Multiple sequence alignment - TraesCS2A01G335000

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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 TraesCS2A01G335000 chr2A 100.000 5494 0 0 1 5494 568583888 568578395 0.000000e+00 10146.0
1 TraesCS2A01G335000 chr2D 91.851 3117 127 46 3 3081 422330070 422327043 0.000000e+00 4231.0
2 TraesCS2A01G335000 chr2D 92.834 2428 116 25 3079 5494 422326930 422324549 0.000000e+00 3467.0
3 TraesCS2A01G335000 chr2B 92.500 1720 81 16 1367 3081 494881775 494880099 0.000000e+00 2418.0
4 TraesCS2A01G335000 chr2B 90.771 1712 110 19 3079 4779 494879953 494878279 0.000000e+00 2242.0
5 TraesCS2A01G335000 chr2B 89.410 1152 51 21 1 1129 494883181 494882078 0.000000e+00 1386.0
6 TraesCS2A01G335000 chr2B 83.569 706 58 33 4815 5494 494878097 494877424 4.710000e-170 608.0
7 TraesCS2A01G335000 chr3A 92.308 208 15 1 2219 2426 723749982 723750188 1.500000e-75 294.0
8 TraesCS2A01G335000 chr1A 100.000 33 0 0 5133 5165 508125256 508125224 1.650000e-05 62.1
9 TraesCS2A01G335000 chr6A 100.000 32 0 0 5133 5164 158316597 158316628 5.940000e-05 60.2
10 TraesCS2A01G335000 chr5D 91.111 45 2 1 5118 5162 31209725 31209683 5.940000e-05 60.2
11 TraesCS2A01G335000 chr7B 100.000 31 0 0 5135 5165 595448407 595448377 2.140000e-04 58.4
12 TraesCS2A01G335000 chr6B 100.000 31 0 0 5133 5163 129485586 129485616 2.140000e-04 58.4
13 TraesCS2A01G335000 chr6B 100.000 31 0 0 5132 5162 561249062 561249092 2.140000e-04 58.4
14 TraesCS2A01G335000 chr4A 100.000 31 0 0 5133 5163 713832916 713832886 2.140000e-04 58.4
15 TraesCS2A01G335000 chr1B 100.000 31 0 0 5133 5163 3122623 3122653 2.140000e-04 58.4
16 TraesCS2A01G335000 chr5A 90.909 44 1 3 5133 5174 474327681 474327723 7.690000e-04 56.5


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 TraesCS2A01G335000 chr2A 568578395 568583888 5493 True 10146.0 10146 100.0000 1 5494 1 chr2A.!!$R1 5493
1 TraesCS2A01G335000 chr2D 422324549 422330070 5521 True 3849.0 4231 92.3425 3 5494 2 chr2D.!!$R1 5491
2 TraesCS2A01G335000 chr2B 494877424 494883181 5757 True 1663.5 2418 89.0625 1 5494 4 chr2B.!!$R1 5493

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
353 365 0.179145 AATACTCTTCGACACCGCCG 60.179 55.000 0.00 0.00 35.37 6.46 F
807 845 0.386113 CGGTGGTTAGGAGCTCTAGC 59.614 60.000 14.64 9.63 42.49 3.42 F
1200 1363 1.206132 TGAGCGGTAGTACATGGTTGG 59.794 52.381 2.06 0.00 0.00 3.77 F
1244 1407 1.527311 GACTTCAGAGGTTGTCGTTGC 59.473 52.381 0.00 0.00 0.00 4.17 F
2321 2495 2.169978 GGCCCTAAAGTAGACGGTGAAT 59.830 50.000 0.00 0.00 0.00 2.57 F
3202 3639 0.179018 AGTCTTGCCACCTGGTGTTC 60.179 55.000 24.32 15.96 37.57 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1357 0.546122 AGACTGCAGTTCACCAACCA 59.454 50.000 22.65 0.0 32.22 3.67 R
1785 1957 2.363306 TGACTGCCTTTTGGTCACAT 57.637 45.000 0.00 0.0 42.99 3.21 R
2850 3024 1.063616 CAAGATCATGTGCTTCGCCAG 59.936 52.381 0.00 0.0 0.00 4.85 R
3182 3619 1.071699 GAACACCAGGTGGCAAGACTA 59.928 52.381 24.13 0.0 37.94 2.59 R
4133 4573 0.109597 CAACTTTGCGCCATCAGGTC 60.110 55.000 4.18 0.0 37.19 3.85 R
4863 5458 0.037447 TCACATTCGGGTCATGGCAA 59.963 50.000 0.00 0.0 0.00 4.52 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
19 20 2.401766 CCGGTTCTGCATGTGAGCC 61.402 63.158 11.59 11.59 0.00 4.70
76 77 1.607148 CTGTTTCCACCCGTCTTTTCC 59.393 52.381 0.00 0.00 0.00 3.13
191 192 0.256177 GAGAAAGGGGGCCAAGGTAG 59.744 60.000 4.39 0.00 0.00 3.18
212 213 1.075151 ATCTTCCCCGACTCCCCTC 60.075 63.158 0.00 0.00 0.00 4.30
245 246 3.988517 GCTACTATTCATCGCCCTACAAC 59.011 47.826 0.00 0.00 0.00 3.32
246 247 3.470645 ACTATTCATCGCCCTACAACC 57.529 47.619 0.00 0.00 0.00 3.77
257 258 3.139077 GCCCTACAACCTACATACATGC 58.861 50.000 0.00 0.00 0.00 4.06
284 285 2.280389 CTCGCCCGCTGCATGTAT 60.280 61.111 0.00 0.00 41.33 2.29
353 365 0.179145 AATACTCTTCGACACCGCCG 60.179 55.000 0.00 0.00 35.37 6.46
371 383 1.134530 CGGACGACGCATCAGAGTTC 61.135 60.000 0.00 0.00 34.82 3.01
549 566 5.907866 TTGTTCTTTTCTCTTTCCCGTTT 57.092 34.783 0.00 0.00 0.00 3.60
580 608 5.163571 GCTCCAAAATCTCCAGATCCTTTTC 60.164 44.000 0.00 0.00 32.75 2.29
766 797 2.213499 GTCTGTCTGCGGATAAATGGG 58.787 52.381 0.00 0.00 31.86 4.00
767 798 0.947244 CTGTCTGCGGATAAATGGGC 59.053 55.000 0.00 0.00 0.00 5.36
805 843 1.760192 GTCGGTGGTTAGGAGCTCTA 58.240 55.000 14.64 1.13 0.00 2.43
806 844 1.677052 GTCGGTGGTTAGGAGCTCTAG 59.323 57.143 14.64 0.00 0.00 2.43
807 845 0.386113 CGGTGGTTAGGAGCTCTAGC 59.614 60.000 14.64 9.63 42.49 3.42
855 893 3.806667 AGGCAGGCATGGGCTCTC 61.807 66.667 0.00 0.00 40.87 3.20
903 941 3.128242 GGAGCATTGACTTGTGGATCTTG 59.872 47.826 0.00 0.00 0.00 3.02
947 988 3.536570 GAAGTAATCAGCTCTGTTCCCC 58.463 50.000 0.00 0.00 0.00 4.81
1013 1054 5.509670 CCGTGCAGATCATGAAGATAGGTAA 60.510 44.000 0.00 0.00 37.00 2.85
1063 1104 6.441924 TCCTCTTCCATCAATCTTCTTGTACT 59.558 38.462 0.00 0.00 0.00 2.73
1067 1108 7.388776 TCTTCCATCAATCTTCTTGTACTGTTG 59.611 37.037 0.00 0.00 0.00 3.33
1188 1351 4.885907 AGTACTAGTATGCTTTGAGCGGTA 59.114 41.667 5.75 0.00 46.26 4.02
1189 1352 4.308899 ACTAGTATGCTTTGAGCGGTAG 57.691 45.455 0.00 0.00 46.26 3.18
1190 1353 3.700038 ACTAGTATGCTTTGAGCGGTAGT 59.300 43.478 0.00 0.00 46.26 2.73
1191 1354 4.885907 ACTAGTATGCTTTGAGCGGTAGTA 59.114 41.667 0.00 0.00 46.26 1.82
1192 1355 4.043037 AGTATGCTTTGAGCGGTAGTAC 57.957 45.455 0.00 0.00 46.26 2.73
1193 1356 3.446161 AGTATGCTTTGAGCGGTAGTACA 59.554 43.478 2.06 0.00 46.26 2.90
1194 1357 3.543680 ATGCTTTGAGCGGTAGTACAT 57.456 42.857 2.06 0.00 46.26 2.29
1195 1358 2.616960 TGCTTTGAGCGGTAGTACATG 58.383 47.619 2.06 0.00 46.26 3.21
1196 1359 1.933853 GCTTTGAGCGGTAGTACATGG 59.066 52.381 2.06 0.00 0.00 3.66
1197 1360 2.677037 GCTTTGAGCGGTAGTACATGGT 60.677 50.000 2.06 0.00 0.00 3.55
1198 1361 3.596214 CTTTGAGCGGTAGTACATGGTT 58.404 45.455 2.06 0.00 0.00 3.67
1199 1362 2.665649 TGAGCGGTAGTACATGGTTG 57.334 50.000 2.06 0.00 0.00 3.77
1200 1363 1.206132 TGAGCGGTAGTACATGGTTGG 59.794 52.381 2.06 0.00 0.00 3.77
1237 1400 8.253810 TCTTATGTATTCAGACTTCAGAGGTTG 58.746 37.037 0.00 0.00 0.00 3.77
1244 1407 1.527311 GACTTCAGAGGTTGTCGTTGC 59.473 52.381 0.00 0.00 0.00 4.17
1271 1434 2.821969 GCATATATTGGCAGGGAAGTGG 59.178 50.000 0.00 0.00 0.00 4.00
1347 1515 7.048629 TCTTAACTGGATAGAGCTGAGATTG 57.951 40.000 0.00 0.00 0.00 2.67
1352 1520 5.221682 ACTGGATAGAGCTGAGATTGATTGG 60.222 44.000 0.00 0.00 0.00 3.16
1353 1521 4.657504 TGGATAGAGCTGAGATTGATTGGT 59.342 41.667 0.00 0.00 0.00 3.67
1354 1522 5.131642 TGGATAGAGCTGAGATTGATTGGTT 59.868 40.000 0.00 0.00 0.00 3.67
1355 1523 6.060788 GGATAGAGCTGAGATTGATTGGTTT 58.939 40.000 0.00 0.00 0.00 3.27
1356 1524 6.545298 GGATAGAGCTGAGATTGATTGGTTTT 59.455 38.462 0.00 0.00 0.00 2.43
1357 1525 7.067981 GGATAGAGCTGAGATTGATTGGTTTTT 59.932 37.037 0.00 0.00 0.00 1.94
1388 1556 6.555315 AGAGCAGAAATTAATTGGTTTAGCG 58.445 36.000 0.39 0.00 0.00 4.26
1552 1721 4.443621 TCTAGTCAGTAGTCACTCGATGG 58.556 47.826 0.00 0.00 30.46 3.51
1595 1765 8.486210 TCTCTTATCATTTGCCATACTGTAACT 58.514 33.333 0.00 0.00 0.00 2.24
1785 1957 5.630121 TCCTATCAGCCTTTTGTCTTTTGA 58.370 37.500 0.00 0.00 0.00 2.69
1806 1979 2.229792 TGTGACCAAAAGGCAGTCATC 58.770 47.619 0.00 0.00 42.14 2.92
1815 1988 4.429854 AAAGGCAGTCATCTATTCCCTC 57.570 45.455 0.00 0.00 0.00 4.30
2048 2222 2.341760 GCAGAACTTACGACTTAGCGTG 59.658 50.000 10.82 0.28 45.23 5.34
2077 2251 7.768240 TCTCTTTTGTTCATTCCATCATGATG 58.232 34.615 25.97 25.97 38.51 3.07
2171 2345 8.779303 CAGTGTTAATTGTGGTACAGATTGTTA 58.221 33.333 0.00 0.00 41.80 2.41
2179 2353 6.350103 TGTGGTACAGATTGTTAACTTGTGA 58.650 36.000 7.22 0.00 41.80 3.58
2180 2354 6.824196 TGTGGTACAGATTGTTAACTTGTGAA 59.176 34.615 7.22 0.00 41.80 3.18
2182 2356 7.012044 GTGGTACAGATTGTTAACTTGTGAACT 59.988 37.037 7.22 0.00 41.80 3.01
2183 2357 8.205512 TGGTACAGATTGTTAACTTGTGAACTA 58.794 33.333 7.22 0.00 0.00 2.24
2184 2358 8.709646 GGTACAGATTGTTAACTTGTGAACTAG 58.290 37.037 7.22 0.00 0.00 2.57
2185 2359 9.257651 GTACAGATTGTTAACTTGTGAACTAGT 57.742 33.333 7.22 0.00 33.54 2.57
2186 2360 8.366671 ACAGATTGTTAACTTGTGAACTAGTC 57.633 34.615 7.22 0.00 31.02 2.59
2187 2361 8.204836 ACAGATTGTTAACTTGTGAACTAGTCT 58.795 33.333 7.22 1.74 31.02 3.24
2188 2362 9.046296 CAGATTGTTAACTTGTGAACTAGTCTT 57.954 33.333 7.22 0.00 31.02 3.01
2189 2363 9.262358 AGATTGTTAACTTGTGAACTAGTCTTC 57.738 33.333 7.22 0.00 31.02 2.87
2190 2364 9.262358 GATTGTTAACTTGTGAACTAGTCTTCT 57.738 33.333 7.22 0.00 31.02 2.85
2230 2404 9.829507 TTCACACTTTTAATGGTTGATGATTTT 57.170 25.926 0.00 0.00 0.00 1.82
2231 2405 9.829507 TCACACTTTTAATGGTTGATGATTTTT 57.170 25.926 0.00 0.00 0.00 1.94
2233 2407 9.829507 ACACTTTTAATGGTTGATGATTTTTGA 57.170 25.926 0.00 0.00 0.00 2.69
2288 2462 4.612264 ACCAATGCTTTTCATGAGCTTT 57.388 36.364 6.93 4.33 40.75 3.51
2291 2465 6.161381 ACCAATGCTTTTCATGAGCTTTTAG 58.839 36.000 6.93 4.11 40.75 1.85
2292 2466 5.579511 CCAATGCTTTTCATGAGCTTTTAGG 59.420 40.000 6.93 2.79 40.75 2.69
2321 2495 2.169978 GGCCCTAAAGTAGACGGTGAAT 59.830 50.000 0.00 0.00 0.00 2.57
2386 2560 5.241506 GGTTGAACAGACCAATTCATCAGAA 59.758 40.000 0.00 0.00 37.14 3.02
2506 2680 2.287009 GCCAAGTTCTGTGGTTTCTTCG 60.287 50.000 0.00 0.00 38.50 3.79
2515 2689 4.019681 TCTGTGGTTTCTTCGGATTATGGT 60.020 41.667 0.00 0.00 0.00 3.55
2518 2692 2.949644 GGTTTCTTCGGATTATGGTGGG 59.050 50.000 0.00 0.00 0.00 4.61
2577 2751 2.517959 TGCTGATCAAAAGGGTTCTGG 58.482 47.619 0.00 0.00 0.00 3.86
2755 2929 9.438228 GGTAATACTATGGAAGAAATAAGAGCC 57.562 37.037 0.00 0.00 0.00 4.70
2936 3110 7.603651 TGAGAAATCAAGTCCTAGACAGTTAC 58.396 38.462 0.00 0.00 34.60 2.50
3072 3246 4.399004 ACAGTATCACCAATCTGCTCTC 57.601 45.455 0.00 0.00 0.00 3.20
3091 3528 8.284945 TGCTCTCATAAAATATATGATTGCCC 57.715 34.615 14.42 0.00 34.37 5.36
3117 3554 4.992688 ACATGTACCGCAATTATTTGGTG 58.007 39.130 0.00 0.00 35.93 4.17
3134 3571 3.444703 GGTGACTGACCATACTAGCAG 57.555 52.381 0.00 0.00 45.34 4.24
3135 3572 3.024547 GGTGACTGACCATACTAGCAGA 58.975 50.000 0.00 0.00 45.34 4.26
3136 3573 3.447586 GGTGACTGACCATACTAGCAGAA 59.552 47.826 0.00 0.00 45.34 3.02
3137 3574 4.100189 GGTGACTGACCATACTAGCAGAAT 59.900 45.833 0.00 0.00 45.34 2.40
3139 3576 6.109359 GTGACTGACCATACTAGCAGAATTT 58.891 40.000 0.00 0.00 32.86 1.82
3141 3578 7.436673 GTGACTGACCATACTAGCAGAATTTAG 59.563 40.741 0.00 0.00 32.86 1.85
3142 3579 7.124298 TGACTGACCATACTAGCAGAATTTAGT 59.876 37.037 0.00 0.00 34.64 2.24
3143 3580 7.852263 ACTGACCATACTAGCAGAATTTAGTT 58.148 34.615 0.00 0.00 32.64 2.24
3144 3581 7.766278 ACTGACCATACTAGCAGAATTTAGTTG 59.234 37.037 0.00 0.00 32.64 3.16
3145 3582 7.847096 TGACCATACTAGCAGAATTTAGTTGA 58.153 34.615 0.00 0.00 32.64 3.18
3146 3583 8.486210 TGACCATACTAGCAGAATTTAGTTGAT 58.514 33.333 0.00 0.00 32.64 2.57
3147 3584 9.982651 GACCATACTAGCAGAATTTAGTTGATA 57.017 33.333 0.00 0.00 32.64 2.15
3176 3613 5.710513 TTTGGTTCAATGATCTGTTCCAG 57.289 39.130 0.00 0.00 0.00 3.86
3182 3619 5.246981 TCAATGATCTGTTCCAGGAAACT 57.753 39.130 2.45 0.00 46.44 2.66
3197 3634 2.427506 GAAACTAGTCTTGCCACCTGG 58.572 52.381 0.00 0.00 38.53 4.45
3202 3639 0.179018 AGTCTTGCCACCTGGTGTTC 60.179 55.000 24.32 15.96 37.57 3.18
3207 3644 1.072266 TGCCACCTGGTGTTCCTATT 58.928 50.000 24.32 0.00 37.57 1.73
3210 3647 1.406887 CCACCTGGTGTTCCTATTCGG 60.407 57.143 24.32 2.15 34.23 4.30
3222 3659 7.078228 GTGTTCCTATTCGGATCAATAAATGC 58.922 38.462 0.00 0.00 41.83 3.56
3223 3660 6.770303 TGTTCCTATTCGGATCAATAAATGCA 59.230 34.615 0.00 0.00 42.70 3.96
3226 3663 8.044060 TCCTATTCGGATCAATAAATGCAATC 57.956 34.615 0.00 0.00 36.69 2.67
3234 3671 7.802720 CGGATCAATAAATGCAATCGAATGTTA 59.197 33.333 1.83 0.00 0.00 2.41
3235 3672 9.462174 GGATCAATAAATGCAATCGAATGTTAA 57.538 29.630 1.83 0.00 0.00 2.01
3327 3764 7.557358 TCATTACAGGTAGCATCAAATGATTGT 59.443 33.333 0.00 0.00 37.79 2.71
3342 3779 7.395206 TCAAATGATTGTCATGAAACTGGATCT 59.605 33.333 0.00 0.00 37.15 2.75
3365 3802 0.394565 ACTGCACCAGAGTCCAGTTC 59.605 55.000 0.00 0.00 35.14 3.01
3405 3842 4.842531 TGAATCAACTTCTGATGGGCTA 57.157 40.909 0.00 0.00 44.43 3.93
3426 3866 3.144657 TCAGCTGCAATTCCTGAAGAA 57.855 42.857 9.47 0.00 39.32 2.52
3428 3868 3.079578 CAGCTGCAATTCCTGAAGAAGA 58.920 45.455 0.00 0.00 38.07 2.87
3492 3932 4.569564 CACTACAACCCTTTTATCGCCTAC 59.430 45.833 0.00 0.00 0.00 3.18
3567 4007 3.751175 ACGATGTTTCTGTTGTACCCATG 59.249 43.478 0.00 0.00 0.00 3.66
3615 4055 2.095853 CAGTGATATTGTCAACGGTGGC 59.904 50.000 0.00 0.00 38.90 5.01
3642 4082 5.711976 ACTGGGAGGTTTTGATTATGTTGAG 59.288 40.000 0.00 0.00 0.00 3.02
3711 4151 2.032528 CGTTCAAGCAGGCTGGGA 59.967 61.111 17.64 0.00 0.00 4.37
3902 4342 3.606595 TGTCCAAGCATCTGAAGAGAG 57.393 47.619 0.00 0.00 0.00 3.20
3905 4345 2.093606 TCCAAGCATCTGAAGAGAGCAG 60.094 50.000 9.38 0.00 34.71 4.24
3917 4357 3.650281 AGAGAGCAGTGATCAGAGAGA 57.350 47.619 11.60 0.00 0.00 3.10
3919 4359 3.887110 AGAGAGCAGTGATCAGAGAGATG 59.113 47.826 11.60 0.00 37.00 2.90
3920 4360 3.633525 GAGAGCAGTGATCAGAGAGATGT 59.366 47.826 11.60 0.00 37.00 3.06
3921 4361 3.633525 AGAGCAGTGATCAGAGAGATGTC 59.366 47.826 11.60 0.00 37.00 3.06
3923 4363 2.543445 GCAGTGATCAGAGAGATGTCGG 60.543 54.545 0.00 0.00 37.00 4.79
3924 4364 2.687425 CAGTGATCAGAGAGATGTCGGT 59.313 50.000 0.00 0.00 37.00 4.69
3925 4365 3.879892 CAGTGATCAGAGAGATGTCGGTA 59.120 47.826 0.00 0.00 37.00 4.02
3926 4366 4.336713 CAGTGATCAGAGAGATGTCGGTAA 59.663 45.833 0.00 0.00 37.00 2.85
3927 4367 4.336993 AGTGATCAGAGAGATGTCGGTAAC 59.663 45.833 0.00 0.00 37.00 2.50
3928 4368 4.096532 GTGATCAGAGAGATGTCGGTAACA 59.903 45.833 0.00 0.00 43.51 2.41
3929 4369 4.705023 TGATCAGAGAGATGTCGGTAACAA 59.295 41.667 0.00 0.00 42.37 2.83
3930 4370 4.703645 TCAGAGAGATGTCGGTAACAAG 57.296 45.455 0.00 0.00 42.37 3.16
3931 4371 4.332828 TCAGAGAGATGTCGGTAACAAGA 58.667 43.478 0.00 0.00 42.37 3.02
3932 4372 4.950475 TCAGAGAGATGTCGGTAACAAGAT 59.050 41.667 0.00 0.00 42.37 2.40
3933 4373 5.039984 CAGAGAGATGTCGGTAACAAGATG 58.960 45.833 0.00 0.00 42.37 2.90
3934 4374 4.950475 AGAGAGATGTCGGTAACAAGATGA 59.050 41.667 0.00 0.00 42.37 2.92
3935 4375 5.067153 AGAGAGATGTCGGTAACAAGATGAG 59.933 44.000 0.00 0.00 42.37 2.90
3936 4376 4.950475 AGAGATGTCGGTAACAAGATGAGA 59.050 41.667 0.00 0.00 42.37 3.27
3937 4377 5.419155 AGAGATGTCGGTAACAAGATGAGAA 59.581 40.000 0.00 0.00 42.37 2.87
3938 4378 6.097554 AGAGATGTCGGTAACAAGATGAGAAT 59.902 38.462 0.00 0.00 42.37 2.40
3939 4379 6.644347 AGATGTCGGTAACAAGATGAGAATT 58.356 36.000 0.00 0.00 42.37 2.17
3940 4380 6.536582 AGATGTCGGTAACAAGATGAGAATTG 59.463 38.462 0.00 0.00 42.37 2.32
3941 4381 5.789521 TGTCGGTAACAAGATGAGAATTGA 58.210 37.500 0.00 0.00 34.03 2.57
3942 4382 6.406370 TGTCGGTAACAAGATGAGAATTGAT 58.594 36.000 0.00 0.00 34.03 2.57
3943 4383 6.313658 TGTCGGTAACAAGATGAGAATTGATG 59.686 38.462 0.00 0.00 34.03 3.07
3944 4384 5.817296 TCGGTAACAAGATGAGAATTGATGG 59.183 40.000 0.00 0.00 0.00 3.51
3945 4385 5.817296 CGGTAACAAGATGAGAATTGATGGA 59.183 40.000 0.00 0.00 0.00 3.41
3946 4386 6.018425 CGGTAACAAGATGAGAATTGATGGAG 60.018 42.308 0.00 0.00 0.00 3.86
3947 4387 5.831702 AACAAGATGAGAATTGATGGAGC 57.168 39.130 0.00 0.00 0.00 4.70
3948 4388 4.851843 ACAAGATGAGAATTGATGGAGCA 58.148 39.130 0.00 0.00 0.00 4.26
3949 4389 4.639310 ACAAGATGAGAATTGATGGAGCAC 59.361 41.667 0.00 0.00 0.00 4.40
3950 4390 4.498894 AGATGAGAATTGATGGAGCACA 57.501 40.909 0.00 0.00 0.00 4.57
3951 4391 5.050126 AGATGAGAATTGATGGAGCACAT 57.950 39.130 0.00 0.00 44.18 3.21
3954 4394 3.285484 GAGAATTGATGGAGCACATGGT 58.715 45.455 0.00 0.00 40.72 3.55
3982 4422 3.445450 GCCTAGTGATGTCAAGAGTGAGA 59.555 47.826 0.00 0.00 33.27 3.27
3983 4423 4.081972 GCCTAGTGATGTCAAGAGTGAGAA 60.082 45.833 0.00 0.00 33.27 2.87
3990 4430 2.029020 TGTCAAGAGTGAGAACCATCCG 60.029 50.000 0.00 0.00 33.27 4.18
3993 4433 3.056536 TCAAGAGTGAGAACCATCCGAAG 60.057 47.826 0.00 0.00 0.00 3.79
4122 4562 2.259204 CAAACGGAGTCGGCGGTA 59.741 61.111 7.21 0.00 45.00 4.02
4133 4573 2.173669 CGGCGGTACAGCAGAATGG 61.174 63.158 19.70 0.00 39.27 3.16
4143 4583 0.106819 AGCAGAATGGACCTGATGGC 60.107 55.000 0.00 0.00 35.86 4.40
4242 4682 1.617018 TAGCGCCCTCTGCTCACATT 61.617 55.000 2.29 0.00 42.85 2.71
4392 4832 1.278985 TGTTGATCCACAGGCTACAGG 59.721 52.381 0.00 0.00 0.00 4.00
4569 5011 4.542075 GCTAGTGTTAGCCAGCCC 57.458 61.111 0.00 0.00 45.34 5.19
4689 5134 1.776034 GATGGCTTGTCGGATTCGCC 61.776 60.000 7.25 7.25 41.06 5.54
4717 5162 5.335897 GGCTTGTAATTTGCAGAGATTGTGA 60.336 40.000 0.00 0.00 0.00 3.58
4798 5379 5.918576 GCTTATACATACATGTAGTGCGACA 59.081 40.000 11.91 0.00 45.46 4.35
4863 5458 2.431057 ACTCACCAGAACGAGTTCAGTT 59.569 45.455 17.00 0.00 39.45 3.16
4876 5471 0.109532 TTCAGTTTGCCATGACCCGA 59.890 50.000 0.00 0.00 0.00 5.14
5021 5623 1.939934 GCACAAAACTGCCCCTTTTTC 59.060 47.619 0.00 0.00 0.00 2.29
5035 5637 0.941542 TTTTTCCGCACGAACTCCTG 59.058 50.000 0.00 0.00 0.00 3.86
5040 5643 2.031163 GCACGAACTCCTGCCAGT 59.969 61.111 0.00 0.00 0.00 4.00
5121 5728 6.149129 TGACCAGCTAATGATACACTGTAG 57.851 41.667 0.00 0.00 0.00 2.74
5122 5729 5.656859 TGACCAGCTAATGATACACTGTAGT 59.343 40.000 0.00 0.00 0.00 2.73
5124 5731 7.040473 ACCAGCTAATGATACACTGTAGTAC 57.960 40.000 0.00 0.00 0.00 2.73
5126 5733 6.040504 CCAGCTAATGATACACTGTAGTACCA 59.959 42.308 0.00 0.00 0.00 3.25
5129 5736 7.342284 AGCTAATGATACACTGTAGTACCAACT 59.658 37.037 0.00 0.00 39.91 3.16
5130 5737 7.980099 GCTAATGATACACTGTAGTACCAACTT 59.020 37.037 0.00 0.00 37.15 2.66
5131 5738 9.302345 CTAATGATACACTGTAGTACCAACTTG 57.698 37.037 0.00 0.00 37.15 3.16
5132 5739 6.904463 TGATACACTGTAGTACCAACTTGA 57.096 37.500 0.00 0.00 37.15 3.02
5133 5740 6.684686 TGATACACTGTAGTACCAACTTGAC 58.315 40.000 0.00 0.00 37.15 3.18
5135 5742 3.382546 ACACTGTAGTACCAACTTGACGT 59.617 43.478 0.00 0.00 37.15 4.34
5136 5743 4.142093 ACACTGTAGTACCAACTTGACGTT 60.142 41.667 0.00 0.00 37.15 3.99
5138 5745 4.340381 ACTGTAGTACCAACTTGACGTTCT 59.660 41.667 0.00 0.00 37.15 3.01
5140 5747 6.039717 ACTGTAGTACCAACTTGACGTTCTTA 59.960 38.462 0.00 0.00 37.15 2.10
5141 5748 6.985117 TGTAGTACCAACTTGACGTTCTTAT 58.015 36.000 0.00 0.00 37.15 1.73
5142 5749 8.109705 TGTAGTACCAACTTGACGTTCTTATA 57.890 34.615 0.00 0.00 37.15 0.98
5144 5751 9.578439 GTAGTACCAACTTGACGTTCTTATATT 57.422 33.333 0.00 0.00 37.15 1.28
5148 5755 8.433421 ACCAACTTGACGTTCTTATATTATGG 57.567 34.615 0.00 0.00 32.27 2.74
5149 5756 7.497909 ACCAACTTGACGTTCTTATATTATGGG 59.502 37.037 0.00 0.00 32.27 4.00
5150 5757 7.713507 CCAACTTGACGTTCTTATATTATGGGA 59.286 37.037 0.00 0.00 32.27 4.37
5151 5758 8.548721 CAACTTGACGTTCTTATATTATGGGAC 58.451 37.037 0.00 0.00 32.27 4.46
5194 5813 2.846039 CAAGCCTGCAAATCTAGCTG 57.154 50.000 0.00 0.00 33.18 4.24
5220 5839 9.248291 GACTAGTTGTAGTAGTAGCAGTAGTAG 57.752 40.741 0.00 0.00 39.78 2.57
5222 5841 9.467258 CTAGTTGTAGTAGTAGCAGTAGTAGAG 57.533 40.741 0.00 0.00 0.00 2.43
5267 5886 9.892130 AAGCTAAGCTTCTTGTAACTATGTATT 57.108 29.630 0.00 0.00 46.77 1.89
5268 5887 9.535878 AGCTAAGCTTCTTGTAACTATGTATTC 57.464 33.333 0.00 0.00 33.89 1.75
5269 5888 9.535878 GCTAAGCTTCTTGTAACTATGTATTCT 57.464 33.333 0.00 0.00 0.00 2.40
5311 5939 0.896226 GTCTGACGGACTTAGGGCTT 59.104 55.000 7.20 0.00 41.46 4.35
5336 5964 2.254350 CGAGGCTCGTCGTTGTGA 59.746 61.111 27.92 0.00 34.72 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 5.824904 ATCCAGATCAAAATTCGTCAAGG 57.175 39.130 0.00 0.00 0.00 3.61
169 170 3.645268 CTTGGCCCCCTTTCTCCCG 62.645 68.421 0.00 0.00 0.00 5.14
170 171 2.360585 CTTGGCCCCCTTTCTCCC 59.639 66.667 0.00 0.00 0.00 4.30
191 192 2.417936 GGAGTCGGGGAAGATCGC 59.582 66.667 0.00 0.00 0.00 4.58
212 213 1.536331 GAATAGTAGCGGACGAGAGGG 59.464 57.143 0.00 0.00 0.00 4.30
245 246 1.202486 ACGGAACCGCATGTATGTAGG 60.202 52.381 13.32 6.87 44.19 3.18
246 247 2.218953 ACGGAACCGCATGTATGTAG 57.781 50.000 13.32 0.00 44.19 2.74
320 321 8.913061 GTCGAAGAGTATTAAATACGCAGGACG 61.913 44.444 0.00 0.00 44.06 4.79
335 336 1.432251 CGGCGGTGTCGAAGAGTAT 59.568 57.895 0.00 0.00 36.95 2.12
353 365 0.802607 GGAACTCTGATGCGTCGTCC 60.803 60.000 0.58 0.00 0.00 4.79
420 432 0.319555 CCCTCTCACGAAACGAAGCA 60.320 55.000 0.00 0.00 0.00 3.91
549 566 2.639347 TGGAGATTTTGGAGCAGAGACA 59.361 45.455 0.00 0.00 0.00 3.41
580 608 2.624838 ACCTCTGAAAACACCATGCTTG 59.375 45.455 0.00 0.00 0.00 4.01
701 732 2.866762 GTGTGGAAGAGTGTTGTCTGTC 59.133 50.000 0.00 0.00 0.00 3.51
702 733 2.420129 GGTGTGGAAGAGTGTTGTCTGT 60.420 50.000 0.00 0.00 0.00 3.41
703 734 2.213499 GGTGTGGAAGAGTGTTGTCTG 58.787 52.381 0.00 0.00 0.00 3.51
704 735 1.837439 TGGTGTGGAAGAGTGTTGTCT 59.163 47.619 0.00 0.00 0.00 3.41
766 797 0.028110 GCTAACGCTAATGGCAGTGC 59.972 55.000 6.55 6.55 41.91 4.40
767 798 0.301687 CGCTAACGCTAATGGCAGTG 59.698 55.000 0.00 0.00 41.91 3.66
780 811 0.527565 TCCTAACCACCGACGCTAAC 59.472 55.000 0.00 0.00 0.00 2.34
805 843 4.453819 CAGATCGGAGAAAACAAAAGAGCT 59.546 41.667 0.00 0.00 43.58 4.09
806 844 4.716943 CAGATCGGAGAAAACAAAAGAGC 58.283 43.478 0.00 0.00 43.58 4.09
807 845 4.453819 AGCAGATCGGAGAAAACAAAAGAG 59.546 41.667 0.00 0.00 43.58 2.85
808 846 4.389374 AGCAGATCGGAGAAAACAAAAGA 58.611 39.130 0.00 0.00 43.58 2.52
809 847 4.378874 GGAGCAGATCGGAGAAAACAAAAG 60.379 45.833 0.00 0.00 43.58 2.27
810 848 3.502211 GGAGCAGATCGGAGAAAACAAAA 59.498 43.478 0.00 0.00 43.58 2.44
839 877 2.850828 AAAGAGAGCCCATGCCTGCC 62.851 60.000 0.00 0.00 38.69 4.85
863 901 1.990327 TCCATCCATCCATCCATCCAG 59.010 52.381 0.00 0.00 0.00 3.86
864 902 1.990327 CTCCATCCATCCATCCATCCA 59.010 52.381 0.00 0.00 0.00 3.41
865 903 1.340795 GCTCCATCCATCCATCCATCC 60.341 57.143 0.00 0.00 0.00 3.51
866 904 1.353358 TGCTCCATCCATCCATCCATC 59.647 52.381 0.00 0.00 0.00 3.51
867 905 1.452540 TGCTCCATCCATCCATCCAT 58.547 50.000 0.00 0.00 0.00 3.41
976 1017 2.159476 TCTGCACGGTGTATCTCGTTAC 60.159 50.000 10.24 0.00 37.53 2.50
1013 1054 1.903183 GGAGCCTCCCTCGCTTATTAT 59.097 52.381 0.00 0.00 41.71 1.28
1097 1138 5.824904 ATTTCTTGCAGATAAGCGAATGT 57.175 34.783 0.00 0.00 37.31 2.71
1183 1346 1.066716 TCACCAACCATGTACTACCGC 60.067 52.381 0.00 0.00 0.00 5.68
1188 1351 2.158682 TGCAGTTCACCAACCATGTACT 60.159 45.455 0.00 0.00 32.22 2.73
1189 1352 2.226330 TGCAGTTCACCAACCATGTAC 58.774 47.619 0.00 0.00 32.22 2.90
1190 1353 2.158682 ACTGCAGTTCACCAACCATGTA 60.159 45.455 15.25 0.00 32.22 2.29
1191 1354 1.321474 CTGCAGTTCACCAACCATGT 58.679 50.000 5.25 0.00 32.22 3.21
1192 1355 1.267806 GACTGCAGTTCACCAACCATG 59.732 52.381 22.65 0.00 32.22 3.66
1193 1356 1.143684 AGACTGCAGTTCACCAACCAT 59.856 47.619 22.65 0.00 32.22 3.55
1194 1357 0.546122 AGACTGCAGTTCACCAACCA 59.454 50.000 22.65 0.00 32.22 3.67
1195 1358 1.680338 AAGACTGCAGTTCACCAACC 58.320 50.000 22.65 5.23 32.22 3.77
1196 1359 3.815401 ACATAAGACTGCAGTTCACCAAC 59.185 43.478 22.65 6.05 0.00 3.77
1197 1360 4.085357 ACATAAGACTGCAGTTCACCAA 57.915 40.909 22.65 4.33 0.00 3.67
1198 1361 3.769739 ACATAAGACTGCAGTTCACCA 57.230 42.857 22.65 5.45 0.00 4.17
1199 1362 5.874810 TGAATACATAAGACTGCAGTTCACC 59.125 40.000 22.65 8.09 0.00 4.02
1200 1363 6.813649 TCTGAATACATAAGACTGCAGTTCAC 59.186 38.462 22.65 8.50 0.00 3.18
1271 1434 5.297029 GCCTGGTAAAAATAGGTGTGATCTC 59.703 44.000 0.00 0.00 34.06 2.75
1330 1498 4.657504 ACCAATCAATCTCAGCTCTATCCA 59.342 41.667 0.00 0.00 0.00 3.41
1361 1529 9.208022 GCTAAACCAATTAATTTCTGCTCTTTT 57.792 29.630 0.00 0.00 0.00 2.27
1362 1530 7.542130 CGCTAAACCAATTAATTTCTGCTCTTT 59.458 33.333 0.00 0.00 0.00 2.52
1363 1531 7.029563 CGCTAAACCAATTAATTTCTGCTCTT 58.970 34.615 0.00 0.00 0.00 2.85
1364 1532 6.374333 TCGCTAAACCAATTAATTTCTGCTCT 59.626 34.615 0.00 0.00 0.00 4.09
1365 1533 6.551736 TCGCTAAACCAATTAATTTCTGCTC 58.448 36.000 0.00 0.00 0.00 4.26
1366 1534 6.509418 TCGCTAAACCAATTAATTTCTGCT 57.491 33.333 0.00 0.00 0.00 4.24
1367 1535 8.342634 TCTATCGCTAAACCAATTAATTTCTGC 58.657 33.333 0.00 0.00 0.00 4.26
1375 1543 9.151471 GCTATCAATCTATCGCTAAACCAATTA 57.849 33.333 0.00 0.00 0.00 1.40
1376 1544 7.661437 TGCTATCAATCTATCGCTAAACCAATT 59.339 33.333 0.00 0.00 0.00 2.32
1377 1545 7.161404 TGCTATCAATCTATCGCTAAACCAAT 58.839 34.615 0.00 0.00 0.00 3.16
1378 1546 6.521162 TGCTATCAATCTATCGCTAAACCAA 58.479 36.000 0.00 0.00 0.00 3.67
1379 1547 6.096673 TGCTATCAATCTATCGCTAAACCA 57.903 37.500 0.00 0.00 0.00 3.67
1380 1548 8.879342 ATATGCTATCAATCTATCGCTAAACC 57.121 34.615 0.00 0.00 0.00 3.27
1504 1672 7.776107 TGTTTCATTTACTTGTGTTCATGGAA 58.224 30.769 0.00 0.00 0.00 3.53
1552 1721 8.504815 TGATAAGAGACATACTACATCGTAAGC 58.495 37.037 0.00 0.00 37.18 3.09
1595 1765 9.226606 ACAAAAATCGATACAAGATGAAACCTA 57.773 29.630 0.00 0.00 0.00 3.08
1785 1957 2.363306 TGACTGCCTTTTGGTCACAT 57.637 45.000 0.00 0.00 42.99 3.21
1806 1979 5.591877 CCAACCAAAGAAGATGAGGGAATAG 59.408 44.000 0.00 0.00 0.00 1.73
1987 2160 7.929245 TCATTTAGCTGTACTGTCACTTTAACA 59.071 33.333 0.00 0.00 0.00 2.41
2048 2222 5.243730 TGATGGAATGAACAAAAGAGAACCC 59.756 40.000 0.00 0.00 0.00 4.11
2077 2251 3.683340 GGTTCAAACGGACAAGAGATACC 59.317 47.826 0.00 0.00 0.00 2.73
2080 2254 3.771577 AGGTTCAAACGGACAAGAGAT 57.228 42.857 0.00 0.00 0.00 2.75
2212 2386 9.434420 GGACATCAAAAATCATCAACCATTAAA 57.566 29.630 0.00 0.00 0.00 1.52
2230 2404 3.885724 TTATCTGCACGAGGACATCAA 57.114 42.857 0.00 0.00 0.00 2.57
2231 2405 3.384467 TCATTATCTGCACGAGGACATCA 59.616 43.478 0.00 0.00 0.00 3.07
2233 2407 4.406648 TTCATTATCTGCACGAGGACAT 57.593 40.909 0.00 0.00 0.00 3.06
2292 2466 2.530958 TACTTTAGGGCCGCCACTGC 62.531 60.000 12.58 0.00 0.00 4.40
2321 2495 5.640158 TTGTCCTTAGTTTCCCTTTCAGA 57.360 39.130 0.00 0.00 0.00 3.27
2378 2552 6.462552 TTTCACAAAACCATGTTCTGATGA 57.537 33.333 0.00 0.00 0.00 2.92
2386 2560 3.491447 GCTCAGCTTTCACAAAACCATGT 60.491 43.478 0.00 0.00 0.00 3.21
2506 2680 3.450457 TGACAAAATGCCCACCATAATCC 59.550 43.478 0.00 0.00 32.67 3.01
2515 2689 2.562298 GACATCCTTGACAAAATGCCCA 59.438 45.455 9.18 0.00 0.00 5.36
2518 2692 3.248266 GCAGACATCCTTGACAAAATGC 58.752 45.455 9.18 0.00 0.00 3.56
2577 2751 6.869388 CACCTTTTCACTTACTACCTTCTCTC 59.131 42.308 0.00 0.00 0.00 3.20
2755 2929 6.000891 TCATGTTCAGTTTTCAAAGGATCG 57.999 37.500 0.00 0.00 0.00 3.69
2850 3024 1.063616 CAAGATCATGTGCTTCGCCAG 59.936 52.381 0.00 0.00 0.00 4.85
2936 3110 3.054878 GTTTTGCAGCTTCATGACTTGG 58.945 45.455 0.00 0.00 0.00 3.61
3011 3185 3.255395 TCAATTGCTTCTCCATCGCAAAA 59.745 39.130 0.00 0.00 45.46 2.44
3091 3528 7.219917 CACCAAATAATTGCGGTACATGTTTAG 59.780 37.037 2.30 0.00 35.10 1.85
3117 3554 7.493367 ACTAAATTCTGCTAGTATGGTCAGTC 58.507 38.462 0.00 0.00 0.00 3.51
3176 3613 2.427506 CAGGTGGCAAGACTAGTTTCC 58.572 52.381 0.00 0.00 0.00 3.13
3182 3619 1.071699 GAACACCAGGTGGCAAGACTA 59.928 52.381 24.13 0.00 37.94 2.59
3202 3639 6.963242 CGATTGCATTTATTGATCCGAATAGG 59.037 38.462 0.00 0.00 42.97 2.57
3207 3644 6.017192 ACATTCGATTGCATTTATTGATCCGA 60.017 34.615 7.21 0.00 0.00 4.55
3261 3698 6.157645 AGAGGCGGAATATGGAGATAAATGAT 59.842 38.462 0.00 0.00 0.00 2.45
3298 3735 7.228108 ATCATTTGATGCTACCTGTAATGACAG 59.772 37.037 2.81 2.81 41.99 3.51
3312 3749 6.811665 CAGTTTCATGACAATCATTTGATGCT 59.188 34.615 0.00 0.00 34.28 3.79
3313 3750 6.035650 CCAGTTTCATGACAATCATTTGATGC 59.964 38.462 0.00 0.00 34.28 3.91
3316 3753 6.897706 TCCAGTTTCATGACAATCATTTGA 57.102 33.333 0.00 0.00 34.28 2.69
3320 3757 7.571919 ACTAGATCCAGTTTCATGACAATCAT 58.428 34.615 0.00 0.00 37.65 2.45
3321 3758 6.950842 ACTAGATCCAGTTTCATGACAATCA 58.049 36.000 0.00 0.00 0.00 2.57
3327 3764 5.422012 TGCAGTACTAGATCCAGTTTCATGA 59.578 40.000 0.00 0.00 0.00 3.07
3342 3779 2.597578 TGGACTCTGGTGCAGTACTA 57.402 50.000 0.00 0.00 38.83 1.82
3365 3802 2.105821 TCAACTGGTAAACCACTGAGGG 59.894 50.000 0.00 0.00 42.01 4.30
3405 3842 3.361281 TCTTCAGGAATTGCAGCTGAT 57.639 42.857 20.43 0.00 0.00 2.90
3413 3850 3.760151 TGCACCATCTTCTTCAGGAATTG 59.240 43.478 0.00 0.00 33.01 2.32
3426 3866 7.129457 TCTGTTATCTAATTCTGCACCATCT 57.871 36.000 0.00 0.00 0.00 2.90
3428 3868 6.100279 TCCTCTGTTATCTAATTCTGCACCAT 59.900 38.462 0.00 0.00 0.00 3.55
3467 3907 4.080526 AGGCGATAAAAGGGTTGTAGTGAT 60.081 41.667 0.00 0.00 0.00 3.06
3492 3932 3.493350 CCCATGTGTCCTCTAAAGATCCG 60.493 52.174 0.00 0.00 0.00 4.18
3567 4007 3.194005 TCTGTCTTTCCAACAGGACAC 57.806 47.619 3.65 0.00 43.48 3.67
3615 4055 1.247567 AATCAAAACCTCCCAGTGCG 58.752 50.000 0.00 0.00 0.00 5.34
3627 4067 7.509141 TTCAGCTGTCTCAACATAATCAAAA 57.491 32.000 14.67 0.00 34.13 2.44
3711 4151 2.093553 GCTCTCTTCAGATGCTTGGACT 60.094 50.000 0.00 0.00 0.00 3.85
3902 4342 2.543445 CCGACATCTCTCTGATCACTGC 60.543 54.545 0.00 0.00 32.05 4.40
3905 4345 4.096532 TGTTACCGACATCTCTCTGATCAC 59.903 45.833 0.00 0.00 32.00 3.06
3917 4357 6.406370 TCAATTCTCATCTTGTTACCGACAT 58.594 36.000 0.00 0.00 38.26 3.06
3919 4359 6.238211 CCATCAATTCTCATCTTGTTACCGAC 60.238 42.308 0.00 0.00 0.00 4.79
3920 4360 5.817296 CCATCAATTCTCATCTTGTTACCGA 59.183 40.000 0.00 0.00 0.00 4.69
3921 4361 5.817296 TCCATCAATTCTCATCTTGTTACCG 59.183 40.000 0.00 0.00 0.00 4.02
3923 4363 6.317140 TGCTCCATCAATTCTCATCTTGTTAC 59.683 38.462 0.00 0.00 0.00 2.50
3924 4364 6.317140 GTGCTCCATCAATTCTCATCTTGTTA 59.683 38.462 0.00 0.00 0.00 2.41
3925 4365 5.125097 GTGCTCCATCAATTCTCATCTTGTT 59.875 40.000 0.00 0.00 0.00 2.83
3926 4366 4.639310 GTGCTCCATCAATTCTCATCTTGT 59.361 41.667 0.00 0.00 0.00 3.16
3927 4367 4.638865 TGTGCTCCATCAATTCTCATCTTG 59.361 41.667 0.00 0.00 0.00 3.02
3928 4368 4.851843 TGTGCTCCATCAATTCTCATCTT 58.148 39.130 0.00 0.00 0.00 2.40
3929 4369 4.498894 TGTGCTCCATCAATTCTCATCT 57.501 40.909 0.00 0.00 0.00 2.90
3930 4370 4.023107 CCATGTGCTCCATCAATTCTCATC 60.023 45.833 0.00 0.00 0.00 2.92
3931 4371 3.889538 CCATGTGCTCCATCAATTCTCAT 59.110 43.478 0.00 0.00 0.00 2.90
3932 4372 3.284617 CCATGTGCTCCATCAATTCTCA 58.715 45.455 0.00 0.00 0.00 3.27
3933 4373 3.066342 CACCATGTGCTCCATCAATTCTC 59.934 47.826 0.00 0.00 0.00 2.87
3934 4374 3.021695 CACCATGTGCTCCATCAATTCT 58.978 45.455 0.00 0.00 0.00 2.40
3935 4375 3.431922 CACCATGTGCTCCATCAATTC 57.568 47.619 0.00 0.00 0.00 2.17
3947 4387 0.251354 ACTAGGCTCTGCACCATGTG 59.749 55.000 0.00 0.00 36.51 3.21
3948 4388 0.251354 CACTAGGCTCTGCACCATGT 59.749 55.000 0.00 0.00 0.00 3.21
3949 4389 0.538584 TCACTAGGCTCTGCACCATG 59.461 55.000 0.00 0.00 0.00 3.66
3950 4390 1.140452 CATCACTAGGCTCTGCACCAT 59.860 52.381 0.00 0.00 0.00 3.55
3951 4391 0.538584 CATCACTAGGCTCTGCACCA 59.461 55.000 0.00 0.00 0.00 4.17
3954 4394 1.560505 TGACATCACTAGGCTCTGCA 58.439 50.000 0.00 0.00 0.00 4.41
3982 4422 0.389948 GTCTCGCACTTCGGATGGTT 60.390 55.000 0.00 0.00 39.05 3.67
3983 4423 1.215647 GTCTCGCACTTCGGATGGT 59.784 57.895 0.00 0.00 39.05 3.55
3990 4430 3.112709 GCACCGGTCTCGCACTTC 61.113 66.667 2.59 0.00 34.56 3.01
3993 4433 4.664677 ACAGCACCGGTCTCGCAC 62.665 66.667 16.80 0.00 34.56 5.34
4086 4526 0.452585 GCGAAACCGTAGAGCTCTCT 59.547 55.000 22.17 0.00 43.40 3.10
4122 4562 1.064906 CCATCAGGTCCATTCTGCTGT 60.065 52.381 0.00 0.00 32.63 4.40
4133 4573 0.109597 CAACTTTGCGCCATCAGGTC 60.110 55.000 4.18 0.00 37.19 3.85
4143 4583 1.487231 CCGAGTCGTCAACTTTGCG 59.513 57.895 12.31 0.00 38.74 4.85
4242 4682 2.210116 GAACGAAGAGAAGTGTTGCCA 58.790 47.619 0.00 0.00 0.00 4.92
4357 4797 7.828717 TGTGGATCAACACATATGAGTTTATGT 59.171 33.333 14.87 2.46 45.70 2.29
4376 4816 0.179062 CTGCCTGTAGCCTGTGGATC 60.179 60.000 0.00 0.00 42.71 3.36
4392 4832 2.331132 GGCTGCTGTTCCACTCTGC 61.331 63.158 0.00 0.00 0.00 4.26
4507 4947 4.981806 GAGCTAGACTCATCAGACAGTT 57.018 45.455 0.00 0.00 45.49 3.16
4627 5072 8.496707 AAATAAAAATAAAAGAGCAGGGCATG 57.503 30.769 0.00 0.00 0.00 4.06
4689 5134 3.503363 TCTCTGCAAATTACAAGCCACTG 59.497 43.478 0.00 0.00 0.00 3.66
4717 5162 7.430760 AAGCTATACCTCTTCATTTCTCACT 57.569 36.000 0.00 0.00 0.00 3.41
4863 5458 0.037447 TCACATTCGGGTCATGGCAA 59.963 50.000 0.00 0.00 0.00 4.52
4876 5471 8.491331 AACTTATTTTGTTGCTTGTTCACATT 57.509 26.923 0.00 0.00 0.00 2.71
4904 5506 4.747108 AGAATATCAGCGTTCTATGTGTGC 59.253 41.667 0.00 0.00 33.15 4.57
5035 5637 2.185004 TTTCTGCAAGGACTACTGGC 57.815 50.000 0.00 0.00 46.97 4.85
5040 5643 2.814097 GCCCTGTTTTCTGCAAGGACTA 60.814 50.000 1.24 0.00 0.00 2.59
5114 5721 3.973657 ACGTCAAGTTGGTACTACAGTG 58.026 45.455 2.34 0.00 33.17 3.66
5122 5729 9.537192 CCATAATATAAGAACGTCAAGTTGGTA 57.463 33.333 2.34 0.00 44.35 3.25
5124 5731 7.713507 TCCCATAATATAAGAACGTCAAGTTGG 59.286 37.037 2.34 0.00 44.35 3.77
5129 5736 9.104965 CTTTGTCCCATAATATAAGAACGTCAA 57.895 33.333 0.00 0.00 0.00 3.18
5130 5737 7.713507 CCTTTGTCCCATAATATAAGAACGTCA 59.286 37.037 0.00 0.00 0.00 4.35
5131 5738 7.172703 CCCTTTGTCCCATAATATAAGAACGTC 59.827 40.741 0.00 0.00 0.00 4.34
5132 5739 6.996282 CCCTTTGTCCCATAATATAAGAACGT 59.004 38.462 0.00 0.00 0.00 3.99
5133 5740 7.221450 TCCCTTTGTCCCATAATATAAGAACG 58.779 38.462 0.00 0.00 0.00 3.95
5135 5742 8.344939 ACTCCCTTTGTCCCATAATATAAGAA 57.655 34.615 0.00 0.00 0.00 2.52
5136 5743 7.947782 ACTCCCTTTGTCCCATAATATAAGA 57.052 36.000 0.00 0.00 0.00 2.10
5140 5747 7.950124 CCAAATACTCCCTTTGTCCCATAATAT 59.050 37.037 0.00 0.00 32.83 1.28
5141 5748 7.294584 CCAAATACTCCCTTTGTCCCATAATA 58.705 38.462 0.00 0.00 32.83 0.98
5142 5749 6.136155 CCAAATACTCCCTTTGTCCCATAAT 58.864 40.000 0.00 0.00 32.83 1.28
5144 5751 4.079443 CCCAAATACTCCCTTTGTCCCATA 60.079 45.833 0.00 0.00 32.83 2.74
5145 5752 3.309848 CCCAAATACTCCCTTTGTCCCAT 60.310 47.826 0.00 0.00 32.83 4.00
5147 5754 2.042569 ACCCAAATACTCCCTTTGTCCC 59.957 50.000 0.00 0.00 32.83 4.46
5148 5755 3.451402 ACCCAAATACTCCCTTTGTCC 57.549 47.619 0.00 0.00 32.83 4.02
5149 5756 5.104067 AGGATACCCAAATACTCCCTTTGTC 60.104 44.000 0.00 0.00 32.83 3.18
5150 5757 4.794067 AGGATACCCAAATACTCCCTTTGT 59.206 41.667 0.00 0.00 32.83 2.83
5151 5758 5.133221 CAGGATACCCAAATACTCCCTTTG 58.867 45.833 0.00 0.00 34.17 2.77
5152 5759 4.386424 GCAGGATACCCAAATACTCCCTTT 60.386 45.833 0.00 0.00 33.88 3.11
5153 5760 3.138468 GCAGGATACCCAAATACTCCCTT 59.862 47.826 0.00 0.00 33.88 3.95
5155 5762 2.441750 TGCAGGATACCCAAATACTCCC 59.558 50.000 0.00 0.00 33.88 4.30
5156 5763 3.857157 TGCAGGATACCCAAATACTCC 57.143 47.619 0.00 0.00 33.88 3.85
5157 5764 3.565902 GCTTGCAGGATACCCAAATACTC 59.434 47.826 0.00 0.00 33.88 2.59
5158 5765 3.555966 GCTTGCAGGATACCCAAATACT 58.444 45.455 0.00 0.00 33.88 2.12
5194 5813 9.248291 CTACTACTGCTACTACTACAACTAGTC 57.752 40.741 0.00 0.00 34.79 2.59


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

AutoCloner maintained by Alex Coulton.