Multiple sequence alignment - TraesCS4D01G289100

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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 TraesCS4D01G289100 chr4D 100.000 6935 0 0 1 6935 460471205 460478139 0.000000e+00 12807.0
1 TraesCS4D01G289100 chr4D 94.737 38 2 0 6306 6343 14938833 14938870 7.510000e-05 60.2
2 TraesCS4D01G289100 chr4D 100.000 30 0 0 6817 6846 57035455 57035426 1.000000e-03 56.5
3 TraesCS4D01G289100 chr4A 94.879 5487 186 36 1 5442 7769879 7764443 0.000000e+00 8488.0
4 TraesCS4D01G289100 chr4A 88.848 807 49 19 5526 6303 7764389 7763595 0.000000e+00 953.0
5 TraesCS4D01G289100 chr4A 79.475 648 68 27 6339 6935 7763589 7762956 3.900000e-107 399.0
6 TraesCS4D01G289100 chr4B 95.274 4592 145 27 879 5436 574940476 574945029 0.000000e+00 7212.0
7 TraesCS4D01G289100 chr4B 92.157 816 52 6 1 814 558731481 558730676 0.000000e+00 1142.0
8 TraesCS4D01G289100 chr4B 90.799 576 20 11 5999 6568 574945677 574946225 0.000000e+00 739.0
9 TraesCS4D01G289100 chr4B 83.142 783 127 4 2 783 244478848 244479626 0.000000e+00 710.0
10 TraesCS4D01G289100 chr4B 85.968 506 42 11 5506 5995 574945068 574945560 1.330000e-141 514.0
11 TraesCS4D01G289100 chr4B 94.444 216 11 1 6720 6935 574946230 574946444 1.440000e-86 331.0
12 TraesCS4D01G289100 chr7A 93.023 817 55 2 1 816 733358518 733359333 0.000000e+00 1192.0
13 TraesCS4D01G289100 chr3B 89.833 777 56 13 1 756 157931521 157932295 0.000000e+00 976.0
14 TraesCS4D01G289100 chr3B 97.222 36 1 0 6306 6341 32597558 32597523 2.090000e-05 62.1
15 TraesCS4D01G289100 chr5D 80.952 819 147 9 2 816 191909333 191908520 2.110000e-179 640.0
16 TraesCS4D01G289100 chr5D 94.286 35 2 0 6316 6350 407531440 407531406 3.000000e-03 54.7
17 TraesCS4D01G289100 chr2B 80.440 818 151 9 4 816 789615127 789614314 3.550000e-172 616.0
18 TraesCS4D01G289100 chrUn 78.036 774 149 12 46 816 465078737 465079492 1.050000e-127 468.0
19 TraesCS4D01G289100 chr7B 80.952 231 43 1 587 816 15773299 15773069 1.540000e-41 182.0
20 TraesCS4D01G289100 chr7B 97.143 35 1 0 6307 6341 671765707 671765741 7.510000e-05 60.2
21 TraesCS4D01G289100 chr5B 80.292 137 26 1 6508 6643 673766319 673766455 1.230000e-17 102.0
22 TraesCS4D01G289100 chr5B 93.023 43 3 0 6307 6349 689994730 689994772 5.810000e-06 63.9
23 TraesCS4D01G289100 chr5A 95.455 44 2 0 6306 6349 586314384 586314341 3.470000e-08 71.3
24 TraesCS4D01G289100 chr5A 97.297 37 1 0 6306 6342 675570254 675570290 5.810000e-06 63.9
25 TraesCS4D01G289100 chr5A 93.023 43 2 1 6818 6859 667210087 667210129 2.090000e-05 62.1
26 TraesCS4D01G289100 chr7D 86.885 61 5 2 6815 6874 139886082 139886140 1.610000e-06 65.8
27 TraesCS4D01G289100 chr7D 97.222 36 1 0 6307 6342 602741724 602741759 2.090000e-05 62.1
28 TraesCS4D01G289100 chr2A 91.489 47 3 1 6814 6860 607429247 607429292 5.810000e-06 63.9
29 TraesCS4D01G289100 chr3A 97.222 36 1 0 6830 6865 66799389 66799354 2.090000e-05 62.1
30 TraesCS4D01G289100 chr6D 92.683 41 2 1 6802 6842 427213166 427213205 2.700000e-04 58.4
31 TraesCS4D01G289100 chr6B 97.143 35 0 1 750 783 667944843 667944877 2.700000e-04 58.4
32 TraesCS4D01G289100 chr6B 100.000 30 0 0 6816 6845 29761791 29761820 1.000000e-03 56.5
33 TraesCS4D01G289100 chr1B 92.308 39 2 1 6307 6345 262576258 262576221 3.000000e-03 54.7


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 TraesCS4D01G289100 chr4D 460471205 460478139 6934 False 12807 12807 100.00000 1 6935 1 chr4D.!!$F2 6934
1 TraesCS4D01G289100 chr4A 7762956 7769879 6923 True 3280 8488 87.73400 1 6935 3 chr4A.!!$R1 6934
2 TraesCS4D01G289100 chr4B 574940476 574946444 5968 False 2199 7212 91.62125 879 6935 4 chr4B.!!$F2 6056
3 TraesCS4D01G289100 chr4B 558730676 558731481 805 True 1142 1142 92.15700 1 814 1 chr4B.!!$R1 813
4 TraesCS4D01G289100 chr4B 244478848 244479626 778 False 710 710 83.14200 2 783 1 chr4B.!!$F1 781
5 TraesCS4D01G289100 chr7A 733358518 733359333 815 False 1192 1192 93.02300 1 816 1 chr7A.!!$F1 815
6 TraesCS4D01G289100 chr3B 157931521 157932295 774 False 976 976 89.83300 1 756 1 chr3B.!!$F1 755
7 TraesCS4D01G289100 chr5D 191908520 191909333 813 True 640 640 80.95200 2 816 1 chr5D.!!$R1 814
8 TraesCS4D01G289100 chr2B 789614314 789615127 813 True 616 616 80.44000 4 816 1 chr2B.!!$R1 812
9 TraesCS4D01G289100 chrUn 465078737 465079492 755 False 468 468 78.03600 46 816 1 chrUn.!!$F1 770

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
795 822 0.038166 GGAGGCAATCAACCCTGTGA 59.962 55.000 0.00 0.00 0.00 3.58 F
1365 1403 0.109412 GTGTTCGTCCGGTAGTCTGG 60.109 60.000 0.00 0.00 41.27 3.86 F
2063 2111 0.667792 GCCGAAAGCACGAGAGACTT 60.668 55.000 0.00 0.00 42.97 3.01 F
3536 3601 2.030540 TCATGAAGTTTTGCTGCAGCTC 60.031 45.455 36.61 25.09 42.66 4.09 F
3544 3609 0.035739 TTGCTGCAGCTCTGACATCA 59.964 50.000 36.61 12.87 42.66 3.07 F
4852 4921 1.153086 GAGTGGGCGCATGGAAGAT 60.153 57.895 10.83 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1705 2.683968 TCAGTAATGTTGACAGCCGAC 58.316 47.619 0.00 0.00 0.00 4.79 R
2243 2291 4.188462 TGCAACATTCCTACAATCCTACG 58.812 43.478 0.00 0.00 0.00 3.51 R
3544 3609 4.660303 TCCCTGCAATAGAACATATCCTGT 59.340 41.667 0.00 0.00 40.84 4.00 R
5376 5454 1.323271 TGGAGAAGCTTCGCTCGGAT 61.323 55.000 26.23 6.01 38.25 4.18 R
5476 5558 2.932855 TGTTTCAACCCGATACCACA 57.067 45.000 0.00 0.00 0.00 4.17 R
6541 6778 0.671781 GTGCAATGCAGAGAGACCGT 60.672 55.000 8.73 0.00 40.08 4.83 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
29 30 4.670896 TCCTCACGATGCAGATGAAATA 57.329 40.909 0.00 0.00 0.00 1.40
251 271 6.624423 TCAGAAGATTAGAATTTTTGCCTGC 58.376 36.000 0.00 0.00 0.00 4.85
625 650 5.728637 AAATTACTGGGCTTCCTTTTCTG 57.271 39.130 0.00 0.00 0.00 3.02
644 669 1.943693 CTTGCCACACAAAACCGCG 60.944 57.895 0.00 0.00 37.96 6.46
661 686 2.609737 CCGCGGGGAGTGATAAGTAATC 60.610 54.545 20.10 0.00 34.06 1.75
674 699 5.885912 TGATAAGTAATCAAGGCAAGGAACC 59.114 40.000 0.00 0.00 41.75 3.62
683 709 0.181350 GGCAAGGAACCGAGGATGAT 59.819 55.000 0.00 0.00 0.00 2.45
793 820 0.251341 GTGGAGGCAATCAACCCTGT 60.251 55.000 0.00 0.00 0.00 4.00
795 822 0.038166 GGAGGCAATCAACCCTGTGA 59.962 55.000 0.00 0.00 0.00 3.58
796 823 1.547675 GGAGGCAATCAACCCTGTGAA 60.548 52.381 0.00 0.00 0.00 3.18
797 824 2.450476 GAGGCAATCAACCCTGTGAAT 58.550 47.619 0.00 0.00 0.00 2.57
798 825 3.620488 GAGGCAATCAACCCTGTGAATA 58.380 45.455 0.00 0.00 0.00 1.75
799 826 4.210331 GAGGCAATCAACCCTGTGAATAT 58.790 43.478 0.00 0.00 0.00 1.28
800 827 3.956199 AGGCAATCAACCCTGTGAATATG 59.044 43.478 0.00 0.00 0.00 1.78
801 828 3.068590 GGCAATCAACCCTGTGAATATGG 59.931 47.826 0.00 0.00 0.00 2.74
802 829 3.068590 GCAATCAACCCTGTGAATATGGG 59.931 47.826 0.00 0.00 46.07 4.00
803 830 3.600448 ATCAACCCTGTGAATATGGGG 57.400 47.619 0.00 0.00 44.97 4.96
807 834 2.071778 CCCTGTGAATATGGGGTTGG 57.928 55.000 0.00 0.00 37.37 3.77
808 835 1.287739 CCCTGTGAATATGGGGTTGGT 59.712 52.381 0.00 0.00 37.37 3.67
809 836 2.292192 CCCTGTGAATATGGGGTTGGTT 60.292 50.000 0.00 0.00 37.37 3.67
810 837 2.760092 CCTGTGAATATGGGGTTGGTTG 59.240 50.000 0.00 0.00 0.00 3.77
811 838 3.430453 CTGTGAATATGGGGTTGGTTGT 58.570 45.455 0.00 0.00 0.00 3.32
812 839 3.426615 TGTGAATATGGGGTTGGTTGTC 58.573 45.455 0.00 0.00 0.00 3.18
813 840 3.181428 TGTGAATATGGGGTTGGTTGTCA 60.181 43.478 0.00 0.00 0.00 3.58
814 841 3.443681 GTGAATATGGGGTTGGTTGTCAG 59.556 47.826 0.00 0.00 0.00 3.51
815 842 3.332187 TGAATATGGGGTTGGTTGTCAGA 59.668 43.478 0.00 0.00 0.00 3.27
816 843 2.871096 TATGGGGTTGGTTGTCAGAC 57.129 50.000 0.00 0.00 0.00 3.51
817 844 1.149101 ATGGGGTTGGTTGTCAGACT 58.851 50.000 1.31 0.00 0.00 3.24
818 845 0.182537 TGGGGTTGGTTGTCAGACTG 59.817 55.000 1.31 0.00 0.00 3.51
819 846 0.182775 GGGGTTGGTTGTCAGACTGT 59.817 55.000 1.59 0.00 0.00 3.55
1066 1093 0.813184 ATTCCATTCCTGCAACGCTG 59.187 50.000 0.00 0.00 0.00 5.18
1112 1149 5.052693 TCCATCGATTCTTCCATTTCCAT 57.947 39.130 0.00 0.00 0.00 3.41
1127 1164 0.704076 TCCATTCCCCCAACTCCTTG 59.296 55.000 0.00 0.00 0.00 3.61
1132 1169 3.406512 TTCCCCCAACTCCTTGAAAAA 57.593 42.857 0.00 0.00 0.00 1.94
1136 1173 2.972021 CCCCAACTCCTTGAAAAACCAT 59.028 45.455 0.00 0.00 0.00 3.55
1349 1387 0.591170 CATGGCGAAAGAAACGGTGT 59.409 50.000 0.00 0.00 0.00 4.16
1365 1403 0.109412 GTGTTCGTCCGGTAGTCTGG 60.109 60.000 0.00 0.00 41.27 3.86
1445 1483 3.545481 GTGATGCTCGTCACCGCG 61.545 66.667 10.33 0.00 42.04 6.46
1454 1492 2.813908 GTCACCGCGGTCCATGTC 60.814 66.667 31.80 11.60 0.00 3.06
1570 1608 3.775654 GGACTCACGCCTCAGGGG 61.776 72.222 6.13 6.13 41.67 4.79
1667 1705 3.585990 GGGTGCCATGCCGAATCG 61.586 66.667 0.00 0.00 0.00 3.34
1756 1794 2.298729 TGCCTTGGGTTAATCTTGTTGC 59.701 45.455 0.00 0.00 0.00 4.17
1927 1973 1.860950 CTCACTGGTCACTTGTTGTCG 59.139 52.381 0.00 0.00 0.00 4.35
1955 2001 6.569226 CGCATCTCATTTTGATAGGGGATTTC 60.569 42.308 0.00 0.00 0.00 2.17
1993 2039 1.398958 TTGGGCCTGGACAAACTTGC 61.399 55.000 4.53 0.00 0.00 4.01
1996 2042 1.616159 GGCCTGGACAAACTTGCTAA 58.384 50.000 0.00 0.00 0.00 3.09
2007 2053 6.405397 GGACAAACTTGCTAAGGAAACAAAGA 60.405 38.462 0.00 0.00 0.00 2.52
2012 2058 4.067972 TGCTAAGGAAACAAAGACGAGT 57.932 40.909 0.00 0.00 0.00 4.18
2021 2068 6.318900 AGGAAACAAAGACGAGTGAGAAAATT 59.681 34.615 0.00 0.00 0.00 1.82
2063 2111 0.667792 GCCGAAAGCACGAGAGACTT 60.668 55.000 0.00 0.00 42.97 3.01
2141 2189 7.284716 CCATATACATCTACGAGTGGGCTTATA 59.715 40.741 0.00 0.00 0.00 0.98
2142 2190 8.851145 CATATACATCTACGAGTGGGCTTATAT 58.149 37.037 0.00 0.00 0.00 0.86
2237 2285 9.730420 GATACATAATATTCAGTTTTTGCGGTT 57.270 29.630 0.00 0.00 0.00 4.44
2243 2291 3.799137 TCAGTTTTTGCGGTTATCGAC 57.201 42.857 0.00 0.00 42.43 4.20
2307 2355 5.089970 TCTGTTCTGTGACCATTATCAGG 57.910 43.478 0.00 0.00 0.00 3.86
2353 2403 7.305474 ACTTGTGCATTAATAAGCTGTTACAC 58.695 34.615 0.00 0.00 0.00 2.90
2884 2935 9.464714 GAATGTGTACCATTGATACTGTAGTAG 57.535 37.037 12.50 0.00 43.87 2.57
3536 3601 2.030540 TCATGAAGTTTTGCTGCAGCTC 60.031 45.455 36.61 25.09 42.66 4.09
3544 3609 0.035739 TTGCTGCAGCTCTGACATCA 59.964 50.000 36.61 12.87 42.66 3.07
3703 3768 3.378427 GGAATGTTGGTAGCTCCATGTTC 59.622 47.826 5.83 9.49 46.60 3.18
3750 3815 2.266554 GGCACAAGAAGATCTGAGACG 58.733 52.381 0.00 0.00 0.00 4.18
3946 4011 7.495606 CAGATGTTGTACTATAGTTGGCAATGA 59.504 37.037 11.40 6.28 0.00 2.57
3965 4030 7.192232 GCAATGATTCTCCTTCAGTAATTGAC 58.808 38.462 0.00 0.00 34.94 3.18
4442 4509 3.433598 GGTATGCCTCAATGCCTGAACTA 60.434 47.826 0.00 0.00 32.17 2.24
4460 4527 7.337942 CCTGAACTAAGAGATGTGCCTTTTAAT 59.662 37.037 0.00 0.00 0.00 1.40
4717 4786 2.539476 GGTTCAACACCAAACAAGCAG 58.461 47.619 0.00 0.00 46.42 4.24
4852 4921 1.153086 GAGTGGGCGCATGGAAGAT 60.153 57.895 10.83 0.00 0.00 2.40
4902 4971 2.273370 ATACAGGTGCTACAACGTCG 57.727 50.000 0.00 0.00 0.00 5.12
5032 5103 3.504863 TCCGTACGAGAATGTGCTTAAC 58.495 45.455 18.76 0.00 0.00 2.01
5083 5154 2.441001 AGATGACATCCCCAACCTCATC 59.559 50.000 11.92 0.00 38.25 2.92
5196 5274 8.850452 GGAATGAACGAAACACAAATAGATTTC 58.150 33.333 0.00 0.00 0.00 2.17
5247 5325 3.056749 AGAGGTTCTTTTATCGCGACACT 60.057 43.478 12.93 0.00 0.00 3.55
5331 5409 6.479001 CAGTTGAGGTTTCGAAACTAGAAGAA 59.521 38.462 33.23 17.90 38.89 2.52
5340 5418 6.531503 TCGAAACTAGAAGAAGGTGATGAT 57.468 37.500 0.00 0.00 0.00 2.45
5384 5462 3.813529 AACTTCTGAAAAATCCGAGCG 57.186 42.857 0.00 0.00 0.00 5.03
5406 5484 6.927294 CGAAGCTTCTCCATTTACCTTTAT 57.073 37.500 23.50 0.00 0.00 1.40
5407 5485 6.719365 CGAAGCTTCTCCATTTACCTTTATG 58.281 40.000 23.50 0.00 0.00 1.90
5443 5525 5.868043 TGATAATGATCATTGACGGCATC 57.132 39.130 27.59 20.68 37.15 3.91
5444 5526 5.554070 TGATAATGATCATTGACGGCATCT 58.446 37.500 27.59 3.04 37.15 2.90
5445 5527 6.700352 TGATAATGATCATTGACGGCATCTA 58.300 36.000 27.59 6.90 37.15 1.98
5446 5528 6.815142 TGATAATGATCATTGACGGCATCTAG 59.185 38.462 27.59 0.00 37.15 2.43
5447 5529 2.759191 TGATCATTGACGGCATCTAGC 58.241 47.619 0.00 0.00 44.65 3.42
5449 5531 8.203563 TAATGATCATTGACGGCATCTAGCCT 62.204 42.308 27.59 0.91 45.33 4.58
5461 5543 3.940221 GCATCTAGCCTTCATCCATCATC 59.060 47.826 0.00 0.00 37.23 2.92
5462 5544 4.565028 GCATCTAGCCTTCATCCATCATCA 60.565 45.833 0.00 0.00 37.23 3.07
5463 5545 5.746284 CATCTAGCCTTCATCCATCATCAT 58.254 41.667 0.00 0.00 0.00 2.45
5464 5546 5.417754 TCTAGCCTTCATCCATCATCATC 57.582 43.478 0.00 0.00 0.00 2.92
5465 5547 4.842380 TCTAGCCTTCATCCATCATCATCA 59.158 41.667 0.00 0.00 0.00 3.07
5466 5548 4.659529 AGCCTTCATCCATCATCATCAT 57.340 40.909 0.00 0.00 0.00 2.45
5467 5549 4.590918 AGCCTTCATCCATCATCATCATC 58.409 43.478 0.00 0.00 0.00 2.92
5468 5550 4.042934 AGCCTTCATCCATCATCATCATCA 59.957 41.667 0.00 0.00 0.00 3.07
5469 5551 4.950475 GCCTTCATCCATCATCATCATCAT 59.050 41.667 0.00 0.00 0.00 2.45
5470 5552 5.066634 GCCTTCATCCATCATCATCATCATC 59.933 44.000 0.00 0.00 0.00 2.92
5471 5553 6.418946 CCTTCATCCATCATCATCATCATCT 58.581 40.000 0.00 0.00 0.00 2.90
5472 5554 7.565680 CCTTCATCCATCATCATCATCATCTA 58.434 38.462 0.00 0.00 0.00 1.98
5473 5555 7.496263 CCTTCATCCATCATCATCATCATCTAC 59.504 40.741 0.00 0.00 0.00 2.59
5474 5556 7.735326 TCATCCATCATCATCATCATCTACT 57.265 36.000 0.00 0.00 0.00 2.57
5475 5557 8.147244 TCATCCATCATCATCATCATCTACTT 57.853 34.615 0.00 0.00 0.00 2.24
5476 5558 8.603304 TCATCCATCATCATCATCATCTACTTT 58.397 33.333 0.00 0.00 0.00 2.66
5477 5559 8.669243 CATCCATCATCATCATCATCTACTTTG 58.331 37.037 0.00 0.00 0.00 2.77
5478 5560 7.742767 TCCATCATCATCATCATCTACTTTGT 58.257 34.615 0.00 0.00 0.00 2.83
5479 5561 7.660208 TCCATCATCATCATCATCTACTTTGTG 59.340 37.037 0.00 0.00 0.00 3.33
5480 5562 7.094762 CCATCATCATCATCATCTACTTTGTGG 60.095 40.741 0.00 0.00 0.00 4.17
5481 5563 6.892485 TCATCATCATCATCTACTTTGTGGT 58.108 36.000 0.00 0.00 0.00 4.16
5482 5564 8.021898 TCATCATCATCATCTACTTTGTGGTA 57.978 34.615 0.00 0.00 0.00 3.25
5483 5565 8.654094 TCATCATCATCATCTACTTTGTGGTAT 58.346 33.333 0.00 0.00 0.00 2.73
5484 5566 8.933807 CATCATCATCATCTACTTTGTGGTATC 58.066 37.037 0.00 0.00 0.00 2.24
5485 5567 7.147976 TCATCATCATCTACTTTGTGGTATCG 58.852 38.462 0.00 0.00 0.00 2.92
5486 5568 5.842907 TCATCATCTACTTTGTGGTATCGG 58.157 41.667 0.00 0.00 0.00 4.18
5487 5569 4.665833 TCATCTACTTTGTGGTATCGGG 57.334 45.455 0.00 0.00 0.00 5.14
5488 5570 4.028131 TCATCTACTTTGTGGTATCGGGT 58.972 43.478 0.00 0.00 0.00 5.28
5489 5571 4.468510 TCATCTACTTTGTGGTATCGGGTT 59.531 41.667 0.00 0.00 0.00 4.11
5490 5572 4.196626 TCTACTTTGTGGTATCGGGTTG 57.803 45.455 0.00 0.00 0.00 3.77
5493 5575 3.822940 ACTTTGTGGTATCGGGTTGAAA 58.177 40.909 0.00 0.00 0.00 2.69
5496 5578 3.426787 TGTGGTATCGGGTTGAAACAT 57.573 42.857 0.00 0.00 0.00 2.71
5498 5580 4.145807 TGTGGTATCGGGTTGAAACATTT 58.854 39.130 0.00 0.00 0.00 2.32
5523 5605 6.910536 TTGCAAATTTTGTTTCCATTACGT 57.089 29.167 10.65 0.00 0.00 3.57
5524 5606 8.420374 TTTGCAAATTTTGTTTCCATTACGTA 57.580 26.923 8.05 0.00 0.00 3.57
5536 5619 5.728351 TCCATTACGTAGCAAAGCATTAC 57.272 39.130 0.00 0.00 0.00 1.89
5559 5642 3.286751 GTGTGCTTGCCTTGCCGA 61.287 61.111 0.00 0.00 0.00 5.54
5566 5649 1.610522 GCTTGCCTTGCCGAATCATAT 59.389 47.619 0.00 0.00 0.00 1.78
5571 5654 4.713553 TGCCTTGCCGAATCATATTAGAA 58.286 39.130 0.00 0.00 0.00 2.10
5574 5665 4.152402 CCTTGCCGAATCATATTAGAACCG 59.848 45.833 0.00 0.00 0.00 4.44
5584 5675 5.909477 TCATATTAGAACCGGTCGTCATTT 58.091 37.500 8.04 0.00 0.00 2.32
5586 5677 3.947910 TTAGAACCGGTCGTCATTTCT 57.052 42.857 8.04 7.87 0.00 2.52
5588 5679 1.343465 AGAACCGGTCGTCATTTCTGT 59.657 47.619 8.04 0.00 0.00 3.41
5590 5681 3.006110 AGAACCGGTCGTCATTTCTGTTA 59.994 43.478 8.04 0.00 0.00 2.41
5591 5682 3.389925 ACCGGTCGTCATTTCTGTTAA 57.610 42.857 0.00 0.00 0.00 2.01
5592 5683 3.062042 ACCGGTCGTCATTTCTGTTAAC 58.938 45.455 0.00 0.00 0.00 2.01
5594 5685 2.414138 CGGTCGTCATTTCTGTTAACCC 59.586 50.000 2.48 0.00 0.00 4.11
5600 5691 4.320870 GTCATTTCTGTTAACCCGAGGAA 58.679 43.478 2.48 0.00 0.00 3.36
5644 5739 8.317891 TGCATTATAAGTTATACAATGACCCG 57.682 34.615 17.18 0.00 0.00 5.28
5664 5759 3.706373 GCGGCAAGGTCTCCTCCA 61.706 66.667 0.00 0.00 30.89 3.86
5718 5813 0.767375 AAGGCTTCCTGAAGTGCTCA 59.233 50.000 8.57 0.00 40.45 4.26
5760 5855 3.312973 CGATAGGCTTAGGATAGGCGTAG 59.687 52.174 0.00 0.00 45.01 3.51
5768 5863 5.241285 GCTTAGGATAGGCGTAGTTACTCTT 59.759 44.000 0.00 0.00 32.71 2.85
5771 5866 8.752005 TTAGGATAGGCGTAGTTACTCTTTTA 57.248 34.615 0.00 0.00 0.00 1.52
5786 5881 9.626045 GTTACTCTTTTAATCCCATGTGAAAAG 57.374 33.333 0.00 0.00 38.09 2.27
5845 5941 2.386661 TGGAAATGAGACTCGCCTTC 57.613 50.000 0.00 0.79 0.00 3.46
5851 5947 2.949451 TGAGACTCGCCTTCTCATTC 57.051 50.000 6.41 0.00 43.69 2.67
5897 5995 6.176975 TGCTGTTTTGACAGAATATAACCG 57.823 37.500 10.51 0.00 39.99 4.44
5911 6009 6.778069 AGAATATAACCGAGACCATTCTCTGA 59.222 38.462 0.70 0.00 45.61 3.27
5914 6012 3.601443 ACCGAGACCATTCTCTGAAAG 57.399 47.619 0.70 0.00 45.61 2.62
5917 6015 4.040461 ACCGAGACCATTCTCTGAAAGAAA 59.960 41.667 0.70 0.00 46.34 2.52
5918 6016 4.997395 CCGAGACCATTCTCTGAAAGAAAA 59.003 41.667 0.46 0.00 46.34 2.29
5919 6017 5.645497 CCGAGACCATTCTCTGAAAGAAAAT 59.355 40.000 0.46 0.00 46.34 1.82
5920 6018 6.402983 CCGAGACCATTCTCTGAAAGAAAATG 60.403 42.308 0.46 0.00 46.34 2.32
5921 6019 6.369890 CGAGACCATTCTCTGAAAGAAAATGA 59.630 38.462 5.13 0.00 46.34 2.57
5922 6020 7.065563 CGAGACCATTCTCTGAAAGAAAATGAT 59.934 37.037 5.13 0.00 46.34 2.45
5923 6021 9.388506 GAGACCATTCTCTGAAAGAAAATGATA 57.611 33.333 5.13 0.00 46.34 2.15
5924 6022 9.171877 AGACCATTCTCTGAAAGAAAATGATAC 57.828 33.333 5.13 0.00 46.34 2.24
5925 6023 9.171877 GACCATTCTCTGAAAGAAAATGATACT 57.828 33.333 5.13 0.00 46.34 2.12
5926 6024 8.954350 ACCATTCTCTGAAAGAAAATGATACTG 58.046 33.333 5.13 0.00 46.34 2.74
5971 6069 7.611467 TCTGTTGAGCCAAAACTGATATACATT 59.389 33.333 0.00 0.00 32.57 2.71
6223 6447 9.660180 GAGGTGGATCTTTATTTATACCATCTC 57.340 37.037 0.00 0.00 43.53 2.75
6303 6529 0.672342 CAAGCCCTAGCCGTACGTAT 59.328 55.000 15.21 4.56 41.25 3.06
6304 6530 0.672342 AAGCCCTAGCCGTACGTATG 59.328 55.000 15.21 7.87 41.25 2.39
6307 6533 1.608590 GCCCTAGCCGTACGTATGTAA 59.391 52.381 15.21 0.00 30.94 2.41
6309 6535 3.490761 GCCCTAGCCGTACGTATGTAAAA 60.491 47.826 15.21 0.00 30.94 1.52
6310 6536 4.797275 GCCCTAGCCGTACGTATGTAAAAT 60.797 45.833 15.21 0.00 30.94 1.82
6311 6537 5.291971 CCCTAGCCGTACGTATGTAAAATT 58.708 41.667 15.21 0.00 30.94 1.82
6312 6538 5.176223 CCCTAGCCGTACGTATGTAAAATTG 59.824 44.000 15.21 0.00 30.94 2.32
6313 6539 5.176223 CCTAGCCGTACGTATGTAAAATTGG 59.824 44.000 15.21 3.30 30.94 3.16
6314 6540 4.757594 AGCCGTACGTATGTAAAATTGGA 58.242 39.130 15.21 0.00 30.94 3.53
6315 6541 5.362263 AGCCGTACGTATGTAAAATTGGAT 58.638 37.500 15.21 0.00 30.94 3.41
6316 6542 5.464389 AGCCGTACGTATGTAAAATTGGATC 59.536 40.000 15.21 0.00 30.94 3.36
6317 6543 5.234757 GCCGTACGTATGTAAAATTGGATCA 59.765 40.000 15.21 0.00 30.94 2.92
6318 6544 6.073440 GCCGTACGTATGTAAAATTGGATCAT 60.073 38.462 15.21 0.00 30.94 2.45
6319 6545 7.507304 CCGTACGTATGTAAAATTGGATCATC 58.493 38.462 15.21 0.00 30.94 2.92
6320 6546 7.384115 CCGTACGTATGTAAAATTGGATCATCT 59.616 37.037 15.21 0.00 30.94 2.90
6321 6547 9.401873 CGTACGTATGTAAAATTGGATCATCTA 57.598 33.333 7.22 0.00 30.94 1.98
6332 6558 8.931385 AAATTGGATCATCTATTTTGAAACGG 57.069 30.769 0.00 0.00 0.00 4.44
6333 6559 7.880160 ATTGGATCATCTATTTTGAAACGGA 57.120 32.000 0.00 0.00 0.00 4.69
6334 6560 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
6335 6561 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
6336 6562 6.055588 GGATCATCTATTTTGAAACGGAGGA 58.944 40.000 0.00 0.00 0.00 3.71
6337 6563 6.542370 GGATCATCTATTTTGAAACGGAGGAA 59.458 38.462 0.00 0.00 0.00 3.36
6541 6778 0.841289 AAAAGGTCCTGGGTTCGACA 59.159 50.000 0.00 0.00 0.00 4.35
6545 6782 2.522436 TCCTGGGTTCGACACGGT 60.522 61.111 0.00 0.00 0.00 4.83
6583 6820 5.808946 CTGTGCACAGGAAAGGTTTACCTC 61.809 50.000 34.65 0.00 42.01 3.85
6603 6840 2.045885 TCCTACATTCCTTCCCCAGACT 59.954 50.000 0.00 0.00 0.00 3.24
6604 6841 2.846827 CCTACATTCCTTCCCCAGACTT 59.153 50.000 0.00 0.00 0.00 3.01
6608 6845 2.118403 TTCCTTCCCCAGACTTCACT 57.882 50.000 0.00 0.00 0.00 3.41
6610 6847 2.418669 TCCTTCCCCAGACTTCACTTT 58.581 47.619 0.00 0.00 0.00 2.66
6613 6850 2.638480 TCCCCAGACTTCACTTTGTG 57.362 50.000 0.00 0.00 34.45 3.33
6624 6861 3.644966 TCACTTTGTGTGGGAGTTTCT 57.355 42.857 0.00 0.00 46.20 2.52
6635 6872 2.378547 TGGGAGTTTCTAGCATTGGGTT 59.621 45.455 0.00 0.00 0.00 4.11
6640 6877 3.826729 AGTTTCTAGCATTGGGTTTGTCC 59.173 43.478 0.00 0.00 0.00 4.02
6643 6880 4.919774 TCTAGCATTGGGTTTGTCCTTA 57.080 40.909 0.00 0.00 36.25 2.69
6644 6881 4.585879 TCTAGCATTGGGTTTGTCCTTAC 58.414 43.478 0.00 0.00 36.25 2.34
6646 6883 4.650972 AGCATTGGGTTTGTCCTTACTA 57.349 40.909 0.00 0.00 36.25 1.82
6647 6884 5.193099 AGCATTGGGTTTGTCCTTACTAT 57.807 39.130 0.00 0.00 36.25 2.12
6648 6885 5.580022 AGCATTGGGTTTGTCCTTACTATT 58.420 37.500 0.00 0.00 36.25 1.73
6649 6886 5.418840 AGCATTGGGTTTGTCCTTACTATTG 59.581 40.000 0.00 0.00 36.25 1.90
6652 6889 7.363793 GCATTGGGTTTGTCCTTACTATTGATT 60.364 37.037 0.00 0.00 36.25 2.57
6653 6890 8.531146 CATTGGGTTTGTCCTTACTATTGATTT 58.469 33.333 0.00 0.00 36.25 2.17
6654 6891 7.696992 TGGGTTTGTCCTTACTATTGATTTC 57.303 36.000 0.00 0.00 36.25 2.17
6655 6892 7.235079 TGGGTTTGTCCTTACTATTGATTTCA 58.765 34.615 0.00 0.00 36.25 2.69
6656 6893 7.393234 TGGGTTTGTCCTTACTATTGATTTCAG 59.607 37.037 0.00 0.00 36.25 3.02
6659 6896 9.444600 GTTTGTCCTTACTATTGATTTCAGGTA 57.555 33.333 0.00 0.00 0.00 3.08
6660 6897 9.667107 TTTGTCCTTACTATTGATTTCAGGTAG 57.333 33.333 0.00 2.40 0.00 3.18
6661 6898 7.272978 TGTCCTTACTATTGATTTCAGGTAGC 58.727 38.462 0.00 0.00 0.00 3.58
6668 6924 1.354031 TGATTTCAGGTAGCTGGCCAA 59.646 47.619 21.22 12.22 0.00 4.52
6691 6947 0.396556 TGCCGCCTGGTAGTGATAGA 60.397 55.000 0.00 0.00 37.67 1.98
6912 7192 8.900983 TTTGAATATGAAAACAAGAAAAGGGG 57.099 30.769 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.685712 CGTAGCTTTAATATTTCATCTGCATCG 59.314 37.037 0.00 0.00 0.00 3.84
29 30 6.761714 CCAAATCCAGAGTACGTAGCTTTAAT 59.238 38.462 0.00 0.00 0.00 1.40
123 125 2.101582 AGTCCCTGATATTCAGTGCGAC 59.898 50.000 4.00 6.26 42.80 5.19
251 271 3.108144 CAAACTGTTTGAAGCAACTCGG 58.892 45.455 25.06 0.00 43.26 4.63
473 495 5.298276 GCCAACGGATTTAATTGATCCAGTA 59.702 40.000 17.71 0.00 42.63 2.74
552 574 8.091952 TGGGTTCTTTACCTTTACCAAAAATT 57.908 30.769 0.00 0.00 46.86 1.82
579 604 9.698309 TTTTGTACAAAATTCACAGAAACTGAA 57.302 25.926 26.05 1.96 35.57 3.02
625 650 2.237066 GCGGTTTTGTGTGGCAAGC 61.237 57.895 0.00 0.00 38.47 4.01
644 669 4.141482 TGCCTTGATTACTTATCACTCCCC 60.141 45.833 0.00 0.00 42.88 4.81
661 686 0.035056 ATCCTCGGTTCCTTGCCTTG 60.035 55.000 0.00 0.00 0.00 3.61
674 699 2.738846 CAAAGCCCGAATATCATCCTCG 59.261 50.000 0.00 0.00 0.00 4.63
683 709 7.685481 TCTCCATATTATTCAAAGCCCGAATA 58.315 34.615 0.00 0.00 34.89 1.75
732 759 6.753913 AATCTTATAGCACTCCTCATTGGA 57.246 37.500 0.00 0.00 43.86 3.53
793 820 3.332187 TCTGACAACCAACCCCATATTCA 59.668 43.478 0.00 0.00 0.00 2.57
795 822 3.333680 AGTCTGACAACCAACCCCATATT 59.666 43.478 10.88 0.00 0.00 1.28
796 823 2.919602 AGTCTGACAACCAACCCCATAT 59.080 45.455 10.88 0.00 0.00 1.78
797 824 2.039746 CAGTCTGACAACCAACCCCATA 59.960 50.000 10.88 0.00 0.00 2.74
798 825 1.149101 AGTCTGACAACCAACCCCAT 58.851 50.000 10.88 0.00 0.00 4.00
799 826 0.182537 CAGTCTGACAACCAACCCCA 59.817 55.000 10.88 0.00 0.00 4.96
800 827 0.182775 ACAGTCTGACAACCAACCCC 59.817 55.000 10.88 0.00 0.00 4.95
801 828 2.104281 ACTACAGTCTGACAACCAACCC 59.896 50.000 10.88 0.00 0.00 4.11
802 829 3.470645 ACTACAGTCTGACAACCAACC 57.529 47.619 10.88 0.00 0.00 3.77
803 830 8.773404 AAATATACTACAGTCTGACAACCAAC 57.227 34.615 10.88 0.00 0.00 3.77
804 831 9.214957 CAAAATATACTACAGTCTGACAACCAA 57.785 33.333 10.88 0.00 0.00 3.67
805 832 7.822334 CCAAAATATACTACAGTCTGACAACCA 59.178 37.037 10.88 0.00 0.00 3.67
806 833 8.038944 TCCAAAATATACTACAGTCTGACAACC 58.961 37.037 10.88 0.00 0.00 3.77
807 834 8.997621 TCCAAAATATACTACAGTCTGACAAC 57.002 34.615 10.88 0.00 0.00 3.32
808 835 9.431887 GTTCCAAAATATACTACAGTCTGACAA 57.568 33.333 10.88 0.00 0.00 3.18
809 836 7.758076 CGTTCCAAAATATACTACAGTCTGACA 59.242 37.037 10.88 0.00 0.00 3.58
810 837 7.222224 CCGTTCCAAAATATACTACAGTCTGAC 59.778 40.741 6.91 0.00 0.00 3.51
811 838 7.123098 TCCGTTCCAAAATATACTACAGTCTGA 59.877 37.037 6.91 0.00 0.00 3.27
812 839 7.262772 TCCGTTCCAAAATATACTACAGTCTG 58.737 38.462 0.00 0.00 0.00 3.51
813 840 7.123847 ACTCCGTTCCAAAATATACTACAGTCT 59.876 37.037 0.00 0.00 0.00 3.24
814 841 7.263496 ACTCCGTTCCAAAATATACTACAGTC 58.737 38.462 0.00 0.00 0.00 3.51
815 842 7.179076 ACTCCGTTCCAAAATATACTACAGT 57.821 36.000 0.00 0.00 0.00 3.55
893 920 2.604046 CCAGACATAGTAGTGGCACC 57.396 55.000 15.27 0.00 0.00 5.01
931 958 7.117236 TGTCGCTTTCATTAACTCGTTAATTCT 59.883 33.333 11.29 0.00 42.11 2.40
1066 1093 1.471287 GGGCGTTGTTAGGTTCAATCC 59.529 52.381 0.00 0.00 0.00 3.01
1112 1149 3.035363 GTTTTTCAAGGAGTTGGGGGAA 58.965 45.455 0.00 0.00 34.09 3.97
1127 1164 5.899547 AGGATCTGGGGATTTATGGTTTTTC 59.100 40.000 0.00 0.00 31.46 2.29
1186 1224 3.453679 AAGGCGGACGAGGAGAGC 61.454 66.667 0.00 0.00 0.00 4.09
1291 1329 0.108186 AATCGATGCGAACAGAGCCA 60.108 50.000 0.00 0.00 39.99 4.75
1349 1387 2.345760 GGCCAGACTACCGGACGAA 61.346 63.158 9.46 0.00 0.00 3.85
1365 1403 1.795162 CGAACGGATTTTGAGCATGGC 60.795 52.381 0.00 0.00 0.00 4.40
1454 1492 1.072965 GGGAGGATAGGCACCATGAAG 59.927 57.143 0.00 0.00 0.00 3.02
1466 1504 1.542175 CAGGGACGAGGGGAGGATA 59.458 63.158 0.00 0.00 0.00 2.59
1544 1582 3.148084 CGTGAGTCCACAACCCCT 58.852 61.111 0.00 0.00 43.34 4.79
1667 1705 2.683968 TCAGTAATGTTGACAGCCGAC 58.316 47.619 0.00 0.00 0.00 4.79
1725 1763 5.816955 TTAACCCAAGGCAAAGCTAAATT 57.183 34.783 0.00 0.00 0.00 1.82
1756 1794 3.817647 GCCAATAGCCTGTCCAGAAATAG 59.182 47.826 0.00 0.00 34.35 1.73
1791 1829 3.057736 CCATTTCCACTGCAGTCTTTCTG 60.058 47.826 18.64 11.85 46.12 3.02
1927 1973 4.394300 CCCCTATCAAAATGAGATGCGATC 59.606 45.833 0.00 0.00 0.00 3.69
1955 2001 5.988561 GCCCAAAGAACTATCAGATCTACAG 59.011 44.000 0.00 0.00 26.56 2.74
1993 2039 5.529791 TCTCACTCGTCTTTGTTTCCTTAG 58.470 41.667 0.00 0.00 0.00 2.18
1996 2042 4.402056 TTCTCACTCGTCTTTGTTTCCT 57.598 40.909 0.00 0.00 0.00 3.36
2007 2053 9.503399 ACCTCTTTTTATAATTTTCTCACTCGT 57.497 29.630 0.00 0.00 0.00 4.18
2021 2068 6.888088 GGCCCTTGAAGTAACCTCTTTTTATA 59.112 38.462 0.00 0.00 0.00 0.98
2063 2111 4.018870 TGTCCAATATAAACACCCAGAGCA 60.019 41.667 0.00 0.00 0.00 4.26
2127 2175 5.347620 TTGTTACATATAAGCCCACTCGT 57.652 39.130 0.00 0.00 0.00 4.18
2141 2189 6.655003 CAGGGATGTACACTCTTTTGTTACAT 59.345 38.462 0.00 0.00 31.79 2.29
2142 2190 5.995282 CAGGGATGTACACTCTTTTGTTACA 59.005 40.000 0.00 0.00 0.00 2.41
2237 2285 5.766670 ACATTCCTACAATCCTACGTCGATA 59.233 40.000 0.00 0.00 0.00 2.92
2243 2291 4.188462 TGCAACATTCCTACAATCCTACG 58.812 43.478 0.00 0.00 0.00 3.51
2307 2355 4.576463 AGTTCATTCCCGATTCAAGCATAC 59.424 41.667 0.00 0.00 0.00 2.39
2372 2422 7.514721 TCCACAAAAAGGTAGACAAGTAAGAT 58.485 34.615 0.00 0.00 0.00 2.40
2853 2904 7.882791 ACAGTATCAATGGTACACATTCTGAAA 59.117 33.333 19.09 4.41 46.67 2.69
3019 3070 4.818546 ACTTTGGAAGAATATGCATCCTCG 59.181 41.667 0.19 0.00 33.02 4.63
3536 3601 7.095313 GCAATAGAACATATCCTGTGATGTCAG 60.095 40.741 0.00 0.00 38.39 3.51
3544 3609 4.660303 TCCCTGCAATAGAACATATCCTGT 59.340 41.667 0.00 0.00 40.84 4.00
3703 3768 7.367159 TGTAAACGGGATTGTTGTTACTATG 57.633 36.000 0.00 0.00 31.10 2.23
3965 4030 4.811557 CGCAGGTCCTCCTAAAATTAGAAG 59.188 45.833 1.75 0.00 43.07 2.85
3992 4057 7.183460 AGTACTCAAGAGTATGGTAACTCCTT 58.817 38.462 12.62 0.00 45.86 3.36
4426 4493 4.478206 TCTCTTAGTTCAGGCATTGAGG 57.522 45.455 0.00 0.00 37.07 3.86
4442 4509 8.635765 TCAAGTAATTAAAAGGCACATCTCTT 57.364 30.769 0.00 0.00 0.00 2.85
4460 4527 6.934645 CAGTGAGGGTCTAAACATTCAAGTAA 59.065 38.462 0.00 0.00 0.00 2.24
4717 4786 1.680314 CTGCCTTCCAAGCTTCCCC 60.680 63.158 0.00 0.00 0.00 4.81
4852 4921 2.423446 TGCATCCTTGAAGCATGCTA 57.577 45.000 23.00 2.60 42.91 3.49
4902 4971 8.898761 CAGATACACATCATAGGACTATAGGAC 58.101 40.741 4.43 0.00 33.21 3.85
5083 5154 3.594603 ACACATACTTGAAGGACTCCG 57.405 47.619 0.00 0.00 0.00 4.63
5196 5274 3.689161 TCTGGCGAACATTTCCTAACATG 59.311 43.478 0.00 0.00 0.00 3.21
5284 5362 3.394836 GGCCGCCTCCTCTTCAGT 61.395 66.667 0.71 0.00 0.00 3.41
5331 5409 3.759581 AGTTGCAAAGACATCATCACCT 58.240 40.909 0.00 0.00 0.00 4.00
5340 5418 4.887071 ACCTGTATGAAAGTTGCAAAGACA 59.113 37.500 0.00 0.00 0.00 3.41
5376 5454 1.323271 TGGAGAAGCTTCGCTCGGAT 61.323 55.000 26.23 6.01 38.25 4.18
5384 5462 7.032377 CCATAAAGGTAAATGGAGAAGCTTC 57.968 40.000 19.11 19.11 44.62 3.86
5405 5483 7.948384 GATCATTATCATGCGGTTTCAAACCAT 60.948 37.037 19.61 7.17 40.60 3.55
5406 5484 6.680131 GATCATTATCATGCGGTTTCAAACCA 60.680 38.462 19.61 0.56 40.60 3.67
5407 5485 5.687285 GATCATTATCATGCGGTTTCAAACC 59.313 40.000 9.53 9.53 38.87 3.27
5439 5521 3.413846 TGATGGATGAAGGCTAGATGC 57.586 47.619 0.00 0.00 41.94 3.91
5442 5524 4.842380 TGATGATGATGGATGAAGGCTAGA 59.158 41.667 0.00 0.00 0.00 2.43
5443 5525 5.161943 TGATGATGATGGATGAAGGCTAG 57.838 43.478 0.00 0.00 0.00 3.42
5444 5526 5.249852 TGATGATGATGATGGATGAAGGCTA 59.750 40.000 0.00 0.00 0.00 3.93
5445 5527 4.042934 TGATGATGATGATGGATGAAGGCT 59.957 41.667 0.00 0.00 0.00 4.58
5446 5528 4.332828 TGATGATGATGATGGATGAAGGC 58.667 43.478 0.00 0.00 0.00 4.35
5447 5529 6.418946 AGATGATGATGATGATGGATGAAGG 58.581 40.000 0.00 0.00 0.00 3.46
5449 5531 8.147244 AGTAGATGATGATGATGATGGATGAA 57.853 34.615 0.00 0.00 0.00 2.57
5451 5533 8.669243 CAAAGTAGATGATGATGATGATGGATG 58.331 37.037 0.00 0.00 0.00 3.51
5452 5534 8.383947 ACAAAGTAGATGATGATGATGATGGAT 58.616 33.333 0.00 0.00 0.00 3.41
5453 5535 7.660208 CACAAAGTAGATGATGATGATGATGGA 59.340 37.037 0.00 0.00 0.00 3.41
5454 5536 7.094762 CCACAAAGTAGATGATGATGATGATGG 60.095 40.741 0.00 0.00 0.00 3.51
5455 5537 7.444487 ACCACAAAGTAGATGATGATGATGATG 59.556 37.037 0.00 0.00 0.00 3.07
5457 5539 6.892485 ACCACAAAGTAGATGATGATGATGA 58.108 36.000 0.00 0.00 0.00 2.92
5461 5543 6.367149 CCGATACCACAAAGTAGATGATGATG 59.633 42.308 0.00 0.00 0.00 3.07
5462 5544 6.459066 CCGATACCACAAAGTAGATGATGAT 58.541 40.000 0.00 0.00 0.00 2.45
5463 5545 5.221441 CCCGATACCACAAAGTAGATGATGA 60.221 44.000 0.00 0.00 0.00 2.92
5464 5546 4.991056 CCCGATACCACAAAGTAGATGATG 59.009 45.833 0.00 0.00 0.00 3.07
5465 5547 4.654262 ACCCGATACCACAAAGTAGATGAT 59.346 41.667 0.00 0.00 0.00 2.45
5466 5548 4.028131 ACCCGATACCACAAAGTAGATGA 58.972 43.478 0.00 0.00 0.00 2.92
5467 5549 4.402056 ACCCGATACCACAAAGTAGATG 57.598 45.455 0.00 0.00 0.00 2.90
5468 5550 4.468510 TCAACCCGATACCACAAAGTAGAT 59.531 41.667 0.00 0.00 0.00 1.98
5469 5551 3.833650 TCAACCCGATACCACAAAGTAGA 59.166 43.478 0.00 0.00 0.00 2.59
5470 5552 4.196626 TCAACCCGATACCACAAAGTAG 57.803 45.455 0.00 0.00 0.00 2.57
5471 5553 4.620589 TTCAACCCGATACCACAAAGTA 57.379 40.909 0.00 0.00 0.00 2.24
5472 5554 3.495434 TTCAACCCGATACCACAAAGT 57.505 42.857 0.00 0.00 0.00 2.66
5473 5555 3.566322 TGTTTCAACCCGATACCACAAAG 59.434 43.478 0.00 0.00 0.00 2.77
5474 5556 3.552875 TGTTTCAACCCGATACCACAAA 58.447 40.909 0.00 0.00 0.00 2.83
5475 5557 3.210232 TGTTTCAACCCGATACCACAA 57.790 42.857 0.00 0.00 0.00 3.33
5476 5558 2.932855 TGTTTCAACCCGATACCACA 57.067 45.000 0.00 0.00 0.00 4.17
5477 5559 4.776795 AAATGTTTCAACCCGATACCAC 57.223 40.909 0.00 0.00 0.00 4.16
5478 5560 5.793030 AAAAATGTTTCAACCCGATACCA 57.207 34.783 0.00 0.00 0.00 3.25
5511 5593 4.413495 TGCTTTGCTACGTAATGGAAAC 57.587 40.909 0.00 0.00 0.00 2.78
5515 5597 4.514506 CGTAATGCTTTGCTACGTAATGG 58.485 43.478 0.00 0.00 34.99 3.16
5549 5632 4.350368 TCTAATATGATTCGGCAAGGCA 57.650 40.909 0.00 0.00 0.00 4.75
5552 5635 4.152402 CCGGTTCTAATATGATTCGGCAAG 59.848 45.833 0.00 0.00 0.00 4.01
5559 5642 5.524971 TGACGACCGGTTCTAATATGATT 57.475 39.130 9.42 0.00 0.00 2.57
5566 5649 3.006110 ACAGAAATGACGACCGGTTCTAA 59.994 43.478 9.42 0.00 0.00 2.10
5571 5654 3.062042 GTTAACAGAAATGACGACCGGT 58.938 45.455 6.92 6.92 0.00 5.28
5574 5665 2.414138 CGGGTTAACAGAAATGACGACC 59.586 50.000 8.10 0.00 0.00 4.79
5584 5675 3.581332 ACATTCTTCCTCGGGTTAACAGA 59.419 43.478 8.10 5.45 0.00 3.41
5586 5677 4.360951 AACATTCTTCCTCGGGTTAACA 57.639 40.909 8.10 0.00 0.00 2.41
5588 5679 6.771749 TGTAAAAACATTCTTCCTCGGGTTAA 59.228 34.615 0.00 0.00 0.00 2.01
5590 5681 5.134661 TGTAAAAACATTCTTCCTCGGGTT 58.865 37.500 0.00 0.00 0.00 4.11
5591 5682 4.721132 TGTAAAAACATTCTTCCTCGGGT 58.279 39.130 0.00 0.00 0.00 5.28
5592 5683 4.156008 CCTGTAAAAACATTCTTCCTCGGG 59.844 45.833 0.00 0.00 0.00 5.14
5594 5685 5.941948 ACCTGTAAAAACATTCTTCCTCG 57.058 39.130 0.00 0.00 0.00 4.63
5626 5721 4.444536 GCCACGGGTCATTGTATAACTTA 58.555 43.478 0.00 0.00 0.00 2.24
5644 5739 3.959991 GAGGAGACCTTGCCGCCAC 62.960 68.421 0.00 0.00 31.76 5.01
5664 5759 2.159014 GGCAAACCGGTTTCCTTTTCTT 60.159 45.455 29.48 2.70 0.00 2.52
5721 5816 2.980233 GCCACAGCCGCAACTTCT 60.980 61.111 0.00 0.00 0.00 2.85
5724 5819 3.309436 TATCGCCACAGCCGCAACT 62.309 57.895 0.00 0.00 34.57 3.16
5760 5855 9.626045 CTTTTCACATGGGATTAAAAGAGTAAC 57.374 33.333 13.22 0.00 38.72 2.50
5768 5863 6.435904 ACCGATTCTTTTCACATGGGATTAAA 59.564 34.615 0.00 0.00 0.00 1.52
5771 5866 4.344104 ACCGATTCTTTTCACATGGGATT 58.656 39.130 0.00 0.00 0.00 3.01
5786 5881 3.576982 TGGAGGACCATATGTACCGATTC 59.423 47.826 1.24 0.00 41.77 2.52
5845 5941 7.031226 TCTGTCAAAGAAAACCAAGAATGAG 57.969 36.000 0.00 0.00 29.54 2.90
5851 5947 6.199719 GCAAGAATCTGTCAAAGAAAACCAAG 59.800 38.462 0.00 0.00 38.79 3.61
5911 6009 8.186821 GCTGCAATCTACAGTATCATTTTCTTT 58.813 33.333 0.00 0.00 37.47 2.52
5914 6012 7.019774 TGCTGCAATCTACAGTATCATTTTC 57.980 36.000 0.00 0.00 37.47 2.29
5917 6015 5.297776 GGTTGCTGCAATCTACAGTATCATT 59.702 40.000 19.11 0.00 37.47 2.57
5918 6016 4.818546 GGTTGCTGCAATCTACAGTATCAT 59.181 41.667 19.11 0.00 37.47 2.45
5919 6017 4.080919 AGGTTGCTGCAATCTACAGTATCA 60.081 41.667 25.64 0.00 32.53 2.15
5920 6018 4.446371 AGGTTGCTGCAATCTACAGTATC 58.554 43.478 25.64 5.14 32.53 2.24
5921 6019 4.494091 AGGTTGCTGCAATCTACAGTAT 57.506 40.909 25.64 0.73 32.53 2.12
5922 6020 3.981071 AGGTTGCTGCAATCTACAGTA 57.019 42.857 25.64 0.00 32.53 2.74
5923 6021 2.816087 CAAGGTTGCTGCAATCTACAGT 59.184 45.455 26.87 10.01 33.23 3.55
5924 6022 2.816087 ACAAGGTTGCTGCAATCTACAG 59.184 45.455 26.87 20.73 33.23 2.74
5925 6023 2.813754 GACAAGGTTGCTGCAATCTACA 59.186 45.455 26.87 0.00 33.23 2.74
5926 6024 3.077359 AGACAAGGTTGCTGCAATCTAC 58.923 45.455 26.87 19.82 33.23 2.59
5971 6069 4.511617 TTGCTTCGCATTTATTTGGTGA 57.488 36.364 0.00 0.00 38.76 4.02
6223 6447 5.003160 TGATAAGGGAATGGTATGAATGCG 58.997 41.667 0.00 0.00 0.00 4.73
6232 6456 3.130450 TCCATGGTGATAAGGGAATGGT 58.870 45.455 12.58 0.00 36.70 3.55
6307 6533 8.748412 TCCGTTTCAAAATAGATGATCCAATTT 58.252 29.630 0.00 0.00 0.00 1.82
6309 6535 7.013655 CCTCCGTTTCAAAATAGATGATCCAAT 59.986 37.037 0.00 0.00 0.00 3.16
6310 6536 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
6311 6537 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
6312 6538 6.055588 TCCTCCGTTTCAAAATAGATGATCC 58.944 40.000 0.00 0.00 0.00 3.36
6313 6539 7.281100 ACTTCCTCCGTTTCAAAATAGATGATC 59.719 37.037 0.00 0.00 0.00 2.92
6314 6540 7.112779 ACTTCCTCCGTTTCAAAATAGATGAT 58.887 34.615 0.00 0.00 0.00 2.45
6315 6541 6.472887 ACTTCCTCCGTTTCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
6316 6542 6.743575 ACTTCCTCCGTTTCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
6317 6543 6.534079 CGTACTTCCTCCGTTTCAAAATAGAT 59.466 38.462 0.00 0.00 0.00 1.98
6318 6544 5.865552 CGTACTTCCTCCGTTTCAAAATAGA 59.134 40.000 0.00 0.00 0.00 1.98
6319 6545 5.636543 ACGTACTTCCTCCGTTTCAAAATAG 59.363 40.000 0.00 0.00 0.00 1.73
6320 6546 5.540911 ACGTACTTCCTCCGTTTCAAAATA 58.459 37.500 0.00 0.00 0.00 1.40
6321 6547 4.383173 ACGTACTTCCTCCGTTTCAAAAT 58.617 39.130 0.00 0.00 0.00 1.82
6322 6548 3.795877 ACGTACTTCCTCCGTTTCAAAA 58.204 40.909 0.00 0.00 0.00 2.44
6323 6549 3.457610 ACGTACTTCCTCCGTTTCAAA 57.542 42.857 0.00 0.00 0.00 2.69
6324 6550 3.383761 GAACGTACTTCCTCCGTTTCAA 58.616 45.455 0.00 0.00 44.04 2.69
6325 6551 2.288395 GGAACGTACTTCCTCCGTTTCA 60.288 50.000 13.68 0.00 44.90 2.69
6326 6552 2.332104 GGAACGTACTTCCTCCGTTTC 58.668 52.381 13.68 0.00 44.90 2.78
6327 6553 2.445565 GGAACGTACTTCCTCCGTTT 57.554 50.000 13.68 0.00 44.90 3.60
6335 6561 4.260784 GCATTCATCCATGGAACGTACTTC 60.261 45.833 20.67 0.60 0.00 3.01
6336 6562 3.627577 GCATTCATCCATGGAACGTACTT 59.372 43.478 20.67 0.00 0.00 2.24
6337 6563 3.118261 AGCATTCATCCATGGAACGTACT 60.118 43.478 20.67 9.51 0.00 2.73
6498 6731 4.262506 GGTACAAGTGAGGAGTAGTTGCTT 60.263 45.833 0.00 0.00 32.92 3.91
6541 6778 0.671781 GTGCAATGCAGAGAGACCGT 60.672 55.000 8.73 0.00 40.08 4.83
6545 6782 1.804601 CACAGTGCAATGCAGAGAGA 58.195 50.000 15.18 0.00 40.08 3.10
6583 6820 2.482494 AGTCTGGGGAAGGAATGTAGG 58.518 52.381 0.00 0.00 0.00 3.18
6585 6822 3.263425 GTGAAGTCTGGGGAAGGAATGTA 59.737 47.826 0.00 0.00 0.00 2.29
6586 6823 2.040412 GTGAAGTCTGGGGAAGGAATGT 59.960 50.000 0.00 0.00 0.00 2.71
6587 6824 2.307098 AGTGAAGTCTGGGGAAGGAATG 59.693 50.000 0.00 0.00 0.00 2.67
6588 6825 2.637165 AGTGAAGTCTGGGGAAGGAAT 58.363 47.619 0.00 0.00 0.00 3.01
6589 6826 2.118403 AGTGAAGTCTGGGGAAGGAA 57.882 50.000 0.00 0.00 0.00 3.36
6591 6828 2.158608 ACAAAGTGAAGTCTGGGGAAGG 60.159 50.000 0.00 0.00 0.00 3.46
6593 6830 2.241176 ACACAAAGTGAAGTCTGGGGAA 59.759 45.455 3.88 0.00 36.96 3.97
6608 6845 3.569194 TGCTAGAAACTCCCACACAAA 57.431 42.857 0.00 0.00 0.00 2.83
6610 6847 3.411446 CAATGCTAGAAACTCCCACACA 58.589 45.455 0.00 0.00 0.00 3.72
6613 6850 2.290960 ACCCAATGCTAGAAACTCCCAC 60.291 50.000 0.00 0.00 0.00 4.61
6615 6852 2.808906 ACCCAATGCTAGAAACTCCC 57.191 50.000 0.00 0.00 0.00 4.30
6624 6861 4.650972 AGTAAGGACAAACCCAATGCTA 57.349 40.909 0.00 0.00 40.05 3.49
6635 6872 7.769044 GCTACCTGAAATCAATAGTAAGGACAA 59.231 37.037 0.00 0.00 0.00 3.18
6640 6877 6.203723 GCCAGCTACCTGAAATCAATAGTAAG 59.796 42.308 0.00 0.00 41.77 2.34
6643 6880 4.455606 GCCAGCTACCTGAAATCAATAGT 58.544 43.478 0.00 0.00 41.77 2.12
6644 6881 3.817647 GGCCAGCTACCTGAAATCAATAG 59.182 47.826 0.00 0.00 41.77 1.73
6646 6883 2.025037 TGGCCAGCTACCTGAAATCAAT 60.025 45.455 0.00 0.00 41.77 2.57
6647 6884 1.354031 TGGCCAGCTACCTGAAATCAA 59.646 47.619 0.00 0.00 41.77 2.57
6648 6885 0.991146 TGGCCAGCTACCTGAAATCA 59.009 50.000 0.00 0.00 41.77 2.57
6649 6886 2.128771 TTGGCCAGCTACCTGAAATC 57.871 50.000 5.11 0.00 41.77 2.17
6652 6889 0.771127 AGTTTGGCCAGCTACCTGAA 59.229 50.000 5.11 0.00 41.77 3.02
6653 6890 0.771127 AAGTTTGGCCAGCTACCTGA 59.229 50.000 5.11 0.00 41.77 3.86
6654 6891 0.883833 CAAGTTTGGCCAGCTACCTG 59.116 55.000 5.11 2.25 38.85 4.00
6655 6892 0.895559 GCAAGTTTGGCCAGCTACCT 60.896 55.000 5.11 0.00 0.00 3.08
6656 6893 1.586541 GCAAGTTTGGCCAGCTACC 59.413 57.895 5.11 0.00 0.00 3.18
6668 6924 1.302511 CACTACCAGGCGGCAAGTT 60.303 57.895 13.08 0.00 31.09 2.66
6675 6931 7.730364 AAATAAATTCTATCACTACCAGGCG 57.270 36.000 0.00 0.00 0.00 5.52
6717 6973 5.363101 TGGTTGCATAGTGATCTTCTGATC 58.637 41.667 0.00 0.00 46.89 2.92
6730 6986 4.678509 ATTACACGTGTTGGTTGCATAG 57.321 40.909 28.55 0.00 0.00 2.23
6893 7173 5.305902 GGGTTCCCCTTTTCTTGTTTTCATA 59.694 40.000 0.00 0.00 41.34 2.15


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

AutoCloner maintained by Alex Coulton.