Multiple sequence alignment - TraesCS1D01G334400

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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 TraesCS1D01G334400 chr1D 100.000 5313 0 0 1 5313 424727000 424732312 0.000000e+00 9812.0
1 TraesCS1D01G334400 chr1D 84.472 161 23 2 5150 5308 468268756 468268916 1.980000e-34 158.0
2 TraesCS1D01G334400 chr1B 93.255 3395 127 46 1 3334 573857631 573860984 0.000000e+00 4907.0
3 TraesCS1D01G334400 chr1B 93.536 1021 43 10 3410 4423 573861014 573862018 0.000000e+00 1498.0
4 TraesCS1D01G334400 chr1B 82.947 733 47 34 4446 5134 573862092 573862790 1.650000e-164 590.0
5 TraesCS1D01G334400 chr1A 94.429 2208 89 21 2237 4421 520571617 520573813 0.000000e+00 3365.0
6 TraesCS1D01G334400 chr1A 91.015 2326 82 54 1 2234 520569239 520571529 0.000000e+00 3020.0
7 TraesCS1D01G334400 chr1A 84.605 734 53 32 4446 5135 520573894 520574611 0.000000e+00 675.0
8 TraesCS1D01G334400 chr1A 82.443 131 21 2 5184 5313 98524346 98524475 4.350000e-21 113.0
9 TraesCS1D01G334400 chr3D 77.824 956 162 32 2323 3260 417162373 417161450 3.620000e-151 545.0
10 TraesCS1D01G334400 chr3D 80.723 664 114 12 3665 4321 417160815 417160159 6.140000e-139 505.0
11 TraesCS1D01G334400 chr3D 76.279 645 86 38 1052 1679 417163870 417163276 1.130000e-71 281.0
12 TraesCS1D01G334400 chr3D 75.112 446 86 21 2831 3259 535744413 535744850 9.090000e-43 185.0
13 TraesCS1D01G334400 chr3D 83.077 130 21 1 5179 5307 349633127 349633256 3.360000e-22 117.0
14 TraesCS1D01G334400 chr3B 81.448 663 109 12 3665 4320 543467862 543467207 1.010000e-146 531.0
15 TraesCS1D01G334400 chr3B 77.368 950 170 31 2327 3260 543469452 543468532 6.100000e-144 521.0
16 TraesCS1D01G334400 chr3B 76.183 655 86 32 1148 1767 543470700 543470081 1.130000e-71 281.0
17 TraesCS1D01G334400 chr3B 81.957 327 57 2 3684 4009 665444 665769 5.240000e-70 276.0
18 TraesCS1D01G334400 chr3B 79.268 164 31 3 5147 5308 451546801 451546639 1.560000e-20 111.0
19 TraesCS1D01G334400 chr3A 81.061 660 113 11 3665 4321 533661707 533662357 2.840000e-142 516.0
20 TraesCS1D01G334400 chr3A 79.356 528 93 10 2742 3260 533660528 533661048 1.820000e-94 357.0
21 TraesCS1D01G334400 chr3A 82.812 320 55 0 2323 2642 533660134 533660453 2.420000e-73 287.0
22 TraesCS1D01G334400 chr3A 86.294 197 23 3 1484 1678 533659018 533659212 1.500000e-50 211.0
23 TraesCS1D01G334400 chr3A 85.057 174 25 1 1142 1314 533658685 533658858 5.470000e-40 176.0
24 TraesCS1D01G334400 chr5D 80.000 670 120 10 3655 4313 478163970 478163304 2.880000e-132 483.0
25 TraesCS1D01G334400 chr5D 74.101 417 70 23 1048 1429 478166309 478165896 2.580000e-28 137.0
26 TraesCS1D01G334400 chr4B 87.253 455 14 15 763 1211 628227110 628227526 3.720000e-131 479.0
27 TraesCS1D01G334400 chr4B 86.593 455 17 17 763 1211 628257580 628257996 3.750000e-126 462.0
28 TraesCS1D01G334400 chr4B 100.000 28 0 0 1176 1203 628227074 628227047 1.000000e-02 52.8
29 TraesCS1D01G334400 chr4B 100.000 28 0 0 1176 1203 628257544 628257517 1.000000e-02 52.8
30 TraesCS1D01G334400 chr5A 79.821 669 112 13 3662 4313 597290139 597289477 2.900000e-127 466.0
31 TraesCS1D01G334400 chr5A 74.568 405 77 19 1048 1429 597292367 597291966 2.560000e-33 154.0
32 TraesCS1D01G334400 chr5A 79.394 165 31 3 5144 5306 31097874 31098037 4.350000e-21 113.0
33 TraesCS1D01G334400 chr5B 79.403 670 116 16 3662 4313 585752607 585751942 2.260000e-123 453.0
34 TraesCS1D01G334400 chr5B 74.830 294 60 10 1149 1429 585754724 585754432 2.600000e-23 121.0
35 TraesCS1D01G334400 chr4A 75.113 442 87 19 2834 3259 741259136 741258702 9.090000e-43 185.0
36 TraesCS1D01G334400 chrUn 74.771 436 87 19 2840 3259 221213140 221213568 1.970000e-39 174.0
37 TraesCS1D01G334400 chr2D 87.786 131 15 1 5184 5313 351980223 351980093 9.220000e-33 152.0
38 TraesCS1D01G334400 chr6B 80.460 174 31 3 5142 5313 581300589 581300761 4.320000e-26 130.0
39 TraesCS1D01G334400 chr4D 80.982 163 29 2 5147 5308 29872074 29871913 1.550000e-25 128.0
40 TraesCS1D01G334400 chr2A 83.077 130 20 2 5179 5307 682557900 682557772 3.360000e-22 117.0


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 TraesCS1D01G334400 chr1D 424727000 424732312 5312 False 9812.000000 9812 100.000000 1 5313 1 chr1D.!!$F1 5312
1 TraesCS1D01G334400 chr1B 573857631 573862790 5159 False 2331.666667 4907 89.912667 1 5134 3 chr1B.!!$F1 5133
2 TraesCS1D01G334400 chr1A 520569239 520574611 5372 False 2353.333333 3365 90.016333 1 5135 3 chr1A.!!$F2 5134
3 TraesCS1D01G334400 chr3D 417160159 417163870 3711 True 443.666667 545 78.275333 1052 4321 3 chr3D.!!$R1 3269
4 TraesCS1D01G334400 chr3B 543467207 543470700 3493 True 444.333333 531 78.333000 1148 4320 3 chr3B.!!$R2 3172
5 TraesCS1D01G334400 chr3A 533658685 533662357 3672 False 309.400000 516 82.916000 1142 4321 5 chr3A.!!$F1 3179
6 TraesCS1D01G334400 chr5D 478163304 478166309 3005 True 310.000000 483 77.050500 1048 4313 2 chr5D.!!$R1 3265
7 TraesCS1D01G334400 chr5A 597289477 597292367 2890 True 310.000000 466 77.194500 1048 4313 2 chr5A.!!$R1 3265
8 TraesCS1D01G334400 chr5B 585751942 585754724 2782 True 287.000000 453 77.116500 1149 4313 2 chr5B.!!$R1 3164

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
987 1090 0.178973 TGTCTGAGGTCGGAGGTTGA 60.179 55.000 0.00 0.0 30.75 3.18 F
988 1091 0.244178 GTCTGAGGTCGGAGGTTGAC 59.756 60.000 0.00 0.0 35.60 3.18 F
994 1097 1.003718 GTCGGAGGTTGACCAAGGG 60.004 63.158 2.56 0.0 38.89 3.95 F
2916 3867 1.002134 CGGGTTCAATGGGACTGCT 60.002 57.895 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2751 3702 0.324943 CAACATCGTCCTTCCCCTGT 59.675 55.000 0.00 0.00 0.00 4.00 R
2916 3867 1.003580 GCCTTGATTCTCCACACTCCA 59.996 52.381 0.00 0.00 0.00 3.86 R
3015 3966 4.223032 TCATTCAGGTAGAGGAACTTCCAC 59.777 45.833 10.57 3.85 41.55 4.02 R
4926 6826 0.179111 ACCGATAGCGACACACATGG 60.179 55.000 0.00 0.00 40.82 3.66 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
60 61 3.560068 GTGTCAATCTTCTCCACGTTTGT 59.440 43.478 0.00 0.00 0.00 2.83
64 65 1.295792 TCTTCTCCACGTTTGTGTGC 58.704 50.000 0.00 0.00 44.92 4.57
89 92 7.246311 CCTATTTGTCTGTTTAGTTGCAGATG 58.754 38.462 0.00 0.00 42.72 2.90
122 125 1.341531 CCGGTATTCAGAGATTCGGCT 59.658 52.381 0.00 0.00 0.00 5.52
232 242 2.183679 GATCTAATCTGATCCCGGCCT 58.816 52.381 0.00 0.00 37.47 5.19
264 274 1.081174 TCCCCCAATATTTTTGGCCCA 59.919 47.619 0.00 0.00 38.23 5.36
313 337 3.322466 CCTTGGACCCTGACCGCT 61.322 66.667 0.00 0.00 0.00 5.52
474 506 2.509561 GAACTCCTTCGCCTCGCC 60.510 66.667 0.00 0.00 0.00 5.54
742 828 0.454620 CGTATCGTATCCTGGAGCGC 60.455 60.000 15.67 0.00 0.00 5.92
798 887 2.359169 CCCTCTTCGTGGCCTGCTA 61.359 63.158 3.32 0.00 0.00 3.49
799 888 1.142748 CCTCTTCGTGGCCTGCTAG 59.857 63.158 3.32 0.00 0.00 3.42
967 1070 3.352222 GCTGCTGCTGCTGTCGTT 61.352 61.111 22.10 0.00 39.81 3.85
972 1075 1.502163 GCTGCTGCTGTCGTTTGTCT 61.502 55.000 8.53 0.00 36.03 3.41
981 1084 0.313043 GTCGTTTGTCTGAGGTCGGA 59.687 55.000 0.00 0.00 0.00 4.55
983 1086 0.388649 CGTTTGTCTGAGGTCGGAGG 60.389 60.000 0.00 0.00 30.75 4.30
984 1087 0.680061 GTTTGTCTGAGGTCGGAGGT 59.320 55.000 0.00 0.00 30.75 3.85
985 1088 1.070289 GTTTGTCTGAGGTCGGAGGTT 59.930 52.381 0.00 0.00 30.75 3.50
986 1089 0.679505 TTGTCTGAGGTCGGAGGTTG 59.320 55.000 0.00 0.00 30.75 3.77
987 1090 0.178973 TGTCTGAGGTCGGAGGTTGA 60.179 55.000 0.00 0.00 30.75 3.18
988 1091 0.244178 GTCTGAGGTCGGAGGTTGAC 59.756 60.000 0.00 0.00 35.60 3.18
994 1097 1.003718 GTCGGAGGTTGACCAAGGG 60.004 63.158 2.56 0.00 38.89 3.95
995 1098 1.460689 TCGGAGGTTGACCAAGGGT 60.461 57.895 2.56 0.00 39.44 4.34
996 1099 1.302511 CGGAGGTTGACCAAGGGTG 60.303 63.158 2.56 0.00 35.25 4.61
1923 2746 4.321230 GCATTTTGTTCGGATCTTTGTCCT 60.321 41.667 0.00 0.00 36.07 3.85
1926 2749 3.040147 TGTTCGGATCTTTGTCCTGAC 57.960 47.619 0.00 0.00 36.07 3.51
1927 2750 2.632996 TGTTCGGATCTTTGTCCTGACT 59.367 45.455 0.00 0.00 36.07 3.41
1989 2817 8.197439 TGTGTTCGTACTTCATATGAATCTCAT 58.803 33.333 18.26 5.34 40.23 2.90
2107 2938 9.760077 TTATTAATCCAAATCTCGGACTAGAAC 57.240 33.333 0.00 0.00 34.69 3.01
2167 2998 4.520179 CATGTGATTGGAGATCAAGGTGA 58.480 43.478 0.00 0.00 38.95 4.02
2176 3007 4.125703 GGAGATCAAGGTGACAAGCTATG 58.874 47.826 0.00 0.00 32.57 2.23
2290 3220 9.713713 AGGTAATTTGTTGTTGTAAAAAGTTGT 57.286 25.926 0.00 0.00 0.00 3.32
2296 3226 6.544622 TGTTGTTGTAAAAAGTTGTAGTCCG 58.455 36.000 0.00 0.00 0.00 4.79
2297 3227 5.738118 TGTTGTAAAAAGTTGTAGTCCGG 57.262 39.130 0.00 0.00 0.00 5.14
2298 3228 5.184711 TGTTGTAAAAAGTTGTAGTCCGGT 58.815 37.500 0.00 0.00 0.00 5.28
2300 3230 5.989551 TGTAAAAAGTTGTAGTCCGGTTC 57.010 39.130 0.00 0.00 0.00 3.62
2301 3231 5.426504 TGTAAAAAGTTGTAGTCCGGTTCA 58.573 37.500 0.00 0.00 0.00 3.18
2303 3233 6.543100 TGTAAAAAGTTGTAGTCCGGTTCAAT 59.457 34.615 0.00 0.00 0.00 2.57
2304 3234 7.714377 TGTAAAAAGTTGTAGTCCGGTTCAATA 59.286 33.333 0.00 0.00 0.00 1.90
2672 3606 5.220359 CGACTGAGCAATTCTTACTGATGTG 60.220 44.000 0.00 0.00 0.00 3.21
2729 3663 8.960591 CAATCCTATCAGTTATGTTTTTGTCCT 58.039 33.333 0.00 0.00 0.00 3.85
2730 3664 7.921786 TCCTATCAGTTATGTTTTTGTCCTG 57.078 36.000 0.00 0.00 0.00 3.86
2731 3665 7.685481 TCCTATCAGTTATGTTTTTGTCCTGA 58.315 34.615 0.00 0.00 32.60 3.86
2732 3666 7.606456 TCCTATCAGTTATGTTTTTGTCCTGAC 59.394 37.037 0.00 0.00 31.01 3.51
2751 3702 4.068599 TGACAAATTCGATGTGCAACCTA 58.931 39.130 0.00 0.00 34.36 3.08
2916 3867 1.002134 CGGGTTCAATGGGACTGCT 60.002 57.895 0.00 0.00 0.00 4.24
3015 3966 1.153289 CCGAGCACATCTCAAGGGG 60.153 63.158 0.00 0.00 41.98 4.79
3260 4220 9.131791 GTGGACATTATAAAATCCAAGGTATGT 57.868 33.333 18.11 2.05 0.00 2.29
3348 4345 3.806941 TCTGCAAGAAGGCAACAGT 57.193 47.368 0.00 0.00 42.31 3.55
3395 4479 8.777865 TTATAGGATAATGTACAAGATGCAGC 57.222 34.615 0.00 0.00 0.00 5.25
3467 4558 8.573035 TGACAAATTTTAGTTACATTCACCCTC 58.427 33.333 0.00 0.00 0.00 4.30
3497 4588 2.602217 GCAGTCGTCAATTTCCACACAC 60.602 50.000 0.00 0.00 0.00 3.82
3600 5041 9.053472 TCTTTGTCCCCTAATTTGTATTCTAGA 57.947 33.333 0.00 0.00 0.00 2.43
3619 5060 3.472652 AGAGCCATTTTGTCGTGTGTAA 58.527 40.909 0.00 0.00 0.00 2.41
3661 5113 1.275010 TGTCCTAACGATGCTGCTTGA 59.725 47.619 0.00 0.00 0.00 3.02
3766 5541 1.081892 CATTCACCCTCTTCTGCGTG 58.918 55.000 0.00 0.00 0.00 5.34
3832 5607 1.140052 TGGGTGGTATGCTACATTCCG 59.860 52.381 0.00 0.00 0.00 4.30
4321 6111 6.162079 CGAGCAAGTGGAGTGATATTGATAT 58.838 40.000 0.00 0.00 0.00 1.63
4323 6113 7.071069 AGCAAGTGGAGTGATATTGATATCA 57.929 36.000 0.00 0.00 44.93 2.15
4385 6176 2.177394 TCGTACTTTGCAGGCATCAA 57.823 45.000 0.00 0.00 0.00 2.57
4437 6239 1.944177 TGCTTACAGGAGGAAGCTCT 58.056 50.000 13.07 0.00 46.68 4.09
4441 6243 3.631250 CTTACAGGAGGAAGCTCTCTCT 58.369 50.000 13.67 3.06 34.39 3.10
4442 6244 1.851304 ACAGGAGGAAGCTCTCTCTG 58.149 55.000 13.67 13.96 37.71 3.35
4443 6245 1.357420 ACAGGAGGAAGCTCTCTCTGA 59.643 52.381 19.04 0.00 36.49 3.27
4444 6246 2.024080 ACAGGAGGAAGCTCTCTCTGAT 60.024 50.000 19.04 8.01 36.49 2.90
4445 6247 3.204158 ACAGGAGGAAGCTCTCTCTGATA 59.796 47.826 19.04 0.00 36.49 2.15
4446 6248 4.140947 ACAGGAGGAAGCTCTCTCTGATAT 60.141 45.833 19.04 3.94 36.49 1.63
4447 6249 5.074377 ACAGGAGGAAGCTCTCTCTGATATA 59.926 44.000 19.04 0.00 36.49 0.86
4456 6304 7.038154 AGCTCTCTCTGATATACAACTGAAC 57.962 40.000 0.00 0.00 0.00 3.18
4506 6354 7.200434 TCTGGATCATCATCATCATCATCAT 57.800 36.000 0.00 0.00 0.00 2.45
4507 6355 7.275920 TCTGGATCATCATCATCATCATCATC 58.724 38.462 0.00 0.00 0.00 2.92
4635 6489 4.398044 GTCCTTTGTTCCTTGTTGACAGAA 59.602 41.667 0.00 0.00 0.00 3.02
4694 6552 5.446143 TGTACTTTTTGCCACGATCAATT 57.554 34.783 0.00 0.00 0.00 2.32
4695 6553 5.218885 TGTACTTTTTGCCACGATCAATTG 58.781 37.500 0.00 0.00 0.00 2.32
4769 6646 5.967364 GCATATGCTTGCATCTTTTGGATGT 60.967 40.000 20.64 0.00 44.24 3.06
4779 6656 5.404946 CATCTTTTGGATGTTACTGGCTTG 58.595 41.667 0.00 0.00 44.88 4.01
4781 6658 4.278170 TCTTTTGGATGTTACTGGCTTGTG 59.722 41.667 0.00 0.00 0.00 3.33
4784 6661 2.290260 TGGATGTTACTGGCTTGTGAGG 60.290 50.000 0.00 0.00 0.00 3.86
4786 6663 2.839486 TGTTACTGGCTTGTGAGGAG 57.161 50.000 0.00 0.00 0.00 3.69
4787 6664 1.270839 TGTTACTGGCTTGTGAGGAGC 60.271 52.381 0.00 0.00 39.41 4.70
4793 6676 1.978473 GCTTGTGAGGAGCCTCTGA 59.022 57.895 16.87 1.55 43.12 3.27
4827 6710 0.108945 GCTTCACAAATGGAGGCTGC 60.109 55.000 0.00 0.00 34.83 5.25
4828 6711 1.542492 CTTCACAAATGGAGGCTGCT 58.458 50.000 7.74 0.00 0.00 4.24
4830 6713 0.401356 TCACAAATGGAGGCTGCTGA 59.599 50.000 7.74 0.00 0.00 4.26
4831 6714 1.202915 TCACAAATGGAGGCTGCTGAA 60.203 47.619 7.74 0.00 0.00 3.02
4840 6723 2.957006 GGAGGCTGCTGAATGAATGAAT 59.043 45.455 0.00 0.00 0.00 2.57
4873 6773 1.068895 CCATGCTGTCTTTGTTTGGCA 59.931 47.619 0.00 0.00 0.00 4.92
4875 6775 1.180907 TGCTGTCTTTGTTTGGCACA 58.819 45.000 0.00 0.00 0.00 4.57
4913 6813 3.006940 TGGGACATATTCGTTGCTTGTC 58.993 45.455 0.00 0.00 36.76 3.18
4920 6820 5.008613 ACATATTCGTTGCTTGTCTGTTTGT 59.991 36.000 0.00 0.00 0.00 2.83
4923 6823 3.497118 TCGTTGCTTGTCTGTTTGTTTG 58.503 40.909 0.00 0.00 0.00 2.93
4924 6824 3.189495 TCGTTGCTTGTCTGTTTGTTTGA 59.811 39.130 0.00 0.00 0.00 2.69
4926 6826 4.204978 CGTTGCTTGTCTGTTTGTTTGATC 59.795 41.667 0.00 0.00 0.00 2.92
4927 6827 4.305989 TGCTTGTCTGTTTGTTTGATCC 57.694 40.909 0.00 0.00 0.00 3.36
4928 6828 3.698539 TGCTTGTCTGTTTGTTTGATCCA 59.301 39.130 0.00 0.00 0.00 3.41
4930 6830 4.682860 GCTTGTCTGTTTGTTTGATCCATG 59.317 41.667 0.00 0.00 0.00 3.66
4931 6831 5.737063 GCTTGTCTGTTTGTTTGATCCATGT 60.737 40.000 0.00 0.00 0.00 3.21
4945 6849 0.179111 CCATGTGTGTCGCTATCGGT 60.179 55.000 0.00 0.00 36.13 4.69
4965 6869 0.901580 GAGAAGGACGTGTACCCCCA 60.902 60.000 0.00 0.00 0.00 4.96
4977 6881 2.723334 TACCCCCAGGCTTGTCCCTT 62.723 60.000 0.00 0.00 36.11 3.95
4978 6882 2.356667 CCCCAGGCTTGTCCCTTC 59.643 66.667 0.00 0.00 31.24 3.46
4979 6883 2.538141 CCCCAGGCTTGTCCCTTCA 61.538 63.158 0.00 0.00 31.24 3.02
4980 6884 1.460255 CCCAGGCTTGTCCCTTCAA 59.540 57.895 0.00 0.00 31.24 2.69
4985 6889 1.147817 AGGCTTGTCCCTTCAATTGGT 59.852 47.619 5.42 0.00 34.51 3.67
4992 6900 4.541705 TGTCCCTTCAATTGGTTTGAGAA 58.458 39.130 5.42 0.00 44.90 2.87
5015 6923 2.100631 GTCCATGTGGAGGCGAACG 61.101 63.158 1.07 0.00 46.49 3.95
5029 6937 1.802337 CGAACGGGGACTCACAGTGA 61.802 60.000 2.48 2.48 0.00 3.41
5048 6959 5.409826 CAGTGATAGGTTTTCTTGGACTGTC 59.590 44.000 0.00 0.00 0.00 3.51
5050 6961 1.594331 AGGTTTTCTTGGACTGTCGC 58.406 50.000 1.07 0.00 0.00 5.19
5051 6962 0.591659 GGTTTTCTTGGACTGTCGCC 59.408 55.000 1.07 0.00 0.00 5.54
5052 6963 1.594331 GTTTTCTTGGACTGTCGCCT 58.406 50.000 1.07 0.00 0.00 5.52
5053 6964 1.947456 GTTTTCTTGGACTGTCGCCTT 59.053 47.619 1.07 0.00 0.00 4.35
5054 6965 1.593196 TTTCTTGGACTGTCGCCTTG 58.407 50.000 1.07 0.00 0.00 3.61
5076 6987 1.265095 CTGACGTTGCATGTTCTTGCT 59.735 47.619 10.95 0.00 43.18 3.91
5100 7011 2.096013 GCTTATCTTCCAACTGGCGAAC 59.904 50.000 0.00 0.00 34.44 3.95
5130 7045 7.356089 TCAGAAACTAACTAACCACTTCTCA 57.644 36.000 0.00 0.00 0.00 3.27
5135 7050 6.334102 ACTAACTAACCACTTCTCAGTCAG 57.666 41.667 0.00 0.00 0.00 3.51
5136 7051 3.669251 ACTAACCACTTCTCAGTCAGC 57.331 47.619 0.00 0.00 0.00 4.26
5137 7052 2.300437 ACTAACCACTTCTCAGTCAGCC 59.700 50.000 0.00 0.00 0.00 4.85
5138 7053 1.131638 AACCACTTCTCAGTCAGCCA 58.868 50.000 0.00 0.00 0.00 4.75
5139 7054 0.683973 ACCACTTCTCAGTCAGCCAG 59.316 55.000 0.00 0.00 0.00 4.85
5140 7055 0.683973 CCACTTCTCAGTCAGCCAGT 59.316 55.000 0.00 0.00 0.00 4.00
5141 7056 1.337635 CCACTTCTCAGTCAGCCAGTC 60.338 57.143 0.00 0.00 0.00 3.51
5142 7057 1.342496 CACTTCTCAGTCAGCCAGTCA 59.658 52.381 0.00 0.00 0.00 3.41
5143 7058 2.042464 ACTTCTCAGTCAGCCAGTCAA 58.958 47.619 0.00 0.00 0.00 3.18
5144 7059 2.224161 ACTTCTCAGTCAGCCAGTCAAC 60.224 50.000 0.00 0.00 0.00 3.18
5145 7060 1.709578 TCTCAGTCAGCCAGTCAACT 58.290 50.000 0.00 0.00 0.00 3.16
5146 7061 1.615883 TCTCAGTCAGCCAGTCAACTC 59.384 52.381 0.00 0.00 0.00 3.01
5147 7062 1.342496 CTCAGTCAGCCAGTCAACTCA 59.658 52.381 0.00 0.00 0.00 3.41
5148 7063 1.973515 TCAGTCAGCCAGTCAACTCAT 59.026 47.619 0.00 0.00 0.00 2.90
5149 7064 2.369860 TCAGTCAGCCAGTCAACTCATT 59.630 45.455 0.00 0.00 0.00 2.57
5150 7065 3.144506 CAGTCAGCCAGTCAACTCATTT 58.855 45.455 0.00 0.00 0.00 2.32
5151 7066 3.188048 CAGTCAGCCAGTCAACTCATTTC 59.812 47.826 0.00 0.00 0.00 2.17
5152 7067 2.158449 GTCAGCCAGTCAACTCATTTCG 59.842 50.000 0.00 0.00 0.00 3.46
5153 7068 2.146342 CAGCCAGTCAACTCATTTCGT 58.854 47.619 0.00 0.00 0.00 3.85
5154 7069 2.158449 CAGCCAGTCAACTCATTTCGTC 59.842 50.000 0.00 0.00 0.00 4.20
5155 7070 1.464997 GCCAGTCAACTCATTTCGTCC 59.535 52.381 0.00 0.00 0.00 4.79
5156 7071 1.726791 CCAGTCAACTCATTTCGTCCG 59.273 52.381 0.00 0.00 0.00 4.79
5157 7072 1.126846 CAGTCAACTCATTTCGTCCGC 59.873 52.381 0.00 0.00 0.00 5.54
5158 7073 0.093026 GTCAACTCATTTCGTCCGCG 59.907 55.000 0.00 0.00 39.92 6.46
5159 7074 1.225745 CAACTCATTTCGTCCGCGC 60.226 57.895 0.00 0.00 38.14 6.86
5160 7075 2.726691 AACTCATTTCGTCCGCGCG 61.727 57.895 25.67 25.67 38.14 6.86
5161 7076 3.913573 CTCATTTCGTCCGCGCGG 61.914 66.667 42.13 42.13 38.14 6.46
5172 7087 3.413023 CGCGCGGGTCCGTTTAAA 61.413 61.111 24.84 0.00 42.09 1.52
5173 7088 2.742738 CGCGCGGGTCCGTTTAAAT 61.743 57.895 24.84 0.00 42.09 1.40
5174 7089 1.419874 CGCGCGGGTCCGTTTAAATA 61.420 55.000 24.84 0.00 42.09 1.40
5175 7090 0.302589 GCGCGGGTCCGTTTAAATAG 59.697 55.000 8.83 0.00 42.09 1.73
5176 7091 1.643880 CGCGGGTCCGTTTAAATAGT 58.356 50.000 11.25 0.00 42.09 2.12
5177 7092 1.325338 CGCGGGTCCGTTTAAATAGTG 59.675 52.381 11.25 0.00 42.09 2.74
5178 7093 2.620242 GCGGGTCCGTTTAAATAGTGA 58.380 47.619 11.25 0.00 42.09 3.41
5179 7094 2.349580 GCGGGTCCGTTTAAATAGTGAC 59.650 50.000 11.25 0.00 42.09 3.67
5180 7095 2.599973 CGGGTCCGTTTAAATAGTGACG 59.400 50.000 0.55 0.00 35.44 4.35
5188 7103 6.456447 CGTTTAAATAGTGACGGTCAGAAA 57.544 37.500 11.83 0.12 32.29 2.52
5189 7104 6.879962 CGTTTAAATAGTGACGGTCAGAAAA 58.120 36.000 11.83 3.70 32.29 2.29
5190 7105 7.007697 CGTTTAAATAGTGACGGTCAGAAAAG 58.992 38.462 11.83 4.60 32.29 2.27
5191 7106 7.306983 CGTTTAAATAGTGACGGTCAGAAAAGT 60.307 37.037 11.83 0.00 32.29 2.66
5192 7107 7.647907 TTAAATAGTGACGGTCAGAAAAGTC 57.352 36.000 11.83 0.00 0.00 3.01
5193 7108 4.866508 ATAGTGACGGTCAGAAAAGTCA 57.133 40.909 11.83 1.05 40.77 3.41
5194 7109 3.099267 AGTGACGGTCAGAAAAGTCAG 57.901 47.619 11.83 0.00 43.22 3.51
5195 7110 2.431057 AGTGACGGTCAGAAAAGTCAGT 59.569 45.455 11.83 5.32 43.22 3.41
5196 7111 2.795470 GTGACGGTCAGAAAAGTCAGTC 59.205 50.000 11.83 0.00 43.22 3.51
5197 7112 2.223971 TGACGGTCAGAAAAGTCAGTCC 60.224 50.000 6.76 0.00 38.52 3.85
5198 7113 1.760613 ACGGTCAGAAAAGTCAGTCCA 59.239 47.619 0.00 0.00 0.00 4.02
5199 7114 2.169769 ACGGTCAGAAAAGTCAGTCCAA 59.830 45.455 0.00 0.00 0.00 3.53
5200 7115 2.544267 CGGTCAGAAAAGTCAGTCCAAC 59.456 50.000 0.00 0.00 0.00 3.77
5201 7116 2.544267 GGTCAGAAAAGTCAGTCCAACG 59.456 50.000 0.00 0.00 0.00 4.10
5202 7117 2.032808 GTCAGAAAAGTCAGTCCAACGC 60.033 50.000 0.00 0.00 0.00 4.84
5203 7118 1.070577 CAGAAAAGTCAGTCCAACGCG 60.071 52.381 3.53 3.53 0.00 6.01
5204 7119 0.384353 GAAAAGTCAGTCCAACGCGC 60.384 55.000 5.73 0.00 0.00 6.86
5205 7120 1.782028 AAAAGTCAGTCCAACGCGCC 61.782 55.000 5.73 0.00 0.00 6.53
5221 7136 3.353836 CCGGCCCAAACAGACGTG 61.354 66.667 0.00 0.00 0.00 4.49
5222 7137 4.025401 CGGCCCAAACAGACGTGC 62.025 66.667 0.00 0.00 0.00 5.34
5223 7138 4.025401 GGCCCAAACAGACGTGCG 62.025 66.667 0.00 0.00 0.00 5.34
5224 7139 3.276846 GCCCAAACAGACGTGCGT 61.277 61.111 0.00 0.00 0.00 5.24
5225 7140 2.935955 CCCAAACAGACGTGCGTC 59.064 61.111 15.92 15.92 44.86 5.19
5226 7141 2.604174 CCCAAACAGACGTGCGTCC 61.604 63.158 19.35 4.01 45.59 4.79
5227 7142 2.544359 CAAACAGACGTGCGTCCG 59.456 61.111 19.35 12.95 45.59 4.79
5228 7143 2.105528 AAACAGACGTGCGTCCGT 59.894 55.556 19.35 13.59 45.59 4.69
5229 7144 1.519898 AAACAGACGTGCGTCCGTT 60.520 52.632 19.35 18.25 44.62 4.44
5230 7145 1.085501 AAACAGACGTGCGTCCGTTT 61.086 50.000 24.43 24.43 45.38 3.60
5231 7146 1.085501 AACAGACGTGCGTCCGTTTT 61.086 50.000 19.35 6.52 41.33 2.43
5232 7147 1.085501 ACAGACGTGCGTCCGTTTTT 61.086 50.000 19.35 0.00 45.59 1.94
5233 7148 0.382636 CAGACGTGCGTCCGTTTTTC 60.383 55.000 19.35 0.00 45.59 2.29
5234 7149 1.435966 GACGTGCGTCCGTTTTTCG 60.436 57.895 13.11 0.00 41.98 3.46
5235 7150 2.081276 GACGTGCGTCCGTTTTTCGT 62.081 55.000 13.11 0.00 41.98 3.85
5236 7151 1.435966 CGTGCGTCCGTTTTTCGTC 60.436 57.895 0.00 0.00 37.94 4.20
5237 7152 1.083209 GTGCGTCCGTTTTTCGTCC 60.083 57.895 0.00 0.00 37.94 4.79
5238 7153 1.521010 TGCGTCCGTTTTTCGTCCA 60.521 52.632 0.00 0.00 37.94 4.02
5239 7154 0.881159 TGCGTCCGTTTTTCGTCCAT 60.881 50.000 0.00 0.00 37.94 3.41
5240 7155 0.179233 GCGTCCGTTTTTCGTCCATC 60.179 55.000 0.00 0.00 37.94 3.51
5241 7156 1.425412 CGTCCGTTTTTCGTCCATCT 58.575 50.000 0.00 0.00 37.94 2.90
5242 7157 1.126113 CGTCCGTTTTTCGTCCATCTG 59.874 52.381 0.00 0.00 37.94 2.90
5243 7158 1.136057 GTCCGTTTTTCGTCCATCTGC 60.136 52.381 0.00 0.00 37.94 4.26
5244 7159 0.168128 CCGTTTTTCGTCCATCTGCC 59.832 55.000 0.00 0.00 37.94 4.85
5245 7160 0.179225 CGTTTTTCGTCCATCTGCCG 60.179 55.000 0.00 0.00 34.52 5.69
5246 7161 1.153353 GTTTTTCGTCCATCTGCCGA 58.847 50.000 0.00 0.00 0.00 5.54
5247 7162 1.136057 GTTTTTCGTCCATCTGCCGAC 60.136 52.381 0.00 0.00 0.00 4.79
5248 7163 0.672401 TTTTCGTCCATCTGCCGACC 60.672 55.000 0.00 0.00 0.00 4.79
5249 7164 2.515996 TTTCGTCCATCTGCCGACCC 62.516 60.000 0.00 0.00 0.00 4.46
5250 7165 3.770040 CGTCCATCTGCCGACCCA 61.770 66.667 0.00 0.00 0.00 4.51
5251 7166 2.911143 GTCCATCTGCCGACCCAT 59.089 61.111 0.00 0.00 0.00 4.00
5252 7167 1.224592 GTCCATCTGCCGACCCATT 59.775 57.895 0.00 0.00 0.00 3.16
5253 7168 0.815615 GTCCATCTGCCGACCCATTC 60.816 60.000 0.00 0.00 0.00 2.67
5254 7169 1.526917 CCATCTGCCGACCCATTCC 60.527 63.158 0.00 0.00 0.00 3.01
5255 7170 1.528824 CATCTGCCGACCCATTCCT 59.471 57.895 0.00 0.00 0.00 3.36
5256 7171 0.816825 CATCTGCCGACCCATTCCTG 60.817 60.000 0.00 0.00 0.00 3.86
5257 7172 0.982852 ATCTGCCGACCCATTCCTGA 60.983 55.000 0.00 0.00 0.00 3.86
5258 7173 1.450312 CTGCCGACCCATTCCTGAC 60.450 63.158 0.00 0.00 0.00 3.51
5259 7174 2.124695 GCCGACCCATTCCTGACC 60.125 66.667 0.00 0.00 0.00 4.02
5260 7175 2.590092 CCGACCCATTCCTGACCC 59.410 66.667 0.00 0.00 0.00 4.46
5261 7176 2.297895 CCGACCCATTCCTGACCCA 61.298 63.158 0.00 0.00 0.00 4.51
5262 7177 1.635817 CCGACCCATTCCTGACCCAT 61.636 60.000 0.00 0.00 0.00 4.00
5263 7178 0.255890 CGACCCATTCCTGACCCATT 59.744 55.000 0.00 0.00 0.00 3.16
5264 7179 1.340991 CGACCCATTCCTGACCCATTT 60.341 52.381 0.00 0.00 0.00 2.32
5265 7180 2.820178 GACCCATTCCTGACCCATTTT 58.180 47.619 0.00 0.00 0.00 1.82
5266 7181 3.173151 GACCCATTCCTGACCCATTTTT 58.827 45.455 0.00 0.00 0.00 1.94
5267 7182 4.349365 GACCCATTCCTGACCCATTTTTA 58.651 43.478 0.00 0.00 0.00 1.52
5268 7183 4.352893 ACCCATTCCTGACCCATTTTTAG 58.647 43.478 0.00 0.00 0.00 1.85
5269 7184 3.132824 CCCATTCCTGACCCATTTTTAGC 59.867 47.826 0.00 0.00 0.00 3.09
5270 7185 3.132824 CCATTCCTGACCCATTTTTAGCC 59.867 47.826 0.00 0.00 0.00 3.93
5271 7186 3.825908 TTCCTGACCCATTTTTAGCCT 57.174 42.857 0.00 0.00 0.00 4.58
5272 7187 3.366052 TCCTGACCCATTTTTAGCCTC 57.634 47.619 0.00 0.00 0.00 4.70
5273 7188 2.647299 TCCTGACCCATTTTTAGCCTCA 59.353 45.455 0.00 0.00 0.00 3.86
5274 7189 3.269381 TCCTGACCCATTTTTAGCCTCAT 59.731 43.478 0.00 0.00 0.00 2.90
5275 7190 4.026052 CCTGACCCATTTTTAGCCTCATT 58.974 43.478 0.00 0.00 0.00 2.57
5276 7191 4.467438 CCTGACCCATTTTTAGCCTCATTT 59.533 41.667 0.00 0.00 0.00 2.32
5277 7192 5.404466 TGACCCATTTTTAGCCTCATTTG 57.596 39.130 0.00 0.00 0.00 2.32
5278 7193 4.183865 GACCCATTTTTAGCCTCATTTGC 58.816 43.478 0.00 0.00 0.00 3.68
5279 7194 3.189285 CCCATTTTTAGCCTCATTTGCG 58.811 45.455 0.00 0.00 0.00 4.85
5280 7195 3.368323 CCCATTTTTAGCCTCATTTGCGT 60.368 43.478 0.00 0.00 0.00 5.24
5281 7196 3.859386 CCATTTTTAGCCTCATTTGCGTC 59.141 43.478 0.00 0.00 0.00 5.19
5282 7197 2.892373 TTTTAGCCTCATTTGCGTCG 57.108 45.000 0.00 0.00 0.00 5.12
5283 7198 1.083489 TTTAGCCTCATTTGCGTCGG 58.917 50.000 0.00 0.00 0.00 4.79
5284 7199 1.366111 TTAGCCTCATTTGCGTCGGC 61.366 55.000 0.00 0.00 40.99 5.54
5285 7200 4.520846 GCCTCATTTGCGTCGGCG 62.521 66.667 4.29 4.29 44.10 6.46
5296 7211 4.492160 GTCGGCGCGGACATGAGA 62.492 66.667 34.74 4.76 36.91 3.27
5297 7212 4.492160 TCGGCGCGGACATGAGAC 62.492 66.667 14.27 0.00 0.00 3.36
5299 7214 4.492160 GGCGCGGACATGAGACGA 62.492 66.667 8.83 0.00 0.00 4.20
5300 7215 2.506217 GCGCGGACATGAGACGAA 60.506 61.111 8.83 0.00 0.00 3.85
5301 7216 2.789203 GCGCGGACATGAGACGAAC 61.789 63.158 8.83 0.00 0.00 3.95
5302 7217 2.497092 CGCGGACATGAGACGAACG 61.497 63.158 0.00 0.00 0.00 3.95
5303 7218 2.789203 GCGGACATGAGACGAACGC 61.789 63.158 0.00 0.00 38.70 4.84
5304 7219 2.497092 CGGACATGAGACGAACGCG 61.497 63.158 3.53 3.53 44.79 6.01
5305 7220 2.689766 GACATGAGACGAACGCGC 59.310 61.111 5.73 0.00 42.48 6.86
5306 7221 3.114483 GACATGAGACGAACGCGCG 62.114 63.158 30.96 30.96 42.48 6.86
5307 7222 4.543736 CATGAGACGAACGCGCGC 62.544 66.667 32.58 23.91 42.48 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.737252 GTGGAGAAGATTGACACGGTTC 59.263 50.000 0.00 0.00 0.00 3.62
60 61 5.278266 GCAACTAAACAGACAAATAGGCACA 60.278 40.000 0.00 0.00 0.00 4.57
64 65 6.801539 TCTGCAACTAAACAGACAAATAGG 57.198 37.500 0.00 0.00 37.99 2.57
89 92 1.349067 ATACCGGGGACAGGATTAGC 58.651 55.000 6.32 0.00 0.00 3.09
122 125 5.930837 AACAACAAAAGGGAAAGTGATCA 57.069 34.783 0.00 0.00 0.00 2.92
168 174 0.320771 ACAAACTGAGCCGCGATTCT 60.321 50.000 8.23 0.42 0.00 2.40
245 255 1.589414 TGGGCCAAAAATATTGGGGG 58.411 50.000 2.13 0.00 39.90 5.40
264 274 1.228552 GTGCATGGGGGCGGATTAT 60.229 57.895 0.00 0.00 36.28 1.28
521 585 2.356553 TTTGGACGGACGCTTCGG 60.357 61.111 0.00 0.00 0.00 4.30
783 872 0.612174 AGACTAGCAGGCCACGAAGA 60.612 55.000 5.01 0.00 0.00 2.87
798 887 4.731612 CGCCAGAGCACGCAGACT 62.732 66.667 0.00 0.00 39.83 3.24
840 938 0.250338 CTGGACGCCCTTAATAGCCC 60.250 60.000 0.00 0.00 0.00 5.19
863 961 2.677542 TACCCGCTCATAGAGGACAT 57.322 50.000 0.00 0.00 37.36 3.06
967 1070 0.679505 CAACCTCCGACCTCAGACAA 59.320 55.000 0.00 0.00 0.00 3.18
981 1084 1.943730 TTGCCACCCTTGGTCAACCT 61.944 55.000 0.10 0.00 45.98 3.50
983 1086 0.318120 CATTGCCACCCTTGGTCAAC 59.682 55.000 3.63 0.00 45.98 3.18
984 1087 0.831288 CCATTGCCACCCTTGGTCAA 60.831 55.000 3.94 3.94 45.98 3.18
985 1088 1.228831 CCATTGCCACCCTTGGTCA 60.229 57.895 0.00 0.00 45.98 4.02
986 1089 2.649129 GCCATTGCCACCCTTGGTC 61.649 63.158 0.00 0.00 45.98 4.02
987 1090 2.604382 GCCATTGCCACCCTTGGT 60.604 61.111 0.00 0.00 45.98 3.67
989 1092 4.440127 GCGCCATTGCCACCCTTG 62.440 66.667 0.00 0.00 0.00 3.61
997 1100 4.811761 GAACGACGGCGCCATTGC 62.812 66.667 28.98 11.02 42.48 3.56
1368 1519 1.376812 CAGCAGCATGGAGAGCACA 60.377 57.895 0.00 0.00 35.86 4.57
1817 2123 2.950309 GGCTGTCCTAGTCGAATACTGA 59.050 50.000 0.00 0.00 39.39 3.41
1820 2126 5.511234 TTTAGGCTGTCCTAGTCGAATAC 57.489 43.478 0.00 0.00 45.21 1.89
1821 2127 6.239232 GGAATTTAGGCTGTCCTAGTCGAATA 60.239 42.308 0.00 0.00 45.21 1.75
1923 2746 2.771943 AGAGTTGTGGTTGGAGAAGTCA 59.228 45.455 0.00 0.00 0.00 3.41
1926 2749 3.475566 TCAGAGTTGTGGTTGGAGAAG 57.524 47.619 0.00 0.00 0.00 2.85
1927 2750 3.743521 CATCAGAGTTGTGGTTGGAGAA 58.256 45.455 0.00 0.00 0.00 2.87
1989 2817 3.263489 TCACGGAGTTTGTTGTTGGTA 57.737 42.857 0.00 0.00 41.61 3.25
2167 2998 0.537188 AGTAGTGCGCCATAGCTTGT 59.463 50.000 4.18 0.00 38.13 3.16
2176 3007 2.361789 TCCCAAATTAAGTAGTGCGCC 58.638 47.619 4.18 0.00 0.00 6.53
2264 3193 9.713713 ACAACTTTTTACAACAACAAATTACCT 57.286 25.926 0.00 0.00 0.00 3.08
2285 3215 5.861727 AGTTTATTGAACCGGACTACAACT 58.138 37.500 9.46 4.42 39.13 3.16
2286 3216 6.549912 AAGTTTATTGAACCGGACTACAAC 57.450 37.500 9.46 1.92 39.13 3.32
2287 3217 8.851541 AATAAGTTTATTGAACCGGACTACAA 57.148 30.769 9.46 9.10 39.13 2.41
2288 3218 8.851541 AAATAAGTTTATTGAACCGGACTACA 57.148 30.769 9.46 0.00 39.13 2.74
2289 3219 8.938906 TGAAATAAGTTTATTGAACCGGACTAC 58.061 33.333 9.46 0.00 39.13 2.73
2290 3220 9.675464 ATGAAATAAGTTTATTGAACCGGACTA 57.325 29.630 9.46 0.00 39.13 2.59
2291 3221 7.989416 TGAAATAAGTTTATTGAACCGGACT 57.011 32.000 9.46 0.00 39.13 3.85
2292 3222 9.634163 AAATGAAATAAGTTTATTGAACCGGAC 57.366 29.630 9.46 1.77 39.13 4.79
2293 3223 9.632807 CAAATGAAATAAGTTTATTGAACCGGA 57.367 29.630 9.46 0.00 39.13 5.14
2294 3224 8.868916 CCAAATGAAATAAGTTTATTGAACCGG 58.131 33.333 0.00 0.00 39.13 5.28
2303 3233 8.801299 TGCAGACATCCAAATGAAATAAGTTTA 58.199 29.630 0.00 0.00 36.67 2.01
2304 3234 7.669427 TGCAGACATCCAAATGAAATAAGTTT 58.331 30.769 0.00 0.00 36.67 2.66
2655 3589 5.376854 ACAACCACATCAGTAAGAATTGC 57.623 39.130 0.00 0.00 0.00 3.56
2672 3606 6.694411 CAGATAAATGAAGCAGCAATACAACC 59.306 38.462 0.00 0.00 0.00 3.77
2729 3663 2.884012 AGGTTGCACATCGAATTTGTCA 59.116 40.909 0.00 0.00 0.00 3.58
2730 3664 3.559238 AGGTTGCACATCGAATTTGTC 57.441 42.857 0.00 0.00 0.00 3.18
2731 3665 3.818210 TGTAGGTTGCACATCGAATTTGT 59.182 39.130 0.00 0.00 0.00 2.83
2732 3666 4.406069 CTGTAGGTTGCACATCGAATTTG 58.594 43.478 0.00 0.00 0.00 2.32
2739 3673 0.618458 TCCCCTGTAGGTTGCACATC 59.382 55.000 0.00 0.00 0.00 3.06
2751 3702 0.324943 CAACATCGTCCTTCCCCTGT 59.675 55.000 0.00 0.00 0.00 4.00
2916 3867 1.003580 GCCTTGATTCTCCACACTCCA 59.996 52.381 0.00 0.00 0.00 3.86
3015 3966 4.223032 TCATTCAGGTAGAGGAACTTCCAC 59.777 45.833 10.57 3.85 41.55 4.02
3260 4220 1.264020 GTGCGTCATCAGAAAACAGCA 59.736 47.619 0.00 0.00 0.00 4.41
3347 4344 1.598601 CCAAAACATGTTGCCAAGCAC 59.401 47.619 12.82 0.00 38.71 4.40
3348 4345 1.483827 TCCAAAACATGTTGCCAAGCA 59.516 42.857 12.82 0.00 36.47 3.91
3395 4479 4.778534 ACTTGATGCCTCTTGACAATTG 57.221 40.909 3.24 3.24 0.00 2.32
3448 4532 8.598916 TGAGTATGAGGGTGAATGTAACTAAAA 58.401 33.333 0.00 0.00 0.00 1.52
3457 4541 3.875727 CTGCTTGAGTATGAGGGTGAATG 59.124 47.826 0.00 0.00 0.00 2.67
3458 4542 3.521126 ACTGCTTGAGTATGAGGGTGAAT 59.479 43.478 0.00 0.00 30.86 2.57
3461 4545 2.736719 CGACTGCTTGAGTATGAGGGTG 60.737 54.545 0.00 0.00 33.83 4.61
3462 4546 1.478510 CGACTGCTTGAGTATGAGGGT 59.521 52.381 0.00 0.00 33.83 4.34
3467 4558 5.446473 GGAAATTGACGACTGCTTGAGTATG 60.446 44.000 0.00 0.00 33.83 2.39
3503 4594 6.650120 TCTACCTCAAGTGAACTGAAAAAGT 58.350 36.000 0.00 0.00 42.60 2.66
3522 4620 9.561069 AATTGTGGATATGTCAATACTTCTACC 57.439 33.333 0.00 0.00 32.52 3.18
3600 5041 4.072131 AGATTACACACGACAAAATGGCT 58.928 39.130 0.00 0.00 0.00 4.75
3619 5060 9.182214 GGACAATTATCCATACATGCATTAGAT 57.818 33.333 0.00 0.00 38.77 1.98
3643 5095 2.988010 ATCAAGCAGCATCGTTAGGA 57.012 45.000 0.00 0.00 0.00 2.94
3661 5113 2.226962 ACCCAATCTGCAGCAGAAAT 57.773 45.000 28.78 17.64 44.04 2.17
3766 5541 3.217626 GAACATTGTCATGGGGAGGATC 58.782 50.000 0.00 0.00 34.27 3.36
3832 5607 1.600957 CTCATGATGGACATTGTCGCC 59.399 52.381 10.56 0.00 37.07 5.54
4321 6111 1.737735 CGGTCGCTGCTGTCATTGA 60.738 57.895 0.00 0.00 0.00 2.57
4323 6113 1.005037 TTCGGTCGCTGCTGTCATT 60.005 52.632 0.00 0.00 0.00 2.57
4437 6239 6.663523 TCCACAGTTCAGTTGTATATCAGAGA 59.336 38.462 0.00 0.00 0.00 3.10
4441 6243 6.850752 TCTCCACAGTTCAGTTGTATATCA 57.149 37.500 0.00 0.00 0.00 2.15
4442 6244 7.766278 ACATTCTCCACAGTTCAGTTGTATATC 59.234 37.037 0.00 0.00 0.00 1.63
4443 6245 7.624549 ACATTCTCCACAGTTCAGTTGTATAT 58.375 34.615 0.00 0.00 0.00 0.86
4444 6246 7.004555 ACATTCTCCACAGTTCAGTTGTATA 57.995 36.000 0.00 0.00 0.00 1.47
4445 6247 5.869579 ACATTCTCCACAGTTCAGTTGTAT 58.130 37.500 0.00 0.00 0.00 2.29
4446 6248 5.290493 ACATTCTCCACAGTTCAGTTGTA 57.710 39.130 0.00 0.00 0.00 2.41
4447 6249 4.156455 ACATTCTCCACAGTTCAGTTGT 57.844 40.909 0.00 0.00 0.00 3.32
4456 6304 9.407380 AGCTATATCTATCTACATTCTCCACAG 57.593 37.037 0.00 0.00 0.00 3.66
4506 6354 0.889186 GCGTCTCCCAGGCTTTTTGA 60.889 55.000 0.00 0.00 32.77 2.69
4507 6355 0.890996 AGCGTCTCCCAGGCTTTTTG 60.891 55.000 0.00 0.00 44.04 2.44
4568 6417 3.434882 CCCACCCAAAAGGCTTTGATTTT 60.435 43.478 14.19 0.00 44.03 1.82
4577 6426 2.922503 CCCACCCACCCAAAAGGC 60.923 66.667 0.00 0.00 40.58 4.35
4580 6429 2.444895 GCACCCACCCACCCAAAA 60.445 61.111 0.00 0.00 0.00 2.44
4720 6582 8.730680 GCAGGAAAAAGAGATACAAATGAACTA 58.269 33.333 0.00 0.00 0.00 2.24
4721 6583 7.231317 TGCAGGAAAAAGAGATACAAATGAACT 59.769 33.333 0.00 0.00 0.00 3.01
4722 6584 7.370383 TGCAGGAAAAAGAGATACAAATGAAC 58.630 34.615 0.00 0.00 0.00 3.18
4723 6585 7.523293 TGCAGGAAAAAGAGATACAAATGAA 57.477 32.000 0.00 0.00 0.00 2.57
4724 6586 7.707624 ATGCAGGAAAAAGAGATACAAATGA 57.292 32.000 0.00 0.00 0.00 2.57
4726 6588 8.139989 GCATATGCAGGAAAAAGAGATACAAAT 58.860 33.333 22.84 0.00 41.59 2.32
4728 6590 6.830324 AGCATATGCAGGAAAAAGAGATACAA 59.170 34.615 28.62 0.00 45.16 2.41
4730 6592 6.874288 AGCATATGCAGGAAAAAGAGATAC 57.126 37.500 28.62 0.00 45.16 2.24
4732 6594 5.451520 GCAAGCATATGCAGGAAAAAGAGAT 60.452 40.000 28.62 0.81 45.70 2.75
4762 6639 3.411446 CTCACAAGCCAGTAACATCCAA 58.589 45.455 0.00 0.00 0.00 3.53
4769 6646 3.935993 GCTCCTCACAAGCCAGTAA 57.064 52.632 0.00 0.00 33.53 2.24
4776 6653 2.301296 TCTTTCAGAGGCTCCTCACAAG 59.699 50.000 17.40 14.33 44.99 3.16
4777 6654 2.329267 TCTTTCAGAGGCTCCTCACAA 58.671 47.619 17.40 7.01 44.99 3.33
4779 6656 3.625649 AATCTTTCAGAGGCTCCTCAC 57.374 47.619 17.40 0.00 44.99 3.51
4781 6658 4.447290 GGTTAATCTTTCAGAGGCTCCTC 58.553 47.826 11.71 7.84 43.03 3.71
4784 6661 3.198872 CCGGTTAATCTTTCAGAGGCTC 58.801 50.000 6.34 6.34 0.00 4.70
4786 6663 1.671328 GCCGGTTAATCTTTCAGAGGC 59.329 52.381 1.90 0.00 35.00 4.70
4787 6664 2.939103 CTGCCGGTTAATCTTTCAGAGG 59.061 50.000 1.90 0.00 0.00 3.69
4790 6673 2.359900 AGCTGCCGGTTAATCTTTCAG 58.640 47.619 1.90 0.00 0.00 3.02
4793 6676 2.488153 GTGAAGCTGCCGGTTAATCTTT 59.512 45.455 1.90 0.00 0.00 2.52
4827 6710 3.635373 CAGGTCCCCATTCATTCATTCAG 59.365 47.826 0.00 0.00 0.00 3.02
4828 6711 3.628002 CCAGGTCCCCATTCATTCATTCA 60.628 47.826 0.00 0.00 0.00 2.57
4830 6713 2.315763 ACCAGGTCCCCATTCATTCATT 59.684 45.455 0.00 0.00 0.00 2.57
4831 6714 1.932338 ACCAGGTCCCCATTCATTCAT 59.068 47.619 0.00 0.00 0.00 2.57
4840 6723 2.917897 GCATGGAACCAGGTCCCCA 61.918 63.158 14.28 14.28 36.80 4.96
4873 6773 1.148949 TGCCAGTGCACATGACTGT 59.851 52.632 21.04 0.00 44.23 3.55
4913 6813 4.935702 ACACACATGGATCAAACAAACAG 58.064 39.130 0.00 0.00 0.00 3.16
4920 6820 2.183478 AGCGACACACATGGATCAAA 57.817 45.000 0.00 0.00 0.00 2.69
4923 6823 2.054363 CGATAGCGACACACATGGATC 58.946 52.381 0.00 0.00 40.82 3.36
4924 6824 1.269778 CCGATAGCGACACACATGGAT 60.270 52.381 0.00 0.00 40.82 3.41
4926 6826 0.179111 ACCGATAGCGACACACATGG 60.179 55.000 0.00 0.00 40.82 3.66
4927 6827 0.923403 CACCGATAGCGACACACATG 59.077 55.000 0.00 0.00 40.82 3.21
4928 6828 0.815095 TCACCGATAGCGACACACAT 59.185 50.000 0.00 0.00 40.82 3.21
4930 6830 0.450583 TCTCACCGATAGCGACACAC 59.549 55.000 0.00 0.00 40.82 3.82
4931 6831 1.132453 CTTCTCACCGATAGCGACACA 59.868 52.381 0.00 0.00 40.82 3.72
4945 6849 0.901580 GGGGGTACACGTCCTTCTCA 60.902 60.000 0.00 0.00 0.00 3.27
4965 6869 1.147817 ACCAATTGAAGGGACAAGCCT 59.852 47.619 7.12 0.00 36.66 4.58
4977 6881 4.037923 GGACTGCTTTCTCAAACCAATTGA 59.962 41.667 7.12 0.00 45.71 2.57
4978 6882 4.202141 TGGACTGCTTTCTCAAACCAATTG 60.202 41.667 0.00 0.00 40.58 2.32
4979 6883 3.960102 TGGACTGCTTTCTCAAACCAATT 59.040 39.130 0.00 0.00 0.00 2.32
4980 6884 3.565307 TGGACTGCTTTCTCAAACCAAT 58.435 40.909 0.00 0.00 0.00 3.16
4985 6889 2.886523 CCACATGGACTGCTTTCTCAAA 59.113 45.455 0.00 0.00 37.39 2.69
4992 6900 1.001641 GCCTCCACATGGACTGCTT 60.002 57.895 9.46 0.00 39.78 3.91
5015 6923 1.867363 ACCTATCACTGTGAGTCCCC 58.133 55.000 16.46 0.00 0.00 4.81
5029 6937 3.335579 GCGACAGTCCAAGAAAACCTAT 58.664 45.455 0.00 0.00 0.00 2.57
5048 6959 4.389576 GCAACGTCAGGCAAGGCG 62.390 66.667 2.42 2.42 0.00 5.52
5050 6961 1.210931 CATGCAACGTCAGGCAAGG 59.789 57.895 12.54 5.77 44.20 3.61
5051 6962 0.311790 AACATGCAACGTCAGGCAAG 59.688 50.000 12.54 10.94 44.20 4.01
5052 6963 0.310543 GAACATGCAACGTCAGGCAA 59.689 50.000 12.54 0.00 44.20 4.52
5053 6964 0.534877 AGAACATGCAACGTCAGGCA 60.535 50.000 11.19 11.19 45.23 4.75
5054 6965 0.593128 AAGAACATGCAACGTCAGGC 59.407 50.000 0.00 0.00 0.00 4.85
5076 6987 2.446435 GCCAGTTGGAAGATAAGCCAA 58.554 47.619 1.45 0.00 41.61 4.52
5100 7011 5.875359 GTGGTTAGTTAGTTTCTGATCCCAG 59.125 44.000 0.00 0.00 41.74 4.45
5130 7045 3.406764 GAAATGAGTTGACTGGCTGACT 58.593 45.455 0.00 0.00 0.00 3.41
5135 7050 1.464997 GGACGAAATGAGTTGACTGGC 59.535 52.381 0.00 0.00 0.00 4.85
5136 7051 1.726791 CGGACGAAATGAGTTGACTGG 59.273 52.381 0.00 0.00 0.00 4.00
5137 7052 1.126846 GCGGACGAAATGAGTTGACTG 59.873 52.381 0.00 0.00 0.00 3.51
5138 7053 1.429463 GCGGACGAAATGAGTTGACT 58.571 50.000 0.00 0.00 0.00 3.41
5139 7054 0.093026 CGCGGACGAAATGAGTTGAC 59.907 55.000 0.00 0.00 43.93 3.18
5140 7055 1.623081 GCGCGGACGAAATGAGTTGA 61.623 55.000 8.83 0.00 43.93 3.18
5141 7056 1.225745 GCGCGGACGAAATGAGTTG 60.226 57.895 8.83 0.00 43.93 3.16
5142 7057 2.726691 CGCGCGGACGAAATGAGTT 61.727 57.895 24.84 0.00 43.93 3.01
5143 7058 3.179265 CGCGCGGACGAAATGAGT 61.179 61.111 24.84 0.00 43.93 3.41
5144 7059 3.913573 CCGCGCGGACGAAATGAG 61.914 66.667 44.86 12.52 43.93 2.90
5155 7070 1.419874 TATTTAAACGGACCCGCGCG 61.420 55.000 25.67 25.67 44.19 6.86
5156 7071 0.302589 CTATTTAAACGGACCCGCGC 59.697 55.000 8.55 0.00 44.19 6.86
5157 7072 1.325338 CACTATTTAAACGGACCCGCG 59.675 52.381 8.55 0.00 44.19 6.46
5158 7073 2.349580 GTCACTATTTAAACGGACCCGC 59.650 50.000 8.55 0.00 44.19 6.13
5159 7074 2.599973 CGTCACTATTTAAACGGACCCG 59.400 50.000 6.94 6.94 46.03 5.28
5165 7080 6.456447 TTTCTGACCGTCACTATTTAAACG 57.544 37.500 0.00 0.00 35.01 3.60
5166 7081 7.858583 ACTTTTCTGACCGTCACTATTTAAAC 58.141 34.615 0.00 0.00 0.00 2.01
5167 7082 7.711772 TGACTTTTCTGACCGTCACTATTTAAA 59.288 33.333 0.00 0.00 32.00 1.52
5168 7083 7.211573 TGACTTTTCTGACCGTCACTATTTAA 58.788 34.615 0.00 0.00 32.00 1.52
5169 7084 6.751157 TGACTTTTCTGACCGTCACTATTTA 58.249 36.000 0.00 0.00 32.00 1.40
5170 7085 5.607477 TGACTTTTCTGACCGTCACTATTT 58.393 37.500 0.00 0.00 32.00 1.40
5171 7086 5.209818 TGACTTTTCTGACCGTCACTATT 57.790 39.130 0.00 0.00 32.00 1.73
5172 7087 4.281182 ACTGACTTTTCTGACCGTCACTAT 59.719 41.667 0.00 0.00 33.32 2.12
5173 7088 3.635373 ACTGACTTTTCTGACCGTCACTA 59.365 43.478 0.00 0.00 33.32 2.74
5174 7089 2.431057 ACTGACTTTTCTGACCGTCACT 59.569 45.455 0.00 0.00 33.32 3.41
5175 7090 2.795470 GACTGACTTTTCTGACCGTCAC 59.205 50.000 0.00 0.00 33.32 3.67
5176 7091 2.223971 GGACTGACTTTTCTGACCGTCA 60.224 50.000 0.29 0.29 35.35 4.35
5177 7092 2.223971 TGGACTGACTTTTCTGACCGTC 60.224 50.000 0.00 0.00 38.02 4.79
5178 7093 1.760613 TGGACTGACTTTTCTGACCGT 59.239 47.619 0.00 0.00 38.02 4.83
5179 7094 2.526304 TGGACTGACTTTTCTGACCG 57.474 50.000 0.00 0.00 38.02 4.79
5180 7095 2.544267 CGTTGGACTGACTTTTCTGACC 59.456 50.000 0.00 0.00 36.49 4.02
5181 7096 2.032808 GCGTTGGACTGACTTTTCTGAC 60.033 50.000 0.00 0.00 0.00 3.51
5182 7097 2.210116 GCGTTGGACTGACTTTTCTGA 58.790 47.619 0.00 0.00 0.00 3.27
5183 7098 1.070577 CGCGTTGGACTGACTTTTCTG 60.071 52.381 0.00 0.00 0.00 3.02
5184 7099 1.217882 CGCGTTGGACTGACTTTTCT 58.782 50.000 0.00 0.00 0.00 2.52
5185 7100 0.384353 GCGCGTTGGACTGACTTTTC 60.384 55.000 8.43 0.00 0.00 2.29
5186 7101 1.647084 GCGCGTTGGACTGACTTTT 59.353 52.632 8.43 0.00 0.00 2.27
5187 7102 2.251642 GGCGCGTTGGACTGACTTT 61.252 57.895 8.43 0.00 0.00 2.66
5188 7103 2.665185 GGCGCGTTGGACTGACTT 60.665 61.111 8.43 0.00 0.00 3.01
5204 7119 3.353836 CACGTCTGTTTGGGCCGG 61.354 66.667 0.00 0.00 0.00 6.13
5205 7120 4.025401 GCACGTCTGTTTGGGCCG 62.025 66.667 0.00 0.00 0.00 6.13
5206 7121 4.025401 CGCACGTCTGTTTGGGCC 62.025 66.667 0.00 0.00 0.00 5.80
5207 7122 3.236618 GACGCACGTCTGTTTGGGC 62.237 63.158 15.56 0.00 41.57 5.36
5208 7123 2.604174 GGACGCACGTCTGTTTGGG 61.604 63.158 21.19 0.00 44.04 4.12
5209 7124 2.935955 GGACGCACGTCTGTTTGG 59.064 61.111 21.19 0.00 44.04 3.28
5210 7125 2.544359 CGGACGCACGTCTGTTTG 59.456 61.111 21.00 5.08 44.19 2.93
5234 7149 0.815615 GAATGGGTCGGCAGATGGAC 60.816 60.000 0.00 0.00 0.00 4.02
5235 7150 1.526887 GAATGGGTCGGCAGATGGA 59.473 57.895 0.00 0.00 0.00 3.41
5236 7151 1.526917 GGAATGGGTCGGCAGATGG 60.527 63.158 0.00 0.00 0.00 3.51
5237 7152 0.816825 CAGGAATGGGTCGGCAGATG 60.817 60.000 0.00 0.00 0.00 2.90
5238 7153 0.982852 TCAGGAATGGGTCGGCAGAT 60.983 55.000 0.00 0.00 0.00 2.90
5239 7154 1.612146 TCAGGAATGGGTCGGCAGA 60.612 57.895 0.00 0.00 0.00 4.26
5240 7155 1.450312 GTCAGGAATGGGTCGGCAG 60.450 63.158 0.00 0.00 0.00 4.85
5241 7156 2.668632 GTCAGGAATGGGTCGGCA 59.331 61.111 0.00 0.00 0.00 5.69
5242 7157 2.124695 GGTCAGGAATGGGTCGGC 60.125 66.667 0.00 0.00 0.00 5.54
5243 7158 1.635817 ATGGGTCAGGAATGGGTCGG 61.636 60.000 0.00 0.00 0.00 4.79
5244 7159 0.255890 AATGGGTCAGGAATGGGTCG 59.744 55.000 0.00 0.00 0.00 4.79
5245 7160 2.532250 AAATGGGTCAGGAATGGGTC 57.468 50.000 0.00 0.00 0.00 4.46
5246 7161 3.274281 AAAAATGGGTCAGGAATGGGT 57.726 42.857 0.00 0.00 0.00 4.51
5247 7162 3.132824 GCTAAAAATGGGTCAGGAATGGG 59.867 47.826 0.00 0.00 0.00 4.00
5248 7163 3.132824 GGCTAAAAATGGGTCAGGAATGG 59.867 47.826 0.00 0.00 0.00 3.16
5249 7164 4.026052 AGGCTAAAAATGGGTCAGGAATG 58.974 43.478 0.00 0.00 0.00 2.67
5250 7165 4.264352 TGAGGCTAAAAATGGGTCAGGAAT 60.264 41.667 0.00 0.00 0.00 3.01
5251 7166 3.075283 TGAGGCTAAAAATGGGTCAGGAA 59.925 43.478 0.00 0.00 0.00 3.36
5252 7167 2.647299 TGAGGCTAAAAATGGGTCAGGA 59.353 45.455 0.00 0.00 0.00 3.86
5253 7168 3.085952 TGAGGCTAAAAATGGGTCAGG 57.914 47.619 0.00 0.00 0.00 3.86
5254 7169 5.413499 CAAATGAGGCTAAAAATGGGTCAG 58.587 41.667 0.00 0.00 0.00 3.51
5255 7170 4.322650 GCAAATGAGGCTAAAAATGGGTCA 60.323 41.667 0.00 0.00 0.00 4.02
5256 7171 4.183865 GCAAATGAGGCTAAAAATGGGTC 58.816 43.478 0.00 0.00 0.00 4.46
5257 7172 3.368323 CGCAAATGAGGCTAAAAATGGGT 60.368 43.478 0.00 0.00 0.00 4.51
5258 7173 3.189285 CGCAAATGAGGCTAAAAATGGG 58.811 45.455 0.00 0.00 0.00 4.00
5259 7174 3.848726 ACGCAAATGAGGCTAAAAATGG 58.151 40.909 0.00 0.00 0.00 3.16
5260 7175 3.543494 CGACGCAAATGAGGCTAAAAATG 59.457 43.478 0.00 0.00 0.00 2.32
5261 7176 3.427503 CCGACGCAAATGAGGCTAAAAAT 60.428 43.478 0.00 0.00 0.00 1.82
5262 7177 2.095466 CCGACGCAAATGAGGCTAAAAA 60.095 45.455 0.00 0.00 0.00 1.94
5263 7178 1.466950 CCGACGCAAATGAGGCTAAAA 59.533 47.619 0.00 0.00 0.00 1.52
5264 7179 1.083489 CCGACGCAAATGAGGCTAAA 58.917 50.000 0.00 0.00 0.00 1.85
5265 7180 1.366111 GCCGACGCAAATGAGGCTAA 61.366 55.000 0.00 0.00 44.06 3.09
5266 7181 1.813753 GCCGACGCAAATGAGGCTA 60.814 57.895 0.00 0.00 44.06 3.93
5267 7182 3.127533 GCCGACGCAAATGAGGCT 61.128 61.111 0.00 0.00 44.06 4.58
5268 7183 4.520846 CGCCGACGCAAATGAGGC 62.521 66.667 0.00 0.00 44.00 4.70
5279 7194 4.492160 TCTCATGTCCGCGCCGAC 62.492 66.667 20.04 20.04 0.00 4.79
5280 7195 4.492160 GTCTCATGTCCGCGCCGA 62.492 66.667 0.00 0.00 0.00 5.54
5282 7197 3.982372 TTCGTCTCATGTCCGCGCC 62.982 63.158 0.00 0.00 0.00 6.53
5283 7198 2.506217 TTCGTCTCATGTCCGCGC 60.506 61.111 0.00 0.00 0.00 6.86
5284 7199 2.497092 CGTTCGTCTCATGTCCGCG 61.497 63.158 0.00 0.00 0.00 6.46
5285 7200 2.789203 GCGTTCGTCTCATGTCCGC 61.789 63.158 0.00 0.00 0.00 5.54
5286 7201 2.497092 CGCGTTCGTCTCATGTCCG 61.497 63.158 0.00 0.00 0.00 4.79
5287 7202 2.789203 GCGCGTTCGTCTCATGTCC 61.789 63.158 8.43 0.00 38.14 4.02
5288 7203 2.689766 GCGCGTTCGTCTCATGTC 59.310 61.111 8.43 0.00 38.14 3.06
5289 7204 3.172575 CGCGCGTTCGTCTCATGT 61.173 61.111 24.19 0.00 38.14 3.21
5290 7205 4.543736 GCGCGCGTTCGTCTCATG 62.544 66.667 32.35 0.00 38.14 3.07


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

AutoCloner maintained by Alex Coulton.