Multiple sequence alignment - TraesCS3D01G386000

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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 TraesCS3D01G386000 chr3D 100.000 3113 0 0 1 3113 501412268 501415380 0.000000e+00 5749.0
1 TraesCS3D01G386000 chr3D 82.753 1264 109 49 997 2188 308985854 308984628 0.000000e+00 1026.0
2 TraesCS3D01G386000 chr3D 81.719 1280 112 65 1 1244 501330649 501331842 0.000000e+00 955.0
3 TraesCS3D01G386000 chr3D 88.395 810 66 9 1374 2181 501331905 501332688 0.000000e+00 950.0
4 TraesCS3D01G386000 chr3A 91.768 2296 136 21 467 2734 640951295 640953565 0.000000e+00 3144.0
5 TraesCS3D01G386000 chr3A 91.785 2191 129 19 467 2629 641011589 641013756 0.000000e+00 3001.0
6 TraesCS3D01G386000 chr3A 83.398 1283 119 46 983 2188 428570307 428569042 0.000000e+00 1103.0
7 TraesCS3D01G386000 chr3A 90.370 810 61 8 1374 2179 640879910 640880706 0.000000e+00 1048.0
8 TraesCS3D01G386000 chr3A 80.191 1151 116 65 106 1244 640878805 640879855 0.000000e+00 760.0
9 TraesCS3D01G386000 chr3A 89.016 437 15 9 1 404 640950823 640951259 7.700000e-141 510.0
10 TraesCS3D01G386000 chr3A 89.016 437 15 9 1 404 641011117 641011553 7.700000e-141 510.0
11 TraesCS3D01G386000 chr3A 87.565 386 35 6 2736 3113 640953634 640954014 4.770000e-118 435.0
12 TraesCS3D01G386000 chr3A 87.565 386 35 6 2736 3113 641013904 641014284 4.770000e-118 435.0
13 TraesCS3D01G386000 chr3A 81.982 111 16 4 2 109 640867183 640867292 1.190000e-14 91.6
14 TraesCS3D01G386000 chr3B 92.362 1689 114 7 1058 2734 663062316 663060631 0.000000e+00 2390.0
15 TraesCS3D01G386000 chr3B 83.267 1255 125 45 998 2185 412595901 412597137 0.000000e+00 1075.0
16 TraesCS3D01G386000 chr3B 87.966 831 65 8 1376 2203 663071922 663071124 0.000000e+00 948.0
17 TraesCS3D01G386000 chr3B 83.847 811 59 36 445 1244 663072734 663071985 0.000000e+00 706.0
18 TraesCS3D01G386000 chr3B 89.564 527 21 11 256 751 663063456 663062933 3.390000e-179 638.0
19 TraesCS3D01G386000 chr3B 88.919 370 26 8 2752 3113 663060542 663060180 2.850000e-120 442.0
20 TraesCS3D01G386000 chr3B 93.970 199 12 0 29 227 663065696 663065498 5.050000e-78 302.0
21 TraesCS3D01G386000 chr3B 85.217 230 29 4 1 227 663079737 663079510 6.710000e-57 231.0
22 TraesCS3D01G386000 chr3B 90.769 65 3 2 609 673 412595524 412595585 1.990000e-12 84.2


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 TraesCS3D01G386000 chr3D 501412268 501415380 3112 False 5749.000000 5749 100.000000 1 3113 1 chr3D.!!$F1 3112
1 TraesCS3D01G386000 chr3D 308984628 308985854 1226 True 1026.000000 1026 82.753000 997 2188 1 chr3D.!!$R1 1191
2 TraesCS3D01G386000 chr3D 501330649 501332688 2039 False 952.500000 955 85.057000 1 2181 2 chr3D.!!$F2 2180
3 TraesCS3D01G386000 chr3A 640950823 640954014 3191 False 1363.000000 3144 89.449667 1 3113 3 chr3A.!!$F3 3112
4 TraesCS3D01G386000 chr3A 641011117 641014284 3167 False 1315.333333 3001 89.455333 1 3113 3 chr3A.!!$F4 3112
5 TraesCS3D01G386000 chr3A 428569042 428570307 1265 True 1103.000000 1103 83.398000 983 2188 1 chr3A.!!$R1 1205
6 TraesCS3D01G386000 chr3A 640878805 640880706 1901 False 904.000000 1048 85.280500 106 2179 2 chr3A.!!$F2 2073
7 TraesCS3D01G386000 chr3B 663060180 663065696 5516 True 943.000000 2390 91.203750 29 3113 4 chr3B.!!$R2 3084
8 TraesCS3D01G386000 chr3B 663071124 663072734 1610 True 827.000000 948 85.906500 445 2203 2 chr3B.!!$R3 1758
9 TraesCS3D01G386000 chr3B 412595524 412597137 1613 False 579.600000 1075 87.018000 609 2185 2 chr3B.!!$F1 1576

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
402 2464 0.31716 TACCAACACAGTGCGAGGAG 59.683 55.0 12.20 0.00 0.00 3.69 F
812 2974 0.45837 CTGCATAAAGTTTGCCGGCC 60.458 55.0 26.77 8.84 39.39 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 4567 0.036388 GGGAGTTTCAGTGGCATCGA 60.036 55.0 0.00 0.0 0.00 3.59 R
2525 5187 0.109153 TGTTGTCTCAGCATGCAGGT 59.891 50.0 21.98 0.0 34.76 4.00 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
60 69 2.727123 ACATGGACACAAGGTGACAA 57.273 45.000 2.98 0.00 36.96 3.18
98 107 1.280457 AACAGGGTCAAGGAGCTAGG 58.720 55.000 0.00 0.00 0.00 3.02
161 172 0.611896 CCCCAGTTGTTCCCATCCAC 60.612 60.000 0.00 0.00 0.00 4.02
227 242 1.138883 GCATCGTAGCGTCTGTCCA 59.861 57.895 0.00 0.00 0.00 4.02
238 2272 2.665794 GCGTCTGTCCAAAAGCTTAAGC 60.666 50.000 20.09 20.09 42.49 3.09
249 2283 3.369381 GCTTAAGCGCATGAGGAGA 57.631 52.632 12.53 0.00 0.00 3.71
252 2286 0.465705 TTAAGCGCATGAGGAGAGGG 59.534 55.000 11.47 0.00 0.00 4.30
349 2403 1.002134 TGCTGCTACAAGGGAAGCC 60.002 57.895 0.00 0.00 37.97 4.35
356 2410 2.678190 GCTACAAGGGAAGCCTAGTGTG 60.678 54.545 0.00 0.00 32.40 3.82
399 2461 1.135972 GCATTACCAACACAGTGCGAG 60.136 52.381 0.00 0.00 0.00 5.03
400 2462 1.464608 CATTACCAACACAGTGCGAGG 59.535 52.381 0.00 2.63 0.00 4.63
401 2463 0.753867 TTACCAACACAGTGCGAGGA 59.246 50.000 12.20 0.00 0.00 3.71
402 2464 0.317160 TACCAACACAGTGCGAGGAG 59.683 55.000 12.20 0.00 0.00 3.69
413 2493 4.655527 CGAGGAGACGCACAAGTT 57.344 55.556 0.00 0.00 0.00 2.66
521 2609 1.378646 GGAGTTGGGTTAGCTGGGC 60.379 63.158 0.00 0.00 0.00 5.36
532 2621 3.006859 GGTTAGCTGGGCTTTGATTTTGT 59.993 43.478 0.00 0.00 40.44 2.83
812 2974 0.458370 CTGCATAAAGTTTGCCGGCC 60.458 55.000 26.77 8.84 39.39 6.13
838 3001 1.070445 CCCCTCTCTGCTAGCAATCAG 59.930 57.143 19.86 14.37 0.00 2.90
849 3012 1.378250 GCAATCAGACCTGCCTGCT 60.378 57.895 12.74 0.00 36.00 4.24
947 3136 0.888619 TCGTGGTGGAGAGCAAGTAG 59.111 55.000 0.00 0.00 31.79 2.57
1108 3645 4.729918 ACCCTAGGACGGACGCGT 62.730 66.667 13.85 13.85 0.00 6.01
1110 3647 2.570181 CCTAGGACGGACGCGTTT 59.430 61.111 15.53 0.00 0.00 3.60
1261 3827 4.838986 TGAGTAACTAGTGAGGCTTCCTTT 59.161 41.667 0.00 0.00 31.76 3.11
1262 3828 5.047235 TGAGTAACTAGTGAGGCTTCCTTTC 60.047 44.000 0.00 0.00 31.76 2.62
1263 3829 3.704800 AACTAGTGAGGCTTCCTTTCC 57.295 47.619 0.00 0.00 31.76 3.13
1264 3830 1.909986 ACTAGTGAGGCTTCCTTTCCC 59.090 52.381 0.00 0.00 31.76 3.97
1265 3831 0.902531 TAGTGAGGCTTCCTTTCCCG 59.097 55.000 0.00 0.00 31.76 5.14
1266 3832 1.128188 AGTGAGGCTTCCTTTCCCGT 61.128 55.000 0.00 0.00 31.76 5.28
1267 3833 0.955919 GTGAGGCTTCCTTTCCCGTG 60.956 60.000 0.00 0.00 31.76 4.94
1268 3834 2.034221 AGGCTTCCTTTCCCGTGC 59.966 61.111 0.00 0.00 0.00 5.34
1269 3835 3.062466 GGCTTCCTTTCCCGTGCC 61.062 66.667 0.00 0.00 0.00 5.01
1270 3836 3.431725 GCTTCCTTTCCCGTGCCG 61.432 66.667 0.00 0.00 0.00 5.69
1271 3837 3.431725 CTTCCTTTCCCGTGCCGC 61.432 66.667 0.00 0.00 0.00 6.53
1275 3841 3.431725 CTTTCCCGTGCCGCCTTC 61.432 66.667 0.00 0.00 0.00 3.46
1334 3915 5.261661 CGTAGTCTGTTAATGGTACTCGAC 58.738 45.833 0.00 0.00 0.00 4.20
1383 3981 5.119931 TGCGAAATGTCTGCTTAATTTGT 57.880 34.783 0.00 0.00 0.00 2.83
1459 4060 2.254350 CGCACGAGTCGTTCCTGA 59.746 61.111 17.16 0.00 38.32 3.86
1469 4070 2.347490 GTTCCTGAGCGGCCAGAA 59.653 61.111 16.73 4.26 36.29 3.02
1533 4146 1.140804 GGCCTCTTGCTCGTCTCTC 59.859 63.158 0.00 0.00 40.92 3.20
1718 4337 3.695606 GGAGCTGCGGAGTGACCA 61.696 66.667 5.62 0.00 38.90 4.02
1779 4398 0.842467 CCACCTCCCTCCACCTTCTT 60.842 60.000 0.00 0.00 0.00 2.52
1850 4469 4.347583 TGATTTTGCTTCCTTTCCCATTGT 59.652 37.500 0.00 0.00 0.00 2.71
2050 4696 0.534877 CAGCGGCATGGGCATAACTA 60.535 55.000 1.45 0.00 43.71 2.24
2091 4737 2.045926 CCCTTCCCGTTCTGCCTG 60.046 66.667 0.00 0.00 0.00 4.85
2240 4901 1.493022 AGTTGGGTACAAAGCACTCCA 59.507 47.619 0.00 0.00 38.54 3.86
2276 4937 7.700022 AATTATATCGAGGTCCTACCACTAC 57.300 40.000 0.00 0.00 41.95 2.73
2279 4940 1.101331 CGAGGTCCTACCACTACCAC 58.899 60.000 0.00 0.00 41.95 4.16
2295 4956 2.665185 ACCGCCAGAACAAGTCGC 60.665 61.111 0.00 0.00 0.00 5.19
2305 4966 2.354188 CAAGTCGCCGACACGTCA 60.354 61.111 20.65 0.00 34.60 4.35
2309 4970 2.019951 GTCGCCGACACGTCATTGT 61.020 57.895 13.23 0.00 32.09 2.71
2315 4976 0.937699 CGACACGTCATTGTCACCGT 60.938 55.000 4.96 0.00 45.38 4.83
2328 4990 2.120274 ACCGTTCCCCTACCGGAA 59.880 61.111 9.46 0.00 44.41 4.30
2357 5019 2.676121 TTGTTCATGGCAGCCGGG 60.676 61.111 7.03 0.68 0.00 5.73
2363 5025 4.115199 ATGGCAGCCGGGAAGTCC 62.115 66.667 7.03 0.00 0.00 3.85
2375 5037 1.021390 GGAAGTCCTCATGCACGTGG 61.021 60.000 18.88 0.08 0.00 4.94
2402 5064 2.534990 GGACTAGCATCCTAGAGCCAT 58.465 52.381 0.00 0.00 43.07 4.40
2426 5088 1.069022 CGTCTTCGTCGTTGAACCCTA 60.069 52.381 0.00 0.00 0.00 3.53
2460 5122 3.761657 CATGTCACCATTGCATACACAC 58.238 45.455 0.00 0.00 0.00 3.82
2462 5124 3.217626 TGTCACCATTGCATACACACAA 58.782 40.909 0.00 0.00 0.00 3.33
2477 5139 3.697542 ACACACAACAAGAAACCCTAACC 59.302 43.478 0.00 0.00 0.00 2.85
2481 5143 2.812011 CAACAAGAAACCCTAACCCTCG 59.188 50.000 0.00 0.00 0.00 4.63
2490 5152 1.087501 CCTAACCCTCGCAAGCTTTC 58.912 55.000 0.00 0.00 37.18 2.62
2492 5154 1.296056 TAACCCTCGCAAGCTTTCGC 61.296 55.000 13.88 6.16 37.18 4.70
2508 5170 2.679716 GCTGCCCCATGTCCTCTT 59.320 61.111 0.00 0.00 0.00 2.85
2513 5175 1.186200 GCCCCATGTCCTCTTTTTCC 58.814 55.000 0.00 0.00 0.00 3.13
2516 5178 2.292455 CCCCATGTCCTCTTTTTCCCAT 60.292 50.000 0.00 0.00 0.00 4.00
2525 5187 3.273434 CTCTTTTTCCCATGAGCGATCA 58.727 45.455 5.53 5.53 0.00 2.92
2571 5233 0.675083 TGAAAGCCGTCCAACTACGA 59.325 50.000 0.00 0.00 45.68 3.43
2584 5246 3.250040 CCAACTACGAGGTTTGTTCAAGG 59.750 47.826 0.00 0.00 0.00 3.61
2590 5252 4.315803 ACGAGGTTTGTTCAAGGTAGATG 58.684 43.478 0.00 0.00 0.00 2.90
2609 5271 1.761784 TGCCAAAACCTTGAACATGCT 59.238 42.857 0.00 0.00 34.14 3.79
2615 5277 5.406175 CCAAAACCTTGAACATGCTATTGTG 59.594 40.000 0.00 0.00 34.14 3.33
2619 5281 4.216257 ACCTTGAACATGCTATTGTGTCAC 59.784 41.667 0.00 0.00 0.00 3.67
2708 5370 7.828717 TCCTTCATTGATTTTAGTGTGATGCTA 59.171 33.333 0.00 0.00 0.00 3.49
2718 5380 2.299013 AGTGTGATGCTAGTCGAAACCA 59.701 45.455 0.00 0.00 0.00 3.67
2721 5383 2.412089 GTGATGCTAGTCGAAACCACAC 59.588 50.000 0.00 0.00 0.00 3.82
2722 5384 2.036604 TGATGCTAGTCGAAACCACACA 59.963 45.455 0.00 0.00 0.00 3.72
2723 5385 1.860676 TGCTAGTCGAAACCACACAC 58.139 50.000 0.00 0.00 0.00 3.82
2734 5396 2.727123 ACCACACACCTTGATGAACA 57.273 45.000 0.00 0.00 0.00 3.18
2750 5479 0.179113 AACAAGCAGGTTTTGGCACG 60.179 50.000 0.00 0.00 0.00 5.34
2802 5539 3.767131 AGGTTTTGGCACCATGGTATTAC 59.233 43.478 19.28 8.64 39.62 1.89
2829 5566 6.055231 TGTCGAAAGAACACCAAATACTTG 57.945 37.500 0.00 0.00 45.01 3.16
2832 5569 6.206692 TCGAAAGAACACCAAATACTTGGCT 61.207 40.000 2.07 0.00 47.00 4.75
2850 5587 8.894768 ACTTGGCTAATCTATAAAGATCACAC 57.105 34.615 0.00 0.00 41.81 3.82
2869 5606 4.795795 CACACGTCTAAACATTTTTGTGCA 59.204 37.500 0.00 0.00 0.00 4.57
2873 5610 5.163703 ACGTCTAAACATTTTTGTGCAGTGA 60.164 36.000 0.00 0.00 0.00 3.41
2904 5641 4.635765 TCCTTGTCGAGAAAATTAGCCATG 59.364 41.667 0.00 0.00 0.00 3.66
2943 5683 4.411327 TCAAGTTTTTCGTTGCTGTTCTG 58.589 39.130 0.00 0.00 0.00 3.02
2975 5715 0.671163 TGTATGGTCGCCGGTGAAAC 60.671 55.000 21.49 16.28 0.00 2.78
2979 5719 2.970324 GTCGCCGGTGAAACTGCA 60.970 61.111 21.49 0.00 43.57 4.41
2981 5721 2.972505 CGCCGGTGAAACTGCACT 60.973 61.111 10.20 0.00 43.57 4.40
2987 5727 3.425758 GCCGGTGAAACTGCACTTTATAC 60.426 47.826 1.90 0.00 43.57 1.47
3007 5747 4.558226 ACTGCAAATGATCCTACACTCA 57.442 40.909 0.00 0.00 0.00 3.41
3015 5755 6.560253 AATGATCCTACACTCAACAAACAC 57.440 37.500 0.00 0.00 0.00 3.32
3045 5785 9.073475 ACAAATGGTATGTTGTTGTGTAATACT 57.927 29.630 0.00 0.00 34.29 2.12
3046 5786 9.340695 CAAATGGTATGTTGTTGTGTAATACTG 57.659 33.333 0.00 0.00 0.00 2.74
3047 5787 8.856153 AATGGTATGTTGTTGTGTAATACTGA 57.144 30.769 0.00 0.00 0.00 3.41
3048 5788 7.661127 TGGTATGTTGTTGTGTAATACTGAC 57.339 36.000 0.00 0.00 0.00 3.51
3049 5789 6.651643 TGGTATGTTGTTGTGTAATACTGACC 59.348 38.462 0.00 0.00 0.00 4.02
3050 5790 6.651643 GGTATGTTGTTGTGTAATACTGACCA 59.348 38.462 0.00 0.00 0.00 4.02
3051 5791 5.994887 TGTTGTTGTGTAATACTGACCAC 57.005 39.130 0.00 0.00 0.00 4.16
3099 5840 8.562892 CAAGTAAATTGGCCAATAGAGTATGAG 58.437 37.037 30.84 11.84 35.08 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 69 5.189539 CCTGTTTCCAAAATGGGGATGTATT 59.810 40.000 0.00 0.00 38.32 1.89
161 172 0.248289 CTGCTCCAATGCTTTTGGGG 59.752 55.000 16.00 14.51 42.94 4.96
227 242 2.421424 CTCCTCATGCGCTTAAGCTTTT 59.579 45.455 24.33 6.49 39.32 2.27
238 2272 4.247380 GGGCCCTCTCCTCATGCG 62.247 72.222 17.04 0.00 0.00 4.73
349 2403 2.287308 GCCTAGCTCGATCACACACTAG 60.287 54.545 0.00 0.00 0.00 2.57
399 2461 1.003866 GTTGTCAACTTGTGCGTCTCC 60.004 52.381 8.53 0.00 0.00 3.71
400 2462 1.003866 GGTTGTCAACTTGTGCGTCTC 60.004 52.381 15.17 0.00 0.00 3.36
401 2463 1.014352 GGTTGTCAACTTGTGCGTCT 58.986 50.000 15.17 0.00 0.00 4.18
402 2464 1.014352 AGGTTGTCAACTTGTGCGTC 58.986 50.000 15.17 0.00 0.00 5.19
413 2493 2.354704 GCTAGCACATACCAGGTTGTCA 60.355 50.000 10.63 0.00 0.00 3.58
498 2584 2.304761 CCAGCTAACCCAACTCCAACTA 59.695 50.000 0.00 0.00 0.00 2.24
521 2609 7.637132 GCAAGAAATGACAACACAAAATCAAAG 59.363 33.333 0.00 0.00 0.00 2.77
532 2621 4.422840 CAACAGTGCAAGAAATGACAACA 58.577 39.130 0.00 0.00 0.00 3.33
591 2689 1.135888 TCGCGTTCCGGTGATATATCG 60.136 52.381 5.77 0.00 37.59 2.92
829 2992 0.107508 GCAGGCAGGTCTGATTGCTA 60.108 55.000 4.84 0.00 40.15 3.49
838 3001 3.875510 AAGGGCAAGCAGGCAGGTC 62.876 63.158 5.17 0.00 46.44 3.85
866 3051 1.250328 TGTCACTACCGGACGTCAAT 58.750 50.000 18.91 4.23 38.10 2.57
968 3157 1.966901 CTATGTGCTACCGGGCCACA 61.967 60.000 21.10 21.10 0.00 4.17
1108 3645 2.160171 CCCTCCCCCACCTGACAAA 61.160 63.158 0.00 0.00 0.00 2.83
1110 3647 3.537506 TCCCTCCCCCACCTGACA 61.538 66.667 0.00 0.00 0.00 3.58
1244 3781 1.909986 GGGAAAGGAAGCCTCACTAGT 59.090 52.381 0.00 0.00 30.89 2.57
1265 3831 4.056125 GCCAAAGGAAGGCGGCAC 62.056 66.667 13.08 4.52 44.25 5.01
1271 3837 1.762370 ACAACAAAGGCCAAAGGAAGG 59.238 47.619 5.01 0.00 0.00 3.46
1272 3838 2.224042 GGACAACAAAGGCCAAAGGAAG 60.224 50.000 5.01 0.00 0.00 3.46
1273 3839 1.760029 GGACAACAAAGGCCAAAGGAA 59.240 47.619 5.01 0.00 0.00 3.36
1274 3840 1.063266 AGGACAACAAAGGCCAAAGGA 60.063 47.619 5.01 0.00 0.00 3.36
1275 3841 1.413118 AGGACAACAAAGGCCAAAGG 58.587 50.000 5.01 0.00 0.00 3.11
1276 3842 3.222603 ACTAGGACAACAAAGGCCAAAG 58.777 45.455 5.01 0.00 0.00 2.77
1277 3843 3.306472 ACTAGGACAACAAAGGCCAAA 57.694 42.857 5.01 0.00 0.00 3.28
1278 3844 4.440826 TTACTAGGACAACAAAGGCCAA 57.559 40.909 5.01 0.00 0.00 4.52
1383 3981 2.931969 CTGCACAGCAATCTCATCGTAA 59.068 45.455 0.00 0.00 38.41 3.18
1459 4060 3.909086 GAAGGTGCTTCTGGCCGCT 62.909 63.158 0.00 0.00 40.92 5.52
1706 4325 2.285773 ATGAGCTGGTCACTCCGCA 61.286 57.895 12.27 0.00 38.28 5.69
1718 4337 0.394899 GGCAAGTAAGGGCATGAGCT 60.395 55.000 0.00 0.00 41.70 4.09
1779 4398 1.004560 CTTCTCGGCTGCCTGTTGA 60.005 57.895 17.92 5.45 0.00 3.18
1936 4567 0.036388 GGGAGTTTCAGTGGCATCGA 60.036 55.000 0.00 0.00 0.00 3.59
2050 4696 2.111043 CACTGCGGTCCCACTGTT 59.889 61.111 0.00 0.00 0.00 3.16
2091 4737 1.322442 AGAAGAAACACTGGCCAAGC 58.678 50.000 7.01 0.00 0.00 4.01
2203 4864 9.832445 GTACCCAACTTCTATAATTGATTCAGA 57.168 33.333 0.00 0.00 0.00 3.27
2205 4866 9.967451 TTGTACCCAACTTCTATAATTGATTCA 57.033 29.630 0.00 0.00 0.00 2.57
2224 4885 1.071699 TGTCTGGAGTGCTTTGTACCC 59.928 52.381 0.00 0.00 0.00 3.69
2225 4886 2.543777 TGTCTGGAGTGCTTTGTACC 57.456 50.000 0.00 0.00 0.00 3.34
2259 4920 0.994247 TGGTAGTGGTAGGACCTCGA 59.006 55.000 0.00 0.00 39.58 4.04
2276 4937 2.317609 CGACTTGTTCTGGCGGTGG 61.318 63.158 0.00 0.00 0.00 4.61
2279 4940 3.423154 GGCGACTTGTTCTGGCGG 61.423 66.667 0.00 0.00 0.00 6.13
2305 4966 0.616891 GGTAGGGGAACGGTGACAAT 59.383 55.000 0.00 0.00 0.00 2.71
2309 4970 2.681064 CCGGTAGGGGAACGGTGA 60.681 66.667 0.00 0.00 42.53 4.02
2328 4990 0.620556 ATGAACAAGGTCAGGCCGAT 59.379 50.000 0.00 0.00 43.70 4.18
2334 4996 0.524862 GCTGCCATGAACAAGGTCAG 59.475 55.000 0.00 12.42 34.39 3.51
2357 5019 1.021390 CCCACGTGCATGAGGACTTC 61.021 60.000 22.45 0.00 33.37 3.01
2363 5025 1.078497 TTAGGCCCACGTGCATGAG 60.078 57.895 14.17 4.33 0.00 2.90
2375 5037 1.723288 AGGATGCTAGTCCTTAGGCC 58.277 55.000 0.00 0.00 46.45 5.19
2395 5057 1.251527 ACGAAGACGACCATGGCTCT 61.252 55.000 13.04 6.51 42.66 4.09
2426 5088 2.744202 GGTGACATGCACTTTCGATTCT 59.256 45.455 16.34 0.00 46.86 2.40
2460 5122 2.812011 CGAGGGTTAGGGTTTCTTGTTG 59.188 50.000 0.00 0.00 0.00 3.33
2462 5124 1.271217 GCGAGGGTTAGGGTTTCTTGT 60.271 52.381 0.00 0.00 0.00 3.16
2490 5152 2.826777 AAAGAGGACATGGGGCAGCG 62.827 60.000 0.00 0.00 0.00 5.18
2492 5154 1.821136 GAAAAAGAGGACATGGGGCAG 59.179 52.381 0.00 0.00 0.00 4.85
2497 5159 3.698040 CTCATGGGAAAAAGAGGACATGG 59.302 47.826 0.00 0.00 37.05 3.66
2508 5170 1.281867 AGGTGATCGCTCATGGGAAAA 59.718 47.619 6.18 0.00 38.64 2.29
2513 5175 0.534427 ATGCAGGTGATCGCTCATGG 60.534 55.000 6.18 0.00 32.98 3.66
2516 5178 1.816679 GCATGCAGGTGATCGCTCA 60.817 57.895 14.21 2.84 0.00 4.26
2525 5187 0.109153 TGTTGTCTCAGCATGCAGGT 59.891 50.000 21.98 0.00 34.76 4.00
2571 5233 3.181434 TGGCATCTACCTTGAACAAACCT 60.181 43.478 0.00 0.00 0.00 3.50
2584 5246 4.846779 TGTTCAAGGTTTTGGCATCTAC 57.153 40.909 0.00 0.00 34.97 2.59
2590 5252 2.531522 AGCATGTTCAAGGTTTTGGC 57.468 45.000 0.00 0.00 34.97 4.52
2609 5271 1.067495 TCATGCGACGGTGACACAATA 60.067 47.619 8.08 0.00 0.00 1.90
2615 5277 2.203800 TTAGATCATGCGACGGTGAC 57.796 50.000 0.00 0.00 0.00 3.67
2708 5370 1.208535 TCAAGGTGTGTGGTTTCGACT 59.791 47.619 0.00 0.00 0.00 4.18
2734 5396 1.904287 TATCGTGCCAAAACCTGCTT 58.096 45.000 0.00 0.00 0.00 3.91
2802 5539 4.364415 TTTGGTGTTCTTTCGACAAAGG 57.636 40.909 0.00 0.00 39.75 3.11
2829 5566 7.371936 AGACGTGTGATCTTTATAGATTAGCC 58.628 38.462 0.00 0.00 41.23 3.93
2845 5582 5.031578 GCACAAAAATGTTTAGACGTGTGA 58.968 37.500 0.00 0.00 0.00 3.58
2849 5586 5.034152 CACTGCACAAAAATGTTTAGACGT 58.966 37.500 0.00 0.00 0.00 4.34
2850 5587 5.270083 TCACTGCACAAAAATGTTTAGACG 58.730 37.500 0.00 0.00 0.00 4.18
2885 5622 5.483811 TGTACATGGCTAATTTTCTCGACA 58.516 37.500 0.00 0.00 0.00 4.35
2915 5654 3.113322 GCAACGAAAAACTTGAGGAACC 58.887 45.455 0.00 0.00 0.00 3.62
2943 5683 4.499040 GCGACCATACACAACAATATTTGC 59.501 41.667 0.00 0.00 0.00 3.68
2979 5719 8.267894 AGTGTAGGATCATTTGCAGTATAAAGT 58.732 33.333 0.00 0.00 0.00 2.66
2981 5721 8.264347 TGAGTGTAGGATCATTTGCAGTATAAA 58.736 33.333 0.00 0.00 0.00 1.40
2987 5727 4.696877 TGTTGAGTGTAGGATCATTTGCAG 59.303 41.667 0.00 0.00 0.00 4.41
3007 5747 6.872920 ACATACCATTTGTTCTGTGTTTGTT 58.127 32.000 0.00 0.00 0.00 2.83
3015 5755 6.272318 ACACAACAACATACCATTTGTTCTG 58.728 36.000 0.00 0.00 42.67 3.02
3045 5785 8.264347 TCAGCACTTCTAATTTATATGTGGTCA 58.736 33.333 8.57 0.00 33.35 4.02
3046 5786 8.662781 TCAGCACTTCTAATTTATATGTGGTC 57.337 34.615 8.57 0.00 33.35 4.02
3047 5787 9.277783 GATCAGCACTTCTAATTTATATGTGGT 57.722 33.333 6.68 6.68 35.49 4.16
3048 5788 9.276590 TGATCAGCACTTCTAATTTATATGTGG 57.723 33.333 0.00 0.00 0.00 4.17
3076 5816 7.224297 TCCTCATACTCTATTGGCCAATTTAC 58.776 38.462 34.85 0.00 32.50 2.01
3083 5824 5.512232 CCTTCTTCCTCATACTCTATTGGCC 60.512 48.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.