Multiple sequence alignment - TraesCS2A01G270400

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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 TraesCS2A01G270400 chr2A 100.000 4511 0 0 1 4511 439191806 439196316 0.000000e+00 8331.0
1 TraesCS2A01G270400 chr2D 90.506 2749 166 46 838 3530 331733928 331736637 0.000000e+00 3542.0
2 TraesCS2A01G270400 chr2D 91.632 968 78 2 3546 4511 5420066 5419100 0.000000e+00 1336.0
3 TraesCS2A01G270400 chr2D 84.091 88 8 6 1141 1223 331734142 331734228 3.740000e-11 80.5
4 TraesCS2A01G270400 chr2B 92.387 2417 131 29 1144 3530 399930811 399933204 0.000000e+00 3395.0
5 TraesCS2A01G270400 chr2B 84.536 194 8 11 932 1123 399930701 399930874 6.000000e-39 172.0
6 TraesCS2A01G270400 chr5D 93.182 968 61 3 3546 4511 308023749 308024713 0.000000e+00 1417.0
7 TraesCS2A01G270400 chr5D 91.632 968 78 2 3546 4511 225746713 225747679 0.000000e+00 1336.0
8 TraesCS2A01G270400 chr6D 91.331 969 80 3 3546 4511 224416634 224417601 0.000000e+00 1321.0
9 TraesCS2A01G270400 chr4A 91.219 968 83 1 3546 4511 159496681 159497648 0.000000e+00 1315.0
10 TraesCS2A01G270400 chr3B 91.012 968 85 1 3546 4511 797015902 797016869 0.000000e+00 1304.0
11 TraesCS2A01G270400 chr3B 90.994 966 85 1 3548 4511 101644922 101643957 0.000000e+00 1301.0
12 TraesCS2A01G270400 chr3B 84.186 645 90 10 2056 2695 752491054 752491691 2.310000e-172 616.0
13 TraesCS2A01G270400 chr3B 89.302 215 20 3 2883 3097 798221937 798221726 2.680000e-67 267.0
14 TraesCS2A01G270400 chr3B 78.820 373 52 24 2947 3304 752492352 752492712 4.540000e-55 226.0
15 TraesCS2A01G270400 chr3B 95.890 73 2 1 2898 2970 798225119 798225048 2.850000e-22 117.0
16 TraesCS2A01G270400 chr7D 91.012 968 80 3 3546 4511 66871326 66870364 0.000000e+00 1299.0
17 TraesCS2A01G270400 chr1D 91.012 968 80 3 3546 4511 162721078 162720116 0.000000e+00 1299.0
18 TraesCS2A01G270400 chr1D 91.379 754 52 8 1 743 437103414 437104165 0.000000e+00 1020.0
19 TraesCS2A01G270400 chr1D 81.116 233 41 3 3096 3326 425573525 425573756 2.770000e-42 183.0
20 TraesCS2A01G270400 chr6A 94.899 745 32 2 1 739 262088709 262089453 0.000000e+00 1160.0
21 TraesCS2A01G270400 chr3D 90.987 466 38 3 1 463 234819244 234819708 3.830000e-175 625.0
22 TraesCS2A01G270400 chr3D 84.653 619 79 12 2081 2694 564929342 564929949 1.800000e-168 603.0
23 TraesCS2A01G270400 chr3D 96.071 280 9 1 462 739 234819839 234820118 5.320000e-124 455.0
24 TraesCS2A01G270400 chr3A 84.259 648 84 11 2056 2695 699483027 699483664 2.310000e-172 616.0
25 TraesCS2A01G270400 chr3A 78.284 373 46 29 2947 3304 699484332 699484684 1.640000e-49 207.0
26 TraesCS2A01G270400 chr5A 90.446 314 20 2 1 314 273451103 273450800 5.430000e-109 405.0
27 TraesCS2A01G270400 chrUn 88.255 298 21 6 461 744 24223433 24223136 1.200000e-90 344.0
28 TraesCS2A01G270400 chrUn 87.640 267 31 2 1 266 24224006 24223741 4.380000e-80 309.0
29 TraesCS2A01G270400 chr7B 86.601 306 17 7 457 739 72086848 72086544 2.620000e-82 316.0


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 TraesCS2A01G270400 chr2A 439191806 439196316 4510 False 8331.00 8331 100.0000 1 4511 1 chr2A.!!$F1 4510
1 TraesCS2A01G270400 chr2D 331733928 331736637 2709 False 1811.25 3542 87.2985 838 3530 2 chr2D.!!$F1 2692
2 TraesCS2A01G270400 chr2D 5419100 5420066 966 True 1336.00 1336 91.6320 3546 4511 1 chr2D.!!$R1 965
3 TraesCS2A01G270400 chr2B 399930701 399933204 2503 False 1783.50 3395 88.4615 932 3530 2 chr2B.!!$F1 2598
4 TraesCS2A01G270400 chr5D 308023749 308024713 964 False 1417.00 1417 93.1820 3546 4511 1 chr5D.!!$F2 965
5 TraesCS2A01G270400 chr5D 225746713 225747679 966 False 1336.00 1336 91.6320 3546 4511 1 chr5D.!!$F1 965
6 TraesCS2A01G270400 chr6D 224416634 224417601 967 False 1321.00 1321 91.3310 3546 4511 1 chr6D.!!$F1 965
7 TraesCS2A01G270400 chr4A 159496681 159497648 967 False 1315.00 1315 91.2190 3546 4511 1 chr4A.!!$F1 965
8 TraesCS2A01G270400 chr3B 797015902 797016869 967 False 1304.00 1304 91.0120 3546 4511 1 chr3B.!!$F1 965
9 TraesCS2A01G270400 chr3B 101643957 101644922 965 True 1301.00 1301 90.9940 3548 4511 1 chr3B.!!$R1 963
10 TraesCS2A01G270400 chr3B 752491054 752492712 1658 False 421.00 616 81.5030 2056 3304 2 chr3B.!!$F2 1248
11 TraesCS2A01G270400 chr7D 66870364 66871326 962 True 1299.00 1299 91.0120 3546 4511 1 chr7D.!!$R1 965
12 TraesCS2A01G270400 chr1D 162720116 162721078 962 True 1299.00 1299 91.0120 3546 4511 1 chr1D.!!$R1 965
13 TraesCS2A01G270400 chr1D 437103414 437104165 751 False 1020.00 1020 91.3790 1 743 1 chr1D.!!$F2 742
14 TraesCS2A01G270400 chr6A 262088709 262089453 744 False 1160.00 1160 94.8990 1 739 1 chr6A.!!$F1 738
15 TraesCS2A01G270400 chr3D 564929342 564929949 607 False 603.00 603 84.6530 2081 2694 1 chr3D.!!$F1 613
16 TraesCS2A01G270400 chr3D 234819244 234820118 874 False 540.00 625 93.5290 1 739 2 chr3D.!!$F2 738
17 TraesCS2A01G270400 chr3A 699483027 699484684 1657 False 411.50 616 81.2715 2056 3304 2 chr3A.!!$F1 1248
18 TraesCS2A01G270400 chrUn 24223136 24224006 870 True 326.50 344 87.9475 1 744 2 chrUn.!!$R1 743

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
102 103 0.179001 TCCCGTGACTCTCACTCACA 60.179 55.0 1.14 0.0 44.85 3.58 F
889 1101 0.257616 GGGGTGCCAGTGCCTATTTA 59.742 55.0 0.00 0.0 36.33 1.40 F
1162 1399 0.977395 GTGCTCCCCGCCTCTATTAT 59.023 55.0 0.00 0.0 38.05 1.28 F
2989 3756 0.663153 GTCTCTGCGCAAACTTTGGT 59.337 50.0 13.05 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 1274 0.665835 CAGTAGTCCTAGCAGAGGCG 59.334 60.0 0.0 0.0 46.25 5.52 R
2374 2647 0.682855 CTAGGCCGCATTCCCCAAAA 60.683 55.0 0.0 0.0 0.00 2.44 R
3097 3878 0.034476 TCAGCTCTGAACTGCCACAG 59.966 55.0 3.2 0.0 36.53 3.66 R
4351 5153 2.102420 CCAATCGTGGTACATCCTGCTA 59.898 50.0 0.0 0.0 44.52 3.49 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
102 103 0.179001 TCCCGTGACTCTCACTCACA 60.179 55.000 1.14 0.00 44.85 3.58
230 236 1.372499 CGGACGGAAAGAGCAACGA 60.372 57.895 0.00 0.00 0.00 3.85
607 791 2.990066 ACATTCCATTCCGTCTCTCC 57.010 50.000 0.00 0.00 0.00 3.71
628 814 8.674263 TCTCCTACCAAACAATAAAACGTAAA 57.326 30.769 0.00 0.00 0.00 2.01
661 847 4.693566 CCGTCTAATTGCTTCTACCAAACA 59.306 41.667 0.00 0.00 0.00 2.83
723 909 0.321298 ATTCCGTCCCACTTGGTTCG 60.321 55.000 0.00 0.00 34.77 3.95
739 925 2.937799 GGTTCGTCAACTAAACACACCA 59.062 45.455 0.00 0.00 32.50 4.17
744 930 4.449743 TCGTCAACTAAACACACCATTAGC 59.550 41.667 0.00 0.00 33.39 3.09
745 931 4.212425 CGTCAACTAAACACACCATTAGCA 59.788 41.667 0.00 0.00 33.39 3.49
746 932 5.277586 CGTCAACTAAACACACCATTAGCAA 60.278 40.000 0.00 0.00 33.39 3.91
747 933 6.500041 GTCAACTAAACACACCATTAGCAAA 58.500 36.000 0.00 0.00 33.39 3.68
748 934 6.416750 GTCAACTAAACACACCATTAGCAAAC 59.583 38.462 0.00 0.00 33.39 2.93
749 935 6.095580 TCAACTAAACACACCATTAGCAAACA 59.904 34.615 0.00 0.00 33.39 2.83
750 936 6.648879 ACTAAACACACCATTAGCAAACAT 57.351 33.333 0.00 0.00 33.39 2.71
751 937 7.753309 ACTAAACACACCATTAGCAAACATA 57.247 32.000 0.00 0.00 33.39 2.29
752 938 8.348285 ACTAAACACACCATTAGCAAACATAT 57.652 30.769 0.00 0.00 33.39 1.78
753 939 9.456147 ACTAAACACACCATTAGCAAACATATA 57.544 29.630 0.00 0.00 33.39 0.86
754 940 9.935682 CTAAACACACCATTAGCAAACATATAG 57.064 33.333 0.00 0.00 0.00 1.31
755 941 6.377327 ACACACCATTAGCAAACATATAGC 57.623 37.500 0.00 0.00 0.00 2.97
756 942 5.885352 ACACACCATTAGCAAACATATAGCA 59.115 36.000 0.00 0.00 0.00 3.49
757 943 6.183360 ACACACCATTAGCAAACATATAGCAC 60.183 38.462 0.00 0.00 0.00 4.40
758 944 5.885352 ACACCATTAGCAAACATATAGCACA 59.115 36.000 0.00 0.00 0.00 4.57
759 945 6.038603 ACACCATTAGCAAACATATAGCACAG 59.961 38.462 0.00 0.00 0.00 3.66
760 946 5.532406 ACCATTAGCAAACATATAGCACAGG 59.468 40.000 0.00 0.00 0.00 4.00
761 947 5.532406 CCATTAGCAAACATATAGCACAGGT 59.468 40.000 0.00 0.00 0.00 4.00
762 948 6.039717 CCATTAGCAAACATATAGCACAGGTT 59.960 38.462 0.00 0.00 0.00 3.50
763 949 7.228507 CCATTAGCAAACATATAGCACAGGTTA 59.771 37.037 0.00 0.00 0.00 2.85
764 950 7.786178 TTAGCAAACATATAGCACAGGTTAG 57.214 36.000 0.00 0.00 0.00 2.34
765 951 5.989477 AGCAAACATATAGCACAGGTTAGA 58.011 37.500 0.00 0.00 0.00 2.10
766 952 6.595682 AGCAAACATATAGCACAGGTTAGAT 58.404 36.000 0.00 0.00 0.00 1.98
767 953 7.735917 AGCAAACATATAGCACAGGTTAGATA 58.264 34.615 0.00 0.00 0.00 1.98
768 954 8.378565 AGCAAACATATAGCACAGGTTAGATAT 58.621 33.333 0.00 0.00 0.00 1.63
769 955 8.446273 GCAAACATATAGCACAGGTTAGATATG 58.554 37.037 0.00 0.00 34.75 1.78
770 956 9.710900 CAAACATATAGCACAGGTTAGATATGA 57.289 33.333 6.67 0.00 33.47 2.15
772 958 9.712305 AACATATAGCACAGGTTAGATATGAAC 57.288 33.333 6.67 0.00 33.47 3.18
773 959 8.029522 ACATATAGCACAGGTTAGATATGAACG 58.970 37.037 6.67 0.00 33.47 3.95
774 960 6.650427 ATAGCACAGGTTAGATATGAACGA 57.350 37.500 0.00 0.00 0.00 3.85
775 961 4.938080 AGCACAGGTTAGATATGAACGAG 58.062 43.478 0.00 0.00 0.00 4.18
776 962 4.402793 AGCACAGGTTAGATATGAACGAGT 59.597 41.667 0.00 0.00 0.00 4.18
777 963 4.504461 GCACAGGTTAGATATGAACGAGTG 59.496 45.833 0.00 11.95 36.31 3.51
778 964 5.043903 CACAGGTTAGATATGAACGAGTGG 58.956 45.833 0.00 0.00 32.81 4.00
779 965 4.710375 ACAGGTTAGATATGAACGAGTGGT 59.290 41.667 0.00 0.00 0.00 4.16
780 966 5.889853 ACAGGTTAGATATGAACGAGTGGTA 59.110 40.000 0.00 0.00 0.00 3.25
781 967 6.183360 ACAGGTTAGATATGAACGAGTGGTAC 60.183 42.308 0.00 0.00 0.00 3.34
782 968 5.889853 AGGTTAGATATGAACGAGTGGTACA 59.110 40.000 0.00 0.00 0.00 2.90
783 969 6.550108 AGGTTAGATATGAACGAGTGGTACAT 59.450 38.462 0.00 0.00 44.52 2.29
784 970 7.069578 AGGTTAGATATGAACGAGTGGTACATT 59.930 37.037 0.00 0.00 44.52 2.71
785 971 7.169308 GGTTAGATATGAACGAGTGGTACATTG 59.831 40.741 0.00 0.00 44.52 2.82
786 972 6.465439 AGATATGAACGAGTGGTACATTGA 57.535 37.500 0.00 0.00 44.52 2.57
787 973 6.873997 AGATATGAACGAGTGGTACATTGAA 58.126 36.000 0.00 0.00 44.52 2.69
788 974 7.327975 AGATATGAACGAGTGGTACATTGAAA 58.672 34.615 0.00 0.00 44.52 2.69
789 975 7.987458 AGATATGAACGAGTGGTACATTGAAAT 59.013 33.333 0.00 0.00 44.52 2.17
790 976 5.856126 TGAACGAGTGGTACATTGAAATC 57.144 39.130 0.00 0.00 44.52 2.17
791 977 5.547465 TGAACGAGTGGTACATTGAAATCT 58.453 37.500 0.00 0.00 44.52 2.40
792 978 5.408299 TGAACGAGTGGTACATTGAAATCTG 59.592 40.000 0.00 0.00 44.52 2.90
793 979 3.684788 ACGAGTGGTACATTGAAATCTGC 59.315 43.478 0.00 0.00 44.52 4.26
794 980 3.242091 CGAGTGGTACATTGAAATCTGCG 60.242 47.826 0.00 0.00 44.52 5.18
795 981 3.932710 GAGTGGTACATTGAAATCTGCGA 59.067 43.478 0.00 0.00 44.52 5.10
796 982 3.684788 AGTGGTACATTGAAATCTGCGAC 59.315 43.478 0.00 0.00 44.52 5.19
797 983 3.006940 TGGTACATTGAAATCTGCGACC 58.993 45.455 0.00 0.00 0.00 4.79
798 984 3.006940 GGTACATTGAAATCTGCGACCA 58.993 45.455 0.00 0.00 0.00 4.02
799 985 3.063997 GGTACATTGAAATCTGCGACCAG 59.936 47.826 0.00 0.00 40.54 4.00
800 986 2.783135 ACATTGAAATCTGCGACCAGT 58.217 42.857 0.00 0.00 40.09 4.00
801 987 2.485426 ACATTGAAATCTGCGACCAGTG 59.515 45.455 0.00 0.00 40.09 3.66
802 988 2.542020 TTGAAATCTGCGACCAGTGA 57.458 45.000 0.00 0.00 40.09 3.41
803 989 2.542020 TGAAATCTGCGACCAGTGAA 57.458 45.000 0.00 0.00 40.09 3.18
804 990 2.143122 TGAAATCTGCGACCAGTGAAC 58.857 47.619 0.00 0.00 40.09 3.18
805 991 2.143122 GAAATCTGCGACCAGTGAACA 58.857 47.619 0.00 0.00 40.09 3.18
806 992 2.479566 AATCTGCGACCAGTGAACAT 57.520 45.000 0.00 0.00 40.09 2.71
807 993 3.610040 AATCTGCGACCAGTGAACATA 57.390 42.857 0.00 0.00 40.09 2.29
808 994 2.363788 TCTGCGACCAGTGAACATAC 57.636 50.000 0.00 0.00 40.09 2.39
809 995 0.992072 CTGCGACCAGTGAACATACG 59.008 55.000 0.00 0.00 34.31 3.06
810 996 0.315886 TGCGACCAGTGAACATACGT 59.684 50.000 0.00 0.00 0.00 3.57
811 997 1.269883 TGCGACCAGTGAACATACGTT 60.270 47.619 0.00 0.00 38.33 3.99
812 998 1.796459 GCGACCAGTGAACATACGTTT 59.204 47.619 0.00 0.00 34.75 3.60
813 999 2.988493 GCGACCAGTGAACATACGTTTA 59.012 45.455 0.00 0.00 34.75 2.01
814 1000 3.181537 GCGACCAGTGAACATACGTTTAC 60.182 47.826 0.00 0.00 40.87 2.01
816 1002 4.682860 CGACCAGTGAACATACGTTTACTT 59.317 41.667 0.00 0.00 46.58 2.24
817 1003 5.858049 CGACCAGTGAACATACGTTTACTTA 59.142 40.000 0.00 0.00 46.58 2.24
818 1004 6.529125 CGACCAGTGAACATACGTTTACTTAT 59.471 38.462 0.00 0.00 46.58 1.73
819 1005 7.062605 CGACCAGTGAACATACGTTTACTTATT 59.937 37.037 0.00 0.00 46.58 1.40
820 1006 8.611654 ACCAGTGAACATACGTTTACTTATTT 57.388 30.769 0.00 0.00 46.58 1.40
821 1007 9.059260 ACCAGTGAACATACGTTTACTTATTTT 57.941 29.630 0.00 0.00 46.58 1.82
822 1008 9.887406 CCAGTGAACATACGTTTACTTATTTTT 57.113 29.630 0.00 0.00 46.58 1.94
889 1101 0.257616 GGGGTGCCAGTGCCTATTTA 59.742 55.000 0.00 0.00 36.33 1.40
890 1102 1.389555 GGGTGCCAGTGCCTATTTAC 58.610 55.000 0.00 0.00 36.33 2.01
892 1104 1.064685 GGTGCCAGTGCCTATTTACCT 60.065 52.381 0.00 0.00 36.33 3.08
893 1105 2.171870 GGTGCCAGTGCCTATTTACCTA 59.828 50.000 0.00 0.00 36.33 3.08
894 1106 3.181443 GGTGCCAGTGCCTATTTACCTAT 60.181 47.826 0.00 0.00 36.33 2.57
897 1109 3.328050 GCCAGTGCCTATTTACCTATCCT 59.672 47.826 0.00 0.00 0.00 3.24
923 1135 5.530176 TTTTAGGCTCTCCCATTTTACCT 57.470 39.130 0.00 0.00 35.39 3.08
924 1136 6.645884 TTTTAGGCTCTCCCATTTTACCTA 57.354 37.500 0.00 0.00 35.39 3.08
925 1137 6.841781 TTTAGGCTCTCCCATTTTACCTAT 57.158 37.500 0.00 0.00 35.39 2.57
926 1138 4.984146 AGGCTCTCCCATTTTACCTATC 57.016 45.455 0.00 0.00 35.39 2.08
927 1139 3.653352 AGGCTCTCCCATTTTACCTATCC 59.347 47.826 0.00 0.00 35.39 2.59
928 1140 3.653352 GGCTCTCCCATTTTACCTATCCT 59.347 47.826 0.00 0.00 0.00 3.24
929 1141 4.104897 GGCTCTCCCATTTTACCTATCCTT 59.895 45.833 0.00 0.00 0.00 3.36
930 1142 5.399152 GGCTCTCCCATTTTACCTATCCTTT 60.399 44.000 0.00 0.00 0.00 3.11
931 1143 5.765677 GCTCTCCCATTTTACCTATCCTTTC 59.234 44.000 0.00 0.00 0.00 2.62
932 1144 6.409810 GCTCTCCCATTTTACCTATCCTTTCT 60.410 42.308 0.00 0.00 0.00 2.52
933 1145 7.138054 TCTCCCATTTTACCTATCCTTTCTC 57.862 40.000 0.00 0.00 0.00 2.87
934 1146 6.676632 TCTCCCATTTTACCTATCCTTTCTCA 59.323 38.462 0.00 0.00 0.00 3.27
935 1147 6.659824 TCCCATTTTACCTATCCTTTCTCAC 58.340 40.000 0.00 0.00 0.00 3.51
958 1170 0.979665 CTTTCAGCCCAGACTCTCCA 59.020 55.000 0.00 0.00 0.00 3.86
1126 1362 2.284331 TCAACTCCGGCCCTGCTA 60.284 61.111 0.00 0.00 0.00 3.49
1127 1363 1.899437 CTCAACTCCGGCCCTGCTAA 61.899 60.000 0.00 0.00 0.00 3.09
1142 1378 1.269673 TGCTAAACTGCGTACGTTCCA 60.270 47.619 17.90 5.50 35.36 3.53
1162 1399 0.977395 GTGCTCCCCGCCTCTATTAT 59.023 55.000 0.00 0.00 38.05 1.28
1163 1400 2.176889 GTGCTCCCCGCCTCTATTATA 58.823 52.381 0.00 0.00 38.05 0.98
1377 1615 7.927629 TCCCTGATTTGTCAAATTTTCTTTCTG 59.072 33.333 12.04 3.23 0.00 3.02
1458 1713 3.261137 AGGTGTAGGTTCTTTCTGTAGGC 59.739 47.826 0.00 0.00 0.00 3.93
1517 1772 9.166173 TGATTTGATCTGGTAGTATCTTTTGTG 57.834 33.333 0.00 0.00 0.00 3.33
1532 1787 5.734720 TCTTTTGTGTCCCTGCTCTATTAG 58.265 41.667 0.00 0.00 0.00 1.73
1538 1793 5.189736 TGTGTCCCTGCTCTATTAGATGTTT 59.810 40.000 0.00 0.00 0.00 2.83
1540 1795 6.258947 GTGTCCCTGCTCTATTAGATGTTTTC 59.741 42.308 0.00 0.00 0.00 2.29
1596 1851 8.658609 CATCAAGTGTTGAAGTTCAAATTTGTT 58.341 29.630 19.63 14.62 43.95 2.83
1597 1852 8.600449 TCAAGTGTTGAAGTTCAAATTTGTTT 57.400 26.923 19.63 10.68 38.22 2.83
1640 1895 3.429492 TCTGTTTATGCTTTGCCATGGA 58.571 40.909 18.40 0.00 0.00 3.41
1651 1906 4.501400 GCTTTGCCATGGAGTACTTTTTGT 60.501 41.667 18.40 0.00 0.00 2.83
1652 1907 5.278758 GCTTTGCCATGGAGTACTTTTTGTA 60.279 40.000 18.40 0.00 0.00 2.41
1724 1983 2.550423 CCTGGCTCCATGAATCTGCTAG 60.550 54.545 0.00 0.00 33.11 3.42
1788 2047 7.990314 TGAGAACGGAACATGATCCATTATAAA 59.010 33.333 20.74 0.30 39.61 1.40
1862 2121 9.717942 AGTGGACTTATCTATTAGATCAAATGC 57.282 33.333 9.47 1.72 36.20 3.56
1915 2174 3.005791 AGCCTTGACTGCATTTGTTTACC 59.994 43.478 0.00 0.00 0.00 2.85
1921 2180 5.035784 GACTGCATTTGTTTACCAGTCTC 57.964 43.478 10.79 0.00 45.39 3.36
1932 2191 7.361457 TGTTTACCAGTCTCTATTAGATGGG 57.639 40.000 13.76 7.34 37.28 4.00
1971 2230 2.099921 TGAAATCGTGGGTGGTGTTTTG 59.900 45.455 0.00 0.00 0.00 2.44
1979 2238 4.116238 GTGGGTGGTGTTTTGTTTATGTG 58.884 43.478 0.00 0.00 0.00 3.21
2112 2383 5.779922 TGATGGTATAGTGGCGAAGATAAC 58.220 41.667 0.00 0.00 0.00 1.89
2123 2394 7.103641 AGTGGCGAAGATAACTCTTTTAATGA 58.896 34.615 0.00 0.00 41.87 2.57
2243 2516 1.063567 AGGGGCACAAGTGGTTTTACA 60.064 47.619 2.00 0.00 0.00 2.41
2443 2716 9.617975 GGTGCTAATAATTTCTAAAGCATCATC 57.382 33.333 0.74 0.00 41.53 2.92
2462 2735 3.939740 TCAATTCCTCTAGGCAGCATT 57.060 42.857 0.00 0.00 34.44 3.56
2474 2747 3.209410 AGGCAGCATTATAAGTGTCTGC 58.791 45.455 20.23 20.23 41.57 4.26
2502 2777 6.315393 TGTGTTTTCCAGTTCTGTTTAGACTC 59.685 38.462 0.00 0.00 31.21 3.36
2512 2788 9.834628 CAGTTCTGTTTAGACTCTTAGAAGTAG 57.165 37.037 0.00 0.00 31.21 2.57
2727 3020 7.901002 TCTTTTCTTTTTAACAATCGGTTTGC 58.099 30.769 0.00 0.00 40.96 3.68
2728 3021 6.591313 TTTCTTTTTAACAATCGGTTTGCC 57.409 33.333 0.00 0.00 40.96 4.52
2740 3033 0.878416 GGTTTGCCGCACAATGAGTA 59.122 50.000 0.00 0.00 38.31 2.59
2751 3044 6.413818 GCCGCACAATGAGTATATTTAACAAC 59.586 38.462 0.00 0.00 0.00 3.32
2822 3588 9.753674 ATCACATGACCTCCTTTCTAATTTTTA 57.246 29.630 0.00 0.00 0.00 1.52
2989 3756 0.663153 GTCTCTGCGCAAACTTTGGT 59.337 50.000 13.05 0.00 0.00 3.67
3039 3806 5.161943 TGATGCTCATCCTCATATCCTTG 57.838 43.478 7.34 0.00 37.02 3.61
3061 3842 9.010029 CCTTGGATGTACTAGTTATTTTGTTGT 57.990 33.333 0.00 0.00 0.00 3.32
3088 3869 5.538433 TCCCTAACAGAAAGGAATGTTTTGG 59.462 40.000 0.00 0.59 40.09 3.28
3089 3870 5.304357 CCCTAACAGAAAGGAATGTTTTGGT 59.696 40.000 0.00 0.00 40.09 3.67
3127 3908 3.815856 TCAGAGCTGACCATCAATCTC 57.184 47.619 0.00 0.00 34.14 2.75
3164 3945 1.904865 CAGGGCCTGCAAGAAAGCA 60.905 57.895 22.68 0.00 43.35 3.91
3236 4017 1.067212 GACCGTATGACGCAGGAGATT 59.933 52.381 0.00 0.00 40.91 2.40
3306 4090 7.165427 AGTTAGTAAGTTAACGTTTGTTCCG 57.835 36.000 5.91 0.00 39.54 4.30
3331 4115 4.480386 CAGCAGTCTGGAAAAAGAACTC 57.520 45.455 1.14 0.00 36.68 3.01
3332 4116 3.879295 CAGCAGTCTGGAAAAAGAACTCA 59.121 43.478 1.14 0.00 36.68 3.41
3333 4117 4.518211 CAGCAGTCTGGAAAAAGAACTCAT 59.482 41.667 1.14 0.00 36.68 2.90
3334 4118 5.702670 CAGCAGTCTGGAAAAAGAACTCATA 59.297 40.000 1.14 0.00 36.68 2.15
3335 4119 6.205464 CAGCAGTCTGGAAAAAGAACTCATAA 59.795 38.462 1.14 0.00 36.68 1.90
3360 4144 4.725556 TCTAGACAAACGACATTGTTGC 57.274 40.909 3.84 0.00 43.31 4.17
3361 4145 2.774439 AGACAAACGACATTGTTGCC 57.226 45.000 3.84 0.00 43.31 4.52
3374 4158 1.598130 GTTGCCGCTCTGTCCAAGT 60.598 57.895 0.00 0.00 0.00 3.16
3376 4160 2.031163 GCCGCTCTGTCCAAGTGT 59.969 61.111 0.00 0.00 0.00 3.55
3379 4163 1.595109 CGCTCTGTCCAAGTGTGCA 60.595 57.895 0.00 0.00 0.00 4.57
3432 4222 6.144078 CTCTAGAGAGAGCTTAGGGAAAAC 57.856 45.833 15.05 0.00 42.86 2.43
3460 4250 5.247507 TCTTGTGGAAGAAATGTTGTGTG 57.752 39.130 0.00 0.00 35.14 3.82
3471 4261 7.750229 AGAAATGTTGTGTGACTAATCATGT 57.250 32.000 0.00 0.00 37.14 3.21
3478 4275 5.359756 TGTGTGACTAATCATGTAGCATCC 58.640 41.667 0.00 0.00 37.14 3.51
3487 4284 0.037326 ATGTAGCATCCGGTATGGCG 60.037 55.000 0.00 0.00 37.80 5.69
3488 4285 1.110518 TGTAGCATCCGGTATGGCGA 61.111 55.000 0.00 0.00 37.80 5.54
3513 4310 4.708726 AGAATGATGCAGTTTAGCCAAC 57.291 40.909 0.00 0.00 35.32 3.77
3530 4327 3.930229 GCCAACGTTTTCCTGTTTCTTTT 59.070 39.130 0.00 0.00 0.00 2.27
3531 4328 4.032445 GCCAACGTTTTCCTGTTTCTTTTC 59.968 41.667 0.00 0.00 0.00 2.29
3532 4329 4.264380 CCAACGTTTTCCTGTTTCTTTTCG 59.736 41.667 0.00 0.00 0.00 3.46
3533 4330 4.950434 ACGTTTTCCTGTTTCTTTTCGA 57.050 36.364 0.00 0.00 0.00 3.71
3534 4331 5.299582 ACGTTTTCCTGTTTCTTTTCGAA 57.700 34.783 0.00 0.00 0.00 3.71
3535 4332 5.701855 ACGTTTTCCTGTTTCTTTTCGAAA 58.298 33.333 6.47 6.47 39.23 3.46
3536 4333 6.151004 ACGTTTTCCTGTTTCTTTTCGAAAA 58.849 32.000 21.35 21.35 42.87 2.29
3537 4334 6.307077 ACGTTTTCCTGTTTCTTTTCGAAAAG 59.693 34.615 34.61 34.61 42.87 2.27
3538 4335 6.237463 CGTTTTCCTGTTTCTTTTCGAAAAGG 60.237 38.462 37.27 26.70 42.87 3.11
3539 4336 4.911514 TCCTGTTTCTTTTCGAAAAGGG 57.088 40.909 37.27 30.85 42.87 3.95
3540 4337 3.634910 TCCTGTTTCTTTTCGAAAAGGGG 59.365 43.478 37.27 29.68 42.87 4.79
3541 4338 3.243737 CCTGTTTCTTTTCGAAAAGGGGG 60.244 47.826 37.27 28.14 42.87 5.40
3564 4361 7.335627 GGGGCTTTAAAAGGTTTAAGCATTAT 58.664 34.615 11.06 0.00 46.43 1.28
3579 4376 0.396811 ATTATACCCGGCCTCTGCAC 59.603 55.000 0.00 0.00 40.13 4.57
3580 4377 0.978667 TTATACCCGGCCTCTGCACA 60.979 55.000 0.00 0.00 40.13 4.57
3597 4395 4.831107 TGCACAACTAAGATGCACATAGA 58.169 39.130 8.72 0.00 44.17 1.98
3634 4432 8.764287 CCTCTCGCACAAAAGAAAAATAAAAAT 58.236 29.630 0.00 0.00 0.00 1.82
3700 4498 0.919710 AGGTGGGCCAATCCTAAGAC 59.080 55.000 13.77 0.00 37.19 3.01
3712 4510 0.254178 CCTAAGACCATGCTGCCACT 59.746 55.000 0.00 0.00 0.00 4.00
3727 4525 3.658757 GCCACTCATGTTGGCTAAAAA 57.341 42.857 25.12 0.00 44.72 1.94
3737 4535 4.850680 TGTTGGCTAAAAATATCCCTCGT 58.149 39.130 0.00 0.00 0.00 4.18
3804 4602 0.242825 CCACGCGTTGTAGAGAGGAA 59.757 55.000 10.22 0.00 0.00 3.36
3853 4653 5.021033 AGATAACCTGCATCAGAGAAGTG 57.979 43.478 0.00 0.00 32.44 3.16
3918 4718 0.167908 CAAATAACGGCAAGCGCTCA 59.832 50.000 12.06 0.00 38.60 4.26
4010 4810 3.330701 ACAAGGAGGATACAAGCCAGAAA 59.669 43.478 0.00 0.00 41.41 2.52
4035 4835 7.911651 ACTATTTGGATGACTGACCATATAGG 58.088 38.462 19.43 8.63 44.53 2.57
4063 4864 7.410087 CGAGCTAATTTGCATTGAAAGAACAAG 60.410 37.037 14.27 0.00 33.22 3.16
4084 4885 8.394971 ACAAGTGTTTTATTGTCTCATCATGA 57.605 30.769 0.00 0.00 34.62 3.07
4113 4914 2.236146 AGACACATTGCGGACTTCCATA 59.764 45.455 0.00 0.00 35.14 2.74
4209 5010 5.300539 TCTTCAGAGGTATCTTCATCTTCCG 59.699 44.000 0.00 0.00 31.64 4.30
4252 5054 4.080129 ACTGGCACATCAGACTGGATTAAT 60.080 41.667 1.81 0.00 38.20 1.40
4348 5150 2.668185 ATTGCACCGTGGACAACCGA 62.668 55.000 0.00 0.00 39.42 4.69
4374 5176 2.679639 GCAGGATGTACCACGATTGGAA 60.680 50.000 0.00 0.00 42.07 3.53
4442 5244 2.025589 TTGCATTACCGTGGCGATAA 57.974 45.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.710326 CGATTCGGAGGTATGACTTCA 57.290 47.619 0.00 0.00 0.00 3.02
88 89 1.687563 TTCGGTGTGAGTGAGAGTCA 58.312 50.000 0.00 0.00 0.00 3.41
102 103 1.270678 CGAGAAGGAAAGGGTTTCGGT 60.271 52.381 0.00 0.00 40.57 4.69
290 296 2.650322 TCCCTGTCTCTCTCTTACCTGT 59.350 50.000 0.00 0.00 0.00 4.00
291 297 3.287222 CTCCCTGTCTCTCTCTTACCTG 58.713 54.545 0.00 0.00 0.00 4.00
628 814 4.526970 AGCAATTAGACGGAATGGAATGT 58.473 39.130 0.00 0.00 0.00 2.71
723 909 5.682943 TGCTAATGGTGTGTTTAGTTGAC 57.317 39.130 0.00 0.00 0.00 3.18
739 925 8.210946 TCTAACCTGTGCTATATGTTTGCTAAT 58.789 33.333 0.00 0.00 0.00 1.73
744 930 9.710900 TCATATCTAACCTGTGCTATATGTTTG 57.289 33.333 0.00 0.00 32.00 2.93
746 932 9.712305 GTTCATATCTAACCTGTGCTATATGTT 57.288 33.333 0.00 0.00 32.00 2.71
747 933 8.029522 CGTTCATATCTAACCTGTGCTATATGT 58.970 37.037 0.00 0.00 32.00 2.29
748 934 8.244113 TCGTTCATATCTAACCTGTGCTATATG 58.756 37.037 0.00 0.00 0.00 1.78
749 935 8.349568 TCGTTCATATCTAACCTGTGCTATAT 57.650 34.615 0.00 0.00 0.00 0.86
750 936 7.447545 ACTCGTTCATATCTAACCTGTGCTATA 59.552 37.037 0.00 0.00 0.00 1.31
751 937 6.265649 ACTCGTTCATATCTAACCTGTGCTAT 59.734 38.462 0.00 0.00 0.00 2.97
752 938 5.593095 ACTCGTTCATATCTAACCTGTGCTA 59.407 40.000 0.00 0.00 0.00 3.49
753 939 4.402793 ACTCGTTCATATCTAACCTGTGCT 59.597 41.667 0.00 0.00 0.00 4.40
754 940 4.504461 CACTCGTTCATATCTAACCTGTGC 59.496 45.833 0.00 0.00 0.00 4.57
755 941 5.043903 CCACTCGTTCATATCTAACCTGTG 58.956 45.833 0.00 0.00 0.00 3.66
756 942 4.710375 ACCACTCGTTCATATCTAACCTGT 59.290 41.667 0.00 0.00 0.00 4.00
757 943 5.263968 ACCACTCGTTCATATCTAACCTG 57.736 43.478 0.00 0.00 0.00 4.00
758 944 5.889853 TGTACCACTCGTTCATATCTAACCT 59.110 40.000 0.00 0.00 0.00 3.50
759 945 6.140303 TGTACCACTCGTTCATATCTAACC 57.860 41.667 0.00 0.00 0.00 2.85
760 946 7.919091 TCAATGTACCACTCGTTCATATCTAAC 59.081 37.037 0.00 0.00 31.81 2.34
761 947 8.002984 TCAATGTACCACTCGTTCATATCTAA 57.997 34.615 0.00 0.00 31.81 2.10
762 948 7.576861 TCAATGTACCACTCGTTCATATCTA 57.423 36.000 0.00 0.00 31.81 1.98
763 949 6.465439 TCAATGTACCACTCGTTCATATCT 57.535 37.500 0.00 0.00 31.81 1.98
764 950 7.534085 TTTCAATGTACCACTCGTTCATATC 57.466 36.000 0.00 0.00 31.81 1.63
765 951 7.987458 AGATTTCAATGTACCACTCGTTCATAT 59.013 33.333 0.00 0.00 31.81 1.78
766 952 7.277760 CAGATTTCAATGTACCACTCGTTCATA 59.722 37.037 0.00 0.00 31.81 2.15
767 953 6.092670 CAGATTTCAATGTACCACTCGTTCAT 59.907 38.462 0.00 0.00 34.22 2.57
768 954 5.408299 CAGATTTCAATGTACCACTCGTTCA 59.592 40.000 0.00 0.00 0.00 3.18
769 955 5.671329 GCAGATTTCAATGTACCACTCGTTC 60.671 44.000 0.00 0.00 0.00 3.95
770 956 4.154195 GCAGATTTCAATGTACCACTCGTT 59.846 41.667 0.00 0.00 0.00 3.85
771 957 3.684788 GCAGATTTCAATGTACCACTCGT 59.315 43.478 0.00 0.00 0.00 4.18
772 958 3.242091 CGCAGATTTCAATGTACCACTCG 60.242 47.826 0.00 0.00 0.00 4.18
773 959 3.932710 TCGCAGATTTCAATGTACCACTC 59.067 43.478 0.00 0.00 0.00 3.51
774 960 3.684788 GTCGCAGATTTCAATGTACCACT 59.315 43.478 0.00 0.00 40.67 4.00
775 961 3.181510 GGTCGCAGATTTCAATGTACCAC 60.182 47.826 0.00 0.00 40.67 4.16
776 962 3.006940 GGTCGCAGATTTCAATGTACCA 58.993 45.455 0.00 0.00 40.67 3.25
777 963 3.006940 TGGTCGCAGATTTCAATGTACC 58.993 45.455 0.00 0.00 40.67 3.34
778 964 3.684788 ACTGGTCGCAGATTTCAATGTAC 59.315 43.478 0.00 0.00 40.67 2.90
779 965 3.684305 CACTGGTCGCAGATTTCAATGTA 59.316 43.478 0.00 0.00 40.67 2.29
780 966 2.485426 CACTGGTCGCAGATTTCAATGT 59.515 45.455 0.00 0.00 40.67 2.71
781 967 2.743664 TCACTGGTCGCAGATTTCAATG 59.256 45.455 0.00 0.00 40.67 2.82
782 968 3.057969 TCACTGGTCGCAGATTTCAAT 57.942 42.857 0.00 0.00 40.67 2.57
783 969 2.542020 TCACTGGTCGCAGATTTCAA 57.458 45.000 0.00 0.00 40.67 2.69
784 970 2.143122 GTTCACTGGTCGCAGATTTCA 58.857 47.619 0.00 0.00 40.67 2.69
785 971 2.143122 TGTTCACTGGTCGCAGATTTC 58.857 47.619 0.00 0.00 40.67 2.17
786 972 2.254546 TGTTCACTGGTCGCAGATTT 57.745 45.000 0.00 0.00 40.67 2.17
787 973 2.479566 ATGTTCACTGGTCGCAGATT 57.520 45.000 0.00 0.00 40.67 2.40
788 974 2.735444 CGTATGTTCACTGGTCGCAGAT 60.735 50.000 0.00 0.00 40.67 2.90
789 975 1.402325 CGTATGTTCACTGGTCGCAGA 60.402 52.381 0.00 0.00 0.00 4.26
790 976 0.992072 CGTATGTTCACTGGTCGCAG 59.008 55.000 0.00 0.00 0.00 5.18
791 977 0.315886 ACGTATGTTCACTGGTCGCA 59.684 50.000 0.00 0.00 0.00 5.10
792 978 1.425412 AACGTATGTTCACTGGTCGC 58.575 50.000 0.00 0.00 30.83 5.19
793 979 4.232221 AGTAAACGTATGTTCACTGGTCG 58.768 43.478 2.63 0.00 35.18 4.79
794 980 7.823149 ATAAGTAAACGTATGTTCACTGGTC 57.177 36.000 4.32 0.00 35.44 4.02
795 981 8.611654 AAATAAGTAAACGTATGTTCACTGGT 57.388 30.769 4.32 0.00 35.44 4.00
796 982 9.887406 AAAAATAAGTAAACGTATGTTCACTGG 57.113 29.630 4.32 0.00 35.44 4.00
823 1009 9.059260 ACACAAAAAGTAAACGTATATTGTCCT 57.941 29.630 0.00 0.00 0.00 3.85
824 1010 9.109533 CACACAAAAAGTAAACGTATATTGTCC 57.890 33.333 0.00 0.00 0.00 4.02
825 1011 9.654417 ACACACAAAAAGTAAACGTATATTGTC 57.346 29.630 0.00 0.00 0.00 3.18
826 1012 9.440784 CACACACAAAAAGTAAACGTATATTGT 57.559 29.630 0.00 0.00 0.00 2.71
827 1013 9.653067 TCACACACAAAAAGTAAACGTATATTG 57.347 29.630 0.00 0.00 0.00 1.90
828 1014 9.872757 CTCACACACAAAAAGTAAACGTATATT 57.127 29.630 0.00 0.00 0.00 1.28
829 1015 9.263538 TCTCACACACAAAAAGTAAACGTATAT 57.736 29.630 0.00 0.00 0.00 0.86
830 1016 8.645730 TCTCACACACAAAAAGTAAACGTATA 57.354 30.769 0.00 0.00 0.00 1.47
831 1017 7.493320 TCTCTCACACACAAAAAGTAAACGTAT 59.507 33.333 0.00 0.00 0.00 3.06
832 1018 6.812656 TCTCTCACACACAAAAAGTAAACGTA 59.187 34.615 0.00 0.00 0.00 3.57
833 1019 5.640357 TCTCTCACACACAAAAAGTAAACGT 59.360 36.000 0.00 0.00 0.00 3.99
834 1020 6.035650 TCTCTCTCACACACAAAAAGTAAACG 59.964 38.462 0.00 0.00 0.00 3.60
835 1021 7.277981 TCTCTCTCTCACACACAAAAAGTAAAC 59.722 37.037 0.00 0.00 0.00 2.01
836 1022 7.327975 TCTCTCTCTCACACACAAAAAGTAAA 58.672 34.615 0.00 0.00 0.00 2.01
846 1032 3.367910 GGGTCAATCTCTCTCTCACACAC 60.368 52.174 0.00 0.00 0.00 3.82
847 1033 2.828520 GGGTCAATCTCTCTCTCACACA 59.171 50.000 0.00 0.00 0.00 3.72
848 1034 2.167487 GGGGTCAATCTCTCTCTCACAC 59.833 54.545 0.00 0.00 0.00 3.82
912 1124 5.527582 CGTGAGAAAGGATAGGTAAAATGGG 59.472 44.000 0.00 0.00 0.00 4.00
913 1125 5.007724 GCGTGAGAAAGGATAGGTAAAATGG 59.992 44.000 0.00 0.00 0.00 3.16
914 1126 5.584649 TGCGTGAGAAAGGATAGGTAAAATG 59.415 40.000 0.00 0.00 0.00 2.32
915 1127 5.585047 GTGCGTGAGAAAGGATAGGTAAAAT 59.415 40.000 0.00 0.00 0.00 1.82
921 1133 2.969628 AGTGCGTGAGAAAGGATAGG 57.030 50.000 0.00 0.00 0.00 2.57
922 1134 4.245660 TGAAAGTGCGTGAGAAAGGATAG 58.754 43.478 0.00 0.00 0.00 2.08
923 1135 4.245660 CTGAAAGTGCGTGAGAAAGGATA 58.754 43.478 0.00 0.00 0.00 2.59
924 1136 3.070018 CTGAAAGTGCGTGAGAAAGGAT 58.930 45.455 0.00 0.00 0.00 3.24
925 1137 2.483876 CTGAAAGTGCGTGAGAAAGGA 58.516 47.619 0.00 0.00 0.00 3.36
926 1138 1.069636 GCTGAAAGTGCGTGAGAAAGG 60.070 52.381 0.00 0.00 35.30 3.11
927 1139 1.069636 GGCTGAAAGTGCGTGAGAAAG 60.070 52.381 0.00 0.00 35.30 2.62
928 1140 0.944386 GGCTGAAAGTGCGTGAGAAA 59.056 50.000 0.00 0.00 35.30 2.52
929 1141 0.884704 GGGCTGAAAGTGCGTGAGAA 60.885 55.000 0.00 0.00 35.30 2.87
930 1142 1.301716 GGGCTGAAAGTGCGTGAGA 60.302 57.895 0.00 0.00 35.30 3.27
931 1143 1.572085 CTGGGCTGAAAGTGCGTGAG 61.572 60.000 0.00 0.00 35.30 3.51
932 1144 1.597854 CTGGGCTGAAAGTGCGTGA 60.598 57.895 0.00 0.00 35.30 4.35
933 1145 1.597854 TCTGGGCTGAAAGTGCGTG 60.598 57.895 0.00 0.00 35.30 5.34
934 1146 1.598130 GTCTGGGCTGAAAGTGCGT 60.598 57.895 0.00 0.00 35.30 5.24
935 1147 1.294659 GAGTCTGGGCTGAAAGTGCG 61.295 60.000 0.00 0.00 35.30 5.34
958 1170 0.325296 TCTCTGGGCCGTCTATTGGT 60.325 55.000 0.00 0.00 0.00 3.67
1058 1273 1.104577 AGTAGTCCTAGCAGAGGCGC 61.105 60.000 0.00 0.00 46.25 6.53
1059 1274 0.665835 CAGTAGTCCTAGCAGAGGCG 59.334 60.000 0.00 0.00 46.25 5.52
1100 1335 3.003173 CGGAGTTGAGAGGGGCCA 61.003 66.667 4.39 0.00 0.00 5.36
1126 1362 1.214367 CACTGGAACGTACGCAGTTT 58.786 50.000 19.99 6.44 37.78 2.66
1127 1363 1.219522 GCACTGGAACGTACGCAGTT 61.220 55.000 19.99 6.78 37.78 3.16
1310 1548 2.623889 ACTAGTGCTGCGATAGTTAGGG 59.376 50.000 9.90 0.00 39.35 3.53
1311 1549 3.566322 AGACTAGTGCTGCGATAGTTAGG 59.434 47.826 15.10 0.00 39.35 2.69
1377 1615 5.709164 AGAACATATATCAATGCAAGCCCTC 59.291 40.000 0.00 0.00 0.00 4.30
1458 1713 7.066163 TCACTGTTTGATATGAGCTTTACATGG 59.934 37.037 0.00 0.00 0.00 3.66
1517 1772 6.587273 AGAAAACATCTAATAGAGCAGGGAC 58.413 40.000 0.00 0.00 36.32 4.46
1538 1793 9.349713 ACAAAGTAGATTAAACATGACCAAGAA 57.650 29.630 0.00 0.00 0.00 2.52
1540 1795 9.398170 CAACAAAGTAGATTAAACATGACCAAG 57.602 33.333 0.00 0.00 0.00 3.61
1596 1851 7.449395 CAGATTAAAGGAATATGGCTCCATGAA 59.551 37.037 11.49 0.00 37.82 2.57
1597 1852 6.944290 CAGATTAAAGGAATATGGCTCCATGA 59.056 38.462 11.49 0.00 37.82 3.07
1672 1927 1.970640 GTCCCAGGCCAAAATTCAAGT 59.029 47.619 5.01 0.00 0.00 3.16
1724 1983 2.410730 CGGTGGAAACTCGACATAACAC 59.589 50.000 0.00 0.00 0.00 3.32
1788 2047 2.626743 GCTGCTATGAATCAATGGGCTT 59.373 45.455 0.00 0.00 0.00 4.35
1915 2174 9.838339 AAAAACATACCCATCTAATAGAGACTG 57.162 33.333 0.00 0.00 36.87 3.51
2050 2311 4.277423 ACAGTTTTCCGTTTGGGTATTGAG 59.723 41.667 0.00 0.00 37.00 3.02
2112 2383 5.128919 AGCATAGCCAGGTCATTAAAAGAG 58.871 41.667 0.00 0.00 0.00 2.85
2123 2394 1.765314 CAGTAAGGAGCATAGCCAGGT 59.235 52.381 0.00 0.00 0.00 4.00
2213 2486 0.906066 TTGTGCCCCTGCTTATCGTA 59.094 50.000 0.00 0.00 38.71 3.43
2243 2516 5.363580 ACCTGTTCTTGAAATGAACCATTGT 59.636 36.000 0.00 0.00 46.83 2.71
2374 2647 0.682855 CTAGGCCGCATTCCCCAAAA 60.683 55.000 0.00 0.00 0.00 2.44
2443 2716 6.939163 ACTTATAATGCTGCCTAGAGGAATTG 59.061 38.462 0.00 0.00 37.39 2.32
2462 2735 5.468746 GGAAAACACACTGCAGACACTTATA 59.531 40.000 23.35 0.00 0.00 0.98
2474 2747 4.701956 AACAGAACTGGAAAACACACTG 57.298 40.909 6.76 0.00 34.19 3.66
2502 2777 5.417580 ACCAGAGCTCAGAACTACTTCTAAG 59.582 44.000 17.77 0.00 34.74 2.18
2512 2788 3.195396 AGAAGATGACCAGAGCTCAGAAC 59.805 47.826 17.77 6.07 0.00 3.01
2727 3020 6.910433 GGTTGTTAAATATACTCATTGTGCGG 59.090 38.462 0.00 0.00 0.00 5.69
2728 3021 7.639850 CAGGTTGTTAAATATACTCATTGTGCG 59.360 37.037 0.00 0.00 0.00 5.34
2733 3026 9.686683 AGAAGCAGGTTGTTAAATATACTCATT 57.313 29.630 0.00 0.00 0.00 2.57
2751 3044 5.992217 ACACTCAAAAGTACTAAGAAGCAGG 59.008 40.000 0.00 0.00 33.25 4.85
2857 3624 1.108776 CGGGGTCTCGGTGAGATAAA 58.891 55.000 0.00 0.00 40.98 1.40
2860 3627 1.454111 CTCGGGGTCTCGGTGAGAT 60.454 63.158 0.00 0.00 40.98 2.75
2989 3756 6.950619 ACTATACATGGAGTAGCATCATCAGA 59.049 38.462 0.00 0.00 35.85 3.27
3058 3839 5.576563 TTCCTTTCTGTTAGGGATCACAA 57.423 39.130 0.00 0.00 33.41 3.33
3061 3842 5.779241 ACATTCCTTTCTGTTAGGGATCA 57.221 39.130 0.00 0.00 27.82 2.92
3097 3878 0.034476 TCAGCTCTGAACTGCCACAG 59.966 55.000 3.20 0.00 36.53 3.66
3291 4072 1.063764 TGGCACGGAACAAACGTTAAC 59.936 47.619 0.00 0.00 43.58 2.01
3296 4080 2.051345 GCTGGCACGGAACAAACG 60.051 61.111 0.00 0.00 36.31 3.60
3334 4118 7.962918 GCAACAATGTCGTTTGTCTAGATTATT 59.037 33.333 0.00 0.00 38.85 1.40
3335 4119 7.414098 GGCAACAATGTCGTTTGTCTAGATTAT 60.414 37.037 0.00 0.00 38.85 1.28
3351 4135 1.237285 GGACAGAGCGGCAACAATGT 61.237 55.000 1.45 0.00 0.00 2.71
3358 4142 2.031012 CACTTGGACAGAGCGGCA 59.969 61.111 1.45 0.00 0.00 5.69
3360 4144 2.320587 GCACACTTGGACAGAGCGG 61.321 63.158 0.00 0.00 0.00 5.52
3361 4145 1.159713 TTGCACACTTGGACAGAGCG 61.160 55.000 0.00 0.00 0.00 5.03
3397 4187 5.901552 CTCTCTCTAGAGTAGGCCTTTTTG 58.098 45.833 12.58 0.00 43.75 2.44
3413 4203 3.432378 TCGTTTTCCCTAAGCTCTCTCT 58.568 45.455 0.00 0.00 0.00 3.10
3417 4207 3.983044 ACATCGTTTTCCCTAAGCTCT 57.017 42.857 0.00 0.00 0.00 4.09
3432 4222 5.362556 ACATTTCTTCCACAAGAACATCG 57.637 39.130 0.00 0.00 46.38 3.84
3460 4250 4.258702 ACCGGATGCTACATGATTAGTC 57.741 45.455 9.46 0.00 0.00 2.59
3471 4261 0.753867 TTTCGCCATACCGGATGCTA 59.246 50.000 9.46 0.00 36.56 3.49
3478 4275 4.282068 CATCATTCTTTTTCGCCATACCG 58.718 43.478 0.00 0.00 0.00 4.02
3487 4284 6.158598 TGGCTAAACTGCATCATTCTTTTTC 58.841 36.000 0.00 0.00 34.04 2.29
3488 4285 6.100404 TGGCTAAACTGCATCATTCTTTTT 57.900 33.333 0.00 0.00 34.04 1.94
3538 4335 3.325425 TGCTTAAACCTTTTAAAGCCCCC 59.675 43.478 0.00 0.00 0.00 5.40
3539 4336 4.610605 TGCTTAAACCTTTTAAAGCCCC 57.389 40.909 0.00 0.00 0.00 5.80
3540 4337 9.309516 GTATAATGCTTAAACCTTTTAAAGCCC 57.690 33.333 0.00 0.00 0.00 5.19
3541 4338 9.309516 GGTATAATGCTTAAACCTTTTAAAGCC 57.690 33.333 0.00 0.00 0.00 4.35
3542 4339 9.309516 GGGTATAATGCTTAAACCTTTTAAAGC 57.690 33.333 0.00 0.00 0.00 3.51
3543 4340 9.511144 CGGGTATAATGCTTAAACCTTTTAAAG 57.489 33.333 0.00 0.00 0.00 1.85
3544 4341 8.468399 CCGGGTATAATGCTTAAACCTTTTAAA 58.532 33.333 0.00 0.00 0.00 1.52
3564 4361 2.925706 TTGTGCAGAGGCCGGGTA 60.926 61.111 2.18 0.00 40.13 3.69
3597 4395 5.957842 TTGTGCGAGAGGATTTTATTTGT 57.042 34.783 0.00 0.00 0.00 2.83
3651 4449 9.091784 CGTTAGCCGTTATATAGACTCTACATA 57.908 37.037 0.00 0.00 0.00 2.29
3700 4498 0.172578 CAACATGAGTGGCAGCATGG 59.827 55.000 25.19 11.44 44.64 3.66
3712 4510 5.530915 CGAGGGATATTTTTAGCCAACATGA 59.469 40.000 0.00 0.00 0.00 3.07
3727 4525 2.307980 TGGAGGATACGACGAGGGATAT 59.692 50.000 0.00 0.00 46.39 1.63
3737 4535 3.065786 GTGTACACGATTGGAGGATACGA 59.934 47.826 10.84 0.00 46.39 3.43
3804 4602 3.167485 TGTACCGGGACTCTGTTTATGT 58.833 45.455 19.95 0.00 0.00 2.29
3918 4718 5.845065 AGGTTTAGAACTCTTCTTAGGGTGT 59.155 40.000 0.00 0.00 41.14 4.16
3986 4786 4.298626 TCTGGCTTGTATCCTCCTTGTAT 58.701 43.478 0.00 0.00 0.00 2.29
4010 4810 7.734865 TCCTATATGGTCAGTCATCCAAATAGT 59.265 37.037 0.00 0.00 37.27 2.12
4035 4835 5.631026 TCTTTCAATGCAAATTAGCTCGTC 58.369 37.500 0.00 0.00 34.99 4.20
4084 4885 2.884012 TCCGCAATGTGTCTTTTGTCAT 59.116 40.909 0.00 0.00 0.00 3.06
4209 5010 7.283127 TGCCAGTTGATAATAACAAGAAGATCC 59.717 37.037 0.00 0.00 33.02 3.36
4252 5054 7.746703 TCTTAGTGGAGTCTATGTATAGAGCA 58.253 38.462 1.93 0.00 39.87 4.26
4274 5076 6.676558 ACCTACATGGGAATGATCAATTCTT 58.323 36.000 0.00 0.00 43.71 2.52
4283 5085 3.181455 CGATGGAACCTACATGGGAATGA 60.181 47.826 0.00 0.00 41.11 2.57
4348 5150 2.384828 TCGTGGTACATCCTGCTACAT 58.615 47.619 0.00 0.00 44.52 2.29
4351 5153 2.102420 CCAATCGTGGTACATCCTGCTA 59.898 50.000 0.00 0.00 44.52 3.49
4374 5176 7.059156 CAGAAGAGATTTAATTGGACCCAGAT 58.941 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.