Multiple sequence alignment - TraesCS6A01G218000

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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 TraesCS6A01G218000 chr6A 100.000 6163 0 0 1 6163 401890969 401884807 0.000000e+00 11382.0
1 TraesCS6A01G218000 chr6A 100.000 33 0 0 4328 4360 401886583 401886551 1.850000e-05 62.1
2 TraesCS6A01G218000 chr6A 100.000 33 0 0 4387 4419 401886642 401886610 1.850000e-05 62.1
3 TraesCS6A01G218000 chr6B 91.047 2837 137 42 964 3757 440559414 440556652 0.000000e+00 3723.0
4 TraesCS6A01G218000 chr6B 98.253 973 16 1 3 974 625072727 625073699 0.000000e+00 1701.0
5 TraesCS6A01G218000 chr6B 94.429 1077 33 15 3953 5027 440556571 440555520 0.000000e+00 1631.0
6 TraesCS6A01G218000 chr6B 93.662 852 50 4 5313 6163 440553502 440552654 0.000000e+00 1271.0
7 TraesCS6A01G218000 chr6B 91.204 216 11 7 5063 5272 440555519 440555306 2.810000e-73 287.0
8 TraesCS6A01G218000 chr6B 94.318 88 5 0 3780 3867 440556660 440556573 1.080000e-27 135.0
9 TraesCS6A01G218000 chr6B 100.000 34 0 0 4387 4420 440556199 440556166 5.160000e-06 63.9
10 TraesCS6A01G218000 chr6D 93.564 2020 78 21 1872 3870 280903185 280905173 0.000000e+00 2963.0
11 TraesCS6A01G218000 chr6D 93.569 1073 38 13 3968 5027 280905190 280906244 0.000000e+00 1570.0
12 TraesCS6A01G218000 chr6D 95.351 882 35 3 964 1840 280902311 280903191 0.000000e+00 1397.0
13 TraesCS6A01G218000 chr6D 93.606 391 23 2 5535 5925 280908689 280909077 3.200000e-162 582.0
14 TraesCS6A01G218000 chr6D 86.667 510 34 19 5060 5540 280906242 280906746 9.090000e-148 534.0
15 TraesCS6A01G218000 chr6D 89.286 196 16 3 5969 6163 278039337 278039146 2.220000e-59 241.0
16 TraesCS6A01G218000 chr6D 100.000 34 0 0 4387 4420 280905558 280905591 5.160000e-06 63.9
17 TraesCS6A01G218000 chr7B 91.770 972 73 6 1 966 615740567 615739597 0.000000e+00 1345.0
18 TraesCS6A01G218000 chr7B 84.615 975 104 15 1 967 749401745 749402681 0.000000e+00 928.0
19 TraesCS6A01G218000 chr7D 91.622 561 42 4 413 968 25205715 25206275 0.000000e+00 771.0
20 TraesCS6A01G218000 chr7D 87.317 410 29 4 1 409 25204581 25204968 1.220000e-121 448.0
21 TraesCS6A01G218000 chr7D 95.402 87 3 1 3868 3954 540863666 540863751 3.000000e-28 137.0
22 TraesCS6A01G218000 chr5A 89.016 437 41 6 2 432 611552396 611552831 9.090000e-148 534.0
23 TraesCS6A01G218000 chr5A 86.425 442 41 10 1 423 639208913 639209354 3.360000e-127 466.0
24 TraesCS6A01G218000 chr5A 93.478 92 5 1 3866 3957 564177636 564177726 1.080000e-27 135.0
25 TraesCS6A01G218000 chr5A 78.378 148 29 3 89 233 611552570 611552717 6.580000e-15 93.5
26 TraesCS6A01G218000 chr5A 100.000 39 0 0 3095 3133 237479117 237479155 8.570000e-09 73.1
27 TraesCS6A01G218000 chr2A 89.327 431 36 8 1 423 489970773 489971201 3.270000e-147 532.0
28 TraesCS6A01G218000 chr2A 83.902 410 49 14 4485 4881 594117039 594117444 5.830000e-100 375.0
29 TraesCS6A01G218000 chr2A 86.528 193 26 0 3526 3718 594115392 594115584 4.840000e-51 213.0
30 TraesCS6A01G218000 chr2A 76.471 357 63 16 5518 5859 606388554 606388904 2.280000e-39 174.0
31 TraesCS6A01G218000 chr2A 84.783 92 12 2 99 188 489970959 489971050 2.370000e-14 91.6
32 TraesCS6A01G218000 chr2B 84.173 417 44 17 4484 4885 529697307 529697716 9.690000e-103 385.0
33 TraesCS6A01G218000 chr2B 77.827 681 95 36 330 968 302101975 302101309 2.710000e-98 370.0
34 TraesCS6A01G218000 chr2B 85.990 207 26 3 3526 3731 529695662 529695866 1.040000e-52 219.0
35 TraesCS6A01G218000 chr2D 83.213 417 51 16 4485 4888 448521717 448521307 1.260000e-96 364.0
36 TraesCS6A01G218000 chr2D 87.368 190 24 0 3529 3718 448523327 448523138 1.040000e-52 219.0
37 TraesCS6A01G218000 chr1D 80.601 366 59 12 5518 5875 389104833 389104472 7.870000e-69 272.0
38 TraesCS6A01G218000 chrUn 93.617 94 3 3 3858 3950 62663392 62663483 3.000000e-28 137.0
39 TraesCS6A01G218000 chrUn 90.385 104 6 4 3865 3966 52071151 52071252 3.880000e-27 134.0
40 TraesCS6A01G218000 chr3B 95.402 87 3 1 3868 3954 686352240 686352325 3.000000e-28 137.0
41 TraesCS6A01G218000 chr3B 92.632 95 5 2 3857 3950 719826047 719826140 1.080000e-27 135.0
42 TraesCS6A01G218000 chr1A 90.476 105 8 2 170 273 518813538 518813641 3.000000e-28 137.0
43 TraesCS6A01G218000 chr1A 87.288 118 9 6 3866 3981 7181364 7181251 5.010000e-26 130.0
44 TraesCS6A01G218000 chr1B 93.478 92 4 2 3868 3959 631232761 631232672 1.080000e-27 135.0
45 TraesCS6A01G218000 chr3D 91.000 100 7 2 3866 3964 362238375 362238277 3.880000e-27 134.0
46 TraesCS6A01G218000 chr3D 82.105 95 16 1 5275 5368 322706648 322706554 5.120000e-11 80.5
47 TraesCS6A01G218000 chr4D 81.579 152 28 0 5708 5859 396250564 396250715 6.490000e-25 126.0


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 TraesCS6A01G218000 chr6A 401884807 401890969 6162 True 11382.000000 11382 100.000000 1 6163 1 chr6A.!!$R1 6162
1 TraesCS6A01G218000 chr6B 625072727 625073699 972 False 1701.000000 1701 98.253000 3 974 1 chr6B.!!$F1 971
2 TraesCS6A01G218000 chr6B 440552654 440559414 6760 True 1185.150000 3723 94.110000 964 6163 6 chr6B.!!$R1 5199
3 TraesCS6A01G218000 chr6D 280902311 280909077 6766 False 1184.983333 2963 93.792833 964 5925 6 chr6D.!!$F1 4961
4 TraesCS6A01G218000 chr7B 615739597 615740567 970 True 1345.000000 1345 91.770000 1 966 1 chr7B.!!$R1 965
5 TraesCS6A01G218000 chr7B 749401745 749402681 936 False 928.000000 928 84.615000 1 967 1 chr7B.!!$F1 966
6 TraesCS6A01G218000 chr7D 25204581 25206275 1694 False 609.500000 771 89.469500 1 968 2 chr7D.!!$F2 967
7 TraesCS6A01G218000 chr2A 594115392 594117444 2052 False 294.000000 375 85.215000 3526 4881 2 chr2A.!!$F3 1355
8 TraesCS6A01G218000 chr2B 302101309 302101975 666 True 370.000000 370 77.827000 330 968 1 chr2B.!!$R1 638
9 TraesCS6A01G218000 chr2B 529695662 529697716 2054 False 302.000000 385 85.081500 3526 4885 2 chr2B.!!$F1 1359
10 TraesCS6A01G218000 chr2D 448521307 448523327 2020 True 291.500000 364 85.290500 3529 4888 2 chr2D.!!$R1 1359

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
577 1326 2.145536 GGCAATCCAAGCAAAAACCAG 58.854 47.619 0.0 0.0 0.00 4.00 F
1081 1889 0.179936 CAATCCCAGTGCTCCTCCTC 59.820 60.000 0.0 0.0 0.00 3.71 F
2169 2979 0.690762 ACCAGTAACAGCGGGTCAAT 59.309 50.000 0.0 0.0 31.39 2.57 F
3887 5331 0.822164 ACTCCCTTCGTCCCGTAATG 59.178 55.000 0.0 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2840 0.038343 CATTGGTTTTCTGTGGGCCG 60.038 55.0 0.00 0.0 0.00 6.13 R
2578 3395 0.179018 GGACTTTGGACCACACTGCT 60.179 55.0 0.00 0.0 0.00 4.24 R
3936 5390 0.267960 ACCTAATCCCTCCGTCCCAT 59.732 55.0 0.00 0.0 0.00 4.00 R
5339 9018 0.248843 GAGAGCACTCAAGGGGACAG 59.751 60.0 6.25 0.0 42.21 3.51 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
345 347 6.266330 AGAGCTAGTTCCAGCAAAATTTCTTT 59.734 34.615 2.55 0.00 44.35 2.52
577 1326 2.145536 GGCAATCCAAGCAAAAACCAG 58.854 47.619 0.00 0.00 0.00 4.00
936 1733 4.084888 GCGACCGGCCGAAGTTTG 62.085 66.667 30.73 11.56 34.80 2.93
1050 1854 0.752376 CTCCCGTACCTGACCTCTCC 60.752 65.000 0.00 0.00 0.00 3.71
1081 1889 0.179936 CAATCCCAGTGCTCCTCCTC 59.820 60.000 0.00 0.00 0.00 3.71
1106 1914 1.959985 CTATCGTCCATGGACTGCTCT 59.040 52.381 35.84 20.29 42.54 4.09
1195 2003 3.521560 TGGCGTCAGTGAGATGTAATTC 58.478 45.455 0.00 0.00 35.60 2.17
1445 2253 3.735029 GCCTCGACGTCACCGACT 61.735 66.667 17.16 0.00 37.88 4.18
1484 2292 4.271816 CCTCCTGGATCCGCGACG 62.272 72.222 8.23 0.00 34.57 5.12
1486 2294 2.518587 TCCTGGATCCGCGACGAT 60.519 61.111 8.23 1.60 0.00 3.73
1535 2343 2.278094 CGCACGATCGTCTATTTTTCGT 59.722 45.455 19.84 0.00 43.18 3.85
1544 2352 7.097128 CGATCGTCTATTTTTCGTCGTCTATTT 60.097 37.037 7.03 0.00 0.00 1.40
1546 2354 6.193410 TCGTCTATTTTTCGTCGTCTATTTCG 59.807 38.462 0.00 0.00 0.00 3.46
1547 2355 6.112343 GTCTATTTTTCGTCGTCTATTTCGC 58.888 40.000 0.00 0.00 0.00 4.70
1560 2368 1.204146 ATTTCGCTGCTTCTCCCCTA 58.796 50.000 0.00 0.00 0.00 3.53
1650 2459 2.361992 CCCCTACCCCGGCAAAAC 60.362 66.667 0.00 0.00 0.00 2.43
1666 2475 3.490526 GCAAAACATGTGGTGTGCTAAAG 59.509 43.478 5.96 0.00 41.14 1.85
1710 2519 2.163412 CCATGTTAACCACCCGATTGTG 59.837 50.000 2.48 0.00 35.98 3.33
1713 2522 3.666274 TGTTAACCACCCGATTGTGTAG 58.334 45.455 2.48 0.00 34.35 2.74
1721 2530 5.045724 ACCACCCGATTGTGTAGGTAATTAA 60.046 40.000 0.00 0.00 34.35 1.40
1743 2552 2.092753 GGTTAGGGGTTGGCTTACCTAC 60.093 54.545 8.83 0.00 40.56 3.18
1832 2641 7.005296 ACTACTCCGATCCACTATAGACAAAT 58.995 38.462 6.78 0.00 0.00 2.32
1843 2652 6.742718 CCACTATAGACAAATTTTGCAACTCG 59.257 38.462 6.78 0.00 0.00 4.18
1854 2663 1.741770 GCAACTCGCACCCCACTAG 60.742 63.158 0.00 0.00 41.79 2.57
1884 2693 5.047164 ACATATGTCCTTTTGCAAAGCATGA 60.047 36.000 12.41 5.11 38.76 3.07
1961 2770 5.067153 TGCGTTTATGCTAAATAAGGCATGT 59.933 36.000 10.16 0.00 46.75 3.21
1982 2791 5.443283 TGTCGGTGAAGTATATCTGGTACT 58.557 41.667 0.00 0.00 33.98 2.73
1983 2792 5.530171 TGTCGGTGAAGTATATCTGGTACTC 59.470 44.000 0.00 0.00 31.44 2.59
1984 2793 5.048852 GTCGGTGAAGTATATCTGGTACTCC 60.049 48.000 0.00 0.00 31.44 3.85
1985 2794 5.071370 CGGTGAAGTATATCTGGTACTCCT 58.929 45.833 0.00 0.00 31.44 3.69
2023 2833 8.999431 ACAGTTATGATCGTGAACTAAAACATT 58.001 29.630 0.00 0.00 32.22 2.71
2024 2834 9.265938 CAGTTATGATCGTGAACTAAAACATTG 57.734 33.333 0.00 0.00 32.22 2.82
2025 2835 8.999431 AGTTATGATCGTGAACTAAAACATTGT 58.001 29.630 0.00 0.00 31.69 2.71
2027 2837 9.605955 TTATGATCGTGAACTAAAACATTGTTG 57.394 29.630 2.13 0.00 0.00 3.33
2028 2838 6.434596 TGATCGTGAACTAAAACATTGTTGG 58.565 36.000 2.13 0.00 0.00 3.77
2029 2839 4.602995 TCGTGAACTAAAACATTGTTGGC 58.397 39.130 2.13 0.00 0.00 4.52
2030 2840 3.733727 CGTGAACTAAAACATTGTTGGCC 59.266 43.478 2.13 0.00 0.00 5.36
2043 2853 3.740495 TTGGCCGGCCCACAGAAAA 62.740 57.895 41.75 24.84 45.34 2.29
2073 2883 2.969950 AGACTGCAACCACCAGTAACTA 59.030 45.455 0.00 0.00 43.17 2.24
2153 2963 4.574674 AATTAGAGCCAAGTCATCACCA 57.425 40.909 0.00 0.00 0.00 4.17
2169 2979 0.690762 ACCAGTAACAGCGGGTCAAT 59.309 50.000 0.00 0.00 31.39 2.57
2170 2980 1.073284 ACCAGTAACAGCGGGTCAATT 59.927 47.619 0.00 0.00 31.39 2.32
2184 2994 2.437716 AATTAGGGCACGCCACGG 60.438 61.111 10.83 0.00 37.98 4.94
2226 3039 7.588497 AGTAATCAGCTGACCTTTTCTTTTT 57.412 32.000 20.97 7.83 0.00 1.94
2229 3042 3.636764 TCAGCTGACCTTTTCTTTTTCCC 59.363 43.478 13.74 0.00 0.00 3.97
2231 3044 4.100035 CAGCTGACCTTTTCTTTTTCCCTT 59.900 41.667 8.42 0.00 0.00 3.95
2232 3045 4.342378 AGCTGACCTTTTCTTTTTCCCTTC 59.658 41.667 0.00 0.00 0.00 3.46
2233 3046 4.099419 GCTGACCTTTTCTTTTTCCCTTCA 59.901 41.667 0.00 0.00 0.00 3.02
2234 3047 5.221521 GCTGACCTTTTCTTTTTCCCTTCAT 60.222 40.000 0.00 0.00 0.00 2.57
2235 3048 6.015434 GCTGACCTTTTCTTTTTCCCTTCATA 60.015 38.462 0.00 0.00 0.00 2.15
2236 3049 7.310052 GCTGACCTTTTCTTTTTCCCTTCATAT 60.310 37.037 0.00 0.00 0.00 1.78
2237 3050 9.243105 CTGACCTTTTCTTTTTCCCTTCATATA 57.757 33.333 0.00 0.00 0.00 0.86
2238 3051 9.020731 TGACCTTTTCTTTTTCCCTTCATATAC 57.979 33.333 0.00 0.00 0.00 1.47
2239 3052 8.950007 ACCTTTTCTTTTTCCCTTCATATACA 57.050 30.769 0.00 0.00 0.00 2.29
2240 3053 9.547279 ACCTTTTCTTTTTCCCTTCATATACAT 57.453 29.630 0.00 0.00 0.00 2.29
2281 3094 7.652105 GTCGATAGTGATCTTGGCACTTAATAA 59.348 37.037 0.00 0.00 43.67 1.40
2417 3232 9.939047 GATTTCGATATTTGTATAGCTTGTACG 57.061 33.333 0.00 0.00 0.00 3.67
2418 3233 8.861033 TTTCGATATTTGTATAGCTTGTACGT 57.139 30.769 0.00 0.00 0.00 3.57
2419 3234 9.949174 TTTCGATATTTGTATAGCTTGTACGTA 57.051 29.630 0.00 0.00 0.00 3.57
2420 3235 8.939586 TCGATATTTGTATAGCTTGTACGTAC 57.060 34.615 18.90 18.90 0.00 3.67
2502 3317 2.896801 GCAGGTCAACCACGCACAG 61.897 63.158 1.33 0.00 38.89 3.66
2560 3377 2.947652 CTGCATATTGTCTGTTGAGGGG 59.052 50.000 0.00 0.00 0.00 4.79
2564 3381 2.586648 ATTGTCTGTTGAGGGGTTCC 57.413 50.000 0.00 0.00 0.00 3.62
2576 3393 6.265876 TGTTGAGGGGTTCCATTTAAACTAAC 59.734 38.462 0.00 0.00 34.83 2.34
2578 3395 5.162969 TGAGGGGTTCCATTTAAACTAACCA 60.163 40.000 20.99 6.33 41.12 3.67
2621 3438 3.550842 CGAGCCAGATGATACACGATTCA 60.551 47.826 0.00 0.00 0.00 2.57
2686 3503 5.583854 GCATGCAGTTCGATCCAGATATTAT 59.416 40.000 14.21 0.00 0.00 1.28
2738 3558 2.668550 GAGGGCGGCGAACAAACT 60.669 61.111 12.98 0.00 0.00 2.66
2739 3559 1.375013 GAGGGCGGCGAACAAACTA 60.375 57.895 12.98 0.00 0.00 2.24
2740 3560 1.359459 GAGGGCGGCGAACAAACTAG 61.359 60.000 12.98 0.00 0.00 2.57
2907 3746 2.072298 GACATCATCATAGAAGGCGGC 58.928 52.381 0.00 0.00 0.00 6.53
2913 3752 1.153449 CATAGAAGGCGGCCGTTGA 60.153 57.895 28.70 6.90 0.00 3.18
2967 3807 1.731720 AGCAGCGGAGTTTTCATCTC 58.268 50.000 0.00 0.00 0.00 2.75
2969 3809 1.663135 GCAGCGGAGTTTTCATCTCTC 59.337 52.381 0.00 0.00 33.06 3.20
2971 3811 3.594134 CAGCGGAGTTTTCATCTCTCTT 58.406 45.455 0.00 0.00 33.06 2.85
3016 3856 8.938906 GGATAGTATGTGAAACGGTCTTTTTAA 58.061 33.333 0.00 0.00 42.39 1.52
3160 4009 9.877178 AATAACAGAGGATAAGTTACTGAACTG 57.123 33.333 0.00 0.00 45.50 3.16
3165 4014 6.380560 AGAGGATAAGTTACTGAACTGGGTAC 59.619 42.308 0.00 0.00 45.50 3.34
3172 4021 7.735326 AGTTACTGAACTGGGTACATTATCT 57.265 36.000 0.00 0.00 44.50 1.98
3225 4074 3.170791 ACTTATCCGTCATCAGCTGTG 57.829 47.619 14.67 11.47 0.00 3.66
3228 4077 1.189752 ATCCGTCATCAGCTGTGACT 58.810 50.000 29.73 18.22 42.88 3.41
3266 4115 6.524101 TGCTTAGTTAAATTAGGGCAAAGG 57.476 37.500 0.00 0.00 0.00 3.11
3319 4168 6.900194 AGCACAATTTCTAATTCTAGGCCTA 58.100 36.000 13.09 13.09 0.00 3.93
3332 4181 3.759086 TCTAGGCCTATATCAGCAAGACG 59.241 47.826 14.30 0.00 0.00 4.18
3370 4219 6.646653 CCAGAAAGAACAAAGGGAAAATAAGC 59.353 38.462 0.00 0.00 0.00 3.09
3449 4298 6.703165 ACATGCTTTCAGGATTTGTTTTCTTC 59.297 34.615 0.00 0.00 0.00 2.87
3476 4325 5.253096 AGCCAAACCCTAGGAATCTTCTTAA 59.747 40.000 11.48 0.00 0.00 1.85
3477 4326 6.068794 AGCCAAACCCTAGGAATCTTCTTAAT 60.069 38.462 11.48 0.00 0.00 1.40
3478 4327 7.128883 AGCCAAACCCTAGGAATCTTCTTAATA 59.871 37.037 11.48 0.00 0.00 0.98
3479 4328 7.778382 GCCAAACCCTAGGAATCTTCTTAATAA 59.222 37.037 11.48 0.00 0.00 1.40
3719 4615 3.350833 CTTGGCCTTCTCAATGTAAGCT 58.649 45.455 3.32 0.00 0.00 3.74
3751 4647 7.115947 GCTGTTAAGTAAACTACCAGTACTGTG 59.884 40.741 21.18 14.60 38.99 3.66
3844 4864 1.202348 GCATGAGGCAAATAACGCGC 61.202 55.000 5.73 0.00 43.97 6.86
3857 4877 3.470567 CGCGCTCAGACGGTTCAC 61.471 66.667 5.56 0.00 0.00 3.18
3875 5319 6.401394 GGTTCACTTTACGTTATACTCCCTT 58.599 40.000 0.00 0.00 0.00 3.95
3882 5326 1.002033 CGTTATACTCCCTTCGTCCCG 60.002 57.143 0.00 0.00 0.00 5.14
3883 5327 2.027385 GTTATACTCCCTTCGTCCCGT 58.973 52.381 0.00 0.00 0.00 5.28
3887 5331 0.822164 ACTCCCTTCGTCCCGTAATG 59.178 55.000 0.00 0.00 0.00 1.90
3888 5332 0.822164 CTCCCTTCGTCCCGTAATGT 59.178 55.000 0.00 0.00 0.00 2.71
3889 5333 2.026641 CTCCCTTCGTCCCGTAATGTA 58.973 52.381 0.00 0.00 0.00 2.29
3890 5334 2.428171 CTCCCTTCGTCCCGTAATGTAA 59.572 50.000 0.00 0.00 0.00 2.41
3892 5336 2.428171 CCCTTCGTCCCGTAATGTAAGA 59.572 50.000 0.00 0.00 0.00 2.10
3895 5339 2.549633 CGTCCCGTAATGTAAGACGT 57.450 50.000 2.88 0.00 43.89 4.34
3896 5340 2.867429 CGTCCCGTAATGTAAGACGTT 58.133 47.619 2.88 0.00 43.89 3.99
3897 5341 3.244976 CGTCCCGTAATGTAAGACGTTT 58.755 45.455 2.88 0.00 43.89 3.60
3950 5404 2.118403 ACATTATGGGACGGAGGGAT 57.882 50.000 0.00 0.00 0.00 3.85
3963 5417 6.012745 GGACGGAGGGATTAGGTTATACTAA 58.987 44.000 0.00 0.00 37.35 2.24
3964 5418 6.666980 GGACGGAGGGATTAGGTTATACTAAT 59.333 42.308 0.00 0.00 44.17 1.73
3965 5419 7.836183 GGACGGAGGGATTAGGTTATACTAATA 59.164 40.741 0.00 0.00 42.19 0.98
3966 5420 8.820153 ACGGAGGGATTAGGTTATACTAATAG 57.180 38.462 0.00 0.00 42.19 1.73
4238 6109 4.713792 AACTCTCCTCCAGAAACAATGT 57.286 40.909 0.00 0.00 0.00 2.71
4255 6126 7.572523 AACAATGTCAATTCTCTTGAGTCAA 57.427 32.000 5.25 5.25 0.00 3.18
4290 6169 1.417517 TGACAGCATCAGTGTCCTGTT 59.582 47.619 12.07 0.00 43.19 3.16
4360 6239 2.821969 GTCCAATTCCATGCTCAACACT 59.178 45.455 0.00 0.00 0.00 3.55
4380 6259 9.776158 CAACACTGAGTTCATTAGTAGTAGTAG 57.224 37.037 0.00 0.00 38.74 2.57
4381 6260 9.517868 AACACTGAGTTCATTAGTAGTAGTAGT 57.482 33.333 0.00 0.00 34.74 2.73
4409 6288 6.669125 TTCTGAAACAATGTCCAATTCCAT 57.331 33.333 0.00 0.00 0.00 3.41
4410 6289 6.028146 TCTGAAACAATGTCCAATTCCATG 57.972 37.500 0.00 0.00 0.00 3.66
4411 6290 4.567971 TGAAACAATGTCCAATTCCATGC 58.432 39.130 0.00 0.00 0.00 4.06
4412 6291 4.283978 TGAAACAATGTCCAATTCCATGCT 59.716 37.500 0.00 0.00 0.00 3.79
4413 6292 4.460948 AACAATGTCCAATTCCATGCTC 57.539 40.909 0.00 0.00 0.00 4.26
4414 6293 3.433343 ACAATGTCCAATTCCATGCTCA 58.567 40.909 0.00 0.00 0.00 4.26
4415 6294 3.833650 ACAATGTCCAATTCCATGCTCAA 59.166 39.130 0.00 0.00 0.00 3.02
4416 6295 4.178540 CAATGTCCAATTCCATGCTCAAC 58.821 43.478 0.00 0.00 0.00 3.18
4417 6296 2.874014 TGTCCAATTCCATGCTCAACA 58.126 42.857 0.00 0.00 0.00 3.33
4418 6297 2.557924 TGTCCAATTCCATGCTCAACAC 59.442 45.455 0.00 0.00 0.00 3.32
4419 6298 2.557924 GTCCAATTCCATGCTCAACACA 59.442 45.455 0.00 0.00 0.00 3.72
4420 6299 3.005684 GTCCAATTCCATGCTCAACACAA 59.994 43.478 0.00 0.00 0.00 3.33
4421 6300 3.005684 TCCAATTCCATGCTCAACACAAC 59.994 43.478 0.00 0.00 0.00 3.32
4422 6301 2.981805 CAATTCCATGCTCAACACAACG 59.018 45.455 0.00 0.00 0.00 4.10
4423 6302 1.960417 TTCCATGCTCAACACAACGA 58.040 45.000 0.00 0.00 0.00 3.85
4424 6303 1.960417 TCCATGCTCAACACAACGAA 58.040 45.000 0.00 0.00 0.00 3.85
4425 6304 1.872952 TCCATGCTCAACACAACGAAG 59.127 47.619 0.00 0.00 0.00 3.79
4939 6831 1.231296 TGCACGCTTACGATTTGGCA 61.231 50.000 0.00 0.00 43.93 4.92
4995 6888 2.092538 CCATCTCCTCACCAAGCTTGAT 60.093 50.000 28.05 8.09 0.00 2.57
4997 6890 1.093159 CTCCTCACCAAGCTTGATGC 58.907 55.000 28.05 0.00 43.29 3.91
5013 6906 0.249489 ATGCCTCCGAACTATCACGC 60.249 55.000 0.00 0.00 0.00 5.34
5021 6914 1.836383 GAACTATCACGCCCGTACAG 58.164 55.000 0.00 0.00 0.00 2.74
5024 6917 1.133790 ACTATCACGCCCGTACAGTTC 59.866 52.381 0.00 0.00 0.00 3.01
5025 6918 1.404391 CTATCACGCCCGTACAGTTCT 59.596 52.381 0.00 0.00 0.00 3.01
5026 6919 0.172803 ATCACGCCCGTACAGTTCTC 59.827 55.000 0.00 0.00 0.00 2.87
5027 6920 1.800315 CACGCCCGTACAGTTCTCG 60.800 63.158 0.00 0.00 0.00 4.04
5028 6921 1.968017 ACGCCCGTACAGTTCTCGA 60.968 57.895 0.00 0.00 0.00 4.04
5029 6922 1.210931 CGCCCGTACAGTTCTCGAA 59.789 57.895 0.00 0.00 0.00 3.71
5030 6923 0.797249 CGCCCGTACAGTTCTCGAAG 60.797 60.000 0.00 0.00 0.00 3.79
5031 6924 0.524862 GCCCGTACAGTTCTCGAAGA 59.475 55.000 0.00 0.00 0.00 2.87
5032 6925 1.134560 GCCCGTACAGTTCTCGAAGAT 59.865 52.381 0.00 0.00 33.89 2.40
5033 6926 2.416972 GCCCGTACAGTTCTCGAAGATT 60.417 50.000 0.00 0.00 33.89 2.40
5034 6927 3.436496 CCCGTACAGTTCTCGAAGATTC 58.564 50.000 0.00 0.00 33.89 2.52
5044 6937 3.314339 CGAAGATTCGTGCTCGTCT 57.686 52.632 8.17 1.80 45.09 4.18
5045 6938 1.618861 CGAAGATTCGTGCTCGTCTT 58.381 50.000 12.17 12.17 45.09 3.01
5046 6939 1.986378 CGAAGATTCGTGCTCGTCTTT 59.014 47.619 13.18 3.54 45.09 2.52
5047 6940 2.408704 CGAAGATTCGTGCTCGTCTTTT 59.591 45.455 13.18 3.83 45.09 2.27
5048 6941 3.719186 CGAAGATTCGTGCTCGTCTTTTG 60.719 47.826 13.18 7.49 45.09 2.44
5049 6942 3.026630 AGATTCGTGCTCGTCTTTTGA 57.973 42.857 8.17 0.00 38.33 2.69
5050 6943 2.731976 AGATTCGTGCTCGTCTTTTGAC 59.268 45.455 8.17 0.00 45.55 3.18
5065 6958 6.529220 GTCTTTTGACAGGATAGCCTATCAT 58.471 40.000 9.18 3.42 46.59 2.45
5118 7018 2.889170 AAAAAGCTCTCCTCCCTTCC 57.111 50.000 0.00 0.00 0.00 3.46
5120 7020 1.284313 AAAGCTCTCCTCCCTTCCTG 58.716 55.000 0.00 0.00 0.00 3.86
5121 7021 1.271127 AAGCTCTCCTCCCTTCCTGC 61.271 60.000 0.00 0.00 0.00 4.85
5229 7129 2.881734 TGTATGCCCAAACCATGTTCA 58.118 42.857 0.00 0.00 0.00 3.18
5238 7138 4.156556 CCCAAACCATGTTCATACACTCAG 59.843 45.833 0.00 0.00 37.03 3.35
5245 7145 6.013725 ACCATGTTCATACACTCAGAAAGGTA 60.014 38.462 0.00 0.00 37.03 3.08
5264 8915 1.039856 ATGCACCCTTTTGTGTGTCC 58.960 50.000 0.00 0.00 38.52 4.02
5277 8954 4.481368 TGTGTGTCCATGTATTACCCTC 57.519 45.455 0.00 0.00 0.00 4.30
5363 9042 1.536073 CCCTTGAGTGCTCTCGGTCA 61.536 60.000 10.97 0.00 43.09 4.02
5382 9061 2.169144 TCATCCGATCTGCACACTTGAT 59.831 45.455 0.00 0.00 0.00 2.57
5401 9080 4.984295 TGATTGTTCAATTCTCCTGTCCA 58.016 39.130 0.00 0.00 0.00 4.02
5412 9091 0.826256 TCCTGTCCAGCTGTACGTGT 60.826 55.000 13.81 0.00 0.00 4.49
5482 9161 2.675423 CTCCTCGTGGACGGGTGA 60.675 66.667 1.10 0.00 38.37 4.02
5502 9181 4.444720 GTGACTTTGTCCTAGTTTGTCTCG 59.555 45.833 0.00 0.00 0.00 4.04
5566 11193 5.431765 CCCTAATCTATGTGCTTTCTGTGT 58.568 41.667 0.00 0.00 0.00 3.72
5568 11195 5.525378 CCTAATCTATGTGCTTTCTGTGTCC 59.475 44.000 0.00 0.00 0.00 4.02
5604 11231 1.938577 GCTAGCACACACAGATCATGG 59.061 52.381 10.63 0.00 0.00 3.66
5739 11366 4.588951 TGTGTCTTCCATCTACTCACAAGT 59.411 41.667 0.00 0.00 39.66 3.16
5784 11411 7.255208 CGTAACCCTACTTCTTATCTCTCCTTC 60.255 44.444 0.00 0.00 0.00 3.46
5789 11416 7.832187 CCCTACTTCTTATCTCTCCTTCGATAT 59.168 40.741 0.00 0.00 0.00 1.63
5800 11427 7.010771 TCTCTCCTTCGATATGGAAAATCCTA 58.989 38.462 1.63 0.00 37.46 2.94
5836 11463 1.665679 CAGCCACGATGGTCAATACAC 59.334 52.381 0.00 0.00 40.46 2.90
5913 11540 9.816787 AATATAAGGTAAAAGAGTTTCCAACCA 57.183 29.630 0.00 0.00 0.00 3.67
5925 11552 6.209788 AGAGTTTCCAACCAGTTTTGTAACAA 59.790 34.615 0.00 0.00 36.70 2.83
5928 11555 7.880713 AGTTTCCAACCAGTTTTGTAACAAAAT 59.119 29.630 0.00 0.00 36.70 1.82
5984 11611 2.504175 TCACCTAATGACTACCCAAGGC 59.496 50.000 0.00 0.00 29.99 4.35
5992 11619 1.831736 GACTACCCAAGGCTAAGCTGA 59.168 52.381 0.00 0.00 0.00 4.26
6018 11645 4.296056 ACCTCCCGTTTCTAACCATAGAT 58.704 43.478 0.00 0.00 37.97 1.98
6030 11657 3.543680 ACCATAGATGAGAACCAACCG 57.456 47.619 0.00 0.00 0.00 4.44
6032 11659 3.711704 ACCATAGATGAGAACCAACCGAT 59.288 43.478 0.00 0.00 0.00 4.18
6063 11690 7.230108 CAGAGATGATAAAGGGCATGTATGTTT 59.770 37.037 0.00 0.00 0.00 2.83
6069 11696 2.806434 AGGGCATGTATGTTTCAAGCA 58.194 42.857 0.00 0.00 32.26 3.91
6071 11698 2.518949 GGCATGTATGTTTCAAGCACG 58.481 47.619 0.00 0.00 32.26 5.34
6074 11701 2.967459 TGTATGTTTCAAGCACGCTG 57.033 45.000 0.00 0.00 0.00 5.18
6084 11711 1.580845 AAGCACGCTGAGTCAATGGC 61.581 55.000 0.00 0.00 0.00 4.40
6085 11712 2.327343 GCACGCTGAGTCAATGGCA 61.327 57.895 0.00 0.00 0.00 4.92
6105 11732 1.479709 ACTCTAGAGCGCATCAACCT 58.520 50.000 19.97 0.00 0.00 3.50
6121 11748 5.147330 TCAACCTTCGACACATATCACTT 57.853 39.130 0.00 0.00 0.00 3.16
6135 11763 5.829924 ACATATCACTTGAAATGATGGTCCC 59.170 40.000 0.00 0.00 37.38 4.46
6149 11777 0.725117 GGTCCCGAAATACAAGTGCG 59.275 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
450 1196 4.498009 CGGTGCTTCAATCAGTGAGTTTTT 60.498 41.667 0.00 0.00 37.61 1.94
799 1589 2.102588 CCCTCGTTCCTTATCCATTCGT 59.897 50.000 0.00 0.00 0.00 3.85
1050 1854 0.181114 TGGGATTGCCTCGATGGAAG 59.819 55.000 0.82 0.00 38.35 3.46
1081 1889 0.969894 GTCCATGGACGATAGAGGGG 59.030 60.000 28.52 0.00 41.38 4.79
1106 1914 1.001633 GGTGGCGTCTCTTTGGAACTA 59.998 52.381 0.00 0.00 0.00 2.24
1195 2003 1.581602 CGCAAAACAAAGTCAACCACG 59.418 47.619 0.00 0.00 0.00 4.94
1535 2343 2.479730 GGAGAAGCAGCGAAATAGACGA 60.480 50.000 0.00 0.00 0.00 4.20
1544 2352 1.204146 ATTTAGGGGAGAAGCAGCGA 58.796 50.000 0.00 0.00 0.00 4.93
1546 2354 2.302260 GGAATTTAGGGGAGAAGCAGC 58.698 52.381 0.00 0.00 0.00 5.25
1547 2355 2.746472 CGGGAATTTAGGGGAGAAGCAG 60.746 54.545 0.00 0.00 0.00 4.24
1686 2495 0.322098 TCGGGTGGTTAACATGGCTG 60.322 55.000 8.10 0.00 0.00 4.85
1710 2519 6.359804 CCAACCCCTAACCTTAATTACCTAC 58.640 44.000 0.00 0.00 0.00 3.18
1713 2522 3.956199 GCCAACCCCTAACCTTAATTACC 59.044 47.826 0.00 0.00 0.00 2.85
1721 2530 0.997363 GGTAAGCCAACCCCTAACCT 59.003 55.000 0.00 0.00 33.02 3.50
1743 2552 8.568676 AGTAGTATGTATGCATGGTAGACTAG 57.431 38.462 10.16 0.00 36.58 2.57
1782 2591 2.513753 CAGTACTTGTCATTTGGGGCA 58.486 47.619 0.00 0.00 0.00 5.36
1843 2652 2.122783 TGTTATTGCTAGTGGGGTGC 57.877 50.000 0.00 0.00 0.00 5.01
1854 2663 7.593875 TTTGCAAAAGGACATATGTTATTGC 57.406 32.000 25.63 25.63 0.00 3.56
1884 2693 7.996098 TTTAATTTAGCAGAAAGTAGCTGGT 57.004 32.000 0.00 0.00 45.16 4.00
1961 2770 5.068636 GGAGTACCAGATATACTTCACCGA 58.931 45.833 0.00 0.00 32.93 4.69
1982 2791 6.734532 TCATAACTGTACCCAACTACTAGGA 58.265 40.000 0.00 0.00 0.00 2.94
1983 2792 7.521748 CGATCATAACTGTACCCAACTACTAGG 60.522 44.444 0.00 0.00 0.00 3.02
1984 2793 7.013083 ACGATCATAACTGTACCCAACTACTAG 59.987 40.741 0.00 0.00 0.00 2.57
1985 2794 6.830324 ACGATCATAACTGTACCCAACTACTA 59.170 38.462 0.00 0.00 0.00 1.82
2024 2834 4.966787 TTCTGTGGGCCGGCCAAC 62.967 66.667 41.48 41.48 40.44 3.77
2025 2835 3.740495 TTTTCTGTGGGCCGGCCAA 62.740 57.895 44.46 35.30 37.98 4.52
2027 2837 3.680786 GTTTTCTGTGGGCCGGCC 61.681 66.667 38.57 38.57 0.00 6.13
2028 2838 3.680786 GGTTTTCTGTGGGCCGGC 61.681 66.667 21.18 21.18 0.00 6.13
2029 2839 1.184970 ATTGGTTTTCTGTGGGCCGG 61.185 55.000 0.00 0.00 0.00 6.13
2030 2840 0.038343 CATTGGTTTTCTGTGGGCCG 60.038 55.000 0.00 0.00 0.00 6.13
2043 2853 1.133823 TGGTTGCAGTCTGTCATTGGT 60.134 47.619 0.93 0.00 0.00 3.67
2073 2883 3.709653 TCCACTGAAACACTACCTCTTGT 59.290 43.478 0.00 0.00 0.00 3.16
2153 2963 2.093128 CCCTAATTGACCCGCTGTTACT 60.093 50.000 0.00 0.00 0.00 2.24
2186 2996 0.968901 TACTACACTGAGGGCCGTGG 60.969 60.000 0.65 3.06 35.51 4.94
2188 2998 1.755380 GATTACTACACTGAGGGCCGT 59.245 52.381 0.00 0.00 0.00 5.68
2189 2999 1.754803 TGATTACTACACTGAGGGCCG 59.245 52.381 0.00 0.00 0.00 6.13
2193 3006 4.440802 GGTCAGCTGATTACTACACTGAGG 60.441 50.000 21.47 0.00 35.02 3.86
2196 3009 4.727507 AGGTCAGCTGATTACTACACTG 57.272 45.455 21.47 0.00 0.00 3.66
2201 3014 8.691661 AAAAAGAAAAGGTCAGCTGATTACTA 57.308 30.769 21.47 0.00 0.00 1.82
2226 3039 7.441157 CGCTTTCTTACAATGTATATGAAGGGA 59.559 37.037 13.03 0.00 0.00 4.20
2229 3042 7.998767 CGACGCTTTCTTACAATGTATATGAAG 59.001 37.037 0.00 0.00 0.00 3.02
2231 3044 6.976349 ACGACGCTTTCTTACAATGTATATGA 59.024 34.615 0.00 0.00 0.00 2.15
2232 3045 7.161829 ACGACGCTTTCTTACAATGTATATG 57.838 36.000 0.00 0.00 0.00 1.78
2233 3046 6.141844 CGACGACGCTTTCTTACAATGTATAT 59.858 38.462 0.00 0.00 0.00 0.86
2234 3047 5.453266 CGACGACGCTTTCTTACAATGTATA 59.547 40.000 0.00 0.00 0.00 1.47
2235 3048 4.264614 CGACGACGCTTTCTTACAATGTAT 59.735 41.667 0.00 0.00 0.00 2.29
2236 3049 3.605056 CGACGACGCTTTCTTACAATGTA 59.395 43.478 0.00 0.00 0.00 2.29
2237 3050 2.407361 CGACGACGCTTTCTTACAATGT 59.593 45.455 0.00 0.00 0.00 2.71
2238 3051 2.659757 TCGACGACGCTTTCTTACAATG 59.340 45.455 1.48 0.00 39.58 2.82
2239 3052 2.937591 TCGACGACGCTTTCTTACAAT 58.062 42.857 1.48 0.00 39.58 2.71
2240 3053 2.404265 TCGACGACGCTTTCTTACAA 57.596 45.000 1.48 0.00 39.58 2.41
2241 3054 2.624316 ATCGACGACGCTTTCTTACA 57.376 45.000 0.00 0.00 39.58 2.41
2306 3120 6.480524 TTGTTGCATGAGTTCACATACTAC 57.519 37.500 0.00 0.00 0.00 2.73
2307 3121 7.105588 AGATTGTTGCATGAGTTCACATACTA 58.894 34.615 0.00 0.00 0.00 1.82
2308 3122 5.942236 AGATTGTTGCATGAGTTCACATACT 59.058 36.000 0.00 0.00 0.00 2.12
2309 3123 6.187125 AGATTGTTGCATGAGTTCACATAC 57.813 37.500 0.00 0.00 0.00 2.39
2310 3124 6.822667 AAGATTGTTGCATGAGTTCACATA 57.177 33.333 0.00 0.00 0.00 2.29
2311 3125 5.717078 AAGATTGTTGCATGAGTTCACAT 57.283 34.783 0.00 0.00 0.00 3.21
2312 3126 5.300034 AGAAAGATTGTTGCATGAGTTCACA 59.700 36.000 0.00 0.00 0.00 3.58
2396 3211 8.718047 TGTACGTACAAGCTATACAAATATCG 57.282 34.615 25.54 0.00 32.40 2.92
2417 3232 4.634443 ACATCTAATTCCGGCACTTTGTAC 59.366 41.667 0.00 0.00 0.00 2.90
2418 3233 4.634004 CACATCTAATTCCGGCACTTTGTA 59.366 41.667 0.00 0.00 0.00 2.41
2419 3234 3.440173 CACATCTAATTCCGGCACTTTGT 59.560 43.478 0.00 0.00 0.00 2.83
2420 3235 3.689161 TCACATCTAATTCCGGCACTTTG 59.311 43.478 0.00 0.00 0.00 2.77
2521 3336 2.035961 GCAGGGATCGATTACTGTAGCA 59.964 50.000 22.96 0.00 33.62 3.49
2560 3377 6.149633 CACTGCTGGTTAGTTTAAATGGAAC 58.850 40.000 0.00 0.00 0.00 3.62
2564 3381 5.009610 ACCACACTGCTGGTTAGTTTAAATG 59.990 40.000 0.00 0.00 42.29 2.32
2576 3393 0.466189 ACTTTGGACCACACTGCTGG 60.466 55.000 0.00 0.00 37.33 4.85
2578 3395 0.179018 GGACTTTGGACCACACTGCT 60.179 55.000 0.00 0.00 0.00 4.24
2907 3746 7.148573 GCACAGATATATGGTAGAAATCAACGG 60.149 40.741 1.85 0.00 0.00 4.44
2936 3776 2.483877 CTCCGCTGCTATTTTGTGACAA 59.516 45.455 0.00 0.00 0.00 3.18
2937 3777 2.076100 CTCCGCTGCTATTTTGTGACA 58.924 47.619 0.00 0.00 0.00 3.58
2971 3811 4.111375 TCCGCAAACAAACTAGCAAAAA 57.889 36.364 0.00 0.00 0.00 1.94
3016 3856 7.986085 ACAGCAGTTCAGTATGTAGATTTTT 57.014 32.000 0.00 0.00 37.40 1.94
3064 3913 5.627780 GCAAAAAGGTAACAGGAACATTACG 59.372 40.000 0.00 0.00 34.36 3.18
3142 3991 6.021030 TGTACCCAGTTCAGTAACTTATCCT 58.979 40.000 0.00 0.00 43.60 3.24
3187 4036 8.974408 CGGATAAGTATCAACAAATCGATACAA 58.026 33.333 0.00 1.29 44.21 2.41
3188 4037 8.139350 ACGGATAAGTATCAACAAATCGATACA 58.861 33.333 0.00 0.00 44.21 2.29
3194 4043 8.365399 TGATGACGGATAAGTATCAACAAATC 57.635 34.615 0.97 0.00 34.40 2.17
3225 4074 8.398878 ACTAAGCATTCCAGATAGTACTAGTC 57.601 38.462 8.85 6.50 0.00 2.59
3266 4115 3.305471 GCTACTGGCCTACTGCTATGTAC 60.305 52.174 3.32 0.00 40.92 2.90
3319 4168 2.098117 GCTTTTGCCGTCTTGCTGATAT 59.902 45.455 0.00 0.00 40.15 1.63
3370 4219 0.892755 ACCATGCACCAATTCAGCAG 59.107 50.000 0.00 0.00 42.14 4.24
3449 4298 2.434702 AGATTCCTAGGGTTTGGCTACG 59.565 50.000 9.46 0.00 0.00 3.51
3476 4325 6.510879 TCACATAACTCACGTCAGACTTAT 57.489 37.500 0.00 0.00 0.00 1.73
3477 4326 5.952526 TCACATAACTCACGTCAGACTTA 57.047 39.130 0.00 0.00 0.00 2.24
3478 4327 4.848562 TCACATAACTCACGTCAGACTT 57.151 40.909 0.00 0.00 0.00 3.01
3479 4328 5.184096 AGAATCACATAACTCACGTCAGACT 59.816 40.000 0.00 0.00 0.00 3.24
3503 4352 2.732289 GGCAAGAGGCTTGGTTTCA 58.268 52.632 9.01 0.00 44.01 2.69
3719 4615 8.537016 ACTGGTAGTTTACTTAACAGCATGATA 58.463 33.333 0.00 0.00 39.69 2.15
3751 4647 1.224069 TGCAGCGTCAGAGAACAAGC 61.224 55.000 0.00 0.00 0.00 4.01
3844 4864 3.009301 ACGTAAAGTGAACCGTCTGAG 57.991 47.619 0.00 0.00 0.00 3.35
3857 4877 5.277047 GGACGAAGGGAGTATAACGTAAAG 58.723 45.833 0.00 0.00 34.26 1.85
3921 5365 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3922 5366 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3923 5367 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3926 5370 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3927 5371 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3929 5373 3.049108 TCCCTCCGTCCCATAATGTAA 57.951 47.619 0.00 0.00 0.00 2.41
3930 5374 2.779429 TCCCTCCGTCCCATAATGTA 57.221 50.000 0.00 0.00 0.00 2.29
3932 5376 3.055094 CCTAATCCCTCCGTCCCATAATG 60.055 52.174 0.00 0.00 0.00 1.90
3936 5390 0.267960 ACCTAATCCCTCCGTCCCAT 59.732 55.000 0.00 0.00 0.00 4.00
3938 5392 2.092598 TAACCTAATCCCTCCGTCCC 57.907 55.000 0.00 0.00 0.00 4.46
4238 6109 6.348498 TGACAGTTTGACTCAAGAGAATTGA 58.652 36.000 3.73 0.00 0.00 2.57
4255 6126 2.916702 TGTCATGTGCTCTGACAGTT 57.083 45.000 13.45 0.00 45.97 3.16
4290 6169 1.116536 TAGCTGGTCACGGTGTGGAA 61.117 55.000 8.17 0.00 33.87 3.53
4382 6261 8.814931 TGGAATTGGACATTGTTTCAGAAATAT 58.185 29.630 0.00 0.00 0.00 1.28
4383 6262 8.187913 TGGAATTGGACATTGTTTCAGAAATA 57.812 30.769 0.00 0.00 0.00 1.40
4384 6263 7.065120 TGGAATTGGACATTGTTTCAGAAAT 57.935 32.000 0.00 0.00 0.00 2.17
4385 6264 6.477053 TGGAATTGGACATTGTTTCAGAAA 57.523 33.333 0.00 0.00 0.00 2.52
4386 6265 6.457355 CATGGAATTGGACATTGTTTCAGAA 58.543 36.000 0.00 0.00 0.00 3.02
4387 6266 5.567224 GCATGGAATTGGACATTGTTTCAGA 60.567 40.000 0.00 0.00 0.00 3.27
4388 6267 4.628333 GCATGGAATTGGACATTGTTTCAG 59.372 41.667 0.00 0.00 0.00 3.02
4389 6268 4.283978 AGCATGGAATTGGACATTGTTTCA 59.716 37.500 0.00 0.00 0.00 2.69
4390 6269 4.824289 AGCATGGAATTGGACATTGTTTC 58.176 39.130 0.00 0.00 0.00 2.78
4391 6270 4.283978 TGAGCATGGAATTGGACATTGTTT 59.716 37.500 0.00 0.00 0.00 2.83
4393 6272 3.433343 TGAGCATGGAATTGGACATTGT 58.567 40.909 0.00 0.00 0.00 2.71
4394 6273 4.178540 GTTGAGCATGGAATTGGACATTG 58.821 43.478 0.00 0.00 0.00 2.82
4395 6274 3.833650 TGTTGAGCATGGAATTGGACATT 59.166 39.130 0.00 0.00 0.00 2.71
4396 6275 3.194116 GTGTTGAGCATGGAATTGGACAT 59.806 43.478 0.00 0.00 0.00 3.06
4397 6276 2.557924 GTGTTGAGCATGGAATTGGACA 59.442 45.455 0.00 0.00 0.00 4.02
4398 6277 2.557924 TGTGTTGAGCATGGAATTGGAC 59.442 45.455 0.00 0.00 0.00 4.02
4399 6278 2.874014 TGTGTTGAGCATGGAATTGGA 58.126 42.857 0.00 0.00 0.00 3.53
4400 6279 3.319755 GTTGTGTTGAGCATGGAATTGG 58.680 45.455 0.00 0.00 0.00 3.16
4401 6280 2.981805 CGTTGTGTTGAGCATGGAATTG 59.018 45.455 0.00 0.00 0.00 2.32
4402 6281 2.884012 TCGTTGTGTTGAGCATGGAATT 59.116 40.909 0.00 0.00 0.00 2.17
4404 6283 1.960417 TCGTTGTGTTGAGCATGGAA 58.040 45.000 0.00 0.00 0.00 3.53
4405 6284 1.872952 CTTCGTTGTGTTGAGCATGGA 59.127 47.619 0.00 0.00 0.00 3.41
4406 6285 1.069022 CCTTCGTTGTGTTGAGCATGG 60.069 52.381 0.00 0.00 0.00 3.66
4407 6286 1.069022 CCCTTCGTTGTGTTGAGCATG 60.069 52.381 0.00 0.00 0.00 4.06
4409 6288 0.179234 TCCCTTCGTTGTGTTGAGCA 59.821 50.000 0.00 0.00 0.00 4.26
4410 6289 1.197721 CATCCCTTCGTTGTGTTGAGC 59.802 52.381 0.00 0.00 0.00 4.26
4411 6290 1.197721 GCATCCCTTCGTTGTGTTGAG 59.802 52.381 0.00 0.00 0.00 3.02
4412 6291 1.234821 GCATCCCTTCGTTGTGTTGA 58.765 50.000 0.00 0.00 0.00 3.18
4413 6292 0.950836 TGCATCCCTTCGTTGTGTTG 59.049 50.000 0.00 0.00 0.00 3.33
4414 6293 1.238439 CTGCATCCCTTCGTTGTGTT 58.762 50.000 0.00 0.00 0.00 3.32
4415 6294 0.108585 ACTGCATCCCTTCGTTGTGT 59.891 50.000 0.00 0.00 0.00 3.72
4416 6295 1.238439 AACTGCATCCCTTCGTTGTG 58.762 50.000 0.00 0.00 0.00 3.33
4417 6296 1.981256 AAACTGCATCCCTTCGTTGT 58.019 45.000 0.00 0.00 0.00 3.32
4418 6297 2.607771 CCAAAACTGCATCCCTTCGTTG 60.608 50.000 0.00 0.00 0.00 4.10
4419 6298 1.613437 CCAAAACTGCATCCCTTCGTT 59.387 47.619 0.00 0.00 0.00 3.85
4420 6299 1.247567 CCAAAACTGCATCCCTTCGT 58.752 50.000 0.00 0.00 0.00 3.85
4421 6300 0.109132 GCCAAAACTGCATCCCTTCG 60.109 55.000 0.00 0.00 0.00 3.79
4422 6301 0.968405 TGCCAAAACTGCATCCCTTC 59.032 50.000 0.00 0.00 32.85 3.46
4423 6302 0.971386 CTGCCAAAACTGCATCCCTT 59.029 50.000 0.00 0.00 38.22 3.95
4424 6303 0.901580 CCTGCCAAAACTGCATCCCT 60.902 55.000 0.00 0.00 38.22 4.20
4425 6304 1.593265 CCTGCCAAAACTGCATCCC 59.407 57.895 0.00 0.00 38.22 3.85
4479 6358 2.306847 GTCCCTCACCTTCTGCAAAAA 58.693 47.619 0.00 0.00 0.00 1.94
4832 6720 2.576615 GACCACTTGAAGAACTTGCCT 58.423 47.619 0.00 0.00 0.00 4.75
4939 6831 3.243737 GGACAAACGGCCATCTTTTTCTT 60.244 43.478 2.24 0.00 0.00 2.52
4995 6888 1.141019 GCGTGATAGTTCGGAGGCA 59.859 57.895 0.00 0.00 0.00 4.75
4997 6890 1.067582 GGGCGTGATAGTTCGGAGG 59.932 63.158 0.00 0.00 0.00 4.30
5013 6906 3.436496 GAATCTTCGAGAACTGTACGGG 58.564 50.000 6.65 0.00 0.00 5.28
5027 6920 3.428870 TCAAAAGACGAGCACGAATCTTC 59.571 43.478 11.40 0.00 42.66 2.87
5028 6921 3.184581 GTCAAAAGACGAGCACGAATCTT 59.815 43.478 11.40 7.07 42.66 2.40
5029 6922 2.731976 GTCAAAAGACGAGCACGAATCT 59.268 45.455 11.40 0.08 42.66 2.40
5030 6923 2.475111 TGTCAAAAGACGAGCACGAATC 59.525 45.455 11.40 0.00 42.66 2.52
5031 6924 2.476619 CTGTCAAAAGACGAGCACGAAT 59.523 45.455 11.40 0.00 42.66 3.34
5032 6925 1.858458 CTGTCAAAAGACGAGCACGAA 59.142 47.619 11.40 0.00 42.66 3.85
5033 6926 1.487482 CTGTCAAAAGACGAGCACGA 58.513 50.000 11.40 0.00 42.66 4.35
5034 6927 0.508641 CCTGTCAAAAGACGAGCACG 59.491 55.000 0.76 0.76 45.75 5.34
5035 6928 1.865865 TCCTGTCAAAAGACGAGCAC 58.134 50.000 0.00 0.00 0.00 4.40
5036 6929 2.839486 ATCCTGTCAAAAGACGAGCA 57.161 45.000 0.00 0.00 0.00 4.26
5037 6930 2.605366 GCTATCCTGTCAAAAGACGAGC 59.395 50.000 0.00 0.00 0.00 5.03
5038 6931 3.118956 AGGCTATCCTGTCAAAAGACGAG 60.119 47.826 0.00 0.00 42.34 4.18
5039 6932 2.832129 AGGCTATCCTGTCAAAAGACGA 59.168 45.455 0.00 0.00 42.34 4.20
5040 6933 3.252974 AGGCTATCCTGTCAAAAGACG 57.747 47.619 0.00 0.00 42.34 4.18
5052 6945 3.718723 AGTGGAGGATGATAGGCTATCC 58.281 50.000 27.21 17.53 42.56 2.59
5053 6946 5.012561 ACAAAGTGGAGGATGATAGGCTATC 59.987 44.000 24.48 24.48 35.74 2.08
5054 6947 4.910304 ACAAAGTGGAGGATGATAGGCTAT 59.090 41.667 6.76 6.76 0.00 2.97
5055 6948 4.298626 ACAAAGTGGAGGATGATAGGCTA 58.701 43.478 0.00 0.00 0.00 3.93
5056 6949 3.118531 ACAAAGTGGAGGATGATAGGCT 58.881 45.455 0.00 0.00 0.00 4.58
5057 6950 3.567478 ACAAAGTGGAGGATGATAGGC 57.433 47.619 0.00 0.00 0.00 3.93
5058 6951 6.127054 TGTTCTACAAAGTGGAGGATGATAGG 60.127 42.308 0.00 0.00 0.00 2.57
5061 6954 5.485353 TCTGTTCTACAAAGTGGAGGATGAT 59.515 40.000 0.00 0.00 0.00 2.45
5065 6958 3.006967 GCTCTGTTCTACAAAGTGGAGGA 59.993 47.826 0.00 0.00 0.00 3.71
5105 6998 0.617249 ACAGCAGGAAGGGAGGAGAG 60.617 60.000 0.00 0.00 0.00 3.20
5111 7011 1.902508 CTCTGTTACAGCAGGAAGGGA 59.097 52.381 7.61 0.00 37.12 4.20
5112 7012 1.677217 GCTCTGTTACAGCAGGAAGGG 60.677 57.143 7.61 0.00 36.82 3.95
5113 7013 1.002430 TGCTCTGTTACAGCAGGAAGG 59.998 52.381 7.61 0.00 42.09 3.46
5120 7020 2.673368 GTGGTACATGCTCTGTTACAGC 59.327 50.000 7.61 0.00 44.52 4.40
5121 7021 3.925379 TGTGGTACATGCTCTGTTACAG 58.075 45.455 5.94 5.94 44.52 2.74
5229 7129 4.384208 GGGTGCATACCTTTCTGAGTGTAT 60.384 45.833 3.34 0.00 46.66 2.29
5245 7145 1.039856 GGACACACAAAAGGGTGCAT 58.960 50.000 0.00 0.00 42.55 3.96
5257 7157 3.454812 AGGAGGGTAATACATGGACACAC 59.545 47.826 0.00 0.00 0.00 3.82
5339 9018 0.248843 GAGAGCACTCAAGGGGACAG 59.751 60.000 6.25 0.00 42.21 3.51
5363 9042 2.941064 CAATCAAGTGTGCAGATCGGAT 59.059 45.455 0.00 0.00 0.00 4.18
5382 9061 3.149196 GCTGGACAGGAGAATTGAACAA 58.851 45.455 1.01 0.00 0.00 2.83
5401 9080 3.036084 GCGCACACACGTACAGCT 61.036 61.111 0.30 0.00 34.88 4.24
5412 9091 4.111016 CGAGTAGTCCGGCGCACA 62.111 66.667 10.83 0.00 0.00 4.57
5482 9161 3.244112 CCCGAGACAAACTAGGACAAAGT 60.244 47.826 0.00 0.00 42.74 2.66
5502 9181 3.284617 GGTCACACATATAACCAACCCC 58.715 50.000 0.00 0.00 0.00 4.95
5566 11193 2.398588 AGCAATTGATCCTAGGACGGA 58.601 47.619 15.42 2.67 37.50 4.69
5568 11195 3.243873 TGCTAGCAATTGATCCTAGGACG 60.244 47.826 16.84 0.00 31.46 4.79
5722 11349 2.637382 TGCCACTTGTGAGTAGATGGAA 59.363 45.455 1.89 0.00 33.90 3.53
5739 11366 4.071961 ACGATGCTATACTCAATTGCCA 57.928 40.909 0.00 0.00 35.71 4.92
5784 11411 5.934043 TCATGCTGTAGGATTTTCCATATCG 59.066 40.000 0.00 0.00 39.61 2.92
5789 11416 5.056480 CGTATCATGCTGTAGGATTTTCCA 58.944 41.667 0.00 0.00 39.61 3.53
5800 11427 0.729116 GCTGCAACGTATCATGCTGT 59.271 50.000 15.37 0.00 42.97 4.40
5836 11463 5.106712 ACGTGTAACTTGCCAATACATTCAG 60.107 40.000 0.00 0.00 32.65 3.02
5913 11540 6.869695 ACGGAAAGGATTTTGTTACAAAACT 58.130 32.000 23.08 14.76 39.27 2.66
5925 11552 5.545063 AATGGTTTTGACGGAAAGGATTT 57.455 34.783 0.00 0.00 43.98 2.17
5928 11555 3.319689 GGAAATGGTTTTGACGGAAAGGA 59.680 43.478 0.00 0.00 0.00 3.36
5984 11611 0.108138 CGGGAGGTTGGTCAGCTTAG 60.108 60.000 0.00 0.00 31.44 2.18
5992 11619 1.072806 GGTTAGAAACGGGAGGTTGGT 59.927 52.381 0.00 0.00 41.96 3.67
6018 11645 1.422024 TGGGAAATCGGTTGGTTCTCA 59.578 47.619 0.00 0.00 29.28 3.27
6030 11657 4.764308 GCCCTTTATCATCTCTGGGAAATC 59.236 45.833 0.00 0.00 36.90 2.17
6032 11659 3.527253 TGCCCTTTATCATCTCTGGGAAA 59.473 43.478 0.00 0.00 36.90 3.13
6063 11690 1.150827 CATTGACTCAGCGTGCTTGA 58.849 50.000 0.00 0.00 0.00 3.02
6069 11696 0.250467 AGTTGCCATTGACTCAGCGT 60.250 50.000 0.00 0.00 0.00 5.07
6071 11698 1.818642 AGAGTTGCCATTGACTCAGC 58.181 50.000 6.31 0.00 43.65 4.26
6074 11701 3.194062 GCTCTAGAGTTGCCATTGACTC 58.806 50.000 20.75 0.00 41.99 3.36
6084 11711 1.929836 GGTTGATGCGCTCTAGAGTTG 59.070 52.381 20.75 14.42 0.00 3.16
6085 11712 1.827969 AGGTTGATGCGCTCTAGAGTT 59.172 47.619 20.75 4.20 0.00 3.01
6105 11732 7.201635 CCATCATTTCAAGTGATATGTGTCGAA 60.202 37.037 10.33 0.00 35.75 3.71
6121 11748 4.849518 TGTATTTCGGGACCATCATTTCA 58.150 39.130 0.00 0.00 0.00 2.69
6135 11763 0.373716 GGGAGCGCACTTGTATTTCG 59.626 55.000 11.47 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.