Multiple sequence alignment - TraesCS3D01G379700

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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 TraesCS3D01G379700 chr3D 100.000 3421 0 0 1 3421 496586496 496583076 0.000000e+00 6318
1 TraesCS3D01G379700 chr3D 87.218 133 10 4 2741 2873 272099895 272100020 9.890000e-31 145
2 TraesCS3D01G379700 chr3B 89.496 2780 170 64 1 2741 655481576 655478880 0.000000e+00 3404
3 TraesCS3D01G379700 chr3B 88.582 543 52 10 2882 3421 655478863 655478328 0.000000e+00 651
4 TraesCS3D01G379700 chr3A 94.541 1612 67 8 1141 2741 638291617 638293218 0.000000e+00 2470
5 TraesCS3D01G379700 chr3A 90.077 776 52 12 1 757 638290575 638291344 0.000000e+00 983
6 TraesCS3D01G379700 chr3A 96.241 133 5 0 2741 2873 74358495 74358627 5.750000e-53 219
7 TraesCS3D01G379700 chr3A 96.269 134 4 1 2741 2873 353180148 353180281 5.750000e-53 219
8 TraesCS3D01G379700 chr3A 88.095 126 11 3 2944 3066 638293652 638293776 2.750000e-31 147
9 TraesCS3D01G379700 chr2B 96.241 133 5 0 2741 2873 501087299 501087167 5.750000e-53 219
10 TraesCS3D01G379700 chr7A 95.522 134 6 0 2741 2874 80838202 80838335 7.440000e-52 215
11 TraesCS3D01G379700 chr4A 95.420 131 6 0 2741 2871 727148649 727148779 3.460000e-50 209
12 TraesCS3D01G379700 chr6A 94.030 134 7 1 2741 2873 569118712 569118579 5.790000e-48 202
13 TraesCS3D01G379700 chr7D 95.868 121 5 0 2741 2861 126967359 126967239 2.690000e-46 196
14 TraesCS3D01G379700 chr2D 93.077 130 7 2 2741 2869 546639248 546639376 4.510000e-44 189


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 TraesCS3D01G379700 chr3D 496583076 496586496 3420 True 6318.0 6318 100.000000 1 3421 1 chr3D.!!$R1 3420
1 TraesCS3D01G379700 chr3B 655478328 655481576 3248 True 2027.5 3404 89.039000 1 3421 2 chr3B.!!$R1 3420
2 TraesCS3D01G379700 chr3A 638290575 638293776 3201 False 1200.0 2470 90.904333 1 3066 3 chr3A.!!$F3 3065

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
245 258 0.249114 GATTCCTCCGTCTCGAAGCC 60.249 60.0 0.00 0.00 0.00 4.35 F
673 698 0.383002 CACAGCACGTACGCAAAGTG 60.383 55.0 16.72 15.16 40.19 3.16 F
1166 1215 0.035458 AGGTTTGAAGCAGTCCGAGG 59.965 55.0 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1121 0.041400 TCGTGCTTGCAATGAACGTG 60.041 50.0 21.21 2.99 35.79 4.49 R
2231 2289 4.887615 TGGAACGCCATGAACACA 57.112 50.0 0.00 0.00 39.92 3.72 R
2948 3387 0.251916 TGCCCTTAGGGTCAACATCG 59.748 55.0 19.76 0.00 46.51 3.84 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
20 21 2.049063 GCGCACTCGAGGACTTGT 60.049 61.111 18.41 0.00 38.10 3.16
25 26 0.868406 CACTCGAGGACTTGTTTGGC 59.132 55.000 18.41 0.00 0.00 4.52
26 27 0.600255 ACTCGAGGACTTGTTTGGCG 60.600 55.000 18.41 0.00 0.00 5.69
27 28 0.319555 CTCGAGGACTTGTTTGGCGA 60.320 55.000 3.91 0.00 0.00 5.54
108 121 6.273825 CACCAATCGTAAAGCAGATAGTACT 58.726 40.000 0.00 0.00 0.00 2.73
109 122 7.423199 CACCAATCGTAAAGCAGATAGTACTA 58.577 38.462 4.77 4.77 0.00 1.82
110 123 7.378995 CACCAATCGTAAAGCAGATAGTACTAC 59.621 40.741 4.31 0.00 0.00 2.73
111 124 7.284944 ACCAATCGTAAAGCAGATAGTACTACT 59.715 37.037 4.31 2.13 0.00 2.57
112 125 7.591795 CCAATCGTAAAGCAGATAGTACTACTG 59.408 40.741 19.73 19.73 35.14 2.74
236 249 0.673644 CAAGCAACCGATTCCTCCGT 60.674 55.000 0.00 0.00 0.00 4.69
245 258 0.249114 GATTCCTCCGTCTCGAAGCC 60.249 60.000 0.00 0.00 0.00 4.35
255 268 1.588861 GTCTCGAAGCCGCTTAATCAC 59.411 52.381 5.38 0.00 35.37 3.06
324 342 2.227194 AGCAGTAACGGAAAAGGGTTG 58.773 47.619 0.00 0.00 0.00 3.77
343 361 3.865011 TGAGCATACCCGTACGTTTAA 57.135 42.857 15.21 0.00 0.00 1.52
354 375 6.223120 ACCCGTACGTTTAACTTACATCTTT 58.777 36.000 15.21 0.00 0.00 2.52
382 403 3.831323 TCTGCTTATCTGAGAGAGGAGG 58.169 50.000 14.12 0.00 0.00 4.30
651 676 2.801063 CCCGTTGATTCATGATTGCAC 58.199 47.619 0.00 0.00 0.00 4.57
673 698 0.383002 CACAGCACGTACGCAAAGTG 60.383 55.000 16.72 15.16 40.19 3.16
674 699 0.808453 ACAGCACGTACGCAAAGTGT 60.808 50.000 16.72 9.20 39.49 3.55
675 700 0.383002 CAGCACGTACGCAAAGTGTG 60.383 55.000 16.72 5.24 39.49 3.82
677 702 0.511221 GCACGTACGCAAAGTGTGAT 59.489 50.000 16.72 0.00 39.49 3.06
693 721 8.434661 CAAAGTGTGATGGTTATTTTTATGCAC 58.565 33.333 0.00 0.00 0.00 4.57
694 722 7.225784 AGTGTGATGGTTATTTTTATGCACA 57.774 32.000 0.00 0.00 0.00 4.57
710 739 2.239201 GCACAAAATTAACGACGAGCC 58.761 47.619 0.00 0.00 0.00 4.70
714 743 3.058501 ACAAAATTAACGACGAGCCTTGG 60.059 43.478 0.00 0.00 0.00 3.61
723 752 0.886490 ACGAGCCTTGGTTGCTTCTG 60.886 55.000 0.00 0.00 39.69 3.02
724 753 0.886490 CGAGCCTTGGTTGCTTCTGT 60.886 55.000 0.00 0.00 39.69 3.41
726 755 0.475906 AGCCTTGGTTGCTTCTGTCT 59.524 50.000 0.00 0.00 34.87 3.41
727 756 0.595095 GCCTTGGTTGCTTCTGTCTG 59.405 55.000 0.00 0.00 0.00 3.51
739 768 4.889832 CTTCTGTCTGAAGCAACAAGTT 57.110 40.909 6.55 0.00 44.62 2.66
741 770 5.983475 CTTCTGTCTGAAGCAACAAGTTAG 58.017 41.667 6.55 0.00 44.62 2.34
757 786 5.981915 ACAAGTTAGTAGAAACGGAACTGAC 59.018 40.000 0.00 0.00 37.00 3.51
761 790 4.416505 AGTAGAAACGGAACTGACGTAG 57.583 45.455 0.00 0.00 44.83 3.51
762 791 8.645498 AGTTAGTAGAAACGGAACTGACGTAGT 61.645 40.741 0.00 0.00 44.83 2.73
782 818 3.049227 CGTGCCTCGTCATTCATCA 57.951 52.632 0.00 0.00 34.52 3.07
788 824 3.063861 TGCCTCGTCATTCATCATTTTCG 59.936 43.478 0.00 0.00 0.00 3.46
789 825 3.063997 GCCTCGTCATTCATCATTTTCGT 59.936 43.478 0.00 0.00 0.00 3.85
790 826 4.270084 GCCTCGTCATTCATCATTTTCGTA 59.730 41.667 0.00 0.00 0.00 3.43
791 827 5.728255 CCTCGTCATTCATCATTTTCGTAC 58.272 41.667 0.00 0.00 0.00 3.67
792 828 5.369947 TCGTCATTCATCATTTTCGTACG 57.630 39.130 9.53 9.53 0.00 3.67
793 829 5.096849 TCGTCATTCATCATTTTCGTACGA 58.903 37.500 15.28 15.28 33.73 3.43
794 830 5.229260 TCGTCATTCATCATTTTCGTACGAG 59.771 40.000 18.64 6.99 32.53 4.18
795 831 5.229260 CGTCATTCATCATTTTCGTACGAGA 59.771 40.000 18.64 11.66 0.00 4.04
797 833 7.515215 CGTCATTCATCATTTTCGTACGAGAAT 60.515 37.037 23.86 23.86 30.42 2.40
798 834 7.789759 GTCATTCATCATTTTCGTACGAGAATC 59.210 37.037 25.96 11.61 28.23 2.52
800 836 7.451281 TTCATCATTTTCGTACGAGAATCTC 57.549 36.000 25.96 0.00 28.23 2.75
802 838 6.913132 TCATCATTTTCGTACGAGAATCTCTC 59.087 38.462 25.96 0.61 40.06 3.20
803 839 6.438259 TCATTTTCGTACGAGAATCTCTCT 57.562 37.500 25.96 7.51 41.26 3.10
815 851 5.247507 AGAATCTCTCTCATTCGTGTCAG 57.752 43.478 0.00 0.00 35.69 3.51
816 852 4.946772 AGAATCTCTCTCATTCGTGTCAGA 59.053 41.667 0.00 0.00 35.69 3.27
817 853 4.898829 ATCTCTCTCATTCGTGTCAGAG 57.101 45.455 0.00 0.00 34.75 3.35
821 857 3.114809 CTCTCATTCGTGTCAGAGATGC 58.885 50.000 0.00 0.00 36.62 3.91
839 875 2.234143 TGCTGATCGTAGATCTCCCTG 58.766 52.381 0.00 0.00 45.12 4.45
841 877 2.030363 GCTGATCGTAGATCTCCCTGTG 60.030 54.545 0.00 0.00 45.12 3.66
843 879 2.235016 GATCGTAGATCTCCCTGTGCT 58.765 52.381 0.00 0.00 45.12 4.40
845 881 3.292492 TCGTAGATCTCCCTGTGCTTA 57.708 47.619 0.00 0.00 0.00 3.09
846 882 3.215151 TCGTAGATCTCCCTGTGCTTAG 58.785 50.000 0.00 0.00 0.00 2.18
847 883 3.118000 TCGTAGATCTCCCTGTGCTTAGA 60.118 47.826 0.00 0.00 0.00 2.10
848 884 3.632604 CGTAGATCTCCCTGTGCTTAGAA 59.367 47.826 0.00 0.00 0.00 2.10
849 885 4.098044 CGTAGATCTCCCTGTGCTTAGAAA 59.902 45.833 0.00 0.00 0.00 2.52
852 888 2.991250 TCTCCCTGTGCTTAGAAATGC 58.009 47.619 0.00 0.00 0.00 3.56
859 895 0.521291 TGCTTAGAAATGCACGGTGC 59.479 50.000 25.55 25.55 45.29 5.01
868 904 3.573491 GCACGGTGCGGATAAGCC 61.573 66.667 18.35 0.00 31.71 4.35
869 905 2.186903 CACGGTGCGGATAAGCCT 59.813 61.111 0.00 0.00 36.02 4.58
870 906 1.449601 CACGGTGCGGATAAGCCTT 60.450 57.895 0.00 0.00 36.02 4.35
871 907 1.024579 CACGGTGCGGATAAGCCTTT 61.025 55.000 0.00 0.00 36.02 3.11
872 908 0.538118 ACGGTGCGGATAAGCCTTTA 59.462 50.000 0.00 0.00 36.02 1.85
881 917 4.215613 GCGGATAAGCCTTTATTTACCCAG 59.784 45.833 0.00 0.00 29.67 4.45
928 965 1.593196 TTGAAGTGTAGCACCTGCAC 58.407 50.000 5.48 5.48 45.10 4.57
997 1039 1.148310 CGAATTCAGCAGTGAACCGT 58.852 50.000 6.22 0.00 45.58 4.83
998 1040 1.136252 CGAATTCAGCAGTGAACCGTG 60.136 52.381 6.22 0.00 45.58 4.94
999 1041 0.593128 AATTCAGCAGTGAACCGTGC 59.407 50.000 0.00 0.00 45.58 5.34
1000 1042 0.534877 ATTCAGCAGTGAACCGTGCA 60.535 50.000 0.00 0.00 45.58 4.57
1001 1043 0.534877 TTCAGCAGTGAACCGTGCAT 60.535 50.000 0.00 0.00 42.47 3.96
1006 1048 1.672356 AGTGAACCGTGCATGGAGC 60.672 57.895 31.74 20.94 45.96 4.70
1016 1058 2.327343 GCATGGAGCTGTCACGCAA 61.327 57.895 0.00 0.00 41.15 4.85
1017 1059 2.249557 GCATGGAGCTGTCACGCAAG 62.250 60.000 0.00 0.00 41.15 4.01
1019 1061 0.671781 ATGGAGCTGTCACGCAAGAC 60.672 55.000 0.00 0.00 43.62 3.01
1035 1077 4.675029 ACGAAAGTGGGGCGACGG 62.675 66.667 0.00 0.00 46.97 4.79
1052 1094 1.885388 GGCCATGCGTGCGTGTATA 60.885 57.895 12.65 0.00 0.00 1.47
1055 1097 1.496934 CCATGCGTGCGTGTATATGA 58.503 50.000 12.65 0.00 0.00 2.15
1059 1107 1.202475 TGCGTGCGTGTATATGACCAT 60.202 47.619 0.00 0.00 0.00 3.55
1065 1113 1.136639 CGTGTATATGACCATTGCGCG 60.137 52.381 0.00 0.00 0.00 6.86
1096 1144 1.264020 GTTCATTGCAAGCACGACTGA 59.736 47.619 4.94 0.00 0.00 3.41
1097 1145 1.812235 TCATTGCAAGCACGACTGAT 58.188 45.000 4.94 0.00 0.00 2.90
1098 1146 1.465777 TCATTGCAAGCACGACTGATG 59.534 47.619 4.94 0.00 0.00 3.07
1100 1148 1.855213 TTGCAAGCACGACTGATGCC 61.855 55.000 0.00 0.00 44.53 4.40
1104 1153 0.250467 AAGCACGACTGATGCCACTT 60.250 50.000 0.00 0.00 44.53 3.16
1117 1166 1.680735 TGCCACTTGCTGAATTCGTTT 59.319 42.857 0.04 0.00 42.00 3.60
1128 1177 0.798776 AATTCGTTTCAGAGCGCTGG 59.201 50.000 18.48 7.07 42.53 4.85
1129 1178 0.320771 ATTCGTTTCAGAGCGCTGGT 60.321 50.000 18.48 0.00 42.53 4.00
1131 1180 0.388134 TCGTTTCAGAGCGCTGGTAC 60.388 55.000 18.48 13.83 42.53 3.34
1132 1181 1.674611 CGTTTCAGAGCGCTGGTACG 61.675 60.000 18.48 22.40 42.53 3.67
1134 1183 0.388134 TTTCAGAGCGCTGGTACGAC 60.388 55.000 18.48 0.00 42.53 4.34
1135 1184 1.520600 TTCAGAGCGCTGGTACGACA 61.521 55.000 18.48 0.00 42.53 4.35
1136 1185 1.515088 CAGAGCGCTGGTACGACAG 60.515 63.158 18.48 0.00 41.41 3.51
1137 1186 2.202623 GAGCGCTGGTACGACAGG 60.203 66.667 18.48 0.00 38.90 4.00
1138 1187 4.436998 AGCGCTGGTACGACAGGC 62.437 66.667 10.39 1.04 38.90 4.85
1139 1188 4.735132 GCGCTGGTACGACAGGCA 62.735 66.667 0.00 0.00 38.90 4.75
1143 1192 1.538204 CGCTGGTACGACAGGCATTAT 60.538 52.381 0.00 0.00 38.90 1.28
1166 1215 0.035458 AGGTTTGAAGCAGTCCGAGG 59.965 55.000 0.00 0.00 0.00 4.63
1177 1226 2.481104 GCAGTCCGAGGATCTCTTTCAG 60.481 54.545 0.00 0.00 0.00 3.02
1922 1980 2.100603 CTCGACTTCGGCCTCGAC 59.899 66.667 10.50 0.00 45.92 4.20
2019 2077 2.058001 ATCGACCTCGCCACCATGA 61.058 57.895 0.00 0.00 39.60 3.07
2020 2078 2.021068 ATCGACCTCGCCACCATGAG 62.021 60.000 0.00 0.00 39.60 2.90
2517 2588 3.067106 ACAGAAATGTAGTTGCGTCCAG 58.933 45.455 0.00 0.00 0.00 3.86
2612 2690 5.450592 TGATGCAAATGCTTGTTCTGTTA 57.549 34.783 6.97 0.00 42.66 2.41
2764 2845 3.309296 TCTGGCTAGATTTAGTGAGGGG 58.691 50.000 0.00 0.00 0.00 4.79
2765 2846 3.052109 TCTGGCTAGATTTAGTGAGGGGA 60.052 47.826 0.00 0.00 0.00 4.81
2766 2847 3.711704 CTGGCTAGATTTAGTGAGGGGAA 59.288 47.826 0.00 0.00 0.00 3.97
2767 2848 3.454812 TGGCTAGATTTAGTGAGGGGAAC 59.545 47.826 0.00 0.00 0.00 3.62
2771 2852 5.398012 GCTAGATTTAGTGAGGGGAACCATT 60.398 44.000 0.00 0.00 44.85 3.16
2772 2853 5.117406 AGATTTAGTGAGGGGAACCATTC 57.883 43.478 0.00 0.00 44.85 2.67
2773 2854 4.790790 AGATTTAGTGAGGGGAACCATTCT 59.209 41.667 0.00 0.00 44.85 2.40
2774 2855 5.254032 AGATTTAGTGAGGGGAACCATTCTT 59.746 40.000 0.00 0.00 44.85 2.52
2775 2856 2.887151 AGTGAGGGGAACCATTCTTG 57.113 50.000 0.00 0.00 44.85 3.02
2776 2857 1.355720 AGTGAGGGGAACCATTCTTGG 59.644 52.381 0.00 0.00 44.85 3.61
2777 2858 0.039618 TGAGGGGAACCATTCTTGGC 59.960 55.000 0.00 0.00 44.85 4.52
2778 2859 0.039618 GAGGGGAACCATTCTTGGCA 59.960 55.000 0.00 0.00 44.85 4.92
2779 2860 0.486879 AGGGGAACCATTCTTGGCAA 59.513 50.000 0.00 0.00 44.85 4.52
2780 2861 1.550869 AGGGGAACCATTCTTGGCAAG 60.551 52.381 21.17 21.17 44.85 4.01
2781 2862 3.908565 AGGGGAACCATTCTTGGCAAGA 61.909 50.000 25.38 25.38 44.85 3.02
2782 2863 5.369306 AGGGGAACCATTCTTGGCAAGAA 62.369 47.826 36.64 36.64 44.85 2.52
2789 2870 2.276732 TTCTTGGCAAGAACCTCCAG 57.723 50.000 32.85 4.65 42.31 3.86
2790 2871 1.434188 TCTTGGCAAGAACCTCCAGA 58.566 50.000 26.78 1.19 33.83 3.86
2791 2872 1.988107 TCTTGGCAAGAACCTCCAGAT 59.012 47.619 26.78 0.00 33.83 2.90
2792 2873 2.376518 TCTTGGCAAGAACCTCCAGATT 59.623 45.455 26.78 0.00 33.83 2.40
2793 2874 2.978156 TGGCAAGAACCTCCAGATTT 57.022 45.000 0.00 0.00 0.00 2.17
2794 2875 3.243359 TGGCAAGAACCTCCAGATTTT 57.757 42.857 0.00 0.00 0.00 1.82
2795 2876 4.380843 TGGCAAGAACCTCCAGATTTTA 57.619 40.909 0.00 0.00 0.00 1.52
2796 2877 4.934356 TGGCAAGAACCTCCAGATTTTAT 58.066 39.130 0.00 0.00 0.00 1.40
2797 2878 5.332743 TGGCAAGAACCTCCAGATTTTATT 58.667 37.500 0.00 0.00 0.00 1.40
2798 2879 5.418840 TGGCAAGAACCTCCAGATTTTATTC 59.581 40.000 0.00 0.00 0.00 1.75
2799 2880 5.449177 GGCAAGAACCTCCAGATTTTATTCG 60.449 44.000 0.00 0.00 0.00 3.34
2800 2881 5.123979 GCAAGAACCTCCAGATTTTATTCGT 59.876 40.000 0.00 0.00 0.00 3.85
2801 2882 6.546395 CAAGAACCTCCAGATTTTATTCGTG 58.454 40.000 0.00 0.00 0.00 4.35
2802 2883 5.805728 AGAACCTCCAGATTTTATTCGTGT 58.194 37.500 0.00 0.00 0.00 4.49
2803 2884 6.238648 AGAACCTCCAGATTTTATTCGTGTT 58.761 36.000 0.00 0.00 0.00 3.32
2804 2885 5.880054 ACCTCCAGATTTTATTCGTGTTG 57.120 39.130 0.00 0.00 0.00 3.33
2805 2886 5.313712 ACCTCCAGATTTTATTCGTGTTGT 58.686 37.500 0.00 0.00 0.00 3.32
2806 2887 5.768164 ACCTCCAGATTTTATTCGTGTTGTT 59.232 36.000 0.00 0.00 0.00 2.83
2807 2888 6.072673 ACCTCCAGATTTTATTCGTGTTGTTC 60.073 38.462 0.00 0.00 0.00 3.18
2808 2889 6.149474 CCTCCAGATTTTATTCGTGTTGTTCT 59.851 38.462 0.00 0.00 0.00 3.01
2809 2890 7.333423 CCTCCAGATTTTATTCGTGTTGTTCTA 59.667 37.037 0.00 0.00 0.00 2.10
2810 2891 8.251750 TCCAGATTTTATTCGTGTTGTTCTAG 57.748 34.615 0.00 0.00 0.00 2.43
2811 2892 7.876068 TCCAGATTTTATTCGTGTTGTTCTAGT 59.124 33.333 0.00 0.00 0.00 2.57
2812 2893 9.146984 CCAGATTTTATTCGTGTTGTTCTAGTA 57.853 33.333 0.00 0.00 0.00 1.82
2817 2898 9.917129 TTTTATTCGTGTTGTTCTAGTAGATGA 57.083 29.630 0.00 0.00 0.00 2.92
2819 2900 7.993821 ATTCGTGTTGTTCTAGTAGATGATG 57.006 36.000 0.00 0.00 0.00 3.07
2820 2901 6.510879 TCGTGTTGTTCTAGTAGATGATGT 57.489 37.500 0.00 0.00 0.00 3.06
2821 2902 7.619964 TCGTGTTGTTCTAGTAGATGATGTA 57.380 36.000 0.00 0.00 0.00 2.29
2822 2903 8.047413 TCGTGTTGTTCTAGTAGATGATGTAA 57.953 34.615 0.00 0.00 0.00 2.41
2823 2904 7.966753 TCGTGTTGTTCTAGTAGATGATGTAAC 59.033 37.037 0.00 0.00 0.00 2.50
2824 2905 7.968956 CGTGTTGTTCTAGTAGATGATGTAACT 59.031 37.037 0.00 0.00 0.00 2.24
2825 2906 9.077674 GTGTTGTTCTAGTAGATGATGTAACTG 57.922 37.037 0.00 0.00 0.00 3.16
2826 2907 8.803235 TGTTGTTCTAGTAGATGATGTAACTGT 58.197 33.333 0.00 0.00 0.00 3.55
2827 2908 9.077674 GTTGTTCTAGTAGATGATGTAACTGTG 57.922 37.037 0.00 0.00 0.00 3.66
2828 2909 8.575649 TGTTCTAGTAGATGATGTAACTGTGA 57.424 34.615 0.00 0.00 0.00 3.58
2829 2910 9.190317 TGTTCTAGTAGATGATGTAACTGTGAT 57.810 33.333 0.00 0.00 0.00 3.06
2832 2913 8.851145 TCTAGTAGATGATGTAACTGTGATTCC 58.149 37.037 0.00 0.00 0.00 3.01
2833 2914 7.423844 AGTAGATGATGTAACTGTGATTCCA 57.576 36.000 0.00 0.00 0.00 3.53
2834 2915 7.495901 AGTAGATGATGTAACTGTGATTCCAG 58.504 38.462 0.00 0.00 38.45 3.86
2835 2916 6.550938 AGATGATGTAACTGTGATTCCAGA 57.449 37.500 8.56 0.00 36.30 3.86
2836 2917 7.134362 AGATGATGTAACTGTGATTCCAGAT 57.866 36.000 8.56 1.31 36.30 2.90
2837 2918 7.215789 AGATGATGTAACTGTGATTCCAGATC 58.784 38.462 8.56 0.00 36.30 2.75
2838 2919 6.298441 TGATGTAACTGTGATTCCAGATCA 57.702 37.500 0.00 5.30 36.30 2.92
2839 2920 6.710278 TGATGTAACTGTGATTCCAGATCAA 58.290 36.000 0.00 0.00 36.30 2.57
2840 2921 7.341030 TGATGTAACTGTGATTCCAGATCAAT 58.659 34.615 0.00 0.00 36.30 2.57
2841 2922 8.485392 TGATGTAACTGTGATTCCAGATCAATA 58.515 33.333 0.00 0.00 36.30 1.90
2842 2923 9.330063 GATGTAACTGTGATTCCAGATCAATAA 57.670 33.333 0.00 0.00 36.30 1.40
2843 2924 9.685276 ATGTAACTGTGATTCCAGATCAATAAA 57.315 29.630 0.00 0.00 36.30 1.40
2844 2925 9.513906 TGTAACTGTGATTCCAGATCAATAAAA 57.486 29.630 0.00 0.00 36.30 1.52
2848 2929 8.400947 ACTGTGATTCCAGATCAATAAAAATCG 58.599 33.333 0.00 0.00 36.30 3.34
2849 2930 7.195646 TGTGATTCCAGATCAATAAAAATCGC 58.804 34.615 0.00 3.27 34.43 4.58
2850 2931 6.638468 GTGATTCCAGATCAATAAAAATCGCC 59.362 38.462 0.00 0.00 0.00 5.54
2851 2932 6.320926 TGATTCCAGATCAATAAAAATCGCCA 59.679 34.615 0.00 0.00 0.00 5.69
2852 2933 6.713762 TTCCAGATCAATAAAAATCGCCAT 57.286 33.333 0.00 0.00 0.00 4.40
2853 2934 6.075762 TCCAGATCAATAAAAATCGCCATG 57.924 37.500 0.00 0.00 0.00 3.66
2854 2935 5.827267 TCCAGATCAATAAAAATCGCCATGA 59.173 36.000 0.00 0.00 0.00 3.07
2855 2936 6.491062 TCCAGATCAATAAAAATCGCCATGAT 59.509 34.615 0.00 0.00 39.67 2.45
2856 2937 6.584942 CCAGATCAATAAAAATCGCCATGATG 59.415 38.462 0.00 0.00 37.39 3.07
2857 2938 6.584942 CAGATCAATAAAAATCGCCATGATGG 59.415 38.462 7.21 7.21 41.55 3.51
2895 2976 5.945310 AGTATCATTTGTGTGCCCTCATAT 58.055 37.500 0.00 0.00 0.00 1.78
2922 3316 3.357021 CGTTAGCATCACATGTTGCATC 58.643 45.455 21.40 11.48 41.77 3.91
2926 3320 3.845178 AGCATCACATGTTGCATCTTTG 58.155 40.909 21.40 0.00 41.77 2.77
2931 3325 6.400303 GCATCACATGTTGCATCTTTGTTTAC 60.400 38.462 15.97 0.00 39.75 2.01
2932 3326 6.389830 TCACATGTTGCATCTTTGTTTACT 57.610 33.333 0.00 0.00 0.00 2.24
2934 3328 7.935520 TCACATGTTGCATCTTTGTTTACTTA 58.064 30.769 0.00 0.00 0.00 2.24
2978 3417 3.217626 CCCTAAGGGCATCTTTAGCAAG 58.782 50.000 0.00 0.00 35.35 4.01
3019 3458 7.733773 TCAAAAGTCATCCCTTATCTCACTA 57.266 36.000 0.00 0.00 0.00 2.74
3068 3510 6.586463 TCGATTCTTAATGTATCAAGATCGCC 59.414 38.462 0.00 0.00 34.93 5.54
3079 3521 8.780846 TGTATCAAGATCGCCTAAAACTTAAA 57.219 30.769 0.00 0.00 0.00 1.52
3083 3525 4.267536 AGATCGCCTAAAACTTAAACCCC 58.732 43.478 0.00 0.00 0.00 4.95
3084 3526 3.793819 TCGCCTAAAACTTAAACCCCT 57.206 42.857 0.00 0.00 0.00 4.79
3085 3527 3.678289 TCGCCTAAAACTTAAACCCCTC 58.322 45.455 0.00 0.00 0.00 4.30
3086 3528 2.417586 CGCCTAAAACTTAAACCCCTCG 59.582 50.000 0.00 0.00 0.00 4.63
3091 3533 6.294899 GCCTAAAACTTAAACCCCTCGAAAAT 60.295 38.462 0.00 0.00 0.00 1.82
3092 3534 7.094248 GCCTAAAACTTAAACCCCTCGAAAATA 60.094 37.037 0.00 0.00 0.00 1.40
3103 3545 6.452242 ACCCCTCGAAAATAATTTTGTTGTC 58.548 36.000 0.00 0.00 32.61 3.18
3105 3547 6.926272 CCCCTCGAAAATAATTTTGTTGTCAA 59.074 34.615 0.00 0.00 32.61 3.18
3117 3559 3.980646 TGTTGTCAATTCTCCCAAACG 57.019 42.857 0.00 0.00 0.00 3.60
3190 3632 5.927954 AAAATTCAAATGCACCACATCAC 57.072 34.783 0.00 0.00 38.34 3.06
3204 3647 3.062639 CCACATCACAATGAACTACGAGC 59.937 47.826 0.00 0.00 36.67 5.03
3224 3667 7.639945 ACGAGCATAAATAAAGTTAATCAGGC 58.360 34.615 0.00 0.00 0.00 4.85
3255 3698 8.538856 CAAACAACTAAACATAACCACAATGTG 58.461 33.333 6.37 6.37 37.62 3.21
3262 3705 7.769272 AAACATAACCACAATGTGTCAAAAG 57.231 32.000 12.79 0.00 37.62 2.27
3296 3739 7.262048 TGAACAAGTCCATTAAAAGAAACACC 58.738 34.615 0.00 0.00 0.00 4.16
3323 3766 1.047002 TGGTGGACCAAAAGCCATTG 58.953 50.000 0.00 0.00 44.35 2.82
3342 3785 3.719268 TGTAGTTCACAAGGGCATCAT 57.281 42.857 0.00 0.00 32.95 2.45
3343 3786 4.835284 TGTAGTTCACAAGGGCATCATA 57.165 40.909 0.00 0.00 32.95 2.15
3348 3791 4.225042 AGTTCACAAGGGCATCATACACTA 59.775 41.667 0.00 0.00 0.00 2.74
3354 3797 1.502231 GGCATCATACACTAGCACCG 58.498 55.000 0.00 0.00 0.00 4.94
3362 3805 1.443872 CACTAGCACCGTCACCGTC 60.444 63.158 0.00 0.00 0.00 4.79
3367 3810 2.428569 CACCGTCACCGTCGACAG 60.429 66.667 17.16 6.83 35.54 3.51
3403 3846 2.354539 CACCGCCAAACTTTGCCG 60.355 61.111 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.521291 CGGAGAAAGCAATCGCCAAA 59.479 50.000 11.09 0.00 39.03 3.28
25 26 1.999051 CGGACGGAGAAAGCAATCG 59.001 57.895 0.00 0.00 0.00 3.34
26 27 1.706287 GGCGGACGGAGAAAGCAATC 61.706 60.000 0.00 0.00 0.00 2.67
27 28 1.745489 GGCGGACGGAGAAAGCAAT 60.745 57.895 0.00 0.00 0.00 3.56
108 121 2.169769 GGGCAACTAGGCATGTACAGTA 59.830 50.000 0.33 0.00 46.44 2.74
109 122 1.065418 GGGCAACTAGGCATGTACAGT 60.065 52.381 0.33 0.00 46.44 3.55
110 123 1.668419 GGGCAACTAGGCATGTACAG 58.332 55.000 0.33 0.00 46.44 2.74
111 124 0.107897 CGGGCAACTAGGCATGTACA 60.108 55.000 0.00 0.00 46.44 2.90
112 125 1.436983 GCGGGCAACTAGGCATGTAC 61.437 60.000 0.00 0.00 46.44 2.90
139 152 1.152881 ATCCGGCCAAGGAATCTGC 60.153 57.895 2.24 0.00 44.50 4.26
236 249 1.470979 GGTGATTAAGCGGCTTCGAGA 60.471 52.381 20.06 4.56 35.61 4.04
245 258 2.103094 TGATCCTGGAGGTGATTAAGCG 59.897 50.000 1.52 0.00 36.34 4.68
255 268 3.839490 AGATAGATGCTTGATCCTGGAGG 59.161 47.826 1.52 0.00 0.00 4.30
324 342 3.774066 AGTTAAACGTACGGGTATGCTC 58.226 45.455 21.06 2.40 0.00 4.26
354 375 6.652481 CCTCTCTCAGATAAGCAGAAACAAAA 59.348 38.462 0.00 0.00 0.00 2.44
358 379 5.451798 CCTCCTCTCTCAGATAAGCAGAAAC 60.452 48.000 0.00 0.00 0.00 2.78
651 676 0.579630 TTTGCGTACGTGCTGTGAAG 59.420 50.000 17.90 0.00 35.36 3.02
693 721 3.058501 ACCAAGGCTCGTCGTTAATTTTG 60.059 43.478 0.00 0.00 0.00 2.44
694 722 3.143728 ACCAAGGCTCGTCGTTAATTTT 58.856 40.909 0.00 0.00 0.00 1.82
704 733 0.886490 CAGAAGCAACCAAGGCTCGT 60.886 55.000 0.00 0.00 41.66 4.18
705 734 0.886490 ACAGAAGCAACCAAGGCTCG 60.886 55.000 0.00 0.00 41.66 5.03
710 739 3.892918 CTTCAGACAGAAGCAACCAAG 57.107 47.619 0.00 0.00 46.54 3.61
723 752 7.345943 GTTTCTACTAACTTGTTGCTTCAGAC 58.654 38.462 0.00 0.00 0.00 3.51
724 753 6.200286 CGTTTCTACTAACTTGTTGCTTCAGA 59.800 38.462 0.00 0.00 0.00 3.27
726 755 5.235616 CCGTTTCTACTAACTTGTTGCTTCA 59.764 40.000 0.00 0.00 0.00 3.02
727 756 5.464389 TCCGTTTCTACTAACTTGTTGCTTC 59.536 40.000 0.00 0.00 0.00 3.86
737 766 4.540824 ACGTCAGTTCCGTTTCTACTAAC 58.459 43.478 0.00 0.00 34.28 2.34
738 767 4.836125 ACGTCAGTTCCGTTTCTACTAA 57.164 40.909 0.00 0.00 34.28 2.24
739 768 4.997395 ACTACGTCAGTTCCGTTTCTACTA 59.003 41.667 0.00 0.00 39.60 1.82
741 770 4.152607 ACTACGTCAGTTCCGTTTCTAC 57.847 45.455 0.00 0.00 39.60 2.59
768 803 4.864916 ACGAAAATGATGAATGACGAGG 57.135 40.909 0.00 0.00 0.00 4.63
776 812 7.258441 AGAGATTCTCGTACGAAAATGATGAA 58.742 34.615 20.85 16.94 35.36 2.57
793 829 4.946772 TCTGACACGAATGAGAGAGATTCT 59.053 41.667 0.00 0.00 39.43 2.40
794 830 5.065859 TCTCTGACACGAATGAGAGAGATTC 59.934 44.000 5.94 0.00 38.10 2.52
795 831 4.946772 TCTCTGACACGAATGAGAGAGATT 59.053 41.667 5.94 0.00 38.10 2.40
797 833 3.944087 TCTCTGACACGAATGAGAGAGA 58.056 45.455 5.94 0.00 39.41 3.10
798 834 4.600032 CATCTCTGACACGAATGAGAGAG 58.400 47.826 13.14 7.47 43.16 3.20
800 836 3.114809 GCATCTCTGACACGAATGAGAG 58.885 50.000 0.00 0.00 38.69 3.20
802 838 2.858941 CAGCATCTCTGACACGAATGAG 59.141 50.000 0.00 0.00 45.72 2.90
803 839 2.493278 TCAGCATCTCTGACACGAATGA 59.507 45.455 0.00 0.00 46.34 2.57
813 849 4.142622 GGAGATCTACGATCAGCATCTCTG 60.143 50.000 15.38 0.00 44.21 3.35
814 850 4.009675 GGAGATCTACGATCAGCATCTCT 58.990 47.826 15.38 2.16 39.57 3.10
815 851 3.128589 GGGAGATCTACGATCAGCATCTC 59.871 52.174 0.00 10.46 39.11 2.75
816 852 3.088532 GGGAGATCTACGATCAGCATCT 58.911 50.000 0.00 0.00 0.00 2.90
817 853 3.088532 AGGGAGATCTACGATCAGCATC 58.911 50.000 0.00 0.00 0.00 3.91
821 857 2.030363 GCACAGGGAGATCTACGATCAG 60.030 54.545 0.00 0.00 0.00 2.90
834 870 2.877097 TGCATTTCTAAGCACAGGGA 57.123 45.000 0.00 0.00 35.51 4.20
841 877 0.521242 CGCACCGTGCATTTCTAAGC 60.521 55.000 22.89 0.00 45.36 3.09
843 879 0.320858 TCCGCACCGTGCATTTCTAA 60.321 50.000 22.89 0.00 45.36 2.10
845 881 0.107897 TATCCGCACCGTGCATTTCT 60.108 50.000 22.89 5.47 45.36 2.52
846 882 0.730265 TTATCCGCACCGTGCATTTC 59.270 50.000 22.89 0.00 45.36 2.17
847 883 0.732571 CTTATCCGCACCGTGCATTT 59.267 50.000 22.89 8.98 45.36 2.32
848 884 1.714899 GCTTATCCGCACCGTGCATT 61.715 55.000 22.89 9.32 45.36 3.56
849 885 2.180204 GCTTATCCGCACCGTGCAT 61.180 57.895 22.89 12.24 45.36 3.96
852 888 1.024579 AAAGGCTTATCCGCACCGTG 61.025 55.000 0.00 0.00 40.77 4.94
854 890 1.878953 ATAAAGGCTTATCCGCACCG 58.121 50.000 0.00 0.00 40.77 4.94
855 891 4.023450 GGTAAATAAAGGCTTATCCGCACC 60.023 45.833 0.00 0.64 40.77 5.01
856 892 4.023450 GGGTAAATAAAGGCTTATCCGCAC 60.023 45.833 0.00 0.00 40.77 5.34
857 893 4.139038 GGGTAAATAAAGGCTTATCCGCA 58.861 43.478 0.00 0.00 40.77 5.69
858 894 4.139038 TGGGTAAATAAAGGCTTATCCGC 58.861 43.478 0.00 0.00 40.77 5.54
859 895 5.617252 TCTGGGTAAATAAAGGCTTATCCG 58.383 41.667 0.00 0.00 40.77 4.18
860 896 7.778382 TCTTTCTGGGTAAATAAAGGCTTATCC 59.222 37.037 0.00 0.00 31.37 2.59
861 897 8.747538 TCTTTCTGGGTAAATAAAGGCTTATC 57.252 34.615 0.00 0.00 31.37 1.75
862 898 9.136323 CATCTTTCTGGGTAAATAAAGGCTTAT 57.864 33.333 0.00 0.00 31.37 1.73
863 899 8.113462 ACATCTTTCTGGGTAAATAAAGGCTTA 58.887 33.333 0.00 0.00 31.37 3.09
864 900 6.954102 ACATCTTTCTGGGTAAATAAAGGCTT 59.046 34.615 0.00 0.00 31.37 4.35
865 901 6.378280 CACATCTTTCTGGGTAAATAAAGGCT 59.622 38.462 0.00 0.00 31.37 4.58
866 902 6.152831 ACACATCTTTCTGGGTAAATAAAGGC 59.847 38.462 0.00 0.00 28.77 4.35
867 903 7.362920 CCACACATCTTTCTGGGTAAATAAAGG 60.363 40.741 0.00 0.00 29.71 3.11
868 904 7.393234 TCCACACATCTTTCTGGGTAAATAAAG 59.607 37.037 0.00 0.00 29.71 1.85
869 905 7.235079 TCCACACATCTTTCTGGGTAAATAAA 58.765 34.615 0.00 0.00 29.71 1.40
870 906 6.785076 TCCACACATCTTTCTGGGTAAATAA 58.215 36.000 0.00 0.00 29.71 1.40
871 907 6.381498 TCCACACATCTTTCTGGGTAAATA 57.619 37.500 0.00 0.00 29.71 1.40
872 908 5.255397 TCCACACATCTTTCTGGGTAAAT 57.745 39.130 0.00 0.00 29.71 1.40
881 917 4.336713 GGAAGGCTTATCCACACATCTTTC 59.663 45.833 0.00 0.00 36.92 2.62
912 949 0.401738 ATGGTGCAGGTGCTACACTT 59.598 50.000 3.18 0.00 42.66 3.16
917 954 2.430694 CAGTAGTATGGTGCAGGTGCTA 59.569 50.000 3.18 0.00 42.66 3.49
918 955 1.208052 CAGTAGTATGGTGCAGGTGCT 59.792 52.381 3.18 0.00 42.66 4.40
919 956 1.066143 ACAGTAGTATGGTGCAGGTGC 60.066 52.381 0.00 0.00 42.50 5.01
920 957 4.672587 ATACAGTAGTATGGTGCAGGTG 57.327 45.455 0.00 0.00 39.43 4.00
950 992 1.371183 CAGAGGAACCTTGGACGCA 59.629 57.895 0.00 0.00 0.00 5.24
960 1002 2.743928 CTGCGTGGCCAGAGGAAC 60.744 66.667 5.11 0.00 34.77 3.62
997 1039 2.743538 GCGTGACAGCTCCATGCA 60.744 61.111 19.51 0.00 43.84 3.96
998 1040 2.249557 CTTGCGTGACAGCTCCATGC 62.250 60.000 18.24 18.24 44.45 4.06
999 1041 0.671472 TCTTGCGTGACAGCTCCATG 60.671 55.000 0.00 0.00 38.13 3.66
1000 1042 0.671781 GTCTTGCGTGACAGCTCCAT 60.672 55.000 4.34 0.00 36.97 3.41
1001 1043 1.300931 GTCTTGCGTGACAGCTCCA 60.301 57.895 4.34 0.00 36.97 3.86
1006 1048 1.071239 CACTTTCGTCTTGCGTGACAG 60.071 52.381 9.12 2.63 42.13 3.51
1016 1058 2.342648 GTCGCCCCACTTTCGTCT 59.657 61.111 0.00 0.00 0.00 4.18
1017 1059 3.110178 CGTCGCCCCACTTTCGTC 61.110 66.667 0.00 0.00 0.00 4.20
1034 1076 1.227999 ATATACACGCACGCATGGCC 61.228 55.000 0.00 0.00 0.00 5.36
1035 1077 0.110688 CATATACACGCACGCATGGC 60.111 55.000 0.00 0.00 0.00 4.40
1036 1078 1.192312 GTCATATACACGCACGCATGG 59.808 52.381 0.00 0.00 0.00 3.66
1037 1079 1.192312 GGTCATATACACGCACGCATG 59.808 52.381 0.00 0.00 0.00 4.06
1038 1080 1.202475 TGGTCATATACACGCACGCAT 60.202 47.619 0.00 0.00 0.00 4.73
1039 1081 0.173708 TGGTCATATACACGCACGCA 59.826 50.000 0.00 0.00 0.00 5.24
1042 1084 2.348498 CGCAATGGTCATATACACGCAC 60.348 50.000 0.00 0.00 0.00 5.34
1065 1113 3.361977 AATGAACGTGTGCCCGCC 61.362 61.111 0.00 0.00 0.00 6.13
1069 1117 1.277495 GCTTGCAATGAACGTGTGCC 61.277 55.000 0.00 0.00 37.48 5.01
1070 1118 0.594540 TGCTTGCAATGAACGTGTGC 60.595 50.000 0.00 6.79 38.78 4.57
1073 1121 0.041400 TCGTGCTTGCAATGAACGTG 60.041 50.000 21.21 2.99 35.79 4.49
1075 1123 0.235665 AGTCGTGCTTGCAATGAACG 59.764 50.000 18.02 18.02 35.64 3.95
1079 1127 1.891178 CATCAGTCGTGCTTGCAATG 58.109 50.000 0.00 0.00 0.00 2.82
1080 1128 0.169672 GCATCAGTCGTGCTTGCAAT 59.830 50.000 0.00 0.00 39.45 3.56
1096 1144 6.054362 TGAAACGAATTCAGCAAGTGGCAT 62.054 41.667 6.22 0.00 43.08 4.40
1097 1145 4.795981 TGAAACGAATTCAGCAAGTGGCA 61.796 43.478 6.22 0.00 43.08 4.92
1098 1146 2.287547 TGAAACGAATTCAGCAAGTGGC 60.288 45.455 6.22 0.00 43.08 5.01
1117 1166 1.923227 CTGTCGTACCAGCGCTCTGA 61.923 60.000 7.13 0.00 42.95 3.27
1123 1172 0.179121 TAATGCCTGTCGTACCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
1124 1173 2.240493 ATAATGCCTGTCGTACCAGC 57.760 50.000 0.00 0.00 0.00 4.85
1128 1177 4.189231 ACCTGAAATAATGCCTGTCGTAC 58.811 43.478 0.00 0.00 0.00 3.67
1129 1178 4.481368 ACCTGAAATAATGCCTGTCGTA 57.519 40.909 0.00 0.00 0.00 3.43
1131 1180 4.155826 TCAAACCTGAAATAATGCCTGTCG 59.844 41.667 0.00 0.00 0.00 4.35
1132 1181 5.643379 TCAAACCTGAAATAATGCCTGTC 57.357 39.130 0.00 0.00 0.00 3.51
1134 1183 4.866486 GCTTCAAACCTGAAATAATGCCTG 59.134 41.667 0.00 0.00 41.05 4.85
1135 1184 4.527816 TGCTTCAAACCTGAAATAATGCCT 59.472 37.500 0.00 0.00 41.05 4.75
1136 1185 4.819769 TGCTTCAAACCTGAAATAATGCC 58.180 39.130 0.00 0.00 41.05 4.40
1137 1186 5.473039 ACTGCTTCAAACCTGAAATAATGC 58.527 37.500 0.00 0.00 41.05 3.56
1138 1187 6.095377 GGACTGCTTCAAACCTGAAATAATG 58.905 40.000 0.00 0.00 41.05 1.90
1139 1188 5.106157 CGGACTGCTTCAAACCTGAAATAAT 60.106 40.000 0.00 0.00 41.05 1.28
1143 1192 1.946768 CGGACTGCTTCAAACCTGAAA 59.053 47.619 0.00 0.00 41.05 2.69
1282 1340 2.715005 CTGCAACCACCACACACG 59.285 61.111 0.00 0.00 0.00 4.49
1286 1344 2.832661 GCACCTGCAACCACCACA 60.833 61.111 0.00 0.00 41.59 4.17
1313 1371 1.001760 CCCCTCCCGGAGAAGAGAA 59.998 63.158 16.69 0.00 30.83 2.87
1315 1373 3.157949 GCCCCTCCCGGAGAAGAG 61.158 72.222 16.69 0.00 0.00 2.85
2231 2289 4.887615 TGGAACGCCATGAACACA 57.112 50.000 0.00 0.00 39.92 3.72
2598 2676 5.450818 TTCCCCTATAACAGAACAAGCAT 57.549 39.130 0.00 0.00 0.00 3.79
2721 2802 9.669353 CCAGATTAACAAATGATAAGAAATCGG 57.331 33.333 0.00 0.00 0.00 4.18
2742 2823 3.906846 CCCCTCACTAAATCTAGCCAGAT 59.093 47.826 0.00 0.00 43.67 2.90
2744 2825 3.309296 TCCCCTCACTAAATCTAGCCAG 58.691 50.000 0.00 0.00 0.00 4.85
2745 2826 3.414759 TCCCCTCACTAAATCTAGCCA 57.585 47.619 0.00 0.00 0.00 4.75
2746 2827 3.181453 GGTTCCCCTCACTAAATCTAGCC 60.181 52.174 0.00 0.00 0.00 3.93
2749 2830 5.970640 AGAATGGTTCCCCTCACTAAATCTA 59.029 40.000 0.00 0.00 0.00 1.98
2750 2831 4.790790 AGAATGGTTCCCCTCACTAAATCT 59.209 41.667 0.00 0.00 0.00 2.40
2751 2832 5.117406 AGAATGGTTCCCCTCACTAAATC 57.883 43.478 0.00 0.00 0.00 2.17
2753 2834 4.508405 CCAAGAATGGTTCCCCTCACTAAA 60.508 45.833 0.00 0.00 42.18 1.85
2754 2835 3.010138 CCAAGAATGGTTCCCCTCACTAA 59.990 47.826 0.00 0.00 42.18 2.24
2756 2837 1.355720 CCAAGAATGGTTCCCCTCACT 59.644 52.381 0.00 0.00 42.18 3.41
2757 2838 1.839424 CCAAGAATGGTTCCCCTCAC 58.161 55.000 0.00 0.00 42.18 3.51
2770 2851 1.774254 TCTGGAGGTTCTTGCCAAGAA 59.226 47.619 15.70 15.70 44.82 2.52
2771 2852 1.434188 TCTGGAGGTTCTTGCCAAGA 58.566 50.000 2.24 2.24 35.26 3.02
2772 2853 2.503895 ATCTGGAGGTTCTTGCCAAG 57.496 50.000 0.00 0.00 0.00 3.61
2773 2854 2.978156 AATCTGGAGGTTCTTGCCAA 57.022 45.000 0.00 0.00 0.00 4.52
2774 2855 2.978156 AAATCTGGAGGTTCTTGCCA 57.022 45.000 0.00 0.00 0.00 4.92
2775 2856 5.449177 CGAATAAAATCTGGAGGTTCTTGCC 60.449 44.000 0.00 0.00 0.00 4.52
2776 2857 5.123979 ACGAATAAAATCTGGAGGTTCTTGC 59.876 40.000 0.00 0.00 0.00 4.01
2777 2858 6.149474 ACACGAATAAAATCTGGAGGTTCTTG 59.851 38.462 0.00 0.00 0.00 3.02
2778 2859 6.238648 ACACGAATAAAATCTGGAGGTTCTT 58.761 36.000 0.00 0.00 0.00 2.52
2779 2860 5.805728 ACACGAATAAAATCTGGAGGTTCT 58.194 37.500 0.00 0.00 0.00 3.01
2780 2861 6.072673 ACAACACGAATAAAATCTGGAGGTTC 60.073 38.462 0.00 0.00 0.00 3.62
2781 2862 5.768164 ACAACACGAATAAAATCTGGAGGTT 59.232 36.000 0.00 0.00 0.00 3.50
2782 2863 5.313712 ACAACACGAATAAAATCTGGAGGT 58.686 37.500 0.00 0.00 0.00 3.85
2783 2864 5.880054 ACAACACGAATAAAATCTGGAGG 57.120 39.130 0.00 0.00 0.00 4.30
2784 2865 7.133891 AGAACAACACGAATAAAATCTGGAG 57.866 36.000 0.00 0.00 0.00 3.86
2785 2866 7.876068 ACTAGAACAACACGAATAAAATCTGGA 59.124 33.333 0.00 0.00 0.00 3.86
2786 2867 8.029642 ACTAGAACAACACGAATAAAATCTGG 57.970 34.615 0.00 0.00 0.00 3.86
2791 2872 9.917129 TCATCTACTAGAACAACACGAATAAAA 57.083 29.630 0.00 0.00 0.00 1.52
2793 2874 9.516314 CATCATCTACTAGAACAACACGAATAA 57.484 33.333 0.00 0.00 0.00 1.40
2794 2875 8.683615 ACATCATCTACTAGAACAACACGAATA 58.316 33.333 0.00 0.00 0.00 1.75
2795 2876 7.548097 ACATCATCTACTAGAACAACACGAAT 58.452 34.615 0.00 0.00 0.00 3.34
2796 2877 6.920817 ACATCATCTACTAGAACAACACGAA 58.079 36.000 0.00 0.00 0.00 3.85
2797 2878 6.510879 ACATCATCTACTAGAACAACACGA 57.489 37.500 0.00 0.00 0.00 4.35
2798 2879 7.968956 AGTTACATCATCTACTAGAACAACACG 59.031 37.037 0.00 0.00 0.00 4.49
2799 2880 9.077674 CAGTTACATCATCTACTAGAACAACAC 57.922 37.037 0.00 0.00 0.00 3.32
2800 2881 8.803235 ACAGTTACATCATCTACTAGAACAACA 58.197 33.333 0.00 0.00 0.00 3.33
2801 2882 9.077674 CACAGTTACATCATCTACTAGAACAAC 57.922 37.037 0.00 0.00 0.00 3.32
2802 2883 9.020731 TCACAGTTACATCATCTACTAGAACAA 57.979 33.333 0.00 0.00 0.00 2.83
2803 2884 8.575649 TCACAGTTACATCATCTACTAGAACA 57.424 34.615 0.00 0.00 0.00 3.18
2806 2887 8.851145 GGAATCACAGTTACATCATCTACTAGA 58.149 37.037 0.00 0.00 0.00 2.43
2807 2888 8.633561 TGGAATCACAGTTACATCATCTACTAG 58.366 37.037 0.00 0.00 0.00 2.57
2808 2889 8.533569 TGGAATCACAGTTACATCATCTACTA 57.466 34.615 0.00 0.00 0.00 1.82
2809 2890 7.343057 TCTGGAATCACAGTTACATCATCTACT 59.657 37.037 0.00 0.00 39.48 2.57
2810 2891 7.492524 TCTGGAATCACAGTTACATCATCTAC 58.507 38.462 0.00 0.00 39.48 2.59
2811 2892 7.660030 TCTGGAATCACAGTTACATCATCTA 57.340 36.000 0.00 0.00 39.48 1.98
2812 2893 6.550938 TCTGGAATCACAGTTACATCATCT 57.449 37.500 0.00 0.00 39.48 2.90
2813 2894 6.988580 TGATCTGGAATCACAGTTACATCATC 59.011 38.462 0.00 0.00 39.48 2.92
2814 2895 6.892485 TGATCTGGAATCACAGTTACATCAT 58.108 36.000 0.00 0.00 39.48 2.45
2815 2896 6.298441 TGATCTGGAATCACAGTTACATCA 57.702 37.500 0.00 0.00 39.48 3.07
2816 2897 7.798596 ATTGATCTGGAATCACAGTTACATC 57.201 36.000 0.00 0.00 39.48 3.06
2817 2898 9.685276 TTTATTGATCTGGAATCACAGTTACAT 57.315 29.630 0.00 0.00 39.48 2.29
2818 2899 9.513906 TTTTATTGATCTGGAATCACAGTTACA 57.486 29.630 0.00 0.00 39.48 2.41
2822 2903 8.400947 CGATTTTTATTGATCTGGAATCACAGT 58.599 33.333 0.00 0.00 39.48 3.55
2823 2904 7.377928 GCGATTTTTATTGATCTGGAATCACAG 59.622 37.037 0.00 0.00 39.84 3.66
2824 2905 7.195646 GCGATTTTTATTGATCTGGAATCACA 58.804 34.615 0.00 0.00 0.00 3.58
2825 2906 6.638468 GGCGATTTTTATTGATCTGGAATCAC 59.362 38.462 0.00 0.00 0.00 3.06
2826 2907 6.320926 TGGCGATTTTTATTGATCTGGAATCA 59.679 34.615 0.00 0.00 0.00 2.57
2827 2908 6.738114 TGGCGATTTTTATTGATCTGGAATC 58.262 36.000 0.00 0.00 0.00 2.52
2828 2909 6.713762 TGGCGATTTTTATTGATCTGGAAT 57.286 33.333 0.00 0.00 0.00 3.01
2829 2910 6.320926 TCATGGCGATTTTTATTGATCTGGAA 59.679 34.615 0.00 0.00 0.00 3.53
2830 2911 5.827267 TCATGGCGATTTTTATTGATCTGGA 59.173 36.000 0.00 0.00 0.00 3.86
2831 2912 6.075762 TCATGGCGATTTTTATTGATCTGG 57.924 37.500 0.00 0.00 0.00 3.86
2832 2913 6.584942 CCATCATGGCGATTTTTATTGATCTG 59.415 38.462 0.00 0.00 29.21 2.90
2833 2914 6.684686 CCATCATGGCGATTTTTATTGATCT 58.315 36.000 0.00 0.00 29.21 2.75
2834 2915 6.939551 CCATCATGGCGATTTTTATTGATC 57.060 37.500 0.00 0.00 29.21 2.92
2868 2949 5.304101 TGAGGGCACACAAATGATACTTTTT 59.696 36.000 0.00 0.00 0.00 1.94
2869 2950 4.832266 TGAGGGCACACAAATGATACTTTT 59.168 37.500 0.00 0.00 0.00 2.27
2870 2951 4.406456 TGAGGGCACACAAATGATACTTT 58.594 39.130 0.00 0.00 0.00 2.66
2871 2952 4.032960 TGAGGGCACACAAATGATACTT 57.967 40.909 0.00 0.00 0.00 2.24
2872 2953 3.719268 TGAGGGCACACAAATGATACT 57.281 42.857 0.00 0.00 0.00 2.12
2873 2954 6.639632 AATATGAGGGCACACAAATGATAC 57.360 37.500 0.00 0.00 0.00 2.24
2874 2955 7.201902 GGAAAATATGAGGGCACACAAATGATA 60.202 37.037 0.00 0.00 0.00 2.15
2875 2956 6.407299 GGAAAATATGAGGGCACACAAATGAT 60.407 38.462 0.00 0.00 0.00 2.45
2876 2957 5.105392 GGAAAATATGAGGGCACACAAATGA 60.105 40.000 0.00 0.00 0.00 2.57
2877 2958 5.111293 GGAAAATATGAGGGCACACAAATG 58.889 41.667 0.00 0.00 0.00 2.32
2878 2959 4.162131 GGGAAAATATGAGGGCACACAAAT 59.838 41.667 0.00 0.00 0.00 2.32
2879 2960 3.513515 GGGAAAATATGAGGGCACACAAA 59.486 43.478 0.00 0.00 0.00 2.83
2886 2967 2.552743 GCTAACGGGAAAATATGAGGGC 59.447 50.000 0.00 0.00 0.00 5.19
2895 2976 3.417101 ACATGTGATGCTAACGGGAAAA 58.583 40.909 0.00 0.00 0.00 2.29
2931 3325 8.368126 GTCAACATCGATGCATTTTCTTTTAAG 58.632 33.333 25.11 0.00 0.00 1.85
2932 3326 7.328249 GGTCAACATCGATGCATTTTCTTTTAA 59.672 33.333 25.11 0.00 0.00 1.52
2934 3328 5.634859 GGTCAACATCGATGCATTTTCTTTT 59.365 36.000 25.11 5.83 0.00 2.27
2947 3386 0.539986 GCCCTTAGGGTCAACATCGA 59.460 55.000 19.76 0.00 46.51 3.59
2948 3387 0.251916 TGCCCTTAGGGTCAACATCG 59.748 55.000 19.76 0.00 46.51 3.84
2978 3417 7.540745 TGACTTTTGAATTTTTAGGATAAGCGC 59.459 33.333 0.00 0.00 0.00 5.92
3043 3485 6.586463 GGCGATCTTGATACATTAAGAATCGA 59.414 38.462 19.93 0.00 36.24 3.59
3045 3487 7.897575 AGGCGATCTTGATACATTAAGAATC 57.102 36.000 1.12 0.65 36.24 2.52
3046 3488 9.778741 TTTAGGCGATCTTGATACATTAAGAAT 57.221 29.630 1.12 0.00 36.24 2.40
3061 3503 4.018688 AGGGGTTTAAGTTTTAGGCGATCT 60.019 41.667 0.00 0.00 0.00 2.75
3066 3508 3.678289 TCGAGGGGTTTAAGTTTTAGGC 58.322 45.455 0.00 0.00 0.00 3.93
3079 3521 6.041069 TGACAACAAAATTATTTTCGAGGGGT 59.959 34.615 0.00 0.00 0.00 4.95
3091 3533 7.436673 CGTTTGGGAGAATTGACAACAAAATTA 59.563 33.333 0.00 0.00 39.54 1.40
3092 3534 6.257630 CGTTTGGGAGAATTGACAACAAAATT 59.742 34.615 0.00 0.00 39.54 1.82
3094 3536 5.105752 CGTTTGGGAGAATTGACAACAAAA 58.894 37.500 0.00 0.00 39.54 2.44
3103 3545 3.369546 AGCAAACGTTTGGGAGAATTG 57.630 42.857 34.94 13.77 38.57 2.32
3105 3547 5.523438 TTTAAGCAAACGTTTGGGAGAAT 57.477 34.783 34.94 10.19 38.57 2.40
3110 3552 8.576936 TTTAGTTATTTAAGCAAACGTTTGGG 57.423 30.769 34.94 16.96 38.57 4.12
3172 3614 4.038883 TCATTGTGATGTGGTGCATTTGAA 59.961 37.500 0.00 0.00 38.06 2.69
3174 3616 3.915536 TCATTGTGATGTGGTGCATTTG 58.084 40.909 0.00 0.00 38.06 2.32
3182 3624 3.062639 GCTCGTAGTTCATTGTGATGTGG 59.937 47.826 0.00 0.00 34.77 4.17
3183 3625 3.679502 TGCTCGTAGTTCATTGTGATGTG 59.320 43.478 0.00 0.00 34.77 3.21
3190 3632 9.988350 AACTTTATTTATGCTCGTAGTTCATTG 57.012 29.630 0.00 0.00 0.00 2.82
3204 3647 8.859090 TGATGGGCCTGATTAACTTTATTTATG 58.141 33.333 4.53 0.00 0.00 1.90
3217 3660 2.893424 AGTTGTTTGATGGGCCTGATT 58.107 42.857 4.53 0.00 0.00 2.57
3221 3664 3.571590 TGTTTAGTTGTTTGATGGGCCT 58.428 40.909 4.53 0.00 0.00 5.19
3223 3666 5.867174 GGTTATGTTTAGTTGTTTGATGGGC 59.133 40.000 0.00 0.00 0.00 5.36
3224 3667 6.866248 GTGGTTATGTTTAGTTGTTTGATGGG 59.134 38.462 0.00 0.00 0.00 4.00
3262 3705 5.695851 AATGGACTTGTTCATTCAGTGTC 57.304 39.130 1.66 0.00 0.00 3.67
3267 3710 9.528018 GTTTCTTTTAATGGACTTGTTCATTCA 57.472 29.630 10.24 0.00 35.50 2.57
3296 3739 3.456280 CTTTTGGTCCACCATGTGTTTG 58.544 45.455 0.00 0.00 46.97 2.93
3323 3766 4.332819 GTGTATGATGCCCTTGTGAACTAC 59.667 45.833 0.00 0.00 0.00 2.73
3338 3781 2.100916 GGTGACGGTGCTAGTGTATGAT 59.899 50.000 0.00 0.00 0.00 2.45
3354 3797 2.733593 GGTGCTGTCGACGGTGAC 60.734 66.667 24.68 19.92 39.37 3.67


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

AutoCloner maintained by Alex Coulton.