Multiple sequence alignment - TraesCS3D01G257500

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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 TraesCS3D01G257500 chr3D 100.000 8587 0 0 1 8587 359680819 359672233 0.000000e+00 15858.0
1 TraesCS3D01G257500 chr3D 89.130 92 8 2 198 288 93604532 93604442 7.050000e-21 113.0
2 TraesCS3D01G257500 chr3D 95.745 47 2 0 202 248 374927622 374927576 9.240000e-10 76.8
3 TraesCS3D01G257500 chr3D 82.051 78 9 5 371 445 592762665 592762740 2.590000e-05 62.1
4 TraesCS3D01G257500 chr3D 94.872 39 2 0 27 65 613796920 613796958 2.590000e-05 62.1
5 TraesCS3D01G257500 chr3A 96.526 5671 124 28 837 6483 479136138 479130517 0.000000e+00 9313.0
6 TraesCS3D01G257500 chr3A 96.330 1880 42 7 6474 8349 479130447 479128591 0.000000e+00 3064.0
7 TraesCS3D01G257500 chr3A 87.456 845 67 19 12 834 479137150 479136323 0.000000e+00 937.0
8 TraesCS3D01G257500 chr3A 80.000 250 39 11 204 446 546420780 546421025 3.190000e-39 174.0
9 TraesCS3D01G257500 chr3A 82.474 97 14 3 202 295 52375415 52375511 1.990000e-11 82.4
10 TraesCS3D01G257500 chr3A 97.297 37 0 1 409 445 723564661 723564626 2.590000e-05 62.1
11 TraesCS3D01G257500 chr3B 97.323 4930 100 12 3370 8296 465932854 465927954 0.000000e+00 8344.0
12 TraesCS3D01G257500 chr3B 92.567 3323 118 54 147 3414 465936104 465932856 0.000000e+00 4649.0
13 TraesCS3D01G257500 chr3B 90.476 84 8 0 8395 8478 432843858 432843941 2.530000e-20 111.0
14 TraesCS3D01G257500 chr2B 81.945 2941 433 64 2448 5347 6186390 6183507 0.000000e+00 2399.0
15 TraesCS3D01G257500 chr2B 81.701 2951 423 70 2447 5356 6215383 6212509 0.000000e+00 2350.0
16 TraesCS3D01G257500 chr2B 81.074 3054 473 69 2458 5458 6204528 6201527 0.000000e+00 2340.0
17 TraesCS3D01G257500 chr2B 84.255 1410 195 19 6189 7585 6211567 6210172 0.000000e+00 1349.0
18 TraesCS3D01G257500 chr2B 83.078 1436 215 19 6184 7613 6182484 6181071 0.000000e+00 1280.0
19 TraesCS3D01G257500 chr2B 83.794 1049 149 14 6563 7598 6200309 6199269 0.000000e+00 976.0
20 TraesCS3D01G257500 chr2B 84.685 222 31 2 1030 1248 6226413 6226192 1.450000e-52 219.0
21 TraesCS3D01G257500 chr2B 86.458 192 24 2 1059 1249 6195682 6195492 8.730000e-50 209.0
22 TraesCS3D01G257500 chr2B 78.486 251 41 12 192 435 768154358 768154602 1.490000e-32 152.0
23 TraesCS3D01G257500 chr2B 90.476 84 8 0 8398 8481 47230614 47230531 2.530000e-20 111.0
24 TraesCS3D01G257500 chr2B 89.412 85 9 0 8400 8484 253719300 253719216 3.280000e-19 108.0
25 TraesCS3D01G257500 chr2B 94.231 52 3 0 28 79 18180848 18180797 7.150000e-11 80.5
26 TraesCS3D01G257500 chr2B 92.157 51 4 0 28 78 177133852 177133802 1.200000e-08 73.1
27 TraesCS3D01G257500 chr2D 81.966 2950 415 75 2447 5356 5299742 5296870 0.000000e+00 2392.0
28 TraesCS3D01G257500 chr2D 81.877 2941 435 58 2448 5347 5285313 5282430 0.000000e+00 2388.0
29 TraesCS3D01G257500 chr2D 83.438 1431 203 20 6189 7600 5296025 5294610 0.000000e+00 1299.0
30 TraesCS3D01G257500 chr2D 82.401 1483 225 27 6176 7650 5281547 5280093 0.000000e+00 1260.0
31 TraesCS3D01G257500 chr2D 86.458 192 24 2 1059 1249 5290526 5290336 8.730000e-50 209.0
32 TraesCS3D01G257500 chr2D 90.805 87 8 0 8398 8484 164019878 164019792 5.450000e-22 117.0
33 TraesCS3D01G257500 chr2D 91.566 83 7 0 8400 8482 645989443 645989525 1.960000e-21 115.0
34 TraesCS3D01G257500 chr2D 91.837 49 4 0 8353 8401 468000866 468000818 1.550000e-07 69.4
35 TraesCS3D01G257500 chr2A 81.311 3050 470 69 2457 5452 3853919 3850916 0.000000e+00 2383.0
36 TraesCS3D01G257500 chr2A 81.350 3051 452 81 2448 5457 3839455 3836481 0.000000e+00 2374.0
37 TraesCS3D01G257500 chr2A 82.330 1562 239 31 6184 7735 3835705 3834171 0.000000e+00 1321.0
38 TraesCS3D01G257500 chr2A 82.043 1498 215 36 2447 3926 3919190 3917729 0.000000e+00 1227.0
39 TraesCS3D01G257500 chr2A 81.929 1483 231 25 6147 7602 3850241 3848769 0.000000e+00 1219.0
40 TraesCS3D01G257500 chr2A 81.812 1446 206 38 3921 5347 3909058 3907651 0.000000e+00 1160.0
41 TraesCS3D01G257500 chr2A 88.442 199 15 7 1019 1213 3857102 3856908 5.180000e-57 233.0
42 TraesCS3D01G257500 chr2A 85.106 188 26 2 1059 1245 3844510 3844324 3.160000e-44 191.0
43 TraesCS3D01G257500 chr2A 94.000 50 3 0 8351 8400 54028977 54029026 9.240000e-10 76.8
44 TraesCS3D01G257500 chr7D 92.683 82 6 0 8400 8481 51445375 51445294 1.510000e-22 119.0
45 TraesCS3D01G257500 chr7D 91.837 49 4 0 8352 8400 92211983 92212031 1.550000e-07 69.4
46 TraesCS3D01G257500 chr7D 88.462 52 6 0 28 79 574703886 574703937 7.200000e-06 63.9
47 TraesCS3D01G257500 chr5B 91.463 82 7 0 8400 8481 428579092 428579011 7.050000e-21 113.0
48 TraesCS3D01G257500 chr5B 97.297 37 1 0 7671 7707 661256496 661256532 7.200000e-06 63.9
49 TraesCS3D01G257500 chr5B 97.297 37 1 0 7671 7707 661271726 661271762 7.200000e-06 63.9
50 TraesCS3D01G257500 chr4D 91.463 82 7 0 8400 8481 69650355 69650436 7.050000e-21 113.0
51 TraesCS3D01G257500 chr4D 97.059 34 0 1 409 442 341525537 341525505 1.000000e-03 56.5
52 TraesCS3D01G257500 chr5D 89.655 87 9 0 8398 8484 335778415 335778329 2.530000e-20 111.0
53 TraesCS3D01G257500 chr5D 81.609 87 14 2 196 281 494082940 494083025 4.300000e-08 71.3
54 TraesCS3D01G257500 chr7B 97.778 45 1 0 8353 8397 642071332 642071376 2.570000e-10 78.7
55 TraesCS3D01G257500 chr7B 93.878 49 2 1 8353 8400 105001001 105000953 1.200000e-08 73.1
56 TraesCS3D01G257500 chr6B 95.833 48 2 0 28 75 343041371 343041324 2.570000e-10 78.7
57 TraesCS3D01G257500 chr6B 90.385 52 5 0 8346 8397 526105036 526105087 1.550000e-07 69.4
58 TraesCS3D01G257500 chr6D 92.308 52 4 0 28 79 218386227 218386278 3.320000e-09 75.0
59 TraesCS3D01G257500 chr6D 91.667 48 4 0 8353 8400 115047184 115047137 5.560000e-07 67.6
60 TraesCS3D01G257500 chr6D 89.796 49 5 0 8352 8400 309579646 309579598 7.200000e-06 63.9
61 TraesCS3D01G257500 chr6A 92.308 52 4 0 28 79 297628391 297628442 3.320000e-09 75.0
62 TraesCS3D01G257500 chr1B 93.617 47 3 0 8351 8397 593740416 593740462 4.300000e-08 71.3
63 TraesCS3D01G257500 chr1A 88.462 52 6 0 28 79 582706603 582706552 7.200000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G257500 chr3D 359672233 359680819 8586 True 15858.000000 15858 100.000000 1 8587 1 chr3D.!!$R2 8586
1 TraesCS3D01G257500 chr3A 479128591 479137150 8559 True 4438.000000 9313 93.437333 12 8349 3 chr3A.!!$R2 8337
2 TraesCS3D01G257500 chr3B 465927954 465936104 8150 True 6496.500000 8344 94.945000 147 8296 2 chr3B.!!$R1 8149
3 TraesCS3D01G257500 chr2B 6210172 6215383 5211 True 1849.500000 2350 82.978000 2447 7585 2 chr2B.!!$R8 5138
4 TraesCS3D01G257500 chr2B 6181071 6186390 5319 True 1839.500000 2399 82.511500 2448 7613 2 chr2B.!!$R6 5165
5 TraesCS3D01G257500 chr2B 6195492 6204528 9036 True 1175.000000 2340 83.775333 1059 7598 3 chr2B.!!$R7 6539
6 TraesCS3D01G257500 chr2D 5294610 5299742 5132 True 1845.500000 2392 82.702000 2447 7600 2 chr2D.!!$R5 5153
7 TraesCS3D01G257500 chr2D 5280093 5285313 5220 True 1824.000000 2388 82.139000 2448 7650 2 chr2D.!!$R4 5202
8 TraesCS3D01G257500 chr2A 3834171 3839455 5284 True 1847.500000 2374 81.840000 2448 7735 2 chr2A.!!$R4 5287
9 TraesCS3D01G257500 chr2A 3848769 3857102 8333 True 1278.333333 2383 83.894000 1019 7602 3 chr2A.!!$R5 6583
10 TraesCS3D01G257500 chr2A 3917729 3919190 1461 True 1227.000000 1227 82.043000 2447 3926 1 chr2A.!!$R3 1479
11 TraesCS3D01G257500 chr2A 3907651 3909058 1407 True 1160.000000 1160 81.812000 3921 5347 1 chr2A.!!$R2 1426

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
974 1192 0.028902 AACAAAAGCCGTGCGTTCTC 59.971 50.000 0.00 0.00 28.93 2.87 F
1491 3928 0.732538 GCAGCGGTTTTACATGGTGC 60.733 55.000 0.00 8.83 46.65 5.01 F
1624 4061 0.764752 GATAGGGGTAGCTGCCACCT 60.765 60.000 26.04 26.04 36.25 4.00 F
1839 4295 3.718434 AGCATCATGGATACCAAAGAGGA 59.282 43.478 10.63 0.00 41.22 3.71 F
3275 5810 3.951663 ACTTACCAAAGGATACACAGGC 58.048 45.455 0.00 0.00 37.01 4.85 F
4217 6803 0.669619 TGGACAGAACGACGCTTGTA 59.330 50.000 0.00 0.00 0.00 2.41 F
5800 8678 3.190744 GCTTAAAACCTTACTCTGTGCCC 59.809 47.826 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 4861 1.680735 ACAATTTCCTTCAGTTGCGCA 59.319 42.857 5.66 5.66 0.0 6.09 R
3299 5834 0.179048 TTGCCCCAGTCATGATAGCG 60.179 55.000 0.00 0.00 0.0 4.26 R
3527 6112 5.059833 CACCCTTGATATCTTCTAACTGCC 58.940 45.833 3.98 0.00 0.0 4.85 R
3898 6483 4.895961 TCAATGAAATTTGCTGCATTGGA 58.104 34.783 21.13 11.28 44.6 3.53 R
5130 7743 2.802247 TCAAAGCATCAACTGACAGTCG 59.198 45.455 8.93 0.00 0.0 4.18 R
5802 8680 0.886490 GTGTCACTGTGGAGCCAAGG 60.886 60.000 8.11 0.00 0.0 3.61 R
7659 10900 1.732941 TAATGCGGCACAGTTACAGG 58.267 50.000 4.03 0.00 0.0 4.00 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
65 66 8.470002 GTCAATAAAAGATGAGGCAATTAAGGT 58.530 33.333 0.00 0.00 0.00 3.50
67 68 5.665916 AAAAGATGAGGCAATTAAGGTGG 57.334 39.130 0.00 0.00 0.00 4.61
72 73 4.864704 TGAGGCAATTAAGGTGGTTTTC 57.135 40.909 0.00 0.00 0.00 2.29
73 74 4.219115 TGAGGCAATTAAGGTGGTTTTCA 58.781 39.130 0.00 0.00 0.00 2.69
135 136 3.057104 TCAAAACGGAGATAGCGAGTTGA 60.057 43.478 0.00 0.00 0.00 3.18
152 153 5.500290 CGAGTTGATAACGCACATAAGGTTC 60.500 44.000 0.00 0.00 36.23 3.62
186 187 2.684374 GGTGGACAACAAAACCTTACGT 59.316 45.455 0.00 0.00 0.00 3.57
187 188 3.129113 GGTGGACAACAAAACCTTACGTT 59.871 43.478 0.00 0.00 35.70 3.99
249 255 3.320541 ACCATGGCAAATCGAACTTTTCA 59.679 39.130 13.04 0.00 0.00 2.69
259 265 6.710692 AATCGAACTTTTCAATGGCAATTC 57.289 33.333 0.00 0.00 0.00 2.17
295 307 2.315901 GACAAATTAGTTGGCACGCAC 58.684 47.619 0.00 0.00 45.59 5.34
322 334 6.482973 ACAATTTTCTGGCCAAAAATACACTG 59.517 34.615 25.54 22.56 35.75 3.66
329 341 2.584791 CCAAAAATACACTGAGCACGC 58.415 47.619 0.00 0.00 0.00 5.34
350 362 4.031991 CGCATTTATCATGTTTGCCAACTG 59.968 41.667 2.01 0.00 33.58 3.16
356 368 9.941325 ATTTATCATGTTTGCCAACTGAATTTA 57.059 25.926 2.01 0.00 33.58 1.40
357 369 8.755696 TTATCATGTTTGCCAACTGAATTTAC 57.244 30.769 2.01 0.00 33.58 2.01
358 370 6.154203 TCATGTTTGCCAACTGAATTTACA 57.846 33.333 2.01 0.00 33.58 2.41
360 372 6.867816 TCATGTTTGCCAACTGAATTTACATC 59.132 34.615 2.01 0.00 33.58 3.06
369 382 2.190161 TGAATTTACATCCTCGCGTCG 58.810 47.619 5.77 0.00 0.00 5.12
389 402 3.057174 TCGCTAAAATTGCCACCGAAAAT 60.057 39.130 0.00 0.00 0.00 1.82
390 403 3.677596 CGCTAAAATTGCCACCGAAAATT 59.322 39.130 0.00 0.00 0.00 1.82
395 408 5.671742 AAATTGCCACCGAAAATTTTCAG 57.328 34.783 26.20 19.32 37.01 3.02
399 412 5.263968 TGCCACCGAAAATTTTCAGTTTA 57.736 34.783 26.20 10.10 37.01 2.01
400 413 5.661458 TGCCACCGAAAATTTTCAGTTTAA 58.339 33.333 26.20 9.26 37.01 1.52
414 427 9.696917 ATTTTCAGTTTAACATGGTCAAATCTC 57.303 29.630 0.00 0.00 0.00 2.75
420 433 3.040147 ACATGGTCAAATCTCGAACGT 57.960 42.857 0.00 0.00 0.00 3.99
555 568 0.526211 TCGAAGGTGACATCACTCGG 59.474 55.000 18.15 5.61 45.73 4.63
590 603 3.257469 TGAGATCAGTGTCCAGCATTC 57.743 47.619 0.00 0.00 0.00 2.67
596 620 3.411446 TCAGTGTCCAGCATTCGAATTT 58.589 40.909 8.21 0.00 0.00 1.82
597 621 3.189080 TCAGTGTCCAGCATTCGAATTTG 59.811 43.478 8.21 9.90 0.00 2.32
598 622 2.095059 AGTGTCCAGCATTCGAATTTGC 60.095 45.455 14.48 14.48 39.17 3.68
599 623 1.885233 TGTCCAGCATTCGAATTTGCA 59.115 42.857 22.09 9.85 41.35 4.08
600 624 2.492881 TGTCCAGCATTCGAATTTGCAT 59.507 40.909 22.09 7.84 41.35 3.96
601 625 2.855963 GTCCAGCATTCGAATTTGCATG 59.144 45.455 22.09 16.63 41.35 4.06
602 626 1.591158 CCAGCATTCGAATTTGCATGC 59.409 47.619 22.09 19.20 41.35 4.06
603 627 1.591158 CAGCATTCGAATTTGCATGCC 59.409 47.619 22.05 8.54 42.60 4.40
604 628 0.932399 GCATTCGAATTTGCATGCCC 59.068 50.000 16.68 0.00 38.72 5.36
605 629 1.472026 GCATTCGAATTTGCATGCCCT 60.472 47.619 16.68 0.00 38.72 5.19
606 630 2.896168 CATTCGAATTTGCATGCCCTT 58.104 42.857 16.68 5.68 0.00 3.95
624 648 4.298332 CCCTTTGCATGAAACTGTTGTAC 58.702 43.478 0.00 0.00 0.00 2.90
627 651 3.600717 TGCATGAAACTGTTGTACACG 57.399 42.857 0.00 0.00 0.00 4.49
776 811 5.075493 CCTTATGAATTGGAATGGAGGGAG 58.925 45.833 0.00 0.00 0.00 4.30
809 844 0.037590 TTTGCGTGATACCCCTGCTT 59.962 50.000 0.00 0.00 0.00 3.91
838 873 5.448654 ACGGTGGGATACAGTTGTATAGTA 58.551 41.667 4.84 0.00 40.99 1.82
839 874 5.533903 ACGGTGGGATACAGTTGTATAGTAG 59.466 44.000 4.84 0.00 40.99 2.57
840 875 5.533903 CGGTGGGATACAGTTGTATAGTAGT 59.466 44.000 4.84 0.00 40.99 2.73
841 876 6.712095 CGGTGGGATACAGTTGTATAGTAGTA 59.288 42.308 4.84 0.00 40.99 1.82
842 877 7.308229 CGGTGGGATACAGTTGTATAGTAGTAC 60.308 44.444 4.84 0.00 40.99 2.73
973 1191 0.454196 AAACAAAAGCCGTGCGTTCT 59.546 45.000 0.00 0.00 28.93 3.01
974 1192 0.028902 AACAAAAGCCGTGCGTTCTC 59.971 50.000 0.00 0.00 28.93 2.87
975 1193 0.814010 ACAAAAGCCGTGCGTTCTCT 60.814 50.000 0.00 0.00 28.93 3.10
985 1203 2.739292 GTGCGTTCTCTTCTGTACACA 58.261 47.619 0.00 0.00 0.00 3.72
1039 1275 2.754658 GGGACGGCGAGGAGAAGA 60.755 66.667 16.62 0.00 0.00 2.87
1335 3772 3.234390 CGTGACAACGCACCAGAG 58.766 61.111 0.00 0.00 43.98 3.35
1393 3830 3.623510 CCATTTCTACTTCCGAGAAAGCC 59.376 47.826 4.36 0.00 44.05 4.35
1448 3885 8.352137 TCTGCCATTAATTTTCTTGATTCTGA 57.648 30.769 0.00 0.00 0.00 3.27
1491 3928 0.732538 GCAGCGGTTTTACATGGTGC 60.733 55.000 0.00 8.83 46.65 5.01
1624 4061 0.764752 GATAGGGGTAGCTGCCACCT 60.765 60.000 26.04 26.04 36.25 4.00
1713 4154 6.687081 TTTTTCTCGCTTCTGAAACCTTTA 57.313 33.333 0.00 0.00 32.72 1.85
1718 4159 7.272037 TCTCGCTTCTGAAACCTTTATTTTT 57.728 32.000 0.00 0.00 0.00 1.94
1839 4295 3.718434 AGCATCATGGATACCAAAGAGGA 59.282 43.478 10.63 0.00 41.22 3.71
2074 4565 4.576463 ACTTTGTCAACTTCTCCACATGTC 59.424 41.667 0.00 0.00 0.00 3.06
2214 4709 4.647424 TTTCAAAATTGCGAGTTGTCCT 57.353 36.364 0.00 0.00 0.00 3.85
2296 4794 6.042781 ACAGAGTATAAGGAAAACAGTGTCCA 59.957 38.462 0.00 0.00 36.28 4.02
2346 4844 7.968956 AGTGACACACGAAGAAATATACTGTAG 59.031 37.037 8.59 0.00 39.64 2.74
2349 4847 9.517609 GACACACGAAGAAATATACTGTAGATT 57.482 33.333 1.99 1.99 0.00 2.40
2430 4929 6.827251 AGTCATATAGTTCTCGTGTCAAGGTA 59.173 38.462 0.00 0.00 0.00 3.08
2431 4930 7.338703 AGTCATATAGTTCTCGTGTCAAGGTAA 59.661 37.037 0.00 0.00 0.00 2.85
2432 4931 8.136165 GTCATATAGTTCTCGTGTCAAGGTAAT 58.864 37.037 0.00 0.00 0.00 1.89
2433 4932 8.692710 TCATATAGTTCTCGTGTCAAGGTAATT 58.307 33.333 0.00 0.00 0.00 1.40
2434 4933 8.755941 CATATAGTTCTCGTGTCAAGGTAATTG 58.244 37.037 0.00 0.00 40.52 2.32
3275 5810 3.951663 ACTTACCAAAGGATACACAGGC 58.048 45.455 0.00 0.00 37.01 4.85
3299 5834 5.746245 CGGAGAAGTCATCAGTATCTTGTTC 59.254 44.000 0.00 0.00 0.00 3.18
3527 6112 4.403752 TGATCCTGATGACAAGACTGGTAG 59.596 45.833 0.00 0.00 0.00 3.18
4217 6803 0.669619 TGGACAGAACGACGCTTGTA 59.330 50.000 0.00 0.00 0.00 2.41
4459 7052 7.604545 ACTCTCAACTAATTAGGCTTCAAGAAC 59.395 37.037 16.73 0.00 0.00 3.01
4503 7096 4.881019 AGACCATAGAAGATTGGATCCG 57.119 45.455 7.39 0.00 36.79 4.18
5365 7978 4.142160 GGTAACCCATCAAAAGAAGCCATC 60.142 45.833 0.00 0.00 0.00 3.51
5662 8539 3.358707 TGCTTTGCCGCCGGTAAC 61.359 61.111 6.04 0.00 0.00 2.50
5800 8678 3.190744 GCTTAAAACCTTACTCTGTGCCC 59.809 47.826 0.00 0.00 0.00 5.36
5801 8679 2.287977 AAAACCTTACTCTGTGCCCC 57.712 50.000 0.00 0.00 0.00 5.80
5802 8680 0.404426 AAACCTTACTCTGTGCCCCC 59.596 55.000 0.00 0.00 0.00 5.40
6087 9106 8.514594 TCAAGGCTATAAAGTGAAGTCATTTTG 58.485 33.333 10.94 0.00 36.63 2.44
6472 9504 5.506832 CGTTTTCAAGGTACGTAATTGCATC 59.493 40.000 14.12 6.52 0.00 3.91
7181 10416 3.627747 GGGAAGTTACTGAGGAGGAGCTA 60.628 52.174 0.00 0.00 0.00 3.32
7328 10563 1.532238 GGCCATACTGAAGGACCCC 59.468 63.158 0.00 0.00 0.00 4.95
7370 10605 0.811616 CGACTAGTGCCTTGGATGCC 60.812 60.000 0.00 0.00 0.00 4.40
7544 10779 5.126061 GGTGCTGATGAACATAAAAGATGGT 59.874 40.000 0.00 0.00 0.00 3.55
7659 10900 2.165437 TGACCACCTTTTGTTGCTGTTC 59.835 45.455 0.00 0.00 0.00 3.18
7788 11049 8.897872 AAATCTTGTGCTTCTGATTTTGATTT 57.102 26.923 0.00 0.00 36.19 2.17
7789 11050 8.897872 AATCTTGTGCTTCTGATTTTGATTTT 57.102 26.923 0.00 0.00 0.00 1.82
7790 11051 7.703298 TCTTGTGCTTCTGATTTTGATTTTG 57.297 32.000 0.00 0.00 0.00 2.44
7791 11052 7.490840 TCTTGTGCTTCTGATTTTGATTTTGA 58.509 30.769 0.00 0.00 0.00 2.69
8013 13221 3.134458 GAGTGTCTGACAAGAACCAAGG 58.866 50.000 12.81 0.00 33.05 3.61
8128 13336 3.764466 CGGAGCAGCGGACTTCCT 61.764 66.667 0.00 0.00 0.00 3.36
8344 13556 2.755542 GATCGATCGCTCGCATGGGT 62.756 60.000 11.09 0.00 44.65 4.51
8349 13561 0.314302 ATCGCTCGCATGGGTACTAC 59.686 55.000 9.86 0.00 0.00 2.73
8350 13562 1.299926 CGCTCGCATGGGTACTACC 60.300 63.158 9.86 0.00 37.60 3.18
8363 13575 4.365514 GGTACTACCCTACTACTCCCTC 57.634 54.545 0.00 0.00 30.04 4.30
8365 13577 1.773653 ACTACCCTACTACTCCCTCCG 59.226 57.143 0.00 0.00 0.00 4.63
8366 13578 1.773653 CTACCCTACTACTCCCTCCGT 59.226 57.143 0.00 0.00 0.00 4.69
8367 13579 1.006020 ACCCTACTACTCCCTCCGTT 58.994 55.000 0.00 0.00 0.00 4.44
8368 13580 1.360507 ACCCTACTACTCCCTCCGTTT 59.639 52.381 0.00 0.00 0.00 3.60
8369 13581 2.030371 CCCTACTACTCCCTCCGTTTC 58.970 57.143 0.00 0.00 0.00 2.78
8370 13582 2.357986 CCCTACTACTCCCTCCGTTTCT 60.358 54.545 0.00 0.00 0.00 2.52
8371 13583 3.117738 CCCTACTACTCCCTCCGTTTCTA 60.118 52.174 0.00 0.00 0.00 2.10
8372 13584 4.530875 CCTACTACTCCCTCCGTTTCTAA 58.469 47.826 0.00 0.00 0.00 2.10
8373 13585 4.952335 CCTACTACTCCCTCCGTTTCTAAA 59.048 45.833 0.00 0.00 0.00 1.85
8374 13586 5.597594 CCTACTACTCCCTCCGTTTCTAAAT 59.402 44.000 0.00 0.00 0.00 1.40
8375 13587 6.774656 CCTACTACTCCCTCCGTTTCTAAATA 59.225 42.308 0.00 0.00 0.00 1.40
8377 13589 9.512588 CTACTACTCCCTCCGTTTCTAAATATA 57.487 37.037 0.00 0.00 0.00 0.86
8378 13590 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
8379 13591 9.205513 ACTACTCCCTCCGTTTCTAAATATAAA 57.794 33.333 0.00 0.00 0.00 1.40
8442 13654 7.761038 ACATCCGTATGTGATTCATAGTAGA 57.239 36.000 0.00 0.00 44.79 2.59
8443 13655 8.178313 ACATCCGTATGTGATTCATAGTAGAA 57.822 34.615 0.00 0.00 44.79 2.10
8444 13656 8.807118 ACATCCGTATGTGATTCATAGTAGAAT 58.193 33.333 0.00 0.00 44.79 2.40
8475 13687 8.899771 ACAAAAACATATATTTAGGAACGGAGG 58.100 33.333 0.00 0.00 0.00 4.30
8476 13688 9.116067 CAAAAACATATATTTAGGAACGGAGGA 57.884 33.333 0.00 0.00 0.00 3.71
8477 13689 9.689501 AAAAACATATATTTAGGAACGGAGGAA 57.310 29.630 0.00 0.00 0.00 3.36
8478 13690 8.904099 AAACATATATTTAGGAACGGAGGAAG 57.096 34.615 0.00 0.00 0.00 3.46
8479 13691 7.613551 ACATATATTTAGGAACGGAGGAAGT 57.386 36.000 0.00 0.00 0.00 3.01
8481 13693 8.804204 ACATATATTTAGGAACGGAGGAAGTAG 58.196 37.037 0.00 0.00 0.00 2.57
8485 13697 3.015675 AGGAACGGAGGAAGTAGTAGG 57.984 52.381 0.00 0.00 0.00 3.18
8486 13698 1.408340 GGAACGGAGGAAGTAGTAGGC 59.592 57.143 0.00 0.00 0.00 3.93
8487 13699 2.097825 GAACGGAGGAAGTAGTAGGCA 58.902 52.381 0.00 0.00 0.00 4.75
8489 13701 1.005687 ACGGAGGAAGTAGTAGGCACT 59.994 52.381 0.00 0.00 46.37 4.40
8492 13704 3.056035 CGGAGGAAGTAGTAGGCACTTTT 60.056 47.826 0.00 0.00 41.75 2.27
8494 13706 4.223255 GGAGGAAGTAGTAGGCACTTTTCT 59.777 45.833 0.00 0.00 41.75 2.52
8495 13707 5.280062 GGAGGAAGTAGTAGGCACTTTTCTT 60.280 44.000 0.00 0.00 41.75 2.52
8497 13709 5.544562 AGGAAGTAGTAGGCACTTTTCTTCT 59.455 40.000 17.09 0.00 41.75 2.85
8498 13710 5.639931 GGAAGTAGTAGGCACTTTTCTTCTG 59.360 44.000 17.09 0.00 41.75 3.02
8503 13715 1.168714 GGCACTTTTCTTCTGCCGAT 58.831 50.000 0.00 0.00 41.15 4.18
8504 13716 1.541588 GGCACTTTTCTTCTGCCGATT 59.458 47.619 0.00 0.00 41.15 3.34
8505 13717 2.589014 GCACTTTTCTTCTGCCGATTG 58.411 47.619 0.00 0.00 0.00 2.67
8506 13718 2.030805 GCACTTTTCTTCTGCCGATTGT 60.031 45.455 0.00 0.00 0.00 2.71
8507 13719 3.550842 GCACTTTTCTTCTGCCGATTGTT 60.551 43.478 0.00 0.00 0.00 2.83
8510 13722 4.097892 ACTTTTCTTCTGCCGATTGTTTGT 59.902 37.500 0.00 0.00 0.00 2.83
8511 13723 3.624326 TTCTTCTGCCGATTGTTTGTG 57.376 42.857 0.00 0.00 0.00 3.33
8512 13724 2.571212 TCTTCTGCCGATTGTTTGTGT 58.429 42.857 0.00 0.00 0.00 3.72
8513 13725 2.948979 TCTTCTGCCGATTGTTTGTGTT 59.051 40.909 0.00 0.00 0.00 3.32
8514 13726 3.380004 TCTTCTGCCGATTGTTTGTGTTT 59.620 39.130 0.00 0.00 0.00 2.83
8516 13728 4.902443 TCTGCCGATTGTTTGTGTTTTA 57.098 36.364 0.00 0.00 0.00 1.52
8517 13729 5.446143 TCTGCCGATTGTTTGTGTTTTAT 57.554 34.783 0.00 0.00 0.00 1.40
8519 13731 6.276847 TCTGCCGATTGTTTGTGTTTTATTT 58.723 32.000 0.00 0.00 0.00 1.40
8521 13733 7.278868 TCTGCCGATTGTTTGTGTTTTATTTTT 59.721 29.630 0.00 0.00 0.00 1.94
8523 13735 7.278868 TGCCGATTGTTTGTGTTTTATTTTTCT 59.721 29.630 0.00 0.00 0.00 2.52
8524 13736 8.119845 GCCGATTGTTTGTGTTTTATTTTTCTT 58.880 29.630 0.00 0.00 0.00 2.52
8533 13745 9.813080 TTGTGTTTTATTTTTCTTTCAAAACCG 57.187 25.926 0.00 0.00 37.97 4.44
8534 13746 9.204570 TGTGTTTTATTTTTCTTTCAAAACCGA 57.795 25.926 0.00 0.00 37.97 4.69
8535 13747 9.683651 GTGTTTTATTTTTCTTTCAAAACCGAG 57.316 29.630 0.00 0.00 37.97 4.63
8536 13748 8.384365 TGTTTTATTTTTCTTTCAAAACCGAGC 58.616 29.630 0.00 0.00 37.97 5.03
8539 13751 4.561735 TTTTCTTTCAAAACCGAGCGAT 57.438 36.364 0.00 0.00 0.00 4.58
8541 13753 4.561735 TTCTTTCAAAACCGAGCGATTT 57.438 36.364 0.00 0.00 0.00 2.17
8542 13754 3.884169 TCTTTCAAAACCGAGCGATTTG 58.116 40.909 11.98 11.98 35.81 2.32
8544 13756 2.679355 TCAAAACCGAGCGATTTGTG 57.321 45.000 15.43 5.15 35.92 3.33
8545 13757 2.214347 TCAAAACCGAGCGATTTGTGA 58.786 42.857 15.43 6.87 35.92 3.58
8546 13758 2.811431 TCAAAACCGAGCGATTTGTGAT 59.189 40.909 15.43 0.00 35.92 3.06
8548 13760 3.915437 AAACCGAGCGATTTGTGATTT 57.085 38.095 0.00 0.00 0.00 2.17
8549 13761 3.471495 AACCGAGCGATTTGTGATTTC 57.529 42.857 0.00 0.00 0.00 2.17
8550 13762 2.699954 ACCGAGCGATTTGTGATTTCT 58.300 42.857 0.00 0.00 0.00 2.52
8551 13763 3.074412 ACCGAGCGATTTGTGATTTCTT 58.926 40.909 0.00 0.00 0.00 2.52
8553 13765 4.023193 ACCGAGCGATTTGTGATTTCTTTT 60.023 37.500 0.00 0.00 0.00 2.27
8554 13766 4.321745 CCGAGCGATTTGTGATTTCTTTTG 59.678 41.667 0.00 0.00 0.00 2.44
8555 13767 4.911610 CGAGCGATTTGTGATTTCTTTTGT 59.088 37.500 0.00 0.00 0.00 2.83
8556 13768 6.077197 CGAGCGATTTGTGATTTCTTTTGTA 58.923 36.000 0.00 0.00 0.00 2.41
8557 13769 6.247165 CGAGCGATTTGTGATTTCTTTTGTAG 59.753 38.462 0.00 0.00 0.00 2.74
8558 13770 7.202016 AGCGATTTGTGATTTCTTTTGTAGA 57.798 32.000 0.00 0.00 0.00 2.59
8560 13772 6.031417 GCGATTTGTGATTTCTTTTGTAGACG 59.969 38.462 0.00 0.00 30.90 4.18
8561 13773 6.031417 CGATTTGTGATTTCTTTTGTAGACGC 59.969 38.462 0.00 0.00 30.90 5.19
8562 13774 6.371809 TTTGTGATTTCTTTTGTAGACGCT 57.628 33.333 0.00 0.00 30.90 5.07
8563 13775 5.342806 TGTGATTTCTTTTGTAGACGCTG 57.657 39.130 0.00 0.00 30.90 5.18
8564 13776 5.053811 TGTGATTTCTTTTGTAGACGCTGA 58.946 37.500 0.00 0.00 30.90 4.26
8565 13777 5.177511 TGTGATTTCTTTTGTAGACGCTGAG 59.822 40.000 0.00 0.00 30.90 3.35
8566 13778 4.690748 TGATTTCTTTTGTAGACGCTGAGG 59.309 41.667 0.00 0.00 30.90 3.86
8567 13779 2.080286 TCTTTTGTAGACGCTGAGGC 57.920 50.000 0.00 0.00 0.00 4.70
8568 13780 1.079503 CTTTTGTAGACGCTGAGGCC 58.920 55.000 0.00 0.00 34.44 5.19
8569 13781 0.685097 TTTTGTAGACGCTGAGGCCT 59.315 50.000 3.86 3.86 34.44 5.19
8571 13783 1.103803 TTGTAGACGCTGAGGCCTAG 58.896 55.000 4.42 4.94 34.44 3.02
8573 13785 1.104630 GTAGACGCTGAGGCCTAGTT 58.895 55.000 4.42 0.00 34.44 2.24
8574 13786 1.477295 GTAGACGCTGAGGCCTAGTTT 59.523 52.381 4.42 1.64 34.44 2.66
8576 13788 0.741221 GACGCTGAGGCCTAGTTTGG 60.741 60.000 4.42 0.00 34.44 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.546526 TCATTGAAAACCACCTTAATTGCC 58.453 37.500 0.00 0.00 0.00 4.52
55 56 7.489574 TTTCATTGAAAACCACCTTAATTGC 57.510 32.000 9.36 0.00 0.00 3.56
72 73 9.746711 CTCTAGATGTTTTACTCGTTTTCATTG 57.253 33.333 0.00 0.00 0.00 2.82
73 74 9.706691 TCTCTAGATGTTTTACTCGTTTTCATT 57.293 29.630 0.00 0.00 0.00 2.57
107 108 7.603651 ACTCGCTATCTCCGTTTTGAATATAT 58.396 34.615 0.00 0.00 0.00 0.86
108 109 6.978338 ACTCGCTATCTCCGTTTTGAATATA 58.022 36.000 0.00 0.00 0.00 0.86
109 110 5.844004 ACTCGCTATCTCCGTTTTGAATAT 58.156 37.500 0.00 0.00 0.00 1.28
110 111 5.258456 ACTCGCTATCTCCGTTTTGAATA 57.742 39.130 0.00 0.00 0.00 1.75
111 112 4.124851 ACTCGCTATCTCCGTTTTGAAT 57.875 40.909 0.00 0.00 0.00 2.57
112 113 3.587797 ACTCGCTATCTCCGTTTTGAA 57.412 42.857 0.00 0.00 0.00 2.69
114 115 3.250744 TCAACTCGCTATCTCCGTTTTG 58.749 45.455 0.00 0.00 0.00 2.44
115 116 3.587797 TCAACTCGCTATCTCCGTTTT 57.412 42.857 0.00 0.00 0.00 2.43
119 120 3.227147 CGTTATCAACTCGCTATCTCCG 58.773 50.000 0.00 0.00 0.00 4.63
120 121 2.981140 GCGTTATCAACTCGCTATCTCC 59.019 50.000 0.00 0.00 45.29 3.71
128 129 3.863424 ACCTTATGTGCGTTATCAACTCG 59.137 43.478 0.00 0.00 0.00 4.18
135 136 4.689071 TCATCGAACCTTATGTGCGTTAT 58.311 39.130 0.00 0.00 46.71 1.89
144 145 4.159879 ACCTCGTTCTTCATCGAACCTTAT 59.840 41.667 0.00 0.00 40.03 1.73
152 153 1.067846 TGTCCACCTCGTTCTTCATCG 60.068 52.381 0.00 0.00 0.00 3.84
194 199 7.230510 CCGAATGTTAGGGATTTATCATTTCCA 59.769 37.037 0.00 0.00 0.00 3.53
211 216 3.951037 CCATGGTCAAATCCCGAATGTTA 59.049 43.478 2.57 0.00 0.00 2.41
249 255 1.665679 CGCGTCACTAGAATTGCCATT 59.334 47.619 0.00 0.00 0.00 3.16
259 265 0.733150 TGTCATCCTCGCGTCACTAG 59.267 55.000 5.77 0.00 0.00 2.57
295 307 5.694006 TGTATTTTTGGCCAGAAAATTGTCG 59.306 36.000 28.05 0.00 37.71 4.35
322 334 3.241322 GCAAACATGATAAATGCGTGCTC 59.759 43.478 0.00 0.00 32.58 4.26
329 341 7.837202 ATTCAGTTGGCAAACATGATAAATG 57.163 32.000 6.76 0.00 38.88 2.32
350 362 1.071436 GCGACGCGAGGATGTAAATTC 60.071 52.381 15.93 0.00 0.00 2.17
356 368 0.108992 TTTTAGCGACGCGAGGATGT 60.109 50.000 15.93 0.00 0.00 3.06
357 369 1.209128 ATTTTAGCGACGCGAGGATG 58.791 50.000 15.93 0.00 0.00 3.51
358 370 1.593006 CAATTTTAGCGACGCGAGGAT 59.407 47.619 15.93 4.91 0.00 3.24
360 372 0.586502 GCAATTTTAGCGACGCGAGG 60.587 55.000 15.93 4.68 0.00 4.63
369 382 5.605564 AAATTTTCGGTGGCAATTTTAGC 57.394 34.783 0.00 0.00 27.77 3.09
389 402 7.860373 CGAGATTTGACCATGTTAAACTGAAAA 59.140 33.333 0.00 0.00 0.00 2.29
390 403 7.227711 TCGAGATTTGACCATGTTAAACTGAAA 59.772 33.333 0.00 0.00 0.00 2.69
395 408 5.788531 CGTTCGAGATTTGACCATGTTAAAC 59.211 40.000 0.00 0.00 0.00 2.01
399 412 3.399330 ACGTTCGAGATTTGACCATGTT 58.601 40.909 0.00 0.00 0.00 2.71
400 413 3.040147 ACGTTCGAGATTTGACCATGT 57.960 42.857 0.00 0.00 0.00 3.21
420 433 0.760572 GGACCCCGATAAATCCCGAA 59.239 55.000 0.00 0.00 0.00 4.30
555 568 8.778358 ACACTGATCTCATCAAACTTTTTAGTC 58.222 33.333 0.00 0.00 39.11 2.59
590 603 0.722848 GCAAAGGGCATGCAAATTCG 59.277 50.000 21.36 3.94 43.29 3.34
601 625 2.137523 CAACAGTTTCATGCAAAGGGC 58.862 47.619 0.00 0.00 45.13 5.19
602 626 3.457610 ACAACAGTTTCATGCAAAGGG 57.542 42.857 0.00 0.00 0.00 3.95
603 627 4.739716 GTGTACAACAGTTTCATGCAAAGG 59.260 41.667 0.00 0.00 0.00 3.11
604 628 4.437495 CGTGTACAACAGTTTCATGCAAAG 59.563 41.667 0.00 0.00 0.00 2.77
605 629 4.346970 CGTGTACAACAGTTTCATGCAAA 58.653 39.130 0.00 0.00 0.00 3.68
606 630 3.790456 GCGTGTACAACAGTTTCATGCAA 60.790 43.478 16.12 0.00 39.74 4.08
624 648 9.988350 AAATCATAGTAGTAATTTTGAAGCGTG 57.012 29.630 0.00 0.00 0.00 5.34
689 715 9.723601 AATGTATGGCACAAAGACATTATTTTT 57.276 25.926 10.14 0.00 46.43 1.94
764 799 0.106967 GGTTCTGCTCCCTCCATTCC 60.107 60.000 0.00 0.00 0.00 3.01
776 811 1.997606 ACGCAAATACGTAGGTTCTGC 59.002 47.619 0.08 4.48 46.19 4.26
809 844 0.322098 CTGTATCCCACCGTTGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
838 873 0.041386 AGGAAAGGCGGAGGAGTACT 59.959 55.000 0.00 0.00 0.00 2.73
839 874 0.460722 GAGGAAAGGCGGAGGAGTAC 59.539 60.000 0.00 0.00 0.00 2.73
840 875 0.686769 GGAGGAAAGGCGGAGGAGTA 60.687 60.000 0.00 0.00 0.00 2.59
841 876 1.990614 GGAGGAAAGGCGGAGGAGT 60.991 63.158 0.00 0.00 0.00 3.85
842 877 2.736826 GGGAGGAAAGGCGGAGGAG 61.737 68.421 0.00 0.00 0.00 3.69
973 1191 2.806745 GCAGCTTGGTGTGTACAGAAGA 60.807 50.000 0.00 0.00 0.00 2.87
974 1192 1.532868 GCAGCTTGGTGTGTACAGAAG 59.467 52.381 0.00 0.00 0.00 2.85
975 1193 1.593196 GCAGCTTGGTGTGTACAGAA 58.407 50.000 0.00 0.00 0.00 3.02
985 1203 2.280552 CCATTGCTGGCAGCTTGGT 61.281 57.895 34.57 20.83 42.97 3.67
1261 3693 2.888863 CTGACCAGAGAGACGGGC 59.111 66.667 0.00 0.00 37.36 6.13
1262 3694 2.888863 GCTGACCAGAGAGACGGG 59.111 66.667 0.47 0.00 39.69 5.28
1263 3695 2.487428 CGCTGACCAGAGAGACGG 59.513 66.667 0.47 0.00 0.00 4.79
1448 3885 5.784578 AATTTTCGTTCTAAACTGGGCTT 57.215 34.783 0.00 0.00 0.00 4.35
1491 3928 9.307121 AGAAACGTGATAGATTTGAATACAGAG 57.693 33.333 0.00 0.00 0.00 3.35
1624 4061 3.994317 TCAGGAGAGATCCCAACATGTA 58.006 45.455 0.00 0.00 0.00 2.29
1718 4159 9.025041 TCAGAGTTTCAGATGAGAGTATTGTAA 57.975 33.333 0.00 0.00 0.00 2.41
1720 4161 7.473735 TCAGAGTTTCAGATGAGAGTATTGT 57.526 36.000 0.00 0.00 0.00 2.71
1721 4162 8.655092 GTTTCAGAGTTTCAGATGAGAGTATTG 58.345 37.037 0.00 0.00 0.00 1.90
1731 4187 4.559862 ATCCCGTTTCAGAGTTTCAGAT 57.440 40.909 0.00 0.00 0.00 2.90
1909 4399 6.908870 CTGTCTTGCAGCAATGTAATACTA 57.091 37.500 8.67 0.00 38.52 1.82
1910 4400 5.808042 CTGTCTTGCAGCAATGTAATACT 57.192 39.130 8.67 0.00 38.52 2.12
2099 4590 5.848406 AGATAGCAGCCATGTTAAGTACTC 58.152 41.667 0.00 0.00 0.00 2.59
2100 4591 5.878406 AGATAGCAGCCATGTTAAGTACT 57.122 39.130 0.00 0.00 0.00 2.73
2170 4665 1.751924 CTAGTAGGGTGTCAGCTGTCC 59.248 57.143 14.67 14.15 0.00 4.02
2214 4709 2.361757 CAACTTGGACTTTGCACCATGA 59.638 45.455 12.28 0.00 36.02 3.07
2346 4844 8.103924 CAGTTGCGCAATGTAAAGAAAATAATC 58.896 33.333 27.79 6.72 0.00 1.75
2349 4847 6.673106 TCAGTTGCGCAATGTAAAGAAAATA 58.327 32.000 27.79 0.00 0.00 1.40
2358 4856 2.177394 TCCTTCAGTTGCGCAATGTA 57.823 45.000 27.79 16.66 0.00 2.29
2363 4861 1.680735 ACAATTTCCTTCAGTTGCGCA 59.319 42.857 5.66 5.66 0.00 6.09
2430 4929 6.294731 GGTTGGCTTGACAGTTATTCTCAATT 60.295 38.462 0.00 0.00 0.00 2.32
2431 4930 5.183904 GGTTGGCTTGACAGTTATTCTCAAT 59.816 40.000 0.00 0.00 0.00 2.57
2432 4931 4.518970 GGTTGGCTTGACAGTTATTCTCAA 59.481 41.667 0.00 0.00 0.00 3.02
2433 4932 4.072131 GGTTGGCTTGACAGTTATTCTCA 58.928 43.478 0.00 0.00 0.00 3.27
2434 4933 4.154918 CAGGTTGGCTTGACAGTTATTCTC 59.845 45.833 0.00 0.00 0.00 2.87
3275 5810 5.255710 ACAAGATACTGATGACTTCTCCG 57.744 43.478 0.00 0.00 0.00 4.63
3299 5834 0.179048 TTGCCCCAGTCATGATAGCG 60.179 55.000 0.00 0.00 0.00 4.26
3527 6112 5.059833 CACCCTTGATATCTTCTAACTGCC 58.940 45.833 3.98 0.00 0.00 4.85
3898 6483 4.895961 TCAATGAAATTTGCTGCATTGGA 58.104 34.783 21.13 11.28 44.60 3.53
4217 6803 4.459685 ACAGTAGTTAGACGATGAGCAACT 59.540 41.667 0.00 0.00 34.10 3.16
4459 7052 5.686159 ACTTTCTGCTCTTCTTCATTGTG 57.314 39.130 0.00 0.00 0.00 3.33
4503 7096 5.989777 TGACAAGCTTGTACTTTTAGACCTC 59.010 40.000 31.20 14.51 42.43 3.85
5130 7743 2.802247 TCAAAGCATCAACTGACAGTCG 59.198 45.455 8.93 0.00 0.00 4.18
5365 7978 4.022935 TCACATTGCTAGAAAAACAGCCTG 60.023 41.667 0.00 0.00 36.95 4.85
5662 8539 4.201871 TGGCTTAACGTGAACAGTTTCTTG 60.202 41.667 0.00 0.00 33.42 3.02
5800 8678 2.034687 CACTGTGGAGCCAAGGGG 59.965 66.667 0.00 0.00 37.18 4.79
5801 8679 1.302832 GTCACTGTGGAGCCAAGGG 60.303 63.158 8.11 0.00 0.00 3.95
5802 8680 0.886490 GTGTCACTGTGGAGCCAAGG 60.886 60.000 8.11 0.00 0.00 3.61
6051 9067 9.330063 TCACTTTATAGCCTTGACTGAATAATG 57.670 33.333 0.00 0.00 0.00 1.90
6093 9112 9.743057 ACTCAGATTCTTATTACTCGATGAAAG 57.257 33.333 0.00 0.00 0.00 2.62
6913 10144 9.686683 ATATAAGACCACAATGAAAGTAAGCTT 57.313 29.630 3.48 3.48 36.30 3.74
7328 10563 6.017026 TCGCCTCATCAAGTAGTAGTATCTTG 60.017 42.308 10.97 10.97 39.59 3.02
7370 10605 1.991430 CACAATTCGCTCGGACTCG 59.009 57.895 0.00 0.00 37.82 4.18
7544 10779 4.758674 AGTTCTACTAGTGAAGCGTACACA 59.241 41.667 5.39 0.00 40.25 3.72
7659 10900 1.732941 TAATGCGGCACAGTTACAGG 58.267 50.000 4.03 0.00 0.00 4.00
7788 11049 5.472820 GGGGAATGCACATTTCAAAAATCAA 59.527 36.000 4.12 0.00 0.00 2.57
7789 11050 5.002516 GGGGAATGCACATTTCAAAAATCA 58.997 37.500 4.12 0.00 0.00 2.57
7790 11051 4.395854 GGGGGAATGCACATTTCAAAAATC 59.604 41.667 4.12 0.00 0.00 2.17
7791 11052 4.334552 GGGGGAATGCACATTTCAAAAAT 58.665 39.130 4.12 0.00 0.00 1.82
7821 11086 6.701841 CAGCAGGATATTACACTCGTTTACAT 59.298 38.462 0.00 0.00 0.00 2.29
7828 11093 5.183014 TGTACAGCAGGATATTACACTCG 57.817 43.478 0.00 0.00 0.00 4.18
8013 13221 3.431725 GCTGGTGCGGTGGTAAGC 61.432 66.667 0.00 0.00 0.00 3.09
8090 13298 1.455849 CCCAAGTCCTGGCTTGACA 59.544 57.895 23.55 0.00 46.34 3.58
8128 13336 3.142838 GTACTGCCGACCCGCCTA 61.143 66.667 0.00 0.00 0.00 3.93
8188 13398 2.728817 CTCGTATGAGACCCCCGC 59.271 66.667 6.03 0.00 45.57 6.13
8189 13399 2.857744 GCCTCGTATGAGACCCCCG 61.858 68.421 13.79 0.00 45.57 5.73
8190 13400 2.857744 CGCCTCGTATGAGACCCCC 61.858 68.421 13.79 0.00 45.57 5.40
8191 13401 2.728817 CGCCTCGTATGAGACCCC 59.271 66.667 13.79 0.00 45.57 4.95
8192 13402 2.728817 CCGCCTCGTATGAGACCC 59.271 66.667 13.79 0.95 45.57 4.46
8194 13404 2.027751 GCCCGCCTCGTATGAGAC 59.972 66.667 13.79 0.23 45.57 3.36
8344 13556 2.975489 CGGAGGGAGTAGTAGGGTAGTA 59.025 54.545 0.00 0.00 0.00 1.82
8349 13561 2.030371 GAAACGGAGGGAGTAGTAGGG 58.970 57.143 0.00 0.00 0.00 3.53
8350 13562 3.015675 AGAAACGGAGGGAGTAGTAGG 57.984 52.381 0.00 0.00 0.00 3.18
8351 13563 6.712179 ATTTAGAAACGGAGGGAGTAGTAG 57.288 41.667 0.00 0.00 0.00 2.57
8352 13564 9.866655 TTATATTTAGAAACGGAGGGAGTAGTA 57.133 33.333 0.00 0.00 0.00 1.82
8353 13565 8.773033 TTATATTTAGAAACGGAGGGAGTAGT 57.227 34.615 0.00 0.00 0.00 2.73
8356 13568 9.916360 AAATTTATATTTAGAAACGGAGGGAGT 57.084 29.630 0.00 0.00 32.25 3.85
8418 13630 8.807118 ATTCTACTATGAATCACATACGGATGT 58.193 33.333 7.68 7.68 40.07 3.06
8419 13631 9.295214 GATTCTACTATGAATCACATACGGATG 57.705 37.037 5.94 5.94 46.81 3.51
8449 13661 8.899771 CCTCCGTTCCTAAATATATGTTTTTGT 58.100 33.333 2.55 0.00 0.00 2.83
8451 13663 9.689501 TTCCTCCGTTCCTAAATATATGTTTTT 57.310 29.630 2.55 0.00 0.00 1.94
8452 13664 9.338622 CTTCCTCCGTTCCTAAATATATGTTTT 57.661 33.333 2.55 0.00 0.00 2.43
8454 13666 8.030913 ACTTCCTCCGTTCCTAAATATATGTT 57.969 34.615 0.00 0.00 0.00 2.71
8455 13667 7.613551 ACTTCCTCCGTTCCTAAATATATGT 57.386 36.000 0.00 0.00 0.00 2.29
8457 13669 8.953223 ACTACTTCCTCCGTTCCTAAATATAT 57.047 34.615 0.00 0.00 0.00 0.86
8458 13670 9.512588 CTACTACTTCCTCCGTTCCTAAATATA 57.487 37.037 0.00 0.00 0.00 0.86
8460 13672 6.774656 CCTACTACTTCCTCCGTTCCTAAATA 59.225 42.308 0.00 0.00 0.00 1.40
8461 13673 5.597594 CCTACTACTTCCTCCGTTCCTAAAT 59.402 44.000 0.00 0.00 0.00 1.40
8463 13675 4.530875 CCTACTACTTCCTCCGTTCCTAA 58.469 47.826 0.00 0.00 0.00 2.69
8464 13676 3.686691 GCCTACTACTTCCTCCGTTCCTA 60.687 52.174 0.00 0.00 0.00 2.94
8465 13677 2.949508 GCCTACTACTTCCTCCGTTCCT 60.950 54.545 0.00 0.00 0.00 3.36
8466 13678 1.408340 GCCTACTACTTCCTCCGTTCC 59.592 57.143 0.00 0.00 0.00 3.62
8468 13680 1.823610 GTGCCTACTACTTCCTCCGTT 59.176 52.381 0.00 0.00 0.00 4.44
8469 13681 1.005687 AGTGCCTACTACTTCCTCCGT 59.994 52.381 0.00 0.00 34.74 4.69
8470 13682 1.765230 AGTGCCTACTACTTCCTCCG 58.235 55.000 0.00 0.00 34.74 4.63
8473 13685 5.544562 AGAAGAAAAGTGCCTACTACTTCCT 59.455 40.000 0.00 0.00 39.57 3.36
8474 13686 5.639931 CAGAAGAAAAGTGCCTACTACTTCC 59.360 44.000 0.00 0.00 39.57 3.46
8475 13687 5.120986 GCAGAAGAAAAGTGCCTACTACTTC 59.879 44.000 0.00 0.00 37.39 3.01
8476 13688 4.998033 GCAGAAGAAAAGTGCCTACTACTT 59.002 41.667 0.00 0.00 39.92 2.24
8477 13689 4.570930 GCAGAAGAAAAGTGCCTACTACT 58.429 43.478 0.00 0.00 35.69 2.57
8478 13690 4.930463 GCAGAAGAAAAGTGCCTACTAC 57.070 45.455 0.00 0.00 35.69 2.73
8485 13697 2.030805 ACAATCGGCAGAAGAAAAGTGC 60.031 45.455 0.00 0.00 36.42 4.40
8486 13698 3.904136 ACAATCGGCAGAAGAAAAGTG 57.096 42.857 0.00 0.00 0.00 3.16
8487 13699 4.097892 ACAAACAATCGGCAGAAGAAAAGT 59.902 37.500 0.00 0.00 0.00 2.66
8489 13701 4.142271 ACACAAACAATCGGCAGAAGAAAA 60.142 37.500 0.00 0.00 0.00 2.29
8492 13704 2.571212 ACACAAACAATCGGCAGAAGA 58.429 42.857 0.00 0.00 0.00 2.87
8494 13706 3.791973 AAACACAAACAATCGGCAGAA 57.208 38.095 0.00 0.00 0.00 3.02
8495 13707 3.791973 AAAACACAAACAATCGGCAGA 57.208 38.095 0.00 0.00 0.00 4.26
8497 13709 6.910536 AAAATAAAACACAAACAATCGGCA 57.089 29.167 0.00 0.00 0.00 5.69
8498 13710 7.626446 AGAAAAATAAAACACAAACAATCGGC 58.374 30.769 0.00 0.00 0.00 5.54
8507 13719 9.813080 CGGTTTTGAAAGAAAAATAAAACACAA 57.187 25.926 0.00 0.00 40.89 3.33
8510 13722 8.384365 GCTCGGTTTTGAAAGAAAAATAAAACA 58.616 29.630 0.00 0.00 40.89 2.83
8511 13723 7.577668 CGCTCGGTTTTGAAAGAAAAATAAAAC 59.422 33.333 0.00 0.00 39.33 2.43
8512 13724 7.488471 TCGCTCGGTTTTGAAAGAAAAATAAAA 59.512 29.630 0.00 0.00 32.02 1.52
8513 13725 6.973474 TCGCTCGGTTTTGAAAGAAAAATAAA 59.027 30.769 0.00 0.00 32.02 1.40
8514 13726 6.496571 TCGCTCGGTTTTGAAAGAAAAATAA 58.503 32.000 0.00 0.00 32.02 1.40
8516 13728 4.927422 TCGCTCGGTTTTGAAAGAAAAAT 58.073 34.783 0.00 0.00 32.02 1.82
8517 13729 4.358494 TCGCTCGGTTTTGAAAGAAAAA 57.642 36.364 0.00 0.00 0.00 1.94
8519 13731 4.561735 AATCGCTCGGTTTTGAAAGAAA 57.438 36.364 0.00 0.00 0.00 2.52
8521 13733 3.314080 ACAAATCGCTCGGTTTTGAAAGA 59.686 39.130 18.24 0.00 35.03 2.52
8523 13735 3.065510 TCACAAATCGCTCGGTTTTGAAA 59.934 39.130 18.24 8.38 35.03 2.69
8524 13736 2.614520 TCACAAATCGCTCGGTTTTGAA 59.385 40.909 18.24 8.61 35.03 2.69
8529 13741 3.074412 AGAAATCACAAATCGCTCGGTT 58.926 40.909 0.00 0.00 0.00 4.44
8531 13743 3.747099 AAGAAATCACAAATCGCTCGG 57.253 42.857 0.00 0.00 0.00 4.63
8532 13744 4.911610 ACAAAAGAAATCACAAATCGCTCG 59.088 37.500 0.00 0.00 0.00 5.03
8533 13745 7.269297 GTCTACAAAAGAAATCACAAATCGCTC 59.731 37.037 0.00 0.00 35.47 5.03
8534 13746 7.078228 GTCTACAAAAGAAATCACAAATCGCT 58.922 34.615 0.00 0.00 35.47 4.93
8535 13747 6.031417 CGTCTACAAAAGAAATCACAAATCGC 59.969 38.462 0.00 0.00 35.47 4.58
8536 13748 6.031417 GCGTCTACAAAAGAAATCACAAATCG 59.969 38.462 0.00 0.00 35.47 3.34
8539 13751 6.037720 TCAGCGTCTACAAAAGAAATCACAAA 59.962 34.615 0.00 0.00 35.47 2.83
8541 13753 5.053811 TCAGCGTCTACAAAAGAAATCACA 58.946 37.500 0.00 0.00 35.47 3.58
8542 13754 5.389935 CCTCAGCGTCTACAAAAGAAATCAC 60.390 44.000 0.00 0.00 35.47 3.06
8544 13756 4.436183 GCCTCAGCGTCTACAAAAGAAATC 60.436 45.833 0.00 0.00 35.47 2.17
8545 13757 3.437049 GCCTCAGCGTCTACAAAAGAAAT 59.563 43.478 0.00 0.00 35.47 2.17
8546 13758 2.806244 GCCTCAGCGTCTACAAAAGAAA 59.194 45.455 0.00 0.00 35.47 2.52
8548 13760 1.337823 GGCCTCAGCGTCTACAAAAGA 60.338 52.381 0.00 0.00 41.24 2.52
8549 13761 1.079503 GGCCTCAGCGTCTACAAAAG 58.920 55.000 0.00 0.00 41.24 2.27
8550 13762 0.685097 AGGCCTCAGCGTCTACAAAA 59.315 50.000 0.00 0.00 41.24 2.44
8551 13763 1.476891 CTAGGCCTCAGCGTCTACAAA 59.523 52.381 9.68 0.00 41.24 2.83
8553 13765 0.034380 ACTAGGCCTCAGCGTCTACA 60.034 55.000 9.68 0.00 41.24 2.74
8554 13766 1.104630 AACTAGGCCTCAGCGTCTAC 58.895 55.000 9.68 0.00 41.24 2.59
8555 13767 1.476891 CAAACTAGGCCTCAGCGTCTA 59.523 52.381 9.68 0.00 41.24 2.59
8556 13768 0.247736 CAAACTAGGCCTCAGCGTCT 59.752 55.000 9.68 0.00 41.24 4.18
8557 13769 0.741221 CCAAACTAGGCCTCAGCGTC 60.741 60.000 9.68 0.00 41.24 5.19
8558 13770 1.296715 CCAAACTAGGCCTCAGCGT 59.703 57.895 9.68 0.00 41.24 5.07


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

AutoCloner maintained by Alex Coulton.