Multiple sequence alignment - TraesCS4A01G301700

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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 TraesCS4A01G301700 chr4A 100.000 3895 0 0 1 3895 598604264 598600370 0.000000e+00 7193.0
1 TraesCS4A01G301700 chr4A 82.054 1655 193 49 900 2503 598607722 598609323 0.000000e+00 1315.0
2 TraesCS4A01G301700 chr4A 100.000 708 0 0 1 708 31617866 31618573 0.000000e+00 1308.0
3 TraesCS4A01G301700 chr4A 88.889 666 50 15 2542 3205 598609442 598610085 0.000000e+00 798.0
4 TraesCS4A01G301700 chr4A 87.413 143 9 4 3294 3427 598610144 598610286 5.210000e-34 156.0
5 TraesCS4A01G301700 chr4A 100.000 33 0 0 765 797 598603361 598603393 1.170000e-05 62.1
6 TraesCS4A01G301700 chr4B 98.791 2399 29 0 989 3387 8117330 8119728 0.000000e+00 4270.0
7 TraesCS4A01G301700 chr4B 98.382 2410 29 1 994 3403 8206321 8208720 0.000000e+00 4226.0
8 TraesCS4A01G301700 chr4B 98.065 2325 29 2 994 3312 8421304 8418990 0.000000e+00 4030.0
9 TraesCS4A01G301700 chr4B 91.259 1453 80 17 900 2321 8366414 8367850 0.000000e+00 1936.0
10 TraesCS4A01G301700 chr4B 79.342 1612 204 65 910 2466 7761175 7762712 0.000000e+00 1013.0
11 TraesCS4A01G301700 chr4B 79.319 1615 205 65 910 2469 7896988 7895448 0.000000e+00 1013.0
12 TraesCS4A01G301700 chr4B 98.238 454 3 2 903 1355 8423010 8422561 0.000000e+00 789.0
13 TraesCS4A01G301700 chr4B 99.455 367 2 0 989 1355 7897514 7897148 0.000000e+00 667.0
14 TraesCS4A01G301700 chr4B 83.711 706 84 13 1796 2478 8175296 8175993 4.240000e-179 638.0
15 TraesCS4A01G301700 chr4B 83.569 706 85 13 1796 2478 8293392 8294089 1.970000e-177 632.0
16 TraesCS4A01G301700 chr4B 87.712 472 50 4 2547 3018 8294118 8294581 9.520000e-151 544.0
17 TraesCS4A01G301700 chr4B 87.500 472 51 4 2547 3018 8176022 8176485 4.430000e-149 538.0
18 TraesCS4A01G301700 chr4B 94.510 255 14 0 3133 3387 8175022 8175276 1.010000e-105 394.0
19 TraesCS4A01G301700 chr4B 93.359 256 16 1 3136 3390 8293110 8293365 1.020000e-100 377.0
20 TraesCS4A01G301700 chr4B 93.590 234 14 1 1587 1820 8418013 8417781 8.010000e-92 348.0
21 TraesCS4A01G301700 chr4B 77.739 566 73 30 2575 3131 8414819 8414298 8.180000e-77 298.0
22 TraesCS4A01G301700 chr4B 84.345 313 33 11 2542 2852 7762865 7763163 3.810000e-75 292.0
23 TraesCS4A01G301700 chr4B 94.086 186 5 3 3469 3654 8205744 8205923 1.070000e-70 278.0
24 TraesCS4A01G301700 chr4B 94.086 186 5 3 3469 3654 8421881 8421702 1.070000e-70 278.0
25 TraesCS4A01G301700 chr4B 88.265 196 9 6 3492 3678 8368679 8368869 5.070000e-54 222.0
26 TraesCS4A01G301700 chr4B 90.090 111 11 0 3385 3495 8119759 8119869 1.130000e-30 145.0
27 TraesCS4A01G301700 chr4B 90.654 107 2 4 901 1002 8206193 8206296 6.790000e-28 135.0
28 TraesCS4A01G301700 chr4B 92.632 95 6 1 3385 3479 8294782 8294875 6.790000e-28 135.0
29 TraesCS4A01G301700 chr4B 90.654 107 2 4 901 1002 8421432 8421329 6.790000e-28 135.0
30 TraesCS4A01G301700 chr4B 91.579 95 7 1 3385 3479 8176686 8176779 3.160000e-26 130.0
31 TraesCS4A01G301700 chr4B 91.489 94 7 1 3294 3387 8294655 8294747 1.140000e-25 128.0
32 TraesCS4A01G301700 chr4B 96.923 65 1 1 733 797 7897682 7897745 1.480000e-19 108.0
33 TraesCS4A01G301700 chr4B 96.875 64 1 1 734 797 8361582 8361520 5.320000e-19 106.0
34 TraesCS4A01G301700 chr4B 97.778 45 1 0 859 903 7897758 7897714 1.160000e-10 78.7
35 TraesCS4A01G301700 chr4B 94.118 51 3 0 3014 3064 8175108 8175158 1.160000e-10 78.7
36 TraesCS4A01G301700 chr4B 94.118 51 3 0 3014 3064 8293193 8293243 1.160000e-10 78.7
37 TraesCS4A01G301700 chr4B 97.778 45 1 0 859 903 8361507 8361551 1.160000e-10 78.7
38 TraesCS4A01G301700 chr4B 97.674 43 1 0 3385 3427 7747041 7747083 1.500000e-09 75.0
39 TraesCS4A01G301700 chr4B 95.652 46 2 0 859 904 7898393 7898348 1.500000e-09 75.0
40 TraesCS4A01G301700 chr4B 95.652 46 2 0 859 904 8115842 8115887 1.500000e-09 75.0
41 TraesCS4A01G301700 chr4B 95.652 46 2 0 859 904 8360857 8360902 1.500000e-09 75.0
42 TraesCS4A01G301700 chr4B 100.000 40 0 0 860 899 8515981 8516020 1.500000e-09 75.0
43 TraesCS4A01G301700 chr4B 95.652 46 2 0 859 904 8954372 8954417 1.500000e-09 75.0
44 TraesCS4A01G301700 chr4B 85.915 71 4 3 733 797 8516063 8515993 1.940000e-08 71.3
45 TraesCS4A01G301700 chr4B 100.000 38 0 0 859 896 8516585 8516622 1.940000e-08 71.3
46 TraesCS4A01G301700 chr4B 97.500 40 1 0 859 898 8110122 8110161 6.980000e-08 69.4
47 TraesCS4A01G301700 chr4B 97.368 38 1 0 3697 3734 8383279 8383316 9.030000e-07 65.8
48 TraesCS4A01G301700 chr4D 92.141 2354 92 24 910 3205 5069613 5071931 0.000000e+00 3236.0
49 TraesCS4A01G301700 chr4D 91.640 1244 73 15 1102 2321 5010364 5009128 0.000000e+00 1692.0
50 TraesCS4A01G301700 chr4D 83.665 704 81 13 1796 2476 5080406 5081098 1.970000e-177 632.0
51 TraesCS4A01G301700 chr4D 92.166 434 21 7 3385 3815 5081887 5082310 5.570000e-168 601.0
52 TraesCS4A01G301700 chr4D 88.962 453 41 5 2549 3000 5081130 5081574 5.690000e-153 551.0
53 TraesCS4A01G301700 chr4D 94.902 255 13 0 3133 3387 5080132 5080386 2.180000e-107 399.0
54 TraesCS4A01G301700 chr4D 88.991 109 6 3 3294 3398 5081755 5081861 3.160000e-26 130.0
55 TraesCS4A01G301700 chr4D 90.769 65 3 2 914 977 5067228 5067166 2.490000e-12 84.2
56 TraesCS4A01G301700 chr4D 100.000 43 0 0 3385 3427 5072114 5072156 3.230000e-11 80.5
57 TraesCS4A01G301700 chr3A 100.000 708 0 0 1 708 154943394 154944101 0.000000e+00 1308.0
58 TraesCS4A01G301700 chr3A 97.743 709 15 1 1 708 674738084 674737376 0.000000e+00 1219.0
59 TraesCS4A01G301700 chr6B 99.859 708 1 0 1 708 118972069 118972776 0.000000e+00 1303.0
60 TraesCS4A01G301700 chr7A 99.718 708 2 0 1 708 570105785 570105078 0.000000e+00 1297.0
61 TraesCS4A01G301700 chr7A 99.576 708 3 0 1 708 27457899 27458606 0.000000e+00 1291.0
62 TraesCS4A01G301700 chr1A 99.718 708 2 0 1 708 44515320 44516027 0.000000e+00 1297.0
63 TraesCS4A01G301700 chr5B 99.435 708 4 0 1 708 661214643 661213936 0.000000e+00 1286.0
64 TraesCS4A01G301700 chrUn 99.849 662 1 0 47 708 464370505 464371166 0.000000e+00 1218.0
65 TraesCS4A01G301700 chrUn 98.592 568 7 1 2928 3495 295774233 295773667 0.000000e+00 1003.0


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 TraesCS4A01G301700 chr4A 598600370 598604264 3894 True 7193.000000 7193 100.000000 1 3895 1 chr4A.!!$R1 3894
1 TraesCS4A01G301700 chr4A 31617866 31618573 707 False 1308.000000 1308 100.000000 1 708 1 chr4A.!!$F1 707
2 TraesCS4A01G301700 chr4A 598607722 598610286 2564 False 756.333333 1315 86.118667 900 3427 3 chr4A.!!$F3 2527
3 TraesCS4A01G301700 chr4B 8205744 8208720 2976 False 1546.333333 4226 94.374000 901 3654 3 chr4B.!!$F9 2753
4 TraesCS4A01G301700 chr4B 8115842 8119869 4027 False 1496.666667 4270 94.844333 859 3495 3 chr4B.!!$F7 2636
5 TraesCS4A01G301700 chr4B 8366414 8368869 2455 False 1079.000000 1936 89.762000 900 3678 2 chr4B.!!$F12 2778
6 TraesCS4A01G301700 chr4B 8414298 8423010 8712 True 979.666667 4030 92.062000 901 3654 6 chr4B.!!$R4 2753
7 TraesCS4A01G301700 chr4B 7761175 7763163 1988 False 652.500000 1013 81.843500 910 2852 2 chr4B.!!$F6 1942
8 TraesCS4A01G301700 chr4B 7895448 7898393 2945 True 458.425000 1013 93.051000 859 2469 4 chr4B.!!$R3 1610
9 TraesCS4A01G301700 chr4B 8175022 8176779 1757 False 355.740000 638 90.283600 1796 3479 5 chr4B.!!$F8 1683
10 TraesCS4A01G301700 chr4B 8293110 8294875 1765 False 315.783333 632 90.479833 1796 3479 6 chr4B.!!$F10 1683
11 TraesCS4A01G301700 chr4D 5009128 5010364 1236 True 1692.000000 1692 91.640000 1102 2321 1 chr4D.!!$R1 1219
12 TraesCS4A01G301700 chr4D 5069613 5072156 2543 False 1658.250000 3236 96.070500 910 3427 2 chr4D.!!$F1 2517
13 TraesCS4A01G301700 chr4D 5080132 5082310 2178 False 462.600000 632 89.737200 1796 3815 5 chr4D.!!$F2 2019
14 TraesCS4A01G301700 chr3A 154943394 154944101 707 False 1308.000000 1308 100.000000 1 708 1 chr3A.!!$F1 707
15 TraesCS4A01G301700 chr3A 674737376 674738084 708 True 1219.000000 1219 97.743000 1 708 1 chr3A.!!$R1 707
16 TraesCS4A01G301700 chr6B 118972069 118972776 707 False 1303.000000 1303 99.859000 1 708 1 chr6B.!!$F1 707
17 TraesCS4A01G301700 chr7A 570105078 570105785 707 True 1297.000000 1297 99.718000 1 708 1 chr7A.!!$R1 707
18 TraesCS4A01G301700 chr7A 27457899 27458606 707 False 1291.000000 1291 99.576000 1 708 1 chr7A.!!$F1 707
19 TraesCS4A01G301700 chr1A 44515320 44516027 707 False 1297.000000 1297 99.718000 1 708 1 chr1A.!!$F1 707
20 TraesCS4A01G301700 chr5B 661213936 661214643 707 True 1286.000000 1286 99.435000 1 708 1 chr5B.!!$R1 707
21 TraesCS4A01G301700 chrUn 464370505 464371166 661 False 1218.000000 1218 99.849000 47 708 1 chrUn.!!$F1 661
22 TraesCS4A01G301700 chrUn 295773667 295774233 566 True 1003.000000 1003 98.592000 2928 3495 1 chrUn.!!$R1 567

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
730 732 0.105658 TATTCGGGCCTCCTGCTACT 60.106 55.000 0.84 0.0 40.92 2.57 F
837 839 0.192566 AGGGCGAACCATATCCCCTA 59.807 55.000 0.00 0.0 44.09 3.53 F
839 841 1.065418 GGGCGAACCATATCCCCTATG 60.065 57.143 0.00 0.0 39.85 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 6005 2.034221 GCAGGGAACTCCACCACC 59.966 66.667 0.0 0.0 40.21 4.61 R
2799 6724 1.773856 TTCATCAACGGCACCCCTGA 61.774 55.000 0.0 0.0 0.00 3.86 R
3491 10759 3.340928 ACAACGGGATAAGCTAACCAAC 58.659 45.455 0.0 0.0 0.00 3.77 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
708 710 1.559682 CTATGCACAACAGGGTAGGGT 59.440 52.381 0.00 0.00 0.00 4.34
709 711 0.777446 ATGCACAACAGGGTAGGGTT 59.223 50.000 0.00 0.00 0.00 4.11
710 712 0.553819 TGCACAACAGGGTAGGGTTT 59.446 50.000 0.00 0.00 0.00 3.27
711 713 1.063567 TGCACAACAGGGTAGGGTTTT 60.064 47.619 0.00 0.00 0.00 2.43
712 714 2.175069 TGCACAACAGGGTAGGGTTTTA 59.825 45.455 0.00 0.00 0.00 1.52
713 715 3.181427 TGCACAACAGGGTAGGGTTTTAT 60.181 43.478 0.00 0.00 0.00 1.40
714 716 3.830178 GCACAACAGGGTAGGGTTTTATT 59.170 43.478 0.00 0.00 0.00 1.40
715 717 4.082408 GCACAACAGGGTAGGGTTTTATTC 60.082 45.833 0.00 0.00 0.00 1.75
716 718 4.155280 CACAACAGGGTAGGGTTTTATTCG 59.845 45.833 0.00 0.00 0.00 3.34
717 719 3.639672 ACAGGGTAGGGTTTTATTCGG 57.360 47.619 0.00 0.00 0.00 4.30
718 720 2.240414 ACAGGGTAGGGTTTTATTCGGG 59.760 50.000 0.00 0.00 0.00 5.14
719 721 1.213678 AGGGTAGGGTTTTATTCGGGC 59.786 52.381 0.00 0.00 0.00 6.13
720 722 1.683943 GGTAGGGTTTTATTCGGGCC 58.316 55.000 0.00 0.00 0.00 5.80
721 723 1.213678 GGTAGGGTTTTATTCGGGCCT 59.786 52.381 0.84 0.00 0.00 5.19
722 724 2.569059 GTAGGGTTTTATTCGGGCCTC 58.431 52.381 0.84 0.00 0.00 4.70
723 725 0.257905 AGGGTTTTATTCGGGCCTCC 59.742 55.000 0.84 0.00 0.00 4.30
724 726 0.257905 GGGTTTTATTCGGGCCTCCT 59.742 55.000 0.84 0.00 0.00 3.69
725 727 1.389555 GGTTTTATTCGGGCCTCCTG 58.610 55.000 0.84 0.00 0.00 3.86
726 728 0.738975 GTTTTATTCGGGCCTCCTGC 59.261 55.000 0.84 0.00 40.16 4.85
727 729 0.623723 TTTTATTCGGGCCTCCTGCT 59.376 50.000 0.84 0.00 40.92 4.24
728 730 1.502690 TTTATTCGGGCCTCCTGCTA 58.497 50.000 0.84 0.00 40.92 3.49
729 731 0.756903 TTATTCGGGCCTCCTGCTAC 59.243 55.000 0.84 0.00 40.92 3.58
730 732 0.105658 TATTCGGGCCTCCTGCTACT 60.106 55.000 0.84 0.00 40.92 2.57
731 733 1.690219 ATTCGGGCCTCCTGCTACTG 61.690 60.000 0.84 0.00 40.92 2.74
732 734 3.854669 CGGGCCTCCTGCTACTGG 61.855 72.222 0.84 0.00 40.92 4.00
733 735 3.483869 GGGCCTCCTGCTACTGGG 61.484 72.222 0.84 0.00 40.92 4.45
734 736 3.483869 GGCCTCCTGCTACTGGGG 61.484 72.222 0.00 0.00 40.92 4.96
735 737 3.483869 GCCTCCTGCTACTGGGGG 61.484 72.222 5.09 5.09 44.68 5.40
736 738 3.483869 CCTCCTGCTACTGGGGGC 61.484 72.222 0.00 0.00 36.33 5.80
737 739 2.366167 CTCCTGCTACTGGGGGCT 60.366 66.667 0.00 0.00 0.00 5.19
738 740 1.075226 CTCCTGCTACTGGGGGCTA 60.075 63.158 0.00 0.00 0.00 3.93
739 741 1.075226 TCCTGCTACTGGGGGCTAG 60.075 63.158 0.00 0.00 0.00 3.42
740 742 2.143419 CCTGCTACTGGGGGCTAGG 61.143 68.421 0.00 0.00 0.00 3.02
741 743 2.040884 TGCTACTGGGGGCTAGGG 60.041 66.667 0.00 0.00 0.00 3.53
742 744 2.040779 GCTACTGGGGGCTAGGGT 60.041 66.667 0.00 0.00 0.00 4.34
743 745 1.693103 GCTACTGGGGGCTAGGGTT 60.693 63.158 0.00 0.00 0.00 4.11
744 746 1.279749 GCTACTGGGGGCTAGGGTTT 61.280 60.000 0.00 0.00 0.00 3.27
745 747 1.296002 CTACTGGGGGCTAGGGTTTT 58.704 55.000 0.00 0.00 0.00 2.43
746 748 2.484602 CTACTGGGGGCTAGGGTTTTA 58.515 52.381 0.00 0.00 0.00 1.52
747 749 1.995868 ACTGGGGGCTAGGGTTTTAT 58.004 50.000 0.00 0.00 0.00 1.40
748 750 2.294194 ACTGGGGGCTAGGGTTTTATT 58.706 47.619 0.00 0.00 0.00 1.40
749 751 2.243994 ACTGGGGGCTAGGGTTTTATTC 59.756 50.000 0.00 0.00 0.00 1.75
750 752 1.213430 TGGGGGCTAGGGTTTTATTCG 59.787 52.381 0.00 0.00 0.00 3.34
751 753 1.478105 GGGGGCTAGGGTTTTATTCGG 60.478 57.143 0.00 0.00 0.00 4.30
752 754 1.478105 GGGGCTAGGGTTTTATTCGGG 60.478 57.143 0.00 0.00 0.00 5.14
753 755 1.315690 GGCTAGGGTTTTATTCGGGC 58.684 55.000 0.00 0.00 0.00 6.13
754 756 1.315690 GCTAGGGTTTTATTCGGGCC 58.684 55.000 0.00 0.00 0.00 5.80
755 757 1.133884 GCTAGGGTTTTATTCGGGCCT 60.134 52.381 0.84 0.00 0.00 5.19
756 758 2.847441 CTAGGGTTTTATTCGGGCCTC 58.153 52.381 0.84 0.00 0.00 4.70
757 759 0.257905 AGGGTTTTATTCGGGCCTCC 59.742 55.000 0.84 0.00 0.00 4.30
758 760 0.257905 GGGTTTTATTCGGGCCTCCT 59.742 55.000 0.84 0.00 0.00 3.69
759 761 1.676746 GGTTTTATTCGGGCCTCCTC 58.323 55.000 0.84 0.00 0.00 3.71
760 762 1.676746 GTTTTATTCGGGCCTCCTCC 58.323 55.000 0.84 0.00 0.00 4.30
761 763 1.212195 GTTTTATTCGGGCCTCCTCCT 59.788 52.381 0.84 0.00 0.00 3.69
762 764 1.129058 TTTATTCGGGCCTCCTCCTC 58.871 55.000 0.84 0.00 0.00 3.71
763 765 0.763223 TTATTCGGGCCTCCTCCTCC 60.763 60.000 0.84 0.00 0.00 4.30
764 766 1.665948 TATTCGGGCCTCCTCCTCCT 61.666 60.000 0.84 0.00 0.00 3.69
765 767 3.849836 TATTCGGGCCTCCTCCTCCTG 62.850 61.905 0.84 0.00 0.00 3.86
766 768 4.465446 CGGGCCTCCTCCTCCTGA 62.465 72.222 0.84 0.00 0.00 3.86
767 769 2.766229 GGGCCTCCTCCTCCTGAC 60.766 72.222 0.84 0.00 0.00 3.51
768 770 2.039624 GGCCTCCTCCTCCTGACA 59.960 66.667 0.00 0.00 0.00 3.58
769 771 2.063378 GGCCTCCTCCTCCTGACAG 61.063 68.421 0.00 0.00 0.00 3.51
770 772 2.730524 GCCTCCTCCTCCTGACAGC 61.731 68.421 0.00 0.00 0.00 4.40
771 773 2.063378 CCTCCTCCTCCTGACAGCC 61.063 68.421 0.00 0.00 0.00 4.85
772 774 2.363018 TCCTCCTCCTGACAGCCG 60.363 66.667 0.00 0.00 0.00 5.52
773 775 4.154347 CCTCCTCCTGACAGCCGC 62.154 72.222 0.00 0.00 0.00 6.53
774 776 4.154347 CTCCTCCTGACAGCCGCC 62.154 72.222 0.00 0.00 0.00 6.13
776 778 4.767255 CCTCCTGACAGCCGCCAC 62.767 72.222 0.00 0.00 0.00 5.01
777 779 3.699894 CTCCTGACAGCCGCCACT 61.700 66.667 0.00 0.00 0.00 4.00
778 780 3.241530 TCCTGACAGCCGCCACTT 61.242 61.111 0.00 0.00 0.00 3.16
779 781 2.281761 CCTGACAGCCGCCACTTT 60.282 61.111 0.00 0.00 0.00 2.66
780 782 2.620112 CCTGACAGCCGCCACTTTG 61.620 63.158 0.00 0.00 0.00 2.77
781 783 2.594303 TGACAGCCGCCACTTTGG 60.594 61.111 0.00 0.00 41.55 3.28
782 784 3.365265 GACAGCCGCCACTTTGGG 61.365 66.667 0.00 0.00 38.19 4.12
790 792 3.860681 CCACTTTGGGCTGCAACT 58.139 55.556 0.50 0.00 32.67 3.16
791 793 2.126951 CCACTTTGGGCTGCAACTT 58.873 52.632 0.50 0.00 32.67 2.66
792 794 0.249573 CCACTTTGGGCTGCAACTTG 60.250 55.000 0.50 0.00 32.67 3.16
793 795 0.249573 CACTTTGGGCTGCAACTTGG 60.250 55.000 0.50 0.00 0.00 3.61
794 796 1.368579 CTTTGGGCTGCAACTTGGG 59.631 57.895 0.50 0.00 0.00 4.12
795 797 2.720358 CTTTGGGCTGCAACTTGGGC 62.720 60.000 0.50 0.00 0.00 5.36
798 800 3.376918 GGCTGCAACTTGGGCCTC 61.377 66.667 4.53 0.00 41.20 4.70
799 801 3.376918 GCTGCAACTTGGGCCTCC 61.377 66.667 4.53 0.00 0.00 4.30
800 802 3.058160 CTGCAACTTGGGCCTCCG 61.058 66.667 4.53 0.00 35.24 4.63
801 803 3.551496 CTGCAACTTGGGCCTCCGA 62.551 63.158 4.53 0.00 35.24 4.55
802 804 3.056328 GCAACTTGGGCCTCCGAC 61.056 66.667 4.53 0.00 35.24 4.79
803 805 2.359975 CAACTTGGGCCTCCGACC 60.360 66.667 4.53 0.00 35.24 4.79
804 806 2.529389 AACTTGGGCCTCCGACCT 60.529 61.111 4.53 0.00 35.24 3.85
805 807 2.154074 AACTTGGGCCTCCGACCTT 61.154 57.895 4.53 0.00 35.24 3.50
806 808 0.838987 AACTTGGGCCTCCGACCTTA 60.839 55.000 4.53 0.00 35.24 2.69
807 809 1.265454 ACTTGGGCCTCCGACCTTAG 61.265 60.000 4.53 0.00 35.24 2.18
808 810 1.972660 CTTGGGCCTCCGACCTTAGG 61.973 65.000 4.53 0.00 35.24 2.69
812 814 4.222847 CCTCCGACCTTAGGCCGC 62.223 72.222 0.26 0.00 0.00 6.53
813 815 3.458163 CTCCGACCTTAGGCCGCA 61.458 66.667 0.26 0.00 0.00 5.69
814 816 3.432051 CTCCGACCTTAGGCCGCAG 62.432 68.421 0.26 0.00 0.00 5.18
831 833 2.515901 GCCCAGGGCGAACCATAT 59.484 61.111 17.05 0.00 43.89 1.78
832 834 1.600916 GCCCAGGGCGAACCATATC 60.601 63.158 17.05 0.00 43.89 1.63
833 835 1.073199 CCCAGGGCGAACCATATCC 59.927 63.158 0.00 0.00 43.89 2.59
834 836 1.073199 CCAGGGCGAACCATATCCC 59.927 63.158 0.00 0.00 43.89 3.85
835 837 1.073199 CAGGGCGAACCATATCCCC 59.927 63.158 0.00 0.00 43.89 4.81
836 838 1.073706 AGGGCGAACCATATCCCCT 60.074 57.895 0.00 0.00 43.89 4.79
837 839 0.192566 AGGGCGAACCATATCCCCTA 59.807 55.000 0.00 0.00 44.09 3.53
838 840 1.203440 AGGGCGAACCATATCCCCTAT 60.203 52.381 0.00 0.00 44.09 2.57
839 841 1.065418 GGGCGAACCATATCCCCTATG 60.065 57.143 0.00 0.00 39.85 2.23
840 842 1.628846 GGCGAACCATATCCCCTATGT 59.371 52.381 0.00 0.00 36.27 2.29
841 843 2.039879 GGCGAACCATATCCCCTATGTT 59.960 50.000 0.00 0.00 36.27 2.71
842 844 3.497942 GGCGAACCATATCCCCTATGTTT 60.498 47.826 0.00 0.00 36.27 2.83
843 845 4.142038 GCGAACCATATCCCCTATGTTTT 58.858 43.478 0.00 0.00 36.27 2.43
844 846 4.583073 GCGAACCATATCCCCTATGTTTTT 59.417 41.667 0.00 0.00 36.27 1.94
845 847 5.278315 GCGAACCATATCCCCTATGTTTTTC 60.278 44.000 0.00 0.00 36.27 2.29
846 848 6.062095 CGAACCATATCCCCTATGTTTTTCT 58.938 40.000 0.00 0.00 36.27 2.52
847 849 6.546034 CGAACCATATCCCCTATGTTTTTCTT 59.454 38.462 0.00 0.00 36.27 2.52
848 850 7.068226 CGAACCATATCCCCTATGTTTTTCTTT 59.932 37.037 0.00 0.00 36.27 2.52
849 851 8.679344 AACCATATCCCCTATGTTTTTCTTTT 57.321 30.769 0.00 0.00 36.27 2.27
850 852 8.679344 ACCATATCCCCTATGTTTTTCTTTTT 57.321 30.769 0.00 0.00 36.27 1.94
851 853 9.777008 ACCATATCCCCTATGTTTTTCTTTTTA 57.223 29.630 0.00 0.00 36.27 1.52
854 856 9.777008 ATATCCCCTATGTTTTTCTTTTTACCA 57.223 29.630 0.00 0.00 0.00 3.25
855 857 7.292713 TCCCCTATGTTTTTCTTTTTACCAC 57.707 36.000 0.00 0.00 0.00 4.16
856 858 7.070629 TCCCCTATGTTTTTCTTTTTACCACT 58.929 34.615 0.00 0.00 0.00 4.00
857 859 7.565768 TCCCCTATGTTTTTCTTTTTACCACTT 59.434 33.333 0.00 0.00 0.00 3.16
1388 5095 2.176055 CGTCTATCCGCCCGATCG 59.824 66.667 8.51 8.51 31.92 3.69
1539 5246 1.830477 AGCTCCAAAAACACCAGCAAA 59.170 42.857 0.00 0.00 32.17 3.68
2799 6724 5.163519 GGTACACAGCAAATGCCTAAATGAT 60.164 40.000 0.94 0.00 43.38 2.45
3431 8831 1.599606 CGTGTGCTAGGAGTCTGCCT 61.600 60.000 0.00 0.00 42.15 4.75
3491 10759 0.317269 CTGTTTGGTCGTGCTTGCAG 60.317 55.000 0.00 0.00 0.00 4.41
3601 11455 6.299141 TGAATGGAGAAGTATAATGGGAAGC 58.701 40.000 0.00 0.00 0.00 3.86
3635 11492 1.597742 TGTTTGGAAGCTGACTCTGC 58.402 50.000 0.00 0.00 0.00 4.26
3680 11858 1.804151 GTTGCACGGAAGCTGTATGAA 59.196 47.619 0.00 0.00 34.99 2.57
3700 11894 5.815581 TGAACTGAAAATAGTGCTGGGTAT 58.184 37.500 0.00 0.00 0.00 2.73
3701 11895 5.880332 TGAACTGAAAATAGTGCTGGGTATC 59.120 40.000 0.00 0.00 0.00 2.24
3702 11896 5.435686 ACTGAAAATAGTGCTGGGTATCA 57.564 39.130 0.00 0.00 0.00 2.15
3703 11897 5.815581 ACTGAAAATAGTGCTGGGTATCAA 58.184 37.500 0.00 0.00 0.00 2.57
3704 11898 6.426587 ACTGAAAATAGTGCTGGGTATCAAT 58.573 36.000 0.00 0.00 0.00 2.57
3705 11899 6.891908 ACTGAAAATAGTGCTGGGTATCAATT 59.108 34.615 0.00 0.00 0.00 2.32
3706 11900 7.099266 TGAAAATAGTGCTGGGTATCAATTG 57.901 36.000 0.00 0.00 0.00 2.32
3707 11901 6.889177 TGAAAATAGTGCTGGGTATCAATTGA 59.111 34.615 11.26 11.26 0.00 2.57
3708 11902 6.949352 AAATAGTGCTGGGTATCAATTGAG 57.051 37.500 14.54 0.00 0.00 3.02
3709 11903 3.287867 AGTGCTGGGTATCAATTGAGG 57.712 47.619 14.54 1.45 0.00 3.86
3710 11904 2.092212 AGTGCTGGGTATCAATTGAGGG 60.092 50.000 14.54 1.78 0.00 4.30
3711 11905 1.215173 TGCTGGGTATCAATTGAGGGG 59.785 52.381 14.54 2.43 0.00 4.79
3712 11906 1.494721 GCTGGGTATCAATTGAGGGGA 59.505 52.381 14.54 0.00 0.00 4.81
3713 11907 2.487986 GCTGGGTATCAATTGAGGGGAG 60.488 54.545 14.54 7.03 0.00 4.30
3714 11908 2.780010 CTGGGTATCAATTGAGGGGAGT 59.220 50.000 14.54 0.00 0.00 3.85
3715 11909 3.973973 CTGGGTATCAATTGAGGGGAGTA 59.026 47.826 14.54 0.00 0.00 2.59
3772 11968 2.959030 GTCCCTTCTTTTGCCTGTCTTT 59.041 45.455 0.00 0.00 0.00 2.52
3774 11970 3.384467 TCCCTTCTTTTGCCTGTCTTTTG 59.616 43.478 0.00 0.00 0.00 2.44
3776 11972 4.114794 CCTTCTTTTGCCTGTCTTTTGTG 58.885 43.478 0.00 0.00 0.00 3.33
3784 11980 7.995463 TTTGCCTGTCTTTTGTGTATTTTAC 57.005 32.000 0.00 0.00 0.00 2.01
3785 11981 6.952773 TGCCTGTCTTTTGTGTATTTTACT 57.047 33.333 0.00 0.00 0.00 2.24
3786 11982 8.453238 TTGCCTGTCTTTTGTGTATTTTACTA 57.547 30.769 0.00 0.00 0.00 1.82
3787 11983 7.867752 TGCCTGTCTTTTGTGTATTTTACTAC 58.132 34.615 0.00 0.00 0.00 2.73
3806 12002 6.228977 ACTACTAGGATTATGGCCCTCTAA 57.771 41.667 0.00 0.00 34.11 2.10
3817 12013 1.074889 GGCCCTCTAAACCCTGTTCAA 59.925 52.381 0.00 0.00 0.00 2.69
3819 12015 2.880167 GCCCTCTAAACCCTGTTCAAGG 60.880 54.545 0.00 0.00 46.94 3.61
3820 12016 2.375509 CCCTCTAAACCCTGTTCAAGGT 59.624 50.000 0.00 0.00 45.78 3.50
3821 12017 3.559384 CCCTCTAAACCCTGTTCAAGGTC 60.559 52.174 0.00 0.00 45.78 3.85
3822 12018 3.072476 CCTCTAAACCCTGTTCAAGGTCA 59.928 47.826 0.00 0.00 45.78 4.02
3827 12023 1.143073 ACCCTGTTCAAGGTCACCTTC 59.857 52.381 5.94 0.00 42.67 3.46
3828 12024 1.421646 CCCTGTTCAAGGTCACCTTCT 59.578 52.381 5.94 0.00 42.67 2.85
3829 12025 2.498167 CCTGTTCAAGGTCACCTTCTG 58.502 52.381 5.94 0.00 42.67 3.02
3831 12027 2.874701 CTGTTCAAGGTCACCTTCTGTG 59.125 50.000 5.94 0.00 42.67 3.66
3832 12028 2.238646 TGTTCAAGGTCACCTTCTGTGT 59.761 45.455 5.94 0.00 42.67 3.72
3833 12029 2.872858 GTTCAAGGTCACCTTCTGTGTC 59.127 50.000 5.94 0.00 42.67 3.67
3834 12030 1.068588 TCAAGGTCACCTTCTGTGTCG 59.931 52.381 5.94 0.00 42.67 4.35
3835 12031 1.120530 AAGGTCACCTTCTGTGTCGT 58.879 50.000 2.03 0.00 40.17 4.34
3836 12032 0.389391 AGGTCACCTTCTGTGTCGTG 59.611 55.000 0.00 0.00 45.61 4.35
3837 12033 0.600255 GGTCACCTTCTGTGTCGTGG 60.600 60.000 0.00 0.00 45.61 4.94
3838 12034 1.069090 TCACCTTCTGTGTCGTGGC 59.931 57.895 0.00 0.00 45.61 5.01
3840 12036 2.358737 CCTTCTGTGTCGTGGCCC 60.359 66.667 0.00 0.00 0.00 5.80
3841 12037 2.738521 CTTCTGTGTCGTGGCCCG 60.739 66.667 0.00 3.30 38.13 6.13
3855 12051 2.912542 CCCGCCGCTCATCTCCTA 60.913 66.667 0.00 0.00 0.00 2.94
3856 12052 2.336809 CCGCCGCTCATCTCCTAC 59.663 66.667 0.00 0.00 0.00 3.18
3857 12053 2.196925 CCGCCGCTCATCTCCTACT 61.197 63.158 0.00 0.00 0.00 2.57
3858 12054 1.736586 CGCCGCTCATCTCCTACTT 59.263 57.895 0.00 0.00 0.00 2.24
3859 12055 0.596083 CGCCGCTCATCTCCTACTTG 60.596 60.000 0.00 0.00 0.00 3.16
3861 12057 1.134670 GCCGCTCATCTCCTACTTGTT 60.135 52.381 0.00 0.00 0.00 2.83
3863 12059 2.932614 CCGCTCATCTCCTACTTGTTTG 59.067 50.000 0.00 0.00 0.00 2.93
3865 12061 3.614616 CGCTCATCTCCTACTTGTTTGTC 59.385 47.826 0.00 0.00 0.00 3.18
3866 12062 3.935828 GCTCATCTCCTACTTGTTTGTCC 59.064 47.826 0.00 0.00 0.00 4.02
3867 12063 4.508662 CTCATCTCCTACTTGTTTGTCCC 58.491 47.826 0.00 0.00 0.00 4.46
3868 12064 3.056107 TCATCTCCTACTTGTTTGTCCCG 60.056 47.826 0.00 0.00 0.00 5.14
3869 12065 2.600790 TCTCCTACTTGTTTGTCCCGA 58.399 47.619 0.00 0.00 0.00 5.14
3872 12068 2.701951 TCCTACTTGTTTGTCCCGAACT 59.298 45.455 0.00 0.00 0.00 3.01
3874 12070 3.992427 CCTACTTGTTTGTCCCGAACTAC 59.008 47.826 0.00 0.00 0.00 2.73
3875 12071 3.832615 ACTTGTTTGTCCCGAACTACT 57.167 42.857 0.00 0.00 0.00 2.57
3876 12072 4.942761 ACTTGTTTGTCCCGAACTACTA 57.057 40.909 0.00 0.00 0.00 1.82
3877 12073 4.625028 ACTTGTTTGTCCCGAACTACTAC 58.375 43.478 0.00 0.00 0.00 2.73
3880 12076 5.633830 TGTTTGTCCCGAACTACTACTAG 57.366 43.478 0.00 0.00 0.00 2.57
3881 12077 4.082571 TGTTTGTCCCGAACTACTACTAGC 60.083 45.833 0.00 0.00 0.00 3.42
3883 12079 3.276857 TGTCCCGAACTACTACTAGCAG 58.723 50.000 0.00 0.00 0.00 4.24
3884 12080 2.033174 GTCCCGAACTACTACTAGCAGC 59.967 54.545 0.00 0.00 0.00 5.25
3885 12081 1.002684 CCCGAACTACTACTAGCAGCG 60.003 57.143 0.00 0.00 0.00 5.18
3886 12082 1.597445 CCGAACTACTACTAGCAGCGC 60.597 57.143 0.00 0.00 0.00 5.92
3888 12084 2.722071 GAACTACTACTAGCAGCGCAG 58.278 52.381 11.47 1.31 0.00 5.18
3889 12085 2.039818 ACTACTACTAGCAGCGCAGA 57.960 50.000 11.47 0.00 0.00 4.26
3890 12086 1.944024 ACTACTACTAGCAGCGCAGAG 59.056 52.381 11.47 2.96 0.00 3.35
3891 12087 1.265635 CTACTACTAGCAGCGCAGAGG 59.734 57.143 11.47 0.00 0.00 3.69
3892 12088 1.299773 CTACTAGCAGCGCAGAGGC 60.300 63.158 11.47 7.81 0.00 4.70
3893 12089 2.009424 CTACTAGCAGCGCAGAGGCA 62.009 60.000 11.47 0.00 41.24 4.75
3894 12090 2.284798 TACTAGCAGCGCAGAGGCAC 62.285 60.000 11.47 0.00 41.24 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
708 710 0.623723 AGCAGGAGGCCCGAATAAAA 59.376 50.000 0.00 0.00 46.50 1.52
709 711 1.140252 GTAGCAGGAGGCCCGAATAAA 59.860 52.381 0.00 0.00 46.50 1.40
710 712 0.756903 GTAGCAGGAGGCCCGAATAA 59.243 55.000 0.00 0.00 46.50 1.40
711 713 0.105658 AGTAGCAGGAGGCCCGAATA 60.106 55.000 0.00 0.00 46.50 1.75
712 714 1.383248 AGTAGCAGGAGGCCCGAAT 60.383 57.895 0.00 0.00 46.50 3.34
713 715 2.038975 AGTAGCAGGAGGCCCGAA 59.961 61.111 0.00 0.00 46.50 4.30
714 716 2.759973 CAGTAGCAGGAGGCCCGA 60.760 66.667 0.00 0.00 46.50 5.14
715 717 3.854669 CCAGTAGCAGGAGGCCCG 61.855 72.222 0.00 0.00 46.50 6.13
716 718 3.483869 CCCAGTAGCAGGAGGCCC 61.484 72.222 0.00 0.00 46.50 5.80
717 719 3.483869 CCCCAGTAGCAGGAGGCC 61.484 72.222 0.00 0.00 46.50 5.19
718 720 3.483869 CCCCCAGTAGCAGGAGGC 61.484 72.222 0.00 0.00 45.30 4.70
719 721 2.605535 TAGCCCCCAGTAGCAGGAGG 62.606 65.000 0.00 0.00 0.00 4.30
720 722 1.075226 TAGCCCCCAGTAGCAGGAG 60.075 63.158 0.00 0.00 0.00 3.69
721 723 1.075226 CTAGCCCCCAGTAGCAGGA 60.075 63.158 0.00 0.00 0.00 3.86
722 724 2.143419 CCTAGCCCCCAGTAGCAGG 61.143 68.421 0.00 0.00 0.00 4.85
723 725 2.143419 CCCTAGCCCCCAGTAGCAG 61.143 68.421 0.00 0.00 0.00 4.24
724 726 2.040884 CCCTAGCCCCCAGTAGCA 60.041 66.667 0.00 0.00 0.00 3.49
725 727 1.279749 AAACCCTAGCCCCCAGTAGC 61.280 60.000 0.00 0.00 0.00 3.58
726 728 1.296002 AAAACCCTAGCCCCCAGTAG 58.704 55.000 0.00 0.00 0.00 2.57
727 729 2.665008 TAAAACCCTAGCCCCCAGTA 57.335 50.000 0.00 0.00 0.00 2.74
728 730 1.995868 ATAAAACCCTAGCCCCCAGT 58.004 50.000 0.00 0.00 0.00 4.00
729 731 2.748465 CGAATAAAACCCTAGCCCCCAG 60.748 54.545 0.00 0.00 0.00 4.45
730 732 1.213430 CGAATAAAACCCTAGCCCCCA 59.787 52.381 0.00 0.00 0.00 4.96
731 733 1.478105 CCGAATAAAACCCTAGCCCCC 60.478 57.143 0.00 0.00 0.00 5.40
732 734 1.478105 CCCGAATAAAACCCTAGCCCC 60.478 57.143 0.00 0.00 0.00 5.80
733 735 1.977056 CCCGAATAAAACCCTAGCCC 58.023 55.000 0.00 0.00 0.00 5.19
734 736 1.315690 GCCCGAATAAAACCCTAGCC 58.684 55.000 0.00 0.00 0.00 3.93
735 737 1.133884 AGGCCCGAATAAAACCCTAGC 60.134 52.381 0.00 0.00 0.00 3.42
736 738 2.486727 GGAGGCCCGAATAAAACCCTAG 60.487 54.545 0.00 0.00 0.00 3.02
737 739 1.491754 GGAGGCCCGAATAAAACCCTA 59.508 52.381 0.00 0.00 0.00 3.53
738 740 0.257905 GGAGGCCCGAATAAAACCCT 59.742 55.000 0.00 0.00 0.00 4.34
739 741 0.257905 AGGAGGCCCGAATAAAACCC 59.742 55.000 0.00 0.00 37.58 4.11
740 742 1.676746 GAGGAGGCCCGAATAAAACC 58.323 55.000 0.00 0.00 37.58 3.27
741 743 1.212195 AGGAGGAGGCCCGAATAAAAC 59.788 52.381 0.00 0.00 37.58 2.43
742 744 1.489230 GAGGAGGAGGCCCGAATAAAA 59.511 52.381 0.00 0.00 37.58 1.52
743 745 1.129058 GAGGAGGAGGCCCGAATAAA 58.871 55.000 0.00 0.00 37.58 1.40
744 746 0.763223 GGAGGAGGAGGCCCGAATAA 60.763 60.000 0.00 0.00 37.58 1.40
745 747 1.152312 GGAGGAGGAGGCCCGAATA 60.152 63.158 0.00 0.00 37.58 1.75
746 748 2.446802 GGAGGAGGAGGCCCGAAT 60.447 66.667 0.00 0.00 37.58 3.34
747 749 3.684628 AGGAGGAGGAGGCCCGAA 61.685 66.667 0.00 0.00 37.58 4.30
748 750 4.465446 CAGGAGGAGGAGGCCCGA 62.465 72.222 0.00 0.00 37.58 5.14
749 751 4.465446 TCAGGAGGAGGAGGCCCG 62.465 72.222 0.00 0.00 37.58 6.13
750 752 2.766229 GTCAGGAGGAGGAGGCCC 60.766 72.222 0.00 0.00 0.00 5.80
751 753 2.039624 TGTCAGGAGGAGGAGGCC 59.960 66.667 0.00 0.00 0.00 5.19
752 754 2.730524 GCTGTCAGGAGGAGGAGGC 61.731 68.421 1.14 0.00 0.00 4.70
753 755 2.063378 GGCTGTCAGGAGGAGGAGG 61.063 68.421 1.14 0.00 0.00 4.30
754 756 2.422231 CGGCTGTCAGGAGGAGGAG 61.422 68.421 1.14 0.00 0.00 3.69
755 757 2.363018 CGGCTGTCAGGAGGAGGA 60.363 66.667 1.14 0.00 0.00 3.71
756 758 4.154347 GCGGCTGTCAGGAGGAGG 62.154 72.222 1.14 0.00 0.00 4.30
757 759 4.154347 GGCGGCTGTCAGGAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
759 761 4.767255 GTGGCGGCTGTCAGGAGG 62.767 72.222 11.43 0.00 0.00 4.30
760 762 2.738213 AAAGTGGCGGCTGTCAGGAG 62.738 60.000 11.43 0.00 0.00 3.69
761 763 2.818169 AAAGTGGCGGCTGTCAGGA 61.818 57.895 11.43 0.00 0.00 3.86
762 764 2.281761 AAAGTGGCGGCTGTCAGG 60.282 61.111 11.43 0.00 0.00 3.86
763 765 2.620112 CCAAAGTGGCGGCTGTCAG 61.620 63.158 11.43 0.00 0.00 3.51
764 766 2.594303 CCAAAGTGGCGGCTGTCA 60.594 61.111 11.43 0.00 0.00 3.58
765 767 3.365265 CCCAAAGTGGCGGCTGTC 61.365 66.667 11.43 0.00 35.79 3.51
773 775 0.249573 CAAGTTGCAGCCCAAAGTGG 60.250 55.000 0.00 0.00 34.68 4.00
774 776 0.249573 CCAAGTTGCAGCCCAAAGTG 60.250 55.000 0.00 0.00 34.68 3.16
775 777 1.402107 CCCAAGTTGCAGCCCAAAGT 61.402 55.000 0.00 0.00 34.68 2.66
776 778 1.368579 CCCAAGTTGCAGCCCAAAG 59.631 57.895 0.00 0.00 34.68 2.77
777 779 2.806009 GCCCAAGTTGCAGCCCAAA 61.806 57.895 0.00 0.00 34.68 3.28
778 780 3.233231 GCCCAAGTTGCAGCCCAA 61.233 61.111 0.00 0.00 0.00 4.12
781 783 3.376918 GAGGCCCAAGTTGCAGCC 61.377 66.667 21.57 21.57 46.13 4.85
782 784 3.376918 GGAGGCCCAAGTTGCAGC 61.377 66.667 0.00 7.41 0.00 5.25
783 785 3.058160 CGGAGGCCCAAGTTGCAG 61.058 66.667 0.00 0.00 0.00 4.41
784 786 3.565214 TCGGAGGCCCAAGTTGCA 61.565 61.111 0.00 0.00 0.00 4.08
785 787 3.056328 GTCGGAGGCCCAAGTTGC 61.056 66.667 0.00 0.00 0.00 4.17
814 816 1.600916 GATATGGTTCGCCCTGGGC 60.601 63.158 28.17 28.17 46.75 5.36
815 817 1.073199 GGATATGGTTCGCCCTGGG 59.927 63.158 8.86 8.86 36.08 4.45
816 818 1.073199 GGGATATGGTTCGCCCTGG 59.927 63.158 0.00 0.00 37.59 4.45
817 819 1.073199 GGGGATATGGTTCGCCCTG 59.927 63.158 0.00 0.00 41.60 4.45
818 820 0.192566 TAGGGGATATGGTTCGCCCT 59.807 55.000 0.00 0.00 46.97 5.19
819 821 1.065418 CATAGGGGATATGGTTCGCCC 60.065 57.143 4.15 0.00 46.97 6.13
820 822 1.628846 ACATAGGGGATATGGTTCGCC 59.371 52.381 0.00 0.00 44.86 5.54
821 823 3.418684 AACATAGGGGATATGGTTCGC 57.581 47.619 0.44 0.00 38.76 4.70
825 827 8.679344 AAAAAGAAAAACATAGGGGATATGGT 57.321 30.769 0.44 0.00 44.00 3.55
828 830 9.777008 TGGTAAAAAGAAAAACATAGGGGATAT 57.223 29.630 0.00 0.00 0.00 1.63
829 831 9.027202 GTGGTAAAAAGAAAAACATAGGGGATA 57.973 33.333 0.00 0.00 0.00 2.59
830 832 7.733047 AGTGGTAAAAAGAAAAACATAGGGGAT 59.267 33.333 0.00 0.00 0.00 3.85
831 833 7.070629 AGTGGTAAAAAGAAAAACATAGGGGA 58.929 34.615 0.00 0.00 0.00 4.81
832 834 7.297936 AGTGGTAAAAAGAAAAACATAGGGG 57.702 36.000 0.00 0.00 0.00 4.79
833 835 9.040939 CAAAGTGGTAAAAAGAAAAACATAGGG 57.959 33.333 0.00 0.00 0.00 3.53
834 836 9.040939 CCAAAGTGGTAAAAAGAAAAACATAGG 57.959 33.333 0.00 0.00 31.35 2.57
835 837 9.040939 CCCAAAGTGGTAAAAAGAAAAACATAG 57.959 33.333 0.00 0.00 35.17 2.23
836 838 7.496263 GCCCAAAGTGGTAAAAAGAAAAACATA 59.504 33.333 0.00 0.00 35.17 2.29
837 839 6.317642 GCCCAAAGTGGTAAAAAGAAAAACAT 59.682 34.615 0.00 0.00 35.17 2.71
838 840 5.644206 GCCCAAAGTGGTAAAAAGAAAAACA 59.356 36.000 0.00 0.00 35.17 2.83
839 841 5.878116 AGCCCAAAGTGGTAAAAAGAAAAAC 59.122 36.000 0.00 0.00 35.17 2.43
840 842 5.877564 CAGCCCAAAGTGGTAAAAAGAAAAA 59.122 36.000 0.00 0.00 35.17 1.94
841 843 5.423886 CAGCCCAAAGTGGTAAAAAGAAAA 58.576 37.500 0.00 0.00 35.17 2.29
842 844 4.141824 CCAGCCCAAAGTGGTAAAAAGAAA 60.142 41.667 0.00 0.00 35.17 2.52
843 845 3.386402 CCAGCCCAAAGTGGTAAAAAGAA 59.614 43.478 0.00 0.00 35.17 2.52
844 846 2.962421 CCAGCCCAAAGTGGTAAAAAGA 59.038 45.455 0.00 0.00 35.17 2.52
845 847 2.037121 CCCAGCCCAAAGTGGTAAAAAG 59.963 50.000 0.00 0.00 35.17 2.27
846 848 2.043227 CCCAGCCCAAAGTGGTAAAAA 58.957 47.619 0.00 0.00 35.17 1.94
847 849 1.710816 CCCAGCCCAAAGTGGTAAAA 58.289 50.000 0.00 0.00 35.17 1.52
848 850 0.178947 CCCCAGCCCAAAGTGGTAAA 60.179 55.000 0.00 0.00 35.17 2.01
849 851 1.462928 CCCCAGCCCAAAGTGGTAA 59.537 57.895 0.00 0.00 35.17 2.85
850 852 3.176297 CCCCAGCCCAAAGTGGTA 58.824 61.111 0.00 0.00 35.17 3.25
851 853 4.621087 GCCCCAGCCCAAAGTGGT 62.621 66.667 0.00 0.00 35.17 4.16
853 855 4.974721 ACGCCCCAGCCCAAAGTG 62.975 66.667 0.00 0.00 34.57 3.16
854 856 4.974721 CACGCCCCAGCCCAAAGT 62.975 66.667 0.00 0.00 34.57 2.66
899 901 4.940483 TGGATTTATTGGGTGGATTGACA 58.060 39.130 0.00 0.00 0.00 3.58
1388 5095 1.732683 CAATTTTGGGGACGCACGC 60.733 57.895 0.00 0.00 0.00 5.34
1495 5202 3.142838 GGGCTTGCGCATGATGGT 61.143 61.111 25.77 0.00 38.10 3.55
2226 6005 2.034221 GCAGGGAACTCCACCACC 59.966 66.667 0.00 0.00 40.21 4.61
2799 6724 1.773856 TTCATCAACGGCACCCCTGA 61.774 55.000 0.00 0.00 0.00 3.86
3491 10759 3.340928 ACAACGGGATAAGCTAACCAAC 58.659 45.455 0.00 0.00 0.00 3.77
3529 10797 7.920682 GCTTTTACTTGATTTTCTCCAGACAAA 59.079 33.333 0.00 0.00 0.00 2.83
3532 10800 6.970484 TGCTTTTACTTGATTTTCTCCAGAC 58.030 36.000 0.00 0.00 0.00 3.51
3533 10801 6.772716 ACTGCTTTTACTTGATTTTCTCCAGA 59.227 34.615 0.00 0.00 0.00 3.86
3534 10802 6.860023 CACTGCTTTTACTTGATTTTCTCCAG 59.140 38.462 0.00 0.00 0.00 3.86
3535 10803 6.321181 ACACTGCTTTTACTTGATTTTCTCCA 59.679 34.615 0.00 0.00 0.00 3.86
3536 10804 6.739112 ACACTGCTTTTACTTGATTTTCTCC 58.261 36.000 0.00 0.00 0.00 3.71
3537 10805 8.560374 ACTACACTGCTTTTACTTGATTTTCTC 58.440 33.333 0.00 0.00 0.00 2.87
3538 10806 8.451908 ACTACACTGCTTTTACTTGATTTTCT 57.548 30.769 0.00 0.00 0.00 2.52
3601 11455 2.602660 CCAAACAAAAGAAGCCAACACG 59.397 45.455 0.00 0.00 0.00 4.49
3680 11858 5.435686 TGATACCCAGCACTATTTTCAGT 57.564 39.130 0.00 0.00 0.00 3.41
3700 11894 3.199442 TCCACTACTCCCCTCAATTGA 57.801 47.619 8.12 8.12 0.00 2.57
3701 11895 4.510167 AATCCACTACTCCCCTCAATTG 57.490 45.455 0.00 0.00 0.00 2.32
3702 11896 5.911178 TGATAATCCACTACTCCCCTCAATT 59.089 40.000 0.00 0.00 0.00 2.32
3703 11897 5.476983 TGATAATCCACTACTCCCCTCAAT 58.523 41.667 0.00 0.00 0.00 2.57
3704 11898 4.890988 TGATAATCCACTACTCCCCTCAA 58.109 43.478 0.00 0.00 0.00 3.02
3705 11899 4.552883 TGATAATCCACTACTCCCCTCA 57.447 45.455 0.00 0.00 0.00 3.86
3706 11900 4.841246 ACATGATAATCCACTACTCCCCTC 59.159 45.833 0.00 0.00 0.00 4.30
3707 11901 4.832492 ACATGATAATCCACTACTCCCCT 58.168 43.478 0.00 0.00 0.00 4.79
3708 11902 5.568620 AACATGATAATCCACTACTCCCC 57.431 43.478 0.00 0.00 0.00 4.81
3709 11903 6.483640 GTGAAACATGATAATCCACTACTCCC 59.516 42.308 0.00 0.00 36.32 4.30
3710 11904 7.225538 CAGTGAAACATGATAATCCACTACTCC 59.774 40.741 0.00 0.00 41.43 3.85
3711 11905 7.766278 ACAGTGAAACATGATAATCCACTACTC 59.234 37.037 0.00 0.00 41.43 2.59
3712 11906 7.624549 ACAGTGAAACATGATAATCCACTACT 58.375 34.615 0.00 0.00 41.43 2.57
3713 11907 7.849804 ACAGTGAAACATGATAATCCACTAC 57.150 36.000 0.00 0.00 41.43 2.73
3715 11909 8.896744 CATAACAGTGAAACATGATAATCCACT 58.103 33.333 0.00 1.18 41.43 4.00
3774 11970 9.433153 GGCCATAATCCTAGTAGTAAAATACAC 57.567 37.037 0.00 0.00 0.00 2.90
3776 11972 8.823794 AGGGCCATAATCCTAGTAGTAAAATAC 58.176 37.037 6.18 0.00 0.00 1.89
3784 11980 6.070710 GGTTTAGAGGGCCATAATCCTAGTAG 60.071 46.154 6.18 0.00 32.74 2.57
3785 11981 5.783875 GGTTTAGAGGGCCATAATCCTAGTA 59.216 44.000 6.18 0.00 32.74 1.82
3786 11982 4.597940 GGTTTAGAGGGCCATAATCCTAGT 59.402 45.833 6.18 0.00 32.74 2.57
3787 11983 4.019231 GGGTTTAGAGGGCCATAATCCTAG 60.019 50.000 19.75 0.00 32.74 3.02
3822 12018 2.426023 GGCCACGACACAGAAGGT 59.574 61.111 0.00 0.00 0.00 3.50
3838 12034 2.912542 TAGGAGATGAGCGGCGGG 60.913 66.667 9.78 0.00 0.00 6.13
3840 12036 0.596083 CAAGTAGGAGATGAGCGGCG 60.596 60.000 0.51 0.51 0.00 6.46
3841 12037 0.461961 ACAAGTAGGAGATGAGCGGC 59.538 55.000 0.00 0.00 0.00 6.53
3843 12039 3.589988 ACAAACAAGTAGGAGATGAGCG 58.410 45.455 0.00 0.00 0.00 5.03
3844 12040 3.935828 GGACAAACAAGTAGGAGATGAGC 59.064 47.826 0.00 0.00 0.00 4.26
3847 12043 3.056107 TCGGGACAAACAAGTAGGAGATG 60.056 47.826 0.00 0.00 0.00 2.90
3848 12044 3.170717 TCGGGACAAACAAGTAGGAGAT 58.829 45.455 0.00 0.00 0.00 2.75
3852 12048 3.121738 AGTTCGGGACAAACAAGTAGG 57.878 47.619 0.00 0.00 0.00 3.18
3854 12050 4.942761 AGTAGTTCGGGACAAACAAGTA 57.057 40.909 0.00 0.00 0.00 2.24
3855 12051 3.832615 AGTAGTTCGGGACAAACAAGT 57.167 42.857 0.00 0.00 0.00 3.16
3856 12052 4.879598 AGTAGTAGTTCGGGACAAACAAG 58.120 43.478 0.00 0.00 0.00 3.16
3857 12053 4.942761 AGTAGTAGTTCGGGACAAACAA 57.057 40.909 0.00 0.00 0.00 2.83
3858 12054 4.082571 GCTAGTAGTAGTTCGGGACAAACA 60.083 45.833 6.47 0.00 0.00 2.83
3859 12055 4.082571 TGCTAGTAGTAGTTCGGGACAAAC 60.083 45.833 6.47 0.00 0.00 2.93
3861 12057 3.689347 TGCTAGTAGTAGTTCGGGACAA 58.311 45.455 6.47 0.00 0.00 3.18
3863 12059 2.033174 GCTGCTAGTAGTAGTTCGGGAC 59.967 54.545 15.62 0.00 30.12 4.46
3865 12061 1.002684 CGCTGCTAGTAGTAGTTCGGG 60.003 57.143 15.62 0.00 30.12 5.14
3866 12062 1.597445 GCGCTGCTAGTAGTAGTTCGG 60.597 57.143 15.62 5.57 30.12 4.30
3867 12063 1.063616 TGCGCTGCTAGTAGTAGTTCG 59.936 52.381 15.62 12.44 30.12 3.95
3868 12064 2.355132 TCTGCGCTGCTAGTAGTAGTTC 59.645 50.000 15.62 8.88 30.12 3.01
3869 12065 2.356382 CTCTGCGCTGCTAGTAGTAGTT 59.644 50.000 15.62 0.00 30.12 2.24
3872 12068 1.309950 CCTCTGCGCTGCTAGTAGTA 58.690 55.000 9.73 0.00 0.00 1.82
3874 12070 1.299773 GCCTCTGCGCTGCTAGTAG 60.300 63.158 9.73 3.05 0.00 2.57
3875 12071 2.052104 TGCCTCTGCGCTGCTAGTA 61.052 57.895 9.73 0.00 41.78 1.82
3876 12072 3.385384 TGCCTCTGCGCTGCTAGT 61.385 61.111 9.73 0.00 41.78 2.57
3877 12073 2.889503 GTGCCTCTGCGCTGCTAG 60.890 66.667 9.73 2.15 44.66 3.42


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

AutoCloner maintained by Alex Coulton.