Multiple sequence alignment - TraesCS6A01G020400

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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 TraesCS6A01G020400 chr6A 100.000 5726 0 0 1 5726 9481425 9487150 0.000000e+00 10575.0
1 TraesCS6A01G020400 chr6A 100.000 117 0 0 5610 5726 217267094 217266978 3.470000e-52 217.0
2 TraesCS6A01G020400 chr6B 91.636 3754 227 38 1 3723 16439530 16443227 0.000000e+00 5112.0
3 TraesCS6A01G020400 chr6B 91.035 3759 235 49 1 3723 15211194 15207502 0.000000e+00 4981.0
4 TraesCS6A01G020400 chr6B 89.225 1420 109 20 3847 5260 16443225 16444606 0.000000e+00 1735.0
5 TraesCS6A01G020400 chr6B 94.725 455 23 1 3847 4300 15207504 15207050 0.000000e+00 706.0
6 TraesCS6A01G020400 chr6B 97.541 122 2 1 5605 5726 124390603 124390483 2.090000e-49 207.0
7 TraesCS6A01G020400 chr6D 91.459 3243 192 42 511 3723 8545351 8542164 0.000000e+00 4375.0
8 TraesCS6A01G020400 chr6D 86.539 3395 255 85 408 3723 34080926 34084197 0.000000e+00 3552.0
9 TraesCS6A01G020400 chr6D 92.338 2258 123 24 401 2636 8807150 8809379 0.000000e+00 3166.0
10 TraesCS6A01G020400 chr6D 91.468 1934 103 29 3134 5036 8560053 8558151 0.000000e+00 2601.0
11 TraesCS6A01G020400 chr6D 92.959 1193 65 9 1206 2381 8561403 8560213 0.000000e+00 1720.0
12 TraesCS6A01G020400 chr6D 93.178 1158 66 9 2574 3723 8809377 8810529 0.000000e+00 1688.0
13 TraesCS6A01G020400 chr6D 91.898 827 38 11 3847 4672 8810527 8811325 0.000000e+00 1129.0
14 TraesCS6A01G020400 chr6D 91.657 827 41 14 3847 4672 8542166 8541367 0.000000e+00 1120.0
15 TraesCS6A01G020400 chr6D 93.957 513 30 1 1 513 8545993 8545482 0.000000e+00 774.0
16 TraesCS6A01G020400 chr6D 87.356 696 28 26 511 1205 8562383 8561747 0.000000e+00 743.0
17 TraesCS6A01G020400 chr6D 93.082 477 31 2 3847 4322 34084195 34084670 0.000000e+00 697.0
18 TraesCS6A01G020400 chr6D 81.855 733 74 22 4541 5260 34084808 34085494 3.870000e-156 562.0
19 TraesCS6A01G020400 chr6D 87.110 481 45 7 4700 5171 8811324 8811796 3.930000e-146 529.0
20 TraesCS6A01G020400 chr6D 93.413 334 20 2 181 513 8562846 8562514 1.430000e-135 494.0
21 TraesCS6A01G020400 chr6D 85.677 384 26 8 5250 5610 34085514 34085891 1.510000e-100 377.0
22 TraesCS6A01G020400 chr6D 92.169 166 12 1 2929 3094 8560216 8560052 3.450000e-57 233.0
23 TraesCS6A01G020400 chr6D 91.667 156 13 0 36 191 8563340 8563185 3.470000e-52 217.0
24 TraesCS6A01G020400 chr6D 99.145 117 1 0 5610 5726 418462627 418462511 1.620000e-50 211.0
25 TraesCS6A01G020400 chr6D 93.204 103 5 2 5510 5611 8555159 8555058 3.570000e-32 150.0
26 TraesCS6A01G020400 chr5B 85.765 3976 352 93 435 4322 556786626 556782777 0.000000e+00 4010.0
27 TraesCS6A01G020400 chr5B 82.014 695 80 21 4444 5128 17672766 17673425 3.020000e-152 549.0
28 TraesCS6A01G020400 chr5B 85.680 419 40 8 4590 5008 556782368 556781970 1.910000e-114 424.0
29 TraesCS6A01G020400 chr7D 80.935 556 81 15 2975 3524 5416418 5416954 3.190000e-112 416.0
30 TraesCS6A01G020400 chr7D 99.153 118 1 0 5609 5726 208557843 208557960 4.490000e-51 213.0
31 TraesCS6A01G020400 chr4A 73.149 1445 262 77 793 2188 737063914 737062547 2.480000e-108 403.0
32 TraesCS6A01G020400 chr4A 80.723 498 67 18 2981 3469 737067780 737067303 1.520000e-95 361.0
33 TraesCS6A01G020400 chr4A 99.145 117 1 0 5610 5726 606665807 606665923 1.620000e-50 211.0
34 TraesCS6A01G020400 chr4A 86.726 113 14 1 4094 4205 737067112 737067000 2.170000e-24 124.0
35 TraesCS6A01G020400 chr4A 81.250 112 20 1 468 578 737065050 737064939 7.900000e-14 89.8
36 TraesCS6A01G020400 chr5D 90.175 285 23 1 4021 4300 42078798 42079082 3.260000e-97 366.0
37 TraesCS6A01G020400 chrUn 100.000 117 0 0 5610 5726 320083 320199 3.470000e-52 217.0
38 TraesCS6A01G020400 chr7B 100.000 116 0 0 5611 5726 37099013 37099128 1.250000e-51 215.0
39 TraesCS6A01G020400 chr1A 99.153 118 1 0 5609 5726 339095840 339095723 4.490000e-51 213.0
40 TraesCS6A01G020400 chr1B 97.541 122 3 0 5605 5726 120345621 120345500 5.810000e-50 209.0


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 TraesCS6A01G020400 chr6A 9481425 9487150 5725 False 10575.000000 10575 100.000000 1 5726 1 chr6A.!!$F1 5725
1 TraesCS6A01G020400 chr6B 16439530 16444606 5076 False 3423.500000 5112 90.430500 1 5260 2 chr6B.!!$F1 5259
2 TraesCS6A01G020400 chr6B 15207050 15211194 4144 True 2843.500000 4981 92.880000 1 4300 2 chr6B.!!$R2 4299
3 TraesCS6A01G020400 chr6D 8541367 8545993 4626 True 2089.666667 4375 92.357667 1 4672 3 chr6D.!!$R2 4671
4 TraesCS6A01G020400 chr6D 8807150 8811796 4646 False 1628.000000 3166 91.131000 401 5171 4 chr6D.!!$F1 4770
5 TraesCS6A01G020400 chr6D 34080926 34085891 4965 False 1297.000000 3552 86.788250 408 5610 4 chr6D.!!$F2 5202
6 TraesCS6A01G020400 chr6D 8555058 8563340 8282 True 879.714286 2601 91.748000 36 5611 7 chr6D.!!$R3 5575
7 TraesCS6A01G020400 chr5B 556781970 556786626 4656 True 2217.000000 4010 85.722500 435 5008 2 chr5B.!!$R1 4573
8 TraesCS6A01G020400 chr5B 17672766 17673425 659 False 549.000000 549 82.014000 4444 5128 1 chr5B.!!$F1 684
9 TraesCS6A01G020400 chr7D 5416418 5416954 536 False 416.000000 416 80.935000 2975 3524 1 chr7D.!!$F1 549
10 TraesCS6A01G020400 chr4A 737062547 737067780 5233 True 244.450000 403 80.462000 468 4205 4 chr4A.!!$R1 3737

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
406 757 0.326904 AGACCAGGCAGATGATCCCA 60.327 55.000 0.00 0.00 0.00 4.37 F
537 1028 0.975040 TGCCAGTGTTTGCCAACCTT 60.975 50.000 0.00 0.00 31.02 3.50 F
1627 2518 1.106285 GGTGTCCAATCATCTTGGGC 58.894 55.000 1.67 1.67 44.14 5.36 F
1762 2655 1.557099 TAGTGCCACTTCTGGTCGAT 58.443 50.000 1.02 0.00 40.17 3.59 F
1766 2659 1.831106 TGCCACTTCTGGTCGATATGT 59.169 47.619 0.00 0.00 40.17 2.29 F
3232 4258 2.288702 TGCTCAGAGAGTGAAGAACAGC 60.289 50.000 0.00 0.00 33.60 4.40 F
3644 4691 3.744660 AGCTGGGTTCTCTTTACAACAG 58.255 45.455 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 2300 0.767375 AGTCCACACATGGCTTGTCT 59.233 50.000 2.62 0.0 46.80 3.41 R
1766 2659 0.907486 CAACAGATCTCAGCCCTCCA 59.093 55.000 0.00 0.0 0.00 3.86 R
3200 4226 1.208052 TCTCTGAGCACCAATACTGCC 59.792 52.381 0.00 0.0 35.01 4.85 R
3617 4662 2.317530 AAGAGAACCCAGCTTATCGC 57.682 50.000 0.00 0.0 39.57 4.58 R
3621 4666 5.163237 ACTGTTGTAAAGAGAACCCAGCTTA 60.163 40.000 0.00 0.0 40.10 3.09 R
4075 5154 0.323725 TCCTTCCCATTTGCAGCTCC 60.324 55.000 0.00 0.0 0.00 4.70 R
5640 11921 1.303236 TTAGGCTGCACAACCGCAT 60.303 52.632 0.50 0.0 42.06 4.73 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
41 42 5.564550 ACTGGTTCTCTTATGCATTGAAGT 58.435 37.500 3.54 1.58 0.00 3.01
47 48 7.433425 GGTTCTCTTATGCATTGAAGTTTATGC 59.567 37.037 3.54 13.90 45.66 3.14
58 59 7.677041 GCATTGAAGTTTATGCCCTTATTTTGC 60.677 37.037 11.02 0.00 40.93 3.68
102 103 3.114616 CTTGGTGCCGTGCGAGAG 61.115 66.667 0.00 0.00 0.00 3.20
108 109 1.069090 TGCCGTGCGAGAGAAACTT 59.931 52.632 0.00 0.00 0.00 2.66
109 110 0.944311 TGCCGTGCGAGAGAAACTTC 60.944 55.000 0.00 0.00 0.00 3.01
166 167 5.426689 TCTTAATGCCTCAGATCACTGTT 57.573 39.130 0.00 0.00 43.81 3.16
172 173 4.569943 TGCCTCAGATCACTGTTAAGAAC 58.430 43.478 0.00 0.00 43.81 3.01
191 541 5.762045 AGAACAATTGAAAGACATGGTTCG 58.238 37.500 13.59 0.00 37.77 3.95
192 542 5.530915 AGAACAATTGAAAGACATGGTTCGA 59.469 36.000 13.59 0.00 37.77 3.71
224 574 3.191791 CACATGACAAGATTGCACCATCA 59.808 43.478 0.00 0.00 0.00 3.07
236 586 6.658816 AGATTGCACCATCAATGTAGTTTACA 59.341 34.615 1.40 0.00 43.80 2.41
271 621 1.369091 CTTGTATGCTCCCACACGCC 61.369 60.000 0.00 0.00 0.00 5.68
278 628 3.371097 CTCCCACACGCCGTAGCAT 62.371 63.158 0.00 0.00 39.83 3.79
289 639 2.798145 CGCCGTAGCATGACATAACAGA 60.798 50.000 0.00 0.00 39.83 3.41
406 757 0.326904 AGACCAGGCAGATGATCCCA 60.327 55.000 0.00 0.00 0.00 4.37
437 788 3.603532 CCAAAGCTCTGCTATTCAGTCA 58.396 45.455 0.00 0.00 43.32 3.41
537 1028 0.975040 TGCCAGTGTTTGCCAACCTT 60.975 50.000 0.00 0.00 31.02 3.50
650 1141 4.019174 AGATGGGTAAAAGCTGGAACATG 58.981 43.478 0.00 0.00 38.20 3.21
727 1221 9.307121 CTATGTCTAACCAGTCAAATCAAGTAG 57.693 37.037 0.00 0.00 0.00 2.57
791 1286 4.843220 AAGTTGCAGTTTTCAGATGAGG 57.157 40.909 0.00 0.00 0.00 3.86
801 1296 4.617253 TTTCAGATGAGGAAGGACGAAA 57.383 40.909 0.00 0.00 0.00 3.46
802 1297 3.876274 TCAGATGAGGAAGGACGAAAG 57.124 47.619 0.00 0.00 0.00 2.62
806 1301 4.099266 CAGATGAGGAAGGACGAAAGAGAT 59.901 45.833 0.00 0.00 0.00 2.75
821 1318 8.586570 ACGAAAGAGATAATAAATGAGAGCTG 57.413 34.615 0.00 0.00 0.00 4.24
839 1336 3.653352 AGCTGTAAAGAGAAGGAAGGGTT 59.347 43.478 0.00 0.00 0.00 4.11
904 1403 6.446434 ACTCCCCTATATATACGACACCTACT 59.554 42.308 0.00 0.00 0.00 2.57
1061 1600 1.229315 AACATGTTCGCCGCGGTAAA 61.229 50.000 28.70 18.32 0.00 2.01
1095 1635 1.550327 TGGTGCCAATTATGCGGAAA 58.450 45.000 0.00 0.00 0.00 3.13
1098 1638 3.123050 GGTGCCAATTATGCGGAAATTC 58.877 45.455 0.00 0.00 0.00 2.17
1102 1642 5.294060 GTGCCAATTATGCGGAAATTCATTT 59.706 36.000 0.00 0.00 0.00 2.32
1142 1684 5.916883 GCGATATTTGTCAGGGAATTTGATG 59.083 40.000 0.00 0.00 0.00 3.07
1143 1685 6.441274 CGATATTTGTCAGGGAATTTGATGG 58.559 40.000 0.00 0.00 0.00 3.51
1148 1690 5.212532 TGTCAGGGAATTTGATGGTTTTG 57.787 39.130 0.00 0.00 0.00 2.44
1201 1744 2.025155 GACGATCAGTTCCAGGAGCTA 58.975 52.381 5.32 0.00 0.00 3.32
1333 2219 2.690778 CCTTTCCTTTGCTCGCCCG 61.691 63.158 0.00 0.00 0.00 6.13
1533 2420 5.048782 TCCTCTTTGTATGTGATTGTGCAAC 60.049 40.000 0.00 0.00 37.35 4.17
1627 2518 1.106285 GGTGTCCAATCATCTTGGGC 58.894 55.000 1.67 1.67 44.14 5.36
1636 2527 4.023707 CCAATCATCTTGGGCGAGAATTAC 60.024 45.833 0.00 0.00 35.96 1.89
1653 2545 7.076842 AGAATTACGGTCTGTTTCATCATTG 57.923 36.000 0.00 0.00 0.00 2.82
1724 2617 4.464951 TGGTTGGACGACTCAACAGTATAT 59.535 41.667 16.14 0.00 44.38 0.86
1762 2655 1.557099 TAGTGCCACTTCTGGTCGAT 58.443 50.000 1.02 0.00 40.17 3.59
1766 2659 1.831106 TGCCACTTCTGGTCGATATGT 59.169 47.619 0.00 0.00 40.17 2.29
1809 2702 5.247507 GCATGTTGCAGTGATTTACCATA 57.752 39.130 0.00 0.00 44.26 2.74
1833 2727 5.986004 AGATCCGACAAAAATTATCCGTC 57.014 39.130 0.00 0.00 0.00 4.79
1938 2842 9.831054 CATTTAGATTTAGATACGACGAACAAC 57.169 33.333 0.00 0.00 0.00 3.32
1945 2849 4.613944 AGATACGACGAACAACTTTGTCA 58.386 39.130 0.00 0.00 41.31 3.58
1953 2857 4.208460 ACGAACAACTTTGTCATCGTACTG 59.792 41.667 16.40 0.00 46.56 2.74
1976 2880 8.495949 ACTGTTTTGTGATTTAGATACGACAAG 58.504 33.333 0.00 0.00 0.00 3.16
1998 2902 4.223477 AGCTGATTGGCCATTGTATTGTTT 59.777 37.500 6.09 0.00 0.00 2.83
2013 2917 9.754382 ATTGTATTGTTTTATGATCTGCATTCC 57.246 29.630 0.00 0.00 38.44 3.01
2181 3088 5.707764 TGTTACCGTTTGATGATTTGGATCA 59.292 36.000 0.00 0.00 45.81 2.92
2205 3112 5.768662 AGACAAATATGATCTGCTTCCCATG 59.231 40.000 0.00 0.00 0.00 3.66
2209 3116 3.947612 ATGATCTGCTTCCCATGAACT 57.052 42.857 0.00 0.00 0.00 3.01
2253 3174 2.871096 AAGTGGTCCAGCCGATTAAA 57.129 45.000 0.00 0.00 41.21 1.52
2254 3175 2.871096 AGTGGTCCAGCCGATTAAAA 57.129 45.000 0.00 0.00 41.21 1.52
2289 3222 3.183172 GTCATTGTCATGATCCGACATCG 59.817 47.826 13.96 9.40 42.69 3.84
2290 3223 3.068024 TCATTGTCATGATCCGACATCGA 59.932 43.478 13.96 11.07 42.69 3.59
2291 3224 3.733443 TTGTCATGATCCGACATCGAT 57.267 42.857 13.96 0.00 42.69 3.59
2325 3267 6.890979 TCATATGTTCCACACACATCAAAA 57.109 33.333 1.90 0.00 38.61 2.44
2339 3281 5.302568 ACACATCAAAAGGCTCAAAGAATCA 59.697 36.000 0.00 0.00 0.00 2.57
2341 3283 5.537674 ACATCAAAAGGCTCAAAGAATCACT 59.462 36.000 0.00 0.00 0.00 3.41
2342 3284 6.041296 ACATCAAAAGGCTCAAAGAATCACTT 59.959 34.615 0.00 0.00 40.98 3.16
2446 3400 7.498239 CCATGACATAGATCAGAGAAACATGTT 59.502 37.037 4.92 4.92 32.47 2.71
2614 3568 4.869861 CACAACATTCCGTGACATAGATCA 59.130 41.667 0.00 0.00 35.02 2.92
2632 3646 3.953712 TCAGAGAAACATGTTCCGCTA 57.046 42.857 12.39 0.00 0.00 4.26
2655 3669 6.916360 ACATTCACATTACTTGGATGGTTT 57.084 33.333 0.00 0.00 0.00 3.27
2676 3690 8.143193 TGGTTTTGTACACTCGAGTTATCTTAA 58.857 33.333 17.26 4.13 0.00 1.85
2821 3836 8.113462 ACTATTCCCTTGCCTAATCAAGTTAAA 58.887 33.333 3.29 0.00 41.29 1.52
2881 3901 3.198635 TGGAATCAGAGGAGTAAGCCAAG 59.801 47.826 0.00 0.00 0.00 3.61
2900 3920 2.805194 AGGAGTCACTACCGCTTTACT 58.195 47.619 0.00 0.00 0.00 2.24
2901 3921 2.754002 AGGAGTCACTACCGCTTTACTC 59.246 50.000 0.00 0.00 34.08 2.59
2955 3975 6.851222 ATCGTGGATTAGCACTTTCATTAG 57.149 37.500 0.00 0.00 0.00 1.73
3062 4087 8.182227 GGCTTTCATAGTTGTATTTAGTTGACC 58.818 37.037 0.00 0.00 0.00 4.02
3232 4258 2.288702 TGCTCAGAGAGTGAAGAACAGC 60.289 50.000 0.00 0.00 33.60 4.40
3318 4346 7.899178 TCATGTCACACTATTGTATTTTCGT 57.101 32.000 0.00 0.00 33.30 3.85
3470 4504 8.946085 TGTAAACTACTCATTTTATTCAGCCTG 58.054 33.333 0.00 0.00 0.00 4.85
3483 4517 4.991153 TTCAGCCTGTATAGAGACACAG 57.009 45.455 0.00 0.00 41.51 3.66
3644 4691 3.744660 AGCTGGGTTCTCTTTACAACAG 58.255 45.455 0.00 0.00 0.00 3.16
3771 4818 7.823745 ATAACTTGTTGATGGTTCAGTCTTT 57.176 32.000 0.00 0.00 32.27 2.52
3805 4852 8.132362 TGTTACAAGCACCTTTTTACATGTAAG 58.868 33.333 17.36 8.89 33.98 2.34
3828 4875 7.637709 AGTTTTCAAAATAAAGGCGTCATTC 57.362 32.000 0.00 0.00 0.00 2.67
4012 5091 7.852971 AATTGTAATGGGATGAGCATTTTTG 57.147 32.000 0.00 0.00 0.00 2.44
4019 5098 4.837860 TGGGATGAGCATTTTTGGTAGTTT 59.162 37.500 0.00 0.00 0.00 2.66
4064 5143 9.787532 TTTTCATGAGCTGCTAATTATTAACAC 57.212 29.630 0.15 0.00 0.00 3.32
4075 5154 7.958567 TGCTAATTATTAACACGTTTCTTTCGG 59.041 33.333 0.00 0.00 0.00 4.30
4300 5413 8.734386 ACTTCTTATCCTAAAGTTTGCTTGATG 58.266 33.333 0.00 0.00 34.71 3.07
4390 5632 2.424246 GTGTACTCAGAGCCAGAGGTAC 59.576 54.545 0.00 0.00 37.43 3.34
4392 5634 3.522343 TGTACTCAGAGCCAGAGGTACTA 59.478 47.826 0.00 0.00 41.55 1.82
4393 5635 3.007473 ACTCAGAGCCAGAGGTACTAC 57.993 52.381 0.00 0.00 41.55 2.73
4511 5785 5.648092 AGGTCACTATAGTTTTGCATCAACC 59.352 40.000 1.56 0.85 0.00 3.77
4552 5832 6.486253 TTGATACACTTCATGTCTTGCTTC 57.514 37.500 0.00 0.00 42.09 3.86
4596 5895 7.759489 TCCTTGCAAATACTCTGTGTTTAAT 57.241 32.000 0.00 0.00 0.00 1.40
4688 5990 4.881850 ACTAACCTGTTGTTCTGTTTCTGG 59.118 41.667 0.00 0.00 38.42 3.86
4697 5999 0.469494 TCTGTTTCTGGTGCAGCTGA 59.531 50.000 20.43 19.92 0.00 4.26
4723 6025 1.566231 CAGGTCCAGGCCTTAATCCTT 59.434 52.381 0.00 0.00 36.58 3.36
4728 6030 4.452825 GTCCAGGCCTTAATCCTTAACTC 58.547 47.826 0.00 0.00 0.00 3.01
4854 6160 0.247736 GTGGGGTCTGTAGCTGTCTG 59.752 60.000 0.00 0.00 0.00 3.51
5008 6325 6.477688 TCTTAGTTCTAGTCGGTTTGTTGTTG 59.522 38.462 0.00 0.00 0.00 3.33
5062 6379 1.307355 TTGTGCCTCGTCGATCGGTA 61.307 55.000 16.41 0.00 40.32 4.02
5063 6380 1.298190 GTGCCTCGTCGATCGGTAC 60.298 63.158 16.41 6.05 40.32 3.34
5064 6381 1.746239 TGCCTCGTCGATCGGTACA 60.746 57.895 16.41 2.82 40.32 2.90
5087 7753 3.738982 TGTGGTACATTGTGGAGAACAG 58.261 45.455 0.00 0.00 44.52 3.16
5089 7755 3.746492 GTGGTACATTGTGGAGAACAGAC 59.254 47.826 0.00 0.00 44.52 3.51
5148 8663 2.165437 GCAAACAAGTCACCACCTTTCA 59.835 45.455 0.00 0.00 0.00 2.69
5150 8665 4.610945 CAAACAAGTCACCACCTTTCATC 58.389 43.478 0.00 0.00 0.00 2.92
5212 9226 8.087982 ACAATTATAGCGGATGATGTGTAAAG 57.912 34.615 0.00 0.00 0.00 1.85
5216 9230 1.934589 CGGATGATGTGTAAAGCCGA 58.065 50.000 0.00 0.00 39.62 5.54
5236 9250 8.197988 AGCCGATAAAAACTAGACATAACAAG 57.802 34.615 0.00 0.00 0.00 3.16
5241 9255 9.543018 GATAAAAACTAGACATAACAAGTGCAC 57.457 33.333 9.40 9.40 0.00 4.57
5254 9303 1.527034 AGTGCACGAATGTCTGCATT 58.473 45.000 12.01 0.00 44.93 3.56
5308 9357 8.246430 ACTAATCATCCATTCTTACGAACCTA 57.754 34.615 0.00 0.00 30.67 3.08
5320 9369 5.474532 TCTTACGAACCTACTAACTCAAGCA 59.525 40.000 0.00 0.00 0.00 3.91
5322 9371 2.924290 CGAACCTACTAACTCAAGCAGC 59.076 50.000 0.00 0.00 0.00 5.25
5328 10497 2.611518 ACTAACTCAAGCAGCTAAGCG 58.388 47.619 0.00 0.00 40.15 4.68
5384 10790 3.822735 TCAATTTGGAGCCTCAACTTCTG 59.177 43.478 0.00 0.00 0.00 3.02
5433 11123 1.723220 CAGCATATGCCTCGGATCTG 58.277 55.000 23.96 9.34 43.38 2.90
5434 11124 1.274447 CAGCATATGCCTCGGATCTGA 59.726 52.381 23.96 3.71 43.38 3.27
5443 11133 2.034878 CCTCGGATCTGACTGAATGGA 58.965 52.381 0.00 0.00 0.00 3.41
5535 11815 0.398696 TAACTGCTTCCGGCCTCAAA 59.601 50.000 0.00 0.00 40.92 2.69
5611 11892 7.803279 AAAGGGCTACAAGTATATTAAGTGC 57.197 36.000 0.00 0.00 0.00 4.40
5612 11893 6.494666 AGGGCTACAAGTATATTAAGTGCA 57.505 37.500 0.00 0.00 0.00 4.57
5613 11894 6.895782 AGGGCTACAAGTATATTAAGTGCAA 58.104 36.000 0.00 0.00 0.00 4.08
5614 11895 7.343357 AGGGCTACAAGTATATTAAGTGCAAA 58.657 34.615 0.00 0.00 0.00 3.68
5615 11896 7.499232 AGGGCTACAAGTATATTAAGTGCAAAG 59.501 37.037 0.00 0.00 0.00 2.77
5616 11897 7.497909 GGGCTACAAGTATATTAAGTGCAAAGA 59.502 37.037 0.00 0.00 0.00 2.52
5617 11898 8.552034 GGCTACAAGTATATTAAGTGCAAAGAG 58.448 37.037 0.00 0.00 0.00 2.85
5618 11899 9.314321 GCTACAAGTATATTAAGTGCAAAGAGA 57.686 33.333 0.00 0.00 0.00 3.10
5620 11901 8.202745 ACAAGTATATTAAGTGCAAAGAGAGC 57.797 34.615 0.00 0.00 0.00 4.09
5621 11902 7.281100 ACAAGTATATTAAGTGCAAAGAGAGCC 59.719 37.037 0.00 0.00 0.00 4.70
5622 11903 7.130681 AGTATATTAAGTGCAAAGAGAGCCT 57.869 36.000 0.00 0.00 0.00 4.58
5623 11904 7.569240 AGTATATTAAGTGCAAAGAGAGCCTT 58.431 34.615 0.00 0.00 36.47 4.35
5624 11905 6.690194 ATATTAAGTGCAAAGAGAGCCTTG 57.310 37.500 0.00 0.00 34.79 3.61
5625 11906 1.613836 AAGTGCAAAGAGAGCCTTGG 58.386 50.000 0.00 0.00 34.79 3.61
5627 11908 4.412075 GCAAAGAGAGCCTTGGCT 57.588 55.556 14.69 14.69 46.15 4.75
5628 11909 2.178856 GCAAAGAGAGCCTTGGCTC 58.821 57.895 28.67 28.67 46.15 4.70
5629 11910 0.607489 GCAAAGAGAGCCTTGGCTCA 60.607 55.000 34.40 0.00 46.15 4.26
5630 11911 1.451067 CAAAGAGAGCCTTGGCTCAG 58.549 55.000 34.40 18.91 39.13 3.35
5631 11912 1.063183 AAAGAGAGCCTTGGCTCAGT 58.937 50.000 34.40 22.13 39.13 3.41
5632 11913 0.324285 AAGAGAGCCTTGGCTCAGTG 59.676 55.000 34.40 0.00 39.13 3.66
5633 11914 1.078567 GAGAGCCTTGGCTCAGTGG 60.079 63.158 34.40 0.00 39.13 4.00
5634 11915 1.835927 GAGAGCCTTGGCTCAGTGGT 61.836 60.000 34.40 19.17 39.13 4.16
5635 11916 1.073897 GAGCCTTGGCTCAGTGGTT 59.926 57.895 30.25 1.25 36.86 3.67
5636 11917 1.228367 AGCCTTGGCTCAGTGGTTG 60.228 57.895 8.56 0.00 0.00 3.77
5637 11918 2.270986 GCCTTGGCTCAGTGGTTGG 61.271 63.158 4.11 0.00 0.00 3.77
5638 11919 1.604593 CCTTGGCTCAGTGGTTGGG 60.605 63.158 0.00 0.00 0.00 4.12
5643 11924 3.281240 CTCAGTGGTTGGGCATGC 58.719 61.111 9.90 9.90 0.00 4.06
5644 11925 2.672651 TCAGTGGTTGGGCATGCG 60.673 61.111 12.44 0.00 0.00 4.73
5645 11926 3.751246 CAGTGGTTGGGCATGCGG 61.751 66.667 12.44 0.00 0.00 5.69
5646 11927 4.284550 AGTGGTTGGGCATGCGGT 62.285 61.111 12.44 0.00 0.00 5.68
5647 11928 3.302344 GTGGTTGGGCATGCGGTT 61.302 61.111 12.44 0.00 0.00 4.44
5648 11929 3.301554 TGGTTGGGCATGCGGTTG 61.302 61.111 12.44 0.00 0.00 3.77
5649 11930 3.302344 GGTTGGGCATGCGGTTGT 61.302 61.111 12.44 0.00 0.00 3.32
5650 11931 2.049248 GTTGGGCATGCGGTTGTG 60.049 61.111 12.44 0.00 0.00 3.33
5651 11932 3.988525 TTGGGCATGCGGTTGTGC 61.989 61.111 12.44 0.00 40.55 4.57
5658 11939 2.112087 TGCGGTTGTGCAGCCTAA 59.888 55.556 3.70 0.00 40.62 2.69
5659 11940 2.258013 TGCGGTTGTGCAGCCTAAC 61.258 57.895 3.70 0.00 40.62 2.34
5660 11941 2.860293 CGGTTGTGCAGCCTAACG 59.140 61.111 3.70 0.00 0.00 3.18
5661 11942 1.666553 CGGTTGTGCAGCCTAACGA 60.667 57.895 3.70 0.00 0.00 3.85
5662 11943 1.866925 GGTTGTGCAGCCTAACGAC 59.133 57.895 0.00 0.00 0.00 4.34
5663 11944 1.574702 GGTTGTGCAGCCTAACGACC 61.575 60.000 5.25 5.25 42.26 4.79
5664 11945 1.302192 TTGTGCAGCCTAACGACCC 60.302 57.895 0.00 0.00 0.00 4.46
5665 11946 2.813908 GTGCAGCCTAACGACCCG 60.814 66.667 0.00 0.00 0.00 5.28
5666 11947 2.992689 TGCAGCCTAACGACCCGA 60.993 61.111 0.00 0.00 0.00 5.14
5667 11948 2.202756 GCAGCCTAACGACCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
5668 11949 3.003113 GCAGCCTAACGACCCGAGT 62.003 63.158 0.00 0.00 0.00 4.18
5669 11950 1.590147 CAGCCTAACGACCCGAGTT 59.410 57.895 0.00 0.00 35.75 3.01
5670 11951 0.458025 CAGCCTAACGACCCGAGTTC 60.458 60.000 0.00 0.00 33.42 3.01
5671 11952 0.896940 AGCCTAACGACCCGAGTTCA 60.897 55.000 0.00 0.00 33.42 3.18
5672 11953 0.037975 GCCTAACGACCCGAGTTCAA 60.038 55.000 0.00 0.00 33.42 2.69
5673 11954 1.405121 GCCTAACGACCCGAGTTCAAT 60.405 52.381 0.00 0.00 33.42 2.57
5674 11955 2.933928 GCCTAACGACCCGAGTTCAATT 60.934 50.000 0.00 0.00 33.42 2.32
5675 11956 2.928116 CCTAACGACCCGAGTTCAATTC 59.072 50.000 0.00 0.00 33.42 2.17
5676 11957 1.804601 AACGACCCGAGTTCAATTCC 58.195 50.000 0.00 0.00 0.00 3.01
5677 11958 0.974383 ACGACCCGAGTTCAATTCCT 59.026 50.000 0.00 0.00 0.00 3.36
5678 11959 2.173519 ACGACCCGAGTTCAATTCCTA 58.826 47.619 0.00 0.00 0.00 2.94
5679 11960 2.165845 ACGACCCGAGTTCAATTCCTAG 59.834 50.000 0.00 0.00 0.00 3.02
5680 11961 2.426024 CGACCCGAGTTCAATTCCTAGA 59.574 50.000 0.00 0.00 0.00 2.43
5681 11962 3.119245 CGACCCGAGTTCAATTCCTAGAA 60.119 47.826 0.00 0.00 0.00 2.10
5682 11963 4.441634 CGACCCGAGTTCAATTCCTAGAAT 60.442 45.833 0.00 0.00 0.00 2.40
5683 11964 5.429130 GACCCGAGTTCAATTCCTAGAATT 58.571 41.667 0.00 0.00 0.00 2.17
5684 11965 5.186198 ACCCGAGTTCAATTCCTAGAATTG 58.814 41.667 19.37 19.37 38.60 2.32
5685 11966 5.045869 ACCCGAGTTCAATTCCTAGAATTGA 60.046 40.000 22.54 22.54 42.82 2.57
5686 11967 5.294552 CCCGAGTTCAATTCCTAGAATTGAC 59.705 44.000 24.95 20.09 43.81 3.18
5687 11968 5.874810 CCGAGTTCAATTCCTAGAATTGACA 59.125 40.000 24.95 16.29 43.81 3.58
5688 11969 6.036517 CCGAGTTCAATTCCTAGAATTGACAG 59.963 42.308 24.95 17.52 43.81 3.51
5689 11970 6.036517 CGAGTTCAATTCCTAGAATTGACAGG 59.963 42.308 24.95 14.49 43.81 4.00
5690 11971 6.784031 AGTTCAATTCCTAGAATTGACAGGT 58.216 36.000 24.95 11.97 43.81 4.00
5691 11972 6.656693 AGTTCAATTCCTAGAATTGACAGGTG 59.343 38.462 24.95 4.88 43.81 4.00
5692 11973 6.373005 TCAATTCCTAGAATTGACAGGTGA 57.627 37.500 22.54 5.42 40.53 4.02
5693 11974 6.962182 TCAATTCCTAGAATTGACAGGTGAT 58.038 36.000 22.54 0.00 40.53 3.06
5694 11975 6.825213 TCAATTCCTAGAATTGACAGGTGATG 59.175 38.462 22.54 1.65 40.53 3.07
5695 11976 4.142609 TCCTAGAATTGACAGGTGATGC 57.857 45.455 0.00 0.00 0.00 3.91
5696 11977 3.519107 TCCTAGAATTGACAGGTGATGCA 59.481 43.478 0.00 0.00 0.00 3.96
5697 11978 3.624861 CCTAGAATTGACAGGTGATGCAC 59.375 47.826 0.00 0.00 0.00 4.57
5698 11979 3.144657 AGAATTGACAGGTGATGCACA 57.855 42.857 0.00 0.00 35.86 4.57
5699 11980 3.079578 AGAATTGACAGGTGATGCACAG 58.920 45.455 0.00 0.00 35.86 3.66
5700 11981 1.830279 ATTGACAGGTGATGCACAGG 58.170 50.000 0.00 0.00 35.86 4.00
5701 11982 0.250858 TTGACAGGTGATGCACAGGG 60.251 55.000 0.00 0.00 35.86 4.45
5702 11983 1.377725 GACAGGTGATGCACAGGGG 60.378 63.158 0.00 0.00 35.86 4.79
5703 11984 2.129555 GACAGGTGATGCACAGGGGT 62.130 60.000 0.00 0.00 35.86 4.95
5704 11985 1.075482 CAGGTGATGCACAGGGGTT 59.925 57.895 0.00 0.00 35.86 4.11
5705 11986 0.540365 CAGGTGATGCACAGGGGTTT 60.540 55.000 0.00 0.00 35.86 3.27
5706 11987 0.188342 AGGTGATGCACAGGGGTTTT 59.812 50.000 0.00 0.00 35.86 2.43
5707 11988 0.603065 GGTGATGCACAGGGGTTTTC 59.397 55.000 0.00 0.00 35.86 2.29
5708 11989 0.603065 GTGATGCACAGGGGTTTTCC 59.397 55.000 0.00 0.00 35.19 3.13
5721 12002 3.861276 GGTTTTCCCCCGTTTATTGAG 57.139 47.619 0.00 0.00 0.00 3.02
5722 12003 2.494471 GGTTTTCCCCCGTTTATTGAGG 59.506 50.000 0.00 0.00 0.00 3.86
5723 12004 3.423749 GTTTTCCCCCGTTTATTGAGGA 58.576 45.455 0.00 0.00 0.00 3.71
5724 12005 4.021229 GTTTTCCCCCGTTTATTGAGGAT 58.979 43.478 0.00 0.00 0.00 3.24
5725 12006 3.570912 TTCCCCCGTTTATTGAGGATC 57.429 47.619 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.022787 AGTCTGGCAAAATAAGGGCATAAA 58.977 37.500 0.00 0.00 38.99 1.40
47 48 4.192429 CCAAAGTCTGGCAAAATAAGGG 57.808 45.455 0.00 0.00 38.76 3.95
96 97 4.395542 TGGACTACTAGAAGTTTCTCTCGC 59.604 45.833 0.00 0.00 38.70 5.03
108 109 8.046867 TCTCCAGATAGAATTGGACTACTAGA 57.953 38.462 0.00 0.00 38.53 2.43
109 110 8.160765 TCTCTCCAGATAGAATTGGACTACTAG 58.839 40.741 0.00 0.00 38.53 2.57
148 149 5.426689 TCTTAACAGTGATCTGAGGCATT 57.573 39.130 0.00 0.00 43.76 3.56
149 150 5.181748 GTTCTTAACAGTGATCTGAGGCAT 58.818 41.667 0.00 0.00 43.76 4.40
166 167 7.227711 TCGAACCATGTCTTTCAATTGTTCTTA 59.772 33.333 5.13 0.00 33.66 2.10
172 173 4.618489 GCTTCGAACCATGTCTTTCAATTG 59.382 41.667 0.00 0.00 0.00 2.32
191 541 5.556355 TCTTGTCATGTGATCATTGCTTC 57.444 39.130 0.00 0.00 31.15 3.86
192 542 6.330278 CAATCTTGTCATGTGATCATTGCTT 58.670 36.000 0.00 0.00 31.15 3.91
224 574 8.288913 GCAATGGCAAAATTTGTAAACTACATT 58.711 29.630 7.60 4.97 38.08 2.71
236 586 5.122711 GCATACAAGAGCAATGGCAAAATTT 59.877 36.000 0.00 0.00 44.61 1.82
271 621 4.045104 GTCCTCTGTTATGTCATGCTACG 58.955 47.826 0.00 0.00 0.00 3.51
278 628 2.642171 AGGGGTCCTCTGTTATGTCA 57.358 50.000 0.00 0.00 0.00 3.58
289 639 6.417503 AAGGTTAATGAATTTAGGGGTCCT 57.582 37.500 0.00 0.00 37.71 3.85
437 788 5.471556 TGTTGATTTTGTCTGGATGCAAT 57.528 34.783 0.00 0.00 0.00 3.56
537 1028 6.464222 ACAGCAGTACTCAACAAAGCTATAA 58.536 36.000 0.00 0.00 33.43 0.98
610 1101 5.245531 CCATCTGTTTACAGCTAAGTGGAA 58.754 41.667 5.00 0.00 43.46 3.53
611 1102 4.323485 CCCATCTGTTTACAGCTAAGTGGA 60.323 45.833 5.00 0.00 43.46 4.02
686 1180 8.265764 GGTTAGACATAGTTTCTTTGGATACCT 58.734 37.037 0.00 0.00 0.00 3.08
791 1286 9.751542 TCTCATTTATTATCTCTTTCGTCCTTC 57.248 33.333 0.00 0.00 0.00 3.46
806 1301 9.823647 CCTTCTCTTTACAGCTCTCATTTATTA 57.176 33.333 0.00 0.00 0.00 0.98
821 1318 3.082548 GGCAACCCTTCCTTCTCTTTAC 58.917 50.000 0.00 0.00 0.00 2.01
839 1336 2.440065 GGATGGCAATGGACGGCA 60.440 61.111 0.00 0.00 43.74 5.69
863 1360 2.450476 GGAGTTGGATTGCAAGTCCAT 58.550 47.619 29.62 13.98 46.30 3.41
864 1361 1.909700 GGAGTTGGATTGCAAGTCCA 58.090 50.000 29.62 20.14 46.30 4.02
904 1403 3.790976 TGAATGGATGGAGATTGGGGTTA 59.209 43.478 0.00 0.00 0.00 2.85
1061 1600 7.660030 ATTGGCACCAAAATAGTAAATAGCT 57.340 32.000 6.14 0.00 39.55 3.32
1095 1635 5.995897 GCGTTACCTATCCACCTAAATGAAT 59.004 40.000 0.00 0.00 0.00 2.57
1098 1638 3.739300 CGCGTTACCTATCCACCTAAATG 59.261 47.826 0.00 0.00 0.00 2.32
1102 1642 2.346766 TCGCGTTACCTATCCACCTA 57.653 50.000 5.77 0.00 0.00 3.08
1142 1684 7.468441 CCACCAAATAAAGACAAAACAAAACC 58.532 34.615 0.00 0.00 0.00 3.27
1143 1685 6.964370 GCCACCAAATAAAGACAAAACAAAAC 59.036 34.615 0.00 0.00 0.00 2.43
1148 1690 6.156519 CCTAGCCACCAAATAAAGACAAAAC 58.843 40.000 0.00 0.00 0.00 2.43
1201 1744 0.252881 TCCCTTCCTGGAGCATCTGT 60.253 55.000 0.00 0.00 38.35 3.41
1225 2111 2.248248 ACCTTGACGATGAAGTCTGGA 58.752 47.619 13.31 0.00 41.47 3.86
1333 2219 1.169661 TTGGATCACACAACACGGGC 61.170 55.000 0.00 0.00 0.00 6.13
1410 2296 1.271001 CCACACATGGCTTGTCTCTGA 60.271 52.381 2.62 0.00 39.82 3.27
1414 2300 0.767375 AGTCCACACATGGCTTGTCT 59.233 50.000 2.62 0.00 46.80 3.41
1533 2420 7.065803 ACCGAAACAATCACAATTCCTATACTG 59.934 37.037 0.00 0.00 0.00 2.74
1627 2518 4.862574 TGATGAAACAGACCGTAATTCTCG 59.137 41.667 0.00 0.00 0.00 4.04
1636 2527 4.690748 ACACTACAATGATGAAACAGACCG 59.309 41.667 0.00 0.00 0.00 4.79
1653 2545 7.966753 TGTCAGATCTACGACATAAAACACTAC 59.033 37.037 10.93 0.00 37.23 2.73
1724 2617 7.766738 TGGCACTAATACGAAAGAACATCAATA 59.233 33.333 0.00 0.00 0.00 1.90
1762 2655 2.323599 CAGATCTCAGCCCTCCACATA 58.676 52.381 0.00 0.00 0.00 2.29
1766 2659 0.907486 CAACAGATCTCAGCCCTCCA 59.093 55.000 0.00 0.00 0.00 3.86
1809 2702 6.649557 GGACGGATAATTTTTGTCGGATCTAT 59.350 38.462 0.00 0.00 0.00 1.98
1833 2727 2.406616 GCTGCCCAATGTGTACGGG 61.407 63.158 0.00 0.00 43.42 5.28
1938 2842 6.043327 TCACAAAACAGTACGATGACAAAG 57.957 37.500 0.00 0.00 0.00 2.77
1945 2849 8.804743 CGTATCTAAATCACAAAACAGTACGAT 58.195 33.333 0.00 0.00 33.87 3.73
1953 2857 7.478667 CAGCTTGTCGTATCTAAATCACAAAAC 59.521 37.037 0.00 0.00 0.00 2.43
1976 2880 3.806625 ACAATACAATGGCCAATCAGC 57.193 42.857 10.96 0.00 0.00 4.26
1998 2902 5.711506 ACTGTTTGTGGAATGCAGATCATAA 59.288 36.000 0.00 0.00 34.33 1.90
2059 2963 5.183140 ACAACAGTACAATGGCCTAATTGTC 59.817 40.000 21.27 14.19 45.47 3.18
2063 2967 4.458989 CACACAACAGTACAATGGCCTAAT 59.541 41.667 3.32 0.00 0.00 1.73
2181 3088 5.378230 TGGGAAGCAGATCATATTTGTCT 57.622 39.130 0.00 0.00 0.00 3.41
2205 3112 6.033341 CAGTACTCATTGAGCTGTCTAGTTC 58.967 44.000 13.64 0.00 35.01 3.01
2209 3116 4.767409 ACACAGTACTCATTGAGCTGTCTA 59.233 41.667 18.49 1.60 38.21 2.59
2254 3175 7.898918 TCATGACAATGACTGAATGGATTTTT 58.101 30.769 0.00 0.00 37.91 1.94
2325 3267 5.176741 AGATGAAGTGATTCTTTGAGCCT 57.823 39.130 0.00 0.00 36.40 4.58
2339 3281 5.775195 CCCCACTTTAAAAAGGAGATGAAGT 59.225 40.000 7.34 0.00 40.31 3.01
2341 3283 5.083821 CCCCCACTTTAAAAAGGAGATGAA 58.916 41.667 7.34 0.00 40.31 2.57
2342 3284 4.672899 CCCCCACTTTAAAAAGGAGATGA 58.327 43.478 7.34 0.00 40.31 2.92
2446 3400 4.669206 AAACATGACAATGGCTGAACAA 57.331 36.364 0.00 0.00 38.19 2.83
2485 3439 8.028540 TGATGTGTGCGGAACATATAATATTC 57.971 34.615 0.00 0.00 40.39 1.75
2491 3445 3.559655 GCTTGATGTGTGCGGAACATATA 59.440 43.478 0.00 0.00 40.39 0.86
2576 3530 5.786401 ATGTTGTGACGATAAAAGAGAGC 57.214 39.130 0.00 0.00 0.00 4.09
2614 3568 3.678056 TGTAGCGGAACATGTTTCTCT 57.322 42.857 13.36 13.57 0.00 3.10
2632 3646 6.916360 AAACCATCCAAGTAATGTGAATGT 57.084 33.333 0.00 0.00 0.00 2.71
2676 3690 5.567037 TGGGATCGATTGACCTGAATATT 57.433 39.130 0.00 0.00 0.00 1.28
2691 3705 4.041740 TCAACTAGTTCGAATGGGATCG 57.958 45.455 4.77 0.00 44.04 3.69
2821 3836 8.325787 TGTATAGACCAAAAACATACATGGACT 58.674 33.333 0.00 0.00 40.26 3.85
2881 3901 2.477525 CGAGTAAAGCGGTAGTGACTCC 60.478 54.545 0.00 0.00 31.61 3.85
3200 4226 1.208052 TCTCTGAGCACCAATACTGCC 59.792 52.381 0.00 0.00 35.01 4.85
3318 4346 8.946085 GTATGGAGATTTCAGTAACACAATGAA 58.054 33.333 0.00 0.00 0.00 2.57
3470 4504 6.043411 GTCACCCAAATCTGTGTCTCTATAC 58.957 44.000 0.00 0.00 34.14 1.47
3483 4517 2.704572 CTCAGTGGAGTCACCCAAATC 58.295 52.381 0.00 0.00 44.64 2.17
3617 4662 2.317530 AAGAGAACCCAGCTTATCGC 57.682 50.000 0.00 0.00 39.57 4.58
3621 4666 5.163237 ACTGTTGTAAAGAGAACCCAGCTTA 60.163 40.000 0.00 0.00 40.10 3.09
3761 4808 9.173939 CTTGTAACATCAATTGAAAGACTGAAC 57.826 33.333 13.09 9.86 0.00 3.18
3766 4813 6.363357 GGTGCTTGTAACATCAATTGAAAGAC 59.637 38.462 13.09 8.90 0.00 3.01
3771 4818 6.403866 AAAGGTGCTTGTAACATCAATTGA 57.596 33.333 11.26 11.26 0.00 2.57
3805 4852 7.637709 AGAATGACGCCTTTATTTTGAAAAC 57.362 32.000 0.00 0.00 0.00 2.43
3821 4868 5.350640 GGGGTAACTCTAACAAAGAATGACG 59.649 44.000 0.00 0.00 32.46 4.35
4064 5143 1.227999 TGCAGCTCCCGAAAGAAACG 61.228 55.000 0.00 0.00 0.00 3.60
4075 5154 0.323725 TCCTTCCCATTTGCAGCTCC 60.324 55.000 0.00 0.00 0.00 4.70
4300 5413 8.233190 TCATTTGTTTGGTTCAATGTTTTTCAC 58.767 29.630 0.00 0.00 0.00 3.18
4365 5607 3.583806 CTCTGGCTCTGAGTACACTTTG 58.416 50.000 6.53 0.00 0.00 2.77
4390 5632 7.593875 AACACTACTCTAGACAACTACGTAG 57.406 40.000 20.97 20.97 35.70 3.51
4391 5633 7.095060 CCAAACACTACTCTAGACAACTACGTA 60.095 40.741 0.00 0.00 0.00 3.57
4392 5634 6.293845 CCAAACACTACTCTAGACAACTACGT 60.294 42.308 0.00 0.00 0.00 3.57
4393 5635 6.084925 CCAAACACTACTCTAGACAACTACG 58.915 44.000 0.00 0.00 0.00 3.51
4574 5854 8.801715 ACAATTAAACACAGAGTATTTGCAAG 57.198 30.769 0.00 0.00 0.00 4.01
4596 5895 5.043737 ACTAAGAACTACAGCCCAAACAA 57.956 39.130 0.00 0.00 0.00 2.83
4637 5939 7.531716 CGTAACCCATTAAGAAATGCTTGTAA 58.468 34.615 0.00 0.00 41.06 2.41
4639 5941 5.621329 GCGTAACCCATTAAGAAATGCTTGT 60.621 40.000 0.00 0.00 41.06 3.16
4645 5947 7.362315 GGTTAGTTGCGTAACCCATTAAGAAAT 60.362 37.037 13.04 0.00 44.39 2.17
4723 6025 6.319152 AGCTTTATCGCTCAAGTCTAGAGTTA 59.681 38.462 12.50 0.00 34.57 2.24
4728 6030 4.047822 CCAGCTTTATCGCTCAAGTCTAG 58.952 47.826 0.00 0.00 38.41 2.43
4787 6090 4.399004 AGCTAGGTTGAGCATGTTCTAG 57.601 45.455 11.09 5.34 45.43 2.43
4822 6126 5.518865 ACAGACCCCACATAAGCAAATTAT 58.481 37.500 0.00 0.00 34.24 1.28
4824 6128 3.778265 ACAGACCCCACATAAGCAAATT 58.222 40.909 0.00 0.00 0.00 1.82
4854 6160 4.078639 AGTAGATGATTAGCTTGCCACC 57.921 45.455 0.00 0.00 0.00 4.61
4897 6205 5.121768 CAGAATTCCAAACGAAACTACGGAT 59.878 40.000 0.65 0.00 37.61 4.18
4948 6258 2.825532 ACCAATAATCCGCAAAACAGCT 59.174 40.909 0.00 0.00 0.00 4.24
4950 6260 3.056891 ACCACCAATAATCCGCAAAACAG 60.057 43.478 0.00 0.00 0.00 3.16
5062 6379 4.365514 TCTCCACAATGTACCACAATGT 57.634 40.909 0.00 0.00 42.48 2.71
5063 6380 4.518590 TGTTCTCCACAATGTACCACAATG 59.481 41.667 0.00 0.00 35.24 2.82
5064 6381 4.724399 TGTTCTCCACAATGTACCACAAT 58.276 39.130 0.00 0.00 29.87 2.71
5110 8469 8.612619 ACTTGTTTGCCTCGTCTTAATAATATG 58.387 33.333 0.00 0.00 0.00 1.78
5148 8663 9.638176 ATCTGCAGAGGAAATTATTTAGTTGAT 57.362 29.630 22.96 0.00 0.00 2.57
5207 9221 9.911980 GTTATGTCTAGTTTTTATCGGCTTTAC 57.088 33.333 0.00 0.00 0.00 2.01
5212 9226 7.903431 CACTTGTTATGTCTAGTTTTTATCGGC 59.097 37.037 0.00 0.00 0.00 5.54
5216 9230 8.227791 CGTGCACTTGTTATGTCTAGTTTTTAT 58.772 33.333 16.19 0.00 0.00 1.40
5241 9255 4.129380 TCCCATTCTAATGCAGACATTCG 58.871 43.478 0.00 0.00 43.08 3.34
5254 9303 5.886609 TCAACTTCCATTGTTCCCATTCTA 58.113 37.500 0.00 0.00 0.00 2.10
5308 9357 2.028930 ACGCTTAGCTGCTTGAGTTAGT 60.029 45.455 7.79 6.22 0.00 2.24
5320 9369 1.470098 CTCCAAAATGCACGCTTAGCT 59.530 47.619 1.76 0.00 0.00 3.32
5322 9371 2.414559 CCACTCCAAAATGCACGCTTAG 60.415 50.000 0.00 0.00 0.00 2.18
5328 10497 3.258123 ACCATTACCACTCCAAAATGCAC 59.742 43.478 0.00 0.00 0.00 4.57
5361 10536 4.077822 AGAAGTTGAGGCTCCAAATTGAG 58.922 43.478 12.86 0.00 34.94 3.02
5384 10790 6.207810 ACCGAGAGTAGAATATCTCCATGTTC 59.792 42.308 0.00 0.00 39.02 3.18
5425 11115 3.099905 ACTTCCATTCAGTCAGATCCGA 58.900 45.455 0.00 0.00 0.00 4.55
5431 11121 3.937706 CCAGCTAACTTCCATTCAGTCAG 59.062 47.826 0.00 0.00 0.00 3.51
5432 11122 3.582647 TCCAGCTAACTTCCATTCAGTCA 59.417 43.478 0.00 0.00 0.00 3.41
5433 11123 4.187694 CTCCAGCTAACTTCCATTCAGTC 58.812 47.826 0.00 0.00 0.00 3.51
5434 11124 3.620966 GCTCCAGCTAACTTCCATTCAGT 60.621 47.826 0.00 0.00 38.21 3.41
5443 11133 3.492102 TCTTGTTGCTCCAGCTAACTT 57.508 42.857 0.00 0.00 42.66 2.66
5561 11842 6.844696 ATATACTTGTATGCGAACTTGGTG 57.155 37.500 3.75 0.00 0.00 4.17
5601 11882 5.591877 CCAAGGCTCTCTTTGCACTTAATAT 59.408 40.000 0.00 0.00 32.41 1.28
5619 11900 2.270986 CCAACCACTGAGCCAAGGC 61.271 63.158 2.02 2.02 42.33 4.35
5620 11901 1.604593 CCCAACCACTGAGCCAAGG 60.605 63.158 0.00 0.00 0.00 3.61
5621 11902 2.270986 GCCCAACCACTGAGCCAAG 61.271 63.158 0.00 0.00 0.00 3.61
5622 11903 2.203480 GCCCAACCACTGAGCCAA 60.203 61.111 0.00 0.00 0.00 4.52
5623 11904 2.844195 ATGCCCAACCACTGAGCCA 61.844 57.895 0.00 0.00 0.00 4.75
5624 11905 2.036256 ATGCCCAACCACTGAGCC 59.964 61.111 0.00 0.00 0.00 4.70
5625 11906 2.998279 GCATGCCCAACCACTGAGC 61.998 63.158 6.36 0.00 0.00 4.26
5626 11907 2.693762 CGCATGCCCAACCACTGAG 61.694 63.158 13.15 0.00 0.00 3.35
5627 11908 2.672651 CGCATGCCCAACCACTGA 60.673 61.111 13.15 0.00 0.00 3.41
5628 11909 3.751246 CCGCATGCCCAACCACTG 61.751 66.667 13.15 0.00 0.00 3.66
5629 11910 3.808218 AACCGCATGCCCAACCACT 62.808 57.895 13.15 0.00 0.00 4.00
5630 11911 3.302344 AACCGCATGCCCAACCAC 61.302 61.111 13.15 0.00 0.00 4.16
5631 11912 3.301554 CAACCGCATGCCCAACCA 61.302 61.111 13.15 0.00 0.00 3.67
5632 11913 3.302344 ACAACCGCATGCCCAACC 61.302 61.111 13.15 0.00 0.00 3.77
5633 11914 2.049248 CACAACCGCATGCCCAAC 60.049 61.111 13.15 0.00 0.00 3.77
5634 11915 3.988525 GCACAACCGCATGCCCAA 61.989 61.111 13.15 0.00 35.73 4.12
5636 11917 4.424566 CTGCACAACCGCATGCCC 62.425 66.667 13.15 0.00 42.06 5.36
5639 11920 1.585267 TTAGGCTGCACAACCGCATG 61.585 55.000 0.50 0.00 42.06 4.06
5640 11921 1.303236 TTAGGCTGCACAACCGCAT 60.303 52.632 0.50 0.00 42.06 4.73
5641 11922 2.112087 TTAGGCTGCACAACCGCA 59.888 55.556 0.50 0.00 40.32 5.69
5642 11923 2.561373 GTTAGGCTGCACAACCGC 59.439 61.111 0.50 0.00 0.00 5.68
5643 11924 1.666553 TCGTTAGGCTGCACAACCG 60.667 57.895 0.50 0.00 0.00 4.44
5644 11925 1.574702 GGTCGTTAGGCTGCACAACC 61.575 60.000 0.50 0.00 0.00 3.77
5645 11926 1.574702 GGGTCGTTAGGCTGCACAAC 61.575 60.000 0.50 3.77 0.00 3.32
5646 11927 1.302192 GGGTCGTTAGGCTGCACAA 60.302 57.895 0.50 0.00 0.00 3.33
5647 11928 2.345991 GGGTCGTTAGGCTGCACA 59.654 61.111 0.50 0.00 0.00 4.57
5648 11929 2.813908 CGGGTCGTTAGGCTGCAC 60.814 66.667 0.50 0.00 0.00 4.57
5649 11930 2.992689 TCGGGTCGTTAGGCTGCA 60.993 61.111 0.50 0.00 0.00 4.41
5650 11931 2.202756 CTCGGGTCGTTAGGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
5651 11932 0.458025 GAACTCGGGTCGTTAGGCTG 60.458 60.000 0.00 0.00 0.00 4.85
5652 11933 0.896940 TGAACTCGGGTCGTTAGGCT 60.897 55.000 0.00 0.00 0.00 4.58
5653 11934 0.037975 TTGAACTCGGGTCGTTAGGC 60.038 55.000 0.00 0.00 0.00 3.93
5654 11935 2.667473 ATTGAACTCGGGTCGTTAGG 57.333 50.000 0.00 0.00 0.00 2.69
5655 11936 2.928116 GGAATTGAACTCGGGTCGTTAG 59.072 50.000 0.00 0.00 0.00 2.34
5656 11937 2.564062 AGGAATTGAACTCGGGTCGTTA 59.436 45.455 0.00 0.00 0.00 3.18
5657 11938 1.346722 AGGAATTGAACTCGGGTCGTT 59.653 47.619 0.00 0.00 0.00 3.85
5658 11939 0.974383 AGGAATTGAACTCGGGTCGT 59.026 50.000 0.00 0.00 0.00 4.34
5659 11940 2.426024 TCTAGGAATTGAACTCGGGTCG 59.574 50.000 0.00 0.00 0.00 4.79
5660 11941 4.467198 TTCTAGGAATTGAACTCGGGTC 57.533 45.455 0.00 0.00 0.00 4.46
5661 11942 5.045869 TCAATTCTAGGAATTGAACTCGGGT 60.046 40.000 24.34 0.00 41.92 5.28
5662 11943 5.294552 GTCAATTCTAGGAATTGAACTCGGG 59.705 44.000 26.66 6.75 45.06 5.14
5663 11944 5.874810 TGTCAATTCTAGGAATTGAACTCGG 59.125 40.000 26.66 7.30 45.06 4.63
5664 11945 6.036517 CCTGTCAATTCTAGGAATTGAACTCG 59.963 42.308 26.66 17.94 45.06 4.18
5665 11946 6.881602 ACCTGTCAATTCTAGGAATTGAACTC 59.118 38.462 26.66 18.75 45.06 3.01
5666 11947 6.656693 CACCTGTCAATTCTAGGAATTGAACT 59.343 38.462 26.66 13.22 45.06 3.01
5667 11948 6.655003 TCACCTGTCAATTCTAGGAATTGAAC 59.345 38.462 26.66 21.66 45.06 3.18
5668 11949 6.778821 TCACCTGTCAATTCTAGGAATTGAA 58.221 36.000 26.66 18.77 45.06 2.69
5669 11950 6.373005 TCACCTGTCAATTCTAGGAATTGA 57.627 37.500 23.36 23.36 42.44 2.57
5670 11951 6.459298 GCATCACCTGTCAATTCTAGGAATTG 60.459 42.308 20.45 20.45 38.60 2.32
5671 11952 5.591877 GCATCACCTGTCAATTCTAGGAATT 59.408 40.000 6.24 0.31 35.55 2.17
5672 11953 5.128919 GCATCACCTGTCAATTCTAGGAAT 58.871 41.667 6.24 0.00 35.55 3.01
5673 11954 4.019411 TGCATCACCTGTCAATTCTAGGAA 60.019 41.667 6.24 0.00 35.55 3.36
5674 11955 3.519107 TGCATCACCTGTCAATTCTAGGA 59.481 43.478 6.24 0.00 35.55 2.94
5675 11956 3.624861 GTGCATCACCTGTCAATTCTAGG 59.375 47.826 0.00 0.00 37.61 3.02
5676 11957 4.256110 TGTGCATCACCTGTCAATTCTAG 58.744 43.478 0.00 0.00 32.73 2.43
5677 11958 4.256110 CTGTGCATCACCTGTCAATTCTA 58.744 43.478 0.00 0.00 32.73 2.10
5678 11959 3.079578 CTGTGCATCACCTGTCAATTCT 58.920 45.455 0.00 0.00 32.73 2.40
5679 11960 2.163010 CCTGTGCATCACCTGTCAATTC 59.837 50.000 0.00 0.00 32.73 2.17
5680 11961 2.165167 CCTGTGCATCACCTGTCAATT 58.835 47.619 0.00 0.00 32.73 2.32
5681 11962 1.615116 CCCTGTGCATCACCTGTCAAT 60.615 52.381 0.00 0.00 32.73 2.57
5682 11963 0.250858 CCCTGTGCATCACCTGTCAA 60.251 55.000 0.00 0.00 32.73 3.18
5683 11964 1.376086 CCCTGTGCATCACCTGTCA 59.624 57.895 0.00 0.00 32.73 3.58
5684 11965 1.377725 CCCCTGTGCATCACCTGTC 60.378 63.158 0.00 0.00 32.73 3.51
5685 11966 1.719063 AACCCCTGTGCATCACCTGT 61.719 55.000 0.00 0.00 32.73 4.00
5686 11967 0.540365 AAACCCCTGTGCATCACCTG 60.540 55.000 0.00 0.00 32.73 4.00
5687 11968 0.188342 AAAACCCCTGTGCATCACCT 59.812 50.000 0.00 0.00 32.73 4.00
5688 11969 0.603065 GAAAACCCCTGTGCATCACC 59.397 55.000 0.00 0.00 32.73 4.02
5689 11970 0.603065 GGAAAACCCCTGTGCATCAC 59.397 55.000 0.00 0.00 34.56 3.06
5690 11971 3.050089 GGAAAACCCCTGTGCATCA 57.950 52.632 0.00 0.00 0.00 3.07
5701 11982 2.494471 CCTCAATAAACGGGGGAAAACC 59.506 50.000 0.00 0.00 39.11 3.27
5702 11983 3.423749 TCCTCAATAAACGGGGGAAAAC 58.576 45.455 0.00 0.00 0.00 2.43
5703 11984 3.810721 TCCTCAATAAACGGGGGAAAA 57.189 42.857 0.00 0.00 0.00 2.29
5704 11985 3.893521 GATCCTCAATAAACGGGGGAAA 58.106 45.455 0.00 0.00 0.00 3.13
5705 11986 3.570912 GATCCTCAATAAACGGGGGAA 57.429 47.619 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.