Multiple sequence alignment - TraesCS1B01G117200

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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 TraesCS1B01G117200 chr1B 100.000 4712 0 0 1 4712 137444194 137448905 0.000000e+00 8702.0
1 TraesCS1B01G117200 chr1B 96.859 2133 45 8 1766 3882 137177900 137180026 0.000000e+00 3548.0
2 TraesCS1B01G117200 chr1B 87.661 1394 94 38 2830 4183 137153075 137154430 0.000000e+00 1550.0
3 TraesCS1B01G117200 chr1B 87.882 1048 81 20 2875 3882 137174670 137175711 0.000000e+00 1190.0
4 TraesCS1B01G117200 chr1B 95.018 562 11 3 1104 1663 137177356 137177902 0.000000e+00 867.0
5 TraesCS1B01G117200 chr1B 86.891 534 37 12 1767 2281 137174123 137174642 6.840000e-158 568.0
6 TraesCS1B01G117200 chr1B 86.910 466 37 8 1767 2209 137152505 137152969 7.040000e-138 501.0
7 TraesCS1B01G117200 chr1B 80.851 564 59 22 1105 1651 137173344 137173875 9.500000e-107 398.0
8 TraesCS1B01G117200 chr1B 91.736 242 14 1 1112 1353 137151808 137152043 9.770000e-87 331.0
9 TraesCS1B01G117200 chr1B 94.898 196 9 1 4203 4397 137154526 137154721 5.920000e-79 305.0
10 TraesCS1B01G117200 chr1B 84.848 297 24 7 4415 4709 137154878 137155155 3.590000e-71 279.0
11 TraesCS1B01G117200 chr1B 85.235 149 15 4 1510 1651 137152097 137152245 3.800000e-31 147.0
12 TraesCS1B01G117200 chr1B 92.771 83 5 1 4628 4709 137180436 137180518 8.280000e-23 119.0
13 TraesCS1B01G117200 chr1B 87.059 85 3 6 3879 3959 453340779 453340699 6.490000e-14 89.8
14 TraesCS1B01G117200 chr1B 100.000 33 0 0 4100 4132 137154307 137154339 1.420000e-05 62.1
15 TraesCS1B01G117200 chr1D 94.774 2143 83 10 1766 3882 84723531 84725670 0.000000e+00 3310.0
16 TraesCS1B01G117200 chr1D 91.932 1636 63 15 51 1663 84721888 84723477 0.000000e+00 2226.0
17 TraesCS1B01G117200 chr1D 91.134 1049 62 19 2829 3866 84569413 84570441 0.000000e+00 1393.0
18 TraesCS1B01G117200 chr1D 87.226 1049 86 21 2875 3882 84612120 84613161 0.000000e+00 1151.0
19 TraesCS1B01G117200 chr1D 87.130 777 61 15 3951 4709 84725738 84726493 0.000000e+00 845.0
20 TraesCS1B01G117200 chr1D 87.605 597 48 14 4132 4709 84613353 84613942 0.000000e+00 669.0
21 TraesCS1B01G117200 chr1D 85.767 541 35 20 1767 2282 84611570 84612093 6.940000e-148 534.0
22 TraesCS1B01G117200 chr1D 83.217 572 38 18 1111 1642 84610750 84611303 5.520000e-129 472.0
23 TraesCS1B01G117200 chr1D 81.803 588 56 22 1108 1655 84565706 84566282 3.350000e-121 446.0
24 TraesCS1B01G117200 chr1D 82.330 515 43 25 4203 4709 84570972 84571446 2.040000e-108 403.0
25 TraesCS1B01G117200 chr1D 85.496 393 33 10 1767 2135 84566392 84566784 5.720000e-104 388.0
26 TraesCS1B01G117200 chr1D 100.000 32 0 0 4101 4132 84570688 84570719 5.090000e-05 60.2
27 TraesCS1B01G117200 chr1A 94.517 2134 76 12 1766 3882 78953954 78956063 0.000000e+00 3254.0
28 TraesCS1B01G117200 chr1A 91.707 1025 61 11 2875 3882 78547294 78548311 0.000000e+00 1400.0
29 TraesCS1B01G117200 chr1A 90.870 920 58 14 2875 3783 78338531 78339435 0.000000e+00 1210.0
30 TraesCS1B01G117200 chr1A 86.873 777 60 17 3951 4709 78956131 78956883 0.000000e+00 832.0
31 TraesCS1B01G117200 chr1A 90.805 609 27 3 1084 1663 78953300 78953908 0.000000e+00 787.0
32 TraesCS1B01G117200 chr1A 86.989 538 33 18 1767 2282 78546744 78547266 5.290000e-159 571.0
33 TraesCS1B01G117200 chr1A 84.068 590 50 16 1082 1651 78543189 78543754 3.230000e-146 529.0
34 TraesCS1B01G117200 chr1A 85.333 450 37 11 4269 4709 78339431 78339860 5.600000e-119 438.0
35 TraesCS1B01G117200 chr1A 85.782 422 35 9 1767 2164 78338004 78338424 1.570000e-114 424.0
36 TraesCS1B01G117200 chr1A 81.714 525 62 20 4196 4709 78548639 78549140 1.580000e-109 407.0
37 TraesCS1B01G117200 chr1A 91.429 210 8 8 840 1043 78953094 78953299 3.590000e-71 279.0
38 TraesCS1B01G117200 chr1A 91.304 161 14 0 1110 1270 78335392 78335552 2.210000e-53 220.0
39 TraesCS1B01G117200 chr1A 85.629 167 17 5 2655 2815 115367925 115367760 8.110000e-38 169.0
40 TraesCS1B01G117200 chr1A 94.505 91 4 1 1265 1355 78335884 78335973 6.360000e-29 139.0
41 TraesCS1B01G117200 chr1A 83.893 149 17 5 1510 1651 78336025 78336173 8.220000e-28 135.0
42 TraesCS1B01G117200 chr1A 88.235 85 3 4 3879 3959 438296519 438296438 1.400000e-15 95.3
43 TraesCS1B01G117200 chr7A 83.190 232 23 10 2829 3056 583787523 583787304 1.030000e-46 198.0
44 TraesCS1B01G117200 chr7A 87.013 77 2 5 3878 3950 688348575 688348647 3.910000e-11 80.5
45 TraesCS1B01G117200 chr7D 97.297 111 3 0 1660 1770 58205448 58205558 6.220000e-44 189.0
46 TraesCS1B01G117200 chr7D 85.714 77 3 5 3878 3950 595350701 595350773 1.820000e-09 75.0
47 TraesCS1B01G117200 chr5B 94.309 123 7 0 1657 1779 493017645 493017767 6.220000e-44 189.0
48 TraesCS1B01G117200 chrUn 95.536 112 5 0 1657 1768 218382245 218382134 3.750000e-41 180.0
49 TraesCS1B01G117200 chrUn 95.536 112 5 0 1657 1768 218399793 218399682 3.750000e-41 180.0
50 TraesCS1B01G117200 chr7B 95.575 113 4 1 1661 1773 562094014 562093903 3.750000e-41 180.0
51 TraesCS1B01G117200 chr2B 95.536 112 5 0 1661 1772 779369532 779369643 3.750000e-41 180.0
52 TraesCS1B01G117200 chr2B 83.529 85 7 2 3879 3959 201440277 201440358 6.540000e-09 73.1
53 TraesCS1B01G117200 chr2B 97.436 39 1 0 2588 2626 777673437 777673475 3.040000e-07 67.6
54 TraesCS1B01G117200 chr6A 89.855 138 10 3 1661 1796 475435162 475435027 1.740000e-39 174.0
55 TraesCS1B01G117200 chr6B 92.562 121 7 2 1660 1778 455146514 455146394 6.270000e-39 172.0
56 TraesCS1B01G117200 chr6B 84.706 85 6 4 3879 3959 14312580 14312499 1.410000e-10 78.7
57 TraesCS1B01G117200 chr3B 90.698 129 9 3 1657 1783 48886467 48886594 8.110000e-38 169.0
58 TraesCS1B01G117200 chr3A 91.803 122 9 1 2703 2823 383695621 383695500 8.110000e-38 169.0
59 TraesCS1B01G117200 chr3A 96.875 32 1 0 2316 2347 550440208 550440239 2.000000e-03 54.7
60 TraesCS1B01G117200 chr6D 90.588 85 1 4 3879 3959 422072020 422072101 6.450000e-19 106.0
61 TraesCS1B01G117200 chr6D 86.585 82 4 4 3879 3956 7414519 7414597 3.020000e-12 84.2
62 TraesCS1B01G117200 chr5A 87.654 81 6 2 3879 3959 622099690 622099766 1.810000e-14 91.6


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 TraesCS1B01G117200 chr1B 137444194 137448905 4711 False 8702.000000 8702 100.000000 1 4712 1 chr1B.!!$F1 4711
1 TraesCS1B01G117200 chr1B 137173344 137180518 7174 False 1115.000000 3548 90.045333 1104 4709 6 chr1B.!!$F3 3605
2 TraesCS1B01G117200 chr1B 137151808 137155155 3347 False 453.585714 1550 90.184000 1112 4709 7 chr1B.!!$F2 3597
3 TraesCS1B01G117200 chr1D 84721888 84726493 4605 False 2127.000000 3310 91.278667 51 4709 3 chr1D.!!$F3 4658
4 TraesCS1B01G117200 chr1D 84610750 84613942 3192 False 706.500000 1151 85.953750 1111 4709 4 chr1D.!!$F2 3598
5 TraesCS1B01G117200 chr1D 84565706 84571446 5740 False 538.040000 1393 88.152600 1108 4709 5 chr1D.!!$F1 3601
6 TraesCS1B01G117200 chr1A 78953094 78956883 3789 False 1288.000000 3254 90.906000 840 4709 4 chr1A.!!$F3 3869
7 TraesCS1B01G117200 chr1A 78543189 78549140 5951 False 726.750000 1400 86.119500 1082 4709 4 chr1A.!!$F2 3627
8 TraesCS1B01G117200 chr1A 78335392 78339860 4468 False 427.666667 1210 88.614500 1110 4709 6 chr1A.!!$F1 3599

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
44 45 0.033796 CCACCATCCCATTCTGCTGT 60.034 55.0 0.00 0.0 0.00 4.40 F
920 922 0.036732 AACACGATGATGCCCACTGT 59.963 50.0 0.00 0.0 0.00 3.55 F
921 923 0.674581 ACACGATGATGCCCACTGTG 60.675 55.0 0.00 0.0 38.48 3.66 F
922 924 0.674581 CACGATGATGCCCACTGTGT 60.675 55.0 7.08 0.0 31.98 3.72 F
2833 14259 0.320073 TTGGTGCTTCGTAGGTTCCG 60.320 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1267 1.146041 CCAATGAATCCTCCGGCGA 59.854 57.895 9.30 0.0 0.00 5.54 R
2632 14058 1.076995 TACTAGCCTCGCCTGAGCA 60.077 57.895 0.00 0.0 41.13 4.26 R
2811 14237 3.602483 GGAACCTACGAAGCACCAATAA 58.398 45.455 0.00 0.0 0.00 1.40 R
2969 14408 2.238395 TGCTACATCTGTGCCCATGTTA 59.762 45.455 0.00 0.0 34.92 2.41 R
4472 16485 0.323302 TGATGGGCGCTTGTTACTGA 59.677 50.000 7.64 0.0 0.00 3.41 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
17 18 4.863415 CCCTGGGGCAAGCTTAAA 57.137 55.556 4.27 0.00 0.00 1.52
18 19 3.065462 CCCTGGGGCAAGCTTAAAA 57.935 52.632 4.27 0.00 0.00 1.52
19 20 1.571955 CCCTGGGGCAAGCTTAAAAT 58.428 50.000 4.27 0.00 0.00 1.82
20 21 2.745968 CCCTGGGGCAAGCTTAAAATA 58.254 47.619 4.27 0.00 0.00 1.40
21 22 2.430694 CCCTGGGGCAAGCTTAAAATAC 59.569 50.000 4.27 0.00 0.00 1.89
22 23 2.430694 CCTGGGGCAAGCTTAAAATACC 59.569 50.000 0.00 0.00 0.00 2.73
23 24 3.365472 CTGGGGCAAGCTTAAAATACCT 58.635 45.455 0.00 0.00 0.00 3.08
24 25 3.769300 CTGGGGCAAGCTTAAAATACCTT 59.231 43.478 0.00 0.00 0.00 3.50
25 26 3.767131 TGGGGCAAGCTTAAAATACCTTC 59.233 43.478 0.00 0.00 0.00 3.46
26 27 3.132289 GGGGCAAGCTTAAAATACCTTCC 59.868 47.826 0.00 0.00 0.00 3.46
27 28 3.767131 GGGCAAGCTTAAAATACCTTCCA 59.233 43.478 0.00 0.00 0.00 3.53
28 29 4.381612 GGGCAAGCTTAAAATACCTTCCAC 60.382 45.833 0.00 0.00 0.00 4.02
29 30 4.381612 GGCAAGCTTAAAATACCTTCCACC 60.382 45.833 0.00 0.00 0.00 4.61
30 31 4.219725 GCAAGCTTAAAATACCTTCCACCA 59.780 41.667 0.00 0.00 0.00 4.17
31 32 5.105351 GCAAGCTTAAAATACCTTCCACCAT 60.105 40.000 0.00 0.00 0.00 3.55
32 33 6.564328 CAAGCTTAAAATACCTTCCACCATC 58.436 40.000 0.00 0.00 0.00 3.51
33 34 5.201243 AGCTTAAAATACCTTCCACCATCC 58.799 41.667 0.00 0.00 0.00 3.51
34 35 4.341235 GCTTAAAATACCTTCCACCATCCC 59.659 45.833 0.00 0.00 0.00 3.85
35 36 5.515106 CTTAAAATACCTTCCACCATCCCA 58.485 41.667 0.00 0.00 0.00 4.37
36 37 4.625225 AAAATACCTTCCACCATCCCAT 57.375 40.909 0.00 0.00 0.00 4.00
37 38 4.625225 AAATACCTTCCACCATCCCATT 57.375 40.909 0.00 0.00 0.00 3.16
38 39 3.884037 ATACCTTCCACCATCCCATTC 57.116 47.619 0.00 0.00 0.00 2.67
39 40 1.686236 ACCTTCCACCATCCCATTCT 58.314 50.000 0.00 0.00 0.00 2.40
40 41 1.285962 ACCTTCCACCATCCCATTCTG 59.714 52.381 0.00 0.00 0.00 3.02
41 42 1.396653 CTTCCACCATCCCATTCTGC 58.603 55.000 0.00 0.00 0.00 4.26
42 43 1.002069 TTCCACCATCCCATTCTGCT 58.998 50.000 0.00 0.00 0.00 4.24
43 44 0.256752 TCCACCATCCCATTCTGCTG 59.743 55.000 0.00 0.00 0.00 4.41
44 45 0.033796 CCACCATCCCATTCTGCTGT 60.034 55.000 0.00 0.00 0.00 4.40
45 46 1.386533 CACCATCCCATTCTGCTGTC 58.613 55.000 0.00 0.00 0.00 3.51
46 47 0.257039 ACCATCCCATTCTGCTGTCC 59.743 55.000 0.00 0.00 0.00 4.02
47 48 0.256752 CCATCCCATTCTGCTGTCCA 59.743 55.000 0.00 0.00 0.00 4.02
48 49 1.133575 CCATCCCATTCTGCTGTCCAT 60.134 52.381 0.00 0.00 0.00 3.41
49 50 2.662866 CATCCCATTCTGCTGTCCATT 58.337 47.619 0.00 0.00 0.00 3.16
50 51 2.425143 TCCCATTCTGCTGTCCATTC 57.575 50.000 0.00 0.00 0.00 2.67
51 52 1.634973 TCCCATTCTGCTGTCCATTCA 59.365 47.619 0.00 0.00 0.00 2.57
52 53 1.747355 CCCATTCTGCTGTCCATTCAC 59.253 52.381 0.00 0.00 0.00 3.18
53 54 2.619849 CCCATTCTGCTGTCCATTCACT 60.620 50.000 0.00 0.00 0.00 3.41
54 55 3.087031 CCATTCTGCTGTCCATTCACTT 58.913 45.455 0.00 0.00 0.00 3.16
55 56 3.119602 CCATTCTGCTGTCCATTCACTTG 60.120 47.826 0.00 0.00 0.00 3.16
74 75 2.265367 TGACCCCAAAGCTGTCTGATA 58.735 47.619 3.17 0.00 0.00 2.15
81 82 3.538591 CAAAGCTGTCTGATATGCTGGA 58.461 45.455 0.00 0.00 35.79 3.86
92 93 8.158789 TGTCTGATATGCTGGATAATTTCATCA 58.841 33.333 0.00 0.00 0.00 3.07
104 105 2.168326 TTTCATCAAGCAGAGCGTCA 57.832 45.000 0.00 0.00 0.00 4.35
111 112 5.463392 TCATCAAGCAGAGCGTCATAATTAC 59.537 40.000 0.00 0.00 0.00 1.89
119 120 5.261370 GAGCGTCATAATTACTGCTCATG 57.739 43.478 18.04 0.00 46.05 3.07
146 147 0.809241 GATCCTCGTCCAGCTGCAAG 60.809 60.000 8.66 0.00 0.00 4.01
158 159 1.926511 GCTGCAAGTGGAATGTCGGG 61.927 60.000 0.00 0.00 35.30 5.14
172 173 0.951040 GTCGGGGAGTTCTGCAAGTG 60.951 60.000 0.00 0.00 33.76 3.16
192 193 7.954248 GCAAGTGAAGATTATATAACATGAGCG 59.046 37.037 0.00 0.00 0.00 5.03
251 252 7.722949 ACCAATTTATGTTGATGAGATGGTT 57.277 32.000 0.00 0.00 33.92 3.67
252 253 8.137745 ACCAATTTATGTTGATGAGATGGTTT 57.862 30.769 0.00 0.00 33.92 3.27
337 338 0.527385 TTCGTTTGCCAGCAACTTGC 60.527 50.000 4.18 5.55 45.46 4.01
367 368 6.036517 GCTGTATATCGTCCCAATCAATCATC 59.963 42.308 0.00 0.00 0.00 2.92
368 369 7.003402 TGTATATCGTCCCAATCAATCATCA 57.997 36.000 0.00 0.00 0.00 3.07
369 370 7.623630 TGTATATCGTCCCAATCAATCATCAT 58.376 34.615 0.00 0.00 0.00 2.45
371 372 9.770097 GTATATCGTCCCAATCAATCATCATAT 57.230 33.333 0.00 0.00 0.00 1.78
475 476 2.594365 AATCCAATCCCAGCCAGCCC 62.594 60.000 0.00 0.00 0.00 5.19
484 485 1.527370 CAGCCAGCCCTACTAACCC 59.473 63.158 0.00 0.00 0.00 4.11
534 535 2.304470 TCGGACCATGAACTGATTCCAA 59.696 45.455 0.00 0.00 33.49 3.53
538 539 2.819608 ACCATGAACTGATTCCAAACCG 59.180 45.455 0.00 0.00 33.49 4.44
553 554 2.816083 CCGCACGGACCGCAATTA 60.816 61.111 15.39 0.00 37.50 1.40
554 555 2.392181 CCGCACGGACCGCAATTAA 61.392 57.895 15.39 0.00 37.50 1.40
555 556 1.711060 CCGCACGGACCGCAATTAAT 61.711 55.000 15.39 0.00 37.50 1.40
556 557 0.931702 CGCACGGACCGCAATTAATA 59.068 50.000 15.39 0.00 0.00 0.98
588 589 6.039829 GTGATTAAGGCCCAGGATTAAGAAAG 59.960 42.308 0.00 0.00 0.00 2.62
602 603 0.744281 AGAAAGGTGGGTTTTGTGCG 59.256 50.000 0.00 0.00 0.00 5.34
619 620 0.965363 GCGGAGGCCCATGAGAAAAA 60.965 55.000 0.00 0.00 0.00 1.94
620 621 0.811281 CGGAGGCCCATGAGAAAAAC 59.189 55.000 0.00 0.00 0.00 2.43
621 622 0.811281 GGAGGCCCATGAGAAAAACG 59.189 55.000 0.00 0.00 0.00 3.60
622 623 1.613255 GGAGGCCCATGAGAAAAACGA 60.613 52.381 0.00 0.00 0.00 3.85
623 624 1.740025 GAGGCCCATGAGAAAAACGAG 59.260 52.381 0.00 0.00 0.00 4.18
624 625 0.811281 GGCCCATGAGAAAAACGAGG 59.189 55.000 0.00 0.00 0.00 4.63
625 626 1.613255 GGCCCATGAGAAAAACGAGGA 60.613 52.381 0.00 0.00 0.00 3.71
630 631 0.690762 TGAGAAAAACGAGGAGGGGG 59.309 55.000 0.00 0.00 0.00 5.40
686 687 3.454573 CATGCCGCCAATGCTGGT 61.455 61.111 0.00 0.00 45.53 4.00
871 873 3.083997 GGGGTGATCGTGAGGGCT 61.084 66.667 0.00 0.00 0.00 5.19
913 915 0.647410 CGAGTCCAACACGATGATGC 59.353 55.000 0.00 0.00 34.12 3.91
914 916 1.009829 GAGTCCAACACGATGATGCC 58.990 55.000 0.00 0.00 0.00 4.40
915 917 0.392998 AGTCCAACACGATGATGCCC 60.393 55.000 0.00 0.00 0.00 5.36
916 918 0.676466 GTCCAACACGATGATGCCCA 60.676 55.000 0.00 0.00 0.00 5.36
917 919 0.676466 TCCAACACGATGATGCCCAC 60.676 55.000 0.00 0.00 0.00 4.61
919 921 0.448990 CAACACGATGATGCCCACTG 59.551 55.000 0.00 0.00 0.00 3.66
920 922 0.036732 AACACGATGATGCCCACTGT 59.963 50.000 0.00 0.00 0.00 3.55
921 923 0.674581 ACACGATGATGCCCACTGTG 60.675 55.000 0.00 0.00 38.48 3.66
922 924 0.674581 CACGATGATGCCCACTGTGT 60.675 55.000 7.08 0.00 31.98 3.72
963 983 2.482333 CCTAGGCCTCTGACCGTCG 61.482 68.421 9.68 0.00 0.00 5.12
964 984 1.451567 CTAGGCCTCTGACCGTCGA 60.452 63.158 9.68 0.00 0.00 4.20
1216 1267 1.752683 AGAAGAGTATCGGTGCGAGT 58.247 50.000 0.00 0.00 42.67 4.18
1297 1688 4.818005 TCATATACGTCCGCTACTTCTTCA 59.182 41.667 0.00 0.00 0.00 3.02
1500 1950 1.879380 TCCATCCTTGTTGCTTCGTTG 59.121 47.619 0.00 0.00 0.00 4.10
1562 2065 9.234827 AGTCAGTGTCATTCATTCATCAAAATA 57.765 29.630 0.00 0.00 0.00 1.40
1681 4944 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1682 4945 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1683 4946 1.753073 TCCCTCCGTTCCGAATTACTC 59.247 52.381 0.00 0.00 0.00 2.59
1686 4962 2.448219 CTCCGTTCCGAATTACTCGTC 58.552 52.381 0.00 0.00 46.65 4.20
1693 4969 5.159209 GTTCCGAATTACTCGTCTCTGAAA 58.841 41.667 0.00 0.00 46.65 2.69
1703 4979 8.858003 TTACTCGTCTCTGAAATGAATGTATC 57.142 34.615 0.00 0.00 0.00 2.24
1708 4984 8.903820 TCGTCTCTGAAATGAATGTATCTAGAA 58.096 33.333 0.00 0.00 0.00 2.10
1709 4985 8.963130 CGTCTCTGAAATGAATGTATCTAGAAC 58.037 37.037 0.00 0.00 0.00 3.01
1739 5015 8.809468 ATACATCTAGATACATCCATACGTGT 57.191 34.615 4.54 0.00 0.00 4.49
1740 5016 6.914259 ACATCTAGATACATCCATACGTGTG 58.086 40.000 4.54 5.16 0.00 3.82
1744 5020 5.592104 AGATACATCCATACGTGTGACAA 57.408 39.130 14.51 0.00 0.00 3.18
1745 5021 5.592054 AGATACATCCATACGTGTGACAAG 58.408 41.667 14.51 0.00 0.00 3.16
1756 5098 4.312443 ACGTGTGACAAGTAATTCGGAAT 58.688 39.130 1.47 0.00 0.00 3.01
1757 5099 4.151689 ACGTGTGACAAGTAATTCGGAATG 59.848 41.667 1.47 0.00 0.00 2.67
1762 5104 3.877508 GACAAGTAATTCGGAATGGAGGG 59.122 47.826 3.59 0.00 0.00 4.30
1763 5105 3.521937 ACAAGTAATTCGGAATGGAGGGA 59.478 43.478 3.59 0.00 0.00 4.20
1894 6924 2.024941 AGAGGGATTCCGGCTCAAAAAT 60.025 45.455 0.00 0.00 38.33 1.82
1909 6939 6.258507 GGCTCAAAAATTCAGTCAATGTTGTT 59.741 34.615 0.00 0.00 0.00 2.83
2527 13943 2.597903 GCCCCCATCTGTTCCCTC 59.402 66.667 0.00 0.00 0.00 4.30
2626 14052 2.003548 GCCCCTCCTCCTCACCAAT 61.004 63.158 0.00 0.00 0.00 3.16
2632 14058 1.912043 CTCCTCCTCACCAATGTCCTT 59.088 52.381 0.00 0.00 0.00 3.36
2811 14237 3.529533 CCGATACCGATACTCGTATCCT 58.470 50.000 10.55 0.93 38.91 3.24
2833 14259 0.320073 TTGGTGCTTCGTAGGTTCCG 60.320 55.000 0.00 0.00 0.00 4.30
3045 14486 9.906660 TCGTCATTCAAAACATAGCTAAAAATT 57.093 25.926 0.00 0.00 0.00 1.82
3162 14612 4.103785 CCCAAGAGAGGATTCATGGTATGT 59.896 45.833 0.00 0.00 0.00 2.29
3522 14973 0.034337 GTGGAGTCCTACAAACGGCA 59.966 55.000 11.33 0.00 0.00 5.69
3553 15004 2.917713 AGGAGTCTCTGTGGATGAGT 57.082 50.000 0.00 0.00 33.59 3.41
3570 15021 1.331756 GAGTTGCTGGTGTTGACTGTG 59.668 52.381 0.00 0.00 0.00 3.66
3577 15028 0.250295 GGTGTTGACTGTGGCTGCTA 60.250 55.000 0.00 0.00 0.00 3.49
3650 15101 3.555547 CGCAATGGTTACGATGATGAGAA 59.444 43.478 0.00 0.00 0.00 2.87
3712 15163 5.995282 ACTTGGTCGATTGTGTATTTCTGAA 59.005 36.000 0.00 0.00 0.00 3.02
3889 15457 1.481363 AGCTAGTTTTACTCCCTCCGC 59.519 52.381 0.00 0.00 0.00 5.54
3907 15475 5.339200 CCTCCGCCCCATAATATAAGATGTT 60.339 44.000 0.00 0.00 0.00 2.71
3908 15476 6.126883 CCTCCGCCCCATAATATAAGATGTTA 60.127 42.308 0.00 0.00 0.00 2.41
3909 15477 7.420214 CCTCCGCCCCATAATATAAGATGTTAT 60.420 40.741 0.29 0.29 33.25 1.89
3910 15478 7.867921 TCCGCCCCATAATATAAGATGTTATT 58.132 34.615 0.00 0.00 31.04 1.40
3911 15479 8.994500 TCCGCCCCATAATATAAGATGTTATTA 58.006 33.333 0.00 0.00 31.04 0.98
3912 15480 9.052759 CCGCCCCATAATATAAGATGTTATTAC 57.947 37.037 0.00 0.00 31.04 1.89
3913 15481 9.607988 CGCCCCATAATATAAGATGTTATTACA 57.392 33.333 0.00 0.00 38.95 2.41
4135 15834 3.999663 GCAAGATGCAGTAACAAGAGACT 59.000 43.478 0.00 0.00 44.26 3.24
4353 16224 4.939052 AGTGGTTCTGAATAGTATCCGG 57.061 45.455 0.00 0.00 0.00 5.14
4413 16426 9.128404 AGTTCTTAAAATAGGTTCTTTTTCCGT 57.872 29.630 0.00 0.00 0.00 4.69
4427 16440 6.565234 TCTTTTTCCGTAACTTTTGAATGCA 58.435 32.000 0.00 0.00 0.00 3.96
4453 16466 1.418637 TGGTGTTTCTAGTCCACCCAC 59.581 52.381 18.81 7.20 46.49 4.61
4472 16485 1.003442 TATGCCCTCCTGGAGCACT 59.997 57.895 18.51 7.84 40.50 4.40
4473 16486 1.050988 TATGCCCTCCTGGAGCACTC 61.051 60.000 18.51 6.94 40.50 3.51
4474 16487 3.005539 GCCCTCCTGGAGCACTCA 61.006 66.667 18.51 0.00 35.39 3.41
4475 16488 3.028921 GCCCTCCTGGAGCACTCAG 62.029 68.421 18.51 3.38 35.39 3.35
4507 16520 3.011818 CCATCAATAGAACTGCTGCACA 58.988 45.455 0.00 0.00 0.00 4.57
4616 16633 9.139174 CTGGTTACCAAATATTTGACAATGAAC 57.861 33.333 26.32 18.15 40.55 3.18
4709 16727 6.289834 ACAAAATGCTTGGTTTGATCAATGA 58.710 32.000 9.40 0.00 37.98 2.57
4710 16728 6.766944 ACAAAATGCTTGGTTTGATCAATGAA 59.233 30.769 9.40 1.90 37.98 2.57
4711 16729 6.790285 AAATGCTTGGTTTGATCAATGAAC 57.210 33.333 9.40 4.55 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.430694 GGTATTTTAAGCTTGCCCCAGG 59.569 50.000 9.86 0.00 0.00 4.45
3 4 3.466395 AGGTATTTTAAGCTTGCCCCA 57.534 42.857 9.86 0.00 0.00 4.96
6 7 4.381612 GGTGGAAGGTATTTTAAGCTTGCC 60.382 45.833 9.86 0.00 42.54 4.52
7 8 4.219725 TGGTGGAAGGTATTTTAAGCTTGC 59.780 41.667 9.86 1.07 43.22 4.01
8 9 5.975693 TGGTGGAAGGTATTTTAAGCTTG 57.024 39.130 9.86 0.00 37.32 4.01
9 10 5.656859 GGATGGTGGAAGGTATTTTAAGCTT 59.343 40.000 3.48 3.48 39.79 3.74
10 11 5.201243 GGATGGTGGAAGGTATTTTAAGCT 58.799 41.667 0.00 0.00 0.00 3.74
11 12 4.341235 GGGATGGTGGAAGGTATTTTAAGC 59.659 45.833 0.00 0.00 0.00 3.09
12 13 5.515106 TGGGATGGTGGAAGGTATTTTAAG 58.485 41.667 0.00 0.00 0.00 1.85
13 14 5.538082 TGGGATGGTGGAAGGTATTTTAA 57.462 39.130 0.00 0.00 0.00 1.52
14 15 5.742562 ATGGGATGGTGGAAGGTATTTTA 57.257 39.130 0.00 0.00 0.00 1.52
15 16 4.625225 ATGGGATGGTGGAAGGTATTTT 57.375 40.909 0.00 0.00 0.00 1.82
16 17 4.232820 AGAATGGGATGGTGGAAGGTATTT 59.767 41.667 0.00 0.00 0.00 1.40
17 18 3.793827 AGAATGGGATGGTGGAAGGTATT 59.206 43.478 0.00 0.00 0.00 1.89
18 19 3.139025 CAGAATGGGATGGTGGAAGGTAT 59.861 47.826 0.00 0.00 0.00 2.73
19 20 2.509548 CAGAATGGGATGGTGGAAGGTA 59.490 50.000 0.00 0.00 0.00 3.08
20 21 1.285962 CAGAATGGGATGGTGGAAGGT 59.714 52.381 0.00 0.00 0.00 3.50
21 22 2.025863 GCAGAATGGGATGGTGGAAGG 61.026 57.143 0.00 0.00 35.86 3.46
22 23 1.064166 AGCAGAATGGGATGGTGGAAG 60.064 52.381 0.00 0.00 35.86 3.46
23 24 1.002069 AGCAGAATGGGATGGTGGAA 58.998 50.000 0.00 0.00 35.86 3.53
24 25 0.256752 CAGCAGAATGGGATGGTGGA 59.743 55.000 0.00 0.00 40.38 4.02
25 26 0.033796 ACAGCAGAATGGGATGGTGG 60.034 55.000 8.95 0.00 46.52 4.61
27 28 0.257039 GGACAGCAGAATGGGATGGT 59.743 55.000 0.00 0.00 35.86 3.55
28 29 0.256752 TGGACAGCAGAATGGGATGG 59.743 55.000 0.00 0.00 35.86 3.51
29 30 2.359981 ATGGACAGCAGAATGGGATG 57.640 50.000 0.00 0.00 35.86 3.51
30 31 2.242965 TGAATGGACAGCAGAATGGGAT 59.757 45.455 0.00 0.00 35.86 3.85
31 32 1.634973 TGAATGGACAGCAGAATGGGA 59.365 47.619 0.00 0.00 35.86 4.37
32 33 1.747355 GTGAATGGACAGCAGAATGGG 59.253 52.381 0.00 0.00 35.86 4.00
33 34 2.719739 AGTGAATGGACAGCAGAATGG 58.280 47.619 0.00 0.00 35.86 3.16
34 35 3.754850 TCAAGTGAATGGACAGCAGAATG 59.245 43.478 0.00 0.00 40.87 2.67
35 36 3.755378 GTCAAGTGAATGGACAGCAGAAT 59.245 43.478 0.00 0.00 0.00 2.40
36 37 3.141398 GTCAAGTGAATGGACAGCAGAA 58.859 45.455 0.00 0.00 0.00 3.02
37 38 2.550855 GGTCAAGTGAATGGACAGCAGA 60.551 50.000 0.00 0.00 33.26 4.26
38 39 1.808945 GGTCAAGTGAATGGACAGCAG 59.191 52.381 0.00 0.00 33.26 4.24
39 40 1.545428 GGGTCAAGTGAATGGACAGCA 60.545 52.381 0.00 0.00 33.26 4.41
40 41 1.168714 GGGTCAAGTGAATGGACAGC 58.831 55.000 0.00 0.00 33.26 4.40
41 42 1.073763 TGGGGTCAAGTGAATGGACAG 59.926 52.381 0.00 0.00 33.26 3.51
42 43 1.144691 TGGGGTCAAGTGAATGGACA 58.855 50.000 0.00 0.00 33.26 4.02
43 44 2.286365 TTGGGGTCAAGTGAATGGAC 57.714 50.000 0.00 0.00 0.00 4.02
44 45 2.875296 CTTTGGGGTCAAGTGAATGGA 58.125 47.619 0.00 0.00 33.98 3.41
45 46 1.273327 GCTTTGGGGTCAAGTGAATGG 59.727 52.381 0.00 0.00 33.98 3.16
46 47 2.029649 CAGCTTTGGGGTCAAGTGAATG 60.030 50.000 0.00 0.00 33.98 2.67
47 48 2.242043 CAGCTTTGGGGTCAAGTGAAT 58.758 47.619 0.00 0.00 33.98 2.57
48 49 1.064017 ACAGCTTTGGGGTCAAGTGAA 60.064 47.619 0.00 0.00 33.98 3.18
49 50 0.550914 ACAGCTTTGGGGTCAAGTGA 59.449 50.000 0.00 0.00 33.98 3.41
50 51 0.954452 GACAGCTTTGGGGTCAAGTG 59.046 55.000 0.00 0.00 33.98 3.16
51 52 0.846693 AGACAGCTTTGGGGTCAAGT 59.153 50.000 4.19 0.00 33.98 3.16
52 53 1.202806 TCAGACAGCTTTGGGGTCAAG 60.203 52.381 4.19 0.00 33.98 3.02
53 54 0.843309 TCAGACAGCTTTGGGGTCAA 59.157 50.000 4.19 0.00 34.04 3.18
54 55 1.067295 ATCAGACAGCTTTGGGGTCA 58.933 50.000 4.19 0.00 34.04 4.02
55 56 3.209410 CATATCAGACAGCTTTGGGGTC 58.791 50.000 0.00 0.00 0.00 4.46
81 82 4.877823 TGACGCTCTGCTTGATGAAATTAT 59.122 37.500 0.00 0.00 0.00 1.28
92 93 3.557595 GCAGTAATTATGACGCTCTGCTT 59.442 43.478 12.35 0.00 42.00 3.91
104 105 5.604231 TCCTGAGACCATGAGCAGTAATTAT 59.396 40.000 0.00 0.00 0.00 1.28
111 112 1.070445 GGATCCTGAGACCATGAGCAG 59.930 57.143 3.84 0.00 0.00 4.24
119 120 0.395862 TGGACGAGGATCCTGAGACC 60.396 60.000 22.02 21.21 39.75 3.85
146 147 0.613777 AGAACTCCCCGACATTCCAC 59.386 55.000 0.00 0.00 0.00 4.02
158 159 9.547753 TTATATAATCTTCACTTGCAGAACTCC 57.452 33.333 0.00 0.00 0.00 3.85
188 189 1.871080 CATGGTTGGATCCTACGCTC 58.129 55.000 18.34 7.10 0.00 5.03
192 193 3.554934 TGATTGCATGGTTGGATCCTAC 58.445 45.455 17.01 17.01 0.00 3.18
235 236 4.646492 GGCCTTAAACCATCTCATCAACAT 59.354 41.667 0.00 0.00 0.00 2.71
251 252 3.042682 TGATGGGATCTTACGGCCTTAA 58.957 45.455 0.00 0.16 0.00 1.85
252 253 2.684943 TGATGGGATCTTACGGCCTTA 58.315 47.619 0.00 0.00 0.00 2.69
337 338 2.816689 TGGGACGATATACAGCAAACG 58.183 47.619 0.00 0.00 0.00 3.60
475 476 1.222661 GGGGGCGTTGGGTTAGTAG 59.777 63.158 0.00 0.00 0.00 2.57
484 485 0.748005 CCATCAAGTAGGGGGCGTTG 60.748 60.000 0.00 0.00 0.00 4.10
538 539 3.408288 TTTATTAATTGCGGTCCGTGC 57.592 42.857 13.94 0.00 0.00 5.34
553 554 8.065007 TCCTGGGCCTTAATCACTTTATTTATT 58.935 33.333 4.53 0.00 0.00 1.40
554 555 7.591821 TCCTGGGCCTTAATCACTTTATTTAT 58.408 34.615 4.53 0.00 0.00 1.40
555 556 6.975949 TCCTGGGCCTTAATCACTTTATTTA 58.024 36.000 4.53 0.00 0.00 1.40
556 557 5.837829 TCCTGGGCCTTAATCACTTTATTT 58.162 37.500 4.53 0.00 0.00 1.40
588 589 2.561037 CCTCCGCACAAAACCCACC 61.561 63.158 0.00 0.00 0.00 4.61
602 603 0.811281 CGTTTTTCTCATGGGCCTCC 59.189 55.000 4.53 0.00 0.00 4.30
648 649 0.251787 ATCCTTTTGAGGTGCCACCC 60.252 55.000 11.06 2.62 39.75 4.61
649 650 1.177401 GATCCTTTTGAGGTGCCACC 58.823 55.000 5.50 5.50 38.99 4.61
650 651 1.177401 GGATCCTTTTGAGGTGCCAC 58.823 55.000 3.84 0.00 0.00 5.01
651 652 0.776810 TGGATCCTTTTGAGGTGCCA 59.223 50.000 14.23 5.40 33.39 4.92
659 660 1.321805 TGGCGGCATGGATCCTTTTG 61.322 55.000 14.23 9.23 0.00 2.44
800 801 0.615850 TCCCTCAACACACACACACA 59.384 50.000 0.00 0.00 0.00 3.72
801 802 1.670811 CTTCCCTCAACACACACACAC 59.329 52.381 0.00 0.00 0.00 3.82
802 803 1.408127 CCTTCCCTCAACACACACACA 60.408 52.381 0.00 0.00 0.00 3.72
861 863 1.113517 GCCCATAGTAGCCCTCACGA 61.114 60.000 0.00 0.00 0.00 4.35
913 915 1.145156 TGTCGTCCAACACAGTGGG 59.855 57.895 5.31 0.00 39.34 4.61
914 916 4.846551 TGTCGTCCAACACAGTGG 57.153 55.556 5.31 0.00 40.33 4.00
920 922 0.533032 TCACTGTGTGTCGTCCAACA 59.467 50.000 7.79 0.00 34.79 3.33
921 923 1.647346 TTCACTGTGTGTCGTCCAAC 58.353 50.000 7.79 0.00 34.79 3.77
922 924 2.209273 CATTCACTGTGTGTCGTCCAA 58.791 47.619 7.79 0.00 34.79 3.53
1167 1218 3.043713 CACTTTCTCGCCGCAGCA 61.044 61.111 0.00 0.00 39.83 4.41
1216 1267 1.146041 CCAATGAATCCTCCGGCGA 59.854 57.895 9.30 0.00 0.00 5.54
1230 1284 1.227556 GCTGTATCGCGGGTCCAAT 60.228 57.895 6.13 0.00 0.00 3.16
1270 1661 3.881795 AGTAGCGGACGTATATGAAACG 58.118 45.455 0.00 1.63 45.64 3.60
1297 1688 1.597027 CCAGGTCGAGTTTGCCGTT 60.597 57.895 0.00 0.00 0.00 4.44
1500 1950 8.692110 TGAATTGAAATGAATTAGACATGCAC 57.308 30.769 0.00 0.00 0.00 4.57
1562 2065 8.624776 CAGAAAGTGAAAGTAACCTTCAGATTT 58.375 33.333 0.00 0.00 0.00 2.17
1681 4944 8.563732 TCTAGATACATTCATTTCAGAGACGAG 58.436 37.037 0.00 0.00 0.00 4.18
1682 4945 8.451908 TCTAGATACATTCATTTCAGAGACGA 57.548 34.615 0.00 0.00 0.00 4.20
1683 4946 8.963130 GTTCTAGATACATTCATTTCAGAGACG 58.037 37.037 0.00 0.00 0.00 4.18
1713 4989 9.244292 ACACGTATGGATGTATCTAGATGTATT 57.756 33.333 15.79 0.00 29.44 1.89
1714 4990 8.678199 CACACGTATGGATGTATCTAGATGTAT 58.322 37.037 15.79 9.11 29.44 2.29
1720 4996 6.313744 TGTCACACGTATGGATGTATCTAG 57.686 41.667 0.00 0.00 0.00 2.43
1723 4999 5.348986 ACTTGTCACACGTATGGATGTATC 58.651 41.667 0.00 0.00 0.00 2.24
1730 5006 4.032445 CCGAATTACTTGTCACACGTATGG 59.968 45.833 0.00 0.00 0.00 2.74
1736 5012 4.693566 TCCATTCCGAATTACTTGTCACAC 59.306 41.667 0.00 0.00 0.00 3.82
1738 5014 4.332819 CCTCCATTCCGAATTACTTGTCAC 59.667 45.833 0.00 0.00 0.00 3.67
1739 5015 4.513442 CCTCCATTCCGAATTACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
1740 5016 3.877508 CCCTCCATTCCGAATTACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
1744 5020 3.385115 ACTCCCTCCATTCCGAATTACT 58.615 45.455 0.00 0.00 0.00 2.24
1745 5021 3.840124 ACTCCCTCCATTCCGAATTAC 57.160 47.619 0.00 0.00 0.00 1.89
1756 5098 6.860034 AGTATGTATGTATGTACTCCCTCCA 58.140 40.000 0.00 0.00 0.00 3.86
1757 5099 7.176490 AGAGTATGTATGTATGTACTCCCTCC 58.824 42.308 7.54 0.00 42.40 4.30
1909 6939 5.707298 GTCAGAGGAAACAATCTTGATGGAA 59.293 40.000 0.00 0.00 0.00 3.53
2406 13814 6.356186 AGTATCGGGGGAGTATTGTAATTC 57.644 41.667 0.00 0.00 0.00 2.17
2527 13943 4.075682 GAGAAGGAGGAAAGAAACTTGGG 58.924 47.826 0.00 0.00 0.00 4.12
2573 13990 4.641645 CCGCTGGCACTGGGTGAA 62.642 66.667 1.57 0.00 38.48 3.18
2632 14058 1.076995 TACTAGCCTCGCCTGAGCA 60.077 57.895 0.00 0.00 41.13 4.26
2811 14237 3.602483 GGAACCTACGAAGCACCAATAA 58.398 45.455 0.00 0.00 0.00 1.40
2969 14408 2.238395 TGCTACATCTGTGCCCATGTTA 59.762 45.455 0.00 0.00 34.92 2.41
3045 14486 7.181665 TGGAATTGATTGAATATTTGGGGTTCA 59.818 33.333 0.00 0.00 0.00 3.18
3522 14973 2.437359 ACTCCTACTACGCGCCGT 60.437 61.111 5.73 5.99 44.35 5.68
3553 15004 1.383456 GCCACAGTCAACACCAGCAA 61.383 55.000 0.00 0.00 0.00 3.91
3570 15021 0.807667 CATCACCGACAGTAGCAGCC 60.808 60.000 0.00 0.00 0.00 4.85
3577 15028 4.646945 AGATAACTCATCATCACCGACAGT 59.353 41.667 0.00 0.00 35.96 3.55
3712 15163 8.572855 ACGGAATAACTAAGAGTTACAGTACT 57.427 34.615 1.29 0.00 42.78 2.73
3735 15186 3.637432 GAGAATCTGGCAGACTATGACG 58.363 50.000 21.37 0.00 41.39 4.35
3829 15311 8.634444 AGAGTCAGAATAGATACAATACACACC 58.366 37.037 0.00 0.00 0.00 4.16
3976 15544 4.469945 CCCTGTGTCCCATAAGTTAAGAGA 59.530 45.833 0.00 0.00 0.00 3.10
3977 15545 4.469945 TCCCTGTGTCCCATAAGTTAAGAG 59.530 45.833 0.00 0.00 0.00 2.85
3984 15552 3.375699 ACTACTCCCTGTGTCCCATAAG 58.624 50.000 0.00 0.00 0.00 1.73
3994 15568 2.766828 GGCAGTGAATACTACTCCCTGT 59.233 50.000 0.00 0.00 34.74 4.00
3995 15569 2.766263 TGGCAGTGAATACTACTCCCTG 59.234 50.000 0.00 0.00 34.74 4.45
4046 15674 1.000385 TCTTGCAATTCAACAAGGCGG 60.000 47.619 0.00 0.00 42.82 6.13
4096 15789 5.664294 TCTTGCAATTCAACAAGGCATAT 57.336 34.783 0.00 0.00 42.82 1.78
4126 15819 5.692204 CGATTCTAACACACAAGTCTCTTGT 59.308 40.000 9.00 9.00 0.00 3.16
4135 15834 2.927477 GCGATCCGATTCTAACACACAA 59.073 45.455 0.00 0.00 0.00 3.33
4353 16224 7.201794 GGGGTAAATTCTGCTATAGGTTTGAAC 60.202 40.741 1.04 0.00 0.00 3.18
4438 16451 2.504175 GGCATAGTGGGTGGACTAGAAA 59.496 50.000 0.00 0.00 31.94 2.52
4439 16452 2.116238 GGCATAGTGGGTGGACTAGAA 58.884 52.381 0.00 0.00 31.94 2.10
4440 16453 1.691482 GGGCATAGTGGGTGGACTAGA 60.691 57.143 0.00 0.00 31.94 2.43
4446 16459 1.694169 AGGAGGGCATAGTGGGTGG 60.694 63.158 0.00 0.00 0.00 4.61
4453 16466 1.053264 AGTGCTCCAGGAGGGCATAG 61.053 60.000 18.83 0.00 41.19 2.23
4472 16485 0.323302 TGATGGGCGCTTGTTACTGA 59.677 50.000 7.64 0.00 0.00 3.41
4473 16486 1.164411 TTGATGGGCGCTTGTTACTG 58.836 50.000 7.64 0.00 0.00 2.74
4474 16487 2.128771 ATTGATGGGCGCTTGTTACT 57.871 45.000 7.64 0.00 0.00 2.24
4475 16488 3.202906 TCTATTGATGGGCGCTTGTTAC 58.797 45.455 7.64 0.00 0.00 2.50
4507 16520 3.524789 TCACTGGGAATGATGTTCATCCT 59.475 43.478 9.83 0.00 35.76 3.24
4555 16570 7.828717 TCTTCTAATTGATGTGGAGTGCATAAA 59.171 33.333 0.00 0.00 0.00 1.40
4556 16571 7.337938 TCTTCTAATTGATGTGGAGTGCATAA 58.662 34.615 0.00 0.00 0.00 1.90
4557 16572 6.888105 TCTTCTAATTGATGTGGAGTGCATA 58.112 36.000 0.00 0.00 0.00 3.14
4596 16611 6.744112 ACGTGTTCATTGTCAAATATTTGGT 58.256 32.000 24.40 9.63 38.66 3.67
4597 16612 6.860539 TGACGTGTTCATTGTCAAATATTTGG 59.139 34.615 24.40 10.77 39.50 3.28
4679 16697 5.277825 TCAAACCAAGCATTTTGTAGAACG 58.722 37.500 0.00 0.00 34.81 3.95


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

AutoCloner maintained by Alex Coulton.