Multiple sequence alignment - TraesCS1B01G443100

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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 TraesCS1B01G443100 chr1B 100.000 4154 0 0 1 4154 664284427 664288580 0.000000e+00 7672.0
1 TraesCS1B01G443100 chr1A 85.876 2032 153 64 1771 3726 573069809 573067836 0.000000e+00 2039.0
2 TraesCS1B01G443100 chr1A 84.103 975 85 41 555 1503 573071023 573070093 0.000000e+00 878.0
3 TraesCS1B01G443100 chr1A 87.909 397 21 9 3755 4149 573067393 573067022 3.810000e-120 442.0
4 TraesCS1B01G443100 chr1A 91.579 285 20 3 10 293 573073002 573072721 1.400000e-104 390.0
5 TraesCS1B01G443100 chr1A 85.433 254 27 7 1531 1777 573070094 573069844 5.330000e-64 255.0
6 TraesCS1B01G443100 chr1D 90.951 1072 59 23 2429 3484 476914042 476912993 0.000000e+00 1408.0
7 TraesCS1B01G443100 chr1D 83.348 1141 78 52 363 1451 476916146 476915066 0.000000e+00 952.0
8 TraesCS1B01G443100 chr1D 91.241 548 35 6 1776 2314 476914663 476914120 0.000000e+00 734.0
9 TraesCS1B01G443100 chr1D 91.795 390 19 10 3762 4149 476912015 476911637 7.910000e-147 531.0
10 TraesCS1B01G443100 chr1D 92.997 357 19 3 1423 1777 476915054 476914702 2.210000e-142 516.0
11 TraesCS1B01G443100 chr1D 84.762 210 22 10 3485 3689 476912938 476912734 7.040000e-48 202.0
12 TraesCS1B01G443100 chr7D 89.305 187 20 0 2626 2812 449775571 449775757 6.940000e-58 235.0
13 TraesCS1B01G443100 chr7D 100.000 28 0 0 421 448 99285263 99285290 8.000000e-03 52.8
14 TraesCS1B01G443100 chr7B 88.770 187 21 0 2626 2812 468124188 468124374 3.230000e-56 230.0
15 TraesCS1B01G443100 chr7B 78.058 278 44 4 6 269 510055233 510055507 4.300000e-35 159.0
16 TraesCS1B01G443100 chr4B 78.448 348 49 12 2673 2999 636616783 636617125 1.960000e-48 204.0
17 TraesCS1B01G443100 chr5A 87.006 177 23 0 2626 2802 258723747 258723923 2.530000e-47 200.0
18 TraesCS1B01G443100 chr4A 87.209 172 21 1 123 294 8579831 8579661 1.180000e-45 195.0
19 TraesCS1B01G443100 chr4A 89.362 47 5 0 402 448 715322992 715323038 4.480000e-05 60.2
20 TraesCS1B01G443100 chr2D 81.702 235 35 8 14 243 372143504 372143273 5.480000e-44 189.0
21 TraesCS1B01G443100 chr2D 82.558 172 25 5 118 289 648308191 648308357 3.350000e-31 147.0
22 TraesCS1B01G443100 chr2D 80.000 105 16 5 5 106 337423164 337423266 5.760000e-09 73.1
23 TraesCS1B01G443100 chr6B 79.422 277 45 5 5 269 437784876 437785152 7.090000e-43 185.0
24 TraesCS1B01G443100 chr6B 77.667 300 47 14 11 293 159124516 159124812 9.240000e-37 165.0
25 TraesCS1B01G443100 chr6B 78.369 282 39 10 9 269 638345477 638345197 3.320000e-36 163.0
26 TraesCS1B01G443100 chr5B 87.407 135 13 4 2704 2836 486362589 486362457 7.190000e-33 152.0
27 TraesCS1B01G443100 chr5B 77.202 193 39 5 6 197 328043464 328043652 1.580000e-19 108.0
28 TraesCS1B01G443100 chr2B 87.407 135 13 4 2704 2836 297449386 297449254 7.190000e-33 152.0
29 TraesCS1B01G443100 chr2B 84.375 160 20 4 2704 2862 644559319 644559474 7.190000e-33 152.0
30 TraesCS1B01G443100 chr2B 90.909 44 4 0 405 448 195622423 195622380 4.480000e-05 60.2
31 TraesCS1B01G443100 chr3A 82.456 171 26 3 123 293 472166511 472166677 3.350000e-31 147.0
32 TraesCS1B01G443100 chr3D 77.824 239 44 6 57 293 64583579 64583810 5.600000e-29 139.0
33 TraesCS1B01G443100 chr3D 81.818 77 14 0 6 82 313260193 313260117 9.640000e-07 65.8
34 TraesCS1B01G443100 chr3B 89.091 110 10 2 2750 2859 467055042 467054935 7.240000e-28 135.0
35 TraesCS1B01G443100 chr3B 75.127 197 29 18 11 197 406632788 406632974 1.600000e-09 75.0
36 TraesCS1B01G443100 chr6A 76.730 159 26 10 11 163 479341049 479341202 1.240000e-10 78.7


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 TraesCS1B01G443100 chr1B 664284427 664288580 4153 False 7672.000000 7672 100.000000 1 4154 1 chr1B.!!$F1 4153
1 TraesCS1B01G443100 chr1A 573067022 573073002 5980 True 800.800000 2039 86.980000 10 4149 5 chr1A.!!$R1 4139
2 TraesCS1B01G443100 chr1D 476911637 476916146 4509 True 723.833333 1408 89.182333 363 4149 6 chr1D.!!$R1 3786

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
297 773 0.036732 TTGACACTGGGCACTGATCC 59.963 55.0 0.00 0.00 0.00 3.36 F
1268 2775 0.098905 TCGTTTCGGCGAGATCTGAG 59.901 55.0 10.46 0.00 35.83 3.35 F
1271 2778 0.098905 TTTCGGCGAGATCTGAGTCG 59.901 55.0 10.46 13.69 39.25 4.18 F
2140 3744 0.461870 TGCACCTATACTGCTTGGCG 60.462 55.0 0.00 0.00 35.53 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 2827 0.673644 ACCCCGCAATCTCTCAAACG 60.674 55.0 0.00 0.0 0.00 3.60 R
2335 3940 0.026674 CACAACAGTCGTGTGTGCAG 59.973 55.0 0.00 0.0 36.84 4.41 R
3006 4657 0.039618 ACCTGAAACCGGGCAATCAT 59.960 50.0 6.32 0.0 33.23 2.45 R
3736 5489 0.036732 TCGCTTCTTGGGACATGCTT 59.963 50.0 0.00 0.0 39.30 3.91 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
50 51 6.208599 TGGTTCTCTGTTGGTTTGGAAATATC 59.791 38.462 0.00 0.00 0.00 1.63
55 56 5.476599 TCTGTTGGTTTGGAAATATCTGTGG 59.523 40.000 0.00 0.00 0.00 4.17
90 92 4.151689 TCGATTTAGGTCAAAGAAGTTGCG 59.848 41.667 0.00 0.00 37.13 4.85
110 112 3.400054 GGGCCCACGAGCTTAGGT 61.400 66.667 19.95 0.00 0.00 3.08
152 154 1.481772 GCTCTCTCATGGCTCTTCTGT 59.518 52.381 0.00 0.00 0.00 3.41
163 165 1.000486 TCTTCTGTCCTCCTCCCGG 60.000 63.158 0.00 0.00 0.00 5.73
176 178 1.076192 TCCCGGAGCTTCTAGGGTC 60.076 63.158 0.73 0.00 44.13 4.46
186 188 2.552367 CTTCTAGGGTCCCTTCTGGTT 58.448 52.381 17.94 0.00 34.61 3.67
294 770 1.545428 GGAATTGACACTGGGCACTGA 60.545 52.381 0.00 0.00 0.00 3.41
295 771 2.440409 GAATTGACACTGGGCACTGAT 58.560 47.619 0.00 0.00 0.00 2.90
296 772 2.119801 ATTGACACTGGGCACTGATC 57.880 50.000 0.00 0.00 0.00 2.92
297 773 0.036732 TTGACACTGGGCACTGATCC 59.963 55.000 0.00 0.00 0.00 3.36
298 774 1.126948 TGACACTGGGCACTGATCCA 61.127 55.000 0.00 0.00 0.00 3.41
303 779 3.963733 TGGGCACTGATCCAGAAAG 57.036 52.632 0.45 0.00 35.18 2.62
315 791 6.385467 ACTGATCCAGAAAGAATAGGCTAGTT 59.615 38.462 0.00 0.00 35.18 2.24
336 1132 0.176680 CCTCTCACATCTCAACCGGG 59.823 60.000 6.32 0.00 0.00 5.73
462 1259 4.036380 GTCCGGACAAACATGAAAAAGACT 59.964 41.667 29.75 0.00 0.00 3.24
510 1326 1.448717 GCTCTTCAGCGTTCCCCTC 60.449 63.158 0.00 0.00 35.39 4.30
529 1345 3.947834 CCTCAAAATGGCCCAAGTAGTAG 59.052 47.826 0.00 0.00 0.00 2.57
530 1346 4.567747 CCTCAAAATGGCCCAAGTAGTAGT 60.568 45.833 0.00 0.00 0.00 2.73
532 1348 5.741011 TCAAAATGGCCCAAGTAGTAGTAG 58.259 41.667 0.00 0.00 0.00 2.57
533 1349 5.249852 TCAAAATGGCCCAAGTAGTAGTAGT 59.750 40.000 0.00 0.00 0.00 2.73
534 1350 6.441284 TCAAAATGGCCCAAGTAGTAGTAGTA 59.559 38.462 0.00 0.00 0.00 1.82
536 1352 4.598036 TGGCCCAAGTAGTAGTAGTAGT 57.402 45.455 0.00 0.00 0.00 2.73
538 1354 5.440610 TGGCCCAAGTAGTAGTAGTAGTAC 58.559 45.833 12.87 12.87 35.87 2.73
559 1375 0.107897 ACTCACAACGGCAAGTGTGA 60.108 50.000 13.06 13.06 38.01 3.58
625 2087 2.415512 CCGACCGTTCTTTCTGGAATTC 59.584 50.000 0.00 0.00 0.00 2.17
651 2114 0.538287 ACAGAAAAGAGGCAGCCCAC 60.538 55.000 8.22 2.52 0.00 4.61
933 2414 3.570550 CGATTCGAAATACTCCTCCTCCT 59.429 47.826 0.00 0.00 0.00 3.69
934 2415 4.320641 CGATTCGAAATACTCCTCCTCCTC 60.321 50.000 0.00 0.00 0.00 3.71
935 2416 2.946785 TCGAAATACTCCTCCTCCTCC 58.053 52.381 0.00 0.00 0.00 4.30
953 2434 1.682344 CCCTAGGGTTTTGCTGCCC 60.682 63.158 20.88 0.00 45.16 5.36
1029 2520 2.202837 CCCCCGTTCGATTCCGTC 60.203 66.667 0.00 0.00 37.05 4.79
1039 2545 4.814294 ATTCCGTCGCGTCTGGCC 62.814 66.667 5.77 0.00 38.94 5.36
1074 2580 1.464997 GCGTGGGTCTGATCTGTTTTC 59.535 52.381 0.00 0.00 0.00 2.29
1075 2581 2.076863 CGTGGGTCTGATCTGTTTTCC 58.923 52.381 0.00 0.00 0.00 3.13
1167 2674 2.607750 ATGGCGGGACTGGTGAGT 60.608 61.111 0.00 0.00 33.98 3.41
1173 2680 1.884444 GGGACTGGTGAGTCTCGTC 59.116 63.158 0.00 0.00 46.96 4.20
1175 2682 1.596895 GGACTGGTGAGTCTCGTCCC 61.597 65.000 11.63 5.12 46.96 4.46
1176 2683 0.609681 GACTGGTGAGTCTCGTCCCT 60.610 60.000 10.21 0.00 44.73 4.20
1177 2684 0.178958 ACTGGTGAGTCTCGTCCCTT 60.179 55.000 10.21 0.00 0.00 3.95
1180 2687 1.605971 GGTGAGTCTCGTCCCTTCCC 61.606 65.000 0.00 0.00 0.00 3.97
1181 2688 1.305046 TGAGTCTCGTCCCTTCCCC 60.305 63.158 0.00 0.00 0.00 4.81
1182 2689 2.039137 AGTCTCGTCCCTTCCCCC 59.961 66.667 0.00 0.00 0.00 5.40
1183 2690 3.459063 GTCTCGTCCCTTCCCCCG 61.459 72.222 0.00 0.00 0.00 5.73
1197 2704 4.016706 CCCGCCTCCCTGTTCGTT 62.017 66.667 0.00 0.00 0.00 3.85
1198 2705 2.032071 CCGCCTCCCTGTTCGTTT 59.968 61.111 0.00 0.00 0.00 3.60
1199 2706 2.033194 CCGCCTCCCTGTTCGTTTC 61.033 63.158 0.00 0.00 0.00 2.78
1203 2710 1.145803 CCTCCCTGTTCGTTTCGTTC 58.854 55.000 0.00 0.00 0.00 3.95
1206 2713 1.203313 CCTGTTCGTTTCGTTCCGC 59.797 57.895 0.00 0.00 0.00 5.54
1211 2718 1.384742 GTTCGTTTCGTTCCGCTAGAC 59.615 52.381 0.00 0.00 0.00 2.59
1212 2719 0.453282 TCGTTTCGTTCCGCTAGACG 60.453 55.000 0.00 0.00 43.15 4.18
1267 2774 0.179171 GTCGTTTCGGCGAGATCTGA 60.179 55.000 10.46 2.79 41.85 3.27
1268 2775 0.098905 TCGTTTCGGCGAGATCTGAG 59.901 55.000 10.46 0.00 35.83 3.35
1271 2778 0.098905 TTTCGGCGAGATCTGAGTCG 59.901 55.000 10.46 13.69 39.25 4.18
1272 2779 1.025113 TTCGGCGAGATCTGAGTCGT 61.025 55.000 17.69 0.00 38.48 4.34
1273 2780 1.010574 CGGCGAGATCTGAGTCGTC 60.011 63.158 0.00 9.57 38.48 4.20
1275 2782 0.736053 GGCGAGATCTGAGTCGTCTT 59.264 55.000 0.00 0.00 37.80 3.01
1276 2783 1.941294 GGCGAGATCTGAGTCGTCTTA 59.059 52.381 0.00 0.00 37.80 2.10
1278 2785 2.597971 GCGAGATCTGAGTCGTCTTACG 60.598 54.545 0.00 0.00 44.19 3.18
1320 2827 5.489792 TGGAATCTGATGTCCTATTAGGC 57.510 43.478 4.73 1.51 34.61 3.93
1324 2831 5.552870 ATCTGATGTCCTATTAGGCGTTT 57.447 39.130 4.73 0.00 34.61 3.60
1326 2833 4.404394 TCTGATGTCCTATTAGGCGTTTGA 59.596 41.667 4.73 2.84 34.61 2.69
1327 2834 4.693283 TGATGTCCTATTAGGCGTTTGAG 58.307 43.478 4.73 0.00 34.61 3.02
1328 2835 4.404394 TGATGTCCTATTAGGCGTTTGAGA 59.596 41.667 4.73 0.00 34.61 3.27
1339 2846 0.673644 CGTTTGAGAGATTGCGGGGT 60.674 55.000 0.00 0.00 0.00 4.95
1340 2847 1.534729 GTTTGAGAGATTGCGGGGTT 58.465 50.000 0.00 0.00 0.00 4.11
1344 2851 1.281867 TGAGAGATTGCGGGGTTGATT 59.718 47.619 0.00 0.00 0.00 2.57
1418 2926 4.990426 CCTTTTGATGCTTTCCGTTTGAAT 59.010 37.500 0.00 0.00 31.67 2.57
1419 2927 5.466393 CCTTTTGATGCTTTCCGTTTGAATT 59.534 36.000 0.00 0.00 31.67 2.17
1438 2986 5.468746 TGAATTCGTGGAAAACAGAGTTAGG 59.531 40.000 0.04 0.00 0.00 2.69
1472 3020 4.413851 GGGATTTAGATCAGGGAGGTCTTT 59.586 45.833 0.00 0.00 33.77 2.52
1477 3025 2.708325 AGATCAGGGAGGTCTTTATGCC 59.292 50.000 0.00 0.00 0.00 4.40
1522 3070 8.417884 CCAATAGGAAGGAAAAAGTTTGTGTAA 58.582 33.333 0.00 0.00 36.89 2.41
1618 3169 7.716799 ATGGAGATTAAACAATTACCAGCAA 57.283 32.000 0.00 0.00 0.00 3.91
1621 3172 9.249053 TGGAGATTAAACAATTACCAGCAAATA 57.751 29.630 0.00 0.00 0.00 1.40
1660 3211 6.071391 GGATTATTTGAACATGGGAGTGTGTT 60.071 38.462 0.00 0.00 40.97 3.32
1711 3265 1.263356 TAGGCAAAGACGTGGTAGCT 58.737 50.000 0.00 0.00 0.00 3.32
1719 3273 5.224888 CAAAGACGTGGTAGCTTTACTGTA 58.775 41.667 0.00 0.00 31.21 2.74
1722 3276 6.129053 AGACGTGGTAGCTTTACTGTATAC 57.871 41.667 0.00 0.00 0.00 1.47
1753 3307 4.218200 TCCATTTTTCATGCACCAGTGTAG 59.782 41.667 0.00 0.00 0.00 2.74
1771 3325 5.830991 AGTGTAGAAGGTCTGCCTATTAGAG 59.169 44.000 0.00 0.00 46.33 2.43
1774 3328 7.284944 GTGTAGAAGGTCTGCCTATTAGAGTTA 59.715 40.741 0.00 0.00 46.33 2.24
1779 3374 6.315714 AGGTCTGCCTATTAGAGTTATGCTA 58.684 40.000 0.00 0.00 44.90 3.49
1835 3430 7.384387 AGTTTTGTCTCTGTACCGAATTACTTC 59.616 37.037 0.00 0.00 0.00 3.01
1837 3432 6.525578 TGTCTCTGTACCGAATTACTTCAT 57.474 37.500 0.00 0.00 0.00 2.57
1873 3468 9.262358 CTAGATTGGTATCTCATGCATCATATG 57.738 37.037 0.00 0.00 41.38 1.78
1899 3495 9.559958 GTTCTAATCAAACATGAACCTAACATG 57.440 33.333 0.00 0.00 46.96 3.21
1904 3504 4.724074 AACATGAACCTAACATGCCATG 57.276 40.909 2.40 2.40 45.95 3.66
1950 3551 3.940209 TTTTGCCTGCCTAGTCATTTG 57.060 42.857 0.00 0.00 0.00 2.32
1956 3557 3.507622 GCCTGCCTAGTCATTTGTTCTTT 59.492 43.478 0.00 0.00 0.00 2.52
1968 3569 9.301897 AGTCATTTGTTCTTTATTAGCTTCCTT 57.698 29.630 0.00 0.00 0.00 3.36
1970 3571 8.739972 TCATTTGTTCTTTATTAGCTTCCTTCC 58.260 33.333 0.00 0.00 0.00 3.46
2100 3704 4.365899 AGAAATACGAGCGTATGTGTGA 57.634 40.909 15.34 0.00 40.73 3.58
2104 3708 5.389642 AATACGAGCGTATGTGTGAATTG 57.610 39.130 15.34 0.00 40.73 2.32
2109 3713 4.561213 CGAGCGTATGTGTGAATTGTTCTA 59.439 41.667 0.00 0.00 0.00 2.10
2120 3724 8.397906 TGTGTGAATTGTTCTAAGTTTCTCTTG 58.602 33.333 0.00 0.00 37.56 3.02
2140 3744 0.461870 TGCACCTATACTGCTTGGCG 60.462 55.000 0.00 0.00 35.53 5.69
2229 3834 4.380867 CCATTGGATTTCACCACTAACTGC 60.381 45.833 0.00 0.00 39.85 4.40
2289 3894 2.979678 AGAGAAGTTTGGTGGCCTTAGA 59.020 45.455 3.32 0.00 0.00 2.10
2314 3919 8.743085 AGATGGATACTAGTAAGTGTTTCGTA 57.257 34.615 6.70 0.00 36.36 3.43
2364 3969 4.099120 CACGACTGTTGTGTAGCTATCTC 58.901 47.826 18.13 0.00 32.68 2.75
2369 3974 7.142021 CGACTGTTGTGTAGCTATCTCAATAT 58.858 38.462 0.00 0.00 0.00 1.28
2394 3999 6.861065 AGATGTATTGGTTAAGGCGTATTG 57.139 37.500 0.00 0.00 0.00 1.90
2395 4000 5.763204 AGATGTATTGGTTAAGGCGTATTGG 59.237 40.000 0.00 0.00 0.00 3.16
2399 4004 6.883217 TGTATTGGTTAAGGCGTATTGGTTTA 59.117 34.615 0.00 0.00 0.00 2.01
2403 4008 5.181622 TGGTTAAGGCGTATTGGTTTACTTG 59.818 40.000 0.00 0.00 0.00 3.16
2405 4010 2.089201 AGGCGTATTGGTTTACTTGGC 58.911 47.619 0.00 0.00 0.00 4.52
2407 4012 3.054948 AGGCGTATTGGTTTACTTGGCTA 60.055 43.478 0.00 0.00 0.00 3.93
2408 4013 3.690628 GGCGTATTGGTTTACTTGGCTAA 59.309 43.478 0.00 0.00 0.00 3.09
2410 4041 5.163591 GGCGTATTGGTTTACTTGGCTAATT 60.164 40.000 0.00 0.00 0.00 1.40
2413 4044 7.642586 GCGTATTGGTTTACTTGGCTAATTTAG 59.357 37.037 0.00 0.00 0.00 1.85
2427 4058 8.177119 TGGCTAATTTAGTTGTTTGACTGATT 57.823 30.769 5.38 0.00 0.00 2.57
2429 4060 9.129209 GGCTAATTTAGTTGTTTGACTGATTTC 57.871 33.333 5.38 0.00 0.00 2.17
2567 4203 6.352682 CTTCTGAAGAAGCAATCATCTCTG 57.647 41.667 12.01 0.00 44.10 3.35
2575 4211 3.533547 AGCAATCATCTCTGCTTCACTC 58.466 45.455 0.00 0.00 46.71 3.51
2581 4217 5.665916 TCATCTCTGCTTCACTCAATGTA 57.334 39.130 0.00 0.00 0.00 2.29
2584 4220 6.537660 TCATCTCTGCTTCACTCAATGTAATG 59.462 38.462 0.00 0.00 0.00 1.90
2587 4223 6.712095 TCTCTGCTTCACTCAATGTAATGTTT 59.288 34.615 0.00 0.00 0.00 2.83
2592 4228 4.793071 TCACTCAATGTAATGTTTTGCCG 58.207 39.130 0.00 0.00 0.00 5.69
2742 4382 5.590530 AGAAGAACCTGCAGTACTATGAG 57.409 43.478 13.81 0.00 0.00 2.90
2838 4478 2.442236 TCATCCCCATTGCTTTCCTC 57.558 50.000 0.00 0.00 0.00 3.71
2914 4557 2.039746 TGATCCCAACATCCACTTCGTT 59.960 45.455 0.00 0.00 0.00 3.85
2978 4621 1.401931 CCATGCAGCAACAGTAAGTGC 60.402 52.381 0.00 0.00 34.62 4.40
2982 4625 1.068954 GCAGCAACAGTAAGTGCCTTC 60.069 52.381 0.00 0.00 0.00 3.46
2983 4626 1.537202 CAGCAACAGTAAGTGCCTTCC 59.463 52.381 0.00 0.00 0.00 3.46
2984 4627 1.421646 AGCAACAGTAAGTGCCTTCCT 59.578 47.619 0.00 0.00 0.00 3.36
2985 4628 1.807142 GCAACAGTAAGTGCCTTCCTC 59.193 52.381 0.00 0.00 0.00 3.71
2986 4629 2.551071 GCAACAGTAAGTGCCTTCCTCT 60.551 50.000 0.00 0.00 0.00 3.69
2987 4630 3.070018 CAACAGTAAGTGCCTTCCTCTG 58.930 50.000 0.00 0.00 0.00 3.35
2988 4631 2.330216 ACAGTAAGTGCCTTCCTCTGT 58.670 47.619 10.97 10.97 31.20 3.41
2990 4633 3.244249 ACAGTAAGTGCCTTCCTCTGTTC 60.244 47.826 10.97 0.00 31.62 3.18
2991 4634 3.007398 CAGTAAGTGCCTTCCTCTGTTCT 59.993 47.826 0.00 0.00 0.00 3.01
2992 4635 2.849294 AAGTGCCTTCCTCTGTTCTC 57.151 50.000 0.00 0.00 0.00 2.87
2993 4636 2.022718 AGTGCCTTCCTCTGTTCTCT 57.977 50.000 0.00 0.00 0.00 3.10
2994 4637 3.176924 AGTGCCTTCCTCTGTTCTCTA 57.823 47.619 0.00 0.00 0.00 2.43
2995 4638 2.829120 AGTGCCTTCCTCTGTTCTCTAC 59.171 50.000 0.00 0.00 0.00 2.59
2996 4639 2.093921 GTGCCTTCCTCTGTTCTCTACC 60.094 54.545 0.00 0.00 0.00 3.18
2999 4650 3.181470 GCCTTCCTCTGTTCTCTACCATC 60.181 52.174 0.00 0.00 0.00 3.51
3006 4657 5.888724 CCTCTGTTCTCTACCATCTTCACTA 59.111 44.000 0.00 0.00 0.00 2.74
3007 4658 6.549364 CCTCTGTTCTCTACCATCTTCACTAT 59.451 42.308 0.00 0.00 0.00 2.12
3014 4665 5.858381 TCTACCATCTTCACTATGATTGCC 58.142 41.667 0.00 0.00 0.00 4.52
3016 4667 2.810274 CCATCTTCACTATGATTGCCCG 59.190 50.000 0.00 0.00 0.00 6.13
3024 4675 1.949525 CTATGATTGCCCGGTTTCAGG 59.050 52.381 0.00 0.00 0.00 3.86
3028 4679 1.815817 ATTGCCCGGTTTCAGGTTGC 61.816 55.000 0.00 0.00 0.00 4.17
3030 4681 2.494530 GCCCGGTTTCAGGTTGCAA 61.495 57.895 0.00 0.00 0.00 4.08
3048 4701 7.410800 GTTGCAATCAACTGAATGAATGAAA 57.589 32.000 0.59 1.76 46.81 2.69
3063 4716 6.032956 TGAATGAAAGAAATGCTGATTGCT 57.967 33.333 0.00 0.00 43.37 3.91
3075 4728 2.988493 GCTGATTGCTTTTTGATGCGAA 59.012 40.909 0.00 0.00 38.95 4.70
3163 4816 4.893608 TCTGATCGAGTAGAGAGAGGATG 58.106 47.826 0.00 0.00 0.00 3.51
3326 4980 6.901265 TGTTTGTGTGACATTGATCTACATG 58.099 36.000 0.00 0.00 0.00 3.21
3480 5140 0.179215 GTTCGCTGCTGGACATTTCG 60.179 55.000 0.00 0.00 0.00 3.46
3537 5251 6.419980 TTTTGAGCTGGTGATTTTGTTTTG 57.580 33.333 0.00 0.00 0.00 2.44
3579 5307 3.574396 TGTCTGTTGAAGATCTCGGTCTT 59.426 43.478 0.00 0.00 40.99 3.01
3590 5318 5.295950 AGATCTCGGTCTTATCAGCATTTG 58.704 41.667 0.00 0.00 0.00 2.32
3591 5319 4.736126 TCTCGGTCTTATCAGCATTTGA 57.264 40.909 0.00 0.00 40.85 2.69
3593 5321 4.870426 TCTCGGTCTTATCAGCATTTGAAC 59.130 41.667 0.00 0.00 39.77 3.18
3594 5322 3.616821 TCGGTCTTATCAGCATTTGAACG 59.383 43.478 0.00 0.00 39.77 3.95
3595 5323 3.616821 CGGTCTTATCAGCATTTGAACGA 59.383 43.478 0.00 0.00 39.77 3.85
3664 5403 2.863809 TGAAGCCCAAAAGAGGAAGAC 58.136 47.619 0.00 0.00 0.00 3.01
3670 5409 2.827921 CCCAAAAGAGGAAGACCATTGG 59.172 50.000 0.00 0.00 37.50 3.16
3671 5410 3.500343 CCAAAAGAGGAAGACCATTGGT 58.500 45.455 8.42 8.42 39.44 3.67
3706 5459 2.907042 ACCAAGGCTAGTAGTTCTGCTT 59.093 45.455 0.00 0.00 0.00 3.91
3726 5479 4.452455 GCTTAAGCTTGAGTTGCTCTTACA 59.548 41.667 20.38 0.00 40.22 2.41
3727 5480 5.049405 GCTTAAGCTTGAGTTGCTCTTACAA 60.049 40.000 20.38 0.00 40.22 2.41
3728 5481 6.513393 GCTTAAGCTTGAGTTGCTCTTACAAA 60.513 38.462 20.38 0.00 40.22 2.83
3730 5483 5.619625 AGCTTGAGTTGCTCTTACAAATC 57.380 39.130 0.00 0.00 43.17 2.17
3731 5484 4.153117 AGCTTGAGTTGCTCTTACAAATCG 59.847 41.667 0.00 0.00 45.18 3.34
3732 5485 4.083802 GCTTGAGTTGCTCTTACAAATCGT 60.084 41.667 0.00 0.00 45.18 3.73
3734 5487 6.347402 GCTTGAGTTGCTCTTACAAATCGTAA 60.347 38.462 0.00 0.00 45.18 3.18
3754 6123 0.449388 GAAGCATGTCCCAAGAAGCG 59.551 55.000 0.00 0.00 0.00 4.68
3769 6207 4.016113 AGAAGCGACACACAAGAAAAAC 57.984 40.909 0.00 0.00 0.00 2.43
3788 6226 1.416401 ACCACATCCATAGGGTAAGCG 59.584 52.381 0.00 0.00 34.93 4.68
3873 6311 1.584724 TGGGAAAAGAGGGCTCTAGG 58.415 55.000 0.00 0.00 39.39 3.02
3956 6395 1.554822 CCCTTTCACCAGGAGGAGGTA 60.555 57.143 0.00 0.00 37.23 3.08
3959 6398 1.879575 TTCACCAGGAGGAGGTATGG 58.120 55.000 0.00 0.00 37.23 2.74
3985 6425 3.011119 CCATCAACCAAATGCCAAATGG 58.989 45.455 0.00 0.00 40.16 3.16
4053 6493 4.098807 GTGTTGGGACATTGTTAAGGTTGT 59.901 41.667 0.00 0.00 39.30 3.32
4079 6519 5.508567 TCATGAGAGCCAACCATCATTTTA 58.491 37.500 0.00 0.00 30.09 1.52
4119 6559 5.904362 AATCTCCAATGGTTAAACTCTGC 57.096 39.130 0.00 0.00 0.00 4.26
4149 6589 2.001076 CTTTTGCCCCAGAAAGAGGT 57.999 50.000 0.00 0.00 35.41 3.85
4150 6590 2.319844 CTTTTGCCCCAGAAAGAGGTT 58.680 47.619 0.00 0.00 35.41 3.50
4151 6591 2.470057 TTTGCCCCAGAAAGAGGTTT 57.530 45.000 0.00 0.00 0.00 3.27
4152 6592 2.470057 TTGCCCCAGAAAGAGGTTTT 57.530 45.000 0.00 0.00 0.00 2.43
4153 6593 2.470057 TGCCCCAGAAAGAGGTTTTT 57.530 45.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.197694 CCTAAATCGACTTCTATAAATCCACAG 57.802 37.037 0.00 0.00 0.00 3.66
68 69 4.084013 ACGCAACTTCTTTGACCTAAATCG 60.084 41.667 0.00 0.00 37.39 3.34
71 72 3.314080 CCACGCAACTTCTTTGACCTAAA 59.686 43.478 0.00 0.00 37.39 1.85
163 165 1.760029 CAGAAGGGACCCTAGAAGCTC 59.240 57.143 15.29 6.50 31.13 4.09
208 684 7.202016 TCAAACTAAGTCCAAACATGATGAC 57.798 36.000 0.00 0.08 0.00 3.06
239 715 6.668323 TGCATGTTTTTGGTTTTTCGAAAAA 58.332 28.000 27.64 27.64 39.88 1.94
243 719 5.862924 TTTGCATGTTTTTGGTTTTTCGA 57.137 30.435 0.00 0.00 0.00 3.71
244 720 6.918043 TTTTTGCATGTTTTTGGTTTTTCG 57.082 29.167 0.00 0.00 0.00 3.46
269 745 2.107378 TGCCCAGTGTCAATTCCTGTTA 59.893 45.455 0.00 0.00 0.00 2.41
270 746 1.133513 TGCCCAGTGTCAATTCCTGTT 60.134 47.619 0.00 0.00 0.00 3.16
272 748 0.883833 GTGCCCAGTGTCAATTCCTG 59.116 55.000 0.00 0.00 0.00 3.86
274 750 0.883833 CAGTGCCCAGTGTCAATTCC 59.116 55.000 0.00 0.00 0.00 3.01
275 751 1.896220 TCAGTGCCCAGTGTCAATTC 58.104 50.000 3.28 0.00 33.58 2.17
278 754 0.036732 GGATCAGTGCCCAGTGTCAA 59.963 55.000 0.00 0.00 33.58 3.18
281 757 1.681666 CTGGATCAGTGCCCAGTGT 59.318 57.895 18.01 0.00 43.71 3.55
294 770 5.072464 GGGAACTAGCCTATTCTTTCTGGAT 59.928 44.000 0.00 0.00 0.00 3.41
295 771 4.409247 GGGAACTAGCCTATTCTTTCTGGA 59.591 45.833 0.00 0.00 0.00 3.86
296 772 4.410555 AGGGAACTAGCCTATTCTTTCTGG 59.589 45.833 0.00 0.00 40.61 3.86
297 773 5.365314 AGAGGGAACTAGCCTATTCTTTCTG 59.635 44.000 0.00 0.00 44.43 3.02
298 774 5.534070 AGAGGGAACTAGCCTATTCTTTCT 58.466 41.667 0.00 0.00 44.43 2.52
299 775 5.364157 TGAGAGGGAACTAGCCTATTCTTTC 59.636 44.000 0.00 0.00 44.43 2.62
300 776 5.129650 GTGAGAGGGAACTAGCCTATTCTTT 59.870 44.000 0.00 0.00 44.43 2.52
301 777 4.651962 GTGAGAGGGAACTAGCCTATTCTT 59.348 45.833 0.00 0.00 44.43 2.52
302 778 4.219919 GTGAGAGGGAACTAGCCTATTCT 58.780 47.826 0.00 0.00 44.43 2.40
303 779 3.961408 TGTGAGAGGGAACTAGCCTATTC 59.039 47.826 0.00 0.00 44.43 1.75
315 791 1.186200 CGGTTGAGATGTGAGAGGGA 58.814 55.000 0.00 0.00 0.00 4.20
380 1176 9.590451 TCCGATCTTTAACGACAATTATTACTT 57.410 29.630 0.00 0.00 0.00 2.24
387 1183 4.035208 GCCATCCGATCTTTAACGACAATT 59.965 41.667 0.00 0.00 0.00 2.32
390 1186 2.167693 AGCCATCCGATCTTTAACGACA 59.832 45.455 0.00 0.00 0.00 4.35
391 1187 2.795470 GAGCCATCCGATCTTTAACGAC 59.205 50.000 0.00 0.00 0.00 4.34
392 1188 2.223971 GGAGCCATCCGATCTTTAACGA 60.224 50.000 0.00 0.00 35.37 3.85
393 1189 2.135933 GGAGCCATCCGATCTTTAACG 58.864 52.381 0.00 0.00 35.37 3.18
447 1243 7.201574 GCCCGTTTAAAAGTCTTTTTCATGTTT 60.202 33.333 15.53 0.00 37.64 2.83
486 1283 3.244249 GGGGAACGCTGAAGAGCTATTAT 60.244 47.826 0.00 0.00 43.77 1.28
510 1326 5.497474 ACTACTACTACTTGGGCCATTTTG 58.503 41.667 7.26 0.43 0.00 2.44
530 1346 4.578871 TGCCGTTGTGAGTAGTACTACTA 58.421 43.478 30.80 16.17 45.63 1.82
532 1348 3.837213 TGCCGTTGTGAGTAGTACTAC 57.163 47.619 23.03 23.03 36.35 2.73
533 1349 3.822735 ACTTGCCGTTGTGAGTAGTACTA 59.177 43.478 1.88 0.00 0.00 1.82
534 1350 2.626743 ACTTGCCGTTGTGAGTAGTACT 59.373 45.455 1.37 1.37 0.00 2.73
536 1352 2.363038 ACACTTGCCGTTGTGAGTAGTA 59.637 45.455 0.00 0.00 37.59 1.82
538 1354 1.526887 CACACTTGCCGTTGTGAGTAG 59.473 52.381 3.22 0.00 37.59 2.57
542 1358 1.131504 GTTTCACACTTGCCGTTGTGA 59.868 47.619 7.15 7.15 39.21 3.58
544 1360 0.098025 CGTTTCACACTTGCCGTTGT 59.902 50.000 0.00 0.00 0.00 3.32
548 1364 2.637025 CCCGTTTCACACTTGCCG 59.363 61.111 0.00 0.00 0.00 5.69
549 1365 2.335011 GCCCGTTTCACACTTGCC 59.665 61.111 0.00 0.00 0.00 4.52
559 1375 2.248835 CGGTTTCAGTCGCCCGTTT 61.249 57.895 0.00 0.00 35.78 3.60
625 2087 1.163554 GCCTCTTTTCTGTGCTCCAG 58.836 55.000 0.00 0.00 42.97 3.86
894 2375 4.410400 GGAGTTGGGGAGGCCGTG 62.410 72.222 0.00 0.00 0.00 4.94
897 2378 2.610532 GAATCGGAGTTGGGGAGGCC 62.611 65.000 0.00 0.00 0.00 5.19
898 2379 1.153147 GAATCGGAGTTGGGGAGGC 60.153 63.158 0.00 0.00 0.00 4.70
899 2380 1.144057 CGAATCGGAGTTGGGGAGG 59.856 63.158 0.00 0.00 0.00 4.30
900 2381 0.535335 TTCGAATCGGAGTTGGGGAG 59.465 55.000 1.76 0.00 0.00 4.30
901 2382 0.978151 TTTCGAATCGGAGTTGGGGA 59.022 50.000 1.76 0.00 0.00 4.81
935 2416 1.682344 GGGCAGCAAAACCCTAGGG 60.682 63.158 27.36 27.36 43.36 3.53
1012 2493 2.202837 GACGGAATCGAACGGGGG 60.203 66.667 11.31 0.00 40.11 5.40
1029 2520 4.899239 GATCCCAGGCCAGACGCG 62.899 72.222 5.01 3.53 38.94 6.01
1052 2558 1.816863 AACAGATCAGACCCACGCGT 61.817 55.000 5.58 5.58 0.00 6.01
1053 2559 0.670546 AAACAGATCAGACCCACGCG 60.671 55.000 3.53 3.53 0.00 6.01
1055 2561 2.076863 GGAAAACAGATCAGACCCACG 58.923 52.381 0.00 0.00 0.00 4.94
1061 2567 3.813166 GACCAAACGGAAAACAGATCAGA 59.187 43.478 0.00 0.00 0.00 3.27
1074 2580 2.317609 CCTGCGACAGACCAAACGG 61.318 63.158 8.20 0.00 32.44 4.44
1075 2581 2.954753 GCCTGCGACAGACCAAACG 61.955 63.158 8.20 0.00 32.44 3.60
1176 2683 4.995058 AACAGGGAGGCGGGGGAA 62.995 66.667 0.00 0.00 0.00 3.97
1180 2687 3.546714 AAACGAACAGGGAGGCGGG 62.547 63.158 0.00 0.00 0.00 6.13
1181 2688 2.032071 AAACGAACAGGGAGGCGG 59.968 61.111 0.00 0.00 0.00 6.13
1182 2689 2.380410 CGAAACGAACAGGGAGGCG 61.380 63.158 0.00 0.00 0.00 5.52
1183 2690 0.883370 AACGAAACGAACAGGGAGGC 60.883 55.000 0.00 0.00 0.00 4.70
1184 2691 1.145803 GAACGAAACGAACAGGGAGG 58.854 55.000 0.00 0.00 0.00 4.30
1267 2774 1.007336 CGCAAAGCCGTAAGACGACT 61.007 55.000 0.00 0.00 46.05 4.18
1268 2775 1.280206 ACGCAAAGCCGTAAGACGAC 61.280 55.000 0.00 0.00 46.05 4.34
1271 2778 1.495951 CCACGCAAAGCCGTAAGAC 59.504 57.895 0.00 0.00 39.83 3.01
1272 2779 2.322081 GCCACGCAAAGCCGTAAGA 61.322 57.895 0.00 0.00 39.83 2.10
1273 2780 2.175811 GCCACGCAAAGCCGTAAG 59.824 61.111 0.00 0.00 39.83 2.34
1308 2815 4.021229 TCTCTCAAACGCCTAATAGGACA 58.979 43.478 11.13 0.00 37.67 4.02
1310 2817 5.601662 CAATCTCTCAAACGCCTAATAGGA 58.398 41.667 11.13 0.00 37.67 2.94
1320 2827 0.673644 ACCCCGCAATCTCTCAAACG 60.674 55.000 0.00 0.00 0.00 3.60
1324 2831 0.911769 ATCAACCCCGCAATCTCTCA 59.088 50.000 0.00 0.00 0.00 3.27
1326 2833 1.004745 ACAATCAACCCCGCAATCTCT 59.995 47.619 0.00 0.00 0.00 3.10
1327 2834 1.463674 ACAATCAACCCCGCAATCTC 58.536 50.000 0.00 0.00 0.00 2.75
1328 2835 2.799126 TACAATCAACCCCGCAATCT 57.201 45.000 0.00 0.00 0.00 2.40
1339 2846 1.735018 CGTGGCACGGATTACAATCAA 59.265 47.619 31.19 0.00 38.08 2.57
1340 2847 1.066787 TCGTGGCACGGATTACAATCA 60.067 47.619 36.30 13.15 42.81 2.57
1344 2851 1.434555 CTTTCGTGGCACGGATTACA 58.565 50.000 36.30 16.19 42.81 2.41
1418 2926 4.100498 ACTCCTAACTCTGTTTTCCACGAA 59.900 41.667 0.00 0.00 0.00 3.85
1419 2927 3.640029 ACTCCTAACTCTGTTTTCCACGA 59.360 43.478 0.00 0.00 0.00 4.35
1438 2986 4.876107 TGATCTAAATCCCTTTCGCAACTC 59.124 41.667 0.00 0.00 0.00 3.01
1506 3054 7.810759 TCTTGTCTTGTTACACAAACTTTTTCC 59.189 33.333 0.00 0.00 37.69 3.13
1507 3055 8.635983 GTCTTGTCTTGTTACACAAACTTTTTC 58.364 33.333 0.00 0.00 37.69 2.29
1508 3056 8.357402 AGTCTTGTCTTGTTACACAAACTTTTT 58.643 29.630 0.00 0.00 37.69 1.94
1509 3057 7.882179 AGTCTTGTCTTGTTACACAAACTTTT 58.118 30.769 0.00 0.00 37.69 2.27
1522 3070 4.750098 CCGACAAACATAGTCTTGTCTTGT 59.250 41.667 11.82 7.31 46.03 3.16
1574 3123 6.878317 TCCATACAGATGCTATAACTATGGC 58.122 40.000 0.00 0.00 40.17 4.40
1649 3200 8.877864 AATAATTCATAGAAAACACACTCCCA 57.122 30.769 0.00 0.00 0.00 4.37
1774 3328 8.593945 TCAAGGGATTTTTCACTTATTAGCAT 57.406 30.769 0.00 0.00 31.19 3.79
1835 3430 3.220110 ACCAATCTAGCAGATGCCAATG 58.780 45.455 0.14 0.00 43.38 2.82
1837 3432 4.349048 AGATACCAATCTAGCAGATGCCAA 59.651 41.667 0.14 0.00 40.82 4.52
1873 3468 9.559958 CATGTTAGGTTCATGTTTGATTAGAAC 57.440 33.333 0.00 0.00 38.17 3.01
1899 3495 5.110940 ACAATTGCAATTTGAAACATGGC 57.889 34.783 21.95 0.00 0.00 4.40
1941 3542 9.959721 AGGAAGCTAATAAAGAACAAATGACTA 57.040 29.630 0.00 0.00 0.00 2.59
1946 3547 8.885693 AGGAAGGAAGCTAATAAAGAACAAAT 57.114 30.769 0.00 0.00 0.00 2.32
1948 3549 7.724061 ACAAGGAAGGAAGCTAATAAAGAACAA 59.276 33.333 0.00 0.00 0.00 2.83
1949 3550 7.231467 ACAAGGAAGGAAGCTAATAAAGAACA 58.769 34.615 0.00 0.00 0.00 3.18
1950 3551 7.608376 AGACAAGGAAGGAAGCTAATAAAGAAC 59.392 37.037 0.00 0.00 0.00 3.01
1956 3557 4.783227 ACCAGACAAGGAAGGAAGCTAATA 59.217 41.667 0.00 0.00 0.00 0.98
1968 3569 3.775316 GGAGAAGGATAACCAGACAAGGA 59.225 47.826 0.00 0.00 38.94 3.36
1970 3571 3.519510 TGGGAGAAGGATAACCAGACAAG 59.480 47.826 0.00 0.00 38.94 3.16
2100 3704 7.196331 GTGCACAAGAGAAACTTAGAACAATT 58.804 34.615 13.17 0.00 37.03 2.32
2104 3708 4.816925 AGGTGCACAAGAGAAACTTAGAAC 59.183 41.667 20.43 0.00 37.03 3.01
2109 3713 5.934625 CAGTATAGGTGCACAAGAGAAACTT 59.065 40.000 20.43 0.00 39.70 2.66
2120 3724 1.017387 GCCAAGCAGTATAGGTGCAC 58.983 55.000 8.80 8.80 43.82 4.57
2140 3744 5.252969 TGAATTTCTTAGCCATGATGCAC 57.747 39.130 0.00 0.00 0.00 4.57
2289 3894 7.642082 ACGAAACACTTACTAGTATCCATCT 57.358 36.000 2.79 0.00 31.96 2.90
2335 3940 0.026674 CACAACAGTCGTGTGTGCAG 59.973 55.000 0.00 0.00 36.84 4.41
2336 3941 0.672091 ACACAACAGTCGTGTGTGCA 60.672 50.000 9.78 0.00 45.64 4.57
2337 3942 1.257936 CTACACAACAGTCGTGTGTGC 59.742 52.381 17.83 0.00 46.72 4.57
2338 3943 1.257936 GCTACACAACAGTCGTGTGTG 59.742 52.381 17.83 10.56 46.72 3.82
2339 3944 1.136305 AGCTACACAACAGTCGTGTGT 59.864 47.619 14.16 14.16 46.72 3.72
2344 3949 4.357018 TGAGATAGCTACACAACAGTCG 57.643 45.455 0.00 0.00 0.00 4.18
2364 3969 8.999431 ACGCCTTAACCAATACATCTAATATTG 58.001 33.333 0.00 0.00 38.99 1.90
2369 3974 7.442969 CCAATACGCCTTAACCAATACATCTAA 59.557 37.037 0.00 0.00 0.00 2.10
2380 3985 5.392272 CCAAGTAAACCAATACGCCTTAACC 60.392 44.000 0.00 0.00 0.00 2.85
2385 3990 2.089201 GCCAAGTAAACCAATACGCCT 58.911 47.619 0.00 0.00 0.00 5.52
2388 3993 8.671028 ACTAAATTAGCCAAGTAAACCAATACG 58.329 33.333 0.00 0.00 0.00 3.06
2394 3999 8.974408 CAAACAACTAAATTAGCCAAGTAAACC 58.026 33.333 0.00 0.00 0.00 3.27
2395 4000 9.738832 TCAAACAACTAAATTAGCCAAGTAAAC 57.261 29.630 0.00 0.00 0.00 2.01
2399 4004 7.284489 TCAGTCAAACAACTAAATTAGCCAAGT 59.716 33.333 0.00 0.00 0.00 3.16
2403 4008 9.129209 GAAATCAGTCAAACAACTAAATTAGCC 57.871 33.333 0.00 0.00 0.00 3.93
2427 4058 9.638239 GGATACTGCACAAATGATTAAAAAGAA 57.362 29.630 0.00 0.00 0.00 2.52
2429 4060 8.984891 TGGATACTGCACAAATGATTAAAAAG 57.015 30.769 0.00 0.00 37.61 2.27
2431 4062 7.980662 CCATGGATACTGCACAAATGATTAAAA 59.019 33.333 5.56 0.00 37.61 1.52
2555 4191 3.268330 TGAGTGAAGCAGAGATGATTGC 58.732 45.455 0.00 0.00 40.57 3.56
2567 4203 5.119125 GGCAAAACATTACATTGAGTGAAGC 59.881 40.000 0.00 0.00 0.00 3.86
2575 4211 3.428198 CACCACGGCAAAACATTACATTG 59.572 43.478 0.00 0.00 0.00 2.82
2581 4217 1.754226 AGAACACCACGGCAAAACATT 59.246 42.857 0.00 0.00 0.00 2.71
2584 4220 0.736053 TCAGAACACCACGGCAAAAC 59.264 50.000 0.00 0.00 0.00 2.43
2587 4223 0.179032 ACATCAGAACACCACGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
2592 4228 2.839486 TCCAGACATCAGAACACCAC 57.161 50.000 0.00 0.00 0.00 4.16
2838 4478 1.825090 TGATGCAAGGTTACAGGCAG 58.175 50.000 0.00 0.00 39.95 4.85
2914 4557 0.609131 GCTTAAGGGCCACTGCTTCA 60.609 55.000 6.18 0.00 37.74 3.02
2978 4621 4.285863 AGATGGTAGAGAACAGAGGAAGG 58.714 47.826 0.00 0.00 0.00 3.46
2982 4625 4.709397 AGTGAAGATGGTAGAGAACAGAGG 59.291 45.833 0.00 0.00 0.00 3.69
2983 4626 5.913137 AGTGAAGATGGTAGAGAACAGAG 57.087 43.478 0.00 0.00 0.00 3.35
2984 4627 7.119387 TCATAGTGAAGATGGTAGAGAACAGA 58.881 38.462 0.00 0.00 0.00 3.41
2985 4628 7.340122 TCATAGTGAAGATGGTAGAGAACAG 57.660 40.000 0.00 0.00 0.00 3.16
2986 4629 7.904558 ATCATAGTGAAGATGGTAGAGAACA 57.095 36.000 0.00 0.00 0.00 3.18
2987 4630 7.170658 GCAATCATAGTGAAGATGGTAGAGAAC 59.829 40.741 0.00 0.00 0.00 3.01
2988 4631 7.212976 GCAATCATAGTGAAGATGGTAGAGAA 58.787 38.462 0.00 0.00 0.00 2.87
2990 4633 5.931146 GGCAATCATAGTGAAGATGGTAGAG 59.069 44.000 0.00 0.00 0.00 2.43
2991 4634 5.221722 GGGCAATCATAGTGAAGATGGTAGA 60.222 44.000 0.00 0.00 0.00 2.59
2992 4635 4.999950 GGGCAATCATAGTGAAGATGGTAG 59.000 45.833 0.00 0.00 0.00 3.18
2993 4636 4.503123 CGGGCAATCATAGTGAAGATGGTA 60.503 45.833 0.00 0.00 0.00 3.25
2994 4637 3.745480 CGGGCAATCATAGTGAAGATGGT 60.745 47.826 0.00 0.00 0.00 3.55
2995 4638 2.810274 CGGGCAATCATAGTGAAGATGG 59.190 50.000 0.00 0.00 0.00 3.51
2996 4639 2.810274 CCGGGCAATCATAGTGAAGATG 59.190 50.000 0.00 0.00 0.00 2.90
2999 4650 2.332063 ACCGGGCAATCATAGTGAAG 57.668 50.000 6.32 0.00 0.00 3.02
3006 4657 0.039618 ACCTGAAACCGGGCAATCAT 59.960 50.000 6.32 0.00 33.23 2.45
3007 4658 0.178975 AACCTGAAACCGGGCAATCA 60.179 50.000 6.32 3.37 33.23 2.57
3014 4665 0.958091 TGATTGCAACCTGAAACCGG 59.042 50.000 0.00 0.00 0.00 5.28
3030 4681 8.311836 AGCATTTCTTTCATTCATTCAGTTGAT 58.688 29.630 0.00 0.00 0.00 2.57
3035 4688 8.595533 CAATCAGCATTTCTTTCATTCATTCAG 58.404 33.333 0.00 0.00 0.00 3.02
3063 4716 3.058450 CCTGCACAATTCGCATCAAAAA 58.942 40.909 0.00 0.00 39.02 1.94
3075 4728 3.058160 GCCTCGTGCCTGCACAAT 61.058 61.111 21.01 0.00 46.47 2.71
3126 4779 0.300789 TCAGATCGTCATCGTCGTCG 59.699 55.000 0.00 0.00 38.33 5.12
3163 4816 7.487484 TGATTGATAAGACAGACAGACTCATC 58.513 38.462 0.00 0.00 0.00 2.92
3326 4980 2.933906 CAAATCCATGGCAAGCAACATC 59.066 45.455 6.96 0.00 0.00 3.06
3480 5140 3.881937 ATCCCTTTTGCTGCTTTCATC 57.118 42.857 0.00 0.00 0.00 2.92
3556 5270 3.766591 AGACCGAGATCTTCAACAGACAT 59.233 43.478 0.00 0.00 32.83 3.06
3570 5298 4.736126 TCAAATGCTGATAAGACCGAGA 57.264 40.909 0.00 0.00 0.00 4.04
3664 5403 5.890985 TGGTAAGGTATGATTTGACCAATGG 59.109 40.000 0.00 0.00 38.27 3.16
3706 5459 6.128553 CGATTTGTAAGAGCAACTCAAGCTTA 60.129 38.462 0.00 0.00 43.58 3.09
3726 5479 3.950397 TGGGACATGCTTCTTACGATTT 58.050 40.909 0.00 0.00 0.00 2.17
3727 5480 3.627395 TGGGACATGCTTCTTACGATT 57.373 42.857 0.00 0.00 0.00 3.34
3728 5481 3.197766 TCTTGGGACATGCTTCTTACGAT 59.802 43.478 0.00 0.00 39.30 3.73
3730 5483 2.972625 TCTTGGGACATGCTTCTTACG 58.027 47.619 0.00 0.00 39.30 3.18
3731 5484 3.127721 GCTTCTTGGGACATGCTTCTTAC 59.872 47.826 0.00 0.00 39.30 2.34
3732 5485 3.347216 GCTTCTTGGGACATGCTTCTTA 58.653 45.455 0.00 0.00 39.30 2.10
3734 5487 1.831580 GCTTCTTGGGACATGCTTCT 58.168 50.000 0.00 0.00 39.30 2.85
3736 5489 0.036732 TCGCTTCTTGGGACATGCTT 59.963 50.000 0.00 0.00 39.30 3.91
3738 5491 4.301505 TCGCTTCTTGGGACATGC 57.698 55.556 0.00 0.00 39.30 4.06
3744 5497 0.588252 CTTGTGTGTCGCTTCTTGGG 59.412 55.000 0.00 0.00 0.00 4.12
3745 5498 1.581934 TCTTGTGTGTCGCTTCTTGG 58.418 50.000 0.00 0.00 0.00 3.61
3754 6123 4.142271 TGGATGTGGTTTTTCTTGTGTGTC 60.142 41.667 0.00 0.00 0.00 3.67
3769 6207 1.878102 GCGCTTACCCTATGGATGTGG 60.878 57.143 0.00 0.00 34.81 4.17
3788 6226 1.133025 CGATGACCCAACCAAGATTGC 59.867 52.381 0.00 0.00 0.00 3.56
3873 6311 3.306294 CCTCCCAGTTGAAATCTTTTGGC 60.306 47.826 0.00 0.00 0.00 4.52
3959 6398 0.176449 GCATTTGGTTGATGGCCTCC 59.824 55.000 3.32 0.00 0.00 4.30
3999 6439 1.526917 GCCCGATGAACCCATCCAG 60.527 63.158 0.00 0.00 44.87 3.86
4053 6493 3.106827 TGATGGTTGGCTCTCATGAGTA 58.893 45.455 21.92 8.43 42.13 2.59
4095 6535 6.945435 TGCAGAGTTTAACCATTGGAGATTTA 59.055 34.615 10.37 0.00 0.00 1.40
4119 6559 0.235404 GGGCAAAAGCGCAATGTTTG 59.765 50.000 11.47 14.96 35.74 2.93
4128 6568 0.242017 CTCTTTCTGGGGCAAAAGCG 59.758 55.000 0.00 0.00 33.46 4.68


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

AutoCloner maintained by Alex Coulton.