Multiple sequence alignment - TraesCS6D01G274400

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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 TraesCS6D01G274400 chr6D 100.000 3985 0 0 1 3985 382799648 382795664 0.000000e+00 7360.0
1 TraesCS6D01G274400 chr6B 91.141 1806 119 19 2191 3983 573160456 573158679 0.000000e+00 2410.0
2 TraesCS6D01G274400 chr6B 92.344 1071 58 18 1127 2192 573161747 573160696 0.000000e+00 1502.0
3 TraesCS6D01G274400 chr6B 84.352 1080 63 44 7 1054 573162879 573161874 0.000000e+00 961.0
4 TraesCS6D01G274400 chr6A 85.290 2223 166 74 119 2272 524869414 524867284 0.000000e+00 2145.0
5 TraesCS6D01G274400 chr6A 88.332 1697 106 41 2264 3892 524867180 524865508 0.000000e+00 1953.0
6 TraesCS6D01G274400 chr7D 80.112 538 78 19 1139 1672 165944610 165945122 1.350000e-99 374.0
7 TraesCS6D01G274400 chr7D 83.621 348 49 6 1139 1485 166204305 166203965 1.790000e-83 320.0
8 TraesCS6D01G274400 chr7A 80.224 536 72 21 1139 1672 167680503 167681006 4.860000e-99 372.0
9 TraesCS6D01G274400 chr7A 84.857 350 43 7 1138 1485 167736204 167735863 1.060000e-90 344.0
10 TraesCS6D01G274400 chr7B 79.626 535 86 16 1139 1672 130120591 130121103 2.930000e-96 363.0
11 TraesCS6D01G274400 chr7B 83.954 349 48 5 1138 1485 130504059 130503718 1.070000e-85 327.0
12 TraesCS6D01G274400 chr1A 81.373 102 14 4 2150 2248 492869013 492868914 1.190000e-10 78.7


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 TraesCS6D01G274400 chr6D 382795664 382799648 3984 True 7360.000000 7360 100.000 1 3985 1 chr6D.!!$R1 3984
1 TraesCS6D01G274400 chr6B 573158679 573162879 4200 True 1624.333333 2410 89.279 7 3983 3 chr6B.!!$R1 3976
2 TraesCS6D01G274400 chr6A 524865508 524869414 3906 True 2049.000000 2145 86.811 119 3892 2 chr6A.!!$R1 3773
3 TraesCS6D01G274400 chr7D 165944610 165945122 512 False 374.000000 374 80.112 1139 1672 1 chr7D.!!$F1 533
4 TraesCS6D01G274400 chr7A 167680503 167681006 503 False 372.000000 372 80.224 1139 1672 1 chr7A.!!$F1 533
5 TraesCS6D01G274400 chr7B 130120591 130121103 512 False 363.000000 363 79.626 1139 1672 1 chr7B.!!$F1 533

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
717 743 0.104304 ACAGACACACCTCGTTCCAC 59.896 55.0 0.0 0.0 0.00 4.02 F
1071 1163 0.037790 AGCCGAGCAGAGACAAGAAC 60.038 55.0 0.0 0.0 0.00 3.01 F
2522 3060 0.239347 CAACCTACACAGCAAGCAGC 59.761 55.0 0.0 0.0 46.19 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2084 0.882927 GCACAAGGGAACACGCAGTA 60.883 55.0 0.00 0.00 41.61 2.74 R
2917 3473 0.174845 CAAGCATGGCTGGGACAATG 59.825 55.0 0.00 0.00 39.62 2.82 R
3532 4124 0.880278 AAACACTGACGACGCAGCAT 60.880 50.0 15.95 5.14 39.51 3.79 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
26 27 1.941294 AGATCTCGTACTGTAGTGCCG 59.059 52.381 0.00 0.00 0.00 5.69
39 40 4.188462 TGTAGTGCCGTCATAAATGGAAG 58.812 43.478 0.00 0.00 35.91 3.46
51 52 3.848272 AAATGGAAGCACGTACAATGG 57.152 42.857 0.00 0.00 0.00 3.16
74 75 3.536917 CGCCGTATGCAGGGAGGA 61.537 66.667 5.48 0.00 41.33 3.71
97 98 8.313292 AGGATCCAGATTAGTACTACTACTACG 58.687 40.741 15.82 0.00 35.54 3.51
98 99 8.093927 GGATCCAGATTAGTACTACTACTACGT 58.906 40.741 6.95 0.00 35.54 3.57
100 101 9.921637 ATCCAGATTAGTACTACTACTACGTAC 57.078 37.037 0.91 0.00 35.54 3.67
101 102 9.137459 TCCAGATTAGTACTACTACTACGTACT 57.863 37.037 0.91 0.00 44.22 2.73
109 110 7.776030 AGTACTACTACTACGTACTACTCTGGA 59.224 40.741 0.00 0.00 41.30 3.86
116 121 5.877012 ACTACGTACTACTCTGGATCGAAAA 59.123 40.000 0.00 0.00 0.00 2.29
126 131 6.055588 ACTCTGGATCGAAAAAGACAAAAGA 58.944 36.000 0.00 0.00 0.00 2.52
127 132 6.203723 ACTCTGGATCGAAAAAGACAAAAGAG 59.796 38.462 0.00 0.00 0.00 2.85
152 162 3.619038 GGATCGATTTGACAGTGGAAGTC 59.381 47.826 0.00 0.00 36.55 3.01
153 163 2.672714 TCGATTTGACAGTGGAAGTCG 58.327 47.619 12.84 12.84 38.83 4.18
161 171 0.318699 CAGTGGAAGTCGCGTCTTGA 60.319 55.000 22.84 6.81 0.00 3.02
180 190 0.246635 ATCAGCCTACCGACACACAC 59.753 55.000 0.00 0.00 0.00 3.82
181 191 1.110518 TCAGCCTACCGACACACACA 61.111 55.000 0.00 0.00 0.00 3.72
182 192 0.667487 CAGCCTACCGACACACACAG 60.667 60.000 0.00 0.00 0.00 3.66
183 193 2.027625 GCCTACCGACACACACAGC 61.028 63.158 0.00 0.00 0.00 4.40
184 194 1.365999 CCTACCGACACACACAGCA 59.634 57.895 0.00 0.00 0.00 4.41
185 195 0.944311 CCTACCGACACACACAGCAC 60.944 60.000 0.00 0.00 0.00 4.40
186 196 0.249280 CTACCGACACACACAGCACA 60.249 55.000 0.00 0.00 0.00 4.57
187 197 0.249280 TACCGACACACACAGCACAG 60.249 55.000 0.00 0.00 0.00 3.66
280 291 8.407064 TCTTCTTATCGTGTCTTTAAGAGATCC 58.593 37.037 0.00 0.00 36.61 3.36
304 316 8.768501 CCATCTATGGCTTGACCTATACTATA 57.231 38.462 0.00 0.00 41.75 1.31
313 325 7.094291 GGCTTGACCTATACTATACACACCTAG 60.094 44.444 0.00 0.00 34.51 3.02
314 326 7.664731 GCTTGACCTATACTATACACACCTAGA 59.335 40.741 0.00 0.00 0.00 2.43
378 395 6.263754 ACCCAACCAGATTTCCAATTCTAAT 58.736 36.000 0.00 0.00 0.00 1.73
379 396 6.730507 ACCCAACCAGATTTCCAATTCTAATT 59.269 34.615 0.00 0.00 0.00 1.40
380 397 7.093333 ACCCAACCAGATTTCCAATTCTAATTC 60.093 37.037 0.00 0.00 0.00 2.17
381 398 7.124750 CCCAACCAGATTTCCAATTCTAATTCT 59.875 37.037 0.00 0.00 0.00 2.40
482 502 2.701951 TCGGGTGACTAACTTGAACCTT 59.298 45.455 0.00 0.00 0.00 3.50
527 551 3.294493 CGGTTGGGCAGTGTTGGG 61.294 66.667 0.00 0.00 0.00 4.12
528 552 3.615709 GGTTGGGCAGTGTTGGGC 61.616 66.667 0.00 0.00 0.00 5.36
529 553 2.837291 GTTGGGCAGTGTTGGGCA 60.837 61.111 0.00 0.00 0.00 5.36
530 554 2.200930 TTGGGCAGTGTTGGGCAT 59.799 55.556 0.00 0.00 0.00 4.40
531 555 1.459158 TTGGGCAGTGTTGGGCATT 60.459 52.632 0.00 0.00 0.00 3.56
532 556 1.053264 TTGGGCAGTGTTGGGCATTT 61.053 50.000 0.00 0.00 0.00 2.32
533 557 1.053264 TGGGCAGTGTTGGGCATTTT 61.053 50.000 0.00 0.00 0.00 1.82
534 558 0.320683 GGGCAGTGTTGGGCATTTTC 60.321 55.000 0.00 0.00 0.00 2.29
535 559 0.681175 GGCAGTGTTGGGCATTTTCT 59.319 50.000 0.00 0.00 0.00 2.52
536 560 1.606224 GGCAGTGTTGGGCATTTTCTG 60.606 52.381 0.00 0.00 0.00 3.02
537 561 1.069049 GCAGTGTTGGGCATTTTCTGT 59.931 47.619 0.00 0.00 0.00 3.41
538 562 2.483538 GCAGTGTTGGGCATTTTCTGTT 60.484 45.455 0.00 0.00 0.00 3.16
539 563 3.125316 CAGTGTTGGGCATTTTCTGTTG 58.875 45.455 0.00 0.00 0.00 3.33
540 564 2.102925 AGTGTTGGGCATTTTCTGTTGG 59.897 45.455 0.00 0.00 0.00 3.77
541 565 1.202627 TGTTGGGCATTTTCTGTTGGC 60.203 47.619 0.00 0.00 37.66 4.52
618 642 1.737793 GAGTAACCACAATGGAAGCCG 59.262 52.381 0.84 0.00 40.96 5.52
682 708 3.670472 CGCTTTCACATGCATGCG 58.330 55.556 26.53 17.70 37.57 4.73
684 710 2.502123 GCTTTCACATGCATGCGCG 61.502 57.895 26.53 15.03 42.97 6.86
695 721 4.016629 ATGCGCGCACACACACAG 62.017 61.111 39.05 0.00 0.00 3.66
697 723 4.360027 GCGCGCACACACACAGAG 62.360 66.667 29.10 0.00 0.00 3.35
703 729 1.212616 GCACACACACAGAGACAGAC 58.787 55.000 0.00 0.00 0.00 3.51
705 731 2.196749 CACACACACAGAGACAGACAC 58.803 52.381 0.00 0.00 0.00 3.67
706 732 1.824852 ACACACACAGAGACAGACACA 59.175 47.619 0.00 0.00 0.00 3.72
707 733 2.196749 CACACACAGAGACAGACACAC 58.803 52.381 0.00 0.00 0.00 3.82
708 734 1.137086 ACACACAGAGACAGACACACC 59.863 52.381 0.00 0.00 0.00 4.16
710 736 1.683917 ACACAGAGACAGACACACCTC 59.316 52.381 0.00 0.00 0.00 3.85
711 737 0.955178 ACAGAGACAGACACACCTCG 59.045 55.000 0.00 0.00 0.00 4.63
712 738 0.955178 CAGAGACAGACACACCTCGT 59.045 55.000 0.00 0.00 0.00 4.18
714 740 1.609555 AGAGACAGACACACCTCGTTC 59.390 52.381 0.00 0.00 0.00 3.95
715 741 0.674534 AGACAGACACACCTCGTTCC 59.325 55.000 0.00 0.00 0.00 3.62
716 742 0.387929 GACAGACACACCTCGTTCCA 59.612 55.000 0.00 0.00 0.00 3.53
717 743 0.104304 ACAGACACACCTCGTTCCAC 59.896 55.000 0.00 0.00 0.00 4.02
718 744 0.600255 CAGACACACCTCGTTCCACC 60.600 60.000 0.00 0.00 0.00 4.61
719 745 1.663702 GACACACCTCGTTCCACCG 60.664 63.158 0.00 0.00 0.00 4.94
720 746 3.041940 CACACCTCGTTCCACCGC 61.042 66.667 0.00 0.00 0.00 5.68
721 747 3.231736 ACACCTCGTTCCACCGCT 61.232 61.111 0.00 0.00 0.00 5.52
722 748 2.030562 CACCTCGTTCCACCGCTT 59.969 61.111 0.00 0.00 0.00 4.68
723 749 1.597027 CACCTCGTTCCACCGCTTT 60.597 57.895 0.00 0.00 0.00 3.51
759 785 6.932356 ACTGTATTTCTAGTTGCCATGATG 57.068 37.500 0.00 0.00 0.00 3.07
760 786 5.297776 ACTGTATTTCTAGTTGCCATGATGC 59.702 40.000 0.00 0.00 0.00 3.91
762 788 2.804986 TTCTAGTTGCCATGATGCCA 57.195 45.000 0.00 0.00 0.00 4.92
763 789 3.301794 TTCTAGTTGCCATGATGCCAT 57.698 42.857 0.00 0.00 0.00 4.40
822 857 1.799258 CTGCCCAGAAACTTTGCGCT 61.799 55.000 9.73 0.00 0.00 5.92
853 892 2.874780 CACGCAGACGGACGCTAC 60.875 66.667 0.00 0.00 46.04 3.58
854 893 3.359523 ACGCAGACGGACGCTACA 61.360 61.111 0.00 0.00 46.04 2.74
868 907 1.269569 CGCTACATCGGCAATGGAGTA 60.270 52.381 11.12 0.00 46.72 2.59
869 908 2.408050 GCTACATCGGCAATGGAGTAG 58.592 52.381 11.12 0.00 46.72 2.57
870 909 2.408050 CTACATCGGCAATGGAGTAGC 58.592 52.381 3.00 0.00 40.94 3.58
871 910 0.179045 ACATCGGCAATGGAGTAGCC 60.179 55.000 0.00 0.00 44.89 3.93
872 911 0.886490 CATCGGCAATGGAGTAGCCC 60.886 60.000 0.00 0.00 45.56 5.19
873 912 2.056906 ATCGGCAATGGAGTAGCCCC 62.057 60.000 0.00 0.00 45.56 5.80
874 913 2.203209 GGCAATGGAGTAGCCCCG 60.203 66.667 0.00 0.00 42.58 5.73
927 966 3.468007 CGCAAGAGAGACAAGGCG 58.532 61.111 0.00 0.00 43.02 5.52
1006 1051 1.415672 TTTCGCCACCACTCCTCCTT 61.416 55.000 0.00 0.00 0.00 3.36
1007 1052 1.415672 TTCGCCACCACTCCTCCTTT 61.416 55.000 0.00 0.00 0.00 3.11
1008 1053 1.376037 CGCCACCACTCCTCCTTTC 60.376 63.158 0.00 0.00 0.00 2.62
1009 1054 1.761174 GCCACCACTCCTCCTTTCA 59.239 57.895 0.00 0.00 0.00 2.69
1011 1056 1.559682 GCCACCACTCCTCCTTTCATA 59.440 52.381 0.00 0.00 0.00 2.15
1071 1163 0.037790 AGCCGAGCAGAGACAAGAAC 60.038 55.000 0.00 0.00 0.00 3.01
1082 1174 4.640201 CAGAGACAAGAACCAAGACCAAAA 59.360 41.667 0.00 0.00 0.00 2.44
1781 1920 4.883354 GGGGCTCCGGCTTCATGG 62.883 72.222 0.00 0.00 38.73 3.66
1783 1922 2.742116 GGGCTCCGGCTTCATGGTA 61.742 63.158 0.00 0.00 38.73 3.25
1863 2002 1.702957 CACCAAGGAGGAGGTAACCAA 59.297 52.381 0.00 0.00 41.22 3.67
1864 2003 2.308866 CACCAAGGAGGAGGTAACCAAT 59.691 50.000 0.00 0.00 41.22 3.16
1865 2004 3.521937 CACCAAGGAGGAGGTAACCAATA 59.478 47.826 0.00 0.00 41.22 1.90
1866 2005 3.522343 ACCAAGGAGGAGGTAACCAATAC 59.478 47.826 0.00 0.00 41.22 1.89
1867 2006 3.780850 CCAAGGAGGAGGTAACCAATACT 59.219 47.826 0.00 0.00 41.22 2.12
1868 2007 4.384208 CCAAGGAGGAGGTAACCAATACTG 60.384 50.000 0.00 0.00 41.22 2.74
1926 2079 1.600957 CATCCATTCTCCACGTGCATC 59.399 52.381 10.91 0.00 0.00 3.91
1931 2084 0.673333 TTCTCCACGTGCATCGCATT 60.673 50.000 10.91 0.00 41.91 3.56
1974 2127 3.374988 CAGTGCGTGATACCACATGAATT 59.625 43.478 0.00 0.00 43.34 2.17
1975 2128 4.570369 CAGTGCGTGATACCACATGAATTA 59.430 41.667 0.00 0.00 43.34 1.40
1976 2129 4.811024 AGTGCGTGATACCACATGAATTAG 59.189 41.667 0.00 0.00 43.34 1.73
1992 2145 8.965172 ACATGAATTAGTATATTCGTTCGACAC 58.035 33.333 0.00 0.00 37.34 3.67
1993 2146 8.964150 CATGAATTAGTATATTCGTTCGACACA 58.036 33.333 0.00 0.00 37.34 3.72
1994 2147 8.331539 TGAATTAGTATATTCGTTCGACACAC 57.668 34.615 0.00 0.00 37.34 3.82
2000 2153 2.281140 TTCGTTCGACACACAACTCA 57.719 45.000 0.00 0.00 0.00 3.41
2003 2156 1.781429 CGTTCGACACACAACTCAGAG 59.219 52.381 0.00 0.00 0.00 3.35
2026 2206 5.731599 CAAGATCTGCATTCTTACCACTC 57.268 43.478 10.69 0.00 32.27 3.51
2053 2234 2.148768 CTTGAGTTGAGATGCACAGCA 58.851 47.619 0.00 0.00 44.86 4.41
2096 2277 9.970553 ATATATAGTACTGTAGAATTCGTCCCA 57.029 33.333 5.39 0.00 0.00 4.37
2099 2280 3.543680 ACTGTAGAATTCGTCCCATGG 57.456 47.619 4.14 4.14 0.00 3.66
2100 2281 2.213499 CTGTAGAATTCGTCCCATGGC 58.787 52.381 6.09 0.00 0.00 4.40
2101 2282 1.557371 TGTAGAATTCGTCCCATGGCA 59.443 47.619 6.09 0.00 0.00 4.92
2102 2283 2.213499 GTAGAATTCGTCCCATGGCAG 58.787 52.381 6.09 0.00 0.00 4.85
2103 2284 0.749454 AGAATTCGTCCCATGGCAGC 60.749 55.000 6.09 0.00 0.00 5.25
2105 2286 0.611618 AATTCGTCCCATGGCAGCAA 60.612 50.000 6.09 0.00 0.00 3.91
2107 2288 1.314534 TTCGTCCCATGGCAGCAATG 61.315 55.000 6.09 2.24 0.00 2.82
2138 2319 8.850156 TCTAGAAGAAGAAACAAAAATCTTGGG 58.150 33.333 0.00 0.00 36.08 4.12
2165 2346 5.687706 GCAATGCCAAGTATACTACTCCCTT 60.688 44.000 5.65 0.00 38.26 3.95
2172 2353 5.579753 AGTATACTACTCCCTTCATCCGA 57.420 43.478 2.75 0.00 32.47 4.55
2177 2358 5.437191 ACTACTCCCTTCATCCGAAAATT 57.563 39.130 0.00 0.00 0.00 1.82
2183 2364 4.700213 TCCCTTCATCCGAAAATTCTTGTC 59.300 41.667 0.00 0.00 0.00 3.18
2200 2621 6.012658 TCTTGTCGGAGAAATGAAAAATGG 57.987 37.500 0.00 0.00 39.69 3.16
2201 2622 5.534654 TCTTGTCGGAGAAATGAAAAATGGT 59.465 36.000 0.00 0.00 39.69 3.55
2244 2665 9.872684 ATACATTTGAATACATCCATTTCTCCT 57.127 29.630 0.00 0.00 0.00 3.69
2259 2680 2.081078 TCCTGACGGAGGGAGTACA 58.919 57.895 0.00 0.00 43.06 2.90
2299 2831 1.404315 GGGTTTTGTTCGGTTTGTGCA 60.404 47.619 0.00 0.00 0.00 4.57
2300 2832 2.545731 GGTTTTGTTCGGTTTGTGCAT 58.454 42.857 0.00 0.00 0.00 3.96
2415 2947 2.094700 CAGTACAGCGGCAAGAAGAGTA 60.095 50.000 1.45 0.00 0.00 2.59
2484 3022 3.747708 GCACTACACCTGGGAAACTCTTT 60.748 47.826 0.00 0.00 0.00 2.52
2522 3060 0.239347 CAACCTACACAGCAAGCAGC 59.761 55.000 0.00 0.00 46.19 5.25
2559 3097 1.602377 GGTTTCCTCTTTCACACACCG 59.398 52.381 0.00 0.00 0.00 4.94
2563 3101 1.616865 TCCTCTTTCACACACCGGTAG 59.383 52.381 6.87 5.57 0.00 3.18
2589 3130 9.492973 GTATTTAACAACTGGAGTTAGTAACCA 57.507 33.333 9.46 0.95 36.32 3.67
2677 3218 6.693466 CAAATAAATCATATGCTGGCCATCA 58.307 36.000 12.49 12.49 35.34 3.07
2685 3226 2.459060 TGCTGGCCATCATTTTTGTG 57.541 45.000 5.51 0.00 0.00 3.33
2687 3228 2.104451 TGCTGGCCATCATTTTTGTGTT 59.896 40.909 5.51 0.00 0.00 3.32
2688 3229 2.481185 GCTGGCCATCATTTTTGTGTTG 59.519 45.455 5.51 0.00 0.00 3.33
2694 3235 5.163673 GGCCATCATTTTTGTGTTGTGTTTT 60.164 36.000 0.00 0.00 0.00 2.43
2695 3236 6.037610 GGCCATCATTTTTGTGTTGTGTTTTA 59.962 34.615 0.00 0.00 0.00 1.52
2717 3271 9.442047 TTTTAAAATTGTCTTGTGGTGTTGAAT 57.558 25.926 0.00 0.00 0.00 2.57
2735 3289 3.888930 TGAATCCAGACCCACAAGTTTTC 59.111 43.478 0.00 0.00 0.00 2.29
2746 3300 4.173256 CCACAAGTTTTCTTTTGAGCGTT 58.827 39.130 0.00 0.00 39.22 4.84
2749 3303 4.857037 ACAAGTTTTCTTTTGAGCGTTGAC 59.143 37.500 0.00 0.00 38.17 3.18
2752 3306 4.083003 AGTTTTCTTTTGAGCGTTGACACA 60.083 37.500 0.00 0.00 0.00 3.72
2755 3309 4.725556 TCTTTTGAGCGTTGACACATAC 57.274 40.909 0.00 0.00 0.00 2.39
2756 3310 4.123506 TCTTTTGAGCGTTGACACATACA 58.876 39.130 0.00 0.00 0.00 2.29
2757 3311 4.754618 TCTTTTGAGCGTTGACACATACAT 59.245 37.500 0.00 0.00 0.00 2.29
2758 3312 4.661993 TTTGAGCGTTGACACATACATC 57.338 40.909 0.00 0.00 0.00 3.06
2759 3313 3.592898 TGAGCGTTGACACATACATCT 57.407 42.857 0.00 0.00 0.00 2.90
2760 3314 3.253230 TGAGCGTTGACACATACATCTG 58.747 45.455 0.00 0.00 0.00 2.90
2762 3316 3.664107 AGCGTTGACACATACATCTGTT 58.336 40.909 0.00 0.00 0.00 3.16
2763 3317 4.816392 AGCGTTGACACATACATCTGTTA 58.184 39.130 0.00 0.00 0.00 2.41
2764 3318 5.419542 AGCGTTGACACATACATCTGTTAT 58.580 37.500 0.00 0.00 0.00 1.89
2765 3319 5.291858 AGCGTTGACACATACATCTGTTATG 59.708 40.000 0.00 0.00 0.00 1.90
2766 3320 5.492854 CGTTGACACATACATCTGTTATGC 58.507 41.667 0.00 0.00 0.00 3.14
2767 3321 5.063312 CGTTGACACATACATCTGTTATGCA 59.937 40.000 0.00 0.00 0.00 3.96
2773 3329 7.483307 ACACATACATCTGTTATGCAAAATCC 58.517 34.615 0.00 0.00 0.00 3.01
2780 3336 6.561737 TCTGTTATGCAAAATCCGTGTAAA 57.438 33.333 0.00 0.00 0.00 2.01
2791 3347 1.536331 TCCGTGTAAAAATTGTCGCCC 59.464 47.619 0.00 0.00 0.00 6.13
2795 3351 3.304123 CGTGTAAAAATTGTCGCCCTTCA 60.304 43.478 0.00 0.00 0.00 3.02
2816 3372 5.895928 TCATGAAGTCTAATCTTGTCTCCG 58.104 41.667 0.00 0.00 0.00 4.63
2836 3392 2.223144 CGTTTCCATGTTTCAGAAGCGA 59.777 45.455 10.73 0.00 43.94 4.93
2880 3436 1.067985 CGAGCTGATAGCATGACCGAT 60.068 52.381 0.00 0.00 45.56 4.18
2917 3473 3.118738 AGACGAGTTAACACATCCATCCC 60.119 47.826 8.61 0.00 0.00 3.85
2919 3475 3.199946 ACGAGTTAACACATCCATCCCAT 59.800 43.478 8.61 0.00 0.00 4.00
2984 3540 6.231951 GGAGTTATAAACCTATCTTGAGGCC 58.768 44.000 0.00 0.00 40.65 5.19
3153 3711 4.261825 CGTGTTTCTGGACTCTCTCTTCTT 60.262 45.833 0.00 0.00 0.00 2.52
3253 3811 1.133253 CTGTGCGAGCCAATTGTCG 59.867 57.895 12.68 12.68 39.25 4.35
3265 3823 2.333926 CAATTGTCGCGGTCAACTCTA 58.666 47.619 16.75 0.00 0.00 2.43
3282 3871 6.314648 TCAACTCTATGTGCATGATTTCAGAC 59.685 38.462 0.00 0.00 0.00 3.51
3319 3908 1.081641 CCTGCTGCAGTTTGCTTCG 60.082 57.895 26.41 6.41 45.31 3.79
3384 3973 1.213678 CCTGCATGATTCTGGAAGGGA 59.786 52.381 0.00 0.00 0.00 4.20
3585 4177 0.661552 CAGATGGCGATGAAAGGCTG 59.338 55.000 0.00 0.00 35.01 4.85
3586 4178 0.543277 AGATGGCGATGAAAGGCTGA 59.457 50.000 0.00 0.00 35.01 4.26
3678 4270 2.756760 GTGGTGTTGCATCCAATCATCT 59.243 45.455 7.24 0.00 35.38 2.90
3708 4300 2.029244 CACATGTTACGCGATCTGAACC 59.971 50.000 15.93 0.00 0.00 3.62
3751 4348 6.611613 TCTATGGTGTGAGAAAGTCAGATT 57.388 37.500 0.00 0.00 35.13 2.40
3786 4383 6.155221 TGCAGGTATACTTTCTGAATCTGAGT 59.845 38.462 10.69 0.00 0.00 3.41
3860 4467 0.109342 CCTTACTGGCTGCCCCTATG 59.891 60.000 17.53 7.32 0.00 2.23
3950 4557 5.640147 TGTTCTTAACCTCATTTCATGGGT 58.360 37.500 0.00 0.00 36.01 4.51
3958 4565 3.433314 CCTCATTTCATGGGTCTCTCCAG 60.433 52.174 0.00 0.00 40.56 3.86
3964 4571 2.182827 CATGGGTCTCTCCAGAGTTGA 58.817 52.381 3.50 0.00 42.60 3.18
3968 4575 2.834549 GGGTCTCTCCAGAGTTGATTGA 59.165 50.000 3.50 0.00 42.60 2.57
3973 4580 5.637387 GTCTCTCCAGAGTTGATTGAAGAAC 59.363 44.000 3.50 0.00 42.60 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.949451 ACAGTACGAGATCTGGCTTG 57.051 50.000 0.00 1.00 36.17 4.01
1 2 3.378742 CACTACAGTACGAGATCTGGCTT 59.621 47.826 0.00 0.00 36.17 4.35
2 3 2.946329 CACTACAGTACGAGATCTGGCT 59.054 50.000 0.00 0.00 36.17 4.75
3 4 2.541999 GCACTACAGTACGAGATCTGGC 60.542 54.545 0.00 0.00 36.17 4.85
4 5 2.033550 GGCACTACAGTACGAGATCTGG 59.966 54.545 0.00 0.00 36.17 3.86
5 6 2.286477 CGGCACTACAGTACGAGATCTG 60.286 54.545 0.00 0.00 37.65 2.90
16 17 3.792401 TCCATTTATGACGGCACTACAG 58.208 45.455 0.00 0.00 0.00 2.74
26 27 5.539582 TTGTACGTGCTTCCATTTATGAC 57.460 39.130 4.97 0.00 0.00 3.06
39 40 1.641677 GATCGGCCATTGTACGTGC 59.358 57.895 2.24 0.00 0.00 5.34
61 62 1.722034 TCTGGATCCTCCCTGCATAC 58.278 55.000 14.23 0.00 35.03 2.39
91 92 5.774498 TCGATCCAGAGTAGTACGTAGTA 57.226 43.478 6.02 6.02 45.11 1.82
94 95 6.595326 TCTTTTTCGATCCAGAGTAGTACGTA 59.405 38.462 0.00 0.00 0.00 3.57
97 98 6.618811 TGTCTTTTTCGATCCAGAGTAGTAC 58.381 40.000 0.00 0.00 0.00 2.73
98 99 6.829229 TGTCTTTTTCGATCCAGAGTAGTA 57.171 37.500 0.00 0.00 0.00 1.82
100 101 7.385205 TCTTTTGTCTTTTTCGATCCAGAGTAG 59.615 37.037 0.00 0.00 0.00 2.57
101 102 7.214381 TCTTTTGTCTTTTTCGATCCAGAGTA 58.786 34.615 0.00 0.00 0.00 2.59
102 103 6.055588 TCTTTTGTCTTTTTCGATCCAGAGT 58.944 36.000 0.00 0.00 0.00 3.24
103 104 6.348050 CCTCTTTTGTCTTTTTCGATCCAGAG 60.348 42.308 0.00 0.00 0.00 3.35
104 105 5.470098 CCTCTTTTGTCTTTTTCGATCCAGA 59.530 40.000 0.00 0.00 0.00 3.86
105 106 5.335191 CCCTCTTTTGTCTTTTTCGATCCAG 60.335 44.000 0.00 0.00 0.00 3.86
106 107 4.518970 CCCTCTTTTGTCTTTTTCGATCCA 59.481 41.667 0.00 0.00 0.00 3.41
109 110 3.826729 CCCCCTCTTTTGTCTTTTTCGAT 59.173 43.478 0.00 0.00 0.00 3.59
116 121 2.266279 TCGATCCCCCTCTTTTGTCTT 58.734 47.619 0.00 0.00 0.00 3.01
126 131 1.210478 CACTGTCAAATCGATCCCCCT 59.790 52.381 0.00 0.00 0.00 4.79
127 132 1.668419 CACTGTCAAATCGATCCCCC 58.332 55.000 0.00 0.00 0.00 5.40
152 162 0.872021 GGTAGGCTGATCAAGACGCG 60.872 60.000 3.53 3.53 39.88 6.01
153 163 0.872021 CGGTAGGCTGATCAAGACGC 60.872 60.000 0.00 0.00 39.88 5.19
161 171 0.246635 GTGTGTGTCGGTAGGCTGAT 59.753 55.000 0.00 0.00 31.86 2.90
180 190 2.637589 CTGTGCTGTGCTGTGCTG 59.362 61.111 0.00 0.00 0.00 4.41
181 191 2.593725 CCTGTGCTGTGCTGTGCT 60.594 61.111 0.00 0.00 0.00 4.40
182 192 2.592574 TCCTGTGCTGTGCTGTGC 60.593 61.111 0.00 0.00 0.00 4.57
183 193 1.226686 GACTCCTGTGCTGTGCTGTG 61.227 60.000 0.00 0.00 0.00 3.66
184 194 1.070445 GACTCCTGTGCTGTGCTGT 59.930 57.895 0.00 0.00 0.00 4.40
185 195 2.025969 CGACTCCTGTGCTGTGCTG 61.026 63.158 0.00 0.00 0.00 4.41
186 196 2.341543 CGACTCCTGTGCTGTGCT 59.658 61.111 0.00 0.00 0.00 4.40
187 197 2.024319 GACGACTCCTGTGCTGTGC 61.024 63.158 0.00 0.00 0.00 4.57
239 250 8.037758 ACGATAAGAAGATGTCAACTGAATTCT 58.962 33.333 7.05 0.00 0.00 2.40
280 291 9.190317 TGTATAGTATAGGTCAAGCCATAGATG 57.810 37.037 0.00 0.00 40.61 2.90
304 316 5.181748 CGGTAGTAACTACTCTAGGTGTGT 58.818 45.833 0.48 0.00 37.16 3.72
313 325 4.043073 GCAAGATGCGGTAGTAACTACTC 58.957 47.826 0.48 0.00 33.87 2.59
314 326 4.043037 GCAAGATGCGGTAGTAACTACT 57.957 45.455 1.86 1.86 33.87 2.57
378 395 7.201803 GCTCCGGTTCTAGAATTAGAGTTAGAA 60.202 40.741 20.61 0.00 37.24 2.10
379 396 6.262720 GCTCCGGTTCTAGAATTAGAGTTAGA 59.737 42.308 20.61 6.13 37.24 2.10
380 397 6.440436 GCTCCGGTTCTAGAATTAGAGTTAG 58.560 44.000 20.61 9.30 37.24 2.34
381 398 5.008415 CGCTCCGGTTCTAGAATTAGAGTTA 59.992 44.000 20.61 1.59 37.24 2.24
384 401 3.304794 CCGCTCCGGTTCTAGAATTAGAG 60.305 52.174 8.75 14.54 42.73 2.43
420 440 2.190161 TCGCCTTAATGTGAACGATCG 58.810 47.619 14.88 14.88 0.00 3.69
436 456 3.012518 CCTTTCCATATCCATGATCGCC 58.987 50.000 0.00 0.00 33.67 5.54
527 551 2.477754 GCTCTTTGCCAACAGAAAATGC 59.522 45.455 0.00 0.00 35.15 3.56
528 552 3.986277 AGCTCTTTGCCAACAGAAAATG 58.014 40.909 0.00 0.00 44.23 2.32
529 553 5.789643 TTAGCTCTTTGCCAACAGAAAAT 57.210 34.783 0.00 0.00 44.23 1.82
530 554 5.590530 TTTAGCTCTTTGCCAACAGAAAA 57.409 34.783 0.00 0.00 44.23 2.29
531 555 4.499696 GCTTTAGCTCTTTGCCAACAGAAA 60.500 41.667 0.00 0.00 44.23 2.52
532 556 3.004734 GCTTTAGCTCTTTGCCAACAGAA 59.995 43.478 0.00 0.00 44.23 3.02
533 557 2.554032 GCTTTAGCTCTTTGCCAACAGA 59.446 45.455 0.00 0.00 44.23 3.41
534 558 2.352127 GGCTTTAGCTCTTTGCCAACAG 60.352 50.000 12.98 0.00 44.23 3.16
535 559 1.613437 GGCTTTAGCTCTTTGCCAACA 59.387 47.619 12.98 0.00 44.23 3.33
536 560 2.354109 GGCTTTAGCTCTTTGCCAAC 57.646 50.000 12.98 0.00 44.23 3.77
539 563 1.613437 TGTTGGCTTTAGCTCTTTGCC 59.387 47.619 11.50 11.50 44.23 4.52
540 564 2.666026 GTGTTGGCTTTAGCTCTTTGC 58.334 47.619 0.00 0.00 41.70 3.68
541 565 2.290641 ACGTGTTGGCTTTAGCTCTTTG 59.709 45.455 0.00 0.00 41.70 2.77
618 642 4.507512 GGGGAATATCAGGAATTCAGGACC 60.508 50.000 7.93 1.82 35.46 4.46
682 708 1.825285 CTGTCTCTGTGTGTGTGCGC 61.825 60.000 0.00 0.00 0.00 6.09
684 710 1.212616 GTCTGTCTCTGTGTGTGTGC 58.787 55.000 0.00 0.00 0.00 4.57
695 721 1.336056 GGAACGAGGTGTGTCTGTCTC 60.336 57.143 0.00 0.00 0.00 3.36
697 723 0.387929 TGGAACGAGGTGTGTCTGTC 59.612 55.000 0.00 0.00 0.00 3.51
703 729 2.989055 AAGCGGTGGAACGAGGTGTG 62.989 60.000 0.00 0.00 38.12 3.82
705 731 0.320073 TAAAGCGGTGGAACGAGGTG 60.320 55.000 0.00 0.00 38.12 4.00
706 732 0.320160 GTAAAGCGGTGGAACGAGGT 60.320 55.000 0.00 0.00 38.12 3.85
707 733 0.037605 AGTAAAGCGGTGGAACGAGG 60.038 55.000 0.00 0.00 38.12 4.63
708 734 1.792006 AAGTAAAGCGGTGGAACGAG 58.208 50.000 0.00 0.00 38.12 4.18
710 736 1.868498 TCAAAGTAAAGCGGTGGAACG 59.132 47.619 0.00 0.00 38.12 3.95
711 737 3.500680 TCATCAAAGTAAAGCGGTGGAAC 59.499 43.478 0.00 0.00 0.00 3.62
712 738 3.745799 TCATCAAAGTAAAGCGGTGGAA 58.254 40.909 0.00 0.00 0.00 3.53
714 740 3.334691 TCTCATCAAAGTAAAGCGGTGG 58.665 45.455 0.00 0.00 0.00 4.61
715 741 4.452455 AGTTCTCATCAAAGTAAAGCGGTG 59.548 41.667 0.00 0.00 0.00 4.94
716 742 4.452455 CAGTTCTCATCAAAGTAAAGCGGT 59.548 41.667 0.00 0.00 0.00 5.68
717 743 4.452455 ACAGTTCTCATCAAAGTAAAGCGG 59.548 41.667 0.00 0.00 0.00 5.52
718 744 5.597813 ACAGTTCTCATCAAAGTAAAGCG 57.402 39.130 0.00 0.00 0.00 4.68
719 745 9.548208 GAAATACAGTTCTCATCAAAGTAAAGC 57.452 33.333 0.00 0.00 0.00 3.51
759 785 1.106285 GGAAACTCCACCATCATGGC 58.894 55.000 2.52 0.00 42.67 4.40
760 786 1.340017 ACGGAAACTCCACCATCATGG 60.340 52.381 0.54 0.54 45.02 3.66
762 788 1.351017 ACACGGAAACTCCACCATCAT 59.649 47.619 0.00 0.00 35.91 2.45
763 789 0.762418 ACACGGAAACTCCACCATCA 59.238 50.000 0.00 0.00 35.91 3.07
765 791 1.604604 CAACACGGAAACTCCACCAT 58.395 50.000 0.00 0.00 35.91 3.55
822 857 5.006261 CCGTCTGCGTGTGAATAATTATCAA 59.994 40.000 0.00 0.00 36.15 2.57
853 892 2.621763 GGCTACTCCATTGCCGATG 58.378 57.895 0.00 0.00 39.52 3.84
874 913 3.599704 GATGCAGATTGCCGGGGC 61.600 66.667 2.18 1.86 44.23 5.80
910 949 1.075425 CTCGCCTTGTCTCTCTTGCG 61.075 60.000 0.00 0.00 43.05 4.85
911 950 1.357991 GCTCGCCTTGTCTCTCTTGC 61.358 60.000 0.00 0.00 0.00 4.01
912 951 1.075425 CGCTCGCCTTGTCTCTCTTG 61.075 60.000 0.00 0.00 0.00 3.02
913 952 1.214062 CGCTCGCCTTGTCTCTCTT 59.786 57.895 0.00 0.00 0.00 2.85
914 953 2.881389 CGCTCGCCTTGTCTCTCT 59.119 61.111 0.00 0.00 0.00 3.10
1006 1051 5.849081 GCGTCGTGATCTTTTGTTTTATGAA 59.151 36.000 0.00 0.00 0.00 2.57
1007 1052 5.050023 TGCGTCGTGATCTTTTGTTTTATGA 60.050 36.000 0.00 0.00 0.00 2.15
1008 1053 5.058008 GTGCGTCGTGATCTTTTGTTTTATG 59.942 40.000 0.00 0.00 0.00 1.90
1009 1054 5.144359 GTGCGTCGTGATCTTTTGTTTTAT 58.856 37.500 0.00 0.00 0.00 1.40
1011 1056 3.181505 TGTGCGTCGTGATCTTTTGTTTT 60.182 39.130 0.00 0.00 0.00 2.43
1071 1163 0.593773 CGGCGTGTTTTTGGTCTTGG 60.594 55.000 0.00 0.00 0.00 3.61
1122 1223 3.093172 CCCCTCCCTCTCCTTGCC 61.093 72.222 0.00 0.00 0.00 4.52
1126 1227 3.443479 ATCGCCCCTCCCTCTCCT 61.443 66.667 0.00 0.00 0.00 3.69
1127 1228 3.237741 CATCGCCCCTCCCTCTCC 61.238 72.222 0.00 0.00 0.00 3.71
1128 1229 3.237741 CCATCGCCCCTCCCTCTC 61.238 72.222 0.00 0.00 0.00 3.20
1129 1230 4.888325 CCCATCGCCCCTCCCTCT 62.888 72.222 0.00 0.00 0.00 3.69
1462 1583 4.680537 AGGTCGGAGGTGGAGCGT 62.681 66.667 0.00 0.00 37.02 5.07
1863 2002 7.063593 TGAAGAGTAGGAGCAGTAATCAGTAT 58.936 38.462 0.00 0.00 0.00 2.12
1864 2003 6.424032 TGAAGAGTAGGAGCAGTAATCAGTA 58.576 40.000 0.00 0.00 0.00 2.74
1865 2004 5.265191 TGAAGAGTAGGAGCAGTAATCAGT 58.735 41.667 0.00 0.00 0.00 3.41
1866 2005 5.843673 TGAAGAGTAGGAGCAGTAATCAG 57.156 43.478 0.00 0.00 0.00 2.90
1867 2006 6.605471 TTTGAAGAGTAGGAGCAGTAATCA 57.395 37.500 0.00 0.00 0.00 2.57
1868 2007 7.268586 TGATTTGAAGAGTAGGAGCAGTAATC 58.731 38.462 0.00 0.00 0.00 1.75
1931 2084 0.882927 GCACAAGGGAACACGCAGTA 60.883 55.000 0.00 0.00 41.61 2.74
1965 2118 8.964150 TGTCGAACGAATATACTAATTCATGTG 58.036 33.333 0.00 0.00 35.93 3.21
1974 2127 6.845302 AGTTGTGTGTCGAACGAATATACTA 58.155 36.000 0.00 0.00 0.00 1.82
1975 2128 5.706916 AGTTGTGTGTCGAACGAATATACT 58.293 37.500 0.00 0.00 0.00 2.12
1976 2129 5.570206 TGAGTTGTGTGTCGAACGAATATAC 59.430 40.000 0.00 1.38 0.00 1.47
2017 2197 3.325135 ACTCAAGTTGGAGGAGTGGTAAG 59.675 47.826 2.34 0.00 40.21 2.34
2096 2277 6.776744 TCTTCTAGAATATCATTGCTGCCAT 58.223 36.000 5.44 0.00 0.00 4.40
2099 2280 7.959689 TCTTCTTCTAGAATATCATTGCTGC 57.040 36.000 5.44 0.00 33.13 5.25
2101 2282 9.896645 TGTTTCTTCTTCTAGAATATCATTGCT 57.103 29.630 5.44 0.00 33.13 3.91
2138 2319 4.474226 GTAGTATACTTGGCATTGCTGC 57.526 45.455 11.40 0.00 42.44 5.25
2148 2329 7.201884 TTTCGGATGAAGGGAGTAGTATACTTG 60.202 40.741 11.40 0.00 43.41 3.16
2149 2330 6.837568 TTTCGGATGAAGGGAGTAGTATACTT 59.162 38.462 11.40 0.00 43.41 2.24
2172 2353 8.940768 TTTTTCATTTCTCCGACAAGAATTTT 57.059 26.923 0.00 0.00 35.30 1.82
2177 2358 5.534654 ACCATTTTTCATTTCTCCGACAAGA 59.465 36.000 0.00 0.00 0.00 3.02
2183 2364 7.538575 AGATACAACCATTTTTCATTTCTCCG 58.461 34.615 0.00 0.00 0.00 4.63
2222 2643 7.012704 CGTCAGGAGAAATGGATGTATTCAAAT 59.987 37.037 0.00 0.00 0.00 2.32
2224 2645 5.817296 CGTCAGGAGAAATGGATGTATTCAA 59.183 40.000 0.00 0.00 0.00 2.69
2227 2648 4.408921 TCCGTCAGGAGAAATGGATGTATT 59.591 41.667 0.00 0.00 42.75 1.89
2244 2665 3.053842 ACTCTAATGTACTCCCTCCGTCA 60.054 47.826 0.00 0.00 0.00 4.35
2314 2846 3.582780 GCTGCTTTTGTACTAGTACGGT 58.417 45.455 24.36 0.00 38.85 4.83
2316 2848 3.367025 GTGGCTGCTTTTGTACTAGTACG 59.633 47.826 24.36 13.32 38.85 3.67
2320 2852 4.392138 GGTTAGTGGCTGCTTTTGTACTAG 59.608 45.833 0.00 0.00 0.00 2.57
2321 2853 4.202377 TGGTTAGTGGCTGCTTTTGTACTA 60.202 41.667 0.00 0.00 0.00 1.82
2322 2854 3.146847 GGTTAGTGGCTGCTTTTGTACT 58.853 45.455 0.00 0.00 0.00 2.73
2323 2855 2.882137 TGGTTAGTGGCTGCTTTTGTAC 59.118 45.455 0.00 0.00 0.00 2.90
2324 2856 2.882137 GTGGTTAGTGGCTGCTTTTGTA 59.118 45.455 0.00 0.00 0.00 2.41
2325 2857 1.681264 GTGGTTAGTGGCTGCTTTTGT 59.319 47.619 0.00 0.00 0.00 2.83
2326 2858 1.956477 AGTGGTTAGTGGCTGCTTTTG 59.044 47.619 0.00 0.00 0.00 2.44
2438 2976 4.384208 GCCACTGAGACAGGGTATATGTTT 60.384 45.833 0.00 0.00 32.12 2.83
2444 2982 1.961180 GCGCCACTGAGACAGGGTAT 61.961 60.000 0.00 0.00 32.12 2.73
2563 3101 9.492973 TGGTTACTAACTCCAGTTGTTAAATAC 57.507 33.333 2.01 0.00 38.90 1.89
2652 3193 4.885413 TGGCCAGCATATGATTTATTTGC 58.115 39.130 0.00 0.00 42.07 3.68
2653 3194 6.693466 TGATGGCCAGCATATGATTTATTTG 58.307 36.000 22.27 0.00 0.00 2.32
2662 3203 4.509970 CACAAAAATGATGGCCAGCATATG 59.490 41.667 35.18 31.15 36.27 1.78
2663 3204 4.162698 ACACAAAAATGATGGCCAGCATAT 59.837 37.500 35.18 24.12 36.27 1.78
2664 3205 3.514706 ACACAAAAATGATGGCCAGCATA 59.485 39.130 35.18 10.64 36.27 3.14
2671 3212 5.482686 AAACACAACACAAAAATGATGGC 57.517 34.783 0.00 0.00 0.00 4.40
2685 3226 7.954786 CACCACAAGACAATTTTAAAACACAAC 59.045 33.333 1.97 0.00 0.00 3.32
2687 3228 7.155328 ACACCACAAGACAATTTTAAAACACA 58.845 30.769 1.97 0.00 0.00 3.72
2688 3229 7.589574 ACACCACAAGACAATTTTAAAACAC 57.410 32.000 1.97 0.00 0.00 3.32
2694 3235 7.147828 TGGATTCAACACCACAAGACAATTTTA 60.148 33.333 0.00 0.00 0.00 1.52
2695 3236 6.048509 GGATTCAACACCACAAGACAATTTT 58.951 36.000 0.00 0.00 0.00 1.82
2701 3242 3.251004 GTCTGGATTCAACACCACAAGAC 59.749 47.826 0.00 0.00 32.44 3.01
2717 3271 3.662759 AAGAAAACTTGTGGGTCTGGA 57.337 42.857 0.00 0.00 0.00 3.86
2735 3289 4.466567 TGTATGTGTCAACGCTCAAAAG 57.533 40.909 0.00 0.00 0.00 2.27
2746 3300 7.446001 TTTTGCATAACAGATGTATGTGTCA 57.554 32.000 0.00 0.00 32.63 3.58
2749 3303 6.634035 CGGATTTTGCATAACAGATGTATGTG 59.366 38.462 0.00 0.00 32.52 3.21
2752 3306 6.318648 ACACGGATTTTGCATAACAGATGTAT 59.681 34.615 0.00 0.00 0.00 2.29
2755 3309 4.985413 ACACGGATTTTGCATAACAGATG 58.015 39.130 0.00 0.00 0.00 2.90
2756 3310 6.751514 TTACACGGATTTTGCATAACAGAT 57.248 33.333 0.00 0.00 0.00 2.90
2757 3311 6.561737 TTTACACGGATTTTGCATAACAGA 57.438 33.333 0.00 0.00 0.00 3.41
2758 3312 7.630470 TTTTTACACGGATTTTGCATAACAG 57.370 32.000 0.00 0.00 0.00 3.16
2759 3313 8.491152 CAATTTTTACACGGATTTTGCATAACA 58.509 29.630 0.00 0.00 0.00 2.41
2760 3314 8.491950 ACAATTTTTACACGGATTTTGCATAAC 58.508 29.630 0.00 0.00 0.00 1.89
2762 3316 7.061210 CGACAATTTTTACACGGATTTTGCATA 59.939 33.333 0.00 0.00 0.00 3.14
2763 3317 6.128956 CGACAATTTTTACACGGATTTTGCAT 60.129 34.615 0.00 0.00 0.00 3.96
2764 3318 5.174035 CGACAATTTTTACACGGATTTTGCA 59.826 36.000 0.00 0.00 0.00 4.08
2765 3319 5.595065 CGACAATTTTTACACGGATTTTGC 58.405 37.500 0.00 0.00 0.00 3.68
2766 3320 5.387958 GGCGACAATTTTTACACGGATTTTG 60.388 40.000 0.00 0.00 0.00 2.44
2767 3321 4.682401 GGCGACAATTTTTACACGGATTTT 59.318 37.500 0.00 0.00 0.00 1.82
2773 3329 2.981400 AGGGCGACAATTTTTACACG 57.019 45.000 0.00 0.00 0.00 4.49
2780 3336 3.157087 ACTTCATGAAGGGCGACAATTT 58.843 40.909 33.11 10.60 42.53 1.82
2791 3347 6.475076 CGGAGACAAGATTAGACTTCATGAAG 59.525 42.308 29.74 29.74 43.79 3.02
2795 3351 5.923733 ACGGAGACAAGATTAGACTTCAT 57.076 39.130 0.00 0.00 0.00 2.57
2816 3372 3.814945 CTCGCTTCTGAAACATGGAAAC 58.185 45.455 0.00 0.00 0.00 2.78
2836 3392 4.295119 AACGCCACGAACCTCGCT 62.295 61.111 0.00 0.00 45.12 4.93
2880 3436 1.019673 CGTCTCCGTCGAGGGAAATA 58.980 55.000 25.74 12.77 41.52 1.40
2917 3473 0.174845 CAAGCATGGCTGGGACAATG 59.825 55.000 0.00 0.00 39.62 2.82
2919 3475 2.277591 GCAAGCATGGCTGGGACAA 61.278 57.895 0.00 0.00 39.62 3.18
2984 3540 0.590195 CCGGACCGGTATCTCTAACG 59.410 60.000 25.54 2.23 42.73 3.18
3023 3581 8.107729 AGAATGATGATCCAAGCATGTATGTAT 58.892 33.333 0.00 0.00 0.00 2.29
3024 3582 7.455891 AGAATGATGATCCAAGCATGTATGTA 58.544 34.615 0.00 0.00 0.00 2.29
3025 3583 6.304624 AGAATGATGATCCAAGCATGTATGT 58.695 36.000 0.00 0.00 0.00 2.29
3026 3584 6.655425 AGAGAATGATGATCCAAGCATGTATG 59.345 38.462 0.00 0.00 0.00 2.39
3064 3622 3.427773 GCTTCTCGTCTTCGAACCATAGT 60.428 47.826 0.00 0.00 45.61 2.12
3153 3711 6.127842 GGAACTAACAAGAAAACACACAAGGA 60.128 38.462 0.00 0.00 0.00 3.36
3253 3811 1.328680 CATGCACATAGAGTTGACCGC 59.671 52.381 0.00 0.00 0.00 5.68
3265 3823 6.330278 CAAATCAGTCTGAAATCATGCACAT 58.670 36.000 6.64 0.00 0.00 3.21
3282 3871 3.094572 AGGTTGGCATCTTCCAAATCAG 58.905 45.455 0.00 0.00 46.63 2.90
3319 3908 1.153667 CAGAGAAGCTGCCGAGTCC 60.154 63.158 0.00 0.00 37.90 3.85
3384 3973 1.599797 GCCACTAACCCGCACAACT 60.600 57.895 0.00 0.00 0.00 3.16
3512 4101 9.817365 GCAGCATATGTACTTATGATTTTGTAG 57.183 33.333 25.27 11.89 32.36 2.74
3532 4124 0.880278 AAACACTGACGACGCAGCAT 60.880 50.000 15.95 5.14 39.51 3.79
3618 4210 9.113876 GATCAATTAAGAAACCACTAAACAACG 57.886 33.333 0.00 0.00 0.00 4.10
3657 4249 2.756760 AGATGATTGGATGCAACACCAC 59.243 45.455 0.12 2.13 35.81 4.16
3663 4255 4.158949 CAGGTTTCAGATGATTGGATGCAA 59.841 41.667 0.79 0.79 0.00 4.08
3678 4270 1.265635 GCGTAACATGTGCAGGTTTCA 59.734 47.619 7.52 0.00 36.63 2.69
3721 4318 8.144478 TGACTTTCTCACACCATAGATATAAGC 58.856 37.037 0.00 0.00 0.00 3.09
3751 4348 7.981789 CAGAAAGTATACCTGCATGTTCTTCTA 59.018 37.037 0.00 0.00 0.00 2.10
3786 4383 3.787676 CGCGCTGCCAACGATTCA 61.788 61.111 5.56 0.00 0.00 2.57
3806 4407 9.258826 CAAAGAATATGGAGTTATCTCAGAGTG 57.741 37.037 0.00 0.00 42.05 3.51
3834 4435 1.271379 GGCAGCCAGTAAGGTTCAAGA 60.271 52.381 6.55 0.00 40.61 3.02
3860 4467 0.928229 GTGGTAACGGACGATGCATC 59.072 55.000 17.10 17.10 42.51 3.91
3950 4557 5.541868 AGTTCTTCAATCAACTCTGGAGAGA 59.458 40.000 10.71 3.57 44.74 3.10
3958 4565 5.825507 ACTTGCAAGTTCTTCAATCAACTC 58.174 37.500 26.36 0.00 35.21 3.01


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

AutoCloner maintained by Alex Coulton.