Multiple sequence alignment - TraesCS2A01G578200

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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 TraesCS2A01G578200 chr2A 100.000 2932 0 0 1 2932 771678336 771681267 0.000000e+00 5415.0
1 TraesCS2A01G578200 chr2A 83.258 221 33 4 2715 2932 139921742 139921961 1.780000e-47 200.0
2 TraesCS2A01G578200 chr2A 81.778 225 39 2 2710 2932 356725116 356724892 1.390000e-43 187.0
3 TraesCS2A01G578200 chr2D 93.392 2149 127 7 793 2932 645933155 645935297 0.000000e+00 3168.0
4 TraesCS2A01G578200 chr2D 78.776 245 35 11 187 425 578925830 578925597 6.550000e-32 148.0
5 TraesCS2A01G578200 chr2B 91.551 1515 101 12 793 2299 789609905 789608410 0.000000e+00 2063.0
6 TraesCS2A01G578200 chr2B 90.572 1294 95 15 1388 2661 789616498 789615212 0.000000e+00 1688.0
7 TraesCS2A01G578200 chr2B 92.000 450 28 3 423 872 789618579 789618138 2.480000e-175 625.0
8 TraesCS2A01G578200 chr2B 89.379 499 39 8 904 1394 789618136 789617644 1.490000e-172 616.0
9 TraesCS2A01G578200 chr2B 87.935 431 39 5 1 425 789619058 789618635 2.030000e-136 496.0
10 TraesCS2A01G578200 chr2B 91.275 149 13 0 517 665 789610203 789610055 1.380000e-48 204.0
11 TraesCS2A01G578200 chr2B 79.259 270 42 7 159 424 789045885 789046144 3.000000e-40 176.0
12 TraesCS2A01G578200 chr2B 96.970 33 1 0 2207 2239 59257757 59257789 4.080000e-04 56.5
13 TraesCS2A01G578200 chr5D 81.744 367 57 10 2337 2700 240506929 240506570 6.140000e-77 298.0
14 TraesCS2A01G578200 chr5D 80.576 139 16 5 291 425 434608626 434608495 2.410000e-16 97.1
15 TraesCS2A01G578200 chr5B 81.768 362 59 7 2336 2696 263218741 263219096 2.210000e-76 296.0
16 TraesCS2A01G578200 chr5B 81.746 126 12 5 304 425 617111786 617111904 8.650000e-16 95.3
17 TraesCS2A01G578200 chr5A 83.062 307 41 10 2337 2639 313310131 313310430 4.820000e-68 268.0
18 TraesCS2A01G578200 chr6B 84.434 212 31 2 2723 2932 34685743 34685532 1.060000e-49 207.0
19 TraesCS2A01G578200 chr6B 78.338 337 58 12 16 342 41912221 41911890 1.380000e-48 204.0
20 TraesCS2A01G578200 chr6B 82.667 225 37 2 2710 2932 652627089 652626865 6.410000e-47 198.0
21 TraesCS2A01G578200 chr3A 83.710 221 32 4 2715 2932 717621300 717621081 3.830000e-49 206.0
22 TraesCS2A01G578200 chr3A 80.189 212 27 10 2047 2253 710868731 710868932 8.470000e-31 145.0
23 TraesCS2A01G578200 chr6A 83.111 225 36 2 2710 2932 55882309 55882085 1.380000e-48 204.0
24 TraesCS2A01G578200 chr6A 77.778 225 37 8 187 409 614407454 614407241 3.070000e-25 126.0
25 TraesCS2A01G578200 chr3D 82.895 228 37 2 2707 2932 582266376 582266603 1.380000e-48 204.0
26 TraesCS2A01G578200 chr3D 77.860 271 42 11 159 425 77398337 77398081 5.060000e-33 152.0
27 TraesCS2A01G578200 chr3D 82.222 135 12 8 295 425 57333704 57333578 4.000000e-19 106.0
28 TraesCS2A01G578200 chr3B 83.645 214 33 2 2721 2932 776503386 776503173 1.780000e-47 200.0
29 TraesCS2A01G578200 chr1D 76.020 392 75 11 26 409 22139481 22139861 4.990000e-43 185.0
30 TraesCS2A01G578200 chr7B 78.992 238 34 11 187 419 711478174 711478400 6.550000e-32 148.0
31 TraesCS2A01G578200 chr1A 78.189 243 40 8 187 425 30337315 30337082 3.050000e-30 143.0
32 TraesCS2A01G578200 chr1B 76.446 242 39 8 187 425 13271008 13271234 6.640000e-22 115.0
33 TraesCS2A01G578200 chr1B 75.362 207 36 11 223 425 430990872 430991067 5.210000e-13 86.1


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 TraesCS2A01G578200 chr2A 771678336 771681267 2931 False 5415.00 5415 100.0000 1 2932 1 chr2A.!!$F2 2931
1 TraesCS2A01G578200 chr2D 645933155 645935297 2142 False 3168.00 3168 93.3920 793 2932 1 chr2D.!!$F1 2139
2 TraesCS2A01G578200 chr2B 789608410 789610203 1793 True 1133.50 2063 91.4130 517 2299 2 chr2B.!!$R1 1782
3 TraesCS2A01G578200 chr2B 789615212 789619058 3846 True 856.25 1688 89.9715 1 2661 4 chr2B.!!$R2 2660

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
150 151 0.108186 CGCATGTAGCTGTTGGGAGA 60.108 55.0 0.0 0.0 42.61 3.71 F
941 1088 0.326522 TGGAAGGGAGATAGCAGGCA 60.327 55.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1220 0.179048 CTATCAGAACCCGCATGCCA 60.179 55.0 13.15 0.0 0.0 4.92 R
2752 4088 0.178990 GACTTGAACCTGGTGGGCTT 60.179 55.0 0.00 0.0 39.1 4.35 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
33 34 0.877743 GTTTTGGCAGCTCTCACTCC 59.122 55.000 0.00 0.00 0.00 3.85
64 65 1.645034 CTTCGACGGTGAGATGCAAT 58.355 50.000 0.00 0.00 0.00 3.56
81 82 5.281693 TGCAATCTATGAAACGTGACTTG 57.718 39.130 0.00 0.00 0.00 3.16
140 141 1.958205 CTAGCCCAGCGCATGTAGC 60.958 63.158 11.47 10.15 41.38 3.58
149 150 1.709147 GCGCATGTAGCTGTTGGGAG 61.709 60.000 0.30 0.00 42.61 4.30
150 151 0.108186 CGCATGTAGCTGTTGGGAGA 60.108 55.000 0.00 0.00 42.61 3.71
157 163 4.157246 TGTAGCTGTTGGGAGAGAAGTAA 58.843 43.478 0.00 0.00 0.00 2.24
199 205 3.641436 ACTTCAATTTGGTGGTTCTTCCC 59.359 43.478 0.00 0.00 34.77 3.97
208 214 1.067071 GTGGTTCTTCCCGAGTACCTG 60.067 57.143 3.97 0.00 43.98 4.00
221 227 1.451567 TACCTGGTCTCGAGCTCCG 60.452 63.158 7.81 3.57 40.25 4.63
243 249 3.265995 GGGGGTGAAAATCCTAGTTCTGA 59.734 47.826 0.00 0.00 0.00 3.27
245 251 4.263331 GGGGTGAAAATCCTAGTTCTGACA 60.263 45.833 0.00 0.00 0.00 3.58
249 255 5.118817 GTGAAAATCCTAGTTCTGACACGAC 59.881 44.000 0.00 0.00 0.00 4.34
257 263 4.258702 AGTTCTGACACGACTTGCTTAT 57.741 40.909 0.00 0.00 0.00 1.73
264 270 1.933853 CACGACTTGCTTATACCTGGC 59.066 52.381 0.00 0.00 0.00 4.85
281 287 2.164219 CTGGCAGTGGCGATATTTTTGT 59.836 45.455 12.58 0.00 42.47 2.83
282 288 2.094803 TGGCAGTGGCGATATTTTTGTG 60.095 45.455 12.58 0.00 42.47 3.33
289 295 3.687212 TGGCGATATTTTTGTGTCGTGAT 59.313 39.130 0.00 0.00 35.51 3.06
291 297 4.034048 GGCGATATTTTTGTGTCGTGATCT 59.966 41.667 0.00 0.00 35.51 2.75
301 307 3.802139 TGTGTCGTGATCTTGTTGAAGAC 59.198 43.478 0.00 0.00 41.12 3.01
315 321 5.912892 TGTTGAAGACATTGCTCGGATATA 58.087 37.500 0.00 0.00 32.00 0.86
330 336 6.238130 GCTCGGATATACTTGGACTTGTTTTC 60.238 42.308 0.00 0.00 0.00 2.29
331 337 6.703319 TCGGATATACTTGGACTTGTTTTCA 58.297 36.000 0.00 0.00 0.00 2.69
332 338 6.816640 TCGGATATACTTGGACTTGTTTTCAG 59.183 38.462 0.00 0.00 0.00 3.02
334 340 7.110155 GGATATACTTGGACTTGTTTTCAGGA 58.890 38.462 0.00 0.00 0.00 3.86
335 341 7.775561 GGATATACTTGGACTTGTTTTCAGGAT 59.224 37.037 0.00 0.00 0.00 3.24
336 342 6.824305 ATACTTGGACTTGTTTTCAGGATG 57.176 37.500 0.00 0.00 37.54 3.51
370 376 4.475016 ACATAGAATCTAGCCTTTGGTGGT 59.525 41.667 0.00 0.00 0.00 4.16
375 381 1.992557 TCTAGCCTTTGGTGGTTGGAT 59.007 47.619 0.00 0.00 0.00 3.41
408 414 2.095252 GCTTGAGCGTCGTTCCCTC 61.095 63.158 6.63 0.00 0.00 4.30
415 421 2.654877 GTCGTTCCCTCGAAGGCA 59.345 61.111 0.00 0.00 41.47 4.75
419 425 0.673644 CGTTCCCTCGAAGGCATTGT 60.674 55.000 0.00 0.00 32.73 2.71
440 504 5.885881 TGTTGTTGTGTAGTTTGTTGATCC 58.114 37.500 0.00 0.00 0.00 3.36
442 506 3.886505 TGTTGTGTAGTTTGTTGATCCCC 59.113 43.478 0.00 0.00 0.00 4.81
445 509 4.798882 TGTGTAGTTTGTTGATCCCCTTT 58.201 39.130 0.00 0.00 0.00 3.11
446 510 4.582656 TGTGTAGTTTGTTGATCCCCTTTG 59.417 41.667 0.00 0.00 0.00 2.77
447 511 3.572255 TGTAGTTTGTTGATCCCCTTTGC 59.428 43.478 0.00 0.00 0.00 3.68
501 565 5.633601 TGATAGCTATTTTCCGTATGCTTCG 59.366 40.000 7.87 0.00 32.72 3.79
585 649 3.377172 GCACGTAATATCTGGCCTTTTGT 59.623 43.478 3.32 0.00 0.00 2.83
714 778 6.517605 AGGAAAGTAACTCTGAAGAAGTCAC 58.482 40.000 0.00 0.00 31.13 3.67
718 782 4.822896 AGTAACTCTGAAGAAGTCACGACT 59.177 41.667 0.00 0.00 44.94 4.18
813 955 6.199937 TCAAATGAGAAAGATAAGCAAGCC 57.800 37.500 0.00 0.00 0.00 4.35
846 988 6.098124 TCAAAATCACCAACTTTCCATCTGTT 59.902 34.615 0.00 0.00 0.00 3.16
863 1010 1.185315 GTTGGGCTGGCATACACATT 58.815 50.000 2.88 0.00 0.00 2.71
898 1045 5.163774 CCGGTCTAAGTGTCTAACTAGTGTC 60.164 48.000 0.00 0.00 38.56 3.67
915 1062 2.202919 CGCCGTCAGCCATGATGA 60.203 61.111 0.00 0.00 43.98 2.92
937 1084 2.494888 TCCATGGAAGGGAGATAGCA 57.505 50.000 13.46 0.00 45.19 3.49
941 1088 0.326522 TGGAAGGGAGATAGCAGGCA 60.327 55.000 0.00 0.00 0.00 4.75
944 1091 1.059006 AAGGGAGATAGCAGGCAGGG 61.059 60.000 0.00 0.00 0.00 4.45
948 1095 1.127343 GAGATAGCAGGCAGGGTCTT 58.873 55.000 0.00 0.00 0.00 3.01
1040 1195 1.536943 GGAGAGAGCGAGGTGGTGTT 61.537 60.000 0.00 0.00 0.00 3.32
1065 1220 0.261696 ACTTCTGGGCCAACCTGTTT 59.738 50.000 8.04 0.00 41.11 2.83
1083 1238 0.254462 TTGGCATGCGGGTTCTGATA 59.746 50.000 12.44 0.00 0.00 2.15
1086 1241 1.510480 GCATGCGGGTTCTGATAGCC 61.510 60.000 0.00 0.00 0.00 3.93
1096 1251 3.144120 CTGATAGCCCTGCGCGAGT 62.144 63.158 12.10 0.00 44.76 4.18
1102 1257 4.451150 CCCTGCGCGAGTTAGGCA 62.451 66.667 12.10 0.00 36.61 4.75
1141 1296 2.685017 AGGACCTCAGCATCCGCA 60.685 61.111 0.00 0.00 42.27 5.69
1145 1300 0.391661 GACCTCAGCATCCGCAAGAA 60.392 55.000 0.00 0.00 42.27 2.52
1149 1304 0.610174 TCAGCATCCGCAAGAAGAGT 59.390 50.000 0.00 0.00 42.27 3.24
1177 1332 4.634703 TGCGCATGAACCCGGTGT 62.635 61.111 5.66 0.00 0.00 4.16
1239 1394 3.087031 CTGCAACTCCATCAACATCCTT 58.913 45.455 0.00 0.00 0.00 3.36
1272 1427 2.342648 GTCTGGGGTCACCGTCAC 59.657 66.667 0.00 0.00 44.64 3.67
1408 2715 8.035394 TGCCTTACAACAATTTTGTCTTGTTTA 58.965 29.630 6.19 0.00 42.58 2.01
1419 2726 9.545105 AATTTTGTCTTGTTTATTTCATGCTCA 57.455 25.926 0.00 0.00 0.00 4.26
1569 2876 6.145535 GCTTGTTCAGTTTACTCATCCTTTG 58.854 40.000 0.00 0.00 0.00 2.77
1745 3052 4.286297 TGAGTTCGGATTTCTGGACATT 57.714 40.909 0.79 0.00 33.04 2.71
1781 3088 1.200483 CGAGCATGTTTCGAGCGTAT 58.800 50.000 14.12 0.00 40.36 3.06
1795 3102 3.423123 CGAGCGTATGAACAACAAGGAAC 60.423 47.826 0.00 0.00 0.00 3.62
1867 3174 0.682855 AAGGAGAGGGAGAGCGTCAG 60.683 60.000 0.00 0.00 0.00 3.51
1933 3240 2.829720 AGTGGTACGGCATAGAGTGAAA 59.170 45.455 0.00 0.00 0.00 2.69
2127 3444 7.406553 TCGAGCAAACAAAATTAGATTATCCG 58.593 34.615 0.00 0.00 0.00 4.18
2151 3468 3.623906 ACATATGTGCTCTGTGCTCTT 57.376 42.857 7.78 1.08 43.37 2.85
2159 3476 1.561643 CTCTGTGCTCTTCTGGGGTA 58.438 55.000 0.00 0.00 0.00 3.69
2196 3516 3.304659 GGCGAATGTGTGTTCTTGTTCAT 60.305 43.478 0.00 0.00 0.00 2.57
2205 3525 1.133025 GTTCTTGTTCATGGGGCATCG 59.867 52.381 0.00 0.00 0.00 3.84
2206 3526 1.031571 TCTTGTTCATGGGGCATCGC 61.032 55.000 0.00 0.00 0.00 4.58
2258 3578 1.243902 GAAGTTGCGGACCATTTCCA 58.756 50.000 0.00 0.00 46.29 3.53
2555 3890 6.096846 ACTTGTTGAGATGTAAGCCAAAAACT 59.903 34.615 0.00 0.00 0.00 2.66
2562 3897 6.303839 AGATGTAAGCCAAAAACTACTTCCA 58.696 36.000 0.00 0.00 0.00 3.53
2563 3898 6.775629 AGATGTAAGCCAAAAACTACTTCCAA 59.224 34.615 0.00 0.00 0.00 3.53
2586 3921 7.272244 CAACCATTTATTTCCCCCATTCTAAC 58.728 38.462 0.00 0.00 0.00 2.34
2639 3974 8.914654 CGAAATCTCAAAATATGCAACTTTGAA 58.085 29.630 17.01 11.20 38.30 2.69
2645 3980 9.474920 CTCAAAATATGCAACTTTGAACCTTAA 57.525 29.630 17.01 0.85 38.30 1.85
2719 4055 2.836479 AAAAACAGTGAACGAACCGG 57.164 45.000 0.00 0.00 0.00 5.28
2737 4073 0.966179 GGTGGTTGGATGGTTGGTTC 59.034 55.000 0.00 0.00 0.00 3.62
2752 4088 1.469335 GGTTCGACAGTGGTCTCCCA 61.469 60.000 0.00 0.00 42.05 4.37
2766 4102 2.283173 CCCAAGCCCACCAGGTTC 60.283 66.667 0.00 0.00 38.26 3.62
2772 4108 1.603739 GCCCACCAGGTTCAAGTCC 60.604 63.158 0.00 0.00 38.26 3.85
2779 4115 0.179020 CAGGTTCAAGTCCTGGTGCA 60.179 55.000 4.27 0.00 46.03 4.57
2780 4116 0.550914 AGGTTCAAGTCCTGGTGCAA 59.449 50.000 0.00 0.00 33.62 4.08
2790 4126 3.834231 AGTCCTGGTGCAAGCATTTATTT 59.166 39.130 0.00 0.00 46.93 1.40
2835 4171 2.094700 GTGATGCACGTTCAGTAGGAGA 60.095 50.000 0.00 0.00 0.00 3.71
2842 4178 4.416620 CACGTTCAGTAGGAGAAGACATC 58.583 47.826 0.00 0.00 0.00 3.06
2846 4182 1.683917 CAGTAGGAGAAGACATCCCCG 59.316 57.143 0.00 0.00 37.57 5.73
2852 4188 1.550976 GAGAAGACATCCCCGTTGACT 59.449 52.381 0.00 0.00 0.00 3.41
2854 4190 3.375699 AGAAGACATCCCCGTTGACTAT 58.624 45.455 0.00 0.00 0.00 2.12
2857 4193 3.104512 AGACATCCCCGTTGACTATGAA 58.895 45.455 0.00 0.00 0.00 2.57
2858 4194 3.133003 AGACATCCCCGTTGACTATGAAG 59.867 47.826 0.00 0.00 0.00 3.02
2874 4210 0.668535 GAAGCGCCTTTGGTGACTTT 59.331 50.000 2.29 0.00 34.74 2.66
2903 4239 3.145286 TCAAAATGACATGTCGGCTCAA 58.855 40.909 20.54 2.48 0.00 3.02
2914 4250 0.107165 TCGGCTCAATCTCTCGGAGA 60.107 55.000 7.60 7.60 43.20 3.71
2926 4262 1.145945 TCTCGGAGATGCTCATAGGGT 59.854 52.381 2.97 0.00 33.89 4.34
2927 4263 2.375509 TCTCGGAGATGCTCATAGGGTA 59.624 50.000 2.97 0.00 33.89 3.69
2928 4264 2.752354 CTCGGAGATGCTCATAGGGTAG 59.248 54.545 0.00 0.00 33.89 3.18
2931 4267 2.493687 GGAGATGCTCATAGGGTAGGGT 60.494 54.545 0.00 0.00 31.08 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.112995 TGAGAGCTGCCAAAACCCAT 59.887 50.000 0.00 0.00 0.00 4.00
48 49 2.492019 TAGATTGCATCTCACCGTCG 57.508 50.000 2.47 0.00 40.76 5.12
49 50 3.982475 TCATAGATTGCATCTCACCGTC 58.018 45.455 2.47 0.00 40.76 4.79
52 53 4.572389 ACGTTTCATAGATTGCATCTCACC 59.428 41.667 2.47 0.00 40.76 4.02
64 65 2.333926 CGGCAAGTCACGTTTCATAGA 58.666 47.619 0.00 0.00 0.00 1.98
70 71 3.645975 CCGCGGCAAGTCACGTTT 61.646 61.111 14.67 0.00 0.00 3.60
81 82 4.171103 AACCATACCCTCCGCGGC 62.171 66.667 23.51 0.00 0.00 6.53
140 141 3.274288 GCCATTACTTCTCTCCCAACAG 58.726 50.000 0.00 0.00 0.00 3.16
149 150 3.585862 TCTGTTGTCGCCATTACTTCTC 58.414 45.455 0.00 0.00 0.00 2.87
150 151 3.678056 TCTGTTGTCGCCATTACTTCT 57.322 42.857 0.00 0.00 0.00 2.85
157 163 6.597672 TGAAGTTAATTATCTGTTGTCGCCAT 59.402 34.615 0.00 0.00 0.00 4.40
171 177 9.974980 GAAGAACCACCAAATTGAAGTTAATTA 57.025 29.630 0.00 0.00 30.47 1.40
172 178 7.931407 GGAAGAACCACCAAATTGAAGTTAATT 59.069 33.333 0.00 0.00 38.79 1.40
195 201 3.277962 GAGACCAGGTACTCGGGAA 57.722 57.895 0.00 0.00 34.60 3.97
221 227 3.265995 TCAGAACTAGGATTTTCACCCCC 59.734 47.826 0.00 0.00 0.00 5.40
243 249 2.677037 GCCAGGTATAAGCAAGTCGTGT 60.677 50.000 0.00 0.00 0.00 4.49
245 251 1.553248 TGCCAGGTATAAGCAAGTCGT 59.447 47.619 0.00 0.00 32.56 4.34
249 255 2.292267 CCACTGCCAGGTATAAGCAAG 58.708 52.381 0.00 0.00 35.79 4.01
257 263 1.128200 AATATCGCCACTGCCAGGTA 58.872 50.000 0.00 0.00 0.00 3.08
264 270 3.120338 ACGACACAAAAATATCGCCACTG 60.120 43.478 0.00 0.00 38.12 3.66
281 287 4.053469 TGTCTTCAACAAGATCACGACA 57.947 40.909 0.00 0.00 40.88 4.35
282 288 5.377358 CAATGTCTTCAACAAGATCACGAC 58.623 41.667 0.00 0.00 42.37 4.34
289 295 2.807967 CCGAGCAATGTCTTCAACAAGA 59.192 45.455 0.00 0.00 42.37 3.02
291 297 2.844946 TCCGAGCAATGTCTTCAACAA 58.155 42.857 0.00 0.00 42.37 2.83
301 307 4.887748 AGTCCAAGTATATCCGAGCAATG 58.112 43.478 0.00 0.00 0.00 2.82
315 321 4.792068 TCATCCTGAAAACAAGTCCAAGT 58.208 39.130 0.00 0.00 0.00 3.16
330 336 9.565213 GATTCTATGTTTTCAGTTTTCATCCTG 57.435 33.333 0.00 0.00 0.00 3.86
331 337 9.525826 AGATTCTATGTTTTCAGTTTTCATCCT 57.474 29.630 0.00 0.00 0.00 3.24
335 341 8.730680 GGCTAGATTCTATGTTTTCAGTTTTCA 58.269 33.333 0.00 0.00 0.00 2.69
336 342 8.951243 AGGCTAGATTCTATGTTTTCAGTTTTC 58.049 33.333 0.00 0.00 0.00 2.29
337 343 8.870075 AGGCTAGATTCTATGTTTTCAGTTTT 57.130 30.769 0.00 0.00 0.00 2.43
338 344 8.870075 AAGGCTAGATTCTATGTTTTCAGTTT 57.130 30.769 0.00 0.00 0.00 2.66
339 345 8.734386 CAAAGGCTAGATTCTATGTTTTCAGTT 58.266 33.333 0.00 0.00 0.00 3.16
340 346 7.337942 CCAAAGGCTAGATTCTATGTTTTCAGT 59.662 37.037 0.00 0.00 0.00 3.41
341 347 7.337942 ACCAAAGGCTAGATTCTATGTTTTCAG 59.662 37.037 0.00 0.00 0.00 3.02
360 366 0.965363 CCGGATCCAACCACCAAAGG 60.965 60.000 13.41 0.00 0.00 3.11
396 402 2.506438 CCTTCGAGGGAACGACGC 60.506 66.667 8.08 0.00 41.97 5.19
408 414 2.490328 ACACAACAACAATGCCTTCG 57.510 45.000 0.00 0.00 0.00 3.79
415 421 6.978080 GGATCAACAAACTACACAACAACAAT 59.022 34.615 0.00 0.00 0.00 2.71
419 425 4.339814 GGGGATCAACAAACTACACAACAA 59.660 41.667 0.00 0.00 0.00 2.83
440 504 4.391405 AAAGTGTGAGAAAAGCAAAGGG 57.609 40.909 0.00 0.00 0.00 3.95
442 506 9.693157 CAAAATAAAAGTGTGAGAAAAGCAAAG 57.307 29.630 0.00 0.00 0.00 2.77
445 509 9.515020 CTACAAAATAAAAGTGTGAGAAAAGCA 57.485 29.630 0.00 0.00 0.00 3.91
446 510 9.516314 ACTACAAAATAAAAGTGTGAGAAAAGC 57.484 29.630 0.00 0.00 0.00 3.51
477 541 5.633601 CGAAGCATACGGAAAATAGCTATCA 59.366 40.000 6.72 0.00 0.00 2.15
501 565 1.666054 CTTCTGGATGCCTTCTCAGC 58.334 55.000 0.00 0.00 0.00 4.26
512 576 4.870021 AATTAGGGTCAAGCTTCTGGAT 57.130 40.909 0.00 0.00 0.00 3.41
585 649 7.065803 GCAATATTGTTGTTCTGCTAGAAGGTA 59.934 37.037 16.61 0.00 34.42 3.08
727 791 3.251484 AGTCATGACTTCTTTCCCCTCA 58.749 45.455 22.89 0.00 38.83 3.86
813 955 4.858935 AGTTGGTGATTTTGACAATGACG 58.141 39.130 0.00 0.00 0.00 4.35
846 988 0.330941 TGAATGTGTATGCCAGCCCA 59.669 50.000 0.00 0.00 0.00 5.36
863 1010 1.794151 TTAGACCGGCGTTGTCGTGA 61.794 55.000 6.01 0.00 37.80 4.35
898 1045 2.202919 TCATCATGGCTGACGGCG 60.203 61.111 4.80 4.80 42.94 6.46
915 1062 2.641815 GCTATCTCCCTTCCATGGATGT 59.358 50.000 17.06 4.15 0.00 3.06
932 1079 2.478872 TAGAAGACCCTGCCTGCTAT 57.521 50.000 0.00 0.00 0.00 2.97
934 1081 2.478872 TATAGAAGACCCTGCCTGCT 57.521 50.000 0.00 0.00 0.00 4.24
935 1082 3.560636 TTTATAGAAGACCCTGCCTGC 57.439 47.619 0.00 0.00 0.00 4.85
936 1083 5.070981 TGAGATTTATAGAAGACCCTGCCTG 59.929 44.000 0.00 0.00 0.00 4.85
937 1084 5.219739 TGAGATTTATAGAAGACCCTGCCT 58.780 41.667 0.00 0.00 0.00 4.75
941 1088 8.317679 GCACATATGAGATTTATAGAAGACCCT 58.682 37.037 10.38 0.00 0.00 4.34
944 1091 8.655092 GCAGCACATATGAGATTTATAGAAGAC 58.345 37.037 10.38 0.00 0.00 3.01
948 1095 7.250032 AGGCAGCACATATGAGATTTATAGA 57.750 36.000 10.38 0.00 0.00 1.98
1040 1195 2.204461 TTGGCCCAGAAGTCGACGA 61.204 57.895 10.46 0.00 0.00 4.20
1065 1220 0.179048 CTATCAGAACCCGCATGCCA 60.179 55.000 13.15 0.00 0.00 4.92
1083 1238 4.148825 CCTAACTCGCGCAGGGCT 62.149 66.667 8.75 0.00 41.64 5.19
1086 1241 2.202932 ATGCCTAACTCGCGCAGG 60.203 61.111 8.75 7.37 35.66 4.85
1096 1251 2.488937 TGTACTCGAACGACATGCCTAA 59.511 45.455 0.00 0.00 0.00 2.69
1132 1287 0.610174 TCACTCTTCTTGCGGATGCT 59.390 50.000 0.00 0.00 43.34 3.79
1141 1296 1.071385 CAGCACCAGGTCACTCTTCTT 59.929 52.381 0.00 0.00 0.00 2.52
1145 1300 2.746359 GCAGCACCAGGTCACTCT 59.254 61.111 0.00 0.00 0.00 3.24
1239 1394 2.007608 CAGACCTCGTCGATGTACTCA 58.992 52.381 4.21 0.00 37.67 3.41
1272 1427 3.423154 GTTCCACCTGCTTCGGCG 61.423 66.667 0.00 0.00 45.37 6.46
1419 2726 7.568199 AGTAAATATTTTTAGCCGATGCAGT 57.432 32.000 5.91 0.00 41.13 4.40
1569 2876 8.778358 CACCTAGGTAAAATAATTCATCAGAGC 58.222 37.037 15.80 0.00 0.00 4.09
1745 3052 1.332686 CTCGATAACGGGATGACGACA 59.667 52.381 0.00 0.00 43.41 4.35
1781 3088 4.638421 AGATCAAACGTTCCTTGTTGTTCA 59.362 37.500 0.00 0.00 0.00 3.18
1795 3102 2.738846 CACTCCACCTCAAGATCAAACG 59.261 50.000 0.00 0.00 0.00 3.60
1933 3240 2.366590 TCGAGCACAATCTATGGCTCAT 59.633 45.455 12.31 0.00 45.24 2.90
2151 3468 2.902608 AGGCATATCGATTACCCCAGA 58.097 47.619 1.71 0.00 0.00 3.86
2205 3525 3.801114 AATTAATTGGGAGCTTTCCGC 57.199 42.857 0.00 0.00 39.57 5.54
2206 3526 4.334481 ACGTAATTAATTGGGAGCTTTCCG 59.666 41.667 11.05 1.09 0.00 4.30
2258 3578 7.759489 TGACTACCATTGAAGCAACTTATTT 57.241 32.000 0.00 0.00 0.00 1.40
2328 3661 5.753744 TGGACATCACAAAATAAACACGAC 58.246 37.500 0.00 0.00 0.00 4.34
2452 3785 6.341316 AGCACCGGACATATATTCATATGAC 58.659 40.000 9.46 5.41 44.70 3.06
2526 3861 5.804639 TGGCTTACATCTCAACAAGTGTAT 58.195 37.500 0.00 0.00 0.00 2.29
2530 3865 6.096846 AGTTTTTGGCTTACATCTCAACAAGT 59.903 34.615 0.00 0.00 0.00 3.16
2555 3890 5.222568 TGGGGGAAATAAATGGTTGGAAGTA 60.223 40.000 0.00 0.00 0.00 2.24
2562 3897 6.962902 TGTTAGAATGGGGGAAATAAATGGTT 59.037 34.615 0.00 0.00 0.00 3.67
2563 3898 6.382859 GTGTTAGAATGGGGGAAATAAATGGT 59.617 38.462 0.00 0.00 0.00 3.55
2586 3921 7.616103 TTTTGCATGTCTAAAACATTACGTG 57.384 32.000 0.00 0.00 46.73 4.49
2704 4040 1.227438 CCACCGGTTCGTTCACTGT 60.227 57.895 2.97 0.00 0.00 3.55
2708 4044 1.524165 CCAACCACCGGTTCGTTCA 60.524 57.895 2.97 0.00 43.05 3.18
2713 4049 0.538746 AACCATCCAACCACCGGTTC 60.539 55.000 2.97 0.00 43.05 3.62
2717 4053 0.825840 AACCAACCATCCAACCACCG 60.826 55.000 0.00 0.00 0.00 4.94
2719 4055 0.596082 CGAACCAACCATCCAACCAC 59.404 55.000 0.00 0.00 0.00 4.16
2752 4088 0.178990 GACTTGAACCTGGTGGGCTT 60.179 55.000 0.00 0.00 39.10 4.35
2766 4102 0.963962 AATGCTTGCACCAGGACTTG 59.036 50.000 0.00 0.00 0.00 3.16
2772 4108 5.063180 TCAGAAATAAATGCTTGCACCAG 57.937 39.130 0.00 0.00 0.00 4.00
2835 4171 3.104512 TCATAGTCAACGGGGATGTCTT 58.895 45.455 0.00 0.00 0.00 3.01
2842 4178 1.429148 GCGCTTCATAGTCAACGGGG 61.429 60.000 0.00 0.00 0.00 5.73
2846 4182 2.159517 CCAAAGGCGCTTCATAGTCAAC 60.160 50.000 7.64 0.00 0.00 3.18
2852 4188 1.003118 AGTCACCAAAGGCGCTTCATA 59.997 47.619 7.64 0.00 0.00 2.15
2854 4190 0.465460 AAGTCACCAAAGGCGCTTCA 60.465 50.000 7.64 0.00 0.00 3.02
2857 4193 0.751643 ACAAAGTCACCAAAGGCGCT 60.752 50.000 7.64 0.00 0.00 5.92
2858 4194 0.317854 GACAAAGTCACCAAAGGCGC 60.318 55.000 0.00 0.00 32.09 6.53
2874 4210 5.106594 CCGACATGTCATTTTGAGATTGACA 60.107 40.000 24.93 7.36 46.64 3.58


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

AutoCloner maintained by Alex Coulton.