Multiple sequence alignment - TraesCS1B01G417000

Loading Multiple Alignment...

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 TraesCS1B01G417000 chr1B 100.000 4687 0 0 1 4687 641549085 641553771 0.000000e+00 8656.0
1 TraesCS1B01G417000 chr1A 88.929 1951 152 41 1014 2947 557193042 557191139 0.000000e+00 2348.0
2 TraesCS1B01G417000 chr1A 94.257 801 35 9 974 1770 557117022 557117815 0.000000e+00 1214.0
3 TraesCS1B01G417000 chr1A 86.944 1011 93 22 2944 3950 557191111 557190136 0.000000e+00 1099.0
4 TraesCS1B01G417000 chr1A 94.942 692 28 3 3048 3739 557119254 557119938 0.000000e+00 1077.0
5 TraesCS1B01G417000 chr1A 91.290 310 21 4 4015 4319 557120203 557120511 7.250000e-113 418.0
6 TraesCS1B01G417000 chr1A 80.924 498 61 11 2232 2706 557118608 557119094 3.450000e-96 363.0
7 TraesCS1B01G417000 chr1A 89.437 284 20 3 3744 4022 557119905 557120183 2.680000e-92 350.0
8 TraesCS1B01G417000 chr1A 90.476 42 3 1 792 833 373763491 373763451 2.000000e-03 54.7
9 TraesCS1B01G417000 chr1D 91.339 1016 36 12 783 1769 464834914 464835906 0.000000e+00 1341.0
10 TraesCS1B01G417000 chr1D 94.942 692 32 2 3048 3739 464837500 464838188 0.000000e+00 1081.0
11 TraesCS1B01G417000 chr1D 80.042 962 118 37 1777 2706 464836426 464837345 0.000000e+00 645.0
12 TraesCS1B01G417000 chr1D 90.994 322 25 3 4016 4333 464838448 464838769 9.320000e-117 431.0
13 TraesCS1B01G417000 chr1D 87.857 280 31 2 4125 4401 464838768 464839047 4.520000e-85 326.0
14 TraesCS1B01G417000 chr1D 90.476 189 12 3 3847 4031 464838251 464838437 1.300000e-60 244.0
15 TraesCS1B01G417000 chr1D 88.462 182 7 3 4507 4687 464839161 464839329 1.710000e-49 207.0
16 TraesCS1B01G417000 chr2D 94.522 785 40 2 1 782 610931441 610930657 0.000000e+00 1208.0
17 TraesCS1B01G417000 chr3B 93.393 787 49 2 1 784 13424855 13424069 0.000000e+00 1162.0
18 TraesCS1B01G417000 chr3B 84.301 637 100 0 3051 3687 243246053 243246689 1.430000e-174 623.0
19 TraesCS1B01G417000 chr3B 90.670 418 34 4 1042 1458 243244296 243244709 6.850000e-153 551.0
20 TraesCS1B01G417000 chr3B 84.236 203 24 8 4316 4515 22108820 22108623 1.720000e-44 191.0
21 TraesCS1B01G417000 chr3B 83.010 206 27 8 4295 4496 22102362 22102161 3.730000e-41 180.0
22 TraesCS1B01G417000 chr3B 80.591 237 34 12 4285 4515 163346816 163346586 6.240000e-39 172.0
23 TraesCS1B01G417000 chr4A 93.367 784 51 1 1 784 738256464 738255682 0.000000e+00 1158.0
24 TraesCS1B01G417000 chr4A 96.875 32 1 0 789 820 3377317 3377286 2.000000e-03 54.7
25 TraesCS1B01G417000 chr7D 93.231 783 53 0 1 783 63996171 63995389 0.000000e+00 1153.0
26 TraesCS1B01G417000 chr7D 94.000 50 0 2 786 835 223819485 223819439 6.510000e-09 73.1
27 TraesCS1B01G417000 chr2A 93.121 785 51 3 1 782 677957685 677958469 0.000000e+00 1147.0
28 TraesCS1B01G417000 chr4D 93.095 782 53 1 1 782 496434346 496435126 0.000000e+00 1144.0
29 TraesCS1B01G417000 chr3D 92.776 789 51 4 1 783 527510464 527509676 0.000000e+00 1136.0
30 TraesCS1B01G417000 chr3D 92.602 784 58 0 1 784 475107462 475106679 0.000000e+00 1127.0
31 TraesCS1B01G417000 chr3D 83.359 637 106 0 3051 3687 168192560 168193196 1.450000e-164 590.0
32 TraesCS1B01G417000 chr3D 90.909 418 33 4 1042 1458 168190755 168191168 1.470000e-154 556.0
33 TraesCS1B01G417000 chr3D 100.000 30 0 0 791 820 4322357 4322386 6.550000e-04 56.5
34 TraesCS1B01G417000 chr6A 92.811 779 56 0 4 782 608663693 608662915 0.000000e+00 1129.0
35 TraesCS1B01G417000 chr3A 82.418 637 112 0 3051 3687 199695080 199694444 1.470000e-154 556.0
36 TraesCS1B01G417000 chr3A 90.909 418 33 3 1042 1458 199697016 199696603 1.470000e-154 556.0
37 TraesCS1B01G417000 chrUn 84.932 219 28 5 4285 4501 83365761 83365976 2.840000e-52 217.0
38 TraesCS1B01G417000 chr7A 84.475 219 28 6 4285 4501 86137011 86136797 1.320000e-50 211.0
39 TraesCS1B01G417000 chr5B 84.896 192 22 7 4316 4504 507628211 507628024 2.230000e-43 187.0
40 TraesCS1B01G417000 chr5B 84.896 192 22 7 4316 4504 507634578 507634391 2.230000e-43 187.0
41 TraesCS1B01G417000 chr5B 81.281 203 22 8 1043 1245 263521923 263521737 2.920000e-32 150.0
42 TraesCS1B01G417000 chr4B 82.938 211 28 8 4295 4501 658523543 658523749 2.880000e-42 183.0
43 TraesCS1B01G417000 chr4B 89.130 46 2 3 789 833 2217001 2216958 2.000000e-03 54.7
44 TraesCS1B01G417000 chr6B 84.127 189 22 8 4316 4501 52801966 52802149 4.820000e-40 176.0
45 TraesCS1B01G417000 chr6B 91.304 46 1 2 789 834 506720240 506720198 5.060000e-05 60.2
46 TraesCS1B01G417000 chr5D 80.822 219 23 10 1027 1245 240084925 240085124 2.260000e-33 154.0
47 TraesCS1B01G417000 chr5A 88.889 108 11 1 1138 1245 313880091 313879985 1.060000e-26 132.0
48 TraesCS1B01G417000 chr5A 94.286 35 2 0 786 820 635404774 635404808 2.000000e-03 54.7
49 TraesCS1B01G417000 chr6D 89.796 49 2 2 786 834 317479744 317479789 5.060000e-05 60.2


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 TraesCS1B01G417000 chr1B 641549085 641553771 4686 False 8656.000000 8656 100.000000 1 4687 1 chr1B.!!$F1 4686
1 TraesCS1B01G417000 chr1A 557190136 557193042 2906 True 1723.500000 2348 87.936500 1014 3950 2 chr1A.!!$R2 2936
2 TraesCS1B01G417000 chr1A 557117022 557120511 3489 False 684.400000 1214 90.170000 974 4319 5 chr1A.!!$F1 3345
3 TraesCS1B01G417000 chr1D 464834914 464839329 4415 False 610.714286 1341 89.158857 783 4687 7 chr1D.!!$F1 3904
4 TraesCS1B01G417000 chr2D 610930657 610931441 784 True 1208.000000 1208 94.522000 1 782 1 chr2D.!!$R1 781
5 TraesCS1B01G417000 chr3B 13424069 13424855 786 True 1162.000000 1162 93.393000 1 784 1 chr3B.!!$R1 783
6 TraesCS1B01G417000 chr3B 243244296 243246689 2393 False 587.000000 623 87.485500 1042 3687 2 chr3B.!!$F1 2645
7 TraesCS1B01G417000 chr4A 738255682 738256464 782 True 1158.000000 1158 93.367000 1 784 1 chr4A.!!$R2 783
8 TraesCS1B01G417000 chr7D 63995389 63996171 782 True 1153.000000 1153 93.231000 1 783 1 chr7D.!!$R1 782
9 TraesCS1B01G417000 chr2A 677957685 677958469 784 False 1147.000000 1147 93.121000 1 782 1 chr2A.!!$F1 781
10 TraesCS1B01G417000 chr4D 496434346 496435126 780 False 1144.000000 1144 93.095000 1 782 1 chr4D.!!$F1 781
11 TraesCS1B01G417000 chr3D 527509676 527510464 788 True 1136.000000 1136 92.776000 1 783 1 chr3D.!!$R2 782
12 TraesCS1B01G417000 chr3D 475106679 475107462 783 True 1127.000000 1127 92.602000 1 784 1 chr3D.!!$R1 783
13 TraesCS1B01G417000 chr3D 168190755 168193196 2441 False 573.000000 590 87.134000 1042 3687 2 chr3D.!!$F2 2645
14 TraesCS1B01G417000 chr6A 608662915 608663693 778 True 1129.000000 1129 92.811000 4 782 1 chr6A.!!$R1 778
15 TraesCS1B01G417000 chr3A 199694444 199697016 2572 True 556.000000 556 86.663500 1042 3687 2 chr3A.!!$R1 2645

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
267 268 0.460284 CGATTCTGGTTCCTCGGTGG 60.460 60.0 0.00 0.0 37.10 4.61 F
857 870 0.601558 TGGTCGGTACTCTGCAAGTC 59.398 55.0 5.04 0.0 39.55 3.01 F
2164 3091 0.306533 GCGCTGAAACCAAAGACGAA 59.693 50.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 3050 0.593128 AGCGCACTGTCATTTTGTCC 59.407 50.0 11.47 0.0 0.0 4.02 R
2506 3623 0.819259 TGAGGTGCACAAAGACAGGC 60.819 55.0 20.43 0.0 0.0 4.85 R
3753 5050 0.035439 GGCCTTGAAGATCACCGGAA 60.035 55.0 9.46 0.0 0.0 4.30 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
210 211 1.338011 CGAAAATGGTGCAATTGCCCT 60.338 47.619 26.94 11.63 41.18 5.19
267 268 0.460284 CGATTCTGGTTCCTCGGTGG 60.460 60.000 0.00 0.00 37.10 4.61
295 296 2.103143 CTCCGATCAACGCTCGCT 59.897 61.111 0.00 0.00 41.07 4.93
334 335 1.188219 AGACAGGCATCTCCACACGT 61.188 55.000 0.00 0.00 37.29 4.49
350 351 3.064324 GTGCCCGGCTTTGCATCT 61.064 61.111 11.61 0.00 40.07 2.90
395 396 2.685017 ACATGGAGCTCGGAGCCA 60.685 61.111 25.49 17.60 43.77 4.75
400 401 2.261671 GAGCTCGGAGCCAAACGA 59.738 61.111 25.49 0.00 43.77 3.85
586 597 3.952675 CAAGCCACGCGTGCAACT 61.953 61.111 33.17 24.79 30.89 3.16
603 614 6.215845 GTGCAACTGTCTGAATAAAATTGGT 58.784 36.000 0.00 0.00 0.00 3.67
664 675 1.105167 ACGTTGACCTGACGGAGACA 61.105 55.000 1.64 0.00 44.34 3.41
716 727 1.804748 GACTAGGGGCAAAACTGAACG 59.195 52.381 0.00 0.00 0.00 3.95
727 738 2.704725 AACTGAACGCAATTCGCATT 57.295 40.000 0.00 0.00 42.60 3.56
754 765 3.755378 GACAAAACTGAGCAGATGGACAT 59.245 43.478 4.21 0.00 0.00 3.06
762 773 2.429971 GAGCAGATGGACATCACTGAGA 59.570 50.000 14.16 0.00 40.22 3.27
857 870 0.601558 TGGTCGGTACTCTGCAAGTC 59.398 55.000 5.04 0.00 39.55 3.01
924 960 1.153127 ACTCGCGCTAGCTCCTACT 60.153 57.895 13.93 0.00 42.32 2.57
968 1008 4.778143 CACCCAGCGCCCTACCAC 62.778 72.222 2.29 0.00 0.00 4.16
972 1012 4.028490 CAGCGCCCTACCACCCAA 62.028 66.667 2.29 0.00 0.00 4.12
975 1015 3.642503 CGCCCTACCACCCAACCA 61.643 66.667 0.00 0.00 0.00 3.67
976 1016 2.355115 GCCCTACCACCCAACCAG 59.645 66.667 0.00 0.00 0.00 4.00
977 1017 2.355115 CCCTACCACCCAACCAGC 59.645 66.667 0.00 0.00 0.00 4.85
978 1018 2.534396 CCCTACCACCCAACCAGCA 61.534 63.158 0.00 0.00 0.00 4.41
979 1019 1.303317 CCTACCACCCAACCAGCAC 60.303 63.158 0.00 0.00 0.00 4.40
980 1020 1.303317 CTACCACCCAACCAGCACC 60.303 63.158 0.00 0.00 0.00 5.01
1515 1561 7.011857 AGAGTTGTGAGTTCTTCAAACTGAATC 59.988 37.037 0.00 0.00 37.32 2.52
1601 1774 2.288091 TGGTCCATTGCATTTGTGTTCG 60.288 45.455 0.00 0.00 0.00 3.95
1716 2022 8.956426 AGATTCTCTAGTGAACTCTGAACTAAG 58.044 37.037 9.32 0.00 0.00 2.18
1880 2777 7.899178 TTTAGTTTCATAATCTCTGTGCGAA 57.101 32.000 0.00 0.00 0.00 4.70
1949 2852 6.627243 TCGTTTGTCTGTAGCTACATTATGT 58.373 36.000 26.22 2.58 35.36 2.29
1950 2853 7.094631 TCGTTTGTCTGTAGCTACATTATGTT 58.905 34.615 26.22 0.00 35.36 2.71
1958 2862 9.297586 TCTGTAGCTACATTATGTTTTCTTACG 57.702 33.333 26.22 9.31 35.36 3.18
1973 2877 0.948678 TTACGCTTCCCTGCAACAAC 59.051 50.000 0.00 0.00 0.00 3.32
2057 2967 6.449698 ACTGGAGCAAATGTTTATTGACAAG 58.550 36.000 0.00 0.00 32.47 3.16
2066 2976 9.426837 CAAATGTTTATTGACAAGGATCAACAT 57.573 29.630 0.00 1.59 41.29 2.71
2082 2992 7.613022 AGGATCAACATTTCACTGACAACATAT 59.387 33.333 0.00 0.00 0.00 1.78
2088 2998 8.389779 ACATTTCACTGACAACATATAACACA 57.610 30.769 0.00 0.00 0.00 3.72
2089 2999 9.013229 ACATTTCACTGACAACATATAACACAT 57.987 29.630 0.00 0.00 0.00 3.21
2090 3000 9.281075 CATTTCACTGACAACATATAACACATG 57.719 33.333 0.00 0.00 0.00 3.21
2091 3001 8.614469 TTTCACTGACAACATATAACACATGA 57.386 30.769 0.00 0.00 0.00 3.07
2092 3002 8.791327 TTCACTGACAACATATAACACATGAT 57.209 30.769 0.00 0.00 0.00 2.45
2093 3003 9.883142 TTCACTGACAACATATAACACATGATA 57.117 29.630 0.00 0.00 0.00 2.15
2130 3050 6.587608 GGATGCTCACATAACAAAAGGAAAAG 59.412 38.462 0.00 0.00 36.35 2.27
2149 3069 0.593128 GGACAAAATGACAGTGCGCT 59.407 50.000 9.73 0.00 0.00 5.92
2162 3089 0.657368 GTGCGCTGAAACCAAAGACG 60.657 55.000 9.73 0.00 0.00 4.18
2163 3090 0.812014 TGCGCTGAAACCAAAGACGA 60.812 50.000 9.73 0.00 0.00 4.20
2164 3091 0.306533 GCGCTGAAACCAAAGACGAA 59.693 50.000 0.00 0.00 0.00 3.85
2165 3092 1.920272 GCGCTGAAACCAAAGACGAAC 60.920 52.381 0.00 0.00 0.00 3.95
2166 3093 1.597663 CGCTGAAACCAAAGACGAACT 59.402 47.619 0.00 0.00 0.00 3.01
2167 3094 2.798283 CGCTGAAACCAAAGACGAACTA 59.202 45.455 0.00 0.00 0.00 2.24
2168 3095 3.362693 CGCTGAAACCAAAGACGAACTAC 60.363 47.826 0.00 0.00 0.00 2.73
2176 3107 6.359480 ACCAAAGACGAACTACAAAAGAAG 57.641 37.500 0.00 0.00 0.00 2.85
2187 3119 9.884465 CGAACTACAAAAGAAGAAGATGAAAAT 57.116 29.630 0.00 0.00 0.00 1.82
2257 3353 0.975135 TGCCAAATTGACCATGGTGG 59.025 50.000 25.52 17.32 45.02 4.61
2259 3355 1.066929 GCCAAATTGACCATGGTGGAC 60.067 52.381 25.52 8.83 40.96 4.02
2345 3443 0.783206 TTGATTTGCTCCTTCCCCCA 59.217 50.000 0.00 0.00 0.00 4.96
2358 3456 2.702592 TCCCCCAAAACTATGCGTAG 57.297 50.000 11.54 11.54 0.00 3.51
2371 3469 1.425412 TGCGTAGGTTCTTTTCTCGC 58.575 50.000 0.00 0.00 41.98 5.03
2429 3528 2.472695 AAGCAAGGCACGTCATTAGA 57.527 45.000 0.00 0.00 0.00 2.10
2439 3538 4.143597 GGCACGTCATTAGATTTCGATACG 60.144 45.833 0.00 0.00 35.38 3.06
2446 3545 7.547961 GTCATTAGATTTCGATACGTCAGTTG 58.452 38.462 0.00 0.00 0.00 3.16
2473 3572 6.457528 GCCTAATTATTGAGCACAGTGAAGAC 60.458 42.308 4.15 0.00 0.00 3.01
2479 3578 0.747255 AGCACAGTGAAGACGAGTGT 59.253 50.000 4.15 0.00 36.17 3.55
2506 3623 5.627499 TTGTTGCTAGCAATTGGAACTAG 57.373 39.130 31.46 10.35 38.28 2.57
2513 3630 2.307098 AGCAATTGGAACTAGCCTGTCT 59.693 45.455 7.72 0.00 0.00 3.41
2519 3636 1.807142 GGAACTAGCCTGTCTTTGTGC 59.193 52.381 0.00 0.00 0.00 4.57
2622 3793 6.469782 ACAATGATGTCTTGTTTCCTGTTT 57.530 33.333 0.00 0.00 33.41 2.83
2649 3820 3.598299 ACTTCTCTCTTGATTGAGCTGC 58.402 45.455 0.00 0.00 34.29 5.25
2689 3861 3.578716 TGTTGTCCTCTAGAACTCCTTGG 59.421 47.826 0.00 0.00 32.63 3.61
2695 3867 4.044825 TCCTCTAGAACTCCTTGGAAGTCT 59.955 45.833 0.00 6.89 0.00 3.24
2710 3882 7.095313 CCTTGGAAGTCTTTATCATGATCATCG 60.095 40.741 12.53 2.07 0.00 3.84
2711 3883 5.698089 TGGAAGTCTTTATCATGATCATCGC 59.302 40.000 12.53 1.61 0.00 4.58
2716 3888 8.304202 AGTCTTTATCATGATCATCGCTTTAC 57.696 34.615 12.53 0.00 0.00 2.01
2732 3904 3.181510 GCTTTACGATTGGCCAGTACAAG 60.182 47.826 5.11 11.85 0.00 3.16
2754 3926 1.129917 TTACGGTGACCAGGTTCCAA 58.870 50.000 1.11 1.24 0.00 3.53
2790 3973 5.295292 GCATTCAGTAGCAGTGTGATGTTAT 59.705 40.000 0.00 0.00 0.00 1.89
2821 4005 8.726988 GTTGATGTAACTTTATAACTCTGGCAA 58.273 33.333 0.00 0.00 36.34 4.52
2834 4018 6.588719 AACTCTGGCAAAACATATAGCAAA 57.411 33.333 0.00 0.00 0.00 3.68
2839 4023 6.047511 TGGCAAAACATATAGCAAAACCAT 57.952 33.333 0.00 0.00 0.00 3.55
2913 4108 6.069963 GGACCCTATAGCACATAATGGATTCT 60.070 42.308 0.00 0.00 0.00 2.40
2969 4228 9.513906 TGTGATGTTTCCTTTCTTGATATAACA 57.486 29.630 0.00 0.00 0.00 2.41
3046 4306 6.942532 TCTGTTTAAAGATACATCCATGGC 57.057 37.500 6.96 0.00 0.00 4.40
3054 4318 7.486407 AAAGATACATCCATGGCTTTTCTTT 57.514 32.000 6.96 13.79 29.72 2.52
3201 4465 3.770040 CGATCCTGTGGGCCGTCA 61.770 66.667 0.00 0.00 0.00 4.35
3236 4500 4.814294 AACGTGATCGCGCTCCCC 62.814 66.667 27.51 0.00 41.18 4.81
3307 4571 1.880819 TACTGGGCCGACGGAAAGAC 61.881 60.000 20.50 0.00 0.00 3.01
3632 4896 0.320771 AGACGCAGGTTGTGATGGAC 60.321 55.000 0.00 0.00 0.00 4.02
3635 4899 3.027170 GCAGGTTGTGATGGACGCG 62.027 63.158 3.53 3.53 0.00 6.01
3687 4951 3.610242 GTCTGTCGATGTTGTGAGCTAAG 59.390 47.826 0.00 0.00 0.00 2.18
3688 4952 3.506067 TCTGTCGATGTTGTGAGCTAAGA 59.494 43.478 0.00 0.00 0.00 2.10
3689 4953 4.022329 TCTGTCGATGTTGTGAGCTAAGAA 60.022 41.667 0.00 0.00 0.00 2.52
3693 4957 6.017933 GTCGATGTTGTGAGCTAAGAAAATG 58.982 40.000 0.00 0.00 0.00 2.32
3714 4978 2.688507 CAACACGTAGCTGGTCATTCT 58.311 47.619 0.00 0.00 0.00 2.40
3716 4980 1.066858 ACACGTAGCTGGTCATTCTGG 60.067 52.381 0.00 0.00 0.00 3.86
3730 5027 5.396772 GGTCATTCTGGTGATATGTCTTCCA 60.397 44.000 6.73 6.73 0.00 3.53
3731 5028 6.115446 GTCATTCTGGTGATATGTCTTCCAA 58.885 40.000 7.89 0.00 32.15 3.53
3732 5029 6.259608 GTCATTCTGGTGATATGTCTTCCAAG 59.740 42.308 7.89 4.24 32.15 3.61
3733 5030 4.142609 TCTGGTGATATGTCTTCCAAGC 57.857 45.455 7.89 0.00 32.15 4.01
3734 5031 3.118261 TCTGGTGATATGTCTTCCAAGCC 60.118 47.826 7.89 0.00 32.15 4.35
3735 5032 2.575735 TGGTGATATGTCTTCCAAGCCA 59.424 45.455 4.97 0.00 0.00 4.75
3736 5033 3.202818 TGGTGATATGTCTTCCAAGCCAT 59.797 43.478 4.97 0.00 0.00 4.40
3737 5034 3.567164 GGTGATATGTCTTCCAAGCCATG 59.433 47.826 0.00 0.00 0.00 3.66
3746 5043 2.118132 CCAAGCCATGGTGCATACC 58.882 57.895 14.67 0.00 44.85 2.73
3754 5051 4.684623 GGTGCATACCTGGCCATT 57.315 55.556 5.51 0.00 43.97 3.16
3755 5052 2.419057 GGTGCATACCTGGCCATTC 58.581 57.895 5.51 0.00 43.97 2.67
3756 5053 1.109323 GGTGCATACCTGGCCATTCC 61.109 60.000 5.51 0.00 43.97 3.01
3757 5054 1.152984 TGCATACCTGGCCATTCCG 60.153 57.895 5.51 0.00 37.80 4.30
3758 5055 1.898574 GCATACCTGGCCATTCCGG 60.899 63.158 5.51 6.54 41.11 5.14
3759 5056 1.531748 CATACCTGGCCATTCCGGT 59.468 57.895 17.73 17.73 41.98 5.28
3760 5057 0.819259 CATACCTGGCCATTCCGGTG 60.819 60.000 21.63 5.04 40.36 4.94
3761 5058 0.986019 ATACCTGGCCATTCCGGTGA 60.986 55.000 21.63 8.54 40.36 4.02
3762 5059 0.986019 TACCTGGCCATTCCGGTGAT 60.986 55.000 21.63 0.73 40.36 3.06
3763 5060 1.526917 CCTGGCCATTCCGGTGATC 60.527 63.158 5.51 0.00 39.73 2.92
3764 5061 1.528824 CTGGCCATTCCGGTGATCT 59.471 57.895 5.51 0.00 36.43 2.75
3765 5062 0.107017 CTGGCCATTCCGGTGATCTT 60.107 55.000 5.51 0.00 36.43 2.40
3766 5063 0.107214 TGGCCATTCCGGTGATCTTC 60.107 55.000 0.00 0.00 37.80 2.87
3767 5064 0.107214 GGCCATTCCGGTGATCTTCA 60.107 55.000 0.00 0.00 36.97 3.02
3782 5079 0.664761 CTTCAAGGCCATGGCGTATG 59.335 55.000 30.86 26.59 43.06 2.39
3812 5112 3.900116 CGTTTGCTCAAATCGTACTTGTG 59.100 43.478 0.00 0.00 32.36 3.33
3817 5117 1.867865 TCAAATCGTACTTGTGCGCAA 59.132 42.857 14.00 12.92 0.00 4.85
3831 5131 3.454941 CGCAAGCGCAAAACTACTT 57.545 47.368 11.47 0.00 38.40 2.24
3832 5132 2.587612 CGCAAGCGCAAAACTACTTA 57.412 45.000 11.47 0.00 38.40 2.24
3833 5133 3.117434 CGCAAGCGCAAAACTACTTAT 57.883 42.857 11.47 0.00 38.40 1.73
3834 5134 4.253352 CGCAAGCGCAAAACTACTTATA 57.747 40.909 11.47 0.00 38.40 0.98
3899 5199 5.858581 GGACAACATTGCAGTTATCAAGTTC 59.141 40.000 0.31 0.00 0.00 3.01
3930 5235 4.955925 TTGCTACGGATTTATTGTGTGG 57.044 40.909 0.00 0.00 0.00 4.17
3956 5261 0.953727 GGCAATATGGATGCTTGCGA 59.046 50.000 4.07 0.00 44.77 5.10
3968 5273 1.287815 CTTGCGAGGTCCACGTACA 59.712 57.895 10.51 0.00 0.00 2.90
3975 5283 2.803956 CGAGGTCCACGTACAAATGTTT 59.196 45.455 0.00 0.00 0.00 2.83
4013 5321 6.694447 ACTCAGGATTTGACAATGGATTTTG 58.306 36.000 0.00 0.00 0.00 2.44
4023 5358 4.492646 ACAATGGATTTTGGGTTCCTCTT 58.507 39.130 0.00 0.00 32.95 2.85
4075 5410 1.215647 GTGACCGCAGTACTCCAGG 59.784 63.158 0.00 0.00 0.00 4.45
4076 5411 2.184579 GACCGCAGTACTCCAGGC 59.815 66.667 0.00 0.00 0.00 4.85
4087 5422 0.915364 ACTCCAGGCCAAAGAGGATC 59.085 55.000 17.83 0.00 41.22 3.36
4119 5455 0.734889 CTGATGTCAATGGTTCGCCC 59.265 55.000 0.00 0.00 36.08 6.13
4135 5471 0.467290 GCCCTCACCAAACTGAACCA 60.467 55.000 0.00 0.00 0.00 3.67
4144 5480 1.270550 CAAACTGAACCATGCCTCCAC 59.729 52.381 0.00 0.00 0.00 4.02
4169 5508 7.778853 ACCCGAGAGATTTAACTCAGAATACTA 59.221 37.037 0.00 0.00 39.14 1.82
4179 5518 8.645814 TTAACTCAGAATACTAGTCCTTGTCA 57.354 34.615 0.00 0.00 0.00 3.58
4186 5525 1.743958 ACTAGTCCTTGTCATCGGTCG 59.256 52.381 0.00 0.00 0.00 4.79
4230 5569 1.125711 GGTACCACACCTGTCCCACT 61.126 60.000 7.15 0.00 44.79 4.00
4240 5579 0.939577 CTGTCCCACTGTGTTCGTCG 60.940 60.000 7.08 0.00 0.00 5.12
4333 5886 4.326826 GTTACCCTTACCCCAACTAACAC 58.673 47.826 0.00 0.00 0.00 3.32
4334 5887 1.706866 ACCCTTACCCCAACTAACACC 59.293 52.381 0.00 0.00 0.00 4.16
4365 5918 0.958822 GGCACCCTAACCAACAAGTG 59.041 55.000 0.00 0.00 0.00 3.16
4379 5932 2.923908 ACAAGTGGTATTGGTCCCCTA 58.076 47.619 0.00 0.00 34.36 3.53
4384 5937 1.053424 GGTATTGGTCCCCTATCGCA 58.947 55.000 0.00 0.00 0.00 5.10
4385 5938 1.270678 GGTATTGGTCCCCTATCGCAC 60.271 57.143 0.00 0.00 0.00 5.34
4391 5944 2.890474 CCCCTATCGCACGCACAC 60.890 66.667 0.00 0.00 0.00 3.82
4401 5954 4.231718 TCGCACGCACACATATATTAGA 57.768 40.909 0.00 0.00 0.00 2.10
4402 5955 4.805219 TCGCACGCACACATATATTAGAT 58.195 39.130 0.00 0.00 0.00 1.98
4403 5956 4.621034 TCGCACGCACACATATATTAGATG 59.379 41.667 0.00 0.00 0.00 2.90
4404 5957 4.201618 CGCACGCACACATATATTAGATGG 60.202 45.833 3.54 0.00 0.00 3.51
4405 5958 4.093408 GCACGCACACATATATTAGATGGG 59.907 45.833 0.00 0.00 33.68 4.00
4406 5959 4.631377 CACGCACACATATATTAGATGGGG 59.369 45.833 5.59 0.00 31.58 4.96
4407 5960 4.191544 CGCACACATATATTAGATGGGGG 58.808 47.826 5.59 2.10 33.98 5.40
4408 5961 4.081142 CGCACACATATATTAGATGGGGGA 60.081 45.833 6.98 0.00 32.44 4.81
4409 5962 5.431765 GCACACATATATTAGATGGGGGAG 58.568 45.833 6.98 0.00 32.44 4.30
4410 5963 5.431765 CACACATATATTAGATGGGGGAGC 58.568 45.833 5.59 0.00 32.44 4.70
4411 5964 5.045651 CACACATATATTAGATGGGGGAGCA 60.046 44.000 5.59 0.00 32.44 4.26
4412 5965 5.190528 ACACATATATTAGATGGGGGAGCAG 59.809 44.000 5.59 0.00 31.58 4.24
4413 5966 4.164988 ACATATATTAGATGGGGGAGCAGC 59.835 45.833 3.54 0.00 0.00 5.25
4414 5967 1.362224 TATTAGATGGGGGAGCAGCC 58.638 55.000 0.00 0.00 0.00 4.85
4415 5968 1.772819 ATTAGATGGGGGAGCAGCCG 61.773 60.000 0.00 0.00 37.63 5.52
4416 5969 2.889521 TTAGATGGGGGAGCAGCCGA 62.890 60.000 0.00 0.00 37.63 5.54
4417 5970 4.554036 GATGGGGGAGCAGCCGAC 62.554 72.222 0.00 0.00 37.63 4.79
4422 5975 3.075005 GGGAGCAGCCGACACCTA 61.075 66.667 0.00 0.00 37.63 3.08
4423 5976 2.184579 GGAGCAGCCGACACCTAC 59.815 66.667 0.00 0.00 0.00 3.18
4424 5977 2.184579 GAGCAGCCGACACCTACC 59.815 66.667 0.00 0.00 0.00 3.18
4425 5978 2.283966 AGCAGCCGACACCTACCT 60.284 61.111 0.00 0.00 0.00 3.08
4426 5979 1.889530 GAGCAGCCGACACCTACCTT 61.890 60.000 0.00 0.00 0.00 3.50
4432 5985 0.170561 CCGACACCTACCTTCTGACG 59.829 60.000 0.00 0.00 0.00 4.35
4443 5996 4.175787 ACCTTCTGACGAGTTCACATAC 57.824 45.455 0.00 0.00 0.00 2.39
4457 6010 2.563620 TCACATACGGTTTACTCCTGCA 59.436 45.455 0.00 0.00 0.00 4.41
4478 6031 4.151883 CACCCCATATCCCTAAAACCATG 58.848 47.826 0.00 0.00 0.00 3.66
4504 6057 4.575973 GGGGGAGCGCTGCATGAT 62.576 66.667 30.47 0.00 0.00 2.45
4507 6060 2.719979 GGAGCGCTGCATGATTGG 59.280 61.111 25.15 0.00 0.00 3.16
4508 6061 2.025727 GAGCGCTGCATGATTGGC 59.974 61.111 18.48 0.00 0.00 4.52
4571 6159 1.373570 GTCTACACCAAGCCTGCATC 58.626 55.000 0.00 0.00 0.00 3.91
4572 6160 0.983467 TCTACACCAAGCCTGCATCA 59.017 50.000 0.00 0.00 0.00 3.07
4573 6161 1.350684 TCTACACCAAGCCTGCATCAA 59.649 47.619 0.00 0.00 0.00 2.57
4574 6162 1.741706 CTACACCAAGCCTGCATCAAG 59.258 52.381 0.00 0.00 0.00 3.02
4586 6174 3.959478 CATCAAGCATGCATGGGAC 57.041 52.632 27.34 11.50 0.00 4.46
4587 6175 1.399714 CATCAAGCATGCATGGGACT 58.600 50.000 27.34 13.64 0.00 3.85
4588 6176 1.754803 CATCAAGCATGCATGGGACTT 59.245 47.619 27.34 18.51 0.00 3.01
4589 6177 1.466856 TCAAGCATGCATGGGACTTC 58.533 50.000 27.34 10.03 0.00 3.01
4590 6178 0.099968 CAAGCATGCATGGGACTTCG 59.900 55.000 27.34 12.60 0.00 3.79
4591 6179 1.660560 AAGCATGCATGGGACTTCGC 61.661 55.000 27.34 10.87 0.00 4.70
4592 6180 2.711311 CATGCATGGGACTTCGCG 59.289 61.111 19.40 0.00 0.00 5.87
4593 6181 2.108514 CATGCATGGGACTTCGCGT 61.109 57.895 19.40 0.00 0.00 6.01
4594 6182 1.815421 ATGCATGGGACTTCGCGTC 60.815 57.895 5.77 0.00 42.07 5.19
4595 6183 3.554692 GCATGGGACTTCGCGTCG 61.555 66.667 5.77 0.16 43.79 5.12
4596 6184 2.180769 CATGGGACTTCGCGTCGA 59.819 61.111 5.77 0.00 43.79 4.20
4597 6185 2.158959 CATGGGACTTCGCGTCGAC 61.159 63.158 5.77 5.18 43.79 4.20
4616 6204 3.421844 GACTGCTTCCTTTGGTGGTAAT 58.578 45.455 0.00 0.00 0.00 1.89
4624 6212 6.262496 GCTTCCTTTGGTGGTAATATCCTAAC 59.738 42.308 0.00 0.00 0.00 2.34
4631 6219 5.546499 TGGTGGTAATATCCTAACCCATCTC 59.454 44.000 0.00 0.00 31.97 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.028130 GAGCTCCGGAAGAAGAGATGA 58.972 52.381 5.23 0.00 0.00 2.92
210 211 2.771943 AGCGAGAATGGGGTAAGAATCA 59.228 45.455 0.00 0.00 0.00 2.57
267 268 0.902531 TGATCGGAGGGTTTCTCACC 59.097 55.000 0.00 0.00 46.46 4.02
295 296 4.357947 GTCTGTCTGCGGTGCCGA 62.358 66.667 15.45 0.00 42.83 5.54
334 335 3.063704 CAGATGCAAAGCCGGGCA 61.064 61.111 23.09 4.17 45.23 5.36
343 344 2.747460 GCCACCTCGCAGATGCAA 60.747 61.111 5.55 0.00 42.21 4.08
395 396 1.352156 GCGGCGTTGAGATCTCGTTT 61.352 55.000 17.76 0.00 0.00 3.60
451 453 3.691744 GACCACAGCGAGAGAGCCG 62.692 68.421 0.00 0.00 38.01 5.52
452 454 2.183046 GACCACAGCGAGAGAGCC 59.817 66.667 0.00 0.00 38.01 4.70
586 597 6.368791 CAGAGACGACCAATTTTATTCAGACA 59.631 38.462 0.00 0.00 0.00 3.41
664 675 0.314302 CTCGTTCCGTGAACTCTGGT 59.686 55.000 12.80 0.00 40.05 4.00
716 727 2.634982 TGTCCTCAAATGCGAATTGC 57.365 45.000 0.00 0.00 46.70 3.56
727 738 3.558931 TCTGCTCAGTTTTGTCCTCAA 57.441 42.857 0.00 0.00 0.00 3.02
754 765 9.010029 GGTTAATTATCCTTTTGTTCTCAGTGA 57.990 33.333 5.46 0.00 0.00 3.41
787 798 4.278975 TGCTTACCACATGTGTCACATA 57.721 40.909 23.79 0.00 36.53 2.29
839 852 0.889306 AGACTTGCAGAGTACCGACC 59.111 55.000 2.17 0.00 39.19 4.79
857 870 0.670546 AACGTGCGACCTGAATCCAG 60.671 55.000 0.00 0.00 40.09 3.86
904 917 2.187493 TAGGAGCTAGCGCGAGTGG 61.187 63.158 18.99 0.00 42.32 4.00
905 918 1.009449 GTAGGAGCTAGCGCGAGTG 60.009 63.158 18.99 0.00 42.32 3.51
906 919 1.153127 AGTAGGAGCTAGCGCGAGT 60.153 57.895 18.99 5.89 42.32 4.18
907 920 1.572447 GAGTAGGAGCTAGCGCGAG 59.428 63.158 12.10 13.72 42.32 5.03
924 960 2.188207 CCGGTGTGTGTGTGTGGA 59.812 61.111 0.00 0.00 0.00 4.02
963 1003 2.836187 GGGTGCTGGTTGGGTGGTA 61.836 63.158 0.00 0.00 0.00 3.25
1515 1561 8.623903 TGGACAGCAAAATTATTATAGCAAGAG 58.376 33.333 0.00 0.00 0.00 2.85
1601 1774 4.247380 CTCCATCCAGGCCGGCTC 62.247 72.222 28.56 16.85 37.29 4.70
1716 2022 3.183237 GGATACAACGACAAACTGCAC 57.817 47.619 0.00 0.00 0.00 4.57
1790 2653 6.761312 TGTTCAAAAGGCAAAATCATCTCAT 58.239 32.000 0.00 0.00 0.00 2.90
1880 2777 2.540383 TGCTCACCAAGTGATAGTCCT 58.460 47.619 0.00 0.00 41.94 3.85
1884 2781 7.144722 TGTAATTTTGCTCACCAAGTGATAG 57.855 36.000 0.00 0.00 41.94 2.08
1917 2814 5.403246 AGCTACAGACAAACGAGATTAGTG 58.597 41.667 0.00 0.00 0.00 2.74
1949 2852 2.264005 TGCAGGGAAGCGTAAGAAAA 57.736 45.000 0.00 0.00 43.02 2.29
1950 2853 1.877443 GTTGCAGGGAAGCGTAAGAAA 59.123 47.619 0.00 0.00 43.02 2.52
1958 2862 1.322442 AAGAGTTGTTGCAGGGAAGC 58.678 50.000 0.00 0.00 0.00 3.86
1999 2909 1.681327 GGCTCTCCGTACCAGACCA 60.681 63.158 0.00 0.00 0.00 4.02
2001 2911 0.824759 ATTGGCTCTCCGTACCAGAC 59.175 55.000 0.00 0.00 34.28 3.51
2057 2967 5.437289 TGTTGTCAGTGAAATGTTGATCC 57.563 39.130 0.00 0.00 0.00 3.36
2066 2976 8.614469 TCATGTGTTATATGTTGTCAGTGAAA 57.386 30.769 0.00 0.00 0.00 2.69
2068 2978 9.883142 TTATCATGTGTTATATGTTGTCAGTGA 57.117 29.630 0.00 0.00 0.00 3.41
2130 3050 0.593128 AGCGCACTGTCATTTTGTCC 59.407 50.000 11.47 0.00 0.00 4.02
2149 3069 6.372103 TCTTTTGTAGTTCGTCTTTGGTTTCA 59.628 34.615 0.00 0.00 0.00 2.69
2187 3119 9.706691 GCTGTTGTATCTTGCCTAATACTAATA 57.293 33.333 0.00 0.00 31.11 0.98
2190 3122 7.361457 AGCTGTTGTATCTTGCCTAATACTA 57.639 36.000 0.00 0.00 31.11 1.82
2257 3353 4.093408 ACACAATATGATTCACTGCACGTC 59.907 41.667 0.00 0.00 0.00 4.34
2259 3355 4.604843 ACACAATATGATTCACTGCACG 57.395 40.909 0.00 0.00 0.00 5.34
2318 3416 4.520492 GGAAGGAGCAAATCAAACAGAGAA 59.480 41.667 0.00 0.00 0.00 2.87
2319 3417 4.074970 GGAAGGAGCAAATCAAACAGAGA 58.925 43.478 0.00 0.00 0.00 3.10
2333 3431 2.379005 CATAGTTTTGGGGGAAGGAGC 58.621 52.381 0.00 0.00 0.00 4.70
2345 3443 6.128634 CGAGAAAAGAACCTACGCATAGTTTT 60.129 38.462 0.00 0.00 0.00 2.43
2358 3456 1.397343 GGATTCGGCGAGAAAAGAACC 59.603 52.381 10.46 0.00 42.91 3.62
2371 3469 8.153479 TCAATTGTTTGATACATAGGATTCGG 57.847 34.615 5.13 0.00 36.94 4.30
2429 3528 1.323534 GCGCAACTGACGTATCGAAAT 59.676 47.619 0.30 0.00 0.00 2.17
2439 3538 4.786609 GCTCAATAATTAGGCGCAACTGAC 60.787 45.833 10.83 0.00 0.00 3.51
2446 3545 2.614057 ACTGTGCTCAATAATTAGGCGC 59.386 45.455 0.00 0.00 0.00 6.53
2473 3572 3.058983 TGCTAGCAACAAAATGACACTCG 60.059 43.478 16.84 0.00 0.00 4.18
2479 3578 5.465532 TCCAATTGCTAGCAACAAAATGA 57.534 34.783 31.51 18.23 38.88 2.57
2506 3623 0.819259 TGAGGTGCACAAAGACAGGC 60.819 55.000 20.43 0.00 0.00 4.85
2513 3630 3.902881 AATTGGTTTGAGGTGCACAAA 57.097 38.095 20.43 8.06 35.34 2.83
2572 3693 7.281100 CCCTTCAAGTAAACTAAGCAAGGATAG 59.719 40.741 0.00 0.00 32.37 2.08
2573 3696 7.037873 TCCCTTCAAGTAAACTAAGCAAGGATA 60.038 37.037 0.00 0.00 32.37 2.59
2616 3787 4.615588 AGAGAGAAGTCCAAGAAACAGG 57.384 45.455 0.00 0.00 0.00 4.00
2617 3788 5.605534 TCAAGAGAGAAGTCCAAGAAACAG 58.394 41.667 0.00 0.00 0.00 3.16
2618 3789 5.614324 TCAAGAGAGAAGTCCAAGAAACA 57.386 39.130 0.00 0.00 0.00 2.83
2619 3790 6.708054 TCAATCAAGAGAGAAGTCCAAGAAAC 59.292 38.462 0.00 0.00 0.00 2.78
2620 3791 6.830912 TCAATCAAGAGAGAAGTCCAAGAAA 58.169 36.000 0.00 0.00 0.00 2.52
2621 3792 6.425210 TCAATCAAGAGAGAAGTCCAAGAA 57.575 37.500 0.00 0.00 0.00 2.52
2622 3793 5.568423 GCTCAATCAAGAGAGAAGTCCAAGA 60.568 44.000 0.00 0.00 37.87 3.02
2649 3820 6.418819 GGACAACACAGAATGAACAAAATCTG 59.581 38.462 11.31 11.31 43.79 2.90
2689 3861 7.418840 AAGCGATGATCATGATAAAGACTTC 57.581 36.000 14.30 3.06 0.00 3.01
2710 3882 2.352388 TGTACTGGCCAATCGTAAAGC 58.648 47.619 7.01 0.00 0.00 3.51
2711 3883 4.000988 ACTTGTACTGGCCAATCGTAAAG 58.999 43.478 7.01 13.39 0.00 1.85
2716 3888 4.208460 CGTAATACTTGTACTGGCCAATCG 59.792 45.833 7.01 0.00 0.00 3.34
2732 3904 2.234414 TGGAACCTGGTCACCGTAATAC 59.766 50.000 15.04 0.00 0.00 1.89
2821 4005 8.584157 TCACTTTGATGGTTTTGCTATATGTTT 58.416 29.630 0.00 0.00 0.00 2.83
2834 4018 4.118168 ACCAGGAATCACTTTGATGGTT 57.882 40.909 0.00 0.00 37.15 3.67
2839 4023 4.462483 GCCATAAACCAGGAATCACTTTGA 59.538 41.667 0.00 0.00 0.00 2.69
2938 4133 5.598005 TCAAGAAAGGAAACATCACAATGGT 59.402 36.000 0.00 0.00 37.19 3.55
2969 4228 9.612620 GATTAAGTGAACGAAAACAATTCTGAT 57.387 29.630 0.00 0.00 0.00 2.90
2973 4232 8.073768 TCCAGATTAAGTGAACGAAAACAATTC 58.926 33.333 0.00 0.00 0.00 2.17
2976 4235 6.316640 TGTCCAGATTAAGTGAACGAAAACAA 59.683 34.615 0.00 0.00 0.00 2.83
3023 4283 6.662755 AGCCATGGATGTATCTTTAAACAGA 58.337 36.000 18.40 0.00 0.00 3.41
3028 4288 8.593945 AAGAAAAGCCATGGATGTATCTTTAA 57.406 30.769 18.40 0.00 0.00 1.52
3029 4289 8.593945 AAAGAAAAGCCATGGATGTATCTTTA 57.406 30.769 24.79 0.00 34.03 1.85
3033 4293 6.633856 ACAAAAGAAAAGCCATGGATGTATC 58.366 36.000 18.40 8.90 0.00 2.24
3035 4295 6.222389 CAACAAAAGAAAAGCCATGGATGTA 58.778 36.000 18.40 0.00 0.00 2.29
3037 4297 4.083696 GCAACAAAAGAAAAGCCATGGATG 60.084 41.667 18.40 0.00 0.00 3.51
3041 4301 4.571580 TGAAGCAACAAAAGAAAAGCCATG 59.428 37.500 0.00 0.00 0.00 3.66
3044 4304 4.432712 TCTGAAGCAACAAAAGAAAAGCC 58.567 39.130 0.00 0.00 0.00 4.35
3045 4305 7.698836 TTATCTGAAGCAACAAAAGAAAAGC 57.301 32.000 0.00 0.00 0.00 3.51
3046 4306 9.086336 TGTTTATCTGAAGCAACAAAAGAAAAG 57.914 29.630 0.00 0.00 0.00 2.27
3054 4318 5.822519 ACAGACTGTTTATCTGAAGCAACAA 59.177 36.000 1.07 0.00 45.46 2.83
3201 4465 1.201880 GTTCTTCGGGAGCTCGTAGTT 59.798 52.381 7.83 0.00 0.00 2.24
3236 4500 1.512926 CTTGGTTCTTGACAGGGTCG 58.487 55.000 0.00 0.00 34.95 4.79
3307 4571 4.335647 AGCAGTGGAAGGTGGCCG 62.336 66.667 0.00 0.00 0.00 6.13
3485 4749 3.406361 GTGACGACGTGCCTGCTG 61.406 66.667 4.58 0.00 0.00 4.41
3632 4896 2.040544 AATGGAAGCCTTCACCGCG 61.041 57.895 6.80 0.00 0.00 6.46
3635 4899 1.909700 TGTCAATGGAAGCCTTCACC 58.090 50.000 6.80 0.00 0.00 4.02
3687 4951 2.031157 ACCAGCTACGTGTTGCATTTTC 60.031 45.455 8.99 0.00 33.84 2.29
3688 4952 1.953686 ACCAGCTACGTGTTGCATTTT 59.046 42.857 8.99 0.00 33.84 1.82
3689 4953 1.535462 GACCAGCTACGTGTTGCATTT 59.465 47.619 8.99 0.00 33.84 2.32
3693 4957 1.128692 GAATGACCAGCTACGTGTTGC 59.871 52.381 0.00 0.00 0.00 4.17
3714 4978 2.575735 TGGCTTGGAAGACATATCACCA 59.424 45.455 0.00 0.00 39.67 4.17
3737 5034 1.109323 GGAATGGCCAGGTATGCACC 61.109 60.000 13.05 1.64 46.19 5.01
3738 5035 1.447317 CGGAATGGCCAGGTATGCAC 61.447 60.000 13.05 0.00 35.94 4.57
3739 5036 1.152984 CGGAATGGCCAGGTATGCA 60.153 57.895 13.05 0.00 35.94 3.96
3740 5037 1.898574 CCGGAATGGCCAGGTATGC 60.899 63.158 13.05 1.55 35.94 3.14
3741 5038 0.819259 CACCGGAATGGCCAGGTATG 60.819 60.000 13.05 1.79 43.94 2.39
3742 5039 0.986019 TCACCGGAATGGCCAGGTAT 60.986 55.000 13.05 0.00 43.94 2.73
3743 5040 0.986019 ATCACCGGAATGGCCAGGTA 60.986 55.000 13.05 2.80 43.94 3.08
3744 5041 2.270874 GATCACCGGAATGGCCAGGT 62.271 60.000 13.05 10.52 43.94 4.00
3745 5042 1.526917 GATCACCGGAATGGCCAGG 60.527 63.158 13.05 9.74 43.94 4.45
3746 5043 0.107017 AAGATCACCGGAATGGCCAG 60.107 55.000 13.05 0.00 43.94 4.85
3747 5044 0.107214 GAAGATCACCGGAATGGCCA 60.107 55.000 8.56 8.56 43.94 5.36
3748 5045 0.107214 TGAAGATCACCGGAATGGCC 60.107 55.000 9.46 0.00 43.94 5.36
3749 5046 1.672881 CTTGAAGATCACCGGAATGGC 59.327 52.381 9.46 0.00 43.94 4.40
3750 5047 2.292267 CCTTGAAGATCACCGGAATGG 58.708 52.381 9.46 0.00 46.41 3.16
3751 5048 1.672881 GCCTTGAAGATCACCGGAATG 59.327 52.381 9.46 0.00 0.00 2.67
3752 5049 1.408822 GGCCTTGAAGATCACCGGAAT 60.409 52.381 9.46 0.00 0.00 3.01
3753 5050 0.035439 GGCCTTGAAGATCACCGGAA 60.035 55.000 9.46 0.00 0.00 4.30
3754 5051 1.198094 TGGCCTTGAAGATCACCGGA 61.198 55.000 9.46 0.00 0.00 5.14
3755 5052 0.107017 ATGGCCTTGAAGATCACCGG 60.107 55.000 3.32 0.00 0.00 5.28
3756 5053 1.019673 CATGGCCTTGAAGATCACCG 58.980 55.000 13.33 0.00 0.00 4.94
3757 5054 1.396653 CCATGGCCTTGAAGATCACC 58.603 55.000 19.85 0.00 0.00 4.02
3758 5055 0.743097 GCCATGGCCTTGAAGATCAC 59.257 55.000 27.24 0.00 34.56 3.06
3759 5056 0.749091 CGCCATGGCCTTGAAGATCA 60.749 55.000 30.79 0.00 37.98 2.92
3760 5057 0.749454 ACGCCATGGCCTTGAAGATC 60.749 55.000 30.79 0.00 37.98 2.75
3761 5058 0.546122 TACGCCATGGCCTTGAAGAT 59.454 50.000 30.79 8.64 37.98 2.40
3762 5059 0.546122 ATACGCCATGGCCTTGAAGA 59.454 50.000 30.79 8.58 37.98 2.87
3763 5060 0.664761 CATACGCCATGGCCTTGAAG 59.335 55.000 30.79 17.70 37.98 3.02
3764 5061 2.792500 CATACGCCATGGCCTTGAA 58.208 52.632 30.79 12.03 37.98 2.69
3765 5062 4.557554 CATACGCCATGGCCTTGA 57.442 55.556 30.79 13.72 37.98 3.02
3782 5079 2.132740 TTTGAGCAAACGCACAATCC 57.867 45.000 0.00 0.00 39.28 3.01
3784 5081 2.287547 ACGATTTGAGCAAACGCACAAT 60.288 40.909 13.65 0.00 39.28 2.71
3812 5112 0.660300 AAGTAGTTTTGCGCTTGCGC 60.660 50.000 29.59 29.59 43.34 6.09
3817 5117 9.938280 TCCAATATATATAAGTAGTTTTGCGCT 57.062 29.630 9.73 0.00 0.00 5.92
3866 5166 2.824936 TGCAATGTTGTCCTTGGTATGG 59.175 45.455 0.00 0.00 0.00 2.74
3872 5172 5.375417 TGATAACTGCAATGTTGTCCTTG 57.625 39.130 11.39 0.00 37.29 3.61
3930 5235 5.178067 GCAAGCATCCATATTGCCAAAATAC 59.822 40.000 0.00 0.00 42.70 1.89
3956 5261 3.143728 GGAAACATTTGTACGTGGACCT 58.856 45.455 0.00 0.00 0.00 3.85
3968 5273 7.936584 TGAGTTTAAGATGAACGGAAACATTT 58.063 30.769 0.00 0.00 33.53 2.32
3975 5283 5.677319 ATCCTGAGTTTAAGATGAACGGA 57.323 39.130 0.00 0.00 32.38 4.69
4013 5321 5.473039 CATTGTCAAATCAAAGAGGAACCC 58.527 41.667 0.00 0.00 0.00 4.11
4023 5358 4.082841 CGGATGTGTCCATTGTCAAATCAA 60.083 41.667 9.75 0.00 45.37 2.57
4075 5410 1.078143 AGGCACGATCCTCTTTGGC 60.078 57.895 0.00 0.00 35.26 4.52
4087 5422 3.842923 ATCAGAGGGCGAGGCACG 61.843 66.667 0.00 0.00 45.66 5.34
4119 5455 1.270550 GGCATGGTTCAGTTTGGTGAG 59.729 52.381 0.00 0.00 0.00 3.51
4125 5461 1.620822 GTGGAGGCATGGTTCAGTTT 58.379 50.000 0.00 0.00 0.00 2.66
4135 5471 0.692419 AATCTCTCGGGTGGAGGCAT 60.692 55.000 0.00 0.00 43.34 4.40
4144 5480 7.045126 AGTATTCTGAGTTAAATCTCTCGGG 57.955 40.000 4.35 0.00 37.58 5.14
4169 5508 0.243907 CACGACCGATGACAAGGACT 59.756 55.000 7.26 0.00 0.00 3.85
4179 5518 0.319083 TAAGCAACCACACGACCGAT 59.681 50.000 0.00 0.00 0.00 4.18
4186 5525 0.250166 ACGGGAGTAAGCAACCACAC 60.250 55.000 0.00 0.00 44.60 3.82
4221 5560 0.939577 CGACGAACACAGTGGGACAG 60.940 60.000 0.00 0.00 41.80 3.51
4230 5569 0.179121 ACAAGCAGACGACGAACACA 60.179 50.000 0.00 0.00 0.00 3.72
4240 5579 3.437049 GGTTCACCTTCATACAAGCAGAC 59.563 47.826 0.00 0.00 0.00 3.51
4306 5649 2.301583 GTTGGGGTAAGGGTAACGTACA 59.698 50.000 0.00 0.00 37.60 2.90
4379 5932 4.805219 TCTAATATATGTGTGCGTGCGAT 58.195 39.130 0.00 0.00 0.00 4.58
4384 5937 4.323485 CCCCCATCTAATATATGTGTGCGT 60.323 45.833 0.00 0.00 0.00 5.24
4385 5938 4.081142 TCCCCCATCTAATATATGTGTGCG 60.081 45.833 0.00 0.00 0.00 5.34
4391 5944 4.445448 GGCTGCTCCCCCATCTAATATATG 60.445 50.000 0.00 0.00 0.00 1.78
4405 5958 3.075005 TAGGTGTCGGCTGCTCCC 61.075 66.667 0.00 0.00 0.00 4.30
4406 5959 2.184579 GTAGGTGTCGGCTGCTCC 59.815 66.667 0.00 0.00 0.00 4.70
4407 5960 1.889530 AAGGTAGGTGTCGGCTGCTC 61.890 60.000 0.00 0.00 0.00 4.26
4408 5961 1.889530 GAAGGTAGGTGTCGGCTGCT 61.890 60.000 0.00 0.00 0.00 4.24
4409 5962 1.448013 GAAGGTAGGTGTCGGCTGC 60.448 63.158 0.00 0.00 0.00 5.25
4410 5963 0.108615 CAGAAGGTAGGTGTCGGCTG 60.109 60.000 0.00 0.00 0.00 4.85
4411 5964 0.251653 TCAGAAGGTAGGTGTCGGCT 60.252 55.000 0.00 0.00 0.00 5.52
4412 5965 0.108756 GTCAGAAGGTAGGTGTCGGC 60.109 60.000 0.00 0.00 0.00 5.54
4413 5966 0.170561 CGTCAGAAGGTAGGTGTCGG 59.829 60.000 0.00 0.00 0.00 4.79
4414 5967 1.130749 CTCGTCAGAAGGTAGGTGTCG 59.869 57.143 0.00 0.00 0.00 4.35
4415 5968 2.161030 ACTCGTCAGAAGGTAGGTGTC 58.839 52.381 0.00 0.00 0.00 3.67
4416 5969 2.289592 ACTCGTCAGAAGGTAGGTGT 57.710 50.000 0.00 0.00 0.00 4.16
4417 5970 2.557056 TGAACTCGTCAGAAGGTAGGTG 59.443 50.000 0.00 0.00 0.00 4.00
4418 5971 2.557490 GTGAACTCGTCAGAAGGTAGGT 59.443 50.000 0.00 0.00 36.74 3.08
4419 5972 2.557056 TGTGAACTCGTCAGAAGGTAGG 59.443 50.000 0.00 0.00 36.74 3.18
4420 5973 3.917329 TGTGAACTCGTCAGAAGGTAG 57.083 47.619 0.00 0.00 36.74 3.18
4421 5974 4.142752 CGTATGTGAACTCGTCAGAAGGTA 60.143 45.833 0.00 0.00 36.74 3.08
4422 5975 3.366070 CGTATGTGAACTCGTCAGAAGGT 60.366 47.826 0.00 0.00 36.74 3.50
4423 5976 3.172050 CGTATGTGAACTCGTCAGAAGG 58.828 50.000 0.00 0.00 36.74 3.46
4424 5977 3.172050 CCGTATGTGAACTCGTCAGAAG 58.828 50.000 0.00 0.00 36.74 2.85
4425 5978 2.555325 ACCGTATGTGAACTCGTCAGAA 59.445 45.455 0.00 0.00 36.74 3.02
4426 5979 2.156917 ACCGTATGTGAACTCGTCAGA 58.843 47.619 0.00 0.00 36.74 3.27
4432 5985 4.863131 CAGGAGTAAACCGTATGTGAACTC 59.137 45.833 0.00 0.00 38.17 3.01
4443 5996 1.376812 GGGGTGCAGGAGTAAACCG 60.377 63.158 0.00 0.00 33.24 4.44
4457 6010 4.058731 TCATGGTTTTAGGGATATGGGGT 58.941 43.478 0.00 0.00 0.00 4.95
4478 6031 3.917760 CGCTCCCCCAGATCGGTC 61.918 72.222 0.00 0.00 30.46 4.79
4501 6054 0.463654 GCCACCGATACTGCCAATCA 60.464 55.000 0.00 0.00 0.00 2.57
4504 6057 2.125310 CGCCACCGATACTGCCAA 60.125 61.111 0.00 0.00 36.29 4.52
4571 6159 0.099968 CGAAGTCCCATGCATGCTTG 59.900 55.000 21.69 23.09 0.00 4.01
4572 6160 1.660560 GCGAAGTCCCATGCATGCTT 61.661 55.000 21.69 18.05 0.00 3.91
4573 6161 2.117156 GCGAAGTCCCATGCATGCT 61.117 57.895 21.69 10.26 0.00 3.79
4574 6162 2.410469 GCGAAGTCCCATGCATGC 59.590 61.111 21.69 11.82 0.00 4.06
4576 6164 1.815421 GACGCGAAGTCCCATGCAT 60.815 57.895 15.93 0.00 43.95 3.96
4578 6166 3.554692 CGACGCGAAGTCCCATGC 61.555 66.667 15.93 0.00 46.92 4.06
4579 6167 2.158959 GTCGACGCGAAGTCCCATG 61.159 63.158 15.93 0.00 46.92 3.66
4580 6168 2.181021 GTCGACGCGAAGTCCCAT 59.819 61.111 15.93 0.00 46.92 4.00
4581 6169 2.981909 AGTCGACGCGAAGTCCCA 60.982 61.111 15.93 0.00 46.92 4.37
4582 6170 2.504244 CAGTCGACGCGAAGTCCC 60.504 66.667 15.93 0.00 46.92 4.46
4583 6171 3.173240 GCAGTCGACGCGAAGTCC 61.173 66.667 15.93 1.69 46.92 3.85
4585 6173 1.729838 GAAGCAGTCGACGCGAAGT 60.730 57.895 15.93 11.45 37.72 3.01
4586 6174 2.437343 GGAAGCAGTCGACGCGAAG 61.437 63.158 15.93 6.11 37.72 3.79
4587 6175 2.416244 AAGGAAGCAGTCGACGCGAA 62.416 55.000 15.93 0.00 37.72 4.70
4588 6176 2.416244 AAAGGAAGCAGTCGACGCGA 62.416 55.000 15.93 0.00 0.00 5.87
4589 6177 2.022129 AAAGGAAGCAGTCGACGCG 61.022 57.895 20.83 3.53 0.00 6.01
4590 6178 1.493311 CAAAGGAAGCAGTCGACGC 59.507 57.895 19.92 19.92 0.00 5.19
4591 6179 0.600255 ACCAAAGGAAGCAGTCGACG 60.600 55.000 10.46 6.47 0.00 5.12
4592 6180 0.868406 CACCAAAGGAAGCAGTCGAC 59.132 55.000 7.70 7.70 0.00 4.20
4593 6181 0.250295 CCACCAAAGGAAGCAGTCGA 60.250 55.000 0.00 0.00 0.00 4.20
4594 6182 0.535102 ACCACCAAAGGAAGCAGTCG 60.535 55.000 0.00 0.00 0.00 4.18
4595 6183 2.561478 TACCACCAAAGGAAGCAGTC 57.439 50.000 0.00 0.00 0.00 3.51
4596 6184 3.525800 ATTACCACCAAAGGAAGCAGT 57.474 42.857 0.00 0.00 0.00 4.40
4597 6185 4.580580 GGATATTACCACCAAAGGAAGCAG 59.419 45.833 0.00 0.00 0.00 4.24
4616 6204 5.076458 TGGATCAGAGAGATGGGTTAGGATA 59.924 44.000 0.00 0.00 37.00 2.59
4624 6212 1.697982 TGCATGGATCAGAGAGATGGG 59.302 52.381 0.00 0.00 37.00 4.00
4631 6219 4.711399 TCACCTAATTGCATGGATCAGAG 58.289 43.478 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.