Multiple sequence alignment - TraesCS1A01G144500

Loading Multiple Alignment...

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 TraesCS1A01G144500 chr1A 100.000 3406 0 0 474 3879 250444948 250441543 0.000000e+00 6290.0
1 TraesCS1A01G144500 chr1A 100.000 259 0 0 1 259 250445421 250445163 2.710000e-131 479.0
2 TraesCS1A01G144500 chr1D 96.097 2024 60 9 808 2827 199278357 199276349 0.000000e+00 3282.0
3 TraesCS1A01G144500 chr1D 93.796 274 14 2 477 750 199278628 199278358 3.610000e-110 409.0
4 TraesCS1A01G144500 chr1D 91.892 259 17 2 1 259 199279232 199278978 3.680000e-95 359.0
5 TraesCS1A01G144500 chr1D 87.789 303 35 2 3271 3573 199261470 199261170 1.710000e-93 353.0
6 TraesCS1A01G144500 chr1D 90.610 213 12 6 2962 3174 199276355 199276151 3.820000e-70 276.0
7 TraesCS1A01G144500 chr1D 94.068 118 7 0 2822 2939 394059793 394059676 3.080000e-41 180.0
8 TraesCS1A01G144500 chr1D 88.489 139 14 2 2822 2959 42025861 42025724 2.400000e-37 167.0
9 TraesCS1A01G144500 chr1B 96.674 1864 51 4 969 2827 279495800 279493943 0.000000e+00 3088.0
10 TraesCS1A01G144500 chr1B 88.559 673 72 4 3211 3879 279492655 279491984 0.000000e+00 811.0
11 TraesCS1A01G144500 chr1B 93.939 132 5 3 2962 3092 279493949 279493820 3.060000e-46 196.0
12 TraesCS1A01G144500 chr1B 93.277 119 7 1 2822 2939 614499131 614499013 1.430000e-39 174.0
13 TraesCS1A01G144500 chr1B 85.235 149 17 4 505 649 279501686 279501539 8.680000e-32 148.0
14 TraesCS1A01G144500 chr1B 97.500 40 1 0 925 964 279501196 279501157 6.950000e-08 69.4
15 TraesCS1A01G144500 chr3B 92.330 691 44 6 1050 1740 104270397 104271078 0.000000e+00 974.0
16 TraesCS1A01G144500 chr3B 72.454 1031 229 46 1627 2640 10963250 10962258 2.950000e-71 279.0
17 TraesCS1A01G144500 chr3B 73.834 386 87 13 2273 2651 10922967 10923345 1.450000e-29 141.0
18 TraesCS1A01G144500 chr5A 94.359 195 11 0 1050 1244 489667470 489667276 2.270000e-77 300.0
19 TraesCS1A01G144500 chr3A 71.778 1226 279 51 1438 2640 11948700 11947519 6.340000e-73 285.0
20 TraesCS1A01G144500 chr3A 75.397 378 79 13 2276 2645 11957824 11957453 1.850000e-38 171.0
21 TraesCS1A01G144500 chr3D 77.807 383 73 11 2264 2640 8936712 8937088 3.900000e-55 226.0
22 TraesCS1A01G144500 chr3D 75.248 404 85 14 2273 2668 8913062 8913458 1.110000e-40 178.0
23 TraesCS1A01G144500 chr3D 94.068 118 6 1 2822 2938 34726317 34726434 1.110000e-40 178.0
24 TraesCS1A01G144500 chr3D 75.405 370 81 9 2276 2640 8928284 8928648 1.850000e-38 171.0
25 TraesCS1A01G144500 chr2A 79.734 301 53 6 3192 3487 52767480 52767777 1.090000e-50 211.0
26 TraesCS1A01G144500 chr4D 70.855 1146 272 48 1451 2565 474942381 474943495 3.930000e-50 209.0
27 TraesCS1A01G144500 chr2B 79.932 294 50 7 3213 3499 80259399 80259690 1.410000e-49 207.0
28 TraesCS1A01G144500 chr2B 88.028 142 13 3 2821 2959 548390 548530 8.620000e-37 165.0
29 TraesCS1A01G144500 chr4A 94.017 117 7 0 2823 2939 618681325 618681209 1.110000e-40 178.0
30 TraesCS1A01G144500 chr4A 74.587 303 67 7 1451 1743 681119421 681119119 1.460000e-24 124.0
31 TraesCS1A01G144500 chr7D 93.220 118 7 1 2822 2938 58772380 58772263 5.150000e-39 172.0
32 TraesCS1A01G144500 chr6B 93.162 117 8 0 2823 2939 647831742 647831626 5.150000e-39 172.0
33 TraesCS1A01G144500 chr6A 92.437 119 8 1 2822 2939 103248227 103248345 6.670000e-38 169.0
34 TraesCS1A01G144500 chr4B 74.503 302 68 6 1451 1743 599331388 599331087 5.260000e-24 122.0


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 TraesCS1A01G144500 chr1A 250441543 250445421 3878 True 3384.5 6290 100.000000 1 3879 2 chr1A.!!$R1 3878
1 TraesCS1A01G144500 chr1D 199276151 199279232 3081 True 1081.5 3282 93.098750 1 3174 4 chr1D.!!$R4 3173
2 TraesCS1A01G144500 chr1B 279491984 279495800 3816 True 1365.0 3088 93.057333 969 3879 3 chr1B.!!$R2 2910
3 TraesCS1A01G144500 chr3B 104270397 104271078 681 False 974.0 974 92.330000 1050 1740 1 chr3B.!!$F2 690
4 TraesCS1A01G144500 chr3B 10962258 10963250 992 True 279.0 279 72.454000 1627 2640 1 chr3B.!!$R1 1013
5 TraesCS1A01G144500 chr3A 11947519 11948700 1181 True 285.0 285 71.778000 1438 2640 1 chr3A.!!$R1 1202
6 TraesCS1A01G144500 chr4D 474942381 474943495 1114 False 209.0 209 70.855000 1451 2565 1 chr4D.!!$F1 1114

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
964 1097 0.030369 GCGTATGTCACCTAGGGTCG 59.97 60.0 14.81 7.74 31.02 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2955 3133 1.134175 CGTGCTCAAACAAAGTTGGGT 59.866 47.619 0.0 0.0 31.14 4.51 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
20 21 1.678627 CTGACCTACACAGATCGAGGG 59.321 57.143 0.00 0.00 37.54 4.30
124 125 2.345760 GGCGGTTCGACAGACCCTA 61.346 63.158 0.00 0.00 33.63 3.53
152 153 1.078497 TCAAACCGCTGCCATCGAT 60.078 52.632 0.00 0.00 0.00 3.59
217 218 4.899239 CACGGAGATCCAGCGGCC 62.899 72.222 0.00 0.00 35.14 6.13
221 222 2.512515 GAGATCCAGCGGCCACAC 60.513 66.667 2.24 0.00 0.00 3.82
226 227 4.641645 CCAGCGGCCACACCTTCA 62.642 66.667 2.24 0.00 35.61 3.02
239 240 4.148825 CTTCACCCGGGGAGCGAG 62.149 72.222 27.92 13.68 0.00 5.03
254 255 1.353804 CGAGCGAGTAGTCAGCCTC 59.646 63.158 9.73 5.63 0.00 4.70
620 753 4.401202 TGAAGCACGGTCTACAAGATATCA 59.599 41.667 5.32 0.00 0.00 2.15
630 763 7.040062 CGGTCTACAAGATATCAGATTCTCCTT 60.040 40.741 5.32 0.00 0.00 3.36
670 803 7.148239 GGAAAGAGATGATAATTCGTTTGGTGT 60.148 37.037 0.00 0.00 0.00 4.16
694 827 3.818773 CGGTTTATGTGGTTTCCTTGTCT 59.181 43.478 0.00 0.00 0.00 3.41
699 832 6.928348 TTATGTGGTTTCCTTGTCTAGAGA 57.072 37.500 0.00 0.00 0.00 3.10
701 834 4.223953 TGTGGTTTCCTTGTCTAGAGAGT 58.776 43.478 0.00 0.00 0.00 3.24
705 838 4.767928 GGTTTCCTTGTCTAGAGAGTGAGA 59.232 45.833 0.00 0.00 0.00 3.27
711 844 3.455849 TGTCTAGAGAGTGAGAGGGAGA 58.544 50.000 0.00 0.00 0.00 3.71
712 845 3.454447 TGTCTAGAGAGTGAGAGGGAGAG 59.546 52.174 0.00 0.00 0.00 3.20
720 853 0.251386 TGAGAGGGAGAGAAGTGCGT 60.251 55.000 0.00 0.00 0.00 5.24
728 861 0.247736 AGAGAAGTGCGTGGCCTTAG 59.752 55.000 3.32 0.00 0.00 2.18
732 865 2.038033 AGAAGTGCGTGGCCTTAGTTTA 59.962 45.455 3.32 0.00 0.00 2.01
743 876 2.574824 GCCTTAGTTTAGGGAGGAACCA 59.425 50.000 0.00 0.00 41.20 3.67
750 883 4.288887 AGTTTAGGGAGGAACCAGTTAAGG 59.711 45.833 0.00 0.00 41.20 2.69
751 884 2.435203 AGGGAGGAACCAGTTAAGGT 57.565 50.000 0.00 0.00 45.91 3.50
752 885 1.985895 AGGGAGGAACCAGTTAAGGTG 59.014 52.381 0.00 0.00 42.25 4.00
753 886 1.703513 GGGAGGAACCAGTTAAGGTGT 59.296 52.381 0.00 0.00 42.25 4.16
754 887 2.908351 GGGAGGAACCAGTTAAGGTGTA 59.092 50.000 0.00 0.00 42.25 2.90
755 888 3.307269 GGGAGGAACCAGTTAAGGTGTAC 60.307 52.174 0.00 0.00 42.25 2.90
756 889 3.581770 GGAGGAACCAGTTAAGGTGTACT 59.418 47.826 0.00 0.00 42.25 2.73
757 890 4.774200 GGAGGAACCAGTTAAGGTGTACTA 59.226 45.833 0.00 0.00 42.25 1.82
758 891 5.337089 GGAGGAACCAGTTAAGGTGTACTAC 60.337 48.000 0.00 0.00 42.25 2.73
759 892 5.400870 AGGAACCAGTTAAGGTGTACTACT 58.599 41.667 0.00 0.00 42.25 2.57
760 893 6.555711 AGGAACCAGTTAAGGTGTACTACTA 58.444 40.000 0.00 0.00 42.25 1.82
761 894 6.435591 AGGAACCAGTTAAGGTGTACTACTAC 59.564 42.308 0.00 0.00 42.25 2.73
762 895 5.886960 ACCAGTTAAGGTGTACTACTACG 57.113 43.478 0.00 0.00 41.30 3.51
763 896 5.316987 ACCAGTTAAGGTGTACTACTACGT 58.683 41.667 0.00 0.00 41.30 3.57
764 897 6.472887 ACCAGTTAAGGTGTACTACTACGTA 58.527 40.000 0.00 0.00 41.30 3.57
765 898 7.112779 ACCAGTTAAGGTGTACTACTACGTAT 58.887 38.462 0.00 0.00 41.30 3.06
766 899 7.066284 ACCAGTTAAGGTGTACTACTACGTATG 59.934 40.741 0.00 0.00 41.30 2.39
767 900 7.066284 CCAGTTAAGGTGTACTACTACGTATGT 59.934 40.741 0.00 0.00 0.00 2.29
768 901 7.907045 CAGTTAAGGTGTACTACTACGTATGTG 59.093 40.741 0.00 0.00 0.00 3.21
769 902 4.889832 AGGTGTACTACTACGTATGTGC 57.110 45.455 0.00 0.51 0.00 4.57
770 903 4.264253 AGGTGTACTACTACGTATGTGCA 58.736 43.478 0.00 3.18 0.00 4.57
771 904 4.701651 AGGTGTACTACTACGTATGTGCAA 59.298 41.667 12.82 0.00 0.00 4.08
772 905 5.183713 AGGTGTACTACTACGTATGTGCAAA 59.816 40.000 12.82 0.00 0.00 3.68
773 906 6.038356 GGTGTACTACTACGTATGTGCAAAT 58.962 40.000 12.82 0.00 0.00 2.32
774 907 6.532657 GGTGTACTACTACGTATGTGCAAATT 59.467 38.462 12.82 0.00 0.00 1.82
775 908 7.701924 GGTGTACTACTACGTATGTGCAAATTA 59.298 37.037 12.82 0.00 0.00 1.40
776 909 8.526681 GTGTACTACTACGTATGTGCAAATTAC 58.473 37.037 12.82 0.00 0.00 1.89
777 910 8.461222 TGTACTACTACGTATGTGCAAATTACT 58.539 33.333 0.00 0.00 0.00 2.24
778 911 7.982371 ACTACTACGTATGTGCAAATTACTC 57.018 36.000 0.00 0.00 0.00 2.59
779 912 5.944049 ACTACGTATGTGCAAATTACTCG 57.056 39.130 0.00 0.00 0.00 4.18
780 913 4.802039 ACTACGTATGTGCAAATTACTCGG 59.198 41.667 0.00 0.00 0.00 4.63
781 914 3.592059 ACGTATGTGCAAATTACTCGGT 58.408 40.909 0.00 0.00 0.00 4.69
782 915 3.615496 ACGTATGTGCAAATTACTCGGTC 59.385 43.478 0.00 0.00 0.00 4.79
783 916 3.000925 CGTATGTGCAAATTACTCGGTCC 59.999 47.826 0.00 0.00 0.00 4.46
784 917 1.816074 TGTGCAAATTACTCGGTCCC 58.184 50.000 0.00 0.00 0.00 4.46
785 918 1.072489 TGTGCAAATTACTCGGTCCCA 59.928 47.619 0.00 0.00 0.00 4.37
786 919 2.290641 TGTGCAAATTACTCGGTCCCAT 60.291 45.455 0.00 0.00 0.00 4.00
787 920 2.752903 GTGCAAATTACTCGGTCCCATT 59.247 45.455 0.00 0.00 0.00 3.16
788 921 3.192633 GTGCAAATTACTCGGTCCCATTT 59.807 43.478 0.00 0.00 0.00 2.32
789 922 3.192422 TGCAAATTACTCGGTCCCATTTG 59.808 43.478 0.00 0.00 37.72 2.32
790 923 3.442273 GCAAATTACTCGGTCCCATTTGA 59.558 43.478 7.03 0.00 37.11 2.69
791 924 4.097892 GCAAATTACTCGGTCCCATTTGAT 59.902 41.667 7.03 0.00 37.11 2.57
792 925 5.394115 GCAAATTACTCGGTCCCATTTGATT 60.394 40.000 7.03 0.00 37.11 2.57
793 926 6.183360 GCAAATTACTCGGTCCCATTTGATTA 60.183 38.462 7.03 0.00 37.11 1.75
794 927 7.629652 GCAAATTACTCGGTCCCATTTGATTAA 60.630 37.037 7.03 0.00 37.11 1.40
795 928 7.948034 AATTACTCGGTCCCATTTGATTAAA 57.052 32.000 0.00 0.00 0.00 1.52
796 929 8.533569 AATTACTCGGTCCCATTTGATTAAAT 57.466 30.769 0.00 0.00 36.97 1.40
797 930 9.635404 AATTACTCGGTCCCATTTGATTAAATA 57.365 29.630 0.00 0.00 34.81 1.40
798 931 9.807921 ATTACTCGGTCCCATTTGATTAAATAT 57.192 29.630 0.00 0.00 34.81 1.28
801 934 9.284968 ACTCGGTCCCATTTGATTAAATATAAG 57.715 33.333 0.00 0.00 34.81 1.73
802 935 9.502091 CTCGGTCCCATTTGATTAAATATAAGA 57.498 33.333 0.00 0.00 34.81 2.10
803 936 9.854668 TCGGTCCCATTTGATTAAATATAAGAA 57.145 29.630 0.00 0.00 34.81 2.52
804 937 9.893305 CGGTCCCATTTGATTAAATATAAGAAC 57.107 33.333 0.00 0.00 34.81 3.01
903 1036 2.594131 TCTGTATGTATGGAGGGTCCG 58.406 52.381 0.00 0.00 40.17 4.79
904 1037 1.618837 CTGTATGTATGGAGGGTCCGG 59.381 57.143 0.00 0.00 40.17 5.14
906 1039 1.617357 GTATGTATGGAGGGTCCGGAC 59.383 57.143 27.04 27.04 40.17 4.79
909 1042 1.075525 TATGGAGGGTCCGGACTGG 60.076 63.158 32.52 0.00 40.17 4.00
917 1050 4.856789 TCCGGACTGGAGTGCTTA 57.143 55.556 0.00 0.00 43.74 3.09
918 1051 3.300032 TCCGGACTGGAGTGCTTAT 57.700 52.632 0.00 0.00 43.74 1.73
924 1057 3.502211 CGGACTGGAGTGCTTATTTTGTT 59.498 43.478 0.00 0.00 33.97 2.83
964 1097 0.030369 GCGTATGTCACCTAGGGTCG 59.970 60.000 14.81 7.74 31.02 4.79
1063 1196 1.816537 GTGCTAGTCCGAGATGCCA 59.183 57.895 0.00 0.00 0.00 4.92
1263 1396 1.302993 GTCCGCCCTGTTTAAGCCA 60.303 57.895 0.00 0.00 0.00 4.75
1293 1426 1.485066 GTTTCATCCCTTCCCTCGCTA 59.515 52.381 0.00 0.00 0.00 4.26
1321 1454 1.418264 TCACCATCGACCAAAACTCCA 59.582 47.619 0.00 0.00 0.00 3.86
1383 1516 2.640302 GCTCACTCCTCAGGCGACA 61.640 63.158 0.00 0.00 0.00 4.35
1390 1523 2.125753 CTCAGGCGACAGTGCTCC 60.126 66.667 0.00 0.00 34.52 4.70
1397 1530 2.359230 GACAGTGCTCCAGGCCAC 60.359 66.667 5.01 0.00 40.92 5.01
1992 2161 0.544357 TGGAGACATCCCCGTTGACT 60.544 55.000 0.00 0.00 46.04 3.41
2031 2208 1.396653 CCTACCCGACGTACTTCCAT 58.603 55.000 0.00 0.00 0.00 3.41
2715 2892 1.133025 GCTATTGTGCCGTGCTGAATT 59.867 47.619 0.00 0.00 0.00 2.17
2745 2922 2.024176 ATTTCAGGATTACGTGCGCT 57.976 45.000 9.73 0.00 32.75 5.92
2824 3002 4.324267 ACCGTGTAATCAGCTAAGCTTTT 58.676 39.130 3.20 0.00 36.40 2.27
2867 3045 9.814899 ATTTCATTAGATAGACTGTTCACAGAG 57.185 33.333 14.00 0.00 46.59 3.35
2868 3046 8.581253 TTCATTAGATAGACTGTTCACAGAGA 57.419 34.615 14.00 0.00 46.59 3.10
2869 3047 8.759481 TCATTAGATAGACTGTTCACAGAGAT 57.241 34.615 14.00 3.76 46.59 2.75
2870 3048 9.194972 TCATTAGATAGACTGTTCACAGAGATT 57.805 33.333 14.00 0.00 46.59 2.40
2873 3051 7.946381 AGATAGACTGTTCACAGAGATTACA 57.054 36.000 14.00 0.00 46.59 2.41
2874 3052 7.767261 AGATAGACTGTTCACAGAGATTACAC 58.233 38.462 14.00 0.00 46.59 2.90
2875 3053 5.791336 AGACTGTTCACAGAGATTACACA 57.209 39.130 14.00 0.00 46.59 3.72
2876 3054 6.352016 AGACTGTTCACAGAGATTACACAT 57.648 37.500 14.00 0.00 46.59 3.21
2877 3055 7.468141 AGACTGTTCACAGAGATTACACATA 57.532 36.000 14.00 0.00 46.59 2.29
2878 3056 8.072321 AGACTGTTCACAGAGATTACACATAT 57.928 34.615 14.00 0.00 46.59 1.78
2879 3057 7.978414 AGACTGTTCACAGAGATTACACATATG 59.022 37.037 14.00 0.00 46.59 1.78
2880 3058 7.044181 ACTGTTCACAGAGATTACACATATGG 58.956 38.462 14.00 0.00 46.59 2.74
2881 3059 6.946340 TGTTCACAGAGATTACACATATGGT 58.054 36.000 7.80 4.97 0.00 3.55
2882 3060 7.041721 TGTTCACAGAGATTACACATATGGTC 58.958 38.462 7.80 0.00 0.00 4.02
2883 3061 6.790232 TCACAGAGATTACACATATGGTCA 57.210 37.500 7.80 0.00 0.00 4.02
2884 3062 7.365497 TCACAGAGATTACACATATGGTCAT 57.635 36.000 7.80 0.00 0.00 3.06
2885 3063 7.436933 TCACAGAGATTACACATATGGTCATC 58.563 38.462 7.80 8.58 0.00 2.92
2886 3064 7.069826 TCACAGAGATTACACATATGGTCATCA 59.930 37.037 7.80 0.00 0.00 3.07
2887 3065 7.876582 CACAGAGATTACACATATGGTCATCAT 59.123 37.037 7.80 0.70 39.78 2.45
2888 3066 9.093458 ACAGAGATTACACATATGGTCATCATA 57.907 33.333 7.80 0.00 42.00 2.15
2889 3067 9.363763 CAGAGATTACACATATGGTCATCATAC 57.636 37.037 7.80 5.46 40.75 2.39
2890 3068 8.246871 AGAGATTACACATATGGTCATCATACG 58.753 37.037 7.80 0.00 40.75 3.06
2891 3069 8.122472 AGATTACACATATGGTCATCATACGA 57.878 34.615 7.80 0.00 40.75 3.43
2892 3070 8.246871 AGATTACACATATGGTCATCATACGAG 58.753 37.037 7.80 0.00 40.75 4.18
2893 3071 7.519032 TTACACATATGGTCATCATACGAGA 57.481 36.000 7.80 0.00 40.75 4.04
2894 3072 5.773575 ACACATATGGTCATCATACGAGAC 58.226 41.667 7.80 0.00 40.75 3.36
2895 3073 5.301805 ACACATATGGTCATCATACGAGACA 59.698 40.000 7.80 0.00 40.75 3.41
2896 3074 5.631096 CACATATGGTCATCATACGAGACAC 59.369 44.000 7.80 0.00 40.75 3.67
2897 3075 5.301805 ACATATGGTCATCATACGAGACACA 59.698 40.000 7.80 0.00 40.75 3.72
2898 3076 4.736126 ATGGTCATCATACGAGACACAA 57.264 40.909 0.00 0.00 33.61 3.33
2899 3077 4.529109 TGGTCATCATACGAGACACAAA 57.471 40.909 0.00 0.00 34.04 2.83
2900 3078 5.084818 TGGTCATCATACGAGACACAAAT 57.915 39.130 0.00 0.00 34.04 2.32
2901 3079 4.869861 TGGTCATCATACGAGACACAAATG 59.130 41.667 0.00 0.00 34.04 2.32
2902 3080 4.260375 GGTCATCATACGAGACACAAATGC 60.260 45.833 0.00 0.00 34.04 3.56
2903 3081 4.568359 GTCATCATACGAGACACAAATGCT 59.432 41.667 0.00 0.00 32.68 3.79
2904 3082 5.063944 GTCATCATACGAGACACAAATGCTT 59.936 40.000 0.00 0.00 32.68 3.91
2905 3083 4.926860 TCATACGAGACACAAATGCTTG 57.073 40.909 0.00 0.00 38.61 4.01
2907 3085 4.388773 TCATACGAGACACAAATGCTTGTC 59.611 41.667 0.00 0.00 44.15 3.18
2908 3086 2.560504 ACGAGACACAAATGCTTGTCA 58.439 42.857 4.66 0.00 44.15 3.58
2909 3087 2.942376 ACGAGACACAAATGCTTGTCAA 59.058 40.909 4.66 0.00 44.15 3.18
2910 3088 3.002656 ACGAGACACAAATGCTTGTCAAG 59.997 43.478 8.31 8.31 44.15 3.02
2945 3123 4.590850 AAAATTCCACAAGAGAGCAACC 57.409 40.909 0.00 0.00 0.00 3.77
2946 3124 2.957402 ATTCCACAAGAGAGCAACCA 57.043 45.000 0.00 0.00 0.00 3.67
2947 3125 2.957402 TTCCACAAGAGAGCAACCAT 57.043 45.000 0.00 0.00 0.00 3.55
2948 3126 4.574674 ATTCCACAAGAGAGCAACCATA 57.425 40.909 0.00 0.00 0.00 2.74
2949 3127 4.574674 TTCCACAAGAGAGCAACCATAT 57.425 40.909 0.00 0.00 0.00 1.78
2950 3128 5.692115 TTCCACAAGAGAGCAACCATATA 57.308 39.130 0.00 0.00 0.00 0.86
2951 3129 5.894298 TCCACAAGAGAGCAACCATATAT 57.106 39.130 0.00 0.00 0.00 0.86
2952 3130 6.252599 TCCACAAGAGAGCAACCATATATT 57.747 37.500 0.00 0.00 0.00 1.28
2953 3131 6.662755 TCCACAAGAGAGCAACCATATATTT 58.337 36.000 0.00 0.00 0.00 1.40
2954 3132 6.767902 TCCACAAGAGAGCAACCATATATTTC 59.232 38.462 0.00 0.00 0.00 2.17
2955 3133 6.543465 CCACAAGAGAGCAACCATATATTTCA 59.457 38.462 0.00 0.00 0.00 2.69
2956 3134 7.412853 CACAAGAGAGCAACCATATATTTCAC 58.587 38.462 0.00 0.00 0.00 3.18
2957 3135 6.543831 ACAAGAGAGCAACCATATATTTCACC 59.456 38.462 0.00 0.00 0.00 4.02
2958 3136 5.625150 AGAGAGCAACCATATATTTCACCC 58.375 41.667 0.00 0.00 0.00 4.61
2959 3137 5.132648 AGAGAGCAACCATATATTTCACCCA 59.867 40.000 0.00 0.00 0.00 4.51
2960 3138 5.765510 AGAGCAACCATATATTTCACCCAA 58.234 37.500 0.00 0.00 0.00 4.12
2961 3139 5.594317 AGAGCAACCATATATTTCACCCAAC 59.406 40.000 0.00 0.00 0.00 3.77
2962 3140 5.518865 AGCAACCATATATTTCACCCAACT 58.481 37.500 0.00 0.00 0.00 3.16
2963 3141 5.957774 AGCAACCATATATTTCACCCAACTT 59.042 36.000 0.00 0.00 0.00 2.66
2964 3142 6.440328 AGCAACCATATATTTCACCCAACTTT 59.560 34.615 0.00 0.00 0.00 2.66
2965 3143 6.534793 GCAACCATATATTTCACCCAACTTTG 59.465 38.462 0.00 0.00 0.00 2.77
2966 3144 7.610865 CAACCATATATTTCACCCAACTTTGT 58.389 34.615 0.00 0.00 0.00 2.83
2967 3145 7.790782 ACCATATATTTCACCCAACTTTGTT 57.209 32.000 0.00 0.00 0.00 2.83
2968 3146 8.201242 ACCATATATTTCACCCAACTTTGTTT 57.799 30.769 0.00 0.00 0.00 2.83
2969 3147 8.093927 ACCATATATTTCACCCAACTTTGTTTG 58.906 33.333 0.00 0.00 0.00 2.93
2970 3148 8.310382 CCATATATTTCACCCAACTTTGTTTGA 58.690 33.333 0.00 0.00 0.00 2.69
2971 3149 9.357652 CATATATTTCACCCAACTTTGTTTGAG 57.642 33.333 0.00 0.00 0.00 3.02
2972 3150 3.518634 TTCACCCAACTTTGTTTGAGC 57.481 42.857 0.00 0.00 0.00 4.26
2973 3151 2.451490 TCACCCAACTTTGTTTGAGCA 58.549 42.857 0.00 0.00 0.00 4.26
2974 3152 2.165437 TCACCCAACTTTGTTTGAGCAC 59.835 45.455 0.00 0.00 0.00 4.40
2975 3153 1.134175 ACCCAACTTTGTTTGAGCACG 59.866 47.619 0.00 0.00 0.00 5.34
3099 3304 4.764308 GCTTCTTCAGATTTTTCTGTCCCT 59.236 41.667 3.15 0.00 38.75 4.20
3114 3319 2.766263 TGTCCCTCGCTCATTCTACAAT 59.234 45.455 0.00 0.00 0.00 2.71
3141 3346 5.794894 TCTTTTGAAATAGACTTCCGCTCT 58.205 37.500 0.00 0.00 0.00 4.09
3249 4476 2.877043 AGGTCGAAACACAACTACGT 57.123 45.000 0.00 0.00 0.00 3.57
3264 4491 4.030134 ACTACGTCGAGCAGAAAATAGG 57.970 45.455 0.00 0.00 0.00 2.57
3269 4496 4.174009 CGTCGAGCAGAAAATAGGAAGAA 58.826 43.478 0.00 0.00 0.00 2.52
3291 4518 8.042944 AGAACTAAGACTACACTAGCAACTAC 57.957 38.462 0.00 0.00 0.00 2.73
3292 4519 6.756299 ACTAAGACTACACTAGCAACTACC 57.244 41.667 0.00 0.00 0.00 3.18
3296 4523 4.831155 AGACTACACTAGCAACTACCAACA 59.169 41.667 0.00 0.00 0.00 3.33
3299 4526 4.145365 ACACTAGCAACTACCAACAACA 57.855 40.909 0.00 0.00 0.00 3.33
3305 4532 2.621055 GCAACTACCAACAACACATGGA 59.379 45.455 0.00 0.00 39.12 3.41
3317 4544 0.033796 CACATGGACTCCCTGGCAAT 60.034 55.000 5.45 0.00 0.00 3.56
3330 4557 2.967270 GGCAATGCCCTCAAGAAGT 58.033 52.632 14.47 0.00 44.06 3.01
3331 4558 2.128771 GGCAATGCCCTCAAGAAGTA 57.871 50.000 14.47 0.00 44.06 2.24
3337 4564 3.478857 TGCCCTCAAGAAGTAAAACGA 57.521 42.857 0.00 0.00 0.00 3.85
3339 4566 3.135994 GCCCTCAAGAAGTAAAACGACA 58.864 45.455 0.00 0.00 0.00 4.35
3346 4573 5.122554 TCAAGAAGTAAAACGACACAAAGCA 59.877 36.000 0.00 0.00 0.00 3.91
3348 4575 5.510671 AGAAGTAAAACGACACAAAGCATG 58.489 37.500 0.00 0.00 0.00 4.06
3349 4576 4.223320 AGTAAAACGACACAAAGCATGG 57.777 40.909 0.00 0.00 0.00 3.66
3350 4577 3.630312 AGTAAAACGACACAAAGCATGGT 59.370 39.130 0.00 0.00 0.00 3.55
3351 4578 3.518634 AAAACGACACAAAGCATGGTT 57.481 38.095 3.82 3.82 0.00 3.67
3360 4587 1.922135 AAAGCATGGTTAGTGCCGCG 61.922 55.000 11.15 0.00 43.50 6.46
3367 4594 3.672447 TTAGTGCCGCGTCCGACA 61.672 61.111 4.92 0.00 36.29 4.35
3385 4612 3.002348 CGACAGAGTGGACAAAGGTTTTC 59.998 47.826 0.00 0.00 0.00 2.29
3403 4630 1.002868 CACCTGGAACTCTGGCAGG 60.003 63.158 15.73 8.05 37.94 4.85
3404 4631 2.227036 ACCTGGAACTCTGGCAGGG 61.227 63.158 14.14 14.14 37.94 4.45
3418 4645 1.364171 CAGGGGAAGCGAGATACGG 59.636 63.158 0.00 0.00 42.83 4.02
3447 4674 2.905996 ATGAGGAAAGCGGCACCCA 61.906 57.895 1.45 4.06 0.00 4.51
3471 4698 2.962786 TCGTTGTTGTCGGCACCG 60.963 61.111 1.73 1.73 41.35 4.94
3499 4726 1.312815 AGCTTTCGCTCAGTTGCTTT 58.687 45.000 0.00 0.00 45.15 3.51
3535 4762 5.580661 TGCTCGTTTTAGTAACAAAAACCC 58.419 37.500 6.00 0.00 41.59 4.11
3539 4766 5.651576 TCGTTTTAGTAACAAAAACCCTGGT 59.348 36.000 6.00 0.00 41.59 4.00
3541 4768 6.404513 CGTTTTAGTAACAAAAACCCTGGTGA 60.405 38.462 6.00 0.00 41.59 4.02
3543 4770 2.946990 AGTAACAAAAACCCTGGTGACG 59.053 45.455 0.00 0.00 0.00 4.35
3547 4774 2.621526 ACAAAAACCCTGGTGACGAATC 59.378 45.455 0.00 0.00 0.00 2.52
3552 4779 2.227194 ACCCTGGTGACGAATCAAAAC 58.773 47.619 0.00 0.00 36.31 2.43
3555 4782 2.349438 CCTGGTGACGAATCAAAACACG 60.349 50.000 0.00 0.00 36.31 4.49
3575 4802 7.599630 ACACGTCGCCTAAAATAATTTTCTA 57.400 32.000 0.00 0.00 34.19 2.10
3582 4809 6.514376 CGCCTAAAATAATTTTCTATGGCGGT 60.514 38.462 20.48 0.00 44.52 5.68
3602 4829 2.095718 GTCAACCGTCATCAGCCTTTTC 60.096 50.000 0.00 0.00 0.00 2.29
3608 4835 1.283321 GTCATCAGCCTTTTCCCTCCT 59.717 52.381 0.00 0.00 0.00 3.69
3610 4837 0.627986 ATCAGCCTTTTCCCTCCTGG 59.372 55.000 0.00 0.00 0.00 4.45
3635 4863 0.680921 CCCTTGGATGCGTTGGTGAT 60.681 55.000 0.00 0.00 0.00 3.06
3645 4873 0.673437 CGTTGGTGATGTTTTGGCCT 59.327 50.000 3.32 0.00 0.00 5.19
3667 4895 4.217754 TGTTTTAGGCGACACATTTGAC 57.782 40.909 0.00 0.00 0.00 3.18
3668 4896 3.628032 TGTTTTAGGCGACACATTTGACA 59.372 39.130 0.00 0.00 0.00 3.58
3669 4897 4.219033 GTTTTAGGCGACACATTTGACAG 58.781 43.478 0.00 0.00 0.00 3.51
3675 4903 3.057019 GCGACACATTTGACAGTCACTA 58.943 45.455 1.52 0.00 0.00 2.74
3676 4904 3.679980 GCGACACATTTGACAGTCACTAT 59.320 43.478 1.52 0.00 0.00 2.12
3677 4905 4.434725 GCGACACATTTGACAGTCACTATG 60.435 45.833 17.62 17.62 0.00 2.23
3683 4911 5.474532 ACATTTGACAGTCACTATGCATGTT 59.525 36.000 18.58 0.00 0.00 2.71
3684 4912 5.611796 TTTGACAGTCACTATGCATGTTC 57.388 39.130 10.16 0.93 0.00 3.18
3692 4920 8.424133 ACAGTCACTATGCATGTTCATATTCTA 58.576 33.333 10.16 0.00 0.00 2.10
3706 4934 6.968131 TCATATTCTACGCTGATTTATGGC 57.032 37.500 0.00 0.00 0.00 4.40
3713 4941 3.238903 CGCTGATTTATGGCGTAACAG 57.761 47.619 10.99 10.99 43.28 3.16
3722 4950 8.128582 TGATTTATGGCGTAACAGAAAATGATC 58.871 33.333 0.00 0.00 35.49 2.92
3724 4952 2.675844 TGGCGTAACAGAAAATGATCGG 59.324 45.455 0.00 0.00 0.00 4.18
3725 4953 2.676342 GGCGTAACAGAAAATGATCGGT 59.324 45.455 0.00 0.00 0.00 4.69
3734 4962 0.324275 AAATGATCGGTGGGTTGGGG 60.324 55.000 0.00 0.00 0.00 4.96
3743 4971 1.133104 GGTGGGTTGGGGAAGGTTAAA 60.133 52.381 0.00 0.00 0.00 1.52
3772 5002 3.380004 TCGATGGCAGTGAAAACAAAGTT 59.620 39.130 0.00 0.00 0.00 2.66
3811 5041 5.351458 TGGACATTAGTTGAGATGATCGTG 58.649 41.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.690219 AATGTCCTCCCTAGGCTGCG 61.690 60.000 2.05 0.00 43.31 5.18
45 46 0.308684 CAACAGACGCTGCACAATGT 59.691 50.000 0.00 0.00 34.37 2.71
54 55 0.034059 CCTTGACCTCAACAGACGCT 59.966 55.000 0.00 0.00 0.00 5.07
111 112 3.590643 CCTCCTAGGGTCTGTCGAA 57.409 57.895 9.46 0.00 0.00 3.71
131 132 1.298157 CGATGGCAGCGGTTTGAGAA 61.298 55.000 18.75 0.00 0.00 2.87
152 153 1.040339 GGGTTTGCCACAAGACACCA 61.040 55.000 2.97 0.00 36.17 4.17
157 158 1.152567 CCCAGGGTTTGCCACAAGA 60.153 57.895 0.00 0.00 36.17 3.02
196 197 4.819761 GCTGGATCTCCGTGCGCA 62.820 66.667 5.66 5.66 39.43 6.09
217 218 3.246112 TCCCCGGGTGAAGGTGTG 61.246 66.667 21.85 0.00 0.00 3.82
544 677 9.120658 TCTCTCCAGGATATTTTTGATATGGAT 57.879 33.333 0.00 0.00 35.20 3.41
598 731 4.933330 TGATATCTTGTAGACCGTGCTTC 58.067 43.478 3.98 0.00 0.00 3.86
651 784 4.260620 CCGGACACCAAACGAATTATCATC 60.261 45.833 0.00 0.00 0.00 2.92
670 803 3.150767 CAAGGAAACCACATAAACCGGA 58.849 45.455 9.46 0.00 0.00 5.14
694 827 4.080582 CACTTCTCTCCCTCTCACTCTCTA 60.081 50.000 0.00 0.00 0.00 2.43
699 832 1.555967 GCACTTCTCTCCCTCTCACT 58.444 55.000 0.00 0.00 0.00 3.41
701 834 0.251386 ACGCACTTCTCTCCCTCTCA 60.251 55.000 0.00 0.00 0.00 3.27
705 838 2.948720 GCCACGCACTTCTCTCCCT 61.949 63.158 0.00 0.00 0.00 4.20
711 844 0.396811 AACTAAGGCCACGCACTTCT 59.603 50.000 5.01 0.00 0.00 2.85
712 845 1.235724 AAACTAAGGCCACGCACTTC 58.764 50.000 5.01 0.00 0.00 3.01
720 853 2.574824 GTTCCTCCCTAAACTAAGGCCA 59.425 50.000 5.01 0.00 35.09 5.36
728 861 4.042560 ACCTTAACTGGTTCCTCCCTAAAC 59.957 45.833 0.00 0.00 36.89 2.01
732 865 1.985895 CACCTTAACTGGTTCCTCCCT 59.014 52.381 0.00 0.00 38.45 4.20
758 891 4.802039 ACCGAGTAATTTGCACATACGTAG 59.198 41.667 0.08 0.00 0.00 3.51
759 892 4.746729 ACCGAGTAATTTGCACATACGTA 58.253 39.130 0.00 0.00 0.00 3.57
760 893 3.592059 ACCGAGTAATTTGCACATACGT 58.408 40.909 0.00 0.00 0.00 3.57
761 894 3.000925 GGACCGAGTAATTTGCACATACG 59.999 47.826 0.00 0.00 0.00 3.06
762 895 3.311596 GGGACCGAGTAATTTGCACATAC 59.688 47.826 0.00 0.00 0.00 2.39
763 896 3.055021 TGGGACCGAGTAATTTGCACATA 60.055 43.478 0.00 0.00 0.00 2.29
764 897 2.290641 TGGGACCGAGTAATTTGCACAT 60.291 45.455 0.00 0.00 0.00 3.21
765 898 1.072489 TGGGACCGAGTAATTTGCACA 59.928 47.619 0.00 0.00 0.00 4.57
766 899 1.816074 TGGGACCGAGTAATTTGCAC 58.184 50.000 0.00 0.00 0.00 4.57
767 900 2.799126 ATGGGACCGAGTAATTTGCA 57.201 45.000 0.00 0.00 0.00 4.08
768 901 3.442273 TCAAATGGGACCGAGTAATTTGC 59.558 43.478 6.33 0.00 37.87 3.68
769 902 5.835113 ATCAAATGGGACCGAGTAATTTG 57.165 39.130 0.00 0.00 38.82 2.32
770 903 7.948034 TTAATCAAATGGGACCGAGTAATTT 57.052 32.000 0.00 0.00 0.00 1.82
771 904 7.948034 TTTAATCAAATGGGACCGAGTAATT 57.052 32.000 0.00 0.00 0.00 1.40
772 905 9.807921 ATATTTAATCAAATGGGACCGAGTAAT 57.192 29.630 0.00 0.00 35.88 1.89
775 908 9.284968 CTTATATTTAATCAAATGGGACCGAGT 57.715 33.333 0.00 0.00 35.88 4.18
776 909 9.502091 TCTTATATTTAATCAAATGGGACCGAG 57.498 33.333 0.00 0.00 35.88 4.63
777 910 9.854668 TTCTTATATTTAATCAAATGGGACCGA 57.145 29.630 0.00 0.00 35.88 4.69
778 911 9.893305 GTTCTTATATTTAATCAAATGGGACCG 57.107 33.333 0.00 0.00 35.88 4.79
793 926 9.019656 TGCTGTACACAATTGGTTCTTATATTT 57.980 29.630 10.83 0.00 0.00 1.40
794 927 8.574251 TGCTGTACACAATTGGTTCTTATATT 57.426 30.769 10.83 0.00 0.00 1.28
839 972 0.806868 CCGATCTGCTGTGCACAATT 59.193 50.000 21.98 3.69 33.79 2.32
852 985 0.321653 GTGGACCAAACAGCCGATCT 60.322 55.000 0.00 0.00 0.00 2.75
903 1036 5.222631 CAAACAAAATAAGCACTCCAGTCC 58.777 41.667 0.00 0.00 0.00 3.85
904 1037 4.681483 GCAAACAAAATAAGCACTCCAGTC 59.319 41.667 0.00 0.00 0.00 3.51
906 1039 3.670055 CGCAAACAAAATAAGCACTCCAG 59.330 43.478 0.00 0.00 0.00 3.86
909 1042 3.361940 GCTCGCAAACAAAATAAGCACTC 59.638 43.478 0.00 0.00 0.00 3.51
910 1043 3.308530 GCTCGCAAACAAAATAAGCACT 58.691 40.909 0.00 0.00 0.00 4.40
911 1044 2.408368 GGCTCGCAAACAAAATAAGCAC 59.592 45.455 0.00 0.00 0.00 4.40
913 1046 2.671596 TGGCTCGCAAACAAAATAAGC 58.328 42.857 0.00 0.00 0.00 3.09
916 1049 4.511617 TGATTGGCTCGCAAACAAAATA 57.488 36.364 0.00 0.00 0.00 1.40
917 1050 3.383620 TGATTGGCTCGCAAACAAAAT 57.616 38.095 0.00 0.00 0.00 1.82
918 1051 2.879002 TGATTGGCTCGCAAACAAAA 57.121 40.000 0.00 0.00 0.00 2.44
1063 1196 2.159099 TGCTAGACTTCATCGGCGATTT 60.159 45.455 21.54 4.63 34.90 2.17
1293 1426 1.153289 GTCGATGGTGATGCTGGCT 60.153 57.895 0.00 0.00 0.00 4.75
1383 1516 3.699894 CGAGTGGCCTGGAGCACT 61.700 66.667 3.32 0.00 46.50 4.40
1493 1626 1.078356 CAGTCTCGGAGGAGGTCGA 60.078 63.158 4.96 0.00 40.85 4.20
1614 1783 2.283604 TCGGTGGAGTAGCAGCCA 60.284 61.111 0.00 0.00 0.00 4.75
1620 1789 1.254026 TGAACTGGTCGGTGGAGTAG 58.746 55.000 0.00 0.00 0.00 2.57
1992 2161 2.628696 TACCGCGAAGTTGCTCCGA 61.629 57.895 8.23 0.00 0.00 4.55
2715 2892 5.411361 CGTAATCCTGAAATTGTTGGACTCA 59.589 40.000 0.00 0.00 0.00 3.41
2801 2978 4.730949 AAGCTTAGCTGATTACACGGTA 57.269 40.909 7.77 0.00 39.62 4.02
2841 3019 9.814899 CTCTGTGAACAGTCTATCTAATGAAAT 57.185 33.333 10.14 0.00 44.12 2.17
2842 3020 9.025041 TCTCTGTGAACAGTCTATCTAATGAAA 57.975 33.333 10.14 0.00 44.12 2.69
2843 3021 8.581253 TCTCTGTGAACAGTCTATCTAATGAA 57.419 34.615 10.14 0.00 44.12 2.57
2844 3022 8.759481 ATCTCTGTGAACAGTCTATCTAATGA 57.241 34.615 10.14 0.00 44.12 2.57
2847 3025 9.462606 TGTAATCTCTGTGAACAGTCTATCTAA 57.537 33.333 10.14 0.00 44.12 2.10
2848 3026 8.894731 GTGTAATCTCTGTGAACAGTCTATCTA 58.105 37.037 10.14 0.00 44.12 1.98
2849 3027 7.394641 TGTGTAATCTCTGTGAACAGTCTATCT 59.605 37.037 10.14 0.00 44.12 1.98
2850 3028 7.539436 TGTGTAATCTCTGTGAACAGTCTATC 58.461 38.462 10.14 0.50 44.12 2.08
2851 3029 7.468141 TGTGTAATCTCTGTGAACAGTCTAT 57.532 36.000 10.14 0.86 44.12 1.98
2852 3030 6.894339 TGTGTAATCTCTGTGAACAGTCTA 57.106 37.500 10.14 0.00 44.12 2.59
2853 3031 5.791336 TGTGTAATCTCTGTGAACAGTCT 57.209 39.130 10.14 0.00 44.12 3.24
2854 3032 7.223582 CCATATGTGTAATCTCTGTGAACAGTC 59.776 40.741 10.14 0.00 44.12 3.51
2855 3033 7.044181 CCATATGTGTAATCTCTGTGAACAGT 58.956 38.462 10.14 0.00 44.12 3.55
2856 3034 7.044181 ACCATATGTGTAATCTCTGTGAACAG 58.956 38.462 3.98 3.98 45.08 3.16
2857 3035 6.946340 ACCATATGTGTAATCTCTGTGAACA 58.054 36.000 1.24 0.00 0.00 3.18
2858 3036 7.041721 TGACCATATGTGTAATCTCTGTGAAC 58.958 38.462 1.24 0.00 0.00 3.18
2859 3037 7.181569 TGACCATATGTGTAATCTCTGTGAA 57.818 36.000 1.24 0.00 0.00 3.18
2860 3038 6.790232 TGACCATATGTGTAATCTCTGTGA 57.210 37.500 1.24 0.00 0.00 3.58
2861 3039 7.212274 TGATGACCATATGTGTAATCTCTGTG 58.788 38.462 16.51 0.00 0.00 3.66
2862 3040 7.365497 TGATGACCATATGTGTAATCTCTGT 57.635 36.000 16.51 0.32 0.00 3.41
2863 3041 9.363763 GTATGATGACCATATGTGTAATCTCTG 57.636 37.037 16.51 0.00 39.69 3.35
2864 3042 8.246871 CGTATGATGACCATATGTGTAATCTCT 58.753 37.037 16.51 10.18 39.69 3.10
2865 3043 8.244113 TCGTATGATGACCATATGTGTAATCTC 58.756 37.037 16.51 9.90 42.59 2.75
2866 3044 8.122472 TCGTATGATGACCATATGTGTAATCT 57.878 34.615 16.51 9.14 42.59 2.40
2867 3045 8.244113 TCTCGTATGATGACCATATGTGTAATC 58.756 37.037 11.84 11.84 42.59 1.75
2868 3046 8.029522 GTCTCGTATGATGACCATATGTGTAAT 58.970 37.037 1.24 0.00 42.59 1.89
2869 3047 7.013846 TGTCTCGTATGATGACCATATGTGTAA 59.986 37.037 1.24 0.00 42.59 2.41
2870 3048 6.488683 TGTCTCGTATGATGACCATATGTGTA 59.511 38.462 1.24 0.00 42.59 2.90
2871 3049 5.301805 TGTCTCGTATGATGACCATATGTGT 59.698 40.000 1.24 0.00 42.59 3.72
2872 3050 5.631096 GTGTCTCGTATGATGACCATATGTG 59.369 44.000 1.24 0.00 42.59 3.21
2873 3051 5.301805 TGTGTCTCGTATGATGACCATATGT 59.698 40.000 1.24 0.00 42.59 2.29
2874 3052 5.772521 TGTGTCTCGTATGATGACCATATG 58.227 41.667 0.00 0.00 43.11 1.78
2875 3053 6.405278 TTGTGTCTCGTATGATGACCATAT 57.595 37.500 10.25 0.00 39.69 1.78
2876 3054 5.845391 TTGTGTCTCGTATGATGACCATA 57.155 39.130 10.25 0.00 36.71 2.74
2877 3055 4.736126 TTGTGTCTCGTATGATGACCAT 57.264 40.909 10.25 0.00 39.25 3.55
2878 3056 4.529109 TTTGTGTCTCGTATGATGACCA 57.471 40.909 10.25 6.76 0.00 4.02
2879 3057 4.260375 GCATTTGTGTCTCGTATGATGACC 60.260 45.833 10.25 5.04 0.00 4.02
2880 3058 4.568359 AGCATTTGTGTCTCGTATGATGAC 59.432 41.667 7.29 7.29 0.00 3.06
2881 3059 4.758688 AGCATTTGTGTCTCGTATGATGA 58.241 39.130 0.00 0.00 0.00 2.92
2882 3060 5.163824 ACAAGCATTTGTGTCTCGTATGATG 60.164 40.000 0.00 0.00 45.54 3.07
2883 3061 4.937620 ACAAGCATTTGTGTCTCGTATGAT 59.062 37.500 0.00 0.00 45.54 2.45
2884 3062 4.314961 ACAAGCATTTGTGTCTCGTATGA 58.685 39.130 0.00 0.00 45.54 2.15
2885 3063 4.668576 ACAAGCATTTGTGTCTCGTATG 57.331 40.909 0.00 0.00 45.54 2.39
2923 3101 4.405358 TGGTTGCTCTCTTGTGGAATTTTT 59.595 37.500 0.00 0.00 0.00 1.94
2924 3102 3.960102 TGGTTGCTCTCTTGTGGAATTTT 59.040 39.130 0.00 0.00 0.00 1.82
2925 3103 3.565307 TGGTTGCTCTCTTGTGGAATTT 58.435 40.909 0.00 0.00 0.00 1.82
2926 3104 3.228188 TGGTTGCTCTCTTGTGGAATT 57.772 42.857 0.00 0.00 0.00 2.17
2927 3105 2.957402 TGGTTGCTCTCTTGTGGAAT 57.043 45.000 0.00 0.00 0.00 3.01
2928 3106 2.957402 ATGGTTGCTCTCTTGTGGAA 57.043 45.000 0.00 0.00 0.00 3.53
2929 3107 5.894298 ATATATGGTTGCTCTCTTGTGGA 57.106 39.130 0.00 0.00 0.00 4.02
2930 3108 6.543465 TGAAATATATGGTTGCTCTCTTGTGG 59.457 38.462 0.00 0.00 0.00 4.17
2931 3109 7.412853 GTGAAATATATGGTTGCTCTCTTGTG 58.587 38.462 0.00 0.00 0.00 3.33
2932 3110 6.543831 GGTGAAATATATGGTTGCTCTCTTGT 59.456 38.462 0.00 0.00 0.00 3.16
2933 3111 6.016777 GGGTGAAATATATGGTTGCTCTCTTG 60.017 42.308 0.00 0.00 0.00 3.02
2934 3112 6.064717 GGGTGAAATATATGGTTGCTCTCTT 58.935 40.000 0.00 0.00 0.00 2.85
2935 3113 5.132648 TGGGTGAAATATATGGTTGCTCTCT 59.867 40.000 0.00 0.00 0.00 3.10
2936 3114 5.376625 TGGGTGAAATATATGGTTGCTCTC 58.623 41.667 0.00 0.00 0.00 3.20
2937 3115 5.387113 TGGGTGAAATATATGGTTGCTCT 57.613 39.130 0.00 0.00 0.00 4.09
2938 3116 5.594317 AGTTGGGTGAAATATATGGTTGCTC 59.406 40.000 0.00 0.00 0.00 4.26
2939 3117 5.518865 AGTTGGGTGAAATATATGGTTGCT 58.481 37.500 0.00 0.00 0.00 3.91
2940 3118 5.852282 AGTTGGGTGAAATATATGGTTGC 57.148 39.130 0.00 0.00 0.00 4.17
2941 3119 7.610865 ACAAAGTTGGGTGAAATATATGGTTG 58.389 34.615 0.00 0.00 0.00 3.77
2942 3120 7.790782 ACAAAGTTGGGTGAAATATATGGTT 57.209 32.000 0.00 0.00 0.00 3.67
2943 3121 7.790782 AACAAAGTTGGGTGAAATATATGGT 57.209 32.000 0.00 0.00 0.00 3.55
2944 3122 8.310382 TCAAACAAAGTTGGGTGAAATATATGG 58.690 33.333 0.00 0.00 0.00 2.74
2945 3123 9.357652 CTCAAACAAAGTTGGGTGAAATATATG 57.642 33.333 0.00 0.00 0.00 1.78
2946 3124 8.034804 GCTCAAACAAAGTTGGGTGAAATATAT 58.965 33.333 0.00 0.00 31.14 0.86
2947 3125 7.014711 TGCTCAAACAAAGTTGGGTGAAATATA 59.985 33.333 0.00 0.00 31.14 0.86
2948 3126 6.183360 TGCTCAAACAAAGTTGGGTGAAATAT 60.183 34.615 0.00 0.00 31.14 1.28
2949 3127 5.127845 TGCTCAAACAAAGTTGGGTGAAATA 59.872 36.000 0.00 0.00 31.14 1.40
2950 3128 4.081198 TGCTCAAACAAAGTTGGGTGAAAT 60.081 37.500 0.00 0.00 31.14 2.17
2951 3129 3.259374 TGCTCAAACAAAGTTGGGTGAAA 59.741 39.130 0.00 0.00 31.14 2.69
2952 3130 2.828520 TGCTCAAACAAAGTTGGGTGAA 59.171 40.909 0.00 0.00 31.14 3.18
2953 3131 2.165437 GTGCTCAAACAAAGTTGGGTGA 59.835 45.455 0.00 0.00 31.14 4.02
2954 3132 2.539476 GTGCTCAAACAAAGTTGGGTG 58.461 47.619 0.00 0.00 31.14 4.61
2955 3133 1.134175 CGTGCTCAAACAAAGTTGGGT 59.866 47.619 0.00 0.00 31.14 4.51
2956 3134 1.403679 TCGTGCTCAAACAAAGTTGGG 59.596 47.619 0.00 0.00 31.69 4.12
2957 3135 2.842208 TCGTGCTCAAACAAAGTTGG 57.158 45.000 0.00 0.00 0.00 3.77
2958 3136 5.508124 TTTTTCGTGCTCAAACAAAGTTG 57.492 34.783 0.00 0.00 0.00 3.16
3099 3304 6.801539 AAAGAACAATTGTAGAATGAGCGA 57.198 33.333 12.39 0.00 0.00 4.93
3114 3319 6.262273 AGCGGAAGTCTATTTCAAAAGAACAA 59.738 34.615 0.00 0.00 0.00 2.83
3216 4443 6.982141 GTGTTTCGACCTATGTATATTGTCCA 59.018 38.462 0.00 0.00 0.00 4.02
3217 4444 6.982141 TGTGTTTCGACCTATGTATATTGTCC 59.018 38.462 0.00 0.00 0.00 4.02
3230 4457 2.877043 ACGTAGTTGTGTTTCGACCT 57.123 45.000 0.00 0.00 37.78 3.85
3249 4476 5.407407 AGTTCTTCCTATTTTCTGCTCGA 57.593 39.130 0.00 0.00 0.00 4.04
3264 4491 7.595604 AGTTGCTAGTGTAGTCTTAGTTCTTC 58.404 38.462 0.00 0.00 0.00 2.87
3269 4496 6.243900 TGGTAGTTGCTAGTGTAGTCTTAGT 58.756 40.000 0.00 0.00 0.00 2.24
3291 4518 1.202927 AGGGAGTCCATGTGTTGTTGG 60.203 52.381 12.30 0.00 34.83 3.77
3292 4519 1.881973 CAGGGAGTCCATGTGTTGTTG 59.118 52.381 15.83 0.00 34.83 3.33
3296 4523 1.380302 GCCAGGGAGTCCATGTGTT 59.620 57.895 21.73 0.00 34.83 3.32
3299 4526 0.033796 CATTGCCAGGGAGTCCATGT 60.034 55.000 21.73 0.78 34.83 3.21
3317 4544 3.135994 GTCGTTTTACTTCTTGAGGGCA 58.864 45.455 0.00 0.00 0.00 5.36
3328 4555 3.630312 ACCATGCTTTGTGTCGTTTTACT 59.370 39.130 0.00 0.00 0.00 2.24
3330 4557 4.640789 AACCATGCTTTGTGTCGTTTTA 57.359 36.364 0.00 0.00 0.00 1.52
3331 4558 3.518634 AACCATGCTTTGTGTCGTTTT 57.481 38.095 0.00 0.00 0.00 2.43
3337 4564 1.613437 GGCACTAACCATGCTTTGTGT 59.387 47.619 14.17 0.73 42.93 3.72
3339 4566 0.881118 CGGCACTAACCATGCTTTGT 59.119 50.000 0.00 0.00 42.93 2.83
3346 4573 2.125269 GGACGCGGCACTAACCAT 60.125 61.111 17.00 0.00 0.00 3.55
3348 4575 4.424566 TCGGACGCGGCACTAACC 62.425 66.667 17.00 2.58 0.00 2.85
3349 4576 3.177249 GTCGGACGCGGCACTAAC 61.177 66.667 17.00 1.14 0.00 2.34
3350 4577 3.620300 CTGTCGGACGCGGCACTAA 62.620 63.158 17.00 0.00 0.00 2.24
3351 4578 4.111016 CTGTCGGACGCGGCACTA 62.111 66.667 17.00 0.00 0.00 2.74
3367 4594 3.053619 AGGTGAAAACCTTTGTCCACTCT 60.054 43.478 0.00 0.00 36.56 3.24
3385 4612 1.002868 CCTGCCAGAGTTCCAGGTG 60.003 63.158 0.00 0.00 40.92 4.00
3403 4630 1.143183 TTGCCGTATCTCGCTTCCC 59.857 57.895 0.00 0.00 38.35 3.97
3404 4631 1.480219 CGTTGCCGTATCTCGCTTCC 61.480 60.000 0.00 0.00 38.35 3.46
3488 4715 6.854892 CAGATTTTGTAGTGAAAGCAACTGAG 59.145 38.462 0.00 0.00 0.00 3.35
3489 4716 6.728200 CAGATTTTGTAGTGAAAGCAACTGA 58.272 36.000 0.00 0.00 0.00 3.41
3499 4726 6.704493 ACTAAAACGAGCAGATTTTGTAGTGA 59.296 34.615 0.00 0.00 31.43 3.41
3535 4762 2.286833 ACGTGTTTTGATTCGTCACCAG 59.713 45.455 0.00 0.00 30.71 4.00
3541 4768 0.233848 GGCGACGTGTTTTGATTCGT 59.766 50.000 0.00 0.00 39.21 3.85
3543 4770 3.799137 TTAGGCGACGTGTTTTGATTC 57.201 42.857 0.00 0.00 0.00 2.52
3547 4774 6.921332 AATTATTTTAGGCGACGTGTTTTG 57.079 33.333 0.00 0.00 0.00 2.44
3552 4779 7.586300 CCATAGAAAATTATTTTAGGCGACGTG 59.414 37.037 2.65 0.00 31.94 4.49
3555 4782 7.853377 GCCATAGAAAATTATTTTAGGCGAC 57.147 36.000 14.87 0.00 31.94 5.19
3582 4809 2.151202 GAAAAGGCTGATGACGGTTGA 58.849 47.619 0.00 0.00 0.00 3.18
3610 4837 2.203209 CGCATCCAAGGGGCTACC 60.203 66.667 3.01 0.00 40.67 3.18
3626 4854 0.673437 AGGCCAAAACATCACCAACG 59.327 50.000 5.01 0.00 0.00 4.10
3645 4873 4.096532 TGTCAAATGTGTCGCCTAAAACAA 59.903 37.500 0.00 0.00 0.00 2.83
3655 4883 4.434725 GCATAGTGACTGTCAAATGTGTCG 60.435 45.833 24.05 8.96 32.64 4.35
3659 4887 5.005740 ACATGCATAGTGACTGTCAAATGT 58.994 37.500 24.05 17.79 29.57 2.71
3667 4895 7.725818 AGAATATGAACATGCATAGTGACTG 57.274 36.000 0.00 0.00 34.50 3.51
3668 4896 7.596621 CGTAGAATATGAACATGCATAGTGACT 59.403 37.037 0.00 0.00 34.50 3.41
3669 4897 7.620188 GCGTAGAATATGAACATGCATAGTGAC 60.620 40.741 0.00 0.20 34.50 3.67
3675 4903 5.299949 TCAGCGTAGAATATGAACATGCAT 58.700 37.500 0.00 0.00 0.00 3.96
3676 4904 4.692228 TCAGCGTAGAATATGAACATGCA 58.308 39.130 0.00 0.00 0.00 3.96
3677 4905 5.852738 ATCAGCGTAGAATATGAACATGC 57.147 39.130 0.00 0.00 0.00 4.06
3683 4911 5.576774 CGCCATAAATCAGCGTAGAATATGA 59.423 40.000 12.52 0.00 44.65 2.15
3684 4912 5.789507 CGCCATAAATCAGCGTAGAATATG 58.210 41.667 0.00 0.00 44.65 1.78
3706 4934 3.063452 CCCACCGATCATTTTCTGTTACG 59.937 47.826 0.00 0.00 0.00 3.18
3713 4941 1.476488 CCCAACCCACCGATCATTTTC 59.524 52.381 0.00 0.00 0.00 2.29
3722 4950 1.781153 TAACCTTCCCCAACCCACCG 61.781 60.000 0.00 0.00 0.00 4.94
3724 4952 2.385135 TTTAACCTTCCCCAACCCAC 57.615 50.000 0.00 0.00 0.00 4.61
3725 4953 3.416414 TTTTTAACCTTCCCCAACCCA 57.584 42.857 0.00 0.00 0.00 4.51
3743 4971 4.582701 TTTCACTGCCATCGAACATTTT 57.417 36.364 0.00 0.00 0.00 1.82
3753 4983 5.799681 CAAAACTTTGTTTTCACTGCCAT 57.200 34.783 5.57 0.00 33.59 4.40
3790 5020 5.233050 CACCACGATCATCTCAACTAATGTC 59.767 44.000 0.00 0.00 0.00 3.06
3831 5061 7.041721 AGTTCAGTAAAATGATAGCATGACGA 58.958 34.615 0.00 0.00 34.26 4.20
3832 5062 7.239166 AGTTCAGTAAAATGATAGCATGACG 57.761 36.000 0.00 0.00 34.26 4.35


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

AutoCloner maintained by Alex Coulton.