Multiple sequence alignment - TraesCS3B01G443800

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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 TraesCS3B01G443800 chr3B 100.000 4371 0 0 1 4371 684247615 684251985 0.000000e+00 8072.0
1 TraesCS3B01G443800 chr3B 82.165 1155 153 31 2310 3440 684266338 684267463 0.000000e+00 942.0
2 TraesCS3B01G443800 chr3B 88.992 645 68 3 202 843 152208546 152207902 0.000000e+00 795.0
3 TraesCS3B01G443800 chr3B 80.910 1011 145 29 2154 3143 683679561 683680544 0.000000e+00 754.0
4 TraesCS3B01G443800 chr3B 84.590 610 76 13 2530 3134 683759369 683759965 1.350000e-164 590.0
5 TraesCS3B01G443800 chr3B 89.765 469 29 12 944 1396 684265049 684265514 2.270000e-162 582.0
6 TraesCS3B01G443800 chr3B 91.346 312 23 4 1074 1383 683758420 683758729 1.450000e-114 424.0
7 TraesCS3B01G443800 chr3B 89.935 308 27 3 1078 1383 684095621 684095926 1.140000e-105 394.0
8 TraesCS3B01G443800 chr3B 76.596 329 52 13 1713 2033 684040409 684040720 1.630000e-34 158.0
9 TraesCS3B01G443800 chr3B 93.814 97 2 4 842 936 684234739 684234833 4.560000e-30 143.0
10 TraesCS3B01G443800 chr3B 78.000 200 27 11 1698 1889 683679300 683679490 4.620000e-20 110.0
11 TraesCS3B01G443800 chr3B 90.625 64 6 0 3279 3342 684389939 684390002 7.790000e-13 86.1
12 TraesCS3B01G443800 chr3A 89.649 2222 189 24 1404 3616 654567971 654570160 0.000000e+00 2791.0
13 TraesCS3B01G443800 chr3A 80.634 1389 207 36 2082 3440 654783325 654784681 0.000000e+00 1018.0
14 TraesCS3B01G443800 chr3A 81.942 958 129 25 2205 3143 654358734 654359666 0.000000e+00 771.0
15 TraesCS3B01G443800 chr3A 82.540 882 118 19 2651 3513 655085637 655086501 0.000000e+00 743.0
16 TraesCS3B01G443800 chr3A 89.375 480 29 18 944 1404 654781931 654782407 6.300000e-163 584.0
17 TraesCS3B01G443800 chr3A 91.534 378 19 12 898 1264 654567119 654567494 3.900000e-140 508.0
18 TraesCS3B01G443800 chr3A 86.709 474 42 16 939 1404 655083031 655083491 1.400000e-139 507.0
19 TraesCS3B01G443800 chr3A 86.504 452 38 18 3865 4297 654579031 654579478 3.960000e-130 475.0
20 TraesCS3B01G443800 chr3A 91.746 315 25 1 1074 1387 654357714 654358028 1.870000e-118 436.0
21 TraesCS3B01G443800 chr3A 90.705 312 25 4 1074 1383 654382605 654382914 3.150000e-111 412.0
22 TraesCS3B01G443800 chr3A 79.200 375 60 9 2113 2482 638437502 638437141 1.210000e-60 244.0
23 TraesCS3B01G443800 chr3A 94.681 94 4 1 3756 3848 654578953 654579046 1.270000e-30 145.0
24 TraesCS3B01G443800 chr3A 93.684 95 4 1 3610 3702 654578846 654578940 1.640000e-29 141.0
25 TraesCS3B01G443800 chr1B 94.124 885 38 13 1 876 134819134 134820013 0.000000e+00 1334.0
26 TraesCS3B01G443800 chr1B 94.444 846 39 7 1 843 476911265 476910425 0.000000e+00 1295.0
27 TraesCS3B01G443800 chr6B 94.340 848 40 8 1 843 590563088 590563932 0.000000e+00 1293.0
28 TraesCS3B01G443800 chr6B 94.008 751 42 3 96 844 288796005 288795256 0.000000e+00 1134.0
29 TraesCS3B01G443800 chr6B 91.304 46 4 0 4046 4091 664222694 664222739 3.650000e-06 63.9
30 TraesCS3B01G443800 chr1A 92.988 656 39 6 198 850 515835571 515836222 0.000000e+00 950.0
31 TraesCS3B01G443800 chr1A 96.552 290 7 3 1 289 321599139 321599426 1.100000e-130 477.0
32 TraesCS3B01G443800 chr1A 96.482 199 5 2 1 198 515835284 515835481 1.170000e-85 327.0
33 TraesCS3B01G443800 chr4A 90.994 644 55 3 203 843 741155766 741155123 0.000000e+00 865.0
34 TraesCS3B01G443800 chr4A 93.617 47 2 1 4045 4091 534781616 534781571 7.840000e-08 69.4
35 TraesCS3B01G443800 chr5D 90.278 648 55 6 198 843 285160840 285161481 0.000000e+00 841.0
36 TraesCS3B01G443800 chr5D 93.182 44 3 0 4046 4089 334892883 334892926 1.010000e-06 65.8
37 TraesCS3B01G443800 chr7D 90.015 651 53 6 198 843 540732718 540733361 0.000000e+00 832.0
38 TraesCS3B01G443800 chr7D 81.300 754 115 15 2675 3405 381001796 381001046 4.870000e-164 588.0
39 TraesCS3B01G443800 chr3D 80.198 909 128 29 2233 3134 519353513 519354376 6.170000e-178 634.0
40 TraesCS3B01G443800 chr3D 89.518 477 31 12 944 1404 519681993 519682466 1.750000e-163 586.0
41 TraesCS3B01G443800 chr3D 90.634 331 29 2 1078 1406 519333598 519333928 5.190000e-119 438.0
42 TraesCS3B01G443800 chr3D 76.831 587 98 23 2094 2662 519334281 519334847 3.310000e-76 296.0
43 TraesCS3B01G443800 chr3D 81.181 271 41 8 1770 2034 519353228 519353494 4.430000e-50 209.0
44 TraesCS3B01G443800 chr7B 81.398 758 117 15 2675 3410 375442138 375441383 8.090000e-167 597.0
45 TraesCS3B01G443800 chr5A 97.586 290 5 2 1 289 41342582 41342870 3.040000e-136 496.0
46 TraesCS3B01G443800 chr5A 95.904 293 10 2 1 292 23255007 23254716 1.420000e-129 473.0
47 TraesCS3B01G443800 chr5A 94.737 38 2 0 4054 4091 157480502 157480465 4.720000e-05 60.2
48 TraesCS3B01G443800 chr4B 93.617 47 2 1 4045 4091 91337718 91337763 7.840000e-08 69.4
49 TraesCS3B01G443800 chr5B 93.182 44 3 0 4046 4089 391755522 391755565 1.010000e-06 65.8


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 TraesCS3B01G443800 chr3B 684247615 684251985 4370 False 8072.000000 8072 100.0000 1 4371 1 chr3B.!!$F4 4370
1 TraesCS3B01G443800 chr3B 152207902 152208546 644 True 795.000000 795 88.9920 202 843 1 chr3B.!!$R1 641
2 TraesCS3B01G443800 chr3B 684265049 684267463 2414 False 762.000000 942 85.9650 944 3440 2 chr3B.!!$F8 2496
3 TraesCS3B01G443800 chr3B 683758420 683759965 1545 False 507.000000 590 87.9680 1074 3134 2 chr3B.!!$F7 2060
4 TraesCS3B01G443800 chr3B 683679300 683680544 1244 False 432.000000 754 79.4550 1698 3143 2 chr3B.!!$F6 1445
5 TraesCS3B01G443800 chr3A 654567119 654570160 3041 False 1649.500000 2791 90.5915 898 3616 2 chr3A.!!$F3 2718
6 TraesCS3B01G443800 chr3A 654781931 654784681 2750 False 801.000000 1018 85.0045 944 3440 2 chr3A.!!$F5 2496
7 TraesCS3B01G443800 chr3A 655083031 655086501 3470 False 625.000000 743 84.6245 939 3513 2 chr3A.!!$F6 2574
8 TraesCS3B01G443800 chr3A 654357714 654359666 1952 False 603.500000 771 86.8440 1074 3143 2 chr3A.!!$F2 2069
9 TraesCS3B01G443800 chr3A 654578846 654579478 632 False 253.666667 475 91.6230 3610 4297 3 chr3A.!!$F4 687
10 TraesCS3B01G443800 chr1B 134819134 134820013 879 False 1334.000000 1334 94.1240 1 876 1 chr1B.!!$F1 875
11 TraesCS3B01G443800 chr1B 476910425 476911265 840 True 1295.000000 1295 94.4440 1 843 1 chr1B.!!$R1 842
12 TraesCS3B01G443800 chr6B 590563088 590563932 844 False 1293.000000 1293 94.3400 1 843 1 chr6B.!!$F1 842
13 TraesCS3B01G443800 chr6B 288795256 288796005 749 True 1134.000000 1134 94.0080 96 844 1 chr6B.!!$R1 748
14 TraesCS3B01G443800 chr1A 515835284 515836222 938 False 638.500000 950 94.7350 1 850 2 chr1A.!!$F2 849
15 TraesCS3B01G443800 chr4A 741155123 741155766 643 True 865.000000 865 90.9940 203 843 1 chr4A.!!$R2 640
16 TraesCS3B01G443800 chr5D 285160840 285161481 641 False 841.000000 841 90.2780 198 843 1 chr5D.!!$F1 645
17 TraesCS3B01G443800 chr7D 540732718 540733361 643 False 832.000000 832 90.0150 198 843 1 chr7D.!!$F1 645
18 TraesCS3B01G443800 chr7D 381001046 381001796 750 True 588.000000 588 81.3000 2675 3405 1 chr7D.!!$R1 730
19 TraesCS3B01G443800 chr3D 519353228 519354376 1148 False 421.500000 634 80.6895 1770 3134 2 chr3D.!!$F3 1364
20 TraesCS3B01G443800 chr3D 519333598 519334847 1249 False 367.000000 438 83.7325 1078 2662 2 chr3D.!!$F2 1584
21 TraesCS3B01G443800 chr7B 375441383 375442138 755 True 597.000000 597 81.3980 2675 3410 1 chr7B.!!$R1 735

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
844 957 0.099436 GCGCCATCATGGTCAAGTTC 59.901 55.0 5.31 0.00 40.46 3.01 F
901 1014 0.108138 CCGATTTTCTCGCCACTCCT 60.108 55.0 0.00 0.00 46.25 3.69 F
904 1017 0.253327 ATTTTCTCGCCACTCCTCCC 59.747 55.0 0.00 0.00 0.00 4.30 F
1829 2623 0.388778 TTGCCACAATGCATTGCTCG 60.389 50.0 33.94 23.33 41.70 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2607 1.094785 GGTGTACCGAGCAATGCATT 58.905 50.000 5.99 5.99 0.0 3.56 R
2099 3223 1.134371 GTGGGCACAGAGGAATAGGTC 60.134 57.143 0.00 0.00 0.0 3.85 R
2425 4976 1.274167 CTTGTGGATGCCTGCAATTGT 59.726 47.619 7.40 0.00 0.0 2.71 R
3520 6172 0.680921 ATCGGTTGGACAATGCAGGG 60.681 55.000 0.00 0.00 0.0 4.45 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
75 76 1.139058 CCGGTGGACTAGCTTAAGCAT 59.861 52.381 28.39 13.90 45.16 3.79
172 175 3.328382 AATTAGGTAGCTGCGTGTGAA 57.672 42.857 7.31 0.00 0.00 3.18
224 317 4.350368 TGTTGAGGCTCACAATCTTGTA 57.650 40.909 18.55 0.00 39.91 2.41
242 335 8.882415 ATCTTGTAAAAGTCGTGTCTTCTTTA 57.118 30.769 0.00 0.00 32.22 1.85
289 382 8.972127 GCTAACATCTCCACCATCTATTATCTA 58.028 37.037 0.00 0.00 0.00 1.98
321 414 4.846779 AACATTTTGCAATAGACGGTGT 57.153 36.364 0.00 0.00 0.00 4.16
403 504 1.889530 GCCTAACTCCCTCACTGCGT 61.890 60.000 0.00 0.00 0.00 5.24
447 548 3.962063 ACCAATATGGCAATCAAGCATCA 59.038 39.130 0.00 0.00 42.67 3.07
676 778 9.944376 AAGTTAGAGCAATCACTTGACTAATTA 57.056 29.630 0.00 0.00 36.35 1.40
839 952 2.819154 CACGCGCCATCATGGTCA 60.819 61.111 5.73 0.00 40.46 4.02
844 957 0.099436 GCGCCATCATGGTCAAGTTC 59.901 55.000 5.31 0.00 40.46 3.01
845 958 1.742761 CGCCATCATGGTCAAGTTCT 58.257 50.000 5.31 0.00 40.46 3.01
847 960 2.159476 CGCCATCATGGTCAAGTTCTTG 60.159 50.000 5.31 6.24 40.46 3.02
851 964 5.739935 GCCATCATGGTCAAGTTCTTGTTTT 60.740 40.000 5.31 0.00 40.46 2.43
852 965 6.516527 GCCATCATGGTCAAGTTCTTGTTTTA 60.517 38.462 5.31 0.13 40.46 1.52
853 966 7.086376 CCATCATGGTCAAGTTCTTGTTTTAG 58.914 38.462 11.52 2.85 31.35 1.85
854 967 6.633500 TCATGGTCAAGTTCTTGTTTTAGG 57.367 37.500 11.52 1.60 0.00 2.69
855 968 6.361433 TCATGGTCAAGTTCTTGTTTTAGGA 58.639 36.000 11.52 3.47 0.00 2.94
856 969 7.004086 TCATGGTCAAGTTCTTGTTTTAGGAT 58.996 34.615 11.52 0.00 0.00 3.24
857 970 7.505585 TCATGGTCAAGTTCTTGTTTTAGGATT 59.494 33.333 11.52 0.00 0.00 3.01
858 971 7.038154 TGGTCAAGTTCTTGTTTTAGGATTG 57.962 36.000 11.52 0.00 0.00 2.67
859 972 5.920840 GGTCAAGTTCTTGTTTTAGGATTGC 59.079 40.000 11.52 0.00 0.00 3.56
860 973 5.920840 GTCAAGTTCTTGTTTTAGGATTGCC 59.079 40.000 11.52 0.00 0.00 4.52
861 974 4.766404 AGTTCTTGTTTTAGGATTGCCG 57.234 40.909 0.00 0.00 39.96 5.69
862 975 4.394729 AGTTCTTGTTTTAGGATTGCCGA 58.605 39.130 0.00 0.00 39.96 5.54
863 976 4.455877 AGTTCTTGTTTTAGGATTGCCGAG 59.544 41.667 0.00 0.00 39.96 4.63
864 977 4.015872 TCTTGTTTTAGGATTGCCGAGT 57.984 40.909 0.00 0.00 39.96 4.18
865 978 4.394729 TCTTGTTTTAGGATTGCCGAGTT 58.605 39.130 0.00 0.00 39.96 3.01
866 979 4.825085 TCTTGTTTTAGGATTGCCGAGTTT 59.175 37.500 0.00 0.00 39.96 2.66
867 980 4.759516 TGTTTTAGGATTGCCGAGTTTC 57.240 40.909 0.00 0.00 39.96 2.78
868 981 4.394729 TGTTTTAGGATTGCCGAGTTTCT 58.605 39.130 0.00 0.00 39.96 2.52
869 982 4.825085 TGTTTTAGGATTGCCGAGTTTCTT 59.175 37.500 0.00 0.00 39.96 2.52
870 983 5.048991 TGTTTTAGGATTGCCGAGTTTCTTC 60.049 40.000 0.00 0.00 39.96 2.87
871 984 4.553330 TTAGGATTGCCGAGTTTCTTCT 57.447 40.909 0.00 0.00 39.96 2.85
872 985 2.979240 AGGATTGCCGAGTTTCTTCTC 58.021 47.619 0.00 0.00 39.96 2.87
873 986 2.010497 GGATTGCCGAGTTTCTTCTCC 58.990 52.381 0.00 0.00 0.00 3.71
874 987 2.615493 GGATTGCCGAGTTTCTTCTCCA 60.615 50.000 0.00 0.00 0.00 3.86
875 988 1.878953 TTGCCGAGTTTCTTCTCCAC 58.121 50.000 0.00 0.00 0.00 4.02
876 989 1.048601 TGCCGAGTTTCTTCTCCACT 58.951 50.000 0.00 0.00 0.00 4.00
877 990 1.000955 TGCCGAGTTTCTTCTCCACTC 59.999 52.381 0.00 0.00 34.68 3.51
878 991 1.000955 GCCGAGTTTCTTCTCCACTCA 59.999 52.381 0.00 0.00 37.40 3.41
879 992 2.928731 GCCGAGTTTCTTCTCCACTCAG 60.929 54.545 0.00 0.00 37.40 3.35
880 993 2.333014 CGAGTTTCTTCTCCACTCAGC 58.667 52.381 0.00 0.00 37.40 4.26
881 994 2.288457 CGAGTTTCTTCTCCACTCAGCA 60.288 50.000 0.00 0.00 37.40 4.41
882 995 3.063485 GAGTTTCTTCTCCACTCAGCAC 58.937 50.000 0.00 0.00 37.48 4.40
883 996 2.147150 GTTTCTTCTCCACTCAGCACC 58.853 52.381 0.00 0.00 0.00 5.01
884 997 0.318441 TTCTTCTCCACTCAGCACCG 59.682 55.000 0.00 0.00 0.00 4.94
885 998 0.539669 TCTTCTCCACTCAGCACCGA 60.540 55.000 0.00 0.00 0.00 4.69
886 999 0.534412 CTTCTCCACTCAGCACCGAT 59.466 55.000 0.00 0.00 0.00 4.18
887 1000 0.976641 TTCTCCACTCAGCACCGATT 59.023 50.000 0.00 0.00 0.00 3.34
888 1001 0.976641 TCTCCACTCAGCACCGATTT 59.023 50.000 0.00 0.00 0.00 2.17
889 1002 1.347707 TCTCCACTCAGCACCGATTTT 59.652 47.619 0.00 0.00 0.00 1.82
890 1003 1.734465 CTCCACTCAGCACCGATTTTC 59.266 52.381 0.00 0.00 0.00 2.29
891 1004 1.347707 TCCACTCAGCACCGATTTTCT 59.652 47.619 0.00 0.00 0.00 2.52
892 1005 1.734465 CCACTCAGCACCGATTTTCTC 59.266 52.381 0.00 0.00 0.00 2.87
894 1007 0.371645 CTCAGCACCGATTTTCTCGC 59.628 55.000 0.00 0.00 46.25 5.03
895 1008 1.019278 TCAGCACCGATTTTCTCGCC 61.019 55.000 0.00 0.00 46.25 5.54
896 1009 1.003839 AGCACCGATTTTCTCGCCA 60.004 52.632 0.00 0.00 46.25 5.69
897 1010 1.134694 GCACCGATTTTCTCGCCAC 59.865 57.895 0.00 0.00 46.25 5.01
898 1011 1.298859 GCACCGATTTTCTCGCCACT 61.299 55.000 0.00 0.00 46.25 4.00
899 1012 0.721718 CACCGATTTTCTCGCCACTC 59.278 55.000 0.00 0.00 46.25 3.51
900 1013 0.391263 ACCGATTTTCTCGCCACTCC 60.391 55.000 0.00 0.00 46.25 3.85
901 1014 0.108138 CCGATTTTCTCGCCACTCCT 60.108 55.000 0.00 0.00 46.25 3.69
902 1015 1.281899 CGATTTTCTCGCCACTCCTC 58.718 55.000 0.00 0.00 41.14 3.71
903 1016 1.657822 GATTTTCTCGCCACTCCTCC 58.342 55.000 0.00 0.00 0.00 4.30
904 1017 0.253327 ATTTTCTCGCCACTCCTCCC 59.747 55.000 0.00 0.00 0.00 4.30
905 1018 1.838073 TTTTCTCGCCACTCCTCCCC 61.838 60.000 0.00 0.00 0.00 4.81
925 1038 2.289694 CCAAACTGTCCATCGTTCTCCT 60.290 50.000 0.00 0.00 0.00 3.69
927 1040 0.811915 ACTGTCCATCGTTCTCCTCG 59.188 55.000 0.00 0.00 0.00 4.63
928 1041 1.095600 CTGTCCATCGTTCTCCTCGA 58.904 55.000 0.00 0.00 41.45 4.04
929 1042 1.064803 CTGTCCATCGTTCTCCTCGAG 59.935 57.143 5.13 5.13 40.57 4.04
930 1043 1.339727 TGTCCATCGTTCTCCTCGAGA 60.340 52.381 15.71 0.00 40.57 4.04
1020 1138 2.341101 GCCGTCTTCCTCCTCGTCA 61.341 63.158 0.00 0.00 0.00 4.35
1168 1301 2.287117 ACATCCTGATGGGGCCCA 60.287 61.111 30.97 30.97 42.91 5.36
1388 1522 0.804989 GCCGACCAGTGAGATTTTGG 59.195 55.000 0.00 0.00 37.98 3.28
1400 1534 1.235756 GATTTTGGATCCCCCTCCCT 58.764 55.000 9.90 0.00 34.12 4.20
1417 1887 1.412361 CCCTCCCACAAACCCTCAAAA 60.412 52.381 0.00 0.00 0.00 2.44
1476 2245 0.458543 AAGATACAGCCGCACACGAG 60.459 55.000 0.00 0.00 43.93 4.18
1477 2246 1.878522 GATACAGCCGCACACGAGG 60.879 63.158 0.00 0.00 43.93 4.63
1478 2247 3.371097 ATACAGCCGCACACGAGGG 62.371 63.158 0.00 0.00 43.93 4.30
1494 2263 2.316586 GGGGGTGGTCACATGGGAT 61.317 63.158 0.00 0.00 0.00 3.85
1518 2291 9.494271 GATGCAACTAGAAATTATGTCCTGATA 57.506 33.333 0.00 0.00 0.00 2.15
1611 2387 8.416329 CCCCCAAATTTCTATTAGTGAAATCAG 58.584 37.037 0.00 0.00 41.54 2.90
1612 2388 8.416329 CCCCAAATTTCTATTAGTGAAATCAGG 58.584 37.037 0.00 0.00 41.54 3.86
1634 2410 1.331756 CATTACAATGTCAGCCGCCTC 59.668 52.381 0.00 0.00 0.00 4.70
1645 2421 1.004918 GCCGCCTCACACACTAACT 60.005 57.895 0.00 0.00 0.00 2.24
1686 2462 5.461737 CAGAGAACAGAGACAACAGAAGTTC 59.538 44.000 0.00 0.00 35.28 3.01
1703 2479 5.531287 AGAAGTTCGAAGCTAACCAATGTTT 59.469 36.000 0.00 0.00 35.87 2.83
1817 2607 2.143122 CGCTAGAAGAAACTTGCCACA 58.857 47.619 0.00 0.00 35.82 4.17
1829 2623 0.388778 TTGCCACAATGCATTGCTCG 60.389 50.000 33.94 23.33 41.70 5.03
1876 2806 7.334858 TCTCTGCACCTTTTTAAAATTTGGTT 58.665 30.769 14.28 3.12 0.00 3.67
1926 2857 5.815581 TGGGTGACTTACAAATAGAAGCAT 58.184 37.500 0.00 0.00 0.00 3.79
1935 2866 9.632638 ACTTACAAATAGAAGCATATGTGGATT 57.367 29.630 4.29 0.00 0.00 3.01
2034 3153 5.815581 TCTTATCACAACATTTAGCCACCT 58.184 37.500 0.00 0.00 0.00 4.00
2047 3171 3.460857 AGCCACCTTCAGATAATCGAC 57.539 47.619 0.00 0.00 0.00 4.20
2050 3174 3.633235 CCACCTTCAGATAATCGACGAG 58.367 50.000 3.01 0.00 0.00 4.18
2057 3181 5.096954 TCAGATAATCGACGAGCTACTTG 57.903 43.478 3.01 0.00 0.00 3.16
2069 3193 1.687123 AGCTACTTGTCTTCACACGGT 59.313 47.619 0.00 0.00 29.76 4.83
2154 3283 2.302587 TGGTGAATTTCCTCCAACCC 57.697 50.000 7.62 0.00 0.00 4.11
2159 3288 4.141597 GGTGAATTTCCTCCAACCCAAAAA 60.142 41.667 0.00 0.00 0.00 1.94
2172 3301 3.218453 ACCCAAAAATGATGTCGTGTCA 58.782 40.909 0.00 0.00 0.00 3.58
2194 3323 2.308570 TCAACCTATGCATTGGTCTGGT 59.691 45.455 29.16 13.83 34.83 4.00
2196 3325 3.845781 ACCTATGCATTGGTCTGGTAG 57.154 47.619 24.76 3.78 29.89 3.18
2250 3387 4.460948 TCTTGATACAACGGGGAAGTAC 57.539 45.455 0.00 0.00 0.00 2.73
2273 3411 4.826556 TCTTTGGTTTGGTTTGAAACAGG 58.173 39.130 10.53 0.00 37.53 4.00
2276 3414 2.234908 TGGTTTGGTTTGAAACAGGGTG 59.765 45.455 10.53 0.00 37.53 4.61
2290 3428 1.004745 CAGGGTGCAGTTGGGAGTTAT 59.995 52.381 0.00 0.00 0.00 1.89
2293 3431 2.359900 GGTGCAGTTGGGAGTTATCTG 58.640 52.381 0.00 0.00 0.00 2.90
2345 4883 3.569701 ACAGTCGAATTGGCAGTGATTTT 59.430 39.130 0.00 0.00 0.00 1.82
2402 4942 6.835174 ACTGATTTCATATACCAGAGTGCAT 58.165 36.000 0.00 0.00 0.00 3.96
2403 4943 7.966812 ACTGATTTCATATACCAGAGTGCATA 58.033 34.615 0.00 0.00 0.00 3.14
2404 4944 8.432013 ACTGATTTCATATACCAGAGTGCATAA 58.568 33.333 0.00 0.00 0.00 1.90
2405 4945 9.445878 CTGATTTCATATACCAGAGTGCATAAT 57.554 33.333 0.00 0.00 0.00 1.28
2406 4946 9.797642 TGATTTCATATACCAGAGTGCATAATT 57.202 29.630 0.00 0.00 0.00 1.40
2411 4951 9.066892 TCATATACCAGAGTGCATAATTTTTCC 57.933 33.333 0.00 0.00 0.00 3.13
2412 4952 9.071276 CATATACCAGAGTGCATAATTTTTCCT 57.929 33.333 0.00 0.00 0.00 3.36
2425 4976 9.377312 GCATAATTTTTCCTAATTTGCAACCTA 57.623 29.630 0.00 0.00 34.87 3.08
2440 4991 1.767759 ACCTACAATTGCAGGCATCC 58.232 50.000 22.53 0.00 35.14 3.51
2447 4998 1.180029 ATTGCAGGCATCCACAAGTC 58.820 50.000 0.00 0.00 0.00 3.01
2450 5001 0.607489 GCAGGCATCCACAAGTCAGT 60.607 55.000 0.00 0.00 0.00 3.41
2479 5033 8.025445 CCCTGAAATTTCTGTCAAATCTAACAG 58.975 37.037 18.64 3.71 43.41 3.16
2505 5059 8.488764 GTTAATCATTTAGTGGATTCTCGCTAC 58.511 37.037 0.00 0.00 35.49 3.58
2508 5062 5.985530 TCATTTAGTGGATTCTCGCTACATG 59.014 40.000 11.58 11.58 38.36 3.21
2512 5066 2.035961 GTGGATTCTCGCTACATGCCTA 59.964 50.000 0.00 0.00 38.78 3.93
2513 5067 2.035961 TGGATTCTCGCTACATGCCTAC 59.964 50.000 0.00 0.00 38.78 3.18
2514 5068 2.035961 GGATTCTCGCTACATGCCTACA 59.964 50.000 0.00 0.00 38.78 2.74
2515 5069 3.306364 GGATTCTCGCTACATGCCTACAT 60.306 47.826 0.00 0.00 38.78 2.29
2526 5080 6.183360 GCTACATGCCTACATTGCTTCTTAAA 60.183 38.462 0.00 0.00 32.87 1.52
2533 5098 7.775093 TGCCTACATTGCTTCTTAAATCTGTAT 59.225 33.333 0.00 0.00 0.00 2.29
2557 5122 7.250032 TCTATGTCCTATGATGCTATTGCTT 57.750 36.000 0.00 0.00 40.48 3.91
2618 5197 3.221771 TGCAAGCCTGTCAAAACATACT 58.778 40.909 0.00 0.00 34.13 2.12
2635 5217 6.458232 ACATACTCTCTAGCTACCTGTTTG 57.542 41.667 0.00 0.00 0.00 2.93
2637 5219 6.095720 ACATACTCTCTAGCTACCTGTTTGAC 59.904 42.308 0.00 0.00 0.00 3.18
2639 5221 5.020132 ACTCTCTAGCTACCTGTTTGACAT 58.980 41.667 0.00 0.00 0.00 3.06
2640 5222 5.105554 ACTCTCTAGCTACCTGTTTGACATG 60.106 44.000 0.00 0.00 0.00 3.21
2668 5272 6.356556 TGCTTATGCCTTTCTATACACATGT 58.643 36.000 0.00 0.00 38.71 3.21
2714 5320 3.234234 AGTGCTATATTTGCAGGGCAT 57.766 42.857 3.73 0.00 41.41 4.40
2746 5352 3.007398 AGAGTCTTCGCCTCATTTCTTGT 59.993 43.478 0.00 0.00 0.00 3.16
2758 5370 9.013490 CGCCTCATTTCTTGTTATAATTTTGAG 57.987 33.333 0.00 0.00 0.00 3.02
2941 5556 0.470766 AAGCCAGTGGGTACGACAAA 59.529 50.000 15.67 0.00 40.38 2.83
3120 5735 4.688419 CCTGCGCGCAAAGTGTGG 62.688 66.667 35.50 26.45 0.00 4.17
3188 5803 2.849120 CTTCGAGGTGCAGGAGCCTG 62.849 65.000 12.17 12.17 46.15 4.85
3354 5996 2.044650 GCTTCTCAGGGGCATGCA 60.045 61.111 21.36 0.00 0.00 3.96
3416 6058 1.133513 AGTGCCTGGATGTTTTCACCA 60.134 47.619 0.00 0.00 32.87 4.17
3452 6104 0.926846 GCACTACTGATCTGCGCTTC 59.073 55.000 9.73 3.62 0.00 3.86
3461 6113 0.037326 ATCTGCGCTTCGGTTCTTCA 60.037 50.000 9.73 0.00 0.00 3.02
3465 6117 1.784062 CGCTTCGGTTCTTCAGCTG 59.216 57.895 7.63 7.63 0.00 4.24
3500 6152 2.538437 CTTCTGCATCGACTTCTCCTG 58.462 52.381 0.00 0.00 0.00 3.86
3514 6166 5.991861 ACTTCTCCTGTAAGATCGTAGAGA 58.008 41.667 13.31 7.89 43.63 3.10
3515 6167 6.053005 ACTTCTCCTGTAAGATCGTAGAGAG 58.947 44.000 13.31 8.29 43.63 3.20
3518 6170 3.878103 TCCTGTAAGATCGTAGAGAGTGC 59.122 47.826 13.31 0.00 43.63 4.40
3520 6172 4.024387 CCTGTAAGATCGTAGAGAGTGCTC 60.024 50.000 13.31 0.00 43.63 4.26
3525 6177 1.032657 TCGTAGAGAGTGCTCCCTGC 61.033 60.000 0.00 0.00 42.30 4.85
3544 6196 2.083774 GCATTGTCCAACCGATCTTCA 58.916 47.619 0.00 0.00 0.00 3.02
3545 6197 2.096496 GCATTGTCCAACCGATCTTCAG 59.904 50.000 0.00 0.00 0.00 3.02
3555 6207 2.744202 ACCGATCTTCAGAAACATGTGC 59.256 45.455 0.00 0.00 0.00 4.57
3557 6209 4.183865 CCGATCTTCAGAAACATGTGCTA 58.816 43.478 0.00 0.00 0.00 3.49
3589 6241 4.900635 ACCTTGCAGTTTAGTTCAAGTG 57.099 40.909 0.00 0.00 35.42 3.16
3605 6257 6.150140 AGTTCAAGTGGTTCTGAAATATGCTC 59.850 38.462 0.00 0.00 0.00 4.26
3641 6293 2.160417 GCAGTACTGGTTTGCTTAGCTG 59.840 50.000 23.95 0.00 35.05 4.24
3658 6310 4.026356 AGCTGTGAAACTTGCTTATCCT 57.974 40.909 0.00 0.00 42.58 3.24
3662 6314 3.753272 TGTGAAACTTGCTTATCCTCTGC 59.247 43.478 0.00 0.00 38.04 4.26
3678 6332 3.325870 CTCTGCGTGGACTTAATGTGAA 58.674 45.455 0.00 0.00 0.00 3.18
3708 6362 4.814041 AGGAGCTCCTGGGCCTCC 62.814 72.222 34.74 19.57 46.55 4.30
3731 6385 2.367512 GGGAGGCCCAGTCATCCT 60.368 66.667 0.00 0.00 44.65 3.24
3732 6386 2.750657 GGGAGGCCCAGTCATCCTG 61.751 68.421 0.00 0.00 44.65 3.86
3733 6387 1.997874 GGAGGCCCAGTCATCCTGT 60.998 63.158 0.00 0.00 39.74 4.00
3734 6388 1.222936 GAGGCCCAGTCATCCTGTG 59.777 63.158 0.00 0.00 39.74 3.66
3735 6389 2.439156 GGCCCAGTCATCCTGTGC 60.439 66.667 0.00 0.00 43.09 4.57
3736 6390 2.439156 GCCCAGTCATCCTGTGCC 60.439 66.667 0.00 0.00 38.48 5.01
3737 6391 2.976490 GCCCAGTCATCCTGTGCCT 61.976 63.158 0.00 0.00 38.48 4.75
3741 6395 1.134280 CCAGTCATCCTGTGCCTTAGG 60.134 57.143 0.00 0.00 39.74 2.69
3752 6406 4.864334 CCTTAGGCCCTGGCGCTG 62.864 72.222 7.64 0.00 43.06 5.18
3753 6407 4.864334 CTTAGGCCCTGGCGCTGG 62.864 72.222 7.64 10.33 43.06 4.85
3811 6466 5.869579 TCTGTTCTGATTGCTAAAACCTCT 58.130 37.500 0.00 0.00 0.00 3.69
3814 6469 5.637810 TGTTCTGATTGCTAAAACCTCTACG 59.362 40.000 0.00 0.00 0.00 3.51
3824 6479 5.391416 GCTAAAACCTCTACGACGAACTACT 60.391 44.000 0.00 0.00 0.00 2.57
3826 6481 1.736681 ACCTCTACGACGAACTACTGC 59.263 52.381 0.00 0.00 0.00 4.40
3842 6497 4.827284 ACTACTGCTGCACACCTTATTTTT 59.173 37.500 0.00 0.00 0.00 1.94
3843 6498 6.001460 ACTACTGCTGCACACCTTATTTTTA 58.999 36.000 0.00 0.00 0.00 1.52
3844 6499 5.782893 ACTGCTGCACACCTTATTTTTAA 57.217 34.783 0.00 0.00 0.00 1.52
3845 6500 5.772521 ACTGCTGCACACCTTATTTTTAAG 58.227 37.500 0.00 0.00 0.00 1.85
3846 6501 5.534654 ACTGCTGCACACCTTATTTTTAAGA 59.465 36.000 0.00 0.00 0.00 2.10
3847 6502 6.040391 ACTGCTGCACACCTTATTTTTAAGAA 59.960 34.615 0.00 0.00 0.00 2.52
3848 6503 6.991938 TGCTGCACACCTTATTTTTAAGAAT 58.008 32.000 0.00 0.00 0.00 2.40
3849 6504 7.441017 TGCTGCACACCTTATTTTTAAGAATT 58.559 30.769 0.00 0.00 0.00 2.17
3850 6505 7.930865 TGCTGCACACCTTATTTTTAAGAATTT 59.069 29.630 0.00 0.00 0.00 1.82
3851 6506 8.435430 GCTGCACACCTTATTTTTAAGAATTTC 58.565 33.333 0.00 0.00 0.00 2.17
3852 6507 9.696917 CTGCACACCTTATTTTTAAGAATTTCT 57.303 29.630 0.00 0.00 0.00 2.52
3853 6508 9.691362 TGCACACCTTATTTTTAAGAATTTCTC 57.309 29.630 0.00 0.00 0.00 2.87
3854 6509 9.691362 GCACACCTTATTTTTAAGAATTTCTCA 57.309 29.630 0.00 0.00 0.00 3.27
3901 6556 5.702349 AGTGTACTAAGTGACACACCTAC 57.298 43.478 8.59 2.61 46.83 3.18
3910 6565 2.806244 GTGACACACCTACCATCACAAC 59.194 50.000 0.00 0.00 39.57 3.32
3920 6575 0.325933 CCATCACAACCAGAGCAGGA 59.674 55.000 0.00 0.00 0.00 3.86
3924 6579 0.179048 CACAACCAGAGCAGGACACA 60.179 55.000 0.00 0.00 0.00 3.72
3927 6582 1.131638 AACCAGAGCAGGACACAGAA 58.868 50.000 0.00 0.00 0.00 3.02
3931 6586 2.027377 CCAGAGCAGGACACAGAAGATT 60.027 50.000 0.00 0.00 0.00 2.40
3992 6648 6.003326 TGCTTCTCCTATGTGTCAATTTTCA 58.997 36.000 0.00 0.00 0.00 2.69
3995 6651 7.395190 TTCTCCTATGTGTCAATTTTCATGG 57.605 36.000 0.00 0.00 0.00 3.66
4052 6714 6.014925 TCCAAAATGCTTAAAAACTACTCCCC 60.015 38.462 0.00 0.00 0.00 4.81
4079 6741 9.447157 CCATTCCATAATTATTGTTGTGGTTTT 57.553 29.630 0.00 0.00 40.20 2.43
4098 6760 7.064016 GTGGTTTTAGTTCAAATTTCTGTTGCA 59.936 33.333 0.00 0.00 0.00 4.08
4099 6761 7.277539 TGGTTTTAGTTCAAATTTCTGTTGCAG 59.722 33.333 0.00 0.00 0.00 4.41
4100 6762 7.491048 GGTTTTAGTTCAAATTTCTGTTGCAGA 59.509 33.333 0.00 0.00 38.87 4.26
4101 6763 8.868916 GTTTTAGTTCAAATTTCTGTTGCAGAA 58.131 29.630 7.41 7.41 46.93 3.02
4119 6781 7.581213 TGCAGAAAAGAAGAAAAGGATTGTA 57.419 32.000 0.00 0.00 0.00 2.41
4212 6889 6.348478 TCAAAATGGAGGATATGGGGTAAA 57.652 37.500 0.00 0.00 0.00 2.01
4221 6898 4.794067 AGGATATGGGGTAAAAACCACTCT 59.206 41.667 0.00 0.00 40.05 3.24
4238 6915 7.719871 ACCACTCTACCATATTCGCTATAAT 57.280 36.000 0.00 0.00 0.00 1.28
4267 6945 5.062183 TCGTCATATTTTTCGAGAGTGCAAG 59.938 40.000 0.00 0.00 0.00 4.01
4279 6957 3.152341 AGAGTGCAAGAAACCAATCTGG 58.848 45.455 0.00 0.00 45.02 3.86
4280 6958 2.229784 GAGTGCAAGAAACCAATCTGGG 59.770 50.000 0.00 0.00 43.37 4.45
4297 6975 7.309744 CCAATCTGGGTAGAATTGCTTTGTTTA 60.310 37.037 0.00 0.00 36.32 2.01
4298 6976 7.961326 ATCTGGGTAGAATTGCTTTGTTTAT 57.039 32.000 0.00 0.00 36.32 1.40
4299 6977 7.775053 TCTGGGTAGAATTGCTTTGTTTATT 57.225 32.000 0.00 0.00 0.00 1.40
4300 6978 8.871629 TCTGGGTAGAATTGCTTTGTTTATTA 57.128 30.769 0.00 0.00 0.00 0.98
4301 6979 9.303116 TCTGGGTAGAATTGCTTTGTTTATTAA 57.697 29.630 0.00 0.00 0.00 1.40
4336 7014 7.687005 TTTTGCTTTGTTTTAATGAGTACGG 57.313 32.000 0.00 0.00 0.00 4.02
4337 7015 4.789784 TGCTTTGTTTTAATGAGTACGGC 58.210 39.130 0.00 0.00 0.00 5.68
4338 7016 4.163552 GCTTTGTTTTAATGAGTACGGCC 58.836 43.478 0.00 0.00 0.00 6.13
4339 7017 4.729595 CTTTGTTTTAATGAGTACGGCCC 58.270 43.478 0.00 0.00 0.00 5.80
4340 7018 3.706600 TGTTTTAATGAGTACGGCCCT 57.293 42.857 0.00 0.00 0.00 5.19
4341 7019 4.023726 TGTTTTAATGAGTACGGCCCTT 57.976 40.909 0.00 0.00 0.00 3.95
4342 7020 4.004982 TGTTTTAATGAGTACGGCCCTTC 58.995 43.478 0.00 0.00 0.00 3.46
4343 7021 2.994186 TTAATGAGTACGGCCCTTCC 57.006 50.000 0.00 0.00 0.00 3.46
4344 7022 1.125633 TAATGAGTACGGCCCTTCCC 58.874 55.000 0.00 0.00 0.00 3.97
4352 7030 4.561452 GGCCCTTCCCGAAGAATC 57.439 61.111 6.01 0.00 40.79 2.52
4364 7042 2.443820 GAAGAATCGAGCGCCTTTTC 57.556 50.000 2.29 2.58 0.00 2.29
4365 7043 1.062733 GAAGAATCGAGCGCCTTTTCC 59.937 52.381 2.29 0.00 0.00 3.13
4366 7044 0.036388 AGAATCGAGCGCCTTTTCCA 60.036 50.000 2.29 0.00 0.00 3.53
4367 7045 0.097150 GAATCGAGCGCCTTTTCCAC 59.903 55.000 2.29 0.00 0.00 4.02
4368 7046 1.635663 AATCGAGCGCCTTTTCCACG 61.636 55.000 2.29 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 9.653067 CGTTTGTGTTTCATATACACTTTTGTA 57.347 29.630 8.36 0.00 44.76 2.41
172 175 3.403936 GCAGAAGATAATGCCCCGT 57.596 52.632 0.00 0.00 36.41 5.28
224 317 4.215613 GCCCATAAAGAAGACACGACTTTT 59.784 41.667 0.00 0.00 35.79 2.27
289 382 8.547173 TCTATTGCAAAATGTTTTGGGGAATAT 58.453 29.630 17.16 0.00 45.73 1.28
403 504 2.158623 AGACCTTCTCATTGTTGCCACA 60.159 45.455 0.00 0.00 0.00 4.17
522 624 6.844097 AAATTAACCGGGCAATCTTTTCTA 57.156 33.333 6.32 0.00 0.00 2.10
676 778 8.924511 AATATTGTGATTGTCTCGGGAAATAT 57.075 30.769 0.00 0.00 0.00 1.28
809 922 1.800032 CGCGTGTTGTTATGCCCAT 59.200 52.632 0.00 0.00 0.00 4.00
818 931 2.689785 CCATGATGGCGCGTGTTGT 61.690 57.895 8.43 0.00 0.00 3.32
839 952 4.825085 TCGGCAATCCTAAAACAAGAACTT 59.175 37.500 0.00 0.00 0.00 2.66
844 957 4.766404 AACTCGGCAATCCTAAAACAAG 57.234 40.909 0.00 0.00 0.00 3.16
845 958 4.825085 AGAAACTCGGCAATCCTAAAACAA 59.175 37.500 0.00 0.00 0.00 2.83
847 960 5.181433 AGAAGAAACTCGGCAATCCTAAAAC 59.819 40.000 0.00 0.00 0.00 2.43
851 964 3.118738 GGAGAAGAAACTCGGCAATCCTA 60.119 47.826 0.00 0.00 37.74 2.94
852 965 2.355209 GGAGAAGAAACTCGGCAATCCT 60.355 50.000 0.00 0.00 37.74 3.24
853 966 2.010497 GGAGAAGAAACTCGGCAATCC 58.990 52.381 0.00 0.00 37.74 3.01
854 967 2.416893 GTGGAGAAGAAACTCGGCAATC 59.583 50.000 0.00 0.00 37.74 2.67
855 968 2.039084 AGTGGAGAAGAAACTCGGCAAT 59.961 45.455 0.00 0.00 37.74 3.56
856 969 1.416401 AGTGGAGAAGAAACTCGGCAA 59.584 47.619 0.00 0.00 37.74 4.52
857 970 1.000955 GAGTGGAGAAGAAACTCGGCA 59.999 52.381 0.00 0.00 37.74 5.69
858 971 1.000955 TGAGTGGAGAAGAAACTCGGC 59.999 52.381 0.00 0.00 42.65 5.54
859 972 2.928731 GCTGAGTGGAGAAGAAACTCGG 60.929 54.545 6.52 6.52 45.94 4.63
860 973 2.288457 TGCTGAGTGGAGAAGAAACTCG 60.288 50.000 0.00 0.00 42.65 4.18
861 974 3.063485 GTGCTGAGTGGAGAAGAAACTC 58.937 50.000 0.00 0.00 40.61 3.01
862 975 2.224402 GGTGCTGAGTGGAGAAGAAACT 60.224 50.000 0.00 0.00 0.00 2.66
863 976 2.147150 GGTGCTGAGTGGAGAAGAAAC 58.853 52.381 0.00 0.00 0.00 2.78
864 977 1.270305 CGGTGCTGAGTGGAGAAGAAA 60.270 52.381 0.00 0.00 0.00 2.52
865 978 0.318441 CGGTGCTGAGTGGAGAAGAA 59.682 55.000 0.00 0.00 0.00 2.52
866 979 0.539669 TCGGTGCTGAGTGGAGAAGA 60.540 55.000 0.00 0.00 0.00 2.87
867 980 0.534412 ATCGGTGCTGAGTGGAGAAG 59.466 55.000 0.00 0.00 0.00 2.85
868 981 0.976641 AATCGGTGCTGAGTGGAGAA 59.023 50.000 0.00 0.00 0.00 2.87
869 982 0.976641 AAATCGGTGCTGAGTGGAGA 59.023 50.000 0.00 0.00 0.00 3.71
870 983 1.734465 GAAAATCGGTGCTGAGTGGAG 59.266 52.381 0.00 0.00 0.00 3.86
871 984 1.347707 AGAAAATCGGTGCTGAGTGGA 59.652 47.619 0.00 0.00 0.00 4.02
872 985 1.734465 GAGAAAATCGGTGCTGAGTGG 59.266 52.381 0.00 0.00 0.00 4.00
884 997 1.657822 GGAGGAGTGGCGAGAAAATC 58.342 55.000 0.00 0.00 0.00 2.17
885 998 0.253327 GGGAGGAGTGGCGAGAAAAT 59.747 55.000 0.00 0.00 0.00 1.82
886 999 1.677552 GGGAGGAGTGGCGAGAAAA 59.322 57.895 0.00 0.00 0.00 2.29
887 1000 2.291043 GGGGAGGAGTGGCGAGAAA 61.291 63.158 0.00 0.00 0.00 2.52
888 1001 2.683933 GGGGAGGAGTGGCGAGAA 60.684 66.667 0.00 0.00 0.00 2.87
889 1002 3.539593 TTGGGGAGGAGTGGCGAGA 62.540 63.158 0.00 0.00 0.00 4.04
890 1003 2.592993 TTTGGGGAGGAGTGGCGAG 61.593 63.158 0.00 0.00 0.00 5.03
891 1004 2.528127 TTTGGGGAGGAGTGGCGA 60.528 61.111 0.00 0.00 0.00 5.54
892 1005 2.359975 GTTTGGGGAGGAGTGGCG 60.360 66.667 0.00 0.00 0.00 5.69
893 1006 1.303643 CAGTTTGGGGAGGAGTGGC 60.304 63.158 0.00 0.00 0.00 5.01
894 1007 0.036875 GACAGTTTGGGGAGGAGTGG 59.963 60.000 0.00 0.00 0.00 4.00
895 1008 0.036875 GGACAGTTTGGGGAGGAGTG 59.963 60.000 0.00 0.00 0.00 3.51
896 1009 0.401395 TGGACAGTTTGGGGAGGAGT 60.401 55.000 0.00 0.00 0.00 3.85
897 1010 0.995024 ATGGACAGTTTGGGGAGGAG 59.005 55.000 0.00 0.00 0.00 3.69
898 1011 0.991920 GATGGACAGTTTGGGGAGGA 59.008 55.000 0.00 0.00 0.00 3.71
899 1012 0.392998 CGATGGACAGTTTGGGGAGG 60.393 60.000 0.00 0.00 0.00 4.30
900 1013 0.324943 ACGATGGACAGTTTGGGGAG 59.675 55.000 0.00 0.00 0.00 4.30
901 1014 0.768622 AACGATGGACAGTTTGGGGA 59.231 50.000 0.00 0.00 0.00 4.81
902 1015 1.165270 GAACGATGGACAGTTTGGGG 58.835 55.000 0.00 0.00 0.00 4.96
903 1016 2.076863 GAGAACGATGGACAGTTTGGG 58.923 52.381 0.00 0.00 0.00 4.12
904 1017 2.076863 GGAGAACGATGGACAGTTTGG 58.923 52.381 0.00 0.00 0.00 3.28
905 1018 2.996621 GAGGAGAACGATGGACAGTTTG 59.003 50.000 0.00 0.00 0.00 2.93
925 1038 3.118555 TGGTGGACAGTTCTTTTTCTCGA 60.119 43.478 0.00 0.00 0.00 4.04
927 1040 5.278512 GGAATGGTGGACAGTTCTTTTTCTC 60.279 44.000 0.00 0.00 0.00 2.87
928 1041 4.584743 GGAATGGTGGACAGTTCTTTTTCT 59.415 41.667 0.00 0.00 0.00 2.52
929 1042 4.262036 GGGAATGGTGGACAGTTCTTTTTC 60.262 45.833 0.00 0.00 0.00 2.29
930 1043 3.641436 GGGAATGGTGGACAGTTCTTTTT 59.359 43.478 0.00 0.00 0.00 1.94
935 1048 1.305930 GCGGGAATGGTGGACAGTTC 61.306 60.000 0.00 0.00 0.00 3.01
966 1079 1.153565 TGGGAGAGGGTTAGGGTTCTT 59.846 52.381 0.00 0.00 0.00 2.52
967 1080 0.797579 TGGGAGAGGGTTAGGGTTCT 59.202 55.000 0.00 0.00 0.00 3.01
1005 1123 1.153997 GCGTGACGAGGAGGAAGAC 60.154 63.158 10.10 0.00 0.00 3.01
1342 1476 3.371063 GAGGAGGTCGTGGTCGCA 61.371 66.667 0.00 0.00 36.96 5.10
1354 1488 1.894756 CGGCGAGGTAGAGGAGGAG 60.895 68.421 0.00 0.00 0.00 3.69
1388 1522 2.448736 GTGGGAGGGAGGGGGATC 60.449 72.222 0.00 0.00 0.00 3.36
1400 1534 1.689892 GGGTTTTGAGGGTTTGTGGGA 60.690 52.381 0.00 0.00 0.00 4.37
1476 2245 2.316586 ATCCCATGTGACCACCCCC 61.317 63.158 0.00 0.00 0.00 5.40
1477 2246 1.076777 CATCCCATGTGACCACCCC 60.077 63.158 0.00 0.00 0.00 4.95
1478 2247 1.754234 GCATCCCATGTGACCACCC 60.754 63.158 0.00 0.00 0.00 4.61
1494 2263 9.276590 CATATCAGGACATAATTTCTAGTTGCA 57.723 33.333 0.00 0.00 0.00 4.08
1599 2372 6.663093 ACATTGTAATGCCCTGATTTCACTAA 59.337 34.615 4.58 0.00 40.04 2.24
1611 2387 0.381801 CGGCTGACATTGTAATGCCC 59.618 55.000 16.46 0.74 40.04 5.36
1612 2388 0.248621 GCGGCTGACATTGTAATGCC 60.249 55.000 13.81 13.81 40.04 4.40
1634 2410 5.921976 TCGTTTATGTGGTAGTTAGTGTGTG 59.078 40.000 0.00 0.00 0.00 3.82
1645 2421 2.167693 CTCTGGGCTCGTTTATGTGGTA 59.832 50.000 0.00 0.00 0.00 3.25
1686 2462 7.772332 AGTCTATAAACATTGGTTAGCTTCG 57.228 36.000 0.00 0.00 35.82 3.79
1817 2607 1.094785 GGTGTACCGAGCAATGCATT 58.905 50.000 5.99 5.99 0.00 3.56
1829 2623 6.415573 AGAAAATGAAGGAGTATGGTGTACC 58.584 40.000 0.00 0.00 0.00 3.34
1876 2806 6.210584 CCCTTCTTCCTTGCCAATTAAGTAAA 59.789 38.462 0.55 0.00 0.00 2.01
1968 3087 6.363065 ACTTGAGGCAATGTGATAATCATCT 58.637 36.000 0.00 0.00 31.93 2.90
1978 3097 5.455392 CAGAGTAAAACTTGAGGCAATGTG 58.545 41.667 0.00 0.00 0.00 3.21
2034 3153 5.066117 ACAAGTAGCTCGTCGATTATCTGAA 59.934 40.000 0.00 0.00 0.00 3.02
2047 3171 1.979469 CGTGTGAAGACAAGTAGCTCG 59.021 52.381 0.00 0.00 32.49 5.03
2050 3174 2.150397 ACCGTGTGAAGACAAGTAGC 57.850 50.000 0.00 0.00 32.49 3.58
2057 3181 7.130269 GGCATATAATTTAACCGTGTGAAGAC 58.870 38.462 0.00 0.00 0.00 3.01
2069 3193 5.335583 GCATGTCGCAGGGCATATAATTTAA 60.336 40.000 0.00 0.00 41.79 1.52
2098 3222 1.204146 GGGCACAGAGGAATAGGTCA 58.796 55.000 0.00 0.00 0.00 4.02
2099 3223 1.134371 GTGGGCACAGAGGAATAGGTC 60.134 57.143 0.00 0.00 0.00 3.85
2137 3263 4.681074 TTTTGGGTTGGAGGAAATTCAC 57.319 40.909 0.00 0.00 0.00 3.18
2141 3267 5.310331 ACATCATTTTTGGGTTGGAGGAAAT 59.690 36.000 0.00 0.00 0.00 2.17
2146 3274 3.255642 ACGACATCATTTTTGGGTTGGAG 59.744 43.478 0.00 0.00 0.00 3.86
2172 3301 3.053395 ACCAGACCAATGCATAGGTTGAT 60.053 43.478 0.00 0.00 38.50 2.57
2194 3323 2.937519 ACTCGGCTGAGATCATCACTA 58.062 47.619 29.29 0.00 45.57 2.74
2196 3325 2.100584 AGAACTCGGCTGAGATCATCAC 59.899 50.000 29.29 4.98 44.18 3.06
2250 3387 4.869861 CCTGTTTCAAACCAAACCAAAGAG 59.130 41.667 0.00 0.00 35.69 2.85
2273 3411 2.290323 ACAGATAACTCCCAACTGCACC 60.290 50.000 0.00 0.00 32.67 5.01
2276 3414 4.321230 CCAAAACAGATAACTCCCAACTGC 60.321 45.833 0.00 0.00 32.67 4.40
2290 3428 1.609208 GCTCAGAAGCCCAAAACAGA 58.391 50.000 0.00 0.00 43.10 3.41
2376 4915 7.112122 TGCACTCTGGTATATGAAATCAGTTT 58.888 34.615 0.00 0.00 0.00 2.66
2391 4931 7.961326 ATTAGGAAAAATTATGCACTCTGGT 57.039 32.000 0.00 0.00 0.00 4.00
2403 4943 9.791801 ATTGTAGGTTGCAAATTAGGAAAAATT 57.208 25.926 0.00 0.00 0.00 1.82
2404 4944 9.791801 AATTGTAGGTTGCAAATTAGGAAAAAT 57.208 25.926 0.00 0.00 0.00 1.82
2405 4945 9.050601 CAATTGTAGGTTGCAAATTAGGAAAAA 57.949 29.630 0.00 0.00 0.00 1.94
2406 4946 8.600449 CAATTGTAGGTTGCAAATTAGGAAAA 57.400 30.769 0.00 0.00 0.00 2.29
2425 4976 1.274167 CTTGTGGATGCCTGCAATTGT 59.726 47.619 7.40 0.00 0.00 2.71
2450 5001 9.973661 TTAGATTTGACAGAAATTTCAGGGATA 57.026 29.630 19.99 2.25 0.00 2.59
2479 5033 7.484035 AGCGAGAATCCACTAAATGATTAAC 57.516 36.000 0.00 0.00 31.56 2.01
2489 5043 3.371102 GCATGTAGCGAGAATCCACTA 57.629 47.619 0.00 0.00 0.00 2.74
2505 5059 6.916387 CAGATTTAAGAAGCAATGTAGGCATG 59.084 38.462 0.00 0.00 35.15 4.06
2508 5062 6.442513 ACAGATTTAAGAAGCAATGTAGGC 57.557 37.500 0.00 0.00 0.00 3.93
2515 5069 9.547753 GGACATAGATACAGATTTAAGAAGCAA 57.452 33.333 0.00 0.00 0.00 3.91
2526 5080 9.880254 ATAGCATCATAGGACATAGATACAGAT 57.120 33.333 0.00 0.00 0.00 2.90
2533 5098 6.864151 AGCAATAGCATCATAGGACATAGA 57.136 37.500 0.00 0.00 45.49 1.98
2575 5140 2.571212 AGCACGGACAGAACATTTCAA 58.429 42.857 0.00 0.00 0.00 2.69
2603 5182 5.971763 AGCTAGAGAGTATGTTTTGACAGG 58.028 41.667 0.00 0.00 0.00 4.00
2618 5197 4.160439 CCATGTCAAACAGGTAGCTAGAGA 59.840 45.833 0.00 0.00 0.00 3.10
2714 5320 2.425312 GGCGAAGACTCTTGAGAGATGA 59.575 50.000 14.61 0.00 44.74 2.92
2746 5352 9.973661 TGAAGTCCTTCATCCTCAAAATTATAA 57.026 29.630 5.64 0.00 43.90 0.98
2771 5386 3.691609 GGGAACTTCACTATTGCCTCTTG 59.308 47.826 0.00 0.00 33.74 3.02
2779 5394 5.324409 TCAAGCAATGGGAACTTCACTATT 58.676 37.500 0.00 0.00 0.00 1.73
2941 5556 2.370445 CCCCAGGGCTTCATCGTCT 61.370 63.158 0.00 0.00 0.00 4.18
3120 5735 1.661341 CCTCACTGTGCTTATCCTGC 58.339 55.000 2.12 0.00 0.00 4.85
3188 5803 2.190578 CCCTGAATCCGCCCAGAC 59.809 66.667 0.00 0.00 32.37 3.51
3354 5996 4.910195 TGGAGTTCACTTCATTAGCATGT 58.090 39.130 0.00 0.00 0.00 3.21
3416 6058 5.711976 AGTAGTGCAGATACTTTGGCAAAAT 59.288 36.000 14.43 6.64 38.10 1.82
3452 6104 3.121030 CCGCCAGCTGAAGAACCG 61.121 66.667 17.39 7.50 0.00 4.44
3461 6113 3.486685 AGATCCATGCCGCCAGCT 61.487 61.111 0.00 0.00 44.23 4.24
3500 6152 3.251487 GGGAGCACTCTCTACGATCTTAC 59.749 52.174 0.00 0.00 39.31 2.34
3518 6170 1.308069 CGGTTGGACAATGCAGGGAG 61.308 60.000 0.00 0.00 0.00 4.30
3520 6172 0.680921 ATCGGTTGGACAATGCAGGG 60.681 55.000 0.00 0.00 0.00 4.45
3525 6177 3.599343 TCTGAAGATCGGTTGGACAATG 58.401 45.455 0.00 0.00 0.00 2.82
3532 6184 4.715896 CACATGTTTCTGAAGATCGGTTG 58.284 43.478 0.00 0.00 0.00 3.77
3544 6196 7.119846 GGTAAATGACTCTTAGCACATGTTTCT 59.880 37.037 0.00 0.00 0.00 2.52
3545 6197 7.119846 AGGTAAATGACTCTTAGCACATGTTTC 59.880 37.037 0.00 0.00 30.78 2.78
3555 6207 7.440523 AAACTGCAAGGTAAATGACTCTTAG 57.559 36.000 0.00 0.00 39.30 2.18
3557 6209 6.998673 ACTAAACTGCAAGGTAAATGACTCTT 59.001 34.615 0.00 0.00 39.30 2.85
3589 6241 7.982354 ACTTACTACAGAGCATATTTCAGAACC 59.018 37.037 0.00 0.00 0.00 3.62
3641 6293 3.181516 CGCAGAGGATAAGCAAGTTTCAC 60.182 47.826 0.00 0.00 0.00 3.18
3658 6310 3.064207 GTTCACATTAAGTCCACGCAGA 58.936 45.455 0.00 0.00 0.00 4.26
3662 6314 5.146460 CACAATGTTCACATTAAGTCCACG 58.854 41.667 4.85 0.00 44.10 4.94
3714 6368 2.367512 AGGATGACTGGGCCTCCC 60.368 66.667 4.53 0.00 45.71 4.30
3715 6369 2.914289 CAGGATGACTGGGCCTCC 59.086 66.667 4.53 2.24 43.70 4.30
3735 6389 4.864334 CAGCGCCAGGGCCTAAGG 62.864 72.222 5.28 5.44 37.98 2.69
3736 6390 4.864334 CCAGCGCCAGGGCCTAAG 62.864 72.222 5.28 1.11 37.98 2.18
3750 6404 1.202330 AGCTCCAATCTCCAGTCCAG 58.798 55.000 0.00 0.00 0.00 3.86
3751 6405 1.556911 GAAGCTCCAATCTCCAGTCCA 59.443 52.381 0.00 0.00 0.00 4.02
3752 6406 1.556911 TGAAGCTCCAATCTCCAGTCC 59.443 52.381 0.00 0.00 0.00 3.85
3753 6407 2.626840 GTGAAGCTCCAATCTCCAGTC 58.373 52.381 0.00 0.00 0.00 3.51
3754 6408 1.066573 CGTGAAGCTCCAATCTCCAGT 60.067 52.381 0.00 0.00 0.00 4.00
3811 6466 0.876399 TGCAGCAGTAGTTCGTCGTA 59.124 50.000 0.00 0.00 0.00 3.43
3814 6469 0.784778 GTGTGCAGCAGTAGTTCGTC 59.215 55.000 0.00 0.00 0.00 4.20
3824 6479 6.398234 TTCTTAAAAATAAGGTGTGCAGCA 57.602 33.333 0.00 0.00 0.00 4.41
3826 6481 9.696917 AGAAATTCTTAAAAATAAGGTGTGCAG 57.303 29.630 0.00 0.00 0.00 4.41
3871 6526 9.903682 GTGTGTCACTTAGTACACTTCTTATAA 57.096 33.333 18.41 0.00 44.99 0.98
3872 6527 8.517878 GGTGTGTCACTTAGTACACTTCTTATA 58.482 37.037 14.18 0.00 44.99 0.98
3873 6528 7.232941 AGGTGTGTCACTTAGTACACTTCTTAT 59.767 37.037 14.18 1.35 44.99 1.73
3888 6543 2.325484 TGTGATGGTAGGTGTGTCACT 58.675 47.619 4.27 0.00 39.78 3.41
3901 6556 0.325933 TCCTGCTCTGGTTGTGATGG 59.674 55.000 0.00 0.00 0.00 3.51
3910 6565 0.972134 TCTTCTGTGTCCTGCTCTGG 59.028 55.000 0.00 0.00 0.00 3.86
3945 6600 6.851330 GCACTAAACAATGTTCTGACACTTAC 59.149 38.462 0.00 0.00 38.91 2.34
3947 6602 5.590259 AGCACTAAACAATGTTCTGACACTT 59.410 36.000 0.00 0.00 38.91 3.16
4019 6675 8.685427 AGTTTTTAAGCATTTTGGAGCATTTTT 58.315 25.926 0.00 0.00 0.00 1.94
4023 6685 7.670364 AGTAGTTTTTAAGCATTTTGGAGCAT 58.330 30.769 0.00 0.00 0.00 3.79
4052 6714 7.123355 ACCACAACAATAATTATGGAATGGG 57.877 36.000 18.14 12.62 0.00 4.00
4089 6751 6.152661 TCCTTTTCTTCTTTTCTGCAACAGAA 59.847 34.615 5.94 5.94 46.93 3.02
4091 6753 5.894807 TCCTTTTCTTCTTTTCTGCAACAG 58.105 37.500 0.00 0.00 0.00 3.16
4197 6874 5.104067 AGAGTGGTTTTTACCCCATATCCTC 60.104 44.000 0.00 0.00 32.32 3.71
4198 6875 4.794067 AGAGTGGTTTTTACCCCATATCCT 59.206 41.667 0.00 0.00 32.32 3.24
4206 6883 6.259387 CGAATATGGTAGAGTGGTTTTTACCC 59.741 42.308 0.00 0.00 35.72 3.69
4212 6889 4.755266 AGCGAATATGGTAGAGTGGTTT 57.245 40.909 0.00 0.00 0.00 3.27
4221 6898 9.297586 GACGATGAAATTATAGCGAATATGGTA 57.702 33.333 6.53 0.00 0.00 3.25
4238 6915 7.674008 GCACTCTCGAAAAATATGACGATGAAA 60.674 37.037 0.00 0.00 34.41 2.69
4252 6929 3.275143 TGGTTTCTTGCACTCTCGAAAA 58.725 40.909 0.00 0.00 0.00 2.29
4256 6933 3.070018 AGATTGGTTTCTTGCACTCTCG 58.930 45.455 0.00 0.00 0.00 4.04
4260 6938 2.242043 CCCAGATTGGTTTCTTGCACT 58.758 47.619 0.00 0.00 35.17 4.40
4267 6945 4.706962 AGCAATTCTACCCAGATTGGTTTC 59.293 41.667 0.00 0.00 39.91 2.78
4311 6989 7.254151 GCCGTACTCATTAAAACAAAGCAAAAA 60.254 33.333 0.00 0.00 0.00 1.94
4312 6990 6.199342 GCCGTACTCATTAAAACAAAGCAAAA 59.801 34.615 0.00 0.00 0.00 2.44
4313 6991 5.688176 GCCGTACTCATTAAAACAAAGCAAA 59.312 36.000 0.00 0.00 0.00 3.68
4314 6992 5.216648 GCCGTACTCATTAAAACAAAGCAA 58.783 37.500 0.00 0.00 0.00 3.91
4315 6993 4.320641 GGCCGTACTCATTAAAACAAAGCA 60.321 41.667 0.00 0.00 0.00 3.91
4316 6994 4.163552 GGCCGTACTCATTAAAACAAAGC 58.836 43.478 0.00 0.00 0.00 3.51
4317 6995 4.457949 AGGGCCGTACTCATTAAAACAAAG 59.542 41.667 0.00 0.00 0.00 2.77
4318 6996 4.400120 AGGGCCGTACTCATTAAAACAAA 58.600 39.130 0.00 0.00 0.00 2.83
4319 6997 4.023726 AGGGCCGTACTCATTAAAACAA 57.976 40.909 0.00 0.00 0.00 2.83
4320 6998 3.706600 AGGGCCGTACTCATTAAAACA 57.293 42.857 0.00 0.00 0.00 2.83
4321 6999 3.376234 GGAAGGGCCGTACTCATTAAAAC 59.624 47.826 0.00 0.00 0.00 2.43
4322 7000 3.613030 GGAAGGGCCGTACTCATTAAAA 58.387 45.455 0.00 0.00 0.00 1.52
4323 7001 2.092807 GGGAAGGGCCGTACTCATTAAA 60.093 50.000 0.54 0.00 37.63 1.52
4324 7002 1.487558 GGGAAGGGCCGTACTCATTAA 59.512 52.381 0.54 0.00 37.63 1.40
4325 7003 1.125633 GGGAAGGGCCGTACTCATTA 58.874 55.000 0.54 0.00 37.63 1.90
4326 7004 1.912971 GGGAAGGGCCGTACTCATT 59.087 57.895 0.54 0.00 37.63 2.57
4327 7005 2.432300 CGGGAAGGGCCGTACTCAT 61.432 63.158 0.54 0.00 37.63 2.90
4328 7006 3.072468 CGGGAAGGGCCGTACTCA 61.072 66.667 0.54 0.00 37.63 3.41
4329 7007 2.294132 CTTCGGGAAGGGCCGTACTC 62.294 65.000 0.54 0.00 37.63 2.59
4330 7008 2.284112 TTCGGGAAGGGCCGTACT 60.284 61.111 0.54 0.00 37.63 2.73
4331 7009 1.891722 TTCTTCGGGAAGGGCCGTAC 61.892 60.000 0.00 0.00 38.88 3.67
4332 7010 0.979187 ATTCTTCGGGAAGGGCCGTA 60.979 55.000 0.00 0.00 38.88 4.02
4333 7011 2.253403 GATTCTTCGGGAAGGGCCGT 62.253 60.000 8.46 0.00 38.88 5.68
4334 7012 1.523938 GATTCTTCGGGAAGGGCCG 60.524 63.158 8.46 0.00 38.88 6.13
4335 7013 1.523938 CGATTCTTCGGGAAGGGCC 60.524 63.158 8.46 0.00 41.74 5.80
4336 7014 1.520666 TCGATTCTTCGGGAAGGGC 59.479 57.895 8.46 0.00 45.53 5.19
4343 7021 1.084370 AAAGGCGCTCGATTCTTCGG 61.084 55.000 7.64 0.00 45.53 4.30
4344 7022 0.721718 AAAAGGCGCTCGATTCTTCG 59.278 50.000 7.64 0.00 46.87 3.79
4345 7023 1.062733 GGAAAAGGCGCTCGATTCTTC 59.937 52.381 7.64 1.08 0.00 2.87
4346 7024 1.087501 GGAAAAGGCGCTCGATTCTT 58.912 50.000 7.64 0.00 0.00 2.52
4347 7025 0.036388 TGGAAAAGGCGCTCGATTCT 60.036 50.000 7.64 0.00 0.00 2.40
4348 7026 0.097150 GTGGAAAAGGCGCTCGATTC 59.903 55.000 7.64 7.26 0.00 2.52
4349 7027 1.635663 CGTGGAAAAGGCGCTCGATT 61.636 55.000 7.64 0.00 0.00 3.34
4350 7028 2.100631 CGTGGAAAAGGCGCTCGAT 61.101 57.895 7.64 0.00 0.00 3.59
4351 7029 2.736995 CGTGGAAAAGGCGCTCGA 60.737 61.111 7.64 0.00 0.00 4.04
4352 7030 4.445545 GCGTGGAAAAGGCGCTCG 62.446 66.667 7.64 1.23 46.55 5.03


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

AutoCloner maintained by Alex Coulton.