Multiple sequence alignment - TraesCS6A01G070700

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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 TraesCS6A01G070700 chr6A 100.000 3885 0 0 934 4818 38550513 38554397 0.000000e+00 7175
1 TraesCS6A01G070700 chr6A 100.000 581 0 0 1 581 38549580 38550160 0.000000e+00 1074
2 TraesCS6A01G070700 chr6B 94.699 3924 149 39 937 4818 71148011 71151917 0.000000e+00 6039
3 TraesCS6A01G070700 chr6B 89.661 590 47 9 1 581 71146731 71147315 0.000000e+00 739
4 TraesCS6A01G070700 chr6B 85.714 133 19 0 16 148 71145654 71145786 1.810000e-29 141
5 TraesCS6A01G070700 chr6D 94.609 3821 132 39 934 4702 34394913 34398711 0.000000e+00 5847
6 TraesCS6A01G070700 chr6D 96.020 201 5 2 273 471 34394363 34394562 1.670000e-84 324
7 TraesCS6A01G070700 chr2B 81.508 557 63 20 2895 3441 378049768 378049242 5.770000e-114 422
8 TraesCS6A01G070700 chr1A 87.903 124 14 1 1000 1122 514553874 514553751 1.400000e-30 145
9 TraesCS6A01G070700 chr1B 91.262 103 9 0 1000 1102 564165507 564165405 1.810000e-29 141


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 TraesCS6A01G070700 chr6A 38549580 38554397 4817 False 4124.500000 7175 100.000000 1 4818 2 chr6A.!!$F1 4817
1 TraesCS6A01G070700 chr6B 71145654 71151917 6263 False 2306.333333 6039 90.024667 1 4818 3 chr6B.!!$F1 4817
2 TraesCS6A01G070700 chr6D 34394363 34398711 4348 False 3085.500000 5847 95.314500 273 4702 2 chr6D.!!$F1 4429
3 TraesCS6A01G070700 chr2B 378049242 378049768 526 True 422.000000 422 81.508000 2895 3441 1 chr2B.!!$R1 546

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
98 1176 0.109319 CGCGCAATTAAACTGGCCTT 60.109 50.0 8.75 0.0 0.0 4.35 F
1427 2895 0.248621 GCGAAATGGGGATCTTTGCG 60.249 55.0 0.00 0.0 35.4 4.85 F
2407 3883 0.457851 TTGGTTTGTTTCTGGTGCCG 59.542 50.0 0.00 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 3243 1.689959 GAAGCATGCGTGAAAAGGTG 58.310 50.0 11.93 0.0 0.00 4.00 R
2512 3988 0.622665 AGCTGGCCTTGCTGATAAGT 59.377 50.0 20.14 0.0 39.56 2.24 R
4328 5842 1.109323 AACAGGCAGGTCAAAGCACC 61.109 55.0 0.00 0.0 36.58 5.01 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
28 656 2.401351 GATACACGGCGGATTCTTACC 58.599 52.381 13.24 0.00 0.00 2.85
37 665 1.568606 GGATTCTTACCGTTCGCCTC 58.431 55.000 0.00 0.00 0.00 4.70
64 692 0.706729 GCGTTACAACCTCTTCGACG 59.293 55.000 0.00 0.00 0.00 5.12
65 693 1.334054 CGTTACAACCTCTTCGACGG 58.666 55.000 0.00 0.00 0.00 4.79
81 709 2.583593 GGCACGTGAGATCTCCGC 60.584 66.667 22.23 18.76 0.00 5.54
82 710 2.951745 GCACGTGAGATCTCCGCG 60.952 66.667 22.23 25.40 34.69 6.46
87 1165 1.148157 CGTGAGATCTCCGCGCAATT 61.148 55.000 20.03 0.00 0.00 2.32
90 1168 2.607635 GTGAGATCTCCGCGCAATTAAA 59.392 45.455 20.03 0.00 0.00 1.52
98 1176 0.109319 CGCGCAATTAAACTGGCCTT 60.109 50.000 8.75 0.00 0.00 4.35
112 1190 3.870606 CCTTACTGGCGACCAACG 58.129 61.111 0.00 0.00 45.66 4.10
136 1214 5.129368 AGCACAACCCCTACATTTATGAT 57.871 39.130 0.00 0.00 0.00 2.45
147 1225 8.321353 CCCCTACATTTATGATGATACAGCTAA 58.679 37.037 0.00 0.00 0.00 3.09
149 1227 9.935241 CCTACATTTATGATGATACAGCTAACT 57.065 33.333 0.00 0.00 0.00 2.24
155 1233 8.706322 TTATGATGATACAGCTAACTCTACCA 57.294 34.615 0.00 0.00 0.00 3.25
156 1234 7.603180 ATGATGATACAGCTAACTCTACCAA 57.397 36.000 0.00 0.00 0.00 3.67
163 1241 5.269991 ACAGCTAACTCTACCAAGGATACA 58.730 41.667 0.00 0.00 41.41 2.29
166 1244 4.337555 GCTAACTCTACCAAGGATACACGA 59.662 45.833 0.00 0.00 41.41 4.35
179 1257 4.899457 AGGATACACGATGGATTCTTACCA 59.101 41.667 0.00 0.00 39.87 3.25
195 1273 1.301244 CCATCAGCCTCGGGAATCG 60.301 63.158 0.00 0.00 40.90 3.34
197 1275 1.457643 ATCAGCCTCGGGAATCGGA 60.458 57.895 0.00 0.00 39.77 4.55
206 1284 3.305471 CCTCGGGAATCGGACTAGAAATC 60.305 52.174 0.00 0.00 39.77 2.17
212 1290 5.213675 GGAATCGGACTAGAAATCTACACG 58.786 45.833 0.00 0.00 0.00 4.49
229 1307 1.518102 CACGCAATCAACTGTTTGCAC 59.482 47.619 19.97 0.00 45.87 4.57
233 1311 3.308530 GCAATCAACTGTTTGCACTACC 58.691 45.455 16.81 0.00 45.27 3.18
247 1325 3.194968 TGCACTACCTAGCCAGTAAGAAC 59.805 47.826 0.00 0.00 0.00 3.01
262 1340 9.623000 GCCAGTAAGAACTTTTATATTTCCCTA 57.377 33.333 0.00 0.00 31.97 3.53
350 1436 2.591715 GCACGCGGGATTAGCCAT 60.592 61.111 15.48 0.00 38.95 4.40
478 1564 3.566210 CACCCCACCCACCGTTCT 61.566 66.667 0.00 0.00 0.00 3.01
479 1565 3.246880 ACCCCACCCACCGTTCTC 61.247 66.667 0.00 0.00 0.00 2.87
540 1650 2.507944 CAGGCTAAGCGGAGGCAT 59.492 61.111 15.18 0.00 44.29 4.40
1110 2562 3.455469 CCCACCGTACGTCCCTCC 61.455 72.222 15.21 0.00 0.00 4.30
1123 2575 2.623502 CGTCCCTCCCTCTCTTCCTTTA 60.624 54.545 0.00 0.00 0.00 1.85
1124 2576 3.659841 GTCCCTCCCTCTCTTCCTTTAT 58.340 50.000 0.00 0.00 0.00 1.40
1125 2577 4.041464 GTCCCTCCCTCTCTTCCTTTATT 58.959 47.826 0.00 0.00 0.00 1.40
1126 2578 4.475381 GTCCCTCCCTCTCTTCCTTTATTT 59.525 45.833 0.00 0.00 0.00 1.40
1247 2715 4.619973 TGGTTGATTGATTCTTTGTGTGC 58.380 39.130 0.00 0.00 0.00 4.57
1275 2743 1.632622 CCTAATTAGGGGGTGGGGGAA 60.633 57.143 22.09 0.00 39.86 3.97
1397 2865 1.344065 TTTCTCGTCTAGGGTTGCCA 58.656 50.000 0.00 0.00 0.00 4.92
1400 2868 0.608640 CTCGTCTAGGGTTGCCAGTT 59.391 55.000 0.00 0.00 0.00 3.16
1401 2869 1.002087 CTCGTCTAGGGTTGCCAGTTT 59.998 52.381 0.00 0.00 0.00 2.66
1402 2870 1.001633 TCGTCTAGGGTTGCCAGTTTC 59.998 52.381 0.00 0.00 0.00 2.78
1403 2871 1.002087 CGTCTAGGGTTGCCAGTTTCT 59.998 52.381 0.00 0.00 0.00 2.52
1404 2872 2.550208 CGTCTAGGGTTGCCAGTTTCTT 60.550 50.000 0.00 0.00 0.00 2.52
1406 2874 3.889538 GTCTAGGGTTGCCAGTTTCTTTT 59.110 43.478 0.00 0.00 0.00 2.27
1425 2893 4.981806 TTTAGCGAAATGGGGATCTTTG 57.018 40.909 0.00 0.00 0.00 2.77
1427 2895 0.248621 GCGAAATGGGGATCTTTGCG 60.249 55.000 0.00 0.00 35.40 4.85
1437 2905 2.565841 GGATCTTTGCGGCTGATACTT 58.434 47.619 0.00 0.00 0.00 2.24
1439 2907 2.760634 TCTTTGCGGCTGATACTTCA 57.239 45.000 0.00 0.00 0.00 3.02
1504 2972 3.181524 CGCTGTCGATTTCGTTACCATTT 60.182 43.478 0.00 0.00 40.80 2.32
1512 2983 7.167136 GTCGATTTCGTTACCATTTAGTAGGAG 59.833 40.741 0.00 0.00 40.80 3.69
1514 2985 5.664294 TTCGTTACCATTTAGTAGGAGCA 57.336 39.130 0.00 0.00 0.00 4.26
1771 3243 1.005867 CACACCAATTGCAGCACCC 60.006 57.895 0.00 0.00 0.00 4.61
1824 3296 8.312896 ACGAAAGATTTCTTTTTACTCTCTCC 57.687 34.615 6.98 0.00 45.37 3.71
1826 3298 7.604545 CGAAAGATTTCTTTTTACTCTCTCCCT 59.395 37.037 6.98 0.00 45.37 4.20
1827 3299 9.290988 GAAAGATTTCTTTTTACTCTCTCCCTT 57.709 33.333 6.98 0.00 45.37 3.95
1833 3308 5.844516 TCTTTTTACTCTCTCCCTTGAGGAA 59.155 40.000 0.00 0.00 46.94 3.36
1960 3435 0.898789 ACGTAGTGGTGGTAGCAGCT 60.899 55.000 23.15 11.29 42.51 4.24
2113 3588 2.290260 CCATGTGGCTGGTTCTAGAACA 60.290 50.000 31.30 18.73 42.85 3.18
2116 3591 2.637382 TGTGGCTGGTTCTAGAACATGA 59.363 45.455 31.30 16.59 42.85 3.07
2180 3655 3.947910 CCATGTGGCTGTTTCTTGAAT 57.052 42.857 0.00 0.00 0.00 2.57
2187 3662 5.115480 GTGGCTGTTTCTTGAATTTGGAAA 58.885 37.500 0.00 0.00 0.00 3.13
2190 3665 6.315891 TGGCTGTTTCTTGAATTTGGAAAAAG 59.684 34.615 11.36 11.36 37.36 2.27
2225 3700 6.368791 TGCACTTGCTGTTTATCTTACTACTG 59.631 38.462 2.33 0.00 42.66 2.74
2231 3706 6.590292 TGCTGTTTATCTTACTACTGCTGTTC 59.410 38.462 0.09 0.00 36.70 3.18
2372 3847 3.568007 TCTTGGTTTGCTGATGGTTACAC 59.432 43.478 0.00 0.00 0.00 2.90
2399 3875 4.105486 GTTCTGTCTGCTTGGTTTGTTTC 58.895 43.478 0.00 0.00 0.00 2.78
2407 3883 0.457851 TTGGTTTGTTTCTGGTGCCG 59.542 50.000 0.00 0.00 0.00 5.69
2419 3895 0.948678 TGGTGCCGAGTTGTAAAAGC 59.051 50.000 0.00 0.00 0.00 3.51
2421 3897 1.197036 GGTGCCGAGTTGTAAAAGCTC 59.803 52.381 0.00 0.00 0.00 4.09
2422 3898 1.871039 GTGCCGAGTTGTAAAAGCTCA 59.129 47.619 0.00 0.00 0.00 4.26
2423 3899 2.289547 GTGCCGAGTTGTAAAAGCTCAA 59.710 45.455 0.00 0.00 0.00 3.02
2435 3911 6.539173 TGTAAAAGCTCAATCTTTGGGACTA 58.461 36.000 0.00 0.00 36.49 2.59
2512 3988 1.625818 GTCTTCCTTCTGGCCTTCTCA 59.374 52.381 3.32 0.00 0.00 3.27
2565 4041 7.226720 TGTTTCAAAGAAGGTAACAGTCTGATC 59.773 37.037 6.91 0.00 41.41 2.92
2604 4081 8.774890 ATATGCAAATAAATTTGTTCTGCACA 57.225 26.923 24.74 19.41 46.63 4.57
2607 4084 7.353497 TGCAAATAAATTTGTTCTGCACATTG 58.647 30.769 21.58 9.10 46.63 2.82
2613 4090 0.953727 TGTTCTGCACATTGCTGGTC 59.046 50.000 5.36 1.00 45.31 4.02
2630 4121 3.138304 TGGTCCAGAAGTTCATTTCACG 58.862 45.455 5.50 0.00 0.00 4.35
2640 4131 7.480855 CAGAAGTTCATTTCACGATCATTTCTG 59.519 37.037 5.50 0.00 33.28 3.02
2649 4140 2.009774 CGATCATTTCTGTGGTCACCC 58.990 52.381 0.00 0.00 0.00 4.61
2662 4153 2.771943 TGGTCACCCTCATGAGTTATCC 59.228 50.000 21.11 15.50 0.00 2.59
2663 4154 2.771943 GGTCACCCTCATGAGTTATCCA 59.228 50.000 21.11 0.00 0.00 3.41
2666 4157 5.059833 GTCACCCTCATGAGTTATCCAATC 58.940 45.833 21.11 0.00 0.00 2.67
2672 4164 7.147320 ACCCTCATGAGTTATCCAATCACATTA 60.147 37.037 21.11 0.00 0.00 1.90
3021 4513 1.346395 TGGTAAGAACGTCACATGGCT 59.654 47.619 0.00 0.00 0.00 4.75
3128 4622 1.518325 TCACAGTAACGTGCAATGGG 58.482 50.000 0.00 0.00 36.80 4.00
3131 4625 0.447801 CAGTAACGTGCAATGGGAGC 59.552 55.000 0.00 0.00 0.00 4.70
3183 4678 8.400184 TGCTATCCAGATGAAAATAAATGAGG 57.600 34.615 0.00 0.00 0.00 3.86
3262 4763 8.662781 TTCTGTGCTTGAGAATATTGGTATAC 57.337 34.615 0.00 0.00 0.00 1.47
3522 5025 1.352352 CTCTTTCCCTTGAAGGAGGCA 59.648 52.381 13.97 0.00 45.90 4.75
3541 5044 6.313744 AGGCAATGTTGTGTTACTAACTTC 57.686 37.500 0.71 0.00 0.00 3.01
3689 5192 3.396560 TGTGAGATGCTGACAGAGTTTG 58.603 45.455 6.65 0.00 0.00 2.93
4231 5736 9.435688 AAATTATGTTTCCTTTCTTGTTATGGC 57.564 29.630 0.00 0.00 0.00 4.40
4235 5740 2.446435 TCCTTTCTTGTTATGGCCTGC 58.554 47.619 3.32 0.00 0.00 4.85
4236 5741 1.478105 CCTTTCTTGTTATGGCCTGCC 59.522 52.381 3.32 0.00 0.00 4.85
4237 5742 2.450476 CTTTCTTGTTATGGCCTGCCT 58.550 47.619 9.97 0.00 36.94 4.75
4238 5743 1.838112 TTCTTGTTATGGCCTGCCTG 58.162 50.000 9.97 0.00 36.94 4.85
4317 5831 2.481795 GGCGTATGATTGCTGGCAAATT 60.482 45.455 12.06 0.00 39.55 1.82
4328 5842 0.388778 TGGCAAATTGAGCATGTGCG 60.389 50.000 0.00 0.00 46.28 5.34
4417 5931 2.758089 GGAGAGCATGTTGGCAGCG 61.758 63.158 0.00 0.00 35.83 5.18
4449 5971 8.681806 TGTTTTGTATGATATTGGTGTGGTATG 58.318 33.333 0.00 0.00 0.00 2.39
4470 5992 6.720112 ATGTGCTGCAATAGGATATTGTTT 57.280 33.333 2.77 0.00 0.00 2.83
4591 6115 6.544931 GGGTACTAAATCTTTTGGGTGGATAC 59.455 42.308 0.00 0.00 0.00 2.24
4605 6132 1.349688 TGGATACGGTCTTTGTTGGCT 59.650 47.619 0.00 0.00 42.51 4.75
4699 6226 1.202592 TGGCGCTGTAACTCAAACAGA 60.203 47.619 7.64 0.00 45.89 3.41
4721 6248 8.946085 ACAGAATTATTGCTTTAGAACGATTGA 58.054 29.630 0.00 0.00 0.00 2.57
4735 6262 5.415701 AGAACGATTGATTATTTGTGGCTGT 59.584 36.000 0.00 0.00 0.00 4.40
4736 6263 4.985413 ACGATTGATTATTTGTGGCTGTG 58.015 39.130 0.00 0.00 0.00 3.66
4738 6265 5.030295 CGATTGATTATTTGTGGCTGTGTC 58.970 41.667 0.00 0.00 0.00 3.67
4742 6269 5.069318 TGATTATTTGTGGCTGTGTCTCAA 58.931 37.500 0.00 0.00 0.00 3.02
4751 6278 1.808945 GCTGTGTCTCAATCAGTTGGG 59.191 52.381 0.00 0.00 37.15 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.813596 GCCGTGTATCCTTGGCAG 58.186 61.111 0.00 0.00 46.76 4.85
2 3 2.660258 ATCCGCCGTGTATCCTTGGC 62.660 60.000 0.00 0.00 44.09 4.52
3 4 0.179056 AATCCGCCGTGTATCCTTGG 60.179 55.000 0.00 0.00 0.00 3.61
4 5 1.202533 AGAATCCGCCGTGTATCCTTG 60.203 52.381 0.00 0.00 0.00 3.61
28 656 2.789203 GCTTGCTACGAGGCGAACG 61.789 63.158 0.00 0.00 34.52 3.95
37 665 1.389106 GAGGTTGTAACGCTTGCTACG 59.611 52.381 0.00 0.00 0.00 3.51
64 692 2.583593 GCGGAGATCTCACGTGCC 60.584 66.667 23.85 3.95 0.00 5.01
65 693 2.951745 CGCGGAGATCTCACGTGC 60.952 66.667 23.85 18.63 31.25 5.34
79 707 0.109319 AAGGCCAGTTTAATTGCGCG 60.109 50.000 5.01 0.00 0.00 6.86
81 709 3.427503 CCAGTAAGGCCAGTTTAATTGCG 60.428 47.826 5.01 0.00 0.00 4.85
82 710 4.110036 CCAGTAAGGCCAGTTTAATTGC 57.890 45.455 5.01 0.00 0.00 3.56
98 1176 1.213537 GCTACGTTGGTCGCCAGTA 59.786 57.895 0.00 0.00 44.19 2.74
112 1190 5.433526 TCATAAATGTAGGGGTTGTGCTAC 58.566 41.667 0.00 0.00 0.00 3.58
136 1214 5.516044 TCCTTGGTAGAGTTAGCTGTATCA 58.484 41.667 0.00 0.00 30.82 2.15
147 1225 3.637229 CCATCGTGTATCCTTGGTAGAGT 59.363 47.826 0.00 0.00 0.00 3.24
149 1227 3.905968 TCCATCGTGTATCCTTGGTAGA 58.094 45.455 0.00 0.00 0.00 2.59
150 1228 4.873746 ATCCATCGTGTATCCTTGGTAG 57.126 45.455 0.00 0.00 0.00 3.18
155 1233 5.365605 TGGTAAGAATCCATCGTGTATCCTT 59.634 40.000 0.00 0.00 0.00 3.36
156 1234 4.899457 TGGTAAGAATCCATCGTGTATCCT 59.101 41.667 0.00 0.00 0.00 3.24
166 1244 3.244353 CGAGGCTGATGGTAAGAATCCAT 60.244 47.826 0.00 0.00 46.78 3.41
179 1257 1.457643 TCCGATTCCCGAGGCTGAT 60.458 57.895 0.00 0.00 41.76 2.90
182 1260 0.824182 CTAGTCCGATTCCCGAGGCT 60.824 60.000 0.00 0.00 41.76 4.58
195 1273 5.348986 TGATTGCGTGTAGATTTCTAGTCC 58.651 41.667 0.00 0.00 0.00 3.85
197 1275 6.311445 CAGTTGATTGCGTGTAGATTTCTAGT 59.689 38.462 0.00 0.00 0.00 2.57
206 1284 2.973224 GCAAACAGTTGATTGCGTGTAG 59.027 45.455 10.63 0.00 42.37 2.74
286 1365 6.169094 TGGACAAATGTTTCTTGAGCAAAAA 58.831 32.000 0.00 0.00 0.00 1.94
350 1436 2.630580 GCCCGCCCCATAATTAATTTCA 59.369 45.455 5.91 0.00 0.00 2.69
471 1557 0.996583 AGAGGGAGAGAGAGAACGGT 59.003 55.000 0.00 0.00 0.00 4.83
474 1560 4.600062 AGAAGAAGAGGGAGAGAGAGAAC 58.400 47.826 0.00 0.00 0.00 3.01
475 1561 4.325030 GGAGAAGAAGAGGGAGAGAGAGAA 60.325 50.000 0.00 0.00 0.00 2.87
476 1562 3.202151 GGAGAAGAAGAGGGAGAGAGAGA 59.798 52.174 0.00 0.00 0.00 3.10
478 1564 2.243736 GGGAGAAGAAGAGGGAGAGAGA 59.756 54.545 0.00 0.00 0.00 3.10
479 1565 2.244769 AGGGAGAAGAAGAGGGAGAGAG 59.755 54.545 0.00 0.00 0.00 3.20
944 2396 3.700350 AGACAGGGGAGGGGAGGG 61.700 72.222 0.00 0.00 0.00 4.30
1124 2576 8.899771 CCCAAGAACTACAAGTAAGAAAAGAAA 58.100 33.333 0.00 0.00 0.00 2.52
1125 2577 8.050930 ACCCAAGAACTACAAGTAAGAAAAGAA 58.949 33.333 0.00 0.00 0.00 2.52
1126 2578 7.571025 ACCCAAGAACTACAAGTAAGAAAAGA 58.429 34.615 0.00 0.00 0.00 2.52
1139 2591 3.279434 CCTGGCATTACCCAAGAACTAC 58.721 50.000 0.00 0.00 37.83 2.73
1141 2593 1.710809 ACCTGGCATTACCCAAGAACT 59.289 47.619 0.00 0.00 37.83 3.01
1247 2715 2.237893 ACCCCCTAATTAGGAACACACG 59.762 50.000 29.75 12.78 46.63 4.49
1397 2865 4.403734 TCCCCATTTCGCTAAAAGAAACT 58.596 39.130 0.00 0.00 39.96 2.66
1400 2868 4.855340 AGATCCCCATTTCGCTAAAAGAA 58.145 39.130 0.00 0.00 0.00 2.52
1401 2869 4.503714 AGATCCCCATTTCGCTAAAAGA 57.496 40.909 0.00 0.00 0.00 2.52
1402 2870 5.343249 CAAAGATCCCCATTTCGCTAAAAG 58.657 41.667 0.00 0.00 0.00 2.27
1403 2871 4.381505 GCAAAGATCCCCATTTCGCTAAAA 60.382 41.667 0.00 0.00 0.00 1.52
1404 2872 3.130340 GCAAAGATCCCCATTTCGCTAAA 59.870 43.478 0.00 0.00 0.00 1.85
1406 2874 2.297701 GCAAAGATCCCCATTTCGCTA 58.702 47.619 0.00 0.00 0.00 4.26
1425 2893 3.945179 CTGATTTTGAAGTATCAGCCGC 58.055 45.455 6.49 0.00 40.74 6.53
1437 2905 4.682563 TCCTAATTTGGGGCTGATTTTGA 58.317 39.130 6.08 0.00 0.00 2.69
1439 2907 6.641161 AAATCCTAATTTGGGGCTGATTTT 57.359 33.333 6.08 0.00 33.78 1.82
1530 3002 8.035984 CGAAATCTCCCTATACTATCTTTTCCC 58.964 40.741 0.00 0.00 0.00 3.97
1531 3003 8.586744 ACGAAATCTCCCTATACTATCTTTTCC 58.413 37.037 0.00 0.00 0.00 3.13
1532 3004 9.628746 GACGAAATCTCCCTATACTATCTTTTC 57.371 37.037 0.00 0.00 0.00 2.29
1771 3243 1.689959 GAAGCATGCGTGAAAAGGTG 58.310 50.000 11.93 0.00 0.00 4.00
1824 3296 6.322456 AGGTTTCTTTCTTTCTTTCCTCAAGG 59.678 38.462 0.00 0.00 32.64 3.61
1826 3298 7.415206 CGAAGGTTTCTTTCTTTCTTTCCTCAA 60.415 37.037 0.00 0.00 32.52 3.02
1827 3299 6.038271 CGAAGGTTTCTTTCTTTCTTTCCTCA 59.962 38.462 0.00 0.00 32.52 3.86
1833 3308 6.113411 TGTCTCGAAGGTTTCTTTCTTTCTT 58.887 36.000 0.00 0.00 32.52 2.52
2113 3588 4.992951 GTGCAGCCAAATTCTTTCTTTCAT 59.007 37.500 0.00 0.00 0.00 2.57
2116 3591 4.677673 AGTGCAGCCAAATTCTTTCTTT 57.322 36.364 0.00 0.00 0.00 2.52
2180 3655 3.882288 GCAGCCAAATTCCTTTTTCCAAA 59.118 39.130 0.00 0.00 0.00 3.28
2187 3662 2.807837 GCAAGTGCAGCCAAATTCCTTT 60.808 45.455 0.00 0.00 41.59 3.11
2190 3665 0.319405 AGCAAGTGCAGCCAAATTCC 59.681 50.000 6.00 0.00 45.16 3.01
2225 3700 0.877743 GTCCTGCCAAGAAGAACAGC 59.122 55.000 0.00 0.00 0.00 4.40
2231 3706 2.012673 GCACATAGTCCTGCCAAGAAG 58.987 52.381 0.00 0.00 0.00 2.85
2372 3847 1.670811 ACCAAGCAGACAGAACAAACG 59.329 47.619 0.00 0.00 0.00 3.60
2399 3875 1.069227 GCTTTTACAACTCGGCACCAG 60.069 52.381 0.00 0.00 0.00 4.00
2407 3883 6.016276 TCCCAAAGATTGAGCTTTTACAACTC 60.016 38.462 0.00 0.00 36.01 3.01
2419 3895 4.697352 CCTGTTGTAGTCCCAAAGATTGAG 59.303 45.833 0.00 0.00 0.00 3.02
2421 3897 4.398319 ACCTGTTGTAGTCCCAAAGATTG 58.602 43.478 0.00 0.00 0.00 2.67
2422 3898 4.104102 TGACCTGTTGTAGTCCCAAAGATT 59.896 41.667 0.00 0.00 31.76 2.40
2423 3899 3.650942 TGACCTGTTGTAGTCCCAAAGAT 59.349 43.478 0.00 0.00 31.76 2.40
2435 3911 2.249139 GTAGTCCTCCTGACCTGTTGT 58.751 52.381 0.00 0.00 45.68 3.32
2512 3988 0.622665 AGCTGGCCTTGCTGATAAGT 59.377 50.000 20.14 0.00 39.56 2.24
2583 4060 6.303733 GCAATGTGCAGAACAAATTTATTTGC 59.696 34.615 13.61 10.15 45.46 3.68
2601 4078 1.901591 ACTTCTGGACCAGCAATGTG 58.098 50.000 17.33 5.35 0.00 3.21
2602 4079 2.158623 TGAACTTCTGGACCAGCAATGT 60.159 45.455 17.33 9.27 0.00 2.71
2604 4081 2.957402 TGAACTTCTGGACCAGCAAT 57.043 45.000 17.33 2.67 0.00 3.56
2607 4084 3.057946 GTGAAATGAACTTCTGGACCAGC 60.058 47.826 17.33 2.80 0.00 4.85
2613 4090 5.808042 ATGATCGTGAAATGAACTTCTGG 57.192 39.130 0.00 0.00 34.16 3.86
2662 4153 9.923786 CATGCCAAAAACATAATAATGTGATTG 57.076 29.630 8.46 8.46 45.79 2.67
2663 4154 9.669887 ACATGCCAAAAACATAATAATGTGATT 57.330 25.926 0.00 0.00 45.79 2.57
2718 4210 6.319658 GCATGGAATAATTTCTCACTGAAGGA 59.680 38.462 0.00 0.00 35.89 3.36
2719 4211 6.320672 AGCATGGAATAATTTCTCACTGAAGG 59.679 38.462 0.00 0.00 35.89 3.46
2815 4307 5.074746 ACCAAGGAACAGAAATTAGGGTT 57.925 39.130 0.00 0.00 0.00 4.11
2816 4308 4.105697 TGACCAAGGAACAGAAATTAGGGT 59.894 41.667 0.00 0.00 0.00 4.34
3128 4622 2.526304 TCACTTGTAGTGTGTGGCTC 57.474 50.000 6.71 0.00 46.03 4.70
3131 4625 2.942376 TGCTTTCACTTGTAGTGTGTGG 59.058 45.455 6.71 0.00 46.03 4.17
3262 4763 4.012374 ACAGCCAACAATTCATCTAGGTG 58.988 43.478 0.00 0.00 0.00 4.00
3522 5025 7.308589 GGCATCTGAAGTTAGTAACACAACATT 60.309 37.037 15.28 0.00 0.00 2.71
3541 5044 2.954318 CCCCTACAGAATTTGGCATCTG 59.046 50.000 13.60 13.60 46.69 2.90
3689 5192 4.830826 AATCGACAAGGACCAGAAAAAC 57.169 40.909 0.00 0.00 0.00 2.43
3924 5428 2.502068 GGTAACCTAGGGTGGGGTAT 57.498 55.000 10.48 0.00 35.34 2.73
4235 5740 4.761235 CATCTAAATGCAGGCATACAGG 57.239 45.455 7.26 0.00 35.31 4.00
4328 5842 1.109323 AACAGGCAGGTCAAAGCACC 61.109 55.000 0.00 0.00 36.58 5.01
4417 5931 7.286775 ACACCAATATCATACAAAACATACCCC 59.713 37.037 0.00 0.00 0.00 4.95
4449 5971 9.778993 CATATAAACAATATCCTATTGCAGCAC 57.221 33.333 0.00 0.00 32.55 4.40
4470 5992 8.854237 ATATTGTACCCAGCCAGATACATATA 57.146 34.615 0.00 0.00 0.00 0.86
4591 6115 0.872388 GTGGTAGCCAACAAAGACCG 59.128 55.000 0.00 0.00 34.18 4.79
4681 6208 3.813529 ATTCTGTTTGAGTTACAGCGC 57.186 42.857 0.00 0.00 42.12 5.92
4721 6248 5.711506 TGATTGAGACACAGCCACAAATAAT 59.288 36.000 0.00 0.00 0.00 1.28
4735 6262 3.496692 CCTTGACCCAACTGATTGAGACA 60.497 47.826 0.00 0.00 38.15 3.41
4736 6263 3.077359 CCTTGACCCAACTGATTGAGAC 58.923 50.000 0.00 0.00 38.15 3.36
4738 6265 3.341823 CTCCTTGACCCAACTGATTGAG 58.658 50.000 0.00 0.00 38.15 3.02
4742 6269 1.912043 CTCCTCCTTGACCCAACTGAT 59.088 52.381 0.00 0.00 0.00 2.90
4751 6278 1.079057 GTTCGCCCTCCTCCTTGAC 60.079 63.158 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.