Multiple sequence alignment - TraesCS6B01G403000

Loading Multiple Alignment...

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 TraesCS6B01G403000 chr6B 100.000 3179 0 0 1 3179 678795216 678798394 0.000000e+00 5871
1 TraesCS6B01G403000 chr6B 84.045 2225 269 32 802 2998 678881208 678883374 0.000000e+00 2063
2 TraesCS6B01G403000 chr6B 83.511 2068 278 41 832 2855 679385445 679383397 0.000000e+00 1871
3 TraesCS6B01G403000 chr6B 79.429 1716 293 39 813 2504 678807336 678809015 0.000000e+00 1158
4 TraesCS6B01G403000 chr6B 78.818 1709 282 51 829 2504 678876247 678877908 0.000000e+00 1077
5 TraesCS6B01G403000 chr6B 92.670 573 42 0 1 573 678880147 678880719 0.000000e+00 826
6 TraesCS6B01G403000 chr6B 91.336 554 45 2 1 552 679387298 679386746 0.000000e+00 754
7 TraesCS6B01G403000 chr6B 89.981 519 49 2 1 519 678811300 678811815 0.000000e+00 667
8 TraesCS6B01G403000 chr6B 81.589 793 102 23 2227 2998 679527262 679526493 1.620000e-172 616
9 TraesCS6B01G403000 chr6B 84.167 600 93 2 1190 1788 679363956 679363358 5.910000e-162 580
10 TraesCS6B01G403000 chrUn 83.749 2203 295 30 832 2998 79396555 79394380 0.000000e+00 2026
11 TraesCS6B01G403000 chrUn 90.734 572 52 1 2 573 79371163 79370593 0.000000e+00 761
12 TraesCS6B01G403000 chrUn 90.734 572 52 1 2 573 79397787 79397217 0.000000e+00 761
13 TraesCS6B01G403000 chrUn 81.589 793 102 23 2227 2998 79369412 79368643 1.620000e-172 616
14 TraesCS6B01G403000 chr6A 83.207 1721 259 18 811 2513 594504076 594505784 0.000000e+00 1550
15 TraesCS6B01G403000 chr6A 94.939 573 29 0 1 573 594503095 594503667 0.000000e+00 898
16 TraesCS6B01G403000 chr6D 78.682 1609 277 38 936 2516 448510884 448509314 0.000000e+00 1011
17 TraesCS6B01G403000 chr6D 93.543 573 37 0 1 573 448040300 448040872 0.000000e+00 854
18 TraesCS6B01G403000 chr6D 79.817 1199 210 23 1322 2505 448037159 448038340 0.000000e+00 845
19 TraesCS6B01G403000 chr6D 87.383 745 79 6 1454 2198 448047853 448048582 0.000000e+00 841
20 TraesCS6B01G403000 chr6D 88.235 323 36 2 834 1154 448041350 448041672 4.970000e-103 385


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 TraesCS6B01G403000 chr6B 678795216 678798394 3178 False 5871.000000 5871 100.000000 1 3179 1 chr6B.!!$F1 3178
1 TraesCS6B01G403000 chr6B 678876247 678883374 7127 False 1322.000000 2063 85.177667 1 2998 3 chr6B.!!$F3 2997
2 TraesCS6B01G403000 chr6B 679383397 679387298 3901 True 1312.500000 1871 87.423500 1 2855 2 chr6B.!!$R3 2854
3 TraesCS6B01G403000 chr6B 678807336 678811815 4479 False 912.500000 1158 84.705000 1 2504 2 chr6B.!!$F2 2503
4 TraesCS6B01G403000 chr6B 679526493 679527262 769 True 616.000000 616 81.589000 2227 2998 1 chr6B.!!$R2 771
5 TraesCS6B01G403000 chr6B 679363358 679363956 598 True 580.000000 580 84.167000 1190 1788 1 chr6B.!!$R1 598
6 TraesCS6B01G403000 chrUn 79394380 79397787 3407 True 1393.500000 2026 87.241500 2 2998 2 chrUn.!!$R2 2996
7 TraesCS6B01G403000 chrUn 79368643 79371163 2520 True 688.500000 761 86.161500 2 2998 2 chrUn.!!$R1 2996
8 TraesCS6B01G403000 chr6A 594503095 594505784 2689 False 1224.000000 1550 89.073000 1 2513 2 chr6A.!!$F1 2512
9 TraesCS6B01G403000 chr6D 448509314 448510884 1570 True 1011.000000 1011 78.682000 936 2516 1 chr6D.!!$R1 1580
10 TraesCS6B01G403000 chr6D 448047853 448048582 729 False 841.000000 841 87.383000 1454 2198 1 chr6D.!!$F1 744
11 TraesCS6B01G403000 chr6D 448037159 448041672 4513 False 694.666667 854 87.198333 1 2505 3 chr6D.!!$F2 2504

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
578 4497 0.039527 CGGGTTTAAACAGGTGCAGC 60.040 55.0 19.57 8.11 0.00 5.25 F
772 5014 0.102481 ACGGAATCGATCGGGACTTG 59.898 55.0 16.41 4.06 40.11 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 11631 0.032952 TGGCGTCGGGATGCTTATAC 59.967 55.0 12.21 0.0 42.72 1.47 R
2594 12692 0.026674 CATCACGTGGTAGCAATGCG 59.973 55.0 17.00 0.0 0.00 4.73 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
82 3983 6.134730 CGACGAGTATAGGTGAAGTTCATAC 58.865 44.000 9.18 7.48 0.00 2.39
136 4037 0.982852 CAGCCAGGATGTACTCCCCA 60.983 60.000 0.00 0.00 46.27 4.96
193 4094 3.015312 AAGGAAGCTACGACCCGGC 62.015 63.158 0.00 0.00 0.00 6.13
216 4117 3.217017 CGGAATCCGGGAGAGCGA 61.217 66.667 14.91 0.00 44.15 4.93
235 4136 3.795905 GGTGGTCTACCCGGAACA 58.204 61.111 0.73 0.00 44.15 3.18
403 4304 4.057943 ACGTAGGAGAGGGCCGGT 62.058 66.667 1.90 0.00 0.00 5.28
552 4454 0.735287 GAGGCGTCCAACTCCGTTAC 60.735 60.000 0.00 0.00 0.00 2.50
565 4484 2.281692 GTTACGGTGGGCGGGTTT 60.282 61.111 0.00 0.00 0.00 3.27
573 4492 0.824595 GTGGGCGGGTTTAAACAGGT 60.825 55.000 19.57 0.00 0.00 4.00
575 4494 1.287815 GGCGGGTTTAAACAGGTGC 59.712 57.895 19.57 15.36 0.00 5.01
576 4495 1.457009 GGCGGGTTTAAACAGGTGCA 61.457 55.000 19.57 0.00 0.00 4.57
578 4497 0.039527 CGGGTTTAAACAGGTGCAGC 60.040 55.000 19.57 8.11 0.00 5.25
580 4499 2.510613 GGGTTTAAACAGGTGCAGCTA 58.489 47.619 19.71 0.00 0.00 3.32
581 4500 2.488153 GGGTTTAAACAGGTGCAGCTAG 59.512 50.000 19.71 15.05 0.00 3.42
582 4501 2.095212 GGTTTAAACAGGTGCAGCTAGC 60.095 50.000 19.71 6.62 45.96 3.42
592 4783 1.806568 GCAGCTAGCGTGAGAGAGT 59.193 57.895 9.55 0.00 0.00 3.24
594 4785 1.606668 GCAGCTAGCGTGAGAGAGTAT 59.393 52.381 9.55 0.00 0.00 2.12
596 4787 3.626977 CAGCTAGCGTGAGAGAGTATTG 58.373 50.000 9.55 0.00 0.00 1.90
599 4790 1.479709 AGCGTGAGAGAGTATTGCCT 58.520 50.000 0.00 0.00 0.00 4.75
604 4795 2.025155 TGAGAGAGTATTGCCTCCGTC 58.975 52.381 0.00 0.00 31.53 4.79
605 4796 1.002251 GAGAGAGTATTGCCTCCGTCG 60.002 57.143 0.00 0.00 31.53 5.12
648 4839 4.057428 GGCGCAGGTCGACTCTGT 62.057 66.667 25.16 5.47 44.55 3.41
650 4841 2.807045 CGCAGGTCGACTCTGTGC 60.807 66.667 24.60 20.97 41.67 4.57
651 4842 2.433318 GCAGGTCGACTCTGTGCC 60.433 66.667 25.16 12.27 34.89 5.01
652 4843 2.126307 CAGGTCGACTCTGTGCCG 60.126 66.667 16.46 0.00 0.00 5.69
653 4844 2.597805 AGGTCGACTCTGTGCCGT 60.598 61.111 16.46 0.00 0.00 5.68
654 4845 1.303074 AGGTCGACTCTGTGCCGTA 60.303 57.895 16.46 0.00 0.00 4.02
675 4914 3.186047 GGACGGTGAATGACGCGG 61.186 66.667 12.47 0.00 35.84 6.46
676 4915 3.849953 GACGGTGAATGACGCGGC 61.850 66.667 12.47 8.67 33.59 6.53
680 4919 3.849953 GTGAATGACGCGGCGACC 61.850 66.667 30.94 19.56 0.00 4.79
704 4943 1.705337 CGAAATCCCGCGAGCACAAT 61.705 55.000 8.23 0.00 0.00 2.71
723 4962 2.291209 TCCATGCAACATGTTGGACT 57.709 45.000 33.56 20.43 43.48 3.85
725 4964 1.887854 CCATGCAACATGTTGGACTGA 59.112 47.619 33.56 9.15 43.48 3.41
742 4984 5.221481 TGGACTGACCAATTAGTACGAAACA 60.221 40.000 0.00 0.00 46.75 2.83
750 4992 8.568732 ACCAATTAGTACGAAACAACAATTTG 57.431 30.769 0.00 0.00 38.83 2.32
755 4997 8.750626 TTAGTACGAAACAACAATTTGTAACG 57.249 30.769 1.76 7.19 45.69 3.18
757 4999 5.232610 ACGAAACAACAATTTGTAACGGA 57.767 34.783 1.76 0.00 45.69 4.69
770 5012 1.336125 GTAACGGAATCGATCGGGACT 59.664 52.381 16.41 0.00 40.11 3.85
772 5014 0.102481 ACGGAATCGATCGGGACTTG 59.898 55.000 16.41 4.06 40.11 3.16
778 5020 3.712091 ATCGATCGGGACTTGACTTAC 57.288 47.619 16.41 0.00 0.00 2.34
779 5021 1.399440 TCGATCGGGACTTGACTTACG 59.601 52.381 16.41 0.00 0.00 3.18
780 5022 1.533338 CGATCGGGACTTGACTTACGG 60.533 57.143 7.38 0.00 0.00 4.02
781 5023 0.175073 ATCGGGACTTGACTTACGGC 59.825 55.000 0.00 0.00 0.00 5.68
782 5024 1.447314 CGGGACTTGACTTACGGCC 60.447 63.158 0.00 0.00 0.00 6.13
783 5025 1.447314 GGGACTTGACTTACGGCCG 60.447 63.158 26.86 26.86 0.00 6.13
784 5026 1.447314 GGACTTGACTTACGGCCGG 60.447 63.158 31.76 14.78 0.00 6.13
787 5644 0.611714 ACTTGACTTACGGCCGGAAT 59.388 50.000 31.76 17.23 0.00 3.01
793 5650 3.118702 TGACTTACGGCCGGAATCAATTA 60.119 43.478 31.76 6.95 0.00 1.40
795 5652 1.873698 TACGGCCGGAATCAATTAGC 58.126 50.000 31.76 0.00 0.00 3.09
801 5658 2.682856 GCCGGAATCAATTAGCTTGACA 59.317 45.455 5.05 0.00 46.37 3.58
802 5659 3.487544 GCCGGAATCAATTAGCTTGACAC 60.488 47.826 5.05 0.00 46.37 3.67
804 5661 4.336433 CCGGAATCAATTAGCTTGACACAT 59.664 41.667 0.00 0.00 46.37 3.21
805 5662 5.504665 CCGGAATCAATTAGCTTGACACATC 60.505 44.000 0.00 0.00 46.37 3.06
807 5664 6.261118 GGAATCAATTAGCTTGACACATCAC 58.739 40.000 0.00 0.00 46.37 3.06
808 5665 4.926860 TCAATTAGCTTGACACATCACG 57.073 40.909 0.00 0.00 38.97 4.35
823 5865 4.497966 CACATCACGTACGTACATAACCTG 59.502 45.833 22.34 15.02 0.00 4.00
825 5867 3.342719 TCACGTACGTACATAACCTGGA 58.657 45.455 22.34 7.12 0.00 3.86
826 5868 3.126858 TCACGTACGTACATAACCTGGAC 59.873 47.826 22.34 0.00 35.10 4.02
827 5869 2.423538 ACGTACGTACATAACCTGGACC 59.576 50.000 21.41 0.00 34.96 4.46
828 5870 2.539547 CGTACGTACATAACCTGGACCG 60.540 54.545 24.50 2.94 34.96 4.79
829 5871 0.819582 ACGTACATAACCTGGACCGG 59.180 55.000 0.00 0.00 34.96 5.28
836 5879 1.389609 TAACCTGGACCGGATCTCGC 61.390 60.000 9.46 0.00 37.59 5.03
847 5890 1.357334 GATCTCGCTCCTCGTCCAC 59.643 63.158 0.00 0.00 39.67 4.02
848 5891 2.381665 GATCTCGCTCCTCGTCCACG 62.382 65.000 0.00 0.00 39.67 4.94
990 6033 2.359230 GGCGTGGCTGCTCTCTTT 60.359 61.111 0.00 0.00 34.52 2.52
1000 6043 2.433145 CTCTCTTTCGCTGCGCCA 60.433 61.111 18.65 3.07 0.00 5.69
1014 6057 3.422303 GCCATGACGTGCAAGCGA 61.422 61.111 3.48 0.00 35.59 4.93
1050 6093 2.509561 GACGCCTCCTTCCTTCGC 60.510 66.667 0.00 0.00 0.00 4.70
1077 6120 1.605738 GCCAGATGATCATGGGGCC 60.606 63.158 26.24 14.39 37.05 5.80
1080 6123 0.477204 CAGATGATCATGGGGCCAGT 59.523 55.000 14.30 0.00 0.00 4.00
1133 6176 2.056481 CTCGACCGTACGGATCCCAC 62.056 65.000 39.52 19.91 38.96 4.61
1149 6192 2.606826 ACCTTCCGGACAGGGGAC 60.607 66.667 26.45 0.00 41.52 4.46
1171 6214 2.932614 CCCATGTTTGCAACGTTTTTCA 59.067 40.909 0.00 0.00 0.00 2.69
1179 6222 2.166459 TGCAACGTTTTTCATCCCAACA 59.834 40.909 0.00 0.00 0.00 3.33
1181 6224 3.775202 CAACGTTTTTCATCCCAACACA 58.225 40.909 0.00 0.00 0.00 3.72
1182 6225 3.708563 ACGTTTTTCATCCCAACACAG 57.291 42.857 0.00 0.00 0.00 3.66
1188 6231 1.302431 CATCCCAACACAGCGGTCA 60.302 57.895 0.00 0.00 0.00 4.02
1227 6276 0.991920 TCAGCTCCTTTTTCCCCGAT 59.008 50.000 0.00 0.00 0.00 4.18
1230 6279 1.075536 AGCTCCTTTTTCCCCGATGTT 59.924 47.619 0.00 0.00 0.00 2.71
1234 6283 3.352648 TCCTTTTTCCCCGATGTTGATC 58.647 45.455 0.00 0.00 0.00 2.92
1236 6285 2.889170 TTTTCCCCGATGTTGATCCA 57.111 45.000 0.00 0.00 0.00 3.41
1248 6297 2.171237 TGTTGATCCATGCCTTCTCGAT 59.829 45.455 0.00 0.00 0.00 3.59
1257 6306 2.202743 CTTCTCGATGGCGCGGAA 60.203 61.111 8.83 0.00 37.46 4.30
1307 6356 4.516195 GCGCCTCTTCTCGGACCC 62.516 72.222 0.00 0.00 0.00 4.46
1309 6358 2.579738 GCCTCTTCTCGGACCCAC 59.420 66.667 0.00 0.00 0.00 4.61
1320 6369 2.269241 GACCCACCTGCTGGCTAC 59.731 66.667 9.95 0.00 39.01 3.58
1337 6386 0.523072 TACCAGTACGACAAGTCCGC 59.477 55.000 0.00 0.00 0.00 5.54
1400 6449 1.992834 TGCTTCCCCCACTATGCGA 60.993 57.895 0.00 0.00 0.00 5.10
1410 6459 2.951642 CCCACTATGCGAACATTTGGAT 59.048 45.455 7.58 0.00 39.20 3.41
1449 6498 3.071602 ACGCCATCCTAACTAATGCAGAT 59.928 43.478 0.00 0.00 0.00 2.90
1450 6499 3.434641 CGCCATCCTAACTAATGCAGATG 59.565 47.826 0.00 0.00 0.00 2.90
1463 6512 1.513158 CAGATGGTTCCTCGAGCGT 59.487 57.895 6.99 0.00 0.00 5.07
1545 11549 4.183858 TATTTCGGCCCGCCCAGG 62.184 66.667 0.00 0.00 40.63 4.45
1567 11571 3.431346 GCTCTACACATTCTCATCCAGCA 60.431 47.826 0.00 0.00 0.00 4.41
1574 11578 4.398358 CACATTCTCATCCAGCAAGTCAAT 59.602 41.667 0.00 0.00 0.00 2.57
1626 11631 1.457643 TGCTAGGGGGATCCGTGAG 60.458 63.158 5.45 1.47 41.52 3.51
1628 11633 0.178970 GCTAGGGGGATCCGTGAGTA 60.179 60.000 5.45 0.00 41.52 2.59
1671 11676 1.004320 TCGCGGTAAGGTGCATTGT 60.004 52.632 6.13 0.00 0.00 2.71
1682 11687 4.141467 AGGTGCATTGTAGCATCCGGAT 62.141 50.000 12.38 12.38 46.75 4.18
1683 11688 4.828154 AGGTGCATTGTAGCATCCGGATA 61.828 47.826 18.63 0.00 46.75 2.59
1723 11728 0.108186 TGACATGGACATGGAGACGC 60.108 55.000 15.94 0.51 42.91 5.19
1737 11742 2.525055 GAGACGCTTCACATCTCTCAC 58.475 52.381 0.00 0.00 34.72 3.51
1752 11757 5.625568 TCTCTCACACAATGATCATGGAT 57.374 39.130 17.33 1.54 36.48 3.41
1765 11770 6.806668 TGATCATGGATAGGACAACTTACA 57.193 37.500 0.00 0.00 0.00 2.41
1788 11793 0.179029 AAACCAACGAGGACCCACAG 60.179 55.000 5.70 0.00 41.22 3.66
1818 11823 3.782443 ACCGATGGGACGCCCTTC 61.782 66.667 14.76 15.49 45.70 3.46
1905 11910 4.009675 GTGAGGATGGTGCTATTGTCAAA 58.990 43.478 0.00 0.00 0.00 2.69
1930 11935 3.737172 GGCTCACCACGCGCATTT 61.737 61.111 5.73 0.00 35.26 2.32
1932 11937 1.499949 GCTCACCACGCGCATTTTA 59.500 52.632 5.73 0.00 0.00 1.52
2022 12027 3.258372 AGAGTGGAACGATGCTACTCAAA 59.742 43.478 17.06 0.00 45.86 2.69
2032 12037 3.185246 TGCTACTCAAAGATAGCCAGC 57.815 47.619 1.07 0.00 42.67 4.85
2097 12102 3.319122 AGTTTGAGTTGCCTGATGGTTTC 59.681 43.478 0.00 0.00 35.27 2.78
2098 12103 2.957402 TGAGTTGCCTGATGGTTTCT 57.043 45.000 0.00 0.00 35.27 2.52
2145 12150 1.951209 TGTTGGAGATGGACTGGCTA 58.049 50.000 0.00 0.00 0.00 3.93
2206 12226 3.505680 TGCATGTAAGTCGAAAAAGGCAT 59.494 39.130 0.00 0.00 0.00 4.40
2224 12244 3.507622 GGCATTATGAGGATTGTTAGGGC 59.492 47.826 0.00 0.00 0.00 5.19
2235 12260 7.285401 TGAGGATTGTTAGGGCATTTATTCTTC 59.715 37.037 0.00 0.00 0.00 2.87
2242 12267 9.288576 TGTTAGGGCATTTATTCTTCTCATATG 57.711 33.333 0.00 0.00 0.00 1.78
2268 12293 3.540617 CGTTGGGTGGATTGTGATCATA 58.459 45.455 0.00 0.00 33.77 2.15
2269 12294 3.561310 CGTTGGGTGGATTGTGATCATAG 59.439 47.826 0.00 0.00 33.77 2.23
2279 12304 9.167311 GTGGATTGTGATCATAGTCTTTTAAGT 57.833 33.333 13.37 0.00 33.77 2.24
2314 12339 6.458232 TGTTACTTGTTTTGCCTAATGTGT 57.542 33.333 0.00 0.00 0.00 3.72
2319 12344 7.107639 ACTTGTTTTGCCTAATGTGTACTTT 57.892 32.000 0.00 0.00 0.00 2.66
2335 12360 8.453238 TGTGTACTTTAATTTCTGGTGCTTAA 57.547 30.769 0.00 0.00 0.00 1.85
2336 12361 8.564574 TGTGTACTTTAATTTCTGGTGCTTAAG 58.435 33.333 0.00 0.00 0.00 1.85
2342 12369 8.700439 TTTAATTTCTGGTGCTTAAGTAGGTT 57.300 30.769 4.02 0.00 0.00 3.50
2513 12554 5.631096 GCAAGGATTTGAGAAGCTAAACAAC 59.369 40.000 0.00 0.00 36.36 3.32
2517 12559 8.814038 AGGATTTGAGAAGCTAAACAACATAT 57.186 30.769 0.00 0.00 0.00 1.78
2518 12560 9.247861 AGGATTTGAGAAGCTAAACAACATATT 57.752 29.630 0.00 0.00 0.00 1.28
2519 12561 9.508567 GGATTTGAGAAGCTAAACAACATATTC 57.491 33.333 0.00 0.00 0.00 1.75
2520 12562 9.214953 GATTTGAGAAGCTAAACAACATATTCG 57.785 33.333 0.00 0.00 0.00 3.34
2521 12563 7.899178 TTGAGAAGCTAAACAACATATTCGA 57.101 32.000 0.00 0.00 0.00 3.71
2522 12564 8.492673 TTGAGAAGCTAAACAACATATTCGAT 57.507 30.769 0.00 0.00 0.00 3.59
2523 12565 7.909267 TGAGAAGCTAAACAACATATTCGATG 58.091 34.615 0.00 0.00 0.00 3.84
2524 12566 7.549134 TGAGAAGCTAAACAACATATTCGATGT 59.451 33.333 0.00 0.00 0.00 3.06
2525 12567 8.268850 AGAAGCTAAACAACATATTCGATGTT 57.731 30.769 0.00 0.00 42.38 2.71
2544 12586 2.163818 TGTGGACTTGACGGTTGATC 57.836 50.000 0.00 0.00 0.00 2.92
2545 12587 1.414550 TGTGGACTTGACGGTTGATCA 59.585 47.619 0.00 0.00 0.00 2.92
2554 12609 0.907704 ACGGTTGATCACCTAGGGCA 60.908 55.000 14.81 2.70 44.69 5.36
2573 12628 4.016444 GGCATGAGGGAAGTTAAACATCA 58.984 43.478 0.00 0.00 0.00 3.07
2575 12630 4.437390 GCATGAGGGAAGTTAAACATCACG 60.437 45.833 0.00 0.00 0.00 4.35
2576 12631 3.670625 TGAGGGAAGTTAAACATCACGG 58.329 45.455 0.00 0.00 0.00 4.94
2592 12690 6.754193 ACATCACGGGTTAATTTTCACAATT 58.246 32.000 0.00 0.00 0.00 2.32
2593 12691 7.213678 ACATCACGGGTTAATTTTCACAATTT 58.786 30.769 0.00 0.00 0.00 1.82
2594 12692 7.383843 ACATCACGGGTTAATTTTCACAATTTC 59.616 33.333 0.00 0.00 0.00 2.17
2595 12693 5.915758 TCACGGGTTAATTTTCACAATTTCG 59.084 36.000 0.00 0.00 0.00 3.46
2596 12694 4.682401 ACGGGTTAATTTTCACAATTTCGC 59.318 37.500 0.00 0.00 0.00 4.70
2597 12695 4.681942 CGGGTTAATTTTCACAATTTCGCA 59.318 37.500 0.00 0.00 0.00 5.10
2598 12696 5.347364 CGGGTTAATTTTCACAATTTCGCAT 59.653 36.000 0.00 0.00 0.00 4.73
2599 12697 6.128688 CGGGTTAATTTTCACAATTTCGCATT 60.129 34.615 0.00 0.00 0.00 3.56
2612 12710 0.108377 TCGCATTGCTACCACGTGAT 60.108 50.000 19.30 0.54 0.00 3.06
2627 12725 0.802494 GTGATGGCAGTAACCAACCG 59.198 55.000 0.00 0.00 44.65 4.44
2631 12729 1.894756 GGCAGTAACCAACCGCACA 60.895 57.895 0.00 0.00 32.79 4.57
2659 12757 1.202639 TGTGCTTTCATCGTGTGACCT 60.203 47.619 0.00 0.00 36.32 3.85
2661 12759 1.069978 TGCTTTCATCGTGTGACCTGA 59.930 47.619 0.00 0.00 36.32 3.86
2699 12797 1.152963 GATGGTGCGGGGCAGTATT 60.153 57.895 0.00 0.00 40.08 1.89
2713 12811 2.804647 CAGTATTGTGTGATACGGCGA 58.195 47.619 16.62 0.00 37.53 5.54
2737 12836 3.129287 GCTTTGGATGTTCGATCCATGTT 59.871 43.478 7.06 0.00 46.51 2.71
2751 12850 6.316140 TCGATCCATGTTGTTCTCCAATAAAG 59.684 38.462 0.00 0.00 35.02 1.85
2801 12900 5.703592 TGAAACAATTACTATTGAGTGGCGT 59.296 36.000 4.99 0.00 43.12 5.68
2802 12901 6.205853 TGAAACAATTACTATTGAGTGGCGTT 59.794 34.615 4.99 0.00 43.12 4.84
2803 12902 5.545658 ACAATTACTATTGAGTGGCGTTG 57.454 39.130 4.99 0.00 43.12 4.10
2804 12903 4.394920 ACAATTACTATTGAGTGGCGTTGG 59.605 41.667 4.99 0.00 43.12 3.77
2805 12904 2.018542 TACTATTGAGTGGCGTTGGC 57.981 50.000 0.00 0.00 36.28 4.52
2806 12905 1.019278 ACTATTGAGTGGCGTTGGCG 61.019 55.000 0.00 0.00 41.24 5.69
2816 12915 3.566261 CGTTGGCGCTCATTGACT 58.434 55.556 7.64 0.00 0.00 3.41
2817 12916 1.133253 CGTTGGCGCTCATTGACTG 59.867 57.895 7.64 0.00 0.00 3.51
2818 12917 1.291184 CGTTGGCGCTCATTGACTGA 61.291 55.000 7.64 0.00 0.00 3.41
2844 12948 5.104259 ACCCTGTAAACTGATGGAGAATC 57.896 43.478 0.00 0.00 35.67 2.52
2871 12975 1.065199 CACATCCCATAGCACTGGTGT 60.065 52.381 2.64 0.58 34.23 4.16
2899 13003 2.355209 GCTAGTCAAGGAAGACAAGGGG 60.355 54.545 0.00 0.00 40.98 4.79
2901 13005 2.986050 AGTCAAGGAAGACAAGGGGTA 58.014 47.619 0.00 0.00 40.98 3.69
2998 13140 5.376854 AACTGCATTCCTCATGTTTGTAC 57.623 39.130 0.00 0.00 34.98 2.90
2999 13141 4.397420 ACTGCATTCCTCATGTTTGTACA 58.603 39.130 0.00 0.00 38.95 2.90
3003 13145 4.023279 GCATTCCTCATGTTTGTACACACA 60.023 41.667 16.69 16.69 37.03 3.72
3005 13147 3.472652 TCCTCATGTTTGTACACACACC 58.527 45.455 16.70 0.00 37.03 4.16
3006 13148 3.118223 TCCTCATGTTTGTACACACACCA 60.118 43.478 16.70 5.94 37.03 4.17
3007 13149 3.629855 CCTCATGTTTGTACACACACCAA 59.370 43.478 16.70 5.14 37.03 3.67
3008 13150 4.097135 CCTCATGTTTGTACACACACCAAA 59.903 41.667 16.70 2.89 37.03 3.28
3009 13151 4.987832 TCATGTTTGTACACACACCAAAC 58.012 39.130 16.70 7.14 45.04 2.93
3013 13155 4.739195 GTTTGTACACACACCAAACACAT 58.261 39.130 7.28 0.00 44.50 3.21
3015 13157 4.624336 TGTACACACACCAAACACATTC 57.376 40.909 0.00 0.00 0.00 2.67
3016 13158 4.010349 TGTACACACACCAAACACATTCA 58.990 39.130 0.00 0.00 0.00 2.57
3017 13159 3.502191 ACACACACCAAACACATTCAC 57.498 42.857 0.00 0.00 0.00 3.18
3019 13161 3.446873 ACACACACCAAACACATTCACAT 59.553 39.130 0.00 0.00 0.00 3.21
3020 13162 4.642437 ACACACACCAAACACATTCACATA 59.358 37.500 0.00 0.00 0.00 2.29
3021 13163 5.214417 CACACACCAAACACATTCACATAG 58.786 41.667 0.00 0.00 0.00 2.23
3022 13164 4.278170 ACACACCAAACACATTCACATAGG 59.722 41.667 0.00 0.00 0.00 2.57
3023 13165 3.255642 ACACCAAACACATTCACATAGGC 59.744 43.478 0.00 0.00 0.00 3.93
3024 13166 2.825532 ACCAAACACATTCACATAGGCC 59.174 45.455 0.00 0.00 0.00 5.19
3028 13170 3.153369 ACACATTCACATAGGCCACAA 57.847 42.857 5.01 0.00 0.00 3.33
3029 13171 2.819608 ACACATTCACATAGGCCACAAC 59.180 45.455 5.01 0.00 0.00 3.32
3030 13172 2.819019 CACATTCACATAGGCCACAACA 59.181 45.455 5.01 0.00 0.00 3.33
3032 13174 3.507233 ACATTCACATAGGCCACAACAAG 59.493 43.478 5.01 0.00 0.00 3.16
3033 13175 3.500448 TTCACATAGGCCACAACAAGA 57.500 42.857 5.01 0.00 0.00 3.02
3034 13176 3.057969 TCACATAGGCCACAACAAGAG 57.942 47.619 5.01 0.00 0.00 2.85
3035 13177 2.637382 TCACATAGGCCACAACAAGAGA 59.363 45.455 5.01 0.00 0.00 3.10
3036 13178 3.072330 TCACATAGGCCACAACAAGAGAA 59.928 43.478 5.01 0.00 0.00 2.87
3037 13179 3.438087 CACATAGGCCACAACAAGAGAAG 59.562 47.826 5.01 0.00 0.00 2.85
3038 13180 3.073062 ACATAGGCCACAACAAGAGAAGT 59.927 43.478 5.01 0.00 0.00 3.01
3039 13181 2.736670 AGGCCACAACAAGAGAAGTT 57.263 45.000 5.01 0.00 0.00 2.66
3040 13182 3.018423 AGGCCACAACAAGAGAAGTTT 57.982 42.857 5.01 0.00 0.00 2.66
3045 13187 5.351458 GCCACAACAAGAGAAGTTTCAAAT 58.649 37.500 0.00 0.00 0.00 2.32
3046 13188 5.812127 GCCACAACAAGAGAAGTTTCAAATT 59.188 36.000 0.00 0.00 0.00 1.82
3047 13189 6.019559 GCCACAACAAGAGAAGTTTCAAATTC 60.020 38.462 0.00 0.00 33.51 2.17
3051 13193 7.970614 ACAACAAGAGAAGTTTCAAATTCAGAC 59.029 33.333 2.84 0.00 35.60 3.51
3052 13194 7.630242 ACAAGAGAAGTTTCAAATTCAGACA 57.370 32.000 2.84 0.00 35.60 3.41
3053 13195 7.475840 ACAAGAGAAGTTTCAAATTCAGACAC 58.524 34.615 2.84 0.00 35.60 3.67
3054 13196 7.121168 ACAAGAGAAGTTTCAAATTCAGACACA 59.879 33.333 2.84 0.00 35.60 3.72
3055 13197 7.256756 AGAGAAGTTTCAAATTCAGACACAG 57.743 36.000 2.84 0.00 35.60 3.66
3056 13198 6.261826 AGAGAAGTTTCAAATTCAGACACAGG 59.738 38.462 2.84 0.00 35.60 4.00
3057 13199 5.888161 AGAAGTTTCAAATTCAGACACAGGT 59.112 36.000 2.84 0.00 35.60 4.00
3058 13200 5.505173 AGTTTCAAATTCAGACACAGGTG 57.495 39.130 0.00 0.00 0.00 4.00
3059 13201 3.988379 TTCAAATTCAGACACAGGTGC 57.012 42.857 0.00 0.00 0.00 5.01
3060 13202 2.929641 TCAAATTCAGACACAGGTGCA 58.070 42.857 0.00 0.00 0.00 4.57
3061 13203 3.286353 TCAAATTCAGACACAGGTGCAA 58.714 40.909 0.00 0.00 0.00 4.08
3063 13205 4.341806 TCAAATTCAGACACAGGTGCAAAT 59.658 37.500 0.00 0.00 0.00 2.32
3064 13206 5.534278 TCAAATTCAGACACAGGTGCAAATA 59.466 36.000 0.00 0.00 0.00 1.40
3065 13207 6.040278 TCAAATTCAGACACAGGTGCAAATAA 59.960 34.615 0.00 0.00 0.00 1.40
3066 13208 6.594788 AATTCAGACACAGGTGCAAATAAT 57.405 33.333 0.00 0.00 0.00 1.28
3067 13209 6.594788 ATTCAGACACAGGTGCAAATAATT 57.405 33.333 0.00 0.00 0.00 1.40
3068 13210 5.627499 TCAGACACAGGTGCAAATAATTC 57.373 39.130 0.00 0.00 0.00 2.17
3095 13489 6.391227 TTTTTAAGGAAAGCAGTGAGGAAG 57.609 37.500 0.00 0.00 0.00 3.46
3097 13491 0.037447 AGGAAAGCAGTGAGGAAGGC 59.963 55.000 0.00 0.00 0.00 4.35
3098 13492 0.250901 GGAAAGCAGTGAGGAAGGCA 60.251 55.000 0.00 0.00 0.00 4.75
3099 13493 0.877743 GAAAGCAGTGAGGAAGGCAC 59.122 55.000 0.00 0.00 36.53 5.01
3100 13494 0.538287 AAAGCAGTGAGGAAGGCACC 60.538 55.000 0.00 0.00 36.95 5.01
3102 13496 1.673665 GCAGTGAGGAAGGCACCAG 60.674 63.158 0.00 0.00 36.95 4.00
3103 13497 1.673665 CAGTGAGGAAGGCACCAGC 60.674 63.158 3.78 0.00 36.95 4.85
3105 13499 3.241530 TGAGGAAGGCACCAGCGT 61.242 61.111 3.78 0.00 43.41 5.07
3111 13505 2.732289 AAGGCACCAGCGTTTTCAT 58.268 47.368 0.00 0.00 45.77 2.57
3112 13506 1.039856 AAGGCACCAGCGTTTTCATT 58.960 45.000 0.00 0.00 45.77 2.57
3113 13507 0.598065 AGGCACCAGCGTTTTCATTC 59.402 50.000 0.00 0.00 43.41 2.67
3114 13508 0.598065 GGCACCAGCGTTTTCATTCT 59.402 50.000 0.00 0.00 43.41 2.40
3115 13509 1.000274 GGCACCAGCGTTTTCATTCTT 60.000 47.619 0.00 0.00 43.41 2.52
3116 13510 2.319472 GCACCAGCGTTTTCATTCTTC 58.681 47.619 0.00 0.00 0.00 2.87
3119 13513 4.358851 CACCAGCGTTTTCATTCTTCAAA 58.641 39.130 0.00 0.00 0.00 2.69
3120 13514 4.803088 CACCAGCGTTTTCATTCTTCAAAA 59.197 37.500 0.00 0.00 0.00 2.44
3122 13516 6.640499 CACCAGCGTTTTCATTCTTCAAAATA 59.360 34.615 0.00 0.00 0.00 1.40
3124 13518 7.872483 ACCAGCGTTTTCATTCTTCAAAATAAT 59.128 29.630 0.00 0.00 0.00 1.28
3141 13535 8.455682 TCAAAATAATAAGAACCCAAACTAGCG 58.544 33.333 0.00 0.00 0.00 4.26
3143 13537 7.549615 AATAATAAGAACCCAAACTAGCGTC 57.450 36.000 0.00 0.00 0.00 5.19
3144 13538 1.792006 AAGAACCCAAACTAGCGTCG 58.208 50.000 0.00 0.00 0.00 5.12
3145 13539 0.037605 AGAACCCAAACTAGCGTCGG 60.038 55.000 0.00 0.00 0.00 4.79
3146 13540 0.320160 GAACCCAAACTAGCGTCGGT 60.320 55.000 1.19 1.19 0.00 4.69
3147 13541 0.968405 AACCCAAACTAGCGTCGGTA 59.032 50.000 3.83 3.83 0.00 4.02
3149 13543 0.804933 CCCAAACTAGCGTCGGTAGC 60.805 60.000 26.86 0.31 37.16 3.58
3150 13544 1.138047 CCAAACTAGCGTCGGTAGCG 61.138 60.000 26.86 16.97 37.16 4.26
3152 13546 0.179179 AAACTAGCGTCGGTAGCGAC 60.179 55.000 31.91 31.91 37.16 5.19
3153 13547 1.023513 AACTAGCGTCGGTAGCGACT 61.024 55.000 35.85 24.76 37.16 4.18
3154 13548 1.023513 ACTAGCGTCGGTAGCGACTT 61.024 55.000 35.85 27.51 37.16 3.01
3155 13549 0.589229 CTAGCGTCGGTAGCGACTTG 60.589 60.000 35.85 25.64 40.04 3.16
3156 13550 1.020861 TAGCGTCGGTAGCGACTTGA 61.021 55.000 35.85 21.91 40.04 3.02
3157 13551 1.443194 GCGTCGGTAGCGACTTGAA 60.443 57.895 35.85 6.48 36.81 2.69
3158 13552 1.671880 GCGTCGGTAGCGACTTGAAC 61.672 60.000 35.85 20.42 36.81 3.18
3159 13553 0.109873 CGTCGGTAGCGACTTGAACT 60.110 55.000 35.85 0.00 36.81 3.01
3161 13555 1.984297 GTCGGTAGCGACTTGAACTTC 59.016 52.381 33.65 9.77 36.12 3.01
3163 13557 1.347320 GGTAGCGACTTGAACTTCGG 58.653 55.000 0.00 0.00 35.73 4.30
3164 13558 1.336609 GGTAGCGACTTGAACTTCGGT 60.337 52.381 0.00 1.10 46.84 4.69
3166 13560 2.349297 AGCGACTTGAACTTCGGTAG 57.651 50.000 0.00 0.00 43.71 3.18
3167 13561 0.714439 GCGACTTGAACTTCGGTAGC 59.286 55.000 0.00 4.85 35.73 3.58
3168 13562 1.669211 GCGACTTGAACTTCGGTAGCT 60.669 52.381 0.00 0.00 35.73 3.32
3169 13563 2.415090 GCGACTTGAACTTCGGTAGCTA 60.415 50.000 10.35 0.00 35.73 3.32
3171 13565 3.731264 CGACTTGAACTTCGGTAGCTAGG 60.731 52.174 0.00 0.00 0.00 3.02
3172 13566 3.163467 ACTTGAACTTCGGTAGCTAGGT 58.837 45.455 0.00 0.00 0.00 3.08
3173 13567 3.577415 ACTTGAACTTCGGTAGCTAGGTT 59.423 43.478 0.00 0.00 0.00 3.50
3174 13568 4.768968 ACTTGAACTTCGGTAGCTAGGTTA 59.231 41.667 0.00 0.00 0.00 2.85
3175 13569 5.244626 ACTTGAACTTCGGTAGCTAGGTTAA 59.755 40.000 0.00 0.00 0.00 2.01
3176 13570 5.064441 TGAACTTCGGTAGCTAGGTTAAC 57.936 43.478 0.00 0.00 0.00 2.01
3177 13571 4.523943 TGAACTTCGGTAGCTAGGTTAACA 59.476 41.667 8.10 0.00 0.00 2.41
3178 13572 4.715527 ACTTCGGTAGCTAGGTTAACAG 57.284 45.455 8.10 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 3968 4.348020 AGGAGGGTATGAACTTCACCTA 57.652 45.455 0.00 0.00 32.66 3.08
82 3983 2.105993 TCATGATGATGCTCAAGGAGGG 59.894 50.000 0.00 0.00 0.00 4.30
410 4311 0.107312 CAGGTCTCCATCTGCTTGGG 60.107 60.000 1.84 0.00 37.37 4.12
412 4313 0.907486 TCCAGGTCTCCATCTGCTTG 59.093 55.000 0.00 0.00 0.00 4.01
437 4338 2.680913 CCGAGACAAGCAAAGGCCG 61.681 63.158 0.00 0.00 42.56 6.13
552 4454 1.858372 CTGTTTAAACCCGCCCACCG 61.858 60.000 15.59 0.00 0.00 4.94
565 4484 0.320374 ACGCTAGCTGCACCTGTTTA 59.680 50.000 13.93 0.00 43.06 2.01
573 4492 0.962855 ACTCTCTCACGCTAGCTGCA 60.963 55.000 13.93 0.00 43.06 4.41
575 4494 3.626977 CAATACTCTCTCACGCTAGCTG 58.373 50.000 13.93 10.24 0.00 4.24
576 4495 2.034053 GCAATACTCTCTCACGCTAGCT 59.966 50.000 13.93 0.00 0.00 3.32
578 4497 2.621055 AGGCAATACTCTCTCACGCTAG 59.379 50.000 0.00 0.00 0.00 3.42
580 4499 1.407258 GAGGCAATACTCTCTCACGCT 59.593 52.381 0.00 0.00 34.65 5.07
581 4500 1.537135 GGAGGCAATACTCTCTCACGC 60.537 57.143 0.00 0.00 37.63 5.34
582 4501 1.268794 CGGAGGCAATACTCTCTCACG 60.269 57.143 0.00 0.00 37.63 4.35
588 4779 0.456221 CACGACGGAGGCAATACTCT 59.544 55.000 0.00 0.00 37.63 3.24
590 4781 1.153628 GCACGACGGAGGCAATACT 60.154 57.895 0.00 0.00 0.00 2.12
592 4783 1.153647 CTGCACGACGGAGGCAATA 60.154 57.895 11.30 0.00 37.06 1.90
594 4785 3.923864 ACTGCACGACGGAGGCAA 61.924 61.111 11.30 0.00 37.39 4.52
628 4819 4.500116 GAGTCGACCTGCGCCTCC 62.500 72.222 13.01 0.00 38.96 4.30
629 4820 3.444805 AGAGTCGACCTGCGCCTC 61.445 66.667 13.01 1.62 44.79 4.70
632 4823 2.807045 CACAGAGTCGACCTGCGC 60.807 66.667 24.90 0.00 40.61 6.09
641 4832 2.604855 CGTCCATATACGGCACAGAGTC 60.605 54.545 0.00 0.00 39.19 3.36
643 4834 2.051879 CGTCCATATACGGCACAGAG 57.948 55.000 0.00 0.00 39.19 3.35
651 4842 2.977829 CGTCATTCACCGTCCATATACG 59.022 50.000 0.00 0.00 42.49 3.06
652 4843 2.729882 GCGTCATTCACCGTCCATATAC 59.270 50.000 0.00 0.00 0.00 1.47
653 4844 2.606065 CGCGTCATTCACCGTCCATATA 60.606 50.000 0.00 0.00 0.00 0.86
654 4845 1.865865 GCGTCATTCACCGTCCATAT 58.134 50.000 0.00 0.00 0.00 1.78
675 4914 2.889018 GGATTTCGTCCCGGTCGC 60.889 66.667 0.00 0.00 41.50 5.19
683 4922 2.508439 TGCTCGCGGGATTTCGTC 60.508 61.111 12.03 0.00 0.00 4.20
684 4923 2.813908 GTGCTCGCGGGATTTCGT 60.814 61.111 12.03 0.00 0.00 3.85
685 4924 1.705337 ATTGTGCTCGCGGGATTTCG 61.705 55.000 12.03 0.00 0.00 3.46
686 4925 0.028110 GATTGTGCTCGCGGGATTTC 59.972 55.000 12.03 0.00 0.00 2.17
687 4926 1.376609 GGATTGTGCTCGCGGGATTT 61.377 55.000 12.03 0.00 0.00 2.17
691 4930 2.514592 ATGGATTGTGCTCGCGGG 60.515 61.111 6.13 2.60 0.00 6.13
704 4943 1.887854 CAGTCCAACATGTTGCATGGA 59.112 47.619 29.42 20.82 39.16 3.41
723 4962 6.922247 TTGTTGTTTCGTACTAATTGGTCA 57.078 33.333 0.00 0.00 0.00 4.02
725 4964 8.192110 ACAAATTGTTGTTTCGTACTAATTGGT 58.808 29.630 0.00 0.00 46.01 3.67
742 4984 5.446741 CCGATCGATTCCGTTACAAATTGTT 60.447 40.000 18.66 0.00 37.05 2.83
750 4992 1.336125 AGTCCCGATCGATTCCGTTAC 59.664 52.381 18.66 2.68 37.05 2.50
753 4995 0.102481 CAAGTCCCGATCGATTCCGT 59.898 55.000 18.66 0.00 37.05 4.69
755 4997 1.409427 AGTCAAGTCCCGATCGATTCC 59.591 52.381 18.66 1.14 0.00 3.01
757 4999 3.488721 CGTAAGTCAAGTCCCGATCGATT 60.489 47.826 18.66 2.80 0.00 3.34
770 5012 0.609151 TGATTCCGGCCGTAAGTCAA 59.391 50.000 26.12 6.86 0.00 3.18
772 5014 1.949465 ATTGATTCCGGCCGTAAGTC 58.051 50.000 26.12 17.69 0.00 3.01
778 5020 1.002468 CAAGCTAATTGATTCCGGCCG 60.002 52.381 21.04 21.04 41.83 6.13
779 5021 2.297701 TCAAGCTAATTGATTCCGGCC 58.702 47.619 0.00 0.00 43.09 6.13
787 5644 4.314961 ACGTGATGTGTCAAGCTAATTGA 58.685 39.130 0.00 0.00 45.79 2.57
793 5650 1.000607 ACGTACGTGATGTGTCAAGCT 60.001 47.619 22.14 0.00 37.35 3.74
795 5652 3.557508 TGTACGTACGTGATGTGTCAAG 58.442 45.455 30.25 0.00 39.38 3.02
801 5658 4.439153 CCAGGTTATGTACGTACGTGATGT 60.439 45.833 30.25 15.36 31.29 3.06
802 5659 4.039703 CCAGGTTATGTACGTACGTGATG 58.960 47.826 30.25 18.66 31.29 3.07
804 5661 3.126858 GTCCAGGTTATGTACGTACGTGA 59.873 47.826 30.25 18.10 31.29 4.35
805 5662 3.429085 GTCCAGGTTATGTACGTACGTG 58.571 50.000 30.25 14.44 0.00 4.49
807 5664 2.539547 CGGTCCAGGTTATGTACGTACG 60.540 54.545 20.18 15.01 0.00 3.67
808 5665 2.223572 CCGGTCCAGGTTATGTACGTAC 60.224 54.545 18.90 18.90 0.00 3.67
826 5868 2.899044 GACGAGGAGCGAGATCCGG 61.899 68.421 0.00 0.00 44.65 5.14
827 5869 2.634777 GACGAGGAGCGAGATCCG 59.365 66.667 1.40 0.00 44.65 4.18
828 5870 1.824329 TGGACGAGGAGCGAGATCC 60.824 63.158 0.00 0.00 44.57 3.36
829 5871 1.357334 GTGGACGAGGAGCGAGATC 59.643 63.158 0.00 0.00 44.57 2.75
916 5959 4.500116 GAGCGACACCTCCTCCGC 62.500 72.222 0.00 0.00 47.00 5.54
972 6015 3.909086 AAAGAGAGCAGCCACGCCC 62.909 63.158 0.00 0.00 0.00 6.13
977 6020 1.375140 CAGCGAAAGAGAGCAGCCA 60.375 57.895 0.00 0.00 35.48 4.75
1000 6043 1.079197 TCCATCGCTTGCACGTCAT 60.079 52.632 0.00 0.00 0.00 3.06
1014 6057 3.917760 GCTACGAGGCGGCTCCAT 61.918 66.667 30.76 21.90 37.29 3.41
1050 6093 3.451556 ATCATCTGGCCAGCGACGG 62.452 63.158 28.91 14.33 0.00 4.79
1062 6105 0.769873 GACTGGCCCCATGATCATCT 59.230 55.000 4.86 0.00 0.00 2.90
1095 6138 1.579429 CCGTTTTGGGGCGAAGAAG 59.421 57.895 0.00 0.00 0.00 2.85
1171 6214 1.003355 CTGACCGCTGTGTTGGGAT 60.003 57.895 0.00 0.00 0.00 3.85
1179 6222 2.661866 GCGAACACTGACCGCTGT 60.662 61.111 10.85 0.00 44.83 4.40
1227 6276 1.554617 TCGAGAAGGCATGGATCAACA 59.445 47.619 0.00 0.00 0.00 3.33
1230 6279 1.071228 CCATCGAGAAGGCATGGATCA 59.929 52.381 0.00 0.00 39.73 2.92
1320 6369 1.445582 GGCGGACTTGTCGTACTGG 60.446 63.158 0.00 0.00 0.00 4.00
1337 6386 2.578786 TGCATACAGCCAGATGAATGG 58.421 47.619 0.00 0.00 44.83 3.16
1400 6449 5.007528 CCGCTTTTGTTGAAATCCAAATGTT 59.992 36.000 0.00 0.00 36.36 2.71
1410 6459 2.392933 CGTAGCCGCTTTTGTTGAAA 57.607 45.000 0.00 0.00 0.00 2.69
1442 6491 0.179062 GCTCGAGGAACCATCTGCAT 60.179 55.000 15.58 0.00 0.00 3.96
1449 6498 1.654954 GCTCTACGCTCGAGGAACCA 61.655 60.000 15.58 0.00 35.14 3.67
1450 6499 1.064458 GCTCTACGCTCGAGGAACC 59.936 63.158 15.58 0.00 35.14 3.62
1463 6512 2.494059 GTTGCCAAGACAGTTGCTCTA 58.506 47.619 0.00 0.00 0.00 2.43
1472 6521 2.521451 TAGCCCGGTTGCCAAGACA 61.521 57.895 0.00 0.00 0.00 3.41
1478 6527 3.766691 TCGAGTAGCCCGGTTGCC 61.767 66.667 0.00 0.00 0.00 4.52
1528 11517 4.183858 CCTGGGCGGGCCGAAATA 62.184 66.667 33.44 11.33 36.85 1.40
1545 11549 3.129871 GCTGGATGAGAATGTGTAGAGC 58.870 50.000 0.00 0.00 0.00 4.09
1567 11571 5.700402 ATAGGCTTACTCCACATTGACTT 57.300 39.130 0.00 0.00 0.00 3.01
1574 11578 9.969001 AAGTTAATTTTATAGGCTTACTCCACA 57.031 29.630 0.00 0.00 0.00 4.17
1626 11631 0.032952 TGGCGTCGGGATGCTTATAC 59.967 55.000 12.21 0.00 42.72 1.47
1628 11633 0.108585 AATGGCGTCGGGATGCTTAT 59.891 50.000 12.21 5.38 42.72 1.73
1723 11728 5.873164 TGATCATTGTGTGAGAGATGTGAAG 59.127 40.000 0.00 0.00 40.92 3.02
1737 11742 6.060136 AGTTGTCCTATCCATGATCATTGTG 58.940 40.000 5.16 0.00 0.00 3.33
1752 11757 3.387374 TGGTTTCCGTGTAAGTTGTCCTA 59.613 43.478 0.00 0.00 0.00 2.94
1765 11770 1.070275 GGTCCTCGTTGGTTTCCGT 59.930 57.895 0.00 0.00 37.07 4.69
1818 11823 3.713288 TGGTCTTGACAGAAGTAACACG 58.287 45.455 3.08 0.00 0.00 4.49
1930 11935 3.908103 AGCCTAGGTGGTTTCAACTCTAA 59.092 43.478 11.31 0.00 40.68 2.10
1932 11937 2.039084 CAGCCTAGGTGGTTTCAACTCT 59.961 50.000 11.31 0.00 40.68 3.24
2032 12037 1.570813 TCAGCGATGTAAATCTGCCG 58.429 50.000 0.00 0.00 0.00 5.69
2097 12102 3.458189 CTTCTGACGGTTAAGCCCATAG 58.542 50.000 0.00 0.00 0.00 2.23
2098 12103 2.169769 CCTTCTGACGGTTAAGCCCATA 59.830 50.000 0.00 0.00 0.00 2.74
2206 12226 9.077885 GAATAAATGCCCTAACAATCCTCATAA 57.922 33.333 0.00 0.00 0.00 1.90
2224 12244 8.081208 ACGCTGACATATGAGAAGAATAAATG 57.919 34.615 10.38 0.00 0.00 2.32
2235 12260 1.935873 CACCCAACGCTGACATATGAG 59.064 52.381 10.38 0.00 0.00 2.90
2242 12267 0.889186 ACAATCCACCCAACGCTGAC 60.889 55.000 0.00 0.00 0.00 3.51
2268 12293 6.482308 ACATGCGTTACTTGACTTAAAAGACT 59.518 34.615 0.00 0.00 0.00 3.24
2269 12294 6.656003 ACATGCGTTACTTGACTTAAAAGAC 58.344 36.000 0.00 0.00 0.00 3.01
2314 12339 9.444600 CCTACTTAAGCACCAGAAATTAAAGTA 57.555 33.333 1.29 0.00 0.00 2.24
2319 12344 7.722285 ACAAACCTACTTAAGCACCAGAAATTA 59.278 33.333 1.29 0.00 0.00 1.40
2335 12360 3.577415 ACTCCGCTTAAGACAAACCTACT 59.423 43.478 6.67 0.00 0.00 2.57
2336 12361 3.922910 ACTCCGCTTAAGACAAACCTAC 58.077 45.455 6.67 0.00 0.00 3.18
2342 12369 5.603596 TCAAAACTACTCCGCTTAAGACAA 58.396 37.500 6.67 0.00 0.00 3.18
2352 12386 8.826710 TGCAAATATCTTATCAAAACTACTCCG 58.173 33.333 0.00 0.00 0.00 4.63
2405 12440 5.394115 GCCCGATTCTTCCACACATTTATTT 60.394 40.000 0.00 0.00 0.00 1.40
2412 12447 0.605319 GTGCCCGATTCTTCCACACA 60.605 55.000 0.00 0.00 0.00 3.72
2466 12502 7.663827 TGCTTTCAAGTGATCATTTTCTCAAT 58.336 30.769 0.00 0.00 0.00 2.57
2477 12513 6.017400 TCAAATCCTTGCTTTCAAGTGATC 57.983 37.500 4.60 0.00 46.33 2.92
2500 12541 7.849804 ACATCGAATATGTTGTTTAGCTTCT 57.150 32.000 0.00 0.00 0.00 2.85
2513 12554 5.500771 CGTCAAGTCCACAACATCGAATATG 60.501 44.000 0.00 0.00 0.00 1.78
2517 12559 2.131972 CGTCAAGTCCACAACATCGAA 58.868 47.619 0.00 0.00 0.00 3.71
2518 12560 1.604438 CCGTCAAGTCCACAACATCGA 60.604 52.381 0.00 0.00 0.00 3.59
2519 12561 0.790207 CCGTCAAGTCCACAACATCG 59.210 55.000 0.00 0.00 0.00 3.84
2520 12562 1.878953 ACCGTCAAGTCCACAACATC 58.121 50.000 0.00 0.00 0.00 3.06
2521 12563 1.946768 CAACCGTCAAGTCCACAACAT 59.053 47.619 0.00 0.00 0.00 2.71
2522 12564 1.066071 TCAACCGTCAAGTCCACAACA 60.066 47.619 0.00 0.00 0.00 3.33
2523 12565 1.658994 TCAACCGTCAAGTCCACAAC 58.341 50.000 0.00 0.00 0.00 3.32
2524 12566 2.158885 TGATCAACCGTCAAGTCCACAA 60.159 45.455 0.00 0.00 0.00 3.33
2525 12567 1.414550 TGATCAACCGTCAAGTCCACA 59.585 47.619 0.00 0.00 0.00 4.17
2526 12568 1.798813 GTGATCAACCGTCAAGTCCAC 59.201 52.381 0.00 0.00 0.00 4.02
2527 12569 1.270625 GGTGATCAACCGTCAAGTCCA 60.271 52.381 0.00 0.00 39.81 4.02
2528 12570 1.439679 GGTGATCAACCGTCAAGTCC 58.560 55.000 0.00 0.00 39.81 3.85
2544 12586 0.471617 CTTCCCTCATGCCCTAGGTG 59.528 60.000 8.29 0.00 0.00 4.00
2545 12587 0.044855 ACTTCCCTCATGCCCTAGGT 59.955 55.000 8.29 0.00 0.00 3.08
2554 12609 4.261801 CCGTGATGTTTAACTTCCCTCAT 58.738 43.478 8.23 0.00 0.00 2.90
2573 12628 4.682401 GCGAAATTGTGAAAATTAACCCGT 59.318 37.500 0.00 0.00 0.00 5.28
2575 12630 6.720012 ATGCGAAATTGTGAAAATTAACCC 57.280 33.333 0.00 0.00 0.00 4.11
2576 12631 6.519419 GCAATGCGAAATTGTGAAAATTAACC 59.481 34.615 11.47 0.00 0.00 2.85
2592 12690 0.319986 TCACGTGGTAGCAATGCGAA 60.320 50.000 17.00 0.00 0.00 4.70
2593 12691 0.108377 ATCACGTGGTAGCAATGCGA 60.108 50.000 17.00 0.00 0.00 5.10
2594 12692 0.026674 CATCACGTGGTAGCAATGCG 59.973 55.000 17.00 0.00 0.00 4.73
2595 12693 0.378257 CCATCACGTGGTAGCAATGC 59.622 55.000 17.00 0.00 43.44 3.56
2616 12714 1.071699 AGTGATGTGCGGTTGGTTACT 59.928 47.619 0.00 0.00 0.00 2.24
2631 12729 8.672161 TCACACGATGAAAGCACAGTAGTGAT 62.672 42.308 4.09 0.00 40.50 3.06
2643 12741 2.674852 CCATCAGGTCACACGATGAAAG 59.325 50.000 7.15 0.00 39.72 2.62
2645 12743 1.066215 CCCATCAGGTCACACGATGAA 60.066 52.381 7.15 0.00 39.72 2.57
2699 12797 0.108377 AAGCATCGCCGTATCACACA 60.108 50.000 0.00 0.00 0.00 3.72
2713 12811 3.003394 TGGATCGAACATCCAAAGCAT 57.997 42.857 3.71 0.00 44.54 3.79
2775 12874 6.555315 GCCACTCAATAGTAATTGTTTCAGG 58.445 40.000 0.00 0.00 42.66 3.86
2781 12880 4.394920 CCAACGCCACTCAATAGTAATTGT 59.605 41.667 0.00 0.00 42.66 2.71
2785 12884 2.352388 GCCAACGCCACTCAATAGTAA 58.648 47.619 0.00 0.00 33.48 2.24
2787 12886 1.019278 CGCCAACGCCACTCAATAGT 61.019 55.000 0.00 0.00 35.91 2.12
2788 12887 1.715585 CGCCAACGCCACTCAATAG 59.284 57.895 0.00 0.00 0.00 1.73
2812 12911 4.407621 TCAGTTTACAGGGTTTCTCAGTCA 59.592 41.667 0.00 0.00 0.00 3.41
2815 12914 4.697352 CCATCAGTTTACAGGGTTTCTCAG 59.303 45.833 0.00 0.00 0.00 3.35
2816 12915 4.349636 TCCATCAGTTTACAGGGTTTCTCA 59.650 41.667 0.00 0.00 0.00 3.27
2817 12916 4.906618 TCCATCAGTTTACAGGGTTTCTC 58.093 43.478 0.00 0.00 0.00 2.87
2818 12917 4.597507 TCTCCATCAGTTTACAGGGTTTCT 59.402 41.667 0.00 0.00 0.00 2.52
2819 12918 4.906618 TCTCCATCAGTTTACAGGGTTTC 58.093 43.478 0.00 0.00 0.00 2.78
2820 12919 4.993705 TCTCCATCAGTTTACAGGGTTT 57.006 40.909 0.00 0.00 0.00 3.27
2844 12948 3.956199 AGTGCTATGGGATGTGAAAATGG 59.044 43.478 0.00 0.00 0.00 3.16
2845 12949 4.202080 CCAGTGCTATGGGATGTGAAAATG 60.202 45.833 0.18 0.00 36.64 2.32
2871 12975 5.077564 TGTCTTCCTTGACTAGCTGACTAA 58.922 41.667 0.00 0.00 37.79 2.24
2998 13140 3.500558 TGTGAATGTGTTTGGTGTGTG 57.499 42.857 0.00 0.00 0.00 3.82
2999 13141 4.278170 CCTATGTGAATGTGTTTGGTGTGT 59.722 41.667 0.00 0.00 0.00 3.72
3003 13145 2.825532 GGCCTATGTGAATGTGTTTGGT 59.174 45.455 0.00 0.00 0.00 3.67
3005 13147 3.255395 TGTGGCCTATGTGAATGTGTTTG 59.745 43.478 3.32 0.00 0.00 2.93
3006 13148 3.495331 TGTGGCCTATGTGAATGTGTTT 58.505 40.909 3.32 0.00 0.00 2.83
3007 13149 3.153369 TGTGGCCTATGTGAATGTGTT 57.847 42.857 3.32 0.00 0.00 3.32
3008 13150 2.819608 GTTGTGGCCTATGTGAATGTGT 59.180 45.455 3.32 0.00 0.00 3.72
3009 13151 2.819019 TGTTGTGGCCTATGTGAATGTG 59.181 45.455 3.32 0.00 0.00 3.21
3010 13152 3.153369 TGTTGTGGCCTATGTGAATGT 57.847 42.857 3.32 0.00 0.00 2.71
3011 13153 3.758023 TCTTGTTGTGGCCTATGTGAATG 59.242 43.478 3.32 0.00 0.00 2.67
3013 13155 3.072330 TCTCTTGTTGTGGCCTATGTGAA 59.928 43.478 3.32 0.00 0.00 3.18
3015 13157 3.057969 TCTCTTGTTGTGGCCTATGTG 57.942 47.619 3.32 0.00 0.00 3.21
3016 13158 3.073062 ACTTCTCTTGTTGTGGCCTATGT 59.927 43.478 3.32 0.00 0.00 2.29
3017 13159 3.679389 ACTTCTCTTGTTGTGGCCTATG 58.321 45.455 3.32 0.00 0.00 2.23
3019 13161 3.857157 AACTTCTCTTGTTGTGGCCTA 57.143 42.857 3.32 0.00 0.00 3.93
3020 13162 2.736670 AACTTCTCTTGTTGTGGCCT 57.263 45.000 3.32 0.00 0.00 5.19
3021 13163 2.687935 TGAAACTTCTCTTGTTGTGGCC 59.312 45.455 0.00 0.00 0.00 5.36
3022 13164 4.370364 TTGAAACTTCTCTTGTTGTGGC 57.630 40.909 0.00 0.00 0.00 5.01
3023 13165 7.035004 TGAATTTGAAACTTCTCTTGTTGTGG 58.965 34.615 0.00 0.00 0.00 4.17
3024 13166 7.970061 TCTGAATTTGAAACTTCTCTTGTTGTG 59.030 33.333 0.00 0.00 0.00 3.33
3028 13170 7.121168 TGTGTCTGAATTTGAAACTTCTCTTGT 59.879 33.333 4.92 0.00 0.00 3.16
3029 13171 7.475015 TGTGTCTGAATTTGAAACTTCTCTTG 58.525 34.615 4.92 0.00 0.00 3.02
3030 13172 7.201767 CCTGTGTCTGAATTTGAAACTTCTCTT 60.202 37.037 4.92 0.00 0.00 2.85
3032 13174 6.038714 ACCTGTGTCTGAATTTGAAACTTCTC 59.961 38.462 4.92 0.00 0.00 2.87
3033 13175 5.888161 ACCTGTGTCTGAATTTGAAACTTCT 59.112 36.000 4.92 0.00 0.00 2.85
3034 13176 5.973565 CACCTGTGTCTGAATTTGAAACTTC 59.026 40.000 4.92 0.00 0.00 3.01
3035 13177 5.679638 GCACCTGTGTCTGAATTTGAAACTT 60.680 40.000 0.00 0.00 0.00 2.66
3036 13178 4.202050 GCACCTGTGTCTGAATTTGAAACT 60.202 41.667 0.00 0.00 0.00 2.66
3037 13179 4.044426 GCACCTGTGTCTGAATTTGAAAC 58.956 43.478 0.00 0.00 0.00 2.78
3038 13180 3.698539 TGCACCTGTGTCTGAATTTGAAA 59.301 39.130 0.00 0.00 0.00 2.69
3039 13181 3.286353 TGCACCTGTGTCTGAATTTGAA 58.714 40.909 0.00 0.00 0.00 2.69
3040 13182 2.929641 TGCACCTGTGTCTGAATTTGA 58.070 42.857 0.00 0.00 0.00 2.69
3045 13187 5.769662 AGAATTATTTGCACCTGTGTCTGAA 59.230 36.000 0.00 0.00 0.00 3.02
3046 13188 5.316167 AGAATTATTTGCACCTGTGTCTGA 58.684 37.500 0.00 0.00 0.00 3.27
3047 13189 5.633830 AGAATTATTTGCACCTGTGTCTG 57.366 39.130 0.00 0.00 0.00 3.51
3081 13475 0.538287 GGTGCCTTCCTCACTGCTTT 60.538 55.000 0.00 0.00 34.97 3.51
3084 13478 1.673665 CTGGTGCCTTCCTCACTGC 60.674 63.158 0.00 0.00 34.97 4.40
3086 13480 2.753029 GCTGGTGCCTTCCTCACT 59.247 61.111 0.00 0.00 34.97 3.41
3088 13482 2.337879 AAACGCTGGTGCCTTCCTCA 62.338 55.000 0.00 0.00 35.36 3.86
3089 13483 1.172812 AAAACGCTGGTGCCTTCCTC 61.173 55.000 0.00 0.00 35.36 3.71
3091 13485 1.285950 GAAAACGCTGGTGCCTTCC 59.714 57.895 0.00 0.00 35.36 3.46
3093 13487 1.000274 GAATGAAAACGCTGGTGCCTT 60.000 47.619 0.00 0.00 35.36 4.35
3094 13488 0.598065 GAATGAAAACGCTGGTGCCT 59.402 50.000 0.00 0.00 35.36 4.75
3095 13489 0.598065 AGAATGAAAACGCTGGTGCC 59.402 50.000 0.00 0.00 35.36 5.01
3097 13491 3.624326 TGAAGAATGAAAACGCTGGTG 57.376 42.857 0.00 0.00 0.00 4.17
3098 13492 4.647424 TTTGAAGAATGAAAACGCTGGT 57.353 36.364 0.00 0.00 0.00 4.00
3099 13493 7.636259 TTATTTTGAAGAATGAAAACGCTGG 57.364 32.000 0.00 0.00 0.00 4.85
3115 13509 8.455682 CGCTAGTTTGGGTTCTTATTATTTTGA 58.544 33.333 0.00 0.00 0.00 2.69
3116 13510 8.241367 ACGCTAGTTTGGGTTCTTATTATTTTG 58.759 33.333 0.00 0.00 0.00 2.44
3119 13513 6.257193 CGACGCTAGTTTGGGTTCTTATTATT 59.743 38.462 0.00 0.00 33.20 1.40
3120 13514 5.751990 CGACGCTAGTTTGGGTTCTTATTAT 59.248 40.000 0.00 0.00 33.20 1.28
3122 13516 3.930848 CGACGCTAGTTTGGGTTCTTATT 59.069 43.478 0.00 0.00 33.20 1.40
3124 13518 2.353011 CCGACGCTAGTTTGGGTTCTTA 60.353 50.000 0.00 0.00 33.20 2.10
3126 13520 0.037605 CCGACGCTAGTTTGGGTTCT 60.038 55.000 0.00 0.00 33.20 3.01
3127 13521 0.320160 ACCGACGCTAGTTTGGGTTC 60.320 55.000 5.12 0.00 33.20 3.62
3128 13522 0.968405 TACCGACGCTAGTTTGGGTT 59.032 50.000 5.05 0.00 33.11 4.11
3129 13523 0.529378 CTACCGACGCTAGTTTGGGT 59.471 55.000 5.10 5.10 34.57 4.51
3130 13524 0.804933 GCTACCGACGCTAGTTTGGG 60.805 60.000 0.00 0.00 32.48 4.12
3131 13525 1.138047 CGCTACCGACGCTAGTTTGG 61.138 60.000 0.00 0.00 36.29 3.28
3134 13528 3.895025 TCGCTACCGACGCTAGTT 58.105 55.556 0.00 0.00 38.82 2.24
3143 13537 0.982673 CGAAGTTCAAGTCGCTACCG 59.017 55.000 3.32 0.00 0.00 4.02
3144 13538 1.336609 ACCGAAGTTCAAGTCGCTACC 60.337 52.381 3.32 0.00 35.93 3.18
3145 13539 2.061740 ACCGAAGTTCAAGTCGCTAC 57.938 50.000 3.32 0.00 35.93 3.58
3146 13540 2.415090 GCTACCGAAGTTCAAGTCGCTA 60.415 50.000 3.32 0.00 35.93 4.26
3147 13541 1.669211 GCTACCGAAGTTCAAGTCGCT 60.669 52.381 3.32 0.00 35.93 4.93
3149 13543 2.349297 AGCTACCGAAGTTCAAGTCG 57.651 50.000 3.32 0.00 37.01 4.18
3150 13544 3.193056 ACCTAGCTACCGAAGTTCAAGTC 59.807 47.826 3.32 0.00 0.00 3.01
3152 13546 3.870633 ACCTAGCTACCGAAGTTCAAG 57.129 47.619 3.32 0.00 0.00 3.02
3153 13547 5.010922 TGTTAACCTAGCTACCGAAGTTCAA 59.989 40.000 2.48 0.00 0.00 2.69
3154 13548 4.523943 TGTTAACCTAGCTACCGAAGTTCA 59.476 41.667 2.48 0.00 0.00 3.18
3155 13549 5.064441 TGTTAACCTAGCTACCGAAGTTC 57.936 43.478 2.48 0.00 0.00 3.01
3156 13550 5.069501 CTGTTAACCTAGCTACCGAAGTT 57.930 43.478 2.48 0.00 0.00 2.66
3157 13551 4.715527 CTGTTAACCTAGCTACCGAAGT 57.284 45.455 2.48 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.