Multiple sequence alignment - TraesCS6D01G160400

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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 TraesCS6D01G160400 chr6D 100.000 5216 0 0 1 5216 138893350 138898565 0.000000e+00 9633.0
1 TraesCS6D01G160400 chr6B 93.420 3146 107 40 848 3959 238153734 238156813 0.000000e+00 4571.0
2 TraesCS6D01G160400 chr6B 94.430 395 20 2 4651 5043 238157737 238158131 1.610000e-169 606.0
3 TraesCS6D01G160400 chr6B 94.695 377 9 2 3956 4332 238156894 238157259 4.530000e-160 575.0
4 TraesCS6D01G160400 chr6B 95.965 347 13 1 4307 4652 238157270 238157616 3.530000e-156 562.0
5 TraesCS6D01G160400 chr6B 90.191 367 18 10 456 811 238153379 238153738 3.680000e-126 462.0
6 TraesCS6D01G160400 chr6B 82.979 423 29 12 331 717 238143829 238144244 5.000000e-90 342.0
7 TraesCS6D01G160400 chr6B 93.421 228 10 4 133 357 238152100 238152325 3.010000e-87 333.0
8 TraesCS6D01G160400 chr6B 90.323 93 6 3 8 99 228227757 228227667 9.180000e-23 119.0
9 TraesCS6D01G160400 chr6B 93.548 62 4 0 133 194 238138975 238139036 5.560000e-15 93.5
10 TraesCS6D01G160400 chr6A 93.319 2889 141 27 2173 5043 181509142 181511996 0.000000e+00 4218.0
11 TraesCS6D01G160400 chr6A 90.231 1863 89 39 514 2357 181507343 181509131 0.000000e+00 2346.0
12 TraesCS6D01G160400 chr6A 89.868 454 35 7 8 455 181504372 181504820 1.630000e-159 573.0
13 TraesCS6D01G160400 chr6A 96.610 59 0 1 5131 5189 181512164 181512220 4.300000e-16 97.1
14 TraesCS6D01G160400 chr4D 93.548 93 5 1 8 100 502385719 502385810 2.530000e-28 137.0
15 TraesCS6D01G160400 chr5A 92.473 93 6 1 8 100 685421044 685421135 1.180000e-26 132.0
16 TraesCS6D01G160400 chr1B 92.473 93 6 1 8 100 264131246 264131155 1.180000e-26 132.0
17 TraesCS6D01G160400 chr1B 89.362 94 9 1 8 100 247070363 247070456 3.300000e-22 117.0
18 TraesCS6D01G160400 chr7B 91.304 92 8 0 8 99 138014032 138014123 5.480000e-25 126.0
19 TraesCS6D01G160400 chr5D 91.304 92 8 0 8 99 227275378 227275469 5.480000e-25 126.0
20 TraesCS6D01G160400 chrUn 89.247 93 8 2 8 100 386876329 386876419 1.190000e-21 115.0


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 TraesCS6D01G160400 chr6D 138893350 138898565 5215 False 9633.000000 9633 100.000 1 5216 1 chr6D.!!$F1 5215
1 TraesCS6D01G160400 chr6B 238152100 238158131 6031 False 1184.833333 4571 93.687 133 5043 6 chr6B.!!$F3 4910
2 TraesCS6D01G160400 chr6A 181504372 181512220 7848 False 1808.525000 4218 92.507 8 5189 4 chr6A.!!$F1 5181

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
129 130 0.251916 TTTGACCTGCCCCATAGACG 59.748 55.000 0.00 0.0 0.00 4.18 F
1054 4506 0.108138 CCAAAGTCTTCTCCCGCGAT 60.108 55.000 8.23 0.0 0.00 4.58 F
1661 5127 0.251209 GGGAGAAAAGACACCCCCAC 60.251 60.000 0.00 0.0 35.21 4.61 F
1665 5131 0.476771 GAAAAGACACCCCCACCTGA 59.523 55.000 0.00 0.0 0.00 3.86 F
1667 5133 0.478507 AAAGACACCCCCACCTGAAG 59.521 55.000 0.00 0.0 0.00 3.02 F
2119 5586 0.631212 GGTCAATGGGGGAGGATTGT 59.369 55.000 0.00 0.0 32.40 2.71 F
2720 6409 1.618343 GGGTGGTTTGGTCCTCATTTG 59.382 52.381 0.00 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 4584 0.179089 AAGCGCCAGAGAGTAGCATG 60.179 55.000 2.29 0.0 0.00 4.06 R
1925 5392 0.261402 CCATAATTCCAGCCCCCACA 59.739 55.000 0.00 0.0 0.00 4.17 R
2915 6604 1.108727 CCACAGCAAGGGCAACTGAA 61.109 55.000 0.00 0.0 44.61 3.02 R
3190 6879 5.594725 ACTTCTATCTTCCAGCTCGTTATCA 59.405 40.000 0.00 0.0 0.00 2.15 R
3382 7071 5.696030 ACATGGACTACATAGCTCACTCTA 58.304 41.667 0.00 0.0 37.84 2.43 R
3672 7361 0.672401 ACCTACAAACATCGGGCACG 60.672 55.000 0.00 0.0 42.74 5.34 R
4326 8134 0.970640 TAGTCGTGCCTAGGTTTGCA 59.029 50.000 11.31 0.0 34.54 4.08 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
71 72 7.530010 ACATTGAGAAACGATGAAGTAATTGG 58.470 34.615 0.00 0.00 41.57 3.16
116 117 6.103997 TGAATACTCGTAGAATGGTTTGACC 58.896 40.000 0.00 0.00 35.26 4.02
117 118 5.934402 ATACTCGTAGAATGGTTTGACCT 57.066 39.130 0.00 0.00 35.66 3.85
119 120 2.673368 CTCGTAGAATGGTTTGACCTGC 59.327 50.000 0.00 0.00 35.66 4.85
121 122 2.092323 GTAGAATGGTTTGACCTGCCC 58.908 52.381 0.00 0.00 39.58 5.36
129 130 0.251916 TTTGACCTGCCCCATAGACG 59.748 55.000 0.00 0.00 0.00 4.18
131 132 2.687200 ACCTGCCCCATAGACGCA 60.687 61.111 0.00 0.00 0.00 5.24
297 300 2.547211 GTGCATTCTCATCCTTCCATCG 59.453 50.000 0.00 0.00 0.00 3.84
306 309 3.957535 CTTCCATCGGCCATGCGC 61.958 66.667 2.24 0.00 0.00 6.09
323 330 0.530870 CGCCGATCCCTTCTTCTTCC 60.531 60.000 0.00 0.00 0.00 3.46
338 345 3.340814 TCTTCCCTCTGCTTCACATTC 57.659 47.619 0.00 0.00 0.00 2.67
350 357 6.148315 TCTGCTTCACATTCTCTTATTGTGTG 59.852 38.462 0.00 0.00 39.44 3.82
384 391 5.175308 GTCTACGAGTTCTGAACCAACTTTC 59.825 44.000 16.48 6.10 34.10 2.62
490 3927 3.065925 GCACCTAATCCAAAGCAGCTAAG 59.934 47.826 0.00 0.00 0.00 2.18
491 3928 4.265073 CACCTAATCCAAAGCAGCTAAGT 58.735 43.478 0.00 0.00 0.00 2.24
592 4040 1.466529 CGTCACTCTCATCCACTCGTG 60.467 57.143 0.00 0.00 0.00 4.35
627 4075 1.153107 CCAGCGCATCTCCATTCCA 60.153 57.895 11.47 0.00 0.00 3.53
638 4086 1.424302 CTCCATTCCAGCCATCATCCT 59.576 52.381 0.00 0.00 0.00 3.24
640 4088 1.547223 CCATTCCAGCCATCATCCTCC 60.547 57.143 0.00 0.00 0.00 4.30
651 4099 1.095600 TCATCCTCCTCGTCGTCTTG 58.904 55.000 0.00 0.00 0.00 3.02
862 4310 5.658634 AGGGAATTAATTGCTTTCCTTCCTC 59.341 40.000 17.81 0.00 39.12 3.71
988 4436 1.001633 CCTATATAACAAGGCCGCCGT 59.998 52.381 3.05 0.00 0.00 5.68
1022 4470 0.109412 GGGACAACTCCGTCTACACG 60.109 60.000 0.00 0.00 46.29 4.49
1047 4499 1.578206 GCACCCGCCAAAGTCTTCTC 61.578 60.000 0.00 0.00 0.00 2.87
1051 4503 2.391389 CGCCAAAGTCTTCTCCCGC 61.391 63.158 0.00 0.00 0.00 6.13
1052 4504 2.391389 GCCAAAGTCTTCTCCCGCG 61.391 63.158 0.00 0.00 0.00 6.46
1053 4505 1.292223 CCAAAGTCTTCTCCCGCGA 59.708 57.895 8.23 0.00 0.00 5.87
1054 4506 0.108138 CCAAAGTCTTCTCCCGCGAT 60.108 55.000 8.23 0.00 0.00 4.58
1102 4554 2.665185 GTTGTTGGCCGAGCGACT 60.665 61.111 0.00 0.00 0.00 4.18
1132 4584 7.375053 GGATTCTGTAGAGGTATGAGATTGAC 58.625 42.308 0.00 0.00 0.00 3.18
1231 4683 3.118992 TCGAGTTGTCTGATCTGATTGGG 60.119 47.826 5.52 0.00 0.00 4.12
1314 4766 6.446318 GCTGAATGTTTGTCCATTCTTGTAA 58.554 36.000 13.28 0.00 47.00 2.41
1316 4768 6.744112 TGAATGTTTGTCCATTCTTGTAACC 58.256 36.000 13.28 0.00 47.00 2.85
1327 4779 9.391006 GTCCATTCTTGTAACCAACATCTTATA 57.609 33.333 0.00 0.00 38.10 0.98
1364 4816 5.237344 GGAATGATACTGCATGTGTTCTACC 59.763 44.000 0.00 0.00 0.00 3.18
1366 4818 2.665649 TACTGCATGTGTTCTACCGG 57.334 50.000 0.00 0.00 0.00 5.28
1367 4819 0.973632 ACTGCATGTGTTCTACCGGA 59.026 50.000 9.46 0.00 0.00 5.14
1368 4820 1.346395 ACTGCATGTGTTCTACCGGAA 59.654 47.619 9.46 0.00 0.00 4.30
1369 4821 2.224426 ACTGCATGTGTTCTACCGGAAA 60.224 45.455 9.46 0.00 35.51 3.13
1370 4822 3.009723 CTGCATGTGTTCTACCGGAAAT 58.990 45.455 9.46 0.00 35.51 2.17
1371 4823 2.746904 TGCATGTGTTCTACCGGAAATG 59.253 45.455 9.46 0.00 35.51 2.32
1373 4825 3.181510 GCATGTGTTCTACCGGAAATGAC 60.182 47.826 9.46 0.14 35.51 3.06
1375 4827 1.392510 GTGTTCTACCGGAAATGACGC 59.607 52.381 9.46 2.89 35.51 5.19
1386 4850 3.786048 CGGAAATGACGCTTTGCTTTATC 59.214 43.478 0.00 0.00 0.00 1.75
1394 4858 3.057526 ACGCTTTGCTTTATCTGGTTTCC 60.058 43.478 0.00 0.00 0.00 3.13
1399 4863 6.517362 GCTTTGCTTTATCTGGTTTCCTTTCT 60.517 38.462 0.00 0.00 0.00 2.52
1414 4878 4.792068 TCCTTTCTTGGTTGTCATCAAGT 58.208 39.130 13.01 0.00 40.67 3.16
1415 4879 5.200483 TCCTTTCTTGGTTGTCATCAAGTT 58.800 37.500 13.01 0.00 40.67 2.66
1416 4880 6.361433 TCCTTTCTTGGTTGTCATCAAGTTA 58.639 36.000 13.01 4.39 40.67 2.24
1420 4884 8.463930 TTTCTTGGTTGTCATCAAGTTAAGAT 57.536 30.769 13.01 0.00 40.67 2.40
1422 4886 8.099364 TCTTGGTTGTCATCAAGTTAAGATTC 57.901 34.615 13.01 0.00 40.67 2.52
1426 4890 7.041167 TGGTTGTCATCAAGTTAAGATTCTGTG 60.041 37.037 0.00 0.00 33.97 3.66
1431 4895 6.880529 TCATCAAGTTAAGATTCTGTGCATCA 59.119 34.615 0.00 0.00 0.00 3.07
1436 4900 5.587844 AGTTAAGATTCTGTGCATCATGTCC 59.412 40.000 0.00 0.00 0.00 4.02
1444 4909 2.224597 TGTGCATCATGTCCAAGTGTCT 60.225 45.455 0.00 0.00 0.00 3.41
1453 4918 6.475504 TCATGTCCAAGTGTCTGTCAAATAT 58.524 36.000 0.00 0.00 0.00 1.28
1454 4919 7.619965 TCATGTCCAAGTGTCTGTCAAATATA 58.380 34.615 0.00 0.00 0.00 0.86
1498 4963 6.808704 GCTTTGTTCTTTCCTGAATAATCACC 59.191 38.462 0.00 0.00 29.65 4.02
1599 5065 8.060931 TGATGGATTGGAAAATGTAATCGAAA 57.939 30.769 0.00 0.00 32.88 3.46
1620 5086 6.092259 CGAAAGACGGGAATTCAGATTTAAGT 59.908 38.462 7.93 0.00 38.46 2.24
1621 5087 7.360946 CGAAAGACGGGAATTCAGATTTAAGTT 60.361 37.037 7.93 0.00 38.46 2.66
1622 5088 6.986904 AGACGGGAATTCAGATTTAAGTTC 57.013 37.500 7.93 0.00 0.00 3.01
1645 5111 3.320610 TTTTGAAATGGTCACTGGGGA 57.679 42.857 0.00 0.00 35.39 4.81
1646 5112 2.584835 TTGAAATGGTCACTGGGGAG 57.415 50.000 0.00 0.00 35.39 4.30
1647 5113 1.741028 TGAAATGGTCACTGGGGAGA 58.259 50.000 0.00 0.00 0.00 3.71
1648 5114 2.061848 TGAAATGGTCACTGGGGAGAA 58.938 47.619 0.00 0.00 0.00 2.87
1649 5115 2.445145 TGAAATGGTCACTGGGGAGAAA 59.555 45.455 0.00 0.00 0.00 2.52
1650 5116 3.117322 TGAAATGGTCACTGGGGAGAAAA 60.117 43.478 0.00 0.00 0.00 2.29
1651 5117 2.887151 ATGGTCACTGGGGAGAAAAG 57.113 50.000 0.00 0.00 0.00 2.27
1652 5118 1.814429 TGGTCACTGGGGAGAAAAGA 58.186 50.000 0.00 0.00 0.00 2.52
1653 5119 1.420138 TGGTCACTGGGGAGAAAAGAC 59.580 52.381 0.00 0.00 0.00 3.01
1654 5120 1.420138 GGTCACTGGGGAGAAAAGACA 59.580 52.381 0.00 0.00 0.00 3.41
1655 5121 2.495084 GTCACTGGGGAGAAAAGACAC 58.505 52.381 0.00 0.00 0.00 3.67
1656 5122 1.420138 TCACTGGGGAGAAAAGACACC 59.580 52.381 0.00 0.00 0.00 4.16
1657 5123 0.771755 ACTGGGGAGAAAAGACACCC 59.228 55.000 0.00 0.00 41.84 4.61
1660 5126 2.160646 GGGAGAAAAGACACCCCCA 58.839 57.895 0.00 0.00 35.21 4.96
1661 5127 0.251209 GGGAGAAAAGACACCCCCAC 60.251 60.000 0.00 0.00 35.21 4.61
1662 5128 0.251209 GGAGAAAAGACACCCCCACC 60.251 60.000 0.00 0.00 0.00 4.61
1663 5129 0.771755 GAGAAAAGACACCCCCACCT 59.228 55.000 0.00 0.00 0.00 4.00
1664 5130 0.478507 AGAAAAGACACCCCCACCTG 59.521 55.000 0.00 0.00 0.00 4.00
1665 5131 0.476771 GAAAAGACACCCCCACCTGA 59.523 55.000 0.00 0.00 0.00 3.86
1666 5132 0.930726 AAAAGACACCCCCACCTGAA 59.069 50.000 0.00 0.00 0.00 3.02
1667 5133 0.478507 AAAGACACCCCCACCTGAAG 59.521 55.000 0.00 0.00 0.00 3.02
1925 5392 5.299279 AGTTTTCAATCTGTCGACAACCATT 59.701 36.000 20.49 14.29 0.00 3.16
2119 5586 0.631212 GGTCAATGGGGGAGGATTGT 59.369 55.000 0.00 0.00 32.40 2.71
2191 5658 5.646793 ACATGATTATCATCAGTATGCCTGC 59.353 40.000 4.51 0.00 42.93 4.85
2221 5709 6.382919 ACCCTTTTCTGTTATGCCTACTTA 57.617 37.500 0.00 0.00 0.00 2.24
2222 5710 6.970191 ACCCTTTTCTGTTATGCCTACTTAT 58.030 36.000 0.00 0.00 0.00 1.73
2223 5711 7.054751 ACCCTTTTCTGTTATGCCTACTTATC 58.945 38.462 0.00 0.00 0.00 1.75
2224 5712 7.054124 CCCTTTTCTGTTATGCCTACTTATCA 58.946 38.462 0.00 0.00 0.00 2.15
2225 5713 7.721399 CCCTTTTCTGTTATGCCTACTTATCAT 59.279 37.037 0.00 0.00 0.00 2.45
2226 5714 8.778358 CCTTTTCTGTTATGCCTACTTATCATC 58.222 37.037 0.00 0.00 0.00 2.92
2227 5715 9.330063 CTTTTCTGTTATGCCTACTTATCATCA 57.670 33.333 0.00 0.00 0.00 3.07
2228 5716 9.679661 TTTTCTGTTATGCCTACTTATCATCAA 57.320 29.630 0.00 0.00 0.00 2.57
2229 5717 8.893219 TTCTGTTATGCCTACTTATCATCAAG 57.107 34.615 0.00 0.00 0.00 3.02
2230 5718 8.250143 TCTGTTATGCCTACTTATCATCAAGA 57.750 34.615 0.00 0.00 0.00 3.02
2231 5719 8.363390 TCTGTTATGCCTACTTATCATCAAGAG 58.637 37.037 0.00 0.00 0.00 2.85
2232 5720 8.023021 TGTTATGCCTACTTATCATCAAGAGT 57.977 34.615 0.00 0.00 0.00 3.24
2233 5721 8.486210 TGTTATGCCTACTTATCATCAAGAGTT 58.514 33.333 0.00 0.00 0.00 3.01
2234 5722 8.768955 GTTATGCCTACTTATCATCAAGAGTTG 58.231 37.037 0.00 0.00 0.00 3.16
2235 5723 6.299805 TGCCTACTTATCATCAAGAGTTGT 57.700 37.500 0.00 0.00 0.00 3.32
2236 5724 7.418337 TGCCTACTTATCATCAAGAGTTGTA 57.582 36.000 0.00 0.00 0.00 2.41
2237 5725 7.847096 TGCCTACTTATCATCAAGAGTTGTAA 58.153 34.615 0.00 0.00 0.00 2.41
2238 5726 8.486210 TGCCTACTTATCATCAAGAGTTGTAAT 58.514 33.333 0.00 0.00 0.00 1.89
2239 5727 8.768955 GCCTACTTATCATCAAGAGTTGTAATG 58.231 37.037 0.00 0.00 0.00 1.90
2281 5769 7.119709 TCAGGTGCTATATTTGTAGTTGCTA 57.880 36.000 0.00 0.00 0.00 3.49
2362 6045 8.314021 TCATAGTGAACACTGATACATGTCTTT 58.686 33.333 16.37 0.00 42.52 2.52
2364 6047 6.291377 AGTGAACACTGATACATGTCTTTGT 58.709 36.000 0.00 0.00 40.75 2.83
2367 6050 8.009974 GTGAACACTGATACATGTCTTTGTTAC 58.990 37.037 0.00 3.15 29.67 2.50
2408 6091 4.323417 TGCGGCTGGATTATTAACATAGG 58.677 43.478 0.00 0.00 0.00 2.57
2504 6191 7.179338 CCACTAACCTATATGCTCCTATGTCTT 59.821 40.741 0.00 0.00 0.00 3.01
2527 6214 4.631131 TCCAAGTGATGTATTAGATGGCG 58.369 43.478 0.00 0.00 0.00 5.69
2539 6226 5.940192 ATTAGATGGCGCATCGAAATAAA 57.060 34.783 10.83 2.48 44.67 1.40
2577 6265 8.848474 TCTCTCTTGTTTTAGGAAATAGTTGG 57.152 34.615 0.00 0.00 0.00 3.77
2615 6303 4.095410 TGCAATTCGCCTCAAACTATTG 57.905 40.909 0.00 0.00 41.33 1.90
2618 6306 4.558860 GCAATTCGCCTCAAACTATTGTTC 59.441 41.667 0.00 0.00 34.53 3.18
2657 6346 3.998913 TTTCCAGGTGATGTGCTATCA 57.001 42.857 0.87 0.87 0.00 2.15
2720 6409 1.618343 GGGTGGTTTGGTCCTCATTTG 59.382 52.381 0.00 0.00 0.00 2.32
2873 6562 8.199449 TGGTATCTGAACTTAAATACTAACGGG 58.801 37.037 0.00 0.00 0.00 5.28
2915 6604 6.231258 TCATTGAGATACACATCTGCTCTT 57.769 37.500 0.00 0.00 41.78 2.85
3142 6831 3.380954 TGCTCTTGCTGTTGTTCATTTCA 59.619 39.130 0.00 0.00 40.48 2.69
3143 6832 4.142204 TGCTCTTGCTGTTGTTCATTTCAA 60.142 37.500 0.00 0.00 40.48 2.69
3190 6879 3.489355 TGATTGGACAGTTCACAGCATT 58.511 40.909 0.00 0.00 0.00 3.56
3382 7071 8.016301 TCAGCTCTGTCTTCAATGATATAGTT 57.984 34.615 0.00 0.00 0.00 2.24
3665 7354 4.156556 TCAGGTAATCAGCATTCTGTTTGC 59.843 41.667 0.00 0.00 41.10 3.68
3672 7361 0.986992 GCATTCTGTTTGCGTGATGC 59.013 50.000 0.00 0.00 46.70 3.91
3706 7395 8.943594 TGTTTGTAGGTATCCTTTTGGTTTAT 57.056 30.769 0.00 0.00 41.38 1.40
3713 7402 6.150474 AGGTATCCTTTTGGTTTATGTGTTCG 59.850 38.462 0.00 0.00 41.38 3.95
3731 7420 6.034577 TGTGTTCGATAACTTTATTCTGCTCG 59.965 38.462 0.00 0.00 36.51 5.03
4016 7789 5.276631 GCCACTAATTTTTGTTTTGGACACG 60.277 40.000 0.00 0.00 38.18 4.49
4168 7941 6.553857 ACCTTTTGGGGTTATGTACATGTTA 58.446 36.000 18.81 0.98 46.08 2.41
4265 8038 7.120285 GGGAGACATTGTTGTGGATATATCATG 59.880 40.741 14.60 9.56 35.79 3.07
4266 8039 7.663081 GGAGACATTGTTGTGGATATATCATGT 59.337 37.037 14.60 12.36 35.79 3.21
4267 8040 9.710900 GAGACATTGTTGTGGATATATCATGTA 57.289 33.333 14.60 0.00 35.79 2.29
4268 8041 9.494271 AGACATTGTTGTGGATATATCATGTAC 57.506 33.333 14.60 8.03 35.79 2.90
4269 8042 9.271828 GACATTGTTGTGGATATATCATGTACA 57.728 33.333 14.60 0.00 35.79 2.90
4270 8043 9.625747 ACATTGTTGTGGATATATCATGTACAA 57.374 29.630 14.60 16.36 33.85 2.41
4273 8046 9.844257 TTGTTGTGGATATATCATGTACAATCA 57.156 29.630 14.60 14.18 0.00 2.57
4290 8063 4.398988 ACAATCATGTACATTTGCACCGAT 59.601 37.500 16.68 8.07 38.24 4.18
4326 8134 1.464997 GAAAAAGGCGAACATCGAGCT 59.535 47.619 3.61 0.00 43.74 4.09
4397 8205 3.532232 AGTAGGGGTCAGGATCTTCTACA 59.468 47.826 12.44 0.00 0.00 2.74
4525 8333 4.959839 ACCACACTTCACACCCTTAATTTT 59.040 37.500 0.00 0.00 0.00 1.82
4526 8334 5.163457 ACCACACTTCACACCCTTAATTTTG 60.163 40.000 0.00 0.00 0.00 2.44
4642 8451 5.800296 ACATAATGCCAAAAAGTTTACCCC 58.200 37.500 0.00 0.00 0.00 4.95
4778 8709 3.821033 AGTTTGTGATGTGGCCTCTAAAC 59.179 43.478 3.32 9.50 0.00 2.01
4787 8718 2.083774 TGGCCTCTAAACAGCAATTCG 58.916 47.619 3.32 0.00 0.00 3.34
5002 8936 8.900511 ACAAATCTCATGTTATGAATCAAACG 57.099 30.769 0.00 0.00 39.11 3.60
5028 8962 9.635404 GACATCTCTATAGCCTATAGGTATTGT 57.365 37.037 20.10 14.50 39.80 2.71
5054 9051 7.781219 TCATACATGTCATCTGATTTCCCAAAT 59.219 33.333 0.00 0.00 0.00 2.32
5055 9052 6.862469 ACATGTCATCTGATTTCCCAAATT 57.138 33.333 0.00 0.00 0.00 1.82
5073 9070 8.695456 TCCCAAATTTTCTTATTCTATCCAAGC 58.305 33.333 0.00 0.00 0.00 4.01
5075 9072 9.874205 CCAAATTTTCTTATTCTATCCAAGCAA 57.126 29.630 0.00 0.00 0.00 3.91
5079 9076 8.877864 TTTTCTTATTCTATCCAAGCAAAGGA 57.122 30.769 0.00 0.00 39.97 3.36
5101 9098 2.103094 GGCCTTCCTTTTGATATTGGGC 59.897 50.000 0.00 0.00 36.70 5.36
5113 9110 1.230074 TATTGGGCCCCATCATGACA 58.770 50.000 22.27 0.00 31.53 3.58
5147 9161 2.874701 GCAAACAGAGAAGTTCTCAGCA 59.125 45.455 29.85 0.00 45.73 4.41
5148 9162 3.059051 GCAAACAGAGAAGTTCTCAGCAG 60.059 47.826 29.85 19.58 45.73 4.24
5189 9203 0.106894 CCAAGCCCGATTCCTACTCC 59.893 60.000 0.00 0.00 0.00 3.85
5190 9204 0.249489 CAAGCCCGATTCCTACTCCG 60.249 60.000 0.00 0.00 0.00 4.63
5191 9205 0.396695 AAGCCCGATTCCTACTCCGA 60.397 55.000 0.00 0.00 0.00 4.55
5192 9206 0.824182 AGCCCGATTCCTACTCCGAG 60.824 60.000 0.00 0.00 0.00 4.63
5193 9207 0.822532 GCCCGATTCCTACTCCGAGA 60.823 60.000 1.33 0.00 0.00 4.04
5194 9208 0.953003 CCCGATTCCTACTCCGAGAC 59.047 60.000 1.33 0.00 0.00 3.36
5195 9209 1.676746 CCGATTCCTACTCCGAGACA 58.323 55.000 1.33 0.00 0.00 3.41
5196 9210 1.604755 CCGATTCCTACTCCGAGACAG 59.395 57.143 1.33 0.00 0.00 3.51
5197 9211 1.604755 CGATTCCTACTCCGAGACAGG 59.395 57.143 1.33 8.27 0.00 4.00
5198 9212 2.657143 GATTCCTACTCCGAGACAGGT 58.343 52.381 15.87 3.46 0.00 4.00
5199 9213 1.835494 TTCCTACTCCGAGACAGGTG 58.165 55.000 15.87 0.00 0.00 4.00
5200 9214 0.697079 TCCTACTCCGAGACAGGTGT 59.303 55.000 15.87 0.57 40.60 4.16
5201 9215 1.911357 TCCTACTCCGAGACAGGTGTA 59.089 52.381 15.87 1.58 38.71 2.90
5202 9216 2.015587 CCTACTCCGAGACAGGTGTAC 58.984 57.143 1.33 0.00 38.71 2.90
5203 9217 1.664659 CTACTCCGAGACAGGTGTACG 59.335 57.143 1.33 3.26 38.71 3.67
5204 9218 0.959372 ACTCCGAGACAGGTGTACGG 60.959 60.000 16.96 16.96 43.87 4.02
5205 9219 2.181021 CCGAGACAGGTGTACGGC 59.819 66.667 12.88 0.00 39.62 5.68
5206 9220 2.202440 CGAGACAGGTGTACGGCG 60.202 66.667 4.80 4.80 0.00 6.46
5207 9221 2.181021 GAGACAGGTGTACGGCGG 59.819 66.667 13.24 0.00 0.00 6.13
5208 9222 3.352338 GAGACAGGTGTACGGCGGG 62.352 68.421 13.24 0.00 0.00 6.13
5209 9223 3.376078 GACAGGTGTACGGCGGGA 61.376 66.667 13.24 0.00 0.00 5.14
5210 9224 3.352338 GACAGGTGTACGGCGGGAG 62.352 68.421 13.24 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.304614 TGATAAACATGCTAGGTACTCCCTC 59.695 44.000 0.00 0.00 44.81 4.30
1 2 5.846714 ATGATAAACATGCTAGGTACTCCCT 59.153 40.000 0.00 0.00 41.62 4.20
2 3 5.546621 TGATAAACATGCTAGGTACTCCC 57.453 43.478 0.00 0.00 41.75 4.30
31 32 9.113876 GTTTCTCAATGTTCATACCGTAAAAAG 57.886 33.333 0.00 0.00 0.00 2.27
44 45 9.055248 CAATTACTTCATCGTTTCTCAATGTTC 57.945 33.333 0.00 0.00 0.00 3.18
47 48 6.470235 GCCAATTACTTCATCGTTTCTCAATG 59.530 38.462 0.00 0.00 0.00 2.82
89 90 6.761242 TCAAACCATTCTACGAGTATTCATGG 59.239 38.462 11.13 11.13 36.54 3.66
109 110 1.751437 GTCTATGGGGCAGGTCAAAC 58.249 55.000 0.00 0.00 0.00 2.93
116 117 1.173043 TTTTTGCGTCTATGGGGCAG 58.827 50.000 0.00 0.00 38.04 4.85
117 118 1.748493 GATTTTTGCGTCTATGGGGCA 59.252 47.619 0.00 0.00 34.35 5.36
119 120 3.278574 TCAGATTTTTGCGTCTATGGGG 58.721 45.455 0.00 0.00 0.00 4.96
121 122 7.541783 TGAATTTTCAGATTTTTGCGTCTATGG 59.458 33.333 0.00 0.00 32.50 2.74
129 130 7.179410 ACGTTGTTGAATTTTCAGATTTTTGC 58.821 30.769 0.00 0.00 38.61 3.68
131 132 8.716909 ACAACGTTGTTGAATTTTCAGATTTTT 58.283 25.926 27.70 0.00 38.47 1.94
258 261 4.242475 TGCACTGTGGATAAACGAGTTAG 58.758 43.478 10.21 0.00 0.00 2.34
306 309 1.414550 GAGGGAAGAAGAAGGGATCGG 59.585 57.143 0.00 0.00 0.00 4.18
308 311 2.158827 GCAGAGGGAAGAAGAAGGGATC 60.159 54.545 0.00 0.00 0.00 3.36
323 330 5.879223 ACAATAAGAGAATGTGAAGCAGAGG 59.121 40.000 0.00 0.00 0.00 3.69
364 371 2.864343 CGAAAGTTGGTTCAGAACTCGT 59.136 45.455 13.13 0.80 32.33 4.18
397 404 5.320549 AGCTCGAAAAATAGTACTTCCGA 57.679 39.130 0.00 1.19 0.00 4.55
424 766 2.279741 CGCTGGCTTTGTTATGCTAGA 58.720 47.619 0.00 0.00 39.63 2.43
517 3959 2.156098 GATTCTGCCGGGTTTGTTACA 58.844 47.619 2.18 0.00 0.00 2.41
602 4050 1.287191 GAGATGCGCTGGCGAGATA 59.713 57.895 19.31 1.99 44.10 1.98
627 4075 1.459455 CGACGAGGAGGATGATGGCT 61.459 60.000 0.00 0.00 0.00 4.75
638 4086 2.868196 CGAGCAAGACGACGAGGA 59.132 61.111 0.00 0.00 0.00 3.71
640 4088 1.865622 GAGCGAGCAAGACGACGAG 60.866 63.158 0.00 0.00 0.00 4.18
723 4171 1.594293 CATTCCTTATCCGCGGCGT 60.594 57.895 23.51 14.55 0.00 5.68
1034 4486 2.391389 CGCGGGAGAAGACTTTGGC 61.391 63.158 0.00 0.00 0.00 4.52
1047 4499 0.645868 GAGACGAAGAAAATCGCGGG 59.354 55.000 6.13 0.00 46.51 6.13
1102 4554 5.277250 TCATACCTCTACAGAATCCCAACA 58.723 41.667 0.00 0.00 0.00 3.33
1132 4584 0.179089 AAGCGCCAGAGAGTAGCATG 60.179 55.000 2.29 0.00 0.00 4.06
1231 4683 3.879892 GACAAACTTCTCCAGGGCATATC 59.120 47.826 0.00 0.00 0.00 1.63
1330 4782 9.139734 ACATGCAGTATCATTCCTTATTCAATT 57.860 29.630 0.00 0.00 0.00 2.32
1331 4783 8.573885 CACATGCAGTATCATTCCTTATTCAAT 58.426 33.333 0.00 0.00 0.00 2.57
1332 4784 7.557358 ACACATGCAGTATCATTCCTTATTCAA 59.443 33.333 0.00 0.00 0.00 2.69
1333 4785 7.056006 ACACATGCAGTATCATTCCTTATTCA 58.944 34.615 0.00 0.00 0.00 2.57
1334 4786 7.502120 ACACATGCAGTATCATTCCTTATTC 57.498 36.000 0.00 0.00 0.00 1.75
1338 4790 5.503927 AGAACACATGCAGTATCATTCCTT 58.496 37.500 0.00 0.00 0.00 3.36
1340 4792 5.237344 GGTAGAACACATGCAGTATCATTCC 59.763 44.000 0.00 0.00 0.00 3.01
1341 4793 5.050769 CGGTAGAACACATGCAGTATCATTC 60.051 44.000 0.00 0.00 0.00 2.67
1342 4794 4.811024 CGGTAGAACACATGCAGTATCATT 59.189 41.667 0.00 0.00 0.00 2.57
1343 4795 4.371786 CGGTAGAACACATGCAGTATCAT 58.628 43.478 0.00 0.00 0.00 2.45
1344 4796 3.430236 CCGGTAGAACACATGCAGTATCA 60.430 47.826 0.00 0.00 0.00 2.15
1345 4797 3.123804 CCGGTAGAACACATGCAGTATC 58.876 50.000 0.00 0.00 0.00 2.24
1346 4798 2.764010 TCCGGTAGAACACATGCAGTAT 59.236 45.455 0.00 0.00 0.00 2.12
1347 4799 2.172679 TCCGGTAGAACACATGCAGTA 58.827 47.619 0.00 0.00 0.00 2.74
1348 4800 0.973632 TCCGGTAGAACACATGCAGT 59.026 50.000 0.00 0.00 0.00 4.40
1364 4816 2.050477 AAAGCAAAGCGTCATTTCCG 57.950 45.000 0.00 0.00 0.00 4.30
1366 4818 4.795278 CCAGATAAAGCAAAGCGTCATTTC 59.205 41.667 0.00 0.00 0.00 2.17
1367 4819 4.218417 ACCAGATAAAGCAAAGCGTCATTT 59.782 37.500 0.00 0.00 0.00 2.32
1368 4820 3.758554 ACCAGATAAAGCAAAGCGTCATT 59.241 39.130 0.00 0.00 0.00 2.57
1369 4821 3.347216 ACCAGATAAAGCAAAGCGTCAT 58.653 40.909 0.00 0.00 0.00 3.06
1370 4822 2.778299 ACCAGATAAAGCAAAGCGTCA 58.222 42.857 0.00 0.00 0.00 4.35
1371 4823 3.831715 AACCAGATAAAGCAAAGCGTC 57.168 42.857 0.00 0.00 0.00 5.19
1373 4825 3.191371 AGGAAACCAGATAAAGCAAAGCG 59.809 43.478 0.00 0.00 0.00 4.68
1375 4827 6.986250 AGAAAGGAAACCAGATAAAGCAAAG 58.014 36.000 0.00 0.00 0.00 2.77
1386 4850 3.699038 TGACAACCAAGAAAGGAAACCAG 59.301 43.478 0.00 0.00 0.00 4.00
1394 4858 7.930217 TCTTAACTTGATGACAACCAAGAAAG 58.070 34.615 20.85 20.15 41.56 2.62
1399 4863 7.502226 ACAGAATCTTAACTTGATGACAACCAA 59.498 33.333 0.00 0.00 32.27 3.67
1414 4878 5.499313 TGGACATGATGCACAGAATCTTAA 58.501 37.500 0.00 0.00 0.00 1.85
1415 4879 5.101648 TGGACATGATGCACAGAATCTTA 57.898 39.130 0.00 0.00 0.00 2.10
1416 4880 3.959293 TGGACATGATGCACAGAATCTT 58.041 40.909 0.00 0.00 0.00 2.40
1420 4884 2.815503 CACTTGGACATGATGCACAGAA 59.184 45.455 0.00 0.00 0.00 3.02
1422 4886 2.156917 ACACTTGGACATGATGCACAG 58.843 47.619 0.00 0.00 0.00 3.66
1426 4890 2.417933 GACAGACACTTGGACATGATGC 59.582 50.000 0.00 0.00 0.00 3.91
1431 4895 7.624549 ACTATATTTGACAGACACTTGGACAT 58.375 34.615 0.00 0.00 0.00 3.06
1453 4918 9.169592 ACAAAGCTTTCAAGTTACAACTAACTA 57.830 29.630 9.23 0.00 41.58 2.24
1454 4919 8.051901 ACAAAGCTTTCAAGTTACAACTAACT 57.948 30.769 9.23 0.00 43.87 2.24
1477 4942 7.121168 GTGATGGTGATTATTCAGGAAAGAACA 59.879 37.037 0.00 0.00 30.85 3.18
1498 4963 6.324512 TCATTTATCTTGGGGAAATGGTGATG 59.675 38.462 6.70 0.00 39.79 3.07
1578 5043 6.687105 CGTCTTTCGATTACATTTTCCAATCC 59.313 38.462 0.00 0.00 42.86 3.01
1599 5065 6.712276 AGAACTTAAATCTGAATTCCCGTCT 58.288 36.000 2.27 0.00 0.00 4.18
1629 5095 2.879103 TTCTCCCCAGTGACCATTTC 57.121 50.000 0.00 0.00 0.00 2.17
1637 5103 1.545651 GGGTGTCTTTTCTCCCCAGTG 60.546 57.143 0.00 0.00 35.72 3.66
1643 5109 0.251209 GGTGGGGGTGTCTTTTCTCC 60.251 60.000 0.00 0.00 0.00 3.71
1644 5110 0.771755 AGGTGGGGGTGTCTTTTCTC 59.228 55.000 0.00 0.00 0.00 2.87
1645 5111 0.478507 CAGGTGGGGGTGTCTTTTCT 59.521 55.000 0.00 0.00 0.00 2.52
1646 5112 0.476771 TCAGGTGGGGGTGTCTTTTC 59.523 55.000 0.00 0.00 0.00 2.29
1647 5113 0.930726 TTCAGGTGGGGGTGTCTTTT 59.069 50.000 0.00 0.00 0.00 2.27
1648 5114 0.478507 CTTCAGGTGGGGGTGTCTTT 59.521 55.000 0.00 0.00 0.00 2.52
1649 5115 0.697854 ACTTCAGGTGGGGGTGTCTT 60.698 55.000 0.00 0.00 0.00 3.01
1650 5116 0.192566 TACTTCAGGTGGGGGTGTCT 59.807 55.000 0.00 0.00 0.00 3.41
1651 5117 1.286248 ATACTTCAGGTGGGGGTGTC 58.714 55.000 0.00 0.00 0.00 3.67
1652 5118 2.653543 TATACTTCAGGTGGGGGTGT 57.346 50.000 0.00 0.00 0.00 4.16
1653 5119 4.080015 TGAAATATACTTCAGGTGGGGGTG 60.080 45.833 0.00 0.00 31.67 4.61
1654 5120 4.116113 TGAAATATACTTCAGGTGGGGGT 58.884 43.478 0.00 0.00 31.67 4.95
1655 5121 4.788925 TGAAATATACTTCAGGTGGGGG 57.211 45.455 0.00 0.00 31.67 5.40
1656 5122 6.889722 TCTTTTGAAATATACTTCAGGTGGGG 59.110 38.462 0.00 0.00 36.69 4.96
1657 5123 7.938140 TCTTTTGAAATATACTTCAGGTGGG 57.062 36.000 0.00 0.00 36.69 4.61
1692 5158 5.704515 AGGACAACAGACAGATTTCATCTTG 59.295 40.000 0.00 0.00 37.58 3.02
1842 5309 0.898320 TCTTCCTCTTCCGCCTTGAG 59.102 55.000 0.00 0.00 0.00 3.02
1925 5392 0.261402 CCATAATTCCAGCCCCCACA 59.739 55.000 0.00 0.00 0.00 4.17
1952 5419 3.118298 TGCCTAGCATCTTGATACTTGCA 60.118 43.478 0.00 0.00 37.56 4.08
2191 5658 1.578583 AACAGAAAAGGGTCGTGTCG 58.421 50.000 0.00 0.00 0.00 4.35
2221 5709 8.408601 GCCAATTACATTACAACTCTTGATGAT 58.591 33.333 0.00 0.00 0.00 2.45
2222 5710 7.392953 TGCCAATTACATTACAACTCTTGATGA 59.607 33.333 0.00 0.00 0.00 2.92
2223 5711 7.537715 TGCCAATTACATTACAACTCTTGATG 58.462 34.615 0.00 0.00 0.00 3.07
2224 5712 7.394359 ACTGCCAATTACATTACAACTCTTGAT 59.606 33.333 0.00 0.00 0.00 2.57
2225 5713 6.714810 ACTGCCAATTACATTACAACTCTTGA 59.285 34.615 0.00 0.00 0.00 3.02
2226 5714 6.913170 ACTGCCAATTACATTACAACTCTTG 58.087 36.000 0.00 0.00 0.00 3.02
2227 5715 8.807948 ATACTGCCAATTACATTACAACTCTT 57.192 30.769 0.00 0.00 0.00 2.85
2228 5716 9.326413 GTATACTGCCAATTACATTACAACTCT 57.674 33.333 0.00 0.00 0.00 3.24
2229 5717 8.273557 CGTATACTGCCAATTACATTACAACTC 58.726 37.037 0.56 0.00 0.00 3.01
2230 5718 7.767198 ACGTATACTGCCAATTACATTACAACT 59.233 33.333 0.56 0.00 0.00 3.16
2231 5719 7.912383 ACGTATACTGCCAATTACATTACAAC 58.088 34.615 0.56 0.00 0.00 3.32
2232 5720 8.495361 AACGTATACTGCCAATTACATTACAA 57.505 30.769 0.56 0.00 0.00 2.41
2233 5721 7.764901 TGAACGTATACTGCCAATTACATTACA 59.235 33.333 0.56 0.00 0.00 2.41
2234 5722 8.133754 TGAACGTATACTGCCAATTACATTAC 57.866 34.615 0.56 0.00 0.00 1.89
2235 5723 7.439955 CCTGAACGTATACTGCCAATTACATTA 59.560 37.037 0.56 0.00 0.00 1.90
2236 5724 6.260050 CCTGAACGTATACTGCCAATTACATT 59.740 38.462 0.56 0.00 0.00 2.71
2237 5725 5.758296 CCTGAACGTATACTGCCAATTACAT 59.242 40.000 0.56 0.00 0.00 2.29
2238 5726 5.113383 CCTGAACGTATACTGCCAATTACA 58.887 41.667 0.56 0.00 0.00 2.41
2239 5727 5.006358 CACCTGAACGTATACTGCCAATTAC 59.994 44.000 0.56 0.00 0.00 1.89
2281 5769 8.495160 TCCAAGGATTCCATATTATGCAATTT 57.505 30.769 5.29 0.00 0.00 1.82
2362 6045 7.476667 CAGTGAACCAAATAAGTGTTGTAACA 58.523 34.615 0.00 0.00 36.38 2.41
2364 6047 6.500041 GCAGTGAACCAAATAAGTGTTGTAA 58.500 36.000 0.00 0.00 0.00 2.41
2367 6050 3.974401 CGCAGTGAACCAAATAAGTGTTG 59.026 43.478 0.00 0.00 0.00 3.33
2408 6091 5.696270 GGAAACCCAACATCAATGAAAAGAC 59.304 40.000 0.00 0.00 0.00 3.01
2504 6191 5.056480 CGCCATCTAATACATCACTTGGAA 58.944 41.667 0.00 0.00 0.00 3.53
2560 6248 8.818622 ATAAGGACCCAACTATTTCCTAAAAC 57.181 34.615 0.00 0.00 37.51 2.43
2615 6303 5.886960 AAAGATGAACAGGCAGTATGAAC 57.113 39.130 0.00 0.00 39.69 3.18
2618 6306 5.183713 TGGAAAAAGATGAACAGGCAGTATG 59.816 40.000 0.00 0.00 40.87 2.39
2657 6346 4.102524 TGAACACCAGTTGTAGATGTTCCT 59.897 41.667 11.66 0.00 45.50 3.36
2720 6409 2.767505 ACAACTGGACGAGAATTCCAC 58.232 47.619 0.65 0.00 38.28 4.02
2860 6549 5.127491 CCAAAGATGCCCCGTTAGTATTTA 58.873 41.667 0.00 0.00 0.00 1.40
2863 6552 2.748465 GCCAAAGATGCCCCGTTAGTAT 60.748 50.000 0.00 0.00 0.00 2.12
2873 6562 1.669999 AATCTGCGGCCAAAGATGCC 61.670 55.000 15.99 0.00 45.70 4.40
2915 6604 1.108727 CCACAGCAAGGGCAACTGAA 61.109 55.000 0.00 0.00 44.61 3.02
3190 6879 5.594725 ACTTCTATCTTCCAGCTCGTTATCA 59.405 40.000 0.00 0.00 0.00 2.15
3382 7071 5.696030 ACATGGACTACATAGCTCACTCTA 58.304 41.667 0.00 0.00 37.84 2.43
3672 7361 0.672401 ACCTACAAACATCGGGCACG 60.672 55.000 0.00 0.00 42.74 5.34
3706 7395 6.034577 CGAGCAGAATAAAGTTATCGAACACA 59.965 38.462 0.00 0.00 38.10 3.72
3713 7402 8.443937 AGAAACAACGAGCAGAATAAAGTTATC 58.556 33.333 0.00 0.00 0.00 1.75
3731 7420 6.127619 CCCATAAGAATCCCTGAAGAAACAAC 60.128 42.308 0.00 0.00 0.00 3.32
3917 7606 1.536766 CACTCCGAATTGTGCATGTGT 59.463 47.619 0.00 0.00 0.00 3.72
4016 7789 3.243501 TGCAGCAAACAAAATCCTCTCAC 60.244 43.478 0.00 0.00 0.00 3.51
4168 7941 9.293404 ACATCCATTTCAAGATGATCGAATATT 57.707 29.630 6.98 0.00 42.04 1.28
4266 8039 4.938226 TCGGTGCAAATGTACATGATTGTA 59.062 37.500 17.46 12.49 37.28 2.41
4267 8040 3.755905 TCGGTGCAAATGTACATGATTGT 59.244 39.130 17.46 0.00 39.98 2.71
4268 8041 4.354071 TCGGTGCAAATGTACATGATTG 57.646 40.909 9.63 12.09 32.02 2.67
4269 8042 4.398988 ACATCGGTGCAAATGTACATGATT 59.601 37.500 9.63 0.00 34.42 2.57
4270 8043 3.947196 ACATCGGTGCAAATGTACATGAT 59.053 39.130 9.63 3.01 34.42 2.45
4271 8044 3.342719 ACATCGGTGCAAATGTACATGA 58.657 40.909 9.63 0.45 34.42 3.07
4272 8045 3.763097 ACATCGGTGCAAATGTACATG 57.237 42.857 9.63 0.00 34.42 3.21
4273 8046 4.782019 AAACATCGGTGCAAATGTACAT 57.218 36.364 1.41 1.41 35.10 2.29
4274 8047 4.576216 AAAACATCGGTGCAAATGTACA 57.424 36.364 10.12 0.00 35.10 2.90
4290 8063 4.381079 CCTTTTTCACGGGTGAGAAAAACA 60.381 41.667 15.51 0.00 44.32 2.83
4326 8134 0.970640 TAGTCGTGCCTAGGTTTGCA 59.029 50.000 11.31 0.00 34.54 4.08
4397 8205 6.500751 TCAAAGTTTCTCTACCTAATGGGACT 59.499 38.462 0.00 0.00 38.76 3.85
4620 8429 5.799213 TGGGGTAAACTTTTTGGCATTATG 58.201 37.500 0.00 0.00 0.00 1.90
4654 8585 2.159627 GGTGAGCACGACAACCTATTTG 59.840 50.000 0.00 0.00 41.49 2.32
4778 8709 4.201485 GCGTTTTTATTGACCGAATTGCTG 60.201 41.667 0.00 0.00 0.00 4.41
4787 8718 5.163784 GGAGACCTAAGCGTTTTTATTGACC 60.164 44.000 0.00 0.00 0.00 4.02
4893 8825 9.381033 CTAGATAGGAATAGCAATCCATTCTTG 57.619 37.037 5.41 4.42 39.55 3.02
4894 8826 9.331466 TCTAGATAGGAATAGCAATCCATTCTT 57.669 33.333 5.41 0.00 39.55 2.52
5002 8936 9.635404 ACAATACCTATAGGCTATAGAGATGTC 57.365 37.037 33.23 0.00 40.43 3.06
5028 8962 6.251255 TGGGAAATCAGATGACATGTATGA 57.749 37.500 0.00 1.48 0.00 2.15
5054 9051 8.877864 TCCTTTGCTTGGATAGAATAAGAAAA 57.122 30.769 0.00 0.00 30.43 2.29
5055 9052 7.557719 CCTCCTTTGCTTGGATAGAATAAGAAA 59.442 37.037 0.00 0.00 32.56 2.52
5066 9063 0.411058 AAGGCCTCCTTTGCTTGGAT 59.589 50.000 5.23 0.00 41.69 3.41
5067 9064 0.251341 GAAGGCCTCCTTTGCTTGGA 60.251 55.000 5.23 0.00 44.82 3.53
5068 9065 1.253593 GGAAGGCCTCCTTTGCTTGG 61.254 60.000 5.23 0.00 44.82 3.61
5069 9066 2.270959 GGAAGGCCTCCTTTGCTTG 58.729 57.895 5.23 0.00 44.82 4.01
5070 9067 4.852388 GGAAGGCCTCCTTTGCTT 57.148 55.556 5.23 0.00 44.82 3.91
5077 9074 3.638627 CCAATATCAAAAGGAAGGCCTCC 59.361 47.826 5.23 9.66 46.28 4.30
5078 9075 3.638627 CCCAATATCAAAAGGAAGGCCTC 59.361 47.826 5.23 0.00 46.28 4.70
5088 9085 3.411454 TGATGGGGCCCAATATCAAAA 57.589 42.857 32.57 4.05 36.95 2.44
5092 9089 2.225091 TGTCATGATGGGGCCCAATATC 60.225 50.000 32.57 23.36 36.95 1.63
5101 9098 1.152819 CTGGGCTGTCATGATGGGG 60.153 63.158 0.00 0.00 0.00 4.96
5113 9110 1.329171 TGTTTGCAGTTTGCTGGGCT 61.329 50.000 2.48 0.00 45.31 5.19
5129 9126 3.894427 TCTCTGCTGAGAACTTCTCTGTT 59.106 43.478 19.80 0.00 45.42 3.16
5147 9161 1.589113 GTTCGCCTGTCTGCTCTCT 59.411 57.895 0.00 0.00 0.00 3.10
5148 9162 1.803519 CGTTCGCCTGTCTGCTCTC 60.804 63.158 0.00 0.00 0.00 3.20
5189 9203 2.202440 CGCCGTACACCTGTCTCG 60.202 66.667 0.00 0.00 0.00 4.04
5190 9204 2.181021 CCGCCGTACACCTGTCTC 59.819 66.667 0.00 0.00 0.00 3.36
5191 9205 3.379445 CCCGCCGTACACCTGTCT 61.379 66.667 0.00 0.00 0.00 3.41
5192 9206 3.352338 CTCCCGCCGTACACCTGTC 62.352 68.421 0.00 0.00 0.00 3.51
5193 9207 3.379445 CTCCCGCCGTACACCTGT 61.379 66.667 0.00 0.00 0.00 4.00
5194 9208 4.814294 GCTCCCGCCGTACACCTG 62.814 72.222 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.