Multiple sequence alignment - TraesCS2D01G012200

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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 TraesCS2D01G012200 chr2D 100.000 7572 0 0 1 7572 5761836 5769407 0.000000e+00 13983.0
1 TraesCS2D01G012200 chr2D 91.748 1030 53 14 568 1583 278844787 278843776 0.000000e+00 1402.0
2 TraesCS2D01G012200 chr2D 89.510 143 9 4 3794 3931 569200961 569200820 7.810000e-40 176.0
3 TraesCS2D01G012200 chr2D 92.982 114 5 3 7139 7252 54963994 54963884 6.080000e-36 163.0
4 TraesCS2D01G012200 chr2D 93.458 107 5 2 7148 7254 233398898 233398794 2.830000e-34 158.0
5 TraesCS2D01G012200 chr2D 89.552 67 7 0 4356 4422 537443725 537443791 1.350000e-12 86.1
6 TraesCS2D01G012200 chr2D 96.078 51 1 1 1521 1571 278843779 278843730 1.750000e-11 82.4
7 TraesCS2D01G012200 chr2D 91.304 46 4 0 4324 4369 299896410 299896365 6.340000e-06 63.9
8 TraesCS2D01G012200 chr2D 97.059 34 0 1 6122 6154 95416542 95416575 1.000000e-03 56.5
9 TraesCS2D01G012200 chr2A 94.085 3821 131 44 194 3993 4222087 4218341 0.000000e+00 5716.0
10 TraesCS2D01G012200 chr2A 96.423 1817 50 8 4324 6133 4218346 4216538 0.000000e+00 2981.0
11 TraesCS2D01G012200 chr2A 96.519 747 18 3 6424 7168 4216461 4215721 0.000000e+00 1229.0
12 TraesCS2D01G012200 chr2A 96.891 193 5 1 7250 7442 4215723 4215532 9.480000e-84 322.0
13 TraesCS2D01G012200 chr2A 96.774 93 3 0 7480 7572 4215536 4215444 1.020000e-33 156.0
14 TraesCS2D01G012200 chr2A 93.056 72 5 0 6241 6312 4216536 4216465 1.040000e-18 106.0
15 TraesCS2D01G012200 chr2A 97.143 35 0 1 6121 6154 631859104 631859138 2.950000e-04 58.4
16 TraesCS2D01G012200 chr2B 95.425 2164 85 3 1419 3581 5662206 5664356 0.000000e+00 3435.0
17 TraesCS2D01G012200 chr2B 91.847 969 54 10 4422 5386 5664508 5665455 0.000000e+00 1328.0
18 TraesCS2D01G012200 chr2B 82.024 1146 114 50 474 1578 5661116 5662210 0.000000e+00 891.0
19 TraesCS2D01G012200 chr2B 90.415 626 49 8 5385 6009 5665559 5666174 0.000000e+00 813.0
20 TraesCS2D01G012200 chr2B 95.499 511 16 4 6456 6960 5666587 5667096 0.000000e+00 809.0
21 TraesCS2D01G012200 chr2B 94.910 334 14 2 3994 4325 415357777 415358109 3.130000e-143 520.0
22 TraesCS2D01G012200 chr2B 88.069 461 21 16 46 497 5660670 5661105 4.050000e-142 516.0
23 TraesCS2D01G012200 chr2B 77.500 1000 121 55 6173 7139 797696494 797697422 8.770000e-139 505.0
24 TraesCS2D01G012200 chr2B 86.323 446 48 8 5683 6123 797696058 797696495 2.470000e-129 473.0
25 TraesCS2D01G012200 chr2B 82.527 372 23 8 6005 6357 5666241 5666589 9.610000e-74 289.0
26 TraesCS2D01G012200 chr2B 93.197 147 7 1 3665 3808 5664363 5664509 5.950000e-51 213.0
27 TraesCS2D01G012200 chr2B 92.593 108 6 2 7167 7274 40438043 40437938 3.660000e-33 154.0
28 TraesCS2D01G012200 chr2B 86.538 104 12 2 4321 4422 418633764 418633661 6.210000e-21 113.0
29 TraesCS2D01G012200 chr2B 88.043 92 10 1 4330 4421 659650662 659650752 2.890000e-19 108.0
30 TraesCS2D01G012200 chr6B 91.945 807 39 14 565 1362 171041976 171042765 0.000000e+00 1107.0
31 TraesCS2D01G012200 chr6B 93.976 249 8 2 1342 1583 171042778 171043026 3.340000e-98 370.0
32 TraesCS2D01G012200 chr6B 91.489 94 6 2 4324 4417 548118516 548118425 2.220000e-25 128.0
33 TraesCS2D01G012200 chr6B 96.078 51 1 1 1521 1571 171043023 171043072 1.750000e-11 82.4
34 TraesCS2D01G012200 chr6B 97.059 34 1 0 6150 6183 554789694 554789727 2.950000e-04 58.4
35 TraesCS2D01G012200 chr3D 98.498 333 5 0 3994 4326 248809901 248810233 8.460000e-164 588.0
36 TraesCS2D01G012200 chr3D 97.885 331 7 0 3994 4324 248807971 248808301 2.370000e-159 573.0
37 TraesCS2D01G012200 chr3D 89.583 96 9 1 4327 4421 138181911 138181816 3.710000e-23 121.0
38 TraesCS2D01G012200 chr7D 96.687 332 11 0 3993 4324 169472002 169471671 3.090000e-153 553.0
39 TraesCS2D01G012200 chr7D 88.525 122 11 3 7136 7256 594802385 594802504 2.200000e-30 145.0
40 TraesCS2D01G012200 chr7D 87.000 100 7 6 4324 4420 18870097 18870001 2.890000e-19 108.0
41 TraesCS2D01G012200 chr7D 94.444 36 0 2 6149 6183 605963530 605963496 4.000000e-03 54.7
42 TraesCS2D01G012200 chr7D 94.286 35 1 1 6121 6154 391585532 391585498 1.400000e-02 52.8
43 TraesCS2D01G012200 chr4B 96.396 333 9 2 3994 4324 316296022 316296353 5.170000e-151 545.0
44 TraesCS2D01G012200 chr4B 94.895 333 14 2 3994 4324 316297942 316298273 1.130000e-142 518.0
45 TraesCS2D01G012200 chr4B 85.567 97 12 2 4327 4422 578050734 578050829 4.830000e-17 100.0
46 TraesCS2D01G012200 chr4B 93.548 62 3 1 3602 3663 41531438 41531498 2.910000e-14 91.6
47 TraesCS2D01G012200 chr4B 83.333 102 14 3 4321 4421 375130991 375131090 2.910000e-14 91.6
48 TraesCS2D01G012200 chr4B 90.625 64 5 1 3604 3667 127851011 127851073 4.870000e-12 84.2
49 TraesCS2D01G012200 chr4B 94.595 37 1 1 6119 6154 584587204 584587240 1.000000e-03 56.5
50 TraesCS2D01G012200 chr6D 95.468 331 12 2 3994 4322 441765307 441765636 6.730000e-145 525.0
51 TraesCS2D01G012200 chr6D 87.755 98 9 3 4324 4420 461683479 461683574 2.230000e-20 111.0
52 TraesCS2D01G012200 chr6D 88.235 68 6 2 3602 3669 273830989 273831054 6.300000e-11 80.5
53 TraesCS2D01G012200 chr1B 94.925 335 13 3 3994 4326 313099735 313100067 8.710000e-144 521.0
54 TraesCS2D01G012200 chr1B 94.262 122 6 1 3813 3933 326768348 326768227 1.300000e-42 185.0
55 TraesCS2D01G012200 chr1B 95.000 60 3 0 3610 3669 156850415 156850356 2.250000e-15 95.3
56 TraesCS2D01G012200 chr1B 85.106 94 12 2 3575 3667 593785987 593785895 2.250000e-15 95.3
57 TraesCS2D01G012200 chr1B 91.176 68 5 1 3602 3669 22328157 22328223 2.910000e-14 91.6
58 TraesCS2D01G012200 chr1B 97.059 34 1 0 6149 6182 3708747 3708780 2.950000e-04 58.4
59 TraesCS2D01G012200 chr1B 100.000 31 0 0 6119 6149 187715045 187715015 2.950000e-04 58.4
60 TraesCS2D01G012200 chr3A 94.595 333 11 2 3993 4324 341642886 341642560 6.780000e-140 508.0
61 TraesCS2D01G012200 chr3A 93.496 123 6 2 3811 3931 114570735 114570857 1.680000e-41 182.0
62 TraesCS2D01G012200 chr3A 94.167 120 5 2 3814 3931 444255474 444255355 1.680000e-41 182.0
63 TraesCS2D01G012200 chr3A 83.654 208 7 10 3811 3991 102531185 102530978 3.630000e-38 171.0
64 TraesCS2D01G012200 chr1A 95.902 122 4 1 3813 3933 293712667 293712546 5.990000e-46 196.0
65 TraesCS2D01G012200 chr1A 80.569 211 13 13 3811 3993 371086992 371087202 3.680000e-28 137.0
66 TraesCS2D01G012200 chr1A 90.769 65 5 1 3602 3666 350017161 350017098 1.350000e-12 86.1
67 TraesCS2D01G012200 chr1D 95.082 122 5 1 3813 3933 226450032 226449911 2.790000e-44 191.0
68 TraesCS2D01G012200 chr1D 86.607 112 14 1 4324 4434 483259401 483259290 1.030000e-23 122.0
69 TraesCS2D01G012200 chr1D 90.769 65 5 1 3602 3666 277362585 277362522 1.350000e-12 86.1
70 TraesCS2D01G012200 chr1D 85.294 68 10 0 4356 4423 159927632 159927699 3.790000e-08 71.3
71 TraesCS2D01G012200 chr5A 93.496 123 6 2 3811 3931 500045187 500045309 1.680000e-41 182.0
72 TraesCS2D01G012200 chr5A 82.812 192 25 8 3811 3996 475529273 475529462 1.690000e-36 165.0
73 TraesCS2D01G012200 chr5A 82.143 112 19 1 7462 7572 689702821 689702710 2.250000e-15 95.3
74 TraesCS2D01G012200 chr5A 84.043 94 12 3 3575 3667 675452034 675451943 3.760000e-13 87.9
75 TraesCS2D01G012200 chr4A 84.211 209 5 11 3814 3994 166730255 166730047 2.170000e-40 178.0
76 TraesCS2D01G012200 chr4A 84.615 91 13 1 3573 3663 724857581 724857670 1.050000e-13 89.8
77 TraesCS2D01G012200 chr4A 89.231 65 6 1 3602 3666 467263387 467263324 6.300000e-11 80.5
78 TraesCS2D01G012200 chr4A 100.000 32 0 0 6149 6180 710665543 710665512 8.210000e-05 60.2
79 TraesCS2D01G012200 chr4A 96.970 33 1 0 6150 6182 137185757 137185789 1.000000e-03 56.5
80 TraesCS2D01G012200 chr4A 94.595 37 1 1 6142 6177 712853328 712853364 1.000000e-03 56.5
81 TraesCS2D01G012200 chr4A 100.000 29 0 0 4376 4404 333523921 333523949 4.000000e-03 54.7
82 TraesCS2D01G012200 chr7B 83.732 209 6 11 3814 3994 559265047 559264839 1.010000e-38 172.0
83 TraesCS2D01G012200 chr7B 94.444 108 6 0 7167 7274 536260633 536260526 4.700000e-37 167.0
84 TraesCS2D01G012200 chr7B 98.837 86 1 0 7167 7252 26879173 26879258 3.660000e-33 154.0
85 TraesCS2D01G012200 chr7B 93.506 77 2 2 3917 3991 715717019 715716944 2.230000e-20 111.0
86 TraesCS2D01G012200 chr7B 85.859 99 14 0 4324 4422 715716947 715716849 1.040000e-18 106.0
87 TraesCS2D01G012200 chr7B 89.855 69 5 2 3602 3669 638921331 638921264 3.760000e-13 87.9
88 TraesCS2D01G012200 chr7B 94.737 38 0 2 6119 6154 508189381 508189418 2.950000e-04 58.4
89 TraesCS2D01G012200 chr7A 83.254 209 7 11 3811 3991 243645598 243645806 4.700000e-37 167.0
90 TraesCS2D01G012200 chr7A 86.420 81 10 1 3581 3661 509222371 509222450 3.760000e-13 87.9
91 TraesCS2D01G012200 chr7A 83.871 93 11 4 3576 3667 83624279 83624368 1.350000e-12 86.1
92 TraesCS2D01G012200 chr3B 95.960 99 2 2 7167 7265 567473600 567473504 7.860000e-35 159.0
93 TraesCS2D01G012200 chr3B 90.000 120 8 4 7135 7252 42629507 42629624 1.320000e-32 152.0
94 TraesCS2D01G012200 chr3B 86.747 83 9 2 3575 3656 132085499 132085580 2.910000e-14 91.6
95 TraesCS2D01G012200 chr3B 100.000 33 0 0 6119 6151 119469109 119469077 2.280000e-05 62.1
96 TraesCS2D01G012200 chr3B 97.143 35 0 1 6121 6154 298711727 298711761 2.950000e-04 58.4
97 TraesCS2D01G012200 chr3B 97.143 35 0 1 6121 6154 663972392 663972426 2.950000e-04 58.4
98 TraesCS2D01G012200 chr3B 97.059 34 0 1 6122 6154 616774395 616774428 1.000000e-03 56.5
99 TraesCS2D01G012200 chr5B 89.167 120 9 3 7148 7264 54462266 54462148 6.120000e-31 147.0
100 TraesCS2D01G012200 chr5B 83.178 107 9 5 7446 7545 646854715 646854611 1.050000e-13 89.8
101 TraesCS2D01G012200 chr5B 84.043 94 13 2 3575 3667 691746152 691746060 1.050000e-13 89.8
102 TraesCS2D01G012200 chr5B 100.000 31 0 0 6149 6179 28405991 28405961 2.950000e-04 58.4
103 TraesCS2D01G012200 chr4D 93.421 76 2 2 3919 3991 503174522 503174597 8.030000e-20 110.0
104 TraesCS2D01G012200 chr4D 89.062 64 6 1 3603 3666 298241454 298241392 2.270000e-10 78.7
105 TraesCS2D01G012200 chr4D 95.238 42 2 0 3622 3663 28974974 28975015 4.900000e-07 67.6
106 TraesCS2D01G012200 chr6A 89.157 83 8 1 4340 4422 592700098 592700179 1.340000e-17 102.0
107 TraesCS2D01G012200 chr6A 94.286 35 2 0 6149 6183 404687739 404687705 4.000000e-03 54.7
108 TraesCS2D01G012200 chr6A 92.308 39 0 3 6150 6186 495448774 495448737 1.400000e-02 52.8
109 TraesCS2D01G012200 chr5D 88.608 79 5 4 3602 3679 281024811 281024886 8.090000e-15 93.5
110 TraesCS2D01G012200 chr5D 91.489 47 4 0 3621 3667 491437579 491437625 1.760000e-06 65.8
111 TraesCS2D01G012200 chr5D 84.615 65 7 3 3581 3643 250068568 250068631 2.280000e-05 62.1
112 TraesCS2D01G012200 chr5D 100.000 33 0 0 6119 6151 527624380 527624348 2.280000e-05 62.1
113 TraesCS2D01G012200 chrUn 92.857 42 3 0 3610 3651 327873548 327873507 2.280000e-05 62.1
114 TraesCS2D01G012200 chrUn 92.857 42 3 0 3610 3651 327882497 327882456 2.280000e-05 62.1
115 TraesCS2D01G012200 chrUn 92.857 42 3 0 3610 3651 446036385 446036426 2.280000e-05 62.1


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 TraesCS2D01G012200 chr2D 5761836 5769407 7571 False 13983.000000 13983 100.000000 1 7572 1 chr2D.!!$F1 7571
1 TraesCS2D01G012200 chr2D 278843730 278844787 1057 True 742.200000 1402 93.913000 568 1583 2 chr2D.!!$R5 1015
2 TraesCS2D01G012200 chr2A 4215444 4222087 6643 True 1751.666667 5716 95.624667 194 7572 6 chr2A.!!$R1 7378
3 TraesCS2D01G012200 chr2B 5660670 5667096 6426 False 1036.750000 3435 89.875375 46 6960 8 chr2B.!!$F3 6914
4 TraesCS2D01G012200 chr2B 797696058 797697422 1364 False 489.000000 505 81.911500 5683 7139 2 chr2B.!!$F4 1456
5 TraesCS2D01G012200 chr6B 171041976 171043072 1096 False 519.800000 1107 93.999667 565 1583 3 chr6B.!!$F2 1018
6 TraesCS2D01G012200 chr3D 248807971 248810233 2262 False 580.500000 588 98.191500 3994 4326 2 chr3D.!!$F1 332
7 TraesCS2D01G012200 chr4B 316296022 316298273 2251 False 531.500000 545 95.645500 3994 4324 2 chr4B.!!$F6 330

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
69 70 1.491668 GGTCCCTCTCCTCTTCTTCC 58.508 60.0 0.00 0.0 0.00 3.46 F
1187 1270 0.249398 TCTCTAGGCAACCTTTCGGC 59.751 55.0 0.00 0.0 34.61 5.54 F
2676 2969 0.329596 ACAGTGCTGAAATCCCCTCC 59.670 55.0 6.17 0.0 0.00 4.30 F
2892 3185 0.107312 GTCAGAGGTGCCATGATGCT 60.107 55.0 0.00 0.0 0.00 3.79 F
3809 4106 0.333993 AGGCTTGCCATCAGATTGGT 59.666 50.0 14.54 0.0 39.11 3.67 F
5550 7900 0.246360 CACGCCATACACCAGAGACA 59.754 55.0 0.00 0.0 0.00 3.41 F
6139 8562 0.635009 ATACTCCCTCCGTCCCAGAA 59.365 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2351 1.749634 ACCAGTAGTAGGACATGACGC 59.250 52.381 0.0 0.0 0.00 5.19 R
2892 3185 2.809446 CTTGATAATCGACGTGCCTCA 58.191 47.619 0.0 0.0 0.00 3.86 R
4502 6741 1.194547 ACAGCAGCATTACAACGAACG 59.805 47.619 0.0 0.0 0.00 3.95 R
4565 6805 7.175641 CCTGAAACAGAGAATACAATGAAAGGT 59.824 37.037 0.0 0.0 32.44 3.50 R
5605 7955 0.449786 CGCGTTCCCATGTGCAATTA 59.550 50.000 0.0 0.0 0.00 1.40 R
6412 8855 0.438830 GCAACTAGACAGTTTCCGCG 59.561 55.000 0.0 0.0 42.51 6.46 R
7230 9689 1.755380 ACTCCCTCCGTTCCGAAATAG 59.245 52.381 0.0 0.0 0.00 1.73 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 4.040645 ATCTCCCGCAAGCTGAGA 57.959 55.556 11.73 11.73 44.27 3.27
18 19 1.519719 ATCTCCCGCAAGCTGAGAC 59.480 57.895 11.62 0.00 43.41 3.36
19 20 1.965754 ATCTCCCGCAAGCTGAGACC 61.966 60.000 11.62 0.00 43.41 3.85
20 21 2.922503 TCCCGCAAGCTGAGACCA 60.923 61.111 0.00 0.00 0.00 4.02
21 22 2.435586 CCCGCAAGCTGAGACCAG 60.436 66.667 0.00 0.00 43.22 4.00
22 23 2.435586 CCGCAAGCTGAGACCAGG 60.436 66.667 0.00 0.00 40.72 4.45
23 24 3.123620 CGCAAGCTGAGACCAGGC 61.124 66.667 0.00 0.00 40.72 4.85
24 25 3.123620 GCAAGCTGAGACCAGGCG 61.124 66.667 0.00 0.00 40.72 5.52
25 26 3.123620 CAAGCTGAGACCAGGCGC 61.124 66.667 0.00 0.00 40.72 6.53
26 27 4.400961 AAGCTGAGACCAGGCGCC 62.401 66.667 21.89 21.89 40.72 6.53
69 70 1.491668 GGTCCCTCTCCTCTTCTTCC 58.508 60.000 0.00 0.00 0.00 3.46
76 77 2.510238 CCTCTTCTTCCGCTGGCG 60.510 66.667 8.08 8.08 39.44 5.69
77 78 3.191539 CTCTTCTTCCGCTGGCGC 61.192 66.667 9.63 0.00 38.24 6.53
78 79 3.655810 CTCTTCTTCCGCTGGCGCT 62.656 63.158 7.64 0.00 38.24 5.92
79 80 3.494336 CTTCTTCCGCTGGCGCTG 61.494 66.667 7.64 1.33 38.24 5.18
112 113 2.920645 CGGAGTGGGGATCGATCGG 61.921 68.421 18.81 0.00 0.00 4.18
214 219 4.460873 CGCGGCCGCCTTTTCTTC 62.461 66.667 42.07 14.11 37.98 2.87
216 221 2.626780 GCGGCCGCCTTTTCTTCTT 61.627 57.895 39.89 0.00 34.56 2.52
217 222 1.502190 CGGCCGCCTTTTCTTCTTC 59.498 57.895 14.67 0.00 0.00 2.87
392 401 2.791927 CGTGCTGATCGAGACGGA 59.208 61.111 5.57 0.00 0.00 4.69
477 486 1.644786 CGGCGGGGTCAGATTTTGTC 61.645 60.000 0.00 0.00 0.00 3.18
506 549 3.119316 AGTGTGGATCGATTCACTCACTC 60.119 47.826 31.68 18.37 36.59 3.51
617 667 8.747538 ATTAAAAACATCCATCTACCTGTACC 57.252 34.615 0.00 0.00 0.00 3.34
618 668 5.772393 AAAACATCCATCTACCTGTACCA 57.228 39.130 0.00 0.00 0.00 3.25
659 709 3.429492 TGCTTGATGCCACCTTTATGAA 58.571 40.909 0.00 0.00 42.00 2.57
723 773 1.833630 GACCAGGTGAGGTGATGATGA 59.166 52.381 0.00 0.00 43.38 2.92
727 786 2.235650 CAGGTGAGGTGATGATGACTGT 59.764 50.000 0.00 0.00 0.00 3.55
728 787 2.909006 AGGTGAGGTGATGATGACTGTT 59.091 45.455 0.00 0.00 0.00 3.16
729 788 3.005554 GGTGAGGTGATGATGACTGTTG 58.994 50.000 0.00 0.00 0.00 3.33
731 790 4.322725 GGTGAGGTGATGATGACTGTTGTA 60.323 45.833 0.00 0.00 0.00 2.41
732 791 5.423015 GTGAGGTGATGATGACTGTTGTAT 58.577 41.667 0.00 0.00 0.00 2.29
735 794 6.381133 TGAGGTGATGATGACTGTTGTATACT 59.619 38.462 4.17 0.00 0.00 2.12
880 949 2.145536 TGTAGCTGTTGTGACATGCTG 58.854 47.619 15.11 4.89 39.19 4.41
940 1010 5.939883 TCACAAATGAACCAGGACTTCATAG 59.060 40.000 5.85 5.19 37.37 2.23
1147 1225 0.391927 GCCTTGGCCGTGTATGTGTA 60.392 55.000 0.00 0.00 0.00 2.90
1149 1227 1.365699 CTTGGCCGTGTATGTGTACC 58.634 55.000 0.00 0.00 0.00 3.34
1153 1234 0.390209 GCCGTGTATGTGTACCGGTT 60.390 55.000 15.04 0.00 42.06 4.44
1164 1245 8.301720 TGTATGTGTACCGGTTATAATCTGATC 58.698 37.037 15.04 0.00 0.00 2.92
1184 1267 4.273148 TCAAGTCTCTAGGCAACCTTTC 57.727 45.455 0.00 0.00 34.61 2.62
1187 1270 0.249398 TCTCTAGGCAACCTTTCGGC 59.751 55.000 0.00 0.00 34.61 5.54
1244 1333 2.358737 GCAGGGGACGGTGTGAAG 60.359 66.667 0.00 0.00 0.00 3.02
1259 1348 2.027745 TGTGAAGAGTGAAGAGGATGCC 60.028 50.000 0.00 0.00 0.00 4.40
1644 1937 5.588240 CATTTTATGCATGTGCTCAGATGT 58.412 37.500 10.16 0.00 42.66 3.06
1645 1938 4.625972 TTTATGCATGTGCTCAGATGTG 57.374 40.909 10.16 0.00 42.66 3.21
1660 1953 6.404623 GCTCAGATGTGCCATTGTTTAACATA 60.405 38.462 0.00 0.00 31.82 2.29
1744 2037 1.689984 TGAAGCCATGCACTTTGTGA 58.310 45.000 1.52 0.00 35.23 3.58
1916 2209 2.693069 AGTGAATATGATAGGCAGCGC 58.307 47.619 0.00 0.00 0.00 5.92
2058 2351 2.606308 GCGCCAAGGCATGATTATCTTG 60.606 50.000 12.19 4.02 42.06 3.02
2147 2440 2.643933 TCGATTGTCACTCAGAGCAG 57.356 50.000 0.00 0.00 0.00 4.24
2253 2546 2.558359 ACCATTAGTTGCACTGGAAAGC 59.442 45.455 0.00 0.00 32.92 3.51
2363 2656 7.596621 TGACGAATTCTCATTGATACAGATAGC 59.403 37.037 3.52 0.00 0.00 2.97
2676 2969 0.329596 ACAGTGCTGAAATCCCCTCC 59.670 55.000 6.17 0.00 0.00 4.30
2846 3139 1.028330 ATGTCTCACCATTGGCGCTG 61.028 55.000 7.64 0.00 0.00 5.18
2892 3185 0.107312 GTCAGAGGTGCCATGATGCT 60.107 55.000 0.00 0.00 0.00 3.79
3039 3332 1.975680 ACAAGACCACGGGTGTCTAAT 59.024 47.619 8.90 0.00 35.25 1.73
3123 3416 4.225267 TCTGAGGAAATAAGGGACCAAGTC 59.775 45.833 0.00 0.00 0.00 3.01
3459 3752 8.435931 AAAGGCCCTTCTTCTAATTGTTTATT 57.564 30.769 0.00 0.00 0.00 1.40
3788 4084 1.139498 TCCCTGAAATGTGCCCTCCA 61.139 55.000 0.00 0.00 0.00 3.86
3809 4106 0.333993 AGGCTTGCCATCAGATTGGT 59.666 50.000 14.54 0.00 39.11 3.67
4064 6301 4.168291 GGGCTTGGCGAGGAGGAG 62.168 72.222 3.44 0.00 0.00 3.69
4160 6399 3.839432 GTCTCCCGGCTCCCTTCG 61.839 72.222 0.00 0.00 0.00 3.79
4326 6565 5.284861 AGTATATGCCGGTCATAACACAA 57.715 39.130 18.34 2.13 40.73 3.33
4327 6566 5.676552 AGTATATGCCGGTCATAACACAAA 58.323 37.500 18.34 1.54 40.73 2.83
4328 6567 4.893424 ATATGCCGGTCATAACACAAAC 57.107 40.909 18.34 0.00 40.73 2.93
4343 6582 3.292460 CACAAACCAAAACCCTGTAGGA 58.708 45.455 0.00 0.00 39.89 2.94
4369 6608 6.228995 TGAGATGAGCATGACATTCTAATCC 58.771 40.000 8.40 2.77 0.00 3.01
4406 6645 3.751175 TCCTGTGTTTTTAGAATCCTGCG 59.249 43.478 0.00 0.00 0.00 5.18
4490 6729 6.403333 TCCTCACTATTTTCGAATGAAACG 57.597 37.500 0.00 0.00 43.54 3.60
4518 6757 8.272866 TGAAATATATCGTTCGTTGTAATGCTG 58.727 33.333 0.00 0.00 0.00 4.41
4728 6968 3.509575 GGCACATTGTAAAGGACATTCCA 59.490 43.478 0.00 0.00 39.61 3.53
4840 7080 4.023193 CCTTTCTTGTTCTGCACCGTAAAT 60.023 41.667 0.00 0.00 0.00 1.40
4842 7082 5.508200 TTCTTGTTCTGCACCGTAAATTT 57.492 34.783 0.00 0.00 0.00 1.82
4903 7145 1.267121 GGTGGTTCAGAGTAGCAGGA 58.733 55.000 0.00 0.00 0.00 3.86
4934 7176 0.954452 CCTCCTGTGAACAAAGGTGC 59.046 55.000 10.39 0.00 34.94 5.01
4935 7177 1.477558 CCTCCTGTGAACAAAGGTGCT 60.478 52.381 10.39 0.00 34.94 4.40
4936 7178 2.224523 CCTCCTGTGAACAAAGGTGCTA 60.225 50.000 10.39 0.00 34.94 3.49
4945 7187 3.268023 ACAAAGGTGCTACTCCTATGC 57.732 47.619 0.00 0.00 34.56 3.14
5024 7266 4.074970 CACTACTGCCTTTCCTTTGTCAT 58.925 43.478 0.00 0.00 0.00 3.06
5160 7402 9.358872 GGATCTATTTTGTTTTCTTTTGCTAGG 57.641 33.333 0.00 0.00 0.00 3.02
5212 7454 9.512435 CATCCATTTCACATTCTATTTGAACTC 57.488 33.333 0.00 0.00 37.52 3.01
5267 7510 9.190858 GTTCAACACAACAAGCATATCAAAATA 57.809 29.630 0.00 0.00 0.00 1.40
5313 7557 5.514274 CCTGTTGGCGGTAAATGATAAAT 57.486 39.130 0.00 0.00 0.00 1.40
5459 7808 2.168496 CCTCTCACCTACGACCTTTCA 58.832 52.381 0.00 0.00 0.00 2.69
5534 7884 7.869937 ACTGATAATTCCTGATAACTCATCACG 59.130 37.037 0.00 0.00 38.79 4.35
5550 7900 0.246360 CACGCCATACACCAGAGACA 59.754 55.000 0.00 0.00 0.00 3.41
5731 8081 7.041372 GCAACTTAACTTCAGGTTCTCATTGTA 60.041 37.037 0.00 0.00 39.17 2.41
5784 8135 9.566432 CCTTTATTTCTTCTATGTAGATTGGCT 57.434 33.333 0.00 0.00 31.40 4.75
5936 8287 3.731216 CGTTACATGAAGCCAGACTATCG 59.269 47.826 0.00 0.00 0.00 2.92
6053 8476 9.508567 GGAGACATTGAAAGAGTAATATTTTGC 57.491 33.333 0.00 0.00 0.00 3.68
6133 8556 4.653868 TCTTCAGATATACTCCCTCCGTC 58.346 47.826 0.00 0.00 0.00 4.79
6134 8557 3.436577 TCAGATATACTCCCTCCGTCC 57.563 52.381 0.00 0.00 0.00 4.79
6135 8558 2.041350 TCAGATATACTCCCTCCGTCCC 59.959 54.545 0.00 0.00 0.00 4.46
6136 8559 2.071372 AGATATACTCCCTCCGTCCCA 58.929 52.381 0.00 0.00 0.00 4.37
6137 8560 2.041891 AGATATACTCCCTCCGTCCCAG 59.958 54.545 0.00 0.00 0.00 4.45
6138 8561 1.526315 TATACTCCCTCCGTCCCAGA 58.474 55.000 0.00 0.00 0.00 3.86
6139 8562 0.635009 ATACTCCCTCCGTCCCAGAA 59.365 55.000 0.00 0.00 0.00 3.02
6140 8563 0.635009 TACTCCCTCCGTCCCAGAAT 59.365 55.000 0.00 0.00 0.00 2.40
6141 8564 0.635009 ACTCCCTCCGTCCCAGAATA 59.365 55.000 0.00 0.00 0.00 1.75
6142 8565 1.007963 ACTCCCTCCGTCCCAGAATAA 59.992 52.381 0.00 0.00 0.00 1.40
6143 8566 1.689273 CTCCCTCCGTCCCAGAATAAG 59.311 57.143 0.00 0.00 0.00 1.73
6147 8570 2.159085 CCTCCGTCCCAGAATAAGTGTC 60.159 54.545 0.00 0.00 0.00 3.67
6173 8596 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
6219 8643 2.935481 ACGATGTAGAACCCGAGAAC 57.065 50.000 0.00 0.00 0.00 3.01
6220 8644 2.165167 ACGATGTAGAACCCGAGAACA 58.835 47.619 0.00 0.00 0.00 3.18
6291 8734 7.550551 CAGTCAATATTCAGAAAGTTCAGGCTA 59.449 37.037 0.00 0.00 0.00 3.93
6320 8763 2.286872 GTCTGCACCATCTCAATCCAG 58.713 52.381 0.00 0.00 0.00 3.86
6364 8807 8.662781 TCCATCAATTCTAGTAACATACAAGC 57.337 34.615 0.00 0.00 0.00 4.01
6378 8821 7.849804 AACATACAAGCTACAGTATGAAAGG 57.150 36.000 27.17 11.16 46.55 3.11
6379 8822 6.947464 ACATACAAGCTACAGTATGAAAGGT 58.053 36.000 27.17 11.65 46.55 3.50
6387 8830 9.686683 AAGCTACAGTATGAAAGGTTGAAATAT 57.313 29.630 0.00 0.00 40.07 1.28
6435 8882 1.461127 GGAAACTGTCTAGTTGCTGCG 59.539 52.381 0.00 0.00 46.14 5.18
6450 8897 1.493772 CTGCGGTCGTTTACAGTGAA 58.506 50.000 0.00 0.00 0.00 3.18
6453 8900 1.142474 CGGTCGTTTACAGTGAACCC 58.858 55.000 0.00 0.00 0.00 4.11
7001 9460 5.333798 CGTAGTACCCGGCAAATAATTCATG 60.334 44.000 0.00 0.00 0.00 3.07
7004 9463 2.958355 ACCCGGCAAATAATTCATGGAG 59.042 45.455 0.00 0.00 0.00 3.86
7175 9634 5.632034 ATTGTATGAAAGGTACTCCCTCC 57.368 43.478 0.00 0.00 45.47 4.30
7176 9635 3.028850 TGTATGAAAGGTACTCCCTCCG 58.971 50.000 0.00 0.00 45.47 4.63
7177 9636 2.249309 ATGAAAGGTACTCCCTCCGT 57.751 50.000 0.00 0.00 45.47 4.69
7178 9637 2.019807 TGAAAGGTACTCCCTCCGTT 57.980 50.000 0.00 0.00 45.47 4.44
7179 9638 1.897802 TGAAAGGTACTCCCTCCGTTC 59.102 52.381 0.00 0.00 45.47 3.95
7180 9639 1.206610 GAAAGGTACTCCCTCCGTTCC 59.793 57.143 0.00 0.00 45.47 3.62
7181 9640 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 45.47 3.53
7182 9641 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
7183 9642 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
7184 9643 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
7185 9644 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
7186 9645 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
7187 9646 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
7188 9647 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
7189 9648 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
7190 9649 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
7191 9650 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
7192 9651 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
7193 9652 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
7194 9653 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
7195 9654 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
7196 9655 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
7197 9656 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
7198 9657 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
7199 9658 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
7200 9659 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
7201 9660 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
7202 9661 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
7203 9662 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
7204 9663 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
7205 9664 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
7206 9665 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
7207 9666 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
7208 9667 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
7209 9668 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
7210 9669 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
7212 9671 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
7213 9672 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
7214 9673 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
7215 9674 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
7237 9696 8.467402 AGTACAAAGTTGAGTCATCTATTTCG 57.533 34.615 4.14 0.00 0.00 3.46
7238 9697 6.727824 ACAAAGTTGAGTCATCTATTTCGG 57.272 37.500 4.14 0.00 0.00 4.30
7239 9698 6.464222 ACAAAGTTGAGTCATCTATTTCGGA 58.536 36.000 4.14 0.00 0.00 4.55
7240 9699 6.934645 ACAAAGTTGAGTCATCTATTTCGGAA 59.065 34.615 4.14 0.00 0.00 4.30
7241 9700 6.969828 AAGTTGAGTCATCTATTTCGGAAC 57.030 37.500 4.14 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.519719 GTCTCAGCTTGCGGGAGAT 59.480 57.895 17.81 0.00 39.63 2.75
1 2 2.650116 GGTCTCAGCTTGCGGGAGA 61.650 63.158 13.22 13.22 35.44 3.71
2 3 2.125350 GGTCTCAGCTTGCGGGAG 60.125 66.667 9.82 9.82 0.00 4.30
4 5 2.435586 CTGGTCTCAGCTTGCGGG 60.436 66.667 0.00 0.00 33.86 6.13
6 7 3.123620 GCCTGGTCTCAGCTTGCG 61.124 66.667 0.00 0.00 39.61 4.85
7 8 3.123620 CGCCTGGTCTCAGCTTGC 61.124 66.667 0.00 0.00 39.61 4.01
8 9 3.123620 GCGCCTGGTCTCAGCTTG 61.124 66.667 0.00 0.00 39.61 4.01
9 10 4.400961 GGCGCCTGGTCTCAGCTT 62.401 66.667 22.15 0.00 39.61 3.74
51 52 1.107945 CGGAAGAAGAGGAGAGGGAC 58.892 60.000 0.00 0.00 0.00 4.46
52 53 0.684805 GCGGAAGAAGAGGAGAGGGA 60.685 60.000 0.00 0.00 0.00 4.20
77 78 2.437359 GTGCTAGCCCAGTGCCAG 60.437 66.667 13.29 0.00 42.71 4.85
78 79 4.393155 CGTGCTAGCCCAGTGCCA 62.393 66.667 13.29 0.00 42.71 4.92
80 81 4.082523 TCCGTGCTAGCCCAGTGC 62.083 66.667 13.29 0.00 41.71 4.40
81 82 2.185350 CTCCGTGCTAGCCCAGTG 59.815 66.667 13.29 0.00 0.00 3.66
87 88 2.370647 GATCCCCACTCCGTGCTAGC 62.371 65.000 8.10 8.10 31.34 3.42
240 249 2.624838 GACGCATTGGATTGGATTGGAT 59.375 45.455 0.00 0.00 0.00 3.41
466 475 1.298157 CTGCCGCGGACAAAATCTGA 61.298 55.000 33.48 0.46 35.44 3.27
467 476 1.135315 CTGCCGCGGACAAAATCTG 59.865 57.895 33.48 9.36 36.68 2.90
506 549 2.033141 CCAGCCAGTGGGTCAGTG 59.967 66.667 11.93 0.00 43.63 3.66
563 613 2.047844 CTGACAGACACGGGGCAG 60.048 66.667 0.00 0.00 0.00 4.85
614 664 2.000701 CAGATGGCACCCCCTGGTA 61.001 63.158 0.00 0.00 45.57 3.25
616 666 2.389449 ATCAGATGGCACCCCCTGG 61.389 63.158 0.00 0.00 37.80 4.45
617 667 1.152819 CATCAGATGGCACCCCCTG 60.153 63.158 1.95 0.00 0.00 4.45
618 668 2.389449 CCATCAGATGGCACCCCCT 61.389 63.158 16.91 0.00 44.70 4.79
659 709 6.323996 AGAAGATGCCACATTCATTCATTCAT 59.676 34.615 0.00 0.00 0.00 2.57
723 773 7.283580 TGGTTTGTTTTGCTAGTATACAACAGT 59.716 33.333 5.50 0.00 0.00 3.55
727 786 8.453238 TTCTGGTTTGTTTTGCTAGTATACAA 57.547 30.769 5.50 5.36 0.00 2.41
728 787 7.308348 GCTTCTGGTTTGTTTTGCTAGTATACA 60.308 37.037 5.50 0.00 0.00 2.29
729 788 7.021790 GCTTCTGGTTTGTTTTGCTAGTATAC 58.978 38.462 0.00 0.00 0.00 1.47
731 790 5.534654 TGCTTCTGGTTTGTTTTGCTAGTAT 59.465 36.000 0.00 0.00 0.00 2.12
732 791 4.884744 TGCTTCTGGTTTGTTTTGCTAGTA 59.115 37.500 0.00 0.00 0.00 1.82
735 794 4.935352 ATGCTTCTGGTTTGTTTTGCTA 57.065 36.364 0.00 0.00 0.00 3.49
843 907 6.713903 ACAGCTACATATCCTTGGATCATTTG 59.286 38.462 5.30 3.49 0.00 2.32
880 949 3.665190 CCAGTTCAAGGGTGAAGTACTC 58.335 50.000 0.00 0.00 44.12 2.59
940 1010 7.040892 ACTGATGCATGTATCATTGGATAACAC 60.041 37.037 24.22 0.00 37.73 3.32
1147 1225 6.551601 AGAGACTTGATCAGATTATAACCGGT 59.448 38.462 0.00 0.00 0.00 5.28
1149 1227 8.240682 CCTAGAGACTTGATCAGATTATAACCG 58.759 40.741 0.00 0.00 0.00 4.44
1153 1234 8.580720 GTTGCCTAGAGACTTGATCAGATTATA 58.419 37.037 0.00 0.00 0.00 0.98
1164 1245 2.996621 CGAAAGGTTGCCTAGAGACTTG 59.003 50.000 0.00 0.00 31.13 3.16
1184 1267 3.191371 AGCAAAATAAGAACCAAGAGCCG 59.809 43.478 0.00 0.00 0.00 5.52
1187 1270 6.317789 TGACAGCAAAATAAGAACCAAGAG 57.682 37.500 0.00 0.00 0.00 2.85
1244 1333 2.611225 AATCGGCATCCTCTTCACTC 57.389 50.000 0.00 0.00 0.00 3.51
1259 1348 5.344128 CCTGTTTGCATGAGAAAGAAAATCG 59.656 40.000 0.00 0.00 0.00 3.34
1644 1937 5.459536 TTGTGCTATGTTAAACAATGGCA 57.540 34.783 0.00 0.00 32.05 4.92
1660 1953 8.454106 GTGAACAATAACTCTATTCATTGTGCT 58.546 33.333 5.99 0.00 39.92 4.40
1673 1966 6.281848 TGTCGAACAAGTGAACAATAACTC 57.718 37.500 0.00 0.00 0.00 3.01
1767 2060 5.182380 TGAATCTCGGTAAACAAAACCATCC 59.818 40.000 0.00 0.00 36.78 3.51
1916 2209 3.388350 AGCTCGATAAAGGAAGGTAAGGG 59.612 47.826 0.00 0.00 0.00 3.95
2058 2351 1.749634 ACCAGTAGTAGGACATGACGC 59.250 52.381 0.00 0.00 0.00 5.19
2147 2440 3.531538 TCGATCCAATCCTTTGTAGTGC 58.468 45.455 0.00 0.00 0.00 4.40
2676 2969 4.025563 CGATAACTCTGTCTACGTGAGAGG 60.026 50.000 15.73 8.65 38.04 3.69
2846 3139 7.329717 CAGAATACAAAGGTATCTTATCTCGGC 59.670 40.741 0.00 0.00 39.28 5.54
2892 3185 2.809446 CTTGATAATCGACGTGCCTCA 58.191 47.619 0.00 0.00 0.00 3.86
3039 3332 5.462530 TGCTAGTGCTGTTTACAACTCTA 57.537 39.130 0.00 0.00 40.48 2.43
3459 3752 4.019792 TGCTGCTCTGAAGTGGAAAATA 57.980 40.909 0.00 0.00 0.00 1.40
3600 3893 5.169295 ACTAGCCTACAAAAAGCGTCTTAG 58.831 41.667 0.00 0.00 0.00 2.18
3638 3931 6.057321 ACCTCCGAACCAAAATATAAGACA 57.943 37.500 0.00 0.00 0.00 3.41
3751 4047 4.829492 CAGGGAAATTTGACTTCAGGAACT 59.171 41.667 0.00 0.00 43.88 3.01
3752 4048 4.827284 TCAGGGAAATTTGACTTCAGGAAC 59.173 41.667 0.00 0.00 0.00 3.62
3788 4084 1.471119 CAATCTGATGGCAAGCCTGT 58.529 50.000 12.96 0.77 36.94 4.00
3931 4228 3.196469 TCAGAGGTTTGAGTGGATGCTAG 59.804 47.826 0.00 0.00 0.00 3.42
4160 6399 1.967319 TCATATTTGCTCGGCTTCCC 58.033 50.000 0.00 0.00 0.00 3.97
4326 6565 4.105697 TCTCAATCCTACAGGGTTTTGGTT 59.894 41.667 0.00 0.00 36.09 3.67
4327 6566 3.655777 TCTCAATCCTACAGGGTTTTGGT 59.344 43.478 0.00 0.00 36.09 3.67
4328 6567 4.301072 TCTCAATCCTACAGGGTTTTGG 57.699 45.455 0.00 0.00 36.09 3.28
4343 6582 7.390996 GGATTAGAATGTCATGCTCATCTCAAT 59.609 37.037 12.79 0.70 0.00 2.57
4406 6645 1.340405 TGCTCAGGGCCTCTTTGATTC 60.340 52.381 0.95 0.00 40.92 2.52
4490 6729 9.250986 GCATTACAACGAACGATATATTTCATC 57.749 33.333 0.14 0.00 0.00 2.92
4502 6741 1.194547 ACAGCAGCATTACAACGAACG 59.805 47.619 0.00 0.00 0.00 3.95
4565 6805 7.175641 CCTGAAACAGAGAATACAATGAAAGGT 59.824 37.037 0.00 0.00 32.44 3.50
4728 6968 8.270744 AGAGTGATATGTTTGAAGAGCCTATTT 58.729 33.333 0.00 0.00 0.00 1.40
4903 7145 8.877864 TTGTTCACAGGAGGAATTTACATAAT 57.122 30.769 0.00 0.00 0.00 1.28
5024 7266 1.968493 AGAGAGAAGTGGCCGTGTAAA 59.032 47.619 0.00 0.00 0.00 2.01
5160 7402 5.527582 ACGGCATAGGAGATAACATTTCAAC 59.472 40.000 0.00 0.00 0.00 3.18
5212 7454 2.242043 ACTTGGCATTTGGAACTGAGG 58.758 47.619 0.00 0.00 0.00 3.86
5267 7510 8.818860 AGGCCAATACATATGCAATATTGATTT 58.181 29.630 19.73 5.20 37.44 2.17
5313 7557 7.647715 GCACATTCTTTGCAGTTAAGAACTAAA 59.352 33.333 12.97 0.00 42.54 1.85
5459 7808 9.699703 TTAAACTTGCAGACACTTTTTAAGTTT 57.300 25.926 14.19 14.19 44.34 2.66
5534 7884 0.905357 AGGTGTCTCTGGTGTATGGC 59.095 55.000 0.00 0.00 0.00 4.40
5550 7900 1.134401 CACTGCACCGATATCCAAGGT 60.134 52.381 0.00 0.00 39.12 3.50
5605 7955 0.449786 CGCGTTCCCATGTGCAATTA 59.550 50.000 0.00 0.00 0.00 1.40
5689 8039 4.852134 AGTTGCAACAAAGCATATGACA 57.148 36.364 30.11 0.00 45.19 3.58
5690 8040 6.863126 AGTTAAGTTGCAACAAAGCATATGAC 59.137 34.615 30.11 13.14 45.19 3.06
5936 8287 6.861065 TTCAAGTCATCTGTTCCAAAGTAC 57.139 37.500 0.00 0.00 0.00 2.73
6053 8476 7.979444 TGGTTCTCTTAAAATAACAGGACAG 57.021 36.000 0.00 0.00 0.00 3.51
6143 8566 3.435671 CCGTCCCAAAATAAGTGAGACAC 59.564 47.826 0.00 0.00 34.10 3.67
6147 8570 3.270877 CCTCCGTCCCAAAATAAGTGAG 58.729 50.000 0.00 0.00 0.00 3.51
6160 8583 0.960286 GCTACATACTCCCTCCGTCC 59.040 60.000 0.00 0.00 0.00 4.79
6161 8584 1.688772 TGCTACATACTCCCTCCGTC 58.311 55.000 0.00 0.00 0.00 4.79
6173 8596 3.820557 AGATATTTGCCGGTTGCTACAT 58.179 40.909 1.90 0.00 42.00 2.29
6205 8628 2.000447 GTGCATGTTCTCGGGTTCTAC 59.000 52.381 0.00 0.00 0.00 2.59
6214 8638 8.097038 TCTTAGGGAATATATGTGCATGTTCTC 58.903 37.037 0.00 0.00 0.00 2.87
6215 8639 7.977818 TCTTAGGGAATATATGTGCATGTTCT 58.022 34.615 0.00 0.00 0.00 3.01
6219 8643 6.538021 GCTCTCTTAGGGAATATATGTGCATG 59.462 42.308 0.00 0.00 0.00 4.06
6220 8644 6.629068 CGCTCTCTTAGGGAATATATGTGCAT 60.629 42.308 0.00 0.00 40.56 3.96
6291 8734 1.806542 GATGGTGCAGACGACAACATT 59.193 47.619 3.26 0.00 45.30 2.71
6340 8783 8.668510 AGCTTGTATGTTACTAGAATTGATGG 57.331 34.615 0.00 0.00 34.17 3.51
6378 8821 8.739972 GGGGATCACCATACATTATATTTCAAC 58.260 37.037 9.87 0.00 42.91 3.18
6379 8822 7.893302 GGGGGATCACCATACATTATATTTCAA 59.107 37.037 17.85 0.00 42.91 2.69
6412 8855 0.438830 GCAACTAGACAGTTTCCGCG 59.561 55.000 0.00 0.00 42.51 6.46
6413 8856 1.461127 CAGCAACTAGACAGTTTCCGC 59.539 52.381 0.00 0.00 42.51 5.54
6414 8857 1.461127 GCAGCAACTAGACAGTTTCCG 59.539 52.381 0.00 0.00 42.51 4.30
6435 8882 1.142474 CGGGTTCACTGTAAACGACC 58.858 55.000 0.00 0.00 0.00 4.79
6450 8897 4.335647 CAGCTGCAGGGTTCGGGT 62.336 66.667 17.12 0.00 0.00 5.28
7001 9460 2.922335 GCAAATTTTCACGCACTCCTCC 60.922 50.000 0.00 0.00 0.00 4.30
7004 9463 2.132740 TGCAAATTTTCACGCACTCC 57.867 45.000 0.00 0.00 0.00 3.85
7079 9538 4.882842 TTGCCTATATACCGAAGCATGA 57.117 40.909 0.00 0.00 0.00 3.07
7087 9546 3.880490 TGCCAAGTTTTGCCTATATACCG 59.120 43.478 0.00 0.00 0.00 4.02
7165 9624 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
7166 9625 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
7167 9626 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
7168 9627 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
7169 9628 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
7170 9629 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
7171 9630 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
7172 9631 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
7173 9632 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
7174 9633 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
7175 9634 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
7176 9635 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
7177 9636 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
7178 9637 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
7179 9638 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
7180 9639 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
7181 9640 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
7182 9641 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
7183 9642 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
7184 9643 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
7185 9644 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
7186 9645 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
7187 9646 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
7188 9647 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
7189 9648 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
7211 9670 9.569167 CGAAATAGATGACTCAACTTTGTACTA 57.431 33.333 0.00 0.00 0.00 1.82
7212 9671 7.545965 CCGAAATAGATGACTCAACTTTGTACT 59.454 37.037 0.00 0.00 0.00 2.73
7213 9672 7.544566 TCCGAAATAGATGACTCAACTTTGTAC 59.455 37.037 0.00 0.00 0.00 2.90
7214 9673 7.608153 TCCGAAATAGATGACTCAACTTTGTA 58.392 34.615 0.00 0.00 0.00 2.41
7215 9674 6.464222 TCCGAAATAGATGACTCAACTTTGT 58.536 36.000 0.00 0.00 0.00 2.83
7216 9675 6.968131 TCCGAAATAGATGACTCAACTTTG 57.032 37.500 0.00 0.00 0.00 2.77
7217 9676 6.090898 CGTTCCGAAATAGATGACTCAACTTT 59.909 38.462 0.00 0.00 0.00 2.66
7218 9677 5.577164 CGTTCCGAAATAGATGACTCAACTT 59.423 40.000 0.00 0.00 0.00 2.66
7219 9678 5.103000 CGTTCCGAAATAGATGACTCAACT 58.897 41.667 0.00 0.00 0.00 3.16
7220 9679 4.267928 CCGTTCCGAAATAGATGACTCAAC 59.732 45.833 0.00 0.00 0.00 3.18
7221 9680 4.158949 TCCGTTCCGAAATAGATGACTCAA 59.841 41.667 0.00 0.00 0.00 3.02
7222 9681 3.697542 TCCGTTCCGAAATAGATGACTCA 59.302 43.478 0.00 0.00 0.00 3.41
7223 9682 4.291783 CTCCGTTCCGAAATAGATGACTC 58.708 47.826 0.00 0.00 0.00 3.36
7224 9683 3.068307 CCTCCGTTCCGAAATAGATGACT 59.932 47.826 0.00 0.00 0.00 3.41
7225 9684 3.381949 CCTCCGTTCCGAAATAGATGAC 58.618 50.000 0.00 0.00 0.00 3.06
7226 9685 2.364324 CCCTCCGTTCCGAAATAGATGA 59.636 50.000 0.00 0.00 0.00 2.92
7227 9686 2.364324 TCCCTCCGTTCCGAAATAGATG 59.636 50.000 0.00 0.00 0.00 2.90
7228 9687 2.628657 CTCCCTCCGTTCCGAAATAGAT 59.371 50.000 0.00 0.00 0.00 1.98
7229 9688 2.029623 CTCCCTCCGTTCCGAAATAGA 58.970 52.381 0.00 0.00 0.00 1.98
7230 9689 1.755380 ACTCCCTCCGTTCCGAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
7231 9690 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
7232 9691 1.856629 TACTCCCTCCGTTCCGAAAT 58.143 50.000 0.00 0.00 0.00 2.17
7233 9692 1.856629 ATACTCCCTCCGTTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
7234 9693 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
7235 9694 2.965671 ATATACTCCCTCCGTTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
7236 9695 5.184479 TCAATTATATACTCCCTCCGTTCCG 59.816 44.000 0.00 0.00 0.00 4.30
7237 9696 6.600882 TCAATTATATACTCCCTCCGTTCC 57.399 41.667 0.00 0.00 0.00 3.62
7238 9697 9.152595 GAATTCAATTATATACTCCCTCCGTTC 57.847 37.037 0.00 0.00 0.00 3.95
7239 9698 8.656806 TGAATTCAATTATATACTCCCTCCGTT 58.343 33.333 5.45 0.00 0.00 4.44
7240 9699 8.202461 TGAATTCAATTATATACTCCCTCCGT 57.798 34.615 5.45 0.00 0.00 4.69
7275 9734 9.528489 AATAACCAGTACACCATCAAATACTTT 57.472 29.630 0.00 0.00 0.00 2.66
7337 9796 4.772886 AGACCCAGCCGTATTTTTAGAT 57.227 40.909 0.00 0.00 0.00 1.98
7481 9940 8.999431 CATCTACAACACCAAATTAGTTACACT 58.001 33.333 0.00 0.00 0.00 3.55
7482 9941 8.780249 ACATCTACAACACCAAATTAGTTACAC 58.220 33.333 0.00 0.00 0.00 2.90
7483 9942 8.911918 ACATCTACAACACCAAATTAGTTACA 57.088 30.769 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.