Multiple sequence alignment - TraesCS4D01G360400

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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 TraesCS4D01G360400 chr4D 100.000 6122 0 0 1 6122 507353504 507347383 0.000000e+00 11306.0
1 TraesCS4D01G360400 chr4D 92.857 140 9 1 3417 3556 507350036 507349898 1.040000e-47 202.0
2 TraesCS4D01G360400 chr4D 92.857 140 9 1 3469 3607 507350088 507349949 1.040000e-47 202.0
3 TraesCS4D01G360400 chr4B 93.990 3078 131 28 946 3998 654201611 654204659 0.000000e+00 4610.0
4 TraesCS4D01G360400 chr4B 89.930 1718 83 47 4037 5688 654204659 654206352 0.000000e+00 2132.0
5 TraesCS4D01G360400 chr4B 90.038 261 12 2 671 917 74304257 74304517 5.920000e-85 326.0
6 TraesCS4D01G360400 chr4B 94.839 155 8 0 3402 3556 654204117 654204271 6.130000e-60 243.0
7 TraesCS4D01G360400 chr5A 93.126 2633 109 32 946 3557 691820691 691823272 0.000000e+00 3794.0
8 TraesCS4D01G360400 chr5A 94.410 161 8 1 4089 4249 691823296 691823455 4.740000e-61 246.0
9 TraesCS4D01G360400 chr5A 93.333 105 6 1 3402 3506 691823169 691823272 2.960000e-33 154.0
10 TraesCS4D01G360400 chr5A 93.258 89 4 2 3520 3607 691823184 691823271 4.980000e-26 130.0
11 TraesCS4D01G360400 chr5A 90.909 44 3 1 4288 4331 682942101 682942143 2.380000e-04 58.4
12 TraesCS4D01G360400 chr7A 81.509 2174 275 71 1172 3279 9486595 9488707 0.000000e+00 1670.0
13 TraesCS4D01G360400 chr7A 84.439 1523 149 35 1795 3279 9688107 9686635 0.000000e+00 1419.0
14 TraesCS4D01G360400 chr7A 92.382 932 38 5 1 917 544156149 544155236 0.000000e+00 1297.0
15 TraesCS4D01G360400 chr7A 89.955 886 71 12 5050 5932 9385326 9386196 0.000000e+00 1127.0
16 TraesCS4D01G360400 chr7A 79.189 1701 283 38 1295 2975 9669848 9668199 0.000000e+00 1114.0
17 TraesCS4D01G360400 chr7A 86.627 830 66 24 3139 3946 9383702 9384508 0.000000e+00 876.0
18 TraesCS4D01G360400 chr7A 94.208 259 15 0 4628 4886 9384816 9385074 4.450000e-106 396.0
19 TraesCS4D01G360400 chr7A 86.139 101 7 5 1181 1277 9642226 9642129 1.090000e-17 102.0
20 TraesCS4D01G360400 chr7D 87.088 1456 138 20 1369 2810 9223956 9225375 0.000000e+00 1602.0
21 TraesCS4D01G360400 chr7D 87.290 1369 112 23 1294 2645 8870162 8871485 0.000000e+00 1507.0
22 TraesCS4D01G360400 chr7D 96.026 931 24 6 1 918 450122683 450123613 0.000000e+00 1502.0
23 TraesCS4D01G360400 chr7D 80.599 2036 287 64 1044 3020 8818647 8820633 0.000000e+00 1472.0
24 TraesCS4D01G360400 chr7D 81.724 1357 194 31 1291 2635 10087846 10086532 0.000000e+00 1083.0
25 TraesCS4D01G360400 chr7D 80.015 1336 192 45 1362 2645 10910346 10909034 0.000000e+00 918.0
26 TraesCS4D01G360400 chr7D 83.640 544 69 13 2698 3225 8871515 8872054 1.530000e-135 494.0
27 TraesCS4D01G360400 chr7D 87.419 310 21 9 3097 3404 8820667 8820960 2.110000e-89 340.0
28 TraesCS4D01G360400 chr7D 80.984 305 23 14 3394 3665 8820991 8821293 6.220000e-50 209.0
29 TraesCS4D01G360400 chr7D 90.400 125 10 2 3448 3572 8821120 8821242 4.910000e-36 163.0
30 TraesCS4D01G360400 chr7D 96.296 54 1 1 3417 3470 8821190 8821242 3.040000e-13 87.9
31 TraesCS4D01G360400 chr2D 96.414 948 18 4 1 932 305771939 305770992 0.000000e+00 1548.0
32 TraesCS4D01G360400 chr2D 95.275 910 29 6 1 896 622863991 622864900 0.000000e+00 1430.0
33 TraesCS4D01G360400 chr2D 83.750 80 12 1 4251 4330 451974407 451974329 2.370000e-09 75.0
34 TraesCS4D01G360400 chr2D 90.741 54 4 1 4246 4299 585063294 585063242 3.060000e-08 71.3
35 TraesCS4D01G360400 chr4A 81.883 1816 229 56 1261 3020 729157299 729159070 0.000000e+00 1439.0
36 TraesCS4D01G360400 chr4A 79.445 1766 264 54 1245 2959 728443571 728441854 0.000000e+00 1158.0
37 TraesCS4D01G360400 chr4A 89.686 892 67 13 5053 5935 728439850 728438975 0.000000e+00 1114.0
38 TraesCS4D01G360400 chr4A 80.840 1477 211 41 1173 2616 729827390 729828827 0.000000e+00 1094.0
39 TraesCS4D01G360400 chr4A 79.838 1602 237 51 1082 2645 728645622 728644069 0.000000e+00 1090.0
40 TraesCS4D01G360400 chr4A 82.616 1277 176 31 1369 2630 729880951 729882196 0.000000e+00 1086.0
41 TraesCS4D01G360400 chr4A 81.887 1314 199 25 1275 2574 729426121 729424833 0.000000e+00 1072.0
42 TraesCS4D01G360400 chr4A 81.537 1327 184 41 1187 2491 731097579 731098866 0.000000e+00 1037.0
43 TraesCS4D01G360400 chr4A 81.059 1341 216 19 1242 2560 730322742 730324066 0.000000e+00 1035.0
44 TraesCS4D01G360400 chr4A 82.621 1030 133 24 2006 2990 729678548 729679576 0.000000e+00 869.0
45 TraesCS4D01G360400 chr4A 94.747 533 26 1 2354 2884 730003141 730002609 0.000000e+00 828.0
46 TraesCS4D01G360400 chr4A 87.219 579 48 5 4334 4889 728440677 728440102 2.410000e-178 636.0
47 TraesCS4D01G360400 chr4A 82.703 688 72 27 3405 4076 730001905 730001249 8.910000e-158 568.0
48 TraesCS4D01G360400 chr4A 89.348 460 36 6 3499 3946 728441481 728441023 3.200000e-157 566.0
49 TraesCS4D01G360400 chr4A 91.967 361 28 1 4526 4886 729986722 729986363 7.080000e-139 505.0
50 TraesCS4D01G360400 chr4A 85.915 497 35 18 3094 3572 728441836 728441357 1.190000e-136 497.0
51 TraesCS4D01G360400 chr4A 84.479 451 64 5 2653 3100 728569667 728569220 2.030000e-119 440.0
52 TraesCS4D01G360400 chr4A 81.746 504 66 14 2795 3279 729159239 729159735 1.240000e-106 398.0
53 TraesCS4D01G360400 chr4A 95.954 173 7 0 5267 5439 729984936 729984764 1.300000e-71 281.0
54 TraesCS4D01G360400 chr4A 90.361 166 13 3 3051 3215 729159074 729159237 1.340000e-51 215.0
55 TraesCS4D01G360400 chr4A 95.385 130 5 1 5769 5897 729263370 729263499 8.040000e-49 206.0
56 TraesCS4D01G360400 chr4A 76.212 433 74 21 4338 4756 729149618 729150035 1.040000e-47 202.0
57 TraesCS4D01G360400 chr4A 91.111 135 11 1 5498 5632 729248546 729248679 1.360000e-41 182.0
58 TraesCS4D01G360400 chr4A 89.524 105 10 1 4327 4430 729992239 729992135 1.380000e-26 132.0
59 TraesCS4D01G360400 chr4A 86.458 96 9 3 3847 3942 729150812 729150903 1.090000e-17 102.0
60 TraesCS4D01G360400 chr4A 86.458 96 9 3 3847 3942 729797291 729797382 1.090000e-17 102.0
61 TraesCS4D01G360400 chr4A 91.304 69 5 1 3846 3914 729159936 729160003 6.530000e-15 93.5
62 TraesCS4D01G360400 chr4A 92.000 50 3 1 3223 3272 728568048 728568000 1.100000e-07 69.4
63 TraesCS4D01G360400 chr4A 81.707 82 10 4 4251 4330 141112005 141111927 5.120000e-06 63.9
64 TraesCS4D01G360400 chr1A 94.421 932 33 5 1 917 30548317 30549244 0.000000e+00 1415.0
65 TraesCS4D01G360400 chr1A 92.800 375 25 2 1 374 586756244 586755871 5.400000e-150 542.0
66 TraesCS4D01G360400 chr1A 76.570 414 56 19 2853 3258 589163788 589163408 8.100000e-44 189.0
67 TraesCS4D01G360400 chr1A 87.500 56 6 1 4250 4304 33218807 33218862 5.120000e-06 63.9
68 TraesCS4D01G360400 chr3B 94.307 931 36 5 1 917 23590886 23589959 0.000000e+00 1410.0
69 TraesCS4D01G360400 chr3B 93.173 249 14 3 671 917 670070837 670071084 4.510000e-96 363.0
70 TraesCS4D01G360400 chr5D 93.790 934 33 6 1 921 345648238 345649159 0.000000e+00 1380.0
71 TraesCS4D01G360400 chr5D 92.857 42 3 0 4289 4330 5570560 5570601 1.840000e-05 62.1
72 TraesCS4D01G360400 chr5D 89.796 49 4 1 4249 4297 386674124 386674077 1.840000e-05 62.1
73 TraesCS4D01G360400 chr1D 93.878 931 29 4 1 917 272696947 272697863 0.000000e+00 1378.0
74 TraesCS4D01G360400 chr3A 95.531 716 28 3 1 714 497667286 497666573 0.000000e+00 1142.0
75 TraesCS4D01G360400 chr6B 92.799 611 27 8 315 910 116286417 116285809 0.000000e+00 869.0
76 TraesCS4D01G360400 chr6B 83.333 66 10 1 4266 4331 213236109 213236045 6.630000e-05 60.2
77 TraesCS4D01G360400 chr1B 91.923 260 7 2 671 916 55542126 55541867 9.760000e-93 351.0
78 TraesCS4D01G360400 chr2A 95.122 41 2 0 4291 4331 585816381 585816341 1.420000e-06 65.8
79 TraesCS4D01G360400 chr7B 88.462 52 5 1 4248 4299 665690686 665690736 1.840000e-05 62.1
80 TraesCS4D01G360400 chr5B 81.333 75 14 0 4257 4331 538722402 538722476 1.840000e-05 62.1
81 TraesCS4D01G360400 chr2B 91.304 46 1 3 4286 4330 602192605 602192648 6.630000e-05 60.2


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 TraesCS4D01G360400 chr4D 507347383 507353504 6121 True 3903.333333 11306 95.238000 1 6122 3 chr4D.!!$R1 6121
1 TraesCS4D01G360400 chr4B 654201611 654206352 4741 False 2328.333333 4610 92.919667 946 5688 3 chr4B.!!$F2 4742
2 TraesCS4D01G360400 chr5A 691820691 691823455 2764 False 1081.000000 3794 93.531750 946 4249 4 chr5A.!!$F2 3303
3 TraesCS4D01G360400 chr7A 9486595 9488707 2112 False 1670.000000 1670 81.509000 1172 3279 1 chr7A.!!$F1 2107
4 TraesCS4D01G360400 chr7A 9686635 9688107 1472 True 1419.000000 1419 84.439000 1795 3279 1 chr7A.!!$R3 1484
5 TraesCS4D01G360400 chr7A 544155236 544156149 913 True 1297.000000 1297 92.382000 1 917 1 chr7A.!!$R4 916
6 TraesCS4D01G360400 chr7A 9668199 9669848 1649 True 1114.000000 1114 79.189000 1295 2975 1 chr7A.!!$R2 1680
7 TraesCS4D01G360400 chr7A 9383702 9386196 2494 False 799.666667 1127 90.263333 3139 5932 3 chr7A.!!$F2 2793
8 TraesCS4D01G360400 chr7D 9223956 9225375 1419 False 1602.000000 1602 87.088000 1369 2810 1 chr7D.!!$F1 1441
9 TraesCS4D01G360400 chr7D 450122683 450123613 930 False 1502.000000 1502 96.026000 1 918 1 chr7D.!!$F2 917
10 TraesCS4D01G360400 chr7D 10086532 10087846 1314 True 1083.000000 1083 81.724000 1291 2635 1 chr7D.!!$R1 1344
11 TraesCS4D01G360400 chr7D 8870162 8872054 1892 False 1000.500000 1507 85.465000 1294 3225 2 chr7D.!!$F4 1931
12 TraesCS4D01G360400 chr7D 10909034 10910346 1312 True 918.000000 918 80.015000 1362 2645 1 chr7D.!!$R2 1283
13 TraesCS4D01G360400 chr7D 8818647 8821293 2646 False 454.380000 1472 87.139600 1044 3665 5 chr7D.!!$F3 2621
14 TraesCS4D01G360400 chr2D 305770992 305771939 947 True 1548.000000 1548 96.414000 1 932 1 chr2D.!!$R1 931
15 TraesCS4D01G360400 chr2D 622863991 622864900 909 False 1430.000000 1430 95.275000 1 896 1 chr2D.!!$F1 895
16 TraesCS4D01G360400 chr4A 729827390 729828827 1437 False 1094.000000 1094 80.840000 1173 2616 1 chr4A.!!$F5 1443
17 TraesCS4D01G360400 chr4A 728644069 728645622 1553 True 1090.000000 1090 79.838000 1082 2645 1 chr4A.!!$R2 1563
18 TraesCS4D01G360400 chr4A 729880951 729882196 1245 False 1086.000000 1086 82.616000 1369 2630 1 chr4A.!!$F6 1261
19 TraesCS4D01G360400 chr4A 729424833 729426121 1288 True 1072.000000 1072 81.887000 1275 2574 1 chr4A.!!$R3 1299
20 TraesCS4D01G360400 chr4A 731097579 731098866 1287 False 1037.000000 1037 81.537000 1187 2491 1 chr4A.!!$F8 1304
21 TraesCS4D01G360400 chr4A 730322742 730324066 1324 False 1035.000000 1035 81.059000 1242 2560 1 chr4A.!!$F7 1318
22 TraesCS4D01G360400 chr4A 729678548 729679576 1028 False 869.000000 869 82.621000 2006 2990 1 chr4A.!!$F3 984
23 TraesCS4D01G360400 chr4A 728438975 728443571 4596 True 794.200000 1158 86.322600 1245 5935 5 chr4A.!!$R5 4690
24 TraesCS4D01G360400 chr4A 730001249 730003141 1892 True 698.000000 828 88.725000 2354 4076 2 chr4A.!!$R8 1722
25 TraesCS4D01G360400 chr4A 729157299 729160003 2704 False 536.375000 1439 86.323500 1261 3914 4 chr4A.!!$F10 2653
26 TraesCS4D01G360400 chr4A 729984764 729986722 1958 True 393.000000 505 93.960500 4526 5439 2 chr4A.!!$R7 913
27 TraesCS4D01G360400 chr4A 728568000 728569667 1667 True 254.700000 440 88.239500 2653 3272 2 chr4A.!!$R6 619
28 TraesCS4D01G360400 chr1A 30548317 30549244 927 False 1415.000000 1415 94.421000 1 917 1 chr1A.!!$F1 916
29 TraesCS4D01G360400 chr3B 23589959 23590886 927 True 1410.000000 1410 94.307000 1 917 1 chr3B.!!$R1 916
30 TraesCS4D01G360400 chr5D 345648238 345649159 921 False 1380.000000 1380 93.790000 1 921 1 chr5D.!!$F2 920
31 TraesCS4D01G360400 chr1D 272696947 272697863 916 False 1378.000000 1378 93.878000 1 917 1 chr1D.!!$F1 916
32 TraesCS4D01G360400 chr3A 497666573 497667286 713 True 1142.000000 1142 95.531000 1 714 1 chr3A.!!$R1 713
33 TraesCS4D01G360400 chr6B 116285809 116286417 608 True 869.000000 869 92.799000 315 910 1 chr6B.!!$R1 595

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
934 970 0.386352 TCCGAGTGTGCGTAAAGTCG 60.386 55.0 13.36 13.36 38.64 4.18 F
1017 1056 0.168788 CAGCATTCACATTCGCCGTT 59.831 50.0 0.00 0.00 0.00 4.44 F
1018 1057 0.447801 AGCATTCACATTCGCCGTTC 59.552 50.0 0.00 0.00 0.00 3.95 F
2347 2542 1.538047 CTGGTTTCACATGGAGGTGG 58.462 55.0 0.00 0.00 39.27 4.61 F
3797 6019 0.179018 AGCTGGGAAAACTGCTCGTT 60.179 50.0 0.00 0.00 41.01 3.85 F
4435 6775 0.328258 AAACTGGGATGGACGGGAAG 59.672 55.0 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2315 1.491670 AATCATCGACGGAAGATGCG 58.508 50.000 10.77 0.00 43.68 4.73 R
2482 2697 1.787012 CACAAGCATGGTTTGAAGGC 58.213 50.000 7.57 0.00 0.00 4.35 R
2939 3475 4.943705 TGTGATTAACAGATCCAAAGCTCC 59.056 41.667 0.00 0.00 33.78 4.70 R
4249 6567 0.257039 GGGACGGAGGGAGTACTACA 59.743 60.000 7.57 0.00 0.00 2.74 R
4662 7024 1.130054 ATCCTAGATGGGGCGCACAT 61.130 55.000 13.89 14.85 36.20 3.21 R
5976 9435 0.030638 CCAAAACAAGGTGCAGGACG 59.969 55.000 0.00 0.00 0.00 4.79 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
195 196 0.670546 CCGACGAAGGATGCAACACT 60.671 55.000 0.00 0.00 0.00 3.55
928 964 3.755628 GGGCTCCGAGTGTGCGTA 61.756 66.667 0.00 0.00 34.26 4.42
929 965 2.260434 GGCTCCGAGTGTGCGTAA 59.740 61.111 0.00 0.00 34.26 3.18
932 968 0.666577 GCTCCGAGTGTGCGTAAAGT 60.667 55.000 0.00 0.00 0.00 2.66
933 969 1.337821 CTCCGAGTGTGCGTAAAGTC 58.662 55.000 0.00 0.00 0.00 3.01
934 970 0.386352 TCCGAGTGTGCGTAAAGTCG 60.386 55.000 13.36 13.36 38.64 4.18
953 989 2.030185 TCGCTACAGTCACAACTCTTCC 60.030 50.000 0.00 0.00 31.71 3.46
959 995 3.055094 ACAGTCACAACTCTTCCACAACT 60.055 43.478 0.00 0.00 31.71 3.16
972 1009 3.740115 TCCACAACTAACAAGAGCTTCC 58.260 45.455 0.00 0.00 0.00 3.46
1017 1056 0.168788 CAGCATTCACATTCGCCGTT 59.831 50.000 0.00 0.00 0.00 4.44
1018 1057 0.447801 AGCATTCACATTCGCCGTTC 59.552 50.000 0.00 0.00 0.00 3.95
1020 1059 1.663643 GCATTCACATTCGCCGTTCTA 59.336 47.619 0.00 0.00 0.00 2.10
1034 1073 4.143179 CGCCGTTCTAAAGAGTCGATTTTT 60.143 41.667 0.00 0.00 0.00 1.94
1332 1416 4.731853 TGGACAGCCATCCGGGGA 62.732 66.667 0.00 0.00 42.24 4.81
2147 2315 1.825622 GGGGTGCTTGCTCTATGCC 60.826 63.158 0.00 0.00 42.00 4.40
2149 2317 2.711924 GTGCTTGCTCTATGCCGC 59.288 61.111 0.00 0.00 42.00 6.53
2347 2542 1.538047 CTGGTTTCACATGGAGGTGG 58.462 55.000 0.00 0.00 39.27 4.61
2482 2697 1.628340 TGGAGATGGGTGGTAGTGTTG 59.372 52.381 0.00 0.00 0.00 3.33
2753 3015 6.411376 TGTAATCGCTCTTCCTTTCCATAAA 58.589 36.000 0.00 0.00 0.00 1.40
2917 3396 9.677567 TTGAGCAAGTTCTTTTTATGTATGTTC 57.322 29.630 0.00 0.00 0.00 3.18
2939 3475 4.805719 TCGCTGTAGCTAATGAATTCAGTG 59.194 41.667 18.22 9.33 39.32 3.66
2976 3512 7.692460 TGTTAATCACAGAGAAATTGCATCT 57.308 32.000 0.00 0.00 0.00 2.90
3065 3995 4.680110 CAGTACACCAGAGTTTTACTGACG 59.320 45.833 0.00 0.00 39.96 4.35
3365 5440 2.724977 TGGAATGAGTCAGACGTGTC 57.275 50.000 0.00 0.00 0.00 3.67
3366 5441 1.960689 TGGAATGAGTCAGACGTGTCA 59.039 47.619 0.00 0.00 0.00 3.58
3367 5442 2.288213 TGGAATGAGTCAGACGTGTCAC 60.288 50.000 0.00 0.00 0.00 3.67
3392 5467 9.037737 ACGCGTGTAACAGTTTTATATTCATAT 57.962 29.630 12.93 0.00 35.74 1.78
3462 5649 8.074370 GTCTAGTGATTTTTGTTTTGTCCCTAC 58.926 37.037 0.00 0.00 0.00 3.18
3557 5745 7.499321 TCTTGGTCTAGCGATTTTTGTTTTA 57.501 32.000 0.00 0.00 0.00 1.52
3560 5748 7.681939 TGGTCTAGCGATTTTTGTTTTATCT 57.318 32.000 0.00 0.00 0.00 1.98
3715 5936 3.565902 CCAAGAACAGAAGGTGTCTTTCC 59.434 47.826 0.00 0.00 39.03 3.13
3733 5954 1.041437 CCGGAGACCTTCCCTACATC 58.959 60.000 0.00 0.00 43.63 3.06
3797 6019 0.179018 AGCTGGGAAAACTGCTCGTT 60.179 50.000 0.00 0.00 41.01 3.85
3812 6034 9.982651 AAACTGCTCGTTATATATATGTCAACT 57.017 29.630 5.44 0.00 33.90 3.16
3920 6145 6.989169 CAGCTGCCTTGAGAAAATAGTAGTAT 59.011 38.462 0.00 0.00 0.00 2.12
3958 6183 6.149807 TCGTTTGTTTTCAACTAAACTGGAGT 59.850 34.615 0.00 0.00 39.73 3.85
3959 6184 6.804783 CGTTTGTTTTCAACTAAACTGGAGTT 59.195 34.615 0.00 0.00 39.73 3.01
3969 6194 3.403936 ACTGGAGTTGTCAGTTGGC 57.596 52.632 0.00 0.00 42.17 4.52
3970 6195 0.839946 ACTGGAGTTGTCAGTTGGCT 59.160 50.000 0.00 0.00 42.17 4.75
3977 6202 1.159713 TTGTCAGTTGGCTGCTGTCG 61.160 55.000 0.00 0.00 42.29 4.35
4001 6259 6.636850 CGGGAGTTTCTTGTTTCATAAACTTG 59.363 38.462 0.00 0.00 41.08 3.16
4012 6270 8.319143 TGTTTCATAAACTTGCTTAGTAGGTC 57.681 34.615 4.35 0.00 41.90 3.85
4107 6378 5.584649 TGGTTTTTAGTATGGATCAAGAGCG 59.415 40.000 0.00 0.00 0.00 5.03
4125 6396 9.302345 TCAAGAGCGTGTAGATTTTCTTATAAG 57.698 33.333 6.11 6.11 0.00 1.73
4165 6483 6.712095 TGGCTGTAATCCTGATGATTAATGTC 59.288 38.462 0.00 0.00 45.24 3.06
4200 6518 5.866633 GGTTCTGATTATCTCGATCATGACC 59.133 44.000 0.00 0.00 34.32 4.02
4249 6567 0.905357 GGCTGTGTCTGGTCTGGTAT 59.095 55.000 0.00 0.00 0.00 2.73
4254 6572 3.764434 CTGTGTCTGGTCTGGTATGTAGT 59.236 47.826 0.00 0.00 0.00 2.73
4278 6596 2.237893 TCCCTCCGTCCCAAAATAAGTC 59.762 50.000 0.00 0.00 0.00 3.01
4284 6602 5.243207 TCCGTCCCAAAATAAGTCTCTTTC 58.757 41.667 0.00 0.00 0.00 2.62
4332 6671 7.129504 ACTTATTTTGGAATGGAGGGAGTATCT 59.870 37.037 0.00 0.00 33.73 1.98
4435 6775 0.328258 AAACTGGGATGGACGGGAAG 59.672 55.000 0.00 0.00 0.00 3.46
4593 6955 7.435305 TGAATTCTGCAATTGATGTTCTTCAA 58.565 30.769 10.34 4.16 39.77 2.69
4595 6957 7.884816 ATTCTGCAATTGATGTTCTTCAAAG 57.115 32.000 10.34 3.75 38.98 2.77
4662 7024 0.249405 CAGCTTTCGCTTGGGCAAAA 60.249 50.000 0.00 0.00 46.47 2.44
4773 7140 5.195185 TCTGCCTTGCTTATCATTTGATGA 58.805 37.500 3.30 0.00 44.55 2.92
4844 7211 3.807209 GCTGACCTCTCCAGTTTTAGCAA 60.807 47.826 0.00 0.00 34.29 3.91
4875 7242 5.221641 TGAGAATTTCTGGAGTTCCTTTCGA 60.222 40.000 3.03 0.00 36.82 3.71
4886 7253 5.106515 GGAGTTCCTTTCGAAGAAGAATTGG 60.107 44.000 0.00 0.00 45.90 3.16
4889 7256 6.427242 AGTTCCTTTCGAAGAAGAATTGGTAC 59.573 38.462 0.00 0.00 45.90 3.34
4890 7257 5.860611 TCCTTTCGAAGAAGAATTGGTACA 58.139 37.500 0.00 0.00 45.90 2.90
4891 7258 5.932303 TCCTTTCGAAGAAGAATTGGTACAG 59.068 40.000 0.00 0.00 45.90 2.74
4901 7297 5.179452 AGAATTGGTACAGGTATTGCTGT 57.821 39.130 0.00 0.00 42.39 4.40
4906 7302 3.774766 TGGTACAGGTATTGCTGTGATCT 59.225 43.478 0.00 0.00 35.26 2.75
4907 7303 4.141937 TGGTACAGGTATTGCTGTGATCTC 60.142 45.833 0.00 0.00 35.26 2.75
4908 7304 4.100189 GGTACAGGTATTGCTGTGATCTCT 59.900 45.833 0.00 0.00 35.26 3.10
4931 7327 7.220030 TCTTCTTCTTTTCTTGTCACTGCTAT 58.780 34.615 0.00 0.00 0.00 2.97
4933 7329 6.524734 TCTTCTTTTCTTGTCACTGCTATCA 58.475 36.000 0.00 0.00 0.00 2.15
4991 7390 1.067142 TCAGAAATAAGCACGTCGCCT 60.067 47.619 6.39 0.00 44.04 5.52
5034 7433 0.395686 AAGCAGCTGAAGCAGACAGA 59.604 50.000 20.43 0.00 45.16 3.41
5035 7434 0.614294 AGCAGCTGAAGCAGACAGAT 59.386 50.000 20.43 0.22 45.16 2.90
5107 7570 5.643777 GCATGGTGGTGATACCTGTATAATC 59.356 44.000 0.00 0.00 41.43 1.75
5227 7693 7.177744 TGGAAAACCTTATCTTTATTCCCACAC 59.822 37.037 0.00 0.00 35.18 3.82
5275 8720 4.454504 TCTGTTTATCTTTCGCTGAAACCC 59.545 41.667 0.55 0.00 30.61 4.11
5332 8777 2.300956 ACACATGTGCCCCAAATGTA 57.699 45.000 25.68 0.00 39.96 2.29
5393 8838 0.798776 CCGGTTCAGTCAGCATTGTC 59.201 55.000 0.00 0.00 0.00 3.18
5538 8984 6.483974 AGAACTGATGATGATTGCTTCAGATC 59.516 38.462 11.78 9.76 38.89 2.75
5542 8988 4.347360 TGATGATTGCTTCAGATCCGAT 57.653 40.909 0.00 0.00 37.89 4.18
5577 9025 7.686938 GTGTCGTACTAAAATTGTATGTGCTTC 59.313 37.037 0.00 0.00 0.00 3.86
5713 9164 4.627035 TCTCATTCAATGACACGCAACTAG 59.373 41.667 0.00 0.00 35.06 2.57
5774 9225 1.942657 CTGGAATGTACATGCCTTCGG 59.057 52.381 29.56 15.20 37.41 4.30
5817 9268 7.824779 AGCTCACTAGATCGTGATACATGTATA 59.175 37.037 18.28 3.45 42.51 1.47
5851 9309 2.062177 GCAATCAGCAGGGGCCATT 61.062 57.895 4.39 0.00 44.79 3.16
5852 9310 1.820581 CAATCAGCAGGGGCCATTG 59.179 57.895 4.39 4.12 42.56 2.82
5888 9346 3.252215 TGCCAAGTTGAAATGAGTAACGG 59.748 43.478 3.87 0.00 0.00 4.44
5896 9354 1.571919 AATGAGTAACGGAGATGCGC 58.428 50.000 0.00 0.00 0.00 6.09
5897 9355 0.595053 ATGAGTAACGGAGATGCGCG 60.595 55.000 0.00 0.00 0.00 6.86
5898 9356 1.944676 GAGTAACGGAGATGCGCGG 60.945 63.158 8.83 0.00 0.00 6.46
5909 9368 1.609840 GATGCGCGGCGTCTCTTATC 61.610 60.000 24.46 13.43 40.94 1.75
5912 9371 2.296480 CGCGGCGTCTCTTATCTGC 61.296 63.158 15.36 0.00 0.00 4.26
5917 9376 1.413382 GCGTCTCTTATCTGCATCCG 58.587 55.000 0.00 0.00 0.00 4.18
5919 9378 2.352225 GCGTCTCTTATCTGCATCCGAT 60.352 50.000 0.00 0.00 0.00 4.18
5922 9381 4.393371 CGTCTCTTATCTGCATCCGATAGA 59.607 45.833 0.00 0.00 39.76 1.98
5924 9383 4.946772 TCTCTTATCTGCATCCGATAGAGG 59.053 45.833 14.11 4.48 39.76 3.69
5925 9384 4.019858 TCTTATCTGCATCCGATAGAGGG 58.980 47.826 0.00 0.00 39.76 4.30
5926 9385 0.901124 ATCTGCATCCGATAGAGGGC 59.099 55.000 0.00 0.00 39.76 5.19
5927 9386 0.469892 TCTGCATCCGATAGAGGGCA 60.470 55.000 0.00 0.00 36.64 5.36
5928 9387 0.394192 CTGCATCCGATAGAGGGCAA 59.606 55.000 0.00 0.00 38.02 4.52
5929 9388 0.106708 TGCATCCGATAGAGGGCAAC 59.893 55.000 0.00 0.00 36.21 4.17
5930 9389 0.394565 GCATCCGATAGAGGGCAACT 59.605 55.000 0.00 0.00 39.76 3.16
5931 9390 1.618837 GCATCCGATAGAGGGCAACTA 59.381 52.381 0.00 0.00 39.76 2.24
5933 9392 1.329256 TCCGATAGAGGGCAACTAGC 58.671 55.000 0.00 0.00 40.54 3.42
5934 9393 0.039074 CCGATAGAGGGCAACTAGCG 60.039 60.000 16.54 16.54 45.23 4.26
5935 9394 0.669077 CGATAGAGGGCAACTAGCGT 59.331 55.000 15.69 0.00 42.25 5.07
5936 9395 1.600663 CGATAGAGGGCAACTAGCGTG 60.601 57.143 15.69 0.00 42.25 5.34
5949 9408 3.585990 GCGTGCAGCCACACACTT 61.586 61.111 7.41 0.00 42.17 3.16
5950 9409 2.328989 CGTGCAGCCACACACTTG 59.671 61.111 7.41 0.00 42.17 3.16
5951 9410 2.723746 GTGCAGCCACACACTTGG 59.276 61.111 1.98 0.00 41.67 3.61
5952 9411 2.519063 TGCAGCCACACACTTGGG 60.519 61.111 0.00 0.00 37.10 4.12
5987 9446 3.753434 CTCGCTCGTCCTGCACCT 61.753 66.667 0.00 0.00 0.00 4.00
5988 9447 3.288308 CTCGCTCGTCCTGCACCTT 62.288 63.158 0.00 0.00 0.00 3.50
5989 9448 3.114616 CGCTCGTCCTGCACCTTG 61.115 66.667 0.00 0.00 0.00 3.61
5990 9449 2.031163 GCTCGTCCTGCACCTTGT 59.969 61.111 0.00 0.00 0.00 3.16
5991 9450 1.598130 GCTCGTCCTGCACCTTGTT 60.598 57.895 0.00 0.00 0.00 2.83
5992 9451 1.166531 GCTCGTCCTGCACCTTGTTT 61.167 55.000 0.00 0.00 0.00 2.83
5993 9452 1.308998 CTCGTCCTGCACCTTGTTTT 58.691 50.000 0.00 0.00 0.00 2.43
5994 9453 1.002468 CTCGTCCTGCACCTTGTTTTG 60.002 52.381 0.00 0.00 0.00 2.44
5995 9454 0.030638 CGTCCTGCACCTTGTTTTGG 59.969 55.000 0.00 0.00 0.00 3.28
5996 9455 0.249447 GTCCTGCACCTTGTTTTGGC 60.249 55.000 0.00 0.00 0.00 4.52
5997 9456 0.396974 TCCTGCACCTTGTTTTGGCT 60.397 50.000 0.00 0.00 0.00 4.75
5998 9457 0.249573 CCTGCACCTTGTTTTGGCTG 60.250 55.000 0.00 0.00 0.00 4.85
5999 9458 0.249573 CTGCACCTTGTTTTGGCTGG 60.250 55.000 0.00 0.00 0.00 4.85
6000 9459 1.595109 GCACCTTGTTTTGGCTGGC 60.595 57.895 0.00 0.00 0.00 4.85
6001 9460 1.069596 CACCTTGTTTTGGCTGGCC 59.930 57.895 4.43 4.43 0.00 5.36
6002 9461 1.382420 ACCTTGTTTTGGCTGGCCA 60.382 52.632 10.55 10.55 45.63 5.36
6010 9469 2.436109 TGGCTGGCCACTTCCTTC 59.564 61.111 10.55 0.00 41.89 3.46
6011 9470 2.747855 GGCTGGCCACTTCCTTCG 60.748 66.667 0.00 0.00 35.81 3.79
6012 9471 3.435186 GCTGGCCACTTCCTTCGC 61.435 66.667 0.00 0.00 0.00 4.70
6013 9472 2.348998 CTGGCCACTTCCTTCGCT 59.651 61.111 0.00 0.00 0.00 4.93
6014 9473 2.032528 TGGCCACTTCCTTCGCTG 59.967 61.111 0.00 0.00 0.00 5.18
6015 9474 2.747855 GGCCACTTCCTTCGCTGG 60.748 66.667 0.00 0.00 0.00 4.85
6016 9475 2.032681 GCCACTTCCTTCGCTGGT 59.967 61.111 0.00 0.00 0.00 4.00
6017 9476 1.600916 GCCACTTCCTTCGCTGGTT 60.601 57.895 0.00 0.00 0.00 3.67
6018 9477 1.578206 GCCACTTCCTTCGCTGGTTC 61.578 60.000 0.00 0.00 0.00 3.62
6019 9478 1.291877 CCACTTCCTTCGCTGGTTCG 61.292 60.000 0.00 0.00 0.00 3.95
6020 9479 0.600255 CACTTCCTTCGCTGGTTCGT 60.600 55.000 0.00 0.00 0.00 3.85
6021 9480 0.106149 ACTTCCTTCGCTGGTTCGTT 59.894 50.000 0.00 0.00 0.00 3.85
6022 9481 0.512952 CTTCCTTCGCTGGTTCGTTG 59.487 55.000 0.00 0.00 0.00 4.10
6023 9482 0.179067 TTCCTTCGCTGGTTCGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
6024 9483 0.179067 TCCTTCGCTGGTTCGTTGTT 60.179 50.000 0.00 0.00 0.00 2.83
6025 9484 0.041312 CCTTCGCTGGTTCGTTGTTG 60.041 55.000 0.00 0.00 0.00 3.33
6026 9485 0.934496 CTTCGCTGGTTCGTTGTTGA 59.066 50.000 0.00 0.00 0.00 3.18
6027 9486 0.653636 TTCGCTGGTTCGTTGTTGAC 59.346 50.000 0.00 0.00 0.00 3.18
6028 9487 0.179094 TCGCTGGTTCGTTGTTGACT 60.179 50.000 0.00 0.00 0.00 3.41
6029 9488 0.042188 CGCTGGTTCGTTGTTGACTG 60.042 55.000 0.00 0.00 0.00 3.51
6030 9489 0.307760 GCTGGTTCGTTGTTGACTGG 59.692 55.000 0.00 0.00 0.00 4.00
6031 9490 0.944386 CTGGTTCGTTGTTGACTGGG 59.056 55.000 0.00 0.00 0.00 4.45
6032 9491 1.098712 TGGTTCGTTGTTGACTGGGC 61.099 55.000 0.00 0.00 0.00 5.36
6033 9492 1.278637 GTTCGTTGTTGACTGGGCG 59.721 57.895 0.00 0.00 0.00 6.13
6034 9493 2.539338 TTCGTTGTTGACTGGGCGC 61.539 57.895 0.00 0.00 0.00 6.53
6035 9494 2.933878 TTCGTTGTTGACTGGGCGCT 62.934 55.000 7.64 0.00 0.00 5.92
6036 9495 2.639286 GTTGTTGACTGGGCGCTG 59.361 61.111 7.64 6.09 0.00 5.18
6037 9496 2.594303 TTGTTGACTGGGCGCTGG 60.594 61.111 7.64 0.00 0.00 4.85
6038 9497 4.641645 TGTTGACTGGGCGCTGGG 62.642 66.667 7.64 0.00 0.00 4.45
6039 9498 4.643387 GTTGACTGGGCGCTGGGT 62.643 66.667 7.64 3.07 0.00 4.51
6040 9499 3.884774 TTGACTGGGCGCTGGGTT 61.885 61.111 7.64 0.00 0.00 4.11
6041 9500 3.842925 TTGACTGGGCGCTGGGTTC 62.843 63.158 7.64 0.00 0.00 3.62
6050 9509 3.426568 GCTGGGTTCGCTGCTGAC 61.427 66.667 10.39 0.00 0.00 3.51
6051 9510 2.345244 CTGGGTTCGCTGCTGACT 59.655 61.111 0.00 0.00 0.00 3.41
6052 9511 2.031012 TGGGTTCGCTGCTGACTG 59.969 61.111 0.00 0.00 0.00 3.51
6053 9512 2.343758 GGGTTCGCTGCTGACTGA 59.656 61.111 0.00 0.00 0.00 3.41
6054 9513 1.078848 GGGTTCGCTGCTGACTGAT 60.079 57.895 0.00 0.00 0.00 2.90
6055 9514 1.086634 GGGTTCGCTGCTGACTGATC 61.087 60.000 0.00 0.00 0.00 2.92
6056 9515 0.390340 GGTTCGCTGCTGACTGATCA 60.390 55.000 0.00 0.00 0.00 2.92
6057 9516 0.718343 GTTCGCTGCTGACTGATCAC 59.282 55.000 0.00 0.00 0.00 3.06
6058 9517 0.733909 TTCGCTGCTGACTGATCACG 60.734 55.000 0.00 0.00 0.00 4.35
6059 9518 2.163390 CGCTGCTGACTGATCACGG 61.163 63.158 0.00 0.00 0.00 4.94
6060 9519 1.079543 GCTGCTGACTGATCACGGT 60.080 57.895 0.00 0.00 38.45 4.83
6061 9520 0.671781 GCTGCTGACTGATCACGGTT 60.672 55.000 0.00 0.00 35.56 4.44
6062 9521 1.073964 CTGCTGACTGATCACGGTTG 58.926 55.000 0.00 0.00 35.56 3.77
6063 9522 0.678950 TGCTGACTGATCACGGTTGA 59.321 50.000 0.00 0.00 35.56 3.18
6064 9523 1.071605 GCTGACTGATCACGGTTGAC 58.928 55.000 0.00 0.00 35.56 3.18
6065 9524 1.337260 GCTGACTGATCACGGTTGACT 60.337 52.381 0.00 0.00 35.56 3.41
6066 9525 2.868044 GCTGACTGATCACGGTTGACTT 60.868 50.000 0.00 0.00 35.56 3.01
6067 9526 3.393800 CTGACTGATCACGGTTGACTTT 58.606 45.455 0.00 0.00 35.56 2.66
6068 9527 4.556233 CTGACTGATCACGGTTGACTTTA 58.444 43.478 0.00 0.00 35.56 1.85
6069 9528 4.556233 TGACTGATCACGGTTGACTTTAG 58.444 43.478 0.00 0.00 35.56 1.85
6070 9529 3.926616 ACTGATCACGGTTGACTTTAGG 58.073 45.455 0.00 0.00 33.38 2.69
6071 9530 3.576982 ACTGATCACGGTTGACTTTAGGA 59.423 43.478 0.00 0.00 33.38 2.94
6072 9531 4.039973 ACTGATCACGGTTGACTTTAGGAA 59.960 41.667 0.00 0.00 33.38 3.36
6073 9532 4.963373 TGATCACGGTTGACTTTAGGAAA 58.037 39.130 0.00 0.00 33.38 3.13
6074 9533 5.369833 TGATCACGGTTGACTTTAGGAAAA 58.630 37.500 0.00 0.00 33.38 2.29
6075 9534 5.823570 TGATCACGGTTGACTTTAGGAAAAA 59.176 36.000 0.00 0.00 33.38 1.94
6109 9568 9.883142 AATCCTAAAACAATTCACAAAAAGTCA 57.117 25.926 0.00 0.00 0.00 3.41
6110 9569 9.883142 ATCCTAAAACAATTCACAAAAAGTCAA 57.117 25.926 0.00 0.00 0.00 3.18
6111 9570 9.712305 TCCTAAAACAATTCACAAAAAGTCAAA 57.288 25.926 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 196 4.838152 GGAATGGCCTCGCTGCGA 62.838 66.667 24.43 24.43 0.00 5.10
925 961 2.924903 TGTGACTGTAGCGACTTTACG 58.075 47.619 0.00 0.00 0.00 3.18
926 962 4.296690 AGTTGTGACTGTAGCGACTTTAC 58.703 43.478 0.00 0.00 33.99 2.01
927 963 4.277672 AGAGTTGTGACTGTAGCGACTTTA 59.722 41.667 0.00 0.00 35.88 1.85
928 964 3.068307 AGAGTTGTGACTGTAGCGACTTT 59.932 43.478 0.00 0.00 35.88 2.66
929 965 2.623889 AGAGTTGTGACTGTAGCGACTT 59.376 45.455 0.00 0.00 35.88 3.01
932 968 2.030185 GGAAGAGTTGTGACTGTAGCGA 60.030 50.000 0.00 0.00 35.88 4.93
933 969 2.288213 TGGAAGAGTTGTGACTGTAGCG 60.288 50.000 0.00 0.00 35.88 4.26
934 970 3.060602 GTGGAAGAGTTGTGACTGTAGC 58.939 50.000 0.00 0.00 35.88 3.58
935 971 4.322080 TGTGGAAGAGTTGTGACTGTAG 57.678 45.455 0.00 0.00 35.88 2.74
936 972 4.161565 AGTTGTGGAAGAGTTGTGACTGTA 59.838 41.667 0.00 0.00 35.88 2.74
937 973 3.055094 AGTTGTGGAAGAGTTGTGACTGT 60.055 43.478 0.00 0.00 35.88 3.55
938 974 3.535561 AGTTGTGGAAGAGTTGTGACTG 58.464 45.455 0.00 0.00 35.88 3.51
939 975 3.914426 AGTTGTGGAAGAGTTGTGACT 57.086 42.857 0.00 0.00 39.32 3.41
940 976 4.873827 TGTTAGTTGTGGAAGAGTTGTGAC 59.126 41.667 0.00 0.00 0.00 3.67
941 977 5.092554 TGTTAGTTGTGGAAGAGTTGTGA 57.907 39.130 0.00 0.00 0.00 3.58
942 978 5.584649 TCTTGTTAGTTGTGGAAGAGTTGTG 59.415 40.000 0.00 0.00 0.00 3.33
943 979 5.741011 TCTTGTTAGTTGTGGAAGAGTTGT 58.259 37.500 0.00 0.00 0.00 3.32
944 980 5.277538 GCTCTTGTTAGTTGTGGAAGAGTTG 60.278 44.000 0.00 0.00 41.09 3.16
953 989 5.695851 AATGGAAGCTCTTGTTAGTTGTG 57.304 39.130 0.00 0.00 0.00 3.33
959 995 4.253685 CGAGGAAATGGAAGCTCTTGTTA 58.746 43.478 0.00 0.00 0.00 2.41
1017 1056 5.869888 GGCTCAGAAAAATCGACTCTTTAGA 59.130 40.000 0.00 0.00 0.00 2.10
1018 1057 5.220303 CGGCTCAGAAAAATCGACTCTTTAG 60.220 44.000 0.00 0.00 0.00 1.85
1020 1059 3.433615 CGGCTCAGAAAAATCGACTCTTT 59.566 43.478 0.00 0.00 0.00 2.52
1034 1073 3.071206 GGAGGACAGCGGCTCAGA 61.071 66.667 0.00 0.00 0.00 3.27
1090 1129 2.524951 TACCTTGGTTTAGGCGGCGG 62.525 60.000 9.78 0.00 38.99 6.13
1185 1234 5.913137 ATTGGAGAGAGGATATCATCGAC 57.087 43.478 11.47 9.89 0.00 4.20
1567 1675 2.999063 GGGAAGGGTCGAACGGGA 60.999 66.667 0.00 0.00 0.00 5.14
1868 2009 2.631062 TCCTGTCATGTACGTTTCCACT 59.369 45.455 0.00 0.00 0.00 4.00
2147 2315 1.491670 AATCATCGACGGAAGATGCG 58.508 50.000 10.77 0.00 43.68 4.73
2149 2317 7.637709 TTATTGTAATCATCGACGGAAGATG 57.362 36.000 9.73 9.73 44.95 2.90
2347 2542 4.470462 CATATCGTACGCTACCAAGGTAC 58.530 47.826 11.24 0.00 34.60 3.34
2482 2697 1.787012 CACAAGCATGGTTTGAAGGC 58.213 50.000 7.57 0.00 0.00 4.35
2939 3475 4.943705 TGTGATTAACAGATCCAAAGCTCC 59.056 41.667 0.00 0.00 33.78 4.70
3092 4033 9.244799 CACAAACTAATATCGTGTATGAAGCTA 57.755 33.333 0.00 0.00 0.00 3.32
3139 5128 7.685481 TCAACCACACCAAGAGATCTTATTTA 58.315 34.615 0.00 0.00 34.28 1.40
3362 5437 1.642728 AAACTGTTACACGCGTGACA 58.357 45.000 42.94 33.52 39.14 3.58
3363 5438 2.724744 AAAACTGTTACACGCGTGAC 57.275 45.000 42.94 31.01 32.40 3.67
3364 5439 6.365518 TGAATATAAAACTGTTACACGCGTGA 59.634 34.615 42.94 24.54 0.00 4.35
3365 5440 6.527089 TGAATATAAAACTGTTACACGCGTG 58.473 36.000 35.99 35.99 0.00 5.34
3366 5441 6.709145 TGAATATAAAACTGTTACACGCGT 57.291 33.333 5.58 5.58 0.00 6.01
3392 5467 1.408266 GGGATTCAAGCCGGCTCTTTA 60.408 52.381 32.93 16.13 0.00 1.85
3394 5469 1.077429 GGGATTCAAGCCGGCTCTT 60.077 57.895 32.93 13.32 0.00 2.85
3397 5472 1.678970 GTTGGGATTCAAGCCGGCT 60.679 57.895 27.08 27.08 35.80 5.52
3398 5473 0.393808 TAGTTGGGATTCAAGCCGGC 60.394 55.000 21.89 21.89 35.80 6.13
3399 5474 1.065418 ACTAGTTGGGATTCAAGCCGG 60.065 52.381 0.00 0.00 35.80 6.13
3400 5475 2.403252 ACTAGTTGGGATTCAAGCCG 57.597 50.000 0.00 0.00 35.80 5.52
3715 5936 1.776662 TGATGTAGGGAAGGTCTCCG 58.223 55.000 0.00 0.00 46.51 4.63
3733 5954 4.059511 TGTTGAATCTTTGCTGCCATTTG 58.940 39.130 0.00 0.00 0.00 2.32
3797 6019 8.007152 CGCGTGCAAAAAGTTGACATATATATA 58.993 33.333 0.00 0.00 36.83 0.86
3920 6145 6.980978 TGAAAACAAACGATATTTTTCTGCCA 59.019 30.769 13.86 0.00 38.32 4.92
3965 6190 2.337879 AAACTCCCGACAGCAGCCAA 62.338 55.000 0.00 0.00 0.00 4.52
3966 6191 2.731691 GAAACTCCCGACAGCAGCCA 62.732 60.000 0.00 0.00 0.00 4.75
3967 6192 2.032681 AAACTCCCGACAGCAGCC 59.967 61.111 0.00 0.00 0.00 4.85
3968 6193 0.603975 AAGAAACTCCCGACAGCAGC 60.604 55.000 0.00 0.00 0.00 5.25
3969 6194 1.151668 CAAGAAACTCCCGACAGCAG 58.848 55.000 0.00 0.00 0.00 4.24
3970 6195 0.468226 ACAAGAAACTCCCGACAGCA 59.532 50.000 0.00 0.00 0.00 4.41
3977 6202 6.420903 GCAAGTTTATGAAACAAGAAACTCCC 59.579 38.462 12.22 6.36 43.79 4.30
4001 6259 5.243283 TCCCTTTCATATCGACCTACTAAGC 59.757 44.000 0.00 0.00 0.00 3.09
4008 6266 3.134804 CACCTTCCCTTTCATATCGACCT 59.865 47.826 0.00 0.00 0.00 3.85
4012 6270 2.874701 CTGCACCTTCCCTTTCATATCG 59.125 50.000 0.00 0.00 0.00 2.92
4087 6351 5.730550 ACACGCTCTTGATCCATACTAAAA 58.269 37.500 0.00 0.00 0.00 1.52
4107 6378 7.281100 ACAGGCAGCTTATAAGAAAATCTACAC 59.719 37.037 16.85 0.00 0.00 2.90
4125 6396 1.821332 GCCATACCAGACAGGCAGC 60.821 63.158 0.00 0.00 46.26 5.25
4165 6483 1.238439 ATCAGAACCTGGCAAACACG 58.762 50.000 0.00 0.00 31.51 4.49
4200 6518 2.014068 GCATTCCTTCCTGAACCTCCG 61.014 57.143 0.00 0.00 0.00 4.63
4249 6567 0.257039 GGGACGGAGGGAGTACTACA 59.743 60.000 7.57 0.00 0.00 2.74
4254 6572 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4317 6656 3.686691 GCAAGCAAGATACTCCCTCCATT 60.687 47.826 0.00 0.00 0.00 3.16
4332 6671 7.938140 ATAATGAGGTTAAGTAAGCAAGCAA 57.062 32.000 3.33 0.00 36.22 3.91
4387 6726 7.210718 ACACAGGCTTAAAATGTTAACTACC 57.789 36.000 7.22 0.00 0.00 3.18
4388 6727 8.776470 TGTACACAGGCTTAAAATGTTAACTAC 58.224 33.333 7.22 0.00 0.00 2.73
4435 6775 2.673368 CGGGCTTGAAGAGTTGTATCAC 59.327 50.000 0.00 0.00 0.00 3.06
4593 6955 0.912486 ATTAGACTTGAGCCCGGCTT 59.088 50.000 14.70 0.00 39.88 4.35
4595 6957 2.614829 TTATTAGACTTGAGCCCGGC 57.385 50.000 0.00 0.00 0.00 6.13
4662 7024 1.130054 ATCCTAGATGGGGCGCACAT 61.130 55.000 13.89 14.85 36.20 3.21
4844 7211 5.240013 ACTCCAGAAATTCTCAGAGCTTT 57.760 39.130 15.65 0.00 30.73 3.51
4875 7242 6.375455 CAGCAATACCTGTACCAATTCTTCTT 59.625 38.462 0.00 0.00 0.00 2.52
4886 7253 5.269505 AGAGATCACAGCAATACCTGTAC 57.730 43.478 0.00 0.00 43.85 2.90
4889 7256 5.021033 AGAAGAGATCACAGCAATACCTG 57.979 43.478 0.00 0.00 38.78 4.00
4890 7257 5.424895 AGAAGAAGAGATCACAGCAATACCT 59.575 40.000 0.00 0.00 0.00 3.08
4891 7258 5.669477 AGAAGAAGAGATCACAGCAATACC 58.331 41.667 0.00 0.00 0.00 2.73
4901 7297 7.440556 CAGTGACAAGAAAAGAAGAAGAGATCA 59.559 37.037 0.00 0.00 0.00 2.92
4906 7302 5.431765 AGCAGTGACAAGAAAAGAAGAAGA 58.568 37.500 0.00 0.00 0.00 2.87
4907 7303 5.747951 AGCAGTGACAAGAAAAGAAGAAG 57.252 39.130 0.00 0.00 0.00 2.85
4908 7304 6.992123 TGATAGCAGTGACAAGAAAAGAAGAA 59.008 34.615 0.00 0.00 0.00 2.52
4931 7327 1.277273 CTGAACACAGCAGGGAGATGA 59.723 52.381 0.00 0.00 37.02 2.92
4933 7329 1.356124 ACTGAACACAGCAGGGAGAT 58.644 50.000 0.00 0.00 37.69 2.75
4991 7390 4.038522 TGTCGGCAATCTTGAATGGAAAAA 59.961 37.500 0.00 0.00 0.00 1.94
5227 7693 5.455056 ACCTACTCTCACAAGTAACACTG 57.545 43.478 0.00 0.00 31.56 3.66
5393 8838 8.319881 AGATCATCACATCCCAAACATATAGAG 58.680 37.037 0.00 0.00 0.00 2.43
5442 8888 6.788598 TTCATCTCTTCTCAGCTCATACTT 57.211 37.500 0.00 0.00 0.00 2.24
5577 9025 7.492020 AGAGAAGTGCTATATATACCTACGACG 59.508 40.741 0.00 0.00 0.00 5.12
5632 9083 9.765795 GCTAGCTATACTTTTCTATGGAAAGAA 57.234 33.333 7.70 0.00 41.66 2.52
5633 9084 8.924303 TGCTAGCTATACTTTTCTATGGAAAGA 58.076 33.333 17.23 0.00 41.66 2.52
5634 9085 9.717942 ATGCTAGCTATACTTTTCTATGGAAAG 57.282 33.333 17.23 2.63 41.66 2.62
5697 9148 9.554724 AAAATTAATACTAGTTGCGTGTCATTG 57.445 29.630 0.00 0.00 0.00 2.82
5817 9268 1.765230 TTGCCGTTGGTGGTTTACTT 58.235 45.000 0.00 0.00 0.00 2.24
5851 9309 0.401356 TGGCACTTGAAGATGCTCCA 59.599 50.000 15.58 6.99 41.74 3.86
5852 9310 1.471684 CTTGGCACTTGAAGATGCTCC 59.528 52.381 15.58 5.08 41.74 4.70
5879 9337 1.226575 CGCGCATCTCCGTTACTCA 60.227 57.895 8.75 0.00 0.00 3.41
5888 9346 2.663630 TAAGAGACGCCGCGCATCTC 62.664 60.000 20.23 20.23 39.38 2.75
5896 9354 1.413382 GATGCAGATAAGAGACGCCG 58.587 55.000 0.00 0.00 0.00 6.46
5897 9355 1.789506 GGATGCAGATAAGAGACGCC 58.210 55.000 0.00 0.00 0.00 5.68
5898 9356 1.001268 TCGGATGCAGATAAGAGACGC 60.001 52.381 0.00 0.00 0.00 5.19
5906 9365 2.103373 GCCCTCTATCGGATGCAGATA 58.897 52.381 0.00 0.00 0.00 1.98
5909 9368 0.394192 TTGCCCTCTATCGGATGCAG 59.606 55.000 0.00 0.00 34.59 4.41
5912 9371 2.353208 GCTAGTTGCCCTCTATCGGATG 60.353 54.545 0.00 0.00 35.15 3.51
5917 9376 1.870167 GCACGCTAGTTGCCCTCTATC 60.870 57.143 7.12 0.00 38.78 2.08
5919 9378 1.254975 TGCACGCTAGTTGCCCTCTA 61.255 55.000 13.86 0.00 38.78 2.43
5922 9381 2.046892 CTGCACGCTAGTTGCCCT 60.047 61.111 13.86 0.00 38.78 5.19
5924 9383 3.804193 GGCTGCACGCTAGTTGCC 61.804 66.667 13.86 1.19 38.78 4.52
5925 9384 3.049674 TGGCTGCACGCTAGTTGC 61.050 61.111 10.59 10.59 39.13 4.17
5926 9385 1.960763 TGTGGCTGCACGCTAGTTG 60.961 57.895 0.50 0.00 39.13 3.16
5927 9386 1.961277 GTGTGGCTGCACGCTAGTT 60.961 57.895 0.50 0.00 39.13 2.24
5928 9387 2.357517 GTGTGGCTGCACGCTAGT 60.358 61.111 0.50 0.00 39.13 2.57
5929 9388 2.357396 TGTGTGGCTGCACGCTAG 60.357 61.111 0.50 0.00 41.94 3.42
5930 9389 2.664851 GTGTGTGGCTGCACGCTA 60.665 61.111 15.36 0.00 44.00 4.26
5933 9392 2.328989 CAAGTGTGTGGCTGCACG 59.671 61.111 0.50 0.00 41.94 5.34
5934 9393 2.723746 CCAAGTGTGTGGCTGCAC 59.276 61.111 0.50 5.96 39.65 4.57
5935 9394 2.519063 CCCAAGTGTGTGGCTGCA 60.519 61.111 0.50 0.00 37.34 4.41
5936 9395 3.982241 GCCCAAGTGTGTGGCTGC 61.982 66.667 0.00 0.00 37.82 5.25
5937 9396 3.297620 GGCCCAAGTGTGTGGCTG 61.298 66.667 0.00 0.00 39.64 4.85
5938 9397 4.954970 CGGCCCAAGTGTGTGGCT 62.955 66.667 0.00 0.00 39.64 4.75
5970 9429 3.288308 AAGGTGCAGGACGAGCGAG 62.288 63.158 0.00 0.00 33.85 5.03
5971 9430 3.303135 AAGGTGCAGGACGAGCGA 61.303 61.111 0.00 0.00 33.85 4.93
5972 9431 3.114616 CAAGGTGCAGGACGAGCG 61.115 66.667 0.00 0.00 33.85 5.03
5973 9432 1.166531 AAACAAGGTGCAGGACGAGC 61.167 55.000 0.00 0.00 0.00 5.03
5974 9433 1.002468 CAAAACAAGGTGCAGGACGAG 60.002 52.381 0.00 0.00 0.00 4.18
5975 9434 1.021202 CAAAACAAGGTGCAGGACGA 58.979 50.000 0.00 0.00 0.00 4.20
5976 9435 0.030638 CCAAAACAAGGTGCAGGACG 59.969 55.000 0.00 0.00 0.00 4.79
5977 9436 0.249447 GCCAAAACAAGGTGCAGGAC 60.249 55.000 0.00 0.00 0.00 3.85
5978 9437 0.396974 AGCCAAAACAAGGTGCAGGA 60.397 50.000 0.00 0.00 0.00 3.86
5979 9438 0.249573 CAGCCAAAACAAGGTGCAGG 60.250 55.000 0.00 0.00 0.00 4.85
5980 9439 0.249573 CCAGCCAAAACAAGGTGCAG 60.250 55.000 0.00 0.00 0.00 4.41
5981 9440 1.821936 CCAGCCAAAACAAGGTGCA 59.178 52.632 0.00 0.00 0.00 4.57
5982 9441 1.595109 GCCAGCCAAAACAAGGTGC 60.595 57.895 0.00 0.00 0.00 5.01
5983 9442 1.069596 GGCCAGCCAAAACAAGGTG 59.930 57.895 3.12 0.00 35.81 4.00
5984 9443 1.382420 TGGCCAGCCAAAACAAGGT 60.382 52.632 9.42 0.00 44.12 3.50
5985 9444 3.548488 TGGCCAGCCAAAACAAGG 58.452 55.556 9.42 0.00 44.12 3.61
5993 9452 2.436109 GAAGGAAGTGGCCAGCCA 59.564 61.111 5.11 7.43 45.02 4.75
5994 9453 2.747855 CGAAGGAAGTGGCCAGCC 60.748 66.667 5.11 8.64 0.00 4.85
5995 9454 3.435186 GCGAAGGAAGTGGCCAGC 61.435 66.667 5.11 0.00 0.00 4.85
5996 9455 2.037136 CAGCGAAGGAAGTGGCCAG 61.037 63.158 5.11 0.00 0.00 4.85
5997 9456 2.032528 CAGCGAAGGAAGTGGCCA 59.967 61.111 0.00 0.00 0.00 5.36
5998 9457 2.747855 CCAGCGAAGGAAGTGGCC 60.748 66.667 0.00 0.00 0.00 5.36
5999 9458 1.578206 GAACCAGCGAAGGAAGTGGC 61.578 60.000 0.16 0.00 32.91 5.01
6000 9459 1.291877 CGAACCAGCGAAGGAAGTGG 61.292 60.000 0.16 0.00 36.05 4.00
6001 9460 0.600255 ACGAACCAGCGAAGGAAGTG 60.600 55.000 0.16 0.00 34.83 3.16
6002 9461 0.106149 AACGAACCAGCGAAGGAAGT 59.894 50.000 0.16 0.00 34.83 3.01
6003 9462 0.512952 CAACGAACCAGCGAAGGAAG 59.487 55.000 0.16 0.00 34.83 3.46
6004 9463 0.179067 ACAACGAACCAGCGAAGGAA 60.179 50.000 0.16 0.00 34.83 3.36
6005 9464 0.179067 AACAACGAACCAGCGAAGGA 60.179 50.000 0.16 0.00 34.83 3.36
6006 9465 0.041312 CAACAACGAACCAGCGAAGG 60.041 55.000 0.00 0.00 34.83 3.46
6007 9466 0.934496 TCAACAACGAACCAGCGAAG 59.066 50.000 0.00 0.00 34.83 3.79
6008 9467 0.653636 GTCAACAACGAACCAGCGAA 59.346 50.000 0.00 0.00 34.83 4.70
6009 9468 0.179094 AGTCAACAACGAACCAGCGA 60.179 50.000 0.00 0.00 34.83 4.93
6010 9469 0.042188 CAGTCAACAACGAACCAGCG 60.042 55.000 0.00 0.00 37.29 5.18
6011 9470 0.307760 CCAGTCAACAACGAACCAGC 59.692 55.000 0.00 0.00 0.00 4.85
6012 9471 0.944386 CCCAGTCAACAACGAACCAG 59.056 55.000 0.00 0.00 0.00 4.00
6013 9472 1.098712 GCCCAGTCAACAACGAACCA 61.099 55.000 0.00 0.00 0.00 3.67
6014 9473 1.652563 GCCCAGTCAACAACGAACC 59.347 57.895 0.00 0.00 0.00 3.62
6015 9474 1.278637 CGCCCAGTCAACAACGAAC 59.721 57.895 0.00 0.00 0.00 3.95
6016 9475 2.539338 GCGCCCAGTCAACAACGAA 61.539 57.895 0.00 0.00 0.00 3.85
6017 9476 2.970324 GCGCCCAGTCAACAACGA 60.970 61.111 0.00 0.00 0.00 3.85
6018 9477 2.972505 AGCGCCCAGTCAACAACG 60.973 61.111 2.29 0.00 0.00 4.10
6019 9478 2.639286 CAGCGCCCAGTCAACAAC 59.361 61.111 2.29 0.00 0.00 3.32
6020 9479 2.594303 CCAGCGCCCAGTCAACAA 60.594 61.111 2.29 0.00 0.00 2.83
6021 9480 4.641645 CCCAGCGCCCAGTCAACA 62.642 66.667 2.29 0.00 0.00 3.33
6022 9481 4.643387 ACCCAGCGCCCAGTCAAC 62.643 66.667 2.29 0.00 0.00 3.18
6023 9482 3.842925 GAACCCAGCGCCCAGTCAA 62.843 63.158 2.29 0.00 0.00 3.18
6024 9483 4.329545 GAACCCAGCGCCCAGTCA 62.330 66.667 2.29 0.00 0.00 3.41
6033 9492 3.426568 GTCAGCAGCGAACCCAGC 61.427 66.667 0.00 0.00 0.00 4.85
6034 9493 2.031516 CAGTCAGCAGCGAACCCAG 61.032 63.158 0.00 0.00 0.00 4.45
6035 9494 1.830587 ATCAGTCAGCAGCGAACCCA 61.831 55.000 0.00 0.00 0.00 4.51
6036 9495 1.078848 ATCAGTCAGCAGCGAACCC 60.079 57.895 0.00 0.00 0.00 4.11
6037 9496 0.390340 TGATCAGTCAGCAGCGAACC 60.390 55.000 0.00 0.00 0.00 3.62
6038 9497 0.718343 GTGATCAGTCAGCAGCGAAC 59.282 55.000 0.00 0.00 34.36 3.95
6039 9498 0.733909 CGTGATCAGTCAGCAGCGAA 60.734 55.000 0.00 0.00 34.36 4.70
6040 9499 1.153958 CGTGATCAGTCAGCAGCGA 60.154 57.895 0.00 0.00 34.36 4.93
6041 9500 2.163390 CCGTGATCAGTCAGCAGCG 61.163 63.158 0.00 0.00 34.36 5.18
6042 9501 0.671781 AACCGTGATCAGTCAGCAGC 60.672 55.000 0.00 0.00 34.36 5.25
6043 9502 1.073964 CAACCGTGATCAGTCAGCAG 58.926 55.000 0.00 0.00 34.36 4.24
6044 9503 0.678950 TCAACCGTGATCAGTCAGCA 59.321 50.000 0.00 0.00 34.36 4.41
6045 9504 1.071605 GTCAACCGTGATCAGTCAGC 58.928 55.000 0.00 0.00 35.80 4.26
6046 9505 2.732412 AGTCAACCGTGATCAGTCAG 57.268 50.000 0.00 0.00 35.80 3.51
6047 9506 3.469008 AAAGTCAACCGTGATCAGTCA 57.531 42.857 0.00 0.00 35.80 3.41
6048 9507 3.927142 CCTAAAGTCAACCGTGATCAGTC 59.073 47.826 0.00 0.00 35.80 3.51
6049 9508 3.576982 TCCTAAAGTCAACCGTGATCAGT 59.423 43.478 0.00 0.00 35.80 3.41
6050 9509 4.188247 TCCTAAAGTCAACCGTGATCAG 57.812 45.455 0.00 0.00 35.80 2.90
6051 9510 4.610605 TTCCTAAAGTCAACCGTGATCA 57.389 40.909 0.00 0.00 35.80 2.92
6052 9511 5.934935 TTTTCCTAAAGTCAACCGTGATC 57.065 39.130 0.00 0.00 35.80 2.92
6083 9542 9.883142 TGACTTTTTGTGAATTGTTTTAGGATT 57.117 25.926 0.00 0.00 0.00 3.01
6084 9543 9.883142 TTGACTTTTTGTGAATTGTTTTAGGAT 57.117 25.926 0.00 0.00 0.00 3.24
6085 9544 9.712305 TTTGACTTTTTGTGAATTGTTTTAGGA 57.288 25.926 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.