Multiple sequence alignment - TraesCS7A01G091500

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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 TraesCS7A01G091500 chr7A 100.000 4663 0 0 1 4663 55884552 55879890 0.000000e+00 8612.0
1 TraesCS7A01G091500 chr7A 85.870 2753 321 47 971 3707 55895508 55892808 0.000000e+00 2867.0
2 TraesCS7A01G091500 chr7A 86.829 1435 172 15 2305 3735 55427221 55425800 0.000000e+00 1587.0
3 TraesCS7A01G091500 chr7A 87.335 1137 134 6 2405 3533 55383712 55382578 0.000000e+00 1293.0
4 TraesCS7A01G091500 chr7A 81.588 1385 206 32 987 2354 55398003 55396651 0.000000e+00 1099.0
5 TraesCS7A01G091500 chr7A 83.158 950 153 4 1016 1960 55428419 55427472 0.000000e+00 861.0
6 TraesCS7A01G091500 chr7A 85.471 647 42 25 3967 4598 112524545 112523936 1.100000e-175 627.0
7 TraesCS7A01G091500 chr7A 92.760 221 15 1 2037 2256 55427450 55427230 7.530000e-83 318.0
8 TraesCS7A01G091500 chr7A 100.000 40 0 0 702 741 55883812 55883773 1.800000e-09 75.0
9 TraesCS7A01G091500 chr7A 100.000 40 0 0 741 780 55883851 55883812 1.800000e-09 75.0
10 TraesCS7A01G091500 chr7A 88.136 59 3 3 4598 4654 6603618 6603674 3.010000e-07 67.6
11 TraesCS7A01G091500 chr4A 95.769 3120 103 7 741 3851 668149217 668146118 0.000000e+00 5003.0
12 TraesCS7A01G091500 chr4A 82.646 2766 384 52 971 3714 668162865 668160174 0.000000e+00 2361.0
13 TraesCS7A01G091500 chr4A 84.166 941 144 5 1020 1959 667861429 667860493 0.000000e+00 907.0
14 TraesCS7A01G091500 chr4A 82.741 956 160 4 1009 1960 668110304 668109350 0.000000e+00 846.0
15 TraesCS7A01G091500 chr4A 85.031 795 55 32 1 741 668149962 668149178 0.000000e+00 750.0
16 TraesCS7A01G091500 chr4A 83.516 637 65 24 3969 4598 668145995 668145392 4.080000e-155 558.0
17 TraesCS7A01G091500 chr4A 85.117 383 41 9 2003 2369 668095513 668095131 1.220000e-100 377.0
18 TraesCS7A01G091500 chr4A 93.243 222 13 2 2037 2256 668109328 668109107 4.500000e-85 326.0
19 TraesCS7A01G091500 chr4A 94.624 93 3 2 3890 3982 668146120 668146030 4.860000e-30 143.0
20 TraesCS7A01G091500 chr4A 92.857 42 3 0 874 915 668148986 668148945 1.400000e-05 62.1
21 TraesCS7A01G091500 chr7D 94.878 3124 119 12 743 3859 53498975 53495886 0.000000e+00 4844.0
22 TraesCS7A01G091500 chr7D 83.728 2747 380 47 987 3707 53509948 53507243 0.000000e+00 2534.0
23 TraesCS7A01G091500 chr7D 86.769 1436 172 15 2305 3735 53484174 53482752 0.000000e+00 1583.0
24 TraesCS7A01G091500 chr7D 86.688 1247 153 11 2448 3690 52696508 52697745 0.000000e+00 1371.0
25 TraesCS7A01G091500 chr7D 84.328 1257 164 20 1020 2272 52821429 52822656 0.000000e+00 1199.0
26 TraesCS7A01G091500 chr7D 81.682 1403 204 33 987 2369 53434394 53433025 0.000000e+00 1118.0
27 TraesCS7A01G091500 chr7D 82.557 1267 187 18 1009 2272 53427225 53425990 0.000000e+00 1085.0
28 TraesCS7A01G091500 chr7D 81.169 1386 213 33 987 2354 52796521 52797876 0.000000e+00 1070.0
29 TraesCS7A01G091500 chr7D 84.681 940 141 2 1020 1959 52829691 52830627 0.000000e+00 935.0
30 TraesCS7A01G091500 chr7D 83.069 945 155 4 1020 1960 53485368 53484425 0.000000e+00 854.0
31 TraesCS7A01G091500 chr7D 91.738 581 36 5 169 741 53499514 53498938 0.000000e+00 797.0
32 TraesCS7A01G091500 chr7D 84.472 644 47 25 3967 4598 53495771 53495169 1.870000e-163 586.0
33 TraesCS7A01G091500 chr7D 92.760 221 15 1 2037 2256 53484403 53484183 7.530000e-83 318.0
34 TraesCS7A01G091500 chr7D 94.565 92 3 2 3891 3982 53495893 53495804 1.750000e-29 141.0
35 TraesCS7A01G091500 chr7D 93.617 47 3 0 12 58 53499707 53499661 2.330000e-08 71.3
36 TraesCS7A01G091500 chr7D 92.857 42 3 0 874 915 53498749 53498708 1.400000e-05 62.1
37 TraesCS7A01G091500 chr6B 82.450 302 40 9 4192 4482 692820980 692820681 7.750000e-63 252.0
38 TraesCS7A01G091500 chr2B 81.148 244 39 5 4255 4495 279272329 279272568 6.160000e-44 189.0
39 TraesCS7A01G091500 chr2B 83.333 66 7 3 4589 4654 708871679 708871740 1.810000e-04 58.4
40 TraesCS7A01G091500 chr1B 84.000 75 7 2 4592 4663 423714239 423714167 3.010000e-07 67.6
41 TraesCS7A01G091500 chr1B 87.097 62 3 2 4595 4653 667646129 667646188 1.080000e-06 65.8
42 TraesCS7A01G091500 chr7B 86.154 65 4 2 4589 4650 594899685 594899747 1.080000e-06 65.8
43 TraesCS7A01G091500 chr7B 86.667 60 6 1 4595 4654 720876141 720876198 1.080000e-06 65.8
44 TraesCS7A01G091500 chr7B 86.207 58 6 1 4597 4654 720831835 720831890 1.400000e-05 62.1
45 TraesCS7A01G091500 chr5D 84.507 71 6 2 4596 4663 535902200 535902132 1.080000e-06 65.8
46 TraesCS7A01G091500 chr1A 86.667 60 4 3 4595 4653 6564833 6564777 3.900000e-06 63.9


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 TraesCS7A01G091500 chr7A 55879890 55884552 4662 True 2920.666667 8612 100.000000 1 4663 3 chr7A.!!$R6 4662
1 TraesCS7A01G091500 chr7A 55892808 55895508 2700 True 2867.000000 2867 85.870000 971 3707 1 chr7A.!!$R3 2736
2 TraesCS7A01G091500 chr7A 55382578 55383712 1134 True 1293.000000 1293 87.335000 2405 3533 1 chr7A.!!$R1 1128
3 TraesCS7A01G091500 chr7A 55396651 55398003 1352 True 1099.000000 1099 81.588000 987 2354 1 chr7A.!!$R2 1367
4 TraesCS7A01G091500 chr7A 55425800 55428419 2619 True 922.000000 1587 87.582333 1016 3735 3 chr7A.!!$R5 2719
5 TraesCS7A01G091500 chr7A 112523936 112524545 609 True 627.000000 627 85.471000 3967 4598 1 chr7A.!!$R4 631
6 TraesCS7A01G091500 chr4A 668160174 668162865 2691 True 2361.000000 2361 82.646000 971 3714 1 chr4A.!!$R3 2743
7 TraesCS7A01G091500 chr4A 668145392 668149962 4570 True 1303.220000 5003 90.359400 1 4598 5 chr4A.!!$R5 4597
8 TraesCS7A01G091500 chr4A 667860493 667861429 936 True 907.000000 907 84.166000 1020 1959 1 chr4A.!!$R1 939
9 TraesCS7A01G091500 chr4A 668109107 668110304 1197 True 586.000000 846 87.992000 1009 2256 2 chr4A.!!$R4 1247
10 TraesCS7A01G091500 chr7D 53507243 53509948 2705 True 2534.000000 2534 83.728000 987 3707 1 chr7D.!!$R3 2720
11 TraesCS7A01G091500 chr7D 52696508 52697745 1237 False 1371.000000 1371 86.688000 2448 3690 1 chr7D.!!$F1 1242
12 TraesCS7A01G091500 chr7D 52821429 52822656 1227 False 1199.000000 1199 84.328000 1020 2272 1 chr7D.!!$F3 1252
13 TraesCS7A01G091500 chr7D 53433025 53434394 1369 True 1118.000000 1118 81.682000 987 2369 1 chr7D.!!$R2 1382
14 TraesCS7A01G091500 chr7D 53425990 53427225 1235 True 1085.000000 1085 82.557000 1009 2272 1 chr7D.!!$R1 1263
15 TraesCS7A01G091500 chr7D 53495169 53499707 4538 True 1083.566667 4844 92.021167 12 4598 6 chr7D.!!$R5 4586
16 TraesCS7A01G091500 chr7D 52796521 52797876 1355 False 1070.000000 1070 81.169000 987 2354 1 chr7D.!!$F2 1367
17 TraesCS7A01G091500 chr7D 52829691 52830627 936 False 935.000000 935 84.681000 1020 1959 1 chr7D.!!$F4 939
18 TraesCS7A01G091500 chr7D 53482752 53485368 2616 True 918.333333 1583 87.532667 1020 3735 3 chr7D.!!$R4 2715

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
162 182 0.888619 TCAGTCGTAGTGGGCAAGAG 59.111 55.000 0.00 0.0 0.00 2.85 F
163 183 0.888619 CAGTCGTAGTGGGCAAGAGA 59.111 55.000 0.00 0.0 0.00 3.10 F
1473 1644 1.000938 GGCAAGAACCAGCTTGAGTTG 60.001 52.381 8.18 0.0 46.31 3.16 F
2220 2416 1.003118 TGCGTAAGAGCTGACCCAAAT 59.997 47.619 0.00 0.0 43.02 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1644 1.180029 AGCATGAGTTGACAATGGGC 58.820 50.0 0.0 0.0 0.00 5.36 R
1773 1944 2.351738 GGCTTCCGAACAACTTCCATTG 60.352 50.0 0.0 0.0 35.59 2.82 R
3387 3602 0.987081 AGCAGCATCTCCATCCCTGT 60.987 55.0 0.0 0.0 0.00 4.00 R
3881 4100 0.112218 CAAATATCCCATCCCCCGCA 59.888 55.0 0.0 0.0 0.00 5.69 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
118 138 1.202604 GGACAACAGGAAGAACGTCCA 60.203 52.381 9.17 0.00 42.04 4.02
119 139 2.135933 GACAACAGGAAGAACGTCCAG 58.864 52.381 9.17 3.98 40.48 3.86
131 151 6.476053 GGAAGAACGTCCAGTATAAATCAGTC 59.524 42.308 0.00 0.00 37.65 3.51
162 182 0.888619 TCAGTCGTAGTGGGCAAGAG 59.111 55.000 0.00 0.00 0.00 2.85
163 183 0.888619 CAGTCGTAGTGGGCAAGAGA 59.111 55.000 0.00 0.00 0.00 3.10
164 184 1.272490 CAGTCGTAGTGGGCAAGAGAA 59.728 52.381 0.00 0.00 0.00 2.87
166 186 2.093973 AGTCGTAGTGGGCAAGAGAATG 60.094 50.000 0.00 0.00 0.00 2.67
208 254 6.237901 ACATACAGAGCAACAAAGGATGTTA 58.762 36.000 0.00 0.00 45.86 2.41
287 340 6.528537 TTAAACATCACTGCCAATAAGCAT 57.471 33.333 0.00 0.00 43.09 3.79
297 350 5.533903 ACTGCCAATAAGCATTCAATAGAGG 59.466 40.000 0.00 0.00 43.09 3.69
339 393 9.632807 TTGAATATAAAAACCCGAAATGACAAG 57.367 29.630 0.00 0.00 0.00 3.16
392 449 3.567478 ATTCTGGATTGGAGGTAGTGC 57.433 47.619 0.00 0.00 0.00 4.40
410 468 9.969001 AGGTAGTGCTTTTCCTACAATTTATAA 57.031 29.630 0.00 0.00 36.17 0.98
444 502 5.544176 AGAAAGAAACATGGAGTCTGGAGTA 59.456 40.000 0.00 0.00 0.00 2.59
449 507 6.440647 AGAAACATGGAGTCTGGAGTATACAA 59.559 38.462 5.50 0.00 0.00 2.41
453 511 7.727181 ACATGGAGTCTGGAGTATACAATTAC 58.273 38.462 5.50 0.00 0.00 1.89
504 562 9.563898 CGCAACATAGATGCATAATTCATATTT 57.436 29.630 0.00 0.00 44.01 1.40
560 618 5.416952 ACCTAAATTCTTGTCTGATGGCAAG 59.583 40.000 4.23 4.23 42.32 4.01
705 763 7.040494 GGTAGTGGGATCAAACTCTTAACTAC 58.960 42.308 3.01 0.00 37.70 2.73
706 764 6.051179 AGTGGGATCAAACTCTTAACTACC 57.949 41.667 0.00 0.00 0.00 3.18
707 765 5.546499 AGTGGGATCAAACTCTTAACTACCA 59.454 40.000 0.00 0.00 0.00 3.25
708 766 6.043938 AGTGGGATCAAACTCTTAACTACCAA 59.956 38.462 0.00 0.00 0.00 3.67
709 767 6.884836 GTGGGATCAAACTCTTAACTACCAAT 59.115 38.462 0.00 0.00 0.00 3.16
710 768 8.044908 GTGGGATCAAACTCTTAACTACCAATA 58.955 37.037 0.00 0.00 0.00 1.90
711 769 8.778059 TGGGATCAAACTCTTAACTACCAATAT 58.222 33.333 0.00 0.00 0.00 1.28
727 785 8.772250 ACTACCAATATATTCCCTATGTGATGG 58.228 37.037 0.00 0.00 0.00 3.51
728 786 7.588866 ACCAATATATTCCCTATGTGATGGT 57.411 36.000 0.00 0.00 0.00 3.55
729 787 8.694171 ACCAATATATTCCCTATGTGATGGTA 57.306 34.615 0.00 0.00 34.71 3.25
730 788 9.122954 ACCAATATATTCCCTATGTGATGGTAA 57.877 33.333 0.00 0.00 34.71 2.85
737 795 8.940397 ATTCCCTATGTGATGGTAATTTTAGG 57.060 34.615 0.00 0.00 0.00 2.69
738 796 6.848069 TCCCTATGTGATGGTAATTTTAGGG 58.152 40.000 5.51 5.51 43.97 3.53
739 797 6.010219 CCCTATGTGATGGTAATTTTAGGGG 58.990 44.000 0.00 0.00 40.55 4.79
746 804 5.732170 TGATGGTAATTTTAGGGGACTACCA 59.268 40.000 1.52 1.52 43.68 3.25
769 827 9.122954 ACCAATATATTCCCTATGTGATGGTAA 57.877 33.333 0.00 0.00 34.71 2.85
847 905 7.804614 TGTCGTATTTGGCATTTTGTATTTC 57.195 32.000 0.00 0.00 0.00 2.17
874 933 7.011389 GTGAAGACAAATGACCGATATCAATGA 59.989 37.037 3.12 0.00 30.82 2.57
875 934 7.716560 TGAAGACAAATGACCGATATCAATGAT 59.283 33.333 0.00 0.00 30.82 2.45
876 935 9.208022 GAAGACAAATGACCGATATCAATGATA 57.792 33.333 5.32 5.32 30.82 2.15
877 936 8.768957 AGACAAATGACCGATATCAATGATAG 57.231 34.615 9.01 0.00 30.82 2.08
878 937 8.588472 AGACAAATGACCGATATCAATGATAGA 58.412 33.333 9.01 0.00 30.82 1.98
879 938 9.376075 GACAAATGACCGATATCAATGATAGAT 57.624 33.333 9.01 0.00 30.82 1.98
880 939 9.730705 ACAAATGACCGATATCAATGATAGATT 57.269 29.630 9.01 0.00 30.82 2.40
881 940 9.983804 CAAATGACCGATATCAATGATAGATTG 57.016 33.333 9.01 0.00 30.82 2.67
882 941 8.728337 AATGACCGATATCAATGATAGATTGG 57.272 34.615 9.01 9.37 30.82 3.16
883 942 7.244886 TGACCGATATCAATGATAGATTGGT 57.755 36.000 14.72 14.72 0.00 3.67
884 943 8.361169 TGACCGATATCAATGATAGATTGGTA 57.639 34.615 14.77 5.01 0.00 3.25
885 944 8.981659 TGACCGATATCAATGATAGATTGGTAT 58.018 33.333 14.77 0.00 37.85 2.73
886 945 9.254133 GACCGATATCAATGATAGATTGGTATG 57.746 37.037 14.77 0.00 35.96 2.39
887 946 8.762645 ACCGATATCAATGATAGATTGGTATGT 58.237 33.333 13.66 0.00 35.96 2.29
902 961 8.874156 AGATTGGTATGTACATGATACATGTCT 58.126 33.333 18.81 13.11 38.47 3.41
903 962 9.144747 GATTGGTATGTACATGATACATGTCTC 57.855 37.037 18.81 2.23 38.47 3.36
904 963 7.595819 TGGTATGTACATGATACATGTCTCA 57.404 36.000 18.81 15.42 38.47 3.27
905 964 7.661040 TGGTATGTACATGATACATGTCTCAG 58.339 38.462 18.81 12.40 38.47 3.35
906 965 7.287696 TGGTATGTACATGATACATGTCTCAGT 59.712 37.037 18.81 16.33 38.47 3.41
907 966 7.810282 GGTATGTACATGATACATGTCTCAGTC 59.190 40.741 18.81 14.40 38.47 3.51
908 967 5.821204 TGTACATGATACATGTCTCAGTCG 58.179 41.667 17.64 11.59 33.76 4.18
909 968 4.991153 ACATGATACATGTCTCAGTCGT 57.009 40.909 17.64 12.11 0.00 4.34
910 969 5.330455 ACATGATACATGTCTCAGTCGTT 57.670 39.130 17.64 0.07 0.00 3.85
911 970 5.724328 ACATGATACATGTCTCAGTCGTTT 58.276 37.500 17.64 0.00 0.00 3.60
912 971 5.807520 ACATGATACATGTCTCAGTCGTTTC 59.192 40.000 17.64 0.00 0.00 2.78
913 972 4.744570 TGATACATGTCTCAGTCGTTTCC 58.255 43.478 9.69 0.00 0.00 3.13
914 973 4.462834 TGATACATGTCTCAGTCGTTTCCT 59.537 41.667 9.69 0.00 0.00 3.36
915 974 5.650703 TGATACATGTCTCAGTCGTTTCCTA 59.349 40.000 9.69 0.00 0.00 2.94
916 975 4.866508 ACATGTCTCAGTCGTTTCCTAA 57.133 40.909 0.00 0.00 0.00 2.69
917 976 5.407407 ACATGTCTCAGTCGTTTCCTAAT 57.593 39.130 0.00 0.00 0.00 1.73
918 977 6.525578 ACATGTCTCAGTCGTTTCCTAATA 57.474 37.500 0.00 0.00 0.00 0.98
919 978 7.113658 ACATGTCTCAGTCGTTTCCTAATAT 57.886 36.000 0.00 0.00 0.00 1.28
920 979 8.234136 ACATGTCTCAGTCGTTTCCTAATATA 57.766 34.615 0.00 0.00 0.00 0.86
921 980 8.692710 ACATGTCTCAGTCGTTTCCTAATATAA 58.307 33.333 0.00 0.00 0.00 0.98
922 981 8.969267 CATGTCTCAGTCGTTTCCTAATATAAC 58.031 37.037 0.00 0.00 0.00 1.89
923 982 8.058667 TGTCTCAGTCGTTTCCTAATATAACA 57.941 34.615 0.00 0.00 0.00 2.41
924 983 8.692710 TGTCTCAGTCGTTTCCTAATATAACAT 58.307 33.333 0.00 0.00 0.00 2.71
925 984 9.530633 GTCTCAGTCGTTTCCTAATATAACATT 57.469 33.333 0.00 0.00 0.00 2.71
950 1009 6.872670 TTTTGCTAAACACAAAAACTACCG 57.127 33.333 0.00 0.00 42.39 4.02
951 1010 5.564048 TTGCTAAACACAAAAACTACCGT 57.436 34.783 0.00 0.00 0.00 4.83
952 1011 6.674694 TTGCTAAACACAAAAACTACCGTA 57.325 33.333 0.00 0.00 0.00 4.02
953 1012 6.674694 TGCTAAACACAAAAACTACCGTAA 57.325 33.333 0.00 0.00 0.00 3.18
954 1013 6.485393 TGCTAAACACAAAAACTACCGTAAC 58.515 36.000 0.00 0.00 0.00 2.50
955 1014 6.093219 TGCTAAACACAAAAACTACCGTAACA 59.907 34.615 0.00 0.00 0.00 2.41
956 1015 7.134163 GCTAAACACAAAAACTACCGTAACAT 58.866 34.615 0.00 0.00 0.00 2.71
957 1016 8.281893 GCTAAACACAAAAACTACCGTAACATA 58.718 33.333 0.00 0.00 0.00 2.29
958 1017 9.584839 CTAAACACAAAAACTACCGTAACATAC 57.415 33.333 0.00 0.00 0.00 2.39
959 1018 7.551035 AACACAAAAACTACCGTAACATACA 57.449 32.000 0.00 0.00 0.00 2.29
960 1019 7.733402 ACACAAAAACTACCGTAACATACAT 57.267 32.000 0.00 0.00 0.00 2.29
961 1020 8.830201 ACACAAAAACTACCGTAACATACATA 57.170 30.769 0.00 0.00 0.00 2.29
962 1021 9.439500 ACACAAAAACTACCGTAACATACATAT 57.561 29.630 0.00 0.00 0.00 1.78
963 1022 9.697250 CACAAAAACTACCGTAACATACATATG 57.303 33.333 0.00 0.00 39.55 1.78
964 1023 8.885722 ACAAAAACTACCGTAACATACATATGG 58.114 33.333 7.80 0.00 38.00 2.74
965 1024 7.486802 AAAACTACCGTAACATACATATGGC 57.513 36.000 7.80 0.00 38.00 4.40
966 1025 5.143376 ACTACCGTAACATACATATGGCC 57.857 43.478 7.80 0.00 38.00 5.36
967 1026 3.412237 ACCGTAACATACATATGGCCC 57.588 47.619 7.80 0.00 38.00 5.80
968 1027 2.706723 ACCGTAACATACATATGGCCCA 59.293 45.455 7.80 0.00 38.00 5.36
969 1028 3.244422 ACCGTAACATACATATGGCCCAG 60.244 47.826 7.80 0.00 38.00 4.45
1112 1268 2.999355 GGTCTTCTGAGAGCATCAACAC 59.001 50.000 1.10 0.00 46.99 3.32
1182 1338 1.971695 GTTCGGCACTGGAAAGGGG 60.972 63.158 0.00 0.00 0.00 4.79
1220 1376 6.096705 CCCTTTAATGTTACATGCCATGAGAA 59.903 38.462 12.53 2.20 0.00 2.87
1473 1644 1.000938 GGCAAGAACCAGCTTGAGTTG 60.001 52.381 8.18 0.00 46.31 3.16
1678 1849 1.827344 ACTCATTCATCGCTGAGGTGA 59.173 47.619 3.75 6.35 42.56 4.02
1773 1944 2.029380 GGTACTTGATTGGGTTGTTGGC 60.029 50.000 0.00 0.00 0.00 4.52
1901 2073 2.636830 CTCTCAAGGTTATGTGGGCAG 58.363 52.381 0.00 0.00 0.00 4.85
2033 2222 7.093322 ACTTTATTGCTCTTGGAATGTGATC 57.907 36.000 0.00 0.00 35.79 2.92
2188 2384 3.390639 AGGATTCAGGAGTGATGATCCAC 59.609 47.826 8.24 0.00 40.53 4.02
2220 2416 1.003118 TGCGTAAGAGCTGACCCAAAT 59.997 47.619 0.00 0.00 43.02 2.32
2354 2557 4.631131 TGCCAATCATATAAGTCCGACTG 58.369 43.478 0.65 0.00 0.00 3.51
2977 3189 1.536418 CTCCCTCACTGGACACCCA 60.536 63.158 0.00 0.00 40.95 4.51
3387 3602 1.412343 TGGATGCGAGCATAGTAAGCA 59.588 47.619 10.85 0.00 42.28 3.91
3389 3604 2.473816 GATGCGAGCATAGTAAGCACA 58.526 47.619 10.85 0.00 40.82 4.57
3409 3624 1.530771 GGATGGAGATGCTGCTGGT 59.469 57.895 0.00 0.00 0.00 4.00
3423 3638 0.246635 GCTGGTAGAAGTTGCCGAGA 59.753 55.000 0.00 0.00 33.59 4.04
3521 3736 0.251634 GAAGCACCTGGAGGGAGAAG 59.748 60.000 0.00 0.00 40.27 2.85
3656 3871 6.578313 TCTGAAGTAGGTATAGAGACACCT 57.422 41.667 0.00 0.00 46.88 4.00
3701 3920 3.887621 ACACCATGCGAGTAGTATTGT 57.112 42.857 0.00 0.00 0.00 2.71
3845 4064 9.691362 GTCACAACATTTATAGAATGGTTTTGT 57.309 29.630 4.06 3.10 29.86 2.83
3859 4078 9.487790 AGAATGGTTTTGTTTATGTTGGTTATG 57.512 29.630 0.00 0.00 0.00 1.90
3860 4079 8.614469 AATGGTTTTGTTTATGTTGGTTATGG 57.386 30.769 0.00 0.00 0.00 2.74
3861 4080 6.525629 TGGTTTTGTTTATGTTGGTTATGGG 58.474 36.000 0.00 0.00 0.00 4.00
3862 4081 6.326583 TGGTTTTGTTTATGTTGGTTATGGGA 59.673 34.615 0.00 0.00 0.00 4.37
3863 4082 7.016661 TGGTTTTGTTTATGTTGGTTATGGGAT 59.983 33.333 0.00 0.00 0.00 3.85
3864 4083 8.532819 GGTTTTGTTTATGTTGGTTATGGGATA 58.467 33.333 0.00 0.00 0.00 2.59
3869 4088 9.480861 TGTTTATGTTGGTTATGGGATATTTGA 57.519 29.630 0.00 0.00 0.00 2.69
3870 4089 9.744468 GTTTATGTTGGTTATGGGATATTTGAC 57.256 33.333 0.00 0.00 0.00 3.18
3871 4090 6.976934 ATGTTGGTTATGGGATATTTGACC 57.023 37.500 0.00 0.00 0.00 4.02
3872 4091 5.205056 TGTTGGTTATGGGATATTTGACCC 58.795 41.667 0.00 0.00 45.74 4.46
3873 4092 5.043732 TGTTGGTTATGGGATATTTGACCCT 60.044 40.000 0.00 0.00 45.74 4.34
3874 4093 5.742562 TGGTTATGGGATATTTGACCCTT 57.257 39.130 0.00 0.00 45.74 3.95
3875 4094 6.098716 TGGTTATGGGATATTTGACCCTTT 57.901 37.500 0.00 0.00 45.74 3.11
3876 4095 6.507568 TGGTTATGGGATATTTGACCCTTTT 58.492 36.000 0.00 0.00 45.74 2.27
3877 4096 6.962902 TGGTTATGGGATATTTGACCCTTTTT 59.037 34.615 0.00 0.00 45.74 1.94
3942 4163 2.158928 TGTTGCTTGCTGCCTTTCATTT 60.159 40.909 0.00 0.00 42.00 2.32
3979 4246 7.483059 GCAGTTGCTCTGTACTGAATTTATTTC 59.517 37.037 6.43 0.00 43.45 2.17
4044 4311 1.143684 TCAGGCTCTTTCAAGTTGGCT 59.856 47.619 2.34 5.89 37.12 4.75
4049 4316 0.185901 TCTTTCAAGTTGGCTGGCCT 59.814 50.000 13.05 0.00 36.94 5.19
4050 4317 1.423541 TCTTTCAAGTTGGCTGGCCTA 59.576 47.619 13.05 2.16 36.94 3.93
4117 4384 5.782893 TGAAGTTGTCAAAGGGGTTAATG 57.217 39.130 0.00 0.00 31.51 1.90
4118 4385 5.205056 TGAAGTTGTCAAAGGGGTTAATGT 58.795 37.500 0.00 0.00 31.51 2.71
4119 4386 5.300792 TGAAGTTGTCAAAGGGGTTAATGTC 59.699 40.000 0.00 0.00 31.51 3.06
4120 4387 4.798882 AGTTGTCAAAGGGGTTAATGTCA 58.201 39.130 0.00 0.00 0.00 3.58
4121 4388 5.205056 AGTTGTCAAAGGGGTTAATGTCAA 58.795 37.500 0.00 0.00 0.00 3.18
4122 4389 5.659079 AGTTGTCAAAGGGGTTAATGTCAAA 59.341 36.000 0.00 0.00 0.00 2.69
4123 4390 5.782893 TGTCAAAGGGGTTAATGTCAAAG 57.217 39.130 0.00 0.00 0.00 2.77
4124 4391 4.586841 TGTCAAAGGGGTTAATGTCAAAGG 59.413 41.667 0.00 0.00 0.00 3.11
4125 4392 4.021456 GTCAAAGGGGTTAATGTCAAAGGG 60.021 45.833 0.00 0.00 0.00 3.95
4126 4393 2.919772 AGGGGTTAATGTCAAAGGGG 57.080 50.000 0.00 0.00 0.00 4.79
4127 4394 2.078611 AGGGGTTAATGTCAAAGGGGT 58.921 47.619 0.00 0.00 0.00 4.95
4128 4395 2.453212 AGGGGTTAATGTCAAAGGGGTT 59.547 45.455 0.00 0.00 0.00 4.11
4129 4396 3.663632 AGGGGTTAATGTCAAAGGGGTTA 59.336 43.478 0.00 0.00 0.00 2.85
4130 4397 3.765511 GGGGTTAATGTCAAAGGGGTTAC 59.234 47.826 0.00 0.00 0.00 2.50
4131 4398 4.409187 GGGTTAATGTCAAAGGGGTTACA 58.591 43.478 0.00 0.00 0.00 2.41
4132 4399 4.461431 GGGTTAATGTCAAAGGGGTTACAG 59.539 45.833 0.00 0.00 0.00 2.74
4133 4400 5.318630 GGTTAATGTCAAAGGGGTTACAGA 58.681 41.667 0.00 0.00 0.00 3.41
4134 4401 5.182570 GGTTAATGTCAAAGGGGTTACAGAC 59.817 44.000 0.00 0.00 0.00 3.51
4135 4402 4.724279 AATGTCAAAGGGGTTACAGACT 57.276 40.909 0.00 0.00 0.00 3.24
4136 4403 4.724279 ATGTCAAAGGGGTTACAGACTT 57.276 40.909 0.00 0.00 0.00 3.01
4137 4404 5.836024 ATGTCAAAGGGGTTACAGACTTA 57.164 39.130 0.00 0.00 0.00 2.24
4138 4405 5.633655 TGTCAAAGGGGTTACAGACTTAA 57.366 39.130 0.00 0.00 0.00 1.85
4178 4445 8.803799 GTTCATTAACTGTGTGTTCGAAATTTT 58.196 29.630 0.00 0.00 39.89 1.82
4189 4456 5.967088 GTGTTCGAAATTTTAAGTCGGTGTT 59.033 36.000 0.00 0.00 35.51 3.32
4201 4469 1.067212 GTCGGTGTTCGGCTCATCTAT 59.933 52.381 0.00 0.00 40.86 1.98
4202 4470 1.067060 TCGGTGTTCGGCTCATCTATG 59.933 52.381 0.00 0.00 39.77 2.23
4214 4483 1.768275 TCATCTATGCCCGGTGAACAT 59.232 47.619 0.00 0.97 0.00 2.71
4273 4551 1.337703 GTGTGGTGCAAGATGCTCAAA 59.662 47.619 3.78 0.00 45.31 2.69
4285 4563 4.338012 AGATGCTCAAATGGTGATGTTCA 58.662 39.130 0.00 0.00 35.07 3.18
4314 4592 6.438186 AATTTTGGGATGTTTGGACATTCT 57.562 33.333 0.00 0.00 46.27 2.40
4323 4601 4.579869 TGTTTGGACATTCTAGGAGCTTC 58.420 43.478 0.00 0.00 0.00 3.86
4331 4609 4.083271 ACATTCTAGGAGCTTCGCAAAAAC 60.083 41.667 0.00 0.00 0.00 2.43
4342 4621 4.267452 GCTTCGCAAAAACAGACAAAATCA 59.733 37.500 0.00 0.00 0.00 2.57
4556 4837 2.218603 ACACGTTGAGCTGGGTAAAAG 58.781 47.619 0.00 0.00 0.00 2.27
4625 4907 9.487790 TTTTTGCAAAATCTTCCGATCTTTATT 57.512 25.926 24.39 0.00 0.00 1.40
4626 4908 8.687824 TTTGCAAAATCTTCCGATCTTTATTC 57.312 30.769 10.02 0.00 0.00 1.75
4627 4909 7.389803 TGCAAAATCTTCCGATCTTTATTCA 57.610 32.000 0.00 0.00 0.00 2.57
4628 4910 7.999679 TGCAAAATCTTCCGATCTTTATTCAT 58.000 30.769 0.00 0.00 0.00 2.57
4629 4911 8.469200 TGCAAAATCTTCCGATCTTTATTCATT 58.531 29.630 0.00 0.00 0.00 2.57
4630 4912 9.305925 GCAAAATCTTCCGATCTTTATTCATTT 57.694 29.630 0.00 0.00 0.00 2.32
4639 4921 9.955208 TCCGATCTTTATTCATTTTCAATCATG 57.045 29.630 0.00 0.00 0.00 3.07
4640 4922 9.188588 CCGATCTTTATTCATTTTCAATCATGG 57.811 33.333 0.00 0.00 0.00 3.66
4641 4923 9.740239 CGATCTTTATTCATTTTCAATCATGGT 57.260 29.630 0.00 0.00 0.00 3.55
4650 4932 8.628630 TCATTTTCAATCATGGTAGTACAACA 57.371 30.769 2.06 0.00 0.00 3.33
4651 4933 9.072375 TCATTTTCAATCATGGTAGTACAACAA 57.928 29.630 2.06 0.00 0.00 2.83
4652 4934 9.689976 CATTTTCAATCATGGTAGTACAACAAA 57.310 29.630 2.06 0.00 0.00 2.83
4653 4935 9.691362 ATTTTCAATCATGGTAGTACAACAAAC 57.309 29.630 2.06 0.00 0.00 2.93
4654 4936 6.474819 TCAATCATGGTAGTACAACAAACG 57.525 37.500 2.06 0.00 0.00 3.60
4655 4937 4.939509 ATCATGGTAGTACAACAAACGC 57.060 40.909 2.06 0.00 0.00 4.84
4656 4938 3.729966 TCATGGTAGTACAACAAACGCA 58.270 40.909 2.06 0.00 0.00 5.24
4657 4939 4.320023 TCATGGTAGTACAACAAACGCAT 58.680 39.130 2.06 0.00 0.00 4.73
4658 4940 4.153296 TCATGGTAGTACAACAAACGCATG 59.847 41.667 2.06 4.42 0.00 4.06
4659 4941 3.729966 TGGTAGTACAACAAACGCATGA 58.270 40.909 0.00 0.00 0.00 3.07
4660 4942 4.127907 TGGTAGTACAACAAACGCATGAA 58.872 39.130 0.00 0.00 0.00 2.57
4661 4943 4.575236 TGGTAGTACAACAAACGCATGAAA 59.425 37.500 0.00 0.00 0.00 2.69
4662 4944 5.239744 TGGTAGTACAACAAACGCATGAAAT 59.760 36.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.759489 AACCTTCTGCATAACTGAATAACAA 57.241 32.000 0.00 0.00 35.88 2.83
77 87 2.734606 CGAGCATGTTTCCGTTCTACAA 59.265 45.455 0.00 0.00 0.00 2.41
87 97 1.197721 CCTGTTGTCCGAGCATGTTTC 59.802 52.381 0.00 0.00 0.00 2.78
131 151 6.018751 CCCACTACGACTGACATATCATTTTG 60.019 42.308 0.00 0.00 33.22 2.44
164 184 8.310382 TGTATGTAAAGCTAAAATGGCAAACAT 58.690 29.630 0.00 0.00 43.07 2.71
166 186 8.026607 TCTGTATGTAAAGCTAAAATGGCAAAC 58.973 33.333 0.00 0.00 0.00 2.93
306 359 9.998106 TTTCGGGTTTTTATATTCAATTTTCCA 57.002 25.926 0.00 0.00 0.00 3.53
339 393 4.969816 AGCGTGTTTCAGTTTGCATATAC 58.030 39.130 0.00 0.00 0.00 1.47
410 468 7.286316 ACTCCATGTTTCTTTCTGTTCTCATTT 59.714 33.333 0.00 0.00 0.00 2.32
453 511 9.666626 CGGAGTATACAAGAAAATAGTCACTAG 57.333 37.037 5.50 0.00 32.08 2.57
467 525 5.119279 GCATCTATGTTGCGGAGTATACAAG 59.881 44.000 5.50 0.00 0.00 3.16
469 527 4.038642 TGCATCTATGTTGCGGAGTATACA 59.961 41.667 5.50 0.00 43.10 2.29
560 618 8.928270 TTAGTTATTCTCGGATTTCAAGTCTC 57.072 34.615 0.00 0.00 0.00 3.36
712 770 8.940397 CCTAAAATTACCATCACATAGGGAAT 57.060 34.615 0.00 0.00 40.19 3.01
715 773 6.010219 CCCCTAAAATTACCATCACATAGGG 58.990 44.000 7.44 7.44 45.20 3.53
716 774 6.715264 GTCCCCTAAAATTACCATCACATAGG 59.285 42.308 0.00 0.00 0.00 2.57
717 775 7.518188 AGTCCCCTAAAATTACCATCACATAG 58.482 38.462 0.00 0.00 0.00 2.23
718 776 7.460214 AGTCCCCTAAAATTACCATCACATA 57.540 36.000 0.00 0.00 0.00 2.29
719 777 6.341408 AGTCCCCTAAAATTACCATCACAT 57.659 37.500 0.00 0.00 0.00 3.21
720 778 5.789574 AGTCCCCTAAAATTACCATCACA 57.210 39.130 0.00 0.00 0.00 3.58
721 779 6.060136 GGTAGTCCCCTAAAATTACCATCAC 58.940 44.000 0.00 0.00 32.69 3.06
722 780 5.732170 TGGTAGTCCCCTAAAATTACCATCA 59.268 40.000 0.00 0.00 36.54 3.07
723 781 6.256643 TGGTAGTCCCCTAAAATTACCATC 57.743 41.667 0.00 0.00 36.54 3.51
724 782 6.661740 TTGGTAGTCCCCTAAAATTACCAT 57.338 37.500 2.39 0.00 39.95 3.55
725 783 6.661740 ATTGGTAGTCCCCTAAAATTACCA 57.338 37.500 0.00 0.00 38.89 3.25
738 796 8.375493 TCACATAGGGAATATATTGGTAGTCC 57.625 38.462 1.78 0.00 37.94 3.85
739 797 9.823647 CATCACATAGGGAATATATTGGTAGTC 57.176 37.037 1.78 0.00 0.00 2.59
847 905 4.803613 TGATATCGGTCATTTGTCTTCACG 59.196 41.667 0.00 0.00 0.00 4.35
876 935 8.874156 AGACATGTATCATGTACATACCAATCT 58.126 33.333 8.32 7.50 36.49 2.40
877 936 9.144747 GAGACATGTATCATGTACATACCAATC 57.855 37.037 15.49 5.68 36.49 2.67
878 937 8.650490 TGAGACATGTATCATGTACATACCAAT 58.350 33.333 18.92 3.11 36.49 3.16
879 938 8.017418 TGAGACATGTATCATGTACATACCAA 57.983 34.615 18.92 0.00 36.49 3.67
880 939 7.287696 ACTGAGACATGTATCATGTACATACCA 59.712 37.037 22.58 3.43 36.49 3.25
881 940 7.661968 ACTGAGACATGTATCATGTACATACC 58.338 38.462 22.58 12.06 36.49 2.73
882 941 7.535599 CGACTGAGACATGTATCATGTACATAC 59.464 40.741 22.58 4.12 36.49 2.39
883 942 7.228706 ACGACTGAGACATGTATCATGTACATA 59.771 37.037 22.58 0.00 36.49 2.29
884 943 6.039829 ACGACTGAGACATGTATCATGTACAT 59.960 38.462 22.58 1.41 38.57 2.29
885 944 5.357032 ACGACTGAGACATGTATCATGTACA 59.643 40.000 22.58 14.83 29.73 2.90
886 945 5.822278 ACGACTGAGACATGTATCATGTAC 58.178 41.667 22.58 12.97 29.73 2.90
887 946 6.451064 AACGACTGAGACATGTATCATGTA 57.549 37.500 22.58 0.92 29.73 2.29
888 947 4.991153 ACGACTGAGACATGTATCATGT 57.009 40.909 22.58 20.44 29.73 3.21
889 948 5.233050 GGAAACGACTGAGACATGTATCATG 59.767 44.000 22.58 17.79 29.73 3.07
890 949 5.127845 AGGAAACGACTGAGACATGTATCAT 59.872 40.000 22.58 13.13 29.73 2.45
891 950 4.462834 AGGAAACGACTGAGACATGTATCA 59.537 41.667 21.21 21.21 0.00 2.15
892 951 5.000012 AGGAAACGACTGAGACATGTATC 58.000 43.478 13.60 13.60 0.00 2.24
893 952 6.525578 TTAGGAAACGACTGAGACATGTAT 57.474 37.500 0.00 0.00 0.00 2.29
894 953 5.970317 TTAGGAAACGACTGAGACATGTA 57.030 39.130 0.00 0.00 0.00 2.29
895 954 4.866508 TTAGGAAACGACTGAGACATGT 57.133 40.909 0.00 0.00 0.00 3.21
896 955 8.969267 GTTATATTAGGAAACGACTGAGACATG 58.031 37.037 0.00 0.00 0.00 3.21
897 956 8.692710 TGTTATATTAGGAAACGACTGAGACAT 58.307 33.333 0.00 0.00 0.00 3.06
898 957 8.058667 TGTTATATTAGGAAACGACTGAGACA 57.941 34.615 0.00 0.00 0.00 3.41
899 958 9.530633 AATGTTATATTAGGAAACGACTGAGAC 57.469 33.333 0.00 0.00 0.00 3.36
926 985 6.867293 ACGGTAGTTTTTGTGTTTAGCAAAAA 59.133 30.769 10.62 10.62 46.79 1.94
927 986 6.388278 ACGGTAGTTTTTGTGTTTAGCAAAA 58.612 32.000 0.00 0.00 42.03 2.44
928 987 5.952033 ACGGTAGTTTTTGTGTTTAGCAAA 58.048 33.333 0.00 0.00 34.47 3.68
929 988 5.564048 ACGGTAGTTTTTGTGTTTAGCAA 57.436 34.783 0.00 0.00 0.00 3.91
930 989 6.093219 TGTTACGGTAGTTTTTGTGTTTAGCA 59.907 34.615 0.00 0.00 0.00 3.49
931 990 6.485393 TGTTACGGTAGTTTTTGTGTTTAGC 58.515 36.000 0.00 0.00 0.00 3.09
932 991 9.584839 GTATGTTACGGTAGTTTTTGTGTTTAG 57.415 33.333 0.00 0.00 0.00 1.85
933 992 9.102757 TGTATGTTACGGTAGTTTTTGTGTTTA 57.897 29.630 0.00 0.00 0.00 2.01
934 993 7.983307 TGTATGTTACGGTAGTTTTTGTGTTT 58.017 30.769 0.00 0.00 0.00 2.83
935 994 7.551035 TGTATGTTACGGTAGTTTTTGTGTT 57.449 32.000 0.00 0.00 0.00 3.32
936 995 7.733402 ATGTATGTTACGGTAGTTTTTGTGT 57.267 32.000 0.00 0.00 0.00 3.72
937 996 9.697250 CATATGTATGTTACGGTAGTTTTTGTG 57.303 33.333 0.00 0.00 0.00 3.33
938 997 8.885722 CCATATGTATGTTACGGTAGTTTTTGT 58.114 33.333 1.24 0.00 31.82 2.83
939 998 7.853929 GCCATATGTATGTTACGGTAGTTTTTG 59.146 37.037 1.24 0.00 31.82 2.44
940 999 7.012610 GGCCATATGTATGTTACGGTAGTTTTT 59.987 37.037 0.00 0.00 31.82 1.94
941 1000 6.484308 GGCCATATGTATGTTACGGTAGTTTT 59.516 38.462 0.00 0.00 31.82 2.43
942 1001 5.993441 GGCCATATGTATGTTACGGTAGTTT 59.007 40.000 0.00 0.00 31.82 2.66
943 1002 5.511888 GGGCCATATGTATGTTACGGTAGTT 60.512 44.000 4.39 0.00 31.82 2.24
944 1003 4.020839 GGGCCATATGTATGTTACGGTAGT 60.021 45.833 4.39 0.00 31.82 2.73
945 1004 4.020928 TGGGCCATATGTATGTTACGGTAG 60.021 45.833 0.00 0.00 31.82 3.18
946 1005 3.902467 TGGGCCATATGTATGTTACGGTA 59.098 43.478 0.00 0.00 31.82 4.02
947 1006 2.706723 TGGGCCATATGTATGTTACGGT 59.293 45.455 0.00 0.00 31.82 4.83
948 1007 3.007506 TCTGGGCCATATGTATGTTACGG 59.992 47.826 6.72 0.00 31.82 4.02
949 1008 4.265904 TCTGGGCCATATGTATGTTACG 57.734 45.455 6.72 0.00 31.82 3.18
950 1009 7.182817 TCTATCTGGGCCATATGTATGTTAC 57.817 40.000 14.22 0.00 31.82 2.50
951 1010 7.995052 ATCTATCTGGGCCATATGTATGTTA 57.005 36.000 14.22 0.00 31.82 2.41
952 1011 6.898171 ATCTATCTGGGCCATATGTATGTT 57.102 37.500 14.22 0.00 31.82 2.71
953 1012 6.353342 CCAATCTATCTGGGCCATATGTATGT 60.353 42.308 14.22 0.00 31.82 2.29
954 1013 6.060136 CCAATCTATCTGGGCCATATGTATG 58.940 44.000 14.22 7.88 0.00 2.39
955 1014 5.733154 ACCAATCTATCTGGGCCATATGTAT 59.267 40.000 14.22 5.09 38.36 2.29
956 1015 5.100811 ACCAATCTATCTGGGCCATATGTA 58.899 41.667 14.22 2.98 38.36 2.29
957 1016 3.918912 ACCAATCTATCTGGGCCATATGT 59.081 43.478 14.22 0.08 38.36 2.29
958 1017 4.581309 ACCAATCTATCTGGGCCATATG 57.419 45.455 14.22 0.00 38.36 1.78
959 1018 5.733154 ACATACCAATCTATCTGGGCCATAT 59.267 40.000 6.72 8.43 38.36 1.78
960 1019 5.100811 ACATACCAATCTATCTGGGCCATA 58.899 41.667 6.72 0.00 38.36 2.74
961 1020 3.918912 ACATACCAATCTATCTGGGCCAT 59.081 43.478 6.72 0.00 38.36 4.40
962 1021 3.326521 ACATACCAATCTATCTGGGCCA 58.673 45.455 5.85 5.85 38.36 5.36
963 1022 4.286032 TGTACATACCAATCTATCTGGGCC 59.714 45.833 0.00 0.00 38.36 5.80
964 1023 5.483685 TGTACATACCAATCTATCTGGGC 57.516 43.478 0.00 0.00 38.36 5.36
965 1024 7.244886 TCATGTACATACCAATCTATCTGGG 57.755 40.000 8.32 0.00 38.36 4.45
966 1025 9.809096 GTATCATGTACATACCAATCTATCTGG 57.191 37.037 8.32 0.00 40.05 3.86
1182 1338 4.280929 ACATTAAAGGGTTCTTGGAAGCAC 59.719 41.667 10.80 2.18 32.75 4.40
1473 1644 1.180029 AGCATGAGTTGACAATGGGC 58.820 50.000 0.00 0.00 0.00 5.36
1773 1944 2.351738 GGCTTCCGAACAACTTCCATTG 60.352 50.000 0.00 0.00 35.59 2.82
2033 2222 3.188048 GTGAGGAGAAAGTCAACATGCAG 59.812 47.826 0.00 0.00 0.00 4.41
2205 2401 4.039603 AGCTTTATTTGGGTCAGCTCTT 57.960 40.909 0.00 0.00 35.95 2.85
2220 2416 1.362224 AGGCCACCTTCAGAGCTTTA 58.638 50.000 5.01 0.00 0.00 1.85
2272 2475 4.431809 CAATGTGTGAACAATTGGTGTGT 58.568 39.130 10.83 0.00 40.60 3.72
2354 2557 9.162764 ACATGACATTTATACAAACTGTACTCC 57.837 33.333 0.00 0.00 35.42 3.85
2371 2574 6.658816 TCACCATTGCTTTACTACATGACATT 59.341 34.615 0.00 0.00 0.00 2.71
2977 3189 3.964031 AGATTCTTGAGCGACCCTAAGAT 59.036 43.478 0.00 0.00 0.00 2.40
3387 3602 0.987081 AGCAGCATCTCCATCCCTGT 60.987 55.000 0.00 0.00 0.00 4.00
3389 3604 1.706995 CCAGCAGCATCTCCATCCCT 61.707 60.000 0.00 0.00 0.00 4.20
3423 3638 1.747355 GCTCAAGCACATACTTGCCAT 59.253 47.619 0.00 0.00 45.43 4.40
3572 3787 3.896648 ACACGAAGCATTAAAGGTGTG 57.103 42.857 0.00 0.50 37.25 3.82
3573 3788 3.252458 GGAACACGAAGCATTAAAGGTGT 59.748 43.478 0.00 0.00 40.04 4.16
3701 3920 1.202806 CCAGGCCTCAAACACTCTTCA 60.203 52.381 0.00 0.00 0.00 3.02
3781 4000 9.136952 ACTTCTACATTAACGTCACAAATAGAC 57.863 33.333 0.00 0.00 0.00 2.59
3782 4001 9.701098 AACTTCTACATTAACGTCACAAATAGA 57.299 29.630 0.00 0.00 0.00 1.98
3783 4002 9.741168 CAACTTCTACATTAACGTCACAAATAG 57.259 33.333 0.00 0.00 0.00 1.73
3784 4003 8.714179 CCAACTTCTACATTAACGTCACAAATA 58.286 33.333 0.00 0.00 0.00 1.40
3785 4004 7.442969 TCCAACTTCTACATTAACGTCACAAAT 59.557 33.333 0.00 0.00 0.00 2.32
3786 4005 6.762187 TCCAACTTCTACATTAACGTCACAAA 59.238 34.615 0.00 0.00 0.00 2.83
3787 4006 6.282167 TCCAACTTCTACATTAACGTCACAA 58.718 36.000 0.00 0.00 0.00 3.33
3788 4007 5.845103 TCCAACTTCTACATTAACGTCACA 58.155 37.500 0.00 0.00 0.00 3.58
3789 4008 6.774354 TTCCAACTTCTACATTAACGTCAC 57.226 37.500 0.00 0.00 0.00 3.67
3790 4009 7.094975 CCAATTCCAACTTCTACATTAACGTCA 60.095 37.037 0.00 0.00 0.00 4.35
3837 4056 6.326583 TCCCATAACCAACATAAACAAAACCA 59.673 34.615 0.00 0.00 0.00 3.67
3845 4064 8.919145 GGTCAAATATCCCATAACCAACATAAA 58.081 33.333 0.00 0.00 0.00 1.40
3848 4067 5.838521 GGGTCAAATATCCCATAACCAACAT 59.161 40.000 0.00 0.00 42.95 2.71
3849 4068 5.043732 AGGGTCAAATATCCCATAACCAACA 60.044 40.000 3.04 0.00 45.64 3.33
3850 4069 5.454966 AGGGTCAAATATCCCATAACCAAC 58.545 41.667 3.04 0.00 45.64 3.77
3851 4070 5.742562 AGGGTCAAATATCCCATAACCAA 57.257 39.130 3.04 0.00 45.64 3.67
3852 4071 5.742562 AAGGGTCAAATATCCCATAACCA 57.257 39.130 3.04 0.00 45.64 3.67
3853 4072 7.432148 AAAAAGGGTCAAATATCCCATAACC 57.568 36.000 3.04 0.00 45.64 2.85
3877 4096 0.631753 TATCCCATCCCCCGCAAAAA 59.368 50.000 0.00 0.00 0.00 1.94
3878 4097 0.856982 ATATCCCATCCCCCGCAAAA 59.143 50.000 0.00 0.00 0.00 2.44
3879 4098 0.856982 AATATCCCATCCCCCGCAAA 59.143 50.000 0.00 0.00 0.00 3.68
3880 4099 0.856982 AAATATCCCATCCCCCGCAA 59.143 50.000 0.00 0.00 0.00 4.85
3881 4100 0.112218 CAAATATCCCATCCCCCGCA 59.888 55.000 0.00 0.00 0.00 5.69
3882 4101 0.404040 TCAAATATCCCATCCCCCGC 59.596 55.000 0.00 0.00 0.00 6.13
3883 4102 1.271926 GGTCAAATATCCCATCCCCCG 60.272 57.143 0.00 0.00 0.00 5.73
3884 4103 2.073776 AGGTCAAATATCCCATCCCCC 58.926 52.381 0.00 0.00 0.00 5.40
3885 4104 3.117131 ACAAGGTCAAATATCCCATCCCC 60.117 47.826 0.00 0.00 0.00 4.81
3886 4105 4.184649 ACAAGGTCAAATATCCCATCCC 57.815 45.455 0.00 0.00 0.00 3.85
3887 4106 4.275936 CGAACAAGGTCAAATATCCCATCC 59.724 45.833 0.00 0.00 0.00 3.51
3888 4107 4.881850 ACGAACAAGGTCAAATATCCCATC 59.118 41.667 0.00 0.00 0.00 3.51
3942 4163 0.187361 AGCAACTGCCAAAAGGGGTA 59.813 50.000 0.00 0.00 43.38 3.69
4002 4269 6.295249 TGACATGTTTCCAGAGTACAAATGA 58.705 36.000 0.00 0.00 0.00 2.57
4116 4383 5.633655 TTAAGTCTGTAACCCCTTTGACA 57.366 39.130 0.00 0.00 0.00 3.58
4117 4384 6.947644 TTTTAAGTCTGTAACCCCTTTGAC 57.052 37.500 0.00 0.00 0.00 3.18
4118 4385 7.388500 CGTATTTTAAGTCTGTAACCCCTTTGA 59.612 37.037 0.00 0.00 0.00 2.69
4119 4386 7.361457 CCGTATTTTAAGTCTGTAACCCCTTTG 60.361 40.741 0.00 0.00 0.00 2.77
4120 4387 6.656270 CCGTATTTTAAGTCTGTAACCCCTTT 59.344 38.462 0.00 0.00 0.00 3.11
4121 4388 6.175471 CCGTATTTTAAGTCTGTAACCCCTT 58.825 40.000 0.00 0.00 0.00 3.95
4122 4389 5.249163 ACCGTATTTTAAGTCTGTAACCCCT 59.751 40.000 0.00 0.00 0.00 4.79
4123 4390 5.491070 ACCGTATTTTAAGTCTGTAACCCC 58.509 41.667 0.00 0.00 0.00 4.95
4124 4391 6.165577 TGACCGTATTTTAAGTCTGTAACCC 58.834 40.000 0.00 0.00 0.00 4.11
4125 4392 7.838771 ATGACCGTATTTTAAGTCTGTAACC 57.161 36.000 0.00 0.00 0.00 2.85
4129 4396 9.148104 GAACTAATGACCGTATTTTAAGTCTGT 57.852 33.333 0.00 0.00 0.00 3.41
4130 4397 9.146984 TGAACTAATGACCGTATTTTAAGTCTG 57.853 33.333 0.00 0.00 0.00 3.51
4131 4398 9.886132 ATGAACTAATGACCGTATTTTAAGTCT 57.114 29.630 0.00 0.00 0.00 3.24
4138 4405 9.444600 ACAGTTAATGAACTAATGACCGTATTT 57.555 29.630 0.00 0.00 44.39 1.40
4178 4445 0.892755 ATGAGCCGAACACCGACTTA 59.107 50.000 0.00 0.00 41.76 2.24
4201 4469 1.889829 CCTTTTAATGTTCACCGGGCA 59.110 47.619 6.32 0.00 0.00 5.36
4202 4470 2.164338 TCCTTTTAATGTTCACCGGGC 58.836 47.619 6.32 0.00 0.00 6.13
4247 4516 2.733026 GCATCTTGCACCACACATTTTC 59.267 45.455 0.00 0.00 44.26 2.29
4273 4551 6.072397 CCAAAATTTTGCATGAACATCACCAT 60.072 34.615 22.90 0.00 36.86 3.55
4285 4563 5.241285 GTCCAAACATCCCAAAATTTTGCAT 59.759 36.000 22.90 14.52 36.86 3.96
4323 4601 4.026640 CACCTGATTTTGTCTGTTTTTGCG 60.027 41.667 0.00 0.00 0.00 4.85
4331 4609 4.336433 ACTGTTCACACCTGATTTTGTCTG 59.664 41.667 0.00 0.00 0.00 3.51
4342 4621 6.767524 TTGAAAACAATACTGTTCACACCT 57.232 33.333 0.00 0.00 45.25 4.00
4400 4680 2.306805 TGGACATTTGAGGAGCTCATGT 59.693 45.455 17.19 15.66 40.39 3.21
4534 4815 0.034337 TTACCCAGCTCAACGTGTCC 59.966 55.000 0.00 0.00 0.00 4.02
4556 4837 7.775053 ATCCATCTTACTCTTGAGTCTATCC 57.225 40.000 6.55 0.00 0.00 2.59
4613 4895 9.955208 CATGATTGAAAATGAATAAAGATCGGA 57.045 29.630 0.00 0.00 0.00 4.55
4614 4896 9.188588 CCATGATTGAAAATGAATAAAGATCGG 57.811 33.333 0.00 0.00 0.00 4.18
4615 4897 9.740239 ACCATGATTGAAAATGAATAAAGATCG 57.260 29.630 0.00 0.00 0.00 3.69
4624 4906 9.072375 TGTTGTACTACCATGATTGAAAATGAA 57.928 29.630 4.98 0.00 0.00 2.57
4625 4907 8.628630 TGTTGTACTACCATGATTGAAAATGA 57.371 30.769 4.98 0.00 0.00 2.57
4626 4908 9.689976 TTTGTTGTACTACCATGATTGAAAATG 57.310 29.630 4.98 0.00 0.00 2.32
4627 4909 9.691362 GTTTGTTGTACTACCATGATTGAAAAT 57.309 29.630 4.98 0.00 0.00 1.82
4628 4910 7.858382 CGTTTGTTGTACTACCATGATTGAAAA 59.142 33.333 4.98 0.00 0.00 2.29
4629 4911 7.356540 CGTTTGTTGTACTACCATGATTGAAA 58.643 34.615 4.98 0.00 0.00 2.69
4630 4912 6.566942 GCGTTTGTTGTACTACCATGATTGAA 60.567 38.462 4.98 0.00 0.00 2.69
4631 4913 5.106869 GCGTTTGTTGTACTACCATGATTGA 60.107 40.000 4.98 0.00 0.00 2.57
4632 4914 5.086058 GCGTTTGTTGTACTACCATGATTG 58.914 41.667 4.98 0.00 0.00 2.67
4633 4915 4.757657 TGCGTTTGTTGTACTACCATGATT 59.242 37.500 4.98 0.00 0.00 2.57
4634 4916 4.320023 TGCGTTTGTTGTACTACCATGAT 58.680 39.130 4.98 0.00 0.00 2.45
4635 4917 3.729966 TGCGTTTGTTGTACTACCATGA 58.270 40.909 4.98 0.00 0.00 3.07
4636 4918 4.153296 TCATGCGTTTGTTGTACTACCATG 59.847 41.667 13.39 13.39 0.00 3.66
4637 4919 4.320023 TCATGCGTTTGTTGTACTACCAT 58.680 39.130 4.98 0.00 0.00 3.55
4638 4920 3.729966 TCATGCGTTTGTTGTACTACCA 58.270 40.909 4.98 0.00 0.00 3.25
4639 4921 4.735662 TTCATGCGTTTGTTGTACTACC 57.264 40.909 4.98 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.