Multiple sequence alignment - TraesCS7A01G020400

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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 TraesCS7A01G020400 chr7A 100.000 3360 0 0 1 3360 8370945 8374304 0.000000e+00 6205.0
1 TraesCS7A01G020400 chr7A 80.620 774 119 13 1254 2021 52682282 52681534 1.350000e-158 569.0
2 TraesCS7A01G020400 chr7A 82.301 339 45 11 1328 1656 8334753 8335086 2.550000e-71 279.0
3 TraesCS7A01G020400 chr7A 84.583 240 17 11 80 312 8333875 8334101 1.570000e-53 220.0
4 TraesCS7A01G020400 chr7A 94.382 89 5 0 1 89 680419033 680419121 1.630000e-28 137.0
5 TraesCS7A01G020400 chr4A 86.366 3220 226 100 258 3360 732769212 732772335 0.000000e+00 3317.0
6 TraesCS7A01G020400 chr4A 79.923 777 129 17 1256 2021 664242003 664241243 2.280000e-151 545.0
7 TraesCS7A01G020400 chr4A 80.000 340 47 14 1332 1653 732725956 732726292 7.250000e-57 231.0
8 TraesCS7A01G020400 chr4A 83.562 219 18 8 84 292 732725102 732725312 4.430000e-44 189.0
9 TraesCS7A01G020400 chr4A 84.507 142 10 4 80 209 732768340 732768481 2.720000e-26 130.0
10 TraesCS7A01G020400 chr4A 77.686 121 14 8 2323 2442 664241049 664240941 1.010000e-05 62.1
11 TraesCS7A01G020400 chr7D 87.587 2860 179 90 587 3360 7444294 7447063 0.000000e+00 3153.0
12 TraesCS7A01G020400 chr7D 80.026 781 127 20 1254 2022 49802033 49801270 4.900000e-153 551.0
13 TraesCS7A01G020400 chr7D 86.957 345 9 19 242 585 7443927 7444236 4.120000e-94 355.0
14 TraesCS7A01G020400 chr7D 76.966 356 44 23 1328 1647 7371694 7372047 5.770000e-38 169.0
15 TraesCS7A01G020400 chr7D 89.286 112 2 2 80 181 7443805 7443916 7.560000e-27 132.0
16 TraesCS7A01G020400 chr7D 77.366 243 22 10 707 943 7371410 7371625 2.740000e-21 113.0
17 TraesCS7A01G020400 chr4B 78.652 801 127 28 1254 2021 86635530 86636319 3.010000e-135 492.0
18 TraesCS7A01G020400 chr7B 80.973 226 28 6 1564 1789 649282486 649282696 7.460000e-37 165.0
19 TraesCS7A01G020400 chr5A 94.382 89 5 0 1 89 77084844 77084756 1.630000e-28 137.0
20 TraesCS7A01G020400 chr5A 91.579 95 8 0 1 95 231070158 231070252 7.560000e-27 132.0
21 TraesCS7A01G020400 chr2B 94.186 86 5 0 1 86 111069074 111069159 7.560000e-27 132.0
22 TraesCS7A01G020400 chr3A 89.423 104 9 2 1 102 261343985 261343882 2.720000e-26 130.0
23 TraesCS7A01G020400 chr6A 90.526 95 9 0 1 95 1814985 1814891 3.520000e-25 126.0
24 TraesCS7A01G020400 chr2A 88.679 106 8 4 1 104 20004700 20004803 3.520000e-25 126.0
25 TraesCS7A01G020400 chr2A 90.625 96 7 2 1 95 27345199 27345293 3.520000e-25 126.0
26 TraesCS7A01G020400 chr1A 89.320 103 8 2 1 103 14170144 14170045 3.520000e-25 126.0


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 TraesCS7A01G020400 chr7A 8370945 8374304 3359 False 6205.000000 6205 100.000000 1 3360 1 chr7A.!!$F1 3359
1 TraesCS7A01G020400 chr7A 52681534 52682282 748 True 569.000000 569 80.620000 1254 2021 1 chr7A.!!$R1 767
2 TraesCS7A01G020400 chr7A 8333875 8335086 1211 False 249.500000 279 83.442000 80 1656 2 chr7A.!!$F3 1576
3 TraesCS7A01G020400 chr4A 732768340 732772335 3995 False 1723.500000 3317 85.436500 80 3360 2 chr4A.!!$F2 3280
4 TraesCS7A01G020400 chr4A 664240941 664242003 1062 True 303.550000 545 78.804500 1256 2442 2 chr4A.!!$R1 1186
5 TraesCS7A01G020400 chr4A 732725102 732726292 1190 False 210.000000 231 81.781000 84 1653 2 chr4A.!!$F1 1569
6 TraesCS7A01G020400 chr7D 7443805 7447063 3258 False 1213.333333 3153 87.943333 80 3360 3 chr7D.!!$F2 3280
7 TraesCS7A01G020400 chr7D 49801270 49802033 763 True 551.000000 551 80.026000 1254 2022 1 chr7D.!!$R1 768
8 TraesCS7A01G020400 chr4B 86635530 86636319 789 False 492.000000 492 78.652000 1254 2021 1 chr4B.!!$F1 767

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
620 1442 0.10339 CACACCACACCACACGTAGA 59.897 55.0 0.0 0.0 0.00 2.59 F
1695 2639 0.03563 CCTTCAGCTTCCTCCAGGTG 60.036 60.0 0.0 0.0 42.62 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 3107 0.037232 GTGGACAGTGGACACTAGGC 60.037 60.0 4.41 2.32 40.2 3.93 R
3039 4086 0.641783 CGAATGGCGCTGAATTTTGC 59.358 50.0 7.64 0.00 0.0 3.68 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 7.906199 AGGTATCTAGCACTAAAATGAGTCT 57.094 36.000 0.00 0.00 0.00 3.24
26 27 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
27 28 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
28 29 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
32 33 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
35 36 9.142014 AGCACTAAAATGAGTCTAGATACATCT 57.858 33.333 12.66 0.00 40.86 2.90
36 37 9.190858 GCACTAAAATGAGTCTAGATACATCTG 57.809 37.037 12.66 7.80 37.76 2.90
55 56 8.862325 ACATCTGTATGTAGACAAATCCAAAA 57.138 30.769 0.00 0.00 44.66 2.44
56 57 8.730680 ACATCTGTATGTAGACAAATCCAAAAC 58.269 33.333 0.00 0.00 44.66 2.43
57 58 8.729756 CATCTGTATGTAGACAAATCCAAAACA 58.270 33.333 0.00 0.00 0.00 2.83
58 59 8.684386 TCTGTATGTAGACAAATCCAAAACAA 57.316 30.769 0.00 0.00 0.00 2.83
59 60 8.783093 TCTGTATGTAGACAAATCCAAAACAAG 58.217 33.333 0.00 0.00 0.00 3.16
60 61 8.458573 TGTATGTAGACAAATCCAAAACAAGT 57.541 30.769 0.00 0.00 0.00 3.16
61 62 9.562408 TGTATGTAGACAAATCCAAAACAAGTA 57.438 29.630 0.00 0.00 0.00 2.24
65 66 9.959749 TGTAGACAAATCCAAAACAAGTAATTC 57.040 29.630 0.00 0.00 0.00 2.17
66 67 9.406828 GTAGACAAATCCAAAACAAGTAATTCC 57.593 33.333 0.00 0.00 0.00 3.01
67 68 7.145323 AGACAAATCCAAAACAAGTAATTCCG 58.855 34.615 0.00 0.00 0.00 4.30
68 69 7.013846 AGACAAATCCAAAACAAGTAATTCCGA 59.986 33.333 0.00 0.00 0.00 4.55
69 70 7.493367 ACAAATCCAAAACAAGTAATTCCGAA 58.507 30.769 0.00 0.00 0.00 4.30
70 71 8.147704 ACAAATCCAAAACAAGTAATTCCGAAT 58.852 29.630 0.00 0.00 0.00 3.34
71 72 8.434661 CAAATCCAAAACAAGTAATTCCGAATG 58.565 33.333 0.00 0.00 0.00 2.67
72 73 6.019779 TCCAAAACAAGTAATTCCGAATGG 57.980 37.500 0.00 0.00 0.00 3.16
73 74 5.770663 TCCAAAACAAGTAATTCCGAATGGA 59.229 36.000 0.00 0.00 44.61 3.41
195 210 0.535102 CAACGCCCTGTCCAGTTTCT 60.535 55.000 0.00 0.00 0.00 2.52
199 214 1.248486 GCCCTGTCCAGTTTCTTTCC 58.752 55.000 0.00 0.00 0.00 3.13
211 226 3.984090 AGTTTCTTTCCTCCTTCCTTCCT 59.016 43.478 0.00 0.00 0.00 3.36
212 227 4.417183 AGTTTCTTTCCTCCTTCCTTCCTT 59.583 41.667 0.00 0.00 0.00 3.36
213 228 4.642466 TTCTTTCCTCCTTCCTTCCTTC 57.358 45.455 0.00 0.00 0.00 3.46
214 229 2.913617 TCTTTCCTCCTTCCTTCCTTCC 59.086 50.000 0.00 0.00 0.00 3.46
215 230 2.743131 TTCCTCCTTCCTTCCTTCCT 57.257 50.000 0.00 0.00 0.00 3.36
216 231 2.743131 TCCTCCTTCCTTCCTTCCTT 57.257 50.000 0.00 0.00 0.00 3.36
375 1090 5.054477 TCTCTTCTTTCCAAACCTACAACG 58.946 41.667 0.00 0.00 0.00 4.10
376 1091 4.773013 TCTTCTTTCCAAACCTACAACGT 58.227 39.130 0.00 0.00 0.00 3.99
377 1092 5.916318 TCTTCTTTCCAAACCTACAACGTA 58.084 37.500 0.00 0.00 0.00 3.57
378 1093 5.754890 TCTTCTTTCCAAACCTACAACGTAC 59.245 40.000 0.00 0.00 0.00 3.67
379 1094 5.021033 TCTTTCCAAACCTACAACGTACA 57.979 39.130 0.00 0.00 0.00 2.90
380 1095 5.426504 TCTTTCCAAACCTACAACGTACAA 58.573 37.500 0.00 0.00 0.00 2.41
381 1096 5.294060 TCTTTCCAAACCTACAACGTACAAC 59.706 40.000 0.00 0.00 0.00 3.32
509 1245 4.033776 TGTAGGTGGCTGGCTGGC 62.034 66.667 11.09 11.09 42.18 4.85
510 1246 3.721706 GTAGGTGGCTGGCTGGCT 61.722 66.667 18.27 1.72 42.34 4.75
511 1247 3.720601 TAGGTGGCTGGCTGGCTG 61.721 66.667 18.27 2.91 42.34 4.85
537 1278 1.202964 CCCAGCCCATGATTGATAGCA 60.203 52.381 0.00 0.00 0.00 3.49
538 1279 2.160205 CCAGCCCATGATTGATAGCAG 58.840 52.381 0.00 0.00 0.00 4.24
539 1280 1.540267 CAGCCCATGATTGATAGCAGC 59.460 52.381 0.00 0.00 0.00 5.25
540 1281 1.424302 AGCCCATGATTGATAGCAGCT 59.576 47.619 0.00 0.00 0.00 4.24
579 1401 1.270199 GCGATGAGGTGATGCATCTCT 60.270 52.381 26.32 21.95 41.72 3.10
581 1403 2.296752 CGATGAGGTGATGCATCTCTCT 59.703 50.000 31.19 24.10 41.72 3.10
583 1405 3.029483 TGAGGTGATGCATCTCTCTCT 57.971 47.619 31.19 20.81 41.72 3.10
585 1407 3.225104 GAGGTGATGCATCTCTCTCTCT 58.775 50.000 27.77 17.92 38.47 3.10
620 1442 0.103390 CACACCACACCACACGTAGA 59.897 55.000 0.00 0.00 0.00 2.59
621 1443 1.045407 ACACCACACCACACGTAGAT 58.955 50.000 0.00 0.00 0.00 1.98
699 1539 0.530870 GTAACCGATCTGGCCTCTGC 60.531 60.000 3.32 0.00 43.94 4.26
700 1540 0.687757 TAACCGATCTGGCCTCTGCT 60.688 55.000 3.32 0.00 43.94 4.24
701 1541 1.965754 AACCGATCTGGCCTCTGCTC 61.966 60.000 3.32 0.00 43.94 4.26
703 1543 2.420890 GATCTGGCCTCTGCTCCG 59.579 66.667 3.32 0.00 37.74 4.63
704 1544 3.160047 ATCTGGCCTCTGCTCCGG 61.160 66.667 3.32 0.00 37.74 5.14
705 1545 3.991924 ATCTGGCCTCTGCTCCGGT 62.992 63.158 3.32 0.00 37.74 5.28
735 1575 4.636435 CACCTTTCCCGGCGGTGT 62.636 66.667 26.32 10.63 42.45 4.16
736 1576 4.636435 ACCTTTCCCGGCGGTGTG 62.636 66.667 26.32 10.02 0.00 3.82
738 1578 4.636435 CTTTCCCGGCGGTGTGGT 62.636 66.667 26.32 0.00 0.00 4.16
739 1579 4.939368 TTTCCCGGCGGTGTGGTG 62.939 66.667 26.32 8.35 0.00 4.17
762 1605 2.733218 GGCGAAACCAAAAGCCGC 60.733 61.111 0.00 0.00 44.45 6.53
763 1606 3.097114 GCGAAACCAAAAGCCGCG 61.097 61.111 0.00 0.00 36.53 6.46
784 1627 1.004595 GCCGTACCTGAAACGATTCC 58.995 55.000 2.72 0.00 42.90 3.01
796 1639 2.712746 GATTCCCCCTCCCTCCCT 59.287 66.667 0.00 0.00 0.00 4.20
832 1704 4.226846 TCCCTCTTCTTTCTTGCATCATCT 59.773 41.667 0.00 0.00 0.00 2.90
840 1712 1.492176 TCTTGCATCATCTTCCCTCCC 59.508 52.381 0.00 0.00 0.00 4.30
841 1713 1.493871 CTTGCATCATCTTCCCTCCCT 59.506 52.381 0.00 0.00 0.00 4.20
842 1714 1.135094 TGCATCATCTTCCCTCCCTC 58.865 55.000 0.00 0.00 0.00 4.30
843 1715 0.399833 GCATCATCTTCCCTCCCTCC 59.600 60.000 0.00 0.00 0.00 4.30
844 1716 1.063183 CATCATCTTCCCTCCCTCCC 58.937 60.000 0.00 0.00 0.00 4.30
853 1728 0.995675 CCCTCCCTCCCATGGACAAT 60.996 60.000 15.22 0.00 0.00 2.71
881 1756 2.042843 TCGCCCTCTCCTTCCTCC 60.043 66.667 0.00 0.00 0.00 4.30
882 1757 3.157949 CGCCCTCTCCTTCCTCCC 61.158 72.222 0.00 0.00 0.00 4.30
883 1758 2.370633 GCCCTCTCCTTCCTCCCT 59.629 66.667 0.00 0.00 0.00 4.20
884 1759 1.764454 GCCCTCTCCTTCCTCCCTC 60.764 68.421 0.00 0.00 0.00 4.30
885 1760 2.023532 CCCTCTCCTTCCTCCCTCT 58.976 63.158 0.00 0.00 0.00 3.69
886 1761 0.105709 CCCTCTCCTTCCTCCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
955 1846 1.011451 GCTCGCCGCATATCTTCCTC 61.011 60.000 0.00 0.00 38.92 3.71
1353 2260 3.020237 GCCGGTCCTCACCTTCCTC 62.020 68.421 1.90 0.00 41.17 3.71
1695 2639 0.035630 CCTTCAGCTTCCTCCAGGTG 60.036 60.000 0.00 0.00 42.62 4.00
1804 2756 1.142314 GTACGCCGCCATACCTCAA 59.858 57.895 0.00 0.00 0.00 3.02
1820 2795 9.046296 CCATACCTCAACTGAATTACTTGTATC 57.954 37.037 0.00 0.00 0.00 2.24
1823 2798 8.324163 ACCTCAACTGAATTACTTGTATCAAC 57.676 34.615 0.00 0.00 0.00 3.18
1846 2830 0.387878 CAGTCACTGACGACCAGCTC 60.388 60.000 0.00 2.06 46.81 4.09
1847 2831 1.442857 GTCACTGACGACCAGCTCG 60.443 63.158 8.95 0.00 46.81 5.03
1859 2848 1.271054 ACCAGCTCGCTTGTCTGAATT 60.271 47.619 0.00 0.00 0.00 2.17
2029 3018 2.135664 CCTCGGAAGGTAATACTGCG 57.864 55.000 0.00 0.00 37.94 5.18
2047 3040 0.673644 CGACACCTCACCATTCCACC 60.674 60.000 0.00 0.00 0.00 4.61
2054 3047 1.228521 CACCATTCCACCAGCACCA 60.229 57.895 0.00 0.00 0.00 4.17
2055 3048 1.228552 ACCATTCCACCAGCACCAC 60.229 57.895 0.00 0.00 0.00 4.16
2056 3049 1.228521 CCATTCCACCAGCACCACA 60.229 57.895 0.00 0.00 0.00 4.17
2058 3051 1.228552 ATTCCACCAGCACCACACC 60.229 57.895 0.00 0.00 0.00 4.16
2060 3053 2.595463 CCACCAGCACCACACCTG 60.595 66.667 0.00 0.00 0.00 4.00
2061 3054 2.510411 CACCAGCACCACACCTGA 59.490 61.111 0.00 0.00 0.00 3.86
2066 3060 1.092348 CAGCACCACACCTGATCATG 58.908 55.000 0.00 0.00 0.00 3.07
2088 3082 4.039609 TGCAGATTCAGAGTTTCAGACAGA 59.960 41.667 0.00 0.00 0.00 3.41
2089 3083 4.388469 GCAGATTCAGAGTTTCAGACAGAC 59.612 45.833 0.00 0.00 0.00 3.51
2090 3084 5.536260 CAGATTCAGAGTTTCAGACAGACA 58.464 41.667 0.00 0.00 0.00 3.41
2113 3107 1.874231 GAGAGATCATGCATGCACCTG 59.126 52.381 25.37 18.85 0.00 4.00
2114 3108 0.311165 GAGATCATGCATGCACCTGC 59.689 55.000 25.37 13.20 42.62 4.85
2133 3143 0.243907 CCTAGTGTCCACTGTCCACG 59.756 60.000 10.15 0.00 42.52 4.94
2149 3159 1.633561 CACGCATGATTGACTCGACT 58.366 50.000 0.00 0.00 0.00 4.18
2152 3162 1.531883 CGCATGATTGACTCGACTCGA 60.532 52.381 0.00 0.29 0.00 4.04
2267 3277 1.466025 CCTGCAGCAGCCTCCAAAAA 61.466 55.000 17.81 0.00 41.13 1.94
2283 3293 4.219070 TCCAAAAATTGCAGAGGATGACAG 59.781 41.667 0.00 0.00 0.00 3.51
2304 3314 2.733593 GCAGCAACAGCAGCAAGC 60.734 61.111 0.00 0.00 40.13 4.01
2317 3330 2.643272 CAAGCAGTGCAGCACCAG 59.357 61.111 22.41 15.87 34.49 4.00
2320 3333 4.039357 GCAGTGCAGCACCAGCAG 62.039 66.667 27.14 13.25 43.63 4.24
2326 3339 2.643272 CAGCACCAGCAGCAACAG 59.357 61.111 0.00 0.00 45.49 3.16
2344 3357 0.740737 AGCAACAACAGGTGCAAGTC 59.259 50.000 8.33 0.00 0.00 3.01
2387 3409 1.000771 GGGAAAACAGAGGAGCCCC 60.001 63.158 0.00 0.00 0.00 5.80
2471 3506 2.859165 TCCCCATGTTCTTGTGAGAC 57.141 50.000 0.00 0.00 0.00 3.36
2472 3507 1.351017 TCCCCATGTTCTTGTGAGACC 59.649 52.381 0.00 0.00 0.00 3.85
2519 3560 1.016130 GGGCACTGTCAGTCATGTCG 61.016 60.000 1.37 0.00 0.00 4.35
2554 3595 2.989840 GTTCTGATCCAGACAACACTCG 59.010 50.000 0.00 0.00 40.46 4.18
2639 3681 2.695359 AGATGTCGCCACGTTTTGTAT 58.305 42.857 0.00 0.00 0.00 2.29
2640 3682 2.415168 AGATGTCGCCACGTTTTGTATG 59.585 45.455 0.00 0.00 0.00 2.39
2641 3683 1.584175 TGTCGCCACGTTTTGTATGT 58.416 45.000 0.00 0.00 0.00 2.29
2642 3684 1.941294 TGTCGCCACGTTTTGTATGTT 59.059 42.857 0.00 0.00 0.00 2.71
2643 3685 2.355132 TGTCGCCACGTTTTGTATGTTT 59.645 40.909 0.00 0.00 0.00 2.83
2644 3686 3.181499 TGTCGCCACGTTTTGTATGTTTT 60.181 39.130 0.00 0.00 0.00 2.43
2645 3687 4.034858 TGTCGCCACGTTTTGTATGTTTTA 59.965 37.500 0.00 0.00 0.00 1.52
2721 3763 8.524870 AATTAACTGCAAATTTGTAAGAGCTG 57.475 30.769 22.21 13.00 0.00 4.24
2763 3805 9.345517 CATTATTTGAGTGAAATACTGTTGGTG 57.654 33.333 4.84 0.00 40.53 4.17
2789 3834 2.390225 AGCAGAGGGGATAGTAGTGG 57.610 55.000 0.00 0.00 0.00 4.00
2797 3842 7.668052 GCAGAGGGGATAGTAGTGGATATATAG 59.332 44.444 0.00 0.00 0.00 1.31
2818 3863 7.703058 ATAGTTGGGAGTTGAAATAAACCAG 57.297 36.000 0.00 0.00 0.00 4.00
2940 3987 4.543692 CACAAGAAAGTGCCAAGAATGAG 58.456 43.478 0.00 0.00 32.04 2.90
2942 3989 4.889409 ACAAGAAAGTGCCAAGAATGAGAA 59.111 37.500 0.00 0.00 0.00 2.87
2948 3995 4.147321 AGTGCCAAGAATGAGAAACACAT 58.853 39.130 0.00 0.00 0.00 3.21
3003 4050 4.636249 ACTTCTTCAGTTGCTTCCTGTAG 58.364 43.478 0.00 0.00 27.32 2.74
3028 4075 0.242286 CCAGTCGATCCCTAGCATCG 59.758 60.000 13.51 13.51 43.77 3.84
3029 4076 0.955178 CAGTCGATCCCTAGCATCGT 59.045 55.000 17.23 2.38 43.07 3.73
3031 4078 0.952280 GTCGATCCCTAGCATCGTCA 59.048 55.000 17.23 2.38 43.07 4.35
3068 4115 3.586039 CGCCATTCGCACTAAACTG 57.414 52.632 0.00 0.00 37.30 3.16
3069 4116 0.521242 CGCCATTCGCACTAAACTGC 60.521 55.000 0.00 0.00 37.30 4.40
3075 4122 2.526304 TCGCACTAAACTGCTCAAGT 57.474 45.000 0.00 0.00 42.60 3.16
3219 4303 5.991606 CACATAGGTGTTGTCTTTCTTCAGA 59.008 40.000 0.00 0.00 40.24 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
1 2 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
2 3 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
6 7 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
9 10 9.142014 AGATGTATCTAGACTCATTTTAGTGCT 57.858 33.333 11.25 2.44 34.85 4.40
10 11 9.190858 CAGATGTATCTAGACTCATTTTAGTGC 57.809 37.037 11.25 0.69 34.85 4.40
19 20 9.713713 GTCTACATACAGATGTATCTAGACTCA 57.286 37.037 25.52 0.00 45.59 3.41
26 27 9.147732 TGGATTTGTCTACATACAGATGTATCT 57.852 33.333 2.47 0.00 45.42 1.98
27 28 9.764363 TTGGATTTGTCTACATACAGATGTATC 57.236 33.333 2.47 0.00 45.42 2.24
29 30 9.952030 TTTTGGATTTGTCTACATACAGATGTA 57.048 29.630 0.00 0.00 44.77 2.29
31 32 8.729756 TGTTTTGGATTTGTCTACATACAGATG 58.270 33.333 0.00 0.00 39.16 2.90
32 33 8.862325 TGTTTTGGATTTGTCTACATACAGAT 57.138 30.769 0.00 0.00 0.00 2.90
33 34 8.684386 TTGTTTTGGATTTGTCTACATACAGA 57.316 30.769 0.00 0.00 0.00 3.41
34 35 8.567948 ACTTGTTTTGGATTTGTCTACATACAG 58.432 33.333 0.00 0.00 0.00 2.74
35 36 8.458573 ACTTGTTTTGGATTTGTCTACATACA 57.541 30.769 0.00 0.00 0.00 2.29
39 40 9.959749 GAATTACTTGTTTTGGATTTGTCTACA 57.040 29.630 0.00 0.00 0.00 2.74
40 41 9.406828 GGAATTACTTGTTTTGGATTTGTCTAC 57.593 33.333 0.00 0.00 0.00 2.59
41 42 8.293867 CGGAATTACTTGTTTTGGATTTGTCTA 58.706 33.333 0.00 0.00 0.00 2.59
42 43 7.013846 TCGGAATTACTTGTTTTGGATTTGTCT 59.986 33.333 0.00 0.00 0.00 3.41
43 44 7.142680 TCGGAATTACTTGTTTTGGATTTGTC 58.857 34.615 0.00 0.00 0.00 3.18
44 45 7.045126 TCGGAATTACTTGTTTTGGATTTGT 57.955 32.000 0.00 0.00 0.00 2.83
45 46 7.938563 TTCGGAATTACTTGTTTTGGATTTG 57.061 32.000 0.00 0.00 0.00 2.32
46 47 7.602265 CCATTCGGAATTACTTGTTTTGGATTT 59.398 33.333 0.00 0.00 0.00 2.17
47 48 7.039363 TCCATTCGGAATTACTTGTTTTGGATT 60.039 33.333 0.00 0.00 38.83 3.01
48 49 6.435904 TCCATTCGGAATTACTTGTTTTGGAT 59.564 34.615 0.00 0.00 38.83 3.41
49 50 5.770663 TCCATTCGGAATTACTTGTTTTGGA 59.229 36.000 0.00 0.00 38.83 3.53
50 51 6.019779 TCCATTCGGAATTACTTGTTTTGG 57.980 37.500 0.00 0.00 38.83 3.28
51 52 6.092748 CCTCCATTCGGAATTACTTGTTTTG 58.907 40.000 0.00 0.00 42.21 2.44
52 53 5.185056 CCCTCCATTCGGAATTACTTGTTTT 59.815 40.000 0.00 0.00 42.21 2.43
53 54 4.705023 CCCTCCATTCGGAATTACTTGTTT 59.295 41.667 0.00 0.00 42.21 2.83
54 55 4.018779 TCCCTCCATTCGGAATTACTTGTT 60.019 41.667 0.00 0.00 42.21 2.83
55 56 3.521937 TCCCTCCATTCGGAATTACTTGT 59.478 43.478 0.00 0.00 42.21 3.16
56 57 4.130118 CTCCCTCCATTCGGAATTACTTG 58.870 47.826 0.00 0.00 42.21 3.16
57 58 3.780850 ACTCCCTCCATTCGGAATTACTT 59.219 43.478 0.00 0.00 42.21 2.24
58 59 3.385115 ACTCCCTCCATTCGGAATTACT 58.615 45.455 0.00 0.00 42.21 2.24
59 60 3.840124 ACTCCCTCCATTCGGAATTAC 57.160 47.619 0.00 0.00 42.21 1.89
60 61 4.291792 TGTACTCCCTCCATTCGGAATTA 58.708 43.478 0.00 0.00 42.21 1.40
61 62 3.112263 TGTACTCCCTCCATTCGGAATT 58.888 45.455 0.00 0.00 42.21 2.17
62 63 2.759355 TGTACTCCCTCCATTCGGAAT 58.241 47.619 0.00 0.00 42.21 3.01
63 64 2.241281 TGTACTCCCTCCATTCGGAA 57.759 50.000 0.00 0.00 42.21 4.30
64 65 2.108168 CTTGTACTCCCTCCATTCGGA 58.892 52.381 0.00 0.00 39.79 4.55
65 66 2.108168 TCTTGTACTCCCTCCATTCGG 58.892 52.381 0.00 0.00 0.00 4.30
66 67 4.021894 CCTATCTTGTACTCCCTCCATTCG 60.022 50.000 0.00 0.00 0.00 3.34
67 68 4.902448 ACCTATCTTGTACTCCCTCCATTC 59.098 45.833 0.00 0.00 0.00 2.67
68 69 4.656112 CACCTATCTTGTACTCCCTCCATT 59.344 45.833 0.00 0.00 0.00 3.16
69 70 4.078571 TCACCTATCTTGTACTCCCTCCAT 60.079 45.833 0.00 0.00 0.00 3.41
70 71 3.271225 TCACCTATCTTGTACTCCCTCCA 59.729 47.826 0.00 0.00 0.00 3.86
71 72 3.912248 TCACCTATCTTGTACTCCCTCC 58.088 50.000 0.00 0.00 0.00 4.30
72 73 5.141182 TCATCACCTATCTTGTACTCCCTC 58.859 45.833 0.00 0.00 0.00 4.30
73 74 5.103473 TCTCATCACCTATCTTGTACTCCCT 60.103 44.000 0.00 0.00 0.00 4.20
74 75 5.141182 TCTCATCACCTATCTTGTACTCCC 58.859 45.833 0.00 0.00 0.00 4.30
75 76 6.491745 TGATCTCATCACCTATCTTGTACTCC 59.508 42.308 0.00 0.00 33.59 3.85
76 77 7.517614 TGATCTCATCACCTATCTTGTACTC 57.482 40.000 0.00 0.00 33.59 2.59
77 78 7.904558 TTGATCTCATCACCTATCTTGTACT 57.095 36.000 0.00 0.00 39.39 2.73
78 79 8.948631 TTTTGATCTCATCACCTATCTTGTAC 57.051 34.615 0.00 0.00 39.39 2.90
181 193 2.553247 GGAGGAAAGAAACTGGACAGGG 60.553 54.545 4.14 0.00 0.00 4.45
183 195 3.778954 AGGAGGAAAGAAACTGGACAG 57.221 47.619 0.00 0.00 0.00 3.51
195 210 3.005529 AGGAAGGAAGGAAGGAGGAAA 57.994 47.619 0.00 0.00 0.00 3.13
216 231 8.426569 AAGATTGGAGGAGATTTCATCAAAAA 57.573 30.769 0.07 0.00 35.87 1.94
238 255 4.152647 TCCTCTCTTAGTTGTGCAGAAGA 58.847 43.478 0.00 0.00 0.00 2.87
239 256 4.527509 TCCTCTCTTAGTTGTGCAGAAG 57.472 45.455 0.00 0.00 0.00 2.85
240 257 4.528206 TGATCCTCTCTTAGTTGTGCAGAA 59.472 41.667 0.00 0.00 0.00 3.02
375 1090 6.542852 CATGTATAGGTTGCTGTTGTTGTAC 58.457 40.000 0.00 0.00 0.00 2.90
376 1091 5.123186 GCATGTATAGGTTGCTGTTGTTGTA 59.877 40.000 0.00 0.00 33.61 2.41
377 1092 4.082787 GCATGTATAGGTTGCTGTTGTTGT 60.083 41.667 0.00 0.00 33.61 3.32
378 1093 4.082841 TGCATGTATAGGTTGCTGTTGTTG 60.083 41.667 0.00 0.00 37.28 3.33
379 1094 4.078537 TGCATGTATAGGTTGCTGTTGTT 58.921 39.130 0.00 0.00 37.28 2.83
380 1095 3.440173 GTGCATGTATAGGTTGCTGTTGT 59.560 43.478 0.00 0.00 37.28 3.32
381 1096 3.439825 TGTGCATGTATAGGTTGCTGTTG 59.560 43.478 0.00 0.00 37.28 3.33
514 1250 0.757935 ATCAATCATGGGCTGGGTGC 60.758 55.000 0.00 0.00 41.94 5.01
515 1251 2.511659 CTATCAATCATGGGCTGGGTG 58.488 52.381 0.00 0.00 0.00 4.61
516 1252 1.202976 GCTATCAATCATGGGCTGGGT 60.203 52.381 0.00 0.00 0.00 4.51
517 1253 1.202964 TGCTATCAATCATGGGCTGGG 60.203 52.381 0.00 0.00 0.00 4.45
518 1254 2.160205 CTGCTATCAATCATGGGCTGG 58.840 52.381 0.00 0.00 0.00 4.85
519 1255 1.540267 GCTGCTATCAATCATGGGCTG 59.460 52.381 0.00 0.00 0.00 4.85
520 1256 1.424302 AGCTGCTATCAATCATGGGCT 59.576 47.619 0.00 0.00 0.00 5.19
521 1257 1.906990 AGCTGCTATCAATCATGGGC 58.093 50.000 0.00 0.00 0.00 5.36
537 1278 4.687219 GCCTCATCTTTTGGTATGGTAGCT 60.687 45.833 0.00 0.00 0.00 3.32
538 1279 3.565902 GCCTCATCTTTTGGTATGGTAGC 59.434 47.826 0.00 0.00 0.00 3.58
539 1280 3.809832 CGCCTCATCTTTTGGTATGGTAG 59.190 47.826 0.00 0.00 0.00 3.18
540 1281 3.452990 TCGCCTCATCTTTTGGTATGGTA 59.547 43.478 0.00 0.00 0.00 3.25
579 1401 2.099405 TGTGTGTGTGTGTGAGAGAGA 58.901 47.619 0.00 0.00 0.00 3.10
581 1403 2.028567 TGTTGTGTGTGTGTGTGAGAGA 60.029 45.455 0.00 0.00 0.00 3.10
583 1405 2.073056 GTGTTGTGTGTGTGTGTGAGA 58.927 47.619 0.00 0.00 0.00 3.27
585 1407 1.533299 GTGTGTTGTGTGTGTGTGTGA 59.467 47.619 0.00 0.00 0.00 3.58
634 1459 1.349357 TGTGGGTAGCATGCAAGTGTA 59.651 47.619 21.98 0.00 0.00 2.90
703 1543 2.342648 GTGACCGGACCAGACACC 59.657 66.667 9.46 0.00 0.00 4.16
704 1544 1.755393 AAGGTGACCGGACCAGACAC 61.755 60.000 9.46 8.16 38.63 3.67
705 1545 1.052124 AAAGGTGACCGGACCAGACA 61.052 55.000 9.46 0.00 38.63 3.41
735 1575 2.517402 GTTTCGCCACCACCACCA 60.517 61.111 0.00 0.00 0.00 4.17
736 1576 3.292159 GGTTTCGCCACCACCACC 61.292 66.667 0.00 0.00 36.73 4.61
737 1577 2.517402 TGGTTTCGCCACCACCAC 60.517 61.111 1.61 0.00 42.27 4.16
746 1586 3.097114 CGCGGCTTTTGGTTTCGC 61.097 61.111 0.00 0.00 42.51 4.70
761 1604 4.143363 GTTTCAGGTACGGCGCGC 62.143 66.667 25.94 25.94 0.00 6.86
762 1605 3.834373 CGTTTCAGGTACGGCGCG 61.834 66.667 6.90 0.00 35.47 6.86
763 1606 1.356527 AATCGTTTCAGGTACGGCGC 61.357 55.000 6.90 0.00 39.38 6.53
784 1627 3.711782 AGGGAAGGGAGGGAGGGG 61.712 72.222 0.00 0.00 0.00 4.79
796 1639 0.252284 AGAGGGAGAAAGCGAGGGAA 60.252 55.000 0.00 0.00 0.00 3.97
832 1704 1.307866 GTCCATGGGAGGGAGGGAA 60.308 63.158 13.02 0.00 34.44 3.97
840 1712 3.815133 CAGGGATTGTCCATGGGAG 57.185 57.895 13.02 0.00 44.05 4.30
869 1744 1.568597 TGAGAGAGGGAGGAAGGAGAG 59.431 57.143 0.00 0.00 0.00 3.20
881 1756 3.019933 GCTTTATAGCCGTGAGAGAGG 57.980 52.381 0.00 0.00 41.74 3.69
955 1846 4.933064 GCGATCGAGCCGGTGGAG 62.933 72.222 21.57 0.00 0.00 3.86
1074 1981 1.354337 CCTTGACGAGCGACACCATG 61.354 60.000 0.00 0.00 0.00 3.66
1792 2736 4.442706 AGTAATTCAGTTGAGGTATGGCG 58.557 43.478 0.00 0.00 0.00 5.69
1793 2737 5.648092 ACAAGTAATTCAGTTGAGGTATGGC 59.352 40.000 8.54 0.00 39.58 4.40
1797 2741 9.431887 GTTGATACAAGTAATTCAGTTGAGGTA 57.568 33.333 8.54 0.00 39.58 3.08
1800 2744 8.993121 ACAGTTGATACAAGTAATTCAGTTGAG 58.007 33.333 8.54 0.00 39.58 3.02
1804 2756 8.150945 ACTGACAGTTGATACAAGTAATTCAGT 58.849 33.333 1.07 16.14 0.00 3.41
1840 2824 1.396301 GAATTCAGACAAGCGAGCTGG 59.604 52.381 0.00 0.00 0.00 4.85
1846 2830 1.391485 CTGGACGAATTCAGACAAGCG 59.609 52.381 6.22 0.00 33.11 4.68
1847 2831 1.734465 CCTGGACGAATTCAGACAAGC 59.266 52.381 6.22 0.00 33.11 4.01
1848 2832 2.350522 CCCTGGACGAATTCAGACAAG 58.649 52.381 6.22 2.39 33.11 3.16
1852 2836 1.218047 CGCCCTGGACGAATTCAGA 59.782 57.895 6.22 0.00 33.11 3.27
1941 2930 3.728373 ACCACCGGGATGAAGGCC 61.728 66.667 6.32 0.00 38.05 5.19
2022 3011 1.195115 ATGGTGAGGTGTCGCAGTAT 58.805 50.000 0.00 0.00 34.60 2.12
2023 3012 0.973632 AATGGTGAGGTGTCGCAGTA 59.026 50.000 0.00 0.00 34.60 2.74
2025 3014 1.021390 GGAATGGTGAGGTGTCGCAG 61.021 60.000 0.00 0.00 34.60 5.18
2026 3015 1.003839 GGAATGGTGAGGTGTCGCA 60.004 57.895 0.00 0.00 34.60 5.10
2027 3016 1.003839 TGGAATGGTGAGGTGTCGC 60.004 57.895 0.00 0.00 0.00 5.19
2028 3017 0.673644 GGTGGAATGGTGAGGTGTCG 60.674 60.000 0.00 0.00 0.00 4.35
2029 3018 0.400213 TGGTGGAATGGTGAGGTGTC 59.600 55.000 0.00 0.00 0.00 3.67
2047 3040 1.092348 CATGATCAGGTGTGGTGCTG 58.908 55.000 0.09 0.00 0.00 4.41
2054 3047 3.199289 TCTGAATCTGCATGATCAGGTGT 59.801 43.478 17.57 0.00 34.30 4.16
2055 3048 3.805207 TCTGAATCTGCATGATCAGGTG 58.195 45.455 17.57 0.19 34.30 4.00
2056 3049 3.455177 ACTCTGAATCTGCATGATCAGGT 59.545 43.478 17.57 13.08 34.30 4.00
2058 3051 5.585047 TGAAACTCTGAATCTGCATGATCAG 59.415 40.000 13.65 13.65 33.57 2.90
2060 3053 5.816258 TCTGAAACTCTGAATCTGCATGATC 59.184 40.000 0.00 0.00 33.57 2.92
2061 3054 5.585445 GTCTGAAACTCTGAATCTGCATGAT 59.415 40.000 0.00 0.00 36.89 2.45
2066 3060 4.388469 GTCTGTCTGAAACTCTGAATCTGC 59.612 45.833 0.00 0.00 0.00 4.26
2088 3082 2.093128 TGCATGCATGATCTCTCAGTGT 60.093 45.455 30.64 0.00 34.12 3.55
2089 3083 2.288186 GTGCATGCATGATCTCTCAGTG 59.712 50.000 30.64 0.46 34.12 3.66
2090 3084 2.562635 GTGCATGCATGATCTCTCAGT 58.437 47.619 30.64 0.00 34.12 3.41
2113 3107 0.037232 GTGGACAGTGGACACTAGGC 60.037 60.000 4.41 2.32 40.20 3.93
2114 3108 0.243907 CGTGGACAGTGGACACTAGG 59.756 60.000 14.80 0.00 40.20 3.02
2133 3143 1.849219 GTCGAGTCGAGTCAATCATGC 59.151 52.381 17.12 0.00 36.23 4.06
2149 3159 4.377021 GCCATTATATTGTCAGGTGTCGA 58.623 43.478 0.00 0.00 0.00 4.20
2152 3162 2.878406 GCGCCATTATATTGTCAGGTGT 59.122 45.455 0.00 0.00 0.00 4.16
2267 3277 2.158928 GCTCTCTGTCATCCTCTGCAAT 60.159 50.000 0.00 0.00 0.00 3.56
2317 3330 0.872881 CCTGTTGTTGCTGTTGCTGC 60.873 55.000 0.00 0.00 40.48 5.25
2320 3333 1.147557 GCACCTGTTGTTGCTGTTGC 61.148 55.000 0.00 0.00 40.20 4.17
2326 3339 0.249031 GGACTTGCACCTGTTGTTGC 60.249 55.000 0.00 0.00 0.00 4.17
2344 3357 1.451567 CAGTCAGGGCTGCATCTGG 60.452 63.158 17.79 3.59 0.00 3.86
2393 3415 3.386402 CACTTGTTAACACCCACCCAATT 59.614 43.478 8.07 0.00 0.00 2.32
2451 3486 2.224769 GGTCTCACAAGAACATGGGGAA 60.225 50.000 0.00 0.00 39.20 3.97
2453 3488 1.826385 GGTCTCACAAGAACATGGGG 58.174 55.000 0.00 0.00 39.20 4.96
2454 3489 1.442769 CGGTCTCACAAGAACATGGG 58.557 55.000 0.00 0.00 39.36 4.00
2519 3560 4.393371 GGATCAGAACCTAAACAGCTTCAC 59.607 45.833 0.00 0.00 0.00 3.18
2721 3763 7.377398 TCAAATAATGCCATTGCCATGTATAC 58.623 34.615 0.00 0.00 36.33 1.47
2763 3805 6.931840 CACTACTATCCCCTCTGCTAAAATTC 59.068 42.308 0.00 0.00 0.00 2.17
2797 3842 4.830600 TCCTGGTTTATTTCAACTCCCAAC 59.169 41.667 0.00 0.00 0.00 3.77
2930 3977 6.916440 TGATTCATGTGTTTCTCATTCTTGG 58.084 36.000 0.00 0.00 0.00 3.61
2932 3979 7.756395 ACTGATTCATGTGTTTCTCATTCTT 57.244 32.000 0.00 0.00 0.00 2.52
2940 3987 6.586463 TCGAAGTCTACTGATTCATGTGTTTC 59.414 38.462 0.00 0.00 0.00 2.78
2942 3989 5.864474 GTCGAAGTCTACTGATTCATGTGTT 59.136 40.000 0.00 0.00 0.00 3.32
2948 3995 4.379186 GGAACGTCGAAGTCTACTGATTCA 60.379 45.833 4.00 0.00 0.00 2.57
3003 4050 2.750712 GCTAGGGATCGACTGGATAGAC 59.249 54.545 4.01 0.00 34.82 2.59
3028 4075 3.360669 GCTGAATTTTGCGTCGTTTTGAC 60.361 43.478 0.00 0.00 44.53 3.18
3029 4076 2.786578 GCTGAATTTTGCGTCGTTTTGA 59.213 40.909 0.00 0.00 0.00 2.69
3031 4078 1.778591 CGCTGAATTTTGCGTCGTTTT 59.221 42.857 14.94 0.00 46.09 2.43
3039 4086 0.641783 CGAATGGCGCTGAATTTTGC 59.358 50.000 7.64 0.00 0.00 3.68
3051 4098 3.312709 GCAGTTTAGTGCGAATGGC 57.687 52.632 0.00 0.00 43.96 4.40
3055 4102 3.202906 AACTTGAGCAGTTTAGTGCGAA 58.797 40.909 4.05 1.51 43.89 4.70
3057 4104 4.928661 ATAACTTGAGCAGTTTAGTGCG 57.071 40.909 4.05 0.00 43.89 5.34
3061 4108 9.760660 GTTGATACAATAACTTGAGCAGTTTAG 57.239 33.333 0.00 0.00 43.89 1.85
3062 4109 9.278978 TGTTGATACAATAACTTGAGCAGTTTA 57.721 29.630 0.00 0.00 43.89 2.01
3063 4110 8.165239 TGTTGATACAATAACTTGAGCAGTTT 57.835 30.769 0.00 0.00 43.89 2.66
3064 4111 8.165239 TTGTTGATACAATAACTTGAGCAGTT 57.835 30.769 0.00 0.00 42.64 3.16
3066 4113 9.462174 TTTTTGTTGATACAATAACTTGAGCAG 57.538 29.630 0.00 0.00 43.43 4.24
3067 4114 9.979578 ATTTTTGTTGATACAATAACTTGAGCA 57.020 25.926 0.00 0.00 43.43 4.26
3114 4198 7.455058 TGGCTTCAAAAGAAGGTACTACAATA 58.545 34.615 7.28 0.00 38.49 1.90
3210 4294 2.811873 GCTGTGGGAGCTTCTGAAGAAA 60.812 50.000 21.06 0.00 45.21 2.52


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

AutoCloner maintained by Alex Coulton.