Multiple sequence alignment - TraesCS6D01G395000

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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 TraesCS6D01G395000 chr6D 100.000 3548 0 0 1 3548 467934751 467931204 0.000000e+00 6553.0
1 TraesCS6D01G395000 chr6D 81.859 441 46 20 936 1360 467977691 467977269 1.220000e-89 340.0
2 TraesCS6D01G395000 chr6D 78.178 527 59 26 169 669 467979516 467979020 5.800000e-73 285.0
3 TraesCS6D01G395000 chr6D 98.734 79 1 0 3470 3548 465182748 465182826 1.330000e-29 141.0
4 TraesCS6D01G395000 chr6D 98.701 77 1 0 3472 3548 1080673 1080749 1.720000e-28 137.0
5 TraesCS6D01G395000 chr6D 98.701 77 1 0 3472 3548 367102655 367102579 1.720000e-28 137.0
6 TraesCS6D01G395000 chr6D 98.701 77 1 0 3472 3548 460314945 460314869 1.720000e-28 137.0
7 TraesCS6D01G395000 chr6A 88.249 3506 301 47 1 3463 614010347 614006910 0.000000e+00 4089.0
8 TraesCS6D01G395000 chr6A 78.691 657 72 36 405 1043 614083832 614083226 3.340000e-100 375.0
9 TraesCS6D01G395000 chr6A 89.272 261 16 7 394 653 614018578 614018329 2.060000e-82 316.0
10 TraesCS6D01G395000 chr6A 88.710 248 18 7 1122 1360 614083194 614082948 9.630000e-76 294.0
11 TraesCS6D01G395000 chr6A 90.854 164 13 2 1118 1279 614018332 614018169 5.960000e-53 219.0
12 TraesCS6D01G395000 chr6A 77.975 395 45 16 379 764 614024485 614024124 3.590000e-50 209.0
13 TraesCS6D01G395000 chr6A 92.453 106 7 1 222 327 614024599 614024495 2.210000e-32 150.0
14 TraesCS6D01G395000 chr6A 92.537 67 5 0 1294 1360 614018181 614018115 2.920000e-16 97.1
15 TraesCS6D01G395000 chr6A 94.118 51 3 0 199 249 614083998 614083948 1.060000e-10 78.7
16 TraesCS6D01G395000 chr6B 85.444 3435 329 82 9 3394 714066761 714063449 0.000000e+00 3415.0
17 TraesCS6D01G395000 chr6B 79.732 523 66 22 850 1360 714080789 714080295 3.390000e-90 342.0
18 TraesCS6D01G395000 chr6B 77.344 512 51 26 191 669 714081378 714080899 3.540000e-60 243.0
19 TraesCS6D01G395000 chr6B 91.667 72 6 0 3392 3463 714060767 714060696 2.250000e-17 100.0
20 TraesCS6D01G395000 chr6B 95.556 45 2 0 2906 2950 436805435 436805391 4.910000e-09 73.1
21 TraesCS6D01G395000 chrUn 84.223 431 51 10 203 620 79606710 79606284 1.530000e-108 403.0
22 TraesCS6D01G395000 chrUn 84.471 425 49 10 203 614 256923910 256924330 1.530000e-108 403.0
23 TraesCS6D01G395000 chr5D 98.734 79 1 0 3470 3548 459311573 459311495 1.330000e-29 141.0
24 TraesCS6D01G395000 chr5D 98.701 77 1 0 3472 3548 2852227 2852151 1.720000e-28 137.0
25 TraesCS6D01G395000 chr4D 98.734 79 1 0 3470 3548 3925683 3925605 1.330000e-29 141.0
26 TraesCS6D01G395000 chr4D 97.561 41 1 0 2906 2946 298241432 298241392 1.770000e-08 71.3
27 TraesCS6D01G395000 chr7D 98.701 77 1 0 3472 3548 552683088 552683012 1.720000e-28 137.0
28 TraesCS6D01G395000 chr1D 98.701 77 1 0 3472 3548 21912085 21912009 1.720000e-28 137.0
29 TraesCS6D01G395000 chr1A 94.000 50 2 1 2903 2952 10076141 10076189 1.370000e-09 75.0
30 TraesCS6D01G395000 chr1A 95.556 45 2 0 2903 2947 104216504 104216548 4.910000e-09 73.1
31 TraesCS6D01G395000 chr1A 87.273 55 6 1 2903 2957 11940854 11940907 1.060000e-05 62.1
32 TraesCS6D01G395000 chr7B 93.750 48 3 0 2903 2950 600566671 600566718 4.910000e-09 73.1
33 TraesCS6D01G395000 chr7B 83.871 62 10 0 2904 2965 648181473 648181412 3.830000e-05 60.2
34 TraesCS6D01G395000 chr4B 95.455 44 2 0 2903 2946 178077875 178077918 1.770000e-08 71.3
35 TraesCS6D01G395000 chr3A 90.385 52 4 1 2907 2958 437869516 437869566 2.290000e-07 67.6


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 TraesCS6D01G395000 chr6D 467931204 467934751 3547 True 6553.000000 6553 100.0000 1 3548 1 chr6D.!!$R3 3547
1 TraesCS6D01G395000 chr6D 467977269 467979516 2247 True 312.500000 340 80.0185 169 1360 2 chr6D.!!$R4 1191
2 TraesCS6D01G395000 chr6A 614006910 614010347 3437 True 4089.000000 4089 88.2490 1 3463 1 chr6A.!!$R1 3462
3 TraesCS6D01G395000 chr6A 614082948 614083998 1050 True 249.233333 375 87.1730 199 1360 3 chr6A.!!$R4 1161
4 TraesCS6D01G395000 chr6B 714060696 714066761 6065 True 1757.500000 3415 88.5555 9 3463 2 chr6B.!!$R2 3454
5 TraesCS6D01G395000 chr6B 714080295 714081378 1083 True 292.500000 342 78.5380 191 1360 2 chr6B.!!$R3 1169

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
691 781 0.107703 CTCTGGGTGTGTGTGTGTGT 60.108 55.0 0.00 0.0 0.00 3.72 F
1437 2757 0.179020 CAAAGCCCACCTCTCACACA 60.179 55.0 0.00 0.0 0.00 3.72 F
2148 3476 0.840722 TCAACCTGAAGGGGTCCTCC 60.841 60.0 0.56 0.0 38.87 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 3203 0.179084 ACATGAGGCACGGGTAATCG 60.179 55.000 0.0 0.0 0.0 3.34 R
2397 3725 0.182775 AATCCCCTTGCATCCGGTAC 59.817 55.000 0.0 0.0 0.0 3.34 R
3300 4637 1.455849 CAACAGGCTCAGTTCCCCA 59.544 57.895 0.0 0.0 0.0 4.96 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
48 49 0.327924 CTCACTAACATGTGGGCCCA 59.672 55.000 24.45 24.45 38.40 5.36
119 120 3.859961 AGTCAGATCACGCGAAATTACAG 59.140 43.478 15.93 0.00 0.00 2.74
193 202 2.842936 CCCCCTACCCCGCTACTG 60.843 72.222 0.00 0.00 0.00 2.74
197 206 0.974010 CCCTACCCCGCTACTGTTCA 60.974 60.000 0.00 0.00 0.00 3.18
202 211 0.320374 CCCCGCTACTGTTCAGTTGA 59.680 55.000 15.89 0.00 0.00 3.18
288 309 2.371910 ACTCTTCGAACCAGCTTAGC 57.628 50.000 0.00 0.00 0.00 3.09
314 335 2.886859 GGACACATCATCCGTAGCG 58.113 57.895 0.00 0.00 0.00 4.26
338 373 3.110178 GCGGTGCGGTGTACTCAC 61.110 66.667 0.00 0.00 43.19 3.51
557 622 2.321213 GGCCATTAGTTGCTAGCCG 58.679 57.895 13.29 0.00 0.00 5.52
558 623 0.179056 GGCCATTAGTTGCTAGCCGA 60.179 55.000 13.29 0.00 0.00 5.54
559 624 1.221414 GCCATTAGTTGCTAGCCGAG 58.779 55.000 13.29 0.00 0.00 4.63
614 695 4.594123 TTGACATGGTCGTACTTCTTCA 57.406 40.909 0.00 0.00 34.95 3.02
617 707 4.219725 TGACATGGTCGTACTTCTTCATCA 59.780 41.667 0.00 0.00 34.95 3.07
645 735 0.894835 AATCAACCGGCACCCAATTC 59.105 50.000 0.00 0.00 0.00 2.17
688 778 0.756294 TACCTCTGGGTGTGTGTGTG 59.244 55.000 0.00 0.00 46.75 3.82
689 779 1.271840 ACCTCTGGGTGTGTGTGTGT 61.272 55.000 0.00 0.00 45.43 3.72
690 780 0.815213 CCTCTGGGTGTGTGTGTGTG 60.815 60.000 0.00 0.00 0.00 3.82
691 781 0.107703 CTCTGGGTGTGTGTGTGTGT 60.108 55.000 0.00 0.00 0.00 3.72
711 801 7.503230 TGTGTGTCTGCATGGATAAATCATAAT 59.497 33.333 0.00 0.00 0.00 1.28
765 855 0.409876 CCCTCCCTCTATCCGATCCA 59.590 60.000 0.00 0.00 0.00 3.41
817 907 1.096386 CACCGTCTCCTCCTACCTCG 61.096 65.000 0.00 0.00 0.00 4.63
914 1084 1.331756 CATTCCTTCCGATTCTTGCCG 59.668 52.381 0.00 0.00 0.00 5.69
918 1088 0.676782 CTTCCGATTCTTGCCGGGTT 60.677 55.000 2.18 0.00 45.36 4.11
927 1097 0.179073 CTTGCCGGGTTGATCGATCT 60.179 55.000 25.02 0.00 0.00 2.75
956 1126 2.430465 AGAACAGCACGCAGATCATTT 58.570 42.857 0.00 0.00 0.00 2.32
989 2288 0.955428 GTCCAAGCGGTCTGATTGCA 60.955 55.000 4.02 0.00 42.63 4.08
990 2289 0.250684 TCCAAGCGGTCTGATTGCAA 60.251 50.000 0.00 0.00 42.63 4.08
1029 2328 1.028868 GCAGCAATCTCGAGGCCTTT 61.029 55.000 6.77 0.00 0.00 3.11
1089 2388 2.630098 CTCCATGGTACGTGATCCATCT 59.370 50.000 12.58 0.00 41.79 2.90
1090 2389 2.628178 TCCATGGTACGTGATCCATCTC 59.372 50.000 12.58 0.00 41.79 2.75
1114 2413 8.896722 TCTCTATCCTTAGTTCCTTACAAACT 57.103 34.615 0.00 0.00 40.06 2.66
1147 2455 0.804989 CCTCTGCTTTTACCGGCAAG 59.195 55.000 0.00 2.33 38.02 4.01
1150 2458 2.749621 CTCTGCTTTTACCGGCAAGAAT 59.250 45.455 0.00 0.00 38.02 2.40
1172 2480 3.070748 GGCTCTGTTTTCCTCTGTTCTC 58.929 50.000 0.00 0.00 0.00 2.87
1193 2510 2.880890 CAACAGTTTGGGTCTTCTCTGG 59.119 50.000 0.00 0.00 0.00 3.86
1429 2749 4.974721 CCGCCACAAAGCCCACCT 62.975 66.667 0.00 0.00 0.00 4.00
1437 2757 0.179020 CAAAGCCCACCTCTCACACA 60.179 55.000 0.00 0.00 0.00 3.72
1473 2793 1.837439 AGGTAATCAGTTGATCGGCCA 59.163 47.619 2.24 0.00 32.75 5.36
1515 2836 1.939934 GCATTTCGATCGATCCACCAA 59.060 47.619 20.18 9.44 0.00 3.67
1516 2837 2.549754 GCATTTCGATCGATCCACCAAT 59.450 45.455 20.18 11.46 0.00 3.16
1517 2838 3.745975 GCATTTCGATCGATCCACCAATA 59.254 43.478 20.18 0.00 0.00 1.90
1518 2839 4.143030 GCATTTCGATCGATCCACCAATAG 60.143 45.833 20.18 9.91 0.00 1.73
1520 2841 4.665833 TTCGATCGATCCACCAATAGTT 57.334 40.909 20.18 0.00 0.00 2.24
1521 2842 4.238761 TCGATCGATCCACCAATAGTTC 57.761 45.455 19.51 0.00 0.00 3.01
1884 3212 1.883084 GCTGGCTCACGATTACCCG 60.883 63.158 0.00 0.00 0.00 5.28
2015 3343 2.109425 ACTTATTTGCTGGTCGGTCC 57.891 50.000 0.00 0.00 0.00 4.46
2057 3385 6.349115 GCATTATCTTGCTGAGGTATGAATGG 60.349 42.308 0.00 0.00 39.57 3.16
2061 3389 0.940126 GCTGAGGTATGAATGGTGCG 59.060 55.000 0.00 0.00 0.00 5.34
2125 3453 3.181436 CCCAATCTATCACATCCCTGCTT 60.181 47.826 0.00 0.00 0.00 3.91
2142 3470 2.290896 TGCTTATGTCAACCTGAAGGGG 60.291 50.000 0.56 0.00 40.27 4.79
2143 3471 2.290960 GCTTATGTCAACCTGAAGGGGT 60.291 50.000 0.56 0.00 42.05 4.95
2148 3476 0.840722 TCAACCTGAAGGGGTCCTCC 60.841 60.000 0.56 0.00 38.87 4.30
2187 3515 3.200825 ACCATTCCATCTCATCGGTCTTT 59.799 43.478 0.00 0.00 0.00 2.52
2229 3557 1.604755 GCCACGTACATTGGTTGTGAA 59.395 47.619 11.28 0.00 39.48 3.18
2254 3582 3.828451 ACAACAGATTTCTTCCACCATGG 59.172 43.478 11.19 11.19 39.43 3.66
2257 3585 2.827322 CAGATTTCTTCCACCATGGCAA 59.173 45.455 13.04 1.04 37.47 4.52
2262 3590 2.722094 TCTTCCACCATGGCAATGTAC 58.278 47.619 13.04 0.00 37.47 2.90
2272 3600 3.266510 TGGCAATGTACTAGGAAGCAG 57.733 47.619 0.00 0.00 0.00 4.24
2273 3601 2.837591 TGGCAATGTACTAGGAAGCAGA 59.162 45.455 0.00 0.00 0.00 4.26
2319 3647 1.873698 TAAGCGCCGTTGTTTCTTCT 58.126 45.000 2.29 0.00 0.00 2.85
2322 3650 1.866925 CGCCGTTGTTTCTTCTCCC 59.133 57.895 0.00 0.00 0.00 4.30
2337 3665 1.067142 TCTCCCGCAGACAACATACAC 60.067 52.381 0.00 0.00 0.00 2.90
2339 3667 1.070914 TCCCGCAGACAACATACACAA 59.929 47.619 0.00 0.00 0.00 3.33
2415 3743 1.837090 GTACCGGATGCAAGGGGAT 59.163 57.895 9.46 0.00 0.00 3.85
2416 3744 0.182775 GTACCGGATGCAAGGGGATT 59.817 55.000 9.46 0.00 0.00 3.01
2423 3751 1.753073 GATGCAAGGGGATTTGTGGAG 59.247 52.381 0.00 0.00 0.00 3.86
2427 3755 1.002857 AAGGGGATTTGTGGAGGAGG 58.997 55.000 0.00 0.00 0.00 4.30
2439 3767 2.367512 AGGAGGCCAGGGTCATCC 60.368 66.667 5.01 0.00 0.00 3.51
2472 3800 1.300963 GTCTGAGCTCCATTGGGCA 59.699 57.895 12.15 4.33 0.00 5.36
2476 3804 3.984193 GAGCTCCATTGGGCAGCGT 62.984 63.158 15.64 4.28 38.26 5.07
2520 3848 3.148084 CACCACCCCGACTTCACT 58.852 61.111 0.00 0.00 0.00 3.41
2529 3857 1.792949 CCCGACTTCACTTTCTTCACG 59.207 52.381 0.00 0.00 0.00 4.35
2532 3860 2.151360 CGACTTCACTTTCTTCACGTCG 59.849 50.000 0.00 0.00 37.32 5.12
2546 3874 1.580385 CGTCGTCTCACCGTCGATG 60.580 63.158 0.00 0.00 40.80 3.84
2559 3887 4.386951 CGATGACACGGCACCCCA 62.387 66.667 0.00 0.00 0.00 4.96
2561 3889 1.524961 GATGACACGGCACCCCATA 59.475 57.895 0.00 0.00 0.00 2.74
2564 3892 1.153429 GACACGGCACCCCATAGAC 60.153 63.158 0.00 0.00 0.00 2.59
2566 3894 1.198759 ACACGGCACCCCATAGACTT 61.199 55.000 0.00 0.00 0.00 3.01
2567 3895 0.035439 CACGGCACCCCATAGACTTT 60.035 55.000 0.00 0.00 0.00 2.66
2568 3896 0.035439 ACGGCACCCCATAGACTTTG 60.035 55.000 0.00 0.00 0.00 2.77
2570 3898 1.037579 GGCACCCCATAGACTTTGCC 61.038 60.000 0.00 0.00 42.57 4.52
2571 3899 1.376609 GCACCCCATAGACTTTGCCG 61.377 60.000 0.00 0.00 0.00 5.69
2579 3907 2.922740 TAGACTTTGCCGGTGTTTCT 57.077 45.000 1.90 1.53 0.00 2.52
2592 3920 2.230992 GGTGTTTCTATGGCATTGCACA 59.769 45.455 4.78 7.44 0.00 4.57
2593 3921 3.119029 GGTGTTTCTATGGCATTGCACAT 60.119 43.478 4.78 13.20 0.00 3.21
2595 3923 3.762823 TGTTTCTATGGCATTGCACATGA 59.237 39.130 4.78 8.80 0.00 3.07
2622 3950 6.951062 TGTGAAGATATGACACCAAAAACA 57.049 33.333 0.00 0.00 34.18 2.83
2637 3965 6.591062 CACCAAAAACATCATGTAGGATTTGG 59.409 38.462 23.01 23.01 41.04 3.28
2658 3986 6.367374 TGGTAGAACAACATGAACTGGATA 57.633 37.500 0.00 0.00 0.00 2.59
2680 4008 7.967303 GGATATTTCTTCTTTCTGAACTTGCAG 59.033 37.037 0.00 0.00 37.24 4.41
2690 4018 5.227569 TCTGAACTTGCAGGAAGATACAA 57.772 39.130 8.96 0.00 36.55 2.41
2695 4023 6.374333 TGAACTTGCAGGAAGATACAATAACC 59.626 38.462 8.96 0.00 35.42 2.85
2697 4025 7.195374 ACTTGCAGGAAGATACAATAACCTA 57.805 36.000 8.96 0.00 35.42 3.08
2710 4038 5.348418 CAATAACCTATTGCATCGACCTG 57.652 43.478 0.00 0.00 39.09 4.00
2725 4053 2.543861 CGACCTGTGTGGATCGGATTAG 60.544 54.545 0.00 0.00 39.71 1.73
2731 4059 1.407618 TGTGGATCGGATTAGGTGTCG 59.592 52.381 0.00 0.00 0.00 4.35
2735 4063 1.955080 GATCGGATTAGGTGTCGGACT 59.045 52.381 9.88 0.00 0.00 3.85
2736 4064 1.100510 TCGGATTAGGTGTCGGACTG 58.899 55.000 9.88 0.00 0.00 3.51
2769 4097 0.036858 TTGTTCATCGACGGGCATGA 60.037 50.000 0.00 0.00 0.00 3.07
2775 4103 3.089284 TCATCGACGGGCATGATATAGT 58.911 45.455 0.00 0.00 0.00 2.12
2778 4106 2.626266 TCGACGGGCATGATATAGTTGT 59.374 45.455 0.00 0.00 0.00 3.32
2808 4136 6.519679 ACATTTTCATAGAAATGCAGCTCA 57.480 33.333 9.53 0.00 46.14 4.26
2816 4144 3.782046 AGAAATGCAGCTCATGAAATGC 58.218 40.909 19.89 19.89 46.21 3.56
2820 4148 0.588233 GCAGCTCATGAAATGCGACG 60.588 55.000 14.12 0.00 46.21 5.12
2823 4151 0.314578 GCTCATGAAATGCGACGTCG 60.315 55.000 32.57 32.57 46.21 5.12
2837 4165 3.420544 GCGACGTCGATGCATATAGTTTG 60.421 47.826 39.74 6.86 43.02 2.93
2838 4166 3.119628 CGACGTCGATGCATATAGTTTGG 59.880 47.826 33.35 0.00 43.02 3.28
2854 4182 2.427095 GTTTGGCAATCCACCTGGTATC 59.573 50.000 0.00 0.00 43.33 2.24
2861 4189 1.568504 TCCACCTGGTATCACCTGTC 58.431 55.000 0.00 0.00 39.58 3.51
2869 4197 1.339727 GGTATCACCTGTCGGGCTTTT 60.340 52.381 0.00 0.00 39.10 2.27
2890 4218 8.989980 GCTTTTACTGTACTTCACTGTCTTAAT 58.010 33.333 0.00 0.00 39.71 1.40
2906 4234 5.706916 GTCTTAATGACACTCCGACAACTA 58.293 41.667 0.00 0.00 44.73 2.24
2907 4235 5.800941 GTCTTAATGACACTCCGACAACTAG 59.199 44.000 0.00 0.00 44.73 2.57
2908 4236 2.656560 ATGACACTCCGACAACTAGC 57.343 50.000 0.00 0.00 0.00 3.42
2910 4238 0.889306 GACACTCCGACAACTAGCCT 59.111 55.000 0.00 0.00 0.00 4.58
2911 4239 2.089980 GACACTCCGACAACTAGCCTA 58.910 52.381 0.00 0.00 0.00 3.93
2912 4240 1.817447 ACACTCCGACAACTAGCCTAC 59.183 52.381 0.00 0.00 0.00 3.18
2913 4241 1.816835 CACTCCGACAACTAGCCTACA 59.183 52.381 0.00 0.00 0.00 2.74
2915 4243 2.895404 ACTCCGACAACTAGCCTACAAA 59.105 45.455 0.00 0.00 0.00 2.83
2916 4244 3.322828 ACTCCGACAACTAGCCTACAAAA 59.677 43.478 0.00 0.00 0.00 2.44
2917 4245 4.202284 ACTCCGACAACTAGCCTACAAAAA 60.202 41.667 0.00 0.00 0.00 1.94
2918 4246 4.060205 TCCGACAACTAGCCTACAAAAAC 58.940 43.478 0.00 0.00 0.00 2.43
2919 4247 3.120786 CCGACAACTAGCCTACAAAAACG 60.121 47.826 0.00 0.00 0.00 3.60
2920 4248 3.492011 CGACAACTAGCCTACAAAAACGT 59.508 43.478 0.00 0.00 0.00 3.99
2921 4249 4.375706 CGACAACTAGCCTACAAAAACGTC 60.376 45.833 0.00 0.00 0.00 4.34
2922 4250 4.700700 ACAACTAGCCTACAAAAACGTCT 58.299 39.130 0.00 0.00 0.00 4.18
2923 4251 5.121105 ACAACTAGCCTACAAAAACGTCTT 58.879 37.500 0.00 0.00 0.00 3.01
2924 4252 6.282930 ACAACTAGCCTACAAAAACGTCTTA 58.717 36.000 0.00 0.00 0.00 2.10
2925 4253 6.932960 ACAACTAGCCTACAAAAACGTCTTAT 59.067 34.615 0.00 0.00 0.00 1.73
2926 4254 8.090214 ACAACTAGCCTACAAAAACGTCTTATA 58.910 33.333 0.00 0.00 0.00 0.98
2927 4255 9.095065 CAACTAGCCTACAAAAACGTCTTATAT 57.905 33.333 0.00 0.00 0.00 0.86
2928 4256 9.662947 AACTAGCCTACAAAAACGTCTTATATT 57.337 29.630 0.00 0.00 0.00 1.28
2929 4257 9.662947 ACTAGCCTACAAAAACGTCTTATATTT 57.337 29.630 0.00 0.00 0.00 1.40
2932 4260 9.005777 AGCCTACAAAAACGTCTTATATTTTGA 57.994 29.630 21.46 9.08 42.48 2.69
2933 4261 9.274065 GCCTACAAAAACGTCTTATATTTTGAG 57.726 33.333 21.46 15.15 42.48 3.02
2988 4316 0.250640 ACTCTGCCTGCTGTTTGGAG 60.251 55.000 0.00 0.00 0.00 3.86
3004 4333 2.259917 TGGAGCACAAAGATGAGGAGA 58.740 47.619 0.00 0.00 0.00 3.71
3008 4337 5.045651 TGGAGCACAAAGATGAGGAGAAATA 60.046 40.000 0.00 0.00 0.00 1.40
3025 4354 7.440556 AGGAGAAATACATCATCTTTGACGATG 59.559 37.037 2.65 2.65 38.09 3.84
3026 4355 6.952743 AGAAATACATCATCTTTGACGATGC 58.047 36.000 3.92 0.00 35.95 3.91
3028 4357 6.682423 AATACATCATCTTTGACGATGCAA 57.318 33.333 3.92 0.00 35.95 4.08
3047 4376 3.061161 GCAATCATGCGTTGTTTTGGATC 59.939 43.478 10.89 0.00 43.83 3.36
3050 4379 2.625314 TCATGCGTTGTTTTGGATCCAA 59.375 40.909 23.63 23.63 0.00 3.53
3061 4390 9.103861 GTTGTTTTGGATCCAAAGTAATTTTCA 57.896 29.630 32.77 20.58 45.15 2.69
3072 4401 8.700051 TCCAAAGTAATTTTCAGTTGGATTTCA 58.300 29.630 0.00 0.00 39.58 2.69
3074 4403 8.479280 CAAAGTAATTTTCAGTTGGATTTCACG 58.521 33.333 0.00 0.00 0.00 4.35
3079 4408 2.679450 TCAGTTGGATTTCACGTACGG 58.321 47.619 21.06 8.79 0.00 4.02
3084 4413 3.663995 TGGATTTCACGTACGGAAAGA 57.336 42.857 25.29 14.59 37.64 2.52
3099 4428 7.382488 CGTACGGAAAGATCATGACAAGATATT 59.618 37.037 7.57 0.00 0.00 1.28
3101 4430 6.422100 ACGGAAAGATCATGACAAGATATTCG 59.578 38.462 0.00 4.80 0.00 3.34
3119 4449 4.864916 TTCGTACTCTGTACCGATACAC 57.135 45.455 0.00 0.00 36.34 2.90
3149 4486 3.385111 CACCTAGGTGGGATACTTCTGAC 59.615 52.174 31.15 0.00 42.00 3.51
3191 4528 3.194062 GAGATCTCAAGCACCACTTAGC 58.806 50.000 18.11 0.00 36.04 3.09
3212 4549 2.840651 CAGGCTTTCCCCTTCTCTTAGA 59.159 50.000 0.00 0.00 31.24 2.10
3250 4587 0.321346 ATACGCGATGATGCCATCCA 59.679 50.000 15.93 0.00 44.87 3.41
3252 4589 0.747644 ACGCGATGATGCCATCCAAA 60.748 50.000 15.93 0.00 44.87 3.28
3268 4605 1.758122 AAATGCCCTGGATTCCGGC 60.758 57.895 13.17 13.17 43.32 6.13
3300 4637 4.479993 GATGCTGCCGACCCTGCT 62.480 66.667 0.00 0.00 0.00 4.24
3314 4651 2.530151 TGCTGGGGAACTGAGCCT 60.530 61.111 0.00 0.00 35.64 4.58
3327 4664 1.876156 CTGAGCCTGTTGGTTCTTCAC 59.124 52.381 0.00 0.00 43.03 3.18
3335 4672 1.954382 GTTGGTTCTTCACTGGGTTCC 59.046 52.381 0.00 0.00 0.00 3.62
3340 4677 3.558533 GGTTCTTCACTGGGTTCCGTAAT 60.559 47.826 0.00 0.00 0.00 1.89
3364 4702 3.726557 AATGATGCTCTTGGGAAGACA 57.273 42.857 0.00 0.00 33.12 3.41
3369 4707 2.551270 TGCTCTTGGGAAGACATACCT 58.449 47.619 0.00 0.00 33.12 3.08
3390 4728 0.470341 GAGACCATTAGGCCCTCCAC 59.530 60.000 0.00 0.00 39.06 4.02
3401 7423 1.271054 GGCCCTCCACTATGTATGCTG 60.271 57.143 0.00 0.00 0.00 4.41
3443 7465 0.538584 CACTAGTGGCATGGCAGAGA 59.461 55.000 28.24 15.14 0.00 3.10
3463 7485 3.898123 AGAGTGTGACACCATTCTACAGT 59.102 43.478 12.81 0.00 34.49 3.55
3464 7486 4.345257 AGAGTGTGACACCATTCTACAGTT 59.655 41.667 12.81 0.00 34.49 3.16
3465 7487 5.538813 AGAGTGTGACACCATTCTACAGTTA 59.461 40.000 12.81 0.00 34.49 2.24
3466 7488 6.041637 AGAGTGTGACACCATTCTACAGTTAA 59.958 38.462 12.81 0.00 34.49 2.01
3467 7489 6.223852 AGTGTGACACCATTCTACAGTTAAG 58.776 40.000 12.81 0.00 34.49 1.85
3468 7490 6.041637 AGTGTGACACCATTCTACAGTTAAGA 59.958 38.462 12.81 0.00 34.49 2.10
3469 7491 6.704493 GTGTGACACCATTCTACAGTTAAGAA 59.296 38.462 3.92 0.00 37.38 2.52
3470 7492 7.225931 GTGTGACACCATTCTACAGTTAAGAAA 59.774 37.037 3.92 0.00 36.60 2.52
3471 7493 7.936847 TGTGACACCATTCTACAGTTAAGAAAT 59.063 33.333 2.45 0.00 36.60 2.17
3472 7494 8.784043 GTGACACCATTCTACAGTTAAGAAATT 58.216 33.333 0.00 0.00 36.60 1.82
3473 7495 8.999431 TGACACCATTCTACAGTTAAGAAATTC 58.001 33.333 0.00 0.00 36.60 2.17
3474 7496 8.029642 ACACCATTCTACAGTTAAGAAATTCG 57.970 34.615 0.00 0.00 36.60 3.34
3475 7497 7.660208 ACACCATTCTACAGTTAAGAAATTCGT 59.340 33.333 0.00 0.00 36.60 3.85
3476 7498 9.146984 CACCATTCTACAGTTAAGAAATTCGTA 57.853 33.333 0.00 0.00 36.60 3.43
3477 7499 9.886132 ACCATTCTACAGTTAAGAAATTCGTAT 57.114 29.630 0.00 0.00 36.60 3.06
3479 7501 9.638300 CATTCTACAGTTAAGAAATTCGTATGC 57.362 33.333 0.00 0.00 36.60 3.14
3480 7502 8.766000 TTCTACAGTTAAGAAATTCGTATGCA 57.234 30.769 0.00 0.00 30.15 3.96
3481 7503 8.766000 TCTACAGTTAAGAAATTCGTATGCAA 57.234 30.769 0.00 0.00 0.00 4.08
3482 7504 9.210329 TCTACAGTTAAGAAATTCGTATGCAAA 57.790 29.630 0.00 0.00 0.00 3.68
3483 7505 9.820229 CTACAGTTAAGAAATTCGTATGCAAAA 57.180 29.630 0.00 0.00 0.00 2.44
3484 7506 8.728088 ACAGTTAAGAAATTCGTATGCAAAAG 57.272 30.769 0.00 0.00 0.00 2.27
3485 7507 8.349983 ACAGTTAAGAAATTCGTATGCAAAAGT 58.650 29.630 0.00 0.00 0.00 2.66
3486 7508 9.180678 CAGTTAAGAAATTCGTATGCAAAAGTT 57.819 29.630 0.00 0.00 0.00 2.66
3490 7512 7.740519 AGAAATTCGTATGCAAAAGTTATGC 57.259 32.000 0.00 0.00 44.08 3.14
3491 7513 6.751888 AGAAATTCGTATGCAAAAGTTATGCC 59.248 34.615 0.00 0.00 43.16 4.40
3492 7514 4.364415 TTCGTATGCAAAAGTTATGCCC 57.636 40.909 0.00 0.00 43.16 5.36
3493 7515 3.348119 TCGTATGCAAAAGTTATGCCCA 58.652 40.909 0.00 0.00 43.16 5.36
3494 7516 3.951037 TCGTATGCAAAAGTTATGCCCAT 59.049 39.130 0.00 0.00 43.16 4.00
3495 7517 4.400884 TCGTATGCAAAAGTTATGCCCATT 59.599 37.500 0.00 0.00 43.16 3.16
3496 7518 5.105554 TCGTATGCAAAAGTTATGCCCATTT 60.106 36.000 0.00 0.00 43.16 2.32
3497 7519 5.580297 CGTATGCAAAAGTTATGCCCATTTT 59.420 36.000 0.00 0.00 43.16 1.82
3498 7520 6.754209 CGTATGCAAAAGTTATGCCCATTTTA 59.246 34.615 0.00 0.00 43.16 1.52
3499 7521 7.276658 CGTATGCAAAAGTTATGCCCATTTTAA 59.723 33.333 0.00 0.00 43.16 1.52
3500 7522 7.614124 ATGCAAAAGTTATGCCCATTTTAAG 57.386 32.000 0.00 0.00 43.16 1.85
3501 7523 6.763355 TGCAAAAGTTATGCCCATTTTAAGA 58.237 32.000 0.00 0.00 43.16 2.10
3502 7524 7.220030 TGCAAAAGTTATGCCCATTTTAAGAA 58.780 30.769 0.00 0.00 43.16 2.52
3503 7525 7.716998 TGCAAAAGTTATGCCCATTTTAAGAAA 59.283 29.630 0.00 0.00 43.16 2.52
3504 7526 8.729756 GCAAAAGTTATGCCCATTTTAAGAAAT 58.270 29.630 0.00 0.00 37.85 2.17
3507 7529 9.448438 AAAGTTATGCCCATTTTAAGAAATTCC 57.552 29.630 0.00 0.00 33.25 3.01
3508 7530 8.144862 AGTTATGCCCATTTTAAGAAATTCCA 57.855 30.769 0.00 0.00 33.25 3.53
3509 7531 8.260114 AGTTATGCCCATTTTAAGAAATTCCAG 58.740 33.333 0.00 0.00 33.25 3.86
3510 7532 6.872585 ATGCCCATTTTAAGAAATTCCAGA 57.127 33.333 0.00 0.00 33.25 3.86
3511 7533 6.284891 TGCCCATTTTAAGAAATTCCAGAG 57.715 37.500 0.00 0.00 33.25 3.35
3512 7534 6.015918 TGCCCATTTTAAGAAATTCCAGAGA 58.984 36.000 0.00 0.00 33.25 3.10
3513 7535 6.153340 TGCCCATTTTAAGAAATTCCAGAGAG 59.847 38.462 0.00 0.00 33.25 3.20
3514 7536 6.378280 GCCCATTTTAAGAAATTCCAGAGAGA 59.622 38.462 0.00 0.00 33.25 3.10
3515 7537 7.069208 GCCCATTTTAAGAAATTCCAGAGAGAT 59.931 37.037 0.00 0.00 33.25 2.75
3516 7538 8.975295 CCCATTTTAAGAAATTCCAGAGAGATT 58.025 33.333 0.00 0.00 33.25 2.40
3520 7542 9.696917 TTTTAAGAAATTCCAGAGAGATTTTGC 57.303 29.630 0.00 0.00 0.00 3.68
3521 7543 6.906157 AAGAAATTCCAGAGAGATTTTGCA 57.094 33.333 0.00 0.00 0.00 4.08
3522 7544 6.906157 AGAAATTCCAGAGAGATTTTGCAA 57.094 33.333 0.00 0.00 0.00 4.08
3523 7545 6.921914 AGAAATTCCAGAGAGATTTTGCAAG 58.078 36.000 0.00 0.00 0.00 4.01
3524 7546 6.492772 AGAAATTCCAGAGAGATTTTGCAAGT 59.507 34.615 0.00 0.00 0.00 3.16
3525 7547 7.667219 AGAAATTCCAGAGAGATTTTGCAAGTA 59.333 33.333 0.00 0.00 0.00 2.24
3526 7548 7.765695 AATTCCAGAGAGATTTTGCAAGTAA 57.234 32.000 0.00 0.00 0.00 2.24
3527 7549 7.765695 ATTCCAGAGAGATTTTGCAAGTAAA 57.234 32.000 0.00 0.00 0.00 2.01
3528 7550 6.808008 TCCAGAGAGATTTTGCAAGTAAAG 57.192 37.500 0.00 0.00 0.00 1.85
3529 7551 6.299141 TCCAGAGAGATTTTGCAAGTAAAGT 58.701 36.000 0.00 0.00 0.00 2.66
3530 7552 6.428159 TCCAGAGAGATTTTGCAAGTAAAGTC 59.572 38.462 0.00 0.00 0.00 3.01
3531 7553 6.302615 CAGAGAGATTTTGCAAGTAAAGTCG 58.697 40.000 0.00 0.00 33.20 4.18
3532 7554 6.146184 CAGAGAGATTTTGCAAGTAAAGTCGA 59.854 38.462 0.00 0.00 33.20 4.20
3533 7555 6.706270 AGAGAGATTTTGCAAGTAAAGTCGAA 59.294 34.615 0.00 0.00 33.20 3.71
3534 7556 7.226720 AGAGAGATTTTGCAAGTAAAGTCGAAA 59.773 33.333 0.00 0.00 33.20 3.46
3535 7557 7.875971 AGAGATTTTGCAAGTAAAGTCGAAAT 58.124 30.769 0.00 0.00 33.20 2.17
3536 7558 8.352942 AGAGATTTTGCAAGTAAAGTCGAAATT 58.647 29.630 0.00 0.00 33.20 1.82
3537 7559 8.507470 AGATTTTGCAAGTAAAGTCGAAATTC 57.493 30.769 0.00 0.00 33.20 2.17
3538 7560 8.134895 AGATTTTGCAAGTAAAGTCGAAATTCA 58.865 29.630 0.00 0.00 33.20 2.57
3539 7561 8.816640 ATTTTGCAAGTAAAGTCGAAATTCAT 57.183 26.923 0.00 0.00 0.00 2.57
3540 7562 9.906660 ATTTTGCAAGTAAAGTCGAAATTCATA 57.093 25.926 0.00 0.00 0.00 2.15
3541 7563 9.906660 TTTTGCAAGTAAAGTCGAAATTCATAT 57.093 25.926 0.00 0.00 0.00 1.78
3542 7564 9.906660 TTTGCAAGTAAAGTCGAAATTCATATT 57.093 25.926 0.00 0.00 0.00 1.28
3543 7565 9.906660 TTGCAAGTAAAGTCGAAATTCATATTT 57.093 25.926 0.00 0.00 36.68 1.40
3544 7566 9.340695 TGCAAGTAAAGTCGAAATTCATATTTG 57.659 29.630 0.00 0.00 34.16 2.32
3545 7567 9.341899 GCAAGTAAAGTCGAAATTCATATTTGT 57.658 29.630 0.00 0.00 34.16 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.928839 ACATGTTAGTGAGTGCTAAGTCAAG 59.071 40.000 0.00 0.00 37.50 3.02
28 29 0.328258 GGGCCCACATGTTAGTGAGT 59.672 55.000 19.95 0.00 42.05 3.41
29 30 0.327924 TGGGCCCACATGTTAGTGAG 59.672 55.000 24.45 0.00 42.05 3.51
48 49 0.892755 CATGTGGCCAGCTTGTGAAT 59.107 50.000 5.11 0.00 0.00 2.57
150 152 2.969238 GGTGGCAGCGGATCGATG 60.969 66.667 0.54 0.98 46.35 3.84
202 211 2.607282 GGATAAGCCGTTGATCGACGAT 60.607 50.000 32.39 19.56 45.47 3.73
288 309 2.146342 GGATGATGTGTCCGCCATTAG 58.854 52.381 0.00 0.00 0.00 1.73
297 318 2.203800 TTCGCTACGGATGATGTGTC 57.796 50.000 0.00 0.00 0.00 3.67
314 335 4.025401 CACCGCACCGCACCTTTC 62.025 66.667 0.00 0.00 0.00 2.62
338 373 1.811266 CGTGTGGATGGAGGCGAAG 60.811 63.158 0.00 0.00 0.00 3.79
375 410 0.032515 TAGCTAGTGGCCAGGCAGTA 60.033 55.000 22.04 11.18 43.05 2.74
403 449 0.901827 TGCTCCATGTGACGTGGTAT 59.098 50.000 22.23 0.00 37.96 2.73
539 593 0.179056 TCGGCTAGCAACTAATGGCC 60.179 55.000 18.24 0.00 36.60 5.36
573 638 4.047125 ACTTGTGGGCGATGGGGG 62.047 66.667 0.00 0.00 0.00 5.40
574 639 2.556840 ATCACTTGTGGGCGATGGGG 62.557 60.000 0.64 0.00 0.00 4.96
575 640 0.680921 AATCACTTGTGGGCGATGGG 60.681 55.000 0.64 0.00 0.00 4.00
614 695 2.026641 CGGTTGATTTGCAGGGATGAT 58.973 47.619 0.00 0.00 0.00 2.45
617 707 1.322538 GCCGGTTGATTTGCAGGGAT 61.323 55.000 1.90 0.00 0.00 3.85
645 735 3.255642 GTGGCTAGCTAGGAGATGAGAAG 59.744 52.174 22.10 0.00 0.00 2.85
688 778 7.811236 CCAATTATGATTTATCCATGCAGACAC 59.189 37.037 0.00 0.00 0.00 3.67
689 779 7.724951 TCCAATTATGATTTATCCATGCAGACA 59.275 33.333 0.00 0.00 0.00 3.41
690 780 8.114331 TCCAATTATGATTTATCCATGCAGAC 57.886 34.615 0.00 0.00 0.00 3.51
691 781 8.888836 ATCCAATTATGATTTATCCATGCAGA 57.111 30.769 0.00 0.00 0.00 4.26
711 801 1.677576 GCATCGAATCCAGCAATCCAA 59.322 47.619 0.00 0.00 0.00 3.53
873 1043 4.107072 TGGATCAAGATTGGGAGAGTCTT 58.893 43.478 0.00 0.00 32.70 3.01
874 1044 3.729108 TGGATCAAGATTGGGAGAGTCT 58.271 45.455 0.00 0.00 0.00 3.24
914 1084 0.032267 GTCCCGAGATCGATCAACCC 59.968 60.000 26.47 11.63 43.02 4.11
918 1088 0.945099 CTTCGTCCCGAGATCGATCA 59.055 55.000 26.47 3.10 43.02 2.92
927 1097 1.006571 GTGCTGTTCTTCGTCCCGA 60.007 57.895 0.00 0.00 0.00 5.14
972 2271 0.597568 TTTGCAATCAGACCGCTTGG 59.402 50.000 0.00 0.00 39.35 3.61
989 2288 6.404513 GCTGCTGCTCTTCATCTTTATCTTTT 60.405 38.462 8.53 0.00 36.03 2.27
990 2289 5.066246 GCTGCTGCTCTTCATCTTTATCTTT 59.934 40.000 8.53 0.00 36.03 2.52
1069 2368 2.628178 GAGATGGATCACGTACCATGGA 59.372 50.000 21.47 0.00 45.41 3.41
1089 2388 8.750298 CAGTTTGTAAGGAACTAAGGATAGAGA 58.250 37.037 0.00 0.00 38.49 3.10
1090 2389 7.982354 CCAGTTTGTAAGGAACTAAGGATAGAG 59.018 40.741 0.00 0.00 38.49 2.43
1114 2413 1.229625 AGAGGACCTGCCATGACCA 60.230 57.895 0.00 0.00 40.02 4.02
1147 2455 3.416156 ACAGAGGAAAACAGAGCCATTC 58.584 45.455 0.00 0.00 0.00 2.67
1150 2458 2.439507 AGAACAGAGGAAAACAGAGCCA 59.560 45.455 0.00 0.00 0.00 4.75
1172 2480 2.880890 CCAGAGAAGACCCAAACTGTTG 59.119 50.000 0.00 0.00 34.25 3.33
1193 2510 3.119096 GGAAGCGTTCCTGCCGAC 61.119 66.667 8.87 0.00 46.57 4.79
1429 2749 4.357947 GGCGCCGAGTGTGTGAGA 62.358 66.667 12.58 0.00 0.00 3.27
1462 2782 3.890674 GGTCACTGGCCGATCAAC 58.109 61.111 0.00 0.00 0.00 3.18
1473 2793 2.426023 GTGGCTGTTCCGGTCACT 59.574 61.111 0.00 0.00 41.56 3.41
1515 2836 5.640147 TCAATGGTTGTTTCCCAGAACTAT 58.360 37.500 0.00 0.00 34.92 2.12
1516 2837 5.055265 TCAATGGTTGTTTCCCAGAACTA 57.945 39.130 0.00 0.00 34.92 2.24
1517 2838 3.909732 TCAATGGTTGTTTCCCAGAACT 58.090 40.909 0.00 0.00 34.92 3.01
1518 2839 4.871933 ATCAATGGTTGTTTCCCAGAAC 57.128 40.909 0.00 0.00 34.92 3.01
1520 2841 7.552050 AATAAATCAATGGTTGTTTCCCAGA 57.448 32.000 0.00 0.00 34.92 3.86
1521 2842 8.096414 AGAAATAAATCAATGGTTGTTTCCCAG 58.904 33.333 11.36 0.00 36.21 4.45
1594 2920 1.805254 GAACCGGTCAGCTACGCTA 59.195 57.895 8.04 0.00 36.40 4.26
1875 3203 0.179084 ACATGAGGCACGGGTAATCG 60.179 55.000 0.00 0.00 0.00 3.34
1884 3212 2.459442 GCTGAGCGACATGAGGCAC 61.459 63.158 13.59 8.76 0.00 5.01
2057 3385 5.460419 TCAATGTTGATTTGTTAAACCGCAC 59.540 36.000 0.00 0.00 31.01 5.34
2125 3453 1.913419 GGACCCCTTCAGGTTGACATA 59.087 52.381 0.00 0.00 41.42 2.29
2142 3470 3.378399 GAGGAAGCAGGCGGAGGAC 62.378 68.421 0.00 0.00 0.00 3.85
2143 3471 3.077556 GAGGAAGCAGGCGGAGGA 61.078 66.667 0.00 0.00 0.00 3.71
2148 3476 1.153549 GTAGGTGAGGAAGCAGGCG 60.154 63.158 0.00 0.00 0.00 5.52
2187 3515 6.126623 TGGCAGATGGTAAATATGTACCTTGA 60.127 38.462 20.68 3.67 43.52 3.02
2229 3557 4.792068 TGGTGGAAGAAATCTGTTGTTCT 58.208 39.130 0.00 0.00 35.59 3.01
2238 3566 3.196254 ACATTGCCATGGTGGAAGAAATC 59.804 43.478 14.67 0.00 40.96 2.17
2254 3582 7.736447 AATTATCTGCTTCCTAGTACATTGC 57.264 36.000 0.00 0.00 0.00 3.56
2257 3585 7.282585 TGCAAATTATCTGCTTCCTAGTACAT 58.717 34.615 0.00 0.00 40.59 2.29
2262 3590 5.819379 TGACTGCAAATTATCTGCTTCCTAG 59.181 40.000 2.52 0.00 40.59 3.02
2300 3628 1.796459 GAGAAGAAACAACGGCGCTTA 59.204 47.619 6.90 0.00 0.00 3.09
2319 3647 0.682292 TGTGTATGTTGTCTGCGGGA 59.318 50.000 0.00 0.00 0.00 5.14
2322 3650 1.136363 CCGTTGTGTATGTTGTCTGCG 60.136 52.381 0.00 0.00 0.00 5.18
2337 3665 4.351938 TCGTGCTCCGGTCCGTTG 62.352 66.667 11.06 3.42 37.11 4.10
2397 3725 0.182775 AATCCCCTTGCATCCGGTAC 59.817 55.000 0.00 0.00 0.00 3.34
2401 3729 0.457035 CACAAATCCCCTTGCATCCG 59.543 55.000 0.00 0.00 0.00 4.18
2415 3743 2.538141 CCCTGGCCTCCTCCACAAA 61.538 63.158 3.32 0.00 31.74 2.83
2416 3744 2.935481 CCCTGGCCTCCTCCACAA 60.935 66.667 3.32 0.00 31.74 3.33
2423 3751 3.866582 CGGATGACCCTGGCCTCC 61.867 72.222 3.32 0.00 0.00 4.30
2439 3767 3.775654 GACAGCCTCCTGGGGTCG 61.776 72.222 0.00 0.00 45.10 4.79
2444 3772 2.583520 GCTCAGACAGCCTCCTGG 59.416 66.667 0.00 0.00 43.17 4.45
2466 3794 4.020617 CAGGAGGACGCTGCCCAA 62.021 66.667 0.00 0.00 0.00 4.12
2472 3800 1.674057 CTTCAACCAGGAGGACGCT 59.326 57.895 0.00 0.00 38.69 5.07
2476 3804 1.072331 GACTTGCTTCAACCAGGAGGA 59.928 52.381 0.00 0.00 38.69 3.71
2502 3830 2.668550 GTGAAGTCGGGGTGGTGC 60.669 66.667 0.00 0.00 0.00 5.01
2520 3848 1.598676 CGGTGAGACGACGTGAAGAAA 60.599 52.381 4.58 0.00 35.47 2.52
2532 3860 0.793478 CGTGTCATCGACGGTGAGAC 60.793 60.000 24.25 24.25 36.75 3.36
2546 3874 1.153429 GTCTATGGGGTGCCGTGTC 60.153 63.158 0.00 0.00 0.00 3.67
2559 3887 3.418684 AGAAACACCGGCAAAGTCTAT 57.581 42.857 0.00 0.00 0.00 1.98
2561 3889 2.922740 TAGAAACACCGGCAAAGTCT 57.077 45.000 0.00 0.37 0.00 3.24
2564 3892 1.135402 GCCATAGAAACACCGGCAAAG 60.135 52.381 0.00 0.00 42.50 2.77
2566 3894 2.562125 GCCATAGAAACACCGGCAA 58.438 52.632 0.00 0.00 42.50 4.52
2567 3895 4.312052 GCCATAGAAACACCGGCA 57.688 55.556 0.00 0.00 42.50 5.69
2568 3896 1.102978 AATGCCATAGAAACACCGGC 58.897 50.000 0.00 0.00 43.28 6.13
2570 3898 1.472082 TGCAATGCCATAGAAACACCG 59.528 47.619 1.53 0.00 0.00 4.94
2571 3899 2.230992 TGTGCAATGCCATAGAAACACC 59.769 45.455 1.53 0.00 0.00 4.16
2579 3907 4.048241 CATTGTCATGTGCAATGCCATA 57.952 40.909 22.48 0.00 44.12 2.74
2592 3920 6.417258 TGGTGTCATATCTTCACATTGTCAT 58.583 36.000 0.00 0.00 34.27 3.06
2593 3921 5.803552 TGGTGTCATATCTTCACATTGTCA 58.196 37.500 0.00 0.00 34.27 3.58
2595 3923 7.523293 TTTTGGTGTCATATCTTCACATTGT 57.477 32.000 0.00 0.00 34.27 2.71
2622 3950 7.402054 TGTTGTTCTACCAAATCCTACATGAT 58.598 34.615 0.00 0.00 0.00 2.45
2637 3965 9.167311 AGAAATATCCAGTTCATGTTGTTCTAC 57.833 33.333 0.00 0.00 31.12 2.59
2658 3986 5.829924 TCCTGCAAGTTCAGAAAGAAGAAAT 59.170 36.000 0.00 0.00 36.78 2.17
2690 4018 4.141711 ACACAGGTCGATGCAATAGGTTAT 60.142 41.667 0.00 0.00 0.00 1.89
2695 4023 1.935873 CCACACAGGTCGATGCAATAG 59.064 52.381 0.00 0.00 0.00 1.73
2697 4025 0.324614 TCCACACAGGTCGATGCAAT 59.675 50.000 0.00 0.00 39.02 3.56
2710 4038 2.798499 CGACACCTAATCCGATCCACAC 60.798 54.545 0.00 0.00 0.00 3.82
2725 4053 2.046892 AGCATGCAGTCCGACACC 60.047 61.111 21.98 0.00 0.00 4.16
2753 4081 3.509967 ACTATATCATGCCCGTCGATGAA 59.490 43.478 6.11 0.00 32.43 2.57
2778 4106 9.409312 CTGCATTTCTATGAAAATGTTGTGTTA 57.591 29.630 13.14 0.00 44.72 2.41
2799 4127 1.065102 GTCGCATTTCATGAGCTGCAT 59.935 47.619 23.34 0.00 37.85 3.96
2808 4136 0.301687 GCATCGACGTCGCATTTCAT 59.698 50.000 32.19 16.81 39.60 2.57
2816 4144 3.119628 CCAAACTATATGCATCGACGTCG 59.880 47.826 31.30 31.30 41.45 5.12
2820 4148 4.811555 TTGCCAAACTATATGCATCGAC 57.188 40.909 0.19 0.00 33.08 4.20
2823 4151 5.710513 TGGATTGCCAAACTATATGCATC 57.289 39.130 0.19 0.00 42.49 3.91
2837 4165 1.680338 GTGATACCAGGTGGATTGCC 58.320 55.000 0.76 0.00 38.94 4.52
2838 4166 1.212935 AGGTGATACCAGGTGGATTGC 59.787 52.381 0.76 0.00 41.95 3.56
2854 4182 1.156736 CAGTAAAAGCCCGACAGGTG 58.843 55.000 0.00 0.00 38.26 4.00
2861 4189 3.432252 CAGTGAAGTACAGTAAAAGCCCG 59.568 47.826 0.00 0.00 0.00 6.13
2890 4218 0.601558 GGCTAGTTGTCGGAGTGTCA 59.398 55.000 0.00 0.00 0.00 3.58
2898 4226 3.492011 ACGTTTTTGTAGGCTAGTTGTCG 59.508 43.478 0.00 0.00 0.00 4.35
2900 4228 4.700700 AGACGTTTTTGTAGGCTAGTTGT 58.299 39.130 0.00 0.00 0.00 3.32
2901 4229 5.668558 AAGACGTTTTTGTAGGCTAGTTG 57.331 39.130 0.00 0.00 0.00 3.16
2903 4231 9.662947 AAATATAAGACGTTTTTGTAGGCTAGT 57.337 29.630 0.00 0.00 0.00 2.57
2906 4234 9.005777 TCAAAATATAAGACGTTTTTGTAGGCT 57.994 29.630 16.32 0.00 39.13 4.58
2907 4235 9.274065 CTCAAAATATAAGACGTTTTTGTAGGC 57.726 33.333 16.32 0.00 39.13 3.93
2921 4249 9.182933 GCTACTACTTCCGTCTCAAAATATAAG 57.817 37.037 0.00 0.00 0.00 1.73
2922 4250 8.689061 TGCTACTACTTCCGTCTCAAAATATAA 58.311 33.333 0.00 0.00 0.00 0.98
2923 4251 8.229253 TGCTACTACTTCCGTCTCAAAATATA 57.771 34.615 0.00 0.00 0.00 0.86
2924 4252 7.108841 TGCTACTACTTCCGTCTCAAAATAT 57.891 36.000 0.00 0.00 0.00 1.28
2925 4253 6.519679 TGCTACTACTTCCGTCTCAAAATA 57.480 37.500 0.00 0.00 0.00 1.40
2926 4254 5.401531 TGCTACTACTTCCGTCTCAAAAT 57.598 39.130 0.00 0.00 0.00 1.82
2927 4255 4.859304 TGCTACTACTTCCGTCTCAAAA 57.141 40.909 0.00 0.00 0.00 2.44
2928 4256 4.219944 ACATGCTACTACTTCCGTCTCAAA 59.780 41.667 0.00 0.00 0.00 2.69
2929 4257 3.762288 ACATGCTACTACTTCCGTCTCAA 59.238 43.478 0.00 0.00 0.00 3.02
2930 4258 3.353557 ACATGCTACTACTTCCGTCTCA 58.646 45.455 0.00 0.00 0.00 3.27
2931 4259 5.066246 ACTTACATGCTACTACTTCCGTCTC 59.934 44.000 0.00 0.00 0.00 3.36
2932 4260 4.948621 ACTTACATGCTACTACTTCCGTCT 59.051 41.667 0.00 0.00 0.00 4.18
2933 4261 5.246145 ACTTACATGCTACTACTTCCGTC 57.754 43.478 0.00 0.00 0.00 4.79
2934 4262 5.649395 TGTACTTACATGCTACTACTTCCGT 59.351 40.000 0.00 0.00 0.00 4.69
2935 4263 6.127810 TGTACTTACATGCTACTACTTCCG 57.872 41.667 0.00 0.00 0.00 4.30
2936 4264 7.098074 ACTGTACTTACATGCTACTACTTCC 57.902 40.000 0.00 0.00 35.36 3.46
2937 4265 8.983307 AAACTGTACTTACATGCTACTACTTC 57.017 34.615 0.00 0.00 35.36 3.01
2938 4266 9.774413 AAAAACTGTACTTACATGCTACTACTT 57.226 29.630 0.00 0.00 35.36 2.24
2970 4298 1.584380 GCTCCAAACAGCAGGCAGAG 61.584 60.000 0.00 0.00 39.43 3.35
2988 4316 6.317140 TGATGTATTTCTCCTCATCTTTGTGC 59.683 38.462 0.00 0.00 37.93 4.57
3025 4354 2.402305 TCCAAAACAACGCATGATTGC 58.598 42.857 0.00 0.00 45.78 3.56
3026 4355 3.613737 GGATCCAAAACAACGCATGATTG 59.386 43.478 6.95 2.42 32.73 2.67
3028 4357 2.824936 TGGATCCAAAACAACGCATGAT 59.175 40.909 13.46 0.00 0.00 2.45
3040 4369 7.930865 CCAACTGAAAATTACTTTGGATCCAAA 59.069 33.333 32.66 32.66 42.77 3.28
3047 4376 8.764287 GTGAAATCCAACTGAAAATTACTTTGG 58.236 33.333 0.00 0.00 35.75 3.28
3050 4379 7.712797 ACGTGAAATCCAACTGAAAATTACTT 58.287 30.769 0.00 0.00 0.00 2.24
3061 4390 3.389925 TTCCGTACGTGAAATCCAACT 57.610 42.857 15.21 0.00 0.00 3.16
3072 4401 3.861276 TGTCATGATCTTTCCGTACGT 57.139 42.857 15.21 0.00 0.00 3.57
3074 4403 8.594881 AATATCTTGTCATGATCTTTCCGTAC 57.405 34.615 0.00 0.00 0.00 3.67
3079 4408 9.469807 AGTACGAATATCTTGTCATGATCTTTC 57.530 33.333 0.00 8.59 0.00 2.62
3084 4413 7.946207 ACAGAGTACGAATATCTTGTCATGAT 58.054 34.615 0.00 6.48 0.00 2.45
3099 4428 2.860136 CGTGTATCGGTACAGAGTACGA 59.140 50.000 9.25 7.61 41.29 3.43
3101 4430 4.784710 GCTTCGTGTATCGGTACAGAGTAC 60.785 50.000 9.25 0.00 41.29 2.73
3149 4486 5.884232 TCTCAATGGGATGACAGATCAAAAG 59.116 40.000 0.00 0.00 38.69 2.27
3191 4528 2.840651 TCTAAGAGAAGGGGAAAGCCTG 59.159 50.000 0.00 0.00 0.00 4.85
3250 4587 1.758122 GCCGGAATCCAGGGCATTT 60.758 57.895 5.05 0.00 46.13 2.32
3268 4605 3.773630 ATCGCGCGGTGTCGTTTG 61.774 61.111 31.69 0.00 38.89 2.93
3300 4637 1.455849 CAACAGGCTCAGTTCCCCA 59.544 57.895 0.00 0.00 0.00 4.96
3314 4651 2.650322 GAACCCAGTGAAGAACCAACA 58.350 47.619 0.00 0.00 0.00 3.33
3327 4664 5.977129 GCATCATTTTTATTACGGAACCCAG 59.023 40.000 0.00 0.00 0.00 4.45
3335 4672 7.026631 TCCCAAGAGCATCATTTTTATTACG 57.973 36.000 0.00 0.00 37.82 3.18
3340 4677 6.009589 TGTCTTCCCAAGAGCATCATTTTTA 58.990 36.000 0.00 0.00 38.41 1.52
3364 4702 3.406498 AGGGCCTAATGGTCTCTAGGTAT 59.594 47.826 2.82 0.00 38.23 2.73
3369 4707 1.578703 TGGAGGGCCTAATGGTCTCTA 59.421 52.381 5.73 0.00 38.23 2.43
3390 4728 4.769688 TGTCTTCCCAACAGCATACATAG 58.230 43.478 0.00 0.00 0.00 2.23
3401 7423 4.254492 GTCTCTTGGTATGTCTTCCCAAC 58.746 47.826 0.00 0.00 34.63 3.77
3443 7465 4.689612 AACTGTAGAATGGTGTCACACT 57.310 40.909 8.12 1.46 34.40 3.55
3464 7486 9.284594 GCATAACTTTTGCATACGAATTTCTTA 57.715 29.630 0.00 0.00 39.90 2.10
3465 7487 7.275560 GGCATAACTTTTGCATACGAATTTCTT 59.724 33.333 6.55 0.00 41.95 2.52
3466 7488 6.751888 GGCATAACTTTTGCATACGAATTTCT 59.248 34.615 6.55 0.00 41.95 2.52
3467 7489 6.019881 GGGCATAACTTTTGCATACGAATTTC 60.020 38.462 6.55 0.00 41.95 2.17
3468 7490 5.810074 GGGCATAACTTTTGCATACGAATTT 59.190 36.000 6.55 0.00 41.95 1.82
3469 7491 5.105554 TGGGCATAACTTTTGCATACGAATT 60.106 36.000 6.55 0.00 41.95 2.17
3470 7492 4.400884 TGGGCATAACTTTTGCATACGAAT 59.599 37.500 6.55 0.00 41.95 3.34
3471 7493 3.759086 TGGGCATAACTTTTGCATACGAA 59.241 39.130 6.55 0.00 41.95 3.85
3472 7494 3.348119 TGGGCATAACTTTTGCATACGA 58.652 40.909 6.55 0.00 41.95 3.43
3473 7495 3.773860 TGGGCATAACTTTTGCATACG 57.226 42.857 6.55 0.00 41.95 3.06
3474 7496 6.983474 AAAATGGGCATAACTTTTGCATAC 57.017 33.333 6.55 0.00 41.95 2.39
3475 7497 8.535335 TCTTAAAATGGGCATAACTTTTGCATA 58.465 29.630 6.55 0.00 41.95 3.14
3476 7498 7.393216 TCTTAAAATGGGCATAACTTTTGCAT 58.607 30.769 6.55 0.00 41.95 3.96
3477 7499 6.763355 TCTTAAAATGGGCATAACTTTTGCA 58.237 32.000 6.55 0.00 41.95 4.08
3478 7500 7.665561 TTCTTAAAATGGGCATAACTTTTGC 57.334 32.000 0.00 0.00 39.41 3.68
3481 7503 9.448438 GGAATTTCTTAAAATGGGCATAACTTT 57.552 29.630 0.00 0.00 35.27 2.66
3482 7504 8.601546 TGGAATTTCTTAAAATGGGCATAACTT 58.398 29.630 0.00 0.00 35.27 2.66
3483 7505 8.144862 TGGAATTTCTTAAAATGGGCATAACT 57.855 30.769 0.00 0.00 35.27 2.24
3484 7506 8.257306 TCTGGAATTTCTTAAAATGGGCATAAC 58.743 33.333 0.00 0.00 35.27 1.89
3485 7507 8.372877 TCTGGAATTTCTTAAAATGGGCATAA 57.627 30.769 0.00 0.00 35.27 1.90
3486 7508 7.838696 TCTCTGGAATTTCTTAAAATGGGCATA 59.161 33.333 0.00 0.00 35.27 3.14
3487 7509 6.669154 TCTCTGGAATTTCTTAAAATGGGCAT 59.331 34.615 0.00 0.00 35.27 4.40
3488 7510 6.015918 TCTCTGGAATTTCTTAAAATGGGCA 58.984 36.000 0.00 0.00 35.27 5.36
3489 7511 6.378280 TCTCTCTGGAATTTCTTAAAATGGGC 59.622 38.462 0.00 0.00 35.27 5.36
3490 7512 7.944729 TCTCTCTGGAATTTCTTAAAATGGG 57.055 36.000 0.00 0.00 35.27 4.00
3494 7516 9.696917 GCAAAATCTCTCTGGAATTTCTTAAAA 57.303 29.630 0.00 0.00 0.00 1.52
3495 7517 8.859090 TGCAAAATCTCTCTGGAATTTCTTAAA 58.141 29.630 0.00 0.00 0.00 1.52
3496 7518 8.408043 TGCAAAATCTCTCTGGAATTTCTTAA 57.592 30.769 0.00 0.00 0.00 1.85
3497 7519 8.408043 TTGCAAAATCTCTCTGGAATTTCTTA 57.592 30.769 0.00 0.00 0.00 2.10
3498 7520 6.906157 TGCAAAATCTCTCTGGAATTTCTT 57.094 33.333 0.00 0.00 0.00 2.52
3499 7521 6.492772 ACTTGCAAAATCTCTCTGGAATTTCT 59.507 34.615 0.00 0.00 0.00 2.52
3500 7522 6.685657 ACTTGCAAAATCTCTCTGGAATTTC 58.314 36.000 0.00 0.00 0.00 2.17
3501 7523 6.661304 ACTTGCAAAATCTCTCTGGAATTT 57.339 33.333 0.00 0.00 0.00 1.82
3502 7524 7.765695 TTACTTGCAAAATCTCTCTGGAATT 57.234 32.000 0.00 0.00 0.00 2.17
3503 7525 7.449704 ACTTTACTTGCAAAATCTCTCTGGAAT 59.550 33.333 0.00 0.00 0.00 3.01
3504 7526 6.772716 ACTTTACTTGCAAAATCTCTCTGGAA 59.227 34.615 0.00 0.00 0.00 3.53
3505 7527 6.299141 ACTTTACTTGCAAAATCTCTCTGGA 58.701 36.000 0.00 0.00 0.00 3.86
3506 7528 6.566197 ACTTTACTTGCAAAATCTCTCTGG 57.434 37.500 0.00 0.00 0.00 3.86
3507 7529 6.146184 TCGACTTTACTTGCAAAATCTCTCTG 59.854 38.462 0.00 0.00 0.00 3.35
3508 7530 6.223852 TCGACTTTACTTGCAAAATCTCTCT 58.776 36.000 0.00 0.00 0.00 3.10
3509 7531 6.467723 TCGACTTTACTTGCAAAATCTCTC 57.532 37.500 0.00 0.00 0.00 3.20
3510 7532 6.861065 TTCGACTTTACTTGCAAAATCTCT 57.139 33.333 0.00 0.00 0.00 3.10
3511 7533 8.507470 AATTTCGACTTTACTTGCAAAATCTC 57.493 30.769 0.00 0.00 0.00 2.75
3512 7534 8.134895 TGAATTTCGACTTTACTTGCAAAATCT 58.865 29.630 0.00 0.00 0.00 2.40
3513 7535 8.280909 TGAATTTCGACTTTACTTGCAAAATC 57.719 30.769 0.00 0.00 0.00 2.17
3514 7536 8.816640 ATGAATTTCGACTTTACTTGCAAAAT 57.183 26.923 0.00 0.00 0.00 1.82
3515 7537 9.906660 ATATGAATTTCGACTTTACTTGCAAAA 57.093 25.926 0.00 0.00 0.00 2.44
3516 7538 9.906660 AATATGAATTTCGACTTTACTTGCAAA 57.093 25.926 0.00 0.00 0.00 3.68
3517 7539 9.906660 AAATATGAATTTCGACTTTACTTGCAA 57.093 25.926 0.00 0.00 28.88 4.08
3518 7540 9.340695 CAAATATGAATTTCGACTTTACTTGCA 57.659 29.630 0.00 0.00 32.87 4.08
3519 7541 9.341899 ACAAATATGAATTTCGACTTTACTTGC 57.658 29.630 0.00 0.00 32.87 4.01


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

AutoCloner maintained by Alex Coulton.