Multiple sequence alignment - TraesCS3A01G025800

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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 TraesCS3A01G025800 chr3A 100.000 4412 0 0 1 4412 13521638 13517227 0.000000e+00 8148.0
1 TraesCS3A01G025800 chr3A 88.365 318 22 7 1440 1755 5993236 5992932 6.970000e-98 368.0
2 TraesCS3A01G025800 chr3A 83.453 278 28 10 979 1241 668027205 668026931 4.410000e-60 243.0
3 TraesCS3A01G025800 chr3B 88.832 4522 290 95 1 4412 8129751 8134167 0.000000e+00 5354.0
4 TraesCS3A01G025800 chr3B 80.682 88 16 1 1158 1245 36492519 36492605 2.850000e-07 67.6
5 TraesCS3A01G025800 chr3D 88.198 4389 303 103 168 4412 6726482 6730799 0.000000e+00 5036.0
6 TraesCS3A01G025800 chr3D 89.373 367 19 6 1386 1752 57606517 57606863 1.130000e-120 444.0
7 TraesCS3A01G025800 chr3D 87.908 306 17 4 4107 4412 47796446 47796731 4.230000e-90 342.0
8 TraesCS3A01G025800 chr3D 89.338 272 14 4 1386 1657 330477815 330477559 1.180000e-85 327.0
9 TraesCS3A01G025800 chr6D 89.459 370 21 5 1386 1755 46527940 46527589 6.730000e-123 451.0
10 TraesCS3A01G025800 chr7D 89.189 370 22 6 1383 1752 103531832 103532183 3.130000e-121 446.0
11 TraesCS3A01G025800 chr4A 89.189 370 22 5 1386 1755 433610654 433610303 3.130000e-121 446.0
12 TraesCS3A01G025800 chr2D 88.828 367 23 5 1386 1752 397123024 397123372 6.780000e-118 435.0
13 TraesCS3A01G025800 chr5D 88.378 370 25 5 1386 1755 16496914 16496563 3.150000e-116 429.0
14 TraesCS3A01G025800 chr4D 88.378 370 25 5 1386 1755 222630757 222630406 3.150000e-116 429.0
15 TraesCS3A01G025800 chr6A 90.566 265 13 3 1488 1752 136654996 136655248 1.520000e-89 340.0
16 TraesCS3A01G025800 chr6A 82.734 278 30 9 979 1241 577803254 577802980 9.540000e-57 231.0
17 TraesCS3A01G025800 chr6B 84.946 93 13 1 158 249 93823954 93824046 4.700000e-15 93.5
18 TraesCS3A01G025800 chr1B 82.955 88 14 1 1158 1245 630060653 630060739 1.320000e-10 78.7
19 TraesCS3A01G025800 chr7B 80.220 91 11 6 1158 1245 253370891 253370977 1.330000e-05 62.1


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 TraesCS3A01G025800 chr3A 13517227 13521638 4411 True 8148 8148 100.000 1 4412 1 chr3A.!!$R2 4411
1 TraesCS3A01G025800 chr3B 8129751 8134167 4416 False 5354 5354 88.832 1 4412 1 chr3B.!!$F1 4411
2 TraesCS3A01G025800 chr3D 6726482 6730799 4317 False 5036 5036 88.198 168 4412 1 chr3D.!!$F1 4244

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
161 170 0.038166 TTTCTCCATTGCGCTTCCCT 59.962 50.0 9.73 0.00 0.00 4.20 F
162 171 0.038166 TTCTCCATTGCGCTTCCCTT 59.962 50.0 9.73 0.00 0.00 3.95 F
850 914 0.110486 TTGGGACCTGCAAGTTCCTC 59.890 55.0 14.11 2.75 36.24 3.71 F
2181 2333 0.179119 GGTCGATTACACCGGTGGAG 60.179 60.0 36.47 18.50 34.19 3.86 F
2274 2429 0.321564 CAATGAGAAGGGCGACACCA 60.322 55.0 0.00 0.00 42.05 4.17 F
3334 3533 0.040870 CGAGGATGAGGACGATGACG 60.041 60.0 0.00 0.00 45.75 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1786 2.362077 GGCAAGTCAAAACCACACTCAT 59.638 45.455 0.0 0.00 0.00 2.90 R
1774 1883 2.751806 CCTGAGATTGCTGACCCTTTTC 59.248 50.000 0.0 0.00 0.00 2.29 R
2225 2380 0.746063 GGATGCATTTTCGATGGGCA 59.254 50.000 0.0 4.42 39.03 5.36 R
3333 3532 0.171455 CCTCTTCTTCCACCTCGTCG 59.829 60.000 0.0 0.00 0.00 5.12 R
3339 3538 0.462759 CGGCATCCTCTTCTTCCACC 60.463 60.000 0.0 0.00 0.00 4.61 R
4225 4449 1.432514 TGAGAAAGATGACTGCGTGC 58.567 50.000 0.0 0.00 0.00 5.34 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
31 32 2.181196 CCTATTCCCCTTCCTCTCCTCT 59.819 54.545 0.00 0.00 0.00 3.69
35 36 0.692756 CCCCTTCCTCTCCTCTTCCC 60.693 65.000 0.00 0.00 0.00 3.97
39 40 0.800239 TTCCTCTCCTCTTCCCCCTT 59.200 55.000 0.00 0.00 0.00 3.95
40 41 0.043334 TCCTCTCCTCTTCCCCCTTG 59.957 60.000 0.00 0.00 0.00 3.61
42 43 1.616628 TCTCCTCTTCCCCCTTGCC 60.617 63.158 0.00 0.00 0.00 4.52
43 44 1.617839 CTCCTCTTCCCCCTTGCCT 60.618 63.158 0.00 0.00 0.00 4.75
44 45 1.151587 TCCTCTTCCCCCTTGCCTT 60.152 57.895 0.00 0.00 0.00 4.35
45 46 1.000396 CCTCTTCCCCCTTGCCTTG 60.000 63.158 0.00 0.00 0.00 3.61
46 47 1.680314 CTCTTCCCCCTTGCCTTGC 60.680 63.158 0.00 0.00 0.00 4.01
48 49 3.868200 CTTCCCCCTTGCCTTGCGT 62.868 63.158 0.00 0.00 0.00 5.24
49 50 3.444818 TTCCCCCTTGCCTTGCGTT 62.445 57.895 0.00 0.00 0.00 4.84
51 52 2.650778 CCCCTTGCCTTGCGTTTC 59.349 61.111 0.00 0.00 0.00 2.78
52 53 2.650778 CCCTTGCCTTGCGTTTCC 59.349 61.111 0.00 0.00 0.00 3.13
53 54 1.903404 CCCTTGCCTTGCGTTTCCT 60.903 57.895 0.00 0.00 0.00 3.36
57 58 0.108585 TTGCCTTGCGTTTCCTCTCT 59.891 50.000 0.00 0.00 0.00 3.10
58 59 0.108585 TGCCTTGCGTTTCCTCTCTT 59.891 50.000 0.00 0.00 0.00 2.85
59 60 0.519077 GCCTTGCGTTTCCTCTCTTG 59.481 55.000 0.00 0.00 0.00 3.02
65 66 2.070028 GCGTTTCCTCTCTTGTCTTCC 58.930 52.381 0.00 0.00 0.00 3.46
79 80 7.176690 TCTCTTGTCTTCCAATTTAAATCCCAC 59.823 37.037 0.10 0.00 31.20 4.61
81 82 5.317808 TGTCTTCCAATTTAAATCCCACGA 58.682 37.500 0.10 0.00 0.00 4.35
86 87 4.398044 TCCAATTTAAATCCCACGAGAAGC 59.602 41.667 0.10 0.00 0.00 3.86
92 93 0.539051 ATCCCACGAGAAGCAAGGAG 59.461 55.000 0.00 0.00 0.00 3.69
93 94 0.541998 TCCCACGAGAAGCAAGGAGA 60.542 55.000 0.00 0.00 0.00 3.71
94 95 0.321671 CCCACGAGAAGCAAGGAGAA 59.678 55.000 0.00 0.00 0.00 2.87
95 96 1.270839 CCCACGAGAAGCAAGGAGAAA 60.271 52.381 0.00 0.00 0.00 2.52
96 97 2.072298 CCACGAGAAGCAAGGAGAAAG 58.928 52.381 0.00 0.00 0.00 2.62
97 98 2.289072 CCACGAGAAGCAAGGAGAAAGA 60.289 50.000 0.00 0.00 0.00 2.52
98 99 3.393800 CACGAGAAGCAAGGAGAAAGAA 58.606 45.455 0.00 0.00 0.00 2.52
101 102 4.202264 ACGAGAAGCAAGGAGAAAGAAAGA 60.202 41.667 0.00 0.00 0.00 2.52
105 106 6.360618 AGAAGCAAGGAGAAAGAAAGAAAGA 58.639 36.000 0.00 0.00 0.00 2.52
109 110 6.830838 AGCAAGGAGAAAGAAAGAAAGAAAGA 59.169 34.615 0.00 0.00 0.00 2.52
113 114 9.467796 AAGGAGAAAGAAAGAAAGAAAGAAAGA 57.532 29.630 0.00 0.00 0.00 2.52
126 127 6.508030 AGAAAGAAAGAAAGAAGAGGAGGT 57.492 37.500 0.00 0.00 0.00 3.85
128 129 5.896073 AAGAAAGAAAGAAGAGGAGGTGA 57.104 39.130 0.00 0.00 0.00 4.02
129 130 5.222079 AGAAAGAAAGAAGAGGAGGTGAC 57.778 43.478 0.00 0.00 0.00 3.67
132 133 3.850752 AGAAAGAAGAGGAGGTGACTGA 58.149 45.455 0.00 0.00 44.43 3.41
134 135 2.990740 AGAAGAGGAGGTGACTGAGT 57.009 50.000 0.00 0.00 44.43 3.41
138 139 1.133325 AGAGGAGGTGACTGAGTGTGT 60.133 52.381 0.00 0.00 44.43 3.72
140 141 2.103263 GAGGAGGTGACTGAGTGTGTTT 59.897 50.000 0.00 0.00 44.43 2.83
159 168 1.453155 TCTTTCTCCATTGCGCTTCC 58.547 50.000 9.73 0.00 0.00 3.46
160 169 0.453390 CTTTCTCCATTGCGCTTCCC 59.547 55.000 9.73 0.00 0.00 3.97
161 170 0.038166 TTTCTCCATTGCGCTTCCCT 59.962 50.000 9.73 0.00 0.00 4.20
162 171 0.038166 TTCTCCATTGCGCTTCCCTT 59.962 50.000 9.73 0.00 0.00 3.95
163 172 0.392998 TCTCCATTGCGCTTCCCTTC 60.393 55.000 9.73 0.00 0.00 3.46
234 243 2.276732 TCTCTTGCTTCCCAAACCTG 57.723 50.000 0.00 0.00 31.94 4.00
235 244 1.202927 TCTCTTGCTTCCCAAACCTGG 60.203 52.381 0.00 0.00 43.10 4.45
236 245 0.827507 TCTTGCTTCCCAAACCTGGC 60.828 55.000 0.00 0.00 41.99 4.85
237 246 0.829182 CTTGCTTCCCAAACCTGGCT 60.829 55.000 0.00 0.00 41.99 4.75
238 247 0.398381 TTGCTTCCCAAACCTGGCTT 60.398 50.000 0.00 0.00 41.99 4.35
239 248 0.480690 TGCTTCCCAAACCTGGCTTA 59.519 50.000 0.00 0.00 41.99 3.09
240 249 1.133325 TGCTTCCCAAACCTGGCTTAA 60.133 47.619 0.00 0.00 41.99 1.85
243 253 1.154430 TCCCAAACCTGGCTTAACCT 58.846 50.000 0.00 0.00 41.99 3.50
245 255 1.075536 CCCAAACCTGGCTTAACCTCT 59.924 52.381 0.00 0.00 41.99 3.69
246 256 2.437413 CCAAACCTGGCTTAACCTCTC 58.563 52.381 0.00 0.00 40.22 3.20
251 266 1.623834 CCTGGCTTAACCTCTCCTCCT 60.624 57.143 0.00 0.00 40.22 3.69
254 269 2.188817 GGCTTAACCTCTCCTCCTTCA 58.811 52.381 0.00 0.00 34.51 3.02
263 278 1.349026 TCTCCTCCTTCACTTGCCTTG 59.651 52.381 0.00 0.00 0.00 3.61
310 325 2.441410 CTTCAAAGCTTTCCTCCTCCC 58.559 52.381 9.23 0.00 0.00 4.30
314 329 1.210885 AAGCTTTCCTCCTCCCCCTG 61.211 60.000 0.00 0.00 0.00 4.45
383 410 2.034558 ACTGCTCATTTTCGTTGGGTTG 59.965 45.455 0.00 0.00 0.00 3.77
441 471 1.149148 GACCACTGAAACCTCGAAGC 58.851 55.000 0.00 0.00 0.00 3.86
443 473 0.250295 CCACTGAAACCTCGAAGCCA 60.250 55.000 0.00 0.00 0.00 4.75
479 513 5.987098 TGATCTCTTCTTGATTTCTCCCTG 58.013 41.667 0.00 0.00 0.00 4.45
484 518 3.623906 TCTTGATTTCTCCCTGCTCTG 57.376 47.619 0.00 0.00 0.00 3.35
489 523 0.612229 TTTCTCCCTGCTCTGCTCTG 59.388 55.000 0.00 0.00 0.00 3.35
490 524 1.897225 TTCTCCCTGCTCTGCTCTGC 61.897 60.000 0.00 0.00 0.00 4.26
491 525 2.284478 TCCCTGCTCTGCTCTGCT 60.284 61.111 0.00 0.00 0.00 4.24
492 526 2.187424 CCCTGCTCTGCTCTGCTC 59.813 66.667 0.00 0.00 0.00 4.26
493 527 2.360767 CCCTGCTCTGCTCTGCTCT 61.361 63.158 0.00 0.00 0.00 4.09
494 528 1.597989 CCTGCTCTGCTCTGCTCTT 59.402 57.895 0.00 0.00 0.00 2.85
495 529 0.460635 CCTGCTCTGCTCTGCTCTTC 60.461 60.000 0.00 0.00 0.00 2.87
496 530 0.533491 CTGCTCTGCTCTGCTCTTCT 59.467 55.000 0.00 0.00 0.00 2.85
497 531 0.531657 TGCTCTGCTCTGCTCTTCTC 59.468 55.000 0.00 0.00 0.00 2.87
498 532 0.819582 GCTCTGCTCTGCTCTTCTCT 59.180 55.000 0.00 0.00 0.00 3.10
499 533 1.205417 GCTCTGCTCTGCTCTTCTCTT 59.795 52.381 0.00 0.00 0.00 2.85
500 534 2.736400 GCTCTGCTCTGCTCTTCTCTTC 60.736 54.545 0.00 0.00 0.00 2.87
501 535 2.756760 CTCTGCTCTGCTCTTCTCTTCT 59.243 50.000 0.00 0.00 0.00 2.85
502 536 2.754552 TCTGCTCTGCTCTTCTCTTCTC 59.245 50.000 0.00 0.00 0.00 2.87
503 537 2.756760 CTGCTCTGCTCTTCTCTTCTCT 59.243 50.000 0.00 0.00 0.00 3.10
504 538 3.947196 CTGCTCTGCTCTTCTCTTCTCTA 59.053 47.826 0.00 0.00 0.00 2.43
505 539 3.947196 TGCTCTGCTCTTCTCTTCTCTAG 59.053 47.826 0.00 0.00 0.00 2.43
534 568 1.066143 TCTTGGGTTTGGCTCTCGATC 60.066 52.381 0.00 0.00 0.00 3.69
535 569 0.391130 TTGGGTTTGGCTCTCGATCG 60.391 55.000 9.36 9.36 0.00 3.69
686 730 1.202325 GCGTTTCCCGTCCAAAAGTTT 60.202 47.619 0.00 0.00 39.32 2.66
687 731 2.723209 CGTTTCCCGTCCAAAAGTTTC 58.277 47.619 0.00 0.00 0.00 2.78
688 732 2.097791 CGTTTCCCGTCCAAAAGTTTCA 59.902 45.455 0.00 0.00 0.00 2.69
689 733 3.702330 GTTTCCCGTCCAAAAGTTTCAG 58.298 45.455 0.00 0.00 0.00 3.02
690 734 3.284793 TTCCCGTCCAAAAGTTTCAGA 57.715 42.857 0.00 0.00 0.00 3.27
693 737 4.017808 TCCCGTCCAAAAGTTTCAGAAAA 58.982 39.130 0.00 0.00 0.00 2.29
698 742 6.312672 CCGTCCAAAAGTTTCAGAAAATTTGT 59.687 34.615 19.30 9.04 38.50 2.83
701 745 6.821160 TCCAAAAGTTTCAGAAAATTTGTCCC 59.179 34.615 19.30 0.00 38.50 4.46
709 753 4.039124 TCAGAAAATTTGTCCCCTTCTTGC 59.961 41.667 0.00 0.00 0.00 4.01
710 754 4.039609 CAGAAAATTTGTCCCCTTCTTGCT 59.960 41.667 0.00 0.00 0.00 3.91
726 770 2.308769 GCTCTCGATGCCGATGCTG 61.309 63.158 0.00 0.00 44.62 4.41
751 795 1.612462 CCAGTGATTCCAGCTGCTTCA 60.612 52.381 8.66 7.76 0.00 3.02
752 796 1.738350 CAGTGATTCCAGCTGCTTCAG 59.262 52.381 8.66 0.00 34.12 3.02
788 839 3.219281 TGGCTTTGTTAACTCCCAGTTC 58.781 45.455 7.22 0.00 39.51 3.01
804 855 3.065371 CCAGTTCCTTGCGGTTATCAATC 59.935 47.826 0.00 0.00 0.00 2.67
805 856 3.689161 CAGTTCCTTGCGGTTATCAATCA 59.311 43.478 0.00 0.00 0.00 2.57
812 863 6.601613 TCCTTGCGGTTATCAATCACTTTAAT 59.398 34.615 0.00 0.00 0.00 1.40
816 867 6.372937 TGCGGTTATCAATCACTTTAATCACA 59.627 34.615 0.00 0.00 0.00 3.58
821 872 5.530519 TCAATCACTTTAATCACACTCGC 57.469 39.130 0.00 0.00 0.00 5.03
822 873 4.994217 TCAATCACTTTAATCACACTCGCA 59.006 37.500 0.00 0.00 0.00 5.10
826 880 1.061131 CTTTAATCACACTCGCAGCCG 59.939 52.381 0.00 0.00 0.00 5.52
843 897 4.966787 GGCGGTTGGGACCTGCAA 62.967 66.667 12.07 0.00 44.20 4.08
844 898 3.365265 GCGGTTGGGACCTGCAAG 61.365 66.667 0.00 0.00 44.20 4.01
850 914 0.110486 TTGGGACCTGCAAGTTCCTC 59.890 55.000 14.11 2.75 36.24 3.71
864 928 6.939730 TGCAAGTTCCTCACAGAATAAATACA 59.060 34.615 0.00 0.00 0.00 2.29
870 934 7.849804 TCCTCACAGAATAAATACAAGAAGC 57.150 36.000 0.00 0.00 0.00 3.86
871 935 7.394016 TCCTCACAGAATAAATACAAGAAGCA 58.606 34.615 0.00 0.00 0.00 3.91
872 936 7.334421 TCCTCACAGAATAAATACAAGAAGCAC 59.666 37.037 0.00 0.00 0.00 4.40
891 955 0.734309 CCAGCAGTTGCATATTCGCA 59.266 50.000 6.90 0.00 45.16 5.10
903 967 1.327303 TATTCGCATTGCATTCCCCC 58.673 50.000 9.69 0.00 0.00 5.40
908 972 2.516930 ATTGCATTCCCCCGCTCG 60.517 61.111 0.00 0.00 0.00 5.03
945 1009 1.244697 TGCCCGAGACAGACAGAGTC 61.245 60.000 0.00 0.00 36.26 3.36
948 1012 2.712709 CCCGAGACAGACAGAGTCTAA 58.287 52.381 0.00 0.00 45.79 2.10
975 1039 2.679837 GCCATGGATGATTATACCTGCG 59.320 50.000 18.40 0.00 0.00 5.18
1324 1391 9.522804 AATTTTGCAGTAATTTAACTTCGTTGA 57.477 25.926 3.74 0.00 0.00 3.18
1433 1532 2.583143 GTGCCTAGTTTGGTTTCCAGT 58.417 47.619 0.00 0.00 33.81 4.00
1434 1533 3.497227 GGTGCCTAGTTTGGTTTCCAGTA 60.497 47.826 0.00 0.00 33.81 2.74
1435 1534 3.501062 GTGCCTAGTTTGGTTTCCAGTAC 59.499 47.826 0.00 0.00 33.81 2.73
1436 1535 2.740447 GCCTAGTTTGGTTTCCAGTACG 59.260 50.000 0.00 0.00 33.81 3.67
1437 1536 3.804759 GCCTAGTTTGGTTTCCAGTACGT 60.805 47.826 0.00 0.00 33.81 3.57
1438 1537 4.561326 GCCTAGTTTGGTTTCCAGTACGTA 60.561 45.833 0.00 0.00 33.81 3.57
1439 1538 5.166398 CCTAGTTTGGTTTCCAGTACGTAG 58.834 45.833 0.00 0.00 33.81 3.51
1483 1582 3.446442 AGTTTGACTTGCCATGAGGAT 57.554 42.857 0.00 0.00 36.89 3.24
1512 1612 7.619512 TGTTATTTTTGGTTGGGGTTAGATT 57.380 32.000 0.00 0.00 0.00 2.40
1556 1656 2.376808 ATCAGGAAAGCTCAGTGACG 57.623 50.000 0.00 0.00 0.00 4.35
1603 1708 1.814394 TGCCTCAATGTAGCTTGCAAG 59.186 47.619 22.44 22.44 0.00 4.01
1604 1709 1.133790 GCCTCAATGTAGCTTGCAAGG 59.866 52.381 27.10 8.94 0.00 3.61
1605 1710 1.133790 CCTCAATGTAGCTTGCAAGGC 59.866 52.381 27.10 18.65 0.00 4.35
1606 1711 1.814394 CTCAATGTAGCTTGCAAGGCA 59.186 47.619 27.10 8.32 36.47 4.75
1607 1712 2.229543 CTCAATGTAGCTTGCAAGGCAA 59.770 45.455 27.10 10.09 46.80 4.52
1646 1751 0.820226 GGCCTTCCTCTTTGGATTGC 59.180 55.000 0.00 0.00 45.68 3.56
1670 1775 6.861572 GCGACATAAATAGACATGTAGTGCTA 59.138 38.462 0.00 0.00 35.55 3.49
1790 1908 5.643379 TTATGTGAAAAGGGTCAGCAATC 57.357 39.130 0.00 0.00 0.00 2.67
1798 1916 3.051940 AGGGTCAGCAATCTCAGGATA 57.948 47.619 0.00 0.00 0.00 2.59
1899 2020 9.864034 GACATGTATATATAGTGTGTGCAAAAC 57.136 33.333 12.94 0.00 0.00 2.43
1912 2033 9.539825 AGTGTGTGCAAAACATGATATTAAAAA 57.460 25.926 0.00 0.00 35.79 1.94
1993 2115 4.285775 GGAAGCAAGGGAGAGAGCTATATT 59.714 45.833 0.00 0.00 36.07 1.28
2060 2188 0.447801 CACGCAGGGTCAAATGTAGC 59.552 55.000 0.00 0.00 0.00 3.58
2061 2189 0.324943 ACGCAGGGTCAAATGTAGCT 59.675 50.000 0.00 0.00 0.00 3.32
2064 2192 2.436417 GCAGGGTCAAATGTAGCTGAA 58.564 47.619 0.00 0.00 0.00 3.02
2076 2204 9.730420 TCAAATGTAGCTGAAACTTTTAAGAAC 57.270 29.630 0.00 0.00 0.00 3.01
2139 2291 8.831550 CATCATCATAGAGATATGCTTGGAATG 58.168 37.037 0.00 0.00 34.43 2.67
2140 2292 7.914859 TCATCATAGAGATATGCTTGGAATGT 58.085 34.615 0.00 0.00 34.43 2.71
2154 2306 6.166982 GCTTGGAATGTACTAAGAAGACACT 58.833 40.000 0.00 0.00 31.56 3.55
2181 2333 0.179119 GGTCGATTACACCGGTGGAG 60.179 60.000 36.47 18.50 34.19 3.86
2189 2341 2.226962 ACACCGGTGGAGTACATAGT 57.773 50.000 36.47 10.42 34.19 2.12
2258 2413 1.885157 CATCCAGCGTTGGTGCAAT 59.115 52.632 18.51 1.00 45.26 3.56
2274 2429 0.321564 CAATGAGAAGGGCGACACCA 60.322 55.000 0.00 0.00 42.05 4.17
2301 2457 4.500477 GCGAAATATGCTTGCAGGTAAAAG 59.500 41.667 0.87 0.00 0.00 2.27
2325 2481 8.177119 AGACAAACAAAAATTGCCTATCTACA 57.823 30.769 0.00 0.00 0.00 2.74
2331 2487 6.597672 ACAAAAATTGCCTATCTACACGATCA 59.402 34.615 0.00 0.00 33.48 2.92
2337 2493 6.399639 TGCCTATCTACACGATCAATGTTA 57.600 37.500 5.02 0.00 33.48 2.41
2338 2494 6.993079 TGCCTATCTACACGATCAATGTTAT 58.007 36.000 5.02 3.39 33.48 1.89
2339 2495 7.441836 TGCCTATCTACACGATCAATGTTATT 58.558 34.615 5.02 0.00 33.48 1.40
2340 2496 7.931407 TGCCTATCTACACGATCAATGTTATTT 59.069 33.333 5.02 0.00 33.48 1.40
2394 2550 8.132362 CAGATAAACATGTGTACCTCTAGTCTC 58.868 40.741 0.00 0.00 0.00 3.36
2406 2562 6.569127 ACCTCTAGTCTCATGAACTCTCTA 57.431 41.667 12.05 3.88 0.00 2.43
2492 2648 0.964358 ATGAACTTCAGGCAGGCAGC 60.964 55.000 0.00 0.00 44.65 5.25
2532 2688 3.517602 CTGATGCAAAACCATGGTGATG 58.482 45.455 20.60 20.61 0.00 3.07
2554 2712 5.287226 TGTCTCTTTGTAAAACGTCTCTCC 58.713 41.667 0.00 0.00 0.00 3.71
2579 2737 2.125225 AGGGGGAACTGGGAGGTC 59.875 66.667 0.00 0.00 0.00 3.85
2603 2761 1.658686 GGCACGATCTCCACGACTCT 61.659 60.000 0.00 0.00 34.70 3.24
2708 2866 3.923864 TGTTGCCGGACAGTCGCT 61.924 61.111 5.05 0.00 0.00 4.93
2926 3092 4.967036 TCATTACATCACACAACACCAGA 58.033 39.130 0.00 0.00 0.00 3.86
2969 3135 2.262423 AGTCTGGTCTTGTTCTTGCC 57.738 50.000 0.00 0.00 0.00 4.52
3037 3219 0.761187 AGCTTCTTGTGCTGAGGACA 59.239 50.000 1.58 1.58 39.56 4.02
3052 3234 1.280421 AGGACAGCTGGGATTCTGTTC 59.720 52.381 19.93 2.47 42.97 3.18
3114 3296 1.611592 CGTCGTCGCCAACAGGTAAC 61.612 60.000 0.00 0.00 0.00 2.50
3116 3298 1.005394 CGTCGCCAACAGGTAACCT 60.005 57.895 0.00 0.00 37.17 3.50
3121 3303 1.338674 CGCCAACAGGTAACCTCATCA 60.339 52.381 0.00 0.00 37.17 3.07
3266 3456 3.822940 CGTAACTCTGGGGTCTAGATCT 58.177 50.000 2.34 0.00 0.00 2.75
3330 3529 0.395862 ACACCGAGGATGAGGACGAT 60.396 55.000 0.00 0.00 0.00 3.73
3333 3532 0.312416 CCGAGGATGAGGACGATGAC 59.688 60.000 0.00 0.00 0.00 3.06
3334 3533 0.040870 CGAGGATGAGGACGATGACG 60.041 60.000 0.00 0.00 45.75 4.35
3335 3534 1.309950 GAGGATGAGGACGATGACGA 58.690 55.000 0.00 0.00 42.66 4.20
3336 3535 1.002251 GAGGATGAGGACGATGACGAC 60.002 57.143 0.00 0.00 42.66 4.34
3337 3536 0.317103 GGATGAGGACGATGACGACG 60.317 60.000 0.00 0.00 42.66 5.12
3338 3537 0.656259 GATGAGGACGATGACGACGA 59.344 55.000 0.00 0.00 42.66 4.20
3339 3538 0.658368 ATGAGGACGATGACGACGAG 59.342 55.000 0.00 0.00 42.66 4.18
3340 3539 1.352404 GAGGACGATGACGACGAGG 59.648 63.158 0.00 0.00 42.66 4.63
3341 3540 1.367599 GAGGACGATGACGACGAGGT 61.368 60.000 0.00 0.00 42.66 3.85
3422 3621 3.056393 CCCGTCTACTGACACCATACAAA 60.056 47.826 0.00 0.00 43.06 2.83
3427 3626 3.695830 ACTGACACCATACAAATCGGT 57.304 42.857 0.00 0.00 0.00 4.69
3457 3656 3.181495 CGGTGTGGTTAACAGAAGCAAAA 60.181 43.478 8.10 0.00 40.26 2.44
3536 3735 4.614535 GCTTCTGTGTGCACAAGAAATAGG 60.615 45.833 28.33 21.99 41.33 2.57
3540 3739 4.910195 TGTGTGCACAAGAAATAGGAGAT 58.090 39.130 23.59 0.00 38.56 2.75
3602 3801 6.093404 CGATGTAACTTGTGAGCTTCTCTAA 58.907 40.000 0.00 0.00 0.00 2.10
3673 3872 4.473196 TGGAATTACAGGCCTGTATCTGAA 59.527 41.667 39.32 28.71 44.54 3.02
3676 3875 1.958288 ACAGGCCTGTATCTGAACCT 58.042 50.000 37.12 8.11 42.90 3.50
3826 4041 5.524646 AGCTTTAAAACAGTACAGTAACGCA 59.475 36.000 0.00 0.00 0.00 5.24
4018 4242 1.212490 CAACGGTGGCGATGCAAAT 59.788 52.632 0.00 0.00 0.00 2.32
4046 4270 0.515564 CGTTTGGGTAAGCTTGGACG 59.484 55.000 9.86 6.47 0.00 4.79
4210 4434 1.278985 TGCACAGGTAACATCAGAGGG 59.721 52.381 0.00 0.00 41.41 4.30
4225 4449 6.548622 ACATCAGAGGGTAATCCATTGATTTG 59.451 38.462 0.00 0.00 41.44 2.32
4246 4470 2.417933 GCACGCAGTCATCTTTCTCAAT 59.582 45.455 0.00 0.00 41.61 2.57
4285 4509 7.967854 TGTGAATATACTGCTAACAAATGCAAC 59.032 33.333 0.00 0.00 38.81 4.17
4363 4587 7.859377 CCAATACATCATTCTGAAATGCAGTAC 59.141 37.037 0.00 0.00 45.14 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.142407 GAGGAGAGGAAGGGGAATAGGTA 59.858 52.174 0.00 0.00 0.00 3.08
9 10 1.948243 AGGAGAGGAAGGGGAATAGGT 59.052 52.381 0.00 0.00 0.00 3.08
10 11 2.181196 AGAGGAGAGGAAGGGGAATAGG 59.819 54.545 0.00 0.00 0.00 2.57
11 12 3.628832 AGAGGAGAGGAAGGGGAATAG 57.371 52.381 0.00 0.00 0.00 1.73
13 14 2.630995 GGAAGAGGAGAGGAAGGGGAAT 60.631 54.545 0.00 0.00 0.00 3.01
14 15 1.273896 GGAAGAGGAGAGGAAGGGGAA 60.274 57.143 0.00 0.00 0.00 3.97
15 16 0.340208 GGAAGAGGAGAGGAAGGGGA 59.660 60.000 0.00 0.00 0.00 4.81
16 17 0.692756 GGGAAGAGGAGAGGAAGGGG 60.693 65.000 0.00 0.00 0.00 4.79
18 19 0.692756 GGGGGAAGAGGAGAGGAAGG 60.693 65.000 0.00 0.00 0.00 3.46
19 20 0.341609 AGGGGGAAGAGGAGAGGAAG 59.658 60.000 0.00 0.00 0.00 3.46
20 21 0.800239 AAGGGGGAAGAGGAGAGGAA 59.200 55.000 0.00 0.00 0.00 3.36
21 22 0.043334 CAAGGGGGAAGAGGAGAGGA 59.957 60.000 0.00 0.00 0.00 3.71
31 32 2.937959 AAACGCAAGGCAAGGGGGAA 62.938 55.000 0.00 0.00 46.39 3.97
35 36 1.866853 GAGGAAACGCAAGGCAAGGG 61.867 60.000 0.00 0.00 46.39 3.95
39 40 0.108585 AAGAGAGGAAACGCAAGGCA 59.891 50.000 0.00 0.00 46.39 4.75
40 41 0.519077 CAAGAGAGGAAACGCAAGGC 59.481 55.000 0.00 0.00 46.39 4.35
43 44 2.910688 AGACAAGAGAGGAAACGCAA 57.089 45.000 0.00 0.00 0.00 4.85
44 45 2.548067 GGAAGACAAGAGAGGAAACGCA 60.548 50.000 0.00 0.00 0.00 5.24
45 46 2.070028 GGAAGACAAGAGAGGAAACGC 58.930 52.381 0.00 0.00 0.00 4.84
46 47 3.386768 TGGAAGACAAGAGAGGAAACG 57.613 47.619 0.00 0.00 0.00 3.60
48 49 8.760980 TTTAAATTGGAAGACAAGAGAGGAAA 57.239 30.769 0.00 0.00 43.48 3.13
49 50 8.940397 ATTTAAATTGGAAGACAAGAGAGGAA 57.060 30.769 0.00 0.00 43.48 3.36
51 52 7.148000 GGGATTTAAATTGGAAGACAAGAGAGG 60.148 40.741 1.43 0.00 43.48 3.69
52 53 7.394359 TGGGATTTAAATTGGAAGACAAGAGAG 59.606 37.037 1.43 0.00 43.48 3.20
53 54 7.176690 GTGGGATTTAAATTGGAAGACAAGAGA 59.823 37.037 1.43 0.00 43.48 3.10
57 58 5.770663 TCGTGGGATTTAAATTGGAAGACAA 59.229 36.000 1.43 0.00 44.54 3.18
58 59 5.317808 TCGTGGGATTTAAATTGGAAGACA 58.682 37.500 1.43 0.00 0.00 3.41
59 60 5.646360 TCTCGTGGGATTTAAATTGGAAGAC 59.354 40.000 1.43 0.00 0.00 3.01
65 66 5.309323 TGCTTCTCGTGGGATTTAAATTG 57.691 39.130 1.43 0.00 0.00 2.32
79 80 4.310769 TCTTTCTTTCTCCTTGCTTCTCG 58.689 43.478 0.00 0.00 0.00 4.04
81 82 6.360618 TCTTTCTTTCTTTCTCCTTGCTTCT 58.639 36.000 0.00 0.00 0.00 2.85
86 87 9.513727 CTTTCTTTCTTTCTTTCTTTCTCCTTG 57.486 33.333 0.00 0.00 0.00 3.61
96 97 9.729023 CCTCTTCTTTCTTTCTTTCTTTCTTTC 57.271 33.333 0.00 0.00 0.00 2.62
97 98 9.467796 TCCTCTTCTTTCTTTCTTTCTTTCTTT 57.532 29.630 0.00 0.00 0.00 2.52
98 99 9.119418 CTCCTCTTCTTTCTTTCTTTCTTTCTT 57.881 33.333 0.00 0.00 0.00 2.52
101 102 7.284261 CACCTCCTCTTCTTTCTTTCTTTCTTT 59.716 37.037 0.00 0.00 0.00 2.52
105 106 6.058833 GTCACCTCCTCTTCTTTCTTTCTTT 58.941 40.000 0.00 0.00 0.00 2.52
109 110 4.656112 TCAGTCACCTCCTCTTCTTTCTTT 59.344 41.667 0.00 0.00 0.00 2.52
113 114 3.323403 CACTCAGTCACCTCCTCTTCTTT 59.677 47.826 0.00 0.00 0.00 2.52
116 117 2.029470 CACACTCAGTCACCTCCTCTTC 60.029 54.545 0.00 0.00 0.00 2.87
118 119 1.133325 ACACACTCAGTCACCTCCTCT 60.133 52.381 0.00 0.00 0.00 3.69
126 127 4.081142 TGGAGAAAGAAACACACTCAGTCA 60.081 41.667 0.00 0.00 0.00 3.41
128 129 4.487714 TGGAGAAAGAAACACACTCAGT 57.512 40.909 0.00 0.00 0.00 3.41
129 130 5.755813 CAATGGAGAAAGAAACACACTCAG 58.244 41.667 0.00 0.00 0.00 3.35
130 131 4.036734 GCAATGGAGAAAGAAACACACTCA 59.963 41.667 0.00 0.00 0.00 3.41
132 133 3.003689 CGCAATGGAGAAAGAAACACACT 59.996 43.478 0.00 0.00 0.00 3.55
134 135 2.287547 GCGCAATGGAGAAAGAAACACA 60.288 45.455 0.30 0.00 0.00 3.72
138 139 2.228822 GGAAGCGCAATGGAGAAAGAAA 59.771 45.455 11.47 0.00 0.00 2.52
140 141 1.453155 GGAAGCGCAATGGAGAAAGA 58.547 50.000 11.47 0.00 0.00 2.52
159 168 0.701147 AAGCCAAGGGAAGGAGAAGG 59.299 55.000 0.00 0.00 0.00 3.46
160 169 1.615384 CCAAGCCAAGGGAAGGAGAAG 60.615 57.143 0.00 0.00 0.00 2.85
161 170 0.405585 CCAAGCCAAGGGAAGGAGAA 59.594 55.000 0.00 0.00 0.00 2.87
162 171 2.078452 CCAAGCCAAGGGAAGGAGA 58.922 57.895 0.00 0.00 0.00 3.71
163 172 1.680314 GCCAAGCCAAGGGAAGGAG 60.680 63.158 0.00 0.00 0.00 3.69
187 196 3.596046 TGGAGGGGGATGTAAGAAAACAT 59.404 43.478 0.00 0.00 42.75 2.71
234 243 2.093394 GTGAAGGAGGAGAGGTTAAGCC 60.093 54.545 0.00 0.00 37.58 4.35
235 244 2.835156 AGTGAAGGAGGAGAGGTTAAGC 59.165 50.000 0.00 0.00 0.00 3.09
236 245 4.826556 CAAGTGAAGGAGGAGAGGTTAAG 58.173 47.826 0.00 0.00 0.00 1.85
237 246 3.008049 GCAAGTGAAGGAGGAGAGGTTAA 59.992 47.826 0.00 0.00 0.00 2.01
238 247 2.567615 GCAAGTGAAGGAGGAGAGGTTA 59.432 50.000 0.00 0.00 0.00 2.85
239 248 1.349357 GCAAGTGAAGGAGGAGAGGTT 59.651 52.381 0.00 0.00 0.00 3.50
240 249 0.980423 GCAAGTGAAGGAGGAGAGGT 59.020 55.000 0.00 0.00 0.00 3.85
243 253 1.349026 CAAGGCAAGTGAAGGAGGAGA 59.651 52.381 0.00 0.00 0.00 3.71
245 255 0.401738 CCAAGGCAAGTGAAGGAGGA 59.598 55.000 0.00 0.00 0.00 3.71
246 256 1.246737 GCCAAGGCAAGTGAAGGAGG 61.247 60.000 6.14 0.00 41.49 4.30
251 266 2.298729 GTTAATGGCCAAGGCAAGTGAA 59.701 45.455 10.96 0.00 42.43 3.18
254 269 1.266178 GGTTAATGGCCAAGGCAAGT 58.734 50.000 10.96 3.13 42.43 3.16
310 325 4.335647 ACCAAGACGGCAGCAGGG 62.336 66.667 0.00 0.00 39.03 4.45
314 329 0.727398 GTTATCACCAAGACGGCAGC 59.273 55.000 0.00 0.00 39.03 5.25
383 410 5.686159 ATATTAGAAATGAGCAGCAGCAC 57.314 39.130 3.17 0.00 45.49 4.40
438 468 5.507637 AGATCAACTGAATGAAGATGGCTT 58.492 37.500 0.00 0.00 36.96 4.35
441 471 7.049133 AGAAGAGATCAACTGAATGAAGATGG 58.951 38.462 0.00 0.00 32.06 3.51
443 473 8.319881 TCAAGAAGAGATCAACTGAATGAAGAT 58.680 33.333 0.00 0.00 32.06 2.40
479 513 0.819582 AGAGAAGAGCAGAGCAGAGC 59.180 55.000 0.00 0.00 0.00 4.09
484 518 3.316308 CCTAGAGAAGAGAAGAGCAGAGC 59.684 52.174 0.00 0.00 0.00 4.09
501 535 5.130350 CAAACCCAAGAAAACTCACCTAGA 58.870 41.667 0.00 0.00 0.00 2.43
502 536 4.278419 CCAAACCCAAGAAAACTCACCTAG 59.722 45.833 0.00 0.00 0.00 3.02
503 537 4.211920 CCAAACCCAAGAAAACTCACCTA 58.788 43.478 0.00 0.00 0.00 3.08
504 538 3.031013 CCAAACCCAAGAAAACTCACCT 58.969 45.455 0.00 0.00 0.00 4.00
505 539 2.483013 GCCAAACCCAAGAAAACTCACC 60.483 50.000 0.00 0.00 0.00 4.02
534 568 0.539051 AGCAAGGGGAGAGACAATCG 59.461 55.000 0.00 0.00 0.00 3.34
535 569 1.472376 CGAGCAAGGGGAGAGACAATC 60.472 57.143 0.00 0.00 0.00 2.67
612 654 5.036090 TGCATAAAACATTCATCGCATCAC 58.964 37.500 0.00 0.00 0.00 3.06
645 688 2.022129 GGAAGGCGACTGTCGTGTG 61.022 63.158 28.38 4.16 42.81 3.82
686 730 4.039124 GCAAGAAGGGGACAAATTTTCTGA 59.961 41.667 0.00 0.00 0.00 3.27
687 731 4.039609 AGCAAGAAGGGGACAAATTTTCTG 59.960 41.667 0.00 0.00 0.00 3.02
688 732 4.226384 AGCAAGAAGGGGACAAATTTTCT 58.774 39.130 0.00 0.00 0.00 2.52
689 733 4.281941 AGAGCAAGAAGGGGACAAATTTTC 59.718 41.667 0.00 0.00 0.00 2.29
690 734 4.226384 AGAGCAAGAAGGGGACAAATTTT 58.774 39.130 0.00 0.00 0.00 1.82
693 737 2.616510 CGAGAGCAAGAAGGGGACAAAT 60.617 50.000 0.00 0.00 0.00 2.32
698 742 0.826715 CATCGAGAGCAAGAAGGGGA 59.173 55.000 0.00 0.00 0.00 4.81
701 745 1.150567 CGGCATCGAGAGCAAGAAGG 61.151 60.000 13.72 0.00 39.00 3.46
726 770 2.413142 GCTGGAATCACTGGCAGGC 61.413 63.158 20.34 5.89 0.00 4.85
734 778 2.105006 TCTGAAGCAGCTGGAATCAC 57.895 50.000 17.12 0.00 0.00 3.06
774 824 1.804748 CGCAAGGAACTGGGAGTTAAC 59.195 52.381 0.00 0.00 38.80 2.01
776 826 3.927555 CGCAAGGAACTGGGAGTTA 57.072 52.632 0.00 0.00 38.80 2.24
804 855 2.159653 GGCTGCGAGTGTGATTAAAGTG 60.160 50.000 0.00 0.00 0.00 3.16
805 856 2.076863 GGCTGCGAGTGTGATTAAAGT 58.923 47.619 0.00 0.00 0.00 2.66
835 889 1.070758 TCTGTGAGGAACTTGCAGGTC 59.929 52.381 0.32 0.00 41.55 3.85
836 890 1.131638 TCTGTGAGGAACTTGCAGGT 58.868 50.000 0.00 0.00 41.55 4.00
839 893 6.939730 TGTATTTATTCTGTGAGGAACTTGCA 59.060 34.615 0.00 0.00 41.55 4.08
842 896 9.793259 TTCTTGTATTTATTCTGTGAGGAACTT 57.207 29.630 0.00 0.00 41.55 2.66
844 898 8.178313 GCTTCTTGTATTTATTCTGTGAGGAAC 58.822 37.037 0.00 0.00 0.00 3.62
850 914 7.144722 TGGTGCTTCTTGTATTTATTCTGTG 57.855 36.000 0.00 0.00 0.00 3.66
864 928 0.752743 TGCAACTGCTGGTGCTTCTT 60.753 50.000 30.23 0.00 42.66 2.52
870 934 1.532505 GCGAATATGCAACTGCTGGTG 60.533 52.381 3.92 3.92 42.66 4.17
871 935 0.734889 GCGAATATGCAACTGCTGGT 59.265 50.000 2.95 0.00 42.66 4.00
872 936 0.734309 TGCGAATATGCAACTGCTGG 59.266 50.000 2.95 0.00 43.02 4.85
891 955 2.516930 CGAGCGGGGGAATGCAAT 60.517 61.111 0.00 0.00 0.00 3.56
945 1009 0.179020 TCATCCATGGCGGCCTTTAG 60.179 55.000 21.46 7.89 33.14 1.85
948 1012 0.478072 TAATCATCCATGGCGGCCTT 59.522 50.000 21.46 11.55 33.14 4.35
1032 1096 2.433318 GTGGACTCCGTGAGCAGC 60.433 66.667 1.36 0.00 32.04 5.25
1279 1346 5.661503 AATTCCACCAAAAGGGGATTTTT 57.338 34.783 0.00 0.00 39.11 1.94
1280 1347 5.661503 AAATTCCACCAAAAGGGGATTTT 57.338 34.783 0.00 0.00 41.91 1.82
1282 1349 4.749476 GCAAAATTCCACCAAAAGGGGATT 60.749 41.667 0.00 0.00 42.91 3.01
1283 1350 3.244875 GCAAAATTCCACCAAAAGGGGAT 60.245 43.478 0.00 0.00 42.91 3.85
1296 1363 8.515473 ACGAAGTTAAATTACTGCAAAATTCC 57.485 30.769 7.05 1.00 37.78 3.01
1339 1409 3.314635 AGAAAACTTCTGCAGCTGTTCTG 59.685 43.478 16.64 3.75 38.91 3.02
1340 1410 3.549794 AGAAAACTTCTGCAGCTGTTCT 58.450 40.909 16.64 10.60 38.91 3.01
1341 1411 3.978718 AGAAAACTTCTGCAGCTGTTC 57.021 42.857 16.64 8.38 38.91 3.18
1367 1441 7.394359 CACCGATTATATCAAATTTCCCATCCT 59.606 37.037 0.00 0.00 0.00 3.24
1386 1460 8.028938 CCAAAATTAAGATCAGAAACACCGATT 58.971 33.333 0.00 0.00 0.00 3.34
1387 1461 7.362920 CCCAAAATTAAGATCAGAAACACCGAT 60.363 37.037 0.00 0.00 0.00 4.18
1389 1463 6.092748 CCCAAAATTAAGATCAGAAACACCG 58.907 40.000 0.00 0.00 0.00 4.94
1463 1562 2.957402 TCCTCATGGCAAGTCAAACT 57.043 45.000 0.00 0.00 0.00 2.66
1556 1656 7.325694 ACAAGGTTGATTTCATCATCAAATCC 58.674 34.615 0.00 0.00 43.30 3.01
1646 1751 8.797266 TTAGCACTACATGTCTATTTATGTCG 57.203 34.615 0.00 0.00 38.41 4.35
1670 1775 8.527810 TCAAAACCACACTCATTTCTACTTTTT 58.472 29.630 0.00 0.00 0.00 1.94
1679 1784 4.432712 GCAAGTCAAAACCACACTCATTT 58.567 39.130 0.00 0.00 0.00 2.32
1681 1786 2.362077 GGCAAGTCAAAACCACACTCAT 59.638 45.455 0.00 0.00 0.00 2.90
1767 1876 5.954150 AGATTGCTGACCCTTTTCACATAAT 59.046 36.000 0.00 0.00 0.00 1.28
1768 1877 5.324409 AGATTGCTGACCCTTTTCACATAA 58.676 37.500 0.00 0.00 0.00 1.90
1769 1878 4.922206 AGATTGCTGACCCTTTTCACATA 58.078 39.130 0.00 0.00 0.00 2.29
1770 1879 3.760684 GAGATTGCTGACCCTTTTCACAT 59.239 43.478 0.00 0.00 0.00 3.21
1772 1881 3.149196 TGAGATTGCTGACCCTTTTCAC 58.851 45.455 0.00 0.00 0.00 3.18
1773 1882 3.415212 CTGAGATTGCTGACCCTTTTCA 58.585 45.455 0.00 0.00 0.00 2.69
1774 1883 2.751806 CCTGAGATTGCTGACCCTTTTC 59.248 50.000 0.00 0.00 0.00 2.29
1798 1916 8.374743 ACAATTTAGGCAAACATAGTGGATTTT 58.625 29.630 0.00 0.00 0.00 1.82
1944 2065 3.019799 TGGGAAAGCAAAACACCTACA 57.980 42.857 0.00 0.00 0.00 2.74
1993 2115 5.006941 CACGCATTGTGTGATGATGATCTAA 59.993 40.000 22.80 0.00 45.59 2.10
2139 2291 7.311408 ACCGAAATACAGTGTCTTCTTAGTAC 58.689 38.462 0.00 0.00 0.00 2.73
2140 2292 7.458409 ACCGAAATACAGTGTCTTCTTAGTA 57.542 36.000 0.00 0.00 0.00 1.82
2225 2380 0.746063 GGATGCATTTTCGATGGGCA 59.254 50.000 0.00 4.42 39.03 5.36
2231 2386 1.135717 CAACGCTGGATGCATTTTCGA 60.136 47.619 0.00 0.00 43.06 3.71
2258 2413 0.904865 AGATGGTGTCGCCCTTCTCA 60.905 55.000 0.00 0.00 34.79 3.27
2301 2457 7.060633 CGTGTAGATAGGCAATTTTTGTTTGTC 59.939 37.037 0.00 0.00 0.00 3.18
2371 2527 7.956328 TGAGACTAGAGGTACACATGTTTAT 57.044 36.000 0.00 0.00 0.00 1.40
2394 2550 8.659925 ATTGCTGTAGAAATAGAGAGTTCATG 57.340 34.615 0.00 0.00 31.96 3.07
2406 2562 3.698040 CTGGCCTGAATTGCTGTAGAAAT 59.302 43.478 3.32 0.00 0.00 2.17
2412 2568 1.980772 GCCTGGCCTGAATTGCTGT 60.981 57.895 11.88 0.00 0.00 4.40
2492 2648 4.947645 TCAGGAAAAAGCTTGTGAAATGG 58.052 39.130 0.00 0.00 0.00 3.16
2532 2688 5.402867 CAGGAGAGACGTTTTACAAAGAGAC 59.597 44.000 0.00 0.00 0.00 3.36
2554 2712 1.376466 CAGTTCCCCCTGTGGACAG 59.624 63.158 0.00 0.00 43.40 3.51
2603 2761 2.722094 GGCACCATTGTTATGACCTGA 58.278 47.619 0.00 0.00 33.37 3.86
2636 2794 1.805943 TCGTCGTACTCGTCCATGAAA 59.194 47.619 0.00 0.00 38.33 2.69
2675 2833 4.711949 CACAGGGCGCTGCTCCTT 62.712 66.667 28.90 7.85 29.31 3.36
2708 2866 7.658982 GCCTATTCTGATGAACTCACAATGATA 59.341 37.037 0.00 0.00 34.71 2.15
2926 3092 9.620259 ACTTTGTTAAAGAAGAGTCTGAAGATT 57.380 29.630 8.18 0.00 41.02 2.40
2956 3122 2.027653 AGAGGCTAGGCAAGAACAAGAC 60.028 50.000 19.70 0.00 0.00 3.01
2969 3135 7.050377 TGGTAAAATTCAAGATCAGAGGCTAG 58.950 38.462 0.00 0.00 0.00 3.42
3055 3237 2.306805 TGCTCTCACCATCACCAAGATT 59.693 45.455 0.00 0.00 33.72 2.40
3114 3296 2.286872 GCTGGTCATTCAGTGATGAGG 58.713 52.381 0.00 0.00 39.48 3.86
3116 3298 1.629861 TGGCTGGTCATTCAGTGATGA 59.370 47.619 0.00 0.00 39.48 2.92
3121 3303 2.559668 CAACAATGGCTGGTCATTCAGT 59.440 45.455 0.00 0.00 35.40 3.41
3158 3340 5.103643 ACTGGTATCAGGATCACTACACCTA 60.104 44.000 8.13 0.00 44.99 3.08
3234 3424 3.372206 CCCAGAGTTACGCATCAGAAAAG 59.628 47.826 0.00 0.00 0.00 2.27
3246 3436 5.056553 AGAGATCTAGACCCCAGAGTTAC 57.943 47.826 0.00 0.00 0.00 2.50
3266 3456 2.642311 TGGTTTCCCTGCAGTATCAAGA 59.358 45.455 13.81 0.00 0.00 3.02
3321 3511 1.366854 CCTCGTCGTCATCGTCCTCA 61.367 60.000 0.00 0.00 38.33 3.86
3330 3529 0.596577 CTTCTTCCACCTCGTCGTCA 59.403 55.000 0.00 0.00 0.00 4.35
3333 3532 0.171455 CCTCTTCTTCCACCTCGTCG 59.829 60.000 0.00 0.00 0.00 5.12
3334 3533 1.546961 TCCTCTTCTTCCACCTCGTC 58.453 55.000 0.00 0.00 0.00 4.20
3335 3534 1.827969 CATCCTCTTCTTCCACCTCGT 59.172 52.381 0.00 0.00 0.00 4.18
3336 3535 1.472376 GCATCCTCTTCTTCCACCTCG 60.472 57.143 0.00 0.00 0.00 4.63
3337 3536 1.134250 GGCATCCTCTTCTTCCACCTC 60.134 57.143 0.00 0.00 0.00 3.85
3338 3537 0.915364 GGCATCCTCTTCTTCCACCT 59.085 55.000 0.00 0.00 0.00 4.00
3339 3538 0.462759 CGGCATCCTCTTCTTCCACC 60.463 60.000 0.00 0.00 0.00 4.61
3340 3539 0.537188 TCGGCATCCTCTTCTTCCAC 59.463 55.000 0.00 0.00 0.00 4.02
3341 3540 0.537188 GTCGGCATCCTCTTCTTCCA 59.463 55.000 0.00 0.00 0.00 3.53
3374 3573 1.736645 CGTGGTTGGTAGTGAGGCG 60.737 63.158 0.00 0.00 0.00 5.52
3380 3579 1.208776 GGATAAGGCGTGGTTGGTAGT 59.791 52.381 0.00 0.00 0.00 2.73
3536 3735 4.720649 TGTACAGAGCCACTACAATCTC 57.279 45.455 0.00 0.00 0.00 2.75
3540 3739 4.081862 GTGGTATGTACAGAGCCACTACAA 60.082 45.833 26.04 6.35 44.35 2.41
3602 3801 2.925724 CTCTCGAGTACATGGGAGAGT 58.074 52.381 13.13 0.00 44.66 3.24
3673 3872 1.059098 TGAGTTGCAGGATCACAGGT 58.941 50.000 0.00 0.00 0.00 4.00
3826 4041 5.765182 GTGCTTTGTTATGGCTGGATATACT 59.235 40.000 0.00 0.00 0.00 2.12
4018 4242 2.674747 GCTTACCCAAACGTCGATGGTA 60.675 50.000 9.90 10.41 34.79 3.25
4046 4270 2.401351 GTGTTCAAGTACCTCGACCAC 58.599 52.381 0.00 0.00 0.00 4.16
4082 4306 2.317371 TGGTCTCTGAAGGAGCTCTT 57.683 50.000 14.64 2.08 41.60 2.85
4210 4434 3.768406 TGCGTGCAAATCAATGGATTAC 58.232 40.909 0.00 0.00 42.87 1.89
4225 4449 1.432514 TGAGAAAGATGACTGCGTGC 58.567 50.000 0.00 0.00 0.00 5.34
4266 4490 4.006989 TCCGTTGCATTTGTTAGCAGTAT 58.993 39.130 0.00 0.00 42.39 2.12
4285 4509 2.481449 GGCATACTGGTCAGTACTTCCG 60.481 54.545 12.40 0.00 45.61 4.30
4363 4587 6.475402 GCTTCCATGTATTAATTTGTTTCCGG 59.525 38.462 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.