Multiple sequence alignment - TraesCS6A01G311800

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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 TraesCS6A01G311800 chr6A 100.000 5778 0 0 1 5778 547825517 547831294 0.000000e+00 10615.0
1 TraesCS6A01G311800 chr6B 91.881 2020 123 24 2814 4803 601882558 601884566 0.000000e+00 2784.0
2 TraesCS6A01G311800 chr6B 95.908 1002 36 3 1001 2001 601880304 601881301 0.000000e+00 1618.0
3 TraesCS6A01G311800 chr6B 93.095 840 39 13 2217 3050 601881737 601882563 0.000000e+00 1212.0
4 TraesCS6A01G311800 chr6B 86.592 895 80 26 103 985 601878869 601879735 0.000000e+00 952.0
5 TraesCS6A01G311800 chr6B 94.037 218 6 2 2000 2217 601881425 601881635 2.010000e-84 324.0
6 TraesCS6A01G311800 chr6D 96.467 1217 35 3 1001 2217 401306164 401307372 0.000000e+00 2002.0
7 TraesCS6A01G311800 chr6D 94.424 1094 38 11 3075 4164 401308362 401309436 0.000000e+00 1661.0
8 TraesCS6A01G311800 chr6D 92.821 599 36 3 2479 3076 401307676 401308268 0.000000e+00 861.0
9 TraesCS6A01G311800 chr6D 92.359 602 30 8 186 778 401305110 401305704 0.000000e+00 843.0
10 TraesCS6A01G311800 chr6D 88.084 663 48 12 4196 4834 401309435 401310090 0.000000e+00 758.0
11 TraesCS6A01G311800 chr6D 94.949 198 6 1 792 985 401305685 401305882 2.020000e-79 307.0
12 TraesCS6A01G311800 chr6D 97.076 171 5 0 2217 2387 401307504 401307674 7.330000e-74 289.0
13 TraesCS6A01G311800 chr6D 94.444 162 7 1 4927 5088 401310159 401310318 1.240000e-61 248.0
14 TraesCS6A01G311800 chr6D 95.876 97 3 1 3 98 401304280 401304376 7.750000e-34 156.0
15 TraesCS6A01G311800 chr6D 89.773 88 3 4 4038 4121 305190130 305190215 2.200000e-19 108.0
16 TraesCS6A01G311800 chr6D 95.161 62 2 1 5096 5156 401310989 401311050 4.770000e-16 97.1
17 TraesCS6A01G311800 chr7A 87.764 662 75 6 1010 1669 211729997 211730654 0.000000e+00 769.0
18 TraesCS6A01G311800 chr7B 88.424 622 70 2 1051 1671 119213897 119214517 0.000000e+00 749.0
19 TraesCS6A01G311800 chr7D 87.781 622 74 2 1051 1671 156809731 156810351 0.000000e+00 726.0
20 TraesCS6A01G311800 chr7D 86.596 567 67 7 5216 5774 417368308 417368873 8.230000e-173 617.0
21 TraesCS6A01G311800 chr7D 85.689 573 66 11 5216 5776 505372462 505371894 1.790000e-164 590.0
22 TraesCS6A01G311800 chr7D 85.166 573 59 16 5216 5776 108083056 108082498 1.090000e-156 564.0
23 TraesCS6A01G311800 chr7D 86.042 523 66 5 5257 5776 465572271 465571753 6.540000e-154 555.0
24 TraesCS6A01G311800 chr2B 83.630 562 82 8 5218 5774 786234105 786234661 2.390000e-143 520.0
25 TraesCS6A01G311800 chr2B 84.766 512 62 10 5269 5775 470909211 470908711 3.110000e-137 499.0
26 TraesCS6A01G311800 chr4D 86.957 460 54 5 5320 5776 17255606 17256062 3.990000e-141 512.0
27 TraesCS6A01G311800 chr3B 84.078 515 67 10 5269 5776 75666172 75665666 3.130000e-132 483.0
28 TraesCS6A01G311800 chr3B 80.068 592 83 20 5196 5776 400306839 400307406 1.940000e-109 407.0
29 TraesCS6A01G311800 chr3D 84.010 394 58 4 5269 5659 469806427 469806036 1.970000e-99 374.0
30 TraesCS6A01G311800 chr3D 86.364 88 8 3 4036 4120 75358689 75358603 6.160000e-15 93.5
31 TraesCS6A01G311800 chrUn 87.356 87 9 1 4038 4122 11032398 11032312 1.320000e-16 99.0
32 TraesCS6A01G311800 chrUn 84.091 88 8 4 4037 4118 9847545 9847632 4.800000e-11 80.5
33 TraesCS6A01G311800 chr5D 87.500 88 6 3 4036 4118 516792227 516792140 4.770000e-16 97.1
34 TraesCS6A01G311800 chr5D 83.871 93 11 1 4038 4126 297499910 297499818 1.030000e-12 86.1
35 TraesCS6A01G311800 chr5B 83.871 93 10 2 4038 4126 337831161 337831070 3.710000e-12 84.2
36 TraesCS6A01G311800 chr3A 83.721 86 9 3 4038 4119 521635881 521635797 6.210000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G311800 chr6A 547825517 547831294 5777 False 10615.00 10615 100.0000 1 5778 1 chr6A.!!$F1 5777
1 TraesCS6A01G311800 chr6B 601878869 601884566 5697 False 1378.00 2784 92.3026 103 4803 5 chr6B.!!$F1 4700
2 TraesCS6A01G311800 chr6D 401304280 401311050 6770 False 722.21 2002 94.1661 3 5156 10 chr6D.!!$F2 5153
3 TraesCS6A01G311800 chr7A 211729997 211730654 657 False 769.00 769 87.7640 1010 1669 1 chr7A.!!$F1 659
4 TraesCS6A01G311800 chr7B 119213897 119214517 620 False 749.00 749 88.4240 1051 1671 1 chr7B.!!$F1 620
5 TraesCS6A01G311800 chr7D 156809731 156810351 620 False 726.00 726 87.7810 1051 1671 1 chr7D.!!$F1 620
6 TraesCS6A01G311800 chr7D 417368308 417368873 565 False 617.00 617 86.5960 5216 5774 1 chr7D.!!$F2 558
7 TraesCS6A01G311800 chr7D 505371894 505372462 568 True 590.00 590 85.6890 5216 5776 1 chr7D.!!$R3 560
8 TraesCS6A01G311800 chr7D 108082498 108083056 558 True 564.00 564 85.1660 5216 5776 1 chr7D.!!$R1 560
9 TraesCS6A01G311800 chr7D 465571753 465572271 518 True 555.00 555 86.0420 5257 5776 1 chr7D.!!$R2 519
10 TraesCS6A01G311800 chr2B 786234105 786234661 556 False 520.00 520 83.6300 5218 5774 1 chr2B.!!$F1 556
11 TraesCS6A01G311800 chr2B 470908711 470909211 500 True 499.00 499 84.7660 5269 5775 1 chr2B.!!$R1 506
12 TraesCS6A01G311800 chr3B 75665666 75666172 506 True 483.00 483 84.0780 5269 5776 1 chr3B.!!$R1 507
13 TraesCS6A01G311800 chr3B 400306839 400307406 567 False 407.00 407 80.0680 5196 5776 1 chr3B.!!$F1 580

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
765 1442 1.133009 TGGCAACCACCCCAATAAACT 60.133 47.619 0.00 0.0 0.0 2.66 F
2347 3853 0.604578 CCCAATTGTGAGTGCCCAAG 59.395 55.000 4.43 0.0 0.0 3.61 F
3758 5601 0.892755 TCGGCGTTGAGGTCAGTTAT 59.107 50.000 6.85 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 4090 0.108585 TGGAGACAGGTCCAGCAAAC 59.891 55.000 0.0 0.0 41.99 2.93 R
3829 5672 1.537202 GCTGTGACCATCAGTTTGACC 59.463 52.381 0.0 0.0 35.60 4.02 R
5161 7710 0.036732 TTGCCTAAGTCCTGCTGTGG 59.963 55.000 0.0 0.0 0.00 4.17 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
23 25 2.386661 ACACTATTGTTCGCCAGAGG 57.613 50.000 0.00 0.00 28.43 3.69
98 100 3.825143 ATGAAAGCAAGGCAAAACACT 57.175 38.095 0.00 0.00 0.00 3.55
99 101 3.608316 TGAAAGCAAGGCAAAACACTT 57.392 38.095 0.00 0.00 0.00 3.16
128 166 5.237048 GCTGGTATTTTTCCAATTCAAGCA 58.763 37.500 0.00 0.00 34.35 3.91
139 177 7.994425 TTCCAATTCAAGCAGACTATTACAA 57.006 32.000 0.00 0.00 0.00 2.41
184 222 4.274459 GGTGCTAGGAAGTTTGCATATGAG 59.726 45.833 6.97 0.00 37.76 2.90
187 835 5.355071 TGCTAGGAAGTTTGCATATGAGTTG 59.645 40.000 6.97 0.00 0.00 3.16
209 857 3.004419 GCTAGAAACCTTCGCCTGTTTTT 59.996 43.478 0.00 0.00 34.97 1.94
215 863 1.602920 CCTTCGCCTGTTTTTGCCTTC 60.603 52.381 0.00 0.00 0.00 3.46
248 898 5.129320 ACCCTGCACTTTTTCTTCTTTTGAT 59.871 36.000 0.00 0.00 0.00 2.57
264 914 1.737838 TGATACCAAAGAAGCCTGCG 58.262 50.000 0.00 0.00 0.00 5.18
283 933 2.281498 GCGCTTGTTTTCACCTGTTTTC 59.719 45.455 0.00 0.00 0.00 2.29
287 938 5.802956 CGCTTGTTTTCACCTGTTTTCTTTA 59.197 36.000 0.00 0.00 0.00 1.85
416 1076 1.688197 CATTGCCAGGGTTGTTTCACT 59.312 47.619 0.00 0.00 0.00 3.41
438 1098 8.733458 TCACTTTGTTTATGATGAAAGAGGATG 58.267 33.333 0.00 0.00 31.24 3.51
440 1100 7.671398 ACTTTGTTTATGATGAAAGAGGATGGT 59.329 33.333 0.00 0.00 31.24 3.55
442 1102 7.395190 TGTTTATGATGAAAGAGGATGGTTG 57.605 36.000 0.00 0.00 0.00 3.77
444 1104 4.598036 ATGATGAAAGAGGATGGTTGGT 57.402 40.909 0.00 0.00 0.00 3.67
630 1291 4.267690 TGAAAATTGCGATGCTAGTCGTAG 59.732 41.667 4.86 0.00 43.27 3.51
653 1314 9.608617 GTAGCATCAATCATTAACATCATGAAG 57.391 33.333 0.00 0.00 34.31 3.02
726 1403 5.665459 CCAGAACTTATTAGAGACCACCAG 58.335 45.833 0.00 0.00 0.00 4.00
765 1442 1.133009 TGGCAACCACCCCAATAAACT 60.133 47.619 0.00 0.00 0.00 2.66
766 1443 2.110188 TGGCAACCACCCCAATAAACTA 59.890 45.455 0.00 0.00 0.00 2.24
767 1444 2.758423 GGCAACCACCCCAATAAACTAG 59.242 50.000 0.00 0.00 0.00 2.57
768 1445 2.758423 GCAACCACCCCAATAAACTAGG 59.242 50.000 0.00 0.00 0.00 3.02
769 1446 3.562609 GCAACCACCCCAATAAACTAGGA 60.563 47.826 0.00 0.00 0.00 2.94
770 1447 4.270008 CAACCACCCCAATAAACTAGGAG 58.730 47.826 0.00 0.00 0.00 3.69
771 1448 2.850568 ACCACCCCAATAAACTAGGAGG 59.149 50.000 0.00 0.00 34.80 4.30
772 1449 3.120108 CCACCCCAATAAACTAGGAGGA 58.880 50.000 0.00 0.00 30.60 3.71
773 1450 3.526019 CCACCCCAATAAACTAGGAGGAA 59.474 47.826 0.00 0.00 30.60 3.36
774 1451 4.385310 CCACCCCAATAAACTAGGAGGAAG 60.385 50.000 0.00 0.00 30.60 3.46
775 1452 4.473559 CACCCCAATAAACTAGGAGGAAGA 59.526 45.833 0.00 0.00 0.00 2.87
776 1453 5.132816 CACCCCAATAAACTAGGAGGAAGAT 59.867 44.000 0.00 0.00 0.00 2.40
777 1454 5.369993 ACCCCAATAAACTAGGAGGAAGATC 59.630 44.000 0.00 0.00 0.00 2.75
778 1455 5.221945 CCCCAATAAACTAGGAGGAAGATCC 60.222 48.000 0.00 0.00 39.89 3.36
779 1456 5.221945 CCCAATAAACTAGGAGGAAGATCCC 60.222 48.000 0.00 0.00 40.53 3.85
780 1457 5.369699 CCAATAAACTAGGAGGAAGATCCCA 59.630 44.000 0.00 0.00 40.53 4.37
781 1458 6.044871 CCAATAAACTAGGAGGAAGATCCCAT 59.955 42.308 0.00 0.00 40.53 4.00
782 1459 6.694445 ATAAACTAGGAGGAAGATCCCATG 57.306 41.667 0.00 0.00 40.53 3.66
783 1460 2.334023 ACTAGGAGGAAGATCCCATGC 58.666 52.381 0.00 0.00 40.53 4.06
784 1461 2.333069 CTAGGAGGAAGATCCCATGCA 58.667 52.381 0.00 0.00 40.53 3.96
785 1462 1.600058 AGGAGGAAGATCCCATGCAA 58.400 50.000 0.00 0.00 40.53 4.08
786 1463 1.925255 AGGAGGAAGATCCCATGCAAA 59.075 47.619 0.00 0.00 40.53 3.68
787 1464 2.312741 AGGAGGAAGATCCCATGCAAAA 59.687 45.455 0.00 0.00 40.53 2.44
788 1465 3.099141 GGAGGAAGATCCCATGCAAAAA 58.901 45.455 0.00 0.00 37.19 1.94
951 1632 5.143660 CGCAATTGTCGTCTTGTCAATTTA 58.856 37.500 7.40 0.00 41.49 1.40
1682 2931 0.869028 GTAAGTTCGTCCGCCGATCC 60.869 60.000 0.00 0.00 46.75 3.36
1708 2957 4.761739 GGAAATTCGGATTGCATCTGGATA 59.238 41.667 0.00 0.00 32.58 2.59
1744 2993 2.500442 CTGACGTGACGCGATCTGC 61.500 63.158 15.93 3.72 44.77 4.26
1746 2995 2.500442 GACGTGACGCGATCTGCTG 61.500 63.158 15.93 0.00 44.77 4.41
1748 2997 2.181777 GTGACGCGATCTGCTGGA 59.818 61.111 15.93 0.00 43.27 3.86
1849 3098 3.517296 TGTGCCTGGATTGAAGGTAAA 57.483 42.857 0.00 0.00 37.13 2.01
1853 3102 3.694072 TGCCTGGATTGAAGGTAAATTCG 59.306 43.478 0.00 0.00 37.13 3.34
1922 3171 4.576463 AGGGTTGATTAGCATCGTGAATTC 59.424 41.667 0.00 0.00 31.08 2.17
1937 3186 9.133627 CATCGTGAATTCTATTACTATGAGTGG 57.866 37.037 7.05 0.00 0.00 4.00
2113 3487 7.876068 CCAACATGTACAGGAAGTAGTTTCTTA 59.124 37.037 15.54 0.00 36.03 2.10
2165 3539 3.495331 TGAGGGCAGCTTTAATTTGTCA 58.505 40.909 0.00 0.00 0.00 3.58
2347 3853 0.604578 CCCAATTGTGAGTGCCCAAG 59.395 55.000 4.43 0.00 0.00 3.61
2367 3873 9.358872 GCCCAAGAATTTTTGTTTCTTCTATAG 57.641 33.333 7.83 0.00 40.53 1.31
2396 3902 2.752144 GCATATCAGTGCAGTGCTTC 57.248 50.000 17.07 9.58 44.43 3.86
2400 3906 4.454847 GCATATCAGTGCAGTGCTTCATAT 59.545 41.667 17.07 11.37 44.43 1.78
2408 3914 6.525628 CAGTGCAGTGCTTCATATTTTGTTAG 59.474 38.462 17.60 0.00 0.00 2.34
2428 3934 1.003233 GGGGTTGTCCTAGTTCTGTGG 59.997 57.143 0.00 0.00 35.33 4.17
2429 3935 1.610886 GGGTTGTCCTAGTTCTGTGGC 60.611 57.143 0.00 0.00 0.00 5.01
2430 3936 1.429463 GTTGTCCTAGTTCTGTGGCG 58.571 55.000 0.00 0.00 0.00 5.69
2515 4021 8.953313 ACTGTAATAACTTAATTTACCTGCACC 58.047 33.333 0.00 0.00 0.00 5.01
2584 4090 7.917505 GGTTTCAGATTTGCCTGACATTAATAG 59.082 37.037 0.00 0.00 42.33 1.73
2594 4100 5.449177 GCCTGACATTAATAGTTTGCTGGAC 60.449 44.000 0.00 0.00 0.00 4.02
2664 4170 3.644265 TGTCTACAGTAGGTGGCTTGAAA 59.356 43.478 7.79 0.00 0.00 2.69
2676 4182 4.739716 GGTGGCTTGAAATATATGTTTGCG 59.260 41.667 1.75 0.00 0.00 4.85
2748 4255 7.512130 TGGCTGTATACTTTGATGATCAATCT 58.488 34.615 8.90 0.00 36.11 2.40
2767 4275 7.623630 TCAATCTTCTAACACTGATTCCATCA 58.376 34.615 0.00 0.00 37.76 3.07
2772 4280 7.984050 TCTTCTAACACTGATTCCATCATCTTC 59.016 37.037 0.00 0.00 38.85 2.87
2797 4305 3.129287 CCTTCCATTGTTTCCCATCGAAG 59.871 47.826 0.00 0.00 0.00 3.79
2830 4338 3.230134 TCTGTTTCCAGAACCCCAAATG 58.770 45.455 0.00 0.00 44.67 2.32
2858 4366 4.052159 TGTTTTGCCATGTCAATTTCGT 57.948 36.364 0.00 0.00 0.00 3.85
2880 4388 2.252976 AACCGCTAAAACACCCGTTA 57.747 45.000 0.00 0.00 33.99 3.18
2882 4390 2.570135 ACCGCTAAAACACCCGTTAAA 58.430 42.857 0.00 0.00 33.99 1.52
2909 4421 5.192176 TGAAGTATGGAAATGCTATGCACA 58.808 37.500 0.00 0.00 43.04 4.57
3273 5114 5.301805 AGGTTGGAATGTTGTGACCTTTTAG 59.698 40.000 0.00 0.00 33.95 1.85
3288 5129 6.583050 TGACCTTTTAGTTTGAACGTTGTTTG 59.417 34.615 5.00 0.00 0.00 2.93
3289 5130 5.346551 ACCTTTTAGTTTGAACGTTGTTTGC 59.653 36.000 5.00 0.00 0.00 3.68
3291 5132 6.090223 CCTTTTAGTTTGAACGTTGTTTGCTT 59.910 34.615 5.00 0.00 0.00 3.91
3418 5261 3.452264 TGCTGAGCTCAAGGTATGTATGT 59.548 43.478 18.85 0.00 0.00 2.29
3603 5446 1.816074 TGCTAAAGCCAAGGTTACCG 58.184 50.000 0.00 0.00 41.18 4.02
3758 5601 0.892755 TCGGCGTTGAGGTCAGTTAT 59.107 50.000 6.85 0.00 0.00 1.89
3904 5747 5.581126 TGTCTTGTTTCTGCTCATTTTGT 57.419 34.783 0.00 0.00 0.00 2.83
3915 5758 5.997746 TCTGCTCATTTTGTGCTAGTAGTTT 59.002 36.000 0.00 0.00 37.71 2.66
3937 5780 8.755018 AGTTTTAAGTTGCAAAGAATTGAATCG 58.245 29.630 0.00 0.00 38.94 3.34
4002 5845 7.745022 TTACGATTTTAGTCATAACCGACAG 57.255 36.000 0.00 0.00 38.43 3.51
4127 5972 7.414266 TGATACAGAGGGAGTATGTGCTATAT 58.586 38.462 0.00 0.00 32.60 0.86
4178 6023 3.645884 CTGCACTTTGAACATTCAAGGG 58.354 45.455 17.61 12.22 46.68 3.95
4235 6080 0.961857 TGCAGTCATTTGGCGCAGAT 60.962 50.000 10.83 0.00 0.00 2.90
4288 6133 3.748568 GTCACCAACCTGAAGATGAAGAC 59.251 47.826 0.00 0.00 0.00 3.01
4365 6210 0.537143 CTTGGGTGTTGCTGGCAGTA 60.537 55.000 17.16 9.18 0.00 2.74
4427 6272 6.376018 CAGGGGAATTCGTTCCTTATTTGTTA 59.624 38.462 9.91 0.00 40.90 2.41
4475 6320 4.518590 TGCAATTCAGTTTAACTGCTGCTA 59.481 37.500 28.66 19.76 45.54 3.49
4549 6412 2.697431 TTAATGTTTGCCTGTGTCGC 57.303 45.000 0.00 0.00 0.00 5.19
4551 6414 0.311790 AATGTTTGCCTGTGTCGCAG 59.688 50.000 6.41 6.41 44.63 5.18
4561 6424 0.249447 TGTGTCGCAGGTCTCAGTTG 60.249 55.000 0.00 0.00 0.00 3.16
4583 6446 4.814234 TGTCGATTACACTTGCAGTTCTTT 59.186 37.500 0.00 0.00 31.43 2.52
4655 6527 1.747325 AAGGCGGTTGTTGCAGCAAT 61.747 50.000 19.30 0.00 0.00 3.56
4656 6528 2.023223 GGCGGTTGTTGCAGCAATG 61.023 57.895 19.30 15.20 0.00 2.82
4657 6529 1.300080 GCGGTTGTTGCAGCAATGT 60.300 52.632 19.30 0.00 0.00 2.71
4658 6530 1.277495 GCGGTTGTTGCAGCAATGTC 61.277 55.000 19.30 10.85 0.00 3.06
4659 6531 0.030504 CGGTTGTTGCAGCAATGTCA 59.969 50.000 19.30 1.54 0.00 3.58
4660 6532 1.490621 GGTTGTTGCAGCAATGTCAC 58.509 50.000 19.30 6.52 0.00 3.67
4661 6533 1.067516 GGTTGTTGCAGCAATGTCACT 59.932 47.619 19.30 0.00 0.00 3.41
4662 6534 2.293122 GGTTGTTGCAGCAATGTCACTA 59.707 45.455 19.30 0.00 0.00 2.74
4663 6535 3.558505 GTTGTTGCAGCAATGTCACTAG 58.441 45.455 19.30 0.00 0.00 2.57
4722 6607 3.133003 TCTGGTTATTGTCTGCTAGCCTC 59.867 47.826 13.29 3.11 0.00 4.70
4725 6610 4.019321 TGGTTATTGTCTGCTAGCCTCTTT 60.019 41.667 13.29 0.00 0.00 2.52
4742 6627 8.593492 AGCCTCTTTGATTATGTTTTGTTTTC 57.407 30.769 0.00 0.00 0.00 2.29
4743 6628 8.424133 AGCCTCTTTGATTATGTTTTGTTTTCT 58.576 29.630 0.00 0.00 0.00 2.52
4779 6664 6.183360 CCAGTTATCAGAATGTACTTGCAGTG 60.183 42.308 0.00 0.00 37.40 3.66
4796 6681 3.860641 CAGTGGTTATTTTGGGCCAATC 58.139 45.455 21.65 8.37 32.26 2.67
4814 6699 6.462768 GGCCAATCTATATGGTGCAATTCAAA 60.463 38.462 0.00 0.00 40.23 2.69
4823 6708 8.938801 ATATGGTGCAATTCAAACATCCTATA 57.061 30.769 0.00 0.00 0.00 1.31
4834 6719 6.711277 TCAAACATCCTATAGCAACACTTCT 58.289 36.000 0.00 0.00 0.00 2.85
4835 6720 6.818644 TCAAACATCCTATAGCAACACTTCTC 59.181 38.462 0.00 0.00 0.00 2.87
4837 6722 3.438297 TCCTATAGCAACACTTCTCGC 57.562 47.619 0.00 0.00 0.00 5.03
4838 6723 3.024547 TCCTATAGCAACACTTCTCGCT 58.975 45.455 0.00 0.00 38.51 4.93
4840 6725 4.276183 TCCTATAGCAACACTTCTCGCTAG 59.724 45.833 0.00 0.00 40.10 3.42
4842 6727 2.071688 AGCAACACTTCTCGCTAGTG 57.928 50.000 0.00 0.00 46.56 2.74
4846 6731 3.425578 CACTTCTCGCTAGTGTGGG 57.574 57.895 2.66 1.20 38.51 4.61
4847 6732 0.108615 CACTTCTCGCTAGTGTGGGG 60.109 60.000 2.66 0.87 38.51 4.96
4848 6733 0.251653 ACTTCTCGCTAGTGTGGGGA 60.252 55.000 2.66 0.00 0.00 4.81
4849 6734 1.115467 CTTCTCGCTAGTGTGGGGAT 58.885 55.000 2.66 0.00 0.00 3.85
4850 6735 1.482593 CTTCTCGCTAGTGTGGGGATT 59.517 52.381 2.66 0.00 0.00 3.01
4851 6736 0.824109 TCTCGCTAGTGTGGGGATTG 59.176 55.000 2.66 0.00 0.00 2.67
4852 6737 0.811616 CTCGCTAGTGTGGGGATTGC 60.812 60.000 2.66 0.00 0.00 3.56
4854 6739 1.609783 GCTAGTGTGGGGATTGCCT 59.390 57.895 0.00 0.00 0.00 4.75
4869 6754 4.722700 CCTCAGCAACCCCCGTGG 62.723 72.222 0.00 0.00 41.37 4.94
4879 6764 2.518933 CCCCGTGGGTGTTTCCTT 59.481 61.111 3.83 0.00 38.25 3.36
4880 6765 1.901464 CCCCGTGGGTGTTTCCTTG 60.901 63.158 3.83 0.00 38.25 3.61
4881 6766 1.152839 CCCGTGGGTGTTTCCTTGT 60.153 57.895 0.00 0.00 36.25 3.16
4882 6767 0.753848 CCCGTGGGTGTTTCCTTGTT 60.754 55.000 0.00 0.00 36.25 2.83
4883 6768 0.383949 CCGTGGGTGTTTCCTTGTTG 59.616 55.000 0.00 0.00 36.25 3.33
4884 6769 1.384525 CGTGGGTGTTTCCTTGTTGA 58.615 50.000 0.00 0.00 36.25 3.18
4885 6770 1.746220 CGTGGGTGTTTCCTTGTTGAA 59.254 47.619 0.00 0.00 36.25 2.69
4895 6780 1.619654 CCTTGTTGAAGGCATCACCA 58.380 50.000 0.00 0.00 42.60 4.17
4903 6788 2.295885 GAAGGCATCACCAAGGAGATG 58.704 52.381 18.50 18.50 43.03 2.90
4904 6789 0.549950 AGGCATCACCAAGGAGATGG 59.450 55.000 22.33 9.11 46.38 3.51
4906 6791 0.548031 GCATCACCAAGGAGATGGGA 59.452 55.000 22.33 1.14 45.18 4.37
4907 6792 1.144503 GCATCACCAAGGAGATGGGAT 59.855 52.381 22.33 3.01 45.18 3.85
4908 6793 2.423947 GCATCACCAAGGAGATGGGATT 60.424 50.000 22.33 0.00 45.18 3.01
4909 6794 3.907221 CATCACCAAGGAGATGGGATTT 58.093 45.455 15.97 0.00 45.18 2.17
4910 6795 3.370840 TCACCAAGGAGATGGGATTTG 57.629 47.619 0.00 0.00 45.18 2.32
4911 6796 1.753073 CACCAAGGAGATGGGATTTGC 59.247 52.381 0.00 0.00 45.18 3.68
4914 6799 2.625087 CCAAGGAGATGGGATTTGCCTT 60.625 50.000 0.00 0.00 36.79 4.35
4915 6800 2.429610 CAAGGAGATGGGATTTGCCTTG 59.570 50.000 0.00 0.00 44.19 3.61
4917 6802 2.043526 AGGAGATGGGATTTGCCTTGTT 59.956 45.455 0.00 0.00 36.66 2.83
4918 6803 2.167075 GGAGATGGGATTTGCCTTGTTG 59.833 50.000 0.00 0.00 36.66 3.33
4919 6804 2.167075 GAGATGGGATTTGCCTTGTTGG 59.833 50.000 0.00 0.00 36.66 3.77
4920 6805 2.178580 GATGGGATTTGCCTTGTTGGA 58.821 47.619 0.00 0.00 38.35 3.53
4921 6806 2.323999 TGGGATTTGCCTTGTTGGAT 57.676 45.000 0.00 0.00 38.35 3.41
4922 6807 2.178580 TGGGATTTGCCTTGTTGGATC 58.821 47.619 0.00 0.00 38.35 3.36
4923 6808 1.482182 GGGATTTGCCTTGTTGGATCC 59.518 52.381 4.20 4.20 36.50 3.36
4924 6809 2.178580 GGATTTGCCTTGTTGGATCCA 58.821 47.619 11.44 11.44 36.95 3.41
4925 6810 2.094026 GGATTTGCCTTGTTGGATCCAC 60.094 50.000 15.91 10.58 36.95 4.02
4931 6816 2.436417 CCTTGTTGGATCCACGATTGT 58.564 47.619 15.91 0.00 38.35 2.71
4960 6845 5.511202 CCATGGGCTTTGTTACTTTTGATGT 60.511 40.000 2.85 0.00 0.00 3.06
5021 6906 0.664166 GGTTTGCGCTGATGTGGTTG 60.664 55.000 9.73 0.00 0.00 3.77
5075 6960 1.805945 CTACGCTGGTGCTTCCGTC 60.806 63.158 0.00 0.00 39.52 4.79
5088 6973 1.252215 TTCCGTCCATGACAGCGGTA 61.252 55.000 13.73 5.28 44.07 4.02
5089 6974 1.518572 CCGTCCATGACAGCGGTAC 60.519 63.158 0.00 0.00 39.41 3.34
5090 6975 1.214325 CGTCCATGACAGCGGTACA 59.786 57.895 0.00 0.00 32.09 2.90
5091 6976 1.076533 CGTCCATGACAGCGGTACAC 61.077 60.000 0.00 0.00 32.09 2.90
5092 6977 1.076533 GTCCATGACAGCGGTACACG 61.077 60.000 0.00 0.00 37.86 4.49
5093 6978 1.080093 CCATGACAGCGGTACACGT 60.080 57.895 0.00 0.00 46.52 4.49
5094 6979 0.171679 CCATGACAGCGGTACACGTA 59.828 55.000 0.00 0.00 46.52 3.57
5150 7699 2.263077 CCGAAGTGGACTTTCGAGATG 58.737 52.381 8.76 0.00 42.00 2.90
5156 7705 4.087182 AGTGGACTTTCGAGATGGTAAGA 58.913 43.478 0.00 0.00 0.00 2.10
5157 7706 4.712337 AGTGGACTTTCGAGATGGTAAGAT 59.288 41.667 0.00 0.00 0.00 2.40
5158 7707 5.044558 GTGGACTTTCGAGATGGTAAGATC 58.955 45.833 0.00 0.00 0.00 2.75
5159 7708 4.709886 TGGACTTTCGAGATGGTAAGATCA 59.290 41.667 0.00 0.00 0.00 2.92
5160 7709 5.363868 TGGACTTTCGAGATGGTAAGATCAT 59.636 40.000 0.00 0.00 0.00 2.45
5161 7710 5.923684 GGACTTTCGAGATGGTAAGATCATC 59.076 44.000 0.00 0.00 40.79 2.92
5162 7711 5.848406 ACTTTCGAGATGGTAAGATCATCC 58.152 41.667 0.00 0.00 41.25 3.51
5163 7712 5.363868 ACTTTCGAGATGGTAAGATCATCCA 59.636 40.000 0.00 0.49 41.25 3.41
5164 7713 4.855715 TCGAGATGGTAAGATCATCCAC 57.144 45.455 0.00 0.00 41.25 4.02
5165 7714 4.215109 TCGAGATGGTAAGATCATCCACA 58.785 43.478 0.00 0.00 41.25 4.17
5166 7715 4.279420 TCGAGATGGTAAGATCATCCACAG 59.721 45.833 0.00 0.00 41.25 3.66
5167 7716 4.314121 GAGATGGTAAGATCATCCACAGC 58.686 47.826 0.00 0.00 41.25 4.40
5168 7717 3.713248 AGATGGTAAGATCATCCACAGCA 59.287 43.478 0.00 0.00 41.25 4.41
5169 7718 3.548745 TGGTAAGATCATCCACAGCAG 57.451 47.619 0.00 0.00 0.00 4.24
5170 7719 2.171237 TGGTAAGATCATCCACAGCAGG 59.829 50.000 0.00 0.00 0.00 4.85
5171 7720 2.435805 GGTAAGATCATCCACAGCAGGA 59.564 50.000 0.00 0.00 43.01 3.86
5172 7721 2.706339 AAGATCATCCACAGCAGGAC 57.294 50.000 0.00 0.00 41.30 3.85
5173 7722 1.876849 AGATCATCCACAGCAGGACT 58.123 50.000 0.00 0.00 41.30 3.85
5174 7723 2.194859 AGATCATCCACAGCAGGACTT 58.805 47.619 0.00 0.00 41.30 3.01
5175 7724 3.378512 AGATCATCCACAGCAGGACTTA 58.621 45.455 0.00 0.00 41.30 2.24
5176 7725 3.387374 AGATCATCCACAGCAGGACTTAG 59.613 47.826 0.00 0.00 41.30 2.18
5177 7726 1.833630 TCATCCACAGCAGGACTTAGG 59.166 52.381 0.00 0.00 41.30 2.69
5178 7727 0.543749 ATCCACAGCAGGACTTAGGC 59.456 55.000 0.00 0.00 41.30 3.93
5179 7728 0.835971 TCCACAGCAGGACTTAGGCA 60.836 55.000 0.00 0.00 31.23 4.75
5180 7729 0.036732 CCACAGCAGGACTTAGGCAA 59.963 55.000 0.00 0.00 0.00 4.52
5181 7730 1.545428 CCACAGCAGGACTTAGGCAAA 60.545 52.381 0.00 0.00 0.00 3.68
5182 7731 2.440409 CACAGCAGGACTTAGGCAAAT 58.560 47.619 0.00 0.00 0.00 2.32
5183 7732 2.421424 CACAGCAGGACTTAGGCAAATC 59.579 50.000 0.00 0.00 0.00 2.17
5184 7733 2.019984 CAGCAGGACTTAGGCAAATCC 58.980 52.381 0.00 0.00 0.00 3.01
5185 7734 1.017387 GCAGGACTTAGGCAAATCCG 58.983 55.000 0.00 0.00 40.77 4.18
5186 7735 1.668419 CAGGACTTAGGCAAATCCGG 58.332 55.000 0.00 0.00 40.77 5.14
5187 7736 0.107165 AGGACTTAGGCAAATCCGGC 60.107 55.000 0.00 0.00 40.77 6.13
5193 7742 4.347865 GGCAAATCCGGCCCTTTA 57.652 55.556 0.00 0.00 45.87 1.85
5194 7743 2.820845 GGCAAATCCGGCCCTTTAT 58.179 52.632 0.00 0.00 45.87 1.40
5199 7748 3.551846 CAAATCCGGCCCTTTATACAGT 58.448 45.455 0.00 0.00 0.00 3.55
5201 7750 1.575419 TCCGGCCCTTTATACAGTGT 58.425 50.000 0.00 0.00 0.00 3.55
5205 7754 1.474498 GGCCCTTTATACAGTGTCCGG 60.474 57.143 0.00 0.00 0.00 5.14
5210 7759 1.191535 TTATACAGTGTCCGGCAGCT 58.808 50.000 0.00 0.00 0.00 4.24
5212 7761 0.972983 ATACAGTGTCCGGCAGCTCT 60.973 55.000 0.00 0.00 0.00 4.09
5214 7763 1.302033 CAGTGTCCGGCAGCTCTTT 60.302 57.895 0.00 0.00 0.00 2.52
5244 7793 0.875908 CCGCACATCCACATACCTCG 60.876 60.000 0.00 0.00 0.00 4.63
5353 7913 7.801547 AAGCAAATCATAGTTCAACAAATCG 57.198 32.000 0.00 0.00 0.00 3.34
5354 7914 6.324819 AGCAAATCATAGTTCAACAAATCGG 58.675 36.000 0.00 0.00 0.00 4.18
5355 7915 6.150976 AGCAAATCATAGTTCAACAAATCGGA 59.849 34.615 0.00 0.00 0.00 4.55
5356 7916 6.974622 GCAAATCATAGTTCAACAAATCGGAT 59.025 34.615 0.00 0.00 0.00 4.18
5357 7917 8.128582 GCAAATCATAGTTCAACAAATCGGATA 58.871 33.333 0.00 0.00 0.00 2.59
5381 7941 7.605410 AATGCCAAAATGAAATCAATGTCTC 57.395 32.000 0.00 0.00 0.00 3.36
5475 8074 2.271173 CTGCTCTGCCTGCATCCA 59.729 61.111 0.00 0.00 39.86 3.41
5491 8090 2.359169 CCAGGCCTACTTCTCCGCA 61.359 63.158 3.98 0.00 0.00 5.69
5532 8158 0.456312 CTTGCCGTGTCGTACTCTCC 60.456 60.000 0.00 0.00 0.00 3.71
5559 8193 4.991687 GTCGTTGATCTCCTTCTTCTTGTT 59.008 41.667 0.00 0.00 0.00 2.83
5655 8290 1.016653 GCGAGTTGCAACCTCTCCTC 61.017 60.000 25.62 14.21 45.45 3.71
5661 8296 1.434188 TGCAACCTCTCCTCCTCAAA 58.566 50.000 0.00 0.00 0.00 2.69
5663 8298 1.611936 GCAACCTCTCCTCCTCAAACC 60.612 57.143 0.00 0.00 0.00 3.27
5707 8343 4.507710 CTTCTCGAGTTCCCATTTGATCA 58.492 43.478 13.13 0.00 0.00 2.92
5776 8412 3.310860 TTCTTCGCCCTCTTCCGGC 62.311 63.158 0.00 0.00 43.38 6.13
5777 8413 4.840005 CTTCGCCCTCTTCCGGCC 62.840 72.222 0.00 0.00 43.98 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 7.041098 CCAGGCTGTATCATAAAAAGGATACAC 60.041 40.741 14.43 7.64 46.51 2.90
44 46 4.215827 CAGCTAAAATGAGATCATCCAGGC 59.784 45.833 0.00 0.34 35.10 4.85
98 100 3.838565 TGGAAAAATACCAGCCTGACAA 58.161 40.909 0.00 0.00 33.22 3.18
99 101 3.517296 TGGAAAAATACCAGCCTGACA 57.483 42.857 0.00 0.00 33.22 3.58
139 177 7.123247 GCACCCTGCAAATATTATGATTCCTAT 59.877 37.037 0.00 0.00 44.26 2.57
184 222 1.464997 CAGGCGAAGGTTTCTAGCAAC 59.535 52.381 0.00 0.00 0.00 4.17
187 835 1.809684 AACAGGCGAAGGTTTCTAGC 58.190 50.000 0.00 0.00 0.00 3.42
225 873 5.009854 TCAAAAGAAGAAAAAGTGCAGGG 57.990 39.130 0.00 0.00 0.00 4.45
226 874 6.642540 GGTATCAAAAGAAGAAAAAGTGCAGG 59.357 38.462 0.00 0.00 0.00 4.85
238 888 6.385033 CAGGCTTCTTTGGTATCAAAAGAAG 58.615 40.000 23.89 23.89 42.59 2.85
240 890 4.218417 GCAGGCTTCTTTGGTATCAAAAGA 59.782 41.667 2.19 0.14 41.70 2.52
241 891 4.488879 GCAGGCTTCTTTGGTATCAAAAG 58.511 43.478 2.19 0.00 41.70 2.27
248 898 3.981308 GCGCAGGCTTCTTTGGTA 58.019 55.556 0.30 0.00 35.83 3.25
264 914 6.811665 ACTAAAGAAAACAGGTGAAAACAAGC 59.188 34.615 0.00 0.00 0.00 4.01
307 960 3.458189 AGACAACTTCCAACTTCTCACG 58.542 45.455 0.00 0.00 0.00 4.35
393 1053 1.053264 AAACAACCCTGGCAATGGCA 61.053 50.000 9.67 9.67 43.71 4.92
416 1076 8.306038 CAACCATCCTCTTTCATCATAAACAAA 58.694 33.333 0.00 0.00 0.00 2.83
438 1098 3.889538 AGGAAGACAAAGCTAAACCAACC 59.110 43.478 0.00 0.00 0.00 3.77
440 1100 8.789762 GTTATTAGGAAGACAAAGCTAAACCAA 58.210 33.333 0.00 0.00 0.00 3.67
442 1102 8.563123 AGTTATTAGGAAGACAAAGCTAAACC 57.437 34.615 0.00 0.00 0.00 3.27
444 1104 9.379791 GCTAGTTATTAGGAAGACAAAGCTAAA 57.620 33.333 0.00 0.00 0.00 1.85
469 1130 2.618241 TGACGCTGGGAATATTTGATGC 59.382 45.455 0.00 0.00 0.00 3.91
485 1146 4.152625 GTGCCGCTGTCATGACGC 62.153 66.667 23.80 23.80 0.00 5.19
566 1227 5.236478 CGGAATTCGGAAAATATGCACTACT 59.764 40.000 7.20 0.00 34.75 2.57
567 1228 5.235616 TCGGAATTCGGAAAATATGCACTAC 59.764 40.000 12.85 0.00 39.77 2.73
568 1229 5.235616 GTCGGAATTCGGAAAATATGCACTA 59.764 40.000 16.39 0.00 39.77 2.74
630 1291 9.692749 AATCTTCATGATGTTAATGATTGATGC 57.307 29.630 8.33 0.00 34.14 3.91
653 1314 9.624697 CAGAATAGAACTACTAGCATCTCAATC 57.375 37.037 0.00 0.00 34.35 2.67
692 1353 7.829725 TCTAATAAGTTCTGGCGTAAGTACAA 58.170 34.615 0.00 0.00 41.68 2.41
765 1442 2.494888 TGCATGGGATCTTCCTCCTA 57.505 50.000 0.00 0.00 36.57 2.94
766 1443 1.600058 TTGCATGGGATCTTCCTCCT 58.400 50.000 0.00 0.00 36.57 3.69
767 1444 2.442236 TTTGCATGGGATCTTCCTCC 57.558 50.000 0.00 0.00 36.57 4.30
792 1469 8.386264 TGAAATCTGATCTTCCTCCTAGTTTTT 58.614 33.333 0.00 0.00 0.00 1.94
793 1470 7.922382 TGAAATCTGATCTTCCTCCTAGTTTT 58.078 34.615 0.00 0.00 0.00 2.43
794 1471 7.502060 TGAAATCTGATCTTCCTCCTAGTTT 57.498 36.000 0.00 0.00 0.00 2.66
795 1472 7.688918 ATGAAATCTGATCTTCCTCCTAGTT 57.311 36.000 0.00 0.00 0.00 2.24
796 1473 7.040062 CGTATGAAATCTGATCTTCCTCCTAGT 60.040 40.741 0.00 0.00 0.00 2.57
797 1474 7.312154 CGTATGAAATCTGATCTTCCTCCTAG 58.688 42.308 0.00 0.00 0.00 3.02
927 1608 0.865111 TGACAAGACGACAATTGCGG 59.135 50.000 20.77 10.12 0.00 5.69
951 1632 7.118723 TGCAACATTGATTAACCTCCTCTTAT 58.881 34.615 0.00 0.00 0.00 1.73
1723 2972 1.022982 AGATCGCGTCACGTCAGGTA 61.023 55.000 5.77 0.00 44.19 3.08
1725 2974 1.869574 CAGATCGCGTCACGTCAGG 60.870 63.158 5.77 0.00 44.19 3.86
1744 2993 4.150627 CGTCTGCATAACGGAAATATCCAG 59.849 45.833 12.56 0.00 46.97 3.86
1746 2995 4.647291 CGTCTGCATAACGGAAATATCC 57.353 45.455 12.56 0.00 42.80 2.59
1849 3098 4.510167 ATCAACCAAGAGGGATTCGAAT 57.490 40.909 11.20 11.20 41.15 3.34
1853 3102 4.221482 AGCAAAATCAACCAAGAGGGATTC 59.779 41.667 0.00 0.00 41.15 2.52
1930 3179 4.767578 AGCAATCAGACATACCACTCAT 57.232 40.909 0.00 0.00 0.00 2.90
1933 3182 4.460382 CCAAAAGCAATCAGACATACCACT 59.540 41.667 0.00 0.00 0.00 4.00
1937 3186 5.156355 CACACCAAAAGCAATCAGACATAC 58.844 41.667 0.00 0.00 0.00 2.39
1943 3192 6.900568 TTAAAACACACCAAAAGCAATCAG 57.099 33.333 0.00 0.00 0.00 2.90
1949 3198 5.236263 CCTCCATTTAAAACACACCAAAAGC 59.764 40.000 0.00 0.00 0.00 3.51
2009 3383 2.569404 AGGAAGGCCTCTTCTGTAACTG 59.431 50.000 5.23 0.00 42.19 3.16
2072 3446 0.453390 GTTGGAACAGCTAGGCATGC 59.547 55.000 9.90 9.90 42.39 4.06
2130 3504 4.383770 GCTGCCCTCAGGTAAACATAGTAA 60.384 45.833 0.00 0.00 40.65 2.24
2133 3507 2.565841 GCTGCCCTCAGGTAAACATAG 58.434 52.381 0.00 0.00 40.65 2.23
2134 3508 2.710096 GCTGCCCTCAGGTAAACATA 57.290 50.000 0.00 0.00 40.65 2.29
2135 3509 3.577389 GCTGCCCTCAGGTAAACAT 57.423 52.632 0.00 0.00 40.65 2.71
2388 3894 5.418840 ACCCCTAACAAAATATGAAGCACTG 59.581 40.000 0.00 0.00 0.00 3.66
2396 3902 7.116736 ACTAGGACAACCCCTAACAAAATATG 58.883 38.462 0.00 0.00 38.26 1.78
2400 3906 5.133153 AGAACTAGGACAACCCCTAACAAAA 59.867 40.000 0.00 0.00 38.26 2.44
2408 3914 1.003233 CCACAGAACTAGGACAACCCC 59.997 57.143 0.00 0.00 36.73 4.95
2428 3934 0.453390 AAAAGAATGGCTAGCAGCGC 59.547 50.000 18.24 0.00 43.62 5.92
2429 3935 5.869753 ATATAAAAGAATGGCTAGCAGCG 57.130 39.130 18.24 0.00 43.62 5.18
2430 3936 7.880105 AGAAATATAAAAGAATGGCTAGCAGC 58.120 34.615 18.24 0.00 41.46 5.25
2561 4067 8.579850 AACTATTAATGTCAGGCAAATCTGAA 57.420 30.769 0.00 0.00 44.30 3.02
2584 4090 0.108585 TGGAGACAGGTCCAGCAAAC 59.891 55.000 0.00 0.00 41.99 2.93
2767 4275 3.766051 GGAAACAATGGAAGGCAGAAGAT 59.234 43.478 0.00 0.00 0.00 2.40
2772 4280 1.631405 TGGGAAACAATGGAAGGCAG 58.369 50.000 0.00 0.00 0.00 4.85
2797 4305 4.305989 TGGAAACAGAACAATCAAGTGC 57.694 40.909 0.00 0.00 35.01 4.40
2830 4338 3.715495 TGACATGGCAAAACAATGTGAC 58.285 40.909 0.00 0.00 0.00 3.67
2858 4366 1.344114 ACGGGTGTTTTAGCGGTTAGA 59.656 47.619 0.00 0.00 37.06 2.10
2880 4388 8.086522 GCATAGCATTTCCATACTTCATGATTT 58.913 33.333 0.00 0.00 36.69 2.17
2882 4390 6.717997 TGCATAGCATTTCCATACTTCATGAT 59.282 34.615 0.00 0.00 32.73 2.45
2909 4421 2.928334 CTGTCATCAGGCCATAAGCTT 58.072 47.619 5.01 3.48 43.05 3.74
3005 4750 0.319297 GACGACTGTAACTGCCCGTT 60.319 55.000 0.00 0.00 39.64 4.44
3006 4751 1.177256 AGACGACTGTAACTGCCCGT 61.177 55.000 0.00 0.00 0.00 5.28
3098 4938 8.890124 TGCACTACTAACAAAATAACTACACA 57.110 30.769 0.00 0.00 0.00 3.72
3141 4981 8.197439 CCATTTCAAGAACCTAAATAATGGGAC 58.803 37.037 0.00 0.00 37.94 4.46
3273 5114 3.246619 TGGAAGCAAACAACGTTCAAAC 58.753 40.909 0.00 0.00 0.00 2.93
3418 5261 9.986833 CATAACTGACGATTTTCAATACAATCA 57.013 29.630 0.00 0.00 30.84 2.57
3758 5601 9.982651 GTAGCCTACATAAATTAGATCAGACAA 57.017 33.333 0.00 0.00 0.00 3.18
3818 5661 5.491070 CATCAGTTTGACCAGTCCAGAATA 58.509 41.667 0.00 0.00 0.00 1.75
3829 5672 1.537202 GCTGTGACCATCAGTTTGACC 59.463 52.381 0.00 0.00 35.60 4.02
3904 5747 7.795482 TCTTTGCAACTTAAAACTACTAGCA 57.205 32.000 0.00 0.00 0.00 3.49
3915 5758 9.176181 GTTACGATTCAATTCTTTGCAACTTAA 57.824 29.630 0.00 0.00 32.61 1.85
3988 5831 5.334879 GCAATGAAAACTGTCGGTTATGACT 60.335 40.000 0.00 0.00 39.64 3.41
4002 5845 7.147976 ACATACTTTCAAGAGGCAATGAAAAC 58.852 34.615 11.64 0.00 42.96 2.43
4095 5940 7.011763 CACATACTCCCTCTGTATCAAAATGTG 59.988 40.741 0.00 0.00 0.00 3.21
4178 6023 5.163854 CGTGTTAGAACTGGTTCATCAATCC 60.164 44.000 14.67 0.00 41.84 3.01
4190 6035 4.295870 TCAAGTAGTGCGTGTTAGAACTG 58.704 43.478 0.00 0.00 31.25 3.16
4235 6080 5.326069 AGTGTAGCTCTCAACTCCTTTCTA 58.674 41.667 0.00 0.00 0.00 2.10
4288 6133 5.466432 TCATCGTGTTAGAAGAGTACTCG 57.534 43.478 17.07 2.96 34.09 4.18
4365 6210 3.855858 ACAGGTTCGTTTTGCAACAAAT 58.144 36.364 0.00 0.00 32.54 2.32
4549 6412 3.921021 GTGTAATCGACAACTGAGACCTG 59.079 47.826 0.00 0.00 40.66 4.00
4551 6414 4.175787 AGTGTAATCGACAACTGAGACC 57.824 45.455 0.00 0.00 40.66 3.85
4583 6446 2.700722 TATAACAGTTGCCATGCGGA 57.299 45.000 0.00 0.00 0.00 5.54
4655 6527 2.352421 GGCAACTAACGAGCTAGTGACA 60.352 50.000 0.00 0.00 32.35 3.58
4656 6528 2.260481 GGCAACTAACGAGCTAGTGAC 58.740 52.381 0.00 0.00 32.35 3.67
4657 6529 2.649331 GGCAACTAACGAGCTAGTGA 57.351 50.000 0.00 0.00 32.35 3.41
4722 6607 9.196552 GGGAGAGAAAACAAAACATAATCAAAG 57.803 33.333 0.00 0.00 0.00 2.77
4725 6610 7.831691 TGGGAGAGAAAACAAAACATAATCA 57.168 32.000 0.00 0.00 0.00 2.57
4742 6627 5.389520 TCTGATAACTGGTCTATGGGAGAG 58.610 45.833 0.00 0.00 33.72 3.20
4743 6628 5.403558 TCTGATAACTGGTCTATGGGAGA 57.596 43.478 0.00 0.00 0.00 3.71
4779 6664 6.496911 ACCATATAGATTGGCCCAAAATAACC 59.503 38.462 0.00 0.00 37.81 2.85
4796 6681 7.281040 AGGATGTTTGAATTGCACCATATAG 57.719 36.000 0.00 0.00 0.00 1.31
4814 6699 4.737946 GCGAGAAGTGTTGCTATAGGATGT 60.738 45.833 1.04 0.00 0.00 3.06
4823 6708 2.071688 CACTAGCGAGAAGTGTTGCT 57.928 50.000 0.00 0.00 39.61 3.91
4834 6719 1.220749 GCAATCCCCACACTAGCGA 59.779 57.895 0.00 0.00 0.00 4.93
4835 6720 1.819632 GGCAATCCCCACACTAGCG 60.820 63.158 0.00 0.00 0.00 4.26
4837 6722 0.911769 TGAGGCAATCCCCACACTAG 59.088 55.000 0.00 0.00 0.00 2.57
4838 6723 0.911769 CTGAGGCAATCCCCACACTA 59.088 55.000 0.00 0.00 0.00 2.74
4840 6725 2.048603 GCTGAGGCAATCCCCACAC 61.049 63.158 0.00 0.00 38.54 3.82
4842 6727 2.356278 TGCTGAGGCAATCCCCAC 59.644 61.111 0.00 0.00 46.36 4.61
4852 6737 4.722700 CCACGGGGGTTGCTGAGG 62.723 72.222 0.00 0.00 0.00 3.86
4863 6748 0.753848 AACAAGGAAACACCCACGGG 60.754 55.000 0.00 0.00 40.05 5.28
4864 6749 0.383949 CAACAAGGAAACACCCACGG 59.616 55.000 0.00 0.00 40.05 4.94
4865 6750 1.384525 TCAACAAGGAAACACCCACG 58.615 50.000 0.00 0.00 40.05 4.94
4866 6751 3.436700 CTTCAACAAGGAAACACCCAC 57.563 47.619 0.00 0.00 40.05 4.61
4880 6765 1.815003 CTCCTTGGTGATGCCTTCAAC 59.185 52.381 0.00 0.00 42.83 3.18
4881 6766 1.704628 TCTCCTTGGTGATGCCTTCAA 59.295 47.619 0.00 0.00 35.70 2.69
4882 6767 1.361204 TCTCCTTGGTGATGCCTTCA 58.639 50.000 0.00 0.00 38.35 3.02
4883 6768 2.295885 CATCTCCTTGGTGATGCCTTC 58.704 52.381 15.77 0.00 38.35 3.46
4884 6769 1.064166 CCATCTCCTTGGTGATGCCTT 60.064 52.381 20.25 0.00 38.84 4.35
4885 6770 0.549950 CCATCTCCTTGGTGATGCCT 59.450 55.000 20.25 0.00 38.84 4.75
4895 6780 2.043526 ACAAGGCAAATCCCATCTCCTT 59.956 45.455 0.00 0.00 34.54 3.36
4903 6788 1.482182 GGATCCAACAAGGCAAATCCC 59.518 52.381 6.95 0.00 33.93 3.85
4904 6789 2.094026 GTGGATCCAACAAGGCAAATCC 60.094 50.000 18.20 0.00 38.30 3.01
4906 6791 1.545582 CGTGGATCCAACAAGGCAAAT 59.454 47.619 18.20 0.00 37.29 2.32
4907 6792 0.958091 CGTGGATCCAACAAGGCAAA 59.042 50.000 18.20 0.00 37.29 3.68
4908 6793 0.109532 TCGTGGATCCAACAAGGCAA 59.890 50.000 18.20 0.00 37.29 4.52
4909 6794 0.327924 ATCGTGGATCCAACAAGGCA 59.672 50.000 18.20 0.00 37.29 4.75
4910 6795 1.133025 CAATCGTGGATCCAACAAGGC 59.867 52.381 18.20 1.30 37.29 4.35
4911 6796 2.162208 CACAATCGTGGATCCAACAAGG 59.838 50.000 18.20 9.16 39.64 3.61
4923 6808 1.507630 CCATGGTGCCACAATCGTG 59.492 57.895 2.57 0.00 43.21 4.35
4924 6809 1.678635 CCCATGGTGCCACAATCGT 60.679 57.895 11.73 0.00 0.00 3.73
4925 6810 3.067480 GCCCATGGTGCCACAATCG 62.067 63.158 11.73 0.00 0.00 3.34
4931 6816 0.178950 TAACAAAGCCCATGGTGCCA 60.179 50.000 18.29 0.00 0.00 4.92
4960 6845 8.203681 AGATCATGTCTCCAAGATGATGATTA 57.796 34.615 12.21 0.00 45.68 1.75
5062 6947 1.021390 GTCATGGACGGAAGCACCAG 61.021 60.000 0.00 0.00 42.34 4.00
5075 6960 0.171679 TACGTGTACCGCTGTCATGG 59.828 55.000 0.00 0.00 41.42 3.66
5088 6973 5.124645 CCTCTATCCAAGTAGTCTACGTGT 58.875 45.833 20.18 8.97 36.60 4.49
5089 6974 4.515944 CCCTCTATCCAAGTAGTCTACGTG 59.484 50.000 16.43 16.43 37.80 4.49
5090 6975 4.411540 TCCCTCTATCCAAGTAGTCTACGT 59.588 45.833 4.34 0.00 0.00 3.57
5091 6976 4.970711 TCCCTCTATCCAAGTAGTCTACG 58.029 47.826 4.34 0.00 0.00 3.51
5092 6977 7.612633 CCTAATCCCTCTATCCAAGTAGTCTAC 59.387 44.444 1.39 1.39 0.00 2.59
5093 6978 7.297588 ACCTAATCCCTCTATCCAAGTAGTCTA 59.702 40.741 0.00 0.00 0.00 2.59
5094 6979 6.104990 ACCTAATCCCTCTATCCAAGTAGTCT 59.895 42.308 0.00 0.00 0.00 3.24
5132 7681 3.320673 ACCATCTCGAAAGTCCACTTC 57.679 47.619 0.00 0.00 34.61 3.01
5150 7699 2.435805 TCCTGCTGTGGATGATCTTACC 59.564 50.000 0.00 0.00 0.00 2.85
5156 7705 2.437281 CCTAAGTCCTGCTGTGGATGAT 59.563 50.000 0.00 0.00 38.52 2.45
5157 7706 1.833630 CCTAAGTCCTGCTGTGGATGA 59.166 52.381 0.00 0.00 38.52 2.92
5158 7707 1.745141 GCCTAAGTCCTGCTGTGGATG 60.745 57.143 0.00 0.00 38.52 3.51
5159 7708 0.543749 GCCTAAGTCCTGCTGTGGAT 59.456 55.000 0.00 0.00 38.52 3.41
5160 7709 0.835971 TGCCTAAGTCCTGCTGTGGA 60.836 55.000 0.00 0.00 0.00 4.02
5161 7710 0.036732 TTGCCTAAGTCCTGCTGTGG 59.963 55.000 0.00 0.00 0.00 4.17
5162 7711 1.896220 TTTGCCTAAGTCCTGCTGTG 58.104 50.000 0.00 0.00 0.00 3.66
5163 7712 2.619074 GGATTTGCCTAAGTCCTGCTGT 60.619 50.000 0.00 0.00 39.06 4.40
5164 7713 2.019984 GGATTTGCCTAAGTCCTGCTG 58.980 52.381 0.00 0.00 39.06 4.41
5165 7714 1.407437 CGGATTTGCCTAAGTCCTGCT 60.407 52.381 0.00 0.00 39.75 4.24
5166 7715 1.017387 CGGATTTGCCTAAGTCCTGC 58.983 55.000 0.00 0.00 39.75 4.85
5167 7716 1.668419 CCGGATTTGCCTAAGTCCTG 58.332 55.000 0.00 0.00 39.75 3.86
5168 7717 0.107165 GCCGGATTTGCCTAAGTCCT 60.107 55.000 5.05 0.00 39.75 3.85
5169 7718 1.101635 GGCCGGATTTGCCTAAGTCC 61.102 60.000 5.05 0.00 45.70 3.85
5170 7719 2.405143 GGCCGGATTTGCCTAAGTC 58.595 57.895 5.05 0.00 45.70 3.01
5171 7720 4.657952 GGCCGGATTTGCCTAAGT 57.342 55.556 5.05 0.00 45.70 2.24
5177 7726 2.293399 CTGTATAAAGGGCCGGATTTGC 59.707 50.000 5.05 0.00 0.00 3.68
5178 7727 3.315191 CACTGTATAAAGGGCCGGATTTG 59.685 47.826 5.05 0.00 0.00 2.32
5179 7728 3.053917 ACACTGTATAAAGGGCCGGATTT 60.054 43.478 5.05 5.20 0.00 2.17
5180 7729 2.508300 ACACTGTATAAAGGGCCGGATT 59.492 45.455 5.05 0.00 0.00 3.01
5181 7730 2.104281 GACACTGTATAAAGGGCCGGAT 59.896 50.000 5.05 0.00 0.00 4.18
5182 7731 1.483415 GACACTGTATAAAGGGCCGGA 59.517 52.381 5.05 0.00 0.00 5.14
5183 7732 1.474498 GGACACTGTATAAAGGGCCGG 60.474 57.143 0.00 0.00 0.00 6.13
5184 7733 1.805120 CGGACACTGTATAAAGGGCCG 60.805 57.143 11.90 11.90 35.17 6.13
5185 7734 1.474498 CCGGACACTGTATAAAGGGCC 60.474 57.143 0.00 0.00 0.00 5.80
5186 7735 1.949465 CCGGACACTGTATAAAGGGC 58.051 55.000 0.00 0.00 0.00 5.19
5187 7736 1.208535 TGCCGGACACTGTATAAAGGG 59.791 52.381 5.05 0.00 0.00 3.95
5188 7737 2.550978 CTGCCGGACACTGTATAAAGG 58.449 52.381 5.05 0.00 0.00 3.11
5189 7738 1.933853 GCTGCCGGACACTGTATAAAG 59.066 52.381 5.05 0.00 0.00 1.85
5190 7739 1.553248 AGCTGCCGGACACTGTATAAA 59.447 47.619 5.05 0.00 0.00 1.40
5191 7740 1.136305 GAGCTGCCGGACACTGTATAA 59.864 52.381 5.05 0.00 0.00 0.98
5192 7741 0.744874 GAGCTGCCGGACACTGTATA 59.255 55.000 5.05 0.00 0.00 1.47
5193 7742 0.972983 AGAGCTGCCGGACACTGTAT 60.973 55.000 5.05 0.00 0.00 2.29
5194 7743 1.185618 AAGAGCTGCCGGACACTGTA 61.186 55.000 5.05 0.00 0.00 2.74
5199 7748 2.434336 ACATATAAAGAGCTGCCGGACA 59.566 45.455 5.05 1.09 0.00 4.02
5201 7750 3.466836 CAACATATAAAGAGCTGCCGGA 58.533 45.455 5.05 0.00 0.00 5.14
5205 7754 2.603173 GGCGCAACATATAAAGAGCTGC 60.603 50.000 10.83 0.00 0.00 5.25
5210 7759 1.329292 GTGCGGCGCAACATATAAAGA 59.671 47.619 38.05 6.00 41.47 2.52
5212 7761 1.087501 TGTGCGGCGCAACATATAAA 58.912 45.000 38.05 7.54 41.47 1.40
5214 7763 0.865111 GATGTGCGGCGCAACATATA 59.135 50.000 38.05 18.22 41.47 0.86
5267 7816 2.880963 TGATCGTCGTGCATGGATTA 57.119 45.000 5.98 0.00 0.00 1.75
5349 7909 7.499292 TGATTTCATTTTGGCATTATCCGATT 58.501 30.769 0.00 0.00 0.00 3.34
5350 7910 7.053316 TGATTTCATTTTGGCATTATCCGAT 57.947 32.000 0.00 0.00 0.00 4.18
5351 7911 6.462552 TGATTTCATTTTGGCATTATCCGA 57.537 33.333 0.00 0.00 0.00 4.55
5352 7912 7.225145 ACATTGATTTCATTTTGGCATTATCCG 59.775 33.333 0.00 0.00 0.00 4.18
5353 7913 8.441312 ACATTGATTTCATTTTGGCATTATCC 57.559 30.769 0.00 0.00 0.00 2.59
5354 7914 9.321562 AGACATTGATTTCATTTTGGCATTATC 57.678 29.630 0.00 0.00 0.00 1.75
5355 7915 9.321562 GAGACATTGATTTCATTTTGGCATTAT 57.678 29.630 0.00 0.00 0.00 1.28
5356 7916 8.312564 TGAGACATTGATTTCATTTTGGCATTA 58.687 29.630 0.00 0.00 0.00 1.90
5357 7917 7.162761 TGAGACATTGATTTCATTTTGGCATT 58.837 30.769 0.00 0.00 0.00 3.56
5381 7941 1.890979 GAGGCCATCCGTCATGCTG 60.891 63.158 5.01 0.00 37.47 4.41
5424 7994 2.025156 CATGCCGCATTTCGCTCC 59.975 61.111 2.16 0.00 39.08 4.70
5430 8000 2.420568 CCTGGAGCATGCCGCATTT 61.421 57.895 15.66 0.00 46.13 2.32
5475 8074 1.826024 CATGCGGAGAAGTAGGCCT 59.174 57.895 11.78 11.78 0.00 5.19
5480 8079 0.249447 CGGATGCATGCGGAGAAGTA 60.249 55.000 30.33 0.00 38.00 2.24
5481 8080 1.522355 CGGATGCATGCGGAGAAGT 60.522 57.895 30.33 0.00 38.00 3.01
5484 8083 2.202919 CACGGATGCATGCGGAGA 60.203 61.111 37.89 0.00 46.28 3.71
5520 8120 1.293963 CGACCGTGGAGAGTACGACA 61.294 60.000 0.00 0.00 43.82 4.35
5521 8121 1.294659 ACGACCGTGGAGAGTACGAC 61.295 60.000 0.00 0.00 43.82 4.34
5532 8158 1.202582 AGAAGGAGATCAACGACCGTG 59.797 52.381 0.00 0.00 0.00 4.94
5559 8193 1.008995 GCGAAAAAGTGGCTTGCGA 60.009 52.632 0.00 0.00 0.00 5.10
5655 8290 0.251916 TGGCGACATAGGGTTTGAGG 59.748 55.000 0.00 0.00 33.40 3.86
5661 8296 1.559682 AGACATTTGGCGACATAGGGT 59.440 47.619 0.00 0.00 42.32 4.34
5663 8298 2.223340 GCAAGACATTTGGCGACATAGG 60.223 50.000 0.00 0.00 42.32 2.57


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

AutoCloner maintained by Alex Coulton.