Multiple sequence alignment - TraesCS7D01G130400

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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 TraesCS7D01G130400 chr7D 100.000 2568 0 0 1 2568 82713482 82716049 0.000000e+00 4743.0
1 TraesCS7D01G130400 chr7B 92.077 1666 70 20 16 1656 31785200 31786828 0.000000e+00 2289.0
2 TraesCS7D01G130400 chr7B 86.604 530 34 21 1667 2192 31786804 31787300 3.730000e-153 551.0
3 TraesCS7D01G130400 chr7B 87.407 270 32 1 2301 2568 31789190 31789459 2.480000e-80 309.0
4 TraesCS7D01G130400 chr7B 93.333 45 3 0 2521 2565 31808338 31808382 1.650000e-07 67.6
5 TraesCS7D01G130400 chr7A 91.381 1079 47 14 574 1626 84689927 84690985 0.000000e+00 1435.0
6 TraesCS7D01G130400 chr7A 96.516 488 16 1 20 506 84687585 84688072 0.000000e+00 806.0
7 TraesCS7D01G130400 chr7A 96.115 489 17 2 20 506 84688284 84688772 0.000000e+00 797.0
8 TraesCS7D01G130400 chr7A 96.115 489 17 2 20 506 84688989 84689477 0.000000e+00 797.0
9 TraesCS7D01G130400 chr7A 83.370 457 41 22 1762 2200 84691043 84691482 8.620000e-105 390.0
10 TraesCS7D01G130400 chr7A 89.899 198 20 0 2371 2568 84700028 84700225 3.280000e-64 255.0
11 TraesCS7D01G130400 chr7A 97.802 91 1 1 502 591 84689536 84689626 3.420000e-34 156.0
12 TraesCS7D01G130400 chr7A 93.069 101 5 2 492 591 84688128 84688227 2.060000e-31 147.0
13 TraesCS7D01G130400 chr7A 93.069 101 5 2 492 591 84688834 84688933 2.060000e-31 147.0
14 TraesCS7D01G130400 chr2B 93.478 46 1 2 93 137 457091272 457091228 1.650000e-07 67.6
15 TraesCS7D01G130400 chr4A 94.737 38 1 1 398 435 157209068 157209032 9.920000e-05 58.4


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 TraesCS7D01G130400 chr7D 82713482 82716049 2567 False 4743.000000 4743 100.000000 1 2568 1 chr7D.!!$F1 2567
1 TraesCS7D01G130400 chr7B 31785200 31789459 4259 False 1049.666667 2289 88.696000 16 2568 3 chr7B.!!$F2 2552
2 TraesCS7D01G130400 chr7A 84687585 84691482 3897 False 584.375000 1435 93.429625 20 2200 8 chr7A.!!$F2 2180

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
914 2712 0.036164 TTAATCGGCATCATCCCCCG 59.964 55.0 0.0 0.0 43.21 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 6058 0.035458 ACTAGAACTGGCGCTGCTTT 59.965 50.0 7.64 0.0 0.0 3.51 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
212 913 7.818930 GGAGTGCTTTTGAATTTAAATGGATGA 59.181 33.333 0.39 0.00 0.00 2.92
232 933 4.392047 TGATTGAGTTGCTGTTGATCTGT 58.608 39.130 0.00 0.00 0.00 3.41
271 972 3.472652 ACGCATCTGTTAAAGTGACCAA 58.527 40.909 0.00 0.00 0.00 3.67
369 1776 0.389391 CTATTCCTGACCGCGGACAT 59.611 55.000 35.90 19.27 0.00 3.06
419 1826 2.136728 TGTTCGTATTGGTGAACCGTG 58.863 47.619 2.98 0.00 42.93 4.94
593 2383 0.600057 CAAGCCTTCCTCTTGTTGGC 59.400 55.000 0.00 0.00 43.52 4.52
609 2399 2.557924 GTTGGCATGTCAACATCTTGGA 59.442 45.455 32.73 0.00 44.51 3.53
610 2400 2.161855 TGGCATGTCAACATCTTGGAC 58.838 47.619 0.00 0.00 33.61 4.02
611 2401 2.224843 TGGCATGTCAACATCTTGGACT 60.225 45.455 0.00 0.00 33.61 3.85
612 2402 2.421424 GGCATGTCAACATCTTGGACTC 59.579 50.000 0.00 0.00 33.61 3.36
613 2403 3.341823 GCATGTCAACATCTTGGACTCT 58.658 45.455 0.00 0.00 33.61 3.24
614 2404 3.755378 GCATGTCAACATCTTGGACTCTT 59.245 43.478 0.00 0.00 33.61 2.85
615 2405 4.379186 GCATGTCAACATCTTGGACTCTTG 60.379 45.833 0.00 0.00 33.61 3.02
616 2406 3.743521 TGTCAACATCTTGGACTCTTGG 58.256 45.455 0.00 0.00 0.00 3.61
662 2452 5.186996 AGAAAATTGTGCGACATTTCTGT 57.813 34.783 12.81 0.00 36.58 3.41
718 2509 1.856629 AATCTTGGCACTGGGAATGG 58.143 50.000 0.00 0.00 0.00 3.16
736 2527 6.459923 GGAATGGGATCTGACTACTGAATAC 58.540 44.000 0.00 0.00 0.00 1.89
743 2534 7.367285 GGATCTGACTACTGAATACTGATCAC 58.633 42.308 0.00 0.00 37.53 3.06
752 2543 4.986622 TGAATACTGATCACAGAGACACG 58.013 43.478 0.00 0.00 46.03 4.49
757 2548 2.952310 CTGATCACAGAGACACGGGATA 59.048 50.000 0.00 0.00 46.03 2.59
822 2613 0.625316 TCTGCCCACCTATGCACATT 59.375 50.000 0.00 0.00 33.17 2.71
876 2674 3.232720 ACCAAAACTACCCCACGAAAT 57.767 42.857 0.00 0.00 0.00 2.17
914 2712 0.036164 TTAATCGGCATCATCCCCCG 59.964 55.000 0.00 0.00 43.21 5.73
945 2744 3.053320 GGGATCTTGTTCTCCCCTTGATT 60.053 47.826 0.00 0.00 44.68 2.57
956 2755 2.237143 TCCCCTTGATTAGCACTGACAG 59.763 50.000 0.00 0.00 0.00 3.51
957 2756 2.012673 CCCTTGATTAGCACTGACAGC 58.987 52.381 1.25 0.00 0.00 4.40
970 2781 2.695666 ACTGACAGCTAGCGACCATATT 59.304 45.455 9.55 0.00 0.00 1.28
1032 2848 2.024871 CGGCTCATCTCCGTCGTC 59.975 66.667 0.00 0.00 41.85 4.20
1283 3106 1.226435 GTCTACAGCCTGCTCGTCG 60.226 63.158 0.00 0.00 0.00 5.12
1284 3107 2.580867 CTACAGCCTGCTCGTCGC 60.581 66.667 0.00 0.00 39.77 5.19
1611 3434 6.911250 ATACCGTTGATGATCTATGTACCA 57.089 37.500 0.00 0.00 0.00 3.25
1614 3437 3.990469 CGTTGATGATCTATGTACCAGGC 59.010 47.826 0.00 0.00 0.00 4.85
1630 3453 3.230567 GCGGTCGCGCAAATTTCG 61.231 61.111 8.75 3.14 34.62 3.46
1645 3468 8.627756 CGCAAATTTCGCTAGTAGTATAATTG 57.372 34.615 0.00 0.32 0.00 2.32
1646 3469 8.273557 CGCAAATTTCGCTAGTAGTATAATTGT 58.726 33.333 0.00 0.00 0.00 2.71
1647 3470 9.931210 GCAAATTTCGCTAGTAGTATAATTGTT 57.069 29.630 0.00 0.00 0.00 2.83
1654 3477 9.426837 TCGCTAGTAGTATAATTGTTTGTTTGT 57.573 29.630 0.00 0.00 0.00 2.83
1708 3531 4.457834 TGTTCCGTGATTTGTTTTGGTT 57.542 36.364 0.00 0.00 0.00 3.67
1710 3533 5.341617 TGTTCCGTGATTTGTTTTGGTTAC 58.658 37.500 0.00 0.00 0.00 2.50
1712 3535 3.301706 CCGTGATTTGTTTTGGTTACGG 58.698 45.455 0.00 0.00 42.89 4.02
1717 3540 4.515944 TGATTTGTTTTGGTTACGGTCGAT 59.484 37.500 0.00 0.00 0.00 3.59
1718 3541 4.471157 TTTGTTTTGGTTACGGTCGATC 57.529 40.909 0.00 0.00 0.00 3.69
1719 3542 3.109044 TGTTTTGGTTACGGTCGATCA 57.891 42.857 0.00 0.00 0.00 2.92
1720 3543 3.666274 TGTTTTGGTTACGGTCGATCAT 58.334 40.909 0.00 0.00 0.00 2.45
1721 3544 4.066490 TGTTTTGGTTACGGTCGATCATT 58.934 39.130 0.00 0.00 0.00 2.57
1737 3560 7.642978 GGTCGATCATTTCATCTTCTTCATTTG 59.357 37.037 0.00 0.00 0.00 2.32
1739 3562 6.417044 CGATCATTTCATCTTCTTCATTTGGC 59.583 38.462 0.00 0.00 0.00 4.52
1742 3565 5.395682 TTTCATCTTCTTCATTTGGCCTG 57.604 39.130 3.32 0.00 0.00 4.85
1762 3585 3.371063 GGACGGACCGACAGCAGA 61.371 66.667 23.38 0.00 0.00 4.26
1763 3586 2.126424 GACGGACCGACAGCAGAC 60.126 66.667 23.38 0.00 0.00 3.51
1764 3587 3.628280 GACGGACCGACAGCAGACC 62.628 68.421 23.38 0.00 0.00 3.85
1765 3588 4.778415 CGGACCGACAGCAGACCG 62.778 72.222 8.64 0.00 34.77 4.79
1770 3593 3.374402 CGACAGCAGACCGAGGGT 61.374 66.667 0.00 0.00 39.44 4.34
1998 3838 5.770162 AGAAAAGGAAAATCAACGATGGTCT 59.230 36.000 0.00 0.00 0.00 3.85
2018 3858 5.331902 GTCTGACAGAATCTCTTTCTCGAG 58.668 45.833 6.76 5.93 42.98 4.04
2019 3859 5.007034 TCTGACAGAATCTCTTTCTCGAGT 58.993 41.667 13.13 0.00 42.98 4.18
2025 3865 7.087639 ACAGAATCTCTTTCTCGAGTAAACTG 58.912 38.462 13.13 14.07 42.98 3.16
2029 3869 4.825634 TCTCTTTCTCGAGTAAACTGACCA 59.174 41.667 13.13 0.00 32.83 4.02
2030 3870 5.477291 TCTCTTTCTCGAGTAAACTGACCAT 59.523 40.000 13.13 0.00 32.83 3.55
2035 3875 3.585862 TCGAGTAAACTGACCATTGAGC 58.414 45.455 0.00 0.00 0.00 4.26
2037 3877 3.369147 CGAGTAAACTGACCATTGAGCAG 59.631 47.826 0.00 0.00 35.81 4.24
2038 3878 3.679389 AGTAAACTGACCATTGAGCAGG 58.321 45.455 9.51 0.00 34.05 4.85
2039 3879 2.664402 AAACTGACCATTGAGCAGGT 57.336 45.000 9.51 0.00 41.83 4.00
2040 3880 2.664402 AACTGACCATTGAGCAGGTT 57.336 45.000 9.51 0.00 38.50 3.50
2041 3881 2.664402 ACTGACCATTGAGCAGGTTT 57.336 45.000 9.51 0.00 38.50 3.27
2042 3882 2.508526 ACTGACCATTGAGCAGGTTTC 58.491 47.619 9.51 0.00 38.50 2.78
2043 3883 1.815003 CTGACCATTGAGCAGGTTTCC 59.185 52.381 0.00 0.00 38.50 3.13
2044 3884 0.804989 GACCATTGAGCAGGTTTCCG 59.195 55.000 0.00 0.00 38.50 4.30
2046 3886 1.135315 CATTGAGCAGGTTTCCGCG 59.865 57.895 0.00 0.00 0.00 6.46
2048 3888 1.021390 ATTGAGCAGGTTTCCGCGAG 61.021 55.000 8.23 0.00 0.00 5.03
2049 3889 2.094757 TTGAGCAGGTTTCCGCGAGA 62.095 55.000 8.23 0.00 0.00 4.04
2051 3891 0.949105 GAGCAGGTTTCCGCGAGAAA 60.949 55.000 8.23 13.22 42.28 2.52
2052 3892 0.534203 AGCAGGTTTCCGCGAGAAAA 60.534 50.000 19.61 9.92 45.93 2.29
2053 3893 0.309612 GCAGGTTTCCGCGAGAAAAA 59.690 50.000 19.61 7.77 45.93 1.94
2090 3930 5.657302 TCAGGTAGACAGATAAAAGGGACTC 59.343 44.000 0.00 0.00 38.49 3.36
2094 3934 4.168101 AGACAGATAAAAGGGACTCCACA 58.832 43.478 0.00 0.00 38.49 4.17
2184 4025 7.201992 GGGCATCTCCAATTTGGTTATATTTCA 60.202 37.037 14.98 0.00 39.03 2.69
2186 4027 9.415544 GCATCTCCAATTTGGTTATATTTCATC 57.584 33.333 14.98 0.00 39.03 2.92
2248 4276 3.313012 ACTAACATGCTAGTCAACGCA 57.687 42.857 2.85 0.00 40.87 5.24
2249 4277 3.659786 ACTAACATGCTAGTCAACGCAA 58.340 40.909 2.85 0.00 39.89 4.85
2252 4280 1.155889 CATGCTAGTCAACGCAACCA 58.844 50.000 0.00 0.00 39.89 3.67
2253 4281 1.535028 CATGCTAGTCAACGCAACCAA 59.465 47.619 0.00 0.00 39.89 3.67
2254 4282 1.669604 TGCTAGTCAACGCAACCAAA 58.330 45.000 0.00 0.00 32.40 3.28
2255 4283 2.017782 TGCTAGTCAACGCAACCAAAA 58.982 42.857 0.00 0.00 32.40 2.44
2256 4284 2.032799 TGCTAGTCAACGCAACCAAAAG 59.967 45.455 0.00 0.00 32.40 2.27
2257 4285 2.032924 GCTAGTCAACGCAACCAAAAGT 59.967 45.455 0.00 0.00 0.00 2.66
2258 4286 2.844122 AGTCAACGCAACCAAAAGTC 57.156 45.000 0.00 0.00 0.00 3.01
2259 4287 1.404035 AGTCAACGCAACCAAAAGTCC 59.596 47.619 0.00 0.00 0.00 3.85
2261 4289 1.819288 TCAACGCAACCAAAAGTCCAA 59.181 42.857 0.00 0.00 0.00 3.53
2262 4290 2.159310 TCAACGCAACCAAAAGTCCAAG 60.159 45.455 0.00 0.00 0.00 3.61
2264 4292 0.102120 CGCAACCAAAAGTCCAAGCA 59.898 50.000 0.00 0.00 0.00 3.91
2267 4295 2.224018 GCAACCAAAAGTCCAAGCATGA 60.224 45.455 0.00 0.00 0.00 3.07
2268 4296 3.740764 GCAACCAAAAGTCCAAGCATGAA 60.741 43.478 0.00 0.00 0.00 2.57
2269 4297 4.440880 CAACCAAAAGTCCAAGCATGAAA 58.559 39.130 0.00 0.00 0.00 2.69
2270 4298 4.751767 ACCAAAAGTCCAAGCATGAAAA 57.248 36.364 0.00 0.00 0.00 2.29
2271 4299 4.696455 ACCAAAAGTCCAAGCATGAAAAG 58.304 39.130 0.00 0.00 0.00 2.27
2273 4301 4.060205 CAAAAGTCCAAGCATGAAAAGGG 58.940 43.478 0.00 0.00 0.00 3.95
2274 4302 1.260544 AGTCCAAGCATGAAAAGGGC 58.739 50.000 0.00 0.00 0.00 5.19
2275 4303 1.203100 AGTCCAAGCATGAAAAGGGCT 60.203 47.619 0.00 0.00 40.14 5.19
2276 4304 2.041620 AGTCCAAGCATGAAAAGGGCTA 59.958 45.455 0.00 0.00 36.76 3.93
2278 4306 2.041620 TCCAAGCATGAAAAGGGCTAGT 59.958 45.455 0.00 0.00 36.76 2.57
2279 4307 2.424956 CCAAGCATGAAAAGGGCTAGTC 59.575 50.000 0.00 0.00 36.76 2.59
2280 4308 3.084039 CAAGCATGAAAAGGGCTAGTCA 58.916 45.455 0.00 0.00 36.76 3.41
2281 4309 3.439857 AGCATGAAAAGGGCTAGTCAA 57.560 42.857 0.00 0.00 35.82 3.18
2282 4310 3.973425 AGCATGAAAAGGGCTAGTCAAT 58.027 40.909 0.00 0.00 35.82 2.57
2283 4311 3.950395 AGCATGAAAAGGGCTAGTCAATC 59.050 43.478 0.00 0.00 35.82 2.67
2284 4312 3.067320 GCATGAAAAGGGCTAGTCAATCC 59.933 47.826 0.00 0.00 0.00 3.01
2286 4314 3.686016 TGAAAAGGGCTAGTCAATCCAC 58.314 45.455 0.00 0.00 0.00 4.02
2287 4315 3.073798 TGAAAAGGGCTAGTCAATCCACA 59.926 43.478 0.00 0.00 0.00 4.17
2288 4316 4.263905 TGAAAAGGGCTAGTCAATCCACAT 60.264 41.667 0.00 0.00 0.00 3.21
2290 4318 5.450818 AAAGGGCTAGTCAATCCACATAA 57.549 39.130 0.00 0.00 0.00 1.90
2291 4319 5.450818 AAGGGCTAGTCAATCCACATAAA 57.549 39.130 0.00 0.00 0.00 1.40
2292 4320 4.781934 AGGGCTAGTCAATCCACATAAAC 58.218 43.478 0.00 0.00 0.00 2.01
2293 4321 4.475016 AGGGCTAGTCAATCCACATAAACT 59.525 41.667 0.00 0.00 0.00 2.66
2295 4323 5.066505 GGGCTAGTCAATCCACATAAACTTG 59.933 44.000 0.00 0.00 0.00 3.16
2296 4324 5.880332 GGCTAGTCAATCCACATAAACTTGA 59.120 40.000 0.00 0.00 0.00 3.02
2297 4325 6.183360 GGCTAGTCAATCCACATAAACTTGAC 60.183 42.308 5.77 5.77 43.70 3.18
2298 4326 6.371548 GCTAGTCAATCCACATAAACTTGACA 59.628 38.462 14.09 2.64 45.04 3.58
2306 5928 9.859427 AATCCACATAAACTTGACAATAACATG 57.141 29.630 0.00 0.00 0.00 3.21
2307 5929 7.825681 TCCACATAAACTTGACAATAACATGG 58.174 34.615 0.00 0.00 0.00 3.66
2309 5931 7.970061 CCACATAAACTTGACAATAACATGGAG 59.030 37.037 0.00 0.00 0.00 3.86
2389 6011 9.559958 CAAATGAAACAACTAGGTCACATTATC 57.440 33.333 0.00 0.00 31.36 1.75
2407 6029 6.043590 ACATTATCAGTGCATATCTCTCCCAA 59.956 38.462 0.00 0.00 0.00 4.12
2409 6031 2.101415 TCAGTGCATATCTCTCCCAACG 59.899 50.000 0.00 0.00 0.00 4.10
2421 6043 1.485066 CTCCCAACGTACAAGGGCTAT 59.515 52.381 8.94 0.00 42.52 2.97
2427 6049 3.705043 ACGTACAAGGGCTATTACTCG 57.295 47.619 0.00 0.00 0.00 4.18
2458 6080 1.275291 AGCAGCGCCAGTTCTAGTTTA 59.725 47.619 2.29 0.00 0.00 2.01
2465 6087 4.007659 CGCCAGTTCTAGTTTAAACCCAT 58.992 43.478 14.72 0.00 0.00 4.00
2492 6114 8.882736 AGACAAATTGACAGGAAAAATCAAAAC 58.117 29.630 0.00 0.00 36.03 2.43
2496 6118 7.967890 ATTGACAGGAAAAATCAAAACCATC 57.032 32.000 0.00 0.00 36.03 3.51
2504 6126 8.458052 AGGAAAAATCAAAACCATCAAAAACAC 58.542 29.630 0.00 0.00 0.00 3.32
2510 6132 5.121454 TCAAAACCATCAAAAACACTTGCAC 59.879 36.000 0.00 0.00 0.00 4.57
2514 6136 5.911752 ACCATCAAAAACACTTGCACATTA 58.088 33.333 0.00 0.00 0.00 1.90
2538 6162 7.389803 AATGCATACAAGTATAACAGCAACA 57.610 32.000 0.00 0.00 34.15 3.33
2541 6165 5.732647 GCATACAAGTATAACAGCAACAACG 59.267 40.000 0.00 0.00 0.00 4.10
2543 6167 3.500680 ACAAGTATAACAGCAACAACGGG 59.499 43.478 0.00 0.00 0.00 5.28
2551 6175 1.336440 CAGCAACAACGGGACAAATCA 59.664 47.619 0.00 0.00 0.00 2.57
2552 6176 1.608590 AGCAACAACGGGACAAATCAG 59.391 47.619 0.00 0.00 0.00 2.90
2556 6180 4.783242 CAACAACGGGACAAATCAGTAAG 58.217 43.478 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.840038 TCCTATGGCAGAACACTCATGT 59.160 45.455 0.00 0.00 42.46 3.21
5 6 3.201290 GTCCTATGGCAGAACACTCATG 58.799 50.000 0.00 0.00 0.00 3.07
6 7 2.159043 CGTCCTATGGCAGAACACTCAT 60.159 50.000 0.00 0.00 0.00 2.90
7 8 1.204704 CGTCCTATGGCAGAACACTCA 59.795 52.381 0.00 0.00 0.00 3.41
8 9 1.476891 TCGTCCTATGGCAGAACACTC 59.523 52.381 0.00 0.00 0.00 3.51
9 10 1.557099 TCGTCCTATGGCAGAACACT 58.443 50.000 0.00 0.00 0.00 3.55
10 11 2.271800 CTTCGTCCTATGGCAGAACAC 58.728 52.381 0.00 0.00 0.00 3.32
11 12 1.899814 ACTTCGTCCTATGGCAGAACA 59.100 47.619 0.00 0.00 0.00 3.18
12 13 2.271800 CACTTCGTCCTATGGCAGAAC 58.728 52.381 0.00 0.00 0.00 3.01
13 14 1.207089 CCACTTCGTCCTATGGCAGAA 59.793 52.381 0.00 0.00 0.00 3.02
14 15 0.824109 CCACTTCGTCCTATGGCAGA 59.176 55.000 0.00 0.00 0.00 4.26
212 913 7.105588 TGTATACAGATCAACAGCAACTCAAT 58.894 34.615 0.08 0.00 0.00 2.57
271 972 4.486125 AAACAAACCAAATGACTGCCTT 57.514 36.364 0.00 0.00 0.00 4.35
302 1004 2.598589 CAAATGTCCGCCACTTTCATG 58.401 47.619 0.00 0.00 0.00 3.07
304 1006 0.958091 CCAAATGTCCGCCACTTTCA 59.042 50.000 0.00 0.00 0.00 2.69
369 1776 1.804151 GCTTGCGGACATGTTTAGACA 59.196 47.619 0.00 0.00 40.71 3.41
419 1826 2.427506 CAGACTTAGGGCAACTCCAAC 58.572 52.381 0.00 0.00 36.21 3.77
593 2383 4.155462 CCAAGAGTCCAAGATGTTGACATG 59.845 45.833 3.74 0.00 36.57 3.21
609 2399 3.637229 CCGACTATCATGGTACCAAGAGT 59.363 47.826 23.08 17.89 0.00 3.24
610 2400 3.005897 CCCGACTATCATGGTACCAAGAG 59.994 52.174 23.08 14.95 0.00 2.85
611 2401 2.963101 CCCGACTATCATGGTACCAAGA 59.037 50.000 21.34 21.34 0.00 3.02
612 2402 2.548067 GCCCGACTATCATGGTACCAAG 60.548 54.545 20.76 15.59 0.00 3.61
613 2403 1.414919 GCCCGACTATCATGGTACCAA 59.585 52.381 20.76 3.13 0.00 3.67
614 2404 1.045407 GCCCGACTATCATGGTACCA 58.955 55.000 18.99 18.99 0.00 3.25
615 2405 1.045407 TGCCCGACTATCATGGTACC 58.955 55.000 4.43 4.43 0.00 3.34
616 2406 2.480845 GTTGCCCGACTATCATGGTAC 58.519 52.381 0.00 0.00 0.00 3.34
662 2452 4.318475 CGAATTCAAGTGTAGCGACAACAA 60.318 41.667 0.00 0.00 37.31 2.83
718 2509 7.013750 TGTGATCAGTATTCAGTAGTCAGATCC 59.986 40.741 0.00 0.00 30.96 3.36
736 2527 1.177401 TCCCGTGTCTCTGTGATCAG 58.823 55.000 0.00 0.00 42.54 2.90
743 2534 4.123497 TGTTGAATATCCCGTGTCTCTG 57.877 45.455 0.00 0.00 0.00 3.35
752 2543 2.808543 GTCTCGCCATGTTGAATATCCC 59.191 50.000 0.00 0.00 0.00 3.85
757 2548 2.783135 ACTTGTCTCGCCATGTTGAAT 58.217 42.857 0.00 0.00 0.00 2.57
822 2613 7.472334 ACGTTGGAAGAGTAGGAATAACTAA 57.528 36.000 0.00 0.00 0.00 2.24
876 2674 7.360353 CCGATTAAATAGATACACGTAGTCCGA 60.360 40.741 0.00 0.00 41.61 4.55
914 2712 4.249661 GAGAACAAGATCCCAGACACTTC 58.750 47.826 0.00 0.00 0.00 3.01
945 2744 0.452184 GTCGCTAGCTGTCAGTGCTA 59.548 55.000 13.93 0.00 41.46 3.49
956 2755 3.001330 GTGTTGTGAATATGGTCGCTAGC 59.999 47.826 4.06 4.06 0.00 3.42
957 2756 3.555956 GGTGTTGTGAATATGGTCGCTAG 59.444 47.826 0.00 0.00 0.00 3.42
970 2781 0.033642 TGATTACGCGGGTGTTGTGA 59.966 50.000 16.34 0.00 0.00 3.58
1179 2998 4.504858 ACGACCTCTCCACATATTTGTTC 58.495 43.478 0.00 0.00 32.34 3.18
1180 2999 4.553330 ACGACCTCTCCACATATTTGTT 57.447 40.909 0.00 0.00 32.34 2.83
1181 3000 4.253685 CAACGACCTCTCCACATATTTGT 58.746 43.478 0.00 0.00 36.15 2.83
1182 3001 3.063997 GCAACGACCTCTCCACATATTTG 59.936 47.826 0.00 0.00 0.00 2.32
1183 3002 3.270877 GCAACGACCTCTCCACATATTT 58.729 45.455 0.00 0.00 0.00 1.40
1185 3004 1.202417 CGCAACGACCTCTCCACATAT 60.202 52.381 0.00 0.00 0.00 1.78
1186 3005 0.172578 CGCAACGACCTCTCCACATA 59.827 55.000 0.00 0.00 0.00 2.29
1187 3006 1.079819 CGCAACGACCTCTCCACAT 60.080 57.895 0.00 0.00 0.00 3.21
1188 3007 2.338620 CGCAACGACCTCTCCACA 59.661 61.111 0.00 0.00 0.00 4.17
1189 3008 3.112709 GCGCAACGACCTCTCCAC 61.113 66.667 0.30 0.00 0.00 4.02
1190 3009 2.449031 AATGCGCAACGACCTCTCCA 62.449 55.000 17.11 0.00 0.00 3.86
1191 3010 1.298859 AAATGCGCAACGACCTCTCC 61.299 55.000 17.11 0.00 0.00 3.71
1192 3011 0.517316 AAAATGCGCAACGACCTCTC 59.483 50.000 17.11 0.00 0.00 3.20
1193 3012 0.517316 GAAAATGCGCAACGACCTCT 59.483 50.000 17.11 0.00 0.00 3.69
1319 3142 2.963499 CCACATCGGTCATGACGAG 58.037 57.895 19.33 15.40 44.24 4.18
1339 3162 4.567318 GTGAGCACCATCCCCATC 57.433 61.111 0.00 0.00 0.00 3.51
1393 3216 3.952628 CTCGTTGCCGTTCCTCCCC 62.953 68.421 0.00 0.00 35.01 4.81
1614 3437 3.230567 GCGAAATTTGCGCGACCG 61.231 61.111 12.10 3.23 45.27 4.79
1679 3502 4.170256 ACAAATCACGGAACAACACAAAC 58.830 39.130 0.00 0.00 0.00 2.93
1692 3515 3.954999 ACCGTAACCAAAACAAATCACG 58.045 40.909 0.00 0.00 0.00 4.35
1708 3531 5.515797 AGAAGATGAAATGATCGACCGTA 57.484 39.130 0.00 0.00 0.00 4.02
1710 3533 4.805719 TGAAGAAGATGAAATGATCGACCG 59.194 41.667 0.00 0.00 0.00 4.79
1712 3535 7.642978 CCAAATGAAGAAGATGAAATGATCGAC 59.357 37.037 0.00 0.00 0.00 4.20
1717 3540 5.718130 AGGCCAAATGAAGAAGATGAAATGA 59.282 36.000 5.01 0.00 0.00 2.57
1718 3541 5.810587 CAGGCCAAATGAAGAAGATGAAATG 59.189 40.000 5.01 0.00 0.00 2.32
1719 3542 5.718130 TCAGGCCAAATGAAGAAGATGAAAT 59.282 36.000 5.01 0.00 0.00 2.17
1720 3543 5.047802 GTCAGGCCAAATGAAGAAGATGAAA 60.048 40.000 5.01 0.00 0.00 2.69
1721 3544 4.460382 GTCAGGCCAAATGAAGAAGATGAA 59.540 41.667 5.01 0.00 0.00 2.57
1755 3578 1.407656 TTTCACCCTCGGTCTGCTGT 61.408 55.000 0.00 0.00 31.02 4.40
1756 3579 0.036010 ATTTCACCCTCGGTCTGCTG 60.036 55.000 0.00 0.00 31.02 4.41
1757 3580 0.036010 CATTTCACCCTCGGTCTGCT 60.036 55.000 0.00 0.00 31.02 4.24
1758 3581 0.321653 ACATTTCACCCTCGGTCTGC 60.322 55.000 0.00 0.00 31.02 4.26
1759 3582 1.442769 CACATTTCACCCTCGGTCTG 58.557 55.000 0.00 0.00 31.02 3.51
1760 3583 0.324943 CCACATTTCACCCTCGGTCT 59.675 55.000 0.00 0.00 31.02 3.85
1761 3584 1.305930 GCCACATTTCACCCTCGGTC 61.306 60.000 0.00 0.00 31.02 4.79
1762 3585 1.303317 GCCACATTTCACCCTCGGT 60.303 57.895 0.00 0.00 35.62 4.69
1763 3586 2.398554 CGCCACATTTCACCCTCGG 61.399 63.158 0.00 0.00 0.00 4.63
1764 3587 1.361668 CTCGCCACATTTCACCCTCG 61.362 60.000 0.00 0.00 0.00 4.63
1765 3588 0.036388 TCTCGCCACATTTCACCCTC 60.036 55.000 0.00 0.00 0.00 4.30
1770 3593 3.145286 TCAAACATCTCGCCACATTTCA 58.855 40.909 0.00 0.00 0.00 2.69
1806 3629 4.530094 GACATGATCGGCATAACGAAAA 57.470 40.909 0.00 0.00 46.92 2.29
1828 3651 9.474920 TCATTTCAAATCTTCAACACCAATAAC 57.525 29.630 0.00 0.00 0.00 1.89
1868 3692 6.151648 CCTCTTCACCTTGCTCAAAATATGAA 59.848 38.462 0.00 0.00 37.67 2.57
2018 3858 3.412386 ACCTGCTCAATGGTCAGTTTAC 58.588 45.455 0.00 0.00 29.18 2.01
2019 3859 3.788227 ACCTGCTCAATGGTCAGTTTA 57.212 42.857 0.00 0.00 29.18 2.01
2025 3865 0.804989 CGGAAACCTGCTCAATGGTC 59.195 55.000 0.00 0.00 35.17 4.02
2029 3869 1.003839 TCGCGGAAACCTGCTCAAT 60.004 52.632 6.13 0.00 0.00 2.57
2030 3870 1.667830 CTCGCGGAAACCTGCTCAA 60.668 57.895 6.13 0.00 0.00 3.02
2051 3891 6.042781 TGTCTACCTGACCTCATAGTTGTTTT 59.957 38.462 0.00 0.00 44.75 2.43
2052 3892 5.542635 TGTCTACCTGACCTCATAGTTGTTT 59.457 40.000 0.00 0.00 44.75 2.83
2053 3893 5.084519 TGTCTACCTGACCTCATAGTTGTT 58.915 41.667 0.00 0.00 44.75 2.83
2054 3894 4.673968 TGTCTACCTGACCTCATAGTTGT 58.326 43.478 0.00 0.00 44.75 3.32
2055 3895 4.950475 TCTGTCTACCTGACCTCATAGTTG 59.050 45.833 0.00 0.00 44.75 3.16
2056 3896 5.194473 TCTGTCTACCTGACCTCATAGTT 57.806 43.478 0.00 0.00 44.75 2.24
2057 3897 4.864483 TCTGTCTACCTGACCTCATAGT 57.136 45.455 0.00 0.00 44.75 2.12
2058 3898 7.825331 TTTATCTGTCTACCTGACCTCATAG 57.175 40.000 0.00 0.00 44.75 2.23
2059 3899 7.287927 CCTTTTATCTGTCTACCTGACCTCATA 59.712 40.741 0.00 0.00 44.75 2.15
2060 3900 6.098982 CCTTTTATCTGTCTACCTGACCTCAT 59.901 42.308 0.00 0.00 44.75 2.90
2061 3901 5.422331 CCTTTTATCTGTCTACCTGACCTCA 59.578 44.000 0.00 0.00 44.75 3.86
2062 3902 5.163395 CCCTTTTATCTGTCTACCTGACCTC 60.163 48.000 0.00 0.00 44.75 3.85
2070 3910 5.187186 TGTGGAGTCCCTTTTATCTGTCTAC 59.813 44.000 6.74 0.00 0.00 2.59
2072 3912 4.020128 GTGTGGAGTCCCTTTTATCTGTCT 60.020 45.833 6.74 0.00 0.00 3.41
2094 3934 2.493278 GCCTTGTCTTATGCACAATGGT 59.507 45.455 0.00 0.00 33.30 3.55
2237 4265 3.303791 GGACTTTTGGTTGCGTTGACTAG 60.304 47.826 0.00 0.00 0.00 2.57
2240 4268 1.133407 TGGACTTTTGGTTGCGTTGAC 59.867 47.619 0.00 0.00 0.00 3.18
2241 4269 1.464734 TGGACTTTTGGTTGCGTTGA 58.535 45.000 0.00 0.00 0.00 3.18
2242 4270 2.192624 CTTGGACTTTTGGTTGCGTTG 58.807 47.619 0.00 0.00 0.00 4.10
2244 4272 0.102300 GCTTGGACTTTTGGTTGCGT 59.898 50.000 0.00 0.00 0.00 5.24
2245 4273 0.102120 TGCTTGGACTTTTGGTTGCG 59.898 50.000 0.00 0.00 0.00 4.85
2246 4274 2.137523 CATGCTTGGACTTTTGGTTGC 58.862 47.619 0.00 0.00 0.00 4.17
2248 4276 4.751767 TTTCATGCTTGGACTTTTGGTT 57.248 36.364 0.00 0.00 0.00 3.67
2249 4277 4.443315 CCTTTTCATGCTTGGACTTTTGGT 60.443 41.667 0.00 0.00 0.00 3.67
2252 4280 3.494924 GCCCTTTTCATGCTTGGACTTTT 60.495 43.478 0.00 0.00 0.00 2.27
2253 4281 2.037641 GCCCTTTTCATGCTTGGACTTT 59.962 45.455 0.00 0.00 0.00 2.66
2254 4282 1.620323 GCCCTTTTCATGCTTGGACTT 59.380 47.619 0.00 0.00 0.00 3.01
2255 4283 1.203100 AGCCCTTTTCATGCTTGGACT 60.203 47.619 0.00 0.00 29.17 3.85
2256 4284 1.260544 AGCCCTTTTCATGCTTGGAC 58.739 50.000 0.00 0.00 29.17 4.02
2257 4285 2.041620 ACTAGCCCTTTTCATGCTTGGA 59.958 45.455 0.00 0.00 36.57 3.53
2258 4286 2.424956 GACTAGCCCTTTTCATGCTTGG 59.575 50.000 0.00 0.00 36.57 3.61
2259 4287 3.084039 TGACTAGCCCTTTTCATGCTTG 58.916 45.455 0.00 0.00 36.57 4.01
2261 4289 3.439857 TTGACTAGCCCTTTTCATGCT 57.560 42.857 0.00 0.00 39.10 3.79
2262 4290 3.067320 GGATTGACTAGCCCTTTTCATGC 59.933 47.826 0.00 0.00 0.00 4.06
2264 4292 4.263905 TGTGGATTGACTAGCCCTTTTCAT 60.264 41.667 0.00 0.00 0.00 2.57
2267 4295 3.806949 TGTGGATTGACTAGCCCTTTT 57.193 42.857 0.00 0.00 0.00 2.27
2268 4296 5.450818 TTATGTGGATTGACTAGCCCTTT 57.549 39.130 0.00 0.00 0.00 3.11
2269 4297 5.044846 AGTTTATGTGGATTGACTAGCCCTT 60.045 40.000 0.00 0.00 0.00 3.95
2270 4298 4.475016 AGTTTATGTGGATTGACTAGCCCT 59.525 41.667 0.00 0.00 0.00 5.19
2271 4299 4.781934 AGTTTATGTGGATTGACTAGCCC 58.218 43.478 0.00 0.00 0.00 5.19
2273 4301 6.371548 TGTCAAGTTTATGTGGATTGACTAGC 59.628 38.462 15.07 0.00 46.23 3.42
2274 4302 7.905604 TGTCAAGTTTATGTGGATTGACTAG 57.094 36.000 15.07 0.00 46.23 2.57
2275 4303 8.862325 ATTGTCAAGTTTATGTGGATTGACTA 57.138 30.769 15.07 9.57 46.23 2.59
2276 4304 7.765695 ATTGTCAAGTTTATGTGGATTGACT 57.234 32.000 15.07 0.00 46.23 3.41
2278 4306 9.072375 TGTTATTGTCAAGTTTATGTGGATTGA 57.928 29.630 0.00 0.00 0.00 2.57
2279 4307 9.859427 ATGTTATTGTCAAGTTTATGTGGATTG 57.141 29.630 0.00 0.00 0.00 2.67
2280 4308 9.859427 CATGTTATTGTCAAGTTTATGTGGATT 57.141 29.630 0.00 0.00 0.00 3.01
2281 4309 8.469200 CCATGTTATTGTCAAGTTTATGTGGAT 58.531 33.333 0.00 0.00 0.00 3.41
2282 4310 7.667635 TCCATGTTATTGTCAAGTTTATGTGGA 59.332 33.333 0.00 0.00 0.00 4.02
2283 4311 7.825681 TCCATGTTATTGTCAAGTTTATGTGG 58.174 34.615 0.00 0.00 0.00 4.17
2284 4312 8.729756 TCTCCATGTTATTGTCAAGTTTATGTG 58.270 33.333 0.00 0.00 0.00 3.21
2326 5948 9.736414 CCTCTATCACTCCAAATTGATGAATAT 57.264 33.333 0.00 0.00 34.28 1.28
2378 6000 6.462500 AGAGATATGCACTGATAATGTGACC 58.538 40.000 0.00 0.00 37.60 4.02
2389 6011 2.159043 ACGTTGGGAGAGATATGCACTG 60.159 50.000 0.00 0.00 0.00 3.66
2407 6029 3.019564 ACGAGTAATAGCCCTTGTACGT 58.980 45.455 0.00 0.00 0.00 3.57
2409 6031 9.533253 TTAATAAACGAGTAATAGCCCTTGTAC 57.467 33.333 0.00 0.00 0.00 2.90
2421 6043 5.791480 GCGCTGCTTTTTAATAAACGAGTAA 59.209 36.000 0.00 0.00 0.00 2.24
2427 6049 4.234574 ACTGGCGCTGCTTTTTAATAAAC 58.765 39.130 7.64 0.00 0.00 2.01
2436 6058 0.035458 ACTAGAACTGGCGCTGCTTT 59.965 50.000 7.64 0.00 0.00 3.51
2458 6080 5.640147 TCCTGTCAATTTGTCTATGGGTTT 58.360 37.500 0.00 0.00 0.00 3.27
2492 6114 6.841443 TTAATGTGCAAGTGTTTTTGATGG 57.159 33.333 0.00 0.00 0.00 3.51
2510 6132 9.949174 TTGCTGTTATACTTGTATGCATTAATG 57.051 29.630 3.54 11.27 0.00 1.90
2514 6136 7.389803 TGTTGCTGTTATACTTGTATGCATT 57.610 32.000 3.54 0.00 0.00 3.56
2522 6144 3.749088 TCCCGTTGTTGCTGTTATACTTG 59.251 43.478 0.00 0.00 0.00 3.16
2524 6146 3.244284 TGTCCCGTTGTTGCTGTTATACT 60.244 43.478 0.00 0.00 0.00 2.12
2525 6147 3.068560 TGTCCCGTTGTTGCTGTTATAC 58.931 45.455 0.00 0.00 0.00 1.47
2538 6162 3.006110 TCGTCTTACTGATTTGTCCCGTT 59.994 43.478 0.00 0.00 0.00 4.44
2541 6165 4.312443 TGTTCGTCTTACTGATTTGTCCC 58.688 43.478 0.00 0.00 0.00 4.46
2543 6167 7.117241 TCATTGTTCGTCTTACTGATTTGTC 57.883 36.000 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.