Multiple sequence alignment - TraesCS5A01G145900

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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 TraesCS5A01G145900 chr5A 100.000 3662 0 0 1 3662 321927582 321931243 0.000000e+00 6763.0
1 TraesCS5A01G145900 chr5D 92.824 2787 126 35 902 3662 233021886 233019148 0.000000e+00 3971.0
2 TraesCS5A01G145900 chr5D 90.418 814 49 18 3 798 233035891 233035089 0.000000e+00 1044.0
3 TraesCS5A01G145900 chr5D 100.000 35 0 0 876 910 233035009 233034975 8.490000e-07 65.8
4 TraesCS5A01G145900 chr5B 91.042 2054 85 36 1 1995 271952681 271954694 0.000000e+00 2682.0
5 TraesCS5A01G145900 chr5B 92.173 1252 61 13 1991 3230 271955436 271956662 0.000000e+00 1735.0
6 TraesCS5A01G145900 chr5B 95.588 136 6 0 3527 3662 271957056 271957191 6.160000e-53 219.0
7 TraesCS5A01G145900 chr5B 80.428 327 21 23 3227 3530 271956726 271957032 3.710000e-50 209.0
8 TraesCS5A01G145900 chr5B 89.796 49 4 1 2229 2276 50469171 50469123 1.100000e-05 62.1
9 TraesCS5A01G145900 chr5B 88.235 51 5 1 2228 2277 327792504 327792554 3.950000e-05 60.2
10 TraesCS5A01G145900 chr3B 96.452 310 9 2 2883 3190 554032557 554032248 9.070000e-141 510.0
11 TraesCS5A01G145900 chr3B 96.452 310 9 2 2883 3190 761575724 761575415 9.070000e-141 510.0
12 TraesCS5A01G145900 chr1B 95.806 310 11 2 2883 3190 646680094 646680403 1.960000e-137 499.0
13 TraesCS5A01G145900 chr1B 95.484 310 12 2 2883 3190 664597327 664597018 9.140000e-136 494.0
14 TraesCS5A01G145900 chr1B 93.182 44 3 0 2228 2271 411570457 411570500 8.490000e-07 65.8
15 TraesCS5A01G145900 chr2B 95.806 310 10 3 2883 3190 797244433 797244741 7.060000e-137 497.0
16 TraesCS5A01G145900 chr7B 95.161 310 13 2 2883 3190 204157807 204157498 4.250000e-134 488.0
17 TraesCS5A01G145900 chr6A 96.233 292 8 3 2901 3190 606596425 606596135 3.310000e-130 475.0
18 TraesCS5A01G145900 chr3A 95.745 47 1 1 2232 2277 296449301 296449255 1.410000e-09 75.0
19 TraesCS5A01G145900 chr1A 95.455 44 2 0 2228 2271 379498312 379498269 1.820000e-08 71.3
20 TraesCS5A01G145900 chr2A 93.333 45 3 0 2228 2272 102688084 102688040 2.360000e-07 67.6
21 TraesCS5A01G145900 chr2D 93.182 44 3 0 2228 2271 234147887 234147930 8.490000e-07 65.8


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 TraesCS5A01G145900 chr5A 321927582 321931243 3661 False 6763.00 6763 100.00000 1 3662 1 chr5A.!!$F1 3661
1 TraesCS5A01G145900 chr5D 233019148 233021886 2738 True 3971.00 3971 92.82400 902 3662 1 chr5D.!!$R1 2760
2 TraesCS5A01G145900 chr5D 233034975 233035891 916 True 554.90 1044 95.20900 3 910 2 chr5D.!!$R2 907
3 TraesCS5A01G145900 chr5B 271952681 271957191 4510 False 1211.25 2682 89.80775 1 3662 4 chr5B.!!$F2 3661

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
230 235 0.179113 CAGCAACCACACCAACCAAC 60.179 55.0 0.00 0.00 0.0 3.77 F
412 418 0.374758 GTACCGAGATCGTACACGCA 59.625 55.0 1.09 0.00 39.6 5.24 F
627 635 0.593773 GATGCGGCGAGAGAGAACTC 60.594 60.0 12.98 0.00 42.9 3.01 F
872 947 0.931702 TTTAGAACCACACACACGCG 59.068 50.0 3.53 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1913 0.249657 CGGTGCAAGAGGCCTCTATC 60.250 60.000 35.31 27.15 43.89 2.08 R
1816 1920 1.130561 GTATGTTTCGGTGCAAGAGGC 59.869 52.381 0.00 0.00 45.13 4.70 R
2590 3451 1.452110 TCACCGAATCCACATGCTTG 58.548 50.000 0.00 0.00 0.00 4.01 R
2729 3593 1.675310 CGGCATTCTCAGGTGGCAA 60.675 57.895 0.00 0.00 40.56 4.52 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
140 145 9.890629 AATTGGATAAGCGATTAAGCATATCTA 57.109 29.630 0.00 5.50 43.38 1.98
230 235 0.179113 CAGCAACCACACCAACCAAC 60.179 55.000 0.00 0.00 0.00 3.77
244 249 3.304928 CCAACCAACTCATTTGCAGAGTC 60.305 47.826 7.48 0.00 45.11 3.36
376 382 8.524870 AACTAAACAATAATGAAAAGCAGCAG 57.475 30.769 0.00 0.00 0.00 4.24
378 384 8.792633 ACTAAACAATAATGAAAAGCAGCAGTA 58.207 29.630 0.00 0.00 0.00 2.74
412 418 0.374758 GTACCGAGATCGTACACGCA 59.625 55.000 1.09 0.00 39.60 5.24
421 427 3.932710 AGATCGTACACGCATCACAAAAT 59.067 39.130 13.04 0.00 39.60 1.82
450 456 2.629051 GACTCCCCAATTTCCACTACG 58.371 52.381 0.00 0.00 0.00 3.51
544 552 2.907910 GCGACAGCAAACAATCAGAT 57.092 45.000 0.00 0.00 44.35 2.90
545 553 2.778659 GCGACAGCAAACAATCAGATC 58.221 47.619 0.00 0.00 44.35 2.75
546 554 2.160219 GCGACAGCAAACAATCAGATCA 59.840 45.455 0.00 0.00 44.35 2.92
547 555 3.727079 GCGACAGCAAACAATCAGATCAG 60.727 47.826 0.00 0.00 44.35 2.90
596 604 2.178912 AATCACCTTCGCCTCGAAAA 57.821 45.000 3.24 0.00 45.23 2.29
627 635 0.593773 GATGCGGCGAGAGAGAACTC 60.594 60.000 12.98 0.00 42.90 3.01
649 657 2.586357 GGCGGGAACAGCGATCTC 60.586 66.667 0.00 0.00 35.00 2.75
697 731 1.680989 GTCGGAATTGGGGGTTGGG 60.681 63.158 0.00 0.00 0.00 4.12
773 814 6.150976 TGAACAGTTGCAGGATTTATTTCGAT 59.849 34.615 0.00 0.00 0.00 3.59
833 907 2.419574 GCTTGTTCGAGTAGGCCCATTA 60.420 50.000 0.00 0.00 0.00 1.90
839 913 2.102588 TCGAGTAGGCCCATTAAAGCTC 59.897 50.000 0.00 0.00 0.00 4.09
869 944 2.030274 GCCCATTTAGAACCACACACAC 60.030 50.000 0.00 0.00 0.00 3.82
870 945 2.225491 CCCATTTAGAACCACACACACG 59.775 50.000 0.00 0.00 0.00 4.49
871 946 2.350388 CCATTTAGAACCACACACACGC 60.350 50.000 0.00 0.00 0.00 5.34
872 947 0.931702 TTTAGAACCACACACACGCG 59.068 50.000 3.53 3.53 0.00 6.01
873 948 1.492319 TTAGAACCACACACACGCGC 61.492 55.000 5.73 0.00 0.00 6.86
874 949 4.643385 GAACCACACACACGCGCG 62.643 66.667 30.96 30.96 0.00 6.86
1321 1396 2.804828 CTTCTGCGGGACCAGGTTCC 62.805 65.000 6.90 6.90 33.64 3.62
1341 1416 2.271497 GAGGAGGACGACGGAGGA 59.729 66.667 0.00 0.00 0.00 3.71
1371 1446 1.153005 CTTCATGGGCCTGGAGCTC 60.153 63.158 4.71 4.71 45.08 4.09
1484 1559 2.493675 TCGTGGTGATCTTCTCCTCTTG 59.506 50.000 0.00 0.00 31.62 3.02
1548 1649 2.956987 GCTGGAGCGCATGTGTTT 59.043 55.556 11.47 0.00 0.00 2.83
1569 1670 7.819900 GTGTTTATGGAACTATCTTCAGTGACT 59.180 37.037 0.00 0.00 39.08 3.41
1570 1671 8.375506 TGTTTATGGAACTATCTTCAGTGACTT 58.624 33.333 0.00 0.00 39.08 3.01
1571 1672 8.660373 GTTTATGGAACTATCTTCAGTGACTTG 58.340 37.037 0.00 0.00 35.31 3.16
1655 1756 1.004745 AGGTAGGTTGCTGACATTGGG 59.995 52.381 0.00 0.00 0.00 4.12
1708 1809 6.494952 ACTTCTGAGTTGACCTAATAGAGGA 58.505 40.000 0.00 0.00 39.55 3.71
1764 1865 3.609175 GCAAGTTAGCAATGACGAAGCAA 60.609 43.478 0.00 0.00 0.00 3.91
1765 1866 4.536065 CAAGTTAGCAATGACGAAGCAAA 58.464 39.130 0.00 0.00 0.00 3.68
1766 1867 4.829064 AGTTAGCAATGACGAAGCAAAA 57.171 36.364 0.00 0.00 0.00 2.44
1767 1868 5.181690 AGTTAGCAATGACGAAGCAAAAA 57.818 34.783 0.00 0.00 0.00 1.94
1802 1906 6.927416 TGATGTTCTTTTCATGGATTCAAGG 58.073 36.000 0.00 0.00 0.00 3.61
1803 1907 6.720748 TGATGTTCTTTTCATGGATTCAAGGA 59.279 34.615 0.00 0.00 0.00 3.36
1804 1908 6.975196 TGTTCTTTTCATGGATTCAAGGAA 57.025 33.333 0.00 0.00 0.00 3.36
1805 1909 7.543359 TGTTCTTTTCATGGATTCAAGGAAT 57.457 32.000 0.00 0.00 34.71 3.01
1806 1910 8.648698 TGTTCTTTTCATGGATTCAAGGAATA 57.351 30.769 0.00 0.00 31.89 1.75
1807 1911 8.742777 TGTTCTTTTCATGGATTCAAGGAATAG 58.257 33.333 0.00 0.96 31.89 1.73
1808 1912 8.960591 GTTCTTTTCATGGATTCAAGGAATAGA 58.039 33.333 4.98 4.98 31.89 1.98
1809 1913 8.743085 TCTTTTCATGGATTCAAGGAATAGAG 57.257 34.615 4.98 0.00 31.89 2.43
1816 1920 7.789202 TGGATTCAAGGAATAGAGATAGAGG 57.211 40.000 0.00 0.00 31.89 3.69
1966 2070 9.543018 GTATTGTGTTTCTCTGTTAAACATAGC 57.457 33.333 11.41 3.36 45.62 2.97
2178 3028 4.844884 TCTGGATCGACTAAACTCAGAGA 58.155 43.478 3.79 0.00 0.00 3.10
2229 3079 7.615403 ACAAAGTACTTGAGCAGAGATAATCA 58.385 34.615 9.34 0.00 38.50 2.57
2384 3235 9.499479 CATAGCAGAGGTATTTATGACATTTCT 57.501 33.333 0.00 0.00 0.00 2.52
2413 3264 2.237392 GCACAGGAAAGGAGAGGTATGT 59.763 50.000 0.00 0.00 0.00 2.29
2455 3306 4.504858 GGACTTCATGAATGTCCTTACGT 58.495 43.478 30.16 16.10 44.84 3.57
2456 3307 4.330074 GGACTTCATGAATGTCCTTACGTG 59.670 45.833 30.16 12.81 44.84 4.49
2457 3308 3.684788 ACTTCATGAATGTCCTTACGTGC 59.315 43.478 8.96 0.00 0.00 5.34
2458 3309 3.610040 TCATGAATGTCCTTACGTGCT 57.390 42.857 0.00 0.00 0.00 4.40
2459 3310 4.729227 TCATGAATGTCCTTACGTGCTA 57.271 40.909 0.00 0.00 0.00 3.49
2460 3311 5.276461 TCATGAATGTCCTTACGTGCTAT 57.724 39.130 0.00 0.00 0.00 2.97
2461 3312 5.289595 TCATGAATGTCCTTACGTGCTATC 58.710 41.667 0.00 0.00 0.00 2.08
2462 3313 5.069119 TCATGAATGTCCTTACGTGCTATCT 59.931 40.000 0.00 0.00 0.00 1.98
2463 3314 5.339008 TGAATGTCCTTACGTGCTATCTT 57.661 39.130 0.00 0.00 0.00 2.40
2766 3630 3.057456 GCCGACTGTAAAGAGAGTTCTGA 60.057 47.826 0.00 0.00 32.79 3.27
2801 3669 5.729229 TGATTTTACCCTCTAACTGGATCCA 59.271 40.000 15.27 15.27 0.00 3.41
2859 3728 6.486941 AGGAAACCACCCGAATAAATTAGAA 58.513 36.000 0.00 0.00 0.00 2.10
2860 3729 6.602009 AGGAAACCACCCGAATAAATTAGAAG 59.398 38.462 0.00 0.00 0.00 2.85
2883 3752 4.967084 ACTTGTGGACATGGTAGTACAA 57.033 40.909 2.06 0.00 33.29 2.41
2887 3761 6.042322 ACTTGTGGACATGGTAGTACAACTTA 59.958 38.462 2.06 0.00 33.29 2.24
2914 3788 4.823442 TCATGTGTGGAAGATGGCATTATC 59.177 41.667 0.00 3.08 30.44 1.75
2946 3822 1.133025 GAATCCGGACCAGCATTTGTG 59.867 52.381 6.12 0.00 0.00 3.33
2975 3851 3.157087 CACTGATGGTAAAAGGGCTTGT 58.843 45.455 0.00 0.00 0.00 3.16
2983 3859 3.868661 GGTAAAAGGGCTTGTTGTGTTTG 59.131 43.478 0.00 0.00 0.00 2.93
3017 3893 8.865590 AATGTTTGTACACATTGTTTTAGTCC 57.134 30.769 10.09 0.00 44.19 3.85
3023 3899 6.995686 TGTACACATTGTTTTAGTCCTCATGT 59.004 34.615 0.00 0.00 0.00 3.21
3037 3913 3.515104 TCCTCATGTATGTCAGCACTTGA 59.485 43.478 0.00 6.06 0.00 3.02
3055 3931 6.197276 CACTTGAACAAAGAGTGAATCACAG 58.803 40.000 16.38 2.57 42.54 3.66
3065 3941 5.546526 AGAGTGAATCACAGAAAGAGAACC 58.453 41.667 16.38 0.00 36.74 3.62
3072 3948 7.604164 TGAATCACAGAAAGAGAACCTTGATAC 59.396 37.037 0.00 0.00 34.79 2.24
3073 3949 6.419484 TCACAGAAAGAGAACCTTGATACA 57.581 37.500 0.00 0.00 34.79 2.29
3074 3950 6.826668 TCACAGAAAGAGAACCTTGATACAA 58.173 36.000 0.00 0.00 34.79 2.41
3075 3951 7.453393 TCACAGAAAGAGAACCTTGATACAAT 58.547 34.615 0.00 0.00 34.79 2.71
3076 3952 8.593679 TCACAGAAAGAGAACCTTGATACAATA 58.406 33.333 0.00 0.00 34.79 1.90
3077 3953 8.660373 CACAGAAAGAGAACCTTGATACAATAC 58.340 37.037 0.00 0.00 34.79 1.89
3081 3957 8.918202 AAAGAGAACCTTGATACAATACACAA 57.082 30.769 0.00 0.00 34.79 3.33
3129 4006 7.008021 AGTGCTGTTGAAATTTTATTGGGAT 57.992 32.000 0.00 0.00 0.00 3.85
3158 4035 4.701651 TCTTCATCAAGTAATGTTGCAGGG 59.298 41.667 0.00 0.00 0.00 4.45
3160 4037 4.406456 TCATCAAGTAATGTTGCAGGGTT 58.594 39.130 0.00 0.00 0.00 4.11
3168 4045 0.393132 TGTTGCAGGGTTGACGACAA 60.393 50.000 0.00 0.00 0.00 3.18
3192 4069 7.578310 ACATGAATAAATCAAGGGAGATGTG 57.422 36.000 0.00 0.00 42.54 3.21
3193 4070 7.121382 ACATGAATAAATCAAGGGAGATGTGT 58.879 34.615 0.00 0.00 42.54 3.72
3208 4085 4.910195 AGATGTGTGCAGGATTTCAACTA 58.090 39.130 0.00 0.00 0.00 2.24
3212 4089 8.432013 AGATGTGTGCAGGATTTCAACTATATA 58.568 33.333 0.00 0.00 0.00 0.86
3262 4206 6.000219 AGCTATGACATTCTGAAAACACACT 59.000 36.000 0.00 0.00 0.00 3.55
3263 4207 6.488006 AGCTATGACATTCTGAAAACACACTT 59.512 34.615 0.00 0.00 0.00 3.16
3264 4208 7.013655 AGCTATGACATTCTGAAAACACACTTT 59.986 33.333 0.00 0.00 0.00 2.66
3265 4209 7.113965 GCTATGACATTCTGAAAACACACTTTG 59.886 37.037 0.00 0.00 0.00 2.77
3266 4210 6.507958 TGACATTCTGAAAACACACTTTGA 57.492 33.333 0.00 0.00 0.00 2.69
3281 4235 7.051623 ACACACTTTGATCTACCACTTTACAA 58.948 34.615 0.00 0.00 0.00 2.41
3284 4238 8.403236 ACACTTTGATCTACCACTTTACAAAAC 58.597 33.333 0.00 0.00 0.00 2.43
3285 4239 7.860872 CACTTTGATCTACCACTTTACAAAACC 59.139 37.037 0.00 0.00 0.00 3.27
3286 4240 6.548441 TTGATCTACCACTTTACAAAACCG 57.452 37.500 0.00 0.00 0.00 4.44
3287 4241 5.856156 TGATCTACCACTTTACAAAACCGA 58.144 37.500 0.00 0.00 0.00 4.69
3306 4260 7.628769 AACCGAAAGTTTTAGTTACAGGAAA 57.371 32.000 3.18 0.00 33.89 3.13
3307 4261 7.019774 ACCGAAAGTTTTAGTTACAGGAAAC 57.980 36.000 0.00 0.00 33.39 2.78
3308 4262 6.131389 CCGAAAGTTTTAGTTACAGGAAACG 58.869 40.000 0.00 0.00 37.15 3.60
3310 4264 6.238184 CGAAAGTTTTAGTTACAGGAAACGGT 60.238 38.462 0.00 0.00 42.94 4.83
3312 4266 8.504812 AAAGTTTTAGTTACAGGAAACGGTTA 57.495 30.769 0.00 0.00 40.14 2.85
3313 4267 7.482654 AGTTTTAGTTACAGGAAACGGTTAC 57.517 36.000 0.00 0.00 40.14 2.50
3318 4273 5.295152 AGTTACAGGAAACGGTTACTTCAG 58.705 41.667 0.00 0.00 44.03 3.02
3332 4287 3.252974 ACTTCAGGGTGATGATTCGAC 57.747 47.619 0.00 0.00 0.00 4.20
3333 4288 2.834549 ACTTCAGGGTGATGATTCGACT 59.165 45.455 0.00 0.00 0.00 4.18
3361 4316 6.270695 ACCAACCAATCCAATGAATTCTTCTT 59.729 34.615 7.05 0.00 0.00 2.52
3371 4326 5.965033 ATGAATTCTTCTTAGCCTCTGGA 57.035 39.130 7.05 0.00 0.00 3.86
3379 4334 4.640771 TCTTAGCCTCTGGATTTTGTGT 57.359 40.909 0.00 0.00 0.00 3.72
3412 4367 7.994425 TCTCTTATCCAACTTTGCACAATAA 57.006 32.000 0.00 0.00 0.00 1.40
3413 4368 8.579850 TCTCTTATCCAACTTTGCACAATAAT 57.420 30.769 0.00 0.00 0.00 1.28
3414 4369 8.461222 TCTCTTATCCAACTTTGCACAATAATG 58.539 33.333 0.00 0.00 0.00 1.90
3415 4370 7.035004 TCTTATCCAACTTTGCACAATAATGC 58.965 34.615 0.00 0.00 46.32 3.56
3416 4371 4.870123 TCCAACTTTGCACAATAATGCT 57.130 36.364 0.00 0.00 46.28 3.79
3417 4372 5.212532 TCCAACTTTGCACAATAATGCTT 57.787 34.783 0.00 0.00 46.28 3.91
3423 4378 2.866198 TGCACAATAATGCTTGCTTCG 58.134 42.857 0.00 0.00 46.28 3.79
3437 4392 7.315247 TGCTTGCTTCGTTGTATATAAACAT 57.685 32.000 0.00 0.00 0.00 2.71
3441 4396 7.851387 TGCTTCGTTGTATATAAACATCCAA 57.149 32.000 7.88 0.00 0.00 3.53
3479 4452 5.431765 AGATCTCCAATCGTTAAACTGCAT 58.568 37.500 0.00 0.00 0.00 3.96
3480 4453 6.582636 AGATCTCCAATCGTTAAACTGCATA 58.417 36.000 0.00 0.00 0.00 3.14
3481 4454 7.220030 AGATCTCCAATCGTTAAACTGCATAT 58.780 34.615 0.00 0.00 0.00 1.78
3482 4455 6.844696 TCTCCAATCGTTAAACTGCATATC 57.155 37.500 0.00 0.00 0.00 1.63
3483 4456 6.345298 TCTCCAATCGTTAAACTGCATATCA 58.655 36.000 0.00 0.00 0.00 2.15
3484 4457 6.992123 TCTCCAATCGTTAAACTGCATATCAT 59.008 34.615 0.00 0.00 0.00 2.45
3485 4458 7.498900 TCTCCAATCGTTAAACTGCATATCATT 59.501 33.333 0.00 0.00 0.00 2.57
3486 4459 7.995289 TCCAATCGTTAAACTGCATATCATTT 58.005 30.769 0.00 0.00 0.00 2.32
3487 4460 8.465999 TCCAATCGTTAAACTGCATATCATTTT 58.534 29.630 0.00 0.00 33.07 1.82
3488 4461 8.745837 CCAATCGTTAAACTGCATATCATTTTC 58.254 33.333 0.00 0.00 31.27 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 121 8.311109 TGTAGATATGCTTAATCGCTTATCCAA 58.689 33.333 14.15 5.67 42.99 3.53
140 145 7.880160 TTGGTAGCTATTGCATTCTATTTGT 57.120 32.000 0.00 0.00 42.74 2.83
155 160 7.880713 TCATGTGAATACTTTGTTTGGTAGCTA 59.119 33.333 0.00 0.00 0.00 3.32
230 235 3.181526 GGGGGACTCTGCAAATGAG 57.818 57.895 0.14 0.14 37.55 2.90
334 340 1.079503 GTTTGTCTGCGTGGATCTCC 58.920 55.000 0.00 0.00 0.00 3.71
376 382 2.559231 GGTACCTCTCCTGCATAGCTAC 59.441 54.545 4.06 0.00 0.00 3.58
378 384 1.710816 GGTACCTCTCCTGCATAGCT 58.289 55.000 4.06 0.00 0.00 3.32
412 418 1.470098 GTCGGCTGCTGATTTTGTGAT 59.530 47.619 15.18 0.00 0.00 3.06
438 444 0.392060 GCCCCGTCGTAGTGGAAATT 60.392 55.000 0.00 0.00 0.00 1.82
450 456 0.806241 TTTGATTTTAGCGCCCCGTC 59.194 50.000 2.29 0.00 0.00 4.79
543 551 0.321653 GGACCTTGCCGTCAACTGAT 60.322 55.000 0.00 0.00 34.24 2.90
544 552 1.070786 GGACCTTGCCGTCAACTGA 59.929 57.895 0.00 0.00 34.24 3.41
545 553 0.817634 TTGGACCTTGCCGTCAACTG 60.818 55.000 0.00 0.00 34.24 3.16
546 554 0.535102 CTTGGACCTTGCCGTCAACT 60.535 55.000 0.00 0.00 34.24 3.16
547 555 1.515521 CCTTGGACCTTGCCGTCAAC 61.516 60.000 0.00 0.00 34.24 3.18
596 604 1.069765 CCGCATCACGCCCTAGATT 59.930 57.895 0.00 0.00 41.76 2.40
617 625 3.453679 GCCGGCGGAGTTCTCTCT 61.454 66.667 33.44 0.00 40.29 3.10
670 698 2.156446 CAATTCCGACGTCGTCCCG 61.156 63.158 33.49 19.79 37.74 5.14
740 781 4.997565 TCCTGCAACTGTTCAAGAAAAAG 58.002 39.130 0.00 0.00 0.00 2.27
746 787 6.306356 CGAAATAAATCCTGCAACTGTTCAAG 59.694 38.462 0.00 0.00 0.00 3.02
747 788 6.016693 TCGAAATAAATCCTGCAACTGTTCAA 60.017 34.615 0.00 0.00 0.00 2.69
748 789 5.471797 TCGAAATAAATCCTGCAACTGTTCA 59.528 36.000 0.00 0.00 0.00 3.18
749 790 5.938322 TCGAAATAAATCCTGCAACTGTTC 58.062 37.500 0.00 0.00 0.00 3.18
846 921 1.427368 TGTGTGGTTCTAAATGGGCCT 59.573 47.619 4.53 0.00 0.00 5.19
855 930 1.952133 GCGCGTGTGTGTGGTTCTA 60.952 57.895 8.43 0.00 0.00 2.10
1029 1104 3.414700 GCAAGCGTGGTGAGACGG 61.415 66.667 0.79 0.00 39.81 4.79
1321 1396 2.045242 TCCGTCGTCCTCCTCCAG 60.045 66.667 0.00 0.00 0.00 3.86
1329 1404 2.435586 TCGTCTCCTCCGTCGTCC 60.436 66.667 0.00 0.00 0.00 4.79
1341 1416 3.760035 ATGAAGCGCCGGTCGTCT 61.760 61.111 17.38 12.59 41.07 4.18
1484 1559 5.828747 TCGCTACTGACCACTTGTATAATC 58.171 41.667 0.00 0.00 0.00 1.75
1548 1649 7.482169 ACAAGTCACTGAAGATAGTTCCATA 57.518 36.000 0.00 0.00 0.00 2.74
1569 1670 2.821378 CTGATGGATGAACCTGCAACAA 59.179 45.455 0.00 0.00 39.86 2.83
1570 1671 2.224843 ACTGATGGATGAACCTGCAACA 60.225 45.455 0.00 0.00 39.86 3.33
1571 1672 2.163010 CACTGATGGATGAACCTGCAAC 59.837 50.000 0.00 0.00 39.86 4.17
1655 1756 5.450550 CCCTTTCAGACTTCACCAGAAAAAC 60.451 44.000 0.00 0.00 32.35 2.43
1715 1816 8.573035 ACGGTTTACATAAGAAAACATGAATGT 58.427 29.630 0.00 0.52 44.20 2.71
1724 1825 6.380095 ACTTGCACGGTTTACATAAGAAAA 57.620 33.333 0.00 0.00 0.00 2.29
1725 1826 6.380095 AACTTGCACGGTTTACATAAGAAA 57.620 33.333 0.00 0.00 0.00 2.52
1739 1840 1.459209 TCGTCATTGCTAACTTGCACG 59.541 47.619 0.00 0.00 43.20 5.34
1776 1877 8.689061 CCTTGAATCCATGAAAAGAACATCATA 58.311 33.333 0.00 0.00 34.61 2.15
1796 1897 5.721225 AGGCCTCTATCTCTATTCCTTGAA 58.279 41.667 0.00 0.00 0.00 2.69
1801 1905 4.081697 GCAAGAGGCCTCTATCTCTATTCC 60.082 50.000 35.31 3.57 39.22 3.01
1802 1906 4.526262 TGCAAGAGGCCTCTATCTCTATTC 59.474 45.833 35.31 13.08 43.89 1.75
1803 1907 4.283212 GTGCAAGAGGCCTCTATCTCTATT 59.717 45.833 35.31 14.73 43.89 1.73
1804 1908 3.831911 GTGCAAGAGGCCTCTATCTCTAT 59.168 47.826 35.31 15.54 43.89 1.98
1805 1909 3.226777 GTGCAAGAGGCCTCTATCTCTA 58.773 50.000 35.31 15.58 43.89 2.43
1806 1910 2.038659 GTGCAAGAGGCCTCTATCTCT 58.961 52.381 35.31 17.14 43.89 3.10
1807 1911 1.069978 GGTGCAAGAGGCCTCTATCTC 59.930 57.143 35.31 25.86 43.89 2.75
1808 1912 1.127343 GGTGCAAGAGGCCTCTATCT 58.873 55.000 35.31 17.96 43.89 1.98
1809 1913 0.249657 CGGTGCAAGAGGCCTCTATC 60.250 60.000 35.31 27.15 43.89 2.08
1816 1920 1.130561 GTATGTTTCGGTGCAAGAGGC 59.869 52.381 0.00 0.00 45.13 4.70
1966 2070 2.531522 TATGCGTGATGACTGGGATG 57.468 50.000 0.00 0.00 0.00 3.51
2413 3264 7.086685 AGTCCACCAAATTAGGTAAGAAAGA 57.913 36.000 0.00 0.00 40.77 2.52
2452 3303 4.798907 CAGATAACACGAAAGATAGCACGT 59.201 41.667 0.00 0.00 39.53 4.49
2453 3304 4.798907 ACAGATAACACGAAAGATAGCACG 59.201 41.667 0.00 0.00 0.00 5.34
2454 3305 7.751047 TTACAGATAACACGAAAGATAGCAC 57.249 36.000 0.00 0.00 0.00 4.40
2455 3306 7.491372 CCTTTACAGATAACACGAAAGATAGCA 59.509 37.037 0.00 0.00 0.00 3.49
2456 3307 7.705325 TCCTTTACAGATAACACGAAAGATAGC 59.295 37.037 0.00 0.00 0.00 2.97
2457 3308 9.239002 CTCCTTTACAGATAACACGAAAGATAG 57.761 37.037 0.00 0.00 0.00 2.08
2458 3309 8.195436 CCTCCTTTACAGATAACACGAAAGATA 58.805 37.037 0.00 0.00 0.00 1.98
2459 3310 7.042335 CCTCCTTTACAGATAACACGAAAGAT 58.958 38.462 0.00 0.00 0.00 2.40
2460 3311 6.209986 TCCTCCTTTACAGATAACACGAAAGA 59.790 38.462 0.00 0.00 0.00 2.52
2461 3312 6.395629 TCCTCCTTTACAGATAACACGAAAG 58.604 40.000 0.00 0.00 0.00 2.62
2462 3313 6.349243 TCCTCCTTTACAGATAACACGAAA 57.651 37.500 0.00 0.00 0.00 3.46
2463 3314 5.988310 TCCTCCTTTACAGATAACACGAA 57.012 39.130 0.00 0.00 0.00 3.85
2590 3451 1.452110 TCACCGAATCCACATGCTTG 58.548 50.000 0.00 0.00 0.00 4.01
2656 3517 5.776716 CCAACCATCCATAGGAATGCTATTT 59.223 40.000 0.00 0.00 34.34 1.40
2695 3556 2.756840 AAAAGGAGCCGTGGTAGTAC 57.243 50.000 0.00 0.00 0.00 2.73
2729 3593 1.675310 CGGCATTCTCAGGTGGCAA 60.675 57.895 0.00 0.00 40.56 4.52
2766 3630 3.525199 AGGGTAAAATCACTGCTGGATCT 59.475 43.478 0.00 0.00 0.00 2.75
2859 3728 4.591498 TGTACTACCATGTCCACAAGTTCT 59.409 41.667 0.00 0.00 0.00 3.01
2860 3729 4.890088 TGTACTACCATGTCCACAAGTTC 58.110 43.478 0.00 0.00 0.00 3.01
2873 3742 9.594478 CACACATGATAATAAGTTGTACTACCA 57.406 33.333 0.00 0.00 0.00 3.25
2883 3752 6.488006 GCCATCTTCCACACATGATAATAAGT 59.512 38.462 0.00 0.00 0.00 2.24
2887 3761 4.795469 TGCCATCTTCCACACATGATAAT 58.205 39.130 0.00 0.00 0.00 1.28
2914 3788 3.126831 GTCCGGATTCTGAACATGCTAG 58.873 50.000 7.81 0.00 0.00 3.42
2969 3845 1.405105 TCTCTGCAAACACAACAAGCC 59.595 47.619 0.00 0.00 0.00 4.35
2975 3851 7.264221 ACAAACATTTATCTCTGCAAACACAA 58.736 30.769 0.00 0.00 0.00 3.33
2983 3859 8.023128 ACAATGTGTACAAACATTTATCTCTGC 58.977 33.333 8.55 0.00 46.19 4.26
3013 3889 3.102972 AGTGCTGACATACATGAGGACT 58.897 45.455 0.00 0.00 31.58 3.85
3017 3893 4.692155 TGTTCAAGTGCTGACATACATGAG 59.308 41.667 0.00 0.00 32.21 2.90
3023 3899 5.237127 CACTCTTTGTTCAAGTGCTGACATA 59.763 40.000 0.00 0.00 34.55 2.29
3037 3913 7.050377 TCTCTTTCTGTGATTCACTCTTTGTT 58.950 34.615 17.26 0.00 35.11 2.83
3055 3931 8.547967 TGTGTATTGTATCAAGGTTCTCTTTC 57.452 34.615 0.00 0.00 32.41 2.62
3089 3965 5.741388 CAGCACTAACTGTCCATAAATCC 57.259 43.478 0.00 0.00 32.78 3.01
3105 3981 6.418057 TCCCAATAAAATTTCAACAGCACT 57.582 33.333 0.00 0.00 0.00 4.40
3135 4012 4.701651 CCCTGCAACATTACTTGATGAAGA 59.298 41.667 0.00 0.00 36.15 2.87
3160 4037 6.128035 CCCTTGATTTATTCATGTTGTCGTCA 60.128 38.462 0.00 0.00 33.34 4.35
3168 4045 7.067859 CACACATCTCCCTTGATTTATTCATGT 59.932 37.037 0.00 0.00 33.34 3.21
3172 4049 5.357878 TGCACACATCTCCCTTGATTTATTC 59.642 40.000 0.00 0.00 0.00 1.75
3192 4069 9.722056 CTTTTGTATATAGTTGAAATCCTGCAC 57.278 33.333 0.00 0.00 0.00 4.57
3193 4070 9.679661 TCTTTTGTATATAGTTGAAATCCTGCA 57.320 29.630 0.00 0.00 0.00 4.41
3237 4181 7.161404 AGTGTGTTTTCAGAATGTCATAGCTA 58.839 34.615 0.00 0.00 37.40 3.32
3239 4183 6.246420 AGTGTGTTTTCAGAATGTCATAGC 57.754 37.500 0.00 0.00 37.40 2.97
3253 4197 7.404671 AAAGTGGTAGATCAAAGTGTGTTTT 57.595 32.000 0.00 0.00 0.00 2.43
3259 4203 7.860872 GGTTTTGTAAAGTGGTAGATCAAAGTG 59.139 37.037 0.00 0.00 0.00 3.16
3262 4206 6.766944 TCGGTTTTGTAAAGTGGTAGATCAAA 59.233 34.615 0.00 0.00 0.00 2.69
3263 4207 6.289834 TCGGTTTTGTAAAGTGGTAGATCAA 58.710 36.000 0.00 0.00 0.00 2.57
3264 4208 5.856156 TCGGTTTTGTAAAGTGGTAGATCA 58.144 37.500 0.00 0.00 0.00 2.92
3265 4209 6.790285 TTCGGTTTTGTAAAGTGGTAGATC 57.210 37.500 0.00 0.00 0.00 2.75
3266 4210 6.769341 ACTTTCGGTTTTGTAAAGTGGTAGAT 59.231 34.615 0.00 0.00 40.85 1.98
3284 4238 6.131389 CGTTTCCTGTAACTAAAACTTTCGG 58.869 40.000 0.00 0.00 31.12 4.30
3285 4239 6.131389 CCGTTTCCTGTAACTAAAACTTTCG 58.869 40.000 0.00 0.00 31.12 3.46
3286 4240 7.019774 ACCGTTTCCTGTAACTAAAACTTTC 57.980 36.000 0.00 0.00 31.12 2.62
3287 4241 7.395190 AACCGTTTCCTGTAACTAAAACTTT 57.605 32.000 0.00 0.00 31.12 2.66
3306 4260 2.253610 TCATCACCCTGAAGTAACCGT 58.746 47.619 0.00 0.00 0.00 4.83
3307 4261 3.543680 ATCATCACCCTGAAGTAACCG 57.456 47.619 0.00 0.00 0.00 4.44
3308 4262 3.871594 CGAATCATCACCCTGAAGTAACC 59.128 47.826 0.00 0.00 0.00 2.85
3310 4264 4.466370 AGTCGAATCATCACCCTGAAGTAA 59.534 41.667 0.00 0.00 0.00 2.24
3312 4266 2.834549 AGTCGAATCATCACCCTGAAGT 59.165 45.455 0.00 0.00 0.00 3.01
3313 4267 3.193263 CAGTCGAATCATCACCCTGAAG 58.807 50.000 0.00 0.00 0.00 3.02
3318 4273 1.473434 GGTCCAGTCGAATCATCACCC 60.473 57.143 0.00 0.00 0.00 4.61
3333 4288 2.988636 TCATTGGATTGGTTGGTCCA 57.011 45.000 0.00 0.00 45.60 4.02
3361 4316 6.439375 TCTTACTACACAAAATCCAGAGGCTA 59.561 38.462 0.00 0.00 0.00 3.93
3412 4367 7.315247 TGTTTATATACAACGAAGCAAGCAT 57.685 32.000 0.00 0.00 0.00 3.79
3413 4368 6.729391 TGTTTATATACAACGAAGCAAGCA 57.271 33.333 0.00 0.00 0.00 3.91
3414 4369 6.851330 GGATGTTTATATACAACGAAGCAAGC 59.149 38.462 0.00 0.00 0.00 4.01
3415 4370 7.915508 TGGATGTTTATATACAACGAAGCAAG 58.084 34.615 0.00 0.00 0.00 4.01
3416 4371 7.851387 TGGATGTTTATATACAACGAAGCAA 57.149 32.000 0.00 0.00 0.00 3.91
3417 4372 7.011950 CCTTGGATGTTTATATACAACGAAGCA 59.988 37.037 16.62 1.67 36.23 3.91
3437 4392 8.543774 GGAGATCTATCATTTAATAGCCTTGGA 58.456 37.037 0.00 0.00 0.00 3.53
3456 4411 4.832248 TGCAGTTTAACGATTGGAGATCT 58.168 39.130 0.00 0.00 0.00 2.75
3479 4452 6.494666 ACAGGGATAACGAGGAAAATGATA 57.505 37.500 0.00 0.00 0.00 2.15
3480 4453 5.368989 GACAGGGATAACGAGGAAAATGAT 58.631 41.667 0.00 0.00 0.00 2.45
3481 4454 4.679639 CGACAGGGATAACGAGGAAAATGA 60.680 45.833 0.00 0.00 0.00 2.57
3482 4455 3.555956 CGACAGGGATAACGAGGAAAATG 59.444 47.826 0.00 0.00 0.00 2.32
3483 4456 3.449737 TCGACAGGGATAACGAGGAAAAT 59.550 43.478 0.00 0.00 0.00 1.82
3484 4457 2.827322 TCGACAGGGATAACGAGGAAAA 59.173 45.455 0.00 0.00 0.00 2.29
3485 4458 2.426024 CTCGACAGGGATAACGAGGAAA 59.574 50.000 0.00 0.00 45.22 3.13
3486 4459 2.022195 CTCGACAGGGATAACGAGGAA 58.978 52.381 0.00 0.00 45.22 3.36
3487 4460 1.676746 CTCGACAGGGATAACGAGGA 58.323 55.000 0.00 0.00 45.22 3.71


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

AutoCloner maintained by Alex Coulton.