Multiple sequence alignment - TraesCS3B01G439100

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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 TraesCS3B01G439100 chr3B 100.000 3542 0 0 1 3542 678172391 678168850 0.000000e+00 6541.0
1 TraesCS3B01G439100 chr3B 95.484 155 7 0 1389 1543 23382152 23382306 7.590000e-62 248.0
2 TraesCS3B01G439100 chr3B 93.443 122 7 1 2403 2524 678149047 678148927 2.810000e-41 180.0
3 TraesCS3B01G439100 chr3B 90.588 85 8 0 226 310 409607301 409607217 2.890000e-21 113.0
4 TraesCS3B01G439100 chr3B 88.372 86 10 0 226 311 99019442 99019527 1.740000e-18 104.0
5 TraesCS3B01G439100 chr3B 100.000 37 0 0 143 179 678172212 678172176 6.340000e-08 69.4
6 TraesCS3B01G439100 chr3B 100.000 37 0 0 180 216 678172249 678172213 6.340000e-08 69.4
7 TraesCS3B01G439100 chr3D 93.832 2756 112 18 1 2727 515677495 515674769 0.000000e+00 4095.0
8 TraesCS3B01G439100 chr3D 92.228 386 21 6 2725 3103 515674721 515674338 4.020000e-149 538.0
9 TraesCS3B01G439100 chr3D 92.473 93 6 1 2403 2495 515668319 515668228 7.980000e-27 132.0
10 TraesCS3B01G439100 chr3D 100.000 37 0 0 143 179 515677314 515677278 6.340000e-08 69.4
11 TraesCS3B01G439100 chr3D 97.297 37 1 0 180 216 515677351 515677315 2.950000e-06 63.9
12 TraesCS3B01G439100 chr3A 92.334 2048 93 20 616 2645 649939778 649937777 0.000000e+00 2854.0
13 TraesCS3B01G439100 chr3A 86.998 423 28 8 2736 3150 649937398 649936995 5.390000e-123 451.0
14 TraesCS3B01G439100 chr3A 97.080 137 4 0 1 137 649940480 649940344 7.650000e-57 231.0
15 TraesCS3B01G439100 chr3A 93.443 122 7 1 2403 2524 649854972 649854852 2.810000e-41 180.0
16 TraesCS3B01G439100 chr3A 80.000 265 29 11 308 570 649940282 649940040 1.310000e-39 174.0
17 TraesCS3B01G439100 chr4B 88.599 421 38 8 3128 3542 643807526 643807942 1.470000e-138 503.0
18 TraesCS3B01G439100 chr4B 85.514 428 52 9 3123 3542 362138092 362138517 4.200000e-119 438.0
19 TraesCS3B01G439100 chr4B 84.651 430 51 10 3123 3542 25966377 25965953 7.070000e-112 414.0
20 TraesCS3B01G439100 chr2D 86.557 424 49 8 3122 3542 629482021 629482439 8.960000e-126 460.0
21 TraesCS3B01G439100 chr2D 91.765 85 7 0 226 310 207242065 207242149 6.210000e-23 119.0
22 TraesCS3B01G439100 chr6B 85.981 428 44 11 3124 3542 681840405 681839985 9.020000e-121 444.0
23 TraesCS3B01G439100 chr7B 89.306 346 30 5 3201 3541 2335779 2336122 9.090000e-116 427.0
24 TraesCS3B01G439100 chr7B 85.308 422 50 9 3123 3542 5200591 5201002 3.270000e-115 425.0
25 TraesCS3B01G439100 chr5B 85.343 423 51 9 3123 3542 648685491 648685077 9.090000e-116 427.0
26 TraesCS3B01G439100 chr1B 83.448 435 49 15 3126 3542 653978844 653978415 1.990000e-102 383.0
27 TraesCS3B01G439100 chr2A 90.698 86 8 0 226 311 16861360 16861445 8.040000e-22 115.0
28 TraesCS3B01G439100 chr2A 90.698 86 8 0 226 311 572446254 572446339 8.040000e-22 115.0
29 TraesCS3B01G439100 chr6D 89.535 86 9 0 225 310 62245316 62245401 3.740000e-20 110.0
30 TraesCS3B01G439100 chr1D 87.912 91 11 0 221 311 355167720 355167810 1.340000e-19 108.0
31 TraesCS3B01G439100 chr7A 86.517 89 10 2 223 310 573673134 573673047 2.910000e-16 97.1


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 TraesCS3B01G439100 chr3B 678168850 678172391 3541 True 2226.600 6541 100.00000 1 3542 3 chr3B.!!$R3 3541
1 TraesCS3B01G439100 chr3D 515674338 515677495 3157 True 1191.575 4095 95.83925 1 3103 4 chr3D.!!$R2 3102
2 TraesCS3B01G439100 chr3A 649936995 649940480 3485 True 927.500 2854 89.10300 1 3150 4 chr3A.!!$R2 3149

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
907 1155 0.037419 TCATAAGCAGCACGCACTGA 60.037 50.0 9.32 0.0 46.13 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2884 3437 0.389426 AATGCGTGTACGTGAGGGAC 60.389 55.0 0.0 0.0 42.22 4.46 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
258 261 5.347907 CGTCCCATAATATAGGAGCGTTTTC 59.652 44.000 0.00 0.00 0.00 2.29
270 273 3.558505 GAGCGTTTTCGACACTAGTGTA 58.441 45.455 27.98 11.50 45.05 2.90
271 274 3.968649 AGCGTTTTCGACACTAGTGTAA 58.031 40.909 27.98 16.93 45.05 2.41
275 278 5.595993 CGTTTTCGACACTAGTGTAATGTG 58.404 41.667 27.98 15.08 45.05 3.21
297 300 8.795842 TGTGAAAAACGGTCTTATATTATGGT 57.204 30.769 0.00 0.00 0.00 3.55
359 362 4.527944 TCTAGAACGACCAGTGATGAGAT 58.472 43.478 0.00 0.00 0.00 2.75
372 375 7.345653 ACCAGTGATGAGATTGGACTATCTTTA 59.654 37.037 0.00 0.00 35.06 1.85
573 578 6.536582 GCAGTGATCTGTCTACATACAAACAT 59.463 38.462 0.00 0.00 43.05 2.71
595 784 2.688507 AGTACTTGACATGTTGGCGAG 58.311 47.619 0.00 0.00 42.79 5.03
622 843 2.063266 CTGGCAATGTTGTGTGCAATC 58.937 47.619 0.00 0.00 42.74 2.67
663 884 2.422276 ATGTTTGCTTCGACAAAGGC 57.578 45.000 1.74 0.00 40.07 4.35
675 896 2.223572 CGACAAAGGCTTCAGCTGTTTT 60.224 45.455 14.67 5.50 41.70 2.43
691 912 4.318974 GCTGTTTTGCCACAAAATGATGAC 60.319 41.667 8.57 0.00 0.00 3.06
695 916 1.265236 GCCACAAAATGATGACCCCA 58.735 50.000 0.00 0.00 0.00 4.96
696 917 1.622811 GCCACAAAATGATGACCCCAA 59.377 47.619 0.00 0.00 0.00 4.12
698 919 2.899256 CCACAAAATGATGACCCCAAGT 59.101 45.455 0.00 0.00 0.00 3.16
699 920 3.056607 CCACAAAATGATGACCCCAAGTC 60.057 47.826 0.00 0.00 46.51 3.01
788 1021 5.195379 GTTGAATATGTACCGCGATCAAAC 58.805 41.667 8.23 0.00 0.00 2.93
797 1030 1.135083 CCGCGATCAAACTACTGACCT 60.135 52.381 8.23 0.00 0.00 3.85
833 1066 0.103572 ATGAAATGGCTTGCGATGGC 59.896 50.000 0.00 0.00 40.52 4.40
834 1067 1.587088 GAAATGGCTTGCGATGGCG 60.587 57.895 0.00 0.00 44.10 5.69
835 1068 1.992233 GAAATGGCTTGCGATGGCGA 61.992 55.000 0.00 0.00 44.10 5.54
836 1069 1.594194 AAATGGCTTGCGATGGCGAA 61.594 50.000 0.00 0.00 44.10 4.70
837 1070 1.996786 AATGGCTTGCGATGGCGAAG 61.997 55.000 0.00 1.80 44.10 3.79
838 1071 3.880846 GGCTTGCGATGGCGAAGG 61.881 66.667 11.61 0.00 44.10 3.46
904 1152 2.663879 GCATATCATAAGCAGCACGCAC 60.664 50.000 0.00 0.00 46.13 5.34
905 1153 2.602257 TATCATAAGCAGCACGCACT 57.398 45.000 0.00 0.00 46.13 4.40
906 1154 1.012086 ATCATAAGCAGCACGCACTG 58.988 50.000 0.00 1.03 46.13 3.66
907 1155 0.037419 TCATAAGCAGCACGCACTGA 60.037 50.000 9.32 0.00 46.13 3.41
908 1156 1.012086 CATAAGCAGCACGCACTGAT 58.988 50.000 9.32 0.00 46.13 2.90
909 1157 1.012086 ATAAGCAGCACGCACTGATG 58.988 50.000 9.32 0.00 46.13 3.07
959 1207 3.353836 CGTTTCCACTGGCACCCG 61.354 66.667 0.00 0.00 0.00 5.28
963 1211 2.969300 TTTCCACTGGCACCCGAACC 62.969 60.000 0.00 0.00 0.00 3.62
1096 1347 3.023949 GCCCTGCTCCACGAGATGT 62.024 63.158 0.00 0.00 0.00 3.06
1396 1647 1.664321 GGTCTACCGCGACATGGTCT 61.664 60.000 8.23 0.00 40.96 3.85
1593 1844 2.551912 CGCGGCCAAGAAGGTGTTT 61.552 57.895 2.24 0.00 40.61 2.83
1638 1889 3.445687 ATCACGTGGACGGCGCTA 61.446 61.111 17.00 0.00 44.95 4.26
1680 1931 4.821589 CGGGGCAAGGAGTCGCTC 62.822 72.222 0.00 0.00 31.66 5.03
1749 2000 1.630878 ACCTTCATCGGCCTTCTCTTT 59.369 47.619 0.00 0.00 0.00 2.52
1863 2114 1.604593 GTGCATGGTGGACCTGCTT 60.605 57.895 16.29 0.00 39.37 3.91
2544 2795 2.631545 GTGTGGTGACTACTGGTAGGTT 59.368 50.000 11.73 0.00 37.49 3.50
2545 2796 2.895404 TGTGGTGACTACTGGTAGGTTC 59.105 50.000 11.73 2.96 37.49 3.62
2546 2797 2.233186 GTGGTGACTACTGGTAGGTTCC 59.767 54.545 11.73 10.11 37.49 3.62
2547 2798 1.475682 GGTGACTACTGGTAGGTTCCG 59.524 57.143 11.73 0.00 37.49 4.30
2548 2799 1.135170 GTGACTACTGGTAGGTTCCGC 60.135 57.143 11.73 2.55 37.49 5.54
2632 2886 1.525619 CCACTTTTTCGTCGACACCTC 59.474 52.381 17.16 0.00 0.00 3.85
2654 2908 5.260424 TCCATTATTTACAGCACACCACAT 58.740 37.500 0.00 0.00 0.00 3.21
2659 3154 2.857186 TACAGCACACCACATCACAT 57.143 45.000 0.00 0.00 0.00 3.21
2660 3155 2.857186 ACAGCACACCACATCACATA 57.143 45.000 0.00 0.00 0.00 2.29
2661 3156 2.426522 ACAGCACACCACATCACATAC 58.573 47.619 0.00 0.00 0.00 2.39
2662 3157 2.038952 ACAGCACACCACATCACATACT 59.961 45.455 0.00 0.00 0.00 2.12
2709 3211 7.213216 TGAAACTTAGCATGCAACTAATCAA 57.787 32.000 21.98 0.00 0.00 2.57
2713 3215 6.615088 ACTTAGCATGCAACTAATCAAAGTG 58.385 36.000 21.98 0.00 0.00 3.16
2730 3232 5.887598 TCAAAGTGCTCCATGCTTGTATATT 59.112 36.000 0.00 0.00 43.37 1.28
2731 3233 7.053498 TCAAAGTGCTCCATGCTTGTATATTA 58.947 34.615 0.00 0.00 43.37 0.98
2733 3235 7.444629 AAGTGCTCCATGCTTGTATATTATG 57.555 36.000 0.00 0.00 43.37 1.90
2734 3236 6.772605 AGTGCTCCATGCTTGTATATTATGA 58.227 36.000 0.00 0.00 43.37 2.15
2884 3437 2.397777 TGTAACAACATGCAACTGCG 57.602 45.000 0.00 0.00 45.83 5.18
2920 3473 3.853671 CGCATTGCCATTTCTGTTTAGAC 59.146 43.478 2.41 0.00 31.21 2.59
2980 3534 4.642885 ACACTCCCAACGAATTTCTTTTGA 59.357 37.500 8.46 0.00 0.00 2.69
3030 3584 2.319032 CGATGCTCGCTTTGCTCG 59.681 61.111 0.00 0.00 31.14 5.03
3044 3598 3.867771 CTCGTCAAGCACTCTGCC 58.132 61.111 0.00 0.00 46.52 4.85
3046 3600 3.114616 CGTCAAGCACTCTGCCCG 61.115 66.667 0.00 0.00 46.52 6.13
3047 3601 2.743928 GTCAAGCACTCTGCCCGG 60.744 66.667 0.00 0.00 46.52 5.73
3049 3603 2.743928 CAAGCACTCTGCCCGGAC 60.744 66.667 0.73 0.00 46.52 4.79
3050 3604 2.925170 AAGCACTCTGCCCGGACT 60.925 61.111 0.73 0.00 46.52 3.85
3051 3605 2.520536 AAGCACTCTGCCCGGACTT 61.521 57.895 0.73 0.00 46.52 3.01
3059 3618 4.083862 GCCCGGACTTCTCGCCTT 62.084 66.667 0.73 0.00 0.00 4.35
3060 3619 2.184579 CCCGGACTTCTCGCCTTC 59.815 66.667 0.73 0.00 0.00 3.46
3063 3622 2.646175 CGGACTTCTCGCCTTCCCA 61.646 63.158 0.00 0.00 0.00 4.37
3065 3624 1.446272 GACTTCTCGCCTTCCCACG 60.446 63.158 0.00 0.00 0.00 4.94
3107 3669 2.609916 CGCTCACGAGTCTCTATCTTCA 59.390 50.000 0.00 0.00 43.93 3.02
3144 3706 2.002127 GAGCATCTTCAGCCGTTCG 58.998 57.895 0.00 0.00 0.00 3.95
3148 3710 3.682292 ATCTTCAGCCGTTCGCCCC 62.682 63.158 0.00 0.00 38.78 5.80
3192 3754 4.072088 GTGACGAACCGGCGCAAG 62.072 66.667 10.83 1.01 45.47 4.01
3193 3755 4.595538 TGACGAACCGGCGCAAGT 62.596 61.111 10.83 1.82 37.93 3.16
3194 3756 3.343421 GACGAACCGGCGCAAGTT 61.343 61.111 10.83 12.36 41.68 2.66
3195 3757 2.888998 GACGAACCGGCGCAAGTTT 61.889 57.895 10.83 0.00 41.68 2.66
3196 3758 2.426752 CGAACCGGCGCAAGTTTG 60.427 61.111 10.83 12.12 41.68 2.93
3197 3759 2.050442 GAACCGGCGCAAGTTTGG 60.050 61.111 10.83 2.92 41.68 3.28
3198 3760 4.279043 AACCGGCGCAAGTTTGGC 62.279 61.111 10.83 0.00 41.68 4.52
3205 3767 4.026226 GCAAGTTTGGCGTTTGGG 57.974 55.556 0.00 0.00 0.00 4.12
3206 3768 1.594021 GCAAGTTTGGCGTTTGGGG 60.594 57.895 0.00 0.00 0.00 4.96
3207 3769 1.068921 CAAGTTTGGCGTTTGGGGG 59.931 57.895 0.00 0.00 0.00 5.40
3221 3783 3.069318 GGGGGCGACTTCGTCTCT 61.069 66.667 2.68 0.00 45.13 3.10
3222 3784 1.751927 GGGGGCGACTTCGTCTCTA 60.752 63.158 2.68 0.00 45.13 2.43
3223 3785 1.108132 GGGGGCGACTTCGTCTCTAT 61.108 60.000 2.68 0.00 45.13 1.98
3224 3786 0.311477 GGGGCGACTTCGTCTCTATC 59.689 60.000 2.88 0.00 42.00 2.08
3225 3787 1.022735 GGGCGACTTCGTCTCTATCA 58.977 55.000 2.88 0.00 44.45 2.15
3226 3788 1.609555 GGGCGACTTCGTCTCTATCAT 59.390 52.381 2.88 0.00 44.45 2.45
3227 3789 2.350964 GGGCGACTTCGTCTCTATCATC 60.351 54.545 2.88 0.00 44.45 2.92
3228 3790 2.566036 GCGACTTCGTCTCTATCATCG 58.434 52.381 0.00 0.00 42.22 3.84
3229 3791 2.032722 GCGACTTCGTCTCTATCATCGT 60.033 50.000 0.00 0.00 42.22 3.73
3230 3792 3.790058 CGACTTCGTCTCTATCATCGTC 58.210 50.000 0.00 0.00 34.11 4.20
3231 3793 3.363182 CGACTTCGTCTCTATCATCGTCC 60.363 52.174 0.00 0.00 34.11 4.79
3232 3794 3.542648 ACTTCGTCTCTATCATCGTCCA 58.457 45.455 0.00 0.00 0.00 4.02
3233 3795 3.312973 ACTTCGTCTCTATCATCGTCCAC 59.687 47.826 0.00 0.00 0.00 4.02
3234 3796 2.219458 TCGTCTCTATCATCGTCCACC 58.781 52.381 0.00 0.00 0.00 4.61
3235 3797 1.947456 CGTCTCTATCATCGTCCACCA 59.053 52.381 0.00 0.00 0.00 4.17
3236 3798 2.554462 CGTCTCTATCATCGTCCACCAT 59.446 50.000 0.00 0.00 0.00 3.55
3237 3799 3.610349 CGTCTCTATCATCGTCCACCATG 60.610 52.174 0.00 0.00 0.00 3.66
3238 3800 3.319405 GTCTCTATCATCGTCCACCATGT 59.681 47.826 0.00 0.00 0.00 3.21
3239 3801 3.570125 TCTCTATCATCGTCCACCATGTC 59.430 47.826 0.00 0.00 0.00 3.06
3240 3802 2.293399 TCTATCATCGTCCACCATGTCG 59.707 50.000 0.00 0.00 0.00 4.35
3241 3803 0.530650 ATCATCGTCCACCATGTCGC 60.531 55.000 0.00 0.00 0.00 5.19
3242 3804 2.173669 CATCGTCCACCATGTCGCC 61.174 63.158 0.00 0.00 0.00 5.54
3243 3805 2.655073 ATCGTCCACCATGTCGCCA 61.655 57.895 0.00 0.00 0.00 5.69
3244 3806 1.971505 ATCGTCCACCATGTCGCCAT 61.972 55.000 0.00 0.00 0.00 4.40
3245 3807 2.463620 CGTCCACCATGTCGCCATG 61.464 63.158 0.00 0.00 46.65 3.66
3252 3814 4.521075 ATGTCGCCATGAGTTCGG 57.479 55.556 0.00 0.00 0.00 4.30
3253 3815 1.815421 ATGTCGCCATGAGTTCGGC 60.815 57.895 0.00 0.00 45.28 5.54
3257 3819 4.750460 GCCATGAGTTCGGCGATA 57.250 55.556 11.76 0.00 38.82 2.92
3258 3820 3.217242 GCCATGAGTTCGGCGATAT 57.783 52.632 11.76 1.32 38.82 1.63
3259 3821 1.512926 GCCATGAGTTCGGCGATATT 58.487 50.000 11.76 0.00 38.82 1.28
3260 3822 2.683968 GCCATGAGTTCGGCGATATTA 58.316 47.619 11.76 0.00 38.82 0.98
3261 3823 2.412089 GCCATGAGTTCGGCGATATTAC 59.588 50.000 11.76 5.77 38.82 1.89
3262 3824 2.661675 CCATGAGTTCGGCGATATTACG 59.338 50.000 11.76 0.00 0.00 3.18
3263 3825 3.305964 CATGAGTTCGGCGATATTACGT 58.694 45.455 11.76 0.00 35.59 3.57
3264 3826 4.469552 CATGAGTTCGGCGATATTACGTA 58.530 43.478 11.76 0.74 35.59 3.57
3265 3827 3.877064 TGAGTTCGGCGATATTACGTAC 58.123 45.455 11.76 2.74 35.59 3.67
3266 3828 3.312146 TGAGTTCGGCGATATTACGTACA 59.688 43.478 11.76 6.67 35.59 2.90
3267 3829 4.201901 TGAGTTCGGCGATATTACGTACAA 60.202 41.667 11.76 0.00 35.59 2.41
3268 3830 4.671377 AGTTCGGCGATATTACGTACAAA 58.329 39.130 11.76 0.00 35.59 2.83
3269 3831 4.500477 AGTTCGGCGATATTACGTACAAAC 59.500 41.667 11.76 0.20 35.59 2.93
3270 3832 4.291540 TCGGCGATATTACGTACAAACT 57.708 40.909 4.99 0.00 35.59 2.66
3271 3833 4.671377 TCGGCGATATTACGTACAAACTT 58.329 39.130 4.99 0.00 35.59 2.66
3272 3834 4.500117 TCGGCGATATTACGTACAAACTTG 59.500 41.667 4.99 0.00 35.59 3.16
3273 3835 4.266029 CGGCGATATTACGTACAAACTTGT 59.734 41.667 0.00 0.07 44.86 3.16
3274 3836 5.486706 GGCGATATTACGTACAAACTTGTG 58.513 41.667 5.34 0.00 42.31 3.33
3275 3837 4.953814 GCGATATTACGTACAAACTTGTGC 59.046 41.667 5.34 3.09 42.31 4.57
3276 3838 5.444877 GCGATATTACGTACAAACTTGTGCA 60.445 40.000 10.62 0.00 42.83 4.57
3277 3839 6.527089 CGATATTACGTACAAACTTGTGCAA 58.473 36.000 10.62 0.05 42.83 4.08
3278 3840 7.010606 CGATATTACGTACAAACTTGTGCAAA 58.989 34.615 10.62 5.13 42.83 3.68
3279 3841 7.005857 CGATATTACGTACAAACTTGTGCAAAC 59.994 37.037 10.62 0.00 42.83 2.93
3280 3842 5.548706 TTACGTACAAACTTGTGCAAACT 57.451 34.783 10.62 0.00 42.83 2.66
3281 3843 4.011058 ACGTACAAACTTGTGCAAACTC 57.989 40.909 10.62 0.00 42.83 3.01
3282 3844 3.026349 CGTACAAACTTGTGCAAACTCG 58.974 45.455 10.62 0.00 42.83 4.18
3283 3845 2.559998 ACAAACTTGTGCAAACTCGG 57.440 45.000 0.00 0.00 40.49 4.63
3284 3846 1.199624 CAAACTTGTGCAAACTCGGC 58.800 50.000 0.00 0.00 0.00 5.54
3285 3847 0.248458 AAACTTGTGCAAACTCGGCG 60.248 50.000 0.00 0.00 0.00 6.46
3286 3848 1.092921 AACTTGTGCAAACTCGGCGA 61.093 50.000 10.14 10.14 0.00 5.54
3287 3849 0.884704 ACTTGTGCAAACTCGGCGAT 60.885 50.000 11.27 0.00 0.00 4.58
3288 3850 0.179215 CTTGTGCAAACTCGGCGATC 60.179 55.000 11.27 0.00 0.00 3.69
3289 3851 0.602638 TTGTGCAAACTCGGCGATCT 60.603 50.000 11.27 0.00 0.00 2.75
3290 3852 1.291184 TGTGCAAACTCGGCGATCTG 61.291 55.000 11.27 9.34 0.00 2.90
3291 3853 1.741401 TGCAAACTCGGCGATCTGG 60.741 57.895 11.27 0.09 0.00 3.86
3292 3854 1.741770 GCAAACTCGGCGATCTGGT 60.742 57.895 11.27 0.88 0.00 4.00
3293 3855 0.459585 GCAAACTCGGCGATCTGGTA 60.460 55.000 11.27 0.00 0.00 3.25
3294 3856 1.278238 CAAACTCGGCGATCTGGTAC 58.722 55.000 11.27 0.00 0.00 3.34
3295 3857 0.179145 AAACTCGGCGATCTGGTACG 60.179 55.000 11.27 0.00 0.00 3.67
3296 3858 1.028330 AACTCGGCGATCTGGTACGA 61.028 55.000 11.27 0.00 0.00 3.43
3297 3859 1.028330 ACTCGGCGATCTGGTACGAA 61.028 55.000 11.27 0.00 32.80 3.85
3298 3860 0.591741 CTCGGCGATCTGGTACGAAC 60.592 60.000 11.27 0.00 32.80 3.95
3299 3861 1.028330 TCGGCGATCTGGTACGAACT 61.028 55.000 4.99 0.00 0.00 3.01
3300 3862 0.591741 CGGCGATCTGGTACGAACTC 60.592 60.000 0.00 0.00 0.00 3.01
3301 3863 0.591741 GGCGATCTGGTACGAACTCG 60.592 60.000 0.00 0.00 46.33 4.18
3302 3864 0.376152 GCGATCTGGTACGAACTCGA 59.624 55.000 6.05 0.00 43.02 4.04
3303 3865 1.855223 GCGATCTGGTACGAACTCGAC 60.855 57.143 6.05 0.14 43.02 4.20
3304 3866 1.591632 CGATCTGGTACGAACTCGACG 60.592 57.143 6.05 0.00 43.02 5.12
3305 3867 1.662629 GATCTGGTACGAACTCGACGA 59.337 52.381 6.05 0.00 43.02 4.20
3306 3868 1.511850 TCTGGTACGAACTCGACGAA 58.488 50.000 6.05 0.00 43.02 3.85
3307 3869 1.872952 TCTGGTACGAACTCGACGAAA 59.127 47.619 6.05 0.00 43.02 3.46
3308 3870 2.485426 TCTGGTACGAACTCGACGAAAT 59.515 45.455 6.05 0.00 43.02 2.17
3309 3871 3.058016 TCTGGTACGAACTCGACGAAATT 60.058 43.478 6.05 0.00 43.02 1.82
3310 3872 3.641648 TGGTACGAACTCGACGAAATTT 58.358 40.909 6.05 0.00 43.02 1.82
3311 3873 3.670055 TGGTACGAACTCGACGAAATTTC 59.330 43.478 8.20 8.20 43.02 2.17
3353 3915 7.458038 AAAAAGTAAAACATGCAAACTACGG 57.542 32.000 0.00 0.00 0.00 4.02
3354 3916 4.155310 AGTAAAACATGCAAACTACGGC 57.845 40.909 0.00 0.00 0.00 5.68
3355 3917 3.566322 AGTAAAACATGCAAACTACGGCA 59.434 39.130 0.00 0.00 45.23 5.69
3356 3918 3.444703 AAAACATGCAAACTACGGCAA 57.555 38.095 0.00 0.00 44.20 4.52
3357 3919 3.444703 AAACATGCAAACTACGGCAAA 57.555 38.095 0.00 0.00 44.20 3.68
3358 3920 2.415697 ACATGCAAACTACGGCAAAC 57.584 45.000 0.00 0.00 44.20 2.93
3359 3921 1.953686 ACATGCAAACTACGGCAAACT 59.046 42.857 0.00 0.00 44.20 2.66
3360 3922 3.142951 ACATGCAAACTACGGCAAACTA 58.857 40.909 0.00 0.00 44.20 2.24
3361 3923 3.058501 ACATGCAAACTACGGCAAACTAC 60.059 43.478 0.00 0.00 44.20 2.73
3362 3924 1.527736 TGCAAACTACGGCAAACTACG 59.472 47.619 0.00 0.00 37.03 3.51
3363 3925 1.723701 GCAAACTACGGCAAACTACGC 60.724 52.381 0.00 0.00 0.00 4.42
3364 3926 1.796459 CAAACTACGGCAAACTACGCT 59.204 47.619 0.00 0.00 0.00 5.07
3365 3927 2.988493 CAAACTACGGCAAACTACGCTA 59.012 45.455 0.00 0.00 0.00 4.26
3366 3928 2.556534 ACTACGGCAAACTACGCTAG 57.443 50.000 0.00 0.00 0.00 3.42
3367 3929 1.197910 CTACGGCAAACTACGCTAGC 58.802 55.000 4.06 4.06 0.00 3.42
3368 3930 0.179129 TACGGCAAACTACGCTAGCC 60.179 55.000 9.66 0.00 41.86 3.93
3369 3931 1.447140 CGGCAAACTACGCTAGCCA 60.447 57.895 9.66 0.00 45.47 4.75
3370 3932 1.693083 CGGCAAACTACGCTAGCCAC 61.693 60.000 9.66 0.00 45.47 5.01
3371 3933 0.391263 GGCAAACTACGCTAGCCACT 60.391 55.000 9.66 0.00 44.59 4.00
3372 3934 1.134907 GGCAAACTACGCTAGCCACTA 60.135 52.381 9.66 0.00 44.59 2.74
3373 3935 1.925185 GCAAACTACGCTAGCCACTAC 59.075 52.381 9.66 0.00 0.00 2.73
3374 3936 2.182825 CAAACTACGCTAGCCACTACG 58.817 52.381 9.66 0.00 0.00 3.51
3375 3937 1.457346 AACTACGCTAGCCACTACGT 58.543 50.000 9.66 2.33 42.22 3.57
3376 3938 1.012841 ACTACGCTAGCCACTACGTC 58.987 55.000 9.66 0.00 39.78 4.34
3377 3939 0.042361 CTACGCTAGCCACTACGTCG 60.042 60.000 9.66 0.00 39.78 5.12
3378 3940 0.740868 TACGCTAGCCACTACGTCGT 60.741 55.000 9.66 2.21 39.78 4.34
3379 3941 1.582937 CGCTAGCCACTACGTCGTG 60.583 63.158 12.97 12.97 34.71 4.35
3380 3942 1.505353 GCTAGCCACTACGTCGTGT 59.495 57.895 17.76 4.28 33.07 4.49
3381 3943 0.522915 GCTAGCCACTACGTCGTGTC 60.523 60.000 17.76 6.31 33.07 3.67
3382 3944 0.098376 CTAGCCACTACGTCGTGTCC 59.902 60.000 17.76 9.18 33.07 4.02
3383 3945 0.606130 TAGCCACTACGTCGTGTCCA 60.606 55.000 17.76 0.00 33.07 4.02
3384 3946 1.214589 GCCACTACGTCGTGTCCAT 59.785 57.895 17.76 0.00 33.07 3.41
3385 3947 0.801067 GCCACTACGTCGTGTCCATC 60.801 60.000 17.76 0.08 33.07 3.51
3386 3948 0.522705 CCACTACGTCGTGTCCATCG 60.523 60.000 17.76 0.00 33.07 3.84
3387 3949 1.132199 CACTACGTCGTGTCCATCGC 61.132 60.000 11.81 0.00 0.00 4.58
3388 3950 1.585521 CTACGTCGTGTCCATCGCC 60.586 63.158 8.47 0.00 0.00 5.54
3389 3951 3.385440 TACGTCGTGTCCATCGCCG 62.385 63.158 8.47 0.00 35.86 6.46
3394 3956 4.856801 GTGTCCATCGCCGGCCAT 62.857 66.667 23.46 11.92 0.00 4.40
3395 3957 4.545706 TGTCCATCGCCGGCCATC 62.546 66.667 23.46 2.07 0.00 3.51
3396 3958 4.241555 GTCCATCGCCGGCCATCT 62.242 66.667 23.46 0.00 0.00 2.90
3397 3959 2.523168 TCCATCGCCGGCCATCTA 60.523 61.111 23.46 0.00 0.00 1.98
3398 3960 2.357517 CCATCGCCGGCCATCTAC 60.358 66.667 23.46 0.00 0.00 2.59
3399 3961 2.421314 CATCGCCGGCCATCTACA 59.579 61.111 23.46 0.00 0.00 2.74
3400 3962 1.004560 CATCGCCGGCCATCTACAT 60.005 57.895 23.46 0.00 0.00 2.29
3401 3963 1.004560 ATCGCCGGCCATCTACATG 60.005 57.895 23.46 2.86 0.00 3.21
3402 3964 3.349006 CGCCGGCCATCTACATGC 61.349 66.667 23.46 0.00 0.00 4.06
3403 3965 2.980233 GCCGGCCATCTACATGCC 60.980 66.667 18.11 0.00 0.00 4.40
3404 3966 2.666190 CCGGCCATCTACATGCCG 60.666 66.667 14.72 14.72 43.59 5.69
3405 3967 2.421314 CGGCCATCTACATGCCGA 59.579 61.111 16.48 0.00 45.25 5.54
3406 3968 1.665916 CGGCCATCTACATGCCGAG 60.666 63.158 16.48 0.00 45.25 4.63
3407 3969 1.748403 GGCCATCTACATGCCGAGA 59.252 57.895 0.00 0.00 0.00 4.04
3408 3970 0.106708 GGCCATCTACATGCCGAGAA 59.893 55.000 0.00 0.00 0.00 2.87
3409 3971 1.506493 GCCATCTACATGCCGAGAAG 58.494 55.000 0.00 0.00 0.00 2.85
3410 3972 1.506493 CCATCTACATGCCGAGAAGC 58.494 55.000 0.00 0.00 0.00 3.86
3411 3973 1.506493 CATCTACATGCCGAGAAGCC 58.494 55.000 0.00 0.00 0.00 4.35
3412 3974 1.069823 CATCTACATGCCGAGAAGCCT 59.930 52.381 0.00 0.00 0.00 4.58
3413 3975 0.461548 TCTACATGCCGAGAAGCCTG 59.538 55.000 0.00 0.00 34.88 4.85
3414 3976 0.176680 CTACATGCCGAGAAGCCTGT 59.823 55.000 0.00 0.39 43.00 4.00
3415 3977 1.409064 CTACATGCCGAGAAGCCTGTA 59.591 52.381 0.00 2.48 41.17 2.74
3416 3978 0.176680 ACATGCCGAGAAGCCTGTAG 59.823 55.000 0.00 0.00 39.44 2.74
3417 3979 0.461548 CATGCCGAGAAGCCTGTAGA 59.538 55.000 0.00 0.00 0.00 2.59
3418 3980 1.134699 CATGCCGAGAAGCCTGTAGAA 60.135 52.381 0.00 0.00 0.00 2.10
3419 3981 0.532573 TGCCGAGAAGCCTGTAGAAG 59.467 55.000 0.00 0.00 0.00 2.85
3420 3982 0.808060 GCCGAGAAGCCTGTAGAAGC 60.808 60.000 0.00 0.00 0.00 3.86
3421 3983 0.526524 CCGAGAAGCCTGTAGAAGCG 60.527 60.000 0.00 0.00 0.00 4.68
3422 3984 0.526524 CGAGAAGCCTGTAGAAGCGG 60.527 60.000 0.00 0.00 0.00 5.52
3423 3985 0.179097 GAGAAGCCTGTAGAAGCGGG 60.179 60.000 0.00 0.00 37.94 6.13
3424 3986 1.153349 GAAGCCTGTAGAAGCGGGG 60.153 63.158 0.00 0.00 35.47 5.73
3425 3987 2.595009 GAAGCCTGTAGAAGCGGGGG 62.595 65.000 0.00 0.00 35.47 5.40
3426 3988 3.400054 GCCTGTAGAAGCGGGGGT 61.400 66.667 0.00 0.00 35.47 4.95
3427 3989 2.062177 GCCTGTAGAAGCGGGGGTA 61.062 63.158 0.00 0.00 35.47 3.69
3428 3990 2.029307 GCCTGTAGAAGCGGGGGTAG 62.029 65.000 0.00 0.00 35.47 3.18
3429 3991 0.686769 CCTGTAGAAGCGGGGGTAGT 60.687 60.000 0.00 0.00 0.00 2.73
3430 3992 0.745468 CTGTAGAAGCGGGGGTAGTC 59.255 60.000 0.00 0.00 0.00 2.59
3431 3993 1.033746 TGTAGAAGCGGGGGTAGTCG 61.034 60.000 0.00 0.00 0.00 4.18
3487 4049 4.791069 GAGCCACCCCCGTCCCTA 62.791 72.222 0.00 0.00 0.00 3.53
3488 4050 4.103928 AGCCACCCCCGTCCCTAT 62.104 66.667 0.00 0.00 0.00 2.57
3489 4051 3.094498 GCCACCCCCGTCCCTATT 61.094 66.667 0.00 0.00 0.00 1.73
3490 4052 2.915869 CCACCCCCGTCCCTATTG 59.084 66.667 0.00 0.00 0.00 1.90
3491 4053 2.192175 CACCCCCGTCCCTATTGC 59.808 66.667 0.00 0.00 0.00 3.56
3492 4054 2.285818 ACCCCCGTCCCTATTGCA 60.286 61.111 0.00 0.00 0.00 4.08
3493 4055 2.192175 CCCCCGTCCCTATTGCAC 59.808 66.667 0.00 0.00 0.00 4.57
3494 4056 2.192175 CCCCGTCCCTATTGCACC 59.808 66.667 0.00 0.00 0.00 5.01
3495 4057 2.192175 CCCGTCCCTATTGCACCC 59.808 66.667 0.00 0.00 0.00 4.61
3496 4058 2.192175 CCGTCCCTATTGCACCCC 59.808 66.667 0.00 0.00 0.00 4.95
3497 4059 2.375345 CCGTCCCTATTGCACCCCT 61.375 63.158 0.00 0.00 0.00 4.79
3498 4060 1.153168 CGTCCCTATTGCACCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
3499 4061 1.453928 GTCCCTATTGCACCCCTGC 60.454 63.158 0.00 0.00 44.52 4.85
3500 4062 2.123726 CCCTATTGCACCCCTGCC 60.124 66.667 0.00 0.00 43.51 4.85
3501 4063 2.123726 CCTATTGCACCCCTGCCC 60.124 66.667 0.00 0.00 43.51 5.36
3502 4064 2.682846 CTATTGCACCCCTGCCCA 59.317 61.111 0.00 0.00 43.51 5.36
3503 4065 1.454479 CTATTGCACCCCTGCCCAG 60.454 63.158 0.00 0.00 43.51 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.376109 CCTCTTCATGGAAGCAAGCAT 58.624 47.619 1.14 0.00 39.29 3.79
174 177 6.239036 GGCACCTTTGTCTTCTGTTTAGAATT 60.239 38.462 0.00 0.00 41.83 2.17
258 261 6.062646 CGTTTTTCACATTACACTAGTGTCG 58.937 40.000 31.11 21.79 43.74 4.35
259 262 6.018507 ACCGTTTTTCACATTACACTAGTGTC 60.019 38.462 31.11 11.71 43.74 3.67
271 274 9.403583 ACCATAATATAAGACCGTTTTTCACAT 57.596 29.630 0.00 0.00 0.00 3.21
297 300 4.956700 CACTTCATTCCTACTCCCTCTGTA 59.043 45.833 0.00 0.00 0.00 2.74
311 314 9.601217 AGTACACATATTAGAACCACTTCATTC 57.399 33.333 0.00 0.00 0.00 2.67
515 520 0.895100 TCTGCTGGTTGGTTGATGCC 60.895 55.000 0.00 0.00 0.00 4.40
573 578 4.242475 CTCGCCAACATGTCAAGTACTTA 58.758 43.478 8.04 0.00 0.00 2.24
622 843 2.951642 TGAGCTTCAAAAGTTGAGTGGG 59.048 45.455 0.00 0.00 41.38 4.61
663 884 2.582728 TTGTGGCAAAACAGCTGAAG 57.417 45.000 23.35 7.88 34.17 3.02
675 896 1.265236 GGGGTCATCATTTTGTGGCA 58.735 50.000 0.00 0.00 0.00 4.92
691 912 3.562732 GACCGTTGGGGACTTGGGG 62.563 68.421 0.00 0.00 39.97 4.96
695 916 2.095978 CTGTCGACCGTTGGGGACTT 62.096 60.000 14.12 0.00 39.97 3.01
696 917 2.522436 TGTCGACCGTTGGGGACT 60.522 61.111 14.12 0.00 39.97 3.85
698 919 3.307906 CCTGTCGACCGTTGGGGA 61.308 66.667 14.12 0.00 39.97 4.81
699 920 2.656069 ATCCTGTCGACCGTTGGGG 61.656 63.158 14.12 5.85 43.62 4.96
788 1021 1.091771 CAATGGCGGCAGGTCAGTAG 61.092 60.000 19.29 0.00 30.81 2.57
797 1030 1.031235 CATGGTTATCAATGGCGGCA 58.969 50.000 16.34 16.34 0.00 5.69
822 1055 4.543084 GCCTTCGCCATCGCAAGC 62.543 66.667 0.00 0.00 35.26 4.01
839 1072 3.121030 CGAGTTGCTGCCCTTCGG 61.121 66.667 0.00 0.00 0.00 4.30
868 1101 1.586422 TATGCGATTGCTTGAGCCTC 58.414 50.000 6.47 0.00 43.34 4.70
911 1159 4.152625 GACTGCCGCGTCATGTGC 62.153 66.667 4.92 0.00 34.11 4.57
912 1160 3.842126 CGACTGCCGCGTCATGTG 61.842 66.667 4.92 0.00 33.54 3.21
1075 1326 3.842923 CTCGTGGAGCAGGGCGAT 61.843 66.667 0.00 0.00 32.79 4.58
1577 1828 0.310854 GTCAAACACCTTCTTGGCCG 59.689 55.000 0.00 0.00 40.22 6.13
1586 1837 3.253955 GCATCGCGTCAAACACCT 58.746 55.556 5.77 0.00 0.00 4.00
1670 1921 1.870580 CGTAGATCTCGAGCGACTCCT 60.871 57.143 7.81 0.87 0.00 3.69
1680 1931 0.167033 CCATCTCGCCGTAGATCTCG 59.833 60.000 0.00 2.90 33.87 4.04
1999 2250 1.664017 CGAGCCTCCAGATCATGCG 60.664 63.158 0.00 0.00 0.00 4.73
2005 2256 2.835431 CGGGTCGAGCCTCCAGAT 60.835 66.667 29.53 0.00 37.43 2.90
2169 2420 0.966920 CCTCCACGTAGAACAGGTGT 59.033 55.000 0.00 0.00 40.66 4.16
2257 2508 2.125793 GTCCGCCACGTACCCTTC 60.126 66.667 0.00 0.00 0.00 3.46
2391 2642 0.599204 GGAGGTTCTTGAACACGCGA 60.599 55.000 15.93 0.00 0.00 5.87
2526 2777 2.532843 GGAACCTACCAGTAGTCACCA 58.467 52.381 4.23 0.00 0.00 4.17
2529 2780 1.180029 GCGGAACCTACCAGTAGTCA 58.820 55.000 4.23 0.00 0.00 3.41
2563 2814 2.920490 CTCTGCTCGACTTGAAGCTTAC 59.080 50.000 0.00 0.00 0.00 2.34
2593 2847 2.359107 CGCCACTGCTGTCCATGT 60.359 61.111 0.00 0.00 34.43 3.21
2632 2886 5.125257 TGATGTGGTGTGCTGTAAATAATGG 59.875 40.000 0.00 0.00 0.00 3.16
2660 3155 9.049523 CATGCTTAGTTCATCATAATGTGTAGT 57.950 33.333 0.00 0.00 34.32 2.73
2661 3156 9.264719 TCATGCTTAGTTCATCATAATGTGTAG 57.735 33.333 0.00 0.00 34.32 2.74
2662 3157 9.612066 TTCATGCTTAGTTCATCATAATGTGTA 57.388 29.630 0.00 0.00 34.32 2.90
2713 3215 7.466996 GCATCTCATAATATACAAGCATGGAGC 60.467 40.741 0.00 0.00 46.19 4.70
2730 3232 6.669154 TGGAGGATACATACATGCATCTCATA 59.331 38.462 0.00 0.00 41.41 2.15
2731 3233 5.486419 TGGAGGATACATACATGCATCTCAT 59.514 40.000 0.00 0.00 41.41 2.90
2733 3235 5.411831 TGGAGGATACATACATGCATCTC 57.588 43.478 0.00 0.00 41.41 2.75
2734 3236 5.104610 GGATGGAGGATACATACATGCATCT 60.105 44.000 0.00 0.00 42.90 2.90
2884 3437 0.389426 AATGCGTGTACGTGAGGGAC 60.389 55.000 0.00 0.00 42.22 4.46
2958 3511 5.181690 TCAAAAGAAATTCGTTGGGAGTG 57.818 39.130 10.89 0.09 0.00 3.51
2959 3512 5.845391 TTCAAAAGAAATTCGTTGGGAGT 57.155 34.783 10.89 0.00 0.00 3.85
2980 3534 9.474920 TCTTTGCTTCGATGAATTTACAAATTT 57.525 25.926 1.89 0.00 38.64 1.82
2982 3536 8.915654 GTTCTTTGCTTCGATGAATTTACAAAT 58.084 29.630 1.89 0.00 0.00 2.32
2983 3537 7.381139 GGTTCTTTGCTTCGATGAATTTACAAA 59.619 33.333 1.89 1.73 0.00 2.83
3030 3584 2.743928 CCGGGCAGAGTGCTTGAC 60.744 66.667 0.00 0.00 44.28 3.18
3043 3597 2.184579 GAAGGCGAGAAGTCCGGG 59.815 66.667 0.00 0.00 0.00 5.73
3044 3598 2.184579 GGAAGGCGAGAAGTCCGG 59.815 66.667 0.00 0.00 0.00 5.14
3046 3600 1.079057 GTGGGAAGGCGAGAAGTCC 60.079 63.158 0.00 0.00 0.00 3.85
3047 3601 1.446272 CGTGGGAAGGCGAGAAGTC 60.446 63.158 0.00 0.00 0.00 3.01
3049 3603 2.815647 GCGTGGGAAGGCGAGAAG 60.816 66.667 0.00 0.00 0.00 2.85
3107 3669 0.108804 CTTAGACGGTGCGTGGATGT 60.109 55.000 0.00 0.00 41.37 3.06
3175 3737 4.072088 CTTGCGCCGGTTCGTCAC 62.072 66.667 4.18 0.00 0.00 3.67
3176 3738 4.595538 ACTTGCGCCGGTTCGTCA 62.596 61.111 4.18 0.00 0.00 4.35
3177 3739 2.888998 AAACTTGCGCCGGTTCGTC 61.889 57.895 4.18 0.00 0.00 4.20
3178 3740 2.898343 AAACTTGCGCCGGTTCGT 60.898 55.556 4.18 0.00 0.00 3.85
3179 3741 2.426752 CAAACTTGCGCCGGTTCG 60.427 61.111 4.18 0.00 0.00 3.95
3180 3742 2.050442 CCAAACTTGCGCCGGTTC 60.050 61.111 4.18 0.00 0.00 3.62
3181 3743 4.279043 GCCAAACTTGCGCCGGTT 62.279 61.111 4.18 7.14 0.00 4.44
3188 3750 1.594021 CCCCAAACGCCAAACTTGC 60.594 57.895 0.00 0.00 0.00 4.01
3189 3751 1.068921 CCCCCAAACGCCAAACTTG 59.931 57.895 0.00 0.00 0.00 3.16
3190 3752 3.544772 CCCCCAAACGCCAAACTT 58.455 55.556 0.00 0.00 0.00 2.66
3212 3774 3.304123 GGTGGACGATGATAGAGACGAAG 60.304 52.174 0.00 0.00 0.00 3.79
3213 3775 2.617308 GGTGGACGATGATAGAGACGAA 59.383 50.000 0.00 0.00 0.00 3.85
3214 3776 2.219458 GGTGGACGATGATAGAGACGA 58.781 52.381 0.00 0.00 0.00 4.20
3215 3777 1.947456 TGGTGGACGATGATAGAGACG 59.053 52.381 0.00 0.00 0.00 4.18
3216 3778 3.319405 ACATGGTGGACGATGATAGAGAC 59.681 47.826 8.57 0.00 35.90 3.36
3217 3779 3.566351 ACATGGTGGACGATGATAGAGA 58.434 45.455 8.57 0.00 35.90 3.10
3218 3780 3.610349 CGACATGGTGGACGATGATAGAG 60.610 52.174 8.57 0.00 35.90 2.43
3219 3781 2.293399 CGACATGGTGGACGATGATAGA 59.707 50.000 8.57 0.00 35.90 1.98
3220 3782 2.666026 CGACATGGTGGACGATGATAG 58.334 52.381 8.57 0.00 35.90 2.08
3221 3783 1.269569 GCGACATGGTGGACGATGATA 60.270 52.381 8.57 0.00 35.90 2.15
3222 3784 0.530650 GCGACATGGTGGACGATGAT 60.531 55.000 8.57 0.00 35.90 2.45
3223 3785 1.153647 GCGACATGGTGGACGATGA 60.154 57.895 8.57 0.00 35.90 2.92
3224 3786 2.173669 GGCGACATGGTGGACGATG 61.174 63.158 0.00 0.67 37.95 3.84
3225 3787 2.186903 GGCGACATGGTGGACGAT 59.813 61.111 0.00 0.00 0.00 3.73
3226 3788 3.307108 TGGCGACATGGTGGACGA 61.307 61.111 0.00 0.00 33.40 4.20
3241 3803 2.661675 CGTAATATCGCCGAACTCATGG 59.338 50.000 0.00 0.00 0.00 3.66
3242 3804 3.305964 ACGTAATATCGCCGAACTCATG 58.694 45.455 0.00 0.00 0.00 3.07
3243 3805 3.637998 ACGTAATATCGCCGAACTCAT 57.362 42.857 0.00 0.00 0.00 2.90
3244 3806 3.312146 TGTACGTAATATCGCCGAACTCA 59.688 43.478 0.00 0.00 0.00 3.41
3245 3807 3.877064 TGTACGTAATATCGCCGAACTC 58.123 45.455 0.00 0.00 0.00 3.01
3246 3808 3.969117 TGTACGTAATATCGCCGAACT 57.031 42.857 0.00 0.00 0.00 3.01
3247 3809 4.500477 AGTTTGTACGTAATATCGCCGAAC 59.500 41.667 0.00 0.00 33.53 3.95
3248 3810 4.671377 AGTTTGTACGTAATATCGCCGAA 58.329 39.130 0.00 0.00 0.00 4.30
3249 3811 4.291540 AGTTTGTACGTAATATCGCCGA 57.708 40.909 0.00 0.00 0.00 5.54
3250 3812 4.266029 ACAAGTTTGTACGTAATATCGCCG 59.734 41.667 0.00 0.00 40.16 6.46
3251 3813 5.486706 CACAAGTTTGTACGTAATATCGCC 58.513 41.667 0.00 0.00 39.91 5.54
3252 3814 4.953814 GCACAAGTTTGTACGTAATATCGC 59.046 41.667 0.00 0.00 39.91 4.58
3253 3815 6.085121 TGCACAAGTTTGTACGTAATATCG 57.915 37.500 0.00 0.00 39.91 2.92
3254 3816 8.013378 AGTTTGCACAAGTTTGTACGTAATATC 58.987 33.333 0.00 0.00 39.91 1.63
3255 3817 7.867752 AGTTTGCACAAGTTTGTACGTAATAT 58.132 30.769 0.00 0.00 39.91 1.28
3256 3818 7.249186 AGTTTGCACAAGTTTGTACGTAATA 57.751 32.000 0.00 0.00 39.91 0.98
3257 3819 6.126568 AGTTTGCACAAGTTTGTACGTAAT 57.873 33.333 0.00 0.00 39.91 1.89
3258 3820 5.548706 AGTTTGCACAAGTTTGTACGTAA 57.451 34.783 0.00 0.00 39.91 3.18
3259 3821 4.259890 CGAGTTTGCACAAGTTTGTACGTA 60.260 41.667 0.00 0.00 39.91 3.57
3260 3822 3.484557 CGAGTTTGCACAAGTTTGTACGT 60.485 43.478 0.00 0.00 39.91 3.57
3261 3823 3.026349 CGAGTTTGCACAAGTTTGTACG 58.974 45.455 0.00 0.00 39.91 3.67
3262 3824 3.359654 CCGAGTTTGCACAAGTTTGTAC 58.640 45.455 0.00 0.00 39.91 2.90
3263 3825 2.223386 GCCGAGTTTGCACAAGTTTGTA 60.223 45.455 0.00 0.00 39.91 2.41
3264 3826 1.469079 GCCGAGTTTGCACAAGTTTGT 60.469 47.619 0.00 0.00 43.36 2.83
3265 3827 1.199624 GCCGAGTTTGCACAAGTTTG 58.800 50.000 0.00 0.00 0.00 2.93
3266 3828 0.248458 CGCCGAGTTTGCACAAGTTT 60.248 50.000 0.00 0.00 0.00 2.66
3267 3829 1.092921 TCGCCGAGTTTGCACAAGTT 61.093 50.000 0.00 0.00 0.00 2.66
3268 3830 0.884704 ATCGCCGAGTTTGCACAAGT 60.885 50.000 0.00 0.00 0.00 3.16
3269 3831 0.179215 GATCGCCGAGTTTGCACAAG 60.179 55.000 0.00 0.00 0.00 3.16
3270 3832 0.602638 AGATCGCCGAGTTTGCACAA 60.603 50.000 0.00 0.00 0.00 3.33
3271 3833 1.005037 AGATCGCCGAGTTTGCACA 60.005 52.632 0.00 0.00 0.00 4.57
3272 3834 1.421485 CAGATCGCCGAGTTTGCAC 59.579 57.895 0.00 0.00 0.00 4.57
3273 3835 1.741401 CCAGATCGCCGAGTTTGCA 60.741 57.895 0.00 0.00 0.00 4.08
3274 3836 0.459585 TACCAGATCGCCGAGTTTGC 60.460 55.000 0.00 0.00 0.00 3.68
3275 3837 1.278238 GTACCAGATCGCCGAGTTTG 58.722 55.000 0.00 0.00 0.00 2.93
3276 3838 0.179145 CGTACCAGATCGCCGAGTTT 60.179 55.000 0.00 0.00 0.00 2.66
3277 3839 1.028330 TCGTACCAGATCGCCGAGTT 61.028 55.000 0.00 0.00 0.00 3.01
3278 3840 1.028330 TTCGTACCAGATCGCCGAGT 61.028 55.000 0.00 0.00 0.00 4.18
3279 3841 0.591741 GTTCGTACCAGATCGCCGAG 60.592 60.000 0.00 0.00 0.00 4.63
3280 3842 1.028330 AGTTCGTACCAGATCGCCGA 61.028 55.000 0.00 0.00 0.00 5.54
3281 3843 0.591741 GAGTTCGTACCAGATCGCCG 60.592 60.000 0.00 0.00 0.00 6.46
3282 3844 0.591741 CGAGTTCGTACCAGATCGCC 60.592 60.000 0.00 0.00 34.11 5.54
3283 3845 0.376152 TCGAGTTCGTACCAGATCGC 59.624 55.000 1.07 0.00 40.80 4.58
3284 3846 1.591632 CGTCGAGTTCGTACCAGATCG 60.592 57.143 1.07 0.00 40.80 3.69
3285 3847 1.662629 TCGTCGAGTTCGTACCAGATC 59.337 52.381 1.07 0.00 40.80 2.75
3286 3848 1.730501 TCGTCGAGTTCGTACCAGAT 58.269 50.000 1.07 0.00 40.80 2.90
3287 3849 1.511850 TTCGTCGAGTTCGTACCAGA 58.488 50.000 1.07 0.00 40.80 3.86
3288 3850 2.320805 TTTCGTCGAGTTCGTACCAG 57.679 50.000 1.07 0.00 40.80 4.00
3289 3851 2.995466 ATTTCGTCGAGTTCGTACCA 57.005 45.000 1.07 0.00 40.80 3.25
3290 3852 3.241146 CGAAATTTCGTCGAGTTCGTACC 60.241 47.826 28.21 0.00 45.09 3.34
3291 3853 3.881186 CGAAATTTCGTCGAGTTCGTAC 58.119 45.455 28.21 0.00 45.09 3.67
3329 3891 6.019398 GCCGTAGTTTGCATGTTTTACTTTTT 60.019 34.615 0.00 0.00 0.00 1.94
3330 3892 5.460748 GCCGTAGTTTGCATGTTTTACTTTT 59.539 36.000 0.00 0.00 0.00 2.27
3331 3893 4.979815 GCCGTAGTTTGCATGTTTTACTTT 59.020 37.500 0.00 0.00 0.00 2.66
3332 3894 4.036971 TGCCGTAGTTTGCATGTTTTACTT 59.963 37.500 0.00 0.00 31.31 2.24
3333 3895 3.566322 TGCCGTAGTTTGCATGTTTTACT 59.434 39.130 0.00 0.00 31.31 2.24
3334 3896 3.891324 TGCCGTAGTTTGCATGTTTTAC 58.109 40.909 0.00 0.00 31.31 2.01
3335 3897 4.569761 TTGCCGTAGTTTGCATGTTTTA 57.430 36.364 0.00 0.00 37.33 1.52
3336 3898 3.444703 TTGCCGTAGTTTGCATGTTTT 57.555 38.095 0.00 0.00 37.33 2.43
3337 3899 3.120041 GTTTGCCGTAGTTTGCATGTTT 58.880 40.909 0.00 0.00 37.33 2.83
3338 3900 2.360801 AGTTTGCCGTAGTTTGCATGTT 59.639 40.909 0.00 0.00 37.33 2.71
3339 3901 1.953686 AGTTTGCCGTAGTTTGCATGT 59.046 42.857 0.00 0.00 37.33 3.21
3340 3902 2.704725 AGTTTGCCGTAGTTTGCATG 57.295 45.000 0.00 0.00 37.33 4.06
3341 3903 2.158841 CGTAGTTTGCCGTAGTTTGCAT 59.841 45.455 0.00 0.00 37.33 3.96
3342 3904 1.527736 CGTAGTTTGCCGTAGTTTGCA 59.472 47.619 0.00 0.00 35.27 4.08
3343 3905 1.723701 GCGTAGTTTGCCGTAGTTTGC 60.724 52.381 0.00 0.00 0.00 3.68
3344 3906 1.796459 AGCGTAGTTTGCCGTAGTTTG 59.204 47.619 0.00 0.00 0.00 2.93
3345 3907 2.159327 AGCGTAGTTTGCCGTAGTTT 57.841 45.000 0.00 0.00 0.00 2.66
3346 3908 2.872370 CTAGCGTAGTTTGCCGTAGTT 58.128 47.619 0.00 0.00 0.00 2.24
3347 3909 1.468736 GCTAGCGTAGTTTGCCGTAGT 60.469 52.381 0.00 0.00 33.18 2.73
3348 3910 1.197910 GCTAGCGTAGTTTGCCGTAG 58.802 55.000 0.00 0.00 33.18 3.51
3349 3911 3.334078 GCTAGCGTAGTTTGCCGTA 57.666 52.632 0.00 0.00 33.18 4.02
3350 3912 4.180496 GCTAGCGTAGTTTGCCGT 57.820 55.556 0.00 0.00 33.18 5.68
3353 3915 1.925185 GTAGTGGCTAGCGTAGTTTGC 59.075 52.381 9.00 0.00 38.81 3.68
3354 3916 2.182825 CGTAGTGGCTAGCGTAGTTTG 58.817 52.381 9.00 0.00 0.00 2.93
3355 3917 1.815003 ACGTAGTGGCTAGCGTAGTTT 59.185 47.619 9.00 0.00 42.51 2.66
3356 3918 1.457346 ACGTAGTGGCTAGCGTAGTT 58.543 50.000 9.00 0.00 42.51 2.24
3357 3919 3.165606 ACGTAGTGGCTAGCGTAGT 57.834 52.632 9.00 5.93 42.51 2.73
3370 3932 1.585521 GGCGATGGACACGACGTAG 60.586 63.158 0.00 0.00 0.00 3.51
3371 3933 2.486504 GGCGATGGACACGACGTA 59.513 61.111 0.00 0.00 0.00 3.57
3379 3941 2.867855 TAGATGGCCGGCGATGGAC 61.868 63.158 29.81 14.46 37.64 4.02
3380 3942 2.523168 TAGATGGCCGGCGATGGA 60.523 61.111 29.81 13.14 0.00 3.41
3381 3943 2.357517 GTAGATGGCCGGCGATGG 60.358 66.667 29.81 0.00 0.00 3.51
3382 3944 1.004560 ATGTAGATGGCCGGCGATG 60.005 57.895 29.81 0.00 0.00 3.84
3383 3945 1.004560 CATGTAGATGGCCGGCGAT 60.005 57.895 25.12 25.12 0.00 4.58
3384 3946 2.421314 CATGTAGATGGCCGGCGA 59.579 61.111 22.54 19.14 0.00 5.54
3385 3947 3.349006 GCATGTAGATGGCCGGCG 61.349 66.667 22.54 0.00 0.00 6.46
3391 3953 1.506493 GCTTCTCGGCATGTAGATGG 58.494 55.000 1.57 0.00 0.00 3.51
3392 3954 1.069823 AGGCTTCTCGGCATGTAGATG 59.930 52.381 0.00 0.00 41.46 2.90
3393 3955 1.069823 CAGGCTTCTCGGCATGTAGAT 59.930 52.381 0.00 0.00 38.88 1.98
3394 3956 0.461548 CAGGCTTCTCGGCATGTAGA 59.538 55.000 0.00 0.00 38.88 2.59
3395 3957 2.983433 CAGGCTTCTCGGCATGTAG 58.017 57.895 0.00 0.00 38.88 2.74
3399 3961 1.137872 CTTCTACAGGCTTCTCGGCAT 59.862 52.381 0.00 0.00 41.46 4.40
3400 3962 0.532573 CTTCTACAGGCTTCTCGGCA 59.467 55.000 0.00 0.00 41.46 5.69
3401 3963 0.808060 GCTTCTACAGGCTTCTCGGC 60.808 60.000 0.00 0.00 38.75 5.54
3402 3964 0.526524 CGCTTCTACAGGCTTCTCGG 60.527 60.000 0.00 0.00 0.00 4.63
3403 3965 0.526524 CCGCTTCTACAGGCTTCTCG 60.527 60.000 0.00 0.00 0.00 4.04
3404 3966 0.179097 CCCGCTTCTACAGGCTTCTC 60.179 60.000 0.00 0.00 0.00 2.87
3405 3967 1.617947 CCCCGCTTCTACAGGCTTCT 61.618 60.000 0.00 0.00 0.00 2.85
3406 3968 1.153349 CCCCGCTTCTACAGGCTTC 60.153 63.158 0.00 0.00 0.00 3.86
3407 3969 2.670148 CCCCCGCTTCTACAGGCTT 61.670 63.158 0.00 0.00 0.00 4.35
3408 3970 2.525284 TACCCCCGCTTCTACAGGCT 62.525 60.000 0.00 0.00 0.00 4.58
3409 3971 2.029307 CTACCCCCGCTTCTACAGGC 62.029 65.000 0.00 0.00 0.00 4.85
3410 3972 0.686769 ACTACCCCCGCTTCTACAGG 60.687 60.000 0.00 0.00 0.00 4.00
3411 3973 0.745468 GACTACCCCCGCTTCTACAG 59.255 60.000 0.00 0.00 0.00 2.74
3412 3974 1.033746 CGACTACCCCCGCTTCTACA 61.034 60.000 0.00 0.00 0.00 2.74
3413 3975 1.732308 CGACTACCCCCGCTTCTAC 59.268 63.158 0.00 0.00 0.00 2.59
3414 3976 2.123428 GCGACTACCCCCGCTTCTA 61.123 63.158 0.00 0.00 46.96 2.10
3415 3977 3.459063 GCGACTACCCCCGCTTCT 61.459 66.667 0.00 0.00 46.96 2.85
3470 4032 4.791069 TAGGGACGGGGGTGGCTC 62.791 72.222 0.00 0.00 0.00 4.70
3471 4033 3.653122 AATAGGGACGGGGGTGGCT 62.653 63.158 0.00 0.00 0.00 4.75
3472 4034 3.094498 AATAGGGACGGGGGTGGC 61.094 66.667 0.00 0.00 0.00 5.01
3473 4035 2.915869 CAATAGGGACGGGGGTGG 59.084 66.667 0.00 0.00 0.00 4.61
3474 4036 2.192175 GCAATAGGGACGGGGGTG 59.808 66.667 0.00 0.00 0.00 4.61
3475 4037 2.285818 TGCAATAGGGACGGGGGT 60.286 61.111 0.00 0.00 0.00 4.95
3476 4038 2.192175 GTGCAATAGGGACGGGGG 59.808 66.667 0.00 0.00 0.00 5.40
3477 4039 2.192175 GGTGCAATAGGGACGGGG 59.808 66.667 0.00 0.00 39.01 5.73
3478 4040 2.192175 GGGTGCAATAGGGACGGG 59.808 66.667 0.00 0.00 39.01 5.28
3479 4041 2.192175 GGGGTGCAATAGGGACGG 59.808 66.667 0.00 0.00 39.01 4.79
3480 4042 1.153168 CAGGGGTGCAATAGGGACG 60.153 63.158 0.00 0.00 39.01 4.79
3481 4043 1.453928 GCAGGGGTGCAATAGGGAC 60.454 63.158 0.00 0.00 37.06 4.46
3482 4044 2.689691 GGCAGGGGTGCAATAGGGA 61.690 63.158 0.00 0.00 36.33 4.20
3483 4045 2.123726 GGCAGGGGTGCAATAGGG 60.124 66.667 0.00 0.00 36.33 3.53
3484 4046 2.123726 GGGCAGGGGTGCAATAGG 60.124 66.667 0.00 0.00 36.33 2.57
3485 4047 1.454479 CTGGGCAGGGGTGCAATAG 60.454 63.158 0.00 0.00 36.33 1.73
3486 4048 2.682846 CTGGGCAGGGGTGCAATA 59.317 61.111 0.00 0.00 36.33 1.90
3487 4049 4.387343 CCTGGGCAGGGGTGCAAT 62.387 66.667 0.00 0.00 44.87 3.56


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

AutoCloner maintained by Alex Coulton.