Multiple sequence alignment - TraesCS4B01G381900

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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 TraesCS4B01G381900 chr4B 100.000 4970 0 0 1 4970 661492217 661497186 0.000000e+00 9178
1 TraesCS4B01G381900 chr4B 93.956 2945 171 4 4 2947 661684632 661681694 0.000000e+00 4446
2 TraesCS4B01G381900 chr4B 93.815 2021 86 10 2973 4970 661681710 661679706 0.000000e+00 3003
3 TraesCS4B01G381900 chr4D 91.254 2950 231 19 4 2947 505993380 505990452 0.000000e+00 3993
4 TraesCS4B01G381900 chr4D 92.792 874 45 2 2974 3847 505990467 505989612 0.000000e+00 1249
5 TraesCS4B01G381900 chr4D 89.513 534 23 6 4042 4575 505989615 505989115 0.000000e+00 645
6 TraesCS4B01G381900 chr4D 94.361 266 11 3 4573 4838 505989063 505988802 5.990000e-109 405
7 TraesCS4B01G381900 chr4D 97.674 129 3 0 4842 4970 505988763 505988635 6.480000e-54 222
8 TraesCS4B01G381900 chr5A 89.755 2938 272 18 5 2936 702142295 702139381 0.000000e+00 3731
9 TraesCS4B01G381900 chr5A 91.710 1146 57 12 3716 4838 702138632 702137502 0.000000e+00 1555
10 TraesCS4B01G381900 chr5A 94.063 758 41 2 2999 3756 702139385 702138632 0.000000e+00 1147
11 TraesCS4B01G381900 chr5A 96.124 129 5 0 4842 4970 702137463 702137335 1.400000e-50 211
12 TraesCS4B01G381900 chrUn 78.947 1501 261 37 2972 4446 88961095 88962566 0.000000e+00 970
13 TraesCS4B01G381900 chrUn 78.098 1283 232 32 3190 4446 88952915 88954174 0.000000e+00 767
14 TraesCS4B01G381900 chrUn 78.098 1283 232 32 3190 4446 269540482 269539223 0.000000e+00 767
15 TraesCS4B01G381900 chrUn 87.349 166 20 1 2972 3137 88952748 88952912 6.570000e-44 189
16 TraesCS4B01G381900 chrUn 87.349 166 20 1 2972 3137 269540649 269540485 6.570000e-44 189
17 TraesCS4B01G381900 chr7B 78.711 1334 237 31 3138 4446 746551792 746550481 0.000000e+00 846
18 TraesCS4B01G381900 chr7B 81.993 883 145 12 3167 4040 746223791 746224668 0.000000e+00 737
19 TraesCS4B01G381900 chr7B 82.135 862 139 12 3167 4018 744679438 744678582 0.000000e+00 725
20 TraesCS4B01G381900 chr7B 81.765 861 142 12 3167 4018 746568813 746567959 0.000000e+00 706
21 TraesCS4B01G381900 chr7B 81.765 861 142 12 3167 4018 746597141 746596287 0.000000e+00 706
22 TraesCS4B01G381900 chr7B 81.900 221 30 7 4226 4442 744678455 744678241 1.420000e-40 178
23 TraesCS4B01G381900 chr7B 81.081 222 32 7 4226 4443 746224773 746224988 8.560000e-38 169
24 TraesCS4B01G381900 chr7A 78.346 1330 233 44 3144 4445 735061301 735059999 0.000000e+00 809
25 TraesCS4B01G381900 chr7A 77.811 1334 246 38 3138 4445 735058398 735057089 0.000000e+00 778
26 TraesCS4B01G381900 chr7D 80.181 883 152 16 3166 4040 632498680 632497813 1.510000e-179 640
27 TraesCS4B01G381900 chr1B 81.129 567 69 21 4004 4554 89697421 89696877 2.140000e-113 420


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 TraesCS4B01G381900 chr4B 661492217 661497186 4969 False 9178.0 9178 100.0000 1 4970 1 chr4B.!!$F1 4969
1 TraesCS4B01G381900 chr4B 661679706 661684632 4926 True 3724.5 4446 93.8855 4 4970 2 chr4B.!!$R1 4966
2 TraesCS4B01G381900 chr4D 505988635 505993380 4745 True 1302.8 3993 93.1188 4 4970 5 chr4D.!!$R1 4966
3 TraesCS4B01G381900 chr5A 702137335 702142295 4960 True 1661.0 3731 92.9130 5 4970 4 chr5A.!!$R1 4965
4 TraesCS4B01G381900 chrUn 88961095 88962566 1471 False 970.0 970 78.9470 2972 4446 1 chrUn.!!$F1 1474
5 TraesCS4B01G381900 chrUn 88952748 88954174 1426 False 478.0 767 82.7235 2972 4446 2 chrUn.!!$F2 1474
6 TraesCS4B01G381900 chrUn 269539223 269540649 1426 True 478.0 767 82.7235 2972 4446 2 chrUn.!!$R1 1474
7 TraesCS4B01G381900 chr7B 746550481 746551792 1311 True 846.0 846 78.7110 3138 4446 1 chr7B.!!$R1 1308
8 TraesCS4B01G381900 chr7B 746567959 746568813 854 True 706.0 706 81.7650 3167 4018 1 chr7B.!!$R2 851
9 TraesCS4B01G381900 chr7B 746596287 746597141 854 True 706.0 706 81.7650 3167 4018 1 chr7B.!!$R3 851
10 TraesCS4B01G381900 chr7B 746223791 746224988 1197 False 453.0 737 81.5370 3167 4443 2 chr7B.!!$F1 1276
11 TraesCS4B01G381900 chr7B 744678241 744679438 1197 True 451.5 725 82.0175 3167 4442 2 chr7B.!!$R4 1275
12 TraesCS4B01G381900 chr7A 735057089 735061301 4212 True 793.5 809 78.0785 3138 4445 2 chr7A.!!$R1 1307
13 TraesCS4B01G381900 chr7D 632497813 632498680 867 True 640.0 640 80.1810 3166 4040 1 chr7D.!!$R1 874
14 TraesCS4B01G381900 chr1B 89696877 89697421 544 True 420.0 420 81.1290 4004 4554 1 chr1B.!!$R1 550

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
527 533 0.036952 CTACGCAGGGGCATATGAGG 60.037 60.0 6.97 0.00 41.24 3.86 F
1512 1522 0.036858 TCATCAATGCCGTCGTTCCA 60.037 50.0 0.00 0.00 0.00 3.53 F
2223 2233 0.030101 TTTGAACGAAAGCCGGCAAG 59.970 50.0 31.54 18.48 43.93 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2213 0.248702 TTGCCGGCTTTCGTTCAAAC 60.249 50.0 29.70 0.00 37.11 2.93 R
3489 3510 0.880441 TGTCGTTTGGACCGATACGA 59.120 50.0 10.39 10.39 45.46 3.43 R
4141 4215 0.971447 AGTCCCTCCTGCCGAACTAC 60.971 60.0 0.00 0.00 0.00 2.73 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
61 62 2.596346 TGACTGATTTTGTGGTGCCAT 58.404 42.857 0.00 0.00 0.00 4.40
78 79 2.164422 GCCATCTACTTCCTTTTGTGGC 59.836 50.000 0.00 0.00 43.29 5.01
188 189 7.771927 AATTGATCAGAGGTTCTTGAAATGT 57.228 32.000 0.00 0.00 0.00 2.71
189 190 6.564709 TTGATCAGAGGTTCTTGAAATGTG 57.435 37.500 0.00 0.00 0.00 3.21
511 517 3.520691 AGGGGTGTTCCTTTTTCCTAC 57.479 47.619 0.00 0.00 32.13 3.18
527 533 0.036952 CTACGCAGGGGCATATGAGG 60.037 60.000 6.97 0.00 41.24 3.86
635 642 1.010797 CATCGTAAGCGGTGCATGC 60.011 57.895 11.82 11.82 42.60 4.06
649 656 1.117150 GCATGCCATTCATTGACCCT 58.883 50.000 6.36 0.00 31.79 4.34
756 763 2.941064 CACTCGTCCTCTATCCACGTTA 59.059 50.000 0.00 0.00 35.05 3.18
760 767 2.686915 CGTCCTCTATCCACGTTACCTT 59.313 50.000 0.00 0.00 0.00 3.50
793 800 0.878961 GTGTGACCTGTCAACCGTCC 60.879 60.000 0.75 0.00 41.85 4.79
833 840 5.063880 AGTTCCTTAGCGTTGAAACTGAAT 58.936 37.500 0.00 0.00 0.00 2.57
857 864 2.159627 CCACGCCTCAGAACAAATACAC 59.840 50.000 0.00 0.00 0.00 2.90
1174 1181 4.192317 GCCCAACTCCAACTATAGTCAAG 58.808 47.826 5.70 6.70 0.00 3.02
1190 1199 9.930693 CTATAGTCAAGTCCAAAACTACTCTTT 57.069 33.333 0.00 0.00 37.17 2.52
1191 1200 6.927294 AGTCAAGTCCAAAACTACTCTTTG 57.073 37.500 0.00 0.00 37.17 2.77
1192 1201 6.415573 AGTCAAGTCCAAAACTACTCTTTGT 58.584 36.000 0.00 0.00 37.17 2.83
1241 1250 0.401979 ATCCATCCCCTCCATTCCGT 60.402 55.000 0.00 0.00 0.00 4.69
1391 1401 5.824624 CACTCCTTCAAGTATGTGCCAATAT 59.175 40.000 0.00 0.00 0.00 1.28
1486 1496 1.659233 CATCAACGCCAACCAAGCA 59.341 52.632 0.00 0.00 0.00 3.91
1512 1522 0.036858 TCATCAATGCCGTCGTTCCA 60.037 50.000 0.00 0.00 0.00 3.53
1513 1523 0.374758 CATCAATGCCGTCGTTCCAG 59.625 55.000 0.00 0.00 0.00 3.86
1525 1535 2.742053 GTCGTTCCAGCTGCTTAATGAA 59.258 45.455 8.66 2.17 0.00 2.57
1545 1555 0.184692 TTGATGGGGCCGCAATCATA 59.815 50.000 27.86 16.07 30.76 2.15
1548 1558 1.252904 ATGGGGCCGCAATCATATGC 61.253 55.000 27.86 0.00 42.94 3.14
1670 1680 3.637229 CGTATCCACTATCTCCAACCAGT 59.363 47.826 0.00 0.00 0.00 4.00
1726 1736 2.095461 CACTCCTTCTCATCGTCCTCA 58.905 52.381 0.00 0.00 0.00 3.86
1730 1740 1.000827 CCTTCTCATCGTCCTCATCCG 60.001 57.143 0.00 0.00 0.00 4.18
1741 1751 4.218200 TCGTCCTCATCCGTTGTTAGTAAA 59.782 41.667 0.00 0.00 0.00 2.01
1747 1757 6.045072 TCATCCGTTGTTAGTAAACAGGAT 57.955 37.500 6.33 6.33 45.04 3.24
1796 1806 2.262915 CCACAGGCTCTCGGTGTC 59.737 66.667 2.54 0.00 39.42 3.67
1815 1825 2.587194 CAATGAGCGGCCTCTCGG 60.587 66.667 17.68 6.39 38.93 4.63
1925 1935 1.060163 GGATTCCTTCGGGGATGGGA 61.060 60.000 0.00 0.00 44.66 4.37
2050 2060 3.288092 GGGGATTTATGACGGCTTCTTT 58.712 45.455 0.00 0.00 0.00 2.52
2147 2157 4.445452 GACAACATCCAGTGCAATGATT 57.555 40.909 17.16 0.00 0.00 2.57
2176 2186 8.160106 ACAACCACTTCTAATCATCTCTTTTCT 58.840 33.333 0.00 0.00 0.00 2.52
2179 2189 8.601546 ACCACTTCTAATCATCTCTTTTCTCTT 58.398 33.333 0.00 0.00 0.00 2.85
2212 2222 2.565391 TCATAGCCCAGAGTTTGAACGA 59.435 45.455 0.00 0.00 0.00 3.85
2221 2231 1.098712 AGTTTGAACGAAAGCCGGCA 61.099 50.000 31.54 0.76 43.93 5.69
2223 2233 0.030101 TTTGAACGAAAGCCGGCAAG 59.970 50.000 31.54 18.48 43.93 4.01
2235 2245 3.090532 GGCAAGGAGGGGTCGGAT 61.091 66.667 0.00 0.00 0.00 4.18
2433 2443 2.203126 GCTGATGAAGGGCGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
2452 2462 1.060553 GGCGTGTATGTGATGAACGTG 59.939 52.381 0.00 0.00 36.65 4.49
2508 2518 2.039084 AGCCCGATCTTGATAACATCCC 59.961 50.000 0.00 0.00 0.00 3.85
2630 2640 3.118738 GGAGGTATGTACACACCCTCTTG 60.119 52.174 19.76 0.00 42.50 3.02
2645 2655 7.605691 CACACCCTCTTGATTATATCATCCTTC 59.394 40.741 0.00 0.00 39.39 3.46
2720 2730 1.483415 TGGGCGATACAGGAGGTAAAC 59.517 52.381 0.00 0.00 35.14 2.01
2740 2750 4.148128 ACAGGATCAAGGCTGAACATAG 57.852 45.455 4.00 0.00 34.49 2.23
2787 2797 2.143925 GAGTGAAGGGGAAACTCAACG 58.856 52.381 0.00 0.00 40.08 4.10
2931 2944 5.163205 TGCTAGACTATTATGGTGCCACATT 60.163 40.000 0.00 0.00 32.39 2.71
2932 2945 6.042666 TGCTAGACTATTATGGTGCCACATTA 59.957 38.462 0.00 0.00 32.39 1.90
2933 2946 7.106239 GCTAGACTATTATGGTGCCACATTAT 58.894 38.462 0.00 0.00 32.39 1.28
2934 2947 7.065085 GCTAGACTATTATGGTGCCACATTATG 59.935 40.741 0.00 0.00 32.39 1.90
2935 2948 7.078249 AGACTATTATGGTGCCACATTATGA 57.922 36.000 0.00 0.00 32.39 2.15
2936 2949 7.517320 AGACTATTATGGTGCCACATTATGAA 58.483 34.615 0.00 0.00 32.39 2.57
2937 2950 7.998383 AGACTATTATGGTGCCACATTATGAAA 59.002 33.333 0.00 0.00 32.39 2.69
2938 2951 8.710749 ACTATTATGGTGCCACATTATGAAAT 57.289 30.769 0.00 0.00 32.39 2.17
2939 2952 9.146586 ACTATTATGGTGCCACATTATGAAATT 57.853 29.630 0.00 0.00 32.39 1.82
2940 2953 9.414295 CTATTATGGTGCCACATTATGAAATTG 57.586 33.333 0.00 0.00 32.39 2.32
2941 2954 3.859443 TGGTGCCACATTATGAAATTGC 58.141 40.909 0.00 0.00 0.00 3.56
2942 2955 3.514706 TGGTGCCACATTATGAAATTGCT 59.485 39.130 0.00 0.00 0.00 3.91
2943 2956 4.708909 TGGTGCCACATTATGAAATTGCTA 59.291 37.500 0.00 0.00 0.00 3.49
2944 2957 5.043248 GGTGCCACATTATGAAATTGCTAC 58.957 41.667 0.00 0.00 0.00 3.58
2945 2958 5.394005 GGTGCCACATTATGAAATTGCTACA 60.394 40.000 0.00 0.00 0.00 2.74
2946 2959 6.275335 GTGCCACATTATGAAATTGCTACAT 58.725 36.000 0.00 0.00 0.00 2.29
2947 2960 6.199531 GTGCCACATTATGAAATTGCTACATG 59.800 38.462 0.00 0.00 0.00 3.21
2948 2961 5.176223 GCCACATTATGAAATTGCTACATGC 59.824 40.000 0.00 0.00 43.25 4.06
2957 2970 2.273449 GCTACATGCACTGGGGCT 59.727 61.111 0.00 0.00 42.31 5.19
2958 2971 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
2959 2972 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
2960 2973 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3112 3125 6.114187 TGAGATAAGTTGTTCACCTCATGT 57.886 37.500 0.00 0.00 0.00 3.21
3224 3239 8.740123 TGAAGAACCTAAAAACTGTGAATGTA 57.260 30.769 0.00 0.00 0.00 2.29
3489 3510 0.549902 TCCCATCACTCCACCACCAT 60.550 55.000 0.00 0.00 0.00 3.55
3555 3576 5.707298 CGGGCTCTATCAATATTTCACCAAT 59.293 40.000 0.00 0.00 0.00 3.16
3745 3811 1.790755 TGTTCGTAACTTCGCATGCT 58.209 45.000 17.13 0.00 0.00 3.79
3808 3874 1.195115 CCCATGACGAAAGGAGGAGA 58.805 55.000 0.00 0.00 0.00 3.71
3999 4071 1.680338 AAATGCTTCCGATGGGCTAC 58.320 50.000 0.00 0.00 0.00 3.58
4072 4145 2.100584 TGCACCATGAACAACAACCTTC 59.899 45.455 0.00 0.00 0.00 3.46
4107 4181 8.340618 TGTTTTCCTTCTCTTGAGAATAATGG 57.659 34.615 12.72 10.64 0.00 3.16
4141 4215 3.680789 GAAAACCCGAAACTGATATGCG 58.319 45.455 0.00 0.00 0.00 4.73
4206 4300 2.296073 AACAAGGTTTCCCGGCAATA 57.704 45.000 0.00 0.00 35.12 1.90
4225 4322 6.016024 GGCAATAGTGATGGAAAGAATATGCA 60.016 38.462 0.00 0.00 0.00 3.96
4242 4342 9.177608 AGAATATGCAAAACTGTATAAGCTCAA 57.822 29.630 0.00 0.00 0.00 3.02
4243 4343 9.956720 GAATATGCAAAACTGTATAAGCTCAAT 57.043 29.630 0.00 0.00 0.00 2.57
4304 4406 5.047235 ACCGAGATTGCTATATTCCAGTACC 60.047 44.000 0.00 0.00 0.00 3.34
4340 4442 1.795286 CTTCTCTGCACCGTCAGTTTC 59.205 52.381 0.00 0.00 35.63 2.78
4474 7493 1.668826 TGGTGGGAGAAACATAGCCT 58.331 50.000 0.00 0.00 0.00 4.58
4531 7550 3.653835 ATAAAAGCCTCCTCACCTTCC 57.346 47.619 0.00 0.00 0.00 3.46
4649 7721 6.093219 CCAGAAGTCTGTATTCACCATTTCTG 59.907 42.308 7.51 0.00 42.27 3.02
4654 7726 6.772716 AGTCTGTATTCACCATTTCTGTGTTT 59.227 34.615 0.00 0.00 35.25 2.83
4779 7851 8.721019 ACCAAAGAAAAATATTGTATGCCATG 57.279 30.769 0.00 0.00 0.00 3.66
4887 7994 2.754552 GGTTTCTACTGATGGCATGCAA 59.245 45.455 21.36 9.21 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.420022 GCACAATGAACATACGCTTCCT 59.580 45.455 0.00 0.00 0.00 3.36
2 3 2.161410 TGCACAATGAACATACGCTTCC 59.839 45.455 0.00 0.00 0.00 3.46
61 62 2.106511 AGCAGCCACAAAAGGAAGTAGA 59.893 45.455 0.00 0.00 0.00 2.59
188 189 7.890515 TCATGAATAAGTGCATTTAACAACCA 58.109 30.769 5.71 1.28 0.00 3.67
189 190 8.647226 GTTCATGAATAAGTGCATTTAACAACC 58.353 33.333 12.12 0.00 0.00 3.77
341 344 4.473196 TGTCTATGAATTGTGGGCCTAAGA 59.527 41.667 4.53 0.00 0.00 2.10
426 432 2.747177 CCACCCTATCTGTAGACACCA 58.253 52.381 0.00 0.00 0.00 4.17
511 517 0.037303 AATCCTCATATGCCCCTGCG 59.963 55.000 0.00 0.00 41.78 5.18
557 563 9.784531 ACCGATCTTCAATAAATGAGACATATT 57.215 29.630 0.00 0.00 39.77 1.28
635 642 0.734889 GCGACAGGGTCAATGAATGG 59.265 55.000 0.00 0.00 32.09 3.16
756 763 4.643334 TCACACGTGCTATCTACATAAGGT 59.357 41.667 17.22 0.00 0.00 3.50
760 767 4.036380 CAGGTCACACGTGCTATCTACATA 59.964 45.833 17.22 0.00 0.00 2.29
793 800 4.572389 AGGAACTTGCTAGCGACATAATTG 59.428 41.667 10.77 0.00 27.25 2.32
833 840 0.179234 TTTGTTCTGAGGCGTGGACA 59.821 50.000 0.00 0.00 0.00 4.02
857 864 1.067060 TGAAGATACGATGACGGGCAG 59.933 52.381 0.00 0.00 44.46 4.85
1174 1181 4.275196 GGTGGACAAAGAGTAGTTTTGGAC 59.725 45.833 3.19 0.00 39.30 4.02
1190 1199 1.227249 TGGGAAAGAAAGGGTGGACA 58.773 50.000 0.00 0.00 0.00 4.02
1191 1200 2.375014 TTGGGAAAGAAAGGGTGGAC 57.625 50.000 0.00 0.00 0.00 4.02
1192 1201 3.304829 CTTTTGGGAAAGAAAGGGTGGA 58.695 45.455 0.00 0.00 44.03 4.02
1486 1496 2.288729 CGACGGCATTGATGATGATGTT 59.711 45.455 0.00 0.00 38.03 2.71
1512 1522 3.640029 CCCCATCAATTCATTAAGCAGCT 59.360 43.478 0.00 0.00 0.00 4.24
1513 1523 3.801293 GCCCCATCAATTCATTAAGCAGC 60.801 47.826 0.00 0.00 0.00 5.25
1525 1535 0.470456 ATGATTGCGGCCCCATCAAT 60.470 50.000 9.59 8.17 33.57 2.57
1545 1555 0.652592 GCTCTTAACGATGCACGCAT 59.347 50.000 3.71 3.71 46.94 4.73
1692 1702 1.063867 AGGAGTGGTCTAGCATACCGT 60.064 52.381 0.00 0.00 40.08 4.83
1726 1736 7.039882 CACTATCCTGTTTACTAACAACGGAT 58.960 38.462 13.16 13.16 44.80 4.18
1730 1740 9.269453 AGAAACACTATCCTGTTTACTAACAAC 57.731 33.333 0.00 0.00 43.05 3.32
1741 1751 6.407865 CCATGAGATGAGAAACACTATCCTGT 60.408 42.308 0.00 0.00 0.00 4.00
1747 1757 6.358974 TCAACCATGAGATGAGAAACACTA 57.641 37.500 0.00 0.00 0.00 2.74
1815 1825 2.831597 GCTGTGGCCAAAGATTTGC 58.168 52.632 28.11 7.83 36.86 3.68
1946 1956 2.372264 CTGAGCCCACTGCACATTATT 58.628 47.619 0.00 0.00 44.83 1.40
2146 2156 6.037786 AGATGATTAGAAGTGGTTGTCGAA 57.962 37.500 0.00 0.00 0.00 3.71
2147 2157 5.419155 AGAGATGATTAGAAGTGGTTGTCGA 59.581 40.000 0.00 0.00 0.00 4.20
2176 2186 4.655963 GGCTATGATTGCCTCCATTAAGA 58.344 43.478 10.67 0.00 46.38 2.10
2203 2213 0.248702 TTGCCGGCTTTCGTTCAAAC 60.249 50.000 29.70 0.00 37.11 2.93
2212 2222 4.366684 CCCCTCCTTGCCGGCTTT 62.367 66.667 29.70 0.00 0.00 3.51
2221 2231 1.007963 TGTTCTATCCGACCCCTCCTT 59.992 52.381 0.00 0.00 0.00 3.36
2223 2233 1.619332 GATGTTCTATCCGACCCCTCC 59.381 57.143 0.00 0.00 0.00 4.30
2235 2245 3.095912 TGTCCTTCTCCGGATGTTCTA 57.904 47.619 3.57 0.00 35.11 2.10
2321 2331 1.000486 CCTCCTCCGTCTCCCTCAA 60.000 63.158 0.00 0.00 0.00 3.02
2433 2443 1.060553 CCACGTTCATCACATACACGC 59.939 52.381 0.00 0.00 34.14 5.34
2523 2533 1.093159 CAACTGCTGCAGATCCTTCC 58.907 55.000 34.28 0.00 35.18 3.46
2630 2640 8.502105 TGCATCACATGAAGGATGATATAATC 57.498 34.615 22.03 0.00 42.73 1.75
2645 2655 8.496751 TCAAAACACAAATAAATGCATCACATG 58.503 29.630 0.00 0.00 39.60 3.21
2720 2730 3.875727 CACTATGTTCAGCCTTGATCCTG 59.124 47.826 0.00 0.00 32.27 3.86
2740 2750 3.485110 TGATGGCGTTGCGATCAC 58.515 55.556 11.65 0.00 45.80 3.06
2787 2797 1.450312 CCCCGAATGCTCTGGTGAC 60.450 63.158 0.00 0.00 0.00 3.67
2902 2915 6.183361 TGGCACCATAATAGTCTAGCAGAAAT 60.183 38.462 0.00 0.00 0.00 2.17
2922 2935 5.649557 TGTAGCAATTTCATAATGTGGCAC 58.350 37.500 11.55 11.55 0.00 5.01
2940 2953 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
2941 2954 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
2942 2955 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3112 3125 9.515226 GTATATGAATGAATTAAAGGGCCTACA 57.485 33.333 6.41 1.09 0.00 2.74
3489 3510 0.880441 TGTCGTTTGGACCGATACGA 59.120 50.000 10.39 10.39 45.46 3.43
3555 3576 5.338632 TCTACCTCATCAACCACCTCTTTA 58.661 41.667 0.00 0.00 0.00 1.85
3808 3874 7.741027 GATGACAGAAACATCATCATGGTAT 57.259 36.000 8.91 0.00 46.98 2.73
3870 3936 3.009723 CACCACCAACACTATGCCTAAG 58.990 50.000 0.00 0.00 0.00 2.18
3999 4071 6.758886 GTCTTTCTGATGTCAACATACCCTAG 59.241 42.308 0.00 0.00 36.57 3.02
4072 4145 7.499232 TCAAGAGAAGGAAAACAAAGACCTAAG 59.501 37.037 0.00 0.00 32.06 2.18
4107 4181 1.399440 GGGTTTTCGGCGATAAAGGAC 59.601 52.381 11.76 0.45 0.00 3.85
4141 4215 0.971447 AGTCCCTCCTGCCGAACTAC 60.971 60.000 0.00 0.00 0.00 2.73
4206 4300 7.039504 ACAGTTTTGCATATTCTTTCCATCACT 60.040 33.333 0.00 0.00 0.00 3.41
4304 4406 2.393768 AAGCATGCGTCGGCTTCTG 61.394 57.895 13.01 0.00 46.82 3.02
4329 4431 5.838531 TTTAATTTGGTGAAACTGACGGT 57.161 34.783 0.00 0.00 36.74 4.83
4340 4442 6.820470 TTTGCGAGAAGTTTTAATTTGGTG 57.180 33.333 0.00 0.00 0.00 4.17
4531 7550 3.056952 CAAGAGCCGAATTGGATTTCG 57.943 47.619 0.00 0.00 46.14 3.46
4583 7655 6.332630 ACATGGAGTCAGAAACTTTGTTTTG 58.667 36.000 0.00 0.00 38.74 2.44
4584 7656 6.530019 ACATGGAGTCAGAAACTTTGTTTT 57.470 33.333 0.00 0.00 38.74 2.43
4779 7851 7.761249 AGCTTATTAAAAATGTCTGGTTGATGC 59.239 33.333 0.00 0.00 0.00 3.91
4887 7994 8.803235 TCTCTGCATTTATACATCGTAATAGGT 58.197 33.333 0.00 0.00 0.00 3.08
4917 8024 9.077885 TCTTGTTTCCTTTTATTCTACAAGCAT 57.922 29.630 0.00 0.00 40.26 3.79


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

AutoCloner maintained by Alex Coulton.