Multiple sequence alignment - TraesCS5D01G551700

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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 TraesCS5D01G551700 chr5D 100.000 2771 0 0 1 2771 557503659 557506429 0.000000e+00 5118.0
1 TraesCS5D01G551700 chr5D 79.613 775 139 11 999 1757 526095828 526095057 3.140000e-149 538.0
2 TraesCS5D01G551700 chr5D 89.836 305 25 3 1993 2297 557510753 557511051 1.200000e-103 387.0
3 TraesCS5D01G551700 chr5D 93.820 178 11 0 2557 2734 321384150 321383973 4.550000e-68 268.0
4 TraesCS5D01G551700 chr5D 73.071 661 125 36 1117 1749 563340013 563340648 4.710000e-43 185.0
5 TraesCS5D01G551700 chr4A 88.693 1813 126 37 1 1769 609563289 609565066 0.000000e+00 2139.0
6 TraesCS5D01G551700 chr4A 89.510 572 35 14 1797 2352 609565393 609565955 0.000000e+00 701.0
7 TraesCS5D01G551700 chr4A 88.441 571 43 11 1796 2352 609569177 609569738 0.000000e+00 667.0
8 TraesCS5D01G551700 chr4A 93.088 217 13 1 2136 2352 609579770 609579984 1.600000e-82 316.0
9 TraesCS5D01G551700 chr4A 90.868 219 11 3 2354 2571 609565999 609566209 4.520000e-73 285.0
10 TraesCS5D01G551700 chr4A 92.857 168 12 0 1604 1771 609568712 609568879 7.670000e-61 244.0
11 TraesCS5D01G551700 chr4A 87.615 218 18 6 2354 2571 609580025 609580233 7.670000e-61 244.0
12 TraesCS5D01G551700 chr4A 95.370 108 5 0 2359 2466 609569784 609569891 3.670000e-39 172.0
13 TraesCS5D01G551700 chr5B 91.171 1008 41 14 1 964 711102757 711103760 0.000000e+00 1325.0
14 TraesCS5D01G551700 chr5B 81.571 1617 204 42 770 2352 705330249 705328693 0.000000e+00 1249.0
15 TraesCS5D01G551700 chr5B 92.168 715 56 0 1000 1714 711103762 711104476 0.000000e+00 1011.0
16 TraesCS5D01G551700 chr5B 87.828 534 41 14 1809 2328 711104882 711105405 3.050000e-169 604.0
17 TraesCS5D01G551700 chr5B 97.024 168 5 0 2567 2734 145828179 145828346 1.620000e-72 283.0
18 TraesCS5D01G551700 chr5B 79.449 399 68 8 999 1385 661028298 661027902 1.260000e-68 270.0
19 TraesCS5D01G551700 chr5B 89.450 218 14 3 2354 2570 705328655 705328446 1.640000e-67 267.0
20 TraesCS5D01G551700 chr5B 73.018 656 125 41 1119 1749 711050378 711049750 1.700000e-42 183.0
21 TraesCS5D01G551700 chr5B 72.315 661 130 40 1117 1749 705566702 705567337 1.030000e-34 158.0
22 TraesCS5D01G551700 chr6B 97.605 167 4 0 2567 2733 229680781 229680947 1.260000e-73 287.0
23 TraesCS5D01G551700 chr6B 97.576 165 4 0 2570 2734 468734655 468734819 1.620000e-72 283.0
24 TraesCS5D01G551700 chr6B 96.951 164 5 0 2569 2732 690750793 690750956 2.720000e-70 276.0
25 TraesCS5D01G551700 chr3A 97.605 167 4 0 2568 2734 731100713 731100879 1.260000e-73 287.0
26 TraesCS5D01G551700 chr6D 97.576 165 4 0 2570 2734 81746768 81746932 1.620000e-72 283.0
27 TraesCS5D01G551700 chr7B 94.886 176 9 0 2568 2743 697802740 697802565 2.720000e-70 276.0
28 TraesCS5D01G551700 chr3B 95.349 172 8 0 2562 2733 592595497 592595326 9.780000e-70 274.0
29 TraesCS5D01G551700 chr3B 76.190 273 48 10 1112 1374 745590710 745590975 8.060000e-26 128.0
30 TraesCS5D01G551700 chr3D 97.297 37 1 0 1473 1509 559899107 559899071 2.300000e-06 63.9
31 TraesCS5D01G551700 chr3D 97.297 37 1 0 1473 1509 560102612 560102576 2.300000e-06 63.9


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 TraesCS5D01G551700 chr5D 557503659 557506429 2770 False 5118.000000 5118 100.0000 1 2771 1 chr5D.!!$F1 2770
1 TraesCS5D01G551700 chr5D 526095057 526095828 771 True 538.000000 538 79.6130 999 1757 1 chr5D.!!$R2 758
2 TraesCS5D01G551700 chr4A 609563289 609569891 6602 False 701.333333 2139 90.9565 1 2571 6 chr4A.!!$F1 2570
3 TraesCS5D01G551700 chr5B 711102757 711105405 2648 False 980.000000 1325 90.3890 1 2328 3 chr5B.!!$F3 2327
4 TraesCS5D01G551700 chr5B 705328446 705330249 1803 True 758.000000 1249 85.5105 770 2570 2 chr5B.!!$R3 1800

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
611 651 0.442699 CTGTCTCGGCCGTAAAAAGC 59.557 55.0 27.15 11.09 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2443 0.770499 TCTTCCACATTGAGGGCACA 59.23 50.0 0.0 0.0 0.0 4.57 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
383 416 1.126846 CATGTCACTCGAAAACGGCTC 59.873 52.381 0.00 0.00 0.00 4.70
494 528 6.742472 GTGACGCATATCACTTATCATAACG 58.258 40.000 5.68 0.00 44.71 3.18
497 531 5.633601 ACGCATATCACTTATCATAACGTGG 59.366 40.000 0.00 0.00 0.00 4.94
611 651 0.442699 CTGTCTCGGCCGTAAAAAGC 59.557 55.000 27.15 11.09 0.00 3.51
669 709 1.600413 GGAACAGCGCACCTCAAAAAG 60.600 52.381 11.47 0.00 0.00 2.27
761 814 0.609131 GGAAGGGCAGCAAGCTAACA 60.609 55.000 0.00 0.00 44.79 2.41
809 862 0.744414 ATCATCGTCGGGCAAAGGTG 60.744 55.000 0.00 0.00 0.00 4.00
958 1011 1.349259 GCTCGCTCGCCGTTCTAAAA 61.349 55.000 0.00 0.00 38.35 1.52
966 1019 2.160813 TCGCCGTTCTAAAAATTGAGCC 59.839 45.455 0.00 0.00 0.00 4.70
979 1032 1.351430 TTGAGCCGCTTCGATTCGTG 61.351 55.000 5.89 2.05 0.00 4.35
980 1033 3.144120 GAGCCGCTTCGATTCGTGC 62.144 63.158 5.89 10.65 0.00 5.34
981 1034 3.188786 GCCGCTTCGATTCGTGCT 61.189 61.111 18.51 0.00 0.00 4.40
982 1035 2.697425 CCGCTTCGATTCGTGCTG 59.303 61.111 18.51 11.90 0.00 4.41
983 1036 2.020559 CGCTTCGATTCGTGCTGC 59.979 61.111 18.51 12.29 0.00 5.25
986 1039 1.741401 CTTCGATTCGTGCTGCCCA 60.741 57.895 5.89 0.00 0.00 5.36
987 1040 1.970917 CTTCGATTCGTGCTGCCCAC 61.971 60.000 5.89 0.00 41.15 4.61
1005 1058 3.785859 GAGGGACGAGGCATGCCA 61.786 66.667 37.18 0.00 38.92 4.92
1101 1157 3.289834 GGCATCATCCGCGGCAAT 61.290 61.111 23.51 6.95 0.00 3.56
1374 1438 3.402681 CCCCACGATCTGGCCACT 61.403 66.667 0.00 0.00 39.01 4.00
1417 1484 1.153449 GACGCCGATGAACATGGGA 60.153 57.895 17.54 0.00 38.77 4.37
1419 1486 1.143838 CGCCGATGAACATGGGAGA 59.856 57.895 17.54 0.00 38.41 3.71
1424 1491 1.405463 CGATGAACATGGGAGAGTCGA 59.595 52.381 0.00 0.00 0.00 4.20
1436 1503 1.062880 GAGAGTCGACCTTCGCTACAG 59.937 57.143 13.01 0.00 40.21 2.74
1660 1736 2.432972 CCTGCATTTTGCCGTGGC 60.433 61.111 3.30 3.30 44.23 5.01
1771 1847 0.777446 CCTCCCCAAACCTTCCTGAA 59.223 55.000 0.00 0.00 0.00 3.02
1772 1848 1.359130 CCTCCCCAAACCTTCCTGAAT 59.641 52.381 0.00 0.00 0.00 2.57
1773 1849 2.621668 CCTCCCCAAACCTTCCTGAATC 60.622 54.545 0.00 0.00 0.00 2.52
1774 1850 1.357761 TCCCCAAACCTTCCTGAATCC 59.642 52.381 0.00 0.00 0.00 3.01
1776 1852 2.450476 CCCAAACCTTCCTGAATCCTG 58.550 52.381 0.00 0.00 0.00 3.86
1777 1853 2.041620 CCCAAACCTTCCTGAATCCTGA 59.958 50.000 0.00 0.00 0.00 3.86
1778 1854 3.309410 CCCAAACCTTCCTGAATCCTGAT 60.309 47.826 0.00 0.00 0.00 2.90
1780 1856 3.550437 AACCTTCCTGAATCCTGATCG 57.450 47.619 0.00 0.00 0.00 3.69
1781 1857 1.765314 ACCTTCCTGAATCCTGATCGG 59.235 52.381 0.00 0.00 0.00 4.18
1782 1858 1.542108 CCTTCCTGAATCCTGATCGGC 60.542 57.143 0.00 0.00 0.00 5.54
1783 1859 0.469917 TTCCTGAATCCTGATCGGCC 59.530 55.000 0.00 0.00 0.00 6.13
1784 1860 1.301244 CCTGAATCCTGATCGGCCG 60.301 63.158 22.12 22.12 0.00 6.13
1785 1861 1.742146 CTGAATCCTGATCGGCCGA 59.258 57.895 33.12 33.12 0.00 5.54
1786 1862 0.598680 CTGAATCCTGATCGGCCGAC 60.599 60.000 33.75 23.91 0.00 4.79
1787 1863 1.301009 GAATCCTGATCGGCCGACC 60.301 63.158 33.75 24.63 0.00 4.79
1788 1864 2.717139 GAATCCTGATCGGCCGACCC 62.717 65.000 33.75 25.13 0.00 4.46
1887 2292 0.034186 TGTGGGCATGTCCAAGGATC 60.034 55.000 23.33 8.95 38.72 3.36
1949 2366 4.270084 ACGGTACATATGCGAAATGACTTG 59.730 41.667 1.58 0.00 0.00 3.16
2005 2443 4.414337 TTGCCCAGTTTATTGTTTGCTT 57.586 36.364 0.00 0.00 0.00 3.91
2030 2472 3.084786 CCCTCAATGTGGAAGAAGGTTC 58.915 50.000 2.45 0.00 0.00 3.62
2031 2473 2.744202 CCTCAATGTGGAAGAAGGTTCG 59.256 50.000 0.00 0.00 0.00 3.95
2077 2519 1.383456 GCACTGCAGGTTGTGGTTCA 61.383 55.000 19.93 0.00 34.99 3.18
2085 2527 5.295950 TGCAGGTTGTGGTTCAAAATAATG 58.704 37.500 0.00 0.00 37.81 1.90
2086 2528 5.069648 TGCAGGTTGTGGTTCAAAATAATGA 59.930 36.000 0.00 0.00 37.81 2.57
2087 2529 6.165577 GCAGGTTGTGGTTCAAAATAATGAT 58.834 36.000 0.00 0.00 37.81 2.45
2122 2564 5.717654 AGGTTGGGTTTGTTTCTTCACTTTA 59.282 36.000 0.00 0.00 0.00 1.85
2124 2566 6.700081 GGTTGGGTTTGTTTCTTCACTTTATC 59.300 38.462 0.00 0.00 0.00 1.75
2125 2567 7.417456 GGTTGGGTTTGTTTCTTCACTTTATCT 60.417 37.037 0.00 0.00 0.00 1.98
2126 2568 7.038154 TGGGTTTGTTTCTTCACTTTATCTG 57.962 36.000 0.00 0.00 0.00 2.90
2127 2569 6.040391 TGGGTTTGTTTCTTCACTTTATCTGG 59.960 38.462 0.00 0.00 0.00 3.86
2128 2570 6.447162 GGTTTGTTTCTTCACTTTATCTGGG 58.553 40.000 0.00 0.00 0.00 4.45
2129 2571 6.040504 GGTTTGTTTCTTCACTTTATCTGGGT 59.959 38.462 0.00 0.00 0.00 4.51
2130 2572 7.229907 GGTTTGTTTCTTCACTTTATCTGGGTA 59.770 37.037 0.00 0.00 0.00 3.69
2134 2576 9.010029 TGTTTCTTCACTTTATCTGGGTATTTC 57.990 33.333 0.00 0.00 0.00 2.17
2162 2606 3.620374 CCATGAACTGAGCATGTCTACAC 59.380 47.826 0.00 0.00 41.11 2.90
2164 2608 2.899900 TGAACTGAGCATGTCTACACCT 59.100 45.455 0.00 0.00 0.00 4.00
2208 2652 4.362677 TCCCTTGAGGAAGCTGTAAGTAT 58.637 43.478 0.00 0.00 43.78 2.12
2235 2679 0.179100 TGCCATCTGCGAGCTTCTAC 60.179 55.000 0.00 0.00 45.60 2.59
2246 2690 4.081642 TGCGAGCTTCTACTGGAGTAAAAT 60.082 41.667 0.00 0.00 0.00 1.82
2282 2728 5.411361 TCTCGTGCTTGTTTGTATTGCTAAT 59.589 36.000 0.00 0.00 0.00 1.73
2405 2893 4.383010 CCTCAGCCCACCCATTTTTAAATC 60.383 45.833 0.00 0.00 0.00 2.17
2432 2920 9.546428 CCTATATTTTGTTGGAATGATTTTCCC 57.454 33.333 2.11 0.00 37.79 3.97
2497 2985 2.057137 TGGTTGCTGCCTATGATTCC 57.943 50.000 0.00 0.00 0.00 3.01
2505 2993 3.336122 CCTATGATTCCCAGGCAGC 57.664 57.895 0.00 0.00 0.00 5.25
2506 2994 0.604780 CCTATGATTCCCAGGCAGCG 60.605 60.000 0.00 0.00 0.00 5.18
2507 2995 0.604780 CTATGATTCCCAGGCAGCGG 60.605 60.000 0.00 0.00 0.00 5.52
2574 3062 7.923414 AAGATGTGTTCCTGTTTTATACTCC 57.077 36.000 0.00 0.00 0.00 3.85
2575 3063 6.415573 AGATGTGTTCCTGTTTTATACTCCC 58.584 40.000 0.00 0.00 0.00 4.30
2576 3064 5.836024 TGTGTTCCTGTTTTATACTCCCT 57.164 39.130 0.00 0.00 0.00 4.20
2577 3065 5.801380 TGTGTTCCTGTTTTATACTCCCTC 58.199 41.667 0.00 0.00 0.00 4.30
2578 3066 5.183969 GTGTTCCTGTTTTATACTCCCTCC 58.816 45.833 0.00 0.00 0.00 4.30
2579 3067 4.081309 TGTTCCTGTTTTATACTCCCTCCG 60.081 45.833 0.00 0.00 0.00 4.63
2580 3068 3.716431 TCCTGTTTTATACTCCCTCCGT 58.284 45.455 0.00 0.00 0.00 4.69
2581 3069 4.098894 TCCTGTTTTATACTCCCTCCGTT 58.901 43.478 0.00 0.00 0.00 4.44
2582 3070 4.533311 TCCTGTTTTATACTCCCTCCGTTT 59.467 41.667 0.00 0.00 0.00 3.60
2583 3071 4.874396 CCTGTTTTATACTCCCTCCGTTTC 59.126 45.833 0.00 0.00 0.00 2.78
2584 3072 5.338137 CCTGTTTTATACTCCCTCCGTTTCT 60.338 44.000 0.00 0.00 0.00 2.52
2585 3073 6.127253 CCTGTTTTATACTCCCTCCGTTTCTA 60.127 42.308 0.00 0.00 0.00 2.10
2586 3074 7.243604 TGTTTTATACTCCCTCCGTTTCTAA 57.756 36.000 0.00 0.00 0.00 2.10
2587 3075 7.678837 TGTTTTATACTCCCTCCGTTTCTAAA 58.321 34.615 0.00 0.00 0.00 1.85
2588 3076 8.323567 TGTTTTATACTCCCTCCGTTTCTAAAT 58.676 33.333 0.00 0.00 0.00 1.40
2589 3077 8.610035 GTTTTATACTCCCTCCGTTTCTAAATG 58.390 37.037 0.00 0.00 0.00 2.32
2590 3078 5.952347 ATACTCCCTCCGTTTCTAAATGT 57.048 39.130 0.00 0.00 0.00 2.71
2591 3079 8.537728 TTATACTCCCTCCGTTTCTAAATGTA 57.462 34.615 0.00 0.00 0.00 2.29
2592 3080 5.750352 ACTCCCTCCGTTTCTAAATGTAA 57.250 39.130 0.00 0.00 0.00 2.41
2593 3081 5.731591 ACTCCCTCCGTTTCTAAATGTAAG 58.268 41.667 0.00 0.00 0.00 2.34
2594 3082 5.247792 ACTCCCTCCGTTTCTAAATGTAAGT 59.752 40.000 0.00 0.00 0.00 2.24
2595 3083 5.727434 TCCCTCCGTTTCTAAATGTAAGTC 58.273 41.667 0.00 0.00 0.00 3.01
2596 3084 5.482878 TCCCTCCGTTTCTAAATGTAAGTCT 59.517 40.000 0.00 0.00 0.00 3.24
2597 3085 6.013984 TCCCTCCGTTTCTAAATGTAAGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2598 3086 6.653740 CCCTCCGTTTCTAAATGTAAGTCTTT 59.346 38.462 0.00 0.00 0.00 2.52
2599 3087 7.360946 CCCTCCGTTTCTAAATGTAAGTCTTTG 60.361 40.741 0.00 0.00 0.00 2.77
2600 3088 7.172703 CCTCCGTTTCTAAATGTAAGTCTTTGT 59.827 37.037 0.00 0.00 0.00 2.83
2601 3089 9.199982 CTCCGTTTCTAAATGTAAGTCTTTGTA 57.800 33.333 0.00 0.00 0.00 2.41
2602 3090 9.199982 TCCGTTTCTAAATGTAAGTCTTTGTAG 57.800 33.333 0.00 0.00 0.00 2.74
2603 3091 9.199982 CCGTTTCTAAATGTAAGTCTTTGTAGA 57.800 33.333 0.00 0.00 0.00 2.59
2611 3099 8.779354 AATGTAAGTCTTTGTAGAGATTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
2612 3100 7.540474 TGTAAGTCTTTGTAGAGATTCCACT 57.460 36.000 0.00 0.00 0.00 4.00
2613 3101 8.645814 TGTAAGTCTTTGTAGAGATTCCACTA 57.354 34.615 0.00 0.00 0.00 2.74
2614 3102 8.740906 TGTAAGTCTTTGTAGAGATTCCACTAG 58.259 37.037 0.00 0.00 0.00 2.57
2615 3103 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
2616 3104 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
2617 3105 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
2629 3117 3.984508 CACTAGGTGGACTACATACGG 57.015 52.381 0.00 0.00 0.00 4.02
2630 3118 3.548770 CACTAGGTGGACTACATACGGA 58.451 50.000 0.00 0.00 0.00 4.69
2631 3119 3.564644 CACTAGGTGGACTACATACGGAG 59.435 52.174 0.00 0.00 0.00 4.63
2632 3120 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
2633 3121 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
2634 3122 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
2635 3123 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
2636 3124 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
2637 3125 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
2638 3126 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
2639 3127 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2640 3128 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
2641 3129 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
2642 3130 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
2643 3131 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
2644 3132 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2645 3133 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2646 3134 6.866480 ACATACGGAGCAAAATGAATGAATT 58.134 32.000 0.00 0.00 0.00 2.17
2647 3135 6.974622 ACATACGGAGCAAAATGAATGAATTC 59.025 34.615 0.00 0.00 37.31 2.17
2663 3151 9.142515 TGAATGAATTCACACTTAAAATGCATC 57.857 29.630 11.07 0.00 41.51 3.91
2664 3152 9.362539 GAATGAATTCACACTTAAAATGCATCT 57.637 29.630 11.07 0.00 36.80 2.90
2685 3173 8.567369 CATCTATATGCATCCGTATGTAGTTC 57.433 38.462 0.19 0.00 32.91 3.01
2686 3174 7.696992 TCTATATGCATCCGTATGTAGTTCA 57.303 36.000 0.19 0.00 32.91 3.18
2687 3175 8.293699 TCTATATGCATCCGTATGTAGTTCAT 57.706 34.615 0.19 0.00 40.25 2.57
2688 3176 9.403583 TCTATATGCATCCGTATGTAGTTCATA 57.596 33.333 0.19 0.00 37.91 2.15
2689 3177 9.670719 CTATATGCATCCGTATGTAGTTCATAG 57.329 37.037 0.19 0.00 39.36 2.23
2690 3178 5.784578 TGCATCCGTATGTAGTTCATAGT 57.215 39.130 0.00 0.00 39.36 2.12
2691 3179 5.528870 TGCATCCGTATGTAGTTCATAGTG 58.471 41.667 0.00 0.00 39.36 2.74
2692 3180 4.923871 GCATCCGTATGTAGTTCATAGTGG 59.076 45.833 0.00 2.99 39.36 4.00
2693 3181 5.278808 GCATCCGTATGTAGTTCATAGTGGA 60.279 44.000 11.01 11.01 43.10 4.02
2694 3182 6.737622 GCATCCGTATGTAGTTCATAGTGGAA 60.738 42.308 12.08 0.00 42.65 3.53
2695 3183 6.971726 TCCGTATGTAGTTCATAGTGGAAT 57.028 37.500 7.73 0.00 39.60 3.01
2696 3184 6.978338 TCCGTATGTAGTTCATAGTGGAATC 58.022 40.000 7.73 0.00 39.60 2.52
2697 3185 6.776116 TCCGTATGTAGTTCATAGTGGAATCT 59.224 38.462 7.73 0.00 39.60 2.40
2698 3186 7.040617 TCCGTATGTAGTTCATAGTGGAATCTC 60.041 40.741 7.73 0.00 39.60 2.75
2699 3187 7.040340 CCGTATGTAGTTCATAGTGGAATCTCT 60.040 40.741 3.20 0.00 39.36 3.10
2700 3188 9.000486 CGTATGTAGTTCATAGTGGAATCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
2702 3190 8.768501 ATGTAGTTCATAGTGGAATCTCTACA 57.231 34.615 0.00 0.00 37.82 2.74
2703 3191 8.589701 TGTAGTTCATAGTGGAATCTCTACAA 57.410 34.615 0.00 0.00 34.07 2.41
2704 3192 9.031537 TGTAGTTCATAGTGGAATCTCTACAAA 57.968 33.333 0.00 0.00 34.07 2.83
2705 3193 9.522804 GTAGTTCATAGTGGAATCTCTACAAAG 57.477 37.037 0.00 0.00 30.38 2.77
2706 3194 8.367660 AGTTCATAGTGGAATCTCTACAAAGA 57.632 34.615 0.00 0.00 29.47 2.52
2707 3195 8.254508 AGTTCATAGTGGAATCTCTACAAAGAC 58.745 37.037 0.00 0.00 29.47 3.01
2708 3196 7.962995 TCATAGTGGAATCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
2709 3197 8.367660 TCATAGTGGAATCTCTACAAAGACTT 57.632 34.615 0.00 0.00 29.47 3.01
2710 3198 9.475620 TCATAGTGGAATCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
2725 3213 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2726 3214 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2727 3215 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2728 3216 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2729 3217 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2743 3233 6.408107 ACGGAGGGAGTATAAATTTCTCTC 57.592 41.667 0.00 0.00 37.66 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 6.366332 GTCGAAAAGCTAAGAAAGACAGATGA 59.634 38.462 0.00 0.00 0.00 2.92
277 305 4.628333 ACGTTTGTTTTCGTTTCTGAGAGA 59.372 37.500 0.00 0.00 36.93 3.10
447 481 4.466567 TGTCGCAATCTGTGTGTTTTAG 57.533 40.909 0.00 0.00 38.94 1.85
490 524 0.035739 GCTCCCACCTTTCCACGTTA 59.964 55.000 0.00 0.00 0.00 3.18
494 528 0.744771 GATCGCTCCCACCTTTCCAC 60.745 60.000 0.00 0.00 0.00 4.02
497 531 1.740025 CAAAGATCGCTCCCACCTTTC 59.260 52.381 0.00 0.00 0.00 2.62
669 709 4.402474 CCCCTTCTCTCTCTCTCTCTTTTC 59.598 50.000 0.00 0.00 0.00 2.29
809 862 2.436824 GCCGAGGAAGAAGGCCAC 60.437 66.667 5.01 0.00 44.80 5.01
914 967 5.784390 ACTGGCCAAGATCTGACTATATGAT 59.216 40.000 7.01 0.00 0.00 2.45
958 1011 0.652592 CGAATCGAAGCGGCTCAATT 59.347 50.000 1.45 3.53 0.00 2.32
966 1019 2.020559 GCAGCACGAATCGAAGCG 59.979 61.111 10.55 10.22 36.81 4.68
986 1039 4.148825 GCATGCCTCGTCCCTCGT 62.149 66.667 6.36 0.00 40.80 4.18
987 1040 4.899239 GGCATGCCTCGTCCCTCG 62.899 72.222 29.98 0.00 41.41 4.63
988 1041 3.112205 ATGGCATGCCTCGTCCCTC 62.112 63.158 35.53 8.06 36.94 4.30
989 1042 3.092511 ATGGCATGCCTCGTCCCT 61.093 61.111 35.53 10.10 36.94 4.20
990 1043 2.592861 GATGGCATGCCTCGTCCC 60.593 66.667 35.53 14.98 36.94 4.46
991 1044 2.969238 CGATGGCATGCCTCGTCC 60.969 66.667 35.53 18.54 34.48 4.79
992 1045 3.643978 GCGATGGCATGCCTCGTC 61.644 66.667 36.46 29.45 38.26 4.20
1005 1058 1.522355 CATGTTCCTCAGCGGCGAT 60.522 57.895 12.98 0.00 0.00 4.58
1101 1157 0.867746 GCACGAAGCACTTGTGATCA 59.132 50.000 9.74 0.00 44.79 2.92
1417 1484 1.088306 CTGTAGCGAAGGTCGACTCT 58.912 55.000 16.46 8.13 43.74 3.24
1419 1486 1.507174 GCTGTAGCGAAGGTCGACT 59.493 57.895 16.46 0.00 43.74 4.18
1660 1736 1.135689 GCATGTGGACGCCTTGTAAAG 60.136 52.381 0.00 0.00 45.69 1.85
1771 1847 3.234730 GGGTCGGCCGATCAGGAT 61.235 66.667 37.42 0.00 45.00 3.24
1788 1864 1.615262 GGAACTCCTCCATTGGGGG 59.385 63.158 16.28 16.28 44.67 5.40
1887 2292 6.748333 TTAACAATCTCTGCAGGAAAGATG 57.252 37.500 15.13 11.48 30.35 2.90
1949 2366 6.480320 CAGATGCTGGTACTCCAAACTAATAC 59.520 42.308 0.00 0.00 43.81 1.89
1965 2382 3.611766 GCAATGTGATATGCAGATGCTGG 60.612 47.826 0.00 0.00 42.12 4.85
2005 2443 0.770499 TCTTCCACATTGAGGGCACA 59.230 50.000 0.00 0.00 0.00 4.57
2030 2472 5.410067 ACATTGATGTTGCCCTTATTTTCG 58.590 37.500 0.00 0.00 37.90 3.46
2085 2527 5.728637 AACCCAACCTTTTCAAGATCATC 57.271 39.130 0.00 0.00 0.00 2.92
2086 2528 5.366477 ACAAACCCAACCTTTTCAAGATCAT 59.634 36.000 0.00 0.00 0.00 2.45
2087 2529 4.714308 ACAAACCCAACCTTTTCAAGATCA 59.286 37.500 0.00 0.00 0.00 2.92
2122 2564 3.756082 TGGCCAAAGAAATACCCAGAT 57.244 42.857 0.61 0.00 0.00 2.90
2124 2566 3.364549 TCATGGCCAAAGAAATACCCAG 58.635 45.455 10.96 0.00 0.00 4.45
2125 2567 3.464720 TCATGGCCAAAGAAATACCCA 57.535 42.857 10.96 0.00 0.00 4.51
2126 2568 3.769300 AGTTCATGGCCAAAGAAATACCC 59.231 43.478 21.42 11.45 0.00 3.69
2127 2569 4.462483 TCAGTTCATGGCCAAAGAAATACC 59.538 41.667 21.42 11.74 0.00 2.73
2128 2570 5.643379 TCAGTTCATGGCCAAAGAAATAC 57.357 39.130 21.42 12.71 0.00 1.89
2129 2571 4.158394 GCTCAGTTCATGGCCAAAGAAATA 59.842 41.667 21.42 11.41 0.00 1.40
2130 2572 3.056322 GCTCAGTTCATGGCCAAAGAAAT 60.056 43.478 21.42 18.59 0.00 2.17
2134 2576 1.250328 TGCTCAGTTCATGGCCAAAG 58.750 50.000 10.96 5.73 0.00 2.77
2162 2606 1.889170 GACCTTTTCCCTGCAAGAAGG 59.111 52.381 4.97 4.97 41.98 3.46
2164 2608 1.142060 TCGACCTTTTCCCTGCAAGAA 59.858 47.619 0.00 0.00 34.07 2.52
2208 2652 2.355756 GCTCGCAGATGGCATAAAGAAA 59.644 45.455 0.00 0.00 45.17 2.52
2246 2690 4.816385 ACAAGCACGAGAAAAGAATCTTGA 59.184 37.500 0.00 0.00 35.24 3.02
2352 2798 1.300481 TTTGCACATTCACGACCGAA 58.700 45.000 0.00 0.00 0.00 4.30
2405 2893 9.546428 GGAAAATCATTCCAACAAAATATAGGG 57.454 33.333 2.41 0.00 38.45 3.53
2432 2920 9.624373 CTTTCTCCTGGGATTGGATATAATATG 57.376 37.037 0.00 0.00 32.56 1.78
2504 2992 1.334869 CATCATTTTCAGTAGGCCCGC 59.665 52.381 0.00 0.00 0.00 6.13
2505 2993 2.917933 TCATCATTTTCAGTAGGCCCG 58.082 47.619 0.00 0.00 0.00 6.13
2506 2994 5.859205 ATTTCATCATTTTCAGTAGGCCC 57.141 39.130 0.00 0.00 0.00 5.80
2507 2995 7.807977 TCTATTTCATCATTTTCAGTAGGCC 57.192 36.000 0.00 0.00 0.00 5.19
2549 3037 8.044908 GGGAGTATAAAACAGGAACACATCTTA 58.955 37.037 0.00 0.00 0.00 2.10
2562 3050 5.750352 AGAAACGGAGGGAGTATAAAACA 57.250 39.130 0.00 0.00 0.00 2.83
2567 3055 8.537728 TTACATTTAGAAACGGAGGGAGTATA 57.462 34.615 0.00 0.00 0.00 1.47
2568 3056 5.952347 ACATTTAGAAACGGAGGGAGTAT 57.048 39.130 0.00 0.00 0.00 2.12
2569 3057 6.438425 ACTTACATTTAGAAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2570 3058 5.247792 ACTTACATTTAGAAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2571 3059 5.731591 ACTTACATTTAGAAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2572 3060 5.482878 AGACTTACATTTAGAAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2573 3061 5.731591 AGACTTACATTTAGAAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
2574 3062 7.172703 ACAAAGACTTACATTTAGAAACGGAGG 59.827 37.037 0.00 0.00 0.00 4.30
2575 3063 8.084590 ACAAAGACTTACATTTAGAAACGGAG 57.915 34.615 0.00 0.00 0.00 4.63
2576 3064 9.199982 CTACAAAGACTTACATTTAGAAACGGA 57.800 33.333 0.00 0.00 0.00 4.69
2577 3065 9.199982 TCTACAAAGACTTACATTTAGAAACGG 57.800 33.333 0.00 0.00 0.00 4.44
2585 3073 9.220767 GTGGAATCTCTACAAAGACTTACATTT 57.779 33.333 0.00 0.00 0.00 2.32
2586 3074 8.598041 AGTGGAATCTCTACAAAGACTTACATT 58.402 33.333 0.00 0.00 29.47 2.71
2587 3075 8.140112 AGTGGAATCTCTACAAAGACTTACAT 57.860 34.615 0.00 0.00 29.47 2.29
2588 3076 7.540474 AGTGGAATCTCTACAAAGACTTACA 57.460 36.000 0.00 0.00 29.47 2.41
2589 3077 8.192110 CCTAGTGGAATCTCTACAAAGACTTAC 58.808 40.741 0.00 0.00 34.57 2.34
2590 3078 7.894364 ACCTAGTGGAATCTCTACAAAGACTTA 59.106 37.037 0.00 0.00 37.04 2.24
2591 3079 6.726764 ACCTAGTGGAATCTCTACAAAGACTT 59.273 38.462 0.00 0.00 37.04 3.01
2592 3080 6.153680 CACCTAGTGGAATCTCTACAAAGACT 59.846 42.308 0.00 0.00 37.04 3.24
2593 3081 6.334202 CACCTAGTGGAATCTCTACAAAGAC 58.666 44.000 0.00 0.00 37.04 3.01
2594 3082 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
2609 3097 3.548770 TCCGTATGTAGTCCACCTAGTG 58.451 50.000 0.00 0.00 0.00 2.74
2610 3098 3.818180 CTCCGTATGTAGTCCACCTAGT 58.182 50.000 0.00 0.00 0.00 2.57
2611 3099 2.553172 GCTCCGTATGTAGTCCACCTAG 59.447 54.545 0.00 0.00 0.00 3.02
2612 3100 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
2613 3101 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
2614 3102 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
2615 3103 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
2616 3104 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2617 3105 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2618 3106 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2619 3107 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
2620 3108 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
2621 3109 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2622 3110 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2623 3111 6.974048 TGAATTCATTCATTTTGCTCCGTATG 59.026 34.615 3.38 0.00 41.51 2.39
2624 3112 7.099266 TGAATTCATTCATTTTGCTCCGTAT 57.901 32.000 3.38 0.00 41.51 3.06
2625 3113 6.507958 TGAATTCATTCATTTTGCTCCGTA 57.492 33.333 3.38 0.00 41.51 4.02
2626 3114 5.389859 TGAATTCATTCATTTTGCTCCGT 57.610 34.783 3.38 0.00 41.51 4.69
2637 3125 9.142515 GATGCATTTTAAGTGTGAATTCATTCA 57.857 29.630 12.12 2.83 43.94 2.57
2638 3126 9.362539 AGATGCATTTTAAGTGTGAATTCATTC 57.637 29.630 12.12 7.96 37.31 2.67
2660 3148 8.190784 TGAACTACATACGGATGCATATAGATG 58.809 37.037 7.78 4.42 36.43 2.90
2661 3149 8.293699 TGAACTACATACGGATGCATATAGAT 57.706 34.615 7.78 0.00 36.43 1.98
2662 3150 7.696992 TGAACTACATACGGATGCATATAGA 57.303 36.000 7.78 0.00 36.43 1.98
2663 3151 9.670719 CTATGAACTACATACGGATGCATATAG 57.329 37.037 7.78 4.48 40.07 1.31
2664 3152 9.185680 ACTATGAACTACATACGGATGCATATA 57.814 33.333 7.78 0.00 40.07 0.86
2665 3153 7.976175 CACTATGAACTACATACGGATGCATAT 59.024 37.037 7.78 0.00 40.07 1.78
2666 3154 7.312899 CACTATGAACTACATACGGATGCATA 58.687 38.462 7.78 6.16 40.07 3.14
2667 3155 6.159293 CACTATGAACTACATACGGATGCAT 58.841 40.000 7.78 0.00 40.07 3.96
2668 3156 5.508994 CCACTATGAACTACATACGGATGCA 60.509 44.000 7.78 0.00 40.07 3.96
2669 3157 4.923871 CCACTATGAACTACATACGGATGC 59.076 45.833 7.78 0.00 40.07 3.91
2670 3158 6.327279 TCCACTATGAACTACATACGGATG 57.673 41.667 5.94 5.94 40.07 3.51
2671 3159 6.971726 TTCCACTATGAACTACATACGGAT 57.028 37.500 0.00 0.00 37.58 4.18
2672 3160 6.776116 AGATTCCACTATGAACTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
2673 3161 6.982852 AGATTCCACTATGAACTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
2674 3162 7.877003 AGAGATTCCACTATGAACTACATACG 58.123 38.462 0.00 0.00 40.07 3.06
2676 3164 9.862149 TGTAGAGATTCCACTATGAACTACATA 57.138 33.333 0.00 0.00 40.07 2.29
2677 3165 8.768501 TGTAGAGATTCCACTATGAACTACAT 57.231 34.615 0.00 0.00 42.39 2.29
2678 3166 8.589701 TTGTAGAGATTCCACTATGAACTACA 57.410 34.615 0.00 0.00 33.29 2.74
2679 3167 9.522804 CTTTGTAGAGATTCCACTATGAACTAC 57.477 37.037 0.00 0.00 0.00 2.73
2680 3168 9.475620 TCTTTGTAGAGATTCCACTATGAACTA 57.524 33.333 0.00 0.00 0.00 2.24
2681 3169 8.254508 GTCTTTGTAGAGATTCCACTATGAACT 58.745 37.037 0.00 0.00 0.00 3.01
2682 3170 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
2683 3171 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
2684 3172 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
2700 3188 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2701 3189 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2702 3190 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2703 3191 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2704 3192 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2705 3193 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2706 3194 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2707 3195 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2708 3196 9.827198 TTATACTCCCTCCGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
2709 3197 9.827198 TTTATACTCCCTCCGTTCCTAAATATA 57.173 33.333 0.00 0.00 0.00 0.86
2710 3198 8.731591 TTTATACTCCCTCCGTTCCTAAATAT 57.268 34.615 0.00 0.00 0.00 1.28
2711 3199 8.731591 ATTTATACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
2712 3200 7.628501 ATTTATACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
2713 3201 7.441903 AATTTATACTCCCTCCGTTCCTAAA 57.558 36.000 0.00 0.00 0.00 1.85
2714 3202 7.346436 AGAAATTTATACTCCCTCCGTTCCTAA 59.654 37.037 0.00 0.00 0.00 2.69
2715 3203 6.842807 AGAAATTTATACTCCCTCCGTTCCTA 59.157 38.462 0.00 0.00 0.00 2.94
2716 3204 5.666265 AGAAATTTATACTCCCTCCGTTCCT 59.334 40.000 0.00 0.00 0.00 3.36
2717 3205 5.926663 AGAAATTTATACTCCCTCCGTTCC 58.073 41.667 0.00 0.00 0.00 3.62
2718 3206 6.818233 AGAGAAATTTATACTCCCTCCGTTC 58.182 40.000 0.00 0.00 0.00 3.95
2719 3207 6.612049 AGAGAGAAATTTATACTCCCTCCGTT 59.388 38.462 12.17 0.00 0.00 4.44
2720 3208 6.137559 AGAGAGAAATTTATACTCCCTCCGT 58.862 40.000 12.17 0.00 0.00 4.69
2721 3209 6.658188 AGAGAGAAATTTATACTCCCTCCG 57.342 41.667 12.17 0.00 0.00 4.63
2722 3210 8.715190 ACTAGAGAGAAATTTATACTCCCTCC 57.285 38.462 0.00 0.93 0.00 4.30
2743 3233 7.441890 TCGATCCTCTATAAGCAGAAACTAG 57.558 40.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.