Multiple sequence alignment - TraesCS1A01G183400

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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 TraesCS1A01G183400 chr1A 100.000 6157 0 0 1 6157 333140201 333134045 0.000000e+00 11370.0
1 TraesCS1A01G183400 chr1D 90.701 6130 275 121 1 5990 269731007 269725033 0.000000e+00 7890.0
2 TraesCS1A01G183400 chr1B 90.941 3102 151 61 3056 6097 342974742 342971711 0.000000e+00 4052.0
3 TraesCS1A01G183400 chr1B 91.071 3091 123 64 1 3042 342977838 342974852 0.000000e+00 4037.0
4 TraesCS1A01G183400 chr4A 86.726 113 10 4 4531 4639 489433340 489433229 3.010000e-23 121.0
5 TraesCS1A01G183400 chr4D 86.607 112 10 4 4532 4639 93070612 93070722 1.080000e-22 119.0
6 TraesCS1A01G183400 chr4B 85.714 112 11 4 4532 4639 130625845 130625955 5.040000e-21 113.0
7 TraesCS1A01G183400 chr3D 95.312 64 3 0 4529 4592 470487154 470487091 1.090000e-17 102.0
8 TraesCS1A01G183400 chr3D 87.805 82 10 0 2835 2916 470488886 470488805 5.080000e-16 97.1
9 TraesCS1A01G183400 chr3A 86.585 82 11 0 2835 2916 612526052 612525971 2.360000e-14 91.6
10 TraesCS1A01G183400 chr7B 83.333 84 14 0 2833 2916 494217915 494217998 1.840000e-10 78.7


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 TraesCS1A01G183400 chr1A 333134045 333140201 6156 True 11370.0 11370 100.000 1 6157 1 chr1A.!!$R1 6156
1 TraesCS1A01G183400 chr1D 269725033 269731007 5974 True 7890.0 7890 90.701 1 5990 1 chr1D.!!$R1 5989
2 TraesCS1A01G183400 chr1B 342971711 342977838 6127 True 4044.5 4052 91.006 1 6097 2 chr1B.!!$R1 6096

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
668 706 0.176910 GCAGTGTAAGCTCCTCCTCC 59.823 60.0 0.00 0.00 0.00 4.30 F
674 712 0.183971 TAAGCTCCTCCTCCTCCTCG 59.816 60.0 0.00 0.00 0.00 4.63 F
2139 2222 0.039617 CCATGGCGACGCAAGAAAAA 60.040 50.0 23.09 0.00 43.62 1.94 F
2201 2284 0.035598 TTCTTCGGCCGTTTCATGGA 59.964 50.0 27.15 10.68 0.00 3.41 F
2357 2448 0.098376 GGTGTCTGTAGCCTCGTACG 59.902 60.0 9.53 9.53 0.00 3.67 F
2358 2449 0.801251 GTGTCTGTAGCCTCGTACGT 59.199 55.0 16.05 0.00 0.00 3.57 F
3756 3972 1.645710 ACCACTCTTGTCCTGTAGGG 58.354 55.0 0.00 0.00 35.41 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2159 0.034863 TCCATGCATGCAGAGCAGAA 60.035 50.000 26.69 0.00 46.36 3.02 R
2182 2265 0.035598 TCCATGAAACGGCCGAAGAA 59.964 50.000 35.90 15.20 0.00 2.52 R
2986 3077 1.139520 GCCACGAAATGCATGGGAC 59.860 57.895 0.00 0.00 33.81 4.46 R
4078 4342 1.342074 TTCTGTGGAGGAGTGAGTGG 58.658 55.000 0.00 0.00 0.00 4.00 R
4250 4528 0.809636 TATGCGTGGCCAATCGACAG 60.810 55.000 19.07 1.21 0.00 3.51 R
4436 4718 3.107017 CGAGCACGTGAAGACATGA 57.893 52.632 22.23 0.00 36.88 3.07 R
5652 5969 0.179140 GGTGCATTGCCATTGGTACG 60.179 55.000 6.12 0.00 0.00 3.67 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
53 55 1.157585 GAAAACAACGGAGGGAGAGC 58.842 55.000 0.00 0.00 0.00 4.09
119 125 0.459237 CCACCAGACTAGCGAGCAAG 60.459 60.000 0.00 0.00 0.00 4.01
120 126 1.080995 CACCAGACTAGCGAGCAAGC 61.081 60.000 0.00 0.00 37.41 4.01
121 127 1.216444 CCAGACTAGCGAGCAAGCA 59.784 57.895 6.21 0.00 40.15 3.91
122 128 0.390340 CCAGACTAGCGAGCAAGCAA 60.390 55.000 6.21 0.00 40.15 3.91
123 129 0.997932 CAGACTAGCGAGCAAGCAAG 59.002 55.000 6.21 0.00 40.15 4.01
124 130 0.739112 AGACTAGCGAGCAAGCAAGC 60.739 55.000 6.21 4.06 40.15 4.01
125 131 1.004560 ACTAGCGAGCAAGCAAGCA 60.005 52.632 12.73 1.12 40.15 3.91
126 132 0.603707 ACTAGCGAGCAAGCAAGCAA 60.604 50.000 12.73 0.00 40.15 3.91
412 434 1.341369 CGCGTTTTTCATTTCCGGGC 61.341 55.000 0.00 0.00 0.00 6.13
470 496 1.841663 CGCCTCCGTCACACTTTTGG 61.842 60.000 0.00 0.00 0.00 3.28
480 507 0.853530 ACACTTTTGGCCCTCTCCTT 59.146 50.000 0.00 0.00 0.00 3.36
499 526 2.570415 TGCCCAAAGAAATGACCGTA 57.430 45.000 0.00 0.00 0.00 4.02
513 540 1.225854 CCGTACGTTCGACTCGACC 60.226 63.158 16.59 0.00 34.89 4.79
515 542 1.630244 CGTACGTTCGACTCGACCCT 61.630 60.000 9.11 0.00 34.89 4.34
524 551 2.811317 CTCGACCCTGCTCGTTGC 60.811 66.667 0.00 0.00 43.25 4.17
586 623 2.160822 AGCAATCTAGCGTGGCTATG 57.839 50.000 0.00 0.00 40.54 2.23
593 630 0.755327 TAGCGTGGCTATGCTCCTGA 60.755 55.000 21.11 0.00 45.95 3.86
597 634 2.659897 GGCTATGCTCCTGACGCG 60.660 66.667 3.53 3.53 0.00 6.01
657 695 3.581755 GGTACGATCAAGTGCAGTGTAA 58.418 45.455 0.00 0.00 0.00 2.41
659 697 2.069273 ACGATCAAGTGCAGTGTAAGC 58.931 47.619 0.00 0.00 0.00 3.09
660 698 2.289072 ACGATCAAGTGCAGTGTAAGCT 60.289 45.455 0.00 0.00 0.00 3.74
662 700 2.169832 TCAAGTGCAGTGTAAGCTCC 57.830 50.000 0.00 0.00 0.00 4.70
663 701 1.694150 TCAAGTGCAGTGTAAGCTCCT 59.306 47.619 0.00 0.00 0.00 3.69
664 702 2.072298 CAAGTGCAGTGTAAGCTCCTC 58.928 52.381 0.00 0.00 0.00 3.71
667 705 0.898320 TGCAGTGTAAGCTCCTCCTC 59.102 55.000 0.00 0.00 0.00 3.71
668 706 0.176910 GCAGTGTAAGCTCCTCCTCC 59.823 60.000 0.00 0.00 0.00 4.30
669 707 1.859302 CAGTGTAAGCTCCTCCTCCT 58.141 55.000 0.00 0.00 0.00 3.69
671 709 1.116308 GTGTAAGCTCCTCCTCCTCC 58.884 60.000 0.00 0.00 0.00 4.30
672 710 1.011595 TGTAAGCTCCTCCTCCTCCT 58.988 55.000 0.00 0.00 0.00 3.69
674 712 0.183971 TAAGCTCCTCCTCCTCCTCG 59.816 60.000 0.00 0.00 0.00 4.63
675 713 1.869824 AAGCTCCTCCTCCTCCTCGT 61.870 60.000 0.00 0.00 0.00 4.18
676 714 1.826487 GCTCCTCCTCCTCCTCGTC 60.826 68.421 0.00 0.00 0.00 4.20
688 733 0.810426 TCCTCGTCGTCGATCTCCTG 60.810 60.000 5.00 0.00 45.21 3.86
689 734 1.010574 CTCGTCGTCGATCTCCTGC 60.011 63.158 5.00 0.00 45.21 4.85
690 735 1.433053 CTCGTCGTCGATCTCCTGCT 61.433 60.000 5.00 0.00 45.21 4.24
691 736 1.297967 CGTCGTCGATCTCCTGCTG 60.298 63.158 0.00 0.00 39.71 4.41
713 758 0.971959 TGCTGCAAACATCCCATCCC 60.972 55.000 0.00 0.00 0.00 3.85
743 788 1.492176 ACCAATCTCATTCCCATCGCT 59.508 47.619 0.00 0.00 0.00 4.93
753 798 2.121538 CCCATCGCTCGTCTCCTCA 61.122 63.158 0.00 0.00 0.00 3.86
754 799 1.459455 CCCATCGCTCGTCTCCTCAT 61.459 60.000 0.00 0.00 0.00 2.90
756 801 0.665298 CATCGCTCGTCTCCTCATCA 59.335 55.000 0.00 0.00 0.00 3.07
828 887 6.427441 GTCTCCATCCCTTTCTTTATTTCCT 58.573 40.000 0.00 0.00 0.00 3.36
830 889 7.067615 GTCTCCATCCCTTTCTTTATTTCCTTC 59.932 40.741 0.00 0.00 0.00 3.46
832 891 5.363868 CCATCCCTTTCTTTATTTCCTTCCC 59.636 44.000 0.00 0.00 0.00 3.97
833 892 4.942944 TCCCTTTCTTTATTTCCTTCCCC 58.057 43.478 0.00 0.00 0.00 4.81
834 893 4.610703 TCCCTTTCTTTATTTCCTTCCCCT 59.389 41.667 0.00 0.00 0.00 4.79
881 940 1.795768 TGTCTTGCTTTACTGCTCCG 58.204 50.000 0.00 0.00 0.00 4.63
911 970 5.178438 CGTTTTCTGAGCTAGCTTTCTTTCT 59.822 40.000 20.42 0.00 0.00 2.52
912 971 6.293135 CGTTTTCTGAGCTAGCTTTCTTTCTT 60.293 38.462 20.42 0.00 0.00 2.52
913 972 7.421599 GTTTTCTGAGCTAGCTTTCTTTCTTT 58.578 34.615 20.42 0.00 0.00 2.52
914 973 6.793492 TTCTGAGCTAGCTTTCTTTCTTTC 57.207 37.500 20.42 2.33 0.00 2.62
996 1064 3.028094 AGCGGAGGTCCAGTATAAAGA 57.972 47.619 0.00 0.00 35.14 2.52
997 1065 3.577919 AGCGGAGGTCCAGTATAAAGAT 58.422 45.455 0.00 0.00 35.14 2.40
998 1066 3.574826 AGCGGAGGTCCAGTATAAAGATC 59.425 47.826 0.00 0.00 35.14 2.75
999 1067 3.612004 GCGGAGGTCCAGTATAAAGATCG 60.612 52.174 0.00 0.00 35.14 3.69
1290 1361 2.670934 GAGCAGCACCACCACCAG 60.671 66.667 0.00 0.00 0.00 4.00
1536 1607 4.802051 TTCTGCAGCATCCCCGCC 62.802 66.667 9.47 0.00 0.00 6.13
1702 1773 2.893637 TCGAAGAGGTTTGCATAGCTC 58.106 47.619 23.61 23.61 41.74 4.09
1703 1774 1.936547 CGAAGAGGTTTGCATAGCTCC 59.063 52.381 26.17 14.75 42.25 4.70
1704 1775 2.677902 CGAAGAGGTTTGCATAGCTCCA 60.678 50.000 26.17 0.00 42.25 3.86
1705 1776 3.549794 GAAGAGGTTTGCATAGCTCCAT 58.450 45.455 26.17 18.28 42.25 3.41
1706 1777 4.708177 GAAGAGGTTTGCATAGCTCCATA 58.292 43.478 26.17 0.00 42.25 2.74
1707 1778 4.348863 AGAGGTTTGCATAGCTCCATAG 57.651 45.455 26.17 0.00 42.25 2.23
1730 1801 5.006358 AGCTAATTAACACGCTGATTAACCG 59.994 40.000 0.00 0.00 0.00 4.44
1737 1808 0.802994 CGCTGATTAACCGCCACGTA 60.803 55.000 0.00 0.00 0.00 3.57
1761 1832 4.812476 CGCTCACGCCGGATTCCA 62.812 66.667 5.05 0.00 0.00 3.53
1771 1842 2.661866 GGATTCCACGGCCGATCG 60.662 66.667 35.90 19.36 0.00 3.69
1804 1875 3.423154 GCCTTGCGTTCGTCAGGG 61.423 66.667 11.61 11.34 34.22 4.45
1997 2068 1.000717 GCTGCAGGTCTAGCTACTAGC 60.001 57.143 17.12 0.00 42.84 3.42
2042 2113 4.798682 CCCCTACGCCCACTCCCT 62.799 72.222 0.00 0.00 0.00 4.20
2043 2114 3.155167 CCCTACGCCCACTCCCTC 61.155 72.222 0.00 0.00 0.00 4.30
2046 2117 2.043248 TACGCCCACTCCCTCCTC 60.043 66.667 0.00 0.00 0.00 3.71
2047 2118 2.575455 CTACGCCCACTCCCTCCTCT 62.575 65.000 0.00 0.00 0.00 3.69
2048 2119 1.284111 TACGCCCACTCCCTCCTCTA 61.284 60.000 0.00 0.00 0.00 2.43
2049 2120 1.830408 CGCCCACTCCCTCCTCTAG 60.830 68.421 0.00 0.00 0.00 2.43
2050 2121 2.137528 GCCCACTCCCTCCTCTAGC 61.138 68.421 0.00 0.00 0.00 3.42
2073 2156 5.221048 GCTCTTTCTCTCTCCATGACTCTAC 60.221 48.000 0.00 0.00 0.00 2.59
2076 2159 3.127250 TCTCTCTCCATGACTCTACCCT 58.873 50.000 0.00 0.00 0.00 4.34
2077 2160 3.529734 TCTCTCTCCATGACTCTACCCTT 59.470 47.826 0.00 0.00 0.00 3.95
2078 2161 3.888930 CTCTCTCCATGACTCTACCCTTC 59.111 52.174 0.00 0.00 0.00 3.46
2079 2162 3.529734 TCTCTCCATGACTCTACCCTTCT 59.470 47.826 0.00 0.00 0.00 2.85
2080 2163 3.636300 CTCTCCATGACTCTACCCTTCTG 59.364 52.174 0.00 0.00 0.00 3.02
2111 2194 1.214062 GGACTCGCAGTCTCACAGG 59.786 63.158 13.59 0.00 44.46 4.00
2112 2195 1.528292 GGACTCGCAGTCTCACAGGT 61.528 60.000 13.59 0.00 44.46 4.00
2138 2221 1.169661 ACCATGGCGACGCAAGAAAA 61.170 50.000 23.09 0.00 43.62 2.29
2139 2222 0.039617 CCATGGCGACGCAAGAAAAA 60.040 50.000 23.09 0.00 43.62 1.94
2163 2246 1.600636 GCACTTGTGCAGGCCACTA 60.601 57.895 19.36 0.00 44.92 2.74
2167 2250 0.322975 CTTGTGCAGGCCACTACTCT 59.677 55.000 5.01 0.00 44.92 3.24
2181 2264 3.055328 ACTACTCTACTCTCCCCCTACC 58.945 54.545 0.00 0.00 0.00 3.18
2182 2265 2.307032 ACTCTACTCTCCCCCTACCT 57.693 55.000 0.00 0.00 0.00 3.08
2183 2266 2.587053 ACTCTACTCTCCCCCTACCTT 58.413 52.381 0.00 0.00 0.00 3.50
2199 2282 0.447801 CCTTCTTCGGCCGTTTCATG 59.552 55.000 27.15 11.97 0.00 3.07
2200 2283 0.447801 CTTCTTCGGCCGTTTCATGG 59.552 55.000 27.15 8.52 0.00 3.66
2201 2284 0.035598 TTCTTCGGCCGTTTCATGGA 59.964 50.000 27.15 10.68 0.00 3.41
2259 2346 2.223572 ACTGCTTTCGTTGCCTTTCTTG 60.224 45.455 0.00 0.00 0.00 3.02
2263 2350 3.242936 GCTTTCGTTGCCTTTCTTGTGTA 60.243 43.478 0.00 0.00 0.00 2.90
2264 2351 4.556699 GCTTTCGTTGCCTTTCTTGTGTAT 60.557 41.667 0.00 0.00 0.00 2.29
2265 2352 5.334569 GCTTTCGTTGCCTTTCTTGTGTATA 60.335 40.000 0.00 0.00 0.00 1.47
2291 2382 6.045318 ACTTCGATCTACAGTCCAATTCATG 58.955 40.000 0.00 0.00 0.00 3.07
2355 2446 3.276857 CTTAGGTGTCTGTAGCCTCGTA 58.723 50.000 0.00 0.00 34.07 3.43
2356 2447 1.461559 AGGTGTCTGTAGCCTCGTAC 58.538 55.000 0.00 0.00 0.00 3.67
2357 2448 0.098376 GGTGTCTGTAGCCTCGTACG 59.902 60.000 9.53 9.53 0.00 3.67
2358 2449 0.801251 GTGTCTGTAGCCTCGTACGT 59.199 55.000 16.05 0.00 0.00 3.57
2400 2491 6.331369 GCTAGAGCTAGTCAAGATCAAGAT 57.669 41.667 6.41 0.00 43.38 2.40
2436 2527 1.673400 CGAGAGAAGCTAGCTACAGCA 59.327 52.381 19.70 0.00 44.35 4.41
2437 2528 2.286950 CGAGAGAAGCTAGCTACAGCAG 60.287 54.545 19.70 5.22 44.35 4.24
2451 2542 2.983229 ACAGCAGCGATCAGAATTTCT 58.017 42.857 0.00 0.00 0.00 2.52
2452 2543 2.676839 ACAGCAGCGATCAGAATTTCTG 59.323 45.455 18.49 18.49 45.59 3.02
2494 2585 4.757149 GGTGACTTGTGAGCTTAATGAAGT 59.243 41.667 0.00 0.00 34.90 3.01
2497 2588 6.647067 GTGACTTGTGAGCTTAATGAAGTACT 59.353 38.462 0.00 0.00 34.90 2.73
2554 2645 2.412605 GTACAGGAGGTACCGCGAT 58.587 57.895 8.23 0.00 45.43 4.58
2927 3018 2.959030 CACCCGTAAGAGATGATCCTCA 59.041 50.000 0.62 0.00 43.02 3.86
2932 3023 5.478679 CCCGTAAGAGATGATCCTCATTACT 59.521 44.000 16.61 4.20 36.91 2.24
2942 3033 7.570607 AGATGATCCTCATTACTTAAACCCTCT 59.429 37.037 0.62 0.00 37.20 3.69
2943 3034 7.510675 TGATCCTCATTACTTAAACCCTCTT 57.489 36.000 0.00 0.00 0.00 2.85
2944 3035 8.618240 TGATCCTCATTACTTAAACCCTCTTA 57.382 34.615 0.00 0.00 0.00 2.10
2945 3036 9.053472 TGATCCTCATTACTTAAACCCTCTTAA 57.947 33.333 0.00 0.00 0.00 1.85
2986 3077 7.659652 AAGAAGAAGATTAACTGTCTTTCCG 57.340 36.000 0.00 0.00 36.13 4.30
3011 3102 2.917701 TGCATTTCGTGGCATGTTAG 57.082 45.000 6.60 0.00 34.58 2.34
3022 3114 7.246674 TCGTGGCATGTTAGAAGATTAATTC 57.753 36.000 6.60 0.00 0.00 2.17
3027 3119 9.466497 TGGCATGTTAGAAGATTAATTCTCTTT 57.534 29.630 5.78 0.45 40.08 2.52
3041 3133 3.844577 TCTCTTTCTACAGCACCGTAC 57.155 47.619 0.00 0.00 0.00 3.67
3042 3134 3.418995 TCTCTTTCTACAGCACCGTACT 58.581 45.455 0.00 0.00 0.00 2.73
3043 3135 4.582869 TCTCTTTCTACAGCACCGTACTA 58.417 43.478 0.00 0.00 0.00 1.82
3044 3136 4.394300 TCTCTTTCTACAGCACCGTACTAC 59.606 45.833 0.00 0.00 0.00 2.73
3045 3137 3.125829 TCTTTCTACAGCACCGTACTACG 59.874 47.826 1.32 1.32 42.11 3.51
3046 3138 2.385013 TCTACAGCACCGTACTACGA 57.615 50.000 10.27 0.00 46.05 3.43
3047 3139 2.274437 TCTACAGCACCGTACTACGAG 58.726 52.381 10.27 3.75 46.05 4.18
3048 3140 2.005451 CTACAGCACCGTACTACGAGT 58.995 52.381 10.27 3.86 46.05 4.18
3049 3141 2.099141 ACAGCACCGTACTACGAGTA 57.901 50.000 10.27 0.00 46.05 2.59
3085 3282 6.500684 AGATTAACGTGCATTGTCAGAAAT 57.499 33.333 0.00 0.00 0.00 2.17
3115 3312 7.873739 AATTCGAATTGAACAGGTGAATTTC 57.126 32.000 22.16 0.00 40.00 2.17
3127 3324 3.120199 AGGTGAATTTCGTTGATCGCTTG 60.120 43.478 0.00 0.00 39.67 4.01
3175 3372 2.097142 CAGCTAGCACATCCAAAGAAGC 59.903 50.000 18.83 0.00 0.00 3.86
3179 3376 2.157738 AGCACATCCAAAGAAGCACTC 58.842 47.619 0.00 0.00 0.00 3.51
3207 3409 5.457140 TGATTAGTTTGCACGAAATGAACC 58.543 37.500 0.00 0.00 0.00 3.62
3212 3414 4.213482 AGTTTGCACGAAATGAACCTAGAC 59.787 41.667 0.00 0.00 0.00 2.59
3222 3424 7.041984 ACGAAATGAACCTAGACTCTTGTTTTC 60.042 37.037 0.00 0.00 0.00 2.29
3227 3433 8.575649 TGAACCTAGACTCTTGTTTTCTTTTT 57.424 30.769 0.00 0.00 0.00 1.94
3298 3508 2.097160 GTGCGACATCTGCTTGCG 59.903 61.111 0.00 0.00 0.00 4.85
3320 3530 5.461078 GCGGAAGATGCTAACGAACTAAATA 59.539 40.000 0.00 0.00 0.00 1.40
3334 3544 9.749490 AACGAACTAAATATACATGTTTGAACG 57.251 29.630 2.30 1.25 0.00 3.95
3367 3577 4.111198 CTCAAGAGTGTGATCCTCATTCG 58.889 47.826 0.00 0.00 0.00 3.34
3403 3613 5.540911 CCTTGTGTTTTATTCTGTGGCATT 58.459 37.500 0.00 0.00 0.00 3.56
3443 3653 9.294614 TGCCATATTTGTCTTGCATTACATATA 57.705 29.630 11.68 11.68 0.00 0.86
3487 3700 5.754890 AGCTGTTTTGGCTTGATTTAACTTG 59.245 36.000 0.00 0.00 36.56 3.16
3490 3703 7.096065 GCTGTTTTGGCTTGATTTAACTTGTAG 60.096 37.037 0.00 0.00 0.00 2.74
3495 3708 9.691362 TTTGGCTTGATTTAACTTGTAGAATTC 57.309 29.630 0.00 0.00 0.00 2.17
3519 3732 6.323739 TCTTTCCCTTAATTTTGTGAAGCTGT 59.676 34.615 0.00 0.00 0.00 4.40
3520 3733 5.452078 TCCCTTAATTTTGTGAAGCTGTG 57.548 39.130 0.00 0.00 0.00 3.66
3573 3788 5.265290 TCCTTCGTATGTCCCCATCTATA 57.735 43.478 0.00 0.00 32.29 1.31
3574 3789 5.262009 TCCTTCGTATGTCCCCATCTATAG 58.738 45.833 0.00 0.00 32.29 1.31
3575 3790 5.014860 TCCTTCGTATGTCCCCATCTATAGA 59.985 44.000 4.57 4.57 32.29 1.98
3576 3791 5.894393 CCTTCGTATGTCCCCATCTATAGAT 59.106 44.000 9.57 9.57 34.56 1.98
3606 3821 7.550551 TCATTTTGCTTATGTTCACTCTCCTAG 59.449 37.037 0.00 0.00 0.00 3.02
3607 3822 6.605471 TTTGCTTATGTTCACTCTCCTAGA 57.395 37.500 0.00 0.00 0.00 2.43
3608 3823 6.605471 TTGCTTATGTTCACTCTCCTAGAA 57.395 37.500 0.00 0.00 0.00 2.10
3613 3828 9.601217 GCTTATGTTCACTCTCCTAGAATTTTA 57.399 33.333 0.00 0.00 0.00 1.52
3696 3912 4.541973 ATTCATATGCGGACAGATGCTA 57.458 40.909 0.00 0.00 43.69 3.49
3742 3958 5.819991 AGAATGTCCACATCAAATACCACT 58.180 37.500 0.00 0.00 35.10 4.00
3749 3965 4.396166 CCACATCAAATACCACTCTTGTCC 59.604 45.833 0.00 0.00 0.00 4.02
3756 3972 1.645710 ACCACTCTTGTCCTGTAGGG 58.354 55.000 0.00 0.00 35.41 3.53
3793 4017 7.579589 TGCATTTACACATATGAACAAAAGC 57.420 32.000 10.38 13.36 0.00 3.51
3951 4182 5.707242 TGTAGACTTGTAACCTCTCACTG 57.293 43.478 0.00 0.00 0.00 3.66
4078 4342 3.468140 GCCAGGTACGTCCTCCCC 61.468 72.222 0.00 0.00 46.24 4.81
4104 4368 3.259374 TCACTCCTCCACAGAATCAGTTC 59.741 47.826 0.00 0.00 34.46 3.01
4126 4390 4.458989 TCATCATCACATGATCGGTCGATA 59.541 41.667 5.81 0.00 46.62 2.92
4172 4450 6.698766 AGCACTTGCAGAAAGAAAAATGTTAG 59.301 34.615 3.62 0.00 45.16 2.34
4250 4528 5.002468 CACATCGTAATCATTGCGTTGTTTC 59.998 40.000 18.44 0.00 45.00 2.78
4437 4719 4.666071 CGTACGCACGTTCGTTTC 57.334 55.556 19.90 11.48 43.31 2.78
4438 4720 1.838754 CGTACGCACGTTCGTTTCA 59.161 52.632 19.90 0.00 43.31 2.69
4468 4750 2.668280 GCTCGTGAACGTTCAGCCC 61.668 63.158 30.38 17.89 37.98 5.19
4498 4796 0.393673 TTGTGTGTGTGGTGTGGGAG 60.394 55.000 0.00 0.00 0.00 4.30
4505 4803 2.154462 GTGTGGTGTGGGAGAAGATTG 58.846 52.381 0.00 0.00 0.00 2.67
4507 4805 2.644299 TGTGGTGTGGGAGAAGATTGAT 59.356 45.455 0.00 0.00 0.00 2.57
4514 4812 2.749076 TGGGAGAAGATTGATTTGTGCG 59.251 45.455 0.00 0.00 0.00 5.34
4519 4817 1.155889 AGATTGATTTGTGCGACGCA 58.844 45.000 20.50 20.50 35.60 5.24
4520 4818 1.739466 AGATTGATTTGTGCGACGCAT 59.261 42.857 27.23 9.97 41.91 4.73
4521 4819 1.841944 GATTGATTTGTGCGACGCATG 59.158 47.619 27.23 0.00 41.91 4.06
4522 4820 0.109827 TTGATTTGTGCGACGCATGG 60.110 50.000 27.23 0.00 41.91 3.66
4523 4821 0.952984 TGATTTGTGCGACGCATGGA 60.953 50.000 27.23 14.59 41.91 3.41
4524 4822 0.378257 GATTTGTGCGACGCATGGAT 59.622 50.000 27.23 18.57 41.91 3.41
4525 4823 0.099259 ATTTGTGCGACGCATGGATG 59.901 50.000 27.23 0.00 41.91 3.51
4526 4824 1.921045 TTTGTGCGACGCATGGATGG 61.921 55.000 27.23 0.00 41.91 3.51
4693 4991 1.219664 CGAACCATAACCCAGCGGA 59.780 57.895 0.00 0.00 0.00 5.54
4694 4992 1.087771 CGAACCATAACCCAGCGGAC 61.088 60.000 0.00 0.00 0.00 4.79
5138 5442 4.097361 GGCGGGTTCCACCTCCTC 62.097 72.222 0.00 0.00 38.64 3.71
5158 5462 4.143333 CGACCTCGCCGGGTGATT 62.143 66.667 11.30 0.84 40.06 2.57
5159 5463 2.511600 GACCTCGCCGGGTGATTG 60.512 66.667 11.30 8.13 40.06 2.67
5160 5464 3.000819 ACCTCGCCGGGTGATTGA 61.001 61.111 11.30 0.00 38.30 2.57
5161 5465 2.311688 GACCTCGCCGGGTGATTGAT 62.312 60.000 11.30 0.00 40.06 2.57
5162 5466 1.595382 CCTCGCCGGGTGATTGATC 60.595 63.158 11.30 0.00 0.00 2.92
5163 5467 1.595382 CTCGCCGGGTGATTGATCC 60.595 63.158 11.30 0.00 0.00 3.36
5218 5522 3.546271 CAGTACCACAATGATCACGTACG 59.454 47.826 15.01 15.01 0.00 3.67
5219 5523 2.736144 ACCACAATGATCACGTACGT 57.264 45.000 16.72 16.72 0.00 3.57
5220 5524 2.333926 ACCACAATGATCACGTACGTG 58.666 47.619 36.46 36.46 46.64 4.49
5221 5525 2.288579 ACCACAATGATCACGTACGTGT 60.289 45.455 38.70 28.57 45.55 4.49
5289 5594 1.347564 ACGCGACGACGTCTGATAG 59.652 57.895 24.36 10.52 44.43 2.08
5300 5605 1.059913 GTCTGATAGGGTGATGGGGG 58.940 60.000 0.00 0.00 0.00 5.40
5307 5612 1.148498 GGGTGATGGGGGATCGAAC 59.852 63.158 0.00 0.00 33.17 3.95
5321 5626 0.618458 TCGAACTGAGGATTTGGGGG 59.382 55.000 0.00 0.00 0.00 5.40
5336 5641 1.078988 GGGGATGTGTAAACGGCGA 60.079 57.895 16.62 0.00 0.00 5.54
5885 6206 7.568349 AGAGAACTATGCCAACAGATTTGATA 58.432 34.615 0.00 0.00 0.00 2.15
5981 6303 2.677836 TGGATTTCATAGTGCGTCTTGC 59.322 45.455 0.00 0.00 46.70 4.01
5982 6304 2.032178 GGATTTCATAGTGCGTCTTGCC 59.968 50.000 0.00 0.00 45.60 4.52
5987 6309 2.209064 ATAGTGCGTCTTGCCGTCGT 62.209 55.000 0.00 0.00 45.60 4.34
5988 6310 2.791396 TAGTGCGTCTTGCCGTCGTC 62.791 60.000 0.00 0.00 45.60 4.20
5991 6313 3.164011 CGTCTTGCCGTCGTCGTC 61.164 66.667 0.71 0.00 35.01 4.20
5992 6314 2.050714 GTCTTGCCGTCGTCGTCA 60.051 61.111 0.71 0.00 35.01 4.35
5995 6317 1.797933 CTTGCCGTCGTCGTCAGAG 60.798 63.158 0.71 0.00 35.01 3.35
6002 6334 2.179517 CGTCGTCAGAGGTGCTCC 59.820 66.667 0.00 0.00 0.00 4.70
6023 6355 1.908066 GCGGAGTTACAACAAGGCCG 61.908 60.000 0.00 0.00 40.17 6.13
6056 6388 1.539065 CCTGCCCAGCTTACATCTACG 60.539 57.143 0.00 0.00 0.00 3.51
6064 6396 1.583054 CTTACATCTACGCTTGGGCC 58.417 55.000 0.00 0.00 34.44 5.80
6077 6409 3.368323 CGCTTGGGCCTTCAAATAACAAT 60.368 43.478 4.53 0.00 34.44 2.71
6097 6429 8.986477 AACAATCCACAACTTATTTGCTTATC 57.014 30.769 0.00 0.00 39.01 1.75
6098 6430 7.250569 ACAATCCACAACTTATTTGCTTATCG 58.749 34.615 0.00 0.00 39.01 2.92
6099 6431 5.229921 TCCACAACTTATTTGCTTATCGC 57.770 39.130 0.00 0.00 39.01 4.58
6100 6432 4.028383 CCACAACTTATTTGCTTATCGCG 58.972 43.478 0.00 0.00 43.27 5.87
6101 6433 4.436852 CCACAACTTATTTGCTTATCGCGT 60.437 41.667 5.77 0.00 43.27 6.01
6102 6434 4.723862 CACAACTTATTTGCTTATCGCGTC 59.276 41.667 5.77 0.00 43.27 5.19
6103 6435 4.201783 ACAACTTATTTGCTTATCGCGTCC 60.202 41.667 5.77 0.00 43.27 4.79
6104 6436 3.527533 ACTTATTTGCTTATCGCGTCCA 58.472 40.909 5.77 0.00 43.27 4.02
6105 6437 3.555956 ACTTATTTGCTTATCGCGTCCAG 59.444 43.478 5.77 1.02 43.27 3.86
6106 6438 0.657840 ATTTGCTTATCGCGTCCAGC 59.342 50.000 5.77 12.41 43.27 4.85
6107 6439 1.366111 TTTGCTTATCGCGTCCAGCC 61.366 55.000 18.73 6.32 44.76 4.85
6108 6440 3.330853 GCTTATCGCGTCCAGCCG 61.331 66.667 5.77 0.00 44.76 5.52
6109 6441 2.411701 CTTATCGCGTCCAGCCGA 59.588 61.111 5.77 0.00 44.76 5.54
6110 6442 1.226859 CTTATCGCGTCCAGCCGAA 60.227 57.895 5.77 0.00 44.76 4.30
6111 6443 1.209275 CTTATCGCGTCCAGCCGAAG 61.209 60.000 5.77 0.00 44.76 3.79
6131 6463 3.551407 GCGTCCTCCCCCTCCATC 61.551 72.222 0.00 0.00 0.00 3.51
6132 6464 2.844839 CGTCCTCCCCCTCCATCC 60.845 72.222 0.00 0.00 0.00 3.51
6133 6465 2.372688 GTCCTCCCCCTCCATCCA 59.627 66.667 0.00 0.00 0.00 3.41
6134 6466 1.768077 GTCCTCCCCCTCCATCCAG 60.768 68.421 0.00 0.00 0.00 3.86
6135 6467 3.174265 CCTCCCCCTCCATCCAGC 61.174 72.222 0.00 0.00 0.00 4.85
6136 6468 3.554342 CTCCCCCTCCATCCAGCG 61.554 72.222 0.00 0.00 0.00 5.18
6140 6472 4.559063 CCCTCCATCCAGCGGCTG 62.559 72.222 22.84 22.84 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.584250 CTCGTGTGCCGACGTACGT 62.584 63.158 23.04 23.04 41.60 3.57
53 55 6.174720 TCTCCTGGGCTATGTATTTTACTG 57.825 41.667 0.00 0.00 0.00 2.74
119 125 4.362476 CCCGGGTTGCTTGCTTGC 62.362 66.667 14.18 0.00 0.00 4.01
120 126 2.597217 TCCCGGGTTGCTTGCTTG 60.597 61.111 22.86 0.00 0.00 4.01
121 127 2.142292 ATCTCCCGGGTTGCTTGCTT 62.142 55.000 22.86 0.00 0.00 3.91
122 128 2.606587 ATCTCCCGGGTTGCTTGCT 61.607 57.895 22.86 0.00 0.00 3.91
123 129 2.044946 ATCTCCCGGGTTGCTTGC 60.045 61.111 22.86 0.00 0.00 4.01
124 130 2.409870 GCATCTCCCGGGTTGCTTG 61.410 63.158 27.41 17.93 32.41 4.01
125 131 2.044946 GCATCTCCCGGGTTGCTT 60.045 61.111 27.41 8.09 32.41 3.91
126 132 4.473520 CGCATCTCCCGGGTTGCT 62.474 66.667 29.60 13.31 32.97 3.91
205 212 0.251916 CCAACTAATCGCCACTGGGA 59.748 55.000 0.00 0.00 37.89 4.37
422 444 2.203750 TTTGGTTGGGCAGGGCAT 59.796 55.556 0.00 0.00 0.00 4.40
470 496 1.680314 CTTTGGGCAAGGAGAGGGC 60.680 63.158 0.00 0.00 0.00 5.19
480 507 2.156098 GTACGGTCATTTCTTTGGGCA 58.844 47.619 0.00 0.00 0.00 5.36
499 526 2.952245 CAGGGTCGAGTCGAACGT 59.048 61.111 23.44 21.47 45.33 3.99
532 559 0.944311 GTACACACAGCCACACGGAG 60.944 60.000 0.00 0.00 0.00 4.63
533 560 1.068417 GTACACACAGCCACACGGA 59.932 57.895 0.00 0.00 0.00 4.69
536 563 1.663695 ACAAGTACACACAGCCACAC 58.336 50.000 0.00 0.00 0.00 3.82
586 623 3.450115 ACTACCCGCGTCAGGAGC 61.450 66.667 4.92 0.00 0.00 4.70
593 630 0.749454 CTACCTACCACTACCCGCGT 60.749 60.000 4.92 0.00 0.00 6.01
597 634 3.560105 CAGTACCTACCTACCACTACCC 58.440 54.545 0.00 0.00 0.00 3.69
657 695 2.279037 GACGAGGAGGAGGAGGAGCT 62.279 65.000 0.00 0.00 0.00 4.09
659 697 1.525077 CGACGAGGAGGAGGAGGAG 60.525 68.421 0.00 0.00 0.00 3.69
660 698 2.254737 GACGACGAGGAGGAGGAGGA 62.255 65.000 0.00 0.00 0.00 3.71
662 700 2.174969 CGACGACGAGGAGGAGGAG 61.175 68.421 0.00 0.00 42.66 3.69
663 701 2.125229 CGACGACGAGGAGGAGGA 60.125 66.667 0.00 0.00 42.66 3.71
664 702 2.125229 TCGACGACGAGGAGGAGG 60.125 66.667 5.75 0.00 43.81 4.30
674 712 1.064946 CCAGCAGGAGATCGACGAC 59.935 63.158 0.00 0.00 36.89 4.34
675 713 2.775856 GCCAGCAGGAGATCGACGA 61.776 63.158 0.00 0.00 36.89 4.20
676 714 2.279120 GCCAGCAGGAGATCGACG 60.279 66.667 0.00 0.00 36.89 5.12
688 733 1.445582 GATGTTTGCAGCAGCCAGC 60.446 57.895 0.00 0.49 46.19 4.85
689 734 1.214589 GGATGTTTGCAGCAGCCAG 59.785 57.895 18.68 0.00 41.62 4.85
690 735 2.277591 GGGATGTTTGCAGCAGCCA 61.278 57.895 22.94 0.00 43.59 4.75
691 736 1.610554 ATGGGATGTTTGCAGCAGCC 61.611 55.000 16.28 16.28 41.30 4.85
713 758 4.280174 GGAATGAGATTGGTGGATGGATTG 59.720 45.833 0.00 0.00 0.00 2.67
743 788 0.395862 GGGAGGTGATGAGGAGACGA 60.396 60.000 0.00 0.00 0.00 4.20
753 798 3.654806 CCATATCTTTCTGGGGAGGTGAT 59.345 47.826 0.00 0.00 0.00 3.06
754 799 3.048600 CCATATCTTTCTGGGGAGGTGA 58.951 50.000 0.00 0.00 0.00 4.02
756 801 1.777272 GCCATATCTTTCTGGGGAGGT 59.223 52.381 0.00 0.00 32.90 3.85
828 887 3.010226 CGAGAGGGAGGGAGGGGAA 62.010 68.421 0.00 0.00 0.00 3.97
856 915 2.229792 CAGTAAAGCAAGACAAGGGCA 58.770 47.619 0.00 0.00 0.00 5.36
881 940 3.187432 AGCTAGCTCAGAAAACGAAAAGC 59.813 43.478 12.68 0.00 0.00 3.51
926 985 0.033504 CAATCTATGGACGGACGGGG 59.966 60.000 0.00 0.00 0.00 5.73
983 1051 3.921021 CGCCATCGATCTTTATACTGGAC 59.079 47.826 0.00 0.00 38.10 4.02
996 1064 2.356313 GGATCGTGCGCCATCGAT 60.356 61.111 24.21 24.21 47.00 3.59
997 1065 4.585526 GGGATCGTGCGCCATCGA 62.586 66.667 18.27 18.27 40.28 3.59
998 1066 4.889856 TGGGATCGTGCGCCATCG 62.890 66.667 4.18 7.73 39.07 3.84
999 1067 2.969238 CTGGGATCGTGCGCCATC 60.969 66.667 4.18 3.53 0.00 3.51
1153 1224 2.035626 CCTGGCCCCGAACATGTT 59.964 61.111 11.78 11.78 0.00 2.71
1281 1352 4.584518 TGCTGGTGCTGGTGGTGG 62.585 66.667 0.00 0.00 40.48 4.61
1517 1588 2.825836 CGGGGATGCTGCAGAACC 60.826 66.667 20.43 16.07 0.00 3.62
1536 1607 2.935955 GCCTTGTTGTCGGTGTCG 59.064 61.111 0.00 0.00 37.82 4.35
1547 1618 2.985847 GCTTCTTGGGCGCCTTGT 60.986 61.111 28.56 0.00 0.00 3.16
1671 1742 4.392921 AACCTCTTCGATCATGGTGTAG 57.607 45.455 0.00 0.00 0.00 2.74
1702 1773 6.545504 AATCAGCGTGTTAATTAGCTATGG 57.454 37.500 0.00 0.00 37.94 2.74
1703 1774 8.009974 GGTTAATCAGCGTGTTAATTAGCTATG 58.990 37.037 0.00 0.00 37.94 2.23
1704 1775 7.095774 CGGTTAATCAGCGTGTTAATTAGCTAT 60.096 37.037 0.00 0.00 41.69 2.97
1705 1776 6.199531 CGGTTAATCAGCGTGTTAATTAGCTA 59.800 38.462 0.83 0.00 41.69 3.32
1706 1777 5.006358 CGGTTAATCAGCGTGTTAATTAGCT 59.994 40.000 0.83 0.00 41.69 3.32
1707 1778 5.195379 CGGTTAATCAGCGTGTTAATTAGC 58.805 41.667 0.00 0.00 41.69 3.09
1730 1801 1.515736 GAGCGGTGTAGTACGTGGC 60.516 63.158 0.00 0.00 0.00 5.01
1761 1832 3.206957 TGATCGACGATCGGCCGT 61.207 61.111 27.66 12.96 46.43 5.68
1771 1842 1.810030 GGCTTGACCCGTGATCGAC 60.810 63.158 0.00 0.00 39.71 4.20
1804 1875 0.250467 TCCAAGAAGCTGGTGCAGTC 60.250 55.000 0.00 0.00 42.74 3.51
2042 2113 3.525609 TGGAGAGAGAAAGAGCTAGAGGA 59.474 47.826 0.00 0.00 0.00 3.71
2043 2114 3.897239 TGGAGAGAGAAAGAGCTAGAGG 58.103 50.000 0.00 0.00 0.00 3.69
2046 2117 4.889409 AGTCATGGAGAGAGAAAGAGCTAG 59.111 45.833 0.00 0.00 0.00 3.42
2047 2118 4.865905 AGTCATGGAGAGAGAAAGAGCTA 58.134 43.478 0.00 0.00 0.00 3.32
2048 2119 3.701040 GAGTCATGGAGAGAGAAAGAGCT 59.299 47.826 0.00 0.00 0.00 4.09
2049 2120 3.701040 AGAGTCATGGAGAGAGAAAGAGC 59.299 47.826 0.00 0.00 0.00 4.09
2050 2121 5.299279 GGTAGAGTCATGGAGAGAGAAAGAG 59.701 48.000 0.00 0.00 0.00 2.85
2073 2156 0.752009 ATGCATGCAGAGCAGAAGGG 60.752 55.000 26.69 0.00 46.36 3.95
2076 2159 0.034863 TCCATGCATGCAGAGCAGAA 60.035 50.000 26.69 0.00 46.36 3.02
2077 2160 0.746923 GTCCATGCATGCAGAGCAGA 60.747 55.000 26.69 14.19 46.36 4.26
2078 2161 0.748367 AGTCCATGCATGCAGAGCAG 60.748 55.000 26.69 12.11 46.36 4.24
2080 2163 1.773054 CGAGTCCATGCATGCAGAGC 61.773 60.000 26.69 15.18 0.00 4.09
2111 2194 1.137404 GTCGCCATGGTGCAATGAC 59.863 57.895 20.97 9.31 0.00 3.06
2112 2195 2.397754 CGTCGCCATGGTGCAATGA 61.398 57.895 20.97 0.00 0.00 2.57
2163 2246 2.307032 AGGTAGGGGGAGAGTAGAGT 57.693 55.000 0.00 0.00 0.00 3.24
2167 2250 2.091994 CGAAGAAGGTAGGGGGAGAGTA 60.092 54.545 0.00 0.00 0.00 2.59
2181 2264 0.447801 CCATGAAACGGCCGAAGAAG 59.552 55.000 35.90 16.21 0.00 2.85
2182 2265 0.035598 TCCATGAAACGGCCGAAGAA 59.964 50.000 35.90 15.20 0.00 2.52
2183 2266 0.251916 ATCCATGAAACGGCCGAAGA 59.748 50.000 35.90 16.61 0.00 2.87
2259 2346 8.320396 TGGACTGTAGATCGAAGTATATACAC 57.680 38.462 15.18 7.64 31.93 2.90
2263 2350 9.078990 TGAATTGGACTGTAGATCGAAGTATAT 57.921 33.333 0.00 0.00 0.00 0.86
2264 2351 8.459911 TGAATTGGACTGTAGATCGAAGTATA 57.540 34.615 0.00 0.00 0.00 1.47
2265 2352 7.348080 TGAATTGGACTGTAGATCGAAGTAT 57.652 36.000 0.00 0.00 0.00 2.12
2355 2446 1.028330 TGCGTGCCTAGCTAGTACGT 61.028 55.000 31.15 0.00 35.67 3.57
2356 2447 0.591741 GTGCGTGCCTAGCTAGTACG 60.592 60.000 29.01 29.01 36.05 3.67
2357 2448 0.454600 TGTGCGTGCCTAGCTAGTAC 59.545 55.000 19.31 15.65 35.28 2.73
2358 2449 0.738975 CTGTGCGTGCCTAGCTAGTA 59.261 55.000 19.31 5.48 35.28 1.82
2400 2491 2.351418 CTCTCGTGCAACAGTGTTTGAA 59.649 45.455 5.57 0.00 35.74 2.69
2451 2542 0.937304 GTGAAGAAACAGCTGCGACA 59.063 50.000 15.27 3.13 0.00 4.35
2452 2543 0.111089 CGTGAAGAAACAGCTGCGAC 60.111 55.000 15.27 5.02 0.00 5.19
2494 2585 2.589720 TCGAGTCAAACACAGGGAGTA 58.410 47.619 0.00 0.00 0.00 2.59
2497 2588 1.001974 CCATCGAGTCAAACACAGGGA 59.998 52.381 0.00 0.00 0.00 4.20
2551 2642 4.592192 ACCGCCCGCATCTGATCG 62.592 66.667 0.00 0.00 0.00 3.69
2737 2828 2.286885 TCCCCCTTGGTCATCCCC 60.287 66.667 0.00 0.00 34.77 4.81
2927 3018 9.623000 ACGCAATATTAAGAGGGTTTAAGTAAT 57.377 29.630 0.00 0.00 0.00 1.89
2932 3023 7.049133 TGCTACGCAATATTAAGAGGGTTTAA 58.951 34.615 0.00 0.00 34.76 1.52
2942 3033 7.655732 TCTTCTTAGCATGCTACGCAATATTAA 59.344 33.333 26.87 11.94 43.62 1.40
2943 3034 7.151976 TCTTCTTAGCATGCTACGCAATATTA 58.848 34.615 26.87 8.27 43.62 0.98
2944 3035 5.991606 TCTTCTTAGCATGCTACGCAATATT 59.008 36.000 26.87 0.00 43.62 1.28
2945 3036 5.541845 TCTTCTTAGCATGCTACGCAATAT 58.458 37.500 26.87 0.79 43.62 1.28
2946 3037 4.944048 TCTTCTTAGCATGCTACGCAATA 58.056 39.130 26.87 10.48 43.62 1.90
2950 3041 3.448686 TCTTCTTCTTAGCATGCTACGC 58.551 45.455 26.87 0.00 0.00 4.42
2954 3045 7.108847 ACAGTTAATCTTCTTCTTAGCATGCT 58.891 34.615 25.99 25.99 0.00 3.79
2960 3051 8.865001 CGGAAAGACAGTTAATCTTCTTCTTAG 58.135 37.037 0.00 0.00 35.31 2.18
2968 3059 4.041198 TGGGACGGAAAGACAGTTAATCTT 59.959 41.667 0.00 0.00 38.05 2.40
2969 3060 3.581332 TGGGACGGAAAGACAGTTAATCT 59.419 43.478 0.00 0.00 0.00 2.40
2970 3061 3.934068 TGGGACGGAAAGACAGTTAATC 58.066 45.455 0.00 0.00 0.00 1.75
2986 3077 1.139520 GCCACGAAATGCATGGGAC 59.860 57.895 0.00 0.00 33.81 4.46
3011 3102 8.608317 GGTGCTGTAGAAAGAGAATTAATCTTC 58.392 37.037 5.99 0.00 38.96 2.87
3022 3114 3.851976 AGTACGGTGCTGTAGAAAGAG 57.148 47.619 0.00 0.00 0.00 2.85
3027 3119 2.274437 CTCGTAGTACGGTGCTGTAGA 58.726 52.381 21.85 4.80 42.81 2.59
3115 3312 3.536158 TTTCTTTCCAAGCGATCAACG 57.464 42.857 0.00 0.00 45.66 4.10
3135 3332 9.057089 GCTAGCTGTTAATTAATCCTGTGTAAT 57.943 33.333 7.70 0.00 0.00 1.89
3139 3336 6.316140 TGTGCTAGCTGTTAATTAATCCTGTG 59.684 38.462 17.23 0.00 0.00 3.66
3141 3338 6.925610 TGTGCTAGCTGTTAATTAATCCTG 57.074 37.500 17.23 0.00 0.00 3.86
3175 3372 5.061684 TCGTGCAAACTAATCAATACGAGTG 59.938 40.000 0.00 0.00 34.83 3.51
3179 3376 6.958752 TCATTTCGTGCAAACTAATCAATACG 59.041 34.615 0.00 0.00 0.00 3.06
3227 3433 9.519191 TCCTGAATCAATTCTAGTTCATTTTCA 57.481 29.630 4.50 0.00 37.67 2.69
3245 3451 6.222038 TGTCTATGGTACTTGTCCTGAATC 57.778 41.667 0.00 0.00 0.00 2.52
3283 3493 2.301902 CTTCCGCAAGCAGATGTCGC 62.302 60.000 0.00 0.00 0.00 5.19
3286 3496 1.376543 CATCTTCCGCAAGCAGATGT 58.623 50.000 10.87 0.00 43.39 3.06
3298 3508 9.472361 TGTATATTTAGTTCGTTAGCATCTTCC 57.528 33.333 0.00 0.00 0.00 3.46
3320 3530 6.602179 CATCAGTTGACGTTCAAACATGTAT 58.398 36.000 0.00 0.00 38.22 2.29
3367 3577 1.880027 ACACAAGGCCAGACGATTTTC 59.120 47.619 5.01 0.00 0.00 2.29
3403 3613 1.344953 ATGGCACGGGGAGAGCAATA 61.345 55.000 0.00 0.00 38.23 1.90
3459 3669 7.447238 AGTTAAATCAAGCCAAAACAGCTAGTA 59.553 33.333 0.00 0.00 40.49 1.82
3490 3703 8.712363 GCTTCACAAAATTAAGGGAAAGAATTC 58.288 33.333 0.00 0.00 34.66 2.17
3495 3708 6.421801 CACAGCTTCACAAAATTAAGGGAAAG 59.578 38.462 0.00 0.00 0.00 2.62
3532 3745 5.957771 AGGAACCTAAGTTGCATCAGATA 57.042 39.130 0.00 0.00 46.06 1.98
3573 3788 7.040201 AGTGAACATAAGCAAAATGACACATCT 60.040 33.333 18.54 6.62 37.48 2.90
3574 3789 7.086376 AGTGAACATAAGCAAAATGACACATC 58.914 34.615 18.54 0.00 37.48 3.06
3575 3790 6.985117 AGTGAACATAAGCAAAATGACACAT 58.015 32.000 18.54 0.00 37.48 3.21
3576 3791 6.262944 AGAGTGAACATAAGCAAAATGACACA 59.737 34.615 18.54 0.00 37.48 3.72
3580 3795 6.240894 AGGAGAGTGAACATAAGCAAAATGA 58.759 36.000 0.58 0.00 0.00 2.57
3617 3832 7.451566 AGGTGAGTAATTAGGACAGCAATTTTT 59.548 33.333 13.91 0.00 0.00 1.94
3618 3833 6.948309 AGGTGAGTAATTAGGACAGCAATTTT 59.052 34.615 13.91 0.00 0.00 1.82
3619 3834 6.485171 AGGTGAGTAATTAGGACAGCAATTT 58.515 36.000 13.91 0.00 0.00 1.82
3637 3853 6.710744 AGTTGGAAGTTATGTGTTTAGGTGAG 59.289 38.462 0.00 0.00 0.00 3.51
3682 3898 2.682856 GGAAAAATAGCATCTGTCCGCA 59.317 45.455 0.00 0.00 0.00 5.69
3696 3912 9.959721 TTCTAATAACACTGCTAGAGGAAAAAT 57.040 29.630 0.00 0.00 0.00 1.82
3749 3965 9.857656 AAATGCATATATGGAATATCCCTACAG 57.142 33.333 11.23 0.00 39.18 2.74
3792 4016 2.185004 ATGAGGGTAGTGTTGTGTGC 57.815 50.000 0.00 0.00 0.00 4.57
3793 4017 5.995282 TCTTTTATGAGGGTAGTGTTGTGTG 59.005 40.000 0.00 0.00 0.00 3.82
3893 4120 9.102757 CCTAACTCTTGTATGTACGTAGACTTA 57.897 37.037 0.00 0.00 0.00 2.24
3896 4123 7.313951 ACCTAACTCTTGTATGTACGTAGAC 57.686 40.000 0.00 0.00 0.00 2.59
3901 4128 5.867716 AGCAAACCTAACTCTTGTATGTACG 59.132 40.000 0.00 0.00 0.00 3.67
3902 4129 6.034683 CGAGCAAACCTAACTCTTGTATGTAC 59.965 42.308 0.00 0.00 0.00 2.90
3903 4130 6.097356 CGAGCAAACCTAACTCTTGTATGTA 58.903 40.000 0.00 0.00 0.00 2.29
3905 4132 4.929808 ACGAGCAAACCTAACTCTTGTATG 59.070 41.667 0.00 0.00 0.00 2.39
3906 4133 5.148651 ACGAGCAAACCTAACTCTTGTAT 57.851 39.130 0.00 0.00 0.00 2.29
3907 4134 4.595762 ACGAGCAAACCTAACTCTTGTA 57.404 40.909 0.00 0.00 0.00 2.41
3908 4135 3.470645 ACGAGCAAACCTAACTCTTGT 57.529 42.857 0.00 0.00 0.00 3.16
3909 4136 3.560068 ACAACGAGCAAACCTAACTCTTG 59.440 43.478 0.00 0.00 0.00 3.02
3910 4137 3.805207 ACAACGAGCAAACCTAACTCTT 58.195 40.909 0.00 0.00 0.00 2.85
3911 4138 3.470645 ACAACGAGCAAACCTAACTCT 57.529 42.857 0.00 0.00 0.00 3.24
3912 4139 4.385146 GTCTACAACGAGCAAACCTAACTC 59.615 45.833 0.00 0.00 0.00 3.01
3951 4182 2.271800 CGTGCTTCCAAGTCTACATCC 58.728 52.381 0.00 0.00 0.00 3.51
4065 4329 2.038490 AGTGGGGGAGGACGTACC 59.962 66.667 0.00 0.00 39.35 3.34
4072 4336 1.687493 GAGGAGTGAGTGGGGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
4078 4342 1.342074 TTCTGTGGAGGAGTGAGTGG 58.658 55.000 0.00 0.00 0.00 4.00
4157 4435 6.669278 AGGAACTCGCTAACATTTTTCTTTC 58.331 36.000 0.00 0.00 0.00 2.62
4172 4450 6.465084 AGGTAATAATTGGATAGGAACTCGC 58.535 40.000 0.00 0.00 41.75 5.03
4250 4528 0.809636 TATGCGTGGCCAATCGACAG 60.810 55.000 19.07 1.21 0.00 3.51
4436 4718 3.107017 CGAGCACGTGAAGACATGA 57.893 52.632 22.23 0.00 36.88 3.07
4468 4750 6.144854 CACCACACACACAATTAGATTCTTG 58.855 40.000 0.00 0.00 0.00 3.02
4498 4796 2.169179 GCGTCGCACAAATCAATCTTC 58.831 47.619 13.44 0.00 0.00 2.87
4505 4803 0.378257 ATCCATGCGTCGCACAAATC 59.622 50.000 24.34 0.00 43.04 2.17
4507 4805 1.501292 CATCCATGCGTCGCACAAA 59.499 52.632 24.34 10.90 43.04 2.83
4519 4817 0.395686 CGAGACCTGCATCCATCCAT 59.604 55.000 0.00 0.00 0.00 3.41
4520 4818 0.687427 TCGAGACCTGCATCCATCCA 60.687 55.000 0.00 0.00 0.00 3.41
4521 4819 0.465705 TTCGAGACCTGCATCCATCC 59.534 55.000 0.00 0.00 0.00 3.51
4522 4820 1.137872 AGTTCGAGACCTGCATCCATC 59.862 52.381 0.00 0.00 0.00 3.51
4523 4821 1.134580 CAGTTCGAGACCTGCATCCAT 60.135 52.381 0.00 0.00 0.00 3.41
4524 4822 0.247460 CAGTTCGAGACCTGCATCCA 59.753 55.000 0.00 0.00 0.00 3.41
4525 4823 0.460987 CCAGTTCGAGACCTGCATCC 60.461 60.000 0.00 0.00 0.00 3.51
4526 4824 0.247736 ACCAGTTCGAGACCTGCATC 59.752 55.000 0.00 0.00 0.00 3.91
4907 5205 2.979197 CTGCTGCTGGTGCTGAAGC 61.979 63.158 0.00 0.00 37.06 3.86
5163 5467 1.134075 CCAGACTGACCGACGTACG 59.866 63.158 15.01 15.01 42.18 3.67
5218 5522 0.892755 TGATCCCTGGACGTACACAC 59.107 55.000 0.00 0.00 0.00 3.82
5219 5523 1.754803 GATGATCCCTGGACGTACACA 59.245 52.381 0.00 0.00 0.00 3.72
5220 5524 1.754803 TGATGATCCCTGGACGTACAC 59.245 52.381 0.00 0.00 0.00 2.90
5221 5525 2.153034 TGATGATCCCTGGACGTACA 57.847 50.000 0.00 0.00 0.00 2.90
5289 5594 1.148498 GTTCGATCCCCCATCACCC 59.852 63.158 0.00 0.00 0.00 4.61
5300 5605 2.565841 CCCCAAATCCTCAGTTCGATC 58.434 52.381 0.00 0.00 0.00 3.69
5307 5612 1.285962 ACACATCCCCCAAATCCTCAG 59.714 52.381 0.00 0.00 0.00 3.35
5321 5626 1.689352 CCGGTCGCCGTTTACACATC 61.689 60.000 15.38 0.00 46.80 3.06
5651 5968 0.525761 GTGCATTGCCATTGGTACGT 59.474 50.000 6.12 0.00 0.00 3.57
5652 5969 0.179140 GGTGCATTGCCATTGGTACG 60.179 55.000 6.12 0.00 0.00 3.67
5653 5970 0.179140 CGGTGCATTGCCATTGGTAC 60.179 55.000 6.12 0.00 0.00 3.34
5654 5971 1.943116 GCGGTGCATTGCCATTGGTA 61.943 55.000 6.12 0.00 0.00 3.25
5735 6052 5.520288 AGACCAAGATACGAAAATGACATCG 59.480 40.000 0.00 0.00 44.33 3.84
5823 6144 1.293062 ATCCCTCTTGCCTCATGTGT 58.707 50.000 0.00 0.00 0.00 3.72
5851 6172 4.307259 TGGCATAGTTCTCTTCCCCTTAT 58.693 43.478 0.00 0.00 0.00 1.73
5905 6226 8.815141 TGAATAATGTTGACATCTTTGGTTTG 57.185 30.769 0.00 0.00 35.10 2.93
5923 6244 9.775854 TGACATGTTTGGTTTTTCATGAATAAT 57.224 25.926 9.40 0.00 39.68 1.28
5938 6259 6.930164 TCCATCTTTGATTTTGACATGTTTGG 59.070 34.615 0.00 0.00 0.00 3.28
5981 6303 2.176055 CACCTCTGACGACGACGG 59.824 66.667 12.58 0.00 44.46 4.79
5982 6304 2.502080 GCACCTCTGACGACGACG 60.502 66.667 5.58 5.58 45.75 5.12
5987 6309 3.062466 CCGGAGCACCTCTGACGA 61.062 66.667 0.00 0.00 39.05 4.20
5988 6310 4.803426 GCCGGAGCACCTCTGACG 62.803 72.222 5.05 0.00 39.05 4.35
6002 6334 1.908066 GCCTTGTTGTAACTCCGCCG 61.908 60.000 0.00 0.00 0.00 6.46
6010 6342 1.540267 CCCATTCGGCCTTGTTGTAA 58.460 50.000 0.00 0.00 0.00 2.41
6038 6370 0.179084 GCGTAGATGTAAGCTGGGCA 60.179 55.000 0.45 0.00 33.08 5.36
6056 6388 3.676291 TTGTTATTTGAAGGCCCAAGC 57.324 42.857 0.00 0.00 38.76 4.01
6114 6446 3.551407 GATGGAGGGGGAGGACGC 61.551 72.222 0.00 0.00 0.00 5.19
6115 6447 2.844839 GGATGGAGGGGGAGGACG 60.845 72.222 0.00 0.00 0.00 4.79
6116 6448 1.768077 CTGGATGGAGGGGGAGGAC 60.768 68.421 0.00 0.00 0.00 3.85
6117 6449 2.705410 CTGGATGGAGGGGGAGGA 59.295 66.667 0.00 0.00 0.00 3.71
6118 6450 3.174265 GCTGGATGGAGGGGGAGG 61.174 72.222 0.00 0.00 0.00 4.30
6119 6451 3.554342 CGCTGGATGGAGGGGGAG 61.554 72.222 0.00 0.00 0.00 4.30
6123 6455 4.559063 CAGCCGCTGGATGGAGGG 62.559 72.222 12.93 0.00 35.19 4.30


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

AutoCloner maintained by Alex Coulton.