Multiple sequence alignment - TraesCS6A01G333500

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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 TraesCS6A01G333500 chr6A 100.000 4360 0 0 1 4360 564583575 564587934 0.000000e+00 8052.0
1 TraesCS6A01G333500 chr6A 96.765 340 10 1 1 339 564539907 564540246 2.280000e-157 566.0
2 TraesCS6A01G333500 chr6A 80.321 686 99 24 2704 3363 564404845 564405520 1.820000e-133 486.0
3 TraesCS6A01G333500 chr6A 95.410 305 14 0 338 642 564540277 564540581 1.820000e-133 486.0
4 TraesCS6A01G333500 chr6A 80.000 680 100 24 2704 3363 564509540 564510203 1.840000e-128 470.0
5 TraesCS6A01G333500 chr6A 86.973 261 29 3 1095 1354 564508023 564508279 5.520000e-74 289.0
6 TraesCS6A01G333500 chr6A 83.969 262 37 4 1094 1354 564403377 564403634 3.370000e-61 246.0
7 TraesCS6A01G333500 chr6A 97.059 68 2 0 641 708 564574637 564574704 9.910000e-22 115.0
8 TraesCS6A01G333500 chr6D 90.757 2153 118 28 1403 3513 421799072 421801185 0.000000e+00 2798.0
9 TraesCS6A01G333500 chr6D 89.554 718 38 8 3671 4351 421801525 421802242 0.000000e+00 876.0
10 TraesCS6A01G333500 chr6D 92.410 527 27 4 844 1357 421798487 421799013 0.000000e+00 739.0
11 TraesCS6A01G333500 chr6D 80.395 658 101 21 2713 3350 421473346 421472697 3.950000e-130 475.0
12 TraesCS6A01G333500 chr6D 85.240 271 34 4 1088 1357 421474785 421474520 1.540000e-69 274.0
13 TraesCS6A01G333500 chr6D 94.969 159 6 2 3518 3674 421801238 421801396 9.360000e-62 248.0
14 TraesCS6A01G333500 chr6D 97.561 41 1 0 1373 1413 421799012 421799052 2.180000e-08 71.3
15 TraesCS6A01G333500 chr6B 93.457 1773 76 19 1740 3473 634977765 634979536 0.000000e+00 2595.0
16 TraesCS6A01G333500 chr6B 88.364 868 44 16 895 1738 634976670 634977504 0.000000e+00 990.0
17 TraesCS6A01G333500 chr6B 79.912 682 105 20 2704 3363 634641795 634642466 5.100000e-129 472.0
18 TraesCS6A01G333500 chr6B 79.185 687 100 29 2704 3363 634941778 634942448 1.860000e-118 436.0
19 TraesCS6A01G333500 chr6B 82.759 348 45 5 4 338 634975607 634975952 3.300000e-76 296.0
20 TraesCS6A01G333500 chr6B 87.843 255 26 3 1101 1354 634940061 634940311 1.190000e-75 294.0
21 TraesCS6A01G333500 chr6B 85.496 262 33 4 1094 1354 634639864 634640121 7.190000e-68 268.0
22 TraesCS6A01G333500 chr6B 95.349 43 2 0 1596 1638 634977456 634977498 7.820000e-08 69.4
23 TraesCS6A01G333500 chr2A 90.058 171 13 3 674 842 726238413 726238245 7.340000e-53 219.0
24 TraesCS6A01G333500 chr7B 80.503 159 27 3 135 293 715857304 715857458 7.660000e-23 119.0
25 TraesCS6A01G333500 chr7B 96.970 33 1 0 1832 1864 80678815 80678783 6.090000e-04 56.5
26 TraesCS6A01G333500 chr7D 78.049 164 29 6 135 296 620722753 620722595 3.590000e-16 97.1
27 TraesCS6A01G333500 chr4D 81.905 105 17 2 372 475 494023929 494024032 2.160000e-13 87.9
28 TraesCS6A01G333500 chr1D 95.349 43 0 1 364 406 398090602 398090642 2.810000e-07 67.6
29 TraesCS6A01G333500 chr1B 80.208 96 5 8 674 768 673593712 673593630 4.710000e-05 60.2
30 TraesCS6A01G333500 chr1B 100.000 29 0 0 504 532 676604053 676604025 2.000000e-03 54.7
31 TraesCS6A01G333500 chr1B 100.000 29 0 0 504 532 676648640 676648612 2.000000e-03 54.7
32 TraesCS6A01G333500 chr3D 86.538 52 7 0 369 420 4861034 4860983 1.690000e-04 58.4


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 TraesCS6A01G333500 chr6A 564583575 564587934 4359 False 8052.00 8052 100.00000 1 4360 1 chr6A.!!$F2 4359
1 TraesCS6A01G333500 chr6A 564539907 564540581 674 False 526.00 566 96.08750 1 642 2 chr6A.!!$F5 641
2 TraesCS6A01G333500 chr6A 564508023 564510203 2180 False 379.50 470 83.48650 1095 3363 2 chr6A.!!$F4 2268
3 TraesCS6A01G333500 chr6A 564403377 564405520 2143 False 366.00 486 82.14500 1094 3363 2 chr6A.!!$F3 2269
4 TraesCS6A01G333500 chr6D 421798487 421802242 3755 False 946.46 2798 93.05020 844 4351 5 chr6D.!!$F1 3507
5 TraesCS6A01G333500 chr6D 421472697 421474785 2088 True 374.50 475 82.81750 1088 3350 2 chr6D.!!$R1 2262
6 TraesCS6A01G333500 chr6B 634975607 634979536 3929 False 987.60 2595 89.98225 4 3473 4 chr6B.!!$F3 3469
7 TraesCS6A01G333500 chr6B 634639864 634642466 2602 False 370.00 472 82.70400 1094 3363 2 chr6B.!!$F1 2269
8 TraesCS6A01G333500 chr6B 634940061 634942448 2387 False 365.00 436 83.51400 1101 3363 2 chr6B.!!$F2 2262

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
703 1046 0.108041 AACACACGGGCCTATTACGG 60.108 55.0 0.84 0.00 0.0 4.02 F
2318 4125 0.110147 ACGACTTCTTCTCTGACGCG 60.110 55.0 3.53 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 4574 0.608640 GTGAGTGACCGACCTCCATT 59.391 55.0 0.0 0.0 0.0 3.16 R
3908 6151 0.039074 GCGGTGTATGATCGAGGGAG 60.039 60.0 0.0 0.0 0.0 4.30 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
165 179 7.271438 TGGCGTTTTTGCAAAATTTAAAAAGTC 59.729 29.630 24.39 12.84 34.92 3.01
230 244 5.235186 CGGATCTGCCACTTGTTCTTATAAG 59.765 44.000 6.11 6.11 35.94 1.73
293 307 4.269183 TGGCTTTGAACTCTCTTCAACAA 58.731 39.130 0.00 0.00 38.05 2.83
453 500 5.071250 TGATGTGTTTAGGAGGTTGTACTGT 59.929 40.000 0.00 0.00 0.00 3.55
514 673 0.737219 ACAGTGCTACGGACCGATAC 59.263 55.000 23.38 12.96 0.00 2.24
535 694 2.675844 CAGGACCGCGTTGAATGATTTA 59.324 45.455 4.92 0.00 0.00 1.40
544 703 4.505300 CGTTGAATGATTTACGTGATCCG 58.495 43.478 0.00 2.55 44.03 4.18
632 975 4.368808 GCGACGCACGTGCACAAT 62.369 61.111 37.03 20.77 44.60 2.71
644 987 2.660612 GCACAATGCAAGGCAACGC 61.661 57.895 0.00 0.00 43.62 4.84
663 1006 3.626680 GAGCGTCAGCACGGCACTA 62.627 63.158 0.00 0.00 46.80 2.74
670 1013 3.929948 GCACGGCACTATGCTCGC 61.930 66.667 10.31 3.60 44.28 5.03
671 1014 3.620428 CACGGCACTATGCTCGCG 61.620 66.667 0.00 0.00 44.28 5.87
672 1015 4.873129 ACGGCACTATGCTCGCGG 62.873 66.667 6.13 0.00 44.28 6.46
682 1025 2.126346 GCTCGCGGCAAAAATGCT 60.126 55.556 6.13 0.00 41.35 3.79
683 1026 1.136565 GCTCGCGGCAAAAATGCTA 59.863 52.632 6.13 0.00 41.35 3.49
684 1027 0.455972 GCTCGCGGCAAAAATGCTAA 60.456 50.000 6.13 0.00 41.35 3.09
685 1028 1.975837 CTCGCGGCAAAAATGCTAAA 58.024 45.000 6.13 0.00 34.73 1.85
686 1029 1.648681 CTCGCGGCAAAAATGCTAAAC 59.351 47.619 6.13 0.00 34.73 2.01
687 1030 1.001268 TCGCGGCAAAAATGCTAAACA 60.001 42.857 6.13 0.00 34.73 2.83
688 1031 1.124116 CGCGGCAAAAATGCTAAACAC 59.876 47.619 0.00 0.00 34.73 3.32
689 1032 2.131183 GCGGCAAAAATGCTAAACACA 58.869 42.857 0.00 0.00 34.73 3.72
690 1033 2.096958 GCGGCAAAAATGCTAAACACAC 60.097 45.455 0.00 0.00 34.73 3.82
691 1034 2.152868 CGGCAAAAATGCTAAACACACG 59.847 45.455 0.40 0.00 34.73 4.49
692 1035 2.474735 GGCAAAAATGCTAAACACACGG 59.525 45.455 0.40 0.00 34.73 4.94
693 1036 2.474735 GCAAAAATGCTAAACACACGGG 59.525 45.455 0.00 0.00 0.00 5.28
694 1037 2.432206 AAAATGCTAAACACACGGGC 57.568 45.000 0.00 0.00 0.00 6.13
695 1038 0.601057 AAATGCTAAACACACGGGCC 59.399 50.000 0.00 0.00 0.00 5.80
696 1039 0.251165 AATGCTAAACACACGGGCCT 60.251 50.000 0.84 0.00 0.00 5.19
697 1040 0.616371 ATGCTAAACACACGGGCCTA 59.384 50.000 0.84 0.00 0.00 3.93
698 1041 0.616371 TGCTAAACACACGGGCCTAT 59.384 50.000 0.84 0.00 0.00 2.57
699 1042 1.003812 TGCTAAACACACGGGCCTATT 59.996 47.619 0.84 0.00 0.00 1.73
700 1043 2.236644 TGCTAAACACACGGGCCTATTA 59.763 45.455 0.84 0.00 0.00 0.98
701 1044 2.610833 GCTAAACACACGGGCCTATTAC 59.389 50.000 0.84 0.00 0.00 1.89
702 1045 1.729284 AAACACACGGGCCTATTACG 58.271 50.000 0.84 0.00 0.00 3.18
703 1046 0.108041 AACACACGGGCCTATTACGG 60.108 55.000 0.84 0.00 0.00 4.02
704 1047 1.227438 CACACGGGCCTATTACGGG 60.227 63.158 0.84 0.00 37.00 5.28
705 1048 2.424302 CACGGGCCTATTACGGGG 59.576 66.667 0.84 0.00 0.00 5.73
706 1049 3.553363 ACGGGCCTATTACGGGGC 61.553 66.667 0.84 0.00 46.89 5.80
707 1050 3.239253 CGGGCCTATTACGGGGCT 61.239 66.667 0.84 0.00 46.80 5.19
708 1051 2.430367 GGGCCTATTACGGGGCTG 59.570 66.667 0.84 0.00 46.80 4.85
709 1052 2.449450 GGGCCTATTACGGGGCTGT 61.449 63.158 0.84 0.00 46.80 4.40
710 1053 1.530283 GGCCTATTACGGGGCTGTT 59.470 57.895 0.00 0.00 46.80 3.16
711 1054 0.760572 GGCCTATTACGGGGCTGTTA 59.239 55.000 0.00 0.00 46.80 2.41
712 1055 1.541889 GGCCTATTACGGGGCTGTTAC 60.542 57.143 0.00 0.00 46.80 2.50
713 1056 1.541889 GCCTATTACGGGGCTGTTACC 60.542 57.143 0.00 0.00 44.48 2.85
718 1061 4.024545 CGGGGCTGTTACCGGGTT 62.025 66.667 4.31 0.00 46.08 4.11
719 1062 2.437449 GGGGCTGTTACCGGGTTT 59.563 61.111 4.31 0.00 0.00 3.27
720 1063 1.684629 GGGGCTGTTACCGGGTTTA 59.315 57.895 4.31 0.00 0.00 2.01
721 1064 0.677731 GGGGCTGTTACCGGGTTTAC 60.678 60.000 4.31 5.04 0.00 2.01
722 1065 0.325933 GGGCTGTTACCGGGTTTACT 59.674 55.000 4.31 0.00 0.00 2.24
723 1066 1.554617 GGGCTGTTACCGGGTTTACTA 59.445 52.381 4.31 0.00 0.00 1.82
724 1067 2.171237 GGGCTGTTACCGGGTTTACTAT 59.829 50.000 4.31 0.00 0.00 2.12
725 1068 3.387699 GGGCTGTTACCGGGTTTACTATA 59.612 47.826 4.31 0.00 0.00 1.31
726 1069 4.141733 GGGCTGTTACCGGGTTTACTATAA 60.142 45.833 4.31 0.00 0.00 0.98
727 1070 5.427378 GGCTGTTACCGGGTTTACTATAAA 58.573 41.667 4.31 0.00 0.00 1.40
728 1071 5.879777 GGCTGTTACCGGGTTTACTATAAAA 59.120 40.000 4.31 0.00 0.00 1.52
729 1072 6.543465 GGCTGTTACCGGGTTTACTATAAAAT 59.457 38.462 4.31 0.00 0.00 1.82
730 1073 7.254898 GGCTGTTACCGGGTTTACTATAAAATC 60.255 40.741 4.31 0.00 0.00 2.17
731 1074 7.496920 GCTGTTACCGGGTTTACTATAAAATCT 59.503 37.037 4.31 0.00 0.00 2.40
732 1075 8.947055 TGTTACCGGGTTTACTATAAAATCTC 57.053 34.615 4.31 0.00 0.00 2.75
733 1076 8.761689 TGTTACCGGGTTTACTATAAAATCTCT 58.238 33.333 4.31 0.00 0.00 3.10
734 1077 9.254133 GTTACCGGGTTTACTATAAAATCTCTC 57.746 37.037 4.31 0.00 0.00 3.20
735 1078 6.824553 ACCGGGTTTACTATAAAATCTCTCC 58.175 40.000 6.32 0.00 0.00 3.71
736 1079 6.384886 ACCGGGTTTACTATAAAATCTCTCCA 59.615 38.462 6.32 0.00 0.00 3.86
737 1080 6.704937 CCGGGTTTACTATAAAATCTCTCCAC 59.295 42.308 0.00 0.00 0.00 4.02
738 1081 6.704937 CGGGTTTACTATAAAATCTCTCCACC 59.295 42.308 0.00 0.00 0.00 4.61
739 1082 6.704937 GGGTTTACTATAAAATCTCTCCACCG 59.295 42.308 0.00 0.00 0.00 4.94
740 1083 6.202379 GGTTTACTATAAAATCTCTCCACCGC 59.798 42.308 0.00 0.00 0.00 5.68
741 1084 3.978687 ACTATAAAATCTCTCCACCGCG 58.021 45.455 0.00 0.00 0.00 6.46
742 1085 1.583054 ATAAAATCTCTCCACCGCGC 58.417 50.000 0.00 0.00 0.00 6.86
743 1086 0.461339 TAAAATCTCTCCACCGCGCC 60.461 55.000 0.00 0.00 0.00 6.53
744 1087 4.514577 AATCTCTCCACCGCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
750 1093 4.690719 TCCACCGCGCCGTGATTT 62.691 61.111 27.01 0.00 35.68 2.17
751 1094 3.732892 CCACCGCGCCGTGATTTT 61.733 61.111 27.01 0.00 35.68 1.82
752 1095 2.202298 CACCGCGCCGTGATTTTC 60.202 61.111 22.08 0.00 35.68 2.29
753 1096 2.666862 ACCGCGCCGTGATTTTCA 60.667 55.556 0.00 0.00 0.00 2.69
754 1097 2.098298 CCGCGCCGTGATTTTCAG 59.902 61.111 0.00 0.00 0.00 3.02
755 1098 2.098298 CGCGCCGTGATTTTCAGG 59.902 61.111 0.00 0.00 32.49 3.86
756 1099 2.677003 CGCGCCGTGATTTTCAGGT 61.677 57.895 0.00 0.00 30.87 4.00
757 1100 1.154225 GCGCCGTGATTTTCAGGTG 60.154 57.895 0.00 0.00 37.33 4.00
758 1101 1.501741 CGCCGTGATTTTCAGGTGG 59.498 57.895 0.00 0.00 30.87 4.61
759 1102 0.953471 CGCCGTGATTTTCAGGTGGA 60.953 55.000 0.00 0.00 30.87 4.02
760 1103 1.463674 GCCGTGATTTTCAGGTGGAT 58.536 50.000 0.00 0.00 30.87 3.41
761 1104 1.133025 GCCGTGATTTTCAGGTGGATG 59.867 52.381 0.00 0.00 30.87 3.51
762 1105 1.745087 CCGTGATTTTCAGGTGGATGG 59.255 52.381 0.00 0.00 30.87 3.51
763 1106 1.745087 CGTGATTTTCAGGTGGATGGG 59.255 52.381 0.00 0.00 0.00 4.00
764 1107 2.102578 GTGATTTTCAGGTGGATGGGG 58.897 52.381 0.00 0.00 0.00 4.96
765 1108 1.114627 GATTTTCAGGTGGATGGGGC 58.885 55.000 0.00 0.00 0.00 5.80
766 1109 0.325577 ATTTTCAGGTGGATGGGGCC 60.326 55.000 0.00 0.00 0.00 5.80
767 1110 1.734420 TTTTCAGGTGGATGGGGCCA 61.734 55.000 4.39 0.00 35.02 5.36
768 1111 1.734420 TTTCAGGTGGATGGGGCCAA 61.734 55.000 4.39 0.00 40.20 4.52
769 1112 1.517538 TTCAGGTGGATGGGGCCAAT 61.518 55.000 4.39 0.00 40.20 3.16
770 1113 1.456331 CAGGTGGATGGGGCCAATC 60.456 63.158 12.89 12.89 40.20 2.67
771 1114 1.623686 AGGTGGATGGGGCCAATCT 60.624 57.895 20.28 0.00 40.20 2.40
772 1115 1.152673 GGTGGATGGGGCCAATCTC 60.153 63.158 20.28 13.17 40.20 2.75
773 1116 1.152673 GTGGATGGGGCCAATCTCC 60.153 63.158 20.28 12.55 40.20 3.71
774 1117 1.309013 TGGATGGGGCCAATCTCCT 60.309 57.895 20.28 0.00 34.31 3.69
775 1118 0.925720 TGGATGGGGCCAATCTCCTT 60.926 55.000 20.28 0.00 34.31 3.36
776 1119 0.178978 GGATGGGGCCAATCTCCTTC 60.179 60.000 20.28 3.60 0.00 3.46
777 1120 0.178978 GATGGGGCCAATCTCCTTCC 60.179 60.000 14.03 0.00 0.00 3.46
778 1121 0.628668 ATGGGGCCAATCTCCTTCCT 60.629 55.000 4.39 0.00 0.00 3.36
779 1122 0.850883 TGGGGCCAATCTCCTTCCTT 60.851 55.000 4.39 0.00 0.00 3.36
780 1123 1.222567 GGGGCCAATCTCCTTCCTTA 58.777 55.000 4.39 0.00 0.00 2.69
781 1124 1.783365 GGGGCCAATCTCCTTCCTTAT 59.217 52.381 4.39 0.00 0.00 1.73
782 1125 2.986728 GGGGCCAATCTCCTTCCTTATA 59.013 50.000 4.39 0.00 0.00 0.98
783 1126 3.397955 GGGGCCAATCTCCTTCCTTATAA 59.602 47.826 4.39 0.00 0.00 0.98
784 1127 4.044698 GGGGCCAATCTCCTTCCTTATAAT 59.955 45.833 4.39 0.00 0.00 1.28
785 1128 5.257262 GGGCCAATCTCCTTCCTTATAATC 58.743 45.833 4.39 0.00 0.00 1.75
786 1129 5.257262 GGCCAATCTCCTTCCTTATAATCC 58.743 45.833 0.00 0.00 0.00 3.01
787 1130 5.222130 GGCCAATCTCCTTCCTTATAATCCA 60.222 44.000 0.00 0.00 0.00 3.41
788 1131 6.306987 GCCAATCTCCTTCCTTATAATCCAA 58.693 40.000 0.00 0.00 0.00 3.53
789 1132 6.950619 GCCAATCTCCTTCCTTATAATCCAAT 59.049 38.462 0.00 0.00 0.00 3.16
790 1133 8.109634 GCCAATCTCCTTCCTTATAATCCAATA 58.890 37.037 0.00 0.00 0.00 1.90
795 1138 9.862149 TCTCCTTCCTTATAATCCAATAAAACC 57.138 33.333 0.00 0.00 0.00 3.27
796 1139 9.868160 CTCCTTCCTTATAATCCAATAAAACCT 57.132 33.333 0.00 0.00 0.00 3.50
799 1142 9.750125 CTTCCTTATAATCCAATAAAACCTTGC 57.250 33.333 0.00 0.00 0.00 4.01
800 1143 8.245195 TCCTTATAATCCAATAAAACCTTGCC 57.755 34.615 0.00 0.00 0.00 4.52
801 1144 7.841729 TCCTTATAATCCAATAAAACCTTGCCA 59.158 33.333 0.00 0.00 0.00 4.92
802 1145 8.650490 CCTTATAATCCAATAAAACCTTGCCAT 58.350 33.333 0.00 0.00 0.00 4.40
803 1146 9.480053 CTTATAATCCAATAAAACCTTGCCATG 57.520 33.333 0.00 0.00 0.00 3.66
804 1147 5.760484 AATCCAATAAAACCTTGCCATGT 57.240 34.783 0.00 0.00 0.00 3.21
805 1148 4.799564 TCCAATAAAACCTTGCCATGTC 57.200 40.909 0.00 0.00 0.00 3.06
806 1149 3.192422 TCCAATAAAACCTTGCCATGTCG 59.808 43.478 0.00 0.00 0.00 4.35
807 1150 3.510719 CAATAAAACCTTGCCATGTCGG 58.489 45.455 0.00 0.00 38.11 4.79
808 1151 2.570415 TAAAACCTTGCCATGTCGGA 57.430 45.000 0.00 0.00 36.56 4.55
809 1152 1.247567 AAAACCTTGCCATGTCGGAG 58.752 50.000 0.00 0.00 36.56 4.63
810 1153 0.609131 AAACCTTGCCATGTCGGAGG 60.609 55.000 0.00 0.00 36.56 4.30
825 1168 4.227618 AGGCACTCCGTAAACCCT 57.772 55.556 0.00 0.00 37.47 4.34
826 1169 1.980844 AGGCACTCCGTAAACCCTC 59.019 57.895 0.00 0.00 37.47 4.30
827 1170 1.078637 GGCACTCCGTAAACCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
828 1171 1.447314 GCACTCCGTAAACCCTCCG 60.447 63.158 0.00 0.00 0.00 4.63
829 1172 1.969862 CACTCCGTAAACCCTCCGT 59.030 57.895 0.00 0.00 0.00 4.69
830 1173 1.176527 CACTCCGTAAACCCTCCGTA 58.823 55.000 0.00 0.00 0.00 4.02
831 1174 1.545582 CACTCCGTAAACCCTCCGTAA 59.454 52.381 0.00 0.00 0.00 3.18
832 1175 1.546029 ACTCCGTAAACCCTCCGTAAC 59.454 52.381 0.00 0.00 0.00 2.50
833 1176 1.545582 CTCCGTAAACCCTCCGTAACA 59.454 52.381 0.00 0.00 0.00 2.41
834 1177 1.545582 TCCGTAAACCCTCCGTAACAG 59.454 52.381 0.00 0.00 0.00 3.16
835 1178 1.404583 CCGTAAACCCTCCGTAACAGG 60.405 57.143 0.00 0.00 0.00 4.00
836 1179 1.730501 GTAAACCCTCCGTAACAGGC 58.269 55.000 0.00 0.00 0.00 4.85
837 1180 0.614812 TAAACCCTCCGTAACAGGCC 59.385 55.000 0.00 0.00 0.00 5.19
838 1181 2.133359 AAACCCTCCGTAACAGGCCC 62.133 60.000 0.00 0.00 0.00 5.80
839 1182 4.157120 CCCTCCGTAACAGGCCCG 62.157 72.222 0.00 0.00 0.00 6.13
840 1183 3.387947 CCTCCGTAACAGGCCCGT 61.388 66.667 0.00 0.00 0.00 5.28
841 1184 2.125673 CTCCGTAACAGGCCCGTG 60.126 66.667 0.00 0.00 0.00 4.94
842 1185 4.382320 TCCGTAACAGGCCCGTGC 62.382 66.667 0.00 0.00 0.00 5.34
867 1210 0.887836 TCGTCTCGCCGTGCCTATAT 60.888 55.000 0.00 0.00 0.00 0.86
882 1225 2.506865 CTATATAACGCGAGCACTCCG 58.493 52.381 15.93 6.90 0.00 4.63
903 1259 1.550524 CGGACGACATATCATCCCCAT 59.449 52.381 0.00 0.00 33.35 4.00
991 1347 2.434884 CTTCGGCTCCGCACACAT 60.435 61.111 2.96 0.00 39.59 3.21
1044 1400 2.055838 GTGATGCTCGTGTCGTGTTTA 58.944 47.619 0.00 0.00 0.00 2.01
1057 1413 3.810896 GTTTAGCCGCCCTTGCCG 61.811 66.667 0.00 0.00 0.00 5.69
1222 1578 4.760047 CGGACCGGAGCAAGGTGG 62.760 72.222 9.46 0.00 43.01 4.61
1224 1580 2.358737 GACCGGAGCAAGGTGGTG 60.359 66.667 9.46 0.00 43.01 4.17
1236 1592 2.357517 GTGGTGGACGTGCTGGAG 60.358 66.667 8.99 0.00 0.00 3.86
1284 1640 2.208349 AGGACCTGGGCCTTCAGT 59.792 61.111 17.79 0.00 33.14 3.41
1359 1715 2.349438 GCAAGTGTTCGTGGTATGTGTG 60.349 50.000 0.00 0.00 0.00 3.82
1360 1716 2.869801 CAAGTGTTCGTGGTATGTGTGT 59.130 45.455 0.00 0.00 0.00 3.72
1361 1717 2.479837 AGTGTTCGTGGTATGTGTGTG 58.520 47.619 0.00 0.00 0.00 3.82
1362 1718 2.159014 AGTGTTCGTGGTATGTGTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
1405 1795 2.483889 GGCCAAAGCTACGCTAGAGATT 60.484 50.000 0.00 0.00 38.25 2.40
1413 1803 3.486474 GCTACGCTAGAGATTTCCGTTTC 59.514 47.826 0.00 0.00 33.79 2.78
1417 1807 3.927142 CGCTAGAGATTTCCGTTTCACTT 59.073 43.478 0.00 0.00 0.00 3.16
1433 1823 7.360861 CCGTTTCACTTGAGCAGATTAATTACA 60.361 37.037 0.00 0.00 0.00 2.41
1475 1865 7.597386 CCATAATACCGTTTACCCTAGTAGTC 58.403 42.308 0.00 0.00 0.00 2.59
1510 1907 3.061563 TCGTTTCCGTCGCTAAAATCATG 59.938 43.478 0.00 0.00 35.01 3.07
1512 1909 4.088648 GTTTCCGTCGCTAAAATCATGTG 58.911 43.478 0.00 0.00 0.00 3.21
1519 1916 5.173312 CGTCGCTAAAATCATGTGGTAGTAG 59.827 44.000 0.00 0.00 0.00 2.57
1520 1917 5.047847 TCGCTAAAATCATGTGGTAGTAGC 58.952 41.667 0.00 0.00 0.00 3.58
1521 1918 4.808895 CGCTAAAATCATGTGGTAGTAGCA 59.191 41.667 0.00 0.00 33.86 3.49
1522 1919 5.293324 CGCTAAAATCATGTGGTAGTAGCAA 59.707 40.000 3.06 0.00 33.86 3.91
1523 1920 6.487103 GCTAAAATCATGTGGTAGTAGCAAC 58.513 40.000 3.06 0.00 34.29 4.17
1524 1921 5.545658 AAAATCATGTGGTAGTAGCAACG 57.454 39.130 3.06 0.00 0.00 4.10
1526 1923 4.672587 ATCATGTGGTAGTAGCAACGAT 57.327 40.909 3.06 3.92 0.00 3.73
1591 2377 3.531538 TCTTAATCAATGGCCAGACGTC 58.468 45.455 13.05 7.70 0.00 4.34
1712 2506 9.197694 ACTAAATCTTAATGCTACTATTGCTCG 57.802 33.333 0.00 0.00 0.00 5.03
1862 2924 9.952341 GTGTATTTGTTCTTTCAAAAGTCAAAC 57.048 29.630 19.45 11.53 40.06 2.93
1874 2936 2.301577 AGTCAAACGCTCCTATGCTC 57.698 50.000 0.00 0.00 0.00 4.26
2118 3795 8.869897 ACATACACGTATATATGCTGCATTTAC 58.130 33.333 21.56 17.24 32.92 2.01
2259 4066 0.242825 CGGGAAGAAGCAGTACGTGA 59.757 55.000 0.00 0.00 0.00 4.35
2267 4074 2.380410 GCAGTACGTGAAGTGGGCG 61.380 63.158 0.00 0.00 0.00 6.13
2295 4102 2.228480 GGCCACTACCTTGGGTCCA 61.228 63.158 0.00 0.00 37.09 4.02
2312 4119 2.030981 GTCCAACGACGACTTCTTCTCT 60.031 50.000 0.00 0.00 0.00 3.10
2318 4125 0.110147 ACGACTTCTTCTCTGACGCG 60.110 55.000 3.53 3.53 0.00 6.01
2327 4134 3.573772 CTCTGACGCGCTCACCCAA 62.574 63.158 5.73 0.00 0.00 4.12
2355 4162 6.681729 TCTACAAGAACCACATTAAGGTCT 57.318 37.500 0.00 0.00 38.76 3.85
2368 4319 5.604650 ACATTAAGGTCTCTCCCTCTTATGG 59.395 44.000 0.00 0.00 36.75 2.74
2370 4321 4.354208 AAGGTCTCTCCCTCTTATGGAA 57.646 45.455 0.00 0.00 36.75 3.53
2403 4387 6.416455 TGCACTGTATAGTTTTTCTTTTTGCG 59.584 34.615 0.00 0.00 34.07 4.85
2471 4470 1.134699 TGGAACAGAGGATGATCACGC 60.135 52.381 0.00 0.00 32.51 5.34
2575 4574 1.874345 GCGACCTCTCCGGAAAGACA 61.874 60.000 6.29 0.00 36.31 3.41
2646 4648 7.309177 CCTCAGTTCACTTCCTATATATCACG 58.691 42.308 0.00 0.00 0.00 4.35
2666 4668 2.929398 CGCCTGTTTATTTTGGCCATTC 59.071 45.455 6.09 0.00 42.15 2.67
2674 4680 3.979101 ATTTTGGCCATTCCGTTCATT 57.021 38.095 6.09 0.00 37.80 2.57
2698 4704 6.790285 AGTTTGATTTGATGGATTTGCAAC 57.210 33.333 0.00 0.00 0.00 4.17
2744 4750 0.804364 ATGTCCGCGTACGTCAAGTA 59.196 50.000 17.90 0.00 37.70 2.24
2772 4778 1.617804 CCCAAGCACATGGTGGAGATT 60.618 52.381 0.00 0.00 38.91 2.40
2868 4877 1.343465 ACCGACTTCGTCTCCAACAAT 59.657 47.619 0.00 0.00 37.74 2.71
2902 4911 2.047274 ACTTCGCCACCATCCACG 60.047 61.111 0.00 0.00 0.00 4.94
2934 4963 4.139038 ACCAGTGGTACGCAAAATAAGTT 58.861 39.130 14.87 0.00 44.14 2.66
3170 5223 1.440060 CGGCTACTTCCGCATGGTA 59.560 57.895 0.00 0.00 43.18 3.25
3202 5255 2.345991 CGCTTCCGTGAAGGGGAA 59.654 61.111 17.31 0.00 45.00 3.97
3450 5511 7.504238 TGGAATTATTTACATCGGGTTGCTAAT 59.496 33.333 0.00 0.00 0.00 1.73
3501 5562 2.696759 CGGGCCAACAAATCGTCCC 61.697 63.158 4.39 0.00 0.00 4.46
3513 5574 2.937959 ATCGTCCCTCTCCTCAGCCC 62.938 65.000 0.00 0.00 0.00 5.19
3515 5576 1.621377 GTCCCTCTCCTCAGCCCTA 59.379 63.158 0.00 0.00 0.00 3.53
3516 5577 0.032017 GTCCCTCTCCTCAGCCCTAA 60.032 60.000 0.00 0.00 0.00 2.69
3517 5578 0.944999 TCCCTCTCCTCAGCCCTAAT 59.055 55.000 0.00 0.00 0.00 1.73
3518 5579 1.133009 TCCCTCTCCTCAGCCCTAATC 60.133 57.143 0.00 0.00 0.00 1.75
3519 5580 1.347062 CCTCTCCTCAGCCCTAATCC 58.653 60.000 0.00 0.00 0.00 3.01
3520 5581 0.965439 CTCTCCTCAGCCCTAATCCG 59.035 60.000 0.00 0.00 0.00 4.18
3521 5582 0.556258 TCTCCTCAGCCCTAATCCGA 59.444 55.000 0.00 0.00 0.00 4.55
3540 5651 6.137794 TCCGAGTTATCTTTTTGTTTGCAA 57.862 33.333 0.00 0.00 0.00 4.08
3589 5700 7.336975 GTGTATGTCAAAACATTGCAGAAAAC 58.663 34.615 0.00 0.00 43.74 2.43
3656 5767 6.350103 TGTATGCAATAAATTCTCGGTGGTA 58.650 36.000 0.00 0.00 0.00 3.25
3790 6033 1.938577 AGAATCATCGCAGCATGTCAC 59.061 47.619 0.00 0.00 39.31 3.67
3791 6034 1.667212 GAATCATCGCAGCATGTCACA 59.333 47.619 0.00 0.00 39.31 3.58
3798 6041 2.352342 TCGCAGCATGTCACATAATGTG 59.648 45.455 8.14 8.14 43.04 3.21
3803 6046 7.336269 GCAGCATGTCACATAATGTGTTGGA 62.336 44.000 0.00 0.00 42.55 3.53
3845 6088 0.815213 TAGCATGCCAAGCGATCACC 60.815 55.000 15.66 0.00 37.01 4.02
3863 6106 5.452078 TCACCACATCAAAATCCTCAAAC 57.548 39.130 0.00 0.00 0.00 2.93
3927 6170 0.039074 CTCCCTCGATCATACACCGC 60.039 60.000 0.00 0.00 0.00 5.68
3931 6174 1.860950 CCTCGATCATACACCGCAAAG 59.139 52.381 0.00 0.00 0.00 2.77
3947 6190 1.136110 CAAAGAACTTTGGTTGCGGGT 59.864 47.619 16.57 0.00 44.47 5.28
3959 6202 0.250124 TTGCGGGTTGTAGTCACCAG 60.250 55.000 0.00 0.00 0.00 4.00
3980 6223 0.545171 AGGTCATCCATGGCAGTGAG 59.455 55.000 6.96 0.00 33.08 3.51
3982 6225 0.107312 GTCATCCATGGCAGTGAGCT 60.107 55.000 6.96 0.00 44.79 4.09
4000 6269 3.183237 GCTCGACGCTTGTGTTAAAAT 57.817 42.857 0.00 0.00 35.14 1.82
4013 6282 7.309805 GCTTGTGTTAAAATGGAAGAGGGTTAT 60.310 37.037 0.00 0.00 0.00 1.89
4076 6354 5.776519 GCATATAGCTAGAATGAGTGCAC 57.223 43.478 18.47 9.40 41.15 4.57
4080 6358 1.821753 AGCTAGAATGAGTGCACGAGT 59.178 47.619 12.01 0.75 0.00 4.18
4092 6370 0.320771 GCACGAGTGGGTCAAGTGAT 60.321 55.000 5.32 0.00 35.03 3.06
4100 6378 3.072915 AGTGGGTCAAGTGATCAACATCA 59.927 43.478 0.00 0.00 36.62 3.07
4106 6384 5.359009 GGTCAAGTGATCAACATCATGGAAT 59.641 40.000 0.00 0.00 41.26 3.01
4126 6404 8.162878 TGGAATGATGCAAAAATTTAAAGCAA 57.837 26.923 13.73 2.56 38.85 3.91
4131 6409 8.151141 TGATGCAAAAATTTAAAGCAACATGA 57.849 26.923 13.73 0.00 38.85 3.07
4138 6416 6.515272 AATTTAAAGCAACATGAGACGGAT 57.485 33.333 0.00 0.00 0.00 4.18
4159 6437 4.970662 TGAAAGCAATGCTAAGTGATCC 57.029 40.909 8.68 0.00 38.25 3.36
4160 6438 4.334552 TGAAAGCAATGCTAAGTGATCCA 58.665 39.130 8.68 0.00 38.25 3.41
4168 6446 6.652481 GCAATGCTAAGTGATCCATACACTAT 59.348 38.462 0.00 0.00 46.01 2.12
4173 6451 7.872993 TGCTAAGTGATCCATACACTATAAAGC 59.127 37.037 0.00 0.71 46.01 3.51
4211 6489 3.282021 CGGTCAGGTGATCCAAATCATT 58.718 45.455 0.00 0.00 43.62 2.57
4220 6498 7.485913 CAGGTGATCCAAATCATTTTTCTAACG 59.514 37.037 0.00 0.00 43.62 3.18
4291 6571 6.017109 CCCGTTTAATTGATGGAACCATAGAG 60.017 42.308 6.31 0.00 36.70 2.43
4351 6631 1.451504 CACACCTCAGAGGGCACAA 59.548 57.895 21.31 0.00 40.58 3.33
4352 6632 0.037303 CACACCTCAGAGGGCACAAT 59.963 55.000 21.31 0.00 40.58 2.71
4353 6633 0.773644 ACACCTCAGAGGGCACAATT 59.226 50.000 21.31 0.00 40.58 2.32
4354 6634 1.145738 ACACCTCAGAGGGCACAATTT 59.854 47.619 21.31 0.00 40.58 1.82
4355 6635 2.242043 CACCTCAGAGGGCACAATTTT 58.758 47.619 21.31 0.00 40.58 1.82
4356 6636 2.029649 CACCTCAGAGGGCACAATTTTG 60.030 50.000 21.31 2.54 40.58 2.44
4357 6637 2.158475 ACCTCAGAGGGCACAATTTTGA 60.158 45.455 21.31 0.00 40.58 2.69
4358 6638 2.229784 CCTCAGAGGGCACAATTTTGAC 59.770 50.000 8.88 0.00 0.00 3.18
4359 6639 2.886523 CTCAGAGGGCACAATTTTGACA 59.113 45.455 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 179 6.494842 TCTGGATTGTTTTCGAACTTGAAAG 58.505 36.000 0.00 0.00 38.92 2.62
230 244 6.196724 CCGAGTGATTAGTGAATTAGACGAAC 59.803 42.308 0.00 0.00 0.00 3.95
293 307 0.037590 TGGTGCGAATAAAGGGTGCT 59.962 50.000 0.00 0.00 0.00 4.40
490 537 3.066190 TCCGTAGCACTGTCCGGG 61.066 66.667 0.00 0.00 40.78 5.73
493 540 1.664321 ATCGGTCCGTAGCACTGTCC 61.664 60.000 11.88 0.00 0.00 4.02
514 673 1.086696 AATCATTCAACGCGGTCCTG 58.913 50.000 12.47 0.13 0.00 3.86
544 703 1.287425 CCTTAAACCGTCCGCATCTC 58.713 55.000 0.00 0.00 0.00 2.75
670 1013 2.152868 CGTGTGTTTAGCATTTTTGCCG 59.847 45.455 0.00 0.00 34.90 5.69
671 1014 2.474735 CCGTGTGTTTAGCATTTTTGCC 59.525 45.455 0.00 0.00 34.90 4.52
672 1015 2.474735 CCCGTGTGTTTAGCATTTTTGC 59.525 45.455 0.00 0.00 0.00 3.68
673 1016 2.474735 GCCCGTGTGTTTAGCATTTTTG 59.525 45.455 0.00 0.00 0.00 2.44
674 1017 2.547007 GGCCCGTGTGTTTAGCATTTTT 60.547 45.455 0.00 0.00 0.00 1.94
675 1018 1.000394 GGCCCGTGTGTTTAGCATTTT 60.000 47.619 0.00 0.00 0.00 1.82
677 1020 0.251165 AGGCCCGTGTGTTTAGCATT 60.251 50.000 0.00 0.00 0.00 3.56
678 1021 0.616371 TAGGCCCGTGTGTTTAGCAT 59.384 50.000 0.00 0.00 0.00 3.79
679 1022 0.616371 ATAGGCCCGTGTGTTTAGCA 59.384 50.000 0.00 0.00 0.00 3.49
680 1023 1.746470 AATAGGCCCGTGTGTTTAGC 58.254 50.000 0.00 0.00 0.00 3.09
681 1024 2.861935 CGTAATAGGCCCGTGTGTTTAG 59.138 50.000 0.00 0.00 0.00 1.85
682 1025 2.418471 CCGTAATAGGCCCGTGTGTTTA 60.418 50.000 0.00 0.00 0.00 2.01
683 1026 1.676615 CCGTAATAGGCCCGTGTGTTT 60.677 52.381 0.00 0.00 0.00 2.83
684 1027 0.108041 CCGTAATAGGCCCGTGTGTT 60.108 55.000 0.00 0.00 0.00 3.32
685 1028 1.518774 CCGTAATAGGCCCGTGTGT 59.481 57.895 0.00 0.00 0.00 3.72
686 1029 1.227438 CCCGTAATAGGCCCGTGTG 60.227 63.158 0.00 0.00 0.00 3.82
687 1030 2.437396 CCCCGTAATAGGCCCGTGT 61.437 63.158 0.00 0.00 0.00 4.49
688 1031 2.424302 CCCCGTAATAGGCCCGTG 59.576 66.667 0.00 0.00 0.00 4.94
689 1032 3.553363 GCCCCGTAATAGGCCCGT 61.553 66.667 0.00 0.00 43.76 5.28
694 1037 1.269936 CGGTAACAGCCCCGTAATAGG 60.270 57.143 0.00 0.00 39.38 2.57
695 1038 1.269936 CCGGTAACAGCCCCGTAATAG 60.270 57.143 0.00 0.00 42.67 1.73
696 1039 0.752054 CCGGTAACAGCCCCGTAATA 59.248 55.000 0.00 0.00 42.67 0.98
697 1040 1.523524 CCGGTAACAGCCCCGTAAT 59.476 57.895 0.00 0.00 42.67 1.89
698 1041 2.658064 CCCGGTAACAGCCCCGTAA 61.658 63.158 0.00 0.00 42.67 3.18
699 1042 3.076278 CCCGGTAACAGCCCCGTA 61.076 66.667 0.00 0.00 42.67 4.02
701 1044 2.182732 TAAACCCGGTAACAGCCCCG 62.183 60.000 0.00 0.00 43.82 5.73
702 1045 0.677731 GTAAACCCGGTAACAGCCCC 60.678 60.000 0.00 0.00 0.00 5.80
703 1046 0.325933 AGTAAACCCGGTAACAGCCC 59.674 55.000 0.00 0.00 0.00 5.19
704 1047 3.548745 ATAGTAAACCCGGTAACAGCC 57.451 47.619 0.00 0.00 0.00 4.85
705 1048 6.983474 TTTTATAGTAAACCCGGTAACAGC 57.017 37.500 0.00 0.00 0.00 4.40
706 1049 8.953368 AGATTTTATAGTAAACCCGGTAACAG 57.047 34.615 0.00 0.00 0.00 3.16
707 1050 8.761689 AGAGATTTTATAGTAAACCCGGTAACA 58.238 33.333 0.00 0.00 0.00 2.41
708 1051 9.254133 GAGAGATTTTATAGTAAACCCGGTAAC 57.746 37.037 0.00 0.00 0.00 2.50
709 1052 8.424133 GGAGAGATTTTATAGTAAACCCGGTAA 58.576 37.037 0.00 0.00 0.00 2.85
710 1053 7.564660 TGGAGAGATTTTATAGTAAACCCGGTA 59.435 37.037 0.00 0.00 0.00 4.02
711 1054 6.384886 TGGAGAGATTTTATAGTAAACCCGGT 59.615 38.462 0.00 0.00 0.00 5.28
712 1055 6.704937 GTGGAGAGATTTTATAGTAAACCCGG 59.295 42.308 0.00 0.00 0.00 5.73
713 1056 6.704937 GGTGGAGAGATTTTATAGTAAACCCG 59.295 42.308 0.00 0.00 0.00 5.28
714 1057 6.704937 CGGTGGAGAGATTTTATAGTAAACCC 59.295 42.308 0.00 0.00 0.00 4.11
715 1058 6.202379 GCGGTGGAGAGATTTTATAGTAAACC 59.798 42.308 0.00 0.00 0.00 3.27
716 1059 6.074463 CGCGGTGGAGAGATTTTATAGTAAAC 60.074 42.308 0.00 0.00 0.00 2.01
717 1060 5.981315 CGCGGTGGAGAGATTTTATAGTAAA 59.019 40.000 0.00 0.00 0.00 2.01
718 1061 5.526115 CGCGGTGGAGAGATTTTATAGTAA 58.474 41.667 0.00 0.00 0.00 2.24
719 1062 4.558095 GCGCGGTGGAGAGATTTTATAGTA 60.558 45.833 8.83 0.00 0.00 1.82
720 1063 3.799232 GCGCGGTGGAGAGATTTTATAGT 60.799 47.826 8.83 0.00 0.00 2.12
721 1064 2.731976 GCGCGGTGGAGAGATTTTATAG 59.268 50.000 8.83 0.00 0.00 1.31
722 1065 2.547218 GGCGCGGTGGAGAGATTTTATA 60.547 50.000 8.83 0.00 0.00 0.98
723 1066 1.583054 GCGCGGTGGAGAGATTTTAT 58.417 50.000 8.83 0.00 0.00 1.40
724 1067 0.461339 GGCGCGGTGGAGAGATTTTA 60.461 55.000 8.83 0.00 0.00 1.52
725 1068 1.745489 GGCGCGGTGGAGAGATTTT 60.745 57.895 8.83 0.00 0.00 1.82
726 1069 2.125106 GGCGCGGTGGAGAGATTT 60.125 61.111 8.83 0.00 0.00 2.17
727 1070 4.514577 CGGCGCGGTGGAGAGATT 62.515 66.667 8.83 0.00 0.00 2.40
733 1076 4.690719 AAATCACGGCGCGGTGGA 62.691 61.111 37.38 27.02 38.46 4.02
734 1077 3.661025 GAAAATCACGGCGCGGTGG 62.661 63.158 37.38 23.60 38.46 4.61
735 1078 2.202298 GAAAATCACGGCGCGGTG 60.202 61.111 34.54 34.54 39.29 4.94
736 1079 2.666862 TGAAAATCACGGCGCGGT 60.667 55.556 15.60 15.60 0.00 5.68
737 1080 2.098298 CTGAAAATCACGGCGCGG 59.902 61.111 14.03 14.03 0.00 6.46
738 1081 2.098298 CCTGAAAATCACGGCGCG 59.902 61.111 6.90 0.00 0.00 6.86
739 1082 1.154225 CACCTGAAAATCACGGCGC 60.154 57.895 6.90 0.00 0.00 6.53
740 1083 0.953471 TCCACCTGAAAATCACGGCG 60.953 55.000 4.80 4.80 0.00 6.46
741 1084 1.133025 CATCCACCTGAAAATCACGGC 59.867 52.381 0.00 0.00 0.00 5.68
742 1085 1.745087 CCATCCACCTGAAAATCACGG 59.255 52.381 0.00 0.00 0.00 4.94
743 1086 1.745087 CCCATCCACCTGAAAATCACG 59.255 52.381 0.00 0.00 0.00 4.35
744 1087 2.102578 CCCCATCCACCTGAAAATCAC 58.897 52.381 0.00 0.00 0.00 3.06
745 1088 1.619432 GCCCCATCCACCTGAAAATCA 60.619 52.381 0.00 0.00 0.00 2.57
746 1089 1.114627 GCCCCATCCACCTGAAAATC 58.885 55.000 0.00 0.00 0.00 2.17
747 1090 0.325577 GGCCCCATCCACCTGAAAAT 60.326 55.000 0.00 0.00 0.00 1.82
748 1091 1.078347 GGCCCCATCCACCTGAAAA 59.922 57.895 0.00 0.00 0.00 2.29
749 1092 1.734420 TTGGCCCCATCCACCTGAAA 61.734 55.000 0.00 0.00 35.50 2.69
750 1093 1.517538 ATTGGCCCCATCCACCTGAA 61.518 55.000 0.00 0.00 35.50 3.02
751 1094 1.935400 ATTGGCCCCATCCACCTGA 60.935 57.895 0.00 0.00 35.50 3.86
752 1095 1.456331 GATTGGCCCCATCCACCTG 60.456 63.158 0.00 0.00 35.50 4.00
753 1096 1.623686 AGATTGGCCCCATCCACCT 60.624 57.895 0.00 0.00 35.50 4.00
754 1097 1.152673 GAGATTGGCCCCATCCACC 60.153 63.158 0.00 0.00 35.50 4.61
755 1098 1.152673 GGAGATTGGCCCCATCCAC 60.153 63.158 0.00 0.00 35.50 4.02
756 1099 0.925720 AAGGAGATTGGCCCCATCCA 60.926 55.000 13.91 0.00 32.21 3.41
757 1100 0.178978 GAAGGAGATTGGCCCCATCC 60.179 60.000 0.00 2.37 0.00 3.51
758 1101 0.178978 GGAAGGAGATTGGCCCCATC 60.179 60.000 0.00 1.40 0.00 3.51
759 1102 0.628668 AGGAAGGAGATTGGCCCCAT 60.629 55.000 0.00 0.00 0.00 4.00
760 1103 0.850883 AAGGAAGGAGATTGGCCCCA 60.851 55.000 0.00 0.00 0.00 4.96
761 1104 1.222567 TAAGGAAGGAGATTGGCCCC 58.777 55.000 0.00 0.00 0.00 5.80
762 1105 4.724279 TTATAAGGAAGGAGATTGGCCC 57.276 45.455 0.00 0.00 0.00 5.80
763 1106 5.222130 TGGATTATAAGGAAGGAGATTGGCC 60.222 44.000 0.00 0.00 0.00 5.36
764 1107 5.880901 TGGATTATAAGGAAGGAGATTGGC 58.119 41.667 0.00 0.00 0.00 4.52
769 1112 9.862149 GGTTTTATTGGATTATAAGGAAGGAGA 57.138 33.333 0.00 0.00 0.00 3.71
770 1113 9.868160 AGGTTTTATTGGATTATAAGGAAGGAG 57.132 33.333 0.00 0.00 0.00 3.69
773 1116 9.750125 GCAAGGTTTTATTGGATTATAAGGAAG 57.250 33.333 0.00 0.00 0.00 3.46
774 1117 8.700973 GGCAAGGTTTTATTGGATTATAAGGAA 58.299 33.333 0.00 0.00 0.00 3.36
775 1118 7.841729 TGGCAAGGTTTTATTGGATTATAAGGA 59.158 33.333 0.00 0.00 0.00 3.36
776 1119 8.017418 TGGCAAGGTTTTATTGGATTATAAGG 57.983 34.615 0.00 0.00 0.00 2.69
777 1120 9.480053 CATGGCAAGGTTTTATTGGATTATAAG 57.520 33.333 0.00 0.00 0.00 1.73
778 1121 8.986991 ACATGGCAAGGTTTTATTGGATTATAA 58.013 29.630 0.00 0.00 0.00 0.98
779 1122 8.546083 ACATGGCAAGGTTTTATTGGATTATA 57.454 30.769 0.00 0.00 0.00 0.98
780 1123 7.436320 ACATGGCAAGGTTTTATTGGATTAT 57.564 32.000 0.00 0.00 0.00 1.28
781 1124 6.405286 CGACATGGCAAGGTTTTATTGGATTA 60.405 38.462 0.00 0.00 0.00 1.75
782 1125 5.624281 CGACATGGCAAGGTTTTATTGGATT 60.624 40.000 0.00 0.00 0.00 3.01
783 1126 4.142182 CGACATGGCAAGGTTTTATTGGAT 60.142 41.667 0.00 0.00 0.00 3.41
784 1127 3.192422 CGACATGGCAAGGTTTTATTGGA 59.808 43.478 0.00 0.00 0.00 3.53
785 1128 3.510719 CGACATGGCAAGGTTTTATTGG 58.489 45.455 0.00 0.00 0.00 3.16
786 1129 3.192422 TCCGACATGGCAAGGTTTTATTG 59.808 43.478 0.00 0.00 37.80 1.90
787 1130 3.426615 TCCGACATGGCAAGGTTTTATT 58.573 40.909 0.00 0.00 37.80 1.40
788 1131 3.016736 CTCCGACATGGCAAGGTTTTAT 58.983 45.455 0.00 0.00 37.80 1.40
789 1132 2.432444 CTCCGACATGGCAAGGTTTTA 58.568 47.619 0.00 0.00 37.80 1.52
790 1133 1.247567 CTCCGACATGGCAAGGTTTT 58.752 50.000 0.00 0.00 37.80 2.43
791 1134 0.609131 CCTCCGACATGGCAAGGTTT 60.609 55.000 8.56 0.00 37.80 3.27
792 1135 1.002134 CCTCCGACATGGCAAGGTT 60.002 57.895 8.56 0.00 37.80 3.50
793 1136 2.671070 CCTCCGACATGGCAAGGT 59.329 61.111 8.56 0.00 37.80 3.50
799 1142 2.187946 GGAGTGCCTCCGACATGG 59.812 66.667 5.60 0.00 41.08 3.66
806 1149 1.078637 GGGTTTACGGAGTGCCTCC 60.079 63.158 10.35 10.35 45.73 4.30
807 1150 0.108281 GAGGGTTTACGGAGTGCCTC 60.108 60.000 0.00 0.00 45.73 4.70
808 1151 1.551019 GGAGGGTTTACGGAGTGCCT 61.551 60.000 0.00 0.00 45.73 4.75
809 1152 1.078637 GGAGGGTTTACGGAGTGCC 60.079 63.158 0.00 0.00 45.73 5.01
810 1153 1.447314 CGGAGGGTTTACGGAGTGC 60.447 63.158 0.00 0.00 45.73 4.40
811 1154 1.176527 TACGGAGGGTTTACGGAGTG 58.823 55.000 0.00 0.00 45.73 3.51
813 1156 1.545582 TGTTACGGAGGGTTTACGGAG 59.454 52.381 0.00 0.00 0.00 4.63
814 1157 1.545582 CTGTTACGGAGGGTTTACGGA 59.454 52.381 0.00 0.00 0.00 4.69
815 1158 1.404583 CCTGTTACGGAGGGTTTACGG 60.405 57.143 0.00 0.00 0.00 4.02
816 1159 2.000429 CCTGTTACGGAGGGTTTACG 58.000 55.000 0.00 0.00 0.00 3.18
817 1160 1.676916 GGCCTGTTACGGAGGGTTTAC 60.677 57.143 0.00 0.00 0.00 2.01
818 1161 0.614812 GGCCTGTTACGGAGGGTTTA 59.385 55.000 0.00 0.00 0.00 2.01
819 1162 1.377612 GGCCTGTTACGGAGGGTTT 59.622 57.895 0.00 0.00 0.00 3.27
820 1163 2.599757 GGGCCTGTTACGGAGGGTT 61.600 63.158 0.84 0.00 0.00 4.11
821 1164 3.007323 GGGCCTGTTACGGAGGGT 61.007 66.667 0.84 0.00 0.00 4.34
822 1165 4.157120 CGGGCCTGTTACGGAGGG 62.157 72.222 2.29 0.00 0.00 4.30
823 1166 3.387947 ACGGGCCTGTTACGGAGG 61.388 66.667 12.85 0.00 0.00 4.30
824 1167 2.125673 CACGGGCCTGTTACGGAG 60.126 66.667 16.73 0.00 0.00 4.63
825 1168 4.382320 GCACGGGCCTGTTACGGA 62.382 66.667 16.73 0.00 0.00 4.69
835 1178 1.152383 GAGACGAAATAGGCACGGGC 61.152 60.000 0.00 0.00 40.13 6.13
836 1179 0.870307 CGAGACGAAATAGGCACGGG 60.870 60.000 0.00 0.00 29.63 5.28
837 1180 1.480219 GCGAGACGAAATAGGCACGG 61.480 60.000 0.00 0.00 33.85 4.94
838 1181 1.480219 GGCGAGACGAAATAGGCACG 61.480 60.000 0.00 0.00 36.32 5.34
839 1182 1.480219 CGGCGAGACGAAATAGGCAC 61.480 60.000 0.00 0.00 35.47 5.01
840 1183 1.226859 CGGCGAGACGAAATAGGCA 60.227 57.895 0.00 0.00 35.47 4.75
841 1184 1.226888 ACGGCGAGACGAAATAGGC 60.227 57.895 16.62 0.00 37.61 3.93
842 1185 1.480219 GCACGGCGAGACGAAATAGG 61.480 60.000 16.62 0.00 37.61 2.57
843 1186 1.480219 GGCACGGCGAGACGAAATAG 61.480 60.000 16.62 0.00 37.61 1.73
844 1187 1.517694 GGCACGGCGAGACGAAATA 60.518 57.895 16.62 0.00 37.61 1.40
845 1188 1.940883 TAGGCACGGCGAGACGAAAT 61.941 55.000 16.62 0.00 37.61 2.17
846 1189 1.940883 ATAGGCACGGCGAGACGAAA 61.941 55.000 16.62 0.00 37.61 3.46
847 1190 1.096967 TATAGGCACGGCGAGACGAA 61.097 55.000 16.62 1.50 37.61 3.85
848 1191 0.887836 ATATAGGCACGGCGAGACGA 60.888 55.000 16.62 4.04 37.61 4.20
903 1259 1.873270 CGGTCGATCACCTGTGTGGA 61.873 60.000 11.12 0.00 44.21 4.02
1148 1504 3.286915 AACCCGTCGGCGTAGAACC 62.287 63.158 9.28 0.00 36.15 3.62
1359 1715 1.517276 CGTTCAACGTGAGACAGACAC 59.483 52.381 0.39 0.00 36.74 3.67
1360 1716 1.535226 CCGTTCAACGTGAGACAGACA 60.535 52.381 9.52 0.00 40.58 3.41
1361 1717 1.129326 CCGTTCAACGTGAGACAGAC 58.871 55.000 9.52 0.00 40.58 3.51
1362 1718 0.596600 GCCGTTCAACGTGAGACAGA 60.597 55.000 9.52 0.00 40.58 3.41
1405 1795 2.613026 TCTGCTCAAGTGAAACGGAA 57.387 45.000 0.00 0.00 45.86 4.30
1413 1803 6.408858 ACGTGTAATTAATCTGCTCAAGTG 57.591 37.500 0.00 0.00 0.00 3.16
1417 1807 4.501559 GCGTACGTGTAATTAATCTGCTCA 59.498 41.667 17.90 0.00 0.00 4.26
1433 1823 0.533491 TGGCTATCTTTGGCGTACGT 59.467 50.000 17.90 0.00 0.00 3.57
1510 1907 5.404946 TGTCTAAATCGTTGCTACTACCAC 58.595 41.667 0.00 0.00 0.00 4.16
1512 1909 5.888105 TCTGTCTAAATCGTTGCTACTACC 58.112 41.667 0.00 0.00 0.00 3.18
1519 1916 3.932710 TGTCCATCTGTCTAAATCGTTGC 59.067 43.478 0.00 0.00 0.00 4.17
1520 1917 4.031765 CGTGTCCATCTGTCTAAATCGTTG 59.968 45.833 0.00 0.00 0.00 4.10
1521 1918 4.082408 TCGTGTCCATCTGTCTAAATCGTT 60.082 41.667 0.00 0.00 0.00 3.85
1522 1919 3.442625 TCGTGTCCATCTGTCTAAATCGT 59.557 43.478 0.00 0.00 0.00 3.73
1523 1920 4.028852 TCGTGTCCATCTGTCTAAATCG 57.971 45.455 0.00 0.00 0.00 3.34
1524 1921 8.491152 CATTATTCGTGTCCATCTGTCTAAATC 58.509 37.037 0.00 0.00 0.00 2.17
1526 1923 7.327975 ACATTATTCGTGTCCATCTGTCTAAA 58.672 34.615 0.00 0.00 0.00 1.85
1621 2415 5.012328 TGGGCAAACGAGTAAAACATTTT 57.988 34.783 0.00 0.00 0.00 1.82
1665 2459 6.952935 AGTGAGCAGTAAGATTTTAACGAG 57.047 37.500 0.00 0.00 0.00 4.18
1666 2460 8.821147 TTTAGTGAGCAGTAAGATTTTAACGA 57.179 30.769 0.00 0.00 0.00 3.85
1667 2461 9.690434 GATTTAGTGAGCAGTAAGATTTTAACG 57.310 33.333 0.00 0.00 0.00 3.18
1674 2468 9.050601 GCATTAAGATTTAGTGAGCAGTAAGAT 57.949 33.333 0.00 0.00 0.00 2.40
1675 2469 8.260818 AGCATTAAGATTTAGTGAGCAGTAAGA 58.739 33.333 0.00 0.00 0.00 2.10
1680 2474 9.703892 ATAGTAGCATTAAGATTTAGTGAGCAG 57.296 33.333 0.00 0.00 0.00 4.24
1697 2491 8.438676 AAGATTTTAACGAGCAATAGTAGCAT 57.561 30.769 0.00 0.00 0.00 3.79
1862 2924 2.030262 GGCCAGAGCATAGGAGCG 59.970 66.667 0.00 0.00 42.56 5.03
1874 2936 3.902218 TGATTAAGATCTTTGGGGCCAG 58.098 45.455 14.36 0.00 33.28 4.85
1994 3538 6.640907 CAGTACAATGAAACCTTTTTGCTACC 59.359 38.462 0.00 0.00 0.00 3.18
2295 4102 2.349627 CGTCAGAGAAGAAGTCGTCGTT 60.350 50.000 0.00 0.00 0.00 3.85
2312 4119 4.228567 TGTTGGGTGAGCGCGTCA 62.229 61.111 8.43 7.68 0.00 4.35
2318 4125 2.543777 TGTAGAACTGTTGGGTGAGC 57.456 50.000 0.00 0.00 0.00 4.26
2348 4155 5.043281 ACTTCCATAAGAGGGAGAGACCTTA 60.043 44.000 0.00 0.00 42.10 2.69
2355 4162 3.055094 GCAACACTTCCATAAGAGGGAGA 60.055 47.826 0.00 0.00 36.25 3.71
2471 4470 2.325761 CCTCGTGAAGGTGTTTACTCG 58.674 52.381 0.00 0.00 40.67 4.18
2554 4553 0.898789 TCTTTCCGGAGAGGTCGCTT 60.899 55.000 21.05 0.00 41.99 4.68
2575 4574 0.608640 GTGAGTGACCGACCTCCATT 59.391 55.000 0.00 0.00 0.00 3.16
2612 4614 4.384647 GGAAGTGAACTGAGGCCATAGATT 60.385 45.833 5.01 0.00 0.00 2.40
2646 4648 3.270027 GGAATGGCCAAAATAAACAGGC 58.730 45.455 10.96 0.00 36.34 4.85
2666 4668 6.851609 TCCATCAAATCAAACTAATGAACGG 58.148 36.000 0.00 0.00 32.06 4.44
2674 4680 7.669427 AGTTGCAAATCCATCAAATCAAACTA 58.331 30.769 0.00 0.00 0.00 2.24
2744 4750 2.879233 ATGTGCTTGGGGTCGACGT 61.879 57.895 9.92 0.00 0.00 4.34
2772 4778 0.251916 CGTAGAACCCTTCCATGCCA 59.748 55.000 0.00 0.00 0.00 4.92
2902 4911 0.323725 TACCACTGGTCGGGGTAGAC 60.324 60.000 3.21 0.00 37.09 2.59
2934 4963 2.032620 GTTCGGGCTAGGAGAAGATGA 58.967 52.381 0.00 0.00 0.00 2.92
2963 5003 0.437295 GCGCGAGTGACACGTTTAAT 59.563 50.000 12.10 0.00 0.00 1.40
2964 5004 1.847975 GCGCGAGTGACACGTTTAA 59.152 52.632 12.10 0.00 0.00 1.52
2966 5013 3.688330 CGCGCGAGTGACACGTTT 61.688 61.111 28.94 0.00 46.66 3.60
3170 5223 0.666913 AAGCGTAGATGGCGTCGTAT 59.333 50.000 0.13 0.00 35.00 3.06
3450 5511 2.802787 GCCTAGCGCTCTTCTATTCA 57.197 50.000 16.34 0.00 0.00 2.57
3476 5537 4.966787 TTGTTGGCCCGCTGTCCC 62.967 66.667 0.00 0.00 0.00 4.46
3481 5542 2.282180 ACGATTTGTTGGCCCGCT 60.282 55.556 0.00 0.00 0.00 5.52
3487 5548 1.279271 AGGAGAGGGACGATTTGTTGG 59.721 52.381 0.00 0.00 0.00 3.77
3501 5562 0.965439 CGGATTAGGGCTGAGGAGAG 59.035 60.000 0.00 0.00 0.00 3.20
3513 5574 8.020819 TGCAAACAAAAAGATAACTCGGATTAG 58.979 33.333 0.00 0.00 0.00 1.73
3515 5576 6.744112 TGCAAACAAAAAGATAACTCGGATT 58.256 32.000 0.00 0.00 0.00 3.01
3516 5577 6.325919 TGCAAACAAAAAGATAACTCGGAT 57.674 33.333 0.00 0.00 0.00 4.18
3517 5578 5.759506 TGCAAACAAAAAGATAACTCGGA 57.240 34.783 0.00 0.00 0.00 4.55
3518 5579 6.420604 ACATTGCAAACAAAAAGATAACTCGG 59.579 34.615 1.71 0.00 39.77 4.63
3519 5580 7.167302 TGACATTGCAAACAAAAAGATAACTCG 59.833 33.333 1.71 0.00 39.77 4.18
3520 5581 8.351495 TGACATTGCAAACAAAAAGATAACTC 57.649 30.769 1.71 0.00 39.77 3.01
3521 5582 8.891671 ATGACATTGCAAACAAAAAGATAACT 57.108 26.923 1.71 0.00 39.77 2.24
3540 5651 6.662234 ACCAAGAAGAAATGATGTGATGACAT 59.338 34.615 0.00 0.00 46.01 3.06
3589 5700 6.889494 TGTATTTGCTTGAATTGTTGCAATG 58.111 32.000 0.59 0.00 43.53 2.82
3636 5747 3.625764 GCTACCACCGAGAATTTATTGCA 59.374 43.478 0.00 0.00 0.00 4.08
3637 5748 3.625764 TGCTACCACCGAGAATTTATTGC 59.374 43.478 0.00 0.00 0.00 3.56
3650 5761 1.975660 TGGAGTTTGTTGCTACCACC 58.024 50.000 0.00 0.00 0.00 4.61
3656 5767 5.471456 CACTTCTCTTATGGAGTTTGTTGCT 59.529 40.000 0.00 0.00 42.40 3.91
3758 6001 3.004839 GCGATGATTCTAGGTGTCTGCTA 59.995 47.826 0.00 0.00 0.00 3.49
3825 6068 0.585357 GTGATCGCTTGGCATGCTAG 59.415 55.000 18.92 15.85 0.00 3.42
3828 6071 2.409055 TGGTGATCGCTTGGCATGC 61.409 57.895 9.90 9.90 0.00 4.06
3845 6088 3.244976 GCGGTTTGAGGATTTTGATGTG 58.755 45.455 0.00 0.00 0.00 3.21
3863 6106 1.597742 CTCCATATTGAGGTTGGCGG 58.402 55.000 0.00 0.00 0.00 6.13
3908 6151 0.039074 GCGGTGTATGATCGAGGGAG 60.039 60.000 0.00 0.00 0.00 4.30
3927 6170 1.136110 ACCCGCAACCAAAGTTCTTTG 59.864 47.619 15.72 15.72 32.45 2.77
3931 6174 0.458260 ACAACCCGCAACCAAAGTTC 59.542 50.000 0.00 0.00 32.45 3.01
3959 6202 0.465097 CACTGCCATGGATGACCTCC 60.465 60.000 18.40 0.00 45.19 4.30
3982 6225 3.132160 TCCATTTTAACACAAGCGTCGA 58.868 40.909 0.00 0.00 0.00 4.20
4000 6269 4.967871 TCTCCCTTAATAACCCTCTTCCA 58.032 43.478 0.00 0.00 0.00 3.53
4030 6299 3.055819 GCTTCTCCTCTATCACCACAACA 60.056 47.826 0.00 0.00 0.00 3.33
4068 6337 1.681486 TTGACCCACTCGTGCACTCA 61.681 55.000 16.19 6.94 0.00 3.41
4076 6354 2.069273 GTTGATCACTTGACCCACTCG 58.931 52.381 0.00 0.00 0.00 4.18
4080 6358 3.786368 TGATGTTGATCACTTGACCCA 57.214 42.857 0.00 0.00 33.40 4.51
4100 6378 8.338072 TGCTTTAAATTTTTGCATCATTCCAT 57.662 26.923 0.00 0.00 0.00 3.41
4106 6384 8.151141 TCATGTTGCTTTAAATTTTTGCATCA 57.849 26.923 17.49 17.49 37.62 3.07
4112 6390 7.206687 TCCGTCTCATGTTGCTTTAAATTTTT 58.793 30.769 0.00 0.00 0.00 1.94
4118 6396 4.574892 TCATCCGTCTCATGTTGCTTTAA 58.425 39.130 0.00 0.00 0.00 1.52
4126 6404 2.768253 TGCTTTCATCCGTCTCATGT 57.232 45.000 0.00 0.00 0.00 3.21
4131 6409 2.119801 AGCATTGCTTTCATCCGTCT 57.880 45.000 5.03 0.00 33.89 4.18
4138 6416 4.334552 TGGATCACTTAGCATTGCTTTCA 58.665 39.130 17.71 0.00 40.44 2.69
4159 6437 5.744345 GGATCGGATCGCTTTATAGTGTATG 59.256 44.000 11.62 0.00 33.54 2.39
4160 6438 5.448768 CGGATCGGATCGCTTTATAGTGTAT 60.449 44.000 11.62 0.00 33.54 2.29
4168 6446 1.067846 CCATCGGATCGGATCGCTTTA 60.068 52.381 12.50 0.00 0.00 1.85
4173 6451 1.154207 CGTCCATCGGATCGGATCG 60.154 63.158 12.50 9.93 32.73 3.69
4243 6523 6.351286 GGGGAGTTACATCGTCCTTTACTTAA 60.351 42.308 0.00 0.00 0.00 1.85
4244 6524 5.127682 GGGGAGTTACATCGTCCTTTACTTA 59.872 44.000 0.00 0.00 0.00 2.24
4291 6571 7.012943 GCTTTTGTTTTGTTTTGTACTTGGTC 58.987 34.615 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.