Multiple sequence alignment - TraesCS2D01G569900

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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 TraesCS2D01G569900 chr2D 100.000 5238 0 0 1 5238 637434454 637429217 0.000000e+00 9673.0
1 TraesCS2D01G569900 chr2D 84.387 1044 100 35 1904 2900 381062550 381063577 0.000000e+00 966.0
2 TraesCS2D01G569900 chr2D 87.731 758 53 22 1904 2635 637755199 637755942 0.000000e+00 848.0
3 TraesCS2D01G569900 chr2D 81.725 974 98 45 978 1908 637751509 637752445 0.000000e+00 739.0
4 TraesCS2D01G569900 chr2D 78.517 1322 133 75 643 1908 381050339 381051565 0.000000e+00 728.0
5 TraesCS2D01G569900 chr2D 83.039 849 71 33 3803 4635 637765277 637766068 0.000000e+00 702.0
6 TraesCS2D01G569900 chr2D 82.921 849 64 38 3803 4635 381083960 381084743 0.000000e+00 689.0
7 TraesCS2D01G569900 chr2D 84.814 619 74 15 3201 3805 381083245 381083857 5.800000e-169 604.0
8 TraesCS2D01G569900 chr2D 84.491 619 78 13 3201 3805 637764560 637765174 3.490000e-166 595.0
9 TraesCS2D01G569900 chr2D 91.007 278 23 2 3201 3478 381075750 381076025 1.780000e-99 374.0
10 TraesCS2D01G569900 chr2D 83.394 277 23 8 4393 4655 380928370 380928103 8.770000e-58 235.0
11 TraesCS2D01G569900 chr2A 91.530 3294 183 29 979 4213 762620873 762624129 0.000000e+00 4449.0
12 TraesCS2D01G569900 chr2A 81.223 1177 119 38 2322 3446 762152159 762151033 0.000000e+00 856.0
13 TraesCS2D01G569900 chr2A 89.228 492 30 9 427 901 762620349 762620834 1.260000e-165 593.0
14 TraesCS2D01G569900 chr2A 80.248 886 82 43 3803 4655 762149080 762148255 9.780000e-162 580.0
15 TraesCS2D01G569900 chr2A 89.209 417 26 5 4310 4724 762624422 762624821 2.180000e-138 503.0
16 TraesCS2D01G569900 chr2A 87.535 353 41 3 3607 3959 762122213 762121864 6.320000e-109 405.0
17 TraesCS2D01G569900 chr2A 84.777 381 44 7 1 381 762619987 762620353 2.300000e-98 370.0
18 TraesCS2D01G569900 chr2A 83.500 400 54 5 3083 3478 762122776 762122385 3.860000e-96 363.0
19 TraesCS2D01G569900 chr2A 82.831 332 43 7 4733 5058 762624995 762625318 8.590000e-73 285.0
20 TraesCS2D01G569900 chr2A 78.897 417 33 14 1605 1996 762154504 762154118 1.130000e-56 231.0
21 TraesCS2D01G569900 chr2A 85.638 188 22 2 3623 3805 762149349 762149162 5.350000e-45 193.0
22 TraesCS2D01G569900 chr2A 76.106 339 76 3 14 352 762591650 762591983 6.970000e-39 172.0
23 TraesCS2D01G569900 chrUn 94.724 1668 80 5 2281 3943 24000458 23998794 0.000000e+00 2586.0
24 TraesCS2D01G569900 chrUn 93.327 1079 44 10 971 2025 24001599 24000525 0.000000e+00 1568.0
25 TraesCS2D01G569900 chrUn 93.673 980 43 8 3988 4956 23998797 23997826 0.000000e+00 1448.0
26 TraesCS2D01G569900 chrUn 87.597 387 22 12 531 904 24001986 24001613 4.850000e-115 425.0
27 TraesCS2D01G569900 chrUn 89.922 129 12 1 5031 5159 23997827 23997700 1.170000e-36 165.0
28 TraesCS2D01G569900 chr2B 80.753 1169 116 40 2322 3440 795275618 795276727 0.000000e+00 811.0
29 TraesCS2D01G569900 chr2B 81.443 873 83 38 3808 4655 795277130 795277948 4.420000e-180 641.0
30 TraesCS2D01G569900 chr2B 80.053 757 68 38 1605 2306 795265460 795266188 7.890000e-133 484.0
31 TraesCS2D01G569900 chr2B 85.101 396 55 1 3083 3478 795287467 795287858 8.170000e-108 401.0
32 TraesCS2D01G569900 chr2B 83.077 390 53 7 3525 3903 795287958 795288345 5.020000e-90 342.0
33 TraesCS2D01G569900 chr7D 79.503 1127 145 43 3223 4331 590594475 590595533 0.000000e+00 723.0
34 TraesCS2D01G569900 chr7D 83.443 610 88 9 3252 3851 590443892 590443286 5.930000e-154 555.0
35 TraesCS2D01G569900 chr7D 86.170 94 9 3 4119 4212 590443107 590443018 1.200000e-16 99.0
36 TraesCS2D01G569900 chr6D 80.455 660 65 29 1740 2372 21514592 21515214 3.720000e-121 446.0
37 TraesCS2D01G569900 chr6D 91.463 164 9 4 1740 1902 242424608 242424449 2.460000e-53 220.0
38 TraesCS2D01G569900 chr6D 97.619 42 1 0 1841 1882 242424440 242424399 7.280000e-09 73.1
39 TraesCS2D01G569900 chr6A 79.697 660 68 34 1740 2372 47269700 47269080 2.920000e-112 416.0
40 TraesCS2D01G569900 chr3B 94.378 249 13 1 1755 2003 433936668 433936421 1.060000e-101 381.0


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 TraesCS2D01G569900 chr2D 637429217 637434454 5237 True 9673.0 9673 100.0000 1 5238 1 chr2D.!!$R2 5237
1 TraesCS2D01G569900 chr2D 381062550 381063577 1027 False 966.0 966 84.3870 1904 2900 1 chr2D.!!$F2 996
2 TraesCS2D01G569900 chr2D 637751509 637755942 4433 False 793.5 848 84.7280 978 2635 2 chr2D.!!$F5 1657
3 TraesCS2D01G569900 chr2D 381050339 381051565 1226 False 728.0 728 78.5170 643 1908 1 chr2D.!!$F1 1265
4 TraesCS2D01G569900 chr2D 637764560 637766068 1508 False 648.5 702 83.7650 3201 4635 2 chr2D.!!$F6 1434
5 TraesCS2D01G569900 chr2D 381083245 381084743 1498 False 646.5 689 83.8675 3201 4635 2 chr2D.!!$F4 1434
6 TraesCS2D01G569900 chr2A 762619987 762625318 5331 False 1240.0 4449 87.5150 1 5058 5 chr2A.!!$F2 5057
7 TraesCS2D01G569900 chr2A 762148255 762154504 6249 True 465.0 856 81.5015 1605 4655 4 chr2A.!!$R2 3050
8 TraesCS2D01G569900 chr2A 762121864 762122776 912 True 384.0 405 85.5175 3083 3959 2 chr2A.!!$R1 876
9 TraesCS2D01G569900 chrUn 23997700 24001986 4286 True 1238.4 2586 91.8486 531 5159 5 chrUn.!!$R1 4628
10 TraesCS2D01G569900 chr2B 795275618 795277948 2330 False 726.0 811 81.0980 2322 4655 2 chr2B.!!$F2 2333
11 TraesCS2D01G569900 chr2B 795265460 795266188 728 False 484.0 484 80.0530 1605 2306 1 chr2B.!!$F1 701
12 TraesCS2D01G569900 chr2B 795287467 795288345 878 False 371.5 401 84.0890 3083 3903 2 chr2B.!!$F3 820
13 TraesCS2D01G569900 chr7D 590594475 590595533 1058 False 723.0 723 79.5030 3223 4331 1 chr7D.!!$F1 1108
14 TraesCS2D01G569900 chr7D 590443018 590443892 874 True 327.0 555 84.8065 3252 4212 2 chr7D.!!$R1 960
15 TraesCS2D01G569900 chr6D 21514592 21515214 622 False 446.0 446 80.4550 1740 2372 1 chr6D.!!$F1 632
16 TraesCS2D01G569900 chr6A 47269080 47269700 620 True 416.0 416 79.6970 1740 2372 1 chr6A.!!$R1 632

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
166 167 0.109086 CGTGTGTGCTGACCTAGAGG 60.109 60.0 0.0 0.0 42.17 3.69 F
322 323 0.174845 GTAGGCCGTGTATGCAGTCA 59.825 55.0 0.0 0.0 0.00 3.41 F
923 963 0.381801 AATCATTCATTCGCCACGCC 59.618 50.0 0.0 0.0 0.00 5.68 F
1767 1879 0.524862 CATCTGCTTTGGTGCCTGAC 59.475 55.0 0.0 0.0 0.00 3.51 F
3153 7898 1.452110 TGATGCTGATGACCAAACCG 58.548 50.0 0.0 0.0 0.00 4.44 F
3495 8357 1.959042 ACGGATCACATCATTGCTCC 58.041 50.0 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 6753 0.391130 TTGTCGATGGCACCTACTGC 60.391 55.000 0.00 0.0 46.31 4.40 R
2187 6814 4.933330 TCCTATTCTGTTCGACAGCATAC 58.067 43.478 9.34 0.0 45.54 2.39 R
2702 7423 0.892755 CACCAGGCCGTAACAGTCTA 59.107 55.000 0.00 0.0 0.00 2.59 R
3226 7971 1.077429 GTGGGGTCTCTGGGCAATC 60.077 63.158 0.00 0.0 0.00 2.67 R
4117 10818 1.030488 TGACGATCGACTCCACCTCC 61.030 60.000 24.34 0.0 0.00 4.30 R
5215 12328 0.037975 TGGCGTCGGAGGAGTAAAAC 60.038 55.000 1.18 0.0 0.00 2.43 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
47 48 3.118334 CCTGCTGGTGAAGAAGATGATCT 60.118 47.826 0.51 0.00 32.35 2.75
69 70 3.499737 GCATGACCTTGCCGACGG 61.500 66.667 10.29 10.29 36.60 4.79
70 71 2.819595 CATGACCTTGCCGACGGG 60.820 66.667 17.22 0.56 0.00 5.28
71 72 4.096003 ATGACCTTGCCGACGGGG 62.096 66.667 17.22 11.14 39.58 5.73
110 111 0.593128 CTTTTCAACGGCCTCACCAG 59.407 55.000 0.00 0.00 39.03 4.00
131 132 2.618053 GGATGTGTACAAGAACCGGAG 58.382 52.381 9.46 0.00 0.00 4.63
151 152 3.269347 GTCAGTTGTGCCGCGTGT 61.269 61.111 4.92 0.00 0.00 4.49
152 153 3.268603 TCAGTTGTGCCGCGTGTG 61.269 61.111 4.92 0.00 0.00 3.82
162 163 2.049526 CGCGTGTGTGCTGACCTA 60.050 61.111 0.00 0.00 0.00 3.08
164 165 1.289066 GCGTGTGTGCTGACCTAGA 59.711 57.895 0.00 0.00 0.00 2.43
166 167 0.109086 CGTGTGTGCTGACCTAGAGG 60.109 60.000 0.00 0.00 42.17 3.69
176 177 3.904717 CTGACCTAGAGGACCACTACAT 58.095 50.000 1.60 0.00 38.94 2.29
185 186 3.181329 AGGACCACTACATCAATCACCA 58.819 45.455 0.00 0.00 0.00 4.17
187 188 3.879295 GGACCACTACATCAATCACCATG 59.121 47.826 0.00 0.00 0.00 3.66
188 189 4.517285 GACCACTACATCAATCACCATGT 58.483 43.478 0.00 0.00 37.08 3.21
190 191 4.263462 ACCACTACATCAATCACCATGTGT 60.263 41.667 0.00 0.00 34.92 3.72
191 192 5.045942 ACCACTACATCAATCACCATGTGTA 60.046 40.000 0.00 0.00 34.92 2.90
198 199 6.433716 ACATCAATCACCATGTGTATGTCAAA 59.566 34.615 0.00 0.00 34.79 2.69
199 200 6.252967 TCAATCACCATGTGTATGTCAAAC 57.747 37.500 0.00 0.00 34.79 2.93
209 210 6.316440 TGTGTATGTCAAACTGTACGAGTA 57.684 37.500 0.00 0.00 33.09 2.59
210 211 6.144854 TGTGTATGTCAAACTGTACGAGTAC 58.855 40.000 6.46 6.46 33.09 2.73
211 212 6.016860 TGTGTATGTCAAACTGTACGAGTACT 60.017 38.462 13.67 0.00 37.00 2.73
212 213 7.173047 TGTGTATGTCAAACTGTACGAGTACTA 59.827 37.037 13.67 1.40 37.00 1.82
221 222 2.086869 GTACGAGTACTAGTGGGCACA 58.913 52.381 17.80 0.00 33.45 4.57
231 232 2.067197 GTGGGCACACCTTAGGAGT 58.933 57.895 8.26 0.00 41.84 3.85
239 240 4.222366 GGCACACCTTAGGAGTAAGTACTT 59.778 45.833 13.68 13.68 36.50 2.24
242 243 6.622549 CACACCTTAGGAGTAAGTACTTCAG 58.377 44.000 12.39 0.00 36.50 3.02
272 273 1.201429 ACGGTCCTTGCCCTTCTCAT 61.201 55.000 0.00 0.00 0.00 2.90
275 276 1.092345 GTCCTTGCCCTTCTCATCGC 61.092 60.000 0.00 0.00 0.00 4.58
313 314 1.214589 GACATCGTGTAGGCCGTGT 59.785 57.895 0.00 0.00 0.00 4.49
322 323 0.174845 GTAGGCCGTGTATGCAGTCA 59.825 55.000 0.00 0.00 0.00 3.41
336 337 3.514539 TGCAGTCATAGGCTATGATCCT 58.485 45.455 33.18 24.92 45.96 3.24
339 340 5.186603 TGCAGTCATAGGCTATGATCCTAAG 59.813 44.000 33.18 21.24 45.96 2.18
340 341 5.395103 GCAGTCATAGGCTATGATCCTAAGG 60.395 48.000 33.18 18.33 45.96 2.69
341 342 5.954752 CAGTCATAGGCTATGATCCTAAGGA 59.045 44.000 33.18 10.86 45.96 3.36
342 343 6.610830 CAGTCATAGGCTATGATCCTAAGGAT 59.389 42.308 33.18 12.89 45.96 3.24
354 355 1.233019 CTAAGGATCATGGCAAGGCG 58.767 55.000 0.00 0.00 0.00 5.52
367 368 1.270041 GCAAGGCGAAACCCAAAATGA 60.270 47.619 0.00 0.00 40.58 2.57
375 376 5.293324 GGCGAAACCCAAAATGAATTAATCC 59.707 40.000 0.00 0.00 0.00 3.01
381 382 7.660030 ACCCAAAATGAATTAATCCGAGAAT 57.340 32.000 0.00 0.00 0.00 2.40
382 383 7.491682 ACCCAAAATGAATTAATCCGAGAATG 58.508 34.615 0.00 0.00 0.00 2.67
383 384 7.341769 ACCCAAAATGAATTAATCCGAGAATGA 59.658 33.333 0.00 0.00 0.00 2.57
384 385 8.362639 CCCAAAATGAATTAATCCGAGAATGAT 58.637 33.333 0.00 0.00 0.00 2.45
385 386 9.754382 CCAAAATGAATTAATCCGAGAATGATT 57.246 29.630 0.00 0.00 36.46 2.57
411 412 9.782900 TCTCTTTCCCATTTTTATTTTATCCCT 57.217 29.630 0.00 0.00 0.00 4.20
416 417 9.967451 TTCCCATTTTTATTTTATCCCTTTTCC 57.033 29.630 0.00 0.00 0.00 3.13
417 418 9.345254 TCCCATTTTTATTTTATCCCTTTTCCT 57.655 29.630 0.00 0.00 0.00 3.36
418 419 9.973661 CCCATTTTTATTTTATCCCTTTTCCTT 57.026 29.630 0.00 0.00 0.00 3.36
424 425 9.699703 TTTATTTTATCCCTTTTCCTTTTGACG 57.300 29.630 0.00 0.00 0.00 4.35
425 426 6.963083 TTTTATCCCTTTTCCTTTTGACGA 57.037 33.333 0.00 0.00 0.00 4.20
426 427 6.569179 TTTATCCCTTTTCCTTTTGACGAG 57.431 37.500 0.00 0.00 0.00 4.18
427 428 3.849563 TCCCTTTTCCTTTTGACGAGA 57.150 42.857 0.00 0.00 0.00 4.04
428 429 3.740115 TCCCTTTTCCTTTTGACGAGAG 58.260 45.455 0.00 0.00 0.00 3.20
429 430 3.389983 TCCCTTTTCCTTTTGACGAGAGA 59.610 43.478 0.00 0.00 0.00 3.10
430 431 4.134563 CCCTTTTCCTTTTGACGAGAGAA 58.865 43.478 0.00 0.00 0.00 2.87
447 448 5.277490 CGAGAGAAATGCTTTTGTCTTGTCA 60.277 40.000 21.01 0.00 43.39 3.58
450 451 5.343249 AGAAATGCTTTTGTCTTGTCACAC 58.657 37.500 1.76 0.00 0.00 3.82
458 459 3.627395 TGTCTTGTCACACTGTTTCCT 57.373 42.857 0.00 0.00 0.00 3.36
460 461 5.092554 TGTCTTGTCACACTGTTTCCTAA 57.907 39.130 0.00 0.00 0.00 2.69
464 465 5.941058 TCTTGTCACACTGTTTCCTAACAAA 59.059 36.000 0.00 0.00 43.33 2.83
482 483 8.579863 CCTAACAAATTGAAGTGGAAGAAATCT 58.420 33.333 0.00 0.00 0.00 2.40
483 484 9.403110 CTAACAAATTGAAGTGGAAGAAATCTG 57.597 33.333 0.00 0.00 0.00 2.90
485 486 8.186709 ACAAATTGAAGTGGAAGAAATCTGAT 57.813 30.769 0.00 0.00 0.00 2.90
493 494 6.051717 AGTGGAAGAAATCTGATTGGTATCG 58.948 40.000 3.22 0.00 33.23 2.92
496 497 5.178438 GGAAGAAATCTGATTGGTATCGCTC 59.822 44.000 3.22 0.00 33.23 5.03
510 511 5.066893 TGGTATCGCTCGTGTTATTTACTCT 59.933 40.000 0.00 0.00 0.00 3.24
512 513 3.677601 TCGCTCGTGTTATTTACTCTCG 58.322 45.455 0.00 0.00 0.00 4.04
514 515 3.176708 GCTCGTGTTATTTACTCTCGCA 58.823 45.455 0.00 0.00 0.00 5.10
515 516 3.797256 GCTCGTGTTATTTACTCTCGCAT 59.203 43.478 0.00 0.00 0.00 4.73
585 586 6.801575 TGTTTTTAGGATGTGTTTTCTGTCC 58.198 36.000 0.00 0.00 0.00 4.02
837 877 1.103803 CCGATTCTTCCTCCTCGTGA 58.896 55.000 0.00 0.00 0.00 4.35
909 949 1.848388 TGCCTGGATCCACTCAATCAT 59.152 47.619 11.44 0.00 0.00 2.45
921 961 2.352651 ACTCAATCATTCATTCGCCACG 59.647 45.455 0.00 0.00 0.00 4.94
923 963 0.381801 AATCATTCATTCGCCACGCC 59.618 50.000 0.00 0.00 0.00 5.68
938 978 1.201429 ACGCCCCAGTCCAGATCTTT 61.201 55.000 0.00 0.00 0.00 2.52
948 988 4.711355 CAGTCCAGATCTTTCTCCTCTTCT 59.289 45.833 0.00 0.00 0.00 2.85
956 996 5.779241 TCTTTCTCCTCTTCTCTCTCTCT 57.221 43.478 0.00 0.00 0.00 3.10
961 1001 4.162320 TCTCCTCTTCTCTCTCTCTGTCTC 59.838 50.000 0.00 0.00 0.00 3.36
962 1002 4.104086 TCCTCTTCTCTCTCTCTGTCTCT 58.896 47.826 0.00 0.00 0.00 3.10
963 1003 4.080919 TCCTCTTCTCTCTCTCTGTCTCTG 60.081 50.000 0.00 0.00 0.00 3.35
964 1004 4.194640 CTCTTCTCTCTCTCTGTCTCTGG 58.805 52.174 0.00 0.00 0.00 3.86
965 1005 3.843619 TCTTCTCTCTCTCTGTCTCTGGA 59.156 47.826 0.00 0.00 0.00 3.86
966 1006 4.288366 TCTTCTCTCTCTCTGTCTCTGGAA 59.712 45.833 0.00 0.00 0.00 3.53
967 1007 4.860802 TCTCTCTCTCTGTCTCTGGAAT 57.139 45.455 0.00 0.00 0.00 3.01
968 1008 4.780815 TCTCTCTCTCTGTCTCTGGAATC 58.219 47.826 0.00 0.00 0.00 2.52
969 1009 4.474651 TCTCTCTCTCTGTCTCTGGAATCT 59.525 45.833 0.00 0.00 0.00 2.40
1234 1313 0.805614 CGCCGTCAGAGAAGAAGAGA 59.194 55.000 0.00 0.00 0.00 3.10
1315 1397 1.981853 GCAAAGGGGGCCGATGAAA 60.982 57.895 0.00 0.00 0.00 2.69
1359 1450 1.482593 GAGGAGAAGCCCGATGAGAAA 59.517 52.381 0.00 0.00 37.37 2.52
1367 1458 1.886655 GCCCGATGAGAAACCAAAGGT 60.887 52.381 0.00 0.00 37.65 3.50
1422 1513 2.496817 GACGCCGAGCTCCTCAAT 59.503 61.111 8.47 0.00 0.00 2.57
1494 1585 2.087009 GGAGACCAACGAGCGAACG 61.087 63.158 0.00 0.00 39.31 3.95
1732 1835 1.622811 AGAGCAGAGACCAGGTTCTTG 59.377 52.381 0.00 0.00 0.00 3.02
1733 1836 1.346068 GAGCAGAGACCAGGTTCTTGT 59.654 52.381 0.00 0.00 0.00 3.16
1735 1838 1.876156 GCAGAGACCAGGTTCTTGTTG 59.124 52.381 0.00 0.00 0.00 3.33
1736 1839 2.746472 GCAGAGACCAGGTTCTTGTTGT 60.746 50.000 0.00 0.00 0.00 3.32
1738 1841 2.104963 AGAGACCAGGTTCTTGTTGTCC 59.895 50.000 0.00 0.00 0.00 4.02
1747 1859 4.956075 AGGTTCTTGTTGTCCACTGAATTT 59.044 37.500 0.00 0.00 0.00 1.82
1748 1860 5.067805 AGGTTCTTGTTGTCCACTGAATTTC 59.932 40.000 0.00 0.00 0.00 2.17
1749 1861 5.163561 GGTTCTTGTTGTCCACTGAATTTCA 60.164 40.000 0.00 0.00 0.00 2.69
1751 1863 6.317789 TCTTGTTGTCCACTGAATTTCATC 57.682 37.500 0.00 0.00 0.00 2.92
1763 1875 3.256558 GAATTTCATCTGCTTTGGTGCC 58.743 45.455 0.00 0.00 0.00 5.01
1767 1879 0.524862 CATCTGCTTTGGTGCCTGAC 59.475 55.000 0.00 0.00 0.00 3.51
1996 6623 4.440802 GGAGGTAACACTCAGACATGCTAG 60.441 50.000 0.00 0.00 39.27 3.42
2005 6632 3.190079 TCAGACATGCTAGCATTCGTTC 58.810 45.455 27.59 19.32 33.90 3.95
2016 6643 6.202762 TGCTAGCATTCGTTCGAATATCATTT 59.797 34.615 14.93 5.60 33.98 2.32
2022 6649 7.564005 GCATTCGTTCGAATATCATTTTCAAGC 60.564 37.037 17.85 10.18 33.98 4.01
2027 6654 7.641411 CGTTCGAATATCATTTTCAAGCTGATT 59.359 33.333 0.00 0.00 32.20 2.57
2120 6747 4.321008 GCTATGGTCAGATGATGCAAATGG 60.321 45.833 0.00 0.00 0.00 3.16
2126 6753 4.624024 GTCAGATGATGCAAATGGTTTGTG 59.376 41.667 0.00 0.00 42.56 3.33
2264 6923 7.396907 TGCTCTGGATTTAGGAATTCAATTCAA 59.603 33.333 12.27 0.00 41.03 2.69
2883 7613 6.942005 TGTCAACTCCTGATGTAATGAAATGT 59.058 34.615 0.00 0.00 36.14 2.71
3029 7765 6.204495 CGATTTTCCAAAAACCAATGGACAAT 59.796 34.615 6.16 6.02 44.63 2.71
3124 7869 5.915196 GGTAAGTGTTCTCATTTTCAACAGC 59.085 40.000 0.00 0.00 30.72 4.40
3153 7898 1.452110 TGATGCTGATGACCAAACCG 58.548 50.000 0.00 0.00 0.00 4.44
3429 8193 2.358195 GGCCTGGGTATTGATTGGTCTT 60.358 50.000 0.00 0.00 0.00 3.01
3495 8357 1.959042 ACGGATCACATCATTGCTCC 58.041 50.000 0.00 0.00 0.00 4.70
3566 9990 5.376625 TCCTTCCATGCCAATCTATGTTAC 58.623 41.667 0.00 0.00 0.00 2.50
3878 10519 6.468543 AGAAGAGGTAATGGTCTTTTCACTC 58.531 40.000 0.00 0.00 33.04 3.51
3975 10621 3.765026 ACATGTCGTTGTTTTGGTTGTC 58.235 40.909 0.00 0.00 0.00 3.18
4031 10677 2.322355 ATGATGCTGCTGTAGGTGTC 57.678 50.000 0.00 0.00 0.00 3.67
4117 10818 2.095532 GGACGATATGGAGACGATACGG 59.904 54.545 0.00 0.00 0.00 4.02
4156 10862 2.283604 TCGCTGCACTGGGAGGTA 60.284 61.111 0.00 0.00 32.28 3.08
4335 11237 6.875726 GGATGAGTGTAGCATAGCATATTGAA 59.124 38.462 0.00 0.00 0.00 2.69
4444 11350 5.630661 TTATTGTTCATGTTGTTACGGGG 57.369 39.130 0.00 0.00 0.00 5.73
4700 11636 7.482743 GCAATACAAGTATGATGGCATTATTCG 59.517 37.037 10.22 0.18 35.94 3.34
4827 11939 2.070305 TATGTGGTGCCCCATTCATG 57.930 50.000 0.00 0.00 44.35 3.07
4918 12030 4.588951 TGGATGTTCACAAGACAGTCTACT 59.411 41.667 2.64 0.00 0.00 2.57
5008 12121 7.988737 TGCCAATGTAGAATTTGTGATTCTAG 58.011 34.615 8.34 0.00 40.18 2.43
5009 12122 7.828717 TGCCAATGTAGAATTTGTGATTCTAGA 59.171 33.333 8.34 8.02 40.18 2.43
5016 12129 7.531280 AGAATTTGTGATTCTAGATGTGACG 57.469 36.000 0.00 0.00 36.68 4.35
5019 12132 4.016113 TGTGATTCTAGATGTGACGTCG 57.984 45.455 11.62 0.00 0.00 5.12
5074 12187 4.120589 CCCTTAGAGCGATCAACCTAAAC 58.879 47.826 2.38 0.00 0.00 2.01
5097 12210 6.433847 CCAAGGGGTTATCATGTACATAGA 57.566 41.667 8.32 9.02 0.00 1.98
5098 12211 6.467677 CCAAGGGGTTATCATGTACATAGAG 58.532 44.000 8.32 0.00 0.00 2.43
5126 12239 8.674925 TCTCTAGTTGATCCCTTAAAAACCTA 57.325 34.615 0.00 0.00 0.00 3.08
5159 12272 7.988028 AGTACATTTGAGAGATAGCCTTAAACC 59.012 37.037 0.00 0.00 0.00 3.27
5160 12273 5.817816 ACATTTGAGAGATAGCCTTAAACCG 59.182 40.000 0.00 0.00 0.00 4.44
5161 12274 5.416271 TTTGAGAGATAGCCTTAAACCGT 57.584 39.130 0.00 0.00 0.00 4.83
5162 12275 5.416271 TTGAGAGATAGCCTTAAACCGTT 57.584 39.130 0.00 0.00 0.00 4.44
5163 12276 6.534475 TTGAGAGATAGCCTTAAACCGTTA 57.466 37.500 0.00 0.00 0.00 3.18
5164 12277 6.145338 TGAGAGATAGCCTTAAACCGTTAG 57.855 41.667 0.00 0.00 0.00 2.34
5165 12278 5.889853 TGAGAGATAGCCTTAAACCGTTAGA 59.110 40.000 0.00 0.00 0.00 2.10
5166 12279 6.039493 TGAGAGATAGCCTTAAACCGTTAGAG 59.961 42.308 0.00 0.00 0.00 2.43
5167 12280 5.302313 AGAGATAGCCTTAAACCGTTAGAGG 59.698 44.000 8.00 8.00 37.30 3.69
5168 12281 5.206587 AGATAGCCTTAAACCGTTAGAGGA 58.793 41.667 14.16 0.00 34.73 3.71
5169 12282 3.889520 AGCCTTAAACCGTTAGAGGAG 57.110 47.619 14.16 0.00 34.73 3.69
5170 12283 3.438183 AGCCTTAAACCGTTAGAGGAGA 58.562 45.455 14.16 0.00 34.73 3.71
5171 12284 3.836562 AGCCTTAAACCGTTAGAGGAGAA 59.163 43.478 14.16 0.00 34.73 2.87
5172 12285 4.285260 AGCCTTAAACCGTTAGAGGAGAAA 59.715 41.667 14.16 0.00 34.73 2.52
5173 12286 5.045797 AGCCTTAAACCGTTAGAGGAGAAAT 60.046 40.000 14.16 0.00 34.73 2.17
5174 12287 5.646793 GCCTTAAACCGTTAGAGGAGAAATT 59.353 40.000 14.16 0.00 34.73 1.82
5175 12288 6.150641 GCCTTAAACCGTTAGAGGAGAAATTT 59.849 38.462 14.16 0.00 34.73 1.82
5176 12289 7.309012 GCCTTAAACCGTTAGAGGAGAAATTTT 60.309 37.037 14.16 0.00 34.73 1.82
5177 12290 8.573885 CCTTAAACCGTTAGAGGAGAAATTTTT 58.426 33.333 6.92 0.00 34.73 1.94
5200 12313 2.525105 GGAGTTATCCCCAAAAGCCA 57.475 50.000 0.00 0.00 40.03 4.75
5201 12314 2.379005 GGAGTTATCCCCAAAAGCCAG 58.621 52.381 0.00 0.00 40.03 4.85
5202 12315 1.751351 GAGTTATCCCCAAAAGCCAGC 59.249 52.381 0.00 0.00 0.00 4.85
5203 12316 0.824109 GTTATCCCCAAAAGCCAGCC 59.176 55.000 0.00 0.00 0.00 4.85
5204 12317 0.325203 TTATCCCCAAAAGCCAGCCC 60.325 55.000 0.00 0.00 0.00 5.19
5205 12318 1.513975 TATCCCCAAAAGCCAGCCCA 61.514 55.000 0.00 0.00 0.00 5.36
5206 12319 2.810488 ATCCCCAAAAGCCAGCCCAG 62.810 60.000 0.00 0.00 0.00 4.45
5207 12320 3.698820 CCCAAAAGCCAGCCCAGC 61.699 66.667 0.00 0.00 0.00 4.85
5208 12321 2.602568 CCAAAAGCCAGCCCAGCT 60.603 61.111 0.00 0.00 44.19 4.24
5209 12322 2.643232 CCAAAAGCCAGCCCAGCTC 61.643 63.158 0.00 0.00 40.49 4.09
5210 12323 1.605738 CAAAAGCCAGCCCAGCTCT 60.606 57.895 0.00 0.00 40.49 4.09
5211 12324 1.303970 AAAAGCCAGCCCAGCTCTC 60.304 57.895 0.00 0.00 40.49 3.20
5212 12325 1.787462 AAAAGCCAGCCCAGCTCTCT 61.787 55.000 0.00 0.00 40.49 3.10
5213 12326 2.195692 AAAGCCAGCCCAGCTCTCTC 62.196 60.000 0.00 0.00 40.49 3.20
5214 12327 3.397439 GCCAGCCCAGCTCTCTCA 61.397 66.667 0.00 0.00 36.40 3.27
5215 12328 2.901813 CCAGCCCAGCTCTCTCAG 59.098 66.667 0.00 0.00 36.40 3.35
5216 12329 1.988956 CCAGCCCAGCTCTCTCAGT 60.989 63.158 0.00 0.00 36.40 3.41
5217 12330 1.551908 CCAGCCCAGCTCTCTCAGTT 61.552 60.000 0.00 0.00 36.40 3.16
5218 12331 0.324285 CAGCCCAGCTCTCTCAGTTT 59.676 55.000 0.00 0.00 36.40 2.66
5219 12332 1.063183 AGCCCAGCTCTCTCAGTTTT 58.937 50.000 0.00 0.00 30.62 2.43
5220 12333 2.027745 CAGCCCAGCTCTCTCAGTTTTA 60.028 50.000 0.00 0.00 36.40 1.52
5221 12334 2.027653 AGCCCAGCTCTCTCAGTTTTAC 60.028 50.000 0.00 0.00 30.62 2.01
5222 12335 2.027653 GCCCAGCTCTCTCAGTTTTACT 60.028 50.000 0.00 0.00 0.00 2.24
5223 12336 3.855858 CCCAGCTCTCTCAGTTTTACTC 58.144 50.000 0.00 0.00 0.00 2.59
5224 12337 3.368948 CCCAGCTCTCTCAGTTTTACTCC 60.369 52.174 0.00 0.00 0.00 3.85
5225 12338 3.513515 CCAGCTCTCTCAGTTTTACTCCT 59.486 47.826 0.00 0.00 0.00 3.69
5226 12339 4.381505 CCAGCTCTCTCAGTTTTACTCCTC 60.382 50.000 0.00 0.00 0.00 3.71
5227 12340 3.767131 AGCTCTCTCAGTTTTACTCCTCC 59.233 47.826 0.00 0.00 0.00 4.30
5228 12341 3.428316 GCTCTCTCAGTTTTACTCCTCCG 60.428 52.174 0.00 0.00 0.00 4.63
5229 12342 4.011023 CTCTCTCAGTTTTACTCCTCCGA 58.989 47.826 0.00 0.00 0.00 4.55
5230 12343 3.757493 TCTCTCAGTTTTACTCCTCCGAC 59.243 47.826 0.00 0.00 0.00 4.79
5231 12344 2.486982 TCTCAGTTTTACTCCTCCGACG 59.513 50.000 0.00 0.00 0.00 5.12
5232 12345 1.068055 TCAGTTTTACTCCTCCGACGC 60.068 52.381 0.00 0.00 0.00 5.19
5233 12346 0.245813 AGTTTTACTCCTCCGACGCC 59.754 55.000 0.00 0.00 0.00 5.68
5234 12347 0.037975 GTTTTACTCCTCCGACGCCA 60.038 55.000 0.00 0.00 0.00 5.69
5235 12348 0.037975 TTTTACTCCTCCGACGCCAC 60.038 55.000 0.00 0.00 0.00 5.01
5236 12349 0.896940 TTTACTCCTCCGACGCCACT 60.897 55.000 0.00 0.00 0.00 4.00
5237 12350 0.896940 TTACTCCTCCGACGCCACTT 60.897 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.436998 CAGGGGCACGTCCTCGAC 62.437 72.222 0.00 0.00 41.53 4.20
24 25 1.280133 TCATCTTCTTCACCAGCAGGG 59.720 52.381 0.00 0.00 44.81 4.45
47 48 1.675310 CGGCAAGGTCATGCTCCAA 60.675 57.895 8.93 0.00 45.68 3.53
82 83 1.247567 CCGTTGAAAAGCCTCACCAT 58.752 50.000 0.00 0.00 0.00 3.55
93 94 1.228124 CCTGGTGAGGCCGTTGAAA 60.228 57.895 0.00 0.00 41.21 2.69
110 111 1.276989 TCCGGTTCTTGTACACATCCC 59.723 52.381 0.00 0.00 0.00 3.85
131 132 3.414700 CGCGGCACAACTGACTCC 61.415 66.667 0.00 0.00 0.00 3.85
151 152 0.114364 TGGTCCTCTAGGTCAGCACA 59.886 55.000 0.00 0.00 36.34 4.57
152 153 0.533032 GTGGTCCTCTAGGTCAGCAC 59.467 60.000 4.80 4.80 34.69 4.40
155 156 3.367646 TGTAGTGGTCCTCTAGGTCAG 57.632 52.381 0.71 0.00 36.34 3.51
162 163 3.452627 GGTGATTGATGTAGTGGTCCTCT 59.547 47.826 0.00 0.00 0.00 3.69
164 165 3.181329 TGGTGATTGATGTAGTGGTCCT 58.819 45.455 0.00 0.00 0.00 3.85
166 167 4.333649 CACATGGTGATTGATGTAGTGGTC 59.666 45.833 0.00 0.00 35.23 4.02
176 177 6.003326 AGTTTGACATACACATGGTGATTGA 58.997 36.000 2.98 0.00 36.96 2.57
185 186 5.779922 ACTCGTACAGTTTGACATACACAT 58.220 37.500 0.00 0.00 26.56 3.21
187 188 6.376978 AGTACTCGTACAGTTTGACATACAC 58.623 40.000 9.62 0.00 38.48 2.90
188 189 6.564709 AGTACTCGTACAGTTTGACATACA 57.435 37.500 9.62 0.00 38.48 2.29
190 191 7.148356 CCACTAGTACTCGTACAGTTTGACATA 60.148 40.741 0.00 0.00 38.48 2.29
191 192 6.349115 CCACTAGTACTCGTACAGTTTGACAT 60.349 42.308 0.00 0.00 38.48 3.06
198 199 2.290514 TGCCCACTAGTACTCGTACAGT 60.291 50.000 0.00 0.00 38.48 3.55
199 200 2.097142 GTGCCCACTAGTACTCGTACAG 59.903 54.545 0.00 0.00 38.48 2.74
209 210 1.203262 TCCTAAGGTGTGCCCACTAGT 60.203 52.381 0.00 0.00 41.53 2.57
210 211 1.482593 CTCCTAAGGTGTGCCCACTAG 59.517 57.143 0.00 0.00 41.53 2.57
211 212 1.203262 ACTCCTAAGGTGTGCCCACTA 60.203 52.381 0.00 0.00 41.53 2.74
212 213 0.473886 ACTCCTAAGGTGTGCCCACT 60.474 55.000 0.00 0.00 41.53 4.00
221 222 6.150034 TCCTGAAGTACTTACTCCTAAGGT 57.850 41.667 8.42 0.00 34.99 3.50
231 232 2.942604 AGGGGCTCCTGAAGTACTTA 57.057 50.000 2.82 0.00 42.98 2.24
257 258 1.221840 GCGATGAGAAGGGCAAGGA 59.778 57.895 0.00 0.00 0.00 3.36
275 276 4.180946 CGACGAGGAGCAGGACGG 62.181 72.222 0.00 0.00 0.00 4.79
304 305 1.119684 ATGACTGCATACACGGCCTA 58.880 50.000 0.00 0.00 31.57 3.93
307 308 1.502231 CCTATGACTGCATACACGGC 58.498 55.000 0.00 0.00 35.94 5.68
313 314 5.275630 AGGATCATAGCCTATGACTGCATA 58.724 41.667 16.39 0.00 46.94 3.14
336 337 0.836606 TCGCCTTGCCATGATCCTTA 59.163 50.000 0.00 0.00 0.00 2.69
339 340 0.101219 GTTTCGCCTTGCCATGATCC 59.899 55.000 0.00 0.00 0.00 3.36
340 341 0.101219 GGTTTCGCCTTGCCATGATC 59.899 55.000 0.00 0.00 0.00 2.92
341 342 1.322538 GGGTTTCGCCTTGCCATGAT 61.323 55.000 0.00 0.00 37.43 2.45
342 343 1.976474 GGGTTTCGCCTTGCCATGA 60.976 57.895 0.00 0.00 37.43 3.07
343 344 1.814772 TTGGGTTTCGCCTTGCCATG 61.815 55.000 0.00 0.00 37.43 3.66
344 345 1.118356 TTTGGGTTTCGCCTTGCCAT 61.118 50.000 0.00 0.00 37.43 4.40
345 346 1.330655 TTTTGGGTTTCGCCTTGCCA 61.331 50.000 0.00 0.00 37.43 4.92
346 347 0.034756 ATTTTGGGTTTCGCCTTGCC 59.965 50.000 0.00 0.00 37.43 4.52
347 348 1.147473 CATTTTGGGTTTCGCCTTGC 58.853 50.000 0.00 0.00 37.43 4.01
348 349 2.810439 TCATTTTGGGTTTCGCCTTG 57.190 45.000 0.00 0.00 37.43 3.61
354 355 7.543756 TCTCGGATTAATTCATTTTGGGTTTC 58.456 34.615 0.00 0.00 0.00 2.78
385 386 9.782900 AGGGATAAAATAAAAATGGGAAAGAGA 57.217 29.630 0.00 0.00 0.00 3.10
390 391 9.967451 GGAAAAGGGATAAAATAAAAATGGGAA 57.033 29.630 0.00 0.00 0.00 3.97
391 392 9.345254 AGGAAAAGGGATAAAATAAAAATGGGA 57.655 29.630 0.00 0.00 0.00 4.37
392 393 9.973661 AAGGAAAAGGGATAAAATAAAAATGGG 57.026 29.630 0.00 0.00 0.00 4.00
398 399 9.699703 CGTCAAAAGGAAAAGGGATAAAATAAA 57.300 29.630 0.00 0.00 0.00 1.40
399 400 9.080097 TCGTCAAAAGGAAAAGGGATAAAATAA 57.920 29.630 0.00 0.00 0.00 1.40
400 401 8.638629 TCGTCAAAAGGAAAAGGGATAAAATA 57.361 30.769 0.00 0.00 0.00 1.40
401 402 7.450323 TCTCGTCAAAAGGAAAAGGGATAAAAT 59.550 33.333 0.00 0.00 0.00 1.82
402 403 6.773685 TCTCGTCAAAAGGAAAAGGGATAAAA 59.226 34.615 0.00 0.00 0.00 1.52
403 404 6.300703 TCTCGTCAAAAGGAAAAGGGATAAA 58.699 36.000 0.00 0.00 0.00 1.40
404 405 5.871834 TCTCGTCAAAAGGAAAAGGGATAA 58.128 37.500 0.00 0.00 0.00 1.75
405 406 5.247564 TCTCTCGTCAAAAGGAAAAGGGATA 59.752 40.000 0.00 0.00 0.00 2.59
406 407 4.041691 TCTCTCGTCAAAAGGAAAAGGGAT 59.958 41.667 0.00 0.00 0.00 3.85
407 408 3.389983 TCTCTCGTCAAAAGGAAAAGGGA 59.610 43.478 0.00 0.00 0.00 4.20
408 409 3.740115 TCTCTCGTCAAAAGGAAAAGGG 58.260 45.455 0.00 0.00 0.00 3.95
409 410 5.751243 TTTCTCTCGTCAAAAGGAAAAGG 57.249 39.130 0.00 0.00 0.00 3.11
410 411 5.626955 GCATTTCTCTCGTCAAAAGGAAAAG 59.373 40.000 0.00 0.00 0.00 2.27
411 412 5.299279 AGCATTTCTCTCGTCAAAAGGAAAA 59.701 36.000 0.00 0.00 0.00 2.29
412 413 4.821805 AGCATTTCTCTCGTCAAAAGGAAA 59.178 37.500 0.00 0.00 0.00 3.13
413 414 4.389374 AGCATTTCTCTCGTCAAAAGGAA 58.611 39.130 0.00 0.00 0.00 3.36
414 415 4.008074 AGCATTTCTCTCGTCAAAAGGA 57.992 40.909 0.00 0.00 0.00 3.36
415 416 4.756084 AAGCATTTCTCTCGTCAAAAGG 57.244 40.909 0.00 0.00 0.00 3.11
416 417 5.973565 ACAAAAGCATTTCTCTCGTCAAAAG 59.026 36.000 0.00 0.00 37.28 2.27
417 418 5.890334 ACAAAAGCATTTCTCTCGTCAAAA 58.110 33.333 0.00 0.00 37.28 2.44
418 419 5.296780 AGACAAAAGCATTTCTCTCGTCAAA 59.703 36.000 5.12 0.00 37.28 2.69
419 420 4.816385 AGACAAAAGCATTTCTCTCGTCAA 59.184 37.500 5.12 0.00 37.28 3.18
420 421 4.380531 AGACAAAAGCATTTCTCTCGTCA 58.619 39.130 5.12 0.00 37.28 4.35
421 422 4.999751 AGACAAAAGCATTTCTCTCGTC 57.000 40.909 0.00 0.00 37.28 4.20
422 423 4.576463 ACAAGACAAAAGCATTTCTCTCGT 59.424 37.500 0.00 0.00 37.28 4.18
423 424 5.100751 ACAAGACAAAAGCATTTCTCTCG 57.899 39.130 0.00 0.00 37.28 4.04
424 425 5.911838 GTGACAAGACAAAAGCATTTCTCTC 59.088 40.000 0.00 0.00 37.28 3.20
425 426 5.357878 TGTGACAAGACAAAAGCATTTCTCT 59.642 36.000 0.00 0.00 37.28 3.10
426 427 5.456822 GTGTGACAAGACAAAAGCATTTCTC 59.543 40.000 0.00 0.00 37.28 2.87
427 428 5.126061 AGTGTGACAAGACAAAAGCATTTCT 59.874 36.000 0.00 0.00 37.28 2.52
428 429 5.230726 CAGTGTGACAAGACAAAAGCATTTC 59.769 40.000 0.00 0.00 37.28 2.17
429 430 5.104374 CAGTGTGACAAGACAAAAGCATTT 58.896 37.500 0.00 0.00 42.41 2.32
430 431 4.158394 ACAGTGTGACAAGACAAAAGCATT 59.842 37.500 0.00 0.00 0.00 3.56
447 448 7.257722 CACTTCAATTTGTTAGGAAACAGTGT 58.742 34.615 0.00 0.00 45.99 3.55
450 451 7.038154 TCCACTTCAATTTGTTAGGAAACAG 57.962 36.000 0.00 0.00 45.99 3.16
458 459 9.130661 TCAGATTTCTTCCACTTCAATTTGTTA 57.869 29.630 0.00 0.00 0.00 2.41
460 461 7.587037 TCAGATTTCTTCCACTTCAATTTGT 57.413 32.000 0.00 0.00 0.00 2.83
464 465 6.723052 ACCAATCAGATTTCTTCCACTTCAAT 59.277 34.615 0.00 0.00 0.00 2.57
482 483 2.665649 AACACGAGCGATACCAATCA 57.334 45.000 0.00 0.00 31.93 2.57
483 484 5.652744 AAATAACACGAGCGATACCAATC 57.347 39.130 0.00 0.00 0.00 2.67
485 486 5.653507 AGTAAATAACACGAGCGATACCAA 58.346 37.500 0.00 0.00 0.00 3.67
493 494 3.176708 TGCGAGAGTAAATAACACGAGC 58.823 45.455 0.00 0.00 0.00 5.03
496 497 3.863424 ACCATGCGAGAGTAAATAACACG 59.137 43.478 0.00 0.00 0.00 4.49
512 513 2.017049 AGAACCGAATAAGCACCATGC 58.983 47.619 0.00 0.00 45.46 4.06
514 515 3.627395 TGAGAACCGAATAAGCACCAT 57.373 42.857 0.00 0.00 0.00 3.55
515 516 3.410631 TTGAGAACCGAATAAGCACCA 57.589 42.857 0.00 0.00 0.00 4.17
654 662 1.969064 TCGAAACCGTGCCCAATGG 60.969 57.895 0.00 0.00 41.27 3.16
724 734 0.462047 CAGATTTCTTCGGGTCCGGG 60.462 60.000 9.68 3.60 40.25 5.73
817 846 0.103208 CACGAGGAGGAAGAATCGGG 59.897 60.000 0.00 0.00 39.42 5.14
837 877 2.846827 AGGAAAGAGGATGGATTTCGGT 59.153 45.455 0.00 0.00 34.47 4.69
909 949 4.337177 TGGGGCGTGGCGAATGAA 62.337 61.111 0.00 0.00 0.00 2.57
921 961 0.915364 AGAAAGATCTGGACTGGGGC 59.085 55.000 0.00 0.00 33.59 5.80
923 963 2.433970 GAGGAGAAAGATCTGGACTGGG 59.566 54.545 0.00 0.00 35.54 4.45
938 978 4.104086 AGACAGAGAGAGAGAAGAGGAGA 58.896 47.826 0.00 0.00 0.00 3.71
948 988 4.525996 CAGATTCCAGAGACAGAGAGAGA 58.474 47.826 0.00 0.00 0.00 3.10
956 996 2.842496 AGCAATCCAGATTCCAGAGACA 59.158 45.455 0.00 0.00 0.00 3.41
961 1001 2.723322 TCCAGCAATCCAGATTCCAG 57.277 50.000 0.00 0.00 0.00 3.86
962 1002 2.940158 CATCCAGCAATCCAGATTCCA 58.060 47.619 0.00 0.00 0.00 3.53
963 1003 1.612463 GCATCCAGCAATCCAGATTCC 59.388 52.381 0.00 0.00 44.79 3.01
964 1004 1.266175 CGCATCCAGCAATCCAGATTC 59.734 52.381 0.00 0.00 46.13 2.52
965 1005 1.134007 TCGCATCCAGCAATCCAGATT 60.134 47.619 0.00 0.00 46.13 2.40
966 1006 0.471191 TCGCATCCAGCAATCCAGAT 59.529 50.000 0.00 0.00 46.13 2.90
967 1007 0.471191 ATCGCATCCAGCAATCCAGA 59.529 50.000 0.00 0.00 46.13 3.86
968 1008 2.174363 TATCGCATCCAGCAATCCAG 57.826 50.000 0.00 0.00 46.13 3.86
969 1009 2.497138 CTTATCGCATCCAGCAATCCA 58.503 47.619 0.00 0.00 46.13 3.41
1140 1207 2.603776 AACGGGGAGAAGTCGGCT 60.604 61.111 0.00 0.00 0.00 5.52
1315 1397 2.715532 TTCTCTGCCGCGCTCTGTTT 62.716 55.000 5.56 0.00 0.00 2.83
1359 1450 3.181433 CCTCCACCTTCTTTACCTTTGGT 60.181 47.826 0.00 0.00 40.16 3.67
1367 1458 0.902531 CTCGGCCTCCACCTTCTTTA 59.097 55.000 0.00 0.00 0.00 1.85
1494 1585 1.335697 GGACACTCGAAGACGCGTTC 61.336 60.000 15.53 7.11 35.24 3.95
1698 1801 1.227674 GCTCTCCGGCCACCTTATG 60.228 63.158 2.24 0.00 0.00 1.90
1732 1835 4.217118 AGCAGATGAAATTCAGTGGACAAC 59.783 41.667 1.10 0.00 0.00 3.32
1733 1836 4.401022 AGCAGATGAAATTCAGTGGACAA 58.599 39.130 1.10 0.00 0.00 3.18
1735 1838 5.159209 CAAAGCAGATGAAATTCAGTGGAC 58.841 41.667 1.10 0.00 0.00 4.02
1736 1839 4.219070 CCAAAGCAGATGAAATTCAGTGGA 59.781 41.667 1.10 0.00 0.00 4.02
1738 1841 4.921515 CACCAAAGCAGATGAAATTCAGTG 59.078 41.667 1.10 2.98 0.00 3.66
1747 1859 0.401356 TCAGGCACCAAAGCAGATGA 59.599 50.000 0.00 0.00 35.83 2.92
1748 1860 0.524862 GTCAGGCACCAAAGCAGATG 59.475 55.000 0.00 0.00 35.83 2.90
1749 1861 0.403271 AGTCAGGCACCAAAGCAGAT 59.597 50.000 0.00 0.00 35.83 2.90
1751 1863 0.595095 GAAGTCAGGCACCAAAGCAG 59.405 55.000 0.00 0.00 35.83 4.24
1767 1879 7.173907 ACAAACCATGTCTGAAGATAACTGAAG 59.826 37.037 0.00 0.00 37.96 3.02
1952 4860 7.835682 ACCTCCTGAATGAAATCAATGTAATGA 59.164 33.333 0.00 0.00 0.00 2.57
1996 6623 7.564005 GCTTGAAAATGATATTCGAACGAATGC 60.564 37.037 25.74 19.05 43.75 3.56
2005 6632 9.941664 ACTTAATCAGCTTGAAAATGATATTCG 57.058 29.630 0.00 0.00 33.40 3.34
2016 6643 4.697352 GGCTCTGAACTTAATCAGCTTGAA 59.303 41.667 1.79 0.00 45.21 2.69
2022 6649 4.456911 TGCAAAGGCTCTGAACTTAATCAG 59.543 41.667 0.00 0.36 42.11 2.90
2027 6654 4.022935 CACAATGCAAAGGCTCTGAACTTA 60.023 41.667 0.00 0.00 41.91 2.24
2110 6737 2.758009 ACTGCACAAACCATTTGCATC 58.242 42.857 1.23 0.00 44.94 3.91
2126 6753 0.391130 TTGTCGATGGCACCTACTGC 60.391 55.000 0.00 0.00 46.31 4.40
2187 6814 4.933330 TCCTATTCTGTTCGACAGCATAC 58.067 43.478 9.34 0.00 45.54 2.39
2367 7061 4.681978 ACTCCGCAGCCAACGTCC 62.682 66.667 0.00 0.00 0.00 4.79
2702 7423 0.892755 CACCAGGCCGTAACAGTCTA 59.107 55.000 0.00 0.00 0.00 2.59
2935 7670 3.820467 CCAGCACATTGACCTTGTTAGAA 59.180 43.478 0.00 0.00 0.00 2.10
3029 7765 5.651576 AGCAGATCTTCTATCATAGCATCGA 59.348 40.000 0.00 0.00 0.00 3.59
3079 7820 3.075148 CAGGCAGCATCAGGATTATCAG 58.925 50.000 0.00 0.00 0.00 2.90
3124 7869 6.470278 TGGTCATCAGCATCAAAGATATAGG 58.530 40.000 0.00 0.00 0.00 2.57
3226 7971 1.077429 GTGGGGTCTCTGGGCAATC 60.077 63.158 0.00 0.00 0.00 2.67
3429 8193 4.594123 TGTCCATAACGTTTCTGACAGA 57.406 40.909 5.91 0.00 0.00 3.41
3566 9990 6.038161 TGAAGAACAGTTGACATAAACACTGG 59.962 38.462 8.65 0.00 32.21 4.00
3895 10536 4.716287 TGATCAGTCATGGTGGTTCTCATA 59.284 41.667 0.00 0.00 0.00 2.15
3900 10541 4.676196 GCATTTGATCAGTCATGGTGGTTC 60.676 45.833 11.52 0.00 33.56 3.62
3967 10613 5.209818 ACTCTTGTTCTATCGACAACCAA 57.790 39.130 0.00 0.00 33.73 3.67
3975 10621 7.169982 AGTCAAACTTCAACTCTTGTTCTATCG 59.830 37.037 0.00 0.00 33.52 2.92
4031 10677 2.223782 CCACAATCACACCCAACAGTTG 60.224 50.000 6.28 6.28 0.00 3.16
4117 10818 1.030488 TGACGATCGACTCCACCTCC 61.030 60.000 24.34 0.00 0.00 4.30
4335 11237 7.771183 ACAAAATCGGCAGTAACAATATCATT 58.229 30.769 0.00 0.00 0.00 2.57
4444 11350 2.169352 TCAATCTTGCTGAGCCTACTCC 59.831 50.000 0.23 0.00 42.74 3.85
4658 11592 7.970061 ACTTGTATTGCATAACTTTAGTGCATG 59.030 33.333 0.00 0.00 46.90 4.06
4659 11593 8.055279 ACTTGTATTGCATAACTTTAGTGCAT 57.945 30.769 0.00 0.00 46.90 3.96
4910 12022 8.474025 AGGACAATTTCTATCTCAAGTAGACTG 58.526 37.037 0.00 0.00 36.93 3.51
4982 12095 7.414222 AGAATCACAAATTCTACATTGGCAT 57.586 32.000 0.00 0.00 36.68 4.40
4989 12102 9.371136 GTCACATCTAGAATCACAAATTCTACA 57.629 33.333 0.00 0.00 39.01 2.74
4990 12103 8.535592 CGTCACATCTAGAATCACAAATTCTAC 58.464 37.037 0.00 0.00 39.01 2.59
4993 12106 7.295952 ACGTCACATCTAGAATCACAAATTC 57.704 36.000 0.00 0.00 0.00 2.17
4996 12109 4.857037 CGACGTCACATCTAGAATCACAAA 59.143 41.667 17.16 0.00 0.00 2.83
5003 12116 2.815503 TGGTTCGACGTCACATCTAGAA 59.184 45.455 17.16 6.05 0.00 2.10
5008 12121 1.710013 ACATGGTTCGACGTCACATC 58.290 50.000 17.16 1.52 0.00 3.06
5009 12122 2.991190 GTTACATGGTTCGACGTCACAT 59.009 45.455 17.16 10.84 0.00 3.21
5016 12129 9.256477 TGATCAATATTAGTTACATGGTTCGAC 57.744 33.333 0.00 0.00 0.00 4.20
5074 12187 6.433847 TCTATGTACATGATAACCCCTTGG 57.566 41.667 18.81 0.00 37.80 3.61
5086 12199 7.880105 TCAACTAGAGATGCTCTATGTACATG 58.120 38.462 18.81 8.56 41.49 3.21
5087 12200 8.648698 ATCAACTAGAGATGCTCTATGTACAT 57.351 34.615 13.93 13.93 41.49 2.29
5097 12210 6.814954 TTTAAGGGATCAACTAGAGATGCT 57.185 37.500 16.23 5.48 34.66 3.79
5098 12211 7.201741 GGTTTTTAAGGGATCAACTAGAGATGC 60.202 40.741 0.00 4.86 33.63 3.91
5129 12242 8.540507 AAGGCTATCTCTCAAATGTACTCTTA 57.459 34.615 0.00 0.00 0.00 2.10
5137 12250 5.817816 ACGGTTTAAGGCTATCTCTCAAATG 59.182 40.000 0.00 0.00 0.00 2.32
5139 12252 5.416271 ACGGTTTAAGGCTATCTCTCAAA 57.584 39.130 0.00 0.00 0.00 2.69
5174 12287 6.014070 GGCTTTTGGGGATAACTCCTTAAAAA 60.014 38.462 0.00 0.00 41.74 1.94
5175 12288 5.482526 GGCTTTTGGGGATAACTCCTTAAAA 59.517 40.000 0.00 0.00 41.74 1.52
5176 12289 5.020795 GGCTTTTGGGGATAACTCCTTAAA 58.979 41.667 0.00 0.00 41.74 1.52
5177 12290 4.044825 TGGCTTTTGGGGATAACTCCTTAA 59.955 41.667 0.00 0.00 41.74 1.85
5178 12291 3.594232 TGGCTTTTGGGGATAACTCCTTA 59.406 43.478 0.00 0.00 41.74 2.69
5179 12292 2.381961 TGGCTTTTGGGGATAACTCCTT 59.618 45.455 0.00 0.00 41.74 3.36
5180 12293 2.000048 TGGCTTTTGGGGATAACTCCT 59.000 47.619 0.00 0.00 41.74 3.69
5181 12294 2.379005 CTGGCTTTTGGGGATAACTCC 58.621 52.381 0.00 0.00 41.26 3.85
5182 12295 1.751351 GCTGGCTTTTGGGGATAACTC 59.249 52.381 0.00 0.00 0.00 3.01
5183 12296 1.619704 GGCTGGCTTTTGGGGATAACT 60.620 52.381 0.00 0.00 0.00 2.24
5184 12297 0.824109 GGCTGGCTTTTGGGGATAAC 59.176 55.000 0.00 0.00 0.00 1.89
5185 12298 0.325203 GGGCTGGCTTTTGGGGATAA 60.325 55.000 0.00 0.00 0.00 1.75
5186 12299 1.309688 GGGCTGGCTTTTGGGGATA 59.690 57.895 0.00 0.00 0.00 2.59
5187 12300 2.039462 GGGCTGGCTTTTGGGGAT 59.961 61.111 0.00 0.00 0.00 3.85
5188 12301 3.516512 TGGGCTGGCTTTTGGGGA 61.517 61.111 0.00 0.00 0.00 4.81
5189 12302 2.999063 CTGGGCTGGCTTTTGGGG 60.999 66.667 0.00 0.00 0.00 4.96
5190 12303 3.698820 GCTGGGCTGGCTTTTGGG 61.699 66.667 0.00 0.00 0.00 4.12
5191 12304 2.602568 AGCTGGGCTGGCTTTTGG 60.603 61.111 0.00 0.00 37.57 3.28
5192 12305 1.593296 GAGAGCTGGGCTGGCTTTTG 61.593 60.000 0.00 0.00 39.88 2.44
5193 12306 1.303970 GAGAGCTGGGCTGGCTTTT 60.304 57.895 0.00 0.00 39.88 2.27
5194 12307 2.195692 GAGAGAGCTGGGCTGGCTTT 62.196 60.000 0.00 1.34 39.88 3.51
5195 12308 2.610233 AGAGAGCTGGGCTGGCTT 60.610 61.111 0.00 0.00 39.88 4.35
5196 12309 3.082701 GAGAGAGCTGGGCTGGCT 61.083 66.667 0.00 4.63 39.88 4.75
5197 12310 3.388703 CTGAGAGAGCTGGGCTGGC 62.389 68.421 0.00 0.00 39.88 4.85
5198 12311 1.551908 AACTGAGAGAGCTGGGCTGG 61.552 60.000 0.00 0.00 39.88 4.85
5199 12312 0.324285 AAACTGAGAGAGCTGGGCTG 59.676 55.000 0.00 0.00 39.88 4.85
5200 12313 1.063183 AAAACTGAGAGAGCTGGGCT 58.937 50.000 0.00 0.00 43.88 5.19
5201 12314 2.027653 AGTAAAACTGAGAGAGCTGGGC 60.028 50.000 0.00 0.00 0.00 5.36
5202 12315 3.368948 GGAGTAAAACTGAGAGAGCTGGG 60.369 52.174 0.00 0.00 0.00 4.45
5203 12316 3.513515 AGGAGTAAAACTGAGAGAGCTGG 59.486 47.826 0.00 0.00 0.00 4.85
5204 12317 4.381505 GGAGGAGTAAAACTGAGAGAGCTG 60.382 50.000 0.00 0.00 0.00 4.24
5205 12318 3.767131 GGAGGAGTAAAACTGAGAGAGCT 59.233 47.826 0.00 0.00 0.00 4.09
5206 12319 3.428316 CGGAGGAGTAAAACTGAGAGAGC 60.428 52.174 0.00 0.00 0.00 4.09
5207 12320 4.011023 TCGGAGGAGTAAAACTGAGAGAG 58.989 47.826 0.00 0.00 0.00 3.20
5208 12321 3.757493 GTCGGAGGAGTAAAACTGAGAGA 59.243 47.826 0.00 0.00 0.00 3.10
5209 12322 3.426426 CGTCGGAGGAGTAAAACTGAGAG 60.426 52.174 0.00 0.00 0.00 3.20
5210 12323 2.486982 CGTCGGAGGAGTAAAACTGAGA 59.513 50.000 0.00 0.00 0.00 3.27
5211 12324 2.864968 CGTCGGAGGAGTAAAACTGAG 58.135 52.381 0.00 0.00 0.00 3.35
5212 12325 1.068055 GCGTCGGAGGAGTAAAACTGA 60.068 52.381 1.18 0.00 0.00 3.41
5213 12326 1.347320 GCGTCGGAGGAGTAAAACTG 58.653 55.000 1.18 0.00 0.00 3.16
5214 12327 0.245813 GGCGTCGGAGGAGTAAAACT 59.754 55.000 1.18 0.00 0.00 2.66
5215 12328 0.037975 TGGCGTCGGAGGAGTAAAAC 60.038 55.000 1.18 0.00 0.00 2.43
5216 12329 0.037975 GTGGCGTCGGAGGAGTAAAA 60.038 55.000 1.18 0.00 0.00 1.52
5217 12330 0.896940 AGTGGCGTCGGAGGAGTAAA 60.897 55.000 1.18 0.00 0.00 2.01
5218 12331 0.896940 AAGTGGCGTCGGAGGAGTAA 60.897 55.000 1.18 0.00 0.00 2.24
5219 12332 1.303888 AAGTGGCGTCGGAGGAGTA 60.304 57.895 1.18 0.00 0.00 2.59
5220 12333 2.600769 AAGTGGCGTCGGAGGAGT 60.601 61.111 1.18 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.