Multiple sequence alignment - TraesCS6D01G136200

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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 TraesCS6D01G136200 chr6D 100.000 3545 0 0 1 3545 104456299 104452755 0.000000e+00 6547
1 TraesCS6D01G136200 chr6B 91.542 1667 89 28 1096 2732 190124309 190122665 0.000000e+00 2250
2 TraesCS6D01G136200 chr6B 88.128 716 41 30 395 1090 190125047 190124356 0.000000e+00 811
3 TraesCS6D01G136200 chr6B 88.632 519 27 12 2720 3227 190122629 190122132 1.410000e-168 603
4 TraesCS6D01G136200 chr6B 91.852 270 11 5 120 378 190125844 190125575 2.010000e-97 366
5 TraesCS6D01G136200 chr6A 92.664 1445 62 17 1097 2508 126346595 126345162 0.000000e+00 2041
6 TraesCS6D01G136200 chr6A 85.976 1148 66 37 12 1099 126347740 126346628 0.000000e+00 1140
7 TraesCS6D01G136200 chr6A 91.785 706 38 9 2538 3227 126344856 126344155 0.000000e+00 965
8 TraesCS6D01G136200 chr6A 93.571 280 17 1 3225 3504 532530735 532530457 1.970000e-112 416
9 TraesCS6D01G136200 chr7D 94.982 279 13 1 3226 3504 622190572 622190849 1.510000e-118 436
10 TraesCS6D01G136200 chr7D 93.571 280 18 0 3226 3505 198028011 198027732 5.470000e-113 418
11 TraesCS6D01G136200 chr7D 88.462 182 19 2 1787 1967 603848574 603848754 5.960000e-53 219
12 TraesCS6D01G136200 chr7D 86.598 194 24 2 1787 1979 603983230 603983422 2.770000e-51 213
13 TraesCS6D01G136200 chr7D 92.929 99 7 0 2148 2246 603983555 603983653 1.030000e-30 145
14 TraesCS6D01G136200 chr3B 93.493 292 17 2 3215 3504 654254330 654254621 1.950000e-117 433
15 TraesCS6D01G136200 chr4B 93.972 282 16 1 3225 3506 165907646 165907366 3.270000e-115 425
16 TraesCS6D01G136200 chr4B 93.617 282 18 0 3225 3506 211720046 211719765 4.230000e-114 422
17 TraesCS6D01G136200 chr4D 93.907 279 17 0 3226 3504 345952521 345952799 4.230000e-114 422
18 TraesCS6D01G136200 chr2D 93.617 282 18 0 3224 3505 581976081 581976362 4.230000e-114 422
19 TraesCS6D01G136200 chr5D 93.571 280 18 0 3225 3504 432046260 432046539 5.470000e-113 418
20 TraesCS6D01G136200 chr7B 86.598 194 23 3 1787 1978 686850749 686850941 9.970000e-51 211
21 TraesCS6D01G136200 chr7B 87.363 182 21 2 1787 1967 686965770 686965590 1.290000e-49 207
22 TraesCS6D01G136200 chr7B 87.363 182 21 2 1787 1967 688163757 688163937 1.290000e-49 207
23 TraesCS6D01G136200 chr7B 93.939 99 6 0 2148 2246 686887431 686887333 2.200000e-32 150
24 TraesCS6D01G136200 chr7A 86.598 194 23 3 1787 1978 696722783 696722591 9.970000e-51 211
25 TraesCS6D01G136200 chr7A 87.363 182 21 2 1787 1967 696553345 696553525 1.290000e-49 207


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 TraesCS6D01G136200 chr6D 104452755 104456299 3544 True 6547.0 6547 100.000000 1 3545 1 chr6D.!!$R1 3544
1 TraesCS6D01G136200 chr6B 190122132 190125844 3712 True 1007.5 2250 90.038500 120 3227 4 chr6B.!!$R1 3107
2 TraesCS6D01G136200 chr6A 126344155 126347740 3585 True 1382.0 2041 90.141667 12 3227 3 chr6A.!!$R2 3215

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
769 1356 0.179048 TCCGCATGCTCGAATTCCAT 60.179 50.0 17.13 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2699 3668 0.321919 AGCAGCACATGGGTACTGTG 60.322 55.0 8.89 8.89 45.39 3.66 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
52 53 8.311109 AGTAAAATTAATTAACCAACCAGCCTG 58.689 33.333 0.01 0.00 0.00 4.85
88 89 6.127479 CCAAGCCCAAACTTGCACTAATAATA 60.127 38.462 0.00 0.00 44.66 0.98
116 120 3.373226 TCCACGTAGGAGCACACC 58.627 61.111 3.02 0.00 43.07 4.16
118 122 1.215647 CCACGTAGGAGCACACCTC 59.784 63.158 0.00 0.00 41.22 3.85
175 179 4.049186 CGAATATGACGGGAAAGAATCGT 58.951 43.478 0.00 0.00 39.99 3.73
315 341 0.547712 TCCTGTCCCCCTCTTTCCAG 60.548 60.000 0.00 0.00 0.00 3.86
323 349 0.252927 CCCTCTTTCCAGTCCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
325 351 0.820871 CTCTTTCCAGTCCCTCCTCG 59.179 60.000 0.00 0.00 0.00 4.63
335 368 0.914417 TCCCTCCTCGCTCCCATTTT 60.914 55.000 0.00 0.00 0.00 1.82
341 374 1.709147 CTCGCTCCCATTTTCCGCAG 61.709 60.000 0.00 0.00 0.00 5.18
367 400 3.428045 GCAAAGCCTAATCGCAATCAACT 60.428 43.478 0.00 0.00 0.00 3.16
368 401 4.100529 CAAAGCCTAATCGCAATCAACTG 58.899 43.478 0.00 0.00 0.00 3.16
369 402 2.292267 AGCCTAATCGCAATCAACTGG 58.708 47.619 0.00 0.00 0.00 4.00
370 403 2.092968 AGCCTAATCGCAATCAACTGGA 60.093 45.455 0.00 0.00 0.00 3.86
371 404 2.289002 GCCTAATCGCAATCAACTGGAG 59.711 50.000 0.00 0.00 0.00 3.86
381 928 5.296780 CGCAATCAACTGGAGTAATAACCAT 59.703 40.000 0.00 0.00 35.54 3.55
491 1043 2.169146 TGCATCTCGCGAGCATGTG 61.169 57.895 30.86 25.54 46.97 3.21
494 1046 1.520120 ATCTCGCGAGCATGTGTGG 60.520 57.895 30.97 5.49 0.00 4.17
495 1047 2.230994 ATCTCGCGAGCATGTGTGGT 62.231 55.000 30.97 0.00 39.13 4.16
496 1048 2.733671 CTCGCGAGCATGTGTGGTG 61.734 63.158 25.07 0.00 35.91 4.17
497 1049 3.043713 CGCGAGCATGTGTGGTGT 61.044 61.111 0.00 0.00 35.91 4.16
498 1050 1.736282 CGCGAGCATGTGTGGTGTA 60.736 57.895 0.00 0.00 35.91 2.90
499 1051 1.787847 GCGAGCATGTGTGGTGTAC 59.212 57.895 0.00 0.00 35.91 2.90
500 1052 0.670546 GCGAGCATGTGTGGTGTACT 60.671 55.000 0.00 0.00 35.91 2.73
525 1088 2.434185 CCGATCACCACCACCACG 60.434 66.667 0.00 0.00 0.00 4.94
526 1089 2.654289 CGATCACCACCACCACGA 59.346 61.111 0.00 0.00 0.00 4.35
527 1090 1.005512 CGATCACCACCACCACGAA 60.006 57.895 0.00 0.00 0.00 3.85
528 1091 0.601576 CGATCACCACCACCACGAAA 60.602 55.000 0.00 0.00 0.00 3.46
529 1092 0.872388 GATCACCACCACCACGAAAC 59.128 55.000 0.00 0.00 0.00 2.78
542 1105 2.025418 CGAAACACTCCCCGAACCG 61.025 63.158 0.00 0.00 0.00 4.44
606 1173 1.451387 CCGTTGGAAAGATCCCCGG 60.451 63.158 0.00 0.00 46.37 5.73
769 1356 0.179048 TCCGCATGCTCGAATTCCAT 60.179 50.000 17.13 0.00 0.00 3.41
797 1384 1.741528 TCCCCGTTTCTTTATTCCGC 58.258 50.000 0.00 0.00 0.00 5.54
804 1391 4.082949 CCGTTTCTTTATTCCGCTTCCTTT 60.083 41.667 0.00 0.00 0.00 3.11
861 1448 1.070577 GTGTGAGTTGTGATGTGACGC 60.071 52.381 0.00 0.00 0.00 5.19
879 1466 4.516195 GAGCCGCTTCGTCCCCTC 62.516 72.222 0.00 0.00 0.00 4.30
886 1473 4.410033 TTCGTCCCCTCCCCCTCC 62.410 72.222 0.00 0.00 0.00 4.30
921 1511 2.783288 CGACCCGACCTTCCTAGCC 61.783 68.421 0.00 0.00 0.00 3.93
930 1520 0.179097 CCTTCCTAGCCAGCGACTTC 60.179 60.000 0.00 0.00 0.00 3.01
1031 1621 5.908341 GAACTCGGAAATAGTTCTCCATCT 58.092 41.667 2.56 0.00 46.08 2.90
1070 1663 1.989966 CTCTTCTCTCCCGCGCGTTA 61.990 60.000 29.95 15.18 0.00 3.18
1088 1681 1.243342 TACCTCGAACCGGAAGCGAA 61.243 55.000 9.46 0.00 33.26 4.70
1102 1735 3.385577 GAAGCGAACTCTACATCCATCC 58.614 50.000 0.00 0.00 0.00 3.51
1109 1742 1.537638 CTCTACATCCATCCTCGACCG 59.462 57.143 0.00 0.00 0.00 4.79
1286 1922 2.066340 CCCTGAGGTAGGCACACAA 58.934 57.895 0.00 0.00 45.89 3.33
1294 1930 2.236395 AGGTAGGCACACAAGTCCATAC 59.764 50.000 0.00 0.00 0.00 2.39
1296 1932 2.479566 AGGCACACAAGTCCATACAG 57.520 50.000 0.00 0.00 0.00 2.74
1300 1936 2.996621 GCACACAAGTCCATACAGAGAC 59.003 50.000 0.00 0.00 0.00 3.36
1301 1937 3.245797 CACACAAGTCCATACAGAGACG 58.754 50.000 0.00 0.00 38.08 4.18
1303 1939 1.135373 ACAAGTCCATACAGAGACGCG 60.135 52.381 3.53 3.53 38.08 6.01
1312 1950 0.384309 ACAGAGACGCGTCAAGAACA 59.616 50.000 37.85 0.00 0.00 3.18
1313 1951 1.202371 ACAGAGACGCGTCAAGAACAA 60.202 47.619 37.85 0.00 0.00 2.83
1315 1953 0.158928 GAGACGCGTCAAGAACAACG 59.841 55.000 37.85 0.00 41.68 4.10
1362 2004 4.631377 GTGTATGTGAGCTGCAACTGAATA 59.369 41.667 1.02 0.00 0.00 1.75
1364 2006 5.525012 TGTATGTGAGCTGCAACTGAATATC 59.475 40.000 1.02 0.00 0.00 1.63
1372 2014 4.033817 GCTGCAACTGAATATCTGTGTCTC 59.966 45.833 0.00 0.00 0.00 3.36
1373 2015 4.507710 TGCAACTGAATATCTGTGTCTCC 58.492 43.478 0.00 0.00 0.00 3.71
1374 2016 4.223700 TGCAACTGAATATCTGTGTCTCCT 59.776 41.667 0.00 0.00 0.00 3.69
1399 2041 0.759346 AGGTTGCGGTTCTTGAGTCT 59.241 50.000 0.00 0.00 0.00 3.24
1535 2180 3.893763 CCGGCGGCAACAACAACA 61.894 61.111 15.42 0.00 0.00 3.33
1792 2446 2.665603 GACCTCAGCCTGGTGGTC 59.334 66.667 17.42 17.42 41.52 4.02
1967 2621 3.537206 GAGGGCGAGCACAACCACT 62.537 63.158 0.00 0.00 0.00 4.00
2365 3044 0.882927 CGCCTCCGTCAAAACCTCAA 60.883 55.000 0.00 0.00 0.00 3.02
2381 3060 2.030805 CCTCAAAGAAAAACCAGCGAGG 60.031 50.000 0.00 0.00 45.67 4.63
2389 3068 4.680537 ACCAGCGAGGACCGGACT 62.681 66.667 9.46 5.62 41.22 3.85
2442 3121 3.706373 GAGCCAGGAACGGAGCCA 61.706 66.667 0.00 0.00 0.00 4.75
2483 3166 0.821517 ATACATCGCCAACACGAGGA 59.178 50.000 5.55 0.00 46.05 3.71
2489 3172 4.657824 CCAACACGAGGACGGCGT 62.658 66.667 14.65 14.65 44.46 5.68
2527 3496 8.850007 CATGTAATGTACTCTAGTAGCTAGGA 57.150 38.462 0.00 0.00 40.20 2.94
2528 3497 9.456147 CATGTAATGTACTCTAGTAGCTAGGAT 57.544 37.037 0.00 0.00 40.20 3.24
2601 3570 8.433421 TCTTTTCCTTATTACTAGGCGAAATG 57.567 34.615 0.00 0.00 32.59 2.32
2661 3630 4.223320 TGAGAAAAATCAAAGTCACCGC 57.777 40.909 0.00 0.00 0.00 5.68
2682 3651 3.727079 GCACATTCTCAGTTCAATCGCTG 60.727 47.826 0.00 0.00 0.00 5.18
2699 3668 7.750458 TCAATCGCTGAAATTTTGTCAATACTC 59.250 33.333 0.00 0.00 0.00 2.59
2700 3669 6.552859 TCGCTGAAATTTTGTCAATACTCA 57.447 33.333 0.00 0.00 0.00 3.41
2707 3676 8.564574 TGAAATTTTGTCAATACTCACAGTACC 58.435 33.333 0.00 0.00 32.84 3.34
2788 3805 2.945668 GTTTGGCGAGCTTATCCAGAAT 59.054 45.455 0.00 0.00 0.00 2.40
2806 3823 1.899437 ATGGGTCCACGTAGGCAGTG 61.899 60.000 0.00 0.00 39.19 3.66
2861 3878 0.466124 AGAATACGCTGGGAAGAGGC 59.534 55.000 0.00 0.00 0.00 4.70
3105 4137 2.280797 GCAACCACGCACCTCTCA 60.281 61.111 0.00 0.00 0.00 3.27
3107 4139 1.237285 GCAACCACGCACCTCTCATT 61.237 55.000 0.00 0.00 0.00 2.57
3108 4140 0.798776 CAACCACGCACCTCTCATTC 59.201 55.000 0.00 0.00 0.00 2.67
3109 4141 0.687354 AACCACGCACCTCTCATTCT 59.313 50.000 0.00 0.00 0.00 2.40
3110 4142 0.247736 ACCACGCACCTCTCATTCTC 59.752 55.000 0.00 0.00 0.00 2.87
3166 4208 4.609691 TTCGACTTTGAAACACACTTCC 57.390 40.909 0.00 0.00 0.00 3.46
3170 4212 5.182380 TCGACTTTGAAACACACTTCCTTTT 59.818 36.000 0.00 0.00 0.00 2.27
3171 4213 5.286082 CGACTTTGAAACACACTTCCTTTTG 59.714 40.000 0.00 0.00 0.00 2.44
3173 4215 4.527509 TTGAAACACACTTCCTTTTGCA 57.472 36.364 0.00 0.00 0.00 4.08
3174 4216 4.527509 TGAAACACACTTCCTTTTGCAA 57.472 36.364 0.00 0.00 0.00 4.08
3188 4230 9.912634 CTTCCTTTTGCAAGTATAAAATCTTCA 57.087 29.630 0.00 0.00 0.00 3.02
3227 4269 4.649674 AGATCTGGCTGAGATACCGTTTTA 59.350 41.667 0.00 0.00 41.91 1.52
3228 4270 4.386867 TCTGGCTGAGATACCGTTTTAG 57.613 45.455 0.00 0.00 0.00 1.85
3229 4271 3.132289 TCTGGCTGAGATACCGTTTTAGG 59.868 47.826 0.00 0.00 37.30 2.69
3230 4272 2.210961 GGCTGAGATACCGTTTTAGGC 58.789 52.381 0.00 0.00 33.69 3.93
3231 4273 2.158943 GGCTGAGATACCGTTTTAGGCT 60.159 50.000 0.00 0.00 33.69 4.58
3232 4274 2.866762 GCTGAGATACCGTTTTAGGCTG 59.133 50.000 0.00 0.00 33.69 4.85
3233 4275 3.458189 CTGAGATACCGTTTTAGGCTGG 58.542 50.000 0.00 0.00 33.69 4.85
3234 4276 2.210961 GAGATACCGTTTTAGGCTGGC 58.789 52.381 0.00 0.00 33.69 4.85
3235 4277 1.134189 AGATACCGTTTTAGGCTGGCC 60.134 52.381 3.00 3.00 33.69 5.36
3236 4278 0.621609 ATACCGTTTTAGGCTGGCCA 59.378 50.000 14.39 4.71 38.92 5.36
3237 4279 0.621609 TACCGTTTTAGGCTGGCCAT 59.378 50.000 5.51 0.00 38.92 4.40
3238 4280 0.621609 ACCGTTTTAGGCTGGCCATA 59.378 50.000 5.51 0.00 38.92 2.74
3239 4281 1.308998 CCGTTTTAGGCTGGCCATAG 58.691 55.000 5.51 0.00 38.92 2.23
3240 4282 1.408266 CCGTTTTAGGCTGGCCATAGT 60.408 52.381 5.51 0.00 38.92 2.12
3241 4283 1.670811 CGTTTTAGGCTGGCCATAGTG 59.329 52.381 5.51 0.00 38.92 2.74
3242 4284 2.024414 GTTTTAGGCTGGCCATAGTGG 58.976 52.381 5.51 0.00 41.55 4.00
3243 4285 0.550914 TTTAGGCTGGCCATAGTGGG 59.449 55.000 5.51 0.00 38.19 4.61
3244 4286 1.352622 TTAGGCTGGCCATAGTGGGG 61.353 60.000 5.51 0.00 38.19 4.96
3245 4287 2.264494 TAGGCTGGCCATAGTGGGGA 62.264 60.000 5.51 0.00 38.19 4.81
3246 4288 2.464403 GGCTGGCCATAGTGGGGAT 61.464 63.158 5.51 0.00 38.19 3.85
3247 4289 1.133809 GGCTGGCCATAGTGGGGATA 61.134 60.000 5.51 0.00 38.19 2.59
3248 4290 0.771127 GCTGGCCATAGTGGGGATAA 59.229 55.000 5.51 0.00 38.19 1.75
3249 4291 1.545651 GCTGGCCATAGTGGGGATAAC 60.546 57.143 5.51 0.00 38.19 1.89
3250 4292 1.774254 CTGGCCATAGTGGGGATAACA 59.226 52.381 5.51 0.00 38.19 2.41
3251 4293 2.376518 CTGGCCATAGTGGGGATAACAT 59.623 50.000 5.51 0.00 38.19 2.71
3252 4294 3.587061 CTGGCCATAGTGGGGATAACATA 59.413 47.826 5.51 0.00 38.19 2.29
3253 4295 3.984090 TGGCCATAGTGGGGATAACATAA 59.016 43.478 0.00 0.00 38.19 1.90
3254 4296 4.417183 TGGCCATAGTGGGGATAACATAAA 59.583 41.667 0.00 0.00 38.19 1.40
3255 4297 5.075761 TGGCCATAGTGGGGATAACATAAAT 59.924 40.000 0.00 0.00 38.19 1.40
3256 4298 6.275855 TGGCCATAGTGGGGATAACATAAATA 59.724 38.462 0.00 0.00 38.19 1.40
3257 4299 6.828785 GGCCATAGTGGGGATAACATAAATAG 59.171 42.308 0.00 0.00 38.19 1.73
3258 4300 7.402862 GCCATAGTGGGGATAACATAAATAGT 58.597 38.462 0.00 0.00 38.19 2.12
3259 4301 8.545472 GCCATAGTGGGGATAACATAAATAGTA 58.455 37.037 0.00 0.00 38.19 1.82
3265 4307 9.959721 GTGGGGATAACATAAATAGTATCATGT 57.040 33.333 0.00 5.05 33.12 3.21
3277 4319 8.873215 AAATAGTATCATGTACTTTGGACTCG 57.127 34.615 11.53 0.00 0.00 4.18
3278 4320 4.683832 AGTATCATGTACTTTGGACTCGC 58.316 43.478 0.00 0.00 0.00 5.03
3279 4321 1.990799 TCATGTACTTTGGACTCGCG 58.009 50.000 0.00 0.00 0.00 5.87
3280 4322 1.542472 TCATGTACTTTGGACTCGCGA 59.458 47.619 9.26 9.26 0.00 5.87
3281 4323 2.029739 TCATGTACTTTGGACTCGCGAA 60.030 45.455 11.33 0.00 0.00 4.70
3282 4324 1.774639 TGTACTTTGGACTCGCGAAC 58.225 50.000 11.33 7.38 0.00 3.95
3283 4325 1.067364 TGTACTTTGGACTCGCGAACA 59.933 47.619 11.33 5.20 0.00 3.18
3284 4326 2.288579 TGTACTTTGGACTCGCGAACAT 60.289 45.455 11.33 0.00 0.00 2.71
3285 4327 1.148310 ACTTTGGACTCGCGAACATG 58.852 50.000 11.33 0.00 0.00 3.21
3286 4328 0.179215 CTTTGGACTCGCGAACATGC 60.179 55.000 11.33 4.66 0.00 4.06
3287 4329 0.602638 TTTGGACTCGCGAACATGCT 60.603 50.000 11.33 0.00 0.00 3.79
3288 4330 0.602638 TTGGACTCGCGAACATGCTT 60.603 50.000 11.33 0.00 0.00 3.91
3289 4331 0.245266 TGGACTCGCGAACATGCTTA 59.755 50.000 11.33 0.00 0.00 3.09
3290 4332 1.134818 TGGACTCGCGAACATGCTTAT 60.135 47.619 11.33 0.00 0.00 1.73
3291 4333 1.258982 GGACTCGCGAACATGCTTATG 59.741 52.381 11.33 0.00 0.00 1.90
3292 4334 1.927174 GACTCGCGAACATGCTTATGT 59.073 47.619 11.33 0.00 36.10 2.29
3293 4335 1.660607 ACTCGCGAACATGCTTATGTG 59.339 47.619 11.33 0.00 34.56 3.21
3294 4336 1.004610 CTCGCGAACATGCTTATGTGG 60.005 52.381 11.33 0.00 34.56 4.17
3295 4337 0.589729 CGCGAACATGCTTATGTGGC 60.590 55.000 0.00 0.00 34.56 5.01
3296 4338 0.451383 GCGAACATGCTTATGTGGCA 59.549 50.000 0.00 0.00 44.05 4.92
3297 4339 1.532505 GCGAACATGCTTATGTGGCAG 60.533 52.381 0.00 0.00 43.15 4.85
3298 4340 1.064505 CGAACATGCTTATGTGGCAGG 59.935 52.381 0.00 0.00 45.30 4.85
3299 4341 0.819582 AACATGCTTATGTGGCAGGC 59.180 50.000 0.00 0.00 43.93 4.85
3300 4342 0.323633 ACATGCTTATGTGGCAGGCA 60.324 50.000 0.00 0.00 43.93 4.75
3301 4343 0.818938 CATGCTTATGTGGCAGGCAA 59.181 50.000 0.00 0.00 43.15 4.52
3302 4344 1.411246 CATGCTTATGTGGCAGGCAAT 59.589 47.619 0.00 0.00 43.15 3.56
3303 4345 1.559368 TGCTTATGTGGCAGGCAATT 58.441 45.000 0.00 0.00 34.56 2.32
3304 4346 2.732763 TGCTTATGTGGCAGGCAATTA 58.267 42.857 0.00 0.00 34.56 1.40
3305 4347 3.095332 TGCTTATGTGGCAGGCAATTAA 58.905 40.909 0.00 0.00 34.56 1.40
3306 4348 3.513119 TGCTTATGTGGCAGGCAATTAAA 59.487 39.130 0.00 0.00 34.56 1.52
3307 4349 4.020751 TGCTTATGTGGCAGGCAATTAAAA 60.021 37.500 0.00 0.00 34.56 1.52
3308 4350 4.934602 GCTTATGTGGCAGGCAATTAAAAA 59.065 37.500 0.00 0.00 0.00 1.94
3335 4377 8.794553 AGAGGAAGATGGTTATAGTAACATACG 58.205 37.037 2.68 0.00 0.00 3.06
3336 4378 8.474710 AGGAAGATGGTTATAGTAACATACGT 57.525 34.615 0.00 0.00 0.00 3.57
3337 4379 9.578576 AGGAAGATGGTTATAGTAACATACGTA 57.421 33.333 0.00 0.00 0.00 3.57
3338 4380 9.837525 GGAAGATGGTTATAGTAACATACGTAG 57.162 37.037 0.08 0.00 0.00 3.51
3344 4386 8.935844 TGGTTATAGTAACATACGTAGATACCG 58.064 37.037 0.08 0.00 0.00 4.02
3345 4387 8.936864 GGTTATAGTAACATACGTAGATACCGT 58.063 37.037 0.08 0.00 42.06 4.83
3349 4391 7.786178 AGTAACATACGTAGATACCGTAACA 57.214 36.000 0.08 0.00 43.24 2.41
3350 4392 8.383318 AGTAACATACGTAGATACCGTAACAT 57.617 34.615 0.08 0.00 43.24 2.71
3351 4393 9.489084 AGTAACATACGTAGATACCGTAACATA 57.511 33.333 0.08 0.00 43.24 2.29
3375 4417 5.880054 AAAATGTGGTGCTACTATGTGTC 57.120 39.130 0.00 0.00 0.00 3.67
3376 4418 4.551702 AATGTGGTGCTACTATGTGTCA 57.448 40.909 0.00 0.00 0.00 3.58
3377 4419 4.760530 ATGTGGTGCTACTATGTGTCAT 57.239 40.909 0.00 0.00 0.00 3.06
3378 4420 3.860641 TGTGGTGCTACTATGTGTCATG 58.139 45.455 0.00 0.00 0.00 3.07
3379 4421 2.609459 GTGGTGCTACTATGTGTCATGC 59.391 50.000 0.00 0.00 0.00 4.06
3380 4422 2.235898 TGGTGCTACTATGTGTCATGCA 59.764 45.455 0.00 0.00 0.00 3.96
3381 4423 3.118298 TGGTGCTACTATGTGTCATGCAT 60.118 43.478 0.00 0.00 34.18 3.96
3382 4424 3.249320 GGTGCTACTATGTGTCATGCATG 59.751 47.826 21.07 21.07 34.18 4.06
3383 4425 4.122046 GTGCTACTATGTGTCATGCATGA 58.878 43.478 25.42 25.42 34.18 3.07
3397 4439 6.381481 TCATGCATGACAATAAATGAGACC 57.619 37.500 25.42 0.00 0.00 3.85
3398 4440 5.887035 TCATGCATGACAATAAATGAGACCA 59.113 36.000 25.42 0.00 0.00 4.02
3399 4441 5.565592 TGCATGACAATAAATGAGACCAC 57.434 39.130 0.00 0.00 0.00 4.16
3400 4442 4.398988 TGCATGACAATAAATGAGACCACC 59.601 41.667 0.00 0.00 0.00 4.61
3401 4443 4.641989 GCATGACAATAAATGAGACCACCT 59.358 41.667 0.00 0.00 0.00 4.00
3402 4444 5.822519 GCATGACAATAAATGAGACCACCTA 59.177 40.000 0.00 0.00 0.00 3.08
3403 4445 6.488006 GCATGACAATAAATGAGACCACCTAT 59.512 38.462 0.00 0.00 0.00 2.57
3404 4446 7.521099 GCATGACAATAAATGAGACCACCTATG 60.521 40.741 0.00 0.00 0.00 2.23
3405 4447 7.194112 TGACAATAAATGAGACCACCTATGA 57.806 36.000 0.00 0.00 0.00 2.15
3406 4448 7.805163 TGACAATAAATGAGACCACCTATGAT 58.195 34.615 0.00 0.00 0.00 2.45
3407 4449 8.933653 TGACAATAAATGAGACCACCTATGATA 58.066 33.333 0.00 0.00 0.00 2.15
3408 4450 9.209175 GACAATAAATGAGACCACCTATGATAC 57.791 37.037 0.00 0.00 0.00 2.24
3409 4451 8.938883 ACAATAAATGAGACCACCTATGATACT 58.061 33.333 0.00 0.00 0.00 2.12
3414 4456 8.964533 AATGAGACCACCTATGATACTAATCT 57.035 34.615 0.00 0.00 32.93 2.40
3417 4459 9.467796 TGAGACCACCTATGATACTAATCTATG 57.532 37.037 0.00 0.00 32.93 2.23
3418 4460 9.688091 GAGACCACCTATGATACTAATCTATGA 57.312 37.037 0.00 0.00 32.93 2.15
3450 4492 9.809395 TGCATTATAGAGGTAGTAACATAGACT 57.191 33.333 0.00 0.00 0.00 3.24
3485 4527 9.804758 ATGCATGTTACTACTCTAAGTTACTTC 57.195 33.333 0.00 0.00 31.82 3.01
3486 4528 8.248945 TGCATGTTACTACTCTAAGTTACTTCC 58.751 37.037 0.00 0.00 31.82 3.46
3487 4529 7.705752 GCATGTTACTACTCTAAGTTACTTCCC 59.294 40.741 0.00 0.00 31.82 3.97
3488 4530 8.746530 CATGTTACTACTCTAAGTTACTTCCCA 58.253 37.037 0.00 0.00 31.82 4.37
3489 4531 8.115490 TGTTACTACTCTAAGTTACTTCCCAC 57.885 38.462 0.00 0.00 31.82 4.61
3490 4532 7.946776 TGTTACTACTCTAAGTTACTTCCCACT 59.053 37.037 0.00 0.00 31.82 4.00
3491 4533 9.454859 GTTACTACTCTAAGTTACTTCCCACTA 57.545 37.037 0.00 0.00 0.00 2.74
3493 4535 8.522542 ACTACTCTAAGTTACTTCCCACTATG 57.477 38.462 0.00 0.00 0.00 2.23
3494 4536 8.334734 ACTACTCTAAGTTACTTCCCACTATGA 58.665 37.037 0.00 0.00 0.00 2.15
3495 4537 7.407393 ACTCTAAGTTACTTCCCACTATGAC 57.593 40.000 0.00 0.00 0.00 3.06
3496 4538 6.380560 ACTCTAAGTTACTTCCCACTATGACC 59.619 42.308 0.00 0.00 0.00 4.02
3497 4539 6.258354 TCTAAGTTACTTCCCACTATGACCA 58.742 40.000 0.00 0.00 0.00 4.02
3498 4540 5.422214 AAGTTACTTCCCACTATGACCAG 57.578 43.478 0.00 0.00 0.00 4.00
3499 4541 3.197983 AGTTACTTCCCACTATGACCAGC 59.802 47.826 0.00 0.00 0.00 4.85
3500 4542 0.912486 ACTTCCCACTATGACCAGCC 59.088 55.000 0.00 0.00 0.00 4.85
3501 4543 1.207791 CTTCCCACTATGACCAGCCT 58.792 55.000 0.00 0.00 0.00 4.58
3502 4544 1.561542 CTTCCCACTATGACCAGCCTT 59.438 52.381 0.00 0.00 0.00 4.35
3503 4545 2.561209 TCCCACTATGACCAGCCTTA 57.439 50.000 0.00 0.00 0.00 2.69
3504 4546 2.840511 TCCCACTATGACCAGCCTTAA 58.159 47.619 0.00 0.00 0.00 1.85
3505 4547 3.393687 TCCCACTATGACCAGCCTTAAT 58.606 45.455 0.00 0.00 0.00 1.40
3506 4548 3.391296 TCCCACTATGACCAGCCTTAATC 59.609 47.826 0.00 0.00 0.00 1.75
3507 4549 3.496870 CCCACTATGACCAGCCTTAATCC 60.497 52.174 0.00 0.00 0.00 3.01
3508 4550 3.392616 CCACTATGACCAGCCTTAATCCT 59.607 47.826 0.00 0.00 0.00 3.24
3509 4551 4.503991 CCACTATGACCAGCCTTAATCCTC 60.504 50.000 0.00 0.00 0.00 3.71
3510 4552 2.918712 ATGACCAGCCTTAATCCTCG 57.081 50.000 0.00 0.00 0.00 4.63
3511 4553 0.830648 TGACCAGCCTTAATCCTCGG 59.169 55.000 0.00 0.00 0.00 4.63
3512 4554 1.120530 GACCAGCCTTAATCCTCGGA 58.879 55.000 0.00 0.00 0.00 4.55
3513 4555 0.831307 ACCAGCCTTAATCCTCGGAC 59.169 55.000 0.00 0.00 0.00 4.79
3514 4556 1.123928 CCAGCCTTAATCCTCGGACT 58.876 55.000 0.00 0.00 0.00 3.85
3515 4557 2.317040 CCAGCCTTAATCCTCGGACTA 58.683 52.381 0.00 0.00 0.00 2.59
3516 4558 2.297597 CCAGCCTTAATCCTCGGACTAG 59.702 54.545 0.00 0.00 0.00 2.57
3517 4559 2.959707 CAGCCTTAATCCTCGGACTAGT 59.040 50.000 0.00 0.00 0.00 2.57
3518 4560 4.142790 CAGCCTTAATCCTCGGACTAGTA 58.857 47.826 0.00 0.00 0.00 1.82
3519 4561 4.583489 CAGCCTTAATCCTCGGACTAGTAA 59.417 45.833 0.00 0.00 0.00 2.24
3520 4562 4.583907 AGCCTTAATCCTCGGACTAGTAAC 59.416 45.833 0.00 0.00 0.00 2.50
3521 4563 4.340381 GCCTTAATCCTCGGACTAGTAACA 59.660 45.833 0.00 0.00 0.00 2.41
3522 4564 5.163478 GCCTTAATCCTCGGACTAGTAACAA 60.163 44.000 0.00 0.00 0.00 2.83
3523 4565 6.628844 GCCTTAATCCTCGGACTAGTAACAAA 60.629 42.308 0.00 0.00 0.00 2.83
3524 4566 7.498443 CCTTAATCCTCGGACTAGTAACAAAT 58.502 38.462 0.00 0.00 0.00 2.32
3525 4567 8.636213 CCTTAATCCTCGGACTAGTAACAAATA 58.364 37.037 0.00 0.00 0.00 1.40
3526 4568 9.680315 CTTAATCCTCGGACTAGTAACAAATAG 57.320 37.037 0.00 0.00 0.00 1.73
3527 4569 7.657023 AATCCTCGGACTAGTAACAAATAGT 57.343 36.000 0.00 0.00 34.96 2.12
3528 4570 8.757982 AATCCTCGGACTAGTAACAAATAGTA 57.242 34.615 0.00 0.00 32.43 1.82
3529 4571 8.757982 ATCCTCGGACTAGTAACAAATAGTAA 57.242 34.615 0.00 0.00 32.43 2.24
3530 4572 8.757982 TCCTCGGACTAGTAACAAATAGTAAT 57.242 34.615 0.00 0.00 32.43 1.89
3531 4573 9.193806 TCCTCGGACTAGTAACAAATAGTAATT 57.806 33.333 0.00 0.00 32.43 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.057456 CGATTTATCCTACTAGCTGGCGT 60.057 47.826 0.00 0.00 0.00 5.68
1 2 3.057456 ACGATTTATCCTACTAGCTGGCG 60.057 47.826 0.00 0.00 0.00 5.69
2 3 4.522722 ACGATTTATCCTACTAGCTGGC 57.477 45.455 0.00 0.00 0.00 4.85
3 4 8.508883 ACTATACGATTTATCCTACTAGCTGG 57.491 38.462 0.00 0.00 0.00 4.85
33 34 2.829120 GCCAGGCTGGTTGGTTAATTAA 59.171 45.455 32.80 0.00 40.46 1.40
41 42 2.048603 GCTAAGCCAGGCTGGTTGG 61.049 63.158 32.80 25.32 39.62 3.77
42 43 3.595819 GCTAAGCCAGGCTGGTTG 58.404 61.111 32.80 18.13 39.62 3.77
76 77 8.428852 TGGAAGTAGCATCTTATTATTAGTGCA 58.571 33.333 0.00 0.00 35.17 4.57
88 89 3.362706 TCCTACGTGGAAGTAGCATCTT 58.637 45.455 0.00 0.00 42.94 2.40
111 115 2.638480 TCCTTCTTGTTGGAGGTGTG 57.362 50.000 0.00 0.00 0.00 3.82
116 120 3.686726 CCGATTCTTCCTTCTTGTTGGAG 59.313 47.826 0.00 0.00 33.46 3.86
118 122 2.749621 CCCGATTCTTCCTTCTTGTTGG 59.250 50.000 0.00 0.00 0.00 3.77
119 123 2.749621 CCCCGATTCTTCCTTCTTGTTG 59.250 50.000 0.00 0.00 0.00 3.33
120 124 2.642807 TCCCCGATTCTTCCTTCTTGTT 59.357 45.455 0.00 0.00 0.00 2.83
121 125 2.266279 TCCCCGATTCTTCCTTCTTGT 58.734 47.619 0.00 0.00 0.00 3.16
122 126 3.274288 CTTCCCCGATTCTTCCTTCTTG 58.726 50.000 0.00 0.00 0.00 3.02
123 127 2.913617 ACTTCCCCGATTCTTCCTTCTT 59.086 45.455 0.00 0.00 0.00 2.52
124 128 2.237392 CACTTCCCCGATTCTTCCTTCT 59.763 50.000 0.00 0.00 0.00 2.85
175 179 2.791655 TGAGCTCGAGTAGACTGGAAA 58.208 47.619 15.13 0.00 30.38 3.13
315 341 1.627297 AAATGGGAGCGAGGAGGGAC 61.627 60.000 0.00 0.00 0.00 4.46
323 349 1.745115 CTGCGGAAAATGGGAGCGA 60.745 57.895 0.00 0.00 0.00 4.93
325 351 2.418083 CCCTGCGGAAAATGGGAGC 61.418 63.158 0.00 0.00 42.11 4.70
367 400 6.724893 TCTCATTCGATGGTTATTACTCCA 57.275 37.500 0.00 0.00 38.14 3.86
368 401 8.608844 AAATCTCATTCGATGGTTATTACTCC 57.391 34.615 0.00 0.00 0.00 3.85
399 946 7.910162 GCTCACTCGCAAAAGATGATTATTTAA 59.090 33.333 0.00 0.00 0.00 1.52
400 947 7.409697 GCTCACTCGCAAAAGATGATTATTTA 58.590 34.615 0.00 0.00 0.00 1.40
401 948 6.261118 GCTCACTCGCAAAAGATGATTATTT 58.739 36.000 0.00 0.00 0.00 1.40
405 953 2.094894 CGCTCACTCGCAAAAGATGATT 59.905 45.455 0.00 0.00 0.00 2.57
409 957 1.993370 GTACGCTCACTCGCAAAAGAT 59.007 47.619 0.00 0.00 0.00 2.40
411 959 0.438830 GGTACGCTCACTCGCAAAAG 59.561 55.000 0.00 0.00 0.00 2.27
412 960 0.249531 TGGTACGCTCACTCGCAAAA 60.250 50.000 0.00 0.00 0.00 2.44
413 961 0.249531 TTGGTACGCTCACTCGCAAA 60.250 50.000 0.00 0.00 0.00 3.68
414 962 0.249531 TTTGGTACGCTCACTCGCAA 60.250 50.000 0.00 0.00 0.00 4.85
415 963 0.249531 TTTTGGTACGCTCACTCGCA 60.250 50.000 0.00 0.00 0.00 5.10
416 964 0.438830 CTTTTGGTACGCTCACTCGC 59.561 55.000 0.00 0.00 0.00 5.03
417 965 0.438830 GCTTTTGGTACGCTCACTCG 59.561 55.000 0.00 0.00 0.00 4.18
491 1043 1.342174 TCGGGTCAAGAAGTACACCAC 59.658 52.381 0.00 0.00 0.00 4.16
494 1046 3.251571 GTGATCGGGTCAAGAAGTACAC 58.748 50.000 0.00 0.00 38.90 2.90
495 1047 2.232941 GGTGATCGGGTCAAGAAGTACA 59.767 50.000 0.00 0.00 38.90 2.90
496 1048 2.232941 TGGTGATCGGGTCAAGAAGTAC 59.767 50.000 0.00 0.00 38.90 2.73
497 1049 2.232941 GTGGTGATCGGGTCAAGAAGTA 59.767 50.000 0.00 0.00 38.90 2.24
498 1050 1.002087 GTGGTGATCGGGTCAAGAAGT 59.998 52.381 0.00 0.00 38.90 3.01
499 1051 1.676014 GGTGGTGATCGGGTCAAGAAG 60.676 57.143 0.00 0.00 38.90 2.85
500 1052 0.323629 GGTGGTGATCGGGTCAAGAA 59.676 55.000 0.00 0.00 38.90 2.52
525 1088 0.249996 TTCGGTTCGGGGAGTGTTTC 60.250 55.000 0.00 0.00 0.00 2.78
526 1089 0.250166 CTTCGGTTCGGGGAGTGTTT 60.250 55.000 0.00 0.00 0.00 2.83
527 1090 1.117142 TCTTCGGTTCGGGGAGTGTT 61.117 55.000 0.00 0.00 0.00 3.32
528 1091 1.532316 TCTTCGGTTCGGGGAGTGT 60.532 57.895 0.00 0.00 0.00 3.55
529 1092 1.080025 GTCTTCGGTTCGGGGAGTG 60.080 63.158 0.00 0.00 0.00 3.51
542 1105 1.446966 GTCGGCTGCCTCTGTCTTC 60.447 63.158 17.92 0.00 0.00 2.87
769 1356 2.533232 AAACGGGGATGGGGGTCA 60.533 61.111 0.00 0.00 0.00 4.02
797 1384 0.393132 GGGCTCGGAGGAAAAGGAAG 60.393 60.000 7.20 0.00 0.00 3.46
889 1476 3.151022 GTCGCAGGAGGGAGGGAG 61.151 72.222 0.00 0.00 37.39 4.30
890 1477 4.779733 GGTCGCAGGAGGGAGGGA 62.780 72.222 0.00 0.00 37.39 4.20
897 1484 3.358076 GAAGGTCGGGTCGCAGGAG 62.358 68.421 0.00 0.00 0.00 3.69
899 1486 4.452733 GGAAGGTCGGGTCGCAGG 62.453 72.222 0.00 0.00 0.00 4.85
900 1487 2.005960 CTAGGAAGGTCGGGTCGCAG 62.006 65.000 0.00 0.00 0.00 5.18
902 1489 2.806237 CTAGGAAGGTCGGGTCGC 59.194 66.667 0.00 0.00 0.00 5.19
930 1520 0.747283 ACGGGACTAGTGGTCTAGCG 60.747 60.000 0.00 2.02 45.32 4.26
1031 1621 3.835395 GAGAAGGGAGAAGAGAAGGTTGA 59.165 47.826 0.00 0.00 0.00 3.18
1070 1663 2.567497 TTCGCTTCCGGTTCGAGGT 61.567 57.895 0.00 0.00 33.56 3.85
1088 1681 2.588620 GGTCGAGGATGGATGTAGAGT 58.411 52.381 0.00 0.00 0.00 3.24
1102 1735 0.037882 CCATGGATCCATCGGTCGAG 60.038 60.000 24.93 11.33 33.90 4.04
1109 1742 0.475475 TGCTGACCCATGGATCCATC 59.525 55.000 24.93 14.86 33.90 3.51
1139 1772 1.153549 GTGCAGGTCGAGGCTAAGG 60.154 63.158 5.40 0.00 0.00 2.69
1142 1775 2.675423 ACGTGCAGGTCGAGGCTA 60.675 61.111 6.15 0.00 0.00 3.93
1286 1922 0.733729 GACGCGTCTCTGTATGGACT 59.266 55.000 31.12 0.00 0.00 3.85
1294 1930 1.190323 GTTGTTCTTGACGCGTCTCTG 59.810 52.381 36.27 25.32 0.00 3.35
1296 1932 0.158928 CGTTGTTCTTGACGCGTCTC 59.841 55.000 36.27 21.50 32.11 3.36
1300 1936 0.506932 ATCACGTTGTTCTTGACGCG 59.493 50.000 3.53 3.53 42.67 6.01
1301 1937 2.663279 AATCACGTTGTTCTTGACGC 57.337 45.000 0.00 0.00 42.67 5.19
1303 1939 6.912591 AGAATCAAAATCACGTTGTTCTTGAC 59.087 34.615 0.00 0.00 29.73 3.18
1312 1950 3.983344 GCAAGCAGAATCAAAATCACGTT 59.017 39.130 0.00 0.00 0.00 3.99
1313 1951 3.568538 GCAAGCAGAATCAAAATCACGT 58.431 40.909 0.00 0.00 0.00 4.49
1315 1953 3.924686 CAGGCAAGCAGAATCAAAATCAC 59.075 43.478 0.00 0.00 0.00 3.06
1373 2015 4.250464 TCAAGAACCGCAACCTATACAAG 58.750 43.478 0.00 0.00 0.00 3.16
1374 2016 4.250464 CTCAAGAACCGCAACCTATACAA 58.750 43.478 0.00 0.00 0.00 2.41
1399 2041 3.006756 GCTCACCCGCTGTAGCTCA 62.007 63.158 0.00 0.00 39.32 4.26
1532 2177 1.673920 CGGCTGGTTGTTGTAGTTGTT 59.326 47.619 0.00 0.00 0.00 2.83
1533 2178 1.305201 CGGCTGGTTGTTGTAGTTGT 58.695 50.000 0.00 0.00 0.00 3.32
1534 2179 1.263217 GACGGCTGGTTGTTGTAGTTG 59.737 52.381 0.00 0.00 0.00 3.16
1535 2180 1.589803 GACGGCTGGTTGTTGTAGTT 58.410 50.000 0.00 0.00 0.00 2.24
1630 2275 2.097038 GTAGTGCTGCTGGTGCGAG 61.097 63.158 0.00 0.00 43.34 5.03
1792 2446 1.029947 GCCATTGGTACCCGTCCTTG 61.030 60.000 10.07 0.00 0.00 3.61
2137 2806 4.849310 GCCAGGTTGCGCCGGATA 62.849 66.667 5.05 0.00 43.70 2.59
2365 3044 1.605753 GGTCCTCGCTGGTTTTTCTT 58.394 50.000 0.00 0.00 37.07 2.52
2381 3060 4.436998 CGGTCAGGCAGTCCGGTC 62.437 72.222 7.63 0.00 43.80 4.79
2398 3077 2.350985 GATCGCGTCTCCGTCGTC 60.351 66.667 5.77 0.00 35.88 4.20
2405 3084 2.651232 CGGAACCGATCGCGTCTC 60.651 66.667 10.32 3.49 42.83 3.36
2489 3172 3.516300 ACATTACATGTTACGACCTCCCA 59.484 43.478 2.30 0.00 41.63 4.37
2526 3495 5.363101 TCCTGAATGACTGACTGCATTATC 58.637 41.667 0.00 0.00 35.05 1.75
2527 3496 5.363562 TCCTGAATGACTGACTGCATTAT 57.636 39.130 0.00 0.00 35.05 1.28
2528 3497 4.824479 TCCTGAATGACTGACTGCATTA 57.176 40.909 0.00 0.00 35.05 1.90
2529 3498 3.708403 TCCTGAATGACTGACTGCATT 57.292 42.857 0.00 0.00 37.43 3.56
2577 3546 8.209917 ACATTTCGCCTAGTAATAAGGAAAAG 57.790 34.615 0.00 0.00 36.08 2.27
2661 3630 3.681417 TCAGCGATTGAACTGAGAATGTG 59.319 43.478 0.00 0.00 37.99 3.21
2682 3651 8.021396 GGGTACTGTGAGTATTGACAAAATTTC 58.979 37.037 0.00 0.00 32.65 2.17
2699 3668 0.321919 AGCAGCACATGGGTACTGTG 60.322 55.000 8.89 8.89 45.39 3.66
2700 3669 0.321919 CAGCAGCACATGGGTACTGT 60.322 55.000 0.00 0.00 40.02 3.55
2788 3805 2.203728 ACTGCCTACGTGGACCCA 60.204 61.111 0.00 0.00 38.35 4.51
2806 3823 3.878699 GTCCAGTAGAGTCTACTACAGCC 59.121 52.174 28.29 13.42 43.38 4.85
2861 3878 2.353145 CGTCCGCGTATTCTCCGG 60.353 66.667 4.92 0.00 43.21 5.14
2955 3974 1.065410 TTTCCACCCAGCTTCCCTGA 61.065 55.000 0.00 0.00 44.64 3.86
3166 4208 9.912634 TCCTTGAAGATTTTATACTTGCAAAAG 57.087 29.630 0.00 0.00 0.00 2.27
3170 4212 9.120538 GGTATCCTTGAAGATTTTATACTTGCA 57.879 33.333 0.00 0.00 0.00 4.08
3171 4213 8.283291 CGGTATCCTTGAAGATTTTATACTTGC 58.717 37.037 0.00 0.00 0.00 4.01
3173 4215 7.937394 CCCGGTATCCTTGAAGATTTTATACTT 59.063 37.037 0.00 0.00 0.00 2.24
3174 4216 7.450903 CCCGGTATCCTTGAAGATTTTATACT 58.549 38.462 0.00 0.00 0.00 2.12
3188 4230 0.104934 ATCTGGAGCCCGGTATCCTT 60.105 55.000 19.77 5.68 36.50 3.36
3211 4253 2.866762 CAGCCTAAAACGGTATCTCAGC 59.133 50.000 0.00 0.00 0.00 4.26
3212 4254 3.458189 CCAGCCTAAAACGGTATCTCAG 58.542 50.000 0.00 0.00 0.00 3.35
3227 4269 2.940421 ATCCCCACTATGGCCAGCCT 62.940 60.000 13.05 0.00 35.79 4.58
3228 4270 1.133809 TATCCCCACTATGGCCAGCC 61.134 60.000 13.05 0.38 35.79 4.85
3229 4271 0.771127 TTATCCCCACTATGGCCAGC 59.229 55.000 13.05 0.00 35.79 4.85
3230 4272 1.774254 TGTTATCCCCACTATGGCCAG 59.226 52.381 13.05 0.00 35.79 4.85
3231 4273 1.900254 TGTTATCCCCACTATGGCCA 58.100 50.000 8.56 8.56 35.79 5.36
3232 4274 4.650972 TTATGTTATCCCCACTATGGCC 57.349 45.455 0.00 0.00 35.79 5.36
3233 4275 7.402862 ACTATTTATGTTATCCCCACTATGGC 58.597 38.462 0.00 0.00 35.79 4.40
3239 4281 9.959721 ACATGATACTATTTATGTTATCCCCAC 57.040 33.333 0.00 0.00 30.05 4.61
3251 4293 9.961265 CGAGTCCAAAGTACATGATACTATTTA 57.039 33.333 0.00 0.00 0.00 1.40
3252 4294 7.438459 GCGAGTCCAAAGTACATGATACTATTT 59.562 37.037 0.00 0.00 0.00 1.40
3253 4295 6.924060 GCGAGTCCAAAGTACATGATACTATT 59.076 38.462 0.00 0.00 0.00 1.73
3254 4296 6.448006 GCGAGTCCAAAGTACATGATACTAT 58.552 40.000 0.00 0.00 0.00 2.12
3255 4297 5.505159 CGCGAGTCCAAAGTACATGATACTA 60.505 44.000 0.00 0.00 0.00 1.82
3256 4298 4.683832 GCGAGTCCAAAGTACATGATACT 58.316 43.478 0.00 0.69 0.00 2.12
3257 4299 3.486108 CGCGAGTCCAAAGTACATGATAC 59.514 47.826 0.00 0.00 0.00 2.24
3258 4300 3.379057 TCGCGAGTCCAAAGTACATGATA 59.621 43.478 3.71 0.00 0.00 2.15
3259 4301 2.165641 TCGCGAGTCCAAAGTACATGAT 59.834 45.455 3.71 0.00 0.00 2.45
3260 4302 1.542472 TCGCGAGTCCAAAGTACATGA 59.458 47.619 3.71 0.00 0.00 3.07
3261 4303 1.990799 TCGCGAGTCCAAAGTACATG 58.009 50.000 3.71 0.00 0.00 3.21
3262 4304 2.288579 TGTTCGCGAGTCCAAAGTACAT 60.289 45.455 9.59 0.00 0.00 2.29
3263 4305 1.067364 TGTTCGCGAGTCCAAAGTACA 59.933 47.619 9.59 4.45 0.00 2.90
3264 4306 1.774639 TGTTCGCGAGTCCAAAGTAC 58.225 50.000 9.59 1.34 0.00 2.73
3265 4307 2.333926 CATGTTCGCGAGTCCAAAGTA 58.666 47.619 9.59 0.00 0.00 2.24
3266 4308 1.148310 CATGTTCGCGAGTCCAAAGT 58.852 50.000 9.59 0.00 0.00 2.66
3267 4309 0.179215 GCATGTTCGCGAGTCCAAAG 60.179 55.000 9.59 6.46 0.00 2.77
3268 4310 0.602638 AGCATGTTCGCGAGTCCAAA 60.603 50.000 9.59 0.00 36.85 3.28
3269 4311 0.602638 AAGCATGTTCGCGAGTCCAA 60.603 50.000 9.59 0.00 36.85 3.53
3270 4312 0.245266 TAAGCATGTTCGCGAGTCCA 59.755 50.000 9.59 8.33 36.85 4.02
3271 4313 1.258982 CATAAGCATGTTCGCGAGTCC 59.741 52.381 9.59 1.91 36.85 3.85
3272 4314 1.927174 ACATAAGCATGTTCGCGAGTC 59.073 47.619 9.59 7.69 42.98 3.36
3273 4315 1.660607 CACATAAGCATGTTCGCGAGT 59.339 47.619 9.59 0.00 42.98 4.18
3274 4316 1.004610 CCACATAAGCATGTTCGCGAG 60.005 52.381 9.59 0.00 42.98 5.03
3275 4317 1.006086 CCACATAAGCATGTTCGCGA 58.994 50.000 3.71 3.71 42.98 5.87
3276 4318 0.589729 GCCACATAAGCATGTTCGCG 60.590 55.000 0.00 0.00 42.98 5.87
3277 4319 0.451383 TGCCACATAAGCATGTTCGC 59.549 50.000 0.00 0.00 42.98 4.70
3278 4320 1.064505 CCTGCCACATAAGCATGTTCG 59.935 52.381 0.00 0.00 42.98 3.95
3279 4321 1.202336 GCCTGCCACATAAGCATGTTC 60.202 52.381 0.00 0.00 42.98 3.18
3280 4322 0.819582 GCCTGCCACATAAGCATGTT 59.180 50.000 0.00 0.00 42.98 2.71
3281 4323 0.323633 TGCCTGCCACATAAGCATGT 60.324 50.000 0.00 0.00 46.58 3.21
3282 4324 0.818938 TTGCCTGCCACATAAGCATG 59.181 50.000 0.00 0.00 40.04 4.06
3283 4325 1.784358 ATTGCCTGCCACATAAGCAT 58.216 45.000 0.00 0.00 40.04 3.79
3284 4326 1.559368 AATTGCCTGCCACATAAGCA 58.441 45.000 0.00 0.00 38.82 3.91
3285 4327 3.799281 TTAATTGCCTGCCACATAAGC 57.201 42.857 0.00 0.00 0.00 3.09
3309 4351 8.794553 CGTATGTTACTATAACCATCTTCCTCT 58.205 37.037 0.00 0.00 0.00 3.69
3310 4352 8.574737 ACGTATGTTACTATAACCATCTTCCTC 58.425 37.037 0.00 0.00 0.00 3.71
3311 4353 8.474710 ACGTATGTTACTATAACCATCTTCCT 57.525 34.615 0.00 0.00 0.00 3.36
3312 4354 9.837525 CTACGTATGTTACTATAACCATCTTCC 57.162 37.037 0.00 0.00 0.00 3.46
3318 4360 8.935844 CGGTATCTACGTATGTTACTATAACCA 58.064 37.037 0.00 0.00 0.00 3.67
3319 4361 8.936864 ACGGTATCTACGTATGTTACTATAACC 58.063 37.037 0.00 0.00 43.60 2.85
3323 4365 9.489084 TGTTACGGTATCTACGTATGTTACTAT 57.511 33.333 0.00 0.00 45.00 2.12
3324 4366 8.880878 TGTTACGGTATCTACGTATGTTACTA 57.119 34.615 0.00 0.00 45.00 1.82
3325 4367 7.786178 TGTTACGGTATCTACGTATGTTACT 57.214 36.000 0.00 0.00 45.00 2.24
3352 4394 5.767665 TGACACATAGTAGCACCACATTTTT 59.232 36.000 0.00 0.00 0.00 1.94
3353 4395 5.312895 TGACACATAGTAGCACCACATTTT 58.687 37.500 0.00 0.00 0.00 1.82
3354 4396 4.905429 TGACACATAGTAGCACCACATTT 58.095 39.130 0.00 0.00 0.00 2.32
3355 4397 4.551702 TGACACATAGTAGCACCACATT 57.448 40.909 0.00 0.00 0.00 2.71
3356 4398 4.445453 CATGACACATAGTAGCACCACAT 58.555 43.478 0.00 0.00 0.00 3.21
3357 4399 3.860641 CATGACACATAGTAGCACCACA 58.139 45.455 0.00 0.00 0.00 4.17
3358 4400 2.609459 GCATGACACATAGTAGCACCAC 59.391 50.000 0.00 0.00 0.00 4.16
3359 4401 2.235898 TGCATGACACATAGTAGCACCA 59.764 45.455 0.00 0.00 30.65 4.17
3360 4402 2.905075 TGCATGACACATAGTAGCACC 58.095 47.619 0.00 0.00 30.65 5.01
3361 4403 4.122046 TCATGCATGACACATAGTAGCAC 58.878 43.478 25.42 0.00 36.06 4.40
3362 4404 4.405116 TCATGCATGACACATAGTAGCA 57.595 40.909 25.42 0.00 37.13 3.49
3374 4416 5.887035 TGGTCTCATTTATTGTCATGCATGA 59.113 36.000 25.42 25.42 0.00 3.07
3375 4417 5.975344 GTGGTCTCATTTATTGTCATGCATG 59.025 40.000 21.07 21.07 0.00 4.06
3376 4418 5.068198 GGTGGTCTCATTTATTGTCATGCAT 59.932 40.000 0.00 0.00 0.00 3.96
3377 4419 4.398988 GGTGGTCTCATTTATTGTCATGCA 59.601 41.667 0.00 0.00 0.00 3.96
3378 4420 4.641989 AGGTGGTCTCATTTATTGTCATGC 59.358 41.667 0.00 0.00 0.00 4.06
3379 4421 7.716560 TCATAGGTGGTCTCATTTATTGTCATG 59.283 37.037 0.00 0.00 0.00 3.07
3380 4422 7.805163 TCATAGGTGGTCTCATTTATTGTCAT 58.195 34.615 0.00 0.00 0.00 3.06
3381 4423 7.194112 TCATAGGTGGTCTCATTTATTGTCA 57.806 36.000 0.00 0.00 0.00 3.58
3382 4424 9.209175 GTATCATAGGTGGTCTCATTTATTGTC 57.791 37.037 0.00 0.00 0.00 3.18
3383 4425 8.938883 AGTATCATAGGTGGTCTCATTTATTGT 58.061 33.333 0.00 0.00 0.00 2.71
3388 4430 9.386122 AGATTAGTATCATAGGTGGTCTCATTT 57.614 33.333 0.00 0.00 32.95 2.32
3389 4431 8.964533 AGATTAGTATCATAGGTGGTCTCATT 57.035 34.615 0.00 0.00 32.95 2.57
3391 4433 9.467796 CATAGATTAGTATCATAGGTGGTCTCA 57.532 37.037 0.00 0.00 32.95 3.27
3392 4434 9.688091 TCATAGATTAGTATCATAGGTGGTCTC 57.312 37.037 0.00 0.00 32.95 3.36
3424 4466 9.809395 AGTCTATGTTACTACCTCTATAATGCA 57.191 33.333 0.00 0.00 0.00 3.96
3459 4501 9.804758 GAAGTAACTTAGAGTAGTAACATGCAT 57.195 33.333 0.00 0.00 0.00 3.96
3460 4502 8.248945 GGAAGTAACTTAGAGTAGTAACATGCA 58.751 37.037 0.00 0.00 0.00 3.96
3461 4503 7.705752 GGGAAGTAACTTAGAGTAGTAACATGC 59.294 40.741 0.00 0.00 0.00 4.06
3462 4504 8.746530 TGGGAAGTAACTTAGAGTAGTAACATG 58.253 37.037 0.00 0.00 0.00 3.21
3463 4505 8.747471 GTGGGAAGTAACTTAGAGTAGTAACAT 58.253 37.037 0.00 0.00 0.00 2.71
3464 4506 7.946776 AGTGGGAAGTAACTTAGAGTAGTAACA 59.053 37.037 0.00 0.00 0.00 2.41
3465 4507 8.347004 AGTGGGAAGTAACTTAGAGTAGTAAC 57.653 38.462 0.00 0.00 0.00 2.50
3467 4509 9.624373 CATAGTGGGAAGTAACTTAGAGTAGTA 57.376 37.037 0.00 0.00 0.00 1.82
3468 4510 8.334734 TCATAGTGGGAAGTAACTTAGAGTAGT 58.665 37.037 0.00 0.00 0.00 2.73
3469 4511 8.623030 GTCATAGTGGGAAGTAACTTAGAGTAG 58.377 40.741 0.00 0.00 0.00 2.57
3470 4512 7.559170 GGTCATAGTGGGAAGTAACTTAGAGTA 59.441 40.741 0.00 0.00 0.00 2.59
3471 4513 6.380560 GGTCATAGTGGGAAGTAACTTAGAGT 59.619 42.308 0.00 0.00 0.00 3.24
3472 4514 6.380274 TGGTCATAGTGGGAAGTAACTTAGAG 59.620 42.308 0.00 0.00 0.00 2.43
3473 4515 6.258354 TGGTCATAGTGGGAAGTAACTTAGA 58.742 40.000 0.00 0.00 0.00 2.10
3474 4516 6.540438 TGGTCATAGTGGGAAGTAACTTAG 57.460 41.667 0.00 0.00 0.00 2.18
3475 4517 5.105064 GCTGGTCATAGTGGGAAGTAACTTA 60.105 44.000 0.00 0.00 0.00 2.24
3476 4518 4.323562 GCTGGTCATAGTGGGAAGTAACTT 60.324 45.833 0.00 0.00 0.00 2.66
3477 4519 3.197983 GCTGGTCATAGTGGGAAGTAACT 59.802 47.826 0.00 0.00 0.00 2.24
3478 4520 3.532542 GCTGGTCATAGTGGGAAGTAAC 58.467 50.000 0.00 0.00 0.00 2.50
3479 4521 2.504175 GGCTGGTCATAGTGGGAAGTAA 59.496 50.000 0.00 0.00 0.00 2.24
3480 4522 2.116238 GGCTGGTCATAGTGGGAAGTA 58.884 52.381 0.00 0.00 0.00 2.24
3481 4523 0.912486 GGCTGGTCATAGTGGGAAGT 59.088 55.000 0.00 0.00 0.00 3.01
3482 4524 1.207791 AGGCTGGTCATAGTGGGAAG 58.792 55.000 0.00 0.00 0.00 3.46
3483 4525 1.668826 AAGGCTGGTCATAGTGGGAA 58.331 50.000 0.00 0.00 0.00 3.97
3484 4526 2.561209 TAAGGCTGGTCATAGTGGGA 57.439 50.000 0.00 0.00 0.00 4.37
3485 4527 3.496870 GGATTAAGGCTGGTCATAGTGGG 60.497 52.174 0.00 0.00 0.00 4.61
3486 4528 3.392616 AGGATTAAGGCTGGTCATAGTGG 59.607 47.826 0.00 0.00 0.00 4.00
3487 4529 4.636249 GAGGATTAAGGCTGGTCATAGTG 58.364 47.826 0.00 0.00 0.00 2.74
3488 4530 3.322254 CGAGGATTAAGGCTGGTCATAGT 59.678 47.826 0.00 0.00 0.00 2.12
3489 4531 3.306364 CCGAGGATTAAGGCTGGTCATAG 60.306 52.174 0.00 0.00 0.00 2.23
3490 4532 2.632996 CCGAGGATTAAGGCTGGTCATA 59.367 50.000 0.00 0.00 0.00 2.15
3491 4533 1.417890 CCGAGGATTAAGGCTGGTCAT 59.582 52.381 0.00 0.00 0.00 3.06
3492 4534 0.830648 CCGAGGATTAAGGCTGGTCA 59.169 55.000 0.00 0.00 0.00 4.02
3493 4535 1.120530 TCCGAGGATTAAGGCTGGTC 58.879 55.000 0.00 0.00 0.00 4.02
3494 4536 0.831307 GTCCGAGGATTAAGGCTGGT 59.169 55.000 0.00 0.00 0.00 4.00
3495 4537 1.123928 AGTCCGAGGATTAAGGCTGG 58.876 55.000 0.00 0.00 0.00 4.85
3496 4538 2.959707 ACTAGTCCGAGGATTAAGGCTG 59.040 50.000 0.00 0.00 0.00 4.85
3497 4539 3.315880 ACTAGTCCGAGGATTAAGGCT 57.684 47.619 0.00 0.00 0.00 4.58
3498 4540 4.340381 TGTTACTAGTCCGAGGATTAAGGC 59.660 45.833 0.00 0.00 0.00 4.35
3499 4541 6.461110 TTGTTACTAGTCCGAGGATTAAGG 57.539 41.667 0.00 0.00 0.00 2.69
3500 4542 9.680315 CTATTTGTTACTAGTCCGAGGATTAAG 57.320 37.037 0.00 0.00 0.00 1.85
3501 4543 9.193806 ACTATTTGTTACTAGTCCGAGGATTAA 57.806 33.333 0.00 0.00 0.00 1.40
3502 4544 8.757982 ACTATTTGTTACTAGTCCGAGGATTA 57.242 34.615 0.00 0.00 0.00 1.75
3503 4545 7.657023 ACTATTTGTTACTAGTCCGAGGATT 57.343 36.000 0.00 0.00 0.00 3.01
3504 4546 8.757982 TTACTATTTGTTACTAGTCCGAGGAT 57.242 34.615 0.00 0.00 30.98 3.24
3505 4547 8.757982 ATTACTATTTGTTACTAGTCCGAGGA 57.242 34.615 0.00 0.00 30.98 3.71


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

AutoCloner maintained by Alex Coulton.