Multiple sequence alignment - TraesCS2D01G054000

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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 TraesCS2D01G054000 chr2D 100.000 2831 0 0 1 2831 21555584 21552754 0.000000e+00 5228
1 TraesCS2D01G054000 chr2D 89.674 368 38 0 1 368 21057393 21057026 1.190000e-128 470
2 TraesCS2D01G054000 chr2D 82.480 371 60 5 1 368 22119731 22120099 1.270000e-83 320
3 TraesCS2D01G054000 chr2D 83.186 339 57 0 1 339 22144656 22144994 7.620000e-81 311
4 TraesCS2D01G054000 chr2A 85.913 1150 155 5 973 2122 22572278 22571136 0.000000e+00 1219
5 TraesCS2D01G054000 chr2A 79.237 891 173 10 983 1869 23960065 23960947 6.700000e-171 610
6 TraesCS2D01G054000 chr2A 84.991 573 78 7 1074 1644 23268638 23268072 2.450000e-160 575
7 TraesCS2D01G054000 chr2A 84.991 573 78 7 1074 1644 23290701 23290135 2.450000e-160 575
8 TraesCS2D01G054000 chr2A 84.775 578 76 10 1071 1644 22836544 22837113 1.140000e-158 569
9 TraesCS2D01G054000 chr2A 92.391 368 28 0 1 368 22573250 22572883 2.500000e-145 525
10 TraesCS2D01G054000 chr2A 83.776 339 55 0 1 339 23959155 23959493 3.520000e-84 322
11 TraesCS2D01G054000 chr2A 81.481 297 45 8 2540 2831 22620784 22620493 4.710000e-58 235
12 TraesCS2D01G054000 chr2A 81.481 297 45 8 2540 2831 22653166 22652875 4.710000e-58 235
13 TraesCS2D01G054000 chr2A 81.481 297 45 8 2540 2831 22800694 22800985 4.710000e-58 235
14 TraesCS2D01G054000 chr2B 78.229 1796 329 39 1074 2831 34478374 34476603 0.000000e+00 1094
15 TraesCS2D01G054000 chr2B 78.179 1801 322 52 1074 2831 34456876 34455104 0.000000e+00 1083
16 TraesCS2D01G054000 chr2B 83.319 1127 166 16 979 2096 34419498 34418385 0.000000e+00 1020
17 TraesCS2D01G054000 chr2B 80.902 1042 182 14 1074 2108 34442901 34441870 0.000000e+00 806
18 TraesCS2D01G054000 chr2B 92.935 368 26 0 1 368 34420395 34420028 1.150000e-148 536
19 TraesCS2D01G054000 chr5A 87.679 349 43 0 1 349 327574217 327574565 9.440000e-110 407
20 TraesCS2D01G054000 chr5D 87.393 349 44 0 1 349 229153650 229153302 4.390000e-108 401
21 TraesCS2D01G054000 chr5D 82.831 332 56 1 16 347 75912820 75912490 2.130000e-76 296
22 TraesCS2D01G054000 chrUn 81.481 297 45 8 2540 2831 146897158 146897449 4.710000e-58 235
23 TraesCS2D01G054000 chrUn 81.481 297 45 8 2540 2831 146912134 146912425 4.710000e-58 235
24 TraesCS2D01G054000 chrUn 81.481 297 45 8 2540 2831 147070703 147070994 4.710000e-58 235
25 TraesCS2D01G054000 chrUn 81.605 299 41 12 2540 2831 154095498 154095789 4.710000e-58 235
26 TraesCS2D01G054000 chrUn 81.481 297 45 8 2540 2831 210800472 210800181 4.710000e-58 235
27 TraesCS2D01G054000 chrUn 81.481 297 45 8 2540 2831 252347217 252346926 4.710000e-58 235


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 TraesCS2D01G054000 chr2D 21552754 21555584 2830 True 5228 5228 100.0000 1 2831 1 chr2D.!!$R2 2830
1 TraesCS2D01G054000 chr2A 22571136 22573250 2114 True 872 1219 89.1520 1 2122 2 chr2A.!!$R5 2121
2 TraesCS2D01G054000 chr2A 23268072 23268638 566 True 575 575 84.9910 1074 1644 1 chr2A.!!$R3 570
3 TraesCS2D01G054000 chr2A 23290135 23290701 566 True 575 575 84.9910 1074 1644 1 chr2A.!!$R4 570
4 TraesCS2D01G054000 chr2A 22836544 22837113 569 False 569 569 84.7750 1071 1644 1 chr2A.!!$F2 573
5 TraesCS2D01G054000 chr2A 23959155 23960947 1792 False 466 610 81.5065 1 1869 2 chr2A.!!$F3 1868
6 TraesCS2D01G054000 chr2B 34476603 34478374 1771 True 1094 1094 78.2290 1074 2831 1 chr2B.!!$R3 1757
7 TraesCS2D01G054000 chr2B 34455104 34456876 1772 True 1083 1083 78.1790 1074 2831 1 chr2B.!!$R2 1757
8 TraesCS2D01G054000 chr2B 34441870 34442901 1031 True 806 806 80.9020 1074 2108 1 chr2B.!!$R1 1034
9 TraesCS2D01G054000 chr2B 34418385 34420395 2010 True 778 1020 88.1270 1 2096 2 chr2B.!!$R4 2095

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
789 1053 0.03601 ACAGTGGCCTCATGTGCTAC 60.036 55.0 15.05 15.05 40.15 3.58 F
1027 1544 0.03601 AACATGGAGAGCGAAGGTGG 60.036 55.0 0.00 0.00 39.88 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 2143 0.319083 TCCGTACTCGCACACCAATT 59.681 50.0 0.0 0.0 35.54 2.32 R
2779 3334 0.465705 AGGTCGCCATGTCCTATGTG 59.534 55.0 0.0 0.0 34.07 3.21 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
320 321 0.387929 TGCTCGTCAACTCTTTCCGT 59.612 50.000 0.00 0.00 0.00 4.69
368 369 1.043022 TGAGACTTGTCTGCTCTGCA 58.957 50.000 8.11 0.00 36.92 4.41
398 616 4.970003 CGTTTGTGCTTAAAGAAGTCCTTG 59.030 41.667 0.00 0.00 34.79 3.61
407 625 8.919145 TGCTTAAAGAAGTCCTTGGAAATTAAA 58.081 29.630 0.00 0.00 34.79 1.52
416 634 7.645402 AGTCCTTGGAAATTAAACTTTACACG 58.355 34.615 0.00 0.00 28.66 4.49
420 638 8.132995 CCTTGGAAATTAAACTTTACACGTTCT 58.867 33.333 0.00 0.00 28.66 3.01
427 645 2.901249 ACTTTACACGTTCTGCACTGT 58.099 42.857 0.00 0.00 0.00 3.55
440 658 0.320596 GCACTGTTGAGAGCAGAGCT 60.321 55.000 7.31 0.00 43.69 4.09
443 661 3.657634 CACTGTTGAGAGCAGAGCTTTA 58.342 45.455 0.00 0.00 39.88 1.85
451 669 8.796475 TGTTGAGAGCAGAGCTTTATAATTTTT 58.204 29.630 0.00 0.00 39.88 1.94
485 703 9.761504 TGACAAAGAATGAATTTTATTTGCTCA 57.238 25.926 8.99 9.02 32.30 4.26
568 800 7.548196 TCTAAATATCTTACCAACAAAGCCG 57.452 36.000 0.00 0.00 0.00 5.52
570 802 6.584185 AAATATCTTACCAACAAAGCCGTT 57.416 33.333 0.00 0.00 0.00 4.44
571 803 3.915437 ATCTTACCAACAAAGCCGTTG 57.085 42.857 4.66 4.66 44.78 4.10
572 804 1.335496 TCTTACCAACAAAGCCGTTGC 59.665 47.619 5.88 0.00 44.01 4.17
573 805 0.386113 TTACCAACAAAGCCGTTGCC 59.614 50.000 5.88 0.00 44.01 4.52
575 807 1.326951 ACCAACAAAGCCGTTGCCTT 61.327 50.000 5.88 0.00 44.01 4.35
577 809 0.102120 CAACAAAGCCGTTGCCTTCA 59.898 50.000 0.00 0.00 41.31 3.02
578 810 1.039856 AACAAAGCCGTTGCCTTCAT 58.960 45.000 0.00 0.00 41.31 2.57
579 811 0.598065 ACAAAGCCGTTGCCTTCATC 59.402 50.000 0.00 0.00 41.31 2.92
580 812 0.597568 CAAAGCCGTTGCCTTCATCA 59.402 50.000 0.00 0.00 38.69 3.07
585 817 3.088532 AGCCGTTGCCTTCATCATTTAA 58.911 40.909 0.00 0.00 38.69 1.52
589 821 5.226396 CCGTTGCCTTCATCATTTAACAAA 58.774 37.500 0.00 0.00 0.00 2.83
593 825 7.754924 CGTTGCCTTCATCATTTAACAAATAGT 59.245 33.333 0.00 0.00 0.00 2.12
641 873 8.780249 GTTTATAAGAGGAGTAAAGCACAACAA 58.220 33.333 0.00 0.00 0.00 2.83
643 875 5.757850 AAGAGGAGTAAAGCACAACAAAG 57.242 39.130 0.00 0.00 0.00 2.77
644 876 5.036117 AGAGGAGTAAAGCACAACAAAGA 57.964 39.130 0.00 0.00 0.00 2.52
647 879 4.335594 AGGAGTAAAGCACAACAAAGACAC 59.664 41.667 0.00 0.00 0.00 3.67
648 880 4.335594 GGAGTAAAGCACAACAAAGACACT 59.664 41.667 0.00 0.00 0.00 3.55
649 881 5.485662 AGTAAAGCACAACAAAGACACTC 57.514 39.130 0.00 0.00 0.00 3.51
650 882 3.782889 AAAGCACAACAAAGACACTCC 57.217 42.857 0.00 0.00 0.00 3.85
672 933 2.859165 ACACATGACAGGGTGTAAGG 57.141 50.000 12.53 0.00 45.77 2.69
677 938 1.198759 TGACAGGGTGTAAGGGGAGC 61.199 60.000 0.00 0.00 0.00 4.70
680 941 2.267961 GGGTGTAAGGGGAGCACG 59.732 66.667 0.00 0.00 34.25 5.34
685 948 1.135170 GTGTAAGGGGAGCACGTCTAC 60.135 57.143 0.00 0.00 0.00 2.59
689 952 0.624785 AGGGGAGCACGTCTACTACT 59.375 55.000 0.00 0.00 0.00 2.57
723 986 9.533253 AATCTTTTGTTCCACATTTCTAACAAG 57.467 29.630 0.00 0.00 41.38 3.16
728 991 5.997746 TGTTCCACATTTCTAACAAGAGGAG 59.002 40.000 0.00 0.00 0.00 3.69
730 993 4.844085 TCCACATTTCTAACAAGAGGAGGA 59.156 41.667 0.00 0.00 0.00 3.71
731 994 4.938226 CCACATTTCTAACAAGAGGAGGAC 59.062 45.833 0.00 0.00 0.00 3.85
734 997 0.809385 TCTAACAAGAGGAGGACGCG 59.191 55.000 3.53 3.53 0.00 6.01
738 1001 0.319641 ACAAGAGGAGGACGCGAAAC 60.320 55.000 15.93 1.49 0.00 2.78
750 1014 0.974836 CGCGAAACGGAAAATTCAGC 59.025 50.000 0.00 0.00 38.44 4.26
751 1015 1.399727 CGCGAAACGGAAAATTCAGCT 60.400 47.619 0.00 0.00 38.44 4.24
753 1017 2.405025 GCGAAACGGAAAATTCAGCTTG 59.595 45.455 0.00 0.00 0.00 4.01
756 1020 4.737765 CGAAACGGAAAATTCAGCTTGAAA 59.262 37.500 3.27 0.00 40.12 2.69
760 1024 9.567848 GAAACGGAAAATTCAGCTTGAAATATA 57.432 29.630 3.27 0.00 40.12 0.86
763 1027 8.137437 ACGGAAAATTCAGCTTGAAATATATGG 58.863 33.333 3.27 0.00 40.12 2.74
764 1028 8.137437 CGGAAAATTCAGCTTGAAATATATGGT 58.863 33.333 3.27 0.00 40.12 3.55
766 1030 9.252962 GAAAATTCAGCTTGAAATATATGGTGG 57.747 33.333 3.27 0.00 40.12 4.61
767 1031 8.537728 AAATTCAGCTTGAAATATATGGTGGA 57.462 30.769 3.27 0.00 40.12 4.02
771 1035 4.823989 AGCTTGAAATATATGGTGGAGCAC 59.176 41.667 9.56 0.00 0.00 4.40
773 1037 5.278169 GCTTGAAATATATGGTGGAGCACAG 60.278 44.000 0.00 0.00 35.86 3.66
774 1038 5.372343 TGAAATATATGGTGGAGCACAGT 57.628 39.130 0.00 0.00 35.86 3.55
783 1047 1.748122 GGAGCACAGTGGCCTCATG 60.748 63.158 3.32 4.41 0.00 3.07
785 1049 1.303074 AGCACAGTGGCCTCATGTG 60.303 57.895 23.17 23.17 45.59 3.21
786 1050 3.271014 CACAGTGGCCTCATGTGC 58.729 61.111 18.32 0.00 38.05 4.57
787 1051 1.303074 CACAGTGGCCTCATGTGCT 60.303 57.895 18.32 0.00 38.05 4.40
788 1052 0.036105 CACAGTGGCCTCATGTGCTA 60.036 55.000 18.32 1.68 38.05 3.49
789 1053 0.036010 ACAGTGGCCTCATGTGCTAC 60.036 55.000 15.05 15.05 40.15 3.58
790 1054 0.036105 CAGTGGCCTCATGTGCTACA 60.036 55.000 21.37 6.92 42.05 2.74
791 1055 0.692476 AGTGGCCTCATGTGCTACAA 59.308 50.000 21.37 2.09 42.05 2.41
792 1056 1.089920 GTGGCCTCATGTGCTACAAG 58.910 55.000 16.96 0.00 39.68 3.16
794 1058 0.393537 GGCCTCATGTGCTACAAGCT 60.394 55.000 0.00 0.00 42.97 3.74
796 1060 2.208431 GCCTCATGTGCTACAAGCTAG 58.792 52.381 0.03 0.00 42.97 3.42
797 1061 2.831333 CCTCATGTGCTACAAGCTAGG 58.169 52.381 0.03 0.00 42.97 3.02
798 1062 2.432146 CCTCATGTGCTACAAGCTAGGA 59.568 50.000 0.03 0.00 42.97 2.94
799 1063 3.452474 CTCATGTGCTACAAGCTAGGAC 58.548 50.000 0.00 0.00 42.97 3.85
800 1064 3.099905 TCATGTGCTACAAGCTAGGACT 58.900 45.455 7.96 0.00 42.97 3.85
801 1065 3.515502 TCATGTGCTACAAGCTAGGACTT 59.484 43.478 7.96 0.00 42.97 3.01
809 1073 2.012673 CAAGCTAGGACTTGCATGACC 58.987 52.381 12.19 12.19 40.53 4.02
822 1086 5.945784 ACTTGCATGACCACTAAACATACAT 59.054 36.000 6.60 0.00 0.00 2.29
828 1092 6.795098 TGACCACTAAACATACATGTGTTC 57.205 37.500 9.11 0.00 41.22 3.18
830 1094 4.693566 ACCACTAAACATACATGTGTTCCG 59.306 41.667 9.11 2.89 41.22 4.30
832 1096 3.687698 ACTAAACATACATGTGTTCCGCC 59.312 43.478 9.11 0.00 41.22 6.13
833 1097 2.192664 AACATACATGTGTTCCGCCA 57.807 45.000 9.11 0.00 41.61 5.69
834 1098 2.192664 ACATACATGTGTTCCGCCAA 57.807 45.000 9.11 0.00 40.03 4.52
835 1099 2.722094 ACATACATGTGTTCCGCCAAT 58.278 42.857 9.11 0.00 40.03 3.16
838 1102 1.167851 ACATGTGTTCCGCCAATCAG 58.832 50.000 0.00 0.00 0.00 2.90
839 1103 0.179156 CATGTGTTCCGCCAATCAGC 60.179 55.000 0.00 0.00 0.00 4.26
840 1104 0.322816 ATGTGTTCCGCCAATCAGCT 60.323 50.000 0.00 0.00 0.00 4.24
845 1109 3.625764 GTGTTCCGCCAATCAGCTATTAA 59.374 43.478 0.00 0.00 0.00 1.40
849 1113 6.127479 TGTTCCGCCAATCAGCTATTAATTTT 60.127 34.615 0.00 0.00 0.00 1.82
850 1114 7.067615 TGTTCCGCCAATCAGCTATTAATTTTA 59.932 33.333 0.00 0.00 0.00 1.52
851 1115 7.759489 TCCGCCAATCAGCTATTAATTTTAT 57.241 32.000 0.00 0.00 0.00 1.40
853 1117 8.946085 TCCGCCAATCAGCTATTAATTTTATAG 58.054 33.333 0.00 0.00 0.00 1.31
855 1119 8.946085 CGCCAATCAGCTATTAATTTTATAGGA 58.054 33.333 0.00 0.00 0.00 2.94
876 1140 4.202080 GGACACATTGGATTGATCATGTGG 60.202 45.833 22.36 9.77 42.40 4.17
877 1141 4.602107 ACACATTGGATTGATCATGTGGA 58.398 39.130 22.36 0.00 42.40 4.02
878 1142 4.643334 ACACATTGGATTGATCATGTGGAG 59.357 41.667 22.36 5.03 42.40 3.86
896 1160 2.093447 GGAGCGATTCATATGGGTAGGG 60.093 54.545 2.13 0.00 0.00 3.53
897 1169 1.909302 AGCGATTCATATGGGTAGGGG 59.091 52.381 2.13 0.00 0.00 4.79
904 1176 1.142060 CATATGGGTAGGGGCGAACAA 59.858 52.381 0.00 0.00 0.00 2.83
905 1177 1.287217 TATGGGTAGGGGCGAACAAA 58.713 50.000 0.00 0.00 0.00 2.83
906 1178 0.629058 ATGGGTAGGGGCGAACAAAT 59.371 50.000 0.00 0.00 0.00 2.32
907 1179 1.287217 TGGGTAGGGGCGAACAAATA 58.713 50.000 0.00 0.00 0.00 1.40
908 1180 1.065272 TGGGTAGGGGCGAACAAATAC 60.065 52.381 0.00 0.00 0.00 1.89
909 1181 1.292992 GGTAGGGGCGAACAAATACG 58.707 55.000 0.00 0.00 0.00 3.06
919 1191 2.345641 CGAACAAATACGCTCCTGTGAG 59.654 50.000 0.00 0.00 41.84 3.51
922 1194 4.111375 ACAAATACGCTCCTGTGAGTAG 57.889 45.455 0.00 0.00 40.95 2.57
926 1198 0.251209 ACGCTCCTGTGAGTAGGACA 60.251 55.000 0.00 0.00 41.85 4.02
930 1202 3.617531 CGCTCCTGTGAGTAGGACATTTT 60.618 47.826 0.00 0.00 41.85 1.82
931 1203 3.935828 GCTCCTGTGAGTAGGACATTTTC 59.064 47.826 0.00 0.00 41.85 2.29
992 1509 1.418097 TTGCCAACTGAGCAGGAGGA 61.418 55.000 12.70 0.00 42.17 3.71
1024 1541 3.190874 GAGTTAACATGGAGAGCGAAGG 58.809 50.000 8.61 0.00 0.00 3.46
1027 1544 0.036010 AACATGGAGAGCGAAGGTGG 60.036 55.000 0.00 0.00 39.88 4.61
1032 1549 1.142097 GAGAGCGAAGGTGGTAGGC 59.858 63.158 0.00 0.00 39.88 3.93
1053 1570 3.214328 CCCAACCTTGCCATCATACTAC 58.786 50.000 0.00 0.00 0.00 2.73
1069 1586 7.468141 TCATACTACCTTGATGATAATCGCT 57.532 36.000 0.00 0.00 0.00 4.93
1160 1677 2.686915 AGCATAGCATTTCCTCTGTTGC 59.313 45.455 0.00 0.00 35.34 4.17
1206 1723 6.382859 TCTCTAACTATGATGCAACCCAGTTA 59.617 38.462 13.37 13.37 0.00 2.24
1212 1729 2.642311 TGATGCAACCCAGTTAGAGGAA 59.358 45.455 0.00 0.00 0.00 3.36
1224 1741 0.984230 TAGAGGAACTTGGCAGTGGG 59.016 55.000 0.00 0.00 41.55 4.61
1266 1783 6.074648 ACCATTTCTTTGGGTTGTAAGATCA 58.925 36.000 0.00 0.00 41.35 2.92
1288 1805 4.530710 AACGAGGCACACAAGTTATCTA 57.469 40.909 0.00 0.00 0.00 1.98
1294 1811 6.183360 CGAGGCACACAAGTTATCTAAAGAAG 60.183 42.308 0.00 0.00 0.00 2.85
1299 1816 8.342634 GCACACAAGTTATCTAAAGAAGTCAAA 58.657 33.333 0.00 0.00 0.00 2.69
1300 1817 9.651718 CACACAAGTTATCTAAAGAAGTCAAAC 57.348 33.333 0.00 0.00 0.00 2.93
1317 1834 6.092748 AGTCAAACTGAAATGTGTGAACAAC 58.907 36.000 0.00 0.00 36.12 3.32
1321 1838 3.064820 ACTGAAATGTGTGAACAACGGAC 59.935 43.478 0.00 0.00 0.00 4.79
1378 1895 2.083774 CACACAAGGCAATCGGTATGT 58.916 47.619 0.00 0.00 0.00 2.29
1383 1900 3.692593 ACAAGGCAATCGGTATGTTAACC 59.307 43.478 2.48 0.00 36.08 2.85
1396 1917 9.458727 TCGGTATGTTAACCCAAATTACATTTA 57.541 29.630 2.48 0.00 36.03 1.40
1524 2046 0.692476 CCCACTGTGGATGGAACTCA 59.308 55.000 27.94 0.00 40.96 3.41
1596 2119 1.451387 GGACCAACCCACCATAGCG 60.451 63.158 0.00 0.00 0.00 4.26
1620 2143 0.473694 ATGTGGAGAGTGTGTGGGGA 60.474 55.000 0.00 0.00 0.00 4.81
1623 2146 1.073923 GTGGAGAGTGTGTGGGGAATT 59.926 52.381 0.00 0.00 0.00 2.17
1645 2168 3.766691 TGCGAGTACGGAAGGGCC 61.767 66.667 0.00 0.00 36.84 5.80
1668 2191 1.668826 ATGGGTGGCTAAAGAGGACA 58.331 50.000 0.00 0.00 0.00 4.02
1681 2204 0.253610 GAGGACAGAGGTCGAGAGGA 59.746 60.000 0.00 0.00 45.28 3.71
1721 2244 5.907662 TGGATGGAGATAGAAAGGATGAGTT 59.092 40.000 0.00 0.00 0.00 3.01
1748 2271 3.192844 AGAAATGCTGCAAAGTGGATGAG 59.807 43.478 6.36 0.00 0.00 2.90
1755 2278 1.135575 GCAAAGTGGATGAGAAAGGCG 60.136 52.381 0.00 0.00 0.00 5.52
1779 2302 0.396695 ATGCAATGCAGGAAGGAGGG 60.397 55.000 14.98 0.00 43.65 4.30
1827 2350 3.536570 TGCTGCAAAGTATACGGCAATA 58.463 40.909 16.77 8.97 42.46 1.90
1850 2373 6.585695 ATGAAGTCATATCAATGCATTCCC 57.414 37.500 9.53 0.00 34.26 3.97
1859 2382 7.779326 TCATATCAATGCATTCCCTACTTCAAA 59.221 33.333 9.53 0.00 32.76 2.69
1860 2383 5.643379 TCAATGCATTCCCTACTTCAAAC 57.357 39.130 9.53 0.00 0.00 2.93
1871 2394 7.069877 TCCCTACTTCAAACTAAGCAAGTAA 57.930 36.000 0.00 0.00 37.50 2.24
1873 2396 6.935208 CCCTACTTCAAACTAAGCAAGTAAGT 59.065 38.462 9.48 9.48 37.50 2.24
1878 2401 4.274950 TCAAACTAAGCAAGTAAGTGGTGC 59.725 41.667 0.00 0.00 37.50 5.01
1884 2407 2.618709 AGCAAGTAAGTGGTGCTTTCAC 59.381 45.455 0.00 0.00 46.25 3.18
1887 2410 3.838244 AGTAAGTGGTGCTTTCACTGA 57.162 42.857 7.67 0.00 43.82 3.41
2002 2530 7.692908 AACACGTGAAAAATTCTTTACATGG 57.307 32.000 25.01 0.00 0.00 3.66
2034 2562 7.658179 TCAATTTGAATAGATCGTATGGAGC 57.342 36.000 0.00 0.00 0.00 4.70
2037 2565 4.790765 TGAATAGATCGTATGGAGCCTG 57.209 45.455 0.00 0.00 0.00 4.85
2050 2578 6.315393 CGTATGGAGCCTGTAAAAGTATTGTT 59.685 38.462 0.00 0.00 0.00 2.83
2055 2583 8.764558 TGGAGCCTGTAAAAGTATTGTTATAGA 58.235 33.333 0.00 0.00 0.00 1.98
2116 2644 3.892588 TCCACACAATAAAACAGTTCCCC 59.107 43.478 0.00 0.00 0.00 4.81
2119 2647 5.221621 CCACACAATAAAACAGTTCCCCATT 60.222 40.000 0.00 0.00 0.00 3.16
2130 2658 9.884636 AAAACAGTTCCCCATTATTAATTAAGC 57.115 29.630 3.94 0.00 0.00 3.09
2131 2659 8.838649 AACAGTTCCCCATTATTAATTAAGCT 57.161 30.769 3.94 0.00 0.00 3.74
2147 2675 7.954788 AATTAAGCTAAGACGATGATTCTCC 57.045 36.000 0.00 0.00 0.00 3.71
2148 2676 6.465439 TTAAGCTAAGACGATGATTCTCCA 57.535 37.500 0.00 0.00 0.00 3.86
2151 2679 6.656632 AGCTAAGACGATGATTCTCCATTA 57.343 37.500 0.00 0.00 0.00 1.90
2154 2682 7.601886 AGCTAAGACGATGATTCTCCATTAATG 59.398 37.037 8.58 8.58 0.00 1.90
2213 2752 8.451748 GGAGTTCTCTAAATTTAATTTCGCACT 58.548 33.333 6.17 3.44 33.82 4.40
2229 2768 7.444558 TTTCGCACTGAAATTTGAAACTAAC 57.555 32.000 0.00 0.00 41.59 2.34
2232 2776 6.690957 TCGCACTGAAATTTGAAACTAACAAG 59.309 34.615 0.00 0.00 0.00 3.16
2254 2798 8.999431 ACAAGTGTATACAATACAAGAAACCAG 58.001 33.333 7.25 0.00 0.00 4.00
2256 2800 9.436957 AAGTGTATACAATACAAGAAACCAGAG 57.563 33.333 7.25 0.00 0.00 3.35
2263 2807 7.227156 ACAATACAAGAAACCAGAGATGTCTT 58.773 34.615 0.00 0.00 0.00 3.01
2264 2808 7.173907 ACAATACAAGAAACCAGAGATGTCTTG 59.826 37.037 9.54 9.54 46.82 3.02
2268 2812 5.825593 AGAAACCAGAGATGTCTTGGTTA 57.174 39.130 19.74 0.00 40.46 2.85
2280 2824 9.202273 GAGATGTCTTGGTTAATCAGATACATC 57.798 37.037 21.14 21.14 40.45 3.06
2281 2825 8.153550 AGATGTCTTGGTTAATCAGATACATCC 58.846 37.037 23.12 13.37 40.83 3.51
2285 2829 8.616076 GTCTTGGTTAATCAGATACATCCAAAG 58.384 37.037 9.20 0.00 34.13 2.77
2292 2836 7.563888 AATCAGATACATCCAAAGACACATG 57.436 36.000 0.00 0.00 0.00 3.21
2298 2842 5.954296 ACATCCAAAGACACATGAAAGAG 57.046 39.130 0.00 0.00 0.00 2.85
2302 2846 7.667219 ACATCCAAAGACACATGAAAGAGTAAT 59.333 33.333 0.00 0.00 0.00 1.89
2304 2848 6.655003 TCCAAAGACACATGAAAGAGTAATCC 59.345 38.462 0.00 0.00 0.00 3.01
2306 2850 7.121759 CCAAAGACACATGAAAGAGTAATCCAT 59.878 37.037 0.00 0.00 0.00 3.41
2308 2852 6.118170 AGACACATGAAAGAGTAATCCATGG 58.882 40.000 4.97 4.97 38.98 3.66
2310 2854 6.248433 ACACATGAAAGAGTAATCCATGGTT 58.752 36.000 12.58 8.15 38.98 3.67
2315 2859 7.831691 TGAAAGAGTAATCCATGGTTTCAAA 57.168 32.000 17.44 0.00 31.35 2.69
2316 2860 7.885297 TGAAAGAGTAATCCATGGTTTCAAAG 58.115 34.615 17.44 0.00 31.35 2.77
2324 2868 6.862469 ATCCATGGTTTCAAAGAACATCAT 57.138 33.333 12.58 0.00 0.00 2.45
2361 2905 6.936968 AAGATAGTATAACCATGTCCCCTC 57.063 41.667 0.00 0.00 0.00 4.30
2367 2911 1.444933 AACCATGTCCCCTCTGTCAA 58.555 50.000 0.00 0.00 0.00 3.18
2368 2912 1.673767 ACCATGTCCCCTCTGTCAAT 58.326 50.000 0.00 0.00 0.00 2.57
2370 2914 1.283029 CCATGTCCCCTCTGTCAATGT 59.717 52.381 0.00 0.00 0.00 2.71
2378 2922 3.452264 CCCCTCTGTCAATGTCTATCACA 59.548 47.826 0.00 0.00 40.18 3.58
2380 2924 5.295950 CCCTCTGTCAATGTCTATCACATC 58.704 45.833 0.00 0.00 45.77 3.06
2383 2927 7.256083 CCCTCTGTCAATGTCTATCACATCATA 60.256 40.741 0.00 0.00 45.77 2.15
2384 2928 7.813627 CCTCTGTCAATGTCTATCACATCATAG 59.186 40.741 0.00 0.00 45.77 2.23
2385 2929 7.150640 TCTGTCAATGTCTATCACATCATAGC 58.849 38.462 0.00 0.00 45.77 2.97
2387 2931 6.703165 TGTCAATGTCTATCACATCATAGCAC 59.297 38.462 0.00 0.00 45.77 4.40
2388 2932 6.703165 GTCAATGTCTATCACATCATAGCACA 59.297 38.462 0.00 0.00 45.77 4.57
2390 2934 5.205759 TGTCTATCACATCATAGCACAGG 57.794 43.478 0.00 0.00 0.00 4.00
2393 2937 5.243954 GTCTATCACATCATAGCACAGGGTA 59.756 44.000 0.00 0.00 0.00 3.69
2394 2938 3.819564 TCACATCATAGCACAGGGTAC 57.180 47.619 0.00 0.00 0.00 3.34
2419 2963 2.514803 TGTTAGGCTCTTTTGGGAAGC 58.485 47.619 0.00 0.00 0.00 3.86
2420 2964 1.468914 GTTAGGCTCTTTTGGGAAGCG 59.531 52.381 0.00 0.00 0.00 4.68
2428 2972 1.686587 CTTTTGGGAAGCGGGAGTTTT 59.313 47.619 0.00 0.00 31.75 2.43
2512 3056 8.988064 ATGATACAAATTACTAGTAGGATGCG 57.012 34.615 2.23 0.00 0.00 4.73
2535 3080 6.358822 GCGTCCAAGTTTTGTTAAGACATTAC 59.641 38.462 0.00 0.00 35.29 1.89
2547 3092 9.521841 TTGTTAAGACATTACATTACATTCCCA 57.478 29.630 0.00 0.00 35.29 4.37
2548 3093 8.952278 TGTTAAGACATTACATTACATTCCCAC 58.048 33.333 0.00 0.00 0.00 4.61
2550 3095 9.521841 TTAAGACATTACATTACATTCCCACAA 57.478 29.630 0.00 0.00 0.00 3.33
2552 3097 8.593945 AGACATTACATTACATTCCCACAAAT 57.406 30.769 0.00 0.00 0.00 2.32
2554 3099 9.730420 GACATTACATTACATTCCCACAAATAC 57.270 33.333 0.00 0.00 0.00 1.89
2555 3100 9.474313 ACATTACATTACATTCCCACAAATACT 57.526 29.630 0.00 0.00 0.00 2.12
2558 3103 9.521841 TTACATTACATTCCCACAAATACTTGA 57.478 29.630 0.00 0.00 36.33 3.02
2559 3104 8.415950 ACATTACATTCCCACAAATACTTGAA 57.584 30.769 0.00 0.00 36.33 2.69
2560 3105 8.522830 ACATTACATTCCCACAAATACTTGAAG 58.477 33.333 0.00 0.00 36.33 3.02
2562 3107 6.575162 ACATTCCCACAAATACTTGAAGAC 57.425 37.500 0.00 0.00 36.33 3.01
2563 3108 6.068010 ACATTCCCACAAATACTTGAAGACA 58.932 36.000 0.00 0.00 36.33 3.41
2564 3109 6.016276 ACATTCCCACAAATACTTGAAGACAC 60.016 38.462 0.00 0.00 36.33 3.67
2566 3111 5.063204 TCCCACAAATACTTGAAGACACTG 58.937 41.667 0.00 0.00 36.33 3.66
2567 3112 4.821805 CCCACAAATACTTGAAGACACTGT 59.178 41.667 0.00 0.00 36.33 3.55
2569 3114 6.147821 CCCACAAATACTTGAAGACACTGTAG 59.852 42.308 0.00 0.00 36.33 2.74
2571 3116 7.441157 CCACAAATACTTGAAGACACTGTAGAA 59.559 37.037 0.00 0.00 36.33 2.10
2572 3117 8.993121 CACAAATACTTGAAGACACTGTAGAAT 58.007 33.333 0.00 0.00 36.33 2.40
2575 3120 9.654663 AAATACTTGAAGACACTGTAGAATACC 57.345 33.333 0.00 0.00 42.12 2.73
2576 3121 6.665992 ACTTGAAGACACTGTAGAATACCA 57.334 37.500 0.00 0.00 42.12 3.25
2577 3122 7.246171 ACTTGAAGACACTGTAGAATACCAT 57.754 36.000 0.00 0.00 42.12 3.55
2578 3123 7.099764 ACTTGAAGACACTGTAGAATACCATG 58.900 38.462 0.00 0.00 42.12 3.66
2579 3124 6.850752 TGAAGACACTGTAGAATACCATGA 57.149 37.500 0.00 0.00 42.12 3.07
2656 3206 8.302515 ACATTTGAAAGCTTCATGGAATATCT 57.697 30.769 0.00 0.00 39.84 1.98
2749 3304 9.955102 AATGTATGCACATAAGATACATCATCT 57.045 29.630 7.20 0.00 44.83 2.90
2750 3305 8.992835 TGTATGCACATAAGATACATCATCTC 57.007 34.615 0.00 0.00 43.56 2.75
2752 3307 9.428097 GTATGCACATAAGATACATCATCTCAA 57.572 33.333 0.00 0.00 43.56 3.02
2793 3348 4.137116 TGAACTACACATAGGACATGGC 57.863 45.455 0.00 0.00 32.08 4.40
2801 3356 2.972713 ACATAGGACATGGCGACCTTAT 59.027 45.455 0.00 0.00 40.51 1.73
2806 3361 4.642429 AGGACATGGCGACCTTATTTATC 58.358 43.478 0.00 0.00 36.23 1.75
2807 3362 4.348168 AGGACATGGCGACCTTATTTATCT 59.652 41.667 0.00 0.00 36.23 1.98
2813 3368 5.357257 TGGCGACCTTATTTATCTGAGAAC 58.643 41.667 0.00 0.00 0.00 3.01
2815 3370 6.322969 TGGCGACCTTATTTATCTGAGAACTA 59.677 38.462 0.00 0.00 0.00 2.24
2817 3372 7.542824 GGCGACCTTATTTATCTGAGAACTATC 59.457 40.741 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 255 6.236889 CGTCGAACTGTTTAATAGACGTCTTC 60.237 42.308 25.44 9.85 43.09 2.87
263 264 3.255725 CAGCCCGTCGAACTGTTTAATA 58.744 45.455 0.00 0.00 0.00 0.98
267 268 1.597027 CCAGCCCGTCGAACTGTTT 60.597 57.895 11.81 0.00 0.00 2.83
269 270 2.915659 TCCAGCCCGTCGAACTGT 60.916 61.111 11.81 0.00 0.00 3.55
320 321 0.955428 GCACCTTTGGCTCGATGTCA 60.955 55.000 0.00 0.00 0.00 3.58
368 369 1.961793 TTAAGCACAAACGCTCACCT 58.038 45.000 0.00 0.00 42.89 4.00
369 370 2.289547 TCTTTAAGCACAAACGCTCACC 59.710 45.455 0.00 0.00 42.89 4.02
391 609 7.283807 ACGTGTAAAGTTTAATTTCCAAGGACT 59.716 33.333 0.00 0.00 0.00 3.85
398 616 6.913673 TGCAGAACGTGTAAAGTTTAATTTCC 59.086 34.615 0.00 0.00 39.06 3.13
407 625 2.901249 ACAGTGCAGAACGTGTAAAGT 58.099 42.857 0.00 0.00 0.00 2.66
410 628 2.863740 CTCAACAGTGCAGAACGTGTAA 59.136 45.455 0.00 0.00 0.00 2.41
416 634 1.586422 TGCTCTCAACAGTGCAGAAC 58.414 50.000 0.00 0.00 42.82 3.01
420 638 3.601277 CTCTGCTCTCAACAGTGCA 57.399 52.632 0.00 0.00 44.92 4.57
459 677 9.761504 TGAGCAAATAAAATTCATTCTTTGTCA 57.238 25.926 0.00 0.00 31.31 3.58
541 773 8.736244 GGCTTTGTTGGTAAGATATTTAGAACA 58.264 33.333 0.00 0.00 0.00 3.18
542 774 7.908601 CGGCTTTGTTGGTAAGATATTTAGAAC 59.091 37.037 0.00 0.00 0.00 3.01
543 775 7.608761 ACGGCTTTGTTGGTAAGATATTTAGAA 59.391 33.333 0.00 0.00 0.00 2.10
544 776 7.107542 ACGGCTTTGTTGGTAAGATATTTAGA 58.892 34.615 0.00 0.00 0.00 2.10
545 777 7.316544 ACGGCTTTGTTGGTAAGATATTTAG 57.683 36.000 0.00 0.00 0.00 1.85
546 778 7.531716 CAACGGCTTTGTTGGTAAGATATTTA 58.468 34.615 8.51 0.00 44.27 1.40
557 789 1.441311 AAGGCAACGGCTTTGTTGG 59.559 52.632 15.32 2.47 46.16 3.77
565 797 3.179048 GTTAAATGATGAAGGCAACGGC 58.821 45.455 0.00 0.00 46.39 5.68
568 800 8.986477 ACTATTTGTTAAATGATGAAGGCAAC 57.014 30.769 0.00 0.00 32.38 4.17
614 846 8.154856 TGTTGTGCTTTACTCCTCTTATAAACT 58.845 33.333 0.00 0.00 0.00 2.66
615 847 8.319143 TGTTGTGCTTTACTCCTCTTATAAAC 57.681 34.615 0.00 0.00 0.00 2.01
620 852 6.482308 GTCTTTGTTGTGCTTTACTCCTCTTA 59.518 38.462 0.00 0.00 0.00 2.10
621 853 5.297029 GTCTTTGTTGTGCTTTACTCCTCTT 59.703 40.000 0.00 0.00 0.00 2.85
632 864 2.092968 TCTGGAGTGTCTTTGTTGTGCT 60.093 45.455 0.00 0.00 0.00 4.40
635 867 3.270877 GTGTCTGGAGTGTCTTTGTTGT 58.729 45.455 0.00 0.00 0.00 3.32
637 869 3.627395 TGTGTCTGGAGTGTCTTTGTT 57.373 42.857 0.00 0.00 0.00 2.83
641 873 2.700371 TGTCATGTGTCTGGAGTGTCTT 59.300 45.455 0.00 0.00 0.00 3.01
643 875 2.611473 CCTGTCATGTGTCTGGAGTGTC 60.611 54.545 0.00 0.00 0.00 3.67
644 876 1.345741 CCTGTCATGTGTCTGGAGTGT 59.654 52.381 0.00 0.00 0.00 3.55
647 879 0.979665 ACCCTGTCATGTGTCTGGAG 59.020 55.000 0.00 0.00 0.00 3.86
648 880 0.686789 CACCCTGTCATGTGTCTGGA 59.313 55.000 0.00 0.00 0.00 3.86
649 881 0.397941 ACACCCTGTCATGTGTCTGG 59.602 55.000 3.16 0.00 41.70 3.86
650 882 3.329386 CTTACACCCTGTCATGTGTCTG 58.671 50.000 10.58 3.72 44.18 3.51
669 930 1.005687 AGTAGTAGACGTGCTCCCCTT 59.994 52.381 0.00 0.00 0.00 3.95
670 931 0.624785 AGTAGTAGACGTGCTCCCCT 59.375 55.000 0.00 0.00 0.00 4.79
671 932 1.472188 AAGTAGTAGACGTGCTCCCC 58.528 55.000 0.00 0.00 0.00 4.81
672 933 3.193056 AGAAAAGTAGTAGACGTGCTCCC 59.807 47.826 0.00 0.00 0.00 4.30
721 984 1.080705 CGTTTCGCGTCCTCCTCTT 60.081 57.895 5.77 0.00 35.54 2.85
722 985 2.567049 CGTTTCGCGTCCTCCTCT 59.433 61.111 5.77 0.00 35.54 3.69
723 986 2.482296 TTCCGTTTCGCGTCCTCCTC 62.482 60.000 5.77 0.00 39.32 3.71
728 991 1.069771 TGAATTTTCCGTTTCGCGTCC 60.070 47.619 5.77 0.00 39.32 4.79
730 993 1.662026 GCTGAATTTTCCGTTTCGCGT 60.662 47.619 5.77 0.00 39.32 6.01
731 994 0.974836 GCTGAATTTTCCGTTTCGCG 59.025 50.000 0.00 0.00 40.95 5.87
734 997 6.769608 ATTTCAAGCTGAATTTTCCGTTTC 57.230 33.333 0.00 0.00 36.11 2.78
738 1001 8.137437 ACCATATATTTCAAGCTGAATTTTCCG 58.863 33.333 0.00 0.00 36.11 4.30
739 1002 9.252962 CACCATATATTTCAAGCTGAATTTTCC 57.747 33.333 0.00 0.00 36.11 3.13
750 1014 5.824624 ACTGTGCTCCACCATATATTTCAAG 59.175 40.000 0.00 0.00 32.73 3.02
751 1015 5.589855 CACTGTGCTCCACCATATATTTCAA 59.410 40.000 0.00 0.00 32.73 2.69
753 1017 4.516698 CCACTGTGCTCCACCATATATTTC 59.483 45.833 1.29 0.00 32.73 2.17
756 1020 2.224621 GCCACTGTGCTCCACCATATAT 60.225 50.000 1.29 0.00 32.73 0.86
760 1024 2.034687 GCCACTGTGCTCCACCAT 59.965 61.111 1.29 0.00 32.73 3.55
761 1025 4.269523 GGCCACTGTGCTCCACCA 62.270 66.667 0.00 0.00 32.73 4.17
763 1027 2.359230 GAGGCCACTGTGCTCCAC 60.359 66.667 5.01 8.77 34.56 4.02
764 1028 2.226315 ATGAGGCCACTGTGCTCCA 61.226 57.895 5.01 6.51 0.00 3.86
766 1030 1.002868 ACATGAGGCCACTGTGCTC 60.003 57.895 5.01 5.44 0.00 4.26
767 1031 1.303074 CACATGAGGCCACTGTGCT 60.303 57.895 16.33 0.00 34.47 4.40
771 1035 0.036105 TGTAGCACATGAGGCCACTG 60.036 55.000 5.01 0.88 0.00 3.66
773 1037 1.089920 CTTGTAGCACATGAGGCCAC 58.910 55.000 5.01 0.00 0.00 5.01
774 1038 0.677731 GCTTGTAGCACATGAGGCCA 60.678 55.000 5.01 0.00 41.89 5.36
783 1047 2.003301 GCAAGTCCTAGCTTGTAGCAC 58.997 52.381 10.60 0.00 45.56 4.40
785 1049 2.386661 TGCAAGTCCTAGCTTGTAGC 57.613 50.000 10.60 0.00 45.47 3.58
786 1050 3.868077 GTCATGCAAGTCCTAGCTTGTAG 59.132 47.826 10.60 0.00 45.47 2.74
787 1051 3.369471 GGTCATGCAAGTCCTAGCTTGTA 60.369 47.826 10.60 7.42 45.47 2.41
788 1052 2.616510 GGTCATGCAAGTCCTAGCTTGT 60.617 50.000 10.60 0.00 45.47 3.16
789 1053 2.012673 GGTCATGCAAGTCCTAGCTTG 58.987 52.381 0.00 5.90 46.21 4.01
790 1054 1.630369 TGGTCATGCAAGTCCTAGCTT 59.370 47.619 6.76 0.00 0.00 3.74
791 1055 1.065854 GTGGTCATGCAAGTCCTAGCT 60.066 52.381 6.76 0.00 0.00 3.32
792 1056 1.065854 AGTGGTCATGCAAGTCCTAGC 60.066 52.381 6.76 0.00 0.00 3.42
794 1058 4.041075 TGTTTAGTGGTCATGCAAGTCCTA 59.959 41.667 6.76 0.00 0.00 2.94
796 1060 3.146066 TGTTTAGTGGTCATGCAAGTCC 58.854 45.455 0.00 0.00 0.00 3.85
797 1061 5.411361 TGTATGTTTAGTGGTCATGCAAGTC 59.589 40.000 0.00 0.00 33.00 3.01
798 1062 5.312895 TGTATGTTTAGTGGTCATGCAAGT 58.687 37.500 0.00 0.00 33.00 3.16
799 1063 5.878332 TGTATGTTTAGTGGTCATGCAAG 57.122 39.130 0.00 0.00 33.00 4.01
800 1064 5.709631 ACATGTATGTTTAGTGGTCATGCAA 59.290 36.000 0.00 0.00 37.90 4.08
801 1065 5.123661 CACATGTATGTTTAGTGGTCATGCA 59.876 40.000 0.00 0.00 39.39 3.96
805 1069 5.703592 GGAACACATGTATGTTTAGTGGTCA 59.296 40.000 10.57 0.00 46.00 4.02
809 1073 4.436852 GGCGGAACACATGTATGTTTAGTG 60.437 45.833 0.00 0.00 42.89 2.74
822 1086 0.323302 TAGCTGATTGGCGGAACACA 59.677 50.000 0.00 0.00 37.29 3.72
828 1092 8.184192 CCTATAAAATTAATAGCTGATTGGCGG 58.816 37.037 0.00 0.00 37.29 6.13
845 1109 9.645128 TGATCAATCCAATGTGTCCTATAAAAT 57.355 29.630 0.00 0.00 0.00 1.82
849 1113 7.662669 CACATGATCAATCCAATGTGTCCTATA 59.337 37.037 14.12 0.00 35.86 1.31
850 1114 6.489022 CACATGATCAATCCAATGTGTCCTAT 59.511 38.462 14.12 0.00 35.86 2.57
851 1115 5.824097 CACATGATCAATCCAATGTGTCCTA 59.176 40.000 14.12 0.00 35.86 2.94
853 1117 4.202080 CCACATGATCAATCCAATGTGTCC 60.202 45.833 18.67 0.00 38.08 4.02
855 1119 4.602107 TCCACATGATCAATCCAATGTGT 58.398 39.130 18.67 6.36 38.08 3.72
861 1125 1.485895 TCGCTCCACATGATCAATCCA 59.514 47.619 0.00 0.00 0.00 3.41
862 1126 2.245159 TCGCTCCACATGATCAATCC 57.755 50.000 0.00 0.00 0.00 3.01
870 1134 2.745821 CCCATATGAATCGCTCCACATG 59.254 50.000 3.65 0.00 0.00 3.21
876 1140 2.093447 CCCCTACCCATATGAATCGCTC 60.093 54.545 3.65 0.00 0.00 5.03
877 1141 1.909302 CCCCTACCCATATGAATCGCT 59.091 52.381 3.65 0.00 0.00 4.93
878 1142 1.679032 GCCCCTACCCATATGAATCGC 60.679 57.143 3.65 0.00 0.00 4.58
904 1176 2.688958 GTCCTACTCACAGGAGCGTATT 59.311 50.000 0.00 0.00 45.49 1.89
905 1177 2.299521 GTCCTACTCACAGGAGCGTAT 58.700 52.381 0.00 0.00 45.49 3.06
906 1178 1.003928 TGTCCTACTCACAGGAGCGTA 59.996 52.381 0.00 0.00 45.49 4.42
907 1179 0.251209 TGTCCTACTCACAGGAGCGT 60.251 55.000 0.00 0.00 45.49 5.07
908 1180 1.107114 ATGTCCTACTCACAGGAGCG 58.893 55.000 0.00 0.00 45.49 5.03
909 1181 3.618690 AAATGTCCTACTCACAGGAGC 57.381 47.619 0.00 0.00 45.49 4.70
959 1400 7.473735 TCAGTTGGCAAATTGTTATTCCATA 57.526 32.000 0.00 0.00 0.00 2.74
961 1402 5.782047 CTCAGTTGGCAAATTGTTATTCCA 58.218 37.500 0.00 0.00 0.00 3.53
962 1403 4.627035 GCTCAGTTGGCAAATTGTTATTCC 59.373 41.667 0.00 0.00 0.00 3.01
967 1408 2.224113 CCTGCTCAGTTGGCAAATTGTT 60.224 45.455 0.00 0.00 39.30 2.83
969 1410 1.614903 TCCTGCTCAGTTGGCAAATTG 59.385 47.619 0.00 3.93 39.30 2.32
992 1509 6.440647 TCTCCATGTTAACTCCATGTACTCTT 59.559 38.462 7.22 0.00 38.39 2.85
1032 1549 2.442236 AGTATGATGGCAAGGTTGGG 57.558 50.000 0.00 0.00 0.00 4.12
1053 1570 5.352569 GGATGGTAAGCGATTATCATCAAGG 59.647 44.000 34.89 0.00 43.44 3.61
1069 1586 6.134535 ACCATAAGACTTGTTGGATGGTAA 57.865 37.500 20.12 0.00 44.02 2.85
1118 1635 5.065914 GCTTCTCTAACCAATCCATGCATA 58.934 41.667 0.00 0.00 0.00 3.14
1160 1677 1.336887 CGGTCCCATAGGATACAAGCG 60.337 57.143 0.00 0.00 46.41 4.68
1206 1723 1.763770 CCCACTGCCAAGTTCCTCT 59.236 57.895 0.00 0.00 32.98 3.69
1212 1729 1.379044 GCATAGCCCACTGCCAAGT 60.379 57.895 0.00 0.00 42.71 3.16
1224 1741 2.094078 TGGTTTGCCAGAATTGCATAGC 60.094 45.455 0.00 0.00 40.46 2.97
1260 1777 2.254546 TGTGTGCCTCGTTTGATCTT 57.745 45.000 0.00 0.00 0.00 2.40
1266 1783 3.740115 AGATAACTTGTGTGCCTCGTTT 58.260 40.909 0.00 0.00 0.00 3.60
1288 1805 7.156876 TCACACATTTCAGTTTGACTTCTTT 57.843 32.000 0.00 0.00 0.00 2.52
1294 1811 5.003402 CGTTGTTCACACATTTCAGTTTGAC 59.997 40.000 0.00 0.00 28.73 3.18
1299 1816 3.064820 GTCCGTTGTTCACACATTTCAGT 59.935 43.478 0.00 0.00 31.06 3.41
1300 1817 3.312421 AGTCCGTTGTTCACACATTTCAG 59.688 43.478 0.00 0.00 31.06 3.02
1317 1834 2.159627 GCACCACTCAACAATTAGTCCG 59.840 50.000 0.00 0.00 0.00 4.79
1487 2009 5.125739 CAGTGGGTAACAAAACAACCTACAA 59.874 40.000 9.46 0.00 44.64 2.41
1524 2046 3.569701 CACTAACAACTGCCTCCAATGTT 59.430 43.478 0.00 0.00 36.03 2.71
1596 2119 3.589988 CCACACACTCTCCACATACTTC 58.410 50.000 0.00 0.00 0.00 3.01
1620 2143 0.319083 TCCGTACTCGCACACCAATT 59.681 50.000 0.00 0.00 35.54 2.32
1623 2146 1.287815 CTTCCGTACTCGCACACCA 59.712 57.895 0.00 0.00 35.54 4.17
1645 2168 2.239654 TCCTCTTTAGCCACCCATTCTG 59.760 50.000 0.00 0.00 0.00 3.02
1653 2176 1.903183 ACCTCTGTCCTCTTTAGCCAC 59.097 52.381 0.00 0.00 0.00 5.01
1668 2191 4.903049 TCTCTAATACTCCTCTCGACCTCT 59.097 45.833 0.00 0.00 0.00 3.69
1681 2204 5.970289 TCCATCCATCACCTCTCTAATACT 58.030 41.667 0.00 0.00 0.00 2.12
1721 2244 4.121317 CCACTTTGCAGCATTTCTTTTGA 58.879 39.130 0.00 0.00 0.00 2.69
1748 2271 1.922545 GCATTGCATTCTTCGCCTTTC 59.077 47.619 3.15 0.00 0.00 2.62
1755 2278 2.756760 TCCTTCCTGCATTGCATTCTTC 59.243 45.455 12.53 0.00 38.13 2.87
1779 2302 3.370366 CGGCAATATGCTTATCTGAGCTC 59.630 47.826 6.82 6.82 44.28 4.09
1822 2345 8.981724 AATGCATTGATATGACTTCATATTGC 57.018 30.769 12.09 19.01 46.36 3.56
1827 2350 6.312529 AGGGAATGCATTGATATGACTTCAT 58.687 36.000 18.59 0.00 40.22 2.57
1838 2361 5.324409 AGTTTGAAGTAGGGAATGCATTGA 58.676 37.500 18.59 0.00 0.00 2.57
1850 2373 7.441458 ACCACTTACTTGCTTAGTTTGAAGTAG 59.559 37.037 0.00 0.00 33.48 2.57
1859 2382 3.771577 AGCACCACTTACTTGCTTAGT 57.228 42.857 0.00 0.00 44.26 2.24
1871 2394 3.769739 TGTATCAGTGAAAGCACCACT 57.230 42.857 0.00 0.00 46.32 4.00
1873 2396 5.316167 AGAATTGTATCAGTGAAAGCACCA 58.684 37.500 0.00 0.00 46.32 4.17
1914 2437 9.570488 GAGAAGATAACATTCTACTTACAACGT 57.430 33.333 0.00 0.00 37.14 3.99
1915 2438 9.569167 TGAGAAGATAACATTCTACTTACAACG 57.431 33.333 0.00 0.00 37.14 4.10
1976 2504 9.239002 CCATGTAAAGAATTTTTCACGTGTTTA 57.761 29.630 16.51 7.47 40.09 2.01
1977 2505 7.762159 ACCATGTAAAGAATTTTTCACGTGTTT 59.238 29.630 16.51 8.47 40.09 2.83
2022 2550 4.694339 ACTTTTACAGGCTCCATACGATC 58.306 43.478 0.00 0.00 0.00 3.69
2026 2554 7.625828 AACAATACTTTTACAGGCTCCATAC 57.374 36.000 0.00 0.00 0.00 2.39
2071 2599 8.597167 TGGAACACTAAGAATATCCATGGATAG 58.403 37.037 32.47 23.96 40.01 2.08
2073 2601 7.392766 TGGAACACTAAGAATATCCATGGAT 57.607 36.000 29.66 29.66 38.54 3.41
2129 2657 7.623089 GCATTAATGGAGAATCATCGTCTTAGC 60.623 40.741 17.02 0.00 36.25 3.09
2130 2658 7.601886 AGCATTAATGGAGAATCATCGTCTTAG 59.398 37.037 17.02 0.00 36.25 2.18
2131 2659 7.445121 AGCATTAATGGAGAATCATCGTCTTA 58.555 34.615 17.02 0.00 36.25 2.10
2136 2664 9.903682 AATTTTAGCATTAATGGAGAATCATCG 57.096 29.630 17.02 0.00 36.25 3.84
2190 2729 9.607285 TTCAGTGCGAAATTAAATTTAGAGAAC 57.393 29.630 0.00 0.00 31.47 3.01
2209 2748 7.275560 ACACTTGTTAGTTTCAAATTTCAGTGC 59.724 33.333 0.00 0.00 30.26 4.40
2210 2749 8.687824 ACACTTGTTAGTTTCAAATTTCAGTG 57.312 30.769 0.00 0.00 30.26 3.66
2227 2766 9.344772 TGGTTTCTTGTATTGTATACACTTGTT 57.655 29.630 4.68 0.00 0.00 2.83
2229 2768 9.214957 TCTGGTTTCTTGTATTGTATACACTTG 57.785 33.333 4.68 0.00 0.00 3.16
2232 2776 8.997621 TCTCTGGTTTCTTGTATTGTATACAC 57.002 34.615 4.68 0.00 0.00 2.90
2239 2783 7.361542 CCAAGACATCTCTGGTTTCTTGTATTG 60.362 40.741 8.41 0.00 40.99 1.90
2242 2786 5.071788 ACCAAGACATCTCTGGTTTCTTGTA 59.928 40.000 8.41 0.00 40.99 2.41
2250 2794 5.485353 TCTGATTAACCAAGACATCTCTGGT 59.515 40.000 8.90 8.90 32.39 4.00
2254 2798 9.202273 GATGTATCTGATTAACCAAGACATCTC 57.798 37.037 14.27 0.00 38.28 2.75
2256 2800 7.933577 TGGATGTATCTGATTAACCAAGACATC 59.066 37.037 13.60 13.60 39.79 3.06
2263 2807 7.552687 GTGTCTTTGGATGTATCTGATTAACCA 59.447 37.037 0.00 0.00 0.00 3.67
2264 2808 7.552687 TGTGTCTTTGGATGTATCTGATTAACC 59.447 37.037 0.00 0.00 0.00 2.85
2268 2812 7.341030 TCATGTGTCTTTGGATGTATCTGATT 58.659 34.615 0.00 0.00 0.00 2.57
2280 2824 6.430925 TGGATTACTCTTTCATGTGTCTTTGG 59.569 38.462 0.00 0.00 0.00 3.28
2281 2825 7.439157 TGGATTACTCTTTCATGTGTCTTTG 57.561 36.000 0.00 0.00 0.00 2.77
2285 2829 5.882557 ACCATGGATTACTCTTTCATGTGTC 59.117 40.000 21.47 0.00 34.94 3.67
2292 2836 8.110860 TCTTTGAAACCATGGATTACTCTTTC 57.889 34.615 21.47 15.84 0.00 2.62
2298 2842 7.601856 TGATGTTCTTTGAAACCATGGATTAC 58.398 34.615 21.47 7.43 0.00 1.89
2302 2846 7.773489 TTATGATGTTCTTTGAAACCATGGA 57.227 32.000 21.47 0.00 0.00 3.41
2306 2850 8.747471 TGCATATTATGATGTTCTTTGAAACCA 58.253 29.630 7.87 0.00 0.00 3.67
2336 2880 7.674772 AGAGGGGACATGGTTATACTATCTTAC 59.325 40.741 0.00 0.00 0.00 2.34
2339 2883 6.019748 CAGAGGGGACATGGTTATACTATCT 58.980 44.000 0.00 0.00 0.00 1.98
2344 2888 3.709653 TGACAGAGGGGACATGGTTATAC 59.290 47.826 0.00 0.00 0.00 1.47
2350 2894 1.283029 ACATTGACAGAGGGGACATGG 59.717 52.381 0.00 0.00 0.00 3.66
2351 2895 2.238144 AGACATTGACAGAGGGGACATG 59.762 50.000 0.00 0.00 0.00 3.21
2357 2901 4.743057 TGTGATAGACATTGACAGAGGG 57.257 45.455 0.00 0.00 0.00 4.30
2361 2905 6.927381 TGCTATGATGTGATAGACATTGACAG 59.073 38.462 0.00 0.00 45.90 3.51
2368 2912 4.039609 CCCTGTGCTATGATGTGATAGACA 59.960 45.833 0.00 0.00 39.53 3.41
2370 2914 4.226384 ACCCTGTGCTATGATGTGATAGA 58.774 43.478 0.00 0.00 0.00 1.98
2394 2938 3.202151 TCCCAAAAGAGCCTAACATAGGG 59.798 47.826 5.62 0.00 46.32 3.53
2396 2940 4.336713 GCTTCCCAAAAGAGCCTAACATAG 59.663 45.833 0.00 0.00 0.00 2.23
2397 2941 4.270008 GCTTCCCAAAAGAGCCTAACATA 58.730 43.478 0.00 0.00 0.00 2.29
2398 2942 3.092301 GCTTCCCAAAAGAGCCTAACAT 58.908 45.455 0.00 0.00 0.00 2.71
2399 2943 2.514803 GCTTCCCAAAAGAGCCTAACA 58.485 47.619 0.00 0.00 0.00 2.41
2408 2952 1.328279 AAACTCCCGCTTCCCAAAAG 58.672 50.000 0.00 0.00 0.00 2.27
2419 2963 7.012327 TGCAATAAGATTATGAGAAAACTCCCG 59.988 37.037 0.00 0.00 0.00 5.14
2420 2964 8.225603 TGCAATAAGATTATGAGAAAACTCCC 57.774 34.615 0.00 0.00 0.00 4.30
2457 3001 9.851686 AGCATACTACATCCAATATTTCAAAGA 57.148 29.630 0.00 0.00 0.00 2.52
2468 3012 9.088987 TGTATCATTAGAGCATACTACATCCAA 57.911 33.333 0.00 0.00 0.00 3.53
2498 3042 3.894759 ACTTGGACGCATCCTACTAGTA 58.105 45.455 0.00 1.89 46.43 1.82
2501 3045 4.250464 CAAAACTTGGACGCATCCTACTA 58.750 43.478 0.00 0.00 46.43 1.82
2502 3046 3.074412 CAAAACTTGGACGCATCCTACT 58.926 45.455 0.00 0.00 46.43 2.57
2512 3056 9.744468 AATGTAATGTCTTAACAAAACTTGGAC 57.256 29.630 0.00 0.00 39.30 4.02
2535 3080 8.739039 TCTTCAAGTATTTGTGGGAATGTAATG 58.261 33.333 0.00 0.00 35.73 1.90
2539 3084 6.016276 GTGTCTTCAAGTATTTGTGGGAATGT 60.016 38.462 0.00 0.00 35.73 2.71
2542 3087 5.530915 CAGTGTCTTCAAGTATTTGTGGGAA 59.469 40.000 0.00 0.00 35.73 3.97
2544 3089 4.821805 ACAGTGTCTTCAAGTATTTGTGGG 59.178 41.667 0.00 0.00 35.73 4.61
2545 3090 6.929049 TCTACAGTGTCTTCAAGTATTTGTGG 59.071 38.462 0.00 0.00 35.73 4.17
2546 3091 7.946655 TCTACAGTGTCTTCAAGTATTTGTG 57.053 36.000 0.00 0.00 35.73 3.33
2550 3095 8.812972 TGGTATTCTACAGTGTCTTCAAGTATT 58.187 33.333 0.00 0.00 0.00 1.89
2552 3097 7.770366 TGGTATTCTACAGTGTCTTCAAGTA 57.230 36.000 0.00 0.00 0.00 2.24
2554 3099 7.323420 TCATGGTATTCTACAGTGTCTTCAAG 58.677 38.462 0.00 0.00 0.00 3.02
2555 3100 7.239763 TCATGGTATTCTACAGTGTCTTCAA 57.760 36.000 0.00 0.00 0.00 2.69
2556 3101 6.850752 TCATGGTATTCTACAGTGTCTTCA 57.149 37.500 0.00 0.00 0.00 3.02
2557 3102 9.988815 ATATTCATGGTATTCTACAGTGTCTTC 57.011 33.333 0.00 0.00 0.00 2.87
2625 3171 7.596494 TCCATGAAGCTTTCAAATGTCTAAAG 58.404 34.615 0.00 0.00 43.95 1.85
2763 3318 7.040892 TGTCCTATGTGTAGTTCATACGTATCC 60.041 40.741 4.74 0.00 37.17 2.59
2766 3321 7.255346 CCATGTCCTATGTGTAGTTCATACGTA 60.255 40.741 0.00 0.00 37.17 3.57
2769 3324 5.696724 GCCATGTCCTATGTGTAGTTCATAC 59.303 44.000 0.00 0.00 34.72 2.39
2779 3334 0.465705 AGGTCGCCATGTCCTATGTG 59.534 55.000 0.00 0.00 34.07 3.21
2793 3348 8.577296 TGGATAGTTCTCAGATAAATAAGGTCG 58.423 37.037 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.