Multiple sequence alignment - TraesCS3B01G281300

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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 TraesCS3B01G281300 chr3B 100.000 4447 0 0 1 4447 451878022 451882468 0.000000e+00 8213.0
1 TraesCS3B01G281300 chr3B 84.668 737 75 23 3734 4447 373330017 373330738 0.000000e+00 701.0
2 TraesCS3B01G281300 chr3A 92.918 1525 49 24 4 1510 471370085 471371568 0.000000e+00 2163.0
3 TraesCS3B01G281300 chr3A 90.663 1221 92 13 2363 3580 471372662 471373863 0.000000e+00 1604.0
4 TraesCS3B01G281300 chr3A 88.769 463 29 13 1510 1963 471371859 471372307 3.020000e-151 545.0
5 TraesCS3B01G281300 chr3A 87.179 351 11 9 1963 2304 471372341 471372666 7.030000e-98 368.0
6 TraesCS3B01G281300 chr3D 92.170 1392 46 24 307 1660 352801465 352802831 0.000000e+00 1908.0
7 TraesCS3B01G281300 chr3D 88.501 1374 113 27 2363 3704 352803749 352805109 0.000000e+00 1620.0
8 TraesCS3B01G281300 chr3D 82.615 742 87 25 3734 4447 276984092 276983365 6.320000e-173 617.0
9 TraesCS3B01G281300 chr3D 92.344 209 11 5 2099 2304 352803547 352803753 4.350000e-75 292.0
10 TraesCS3B01G281300 chr3D 95.882 170 6 1 94 263 352801294 352801462 1.580000e-69 274.0
11 TraesCS3B01G281300 chr3D 93.846 65 3 1 1963 2027 352803386 352803449 3.660000e-16 97.1
12 TraesCS3B01G281300 chr3D 93.878 49 3 0 2019 2067 352803489 352803537 1.720000e-09 75.0
13 TraesCS3B01G281300 chr6D 83.473 714 61 31 3772 4446 397279431 397278736 2.940000e-171 612.0
14 TraesCS3B01G281300 chr2B 82.256 727 89 20 3734 4435 77778204 77778915 3.830000e-165 592.0
15 TraesCS3B01G281300 chr2B 84.222 450 52 10 4005 4435 587716034 587715585 1.910000e-113 420.0
16 TraesCS3B01G281300 chr2A 81.361 735 96 21 3727 4435 738715850 738715131 1.080000e-155 560.0
17 TraesCS3B01G281300 chr2A 80.556 756 90 32 3735 4446 214935969 214936711 3.050000e-146 529.0
18 TraesCS3B01G281300 chr2A 87.843 255 19 5 4203 4445 403633265 403633519 5.630000e-74 289.0
19 TraesCS3B01G281300 chr7D 81.532 731 87 29 3733 4435 12731323 12730613 3.890000e-155 558.0
20 TraesCS3B01G281300 chr4A 80.769 728 100 18 3734 4435 81081877 81082590 2.350000e-147 532.0
21 TraesCS3B01G281300 chrUn 77.907 344 55 10 1156 1492 93651295 93650966 1.260000e-45 195.0


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 TraesCS3B01G281300 chr3B 451878022 451882468 4446 False 8213.000000 8213 100.000000 1 4447 1 chr3B.!!$F2 4446
1 TraesCS3B01G281300 chr3B 373330017 373330738 721 False 701.000000 701 84.668000 3734 4447 1 chr3B.!!$F1 713
2 TraesCS3B01G281300 chr3A 471370085 471373863 3778 False 1170.000000 2163 89.882250 4 3580 4 chr3A.!!$F1 3576
3 TraesCS3B01G281300 chr3D 352801294 352805109 3815 False 711.016667 1908 92.770167 94 3704 6 chr3D.!!$F1 3610
4 TraesCS3B01G281300 chr3D 276983365 276984092 727 True 617.000000 617 82.615000 3734 4447 1 chr3D.!!$R1 713
5 TraesCS3B01G281300 chr6D 397278736 397279431 695 True 612.000000 612 83.473000 3772 4446 1 chr6D.!!$R1 674
6 TraesCS3B01G281300 chr2B 77778204 77778915 711 False 592.000000 592 82.256000 3734 4435 1 chr2B.!!$F1 701
7 TraesCS3B01G281300 chr2A 738715131 738715850 719 True 560.000000 560 81.361000 3727 4435 1 chr2A.!!$R1 708
8 TraesCS3B01G281300 chr2A 214935969 214936711 742 False 529.000000 529 80.556000 3735 4446 1 chr2A.!!$F1 711
9 TraesCS3B01G281300 chr7D 12730613 12731323 710 True 558.000000 558 81.532000 3733 4435 1 chr7D.!!$R1 702
10 TraesCS3B01G281300 chr4A 81081877 81082590 713 False 532.000000 532 80.769000 3734 4435 1 chr4A.!!$F1 701

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
905 939 0.183492 TTGTGTCTCTGCTTTGGGCT 59.817 50.0 0.0 0.0 42.39 5.19 F
1040 1078 0.394938 ACATTGACACTGGGCACGTA 59.605 50.0 0.0 0.0 0.00 3.57 F
1805 2146 0.176219 CAAGCAGGGAGAGAGAGCAG 59.824 60.0 0.0 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 2127 0.176219 CTGCTCTCTCTCCCTGCTTG 59.824 60.0 0.0 0.0 0.0 4.01 R
2309 3052 0.317770 GCAACATGTCAACACCCGTG 60.318 55.0 0.0 0.0 0.0 4.94 R
3779 4549 0.184211 AACGTTTAGGTGGCAGGGTT 59.816 50.0 0.0 0.0 0.0 4.11 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
56 57 1.536766 CATCTTGTGACCATTGCACGT 59.463 47.619 0.00 0.00 39.07 4.49
57 58 2.535012 TCTTGTGACCATTGCACGTA 57.465 45.000 0.00 0.00 39.07 3.57
58 59 2.839975 TCTTGTGACCATTGCACGTAA 58.160 42.857 0.00 0.00 39.07 3.18
59 60 3.206964 TCTTGTGACCATTGCACGTAAA 58.793 40.909 0.00 0.00 39.07 2.01
60 61 3.628032 TCTTGTGACCATTGCACGTAAAA 59.372 39.130 0.00 0.00 39.07 1.52
61 62 3.341857 TGTGACCATTGCACGTAAAAC 57.658 42.857 0.00 0.00 39.07 2.43
85 86 9.701098 AACTAAAACTATGATGACGAACTTGTA 57.299 29.630 0.00 0.00 0.00 2.41
266 267 0.537143 ACAAAGGCCGCATCAGTCAA 60.537 50.000 0.00 0.00 0.00 3.18
281 282 1.065491 AGTCAACATGCGGCATCCTAA 60.065 47.619 13.53 0.00 0.00 2.69
282 283 1.949525 GTCAACATGCGGCATCCTAAT 59.050 47.619 13.53 0.00 0.00 1.73
283 284 3.138304 GTCAACATGCGGCATCCTAATA 58.862 45.455 13.53 0.00 0.00 0.98
284 285 3.563808 GTCAACATGCGGCATCCTAATAA 59.436 43.478 13.53 0.00 0.00 1.40
285 286 3.814842 TCAACATGCGGCATCCTAATAAG 59.185 43.478 13.53 1.68 0.00 1.73
286 287 2.783135 ACATGCGGCATCCTAATAAGG 58.217 47.619 13.53 0.92 45.21 2.69
287 288 1.470098 CATGCGGCATCCTAATAAGGC 59.530 52.381 13.53 0.00 43.31 4.35
288 289 0.472044 TGCGGCATCCTAATAAGGCA 59.528 50.000 0.00 0.00 43.31 4.75
289 290 1.160137 GCGGCATCCTAATAAGGCAG 58.840 55.000 0.00 0.00 43.31 4.85
290 291 1.543429 GCGGCATCCTAATAAGGCAGT 60.543 52.381 0.00 0.00 43.31 4.40
291 292 2.146342 CGGCATCCTAATAAGGCAGTG 58.854 52.381 0.00 0.00 43.31 3.66
292 293 2.224281 CGGCATCCTAATAAGGCAGTGA 60.224 50.000 0.00 0.00 43.31 3.41
293 294 3.406764 GGCATCCTAATAAGGCAGTGAG 58.593 50.000 0.00 0.00 43.31 3.51
294 295 3.181450 GGCATCCTAATAAGGCAGTGAGT 60.181 47.826 0.00 0.00 43.31 3.41
295 296 4.040461 GGCATCCTAATAAGGCAGTGAGTA 59.960 45.833 0.00 0.00 43.31 2.59
296 297 5.454755 GGCATCCTAATAAGGCAGTGAGTAA 60.455 44.000 0.00 0.00 43.31 2.24
297 298 5.467063 GCATCCTAATAAGGCAGTGAGTAAC 59.533 44.000 0.00 0.00 43.31 2.50
298 299 6.686632 GCATCCTAATAAGGCAGTGAGTAACT 60.687 42.308 0.00 0.00 43.31 2.24
326 327 0.243907 TCGGGCGAGAAGAGAAACAG 59.756 55.000 0.00 0.00 0.00 3.16
333 334 3.555168 GCGAGAAGAGAAACAGAAGGGAA 60.555 47.826 0.00 0.00 0.00 3.97
335 336 4.629200 CGAGAAGAGAAACAGAAGGGAATG 59.371 45.833 0.00 0.00 0.00 2.67
463 464 1.645034 CCGTATGACCTGCACAAGAG 58.355 55.000 0.00 0.00 0.00 2.85
498 503 6.142480 CGGCGTCATCTATCTAACAAGTAAAG 59.858 42.308 0.00 0.00 0.00 1.85
502 507 7.112287 CGTCATCTATCTAACAAGTAAAGAGCG 59.888 40.741 0.00 0.00 0.00 5.03
508 513 2.032634 CAAGTAAAGAGCGGCGCCA 61.033 57.895 30.40 0.53 0.00 5.69
535 540 1.988846 GGAAGGGATGGATAAGGGGAG 59.011 57.143 0.00 0.00 0.00 4.30
540 545 1.662686 GATGGATAAGGGGAGGGAGG 58.337 60.000 0.00 0.00 0.00 4.30
750 770 2.359404 GAGGAGACCACGAGGGGA 59.641 66.667 3.29 0.00 42.91 4.81
751 771 1.755008 GAGGAGACCACGAGGGGAG 60.755 68.421 3.29 0.00 42.91 4.30
754 774 4.400251 AGACCACGAGGGGAGGGG 62.400 72.222 3.29 0.00 42.91 4.79
761 781 3.036959 GAGGGGAGGGGGAGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
762 782 3.039526 AGGGGAGGGGGAGGAGAG 61.040 72.222 0.00 0.00 0.00 3.20
764 784 3.036959 GGGAGGGGGAGGAGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
901 935 8.127327 CCATTATTCTATTGTGTCTCTGCTTTG 58.873 37.037 0.00 0.00 0.00 2.77
904 938 1.251251 ATTGTGTCTCTGCTTTGGGC 58.749 50.000 0.00 0.00 42.22 5.36
905 939 0.183492 TTGTGTCTCTGCTTTGGGCT 59.817 50.000 0.00 0.00 42.39 5.19
924 958 1.345415 CTTTTGCAAGCTTGGATGGGT 59.655 47.619 27.10 0.00 0.00 4.51
1017 1055 1.196808 CACACTACCCACATTTCGCAC 59.803 52.381 0.00 0.00 0.00 5.34
1024 1062 0.597568 CCACATTTCGCACCACACAT 59.402 50.000 0.00 0.00 0.00 3.21
1040 1078 0.394938 ACATTGACACTGGGCACGTA 59.605 50.000 0.00 0.00 0.00 3.57
1144 1182 4.451150 GCTGTCCGCCATCGACCA 62.451 66.667 0.00 0.00 38.10 4.02
1545 1885 3.003378 GCTCCTTGCAGAAAACGTTTACT 59.997 43.478 15.03 0.00 42.31 2.24
1546 1886 4.212636 GCTCCTTGCAGAAAACGTTTACTA 59.787 41.667 15.03 1.17 42.31 1.82
1547 1887 5.614887 GCTCCTTGCAGAAAACGTTTACTAG 60.615 44.000 15.03 10.08 42.31 2.57
1548 1888 4.753107 TCCTTGCAGAAAACGTTTACTAGG 59.247 41.667 15.03 17.42 0.00 3.02
1549 1889 4.464112 CTTGCAGAAAACGTTTACTAGGC 58.536 43.478 15.03 13.73 0.00 3.93
1550 1890 3.468770 TGCAGAAAACGTTTACTAGGCA 58.531 40.909 15.03 15.98 0.00 4.75
1551 1891 3.878103 TGCAGAAAACGTTTACTAGGCAA 59.122 39.130 15.03 3.35 0.00 4.52
1598 1939 8.592105 TTTCATCCATTTCACATTTTCTTGTC 57.408 30.769 0.00 0.00 0.00 3.18
1693 2034 8.225603 TCGGATCGGGTATTAGTATATTTACC 57.774 38.462 0.00 0.00 32.07 2.85
1712 2053 0.813184 CTCATGCTGCCAATTTCCGT 59.187 50.000 0.00 0.00 0.00 4.69
1719 2060 1.000717 CTGCCAATTTCCGTCCGTTTT 60.001 47.619 0.00 0.00 0.00 2.43
1763 2104 9.072294 GTCCGTATTAGTAAACGTTTTAAGCTA 57.928 33.333 20.19 13.10 37.40 3.32
1786 2127 1.571955 AAAGGGGGCATGGACATTTC 58.428 50.000 0.00 0.00 0.00 2.17
1805 2146 0.176219 CAAGCAGGGAGAGAGAGCAG 59.824 60.000 0.00 0.00 0.00 4.24
1816 2157 1.001641 GAGAGCAGCCCACCACATT 60.002 57.895 0.00 0.00 0.00 2.71
1840 2181 3.316308 AGAAACCATCGCCATGAATTAGC 59.684 43.478 0.00 0.00 30.57 3.09
1867 2466 4.369182 GACGTCTGAAGTCAGGAAGAAAA 58.631 43.478 17.05 0.00 43.91 2.29
1972 2618 3.065095 GGATTCATTTCTCAGAGCAGTGC 59.935 47.826 7.13 7.13 0.00 4.40
2090 2831 2.931325 GGATACATCGCGTTGTTGGTAA 59.069 45.455 26.10 9.88 0.00 2.85
2125 2866 1.210722 TGCCGGCACCACATATTTCTA 59.789 47.619 29.03 0.00 0.00 2.10
2130 2871 4.438200 CCGGCACCACATATTTCTAACAAC 60.438 45.833 0.00 0.00 0.00 3.32
2251 2993 9.986833 CATCTGAATAACAATAACGAATGTCAA 57.013 29.630 0.00 0.00 0.00 3.18
2261 3003 1.880027 ACGAATGTCAAGGTTTCAGGC 59.120 47.619 0.00 0.00 0.00 4.85
2264 3006 1.915141 ATGTCAAGGTTTCAGGCCTG 58.085 50.000 27.87 27.87 36.30 4.85
2279 3022 4.158394 TCAGGCCTGATATTGCAAACTTTC 59.842 41.667 32.00 0.00 34.14 2.62
2281 3024 5.357878 CAGGCCTGATATTGCAAACTTTCTA 59.642 40.000 29.88 0.00 0.00 2.10
2297 3040 9.244799 CAAACTTTCTACCTTGTCATTTTAACC 57.755 33.333 0.00 0.00 0.00 2.85
2304 3047 5.768317 ACCTTGTCATTTTAACCGATGTTG 58.232 37.500 0.00 0.00 35.87 3.33
2307 3050 5.384063 TGTCATTTTAACCGATGTTGCAT 57.616 34.783 0.00 0.00 35.87 3.96
2309 3052 4.031652 GTCATTTTAACCGATGTTGCATGC 59.968 41.667 11.82 11.82 35.87 4.06
2310 3053 3.650070 TTTTAACCGATGTTGCATGCA 57.350 38.095 18.46 18.46 35.87 3.96
2311 3054 2.627863 TTAACCGATGTTGCATGCAC 57.372 45.000 22.58 16.00 35.87 4.57
2313 3056 2.100797 CCGATGTTGCATGCACGG 59.899 61.111 26.66 26.66 34.77 4.94
2314 3057 2.100797 CGATGTTGCATGCACGGG 59.899 61.111 22.58 4.40 0.00 5.28
2315 3058 2.689785 CGATGTTGCATGCACGGGT 61.690 57.895 22.58 6.83 0.00 5.28
2316 3059 1.153978 GATGTTGCATGCACGGGTG 60.154 57.895 22.58 0.00 0.00 4.61
2318 3061 1.462731 ATGTTGCATGCACGGGTGTT 61.463 50.000 22.58 0.00 0.00 3.32
2319 3062 1.661197 GTTGCATGCACGGGTGTTG 60.661 57.895 22.58 0.81 0.00 3.33
2321 3064 2.069465 TTGCATGCACGGGTGTTGAC 62.069 55.000 22.58 0.00 0.00 3.18
2322 3065 2.551006 GCATGCACGGGTGTTGACA 61.551 57.895 14.21 0.00 0.00 3.58
2323 3066 1.865788 GCATGCACGGGTGTTGACAT 61.866 55.000 14.21 0.00 0.00 3.06
2324 3067 0.109643 CATGCACGGGTGTTGACATG 60.110 55.000 0.00 0.00 0.00 3.21
2325 3068 0.537143 ATGCACGGGTGTTGACATGT 60.537 50.000 0.00 0.00 0.00 3.21
2326 3069 0.749818 TGCACGGGTGTTGACATGTT 60.750 50.000 0.00 0.00 0.00 2.71
2327 3070 0.317770 GCACGGGTGTTGACATGTTG 60.318 55.000 0.00 0.00 0.00 3.33
2328 3071 0.317770 CACGGGTGTTGACATGTTGC 60.318 55.000 0.00 0.00 0.00 4.17
2329 3072 0.749818 ACGGGTGTTGACATGTTGCA 60.750 50.000 0.00 0.00 0.00 4.08
2330 3073 0.597568 CGGGTGTTGACATGTTGCAT 59.402 50.000 0.00 0.00 0.00 3.96
2331 3074 1.666599 CGGGTGTTGACATGTTGCATG 60.667 52.381 0.00 7.48 0.00 4.06
2332 3075 1.340889 GGGTGTTGACATGTTGCATGT 59.659 47.619 13.74 13.74 34.52 3.21
2333 3076 2.224018 GGGTGTTGACATGTTGCATGTT 60.224 45.455 14.80 1.11 31.52 2.71
2334 3077 3.456280 GGTGTTGACATGTTGCATGTTT 58.544 40.909 14.80 0.00 31.52 2.83
2335 3078 3.245754 GGTGTTGACATGTTGCATGTTTG 59.754 43.478 14.80 0.00 31.52 2.93
2369 3112 4.629251 TTTTTGGGAGCAAAATGTTTGC 57.371 36.364 16.08 16.08 45.22 3.68
2380 3123 6.529463 GCAAAATGTTTGCAAACTAGATGT 57.471 33.333 35.09 18.12 44.34 3.06
2381 3124 7.636259 GCAAAATGTTTGCAAACTAGATGTA 57.364 32.000 35.09 18.71 44.34 2.29
2382 3125 8.243289 GCAAAATGTTTGCAAACTAGATGTAT 57.757 30.769 35.09 19.94 44.34 2.29
2383 3126 8.711457 GCAAAATGTTTGCAAACTAGATGTATT 58.289 29.630 35.09 23.66 44.34 1.89
2385 3128 9.979578 AAAATGTTTGCAAACTAGATGTATTCA 57.020 25.926 35.09 16.33 39.59 2.57
2410 3153 9.453325 CATTATACCTTTCTCGTTCTAACTCTC 57.547 37.037 0.00 0.00 0.00 3.20
2412 3155 9.896645 TTATACCTTTCTCGTTCTAACTCTCTA 57.103 33.333 0.00 0.00 0.00 2.43
2413 3156 8.983702 ATACCTTTCTCGTTCTAACTCTCTAT 57.016 34.615 0.00 0.00 0.00 1.98
2414 3157 7.090953 ACCTTTCTCGTTCTAACTCTCTATG 57.909 40.000 0.00 0.00 0.00 2.23
2418 3161 4.941873 TCTCGTTCTAACTCTCTATGTGCA 59.058 41.667 0.00 0.00 0.00 4.57
2419 3162 5.590663 TCTCGTTCTAACTCTCTATGTGCAT 59.409 40.000 0.00 0.00 0.00 3.96
2420 3163 6.766467 TCTCGTTCTAACTCTCTATGTGCATA 59.234 38.462 0.00 0.00 0.00 3.14
2421 3164 6.960468 TCGTTCTAACTCTCTATGTGCATAG 58.040 40.000 11.81 11.81 41.58 2.23
2496 3239 4.379243 CTCGCAGACGGGCTTGGT 62.379 66.667 0.00 0.00 40.63 3.67
2514 3257 2.563620 TGGTGCTGCACAATTCATCAAT 59.436 40.909 31.35 0.00 35.86 2.57
2606 3349 1.422402 GAACCCACCCAAGTTACCTCA 59.578 52.381 0.00 0.00 0.00 3.86
2622 3365 3.660571 CAGGGGCCACCACCATCA 61.661 66.667 0.00 0.00 43.89 3.07
2631 3374 1.004628 CCACCACCATCATTCCAGTCA 59.995 52.381 0.00 0.00 0.00 3.41
2665 3408 1.291184 TTTCGCCACAGATGTCAGCG 61.291 55.000 16.75 16.75 44.49 5.18
2667 3410 3.857854 GCCACAGATGTCAGCGCG 61.858 66.667 0.00 0.00 0.00 6.86
2670 3413 2.125912 ACAGATGTCAGCGCGGAC 60.126 61.111 30.18 30.18 38.29 4.79
2705 3448 1.065418 CAAGGCCGAATACTTCCAGGT 60.065 52.381 0.00 0.00 0.00 4.00
2841 3584 2.050144 ACCAGACACCTTCTCACACAT 58.950 47.619 0.00 0.00 28.96 3.21
2868 3611 1.500736 CCAAAGGATGGGGGCTTCTAT 59.499 52.381 0.00 0.00 46.27 1.98
2923 3666 3.039202 GCGAAGGATGTTGCCACGG 62.039 63.158 0.00 0.00 33.16 4.94
2973 3716 2.666098 GGACGGGAAGGCAAGGCTA 61.666 63.158 0.00 0.00 0.00 3.93
2974 3717 1.298667 GACGGGAAGGCAAGGCTAA 59.701 57.895 0.00 0.00 0.00 3.09
3063 3806 3.684788 ACAATGTGCTATTTGTCTCGGAC 59.315 43.478 0.00 0.00 30.43 4.79
3069 3812 2.094182 GCTATTTGTCTCGGACTGGACA 60.094 50.000 5.77 2.51 40.17 4.02
3096 3839 5.665459 CTTGGATTCTTTGAGGTCGACTAT 58.335 41.667 16.46 4.36 0.00 2.12
3131 3874 5.044919 CCCCTAGCCATATCATACCATTCAA 60.045 44.000 0.00 0.00 0.00 2.69
3135 3878 7.766278 CCTAGCCATATCATACCATTCAACTAC 59.234 40.741 0.00 0.00 0.00 2.73
3139 3882 6.128553 CCATATCATACCATTCAACTACGCAC 60.129 42.308 0.00 0.00 0.00 5.34
3241 3984 4.564782 AAGCATCTCAATGAGTTCAGGA 57.435 40.909 10.36 0.00 34.61 3.86
3303 4046 0.818938 TCAATGGCATGTGTGGATGC 59.181 50.000 0.00 0.00 46.82 3.91
3342 4087 0.106819 GGCAATCTGGAGGCATGAGT 60.107 55.000 0.00 0.00 0.00 3.41
3358 4103 5.584649 GGCATGAGTAAATACTACACTTGCA 59.415 40.000 16.21 0.00 39.25 4.08
3365 4110 8.391075 AGTAAATACTACACTTGCAATGTTGT 57.609 30.769 21.88 21.88 39.04 3.32
3417 4162 6.341408 ACTATCCATGTAATTCAGGGGTTT 57.659 37.500 8.17 0.00 46.65 3.27
3432 4177 5.555542 TCAGGGGTTTGGCTAATATATGGAT 59.444 40.000 0.00 0.00 0.00 3.41
3469 4214 2.700722 TGTGAAAGTGTAGTGTGCCA 57.299 45.000 0.00 0.00 0.00 4.92
3486 4231 7.215789 AGTGTGCCATTTAATTGTTGATTTGA 58.784 30.769 0.00 0.00 0.00 2.69
3533 4278 7.654520 TGGGACTAATATTACACGCTAATTGAC 59.345 37.037 0.00 0.00 0.00 3.18
3537 4282 8.912658 ACTAATATTACACGCTAATTGACGATG 58.087 33.333 8.68 6.13 0.00 3.84
3538 4283 7.709269 AATATTACACGCTAATTGACGATGT 57.291 32.000 8.68 10.46 0.00 3.06
3540 4285 3.232213 ACACGCTAATTGACGATGTCT 57.768 42.857 8.68 0.00 33.15 3.41
3549 4294 4.921470 ATTGACGATGTCTAAAACCGTG 57.079 40.909 0.00 0.00 33.32 4.94
3556 4301 4.557205 GATGTCTAAAACCGTGAGTGTCT 58.443 43.478 0.00 0.00 0.00 3.41
3557 4302 3.973657 TGTCTAAAACCGTGAGTGTCTC 58.026 45.455 0.00 0.00 0.00 3.36
3558 4303 2.978489 GTCTAAAACCGTGAGTGTCTCG 59.022 50.000 0.00 0.00 32.35 4.04
3573 4318 1.212934 TCTCGGTAGGGGTGGAGAGT 61.213 60.000 0.00 0.00 32.18 3.24
3580 4325 2.593956 GGGGTGGAGAGTGTGACCC 61.594 68.421 0.00 0.00 46.55 4.46
3581 4326 2.593956 GGGTGGAGAGTGTGACCCC 61.594 68.421 0.00 0.00 42.13 4.95
3582 4327 2.593956 GGTGGAGAGTGTGACCCCC 61.594 68.421 0.00 0.00 0.00 5.40
3583 4328 1.841556 GTGGAGAGTGTGACCCCCA 60.842 63.158 0.00 0.00 0.00 4.96
3584 4329 1.074090 TGGAGAGTGTGACCCCCAA 60.074 57.895 0.00 0.00 0.00 4.12
3585 4330 0.696143 TGGAGAGTGTGACCCCCAAA 60.696 55.000 0.00 0.00 0.00 3.28
3586 4331 0.036875 GGAGAGTGTGACCCCCAAAG 59.963 60.000 0.00 0.00 0.00 2.77
3587 4332 0.036875 GAGAGTGTGACCCCCAAAGG 59.963 60.000 0.00 0.00 0.00 3.11
3598 4343 4.395519 CCAAAGGGATCACGCACA 57.604 55.556 0.00 0.00 35.59 4.57
3600 4345 0.958091 CCAAAGGGATCACGCACAAA 59.042 50.000 0.00 0.00 35.59 2.83
3601 4346 1.068333 CCAAAGGGATCACGCACAAAG 60.068 52.381 0.00 0.00 35.59 2.77
3606 4359 2.693074 AGGGATCACGCACAAAGTTTTT 59.307 40.909 0.00 0.00 0.00 1.94
3607 4360 3.886505 AGGGATCACGCACAAAGTTTTTA 59.113 39.130 0.00 0.00 0.00 1.52
3616 4369 3.794564 GCACAAAGTTTTTACCAGGTTCG 59.205 43.478 0.00 0.00 0.00 3.95
3619 4372 1.612676 AGTTTTTACCAGGTTCGGGC 58.387 50.000 0.00 0.00 0.00 6.13
3689 4459 1.635487 TGAGGGGTTCCAGATTGAAGG 59.365 52.381 0.00 0.00 34.83 3.46
3709 4479 3.089573 GTAGTGATAACTACCCACGCC 57.910 52.381 9.05 0.00 37.27 5.68
3710 4480 1.861982 AGTGATAACTACCCACGCCT 58.138 50.000 0.00 0.00 36.06 5.52
3711 4481 1.755380 AGTGATAACTACCCACGCCTC 59.245 52.381 0.00 0.00 36.06 4.70
3712 4482 1.755380 GTGATAACTACCCACGCCTCT 59.245 52.381 0.00 0.00 0.00 3.69
3713 4483 2.954318 GTGATAACTACCCACGCCTCTA 59.046 50.000 0.00 0.00 0.00 2.43
3714 4484 3.004524 GTGATAACTACCCACGCCTCTAG 59.995 52.174 0.00 0.00 0.00 2.43
3715 4485 1.396653 TAACTACCCACGCCTCTAGC 58.603 55.000 0.00 0.00 38.52 3.42
3716 4486 1.328430 AACTACCCACGCCTCTAGCC 61.328 60.000 0.00 0.00 38.78 3.93
3717 4487 2.443390 TACCCACGCCTCTAGCCC 60.443 66.667 0.00 0.00 38.78 5.19
3725 4495 2.122989 CCTCTAGCCCCCGCCTTA 60.123 66.667 0.00 0.00 34.57 2.69
3726 4496 1.536662 CCTCTAGCCCCCGCCTTAT 60.537 63.158 0.00 0.00 34.57 1.73
3727 4497 0.252103 CCTCTAGCCCCCGCCTTATA 60.252 60.000 0.00 0.00 34.57 0.98
3728 4498 1.187087 CTCTAGCCCCCGCCTTATAG 58.813 60.000 0.00 0.00 34.57 1.31
3729 4499 0.781920 TCTAGCCCCCGCCTTATAGA 59.218 55.000 0.00 0.00 34.57 1.98
3730 4500 1.148446 TCTAGCCCCCGCCTTATAGAA 59.852 52.381 0.00 0.00 34.57 2.10
3731 4501 1.550976 CTAGCCCCCGCCTTATAGAAG 59.449 57.143 0.00 0.00 34.57 2.85
3779 4549 7.396623 CCTAGTTCCTTAGTTCTCCTCAGTTTA 59.603 40.741 0.00 0.00 0.00 2.01
3780 4552 7.613551 AGTTCCTTAGTTCTCCTCAGTTTAA 57.386 36.000 0.00 0.00 0.00 1.52
3784 4556 5.248705 CCTTAGTTCTCCTCAGTTTAACCCT 59.751 44.000 0.00 0.00 0.00 4.34
3792 4564 2.304761 CTCAGTTTAACCCTGCCACCTA 59.695 50.000 0.00 0.00 0.00 3.08
3864 4638 0.536460 ACGAAGCATTCCGTTGGGTT 60.536 50.000 0.00 0.00 43.81 4.11
3929 4703 0.598065 GACCTCAAAAGTGCGCCATT 59.402 50.000 4.18 0.00 0.00 3.16
3941 4715 2.451990 CGCCATTGACGTCGCATCA 61.452 57.895 11.62 0.00 0.00 3.07
3952 4726 2.124612 CGCATCACAGCCCATGGA 60.125 61.111 15.22 0.00 0.00 3.41
3960 4734 3.415087 AGCCCATGGACTGAGCCC 61.415 66.667 15.22 0.00 0.00 5.19
3978 4752 2.357034 GTGCGACACGTGGGTCAT 60.357 61.111 21.57 0.00 37.66 3.06
3979 4753 2.048597 TGCGACACGTGGGTCATC 60.049 61.111 21.57 6.77 37.66 2.92
3980 4754 2.261671 GCGACACGTGGGTCATCT 59.738 61.111 21.57 0.00 37.66 2.90
3981 4755 2.094659 GCGACACGTGGGTCATCTG 61.095 63.158 21.57 5.69 37.66 2.90
3982 4756 1.289066 CGACACGTGGGTCATCTGT 59.711 57.895 21.57 0.00 37.66 3.41
3986 4760 2.218603 ACACGTGGGTCATCTGTTTTC 58.781 47.619 21.57 0.00 0.00 2.29
3987 4761 2.158813 ACACGTGGGTCATCTGTTTTCT 60.159 45.455 21.57 0.00 0.00 2.52
3988 4762 2.480419 CACGTGGGTCATCTGTTTTCTC 59.520 50.000 7.95 0.00 0.00 2.87
3990 4764 3.138304 CGTGGGTCATCTGTTTTCTCAA 58.862 45.455 0.00 0.00 0.00 3.02
3991 4765 3.563808 CGTGGGTCATCTGTTTTCTCAAA 59.436 43.478 0.00 0.00 0.00 2.69
3992 4766 4.036262 CGTGGGTCATCTGTTTTCTCAAAA 59.964 41.667 0.00 0.00 0.00 2.44
3993 4767 5.449862 CGTGGGTCATCTGTTTTCTCAAAAA 60.450 40.000 0.00 0.00 31.13 1.94
3994 4768 5.979517 GTGGGTCATCTGTTTTCTCAAAAAG 59.020 40.000 0.00 0.00 35.10 2.27
3995 4769 5.890985 TGGGTCATCTGTTTTCTCAAAAAGA 59.109 36.000 0.00 0.00 35.10 2.52
3996 4770 6.379703 TGGGTCATCTGTTTTCTCAAAAAGAA 59.620 34.615 0.00 0.00 42.35 2.52
4044 4843 5.049828 CCTGCATGAATAGTGTCGAATACA 58.950 41.667 0.00 0.00 35.06 2.29
4116 4931 8.110860 TGAGTTGATTCAAGTTCCTAAATTCC 57.889 34.615 8.12 0.00 0.00 3.01
4128 4943 9.866655 AAGTTCCTAAATTCCTCATATATGCAA 57.133 29.630 7.92 1.50 0.00 4.08
4296 5136 5.895636 TTGACCTCATTAATTTGCGTCAT 57.104 34.783 5.65 0.00 30.66 3.06
4365 5207 5.792741 TCCAAAATAGGCAGTTTCCAAATG 58.207 37.500 0.00 0.00 0.00 2.32
4367 5209 5.409214 CCAAAATAGGCAGTTTCCAAATGTG 59.591 40.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.082571 GGTTAATGGCATTAGGCTAGCATG 60.083 45.833 18.24 12.82 44.01 4.06
5 6 3.486383 TGGTTAATGGCATTAGGCTAGC 58.514 45.455 18.52 6.04 44.01 3.42
57 58 9.878599 CAAGTTCGTCATCATAGTTTTAGTTTT 57.121 29.630 0.00 0.00 0.00 2.43
58 59 9.052759 ACAAGTTCGTCATCATAGTTTTAGTTT 57.947 29.630 0.00 0.00 0.00 2.66
59 60 8.603242 ACAAGTTCGTCATCATAGTTTTAGTT 57.397 30.769 0.00 0.00 0.00 2.24
60 61 9.701098 TTACAAGTTCGTCATCATAGTTTTAGT 57.299 29.630 0.00 0.00 0.00 2.24
61 62 9.953825 GTTACAAGTTCGTCATCATAGTTTTAG 57.046 33.333 0.00 0.00 0.00 1.85
85 86 4.402793 CCATAGGTGAGCTACAGTACAGTT 59.597 45.833 0.00 0.00 0.00 3.16
247 248 0.537143 TTGACTGATGCGGCCTTTGT 60.537 50.000 0.00 0.00 0.00 2.83
252 253 1.430632 CATGTTGACTGATGCGGCC 59.569 57.895 0.00 0.00 0.00 6.13
266 267 2.783135 CCTTATTAGGATGCCGCATGT 58.217 47.619 11.49 0.00 45.05 3.21
288 289 2.527100 GATTACGCGCAGTTACTCACT 58.473 47.619 5.73 0.00 35.35 3.41
289 290 1.252015 CGATTACGCGCAGTTACTCAC 59.748 52.381 5.73 0.00 0.00 3.51
290 291 1.541475 CGATTACGCGCAGTTACTCA 58.459 50.000 5.73 0.00 0.00 3.41
291 292 0.844503 CCGATTACGCGCAGTTACTC 59.155 55.000 5.73 0.00 38.29 2.59
292 293 0.526954 CCCGATTACGCGCAGTTACT 60.527 55.000 5.73 0.00 38.29 2.24
293 294 1.922189 CCCGATTACGCGCAGTTAC 59.078 57.895 5.73 0.00 38.29 2.50
294 295 1.879430 GCCCGATTACGCGCAGTTA 60.879 57.895 5.73 0.36 41.99 2.24
295 296 3.192922 GCCCGATTACGCGCAGTT 61.193 61.111 5.73 0.00 41.99 3.16
301 302 0.935366 CTCTTCTCGCCCGATTACGC 60.935 60.000 0.00 0.00 38.29 4.42
302 303 0.661552 TCTCTTCTCGCCCGATTACG 59.338 55.000 0.00 0.00 39.43 3.18
303 304 2.858941 GTTTCTCTTCTCGCCCGATTAC 59.141 50.000 0.00 0.00 0.00 1.89
326 327 0.396278 CCTGCTTCCCCATTCCCTTC 60.396 60.000 0.00 0.00 0.00 3.46
333 334 2.361610 CGTTGCCTGCTTCCCCAT 60.362 61.111 0.00 0.00 0.00 4.00
372 373 4.479993 GCCGCCCTCATGCTCACT 62.480 66.667 0.00 0.00 0.00 3.41
402 403 1.227497 GATCAGCGGCTTCCTCCTG 60.227 63.158 0.00 0.00 0.00 3.86
540 545 2.911926 AAGCTCAAGGCACCCCTCC 61.912 63.158 0.00 0.00 41.90 4.30
750 770 2.204705 ACCTCCTCTCCTCCCCCT 60.205 66.667 0.00 0.00 0.00 4.79
751 771 2.041405 CACCTCCTCTCCTCCCCC 60.041 72.222 0.00 0.00 0.00 5.40
754 774 3.151022 CGCCACCTCCTCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
756 776 2.363147 GACGCCACCTCCTCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
757 777 3.462678 GGACGCCACCTCCTCTCC 61.463 72.222 0.00 0.00 0.00 3.71
761 781 1.128188 AGAAAAGGACGCCACCTCCT 61.128 55.000 0.00 0.00 40.11 3.69
762 782 0.673956 GAGAAAAGGACGCCACCTCC 60.674 60.000 0.00 0.00 39.62 4.30
764 784 1.004918 CGAGAAAAGGACGCCACCT 60.005 57.895 0.00 0.00 42.69 4.00
876 908 8.127327 CCAAAGCAGAGACACAATAGAATAATG 58.873 37.037 0.00 0.00 0.00 1.90
877 909 7.284034 CCCAAAGCAGAGACACAATAGAATAAT 59.716 37.037 0.00 0.00 0.00 1.28
880 912 4.946157 CCCAAAGCAGAGACACAATAGAAT 59.054 41.667 0.00 0.00 0.00 2.40
883 915 2.421424 GCCCAAAGCAGAGACACAATAG 59.579 50.000 0.00 0.00 42.97 1.73
884 916 2.436417 GCCCAAAGCAGAGACACAATA 58.564 47.619 0.00 0.00 42.97 1.90
885 917 1.251251 GCCCAAAGCAGAGACACAAT 58.749 50.000 0.00 0.00 42.97 2.71
887 919 4.481195 GCCCAAAGCAGAGACACA 57.519 55.556 0.00 0.00 42.97 3.72
901 935 0.322648 ATCCAAGCTTGCAAAAGCCC 59.677 50.000 21.43 0.00 46.61 5.19
904 938 1.345415 ACCCATCCAAGCTTGCAAAAG 59.655 47.619 21.43 11.14 0.00 2.27
905 939 1.422531 ACCCATCCAAGCTTGCAAAA 58.577 45.000 21.43 6.25 0.00 2.44
924 958 1.358725 GCTGAATGTACGAGCGGCAA 61.359 55.000 1.45 0.00 33.01 4.52
986 1021 0.173708 GGTAGTGTGAGCCTTCGAGG 59.826 60.000 0.00 0.00 38.80 4.63
1017 1055 0.822944 TGCCCAGTGTCAATGTGTGG 60.823 55.000 0.00 0.00 0.00 4.17
1024 1062 1.301401 GCTACGTGCCCAGTGTCAA 60.301 57.895 0.00 0.00 35.15 3.18
1040 1078 2.291209 TTGATGACAACATGGTGGCT 57.709 45.000 19.55 2.80 36.82 4.75
1050 1088 1.075212 TGCCAGGGTGATTGATGACAA 59.925 47.619 0.00 0.00 40.42 3.18
1451 1498 3.386726 CCGGAATAGTGGTAGGATCAACA 59.613 47.826 0.00 0.00 0.00 3.33
1457 1504 2.832643 TGACCGGAATAGTGGTAGGA 57.167 50.000 9.46 0.00 38.99 2.94
1545 1885 1.140852 ACTGCGAATGCCTATTGCCTA 59.859 47.619 0.00 0.00 41.78 3.93
1546 1886 0.107017 ACTGCGAATGCCTATTGCCT 60.107 50.000 0.00 0.00 41.78 4.75
1547 1887 0.308993 GACTGCGAATGCCTATTGCC 59.691 55.000 0.00 0.00 41.78 4.52
1548 1888 0.308993 GGACTGCGAATGCCTATTGC 59.691 55.000 0.00 0.00 41.78 3.56
1549 1889 0.583438 CGGACTGCGAATGCCTATTG 59.417 55.000 0.00 0.00 41.78 1.90
1550 1890 1.160329 GCGGACTGCGAATGCCTATT 61.160 55.000 0.00 0.00 41.78 1.73
1551 1891 1.595382 GCGGACTGCGAATGCCTAT 60.595 57.895 0.00 0.00 41.78 2.57
1667 2008 8.686334 GGTAAATATACTAATACCCGATCCGAA 58.314 37.037 0.00 0.00 33.25 4.30
1670 2011 9.193806 TGAGGTAAATATACTAATACCCGATCC 57.806 37.037 0.00 0.00 38.86 3.36
1680 2021 7.073457 TGGCAGCATGAGGTAAATATACTAA 57.927 36.000 0.00 0.00 39.69 2.24
1692 2033 0.101759 CGGAAATTGGCAGCATGAGG 59.898 55.000 0.00 0.00 39.69 3.86
1693 2034 0.813184 ACGGAAATTGGCAGCATGAG 59.187 50.000 0.00 0.00 39.69 2.90
1697 2038 2.331893 CGGACGGAAATTGGCAGCA 61.332 57.895 0.00 0.00 0.00 4.41
1769 2110 0.413037 TTGAAATGTCCATGCCCCCT 59.587 50.000 0.00 0.00 0.00 4.79
1770 2111 0.826062 CTTGAAATGTCCATGCCCCC 59.174 55.000 0.00 0.00 0.00 5.40
1786 2127 0.176219 CTGCTCTCTCTCCCTGCTTG 59.824 60.000 0.00 0.00 0.00 4.01
1805 2146 2.243810 TGGTTTCTTAATGTGGTGGGC 58.756 47.619 0.00 0.00 0.00 5.36
1816 2157 5.008613 GCTAATTCATGGCGATGGTTTCTTA 59.991 40.000 8.98 0.52 0.00 2.10
1872 2471 1.239347 GTGGTTTCTTGAGGTCTGCC 58.761 55.000 0.00 0.00 0.00 4.85
1874 2473 3.480470 ACATGTGGTTTCTTGAGGTCTG 58.520 45.455 0.00 0.00 0.00 3.51
1875 2474 3.864789 ACATGTGGTTTCTTGAGGTCT 57.135 42.857 0.00 0.00 0.00 3.85
1966 2612 1.214589 CATTTGGGAGCTGCACTGC 59.785 57.895 7.79 0.00 35.62 4.40
1972 2618 2.229784 GTCTTGGTTCATTTGGGAGCTG 59.770 50.000 0.00 0.00 0.00 4.24
2090 2831 2.746472 GCCGGCACTTTCTATCTTCCAT 60.746 50.000 24.80 0.00 0.00 3.41
2125 2866 1.014352 GTGTCGGTGCTTCAGTTGTT 58.986 50.000 0.00 0.00 0.00 2.83
2130 2871 1.299850 TGACGTGTCGGTGCTTCAG 60.300 57.895 0.00 0.00 0.00 3.02
2251 2993 2.025037 TGCAATATCAGGCCTGAAACCT 60.025 45.455 38.02 24.20 43.58 3.50
2261 3003 7.094205 ACAAGGTAGAAAGTTTGCAATATCAGG 60.094 37.037 0.00 0.00 0.00 3.86
2264 3006 7.816640 TGACAAGGTAGAAAGTTTGCAATATC 58.183 34.615 0.00 0.00 0.00 1.63
2279 3022 6.737254 ACATCGGTTAAAATGACAAGGTAG 57.263 37.500 1.86 0.00 0.00 3.18
2281 3024 5.768317 CAACATCGGTTAAAATGACAAGGT 58.232 37.500 1.86 0.00 34.87 3.50
2297 3040 2.100797 CCCGTGCATGCAACATCG 59.899 61.111 24.58 20.94 0.00 3.84
2304 3047 1.865788 ATGTCAACACCCGTGCATGC 61.866 55.000 11.82 11.82 0.00 4.06
2307 3050 0.749818 AACATGTCAACACCCGTGCA 60.750 50.000 0.00 0.00 0.00 4.57
2309 3052 0.317770 GCAACATGTCAACACCCGTG 60.318 55.000 0.00 0.00 0.00 4.94
2310 3053 0.749818 TGCAACATGTCAACACCCGT 60.750 50.000 0.00 0.00 0.00 5.28
2311 3054 0.597568 ATGCAACATGTCAACACCCG 59.402 50.000 0.00 0.00 0.00 5.28
2313 3056 2.798976 ACATGCAACATGTCAACACC 57.201 45.000 7.38 0.00 0.00 4.16
2314 3057 3.302610 GCAAACATGCAACATGTCAACAC 60.303 43.478 13.20 0.00 34.41 3.32
2315 3058 2.864946 GCAAACATGCAACATGTCAACA 59.135 40.909 13.20 0.00 34.41 3.33
2316 3059 2.864946 TGCAAACATGCAACATGTCAAC 59.135 40.909 13.20 6.73 42.40 3.18
2318 3061 2.884894 TGCAAACATGCAACATGTCA 57.115 40.000 13.20 5.28 42.40 3.58
2348 3091 9.134268 AGTTTGCAAACATTTTGCTCCCAAAAA 62.134 33.333 36.46 11.18 42.98 1.94
2349 3092 7.743857 AGTTTGCAAACATTTTGCTCCCAAAA 61.744 34.615 36.46 11.74 43.36 2.44
2350 3093 3.272574 TGCAAACATTTTGCTCCCAAA 57.727 38.095 20.94 1.02 45.13 3.28
2351 3094 2.996249 TGCAAACATTTTGCTCCCAA 57.004 40.000 20.94 1.66 45.13 4.12
2352 3095 2.941720 GTTTGCAAACATTTTGCTCCCA 59.058 40.909 32.21 1.99 45.13 4.37
2353 3096 3.205338 AGTTTGCAAACATTTTGCTCCC 58.795 40.909 36.46 11.70 45.13 4.30
2354 3097 5.288804 TCTAGTTTGCAAACATTTTGCTCC 58.711 37.500 36.46 12.18 45.13 4.70
2355 3098 6.421801 ACATCTAGTTTGCAAACATTTTGCTC 59.578 34.615 36.46 12.87 45.13 4.26
2356 3099 6.282930 ACATCTAGTTTGCAAACATTTTGCT 58.717 32.000 36.46 20.57 45.13 3.91
2357 3100 6.529463 ACATCTAGTTTGCAAACATTTTGC 57.471 33.333 36.46 15.22 45.11 3.68
2359 3102 9.979578 TGAATACATCTAGTTTGCAAACATTTT 57.020 25.926 36.46 22.18 41.30 1.82
2382 3125 9.798994 GAGTTAGAACGAGAAAGGTATAATGAA 57.201 33.333 0.00 0.00 0.00 2.57
2383 3126 9.186837 AGAGTTAGAACGAGAAAGGTATAATGA 57.813 33.333 0.00 0.00 0.00 2.57
2384 3127 9.453325 GAGAGTTAGAACGAGAAAGGTATAATG 57.547 37.037 0.00 0.00 0.00 1.90
2385 3128 9.411189 AGAGAGTTAGAACGAGAAAGGTATAAT 57.589 33.333 0.00 0.00 0.00 1.28
2386 3129 8.804912 AGAGAGTTAGAACGAGAAAGGTATAA 57.195 34.615 0.00 0.00 0.00 0.98
2388 3131 8.842280 CATAGAGAGTTAGAACGAGAAAGGTAT 58.158 37.037 0.00 0.00 0.00 2.73
2410 3153 2.487934 GGTCACCTGCTATGCACATAG 58.512 52.381 12.40 12.40 42.76 2.23
2412 3155 0.462581 CGGTCACCTGCTATGCACAT 60.463 55.000 0.00 0.00 33.79 3.21
2413 3156 1.079197 CGGTCACCTGCTATGCACA 60.079 57.895 0.00 0.00 33.79 4.57
2414 3157 0.391130 TTCGGTCACCTGCTATGCAC 60.391 55.000 0.00 0.00 33.79 4.57
2418 3161 2.906354 GTGAATTCGGTCACCTGCTAT 58.094 47.619 0.04 0.00 41.79 2.97
2419 3162 2.380084 GTGAATTCGGTCACCTGCTA 57.620 50.000 0.04 0.00 41.79 3.49
2420 3163 3.233355 GTGAATTCGGTCACCTGCT 57.767 52.632 0.04 0.00 41.79 4.24
2496 3239 2.028930 TGCATTGATGAATTGTGCAGCA 60.029 40.909 0.00 0.00 40.51 4.41
2499 3242 4.142795 GCAATTGCATTGATGAATTGTGCA 60.143 37.500 25.36 0.00 42.83 4.57
2606 3349 2.228841 GAATGATGGTGGTGGCCCCT 62.229 60.000 0.00 0.00 0.00 4.79
2622 3365 1.281867 TGGAAGCCGAATGACTGGAAT 59.718 47.619 0.00 0.00 0.00 3.01
2667 3410 0.464036 TGACATGGGCGATACAGTCC 59.536 55.000 0.00 0.00 36.18 3.85
2670 3413 1.586422 CCTTGACATGGGCGATACAG 58.414 55.000 0.00 0.00 0.00 2.74
2705 3448 3.838317 AGTTGAGCAGTACTGACCCATTA 59.162 43.478 27.08 3.86 0.00 1.90
2868 3611 1.003839 CGGGTAGAAGCAGTTGCCA 60.004 57.895 0.00 0.00 43.38 4.92
2974 3717 1.756538 CCACTTGGCAAACTCCAAAGT 59.243 47.619 0.00 0.00 44.73 2.66
2997 3740 4.202545 GGATCAATCTTCACATCCCCTGAT 60.203 45.833 0.00 0.00 30.17 2.90
3057 3800 0.671781 CAAGCCTTGTCCAGTCCGAG 60.672 60.000 0.00 0.00 0.00 4.63
3063 3806 2.503895 AGAATCCAAGCCTTGTCCAG 57.496 50.000 3.37 0.00 0.00 3.86
3069 3812 3.425659 GACCTCAAAGAATCCAAGCCTT 58.574 45.455 0.00 0.00 0.00 4.35
3139 3882 2.625906 CGCGACCGCCATGTAATG 59.374 61.111 0.00 0.00 46.21 1.90
3179 3922 3.330720 CCCGGGTGCCCTTCTTCT 61.331 66.667 14.18 0.00 0.00 2.85
3195 3938 1.349688 TCCACACACTGGGTCATAACC 59.650 52.381 0.00 0.00 45.65 2.85
3219 3962 4.914983 TCCTGAACTCATTGAGATGCTTT 58.085 39.130 20.33 3.51 33.32 3.51
3241 3984 9.987272 CTTTTAAAAGAAACCCTTCATCTCATT 57.013 29.630 21.12 0.00 38.28 2.57
3303 4046 4.252878 GCCACAAATTTATCCAAACCCAG 58.747 43.478 0.00 0.00 0.00 4.45
3342 4087 8.384607 TCACAACATTGCAAGTGTAGTATTTA 57.615 30.769 14.14 0.00 33.84 1.40
3417 4162 4.080356 GGGCAGTCATCCATATATTAGCCA 60.080 45.833 0.00 0.00 40.06 4.75
3432 4177 4.211125 TCACAAACTTTATTGGGCAGTCA 58.789 39.130 0.00 0.00 33.63 3.41
3486 4231 7.226720 GTCCCACTAATTTGTCGTCATCAATAT 59.773 37.037 0.00 0.00 0.00 1.28
3520 4265 3.232213 AGACATCGTCAATTAGCGTGT 57.768 42.857 0.00 5.29 34.60 4.49
3533 4278 3.314553 ACACTCACGGTTTTAGACATCG 58.685 45.455 0.00 0.00 0.00 3.84
3537 4282 2.978489 CGAGACACTCACGGTTTTAGAC 59.022 50.000 0.00 0.00 0.00 2.59
3538 4283 2.030540 CCGAGACACTCACGGTTTTAGA 60.031 50.000 0.00 0.00 43.93 2.10
3540 4285 2.427232 CCGAGACACTCACGGTTTTA 57.573 50.000 0.00 0.00 43.93 1.52
3549 4294 1.321074 CCACCCCTACCGAGACACTC 61.321 65.000 0.00 0.00 0.00 3.51
3556 4301 1.000019 CACTCTCCACCCCTACCGA 60.000 63.158 0.00 0.00 0.00 4.69
3557 4302 1.305046 ACACTCTCCACCCCTACCG 60.305 63.158 0.00 0.00 0.00 4.02
3558 4303 0.252103 TCACACTCTCCACCCCTACC 60.252 60.000 0.00 0.00 0.00 3.18
3560 4305 0.252103 GGTCACACTCTCCACCCCTA 60.252 60.000 0.00 0.00 0.00 3.53
3561 4306 1.536662 GGTCACACTCTCCACCCCT 60.537 63.158 0.00 0.00 0.00 4.79
3562 4307 2.593956 GGGTCACACTCTCCACCCC 61.594 68.421 0.00 0.00 42.60 4.95
3580 4325 0.893270 TTGTGCGTGATCCCTTTGGG 60.893 55.000 0.00 0.00 46.11 4.12
3581 4326 0.958091 TTTGTGCGTGATCCCTTTGG 59.042 50.000 0.00 0.00 0.00 3.28
3582 4327 1.608590 ACTTTGTGCGTGATCCCTTTG 59.391 47.619 0.00 0.00 0.00 2.77
3583 4328 1.981256 ACTTTGTGCGTGATCCCTTT 58.019 45.000 0.00 0.00 0.00 3.11
3584 4329 1.981256 AACTTTGTGCGTGATCCCTT 58.019 45.000 0.00 0.00 0.00 3.95
3585 4330 1.981256 AAACTTTGTGCGTGATCCCT 58.019 45.000 0.00 0.00 0.00 4.20
3586 4331 2.793278 AAAACTTTGTGCGTGATCCC 57.207 45.000 0.00 0.00 0.00 3.85
3587 4332 3.978855 GGTAAAAACTTTGTGCGTGATCC 59.021 43.478 0.00 0.00 0.00 3.36
3588 4333 4.602995 TGGTAAAAACTTTGTGCGTGATC 58.397 39.130 0.00 0.00 0.00 2.92
3590 4335 3.181495 CCTGGTAAAAACTTTGTGCGTGA 60.181 43.478 0.00 0.00 0.00 4.35
3591 4336 3.112580 CCTGGTAAAAACTTTGTGCGTG 58.887 45.455 0.00 0.00 0.00 5.34
3592 4337 2.756207 ACCTGGTAAAAACTTTGTGCGT 59.244 40.909 0.00 0.00 0.00 5.24
3593 4338 3.430333 ACCTGGTAAAAACTTTGTGCG 57.570 42.857 0.00 0.00 0.00 5.34
3595 4340 4.356289 CCGAACCTGGTAAAAACTTTGTG 58.644 43.478 0.00 0.00 0.00 3.33
3597 4342 3.797524 GCCCGAACCTGGTAAAAACTTTG 60.798 47.826 0.00 0.00 0.00 2.77
3598 4343 2.363038 GCCCGAACCTGGTAAAAACTTT 59.637 45.455 0.00 0.00 0.00 2.66
3600 4345 1.612676 GCCCGAACCTGGTAAAAACT 58.387 50.000 0.00 0.00 0.00 2.66
3601 4346 0.599558 GGCCCGAACCTGGTAAAAAC 59.400 55.000 0.00 0.00 0.00 2.43
3606 4359 2.686106 GAGGGCCCGAACCTGGTA 60.686 66.667 18.44 0.00 38.79 3.25
3607 4360 4.974438 TGAGGGCCCGAACCTGGT 62.974 66.667 18.44 0.00 38.79 4.00
3633 4386 4.818546 CCACCATCAATCAGAAGGTATCAC 59.181 45.833 0.00 0.00 46.15 3.06
3634 4387 4.721274 TCCACCATCAATCAGAAGGTATCA 59.279 41.667 0.00 0.00 46.15 2.15
3635 4388 5.296151 TCCACCATCAATCAGAAGGTATC 57.704 43.478 0.00 0.00 46.15 2.24
3637 4390 5.222027 TGTTTCCACCATCAATCAGAAGGTA 60.222 40.000 0.00 0.00 46.15 3.08
3639 4392 4.081406 TGTTTCCACCATCAATCAGAAGG 58.919 43.478 0.00 0.00 40.94 3.46
3708 4478 0.252103 TATAAGGCGGGGGCTAGAGG 60.252 60.000 0.00 0.00 37.50 3.69
3709 4479 1.187087 CTATAAGGCGGGGGCTAGAG 58.813 60.000 0.00 0.00 37.50 2.43
3710 4480 0.781920 TCTATAAGGCGGGGGCTAGA 59.218 55.000 0.00 0.00 37.50 2.43
3711 4481 1.550976 CTTCTATAAGGCGGGGGCTAG 59.449 57.143 0.00 0.00 37.50 3.42
3712 4482 1.640917 CTTCTATAAGGCGGGGGCTA 58.359 55.000 0.00 0.00 37.50 3.93
3713 4483 1.128188 CCTTCTATAAGGCGGGGGCT 61.128 60.000 0.00 0.00 45.78 5.19
3714 4484 1.375326 CCTTCTATAAGGCGGGGGC 59.625 63.158 0.00 0.00 45.78 5.80
3726 4496 8.445588 GGTATGAAAATAGAAATCCCCCTTCTA 58.554 37.037 0.00 0.00 39.18 2.10
3727 4497 7.298374 GGTATGAAAATAGAAATCCCCCTTCT 58.702 38.462 0.00 0.00 37.00 2.85
3728 4498 6.493802 GGGTATGAAAATAGAAATCCCCCTTC 59.506 42.308 0.00 0.00 0.00 3.46
3729 4499 6.382087 GGGTATGAAAATAGAAATCCCCCTT 58.618 40.000 0.00 0.00 0.00 3.95
3730 4500 5.162870 GGGGTATGAAAATAGAAATCCCCCT 60.163 44.000 0.00 0.00 44.41 4.79
3731 4501 5.084519 GGGGTATGAAAATAGAAATCCCCC 58.915 45.833 0.00 0.00 44.41 5.40
3750 4520 3.340357 AGGAGAACTAAGGAACTAGGGGT 59.660 47.826 0.00 0.00 38.49 4.95
3779 4549 0.184211 AACGTTTAGGTGGCAGGGTT 59.816 50.000 0.00 0.00 0.00 4.11
3780 4552 0.250597 GAACGTTTAGGTGGCAGGGT 60.251 55.000 0.46 0.00 0.00 4.34
3784 4556 0.759959 TGAGGAACGTTTAGGTGGCA 59.240 50.000 0.46 0.00 0.00 4.92
3792 4564 3.211865 GAGGGAAAAGTGAGGAACGTTT 58.788 45.455 0.46 0.00 42.24 3.60
3864 4638 5.680619 AGTAACGATCAATGATGGGCTTTA 58.319 37.500 9.93 0.00 0.00 1.85
3929 4703 2.432456 GGCTGTGATGCGACGTCA 60.432 61.111 17.16 0.00 0.00 4.35
3952 4726 4.664677 GTGTCGCACGGGCTCAGT 62.665 66.667 8.62 0.00 38.10 3.41
3986 4760 5.598416 ACCCAAGACCTTTTCTTTTTGAG 57.402 39.130 0.00 0.00 42.37 3.02
3987 4761 5.337975 CCAACCCAAGACCTTTTCTTTTTGA 60.338 40.000 0.00 0.00 42.37 2.69
3988 4762 4.875536 CCAACCCAAGACCTTTTCTTTTTG 59.124 41.667 0.00 0.00 42.37 2.44
3990 4764 3.118408 GCCAACCCAAGACCTTTTCTTTT 60.118 43.478 0.00 0.00 42.37 2.27
3991 4765 2.434336 GCCAACCCAAGACCTTTTCTTT 59.566 45.455 0.00 0.00 42.37 2.52
3992 4766 2.039418 GCCAACCCAAGACCTTTTCTT 58.961 47.619 0.00 0.00 46.29 2.52
3993 4767 1.704641 GCCAACCCAAGACCTTTTCT 58.295 50.000 0.00 0.00 35.32 2.52
3994 4768 0.679505 GGCCAACCCAAGACCTTTTC 59.320 55.000 0.00 0.00 0.00 2.29
3995 4769 2.834631 GGCCAACCCAAGACCTTTT 58.165 52.632 0.00 0.00 0.00 2.27
3996 4770 4.619233 GGCCAACCCAAGACCTTT 57.381 55.556 0.00 0.00 0.00 3.11
4082 4881 9.436957 GGAACTTGAATCAACTCAACTAGAATA 57.563 33.333 0.00 0.00 32.00 1.75
4087 4886 9.793259 ATTTAGGAACTTGAATCAACTCAACTA 57.207 29.630 0.00 0.00 41.75 2.24
4116 4931 8.986847 GCTATTACATAGGCTTGCATATATGAG 58.013 37.037 17.10 6.96 33.43 2.90
4123 4938 8.641498 AAATTAGCTATTACATAGGCTTGCAT 57.359 30.769 0.00 0.00 33.43 3.96
4349 5191 3.561143 ACACACATTTGGAAACTGCCTA 58.439 40.909 0.00 0.00 0.00 3.93
4395 5241 4.611367 TCACACAAAACCCCCTCTTTTTA 58.389 39.130 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.