Multiple sequence alignment - TraesCS2A01G217600

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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 TraesCS2A01G217600 chr2A 100.000 4382 0 0 1 4382 204888633 204884252 0.000000e+00 8093.0
1 TraesCS2A01G217600 chr2D 95.985 2615 93 8 1775 4382 190355617 190353008 0.000000e+00 4237.0
2 TraesCS2A01G217600 chr2D 95.082 793 37 1 367 1159 190362864 190362074 0.000000e+00 1247.0
3 TraesCS2A01G217600 chr2D 86.183 427 32 18 1217 1631 190361975 190361564 1.870000e-118 436.0
4 TraesCS2A01G217600 chr2D 97.778 45 1 0 1708 1752 190355647 190355603 1.310000e-10 78.7
5 TraesCS2A01G217600 chr2B 94.620 1933 79 16 1775 3683 247390892 247388961 0.000000e+00 2970.0
6 TraesCS2A01G217600 chr2B 94.264 802 41 2 367 1165 247392522 247391723 0.000000e+00 1221.0
7 TraesCS2A01G217600 chr2B 88.778 704 62 5 3695 4382 247388896 247388194 0.000000e+00 846.0
8 TraesCS2A01G217600 chr2B 86.000 500 44 14 1271 1752 247391369 247390878 3.020000e-141 512.0
9 TraesCS2A01G217600 chr1D 90.814 381 21 4 1 373 492536496 492536870 8.460000e-137 497.0
10 TraesCS2A01G217600 chr1D 90.566 371 21 8 1 363 481809684 481810048 3.070000e-131 479.0
11 TraesCS2A01G217600 chr1D 90.212 378 22 11 1 369 481811528 481811899 3.070000e-131 479.0
12 TraesCS2A01G217600 chr7D 91.105 371 19 8 1 363 192056820 192057184 1.420000e-134 490.0
13 TraesCS2A01G217600 chr5B 89.757 371 24 6 4 366 658840171 658839807 3.090000e-126 462.0
14 TraesCS2A01G217600 chr5B 88.978 372 25 9 4 366 658806192 658805828 3.110000e-121 446.0
15 TraesCS2A01G217600 chr5B 88.949 371 27 7 4 366 658875580 658875216 3.110000e-121 446.0
16 TraesCS2A01G217600 chr5B 89.101 367 26 9 8 366 685675581 685675221 1.120000e-120 444.0
17 TraesCS2A01G217600 chr5B 88.679 371 28 8 4 366 658857871 658857507 1.450000e-119 440.0


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 TraesCS2A01G217600 chr2A 204884252 204888633 4381 True 8093.00 8093 100.0000 1 4382 1 chr2A.!!$R1 4381
1 TraesCS2A01G217600 chr2D 190353008 190355647 2639 True 2157.85 4237 96.8815 1708 4382 2 chr2D.!!$R1 2674
2 TraesCS2A01G217600 chr2D 190361564 190362864 1300 True 841.50 1247 90.6325 367 1631 2 chr2D.!!$R2 1264
3 TraesCS2A01G217600 chr2B 247388194 247392522 4328 True 1387.25 2970 90.9155 367 4382 4 chr2B.!!$R1 4015
4 TraesCS2A01G217600 chr1D 481809684 481811899 2215 False 479.00 479 90.3890 1 369 2 chr1D.!!$F2 368

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
363 2214 0.447801 GCATGTCCACTCGCGATTTT 59.552 50.0 10.36 0.0 0.00 1.82 F
1331 3482 0.478507 ACTGTGCCTTTGGGTAGCTT 59.521 50.0 0.00 0.0 34.45 3.74 F
2426 4604 0.796312 CACTTGGCCGTGTGTCATAC 59.204 55.0 16.85 0.0 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 3545 0.179040 TTCCCCGTGTTCTGTTGGTC 60.179 55.000 0.00 0.0 0.0 4.02 R
3268 5450 0.034089 GGTTGCCTTGGCTCTGGTAT 60.034 55.000 13.18 0.0 0.0 2.73 R
3909 6155 2.612721 GCCGAATTCACAGCCCAAATTT 60.613 45.455 6.22 0.0 0.0 1.82 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
39 40 1.662629 CTCATCACGTGTGCCTTCATC 59.337 52.381 16.51 0.00 0.00 2.92
60 61 3.262151 TCGTGTCCCTTCCAACATAATCA 59.738 43.478 0.00 0.00 0.00 2.57
74 75 6.350906 CAACATAATCAAAAGGCCCATGATT 58.649 36.000 23.70 23.70 43.91 2.57
110 111 3.610040 TCACTTGAGTTGCGGTATCAT 57.390 42.857 0.00 0.00 0.00 2.45
158 159 3.849645 GCCAGATCGTTGAATTATTGCCG 60.850 47.826 0.00 0.00 0.00 5.69
187 188 2.880890 GCTAGGTGTGGGATTAATGCAG 59.119 50.000 9.34 0.00 0.00 4.41
188 189 2.442236 AGGTGTGGGATTAATGCAGG 57.558 50.000 9.34 0.00 0.00 4.85
189 190 1.063717 AGGTGTGGGATTAATGCAGGG 60.064 52.381 9.34 0.00 0.00 4.45
235 236 4.359971 GCATGTGTCAGATGCAAATACA 57.640 40.909 25.63 0.00 44.74 2.29
236 237 4.100529 GCATGTGTCAGATGCAAATACAC 58.899 43.478 25.63 14.51 44.74 2.90
245 246 3.618594 AGATGCAAATACACACACGCTAG 59.381 43.478 0.00 0.00 0.00 3.42
260 261 3.058155 CACGCTAGACCGAATGCTATACT 60.058 47.826 0.00 0.00 0.00 2.12
267 268 2.228343 ACCGAATGCTATACTACGAGGC 59.772 50.000 0.00 0.00 0.00 4.70
283 284 2.288030 CGAGGCGAATTCCTTATACGGT 60.288 50.000 0.00 0.00 36.38 4.83
285 286 2.696707 AGGCGAATTCCTTATACGGTCA 59.303 45.455 0.00 0.00 30.82 4.02
292 293 3.393426 TCCTTATACGGTCAGAGGGTT 57.607 47.619 0.00 0.00 0.00 4.11
293 294 4.524802 TCCTTATACGGTCAGAGGGTTA 57.475 45.455 0.00 0.00 0.00 2.85
363 2214 0.447801 GCATGTCCACTCGCGATTTT 59.552 50.000 10.36 0.00 0.00 1.82
380 2231 5.783111 CGATTTTTCCATTTTTCAGTCCCT 58.217 37.500 0.00 0.00 0.00 4.20
381 2232 5.634859 CGATTTTTCCATTTTTCAGTCCCTG 59.365 40.000 0.00 0.00 0.00 4.45
506 2357 1.228429 GCCCAAACAGCACCTACCA 60.228 57.895 0.00 0.00 0.00 3.25
508 2359 0.609131 CCCAAACAGCACCTACCAGG 60.609 60.000 0.00 0.00 42.49 4.45
687 2541 0.602638 TCGGCAAGACAATCAACGCT 60.603 50.000 0.00 0.00 0.00 5.07
738 2592 1.080093 CAAGGACGTGGCGCTCTAA 60.080 57.895 7.64 0.00 0.00 2.10
831 2685 1.966451 CGGCACCAACCTGAACCTC 60.966 63.158 0.00 0.00 0.00 3.85
891 2745 1.808133 GCCAAGCTAACGAGATCCCTG 60.808 57.143 0.00 0.00 0.00 4.45
1131 2985 1.005867 GTACGAGACCGGCAACCAA 60.006 57.895 0.00 0.00 40.78 3.67
1146 3000 3.119955 GCAACCAATTCTTTACGGAGACC 60.120 47.826 0.00 0.00 0.00 3.85
1177 3156 5.080068 GCAAGTCGTTGTACAATTTAGAGC 58.920 41.667 12.26 9.08 35.92 4.09
1184 3163 6.480651 TCGTTGTACAATTTAGAGCACAAGAA 59.519 34.615 12.26 0.00 0.00 2.52
1193 3172 7.807977 ATTTAGAGCACAAGAAAGAAACTGA 57.192 32.000 0.00 0.00 0.00 3.41
1235 3378 9.558396 AATTCCATTTTTGTCTTGAGCATTAAA 57.442 25.926 0.00 0.00 0.00 1.52
1289 3432 7.907389 ACTCAAGAGTTGGACTATCAACAATA 58.093 34.615 9.85 0.00 46.74 1.90
1291 3434 9.388506 CTCAAGAGTTGGACTATCAACAATAAT 57.611 33.333 9.85 0.00 46.74 1.28
1318 3469 6.734104 AGATCATAAGACTGAAAACTGTGC 57.266 37.500 0.00 0.00 0.00 4.57
1319 3470 5.645497 AGATCATAAGACTGAAAACTGTGCC 59.355 40.000 0.00 0.00 0.00 5.01
1321 3472 5.376625 TCATAAGACTGAAAACTGTGCCTT 58.623 37.500 0.00 0.00 0.00 4.35
1331 3482 0.478507 ACTGTGCCTTTGGGTAGCTT 59.521 50.000 0.00 0.00 34.45 3.74
1332 3483 1.702957 ACTGTGCCTTTGGGTAGCTTA 59.297 47.619 0.00 0.00 34.45 3.09
1336 3487 4.924625 TGTGCCTTTGGGTAGCTTATAAA 58.075 39.130 0.00 0.00 34.45 1.40
1369 3520 9.672673 AAGTAAGACATCATACAGTTTTGCTAT 57.327 29.630 0.00 0.00 27.87 2.97
1370 3521 9.672673 AGTAAGACATCATACAGTTTTGCTATT 57.327 29.630 0.00 0.00 0.00 1.73
1373 3524 9.630098 AAGACATCATACAGTTTTGCTATTTTG 57.370 29.630 0.00 0.00 0.00 2.44
1374 3525 7.756722 AGACATCATACAGTTTTGCTATTTTGC 59.243 33.333 0.00 0.00 0.00 3.68
1376 3527 8.739039 ACATCATACAGTTTTGCTATTTTGCTA 58.261 29.630 0.00 0.00 0.00 3.49
1377 3528 9.229784 CATCATACAGTTTTGCTATTTTGCTAG 57.770 33.333 0.00 0.00 0.00 3.42
1378 3529 8.560355 TCATACAGTTTTGCTATTTTGCTAGA 57.440 30.769 0.00 0.00 0.00 2.43
1383 3534 8.960591 ACAGTTTTGCTATTTTGCTAGATATGT 58.039 29.630 0.00 0.00 0.00 2.29
1384 3535 9.443283 CAGTTTTGCTATTTTGCTAGATATGTC 57.557 33.333 0.00 0.00 0.00 3.06
1396 3548 7.661536 TGCTAGATATGTCTATAATGGGACC 57.338 40.000 0.00 0.00 36.40 4.46
1410 3562 1.599797 GGACCAACAGAACACGGGG 60.600 63.158 0.00 0.00 0.00 5.73
1414 3566 1.700739 ACCAACAGAACACGGGGAATA 59.299 47.619 0.00 0.00 0.00 1.75
1416 3568 2.290071 CCAACAGAACACGGGGAATAGT 60.290 50.000 0.00 0.00 0.00 2.12
1444 3596 8.490355 CAAAGGTTCAGTTTGCTTAATCAAATC 58.510 33.333 7.66 2.97 38.12 2.17
1590 3759 2.921121 TCGTTCATTCGCTACATGTCAC 59.079 45.455 0.00 0.00 0.00 3.67
1705 3874 5.874810 TGCTTTTCTGTGTCCTATACATCAC 59.125 40.000 0.00 0.00 41.10 3.06
1746 3915 7.775120 AGGTAAGCAGTTCAATAAATTCCATG 58.225 34.615 0.00 0.00 0.00 3.66
1747 3916 6.476706 GGTAAGCAGTTCAATAAATTCCATGC 59.523 38.462 0.00 0.00 0.00 4.06
1748 3917 4.675510 AGCAGTTCAATAAATTCCATGCG 58.324 39.130 0.00 0.00 36.31 4.73
1749 3918 3.243643 GCAGTTCAATAAATTCCATGCGC 59.756 43.478 0.00 0.00 0.00 6.09
1750 3919 4.675510 CAGTTCAATAAATTCCATGCGCT 58.324 39.130 9.73 0.00 0.00 5.92
1751 3920 5.733091 GCAGTTCAATAAATTCCATGCGCTA 60.733 40.000 9.73 0.00 0.00 4.26
1752 3921 6.441274 CAGTTCAATAAATTCCATGCGCTAT 58.559 36.000 9.73 0.00 0.00 2.97
1753 3922 6.580041 CAGTTCAATAAATTCCATGCGCTATC 59.420 38.462 9.73 0.00 0.00 2.08
1754 3923 6.488006 AGTTCAATAAATTCCATGCGCTATCT 59.512 34.615 9.73 0.00 0.00 1.98
1755 3924 6.245115 TCAATAAATTCCATGCGCTATCTG 57.755 37.500 9.73 0.61 0.00 2.90
1756 3925 4.691860 ATAAATTCCATGCGCTATCTGC 57.308 40.909 9.73 0.00 38.57 4.26
1758 3927 1.971481 ATTCCATGCGCTATCTGCAA 58.029 45.000 9.73 0.00 46.87 4.08
1759 3928 1.748950 TTCCATGCGCTATCTGCAAA 58.251 45.000 9.73 0.00 46.87 3.68
1760 3929 1.748950 TCCATGCGCTATCTGCAAAA 58.251 45.000 9.73 0.00 46.87 2.44
1761 3930 2.090760 TCCATGCGCTATCTGCAAAAA 58.909 42.857 9.73 0.00 46.87 1.94
2006 4175 2.613223 GCTACAGACAACTTCTCACCCC 60.613 54.545 0.00 0.00 28.96 4.95
2028 4197 3.243068 CGCAAAATATTAGGACAGGGTGC 60.243 47.826 0.00 0.00 0.00 5.01
2055 4224 4.344390 TGGGCCCGTTTACAAAGTATTTTT 59.656 37.500 19.37 0.00 35.03 1.94
2056 4225 4.925054 GGGCCCGTTTACAAAGTATTTTTC 59.075 41.667 5.69 0.00 35.03 2.29
2057 4226 4.925054 GGCCCGTTTACAAAGTATTTTTCC 59.075 41.667 0.00 0.00 35.03 3.13
2121 4291 6.647067 CGAACCATTCTAAGTTATGGAGGATC 59.353 42.308 9.67 2.30 43.25 3.36
2288 4458 2.104967 CTGGGTTGTTGCATCCATGAT 58.895 47.619 0.00 0.00 0.00 2.45
2370 4544 8.688747 TTTCGGTAGGTTTTTGGAGTAATTTA 57.311 30.769 0.00 0.00 0.00 1.40
2426 4604 0.796312 CACTTGGCCGTGTGTCATAC 59.204 55.000 16.85 0.00 0.00 2.39
2567 4745 5.659971 AGGGATCTGAAAGCAAGCAATATTT 59.340 36.000 0.00 0.00 0.00 1.40
2626 4804 1.620323 GGCATGGCAAGGATATTTCCC 59.380 52.381 15.47 0.00 43.76 3.97
2680 4858 6.598064 GGCTTGTTGGAACATAGTAAGTACAT 59.402 38.462 0.00 0.00 39.30 2.29
2885 5063 5.068198 GCAGGATTTCAGCATTATGGAGAAA 59.932 40.000 0.00 0.00 33.33 2.52
2971 5149 7.276218 TCTCGATTTTTCATTTCCATGAATTGC 59.724 33.333 0.00 0.00 46.68 3.56
3098 5280 1.466856 TTTCAGGCATGGCAGATGTC 58.533 50.000 22.64 0.00 0.00 3.06
3110 5292 2.416893 GGCAGATGTCGGAAGAAGAAAC 59.583 50.000 0.00 0.00 45.01 2.78
3189 5371 5.692115 TGAAATATCTCAGGTTGGCACTA 57.308 39.130 0.00 0.00 0.00 2.74
3324 5506 6.859112 ACCAGAGTAGATGTGTCAGTAAAT 57.141 37.500 0.00 0.00 0.00 1.40
3623 5815 1.270839 TGGAACTAGCACAAGACCTGC 60.271 52.381 0.00 0.00 34.63 4.85
3669 5862 2.100916 CCACCAACTATCTACCGTCAGG 59.899 54.545 0.00 0.00 45.13 3.86
3737 5983 3.952967 GAGAAGGTATTCTACACTCCCGT 59.047 47.826 0.00 0.00 45.98 5.28
3928 6174 3.911868 TCAAATTTGGGCTGTGAATTCG 58.088 40.909 17.90 0.00 0.00 3.34
3950 6196 4.260784 CGGCTCACTAACAATAAGAATGCC 60.261 45.833 0.00 0.00 0.00 4.40
4052 6306 7.945033 TGAGATTTTGTTCATAAGTTTTGGC 57.055 32.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.461693 GTGATGAGCAGCCTCTCCAC 60.462 60.000 0.00 1.52 38.93 4.02
39 40 3.605634 TGATTATGTTGGAAGGGACACG 58.394 45.455 0.00 0.00 0.00 4.49
60 61 2.034124 CCGATGAATCATGGGCCTTTT 58.966 47.619 11.27 0.00 33.35 2.27
74 75 4.122046 CAAGTGATACAATGCTCCGATGA 58.878 43.478 0.00 0.00 0.00 2.92
110 111 1.134128 ACATGCGGGCAACATATCTGA 60.134 47.619 0.00 0.00 39.74 3.27
138 139 4.536364 ACGGCAATAATTCAACGATCTG 57.464 40.909 0.00 0.00 0.00 2.90
158 159 1.675641 CCACACCTAGCAGCCCAAC 60.676 63.158 0.00 0.00 0.00 3.77
164 165 2.880890 GCATTAATCCCACACCTAGCAG 59.119 50.000 0.00 0.00 0.00 4.24
167 168 3.480470 CCTGCATTAATCCCACACCTAG 58.520 50.000 0.00 0.00 0.00 3.02
169 170 1.063717 CCCTGCATTAATCCCACACCT 60.064 52.381 0.00 0.00 0.00 4.00
225 226 3.370978 GTCTAGCGTGTGTGTATTTGCAT 59.629 43.478 0.00 0.00 0.00 3.96
234 235 0.992072 CATTCGGTCTAGCGTGTGTG 59.008 55.000 1.14 0.00 0.00 3.82
235 236 0.736325 GCATTCGGTCTAGCGTGTGT 60.736 55.000 1.14 0.00 0.00 3.72
236 237 0.458543 AGCATTCGGTCTAGCGTGTG 60.459 55.000 1.14 3.57 0.00 3.82
245 246 3.670091 GCCTCGTAGTATAGCATTCGGTC 60.670 52.174 0.00 0.00 0.00 4.79
260 261 3.058016 CCGTATAAGGAATTCGCCTCGTA 60.058 47.826 0.00 0.00 37.26 3.43
267 268 4.547532 CCTCTGACCGTATAAGGAATTCG 58.452 47.826 12.02 0.00 34.73 3.34
283 284 3.678806 CGTGCAGCTTTATAACCCTCTGA 60.679 47.826 0.00 0.00 0.00 3.27
285 286 2.906354 CGTGCAGCTTTATAACCCTCT 58.094 47.619 0.00 0.00 0.00 3.69
317 326 2.776072 CGCGTCCGAAATCCACAC 59.224 61.111 0.00 0.00 36.29 3.82
381 2232 4.295119 ATCGCACGGCCGGGATAC 62.295 66.667 36.21 13.44 36.85 2.24
450 2301 3.426568 GCGCAGAACAGCTGGTCC 61.427 66.667 28.05 12.90 45.03 4.46
470 2321 1.219522 GCTGTACTTGTCGTTGGCGT 61.220 55.000 0.00 0.00 39.49 5.68
479 2330 1.318576 GCTGTTTGGGCTGTACTTGT 58.681 50.000 0.00 0.00 0.00 3.16
508 2359 1.369321 CGAGGGATCTAAGGCTGGC 59.631 63.158 0.00 0.00 0.00 4.85
583 2434 4.097361 GACCTTGTCGGAGCCCCC 62.097 72.222 0.00 0.00 36.31 5.40
584 2435 1.684734 TAGACCTTGTCGGAGCCCC 60.685 63.158 0.00 0.00 37.67 5.80
674 2528 1.151668 GCTGTCAGCGTTGATTGTCT 58.848 50.000 9.53 0.00 35.39 3.41
678 2532 2.247790 GGTGCTGTCAGCGTTGATT 58.752 52.632 19.68 0.00 46.26 2.57
846 2700 1.583967 CTCGTCGAACTGCCTAGCG 60.584 63.158 0.00 0.00 0.00 4.26
1127 2981 2.968675 CGGTCTCCGTAAAGAATTGGT 58.031 47.619 0.00 0.00 42.73 3.67
1160 3044 6.223138 TCTTGTGCTCTAAATTGTACAACG 57.777 37.500 11.22 0.20 34.76 4.10
1210 3189 9.729281 ATTTAATGCTCAAGACAAAAATGGAAT 57.271 25.926 0.00 0.00 0.00 3.01
1254 3397 6.438741 AGTCCAACTCTTGAGTCTGATGATAA 59.561 38.462 3.58 0.00 0.00 1.75
1255 3398 5.954752 AGTCCAACTCTTGAGTCTGATGATA 59.045 40.000 3.58 0.00 0.00 2.15
1256 3399 4.776837 AGTCCAACTCTTGAGTCTGATGAT 59.223 41.667 3.58 0.00 0.00 2.45
1259 3402 5.954752 TGATAGTCCAACTCTTGAGTCTGAT 59.045 40.000 3.58 0.00 0.00 2.90
1260 3403 5.325239 TGATAGTCCAACTCTTGAGTCTGA 58.675 41.667 3.58 1.57 0.00 3.27
1261 3404 5.651387 TGATAGTCCAACTCTTGAGTCTG 57.349 43.478 3.58 5.21 0.00 3.51
1262 3405 5.540337 TGTTGATAGTCCAACTCTTGAGTCT 59.460 40.000 3.58 0.07 44.87 3.24
1263 3406 5.784177 TGTTGATAGTCCAACTCTTGAGTC 58.216 41.667 3.58 0.00 44.87 3.36
1264 3407 5.808366 TGTTGATAGTCCAACTCTTGAGT 57.192 39.130 0.00 0.00 44.87 3.41
1265 3408 8.777865 TTATTGTTGATAGTCCAACTCTTGAG 57.222 34.615 0.00 0.00 44.87 3.02
1318 3469 9.936759 TTTTCATTTTTATAAGCTACCCAAAGG 57.063 29.630 0.00 0.00 40.04 3.11
1352 3503 9.177608 TCTAGCAAAATAGCAAAACTGTATGAT 57.822 29.630 0.00 0.00 36.85 2.45
1353 3504 8.560355 TCTAGCAAAATAGCAAAACTGTATGA 57.440 30.769 0.00 0.00 36.85 2.15
1358 3509 9.443283 GACATATCTAGCAAAATAGCAAAACTG 57.557 33.333 0.00 0.00 36.85 3.16
1369 3520 9.944376 GTCCCATTATAGACATATCTAGCAAAA 57.056 33.333 0.00 0.00 40.84 2.44
1370 3521 8.540388 GGTCCCATTATAGACATATCTAGCAAA 58.460 37.037 0.00 0.00 40.84 3.68
1372 3523 7.189087 TGGTCCCATTATAGACATATCTAGCA 58.811 38.462 0.00 0.00 40.84 3.49
1373 3524 7.661536 TGGTCCCATTATAGACATATCTAGC 57.338 40.000 0.00 0.00 40.84 3.42
1374 3525 9.035890 TGTTGGTCCCATTATAGACATATCTAG 57.964 37.037 0.00 0.00 40.84 2.43
1376 3527 7.734865 TCTGTTGGTCCCATTATAGACATATCT 59.265 37.037 0.00 0.00 39.15 1.98
1377 3528 7.907389 TCTGTTGGTCCCATTATAGACATATC 58.093 38.462 0.00 0.00 34.58 1.63
1378 3529 7.872061 TCTGTTGGTCCCATTATAGACATAT 57.128 36.000 0.00 0.00 34.58 1.78
1380 3531 6.069673 TGTTCTGTTGGTCCCATTATAGACAT 60.070 38.462 0.00 0.00 34.58 3.06
1381 3532 5.249622 TGTTCTGTTGGTCCCATTATAGACA 59.750 40.000 0.00 0.00 34.58 3.41
1382 3533 5.585047 GTGTTCTGTTGGTCCCATTATAGAC 59.415 44.000 0.00 0.00 0.00 2.59
1383 3534 5.625886 CGTGTTCTGTTGGTCCCATTATAGA 60.626 44.000 0.00 0.00 0.00 1.98
1384 3535 4.570772 CGTGTTCTGTTGGTCCCATTATAG 59.429 45.833 0.00 0.00 0.00 1.31
1393 3545 0.179040 TTCCCCGTGTTCTGTTGGTC 60.179 55.000 0.00 0.00 0.00 4.02
1396 3548 3.053831 ACTATTCCCCGTGTTCTGTTG 57.946 47.619 0.00 0.00 0.00 3.33
1410 3562 7.203255 AGCAAACTGAACCTTTGTACTATTC 57.797 36.000 0.00 0.00 32.18 1.75
1414 3566 7.284489 TGATTAAGCAAACTGAACCTTTGTACT 59.716 33.333 0.00 0.00 32.18 2.73
1416 3568 7.575414 TGATTAAGCAAACTGAACCTTTGTA 57.425 32.000 0.00 0.00 32.18 2.41
1444 3596 3.056749 GCTCCTTCCAGTATATGTACCCG 60.057 52.174 0.00 0.00 0.00 5.28
1516 3670 7.826744 AGCTCTTTCATACTTTTAGAAGGGAAG 59.173 37.037 0.00 0.00 37.19 3.46
1590 3759 6.263842 TGCCCTGAATATTGCAAGAGAATAAG 59.736 38.462 4.94 0.00 0.00 1.73
1705 3874 5.236478 TGCTTACCTCTTTTTCTTCGTCTTG 59.764 40.000 0.00 0.00 0.00 3.02
1773 3942 5.518848 TCATCATTAGCGCATGGATTTTT 57.481 34.783 11.47 0.00 0.00 1.94
1774 3943 5.717078 ATCATCATTAGCGCATGGATTTT 57.283 34.783 11.47 0.00 0.00 1.82
1775 3944 5.942236 ACTATCATCATTAGCGCATGGATTT 59.058 36.000 11.47 0.14 0.00 2.17
1776 3945 5.353400 CACTATCATCATTAGCGCATGGATT 59.647 40.000 11.47 0.00 0.00 3.01
1777 3946 4.874396 CACTATCATCATTAGCGCATGGAT 59.126 41.667 11.47 7.36 0.00 3.41
1778 3947 4.248058 CACTATCATCATTAGCGCATGGA 58.752 43.478 11.47 1.18 0.00 3.41
1779 3948 3.373130 CCACTATCATCATTAGCGCATGG 59.627 47.826 11.47 0.00 0.00 3.66
1780 3949 3.181513 GCCACTATCATCATTAGCGCATG 60.182 47.826 11.47 5.65 0.00 4.06
1781 3950 3.005554 GCCACTATCATCATTAGCGCAT 58.994 45.455 11.47 0.00 0.00 4.73
1782 3951 2.224257 TGCCACTATCATCATTAGCGCA 60.224 45.455 11.47 0.00 0.00 6.09
1901 4070 5.226194 AGCCTCAGGATTTCATCTATGTC 57.774 43.478 0.00 0.00 0.00 3.06
2006 4175 3.243068 GCACCCTGTCCTAATATTTTGCG 60.243 47.826 0.00 0.00 0.00 4.85
2028 4197 1.000394 CTTTGTAAACGGGCCCAAAGG 60.000 52.381 24.92 7.89 39.87 3.11
2055 4224 9.839817 TTATTGAGGAAATATGAATACAACGGA 57.160 29.630 0.00 0.00 30.74 4.69
2096 4265 5.914033 TCCTCCATAACTTAGAATGGTTCG 58.086 41.667 14.50 7.57 42.77 3.95
2098 4267 6.099845 ACGATCCTCCATAACTTAGAATGGTT 59.900 38.462 14.50 0.00 42.77 3.67
2114 4284 4.142403 TGCAAAAATCATGAACGATCCTCC 60.142 41.667 0.00 0.00 0.00 4.30
2121 4291 3.574284 TCCCTGCAAAAATCATGAACG 57.426 42.857 0.00 0.00 0.00 3.95
2370 4544 4.079212 AGGGGCATACAATTGGACATTAGT 60.079 41.667 10.83 0.00 0.00 2.24
2378 4552 2.442236 ACAGAGGGGCATACAATTGG 57.558 50.000 10.83 0.00 0.00 3.16
2426 4604 2.089980 CCTCCTGTTTGGATCTGCAAG 58.910 52.381 0.00 0.00 45.16 4.01
2482 4660 0.553333 GCCCTTGGGCTATTCCTTCT 59.447 55.000 22.47 0.00 34.39 2.85
2567 4745 6.600882 AGGATTTAACTCGGAGTCTAACAA 57.399 37.500 11.71 1.03 0.00 2.83
2626 4804 4.572985 TTTTGTTTGAGTGGCATCTGAG 57.427 40.909 0.00 0.00 0.00 3.35
2705 4883 6.019108 AGAAGGAAAATGCTTGGGTAGAAAT 58.981 36.000 0.00 0.00 0.00 2.17
2971 5149 3.511540 GGGAAAGAATGAAAAGACCCCTG 59.488 47.826 0.00 0.00 0.00 4.45
3050 5232 6.313411 CGGTCCTTACATAAATTTGACGGTAA 59.687 38.462 0.00 3.83 0.00 2.85
3098 5280 2.749076 TCATGCCATGTTTCTTCTTCCG 59.251 45.455 4.31 0.00 0.00 4.30
3110 5292 6.928492 TGATTGATCAATGAATTCATGCCATG 59.072 34.615 25.37 15.23 36.56 3.66
3189 5371 4.644685 ACTGCTTTTACTTGGACACACATT 59.355 37.500 0.00 0.00 0.00 2.71
3268 5450 0.034089 GGTTGCCTTGGCTCTGGTAT 60.034 55.000 13.18 0.00 0.00 2.73
3324 5506 9.134055 TCATTTCTGGTGCATGATAAATTGATA 57.866 29.630 0.00 0.00 0.00 2.15
3669 5862 3.460857 AGATATGTCTCAAAGGACGGC 57.539 47.619 0.00 0.00 38.91 5.68
3737 5983 7.979786 ATGAGATTTCTAGAGTTGGGAGTAA 57.020 36.000 0.00 0.00 0.00 2.24
3854 6100 4.765281 TTGTTTCTAGACGTGTGTTTCG 57.235 40.909 0.00 0.00 0.00 3.46
3909 6155 2.612721 GCCGAATTCACAGCCCAAATTT 60.613 45.455 6.22 0.00 0.00 1.82
3928 6174 4.260784 CGGCATTCTTATTGTTAGTGAGCC 60.261 45.833 0.00 0.00 0.00 4.70
4061 6315 3.634910 GCTCCCGAAAATTTTGGCCTATA 59.365 43.478 8.47 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.