Multiple sequence alignment - TraesCS3A01G261700

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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 TraesCS3A01G261700 chr3A 100.000 4493 0 0 1 4493 484638247 484633755 0.000000e+00 8298.0
1 TraesCS3A01G261700 chr3A 73.897 816 172 30 1266 2068 448701981 448702768 5.690000e-74 289.0
2 TraesCS3A01G261700 chr3A 71.887 811 171 45 1270 2053 598553492 598554272 9.930000e-42 182.0
3 TraesCS3A01G261700 chr3A 71.902 815 158 52 1276 2053 623610125 623610905 2.150000e-38 171.0
4 TraesCS3A01G261700 chr3A 71.785 801 164 48 1284 2053 625210518 625209749 2.150000e-38 171.0
5 TraesCS3A01G261700 chr3B 93.747 4478 222 29 1 4464 473695664 473691231 0.000000e+00 6665.0
6 TraesCS3A01G261700 chr3B 73.432 813 175 30 1269 2068 431040213 431040997 2.660000e-67 267.0
7 TraesCS3A01G261700 chr3B 71.144 804 183 39 1270 2053 602331249 602332023 2.160000e-33 154.0
8 TraesCS3A01G261700 chr3D 93.664 2336 109 19 1 2326 363598923 363596617 0.000000e+00 3458.0
9 TraesCS3A01G261700 chr3D 92.595 1337 86 7 2323 3657 363595635 363594310 0.000000e+00 1908.0
10 TraesCS3A01G261700 chr3D 90.808 631 40 9 3746 4371 363594077 363593460 0.000000e+00 828.0
11 TraesCS3A01G261700 chr3D 74.293 813 168 30 1269 2068 331657185 331657969 5.650000e-79 305.0
12 TraesCS3A01G261700 chr3D 72.025 815 157 52 1276 2053 480842451 480843231 4.620000e-40 176.0
13 TraesCS3A01G261700 chr3D 71.640 811 173 44 1270 2053 455869728 455870508 2.150000e-38 171.0
14 TraesCS3A01G261700 chr3D 71.163 808 169 46 1278 2053 482190987 482190212 4.690000e-30 143.0
15 TraesCS3A01G261700 chr6D 90.064 936 89 2 1 936 14169163 14170094 0.000000e+00 1210.0
16 TraesCS3A01G261700 chr5A 86.511 897 117 4 1 895 46423206 46422312 0.000000e+00 983.0
17 TraesCS3A01G261700 chr5A 75.556 810 138 37 1277 2059 41373873 41374649 1.200000e-90 344.0
18 TraesCS3A01G261700 chr2B 100.000 29 0 0 2855 2883 765296337 765296309 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G261700 chr3A 484633755 484638247 4492 True 8298.000000 8298 100.000000 1 4493 1 chr3A.!!$R1 4492
1 TraesCS3A01G261700 chr3A 448701981 448702768 787 False 289.000000 289 73.897000 1266 2068 1 chr3A.!!$F1 802
2 TraesCS3A01G261700 chr3B 473691231 473695664 4433 True 6665.000000 6665 93.747000 1 4464 1 chr3B.!!$R1 4463
3 TraesCS3A01G261700 chr3B 431040213 431040997 784 False 267.000000 267 73.432000 1269 2068 1 chr3B.!!$F1 799
4 TraesCS3A01G261700 chr3D 363593460 363598923 5463 True 2064.666667 3458 92.355667 1 4371 3 chr3D.!!$R2 4370
5 TraesCS3A01G261700 chr3D 331657185 331657969 784 False 305.000000 305 74.293000 1269 2068 1 chr3D.!!$F1 799
6 TraesCS3A01G261700 chr6D 14169163 14170094 931 False 1210.000000 1210 90.064000 1 936 1 chr6D.!!$F1 935
7 TraesCS3A01G261700 chr5A 46422312 46423206 894 True 983.000000 983 86.511000 1 895 1 chr5A.!!$R1 894
8 TraesCS3A01G261700 chr5A 41373873 41374649 776 False 344.000000 344 75.556000 1277 2059 1 chr5A.!!$F1 782


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
756 757 1.134965 GGAGAGATCACCGAGGTTGTG 60.135 57.143 0.0 0.0 35.01 3.33 F
1070 1073 0.099968 CTGTCATTTGCAGCATCCCG 59.900 55.000 0.0 0.0 0.00 5.14 F
2761 3775 0.543174 AGGAGGCGACAAGGACTTCT 60.543 55.000 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2706 3720 0.036952 CCTTCACTGTGATCTGCCGT 60.037 55.0 11.86 0.00 0.00 5.68 R
2871 3885 0.548031 CATAGCTTTCCAGGGAGCCA 59.452 55.0 11.01 0.21 39.71 4.75 R
4148 5327 0.324738 TTGTGCTCCCAAAACCACCA 60.325 50.0 0.00 0.00 0.00 4.17 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
57 58 2.224769 TGAAAAGCTAGGTCAAGGTGGG 60.225 50.000 0.00 0.00 0.00 4.61
223 224 5.640147 TCTTAGGATTTTGCTTGGAAGGAA 58.360 37.500 0.00 0.00 34.39 3.36
282 283 5.362430 TGGTTCACTTGAAAGGTATGCTTTT 59.638 36.000 0.00 0.00 35.58 2.27
294 295 4.889995 AGGTATGCTTTTAAAGATGGCTCC 59.110 41.667 9.10 3.08 0.00 4.70
432 433 3.697166 ACCCCACAACATTCTATTGGAC 58.303 45.455 0.00 0.00 0.00 4.02
456 457 5.048434 CCAAAACTTCTGTCCAAAGATCTCC 60.048 44.000 0.00 0.00 0.00 3.71
756 757 1.134965 GGAGAGATCACCGAGGTTGTG 60.135 57.143 0.00 0.00 35.01 3.33
843 844 1.400142 AGAGTCGTCGAGATGCTTGAG 59.600 52.381 0.00 0.00 0.00 3.02
865 866 3.723348 GCACAACCGGCCTCGAAC 61.723 66.667 0.00 0.00 39.00 3.95
906 907 6.374333 TCTTGAGTTGACAGGGTTTATATTGC 59.626 38.462 0.00 0.00 0.00 3.56
910 911 6.485171 AGTTGACAGGGTTTATATTGCTCTT 58.515 36.000 0.00 0.00 0.00 2.85
936 938 3.004629 CACTTGCTCCAGTGTTGCATAAA 59.995 43.478 7.89 0.00 39.59 1.40
946 949 5.794945 CCAGTGTTGCATAAATCTGTAAACG 59.205 40.000 0.00 0.00 0.00 3.60
1070 1073 0.099968 CTGTCATTTGCAGCATCCCG 59.900 55.000 0.00 0.00 0.00 5.14
1071 1074 1.314534 TGTCATTTGCAGCATCCCGG 61.315 55.000 0.00 0.00 0.00 5.73
1082 1085 1.143073 AGCATCCCGGTTCTTTATCCC 59.857 52.381 0.00 0.00 0.00 3.85
1093 1096 6.376018 CCGGTTCTTTATCCCAGAAAATAACA 59.624 38.462 0.00 0.00 31.98 2.41
1119 1122 2.851263 TTCCTTCCACGTATGCTTGT 57.149 45.000 0.00 0.00 0.00 3.16
1182 1185 6.306356 CACAAAAGACATTCGCCATCTTTAAG 59.694 38.462 0.00 0.00 40.85 1.85
1183 1186 6.206634 ACAAAAGACATTCGCCATCTTTAAGA 59.793 34.615 0.00 0.00 40.85 2.10
1184 1187 5.803020 AAGACATTCGCCATCTTTAAGAC 57.197 39.130 0.00 0.00 28.03 3.01
1185 1188 5.091261 AGACATTCGCCATCTTTAAGACT 57.909 39.130 0.00 0.00 0.00 3.24
1186 1189 5.491982 AGACATTCGCCATCTTTAAGACTT 58.508 37.500 0.00 0.00 0.00 3.01
1187 1190 5.940470 AGACATTCGCCATCTTTAAGACTTT 59.060 36.000 0.00 0.00 0.00 2.66
1188 1191 7.103641 AGACATTCGCCATCTTTAAGACTTTA 58.896 34.615 0.00 0.00 0.00 1.85
1189 1192 7.606456 AGACATTCGCCATCTTTAAGACTTTAA 59.394 33.333 0.00 0.00 0.00 1.52
1200 1203 1.173913 AGACTTTAACAATGCCCGGC 58.826 50.000 1.04 1.04 0.00 6.13
1230 1233 3.373439 GCATTCTCACGATCTTGCTCTTT 59.627 43.478 0.00 0.00 0.00 2.52
1347 1350 3.450115 GGCACGGGACTCTACGCT 61.450 66.667 0.00 0.00 0.00 5.07
2016 2037 2.821366 CAGGTGCTGCCGATGGTC 60.821 66.667 0.00 0.00 43.70 4.02
2072 2093 3.003113 GCCGCTCCTACGACAAGGT 62.003 63.158 0.00 0.00 37.91 3.50
2076 2097 1.465794 GCTCCTACGACAAGGTCTCT 58.534 55.000 0.00 0.00 37.91 3.10
2079 2100 1.075050 TCCTACGACAAGGTCTCTGGT 59.925 52.381 0.00 0.00 37.91 4.00
2085 2106 3.387050 ACGACAAGGTCTCTGGTTTTAGT 59.613 43.478 0.00 0.00 0.00 2.24
2088 2109 4.451900 ACAAGGTCTCTGGTTTTAGTGTG 58.548 43.478 0.00 0.00 0.00 3.82
2156 2181 2.746362 CCTTCTGCTTTCAGGCTTACAG 59.254 50.000 0.00 0.00 40.69 2.74
2218 2245 8.883789 TTGCCGTCGTTTATTCTAAATTTTAG 57.116 30.769 9.48 9.48 0.00 1.85
2370 3384 5.809562 CACATAGACTAGCTCAAGAGTTTGG 59.190 44.000 0.00 0.00 34.97 3.28
2425 3439 3.840666 TGCATTGCATTTTAAACCCCCTA 59.159 39.130 7.38 0.00 31.71 3.53
2613 3627 5.591877 AGCTCATCATCCAAAAAGATACACC 59.408 40.000 0.00 0.00 0.00 4.16
2639 3653 2.744202 CCGAAGTGGAAAGGATGACAAG 59.256 50.000 0.00 0.00 42.00 3.16
2738 3752 3.209410 CAGTGAAGGTGCTGAAGAACTT 58.791 45.455 0.00 0.00 34.87 2.66
2739 3753 3.629398 CAGTGAAGGTGCTGAAGAACTTT 59.371 43.478 0.00 0.00 34.87 2.66
2745 3759 5.048846 AGGTGCTGAAGAACTTTAAAGGA 57.951 39.130 19.14 0.00 0.00 3.36
2761 3775 0.543174 AGGAGGCGACAAGGACTTCT 60.543 55.000 0.00 0.00 0.00 2.85
2838 3852 3.614698 TTTTGCTTGCAGGGGCCG 61.615 61.111 0.00 0.00 40.13 6.13
2871 3885 5.480422 TCTGATATACGAGTACATGCCCAAT 59.520 40.000 0.00 0.00 0.00 3.16
2913 3927 0.457443 TCAGCAGCTATGACTCCGTG 59.543 55.000 0.00 0.00 0.00 4.94
2961 3975 3.181454 ACTGGGAGAAACTGTTCGACATT 60.181 43.478 0.00 0.00 38.90 2.71
2967 3981 2.995466 AACTGTTCGACATTGCCATG 57.005 45.000 0.00 0.00 36.34 3.66
3081 4095 3.265479 AGGAGCTATGCCCAAAGATATCC 59.735 47.826 0.00 0.00 0.00 2.59
3177 4191 1.264749 TGGTGTCCAGGAGATTCGGG 61.265 60.000 0.00 0.00 0.00 5.14
3188 4202 0.974010 AGATTCGGGCCGGTCACTAA 60.974 55.000 27.98 12.37 0.00 2.24
3210 4224 1.747709 AGTCCGACGTGTACAGCTAT 58.252 50.000 0.00 0.00 0.00 2.97
3254 4268 0.034059 AGGGCAAAGAGACACGTCAG 59.966 55.000 0.00 0.00 0.00 3.51
3394 4408 2.290287 ATAGTCGGGCTGTGGTGCA 61.290 57.895 0.00 0.00 34.04 4.57
3465 4479 4.874977 GAGGGTAGCAGCGCGGAC 62.875 72.222 13.03 0.54 0.00 4.79
3499 4513 2.231721 AGAAGAACCTCCTGAAGCGTAC 59.768 50.000 0.00 0.00 0.00 3.67
3552 4569 3.323751 AATGCACCTGCTTTTGGATTC 57.676 42.857 0.00 0.00 42.66 2.52
3572 4592 1.871039 CGTGTAGTGTTGGTTTCAGGG 59.129 52.381 0.00 0.00 0.00 4.45
3576 4596 1.222567 AGTGTTGGTTTCAGGGGAGT 58.777 50.000 0.00 0.00 0.00 3.85
3578 4598 2.372172 AGTGTTGGTTTCAGGGGAGTAG 59.628 50.000 0.00 0.00 0.00 2.57
3640 4661 6.149633 GGTTTTAGTGCCAGATAACTTGTTG 58.850 40.000 0.00 0.00 0.00 3.33
3641 4662 5.957842 TTTAGTGCCAGATAACTTGTTGG 57.042 39.130 0.00 0.00 0.00 3.77
3688 4815 6.435428 ACAAACCAAACAATAAGACACGATC 58.565 36.000 0.00 0.00 0.00 3.69
3689 4816 6.038825 ACAAACCAAACAATAAGACACGATCA 59.961 34.615 0.00 0.00 0.00 2.92
3690 4817 6.817765 AACCAAACAATAAGACACGATCAT 57.182 33.333 0.00 0.00 0.00 2.45
3691 4818 6.422776 ACCAAACAATAAGACACGATCATC 57.577 37.500 0.00 0.00 0.00 2.92
3692 4819 5.937540 ACCAAACAATAAGACACGATCATCA 59.062 36.000 0.00 0.00 0.00 3.07
3693 4820 6.429692 ACCAAACAATAAGACACGATCATCAA 59.570 34.615 0.00 0.00 0.00 2.57
3701 4828 2.413112 GACACGATCATCAACACCACAG 59.587 50.000 0.00 0.00 0.00 3.66
3716 4843 0.604073 CACAGGCACATTTGATGGCA 59.396 50.000 0.00 0.00 44.76 4.92
3900 5076 3.873952 GCTGTTCTGGGAGTTGATGTATC 59.126 47.826 0.00 0.00 0.00 2.24
4108 5287 1.585006 CTACGAGGAACAGCACCGT 59.415 57.895 0.00 0.00 37.27 4.83
4132 5311 1.093159 GGCTTCATGGCTTCTCAGTG 58.907 55.000 0.00 0.00 38.32 3.66
4134 5313 2.430465 GCTTCATGGCTTCTCAGTGAA 58.570 47.619 0.00 0.00 0.00 3.18
4146 5325 6.279513 CTTCTCAGTGAAGGATTACTCTGT 57.720 41.667 4.53 0.00 46.25 3.41
4147 5326 5.906113 TCTCAGTGAAGGATTACTCTGTC 57.094 43.478 0.00 0.00 0.00 3.51
4148 5327 5.575157 TCTCAGTGAAGGATTACTCTGTCT 58.425 41.667 0.00 0.00 0.00 3.41
4149 5328 5.417266 TCTCAGTGAAGGATTACTCTGTCTG 59.583 44.000 0.00 0.00 0.00 3.51
4150 5329 4.464244 TCAGTGAAGGATTACTCTGTCTGG 59.536 45.833 0.00 0.00 0.00 3.86
4205 5388 4.627467 ACTATTTGTAGCAAGAGAACAGCG 59.373 41.667 0.00 0.00 0.00 5.18
4239 5422 1.202568 CGCCATGCTCTATCTGGAACA 60.203 52.381 0.00 0.00 31.38 3.18
4255 5438 2.350484 GGAACAGTGCCGCTAAAACTTC 60.350 50.000 0.00 0.00 0.00 3.01
4256 5439 0.865769 ACAGTGCCGCTAAAACTTCG 59.134 50.000 0.00 0.00 0.00 3.79
4307 5491 3.645660 TGGAGCACGGGCATTCCA 61.646 61.111 16.16 16.16 40.81 3.53
4321 5506 1.479323 CATTCCAATGAGTGCTTGGGG 59.521 52.381 2.16 0.00 42.83 4.96
4337 5522 4.704833 GGCTCCGGCACTGCTTCA 62.705 66.667 0.00 0.00 40.87 3.02
4379 5564 3.097137 CTGCTGCTGCTGCTTAGCG 62.097 63.158 27.67 10.25 44.01 4.26
4416 5601 2.217750 TGCTGTGCAGATTACGTTTGT 58.782 42.857 3.02 0.00 33.32 2.83
4464 5649 3.004315 CACACCGATAAAAGTGCCTTGTT 59.996 43.478 0.00 0.00 37.51 2.83
4465 5650 3.004315 ACACCGATAAAAGTGCCTTGTTG 59.996 43.478 0.00 0.00 37.51 3.33
4466 5651 3.252215 CACCGATAAAAGTGCCTTGTTGA 59.748 43.478 0.00 0.00 0.00 3.18
4467 5652 3.886505 ACCGATAAAAGTGCCTTGTTGAA 59.113 39.130 0.00 0.00 0.00 2.69
4468 5653 4.226761 CCGATAAAAGTGCCTTGTTGAAC 58.773 43.478 0.00 0.00 0.00 3.18
4469 5654 4.261405 CCGATAAAAGTGCCTTGTTGAACA 60.261 41.667 0.00 0.00 0.00 3.18
4470 5655 4.911610 CGATAAAAGTGCCTTGTTGAACAG 59.088 41.667 0.00 0.00 0.00 3.16
4471 5656 5.277779 CGATAAAAGTGCCTTGTTGAACAGA 60.278 40.000 0.00 0.00 0.00 3.41
4472 5657 6.568462 CGATAAAAGTGCCTTGTTGAACAGAT 60.568 38.462 0.00 0.00 0.00 2.90
4473 5658 5.343307 AAAAGTGCCTTGTTGAACAGATT 57.657 34.783 0.00 0.00 0.00 2.40
4474 5659 5.343307 AAAGTGCCTTGTTGAACAGATTT 57.657 34.783 0.00 0.00 0.00 2.17
4475 5660 5.343307 AAGTGCCTTGTTGAACAGATTTT 57.657 34.783 0.00 0.00 0.00 1.82
4476 5661 4.936891 AGTGCCTTGTTGAACAGATTTTC 58.063 39.130 0.00 0.00 0.00 2.29
4477 5662 4.051237 GTGCCTTGTTGAACAGATTTTCC 58.949 43.478 0.00 0.00 0.00 3.13
4478 5663 3.703556 TGCCTTGTTGAACAGATTTTCCA 59.296 39.130 0.00 0.00 0.00 3.53
4479 5664 4.161189 TGCCTTGTTGAACAGATTTTCCAA 59.839 37.500 0.00 0.00 0.00 3.53
4480 5665 4.507756 GCCTTGTTGAACAGATTTTCCAAC 59.492 41.667 0.00 0.00 0.00 3.77
4481 5666 5.659463 CCTTGTTGAACAGATTTTCCAACA 58.341 37.500 0.00 0.00 30.99 3.33
4482 5667 6.282930 CCTTGTTGAACAGATTTTCCAACAT 58.717 36.000 0.00 0.00 32.03 2.71
4483 5668 6.762661 CCTTGTTGAACAGATTTTCCAACATT 59.237 34.615 0.00 0.00 32.03 2.71
4484 5669 7.254522 CCTTGTTGAACAGATTTTCCAACATTG 60.255 37.037 0.00 0.00 32.03 2.82
4485 5670 6.871844 TGTTGAACAGATTTTCCAACATTGA 58.128 32.000 0.00 0.00 29.42 2.57
4486 5671 6.979817 TGTTGAACAGATTTTCCAACATTGAG 59.020 34.615 0.00 0.00 29.42 3.02
4487 5672 5.531634 TGAACAGATTTTCCAACATTGAGC 58.468 37.500 0.00 0.00 0.00 4.26
4488 5673 5.068855 TGAACAGATTTTCCAACATTGAGCA 59.931 36.000 0.00 0.00 0.00 4.26
4489 5674 5.534207 ACAGATTTTCCAACATTGAGCAA 57.466 34.783 0.00 0.00 0.00 3.91
4490 5675 6.105397 ACAGATTTTCCAACATTGAGCAAT 57.895 33.333 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.287608 GCCTCTGTAAACAGCACCAAAC 60.288 50.000 5.21 0.00 43.46 2.93
223 224 6.016555 AGTCATAAATTAGTGCCCTTTTGGT 58.983 36.000 0.00 0.00 38.10 3.67
282 283 1.209504 CCACCTTCGGAGCCATCTTTA 59.790 52.381 0.00 0.00 0.00 1.85
294 295 5.123344 CCAACCTAAAGTATTTCCACCTTCG 59.877 44.000 0.00 0.00 40.09 3.79
432 433 5.048434 GGAGATCTTTGGACAGAAGTTTTGG 60.048 44.000 0.00 0.00 0.00 3.28
456 457 1.982073 GCTTGGCCAGTCCGAAATCG 61.982 60.000 5.11 0.00 37.80 3.34
555 556 4.510038 ACTTACTGCTCCAAATTGCTTG 57.490 40.909 0.00 0.00 34.52 4.01
654 655 6.293845 GGAAATATTGGCTGCTAGATTCAGTG 60.294 42.308 0.00 0.00 34.21 3.66
756 757 3.745797 GCCCAACCACTATCATCTTCCTC 60.746 52.174 0.00 0.00 0.00 3.71
865 866 1.035139 AAGAGCACTTTTGGTGGCAG 58.965 50.000 0.00 0.00 45.44 4.85
991 994 0.886490 CCAGCGGACATATGGAAGCC 60.886 60.000 7.80 2.19 36.09 4.35
1070 1073 8.581578 TGTTGTTATTTTCTGGGATAAAGAACC 58.418 33.333 0.00 0.00 35.62 3.62
1071 1074 9.406828 GTGTTGTTATTTTCTGGGATAAAGAAC 57.593 33.333 0.00 0.00 36.50 3.01
1082 1085 6.868339 GGAAGGAATGGTGTTGTTATTTTCTG 59.132 38.462 0.00 0.00 0.00 3.02
1093 1096 3.343617 CATACGTGGAAGGAATGGTGTT 58.656 45.455 0.00 0.00 0.00 3.32
1145 1148 3.402691 TTTTGTGGCGTGTGCGGTG 62.403 57.895 0.00 0.00 44.10 4.94
1146 1149 3.119709 CTTTTGTGGCGTGTGCGGT 62.120 57.895 0.00 0.00 44.10 5.68
1147 1150 2.353376 CTTTTGTGGCGTGTGCGG 60.353 61.111 0.00 0.00 44.10 5.69
1148 1151 1.654137 GTCTTTTGTGGCGTGTGCG 60.654 57.895 0.00 0.00 44.10 5.34
1182 1185 0.885196 TGCCGGGCATTGTTAAAGTC 59.115 50.000 19.77 0.00 31.71 3.01
1183 1186 1.272212 CTTGCCGGGCATTGTTAAAGT 59.728 47.619 24.49 0.00 38.76 2.66
1184 1187 1.994916 CTTGCCGGGCATTGTTAAAG 58.005 50.000 24.49 11.49 38.76 1.85
1185 1188 0.037790 GCTTGCCGGGCATTGTTAAA 60.038 50.000 24.49 4.67 38.76 1.52
1186 1189 1.589113 GCTTGCCGGGCATTGTTAA 59.411 52.632 24.49 5.50 38.76 2.01
1187 1190 2.347322 GGCTTGCCGGGCATTGTTA 61.347 57.895 24.49 6.33 38.76 2.41
1188 1191 3.694538 GGCTTGCCGGGCATTGTT 61.695 61.111 24.49 0.00 38.76 2.83
1200 1203 2.753966 CGTGAGAATGCCGGGCTTG 61.754 63.158 21.46 0.00 0.00 4.01
1211 1214 2.738846 GCAAAGAGCAAGATCGTGAGAA 59.261 45.455 13.18 0.00 44.07 2.87
1347 1350 0.664166 GGAACGCGAGGTTGACGTAA 60.664 55.000 15.93 0.00 39.50 3.18
1553 1556 1.445942 CATAGGTAGGTGGCCACGG 59.554 63.158 29.08 7.33 0.00 4.94
2016 2037 1.582680 GTAATTGGGCGCGCTTTCG 60.583 57.895 32.29 0.00 39.07 3.46
2072 2093 4.380531 CAGCTTCACACTAAAACCAGAGA 58.619 43.478 0.00 0.00 0.00 3.10
2076 2097 2.618241 CTGCAGCTTCACACTAAAACCA 59.382 45.455 0.00 0.00 0.00 3.67
2079 2100 2.549754 GCTCTGCAGCTTCACACTAAAA 59.450 45.455 9.47 0.00 43.09 1.52
2346 3360 5.809562 CCAAACTCTTGAGCTAGTCTATGTG 59.190 44.000 0.00 0.00 34.14 3.21
2370 3384 2.627699 TGGCAAGGAAATCACCAACTTC 59.372 45.455 0.00 0.00 0.00 3.01
2577 3591 1.425066 TGATGAGCTCCCAGTTTTGGT 59.575 47.619 12.15 0.00 43.40 3.67
2639 3653 1.457346 CATCCTGTGAGCAAAGGTCC 58.543 55.000 6.60 0.00 34.94 4.46
2706 3720 0.036952 CCTTCACTGTGATCTGCCGT 60.037 55.000 11.86 0.00 0.00 5.68
2738 3752 1.975680 AGTCCTTGTCGCCTCCTTTAA 59.024 47.619 0.00 0.00 0.00 1.52
2739 3753 1.640917 AGTCCTTGTCGCCTCCTTTA 58.359 50.000 0.00 0.00 0.00 1.85
2745 3759 3.614399 CAAGAAGTCCTTGTCGCCT 57.386 52.632 0.00 0.00 45.52 5.52
2761 3775 1.478510 GATGCTCTCGACCTCCTTCAA 59.521 52.381 0.00 0.00 0.00 2.69
2838 3852 2.417239 CTCGTATATCAGAGCCCTCGTC 59.583 54.545 0.00 0.00 34.09 4.20
2871 3885 0.548031 CATAGCTTTCCAGGGAGCCA 59.452 55.000 11.01 0.21 39.71 4.75
2913 3927 2.554893 CCATAGCGAGTAGTTCTCCTCC 59.445 54.545 0.00 0.00 39.84 4.30
2997 4011 1.447140 GTTAGCACCGTCATCGCCA 60.447 57.895 0.00 0.00 35.54 5.69
3081 4095 2.151202 AGGTTTGCTACACCAACATCG 58.849 47.619 2.88 0.00 36.67 3.84
3177 4191 1.012486 CGGACTTGTTAGTGACCGGC 61.012 60.000 0.00 0.00 37.84 6.13
3188 4202 0.318445 GCTGTACACGTCGGACTTGT 60.318 55.000 21.62 21.62 34.78 3.16
3210 4224 2.606213 TCCAGGACCATCACGCCA 60.606 61.111 0.00 0.00 0.00 5.69
3270 4284 0.451783 GGGCGAAATACTTGCTGGTG 59.548 55.000 0.00 0.00 0.00 4.17
3499 4513 8.099364 ACATTGTTTACAACCATGTCTTCTAG 57.901 34.615 0.00 0.00 42.15 2.43
3552 4569 1.871039 CCCTGAAACCAACACTACACG 59.129 52.381 0.00 0.00 0.00 4.49
3572 4592 2.680312 TGAAGTGCTCATGCTACTCC 57.320 50.000 0.00 0.00 40.48 3.85
3576 4596 3.599343 ACGAAATGAAGTGCTCATGCTA 58.401 40.909 0.00 0.00 44.43 3.49
3578 4598 2.907910 ACGAAATGAAGTGCTCATGC 57.092 45.000 0.00 0.00 44.43 4.06
3621 4642 4.323417 CACCAACAAGTTATCTGGCACTA 58.677 43.478 0.00 0.00 31.74 2.74
3626 4647 4.218200 TGATTGCACCAACAAGTTATCTGG 59.782 41.667 0.00 0.00 31.96 3.86
3640 4661 7.042187 TGTTTGTTTTCAACATATGATTGCACC 60.042 33.333 10.38 1.37 41.79 5.01
3641 4662 7.849496 TGTTTGTTTTCAACATATGATTGCAC 58.151 30.769 10.38 8.22 41.79 4.57
3666 4793 6.627395 TGATCGTGTCTTATTGTTTGGTTT 57.373 33.333 0.00 0.00 0.00 3.27
3667 4794 6.429692 TGATGATCGTGTCTTATTGTTTGGTT 59.570 34.615 0.00 0.00 0.00 3.67
3668 4795 5.937540 TGATGATCGTGTCTTATTGTTTGGT 59.062 36.000 0.00 0.00 0.00 3.67
3669 4796 6.421377 TGATGATCGTGTCTTATTGTTTGG 57.579 37.500 0.00 0.00 0.00 3.28
3670 4797 7.269084 GTGTTGATGATCGTGTCTTATTGTTTG 59.731 37.037 0.00 0.00 0.00 2.93
3688 4815 1.250328 ATGTGCCTGTGGTGTTGATG 58.750 50.000 0.00 0.00 0.00 3.07
3689 4816 1.999648 AATGTGCCTGTGGTGTTGAT 58.000 45.000 0.00 0.00 0.00 2.57
3690 4817 1.408340 CAAATGTGCCTGTGGTGTTGA 59.592 47.619 0.00 0.00 0.00 3.18
3691 4818 1.408340 TCAAATGTGCCTGTGGTGTTG 59.592 47.619 0.00 0.00 0.00 3.33
3692 4819 1.774110 TCAAATGTGCCTGTGGTGTT 58.226 45.000 0.00 0.00 0.00 3.32
3693 4820 1.614903 CATCAAATGTGCCTGTGGTGT 59.385 47.619 0.00 0.00 0.00 4.16
3701 4828 2.273557 GTCATTGCCATCAAATGTGCC 58.726 47.619 0.00 0.00 35.56 5.01
3716 4843 2.026641 AGCAGTGCTTTGTGTGTCATT 58.973 42.857 13.14 0.00 33.89 2.57
3757 4933 2.204461 TTCGTCTTGGCCGTCTCCA 61.204 57.895 0.00 0.00 0.00 3.86
4108 5287 1.679977 GAAGCCATGAAGCCCTGCA 60.680 57.895 0.00 0.00 0.00 4.41
4132 5311 3.515901 ACCACCAGACAGAGTAATCCTTC 59.484 47.826 0.00 0.00 0.00 3.46
4134 5313 3.191888 ACCACCAGACAGAGTAATCCT 57.808 47.619 0.00 0.00 0.00 3.24
4140 5319 1.133792 CCCAAAACCACCAGACAGAGT 60.134 52.381 0.00 0.00 0.00 3.24
4142 5321 1.142870 CTCCCAAAACCACCAGACAGA 59.857 52.381 0.00 0.00 0.00 3.41
4143 5322 1.609208 CTCCCAAAACCACCAGACAG 58.391 55.000 0.00 0.00 0.00 3.51
4146 5325 0.467290 GTGCTCCCAAAACCACCAGA 60.467 55.000 0.00 0.00 0.00 3.86
4147 5326 0.754957 TGTGCTCCCAAAACCACCAG 60.755 55.000 0.00 0.00 0.00 4.00
4148 5327 0.324738 TTGTGCTCCCAAAACCACCA 60.325 50.000 0.00 0.00 0.00 4.17
4149 5328 0.389025 CTTGTGCTCCCAAAACCACC 59.611 55.000 0.00 0.00 0.00 4.61
4150 5329 1.338020 CTCTTGTGCTCCCAAAACCAC 59.662 52.381 0.00 0.00 0.00 4.16
4239 5422 2.443887 TACGAAGTTTTAGCGGCACT 57.556 45.000 1.45 0.00 37.78 4.40
4255 5438 2.160117 CGTGCAATGCAAAAGCTTTACG 60.160 45.455 10.44 11.95 41.47 3.18
4256 5439 2.155539 CCGTGCAATGCAAAAGCTTTAC 59.844 45.455 10.44 8.62 41.47 2.01
4321 5506 3.123620 CTGAAGCAGTGCCGGAGC 61.124 66.667 12.58 2.48 40.48 4.70
4374 5559 1.899814 ACCTTGGACATGTCTCGCTAA 59.100 47.619 24.50 11.44 0.00 3.09
4379 5564 2.227388 CAGCAAACCTTGGACATGTCTC 59.773 50.000 24.50 15.19 0.00 3.36
4416 5601 2.106857 ACGGTCACCCCACTTCAATTAA 59.893 45.455 0.00 0.00 0.00 1.40
4437 5622 2.422597 CACTTTTATCGGTGTGCTCCA 58.577 47.619 0.00 0.00 0.00 3.86
4458 5643 5.659463 TGTTGGAAAATCTGTTCAACAAGG 58.341 37.500 0.00 0.00 31.57 3.61
4461 5646 6.871844 TCAATGTTGGAAAATCTGTTCAACA 58.128 32.000 9.17 9.17 35.26 3.33
4464 5649 5.068855 TGCTCAATGTTGGAAAATCTGTTCA 59.931 36.000 0.00 0.00 0.00 3.18
4465 5650 5.531634 TGCTCAATGTTGGAAAATCTGTTC 58.468 37.500 0.00 0.00 0.00 3.18
4466 5651 5.534207 TGCTCAATGTTGGAAAATCTGTT 57.466 34.783 0.00 0.00 0.00 3.16
4467 5652 5.534207 TTGCTCAATGTTGGAAAATCTGT 57.466 34.783 0.00 0.00 0.00 3.41
4468 5653 5.350365 CCATTGCTCAATGTTGGAAAATCTG 59.650 40.000 18.07 0.00 44.97 2.90
4469 5654 5.484715 CCATTGCTCAATGTTGGAAAATCT 58.515 37.500 18.07 0.00 44.97 2.40
4470 5655 5.789710 CCATTGCTCAATGTTGGAAAATC 57.210 39.130 18.07 0.00 44.97 2.17



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

AutoCloner maintained by Alex Coulton.