Multiple sequence alignment - TraesCS3A01G124100

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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 TraesCS3A01G124100 chr3A 100.000 2709 0 0 1750 4458 100188917 100191625 0.000000e+00 5003.0
1 TraesCS3A01G124100 chr3A 100.000 1607 0 0 1 1607 100187168 100188774 0.000000e+00 2968.0
2 TraesCS3A01G124100 chr3A 90.909 77 3 3 2070 2144 100189189 100189263 2.840000e-17 100.0
3 TraesCS3A01G124100 chr3A 90.909 77 3 3 2022 2096 100189237 100189311 2.840000e-17 100.0
4 TraesCS3A01G124100 chr3D 92.522 2728 109 34 1752 4458 84014637 84017290 0.000000e+00 3819.0
5 TraesCS3A01G124100 chr3D 94.498 927 33 8 688 1607 84013680 84014595 0.000000e+00 1413.0
6 TraesCS3A01G124100 chr3D 88.112 715 56 10 1 697 84012567 84013270 0.000000e+00 822.0
7 TraesCS3A01G124100 chr3D 90.426 188 18 0 1417 1604 84014591 84014778 9.580000e-62 248.0
8 TraesCS3A01G124100 chr3D 89.474 190 20 0 1417 1606 84014498 84014687 1.600000e-59 241.0
9 TraesCS3A01G124100 chr3D 88.542 96 10 1 1417 1511 84014683 84014778 1.010000e-21 115.0
10 TraesCS3A01G124100 chr3B 93.251 2267 107 20 2085 4345 132529608 132527382 0.000000e+00 3297.0
11 TraesCS3A01G124100 chr3B 95.740 845 23 3 763 1607 132530766 132529935 0.000000e+00 1349.0
12 TraesCS3A01G124100 chr3B 87.344 719 59 13 1 703 132531632 132530930 0.000000e+00 795.0
13 TraesCS3A01G124100 chr3B 94.783 345 18 0 1752 2096 132529893 132529549 5.070000e-149 538.0
14 TraesCS3A01G124100 chr3B 89.474 190 20 0 1417 1606 132530032 132529843 1.600000e-59 241.0
15 TraesCS3A01G124100 chr3B 89.362 188 20 0 1417 1604 132529939 132529752 2.070000e-58 237.0
16 TraesCS3A01G124100 chr3B 93.913 115 7 0 4344 4458 132527300 132527186 1.650000e-39 174.0
17 TraesCS3A01G124100 chr3B 90.625 96 8 1 1417 1511 132529847 132529752 4.680000e-25 126.0
18 TraesCS3A01G124100 chr5B 97.297 37 1 0 954 990 458153549 458153513 3.720000e-06 63.9
19 TraesCS3A01G124100 chr5D 97.059 34 1 0 957 990 381918878 381918845 1.730000e-04 58.4
20 TraesCS3A01G124100 chr6D 94.444 36 1 1 963 998 303637929 303637895 2.000000e-03 54.7
21 TraesCS3A01G124100 chr6D 100.000 28 0 0 964 991 132762062 132762035 8.000000e-03 52.8
22 TraesCS3A01G124100 chr6B 94.444 36 1 1 963 998 469302975 469302941 2.000000e-03 54.7
23 TraesCS3A01G124100 chr6A 94.444 36 1 1 963 998 412385191 412385157 2.000000e-03 54.7
24 TraesCS3A01G124100 chr1D 100.000 28 0 0 962 989 462462272 462462299 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G124100 chr3A 100187168 100191625 4457 False 2042.750000 5003 95.454500 1 4458 4 chr3A.!!$F1 4457
1 TraesCS3A01G124100 chr3D 84012567 84017290 4723 False 1109.666667 3819 90.595667 1 4458 6 chr3D.!!$F1 4457
2 TraesCS3A01G124100 chr3B 132527186 132531632 4446 True 844.625000 3297 91.811500 1 4458 8 chr3B.!!$R1 4457

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
870 1355 0.037734 CACCAACCCTAACCCCAGTC 59.962 60.000 0.0 0.0 0.00 3.51 F
993 1478 0.543174 ATCTAGATCCGCCCCTGGTC 60.543 60.000 0.0 0.0 0.00 4.02 F
1782 2267 1.209019 GATTGAGGAGAAGGCTGCTGA 59.791 52.381 0.0 0.0 43.46 4.26 F
2069 2554 1.361204 TGACCAGAATGAAGGCTCCA 58.639 50.000 0.0 0.0 39.69 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2585 0.622665 CCTGGAGCCTTCATTCTGGT 59.377 55.000 0.00 0.00 0.0 4.00 R
2101 2586 0.914644 TCCTGGAGCCTTCATTCTGG 59.085 55.000 0.00 0.00 0.0 3.86 R
2839 3339 1.589803 AACAAAGGCGCGAGTTACTT 58.410 45.000 12.10 2.14 0.0 2.24 R
3842 4344 1.459592 CTGAAGTAACCGGAAACAGCG 59.540 52.381 9.46 0.00 0.0 5.18 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
30 31 5.221925 TGTTGAACCTCTTGAGGAAGCTAAT 60.222 40.000 22.10 0.00 0.00 1.73
61 62 5.522456 TCGTTGAAGTAAAAGACGAAGCTA 58.478 37.500 0.00 0.00 39.46 3.32
94 95 2.639839 TCCTATTATCTTGGCAGCCTCC 59.360 50.000 14.15 0.00 0.00 4.30
104 105 2.914289 CAGCCTCCAGGACCATCC 59.086 66.667 0.00 0.00 37.39 3.51
153 154 0.249120 CCAGCGTTGTGGACCATCTA 59.751 55.000 0.00 0.00 40.44 1.98
166 167 0.394352 CCATCTACCAAAGGCGCCTT 60.394 55.000 35.84 35.84 37.98 4.35
194 195 2.019249 CAAGCATCGATTCCATGTGGT 58.981 47.619 0.00 0.00 36.34 4.16
226 227 5.242838 TGGTCACTTGATTTTGGTATTGGAC 59.757 40.000 0.00 0.00 0.00 4.02
259 260 0.378257 CATTGATGTGGTGCGTAGGC 59.622 55.000 0.00 0.00 40.52 3.93
280 282 2.724839 CGCGCAAGTTTTGTAGATGGAC 60.725 50.000 8.75 0.00 41.68 4.02
288 290 6.665992 AGTTTTGTAGATGGACTGTAGTGA 57.334 37.500 0.00 0.00 0.00 3.41
290 292 7.155328 AGTTTTGTAGATGGACTGTAGTGAAG 58.845 38.462 0.00 0.00 0.00 3.02
311 313 2.628657 GGGGCGTCTTATATGAGAGTGT 59.371 50.000 0.00 0.00 0.00 3.55
313 315 4.280174 GGGGCGTCTTATATGAGAGTGTAA 59.720 45.833 0.00 0.00 0.00 2.41
325 327 0.110644 GAGTGTAAGTTGCAGTGCGC 60.111 55.000 11.20 0.00 42.89 6.09
329 331 2.616330 TAAGTTGCAGTGCGCTGGC 61.616 57.895 27.56 19.50 42.78 4.85
449 462 7.948278 AGTCGCTTGACATAATAGTTATTCC 57.052 36.000 0.00 0.00 45.40 3.01
688 709 3.825585 GCCCACCTCTATACTGTACTACC 59.174 52.174 0.00 0.00 0.00 3.18
690 711 5.071370 CCCACCTCTATACTGTACTACCAG 58.929 50.000 0.00 0.00 38.45 4.00
691 712 5.163120 CCCACCTCTATACTGTACTACCAGA 60.163 48.000 0.00 0.00 36.30 3.86
720 1162 1.967066 CCACCAAAGTGCCATAAACCA 59.033 47.619 0.00 0.00 43.09 3.67
732 1201 6.096846 AGTGCCATAAACCAAAATACATCTCC 59.903 38.462 0.00 0.00 0.00 3.71
794 1279 2.289547 AGTTTTGAAAAAGCGCGCTCTA 59.710 40.909 36.57 16.23 0.00 2.43
818 1303 1.590591 TTCGAGATCCCCCAAATCCA 58.409 50.000 0.00 0.00 0.00 3.41
819 1304 1.819753 TCGAGATCCCCCAAATCCAT 58.180 50.000 0.00 0.00 0.00 3.41
820 1305 1.699634 TCGAGATCCCCCAAATCCATC 59.300 52.381 0.00 0.00 0.00 3.51
821 1306 1.271597 CGAGATCCCCCAAATCCATCC 60.272 57.143 0.00 0.00 0.00 3.51
822 1307 1.076187 GAGATCCCCCAAATCCATCCC 59.924 57.143 0.00 0.00 0.00 3.85
823 1308 0.115152 GATCCCCCAAATCCATCCCC 59.885 60.000 0.00 0.00 0.00 4.81
824 1309 0.330834 ATCCCCCAAATCCATCCCCT 60.331 55.000 0.00 0.00 0.00 4.79
825 1310 0.998945 TCCCCCAAATCCATCCCCTC 60.999 60.000 0.00 0.00 0.00 4.30
826 1311 1.543690 CCCCAAATCCATCCCCTCC 59.456 63.158 0.00 0.00 0.00 4.30
870 1355 0.037734 CACCAACCCTAACCCCAGTC 59.962 60.000 0.00 0.00 0.00 3.51
941 1426 3.141488 CTCCGCCGCACTCCTAGT 61.141 66.667 0.00 0.00 0.00 2.57
978 1463 4.155733 CACCCGGCGCACCATCTA 62.156 66.667 10.83 0.00 34.57 1.98
993 1478 0.543174 ATCTAGATCCGCCCCTGGTC 60.543 60.000 0.00 0.00 0.00 4.02
1456 1941 6.827762 GGAAATGAAGAAAGATGAGGTGATCT 59.172 38.462 0.00 0.00 33.91 2.75
1536 2021 5.753716 AGATTGGAGGAGGAAATGAAGAAG 58.246 41.667 0.00 0.00 0.00 2.85
1782 2267 1.209019 GATTGAGGAGAAGGCTGCTGA 59.791 52.381 0.00 0.00 43.46 4.26
1802 2287 3.203059 GAGATATCTAGGGAGAGGGGGA 58.797 54.545 4.89 0.00 34.35 4.81
1803 2288 3.204382 GAGATATCTAGGGAGAGGGGGAG 59.796 56.522 4.89 0.00 34.35 4.30
1820 2305 2.158549 GGGAGATTGGAGGAGGAAATGG 60.159 54.545 0.00 0.00 0.00 3.16
1828 2313 3.264450 TGGAGGAGGAAATGGAGAAAGAC 59.736 47.826 0.00 0.00 0.00 3.01
1868 2353 3.196685 CGAAAGAGAGATTGGGGAGAAGT 59.803 47.826 0.00 0.00 0.00 3.01
1940 2425 4.102367 AGCTGGAGTTGAAGGATAAGGATC 59.898 45.833 0.00 0.00 0.00 3.36
2056 2541 2.363683 GAAGGCTCCAAGATTGACCAG 58.636 52.381 0.00 0.00 0.00 4.00
2057 2542 1.661463 AGGCTCCAAGATTGACCAGA 58.339 50.000 0.00 0.00 0.00 3.86
2058 2543 1.988107 AGGCTCCAAGATTGACCAGAA 59.012 47.619 0.00 0.00 0.00 3.02
2059 2544 2.579860 AGGCTCCAAGATTGACCAGAAT 59.420 45.455 0.00 0.00 0.00 2.40
2060 2545 2.686915 GGCTCCAAGATTGACCAGAATG 59.313 50.000 0.00 0.00 0.00 2.67
2061 2546 3.614092 GCTCCAAGATTGACCAGAATGA 58.386 45.455 0.00 0.00 39.69 2.57
2062 2547 4.012374 GCTCCAAGATTGACCAGAATGAA 58.988 43.478 0.00 0.00 39.69 2.57
2063 2548 4.096081 GCTCCAAGATTGACCAGAATGAAG 59.904 45.833 0.00 0.00 39.69 3.02
2064 2549 4.592942 TCCAAGATTGACCAGAATGAAGG 58.407 43.478 0.00 0.00 39.69 3.46
2065 2550 3.129988 CCAAGATTGACCAGAATGAAGGC 59.870 47.826 0.00 0.00 39.69 4.35
2066 2551 4.015084 CAAGATTGACCAGAATGAAGGCT 58.985 43.478 0.00 0.00 39.69 4.58
2067 2552 3.883669 AGATTGACCAGAATGAAGGCTC 58.116 45.455 0.00 0.00 39.69 4.70
2068 2553 2.496899 TTGACCAGAATGAAGGCTCC 57.503 50.000 0.00 0.00 39.69 4.70
2069 2554 1.361204 TGACCAGAATGAAGGCTCCA 58.639 50.000 0.00 0.00 39.69 3.86
2070 2555 1.704628 TGACCAGAATGAAGGCTCCAA 59.295 47.619 0.00 0.00 39.69 3.53
2071 2556 2.290514 TGACCAGAATGAAGGCTCCAAG 60.291 50.000 0.00 0.00 39.69 3.61
2072 2557 1.988107 ACCAGAATGAAGGCTCCAAGA 59.012 47.619 0.00 0.00 39.69 3.02
2073 2558 2.579860 ACCAGAATGAAGGCTCCAAGAT 59.420 45.455 0.00 0.00 39.69 2.40
2074 2559 3.011032 ACCAGAATGAAGGCTCCAAGATT 59.989 43.478 0.00 0.00 39.69 2.40
2075 2560 3.380637 CCAGAATGAAGGCTCCAAGATTG 59.619 47.826 0.00 0.00 39.69 2.67
2076 2561 4.267536 CAGAATGAAGGCTCCAAGATTGA 58.732 43.478 0.00 0.00 39.69 2.57
2077 2562 4.096081 CAGAATGAAGGCTCCAAGATTGAC 59.904 45.833 0.00 0.00 39.69 3.18
2078 2563 2.496899 TGAAGGCTCCAAGATTGACC 57.503 50.000 0.00 0.00 0.00 4.02
2079 2564 1.704628 TGAAGGCTCCAAGATTGACCA 59.295 47.619 0.00 0.00 0.00 4.02
2080 2565 2.290514 TGAAGGCTCCAAGATTGACCAG 60.291 50.000 0.00 0.00 0.00 4.00
2081 2566 1.661463 AGGCTCCAAGATTGACCAGA 58.339 50.000 0.00 0.00 0.00 3.86
2082 2567 1.988107 AGGCTCCAAGATTGACCAGAA 59.012 47.619 0.00 0.00 0.00 3.02
2083 2568 2.579860 AGGCTCCAAGATTGACCAGAAT 59.420 45.455 0.00 0.00 0.00 2.40
2084 2569 2.686915 GGCTCCAAGATTGACCAGAATG 59.313 50.000 0.00 0.00 0.00 2.67
2085 2570 3.614092 GCTCCAAGATTGACCAGAATGA 58.386 45.455 0.00 0.00 39.69 2.57
2086 2571 4.012374 GCTCCAAGATTGACCAGAATGAA 58.988 43.478 0.00 0.00 39.69 2.57
2087 2572 4.096081 GCTCCAAGATTGACCAGAATGAAG 59.904 45.833 0.00 0.00 39.69 3.02
2088 2573 4.592942 TCCAAGATTGACCAGAATGAAGG 58.407 43.478 0.00 0.00 39.69 3.46
2089 2574 3.129988 CCAAGATTGACCAGAATGAAGGC 59.870 47.826 0.00 0.00 39.69 4.35
2090 2575 4.015084 CAAGATTGACCAGAATGAAGGCT 58.985 43.478 0.00 0.00 39.69 4.58
2091 2576 3.883669 AGATTGACCAGAATGAAGGCTC 58.116 45.455 0.00 0.00 39.69 4.70
2092 2577 2.496899 TTGACCAGAATGAAGGCTCC 57.503 50.000 0.00 0.00 39.69 4.70
2093 2578 1.361204 TGACCAGAATGAAGGCTCCA 58.639 50.000 0.00 0.00 39.69 3.86
2094 2579 1.704628 TGACCAGAATGAAGGCTCCAA 59.295 47.619 0.00 0.00 39.69 3.53
2095 2580 2.290514 TGACCAGAATGAAGGCTCCAAG 60.291 50.000 0.00 0.00 39.69 3.61
2096 2581 1.988107 ACCAGAATGAAGGCTCCAAGA 59.012 47.619 0.00 0.00 39.69 3.02
2097 2582 2.579860 ACCAGAATGAAGGCTCCAAGAT 59.420 45.455 0.00 0.00 39.69 2.40
2098 2583 3.011032 ACCAGAATGAAGGCTCCAAGATT 59.989 43.478 0.00 0.00 39.69 2.40
2099 2584 3.380637 CCAGAATGAAGGCTCCAAGATTG 59.619 47.826 0.00 0.00 39.69 2.67
2100 2585 4.267536 CAGAATGAAGGCTCCAAGATTGA 58.732 43.478 0.00 0.00 39.69 2.57
2101 2586 4.096081 CAGAATGAAGGCTCCAAGATTGAC 59.904 45.833 0.00 0.00 39.69 3.18
2102 2587 2.496899 TGAAGGCTCCAAGATTGACC 57.503 50.000 0.00 0.00 0.00 4.02
2103 2588 1.704628 TGAAGGCTCCAAGATTGACCA 59.295 47.619 0.00 0.00 0.00 4.02
2317 2803 6.212888 AGGATCCATATCTTTTGTGCAAAC 57.787 37.500 15.82 0.00 32.29 2.93
2384 2880 7.708752 CCAGTATCTCTTTTCTGTCAATCCTAC 59.291 40.741 0.00 0.00 0.00 3.18
2395 2891 6.957631 TCTGTCAATCCTACCACATAACATT 58.042 36.000 0.00 0.00 0.00 2.71
2409 2905 7.012515 ACCACATAACATTGACGTGTCTTAAAA 59.987 33.333 0.00 0.00 0.00 1.52
2410 2906 8.020819 CCACATAACATTGACGTGTCTTAAAAT 58.979 33.333 0.00 0.00 0.00 1.82
2470 2966 5.757850 ACTCACTTGTTTGATTTCCAGAC 57.242 39.130 0.00 0.00 0.00 3.51
2549 3046 9.204570 TGCCGCTCTAATTTAAGAATCTTATAC 57.795 33.333 3.28 0.00 0.00 1.47
2655 3155 4.103627 TCAATCCTATCACCTGACATGCAT 59.896 41.667 0.00 0.00 0.00 3.96
2728 3228 9.688592 ATCTCAGTTGTTTGATTTTCAGATTTC 57.311 29.630 0.00 0.00 0.00 2.17
2892 3392 0.608640 ACTAACCCTCCGCACAAGAG 59.391 55.000 0.00 0.00 0.00 2.85
2895 3395 2.046892 CCCTCCGCACAAGAGTGG 60.047 66.667 0.00 0.00 45.98 4.00
3178 3678 2.742053 CCTCAACAACATACCAGTTCCG 59.258 50.000 0.00 0.00 0.00 4.30
3388 3888 4.807834 CATCATGATGGTGTGTCTAGACAC 59.192 45.833 37.98 37.98 45.92 3.67
3418 3918 1.217057 ATGCCCCTCCATTGACACCT 61.217 55.000 0.00 0.00 0.00 4.00
3532 4032 2.555732 TCCTCGGTTACCCCTGTATT 57.444 50.000 0.00 0.00 0.00 1.89
3543 4043 3.898482 ACCCCTGTATTCTGTTAATGGC 58.102 45.455 0.00 0.00 0.00 4.40
3564 4064 2.674747 CGCAGAAAATTCATGTTGGGGG 60.675 50.000 0.00 0.00 0.00 5.40
3570 4070 2.086610 ATTCATGTTGGGGGCATACC 57.913 50.000 0.00 0.00 39.11 2.73
3628 4128 9.832445 GTCAGTTTGTGGAGGATAGATAATAAA 57.168 33.333 0.00 0.00 0.00 1.40
3679 4179 5.048083 TCAGAAAAGTTGAACAGTTGCTTGT 60.048 36.000 0.00 0.00 0.00 3.16
3842 4344 1.188863 ATTCATGGCCTGTTGCTTCC 58.811 50.000 3.32 0.00 40.92 3.46
3850 4352 0.040067 CCTGTTGCTTCCGCTGTTTC 60.040 55.000 0.00 0.00 36.97 2.78
3852 4354 1.082104 GTTGCTTCCGCTGTTTCCG 60.082 57.895 0.00 0.00 36.97 4.30
3871 4373 5.801531 TCCGGTTACTTCAGTATATGCAT 57.198 39.130 3.79 3.79 0.00 3.96
3872 4374 6.169557 TCCGGTTACTTCAGTATATGCATT 57.830 37.500 3.54 0.00 0.00 3.56
3873 4375 7.292713 TCCGGTTACTTCAGTATATGCATTA 57.707 36.000 3.54 0.00 0.00 1.90
3874 4376 7.149973 TCCGGTTACTTCAGTATATGCATTAC 58.850 38.462 3.54 7.66 0.00 1.89
3875 4377 6.926826 CCGGTTACTTCAGTATATGCATTACA 59.073 38.462 3.54 0.00 0.00 2.41
3876 4378 7.439955 CCGGTTACTTCAGTATATGCATTACAA 59.560 37.037 3.54 0.00 0.00 2.41
3877 4379 8.988934 CGGTTACTTCAGTATATGCATTACAAT 58.011 33.333 3.54 0.00 0.00 2.71
3997 4499 7.645340 CAGAGAGTTTGTGTTTGGAGTTTTATG 59.355 37.037 0.00 0.00 0.00 1.90
4089 4591 8.391106 GTTTATCTGTAGCCATCTTGTGTAAAG 58.609 37.037 0.00 0.00 0.00 1.85
4108 4610 4.437682 AAGTCCACTGAAGAATTGACCA 57.562 40.909 0.00 0.00 0.00 4.02
4169 4673 1.404391 CAGCTTGTCCATTGATCCTGC 59.596 52.381 0.00 0.00 0.00 4.85
4214 4718 3.420300 TTTAACTCGGGTGGTTGCATA 57.580 42.857 0.00 0.00 0.00 3.14
4215 4719 2.389962 TAACTCGGGTGGTTGCATAC 57.610 50.000 0.00 0.00 0.00 2.39
4216 4720 0.690762 AACTCGGGTGGTTGCATACT 59.309 50.000 0.00 0.00 0.00 2.12
4217 4721 0.690762 ACTCGGGTGGTTGCATACTT 59.309 50.000 0.00 0.00 0.00 2.24
4218 4722 1.086696 CTCGGGTGGTTGCATACTTG 58.913 55.000 0.00 0.00 0.00 3.16
4229 4733 3.903876 CATACTTGCATCGTGTGGC 57.096 52.632 5.76 0.00 0.00 5.01
4238 4742 1.875514 GCATCGTGTGGCATATCATGT 59.124 47.619 0.00 0.00 0.00 3.21
4279 4783 1.651737 TCTGGTCCCTCAATTTCCGA 58.348 50.000 0.00 0.00 0.00 4.55
4293 4797 0.601057 TTCCGAGTGCTTCATCGACA 59.399 50.000 0.00 0.00 41.40 4.35
4294 4798 0.817654 TCCGAGTGCTTCATCGACAT 59.182 50.000 0.00 0.00 41.40 3.06
4337 4841 9.545105 CACTCATCTTAGATATTTTCTCAGCTT 57.455 33.333 0.00 0.00 35.79 3.74
4351 4938 9.836864 ATTTTCTCAGCTTTTTCCTATTTTGTT 57.163 25.926 0.00 0.00 0.00 2.83
4394 4989 3.728385 AAGTAGAAATGGCCTGCTCTT 57.272 42.857 3.32 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.827302 AGATAATAGGAATCGTGGACGCT 59.173 43.478 0.00 0.00 39.60 5.07
94 95 4.227134 CGCCTCCGGATGGTCCTG 62.227 72.222 3.57 0.00 33.30 3.86
130 131 3.050275 GTCCACAACGCTGGCCTC 61.050 66.667 3.32 0.00 0.00 4.70
141 142 1.004277 GCCTTTGGTAGATGGTCCACA 59.996 52.381 0.00 0.00 33.12 4.17
153 154 0.606673 GAGAAGAAGGCGCCTTTGGT 60.607 55.000 40.31 27.89 36.26 3.67
166 167 2.196749 GAATCGATGCTTGCGAGAAGA 58.803 47.619 4.70 0.00 41.49 2.87
175 176 2.019249 CACCACATGGAATCGATGCTT 58.981 47.619 4.53 0.00 38.94 3.91
194 195 1.434188 ATCAAGTGACCAGGACCACA 58.566 50.000 15.72 0.00 35.84 4.17
226 227 5.335113 CCACATCAATGGTAAATATGCTCCG 60.335 44.000 0.00 0.00 34.77 4.63
259 260 1.463056 TCCATCTACAAAACTTGCGCG 59.537 47.619 0.00 0.00 0.00 6.86
280 282 0.608640 AAGACGCCCCTTCACTACAG 59.391 55.000 0.00 0.00 0.00 2.74
288 290 3.322254 CACTCTCATATAAGACGCCCCTT 59.678 47.826 0.00 0.00 0.00 3.95
290 292 2.628657 ACACTCTCATATAAGACGCCCC 59.371 50.000 0.00 0.00 0.00 5.80
325 327 2.014857 CTCACACAATCAGATGGCCAG 58.985 52.381 13.05 0.00 0.00 4.85
329 331 3.119602 CCAAAGCTCACACAATCAGATGG 60.120 47.826 0.00 0.00 0.00 3.51
334 336 1.689984 TGCCAAAGCTCACACAATCA 58.310 45.000 0.00 0.00 40.80 2.57
381 383 9.092876 CCTGCTGTTAAAAAGTCAACAAAAATA 57.907 29.630 0.00 0.00 34.43 1.40
419 421 7.235430 ACTATTATGTCAAGCGACTAAAAGC 57.765 36.000 0.00 0.00 43.06 3.51
449 462 1.133598 TGTACCACTTGATCGGCGTAG 59.866 52.381 6.85 3.21 0.00 3.51
499 512 9.988815 ACAACTATGGTTTTGCACAATTTATTA 57.011 25.926 0.00 0.00 32.73 0.98
508 521 6.089417 GCATTTCTACAACTATGGTTTTGCAC 59.911 38.462 0.00 0.00 32.73 4.57
595 613 8.777865 TTTTGATTGACACAATGTTTACCAAA 57.222 26.923 1.64 3.15 0.00 3.28
642 660 1.393603 GCTATTTGGAGAGGGCCAAC 58.606 55.000 6.18 0.00 46.99 3.77
705 1147 7.906327 AGATGTATTTTGGTTTATGGCACTTT 58.094 30.769 0.00 0.00 0.00 2.66
720 1162 4.941873 GGAAAGTGACCGGAGATGTATTTT 59.058 41.667 9.46 0.00 0.00 1.82
732 1201 3.364964 CCTCGAATTTTGGAAAGTGACCG 60.365 47.826 0.00 0.00 0.00 4.79
794 1279 4.405680 GGATTTGGGGGATCTCGAAATTTT 59.594 41.667 3.42 0.00 0.00 1.82
818 1303 3.462501 GAGGGGAGGGGAGGGGAT 61.463 72.222 0.00 0.00 0.00 3.85
823 1308 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
941 1426 2.682876 GCGCCCGAATTCGTGGAAA 61.683 57.895 28.58 0.00 37.74 3.13
993 1478 2.749839 TTGCCCTCCATTTCGGCG 60.750 61.111 0.00 0.00 46.12 6.46
1278 1763 3.764466 CCGCGGTTGAGCTCCTCT 61.764 66.667 19.50 0.00 34.40 3.69
1410 1895 1.366082 TCCTCCAATCTCCCCAGAAGA 59.634 52.381 0.00 0.00 30.24 2.87
1456 1941 4.082523 CTCCCTTTCGAGCCGGCA 62.083 66.667 31.54 4.59 0.00 5.69
1749 2234 2.761208 TCCTCAATCTCCCTTTCGAGAC 59.239 50.000 0.00 0.00 41.60 3.36
1750 2235 3.027412 CTCCTCAATCTCCCTTTCGAGA 58.973 50.000 0.00 0.00 42.93 4.04
1782 2267 3.181366 TCTCCCCCTCTCCCTAGATATCT 60.181 52.174 10.73 10.73 0.00 1.98
1802 2287 3.740780 TCTCCATTTCCTCCTCCAATCT 58.259 45.455 0.00 0.00 0.00 2.40
1803 2288 4.510167 TTCTCCATTTCCTCCTCCAATC 57.490 45.455 0.00 0.00 0.00 2.67
1828 2313 1.586564 GAGCCGACGAATCACCTCG 60.587 63.158 0.00 0.00 44.50 4.63
1868 2353 3.176411 TCTCCCTTGAAATCTCAGCAGA 58.824 45.455 0.00 0.00 31.69 4.26
1910 2395 0.761187 TTCAACTCCAGCTGCTGTCT 59.239 50.000 26.41 6.99 0.00 3.41
1911 2396 1.155042 CTTCAACTCCAGCTGCTGTC 58.845 55.000 26.41 0.00 0.00 3.51
1919 2404 5.885449 AGATCCTTATCCTTCAACTCCAG 57.115 43.478 0.00 0.00 31.98 3.86
2056 2541 3.379688 GGTCAATCTTGGAGCCTTCATTC 59.620 47.826 0.00 0.00 0.00 2.67
2057 2542 3.245371 TGGTCAATCTTGGAGCCTTCATT 60.245 43.478 0.00 0.00 31.96 2.57
2058 2543 2.309755 TGGTCAATCTTGGAGCCTTCAT 59.690 45.455 0.00 0.00 31.96 2.57
2059 2544 1.704628 TGGTCAATCTTGGAGCCTTCA 59.295 47.619 0.00 0.00 31.96 3.02
2060 2545 2.026822 TCTGGTCAATCTTGGAGCCTTC 60.027 50.000 0.00 0.00 31.96 3.46
2061 2546 1.988107 TCTGGTCAATCTTGGAGCCTT 59.012 47.619 0.00 0.00 31.96 4.35
2062 2547 1.661463 TCTGGTCAATCTTGGAGCCT 58.339 50.000 0.00 0.00 31.96 4.58
2063 2548 2.496899 TTCTGGTCAATCTTGGAGCC 57.503 50.000 0.00 0.00 31.96 4.70
2064 2549 3.614092 TCATTCTGGTCAATCTTGGAGC 58.386 45.455 0.00 0.00 0.00 4.70
2065 2550 4.639310 CCTTCATTCTGGTCAATCTTGGAG 59.361 45.833 0.00 0.00 0.00 3.86
2066 2551 4.592942 CCTTCATTCTGGTCAATCTTGGA 58.407 43.478 0.00 0.00 0.00 3.53
2067 2552 3.129988 GCCTTCATTCTGGTCAATCTTGG 59.870 47.826 0.00 0.00 0.00 3.61
2068 2553 4.015084 AGCCTTCATTCTGGTCAATCTTG 58.985 43.478 0.00 0.00 0.00 3.02
2069 2554 4.268359 GAGCCTTCATTCTGGTCAATCTT 58.732 43.478 0.00 0.00 0.00 2.40
2070 2555 3.371380 GGAGCCTTCATTCTGGTCAATCT 60.371 47.826 0.00 0.00 0.00 2.40
2071 2556 2.948315 GGAGCCTTCATTCTGGTCAATC 59.052 50.000 0.00 0.00 0.00 2.67
2072 2557 2.309755 TGGAGCCTTCATTCTGGTCAAT 59.690 45.455 0.00 0.00 0.00 2.57
2073 2558 1.704628 TGGAGCCTTCATTCTGGTCAA 59.295 47.619 0.00 0.00 0.00 3.18
2074 2559 1.361204 TGGAGCCTTCATTCTGGTCA 58.639 50.000 0.00 0.00 0.00 4.02
2075 2560 2.026822 TCTTGGAGCCTTCATTCTGGTC 60.027 50.000 0.00 0.00 0.00 4.02
2076 2561 1.988107 TCTTGGAGCCTTCATTCTGGT 59.012 47.619 0.00 0.00 0.00 4.00
2077 2562 2.795231 TCTTGGAGCCTTCATTCTGG 57.205 50.000 0.00 0.00 0.00 3.86
2078 2563 4.096081 GTCAATCTTGGAGCCTTCATTCTG 59.904 45.833 0.00 0.00 0.00 3.02
2079 2564 4.268359 GTCAATCTTGGAGCCTTCATTCT 58.732 43.478 0.00 0.00 0.00 2.40
2080 2565 3.379688 GGTCAATCTTGGAGCCTTCATTC 59.620 47.826 0.00 0.00 0.00 2.67
2081 2566 3.245371 TGGTCAATCTTGGAGCCTTCATT 60.245 43.478 0.00 0.00 31.96 2.57
2082 2567 2.309755 TGGTCAATCTTGGAGCCTTCAT 59.690 45.455 0.00 0.00 31.96 2.57
2083 2568 1.704628 TGGTCAATCTTGGAGCCTTCA 59.295 47.619 0.00 0.00 31.96 3.02
2084 2569 2.026822 TCTGGTCAATCTTGGAGCCTTC 60.027 50.000 0.00 0.00 31.96 3.46
2085 2570 1.988107 TCTGGTCAATCTTGGAGCCTT 59.012 47.619 0.00 0.00 31.96 4.35
2086 2571 1.661463 TCTGGTCAATCTTGGAGCCT 58.339 50.000 0.00 0.00 31.96 4.58
2087 2572 2.496899 TTCTGGTCAATCTTGGAGCC 57.503 50.000 0.00 0.00 31.96 4.70
2088 2573 3.614092 TCATTCTGGTCAATCTTGGAGC 58.386 45.455 0.00 0.00 0.00 4.70
2089 2574 4.639310 CCTTCATTCTGGTCAATCTTGGAG 59.361 45.833 0.00 0.00 0.00 3.86
2090 2575 4.592942 CCTTCATTCTGGTCAATCTTGGA 58.407 43.478 0.00 0.00 0.00 3.53
2091 2576 3.129988 GCCTTCATTCTGGTCAATCTTGG 59.870 47.826 0.00 0.00 0.00 3.61
2092 2577 4.015084 AGCCTTCATTCTGGTCAATCTTG 58.985 43.478 0.00 0.00 0.00 3.02
2093 2578 4.268359 GAGCCTTCATTCTGGTCAATCTT 58.732 43.478 0.00 0.00 0.00 2.40
2094 2579 3.371380 GGAGCCTTCATTCTGGTCAATCT 60.371 47.826 0.00 0.00 0.00 2.40
2095 2580 2.948315 GGAGCCTTCATTCTGGTCAATC 59.052 50.000 0.00 0.00 0.00 2.67
2096 2581 2.309755 TGGAGCCTTCATTCTGGTCAAT 59.690 45.455 0.00 0.00 0.00 2.57
2097 2582 1.704628 TGGAGCCTTCATTCTGGTCAA 59.295 47.619 0.00 0.00 0.00 3.18
2098 2583 1.280133 CTGGAGCCTTCATTCTGGTCA 59.720 52.381 0.00 0.00 0.00 4.02
2099 2584 1.407989 CCTGGAGCCTTCATTCTGGTC 60.408 57.143 0.00 0.00 0.00 4.02
2100 2585 0.622665 CCTGGAGCCTTCATTCTGGT 59.377 55.000 0.00 0.00 0.00 4.00
2101 2586 0.914644 TCCTGGAGCCTTCATTCTGG 59.085 55.000 0.00 0.00 0.00 3.86
2102 2587 2.950309 CAATCCTGGAGCCTTCATTCTG 59.050 50.000 1.52 0.00 0.00 3.02
2103 2588 2.848694 TCAATCCTGGAGCCTTCATTCT 59.151 45.455 1.52 0.00 0.00 2.40
2203 2688 4.934356 AGAATTTGAGAAGTTATGGGGCA 58.066 39.130 0.00 0.00 0.00 5.36
2300 2786 8.468720 TTGATCATGTTTGCACAAAAGATATG 57.531 30.769 0.00 2.04 36.16 1.78
2301 2787 9.093970 CATTGATCATGTTTGCACAAAAGATAT 57.906 29.630 0.00 0.00 36.16 1.63
2350 2846 6.716628 ACAGAAAAGAGATACTGGCAAATTGA 59.283 34.615 0.00 0.00 35.08 2.57
2384 2880 6.474819 TTAAGACACGTCAATGTTATGTGG 57.525 37.500 0.00 0.00 38.02 4.17
2395 2891 9.961265 CTCCTATACATATTTTAAGACACGTCA 57.039 33.333 0.00 0.00 0.00 4.35
2448 2944 5.440610 AGTCTGGAAATCAAACAAGTGAGT 58.559 37.500 0.00 0.00 0.00 3.41
2470 2966 6.524101 AGAAAACTCAAGTAGCTCTAGGAG 57.476 41.667 0.00 0.00 35.32 3.69
2549 3046 5.437289 TGCACAAAAAGTACAGATCCTTG 57.563 39.130 0.00 0.00 0.00 3.61
2614 3114 8.830915 AGGATTGACAGAAAAGAGATACTAGA 57.169 34.615 0.00 0.00 0.00 2.43
2720 3220 3.762407 TTTCGTGTCCTGGAAATCTGA 57.238 42.857 0.00 0.00 0.00 3.27
2728 3228 2.160417 GCTCTCATTTTTCGTGTCCTGG 59.840 50.000 0.00 0.00 0.00 4.45
2839 3339 1.589803 AACAAAGGCGCGAGTTACTT 58.410 45.000 12.10 2.14 0.00 2.24
2895 3395 3.393800 TCTGTCTTTGAAGTGCTAGCAC 58.606 45.455 35.56 35.56 46.50 4.40
3178 3678 2.095567 TGAAATTGAGCTTCGCTGCTTC 60.096 45.455 0.00 0.00 44.17 3.86
3388 3888 1.625818 GGAGGGGCATACCTGTATCTG 59.374 57.143 0.00 0.00 42.10 2.90
3418 3918 3.647636 TCCAATGTTCCAAAACCCTTCA 58.352 40.909 0.00 0.00 34.28 3.02
3532 4032 4.217334 TGAATTTTCTGCGCCATTAACAGA 59.783 37.500 4.18 0.00 38.62 3.41
3543 4043 2.609350 CCCCAACATGAATTTTCTGCG 58.391 47.619 0.00 0.00 0.00 5.18
3564 4064 5.047802 CCAACCTTAATGATGATGGGTATGC 60.048 44.000 0.00 0.00 0.00 3.14
3570 4070 5.829391 TGATCACCAACCTTAATGATGATGG 59.171 40.000 0.00 0.00 31.96 3.51
3572 4072 9.071276 GTAATGATCACCAACCTTAATGATGAT 57.929 33.333 0.00 0.00 31.96 2.45
3628 4128 8.958119 TTTACATAGAACTGAACAAACTGACT 57.042 30.769 0.00 0.00 0.00 3.41
3679 4179 7.711846 TGCTTCTTTGAGTGTAAATAAGCAAA 58.288 30.769 16.46 0.00 46.95 3.68
3755 4257 3.303938 TGAATTGTTTCTCAGGGGCAAA 58.696 40.909 0.00 0.00 32.78 3.68
3842 4344 1.459592 CTGAAGTAACCGGAAACAGCG 59.540 52.381 9.46 0.00 0.00 5.18
3850 4352 6.926826 TGTAATGCATATACTGAAGTAACCGG 59.073 38.462 0.00 0.00 33.76 5.28
3997 4499 6.575162 ATGTTTCACAAATTCACCTACTCC 57.425 37.500 0.00 0.00 0.00 3.85
4031 4533 6.387041 AGCGCTGATAGTAGTAACATTGTA 57.613 37.500 10.39 0.00 0.00 2.41
4044 4546 4.410492 AACTGAAAACAAGCGCTGATAG 57.590 40.909 12.58 4.02 0.00 2.08
4089 4591 5.712152 AAATGGTCAATTCTTCAGTGGAC 57.288 39.130 0.00 0.00 0.00 4.02
4108 4610 2.978278 TGAAGCAAATCCACCCCAAAAT 59.022 40.909 0.00 0.00 0.00 1.82
4169 4673 2.996621 GTCCTGAATTGGAACTGAGTCG 59.003 50.000 0.00 0.00 37.93 4.18
4214 4718 1.942657 GATATGCCACACGATGCAAGT 59.057 47.619 0.00 0.00 41.50 3.16
4215 4719 1.941975 TGATATGCCACACGATGCAAG 59.058 47.619 0.00 0.00 41.50 4.01
4216 4720 2.035530 TGATATGCCACACGATGCAA 57.964 45.000 0.00 0.00 41.50 4.08
4217 4721 1.874872 CATGATATGCCACACGATGCA 59.125 47.619 0.00 0.00 42.52 3.96
4218 4722 1.875514 ACATGATATGCCACACGATGC 59.124 47.619 0.00 0.00 0.00 3.91
4219 4723 4.083855 GGTTACATGATATGCCACACGATG 60.084 45.833 0.00 0.00 0.00 3.84
4220 4724 4.065088 GGTTACATGATATGCCACACGAT 58.935 43.478 0.00 0.00 0.00 3.73
4221 4725 3.118592 TGGTTACATGATATGCCACACGA 60.119 43.478 0.00 0.00 0.00 4.35
4238 4742 7.824289 CCAGAAGACTCTTTCATTACATGGTTA 59.176 37.037 0.00 0.00 0.00 2.85
4255 4759 3.009584 GGAAATTGAGGGACCAGAAGACT 59.990 47.826 0.00 0.00 0.00 3.24
4256 4760 3.348119 GGAAATTGAGGGACCAGAAGAC 58.652 50.000 0.00 0.00 0.00 3.01
4279 4783 4.999950 AGAAAGAAATGTCGATGAAGCACT 59.000 37.500 0.00 0.00 0.00 4.40
4293 4797 5.245531 TGAGTGCGTGGATAAGAAAGAAAT 58.754 37.500 0.00 0.00 0.00 2.17
4294 4798 4.637276 TGAGTGCGTGGATAAGAAAGAAA 58.363 39.130 0.00 0.00 0.00 2.52
4337 4841 8.203485 AGCAATCAAGACAACAAAATAGGAAAA 58.797 29.630 0.00 0.00 0.00 2.29
4351 4938 2.813754 GCAGTTACCAGCAATCAAGACA 59.186 45.455 0.00 0.00 0.00 3.41
4381 4976 0.323999 TGCATCAAGAGCAGGCCATT 60.324 50.000 5.01 0.00 37.02 3.16
4394 4989 3.908643 AGCAGAAGAAGAGATGCATCA 57.091 42.857 27.81 0.00 41.14 3.07


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

AutoCloner maintained by Alex Coulton.