Multiple sequence alignment - TraesCS3A01G161800

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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 TraesCS3A01G161800 chr3A 100.000 5384 0 0 1 5384 163934091 163928708 0.000000e+00 9943.0
1 TraesCS3A01G161800 chr3A 98.440 577 7 1 4810 5384 529165295 529165871 0.000000e+00 1014.0
2 TraesCS3A01G161800 chr3A 88.173 854 67 7 1167 2011 262223899 262224727 0.000000e+00 987.0
3 TraesCS3A01G161800 chr3A 92.100 519 37 3 2510 3028 262225138 262225652 0.000000e+00 728.0
4 TraesCS3A01G161800 chr3A 93.365 422 26 2 2067 2487 262224725 262225145 1.650000e-174 623.0
5 TraesCS3A01G161800 chr3A 84.067 659 37 23 4201 4809 262521844 262522484 1.680000e-159 573.0
6 TraesCS3A01G161800 chr3A 94.624 186 2 1 4810 4987 529170010 529170195 1.140000e-71 281.0
7 TraesCS3A01G161800 chr3A 98.425 127 2 0 4861 4987 163924335 163924209 1.950000e-54 224.0
8 TraesCS3A01G161800 chr3A 87.500 96 12 0 280 375 81701952 81701857 1.590000e-20 111.0
9 TraesCS3A01G161800 chr3A 98.413 63 1 0 4810 4872 163924420 163924358 1.590000e-20 111.0
10 TraesCS3A01G161800 chr3D 98.920 3333 32 4 1 3333 144302456 144299128 0.000000e+00 5952.0
11 TraesCS3A01G161800 chr3D 94.797 1307 28 11 3534 4809 144299147 144297850 0.000000e+00 2001.0
12 TraesCS3A01G161800 chr3D 89.323 871 60 7 1160 2022 192173792 192172947 0.000000e+00 1062.0
13 TraesCS3A01G161800 chr3D 90.909 649 52 6 3553 4197 192148919 192148274 0.000000e+00 865.0
14 TraesCS3A01G161800 chr3D 93.795 419 24 2 2069 2487 192172957 192172541 3.540000e-176 628.0
15 TraesCS3A01G161800 chr3D 84.793 651 40 23 4197 4806 192059817 192059185 2.780000e-167 599.0
16 TraesCS3A01G161800 chr3D 90.606 330 14 2 2510 2839 192172548 192172236 6.450000e-114 422.0
17 TraesCS3A01G161800 chr3D 94.359 195 11 0 2834 3028 192153260 192153066 3.150000e-77 300.0
18 TraesCS3A01G161800 chr3D 100.000 34 0 0 339 372 70271902 70271869 4.500000e-06 63.9
19 TraesCS3A01G161800 chr3D 100.000 32 0 0 341 372 70258315 70258284 5.820000e-05 60.2
20 TraesCS3A01G161800 chr3D 100.000 32 0 0 339 370 70260779 70260748 5.820000e-05 60.2
21 TraesCS3A01G161800 chr3B 97.689 3029 65 5 1 3028 207458863 207455839 0.000000e+00 5201.0
22 TraesCS3A01G161800 chr3B 92.741 1295 32 17 3534 4775 207453181 207451896 0.000000e+00 1814.0
23 TraesCS3A01G161800 chr3B 87.858 873 68 10 1162 2022 275656714 275657560 0.000000e+00 990.0
24 TraesCS3A01G161800 chr3B 91.843 613 44 5 3555 4164 275712118 275712727 0.000000e+00 850.0
25 TraesCS3A01G161800 chr3B 93.642 519 32 1 2510 3028 275657958 275658475 0.000000e+00 774.0
26 TraesCS3A01G161800 chr3B 93.795 419 23 2 2069 2487 275657550 275657965 1.270000e-175 627.0
27 TraesCS3A01G161800 chr3B 96.753 308 9 1 3027 3333 207453469 207453162 3.720000e-141 512.0
28 TraesCS3A01G161800 chr3B 79.348 644 50 33 4197 4809 275911929 275912520 5.090000e-100 375.0
29 TraesCS3A01G161800 chr1B 99.304 575 4 0 4810 5384 327225253 327224679 0.000000e+00 1040.0
30 TraesCS3A01G161800 chr1B 98.876 178 2 0 4810 4987 327220540 327220363 8.700000e-83 318.0
31 TraesCS3A01G161800 chr1B 77.778 288 56 7 5101 5384 252371461 252371178 2.580000e-38 171.0
32 TraesCS3A01G161800 chr1B 92.308 39 3 0 638 676 57784880 57784918 7.530000e-04 56.5
33 TraesCS3A01G161800 chr2B 99.133 577 5 0 4808 5384 542909669 542910245 0.000000e+00 1038.0
34 TraesCS3A01G161800 chr2B 98.315 178 3 0 4810 4987 542914384 542914561 4.050000e-81 313.0
35 TraesCS3A01G161800 chr2B 90.556 180 15 2 3029 3207 547003593 547003415 2.510000e-58 237.0
36 TraesCS3A01G161800 chr7A 89.446 578 59 2 4808 5384 185470508 185471084 0.000000e+00 728.0
37 TraesCS3A01G161800 chr7A 97.537 203 5 0 3332 3534 319592002 319591800 1.110000e-91 348.0
38 TraesCS3A01G161800 chr7A 95.000 220 7 4 3318 3534 42965971 42966189 5.160000e-90 342.0
39 TraesCS3A01G161800 chr7A 96.602 206 6 1 3323 3528 100247238 100247442 1.860000e-89 340.0
40 TraesCS3A01G161800 chr7A 92.045 176 14 0 3027 3202 575454227 575454052 1.160000e-61 248.0
41 TraesCS3A01G161800 chr2A 85.983 478 62 5 4909 5384 3419750 3419276 1.730000e-139 507.0
42 TraesCS3A01G161800 chr2A 96.226 212 6 2 3325 3534 19253309 19253520 3.990000e-91 346.0
43 TraesCS3A01G161800 chr2A 95.775 213 9 0 3322 3534 552491893 552491681 1.440000e-90 344.0
44 TraesCS3A01G161800 chr4D 97.537 203 5 0 3332 3534 313597754 313597552 1.110000e-91 348.0
45 TraesCS3A01G161800 chr4D 96.721 183 5 1 4810 4991 23581579 23581761 2.440000e-78 303.0
46 TraesCS3A01G161800 chr4D 93.333 180 12 0 3027 3206 69178213 69178034 3.200000e-67 267.0
47 TraesCS3A01G161800 chr4D 91.379 174 15 0 3029 3202 497251813 497251986 6.970000e-59 239.0
48 TraesCS3A01G161800 chr4D 80.906 309 40 7 90 398 475310754 475310465 5.430000e-55 226.0
49 TraesCS3A01G161800 chr1D 97.537 203 5 0 3332 3534 223524581 223524379 1.110000e-91 348.0
50 TraesCS3A01G161800 chr1A 97.101 207 5 1 3329 3534 127703754 127703960 1.110000e-91 348.0
51 TraesCS3A01G161800 chr1A 97.487 199 5 0 3336 3534 420384899 420385097 1.860000e-89 340.0
52 TraesCS3A01G161800 chr6B 81.407 398 52 9 1 398 126791187 126790812 6.770000e-79 305.0
53 TraesCS3A01G161800 chr2D 92.179 179 14 0 3026 3204 142434192 142434370 2.490000e-63 254.0
54 TraesCS3A01G161800 chr2D 81.022 137 26 0 5110 5246 543306218 543306082 5.700000e-20 110.0
55 TraesCS3A01G161800 chr2D 79.137 139 25 3 5110 5246 589755468 589755332 5.740000e-15 93.5
56 TraesCS3A01G161800 chr5D 90.217 184 17 1 3027 3209 60522582 60522765 6.970000e-59 239.0
57 TraesCS3A01G161800 chr5A 91.429 175 13 2 3029 3202 578233638 578233465 6.970000e-59 239.0
58 TraesCS3A01G161800 chr5A 89.583 144 12 3 4846 4987 207520017 207520159 4.280000e-41 180.0
59 TraesCS3A01G161800 chr4A 81.250 256 30 11 134 389 682064776 682064539 1.980000e-44 191.0


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 TraesCS3A01G161800 chr3A 163928708 163934091 5383 True 9943.000000 9943 100.000000 1 5384 1 chr3A.!!$R2 5383
1 TraesCS3A01G161800 chr3A 529165295 529165871 576 False 1014.000000 1014 98.440000 4810 5384 1 chr3A.!!$F2 574
2 TraesCS3A01G161800 chr3A 262223899 262225652 1753 False 779.333333 987 91.212667 1167 3028 3 chr3A.!!$F4 1861
3 TraesCS3A01G161800 chr3A 262521844 262522484 640 False 573.000000 573 84.067000 4201 4809 1 chr3A.!!$F1 608
4 TraesCS3A01G161800 chr3D 144297850 144302456 4606 True 3976.500000 5952 96.858500 1 4809 2 chr3D.!!$R6 4808
5 TraesCS3A01G161800 chr3D 192148274 192148919 645 True 865.000000 865 90.909000 3553 4197 1 chr3D.!!$R3 644
6 TraesCS3A01G161800 chr3D 192172236 192173792 1556 True 704.000000 1062 91.241333 1160 2839 3 chr3D.!!$R7 1679
7 TraesCS3A01G161800 chr3D 192059185 192059817 632 True 599.000000 599 84.793000 4197 4806 1 chr3D.!!$R2 609
8 TraesCS3A01G161800 chr3B 207451896 207458863 6967 True 2509.000000 5201 95.727667 1 4775 3 chr3B.!!$R1 4774
9 TraesCS3A01G161800 chr3B 275712118 275712727 609 False 850.000000 850 91.843000 3555 4164 1 chr3B.!!$F1 609
10 TraesCS3A01G161800 chr3B 275656714 275658475 1761 False 797.000000 990 91.765000 1162 3028 3 chr3B.!!$F3 1866
11 TraesCS3A01G161800 chr3B 275911929 275912520 591 False 375.000000 375 79.348000 4197 4809 1 chr3B.!!$F2 612
12 TraesCS3A01G161800 chr1B 327224679 327225253 574 True 1040.000000 1040 99.304000 4810 5384 1 chr1B.!!$R3 574
13 TraesCS3A01G161800 chr2B 542909669 542910245 576 False 1038.000000 1038 99.133000 4808 5384 1 chr2B.!!$F1 576
14 TraesCS3A01G161800 chr7A 185470508 185471084 576 False 728.000000 728 89.446000 4808 5384 1 chr7A.!!$F3 576

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
176 177 0.606604 ATTGCCTTTCAGCTTGCCTG 59.393 50.000 0.00 0.0 43.17 4.85 F
720 721 1.001158 GCTAGCTGTCGATCCCTGTAC 60.001 57.143 7.70 0.0 0.00 2.90 F
1117 1118 1.003839 GGAGTGTTCATGGCGGTCA 60.004 57.895 0.00 0.0 0.00 4.02 F
1209 1210 1.064017 GTCACCCAAATCCCTGCCATA 60.064 52.381 0.00 0.0 0.00 2.74 F
2808 2822 1.311859 ATGTGGCACCAGAATATGCG 58.688 50.000 16.26 0.0 43.02 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1304 0.323629 TTGTCTGATTCCCGGTCACC 59.676 55.000 0.0 0.0 0.00 4.02 R
1620 1621 1.134699 GGAGTGCCATTGACGATCTCA 60.135 52.381 0.0 0.0 0.00 3.27 R
2808 2822 4.380531 TCTCATTCAACAGTCCAGTGTTC 58.619 43.478 0.0 0.0 38.65 3.18 R
3327 5713 4.038042 TGTTGTTGTTGTTGTTGTTGAGGA 59.962 37.500 0.0 0.0 0.00 3.71 R
4551 6982 1.926561 TACAGCAGCACATCATCGTC 58.073 50.000 0.0 0.0 0.00 4.20 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
35 36 7.925993 TGTTCCAAAACTGTTGTAGTATGAAG 58.074 34.615 0.00 0.00 39.18 3.02
176 177 0.606604 ATTGCCTTTCAGCTTGCCTG 59.393 50.000 0.00 0.00 43.17 4.85
257 258 3.159356 GACATAGGTCCAGGACAACCCT 61.159 54.545 21.75 11.51 39.14 4.34
391 392 7.759489 ATTTACAATGGTTGCTCTTGTTCTA 57.241 32.000 0.00 0.00 35.00 2.10
426 427 4.074970 GGCTGCAATATTACTAGTGGCAT 58.925 43.478 5.39 0.00 0.00 4.40
661 662 1.154430 TGCTACCCTGGGTTTTCCTT 58.846 50.000 26.00 0.00 40.46 3.36
720 721 1.001158 GCTAGCTGTCGATCCCTGTAC 60.001 57.143 7.70 0.00 0.00 2.90
1117 1118 1.003839 GGAGTGTTCATGGCGGTCA 60.004 57.895 0.00 0.00 0.00 4.02
1209 1210 1.064017 GTCACCCAAATCCCTGCCATA 60.064 52.381 0.00 0.00 0.00 2.74
1303 1304 1.813513 AACGATCCAAGACAAGCCTG 58.186 50.000 0.00 0.00 0.00 4.85
1620 1621 5.364446 TGGATATGGTGTAGTTTATCGTGGT 59.636 40.000 0.00 0.00 0.00 4.16
1904 1905 2.025131 GTGGAGGGTACTCAGAGGTACT 60.025 54.545 1.53 0.00 45.81 2.73
1914 1915 6.656693 GGTACTCAGAGGTACTTTGTACTGTA 59.343 42.308 1.53 0.00 41.71 2.74
1969 1974 7.509141 TTATCATTGGTCACATATCGCATTT 57.491 32.000 0.00 0.00 0.00 2.32
2047 2060 2.816087 GACCTTCAATGCTCTGCAGAAA 59.184 45.455 18.85 9.60 43.65 2.52
2048 2061 3.225104 ACCTTCAATGCTCTGCAGAAAA 58.775 40.909 18.85 9.20 43.65 2.29
2808 2822 1.311859 ATGTGGCACCAGAATATGCG 58.688 50.000 16.26 0.00 43.02 4.73
3319 5705 7.123218 ACATCTTTATGCACCATGAGGTTGC 62.123 44.000 0.00 0.00 40.17 4.17
3329 5715 4.228912 CCATGAGGTTGCGAATTAATCC 57.771 45.455 0.00 0.00 0.00 3.01
3330 5716 3.885297 CCATGAGGTTGCGAATTAATCCT 59.115 43.478 0.00 0.00 0.00 3.24
3331 5717 4.023707 CCATGAGGTTGCGAATTAATCCTC 60.024 45.833 10.35 10.35 41.00 3.71
3332 5718 4.214986 TGAGGTTGCGAATTAATCCTCA 57.785 40.909 14.32 14.32 45.76 3.86
3333 5719 4.584874 TGAGGTTGCGAATTAATCCTCAA 58.415 39.130 15.44 0.00 45.23 3.02
3334 5720 4.394920 TGAGGTTGCGAATTAATCCTCAAC 59.605 41.667 15.44 8.51 45.23 3.18
3335 5721 4.331968 AGGTTGCGAATTAATCCTCAACA 58.668 39.130 9.36 0.00 38.63 3.33
3336 5722 4.764823 AGGTTGCGAATTAATCCTCAACAA 59.235 37.500 9.36 0.75 38.63 2.83
3337 5723 4.857037 GGTTGCGAATTAATCCTCAACAAC 59.143 41.667 9.36 10.47 38.63 3.32
3338 5724 5.457140 GTTGCGAATTAATCCTCAACAACA 58.543 37.500 3.01 0.00 37.67 3.33
3339 5725 5.697473 TGCGAATTAATCCTCAACAACAA 57.303 34.783 0.00 0.00 0.00 2.83
3340 5726 5.457140 TGCGAATTAATCCTCAACAACAAC 58.543 37.500 0.00 0.00 0.00 3.32
3341 5727 5.009110 TGCGAATTAATCCTCAACAACAACA 59.991 36.000 0.00 0.00 0.00 3.33
3342 5728 5.918011 GCGAATTAATCCTCAACAACAACAA 59.082 36.000 0.00 0.00 0.00 2.83
3343 5729 6.129194 GCGAATTAATCCTCAACAACAACAAC 60.129 38.462 0.00 0.00 0.00 3.32
3344 5730 6.915300 CGAATTAATCCTCAACAACAACAACA 59.085 34.615 0.00 0.00 0.00 3.33
3345 5731 7.433719 CGAATTAATCCTCAACAACAACAACAA 59.566 33.333 0.00 0.00 0.00 2.83
3346 5732 8.419076 AATTAATCCTCAACAACAACAACAAC 57.581 30.769 0.00 0.00 0.00 3.32
3347 5733 5.398603 AATCCTCAACAACAACAACAACA 57.601 34.783 0.00 0.00 0.00 3.33
3348 5734 4.855715 TCCTCAACAACAACAACAACAA 57.144 36.364 0.00 0.00 0.00 2.83
3349 5735 4.551388 TCCTCAACAACAACAACAACAAC 58.449 39.130 0.00 0.00 0.00 3.32
3350 5736 4.038042 TCCTCAACAACAACAACAACAACA 59.962 37.500 0.00 0.00 0.00 3.33
3351 5737 4.747108 CCTCAACAACAACAACAACAACAA 59.253 37.500 0.00 0.00 0.00 2.83
3352 5738 5.332959 CCTCAACAACAACAACAACAACAAC 60.333 40.000 0.00 0.00 0.00 3.32
3353 5739 5.109210 TCAACAACAACAACAACAACAACA 58.891 33.333 0.00 0.00 0.00 3.33
3354 5740 5.580691 TCAACAACAACAACAACAACAACAA 59.419 32.000 0.00 0.00 0.00 2.83
3355 5741 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3356 5742 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3357 5743 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3358 5744 6.128282 ACAACAACAACAACAACAACAACAAA 60.128 30.769 0.00 0.00 0.00 2.83
3359 5745 6.042144 ACAACAACAACAACAACAACAAAG 57.958 33.333 0.00 0.00 0.00 2.77
3360 5746 4.723879 ACAACAACAACAACAACAAAGC 57.276 36.364 0.00 0.00 0.00 3.51
3361 5747 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
3362 5748 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
3363 5749 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
3364 5750 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
3365 5751 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
3366 5752 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
3367 5753 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
3368 5754 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
3369 5755 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
3370 5756 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
3371 5757 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
3372 5758 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
3373 5759 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
3374 5760 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
3375 5761 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
3376 5762 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
3377 5763 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
3378 5764 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
3379 5765 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
3380 5766 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
3389 5775 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
3390 5776 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
3391 5777 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
3392 5778 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
3393 5779 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
3394 5780 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
3395 5781 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
3396 5782 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
3397 5783 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
3398 5784 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
3399 5785 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
3400 5786 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
3415 5801 3.531538 GTGAAACCCATAAGATCTCGCA 58.468 45.455 0.00 0.00 0.00 5.10
3416 5802 3.938963 GTGAAACCCATAAGATCTCGCAA 59.061 43.478 0.00 0.00 0.00 4.85
3417 5803 3.938963 TGAAACCCATAAGATCTCGCAAC 59.061 43.478 0.00 0.00 0.00 4.17
3418 5804 2.622064 ACCCATAAGATCTCGCAACC 57.378 50.000 0.00 0.00 0.00 3.77
3419 5805 1.837439 ACCCATAAGATCTCGCAACCA 59.163 47.619 0.00 0.00 0.00 3.67
3420 5806 2.238646 ACCCATAAGATCTCGCAACCAA 59.761 45.455 0.00 0.00 0.00 3.67
3421 5807 2.614057 CCCATAAGATCTCGCAACCAAC 59.386 50.000 0.00 0.00 0.00 3.77
3422 5808 3.535561 CCATAAGATCTCGCAACCAACT 58.464 45.455 0.00 0.00 0.00 3.16
3423 5809 3.557595 CCATAAGATCTCGCAACCAACTC 59.442 47.826 0.00 0.00 0.00 3.01
3424 5810 2.839486 AAGATCTCGCAACCAACTCA 57.161 45.000 0.00 0.00 0.00 3.41
3425 5811 3.340814 AAGATCTCGCAACCAACTCAT 57.659 42.857 0.00 0.00 0.00 2.90
3426 5812 2.625737 AGATCTCGCAACCAACTCATG 58.374 47.619 0.00 0.00 0.00 3.07
3434 5820 3.915575 CCAACTCATGGCTCTGGC 58.084 61.111 0.00 0.00 43.80 4.85
3435 5821 1.001764 CCAACTCATGGCTCTGGCA 60.002 57.895 0.00 0.00 43.80 4.92
3436 5822 1.310933 CCAACTCATGGCTCTGGCAC 61.311 60.000 0.00 0.00 43.80 5.01
3437 5823 1.376424 AACTCATGGCTCTGGCACG 60.376 57.895 0.00 0.00 41.84 5.34
3438 5824 2.116983 AACTCATGGCTCTGGCACGT 62.117 55.000 0.00 0.00 41.84 4.49
3439 5825 2.046988 TCATGGCTCTGGCACGTG 60.047 61.111 12.28 12.28 41.84 4.49
3440 5826 3.129502 CATGGCTCTGGCACGTGG 61.130 66.667 18.88 0.08 41.84 4.94
3441 5827 3.321648 ATGGCTCTGGCACGTGGA 61.322 61.111 18.88 5.20 41.84 4.02
3442 5828 2.673200 ATGGCTCTGGCACGTGGAT 61.673 57.895 18.88 0.00 41.84 3.41
3443 5829 2.045926 GGCTCTGGCACGTGGATT 60.046 61.111 18.88 0.00 40.87 3.01
3444 5830 2.401766 GGCTCTGGCACGTGGATTG 61.402 63.158 18.88 0.00 40.87 2.67
3445 5831 3.044059 GCTCTGGCACGTGGATTGC 62.044 63.158 18.88 1.36 39.41 3.56
3446 5832 1.672030 CTCTGGCACGTGGATTGCA 60.672 57.895 18.88 0.00 42.12 4.08
3447 5833 1.228094 TCTGGCACGTGGATTGCAA 60.228 52.632 18.88 0.00 42.12 4.08
3448 5834 1.210931 CTGGCACGTGGATTGCAAG 59.789 57.895 18.88 0.70 42.12 4.01
3449 5835 2.126346 GGCACGTGGATTGCAAGC 60.126 61.111 18.88 6.04 42.12 4.01
3450 5836 2.629656 GGCACGTGGATTGCAAGCT 61.630 57.895 18.88 0.00 42.12 3.74
3451 5837 1.286880 GCACGTGGATTGCAAGCTT 59.713 52.632 18.88 0.00 39.93 3.74
3452 5838 0.730494 GCACGTGGATTGCAAGCTTC 60.730 55.000 18.88 2.00 39.93 3.86
3453 5839 0.109597 CACGTGGATTGCAAGCTTCC 60.110 55.000 15.27 12.46 0.00 3.46
3454 5840 0.537143 ACGTGGATTGCAAGCTTCCA 60.537 50.000 15.27 15.05 37.20 3.53
3456 5842 2.256391 TGGATTGCAAGCTTCCACG 58.744 52.632 15.27 0.00 34.65 4.94
3457 5843 1.153958 GGATTGCAAGCTTCCACGC 60.154 57.895 15.27 0.00 0.00 5.34
3458 5844 1.580942 GATTGCAAGCTTCCACGCA 59.419 52.632 7.61 5.16 0.00 5.24
3459 5845 0.730494 GATTGCAAGCTTCCACGCAC 60.730 55.000 7.61 0.00 33.29 5.34
3460 5846 2.146073 ATTGCAAGCTTCCACGCACC 62.146 55.000 8.57 0.00 33.29 5.01
3461 5847 2.980233 GCAAGCTTCCACGCACCT 60.980 61.111 0.00 0.00 0.00 4.00
3462 5848 2.970974 GCAAGCTTCCACGCACCTC 61.971 63.158 0.00 0.00 0.00 3.85
3463 5849 1.302033 CAAGCTTCCACGCACCTCT 60.302 57.895 0.00 0.00 0.00 3.69
3464 5850 1.302033 AAGCTTCCACGCACCTCTG 60.302 57.895 0.00 0.00 0.00 3.35
3465 5851 2.031163 GCTTCCACGCACCTCTGT 59.969 61.111 0.00 0.00 0.00 3.41
3466 5852 2.029844 GCTTCCACGCACCTCTGTC 61.030 63.158 0.00 0.00 0.00 3.51
3467 5853 1.374758 CTTCCACGCACCTCTGTCC 60.375 63.158 0.00 0.00 0.00 4.02
3468 5854 2.099652 CTTCCACGCACCTCTGTCCA 62.100 60.000 0.00 0.00 0.00 4.02
3469 5855 1.480212 TTCCACGCACCTCTGTCCAT 61.480 55.000 0.00 0.00 0.00 3.41
3470 5856 0.613572 TCCACGCACCTCTGTCCATA 60.614 55.000 0.00 0.00 0.00 2.74
3471 5857 0.179100 CCACGCACCTCTGTCCATAG 60.179 60.000 0.00 0.00 0.00 2.23
3472 5858 0.807667 CACGCACCTCTGTCCATAGC 60.808 60.000 0.00 0.00 0.00 2.97
3473 5859 0.972983 ACGCACCTCTGTCCATAGCT 60.973 55.000 0.00 0.00 0.00 3.32
3474 5860 1.032794 CGCACCTCTGTCCATAGCTA 58.967 55.000 0.00 0.00 0.00 3.32
3475 5861 1.000827 CGCACCTCTGTCCATAGCTAG 60.001 57.143 0.00 0.00 0.00 3.42
3476 5862 1.270041 GCACCTCTGTCCATAGCTAGC 60.270 57.143 6.62 6.62 0.00 3.42
3477 5863 2.315176 CACCTCTGTCCATAGCTAGCT 58.685 52.381 23.12 23.12 0.00 3.32
3478 5864 2.295909 CACCTCTGTCCATAGCTAGCTC 59.704 54.545 23.26 7.00 0.00 4.09
3479 5865 2.176798 ACCTCTGTCCATAGCTAGCTCT 59.823 50.000 23.26 9.05 0.00 4.09
3480 5866 3.230134 CCTCTGTCCATAGCTAGCTCTT 58.770 50.000 23.26 7.47 0.00 2.85
3481 5867 3.640967 CCTCTGTCCATAGCTAGCTCTTT 59.359 47.826 23.26 4.57 0.00 2.52
3482 5868 4.501229 CCTCTGTCCATAGCTAGCTCTTTG 60.501 50.000 23.26 16.78 0.00 2.77
3483 5869 3.386078 TCTGTCCATAGCTAGCTCTTTGG 59.614 47.826 23.26 24.37 36.78 3.28
3484 5870 3.107601 TGTCCATAGCTAGCTCTTTGGT 58.892 45.455 27.50 8.05 36.79 3.67
3485 5871 3.118629 TGTCCATAGCTAGCTCTTTGGTG 60.119 47.826 27.50 16.61 36.79 4.17
3486 5872 3.133003 GTCCATAGCTAGCTCTTTGGTGA 59.867 47.826 27.50 15.24 36.79 4.02
3487 5873 3.969976 TCCATAGCTAGCTCTTTGGTGAT 59.030 43.478 27.50 12.14 36.79 3.06
3488 5874 5.011125 GTCCATAGCTAGCTCTTTGGTGATA 59.989 44.000 27.50 14.48 36.79 2.15
3489 5875 5.011125 TCCATAGCTAGCTCTTTGGTGATAC 59.989 44.000 27.50 0.00 36.79 2.24
3490 5876 5.011533 CCATAGCTAGCTCTTTGGTGATACT 59.988 44.000 23.26 0.00 32.65 2.12
3491 5877 4.664150 AGCTAGCTCTTTGGTGATACTC 57.336 45.455 12.68 0.00 0.00 2.59
3492 5878 3.386402 AGCTAGCTCTTTGGTGATACTCC 59.614 47.826 12.68 0.00 0.00 3.85
3493 5879 3.133003 GCTAGCTCTTTGGTGATACTCCA 59.867 47.826 7.70 0.00 0.00 3.86
3494 5880 4.383118 GCTAGCTCTTTGGTGATACTCCAA 60.383 45.833 7.70 0.00 42.29 3.53
3495 5881 4.851639 AGCTCTTTGGTGATACTCCAAT 57.148 40.909 6.20 0.00 43.25 3.16
3496 5882 4.775236 AGCTCTTTGGTGATACTCCAATC 58.225 43.478 6.20 0.00 43.25 2.67
3497 5883 3.879892 GCTCTTTGGTGATACTCCAATCC 59.120 47.826 6.20 0.00 43.25 3.01
3498 5884 4.384647 GCTCTTTGGTGATACTCCAATCCT 60.385 45.833 6.20 0.00 43.25 3.24
3499 5885 5.749462 CTCTTTGGTGATACTCCAATCCTT 58.251 41.667 6.20 0.00 43.25 3.36
3500 5886 5.745227 TCTTTGGTGATACTCCAATCCTTC 58.255 41.667 6.20 0.00 43.25 3.46
3501 5887 5.250543 TCTTTGGTGATACTCCAATCCTTCA 59.749 40.000 6.20 0.00 43.25 3.02
3502 5888 4.760530 TGGTGATACTCCAATCCTTCAG 57.239 45.455 0.00 0.00 31.50 3.02
3503 5889 4.361783 TGGTGATACTCCAATCCTTCAGA 58.638 43.478 0.00 0.00 31.50 3.27
3504 5890 4.971282 TGGTGATACTCCAATCCTTCAGAT 59.029 41.667 0.00 0.00 36.48 2.90
3505 5891 5.070981 TGGTGATACTCCAATCCTTCAGATC 59.929 44.000 0.00 0.00 32.47 2.75
3506 5892 5.306678 GGTGATACTCCAATCCTTCAGATCT 59.693 44.000 0.00 0.00 32.47 2.75
3507 5893 6.454795 GTGATACTCCAATCCTTCAGATCTC 58.545 44.000 0.00 0.00 32.47 2.75
3508 5894 6.267471 GTGATACTCCAATCCTTCAGATCTCT 59.733 42.308 0.00 0.00 32.47 3.10
3509 5895 6.493115 TGATACTCCAATCCTTCAGATCTCTC 59.507 42.308 0.00 0.00 32.47 3.20
3510 5896 4.882559 ACTCCAATCCTTCAGATCTCTCT 58.117 43.478 0.00 0.00 32.47 3.10
3511 5897 5.279685 ACTCCAATCCTTCAGATCTCTCTT 58.720 41.667 0.00 0.00 32.47 2.85
3512 5898 6.439487 ACTCCAATCCTTCAGATCTCTCTTA 58.561 40.000 0.00 0.00 32.47 2.10
3513 5899 6.900186 ACTCCAATCCTTCAGATCTCTCTTAA 59.100 38.462 0.00 0.00 32.47 1.85
3514 5900 7.118496 TCCAATCCTTCAGATCTCTCTTAAC 57.882 40.000 0.00 0.00 32.47 2.01
3515 5901 5.982516 CCAATCCTTCAGATCTCTCTTAACG 59.017 44.000 0.00 0.00 32.47 3.18
3516 5902 5.782893 ATCCTTCAGATCTCTCTTAACGG 57.217 43.478 0.00 0.00 0.00 4.44
3517 5903 4.856509 TCCTTCAGATCTCTCTTAACGGA 58.143 43.478 0.00 0.00 0.00 4.69
3518 5904 4.641094 TCCTTCAGATCTCTCTTAACGGAC 59.359 45.833 0.00 0.00 0.00 4.79
3519 5905 4.642885 CCTTCAGATCTCTCTTAACGGACT 59.357 45.833 0.00 0.00 0.00 3.85
3520 5906 5.220970 CCTTCAGATCTCTCTTAACGGACTC 60.221 48.000 0.00 0.00 0.00 3.36
3521 5907 4.200874 TCAGATCTCTCTTAACGGACTCC 58.799 47.826 0.00 0.00 0.00 3.85
3522 5908 4.080243 TCAGATCTCTCTTAACGGACTCCT 60.080 45.833 0.00 0.00 0.00 3.69
3523 5909 4.274950 CAGATCTCTCTTAACGGACTCCTC 59.725 50.000 0.00 0.00 0.00 3.71
3524 5910 3.002038 TCTCTCTTAACGGACTCCTCC 57.998 52.381 0.00 0.00 0.00 4.30
3525 5911 2.025898 CTCTCTTAACGGACTCCTCCC 58.974 57.143 0.00 0.00 31.93 4.30
3526 5912 1.356738 TCTCTTAACGGACTCCTCCCA 59.643 52.381 0.00 0.00 31.93 4.37
3527 5913 2.024273 TCTCTTAACGGACTCCTCCCAT 60.024 50.000 0.00 0.00 31.93 4.00
3528 5914 2.101582 CTCTTAACGGACTCCTCCCATG 59.898 54.545 0.00 0.00 31.93 3.66
3529 5915 1.831736 CTTAACGGACTCCTCCCATGT 59.168 52.381 0.00 0.00 31.93 3.21
3530 5916 1.946984 TAACGGACTCCTCCCATGTT 58.053 50.000 0.00 0.00 31.93 2.71
3531 5917 1.946984 AACGGACTCCTCCCATGTTA 58.053 50.000 0.00 0.00 31.93 2.41
3532 5918 1.946984 ACGGACTCCTCCCATGTTAA 58.053 50.000 0.00 0.00 31.93 2.01
3533 5919 2.262637 ACGGACTCCTCCCATGTTAAA 58.737 47.619 0.00 0.00 31.93 1.52
3534 5920 2.236395 ACGGACTCCTCCCATGTTAAAG 59.764 50.000 0.00 0.00 31.93 1.85
3535 5921 2.420129 CGGACTCCTCCCATGTTAAAGG 60.420 54.545 0.00 0.00 31.93 3.11
3536 5922 2.644676 GACTCCTCCCATGTTAAAGGC 58.355 52.381 0.00 0.00 0.00 4.35
3537 5923 2.239907 GACTCCTCCCATGTTAAAGGCT 59.760 50.000 0.00 0.00 0.00 4.58
3538 5924 2.025887 ACTCCTCCCATGTTAAAGGCTG 60.026 50.000 0.00 0.00 0.00 4.85
3680 6074 7.386299 GGCATAACTTGATCACTTGTAGGATAG 59.614 40.741 0.00 0.00 0.00 2.08
3795 6189 0.472471 GGGGGTCATTCCTTGCGATA 59.528 55.000 0.00 0.00 36.25 2.92
4260 6659 2.414994 AATGATGTGAGCAGGACAGG 57.585 50.000 0.00 0.00 0.00 4.00
4437 6837 3.335579 AGTAACGATGGAAGCTTTGACC 58.664 45.455 0.00 0.00 0.00 4.02
4440 6840 1.202758 ACGATGGAAGCTTTGACCACA 60.203 47.619 7.48 0.00 36.49 4.17
4462 6863 2.270352 AGGGCTGATGAAAAACGTGA 57.730 45.000 0.00 0.00 0.00 4.35
4463 6864 1.880027 AGGGCTGATGAAAAACGTGAC 59.120 47.619 0.00 0.00 0.00 3.67
4551 6982 7.499321 TTATTTGTACCTACACCAGTTGTTG 57.501 36.000 0.00 0.00 39.91 3.33
4552 6983 4.757019 TTGTACCTACACCAGTTGTTGA 57.243 40.909 0.00 0.00 39.91 3.18
4553 6984 4.062677 TGTACCTACACCAGTTGTTGAC 57.937 45.455 0.00 0.00 39.91 3.18
4556 6987 2.367567 ACCTACACCAGTTGTTGACGAT 59.632 45.455 0.00 0.00 39.91 3.73
4586 7020 3.314080 TGCTGTAAGTTGTTAACAGTGCC 59.686 43.478 8.56 0.00 35.30 5.01
4627 7070 2.297315 TGAGTACTGGCACAAGAGAGTG 59.703 50.000 0.00 0.00 38.70 3.51
4630 7073 1.418334 ACTGGCACAAGAGAGTGTCT 58.582 50.000 0.00 0.00 44.21 3.41
4799 7274 4.641645 CAACAGCACGAGCCCCCA 62.642 66.667 0.00 0.00 43.56 4.96
4865 7342 0.314302 ACGGCGCACCTCTCATATAC 59.686 55.000 10.83 0.00 0.00 1.47
4993 7470 0.834687 TTGGTCTCTAACACGCCCCT 60.835 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 7.865385 TCAGAATACAACAATTTGGTAAACTGC 59.135 33.333 0.78 0.00 37.00 4.40
176 177 1.270893 GGGGTGGTGAGACTTCTGAAC 60.271 57.143 0.00 0.00 0.00 3.18
228 229 4.710375 GTCCTGGACCTATGTCTTAGAACA 59.290 45.833 16.14 0.00 41.47 3.18
372 373 5.700832 TGTACTAGAACAAGAGCAACCATTG 59.299 40.000 0.00 0.00 0.00 2.82
391 392 4.982241 ATTGCAGCCAGGTATATGTACT 57.018 40.909 0.00 0.00 0.00 2.73
611 612 1.069358 GGGAATTTTCACGGGCACAAA 59.931 47.619 0.00 0.00 0.00 2.83
661 662 1.134551 GCTTTGTTTGGTTGCAAGGGA 60.135 47.619 0.00 0.00 0.00 4.20
720 721 1.955529 GCAGCACCGACACATACACG 61.956 60.000 0.00 0.00 0.00 4.49
1117 1118 6.205658 GTGAGCCAGACAGTTAAAAAGAAGAT 59.794 38.462 0.00 0.00 0.00 2.40
1209 1210 5.259632 CTCACTTCCTTGATTTCCTTGGAT 58.740 41.667 0.00 0.00 0.00 3.41
1303 1304 0.323629 TTGTCTGATTCCCGGTCACC 59.676 55.000 0.00 0.00 0.00 4.02
1620 1621 1.134699 GGAGTGCCATTGACGATCTCA 60.135 52.381 0.00 0.00 0.00 3.27
1969 1974 9.444600 GTACCAAGGATATGTTTTTCTCTTGTA 57.555 33.333 0.00 0.00 0.00 2.41
2047 2060 9.691362 ATCATTGCAGTTAAACGAGTTTTATTT 57.309 25.926 6.53 0.00 34.23 1.40
2048 2061 9.691362 AATCATTGCAGTTAAACGAGTTTTATT 57.309 25.926 6.53 0.00 34.23 1.40
2808 2822 4.380531 TCTCATTCAACAGTCCAGTGTTC 58.619 43.478 0.00 0.00 38.65 3.18
3319 5705 6.915300 TGTTGTTGTTGTTGAGGATTAATTCG 59.085 34.615 0.00 0.00 0.00 3.34
3320 5706 8.539674 GTTGTTGTTGTTGTTGAGGATTAATTC 58.460 33.333 0.00 0.00 0.00 2.17
3321 5707 8.037758 TGTTGTTGTTGTTGTTGAGGATTAATT 58.962 29.630 0.00 0.00 0.00 1.40
3322 5708 7.551585 TGTTGTTGTTGTTGTTGAGGATTAAT 58.448 30.769 0.00 0.00 0.00 1.40
3323 5709 6.925211 TGTTGTTGTTGTTGTTGAGGATTAA 58.075 32.000 0.00 0.00 0.00 1.40
3324 5710 6.516739 TGTTGTTGTTGTTGTTGAGGATTA 57.483 33.333 0.00 0.00 0.00 1.75
3325 5711 5.398603 TGTTGTTGTTGTTGTTGAGGATT 57.601 34.783 0.00 0.00 0.00 3.01
3326 5712 5.167845 GTTGTTGTTGTTGTTGTTGAGGAT 58.832 37.500 0.00 0.00 0.00 3.24
3327 5713 4.038042 TGTTGTTGTTGTTGTTGTTGAGGA 59.962 37.500 0.00 0.00 0.00 3.71
3328 5714 4.302455 TGTTGTTGTTGTTGTTGTTGAGG 58.698 39.130 0.00 0.00 0.00 3.86
3329 5715 5.233050 TGTTGTTGTTGTTGTTGTTGTTGAG 59.767 36.000 0.00 0.00 0.00 3.02
3330 5716 5.109210 TGTTGTTGTTGTTGTTGTTGTTGA 58.891 33.333 0.00 0.00 0.00 3.18
3331 5717 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3332 5718 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
3333 5719 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3334 5720 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3335 5721 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
3336 5722 5.503194 GCTTTGTTGTTGTTGTTGTTGTTGT 60.503 36.000 0.00 0.00 0.00 3.32
3337 5723 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
3338 5724 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
3339 5725 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
3340 5726 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
3341 5727 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
3342 5728 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
3343 5729 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
3344 5730 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
3345 5731 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
3346 5732 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
3347 5733 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
3348 5734 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
3349 5735 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
3350 5736 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
3351 5737 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
3352 5738 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
3353 5739 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
3354 5740 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
3355 5741 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
3356 5742 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
3357 5743 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
3358 5744 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
3359 5745 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
3370 5756 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
3371 5757 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
3372 5758 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
3373 5759 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
3374 5760 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
3375 5761 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
3376 5762 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
3377 5763 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
3378 5764 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
3379 5765 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
3380 5766 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
3381 5767 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
3382 5768 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
3383 5769 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
3384 5770 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
3385 5771 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
3386 5772 3.454812 TCTTATGGGTTTCACCTCTAGCC 59.545 47.826 0.00 0.00 38.64 3.93
3387 5773 4.755266 TCTTATGGGTTTCACCTCTAGC 57.245 45.455 0.00 0.00 38.64 3.42
3388 5774 6.515862 CGAGATCTTATGGGTTTCACCTCTAG 60.516 46.154 0.00 0.00 38.64 2.43
3389 5775 5.302059 CGAGATCTTATGGGTTTCACCTCTA 59.698 44.000 0.00 0.00 38.64 2.43
3390 5776 4.100189 CGAGATCTTATGGGTTTCACCTCT 59.900 45.833 0.00 0.00 38.64 3.69
3391 5777 4.372656 CGAGATCTTATGGGTTTCACCTC 58.627 47.826 0.00 0.00 38.64 3.85
3392 5778 3.432326 GCGAGATCTTATGGGTTTCACCT 60.432 47.826 0.00 0.00 38.64 4.00
3393 5779 2.872858 GCGAGATCTTATGGGTTTCACC 59.127 50.000 0.00 0.00 37.60 4.02
3394 5780 3.531538 TGCGAGATCTTATGGGTTTCAC 58.468 45.455 0.00 0.00 0.00 3.18
3395 5781 3.904800 TGCGAGATCTTATGGGTTTCA 57.095 42.857 0.00 0.00 0.00 2.69
3396 5782 3.312697 GGTTGCGAGATCTTATGGGTTTC 59.687 47.826 0.00 0.00 0.00 2.78
3397 5783 3.279434 GGTTGCGAGATCTTATGGGTTT 58.721 45.455 0.00 0.00 0.00 3.27
3398 5784 2.238646 TGGTTGCGAGATCTTATGGGTT 59.761 45.455 0.00 0.00 0.00 4.11
3399 5785 1.837439 TGGTTGCGAGATCTTATGGGT 59.163 47.619 0.00 0.00 0.00 4.51
3400 5786 2.614057 GTTGGTTGCGAGATCTTATGGG 59.386 50.000 0.00 0.00 0.00 4.00
3401 5787 3.535561 AGTTGGTTGCGAGATCTTATGG 58.464 45.455 0.00 0.00 0.00 2.74
3402 5788 4.183865 TGAGTTGGTTGCGAGATCTTATG 58.816 43.478 0.00 0.00 0.00 1.90
3403 5789 4.471904 TGAGTTGGTTGCGAGATCTTAT 57.528 40.909 0.00 0.00 0.00 1.73
3404 5790 3.953712 TGAGTTGGTTGCGAGATCTTA 57.046 42.857 0.00 0.00 0.00 2.10
3405 5791 2.839486 TGAGTTGGTTGCGAGATCTT 57.161 45.000 0.00 0.00 0.00 2.40
3406 5792 2.625737 CATGAGTTGGTTGCGAGATCT 58.374 47.619 0.00 0.00 0.00 2.75
3407 5793 1.667724 CCATGAGTTGGTTGCGAGATC 59.332 52.381 0.00 0.00 40.99 2.75
3408 5794 1.742761 CCATGAGTTGGTTGCGAGAT 58.257 50.000 0.00 0.00 40.99 2.75
3409 5795 3.231734 CCATGAGTTGGTTGCGAGA 57.768 52.632 0.00 0.00 40.99 4.04
3418 5804 1.642037 CGTGCCAGAGCCATGAGTTG 61.642 60.000 0.00 0.00 38.69 3.16
3419 5805 1.376424 CGTGCCAGAGCCATGAGTT 60.376 57.895 0.00 0.00 38.69 3.01
3420 5806 2.267006 CGTGCCAGAGCCATGAGT 59.733 61.111 0.00 0.00 38.69 3.41
3421 5807 2.104859 CACGTGCCAGAGCCATGAG 61.105 63.158 0.82 0.00 38.69 2.90
3422 5808 2.046988 CACGTGCCAGAGCCATGA 60.047 61.111 0.82 0.00 38.69 3.07
3423 5809 2.881539 ATCCACGTGCCAGAGCCATG 62.882 60.000 10.91 0.00 38.69 3.66
3424 5810 2.202236 AATCCACGTGCCAGAGCCAT 62.202 55.000 10.91 0.00 38.69 4.40
3425 5811 2.894257 AATCCACGTGCCAGAGCCA 61.894 57.895 10.91 0.00 38.69 4.75
3426 5812 2.045926 AATCCACGTGCCAGAGCC 60.046 61.111 10.91 0.00 38.69 4.70
3427 5813 3.044059 GCAATCCACGTGCCAGAGC 62.044 63.158 10.91 6.26 35.91 4.09
3428 5814 1.236616 TTGCAATCCACGTGCCAGAG 61.237 55.000 10.91 0.00 41.49 3.35
3429 5815 1.228094 TTGCAATCCACGTGCCAGA 60.228 52.632 10.91 2.25 41.49 3.86
3430 5816 1.210931 CTTGCAATCCACGTGCCAG 59.789 57.895 10.91 0.00 41.49 4.85
3431 5817 2.918345 GCTTGCAATCCACGTGCCA 61.918 57.895 10.91 0.00 41.49 4.92
3432 5818 2.126346 GCTTGCAATCCACGTGCC 60.126 61.111 10.91 0.00 41.49 5.01
3433 5819 0.730494 GAAGCTTGCAATCCACGTGC 60.730 55.000 10.91 0.00 42.55 5.34
3434 5820 0.109597 GGAAGCTTGCAATCCACGTG 60.110 55.000 13.73 9.08 33.30 4.49
3435 5821 0.537143 TGGAAGCTTGCAATCCACGT 60.537 50.000 19.21 0.00 38.30 4.49
3436 5822 2.256391 TGGAAGCTTGCAATCCACG 58.744 52.632 19.21 0.00 38.30 4.94
3438 5824 1.865788 GCGTGGAAGCTTGCAATCCA 61.866 55.000 23.11 14.87 40.84 3.41
3439 5825 1.153958 GCGTGGAAGCTTGCAATCC 60.154 57.895 23.11 8.45 0.00 3.01
3440 5826 0.730494 GTGCGTGGAAGCTTGCAATC 60.730 55.000 23.11 16.57 39.34 2.67
3441 5827 1.286880 GTGCGTGGAAGCTTGCAAT 59.713 52.632 23.11 0.00 39.34 3.56
3442 5828 2.721231 GTGCGTGGAAGCTTGCAA 59.279 55.556 23.11 4.28 39.34 4.08
3443 5829 3.286751 GGTGCGTGGAAGCTTGCA 61.287 61.111 17.55 17.55 38.13 4.08
3444 5830 2.970974 GAGGTGCGTGGAAGCTTGC 61.971 63.158 11.58 11.58 38.13 4.01
3445 5831 1.302033 AGAGGTGCGTGGAAGCTTG 60.302 57.895 2.10 0.00 38.13 4.01
3446 5832 1.302033 CAGAGGTGCGTGGAAGCTT 60.302 57.895 0.00 0.00 38.13 3.74
3447 5833 2.345244 CAGAGGTGCGTGGAAGCT 59.655 61.111 0.00 0.00 38.13 3.74
3448 5834 2.029844 GACAGAGGTGCGTGGAAGC 61.030 63.158 0.00 0.00 37.71 3.86
3449 5835 1.374758 GGACAGAGGTGCGTGGAAG 60.375 63.158 0.00 0.00 0.00 3.46
3450 5836 1.480212 ATGGACAGAGGTGCGTGGAA 61.480 55.000 0.00 0.00 38.35 3.53
3451 5837 0.613572 TATGGACAGAGGTGCGTGGA 60.614 55.000 0.00 0.00 38.35 4.02
3452 5838 0.179100 CTATGGACAGAGGTGCGTGG 60.179 60.000 0.00 0.00 38.35 4.94
3453 5839 0.807667 GCTATGGACAGAGGTGCGTG 60.808 60.000 0.00 0.00 38.35 5.34
3454 5840 0.972983 AGCTATGGACAGAGGTGCGT 60.973 55.000 0.00 0.00 38.35 5.24
3455 5841 1.000827 CTAGCTATGGACAGAGGTGCG 60.001 57.143 8.72 0.00 38.35 5.34
3456 5842 1.270041 GCTAGCTATGGACAGAGGTGC 60.270 57.143 7.70 6.81 32.24 5.01
3457 5843 2.295909 GAGCTAGCTATGGACAGAGGTG 59.704 54.545 19.38 1.29 32.24 4.00
3458 5844 2.176798 AGAGCTAGCTATGGACAGAGGT 59.823 50.000 19.38 4.03 34.50 3.85
3459 5845 2.875296 AGAGCTAGCTATGGACAGAGG 58.125 52.381 19.38 0.00 0.00 3.69
3460 5846 4.501229 CCAAAGAGCTAGCTATGGACAGAG 60.501 50.000 27.69 9.84 30.53 3.35
3461 5847 3.386078 CCAAAGAGCTAGCTATGGACAGA 59.614 47.826 27.69 0.00 30.53 3.41
3462 5848 3.133721 ACCAAAGAGCTAGCTATGGACAG 59.866 47.826 33.71 17.94 32.26 3.51
3463 5849 3.107601 ACCAAAGAGCTAGCTATGGACA 58.892 45.455 33.71 0.00 32.26 4.02
3464 5850 3.133003 TCACCAAAGAGCTAGCTATGGAC 59.867 47.826 33.71 18.05 32.26 4.02
3465 5851 3.374764 TCACCAAAGAGCTAGCTATGGA 58.625 45.455 33.71 19.25 32.26 3.41
3466 5852 3.827008 TCACCAAAGAGCTAGCTATGG 57.173 47.619 28.91 28.91 33.36 2.74
3467 5853 6.095432 AGTATCACCAAAGAGCTAGCTATG 57.905 41.667 19.38 16.41 0.00 2.23
3468 5854 5.245075 GGAGTATCACCAAAGAGCTAGCTAT 59.755 44.000 19.38 12.73 36.25 2.97
3469 5855 4.585162 GGAGTATCACCAAAGAGCTAGCTA 59.415 45.833 19.38 0.00 36.25 3.32
3470 5856 3.386402 GGAGTATCACCAAAGAGCTAGCT 59.614 47.826 19.45 19.45 36.25 3.32
3471 5857 3.133003 TGGAGTATCACCAAAGAGCTAGC 59.867 47.826 6.62 6.62 36.25 3.42
3472 5858 5.344743 TTGGAGTATCACCAAAGAGCTAG 57.655 43.478 0.00 0.00 43.22 3.42
3481 5867 4.361783 TCTGAAGGATTGGAGTATCACCA 58.638 43.478 0.00 0.00 36.25 4.17
3482 5868 5.306678 AGATCTGAAGGATTGGAGTATCACC 59.693 44.000 0.00 0.00 33.06 4.02
3483 5869 6.267471 AGAGATCTGAAGGATTGGAGTATCAC 59.733 42.308 0.00 0.00 33.06 3.06
3484 5870 6.380414 AGAGATCTGAAGGATTGGAGTATCA 58.620 40.000 0.00 0.00 33.06 2.15
3485 5871 6.721208 AGAGAGATCTGAAGGATTGGAGTATC 59.279 42.308 0.00 0.00 34.33 2.24
3486 5872 6.623329 AGAGAGATCTGAAGGATTGGAGTAT 58.377 40.000 0.00 0.00 34.33 2.12
3487 5873 6.024563 AGAGAGATCTGAAGGATTGGAGTA 57.975 41.667 0.00 0.00 34.33 2.59
3488 5874 4.882559 AGAGAGATCTGAAGGATTGGAGT 58.117 43.478 0.00 0.00 34.33 3.85
3489 5875 5.874897 AAGAGAGATCTGAAGGATTGGAG 57.125 43.478 0.00 0.00 34.33 3.86
3490 5876 6.183360 CGTTAAGAGAGATCTGAAGGATTGGA 60.183 42.308 0.00 0.00 34.33 3.53
3491 5877 5.982516 CGTTAAGAGAGATCTGAAGGATTGG 59.017 44.000 0.00 0.00 34.33 3.16
3492 5878 5.982516 CCGTTAAGAGAGATCTGAAGGATTG 59.017 44.000 0.00 0.00 34.33 2.67
3493 5879 5.894393 TCCGTTAAGAGAGATCTGAAGGATT 59.106 40.000 0.00 0.00 34.33 3.01
3494 5880 5.300792 GTCCGTTAAGAGAGATCTGAAGGAT 59.699 44.000 0.00 0.00 37.37 3.24
3495 5881 4.641094 GTCCGTTAAGAGAGATCTGAAGGA 59.359 45.833 0.00 0.00 0.00 3.36
3496 5882 4.642885 AGTCCGTTAAGAGAGATCTGAAGG 59.357 45.833 0.00 0.00 0.00 3.46
3497 5883 5.220970 GGAGTCCGTTAAGAGAGATCTGAAG 60.221 48.000 0.00 0.00 0.00 3.02
3498 5884 4.641094 GGAGTCCGTTAAGAGAGATCTGAA 59.359 45.833 0.00 0.00 0.00 3.02
3499 5885 4.080243 AGGAGTCCGTTAAGAGAGATCTGA 60.080 45.833 0.00 0.00 0.00 3.27
3500 5886 4.204012 AGGAGTCCGTTAAGAGAGATCTG 58.796 47.826 0.00 0.00 0.00 2.90
3501 5887 4.457466 GAGGAGTCCGTTAAGAGAGATCT 58.543 47.826 2.76 0.00 0.00 2.75
3502 5888 3.566742 GGAGGAGTCCGTTAAGAGAGATC 59.433 52.174 2.76 0.00 31.37 2.75
3503 5889 3.558033 GGAGGAGTCCGTTAAGAGAGAT 58.442 50.000 2.76 0.00 31.37 2.75
3504 5890 2.356947 GGGAGGAGTCCGTTAAGAGAGA 60.357 54.545 2.76 0.00 45.05 3.10
3505 5891 2.025898 GGGAGGAGTCCGTTAAGAGAG 58.974 57.143 2.76 0.00 45.05 3.20
3506 5892 1.356738 TGGGAGGAGTCCGTTAAGAGA 59.643 52.381 2.76 0.00 45.05 3.10
3507 5893 1.848652 TGGGAGGAGTCCGTTAAGAG 58.151 55.000 2.76 0.00 45.05 2.85
3508 5894 2.108168 CATGGGAGGAGTCCGTTAAGA 58.892 52.381 2.76 0.00 45.05 2.10
3509 5895 1.831736 ACATGGGAGGAGTCCGTTAAG 59.168 52.381 2.76 0.00 45.05 1.85
3510 5896 1.946984 ACATGGGAGGAGTCCGTTAA 58.053 50.000 2.76 0.00 45.05 2.01
3511 5897 1.946984 AACATGGGAGGAGTCCGTTA 58.053 50.000 2.76 0.00 45.05 3.18
3512 5898 1.946984 TAACATGGGAGGAGTCCGTT 58.053 50.000 2.76 3.37 45.05 4.44
3513 5899 1.946984 TTAACATGGGAGGAGTCCGT 58.053 50.000 2.76 0.00 45.05 4.69
3514 5900 2.420129 CCTTTAACATGGGAGGAGTCCG 60.420 54.545 2.76 0.00 45.05 4.79
3515 5901 2.684038 GCCTTTAACATGGGAGGAGTCC 60.684 54.545 0.00 0.00 43.05 3.85
3516 5902 2.239907 AGCCTTTAACATGGGAGGAGTC 59.760 50.000 0.00 0.00 0.00 3.36
3517 5903 2.025887 CAGCCTTTAACATGGGAGGAGT 60.026 50.000 0.00 0.00 0.00 3.85
3518 5904 2.648059 CAGCCTTTAACATGGGAGGAG 58.352 52.381 0.00 0.00 0.00 3.69
3519 5905 1.340991 GCAGCCTTTAACATGGGAGGA 60.341 52.381 0.00 0.00 0.00 3.71
3520 5906 1.106285 GCAGCCTTTAACATGGGAGG 58.894 55.000 0.00 0.00 0.00 4.30
3521 5907 0.734889 CGCAGCCTTTAACATGGGAG 59.265 55.000 0.00 0.00 0.00 4.30
3522 5908 0.326595 TCGCAGCCTTTAACATGGGA 59.673 50.000 0.00 0.00 32.90 4.37
3523 5909 1.173043 TTCGCAGCCTTTAACATGGG 58.827 50.000 0.00 0.00 0.00 4.00
3524 5910 3.508744 AATTCGCAGCCTTTAACATGG 57.491 42.857 0.00 0.00 0.00 3.66
3525 5911 5.687285 GGATTAATTCGCAGCCTTTAACATG 59.313 40.000 0.00 0.00 0.00 3.21
3526 5912 5.594317 AGGATTAATTCGCAGCCTTTAACAT 59.406 36.000 0.00 0.00 0.00 2.71
3527 5913 4.947388 AGGATTAATTCGCAGCCTTTAACA 59.053 37.500 0.00 0.00 0.00 2.41
3528 5914 5.065988 TGAGGATTAATTCGCAGCCTTTAAC 59.934 40.000 0.00 0.00 0.00 2.01
3529 5915 5.189928 TGAGGATTAATTCGCAGCCTTTAA 58.810 37.500 0.00 0.00 0.00 1.52
3530 5916 4.776349 TGAGGATTAATTCGCAGCCTTTA 58.224 39.130 0.00 0.00 0.00 1.85
3531 5917 3.620488 TGAGGATTAATTCGCAGCCTTT 58.380 40.909 0.00 0.00 0.00 3.11
3532 5918 3.209410 CTGAGGATTAATTCGCAGCCTT 58.791 45.455 13.74 0.00 0.00 4.35
3533 5919 2.843701 CTGAGGATTAATTCGCAGCCT 58.156 47.619 13.74 2.90 0.00 4.58
3534 5920 1.265365 GCTGAGGATTAATTCGCAGCC 59.735 52.381 31.54 18.71 42.75 4.85
3535 5921 1.265365 GGCTGAGGATTAATTCGCAGC 59.735 52.381 32.94 32.94 45.40 5.25
3536 5922 2.843701 AGGCTGAGGATTAATTCGCAG 58.156 47.619 20.02 20.02 33.16 5.18
3537 5923 3.281727 AAGGCTGAGGATTAATTCGCA 57.718 42.857 0.00 0.00 0.00 5.10
3538 5924 3.378427 ACAAAGGCTGAGGATTAATTCGC 59.622 43.478 0.00 0.00 0.00 4.70
4074 6471 6.587206 TGCATGACATAAACAAGGATGAAA 57.413 33.333 0.00 0.00 0.00 2.69
4260 6659 2.815722 GCGGTTATGCCTCGATCTC 58.184 57.895 0.00 0.00 34.25 2.75
4437 6837 3.490526 CGTTTTTCATCAGCCCTTTTGTG 59.509 43.478 0.00 0.00 0.00 3.33
4440 6840 3.383185 TCACGTTTTTCATCAGCCCTTTT 59.617 39.130 0.00 0.00 0.00 2.27
4551 6982 1.926561 TACAGCAGCACATCATCGTC 58.073 50.000 0.00 0.00 0.00 4.20
4552 6983 2.274437 CTTACAGCAGCACATCATCGT 58.726 47.619 0.00 0.00 0.00 3.73
4553 6984 2.274437 ACTTACAGCAGCACATCATCG 58.726 47.619 0.00 0.00 0.00 3.84
4556 6987 2.849942 ACAACTTACAGCAGCACATCA 58.150 42.857 0.00 0.00 0.00 3.07
4586 7020 2.717580 TGAGCCTACAACTGTACACG 57.282 50.000 0.00 0.00 0.00 4.49
4627 7070 8.755018 CAACTTTCCATTAAATTCACACAAGAC 58.245 33.333 0.00 0.00 0.00 3.01
4630 7073 8.877779 CAACAACTTTCCATTAAATTCACACAA 58.122 29.630 0.00 0.00 0.00 3.33
4799 7274 5.853572 TTTCCTATTTACACTCCCTTGGT 57.146 39.130 0.00 0.00 0.00 3.67
4993 7470 0.321564 CATTCCCGGTTCAGACTGCA 60.322 55.000 0.00 0.00 0.00 4.41
5324 7801 4.500545 CGTTCTAGTGCAGAGGCTGAATAT 60.501 45.833 0.00 0.00 41.91 1.28


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

AutoCloner maintained by Alex Coulton.