Multiple sequence alignment - TraesCS7A01G461100

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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 TraesCS7A01G461100 chr7A 100.000 5677 0 0 1 5677 657351290 657356966 0.000000e+00 10484.0
1 TraesCS7A01G461100 chr7B 94.250 4626 217 20 1 4597 624349192 624353797 0.000000e+00 7023.0
2 TraesCS7A01G461100 chr7B 88.432 389 37 4 5193 5580 624354238 624354619 4.010000e-126 462.0
3 TraesCS7A01G461100 chr7B 81.921 354 26 13 4649 4989 624353793 624354121 1.210000e-66 265.0
4 TraesCS7A01G461100 chr7B 96.429 56 2 0 5576 5631 624356400 624356455 6.060000e-15 93.5
5 TraesCS7A01G461100 chr7D 92.791 4730 261 45 1 4702 568596585 568601262 0.000000e+00 6772.0
6 TraesCS7A01G461100 chr7D 87.473 471 46 8 5211 5677 568615607 568616068 1.080000e-146 531.0
7 TraesCS7A01G461100 chr7D 80.786 229 16 12 4851 5079 568601256 568601456 2.740000e-33 154.0
8 TraesCS7A01G461100 chr7D 95.349 43 1 1 5151 5193 568601491 568601532 3.670000e-07 67.6
9 TraesCS7A01G461100 chr5D 93.706 2860 158 19 1545 4392 534864656 534867505 0.000000e+00 4265.0
10 TraesCS7A01G461100 chr5D 91.821 2861 198 23 1545 4396 534856553 534859386 0.000000e+00 3954.0
11 TraesCS7A01G461100 chr5D 78.588 425 68 15 978 1388 534856024 534856439 5.640000e-65 259.0
12 TraesCS7A01G461100 chr4A 93.202 2883 167 23 1530 4395 636680485 636677615 0.000000e+00 4211.0
13 TraesCS7A01G461100 chr4A 93.234 2616 156 16 1914 4515 636687186 636684578 0.000000e+00 3831.0
14 TraesCS7A01G461100 chr4A 79.639 388 67 8 954 1335 636688062 636687681 9.380000e-68 268.0
15 TraesCS7A01G461100 chr4A 76.380 453 58 28 1144 1568 636965885 636965454 1.250000e-46 198.0
16 TraesCS7A01G461100 chr5B 94.635 2535 134 2 1848 4382 675423319 675425851 0.000000e+00 3927.0
17 TraesCS7A01G461100 chr5B 94.947 2474 125 0 1925 4398 674892239 674894712 0.000000e+00 3877.0
18 TraesCS7A01G461100 chr5B 93.943 2559 149 6 1847 4401 675080129 675082685 0.000000e+00 3862.0
19 TraesCS7A01G461100 chr5B 80.357 336 48 11 1065 1388 675079098 675079427 7.350000e-59 239.0


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 TraesCS7A01G461100 chr7A 657351290 657356966 5676 False 10484.000 10484 100.0000 1 5677 1 chr7A.!!$F1 5676
1 TraesCS7A01G461100 chr7B 624349192 624356455 7263 False 1960.875 7023 90.2580 1 5631 4 chr7B.!!$F1 5630
2 TraesCS7A01G461100 chr7D 568596585 568601532 4947 False 2331.200 6772 89.6420 1 5193 3 chr7D.!!$F2 5192
3 TraesCS7A01G461100 chr5D 534864656 534867505 2849 False 4265.000 4265 93.7060 1545 4392 1 chr5D.!!$F1 2847
4 TraesCS7A01G461100 chr5D 534856024 534859386 3362 False 2106.500 3954 85.2045 978 4396 2 chr5D.!!$F2 3418
5 TraesCS7A01G461100 chr4A 636677615 636680485 2870 True 4211.000 4211 93.2020 1530 4395 1 chr4A.!!$R1 2865
6 TraesCS7A01G461100 chr4A 636684578 636688062 3484 True 2049.500 3831 86.4365 954 4515 2 chr4A.!!$R3 3561
7 TraesCS7A01G461100 chr5B 675423319 675425851 2532 False 3927.000 3927 94.6350 1848 4382 1 chr5B.!!$F2 2534
8 TraesCS7A01G461100 chr5B 674892239 674894712 2473 False 3877.000 3877 94.9470 1925 4398 1 chr5B.!!$F1 2473
9 TraesCS7A01G461100 chr5B 675079098 675082685 3587 False 2050.500 3862 87.1500 1065 4401 2 chr5B.!!$F3 3336

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
283 286 0.471022 TGCCTGTCTGTGGTACCTGA 60.471 55.000 14.36 6.11 0.00 3.86 F
928 936 0.519077 GTGCTAGTGTTGGCTCAAGC 59.481 55.000 0.00 0.00 41.14 4.01 F
2459 2843 1.286248 GGGATGTCCAAGTGTACCCT 58.714 55.000 0.86 0.00 37.91 4.34 F
2894 3278 1.340114 CCTTCAAAGGCCCAGAGGTAC 60.340 57.143 0.00 0.00 39.76 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2286 1.788258 ATCTGTGAGAACAGTGCACG 58.212 50.000 12.01 9.15 38.75 5.34 R
2597 2981 1.068333 CATTTCTTTGTGGCTGGGTCG 60.068 52.381 0.00 0.00 0.00 4.79 R
3554 3938 1.178276 CTGTACGGCAGGACTTCTCT 58.822 55.000 0.00 0.00 41.42 3.10 R
4735 5134 0.044855 AGGAACATAGGGTGGAGGCT 59.955 55.000 0.00 0.00 0.00 4.58 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
89 90 1.325943 GCGCTGTAGATCTGCTGTTTC 59.674 52.381 16.80 5.33 38.56 2.78
102 103 1.462541 GCTGTTTCGTTCGTCATGCTC 60.463 52.381 0.00 0.00 0.00 4.26
103 104 2.061773 CTGTTTCGTTCGTCATGCTCT 58.938 47.619 0.00 0.00 0.00 4.09
105 106 1.390463 GTTTCGTTCGTCATGCTCTCC 59.610 52.381 0.00 0.00 0.00 3.71
117 118 2.291043 GCTCTCCTGTTCCGGGGAA 61.291 63.158 0.00 0.00 31.89 3.97
134 135 1.614385 GAACGATTTCGCTCTGACGA 58.386 50.000 0.00 0.00 44.43 4.20
140 141 5.741639 ACGATTTCGCTCTGACGAGAGTAT 61.742 45.833 0.00 0.00 46.76 2.12
142 143 8.406305 ACGATTTCGCTCTGACGAGAGTATAC 62.406 46.154 0.00 0.00 46.76 1.47
149 150 1.930100 ACGAGAGTATACGCGTCGG 59.070 57.895 18.63 0.98 46.88 4.79
153 154 0.812811 AGAGTATACGCGTCGGCTGA 60.813 55.000 18.63 0.00 36.88 4.26
166 167 1.713937 CGGCTGATTTATGTGCGGCA 61.714 55.000 0.00 0.00 35.66 5.69
167 168 0.670162 GGCTGATTTATGTGCGGCAT 59.330 50.000 5.72 0.00 41.42 4.40
169 170 1.335324 GCTGATTTATGTGCGGCATCC 60.335 52.381 5.72 0.00 38.94 3.51
186 187 3.197790 CAAGGGCGCGGATCTGTG 61.198 66.667 8.83 10.90 0.00 3.66
206 207 1.104577 GTTCCGGTGCTGGTTTTGGA 61.105 55.000 0.00 0.00 0.00 3.53
283 286 0.471022 TGCCTGTCTGTGGTACCTGA 60.471 55.000 14.36 6.11 0.00 3.86
296 299 2.353323 GTACCTGATCGGGTTTGTTCC 58.647 52.381 30.92 9.06 40.48 3.62
390 395 2.634453 TGCATGACTTTCTCTCTGACCA 59.366 45.455 0.00 0.00 0.00 4.02
461 467 2.897271 TGTATGGATGGTTGCACCTT 57.103 45.000 6.83 1.12 39.58 3.50
569 576 4.616802 GTGCATAAAACTGTGATTCCGTTG 59.383 41.667 0.00 0.00 0.00 4.10
607 615 2.068831 TCCCATTTACCCCAAGTCCT 57.931 50.000 0.00 0.00 0.00 3.85
615 623 0.984995 ACCCCAAGTCCTGTCTTAGC 59.015 55.000 0.00 0.00 0.00 3.09
628 636 6.265649 GTCCTGTCTTAGCCTGTAATCATCTA 59.734 42.308 0.00 0.00 0.00 1.98
629 637 6.265649 TCCTGTCTTAGCCTGTAATCATCTAC 59.734 42.308 0.00 0.00 0.00 2.59
633 641 7.778382 TGTCTTAGCCTGTAATCATCTACTACA 59.222 37.037 0.00 0.00 0.00 2.74
681 689 8.792830 TTTATTCTGGTGAAGTTTCTCTATGG 57.207 34.615 0.00 0.00 35.44 2.74
683 691 5.825593 TCTGGTGAAGTTTCTCTATGGTT 57.174 39.130 0.00 0.00 0.00 3.67
684 692 6.187727 TCTGGTGAAGTTTCTCTATGGTTT 57.812 37.500 0.00 0.00 0.00 3.27
705 713 8.308207 TGGTTTATCCCTTTATTAGTTTTGCAC 58.692 33.333 0.00 0.00 34.77 4.57
852 860 8.871629 TTATTTCTTAAACATTGGCTGGTCTA 57.128 30.769 0.00 0.00 0.00 2.59
922 930 0.593128 CTGTTGGTGCTAGTGTTGGC 59.407 55.000 0.00 0.00 0.00 4.52
928 936 0.519077 GTGCTAGTGTTGGCTCAAGC 59.481 55.000 0.00 0.00 41.14 4.01
993 1009 4.638421 CAGGTCTTGTTGGTTGAAGTGTTA 59.362 41.667 0.00 0.00 0.00 2.41
1020 1036 9.717892 GTTAAAATATTAAGGTAGCAGTGCTTC 57.282 33.333 25.23 18.59 34.48 3.86
1046 1062 6.095300 TGACTTCTGGGCATACAACAATATTG 59.905 38.462 14.01 14.01 0.00 1.90
1049 1065 6.007485 TCTGGGCATACAACAATATTGGTA 57.993 37.500 19.37 12.55 0.00 3.25
1051 1067 6.007485 TGGGCATACAACAATATTGGTAGA 57.993 37.500 19.37 4.79 0.00 2.59
1089 1105 8.531146 AGACAATTGTGATTTTAATTACCTGGG 58.469 33.333 17.58 0.00 0.00 4.45
1099 1115 7.639113 TTTTAATTACCTGGGCAGAGTATTG 57.361 36.000 0.00 0.00 0.00 1.90
1176 1200 7.012704 TGTTTGATTCTGATAGCTTGCTATTCC 59.987 37.037 15.23 5.68 0.00 3.01
1282 1306 5.637006 TGGACAAAAAGAACAATATCCGG 57.363 39.130 0.00 0.00 0.00 5.14
1347 1371 8.230486 CCTGAACAGTGACATTATTGAGTTTAC 58.770 37.037 0.00 0.00 0.00 2.01
1398 1433 3.515502 TGTAGCCTGCTCATTCTACTGTT 59.484 43.478 0.00 0.00 34.19 3.16
1399 1434 3.710209 AGCCTGCTCATTCTACTGTTT 57.290 42.857 0.00 0.00 0.00 2.83
1400 1435 3.604582 AGCCTGCTCATTCTACTGTTTC 58.395 45.455 0.00 0.00 0.00 2.78
1401 1436 2.349886 GCCTGCTCATTCTACTGTTTCG 59.650 50.000 0.00 0.00 0.00 3.46
1407 1448 6.831769 TGCTCATTCTACTGTTTCGATTTTC 58.168 36.000 0.00 0.00 0.00 2.29
1415 1456 4.989044 ACTGTTTCGATTTTCAAAACCGT 58.011 34.783 0.00 0.00 33.06 4.83
1431 1472 4.965119 AACCGTATCTCTTTGAATTGGC 57.035 40.909 0.00 0.00 0.00 4.52
1436 1477 6.093633 ACCGTATCTCTTTGAATTGGCTAAAC 59.906 38.462 0.00 0.00 0.00 2.01
1686 1765 7.609760 TGATATGAAGTTCATGTGGTTGTAC 57.390 36.000 25.48 8.11 37.70 2.90
1790 1872 4.828387 TGGTTCGCCTTATGTTTACCTTTT 59.172 37.500 0.00 0.00 38.36 2.27
1886 2270 7.995289 TGTAATCATATGGATTGTGTTCAACC 58.005 34.615 2.13 0.00 45.70 3.77
1902 2286 4.545823 TCAACCGTCAAACAAGATGTTC 57.454 40.909 0.00 0.00 40.14 3.18
2441 2825 2.431954 ATGAAGATGTGCTCCTTGGG 57.568 50.000 0.00 0.00 0.00 4.12
2459 2843 1.286248 GGGATGTCCAAGTGTACCCT 58.714 55.000 0.86 0.00 37.91 4.34
2597 2981 2.772287 CTGTGGGGTGAGAACTTCTTC 58.228 52.381 0.00 0.00 0.00 2.87
2894 3278 1.340114 CCTTCAAAGGCCCAGAGGTAC 60.340 57.143 0.00 0.00 39.76 3.34
2984 3368 4.502259 CCTGATGGTCCTCTTATGCTGTAC 60.502 50.000 0.00 0.00 0.00 2.90
3428 3812 4.346709 TGTACCATTGAAGAGTCTGGTGAA 59.653 41.667 10.48 0.00 41.92 3.18
3554 3938 3.082548 CTCCTTCCGTGAGACTGTTCTA 58.917 50.000 0.00 0.00 29.47 2.10
4046 4430 1.071699 GAGCCTGTGTACCTGGTTGAA 59.928 52.381 3.84 0.00 34.73 2.69
4331 4715 1.147153 GATCCGCAAGAGGAAGGGG 59.853 63.158 0.00 0.00 44.50 4.79
4367 4751 2.626743 GACCCCTCTATCCGATTTCGAA 59.373 50.000 0.67 0.00 43.02 3.71
4429 4813 4.023963 GGTCTTGTGTTGTTAAAGAGAGCC 60.024 45.833 0.00 0.00 30.84 4.70
4498 4894 5.872617 TCGTGATACTGGGAACTATGTTTTG 59.127 40.000 0.00 0.00 0.00 2.44
4499 4895 5.872617 CGTGATACTGGGAACTATGTTTTGA 59.127 40.000 0.00 0.00 0.00 2.69
4572 4968 3.129287 CACTGGTTCTTTTGCTCTTGTGT 59.871 43.478 0.00 0.00 0.00 3.72
4599 4995 8.218338 TGATCTTTAGATTTGCCTGATTCTTC 57.782 34.615 0.00 0.00 34.37 2.87
4604 5000 2.448926 TTTGCCTGATTCTTCGTCGA 57.551 45.000 0.00 0.00 0.00 4.20
4635 5031 5.008619 TGCTTTCTCATGAAAAAGTTGCA 57.991 34.783 19.98 11.84 41.09 4.08
4638 5034 5.924825 GCTTTCTCATGAAAAAGTTGCATCT 59.075 36.000 19.98 0.00 41.09 2.90
4639 5035 6.423001 GCTTTCTCATGAAAAAGTTGCATCTT 59.577 34.615 19.98 4.13 41.09 2.40
4640 5036 7.359014 GCTTTCTCATGAAAAAGTTGCATCTTC 60.359 37.037 19.98 0.00 41.09 2.87
4642 5038 6.675026 TCTCATGAAAAAGTTGCATCTTCTG 58.325 36.000 10.38 4.67 0.00 3.02
4643 5039 6.487668 TCTCATGAAAAAGTTGCATCTTCTGA 59.512 34.615 10.38 7.98 0.00 3.27
4644 5040 7.176165 TCTCATGAAAAAGTTGCATCTTCTGAT 59.824 33.333 10.38 0.00 0.00 2.90
4645 5041 7.310664 TCATGAAAAAGTTGCATCTTCTGATC 58.689 34.615 10.38 7.42 0.00 2.92
4646 5042 6.638096 TGAAAAAGTTGCATCTTCTGATCA 57.362 33.333 10.38 9.50 0.00 2.92
4647 5043 6.675026 TGAAAAAGTTGCATCTTCTGATCAG 58.325 36.000 17.07 17.07 0.00 2.90
4727 5126 8.766994 TTGCCTGCTCTTATTATTATTTCCTT 57.233 30.769 0.00 0.00 0.00 3.36
4750 5149 1.794714 CACTAGCCTCCACCCTATGT 58.205 55.000 0.00 0.00 0.00 2.29
4751 5150 2.119495 CACTAGCCTCCACCCTATGTT 58.881 52.381 0.00 0.00 0.00 2.71
4752 5151 2.103263 CACTAGCCTCCACCCTATGTTC 59.897 54.545 0.00 0.00 0.00 3.18
4753 5152 1.694696 CTAGCCTCCACCCTATGTTCC 59.305 57.143 0.00 0.00 0.00 3.62
4754 5153 0.044855 AGCCTCCACCCTATGTTCCT 59.955 55.000 0.00 0.00 0.00 3.36
4757 5156 1.765314 CCTCCACCCTATGTTCCTCAG 59.235 57.143 0.00 0.00 0.00 3.35
4762 5161 0.531532 CCCTATGTTCCTCAGCAGCG 60.532 60.000 0.00 0.00 0.00 5.18
4771 5170 2.076100 TCCTCAGCAGCGTGTTTTATG 58.924 47.619 0.00 0.00 0.00 1.90
4777 5176 1.732405 GCAGCGTGTTTTATGCCCTTC 60.732 52.381 0.00 0.00 42.47 3.46
4778 5177 1.812571 CAGCGTGTTTTATGCCCTTCT 59.187 47.619 0.00 0.00 42.47 2.85
4779 5178 2.228822 CAGCGTGTTTTATGCCCTTCTT 59.771 45.455 0.00 0.00 42.47 2.52
4780 5179 3.438781 CAGCGTGTTTTATGCCCTTCTTA 59.561 43.478 0.00 0.00 42.47 2.10
4781 5180 4.096382 CAGCGTGTTTTATGCCCTTCTTAT 59.904 41.667 0.00 0.00 42.47 1.73
4782 5181 4.705023 AGCGTGTTTTATGCCCTTCTTATT 59.295 37.500 0.00 0.00 42.47 1.40
4783 5182 5.883673 AGCGTGTTTTATGCCCTTCTTATTA 59.116 36.000 0.00 0.00 42.47 0.98
4784 5183 5.969435 GCGTGTTTTATGCCCTTCTTATTAC 59.031 40.000 0.00 0.00 35.18 1.89
4787 5186 7.480810 GTGTTTTATGCCCTTCTTATTACAGG 58.519 38.462 0.00 0.00 0.00 4.00
4799 5198 5.815581 TCTTATTACAGGCACTTCATGGTT 58.184 37.500 0.00 0.00 34.60 3.67
4802 5201 2.071778 ACAGGCACTTCATGGTTGTT 57.928 45.000 0.00 0.00 34.60 2.83
4831 5230 6.631971 TTGTAGCAAAAGATGTGTTCATGA 57.368 33.333 0.00 0.00 34.06 3.07
4836 5235 7.275888 AGCAAAAGATGTGTTCATGAAAGTA 57.724 32.000 10.35 0.00 34.06 2.24
4839 5238 7.536622 GCAAAAGATGTGTTCATGAAAGTAGAG 59.463 37.037 10.35 0.00 34.06 2.43
4850 5249 3.969553 TGAAAGTAGAGGCTGCTCTCTA 58.030 45.455 18.06 18.06 43.26 2.43
4851 5250 4.541705 TGAAAGTAGAGGCTGCTCTCTAT 58.458 43.478 22.16 12.29 44.97 1.98
4852 5251 5.696030 TGAAAGTAGAGGCTGCTCTCTATA 58.304 41.667 22.16 8.16 44.97 1.31
4853 5252 6.129874 TGAAAGTAGAGGCTGCTCTCTATAA 58.870 40.000 22.16 7.63 44.97 0.98
4854 5253 6.780031 TGAAAGTAGAGGCTGCTCTCTATAAT 59.220 38.462 22.16 14.69 44.97 1.28
4855 5254 7.288852 TGAAAGTAGAGGCTGCTCTCTATAATT 59.711 37.037 22.16 18.06 44.97 1.40
4856 5255 7.610580 AAGTAGAGGCTGCTCTCTATAATTT 57.389 36.000 22.16 14.83 44.97 1.82
4857 5256 7.227049 AGTAGAGGCTGCTCTCTATAATTTC 57.773 40.000 22.16 13.05 44.97 2.17
4858 5257 5.482163 AGAGGCTGCTCTCTATAATTTCC 57.518 43.478 15.90 0.00 41.86 3.13
4859 5258 5.154418 AGAGGCTGCTCTCTATAATTTCCT 58.846 41.667 15.90 0.00 41.86 3.36
4860 5259 5.011943 AGAGGCTGCTCTCTATAATTTCCTG 59.988 44.000 15.90 0.00 41.86 3.86
4895 5294 3.876320 CAGCTTCTTTCCTCTAGGATTGC 59.124 47.826 0.00 1.19 44.98 3.56
4913 5312 3.382832 CGTTCTGCCGGTCTCCCT 61.383 66.667 1.90 0.00 0.00 4.20
4938 5347 2.527951 CTTGCGAGTCCCTCCCCTTG 62.528 65.000 0.00 0.00 0.00 3.61
4964 5373 3.011517 ATCTCCCTTGCTGCCGGT 61.012 61.111 1.90 0.00 0.00 5.28
4976 5385 2.045340 GCCGGTAGCCATGGTGTT 60.045 61.111 14.67 2.08 34.35 3.32
4989 5398 1.227321 GGTGTTCGTGTTCGGTGGA 60.227 57.895 0.00 0.00 37.69 4.02
4996 5405 1.579429 GTGTTCGGTGGAATGGTGC 59.421 57.895 0.00 0.00 34.05 5.01
5001 5410 0.109532 TCGGTGGAATGGTGCTTTGA 59.890 50.000 0.00 0.00 0.00 2.69
5005 5414 3.588955 GGTGGAATGGTGCTTTGAATTC 58.411 45.455 0.00 0.00 0.00 2.17
5027 5436 1.489230 AGGTGAAGTTTTCTCCACGGT 59.511 47.619 11.24 0.00 43.90 4.83
5030 5439 2.287103 GTGAAGTTTTCTCCACGGTCAC 59.713 50.000 0.00 0.00 31.30 3.67
5038 5447 0.389948 CTCCACGGTCACTAAGGTGC 60.390 60.000 0.00 0.00 42.72 5.01
5040 5449 1.671742 CACGGTCACTAAGGTGCCT 59.328 57.895 0.00 0.00 42.72 4.75
5079 5488 0.909610 TCGGTGGGGCATCTTCTTCT 60.910 55.000 0.00 0.00 0.00 2.85
5080 5489 0.462759 CGGTGGGGCATCTTCTTCTC 60.463 60.000 0.00 0.00 0.00 2.87
5084 5493 0.472044 GGGGCATCTTCTTCTCTCCC 59.528 60.000 0.00 0.00 0.00 4.30
5086 5495 1.843206 GGGCATCTTCTTCTCTCCCTT 59.157 52.381 0.00 0.00 0.00 3.95
5087 5496 2.421248 GGGCATCTTCTTCTCTCCCTTG 60.421 54.545 0.00 0.00 0.00 3.61
5088 5497 2.421248 GGCATCTTCTTCTCTCCCTTGG 60.421 54.545 0.00 0.00 0.00 3.61
5091 5500 0.254462 CTTCTTCTCTCCCTTGGGGC 59.746 60.000 5.78 0.00 43.94 5.80
5097 5506 4.064768 CTCCCTTGGGGCCATGCA 62.065 66.667 4.39 0.00 43.94 3.96
5117 5526 1.494721 AGGTGGCAAAGAGGTTGAGAA 59.505 47.619 0.00 0.00 39.87 2.87
5120 5529 3.132111 GGTGGCAAAGAGGTTGAGAAAAA 59.868 43.478 0.00 0.00 39.87 1.94
5128 5537 7.630728 GCAAAGAGGTTGAGAAAAAGTTTACCT 60.631 37.037 5.37 5.37 39.87 3.08
5131 5540 4.820173 AGGTTGAGAAAAAGTTTACCTCCG 59.180 41.667 12.09 0.00 28.75 4.63
5132 5541 4.023450 GGTTGAGAAAAAGTTTACCTCCGG 60.023 45.833 0.00 0.00 0.00 5.14
5135 5544 2.145536 GAAAAAGTTTACCTCCGGCGA 58.854 47.619 9.30 0.00 0.00 5.54
5136 5545 1.804601 AAAAGTTTACCTCCGGCGAG 58.195 50.000 9.30 3.68 35.72 5.03
5144 5553 3.857764 CTCCGGCGAGGGATACTT 58.142 61.111 9.30 0.00 41.52 2.24
5145 5554 2.125178 CTCCGGCGAGGGATACTTT 58.875 57.895 9.30 0.00 41.52 2.66
5146 5555 0.249489 CTCCGGCGAGGGATACTTTG 60.249 60.000 9.30 0.00 41.52 2.77
5147 5556 1.227556 CCGGCGAGGGATACTTTGG 60.228 63.158 9.30 0.00 35.97 3.28
5148 5557 4.142780 GGCGAGGGATACTTTGGC 57.857 61.111 0.00 0.00 45.50 4.52
5149 5558 1.887707 GGCGAGGGATACTTTGGCG 60.888 63.158 0.00 0.00 42.86 5.69
5150 5559 2.534903 GCGAGGGATACTTTGGCGC 61.535 63.158 0.00 0.00 36.12 6.53
5151 5560 1.887707 CGAGGGATACTTTGGCGCC 60.888 63.158 22.73 22.73 0.00 6.53
5152 5561 1.526225 GAGGGATACTTTGGCGCCC 60.526 63.158 26.77 5.93 39.12 6.13
5153 5562 2.518587 GGGATACTTTGGCGCCCC 60.519 66.667 26.77 15.92 32.50 5.80
5154 5563 2.518587 GGATACTTTGGCGCCCCC 60.519 66.667 26.77 9.61 0.00 5.40
5155 5564 2.595655 GATACTTTGGCGCCCCCT 59.404 61.111 26.77 6.07 0.00 4.79
5156 5565 1.076995 GATACTTTGGCGCCCCCTT 60.077 57.895 26.77 8.59 0.00 3.95
5209 5618 7.050377 GTCTGATTTGGTGGATAAGAAGATGA 58.950 38.462 0.00 0.00 0.00 2.92
5233 5642 0.700564 AAGGGAGATGGAAGCTGCAA 59.299 50.000 1.02 0.00 45.08 4.08
5234 5643 0.700564 AGGGAGATGGAAGCTGCAAA 59.299 50.000 1.02 0.00 45.08 3.68
5256 5665 4.610605 TGAGGTTGGTGTTCTTTATCGA 57.389 40.909 0.00 0.00 0.00 3.59
5278 5687 0.966179 TCTTTGTGGCAGAGCTACGA 59.034 50.000 0.00 0.00 42.93 3.43
5279 5688 1.550524 TCTTTGTGGCAGAGCTACGAT 59.449 47.619 0.00 0.00 42.93 3.73
5280 5689 1.662629 CTTTGTGGCAGAGCTACGATG 59.337 52.381 0.00 0.00 42.93 3.84
5315 5724 4.812476 TCCACCGCCTCGCAATCG 62.812 66.667 0.00 0.00 0.00 3.34
5323 5732 1.148759 GCCTCGCAATCGACTCTTCC 61.149 60.000 0.00 0.00 40.21 3.46
5324 5733 0.173481 CCTCGCAATCGACTCTTCCA 59.827 55.000 0.00 0.00 40.21 3.53
5351 5760 0.896226 GGCGACCACTCTTAGTCCTT 59.104 55.000 0.00 0.00 0.00 3.36
5365 5774 1.203100 AGTCCTTTTGGCCTTGATGCT 60.203 47.619 3.32 0.00 40.12 3.79
5366 5775 1.620323 GTCCTTTTGGCCTTGATGCTT 59.380 47.619 3.32 0.00 40.12 3.91
5368 5777 3.091545 TCCTTTTGGCCTTGATGCTTAG 58.908 45.455 3.32 0.00 40.12 2.18
5374 5783 0.179006 GCCTTGATGCTTAGGGGGAG 60.179 60.000 0.00 0.00 31.95 4.30
5383 5792 1.580059 CTTAGGGGGAGGTAGTGCAA 58.420 55.000 0.00 0.00 0.00 4.08
5397 5806 0.179045 GTGCAACTCTGACCAGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
5421 5830 4.130118 GCGGTATCAATGGTCTCATTCTT 58.870 43.478 0.00 0.00 41.29 2.52
5423 5832 5.406780 GCGGTATCAATGGTCTCATTCTTAG 59.593 44.000 0.00 0.00 41.29 2.18
5433 5842 2.432146 TCTCATTCTTAGGCATGCGTCT 59.568 45.455 17.50 9.01 0.00 4.18
5438 5847 1.485838 CTTAGGCATGCGTCTCTGCG 61.486 60.000 17.50 0.00 39.30 5.18
5439 5848 1.944234 TTAGGCATGCGTCTCTGCGA 61.944 55.000 17.50 0.00 39.30 5.10
5446 5855 1.640428 TGCGTCTCTGCGAAAATAGG 58.360 50.000 0.00 0.00 37.81 2.57
5474 5883 4.388499 CCCCGTCGTCCCAAGTGG 62.388 72.222 0.00 0.00 0.00 4.00
5477 5886 4.657824 CGTCGTCCCAAGTGGCGT 62.658 66.667 0.00 0.00 35.82 5.68
5478 5887 2.652530 GTCGTCCCAAGTGGCGTA 59.347 61.111 0.00 0.00 35.82 4.42
5480 5889 1.904865 TCGTCCCAAGTGGCGTAGT 60.905 57.895 0.00 0.00 35.82 2.73
5482 5891 1.079336 GTCCCAAGTGGCGTAGTCC 60.079 63.158 0.00 0.00 0.00 3.85
5483 5892 2.267961 CCCAAGTGGCGTAGTCCC 59.732 66.667 0.00 0.00 0.00 4.46
5484 5893 2.267961 CCAAGTGGCGTAGTCCCC 59.732 66.667 0.00 0.00 0.00 4.81
5486 5895 2.283388 AAGTGGCGTAGTCCCCGA 60.283 61.111 0.00 0.00 0.00 5.14
5487 5896 1.684734 AAGTGGCGTAGTCCCCGAT 60.685 57.895 0.00 0.00 0.00 4.18
5488 5897 1.956629 AAGTGGCGTAGTCCCCGATG 61.957 60.000 0.00 0.00 0.00 3.84
5489 5898 2.043752 TGGCGTAGTCCCCGATGA 60.044 61.111 0.00 0.00 0.00 2.92
5490 5899 1.456892 TGGCGTAGTCCCCGATGAT 60.457 57.895 0.00 0.00 0.00 2.45
5491 5900 1.006102 GGCGTAGTCCCCGATGATG 60.006 63.158 0.00 0.00 0.00 3.07
5492 5901 1.006102 GCGTAGTCCCCGATGATGG 60.006 63.158 0.00 0.00 0.00 3.51
5493 5902 1.745320 GCGTAGTCCCCGATGATGGT 61.745 60.000 0.00 0.00 0.00 3.55
5504 5913 2.874701 CCGATGATGGTGAGATTGGAAC 59.125 50.000 0.00 0.00 0.00 3.62
5546 5955 4.275936 CACCCAATCGTGTTTTCTCTTCTT 59.724 41.667 0.00 0.00 0.00 2.52
5550 5959 5.909610 CCAATCGTGTTTTCTCTTCTTTGTC 59.090 40.000 0.00 0.00 0.00 3.18
5551 5960 6.238484 CCAATCGTGTTTTCTCTTCTTTGTCT 60.238 38.462 0.00 0.00 0.00 3.41
5552 5961 5.718649 TCGTGTTTTCTCTTCTTTGTCTG 57.281 39.130 0.00 0.00 0.00 3.51
5572 5981 0.398318 GGGTCCTCTTTGCAGTCACT 59.602 55.000 0.00 0.00 0.00 3.41
5574 5983 1.070758 GGTCCTCTTTGCAGTCACTGA 59.929 52.381 9.70 0.00 32.44 3.41
5619 7813 4.901197 TGAAGGCCTGATGTAAAGTGTA 57.099 40.909 5.69 0.00 0.00 2.90
5623 7817 3.007635 GGCCTGATGTAAAGTGTACACC 58.992 50.000 22.28 7.67 0.00 4.16
5631 7825 5.136816 TGTAAAGTGTACACCGATGCTTA 57.863 39.130 22.28 7.97 0.00 3.09
5632 7826 5.726397 TGTAAAGTGTACACCGATGCTTAT 58.274 37.500 22.28 0.00 0.00 1.73
5633 7827 5.808540 TGTAAAGTGTACACCGATGCTTATC 59.191 40.000 22.28 6.60 0.00 1.75
5634 7828 4.737855 AAGTGTACACCGATGCTTATCT 57.262 40.909 22.28 0.00 0.00 1.98
5635 7829 5.847111 AAGTGTACACCGATGCTTATCTA 57.153 39.130 22.28 0.00 0.00 1.98
5636 7830 5.847111 AGTGTACACCGATGCTTATCTAA 57.153 39.130 22.28 0.00 0.00 2.10
5637 7831 6.406692 AGTGTACACCGATGCTTATCTAAT 57.593 37.500 22.28 0.00 0.00 1.73
5638 7832 6.216569 AGTGTACACCGATGCTTATCTAATG 58.783 40.000 22.28 0.00 0.00 1.90
5639 7833 6.040504 AGTGTACACCGATGCTTATCTAATGA 59.959 38.462 22.28 0.00 0.00 2.57
5640 7834 6.700081 GTGTACACCGATGCTTATCTAATGAA 59.300 38.462 15.42 0.00 0.00 2.57
5641 7835 7.223971 GTGTACACCGATGCTTATCTAATGAAA 59.776 37.037 15.42 0.00 0.00 2.69
5642 7836 7.766738 TGTACACCGATGCTTATCTAATGAAAA 59.233 33.333 0.00 0.00 0.00 2.29
5643 7837 7.624360 ACACCGATGCTTATCTAATGAAAAA 57.376 32.000 0.00 0.00 0.00 1.94
5644 7838 7.697691 ACACCGATGCTTATCTAATGAAAAAG 58.302 34.615 0.00 0.00 0.00 2.27
5645 7839 7.336931 ACACCGATGCTTATCTAATGAAAAAGT 59.663 33.333 0.00 0.00 0.00 2.66
5646 7840 7.852945 CACCGATGCTTATCTAATGAAAAAGTC 59.147 37.037 0.00 0.00 0.00 3.01
5647 7841 7.770897 ACCGATGCTTATCTAATGAAAAAGTCT 59.229 33.333 0.00 0.00 0.00 3.24
5648 7842 8.616076 CCGATGCTTATCTAATGAAAAAGTCTT 58.384 33.333 0.00 0.00 0.00 3.01
5649 7843 9.430838 CGATGCTTATCTAATGAAAAAGTCTTG 57.569 33.333 0.00 0.00 0.00 3.02
5653 7847 9.561270 GCTTATCTAATGAAAAAGTCTTGAACC 57.439 33.333 0.00 0.00 0.00 3.62
5657 7851 7.861630 TCTAATGAAAAAGTCTTGAACCTTCG 58.138 34.615 0.00 0.00 0.00 3.79
5658 7852 4.893424 TGAAAAAGTCTTGAACCTTCGG 57.107 40.909 0.00 0.00 0.00 4.30
5659 7853 4.519213 TGAAAAAGTCTTGAACCTTCGGA 58.481 39.130 0.00 0.00 0.00 4.55
5660 7854 5.130350 TGAAAAAGTCTTGAACCTTCGGAT 58.870 37.500 0.00 0.00 0.00 4.18
5661 7855 5.238650 TGAAAAAGTCTTGAACCTTCGGATC 59.761 40.000 0.00 0.00 0.00 3.36
5662 7856 3.336138 AAGTCTTGAACCTTCGGATCC 57.664 47.619 0.00 0.00 0.00 3.36
5663 7857 2.541466 AGTCTTGAACCTTCGGATCCT 58.459 47.619 10.75 0.00 0.00 3.24
5664 7858 2.498078 AGTCTTGAACCTTCGGATCCTC 59.502 50.000 10.75 0.00 0.00 3.71
5665 7859 2.498078 GTCTTGAACCTTCGGATCCTCT 59.502 50.000 10.75 0.00 0.00 3.69
5666 7860 2.497675 TCTTGAACCTTCGGATCCTCTG 59.502 50.000 10.75 0.00 0.00 3.35
5667 7861 1.938585 TGAACCTTCGGATCCTCTGT 58.061 50.000 10.75 0.00 0.00 3.41
5668 7862 2.257207 TGAACCTTCGGATCCTCTGTT 58.743 47.619 10.75 7.77 0.00 3.16
5669 7863 3.437213 TGAACCTTCGGATCCTCTGTTA 58.563 45.455 10.75 0.00 0.00 2.41
5670 7864 3.447586 TGAACCTTCGGATCCTCTGTTAG 59.552 47.826 10.75 0.00 0.00 2.34
5671 7865 3.383698 ACCTTCGGATCCTCTGTTAGA 57.616 47.619 10.75 0.00 0.00 2.10
5672 7866 3.709587 ACCTTCGGATCCTCTGTTAGAA 58.290 45.455 10.75 3.08 0.00 2.10
5673 7867 4.094476 ACCTTCGGATCCTCTGTTAGAAA 58.906 43.478 10.75 0.00 0.00 2.52
5674 7868 4.530946 ACCTTCGGATCCTCTGTTAGAAAA 59.469 41.667 10.75 0.00 0.00 2.29
5675 7869 5.012768 ACCTTCGGATCCTCTGTTAGAAAAA 59.987 40.000 10.75 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.203287 GAATCCAGCAAAGGGAACAGC 59.797 52.381 0.00 0.00 38.09 4.40
16 17 1.202879 ACGAATCCAGCAAAGGGAACA 60.203 47.619 0.00 0.00 38.09 3.18
89 90 0.109086 ACAGGAGAGCATGACGAACG 60.109 55.000 0.00 0.00 0.00 3.95
117 118 0.803117 TCTCGTCAGAGCGAAATCGT 59.197 50.000 4.59 0.00 44.02 3.73
134 135 0.812811 TCAGCCGACGCGTATACTCT 60.813 55.000 13.97 2.09 41.18 3.24
140 141 1.202325 ACATAAATCAGCCGACGCGTA 60.202 47.619 13.97 0.00 41.18 4.42
142 143 0.043053 CACATAAATCAGCCGACGCG 60.043 55.000 3.53 3.53 41.18 6.01
145 146 0.304705 CCGCACATAAATCAGCCGAC 59.695 55.000 0.00 0.00 0.00 4.79
149 150 1.335324 GGATGCCGCACATAAATCAGC 60.335 52.381 0.00 0.00 39.84 4.26
153 154 1.682854 CCTTGGATGCCGCACATAAAT 59.317 47.619 0.00 0.00 39.84 1.40
167 168 4.161295 CAGATCCGCGCCCTTGGA 62.161 66.667 0.00 2.25 38.95 3.53
169 170 3.197790 CACAGATCCGCGCCCTTG 61.198 66.667 0.00 0.00 0.00 3.61
186 187 1.362355 CAAAACCAGCACCGGAACC 59.638 57.895 9.46 0.00 0.00 3.62
461 467 5.105797 ACAGTCATTGAGTTGAACTTTGCAA 60.106 36.000 0.00 0.00 0.00 4.08
466 472 7.642669 CACATAACAGTCATTGAGTTGAACTT 58.357 34.615 0.00 0.00 0.00 2.66
543 550 5.048083 ACGGAATCACAGTTTTATGCACAAT 60.048 36.000 0.00 0.00 0.00 2.71
607 615 7.778382 TGTAGTAGATGATTACAGGCTAAGACA 59.222 37.037 0.00 0.00 0.00 3.41
615 623 8.873830 CAAAACAGTGTAGTAGATGATTACAGG 58.126 37.037 0.00 0.00 31.44 4.00
628 636 5.825679 TGTAGGAATTGCAAAACAGTGTAGT 59.174 36.000 1.71 0.00 0.00 2.73
629 637 6.312399 TGTAGGAATTGCAAAACAGTGTAG 57.688 37.500 1.71 0.00 0.00 2.74
633 641 6.594788 ATCATGTAGGAATTGCAAAACAGT 57.405 33.333 1.71 0.00 0.00 3.55
681 689 9.569167 GAGTGCAAAACTAATAAAGGGATAAAC 57.431 33.333 0.00 0.00 40.07 2.01
683 691 8.113462 AGGAGTGCAAAACTAATAAAGGGATAA 58.887 33.333 0.00 0.00 40.07 1.75
684 692 7.556275 CAGGAGTGCAAAACTAATAAAGGGATA 59.444 37.037 0.00 0.00 40.07 2.59
695 703 3.857157 ACTTCCAGGAGTGCAAAACTA 57.143 42.857 0.00 0.00 40.07 2.24
705 713 3.778954 ACCTTCAAGAACTTCCAGGAG 57.221 47.619 12.74 0.00 0.00 3.69
763 771 3.443681 CCACAATTTTAGGGGCTACACAG 59.556 47.826 0.00 0.00 0.00 3.66
839 847 4.178540 CAAAGCAATTAGACCAGCCAATG 58.821 43.478 0.00 0.00 0.00 2.82
845 853 2.821969 AGCCACAAAGCAATTAGACCAG 59.178 45.455 0.00 0.00 34.23 4.00
852 860 5.982890 AGTACAATAGCCACAAAGCAATT 57.017 34.783 0.00 0.00 34.23 2.32
967 983 3.885297 ACTTCAACCAACAAGACCTGATG 59.115 43.478 0.00 0.00 0.00 3.07
993 1009 9.462606 AAGCACTGCTACCTTAATATTTTAACT 57.537 29.630 3.33 0.00 38.25 2.24
1018 1034 3.072330 TGTTGTATGCCCAGAAGTCAGAA 59.928 43.478 0.00 0.00 0.00 3.02
1020 1036 3.057969 TGTTGTATGCCCAGAAGTCAG 57.942 47.619 0.00 0.00 0.00 3.51
1074 1090 7.839200 ACAATACTCTGCCCAGGTAATTAAAAT 59.161 33.333 0.00 0.00 0.00 1.82
1089 1105 9.967346 TCTGACACTAATATAACAATACTCTGC 57.033 33.333 0.00 0.00 0.00 4.26
1176 1200 5.393461 GCTGGAAATATGGTTCCTGTTCAAG 60.393 44.000 12.22 0.00 46.29 3.02
1282 1306 4.094887 ACATGAGCAATAACCGACATGTTC 59.905 41.667 0.00 0.00 43.30 3.18
1347 1371 7.046652 ACATCAATCAACAAGATCCTACTGAG 58.953 38.462 0.00 0.00 35.39 3.35
1398 1433 7.429636 AAGAGATACGGTTTTGAAAATCGAA 57.570 32.000 27.54 0.00 0.00 3.71
1399 1434 7.171848 TCAAAGAGATACGGTTTTGAAAATCGA 59.828 33.333 27.54 12.88 36.81 3.59
1400 1435 7.295201 TCAAAGAGATACGGTTTTGAAAATCG 58.705 34.615 20.40 20.40 36.81 3.34
1401 1436 9.626045 ATTCAAAGAGATACGGTTTTGAAAATC 57.374 29.630 16.90 0.00 46.40 2.17
1407 1448 5.572896 GCCAATTCAAAGAGATACGGTTTTG 59.427 40.000 0.00 0.00 33.09 2.44
1415 1456 9.959721 ACTAAGTTTAGCCAATTCAAAGAGATA 57.040 29.630 0.00 0.00 34.09 1.98
1659 1728 8.442632 ACAACCACATGAACTTCATATCATAG 57.557 34.615 0.00 0.00 34.28 2.23
1662 1737 7.394016 AGTACAACCACATGAACTTCATATCA 58.606 34.615 0.00 0.00 34.28 2.15
1811 1893 4.404640 AGTAGGACACAGCAGTACAGTAA 58.595 43.478 0.00 0.00 0.00 2.24
1872 2256 3.181495 TGTTTGACGGTTGAACACAATCC 60.181 43.478 0.00 0.00 0.00 3.01
1886 2270 2.286125 TGCACGAACATCTTGTTTGACG 60.286 45.455 13.23 6.54 42.88 4.35
1902 2286 1.788258 ATCTGTGAGAACAGTGCACG 58.212 50.000 12.01 9.15 38.75 5.34
2441 2825 1.906574 TCAGGGTACACTTGGACATCC 59.093 52.381 0.00 0.00 0.00 3.51
2459 2843 2.380064 ATGCAACAGTCCCCTTTTCA 57.620 45.000 0.00 0.00 0.00 2.69
2597 2981 1.068333 CATTTCTTTGTGGCTGGGTCG 60.068 52.381 0.00 0.00 0.00 4.79
2633 3017 1.448540 CTTGCAGGTAGCTGTCCCG 60.449 63.158 22.21 6.11 45.94 5.14
2894 3278 3.488721 CCTCGTATAAGTTCTCCACACGG 60.489 52.174 0.00 0.00 0.00 4.94
2984 3368 2.208431 GCTGGAATCATCTTGGAGACG 58.792 52.381 0.00 0.00 0.00 4.18
3428 3812 2.440627 TCCAGCTCCAGCAATGATATGT 59.559 45.455 0.48 0.00 45.16 2.29
3554 3938 1.178276 CTGTACGGCAGGACTTCTCT 58.822 55.000 0.00 0.00 41.42 3.10
4046 4430 1.697754 ATTCTCCGGGGCCTGGATT 60.698 57.895 33.90 18.82 34.32 3.01
4367 4751 5.302823 AGCACCAAAAATTTAGAGCTTGTCT 59.697 36.000 0.00 0.00 39.59 3.41
4429 4813 5.687730 AGACTCATCGATACAAAATAGTGCG 59.312 40.000 0.00 0.00 0.00 5.34
4498 4894 3.130516 TCCGTTACATCACCAGACATCTC 59.869 47.826 0.00 0.00 0.00 2.75
4499 4895 3.096852 TCCGTTACATCACCAGACATCT 58.903 45.455 0.00 0.00 0.00 2.90
4572 4968 8.585471 AGAATCAGGCAAATCTAAAGATCAAA 57.415 30.769 0.00 0.00 32.75 2.69
4599 4995 6.993175 TGAGAAAGCAAGATTATATCGACG 57.007 37.500 0.00 0.00 0.00 5.12
4635 5031 6.610830 AGAATAGTGACCACTGATCAGAAGAT 59.389 38.462 29.27 8.14 42.52 2.40
4638 5034 5.163612 CGAGAATAGTGACCACTGATCAGAA 60.164 44.000 29.27 6.26 42.52 3.02
4639 5035 4.336713 CGAGAATAGTGACCACTGATCAGA 59.663 45.833 29.27 3.06 42.52 3.27
4640 5036 4.097135 ACGAGAATAGTGACCACTGATCAG 59.903 45.833 21.37 21.37 42.52 2.90
4642 5038 4.640789 ACGAGAATAGTGACCACTGATC 57.359 45.455 12.54 10.02 42.52 2.92
4643 5039 4.438880 CGAACGAGAATAGTGACCACTGAT 60.439 45.833 12.54 1.58 42.52 2.90
4644 5040 3.119955 CGAACGAGAATAGTGACCACTGA 60.120 47.826 12.54 0.00 42.52 3.41
4645 5041 3.172050 CGAACGAGAATAGTGACCACTG 58.828 50.000 12.54 0.00 42.52 3.66
4646 5042 2.818432 ACGAACGAGAATAGTGACCACT 59.182 45.455 7.86 7.86 45.02 4.00
4647 5043 3.213249 ACGAACGAGAATAGTGACCAC 57.787 47.619 0.14 0.00 0.00 4.16
4684 5080 6.074941 GCAGGCAAAAATAATGCAAACAAAAC 60.075 34.615 0.00 0.00 45.60 2.43
4727 5126 2.592993 GGGTGGAGGCTAGTGCACA 61.593 63.158 21.04 4.13 40.37 4.57
4735 5134 0.044855 AGGAACATAGGGTGGAGGCT 59.955 55.000 0.00 0.00 0.00 4.58
4750 5149 2.248280 TAAAACACGCTGCTGAGGAA 57.752 45.000 0.00 0.00 0.00 3.36
4751 5150 2.076100 CATAAAACACGCTGCTGAGGA 58.924 47.619 0.00 0.00 0.00 3.71
4752 5151 1.466360 GCATAAAACACGCTGCTGAGG 60.466 52.381 0.00 0.00 0.00 3.86
4753 5152 1.466360 GGCATAAAACACGCTGCTGAG 60.466 52.381 0.00 0.00 35.03 3.35
4754 5153 0.521291 GGCATAAAACACGCTGCTGA 59.479 50.000 0.00 0.00 35.03 4.26
4757 5156 0.243636 AAGGGCATAAAACACGCTGC 59.756 50.000 0.00 0.00 0.00 5.25
4762 5161 7.480810 CCTGTAATAAGAAGGGCATAAAACAC 58.519 38.462 0.00 0.00 0.00 3.32
4771 5170 3.283259 AGTGCCTGTAATAAGAAGGGC 57.717 47.619 0.00 0.00 39.93 5.19
4777 5176 5.415701 ACAACCATGAAGTGCCTGTAATAAG 59.584 40.000 0.00 0.00 0.00 1.73
4778 5177 5.321102 ACAACCATGAAGTGCCTGTAATAA 58.679 37.500 0.00 0.00 0.00 1.40
4779 5178 4.917385 ACAACCATGAAGTGCCTGTAATA 58.083 39.130 0.00 0.00 0.00 0.98
4780 5179 3.766545 ACAACCATGAAGTGCCTGTAAT 58.233 40.909 0.00 0.00 0.00 1.89
4781 5180 3.222173 ACAACCATGAAGTGCCTGTAA 57.778 42.857 0.00 0.00 0.00 2.41
4782 5181 2.949177 ACAACCATGAAGTGCCTGTA 57.051 45.000 0.00 0.00 0.00 2.74
4783 5182 2.071778 AACAACCATGAAGTGCCTGT 57.928 45.000 0.00 0.00 0.00 4.00
4784 5183 4.582701 TTAAACAACCATGAAGTGCCTG 57.417 40.909 0.00 0.00 0.00 4.85
4787 5186 7.245419 ACAAATTTAAACAACCATGAAGTGC 57.755 32.000 0.00 0.00 0.00 4.40
4799 5198 9.593134 ACACATCTTTTGCTACAAATTTAAACA 57.407 25.926 0.00 0.00 0.00 2.83
4802 5201 9.809096 TGAACACATCTTTTGCTACAAATTTAA 57.191 25.926 0.00 0.00 0.00 1.52
4839 5238 4.967036 ACAGGAAATTATAGAGAGCAGCC 58.033 43.478 0.00 0.00 0.00 4.85
4850 5249 4.697352 GCATGCTCGGATACAGGAAATTAT 59.303 41.667 11.37 0.00 0.00 1.28
4851 5250 4.065088 GCATGCTCGGATACAGGAAATTA 58.935 43.478 11.37 0.00 0.00 1.40
4852 5251 2.880890 GCATGCTCGGATACAGGAAATT 59.119 45.455 11.37 0.00 0.00 1.82
4853 5252 2.158769 TGCATGCTCGGATACAGGAAAT 60.159 45.455 20.33 0.00 0.00 2.17
4854 5253 1.209261 TGCATGCTCGGATACAGGAAA 59.791 47.619 20.33 0.00 0.00 3.13
4855 5254 0.829990 TGCATGCTCGGATACAGGAA 59.170 50.000 20.33 0.00 0.00 3.36
4856 5255 0.390492 CTGCATGCTCGGATACAGGA 59.610 55.000 20.33 0.00 0.00 3.86
4857 5256 1.226686 GCTGCATGCTCGGATACAGG 61.227 60.000 20.33 0.00 38.95 4.00
4858 5257 2.232750 GCTGCATGCTCGGATACAG 58.767 57.895 20.33 6.13 38.95 2.74
4859 5258 4.443857 GCTGCATGCTCGGATACA 57.556 55.556 20.33 0.00 38.95 2.29
4906 5305 4.432741 GCAAGGGGGCAGGGAGAC 62.433 72.222 0.00 0.00 0.00 3.36
4938 5347 1.225704 CAAGGGAGATGGAGGCCAC 59.774 63.158 5.01 0.00 35.80 5.01
4964 5373 1.803334 GAACACGAACACCATGGCTA 58.197 50.000 13.04 0.00 0.00 3.93
4976 5385 0.601576 CACCATTCCACCGAACACGA 60.602 55.000 0.00 0.00 0.00 4.35
4989 5398 5.324409 TCACCTAGAATTCAAAGCACCATT 58.676 37.500 8.44 0.00 0.00 3.16
4996 5405 8.293157 GGAGAAAACTTCACCTAGAATTCAAAG 58.707 37.037 8.44 4.61 37.43 2.77
5001 5410 5.701290 CGTGGAGAAAACTTCACCTAGAATT 59.299 40.000 0.00 0.00 40.56 2.17
5005 5414 3.244112 ACCGTGGAGAAAACTTCACCTAG 60.244 47.826 0.00 0.00 40.56 3.02
5030 5439 1.415659 CAGATCTGGGAGGCACCTTAG 59.584 57.143 15.38 0.40 38.98 2.18
5084 5493 3.072468 CACCTGCATGGCCCCAAG 61.072 66.667 0.00 0.00 40.22 3.61
5097 5506 1.140312 TCTCAACCTCTTTGCCACCT 58.860 50.000 0.00 0.00 34.88 4.00
5103 5512 7.772166 AGGTAAACTTTTTCTCAACCTCTTTG 58.228 34.615 0.00 0.00 30.03 2.77
5128 5537 1.682451 CCAAAGTATCCCTCGCCGGA 61.682 60.000 5.05 0.00 36.02 5.14
5131 5540 1.887707 CGCCAAAGTATCCCTCGCC 60.888 63.158 0.00 0.00 0.00 5.54
5132 5541 2.534903 GCGCCAAAGTATCCCTCGC 61.535 63.158 0.00 0.00 0.00 5.03
5135 5544 2.595655 GGGCGCCAAAGTATCCCT 59.404 61.111 30.85 0.00 34.19 4.20
5136 5545 2.518587 GGGGCGCCAAAGTATCCC 60.519 66.667 30.85 13.99 36.25 3.85
5137 5546 2.518587 GGGGGCGCCAAAGTATCC 60.519 66.667 30.85 18.11 0.00 2.59
5138 5547 1.076995 AAGGGGGCGCCAAAGTATC 60.077 57.895 30.85 8.62 0.00 2.24
5139 5548 1.379843 CAAGGGGGCGCCAAAGTAT 60.380 57.895 30.85 5.75 0.00 2.12
5140 5549 2.034999 CAAGGGGGCGCCAAAGTA 59.965 61.111 30.85 0.00 0.00 2.24
5150 5559 4.060667 ATGGAACCGGCAAGGGGG 62.061 66.667 0.00 0.00 46.96 5.40
5151 5560 2.755469 CATGGAACCGGCAAGGGG 60.755 66.667 0.00 0.00 46.96 4.79
5152 5561 2.755469 CCATGGAACCGGCAAGGG 60.755 66.667 5.56 0.00 46.96 3.95
5153 5562 3.451894 GCCATGGAACCGGCAAGG 61.452 66.667 18.40 0.00 44.22 3.61
5154 5563 3.814268 CGCCATGGAACCGGCAAG 61.814 66.667 18.40 0.00 44.94 4.01
5155 5564 3.851897 TTCGCCATGGAACCGGCAA 62.852 57.895 18.40 0.00 44.94 4.52
5156 5565 4.337177 TTCGCCATGGAACCGGCA 62.337 61.111 18.40 0.00 44.94 5.69
5209 5618 1.009429 AGCTTCCATCTCCCTTCTCCT 59.991 52.381 0.00 0.00 0.00 3.69
5233 5642 5.556915 TCGATAAAGAACACCAACCTCATT 58.443 37.500 0.00 0.00 0.00 2.57
5234 5643 5.160607 TCGATAAAGAACACCAACCTCAT 57.839 39.130 0.00 0.00 0.00 2.90
5256 5665 1.002544 GTAGCTCTGCCACAAAGACCT 59.997 52.381 0.00 0.00 0.00 3.85
5323 5732 2.743928 GTGGTCGCCCTTCAGCTG 60.744 66.667 7.63 7.63 0.00 4.24
5324 5733 2.925170 AGTGGTCGCCCTTCAGCT 60.925 61.111 0.00 0.00 0.00 4.24
5346 5755 1.260544 AGCATCAAGGCCAAAAGGAC 58.739 50.000 5.01 0.00 0.00 3.85
5351 5760 1.619432 CCCCTAAGCATCAAGGCCAAA 60.619 52.381 5.01 0.00 0.00 3.28
5365 5774 1.203389 AGTTGCACTACCTCCCCCTAA 60.203 52.381 0.00 0.00 0.00 2.69
5366 5775 0.416231 AGTTGCACTACCTCCCCCTA 59.584 55.000 0.00 0.00 0.00 3.53
5368 5777 0.910088 AGAGTTGCACTACCTCCCCC 60.910 60.000 0.00 0.00 0.00 5.40
5374 5783 1.338200 CCTGGTCAGAGTTGCACTACC 60.338 57.143 0.00 0.00 0.00 3.18
5383 5792 2.872388 CGCCACACCTGGTCAGAGT 61.872 63.158 0.00 0.00 40.17 3.24
5392 5801 0.107214 CCATTGATACCGCCACACCT 60.107 55.000 0.00 0.00 0.00 4.00
5393 5802 0.393808 ACCATTGATACCGCCACACC 60.394 55.000 0.00 0.00 0.00 4.16
5397 5806 1.199615 TGAGACCATTGATACCGCCA 58.800 50.000 0.00 0.00 0.00 5.69
5404 5813 5.378230 TGCCTAAGAATGAGACCATTGAT 57.622 39.130 0.00 0.00 42.66 2.57
5421 5830 1.944234 TTCGCAGAGACGCATGCCTA 61.944 55.000 13.15 0.00 39.30 3.93
5423 5832 1.911293 TTTTCGCAGAGACGCATGCC 61.911 55.000 13.15 0.00 39.30 4.40
5433 5842 2.703536 TCCATAGCCCTATTTTCGCAGA 59.296 45.455 0.00 0.00 0.00 4.26
5438 5847 2.796557 GGCCTCCATAGCCCTATTTTC 58.203 52.381 0.00 0.00 45.16 2.29
5439 5848 2.980246 GGCCTCCATAGCCCTATTTT 57.020 50.000 0.00 0.00 45.16 1.82
5457 5866 4.388499 CCACTTGGGACGACGGGG 62.388 72.222 0.00 0.00 40.01 5.73
5460 5869 3.271706 TACGCCACTTGGGACGACG 62.272 63.158 0.00 0.00 40.01 5.12
5474 5883 1.006102 CCATCATCGGGGACTACGC 60.006 63.158 0.00 0.00 0.00 4.42
5476 5885 1.341531 CTCACCATCATCGGGGACTAC 59.658 57.143 0.00 0.00 31.82 2.73
5477 5886 1.216930 TCTCACCATCATCGGGGACTA 59.783 52.381 0.00 0.00 31.82 2.59
5478 5887 0.032117 TCTCACCATCATCGGGGACT 60.032 55.000 0.00 0.00 31.82 3.85
5480 5889 1.417517 CAATCTCACCATCATCGGGGA 59.582 52.381 0.00 0.00 35.55 4.81
5482 5891 1.417517 TCCAATCTCACCATCATCGGG 59.582 52.381 0.00 0.00 0.00 5.14
5483 5892 2.874701 GTTCCAATCTCACCATCATCGG 59.125 50.000 0.00 0.00 0.00 4.18
5484 5893 2.874701 GGTTCCAATCTCACCATCATCG 59.125 50.000 0.00 0.00 0.00 3.84
5486 5895 4.079615 TCATGGTTCCAATCTCACCATCAT 60.080 41.667 0.00 0.00 46.51 2.45
5487 5896 3.266513 TCATGGTTCCAATCTCACCATCA 59.733 43.478 0.00 0.00 46.51 3.07
5488 5897 3.889815 TCATGGTTCCAATCTCACCATC 58.110 45.455 0.00 0.00 46.51 3.51
5490 5899 3.561960 CCTTCATGGTTCCAATCTCACCA 60.562 47.826 0.00 0.00 44.75 4.17
5491 5900 3.019564 CCTTCATGGTTCCAATCTCACC 58.980 50.000 0.00 0.00 0.00 4.02
5492 5901 3.944015 CTCCTTCATGGTTCCAATCTCAC 59.056 47.826 0.00 0.00 37.07 3.51
5493 5902 3.588842 ACTCCTTCATGGTTCCAATCTCA 59.411 43.478 0.00 0.00 37.07 3.27
5504 5913 3.383761 GTGCAAAACAACTCCTTCATGG 58.616 45.455 0.00 0.00 37.10 3.66
5546 5955 0.110486 GCAAAGAGGACCCCAGACAA 59.890 55.000 0.00 0.00 0.00 3.18
5550 5959 0.322008 GACTGCAAAGAGGACCCCAG 60.322 60.000 0.00 0.00 0.00 4.45
5551 5960 1.059584 TGACTGCAAAGAGGACCCCA 61.060 55.000 0.00 0.00 0.00 4.96
5552 5961 0.606673 GTGACTGCAAAGAGGACCCC 60.607 60.000 0.00 0.00 0.00 4.95
5619 7813 7.336931 ACTTTTTCATTAGATAAGCATCGGTGT 59.663 33.333 0.00 0.00 36.20 4.16
5623 7817 9.430838 CAAGACTTTTTCATTAGATAAGCATCG 57.569 33.333 0.00 0.00 36.20 3.84
5631 7825 8.507249 CGAAGGTTCAAGACTTTTTCATTAGAT 58.493 33.333 0.00 0.00 0.00 1.98
5632 7826 7.861630 CGAAGGTTCAAGACTTTTTCATTAGA 58.138 34.615 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.