Multiple sequence alignment - TraesCS1B01G429100

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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 TraesCS1B01G429100 chr1B 100.000 3118 0 0 1 3118 653939828 653936711 0.000000e+00 5758.0
1 TraesCS1B01G429100 chr1B 84.126 1367 150 20 897 2247 653890668 653889353 0.000000e+00 1260.0
2 TraesCS1B01G429100 chr1B 82.857 840 124 17 883 1715 653975618 653974792 0.000000e+00 736.0
3 TraesCS1B01G429100 chr1B 86.184 304 18 6 546 842 653891173 653890887 1.090000e-79 307.0
4 TraesCS1B01G429100 chr1B 83.871 310 27 7 2255 2552 653889384 653889086 1.100000e-69 274.0
5 TraesCS1B01G429100 chr1B 94.872 39 2 0 2077 2115 653974789 653974751 9.340000e-06 62.1
6 TraesCS1B01G429100 chr1B 90.909 44 1 3 2206 2247 653937585 653937543 4.340000e-04 56.5
7 TraesCS1B01G429100 chr1B 90.909 44 1 3 2244 2286 653937623 653937582 4.340000e-04 56.5
8 TraesCS1B01G429100 chr1D 95.921 1373 41 6 877 2247 470648574 470647215 0.000000e+00 2211.0
9 TraesCS1B01G429100 chr1D 85.578 1366 141 16 897 2247 470625878 470624554 0.000000e+00 1380.0
10 TraesCS1B01G429100 chr1D 92.481 798 29 17 1 786 470649899 470649121 0.000000e+00 1112.0
11 TraesCS1B01G429100 chr1D 81.764 1179 186 16 947 2115 470657116 470655957 0.000000e+00 959.0
12 TraesCS1B01G429100 chr1D 88.994 318 17 7 2244 2544 470647258 470646942 8.160000e-101 377.0
13 TraesCS1B01G429100 chr1D 73.280 1134 234 56 971 2070 470798140 470799238 4.950000e-93 351.0
14 TraesCS1B01G429100 chr1D 84.539 304 23 10 546 842 470626313 470626027 2.370000e-71 279.0
15 TraesCS1B01G429100 chr1D 83.810 315 23 8 2255 2552 470624585 470624282 1.100000e-69 274.0
16 TraesCS1B01G429100 chr1D 92.473 93 4 2 763 852 470649028 470648936 2.520000e-26 130.0
17 TraesCS1B01G429100 chr1A 95.636 1375 47 5 877 2247 564345921 564344556 0.000000e+00 2194.0
18 TraesCS1B01G429100 chr1A 88.155 1393 125 20 877 2247 564313928 564312554 0.000000e+00 1622.0
19 TraesCS1B01G429100 chr1A 86.564 1362 145 15 897 2247 564334752 564333418 0.000000e+00 1467.0
20 TraesCS1B01G429100 chr1A 90.698 860 35 13 1 852 564347402 564346580 0.000000e+00 1103.0
21 TraesCS1B01G429100 chr1A 81.888 1176 188 15 947 2115 564373463 564372306 0.000000e+00 968.0
22 TraesCS1B01G429100 chr1A 88.478 460 28 9 2244 2689 564344599 564344151 1.650000e-147 532.0
23 TraesCS1B01G429100 chr1A 85.078 449 40 10 2244 2670 564312597 564312154 1.720000e-117 433.0
24 TraesCS1B01G429100 chr1A 84.464 457 46 11 2244 2689 564333461 564333019 7.990000e-116 427.0
25 TraesCS1B01G429100 chr1A 75.831 662 130 23 945 1593 564576001 564576645 3.020000e-80 309.0
26 TraesCS1B01G429100 chr1A 84.298 242 13 15 608 849 564314371 564314155 2.440000e-51 213.0
27 TraesCS1B01G429100 chr1A 84.667 150 9 12 702 850 564335020 564334884 1.510000e-28 137.0
28 TraesCS1B01G429100 chr2D 92.944 411 25 3 2691 3100 640367314 640367721 2.070000e-166 595.0
29 TraesCS1B01G429100 chr2D 91.463 410 30 4 2691 3099 3732210 3731805 2.720000e-155 558.0
30 TraesCS1B01G429100 chr3D 91.505 412 31 4 2691 3100 424493760 424493351 5.840000e-157 564.0
31 TraesCS1B01G429100 chr7D 91.525 413 28 5 2691 3100 133690521 133690113 2.100000e-156 562.0
32 TraesCS1B01G429100 chr7D 91.463 410 31 3 2691 3099 589510794 589511200 7.550000e-156 560.0
33 TraesCS1B01G429100 chr4A 91.687 409 29 5 2691 3099 139718055 139717652 2.100000e-156 562.0
34 TraesCS1B01G429100 chr7A 91.241 411 30 6 2691 3099 127763178 127762772 3.510000e-154 555.0
35 TraesCS1B01G429100 chr5A 91.400 407 31 3 2691 3096 428152031 428152434 3.510000e-154 555.0
36 TraesCS1B01G429100 chr5A 89.498 438 38 8 2667 3099 380827011 380826577 5.880000e-152 547.0


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 TraesCS1B01G429100 chr1B 653936711 653939828 3117 True 1957.000000 5758 93.939333 1 3118 3 chr1B.!!$R2 3117
1 TraesCS1B01G429100 chr1B 653889086 653891173 2087 True 613.666667 1260 84.727000 546 2552 3 chr1B.!!$R1 2006
2 TraesCS1B01G429100 chr1B 653974751 653975618 867 True 399.050000 736 88.864500 883 2115 2 chr1B.!!$R3 1232
3 TraesCS1B01G429100 chr1D 470655957 470657116 1159 True 959.000000 959 81.764000 947 2115 1 chr1D.!!$R1 1168
4 TraesCS1B01G429100 chr1D 470646942 470649899 2957 True 957.500000 2211 92.467250 1 2544 4 chr1D.!!$R3 2543
5 TraesCS1B01G429100 chr1D 470624282 470626313 2031 True 644.333333 1380 84.642333 546 2552 3 chr1D.!!$R2 2006
6 TraesCS1B01G429100 chr1D 470798140 470799238 1098 False 351.000000 351 73.280000 971 2070 1 chr1D.!!$F1 1099
7 TraesCS1B01G429100 chr1A 564344151 564347402 3251 True 1276.333333 2194 91.604000 1 2689 3 chr1A.!!$R4 2688
8 TraesCS1B01G429100 chr1A 564372306 564373463 1157 True 968.000000 968 81.888000 947 2115 1 chr1A.!!$R1 1168
9 TraesCS1B01G429100 chr1A 564312154 564314371 2217 True 756.000000 1622 85.843667 608 2670 3 chr1A.!!$R2 2062
10 TraesCS1B01G429100 chr1A 564333019 564335020 2001 True 677.000000 1467 85.231667 702 2689 3 chr1A.!!$R3 1987
11 TraesCS1B01G429100 chr1A 564576001 564576645 644 False 309.000000 309 75.831000 945 1593 1 chr1A.!!$F1 648

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
852 1023 0.108615 CAGCTCCTAAGTGGGTGACG 60.109 60.0 0.0 0.0 36.2 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2580 3587 0.179225 GCGTGCACCGTGTCAAATAG 60.179 55.0 12.15 0.0 39.32 1.73 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
64 65 3.214328 ACTAATTGGCCAATCGACATCC 58.786 45.455 30.74 0.00 0.00 3.51
147 148 3.092301 GGGAGCTTGGCAAGTTTTATCT 58.908 45.455 26.71 14.79 0.00 1.98
148 149 4.270008 GGGAGCTTGGCAAGTTTTATCTA 58.730 43.478 26.71 0.00 0.00 1.98
149 150 4.336713 GGGAGCTTGGCAAGTTTTATCTAG 59.663 45.833 26.71 0.00 0.00 2.43
150 151 5.186198 GGAGCTTGGCAAGTTTTATCTAGA 58.814 41.667 26.71 0.00 0.00 2.43
151 152 5.295540 GGAGCTTGGCAAGTTTTATCTAGAG 59.704 44.000 26.71 0.00 0.00 2.43
192 193 9.457436 TTGCATGCAGATATGATTATGAATAGT 57.543 29.630 21.50 0.00 0.00 2.12
484 491 2.709397 TCAGATGCATCATCCATGGAGT 59.291 45.455 27.81 5.91 41.36 3.85
536 543 2.559440 CTTGCTACTTCAGGATGCCTC 58.441 52.381 0.00 0.00 34.76 4.70
537 544 1.571955 TGCTACTTCAGGATGCCTCA 58.428 50.000 0.00 0.00 34.76 3.86
538 545 2.121948 TGCTACTTCAGGATGCCTCAT 58.878 47.619 0.00 0.00 34.76 2.90
539 546 2.158856 TGCTACTTCAGGATGCCTCATG 60.159 50.000 0.00 0.00 34.76 3.07
579 586 3.054582 ACTGACAGTGATCTCCATTGCAT 60.055 43.478 7.47 0.00 36.10 3.96
641 681 1.142314 GCCGGCTCGTGGTATGTTA 59.858 57.895 22.15 0.00 0.00 2.41
673 713 5.163844 GCGAGAACAATAGAGAAGGGTTTTC 60.164 44.000 0.00 0.00 0.00 2.29
800 971 8.014322 TGTTGTGATCTCATTACGTTTACTTC 57.986 34.615 0.00 0.00 0.00 3.01
801 972 7.654116 TGTTGTGATCTCATTACGTTTACTTCA 59.346 33.333 0.00 0.00 0.00 3.02
802 973 8.656849 GTTGTGATCTCATTACGTTTACTTCAT 58.343 33.333 0.00 0.00 0.00 2.57
803 974 8.771920 TGTGATCTCATTACGTTTACTTCATT 57.228 30.769 0.00 0.00 0.00 2.57
804 975 8.655970 TGTGATCTCATTACGTTTACTTCATTG 58.344 33.333 0.00 0.00 0.00 2.82
805 976 7.636359 GTGATCTCATTACGTTTACTTCATTGC 59.364 37.037 0.00 0.00 0.00 3.56
806 977 7.549134 TGATCTCATTACGTTTACTTCATTGCT 59.451 33.333 0.00 0.00 0.00 3.91
807 978 7.667043 TCTCATTACGTTTACTTCATTGCTT 57.333 32.000 0.00 0.00 0.00 3.91
852 1023 0.108615 CAGCTCCTAAGTGGGTGACG 60.109 60.000 0.00 0.00 36.20 4.35
853 1024 0.251653 AGCTCCTAAGTGGGTGACGA 60.252 55.000 0.00 0.00 36.20 4.20
854 1025 0.108756 GCTCCTAAGTGGGTGACGAC 60.109 60.000 0.00 0.00 39.69 4.34
856 1027 0.178955 TCCTAAGTGGGTGACGACCA 60.179 55.000 0.00 0.00 45.25 4.02
865 1036 3.851128 TGACGACCACCCAACGCA 61.851 61.111 0.00 0.00 0.00 5.24
866 1037 3.343421 GACGACCACCCAACGCAC 61.343 66.667 0.00 0.00 0.00 5.34
872 1043 1.172180 ACCACCCAACGCACATCAAG 61.172 55.000 0.00 0.00 0.00 3.02
873 1044 1.172180 CCACCCAACGCACATCAAGT 61.172 55.000 0.00 0.00 0.00 3.16
991 1911 5.106118 GCCAACTTTCCCTTTCAGTATTCTC 60.106 44.000 0.00 0.00 0.00 2.87
1060 1982 5.664908 ACTGATGATCTAGTGGTGGAAATCT 59.335 40.000 0.00 0.00 0.00 2.40
1248 2176 7.402650 TCCCCAAATGATGAAGAAATTAATGGT 59.597 33.333 0.00 0.00 0.00 3.55
1331 2259 9.141400 CCTAGTTCTTTGTAAGTACAAGATCAC 57.859 37.037 4.23 1.90 45.77 3.06
1381 2309 2.937519 TCATGTGTAACCCTGCAACAA 58.062 42.857 0.00 0.00 34.36 2.83
1392 2320 0.109342 CTGCAACAAGGGAGTGGAGT 59.891 55.000 0.00 0.00 0.00 3.85
1806 2765 0.390998 GTGCACTTCCAGAGGAGAGC 60.391 60.000 10.32 0.00 31.21 4.09
1807 2766 1.153667 GCACTTCCAGAGGAGAGCG 60.154 63.158 0.00 0.00 31.21 5.03
1808 2767 1.515020 CACTTCCAGAGGAGAGCGG 59.485 63.158 0.00 0.00 31.21 5.52
1809 2768 1.077625 ACTTCCAGAGGAGAGCGGT 59.922 57.895 0.00 0.00 31.21 5.68
1810 2769 0.968393 ACTTCCAGAGGAGAGCGGTC 60.968 60.000 6.48 6.48 31.21 4.79
1993 2955 5.238583 TGATTCGGAAAGAAAGGTTCTCTC 58.761 41.667 0.00 0.00 42.91 3.20
2116 3087 3.983344 GTGGCATGCTACTCAAAACTTTG 59.017 43.478 25.31 0.00 39.48 2.77
2149 3120 6.998074 TCCTCTTTTGAGCATAGACAAGAAAA 59.002 34.615 0.00 0.00 44.93 2.29
2215 3186 4.624336 TGTGCGTATTTGTGTCTGTTTT 57.376 36.364 0.00 0.00 0.00 2.43
2216 3187 5.736486 TGTGCGTATTTGTGTCTGTTTTA 57.264 34.783 0.00 0.00 0.00 1.52
2217 3188 5.503498 TGTGCGTATTTGTGTCTGTTTTAC 58.497 37.500 0.00 0.00 0.00 2.01
2218 3189 5.064834 TGTGCGTATTTGTGTCTGTTTTACA 59.935 36.000 0.00 0.00 0.00 2.41
2219 3190 5.966503 GTGCGTATTTGTGTCTGTTTTACAA 59.033 36.000 0.00 0.00 32.93 2.41
2220 3191 5.966503 TGCGTATTTGTGTCTGTTTTACAAC 59.033 36.000 0.00 0.00 34.38 3.32
2221 3192 5.966503 GCGTATTTGTGTCTGTTTTACAACA 59.033 36.000 0.00 0.00 40.82 3.33
2222 3193 6.469595 GCGTATTTGTGTCTGTTTTACAACAA 59.530 34.615 0.00 0.00 42.53 2.83
2223 3194 7.166804 GCGTATTTGTGTCTGTTTTACAACAAT 59.833 33.333 0.00 0.00 42.53 2.71
2224 3195 8.468349 CGTATTTGTGTCTGTTTTACAACAATG 58.532 33.333 0.00 0.00 42.53 2.82
2225 3196 7.769272 ATTTGTGTCTGTTTTACAACAATGG 57.231 32.000 0.00 0.00 42.53 3.16
2226 3197 6.516739 TTGTGTCTGTTTTACAACAATGGA 57.483 33.333 0.00 0.00 42.53 3.41
2227 3198 6.707440 TGTGTCTGTTTTACAACAATGGAT 57.293 33.333 0.00 0.00 42.53 3.41
2228 3199 7.106439 TGTGTCTGTTTTACAACAATGGATT 57.894 32.000 0.00 0.00 42.53 3.01
2229 3200 8.226819 TGTGTCTGTTTTACAACAATGGATTA 57.773 30.769 0.00 0.00 42.53 1.75
2230 3201 8.349245 TGTGTCTGTTTTACAACAATGGATTAG 58.651 33.333 0.00 0.00 42.53 1.73
2231 3202 7.807907 GTGTCTGTTTTACAACAATGGATTAGG 59.192 37.037 0.00 0.00 42.53 2.69
2232 3203 7.504238 TGTCTGTTTTACAACAATGGATTAGGT 59.496 33.333 0.00 0.00 42.53 3.08
2233 3204 8.357402 GTCTGTTTTACAACAATGGATTAGGTT 58.643 33.333 0.00 0.00 42.53 3.50
2234 3205 8.356657 TCTGTTTTACAACAATGGATTAGGTTG 58.643 33.333 0.00 0.00 42.53 3.77
2235 3206 7.437748 TGTTTTACAACAATGGATTAGGTTGG 58.562 34.615 0.00 0.00 43.61 3.77
2236 3207 7.070074 TGTTTTACAACAATGGATTAGGTTGGT 59.930 33.333 0.00 0.00 43.61 3.67
2237 3208 8.578151 GTTTTACAACAATGGATTAGGTTGGTA 58.422 33.333 0.00 0.00 43.61 3.25
2238 3209 8.707796 TTTACAACAATGGATTAGGTTGGTAA 57.292 30.769 0.00 0.00 43.61 2.85
2239 3210 6.584185 ACAACAATGGATTAGGTTGGTAAC 57.416 37.500 0.00 0.00 43.61 2.50
2331 3306 1.468054 CGCAAATGAGCTTAACTGGCC 60.468 52.381 0.00 0.00 0.00 5.36
2408 3383 7.175641 CACCTTCTGAATGTTCTTACCAGAATT 59.824 37.037 0.00 0.00 41.26 2.17
2410 3385 9.231297 CCTTCTGAATGTTCTTACCAGAATTTA 57.769 33.333 0.00 0.00 41.26 1.40
2418 3393 8.209802 TGTTCTTACCAGAATTTAAGGGACTA 57.790 34.615 0.00 0.00 41.26 2.59
2494 3498 5.653255 ATTAAGGTAATCTGTGATGGGCT 57.347 39.130 0.00 0.00 0.00 5.19
2527 3531 4.527509 TCACTGACACTCCTCATTCTTC 57.472 45.455 0.00 0.00 0.00 2.87
2557 3564 7.043986 CCAATGTGAACAATGTTTTTGCATTTG 60.044 33.333 0.00 3.03 37.00 2.32
2566 3573 9.719279 ACAATGTTTTTGCATTTGTAAAATCAG 57.281 25.926 16.88 10.49 40.18 2.90
2597 3604 3.002862 TGTTTCTATTTGACACGGTGCAC 59.997 43.478 8.80 8.80 0.00 4.57
2616 3623 3.485216 GCACGCACATGTTTCCTACATAC 60.485 47.826 0.00 0.00 45.71 2.39
2689 3696 7.637709 AAAAATGTTAAAAGTGCGAGGAATC 57.362 32.000 0.00 0.00 0.00 2.52
2690 3697 5.957842 AATGTTAAAAGTGCGAGGAATCA 57.042 34.783 0.00 0.00 0.00 2.57
2691 3698 5.957842 ATGTTAAAAGTGCGAGGAATCAA 57.042 34.783 0.00 0.00 0.00 2.57
2692 3699 5.759506 TGTTAAAAGTGCGAGGAATCAAA 57.240 34.783 0.00 0.00 0.00 2.69
2693 3700 6.137794 TGTTAAAAGTGCGAGGAATCAAAA 57.862 33.333 0.00 0.00 0.00 2.44
2694 3701 6.744112 TGTTAAAAGTGCGAGGAATCAAAAT 58.256 32.000 0.00 0.00 0.00 1.82
2695 3702 6.640499 TGTTAAAAGTGCGAGGAATCAAAATG 59.360 34.615 0.00 0.00 0.00 2.32
2696 3703 2.927553 AGTGCGAGGAATCAAAATGC 57.072 45.000 0.00 0.00 0.00 3.56
2697 3704 1.474077 AGTGCGAGGAATCAAAATGCC 59.526 47.619 0.00 0.00 0.00 4.40
2698 3705 1.202114 GTGCGAGGAATCAAAATGCCA 59.798 47.619 0.00 0.00 32.04 4.92
2699 3706 1.891811 TGCGAGGAATCAAAATGCCAA 59.108 42.857 0.00 0.00 32.04 4.52
2700 3707 2.298446 TGCGAGGAATCAAAATGCCAAA 59.702 40.909 0.00 0.00 32.04 3.28
2701 3708 2.667969 GCGAGGAATCAAAATGCCAAAC 59.332 45.455 0.00 0.00 32.04 2.93
2702 3709 2.916716 CGAGGAATCAAAATGCCAAACG 59.083 45.455 0.00 0.00 32.04 3.60
2703 3710 3.253230 GAGGAATCAAAATGCCAAACGG 58.747 45.455 0.00 0.00 32.04 4.44
2704 3711 2.896685 AGGAATCAAAATGCCAAACGGA 59.103 40.909 0.00 0.00 32.04 4.69
2705 3712 3.056607 AGGAATCAAAATGCCAAACGGAG 60.057 43.478 0.00 0.00 32.04 4.63
2706 3713 3.056891 GGAATCAAAATGCCAAACGGAGA 60.057 43.478 0.00 0.00 29.64 3.71
2707 3714 3.575965 ATCAAAATGCCAAACGGAGAC 57.424 42.857 0.00 0.00 0.00 3.36
2708 3715 1.611491 TCAAAATGCCAAACGGAGACC 59.389 47.619 0.00 0.00 0.00 3.85
2709 3716 1.339610 CAAAATGCCAAACGGAGACCA 59.660 47.619 0.00 0.00 0.00 4.02
2710 3717 1.698506 AAATGCCAAACGGAGACCAA 58.301 45.000 0.00 0.00 0.00 3.67
2711 3718 1.247567 AATGCCAAACGGAGACCAAG 58.752 50.000 0.00 0.00 0.00 3.61
2712 3719 1.244019 ATGCCAAACGGAGACCAAGC 61.244 55.000 0.00 0.00 0.00 4.01
2713 3720 1.600916 GCCAAACGGAGACCAAGCT 60.601 57.895 0.00 0.00 0.00 3.74
2714 3721 1.578206 GCCAAACGGAGACCAAGCTC 61.578 60.000 0.00 0.00 0.00 4.09
2721 3728 3.776616 GAGACCAAGCTCCATGGAG 57.223 57.895 33.73 33.73 44.56 3.86
2722 3729 0.179936 GAGACCAAGCTCCATGGAGG 59.820 60.000 36.92 26.01 42.19 4.30
2723 3730 1.452833 GACCAAGCTCCATGGAGGC 60.453 63.158 36.92 28.76 42.19 4.70
2724 3731 2.123982 CCAAGCTCCATGGAGGCC 60.124 66.667 36.92 23.97 42.19 5.19
2725 3732 2.687610 CCAAGCTCCATGGAGGCCT 61.688 63.158 36.92 25.64 42.19 5.19
2726 3733 1.305623 CAAGCTCCATGGAGGCCTT 59.694 57.895 36.92 29.06 42.19 4.35
2727 3734 0.324091 CAAGCTCCATGGAGGCCTTT 60.324 55.000 36.92 19.63 42.19 3.11
2728 3735 1.064463 CAAGCTCCATGGAGGCCTTTA 60.064 52.381 36.92 4.58 42.19 1.85
2729 3736 1.527457 AGCTCCATGGAGGCCTTTAT 58.473 50.000 36.92 14.36 42.19 1.40
2730 3737 1.855599 AGCTCCATGGAGGCCTTTATT 59.144 47.619 36.92 13.75 42.19 1.40
2731 3738 2.245806 AGCTCCATGGAGGCCTTTATTT 59.754 45.455 36.92 13.14 42.19 1.40
2732 3739 2.363359 GCTCCATGGAGGCCTTTATTTG 59.637 50.000 36.92 13.51 42.19 2.32
2733 3740 3.902218 CTCCATGGAGGCCTTTATTTGA 58.098 45.455 31.14 3.17 38.51 2.69
2734 3741 4.280819 CTCCATGGAGGCCTTTATTTGAA 58.719 43.478 31.14 0.00 38.51 2.69
2735 3742 4.682563 TCCATGGAGGCCTTTATTTGAAA 58.317 39.130 11.44 0.00 37.29 2.69
2736 3743 5.090139 TCCATGGAGGCCTTTATTTGAAAA 58.910 37.500 11.44 0.00 37.29 2.29
2737 3744 5.046663 TCCATGGAGGCCTTTATTTGAAAAC 60.047 40.000 11.44 0.00 37.29 2.43
2738 3745 5.046376 CCATGGAGGCCTTTATTTGAAAACT 60.046 40.000 6.77 0.00 0.00 2.66
2739 3746 6.466812 CATGGAGGCCTTTATTTGAAAACTT 58.533 36.000 6.77 0.00 0.00 2.66
2740 3747 6.493189 TGGAGGCCTTTATTTGAAAACTTT 57.507 33.333 6.77 0.00 0.00 2.66
2741 3748 7.604657 TGGAGGCCTTTATTTGAAAACTTTA 57.395 32.000 6.77 0.00 0.00 1.85
2742 3749 8.024145 TGGAGGCCTTTATTTGAAAACTTTAA 57.976 30.769 6.77 0.00 0.00 1.52
2743 3750 8.487028 TGGAGGCCTTTATTTGAAAACTTTAAA 58.513 29.630 6.77 0.00 0.00 1.52
2744 3751 9.332502 GGAGGCCTTTATTTGAAAACTTTAAAA 57.667 29.630 6.77 0.00 0.00 1.52
2818 3825 7.872993 ACCTAGATACATAATGTACATGTGTGC 59.127 37.037 25.77 19.80 35.42 4.57
2819 3826 7.872483 CCTAGATACATAATGTACATGTGTGCA 59.128 37.037 25.77 14.40 44.32 4.57
2820 3827 9.260002 CTAGATACATAATGTACATGTGTGCAA 57.740 33.333 25.77 13.89 43.49 4.08
2821 3828 8.504812 AGATACATAATGTACATGTGTGCAAA 57.495 30.769 25.77 13.64 43.49 3.68
2822 3829 9.123902 AGATACATAATGTACATGTGTGCAAAT 57.876 29.630 25.77 16.51 43.49 2.32
2823 3830 9.734620 GATACATAATGTACATGTGTGCAAATT 57.265 29.630 25.77 6.78 43.49 1.82
2825 3832 8.830201 ACATAATGTACATGTGTGCAAATTTT 57.170 26.923 20.33 1.42 43.49 1.82
2826 3833 9.920133 ACATAATGTACATGTGTGCAAATTTTA 57.080 25.926 20.33 3.42 43.49 1.52
2829 3836 7.830940 ATGTACATGTGTGCAAATTTTATGG 57.169 32.000 7.78 0.00 43.49 2.74
2830 3837 5.636965 TGTACATGTGTGCAAATTTTATGGC 59.363 36.000 9.11 0.00 37.70 4.40
2831 3838 4.002316 ACATGTGTGCAAATTTTATGGCC 58.998 39.130 0.00 0.00 0.00 5.36
2832 3839 2.681706 TGTGTGCAAATTTTATGGCCG 58.318 42.857 0.00 0.00 0.00 6.13
2833 3840 2.297315 TGTGTGCAAATTTTATGGCCGA 59.703 40.909 0.00 0.00 0.00 5.54
2834 3841 3.243873 TGTGTGCAAATTTTATGGCCGAA 60.244 39.130 0.00 0.00 0.00 4.30
2835 3842 3.743396 GTGTGCAAATTTTATGGCCGAAA 59.257 39.130 0.00 0.00 0.00 3.46
2836 3843 4.391523 GTGTGCAAATTTTATGGCCGAAAT 59.608 37.500 0.00 1.77 0.00 2.17
2837 3844 5.578727 GTGTGCAAATTTTATGGCCGAAATA 59.421 36.000 10.74 0.00 0.00 1.40
2838 3845 5.578727 TGTGCAAATTTTATGGCCGAAATAC 59.421 36.000 10.74 7.12 0.00 1.89
2839 3846 5.578727 GTGCAAATTTTATGGCCGAAATACA 59.421 36.000 10.74 7.95 0.00 2.29
2840 3847 6.257630 GTGCAAATTTTATGGCCGAAATACAT 59.742 34.615 10.74 0.00 0.00 2.29
2841 3848 6.820656 TGCAAATTTTATGGCCGAAATACATT 59.179 30.769 10.74 3.31 0.00 2.71
2842 3849 7.981789 TGCAAATTTTATGGCCGAAATACATTA 59.018 29.630 10.74 0.00 0.00 1.90
2843 3850 8.821894 GCAAATTTTATGGCCGAAATACATTAA 58.178 29.630 10.74 0.00 0.00 1.40
2885 3892 8.648557 AAAAGACAAATCTGGAGCTTTTTAAC 57.351 30.769 0.00 0.00 34.48 2.01
2886 3893 6.959639 AGACAAATCTGGAGCTTTTTAACA 57.040 33.333 0.00 0.00 32.29 2.41
2887 3894 7.530426 AGACAAATCTGGAGCTTTTTAACAT 57.470 32.000 0.00 0.00 32.29 2.71
2888 3895 8.635765 AGACAAATCTGGAGCTTTTTAACATA 57.364 30.769 0.00 0.00 32.29 2.29
2889 3896 9.247861 AGACAAATCTGGAGCTTTTTAACATAT 57.752 29.630 0.00 0.00 32.29 1.78
2890 3897 9.294030 GACAAATCTGGAGCTTTTTAACATATG 57.706 33.333 0.00 0.00 0.00 1.78
2891 3898 8.806146 ACAAATCTGGAGCTTTTTAACATATGT 58.194 29.630 1.41 1.41 0.00 2.29
2894 3901 9.686683 AATCTGGAGCTTTTTAACATATGTACT 57.313 29.630 9.21 0.00 0.00 2.73
2895 3902 8.492673 TCTGGAGCTTTTTAACATATGTACTG 57.507 34.615 9.21 0.00 0.00 2.74
2896 3903 8.100791 TCTGGAGCTTTTTAACATATGTACTGT 58.899 33.333 9.21 0.00 0.00 3.55
2897 3904 8.630054 TGGAGCTTTTTAACATATGTACTGTT 57.370 30.769 9.21 4.60 39.93 3.16
2898 3905 8.726988 TGGAGCTTTTTAACATATGTACTGTTC 58.273 33.333 9.21 4.58 37.89 3.18
2899 3906 8.726988 GGAGCTTTTTAACATATGTACTGTTCA 58.273 33.333 9.21 0.00 37.89 3.18
2914 3921 8.322906 TGTACTGTTCATCTTAAAAGTCCATG 57.677 34.615 0.00 0.00 0.00 3.66
2915 3922 8.154203 TGTACTGTTCATCTTAAAAGTCCATGA 58.846 33.333 0.00 0.00 0.00 3.07
2916 3923 9.167311 GTACTGTTCATCTTAAAAGTCCATGAT 57.833 33.333 0.00 0.00 0.00 2.45
2917 3924 8.641498 ACTGTTCATCTTAAAAGTCCATGATT 57.359 30.769 0.00 0.00 0.00 2.57
2918 3925 9.082313 ACTGTTCATCTTAAAAGTCCATGATTT 57.918 29.630 0.00 0.00 0.00 2.17
2919 3926 9.918630 CTGTTCATCTTAAAAGTCCATGATTTT 57.081 29.630 0.00 1.51 33.42 1.82
2920 3927 9.695526 TGTTCATCTTAAAAGTCCATGATTTTG 57.304 29.630 0.00 0.00 31.41 2.44
2921 3928 9.696917 GTTCATCTTAAAAGTCCATGATTTTGT 57.303 29.630 0.00 0.00 31.41 2.83
2942 3949 1.654220 TTTTTCTGTGCAGCTCGCC 59.346 52.632 5.82 0.00 41.33 5.54
2943 3950 2.116736 TTTTTCTGTGCAGCTCGCCG 62.117 55.000 5.82 0.00 41.33 6.46
2944 3951 3.807631 TTTCTGTGCAGCTCGCCGT 62.808 57.895 5.82 0.00 41.33 5.68
2945 3952 3.807631 TTCTGTGCAGCTCGCCGTT 62.808 57.895 5.82 0.00 41.33 4.44
2946 3953 3.782244 CTGTGCAGCTCGCCGTTC 61.782 66.667 5.82 0.00 41.33 3.95
2947 3954 4.600576 TGTGCAGCTCGCCGTTCA 62.601 61.111 5.82 0.00 41.33 3.18
2948 3955 3.345808 GTGCAGCTCGCCGTTCAA 61.346 61.111 5.82 0.00 41.33 2.69
2949 3956 2.358615 TGCAGCTCGCCGTTCAAT 60.359 55.556 5.82 0.00 41.33 2.57
2950 3957 2.099062 GCAGCTCGCCGTTCAATG 59.901 61.111 0.00 0.00 32.94 2.82
2951 3958 2.680913 GCAGCTCGCCGTTCAATGT 61.681 57.895 0.00 0.00 32.94 2.71
2952 3959 1.358725 GCAGCTCGCCGTTCAATGTA 61.359 55.000 0.00 0.00 32.94 2.29
2953 3960 1.290203 CAGCTCGCCGTTCAATGTAT 58.710 50.000 0.00 0.00 0.00 2.29
2954 3961 1.665679 CAGCTCGCCGTTCAATGTATT 59.334 47.619 0.00 0.00 0.00 1.89
2955 3962 2.095853 CAGCTCGCCGTTCAATGTATTT 59.904 45.455 0.00 0.00 0.00 1.40
2956 3963 2.351726 AGCTCGCCGTTCAATGTATTTC 59.648 45.455 0.00 0.00 0.00 2.17
2957 3964 2.095213 GCTCGCCGTTCAATGTATTTCA 59.905 45.455 0.00 0.00 0.00 2.69
2958 3965 3.242739 GCTCGCCGTTCAATGTATTTCAT 60.243 43.478 0.00 0.00 38.57 2.57
2959 3966 4.518217 CTCGCCGTTCAATGTATTTCATC 58.482 43.478 0.00 0.00 35.48 2.92
2960 3967 3.311322 TCGCCGTTCAATGTATTTCATCC 59.689 43.478 0.00 0.00 35.48 3.51
2961 3968 3.312421 CGCCGTTCAATGTATTTCATCCT 59.688 43.478 0.00 0.00 35.48 3.24
2962 3969 4.601019 GCCGTTCAATGTATTTCATCCTG 58.399 43.478 0.00 0.00 35.48 3.86
2963 3970 4.335315 GCCGTTCAATGTATTTCATCCTGA 59.665 41.667 0.00 0.00 35.48 3.86
2964 3971 5.163663 GCCGTTCAATGTATTTCATCCTGAA 60.164 40.000 0.00 0.00 35.48 3.02
2979 3986 9.474920 TTTCATCCTGAAAATTTTCACACATAC 57.525 29.630 26.01 2.67 42.72 2.39
2980 3987 8.175925 TCATCCTGAAAATTTTCACACATACA 57.824 30.769 26.01 6.95 41.88 2.29
2981 3988 8.081633 TCATCCTGAAAATTTTCACACATACAC 58.918 33.333 26.01 1.31 41.88 2.90
2982 3989 7.581213 TCCTGAAAATTTTCACACATACACT 57.419 32.000 26.01 0.00 41.88 3.55
2983 3990 8.006298 TCCTGAAAATTTTCACACATACACTT 57.994 30.769 26.01 0.00 41.88 3.16
2984 3991 8.474025 TCCTGAAAATTTTCACACATACACTTT 58.526 29.630 26.01 0.00 41.88 2.66
2985 3992 9.743057 CCTGAAAATTTTCACACATACACTTTA 57.257 29.630 26.01 4.03 41.88 1.85
2990 3997 9.691362 AAATTTTCACACATACACTTTACATCC 57.309 29.630 0.00 0.00 0.00 3.51
2991 3998 8.635765 ATTTTCACACATACACTTTACATCCT 57.364 30.769 0.00 0.00 0.00 3.24
2992 3999 8.458573 TTTTCACACATACACTTTACATCCTT 57.541 30.769 0.00 0.00 0.00 3.36
2993 4000 7.433708 TTCACACATACACTTTACATCCTTG 57.566 36.000 0.00 0.00 0.00 3.61
2994 4001 5.411361 TCACACATACACTTTACATCCTTGC 59.589 40.000 0.00 0.00 0.00 4.01
2995 4002 5.181056 CACACATACACTTTACATCCTTGCA 59.819 40.000 0.00 0.00 0.00 4.08
2996 4003 5.945784 ACACATACACTTTACATCCTTGCAT 59.054 36.000 0.00 0.00 0.00 3.96
2997 4004 7.065683 CACACATACACTTTACATCCTTGCATA 59.934 37.037 0.00 0.00 0.00 3.14
2998 4005 7.065803 ACACATACACTTTACATCCTTGCATAC 59.934 37.037 0.00 0.00 0.00 2.39
2999 4006 7.065683 CACATACACTTTACATCCTTGCATACA 59.934 37.037 0.00 0.00 0.00 2.29
3000 4007 7.775093 ACATACACTTTACATCCTTGCATACAT 59.225 33.333 0.00 0.00 0.00 2.29
3001 4008 6.441093 ACACTTTACATCCTTGCATACATG 57.559 37.500 0.00 0.00 0.00 3.21
3002 4009 5.945784 ACACTTTACATCCTTGCATACATGT 59.054 36.000 2.69 2.69 33.95 3.21
3003 4010 6.127925 ACACTTTACATCCTTGCATACATGTG 60.128 38.462 9.11 0.00 31.83 3.21
3004 4011 5.945784 ACTTTACATCCTTGCATACATGTGT 59.054 36.000 9.11 0.00 31.83 3.72
3005 4012 7.065683 CACTTTACATCCTTGCATACATGTGTA 59.934 37.037 9.11 0.00 31.83 2.90
3006 4013 7.609918 ACTTTACATCCTTGCATACATGTGTAA 59.390 33.333 9.11 1.48 33.76 2.41
3007 4014 8.518430 TTTACATCCTTGCATACATGTGTAAT 57.482 30.769 9.11 0.00 32.76 1.89
3008 4015 8.518430 TTACATCCTTGCATACATGTGTAATT 57.482 30.769 9.11 0.00 33.76 1.40
3009 4016 7.408756 ACATCCTTGCATACATGTGTAATTT 57.591 32.000 9.11 0.00 33.76 1.82
3010 4017 7.839907 ACATCCTTGCATACATGTGTAATTTT 58.160 30.769 9.11 0.00 33.76 1.82
3011 4018 8.313292 ACATCCTTGCATACATGTGTAATTTTT 58.687 29.630 9.11 0.00 33.76 1.94
3039 4046 9.418045 GGAATTTTCCGAAACTGAAATTTATGA 57.582 29.630 0.00 0.00 37.65 2.15
3046 4053 9.973450 TCCGAAACTGAAATTTATGAATTTTGA 57.027 25.926 9.33 0.36 43.61 2.69
3072 4079 5.419239 TTTCAAAATAAAGGGCTCCATGG 57.581 39.130 4.97 4.97 0.00 3.66
3073 4080 4.329638 TCAAAATAAAGGGCTCCATGGA 57.670 40.909 15.27 15.27 0.00 3.41
3074 4081 4.280819 TCAAAATAAAGGGCTCCATGGAG 58.719 43.478 33.73 33.73 44.56 3.86
3082 4089 3.947173 CTCCATGGAGCTCGGTCT 58.053 61.111 28.45 0.00 35.31 3.85
3083 4090 1.739049 CTCCATGGAGCTCGGTCTC 59.261 63.158 28.45 0.00 35.31 3.36
3091 4098 0.729690 GAGCTCGGTCTCCAAAATGC 59.270 55.000 0.00 0.00 0.00 3.56
3092 4099 0.678048 AGCTCGGTCTCCAAAATGCC 60.678 55.000 0.00 0.00 0.00 4.40
3093 4100 1.657751 GCTCGGTCTCCAAAATGCCC 61.658 60.000 0.00 0.00 0.00 5.36
3094 4101 0.035056 CTCGGTCTCCAAAATGCCCT 60.035 55.000 0.00 0.00 0.00 5.19
3095 4102 1.209504 CTCGGTCTCCAAAATGCCCTA 59.790 52.381 0.00 0.00 0.00 3.53
3096 4103 1.065709 TCGGTCTCCAAAATGCCCTAC 60.066 52.381 0.00 0.00 0.00 3.18
3097 4104 1.065418 CGGTCTCCAAAATGCCCTACT 60.065 52.381 0.00 0.00 0.00 2.57
3098 4105 2.644676 GGTCTCCAAAATGCCCTACTC 58.355 52.381 0.00 0.00 0.00 2.59
3099 4106 2.280628 GTCTCCAAAATGCCCTACTCG 58.719 52.381 0.00 0.00 0.00 4.18
3100 4107 1.017387 CTCCAAAATGCCCTACTCGC 58.983 55.000 0.00 0.00 0.00 5.03
3101 4108 0.742990 TCCAAAATGCCCTACTCGCG 60.743 55.000 0.00 0.00 0.00 5.87
3102 4109 0.742990 CCAAAATGCCCTACTCGCGA 60.743 55.000 9.26 9.26 0.00 5.87
3103 4110 0.652592 CAAAATGCCCTACTCGCGAG 59.347 55.000 33.45 33.45 0.00 5.03
3104 4111 0.462047 AAAATGCCCTACTCGCGAGG 60.462 55.000 36.93 22.96 0.00 4.63
3105 4112 1.327690 AAATGCCCTACTCGCGAGGA 61.328 55.000 36.93 30.28 35.99 3.71
3106 4113 1.327690 AATGCCCTACTCGCGAGGAA 61.328 55.000 36.93 24.20 35.99 3.36
3107 4114 1.115930 ATGCCCTACTCGCGAGGAAT 61.116 55.000 36.93 19.58 35.99 3.01
3108 4115 1.300233 GCCCTACTCGCGAGGAATG 60.300 63.158 36.93 23.88 35.99 2.67
3109 4116 1.300233 CCCTACTCGCGAGGAATGC 60.300 63.158 36.93 0.00 35.99 3.56
3110 4117 1.300233 CCTACTCGCGAGGAATGCC 60.300 63.158 36.93 0.00 35.99 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.697507 ACTAGGAAAATCATGGGCTAAATAAG 57.302 34.615 0.00 0.00 0.00 1.73
147 148 4.825422 GCAATGGCATGCTAGATACTCTA 58.175 43.478 18.92 0.00 43.06 2.43
148 149 3.672808 GCAATGGCATGCTAGATACTCT 58.327 45.455 18.92 0.00 43.06 3.24
191 192 7.065324 TGCATGCTAGGTACATAAAACTTGTAC 59.935 37.037 20.33 5.61 45.57 2.90
192 193 7.065324 GTGCATGCTAGGTACATAAAACTTGTA 59.935 37.037 20.33 0.00 0.00 2.41
193 194 5.943416 TGCATGCTAGGTACATAAAACTTGT 59.057 36.000 20.33 0.00 0.00 3.16
484 491 1.937350 TCCCAGGTCCTCAGGAGATAA 59.063 52.381 0.00 0.00 29.39 1.75
513 520 1.293924 CATCCTGAAGTAGCAAGGCG 58.706 55.000 0.00 0.00 0.00 5.52
579 586 4.522789 GCCTACATGTTTGGAAGGAGAAAA 59.477 41.667 14.60 0.00 33.90 2.29
632 672 4.466827 TCTCGCTATGGACTAACATACCA 58.533 43.478 0.00 0.00 38.09 3.25
633 673 5.221130 GTTCTCGCTATGGACTAACATACC 58.779 45.833 0.00 0.00 32.39 2.73
641 681 5.133941 TCTCTATTGTTCTCGCTATGGACT 58.866 41.667 0.00 0.00 0.00 3.85
800 971 4.626604 ACAAAAAGTGACACACAAGCAATG 59.373 37.500 8.59 0.00 36.74 2.82
801 972 4.819769 ACAAAAAGTGACACACAAGCAAT 58.180 34.783 8.59 0.00 36.74 3.56
802 973 4.250116 ACAAAAAGTGACACACAAGCAA 57.750 36.364 8.59 0.00 36.74 3.91
803 974 3.932545 ACAAAAAGTGACACACAAGCA 57.067 38.095 8.59 0.00 36.74 3.91
804 975 4.233789 TCAACAAAAAGTGACACACAAGC 58.766 39.130 8.59 0.00 36.74 4.01
805 976 5.118510 GGTTCAACAAAAAGTGACACACAAG 59.881 40.000 8.59 0.00 36.74 3.16
806 977 4.985409 GGTTCAACAAAAAGTGACACACAA 59.015 37.500 8.59 0.00 36.74 3.33
807 978 4.038042 TGGTTCAACAAAAAGTGACACACA 59.962 37.500 8.59 0.00 36.74 3.72
852 1023 1.169661 TTGATGTGCGTTGGGTGGTC 61.170 55.000 0.00 0.00 0.00 4.02
853 1024 1.152860 TTGATGTGCGTTGGGTGGT 60.153 52.632 0.00 0.00 0.00 4.16
854 1025 1.172180 ACTTGATGTGCGTTGGGTGG 61.172 55.000 0.00 0.00 0.00 4.61
856 1027 2.330254 CACTTGATGTGCGTTGGGT 58.670 52.632 0.00 0.00 40.06 4.51
865 1036 3.577848 TGCTTTATTTGGGCACTTGATGT 59.422 39.130 0.00 0.00 0.00 3.06
866 1037 4.082081 TCTGCTTTATTTGGGCACTTGATG 60.082 41.667 0.00 0.00 32.33 3.07
872 1043 5.237048 TGAAAATCTGCTTTATTTGGGCAC 58.763 37.500 0.00 0.00 32.33 5.01
873 1044 5.480642 TGAAAATCTGCTTTATTTGGGCA 57.519 34.783 0.00 0.00 34.66 5.36
874 1045 6.990341 ATTGAAAATCTGCTTTATTTGGGC 57.010 33.333 0.00 0.00 0.00 5.36
875 1046 8.550710 TCAATTGAAAATCTGCTTTATTTGGG 57.449 30.769 5.45 0.00 0.00 4.12
991 1911 8.416329 CACCTTCTTAGAATCCATTTTTATGGG 58.584 37.037 4.46 0.00 41.95 4.00
1248 2176 1.086696 GCGGCAAGAATGTAAGAGCA 58.913 50.000 0.00 0.00 0.00 4.26
1392 2320 4.838423 TGAGTATCAGGAACAGGAAGTGAA 59.162 41.667 0.00 0.00 42.56 3.18
1806 2765 0.655733 GCAATTGTATGACCGGACCG 59.344 55.000 9.46 6.99 0.00 4.79
1807 2766 1.670811 CTGCAATTGTATGACCGGACC 59.329 52.381 9.46 0.00 0.00 4.46
1808 2767 2.356135 ACTGCAATTGTATGACCGGAC 58.644 47.619 9.46 1.07 0.00 4.79
1809 2768 2.779755 ACTGCAATTGTATGACCGGA 57.220 45.000 9.46 0.00 0.00 5.14
1810 2769 3.848272 AAACTGCAATTGTATGACCGG 57.152 42.857 7.40 0.00 0.00 5.28
2116 3087 5.956068 ATGCTCAAAAGAGGAAAGAACTC 57.044 39.130 0.00 0.00 35.20 3.01
2123 3094 6.114187 TCTTGTCTATGCTCAAAAGAGGAA 57.886 37.500 0.00 0.00 0.00 3.36
2149 3120 9.905713 TCAGCTAGAACCAGAATAATTAACAAT 57.094 29.630 0.00 0.00 0.00 2.71
2163 3134 4.632153 GAGTTTCTTGTCAGCTAGAACCA 58.368 43.478 0.00 0.00 36.49 3.67
2215 3186 7.232188 TGTTACCAACCTAATCCATTGTTGTA 58.768 34.615 0.00 0.00 37.08 2.41
2216 3187 6.071984 TGTTACCAACCTAATCCATTGTTGT 58.928 36.000 0.00 0.00 37.08 3.32
2217 3188 6.582677 TGTTACCAACCTAATCCATTGTTG 57.417 37.500 0.00 0.00 38.20 3.33
2218 3189 6.154363 CCATGTTACCAACCTAATCCATTGTT 59.846 38.462 0.00 0.00 0.00 2.83
2219 3190 5.656416 CCATGTTACCAACCTAATCCATTGT 59.344 40.000 0.00 0.00 0.00 2.71
2220 3191 5.656416 ACCATGTTACCAACCTAATCCATTG 59.344 40.000 0.00 0.00 0.00 2.82
2221 3192 5.656416 CACCATGTTACCAACCTAATCCATT 59.344 40.000 0.00 0.00 0.00 3.16
2222 3193 5.200483 CACCATGTTACCAACCTAATCCAT 58.800 41.667 0.00 0.00 0.00 3.41
2223 3194 4.043561 ACACCATGTTACCAACCTAATCCA 59.956 41.667 0.00 0.00 0.00 3.41
2224 3195 4.595986 ACACCATGTTACCAACCTAATCC 58.404 43.478 0.00 0.00 0.00 3.01
2225 3196 5.475564 ACAACACCATGTTACCAACCTAATC 59.524 40.000 0.00 0.00 38.77 1.75
2226 3197 5.390387 ACAACACCATGTTACCAACCTAAT 58.610 37.500 0.00 0.00 38.77 1.73
2227 3198 4.794334 ACAACACCATGTTACCAACCTAA 58.206 39.130 0.00 0.00 38.77 2.69
2228 3199 4.440826 ACAACACCATGTTACCAACCTA 57.559 40.909 0.00 0.00 38.77 3.08
2229 3200 3.306472 ACAACACCATGTTACCAACCT 57.694 42.857 0.00 0.00 38.77 3.50
2230 3201 3.131400 ACAACAACACCATGTTACCAACC 59.869 43.478 0.00 0.00 41.44 3.77
2231 3202 4.379339 ACAACAACACCATGTTACCAAC 57.621 40.909 0.00 0.00 41.44 3.77
2232 3203 4.948004 TGTACAACAACACCATGTTACCAA 59.052 37.500 0.00 0.00 41.44 3.67
2233 3204 4.524053 TGTACAACAACACCATGTTACCA 58.476 39.130 0.00 0.00 41.44 3.25
2234 3205 5.502153 TTGTACAACAACACCATGTTACC 57.498 39.130 3.59 0.00 41.44 2.85
2235 3206 7.640852 TGTATTGTACAACAACACCATGTTAC 58.359 34.615 11.22 5.64 41.40 2.50
2236 3207 7.803279 TGTATTGTACAACAACACCATGTTA 57.197 32.000 11.22 0.00 41.40 2.41
2237 3208 6.701145 TGTATTGTACAACAACACCATGTT 57.299 33.333 11.22 0.00 41.40 2.71
2238 3209 6.701145 TTGTATTGTACAACAACACCATGT 57.299 33.333 19.89 1.61 43.23 3.21
2250 3221 7.406916 ACCAACCTAATCCATTGTATTGTACA 58.593 34.615 0.00 0.00 36.79 2.90
2251 3222 7.875327 ACCAACCTAATCCATTGTATTGTAC 57.125 36.000 0.00 0.00 0.00 2.90
2331 3306 3.953612 TGCATAAGTTAGAATGGCCCTTG 59.046 43.478 0.00 0.00 0.00 3.61
2494 3498 4.096681 AGTGTCAGTGAATCCTCCACATA 58.903 43.478 10.77 0.00 37.01 2.29
2527 3531 6.707711 CAAAAACATTGTTCACATTGGACAG 58.292 36.000 1.83 0.00 33.04 3.51
2580 3587 0.179225 GCGTGCACCGTGTCAAATAG 60.179 55.000 12.15 0.00 39.32 1.73
2616 3623 6.312399 TGCTAAAGTGTGAAATTGTACAGG 57.688 37.500 0.00 0.00 0.00 4.00
2689 3696 1.339610 TGGTCTCCGTTTGGCATTTTG 59.660 47.619 0.00 0.00 34.14 2.44
2690 3697 1.698506 TGGTCTCCGTTTGGCATTTT 58.301 45.000 0.00 0.00 34.14 1.82
2691 3698 1.613437 CTTGGTCTCCGTTTGGCATTT 59.387 47.619 0.00 0.00 34.14 2.32
2692 3699 1.247567 CTTGGTCTCCGTTTGGCATT 58.752 50.000 0.00 0.00 34.14 3.56
2693 3700 1.244019 GCTTGGTCTCCGTTTGGCAT 61.244 55.000 0.00 0.00 34.14 4.40
2694 3701 1.896660 GCTTGGTCTCCGTTTGGCA 60.897 57.895 0.00 0.00 34.14 4.92
2695 3702 1.578206 GAGCTTGGTCTCCGTTTGGC 61.578 60.000 0.00 0.00 34.14 4.52
2696 3703 0.955919 GGAGCTTGGTCTCCGTTTGG 60.956 60.000 0.00 0.00 42.74 3.28
2697 3704 2.544726 GGAGCTTGGTCTCCGTTTG 58.455 57.895 0.00 0.00 42.74 2.93
2703 3710 0.179936 CCTCCATGGAGCTTGGTCTC 59.820 60.000 32.97 0.00 40.69 3.36
2704 3711 1.919600 GCCTCCATGGAGCTTGGTCT 61.920 60.000 32.97 0.00 40.69 3.85
2705 3712 1.452833 GCCTCCATGGAGCTTGGTC 60.453 63.158 32.97 14.43 40.69 4.02
2706 3713 2.679716 GCCTCCATGGAGCTTGGT 59.320 61.111 32.97 0.00 40.69 3.67
2707 3714 2.123982 GGCCTCCATGGAGCTTGG 60.124 66.667 32.97 22.55 40.69 3.61
2708 3715 0.324091 AAAGGCCTCCATGGAGCTTG 60.324 55.000 32.97 21.57 40.69 4.01
2709 3716 1.298953 TAAAGGCCTCCATGGAGCTT 58.701 50.000 32.97 26.98 40.69 3.74
2710 3717 1.527457 ATAAAGGCCTCCATGGAGCT 58.473 50.000 32.97 23.24 40.69 4.09
2711 3718 2.363359 CAAATAAAGGCCTCCATGGAGC 59.637 50.000 32.97 26.44 40.69 4.70
2712 3719 3.902218 TCAAATAAAGGCCTCCATGGAG 58.098 45.455 31.69 31.69 41.63 3.86
2713 3720 4.329638 TTCAAATAAAGGCCTCCATGGA 57.670 40.909 15.27 15.27 38.35 3.41
2714 3721 5.046376 AGTTTTCAAATAAAGGCCTCCATGG 60.046 40.000 5.23 4.97 39.35 3.66
2715 3722 6.041423 AGTTTTCAAATAAAGGCCTCCATG 57.959 37.500 5.23 1.29 0.00 3.66
2716 3723 6.686484 AAGTTTTCAAATAAAGGCCTCCAT 57.314 33.333 5.23 0.00 0.00 3.41
2717 3724 6.493189 AAAGTTTTCAAATAAAGGCCTCCA 57.507 33.333 5.23 0.00 0.00 3.86
2718 3725 8.896320 TTTAAAGTTTTCAAATAAAGGCCTCC 57.104 30.769 5.23 0.00 0.00 4.30
2792 3799 7.872993 GCACACATGTACATTATGTATCTAGGT 59.127 37.037 17.98 4.03 36.67 3.08
2793 3800 7.872483 TGCACACATGTACATTATGTATCTAGG 59.128 37.037 17.98 9.14 36.67 3.02
2794 3801 8.816640 TGCACACATGTACATTATGTATCTAG 57.183 34.615 17.98 9.67 36.67 2.43
2795 3802 9.606631 TTTGCACACATGTACATTATGTATCTA 57.393 29.630 17.98 9.97 36.67 1.98
2796 3803 8.504812 TTTGCACACATGTACATTATGTATCT 57.495 30.769 17.98 0.00 36.67 1.98
2797 3804 9.734620 AATTTGCACACATGTACATTATGTATC 57.265 29.630 17.98 14.10 36.67 2.24
2799 3806 9.920133 AAAATTTGCACACATGTACATTATGTA 57.080 25.926 17.98 0.29 36.67 2.29
2800 3807 8.830201 AAAATTTGCACACATGTACATTATGT 57.170 26.923 14.24 14.24 39.23 2.29
2803 3810 9.363763 CCATAAAATTTGCACACATGTACATTA 57.636 29.630 5.37 0.00 0.00 1.90
2804 3811 7.148440 GCCATAAAATTTGCACACATGTACATT 60.148 33.333 5.37 0.00 0.00 2.71
2805 3812 6.313411 GCCATAAAATTTGCACACATGTACAT 59.687 34.615 1.41 1.41 0.00 2.29
2806 3813 5.636965 GCCATAAAATTTGCACACATGTACA 59.363 36.000 0.00 0.00 0.00 2.90
2807 3814 5.063312 GGCCATAAAATTTGCACACATGTAC 59.937 40.000 0.00 0.00 0.00 2.90
2808 3815 5.174395 GGCCATAAAATTTGCACACATGTA 58.826 37.500 0.00 0.00 0.00 2.29
2809 3816 4.002316 GGCCATAAAATTTGCACACATGT 58.998 39.130 0.00 0.00 0.00 3.21
2810 3817 3.062369 CGGCCATAAAATTTGCACACATG 59.938 43.478 2.24 0.00 0.00 3.21
2811 3818 3.056250 TCGGCCATAAAATTTGCACACAT 60.056 39.130 2.24 0.00 0.00 3.21
2812 3819 2.297315 TCGGCCATAAAATTTGCACACA 59.703 40.909 2.24 0.00 0.00 3.72
2813 3820 2.953020 TCGGCCATAAAATTTGCACAC 58.047 42.857 2.24 0.00 0.00 3.82
2814 3821 3.667497 TTCGGCCATAAAATTTGCACA 57.333 38.095 2.24 0.00 0.00 4.57
2815 3822 5.578727 TGTATTTCGGCCATAAAATTTGCAC 59.421 36.000 2.24 1.81 0.00 4.57
2816 3823 5.724328 TGTATTTCGGCCATAAAATTTGCA 58.276 33.333 2.24 3.75 0.00 4.08
2817 3824 6.843069 ATGTATTTCGGCCATAAAATTTGC 57.157 33.333 2.24 0.00 0.00 3.68
2859 3866 9.098355 GTTAAAAAGCTCCAGATTTGTCTTTTT 57.902 29.630 16.98 16.98 42.61 1.94
2860 3867 8.257306 TGTTAAAAAGCTCCAGATTTGTCTTTT 58.743 29.630 0.00 0.00 33.52 2.27
2861 3868 7.781056 TGTTAAAAAGCTCCAGATTTGTCTTT 58.219 30.769 0.00 0.00 33.52 2.52
2862 3869 7.346751 TGTTAAAAAGCTCCAGATTTGTCTT 57.653 32.000 0.00 0.00 33.52 3.01
2863 3870 6.959639 TGTTAAAAAGCTCCAGATTTGTCT 57.040 33.333 0.00 0.00 33.52 3.41
2864 3871 9.294030 CATATGTTAAAAAGCTCCAGATTTGTC 57.706 33.333 0.00 0.00 33.52 3.18
2865 3872 8.806146 ACATATGTTAAAAAGCTCCAGATTTGT 58.194 29.630 1.41 0.00 33.52 2.83
2868 3875 9.686683 AGTACATATGTTAAAAAGCTCCAGATT 57.313 29.630 14.77 0.00 0.00 2.40
2869 3876 9.113838 CAGTACATATGTTAAAAAGCTCCAGAT 57.886 33.333 14.77 0.00 0.00 2.90
2870 3877 8.100791 ACAGTACATATGTTAAAAAGCTCCAGA 58.899 33.333 14.77 0.00 0.00 3.86
2871 3878 8.268850 ACAGTACATATGTTAAAAAGCTCCAG 57.731 34.615 14.77 0.00 0.00 3.86
2872 3879 8.630054 AACAGTACATATGTTAAAAAGCTCCA 57.370 30.769 14.77 0.00 39.06 3.86
2873 3880 8.726988 TGAACAGTACATATGTTAAAAAGCTCC 58.273 33.333 14.77 0.00 40.86 4.70
2888 3895 8.950210 CATGGACTTTTAAGATGAACAGTACAT 58.050 33.333 0.00 0.00 36.43 2.29
2889 3896 8.154203 TCATGGACTTTTAAGATGAACAGTACA 58.846 33.333 0.00 0.00 29.71 2.90
2890 3897 8.547967 TCATGGACTTTTAAGATGAACAGTAC 57.452 34.615 0.00 0.00 0.00 2.73
2891 3898 9.739276 AATCATGGACTTTTAAGATGAACAGTA 57.261 29.630 0.00 0.00 0.00 2.74
2892 3899 8.641498 AATCATGGACTTTTAAGATGAACAGT 57.359 30.769 0.00 0.00 0.00 3.55
2893 3900 9.918630 AAAATCATGGACTTTTAAGATGAACAG 57.081 29.630 0.00 0.00 0.00 3.16
2894 3901 9.695526 CAAAATCATGGACTTTTAAGATGAACA 57.304 29.630 0.00 0.00 0.00 3.18
2895 3902 9.696917 ACAAAATCATGGACTTTTAAGATGAAC 57.303 29.630 0.00 0.00 0.00 3.18
2933 3940 1.358725 TACATTGAACGGCGAGCTGC 61.359 55.000 16.62 0.00 45.38 5.25
2934 3941 1.290203 ATACATTGAACGGCGAGCTG 58.710 50.000 16.62 6.03 0.00 4.24
2935 3942 2.024176 AATACATTGAACGGCGAGCT 57.976 45.000 16.62 0.00 0.00 4.09
2936 3943 2.095213 TGAAATACATTGAACGGCGAGC 59.905 45.455 16.62 5.20 0.00 5.03
2937 3944 4.518217 GATGAAATACATTGAACGGCGAG 58.482 43.478 16.62 0.00 39.56 5.03
2938 3945 3.311322 GGATGAAATACATTGAACGGCGA 59.689 43.478 16.62 0.00 39.56 5.54
2939 3946 3.312421 AGGATGAAATACATTGAACGGCG 59.688 43.478 4.80 4.80 39.56 6.46
2940 3947 4.335315 TCAGGATGAAATACATTGAACGGC 59.665 41.667 0.00 0.00 45.97 5.68
2955 3962 8.081633 GTGTATGTGTGAAAATTTTCAGGATGA 58.918 33.333 29.34 14.88 46.80 2.92
2956 3963 8.084073 AGTGTATGTGTGAAAATTTTCAGGATG 58.916 33.333 29.34 0.00 46.80 3.51
2957 3964 8.181904 AGTGTATGTGTGAAAATTTTCAGGAT 57.818 30.769 29.34 22.21 46.80 3.24
2958 3965 7.581213 AGTGTATGTGTGAAAATTTTCAGGA 57.419 32.000 29.34 18.15 46.80 3.86
2959 3966 8.647143 AAAGTGTATGTGTGAAAATTTTCAGG 57.353 30.769 29.34 0.00 46.80 3.86
2964 3971 9.691362 GGATGTAAAGTGTATGTGTGAAAATTT 57.309 29.630 0.00 0.00 0.00 1.82
2965 3972 9.077885 AGGATGTAAAGTGTATGTGTGAAAATT 57.922 29.630 0.00 0.00 0.00 1.82
2966 3973 8.635765 AGGATGTAAAGTGTATGTGTGAAAAT 57.364 30.769 0.00 0.00 0.00 1.82
2967 3974 8.349245 CAAGGATGTAAAGTGTATGTGTGAAAA 58.651 33.333 0.00 0.00 0.00 2.29
2968 3975 7.521423 GCAAGGATGTAAAGTGTATGTGTGAAA 60.521 37.037 0.00 0.00 0.00 2.69
2969 3976 6.072728 GCAAGGATGTAAAGTGTATGTGTGAA 60.073 38.462 0.00 0.00 0.00 3.18
2970 3977 5.411361 GCAAGGATGTAAAGTGTATGTGTGA 59.589 40.000 0.00 0.00 0.00 3.58
2971 3978 5.181056 TGCAAGGATGTAAAGTGTATGTGTG 59.819 40.000 0.00 0.00 0.00 3.82
2972 3979 5.312895 TGCAAGGATGTAAAGTGTATGTGT 58.687 37.500 0.00 0.00 0.00 3.72
2973 3980 5.878332 TGCAAGGATGTAAAGTGTATGTG 57.122 39.130 0.00 0.00 0.00 3.21
2974 3981 7.109501 TGTATGCAAGGATGTAAAGTGTATGT 58.890 34.615 0.00 0.00 0.00 2.29
2975 3982 7.552458 TGTATGCAAGGATGTAAAGTGTATG 57.448 36.000 0.00 0.00 0.00 2.39
2976 3983 7.775093 ACATGTATGCAAGGATGTAAAGTGTAT 59.225 33.333 0.00 0.00 0.00 2.29
2977 3984 7.065683 CACATGTATGCAAGGATGTAAAGTGTA 59.934 37.037 0.00 0.00 0.00 2.90
2978 3985 5.945784 ACATGTATGCAAGGATGTAAAGTGT 59.054 36.000 0.00 0.00 0.00 3.55
2979 3986 6.127925 ACACATGTATGCAAGGATGTAAAGTG 60.128 38.462 0.00 0.00 0.00 3.16
2980 3987 5.945784 ACACATGTATGCAAGGATGTAAAGT 59.054 36.000 0.00 1.15 0.00 2.66
2981 3988 6.441093 ACACATGTATGCAAGGATGTAAAG 57.559 37.500 0.00 0.66 0.00 1.85
2982 3989 7.929941 TTACACATGTATGCAAGGATGTAAA 57.070 32.000 0.00 3.99 30.53 2.01
2983 3990 8.518430 AATTACACATGTATGCAAGGATGTAA 57.482 30.769 0.00 11.55 36.16 2.41
2984 3991 8.518430 AAATTACACATGTATGCAAGGATGTA 57.482 30.769 0.00 2.28 0.00 2.29
2985 3992 7.408756 AAATTACACATGTATGCAAGGATGT 57.591 32.000 0.00 0.00 0.00 3.06
2986 3993 8.706492 AAAAATTACACATGTATGCAAGGATG 57.294 30.769 0.00 0.00 0.00 3.51
3013 4020 9.418045 TCATAAATTTCAGTTTCGGAAAATTCC 57.582 29.630 4.46 1.92 44.05 3.01
3020 4027 9.973450 TCAAAATTCATAAATTTCAGTTTCGGA 57.027 25.926 0.00 0.00 42.82 4.55
3048 4055 6.043706 TCCATGGAGCCCTTTATTTTGAAAAA 59.956 34.615 11.44 0.00 0.00 1.94
3049 4056 5.545723 TCCATGGAGCCCTTTATTTTGAAAA 59.454 36.000 11.44 0.00 0.00 2.29
3050 4057 5.090139 TCCATGGAGCCCTTTATTTTGAAA 58.910 37.500 11.44 0.00 0.00 2.69
3051 4058 4.682563 TCCATGGAGCCCTTTATTTTGAA 58.317 39.130 11.44 0.00 0.00 2.69
3052 4059 4.280819 CTCCATGGAGCCCTTTATTTTGA 58.719 43.478 28.45 0.00 35.31 2.69
3053 4060 4.660789 CTCCATGGAGCCCTTTATTTTG 57.339 45.455 28.45 1.40 35.31 2.44
3065 4072 1.739049 GAGACCGAGCTCCATGGAG 59.261 63.158 33.73 33.73 44.56 3.86
3066 4073 3.941081 GAGACCGAGCTCCATGGA 58.059 61.111 15.27 15.27 0.00 3.41
3072 4079 0.729690 GCATTTTGGAGACCGAGCTC 59.270 55.000 2.73 2.73 0.00 4.09
3073 4080 0.678048 GGCATTTTGGAGACCGAGCT 60.678 55.000 0.00 0.00 0.00 4.09
3074 4081 1.657751 GGGCATTTTGGAGACCGAGC 61.658 60.000 0.00 0.00 0.00 5.03
3075 4082 0.035056 AGGGCATTTTGGAGACCGAG 60.035 55.000 0.00 0.00 0.00 4.63
3076 4083 1.065709 GTAGGGCATTTTGGAGACCGA 60.066 52.381 0.00 0.00 0.00 4.69
3077 4084 1.065418 AGTAGGGCATTTTGGAGACCG 60.065 52.381 0.00 0.00 0.00 4.79
3078 4085 2.644676 GAGTAGGGCATTTTGGAGACC 58.355 52.381 0.00 0.00 0.00 3.85
3079 4086 2.280628 CGAGTAGGGCATTTTGGAGAC 58.719 52.381 0.00 0.00 0.00 3.36
3080 4087 1.406887 GCGAGTAGGGCATTTTGGAGA 60.407 52.381 0.00 0.00 0.00 3.71
3081 4088 1.017387 GCGAGTAGGGCATTTTGGAG 58.983 55.000 0.00 0.00 0.00 3.86
3082 4089 0.742990 CGCGAGTAGGGCATTTTGGA 60.743 55.000 0.00 0.00 0.00 3.53
3083 4090 0.742990 TCGCGAGTAGGGCATTTTGG 60.743 55.000 3.71 0.00 0.00 3.28
3084 4091 0.652592 CTCGCGAGTAGGGCATTTTG 59.347 55.000 27.79 0.00 0.00 2.44
3085 4092 0.462047 CCTCGCGAGTAGGGCATTTT 60.462 55.000 32.41 0.00 0.00 1.82
3086 4093 1.144057 CCTCGCGAGTAGGGCATTT 59.856 57.895 32.41 0.00 0.00 2.32
3087 4094 1.327690 TTCCTCGCGAGTAGGGCATT 61.328 55.000 32.41 0.00 34.66 3.56
3088 4095 1.115930 ATTCCTCGCGAGTAGGGCAT 61.116 55.000 32.41 13.05 34.66 4.40
3089 4096 1.756950 ATTCCTCGCGAGTAGGGCA 60.757 57.895 32.41 11.15 34.66 5.36
3090 4097 1.300233 CATTCCTCGCGAGTAGGGC 60.300 63.158 32.41 0.00 34.66 5.19
3091 4098 1.300233 GCATTCCTCGCGAGTAGGG 60.300 63.158 32.41 19.73 34.66 3.53
3092 4099 1.300233 GGCATTCCTCGCGAGTAGG 60.300 63.158 32.41 22.30 35.26 3.18
3093 4100 0.103208 AAGGCATTCCTCGCGAGTAG 59.897 55.000 32.41 19.49 43.40 2.57
3094 4101 0.535335 AAAGGCATTCCTCGCGAGTA 59.465 50.000 32.41 21.12 43.40 2.59
3095 4102 1.021390 CAAAGGCATTCCTCGCGAGT 61.021 55.000 32.41 13.69 43.40 4.18
3096 4103 1.021390 ACAAAGGCATTCCTCGCGAG 61.021 55.000 29.06 29.06 43.40 5.03
3097 4104 0.605319 AACAAAGGCATTCCTCGCGA 60.605 50.000 9.26 9.26 43.40 5.87
3098 4105 0.240945 AAACAAAGGCATTCCTCGCG 59.759 50.000 0.00 0.00 43.40 5.87


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

AutoCloner maintained by Alex Coulton.