Multiple sequence alignment - TraesCS2B01G144400

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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 TraesCS2B01G144400 chr2B 100.000 6379 0 0 1 6379 110485223 110478845 0.000000e+00 11780.0
1 TraesCS2B01G144400 chr2B 79.613 2271 269 84 1841 4047 545757984 545760124 0.000000e+00 1450.0
2 TraesCS2B01G144400 chr2B 86.027 365 50 1 4599 4963 129315907 129315544 2.160000e-104 390.0
3 TraesCS2B01G144400 chr2B 84.239 368 32 13 4222 4583 545760515 545760862 1.020000e-87 335.0
4 TraesCS2B01G144400 chr2B 82.203 354 52 4 2713 3058 110473335 110472985 1.740000e-75 294.0
5 TraesCS2B01G144400 chr2B 93.750 128 8 0 1497 1624 34111054 34111181 6.530000e-45 193.0
6 TraesCS2B01G144400 chr2B 92.537 134 9 1 1493 1625 136176803 136176670 2.350000e-44 191.0
7 TraesCS2B01G144400 chr2B 86.628 172 22 1 4599 4770 545761050 545761220 8.440000e-44 189.0
8 TraesCS2B01G144400 chr2B 79.268 164 14 8 3138 3292 110468714 110468562 5.260000e-16 97.1
9 TraesCS2B01G144400 chr2D 94.352 4320 154 26 1736 6017 73103192 73098925 0.000000e+00 6543.0
10 TraesCS2B01G144400 chr2D 90.665 1489 106 20 38 1499 73104939 73103457 0.000000e+00 1949.0
11 TraesCS2B01G144400 chr2D 80.345 2437 308 77 1878 4254 467060137 467062462 0.000000e+00 1688.0
12 TraesCS2B01G144400 chr2D 81.958 521 69 19 3641 4146 310718654 310718144 9.890000e-113 418.0
13 TraesCS2B01G144400 chr2D 80.588 340 31 19 4256 4583 467062614 467062930 4.970000e-56 230.0
14 TraesCS2B01G144400 chr2D 79.430 316 48 10 1194 1494 628656378 628656065 2.330000e-49 207.0
15 TraesCS2B01G144400 chr2D 91.228 114 9 1 3459 3572 310718775 310718663 3.080000e-33 154.0
16 TraesCS2B01G144400 chr2D 85.714 126 18 0 4916 5041 467063294 467063419 4.010000e-27 134.0
17 TraesCS2B01G144400 chr2A 92.400 1750 92 15 3997 5720 71667479 71665745 0.000000e+00 2457.0
18 TraesCS2B01G144400 chr2A 94.668 1444 60 9 1622 3060 71669893 71668462 0.000000e+00 2224.0
19 TraesCS2B01G144400 chr2A 90.366 955 44 13 3071 4012 71668416 71667497 0.000000e+00 1210.0
20 TraesCS2B01G144400 chr2A 89.016 965 51 17 545 1499 71670810 71669891 0.000000e+00 1144.0
21 TraesCS2B01G144400 chr2A 81.624 1453 173 50 3165 4583 607912873 607914265 0.000000e+00 1118.0
22 TraesCS2B01G144400 chr2A 84.680 1077 131 15 1910 2975 607911661 607912714 0.000000e+00 1044.0
23 TraesCS2B01G144400 chr2A 86.817 531 45 14 1 517 71671326 71670807 2.580000e-158 569.0
24 TraesCS2B01G144400 chr2A 81.636 648 65 23 3948 4581 71629085 71628478 7.430000e-134 488.0
25 TraesCS2B01G144400 chr2A 80.651 522 50 25 5877 6366 71664585 71664083 2.190000e-94 357.0
26 TraesCS2B01G144400 chr2A 77.426 474 59 17 4915 5375 607914614 607915052 8.270000e-59 239.0
27 TraesCS2B01G144400 chr2A 87.681 138 11 3 5718 5853 71664922 71664789 8.560000e-34 156.0
28 TraesCS2B01G144400 chr5D 82.335 1336 174 37 1622 2930 496980195 496981495 0.000000e+00 1103.0
29 TraesCS2B01G144400 chr5D 82.308 520 65 15 3641 4146 325879693 325879187 5.910000e-115 425.0
30 TraesCS2B01G144400 chr5D 82.993 441 57 5 4599 5039 496981751 496982173 3.610000e-102 383.0
31 TraesCS2B01G144400 chr5D 91.228 114 9 1 3459 3572 325879814 325879702 3.080000e-33 154.0
32 TraesCS2B01G144400 chr6A 80.650 1261 184 26 1622 2873 539181027 539182236 0.000000e+00 922.0
33 TraesCS2B01G144400 chr6A 82.955 440 54 7 4601 5039 539185233 539185652 1.680000e-100 377.0
34 TraesCS2B01G144400 chr6A 76.744 172 21 14 5999 6165 533414398 533414555 1.910000e-10 78.7
35 TraesCS2B01G144400 chr5B 83.813 939 129 12 1945 2873 615840803 615841728 0.000000e+00 870.0
36 TraesCS2B01G144400 chr5B 81.574 521 71 17 3641 4146 231713359 231713869 2.140000e-109 407.0
37 TraesCS2B01G144400 chr5B 85.434 357 51 1 4599 4954 271210672 271211028 2.810000e-98 370.0
38 TraesCS2B01G144400 chr5B 86.513 304 39 2 4599 4901 615841883 615842185 3.690000e-87 333.0
39 TraesCS2B01G144400 chr5B 93.023 129 9 0 1496 1624 482500814 482500942 8.440000e-44 189.0
40 TraesCS2B01G144400 chr5B 89.167 120 12 1 3453 3572 231713232 231713350 1.430000e-31 148.0
41 TraesCS2B01G144400 chr5B 88.312 77 9 0 4963 5039 615842220 615842296 6.810000e-15 93.5
42 TraesCS2B01G144400 chr5A 81.989 1066 149 23 1622 2677 621194789 621195821 0.000000e+00 865.0
43 TraesCS2B01G144400 chr5A 89.130 368 36 3 2508 2873 621195825 621196190 7.540000e-124 455.0
44 TraesCS2B01G144400 chr5A 84.842 442 54 8 4599 5039 621196362 621196791 3.530000e-117 433.0
45 TraesCS2B01G144400 chr5A 81.043 422 58 15 3641 4048 243870401 243869988 3.710000e-82 316.0
46 TraesCS2B01G144400 chr5A 91.228 114 9 1 3459 3572 243870522 243870410 3.080000e-33 154.0
47 TraesCS2B01G144400 chr4D 82.308 520 68 18 3641 4146 23119062 23118553 4.570000e-116 429.0
48 TraesCS2B01G144400 chr1D 81.958 521 68 14 3641 4146 428589068 428589577 9.890000e-113 418.0
49 TraesCS2B01G144400 chr1D 87.143 140 13 3 1359 1494 252477055 252477193 3.080000e-33 154.0
50 TraesCS2B01G144400 chr1D 88.333 120 13 1 3453 3572 428588941 428589059 6.670000e-30 143.0
51 TraesCS2B01G144400 chr7B 81.609 522 69 17 3641 4146 92829864 92829354 2.140000e-109 407.0
52 TraesCS2B01G144400 chr1B 81.574 521 71 19 3641 4146 498712430 498712940 2.140000e-109 407.0
53 TraesCS2B01G144400 chr1B 91.176 136 11 1 1489 1624 626226872 626227006 3.930000e-42 183.0
54 TraesCS2B01G144400 chr1B 90.000 120 11 1 3453 3572 498712303 498712421 3.080000e-33 154.0
55 TraesCS2B01G144400 chrUn 91.791 134 11 0 1490 1623 304504659 304504526 3.040000e-43 187.0
56 TraesCS2B01G144400 chr6B 91.791 134 11 0 1497 1630 439064791 439064658 3.040000e-43 187.0
57 TraesCS2B01G144400 chr3D 91.791 134 11 0 1490 1623 52810886 52811019 3.040000e-43 187.0
58 TraesCS2B01G144400 chr3B 92.366 131 10 0 1493 1623 184611445 184611575 3.040000e-43 187.0
59 TraesCS2B01G144400 chr4A 90.511 137 11 2 1489 1624 173652815 173652950 5.080000e-41 180.0
60 TraesCS2B01G144400 chr4A 97.143 35 1 0 5706 5740 665735903 665735869 6.910000e-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 TraesCS2B01G144400 chr2B 110478845 110485223 6378 True 11780.000000 11780 100.000000 1 6379 1 chr2B.!!$R3 6378
1 TraesCS2B01G144400 chr2B 545757984 545761220 3236 False 658.000000 1450 83.493333 1841 4770 3 chr2B.!!$F2 2929
2 TraesCS2B01G144400 chr2D 73098925 73104939 6014 True 4246.000000 6543 92.508500 38 6017 2 chr2D.!!$R2 5979
3 TraesCS2B01G144400 chr2D 467060137 467063419 3282 False 684.000000 1688 82.215667 1878 5041 3 chr2D.!!$F1 3163
4 TraesCS2B01G144400 chr2D 310718144 310718775 631 True 286.000000 418 86.593000 3459 4146 2 chr2D.!!$R3 687
5 TraesCS2B01G144400 chr2A 71664083 71671326 7243 True 1159.571429 2457 88.799857 1 6366 7 chr2A.!!$R2 6365
6 TraesCS2B01G144400 chr2A 607911661 607915052 3391 False 800.333333 1118 81.243333 1910 5375 3 chr2A.!!$F1 3465
7 TraesCS2B01G144400 chr2A 71628478 71629085 607 True 488.000000 488 81.636000 3948 4581 1 chr2A.!!$R1 633
8 TraesCS2B01G144400 chr5D 496980195 496982173 1978 False 743.000000 1103 82.664000 1622 5039 2 chr5D.!!$F1 3417
9 TraesCS2B01G144400 chr5D 325879187 325879814 627 True 289.500000 425 86.768000 3459 4146 2 chr5D.!!$R1 687
10 TraesCS2B01G144400 chr6A 539181027 539185652 4625 False 649.500000 922 81.802500 1622 5039 2 chr6A.!!$F2 3417
11 TraesCS2B01G144400 chr5B 615840803 615842296 1493 False 432.166667 870 86.212667 1945 5039 3 chr5B.!!$F4 3094
12 TraesCS2B01G144400 chr5B 231713232 231713869 637 False 277.500000 407 85.370500 3453 4146 2 chr5B.!!$F3 693
13 TraesCS2B01G144400 chr5A 621194789 621196791 2002 False 584.333333 865 85.320333 1622 5039 3 chr5A.!!$F1 3417
14 TraesCS2B01G144400 chr5A 243869988 243870522 534 True 235.000000 316 86.135500 3459 4048 2 chr5A.!!$R1 589
15 TraesCS2B01G144400 chr4D 23118553 23119062 509 True 429.000000 429 82.308000 3641 4146 1 chr4D.!!$R1 505
16 TraesCS2B01G144400 chr1D 428588941 428589577 636 False 280.500000 418 85.145500 3453 4146 2 chr1D.!!$F2 693
17 TraesCS2B01G144400 chr7B 92829354 92829864 510 True 407.000000 407 81.609000 3641 4146 1 chr7B.!!$R1 505
18 TraesCS2B01G144400 chr1B 498712303 498712940 637 False 280.500000 407 85.787000 3453 4146 2 chr1B.!!$F2 693

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
176 185 0.166814 GCGAAATCGAAAGCACAGCT 59.833 50.000 7.06 0.0 40.86 4.24 F
643 668 0.405585 ATTTGTGGGAGGTGAGGGTG 59.594 55.000 0.00 0.0 0.00 4.61 F
931 970 0.610174 TCTCTGTGATGCCAGGTGAC 59.390 55.000 0.00 0.0 33.14 3.67 F
1515 1554 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.0 44.66 2.17 F
1518 1557 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 F
1519 1558 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.0 44.66 2.24 F
3066 3497 1.073284 ACATGAAGTGGCCTAAACGGT 59.927 47.619 3.32 0.0 34.25 4.83 F
4522 7106 2.038952 TGTCACATTCAGTTCAGAGGGG 59.961 50.000 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1535 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 R
1499 1538 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
2108 2328 2.287915 GGCAACTTATCGGCAGTACATG 59.712 50.000 0.00 0.00 0.00 3.21 R
2810 3227 2.519771 TCCTTTCCATTGCAGCATCT 57.480 45.000 0.00 0.00 0.00 2.90 R
3193 3661 6.043243 AGGACAACTTCTAGATGACAAAAGGA 59.957 38.462 12.31 0.00 0.00 3.36 R
3415 3965 9.082313 GTAAAGGGAATGGATTTCATACATGAT 57.918 33.333 0.00 0.00 33.05 2.45 R
4717 7477 0.246912 GTTCATCGCGCTGTTTCTCG 60.247 55.000 10.07 0.00 0.00 4.04 R
6302 10169 0.321653 GACGGCACTTCCCTTGTGAT 60.322 55.000 0.00 0.00 37.60 3.06 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
31 32 2.235016 TCAGGGTTCAATTTCAACGGG 58.765 47.619 0.00 0.00 0.00 5.28
49 54 1.613520 GGGGCTCTACCAGTTCAAACC 60.614 57.143 0.00 0.00 42.05 3.27
51 56 2.224793 GGGCTCTACCAGTTCAAACCTT 60.225 50.000 0.00 0.00 42.05 3.50
55 60 5.181433 GGCTCTACCAGTTCAAACCTTAAAG 59.819 44.000 0.00 0.00 38.86 1.85
84 93 2.754946 ATACTTTTCTCGGCCGTCAA 57.245 45.000 27.15 16.13 0.00 3.18
98 107 1.678269 CGTCAAGCGTCAGCAGCTAC 61.678 60.000 0.00 0.00 45.31 3.58
137 146 3.003173 TCTGTTCTCCGGCCCCTG 61.003 66.667 0.00 0.00 0.00 4.45
155 164 1.900016 GGAAAACGGGGCGAAACCT 60.900 57.895 0.00 0.00 39.10 3.50
156 165 1.284715 GAAAACGGGGCGAAACCTG 59.715 57.895 0.00 0.00 42.81 4.00
157 166 2.137425 GAAAACGGGGCGAAACCTGG 62.137 60.000 0.00 0.00 41.38 4.45
172 181 0.179189 CCTGGCGAAATCGAAAGCAC 60.179 55.000 7.06 0.00 43.02 4.40
176 185 0.166814 GCGAAATCGAAAGCACAGCT 59.833 50.000 7.06 0.00 40.86 4.24
252 267 4.475444 TCCCCCTCGCCGGATCTT 62.475 66.667 5.05 0.00 33.16 2.40
257 272 2.482333 CCTCGCCGGATCTTCTCGT 61.482 63.158 5.05 0.00 33.16 4.18
259 274 2.352457 CGCCGGATCTTCTCGTCG 60.352 66.667 5.05 0.00 0.00 5.12
299 314 0.818296 CGTCCGAGATGAGGTTCCTT 59.182 55.000 0.00 0.00 0.00 3.36
356 372 1.363807 CGCGACAGGCTCATGGATA 59.636 57.895 0.00 0.00 40.44 2.59
385 403 5.890419 CCCTTCCTAAGATGCTTTGATTCTT 59.110 40.000 0.00 0.00 34.29 2.52
387 405 6.039159 CCTTCCTAAGATGCTTTGATTCTTCC 59.961 42.308 0.00 0.00 32.28 3.46
399 417 7.335422 TGCTTTGATTCTTCCTAGATGTTTCTC 59.665 37.037 0.00 0.00 33.17 2.87
410 428 4.247267 AGATGTTTCTCCGTTTCGTACA 57.753 40.909 0.00 0.00 0.00 2.90
476 494 4.452733 GAGAGGGGCGTGGTTCGG 62.453 72.222 0.00 0.00 40.26 4.30
504 522 3.146828 AACTGGGTGGTTCTGGGGC 62.147 63.158 0.00 0.00 0.00 5.80
531 549 3.435186 GTCGGGCTCTGGCTTTGC 61.435 66.667 0.00 0.00 38.73 3.68
543 561 3.554692 CTTTGCGGCGCTACGAGG 61.555 66.667 33.26 12.55 35.47 4.63
551 576 1.226435 GCGCTACGAGGTGTCAGAG 60.226 63.158 0.00 0.00 0.00 3.35
562 587 2.298729 AGGTGTCAGAGCTCTTCAGAAC 59.701 50.000 15.27 4.93 0.00 3.01
573 598 1.347817 CTTCAGAACTGACGAGCGGC 61.348 60.000 3.88 0.00 39.66 6.53
575 600 3.362797 AGAACTGACGAGCGGCGA 61.363 61.111 12.98 0.00 44.57 5.54
576 601 2.876645 GAACTGACGAGCGGCGAG 60.877 66.667 12.98 3.03 44.57 5.03
643 668 0.405585 ATTTGTGGGAGGTGAGGGTG 59.594 55.000 0.00 0.00 0.00 4.61
673 698 5.420409 GTTTGATCAAGAGGAAGGATACGT 58.580 41.667 8.41 0.00 46.39 3.57
686 711 1.644786 GATACGTTGGGTGCCACTGC 61.645 60.000 0.00 0.00 30.78 4.40
733 758 8.883731 AGATTTACTTACGAATGTTTCATGGAG 58.116 33.333 0.00 0.00 0.00 3.86
766 792 8.325787 GGATTTTGGTGGTTTAGGGATTTTATT 58.674 33.333 0.00 0.00 0.00 1.40
778 804 4.055360 GGGATTTTATTATGGGTTTGCGC 58.945 43.478 0.00 0.00 0.00 6.09
792 827 5.106475 TGGGTTTGCGCTAACTAGTTTATTG 60.106 40.000 28.73 3.16 0.00 1.90
800 835 5.231568 CGCTAACTAGTTTATTGTCCTTCCG 59.768 44.000 14.49 0.00 0.00 4.30
812 847 3.146066 TGTCCTTCCGGTTTGATTTGAG 58.854 45.455 0.00 0.00 0.00 3.02
821 856 6.234920 TCCGGTTTGATTTGAGAGTGAATTA 58.765 36.000 0.00 0.00 0.00 1.40
822 857 6.712998 TCCGGTTTGATTTGAGAGTGAATTAA 59.287 34.615 0.00 0.00 0.00 1.40
824 859 6.801862 CGGTTTGATTTGAGAGTGAATTAACC 59.198 38.462 0.00 0.00 32.59 2.85
836 871 3.189702 GTGAATTAACCGCTTGGCAAGTA 59.810 43.478 26.71 9.87 35.53 2.24
837 872 3.189702 TGAATTAACCGCTTGGCAAGTAC 59.810 43.478 26.71 11.47 35.53 2.73
839 874 1.803334 TAACCGCTTGGCAAGTACTG 58.197 50.000 26.71 15.32 35.53 2.74
846 882 3.676049 CGCTTGGCAAGTACTGATCTGTA 60.676 47.826 26.71 8.27 0.00 2.74
855 891 6.091441 GCAAGTACTGATCTGTAAAAGTCTGG 59.909 42.308 13.39 5.87 0.00 3.86
857 893 7.164230 AGTACTGATCTGTAAAAGTCTGGAG 57.836 40.000 13.39 0.00 0.00 3.86
864 900 4.899457 TCTGTAAAAGTCTGGAGGTCTTCA 59.101 41.667 0.00 0.00 0.00 3.02
866 902 5.794894 TGTAAAAGTCTGGAGGTCTTCATC 58.205 41.667 0.00 0.00 0.00 2.92
867 903 3.990959 AAAGTCTGGAGGTCTTCATCC 57.009 47.619 0.00 0.00 43.89 3.51
869 905 2.465813 AGTCTGGAGGTCTTCATCCTG 58.534 52.381 0.94 0.80 43.95 3.86
884 920 4.843728 TCATCCTGGATAACACTTCAACC 58.156 43.478 9.27 0.00 0.00 3.77
904 943 4.910195 ACCAAGTACTGATCATGCTCAAA 58.090 39.130 0.00 0.00 0.00 2.69
931 970 0.610174 TCTCTGTGATGCCAGGTGAC 59.390 55.000 0.00 0.00 33.14 3.67
962 1001 2.356227 GGAGATGAGAGTGGAAAACCCC 60.356 54.545 0.00 0.00 0.00 4.95
1020 1059 2.765689 TGGACAACCCATTGAACCTT 57.234 45.000 0.00 0.00 40.82 3.50
1048 1087 1.678101 GTTCAGTGCAGCCAAACTTCT 59.322 47.619 0.00 0.00 0.00 2.85
1072 1111 2.264794 CCTTCTACGCCCGCAAGT 59.735 61.111 0.00 0.00 0.00 3.16
1083 1122 2.328099 CCGCAAGTCAGGAAGTGCC 61.328 63.158 0.00 0.00 33.33 5.01
1401 1440 1.399089 GTAGACGTGTGAGCTCTCTCC 59.601 57.143 16.19 5.70 38.58 3.71
1408 1447 3.160748 GAGCTCTCTCCCCCTGCC 61.161 72.222 6.43 0.00 33.19 4.85
1494 1533 6.991938 TGGTTGAAGGAATTGAAATTGGTAG 58.008 36.000 0.00 0.00 0.00 3.18
1496 1535 6.295292 GGTTGAAGGAATTGAAATTGGTAGCT 60.295 38.462 0.00 0.00 0.00 3.32
1497 1536 7.093945 GGTTGAAGGAATTGAAATTGGTAGCTA 60.094 37.037 0.00 0.00 0.00 3.32
1498 1537 7.391148 TGAAGGAATTGAAATTGGTAGCTAC 57.609 36.000 15.88 15.88 0.00 3.58
1499 1538 7.175104 TGAAGGAATTGAAATTGGTAGCTACT 58.825 34.615 22.74 2.89 0.00 2.57
1500 1539 7.336931 TGAAGGAATTGAAATTGGTAGCTACTC 59.663 37.037 22.74 12.68 0.00 2.59
1501 1540 6.122964 AGGAATTGAAATTGGTAGCTACTCC 58.877 40.000 22.74 16.46 0.00 3.85
1502 1541 5.299531 GGAATTGAAATTGGTAGCTACTCCC 59.700 44.000 22.74 7.85 0.00 4.30
1503 1542 5.717119 ATTGAAATTGGTAGCTACTCCCT 57.283 39.130 22.74 4.96 0.00 4.20
1504 1543 4.755266 TGAAATTGGTAGCTACTCCCTC 57.245 45.455 22.74 13.31 0.00 4.30
1505 1544 3.454812 TGAAATTGGTAGCTACTCCCTCC 59.545 47.826 22.74 6.36 0.00 4.30
1506 1545 1.705873 ATTGGTAGCTACTCCCTCCG 58.294 55.000 22.74 0.00 0.00 4.63
1507 1546 0.333993 TTGGTAGCTACTCCCTCCGT 59.666 55.000 22.74 0.00 0.00 4.69
1508 1547 0.106819 TGGTAGCTACTCCCTCCGTC 60.107 60.000 22.74 4.13 0.00 4.79
1509 1548 0.822944 GGTAGCTACTCCCTCCGTCC 60.823 65.000 22.74 0.00 0.00 4.79
1510 1549 1.147824 TAGCTACTCCCTCCGTCCG 59.852 63.158 0.00 0.00 0.00 4.79
1511 1550 2.335092 TAGCTACTCCCTCCGTCCGG 62.335 65.000 0.00 0.00 0.00 5.14
1512 1551 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
1513 1552 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
1514 1553 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
1515 1554 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1516 1555 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1517 1556 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1518 1557 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1519 1558 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1520 1559 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1521 1560 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1522 1561 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1523 1562 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1524 1563 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1525 1564 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1526 1565 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1527 1566 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1528 1567 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1529 1568 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1530 1569 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1531 1570 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1532 1571 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
1533 1572 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
1534 1573 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1609 1648 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1610 1649 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1611 1650 6.350110 CCATTTTGATGACAAGTATTTCCGGT 60.350 38.462 0.00 0.00 37.32 5.28
1612 1651 5.873179 TTTGATGACAAGTATTTCCGGTC 57.127 39.130 0.00 0.00 37.32 4.79
1613 1652 4.545208 TGATGACAAGTATTTCCGGTCA 57.455 40.909 0.00 0.00 42.07 4.02
1614 1653 4.503910 TGATGACAAGTATTTCCGGTCAG 58.496 43.478 0.00 0.00 41.27 3.51
1615 1654 4.221924 TGATGACAAGTATTTCCGGTCAGA 59.778 41.667 0.00 0.00 41.27 3.27
1616 1655 4.188247 TGACAAGTATTTCCGGTCAGAG 57.812 45.455 0.00 0.00 33.88 3.35
1617 1656 3.056107 TGACAAGTATTTCCGGTCAGAGG 60.056 47.826 0.00 0.00 33.88 3.69
1618 1657 2.236395 ACAAGTATTTCCGGTCAGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
1619 1658 2.500098 CAAGTATTTCCGGTCAGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
1620 1659 2.389715 AGTATTTCCGGTCAGAGGGAG 58.610 52.381 0.00 0.00 33.01 4.30
1639 1678 3.321396 GGAGTACCTACTAGGACATTGGC 59.679 52.174 9.28 0.00 37.67 4.52
1642 1681 4.650131 AGTACCTACTAGGACATTGGCTTC 59.350 45.833 9.28 0.00 37.67 3.86
1660 1699 9.832445 ATTGGCTTCGTTTCTTCTTCTATATAA 57.168 29.630 0.00 0.00 0.00 0.98
1719 1761 3.071023 TGAGAAATCGTGTCCAGGTTTCT 59.929 43.478 4.38 4.38 40.65 2.52
1819 2012 3.196469 GGAGATGGAATGCTCGATATCCA 59.804 47.826 9.99 9.99 43.80 3.41
1866 2059 2.093764 CAGACAGGACATCAAGGAGGAC 60.094 54.545 0.00 0.00 0.00 3.85
2066 2284 2.548057 TGTGAAAAATCTCACTGCCGTC 59.452 45.455 5.43 0.00 45.03 4.79
2108 2328 4.260375 CGTATGCCTGTATTGCTTTCTGTC 60.260 45.833 0.00 0.00 0.00 3.51
2126 2347 4.159693 TCTGTCATGTACTGCCGATAAGTT 59.840 41.667 0.00 0.00 0.00 2.66
2386 2619 3.738282 GCGTCTTGCACTATCAGGATAAG 59.262 47.826 0.00 0.00 45.45 1.73
2810 3227 2.680805 GGCTGCAAGACAGGTTGCTATA 60.681 50.000 9.77 0.00 46.27 1.31
3018 3449 5.659463 TGCTTGCTTGTTTTATTGTCTGTT 58.341 33.333 0.00 0.00 0.00 3.16
3066 3497 1.073284 ACATGAAGTGGCCTAAACGGT 59.927 47.619 3.32 0.00 34.25 4.83
3076 3541 2.223479 GGCCTAAACGGTGCACATAATG 60.223 50.000 20.43 4.99 34.25 1.90
3193 3661 6.966534 ACAATGACAGAAAACTCAAATCCT 57.033 33.333 0.00 0.00 0.00 3.24
3217 3694 6.231211 TCCTTTTGTCATCTAGAAGTTGTCC 58.769 40.000 0.00 0.00 0.00 4.02
3305 3795 4.478206 TTGACAAATTTGACCTTTGGCA 57.522 36.364 24.64 0.63 47.00 4.92
3415 3965 9.073475 GTATTCCAATATGTTTGCCTTACCATA 57.927 33.333 0.00 0.00 0.00 2.74
3780 4331 2.117051 AGGCAGAGATCAGCTCATCAA 58.883 47.619 0.00 0.00 46.45 2.57
3861 4446 3.395639 TCGGCTTTCGTTATGTTGACTT 58.604 40.909 0.00 0.00 40.32 3.01
3862 4447 3.810941 TCGGCTTTCGTTATGTTGACTTT 59.189 39.130 0.00 0.00 40.32 2.66
3863 4448 4.273969 TCGGCTTTCGTTATGTTGACTTTT 59.726 37.500 0.00 0.00 40.32 2.27
3864 4449 4.973663 CGGCTTTCGTTATGTTGACTTTTT 59.026 37.500 0.00 0.00 0.00 1.94
4414 6285 5.390779 GCTGAATTGTTTTGTGTTTGCTTGT 60.391 36.000 0.00 0.00 0.00 3.16
4459 7033 5.965918 GCGTAGATCTTTTATTGCTGGTTTC 59.034 40.000 0.00 0.00 0.00 2.78
4522 7106 2.038952 TGTCACATTCAGTTCAGAGGGG 59.961 50.000 0.00 0.00 0.00 4.79
4796 7556 3.244561 TGTTTCTGAAGTAAGGGCAGGAG 60.245 47.826 0.00 0.00 0.00 3.69
4798 7558 0.615331 CTGAAGTAAGGGCAGGAGCA 59.385 55.000 0.00 0.00 44.61 4.26
4799 7559 0.615331 TGAAGTAAGGGCAGGAGCAG 59.385 55.000 0.00 0.00 44.61 4.24
4804 7564 2.202236 TAAGGGCAGGAGCAGCAAGG 62.202 60.000 0.00 0.00 44.61 3.61
4825 7585 1.412710 TCCGACCCTTCTGATACATGC 59.587 52.381 0.00 0.00 0.00 4.06
4975 7764 0.871057 ACAAAGAGCAAGAGAAGCGC 59.129 50.000 0.00 0.00 37.01 5.92
5194 8000 8.414629 AATAAGAATCCAGATTTAATGGCTCC 57.585 34.615 0.00 0.00 37.76 4.70
5254 8060 0.671796 TCGAAGTTCTTCCACGAGCA 59.328 50.000 0.56 0.00 0.00 4.26
5261 8067 1.878953 TCTTCCACGAGCAAACTTCC 58.121 50.000 0.00 0.00 0.00 3.46
5264 8070 0.179067 TCCACGAGCAAACTTCCGTT 60.179 50.000 0.00 0.00 32.50 4.44
5273 8079 0.751643 AAACTTCCGTTGGCAGCAGT 60.752 50.000 1.39 0.00 32.65 4.40
5434 8240 1.012841 GAGCATGCTGTAGCCAGAAC 58.987 55.000 28.27 1.91 41.50 3.01
5439 8245 1.079819 GCTGTAGCCAGAACGAGCA 60.080 57.895 0.00 0.00 41.50 4.26
5543 8349 4.589216 TTTCAGGATTTGGTTTGAGCAG 57.411 40.909 0.00 0.00 0.00 4.24
5545 8351 2.158475 TCAGGATTTGGTTTGAGCAGGT 60.158 45.455 0.00 0.00 0.00 4.00
5596 8416 4.202245 TCCCTTTGTACTAGACACATGC 57.798 45.455 0.00 0.00 37.96 4.06
5605 8425 4.220693 ACTAGACACATGCATTGCCTTA 57.779 40.909 6.12 0.00 0.00 2.69
5630 8450 4.131714 CAATTGAAGTTTCACGTACGTCG 58.868 43.478 19.94 14.17 46.00 5.12
5712 8533 8.491045 TGAGATTGTGACATATATTACTCCCA 57.509 34.615 0.00 0.00 0.00 4.37
5791 9438 2.735772 CCATAGAGGCTGGCGTGGT 61.736 63.158 0.00 0.00 0.00 4.16
5805 9452 1.823470 GTGGTGAGCACAGGCACAA 60.823 57.895 10.26 0.00 42.28 3.33
5806 9453 1.151221 TGGTGAGCACAGGCACAAT 59.849 52.632 2.75 0.00 42.28 2.71
5848 9495 2.045131 GGCCAGGCTGCTTCTGAAG 61.045 63.158 12.43 13.02 34.36 3.02
5854 9501 1.141657 AGGCTGCTTCTGAAGTTGACA 59.858 47.619 17.97 7.18 0.00 3.58
5874 9521 1.889545 GAGCTGGAAGTTGCAGTTCT 58.110 50.000 26.62 16.46 41.44 3.01
5888 9716 3.681417 TGCAGTTCTCGAAGTGATGATTG 59.319 43.478 16.47 0.00 42.77 2.67
5894 9727 1.089112 CGAAGTGATGATTGGCTGCA 58.911 50.000 0.50 0.00 0.00 4.41
5895 9728 1.063616 CGAAGTGATGATTGGCTGCAG 59.936 52.381 10.11 10.11 0.00 4.41
5896 9729 0.815734 AAGTGATGATTGGCTGCAGC 59.184 50.000 30.88 30.88 41.14 5.25
5897 9730 0.323087 AGTGATGATTGGCTGCAGCA 60.323 50.000 37.63 20.97 44.36 4.41
5944 9778 3.047877 GGGACCTGAACGTTGCCG 61.048 66.667 5.00 0.00 40.83 5.69
5986 9834 2.031012 CCGCTGAGCAGTCAACCA 59.969 61.111 4.88 0.00 30.14 3.67
6043 9891 9.467258 AGCCAAATTTATTCATCAAATATCACG 57.533 29.630 0.00 0.00 29.96 4.35
6044 9892 9.248291 GCCAAATTTATTCATCAAATATCACGT 57.752 29.630 0.00 0.00 29.96 4.49
6050 9898 8.940768 TTATTCATCAAATATCACGTCACAGA 57.059 30.769 0.00 0.00 29.96 3.41
6051 9899 6.892310 TTCATCAAATATCACGTCACAGAG 57.108 37.500 0.00 0.00 0.00 3.35
6052 9900 5.965922 TCATCAAATATCACGTCACAGAGT 58.034 37.500 0.00 0.00 0.00 3.24
6053 9901 5.807011 TCATCAAATATCACGTCACAGAGTG 59.193 40.000 0.00 0.00 39.55 3.51
6054 9902 5.134202 TCAAATATCACGTCACAGAGTGT 57.866 39.130 0.00 0.00 39.25 3.55
6076 9924 9.656323 AGTGTGGGATAGTATAACTTAGATCAA 57.344 33.333 0.00 0.00 0.00 2.57
6115 9963 2.125673 GGCGCTTCGAACCTAGCA 60.126 61.111 7.64 0.00 37.23 3.49
6122 9970 2.066262 CTTCGAACCTAGCAAAAGCGA 58.934 47.619 0.00 0.00 0.00 4.93
6134 9982 3.743396 AGCAAAAGCGAGAACTTGACTAG 59.257 43.478 0.00 0.00 0.00 2.57
6136 9984 4.376514 GCAAAAGCGAGAACTTGACTAGAC 60.377 45.833 0.00 0.00 0.00 2.59
6161 10009 2.845967 GTGCTTCAAAGTTGACAACACG 59.154 45.455 20.08 8.01 36.83 4.49
6214 10064 9.642343 TGAGCTACCTTAAGATTAATCTCACTA 57.358 33.333 18.19 4.96 35.76 2.74
6293 10160 4.196778 TTGGGCCGCAACTGGACA 62.197 61.111 0.00 0.00 39.59 4.02
6294 10161 3.723097 TTGGGCCGCAACTGGACAA 62.723 57.895 0.00 0.00 39.59 3.18
6297 10164 2.268076 GGCCGCAACTGGACAATGT 61.268 57.895 0.00 0.00 36.84 2.71
6317 10184 0.961019 TGCAATCACAAGGGAAGTGC 59.039 50.000 4.84 4.84 36.93 4.40
6327 10194 1.374758 GGGAAGTGCCGTCTCACAG 60.375 63.158 0.00 0.00 39.35 3.66
6335 10202 2.740055 CGTCTCACAGCACCAGCC 60.740 66.667 0.00 0.00 43.56 4.85
6353 10220 1.593006 GCCGACGATTATGTTGTGAGG 59.407 52.381 0.00 0.00 0.00 3.86
6362 10229 5.616866 CGATTATGTTGTGAGGGTTGTTGTC 60.617 44.000 0.00 0.00 0.00 3.18
6366 10233 1.979855 TGTGAGGGTTGTTGTCATGG 58.020 50.000 0.00 0.00 0.00 3.66
6367 10234 1.492599 TGTGAGGGTTGTTGTCATGGA 59.507 47.619 0.00 0.00 0.00 3.41
6368 10235 1.880027 GTGAGGGTTGTTGTCATGGAC 59.120 52.381 0.00 0.00 0.00 4.02
6369 10236 1.774254 TGAGGGTTGTTGTCATGGACT 59.226 47.619 0.00 0.00 33.15 3.85
6370 10237 2.174639 TGAGGGTTGTTGTCATGGACTT 59.825 45.455 0.00 0.00 33.15 3.01
6371 10238 3.392947 TGAGGGTTGTTGTCATGGACTTA 59.607 43.478 0.00 0.00 33.15 2.24
6372 10239 4.141367 TGAGGGTTGTTGTCATGGACTTAA 60.141 41.667 0.00 0.00 33.15 1.85
6373 10240 4.798882 AGGGTTGTTGTCATGGACTTAAA 58.201 39.130 0.00 0.00 33.15 1.52
6374 10241 4.583073 AGGGTTGTTGTCATGGACTTAAAC 59.417 41.667 0.00 0.44 33.15 2.01
6375 10242 4.261867 GGGTTGTTGTCATGGACTTAAACC 60.262 45.833 14.03 14.03 37.66 3.27
6376 10243 4.261867 GGTTGTTGTCATGGACTTAAACCC 60.262 45.833 12.52 0.00 35.17 4.11
6377 10244 4.447138 TGTTGTCATGGACTTAAACCCT 57.553 40.909 0.00 0.00 33.15 4.34
6378 10245 5.570205 TGTTGTCATGGACTTAAACCCTA 57.430 39.130 0.00 0.00 33.15 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.886542 AGAGCCCCGTTGAAATTGAAC 59.113 47.619 0.00 0.00 0.00 3.18
26 27 0.834687 TGAACTGGTAGAGCCCCGTT 60.835 55.000 0.00 0.00 36.04 4.44
31 32 2.861147 AGGTTTGAACTGGTAGAGCC 57.139 50.000 0.00 0.00 37.90 4.70
55 60 6.484540 GGCCGAGAAAAGTATACTTTAAAGC 58.515 40.000 26.94 22.73 44.69 3.51
66 75 1.938016 GCTTGACGGCCGAGAAAAGTA 60.938 52.381 35.90 6.71 0.00 2.24
84 93 2.271800 GTATTTGTAGCTGCTGACGCT 58.728 47.619 13.43 0.00 41.35 5.07
98 107 3.134804 ACGGAGATGGGAGAAGGTATTTG 59.865 47.826 0.00 0.00 0.00 2.32
137 146 1.900016 AGGTTTCGCCCCGTTTTCC 60.900 57.895 0.00 0.00 38.26 3.13
146 155 1.136774 GATTTCGCCAGGTTTCGCC 59.863 57.895 0.00 0.00 37.58 5.54
155 164 0.516877 CTGTGCTTTCGATTTCGCCA 59.483 50.000 0.00 0.00 39.60 5.69
156 165 0.794605 GCTGTGCTTTCGATTTCGCC 60.795 55.000 0.00 0.00 39.60 5.54
157 166 0.166814 AGCTGTGCTTTCGATTTCGC 59.833 50.000 0.00 0.00 33.89 4.70
235 250 4.475444 AAGATCCGGCGAGGGGGA 62.475 66.667 9.30 0.00 41.52 4.81
240 255 1.009449 GACGAGAAGATCCGGCGAG 60.009 63.158 9.30 0.00 0.00 5.03
299 314 2.112297 AGCGGCGAAAAGTTGGGA 59.888 55.556 12.98 0.00 0.00 4.37
385 403 3.508793 ACGAAACGGAGAAACATCTAGGA 59.491 43.478 0.00 0.00 0.00 2.94
387 405 5.396484 TGTACGAAACGGAGAAACATCTAG 58.604 41.667 0.00 0.00 0.00 2.43
399 417 2.031508 AGCAAAACCATGTACGAAACGG 60.032 45.455 0.00 0.00 0.00 4.44
410 428 1.541147 CACGATCCACAGCAAAACCAT 59.459 47.619 0.00 0.00 0.00 3.55
504 522 1.328680 CAGAGCCCGACATTTCATTCG 59.671 52.381 0.00 0.00 34.93 3.34
531 549 4.111016 TGACACCTCGTAGCGCCG 62.111 66.667 2.29 0.45 0.00 6.46
533 551 1.226435 CTCTGACACCTCGTAGCGC 60.226 63.158 0.00 0.00 0.00 5.92
543 561 3.005261 TCAGTTCTGAAGAGCTCTGACAC 59.995 47.826 19.06 10.05 33.18 3.67
573 598 0.095935 CAAACTGGATTCAGCGCTCG 59.904 55.000 7.13 3.29 44.59 5.03
575 600 1.609208 AACAAACTGGATTCAGCGCT 58.391 45.000 2.64 2.64 44.59 5.92
576 601 2.319472 GAAACAAACTGGATTCAGCGC 58.681 47.619 0.00 0.00 44.59 5.92
579 604 5.376854 AATCCGAAACAAACTGGATTCAG 57.623 39.130 0.00 0.00 45.67 3.02
643 668 5.163713 CCTTCCTCTTGATCAAACCGATTTC 60.164 44.000 9.88 0.00 33.17 2.17
686 711 0.037882 ACTGATCTGCACACAGGACG 60.038 55.000 12.51 0.00 44.59 4.79
733 758 2.696759 CCACCAAAATCCGTCCGGC 61.697 63.158 0.00 0.00 34.68 6.13
766 792 3.899052 ACTAGTTAGCGCAAACCCATA 57.101 42.857 11.47 0.00 0.00 2.74
800 835 6.801862 CGGTTAATTCACTCTCAAATCAAACC 59.198 38.462 0.00 0.00 32.63 3.27
812 847 1.810151 TGCCAAGCGGTTAATTCACTC 59.190 47.619 0.00 0.00 33.28 3.51
821 856 0.107831 TCAGTACTTGCCAAGCGGTT 59.892 50.000 3.88 0.00 33.28 4.44
822 857 0.324943 ATCAGTACTTGCCAAGCGGT 59.675 50.000 3.88 0.00 33.28 5.68
824 859 1.662629 CAGATCAGTACTTGCCAAGCG 59.337 52.381 3.88 0.00 0.00 4.68
836 871 4.841246 ACCTCCAGACTTTTACAGATCAGT 59.159 41.667 0.00 0.00 0.00 3.41
837 872 5.186797 AGACCTCCAGACTTTTACAGATCAG 59.813 44.000 0.00 0.00 0.00 2.90
839 874 5.669164 AGACCTCCAGACTTTTACAGATC 57.331 43.478 0.00 0.00 0.00 2.75
846 882 3.913163 AGGATGAAGACCTCCAGACTTTT 59.087 43.478 0.00 0.00 34.07 2.27
855 891 4.407296 AGTGTTATCCAGGATGAAGACCTC 59.593 45.833 12.80 2.87 39.69 3.85
857 893 4.762289 AGTGTTATCCAGGATGAAGACC 57.238 45.455 12.80 0.00 39.69 3.85
864 900 4.927267 TGGTTGAAGTGTTATCCAGGAT 57.073 40.909 7.27 7.27 0.00 3.24
866 902 4.398319 ACTTGGTTGAAGTGTTATCCAGG 58.602 43.478 0.00 0.00 43.71 4.45
867 903 6.147821 CAGTACTTGGTTGAAGTGTTATCCAG 59.852 42.308 0.00 0.00 45.05 3.86
869 905 6.228258 TCAGTACTTGGTTGAAGTGTTATCC 58.772 40.000 0.00 0.00 45.05 2.59
884 920 6.673154 TCATTTGAGCATGATCAGTACTTG 57.327 37.500 14.16 8.63 0.00 3.16
904 943 4.401519 CCTGGCATCACAGAGAAAATTCAT 59.598 41.667 0.00 0.00 40.97 2.57
931 970 0.810426 TCTCATCTCCGAGTCCGACG 60.810 60.000 0.00 0.00 38.22 5.12
1020 1059 2.061220 CTGCACTGAACCAGGAGGA 58.939 57.895 0.00 0.00 38.69 3.71
1048 1087 4.143333 GGCGTAGAAGGCCGAGCA 62.143 66.667 0.00 0.00 39.53 4.26
1072 1111 1.597854 CTGTTGCGGCACTTCCTGA 60.598 57.895 0.05 0.00 0.00 3.86
1401 1440 1.122227 CCCAAATTACATGGCAGGGG 58.878 55.000 3.46 0.00 36.58 4.79
1494 1533 3.217743 CCGGACGGAGGGAGTAGC 61.218 72.222 4.40 0.00 37.50 3.58
1496 1535 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1497 1536 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1498 1537 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1499 1538 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1500 1539 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1501 1540 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1502 1541 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1503 1542 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1504 1543 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1505 1544 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1506 1545 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1507 1546 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1508 1547 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1509 1548 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1583 1622 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1584 1623 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1585 1624 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1586 1625 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1587 1626 6.620678 ACCGGAAATACTTGTCATCAAAATG 58.379 36.000 9.46 0.00 32.87 2.32
1588 1627 6.432783 TGACCGGAAATACTTGTCATCAAAAT 59.567 34.615 9.46 0.00 31.45 1.82
1589 1628 5.765677 TGACCGGAAATACTTGTCATCAAAA 59.234 36.000 9.46 0.00 31.45 2.44
1590 1629 5.309638 TGACCGGAAATACTTGTCATCAAA 58.690 37.500 9.46 0.00 31.45 2.69
1591 1630 4.900684 TGACCGGAAATACTTGTCATCAA 58.099 39.130 9.46 0.00 31.45 2.57
1592 1631 4.221924 TCTGACCGGAAATACTTGTCATCA 59.778 41.667 9.46 0.00 35.59 3.07
1593 1632 4.755411 TCTGACCGGAAATACTTGTCATC 58.245 43.478 9.46 0.00 35.59 2.92
1594 1633 4.383118 CCTCTGACCGGAAATACTTGTCAT 60.383 45.833 9.46 0.00 35.59 3.06
1595 1634 3.056107 CCTCTGACCGGAAATACTTGTCA 60.056 47.826 9.46 0.00 34.95 3.58
1596 1635 3.522553 CCTCTGACCGGAAATACTTGTC 58.477 50.000 9.46 0.00 0.00 3.18
1597 1636 2.236395 CCCTCTGACCGGAAATACTTGT 59.764 50.000 9.46 0.00 0.00 3.16
1598 1637 2.500098 TCCCTCTGACCGGAAATACTTG 59.500 50.000 9.46 0.00 0.00 3.16
1599 1638 2.766828 CTCCCTCTGACCGGAAATACTT 59.233 50.000 9.46 0.00 0.00 2.24
1600 1639 2.292323 ACTCCCTCTGACCGGAAATACT 60.292 50.000 9.46 0.00 0.00 2.12
1601 1640 2.108970 ACTCCCTCTGACCGGAAATAC 58.891 52.381 9.46 0.00 0.00 1.89
1602 1641 2.544844 ACTCCCTCTGACCGGAAATA 57.455 50.000 9.46 0.00 0.00 1.40
1603 1642 2.108970 GTACTCCCTCTGACCGGAAAT 58.891 52.381 9.46 0.00 0.00 2.17
1604 1643 1.553706 GTACTCCCTCTGACCGGAAA 58.446 55.000 9.46 0.00 0.00 3.13
1605 1644 0.324091 GGTACTCCCTCTGACCGGAA 60.324 60.000 9.46 0.00 0.00 4.30
1606 1645 1.212934 AGGTACTCCCTCTGACCGGA 61.213 60.000 9.46 0.00 40.71 5.14
1607 1646 0.549950 TAGGTACTCCCTCTGACCGG 59.450 60.000 0.00 0.00 44.81 5.28
1608 1647 1.212441 AGTAGGTACTCCCTCTGACCG 59.788 57.143 0.00 0.00 44.81 4.79
1609 1648 3.181441 CCTAGTAGGTACTCCCTCTGACC 60.181 56.522 8.17 0.00 44.81 4.02
1610 1649 3.715834 TCCTAGTAGGTACTCCCTCTGAC 59.284 52.174 16.02 0.00 44.81 3.51
1611 1650 3.715834 GTCCTAGTAGGTACTCCCTCTGA 59.284 52.174 16.02 0.00 44.81 3.27
1612 1651 3.458857 TGTCCTAGTAGGTACTCCCTCTG 59.541 52.174 16.02 0.00 44.81 3.35
1613 1652 3.745489 TGTCCTAGTAGGTACTCCCTCT 58.255 50.000 16.02 0.00 44.81 3.69
1614 1653 4.727792 ATGTCCTAGTAGGTACTCCCTC 57.272 50.000 16.02 0.00 44.81 4.30
1616 1655 3.896272 CCAATGTCCTAGTAGGTACTCCC 59.104 52.174 16.02 0.08 41.75 4.30
1617 1656 3.321396 GCCAATGTCCTAGTAGGTACTCC 59.679 52.174 16.02 1.69 41.75 3.85
1618 1657 4.216708 AGCCAATGTCCTAGTAGGTACTC 58.783 47.826 16.02 6.35 41.75 2.59
1619 1658 4.267341 AGCCAATGTCCTAGTAGGTACT 57.733 45.455 16.02 0.00 46.37 2.73
1620 1659 4.499357 CGAAGCCAATGTCCTAGTAGGTAC 60.499 50.000 16.02 12.67 36.53 3.34
1660 1699 5.653769 ACACAGAATACCAGCTGCAATTATT 59.346 36.000 8.66 7.88 35.57 1.40
1664 1706 3.077484 ACACAGAATACCAGCTGCAAT 57.923 42.857 8.66 0.06 35.57 3.56
1667 1709 2.813754 TGAAACACAGAATACCAGCTGC 59.186 45.455 8.66 0.00 35.57 5.25
1719 1761 3.041946 GCTCTCAGAGGATAAAAGGGGA 58.958 50.000 3.18 0.00 0.00 4.81
1819 2012 5.359009 GGATTCACATGATGTTTCACTCCAT 59.641 40.000 0.00 0.00 33.85 3.41
2027 2221 6.662414 TTCACAGCAAGCAATATACAGTAC 57.338 37.500 0.00 0.00 0.00 2.73
2108 2328 2.287915 GGCAACTTATCGGCAGTACATG 59.712 50.000 0.00 0.00 0.00 3.21
2810 3227 2.519771 TCCTTTCCATTGCAGCATCT 57.480 45.000 0.00 0.00 0.00 2.90
3018 3449 7.278461 TCTTCATCGTGGTTAAATTTTCCAA 57.722 32.000 13.77 3.70 32.82 3.53
3193 3661 6.043243 AGGACAACTTCTAGATGACAAAAGGA 59.957 38.462 12.31 0.00 0.00 3.36
3305 3795 9.565090 TCAATGATTATTAAGTGCTAGCAGAAT 57.435 29.630 20.03 19.00 0.00 2.40
3415 3965 9.082313 GTAAAGGGAATGGATTTCATACATGAT 57.918 33.333 0.00 0.00 33.05 2.45
3871 4456 9.063615 ACCTTAAATTGTTTTCTAAGTCGACAT 57.936 29.630 19.50 8.71 0.00 3.06
3872 4457 8.441312 ACCTTAAATTGTTTTCTAAGTCGACA 57.559 30.769 19.50 0.00 0.00 4.35
3940 4536 9.268268 GGTCATAAATATTCAGTCGGTCATTTA 57.732 33.333 0.00 0.00 0.00 1.40
3965 4561 4.507710 TGTTCTAGCATTTGAGCTACTGG 58.492 43.478 0.00 0.00 44.50 4.00
4414 6285 3.633525 GCATGGCCATAGAAGAATGTGAA 59.366 43.478 20.30 0.00 0.00 3.18
4522 7106 5.529800 TCTTTAGGTGGAGTAACAAAGCAAC 59.470 40.000 0.00 0.00 0.00 4.17
4717 7477 0.246912 GTTCATCGCGCTGTTTCTCG 60.247 55.000 10.07 0.00 0.00 4.04
4796 7556 4.021925 AGGGTCGGACCTTGCTGC 62.022 66.667 25.39 8.78 37.69 5.25
4804 7564 2.803492 GCATGTATCAGAAGGGTCGGAC 60.803 54.545 0.00 0.00 30.30 4.79
4825 7585 3.254060 CACCGGTCTTCTGTCATACTTG 58.746 50.000 2.59 0.00 0.00 3.16
4975 7764 5.130292 AGTCATGCAAGGTTTTCAGAATG 57.870 39.130 0.00 0.00 37.54 2.67
5175 7981 4.078980 ACCAGGAGCCATTAAATCTGGATT 60.079 41.667 13.29 0.00 43.05 3.01
5188 7994 0.472471 AGAAACGAAACCAGGAGCCA 59.528 50.000 0.00 0.00 0.00 4.75
5194 8000 2.872245 TCTTCTGCAGAAACGAAACCAG 59.128 45.455 28.16 14.31 33.07 4.00
5232 8038 2.263077 CTCGTGGAAGAACTTCGATGG 58.737 52.381 15.07 6.60 40.37 3.51
5289 8095 1.102222 ACCTCTGCGACCCTCGATAC 61.102 60.000 0.00 0.00 43.74 2.24
5465 8271 2.183478 TGCTATATGCCATTGTCGGG 57.817 50.000 0.00 0.00 42.00 5.14
5545 8351 6.322969 TGATAATACTCGGAGAAGGTTAGCAA 59.677 38.462 12.86 0.00 34.09 3.91
5605 8425 3.059188 CGTACGTGAAACTTCAATTGGCT 60.059 43.478 7.22 0.00 39.21 4.75
5630 8450 5.574830 GCGAGATATTATCACTCATGTCCAC 59.425 44.000 6.46 0.00 0.00 4.02
5752 9399 1.153168 CATGCCCCCTAACGGACAG 60.153 63.158 0.00 0.00 0.00 3.51
5753 9400 2.994699 CATGCCCCCTAACGGACA 59.005 61.111 0.00 0.00 0.00 4.02
5754 9401 2.516225 GCATGCCCCCTAACGGAC 60.516 66.667 6.36 0.00 0.00 4.79
5755 9402 3.012119 TGCATGCCCCCTAACGGA 61.012 61.111 16.68 0.00 0.00 4.69
5791 9438 1.672737 CGTCTATTGTGCCTGTGCTCA 60.673 52.381 0.00 0.00 39.09 4.26
5834 9481 1.141657 TGTCAACTTCAGAAGCAGCCT 59.858 47.619 10.33 0.00 0.00 4.58
5848 9495 1.265365 GCAACTTCCAGCTCTGTCAAC 59.735 52.381 0.00 0.00 0.00 3.18
5854 9501 1.419387 AGAACTGCAACTTCCAGCTCT 59.581 47.619 0.00 0.00 32.50 4.09
5874 9521 1.338960 TGCAGCCAATCATCACTTCGA 60.339 47.619 0.00 0.00 0.00 3.71
5915 9748 1.305381 AGGTCCCCGTCCAGAGAAG 60.305 63.158 0.00 0.00 0.00 2.85
5920 9753 2.663196 GTTCAGGTCCCCGTCCAG 59.337 66.667 0.00 0.00 0.00 3.86
5950 9784 1.817099 CTTCCTGCGATCTGGCCAC 60.817 63.158 0.00 0.00 0.00 5.01
6006 9854 9.866655 ATGAATAAATTTGGCTATTACCTCTCA 57.133 29.630 0.00 0.00 0.00 3.27
6046 9894 8.280084 TCTAAGTTATACTATCCCACACTCTGT 58.720 37.037 0.00 0.00 0.00 3.41
6047 9895 8.693120 TCTAAGTTATACTATCCCACACTCTG 57.307 38.462 0.00 0.00 0.00 3.35
6048 9896 9.523168 GATCTAAGTTATACTATCCCACACTCT 57.477 37.037 0.00 0.00 0.00 3.24
6050 9898 9.656323 TTGATCTAAGTTATACTATCCCACACT 57.344 33.333 0.00 0.00 0.00 3.55
6051 9899 9.915629 CTTGATCTAAGTTATACTATCCCACAC 57.084 37.037 0.00 0.00 0.00 3.82
6052 9900 9.090103 CCTTGATCTAAGTTATACTATCCCACA 57.910 37.037 0.00 0.00 34.45 4.17
6053 9901 8.532819 CCCTTGATCTAAGTTATACTATCCCAC 58.467 40.741 0.00 0.00 34.45 4.61
6054 9902 7.678598 CCCCTTGATCTAAGTTATACTATCCCA 59.321 40.741 0.00 0.00 34.45 4.37
6055 9903 7.679025 ACCCCTTGATCTAAGTTATACTATCCC 59.321 40.741 0.00 0.00 34.45 3.85
6056 9904 8.667592 ACCCCTTGATCTAAGTTATACTATCC 57.332 38.462 0.00 0.00 34.45 2.59
6057 9905 9.930693 CAACCCCTTGATCTAAGTTATACTATC 57.069 37.037 0.00 0.00 34.45 2.08
6058 9906 8.881262 CCAACCCCTTGATCTAAGTTATACTAT 58.119 37.037 0.00 0.00 34.45 2.12
6059 9907 7.847848 ACCAACCCCTTGATCTAAGTTATACTA 59.152 37.037 0.00 0.00 34.45 1.82
6060 9908 6.677076 ACCAACCCCTTGATCTAAGTTATACT 59.323 38.462 0.00 0.00 34.45 2.12
6097 9945 3.255379 GCTAGGTTCGAAGCGCCG 61.255 66.667 20.64 13.86 0.00 6.46
6103 9951 2.066262 CTCGCTTTTGCTAGGTTCGAA 58.934 47.619 0.00 0.00 44.80 3.71
6104 9952 1.271379 TCTCGCTTTTGCTAGGTTCGA 59.729 47.619 0.00 0.00 44.80 3.71
6106 9954 3.067833 AGTTCTCGCTTTTGCTAGGTTC 58.932 45.455 0.00 0.00 44.80 3.62
6107 9955 3.127425 AGTTCTCGCTTTTGCTAGGTT 57.873 42.857 0.00 0.00 44.80 3.50
6115 9963 5.203060 AGTCTAGTCAAGTTCTCGCTTTT 57.797 39.130 0.00 0.00 0.00 2.27
6122 9970 6.209589 TGAAGCACATAGTCTAGTCAAGTTCT 59.790 38.462 0.00 0.00 0.00 3.01
6134 9982 5.673337 TGTCAACTTTGAAGCACATAGTC 57.327 39.130 7.25 0.00 39.22 2.59
6136 9984 5.682862 GTGTTGTCAACTTTGAAGCACATAG 59.317 40.000 16.45 0.00 39.21 2.23
6214 10064 6.772716 CCAAGGATGGTGCTATTGTTATAGTT 59.227 38.462 0.00 0.00 42.18 2.24
6293 10160 3.642848 ACTTCCCTTGTGATTGCAACATT 59.357 39.130 0.00 0.00 0.00 2.71
6294 10161 3.006110 CACTTCCCTTGTGATTGCAACAT 59.994 43.478 0.00 0.00 37.60 2.71
6297 10164 1.340889 GCACTTCCCTTGTGATTGCAA 59.659 47.619 0.00 0.00 37.60 4.08
6302 10169 0.321653 GACGGCACTTCCCTTGTGAT 60.322 55.000 0.00 0.00 37.60 3.06
6317 10184 2.740055 GCTGGTGCTGTGAGACGG 60.740 66.667 0.00 0.00 36.03 4.79
6327 10194 0.810031 ACATAATCGTCGGCTGGTGC 60.810 55.000 0.00 0.00 38.76 5.01
6335 10202 2.888594 ACCCTCACAACATAATCGTCG 58.111 47.619 0.00 0.00 0.00 5.12
6353 10220 4.261867 GGGTTTAAGTCCATGACAACAACC 60.262 45.833 0.00 10.61 36.77 3.77


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

AutoCloner maintained by Alex Coulton.