Multiple sequence alignment - TraesCS7D01G049300

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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 TraesCS7D01G049300 chr7D 100.000 5765 0 0 1 5765 25292942 25287178 0.000000e+00 10647.0
1 TraesCS7D01G049300 chr7D 81.500 400 51 17 1083 1476 25338665 25338283 2.020000e-79 307.0
2 TraesCS7D01G049300 chr7A 92.916 2894 148 21 1771 4637 26104917 26102054 0.000000e+00 4156.0
3 TraesCS7D01G049300 chr7A 93.649 1795 78 18 5 1786 26106737 26104966 0.000000e+00 2651.0
4 TraesCS7D01G049300 chr7A 80.245 1468 231 41 3176 4617 26241110 26239676 0.000000e+00 1050.0
5 TraesCS7D01G049300 chr7A 88.604 781 82 4 3821 4598 26057509 26056733 0.000000e+00 942.0
6 TraesCS7D01G049300 chr7A 83.537 492 72 7 3056 3545 26058565 26058081 8.810000e-123 451.0
7 TraesCS7D01G049300 chr7A 78.476 525 84 21 5082 5591 26101533 26101023 3.350000e-82 316.0
8 TraesCS7D01G049300 chr7A 86.926 283 34 3 1190 1469 26060165 26059883 1.210000e-81 315.0
9 TraesCS7D01G049300 chr7A 82.199 382 50 15 4683 5054 26102050 26101677 4.340000e-81 313.0
10 TraesCS7D01G049300 chr7A 89.247 186 20 0 3557 3742 26057818 26057633 3.470000e-57 233.0
11 TraesCS7D01G049300 chr7A 80.000 115 17 5 1597 1708 625379420 625379309 4.790000e-11 80.5
12 TraesCS7D01G049300 chr4A 90.903 3023 213 31 1870 4854 709421258 709418260 0.000000e+00 4002.0
13 TraesCS7D01G049300 chr4A 90.870 3023 214 31 1870 4854 709568885 709565887 0.000000e+00 3997.0
14 TraesCS7D01G049300 chr4A 90.931 2944 207 30 1870 4777 709274927 709272008 0.000000e+00 3903.0
15 TraesCS7D01G049300 chr4A 91.127 2919 198 31 1870 4753 709615331 709612439 0.000000e+00 3899.0
16 TraesCS7D01G049300 chr4A 84.348 1955 223 36 3117 5055 709207285 709205398 0.000000e+00 1838.0
17 TraesCS7D01G049300 chr4A 88.446 978 65 22 825 1786 709616464 709615519 0.000000e+00 1136.0
18 TraesCS7D01G049300 chr4A 87.888 966 66 29 828 1786 709422367 709421446 0.000000e+00 1088.0
19 TraesCS7D01G049300 chr4A 87.578 966 66 31 828 1786 709276033 709275115 0.000000e+00 1070.0
20 TraesCS7D01G049300 chr4A 86.957 966 64 32 828 1786 709569983 709569073 0.000000e+00 1029.0
21 TraesCS7D01G049300 chr4A 79.040 1479 246 30 3176 4617 709717807 709716356 0.000000e+00 955.0
22 TraesCS7D01G049300 chr4A 92.857 588 30 6 1 584 709570688 709570109 0.000000e+00 843.0
23 TraesCS7D01G049300 chr4A 92.517 588 32 6 1 584 709423072 709422493 0.000000e+00 832.0
24 TraesCS7D01G049300 chr4A 92.164 587 35 6 1 584 709276737 709276159 0.000000e+00 819.0
25 TraesCS7D01G049300 chr4A 93.838 357 18 4 239 594 709616923 709616570 8.500000e-148 534.0
26 TraesCS7D01G049300 chr4A 89.935 308 30 1 5459 5765 709563644 709563337 4.190000e-106 396.0
27 TraesCS7D01G049300 chr4A 89.610 308 31 1 5459 5765 709266144 709265837 1.950000e-104 390.0
28 TraesCS7D01G049300 chr4A 89.610 308 31 1 5459 5765 709268233 709267926 1.950000e-104 390.0
29 TraesCS7D01G049300 chr4A 89.610 308 31 1 5459 5765 709416014 709415707 1.950000e-104 390.0
30 TraesCS7D01G049300 chr4A 89.836 305 30 1 5462 5765 709610860 709610556 1.950000e-104 390.0
31 TraesCS7D01G049300 chr4A 77.311 714 111 24 5082 5751 709205257 709204551 1.960000e-99 374.0
32 TraesCS7D01G049300 chr4A 88.636 308 34 1 5459 5765 709270322 709270015 1.960000e-99 374.0
33 TraesCS7D01G049300 chr4A 90.769 260 24 0 1210 1469 709209630 709209371 1.190000e-91 348.0
34 TraesCS7D01G049300 chr4A 94.241 191 9 2 4786 4975 709612446 709612257 2.030000e-74 291.0
35 TraesCS7D01G049300 chr4A 89.474 190 16 2 5236 5424 709268418 709268232 2.690000e-58 237.0
36 TraesCS7D01G049300 chr4A 89.474 190 16 2 5236 5424 709270507 709270321 2.690000e-58 237.0
37 TraesCS7D01G049300 chr4A 88.947 190 17 2 5236 5424 709266329 709266143 1.250000e-56 231.0
38 TraesCS7D01G049300 chr4A 86.603 209 18 4 14 220 709618587 709618387 7.520000e-54 222.0
39 TraesCS7D01G049300 chr4A 93.836 146 7 2 4831 4975 709272005 709271861 9.730000e-53 219.0
40 TraesCS7D01G049300 chr4A 87.368 190 20 2 5236 5424 709563829 709563643 1.260000e-51 215.0
41 TraesCS7D01G049300 chr4A 87.368 190 20 2 5236 5424 709611048 709610862 1.260000e-51 215.0
42 TraesCS7D01G049300 chr4A 86.316 190 22 2 5236 5424 709416199 709416013 2.720000e-48 204.0
43 TraesCS7D01G049300 chr4A 95.312 128 5 1 4848 4975 709417700 709417574 9.790000e-48 202.0
44 TraesCS7D01G049300 chr4A 95.312 128 5 1 4848 4975 709565327 709565201 9.790000e-48 202.0
45 TraesCS7D01G049300 chr4A 90.909 77 7 0 4980 5056 709266413 709266337 2.840000e-18 104.0
46 TraesCS7D01G049300 chr4A 90.909 77 7 0 4980 5056 709268502 709268426 2.840000e-18 104.0
47 TraesCS7D01G049300 chr4A 90.909 77 7 0 4980 5056 709270591 709270515 2.840000e-18 104.0
48 TraesCS7D01G049300 chr4A 97.059 34 1 0 1114 1147 709209911 709209878 2.240000e-04 58.4
49 TraesCS7D01G049300 chrUn 89.218 2124 169 30 1870 3957 350559187 350561286 0.000000e+00 2599.0
50 TraesCS7D01G049300 chrUn 87.822 969 67 29 825 1786 346599901 346600825 0.000000e+00 1088.0
51 TraesCS7D01G049300 chrUn 93.220 472 22 5 115 584 346599315 346599778 0.000000e+00 686.0
52 TraesCS7D01G049300 chrUn 88.329 377 34 8 1870 2242 346601013 346601383 1.470000e-120 444.0
53 TraesCS7D01G049300 chr3D 80.193 207 29 11 5090 5293 125693256 125693453 1.670000e-30 145.0
54 TraesCS7D01G049300 chr3D 100.000 32 0 0 1871 1902 13034614 13034583 6.240000e-05 60.2
55 TraesCS7D01G049300 chr5B 81.443 97 8 9 1624 1714 653429914 653430006 2.880000e-08 71.3
56 TraesCS7D01G049300 chr5B 78.378 111 18 5 1601 1708 599794687 599794580 3.730000e-07 67.6
57 TraesCS7D01G049300 chr6A 100.000 31 0 0 1872 1902 158073946 158073976 2.240000e-04 58.4


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 TraesCS7D01G049300 chr7D 25287178 25292942 5764 True 10647.000000 10647 100.000000 1 5765 1 chr7D.!!$R1 5764
1 TraesCS7D01G049300 chr7A 26101023 26106737 5714 True 1859.000000 4156 86.810000 5 5591 4 chr7A.!!$R4 5586
2 TraesCS7D01G049300 chr7A 26239676 26241110 1434 True 1050.000000 1050 80.245000 3176 4617 1 chr7A.!!$R1 1441
3 TraesCS7D01G049300 chr7A 26056733 26060165 3432 True 485.250000 942 87.078500 1190 4598 4 chr7A.!!$R3 3408
4 TraesCS7D01G049300 chr4A 709415707 709423072 7365 True 1119.666667 4002 90.424333 1 5765 6 chr4A.!!$R4 5764
5 TraesCS7D01G049300 chr4A 709563337 709570688 7351 True 1113.666667 3997 90.549833 1 5765 6 chr4A.!!$R5 5764
6 TraesCS7D01G049300 chr4A 709610556 709618587 8031 True 955.285714 3899 90.208429 14 5765 7 chr4A.!!$R6 5751
7 TraesCS7D01G049300 chr4A 709716356 709717807 1451 True 955.000000 955 79.040000 3176 4617 1 chr4A.!!$R1 1441
8 TraesCS7D01G049300 chr4A 709204551 709209911 5360 True 654.600000 1838 87.371750 1114 5751 4 chr4A.!!$R2 4637
9 TraesCS7D01G049300 chr4A 709265837 709276737 10900 True 629.384615 3903 90.229769 1 5765 13 chr4A.!!$R3 5764
10 TraesCS7D01G049300 chrUn 350559187 350561286 2099 False 2599.000000 2599 89.218000 1870 3957 1 chrUn.!!$F1 2087
11 TraesCS7D01G049300 chrUn 346599315 346601383 2068 False 739.333333 1088 89.790333 115 2242 3 chrUn.!!$F2 2127

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
820 2279 0.250295 TTCTTCACTGAACTGGGCCG 60.250 55.000 0.00 0.0 0.0 6.13 F
2058 4243 0.251474 ATGCTGCATGTTGAGGTGGT 60.251 50.000 15.44 0.0 0.0 4.16 F
2752 5331 1.486310 ACTCACTCTTTGCACAGGACA 59.514 47.619 0.00 0.0 0.0 4.02 F
3386 6153 1.227943 GGACCAGTTCAGCAGCACA 60.228 57.895 0.00 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2700 5279 1.538047 GCCCAAGAGTTTGCAGATCA 58.462 50.0 0.0 0.0 32.79 2.92 R
3386 6153 0.394565 AGAAGCTGTCCTTGTCGCTT 59.605 50.0 0.0 0.0 44.61 4.68 R
4587 7708 0.320421 ACTTGTAACGCCTGTCGCAT 60.320 50.0 0.0 0.0 43.23 4.73 R
5163 13032 0.845102 ATCTTTTCCCCCTCCACCGT 60.845 55.0 0.0 0.0 0.00 4.83 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
44 49 1.000274 CAAACCTGCCCAGTACAAAGC 60.000 52.381 0.00 0.00 0.00 3.51
55 60 4.044426 CCAGTACAAAGCAAAAGAGCAAC 58.956 43.478 0.00 0.00 36.85 4.17
155 162 2.568509 CACCCAGCAAATTTCAGGGATT 59.431 45.455 20.49 2.50 42.25 3.01
193 200 2.178984 TCCACCAAATTTCCAGGAAGGT 59.821 45.455 1.07 3.44 39.02 3.50
309 1761 8.750298 AGCTAGAGAACAAGTAAAGTATAAGCA 58.250 33.333 0.00 0.00 0.00 3.91
474 1926 4.342092 CCAATGGGACCCAACAATATCTTC 59.658 45.833 19.58 0.00 36.95 2.87
496 1948 8.783093 TCTTCTTTTAACCACTCATACATTGTG 58.217 33.333 0.00 0.00 0.00 3.33
497 1949 6.908825 TCTTTTAACCACTCATACATTGTGC 58.091 36.000 0.00 0.00 0.00 4.57
599 2051 2.675348 GCAACTCTATCAAGCCACTGAC 59.325 50.000 0.00 0.00 0.00 3.51
600 2052 3.265791 CAACTCTATCAAGCCACTGACC 58.734 50.000 0.00 0.00 0.00 4.02
602 2054 2.499289 ACTCTATCAAGCCACTGACCAG 59.501 50.000 0.00 0.00 0.00 4.00
732 2191 1.973515 TCAGAGCACCAAGAGTCATGT 59.026 47.619 0.00 0.00 0.00 3.21
793 2252 6.976934 TTCTCCCAGCAAAATAAAACTCTT 57.023 33.333 0.00 0.00 0.00 2.85
794 2253 6.976934 TCTCCCAGCAAAATAAAACTCTTT 57.023 33.333 0.00 0.00 0.00 2.52
820 2279 0.250295 TTCTTCACTGAACTGGGCCG 60.250 55.000 0.00 0.00 0.00 6.13
823 2282 1.407656 TTCACTGAACTGGGCCGTCT 61.408 55.000 0.00 0.00 0.00 4.18
943 2405 3.118454 CAGCAACGTACCCAGCCG 61.118 66.667 0.00 0.00 0.00 5.52
1008 2470 1.305633 CAGCCCTCCAGAGACCAGA 60.306 63.158 0.00 0.00 0.00 3.86
1009 2471 1.305718 AGCCCTCCAGAGACCAGAC 60.306 63.158 0.00 0.00 0.00 3.51
1010 2472 2.363172 GCCCTCCAGAGACCAGACC 61.363 68.421 0.00 0.00 0.00 3.85
1179 2659 2.943033 GCCTCTCTGTGTCTCTCTCTAC 59.057 54.545 0.00 0.00 0.00 2.59
1210 2887 1.348064 TGGTCACTTACTCCCTGGTG 58.652 55.000 0.00 0.00 0.00 4.17
1462 3146 2.431942 CGTTCTGGTCCGAACCCG 60.432 66.667 16.10 6.57 45.83 5.28
1558 3258 4.591321 ATGGTCCTTCATAGAGCCAAAA 57.409 40.909 0.00 0.00 31.87 2.44
1569 3269 9.494271 CTTCATAGAGCCAAAATATAAGTAGCA 57.506 33.333 0.00 0.00 0.00 3.49
1570 3270 9.494271 TTCATAGAGCCAAAATATAAGTAGCAG 57.506 33.333 0.00 0.00 0.00 4.24
1571 3271 8.651389 TCATAGAGCCAAAATATAAGTAGCAGT 58.349 33.333 0.00 0.00 0.00 4.40
1572 3272 9.277783 CATAGAGCCAAAATATAAGTAGCAGTT 57.722 33.333 0.00 0.00 0.00 3.16
1573 3273 7.793927 AGAGCCAAAATATAAGTAGCAGTTC 57.206 36.000 0.00 0.00 0.00 3.01
1574 3274 7.338710 AGAGCCAAAATATAAGTAGCAGTTCA 58.661 34.615 0.00 0.00 0.00 3.18
1575 3275 7.829211 AGAGCCAAAATATAAGTAGCAGTTCAA 59.171 33.333 0.00 0.00 0.00 2.69
1576 3276 8.348285 AGCCAAAATATAAGTAGCAGTTCAAA 57.652 30.769 0.00 0.00 0.00 2.69
1577 3277 8.462016 AGCCAAAATATAAGTAGCAGTTCAAAG 58.538 33.333 0.00 0.00 0.00 2.77
1578 3278 7.702348 GCCAAAATATAAGTAGCAGTTCAAAGG 59.298 37.037 0.00 0.00 0.00 3.11
1579 3279 8.956426 CCAAAATATAAGTAGCAGTTCAAAGGA 58.044 33.333 0.00 0.00 0.00 3.36
1585 3285 2.957402 AGCAGTTCAAAGGATGGTCA 57.043 45.000 0.00 0.00 0.00 4.02
1631 3331 0.721154 ATACATCACACGTTGCTGCG 59.279 50.000 0.00 0.00 37.94 5.18
1639 3339 1.599518 ACGTTGCTGCGGGAATTGA 60.600 52.632 1.67 0.00 35.98 2.57
1902 3871 7.923878 GGGTGCTAGCTATTTAGATATAGAAGC 59.076 40.741 17.23 0.00 38.18 3.86
1920 3892 5.426504 AGAAGCTAGGAATGTGAACATGAG 58.573 41.667 0.00 0.00 36.56 2.90
1934 3906 8.862325 TGTGAACATGAGTATTTGGATTAACT 57.138 30.769 0.00 0.00 0.00 2.24
2058 4243 0.251474 ATGCTGCATGTTGAGGTGGT 60.251 50.000 15.44 0.00 0.00 4.16
2064 4249 1.545428 GCATGTTGAGGTGGTCCTTCA 60.545 52.381 0.00 0.00 45.24 3.02
2148 4341 3.954258 GGGTGTCCCTATTCATTTTCTGG 59.046 47.826 0.00 0.00 41.34 3.86
2150 4343 4.640647 GGTGTCCCTATTCATTTTCTGGAC 59.359 45.833 0.00 0.00 40.88 4.02
2202 4743 7.947782 TTAAGTACTCCCTCCAATTCCATAT 57.052 36.000 0.00 0.00 0.00 1.78
2409 4981 3.968724 GTCAAGAAAAACATGTCACGCTC 59.031 43.478 0.00 0.00 0.00 5.03
2411 4983 5.050363 GTCAAGAAAAACATGTCACGCTCTA 60.050 40.000 0.00 0.00 0.00 2.43
2413 4985 5.786401 AGAAAAACATGTCACGCTCTATC 57.214 39.130 0.00 0.00 0.00 2.08
2414 4986 5.482908 AGAAAAACATGTCACGCTCTATCT 58.517 37.500 0.00 0.00 0.00 1.98
2415 4987 5.934625 AGAAAAACATGTCACGCTCTATCTT 59.065 36.000 0.00 0.00 0.00 2.40
2476 5053 9.613428 ACTTCACATTTATCCGAAGATAATGAA 57.387 29.630 5.09 8.75 43.01 2.57
2534 5112 5.646577 AAACTCTCTATCGTGCAACTACT 57.353 39.130 0.00 0.00 31.75 2.57
2537 5115 4.201832 ACTCTCTATCGTGCAACTACTTCG 60.202 45.833 0.00 0.00 31.75 3.79
2568 5146 8.235226 GCATACACTGATCATTTCATATCCAAG 58.765 37.037 0.00 0.00 32.72 3.61
2610 5188 8.522830 ACCAGGAACTTTACACATGAATATTTG 58.477 33.333 0.00 0.00 34.60 2.32
2626 5204 7.106239 TGAATATTTGGAAGTTGAGAGAGGTC 58.894 38.462 0.00 0.00 0.00 3.85
2638 5216 6.377146 AGTTGAGAGAGGTCTGAGAAGATAAC 59.623 42.308 0.00 0.00 30.97 1.89
2656 5234 3.814504 AACTCCCCTGTTGACATGAAT 57.185 42.857 0.00 0.00 0.00 2.57
2716 5295 5.464057 TGCAAAAATGATCTGCAAACTCTTG 59.536 36.000 4.24 0.00 42.84 3.02
2748 5327 2.831333 ACTCACTCACTCTTTGCACAG 58.169 47.619 0.00 0.00 0.00 3.66
2752 5331 1.486310 ACTCACTCTTTGCACAGGACA 59.514 47.619 0.00 0.00 0.00 4.02
2755 5334 2.092968 TCACTCTTTGCACAGGACAAGT 60.093 45.455 0.00 0.00 0.00 3.16
2757 5336 2.292267 CTCTTTGCACAGGACAAGTGT 58.708 47.619 0.00 0.00 39.17 3.55
2793 5373 7.220491 CGATGCAAGCATTTTGTTCATATGTTA 59.780 33.333 9.16 0.00 36.70 2.41
2870 5450 6.403866 AAGGAAACATGACTGCACAATAAA 57.596 33.333 0.00 0.00 0.00 1.40
2931 5511 6.764085 CCACAAATGAATGCAACAATCCATAT 59.236 34.615 0.00 0.00 0.00 1.78
2943 5524 8.916062 TGCAACAATCCATATATTGAATCACTT 58.084 29.630 5.41 0.00 38.84 3.16
3084 5840 5.028549 TGCCCTTTAATGCAACAGAAAAA 57.971 34.783 0.00 0.00 33.87 1.94
3114 5872 5.293569 AGGACTGTAACAAAACTGTTTCTCG 59.706 40.000 6.20 1.44 32.42 4.04
3128 5886 2.031012 CTCGTGCACTTGAGCCCA 59.969 61.111 16.19 0.00 0.00 5.36
3254 6018 1.784036 CGCCACACTGCACATTGTCA 61.784 55.000 0.00 0.00 0.00 3.58
3386 6153 1.227943 GGACCAGTTCAGCAGCACA 60.228 57.895 0.00 0.00 0.00 4.57
3809 6912 1.683943 CCGGATTGGTGAATCATGCT 58.316 50.000 0.00 0.00 39.98 3.79
3987 7093 3.770040 CCGCTGTGGTCATCCGGA 61.770 66.667 6.61 6.61 39.21 5.14
4215 7324 2.040544 GCTACAGCGTGTGGGCATT 61.041 57.895 1.58 0.00 33.17 3.56
4587 7708 0.685097 ACTTTGCCTACTTCCTCGCA 59.315 50.000 0.00 0.00 0.00 5.10
4660 7781 0.179124 ATGCGCGTGGTTTGTTTGTT 60.179 45.000 8.43 0.00 0.00 2.83
4823 7955 5.084818 TGGATACATTTCAGTGTCACGAT 57.915 39.130 0.00 0.00 46.17 3.73
4846 7980 1.541147 CGGCCTTTGTGTGATTGATGT 59.459 47.619 0.00 0.00 0.00 3.06
4882 8583 7.221450 ACTTTATTACCAAGTGCTCAGTTGTA 58.779 34.615 14.26 6.30 39.48 2.41
4890 8591 6.320164 ACCAAGTGCTCAGTTGTATACAAAAA 59.680 34.615 19.63 7.60 39.48 1.94
4903 8604 9.240159 GTTGTATACAAAAACCAAAAAGATCGT 57.760 29.630 19.63 0.00 37.63 3.73
4927 8628 1.067635 ACCGATCAAAGGCAATGCAAC 60.068 47.619 7.79 0.00 0.00 4.17
4978 12215 3.838317 ACACTGCTACCTCACAAATAGGA 59.162 43.478 0.00 0.00 37.57 2.94
5016 12253 4.270325 GCTATCCAAAGTTTAGTGTAGCCG 59.730 45.833 8.70 0.00 0.00 5.52
5017 12254 4.546829 ATCCAAAGTTTAGTGTAGCCGA 57.453 40.909 0.00 0.00 0.00 5.54
5056 12294 6.770303 TGATTGTCATGTTTTGAGACTGGTAA 59.230 34.615 0.00 0.00 34.17 2.85
5057 12295 7.284261 TGATTGTCATGTTTTGAGACTGGTAAA 59.716 33.333 0.00 0.00 34.17 2.01
5061 12299 9.126151 TGTCATGTTTTGAGACTGGTAAAATTA 57.874 29.630 0.00 0.00 34.17 1.40
5071 12309 7.224753 TGAGACTGGTAAAATTATCAATCGAGC 59.775 37.037 0.00 0.00 26.26 5.03
5072 12310 6.201044 AGACTGGTAAAATTATCAATCGAGCG 59.799 38.462 0.00 0.00 26.26 5.03
5073 12311 6.046593 ACTGGTAAAATTATCAATCGAGCGA 58.953 36.000 0.00 0.00 0.00 4.93
5075 12313 5.051307 TGGTAAAATTATCAATCGAGCGACG 60.051 40.000 0.00 0.00 44.09 5.12
5115 12984 2.142761 CCGGGGATCAGGAGCATCA 61.143 63.158 0.00 0.00 36.25 3.07
5126 12995 2.435069 CAGGAGCATCACCAGAGAGATT 59.565 50.000 0.00 0.00 36.25 2.40
5127 12996 2.435069 AGGAGCATCACCAGAGAGATTG 59.565 50.000 0.00 0.00 36.25 2.67
5133 13002 4.582869 CATCACCAGAGAGATTGGTTTCA 58.417 43.478 0.00 0.00 46.57 2.69
5137 13006 3.588842 ACCAGAGAGATTGGTTTCATGGA 59.411 43.478 0.00 0.00 46.57 3.41
5150 13019 8.415950 TTGGTTTCATGGATTACAACTTACAT 57.584 30.769 0.00 0.00 0.00 2.29
5156 13025 4.929479 TGGATTACAACTTACATGCCCTT 58.071 39.130 0.00 0.00 0.00 3.95
5177 13046 2.606519 CTGACGGTGGAGGGGGAA 60.607 66.667 0.00 0.00 0.00 3.97
5195 13064 3.610911 GGAAAAGATGGTGGTAGGTGAG 58.389 50.000 0.00 0.00 0.00 3.51
5197 13066 4.508662 GAAAAGATGGTGGTAGGTGAGAG 58.491 47.826 0.00 0.00 0.00 3.20
5204 13073 1.137282 GTGGTAGGTGAGAGCCTTAGC 59.863 57.143 0.00 0.00 39.94 3.09
5223 13096 6.377146 CCTTAGCTCTAGGGTGATCTAGAATC 59.623 46.154 0.00 0.00 43.37 2.52
5325 14481 1.388133 GATTGGGGGCCTTTGGTCT 59.612 57.895 0.84 0.00 0.00 3.85
5382 14538 1.804151 TCGTGCTTGCAAGTTGATACC 59.196 47.619 26.55 9.43 0.00 2.73
5383 14539 1.806542 CGTGCTTGCAAGTTGATACCT 59.193 47.619 26.55 0.00 0.00 3.08
5384 14540 2.413239 CGTGCTTGCAAGTTGATACCTG 60.413 50.000 26.55 0.00 0.00 4.00
5394 14550 4.213564 AGTTGATACCTGCTTCCTTGAG 57.786 45.455 0.00 0.00 0.00 3.02
5448 14604 3.122369 GCCATGGCTGCCTAAATCT 57.878 52.632 29.98 0.00 38.26 2.40
5449 14605 0.957362 GCCATGGCTGCCTAAATCTC 59.043 55.000 29.98 0.00 38.26 2.75
5456 14612 2.437651 GGCTGCCTAAATCTCTCCTTCT 59.562 50.000 12.43 0.00 0.00 2.85
5520 14723 1.141858 CCCTCCTGAGAAGGTTATGCC 59.858 57.143 0.00 0.00 37.58 4.40
5521 14724 1.839994 CCTCCTGAGAAGGTTATGCCA 59.160 52.381 0.00 0.00 40.61 4.92
5545 14748 3.057736 ACTTGTTAAGTCTCTTCGCGCTA 60.058 43.478 5.56 0.00 37.02 4.26
5595 14798 0.339162 TGGTTGAATCATGGGGCCAT 59.661 50.000 4.39 0.00 37.08 4.40
5635 14856 3.449918 TGATCCACTCCACCAATAGACA 58.550 45.455 0.00 0.00 0.00 3.41
5652 14873 3.827722 AGACAAATCGTTGAAGGGGAAA 58.172 40.909 0.00 0.00 38.20 3.13
5669 14891 2.673523 AGGTGCACCTCATGAGCC 59.326 61.111 33.20 12.29 44.77 4.70
5681 14903 2.954989 CTCATGAGCCAGTAGAGTGCTA 59.045 50.000 10.38 0.00 34.99 3.49
5694 14916 0.389948 AGTGCTAAAGAACCGAGGCG 60.390 55.000 0.00 0.00 0.00 5.52
5726 14951 3.814625 TGTTTGCCATGTCACAGTCTTA 58.185 40.909 0.00 0.00 0.00 2.10
5727 14952 3.814842 TGTTTGCCATGTCACAGTCTTAG 59.185 43.478 0.00 0.00 0.00 2.18
5734 14959 1.534163 TGTCACAGTCTTAGTCGGTCG 59.466 52.381 0.00 0.00 0.00 4.79
5757 14982 7.434602 GTCGGTCTTGACTAACAAATAGTATCC 59.565 40.741 0.61 0.00 45.00 2.59
5758 14983 7.123098 TCGGTCTTGACTAACAAATAGTATCCA 59.877 37.037 0.61 0.00 45.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.455543 TGCTGAAGGTGGATGATCATACA 59.544 43.478 17.05 17.05 0.00 2.29
44 49 4.985413 TGTCTTCACTTGTTGCTCTTTTG 58.015 39.130 0.00 0.00 0.00 2.44
55 60 0.689623 AGGGAGGCTGTCTTCACTTG 59.310 55.000 0.00 0.00 0.00 3.16
155 162 4.950475 TGGTGGAAATTTTATATGGCGTGA 59.050 37.500 0.00 0.00 0.00 4.35
193 200 5.339008 AGTTCTGCTTGGTTACATCGATA 57.661 39.130 0.00 0.00 0.00 2.92
309 1761 5.361571 TGTGATAATGCTGAATCTGCCAATT 59.638 36.000 9.59 6.34 0.00 2.32
435 1887 0.850100 TTGGAAAGCTTGTCTCCCCA 59.150 50.000 12.19 5.34 0.00 4.96
474 1926 6.913170 AGCACAATGTATGAGTGGTTAAAAG 58.087 36.000 0.00 0.00 40.68 2.27
496 1948 4.034510 AGCAATCGCAGATTTACTACAAGC 59.965 41.667 1.76 0.00 45.12 4.01
497 1949 5.496387 CAGCAATCGCAGATTTACTACAAG 58.504 41.667 1.76 0.00 45.12 3.16
599 2051 2.159448 TCGTTTGTGTTGCTTTGTCTGG 60.159 45.455 0.00 0.00 0.00 3.86
600 2052 3.100817 CTCGTTTGTGTTGCTTTGTCTG 58.899 45.455 0.00 0.00 0.00 3.51
602 2054 3.398954 TCTCGTTTGTGTTGCTTTGTC 57.601 42.857 0.00 0.00 0.00 3.18
681 2140 6.665248 CCCTTAAAATCTCATTCCTTGGACTT 59.335 38.462 0.00 0.00 0.00 3.01
732 2191 7.904205 ACAGTGATGATATAGCAAGATGATGA 58.096 34.615 0.00 0.00 0.00 2.92
793 2252 6.460953 GCCCAGTTCAGTGAAGAAAATGTTAA 60.461 38.462 5.62 0.00 0.00 2.01
794 2253 5.009610 GCCCAGTTCAGTGAAGAAAATGTTA 59.990 40.000 5.62 0.00 0.00 2.41
804 2263 1.070786 GACGGCCCAGTTCAGTGAA 59.929 57.895 0.08 0.08 0.00 3.18
820 2279 1.606601 GGGGTTGAAAGGGCCAGAC 60.607 63.158 6.18 0.00 0.00 3.51
823 2282 2.543797 ATCGGGGTTGAAAGGGCCA 61.544 57.895 6.18 0.00 0.00 5.36
1008 2470 3.012502 TGATCCTCCTACTAGTTGGTGGT 59.987 47.826 30.74 22.43 39.20 4.16
1009 2471 3.643237 TGATCCTCCTACTAGTTGGTGG 58.357 50.000 28.29 28.29 39.41 4.61
1010 2472 4.466370 TGTTGATCCTCCTACTAGTTGGTG 59.534 45.833 20.72 18.13 0.00 4.17
1179 2659 1.604604 AGTGACCATGAAAACACGGG 58.395 50.000 0.00 0.00 38.15 5.28
1199 2876 0.399376 ACACACCACACCAGGGAGTA 60.399 55.000 0.00 0.00 0.00 2.59
1210 2887 2.730928 GCATGCATGTTTTACACACCAC 59.269 45.455 26.79 2.60 38.61 4.16
1259 2943 2.732016 CTGGTCGTCCCGTTGACA 59.268 61.111 0.00 0.00 44.71 3.58
1462 3146 4.092968 AGAGTGCGTGAAATTAATTCGGTC 59.907 41.667 0.10 0.00 41.18 4.79
1558 3258 7.806180 ACCATCCTTTGAACTGCTACTTATAT 58.194 34.615 0.00 0.00 0.00 0.86
1569 3269 4.580580 GTGTTTCTGACCATCCTTTGAACT 59.419 41.667 0.00 0.00 0.00 3.01
1570 3270 4.338118 TGTGTTTCTGACCATCCTTTGAAC 59.662 41.667 0.00 0.00 0.00 3.18
1571 3271 4.531854 TGTGTTTCTGACCATCCTTTGAA 58.468 39.130 0.00 0.00 0.00 2.69
1572 3272 4.163441 TGTGTTTCTGACCATCCTTTGA 57.837 40.909 0.00 0.00 0.00 2.69
1573 3273 4.763793 AGATGTGTTTCTGACCATCCTTTG 59.236 41.667 0.00 0.00 36.98 2.77
1574 3274 4.990526 AGATGTGTTTCTGACCATCCTTT 58.009 39.130 0.00 0.00 36.98 3.11
1575 3275 4.647564 AGATGTGTTTCTGACCATCCTT 57.352 40.909 0.00 0.00 36.98 3.36
1576 3276 4.647564 AAGATGTGTTTCTGACCATCCT 57.352 40.909 0.00 0.00 36.98 3.24
1577 3277 8.682936 ATAATAAGATGTGTTTCTGACCATCC 57.317 34.615 0.00 0.00 36.98 3.51
1617 3317 3.741830 TTCCCGCAGCAACGTGTGA 62.742 57.895 0.00 0.00 0.00 3.58
1746 3526 9.822185 ATTGCTCCAAATATTCAGTAAATTTCC 57.178 29.630 0.00 0.00 0.00 3.13
1902 3871 7.770433 TCCAAATACTCATGTTCACATTCCTAG 59.230 37.037 0.00 0.00 33.61 3.02
2058 4243 6.101150 ACATATAACTATGCCACCTTGAAGGA 59.899 38.462 19.83 0.00 36.86 3.36
2323 4893 6.049263 ACATCGAACTGTGACTTTCTTTTC 57.951 37.500 0.00 0.00 0.00 2.29
2381 4951 7.201266 GCGTGACATGTTTTTCTTGACATTATC 60.201 37.037 0.00 0.00 34.42 1.75
2476 5053 2.939103 GAGGAGCATGTGTCGCTATTTT 59.061 45.455 0.00 0.00 40.63 1.82
2521 5099 3.181520 GCATTTCGAAGTAGTTGCACGAT 60.182 43.478 0.00 0.00 33.25 3.73
2534 5112 6.682423 AATGATCAGTGTATGCATTTCGAA 57.318 33.333 3.54 0.00 0.00 3.71
2610 5188 3.426615 TCTCAGACCTCTCTCAACTTCC 58.573 50.000 0.00 0.00 0.00 3.46
2626 5204 4.467795 TCAACAGGGGAGTTATCTTCTCAG 59.532 45.833 0.00 0.00 34.04 3.35
2638 5216 3.641434 AGATTCATGTCAACAGGGGAG 57.359 47.619 0.00 0.00 0.00 4.30
2684 5263 4.562082 CAGATCATTTTTGCACCACACAT 58.438 39.130 0.00 0.00 0.00 3.21
2700 5279 1.538047 GCCCAAGAGTTTGCAGATCA 58.462 50.000 0.00 0.00 32.79 2.92
2716 5295 3.112709 GTGAGTTCTCACGCGCCC 61.113 66.667 15.59 0.00 0.00 6.13
2775 5355 7.579589 TGTTGCTAACATATGAACAAAATGC 57.420 32.000 10.38 3.05 36.25 3.56
2793 5373 5.456548 TGATGATTTGTTGACATGTTGCT 57.543 34.783 0.00 0.00 0.00 3.91
2870 5450 5.111293 GCTGGTGTTGCAAGCATATAAAAT 58.889 37.500 0.00 0.00 43.67 1.82
2931 5511 8.044574 TGGAATGATCCCTAAGTGATTCAATA 57.955 34.615 0.00 0.00 45.95 1.90
2943 5524 9.713684 AAAATCTTACAAATGGAATGATCCCTA 57.286 29.630 0.00 0.00 45.95 3.53
2991 5572 8.766994 CCTAATCAAGGGAATAGGAAAATCAA 57.233 34.615 0.45 0.00 45.80 2.57
3084 5840 7.404671 ACAGTTTTGTTACAGTCCTTCAATT 57.595 32.000 0.00 0.00 32.28 2.32
3092 5849 5.957796 CACGAGAAACAGTTTTGTTACAGTC 59.042 40.000 0.00 0.00 46.54 3.51
3097 5854 4.393680 AGTGCACGAGAAACAGTTTTGTTA 59.606 37.500 12.01 0.00 46.54 2.41
3114 5872 2.595463 TGCTGGGCTCAAGTGCAC 60.595 61.111 9.40 9.40 36.79 4.57
3128 5886 2.029623 GATCATTTGCCATGGACTGCT 58.970 47.619 18.40 0.00 0.00 4.24
3386 6153 0.394565 AGAAGCTGTCCTTGTCGCTT 59.605 50.000 0.00 0.00 44.61 4.68
3661 6679 1.286501 CACGTTGTACTGCACACTGT 58.713 50.000 0.00 0.00 36.69 3.55
3809 6912 1.451927 GGTCCAGCGGATGCATGAA 60.452 57.895 2.46 0.00 46.23 2.57
3987 7093 3.798878 CGATCGACATGAACAGCAGTATT 59.201 43.478 10.26 0.00 0.00 1.89
4200 7309 2.985282 CCAATGCCCACACGCTGT 60.985 61.111 0.00 0.00 0.00 4.40
4225 7334 2.819595 CATGGCCCCGACGTTCAG 60.820 66.667 0.00 0.00 0.00 3.02
4587 7708 0.320421 ACTTGTAACGCCTGTCGCAT 60.320 50.000 0.00 0.00 43.23 4.73
4660 7781 1.067295 AGCCCTTGTCAACCTCATGA 58.933 50.000 0.00 0.00 0.00 3.07
4823 7955 0.958091 CAATCACACAAAGGCCGGAA 59.042 50.000 5.05 0.00 0.00 4.30
4846 7980 5.149973 TGGTAATAAAGTAAGGTCGTGCA 57.850 39.130 0.00 0.00 0.00 4.57
4882 8583 9.673454 GTAGAACGATCTTTTTGGTTTTTGTAT 57.327 29.630 0.00 0.00 37.10 2.29
4890 8591 4.261578 TCGGTAGAACGATCTTTTTGGT 57.738 40.909 0.00 0.00 38.06 3.67
4903 8604 2.682856 GCATTGCCTTTGATCGGTAGAA 59.317 45.455 0.00 0.00 0.00 2.10
5016 12253 5.771469 TGACAATCAACATGTGGAAATGTC 58.229 37.500 28.83 28.83 39.89 3.06
5017 12254 5.787953 TGACAATCAACATGTGGAAATGT 57.212 34.783 19.58 19.58 42.62 2.71
5066 12304 1.129879 GCAATTACGTCGTCGCTCGA 61.130 55.000 0.00 0.00 46.83 4.04
5067 12305 1.132199 AGCAATTACGTCGTCGCTCG 61.132 55.000 0.00 7.80 41.18 5.03
5071 12309 1.983605 ACTTGAGCAATTACGTCGTCG 59.016 47.619 0.00 0.00 43.34 5.12
5072 12310 2.472397 GCACTTGAGCAATTACGTCGTC 60.472 50.000 0.00 0.00 0.00 4.20
5073 12311 1.459592 GCACTTGAGCAATTACGTCGT 59.540 47.619 2.21 2.21 0.00 4.34
5075 12313 2.222596 CGAGCACTTGAGCAATTACGTC 60.223 50.000 0.00 0.00 36.85 4.34
5076 12314 1.726791 CGAGCACTTGAGCAATTACGT 59.273 47.619 0.00 0.00 36.85 3.57
5077 12315 1.527793 GCGAGCACTTGAGCAATTACG 60.528 52.381 0.00 0.00 36.85 3.18
5079 12317 1.086696 GGCGAGCACTTGAGCAATTA 58.913 50.000 0.00 0.00 36.85 1.40
5080 12318 1.878775 GGCGAGCACTTGAGCAATT 59.121 52.632 0.00 0.00 36.85 2.32
5101 12970 1.070445 CTCTGGTGATGCTCCTGATCC 59.930 57.143 0.00 0.00 33.67 3.36
5126 12995 7.576666 GCATGTAAGTTGTAATCCATGAAACCA 60.577 37.037 0.00 0.00 33.28 3.67
5127 12996 6.751888 GCATGTAAGTTGTAATCCATGAAACC 59.248 38.462 0.00 0.00 33.28 3.27
5133 13002 5.129368 AGGGCATGTAAGTTGTAATCCAT 57.871 39.130 0.00 0.00 0.00 3.41
5163 13032 0.845102 ATCTTTTCCCCCTCCACCGT 60.845 55.000 0.00 0.00 0.00 4.83
5177 13046 2.237392 GCTCTCACCTACCACCATCTTT 59.763 50.000 0.00 0.00 0.00 2.52
5197 13066 2.604139 AGATCACCCTAGAGCTAAGGC 58.396 52.381 8.80 0.00 31.46 4.35
5204 13073 6.015519 CCAACAGATTCTAGATCACCCTAGAG 60.016 46.154 0.00 0.00 44.03 2.43
5211 13080 5.221342 ACGGATCCAACAGATTCTAGATCAC 60.221 44.000 13.41 0.00 34.42 3.06
5223 13096 1.732259 CCTTTTCGACGGATCCAACAG 59.268 52.381 13.41 0.72 0.00 3.16
5254 14409 7.073854 ACCCTAGCTTGACCAAGTATATAAGA 58.926 38.462 10.96 0.00 40.45 2.10
5308 14464 1.388133 GAGACCAAAGGCCCCCAAT 59.612 57.895 0.00 0.00 0.00 3.16
5325 14481 1.006825 CGCTTGACACGGTTCGATGA 61.007 55.000 0.00 0.00 0.00 2.92
5394 14550 0.962489 TTCTCGAGCCCAGCTATAGC 59.038 55.000 17.33 17.33 39.88 2.97
5434 14590 1.885049 AGGAGAGATTTAGGCAGCCA 58.115 50.000 15.80 0.00 0.00 4.75
5436 14592 3.836365 AGAAGGAGAGATTTAGGCAGC 57.164 47.619 0.00 0.00 0.00 5.25
5437 14593 6.478512 ACTAAGAAGGAGAGATTTAGGCAG 57.521 41.667 0.00 0.00 0.00 4.85
5441 14597 6.536941 GCACCAACTAAGAAGGAGAGATTTAG 59.463 42.308 0.00 0.00 0.00 1.85
5443 14599 5.249420 GCACCAACTAAGAAGGAGAGATTT 58.751 41.667 0.00 0.00 0.00 2.17
5444 14600 4.621747 CGCACCAACTAAGAAGGAGAGATT 60.622 45.833 0.00 0.00 0.00 2.40
5446 14602 2.231478 CGCACCAACTAAGAAGGAGAGA 59.769 50.000 0.00 0.00 0.00 3.10
5447 14603 2.611518 CGCACCAACTAAGAAGGAGAG 58.388 52.381 0.00 0.00 0.00 3.20
5448 14604 1.337823 GCGCACCAACTAAGAAGGAGA 60.338 52.381 0.30 0.00 0.00 3.71
5449 14605 1.079503 GCGCACCAACTAAGAAGGAG 58.920 55.000 0.30 0.00 0.00 3.69
5456 14612 2.666862 CACGGGCGCACCAACTAA 60.667 61.111 10.83 0.00 40.22 2.24
5545 14748 2.044252 TCGAGTAGCTTCCCGCCT 60.044 61.111 0.00 0.00 40.39 5.52
5595 14798 3.387012 TCATGGGAATCTGACTGGATGA 58.613 45.455 0.00 0.00 0.00 2.92
5635 14856 2.890945 CACCTTTCCCCTTCAACGATTT 59.109 45.455 0.00 0.00 0.00 2.17
5669 14891 4.416620 CTCGGTTCTTTAGCACTCTACTG 58.583 47.826 0.00 0.00 0.00 2.74
5694 14916 2.725815 GCAAACAACGTCAGCGGC 60.726 61.111 0.00 0.00 43.45 6.53
5726 14951 1.538950 GTTAGTCAAGACCGACCGACT 59.461 52.381 0.00 0.00 41.45 4.18
5727 14952 1.267806 TGTTAGTCAAGACCGACCGAC 59.732 52.381 0.00 0.00 36.52 4.79
5734 14959 9.444600 TTTGGATACTATTTGTTAGTCAAGACC 57.555 33.333 0.00 0.00 40.41 3.85


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

AutoCloner maintained by Alex Coulton.