Multiple sequence alignment - TraesCS3D01G467000

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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 TraesCS3D01G467000 chr3D 100.000 3518 0 0 1 3518 570157391 570160908 0.000000e+00 6497.0
1 TraesCS3D01G467000 chr3D 91.216 740 60 4 1 738 489527641 489528377 0.000000e+00 1002.0
2 TraesCS3D01G467000 chr3A 93.898 1475 62 5 1060 2517 702962696 702964159 0.000000e+00 2200.0
3 TraesCS3D01G467000 chr3A 88.430 242 25 3 2406 2647 702968055 702968293 4.440000e-74 289.0
4 TraesCS3D01G467000 chr3A 89.326 178 12 3 809 986 702962213 702962383 2.130000e-52 217.0
5 TraesCS3D01G467000 chr3A 92.391 92 7 0 2959 3050 709206283 709206374 7.920000e-27 132.0
6 TraesCS3D01G467000 chr3A 98.039 51 1 0 988 1038 702962599 702962649 4.840000e-14 89.8
7 TraesCS3D01G467000 chr1B 92.141 738 54 3 1 737 681154834 681155568 0.000000e+00 1038.0
8 TraesCS3D01G467000 chr1D 91.746 739 58 2 1 738 296632669 296631933 0.000000e+00 1024.0
9 TraesCS3D01G467000 chr7A 91.622 740 60 2 1 738 634328030 634327291 0.000000e+00 1022.0
10 TraesCS3D01G467000 chr3B 91.498 741 59 3 1 739 799300393 799301131 0.000000e+00 1016.0
11 TraesCS3D01G467000 chr3B 90.070 574 31 5 2945 3516 757044038 757044587 0.000000e+00 721.0
12 TraesCS3D01G467000 chr3B 90.070 574 31 5 2945 3516 757181199 757181748 0.000000e+00 721.0
13 TraesCS3D01G467000 chr3B 89.547 574 34 5 2945 3516 756940022 756940571 0.000000e+00 704.0
14 TraesCS3D01G467000 chr7D 91.610 739 52 8 1 736 636717026 636717757 0.000000e+00 1013.0
15 TraesCS3D01G467000 chr7D 91.351 740 59 4 1 738 7528493 7527757 0.000000e+00 1007.0
16 TraesCS3D01G467000 chr7D 81.579 190 31 4 2689 2875 560319413 560319601 1.690000e-33 154.0
17 TraesCS3D01G467000 chr5B 91.475 739 59 3 1 738 505219414 505218679 0.000000e+00 1013.0
18 TraesCS3D01G467000 chr5B 88.316 291 33 1 2663 2952 144719660 144719370 7.230000e-92 348.0
19 TraesCS3D01G467000 chr4D 91.228 741 61 3 1 739 346204404 346203666 0.000000e+00 1005.0
20 TraesCS3D01G467000 chrUn 90.070 574 31 5 2945 3516 351095100 351094551 0.000000e+00 721.0
21 TraesCS3D01G467000 chrUn 89.831 531 28 5 2945 3473 473084766 473084260 0.000000e+00 658.0
22 TraesCS3D01G467000 chrUn 82.143 140 23 2 2814 2952 55537074 55537212 6.170000e-23 119.0
23 TraesCS3D01G467000 chrUn 82.143 140 23 2 2814 2952 286792408 286792270 6.170000e-23 119.0
24 TraesCS3D01G467000 chr4A 93.471 291 18 1 2663 2952 473846009 473846299 6.980000e-117 431.0
25 TraesCS3D01G467000 chr7B 89.153 295 25 6 2663 2953 549786274 549786565 9.280000e-96 361.0
26 TraesCS3D01G467000 chr2A 81.100 418 66 10 3053 3465 695433463 695433054 4.380000e-84 322.0
27 TraesCS3D01G467000 chr6A 82.101 257 40 6 2699 2952 294812323 294812070 7.650000e-52 215.0
28 TraesCS3D01G467000 chr2D 89.189 148 13 3 3048 3193 65515468 65515322 7.760000e-42 182.0
29 TraesCS3D01G467000 chr4B 91.200 125 10 1 2829 2952 177608022 177608146 6.040000e-38 169.0
30 TraesCS3D01G467000 chr2B 91.200 125 10 1 2829 2952 550619249 550619373 6.040000e-38 169.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G467000 chr3D 570157391 570160908 3517 False 6497.00 6497 100.00000 1 3518 1 chr3D.!!$F2 3517
1 TraesCS3D01G467000 chr3D 489527641 489528377 736 False 1002.00 1002 91.21600 1 738 1 chr3D.!!$F1 737
2 TraesCS3D01G467000 chr3A 702962213 702968293 6080 False 698.95 2200 92.42325 809 2647 4 chr3A.!!$F2 1838
3 TraesCS3D01G467000 chr1B 681154834 681155568 734 False 1038.00 1038 92.14100 1 737 1 chr1B.!!$F1 736
4 TraesCS3D01G467000 chr1D 296631933 296632669 736 True 1024.00 1024 91.74600 1 738 1 chr1D.!!$R1 737
5 TraesCS3D01G467000 chr7A 634327291 634328030 739 True 1022.00 1022 91.62200 1 738 1 chr7A.!!$R1 737
6 TraesCS3D01G467000 chr3B 799300393 799301131 738 False 1016.00 1016 91.49800 1 739 1 chr3B.!!$F4 738
7 TraesCS3D01G467000 chr3B 757044038 757044587 549 False 721.00 721 90.07000 2945 3516 1 chr3B.!!$F2 571
8 TraesCS3D01G467000 chr3B 757181199 757181748 549 False 721.00 721 90.07000 2945 3516 1 chr3B.!!$F3 571
9 TraesCS3D01G467000 chr3B 756940022 756940571 549 False 704.00 704 89.54700 2945 3516 1 chr3B.!!$F1 571
10 TraesCS3D01G467000 chr7D 636717026 636717757 731 False 1013.00 1013 91.61000 1 736 1 chr7D.!!$F2 735
11 TraesCS3D01G467000 chr7D 7527757 7528493 736 True 1007.00 1007 91.35100 1 738 1 chr7D.!!$R1 737
12 TraesCS3D01G467000 chr5B 505218679 505219414 735 True 1013.00 1013 91.47500 1 738 1 chr5B.!!$R2 737
13 TraesCS3D01G467000 chr4D 346203666 346204404 738 True 1005.00 1005 91.22800 1 739 1 chr4D.!!$R1 738
14 TraesCS3D01G467000 chrUn 351094551 351095100 549 True 721.00 721 90.07000 2945 3516 1 chrUn.!!$R2 571
15 TraesCS3D01G467000 chrUn 473084260 473084766 506 True 658.00 658 89.83100 2945 3473 1 chrUn.!!$R3 528

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
838 843 0.177373 CGCTACCCTAAGACCCAACC 59.823 60.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 6798 0.034059 AGCGGGGAATGCTCGATTAG 59.966 55.0 0.0 0.0 38.62 1.73 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
75 78 8.435982 ACTAATAAATCTTCAGATCCTTCCCAG 58.564 37.037 0.00 0.00 32.75 4.45
293 297 1.971149 AGATGGTGGATCTGGGTTCA 58.029 50.000 0.00 0.00 40.19 3.18
300 304 1.991813 TGGATCTGGGTTCATGGTTCA 59.008 47.619 0.00 0.00 0.00 3.18
404 408 1.376812 GCCCCGGTCTGATTCGTTT 60.377 57.895 0.00 0.00 0.00 3.60
414 418 4.379082 GGTCTGATTCGTTTAACGGCAATT 60.379 41.667 17.59 0.00 42.81 2.32
484 488 4.847516 CGATGGAGCCGCGTCGAA 62.848 66.667 4.92 0.00 36.25 3.71
488 492 4.415332 GGAGCCGCGTCGAACTCA 62.415 66.667 4.92 0.00 33.70 3.41
533 537 0.991146 TCCTTTGGTGGCTGCTATGA 59.009 50.000 0.00 0.00 0.00 2.15
566 570 1.003112 GGTGACGGGCATTGGTGTA 60.003 57.895 0.00 0.00 0.00 2.90
572 576 0.887933 CGGGCATTGGTGTAAAGCTT 59.112 50.000 0.00 0.00 33.66 3.74
581 585 6.127619 GCATTGGTGTAAAGCTTAGAGGATTT 60.128 38.462 0.00 0.00 30.62 2.17
585 589 6.433093 TGGTGTAAAGCTTAGAGGATTTTTCC 59.567 38.462 0.00 0.00 0.00 3.13
622 626 2.067365 ACTTCTTGGTTGGTGTTCCC 57.933 50.000 0.00 0.00 0.00 3.97
632 636 0.965866 TGGTGTTCCCGTGTGCAAAA 60.966 50.000 0.00 0.00 35.15 2.44
644 648 2.857748 GTGTGCAAAAGCTAGCGTTTTT 59.142 40.909 23.49 15.75 34.45 1.94
652 656 4.733972 AAGCTAGCGTTTTTCTGTCTTC 57.266 40.909 9.55 0.00 0.00 2.87
689 693 2.543641 GGTATGTACGTGGCTTGTACC 58.456 52.381 14.34 0.00 41.13 3.34
783 788 3.790091 GGATAACCCGAACAGTCTTACC 58.210 50.000 0.00 0.00 0.00 2.85
784 789 3.450096 GGATAACCCGAACAGTCTTACCT 59.550 47.826 0.00 0.00 0.00 3.08
785 790 4.646492 GGATAACCCGAACAGTCTTACCTA 59.354 45.833 0.00 0.00 0.00 3.08
786 791 5.303845 GGATAACCCGAACAGTCTTACCTAT 59.696 44.000 0.00 0.00 0.00 2.57
787 792 6.183360 GGATAACCCGAACAGTCTTACCTATT 60.183 42.308 0.00 0.00 0.00 1.73
788 793 5.494390 AACCCGAACAGTCTTACCTATTT 57.506 39.130 0.00 0.00 0.00 1.40
789 794 5.494390 ACCCGAACAGTCTTACCTATTTT 57.506 39.130 0.00 0.00 0.00 1.82
790 795 5.872963 ACCCGAACAGTCTTACCTATTTTT 58.127 37.500 0.00 0.00 0.00 1.94
834 839 1.134877 GTGTTCGCTACCCTAAGACCC 60.135 57.143 0.00 0.00 0.00 4.46
836 841 1.551883 GTTCGCTACCCTAAGACCCAA 59.448 52.381 0.00 0.00 0.00 4.12
838 843 0.177373 CGCTACCCTAAGACCCAACC 59.823 60.000 0.00 0.00 0.00 3.77
839 844 1.282382 GCTACCCTAAGACCCAACCA 58.718 55.000 0.00 0.00 0.00 3.67
840 845 1.631898 GCTACCCTAAGACCCAACCAA 59.368 52.381 0.00 0.00 0.00 3.67
841 846 2.241430 GCTACCCTAAGACCCAACCAAT 59.759 50.000 0.00 0.00 0.00 3.16
866 871 3.742369 TGGTTTAGAAAACGAGCTAACCG 59.258 43.478 5.12 0.00 0.00 4.44
869 874 4.782019 TTAGAAAACGAGCTAACCGGTA 57.218 40.909 8.00 0.00 0.00 4.02
873 878 1.251251 AACGAGCTAACCGGTACTGT 58.749 50.000 8.00 4.67 0.00 3.55
931 936 3.433306 TCCACCTGAATTCGGACAAAT 57.567 42.857 16.17 0.00 0.00 2.32
953 958 2.946133 CGTACACGTGCTAATTCGAC 57.054 50.000 17.22 0.29 34.11 4.20
958 963 1.076533 ACGTGCTAATTCGACGGCAG 61.077 55.000 0.00 0.00 37.42 4.85
971 976 2.668556 CGACGGCAGGCTACATACTATG 60.669 54.545 0.00 0.00 0.00 2.23
982 987 4.319333 GCTACATACTATGAGTGCGTACGT 60.319 45.833 17.90 0.00 0.00 3.57
1038 1257 0.041312 CACAACAAGCACCAGTACGC 60.041 55.000 0.00 0.00 0.00 4.42
1040 1259 0.041312 CAACAAGCACCAGTACGCAC 60.041 55.000 0.00 0.00 0.00 5.34
1041 1260 0.462937 AACAAGCACCAGTACGCACA 60.463 50.000 0.00 0.00 0.00 4.57
1042 1261 0.462937 ACAAGCACCAGTACGCACAA 60.463 50.000 0.00 0.00 0.00 3.33
1043 1262 0.874390 CAAGCACCAGTACGCACAAT 59.126 50.000 0.00 0.00 0.00 2.71
1045 1264 0.034756 AGCACCAGTACGCACAATCA 59.965 50.000 0.00 0.00 0.00 2.57
1046 1265 0.871722 GCACCAGTACGCACAATCAA 59.128 50.000 0.00 0.00 0.00 2.57
1047 1266 1.468520 GCACCAGTACGCACAATCAAT 59.531 47.619 0.00 0.00 0.00 2.57
1091 1337 1.614413 GAACCCTAGCTAGGTCCATCG 59.386 57.143 33.00 20.99 42.03 3.84
1092 1338 0.556747 ACCCTAGCTAGGTCCATCGT 59.443 55.000 33.00 21.59 42.03 3.73
1093 1339 1.779092 ACCCTAGCTAGGTCCATCGTA 59.221 52.381 33.00 0.00 42.03 3.43
1094 1340 2.379226 ACCCTAGCTAGGTCCATCGTAT 59.621 50.000 33.00 8.52 42.03 3.06
1095 1341 3.018149 CCCTAGCTAGGTCCATCGTATC 58.982 54.545 33.00 0.00 42.03 2.24
1096 1342 2.678836 CCTAGCTAGGTCCATCGTATCG 59.321 54.545 28.90 1.25 38.69 2.92
1121 1367 0.702316 AAGAAAAGTATGGCCCCGGT 59.298 50.000 0.00 0.00 0.00 5.28
1132 1378 2.765807 CCCCGGTGGCTGAGATCT 60.766 66.667 0.00 0.00 0.00 2.75
1165 1411 1.376609 GGGCTACAAGTTCATGCCGG 61.377 60.000 0.00 0.00 44.07 6.13
1184 1430 1.818363 CCGACGAGGAGGTGATCGA 60.818 63.158 0.00 0.00 45.00 3.59
1305 1551 2.283388 AACGGGCTGGACGAGGTA 60.283 61.111 0.00 0.00 34.93 3.08
1407 1653 1.221021 GTGGGTCGGGATGAAGGTC 59.779 63.158 0.00 0.00 0.00 3.85
1473 1719 3.522553 GCAGGTGTACAGGATGAACTAC 58.477 50.000 0.00 0.00 39.69 2.73
1478 1724 4.495422 GTGTACAGGATGAACTACCAGTG 58.505 47.826 0.00 0.00 39.69 3.66
1484 1730 2.436115 GAACTACCAGTGGGGCGC 60.436 66.667 15.21 0.00 42.05 6.53
1534 1780 1.604278 TCATGCTCGAGTACTCCATCG 59.396 52.381 17.23 6.60 40.26 3.84
1535 1781 1.335182 CATGCTCGAGTACTCCATCGT 59.665 52.381 17.23 0.00 39.86 3.73
1536 1782 1.015109 TGCTCGAGTACTCCATCGTC 58.985 55.000 17.23 4.32 39.86 4.20
1542 1788 1.585521 GTACTCCATCGTCGCACCG 60.586 63.158 0.00 0.00 0.00 4.94
1590 1836 3.556004 GCAAGATCTCCTTTAGCGGCTAT 60.556 47.826 11.04 0.00 31.42 2.97
1636 1882 0.589229 CGGCTATGTCGACGACTGTC 60.589 60.000 26.86 17.23 41.91 3.51
1643 1889 0.589229 GTCGACGACTGTCATAGCGG 60.589 60.000 20.52 0.00 45.80 5.52
1665 1911 2.102553 GCCGCTACTCGTCCACTC 59.897 66.667 0.00 0.00 36.19 3.51
1686 1932 3.869272 GCCGCACTGCCATCTTCG 61.869 66.667 0.00 0.00 0.00 3.79
1694 1940 1.816835 ACTGCCATCTTCGACGACTAA 59.183 47.619 0.00 0.00 0.00 2.24
1704 1950 6.245115 TCTTCGACGACTAAGTGTTATTCA 57.755 37.500 0.00 0.00 0.00 2.57
1712 1958 5.568023 CGACTAAGTGTTATTCAGAACCCCA 60.568 44.000 0.00 0.00 0.00 4.96
1816 2077 4.512484 TGATCAAGATACGCAACCATTGA 58.488 39.130 0.00 0.00 0.00 2.57
1826 2087 2.924926 CGCAACCATTGATTGATGTTGG 59.075 45.455 0.00 0.00 0.00 3.77
1829 2090 3.880047 ACCATTGATTGATGTTGGCTG 57.120 42.857 0.00 0.00 0.00 4.85
1851 2112 1.814169 GCCGGGATTCTCGTCAACC 60.814 63.158 2.18 0.00 0.00 3.77
1852 2113 1.153429 CCGGGATTCTCGTCAACCC 60.153 63.158 5.04 0.00 37.42 4.11
1853 2114 1.153429 CGGGATTCTCGTCAACCCC 60.153 63.158 0.00 0.00 37.49 4.95
1854 2115 1.223763 GGGATTCTCGTCAACCCCC 59.776 63.158 0.00 0.00 35.00 5.40
1894 2155 3.141398 GTGGATGACGGTATGATGCAAT 58.859 45.455 0.00 0.00 0.00 3.56
1900 2161 1.768275 ACGGTATGATGCAATCCCAGA 59.232 47.619 0.00 0.00 44.73 3.86
1913 2174 4.320788 GCAATCCCAGATGTTTAGCTATGC 60.321 45.833 0.00 0.00 0.00 3.14
1919 2180 1.264288 GATGTTTAGCTATGCCGTGGC 59.736 52.381 3.30 3.30 42.35 5.01
1958 2219 5.485708 AGCCAACTAGGAACTATGAAGAACT 59.514 40.000 0.00 0.00 41.70 3.01
1991 2252 1.195448 GACGACACAGCAGTTTGATGG 59.805 52.381 0.00 0.00 38.24 3.51
1996 2257 2.620115 ACACAGCAGTTTGATGGTCAAG 59.380 45.455 0.00 0.00 38.24 3.02
2043 2304 1.134759 GGCTTCCCTTCGACTTCTACC 60.135 57.143 0.00 0.00 0.00 3.18
2046 2307 0.609957 TCCCTTCGACTTCTACCGCA 60.610 55.000 0.00 0.00 0.00 5.69
2102 2363 2.028020 AGATCGACCAAGAAACCCACTC 60.028 50.000 0.00 0.00 0.00 3.51
2121 2382 0.605589 CCCCGGAGAAGTTTGTGGAC 60.606 60.000 0.73 0.00 0.00 4.02
2186 2447 1.685517 GGAGAAGTACGTCCCCATACC 59.314 57.143 4.48 0.00 0.00 2.73
2202 2463 2.510064 TACCGCCGGTGATTGACCAC 62.510 60.000 21.20 0.00 46.55 4.16
2238 2499 0.674534 AGGAGCAGTTCTTCGACGTT 59.325 50.000 0.00 0.00 0.00 3.99
2268 2529 2.333014 GAACTTCAAGTGCTCCTCGAG 58.667 52.381 5.13 5.13 0.00 4.04
2301 2562 1.210155 CGCTACTGCTGGGCAAAAC 59.790 57.895 10.28 0.00 38.41 2.43
2481 2742 3.334583 TGTGTCCAATGCCTCTTCTAC 57.665 47.619 0.00 0.00 0.00 2.59
2549 6816 2.533318 CTAATCGAGCATTCCCCGC 58.467 57.895 0.00 0.00 0.00 6.13
2634 6901 9.658799 TTATGACCAATGAAATATAGCTCTAGC 57.341 33.333 0.00 0.00 42.49 3.42
2646 6913 0.750249 GCTCTAGCTCCACTTCCTCC 59.250 60.000 0.00 0.00 38.21 4.30
2647 6914 1.687996 GCTCTAGCTCCACTTCCTCCT 60.688 57.143 0.00 0.00 38.21 3.69
2648 6915 2.306847 CTCTAGCTCCACTTCCTCCTC 58.693 57.143 0.00 0.00 0.00 3.71
2649 6916 1.063567 TCTAGCTCCACTTCCTCCTCC 60.064 57.143 0.00 0.00 0.00 4.30
2650 6917 1.011595 TAGCTCCACTTCCTCCTCCT 58.988 55.000 0.00 0.00 0.00 3.69
2651 6918 0.617249 AGCTCCACTTCCTCCTCCTG 60.617 60.000 0.00 0.00 0.00 3.86
2652 6919 1.621672 GCTCCACTTCCTCCTCCTGG 61.622 65.000 0.00 0.00 0.00 4.45
2653 6920 1.613630 TCCACTTCCTCCTCCTGGC 60.614 63.158 0.00 0.00 0.00 4.85
2654 6921 2.674220 CCACTTCCTCCTCCTGGCC 61.674 68.421 0.00 0.00 0.00 5.36
2655 6922 2.285743 ACTTCCTCCTCCTGGCCC 60.286 66.667 0.00 0.00 0.00 5.80
2656 6923 3.093172 CTTCCTCCTCCTGGCCCC 61.093 72.222 0.00 0.00 0.00 5.80
2684 6951 4.120331 GCACCACCAAGCGATGCC 62.120 66.667 0.00 0.00 0.00 4.40
2685 6952 3.803082 CACCACCAAGCGATGCCG 61.803 66.667 0.00 0.00 39.16 5.69
2687 6954 4.776322 CCACCAAGCGATGCCGGA 62.776 66.667 5.05 0.00 36.06 5.14
2688 6955 3.197790 CACCAAGCGATGCCGGAG 61.198 66.667 5.05 0.00 36.06 4.63
2773 7040 4.436998 CCACTCGTGGCGACTCCC 62.437 72.222 2.72 0.00 44.73 4.30
2774 7041 4.436998 CACTCGTGGCGACTCCCC 62.437 72.222 0.00 0.00 0.00 4.81
2775 7042 4.988716 ACTCGTGGCGACTCCCCA 62.989 66.667 0.00 0.00 0.00 4.96
2781 7048 4.021925 GGCGACTCCCCACTGCTT 62.022 66.667 0.00 0.00 0.00 3.91
2782 7049 2.435059 GCGACTCCCCACTGCTTC 60.435 66.667 0.00 0.00 0.00 3.86
2783 7050 3.059982 CGACTCCCCACTGCTTCA 58.940 61.111 0.00 0.00 0.00 3.02
2784 7051 1.374758 CGACTCCCCACTGCTTCAC 60.375 63.158 0.00 0.00 0.00 3.18
2785 7052 1.754745 GACTCCCCACTGCTTCACA 59.245 57.895 0.00 0.00 0.00 3.58
2786 7053 0.603975 GACTCCCCACTGCTTCACAC 60.604 60.000 0.00 0.00 0.00 3.82
2787 7054 1.302832 CTCCCCACTGCTTCACACC 60.303 63.158 0.00 0.00 0.00 4.16
2788 7055 1.770110 TCCCCACTGCTTCACACCT 60.770 57.895 0.00 0.00 0.00 4.00
2789 7056 1.302832 CCCCACTGCTTCACACCTC 60.303 63.158 0.00 0.00 0.00 3.85
2790 7057 1.302832 CCCACTGCTTCACACCTCC 60.303 63.158 0.00 0.00 0.00 4.30
2791 7058 1.757306 CCACTGCTTCACACCTCCT 59.243 57.895 0.00 0.00 0.00 3.69
2792 7059 0.321122 CCACTGCTTCACACCTCCTC 60.321 60.000 0.00 0.00 0.00 3.71
2793 7060 0.321122 CACTGCTTCACACCTCCTCC 60.321 60.000 0.00 0.00 0.00 4.30
2794 7061 1.298014 CTGCTTCACACCTCCTCCC 59.702 63.158 0.00 0.00 0.00 4.30
2795 7062 2.266055 GCTTCACACCTCCTCCCG 59.734 66.667 0.00 0.00 0.00 5.14
2796 7063 2.266055 CTTCACACCTCCTCCCGC 59.734 66.667 0.00 0.00 0.00 6.13
2797 7064 3.316573 CTTCACACCTCCTCCCGCC 62.317 68.421 0.00 0.00 0.00 6.13
2798 7065 4.631740 TCACACCTCCTCCCGCCA 62.632 66.667 0.00 0.00 0.00 5.69
2799 7066 3.402681 CACACCTCCTCCCGCCAT 61.403 66.667 0.00 0.00 0.00 4.40
2800 7067 3.402681 ACACCTCCTCCCGCCATG 61.403 66.667 0.00 0.00 0.00 3.66
2801 7068 4.181010 CACCTCCTCCCGCCATGG 62.181 72.222 7.63 7.63 37.55 3.66
2807 7074 4.738998 CTCCCGCCATGGCCAACA 62.739 66.667 30.79 11.38 37.98 3.33
2811 7078 3.443045 CGCCATGGCCAACACCTC 61.443 66.667 30.79 0.24 37.98 3.85
2812 7079 3.070576 GCCATGGCCAACACCTCC 61.071 66.667 27.24 0.00 34.56 4.30
2813 7080 2.751436 CCATGGCCAACACCTCCG 60.751 66.667 10.96 0.00 0.00 4.63
2814 7081 2.751436 CATGGCCAACACCTCCGG 60.751 66.667 10.96 0.00 0.00 5.14
2815 7082 2.933287 ATGGCCAACACCTCCGGA 60.933 61.111 10.96 2.93 0.00 5.14
2816 7083 2.308722 ATGGCCAACACCTCCGGAT 61.309 57.895 10.96 0.00 0.00 4.18
2817 7084 1.863155 ATGGCCAACACCTCCGGATT 61.863 55.000 10.96 0.00 0.00 3.01
2818 7085 1.749258 GGCCAACACCTCCGGATTC 60.749 63.158 3.57 0.00 0.00 2.52
2819 7086 1.749258 GCCAACACCTCCGGATTCC 60.749 63.158 3.57 0.00 0.00 3.01
2829 7096 2.743718 CGGATTCCGGCTAGCCAT 59.256 61.111 32.47 19.13 44.15 4.40
2830 7097 1.669115 CGGATTCCGGCTAGCCATG 60.669 63.158 32.47 22.41 44.15 3.66
2831 7098 1.302832 GGATTCCGGCTAGCCATGG 60.303 63.158 32.47 25.39 35.37 3.66
2832 7099 1.968540 GATTCCGGCTAGCCATGGC 60.969 63.158 32.47 30.12 42.33 4.40
2838 7105 4.277009 GCTAGCCATGGCCTCCCC 62.277 72.222 33.14 13.42 43.17 4.81
2839 7106 3.946201 CTAGCCATGGCCTCCCCG 61.946 72.222 33.14 11.25 43.17 5.73
2864 7131 4.193893 CCGCCATGGATCCAGCCA 62.194 66.667 21.33 0.00 42.00 4.75
2866 7133 1.970114 CGCCATGGATCCAGCCATC 60.970 63.158 21.33 6.41 45.36 3.51
2867 7134 1.605738 GCCATGGATCCAGCCATCC 60.606 63.158 21.33 1.45 45.36 3.51
2870 7137 4.167720 TGGATCCAGCCATCCACA 57.832 55.556 11.44 0.00 46.34 4.17
2871 7138 1.917495 TGGATCCAGCCATCCACAG 59.083 57.895 11.44 0.00 46.34 3.66
2872 7139 1.527844 GGATCCAGCCATCCACAGC 60.528 63.158 6.95 0.00 42.02 4.40
2873 7140 1.527844 GATCCAGCCATCCACAGCC 60.528 63.158 0.00 0.00 0.00 4.85
2874 7141 1.992519 GATCCAGCCATCCACAGCCT 61.993 60.000 0.00 0.00 0.00 4.58
2875 7142 0.695462 ATCCAGCCATCCACAGCCTA 60.695 55.000 0.00 0.00 0.00 3.93
2876 7143 1.153086 CCAGCCATCCACAGCCTAC 60.153 63.158 0.00 0.00 0.00 3.18
2877 7144 1.630126 CCAGCCATCCACAGCCTACT 61.630 60.000 0.00 0.00 0.00 2.57
2878 7145 0.179062 CAGCCATCCACAGCCTACTC 60.179 60.000 0.00 0.00 0.00 2.59
2879 7146 1.227380 GCCATCCACAGCCTACTCG 60.227 63.158 0.00 0.00 0.00 4.18
2880 7147 1.227380 CCATCCACAGCCTACTCGC 60.227 63.158 0.00 0.00 0.00 5.03
2881 7148 1.589993 CATCCACAGCCTACTCGCG 60.590 63.158 0.00 0.00 0.00 5.87
2882 7149 2.052690 ATCCACAGCCTACTCGCGT 61.053 57.895 5.77 0.00 0.00 6.01
2883 7150 2.005960 ATCCACAGCCTACTCGCGTC 62.006 60.000 5.77 0.00 0.00 5.19
2884 7151 2.577112 CACAGCCTACTCGCGTCG 60.577 66.667 5.77 0.58 0.00 5.12
2885 7152 3.054503 ACAGCCTACTCGCGTCGT 61.055 61.111 5.77 7.56 0.00 4.34
2886 7153 2.577112 CAGCCTACTCGCGTCGTG 60.577 66.667 5.77 0.00 0.00 4.35
2887 7154 4.477975 AGCCTACTCGCGTCGTGC 62.478 66.667 5.77 5.81 41.47 5.34
2898 7165 4.760047 GTCGTGCCGCCAGTGGAT 62.760 66.667 15.20 0.00 0.00 3.41
2899 7166 4.451150 TCGTGCCGCCAGTGGATC 62.451 66.667 15.20 0.68 0.00 3.36
2901 7168 4.408821 GTGCCGCCAGTGGATCCA 62.409 66.667 15.20 11.44 0.00 3.41
2902 7169 4.100084 TGCCGCCAGTGGATCCAG 62.100 66.667 16.81 4.68 0.00 3.86
2904 7171 4.864334 CCGCCAGTGGATCCAGCC 62.864 72.222 16.81 4.14 0.00 4.85
2905 7172 4.100084 CGCCAGTGGATCCAGCCA 62.100 66.667 16.81 0.00 35.02 4.75
2906 7173 2.599597 GCCAGTGGATCCAGCCAT 59.400 61.111 16.81 0.00 40.68 4.40
2907 7174 1.527844 GCCAGTGGATCCAGCCATC 60.528 63.158 16.81 2.41 40.68 3.51
2908 7175 1.150081 CCAGTGGATCCAGCCATCC 59.850 63.158 16.81 1.55 42.68 3.51
2911 7178 2.910360 TGGATCCAGCCATCCACG 59.090 61.111 11.44 0.00 46.34 4.94
2912 7179 2.111878 GGATCCAGCCATCCACGG 59.888 66.667 6.95 0.00 42.02 4.94
2920 7187 3.411517 CCATCCACGGCCTCCCTT 61.412 66.667 0.00 0.00 0.00 3.95
2921 7188 2.124570 CATCCACGGCCTCCCTTG 60.125 66.667 0.00 0.00 0.00 3.61
2922 7189 2.285368 ATCCACGGCCTCCCTTGA 60.285 61.111 0.00 0.00 32.32 3.02
2923 7190 1.694169 ATCCACGGCCTCCCTTGAT 60.694 57.895 0.00 0.00 32.32 2.57
2924 7191 1.987807 ATCCACGGCCTCCCTTGATG 61.988 60.000 0.00 0.00 32.32 3.07
2925 7192 2.825836 CACGGCCTCCCTTGATGC 60.826 66.667 0.00 0.00 32.32 3.91
2926 7193 4.473520 ACGGCCTCCCTTGATGCG 62.474 66.667 0.00 0.00 33.40 4.73
2930 7197 4.473520 CCTCCCTTGATGCGCCGT 62.474 66.667 4.18 0.00 0.00 5.68
2931 7198 2.892425 CTCCCTTGATGCGCCGTC 60.892 66.667 4.18 3.57 0.00 4.79
2932 7199 4.812476 TCCCTTGATGCGCCGTCG 62.812 66.667 4.18 0.00 39.07 5.12
2979 7246 7.849804 AATGTTAATAGTGTGGCTTACTCTG 57.150 36.000 6.52 0.00 35.03 3.35
2989 7256 4.645136 TGTGGCTTACTCTGTAGGTATCTG 59.355 45.833 0.00 0.00 0.00 2.90
3012 7279 6.234920 TGCTAAGATGCTACAAAACCTACAA 58.765 36.000 0.00 0.00 0.00 2.41
3013 7280 6.712998 TGCTAAGATGCTACAAAACCTACAAA 59.287 34.615 0.00 0.00 0.00 2.83
3014 7281 7.094805 TGCTAAGATGCTACAAAACCTACAAAG 60.095 37.037 0.00 0.00 0.00 2.77
3015 7282 7.119262 GCTAAGATGCTACAAAACCTACAAAGA 59.881 37.037 0.00 0.00 0.00 2.52
3016 7283 7.817418 AAGATGCTACAAAACCTACAAAGAA 57.183 32.000 0.00 0.00 0.00 2.52
3017 7284 7.817418 AGATGCTACAAAACCTACAAAGAAA 57.183 32.000 0.00 0.00 0.00 2.52
3018 7285 7.875971 AGATGCTACAAAACCTACAAAGAAAG 58.124 34.615 0.00 0.00 0.00 2.62
3019 7286 7.502561 AGATGCTACAAAACCTACAAAGAAAGT 59.497 33.333 0.00 0.00 0.00 2.66
3020 7287 7.399245 TGCTACAAAACCTACAAAGAAAGTT 57.601 32.000 0.00 0.00 0.00 2.66
3021 7288 7.477494 TGCTACAAAACCTACAAAGAAAGTTC 58.523 34.615 0.00 0.00 0.00 3.01
3022 7289 7.338449 TGCTACAAAACCTACAAAGAAAGTTCT 59.662 33.333 0.00 0.00 39.74 3.01
3026 7293 9.850628 ACAAAACCTACAAAGAAAGTTCTTAAC 57.149 29.630 6.72 0.00 46.22 2.01
3027 7294 9.006215 CAAAACCTACAAAGAAAGTTCTTAACG 57.994 33.333 6.72 2.38 46.22 3.18
3028 7295 6.856135 ACCTACAAAGAAAGTTCTTAACGG 57.144 37.500 6.72 7.85 46.22 4.44
3029 7296 5.761726 ACCTACAAAGAAAGTTCTTAACGGG 59.238 40.000 6.72 9.45 46.22 5.28
3030 7297 5.761726 CCTACAAAGAAAGTTCTTAACGGGT 59.238 40.000 6.72 4.24 46.22 5.28
3031 7298 5.746307 ACAAAGAAAGTTCTTAACGGGTC 57.254 39.130 6.72 0.00 46.22 4.46
3032 7299 5.187687 ACAAAGAAAGTTCTTAACGGGTCA 58.812 37.500 6.72 0.00 46.22 4.02
3033 7300 5.648960 ACAAAGAAAGTTCTTAACGGGTCAA 59.351 36.000 6.72 0.00 46.22 3.18
3053 7320 7.246311 GGTCAATCATAGATTAAATCATGCGG 58.754 38.462 0.00 0.00 0.00 5.69
3099 7367 1.577328 CCACCTCCGACATGCAACAC 61.577 60.000 0.00 0.00 0.00 3.32
3104 7372 2.030007 CCTCCGACATGCAACACAATTT 60.030 45.455 0.00 0.00 0.00 1.82
3185 7453 2.176792 GCTACTTGCAAGTGCGCC 59.823 61.111 36.50 19.83 45.83 6.53
3234 7502 1.809684 CCTCCGACCCTTTTTGTCTC 58.190 55.000 0.00 0.00 0.00 3.36
3252 7520 4.102524 TGTCTCAGTTACAATTCCACACCT 59.897 41.667 0.00 0.00 0.00 4.00
3267 7535 2.187685 CCTGCCATGCTACTGCGA 59.812 61.111 0.00 0.00 43.34 5.10
3312 7580 1.414158 ATCGAATCCACCCTCGACAT 58.586 50.000 0.00 0.00 46.01 3.06
3341 7610 1.128809 TTTCGGTAGAGGGGGCAACA 61.129 55.000 0.00 0.00 39.74 3.33
3376 7645 3.433598 GCTGCAACTCCATCCCTAACATA 60.434 47.826 0.00 0.00 0.00 2.29
3377 7646 4.130118 CTGCAACTCCATCCCTAACATAC 58.870 47.826 0.00 0.00 0.00 2.39
3385 7654 3.214328 CATCCCTAACATACAACTGGGC 58.786 50.000 0.00 0.00 34.89 5.36
3386 7655 2.270858 TCCCTAACATACAACTGGGCA 58.729 47.619 0.00 0.00 34.89 5.36
3405 7674 4.996758 GGGCACACTTTTTCTATTTGCAAT 59.003 37.500 0.00 0.00 0.00 3.56
3407 7676 6.365050 GGCACACTTTTTCTATTTGCAATTG 58.635 36.000 0.00 0.00 0.00 2.32
3436 7705 5.125356 TCAATATGCAATTGAGGTGTCGAT 58.875 37.500 10.34 0.00 33.55 3.59
3443 7712 4.731773 GCAATTGAGGTGTCGATCCATTTC 60.732 45.833 10.34 2.61 0.00 2.17
3509 7778 5.515359 CCCAATTGCATGTCCATCCTCTATA 60.515 44.000 0.00 0.00 0.00 1.31
3516 7785 6.109359 GCATGTCCATCCTCTATATACAACC 58.891 44.000 0.00 0.00 0.00 3.77
3517 7786 5.977489 TGTCCATCCTCTATATACAACCG 57.023 43.478 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.577303 AGGATCTGAAGATTTATTAGTTGGCA 58.423 34.615 0.00 0.00 34.37 4.92
48 49 8.781951 TGGGAAGGATCTGAAGATTTATTAGTT 58.218 33.333 0.00 0.00 34.37 2.24
75 78 1.226018 CAAAAACGGATCGCCTCGC 60.226 57.895 0.00 0.00 0.00 5.03
181 184 4.307908 GCAAACGCCGTCGCAACT 62.308 61.111 6.72 0.00 39.84 3.16
293 297 0.700564 ACCAGCCTGTCATGAACCAT 59.299 50.000 0.00 0.00 0.00 3.55
300 304 2.357154 GGAAACCATACCAGCCTGTCAT 60.357 50.000 0.00 0.00 0.00 3.06
303 307 1.282157 GAGGAAACCATACCAGCCTGT 59.718 52.381 0.00 0.00 0.00 4.00
309 313 2.307686 GTTGGAGGAGGAAACCATACCA 59.692 50.000 0.00 0.00 33.56 3.25
354 358 0.537188 ACGCCATCGAACTCCAGATT 59.463 50.000 0.00 0.00 39.41 2.40
381 385 0.394352 GAATCAGACCGGGGCAACAT 60.394 55.000 6.32 0.00 39.74 2.71
414 418 3.267483 GCTCACCAATAAAGGCGAAGTA 58.733 45.455 0.00 0.00 0.00 2.24
443 447 0.322456 TATGCAGCTTTGCGGACCTT 60.322 50.000 0.00 0.00 37.69 3.50
484 488 1.270907 GATCACCTCCACACCTGAGT 58.729 55.000 0.00 0.00 0.00 3.41
488 492 1.229209 ACGGATCACCTCCACACCT 60.229 57.895 0.00 0.00 45.24 4.00
508 512 1.269778 GCAGCCACCAAAGGAGAAAAC 60.270 52.381 0.00 0.00 0.00 2.43
566 570 5.561679 AGACGGAAAAATCCTCTAAGCTTT 58.438 37.500 3.20 0.00 0.00 3.51
572 576 6.059484 ACAAACAAGACGGAAAAATCCTCTA 58.941 36.000 0.00 0.00 0.00 2.43
581 585 9.505995 GAAGTAAAATTACAAACAAGACGGAAA 57.494 29.630 6.13 0.00 36.12 3.13
585 589 8.953990 CCAAGAAGTAAAATTACAAACAAGACG 58.046 33.333 6.13 0.00 36.12 4.18
632 636 3.991121 GAGAAGACAGAAAAACGCTAGCT 59.009 43.478 13.93 0.00 0.00 3.32
644 648 4.162320 ACCTGACAAAACTGAGAAGACAGA 59.838 41.667 0.00 0.00 40.63 3.41
652 656 2.240493 ACCGACCTGACAAAACTGAG 57.760 50.000 0.00 0.00 0.00 3.35
762 767 3.450096 AGGTAAGACTGTTCGGGTTATCC 59.550 47.826 0.00 0.00 0.00 2.59
763 768 4.732672 AGGTAAGACTGTTCGGGTTATC 57.267 45.455 0.00 0.00 0.00 1.75
764 769 6.803366 AATAGGTAAGACTGTTCGGGTTAT 57.197 37.500 0.00 0.00 0.00 1.89
765 770 6.610075 AAATAGGTAAGACTGTTCGGGTTA 57.390 37.500 0.00 0.00 0.00 2.85
766 771 5.494390 AAATAGGTAAGACTGTTCGGGTT 57.506 39.130 0.00 0.00 0.00 4.11
767 772 5.494390 AAAATAGGTAAGACTGTTCGGGT 57.506 39.130 0.00 0.00 0.00 5.28
788 793 7.201427 CGTAATAAGACGTTCGGGTCATAAAAA 60.201 37.037 0.00 0.00 39.42 1.94
789 794 6.253298 CGTAATAAGACGTTCGGGTCATAAAA 59.747 38.462 0.00 0.00 39.42 1.52
790 795 5.743398 CGTAATAAGACGTTCGGGTCATAAA 59.257 40.000 0.00 0.00 39.42 1.40
791 796 5.273170 CGTAATAAGACGTTCGGGTCATAA 58.727 41.667 0.00 0.00 39.42 1.90
792 797 4.847633 CGTAATAAGACGTTCGGGTCATA 58.152 43.478 0.00 0.00 39.42 2.15
793 798 3.699067 CGTAATAAGACGTTCGGGTCAT 58.301 45.455 0.00 0.00 39.42 3.06
794 799 3.135414 CGTAATAAGACGTTCGGGTCA 57.865 47.619 0.00 0.00 39.42 4.02
804 809 3.793492 GGGTAGCGAACACGTAATAAGAC 59.207 47.826 0.00 0.00 0.00 3.01
805 810 3.696051 AGGGTAGCGAACACGTAATAAGA 59.304 43.478 0.00 0.00 36.23 2.10
806 811 4.037858 AGGGTAGCGAACACGTAATAAG 57.962 45.455 0.00 0.00 36.23 1.73
807 812 5.356751 TCTTAGGGTAGCGAACACGTAATAA 59.643 40.000 0.00 0.00 36.23 1.40
838 843 5.942872 AGCTCGTTTTCTAAACCATCATTG 58.057 37.500 0.00 0.00 0.00 2.82
839 844 7.361799 GGTTAGCTCGTTTTCTAAACCATCATT 60.362 37.037 4.70 0.00 0.00 2.57
840 845 6.093633 GGTTAGCTCGTTTTCTAAACCATCAT 59.906 38.462 4.70 0.00 0.00 2.45
841 846 5.410439 GGTTAGCTCGTTTTCTAAACCATCA 59.590 40.000 4.70 0.00 0.00 3.07
847 852 3.993920 ACCGGTTAGCTCGTTTTCTAAA 58.006 40.909 0.00 0.00 0.00 1.85
850 855 2.560105 AGTACCGGTTAGCTCGTTTTCT 59.440 45.455 15.04 0.00 0.00 2.52
852 857 2.036346 ACAGTACCGGTTAGCTCGTTTT 59.964 45.455 15.04 0.00 0.00 2.43
946 951 0.178068 ATGTAGCCTGCCGTCGAATT 59.822 50.000 0.00 0.00 0.00 2.17
947 952 1.037493 TATGTAGCCTGCCGTCGAAT 58.963 50.000 0.00 0.00 0.00 3.34
948 953 0.101759 GTATGTAGCCTGCCGTCGAA 59.898 55.000 0.00 0.00 0.00 3.71
953 958 2.558795 ACTCATAGTATGTAGCCTGCCG 59.441 50.000 9.94 0.00 0.00 5.69
958 963 3.644884 ACGCACTCATAGTATGTAGCC 57.355 47.619 9.94 2.00 0.00 3.93
982 987 2.157834 ATGGACTGAAAACGTGCGTA 57.842 45.000 0.00 0.00 0.00 4.42
986 991 8.142994 AGCTTTATATATGGACTGAAAACGTG 57.857 34.615 0.00 0.00 0.00 4.49
987 992 9.477484 CTAGCTTTATATATGGACTGAAAACGT 57.523 33.333 0.00 0.00 0.00 3.99
988 993 8.436200 GCTAGCTTTATATATGGACTGAAAACG 58.564 37.037 7.70 0.00 0.00 3.60
1038 1257 2.611751 TCGCCGGTATTGATTGATTGTG 59.388 45.455 1.90 0.00 0.00 3.33
1040 1259 3.748048 AGATCGCCGGTATTGATTGATTG 59.252 43.478 1.90 0.00 0.00 2.67
1041 1260 3.997021 GAGATCGCCGGTATTGATTGATT 59.003 43.478 1.90 0.00 0.00 2.57
1042 1261 3.589988 GAGATCGCCGGTATTGATTGAT 58.410 45.455 1.90 0.00 0.00 2.57
1043 1262 2.607038 CGAGATCGCCGGTATTGATTGA 60.607 50.000 1.90 0.00 0.00 2.57
1045 1264 1.340248 ACGAGATCGCCGGTATTGATT 59.660 47.619 1.90 0.00 44.43 2.57
1046 1265 0.959553 ACGAGATCGCCGGTATTGAT 59.040 50.000 1.90 1.43 44.43 2.57
1047 1266 0.309922 GACGAGATCGCCGGTATTGA 59.690 55.000 1.90 0.00 44.43 2.57
1091 1337 6.147328 GGCCATACTTTTCTTGGATACGATAC 59.853 42.308 0.00 0.00 42.51 2.24
1092 1338 6.228258 GGCCATACTTTTCTTGGATACGATA 58.772 40.000 0.00 0.00 42.51 2.92
1093 1339 5.063880 GGCCATACTTTTCTTGGATACGAT 58.936 41.667 0.00 0.00 42.51 3.73
1094 1340 4.448210 GGCCATACTTTTCTTGGATACGA 58.552 43.478 0.00 0.00 42.51 3.43
1095 1341 3.564225 GGGCCATACTTTTCTTGGATACG 59.436 47.826 4.39 0.00 42.51 3.06
1096 1342 3.889538 GGGGCCATACTTTTCTTGGATAC 59.110 47.826 4.39 0.00 31.94 2.24
1121 1367 3.092511 GGCCCCAGATCTCAGCCA 61.093 66.667 18.19 0.00 43.32 4.75
1165 1411 2.413765 GATCACCTCCTCGTCGGC 59.586 66.667 0.00 0.00 0.00 5.54
1184 1430 0.824759 GCGTGGGATGAGGTAGAACT 59.175 55.000 0.00 0.00 0.00 3.01
1236 1482 0.249073 GTGGGTCCTCGTCGATGATG 60.249 60.000 7.99 5.63 0.00 3.07
1305 1551 4.771127 AACGCATGTTCCACGTCT 57.229 50.000 0.00 0.00 39.49 4.18
1328 1574 2.795973 CATACTCGCCGGACGTGA 59.204 61.111 21.26 6.64 44.19 4.35
1330 1576 4.203076 GGCATACTCGCCGGACGT 62.203 66.667 5.05 0.00 43.52 4.34
1407 1653 2.282462 AGCTTCCCCTTGTTGCCG 60.282 61.111 0.00 0.00 0.00 5.69
1542 1788 2.045926 ATGGAAGCACAGTCGGCC 60.046 61.111 0.00 0.00 0.00 6.13
1551 1797 0.178995 TGCACACCTTGATGGAAGCA 60.179 50.000 0.00 0.00 39.71 3.91
1627 1873 1.589196 GGCCGCTATGACAGTCGTC 60.589 63.158 0.00 0.00 42.93 4.20
1686 1932 5.575995 GGGTTCTGAATAACACTTAGTCGTC 59.424 44.000 0.00 0.00 33.20 4.20
1694 1940 4.652822 GTCTTGGGGTTCTGAATAACACT 58.347 43.478 0.00 0.00 33.12 3.55
1704 1950 1.339151 GCATCTTCGTCTTGGGGTTCT 60.339 52.381 0.00 0.00 0.00 3.01
1712 1958 1.517832 CCTCCGGCATCTTCGTCTT 59.482 57.895 0.00 0.00 0.00 3.01
1816 2077 3.826637 GCAAGCAGCCAACATCAAT 57.173 47.368 0.00 0.00 37.23 2.57
1826 2087 2.439156 AGAATCCCGGCAAGCAGC 60.439 61.111 0.00 0.00 44.65 5.25
1829 2090 2.125106 ACGAGAATCCCGGCAAGC 60.125 61.111 0.00 0.00 0.00 4.01
1852 2113 3.706373 CGACACAGGGACAGGGGG 61.706 72.222 0.00 0.00 0.00 5.40
1853 2114 3.706373 CCGACACAGGGACAGGGG 61.706 72.222 0.00 0.00 0.00 4.79
1854 2115 4.394712 GCCGACACAGGGACAGGG 62.395 72.222 0.00 0.00 0.00 4.45
1855 2116 4.394712 GGCCGACACAGGGACAGG 62.395 72.222 0.00 0.00 30.75 4.00
1856 2117 4.742201 CGGCCGACACAGGGACAG 62.742 72.222 24.07 0.00 30.75 3.51
1865 2126 4.429212 CGTCATCCACGGCCGACA 62.429 66.667 35.90 15.48 45.46 4.35
1894 2155 2.224281 CGGCATAGCTAAACATCTGGGA 60.224 50.000 0.00 0.00 0.00 4.37
1900 2161 1.308998 GCCACGGCATAGCTAAACAT 58.691 50.000 2.36 0.00 41.49 2.71
1919 2180 1.153469 GGCTCTGCTTCTCCTTCCG 60.153 63.158 0.00 0.00 0.00 4.30
1958 2219 1.797046 GTGTCGTCGTCTCAGTGTAGA 59.203 52.381 0.00 0.00 0.00 2.59
1991 2252 1.470098 CAGGTGGTTGCATAGCTTGAC 59.530 52.381 0.00 0.00 0.00 3.18
1996 2257 0.677731 TCAGCAGGTGGTTGCATAGC 60.678 55.000 0.00 0.00 46.47 2.97
2043 2304 0.521735 CATCATCCATGCCTGATGCG 59.478 55.000 17.54 4.82 45.60 4.73
2046 2307 0.481128 TGCCATCATCCATGCCTGAT 59.519 50.000 3.18 3.18 32.37 2.90
2066 2327 3.986572 GTCGATCTGAAGTGGCATGATAG 59.013 47.826 0.00 0.00 0.00 2.08
2079 2340 1.974957 TGGGTTTCTTGGTCGATCTGA 59.025 47.619 0.00 0.00 0.00 3.27
2102 2363 0.605589 GTCCACAAACTTCTCCGGGG 60.606 60.000 0.00 0.00 0.00 5.73
2150 2411 1.065199 TCTCCGGCATGCAGAATTCTT 60.065 47.619 21.36 0.00 0.00 2.52
2213 2474 1.294659 GAAGAACTGCTCCTGTGGCG 61.295 60.000 0.00 0.00 0.00 5.69
2217 2478 0.039074 CGTCGAAGAACTGCTCCTGT 60.039 55.000 0.00 0.00 39.69 4.00
2238 2499 2.028112 CACTTGAAGTTCCGGATCCTCA 60.028 50.000 4.15 7.44 0.00 3.86
2292 2553 1.976474 GCCAGGATCGTTTTGCCCA 60.976 57.895 0.00 0.00 0.00 5.36
2301 2562 2.338577 AATCTCCAAAGCCAGGATCG 57.661 50.000 0.00 0.00 33.99 3.69
2500 2761 0.549469 TTTAAAGGAGGATCGCCCCC 59.451 55.000 0.00 0.00 34.37 5.40
2531 6798 0.034059 AGCGGGGAATGCTCGATTAG 59.966 55.000 0.00 0.00 38.62 1.73
2536 6803 3.204827 CCAAGCGGGGAATGCTCG 61.205 66.667 0.00 0.00 43.14 5.03
2539 6806 3.521796 GAGCCAAGCGGGGAATGC 61.522 66.667 0.42 0.00 37.04 3.56
2545 6812 2.753043 ATTGCAGAGCCAAGCGGG 60.753 61.111 0.00 0.00 40.85 6.13
2547 6814 1.263484 CATAGATTGCAGAGCCAAGCG 59.737 52.381 0.00 0.00 36.31 4.68
2549 6816 3.314635 GGAACATAGATTGCAGAGCCAAG 59.685 47.826 0.00 0.00 0.00 3.61
2629 6896 1.063567 GGAGGAGGAAGTGGAGCTAGA 60.064 57.143 0.00 0.00 0.00 2.43
2633 6900 1.621672 CCAGGAGGAGGAAGTGGAGC 61.622 65.000 0.00 0.00 36.89 4.70
2634 6901 1.621672 GCCAGGAGGAGGAAGTGGAG 61.622 65.000 0.00 0.00 36.89 3.86
2638 6905 2.285743 GGGCCAGGAGGAGGAAGT 60.286 66.667 4.39 0.00 36.89 3.01
2639 6906 3.093172 GGGGCCAGGAGGAGGAAG 61.093 72.222 4.39 0.00 36.89 3.46
2668 6935 3.803082 CGGCATCGCTTGGTGGTG 61.803 66.667 0.00 0.00 0.00 4.17
2670 6937 4.776322 TCCGGCATCGCTTGGTGG 62.776 66.667 0.00 0.00 34.56 4.61
2671 6938 3.197790 CTCCGGCATCGCTTGGTG 61.198 66.667 0.00 0.00 34.56 4.17
2757 7024 4.436998 GGGGAGTCGCCACGAGTG 62.437 72.222 20.82 0.00 39.77 3.51
2758 7025 4.988716 TGGGGAGTCGCCACGAGT 62.989 66.667 24.17 0.00 46.01 4.18
2764 7031 3.959991 GAAGCAGTGGGGAGTCGCC 62.960 68.421 19.10 19.10 36.97 5.54
2765 7032 2.435059 GAAGCAGTGGGGAGTCGC 60.435 66.667 0.00 0.00 0.00 5.19
2766 7033 1.374758 GTGAAGCAGTGGGGAGTCG 60.375 63.158 0.00 0.00 0.00 4.18
2767 7034 0.603975 GTGTGAAGCAGTGGGGAGTC 60.604 60.000 0.00 0.00 0.00 3.36
2768 7035 1.451936 GTGTGAAGCAGTGGGGAGT 59.548 57.895 0.00 0.00 0.00 3.85
2769 7036 1.302832 GGTGTGAAGCAGTGGGGAG 60.303 63.158 0.00 0.00 0.00 4.30
2770 7037 1.768684 GAGGTGTGAAGCAGTGGGGA 61.769 60.000 0.00 0.00 0.00 4.81
2771 7038 1.302832 GAGGTGTGAAGCAGTGGGG 60.303 63.158 0.00 0.00 0.00 4.96
2772 7039 1.302832 GGAGGTGTGAAGCAGTGGG 60.303 63.158 0.00 0.00 0.00 4.61
2773 7040 0.321122 GAGGAGGTGTGAAGCAGTGG 60.321 60.000 0.00 0.00 0.00 4.00
2774 7041 0.321122 GGAGGAGGTGTGAAGCAGTG 60.321 60.000 0.00 0.00 0.00 3.66
2775 7042 1.484444 GGGAGGAGGTGTGAAGCAGT 61.484 60.000 0.00 0.00 0.00 4.40
2776 7043 1.298014 GGGAGGAGGTGTGAAGCAG 59.702 63.158 0.00 0.00 0.00 4.24
2777 7044 2.583441 CGGGAGGAGGTGTGAAGCA 61.583 63.158 0.00 0.00 0.00 3.91
2778 7045 2.266055 CGGGAGGAGGTGTGAAGC 59.734 66.667 0.00 0.00 0.00 3.86
2779 7046 2.266055 GCGGGAGGAGGTGTGAAG 59.734 66.667 0.00 0.00 0.00 3.02
2780 7047 3.319198 GGCGGGAGGAGGTGTGAA 61.319 66.667 0.00 0.00 0.00 3.18
2781 7048 3.924013 ATGGCGGGAGGAGGTGTGA 62.924 63.158 0.00 0.00 0.00 3.58
2782 7049 3.402681 ATGGCGGGAGGAGGTGTG 61.403 66.667 0.00 0.00 0.00 3.82
2783 7050 3.402681 CATGGCGGGAGGAGGTGT 61.403 66.667 0.00 0.00 0.00 4.16
2784 7051 4.181010 CCATGGCGGGAGGAGGTG 62.181 72.222 0.00 0.00 0.00 4.00
2790 7057 4.738998 TGTTGGCCATGGCGGGAG 62.739 66.667 29.90 0.00 43.06 4.30
2794 7061 3.443045 GAGGTGTTGGCCATGGCG 61.443 66.667 29.90 0.00 43.06 5.69
2795 7062 3.070576 GGAGGTGTTGGCCATGGC 61.071 66.667 29.47 29.47 41.06 4.40
2796 7063 2.751436 CGGAGGTGTTGGCCATGG 60.751 66.667 6.09 7.63 0.00 3.66
2813 7080 1.302832 CCATGGCTAGCCGGAATCC 60.303 63.158 28.28 3.51 39.42 3.01
2814 7081 1.968540 GCCATGGCTAGCCGGAATC 60.969 63.158 29.98 12.52 39.42 2.52
2815 7082 2.113986 GCCATGGCTAGCCGGAAT 59.886 61.111 29.98 14.12 39.42 3.01
2816 7083 4.189580 GGCCATGGCTAGCCGGAA 62.190 66.667 34.70 12.22 39.87 4.30
2821 7088 4.277009 GGGGAGGCCATGGCTAGC 62.277 72.222 34.70 22.90 38.98 3.42
2822 7089 3.946201 CGGGGAGGCCATGGCTAG 61.946 72.222 34.70 16.15 38.98 3.42
2847 7114 3.502621 ATGGCTGGATCCATGGCGG 62.503 63.158 16.63 4.00 44.72 6.13
2848 7115 1.970114 GATGGCTGGATCCATGGCG 60.970 63.158 16.63 4.42 46.29 5.69
2849 7116 1.605738 GGATGGCTGGATCCATGGC 60.606 63.158 16.63 20.48 46.29 4.40
2850 7117 1.848400 TGGATGGCTGGATCCATGG 59.152 57.895 16.63 4.97 45.85 3.66
2854 7121 1.527844 GCTGTGGATGGCTGGATCC 60.528 63.158 4.20 4.20 42.23 3.36
2855 7122 1.527844 GGCTGTGGATGGCTGGATC 60.528 63.158 0.00 0.00 0.00 3.36
2856 7123 0.695462 TAGGCTGTGGATGGCTGGAT 60.695 55.000 0.00 0.00 40.59 3.41
2857 7124 1.306911 TAGGCTGTGGATGGCTGGA 60.307 57.895 0.00 0.00 40.59 3.86
2858 7125 1.153086 GTAGGCTGTGGATGGCTGG 60.153 63.158 0.00 0.00 40.59 4.85
2859 7126 0.179062 GAGTAGGCTGTGGATGGCTG 60.179 60.000 0.00 0.00 40.59 4.85
2860 7127 1.680522 CGAGTAGGCTGTGGATGGCT 61.681 60.000 0.00 0.00 42.95 4.75
2861 7128 1.227380 CGAGTAGGCTGTGGATGGC 60.227 63.158 0.00 0.00 0.00 4.40
2862 7129 1.227380 GCGAGTAGGCTGTGGATGG 60.227 63.158 0.00 0.00 0.00 3.51
2863 7130 1.589993 CGCGAGTAGGCTGTGGATG 60.590 63.158 0.00 0.00 0.00 3.51
2864 7131 2.052690 ACGCGAGTAGGCTGTGGAT 61.053 57.895 15.93 0.00 46.88 3.41
2865 7132 2.675423 ACGCGAGTAGGCTGTGGA 60.675 61.111 15.93 0.00 46.88 4.02
2884 7151 4.408821 TGGATCCACTGGCGGCAC 62.409 66.667 11.44 0.00 0.00 5.01
2885 7152 4.100084 CTGGATCCACTGGCGGCA 62.100 66.667 11.44 12.58 0.00 5.69
2887 7154 4.864334 GGCTGGATCCACTGGCGG 62.864 72.222 11.44 0.49 0.00 6.13
2888 7155 3.411114 ATGGCTGGATCCACTGGCG 62.411 63.158 11.44 1.33 39.25 5.69
2889 7156 1.527844 GATGGCTGGATCCACTGGC 60.528 63.158 11.44 15.37 39.25 4.85
2890 7157 1.150081 GGATGGCTGGATCCACTGG 59.850 63.158 11.44 2.19 41.59 4.00
2891 7158 1.917495 TGGATGGCTGGATCCACTG 59.083 57.895 11.44 3.05 45.85 3.66
2892 7159 4.506076 TGGATGGCTGGATCCACT 57.494 55.556 11.44 0.00 45.85 4.00
2895 7162 2.111878 CCGTGGATGGCTGGATCC 59.888 66.667 4.20 4.20 42.23 3.36
2903 7170 3.411517 AAGGGAGGCCGTGGATGG 61.412 66.667 0.00 0.00 0.00 3.51
2904 7171 1.987807 ATCAAGGGAGGCCGTGGATG 61.988 60.000 0.00 0.00 31.64 3.51
2905 7172 1.694169 ATCAAGGGAGGCCGTGGAT 60.694 57.895 0.00 0.00 28.28 3.41
2906 7173 2.285368 ATCAAGGGAGGCCGTGGA 60.285 61.111 0.00 0.00 0.00 4.02
2907 7174 2.124570 CATCAAGGGAGGCCGTGG 60.125 66.667 0.00 0.00 0.00 4.94
2908 7175 2.825836 GCATCAAGGGAGGCCGTG 60.826 66.667 0.00 0.00 44.73 4.94
2913 7180 4.473520 ACGGCGCATCAAGGGAGG 62.474 66.667 10.83 0.00 0.00 4.30
2914 7181 2.892425 GACGGCGCATCAAGGGAG 60.892 66.667 10.83 0.00 0.00 4.30
2915 7182 4.812476 CGACGGCGCATCAAGGGA 62.812 66.667 10.83 0.00 0.00 4.20
2935 7202 1.550130 TATTCGGGATGGCCGGATCC 61.550 60.000 5.05 10.05 42.33 3.36
2936 7203 0.323629 TTATTCGGGATGGCCGGATC 59.676 55.000 5.05 0.00 42.33 3.36
2937 7204 0.768622 TTTATTCGGGATGGCCGGAT 59.231 50.000 5.05 0.00 42.33 4.18
2938 7205 0.768622 ATTTATTCGGGATGGCCGGA 59.231 50.000 5.05 0.00 41.25 5.14
2939 7206 0.881118 CATTTATTCGGGATGGCCGG 59.119 55.000 0.00 0.00 35.92 6.13
2940 7207 1.604604 ACATTTATTCGGGATGGCCG 58.395 50.000 0.00 0.00 33.83 6.13
2941 7208 5.722021 ATTAACATTTATTCGGGATGGCC 57.278 39.130 0.00 0.00 0.00 5.36
2942 7209 7.040686 ACACTATTAACATTTATTCGGGATGGC 60.041 37.037 0.00 0.00 0.00 4.40
2943 7210 8.289618 CACACTATTAACATTTATTCGGGATGG 58.710 37.037 0.00 0.00 0.00 3.51
2947 7214 6.262273 AGCCACACTATTAACATTTATTCGGG 59.738 38.462 0.00 0.00 0.00 5.14
2962 7229 4.611367 ACCTACAGAGTAAGCCACACTAT 58.389 43.478 0.00 0.00 0.00 2.12
2979 7246 6.576662 TGTAGCATCTTAGCAGATACCTAC 57.423 41.667 12.47 12.47 37.71 3.18
2989 7256 6.737254 TTGTAGGTTTTGTAGCATCTTAGC 57.263 37.500 0.00 0.00 0.00 3.09
3013 7280 5.617252 TGATTGACCCGTTAAGAACTTTCT 58.383 37.500 0.00 0.00 39.74 2.52
3014 7281 5.934935 TGATTGACCCGTTAAGAACTTTC 57.065 39.130 0.00 0.00 0.00 2.62
3015 7282 7.391620 TCTATGATTGACCCGTTAAGAACTTT 58.608 34.615 0.00 0.00 0.00 2.66
3016 7283 6.942976 TCTATGATTGACCCGTTAAGAACTT 58.057 36.000 0.00 0.00 0.00 2.66
3017 7284 6.540438 TCTATGATTGACCCGTTAAGAACT 57.460 37.500 0.00 0.00 0.00 3.01
3018 7285 7.787725 AATCTATGATTGACCCGTTAAGAAC 57.212 36.000 0.00 0.00 0.00 3.01
3019 7286 9.893634 TTTAATCTATGATTGACCCGTTAAGAA 57.106 29.630 3.35 0.00 0.00 2.52
3022 7289 9.839817 TGATTTAATCTATGATTGACCCGTTAA 57.160 29.630 6.50 0.00 0.00 2.01
3024 7291 8.786898 CATGATTTAATCTATGATTGACCCGTT 58.213 33.333 6.50 0.00 0.00 4.44
3025 7292 7.094634 GCATGATTTAATCTATGATTGACCCGT 60.095 37.037 15.98 0.00 0.00 5.28
3026 7293 7.246311 GCATGATTTAATCTATGATTGACCCG 58.754 38.462 15.98 0.00 0.00 5.28
3027 7294 7.246311 CGCATGATTTAATCTATGATTGACCC 58.754 38.462 15.98 2.65 0.00 4.46
3028 7295 7.094634 ACCGCATGATTTAATCTATGATTGACC 60.095 37.037 15.98 3.12 0.00 4.02
3029 7296 7.747799 CACCGCATGATTTAATCTATGATTGAC 59.252 37.037 15.98 3.58 0.00 3.18
3030 7297 7.661027 TCACCGCATGATTTAATCTATGATTGA 59.339 33.333 15.98 12.23 29.99 2.57
3031 7298 7.747799 GTCACCGCATGATTTAATCTATGATTG 59.252 37.037 15.98 10.91 40.28 2.67
3032 7299 7.094634 GGTCACCGCATGATTTAATCTATGATT 60.095 37.037 15.98 0.00 40.28 2.57
3033 7300 6.372659 GGTCACCGCATGATTTAATCTATGAT 59.627 38.462 15.98 0.00 40.28 2.45
3066 7333 2.500504 GGAGGTGGAGTTACAACTAGGG 59.499 54.545 0.00 0.00 38.83 3.53
3067 7334 2.165845 CGGAGGTGGAGTTACAACTAGG 59.834 54.545 0.00 0.00 38.83 3.02
3099 7367 4.670896 ACTGGGTCACAAAAGGAAATTG 57.329 40.909 0.00 0.00 0.00 2.32
3104 7372 1.341482 TGCAACTGGGTCACAAAAGGA 60.341 47.619 0.00 0.00 0.00 3.36
3181 7449 0.733909 GTTGCATCTCAAAAGGGCGC 60.734 55.000 0.00 0.00 36.26 6.53
3182 7450 0.883833 AGTTGCATCTCAAAAGGGCG 59.116 50.000 0.00 0.00 36.26 6.13
3183 7451 1.888512 TCAGTTGCATCTCAAAAGGGC 59.111 47.619 0.00 0.00 36.26 5.19
3184 7452 2.094854 GCTCAGTTGCATCTCAAAAGGG 60.095 50.000 0.00 0.00 36.26 3.95
3185 7453 2.555325 TGCTCAGTTGCATCTCAAAAGG 59.445 45.455 0.00 0.00 38.12 3.11
3206 7474 3.717294 GGTCGGAGGCACCCACAT 61.717 66.667 0.87 0.00 34.64 3.21
3226 7494 6.183360 GGTGTGGAATTGTAACTGAGACAAAA 60.183 38.462 0.00 0.00 40.07 2.44
3234 7502 2.228822 GGCAGGTGTGGAATTGTAACTG 59.771 50.000 0.00 0.00 0.00 3.16
3252 7520 2.512286 GCTCGCAGTAGCATGGCA 60.512 61.111 0.00 0.00 42.30 4.92
3267 7535 4.134563 AGGACAACAACAAAATACGAGCT 58.865 39.130 0.00 0.00 0.00 4.09
3312 7580 2.143122 CTCTACCGAAAACAGCTTGCA 58.857 47.619 0.00 0.00 0.00 4.08
3341 7610 2.435437 AGTTGCAGCTGGGACAAAAATT 59.565 40.909 17.12 0.00 38.70 1.82
3376 7645 2.456577 AGAAAAAGTGTGCCCAGTTGT 58.543 42.857 0.00 0.00 34.44 3.32
3377 7646 4.853924 ATAGAAAAAGTGTGCCCAGTTG 57.146 40.909 0.00 0.00 34.44 3.16
3407 7676 3.973657 CTCAATTGCATATTGAGGGTGC 58.026 45.455 26.92 0.00 46.75 5.01
3413 7682 4.512484 TCGACACCTCAATTGCATATTGA 58.488 39.130 17.56 17.56 36.67 2.57
3436 7705 1.243902 GCAACTTGGGACGAAATGGA 58.756 50.000 0.00 0.00 0.00 3.41
3443 7712 0.958091 TGGAATTGCAACTTGGGACG 59.042 50.000 0.00 0.00 0.00 4.79
3489 7758 7.500629 TGTATATAGAGGATGGACATGCAAT 57.499 36.000 6.58 0.33 0.00 3.56


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

AutoCloner maintained by Alex Coulton.