTTTTGGTTGATC 59.118 45.455 0.00 0.00 0.00 2.92
2201 2310 2.350388 CCGGACACTTTTTGGTTGATCG 60.350 50.000 0.00 0.00 0.00 3.69
2202 2311 2.546368 CGGACACTTTTTGGTTGATCGA 59.454 45.455 0.00 0.00 0.00 3.59
2203 2312 3.606153 CGGACACTTTTTGGTTGATCGAC 60.606 47.826 4.31 4.31 0.00 4.20
2204 2313 3.314080 GGACACTTTTTGGTTGATCGACA 59.686 43.478 15.11 0.00 0.00 4.35
2205 2314 4.023193 GGACACTTTTTGGTTGATCGACAT 60.023 41.667 15.11 0.00 0.00 3.06
2235 2346 7.063074 CCAATACCAGACAAGTAGTTTTAGTCG 59.937 40.741 0.00 0.00 34.56 4.18
2240 2351 6.583050 CCAGACAAGTAGTTTTAGTCGAAGAG 59.417 42.308 0.00 0.00 36.95 2.85
2243 2354 8.411683 AGACAAGTAGTTTTAGTCGAAGAGAAA 58.588 33.333 0.00 0.00 36.95 2.52
2244 2355 8.937634 ACAAGTAGTTTTAGTCGAAGAGAAAA 57.062 30.769 0.00 0.00 36.95 2.29
2245 2356 8.815189 ACAAGTAGTTTTAGTCGAAGAGAAAAC 58.185 33.333 13.46 13.46 45.92 2.43
2246 2357 7.943413 AGTAGTTTTAGTCGAAGAGAAAACC 57.057 36.000 15.94 7.29 46.34 3.27
2293 2405 2.474712 GCGTACGAGGCAAACTGC 59.525 61.111 21.65 0.00 44.08 4.40
2294 2406 2.769617 CGTACGAGGCAAACTGCG 59.230 61.111 10.44 0.00 46.21 5.18
2312 2426 2.607187 GCGAGTGCAGTACAGTATGTT 58.393 47.619 0.00 0.00 45.52 2.71
2380 2495 6.604795 AGGCAGCATGTAGATTTTGTATTTCT 59.395 34.615 0.00 0.00 39.31 2.52
2382 2497 7.221452 GGCAGCATGTAGATTTTGTATTTCTTG 59.779 37.037 0.00 0.00 39.31 3.02
2383 2498 7.970061 GCAGCATGTAGATTTTGTATTTCTTGA 59.030 33.333 0.00 0.00 39.31 3.02
2387 2502 9.956720 CATGTAGATTTTGTATTTCTTGATCCC 57.043 33.333 0.00 0.00 0.00 3.85
2400 2515 5.880054 TCTTGATCCCTTTTTCATTCGTC 57.120 39.130 0.00 0.00 0.00 4.20
2420 2535 5.580691 TCGTCTGTAATGAAAACTATGCTGG 59.419 40.000 0.00 0.00 0.00 4.85
2424 2539 5.953183 TGTAATGAAAACTATGCTGGCAAG 58.047 37.500 0.00 1.87 0.00 4.01
2441 2556 4.584327 GCAAGAAGCCCTGAAAAGTAAA 57.416 40.909 0.00 0.00 37.23 2.01
2442 2557 4.944048 GCAAGAAGCCCTGAAAAGTAAAA 58.056 39.130 0.00 0.00 37.23 1.52
2443 2558 5.356426 GCAAGAAGCCCTGAAAAGTAAAAA 58.644 37.500 0.00 0.00 37.23 1.94
2567 2683 1.067669 TGAGACTGTGAGTGTGACTGC 59.932 52.381 0.00 0.00 0.00 4.40
2571 2687 2.939103 GACTGTGAGTGTGACTGCTTTT 59.061 45.455 0.00 0.00 0.00 2.27
2572 2688 4.119862 GACTGTGAGTGTGACTGCTTTTA 58.880 43.478 0.00 0.00 0.00 1.52
2616 2732 0.468029 ACAACAGAAGCAGGTTGGGG 60.468 55.000 9.06 0.00 46.56 4.96
2685 2802 1.281867 CTGGTCTACAGGGCCATTGAA 59.718 52.381 6.18 0.00 43.70 2.69
2693 2810 2.225343 ACAGGGCCATTGAATTTCAGGA 60.225 45.455 6.18 0.00 0.00 3.86
2729 2846 3.853671 GTCATTGACGAAATCATTGGTGC 59.146 43.478 0.13 0.00 38.63 5.01
2823 2940 5.245531 TCGTAGTTTAGAGAAGAACCGGTA 58.754 41.667 8.00 0.00 0.00 4.02
2847 2964 2.432628 GTGAAGCCGTGTCCCTCG 60.433 66.667 0.00 0.00 0.00 4.63
2848 2965 2.915659 TGAAGCCGTGTCCCTCGT 60.916 61.111 0.00 0.00 0.00 4.18
2911 3029 7.795431 TGATTTTACGCTAAGATTTTTGCAG 57.205 32.000 3.55 0.00 35.21 4.41
2973 3097 8.364142 AGTCACTTAGATATAGAACAATGAGGC 58.636 37.037 0.00 0.00 0.00 4.70
2974 3098 8.364142 GTCACTTAGATATAGAACAATGAGGCT 58.636 37.037 0.00 0.00 0.00 4.58
2976 3100 9.853555 CACTTAGATATAGAACAATGAGGCTAG 57.146 37.037 0.00 0.00 0.00 3.42
3018 3159 8.579682 ACAGTTTTGCTAAAGCTTATTGAAAG 57.420 30.769 0.00 0.00 42.66 2.62
3028 3169 2.287248 GCTTATTGAAAGATGCCTCCGC 60.287 50.000 0.00 0.00 0.00 5.54
3050 3191 7.825270 TCCGCTGATGGTAGTTTATTTTAGAAA 59.175 33.333 0.00 0.00 0.00 2.52
3062 3203 8.953313 AGTTTATTTTAGAAAATACTCCCACCG 58.047 33.333 6.89 0.00 39.75 4.94
3063 3204 8.733458 GTTTATTTTAGAAAATACTCCCACCGT 58.267 33.333 6.89 0.00 39.75 4.83
3064 3205 9.956640 TTTATTTTAGAAAATACTCCCACCGTA 57.043 29.630 6.89 0.00 39.75 4.02
3065 3206 9.956640 TTATTTTAGAAAATACTCCCACCGTAA 57.043 29.630 6.89 0.00 39.75 3.18
3066 3207 8.866970 ATTTTAGAAAATACTCCCACCGTAAA 57.133 30.769 0.00 0.00 36.88 2.01
3067 3208 7.671495 TTTAGAAAATACTCCCACCGTAAAC 57.329 36.000 0.00 0.00 0.00 2.01
3068 3209 5.494390 AGAAAATACTCCCACCGTAAACT 57.506 39.130 0.00 0.00 0.00 2.66
3069 3210 6.610075 AGAAAATACTCCCACCGTAAACTA 57.390 37.500 0.00 0.00 0.00 2.24
3070 3211 7.008021 AGAAAATACTCCCACCGTAAACTAA 57.992 36.000 0.00 0.00 0.00 2.24
3071 3212 7.627311 AGAAAATACTCCCACCGTAAACTAAT 58.373 34.615 0.00 0.00 0.00 1.73
3072 3213 8.761689 AGAAAATACTCCCACCGTAAACTAATA 58.238 33.333 0.00 0.00 0.00 0.98
3073 3214 9.551734 GAAAATACTCCCACCGTAAACTAATAT 57.448 33.333 0.00 0.00 0.00 1.28
3077 3218 7.902920 ACTCCCACCGTAAACTAATATAAGA 57.097 36.000 0.00 0.00 0.00 2.10
3078 3219 7.949434 ACTCCCACCGTAAACTAATATAAGAG 58.051 38.462 0.00 0.00 0.00 2.85
3079 3220 6.752168 TCCCACCGTAAACTAATATAAGAGC 58.248 40.000 0.00 0.00 0.00 4.09
3080 3221 5.632347 CCCACCGTAAACTAATATAAGAGCG 59.368 44.000 0.00 0.00 0.00 5.03
3081 3222 6.211515 CCACCGTAAACTAATATAAGAGCGT 58.788 40.000 0.00 0.00 0.00 5.07
3082 3223 6.698766 CCACCGTAAACTAATATAAGAGCGTT 59.301 38.462 0.00 0.00 0.00 4.84
3083 3224 7.223387 CCACCGTAAACTAATATAAGAGCGTTT 59.777 37.037 0.00 0.00 0.00 3.60
3084 3225 9.236691 CACCGTAAACTAATATAAGAGCGTTTA 57.763 33.333 0.00 0.00 0.00 2.01
3085 3226 9.455847 ACCGTAAACTAATATAAGAGCGTTTAG 57.544 33.333 0.00 0.00 30.36 1.85
3086 3227 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3139 3280 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
3140 3281 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
3141 3282 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
3142 3283 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
3143 3284 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
3164 3305 9.543783 GGGAGTACCTCTGTAATTTAATGTAAG 57.456 37.037 0.00 0.00 35.85 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.156736 CTTGTACTGGGCTTTCCGTG 58.843 55.000 0.00 0.00 38.76 4.94
63 64 0.605589 GTCGGCTTGTACTGGGCTTT 60.606 55.000 0.00 0.00 0.00 3.51
69 70 0.240145 TCACGAGTCGGCTTGTACTG 59.760 55.000 18.30 3.27 37.24 2.74
70 71 0.240411 GTCACGAGTCGGCTTGTACT 59.760 55.000 18.30 0.00 37.24 2.73
91 92 0.036732 TGAGTGGGCTGGCTGTTTAG 59.963 55.000 0.00 0.00 0.00 1.85
100 101 0.588252 CAAACGAACTGAGTGGGCTG 59.412 55.000 0.00 0.00 0.00 4.85
104 105 1.841663 CGCCCAAACGAACTGAGTGG 61.842 60.000 0.00 0.00 34.06 4.00
116 117 1.000233 ATCCAATCTGCCGCCCAAA 60.000 52.632 0.00 0.00 0.00 3.28
118 119 2.192979 GATCCAATCTGCCGCCCA 59.807 61.111 0.00 0.00 0.00 5.36
196 197 1.974875 TGAGCGACTTCAGCCGGTA 60.975 57.895 1.90 0.00 36.60 4.02
217 218 2.041686 AGAGGCGAGTCCAGACGAC 61.042 63.158 0.00 0.00 42.32 4.34
218 219 2.041115 CAGAGGCGAGTCCAGACGA 61.041 63.158 0.00 0.00 37.29 4.20
222 223 1.227205 GATGCAGAGGCGAGTCCAG 60.227 63.158 0.00 0.00 45.35 3.86
256 257 3.179265 CATCACGGTCACGGCGAC 61.179 66.667 16.62 0.87 46.48 5.19
313 314 2.013400 CATGCATGGCGGTAACAACTA 58.987 47.619 19.40 0.00 0.00 2.24
314 315 0.810648 CATGCATGGCGGTAACAACT 59.189 50.000 19.40 0.00 0.00 3.16
315 316 0.801836 GCATGCATGGCGGTAACAAC 60.802 55.000 27.34 3.43 0.00 3.32
316 317 1.510383 GCATGCATGGCGGTAACAA 59.490 52.632 27.34 0.00 0.00 2.83
317 318 3.195683 GCATGCATGGCGGTAACA 58.804 55.556 27.34 0.00 0.00 2.41
337 338 1.859398 CAAGCACGCACACATACGT 59.141 52.632 0.00 0.00 44.75 3.57
399 407 5.104259 ACCATCACTTTACTCAATCCTCC 57.896 43.478 0.00 0.00 0.00 4.30
407 415 6.166279 TGACTGAATGACCATCACTTTACTC 58.834 40.000 0.00 0.00 0.00 2.59
426 476 3.377485 CCATGCCTCTTTCTCAATGACTG 59.623 47.826 0.00 0.00 0.00 3.51
445 495 0.176219 CGCCCATTTGTTGCATCCAT 59.824 50.000 0.00 0.00 0.00 3.41
467 517 5.123936 TGAATGCCTGAGATGAGATCAAAG 58.876 41.667 0.00 0.00 0.00 2.77
547 625 9.495754 GCAATTTTTAAAAACAGCAATACAACA 57.504 25.926 23.66 0.00 33.67 3.33
549 627 7.852945 CGGCAATTTTTAAAAACAGCAATACAA 59.147 29.630 26.94 3.24 34.56 2.41
550 628 7.011482 ACGGCAATTTTTAAAAACAGCAATACA 59.989 29.630 26.94 3.66 34.56 2.29
603 681 1.642360 CGATACGGCGACATCAATACG 59.358 52.381 16.62 2.06 0.00 3.06
634 712 0.878416 CGGTCTCGGAGGATCTCATC 59.122 60.000 4.96 0.00 33.73 2.92
759 837 1.302993 GCTTTCGGGCTGGTTGGTA 60.303 57.895 0.00 0.00 0.00 3.25
895 984 2.723746 GTGCTGGTTGGTGCTGTG 59.276 61.111 0.00 0.00 0.00 3.66
896 985 2.519302 GGTGCTGGTTGGTGCTGT 60.519 61.111 0.00 0.00 0.00 4.40
897 986 2.519063 TGGTGCTGGTTGGTGCTG 60.519 61.111 0.00 0.00 0.00 4.41
898 987 2.519302 GTGGTGCTGGTTGGTGCT 60.519 61.111 0.00 0.00 0.00 4.40
899 988 3.964875 CGTGGTGCTGGTTGGTGC 61.965 66.667 0.00 0.00 0.00 5.01
900 989 3.964875 GCGTGGTGCTGGTTGGTG 61.965 66.667 0.00 0.00 41.73 4.17
950 1054 0.246086 AGCCTCGAGTCTGAAAGCTG 59.754 55.000 12.31 0.00 0.00 4.24
956 1060 2.438614 CCCGAGCCTCGAGTCTGA 60.439 66.667 17.19 0.00 43.74 3.27
968 1072 2.032860 ATGAATGAGACGGCCCCGAG 62.033 60.000 14.44 0.00 42.83 4.63
981 1085 3.513912 CCATGGGATGATGGGAATGAATG 59.486 47.826 2.85 0.00 39.53 2.67
982 1086 3.403394 TCCATGGGATGATGGGAATGAAT 59.597 43.478 13.02 0.00 42.95 2.57
983 1087 2.790585 TCCATGGGATGATGGGAATGAA 59.209 45.455 13.02 0.00 42.95 2.57
984 1088 2.108776 GTCCATGGGATGATGGGAATGA 59.891 50.000 13.02 0.00 42.95 2.57
985 1089 2.522185 GTCCATGGGATGATGGGAATG 58.478 52.381 13.02 0.00 42.95 2.67
986 1090 1.430464 GGTCCATGGGATGATGGGAAT 59.570 52.381 13.02 0.00 42.95 3.01
987 1091 0.852842 GGTCCATGGGATGATGGGAA 59.147 55.000 13.02 0.00 42.95 3.97
988 1092 1.418097 CGGTCCATGGGATGATGGGA 61.418 60.000 13.02 0.00 42.95 4.37
989 1093 1.073722 CGGTCCATGGGATGATGGG 59.926 63.158 13.02 0.00 42.95 4.00
990 1094 0.694771 ATCGGTCCATGGGATGATGG 59.305 55.000 13.02 0.00 43.96 3.51
991 1095 1.673923 CGATCGGTCCATGGGATGATG 60.674 57.143 13.02 4.49 32.46 3.07
992 1096 0.610174 CGATCGGTCCATGGGATGAT 59.390 55.000 13.02 12.20 34.12 2.45
993 1097 1.471829 CCGATCGGTCCATGGGATGA 61.472 60.000 26.35 7.54 32.73 2.92
994 1098 1.004560 CCGATCGGTCCATGGGATG 60.005 63.158 26.35 1.53 32.73 3.51
995 1099 3.471620 CCGATCGGTCCATGGGAT 58.528 61.111 26.35 6.81 32.73 3.85
1356 1465 6.473455 CGTGATCATATTATAATGAGCTCGCA 59.527 38.462 9.64 0.00 45.80 5.10
1925 2034 4.529219 CCCTGCTGCGTCGCCATA 62.529 66.667 15.88 0.00 0.00 2.74
1955 2064 0.389391 CGGCCATGTCCCTGTAGTAG 59.611 60.000 2.24 0.00 0.00 2.57
1985 2094 1.759236 GGGGTCGAACTCCCACTTT 59.241 57.895 11.43 0.00 46.26 2.66
2096 2205 1.966451 GTTGACCCACCCGAGCTTG 60.966 63.158 0.00 0.00 0.00 4.01
2098 2207 1.229082 TAGTTGACCCACCCGAGCT 60.229 57.895 0.00 0.00 0.00 4.09
2200 2309 2.159296 TGTCTGGTATTGGTCGATGTCG 60.159 50.000 0.00 0.00 41.45 4.35
2201 2310 3.520290 TGTCTGGTATTGGTCGATGTC 57.480 47.619 0.00 0.00 0.00 3.06
2202 2311 3.260884 ACTTGTCTGGTATTGGTCGATGT 59.739 43.478 0.00 0.00 0.00 3.06
2203 2312 3.861840 ACTTGTCTGGTATTGGTCGATG 58.138 45.455 0.00 0.00 0.00 3.84
2204 2313 4.710375 ACTACTTGTCTGGTATTGGTCGAT 59.290 41.667 0.00 0.00 0.00 3.59
2205 2314 4.084287 ACTACTTGTCTGGTATTGGTCGA 58.916 43.478 0.00 0.00 0.00 4.20
2235 2346 3.067833 CACTTCTCCGGGTTTTCTCTTC 58.932 50.000 0.00 0.00 0.00 2.87
2240 2351 1.607148 CCAACACTTCTCCGGGTTTTC 59.393 52.381 0.00 0.00 0.00 2.29
2243 2354 1.228154 GCCAACACTTCTCCGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
2244 2355 2.430367 GCCAACACTTCTCCGGGT 59.570 61.111 0.00 0.00 0.00 5.28
2245 2356 2.359975 GGCCAACACTTCTCCGGG 60.360 66.667 0.00 0.00 0.00 5.73
2246 2357 0.537371 AAAGGCCAACACTTCTCCGG 60.537 55.000 5.01 0.00 0.00 5.14
2293 2405 6.887376 AATAAACATACTGTACTGCACTCG 57.113 37.500 0.00 0.00 0.00 4.18
2294 2406 8.480643 AGAAATAAACATACTGTACTGCACTC 57.519 34.615 0.00 0.00 0.00 3.51
2333 2447 7.181845 TGCCTCATGTTCCCATGTATGTATATA 59.818 37.037 2.91 0.00 46.99 0.86
2334 2448 6.012596 TGCCTCATGTTCCCATGTATGTATAT 60.013 38.462 2.91 0.00 46.99 0.86
2335 2449 5.309282 TGCCTCATGTTCCCATGTATGTATA 59.691 40.000 2.91 0.00 46.99 1.47
2336 2450 4.104579 TGCCTCATGTTCCCATGTATGTAT 59.895 41.667 2.91 0.00 46.99 2.29
2340 2454 2.750807 GCTGCCTCATGTTCCCATGTAT 60.751 50.000 2.91 0.00 46.99 2.29
2380 2495 5.070001 ACAGACGAATGAAAAAGGGATCAA 58.930 37.500 0.00 0.00 0.00 2.57
2382 2497 6.737254 TTACAGACGAATGAAAAAGGGATC 57.263 37.500 0.00 0.00 0.00 3.36
2383 2498 6.884295 TCATTACAGACGAATGAAAAAGGGAT 59.116 34.615 0.00 0.00 39.71 3.85
2400 2515 5.565592 TGCCAGCATAGTTTTCATTACAG 57.434 39.130 0.00 0.00 0.00 2.74
2420 2535 4.584327 TTTACTTTTCAGGGCTTCTTGC 57.416 40.909 0.00 0.00 41.94 4.01
2455 2570 6.852664 CCATCTTGGTAAAAATGTCACTACC 58.147 40.000 0.00 0.00 35.37 3.18
2582 2698 6.680378 GCTTCTGTTGTCTGAAAAGGCTAAAA 60.680 38.462 0.00 0.00 32.68 1.52
2586 2702 2.620585 GCTTCTGTTGTCTGAAAAGGCT 59.379 45.455 0.00 0.00 32.68 4.58
2587 2703 2.358898 TGCTTCTGTTGTCTGAAAAGGC 59.641 45.455 0.00 0.00 32.68 4.35
2588 2704 3.004106 CCTGCTTCTGTTGTCTGAAAAGG 59.996 47.826 0.00 0.00 33.55 3.11
2589 2705 3.629398 ACCTGCTTCTGTTGTCTGAAAAG 59.371 43.478 0.00 0.00 32.68 2.27
2590 2706 3.620488 ACCTGCTTCTGTTGTCTGAAAA 58.380 40.909 0.00 0.00 32.68 2.29
2594 2710 1.605710 CCAACCTGCTTCTGTTGTCTG 59.394 52.381 0.00 0.00 40.12 3.51
2616 2732 5.390991 CCTCTTTCATTTCTCTAACCAACGC 60.391 44.000 0.00 0.00 0.00 4.84
2710 2827 5.185454 TCTAGCACCAATGATTTCGTCAAT 58.815 37.500 0.00 0.00 40.97 2.57
2729 2846 7.069331 AGAGGTCCAATTTGTCTCTGTATCTAG 59.931 40.741 11.06 0.00 34.01 2.43
2769 2886 4.984295 TCTGATCCTTGATTGTGTTTGGA 58.016 39.130 0.00 0.00 0.00 3.53
2823 2940 1.021968 GACACGGCTTCACCAACTTT 58.978 50.000 0.00 0.00 39.03 2.66
2847 2964 3.118261 TGTGCAATAGATGGAAGAGGGAC 60.118 47.826 0.00 0.00 0.00 4.46
2848 2965 3.114606 TGTGCAATAGATGGAAGAGGGA 58.885 45.455 0.00 0.00 0.00 4.20
2961 3085 7.854166 AAGATCTATCTAGCCTCATTGTTCT 57.146 36.000 0.00 0.00 35.76 3.01
2962 3086 8.900983 AAAAGATCTATCTAGCCTCATTGTTC 57.099 34.615 0.00 0.00 35.76 3.18
2965 3089 8.899427 TTGAAAAGATCTATCTAGCCTCATTG 57.101 34.615 0.00 0.00 35.76 2.82
2969 3093 9.988815 TGTTATTGAAAAGATCTATCTAGCCTC 57.011 33.333 0.00 0.00 35.76 4.70
2971 3095 9.771534 ACTGTTATTGAAAAGATCTATCTAGCC 57.228 33.333 0.00 0.00 35.76 3.93
2982 3106 9.030301 GCTTTAGCAAAACTGTTATTGAAAAGA 57.970 29.630 24.04 9.86 41.59 2.52
2983 3107 9.034544 AGCTTTAGCAAAACTGTTATTGAAAAG 57.965 29.630 20.62 20.62 45.16 2.27
3003 3144 5.296780 CGGAGGCATCTTTCAATAAGCTTTA 59.703 40.000 3.20 0.00 0.00 1.85
3018 3159 0.320247 CTACCATCAGCGGAGGCATC 60.320 60.000 0.00 0.00 43.41 3.91
3055 3196 6.515531 CGCTCTTATATTAGTTTACGGTGGGA 60.516 42.308 0.00 0.00 0.00 4.37
3056 3197 5.632347 CGCTCTTATATTAGTTTACGGTGGG 59.368 44.000 0.00 0.00 0.00 4.61
3057 3198 6.211515 ACGCTCTTATATTAGTTTACGGTGG 58.788 40.000 0.00 0.00 0.00 4.61
3058 3199 7.689953 AACGCTCTTATATTAGTTTACGGTG 57.310 36.000 0.00 0.00 0.00 4.94
3059 3200 9.455847 CTAAACGCTCTTATATTAGTTTACGGT 57.544 33.333 0.00 0.00 34.29 4.83
3060 3201 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3113 3254 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3114 3255 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
3115 3256 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
3116 3257 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
3117 3258 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.