Multiple sequence alignment - TraesCS1A01G186400

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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 TraesCS1A01G186400 chr1A 100.000 2954 0 0 1 2954 337654620 337657573 0.000000e+00 5456.0
1 TraesCS1A01G186400 chr1D 86.880 1372 122 22 693 2059 262303857 262302539 0.000000e+00 1483.0
2 TraesCS1A01G186400 chr1D 91.822 697 31 10 1 696 262311100 262310429 0.000000e+00 948.0
3 TraesCS1A01G186400 chr1D 92.857 252 18 0 1569 1820 262294417 262294166 1.670000e-97 366.0
4 TraesCS1A01G186400 chr1B 90.603 979 90 2 972 1949 349541343 349542320 0.000000e+00 1297.0
5 TraesCS1A01G186400 chr1B 91.535 697 48 5 1 696 349511669 349512355 0.000000e+00 950.0
6 TraesCS1A01G186400 chr1B 86.408 721 57 19 2195 2895 349542948 349543647 0.000000e+00 750.0
7 TraesCS1A01G186400 chr1B 91.371 197 15 2 693 888 349539827 349540022 4.850000e-68 268.0
8 TraesCS1A01G186400 chr1B 78.475 223 44 4 120 340 349569773 349569553 3.070000e-30 143.0
9 TraesCS1A01G186400 chr1B 94.231 52 3 0 2903 2954 349546318 349546369 2.440000e-11 80.5
10 TraesCS1A01G186400 chr3A 81.588 277 39 8 119 389 483743616 483743346 4.960000e-53 219.0
11 TraesCS1A01G186400 chr2D 80.212 283 53 1 114 393 599003472 599003754 2.980000e-50 209.0


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 TraesCS1A01G186400 chr1A 337654620 337657573 2953 False 5456.000 5456 100.00000 1 2954 1 chr1A.!!$F1 2953
1 TraesCS1A01G186400 chr1D 262302539 262303857 1318 True 1483.000 1483 86.88000 693 2059 1 chr1D.!!$R2 1366
2 TraesCS1A01G186400 chr1D 262310429 262311100 671 True 948.000 948 91.82200 1 696 1 chr1D.!!$R3 695
3 TraesCS1A01G186400 chr1B 349511669 349512355 686 False 950.000 950 91.53500 1 696 1 chr1B.!!$F1 695
4 TraesCS1A01G186400 chr1B 349539827 349546369 6542 False 598.875 1297 90.65325 693 2954 4 chr1B.!!$F2 2261

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
744 746 0.035317 TCGCAGATGTGAAGCTGGTT 59.965 50.0 0.00 0.00 32.83 3.67 F
1383 2687 0.299300 TCGACGACAAAGTTTGCGTG 59.701 50.0 29.45 22.87 41.13 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 3106 0.033366 CCATCACCACGTCTGTGTCA 59.967 55.0 12.94 0.00 44.92 3.58 R
2692 4455 0.106335 TTTTACTTGCCCGACGGTCA 59.894 50.0 13.94 2.38 0.00 4.02 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
32 33 0.536006 AAGAGCTGCAAGACACCACC 60.536 55.000 1.02 0.00 34.07 4.61
34 35 1.510480 GAGCTGCAAGACACCACCAC 61.510 60.000 1.02 0.00 34.07 4.16
35 36 2.896801 GCTGCAAGACACCACCACG 61.897 63.158 0.00 0.00 34.07 4.94
36 37 2.203139 TGCAAGACACCACCACGG 60.203 61.111 0.00 0.00 42.50 4.94
55 56 1.937546 GCCATGAAACCCGGCTCAAG 61.938 60.000 0.00 0.00 42.78 3.02
62 63 0.467290 AACCCGGCTCAAGCTCAAAA 60.467 50.000 0.00 0.00 41.70 2.44
328 329 0.603975 GTGAACAGGTCCTGCTCCAC 60.604 60.000 19.40 18.31 34.37 4.02
441 442 0.729140 GGCTGCCATTGTTTCGTTCG 60.729 55.000 15.17 0.00 0.00 3.95
448 449 1.070175 CATTGTTTCGTTCGCCGTCTT 60.070 47.619 0.00 0.00 37.94 3.01
503 504 5.417894 ACTGATAGACACCGTATTCTTCACA 59.582 40.000 0.00 0.00 0.00 3.58
504 505 6.096987 ACTGATAGACACCGTATTCTTCACAT 59.903 38.462 0.00 0.00 0.00 3.21
505 506 6.873997 TGATAGACACCGTATTCTTCACATT 58.126 36.000 0.00 0.00 0.00 2.71
506 507 7.327975 TGATAGACACCGTATTCTTCACATTT 58.672 34.615 0.00 0.00 0.00 2.32
529 530 1.395635 TGTATACCTCCGTGCGTCAT 58.604 50.000 0.00 0.00 0.00 3.06
558 559 1.263217 CGGTTGGCAGTCAAAGTACAC 59.737 52.381 0.00 0.00 37.08 2.90
601 603 4.450080 CCATGAGATGACGGTGACATATTG 59.550 45.833 0.00 0.00 0.00 1.90
619 621 2.873170 TGTTTACGCTCAGCATTTCG 57.127 45.000 0.00 0.00 0.00 3.46
667 669 2.119655 GGATGGCTTGGCTCTGCAG 61.120 63.158 7.63 7.63 0.00 4.41
732 734 3.812053 GAGAACAATGGCTAATCGCAGAT 59.188 43.478 0.00 0.00 45.12 2.90
744 746 0.035317 TCGCAGATGTGAAGCTGGTT 59.965 50.000 0.00 0.00 32.83 3.67
761 763 1.904865 TTAGCGACGGGTGGTGAGT 60.905 57.895 0.00 0.00 0.00 3.41
769 771 2.737376 GGTGGTGAGTCCGTTCGC 60.737 66.667 0.00 0.00 39.52 4.70
787 789 4.561735 TCGCGGAAGAAAAGTGAAAATT 57.438 36.364 6.13 0.00 0.00 1.82
819 821 4.129380 CAATCACCAACTTCTCTCACACA 58.871 43.478 0.00 0.00 0.00 3.72
851 853 3.498397 AGAAGTGTTGACCAATTGCTACG 59.502 43.478 0.00 0.00 30.08 3.51
854 857 3.250040 AGTGTTGACCAATTGCTACGTTC 59.750 43.478 0.00 0.00 0.00 3.95
888 891 2.356135 GTCACCGGTGATGCAAATAGT 58.644 47.619 38.11 0.00 42.18 2.12
889 892 3.527533 GTCACCGGTGATGCAAATAGTA 58.472 45.455 38.11 10.43 42.18 1.82
890 893 3.555956 GTCACCGGTGATGCAAATAGTAG 59.444 47.826 38.11 6.51 42.18 2.57
891 894 3.449377 TCACCGGTGATGCAAATAGTAGA 59.551 43.478 33.23 5.93 34.14 2.59
892 895 3.555956 CACCGGTGATGCAAATAGTAGAC 59.444 47.826 31.31 0.00 0.00 2.59
893 896 3.196901 ACCGGTGATGCAAATAGTAGACA 59.803 43.478 6.12 0.00 0.00 3.41
894 897 3.555956 CCGGTGATGCAAATAGTAGACAC 59.444 47.826 0.00 0.00 0.00 3.67
896 899 4.032900 CGGTGATGCAAATAGTAGACACAC 59.967 45.833 0.00 0.00 0.00 3.82
897 900 4.935205 GGTGATGCAAATAGTAGACACACA 59.065 41.667 0.00 0.00 0.00 3.72
898 901 5.411361 GGTGATGCAAATAGTAGACACACAA 59.589 40.000 0.00 0.00 0.00 3.33
899 902 6.402550 GGTGATGCAAATAGTAGACACACAAG 60.403 42.308 0.00 0.00 0.00 3.16
900 903 6.147821 GTGATGCAAATAGTAGACACACAAGT 59.852 38.462 0.00 0.00 0.00 3.16
901 904 7.330946 GTGATGCAAATAGTAGACACACAAGTA 59.669 37.037 0.00 0.00 0.00 2.24
902 905 7.875554 TGATGCAAATAGTAGACACACAAGTAA 59.124 33.333 0.00 0.00 0.00 2.24
903 906 8.792830 ATGCAAATAGTAGACACACAAGTAAT 57.207 30.769 0.00 0.00 0.00 1.89
904 907 8.251750 TGCAAATAGTAGACACACAAGTAATC 57.748 34.615 0.00 0.00 0.00 1.75
905 908 7.875554 TGCAAATAGTAGACACACAAGTAATCA 59.124 33.333 0.00 0.00 0.00 2.57
906 909 8.717821 GCAAATAGTAGACACACAAGTAATCAA 58.282 33.333 0.00 0.00 0.00 2.57
928 931 2.890371 GCTTCCCATGGCTGCAAG 59.110 61.111 6.09 6.43 0.00 4.01
1023 2326 4.241590 TGATTTCAGCACATTGAACCAC 57.758 40.909 0.00 0.00 36.84 4.16
1060 2363 1.200948 GGAAGACAACAATGGCAGCTC 59.799 52.381 0.00 0.00 36.86 4.09
1160 2463 5.115773 GCTTGAGCTACGAGTATATCAAACG 59.884 44.000 0.00 0.00 38.21 3.60
1222 2525 1.761174 GTGGAGAAGAAGGTGCCCA 59.239 57.895 0.00 0.00 0.00 5.36
1246 2549 1.153369 ATCCACGATGGCAAGACCG 60.153 57.895 0.00 0.00 43.94 4.79
1257 2560 1.134560 GGCAAGACCGTACTCGATTCT 59.865 52.381 0.00 0.00 39.71 2.40
1260 2563 3.099362 CAAGACCGTACTCGATTCTTCG 58.901 50.000 0.00 0.00 46.87 3.79
1262 2565 1.457346 ACCGTACTCGATTCTTCGGT 58.543 50.000 11.57 11.57 45.53 4.69
1374 2677 1.440850 CGCCTACGTCGACGACAAA 60.441 57.895 41.52 22.35 43.02 2.83
1380 2683 0.299597 ACGTCGACGACAAAGTTTGC 59.700 50.000 41.52 7.61 43.02 3.68
1383 2687 0.299300 TCGACGACAAAGTTTGCGTG 59.701 50.000 29.45 22.87 41.13 5.34
1396 2700 3.006967 AGTTTGCGTGTTCTCATACCTCT 59.993 43.478 0.00 0.00 0.00 3.69
1418 2723 4.950050 TGTTCAGTCTTCCTTGTCTTCTC 58.050 43.478 0.00 0.00 0.00 2.87
1419 2724 4.405680 TGTTCAGTCTTCCTTGTCTTCTCA 59.594 41.667 0.00 0.00 0.00 3.27
1423 2728 6.226787 TCAGTCTTCCTTGTCTTCTCAATTC 58.773 40.000 0.00 0.00 0.00 2.17
1431 2736 6.037098 CCTTGTCTTCTCAATTCTACCTACG 58.963 44.000 0.00 0.00 0.00 3.51
1456 2761 2.093128 ACGACAAGGTTTGTGTCTTCCT 60.093 45.455 0.00 0.00 45.52 3.36
1458 2763 3.541632 GACAAGGTTTGTGTCTTCCTCA 58.458 45.455 0.00 0.00 45.52 3.86
1463 2768 3.910627 AGGTTTGTGTCTTCCTCACCTAT 59.089 43.478 0.00 0.00 35.25 2.57
1468 2773 2.497675 GTGTCTTCCTCACCTATGCTGA 59.502 50.000 0.00 0.00 0.00 4.26
1493 2798 0.828022 TGTCACACGGTCTTCCTTGT 59.172 50.000 0.00 0.00 45.20 3.16
1528 2833 5.220510 CGCTTATGTCGGTGTTAATAAAGCA 60.221 40.000 0.00 0.00 0.00 3.91
1529 2834 6.192360 GCTTATGTCGGTGTTAATAAAGCAG 58.808 40.000 0.00 0.00 0.00 4.24
1530 2835 6.183360 GCTTATGTCGGTGTTAATAAAGCAGT 60.183 38.462 0.00 0.00 0.00 4.40
1547 2852 1.304217 GTGACGGAGGTGGAGAGGA 60.304 63.158 0.00 0.00 0.00 3.71
1548 2853 0.684805 GTGACGGAGGTGGAGAGGAT 60.685 60.000 0.00 0.00 0.00 3.24
1579 2884 2.126071 GAGACGCTTGCGGTGCTA 60.126 61.111 19.19 0.00 0.00 3.49
1623 2928 1.067635 CAAGCATTCCAACGGAAAGGG 60.068 52.381 0.00 0.00 45.41 3.95
1630 2935 0.881796 CCAACGGAAAGGGCTTCTTC 59.118 55.000 0.00 0.00 33.94 2.87
1666 2971 1.180029 GGTACCTTGACCTCGCAGTA 58.820 55.000 4.06 0.00 36.47 2.74
1696 3001 3.429141 CACTGGCTCAAGGCGCAG 61.429 66.667 10.83 0.00 44.42 5.18
1697 3002 3.946201 ACTGGCTCAAGGCGCAGT 61.946 61.111 10.83 0.00 42.90 4.40
1699 3004 4.254709 TGGCTCAAGGCGCAGTGT 62.255 61.111 10.83 0.00 44.42 3.55
1708 3013 1.726853 AGGCGCAGTGTAAGATGTTC 58.273 50.000 10.83 0.00 0.00 3.18
1723 3028 2.029964 TTCGGCGTGGTGTTCCTC 59.970 61.111 6.85 0.00 34.23 3.71
1769 3074 2.281208 CCTGGGCGAAACGGTTCA 60.281 61.111 14.64 0.00 32.89 3.18
1780 3085 0.966920 AACGGTTCACTGAGACCGAT 59.033 50.000 26.18 17.86 40.83 4.18
1828 3133 1.137086 GACGTGGTGATGGAGTATGCT 59.863 52.381 0.00 0.00 0.00 3.79
1851 3156 2.511600 GCGCCAGGCTTATCGTGT 60.512 61.111 10.54 0.00 39.11 4.49
1900 3205 2.325583 AGTGAAACGCTTCAGACCAA 57.674 45.000 0.51 0.00 45.86 3.67
1907 3212 1.796796 GCTTCAGACCAATGCGACC 59.203 57.895 0.00 0.00 0.00 4.79
1936 3241 3.467803 GACTACCCAAGCATAGCGAAAT 58.532 45.455 0.00 0.00 0.00 2.17
1940 3245 2.684881 ACCCAAGCATAGCGAAATCAAG 59.315 45.455 0.00 0.00 0.00 3.02
1949 3254 2.983229 AGCGAAATCAAGCTGATCACT 58.017 42.857 0.00 0.00 42.82 3.41
1950 3255 3.341823 AGCGAAATCAAGCTGATCACTT 58.658 40.909 0.00 0.00 42.82 3.16
1951 3256 4.507710 AGCGAAATCAAGCTGATCACTTA 58.492 39.130 9.32 2.13 42.82 2.24
1952 3257 5.121811 AGCGAAATCAAGCTGATCACTTAT 58.878 37.500 9.32 3.75 42.82 1.73
1953 3258 5.007430 AGCGAAATCAAGCTGATCACTTATG 59.993 40.000 9.32 0.07 42.82 1.90
1954 3259 5.220739 GCGAAATCAAGCTGATCACTTATGT 60.221 40.000 9.32 2.33 35.76 2.29
1955 3260 6.018751 GCGAAATCAAGCTGATCACTTATGTA 60.019 38.462 9.32 0.11 35.76 2.29
1956 3261 7.340699 CGAAATCAAGCTGATCACTTATGTAC 58.659 38.462 9.32 0.00 35.76 2.90
1957 3262 6.834959 AATCAAGCTGATCACTTATGTACG 57.165 37.500 9.32 0.00 35.76 3.67
1958 3263 5.324784 TCAAGCTGATCACTTATGTACGT 57.675 39.130 9.32 0.00 0.00 3.57
1959 3264 6.445357 TCAAGCTGATCACTTATGTACGTA 57.555 37.500 9.32 0.00 0.00 3.57
1960 3265 7.039313 TCAAGCTGATCACTTATGTACGTAT 57.961 36.000 0.00 0.00 0.00 3.06
1961 3266 8.161699 TCAAGCTGATCACTTATGTACGTATA 57.838 34.615 0.00 0.00 0.00 1.47
1987 3292 9.936329 ATATGTATTTGGGAGTTTAGTTTCCAT 57.064 29.630 0.00 0.00 35.09 3.41
1988 3293 7.696992 TGTATTTGGGAGTTTAGTTTCCATC 57.303 36.000 0.00 0.00 35.09 3.51
1989 3294 7.235079 TGTATTTGGGAGTTTAGTTTCCATCA 58.765 34.615 0.00 0.00 35.09 3.07
1990 3295 7.726291 TGTATTTGGGAGTTTAGTTTCCATCAA 59.274 33.333 0.00 0.00 35.09 2.57
1991 3296 6.648879 TTTGGGAGTTTAGTTTCCATCAAG 57.351 37.500 0.00 0.00 35.09 3.02
1992 3297 5.319043 TGGGAGTTTAGTTTCCATCAAGT 57.681 39.130 0.00 0.00 35.09 3.16
1993 3298 5.313712 TGGGAGTTTAGTTTCCATCAAGTC 58.686 41.667 0.00 0.00 35.09 3.01
1994 3299 5.073144 TGGGAGTTTAGTTTCCATCAAGTCT 59.927 40.000 0.00 0.00 35.09 3.24
1997 3302 5.238583 AGTTTAGTTTCCATCAAGTCTCCG 58.761 41.667 0.00 0.00 0.00 4.63
1998 3303 2.100605 AGTTTCCATCAAGTCTCCGC 57.899 50.000 0.00 0.00 0.00 5.54
2000 3305 1.464997 GTTTCCATCAAGTCTCCGCAC 59.535 52.381 0.00 0.00 0.00 5.34
2052 3358 5.482526 TGCTTTGTGAGGGTATAAGAGTGTA 59.517 40.000 0.00 0.00 0.00 2.90
2059 3365 9.025041 TGTGAGGGTATAAGAGTGTATCATATG 57.975 37.037 0.00 0.00 0.00 1.78
2087 3393 3.454812 TAACTTATGTTGGAGGGAGCCTC 59.545 47.826 4.33 0.00 42.06 4.70
2100 3406 0.878086 GAGCCTCCTAGCGCAATGAC 60.878 60.000 11.47 0.00 38.01 3.06
2101 3407 1.153369 GCCTCCTAGCGCAATGACA 60.153 57.895 11.47 0.00 0.00 3.58
2105 3411 1.662629 CTCCTAGCGCAATGACAAGTG 59.337 52.381 11.47 0.00 0.00 3.16
2106 3412 1.275010 TCCTAGCGCAATGACAAGTGA 59.725 47.619 11.47 0.00 0.00 3.41
2117 3423 6.086765 CGCAATGACAAGTGAGTTATGTTTTC 59.913 38.462 0.00 0.00 0.00 2.29
2119 3425 7.596248 GCAATGACAAGTGAGTTATGTTTTCAT 59.404 33.333 0.00 0.00 43.60 2.57
2120 3426 9.467258 CAATGACAAGTGAGTTATGTTTTCATT 57.533 29.630 0.00 0.00 41.25 2.57
2121 3427 9.683069 AATGACAAGTGAGTTATGTTTTCATTC 57.317 29.630 0.00 0.00 41.25 2.67
2122 3428 8.219546 TGACAAGTGAGTTATGTTTTCATTCA 57.780 30.769 0.00 0.00 41.25 2.57
2123 3429 8.849168 TGACAAGTGAGTTATGTTTTCATTCAT 58.151 29.630 0.00 0.00 41.25 2.57
2124 3430 9.121517 GACAAGTGAGTTATGTTTTCATTCATG 57.878 33.333 0.00 0.00 41.25 3.07
2125 3431 8.632679 ACAAGTGAGTTATGTTTTCATTCATGT 58.367 29.630 0.00 0.00 41.25 3.21
2143 3449 7.854557 TTCATGTCATCTAGGTTCAAATCTG 57.145 36.000 0.00 0.00 0.00 2.90
2148 3454 5.582665 GTCATCTAGGTTCAAATCTGTCCAC 59.417 44.000 0.00 0.00 0.00 4.02
2154 3460 3.009143 GGTTCAAATCTGTCCACCTACCT 59.991 47.826 0.00 0.00 0.00 3.08
2156 3462 5.420409 GTTCAAATCTGTCCACCTACCTAG 58.580 45.833 0.00 0.00 0.00 3.02
2158 3464 5.834460 TCAAATCTGTCCACCTACCTAGTA 58.166 41.667 0.00 0.00 0.00 1.82
2160 3466 6.154021 TCAAATCTGTCCACCTACCTAGTAAC 59.846 42.308 0.00 0.00 0.00 2.50
2161 3467 4.942363 TCTGTCCACCTACCTAGTAACT 57.058 45.455 0.00 0.00 0.00 2.24
2163 3469 4.290459 TCTGTCCACCTACCTAGTAACTGA 59.710 45.833 0.00 0.00 0.00 3.41
2164 3470 5.001833 TGTCCACCTACCTAGTAACTGAA 57.998 43.478 0.00 0.00 0.00 3.02
2166 3472 5.015515 GTCCACCTACCTAGTAACTGAAGT 58.984 45.833 0.00 0.00 0.00 3.01
2167 3473 5.479724 GTCCACCTACCTAGTAACTGAAGTT 59.520 44.000 0.71 0.71 41.73 2.66
2168 3474 6.660949 GTCCACCTACCTAGTAACTGAAGTTA 59.339 42.308 0.00 0.00 39.31 2.24
2169 3475 7.177392 GTCCACCTACCTAGTAACTGAAGTTAA 59.823 40.741 4.52 0.00 41.58 2.01
2170 3476 7.729881 TCCACCTACCTAGTAACTGAAGTTAAA 59.270 37.037 4.52 0.00 41.58 1.52
2171 3477 8.537858 CCACCTACCTAGTAACTGAAGTTAAAT 58.462 37.037 4.52 0.53 41.58 1.40
2172 3478 9.367444 CACCTACCTAGTAACTGAAGTTAAATG 57.633 37.037 4.52 0.00 41.58 2.32
2173 3479 8.537858 ACCTACCTAGTAACTGAAGTTAAATGG 58.462 37.037 4.52 8.98 41.58 3.16
2174 3480 8.537858 CCTACCTAGTAACTGAAGTTAAATGGT 58.462 37.037 18.07 18.07 41.58 3.55
2175 3481 9.939802 CTACCTAGTAACTGAAGTTAAATGGTT 57.060 33.333 18.69 9.70 41.58 3.67
2176 3482 8.843885 ACCTAGTAACTGAAGTTAAATGGTTC 57.156 34.615 4.52 0.00 41.58 3.62
2177 3483 8.434392 ACCTAGTAACTGAAGTTAAATGGTTCA 58.566 33.333 4.52 0.00 41.58 3.18
2182 3488 9.959749 GTAACTGAAGTTAAATGGTTCAAATCA 57.040 29.630 4.52 0.00 41.58 2.57
2184 3490 9.480053 AACTGAAGTTAAATGGTTCAAATCATG 57.520 29.630 0.00 0.00 36.32 3.07
2185 3491 7.599998 ACTGAAGTTAAATGGTTCAAATCATGC 59.400 33.333 0.00 0.00 28.30 4.06
2186 3492 6.873076 TGAAGTTAAATGGTTCAAATCATGCC 59.127 34.615 0.00 0.00 28.30 4.40
2187 3493 6.357579 AGTTAAATGGTTCAAATCATGCCA 57.642 33.333 0.00 0.00 28.30 4.92
2188 3494 6.949715 AGTTAAATGGTTCAAATCATGCCAT 58.050 32.000 0.00 0.00 41.22 4.40
2189 3495 7.043565 AGTTAAATGGTTCAAATCATGCCATC 58.956 34.615 0.00 0.00 38.82 3.51
2190 3496 5.687166 AAATGGTTCAAATCATGCCATCT 57.313 34.783 0.00 0.00 38.82 2.90
2191 3497 6.795144 AAATGGTTCAAATCATGCCATCTA 57.205 33.333 0.00 0.00 38.82 1.98
2193 3499 5.114764 TGGTTCAAATCATGCCATCTAGA 57.885 39.130 0.00 0.00 0.00 2.43
2194 3500 5.698104 TGGTTCAAATCATGCCATCTAGAT 58.302 37.500 0.00 0.00 0.00 1.98
2195 3501 6.131264 TGGTTCAAATCATGCCATCTAGATT 58.869 36.000 1.33 0.00 32.45 2.40
2197 3503 7.124599 TGGTTCAAATCATGCCATCTAGATTTT 59.875 33.333 1.33 0.00 38.30 1.82
2200 3506 8.296211 TCAAATCATGCCATCTAGATTTTCAA 57.704 30.769 1.33 0.00 38.30 2.69
2201 3507 8.410912 TCAAATCATGCCATCTAGATTTTCAAG 58.589 33.333 1.33 0.00 38.30 3.02
2205 3950 7.795047 TCATGCCATCTAGATTTTCAAGACTA 58.205 34.615 1.33 0.00 0.00 2.59
2221 3966 4.213564 AGACTATGTTTTGCCTCCTGAG 57.786 45.455 0.00 0.00 0.00 3.35
2224 3969 4.327680 ACTATGTTTTGCCTCCTGAGAAC 58.672 43.478 0.00 0.00 0.00 3.01
2228 3973 0.984230 TTTGCCTCCTGAGAACCGAT 59.016 50.000 0.00 0.00 0.00 4.18
2238 3983 4.588951 TCCTGAGAACCGATGTGCTATTAT 59.411 41.667 0.00 0.00 26.98 1.28
2247 3992 4.036734 CCGATGTGCTATTATGCTTTTGGT 59.963 41.667 0.00 0.00 0.00 3.67
2249 3994 4.108699 TGTGCTATTATGCTTTTGGTGC 57.891 40.909 0.00 0.00 0.00 5.01
2253 3998 3.491447 GCTATTATGCTTTTGGTGCCCAG 60.491 47.826 0.00 0.00 33.81 4.45
2262 4007 4.747810 CTTTTGGTGCCCAGTATCAATTC 58.252 43.478 0.00 0.00 33.81 2.17
2263 4008 3.737559 TTGGTGCCCAGTATCAATTCT 57.262 42.857 0.00 0.00 33.81 2.40
2267 4012 2.945668 GTGCCCAGTATCAATTCTGTCC 59.054 50.000 0.00 0.00 0.00 4.02
2289 4034 1.068541 GTTGTCGACCATTTCCTTGGC 60.069 52.381 14.12 0.00 40.68 4.52
2291 4036 0.322546 GTCGACCATTTCCTTGGCCT 60.323 55.000 3.51 0.00 40.68 5.19
2293 4038 1.209504 TCGACCATTTCCTTGGCCTAG 59.790 52.381 7.29 7.29 40.68 3.02
2297 4042 4.444306 CGACCATTTCCTTGGCCTAGAATA 60.444 45.833 16.43 0.33 40.68 1.75
2310 4055 7.009179 TGGCCTAGAATATCCTTGATAACTG 57.991 40.000 3.32 0.00 0.00 3.16
2312 4057 7.733047 TGGCCTAGAATATCCTTGATAACTGTA 59.267 37.037 3.32 0.00 0.00 2.74
2313 4058 8.594550 GGCCTAGAATATCCTTGATAACTGTAA 58.405 37.037 0.00 0.00 0.00 2.41
2314 4059 9.646427 GCCTAGAATATCCTTGATAACTGTAAG 57.354 37.037 0.00 0.00 42.29 2.34
2319 4064 9.442047 GAATATCCTTGATAACTGTAAGATGGG 57.558 37.037 0.00 0.00 37.43 4.00
2320 4065 6.831664 ATCCTTGATAACTGTAAGATGGGT 57.168 37.500 0.00 0.00 37.43 4.51
2321 4066 6.636454 TCCTTGATAACTGTAAGATGGGTT 57.364 37.500 0.00 0.00 37.43 4.11
2322 4067 7.743116 TCCTTGATAACTGTAAGATGGGTTA 57.257 36.000 0.00 0.00 37.43 2.85
2323 4068 8.331931 TCCTTGATAACTGTAAGATGGGTTAT 57.668 34.615 0.00 0.00 37.51 1.89
2324 4069 8.210946 TCCTTGATAACTGTAAGATGGGTTATG 58.789 37.037 0.00 0.00 35.74 1.90
2325 4070 7.993183 CCTTGATAACTGTAAGATGGGTTATGT 59.007 37.037 0.00 0.00 35.74 2.29
2352 4097 2.285977 GGTTATGCCCCTTACACTTCG 58.714 52.381 0.00 0.00 0.00 3.79
2358 4103 1.217244 CCCTTACACTTCGGACCCG 59.783 63.158 1.31 1.31 41.35 5.28
2359 4104 1.447314 CCTTACACTTCGGACCCGC 60.447 63.158 3.13 0.00 39.59 6.13
2360 4105 1.447314 CTTACACTTCGGACCCGCC 60.447 63.158 3.13 0.00 39.59 6.13
2525 4271 4.202567 ACAAGGGCTTCTGGTAGAAAATCA 60.203 41.667 0.00 0.00 33.19 2.57
2531 4277 4.873259 GCTTCTGGTAGAAAATCAGAGGAC 59.127 45.833 1.96 0.00 38.55 3.85
2557 4303 6.436532 ACGTTAGTTCTAAGAGAGGGAATTGA 59.563 38.462 0.00 0.00 0.00 2.57
2559 4305 7.982354 CGTTAGTTCTAAGAGAGGGAATTGAAT 59.018 37.037 0.00 0.00 0.00 2.57
2571 4317 8.221965 AGAGGGAATTGAATAAACCGAAATAC 57.778 34.615 0.00 0.00 0.00 1.89
2573 4319 6.893005 AGGGAATTGAATAAACCGAAATACCA 59.107 34.615 0.00 0.00 0.00 3.25
2574 4320 6.976349 GGGAATTGAATAAACCGAAATACCAC 59.024 38.462 0.00 0.00 0.00 4.16
2575 4321 7.363094 GGGAATTGAATAAACCGAAATACCACA 60.363 37.037 0.00 0.00 0.00 4.17
2576 4322 8.194769 GGAATTGAATAAACCGAAATACCACAT 58.805 33.333 0.00 0.00 0.00 3.21
2593 4339 9.914834 AATACCACATAACATATTGGTGTAAGT 57.085 29.630 4.99 0.00 42.48 2.24
2600 4346 5.484173 ACATATTGGTGTAAGTCATTGCG 57.516 39.130 0.00 0.00 0.00 4.85
2639 4402 9.607988 TCAATATTGAGGTACGTTGATGTAATT 57.392 29.630 14.23 0.00 32.50 1.40
2666 4429 0.605589 GTTGGGCCTCGCTTGTAAGT 60.606 55.000 4.53 0.00 0.00 2.24
2673 4436 1.556591 CTCGCTTGTAAGTGCACGCA 61.557 55.000 12.01 9.38 36.50 5.24
2692 4455 6.321717 CACGCATGACAAAATACCTAAACAT 58.678 36.000 0.00 0.00 0.00 2.71
2753 4516 4.524328 CCTTTGGTCCAACTGAGCTTAAAT 59.476 41.667 2.98 0.00 42.12 1.40
2754 4517 5.011023 CCTTTGGTCCAACTGAGCTTAAATT 59.989 40.000 2.98 0.00 42.12 1.82
2755 4518 6.462909 CCTTTGGTCCAACTGAGCTTAAATTT 60.463 38.462 2.98 0.00 42.12 1.82
2756 4519 5.705609 TGGTCCAACTGAGCTTAAATTTC 57.294 39.130 0.00 0.00 42.12 2.17
2853 4619 6.603599 AGGTATTTTAGAGCAAGGAAATGGTC 59.396 38.462 0.00 0.00 45.77 4.02
2895 4661 5.685511 CGAAACCATGACGAAAAGACAAAAT 59.314 36.000 0.00 0.00 0.00 1.82
2897 4663 6.826893 AACCATGACGAAAAGACAAAATTG 57.173 33.333 0.00 0.00 0.00 2.32
2900 4666 7.484975 ACCATGACGAAAAGACAAAATTGTAA 58.515 30.769 0.00 0.00 42.43 2.41
2942 7371 8.495148 CAATGGCAAAATTGAGTAACCTAAAAC 58.505 33.333 0.00 0.00 39.46 2.43
2949 7378 9.961264 AAAATTGAGTAACCTAAAACCCAAAAA 57.039 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.439540 CCGGGTTTCATGGCCGTG 61.440 66.667 19.62 19.62 0.00 4.94
55 56 1.008538 CTGCCGTGGTGTTTTGAGC 60.009 57.895 0.00 0.00 0.00 4.26
62 63 0.395173 AACTTTTCCTGCCGTGGTGT 60.395 50.000 0.00 0.00 0.00 4.16
343 344 2.402388 CGCTGCAGATGAAAGGCG 59.598 61.111 20.43 8.27 36.89 5.52
454 455 2.392662 CACTGATAGAGCAGGGGAGAA 58.607 52.381 0.00 0.00 40.20 2.87
457 458 0.325577 TGCACTGATAGAGCAGGGGA 60.326 55.000 0.00 0.00 39.70 4.81
459 460 1.065926 TGTTGCACTGATAGAGCAGGG 60.066 52.381 0.00 0.00 42.43 4.45
460 461 2.005451 GTGTTGCACTGATAGAGCAGG 58.995 52.381 0.00 0.00 42.43 4.85
461 462 2.969990 AGTGTTGCACTGATAGAGCAG 58.030 47.619 0.53 0.00 43.63 4.24
471 472 2.610479 CGGTGTCTATCAGTGTTGCACT 60.610 50.000 0.00 0.00 46.51 4.40
484 485 6.460781 ACAAATGTGAAGAATACGGTGTCTA 58.539 36.000 0.00 0.00 0.00 2.59
503 504 3.372822 CGCACGGAGGTATACAAACAAAT 59.627 43.478 5.01 0.00 0.00 2.32
504 505 2.737783 CGCACGGAGGTATACAAACAAA 59.262 45.455 5.01 0.00 0.00 2.83
505 506 2.288948 ACGCACGGAGGTATACAAACAA 60.289 45.455 5.01 0.00 0.00 2.83
506 507 1.273048 ACGCACGGAGGTATACAAACA 59.727 47.619 5.01 0.00 0.00 2.83
519 520 3.463505 GTCACTGATGACGCACGG 58.536 61.111 0.00 0.00 45.66 4.94
529 530 4.228567 TGCCAACCGCGTCACTGA 62.229 61.111 4.92 0.00 42.08 3.41
601 603 1.463444 ACCGAAATGCTGAGCGTAAAC 59.537 47.619 0.00 0.00 0.00 2.01
619 621 1.205893 AGAAGAATCTCGAGGTGCACC 59.794 52.381 29.22 29.22 0.00 5.01
732 734 0.666274 CGTCGCTAACCAGCTTCACA 60.666 55.000 0.00 0.00 46.26 3.58
744 746 2.282674 ACTCACCACCCGTCGCTA 60.283 61.111 0.00 0.00 0.00 4.26
769 771 7.414436 TGTCACTAATTTTCACTTTTCTTCCG 58.586 34.615 0.00 0.00 0.00 4.30
787 789 4.019792 AGTTGGTGATTGCATGTCACTA 57.980 40.909 23.73 18.57 44.15 2.74
819 821 3.139077 GTCAACACTTCTCCACGGAATT 58.861 45.455 0.00 0.00 0.00 2.17
851 853 4.342772 GGTGACGTATCATGCATTTGAAC 58.657 43.478 0.00 0.00 37.14 3.18
888 891 5.860182 GCGTACTTGATTACTTGTGTGTCTA 59.140 40.000 0.00 0.00 0.00 2.59
889 892 4.684703 GCGTACTTGATTACTTGTGTGTCT 59.315 41.667 0.00 0.00 0.00 3.41
890 893 4.684703 AGCGTACTTGATTACTTGTGTGTC 59.315 41.667 0.00 0.00 0.00 3.67
891 894 4.628074 AGCGTACTTGATTACTTGTGTGT 58.372 39.130 0.00 0.00 0.00 3.72
892 895 5.389516 GGAAGCGTACTTGATTACTTGTGTG 60.390 44.000 0.00 0.00 35.82 3.82
893 896 4.689345 GGAAGCGTACTTGATTACTTGTGT 59.311 41.667 0.00 0.00 35.82 3.72
894 897 4.092968 GGGAAGCGTACTTGATTACTTGTG 59.907 45.833 0.00 0.00 35.82 3.33
896 899 4.250464 TGGGAAGCGTACTTGATTACTTG 58.750 43.478 0.00 0.00 35.82 3.16
897 900 4.546829 TGGGAAGCGTACTTGATTACTT 57.453 40.909 0.00 0.00 35.82 2.24
898 901 4.442706 CATGGGAAGCGTACTTGATTACT 58.557 43.478 0.00 0.00 35.82 2.24
899 902 3.560068 CCATGGGAAGCGTACTTGATTAC 59.440 47.826 2.85 0.00 35.82 1.89
900 903 3.804036 CCATGGGAAGCGTACTTGATTA 58.196 45.455 2.85 0.00 35.82 1.75
901 904 2.643551 CCATGGGAAGCGTACTTGATT 58.356 47.619 2.85 0.00 35.82 2.57
902 905 1.747206 GCCATGGGAAGCGTACTTGAT 60.747 52.381 15.13 0.00 35.82 2.57
903 906 0.392461 GCCATGGGAAGCGTACTTGA 60.392 55.000 15.13 0.00 35.82 3.02
904 907 0.392998 AGCCATGGGAAGCGTACTTG 60.393 55.000 15.13 0.00 35.82 3.16
905 908 0.392998 CAGCCATGGGAAGCGTACTT 60.393 55.000 15.13 0.00 39.43 2.24
906 909 1.221840 CAGCCATGGGAAGCGTACT 59.778 57.895 15.13 0.00 0.00 2.73
928 931 0.247460 GGAAATGGGAAGTTGCAGGC 59.753 55.000 0.00 0.00 0.00 4.85
930 933 3.160269 AGAAGGAAATGGGAAGTTGCAG 58.840 45.455 0.00 0.00 0.00 4.41
931 934 3.243359 AGAAGGAAATGGGAAGTTGCA 57.757 42.857 0.00 0.00 0.00 4.08
932 935 3.696548 CCTAGAAGGAAATGGGAAGTTGC 59.303 47.826 0.00 0.00 37.67 4.17
933 936 5.179452 TCCTAGAAGGAAATGGGAAGTTG 57.821 43.478 0.00 0.00 42.51 3.16
964 967 8.422080 CATCGTTTTTGGATGTTTATATAGCG 57.578 34.615 0.00 0.00 37.18 4.26
990 2293 3.252944 TGCTGAAATCAATGCGAGAACAA 59.747 39.130 0.00 0.00 0.00 2.83
1023 2326 1.166129 TCCGTCTCTCTGTTCTTCCG 58.834 55.000 0.00 0.00 0.00 4.30
1060 2363 2.557920 AGCAACTTCAGGTCTCCTTG 57.442 50.000 0.00 0.00 0.00 3.61
1222 2525 2.700371 TCTTGCCATCGTGGATGAGTAT 59.300 45.455 7.16 0.00 42.09 2.12
1257 2560 0.599060 TGTACTGCACGATGACCGAA 59.401 50.000 0.00 0.00 41.76 4.30
1260 2563 1.200483 CGATGTACTGCACGATGACC 58.800 55.000 0.00 0.00 0.00 4.02
1262 2565 1.531058 CGTCGATGTACTGCACGATGA 60.531 52.381 8.25 0.00 38.58 2.92
1346 2649 4.530857 CGTAGGCGGCCCAGAAGG 62.531 72.222 17.02 0.99 39.47 3.46
1374 2677 3.006967 AGAGGTATGAGAACACGCAAACT 59.993 43.478 0.00 0.00 0.00 2.66
1380 2683 4.169508 CTGAACAGAGGTATGAGAACACG 58.830 47.826 0.00 0.00 0.00 4.49
1383 2687 5.652994 AGACTGAACAGAGGTATGAGAAC 57.347 43.478 8.87 0.00 0.00 3.01
1396 2700 4.405680 TGAGAAGACAAGGAAGACTGAACA 59.594 41.667 0.00 0.00 0.00 3.18
1418 2723 3.181517 TGTCGTCGACGTAGGTAGAATTG 60.182 47.826 34.40 4.90 40.80 2.32
1419 2724 3.002791 TGTCGTCGACGTAGGTAGAATT 58.997 45.455 34.40 0.00 40.80 2.17
1423 2728 1.061711 CCTTGTCGTCGACGTAGGTAG 59.938 57.143 34.40 23.37 40.80 3.18
1431 2736 1.257155 GACACAAACCTTGTCGTCGAC 59.743 52.381 18.51 18.51 43.23 4.20
1468 2773 2.616842 GGAAGACCGTGTGACAATTTGT 59.383 45.455 0.63 0.63 0.00 2.83
1481 2786 4.500035 GGAGAATAGCTACAAGGAAGACCG 60.500 50.000 0.00 0.00 41.83 4.79
1493 2798 4.421033 CGACATAAGCGGAGAATAGCTA 57.579 45.455 0.00 0.00 43.78 3.32
1528 2833 1.304547 CCTCTCCACCTCCGTCACT 60.305 63.158 0.00 0.00 0.00 3.41
1529 2834 0.684805 ATCCTCTCCACCTCCGTCAC 60.685 60.000 0.00 0.00 0.00 3.67
1530 2835 0.684479 CATCCTCTCCACCTCCGTCA 60.684 60.000 0.00 0.00 0.00 4.35
1547 2852 1.405821 CGTCTCGCTAACCTTCTCCAT 59.594 52.381 0.00 0.00 0.00 3.41
1548 2853 0.809385 CGTCTCGCTAACCTTCTCCA 59.191 55.000 0.00 0.00 0.00 3.86
1579 2884 0.990374 ATGCCTCCTCAAGTTGCTCT 59.010 50.000 0.00 0.00 0.00 4.09
1609 2914 0.476771 AGAAGCCCTTTCCGTTGGAA 59.523 50.000 0.00 0.00 40.27 3.53
1612 2917 0.517316 CGAAGAAGCCCTTTCCGTTG 59.483 55.000 0.00 0.00 36.40 4.10
1623 2928 4.083862 AGTCCCCGGCGAAGAAGC 62.084 66.667 9.30 0.00 0.00 3.86
1654 2959 1.676678 GGCATCCTACTGCGAGGTCA 61.677 60.000 0.00 0.00 43.23 4.02
1680 2985 3.946201 ACTGCGCCTTGAGCCAGT 61.946 61.111 4.18 0.00 43.74 4.00
1696 3001 0.719465 CCACGCCGAACATCTTACAC 59.281 55.000 0.00 0.00 0.00 2.90
1697 3002 0.319083 ACCACGCCGAACATCTTACA 59.681 50.000 0.00 0.00 0.00 2.41
1699 3004 0.319083 ACACCACGCCGAACATCTTA 59.681 50.000 0.00 0.00 0.00 2.10
1708 3013 4.351938 TCGAGGAACACCACGCCG 62.352 66.667 0.00 0.00 37.60 6.46
1751 3056 2.281276 GAACCGTTTCGCCCAGGT 60.281 61.111 0.00 0.00 38.88 4.00
1753 3058 1.597027 AGTGAACCGTTTCGCCCAG 60.597 57.895 2.33 0.00 42.37 4.45
1801 3106 0.033366 CCATCACCACGTCTGTGTCA 59.967 55.000 12.94 0.00 44.92 3.58
1870 3175 1.498865 CGTTTCACTTGGCACTCGCT 61.499 55.000 0.00 0.00 38.60 4.93
1875 3180 0.380378 TGAAGCGTTTCACTTGGCAC 59.620 50.000 10.92 0.00 38.37 5.01
1900 3205 1.530293 GTAGTCGATACTCGGTCGCAT 59.470 52.381 0.00 0.00 40.88 4.73
1907 3212 1.674441 TGCTTGGGTAGTCGATACTCG 59.326 52.381 0.00 0.00 37.73 4.18
1922 3227 3.064408 TCAGCTTGATTTCGCTATGCTTG 59.936 43.478 0.00 0.00 34.58 4.01
1936 3241 5.324784 ACGTACATAAGTGATCAGCTTGA 57.675 39.130 16.19 0.00 0.00 3.02
1961 3266 9.936329 ATGGAAACTAAACTCCCAAATACATAT 57.064 29.630 0.00 0.00 0.00 1.78
1987 3292 2.355837 GTGCGTGCGGAGACTTGA 60.356 61.111 0.00 0.00 0.00 3.02
1988 3293 2.356313 AGTGCGTGCGGAGACTTG 60.356 61.111 0.00 0.00 0.00 3.16
1989 3294 2.356313 CAGTGCGTGCGGAGACTT 60.356 61.111 0.00 0.00 0.00 3.01
1990 3295 2.856628 TTCAGTGCGTGCGGAGACT 61.857 57.895 0.00 0.00 0.00 3.24
1991 3296 2.355837 TTCAGTGCGTGCGGAGAC 60.356 61.111 0.00 0.00 0.00 3.36
1992 3297 2.355837 GTTCAGTGCGTGCGGAGA 60.356 61.111 0.00 0.00 0.00 3.71
1993 3298 2.661537 TGTTCAGTGCGTGCGGAG 60.662 61.111 0.00 0.00 0.00 4.63
1994 3299 2.916502 AAGTGTTCAGTGCGTGCGGA 62.917 55.000 0.00 0.00 0.00 5.54
1997 3302 1.655350 GCAAGTGTTCAGTGCGTGC 60.655 57.895 0.00 0.00 0.00 5.34
1998 3303 0.041839 GAGCAAGTGTTCAGTGCGTG 60.042 55.000 0.00 0.00 43.16 5.34
2000 3305 1.783284 TAGAGCAAGTGTTCAGTGCG 58.217 50.000 0.00 0.00 43.16 5.34
2059 3365 7.201794 GGCTCCCTCCAACATAAGTTATTTAAC 60.202 40.741 0.00 0.00 35.85 2.01
2063 3369 4.478686 AGGCTCCCTCCAACATAAGTTATT 59.521 41.667 0.00 0.00 35.85 1.40
2082 3388 1.144936 GTCATTGCGCTAGGAGGCT 59.855 57.895 9.73 0.00 0.00 4.58
2087 3393 1.662629 CTCACTTGTCATTGCGCTAGG 59.337 52.381 9.73 2.03 0.00 3.02
2092 3398 4.668576 ACATAACTCACTTGTCATTGCG 57.331 40.909 0.00 0.00 0.00 4.85
2100 3406 9.121517 GACATGAATGAAAACATAACTCACTTG 57.878 33.333 0.00 0.00 0.00 3.16
2101 3407 8.849168 TGACATGAATGAAAACATAACTCACTT 58.151 29.630 0.00 0.00 0.00 3.16
2117 3423 8.343366 CAGATTTGAACCTAGATGACATGAATG 58.657 37.037 0.00 0.00 0.00 2.67
2119 3425 7.397221 ACAGATTTGAACCTAGATGACATGAA 58.603 34.615 0.00 0.00 0.00 2.57
2120 3426 6.950842 ACAGATTTGAACCTAGATGACATGA 58.049 36.000 0.00 0.00 0.00 3.07
2121 3427 6.259608 GGACAGATTTGAACCTAGATGACATG 59.740 42.308 0.00 0.00 0.00 3.21
2122 3428 6.070021 TGGACAGATTTGAACCTAGATGACAT 60.070 38.462 0.00 0.00 0.00 3.06
2123 3429 5.248248 TGGACAGATTTGAACCTAGATGACA 59.752 40.000 0.00 0.00 0.00 3.58
2124 3430 5.582665 GTGGACAGATTTGAACCTAGATGAC 59.417 44.000 0.00 0.00 0.00 3.06
2125 3431 5.338381 GGTGGACAGATTTGAACCTAGATGA 60.338 44.000 0.00 0.00 0.00 2.92
2143 3449 5.015515 ACTTCAGTTACTAGGTAGGTGGAC 58.984 45.833 0.00 0.00 0.00 4.02
2148 3454 8.537858 ACCATTTAACTTCAGTTACTAGGTAGG 58.462 37.037 11.62 5.69 39.92 3.18
2156 3462 9.959749 TGATTTGAACCATTTAACTTCAGTTAC 57.040 29.630 0.00 0.00 39.92 2.50
2158 3464 9.480053 CATGATTTGAACCATTTAACTTCAGTT 57.520 29.630 0.00 0.00 41.73 3.16
2160 3466 7.063780 GGCATGATTTGAACCATTTAACTTCAG 59.936 37.037 0.00 0.00 0.00 3.02
2161 3467 6.873076 GGCATGATTTGAACCATTTAACTTCA 59.127 34.615 0.00 0.00 0.00 3.02
2163 3469 6.767456 TGGCATGATTTGAACCATTTAACTT 58.233 32.000 0.00 0.00 0.00 2.66
2164 3470 6.357579 TGGCATGATTTGAACCATTTAACT 57.642 33.333 0.00 0.00 0.00 2.24
2166 3472 7.185318 AGATGGCATGATTTGAACCATTTAA 57.815 32.000 3.81 0.00 41.15 1.52
2167 3473 6.795144 AGATGGCATGATTTGAACCATTTA 57.205 33.333 3.81 0.00 41.15 1.40
2168 3474 5.687166 AGATGGCATGATTTGAACCATTT 57.313 34.783 3.81 0.00 41.15 2.32
2169 3475 6.131264 TCTAGATGGCATGATTTGAACCATT 58.869 36.000 3.81 0.00 41.15 3.16
2170 3476 5.698104 TCTAGATGGCATGATTTGAACCAT 58.302 37.500 3.81 0.00 43.72 3.55
2171 3477 5.114764 TCTAGATGGCATGATTTGAACCA 57.885 39.130 3.81 0.00 34.28 3.67
2172 3478 6.645790 AATCTAGATGGCATGATTTGAACC 57.354 37.500 3.81 0.00 0.00 3.62
2173 3479 8.192774 TGAAAATCTAGATGGCATGATTTGAAC 58.807 33.333 19.12 14.98 38.59 3.18
2174 3480 8.296211 TGAAAATCTAGATGGCATGATTTGAA 57.704 30.769 19.12 11.24 38.59 2.69
2175 3481 7.885009 TGAAAATCTAGATGGCATGATTTGA 57.115 32.000 19.12 10.34 38.59 2.69
2176 3482 8.410912 TCTTGAAAATCTAGATGGCATGATTTG 58.589 33.333 19.12 10.60 38.59 2.32
2177 3483 8.411683 GTCTTGAAAATCTAGATGGCATGATTT 58.588 33.333 3.81 11.34 39.78 2.17
2179 3485 7.288560 AGTCTTGAAAATCTAGATGGCATGAT 58.711 34.615 3.81 0.00 31.48 2.45
2180 3486 6.656902 AGTCTTGAAAATCTAGATGGCATGA 58.343 36.000 3.81 9.44 31.48 3.07
2181 3487 6.939132 AGTCTTGAAAATCTAGATGGCATG 57.061 37.500 3.81 7.46 31.48 4.06
2182 3488 8.216423 ACATAGTCTTGAAAATCTAGATGGCAT 58.784 33.333 5.86 0.00 31.48 4.40
2183 3489 7.568349 ACATAGTCTTGAAAATCTAGATGGCA 58.432 34.615 5.86 2.27 31.48 4.92
2184 3490 8.443953 AACATAGTCTTGAAAATCTAGATGGC 57.556 34.615 5.86 0.00 31.48 4.40
2188 3494 8.730680 GGCAAAACATAGTCTTGAAAATCTAGA 58.269 33.333 0.00 0.00 0.00 2.43
2189 3495 8.734386 AGGCAAAACATAGTCTTGAAAATCTAG 58.266 33.333 0.00 0.00 0.00 2.43
2190 3496 8.635765 AGGCAAAACATAGTCTTGAAAATCTA 57.364 30.769 0.00 0.00 0.00 1.98
2191 3497 7.309438 GGAGGCAAAACATAGTCTTGAAAATCT 60.309 37.037 0.00 0.00 0.00 2.40
2193 3499 6.494835 AGGAGGCAAAACATAGTCTTGAAAAT 59.505 34.615 0.00 0.00 0.00 1.82
2194 3500 5.833131 AGGAGGCAAAACATAGTCTTGAAAA 59.167 36.000 0.00 0.00 0.00 2.29
2195 3501 5.241506 CAGGAGGCAAAACATAGTCTTGAAA 59.758 40.000 0.00 0.00 0.00 2.69
2197 3503 4.041567 TCAGGAGGCAAAACATAGTCTTGA 59.958 41.667 0.00 0.00 0.00 3.02
2200 3506 3.840666 TCTCAGGAGGCAAAACATAGTCT 59.159 43.478 0.00 0.00 0.00 3.24
2201 3507 4.207891 TCTCAGGAGGCAAAACATAGTC 57.792 45.455 0.00 0.00 0.00 2.59
2205 3950 2.519013 GGTTCTCAGGAGGCAAAACAT 58.481 47.619 0.00 0.00 0.00 2.71
2221 3966 5.424121 AAAGCATAATAGCACATCGGTTC 57.576 39.130 0.00 0.00 36.85 3.62
2224 3969 4.036734 ACCAAAAGCATAATAGCACATCGG 59.963 41.667 0.00 0.00 36.85 4.18
2228 3973 3.119173 GGCACCAAAAGCATAATAGCACA 60.119 43.478 0.00 0.00 36.85 4.57
2247 3992 2.419990 CGGACAGAATTGATACTGGGCA 60.420 50.000 0.00 0.00 38.30 5.36
2249 3994 2.170607 ACCGGACAGAATTGATACTGGG 59.829 50.000 9.46 0.00 38.30 4.45
2253 3998 3.306166 CGACAACCGGACAGAATTGATAC 59.694 47.826 9.46 0.00 33.91 2.24
2283 4028 4.982241 TCAAGGATATTCTAGGCCAAGG 57.018 45.455 5.01 0.00 0.00 3.61
2285 4030 7.072454 ACAGTTATCAAGGATATTCTAGGCCAA 59.928 37.037 5.01 0.00 0.00 4.52
2293 4038 9.442047 CCCATCTTACAGTTATCAAGGATATTC 57.558 37.037 0.00 0.00 0.00 1.75
2297 4042 6.831664 ACCCATCTTACAGTTATCAAGGAT 57.168 37.500 0.00 0.00 0.00 3.24
2310 4055 6.838382 ACCCATCTTACATAACCCATCTTAC 58.162 40.000 0.00 0.00 0.00 2.34
2312 4057 5.994416 ACCCATCTTACATAACCCATCTT 57.006 39.130 0.00 0.00 0.00 2.40
2313 4058 5.994416 AACCCATCTTACATAACCCATCT 57.006 39.130 0.00 0.00 0.00 2.90
2314 4059 6.151144 GCATAACCCATCTTACATAACCCATC 59.849 42.308 0.00 0.00 0.00 3.51
2315 4060 6.010219 GCATAACCCATCTTACATAACCCAT 58.990 40.000 0.00 0.00 0.00 4.00
2316 4061 5.381757 GCATAACCCATCTTACATAACCCA 58.618 41.667 0.00 0.00 0.00 4.51
2317 4062 4.765339 GGCATAACCCATCTTACATAACCC 59.235 45.833 0.00 0.00 0.00 4.11
2318 4063 5.959618 GGCATAACCCATCTTACATAACC 57.040 43.478 0.00 0.00 0.00 2.85
2344 4089 3.384532 GGGCGGGTCCGAAGTGTA 61.385 66.667 14.15 0.00 42.83 2.90
2379 4124 7.655521 TTCGGAGAGAGATGGTCTATTTTAA 57.344 36.000 0.00 0.00 38.43 1.52
2390 4135 1.480137 ACTTGGCTTCGGAGAGAGATG 59.520 52.381 0.00 0.00 38.43 2.90
2397 4142 0.249868 TGTGTGACTTGGCTTCGGAG 60.250 55.000 0.00 0.00 0.00 4.63
2463 4209 1.749258 GGCCGCTCGGAATCCTTTT 60.749 57.895 13.11 0.00 37.50 2.27
2484 4230 3.812019 CGAGTCACCCCCTCGTCG 61.812 72.222 1.87 0.00 45.09 5.12
2501 4247 3.418684 TTTCTACCAGAAGCCCTTGTC 57.581 47.619 0.00 0.00 35.37 3.18
2525 4271 5.558818 TCTCTTAGAACTAACGTGTCCTCT 58.441 41.667 0.00 0.00 0.00 3.69
2531 4277 5.640189 TTCCCTCTCTTAGAACTAACGTG 57.360 43.478 0.00 0.00 0.00 4.49
2560 4306 8.410141 CCAATATGTTATGTGGTATTTCGGTTT 58.590 33.333 0.00 0.00 0.00 3.27
2571 4317 7.857734 TGACTTACACCAATATGTTATGTGG 57.142 36.000 8.30 0.00 37.17 4.17
2573 4319 8.405531 GCAATGACTTACACCAATATGTTATGT 58.594 33.333 0.00 0.00 33.85 2.29
2574 4320 7.587392 CGCAATGACTTACACCAATATGTTATG 59.413 37.037 0.00 0.00 33.85 1.90
2575 4321 7.255104 CCGCAATGACTTACACCAATATGTTAT 60.255 37.037 0.00 0.00 33.85 1.89
2576 4322 6.037720 CCGCAATGACTTACACCAATATGTTA 59.962 38.462 0.00 0.00 33.85 2.41
2577 4323 5.163663 CCGCAATGACTTACACCAATATGTT 60.164 40.000 0.00 0.00 33.85 2.71
2585 4331 1.933853 CTAGCCGCAATGACTTACACC 59.066 52.381 0.00 0.00 0.00 4.16
2593 4339 3.133901 TGAAATAGACCTAGCCGCAATGA 59.866 43.478 0.00 0.00 0.00 2.57
2600 4346 7.454225 ACCTCAATATTGAAATAGACCTAGCC 58.546 38.462 18.47 0.00 36.64 3.93
2666 4429 2.158559 AGGTATTTTGTCATGCGTGCA 58.841 42.857 0.00 0.00 0.00 4.57
2673 4436 6.657541 ACGGTCATGTTTAGGTATTTTGTCAT 59.342 34.615 0.00 0.00 0.00 3.06
2692 4455 0.106335 TTTTACTTGCCCGACGGTCA 59.894 50.000 13.94 2.38 0.00 4.02
2809 4575 2.930040 CCTAGGTGTATGTGCTGAAACG 59.070 50.000 0.00 0.00 0.00 3.60
2810 4576 3.939066 ACCTAGGTGTATGTGCTGAAAC 58.061 45.455 15.42 0.00 0.00 2.78
2853 4619 1.883021 GTCCGGTGAAATGCCCTTG 59.117 57.895 0.00 0.00 0.00 3.61
2856 4622 1.238625 TTTCGTCCGGTGAAATGCCC 61.239 55.000 16.92 0.00 30.75 5.36


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

AutoCloner maintained by Alex Coulton.