Multiple sequence alignment - TraesCS7B01G222900

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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 TraesCS7B01G222900 chr7B 100.000 3479 0 0 1 3479 418859510 418856032 0.000000e+00 6425.0
1 TraesCS7B01G222900 chr7A 91.689 2599 142 34 403 2958 466205403 466202836 0.000000e+00 3535.0
2 TraesCS7B01G222900 chr7A 88.449 303 13 2 115 417 466205698 466205418 2.570000e-91 346.0
3 TraesCS7B01G222900 chr7A 97.297 111 3 0 2 112 466207064 466206954 4.580000e-44 189.0
4 TraesCS7B01G222900 chr7D 96.400 1361 38 6 1 1354 407716162 407714806 0.000000e+00 2231.0
5 TraesCS7B01G222900 chr7D 92.147 1579 97 18 1387 2958 407714805 407713247 0.000000e+00 2204.0
6 TraesCS7B01G222900 chr7D 93.900 459 21 3 3023 3479 407713258 407712805 0.000000e+00 686.0
7 TraesCS7B01G222900 chr7D 93.333 60 3 1 2959 3018 41749070 41749128 1.720000e-13 87.9
8 TraesCS7B01G222900 chr4A 100.000 62 0 0 2959 3020 642556902 642556963 7.890000e-22 115.0
9 TraesCS7B01G222900 chr1B 96.667 60 1 1 2959 3018 595541257 595541315 7.950000e-17 99.0
10 TraesCS7B01G222900 chr3A 91.935 62 5 0 2959 3020 607445256 607445195 1.720000e-13 87.9
11 TraesCS7B01G222900 chr5D 91.935 62 4 1 2959 3020 556378998 556378938 6.190000e-13 86.1
12 TraesCS7B01G222900 chr5D 90.000 60 4 2 2959 3017 423222746 423222804 3.720000e-10 76.8
13 TraesCS7B01G222900 chr5B 90.476 63 4 2 2959 3020 54826471 54826410 8.000000e-12 82.4
14 TraesCS7B01G222900 chr4D 90.476 63 4 2 2959 3020 89536061 89536000 8.000000e-12 82.4
15 TraesCS7B01G222900 chrUn 90.323 62 4 2 2959 3020 108274780 108274839 2.880000e-11 80.5
16 TraesCS7B01G222900 chr7B 100.000 3479 0 0 1 3479 418859510 418856032 0.000000e+00 6425.0
17 TraesCS7B01G222900 chr7A 91.689 2599 142 34 403 2958 466205403 466202836 0.000000e+00 3535.0
18 TraesCS7B01G222900 chr7A 88.449 303 13 2 115 417 466205698 466205418 2.570000e-91 346.0
19 TraesCS7B01G222900 chr7A 97.297 111 3 0 2 112 466207064 466206954 4.580000e-44 189.0
20 TraesCS7B01G222900 chr7D 96.400 1361 38 6 1 1354 407716162 407714806 0.000000e+00 2231.0
21 TraesCS7B01G222900 chr7D 92.147 1579 97 18 1387 2958 407714805 407713247 0.000000e+00 2204.0
22 TraesCS7B01G222900 chr7D 93.900 459 21 3 3023 3479 407713258 407712805 0.000000e+00 686.0
23 TraesCS7B01G222900 chr7D 93.333 60 3 1 2959 3018 41749070 41749128 1.720000e-13 87.9
24 TraesCS7B01G222900 chr4A 100.000 62 0 0 2959 3020 642556902 642556963 7.890000e-22 115.0
25 TraesCS7B01G222900 chr1B 96.667 60 1 1 2959 3018 595541257 595541315 7.950000e-17 99.0
26 TraesCS7B01G222900 chr3A 91.935 62 5 0 2959 3020 607445256 607445195 1.720000e-13 87.9
27 TraesCS7B01G222900 chr5D 91.935 62 4 1 2959 3020 556378998 556378938 6.190000e-13 86.1
28 TraesCS7B01G222900 chr5D 90.000 60 4 2 2959 3017 423222746 423222804 3.720000e-10 76.8
29 TraesCS7B01G222900 chr5B 90.476 63 4 2 2959 3020 54826471 54826410 8.000000e-12 82.4
30 TraesCS7B01G222900 chr4D 90.476 63 4 2 2959 3020 89536061 89536000 8.000000e-12 82.4
31 TraesCS7B01G222900 chrUn 90.323 62 4 2 2959 3020 108274780 108274839 2.880000e-11 80.5


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 TraesCS7B01G222900 chr7B 418856032 418859510 3478 True 6425.000000 6425 100.000000 1 3479 2 chr7B.!!$R1 3478
1 TraesCS7B01G222900 chr7A 466202836 466207064 4228 True 1356.666667 3535 92.478333 2 2958 6 chr7A.!!$R1 2956
2 TraesCS7B01G222900 chr7D 407712805 407716162 3357 True 1707.000000 2231 94.149000 1 3479 6 chr7D.!!$R1 3478

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
938 2230 0.109504 GACCTCTCGCACACACTCTC 60.11 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 3974 0.310543 TGTTGTCATTTGCAGTCGGC 59.689 50.0 0.0 0.0 45.13 5.54 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
33 34 7.702772 TCTTAGCTTCTGAAAATAGCTTCGTAG 59.297 37.037 6.88 2.02 42.30 3.51
91 92 3.181491 GCAGTTAGAAAACCACTTGTGCA 60.181 43.478 0.00 0.00 36.15 4.57
331 1585 0.889186 TTTCCGGCAGAGCAAACTCC 60.889 55.000 0.00 0.00 44.65 3.85
394 1649 2.158842 AGCTCCAATAGTCACTGCATCC 60.159 50.000 0.00 0.00 0.00 3.51
476 1760 1.811965 TGTCCCATTCAGTTTCATGCG 59.188 47.619 0.00 0.00 0.00 4.73
558 1842 3.007831 TGGCCTTGAAATTTTGATGGACC 59.992 43.478 3.32 5.80 0.00 4.46
562 1852 4.923281 CCTTGAAATTTTGATGGACCGAAC 59.077 41.667 0.00 0.00 0.00 3.95
591 1881 3.873952 ACGATCTTTCTTGCCTTATCAGC 59.126 43.478 0.00 0.00 0.00 4.26
592 1882 3.873361 CGATCTTTCTTGCCTTATCAGCA 59.127 43.478 0.00 0.00 38.81 4.41
616 1906 1.693062 AGCCCAGATACATCAGCTCTG 59.307 52.381 0.00 0.00 36.89 3.35
618 1908 2.547642 GCCCAGATACATCAGCTCTGAC 60.548 54.545 1.15 0.00 43.11 3.51
619 1909 2.964464 CCCAGATACATCAGCTCTGACT 59.036 50.000 1.15 0.00 43.11 3.41
658 1948 4.940046 TCTCTCTTCAATGAACAGGCATTC 59.060 41.667 0.00 0.00 36.39 2.67
795 2085 6.925610 TCATTATCGCTTCATGCTTTTAGT 57.074 33.333 0.00 0.00 40.11 2.24
927 2217 4.177026 CTCAACACCATAAAGACCTCTCG 58.823 47.826 0.00 0.00 0.00 4.04
937 2229 0.538516 AGACCTCTCGCACACACTCT 60.539 55.000 0.00 0.00 0.00 3.24
938 2230 0.109504 GACCTCTCGCACACACTCTC 60.110 60.000 0.00 0.00 0.00 3.20
951 2243 3.065786 ACACACTCTCACAAATTGCACAG 59.934 43.478 0.00 0.00 0.00 3.66
1222 2515 1.303643 GCCCTGGAACAACCTCAGG 60.304 63.158 0.00 0.00 45.57 3.86
1275 2568 6.210796 GTTTGGTTATCAGTTACCACAAACC 58.789 40.000 0.00 0.00 43.80 3.27
1277 2570 5.067273 TGGTTATCAGTTACCACAAACCAG 58.933 41.667 0.00 0.00 39.81 4.00
1301 2594 4.930963 TGTTGTTTCTTCGCAATCATGTT 58.069 34.783 0.00 0.00 0.00 2.71
1303 2596 5.912396 TGTTGTTTCTTCGCAATCATGTTAC 59.088 36.000 0.00 0.00 0.00 2.50
1344 2637 2.479275 GGCTGAAACGAAGTACAGTTCC 59.521 50.000 0.00 0.00 45.00 3.62
1350 2676 3.279853 ACGAAGTACAGTTCCGAGTTC 57.720 47.619 0.00 0.00 41.94 3.01
1354 2680 4.153835 CGAAGTACAGTTCCGAGTTCTAGT 59.846 45.833 0.00 0.00 0.00 2.57
1355 2681 5.349817 CGAAGTACAGTTCCGAGTTCTAGTA 59.650 44.000 0.00 0.00 0.00 1.82
1356 2682 6.128445 CGAAGTACAGTTCCGAGTTCTAGTAA 60.128 42.308 0.00 0.00 0.00 2.24
1357 2683 7.413877 CGAAGTACAGTTCCGAGTTCTAGTAAT 60.414 40.741 0.00 0.00 0.00 1.89
1358 2684 8.798859 AAGTACAGTTCCGAGTTCTAGTAATA 57.201 34.615 0.00 0.00 0.00 0.98
1359 2685 8.207521 AGTACAGTTCCGAGTTCTAGTAATAC 57.792 38.462 0.00 0.00 0.00 1.89
1360 2686 7.826252 AGTACAGTTCCGAGTTCTAGTAATACA 59.174 37.037 0.00 0.00 0.00 2.29
1361 2687 7.458409 ACAGTTCCGAGTTCTAGTAATACAA 57.542 36.000 0.00 0.00 0.00 2.41
1362 2688 7.311408 ACAGTTCCGAGTTCTAGTAATACAAC 58.689 38.462 0.00 0.00 0.00 3.32
1363 2689 6.750963 CAGTTCCGAGTTCTAGTAATACAACC 59.249 42.308 0.00 0.00 0.00 3.77
1364 2690 6.662663 AGTTCCGAGTTCTAGTAATACAACCT 59.337 38.462 0.00 0.00 0.00 3.50
1365 2691 7.831193 AGTTCCGAGTTCTAGTAATACAACCTA 59.169 37.037 0.00 0.00 0.00 3.08
1366 2692 7.798596 TCCGAGTTCTAGTAATACAACCTAG 57.201 40.000 0.00 0.00 0.00 3.02
1367 2693 7.568349 TCCGAGTTCTAGTAATACAACCTAGA 58.432 38.462 0.00 0.00 36.34 2.43
1368 2694 8.216423 TCCGAGTTCTAGTAATACAACCTAGAT 58.784 37.037 0.00 0.00 37.58 1.98
1369 2695 9.499479 CCGAGTTCTAGTAATACAACCTAGATA 57.501 37.037 0.00 0.00 37.58 1.98
1409 2735 3.118298 ACATGCTTTGATTAAATGGGGGC 60.118 43.478 0.00 0.00 0.00 5.80
1412 2738 2.223805 GCTTTGATTAAATGGGGGCTCG 60.224 50.000 0.00 0.00 0.00 5.03
1416 2742 2.291282 TGATTAAATGGGGGCTCGTGTT 60.291 45.455 0.00 0.00 0.00 3.32
1418 2744 1.540267 TAAATGGGGGCTCGTGTTTG 58.460 50.000 0.00 0.00 0.00 2.93
1521 2851 5.435291 AGAGAATTTGCATGTAAGAGAGGG 58.565 41.667 0.00 0.00 0.00 4.30
1539 2869 4.830600 AGAGGGGAATGCGAAAAGTAAAAA 59.169 37.500 0.00 0.00 0.00 1.94
1573 2905 8.561738 AATACGAAGGTAAACAAGATTGTGAT 57.438 30.769 0.00 0.00 41.31 3.06
1575 2907 7.596749 ACGAAGGTAAACAAGATTGTGATAG 57.403 36.000 0.00 0.00 41.31 2.08
1592 2924 5.411361 TGTGATAGACAAAACAATTCCCTCG 59.589 40.000 0.00 0.00 0.00 4.63
1607 2939 2.884639 TCCCTCGCCAAAGAAAAGAAAG 59.115 45.455 0.00 0.00 0.00 2.62
1667 2999 7.986085 AACATACTAGCATGTCTCAAGTTTT 57.014 32.000 9.06 0.00 38.19 2.43
1668 3000 7.986085 ACATACTAGCATGTCTCAAGTTTTT 57.014 32.000 2.51 0.00 33.89 1.94
1725 3057 2.827652 TGTTGTCATGAACTACACGCA 58.172 42.857 0.00 0.00 38.45 5.24
1767 3099 1.932604 GCTTGTCTGTCACCGTCTCAG 60.933 57.143 0.00 0.00 0.00 3.35
1890 3222 4.141756 CCTGCATATTCTGAAGACCTGAGT 60.142 45.833 0.00 0.00 31.16 3.41
1901 3233 4.407621 TGAAGACCTGAGTAAAGTGGAACA 59.592 41.667 0.00 0.00 41.43 3.18
1945 3277 5.766150 TGGAAACATAAACACTGGAGTTG 57.234 39.130 0.00 0.00 33.40 3.16
2022 3354 4.934797 TGGGAGAAAGATTGACCTGAAT 57.065 40.909 0.00 0.00 0.00 2.57
2049 3381 2.572284 GGCTACGGTTCGCTGTCT 59.428 61.111 0.00 0.00 37.89 3.41
2113 3445 0.395586 TCCTTGGTTTGCACTGCACT 60.396 50.000 2.26 0.00 38.71 4.40
2114 3446 0.249155 CCTTGGTTTGCACTGCACTG 60.249 55.000 2.26 0.00 38.71 3.66
2115 3447 0.872881 CTTGGTTTGCACTGCACTGC 60.873 55.000 10.99 10.99 38.71 4.40
2116 3448 1.602327 TTGGTTTGCACTGCACTGCA 61.602 50.000 15.89 15.89 45.59 4.41
2117 3449 1.589727 GGTTTGCACTGCACTGCAC 60.590 57.895 18.97 9.80 46.90 4.57
2118 3450 1.139308 GTTTGCACTGCACTGCACA 59.861 52.632 18.97 11.25 46.90 4.57
2119 3451 1.139308 TTTGCACTGCACTGCACAC 59.861 52.632 18.97 0.00 46.90 3.82
2120 3452 1.314534 TTTGCACTGCACTGCACACT 61.315 50.000 18.97 0.00 46.90 3.55
2161 3494 5.151297 TCTTGCTCATGTTCACTGACATA 57.849 39.130 0.00 0.00 38.15 2.29
2193 3526 2.170166 TGGTTGATTTCAGATGGCCAC 58.830 47.619 8.16 1.58 0.00 5.01
2213 3546 0.394899 GGGAGGATTGCAACCAGAGG 60.395 60.000 16.93 0.00 0.00 3.69
2216 3549 1.380380 GGATTGCAACCAGAGGGGG 60.380 63.158 0.00 0.00 42.91 5.40
2339 3672 0.702902 TGGGAGTAAGTCGAGGGAGT 59.297 55.000 0.00 0.00 0.00 3.85
2366 3699 3.728718 GGCATATACGCCGTTCATTTTTG 59.271 43.478 0.00 0.00 43.52 2.44
2424 3759 1.443194 GCTGTTCGTCGCTTCGGTA 60.443 57.895 0.00 0.00 0.00 4.02
2469 3804 3.245052 ACCCTAGAGCTGACAAAAGCAAT 60.245 43.478 0.00 0.00 46.08 3.56
2621 3969 1.763120 AGGCAGTTCCTGTGCATCA 59.237 52.632 0.00 0.00 45.54 3.07
2622 3970 0.330604 AGGCAGTTCCTGTGCATCAT 59.669 50.000 0.00 0.00 45.54 2.45
2623 3971 0.737219 GGCAGTTCCTGTGCATCATC 59.263 55.000 0.00 0.00 43.12 2.92
2624 3972 1.681166 GGCAGTTCCTGTGCATCATCT 60.681 52.381 0.00 0.00 43.12 2.90
2625 3973 2.420547 GGCAGTTCCTGTGCATCATCTA 60.421 50.000 0.00 0.00 43.12 1.98
2626 3974 2.871022 GCAGTTCCTGTGCATCATCTAG 59.129 50.000 0.00 0.00 40.86 2.43
2627 3975 2.871022 CAGTTCCTGTGCATCATCTAGC 59.129 50.000 0.00 0.00 0.00 3.42
2628 3976 2.158842 AGTTCCTGTGCATCATCTAGCC 60.159 50.000 0.00 0.00 0.00 3.93
2671 4019 0.677731 TGCATAGCTCCAACCTGCAC 60.678 55.000 0.00 0.00 37.88 4.57
2707 4068 0.106967 GTCTTCCCCTCCAATGAGCC 60.107 60.000 0.00 0.00 37.29 4.70
2732 4093 2.181021 CGTGTGTCTAGGGGCGTC 59.819 66.667 0.00 0.00 0.00 5.19
2736 4097 2.282674 TGTCTAGGGGCGTCGTGT 60.283 61.111 0.00 0.00 0.00 4.49
2748 4109 3.244579 GGGCGTCGTGTGATTAATTACTC 59.755 47.826 11.24 7.06 0.00 2.59
2782 4143 5.718649 GCTTGTGCAATCGAATAGTAGAA 57.281 39.130 0.00 0.00 39.41 2.10
2783 4144 5.732288 GCTTGTGCAATCGAATAGTAGAAG 58.268 41.667 0.00 0.00 39.41 2.85
2784 4145 5.520288 GCTTGTGCAATCGAATAGTAGAAGA 59.480 40.000 11.80 0.00 39.41 2.87
2887 4248 3.255725 GCACCGTTACACTAACATGCTA 58.744 45.455 0.00 0.00 42.55 3.49
2916 4277 3.160777 TCTCCTCGGAAGCGTTTTATC 57.839 47.619 0.00 0.00 0.00 1.75
2917 4278 2.494471 TCTCCTCGGAAGCGTTTTATCA 59.506 45.455 0.00 0.00 0.00 2.15
2949 4311 3.157932 GCTTTCTGCTCTCATCGTAGT 57.842 47.619 0.00 0.00 38.95 2.73
2950 4312 3.516615 GCTTTCTGCTCTCATCGTAGTT 58.483 45.455 0.00 0.00 38.95 2.24
2951 4313 3.929610 GCTTTCTGCTCTCATCGTAGTTT 59.070 43.478 0.00 0.00 38.95 2.66
2952 4314 4.201666 GCTTTCTGCTCTCATCGTAGTTTG 60.202 45.833 0.00 0.00 38.95 2.93
2953 4315 4.521130 TTCTGCTCTCATCGTAGTTTGT 57.479 40.909 0.00 0.00 0.00 2.83
2954 4316 4.521130 TCTGCTCTCATCGTAGTTTGTT 57.479 40.909 0.00 0.00 0.00 2.83
2955 4317 4.883083 TCTGCTCTCATCGTAGTTTGTTT 58.117 39.130 0.00 0.00 0.00 2.83
2956 4318 4.686091 TCTGCTCTCATCGTAGTTTGTTTG 59.314 41.667 0.00 0.00 0.00 2.93
2957 4319 4.627058 TGCTCTCATCGTAGTTTGTTTGA 58.373 39.130 0.00 0.00 0.00 2.69
2958 4320 5.053811 TGCTCTCATCGTAGTTTGTTTGAA 58.946 37.500 0.00 0.00 0.00 2.69
2959 4321 5.700832 TGCTCTCATCGTAGTTTGTTTGAAT 59.299 36.000 0.00 0.00 0.00 2.57
2960 4322 6.017933 GCTCTCATCGTAGTTTGTTTGAATG 58.982 40.000 0.00 0.00 0.00 2.67
2961 4323 6.480524 TCTCATCGTAGTTTGTTTGAATGG 57.519 37.500 0.00 0.00 0.00 3.16
2962 4324 5.041951 TCATCGTAGTTTGTTTGAATGGC 57.958 39.130 0.00 0.00 0.00 4.40
2963 4325 4.759693 TCATCGTAGTTTGTTTGAATGGCT 59.240 37.500 0.00 0.00 0.00 4.75
2964 4326 4.481930 TCGTAGTTTGTTTGAATGGCTG 57.518 40.909 0.00 0.00 0.00 4.85
2965 4327 2.979813 CGTAGTTTGTTTGAATGGCTGC 59.020 45.455 0.00 0.00 0.00 5.25
2966 4328 3.549827 CGTAGTTTGTTTGAATGGCTGCA 60.550 43.478 0.50 0.00 0.00 4.41
2967 4329 3.756933 AGTTTGTTTGAATGGCTGCAT 57.243 38.095 0.50 0.00 0.00 3.96
2968 4330 3.395639 AGTTTGTTTGAATGGCTGCATG 58.604 40.909 0.50 0.00 0.00 4.06
2969 4331 1.798283 TTGTTTGAATGGCTGCATGC 58.202 45.000 11.82 11.82 41.94 4.06
2970 4332 0.680061 TGTTTGAATGGCTGCATGCA 59.320 45.000 21.29 21.29 45.15 3.96
2971 4333 1.276705 TGTTTGAATGGCTGCATGCAT 59.723 42.857 22.97 5.46 45.15 3.96
2972 4334 1.931172 GTTTGAATGGCTGCATGCATC 59.069 47.619 22.97 17.75 45.15 3.91
2973 4335 0.101579 TTGAATGGCTGCATGCATCG 59.898 50.000 22.97 12.00 45.15 3.84
2974 4336 0.748729 TGAATGGCTGCATGCATCGA 60.749 50.000 22.97 15.35 45.15 3.59
2975 4337 0.596577 GAATGGCTGCATGCATCGAT 59.403 50.000 22.97 17.12 45.15 3.59
2976 4338 1.000607 GAATGGCTGCATGCATCGATT 60.001 47.619 25.46 25.46 45.15 3.34
2977 4339 0.313987 ATGGCTGCATGCATCGATTG 59.686 50.000 22.97 9.56 45.15 2.67
2978 4340 0.748729 TGGCTGCATGCATCGATTGA 60.749 50.000 22.97 0.00 45.15 2.57
2979 4341 0.596577 GGCTGCATGCATCGATTGAT 59.403 50.000 22.97 0.00 45.15 2.57
2988 4350 0.873054 CATCGATTGATGCAGAGGCC 59.127 55.000 10.05 0.00 45.06 5.19
2989 4351 0.602106 ATCGATTGATGCAGAGGCCG 60.602 55.000 0.00 0.00 40.13 6.13
2990 4352 2.249535 CGATTGATGCAGAGGCCGG 61.250 63.158 0.00 0.00 40.13 6.13
2991 4353 1.146930 GATTGATGCAGAGGCCGGA 59.853 57.895 5.05 0.00 40.13 5.14
2992 4354 0.883814 GATTGATGCAGAGGCCGGAG 60.884 60.000 5.05 0.00 40.13 4.63
3009 4371 2.394930 GAGGCTCTGTCTCCTTTTCC 57.605 55.000 7.40 0.00 31.71 3.13
3010 4372 1.625818 GAGGCTCTGTCTCCTTTTCCA 59.374 52.381 7.40 0.00 31.71 3.53
3011 4373 2.039084 GAGGCTCTGTCTCCTTTTCCAA 59.961 50.000 7.40 0.00 31.71 3.53
3012 4374 2.443255 AGGCTCTGTCTCCTTTTCCAAA 59.557 45.455 0.00 0.00 0.00 3.28
3013 4375 3.117512 AGGCTCTGTCTCCTTTTCCAAAA 60.118 43.478 0.00 0.00 0.00 2.44
3014 4376 3.636764 GGCTCTGTCTCCTTTTCCAAAAA 59.363 43.478 0.00 0.00 0.00 1.94
3109 4471 4.376146 GCAAACCAGTTTATGCCTTTTGA 58.624 39.130 0.00 0.00 0.00 2.69
3150 4512 7.813645 GGATTACGACAATCCAGTTTAGTTTT 58.186 34.615 21.15 0.00 44.33 2.43
3155 4517 6.543100 ACGACAATCCAGTTTAGTTTTTACCA 59.457 34.615 0.00 0.00 0.00 3.25
3163 4525 9.191479 TCCAGTTTAGTTTTTACCAAGAAATCA 57.809 29.630 0.00 0.00 0.00 2.57
3172 4534 3.795688 ACCAAGAAATCAGAAGGAGCA 57.204 42.857 0.00 0.00 0.00 4.26
3173 4535 3.683802 ACCAAGAAATCAGAAGGAGCAG 58.316 45.455 0.00 0.00 0.00 4.24
3240 4604 0.779997 AGGGGACATTGCCAGAAACT 59.220 50.000 0.00 0.00 0.00 2.66
3256 4620 1.326951 AACTGTTGGCAACCCACCAC 61.327 55.000 26.31 1.84 41.97 4.16
3271 4635 3.070018 CCACCACTGATTCACTTCTCAC 58.930 50.000 0.00 0.00 0.00 3.51
3345 4709 1.004862 TCAGAGCGAGGAGGAAGAGAA 59.995 52.381 0.00 0.00 0.00 2.87
3346 4710 1.134175 CAGAGCGAGGAGGAAGAGAAC 59.866 57.143 0.00 0.00 0.00 3.01
3354 4718 1.486211 GAGGAAGAGAACGGGGATGA 58.514 55.000 0.00 0.00 0.00 2.92
3376 4740 1.200839 GAAGTGTCGTGCCGTTTCG 59.799 57.895 0.00 0.00 0.00 3.46
3404 4768 1.489230 ACCGGATACCCTGGATTTGAC 59.511 52.381 9.46 0.00 32.72 3.18
3405 4769 1.768870 CCGGATACCCTGGATTTGACT 59.231 52.381 0.00 0.00 0.00 3.41
3413 4777 5.104259 ACCCTGGATTTGACTACATTCTC 57.896 43.478 0.00 0.00 0.00 2.87
3416 4780 5.398353 CCCTGGATTTGACTACATTCTCCAT 60.398 44.000 0.00 0.00 32.16 3.41
3417 4781 6.183361 CCCTGGATTTGACTACATTCTCCATA 60.183 42.308 0.00 0.00 32.16 2.74
3418 4782 6.933521 CCTGGATTTGACTACATTCTCCATAG 59.066 42.308 0.00 0.00 32.16 2.23
3419 4783 6.830912 TGGATTTGACTACATTCTCCATAGG 58.169 40.000 0.00 0.00 0.00 2.57
3447 4811 7.261325 CCTCGTAGATCTTTCTTCAATCTTGA 58.739 38.462 0.00 0.00 33.89 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 6.764308 AACTGCAAATGAAGTATGCACTAT 57.236 33.333 0.00 0.00 44.52 2.12
91 92 9.499479 GGATATGAGATGAATGTTGATGTTACT 57.501 33.333 0.00 0.00 0.00 2.24
476 1760 2.370647 GATACACCCGCCCTCAGAGC 62.371 65.000 0.00 0.00 0.00 4.09
558 1842 5.472822 CAAGAAAGATCGTAATCACGTTCG 58.527 41.667 0.00 0.00 46.62 3.95
591 1881 4.649692 AGCTGATGTATCTGGGCTATTTG 58.350 43.478 0.00 0.00 0.00 2.32
592 1882 4.596643 AGAGCTGATGTATCTGGGCTATTT 59.403 41.667 0.00 0.00 31.94 1.40
658 1948 2.137810 TTTTAAAGGATGGCGGGAGG 57.862 50.000 0.00 0.00 0.00 4.30
686 1976 6.428159 CCATAGAATGGCTCATGTTTACCTAC 59.572 42.308 0.00 0.00 44.70 3.18
795 2085 0.416231 AGTGGAGTAGTGGGGCCTAA 59.584 55.000 0.84 0.00 0.00 2.69
927 2217 2.223548 TGCAATTTGTGAGAGTGTGTGC 60.224 45.455 0.00 0.00 0.00 4.57
937 2229 3.065233 GTGTCTGTCTGTGCAATTTGTGA 59.935 43.478 0.00 0.00 0.00 3.58
938 2230 3.181498 TGTGTCTGTCTGTGCAATTTGTG 60.181 43.478 0.00 0.00 0.00 3.33
951 2243 4.519730 ACTTCACTACTACCTGTGTCTGTC 59.480 45.833 0.00 0.00 35.82 3.51
993 2285 0.177604 AAGAGCTCTTCATGGCCTCG 59.822 55.000 23.49 0.00 0.00 4.63
1073 2366 2.504367 GCCTAAGCTCAAGGTTGTTGA 58.496 47.619 14.75 0.00 36.43 3.18
1222 2515 2.102252 CAGGACACTCATTAGGCCTCTC 59.898 54.545 9.68 0.00 0.00 3.20
1275 2568 4.350346 TGATTGCGAAGAAACAACAACTG 58.650 39.130 0.00 0.00 0.00 3.16
1277 2570 4.739716 ACATGATTGCGAAGAAACAACAAC 59.260 37.500 0.00 0.00 0.00 3.32
1303 2596 9.653287 TTCAGCCTATATACCATCTTATTTTCG 57.347 33.333 0.00 0.00 0.00 3.46
1320 2613 4.803098 ACTGTACTTCGTTTCAGCCTAT 57.197 40.909 0.00 0.00 0.00 2.57
1370 2696 9.571810 CAAAGCATGTTTACATTCATAAAGCTA 57.428 29.630 0.00 0.00 33.61 3.32
1371 2697 8.306038 TCAAAGCATGTTTACATTCATAAAGCT 58.694 29.630 0.00 0.00 33.61 3.74
1372 2698 8.464770 TCAAAGCATGTTTACATTCATAAAGC 57.535 30.769 0.00 0.00 33.61 3.51
1380 2706 9.165035 CCCATTTAATCAAAGCATGTTTACATT 57.835 29.630 0.00 0.09 33.61 2.71
1381 2707 7.769970 CCCCATTTAATCAAAGCATGTTTACAT 59.230 33.333 0.00 0.00 36.96 2.29
1382 2708 7.102346 CCCCATTTAATCAAAGCATGTTTACA 58.898 34.615 0.00 0.00 0.00 2.41
1383 2709 6.538381 CCCCCATTTAATCAAAGCATGTTTAC 59.462 38.462 0.00 0.00 0.00 2.01
1384 2710 6.648192 CCCCCATTTAATCAAAGCATGTTTA 58.352 36.000 0.00 0.00 0.00 2.01
1385 2711 5.499313 CCCCCATTTAATCAAAGCATGTTT 58.501 37.500 0.00 0.00 0.00 2.83
1405 2731 2.433436 ACTTATTCAAACACGAGCCCC 58.567 47.619 0.00 0.00 0.00 5.80
1482 2811 7.646922 GCAAATTCTCTATGTTCCATTGACATC 59.353 37.037 0.00 0.00 38.58 3.06
1490 2819 7.828717 TCTTACATGCAAATTCTCTATGTTCCA 59.171 33.333 0.00 0.00 34.22 3.53
1539 2869 9.620660 CTTGTTTACCTTCGTATTTATTTGCTT 57.379 29.630 0.00 0.00 0.00 3.91
1553 2883 8.547967 TGTCTATCACAATCTTGTTTACCTTC 57.452 34.615 0.00 0.00 39.91 3.46
1569 2901 5.673818 GCGAGGGAATTGTTTTGTCTATCAC 60.674 44.000 0.00 0.00 0.00 3.06
1573 2905 3.078837 GGCGAGGGAATTGTTTTGTCTA 58.921 45.455 0.00 0.00 0.00 2.59
1575 2907 1.611491 TGGCGAGGGAATTGTTTTGTC 59.389 47.619 0.00 0.00 0.00 3.18
1592 2924 6.925718 AGCTTGTTATCTTTCTTTTCTTTGGC 59.074 34.615 0.00 0.00 0.00 4.52
1628 2960 7.659799 TGCTAGTATGTTACCGCAATATCAATT 59.340 33.333 0.00 0.00 34.21 2.32
1630 2962 6.517605 TGCTAGTATGTTACCGCAATATCAA 58.482 36.000 0.00 0.00 34.21 2.57
1693 3025 4.967036 TCATGACAACAAGACATACACCA 58.033 39.130 0.00 0.00 31.42 4.17
1725 3057 1.168714 GCAAGATTCCACGCCTCTTT 58.831 50.000 0.00 0.00 0.00 2.52
1734 3066 1.074405 AGACAAGCCAGCAAGATTCCA 59.926 47.619 0.00 0.00 0.00 3.53
1735 3067 1.471684 CAGACAAGCCAGCAAGATTCC 59.528 52.381 0.00 0.00 0.00 3.01
1767 3099 5.685511 TCTGAAAATTGTTAGCGAAACTTGC 59.314 36.000 6.55 0.00 38.99 4.01
1890 3222 6.109156 TCTTCATAGCAGTGTTCCACTTTA 57.891 37.500 0.00 0.00 42.59 1.85
1901 3233 5.426504 CATGGTCTTCTTCTTCATAGCAGT 58.573 41.667 0.00 0.00 0.00 4.40
1945 3277 1.153549 CCGGCCTCTCTTGTACTGC 60.154 63.158 0.00 0.00 0.00 4.40
2040 3372 1.005748 CAGAGCACCAGACAGCGAA 60.006 57.895 0.00 0.00 35.48 4.70
2096 3428 0.872881 GCAGTGCAGTGCAAACCAAG 60.873 55.000 35.84 7.31 41.47 3.61
2113 3445 5.817296 GGAGTTTGATCATACATAGTGTGCA 59.183 40.000 17.09 0.00 0.00 4.57
2114 3446 5.817296 TGGAGTTTGATCATACATAGTGTGC 59.183 40.000 17.09 3.05 0.00 4.57
2115 3447 7.930325 AGATGGAGTTTGATCATACATAGTGTG 59.070 37.037 17.09 0.00 0.00 3.82
2116 3448 8.027524 AGATGGAGTTTGATCATACATAGTGT 57.972 34.615 17.09 0.00 0.00 3.55
2117 3449 8.771766 CAAGATGGAGTTTGATCATACATAGTG 58.228 37.037 17.09 4.20 0.00 2.74
2118 3450 7.443575 GCAAGATGGAGTTTGATCATACATAGT 59.556 37.037 17.09 2.40 0.00 2.12
2119 3451 7.660617 AGCAAGATGGAGTTTGATCATACATAG 59.339 37.037 17.09 1.91 0.00 2.23
2120 3452 7.512130 AGCAAGATGGAGTTTGATCATACATA 58.488 34.615 17.09 4.77 0.00 2.29
2161 3494 4.951715 TGAAATCAACCAAGCAGCTCATAT 59.048 37.500 0.00 0.00 0.00 1.78
2193 3526 0.745845 CTCTGGTTGCAATCCTCCCG 60.746 60.000 7.36 0.00 0.00 5.14
2213 3546 2.045536 CCAGCTGCTCTTCACCCC 60.046 66.667 8.66 0.00 0.00 4.95
2216 3549 3.559242 GTGATATTCCAGCTGCTCTTCAC 59.441 47.826 8.66 12.76 0.00 3.18
2366 3699 2.880890 AGTGACCACTTCAACTTGCATC 59.119 45.455 0.00 0.00 38.83 3.91
2444 3779 1.276622 TTTGTCAGCTCTAGGGTCCC 58.723 55.000 0.00 0.00 0.00 4.46
2469 3804 5.045215 CACACACCGTTGTTCTACTTCTTA 58.955 41.667 0.00 0.00 31.66 2.10
2621 3969 2.093500 TGTCATTTGCAGTCGGCTAGAT 60.093 45.455 0.00 0.00 45.15 1.98
2622 3970 1.275010 TGTCATTTGCAGTCGGCTAGA 59.725 47.619 0.00 0.00 45.15 2.43
2623 3971 1.725641 TGTCATTTGCAGTCGGCTAG 58.274 50.000 0.00 0.00 45.15 3.42
2624 3972 1.804151 GTTGTCATTTGCAGTCGGCTA 59.196 47.619 0.00 0.00 45.15 3.93
2625 3973 0.593128 GTTGTCATTTGCAGTCGGCT 59.407 50.000 0.00 0.00 45.15 5.52
2626 3974 0.310543 TGTTGTCATTTGCAGTCGGC 59.689 50.000 0.00 0.00 45.13 5.54
2627 3975 1.069022 CCTGTTGTCATTTGCAGTCGG 60.069 52.381 0.00 0.00 0.00 4.79
2628 3976 1.872952 TCCTGTTGTCATTTGCAGTCG 59.127 47.619 0.00 0.00 0.00 4.18
2671 4019 3.606595 AGACCATATCTGCATGATCCG 57.393 47.619 0.00 0.00 35.81 4.18
2732 4093 8.928270 AACTTCCTAGAGTAATTAATCACACG 57.072 34.615 14.80 0.44 0.00 4.49
2736 4097 9.959721 AGCAAAACTTCCTAGAGTAATTAATCA 57.040 29.630 14.80 1.24 0.00 2.57
2782 4143 8.654997 ACATGAACATTAGCTAATCCACTATCT 58.345 33.333 16.21 0.00 0.00 1.98
2783 4144 8.839310 ACATGAACATTAGCTAATCCACTATC 57.161 34.615 16.21 8.76 0.00 2.08
2887 4248 3.677424 CGCTTCCGAGGAGAAGAAGATTT 60.677 47.826 5.50 0.00 45.08 2.17
2916 4277 1.512734 GAAAGCTGCACGCCGATTG 60.513 57.895 1.02 0.00 40.39 2.67
2917 4278 1.672356 AGAAAGCTGCACGCCGATT 60.672 52.632 1.02 0.00 40.39 3.34
2934 4296 4.686091 TCAAACAAACTACGATGAGAGCAG 59.314 41.667 0.00 0.00 0.00 4.24
2945 4307 3.976169 TGCAGCCATTCAAACAAACTAC 58.024 40.909 0.00 0.00 0.00 2.73
2946 4308 4.558178 CATGCAGCCATTCAAACAAACTA 58.442 39.130 0.00 0.00 0.00 2.24
2947 4309 3.395639 CATGCAGCCATTCAAACAAACT 58.604 40.909 0.00 0.00 0.00 2.66
2948 4310 2.096119 GCATGCAGCCATTCAAACAAAC 60.096 45.455 14.21 0.00 37.23 2.93
2949 4311 2.144730 GCATGCAGCCATTCAAACAAA 58.855 42.857 14.21 0.00 37.23 2.83
2950 4312 1.070289 TGCATGCAGCCATTCAAACAA 59.930 42.857 18.46 0.00 44.83 2.83
2951 4313 0.680061 TGCATGCAGCCATTCAAACA 59.320 45.000 18.46 0.00 44.83 2.83
2952 4314 1.931172 GATGCATGCAGCCATTCAAAC 59.069 47.619 25.21 2.67 44.83 2.93
2953 4315 1.470112 CGATGCATGCAGCCATTCAAA 60.470 47.619 28.76 0.00 44.83 2.69
2954 4316 0.101579 CGATGCATGCAGCCATTCAA 59.898 50.000 28.76 0.09 44.83 2.69
2955 4317 0.748729 TCGATGCATGCAGCCATTCA 60.749 50.000 28.76 6.25 44.83 2.57
2956 4318 0.596577 ATCGATGCATGCAGCCATTC 59.403 50.000 28.76 18.01 44.83 2.67
2957 4319 1.037493 AATCGATGCATGCAGCCATT 58.963 45.000 28.76 24.66 44.83 3.16
2958 4320 0.313987 CAATCGATGCATGCAGCCAT 59.686 50.000 28.76 20.10 44.83 4.40
2959 4321 0.748729 TCAATCGATGCATGCAGCCA 60.749 50.000 28.76 18.55 44.83 4.75
2960 4322 0.596577 ATCAATCGATGCATGCAGCC 59.403 50.000 28.76 19.54 44.83 4.85
2961 4323 1.686464 CATCAATCGATGCATGCAGC 58.314 50.000 25.69 25.69 42.54 5.25
2970 4332 0.602106 CGGCCTCTGCATCAATCGAT 60.602 55.000 0.00 0.00 40.13 3.59
2971 4333 1.227350 CGGCCTCTGCATCAATCGA 60.227 57.895 0.00 0.00 40.13 3.59
2972 4334 2.249535 CCGGCCTCTGCATCAATCG 61.250 63.158 0.00 0.00 40.13 3.34
2973 4335 0.883814 CTCCGGCCTCTGCATCAATC 60.884 60.000 0.00 0.00 40.13 2.67
2974 4336 1.147824 CTCCGGCCTCTGCATCAAT 59.852 57.895 0.00 0.00 40.13 2.57
2975 4337 2.586245 CTCCGGCCTCTGCATCAA 59.414 61.111 0.00 0.00 40.13 2.57
2976 4338 3.473647 CCTCCGGCCTCTGCATCA 61.474 66.667 0.00 0.00 40.13 3.07
2977 4339 4.925861 GCCTCCGGCCTCTGCATC 62.926 72.222 0.00 0.00 44.06 3.91
2990 4352 1.625818 TGGAAAAGGAGACAGAGCCTC 59.374 52.381 0.00 0.00 32.07 4.70
2991 4353 1.734655 TGGAAAAGGAGACAGAGCCT 58.265 50.000 0.00 0.00 35.61 4.58
2992 4354 2.568623 TTGGAAAAGGAGACAGAGCC 57.431 50.000 0.00 0.00 0.00 4.70
2993 4355 4.918810 TTTTTGGAAAAGGAGACAGAGC 57.081 40.909 0.00 0.00 0.00 4.09
3015 4377 8.766000 AAATTCCTCAAACAAACTACGTTTTT 57.234 26.923 0.00 0.00 34.40 1.94
3016 4378 9.511144 CTAAATTCCTCAAACAAACTACGTTTT 57.489 29.630 0.00 0.00 34.40 2.43
3017 4379 7.646526 GCTAAATTCCTCAAACAAACTACGTTT 59.353 33.333 0.00 0.00 37.04 3.60
3018 4380 7.136772 GCTAAATTCCTCAAACAAACTACGTT 58.863 34.615 0.00 0.00 0.00 3.99
3019 4381 6.293790 GGCTAAATTCCTCAAACAAACTACGT 60.294 38.462 0.00 0.00 0.00 3.57
3020 4382 6.072673 AGGCTAAATTCCTCAAACAAACTACG 60.073 38.462 0.00 0.00 0.00 3.51
3021 4383 7.215719 AGGCTAAATTCCTCAAACAAACTAC 57.784 36.000 0.00 0.00 0.00 2.73
3042 4404 1.003580 TCATGTTCCCACAGAAGAGGC 59.996 52.381 0.00 0.00 35.94 4.70
3093 4455 4.520492 ACCAGACTCAAAAGGCATAAACTG 59.480 41.667 0.00 0.00 30.24 3.16
3109 4471 4.099573 CGTAATCCACCTCAATACCAGACT 59.900 45.833 0.00 0.00 0.00 3.24
3146 4508 6.863645 GCTCCTTCTGATTTCTTGGTAAAAAC 59.136 38.462 0.00 0.00 0.00 2.43
3150 4512 5.241403 TGCTCCTTCTGATTTCTTGGTAA 57.759 39.130 0.00 0.00 0.00 2.85
3153 4515 2.422832 GCTGCTCCTTCTGATTTCTTGG 59.577 50.000 0.00 0.00 0.00 3.61
3155 4517 3.345414 CAGCTGCTCCTTCTGATTTCTT 58.655 45.455 0.00 0.00 0.00 2.52
3163 4525 0.112025 AAAAGGCAGCTGCTCCTTCT 59.888 50.000 35.82 22.11 41.54 2.85
3172 4534 4.666512 TCTTCCTTAATGAAAAGGCAGCT 58.333 39.130 0.00 0.00 44.89 4.24
3173 4535 5.391312 TTCTTCCTTAATGAAAAGGCAGC 57.609 39.130 0.00 0.00 44.89 5.25
3240 4604 1.756172 CAGTGGTGGGTTGCCAACA 60.756 57.895 10.18 0.00 37.81 3.33
3345 4709 0.836400 ACACTTCCTGTCATCCCCGT 60.836 55.000 0.00 0.00 0.00 5.28
3346 4710 1.983224 ACACTTCCTGTCATCCCCG 59.017 57.895 0.00 0.00 0.00 5.73
3393 4757 5.102953 TGGAGAATGTAGTCAAATCCAGG 57.897 43.478 0.00 0.00 33.09 4.45
3404 4768 3.508012 CGAGGGACCTATGGAGAATGTAG 59.492 52.174 0.00 0.00 0.00 2.74
3405 4769 3.117246 ACGAGGGACCTATGGAGAATGTA 60.117 47.826 0.00 0.00 0.00 2.29
3413 4777 3.443145 AGATCTACGAGGGACCTATGG 57.557 52.381 0.00 0.00 0.00 2.74
3416 4780 4.792513 AGAAAGATCTACGAGGGACCTA 57.207 45.455 0.00 0.00 32.88 3.08
3417 4781 3.673543 AGAAAGATCTACGAGGGACCT 57.326 47.619 0.00 0.00 32.88 3.85
3418 4782 3.700038 TGAAGAAAGATCTACGAGGGACC 59.300 47.826 0.00 0.00 33.77 4.46
3419 4783 4.985538 TGAAGAAAGATCTACGAGGGAC 57.014 45.455 0.00 0.00 33.77 4.46
3447 4811 7.390027 CGTGAATATCTCATCCTTCCCTAATT 58.610 38.462 0.00 0.00 36.14 1.40


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

AutoCloner maintained by Alex Coulton.