Multiple sequence alignment - TraesCS3A01G300600

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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 TraesCS3A01G300600 chr3A 100.000 4504 0 0 1 4504 534530495 534534998 0.000000e+00 8318
1 TraesCS3A01G300600 chr3A 93.947 760 45 1 1 759 73871161 73871920 0.000000e+00 1147
2 TraesCS3A01G300600 chr3D 93.220 3009 141 19 774 3743 415655525 415652541 0.000000e+00 4368
3 TraesCS3A01G300600 chr3D 92.098 772 59 2 1 771 586598863 586598093 0.000000e+00 1086
4 TraesCS3A01G300600 chr3D 87.477 543 29 20 3995 4504 415647810 415647274 1.400000e-164 590
5 TraesCS3A01G300600 chr3B 91.895 2369 139 23 774 3125 542165495 542163163 0.000000e+00 3262
6 TraesCS3A01G300600 chr3B 91.902 778 60 3 1 777 52193304 52192529 0.000000e+00 1085
7 TraesCS3A01G300600 chr3B 89.150 553 27 19 3167 3709 542163071 542162542 0.000000e+00 658
8 TraesCS3A01G300600 chr3B 84.140 372 20 7 4169 4504 542135099 542134731 1.560000e-84 324
9 TraesCS3A01G300600 chr4A 92.866 771 54 1 2 771 595416643 595415873 0.000000e+00 1118
10 TraesCS3A01G300600 chr1B 92.866 771 54 1 1 770 185229036 185228266 0.000000e+00 1118
11 TraesCS3A01G300600 chr5D 93.026 760 51 2 1 758 367422170 367421411 0.000000e+00 1109
12 TraesCS3A01G300600 chr7A 92.487 772 56 2 1 771 82126719 82125949 0.000000e+00 1103
13 TraesCS3A01G300600 chr6B 92.468 770 56 2 1 769 132110955 132111723 0.000000e+00 1099
14 TraesCS3A01G300600 chr7B 92.078 770 59 2 1 769 21255681 21256449 0.000000e+00 1083
15 TraesCS3A01G300600 chr7D 94.118 493 23 4 2198 2690 6141958 6141472 0.000000e+00 745
16 TraesCS3A01G300600 chr7D 94.903 412 16 2 2622 3031 6141475 6141067 1.370000e-179 640
17 TraesCS3A01G300600 chr7D 82.835 769 69 35 3014 3743 6141037 6140293 8.220000e-177 630
18 TraesCS3A01G300600 chr7D 84.615 260 23 8 917 1161 6142232 6141975 4.500000e-60 243
19 TraesCS3A01G300600 chr7D 100.000 55 0 0 4450 4504 6136955 6136901 7.970000e-18 102
20 TraesCS3A01G300600 chr5A 85.518 656 49 14 1322 1969 54731625 54731008 1.060000e-180 643


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 TraesCS3A01G300600 chr3A 534530495 534534998 4503 False 8318 8318 100.0000 1 4504 1 chr3A.!!$F2 4503
1 TraesCS3A01G300600 chr3A 73871161 73871920 759 False 1147 1147 93.9470 1 759 1 chr3A.!!$F1 758
2 TraesCS3A01G300600 chr3D 415652541 415655525 2984 True 4368 4368 93.2200 774 3743 1 chr3D.!!$R2 2969
3 TraesCS3A01G300600 chr3D 586598093 586598863 770 True 1086 1086 92.0980 1 771 1 chr3D.!!$R3 770
4 TraesCS3A01G300600 chr3D 415647274 415647810 536 True 590 590 87.4770 3995 4504 1 chr3D.!!$R1 509
5 TraesCS3A01G300600 chr3B 542162542 542165495 2953 True 1960 3262 90.5225 774 3709 2 chr3B.!!$R3 2935
6 TraesCS3A01G300600 chr3B 52192529 52193304 775 True 1085 1085 91.9020 1 777 1 chr3B.!!$R1 776
7 TraesCS3A01G300600 chr4A 595415873 595416643 770 True 1118 1118 92.8660 2 771 1 chr4A.!!$R1 769
8 TraesCS3A01G300600 chr1B 185228266 185229036 770 True 1118 1118 92.8660 1 770 1 chr1B.!!$R1 769
9 TraesCS3A01G300600 chr5D 367421411 367422170 759 True 1109 1109 93.0260 1 758 1 chr5D.!!$R1 757
10 TraesCS3A01G300600 chr7A 82125949 82126719 770 True 1103 1103 92.4870 1 771 1 chr7A.!!$R1 770
11 TraesCS3A01G300600 chr6B 132110955 132111723 768 False 1099 1099 92.4680 1 769 1 chr6B.!!$F1 768
12 TraesCS3A01G300600 chr7B 21255681 21256449 768 False 1083 1083 92.0780 1 769 1 chr7B.!!$F1 768
13 TraesCS3A01G300600 chr7D 6136901 6142232 5331 True 472 745 91.2942 917 4504 5 chr7D.!!$R1 3587
14 TraesCS3A01G300600 chr5A 54731008 54731625 617 True 643 643 85.5180 1322 1969 1 chr5A.!!$R1 647

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
935 941 0.615850 CTTCCTTCTTTCCTCCGCCT 59.384 55.0 0.0 0.0 0.00 5.52 F
1229 1269 0.103876 AGGAAGAAGGTTCTGGGGGT 60.104 55.0 0.0 0.0 37.65 4.95 F
2138 2189 0.615850 GTTCCTCAAGAGACAGGGGG 59.384 60.0 0.0 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2754 2870 0.034059 CTCCGAGCAACTGAACCACT 59.966 55.0 0.0 0.0 0.00 4.00 R
3031 3149 2.229784 GCCAACAGATGTCCTCAAAAGG 59.770 50.0 0.0 0.0 44.89 3.11 R
3864 4122 0.108138 GTGACACCTCTGAATCCGGG 60.108 60.0 0.0 0.0 0.00 5.73 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
60 61 2.827921 GTTAGGGTTGAGGGAGACGTTA 59.172 50.000 0.00 0.00 0.00 3.18
71 72 2.202531 GACGTTACCGAGGCCGTC 60.203 66.667 11.74 11.74 42.22 4.79
160 161 1.304962 TAGGAGCCAGCGGAGTTGA 60.305 57.895 0.00 0.00 42.98 3.18
282 284 3.459969 AGACCCTTCTTCTTCCTTGTTGT 59.540 43.478 0.00 0.00 0.00 3.32
308 310 1.683943 TTGCTGCTGCTGTTCTTCTT 58.316 45.000 17.00 0.00 40.48 2.52
312 314 2.292845 GCTGCTGCTGTTCTTCTTCTTT 59.707 45.455 8.53 0.00 36.03 2.52
315 317 4.960938 TGCTGCTGTTCTTCTTCTTTCTA 58.039 39.130 0.00 0.00 0.00 2.10
317 319 6.000219 TGCTGCTGTTCTTCTTCTTTCTATT 59.000 36.000 0.00 0.00 0.00 1.73
403 405 3.082548 TCGGATGACTCGAGTTCTCTTT 58.917 45.455 21.08 1.11 32.51 2.52
496 498 2.180946 TGTCCATGCCCTCTCAGTAT 57.819 50.000 0.00 0.00 0.00 2.12
499 501 2.435805 GTCCATGCCCTCTCAGTATTGA 59.564 50.000 0.00 0.00 0.00 2.57
517 519 7.391554 CAGTATTGATGTCAAGAAAGGAGGAAA 59.608 37.037 1.65 0.00 39.47 3.13
518 520 8.112183 AGTATTGATGTCAAGAAAGGAGGAAAT 58.888 33.333 1.65 0.00 39.47 2.17
634 636 0.977627 ATGATGACACAGGGCTCCGA 60.978 55.000 0.00 0.00 0.00 4.55
681 683 9.895138 TGTTTTAGGGTATTCTAGGTGTTTATC 57.105 33.333 0.00 0.00 0.00 1.75
750 752 8.251026 ACTCTGTACTGATTCGTGATTTGAATA 58.749 33.333 2.62 0.00 36.24 1.75
880 882 4.973055 CCAACGGTCGGTTCGGCA 62.973 66.667 0.00 0.00 36.49 5.69
924 930 7.388638 TCGAAATAAATATCCCCTTCCTTCT 57.611 36.000 0.00 0.00 0.00 2.85
935 941 0.615850 CTTCCTTCTTTCCTCCGCCT 59.384 55.000 0.00 0.00 0.00 5.52
974 1001 1.521681 CCCTTTCCCGATCAGTCGC 60.522 63.158 0.00 0.00 46.32 5.19
1007 1035 3.202001 CGCCGCCGACATGGATTT 61.202 61.111 0.00 0.00 42.00 2.17
1086 1120 3.815401 TCTTTGTCTGCTGCTTCCTTAAC 59.185 43.478 0.00 0.00 0.00 2.01
1087 1121 2.928801 TGTCTGCTGCTTCCTTAACA 57.071 45.000 0.00 0.00 0.00 2.41
1229 1269 0.103876 AGGAAGAAGGTTCTGGGGGT 60.104 55.000 0.00 0.00 37.65 4.95
1545 1588 3.878519 GCCGACGACGAGGAGGAG 61.879 72.222 9.28 0.00 42.66 3.69
1623 1666 3.393970 TCCTCGGCCTGCCTCTTG 61.394 66.667 6.60 0.00 0.00 3.02
1681 1732 3.192844 TGCTACTACTTCAGAAGAACCCG 59.807 47.826 17.56 3.60 0.00 5.28
1698 1749 1.425412 CCGTCAGTTTCGTCGGATTT 58.575 50.000 0.00 0.00 44.86 2.17
1712 1763 3.251004 GTCGGATTTAATGGGAGCATGTC 59.749 47.826 0.00 0.00 0.00 3.06
1959 2010 4.946157 AGCGAGATTTTGGATGTTCTGAAT 59.054 37.500 0.00 0.00 0.00 2.57
2027 2078 3.370366 CCACTCGAGAATGCTGAAGAAAG 59.630 47.826 21.68 0.00 0.00 2.62
2028 2079 2.999355 ACTCGAGAATGCTGAAGAAAGC 59.001 45.455 21.68 0.00 43.82 3.51
2046 2097 3.407424 AGCAGTGAAGTTGTATGCTCA 57.593 42.857 0.00 0.00 43.46 4.26
2063 2114 2.309136 TCAGGTGGAGATGTCACTGA 57.691 50.000 6.94 6.94 35.61 3.41
2095 2146 1.134521 GTTCCACCCACAGCGATGATA 60.135 52.381 8.12 0.00 0.00 2.15
2104 2155 3.056322 CCACAGCGATGATATGGATGAGA 60.056 47.826 8.12 0.00 31.69 3.27
2138 2189 0.615850 GTTCCTCAAGAGACAGGGGG 59.384 60.000 0.00 0.00 0.00 5.40
2145 2196 2.191400 CAAGAGACAGGGGGAGATGAA 58.809 52.381 0.00 0.00 0.00 2.57
2149 2200 2.774234 GAGACAGGGGGAGATGAATCAA 59.226 50.000 0.00 0.00 0.00 2.57
2154 2205 4.088634 CAGGGGGAGATGAATCAAAACAA 58.911 43.478 0.00 0.00 0.00 2.83
2168 2219 3.387374 TCAAAACAATCCATGCCACAGTT 59.613 39.130 0.00 0.00 0.00 3.16
2237 2288 5.710099 TGAGTGATGATAAGGGTTTGGAAAC 59.290 40.000 0.00 0.00 38.17 2.78
2247 2298 2.623416 GGGTTTGGAAACTGAGAGGTTG 59.377 50.000 2.44 0.00 38.89 3.77
2289 2340 1.656587 TGGGGTATGAGAACACAGCT 58.343 50.000 0.00 0.00 0.00 4.24
2294 2345 3.265791 GGTATGAGAACACAGCTGAAGG 58.734 50.000 23.35 11.87 0.00 3.46
2582 2633 2.119655 CATCTGCCTGCTTGGAGCC 61.120 63.158 0.49 0.00 41.51 4.70
2587 2638 2.370445 GCCTGCTTGGAGCCTCCTA 61.370 63.158 12.94 3.09 41.51 2.94
2642 2693 2.821378 TGTGCCTCAATGTTCCATCAAG 59.179 45.455 0.00 0.00 0.00 3.02
2754 2870 1.421268 ACTGACAGATCAAAGCCACCA 59.579 47.619 10.08 0.00 33.30 4.17
2982 3100 3.253188 TCTTTTCCAGACATCTTTTGGCG 59.747 43.478 0.00 0.00 38.94 5.69
3031 3149 4.328440 GTGCGTCATATGAGATTATCCTGC 59.672 45.833 5.42 2.19 0.00 4.85
3073 3237 5.105392 TGGCATTGCATTTTAGTTCCTTAGG 60.105 40.000 11.39 0.00 0.00 2.69
3158 3341 8.355913 AGACAGGTACACAAAAGTAGTTACTAC 58.644 37.037 14.13 14.13 37.23 2.73
3333 3556 3.524095 TCATTACCATTATGCCCCAGG 57.476 47.619 0.00 0.00 0.00 4.45
3461 3708 1.065928 GGATGCTACACCGACTCCG 59.934 63.158 0.00 0.00 0.00 4.63
3463 3710 2.005960 GATGCTACACCGACTCCGCT 62.006 60.000 0.00 0.00 0.00 5.52
3539 3788 0.109179 TGCATTTTGCTGATGTCGGC 60.109 50.000 6.87 6.87 45.31 5.54
3571 3820 1.841103 TGTGGTGCTGGGAGCTGTA 60.841 57.895 0.00 0.00 42.97 2.74
3581 3830 1.007118 TGGGAGCTGTAGGAGACATCA 59.993 52.381 0.00 0.00 37.45 3.07
3628 3878 4.848357 AGATTTGGTGCTGTAGCTGTAAT 58.152 39.130 5.38 0.67 42.66 1.89
3723 3978 5.972107 ATTGTACTGTACTCGTTACCTGT 57.028 39.130 17.98 0.00 0.00 4.00
3730 3985 3.758554 TGTACTCGTTACCTGTCCCTAAC 59.241 47.826 0.00 0.00 0.00 2.34
3737 3992 1.426751 ACCTGTCCCTAACGGTGAAA 58.573 50.000 0.00 0.00 34.75 2.69
3743 3998 2.036862 GTCCCTAACGGTGAAACAGAGT 59.963 50.000 0.00 0.00 39.98 3.24
3744 3999 2.036733 TCCCTAACGGTGAAACAGAGTG 59.963 50.000 0.00 0.00 39.98 3.51
3745 4000 2.413837 CCTAACGGTGAAACAGAGTGG 58.586 52.381 0.00 0.00 39.98 4.00
3746 4001 2.224209 CCTAACGGTGAAACAGAGTGGT 60.224 50.000 0.00 0.00 39.98 4.16
3747 4002 2.413310 AACGGTGAAACAGAGTGGTT 57.587 45.000 0.00 0.00 39.98 3.67
3748 4003 2.413310 ACGGTGAAACAGAGTGGTTT 57.587 45.000 0.00 0.00 43.30 3.27
3749 4004 2.718563 ACGGTGAAACAGAGTGGTTTT 58.281 42.857 0.00 0.00 40.85 2.43
3750 4005 3.086282 ACGGTGAAACAGAGTGGTTTTT 58.914 40.909 0.00 0.00 40.85 1.94
3751 4006 3.128068 ACGGTGAAACAGAGTGGTTTTTC 59.872 43.478 0.00 0.00 40.85 2.29
3752 4007 3.377172 CGGTGAAACAGAGTGGTTTTTCT 59.623 43.478 0.00 0.00 40.85 2.52
3753 4008 4.142469 CGGTGAAACAGAGTGGTTTTTCTT 60.142 41.667 0.00 0.00 40.85 2.52
3754 4009 5.621329 CGGTGAAACAGAGTGGTTTTTCTTT 60.621 40.000 0.00 0.00 40.85 2.52
3755 4010 6.163476 GGTGAAACAGAGTGGTTTTTCTTTT 58.837 36.000 0.00 0.00 40.85 2.27
3756 4011 6.090763 GGTGAAACAGAGTGGTTTTTCTTTTG 59.909 38.462 0.00 0.00 40.85 2.44
3757 4012 6.645003 GTGAAACAGAGTGGTTTTTCTTTTGT 59.355 34.615 0.00 0.00 40.85 2.83
3758 4013 7.170828 GTGAAACAGAGTGGTTTTTCTTTTGTT 59.829 33.333 0.00 0.00 40.85 2.83
3759 4014 7.170658 TGAAACAGAGTGGTTTTTCTTTTGTTG 59.829 33.333 0.00 0.00 40.85 3.33
3760 4015 6.339587 ACAGAGTGGTTTTTCTTTTGTTGA 57.660 33.333 0.00 0.00 0.00 3.18
3761 4016 6.156519 ACAGAGTGGTTTTTCTTTTGTTGAC 58.843 36.000 0.00 0.00 0.00 3.18
3762 4017 6.155827 CAGAGTGGTTTTTCTTTTGTTGACA 58.844 36.000 0.00 0.00 0.00 3.58
3763 4018 6.813152 CAGAGTGGTTTTTCTTTTGTTGACAT 59.187 34.615 0.00 0.00 0.00 3.06
3764 4019 6.813152 AGAGTGGTTTTTCTTTTGTTGACATG 59.187 34.615 0.00 0.00 0.00 3.21
3768 4023 6.070767 TGGTTTTTCTTTTGTTGACATGGGTA 60.071 34.615 0.00 0.00 0.00 3.69
3771 4026 8.722394 GTTTTTCTTTTGTTGACATGGGTAAAA 58.278 29.630 0.00 0.00 0.00 1.52
3781 4036 5.630121 TGACATGGGTAAAACAGAGATTGT 58.370 37.500 0.00 0.00 43.45 2.71
3794 4049 3.696051 CAGAGATTGTTGGTGGTATTGGG 59.304 47.826 0.00 0.00 0.00 4.12
3795 4050 2.427095 GAGATTGTTGGTGGTATTGGGC 59.573 50.000 0.00 0.00 0.00 5.36
3796 4051 2.175202 GATTGTTGGTGGTATTGGGCA 58.825 47.619 0.00 0.00 0.00 5.36
3798 4053 1.626686 TGTTGGTGGTATTGGGCAAG 58.373 50.000 0.00 0.00 0.00 4.01
3799 4054 1.133325 TGTTGGTGGTATTGGGCAAGT 60.133 47.619 0.00 0.00 0.00 3.16
3801 4056 3.158676 GTTGGTGGTATTGGGCAAGTTA 58.841 45.455 0.00 0.00 0.00 2.24
3802 4057 3.527507 TGGTGGTATTGGGCAAGTTAA 57.472 42.857 0.00 0.00 0.00 2.01
3803 4058 4.054359 TGGTGGTATTGGGCAAGTTAAT 57.946 40.909 0.00 0.00 0.00 1.40
3804 4059 4.020543 TGGTGGTATTGGGCAAGTTAATC 58.979 43.478 0.00 0.00 0.00 1.75
3807 4062 4.947388 GTGGTATTGGGCAAGTTAATCTCA 59.053 41.667 0.00 0.00 0.00 3.27
3808 4063 4.947388 TGGTATTGGGCAAGTTAATCTCAC 59.053 41.667 0.00 0.00 0.00 3.51
3809 4064 4.338400 GGTATTGGGCAAGTTAATCTCACC 59.662 45.833 0.00 0.00 0.00 4.02
3811 4066 1.707989 TGGGCAAGTTAATCTCACCCA 59.292 47.619 0.00 0.00 44.10 4.51
3813 4068 2.290960 GGGCAAGTTAATCTCACCCACT 60.291 50.000 0.00 0.00 39.57 4.00
3816 4071 4.081087 GGCAAGTTAATCTCACCCACTCTA 60.081 45.833 0.00 0.00 0.00 2.43
3818 4073 5.755861 GCAAGTTAATCTCACCCACTCTATC 59.244 44.000 0.00 0.00 0.00 2.08
3819 4074 5.776173 AGTTAATCTCACCCACTCTATCG 57.224 43.478 0.00 0.00 0.00 2.92
3820 4075 5.446860 AGTTAATCTCACCCACTCTATCGA 58.553 41.667 0.00 0.00 0.00 3.59
3821 4076 5.892119 AGTTAATCTCACCCACTCTATCGAA 59.108 40.000 0.00 0.00 0.00 3.71
3822 4077 6.551601 AGTTAATCTCACCCACTCTATCGAAT 59.448 38.462 0.00 0.00 0.00 3.34
3823 4078 5.878406 AATCTCACCCACTCTATCGAATT 57.122 39.130 0.00 0.00 0.00 2.17
3826 4084 5.446860 TCTCACCCACTCTATCGAATTAGT 58.553 41.667 0.00 0.00 0.00 2.24
3830 4088 6.323996 TCACCCACTCTATCGAATTAGTCATT 59.676 38.462 0.00 0.00 0.00 2.57
3831 4089 7.504574 TCACCCACTCTATCGAATTAGTCATTA 59.495 37.037 0.00 0.00 0.00 1.90
3843 4101 9.481340 TCGAATTAGTCATTATTCTCCTGATTG 57.519 33.333 0.00 0.00 0.00 2.67
3844 4102 9.481340 CGAATTAGTCATTATTCTCCTGATTGA 57.519 33.333 0.00 0.00 0.00 2.57
3857 4115 9.727859 ATTCTCCTGATTGATCTCTGAATTATG 57.272 33.333 0.00 0.00 0.00 1.90
3858 4116 8.260099 TCTCCTGATTGATCTCTGAATTATGT 57.740 34.615 0.00 0.00 0.00 2.29
3860 4118 8.672823 TCCTGATTGATCTCTGAATTATGTTG 57.327 34.615 0.00 0.00 0.00 3.33
3861 4119 7.718314 TCCTGATTGATCTCTGAATTATGTTGG 59.282 37.037 0.00 0.00 0.00 3.77
3862 4120 7.268199 TGATTGATCTCTGAATTATGTTGGC 57.732 36.000 0.00 0.00 0.00 4.52
3863 4121 6.263842 TGATTGATCTCTGAATTATGTTGGCC 59.736 38.462 0.00 0.00 0.00 5.36
3864 4122 4.464008 TGATCTCTGAATTATGTTGGCCC 58.536 43.478 0.00 0.00 0.00 5.80
3865 4123 3.297134 TCTCTGAATTATGTTGGCCCC 57.703 47.619 0.00 0.00 0.00 5.80
3866 4124 2.091885 TCTCTGAATTATGTTGGCCCCC 60.092 50.000 0.00 0.00 0.00 5.40
3867 4125 1.032014 CTGAATTATGTTGGCCCCCG 58.968 55.000 0.00 0.00 0.00 5.73
3872 4130 0.106419 TTATGTTGGCCCCCGGATTC 60.106 55.000 0.73 0.00 0.00 2.52
3873 4131 1.282653 TATGTTGGCCCCCGGATTCA 61.283 55.000 0.73 0.00 0.00 2.57
3874 4132 2.440247 GTTGGCCCCCGGATTCAG 60.440 66.667 0.73 0.00 0.00 3.02
3875 4133 2.612430 TTGGCCCCCGGATTCAGA 60.612 61.111 0.73 0.00 0.00 3.27
3876 4134 2.679342 TTGGCCCCCGGATTCAGAG 61.679 63.158 0.73 0.00 0.00 3.35
3877 4135 3.878667 GGCCCCCGGATTCAGAGG 61.879 72.222 0.73 0.00 0.00 3.69
3878 4136 3.090532 GCCCCCGGATTCAGAGGT 61.091 66.667 0.73 0.00 0.00 3.85
3879 4137 2.911143 CCCCCGGATTCAGAGGTG 59.089 66.667 0.73 0.00 0.00 4.00
3880 4138 1.995626 CCCCCGGATTCAGAGGTGT 60.996 63.158 0.73 0.00 0.00 4.16
3882 4140 1.264749 CCCCGGATTCAGAGGTGTCA 61.265 60.000 0.73 0.00 0.00 3.58
3884 4142 0.608130 CCGGATTCAGAGGTGTCACA 59.392 55.000 5.12 0.00 0.00 3.58
3885 4143 1.001974 CCGGATTCAGAGGTGTCACAA 59.998 52.381 5.12 0.00 0.00 3.33
3886 4144 2.069273 CGGATTCAGAGGTGTCACAAC 58.931 52.381 5.12 0.00 0.00 3.32
3887 4145 2.289072 CGGATTCAGAGGTGTCACAACT 60.289 50.000 0.00 0.00 32.17 3.16
3888 4146 3.744660 GGATTCAGAGGTGTCACAACTT 58.255 45.455 0.00 0.00 28.17 2.66
3890 4148 4.932200 GGATTCAGAGGTGTCACAACTTAG 59.068 45.833 0.00 0.00 28.17 2.18
3891 4149 5.511545 GGATTCAGAGGTGTCACAACTTAGT 60.512 44.000 0.00 0.00 28.17 2.24
3892 4150 4.322080 TCAGAGGTGTCACAACTTAGTG 57.678 45.455 0.00 0.00 40.85 2.74
3893 4151 3.704566 TCAGAGGTGTCACAACTTAGTGT 59.295 43.478 0.00 0.00 40.37 3.55
3894 4152 4.161565 TCAGAGGTGTCACAACTTAGTGTT 59.838 41.667 0.00 0.00 40.37 3.32
3911 5932 8.312564 ACTTAGTGTTGTATTACCTTCCTTCTC 58.687 37.037 0.00 0.00 0.00 2.87
3912 5933 6.051179 AGTGTTGTATTACCTTCCTTCTCC 57.949 41.667 0.00 0.00 0.00 3.71
3919 5940 4.891992 TTACCTTCCTTCTCCAGTTCAG 57.108 45.455 0.00 0.00 0.00 3.02
3922 5943 3.459969 ACCTTCCTTCTCCAGTTCAGTTT 59.540 43.478 0.00 0.00 0.00 2.66
3923 5944 4.068599 CCTTCCTTCTCCAGTTCAGTTTC 58.931 47.826 0.00 0.00 0.00 2.78
3925 5946 5.372373 CTTCCTTCTCCAGTTCAGTTTCTT 58.628 41.667 0.00 0.00 0.00 2.52
3927 5948 6.688073 TCCTTCTCCAGTTCAGTTTCTTAT 57.312 37.500 0.00 0.00 0.00 1.73
3930 5951 8.656806 TCCTTCTCCAGTTCAGTTTCTTATAAA 58.343 33.333 0.00 0.00 0.00 1.40
3931 5952 9.284968 CCTTCTCCAGTTCAGTTTCTTATAAAA 57.715 33.333 0.00 0.00 0.00 1.52
3946 5967 6.408869 TCTTATAAAAGAAAACGATCCCGGT 58.591 36.000 0.00 0.00 38.81 5.28
3950 5971 5.970317 AAAAGAAAACGATCCCGGTAAAT 57.030 34.783 0.00 0.00 40.78 1.40
3958 5979 5.349061 ACGATCCCGGTAAATTTAAGACT 57.651 39.130 0.00 0.00 40.78 3.24
3968 5989 7.388500 CCGGTAAATTTAAGACTCTGGTTAACA 59.612 37.037 8.10 0.00 0.00 2.41
3975 5996 8.842358 TTTAAGACTCTGGTTAACATTACAGG 57.158 34.615 8.10 3.04 0.00 4.00
3978 5999 6.702329 AGACTCTGGTTAACATTACAGGAAG 58.298 40.000 8.10 3.03 0.00 3.46
3979 6000 5.805728 ACTCTGGTTAACATTACAGGAAGG 58.194 41.667 8.10 1.22 0.00 3.46
3980 6001 5.309806 ACTCTGGTTAACATTACAGGAAGGT 59.690 40.000 8.10 1.73 32.12 3.50
3981 6002 6.183361 ACTCTGGTTAACATTACAGGAAGGTT 60.183 38.462 8.10 0.18 44.02 3.50
3982 6003 6.607019 TCTGGTTAACATTACAGGAAGGTTT 58.393 36.000 8.10 0.00 38.91 3.27
3983 6004 7.747690 TCTGGTTAACATTACAGGAAGGTTTA 58.252 34.615 8.10 0.00 38.91 2.01
3984 6005 8.219178 TCTGGTTAACATTACAGGAAGGTTTAA 58.781 33.333 8.10 0.00 38.91 1.52
3986 6007 9.369672 TGGTTAACATTACAGGAAGGTTTAAAT 57.630 29.630 8.10 0.00 38.91 1.40
3992 6013 9.462606 ACATTACAGGAAGGTTTAAATAGAAGG 57.537 33.333 0.00 0.00 0.00 3.46
3993 6014 9.462606 CATTACAGGAAGGTTTAAATAGAAGGT 57.537 33.333 0.00 0.00 0.00 3.50
4036 6057 9.732130 AGATTGGATAGTTTATCAGCCTAAATC 57.268 33.333 0.00 0.00 36.91 2.17
4051 6072 4.320494 GCCTAAATCATAAGCAACCCATCG 60.320 45.833 0.00 0.00 0.00 3.84
4062 6083 1.760479 AACCCATCGACGTGGAACCA 61.760 55.000 3.81 0.00 42.02 3.67
4074 6103 1.059584 TGGAACCAGTGGAAGGCTCA 61.060 55.000 18.40 2.39 0.00 4.26
4076 6105 1.272147 GGAACCAGTGGAAGGCTCATT 60.272 52.381 18.40 0.00 0.00 2.57
4077 6106 2.087646 GAACCAGTGGAAGGCTCATTC 58.912 52.381 18.40 2.41 0.00 2.67
4078 6107 1.067295 ACCAGTGGAAGGCTCATTCA 58.933 50.000 18.40 0.00 0.00 2.57
4079 6108 1.004044 ACCAGTGGAAGGCTCATTCAG 59.996 52.381 18.40 0.00 0.00 3.02
4080 6109 1.004044 CCAGTGGAAGGCTCATTCAGT 59.996 52.381 1.68 0.00 0.00 3.41
4081 6110 2.354259 CAGTGGAAGGCTCATTCAGTC 58.646 52.381 0.00 0.00 0.00 3.51
4082 6111 1.980765 AGTGGAAGGCTCATTCAGTCA 59.019 47.619 0.00 0.00 0.00 3.41
4083 6112 2.575279 AGTGGAAGGCTCATTCAGTCAT 59.425 45.455 0.00 0.00 0.00 3.06
4084 6113 3.009916 AGTGGAAGGCTCATTCAGTCATT 59.990 43.478 0.00 0.00 0.00 2.57
4117 6147 2.798148 ATCCGAAGCGTCCCACCAAC 62.798 60.000 0.00 0.00 0.00 3.77
4145 6175 2.029073 ACAACACCTCGCGTCCAG 59.971 61.111 5.77 0.00 0.00 3.86
4175 6205 0.388659 ATTTGCTTTGCTGCACGGAA 59.611 45.000 0.00 0.99 43.20 4.30
4179 6209 0.936297 GCTTTGCTGCACGGAACTTG 60.936 55.000 0.00 0.00 0.00 3.16
4200 6230 2.568623 ACTACAGAGCCCAAAACCAG 57.431 50.000 0.00 0.00 0.00 4.00
4232 6271 2.813726 GCAACCAAAACCCCCACCC 61.814 63.158 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.613691 GGAGAAACTTATTCCGACGCA 58.386 47.619 0.00 0.00 0.00 5.24
178 179 4.697756 CCAAAGCCCGCGACCTCA 62.698 66.667 8.23 0.00 0.00 3.86
282 284 3.760151 AGAACAGCAGCAGCAAATCATAA 59.240 39.130 3.17 0.00 45.49 1.90
308 310 4.397103 CACCAGCATCAGCAAATAGAAAGA 59.603 41.667 0.00 0.00 45.49 2.52
312 314 2.646930 CCACCAGCATCAGCAAATAGA 58.353 47.619 0.00 0.00 45.49 1.98
315 317 0.040058 TCCCACCAGCATCAGCAAAT 59.960 50.000 0.00 0.00 45.49 2.32
317 319 1.001764 CTCCCACCAGCATCAGCAA 60.002 57.895 0.00 0.00 45.49 3.91
373 375 1.601419 GAGTCATCCGACCGGTCCAA 61.601 60.000 28.52 17.03 43.73 3.53
403 405 0.974383 GAAGTGTCCCTTCCGGAAGA 59.026 55.000 39.78 22.34 44.47 2.87
496 498 6.375455 GCTATTTCCTCCTTTCTTGACATCAA 59.625 38.462 0.00 0.00 0.00 2.57
499 501 4.878397 CGCTATTTCCTCCTTTCTTGACAT 59.122 41.667 0.00 0.00 0.00 3.06
517 519 0.462937 TACAATTGCCGCCACGCTAT 60.463 50.000 5.05 0.00 0.00 2.97
518 520 1.079057 TACAATTGCCGCCACGCTA 60.079 52.632 5.05 0.00 0.00 4.26
634 636 7.823745 AACAACCATAACACAAGAAGATCTT 57.176 32.000 7.95 7.95 37.14 2.40
697 699 5.648092 GTGACCCTTACAAGCATACTGAAAT 59.352 40.000 0.00 0.00 0.00 2.17
705 707 3.182152 AGTAGGTGACCCTTACAAGCAT 58.818 45.455 0.00 0.00 42.66 3.79
771 773 0.811616 CTTGGCTGGATCCTGCGTAC 60.812 60.000 30.38 20.20 40.98 3.67
772 774 1.522092 CTTGGCTGGATCCTGCGTA 59.478 57.895 30.38 21.58 40.98 4.42
852 854 3.989787 CCGTTGGGGCAAGGCAAC 61.990 66.667 0.00 0.00 0.00 4.17
853 855 4.531426 ACCGTTGGGGCAAGGCAA 62.531 61.111 0.00 0.00 40.62 4.52
854 856 4.966787 GACCGTTGGGGCAAGGCA 62.967 66.667 0.00 0.00 42.95 4.75
880 882 2.386661 AATTCGAACCGACTGCATCT 57.613 45.000 0.00 0.00 34.89 2.90
924 930 3.335729 GGGGGAAGGCGGAGGAAA 61.336 66.667 0.00 0.00 0.00 3.13
935 941 0.341609 GGGGAATGGATTTGGGGGAA 59.658 55.000 0.00 0.00 0.00 3.97
998 1026 0.611618 TCGCTTGGGCAAATCCATGT 60.612 50.000 0.00 0.00 36.58 3.21
1007 1035 4.087892 GGAGAGCTCGCTTGGGCA 62.088 66.667 17.35 0.00 38.60 5.36
1086 1120 2.080286 AACAAGAACGGACGGATCTG 57.920 50.000 0.00 0.00 37.24 2.90
1087 1121 2.224209 ACAAACAAGAACGGACGGATCT 60.224 45.455 0.00 0.00 0.00 2.75
1335 1378 0.782384 GCGTGGTGTAGTTCGTCTTG 59.218 55.000 0.00 0.00 0.00 3.02
1362 1405 1.868251 GTCGTAGCGCAGGAAGTCG 60.868 63.158 11.47 3.37 0.00 4.18
1470 1513 2.125912 CCGGAAGACAGCACCTCG 60.126 66.667 0.00 0.00 0.00 4.63
1536 1579 3.775654 GGCACCACCTCCTCCTCG 61.776 72.222 0.00 0.00 34.51 4.63
1599 1642 4.803426 CAGGCCGAGGACACGAGC 62.803 72.222 0.00 0.00 35.09 5.03
1681 1732 4.201783 CCCATTAAATCCGACGAAACTGAC 60.202 45.833 0.00 0.00 0.00 3.51
1698 1749 3.493176 CGACATCAGACATGCTCCCATTA 60.493 47.826 0.00 0.00 0.00 1.90
1712 1763 1.340658 CTCGTGAACACCGACATCAG 58.659 55.000 0.00 0.00 0.00 2.90
1745 1796 1.676006 GTTCATACTGAATTGGCCCCG 59.324 52.381 0.00 0.00 38.79 5.73
1812 1863 3.451894 GGGCCGTGCAAAGGGATG 61.452 66.667 11.00 0.00 35.32 3.51
1959 2010 2.630098 CTCGCCTATCCCAGAATCTTCA 59.370 50.000 0.00 0.00 0.00 3.02
2027 2078 2.417933 CCTGAGCATACAACTTCACTGC 59.582 50.000 0.00 0.00 0.00 4.40
2028 2079 3.434641 CACCTGAGCATACAACTTCACTG 59.565 47.826 0.00 0.00 0.00 3.66
2046 2097 2.614259 ACTTCAGTGACATCTCCACCT 58.386 47.619 0.00 0.00 35.23 4.00
2095 2146 5.643421 AATCCTAGCTTGTTCTCATCCAT 57.357 39.130 0.00 0.00 0.00 3.41
2138 2189 5.751990 GGCATGGATTGTTTTGATTCATCTC 59.248 40.000 0.00 0.00 0.00 2.75
2145 2196 3.579586 ACTGTGGCATGGATTGTTTTGAT 59.420 39.130 0.00 0.00 0.00 2.57
2149 2200 2.037511 CCAACTGTGGCATGGATTGTTT 59.962 45.455 0.00 0.00 38.35 2.83
2168 2219 4.018490 CAGAATTTCATCCATGGTGACCA 58.982 43.478 6.84 6.84 38.19 4.02
2237 2288 4.815533 TCTTCTTGATCCAACCTCTCAG 57.184 45.455 0.00 0.00 0.00 3.35
2247 2298 4.425520 ACGAGTCGAATTCTTCTTGATCC 58.574 43.478 21.50 0.00 0.00 3.36
2289 2340 2.733956 ACAAGTTTCTTGGCACCTTCA 58.266 42.857 12.95 0.00 0.00 3.02
2294 2345 5.163513 CCATATCAACAAGTTTCTTGGCAC 58.836 41.667 12.95 0.00 0.00 5.01
2516 2567 1.466167 CAGGTTGCTCTGAATGGAACG 59.534 52.381 0.00 0.00 36.76 3.95
2642 2693 4.529769 TCTGATCATGATCCCTATGACCAC 59.470 45.833 28.61 4.68 37.38 4.16
2754 2870 0.034059 CTCCGAGCAACTGAACCACT 59.966 55.000 0.00 0.00 0.00 4.00
2816 2932 3.508793 ACCATGCTGAATTGAGTCTTTGG 59.491 43.478 0.00 0.00 0.00 3.28
2956 3074 6.572519 CCAAAAGATGTCTGGAAAAGAAACA 58.427 36.000 0.00 0.00 36.40 2.83
2982 3100 4.796312 ACACTTCGCACACAAAAATACAAC 59.204 37.500 0.00 0.00 0.00 3.32
3031 3149 2.229784 GCCAACAGATGTCCTCAAAAGG 59.770 50.000 0.00 0.00 44.89 3.11
3158 3341 5.066505 GGCCACTAATGTGAATGTTCTAAGG 59.933 44.000 0.00 0.00 46.55 2.69
3164 3347 3.766545 AGTGGCCACTAATGTGAATGTT 58.233 40.909 37.12 8.23 46.55 2.71
3274 3489 5.490213 GCACTGTGCGTAGATGTATTTAAC 58.510 41.667 17.93 0.00 31.71 2.01
3345 3568 5.011023 ACTGTGGGGAATAAAAGCTTGAAAG 59.989 40.000 0.00 0.00 0.00 2.62
3408 3655 1.970640 TGCTCTTGCAGTCTCCTGTTA 59.029 47.619 0.00 0.00 45.31 2.41
3461 3708 2.171489 GACGGTTTGAACGCCTCAGC 62.171 60.000 0.00 0.00 34.81 4.26
3463 3710 0.599204 GAGACGGTTTGAACGCCTCA 60.599 55.000 0.00 0.00 34.00 3.86
3539 3788 1.462283 CACCACACGAAGAATCAGCAG 59.538 52.381 0.00 0.00 0.00 4.24
3540 3789 1.511850 CACCACACGAAGAATCAGCA 58.488 50.000 0.00 0.00 0.00 4.41
3571 3820 4.466726 GGTTACAACTAGGTGATGTCTCCT 59.533 45.833 16.48 8.52 42.06 3.69
3628 3878 6.652062 GCAAGCCTTTTACACTAGTTAACCTA 59.348 38.462 0.88 0.00 0.00 3.08
3644 3897 1.134729 CCAAACACACTGCAAGCCTTT 60.135 47.619 0.00 0.00 37.60 3.11
3723 3978 2.036733 CACTCTGTTTCACCGTTAGGGA 59.963 50.000 0.00 0.00 43.47 4.20
3730 3985 3.377172 AGAAAAACCACTCTGTTTCACCG 59.623 43.478 0.00 0.00 37.46 4.94
3737 3992 6.156519 GTCAACAAAAGAAAAACCACTCTGT 58.843 36.000 0.00 0.00 0.00 3.41
3743 3998 5.181748 CCCATGTCAACAAAAGAAAAACCA 58.818 37.500 0.00 0.00 0.00 3.67
3744 3999 5.182487 ACCCATGTCAACAAAAGAAAAACC 58.818 37.500 0.00 0.00 0.00 3.27
3745 4000 7.835634 TTACCCATGTCAACAAAAGAAAAAC 57.164 32.000 0.00 0.00 0.00 2.43
3746 4001 8.722394 GTTTTACCCATGTCAACAAAAGAAAAA 58.278 29.630 0.00 0.00 0.00 1.94
3747 4002 7.878127 TGTTTTACCCATGTCAACAAAAGAAAA 59.122 29.630 0.00 0.00 29.36 2.29
3748 4003 7.386851 TGTTTTACCCATGTCAACAAAAGAAA 58.613 30.769 0.00 0.00 29.36 2.52
3749 4004 6.936279 TGTTTTACCCATGTCAACAAAAGAA 58.064 32.000 0.00 0.00 29.36 2.52
3750 4005 6.378564 TCTGTTTTACCCATGTCAACAAAAGA 59.621 34.615 0.00 0.00 31.10 2.52
3751 4006 6.568869 TCTGTTTTACCCATGTCAACAAAAG 58.431 36.000 0.00 0.00 31.10 2.27
3752 4007 6.378564 TCTCTGTTTTACCCATGTCAACAAAA 59.621 34.615 0.00 0.00 31.10 2.44
3753 4008 5.888724 TCTCTGTTTTACCCATGTCAACAAA 59.111 36.000 0.00 0.00 31.10 2.83
3754 4009 5.441500 TCTCTGTTTTACCCATGTCAACAA 58.558 37.500 0.00 0.00 31.10 2.83
3755 4010 5.042463 TCTCTGTTTTACCCATGTCAACA 57.958 39.130 0.00 0.00 0.00 3.33
3756 4011 6.016276 ACAATCTCTGTTTTACCCATGTCAAC 60.016 38.462 0.00 0.00 32.99 3.18
3757 4012 6.068010 ACAATCTCTGTTTTACCCATGTCAA 58.932 36.000 0.00 0.00 32.99 3.18
3758 4013 5.630121 ACAATCTCTGTTTTACCCATGTCA 58.370 37.500 0.00 0.00 32.99 3.58
3759 4014 6.381801 CAACAATCTCTGTTTTACCCATGTC 58.618 40.000 0.00 0.00 46.49 3.06
3760 4015 5.243730 CCAACAATCTCTGTTTTACCCATGT 59.756 40.000 0.00 0.00 46.49 3.21
3761 4016 5.243730 ACCAACAATCTCTGTTTTACCCATG 59.756 40.000 0.00 0.00 46.49 3.66
3762 4017 5.243730 CACCAACAATCTCTGTTTTACCCAT 59.756 40.000 0.00 0.00 46.49 4.00
3763 4018 4.582656 CACCAACAATCTCTGTTTTACCCA 59.417 41.667 0.00 0.00 46.49 4.51
3764 4019 4.022329 CCACCAACAATCTCTGTTTTACCC 60.022 45.833 0.00 0.00 46.49 3.69
3768 4023 6.239289 CCAATACCACCAACAATCTCTGTTTT 60.239 38.462 0.00 0.00 46.49 2.43
3771 4026 4.335416 CCAATACCACCAACAATCTCTGT 58.665 43.478 0.00 0.00 41.27 3.41
3781 4036 2.390225 AACTTGCCCAATACCACCAA 57.610 45.000 0.00 0.00 0.00 3.67
3786 4041 4.338400 GGTGAGATTAACTTGCCCAATACC 59.662 45.833 0.00 0.00 0.00 2.73
3787 4042 4.338400 GGGTGAGATTAACTTGCCCAATAC 59.662 45.833 0.00 0.00 40.26 1.89
3788 4043 4.017958 TGGGTGAGATTAACTTGCCCAATA 60.018 41.667 0.00 0.00 43.99 1.90
3789 4044 3.245586 TGGGTGAGATTAACTTGCCCAAT 60.246 43.478 0.00 0.00 43.99 3.16
3790 4045 2.109128 TGGGTGAGATTAACTTGCCCAA 59.891 45.455 0.00 0.00 43.99 4.12
3792 4047 2.092323 GTGGGTGAGATTAACTTGCCC 58.908 52.381 0.00 0.00 40.63 5.36
3794 4049 3.944087 AGAGTGGGTGAGATTAACTTGC 58.056 45.455 0.00 0.00 0.00 4.01
3795 4050 5.980116 CGATAGAGTGGGTGAGATTAACTTG 59.020 44.000 0.00 0.00 39.76 3.16
3796 4051 5.892119 TCGATAGAGTGGGTGAGATTAACTT 59.108 40.000 0.00 0.00 42.67 2.66
3798 4053 5.769484 TCGATAGAGTGGGTGAGATTAAC 57.231 43.478 0.00 0.00 42.67 2.01
3818 4073 9.481340 TCAATCAGGAGAATAATGACTAATTCG 57.519 33.333 0.00 0.00 37.22 3.34
3823 4078 9.599056 AGAGATCAATCAGGAGAATAATGACTA 57.401 33.333 0.00 0.00 0.00 2.59
3826 4084 8.488308 TCAGAGATCAATCAGGAGAATAATGA 57.512 34.615 0.00 0.00 0.00 2.57
3831 4089 9.727859 CATAATTCAGAGATCAATCAGGAGAAT 57.272 33.333 0.00 0.00 0.00 2.40
3843 4101 3.823304 GGGGCCAACATAATTCAGAGATC 59.177 47.826 4.39 0.00 0.00 2.75
3844 4102 3.437052 GGGGGCCAACATAATTCAGAGAT 60.437 47.826 4.39 0.00 0.00 2.75
3848 4106 1.032014 CGGGGGCCAACATAATTCAG 58.968 55.000 4.39 0.00 0.00 3.02
3857 4115 2.440247 CTGAATCCGGGGGCCAAC 60.440 66.667 4.39 0.00 0.00 3.77
3858 4116 2.612430 TCTGAATCCGGGGGCCAA 60.612 61.111 4.39 0.00 0.00 4.52
3860 4118 3.878667 CCTCTGAATCCGGGGGCC 61.879 72.222 0.00 0.00 31.31 5.80
3861 4119 3.090532 ACCTCTGAATCCGGGGGC 61.091 66.667 0.00 0.00 43.48 5.80
3862 4120 1.972660 GACACCTCTGAATCCGGGGG 61.973 65.000 0.00 0.00 45.27 5.40
3863 4121 1.264749 TGACACCTCTGAATCCGGGG 61.265 60.000 0.00 0.00 0.00 5.73
3864 4122 0.108138 GTGACACCTCTGAATCCGGG 60.108 60.000 0.00 0.00 0.00 5.73
3865 4123 0.608130 TGTGACACCTCTGAATCCGG 59.392 55.000 2.45 0.00 0.00 5.14
3866 4124 2.069273 GTTGTGACACCTCTGAATCCG 58.931 52.381 2.45 0.00 0.00 4.18
3867 4125 3.409026 AGTTGTGACACCTCTGAATCC 57.591 47.619 2.45 0.00 0.00 3.01
3872 4130 4.060038 ACACTAAGTTGTGACACCTCTG 57.940 45.455 2.45 0.00 40.12 3.35
3873 4131 4.755266 AACACTAAGTTGTGACACCTCT 57.245 40.909 2.45 0.00 39.49 3.69
3884 4142 8.657712 AGAAGGAAGGTAATACAACACTAAGTT 58.342 33.333 0.00 0.00 42.42 2.66
3885 4143 8.203681 AGAAGGAAGGTAATACAACACTAAGT 57.796 34.615 0.00 0.00 0.00 2.24
3886 4144 7.764901 GGAGAAGGAAGGTAATACAACACTAAG 59.235 40.741 0.00 0.00 0.00 2.18
3887 4145 7.236019 TGGAGAAGGAAGGTAATACAACACTAA 59.764 37.037 0.00 0.00 0.00 2.24
3888 4146 6.727231 TGGAGAAGGAAGGTAATACAACACTA 59.273 38.462 0.00 0.00 0.00 2.74
3890 4148 5.801380 TGGAGAAGGAAGGTAATACAACAC 58.199 41.667 0.00 0.00 0.00 3.32
3891 4149 5.546499 ACTGGAGAAGGAAGGTAATACAACA 59.454 40.000 0.00 0.00 0.00 3.33
3892 4150 6.051179 ACTGGAGAAGGAAGGTAATACAAC 57.949 41.667 0.00 0.00 0.00 3.32
3893 4151 6.271391 TGAACTGGAGAAGGAAGGTAATACAA 59.729 38.462 0.00 0.00 0.00 2.41
3894 4152 5.783360 TGAACTGGAGAAGGAAGGTAATACA 59.217 40.000 0.00 0.00 0.00 2.29
3895 4153 6.070710 ACTGAACTGGAGAAGGAAGGTAATAC 60.071 42.308 0.00 0.00 0.00 1.89
3896 4154 6.023603 ACTGAACTGGAGAAGGAAGGTAATA 58.976 40.000 0.00 0.00 0.00 0.98
3897 4155 4.846940 ACTGAACTGGAGAAGGAAGGTAAT 59.153 41.667 0.00 0.00 0.00 1.89
3901 5922 3.778954 AACTGAACTGGAGAAGGAAGG 57.221 47.619 0.00 0.00 0.00 3.46
3922 5943 6.408869 ACCGGGATCGTTTTCTTTTATAAGA 58.591 36.000 6.32 0.00 35.13 2.10
3923 5944 6.673154 ACCGGGATCGTTTTCTTTTATAAG 57.327 37.500 6.32 0.00 33.95 1.73
3925 5946 8.735692 ATTTACCGGGATCGTTTTCTTTTATA 57.264 30.769 6.32 0.00 33.95 0.98
3927 5948 7.451501 AATTTACCGGGATCGTTTTCTTTTA 57.548 32.000 6.32 0.00 33.95 1.52
3930 5951 5.970317 AAATTTACCGGGATCGTTTTCTT 57.030 34.783 6.32 0.00 33.95 2.52
3931 5952 6.880529 TCTTAAATTTACCGGGATCGTTTTCT 59.119 34.615 6.32 0.00 33.95 2.52
3932 5953 6.963242 GTCTTAAATTTACCGGGATCGTTTTC 59.037 38.462 6.32 0.00 33.95 2.29
3933 5954 6.656270 AGTCTTAAATTTACCGGGATCGTTTT 59.344 34.615 6.32 0.45 33.95 2.43
3934 5955 6.175471 AGTCTTAAATTTACCGGGATCGTTT 58.825 36.000 6.32 1.30 33.95 3.60
3935 5956 5.737860 AGTCTTAAATTTACCGGGATCGTT 58.262 37.500 6.32 0.00 33.95 3.85
3936 5957 5.128335 AGAGTCTTAAATTTACCGGGATCGT 59.872 40.000 6.32 0.00 33.95 3.73
3937 5958 5.462398 CAGAGTCTTAAATTTACCGGGATCG 59.538 44.000 6.32 0.00 0.00 3.69
3938 5959 5.758784 CCAGAGTCTTAAATTTACCGGGATC 59.241 44.000 6.32 0.00 0.00 3.36
3939 5960 5.191124 ACCAGAGTCTTAAATTTACCGGGAT 59.809 40.000 6.32 0.00 0.00 3.85
3940 5961 4.533311 ACCAGAGTCTTAAATTTACCGGGA 59.467 41.667 6.32 0.00 0.00 5.14
3943 5964 8.314143 TGTTAACCAGAGTCTTAAATTTACCG 57.686 34.615 2.48 0.00 0.00 4.02
3950 5971 8.653191 TCCTGTAATGTTAACCAGAGTCTTAAA 58.347 33.333 10.18 0.00 0.00 1.52
3958 5979 5.836024 ACCTTCCTGTAATGTTAACCAGA 57.164 39.130 10.18 0.00 0.00 3.86
3971 5992 7.523415 TGAACCTTCTATTTAAACCTTCCTGT 58.477 34.615 0.00 0.00 0.00 4.00
3972 5993 7.996098 TGAACCTTCTATTTAAACCTTCCTG 57.004 36.000 0.00 0.00 0.00 3.86
3973 5994 9.601810 ATTTGAACCTTCTATTTAAACCTTCCT 57.398 29.630 0.00 0.00 0.00 3.36
3986 6007 9.627123 TCTTTTCTCAGAAATTTGAACCTTCTA 57.373 29.630 0.00 0.00 0.00 2.10
3988 6009 9.755804 AATCTTTTCTCAGAAATTTGAACCTTC 57.244 29.630 0.00 0.00 0.00 3.46
3990 6011 8.146412 CCAATCTTTTCTCAGAAATTTGAACCT 58.854 33.333 14.87 0.00 0.00 3.50
3992 6013 9.702494 ATCCAATCTTTTCTCAGAAATTTGAAC 57.298 29.630 14.87 0.00 0.00 3.18
4036 6057 1.327460 CACGTCGATGGGTTGCTTATG 59.673 52.381 9.90 0.00 0.00 1.90
4051 6072 0.602905 CCTTCCACTGGTTCCACGTC 60.603 60.000 0.00 0.00 0.00 4.34
4062 6083 1.980765 TGACTGAATGAGCCTTCCACT 59.019 47.619 0.00 0.00 0.00 4.00
4074 6103 3.094572 CCCTTCTGCCAAATGACTGAAT 58.905 45.455 0.00 0.00 0.00 2.57
4076 6105 1.704628 TCCCTTCTGCCAAATGACTGA 59.295 47.619 0.00 0.00 0.00 3.41
4077 6106 2.205022 TCCCTTCTGCCAAATGACTG 57.795 50.000 0.00 0.00 0.00 3.51
4078 6107 2.978156 TTCCCTTCTGCCAAATGACT 57.022 45.000 0.00 0.00 0.00 3.41
4079 6108 3.118992 GGATTTCCCTTCTGCCAAATGAC 60.119 47.826 0.00 0.00 0.00 3.06
4080 6109 3.099141 GGATTTCCCTTCTGCCAAATGA 58.901 45.455 0.00 0.00 0.00 2.57
4081 6110 2.159198 CGGATTTCCCTTCTGCCAAATG 60.159 50.000 0.00 0.00 0.00 2.32
4082 6111 2.102578 CGGATTTCCCTTCTGCCAAAT 58.897 47.619 0.00 0.00 0.00 2.32
4083 6112 1.074727 TCGGATTTCCCTTCTGCCAAA 59.925 47.619 0.00 0.00 0.00 3.28
4084 6113 0.695924 TCGGATTTCCCTTCTGCCAA 59.304 50.000 0.00 0.00 0.00 4.52
4162 6192 1.098869 TTCAAGTTCCGTGCAGCAAA 58.901 45.000 0.00 0.00 0.00 3.68
4175 6205 3.857157 TTTGGGCTCTGTAGTTCAAGT 57.143 42.857 0.00 0.00 0.00 3.16
4179 6209 2.814336 CTGGTTTTGGGCTCTGTAGTTC 59.186 50.000 0.00 0.00 0.00 3.01
4259 6298 4.598894 CCTCCGCGAGCTCCATGG 62.599 72.222 8.23 4.97 0.00 3.66
4353 6407 0.560688 GGATGGAGAGAGGGGAGACT 59.439 60.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.