Multiple sequence alignment - TraesCS1D01G092000

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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 TraesCS1D01G092000 chr1D 100.000 3068 0 0 1 3068 78920463 78923530 0.000000e+00 5666
1 TraesCS1D01G092000 chr1B 91.029 2274 166 18 813 3064 123434115 123431858 0.000000e+00 3035
2 TraesCS1D01G092000 chr7D 95.777 521 11 2 1 510 528056330 528055810 0.000000e+00 830
3 TraesCS1D01G092000 chr7D 94.565 276 12 3 453 725 528055830 528055555 1.020000e-114 424
4 TraesCS1D01G092000 chr7D 77.029 579 84 36 175 724 282955229 282954671 1.390000e-73 287
5 TraesCS1D01G092000 chr3A 86.957 759 59 20 1 724 747037831 747037078 0.000000e+00 817
6 TraesCS1D01G092000 chr5A 90.291 515 40 1 1 505 12557822 12558336 0.000000e+00 665
7 TraesCS1D01G092000 chr5A 91.935 248 20 0 478 725 12558349 12558596 6.300000e-92 348
8 TraesCS1D01G092000 chr5D 84.050 721 80 19 1 704 245774366 245773664 0.000000e+00 662
9 TraesCS1D01G092000 chr5D 81.529 314 38 14 175 474 515226998 515227305 1.100000e-59 241
10 TraesCS1D01G092000 chr5D 91.919 99 8 0 39 137 564898743 564898645 4.130000e-29 139
11 TraesCS1D01G092000 chr5D 86.607 112 12 3 10 119 334971167 334971277 1.490000e-23 121
12 TraesCS1D01G092000 chr7B 82.038 373 50 8 169 529 744305907 744306274 4.970000e-78 302
13 TraesCS1D01G092000 chr2B 91.129 124 9 2 1 123 238631449 238631571 1.890000e-37 167
14 TraesCS1D01G092000 chr2B 87.640 89 11 0 636 724 745780830 745780918 1.500000e-18 104
15 TraesCS1D01G092000 chr2B 83.810 105 15 2 630 732 607249651 607249755 7.000000e-17 99
16 TraesCS1D01G092000 chr2D 87.597 129 9 3 1 123 640723390 640723517 3.190000e-30 143
17 TraesCS1D01G092000 chr6B 83.916 143 19 3 39 178 698135591 698135732 1.920000e-27 134
18 TraesCS1D01G092000 chr6B 85.567 97 12 2 630 724 653860885 653860981 1.950000e-17 100
19 TraesCS1D01G092000 chr4D 75.379 264 40 15 456 715 473868310 473868552 1.500000e-18 104


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 TraesCS1D01G092000 chr1D 78920463 78923530 3067 False 5666.0 5666 100.000 1 3068 1 chr1D.!!$F1 3067
1 TraesCS1D01G092000 chr1B 123431858 123434115 2257 True 3035.0 3035 91.029 813 3064 1 chr1B.!!$R1 2251
2 TraesCS1D01G092000 chr7D 528055555 528056330 775 True 627.0 830 95.171 1 725 2 chr7D.!!$R2 724
3 TraesCS1D01G092000 chr7D 282954671 282955229 558 True 287.0 287 77.029 175 724 1 chr7D.!!$R1 549
4 TraesCS1D01G092000 chr3A 747037078 747037831 753 True 817.0 817 86.957 1 724 1 chr3A.!!$R1 723
5 TraesCS1D01G092000 chr5A 12557822 12558596 774 False 506.5 665 91.113 1 725 2 chr5A.!!$F1 724
6 TraesCS1D01G092000 chr5D 245773664 245774366 702 True 662.0 662 84.050 1 704 1 chr5D.!!$R1 703

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
746 819 0.040425 CAAGAAGGGAAACGCAACGG 60.04 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2535 2626 0.468226 TTCATCCGGGCCATCAGTAC 59.532 55.0 4.39 0.0 0.0 2.73 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
186 187 1.576356 GCAACCGGCAATCACAAAAA 58.424 45.000 0.00 0.00 43.97 1.94
227 228 1.064758 TGCTACAATGGTGATGGGGTC 60.065 52.381 0.00 0.00 0.00 4.46
437 464 2.433970 TCCTGCATACATGGATTCGACA 59.566 45.455 0.00 0.00 0.00 4.35
562 630 1.293498 GTCCTGTGCTCGTCCATGT 59.707 57.895 0.00 0.00 0.00 3.21
633 703 0.974383 GGGGAGGAAACGAGTGAAGA 59.026 55.000 0.00 0.00 0.00 2.87
728 801 3.322514 GCCTATAAGCGGCCAATCA 57.677 52.632 2.24 0.00 41.73 2.57
729 802 1.604604 GCCTATAAGCGGCCAATCAA 58.395 50.000 2.24 0.00 41.73 2.57
730 803 1.537202 GCCTATAAGCGGCCAATCAAG 59.463 52.381 2.24 0.00 41.73 3.02
731 804 2.810400 GCCTATAAGCGGCCAATCAAGA 60.810 50.000 2.24 0.00 41.73 3.02
732 805 3.476552 CCTATAAGCGGCCAATCAAGAA 58.523 45.455 2.24 0.00 0.00 2.52
733 806 3.499918 CCTATAAGCGGCCAATCAAGAAG 59.500 47.826 2.24 0.00 0.00 2.85
734 807 1.750193 TAAGCGGCCAATCAAGAAGG 58.250 50.000 2.24 0.00 0.00 3.46
735 808 0.967380 AAGCGGCCAATCAAGAAGGG 60.967 55.000 2.24 0.00 0.00 3.95
736 809 1.378514 GCGGCCAATCAAGAAGGGA 60.379 57.895 2.24 0.00 0.00 4.20
737 810 0.965363 GCGGCCAATCAAGAAGGGAA 60.965 55.000 2.24 0.00 0.00 3.97
738 811 1.544724 CGGCCAATCAAGAAGGGAAA 58.455 50.000 2.24 0.00 0.00 3.13
739 812 1.202348 CGGCCAATCAAGAAGGGAAAC 59.798 52.381 2.24 0.00 0.00 2.78
740 813 1.202348 GGCCAATCAAGAAGGGAAACG 59.798 52.381 0.00 0.00 0.00 3.60
741 814 1.402852 GCCAATCAAGAAGGGAAACGC 60.403 52.381 0.00 0.00 0.00 4.84
742 815 1.885887 CCAATCAAGAAGGGAAACGCA 59.114 47.619 0.00 0.00 0.00 5.24
743 816 2.295909 CCAATCAAGAAGGGAAACGCAA 59.704 45.455 0.00 0.00 0.00 4.85
744 817 3.308530 CAATCAAGAAGGGAAACGCAAC 58.691 45.455 0.00 0.00 0.00 4.17
745 818 0.941542 TCAAGAAGGGAAACGCAACG 59.058 50.000 0.00 0.00 0.00 4.10
746 819 0.040425 CAAGAAGGGAAACGCAACGG 60.040 55.000 0.00 0.00 0.00 4.44
747 820 0.464916 AAGAAGGGAAACGCAACGGT 60.465 50.000 0.00 0.00 0.00 4.83
748 821 0.464916 AGAAGGGAAACGCAACGGTT 60.465 50.000 0.00 0.00 40.41 4.44
749 822 0.382873 GAAGGGAAACGCAACGGTTT 59.617 50.000 0.00 0.00 36.71 3.27
767 840 3.492337 GTTTCAAACCATACCCAGACCA 58.508 45.455 0.00 0.00 0.00 4.02
768 841 2.871096 TCAAACCATACCCAGACCAC 57.129 50.000 0.00 0.00 0.00 4.16
769 842 1.353022 TCAAACCATACCCAGACCACC 59.647 52.381 0.00 0.00 0.00 4.61
770 843 1.074727 CAAACCATACCCAGACCACCA 59.925 52.381 0.00 0.00 0.00 4.17
771 844 0.696501 AACCATACCCAGACCACCAC 59.303 55.000 0.00 0.00 0.00 4.16
772 845 0.178873 ACCATACCCAGACCACCACT 60.179 55.000 0.00 0.00 0.00 4.00
773 846 1.079825 ACCATACCCAGACCACCACTA 59.920 52.381 0.00 0.00 0.00 2.74
774 847 1.485066 CCATACCCAGACCACCACTAC 59.515 57.143 0.00 0.00 0.00 2.73
775 848 2.184533 CATACCCAGACCACCACTACA 58.815 52.381 0.00 0.00 0.00 2.74
776 849 2.634639 TACCCAGACCACCACTACAT 57.365 50.000 0.00 0.00 0.00 2.29
777 850 2.634639 ACCCAGACCACCACTACATA 57.365 50.000 0.00 0.00 0.00 2.29
778 851 2.910544 ACCCAGACCACCACTACATAA 58.089 47.619 0.00 0.00 0.00 1.90
779 852 3.460825 ACCCAGACCACCACTACATAAT 58.539 45.455 0.00 0.00 0.00 1.28
780 853 3.850173 ACCCAGACCACCACTACATAATT 59.150 43.478 0.00 0.00 0.00 1.40
781 854 5.034200 ACCCAGACCACCACTACATAATTA 58.966 41.667 0.00 0.00 0.00 1.40
782 855 5.489637 ACCCAGACCACCACTACATAATTAA 59.510 40.000 0.00 0.00 0.00 1.40
783 856 6.055588 CCCAGACCACCACTACATAATTAAG 58.944 44.000 0.00 0.00 0.00 1.85
784 857 5.527582 CCAGACCACCACTACATAATTAAGC 59.472 44.000 0.00 0.00 0.00 3.09
785 858 6.349300 CAGACCACCACTACATAATTAAGCT 58.651 40.000 0.00 0.00 0.00 3.74
786 859 7.418597 CCAGACCACCACTACATAATTAAGCTA 60.419 40.741 0.00 0.00 0.00 3.32
787 860 7.438459 CAGACCACCACTACATAATTAAGCTAC 59.562 40.741 0.00 0.00 0.00 3.58
788 861 7.344871 AGACCACCACTACATAATTAAGCTACT 59.655 37.037 0.00 0.00 0.00 2.57
789 862 7.272978 ACCACCACTACATAATTAAGCTACTG 58.727 38.462 0.00 0.00 0.00 2.74
790 863 7.093024 ACCACCACTACATAATTAAGCTACTGT 60.093 37.037 0.00 0.00 0.00 3.55
791 864 7.438459 CCACCACTACATAATTAAGCTACTGTC 59.562 40.741 0.00 0.00 0.00 3.51
792 865 7.979537 CACCACTACATAATTAAGCTACTGTCA 59.020 37.037 0.00 0.00 0.00 3.58
793 866 8.537016 ACCACTACATAATTAAGCTACTGTCAA 58.463 33.333 0.00 0.00 0.00 3.18
794 867 9.378551 CCACTACATAATTAAGCTACTGTCAAA 57.621 33.333 0.00 0.00 0.00 2.69
828 901 8.380867 ACTACATAATTAAGCACCCTATTACCC 58.619 37.037 0.00 0.00 0.00 3.69
839 912 2.227194 CCTATTACCCCGCCAACAATC 58.773 52.381 0.00 0.00 0.00 2.67
873 948 2.573915 GTCCATCCCATCTCTAATCCCC 59.426 54.545 0.00 0.00 0.00 4.81
874 949 2.184339 TCCATCCCATCTCTAATCCCCA 59.816 50.000 0.00 0.00 0.00 4.96
875 950 3.181380 TCCATCCCATCTCTAATCCCCAT 60.181 47.826 0.00 0.00 0.00 4.00
876 951 3.595138 CCATCCCATCTCTAATCCCCATT 59.405 47.826 0.00 0.00 0.00 3.16
877 952 4.569228 CCATCCCATCTCTAATCCCCATTG 60.569 50.000 0.00 0.00 0.00 2.82
881 959 2.645838 TCTCTAATCCCCATTGCTGC 57.354 50.000 0.00 0.00 0.00 5.25
885 963 1.952296 CTAATCCCCATTGCTGCAGAC 59.048 52.381 20.43 9.67 0.00 3.51
891 969 2.816958 ATTGCTGCAGACCGCGAG 60.817 61.111 20.43 0.00 46.97 5.03
912 990 1.138266 GCATCACCGCCTAGAACCTTA 59.862 52.381 0.00 0.00 0.00 2.69
934 1012 1.739562 CCAGCACTCCTGAAGCGAC 60.740 63.158 0.00 0.00 44.64 5.19
935 1013 1.739562 CAGCACTCCTGAAGCGACC 60.740 63.158 0.00 0.00 44.64 4.79
946 1024 3.491104 CCTGAAGCGACCAGAATAGGTAC 60.491 52.174 4.91 0.00 43.38 3.34
947 1025 2.098607 TGAAGCGACCAGAATAGGTACG 59.901 50.000 0.00 0.00 43.38 3.67
948 1026 1.760192 AGCGACCAGAATAGGTACGT 58.240 50.000 0.00 0.00 43.38 3.57
949 1027 2.923121 AGCGACCAGAATAGGTACGTA 58.077 47.619 0.00 0.00 43.38 3.57
966 1044 6.016943 AGGTACGTAGAAACTAGAGCATCATC 60.017 42.308 0.00 0.00 37.82 2.92
976 1054 1.415659 AGAGCATCATCACCCAGCTAC 59.584 52.381 0.00 0.00 37.82 3.58
1053 1138 1.219393 CCTTGGCGACCTCTTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
1222 1307 1.413767 CGAAGATGAACGTGCCTCCG 61.414 60.000 0.00 0.00 0.00 4.63
1326 1411 1.139734 CGGTGGTCTCATCGTCCTG 59.860 63.158 0.00 0.00 42.14 3.86
1347 1432 3.537206 AAGCAGGACCGCTCCACAC 62.537 63.158 10.58 0.00 42.89 3.82
1348 1433 4.314440 GCAGGACCGCTCCACACA 62.314 66.667 0.00 0.00 39.39 3.72
1380 1465 4.690748 GTCATGAATCTTTTCACCGACTCA 59.309 41.667 0.00 0.00 44.36 3.41
1382 1467 5.352293 TCATGAATCTTTTCACCGACTCATG 59.648 40.000 0.00 4.81 44.36 3.07
1395 1480 0.723414 ACTCATGCATCAGTTTCGCG 59.277 50.000 0.00 0.00 0.00 5.87
1516 1601 1.666553 TACACGGCCAAGCTTGACG 60.667 57.895 29.35 29.35 35.52 4.35
1585 1670 0.594602 CATATGGGGCATTGACGCTG 59.405 55.000 8.17 0.00 0.00 5.18
1592 1677 2.463620 GCATTGACGCTGCCGATCA 61.464 57.895 0.00 0.00 38.29 2.92
1722 1807 0.980423 TCATCCATCGTCAACACCCA 59.020 50.000 0.00 0.00 0.00 4.51
1766 1851 4.028852 AGGTGAACGTTGAAGAAAAAGC 57.971 40.909 5.00 0.00 0.00 3.51
1833 1918 0.249489 AGAGGTGCGTGTCTGTTGAC 60.249 55.000 0.00 0.00 43.20 3.18
1866 1951 1.349688 TCTACCATTGAAGGCAACCGT 59.650 47.619 0.00 0.00 36.72 4.83
1886 1971 3.665190 GTGTCTTCTACTTTGGTGGAGG 58.335 50.000 0.00 0.00 34.54 4.30
1893 1978 0.689623 ACTTTGGTGGAGGAGAGCAG 59.310 55.000 0.00 0.00 0.00 4.24
1902 1987 1.544691 GGAGGAGAGCAGTACGACAAA 59.455 52.381 0.00 0.00 0.00 2.83
1906 1991 0.679505 AGAGCAGTACGACAAAGGCA 59.320 50.000 0.00 0.00 0.00 4.75
2061 2146 3.246112 CCGTGGGTCCCAACTGGA 61.246 66.667 13.78 0.00 42.41 3.86
2071 2156 1.553248 TCCCAACTGGAGTATGAACCG 59.447 52.381 0.00 0.00 38.61 4.44
2079 2164 2.132762 GGAGTATGAACCGCATAACCG 58.867 52.381 0.00 0.00 40.97 4.44
2104 2189 1.331214 GTGGCAATGGGGTATGATGG 58.669 55.000 0.00 0.00 0.00 3.51
2105 2190 0.469705 TGGCAATGGGGTATGATGGC 60.470 55.000 0.00 0.00 37.12 4.40
2107 2192 0.675633 GCAATGGGGTATGATGGCAC 59.324 55.000 0.00 0.00 0.00 5.01
2110 2195 1.521764 ATGGGGTATGATGGCACTGA 58.478 50.000 0.00 0.00 0.00 3.41
2128 2213 7.334671 TGGCACTGAATAATATTGTAAACGTCA 59.665 33.333 0.00 0.00 0.00 4.35
2145 2230 3.244215 ACGTCAGGTGTGATTGATTGAGT 60.244 43.478 0.00 0.00 34.36 3.41
2147 2232 4.377738 CGTCAGGTGTGATTGATTGAGTTG 60.378 45.833 0.00 0.00 34.36 3.16
2155 2240 6.476380 GTGTGATTGATTGAGTTGCAAGAAAA 59.524 34.615 0.00 0.00 40.42 2.29
2195 2282 9.717942 TTTGGGGTATTGTATTTCAAATTTGAG 57.282 29.630 19.64 0.00 39.62 3.02
2196 2283 8.657387 TGGGGTATTGTATTTCAAATTTGAGA 57.343 30.769 19.64 16.46 39.62 3.27
2211 2298 9.342308 TCAAATTTGAGAGTTGAATGTTCTACT 57.658 29.630 16.91 9.10 39.20 2.57
2213 2300 7.678947 ATTTGAGAGTTGAATGTTCTACTGG 57.321 36.000 13.18 0.00 41.96 4.00
2216 2303 5.540337 TGAGAGTTGAATGTTCTACTGGTCT 59.460 40.000 13.18 6.10 41.96 3.85
2217 2304 6.031751 AGAGTTGAATGTTCTACTGGTCTC 57.968 41.667 13.18 1.47 41.96 3.36
2236 2323 9.482627 CTGGTCTCTATATGTCTGTTAAAATCC 57.517 37.037 0.00 0.00 0.00 3.01
2265 2352 4.717233 TGTCAGTTGCAAGTTTGTTCAT 57.283 36.364 3.38 0.00 0.00 2.57
2266 2353 4.422840 TGTCAGTTGCAAGTTTGTTCATG 58.577 39.130 3.38 0.00 0.00 3.07
2278 2365 7.487829 GCAAGTTTGTTCATGTAACTCTTGAAA 59.512 33.333 23.27 11.42 40.27 2.69
2291 2378 4.120589 ACTCTTGAAAGTCGAGTTGTTCC 58.879 43.478 6.19 0.00 34.55 3.62
2332 2421 9.582648 AAATAATAAGTAGAACAACCACCAAGT 57.417 29.630 0.00 0.00 0.00 3.16
2334 2423 9.886132 ATAATAAGTAGAACAACCACCAAGTAG 57.114 33.333 0.00 0.00 0.00 2.57
2345 2434 5.359194 ACCACCAAGTAGGAGACATATTG 57.641 43.478 0.00 0.00 41.22 1.90
2349 2438 3.181465 CCAAGTAGGAGACATATTGCGGT 60.181 47.826 0.00 0.00 41.22 5.68
2351 2440 5.223382 CAAGTAGGAGACATATTGCGGTAG 58.777 45.833 0.00 0.00 0.00 3.18
2409 2500 0.396695 GTCCACGAGGTAGGATGGGA 60.397 60.000 0.00 0.00 36.11 4.37
2426 2517 2.680352 ATCCGTCCACGCCTCACT 60.680 61.111 0.00 0.00 38.18 3.41
2435 2526 0.589229 CACGCCTCACTATCGTCGAC 60.589 60.000 5.18 5.18 33.84 4.20
2444 2535 5.213913 TCACTATCGTCGACTAGAACAAC 57.786 43.478 14.70 0.00 0.00 3.32
2446 2537 2.539346 ATCGTCGACTAGAACAACCG 57.461 50.000 14.70 0.00 0.00 4.44
2454 2545 3.305608 CGACTAGAACAACCGGTAAACCT 60.306 47.826 8.00 6.10 0.00 3.50
2460 2551 4.353737 GAACAACCGGTAAACCTTTGTTC 58.646 43.478 23.11 23.11 46.87 3.18
2465 2556 2.352323 CCGGTAAACCTTTGTTCATGGC 60.352 50.000 0.00 0.00 32.15 4.40
2466 2557 2.294791 CGGTAAACCTTTGTTCATGGCA 59.705 45.455 0.00 0.00 32.15 4.92
2475 2566 0.321564 TGTTCATGGCAGGTTCCTCG 60.322 55.000 0.00 0.00 0.00 4.63
2478 2569 0.321564 TCATGGCAGGTTCCTCGTTG 60.322 55.000 0.00 0.00 0.00 4.10
2479 2570 1.002134 ATGGCAGGTTCCTCGTTGG 60.002 57.895 0.00 0.00 37.10 3.77
2484 2575 2.046217 GGTTCCTCGTTGGCCTCC 60.046 66.667 3.32 0.00 35.26 4.30
2487 2578 0.539986 GTTCCTCGTTGGCCTCCATA 59.460 55.000 3.32 0.00 31.53 2.74
2492 2583 2.421388 CCTCGTTGGCCTCCATAATGAA 60.421 50.000 3.32 0.00 31.53 2.57
2530 2621 2.214347 TCGTTTTCTCGAATGGTTGCA 58.786 42.857 0.00 0.00 36.89 4.08
2531 2622 2.032377 TCGTTTTCTCGAATGGTTGCAC 60.032 45.455 0.00 0.00 36.89 4.57
2535 2626 1.452110 TCTCGAATGGTTGCACATGG 58.548 50.000 0.00 0.00 0.00 3.66
2547 2638 1.103398 GCACATGGTACTGATGGCCC 61.103 60.000 0.00 0.00 0.00 5.80
2554 2645 0.468226 GTACTGATGGCCCGGATGAA 59.532 55.000 0.73 0.00 0.00 2.57
2558 2649 3.460672 GATGGCCCGGATGAAGCGA 62.461 63.158 0.73 0.00 0.00 4.93
2559 2650 3.757248 ATGGCCCGGATGAAGCGAC 62.757 63.158 0.73 0.00 0.00 5.19
2565 2656 1.656652 CCGGATGAAGCGACTGAATT 58.343 50.000 0.00 0.00 0.00 2.17
2571 2662 4.090642 GGATGAAGCGACTGAATTATAGCG 59.909 45.833 0.00 0.00 0.00 4.26
2577 2668 3.550275 GCGACTGAATTATAGCGAACACA 59.450 43.478 0.00 0.00 0.00 3.72
2594 2685 6.972328 GCGAACACAAATAATGATACATTGGT 59.028 34.615 7.16 0.00 0.00 3.67
2618 2709 6.393720 GCGCATGCAAAAATTAATATAGGG 57.606 37.500 19.57 0.00 42.15 3.53
2619 2710 5.348451 GCGCATGCAAAAATTAATATAGGGG 59.652 40.000 19.57 0.00 42.15 4.79
2620 2711 5.348451 CGCATGCAAAAATTAATATAGGGGC 59.652 40.000 19.57 0.00 0.00 5.80
2624 2715 7.667575 TGCAAAAATTAATATAGGGGCTTCA 57.332 32.000 0.00 0.00 0.00 3.02
2666 2757 4.973168 ACTTCTCTTGGACAAGCAACATA 58.027 39.130 7.18 0.00 38.28 2.29
2720 2811 3.113322 TCGCATGCTAAGACGACATTAC 58.887 45.455 17.13 0.00 0.00 1.89
2728 2820 5.587443 TGCTAAGACGACATTACACTAGCTA 59.413 40.000 0.00 0.00 0.00 3.32
2740 2832 9.534565 ACATTACACTAGCTATTTGACATACTG 57.465 33.333 9.02 0.86 0.00 2.74
2762 2854 5.833082 TGAATCGACTTTAAGCTAGCTAGG 58.167 41.667 19.70 6.36 0.00 3.02
2763 2855 5.360144 TGAATCGACTTTAAGCTAGCTAGGT 59.640 40.000 19.70 19.65 35.17 3.08
2773 2865 8.763984 TTTAAGCTAGCTAGGTCATACTTAGT 57.236 34.615 24.86 9.27 31.24 2.24
2784 2876 6.216569 AGGTCATACTTAGTGCAATACGATG 58.783 40.000 4.56 4.12 0.00 3.84
2796 2888 5.059221 GTGCAATACGATGAAAAGAAAACCG 59.941 40.000 0.00 0.00 0.00 4.44
2821 2913 5.163602 TGACGGACTAAAAACAAGCAAATGT 60.164 36.000 0.00 0.00 34.24 2.71
2827 2919 8.874816 GGACTAAAAACAAGCAAATGTAAAACA 58.125 29.630 0.00 0.00 32.02 2.83
2848 2940 7.750229 AACATTTATTATCATGGCGATGACT 57.250 32.000 14.05 6.26 41.52 3.41
2861 2953 1.725164 CGATGACTCATGCCATGATCG 59.275 52.381 8.03 10.64 38.85 3.69
2864 2956 1.207811 TGACTCATGCCATGATCGTGT 59.792 47.619 8.03 2.26 38.85 4.49
2872 2964 1.511850 CCATGATCGTGTGTGTGTGT 58.488 50.000 13.81 0.00 0.00 3.72
2873 2965 2.682836 CCATGATCGTGTGTGTGTGTA 58.317 47.619 13.81 0.00 0.00 2.90
2874 2966 2.667969 CCATGATCGTGTGTGTGTGTAG 59.332 50.000 13.81 0.00 0.00 2.74
2875 2967 3.317150 CATGATCGTGTGTGTGTGTAGT 58.683 45.455 6.77 0.00 0.00 2.73
2876 2968 3.446310 TGATCGTGTGTGTGTGTAGTT 57.554 42.857 0.00 0.00 0.00 2.24
2877 2969 3.787785 TGATCGTGTGTGTGTGTAGTTT 58.212 40.909 0.00 0.00 0.00 2.66
2896 2988 3.799281 TTTTTCAGCACCAACTCCTTG 57.201 42.857 0.00 0.00 0.00 3.61
2908 3000 3.258123 CCAACTCCTTGGTTAATTGGTGG 59.742 47.826 0.00 0.00 42.09 4.61
2921 3013 0.110295 TTGGTGGAGTGTGTGGATGG 59.890 55.000 0.00 0.00 0.00 3.51
2949 3041 7.987750 TGACTAGCTACATTCTATCTGGTAG 57.012 40.000 0.00 0.00 37.01 3.18
2963 3055 4.991153 TCTGGTAGAAGCTATGACTGTG 57.009 45.455 0.00 0.00 0.00 3.66
2967 3059 2.001812 AGAAGCTATGACTGTGTGCG 57.998 50.000 0.00 0.00 0.00 5.34
2971 3063 1.991430 CTATGACTGTGTGCGTCGC 59.009 57.895 11.10 11.10 34.17 5.19
2989 3081 1.506493 GCTTGATGCATAGACCGAGG 58.494 55.000 0.00 0.00 42.31 4.63
2995 3087 3.646162 TGATGCATAGACCGAGGGTAATT 59.354 43.478 0.00 0.00 35.25 1.40
2998 3090 3.321111 TGCATAGACCGAGGGTAATTCTC 59.679 47.826 0.00 0.00 35.25 2.87
2999 3091 3.306156 GCATAGACCGAGGGTAATTCTCC 60.306 52.174 0.00 0.00 35.25 3.71
3005 3097 4.332828 ACCGAGGGTAATTCTCCTTTTTG 58.667 43.478 1.63 0.00 32.11 2.44
3006 3098 4.042435 ACCGAGGGTAATTCTCCTTTTTGA 59.958 41.667 1.63 0.00 32.11 2.69
3009 3101 6.152831 CCGAGGGTAATTCTCCTTTTTGAATT 59.847 38.462 0.00 0.00 42.98 2.17
3010 3102 7.309805 CCGAGGGTAATTCTCCTTTTTGAATTT 60.310 37.037 6.32 0.00 41.40 1.82
3011 3103 8.088365 CGAGGGTAATTCTCCTTTTTGAATTTT 58.912 33.333 6.32 0.00 41.40 1.82
3012 3104 9.778741 GAGGGTAATTCTCCTTTTTGAATTTTT 57.221 29.630 6.32 0.00 41.40 1.94
3057 3150 4.927267 TGGTTAACAGATTGGATCACCT 57.073 40.909 8.10 0.00 37.04 4.00
3059 3152 5.741011 TGGTTAACAGATTGGATCACCTAC 58.259 41.667 8.10 0.00 37.04 3.18
3060 3153 5.249622 TGGTTAACAGATTGGATCACCTACA 59.750 40.000 8.10 0.00 37.04 2.74
3061 3154 6.069673 TGGTTAACAGATTGGATCACCTACAT 60.070 38.462 8.10 0.00 37.04 2.29
3062 3155 7.126573 TGGTTAACAGATTGGATCACCTACATA 59.873 37.037 8.10 0.00 37.04 2.29
3063 3156 7.441458 GGTTAACAGATTGGATCACCTACATAC 59.559 40.741 8.10 0.00 37.04 2.39
3065 3158 5.219739 ACAGATTGGATCACCTACATACCT 58.780 41.667 0.00 0.00 37.04 3.08
3066 3159 6.382087 ACAGATTGGATCACCTACATACCTA 58.618 40.000 0.00 0.00 37.04 3.08
3067 3160 6.267928 ACAGATTGGATCACCTACATACCTAC 59.732 42.308 0.00 0.00 37.04 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 3.854286 AAAAAGCTCGTAGTTGTCACG 57.146 42.857 0.00 0.00 40.72 4.35
437 464 1.269998 CCGTCGTCTCCTGAGTTTCTT 59.730 52.381 0.00 0.00 0.00 2.52
562 630 3.052745 GCAGATCGACATCGCATCTTTA 58.947 45.455 11.20 0.00 35.60 1.85
600 668 0.037605 CTCCCCAGCGTAACGACTTT 60.038 55.000 0.00 0.00 0.00 2.66
633 703 0.036765 TGGTAGCCGCACGATCTTTT 60.037 50.000 0.00 0.00 0.00 2.27
725 798 1.535462 CGTTGCGTTTCCCTTCTTGAT 59.465 47.619 0.00 0.00 0.00 2.57
726 799 0.941542 CGTTGCGTTTCCCTTCTTGA 59.058 50.000 0.00 0.00 0.00 3.02
727 800 0.040425 CCGTTGCGTTTCCCTTCTTG 60.040 55.000 0.00 0.00 0.00 3.02
728 801 0.464916 ACCGTTGCGTTTCCCTTCTT 60.465 50.000 0.00 0.00 0.00 2.52
729 802 0.464916 AACCGTTGCGTTTCCCTTCT 60.465 50.000 0.00 0.00 0.00 2.85
730 803 0.382873 AAACCGTTGCGTTTCCCTTC 59.617 50.000 0.00 0.00 29.99 3.46
731 804 0.382873 GAAACCGTTGCGTTTCCCTT 59.617 50.000 3.37 0.00 43.80 3.95
732 805 2.027325 GAAACCGTTGCGTTTCCCT 58.973 52.632 3.37 0.00 43.80 4.20
733 806 4.620437 GAAACCGTTGCGTTTCCC 57.380 55.556 3.37 0.00 43.80 3.97
736 809 1.631284 GGTTTGAAACCGTTGCGTTT 58.369 45.000 11.83 0.00 42.62 3.60
737 810 3.332421 GGTTTGAAACCGTTGCGTT 57.668 47.368 11.83 0.00 42.62 4.84
746 819 3.254903 GTGGTCTGGGTATGGTTTGAAAC 59.745 47.826 0.00 0.00 0.00 2.78
747 820 3.492337 GTGGTCTGGGTATGGTTTGAAA 58.508 45.455 0.00 0.00 0.00 2.69
748 821 2.224917 GGTGGTCTGGGTATGGTTTGAA 60.225 50.000 0.00 0.00 0.00 2.69
749 822 1.353022 GGTGGTCTGGGTATGGTTTGA 59.647 52.381 0.00 0.00 0.00 2.69
750 823 1.074727 TGGTGGTCTGGGTATGGTTTG 59.925 52.381 0.00 0.00 0.00 2.93
751 824 1.074889 GTGGTGGTCTGGGTATGGTTT 59.925 52.381 0.00 0.00 0.00 3.27
752 825 0.696501 GTGGTGGTCTGGGTATGGTT 59.303 55.000 0.00 0.00 0.00 3.67
753 826 0.178873 AGTGGTGGTCTGGGTATGGT 60.179 55.000 0.00 0.00 0.00 3.55
754 827 1.485066 GTAGTGGTGGTCTGGGTATGG 59.515 57.143 0.00 0.00 0.00 2.74
755 828 2.184533 TGTAGTGGTGGTCTGGGTATG 58.815 52.381 0.00 0.00 0.00 2.39
756 829 2.634639 TGTAGTGGTGGTCTGGGTAT 57.365 50.000 0.00 0.00 0.00 2.73
757 830 2.634639 ATGTAGTGGTGGTCTGGGTA 57.365 50.000 0.00 0.00 0.00 3.69
758 831 2.634639 TATGTAGTGGTGGTCTGGGT 57.365 50.000 0.00 0.00 0.00 4.51
759 832 4.503714 AATTATGTAGTGGTGGTCTGGG 57.496 45.455 0.00 0.00 0.00 4.45
760 833 5.527582 GCTTAATTATGTAGTGGTGGTCTGG 59.472 44.000 0.84 0.00 0.00 3.86
761 834 6.349300 AGCTTAATTATGTAGTGGTGGTCTG 58.651 40.000 0.84 0.00 0.00 3.51
762 835 6.561519 AGCTTAATTATGTAGTGGTGGTCT 57.438 37.500 0.84 0.00 0.00 3.85
763 836 7.438459 CAGTAGCTTAATTATGTAGTGGTGGTC 59.562 40.741 0.00 0.00 0.00 4.02
764 837 7.093024 ACAGTAGCTTAATTATGTAGTGGTGGT 60.093 37.037 0.00 0.00 0.00 4.16
765 838 7.272978 ACAGTAGCTTAATTATGTAGTGGTGG 58.727 38.462 0.00 0.00 0.00 4.61
766 839 7.979537 TGACAGTAGCTTAATTATGTAGTGGTG 59.020 37.037 0.00 0.00 0.00 4.17
767 840 8.074613 TGACAGTAGCTTAATTATGTAGTGGT 57.925 34.615 0.00 0.00 0.00 4.16
768 841 8.942338 TTGACAGTAGCTTAATTATGTAGTGG 57.058 34.615 0.00 0.00 0.00 4.00
795 868 7.453439 AGGGTGCTTAATTATGTAGTGGTTTTT 59.547 33.333 0.84 0.00 0.00 1.94
796 869 6.951778 AGGGTGCTTAATTATGTAGTGGTTTT 59.048 34.615 0.84 0.00 0.00 2.43
797 870 6.490492 AGGGTGCTTAATTATGTAGTGGTTT 58.510 36.000 0.84 0.00 0.00 3.27
798 871 6.074698 AGGGTGCTTAATTATGTAGTGGTT 57.925 37.500 0.84 0.00 0.00 3.67
799 872 5.710409 AGGGTGCTTAATTATGTAGTGGT 57.290 39.130 0.84 0.00 0.00 4.16
800 873 9.216117 GTAATAGGGTGCTTAATTATGTAGTGG 57.784 37.037 0.84 0.00 0.00 4.00
801 874 9.216117 GGTAATAGGGTGCTTAATTATGTAGTG 57.784 37.037 0.84 0.00 0.00 2.74
802 875 8.380867 GGGTAATAGGGTGCTTAATTATGTAGT 58.619 37.037 0.84 0.00 0.00 2.73
803 876 7.827729 GGGGTAATAGGGTGCTTAATTATGTAG 59.172 40.741 0.84 0.00 0.00 2.74
804 877 7.527531 CGGGGTAATAGGGTGCTTAATTATGTA 60.528 40.741 0.84 0.00 0.00 2.29
805 878 6.549242 GGGGTAATAGGGTGCTTAATTATGT 58.451 40.000 0.84 0.00 0.00 2.29
806 879 5.646360 CGGGGTAATAGGGTGCTTAATTATG 59.354 44.000 0.00 0.00 0.00 1.90
807 880 5.805424 GCGGGGTAATAGGGTGCTTAATTAT 60.805 44.000 0.00 0.00 0.00 1.28
808 881 4.505390 GCGGGGTAATAGGGTGCTTAATTA 60.505 45.833 0.00 0.00 0.00 1.40
809 882 3.749632 GCGGGGTAATAGGGTGCTTAATT 60.750 47.826 0.00 0.00 0.00 1.40
810 883 2.224695 GCGGGGTAATAGGGTGCTTAAT 60.225 50.000 0.00 0.00 0.00 1.40
811 884 1.141455 GCGGGGTAATAGGGTGCTTAA 59.859 52.381 0.00 0.00 0.00 1.85
828 901 1.937546 GCTTCTGGGATTGTTGGCGG 61.938 60.000 0.00 0.00 0.00 6.13
839 912 0.460987 GATGGACGAGTGCTTCTGGG 60.461 60.000 0.00 0.00 0.00 4.45
873 948 3.092192 CTCGCGGTCTGCAGCAATG 62.092 63.158 9.47 0.00 46.97 2.82
874 949 2.816958 CTCGCGGTCTGCAGCAAT 60.817 61.111 9.47 0.00 46.97 3.56
881 959 2.887568 GTGATGCCTCGCGGTCTG 60.888 66.667 6.13 0.00 0.00 3.51
894 972 2.431057 CTGTAAGGTTCTAGGCGGTGAT 59.569 50.000 0.00 0.00 0.00 3.06
898 976 0.179081 GGCTGTAAGGTTCTAGGCGG 60.179 60.000 0.00 0.00 0.00 6.13
905 983 1.443802 GAGTGCTGGCTGTAAGGTTC 58.556 55.000 0.00 0.00 0.00 3.62
912 990 1.374190 CTTCAGGAGTGCTGGCTGT 59.626 57.895 12.15 0.00 0.00 4.40
934 1012 7.520292 GCTCTAGTTTCTACGTACCTATTCTGG 60.520 44.444 0.00 0.00 0.00 3.86
935 1013 7.012138 TGCTCTAGTTTCTACGTACCTATTCTG 59.988 40.741 0.00 0.00 0.00 3.02
946 1024 4.979197 GGTGATGATGCTCTAGTTTCTACG 59.021 45.833 0.00 0.00 0.00 3.51
947 1025 5.163405 TGGGTGATGATGCTCTAGTTTCTAC 60.163 44.000 0.00 0.00 0.00 2.59
948 1026 4.962362 TGGGTGATGATGCTCTAGTTTCTA 59.038 41.667 0.00 0.00 0.00 2.10
949 1027 3.776969 TGGGTGATGATGCTCTAGTTTCT 59.223 43.478 0.00 0.00 0.00 2.52
966 1044 1.139058 GTGGTGGATAGTAGCTGGGTG 59.861 57.143 0.00 0.00 0.00 4.61
976 1054 1.741706 AGTGACGTACGTGGTGGATAG 59.258 52.381 28.16 0.00 0.00 2.08
1053 1138 1.225583 GTCTACGTCGTCGGTGTCG 60.226 63.158 0.00 0.00 41.85 4.35
1222 1307 0.670854 GTGTTGAGGAAGAGGCGTCC 60.671 60.000 2.06 0.00 35.17 4.79
1347 1432 5.428496 AAAGATTCATGACGCATACCATG 57.572 39.130 0.00 0.00 40.97 3.66
1348 1433 5.589855 TGAAAAGATTCATGACGCATACCAT 59.410 36.000 0.00 0.00 40.59 3.55
1380 1465 2.793946 GCCGCGAAACTGATGCAT 59.206 55.556 8.23 0.00 0.00 3.96
1497 1582 1.866925 GTCAAGCTTGGCCGTGTAC 59.133 57.895 25.73 11.19 0.00 2.90
1516 1601 1.444895 CCACCGCAAATTGCTCAGC 60.445 57.895 16.42 0.00 42.25 4.26
1592 1677 1.063642 TGAGACCACCGATCATCTCCT 60.064 52.381 0.00 0.00 37.40 3.69
1766 1851 1.153939 CTTCTCACAGGCTCGACCG 60.154 63.158 0.00 0.00 46.52 4.79
1833 1918 5.063204 TCAATGGTAGAGAACTTGTTGGTG 58.937 41.667 0.00 0.00 0.00 4.17
1846 1931 1.349688 ACGGTTGCCTTCAATGGTAGA 59.650 47.619 0.00 0.00 34.29 2.59
1866 1951 3.578716 CTCCTCCACCAAAGTAGAAGACA 59.421 47.826 0.00 0.00 0.00 3.41
1886 1971 1.336887 TGCCTTTGTCGTACTGCTCTC 60.337 52.381 0.00 0.00 0.00 3.20
1893 1978 0.878416 TGCCAATGCCTTTGTCGTAC 59.122 50.000 0.00 0.00 36.33 3.67
1902 1987 2.742428 ACATGTAGATGCCAATGCCT 57.258 45.000 0.00 0.00 36.33 4.75
1906 1991 3.118261 AGGTCGAACATGTAGATGCCAAT 60.118 43.478 1.87 0.00 32.14 3.16
1912 1997 5.670792 TTGGTAAGGTCGAACATGTAGAT 57.329 39.130 1.87 0.00 0.00 1.98
2061 2146 2.691526 TCTCGGTTATGCGGTTCATACT 59.308 45.455 0.00 0.00 37.38 2.12
2071 2156 1.378531 TGCCACAATCTCGGTTATGC 58.621 50.000 0.00 0.00 0.00 3.14
2079 2164 2.435372 TACCCCATTGCCACAATCTC 57.565 50.000 0.00 0.00 0.00 2.75
2104 2189 7.850982 CCTGACGTTTACAATATTATTCAGTGC 59.149 37.037 0.00 0.00 0.00 4.40
2105 2190 8.879759 ACCTGACGTTTACAATATTATTCAGTG 58.120 33.333 0.00 0.00 0.00 3.66
2107 2192 8.879759 ACACCTGACGTTTACAATATTATTCAG 58.120 33.333 0.00 0.00 0.00 3.02
2110 2195 8.780846 TCACACCTGACGTTTACAATATTATT 57.219 30.769 0.00 0.00 0.00 1.40
2128 2213 3.489355 TGCAACTCAATCAATCACACCT 58.511 40.909 0.00 0.00 0.00 4.00
2171 2256 8.657387 TCTCAAATTTGAAATACAATACCCCA 57.343 30.769 20.82 0.00 38.36 4.96
2194 2281 5.777732 AGAGACCAGTAGAACATTCAACTCT 59.222 40.000 0.00 0.00 0.00 3.24
2195 2282 6.031751 AGAGACCAGTAGAACATTCAACTC 57.968 41.667 0.00 0.00 0.00 3.01
2196 2283 7.726033 ATAGAGACCAGTAGAACATTCAACT 57.274 36.000 0.00 0.00 0.00 3.16
2211 2298 9.213777 AGGATTTTAACAGACATATAGAGACCA 57.786 33.333 0.00 0.00 0.00 4.02
2236 2323 4.761235 ACTTGCAACTGACATGAATGAG 57.239 40.909 0.00 0.00 0.00 2.90
2241 2328 4.157472 TGAACAAACTTGCAACTGACATGA 59.843 37.500 0.00 0.00 0.00 3.07
2278 2365 3.467803 CAAAGGAAGGAACAACTCGACT 58.532 45.455 0.00 0.00 0.00 4.18
2310 2397 7.016858 TCCTACTTGGTGGTTGTTCTACTTATT 59.983 37.037 0.00 0.00 37.07 1.40
2327 2416 3.181465 ACCGCAATATGTCTCCTACTTGG 60.181 47.826 0.00 0.00 37.10 3.61
2328 2417 4.060038 ACCGCAATATGTCTCCTACTTG 57.940 45.455 0.00 0.00 0.00 3.16
2329 2418 5.138276 TCTACCGCAATATGTCTCCTACTT 58.862 41.667 0.00 0.00 0.00 2.24
2332 2421 4.519350 CACTCTACCGCAATATGTCTCCTA 59.481 45.833 0.00 0.00 0.00 2.94
2334 2423 3.068307 ACACTCTACCGCAATATGTCTCC 59.932 47.826 0.00 0.00 0.00 3.71
2409 2500 0.755698 ATAGTGAGGCGTGGACGGAT 60.756 55.000 0.71 0.00 40.23 4.18
2413 2504 4.711980 CGATAGTGAGGCGTGGAC 57.288 61.111 0.00 0.00 0.00 4.02
2426 2517 2.352651 CCGGTTGTTCTAGTCGACGATA 59.647 50.000 10.46 0.00 0.00 2.92
2435 2526 4.818005 ACAAAGGTTTACCGGTTGTTCTAG 59.182 41.667 15.04 5.61 42.51 2.43
2444 2535 2.352323 GCCATGAACAAAGGTTTACCGG 60.352 50.000 0.00 0.00 42.08 5.28
2446 2537 3.306019 CCTGCCATGAACAAAGGTTTACC 60.306 47.826 0.00 0.00 37.36 2.85
2454 2545 2.238521 GAGGAACCTGCCATGAACAAA 58.761 47.619 0.00 0.00 0.00 2.83
2460 2551 1.308069 CCAACGAGGAACCTGCCATG 61.308 60.000 0.00 0.00 41.22 3.66
2465 2556 1.376037 GAGGCCAACGAGGAACCTG 60.376 63.158 5.01 0.00 41.22 4.00
2466 2557 2.593956 GGAGGCCAACGAGGAACCT 61.594 63.158 5.01 0.00 41.22 3.50
2475 2566 3.018423 ACCTTCATTATGGAGGCCAAC 57.982 47.619 19.01 0.00 36.95 3.77
2478 2569 2.553247 GGCTACCTTCATTATGGAGGCC 60.553 54.545 19.01 10.98 37.35 5.19
2479 2570 2.784347 GGCTACCTTCATTATGGAGGC 58.216 52.381 19.01 5.64 0.00 4.70
2484 2575 2.872038 GCCCTCGGCTACCTTCATTATG 60.872 54.545 0.00 0.00 46.69 1.90
2487 2578 1.527370 GCCCTCGGCTACCTTCATT 59.473 57.895 0.00 0.00 46.69 2.57
2509 2600 5.976927 TGTGCAACCATTCGAGAAAACGAA 61.977 41.667 0.00 0.00 45.87 3.85
2511 2602 2.286713 TGTGCAACCATTCGAGAAAACG 60.287 45.455 0.00 0.00 34.36 3.60
2513 2604 3.305267 CCATGTGCAACCATTCGAGAAAA 60.305 43.478 0.00 0.00 34.36 2.29
2528 2619 1.103398 GGGCCATCAGTACCATGTGC 61.103 60.000 4.39 0.00 0.00 4.57
2530 2621 1.526887 CGGGCCATCAGTACCATGT 59.473 57.895 4.39 0.00 0.00 3.21
2531 2622 1.227943 CCGGGCCATCAGTACCATG 60.228 63.158 4.39 0.00 0.00 3.66
2535 2626 0.468226 TTCATCCGGGCCATCAGTAC 59.532 55.000 4.39 0.00 0.00 2.73
2547 2638 4.090642 GCTATAATTCAGTCGCTTCATCCG 59.909 45.833 0.00 0.00 0.00 4.18
2554 2645 3.797256 GTGTTCGCTATAATTCAGTCGCT 59.203 43.478 0.00 0.00 0.00 4.93
2558 2649 9.935682 CATTATTTGTGTTCGCTATAATTCAGT 57.064 29.630 0.00 0.00 0.00 3.41
2571 2662 7.044117 CGCACCAATGTATCATTATTTGTGTTC 60.044 37.037 0.00 0.00 34.34 3.18
2577 2668 5.512753 TGCGCACCAATGTATCATTATTT 57.487 34.783 5.66 0.00 0.00 1.40
2619 2710 9.482627 GTATTCATAGGGCTGTATATATGAAGC 57.517 37.037 11.24 11.24 43.86 3.86
2634 2725 8.380630 GCTTGTCCAAGAGAAGTATTCATAGGG 61.381 44.444 11.12 0.00 42.34 3.53
2646 2737 5.316167 ACATATGTTGCTTGTCCAAGAGAA 58.684 37.500 11.12 0.30 40.79 2.87
2649 2740 5.185454 CCTACATATGTTGCTTGTCCAAGA 58.815 41.667 14.77 0.00 40.79 3.02
2688 2779 5.235186 GTCTTAGCATGCGATAGTGTTCATT 59.765 40.000 13.01 0.00 39.35 2.57
2720 2811 7.862873 TCGATTCAGTATGTCAAATAGCTAGTG 59.137 37.037 0.00 0.00 37.40 2.74
2728 2820 8.391106 GCTTAAAGTCGATTCAGTATGTCAAAT 58.609 33.333 0.00 0.00 37.40 2.32
2740 2832 5.834169 ACCTAGCTAGCTTAAAGTCGATTC 58.166 41.667 24.88 0.00 0.00 2.52
2762 2854 7.694388 TTCATCGTATTGCACTAAGTATGAC 57.306 36.000 0.00 0.00 0.00 3.06
2763 2855 8.710835 TTTTCATCGTATTGCACTAAGTATGA 57.289 30.769 0.00 0.00 0.00 2.15
2773 2865 5.150683 CGGTTTTCTTTTCATCGTATTGCA 58.849 37.500 0.00 0.00 0.00 4.08
2796 2888 3.955771 TGCTTGTTTTTAGTCCGTCAC 57.044 42.857 0.00 0.00 0.00 3.67
2821 2913 9.891828 GTCATCGCCATGATAATAAATGTTTTA 57.108 29.630 0.00 0.00 41.26 1.52
2827 2919 7.414873 GCATGAGTCATCGCCATGATAATAAAT 60.415 37.037 1.56 0.00 41.26 1.40
2841 2933 1.725164 CGATCATGGCATGAGTCATCG 59.275 52.381 31.39 28.91 43.53 3.84
2848 2940 1.338960 ACACACACGATCATGGCATGA 60.339 47.619 30.53 30.53 44.55 3.07
2876 2968 3.799281 CAAGGAGTTGGTGCTGAAAAA 57.201 42.857 0.00 0.00 0.00 1.94
2889 2981 3.397955 ACTCCACCAATTAACCAAGGAGT 59.602 43.478 5.45 5.45 46.90 3.85
2896 2988 2.556622 CCACACACTCCACCAATTAACC 59.443 50.000 0.00 0.00 0.00 2.85
2897 2989 3.482436 TCCACACACTCCACCAATTAAC 58.518 45.455 0.00 0.00 0.00 2.01
2899 2991 3.561097 CCATCCACACACTCCACCAATTA 60.561 47.826 0.00 0.00 0.00 1.40
2904 2996 1.002134 CCCATCCACACACTCCACC 60.002 63.158 0.00 0.00 0.00 4.61
2908 3000 0.035152 TCATGCCCATCCACACACTC 60.035 55.000 0.00 0.00 0.00 3.51
2921 3013 6.098679 CAGATAGAATGTAGCTAGTCATGCC 58.901 44.000 0.00 0.00 0.00 4.40
2949 3041 1.656095 GACGCACACAGTCATAGCTTC 59.344 52.381 0.00 0.00 38.42 3.86
2951 3043 0.456824 CGACGCACACAGTCATAGCT 60.457 55.000 0.00 0.00 38.46 3.32
2958 3050 1.300931 ATCAAGCGACGCACACAGT 60.301 52.632 23.70 0.00 0.00 3.55
2963 3055 0.042708 CTATGCATCAAGCGACGCAC 60.043 55.000 23.70 4.42 44.23 5.34
2971 3063 1.414181 ACCCTCGGTCTATGCATCAAG 59.586 52.381 0.19 0.00 0.00 3.02
2980 3072 3.967467 AGGAGAATTACCCTCGGTCTA 57.033 47.619 0.00 0.00 37.09 2.59
2983 3075 4.042435 TCAAAAAGGAGAATTACCCTCGGT 59.958 41.667 0.00 0.00 40.16 4.69
3011 3103 5.993748 AAAAATAGCCCCGATCAGAAAAA 57.006 34.783 0.00 0.00 0.00 1.94
3040 3133 6.844388 AGGTATGTAGGTGATCCAATCTGTTA 59.156 38.462 0.00 0.00 35.89 2.41


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

AutoCloner maintained by Alex Coulton.