Multiple sequence alignment - TraesCS4B01G064400

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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 TraesCS4B01G064400 chr4B 100.000 2375 0 0 1 2375 57522947 57525321 0.000000e+00 4386
1 TraesCS4B01G064400 chr4B 90.533 1088 62 19 417 1496 57275562 57274508 0.000000e+00 1400
2 TraesCS4B01G064400 chr4B 88.359 713 46 24 792 1496 57279635 57278952 0.000000e+00 822
3 TraesCS4B01G064400 chr4B 89.744 273 25 2 1861 2133 495127992 495127723 1.750000e-91 346
4 TraesCS4B01G064400 chr4B 82.284 429 35 17 1 422 57275921 57275527 1.360000e-87 333
5 TraesCS4B01G064400 chr4B 89.286 112 12 0 1222 1333 57530228 57530339 8.850000e-30 141
6 TraesCS4B01G064400 chr4A 89.735 867 53 23 637 1496 561112768 561111931 0.000000e+00 1075
7 TraesCS4B01G064400 chr4A 88.983 118 13 0 1222 1339 561105830 561105713 1.900000e-31 147
8 TraesCS4B01G064400 chr4A 90.385 104 4 2 497 600 561113923 561113826 5.330000e-27 132
9 TraesCS4B01G064400 chr7D 90.809 729 37 4 1498 2225 180972283 180971584 0.000000e+00 948
10 TraesCS4B01G064400 chr7D 88.705 363 34 4 1863 2225 54942793 54942438 1.010000e-118 436
11 TraesCS4B01G064400 chr7D 82.263 327 46 7 1498 1823 54943101 54942786 3.010000e-69 272
12 TraesCS4B01G064400 chr7D 81.595 326 45 8 1498 1810 591564793 591565116 3.030000e-64 255
13 TraesCS4B01G064400 chr7D 96.078 153 6 0 2223 2375 180971456 180971304 1.410000e-62 250
14 TraesCS4B01G064400 chr7B 89.849 729 51 7 1498 2225 192018788 192018082 0.000000e+00 915
15 TraesCS4B01G064400 chr7B 95.425 153 7 0 2223 2375 192017954 192017802 6.560000e-61 244
16 TraesCS4B01G064400 chr7B 80.071 281 44 8 1552 1823 17330228 17329951 5.180000e-47 198
17 TraesCS4B01G064400 chr4D 88.756 587 31 16 919 1496 39258592 39259152 0.000000e+00 686
18 TraesCS4B01G064400 chr4D 80.341 646 43 27 1 640 39257572 39258139 1.700000e-111 412
19 TraesCS4B01G064400 chr4D 91.901 284 17 4 639 918 39258178 39258459 2.210000e-105 392
20 TraesCS4B01G064400 chr4D 92.199 141 8 1 1190 1330 39336329 39336466 1.860000e-46 196
21 TraesCS4B01G064400 chr4D 91.892 111 9 0 1229 1339 39274018 39274128 3.160000e-34 156
22 TraesCS4B01G064400 chr5B 95.707 396 17 0 1980 2375 696415983 696416378 2.570000e-179 638
23 TraesCS4B01G064400 chr3D 90.152 264 24 1 1964 2225 97907465 97907728 2.260000e-90 342
24 TraesCS4B01G064400 chr3D 84.058 276 35 9 1498 1768 585095548 585095277 8.420000e-65 257
25 TraesCS4B01G064400 chr7A 82.934 334 44 10 1498 1823 682013583 682013911 2.990000e-74 289
26 TraesCS4B01G064400 chr1D 84.946 279 38 4 1498 1772 9388138 9387860 1.800000e-71 279
27 TraesCS4B01G064400 chr2B 84.116 277 38 5 1498 1769 88205930 88206205 1.810000e-66 263
28 TraesCS4B01G064400 chr2B 81.685 273 46 4 1498 1768 581432978 581432708 8.540000e-55 224
29 TraesCS4B01G064400 chr5A 84.000 275 40 4 1498 1769 638815032 638815305 6.510000e-66 261
30 TraesCS4B01G064400 chr2A 88.182 110 13 0 1223 1332 541387022 541386913 5.330000e-27 132


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 TraesCS4B01G064400 chr4B 57522947 57525321 2374 False 4386.000000 4386 100.000000 1 2375 1 chr4B.!!$F1 2374
1 TraesCS4B01G064400 chr4B 57274508 57279635 5127 True 851.666667 1400 87.058667 1 1496 3 chr4B.!!$R2 1495
2 TraesCS4B01G064400 chr4A 561111931 561113923 1992 True 603.500000 1075 90.060000 497 1496 2 chr4A.!!$R2 999
3 TraesCS4B01G064400 chr7D 180971304 180972283 979 True 599.000000 948 93.443500 1498 2375 2 chr7D.!!$R2 877
4 TraesCS4B01G064400 chr7D 54942438 54943101 663 True 354.000000 436 85.484000 1498 2225 2 chr7D.!!$R1 727
5 TraesCS4B01G064400 chr7B 192017802 192018788 986 True 579.500000 915 92.637000 1498 2375 2 chr7B.!!$R2 877
6 TraesCS4B01G064400 chr4D 39257572 39259152 1580 False 496.666667 686 86.999333 1 1496 3 chr4D.!!$F3 1495

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
990 4921 0.040425 CACAAAGGCAACGCTACACC 60.04 55.0 0.0 0.0 46.39 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 5787 0.036765 GGCGGTGATACAGTGGACAA 60.037 55.0 0.0 0.0 0.0 3.18 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
122 3845 7.388460 TGAATGCACAAACTTTTTCCAAAAT 57.612 28.000 0.00 0.00 0.00 1.82
128 3851 6.238076 GCACAAACTTTTTCCAAAATCGTGAT 60.238 34.615 0.00 0.00 0.00 3.06
220 3944 6.669485 AATTGCGAACATTTTCTAAACGTC 57.331 33.333 0.00 0.00 0.00 4.34
263 3987 9.685828 TTGTGGCAGTATTTTAACATAAGAAAC 57.314 29.630 0.00 0.00 0.00 2.78
264 3988 8.851145 TGTGGCAGTATTTTAACATAAGAAACA 58.149 29.630 0.00 0.00 0.00 2.83
265 3989 9.341899 GTGGCAGTATTTTAACATAAGAAACAG 57.658 33.333 0.00 0.00 0.00 3.16
266 3990 8.519526 TGGCAGTATTTTAACATAAGAAACAGG 58.480 33.333 0.00 0.00 0.00 4.00
267 3991 7.488150 GGCAGTATTTTAACATAAGAAACAGGC 59.512 37.037 0.00 0.00 0.00 4.85
268 3992 7.488150 GCAGTATTTTAACATAAGAAACAGGCC 59.512 37.037 0.00 0.00 0.00 5.19
269 3993 7.973944 CAGTATTTTAACATAAGAAACAGGCCC 59.026 37.037 0.00 0.00 0.00 5.80
270 3994 7.893833 AGTATTTTAACATAAGAAACAGGCCCT 59.106 33.333 0.00 0.00 0.00 5.19
271 3995 6.584185 TTTTAACATAAGAAACAGGCCCTC 57.416 37.500 0.00 0.00 0.00 4.30
272 3996 2.403252 ACATAAGAAACAGGCCCTCG 57.597 50.000 0.00 0.00 0.00 4.63
273 3997 1.906574 ACATAAGAAACAGGCCCTCGA 59.093 47.619 0.00 0.00 0.00 4.04
274 3998 2.304761 ACATAAGAAACAGGCCCTCGAA 59.695 45.455 0.00 0.00 0.00 3.71
275 3999 3.244770 ACATAAGAAACAGGCCCTCGAAA 60.245 43.478 0.00 0.00 0.00 3.46
276 4000 2.358322 AAGAAACAGGCCCTCGAAAA 57.642 45.000 0.00 0.00 0.00 2.29
277 4001 2.358322 AGAAACAGGCCCTCGAAAAA 57.642 45.000 0.00 0.00 0.00 1.94
351 4075 5.411361 TGAGACAAAAATTACTAGTGCGCAT 59.589 36.000 15.91 5.37 0.00 4.73
357 4081 7.849026 ACAAAAATTACTAGTGCGCATAATACG 59.151 33.333 15.91 5.74 0.00 3.06
382 4106 0.817654 GTGCTGGCCCATTTTAGGTC 59.182 55.000 0.00 0.00 0.00 3.85
408 4132 1.001378 GCAGTGCGATTGGTGACTTTT 60.001 47.619 0.00 0.00 0.00 2.27
409 4133 2.543653 GCAGTGCGATTGGTGACTTTTT 60.544 45.455 0.00 0.00 0.00 1.94
432 4156 4.093952 GCAGTGCAGTGCGCGATT 62.094 61.111 29.43 2.88 46.97 3.34
434 4158 3.425713 AGTGCAGTGCGCGATTGG 61.426 61.111 22.20 0.00 46.97 3.16
435 4159 3.726517 GTGCAGTGCGCGATTGGT 61.727 61.111 12.10 0.00 46.97 3.67
436 4160 3.725459 TGCAGTGCGCGATTGGTG 61.725 61.111 12.10 0.00 46.97 4.17
437 4161 3.422303 GCAGTGCGCGATTGGTGA 61.422 61.111 12.10 0.00 0.00 4.02
438 4162 2.476051 CAGTGCGCGATTGGTGAC 59.524 61.111 12.10 0.00 0.00 3.67
439 4163 2.029288 CAGTGCGCGATTGGTGACT 61.029 57.895 12.10 0.00 0.00 3.41
440 4164 1.301716 AGTGCGCGATTGGTGACTT 60.302 52.632 12.10 0.00 0.00 3.01
441 4165 0.884704 AGTGCGCGATTGGTGACTTT 60.885 50.000 12.10 0.00 0.00 2.66
442 4166 0.452784 GTGCGCGATTGGTGACTTTC 60.453 55.000 12.10 0.00 0.00 2.62
443 4167 1.134694 GCGCGATTGGTGACTTTCC 59.865 57.895 12.10 0.00 0.00 3.13
444 4168 1.573829 GCGCGATTGGTGACTTTCCA 61.574 55.000 12.10 0.00 0.00 3.53
445 4169 0.443869 CGCGATTGGTGACTTTCCAG 59.556 55.000 0.00 0.00 36.28 3.86
446 4170 0.169009 GCGATTGGTGACTTTCCAGC 59.831 55.000 0.00 0.00 36.28 4.85
447 4171 0.443869 CGATTGGTGACTTTCCAGCG 59.556 55.000 0.00 0.00 37.36 5.18
448 4172 0.169009 GATTGGTGACTTTCCAGCGC 59.831 55.000 0.00 0.00 37.36 5.92
449 4173 0.537143 ATTGGTGACTTTCCAGCGCA 60.537 50.000 11.47 0.00 37.36 6.09
450 4174 0.537143 TTGGTGACTTTCCAGCGCAT 60.537 50.000 11.47 0.00 37.36 4.73
451 4175 1.236616 TGGTGACTTTCCAGCGCATG 61.237 55.000 11.47 4.88 37.36 4.06
483 4207 4.072088 GCCTTTGTGCGTCGTCCG 62.072 66.667 0.00 0.00 40.40 4.79
509 4239 1.745864 GACGGCTCGACTGAGAGGA 60.746 63.158 1.50 0.00 45.57 3.71
608 4352 3.462021 CTGGCTGCTCTAATTAGTGTCC 58.538 50.000 12.19 12.03 0.00 4.02
609 4353 2.837591 TGGCTGCTCTAATTAGTGTCCA 59.162 45.455 12.19 14.00 0.00 4.02
652 4441 1.992834 TGGTGCCAATCCCTAGCGA 60.993 57.895 0.00 0.00 0.00 4.93
657 4446 1.064758 TGCCAATCCCTAGCGATTTGT 60.065 47.619 0.00 0.00 29.85 2.83
755 4548 2.500098 ACTGTTAGCCGCTTCTTATCCA 59.500 45.455 0.00 0.00 0.00 3.41
842 4636 5.353678 AGTTTAGTCTAAGACGTACGCTGAT 59.646 40.000 16.72 1.75 37.67 2.90
869 4663 2.665777 GCGCTAGCAAACTCGATCA 58.334 52.632 16.45 0.00 44.35 2.92
894 4688 4.352600 CATCTCCATGCTCAAAGTCAAC 57.647 45.455 0.00 0.00 0.00 3.18
940 4866 9.793259 TTTCATTTCCCTATATAAACTGCCTAG 57.207 33.333 0.00 0.00 0.00 3.02
978 4904 3.181397 CAACTCAAAGCACACACAAAGG 58.819 45.455 0.00 0.00 0.00 3.11
990 4921 0.040425 CACAAAGGCAACGCTACACC 60.040 55.000 0.00 0.00 46.39 4.16
994 4925 0.107831 AAGGCAACGCTACACCAAGA 59.892 50.000 0.00 0.00 46.39 3.02
995 4926 0.324943 AGGCAACGCTACACCAAGAT 59.675 50.000 0.00 0.00 46.39 2.40
1008 4939 5.818136 ACACCAAGATCATTATGGTTTCG 57.182 39.130 9.08 3.30 44.92 3.46
1030 4961 0.320683 CATGAAGCTGTCGGTCACCA 60.321 55.000 0.00 0.00 0.00 4.17
1050 4981 2.124693 CGTCCTCCTCCTCTCAGGC 61.125 68.421 0.00 0.00 34.61 4.85
1058 4989 2.219325 CTCCTCTCAGGCACGTCCAC 62.219 65.000 6.78 0.00 34.61 4.02
1059 4990 2.279069 CCTCTCAGGCACGTCCACT 61.279 63.158 6.78 0.00 37.29 4.00
1060 4991 1.214062 CTCTCAGGCACGTCCACTC 59.786 63.158 6.78 0.00 37.29 3.51
1061 4992 2.126307 CTCAGGCACGTCCACTCG 60.126 66.667 6.78 0.00 37.29 4.18
1062 4993 2.910479 TCAGGCACGTCCACTCGT 60.910 61.111 6.78 0.00 45.10 4.18
1063 4994 1.583495 CTCAGGCACGTCCACTCGTA 61.583 60.000 6.78 0.00 42.27 3.43
1064 4995 1.174078 TCAGGCACGTCCACTCGTAA 61.174 55.000 6.78 0.00 42.27 3.18
1065 4996 0.108804 CAGGCACGTCCACTCGTAAT 60.109 55.000 6.78 0.00 42.27 1.89
1066 4997 0.606604 AGGCACGTCCACTCGTAATT 59.393 50.000 6.78 0.00 42.27 1.40
1072 5003 4.100529 CACGTCCACTCGTAATTTCGTAT 58.899 43.478 4.34 0.00 42.27 3.06
1074 5005 5.170270 CACGTCCACTCGTAATTTCGTATAC 59.830 44.000 4.34 0.00 42.27 1.47
1083 5014 4.322804 CGTAATTTCGTATACTCGCATCCC 59.677 45.833 0.56 0.00 0.00 3.85
1088 5019 5.717078 TTCGTATACTCGCATCCCTAATT 57.283 39.130 0.56 0.00 0.00 1.40
1091 5022 4.379186 CGTATACTCGCATCCCTAATTCGT 60.379 45.833 0.56 0.00 0.00 3.85
1092 5023 5.163824 CGTATACTCGCATCCCTAATTCGTA 60.164 44.000 0.56 0.00 0.00 3.43
1093 5024 5.717078 ATACTCGCATCCCTAATTCGTAA 57.283 39.130 0.00 0.00 0.00 3.18
1094 5025 3.978687 ACTCGCATCCCTAATTCGTAAG 58.021 45.455 0.00 0.00 0.00 2.34
1095 5026 3.243771 ACTCGCATCCCTAATTCGTAAGG 60.244 47.826 0.00 0.00 38.47 2.69
1096 5027 1.798813 CGCATCCCTAATTCGTAAGGC 59.201 52.381 0.00 0.00 38.47 4.35
1097 5028 2.548067 CGCATCCCTAATTCGTAAGGCT 60.548 50.000 0.00 0.00 38.47 4.58
1098 5029 3.067833 GCATCCCTAATTCGTAAGGCTC 58.932 50.000 0.00 0.00 38.47 4.70
1099 5030 3.494398 GCATCCCTAATTCGTAAGGCTCA 60.494 47.826 0.00 0.00 38.47 4.26
1100 5031 4.703897 CATCCCTAATTCGTAAGGCTCAA 58.296 43.478 0.00 0.00 38.47 3.02
1101 5032 4.402056 TCCCTAATTCGTAAGGCTCAAG 57.598 45.455 0.00 0.00 38.47 3.02
1102 5033 2.872858 CCCTAATTCGTAAGGCTCAAGC 59.127 50.000 0.00 0.00 41.14 4.01
1117 5048 1.556911 TCAAGCTGAGAGATGGGTTCC 59.443 52.381 0.00 0.00 0.00 3.62
1122 5053 3.075134 AGCTGAGAGATGGGTTCCTTTTT 59.925 43.478 0.00 0.00 0.00 1.94
1123 5054 3.192212 GCTGAGAGATGGGTTCCTTTTTG 59.808 47.826 0.00 0.00 0.00 2.44
1124 5055 4.655963 CTGAGAGATGGGTTCCTTTTTGA 58.344 43.478 0.00 0.00 0.00 2.69
1125 5056 4.398319 TGAGAGATGGGTTCCTTTTTGAC 58.602 43.478 0.00 0.00 0.00 3.18
1531 5469 3.306472 AACCACCACTTTGAAGGCTAA 57.694 42.857 0.00 0.00 0.00 3.09
1541 5479 3.896648 TTGAAGGCTAAGTTTGCGAAG 57.103 42.857 3.21 0.00 0.00 3.79
1548 5487 5.186198 AGGCTAAGTTTGCGAAGAACATAT 58.814 37.500 3.21 0.00 0.00 1.78
1620 5559 0.036765 AACACTGATCGGCGGCTTTA 60.037 50.000 7.21 0.00 0.00 1.85
1650 5589 2.542595 GACCGCGTTTATAACAGATGGG 59.457 50.000 4.92 0.00 0.00 4.00
1670 5610 0.250727 GCCTGCCAGTTAGGTTGACA 60.251 55.000 0.00 0.00 40.61 3.58
1702 5642 9.161629 CCACTTAACATCTCACATATAACAACA 57.838 33.333 0.00 0.00 0.00 3.33
1858 5798 2.340809 CCGCCGTTGTCCACTGTA 59.659 61.111 0.00 0.00 0.00 2.74
1859 5799 1.079405 CCGCCGTTGTCCACTGTAT 60.079 57.895 0.00 0.00 0.00 2.29
1934 5874 3.382832 CGTCCTTCCCACGCTCCT 61.383 66.667 0.00 0.00 0.00 3.69
1970 5910 0.560193 CATCCTCTCCTCCCTCTCCA 59.440 60.000 0.00 0.00 0.00 3.86
1971 5911 0.859760 ATCCTCTCCTCCCTCTCCAG 59.140 60.000 0.00 0.00 0.00 3.86
1978 5918 3.368190 CTCCCTCTCCAGCGTGCAG 62.368 68.421 0.00 0.00 0.00 4.41
2049 5989 1.341531 CCTCCGTGTGTTCTTCAGAGT 59.658 52.381 0.00 0.00 0.00 3.24
2140 6080 3.691342 CTGCCGGTTCTCGACCCA 61.691 66.667 1.90 0.00 46.35 4.51
2246 6316 4.947147 GCGGCCTTCCACCACACA 62.947 66.667 0.00 0.00 0.00 3.72
2275 6345 1.812922 CGTGAGCATGCTCCAGGAC 60.813 63.158 37.92 28.70 42.09 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 3830 8.661352 AATGATCACGATTTTGGAAAAAGTTT 57.339 26.923 0.00 0.00 0.00 2.66
148 3871 8.502161 AAAAATGTACACGAATACAGAAAAGC 57.498 30.769 0.00 0.00 38.43 3.51
179 3902 5.947519 CGCAATTTAGAAAAATGTTCATGCG 59.052 36.000 10.54 10.54 44.28 4.73
220 3944 9.206870 ACTGCCACAAAATTTAAATATGTTCAG 57.793 29.630 23.82 23.82 32.63 3.02
278 4002 7.329588 ACTTCGACCTGTTTCTTATGTTTTT 57.670 32.000 0.00 0.00 0.00 1.94
279 4003 6.937436 ACTTCGACCTGTTTCTTATGTTTT 57.063 33.333 0.00 0.00 0.00 2.43
280 4004 8.441312 TTTACTTCGACCTGTTTCTTATGTTT 57.559 30.769 0.00 0.00 0.00 2.83
281 4005 8.441312 TTTTACTTCGACCTGTTTCTTATGTT 57.559 30.769 0.00 0.00 0.00 2.71
282 4006 8.441312 TTTTTACTTCGACCTGTTTCTTATGT 57.559 30.769 0.00 0.00 0.00 2.29
311 4035 1.001520 TCTCATCGAGTTTTCGGCCAA 59.998 47.619 2.24 0.00 46.67 4.52
351 4075 0.742990 GCCAGCACACTGCCGTATTA 60.743 55.000 0.00 0.00 46.52 0.98
408 4132 2.974148 CACTGCACTGCGCTGGAA 60.974 61.111 18.98 1.48 43.49 3.53
423 4147 0.452784 GAAAGTCACCAATCGCGCAC 60.453 55.000 8.75 0.00 0.00 5.34
424 4148 1.573829 GGAAAGTCACCAATCGCGCA 61.574 55.000 8.75 0.00 0.00 6.09
425 4149 1.134694 GGAAAGTCACCAATCGCGC 59.865 57.895 0.00 0.00 0.00 6.86
426 4150 0.443869 CTGGAAAGTCACCAATCGCG 59.556 55.000 0.00 0.00 36.95 5.87
427 4151 0.169009 GCTGGAAAGTCACCAATCGC 59.831 55.000 0.00 0.00 36.95 4.58
428 4152 0.443869 CGCTGGAAAGTCACCAATCG 59.556 55.000 0.00 0.00 36.95 3.34
429 4153 0.169009 GCGCTGGAAAGTCACCAATC 59.831 55.000 0.00 0.00 36.95 2.67
430 4154 0.537143 TGCGCTGGAAAGTCACCAAT 60.537 50.000 9.73 0.00 36.95 3.16
431 4155 0.537143 ATGCGCTGGAAAGTCACCAA 60.537 50.000 9.73 0.00 36.95 3.67
432 4156 1.073025 ATGCGCTGGAAAGTCACCA 59.927 52.632 9.73 0.00 35.96 4.17
448 4172 4.776322 TCCTGTTCCGCGCCCATG 62.776 66.667 0.00 0.00 0.00 3.66
449 4173 4.473520 CTCCTGTTCCGCGCCCAT 62.474 66.667 0.00 0.00 0.00 4.00
454 4178 2.358737 AAAGGCTCCTGTTCCGCG 60.359 61.111 0.00 0.00 0.00 6.46
455 4179 1.600916 ACAAAGGCTCCTGTTCCGC 60.601 57.895 0.00 0.00 0.00 5.54
509 4239 2.091885 TGGAAAAGGTTCAGGTTCAGCT 60.092 45.455 0.00 0.00 35.25 4.24
546 4282 7.315142 TCGCAAATGCTTTTTCTATCTGATTT 58.685 30.769 3.63 0.00 39.32 2.17
608 4352 2.228582 TCATTTTCCGAAGTGCCATGTG 59.771 45.455 0.00 0.00 0.00 3.21
609 4353 2.513753 TCATTTTCCGAAGTGCCATGT 58.486 42.857 0.00 0.00 0.00 3.21
657 4446 2.727123 TCTCAGTTGAAAGGTGGCAA 57.273 45.000 0.00 0.00 0.00 4.52
842 4636 2.357637 AGTTTGCTAGCGCTTTTGTCAA 59.642 40.909 18.68 10.16 36.97 3.18
854 4648 4.510711 AGATGCATTGATCGAGTTTGCTAG 59.489 41.667 0.00 0.00 34.47 3.42
894 4688 2.802667 CTCTGGCGTGGCGATTTCG 61.803 63.158 0.00 0.00 43.27 3.46
936 4862 0.108207 CAGAGCCATGGAAGCCTAGG 59.892 60.000 18.40 3.67 0.00 3.02
978 4904 1.438651 TGATCTTGGTGTAGCGTTGC 58.561 50.000 0.00 0.00 0.00 4.17
990 4921 3.631686 TGGCCGAAACCATAATGATCTTG 59.368 43.478 0.00 0.00 33.75 3.02
1008 4939 2.045926 ACCGACAGCTTCATGGCC 60.046 61.111 0.00 0.00 0.00 5.36
1030 4961 0.184933 CCTGAGAGGAGGAGGACGAT 59.815 60.000 0.00 0.00 37.67 3.73
1050 4981 2.322161 ACGAAATTACGAGTGGACGTG 58.678 47.619 0.00 0.00 46.02 4.49
1058 4989 5.283247 GGATGCGAGTATACGAAATTACGAG 59.717 44.000 0.00 0.00 37.03 4.18
1059 4990 5.149273 GGATGCGAGTATACGAAATTACGA 58.851 41.667 0.00 0.00 37.03 3.43
1060 4991 4.322804 GGGATGCGAGTATACGAAATTACG 59.677 45.833 0.00 0.00 39.31 3.18
1061 4992 5.467705 AGGGATGCGAGTATACGAAATTAC 58.532 41.667 0.00 0.00 35.09 1.89
1062 4993 5.717078 AGGGATGCGAGTATACGAAATTA 57.283 39.130 0.00 0.00 35.09 1.40
1063 4994 4.602340 AGGGATGCGAGTATACGAAATT 57.398 40.909 0.00 0.00 35.09 1.82
1064 4995 5.717078 TTAGGGATGCGAGTATACGAAAT 57.283 39.130 0.00 0.00 35.09 2.17
1065 4996 5.717078 ATTAGGGATGCGAGTATACGAAA 57.283 39.130 0.00 0.00 35.09 3.46
1066 4997 5.618418 CGAATTAGGGATGCGAGTATACGAA 60.618 44.000 0.00 0.00 39.27 3.85
1072 5003 4.022589 CCTTACGAATTAGGGATGCGAGTA 60.023 45.833 0.00 0.00 39.27 2.59
1074 5005 3.318017 CCTTACGAATTAGGGATGCGAG 58.682 50.000 0.00 0.00 39.27 5.03
1083 5014 4.433615 TCAGCTTGAGCCTTACGAATTAG 58.566 43.478 0.00 0.00 43.38 1.73
1088 5019 1.474478 CTCTCAGCTTGAGCCTTACGA 59.526 52.381 0.00 0.00 43.95 3.43
1091 5022 2.433604 CCATCTCTCAGCTTGAGCCTTA 59.566 50.000 8.27 0.00 43.95 2.69
1092 5023 1.209990 CCATCTCTCAGCTTGAGCCTT 59.790 52.381 8.27 0.00 43.95 4.35
1093 5024 0.831966 CCATCTCTCAGCTTGAGCCT 59.168 55.000 8.27 0.00 43.95 4.58
1094 5025 0.179051 CCCATCTCTCAGCTTGAGCC 60.179 60.000 8.27 0.00 43.95 4.70
1095 5026 0.540923 ACCCATCTCTCAGCTTGAGC 59.459 55.000 8.27 0.00 43.95 4.26
1096 5027 2.419851 GGAACCCATCTCTCAGCTTGAG 60.420 54.545 7.07 7.07 45.59 3.02
1097 5028 1.556911 GGAACCCATCTCTCAGCTTGA 59.443 52.381 0.00 0.00 0.00 3.02
1098 5029 1.558756 AGGAACCCATCTCTCAGCTTG 59.441 52.381 0.00 0.00 0.00 4.01
1099 5030 1.963985 AGGAACCCATCTCTCAGCTT 58.036 50.000 0.00 0.00 0.00 3.74
1100 5031 1.963985 AAGGAACCCATCTCTCAGCT 58.036 50.000 0.00 0.00 0.00 4.24
1101 5032 2.797177 AAAGGAACCCATCTCTCAGC 57.203 50.000 0.00 0.00 0.00 4.26
1102 5033 4.457257 GTCAAAAAGGAACCCATCTCTCAG 59.543 45.833 0.00 0.00 0.00 3.35
1117 5048 5.014483 CACGCACACAAAAATGTCAAAAAG 58.986 37.500 0.00 0.00 0.00 2.27
1122 5053 2.524034 CACACGCACACAAAAATGTCA 58.476 42.857 0.00 0.00 0.00 3.58
1123 5054 1.255084 GCACACGCACACAAAAATGTC 59.745 47.619 0.00 0.00 38.36 3.06
1124 5055 1.135141 AGCACACGCACACAAAAATGT 60.135 42.857 0.00 0.00 42.27 2.71
1125 5056 1.255859 CAGCACACGCACACAAAAATG 59.744 47.619 0.00 0.00 42.27 2.32
1450 5387 5.682943 TGAATTACACTGCCAAACTACAC 57.317 39.130 0.00 0.00 0.00 2.90
1496 5434 4.873259 GTGGTGGTTTTGTGCAATTTACTT 59.127 37.500 0.00 0.00 0.00 2.24
1641 5580 3.267233 TGGCAGGCCCCATCTGTT 61.267 61.111 8.02 0.00 34.89 3.16
1650 5589 0.960861 GTCAACCTAACTGGCAGGCC 60.961 60.000 20.34 2.62 40.22 5.19
1670 5610 3.244875 TGTGAGATGTTAAGTGGTGCCAT 60.245 43.478 0.00 0.00 0.00 4.40
1709 5649 6.870439 AGGTCACACATGATGATAACGATATG 59.130 38.462 0.00 0.00 37.14 1.78
1713 5653 4.736126 AGGTCACACATGATGATAACGA 57.264 40.909 0.00 0.00 37.14 3.85
1840 5780 3.869473 TACAGTGGACAACGGCGGC 62.869 63.158 13.24 0.00 0.00 6.53
1841 5781 1.079405 ATACAGTGGACAACGGCGG 60.079 57.895 13.24 0.00 0.00 6.13
1842 5782 0.389296 TGATACAGTGGACAACGGCG 60.389 55.000 4.80 4.80 0.00 6.46
1843 5783 1.076332 GTGATACAGTGGACAACGGC 58.924 55.000 0.00 0.00 0.00 5.68
1844 5784 1.722011 GGTGATACAGTGGACAACGG 58.278 55.000 0.00 0.00 0.00 4.44
1845 5785 1.346365 CGGTGATACAGTGGACAACG 58.654 55.000 8.84 8.84 37.14 4.10
1846 5786 1.076332 GCGGTGATACAGTGGACAAC 58.924 55.000 0.00 0.00 0.00 3.32
1847 5787 0.036765 GGCGGTGATACAGTGGACAA 60.037 55.000 0.00 0.00 0.00 3.18
1848 5788 1.594833 GGCGGTGATACAGTGGACA 59.405 57.895 0.00 0.00 0.00 4.02
1849 5789 1.518572 CGGCGGTGATACAGTGGAC 60.519 63.158 0.00 0.00 0.00 4.02
1850 5790 2.889617 CGGCGGTGATACAGTGGA 59.110 61.111 0.00 0.00 0.00 4.02
1851 5791 2.890474 GCGGCGGTGATACAGTGG 60.890 66.667 9.78 0.00 0.00 4.00
1852 5792 2.890474 GGCGGCGGTGATACAGTG 60.890 66.667 9.78 0.00 0.00 3.66
1853 5793 4.157120 GGGCGGCGGTGATACAGT 62.157 66.667 9.78 0.00 0.00 3.55
1978 5918 4.500116 GAGACCGCGGAGTCCAGC 62.500 72.222 35.90 12.49 37.49 4.85
2027 5967 1.340248 TCTGAAGAACACACGGAGGTC 59.660 52.381 0.00 0.00 0.00 3.85
2246 6316 4.148825 GCTCACGGCATCCTCGGT 62.149 66.667 0.00 0.00 41.35 4.69
2264 6334 2.235016 GATCTAGTCGTCCTGGAGCAT 58.765 52.381 0.00 0.00 37.08 3.79
2350 6420 1.140852 CCCTTCCGCACCTCATATTCA 59.859 52.381 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.