Multiple sequence alignment - TraesCS1A01G006900

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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 TraesCS1A01G006900 chr1A 100.000 3954 0 0 1 3954 3672050 3668097 0.000000e+00 7302.0
1 TraesCS1A01G006900 chr1A 85.791 2963 377 28 2 2947 3491363 3488428 0.000000e+00 3099.0
2 TraesCS1A01G006900 chr1A 85.168 2953 417 18 16 2954 3503408 3500463 0.000000e+00 3007.0
3 TraesCS1A01G006900 chr1A 86.000 2550 342 12 414 2951 3453864 3451318 0.000000e+00 2717.0
4 TraesCS1A01G006900 chr1A 85.734 729 98 6 2 728 3656915 3656191 0.000000e+00 765.0
5 TraesCS1A01G006900 chr1A 82.828 396 46 14 3166 3558 2925672 2926048 6.330000e-88 335.0
6 TraesCS1A01G006900 chr1A 84.133 271 33 7 2950 3216 3488370 3488106 1.820000e-63 254.0
7 TraesCS1A01G006900 chr1A 81.818 297 34 12 2950 3241 2986014 2986295 8.540000e-57 231.0
8 TraesCS1A01G006900 chr1A 84.255 235 24 6 3261 3485 2986367 2986598 2.390000e-52 217.0
9 TraesCS1A01G006900 chr1A 85.714 147 11 6 2953 3091 2977620 2977764 3.180000e-31 147.0
10 TraesCS1A01G006900 chr1A 78.191 188 28 8 3285 3467 3450730 3450551 1.500000e-19 108.0
11 TraesCS1A01G006900 chr1A 94.000 50 3 0 3659 3708 3658856 3658807 4.240000e-10 76.8
12 TraesCS1A01G006900 chr1B 86.579 2958 375 16 2 2951 3965003 3967946 0.000000e+00 3243.0
13 TraesCS1A01G006900 chr1B 86.338 2957 391 10 2 2951 4510391 4507441 0.000000e+00 3210.0
14 TraesCS1A01G006900 chr1B 85.990 2955 406 6 2 2951 3951597 3954548 0.000000e+00 3157.0
15 TraesCS1A01G006900 chr1B 85.244 2948 417 15 16 2951 4096036 4098977 0.000000e+00 3018.0
16 TraesCS1A01G006900 chr1B 85.101 2960 402 19 1 2947 4591183 4588250 0.000000e+00 2987.0
17 TraesCS1A01G006900 chr1B 86.076 553 68 6 2405 2952 3156376 3156924 1.580000e-163 586.0
18 TraesCS1A01G006900 chr1B 89.130 322 34 1 2626 2947 4153928 4154248 2.210000e-107 399.0
19 TraesCS1A01G006900 chr1B 81.481 297 37 11 2950 3241 4759011 4758728 1.110000e-55 228.0
20 TraesCS1A01G006900 chr1B 83.333 234 26 5 3263 3485 4758654 4758423 1.860000e-48 204.0
21 TraesCS1A01G006900 chr1B 80.597 268 37 9 2954 3216 4015181 4015438 4.030000e-45 193.0
22 TraesCS1A01G006900 chr1B 82.938 211 26 6 2953 3155 4558038 4557830 8.730000e-42 182.0
23 TraesCS1A01G006900 chr1B 80.162 247 35 9 3017 3261 3945993 3946227 5.250000e-39 172.0
24 TraesCS1A01G006900 chr1B 80.693 202 30 6 2953 3152 4118134 4118328 8.850000e-32 148.0
25 TraesCS1A01G006900 chr1B 80.240 167 21 7 3285 3447 4479729 4479571 8.980000e-22 115.0
26 TraesCS1A01G006900 chr1D 86.525 2961 380 13 2 2951 620695 617743 0.000000e+00 3240.0
27 TraesCS1A01G006900 chr1D 82.511 446 40 18 3520 3951 616588 616167 1.350000e-94 357.0
28 TraesCS1A01G006900 chr1D 85.171 263 36 2 2954 3216 694419 694160 2.340000e-67 267.0
29 TraesCS1A01G006900 chr3D 85.902 305 23 5 3486 3789 560072520 560072235 1.380000e-79 307.0
30 TraesCS1A01G006900 chr3D 88.372 129 12 2 3352 3479 560072714 560072588 6.840000e-33 152.0


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 TraesCS1A01G006900 chr1A 3668097 3672050 3953 True 7302.0 7302 100.0000 1 3954 1 chr1A.!!$R2 3953
1 TraesCS1A01G006900 chr1A 3500463 3503408 2945 True 3007.0 3007 85.1680 16 2954 1 chr1A.!!$R1 2938
2 TraesCS1A01G006900 chr1A 3488106 3491363 3257 True 1676.5 3099 84.9620 2 3216 2 chr1A.!!$R4 3214
3 TraesCS1A01G006900 chr1A 3450551 3453864 3313 True 1412.5 2717 82.0955 414 3467 2 chr1A.!!$R3 3053
4 TraesCS1A01G006900 chr1A 3656191 3658856 2665 True 420.9 765 89.8670 2 3708 2 chr1A.!!$R5 3706
5 TraesCS1A01G006900 chr1A 2986014 2986598 584 False 224.0 231 83.0365 2950 3485 2 chr1A.!!$F3 535
6 TraesCS1A01G006900 chr1B 3965003 3967946 2943 False 3243.0 3243 86.5790 2 2951 1 chr1B.!!$F4 2949
7 TraesCS1A01G006900 chr1B 4507441 4510391 2950 True 3210.0 3210 86.3380 2 2951 1 chr1B.!!$R2 2949
8 TraesCS1A01G006900 chr1B 3951597 3954548 2951 False 3157.0 3157 85.9900 2 2951 1 chr1B.!!$F3 2949
9 TraesCS1A01G006900 chr1B 4096036 4098977 2941 False 3018.0 3018 85.2440 16 2951 1 chr1B.!!$F6 2935
10 TraesCS1A01G006900 chr1B 4588250 4591183 2933 True 2987.0 2987 85.1010 1 2947 1 chr1B.!!$R4 2946
11 TraesCS1A01G006900 chr1B 3156376 3156924 548 False 586.0 586 86.0760 2405 2952 1 chr1B.!!$F1 547
12 TraesCS1A01G006900 chr1B 4758423 4759011 588 True 216.0 228 82.4070 2950 3485 2 chr1B.!!$R5 535
13 TraesCS1A01G006900 chr1D 616167 620695 4528 True 1798.5 3240 84.5180 2 3951 2 chr1D.!!$R2 3949

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
313 2253 0.116541 TATACCCCAGGAGCTAGGCC 59.883 60.0 0.00 0.0 0.00 5.19 F
1027 2967 0.039618 TGGCCCAATTCCAAGGAGTC 59.960 55.0 0.00 0.0 0.00 3.36 F
1468 3411 0.046397 ACCTGAGGAATTAGGGGCCT 59.954 55.0 4.99 0.0 38.42 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 4059 0.478072 TGCCCATCTTGGAGTTGTGT 59.522 50.0 0.00 0.0 40.96 3.72 R
2807 4772 0.106149 GGCCGTCGGTCCAGAATATT 59.894 55.0 13.94 0.0 0.00 1.28 R
3223 5405 1.071605 CCGAGAACAGCCGAAAGAAG 58.928 55.0 0.00 0.0 0.00 2.85 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
25 1965 4.398319 ACAAATTCCGTCTGAGATTGGTT 58.602 39.130 4.01 0.00 0.00 3.67
42 1982 1.312815 GTTGCCTGCAAAGTCTCACT 58.687 50.000 6.07 0.00 37.70 3.41
58 1998 1.005630 ACTCAGCTTGGTCTCGCAC 60.006 57.895 0.00 0.00 0.00 5.34
59 1999 1.005748 CTCAGCTTGGTCTCGCACA 60.006 57.895 0.00 0.00 0.00 4.57
72 2012 2.820197 TCTCGCACATAACAGACTCACT 59.180 45.455 0.00 0.00 0.00 3.41
187 2127 3.181434 TGGAAGGCTTGTCAACCTACAAT 60.181 43.478 3.46 0.00 38.61 2.71
210 2150 4.066646 TCTACAGCTAAGCAACAACACA 57.933 40.909 0.00 0.00 0.00 3.72
313 2253 0.116541 TATACCCCAGGAGCTAGGCC 59.883 60.000 0.00 0.00 0.00 5.19
339 2279 6.379133 AGCTAATCCATTTGCAAGATCTTGAA 59.621 34.615 34.43 24.79 42.93 2.69
344 2284 5.302568 TCCATTTGCAAGATCTTGAACTTGT 59.697 36.000 34.43 14.27 43.41 3.16
394 2334 5.530171 CCAATCTCCATAACCAATCTCACTG 59.470 44.000 0.00 0.00 0.00 3.66
488 2428 5.289083 AGGCTAAACCATCTTGATCTCTC 57.711 43.478 0.00 0.00 43.14 3.20
626 2566 9.553064 CTACTTGCTGAATCTCCAGTATTTAAT 57.447 33.333 0.00 0.00 36.57 1.40
627 2567 8.814038 ACTTGCTGAATCTCCAGTATTTAATT 57.186 30.769 0.00 0.00 36.57 1.40
652 2592 5.876357 TGTCCTATAACCAAATATCTGGCC 58.124 41.667 0.00 0.00 40.45 5.36
669 2609 3.106738 CCCTATTCCTGGCAGCTTG 57.893 57.895 9.56 0.00 0.00 4.01
676 2616 0.612732 TCCTGGCAGCTTGGGAAATG 60.613 55.000 9.56 0.00 0.00 2.32
683 2623 2.094545 GCAGCTTGGGAAATGTAACCAG 60.095 50.000 0.00 0.00 35.37 4.00
703 2643 3.130693 CAGGCTAGTACAACTACACCTCC 59.869 52.174 0.00 0.00 32.60 4.30
706 2646 4.202131 GGCTAGTACAACTACACCTCCATC 60.202 50.000 0.00 0.00 0.00 3.51
715 2655 1.463674 ACACCTCCATCAAAATCGGC 58.536 50.000 0.00 0.00 0.00 5.54
751 2691 2.093341 CCCCAAGAAATTGGCAATCTGG 60.093 50.000 14.04 16.12 40.74 3.86
771 2711 5.411361 TCTGGTGAACCTCGAACATTTAATG 59.589 40.000 3.07 3.07 36.82 1.90
829 2769 3.860641 ACTTTTGGGAAGTTGCAAAGTG 58.139 40.909 0.00 0.00 36.54 3.16
879 2819 4.737855 TTTATCAGGTTCTCTTCCTCGG 57.262 45.455 0.00 0.00 32.37 4.63
918 2858 0.752658 GCCTTGTTGAACTTGGGCTT 59.247 50.000 15.35 0.00 36.96 4.35
920 2860 2.364002 GCCTTGTTGAACTTGGGCTTTA 59.636 45.455 15.35 0.00 36.96 1.85
930 2870 5.180492 TGAACTTGGGCTTTATAACAACTCG 59.820 40.000 0.00 0.00 0.00 4.18
942 2882 0.250338 ACAACTCGCTTTCAGGACCC 60.250 55.000 0.00 0.00 0.00 4.46
976 2916 2.664402 ATGTTCAGGTGGCAGACTTT 57.336 45.000 0.00 0.00 0.00 2.66
1007 2947 8.462811 TCTCAGTGTCTCTTCTAATATGTTCAC 58.537 37.037 0.00 0.00 0.00 3.18
1014 2954 4.473196 TCTTCTAATATGTTCACTGGCCCA 59.527 41.667 0.00 0.00 0.00 5.36
1027 2967 0.039618 TGGCCCAATTCCAAGGAGTC 59.960 55.000 0.00 0.00 0.00 3.36
1058 2998 8.419076 ACATGTGTGAGTTTGGTTAAAATTTC 57.581 30.769 0.00 0.00 0.00 2.17
1064 3004 6.481976 GTGAGTTTGGTTAAAATTTCCCTTGG 59.518 38.462 0.00 0.00 0.00 3.61
1068 3008 6.771934 TTGGTTAAAATTTCCCTTGGGAAT 57.228 33.333 20.50 9.32 0.00 3.01
1106 3046 6.814506 AGATATATCTCAGCATTTTGGTGC 57.185 37.500 9.57 0.00 44.81 5.01
1191 3131 2.026262 CCTAGGTGCATGTACCCAACTT 60.026 50.000 27.17 12.50 41.83 2.66
1242 3182 0.616371 CGGGTTCCATACCTCCAACA 59.384 55.000 0.00 0.00 46.86 3.33
1261 3201 6.605594 TCCAACACTTTCTAAATTGTCCAACT 59.394 34.615 0.00 0.00 31.63 3.16
1264 3204 9.965824 CAACACTTTCTAAATTGTCCAACTTAT 57.034 29.630 0.00 0.00 31.63 1.73
1332 3272 7.254795 CCACCAGAAGTCTGTAGTTTAACAAAG 60.255 40.741 7.51 0.00 42.27 2.77
1341 3281 9.303537 GTCTGTAGTTTAACAAAGCTATCTAGG 57.696 37.037 0.00 0.00 0.00 3.02
1360 3300 3.554934 AGGCTGAACTTGTCATCAAACA 58.445 40.909 0.00 0.00 35.07 2.83
1368 3308 9.681692 CTGAACTTGTCATCAAACAAATTATCA 57.318 29.630 0.00 0.00 38.60 2.15
1398 3338 6.926272 CCATACCTACACAGATAGAAAAGCTC 59.074 42.308 0.00 0.00 0.00 4.09
1413 3353 7.086230 AGAAAAGCTCAGCAATCTAGAATTG 57.914 36.000 0.00 3.69 0.00 2.32
1459 3399 6.617371 ACTGAGTGGATTAATACCTGAGGAAT 59.383 38.462 4.99 0.00 0.00 3.01
1468 3411 0.046397 ACCTGAGGAATTAGGGGCCT 59.954 55.000 4.99 0.00 38.42 5.19
1469 3412 0.475906 CCTGAGGAATTAGGGGCCTG 59.524 60.000 0.84 0.00 30.70 4.85
1470 3413 0.179006 CTGAGGAATTAGGGGCCTGC 60.179 60.000 0.84 0.00 30.70 4.85
1482 3425 1.686115 GGGGCCTGCATGAAACTACAT 60.686 52.381 0.84 0.00 0.00 2.29
1527 3470 0.899717 TCAATGGGAGTTTGCCTGGC 60.900 55.000 12.87 12.87 0.00 4.85
1529 3472 2.713531 AATGGGAGTTTGCCTGGCGT 62.714 55.000 14.98 0.00 0.00 5.68
1533 3476 2.594592 AGTTTGCCTGGCGTGGTC 60.595 61.111 14.98 2.81 0.00 4.02
1546 3489 1.198178 GCGTGGTCGGAAATTTAGCAA 59.802 47.619 0.00 0.00 37.56 3.91
1663 3606 6.117911 TGTCACATAATAAGTTCAATGGCG 57.882 37.500 0.00 0.00 0.00 5.69
1691 3634 0.612732 TCCTCCTTTGCAAGCATGGG 60.613 55.000 0.00 9.94 0.00 4.00
1729 3672 4.219725 TCGATGTGTCCTACAATGACTTGA 59.780 41.667 0.00 0.00 43.77 3.02
1754 3697 2.203294 AGTCCCAACAACACGGCC 60.203 61.111 0.00 0.00 0.00 6.13
1756 3699 1.901464 GTCCCAACAACACGGCCAT 60.901 57.895 2.24 0.00 0.00 4.40
1773 3716 3.332034 GCCATTTCAAAATGCTTCAGCT 58.668 40.909 9.48 0.00 43.38 4.24
1783 3726 6.264292 TCAAAATGCTTCAGCTAGTTGGTTTA 59.736 34.615 6.75 0.00 42.66 2.01
1838 3781 2.497273 GCCTGCCACCTTGTTATTCAAT 59.503 45.455 0.00 0.00 35.35 2.57
1849 3795 7.552687 CACCTTGTTATTCAATTCCAGTAGCTA 59.447 37.037 0.00 0.00 35.35 3.32
1858 3804 4.679373 ATTCCAGTAGCTAGTCACCATG 57.321 45.455 0.00 0.00 0.00 3.66
1862 3808 3.195610 CCAGTAGCTAGTCACCATGAACA 59.804 47.826 0.00 0.00 0.00 3.18
1888 3834 6.076981 AGATACTTGGTTTGCTTTTGTCAG 57.923 37.500 0.00 0.00 0.00 3.51
1942 3888 7.545489 TGCTGCAATTGTTGTCATAATAATGA 58.455 30.769 7.40 0.00 39.87 2.57
2088 4037 6.957631 TGATAACTACATCATTGGAACTGGT 58.042 36.000 0.00 0.00 29.93 4.00
2100 4049 1.369625 GAACTGGTGGATACGGCAAG 58.630 55.000 0.00 0.00 42.51 4.01
2110 4059 2.429610 GGATACGGCAAGGTCTACAAGA 59.570 50.000 0.00 0.00 0.00 3.02
2167 4116 1.134848 AGCTTCATCAGACCGAAGAGC 60.135 52.381 13.45 2.55 40.94 4.09
2330 4279 3.828451 CTCCACAGGACATTGGAAAATGT 59.172 43.478 3.84 3.84 45.32 2.71
2340 4289 2.128771 TGGAAAATGTGGAGCTAGCC 57.871 50.000 12.13 2.59 0.00 3.93
2364 4313 5.046288 AGGAATTAGATTGGCAGAAGAGG 57.954 43.478 0.00 0.00 0.00 3.69
2472 4421 6.408858 AGCAACAACATCTTACTTGATACG 57.591 37.500 0.00 0.00 0.00 3.06
2488 4437 3.007506 TGATACGACCTTGAAGGCTTTCA 59.992 43.478 11.96 7.24 39.63 2.69
2524 4473 2.091541 CGGCAAGAATTCTTAAGCCCA 58.908 47.619 29.84 0.00 40.15 5.36
2592 4547 5.839063 AGCTCCTGGTATGTACTAGCATAAA 59.161 40.000 0.00 0.00 37.22 1.40
2593 4548 6.326583 AGCTCCTGGTATGTACTAGCATAAAA 59.673 38.462 0.00 0.00 37.22 1.52
2636 4593 5.106038 GCATTCATCTCAGTCCATTTGTTCA 60.106 40.000 0.00 0.00 0.00 3.18
2735 4700 1.671850 GCGTGGTTGTGCTAGAGCTAA 60.672 52.381 2.72 0.00 42.66 3.09
2782 4747 2.754946 TAGACGGTAGTTTGCCAAGG 57.245 50.000 0.00 0.00 0.00 3.61
2807 4772 7.328737 GGAGGAACAAGCTATACTAGTGAAAA 58.671 38.462 5.39 0.00 0.00 2.29
2820 4785 8.888579 ATACTAGTGAAAAATATTCTGGACCG 57.111 34.615 5.39 0.00 0.00 4.79
2829 4794 1.910580 ATTCTGGACCGACGGCCAAT 61.911 55.000 24.03 15.97 30.91 3.16
2919 4884 0.112995 TCTCCACAAGCAAGGCCAAT 59.887 50.000 5.01 0.00 0.00 3.16
2926 4891 2.567564 AAGCAAGGCCAATCATGCGC 62.568 55.000 5.01 0.00 43.39 6.09
2947 4912 3.009723 CGAGGCATACCAAACACTCATT 58.990 45.455 0.00 0.00 39.06 2.57
2968 5140 5.344743 TTCAGTAGGATGAGTTGATGACC 57.655 43.478 0.00 0.00 0.00 4.02
3003 5175 4.106029 TGTATTTGTAGACACTCTCCGC 57.894 45.455 0.00 0.00 0.00 5.54
3010 5183 4.127907 TGTAGACACTCTCCGCTATAGTG 58.872 47.826 6.31 6.31 44.89 2.74
3106 5287 4.900635 ATTTCTCTGTTTGTTCGCTTGT 57.099 36.364 0.00 0.00 0.00 3.16
3107 5288 3.944422 TTCTCTGTTTGTTCGCTTGTC 57.056 42.857 0.00 0.00 0.00 3.18
3119 5300 2.613691 TCGCTTGTCGATTTCTAACCC 58.386 47.619 0.00 0.00 43.16 4.11
3159 5341 4.978083 TTTACGGGTTGCTTGTAAAACA 57.022 36.364 0.00 0.00 35.71 2.83
3160 5342 2.855660 ACGGGTTGCTTGTAAAACAC 57.144 45.000 0.00 0.00 0.00 3.32
3161 5343 2.371306 ACGGGTTGCTTGTAAAACACT 58.629 42.857 0.00 0.00 0.00 3.55
3162 5344 2.356695 ACGGGTTGCTTGTAAAACACTC 59.643 45.455 0.00 0.00 0.00 3.51
3163 5345 2.616842 CGGGTTGCTTGTAAAACACTCT 59.383 45.455 0.00 0.00 0.00 3.24
3164 5346 3.810941 CGGGTTGCTTGTAAAACACTCTA 59.189 43.478 0.00 0.00 0.00 2.43
3170 5352 6.344572 TGCTTGTAAAACACTCTATATGCG 57.655 37.500 0.00 0.00 0.00 4.73
3174 5356 4.569162 TGTAAAACACTCTATATGCGGTGC 59.431 41.667 0.00 0.00 33.53 5.01
3179 5361 3.578716 ACACTCTATATGCGGTGCCTATT 59.421 43.478 0.00 0.00 33.53 1.73
3180 5362 4.177026 CACTCTATATGCGGTGCCTATTC 58.823 47.826 0.00 0.00 0.00 1.75
3198 5380 8.770828 TGCCTATTCTTATATTTGTTTAGACGC 58.229 33.333 0.00 0.00 0.00 5.19
3216 5398 1.442769 GCAGTACCCACATGTGACAG 58.557 55.000 27.46 16.72 0.00 3.51
3218 5400 2.416747 CAGTACCCACATGTGACAGTG 58.583 52.381 27.46 18.13 35.56 3.66
3219 5401 2.037121 CAGTACCCACATGTGACAGTGA 59.963 50.000 27.46 3.27 37.97 3.41
3220 5402 2.037251 AGTACCCACATGTGACAGTGAC 59.963 50.000 27.46 14.49 37.97 3.67
3221 5403 0.836606 ACCCACATGTGACAGTGACA 59.163 50.000 27.46 0.00 37.97 3.58
3222 5404 1.211703 ACCCACATGTGACAGTGACAA 59.788 47.619 27.46 0.00 37.97 3.18
3223 5405 1.603802 CCCACATGTGACAGTGACAAC 59.396 52.381 27.46 0.00 37.97 3.32
3241 5423 1.784525 ACTTCTTTCGGCTGTTCTCG 58.215 50.000 0.00 0.00 0.00 4.04
3243 5425 0.320421 TTCTTTCGGCTGTTCTCGGG 60.320 55.000 0.00 0.00 0.00 5.14
3268 5548 3.482436 GGTACTTGAAATGGTGGTCACA 58.518 45.455 3.40 0.00 0.00 3.58
3278 5558 5.705609 AATGGTGGTCACACTTTATTGTC 57.294 39.130 3.40 0.00 46.85 3.18
3315 5601 3.244044 GCAAAATACCTTGGACCAAGCAA 60.244 43.478 26.34 16.96 39.85 3.91
3321 5607 0.593128 CTTGGACCAAGCAAGAACGG 59.407 55.000 21.10 0.00 34.63 4.44
3332 5618 2.485426 AGCAAGAACGGTCACAATGATG 59.515 45.455 1.87 0.00 0.00 3.07
3333 5619 2.226437 GCAAGAACGGTCACAATGATGT 59.774 45.455 1.87 0.00 41.61 3.06
3334 5620 3.667960 GCAAGAACGGTCACAATGATGTC 60.668 47.826 1.87 0.00 37.82 3.06
3342 5637 3.120477 GGTCACAATGATGTCGCGTAAAA 60.120 43.478 5.77 0.00 37.82 1.52
3350 5646 3.185594 TGATGTCGCGTAAAAAGGAACAG 59.814 43.478 5.77 0.00 0.00 3.16
3386 5683 3.242543 CGCAGAGCTAGGTGCATAAAAAG 60.243 47.826 13.85 0.00 45.94 2.27
3402 5699 8.207545 TGCATAAAAAGGAAAAATTACCACAGT 58.792 29.630 0.00 0.00 0.00 3.55
3403 5700 9.699703 GCATAAAAAGGAAAAATTACCACAGTA 57.300 29.630 0.00 0.00 0.00 2.74
3447 5750 2.249214 AGGGTTGTAGGGCAGGAGTATA 59.751 50.000 0.00 0.00 0.00 1.47
3471 6034 5.365021 AGTTCTTGTCCTTATGATGGAGG 57.635 43.478 0.00 0.00 33.78 4.30
3476 6039 5.667172 TCTTGTCCTTATGATGGAGGATTGA 59.333 40.000 3.25 1.12 43.54 2.57
3482 6097 5.944599 CCTTATGATGGAGGATTGATCAAGG 59.055 44.000 14.54 0.11 34.91 3.61
3484 6099 4.701651 TGATGGAGGATTGATCAAGGAG 57.298 45.455 14.54 0.00 0.00 3.69
3485 6100 3.393609 TGATGGAGGATTGATCAAGGAGG 59.606 47.826 14.54 0.00 0.00 4.30
3487 6102 2.131023 GGAGGATTGATCAAGGAGGGT 58.869 52.381 14.54 0.00 0.00 4.34
3489 6104 3.434310 GGAGGATTGATCAAGGAGGGTTC 60.434 52.174 14.54 4.46 0.00 3.62
3490 6105 2.171448 AGGATTGATCAAGGAGGGTTCG 59.829 50.000 14.54 0.00 0.00 3.95
3494 6109 0.806492 GATCAAGGAGGGTTCGCGAC 60.806 60.000 9.15 3.93 0.00 5.19
3498 6113 0.673644 AAGGAGGGTTCGCGACATTG 60.674 55.000 9.15 0.00 0.00 2.82
3499 6114 1.079405 GGAGGGTTCGCGACATTGA 60.079 57.895 9.15 0.00 0.00 2.57
3524 6139 4.647611 TGGAACAAAGGATGACGTACAAT 58.352 39.130 0.00 0.00 31.92 2.71
3537 6152 7.958025 GGATGACGTACAATCTTCTTTTTCTTC 59.042 37.037 0.00 0.00 0.00 2.87
3547 6162 9.084164 CAATCTTCTTTTTCTTCATGCCTAATG 57.916 33.333 0.00 0.00 37.66 1.90
3572 6187 6.541641 GCAAACTTAACAGAGGATGAGATGAT 59.458 38.462 0.00 0.00 0.00 2.45
3583 6198 9.974980 CAGAGGATGAGATGATATGATATGAAG 57.025 37.037 0.00 0.00 0.00 3.02
3584 6199 9.150028 AGAGGATGAGATGATATGATATGAAGG 57.850 37.037 0.00 0.00 0.00 3.46
3585 6200 9.145442 GAGGATGAGATGATATGATATGAAGGA 57.855 37.037 0.00 0.00 0.00 3.36
3586 6201 9.503369 AGGATGAGATGATATGATATGAAGGAA 57.497 33.333 0.00 0.00 0.00 3.36
3591 6206 9.558396 GAGATGATATGATATGAAGGAAATCCC 57.442 37.037 0.00 0.00 36.42 3.85
3592 6207 8.501070 AGATGATATGATATGAAGGAAATCCCC 58.499 37.037 0.00 0.00 36.42 4.81
3593 6208 7.587375 TGATATGATATGAAGGAAATCCCCA 57.413 36.000 0.00 0.00 36.42 4.96
3594 6209 8.178662 TGATATGATATGAAGGAAATCCCCAT 57.821 34.615 9.12 9.12 36.42 4.00
3595 6210 9.295224 TGATATGATATGAAGGAAATCCCCATA 57.705 33.333 11.94 11.94 36.87 2.74
3634 6249 4.860022 AGCTAGCAATGTCCCATAACTTT 58.140 39.130 18.83 0.00 0.00 2.66
3635 6250 5.264395 AGCTAGCAATGTCCCATAACTTTT 58.736 37.500 18.83 0.00 0.00 2.27
3636 6251 5.716703 AGCTAGCAATGTCCCATAACTTTTT 59.283 36.000 18.83 0.00 0.00 1.94
3670 6285 6.552445 ACTAGATACCAATTCAACTCAGCT 57.448 37.500 0.00 0.00 0.00 4.24
3671 6286 7.661536 ACTAGATACCAATTCAACTCAGCTA 57.338 36.000 0.00 0.00 0.00 3.32
3672 6287 7.721402 ACTAGATACCAATTCAACTCAGCTAG 58.279 38.462 0.00 0.00 0.00 3.42
3673 6288 6.552445 AGATACCAATTCAACTCAGCTAGT 57.448 37.500 0.00 0.00 41.49 2.57
3674 6289 6.344500 AGATACCAATTCAACTCAGCTAGTG 58.656 40.000 0.00 0.00 38.88 2.74
3675 6290 3.077359 ACCAATTCAACTCAGCTAGTGC 58.923 45.455 0.00 0.00 38.88 4.40
3676 6291 3.076621 CCAATTCAACTCAGCTAGTGCA 58.923 45.455 0.00 0.00 42.74 4.57
3677 6292 3.503363 CCAATTCAACTCAGCTAGTGCAA 59.497 43.478 0.00 0.00 42.74 4.08
3678 6293 4.157289 CCAATTCAACTCAGCTAGTGCAAT 59.843 41.667 0.00 0.00 42.74 3.56
3679 6294 5.330295 CAATTCAACTCAGCTAGTGCAATC 58.670 41.667 0.00 0.00 42.74 2.67
3680 6295 3.683365 TCAACTCAGCTAGTGCAATCA 57.317 42.857 0.00 0.00 42.74 2.57
3681 6296 3.329386 TCAACTCAGCTAGTGCAATCAC 58.671 45.455 0.00 0.00 43.44 3.06
3688 6303 3.063588 CAGCTAGTGCAATCACAGACATG 59.936 47.826 0.00 0.00 45.49 3.21
3692 6307 3.005554 AGTGCAATCACAGACATGCTAC 58.994 45.455 0.00 5.33 45.49 3.58
3722 6337 8.251026 CAGGATGTACAACAGTATAGAGAACAA 58.749 37.037 0.00 0.00 0.00 2.83
3723 6338 8.251721 AGGATGTACAACAGTATAGAGAACAAC 58.748 37.037 0.00 0.00 0.00 3.32
3724 6339 8.251721 GGATGTACAACAGTATAGAGAACAACT 58.748 37.037 0.00 0.00 0.00 3.16
3725 6340 9.291664 GATGTACAACAGTATAGAGAACAACTC 57.708 37.037 0.00 0.00 45.22 3.01
3726 6341 7.600065 TGTACAACAGTATAGAGAACAACTCC 58.400 38.462 0.00 0.00 45.96 3.85
3730 6345 5.833340 ACAGTATAGAGAACAACTCCCTCT 58.167 41.667 0.00 0.00 45.96 3.69
3731 6346 6.971340 ACAGTATAGAGAACAACTCCCTCTA 58.029 40.000 0.00 0.00 45.96 2.43
3734 6349 8.356657 CAGTATAGAGAACAACTCCCTCTATTG 58.643 40.741 14.04 6.31 43.75 1.90
3735 6350 4.479786 AGAGAACAACTCCCTCTATTGC 57.520 45.455 0.00 0.00 45.96 3.56
3738 6353 3.198853 AGAACAACTCCCTCTATTGCTCC 59.801 47.826 0.00 0.00 0.00 4.70
3739 6354 2.551270 ACAACTCCCTCTATTGCTCCA 58.449 47.619 0.00 0.00 0.00 3.86
3740 6355 2.237392 ACAACTCCCTCTATTGCTCCAC 59.763 50.000 0.00 0.00 0.00 4.02
3741 6356 2.503356 CAACTCCCTCTATTGCTCCACT 59.497 50.000 0.00 0.00 0.00 4.00
3743 6358 4.206244 ACTCCCTCTATTGCTCCACTAT 57.794 45.455 0.00 0.00 0.00 2.12
3748 6363 7.956315 ACTCCCTCTATTGCTCCACTATTATTA 59.044 37.037 0.00 0.00 0.00 0.98
3760 6375 9.516314 GCTCCACTATTATTATTCCAAAACAAC 57.484 33.333 0.00 0.00 0.00 3.32
3769 6384 9.581289 TTATTATTCCAAAACAACAGGAAGAGA 57.419 29.630 0.00 0.00 43.99 3.10
3774 6395 4.580167 CCAAAACAACAGGAAGAGACATCA 59.420 41.667 0.00 0.00 0.00 3.07
3781 6402 4.248859 ACAGGAAGAGACATCATTCAACG 58.751 43.478 0.00 0.00 0.00 4.10
3805 6429 7.283127 ACGAATTGCAGTGGTATATGAAAGATT 59.717 33.333 0.00 0.00 0.00 2.40
3809 6433 7.320443 TGCAGTGGTATATGAAAGATTCAAC 57.680 36.000 0.00 0.00 43.95 3.18
3813 6437 8.116753 CAGTGGTATATGAAAGATTCAACGAAC 58.883 37.037 0.00 0.00 43.95 3.95
3825 6449 1.601903 TCAACGAACTTGTCCATGCAC 59.398 47.619 0.00 0.00 0.00 4.57
3831 6455 3.550639 CGAACTTGTCCATGCACAAACAT 60.551 43.478 3.35 0.00 35.83 2.71
3834 6458 3.057315 ACTTGTCCATGCACAAACATAGC 60.057 43.478 3.35 0.00 35.83 2.97
3845 6469 1.014352 AAACATAGCGCCGACCATTC 58.986 50.000 2.29 0.00 0.00 2.67
3849 6473 0.106708 ATAGCGCCGACCATTCACAT 59.893 50.000 2.29 0.00 0.00 3.21
3860 6484 4.026228 CGACCATTCACATCGAGATCAAAG 60.026 45.833 0.00 0.00 38.10 2.77
3872 6497 4.645136 TCGAGATCAAAGCTACACCATAGT 59.355 41.667 0.00 0.00 0.00 2.12
3902 6530 5.630680 TCGTTACTTTCAGGTACGAATTGAC 59.369 40.000 0.00 0.00 0.00 3.18
3943 6571 1.064463 TCCCAATTCATCCTCCTGCAC 60.064 52.381 0.00 0.00 0.00 4.57
3951 6579 1.067295 ATCCTCCTGCACCAACAGAA 58.933 50.000 0.00 0.00 40.25 3.02
3952 6580 0.843309 TCCTCCTGCACCAACAGAAA 59.157 50.000 0.00 0.00 40.25 2.52
3953 6581 1.425066 TCCTCCTGCACCAACAGAAAT 59.575 47.619 0.00 0.00 40.25 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.726416 CAACCAATCTCAGACGGAATTTG 58.274 43.478 0.00 0.00 0.00 2.32
12 1952 0.807496 GCAGGCAACCAATCTCAGAC 59.193 55.000 0.00 0.00 37.17 3.51
25 1965 0.469494 TGAGTGAGACTTTGCAGGCA 59.531 50.000 0.00 0.00 0.00 4.75
42 1982 0.894835 TATGTGCGAGACCAAGCTGA 59.105 50.000 0.00 0.00 0.00 4.26
58 1998 6.703607 GGAATATGTCCAGTGAGTCTGTTATG 59.296 42.308 0.00 0.00 46.97 1.90
59 1999 6.821388 GGAATATGTCCAGTGAGTCTGTTAT 58.179 40.000 0.00 0.00 46.97 1.89
187 2127 4.878971 TGTGTTGTTGCTTAGCTGTAGAAA 59.121 37.500 5.60 0.00 0.00 2.52
234 2174 5.576563 TTAGTTGGGTCAGATTTCCAAGA 57.423 39.130 0.00 0.00 40.71 3.02
313 2253 5.769484 AGATCTTGCAAATGGATTAGCTG 57.231 39.130 0.00 0.00 0.00 4.24
339 2279 8.306761 GGACCTGAAATATGATTTGAAACAAGT 58.693 33.333 0.00 0.00 0.00 3.16
344 2284 9.874205 GAATTGGACCTGAAATATGATTTGAAA 57.126 29.630 0.00 0.00 0.00 2.69
352 2292 7.255730 GGAGATTGGAATTGGACCTGAAATATG 60.256 40.741 0.00 0.00 0.00 1.78
355 2295 4.958581 GGAGATTGGAATTGGACCTGAAAT 59.041 41.667 0.00 0.00 0.00 2.17
401 2341 9.921637 TTTGATTTCTAGAGAGAGAAAGTCTTC 57.078 33.333 5.02 0.00 45.98 2.87
410 2350 7.555087 ACCTGTGATTTGATTTCTAGAGAGAG 58.445 38.462 0.00 0.00 31.77 3.20
419 2359 6.564328 GGTATTGGACCTGTGATTTGATTTC 58.436 40.000 0.00 0.00 45.89 2.17
467 2407 4.384940 GGAGAGATCAAGATGGTTTAGCC 58.615 47.826 0.00 0.00 37.90 3.93
488 2428 5.212532 TGAACCTGTGATTTGATTTTGGG 57.787 39.130 0.00 0.00 0.00 4.12
626 2566 7.286775 GGCCAGATATTTGGTTATAGGACAAAA 59.713 37.037 13.50 0.00 40.49 2.44
627 2567 6.775629 GGCCAGATATTTGGTTATAGGACAAA 59.224 38.462 13.50 0.00 40.49 2.83
636 2576 5.615261 AGGAATAGGGCCAGATATTTGGTTA 59.385 40.000 13.50 5.27 40.49 2.85
652 2592 0.466922 CCCAAGCTGCCAGGAATAGG 60.467 60.000 9.31 0.00 0.00 2.57
669 2609 3.646736 ACTAGCCTGGTTACATTTCCC 57.353 47.619 0.00 0.00 0.00 3.97
676 2616 5.405797 GTGTAGTTGTACTAGCCTGGTTAC 58.594 45.833 0.00 0.00 30.12 2.50
683 2623 3.094572 TGGAGGTGTAGTTGTACTAGCC 58.905 50.000 0.00 0.00 30.12 3.93
715 2655 1.148498 GGGGAATGGAGCCGGTTAG 59.852 63.158 1.90 0.00 0.00 2.34
771 2711 5.163754 CCCCGAAATTCTGTTCTGATACAAC 60.164 44.000 0.00 0.00 0.00 3.32
785 2725 3.881220 TCTGGTATTGACCCCGAAATTC 58.119 45.455 0.00 0.00 46.32 2.17
805 2745 4.935205 ACTTTGCAACTTCCCAAAAGTTTC 59.065 37.500 0.00 0.00 38.32 2.78
855 2795 6.183360 CCCGAGGAAGAGAACCTGATAAATTA 60.183 42.308 0.00 0.00 37.93 1.40
879 2819 2.810852 GCCGATGAGATCTCCAAATTCC 59.189 50.000 20.03 0.00 0.00 3.01
918 2858 4.933400 GGTCCTGAAAGCGAGTTGTTATAA 59.067 41.667 0.00 0.00 0.00 0.98
920 2860 3.335579 GGTCCTGAAAGCGAGTTGTTAT 58.664 45.455 0.00 0.00 0.00 1.89
930 2870 0.392595 CGGGTAAGGGTCCTGAAAGC 60.393 60.000 0.00 0.00 33.49 3.51
942 2882 5.763204 ACCTGAACATATATTTGCGGGTAAG 59.237 40.000 8.44 0.00 0.00 2.34
1007 2947 0.040204 ACTCCTTGGAATTGGGCCAG 59.960 55.000 6.23 0.00 36.64 4.85
1014 2954 6.656693 CACATGTCTTTAGACTCCTTGGAATT 59.343 38.462 10.92 0.00 44.99 2.17
1027 2967 6.377327 AACCAAACTCACACATGTCTTTAG 57.623 37.500 0.00 0.00 0.00 1.85
1039 2979 6.481976 CCAAGGGAAATTTTAACCAAACTCAC 59.518 38.462 9.32 0.00 0.00 3.51
1040 2980 6.408662 CCCAAGGGAAATTTTAACCAAACTCA 60.409 38.462 0.00 0.00 37.50 3.41
1058 2998 4.668636 TGTTAGTTGGTTATTCCCAAGGG 58.331 43.478 0.00 0.00 44.92 3.95
1191 3131 4.459390 TTGTGCTAGATTTAGTGCCGTA 57.541 40.909 0.00 0.00 0.00 4.02
1242 3182 9.793259 TCTGATAAGTTGGACAATTTAGAAAGT 57.207 29.630 6.26 0.00 0.00 2.66
1315 3255 9.303537 CCTAGATAGCTTTGTTAAACTACAGAC 57.696 37.037 0.00 0.00 0.00 3.51
1332 3272 4.392921 TGACAAGTTCAGCCTAGATAGC 57.607 45.455 0.00 0.00 0.00 2.97
1341 3281 6.833342 AATTTGTTTGATGACAAGTTCAGC 57.167 33.333 0.00 0.00 40.33 4.26
1360 3300 8.275187 TGTGTAGGTATGGATCCTGATAATTT 57.725 34.615 14.23 0.00 36.60 1.82
1368 3308 6.470456 TCTATCTGTGTAGGTATGGATCCT 57.530 41.667 14.23 0.89 38.91 3.24
1413 3353 7.212976 TCAGTCTGTTCCAAGATATATCAAGC 58.787 38.462 15.08 0.99 0.00 4.01
1426 3366 5.762179 ATTAATCCACTCAGTCTGTTCCA 57.238 39.130 0.00 0.00 0.00 3.53
1459 3399 0.704076 AGTTTCATGCAGGCCCCTAA 59.296 50.000 0.00 0.00 0.00 2.69
1468 3411 6.003326 TCTTCAAGGAATGTAGTTTCATGCA 58.997 36.000 0.00 0.00 0.00 3.96
1469 3412 6.500684 TCTTCAAGGAATGTAGTTTCATGC 57.499 37.500 0.00 0.00 0.00 4.06
1470 3413 8.272545 TGATCTTCAAGGAATGTAGTTTCATG 57.727 34.615 0.00 0.00 0.00 3.07
1482 3425 6.152661 AGTTGTTGTTGTTGATCTTCAAGGAA 59.847 34.615 0.00 0.00 37.00 3.36
1527 3470 2.727916 GCTTGCTAAATTTCCGACCACG 60.728 50.000 0.00 0.00 39.43 4.94
1529 3472 1.816224 GGCTTGCTAAATTTCCGACCA 59.184 47.619 0.00 0.00 0.00 4.02
1533 3476 1.913317 GCAGGCTTGCTAAATTTCCG 58.087 50.000 14.45 0.00 46.95 4.30
1546 3489 5.061853 CACATCTAACATAATCTGCAGGCT 58.938 41.667 15.13 3.64 0.00 4.58
1557 3500 9.448438 AGTTTATTGTTGCTCACATCTAACATA 57.552 29.630 0.00 0.00 34.43 2.29
1581 3524 1.523711 CGGCAACACACCACTGAGT 60.524 57.895 0.00 0.00 0.00 3.41
1619 3562 7.699812 GTGACAAATTCAGAAATTCTAGCATCC 59.300 37.037 0.00 0.00 33.93 3.51
1651 3594 0.532115 GGAATGCCGCCATTGAACTT 59.468 50.000 0.00 0.00 41.60 2.66
1663 3606 0.749049 GCAAAGGAGGATGGAATGCC 59.251 55.000 0.00 0.00 33.77 4.40
1691 3634 3.557595 CACATCGAGTATTGAAAGGCTCC 59.442 47.826 0.00 0.00 28.09 4.70
1754 3697 6.090358 CCAACTAGCTGAAGCATTTTGAAATG 59.910 38.462 11.19 11.19 46.55 2.32
1756 3699 5.068987 ACCAACTAGCTGAAGCATTTTGAAA 59.931 36.000 4.90 0.00 45.16 2.69
1783 3726 8.755028 GTTACCACATAAACCTTTATTGGGAAT 58.245 33.333 13.82 0.00 36.99 3.01
1838 3781 3.708451 TCATGGTGACTAGCTACTGGAA 58.292 45.455 0.00 0.00 0.00 3.53
1849 3795 6.207417 CCAAGTATCTTTTGTTCATGGTGACT 59.793 38.462 0.00 0.00 0.00 3.41
1858 3804 7.770801 AAAGCAAACCAAGTATCTTTTGTTC 57.229 32.000 0.00 0.00 32.57 3.18
1862 3808 7.327214 TGACAAAAGCAAACCAAGTATCTTTT 58.673 30.769 0.00 0.00 35.06 2.27
1888 3834 2.494073 TGAAACCCACCACAAGAACAAC 59.506 45.455 0.00 0.00 0.00 3.32
1942 3888 6.932400 TGTGGTTTTCTATTGTTACGACTGAT 59.068 34.615 0.00 0.00 0.00 2.90
1956 3902 4.497291 AGTGACACCTTGTGGTTTTCTA 57.503 40.909 0.84 0.00 46.05 2.10
1974 3923 1.625818 AGGTCCCTTGCTTCAGTAGTG 59.374 52.381 0.00 0.00 0.00 2.74
2070 4019 4.220693 TCCACCAGTTCCAATGATGTAG 57.779 45.455 0.00 0.00 0.00 2.74
2085 4034 0.907704 AGACCTTGCCGTATCCACCA 60.908 55.000 0.00 0.00 0.00 4.17
2088 4037 1.855295 TGTAGACCTTGCCGTATCCA 58.145 50.000 0.00 0.00 0.00 3.41
2100 4049 3.746045 TGGAGTTGTGTCTTGTAGACC 57.254 47.619 4.52 0.00 44.44 3.85
2110 4059 0.478072 TGCCCATCTTGGAGTTGTGT 59.522 50.000 0.00 0.00 40.96 3.72
2167 4116 5.869753 AATCTTCTTTCATCGTCCAACTG 57.130 39.130 0.00 0.00 0.00 3.16
2208 4157 4.443913 TCGTTGTCGGATCTGTGATAAA 57.556 40.909 0.42 0.00 37.69 1.40
2330 4279 3.384168 TCTAATTCCTTGGCTAGCTCCA 58.616 45.455 15.72 1.57 0.00 3.86
2340 4289 5.298777 CCTCTTCTGCCAATCTAATTCCTTG 59.701 44.000 0.00 0.00 0.00 3.61
2472 4421 3.679389 TGAGATGAAAGCCTTCAAGGTC 58.321 45.455 5.03 0.00 44.64 3.85
2488 4437 0.811616 GCCGTGCCGAAATCTGAGAT 60.812 55.000 0.00 0.00 0.00 2.75
2524 4473 2.744202 GTGCACTCCAGTTCGATGAATT 59.256 45.455 10.32 0.00 0.00 2.17
2735 4700 1.133262 CCTTGGATGCTTCCCCATCAT 60.133 52.381 15.62 0.00 42.63 2.45
2782 4747 6.466885 TTCACTAGTATAGCTTGTTCCTCC 57.533 41.667 0.00 0.00 44.39 4.30
2807 4772 0.106149 GGCCGTCGGTCCAGAATATT 59.894 55.000 13.94 0.00 0.00 1.28
2820 4785 1.240256 TGTTGGTGTTATTGGCCGTC 58.760 50.000 0.00 0.00 0.00 4.79
2829 4794 5.492895 TCTCTTCTGTTGTTGTTGGTGTTA 58.507 37.500 0.00 0.00 0.00 2.41
2926 4891 2.093306 TGAGTGTTTGGTATGCCTCG 57.907 50.000 0.16 0.00 35.27 4.63
2947 4912 3.706594 GGGTCATCAACTCATCCTACTGA 59.293 47.826 0.00 0.00 0.00 3.41
2993 5165 3.181485 GCTTTCACTATAGCGGAGAGTGT 60.181 47.826 13.78 0.00 45.83 3.55
3003 5175 4.268644 CACATGACGGTGCTTTCACTATAG 59.731 45.833 0.00 0.00 42.72 1.31
3029 5204 2.119886 CCTTGCGGGAAAAACCACA 58.880 52.632 0.00 0.00 41.20 4.17
3118 5299 9.445786 CCGTAAAACAAGTTATATTTATGCAGG 57.554 33.333 0.00 0.00 0.00 4.85
3119 5300 9.445786 CCCGTAAAACAAGTTATATTTATGCAG 57.554 33.333 0.00 0.00 0.00 4.41
3133 5315 3.430333 ACAAGCAACCCGTAAAACAAG 57.570 42.857 0.00 0.00 0.00 3.16
3141 5323 2.356695 GAGTGTTTTACAAGCAACCCGT 59.643 45.455 0.00 0.00 0.00 5.28
3158 5340 3.876274 ATAGGCACCGCATATAGAGTG 57.124 47.619 0.00 0.00 33.69 3.51
3159 5341 4.090090 AGAATAGGCACCGCATATAGAGT 58.910 43.478 0.00 0.00 34.37 3.24
3160 5342 4.727507 AGAATAGGCACCGCATATAGAG 57.272 45.455 0.00 0.00 34.37 2.43
3161 5343 6.791867 ATAAGAATAGGCACCGCATATAGA 57.208 37.500 0.00 0.00 34.37 1.98
3162 5344 9.547753 AAATATAAGAATAGGCACCGCATATAG 57.452 33.333 0.00 0.00 34.37 1.31
3163 5345 9.325198 CAAATATAAGAATAGGCACCGCATATA 57.675 33.333 0.00 0.00 34.37 0.86
3164 5346 7.829211 ACAAATATAAGAATAGGCACCGCATAT 59.171 33.333 0.00 0.00 37.11 1.78
3179 5361 7.707893 GGGTACTGCGTCTAAACAAATATAAGA 59.292 37.037 0.00 0.00 0.00 2.10
3180 5362 7.493320 TGGGTACTGCGTCTAAACAAATATAAG 59.507 37.037 0.00 0.00 0.00 1.73
3197 5379 1.270839 ACTGTCACATGTGGGTACTGC 60.271 52.381 25.16 8.01 0.00 4.40
3198 5380 2.037121 TCACTGTCACATGTGGGTACTG 59.963 50.000 25.16 20.06 35.15 2.74
3216 5398 1.940613 ACAGCCGAAAGAAGTTGTCAC 59.059 47.619 0.00 0.00 0.00 3.67
3218 5400 2.872858 AGAACAGCCGAAAGAAGTTGTC 59.127 45.455 0.00 0.00 0.00 3.18
3219 5401 2.872858 GAGAACAGCCGAAAGAAGTTGT 59.127 45.455 0.00 0.00 0.00 3.32
3220 5402 2.096713 CGAGAACAGCCGAAAGAAGTTG 60.097 50.000 0.00 0.00 0.00 3.16
3221 5403 2.135933 CGAGAACAGCCGAAAGAAGTT 58.864 47.619 0.00 0.00 0.00 2.66
3222 5404 1.605712 CCGAGAACAGCCGAAAGAAGT 60.606 52.381 0.00 0.00 0.00 3.01
3223 5405 1.071605 CCGAGAACAGCCGAAAGAAG 58.928 55.000 0.00 0.00 0.00 2.85
3241 5423 3.089284 CACCATTTCAAGTACCCTTCCC 58.911 50.000 0.00 0.00 0.00 3.97
3243 5425 3.756963 GACCACCATTTCAAGTACCCTTC 59.243 47.826 0.00 0.00 0.00 3.46
3268 5548 7.554476 GCTTTGATTCCTAGAGGACAATAAAGT 59.446 37.037 16.82 0.00 45.39 2.66
3278 5558 6.830838 AGGTATTTTGCTTTGATTCCTAGAGG 59.169 38.462 0.00 0.00 0.00 3.69
3294 5580 4.280677 TCTTGCTTGGTCCAAGGTATTTTG 59.719 41.667 28.96 6.33 41.31 2.44
3315 5601 2.337583 CGACATCATTGTGACCGTTCT 58.662 47.619 0.00 0.00 35.79 3.01
3321 5607 3.715618 TTTACGCGACATCATTGTGAC 57.284 42.857 15.93 0.00 35.79 3.67
3332 5618 3.430895 TCATCTGTTCCTTTTTACGCGAC 59.569 43.478 15.93 0.00 0.00 5.19
3333 5619 3.655486 TCATCTGTTCCTTTTTACGCGA 58.345 40.909 15.93 0.00 0.00 5.87
3334 5620 4.398549 TTCATCTGTTCCTTTTTACGCG 57.601 40.909 3.53 3.53 0.00 6.01
3342 5637 5.334879 GCGTGTTTACATTCATCTGTTCCTT 60.335 40.000 0.00 0.00 0.00 3.36
3350 5646 3.372206 AGCTCTGCGTGTTTACATTCATC 59.628 43.478 0.00 0.00 0.00 2.92
3402 5699 9.638176 CCTCTGTAAGTCCCTTTACTTAGTATA 57.362 37.037 0.00 0.00 41.42 1.47
3403 5700 7.564292 CCCTCTGTAAGTCCCTTTACTTAGTAT 59.436 40.741 0.00 0.00 41.42 2.12
3415 5718 2.500504 CCTACAACCCTCTGTAAGTCCC 59.499 54.545 0.00 0.00 31.51 4.46
3447 5750 6.012508 TCCTCCATCATAAGGACAAGAACTTT 60.013 38.462 0.00 0.00 36.75 2.66
3471 6034 1.943340 GCGAACCCTCCTTGATCAATC 59.057 52.381 8.96 0.70 0.00 2.67
3476 6039 1.218316 GTCGCGAACCCTCCTTGAT 59.782 57.895 12.06 0.00 0.00 2.57
3482 6097 0.669318 TGTCAATGTCGCGAACCCTC 60.669 55.000 12.06 0.00 0.00 4.30
3484 6099 0.096976 CATGTCAATGTCGCGAACCC 59.903 55.000 12.06 0.00 0.00 4.11
3485 6100 0.096976 CCATGTCAATGTCGCGAACC 59.903 55.000 12.06 0.00 31.27 3.62
3487 6102 1.463056 GTTCCATGTCAATGTCGCGAA 59.537 47.619 12.06 1.13 31.27 4.70
3489 6104 0.795698 TGTTCCATGTCAATGTCGCG 59.204 50.000 0.00 0.00 31.27 5.87
3490 6105 2.987413 TTGTTCCATGTCAATGTCGC 57.013 45.000 0.00 0.00 31.27 5.19
3494 6109 5.404946 GTCATCCTTTGTTCCATGTCAATG 58.595 41.667 0.00 0.00 0.00 2.82
3498 6113 3.074412 ACGTCATCCTTTGTTCCATGTC 58.926 45.455 0.00 0.00 0.00 3.06
3499 6114 3.140325 ACGTCATCCTTTGTTCCATGT 57.860 42.857 0.00 0.00 0.00 3.21
3512 6127 8.495949 TGAAGAAAAAGAAGATTGTACGTCATC 58.504 33.333 0.00 0.00 0.00 2.92
3513 6128 8.378172 TGAAGAAAAAGAAGATTGTACGTCAT 57.622 30.769 0.00 0.00 0.00 3.06
3514 6129 7.780008 TGAAGAAAAAGAAGATTGTACGTCA 57.220 32.000 0.00 0.00 0.00 4.35
3515 6130 7.269297 GCATGAAGAAAAAGAAGATTGTACGTC 59.731 37.037 0.00 0.00 0.00 4.34
3516 6131 7.078228 GCATGAAGAAAAAGAAGATTGTACGT 58.922 34.615 0.00 0.00 0.00 3.57
3517 6132 6.524586 GGCATGAAGAAAAAGAAGATTGTACG 59.475 38.462 0.00 0.00 0.00 3.67
3518 6133 7.597386 AGGCATGAAGAAAAAGAAGATTGTAC 58.403 34.615 0.00 0.00 0.00 2.90
3524 6139 6.624423 GCATTAGGCATGAAGAAAAAGAAGA 58.376 36.000 0.00 0.00 43.97 2.87
3547 6162 5.877012 TCATCTCATCCTCTGTTAAGTTTGC 59.123 40.000 0.00 0.00 0.00 3.68
3559 6174 9.145442 TCCTTCATATCATATCATCTCATCCTC 57.855 37.037 0.00 0.00 0.00 3.71
3572 6187 9.295224 TCATATGGGGATTTCCTTCATATCATA 57.705 33.333 16.04 0.00 38.93 2.15
3579 6194 4.726317 TCTGTCATATGGGGATTTCCTTCA 59.274 41.667 2.13 0.00 35.95 3.02
3583 6198 4.437682 TGTCTGTCATATGGGGATTTCC 57.562 45.455 2.13 0.00 0.00 3.13
3584 6199 5.192927 TGTTGTCTGTCATATGGGGATTTC 58.807 41.667 2.13 0.00 0.00 2.17
3585 6200 5.191727 TGTTGTCTGTCATATGGGGATTT 57.808 39.130 2.13 0.00 0.00 2.17
3586 6201 4.860802 TGTTGTCTGTCATATGGGGATT 57.139 40.909 2.13 0.00 0.00 3.01
3587 6202 4.413189 TCATGTTGTCTGTCATATGGGGAT 59.587 41.667 2.13 0.00 0.00 3.85
3589 6204 4.132336 CTCATGTTGTCTGTCATATGGGG 58.868 47.826 2.13 0.00 0.00 4.96
3590 6205 5.027293 TCTCATGTTGTCTGTCATATGGG 57.973 43.478 2.13 0.00 0.00 4.00
3591 6206 4.510711 GCTCTCATGTTGTCTGTCATATGG 59.489 45.833 2.13 0.00 0.00 2.74
3592 6207 5.358090 AGCTCTCATGTTGTCTGTCATATG 58.642 41.667 0.00 0.00 0.00 1.78
3593 6208 5.611128 AGCTCTCATGTTGTCTGTCATAT 57.389 39.130 0.00 0.00 0.00 1.78
3594 6209 5.451103 GCTAGCTCTCATGTTGTCTGTCATA 60.451 44.000 7.70 0.00 0.00 2.15
3595 6210 3.977134 AGCTCTCATGTTGTCTGTCAT 57.023 42.857 0.00 0.00 0.00 3.06
3645 6260 7.398024 AGCTGAGTTGAATTGGTATCTAGTTT 58.602 34.615 0.00 0.00 0.00 2.66
3648 6263 7.651304 CACTAGCTGAGTTGAATTGGTATCTAG 59.349 40.741 0.00 0.00 35.64 2.43
3649 6264 7.492524 CACTAGCTGAGTTGAATTGGTATCTA 58.507 38.462 0.00 0.00 35.64 1.98
3670 6285 3.339253 AGCATGTCTGTGATTGCACTA 57.661 42.857 0.00 0.00 45.36 2.74
3671 6286 2.195741 AGCATGTCTGTGATTGCACT 57.804 45.000 0.00 0.00 45.36 4.40
3672 6287 2.096496 GGTAGCATGTCTGTGATTGCAC 59.904 50.000 0.00 0.00 45.35 4.57
3673 6288 2.290197 TGGTAGCATGTCTGTGATTGCA 60.290 45.455 0.00 0.00 37.56 4.08
3674 6289 2.358957 TGGTAGCATGTCTGTGATTGC 58.641 47.619 0.00 0.00 35.34 3.56
3675 6290 3.752747 TGTTGGTAGCATGTCTGTGATTG 59.247 43.478 0.00 0.00 0.00 2.67
3676 6291 4.005650 CTGTTGGTAGCATGTCTGTGATT 58.994 43.478 0.00 0.00 0.00 2.57
3677 6292 3.603532 CTGTTGGTAGCATGTCTGTGAT 58.396 45.455 0.00 0.00 0.00 3.06
3678 6293 2.289631 CCTGTTGGTAGCATGTCTGTGA 60.290 50.000 0.00 0.00 0.00 3.58
3679 6294 2.079158 CCTGTTGGTAGCATGTCTGTG 58.921 52.381 0.00 0.00 0.00 3.66
3680 6295 1.977854 TCCTGTTGGTAGCATGTCTGT 59.022 47.619 0.00 0.00 34.23 3.41
3681 6296 2.768253 TCCTGTTGGTAGCATGTCTG 57.232 50.000 0.00 0.00 34.23 3.51
3688 6303 3.670625 TGTTGTACATCCTGTTGGTAGC 58.329 45.455 0.00 0.00 34.23 3.58
3692 6307 6.873997 TCTATACTGTTGTACATCCTGTTGG 58.126 40.000 0.00 0.00 0.00 3.77
3709 6324 7.014808 GCAATAGAGGGAGTTGTTCTCTATACT 59.985 40.741 11.11 0.00 45.03 2.12
3722 6337 2.559381 AGTGGAGCAATAGAGGGAGT 57.441 50.000 0.00 0.00 0.00 3.85
3723 6338 6.865834 ATAATAGTGGAGCAATAGAGGGAG 57.134 41.667 0.00 0.00 0.00 4.30
3724 6339 8.917414 ATAATAATAGTGGAGCAATAGAGGGA 57.083 34.615 0.00 0.00 0.00 4.20
3725 6340 9.606631 GAATAATAATAGTGGAGCAATAGAGGG 57.393 37.037 0.00 0.00 0.00 4.30
3726 6341 9.606631 GGAATAATAATAGTGGAGCAATAGAGG 57.393 37.037 0.00 0.00 0.00 3.69
3734 6349 9.516314 GTTGTTTTGGAATAATAATAGTGGAGC 57.484 33.333 0.00 0.00 0.00 4.70
3743 6358 9.581289 TCTCTTCCTGTTGTTTTGGAATAATAA 57.419 29.630 0.00 0.00 38.91 1.40
3748 6363 5.200483 TGTCTCTTCCTGTTGTTTTGGAAT 58.800 37.500 0.00 0.00 38.91 3.01
3754 6369 6.064060 TGAATGATGTCTCTTCCTGTTGTTT 58.936 36.000 0.00 0.00 0.00 2.83
3755 6370 5.624159 TGAATGATGTCTCTTCCTGTTGTT 58.376 37.500 0.00 0.00 0.00 2.83
3760 6375 4.498241 TCGTTGAATGATGTCTCTTCCTG 58.502 43.478 0.00 0.00 0.00 3.86
3761 6376 4.808414 TCGTTGAATGATGTCTCTTCCT 57.192 40.909 0.00 0.00 0.00 3.36
3766 6381 4.973396 TGCAATTCGTTGAATGATGTCTC 58.027 39.130 0.00 0.00 32.14 3.36
3767 6382 4.456911 ACTGCAATTCGTTGAATGATGTCT 59.543 37.500 0.00 0.00 32.14 3.41
3768 6383 4.556135 CACTGCAATTCGTTGAATGATGTC 59.444 41.667 0.00 0.00 32.14 3.06
3769 6384 4.478699 CACTGCAATTCGTTGAATGATGT 58.521 39.130 0.00 0.00 32.14 3.06
3774 6395 6.542005 TCATATACCACTGCAATTCGTTGAAT 59.458 34.615 0.00 0.00 33.25 2.57
3781 6402 8.623903 TGAATCTTTCATATACCACTGCAATTC 58.376 33.333 0.00 0.00 34.08 2.17
3805 6429 1.601903 GTGCATGGACAAGTTCGTTGA 59.398 47.619 13.07 0.00 38.60 3.18
3809 6433 2.223456 TGTTTGTGCATGGACAAGTTCG 60.223 45.455 28.19 0.00 37.16 3.95
3813 6437 3.504863 GCTATGTTTGTGCATGGACAAG 58.495 45.455 28.19 19.30 37.16 3.16
3825 6449 0.732571 AATGGTCGGCGCTATGTTTG 59.267 50.000 7.64 0.00 0.00 2.93
3831 6455 0.529773 GATGTGAATGGTCGGCGCTA 60.530 55.000 7.64 0.00 0.00 4.26
3834 6458 1.482621 CTCGATGTGAATGGTCGGCG 61.483 60.000 0.00 0.00 0.00 6.46
3845 6469 3.553511 GGTGTAGCTTTGATCTCGATGTG 59.446 47.826 0.00 0.00 0.00 3.21
3849 6473 4.645136 ACTATGGTGTAGCTTTGATCTCGA 59.355 41.667 0.00 0.00 0.00 4.04
3879 6504 5.442390 CGTCAATTCGTACCTGAAAGTAACG 60.442 44.000 0.00 0.00 40.29 3.18
3880 6505 5.667156 GCGTCAATTCGTACCTGAAAGTAAC 60.667 44.000 0.00 0.00 0.00 2.50
3882 6507 3.922240 GCGTCAATTCGTACCTGAAAGTA 59.078 43.478 0.00 0.00 0.00 2.24
3883 6508 2.735134 GCGTCAATTCGTACCTGAAAGT 59.265 45.455 0.00 0.00 0.00 2.66
3884 6509 2.222508 CGCGTCAATTCGTACCTGAAAG 60.223 50.000 0.00 0.00 0.00 2.62
3914 6542 2.554032 GGATGAATTGGGATTGCCTACG 59.446 50.000 0.00 0.00 0.00 3.51
3922 6550 1.854939 TGCAGGAGGATGAATTGGGAT 59.145 47.619 0.00 0.00 0.00 3.85
3928 6556 1.355381 TGTTGGTGCAGGAGGATGAAT 59.645 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.