Multiple sequence alignment - TraesCS5A01G152100

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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 TraesCS5A01G152100 chr5A 100.000 4420 0 0 1 4420 329226975 329222556 0.000000e+00 8163
1 TraesCS5A01G152100 chr5D 93.983 2626 113 18 1812 4420 245188503 245185906 0.000000e+00 3932
2 TraesCS5A01G152100 chr5D 93.772 1702 54 14 1 1691 245190386 245188726 0.000000e+00 2508
3 TraesCS5A01G152100 chr5B 95.160 2004 66 8 1788 3771 278448100 278446108 0.000000e+00 3134
4 TraesCS5A01G152100 chr5B 90.941 1711 90 24 2 1689 278449955 278448287 0.000000e+00 2241
5 TraesCS5A01G152100 chr5B 91.811 403 33 0 4018 4420 278444690 278444288 2.980000e-156 562
6 TraesCS5A01G152100 chr5B 90.547 201 10 6 3777 3975 278446014 278445821 1.580000e-64 257
7 TraesCS5A01G152100 chr2A 92.840 838 50 4 758 1593 277333293 277334122 0.000000e+00 1206
8 TraesCS5A01G152100 chr2A 88.338 343 22 10 198 535 277332968 277333297 3.200000e-106 396
9 TraesCS5A01G152100 chr2A 89.011 91 8 1 1785 1873 277334337 277334427 1.300000e-20 111
10 TraesCS5A01G152100 chr3D 94.539 531 22 3 1160 1690 528821303 528821826 0.000000e+00 813
11 TraesCS5A01G152100 chr3D 91.905 210 8 3 198 403 528820616 528820820 7.240000e-73 285
12 TraesCS5A01G152100 chr3D 93.525 139 8 1 449 586 528821167 528821305 5.790000e-49 206
13 TraesCS5A01G152100 chr3D 89.691 97 8 1 1785 1879 528821997 528822093 6.000000e-24 122
14 TraesCS5A01G152100 chr7D 94.340 530 22 4 1160 1689 99932192 99932713 0.000000e+00 806
15 TraesCS5A01G152100 chr7D 89.367 395 22 6 198 586 99931814 99932194 3.090000e-131 479
16 TraesCS5A01G152100 chr7D 91.489 94 6 1 1785 1876 99932883 99932976 1.290000e-25 128
17 TraesCS5A01G152100 chr7B 89.247 93 7 2 1785 1874 137025308 137025400 3.610000e-21 113


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 TraesCS5A01G152100 chr5A 329222556 329226975 4419 True 8163.0 8163 100.00000 1 4420 1 chr5A.!!$R1 4419
1 TraesCS5A01G152100 chr5D 245185906 245190386 4480 True 3220.0 3932 93.87750 1 4420 2 chr5D.!!$R1 4419
2 TraesCS5A01G152100 chr5B 278444288 278449955 5667 True 1548.5 3134 92.11475 2 4420 4 chr5B.!!$R1 4418
3 TraesCS5A01G152100 chr2A 277332968 277334427 1459 False 571.0 1206 90.06300 198 1873 3 chr2A.!!$F1 1675
4 TraesCS5A01G152100 chr3D 528820616 528822093 1477 False 356.5 813 92.41500 198 1879 4 chr3D.!!$F1 1681
5 TraesCS5A01G152100 chr7D 99931814 99932976 1162 False 471.0 806 91.73200 198 1876 3 chr7D.!!$F1 1678

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
664 1002 0.532862 GACTCTGGTGTGGTGTGGTG 60.533 60.000 0.0 0.0 0.0 4.17 F
1243 1600 1.135257 CCTTCTTCATCGTCGTCAGCT 60.135 52.381 0.0 0.0 0.0 4.24 F
1959 2467 0.249489 ATCCAGTCATTCGCGCCTAC 60.249 55.000 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 2055 0.112995 TCAGCAGGCCAATCTGGTTT 59.887 50.0 5.01 0.0 42.74 3.27 R
2312 2830 0.179062 ATGCCGTGAAGGAGATGAGC 60.179 55.0 0.00 0.0 45.00 4.26 R
3549 4074 0.475906 AGCAAGTGCAGAGAAACCCT 59.524 50.0 6.00 0.0 45.16 4.34 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
36 37 4.202305 ACTTCTGTCAGAAAAGAGGTGGAG 60.202 45.833 15.97 3.41 33.19 3.86
72 73 1.442017 GGCAAACCGTTGATCGTGC 60.442 57.895 0.00 0.00 36.83 5.34
191 192 2.879168 CATGCATGCAACAGCCGA 59.121 55.556 26.68 0.00 0.00 5.54
196 197 1.005294 GCATGCAACAGCCGAACAAG 61.005 55.000 14.21 0.00 0.00 3.16
233 235 7.030165 ACGTGTTGACTGATCAGAAATACTAG 58.970 38.462 29.27 17.82 35.83 2.57
263 265 3.166489 AGACGGCAGTAACAGATAAGC 57.834 47.619 0.00 0.00 0.00 3.09
337 339 3.366679 CGATGTGACCGTACCAGTTAAGT 60.367 47.826 0.00 0.00 0.00 2.24
338 340 4.563061 GATGTGACCGTACCAGTTAAGTT 58.437 43.478 0.00 0.00 0.00 2.66
339 341 5.619757 CGATGTGACCGTACCAGTTAAGTTA 60.620 44.000 0.00 0.00 0.00 2.24
340 342 5.528043 TGTGACCGTACCAGTTAAGTTAA 57.472 39.130 0.00 0.00 0.00 2.01
341 343 5.531634 TGTGACCGTACCAGTTAAGTTAAG 58.468 41.667 0.00 0.00 0.00 1.85
406 411 6.473758 TGATTGCCATTTTGAAATGATGGAA 58.526 32.000 16.00 9.18 46.72 3.53
407 412 6.940867 TGATTGCCATTTTGAAATGATGGAAA 59.059 30.769 16.00 8.31 46.72 3.13
417 422 9.504708 TTTTGAAATGATGGAAAATGCATTACT 57.495 25.926 13.39 2.71 31.30 2.24
418 423 8.481974 TTGAAATGATGGAAAATGCATTACTG 57.518 30.769 13.39 0.00 31.30 2.74
419 424 7.838884 TGAAATGATGGAAAATGCATTACTGA 58.161 30.769 13.39 0.00 31.30 3.41
421 426 8.483307 AAATGATGGAAAATGCATTACTGAAC 57.517 30.769 13.39 4.68 31.30 3.18
422 427 6.839124 TGATGGAAAATGCATTACTGAACT 57.161 33.333 13.39 0.00 0.00 3.01
423 428 7.230849 TGATGGAAAATGCATTACTGAACTT 57.769 32.000 13.39 0.70 0.00 2.66
425 430 8.801299 TGATGGAAAATGCATTACTGAACTTTA 58.199 29.630 13.39 0.00 0.00 1.85
427 432 8.177119 TGGAAAATGCATTACTGAACTTTACT 57.823 30.769 13.39 0.00 0.00 2.24
428 433 8.637986 TGGAAAATGCATTACTGAACTTTACTT 58.362 29.630 13.39 0.00 0.00 2.24
429 434 9.129209 GGAAAATGCATTACTGAACTTTACTTC 57.871 33.333 13.39 7.63 0.00 3.01
445 453 1.581149 ACTTCAGGGGGCCTCTATACT 59.419 52.381 5.06 0.00 0.00 2.12
522 840 4.607293 AATGCAAAAGACTTCTTTCCCC 57.393 40.909 4.71 0.00 44.69 4.81
664 1002 0.532862 GACTCTGGTGTGGTGTGGTG 60.533 60.000 0.00 0.00 0.00 4.17
670 1008 1.377987 GTGTGGTGTGGTGTGGTGT 60.378 57.895 0.00 0.00 0.00 4.16
671 1009 1.377856 TGTGGTGTGGTGTGGTGTG 60.378 57.895 0.00 0.00 0.00 3.82
672 1010 2.118404 GTGGTGTGGTGTGGTGTGG 61.118 63.158 0.00 0.00 0.00 4.17
673 1011 2.274104 GGTGTGGTGTGGTGTGGT 59.726 61.111 0.00 0.00 0.00 4.16
674 1012 2.118404 GGTGTGGTGTGGTGTGGTG 61.118 63.158 0.00 0.00 0.00 4.17
730 1068 4.432980 AACCAGCACTTGTACCTTTACT 57.567 40.909 0.00 0.00 0.00 2.24
731 1069 4.004196 ACCAGCACTTGTACCTTTACTC 57.996 45.455 0.00 0.00 0.00 2.59
801 1139 2.433145 ACATGCGTGGAGTGAGCG 60.433 61.111 11.36 0.00 0.00 5.03
824 1162 6.596703 CGTGAGCCTGACATATAAAATCATG 58.403 40.000 0.00 0.00 0.00 3.07
836 1174 7.652909 ACATATAAAATCATGTGCAAATTCGGG 59.347 33.333 0.00 0.00 34.15 5.14
876 1216 1.266718 CAAACACCACCCATCGTCTTG 59.733 52.381 0.00 0.00 0.00 3.02
886 1226 1.197721 CCATCGTCTTGTCTTGCAACC 59.802 52.381 0.00 0.00 32.90 3.77
887 1227 2.146342 CATCGTCTTGTCTTGCAACCT 58.854 47.619 0.00 0.00 32.90 3.50
888 1228 1.865865 TCGTCTTGTCTTGCAACCTC 58.134 50.000 0.00 0.00 32.90 3.85
889 1229 1.138069 TCGTCTTGTCTTGCAACCTCA 59.862 47.619 0.00 0.00 32.90 3.86
890 1230 2.146342 CGTCTTGTCTTGCAACCTCAT 58.854 47.619 0.00 0.00 32.90 2.90
891 1231 2.549754 CGTCTTGTCTTGCAACCTCATT 59.450 45.455 0.00 0.00 32.90 2.57
892 1232 3.003689 CGTCTTGTCTTGCAACCTCATTT 59.996 43.478 0.00 0.00 32.90 2.32
893 1233 4.540824 GTCTTGTCTTGCAACCTCATTTC 58.459 43.478 0.00 0.00 32.90 2.17
894 1234 4.036734 GTCTTGTCTTGCAACCTCATTTCA 59.963 41.667 0.00 0.00 32.90 2.69
895 1235 4.828939 TCTTGTCTTGCAACCTCATTTCAT 59.171 37.500 0.00 0.00 32.90 2.57
896 1236 5.302568 TCTTGTCTTGCAACCTCATTTCATT 59.697 36.000 0.00 0.00 32.90 2.57
897 1237 5.534207 TGTCTTGCAACCTCATTTCATTT 57.466 34.783 0.00 0.00 0.00 2.32
898 1238 5.531634 TGTCTTGCAACCTCATTTCATTTC 58.468 37.500 0.00 0.00 0.00 2.17
899 1239 5.068855 TGTCTTGCAACCTCATTTCATTTCA 59.931 36.000 0.00 0.00 0.00 2.69
900 1240 5.632347 GTCTTGCAACCTCATTTCATTTCAG 59.368 40.000 0.00 0.00 0.00 3.02
901 1241 3.916761 TGCAACCTCATTTCATTTCAGC 58.083 40.909 0.00 0.00 0.00 4.26
902 1242 3.256558 GCAACCTCATTTCATTTCAGCC 58.743 45.455 0.00 0.00 0.00 4.85
954 1305 3.050619 GCACATTCTTATACGTCCGAGG 58.949 50.000 0.00 0.00 0.00 4.63
1099 1456 6.404293 CCATTACAACAATAAAAGAGGGGACG 60.404 42.308 0.00 0.00 0.00 4.79
1168 1525 1.671054 AACAAGATGACCACGGCGG 60.671 57.895 13.24 0.00 42.50 6.13
1170 1527 4.778143 AAGATGACCACGGCGGCC 62.778 66.667 13.24 9.54 39.03 6.13
1243 1600 1.135257 CCTTCTTCATCGTCGTCAGCT 60.135 52.381 0.00 0.00 0.00 4.24
1383 1740 3.859414 GAGCTCATGGGCGAGGCT 61.859 66.667 12.97 0.00 37.29 4.58
1386 1743 3.094062 GCTCATGGGCGAGGCTGTA 62.094 63.158 0.00 0.00 33.36 2.74
1636 1993 9.521841 TCTCTAGAAAGAATAGTTGAGTTGAGA 57.478 33.333 0.00 0.00 0.00 3.27
1637 1994 9.567848 CTCTAGAAAGAATAGTTGAGTTGAGAC 57.432 37.037 0.00 0.00 0.00 3.36
1638 1995 9.303116 TCTAGAAAGAATAGTTGAGTTGAGACT 57.697 33.333 0.00 0.00 39.32 3.24
1639 1996 9.921637 CTAGAAAGAATAGTTGAGTTGAGACTT 57.078 33.333 0.00 0.00 35.88 3.01
1640 1997 8.600449 AGAAAGAATAGTTGAGTTGAGACTTG 57.400 34.615 0.00 0.00 35.88 3.16
1641 1998 7.659390 AGAAAGAATAGTTGAGTTGAGACTTGG 59.341 37.037 0.00 0.00 35.88 3.61
1645 2002 4.329462 AGTTGAGTTGAGACTTGGAGTC 57.671 45.455 0.00 0.00 45.38 3.36
1690 2047 5.821470 TCATTCATGCCAACAACAACAAAAT 59.179 32.000 0.00 0.00 0.00 1.82
1691 2048 5.731599 TTCATGCCAACAACAACAAAATC 57.268 34.783 0.00 0.00 0.00 2.17
1692 2049 5.021033 TCATGCCAACAACAACAAAATCT 57.979 34.783 0.00 0.00 0.00 2.40
1693 2050 5.426504 TCATGCCAACAACAACAAAATCTT 58.573 33.333 0.00 0.00 0.00 2.40
1696 2053 5.355596 TGCCAACAACAACAAAATCTTAGG 58.644 37.500 0.00 0.00 0.00 2.69
1697 2054 4.749598 GCCAACAACAACAAAATCTTAGGG 59.250 41.667 0.00 0.00 0.00 3.53
1698 2055 5.452636 GCCAACAACAACAAAATCTTAGGGA 60.453 40.000 0.00 0.00 0.00 4.20
1699 2056 6.578023 CCAACAACAACAAAATCTTAGGGAA 58.422 36.000 0.00 0.00 0.00 3.97
1700 2057 7.044798 CCAACAACAACAAAATCTTAGGGAAA 58.955 34.615 0.00 0.00 0.00 3.13
1725 2225 1.422531 TTGGCCTGCTGAAACCAAAT 58.577 45.000 3.32 0.00 39.17 2.32
1738 2238 6.200286 GCTGAAACCAAATGATGCATGATAAG 59.800 38.462 2.46 0.00 0.00 1.73
1741 2241 8.747471 TGAAACCAAATGATGCATGATAAGTAA 58.253 29.630 2.46 0.00 0.00 2.24
1742 2242 9.754382 GAAACCAAATGATGCATGATAAGTAAT 57.246 29.630 2.46 0.00 0.00 1.89
1781 2281 8.183536 TGGAACAAATCATATGTGAGATTTTCG 58.816 33.333 1.90 0.00 41.20 3.46
1783 2283 9.941664 GAACAAATCATATGTGAGATTTTCGAT 57.058 29.630 1.90 0.00 41.20 3.59
1808 2308 5.449107 AAAATCATATGTGAGATGGCAGC 57.551 39.130 1.90 0.00 37.87 5.25
1823 2323 3.329889 AGCGAGTGGGATTGGCCA 61.330 61.111 0.00 0.00 38.95 5.36
1952 2460 0.309922 GCATGGCATCCAGTCATTCG 59.690 55.000 0.00 0.00 40.35 3.34
1959 2467 0.249489 ATCCAGTCATTCGCGCCTAC 60.249 55.000 0.00 0.00 0.00 3.18
2119 2637 8.853126 TGAAAGATCATGAGTTGTGAGAATTTT 58.147 29.630 0.09 0.00 0.00 1.82
2189 2707 2.094494 TGCCACAAAACTGCTCGAAAAA 60.094 40.909 0.00 0.00 0.00 1.94
2345 2863 2.628194 CGGCATTCGTATGTTTCTCG 57.372 50.000 3.87 0.00 34.12 4.04
2364 2882 5.842907 TCTCGATCTCTGAACACTTGAAAA 58.157 37.500 0.00 0.00 0.00 2.29
2615 3133 1.448717 GAGGAAGCAGAAGCCCGAC 60.449 63.158 0.00 0.00 43.56 4.79
2691 3209 7.941919 ACAAAAGGAAAGAGTTATCTGAAACC 58.058 34.615 0.00 0.00 35.37 3.27
2697 3215 2.230508 AGAGTTATCTGAAACCGACGCA 59.769 45.455 0.00 0.00 33.30 5.24
2736 3254 3.777106 TGGATGCTATGAACTGGGATC 57.223 47.619 0.00 0.00 33.20 3.36
2818 3343 3.378427 GCAGGTATGGTTCATTTGAGGAC 59.622 47.826 0.00 0.00 0.00 3.85
2976 3501 4.983671 GGTGAGACCAAAAACTGAAACT 57.016 40.909 0.00 0.00 38.42 2.66
3137 3662 4.844420 GAGCCGATCCAGAAGGTG 57.156 61.111 0.00 0.00 35.89 4.00
3158 3683 1.957186 GTACAAAGGCGCGACCACA 60.957 57.895 9.25 0.00 43.14 4.17
3200 3725 4.950479 AAGCAGATCTTCAGGCCG 57.050 55.556 0.00 0.00 0.00 6.13
3473 3998 0.179134 TTCGGGGTTTTGTTGTTGCG 60.179 50.000 0.00 0.00 0.00 4.85
3688 4217 2.161410 TGCAAATCTTATGACACCGTGC 59.839 45.455 0.00 0.00 0.00 5.34
3695 4224 0.673333 TATGACACCGTGCTTGGCTG 60.673 55.000 0.00 0.00 0.00 4.85
3813 4430 7.000472 TGATGTGAATTTGAGAGGAAGTTTCT 59.000 34.615 0.00 0.00 0.00 2.52
3818 4435 4.788925 TTTGAGAGGAAGTTTCTTCCCA 57.211 40.909 20.56 11.62 39.39 4.37
3835 4452 2.093341 TCCCACGTGAACTAATAAGGGC 60.093 50.000 19.30 0.00 35.03 5.19
3922 4539 4.696877 TGTGTGGCAAGAGTTGATTAGATG 59.303 41.667 0.00 0.00 0.00 2.90
3968 4587 5.464389 GCAATGTTACGTCCGGATATAAAGT 59.536 40.000 7.81 4.20 0.00 2.66
3981 4633 5.573282 CGGATATAAAGTCAATCTGGCTACG 59.427 44.000 0.00 0.00 28.54 3.51
4002 5703 5.078256 ACGGTGGACTAAGAGGGATATAAG 58.922 45.833 0.00 0.00 0.00 1.73
4014 5715 6.458784 AGAGGGATATAAGGGGTTTAAGTCA 58.541 40.000 0.00 0.00 0.00 3.41
4040 5747 3.157087 ACTTTGGCCACCACTTTGATAG 58.843 45.455 3.88 0.00 30.78 2.08
4054 5761 4.021981 ACTTTGATAGGGCAGTTTTGAAGC 60.022 41.667 0.00 0.00 0.00 3.86
4055 5762 3.153369 TGATAGGGCAGTTTTGAAGCA 57.847 42.857 0.00 0.00 0.00 3.91
4120 5827 2.700371 TGGCAGTAGTATGATGTGGGAG 59.300 50.000 0.00 0.00 0.00 4.30
4143 5850 5.523916 AGATATTTATGTGTTCAGTGTCGGC 59.476 40.000 0.00 0.00 0.00 5.54
4222 5929 2.545537 AGAAAGGGTCAAAGTCGTCC 57.454 50.000 0.00 0.00 0.00 4.79
4224 5931 0.250166 AAAGGGTCAAAGTCGTCCGG 60.250 55.000 0.00 0.00 0.00 5.14
4227 5934 1.364901 GGTCAAAGTCGTCCGGTCA 59.635 57.895 0.00 0.00 0.00 4.02
4284 5991 8.547967 TCATGTTTAGTTTCCTGCTTAGTAAG 57.452 34.615 5.47 5.47 0.00 2.34
4356 6063 0.251787 AGGGTGAAGTTCCAATGGGC 60.252 55.000 0.00 0.00 0.00 5.36
4411 6118 1.340405 TGCTTGAGGATGGAGGCTTTC 60.340 52.381 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 0.996727 GCAAACACCGCACGATCAAC 60.997 55.000 0.00 0.00 0.00 3.18
188 189 1.862201 TCTTAACGTGTGCTTGTTCGG 59.138 47.619 0.00 0.00 0.00 4.30
189 190 2.655577 CGTCTTAACGTGTGCTTGTTCG 60.656 50.000 0.00 0.00 43.94 3.95
190 191 2.887733 CGTCTTAACGTGTGCTTGTTC 58.112 47.619 0.00 0.00 43.94 3.18
233 235 5.942872 TGTTACTGCCGTCTACTACTTAAC 58.057 41.667 0.00 0.00 0.00 2.01
337 339 8.859090 TGTACTAGTAGTGCTAAACAACCTTAA 58.141 33.333 17.78 0.00 31.77 1.85
338 340 8.408043 TGTACTAGTAGTGCTAAACAACCTTA 57.592 34.615 17.78 0.00 31.77 2.69
339 341 7.294017 TGTACTAGTAGTGCTAAACAACCTT 57.706 36.000 17.78 0.00 31.77 3.50
340 342 6.906157 TGTACTAGTAGTGCTAAACAACCT 57.094 37.500 17.78 0.00 31.77 3.50
341 343 7.318141 TGATGTACTAGTAGTGCTAAACAACC 58.682 38.462 17.78 8.65 32.68 3.77
417 422 1.074889 GGCCCCCTGAAGTAAAGTTCA 59.925 52.381 0.00 0.58 35.16 3.18
418 423 1.354705 AGGCCCCCTGAAGTAAAGTTC 59.645 52.381 0.00 0.00 29.57 3.01
419 424 1.354705 GAGGCCCCCTGAAGTAAAGTT 59.645 52.381 0.00 0.00 31.76 2.66
421 426 1.290134 AGAGGCCCCCTGAAGTAAAG 58.710 55.000 0.00 0.00 31.76 1.85
422 427 2.653543 TAGAGGCCCCCTGAAGTAAA 57.346 50.000 0.00 0.00 31.76 2.01
423 428 2.889522 ATAGAGGCCCCCTGAAGTAA 57.110 50.000 0.00 0.00 31.76 2.24
425 430 1.581149 AGTATAGAGGCCCCCTGAAGT 59.419 52.381 0.00 0.00 31.76 3.01
427 432 2.795960 ACTAGTATAGAGGCCCCCTGAA 59.204 50.000 0.00 0.00 42.77 3.02
428 433 2.110188 CACTAGTATAGAGGCCCCCTGA 59.890 54.545 0.00 0.00 42.77 3.86
429 434 2.530701 CACTAGTATAGAGGCCCCCTG 58.469 57.143 0.00 0.00 42.77 4.45
431 436 1.939980 CCACTAGTATAGAGGCCCCC 58.060 60.000 0.00 0.00 42.41 5.40
468 786 6.662755 TGTTCCTCACCTAATTAGCATTCAT 58.337 36.000 6.99 0.00 0.00 2.57
563 881 2.127609 GCGCGTGTCACTTTCAGC 60.128 61.111 8.43 0.00 0.00 4.26
664 1002 2.890311 TCAATCAAATCCACCACACCAC 59.110 45.455 0.00 0.00 0.00 4.16
670 1008 8.717717 ACTTCTATCTATCAATCAAATCCACCA 58.282 33.333 0.00 0.00 0.00 4.17
671 1009 8.997323 CACTTCTATCTATCAATCAAATCCACC 58.003 37.037 0.00 0.00 0.00 4.61
672 1010 9.553064 ACACTTCTATCTATCAATCAAATCCAC 57.447 33.333 0.00 0.00 0.00 4.02
673 1011 9.770097 GACACTTCTATCTATCAATCAAATCCA 57.230 33.333 0.00 0.00 0.00 3.41
674 1012 8.920665 CGACACTTCTATCTATCAATCAAATCC 58.079 37.037 0.00 0.00 0.00 3.01
801 1139 7.358066 CACATGATTTTATATGTCAGGCTCAC 58.642 38.462 0.00 0.00 35.46 3.51
824 1162 2.573340 CCAGCCCCGAATTTGCAC 59.427 61.111 0.00 0.00 0.00 4.57
836 1174 2.039348 TGTAAGTTTGGTCTACCCAGCC 59.961 50.000 0.00 0.00 46.31 4.85
876 1216 5.531634 TGAAATGAAATGAGGTTGCAAGAC 58.468 37.500 0.00 0.00 0.00 3.01
886 1226 6.022163 AGTTTGAGGCTGAAATGAAATGAG 57.978 37.500 1.68 0.00 0.00 2.90
887 1227 6.409524 AAGTTTGAGGCTGAAATGAAATGA 57.590 33.333 1.68 0.00 0.00 2.57
888 1228 6.702723 TGAAAGTTTGAGGCTGAAATGAAATG 59.297 34.615 1.68 0.00 0.00 2.32
889 1229 6.819284 TGAAAGTTTGAGGCTGAAATGAAAT 58.181 32.000 1.68 0.00 0.00 2.17
890 1230 6.219417 TGAAAGTTTGAGGCTGAAATGAAA 57.781 33.333 1.68 0.00 0.00 2.69
891 1231 5.737063 GCTGAAAGTTTGAGGCTGAAATGAA 60.737 40.000 1.68 0.00 35.30 2.57
892 1232 4.261741 GCTGAAAGTTTGAGGCTGAAATGA 60.262 41.667 1.68 0.00 35.30 2.57
893 1233 3.985925 GCTGAAAGTTTGAGGCTGAAATG 59.014 43.478 1.68 0.00 35.30 2.32
894 1234 3.304928 CGCTGAAAGTTTGAGGCTGAAAT 60.305 43.478 1.68 0.00 35.30 2.17
895 1235 2.033299 CGCTGAAAGTTTGAGGCTGAAA 59.967 45.455 4.18 0.00 35.30 2.69
896 1236 1.603802 CGCTGAAAGTTTGAGGCTGAA 59.396 47.619 4.18 0.00 35.30 3.02
897 1237 1.229428 CGCTGAAAGTTTGAGGCTGA 58.771 50.000 4.18 0.00 35.30 4.26
898 1238 0.386478 GCGCTGAAAGTTTGAGGCTG 60.386 55.000 0.00 0.00 35.30 4.85
899 1239 1.518903 GGCGCTGAAAGTTTGAGGCT 61.519 55.000 7.64 0.00 35.30 4.58
900 1240 1.081175 GGCGCTGAAAGTTTGAGGC 60.081 57.895 7.64 5.75 35.30 4.70
901 1241 0.239347 CTGGCGCTGAAAGTTTGAGG 59.761 55.000 7.64 0.00 35.30 3.86
902 1242 0.947244 ACTGGCGCTGAAAGTTTGAG 59.053 50.000 7.64 0.00 35.30 3.02
954 1305 2.028020 AGTGCAACCTCCTGTAAGCTAC 60.028 50.000 0.00 0.00 37.80 3.58
1113 1470 2.417933 CGGCTTCATTTTCTCTGGTGAG 59.582 50.000 0.00 0.00 41.51 3.51
1209 1566 3.708220 GAAGGCGACGAGGGAGCTG 62.708 68.421 0.00 0.00 0.00 4.24
1243 1600 2.046864 CGAAGAGCAGGGAGACGGA 61.047 63.158 0.00 0.00 0.00 4.69
1383 1740 2.284331 TCGCCAGAGCCCCTTACA 60.284 61.111 0.00 0.00 34.57 2.41
1386 1743 4.722535 TCCTCGCCAGAGCCCCTT 62.723 66.667 0.00 0.00 43.05 3.95
1395 1752 2.031012 CAGTTGCACTCCTCGCCA 59.969 61.111 0.00 0.00 0.00 5.69
1425 1782 1.594836 GGCGTTGTCGTACACCCAA 60.595 57.895 0.00 0.00 39.49 4.12
1636 1993 3.612004 CGAGCTAGAAAACGACTCCAAGT 60.612 47.826 0.00 0.00 0.00 3.16
1637 1994 2.917971 CGAGCTAGAAAACGACTCCAAG 59.082 50.000 0.00 0.00 0.00 3.61
1638 1995 2.352421 CCGAGCTAGAAAACGACTCCAA 60.352 50.000 0.00 0.00 0.00 3.53
1639 1996 1.201647 CCGAGCTAGAAAACGACTCCA 59.798 52.381 0.00 0.00 0.00 3.86
1640 1997 1.201880 ACCGAGCTAGAAAACGACTCC 59.798 52.381 0.00 0.00 0.00 3.85
1641 1998 2.633199 ACCGAGCTAGAAAACGACTC 57.367 50.000 0.00 0.00 0.00 3.36
1645 2002 3.872560 ACAAAACCGAGCTAGAAAACG 57.127 42.857 0.00 0.00 0.00 3.60
1690 2047 2.025321 GGCCAATCTGGTTTCCCTAAGA 60.025 50.000 0.00 0.00 40.46 2.10
1691 2048 2.024941 AGGCCAATCTGGTTTCCCTAAG 60.025 50.000 5.01 0.00 40.46 2.18
1692 2049 2.000048 AGGCCAATCTGGTTTCCCTAA 59.000 47.619 5.01 0.00 40.46 2.69
1693 2050 1.284785 CAGGCCAATCTGGTTTCCCTA 59.715 52.381 5.01 0.00 40.46 3.53
1696 2053 0.613012 AGCAGGCCAATCTGGTTTCC 60.613 55.000 5.01 0.00 42.05 3.13
1697 2054 0.529378 CAGCAGGCCAATCTGGTTTC 59.471 55.000 5.01 0.00 42.74 2.78
1698 2055 0.112995 TCAGCAGGCCAATCTGGTTT 59.887 50.000 5.01 0.00 42.74 3.27
1699 2056 0.112995 TTCAGCAGGCCAATCTGGTT 59.887 50.000 5.01 0.00 42.74 3.67
1700 2057 0.112995 TTTCAGCAGGCCAATCTGGT 59.887 50.000 5.01 0.00 45.11 4.00
1702 2059 0.529378 GGTTTCAGCAGGCCAATCTG 59.471 55.000 5.01 9.12 37.79 2.90
1704 2061 0.968405 TTGGTTTCAGCAGGCCAATC 59.032 50.000 5.01 0.00 36.23 2.67
1706 2063 1.070445 CATTTGGTTTCAGCAGGCCAA 59.930 47.619 5.01 0.00 39.00 4.52
1707 2064 0.680618 CATTTGGTTTCAGCAGGCCA 59.319 50.000 5.01 0.00 0.00 5.36
1708 2065 0.968405 TCATTTGGTTTCAGCAGGCC 59.032 50.000 0.00 0.00 0.00 5.19
1709 2066 2.613691 CATCATTTGGTTTCAGCAGGC 58.386 47.619 0.00 0.00 0.00 4.85
1711 2068 3.306917 TGCATCATTTGGTTTCAGCAG 57.693 42.857 0.00 0.00 0.00 4.24
1785 2285 5.506815 CGCTGCCATCTCACATATGATTTTT 60.507 40.000 10.38 0.00 33.22 1.94
1786 2286 4.023450 CGCTGCCATCTCACATATGATTTT 60.023 41.667 10.38 0.00 33.22 1.82
1787 2287 3.501062 CGCTGCCATCTCACATATGATTT 59.499 43.478 10.38 0.00 33.22 2.17
1788 2288 3.072211 CGCTGCCATCTCACATATGATT 58.928 45.455 10.38 0.00 33.22 2.57
1789 2289 2.301009 TCGCTGCCATCTCACATATGAT 59.699 45.455 10.38 0.00 33.22 2.45
1790 2290 1.688197 TCGCTGCCATCTCACATATGA 59.312 47.619 10.38 0.00 0.00 2.15
1791 2291 2.067013 CTCGCTGCCATCTCACATATG 58.933 52.381 0.00 0.00 0.00 1.78
1792 2292 1.690893 ACTCGCTGCCATCTCACATAT 59.309 47.619 0.00 0.00 0.00 1.78
1793 2293 1.114627 ACTCGCTGCCATCTCACATA 58.885 50.000 0.00 0.00 0.00 2.29
1794 2294 0.461516 CACTCGCTGCCATCTCACAT 60.462 55.000 0.00 0.00 0.00 3.21
1795 2295 1.079612 CACTCGCTGCCATCTCACA 60.080 57.895 0.00 0.00 0.00 3.58
1796 2296 1.812922 CCACTCGCTGCCATCTCAC 60.813 63.158 0.00 0.00 0.00 3.51
1797 2297 2.580815 CCACTCGCTGCCATCTCA 59.419 61.111 0.00 0.00 0.00 3.27
1798 2298 2.037620 ATCCCACTCGCTGCCATCTC 62.038 60.000 0.00 0.00 0.00 2.75
1799 2299 1.630126 AATCCCACTCGCTGCCATCT 61.630 55.000 0.00 0.00 0.00 2.90
1800 2300 1.153086 AATCCCACTCGCTGCCATC 60.153 57.895 0.00 0.00 0.00 3.51
1801 2301 1.452651 CAATCCCACTCGCTGCCAT 60.453 57.895 0.00 0.00 0.00 4.40
1802 2302 2.046023 CAATCCCACTCGCTGCCA 60.046 61.111 0.00 0.00 0.00 4.92
1803 2303 2.825836 CCAATCCCACTCGCTGCC 60.826 66.667 0.00 0.00 0.00 4.85
1804 2304 3.512516 GCCAATCCCACTCGCTGC 61.513 66.667 0.00 0.00 0.00 5.25
1805 2305 2.825836 GGCCAATCCCACTCGCTG 60.826 66.667 0.00 0.00 0.00 5.18
1806 2306 3.329889 TGGCCAATCCCACTCGCT 61.330 61.111 0.61 0.00 0.00 4.93
1807 2307 2.825836 CTGGCCAATCCCACTCGC 60.826 66.667 7.01 0.00 0.00 5.03
1808 2308 2.825836 GCTGGCCAATCCCACTCG 60.826 66.667 7.01 0.00 0.00 4.18
1823 2323 3.076092 CTGCCCTCTGGTTCAGCT 58.924 61.111 0.00 0.00 0.00 4.24
1952 2460 1.993370 CACTTTGACAGTAGTAGGCGC 59.007 52.381 0.00 0.00 32.76 6.53
1959 2467 6.974932 ATGCTATTGACACTTTGACAGTAG 57.025 37.500 4.58 4.58 36.22 2.57
2021 2529 6.992123 TCATATCACTATTTTCTGGCGTTGAT 59.008 34.615 0.00 0.00 0.00 2.57
2137 2655 6.018589 TGTTTCACAGTTTCAACATGACAA 57.981 33.333 0.00 0.00 0.00 3.18
2168 2686 1.098869 TTTCGAGCAGTTTTGTGGCA 58.901 45.000 0.00 0.00 0.00 4.92
2189 2707 2.569404 GACCATCCTCTTGTTCCTCAGT 59.431 50.000 0.00 0.00 0.00 3.41
2312 2830 0.179062 ATGCCGTGAAGGAGATGAGC 60.179 55.000 0.00 0.00 45.00 4.26
2364 2882 5.823045 GGCATGCCTTACTTCTAGTACATTT 59.177 40.000 29.98 0.00 28.93 2.32
2368 2886 4.120589 GTGGCATGCCTTACTTCTAGTAC 58.879 47.826 35.53 17.80 36.94 2.73
2516 3034 1.760613 TCAATCTTCTCCGCCCGTATT 59.239 47.619 0.00 0.00 0.00 1.89
2691 3209 4.523813 ACTTTATCAACTTGTTTGCGTCG 58.476 39.130 0.00 0.00 34.88 5.12
2697 3215 7.986889 AGCATCCAAAACTTTATCAACTTGTTT 59.013 29.630 0.00 0.00 33.04 2.83
2778 3296 1.805943 TGCACATGGTGAAGATGTTCG 59.194 47.619 0.00 0.00 35.23 3.95
2818 3343 0.647410 CGTCTAGCTTTGCATCACCG 59.353 55.000 0.00 0.00 0.00 4.94
2906 3431 8.227791 TGCGAAATAGATTTTAGTCTTGTTGTC 58.772 33.333 0.00 0.00 0.00 3.18
2976 3501 5.644636 GTCAGGTTTAACGGTTGATGGATAA 59.355 40.000 3.07 0.00 0.00 1.75
3137 3662 3.122971 GTCGCGCCTTTGTACCCC 61.123 66.667 0.00 0.00 0.00 4.95
3158 3683 3.118482 CCTTGTCCATCATGCTGTAGTCT 60.118 47.826 0.00 0.00 0.00 3.24
3200 3725 1.755179 TTATGCCTTTCTGCTCCAGC 58.245 50.000 0.00 0.00 42.50 4.85
3435 3960 3.179599 CGAACGAACAAGAAATGGTTTGC 59.820 43.478 0.00 0.00 32.72 3.68
3438 3963 2.292292 CCCGAACGAACAAGAAATGGTT 59.708 45.455 0.00 0.00 0.00 3.67
3439 3964 1.877443 CCCGAACGAACAAGAAATGGT 59.123 47.619 0.00 0.00 0.00 3.55
3473 3998 1.880941 ATCTAGACCCTCCCACAACC 58.119 55.000 0.00 0.00 0.00 3.77
3501 4026 3.990092 TGTCCTATACATAAAGGCAGCG 58.010 45.455 0.00 0.00 31.43 5.18
3540 4065 4.023622 GTGCAGAGAAACCCTTCTTCTTTC 60.024 45.833 0.00 0.00 42.19 2.62
3544 4069 3.133141 AGTGCAGAGAAACCCTTCTTC 57.867 47.619 0.00 0.00 42.19 2.87
3546 4071 2.856222 CAAGTGCAGAGAAACCCTTCT 58.144 47.619 0.00 0.00 44.93 2.85
3547 4072 1.268079 GCAAGTGCAGAGAAACCCTTC 59.732 52.381 0.00 0.00 41.59 3.46
3549 4074 0.475906 AGCAAGTGCAGAGAAACCCT 59.524 50.000 6.00 0.00 45.16 4.34
3550 4075 1.000938 CAAGCAAGTGCAGAGAAACCC 60.001 52.381 6.00 0.00 45.16 4.11
3688 4217 1.026718 CCGTTTCCCTAGCAGCCAAG 61.027 60.000 0.00 0.00 0.00 3.61
3695 4224 0.544697 TCCCATTCCGTTTCCCTAGC 59.455 55.000 0.00 0.00 0.00 3.42
3775 4392 3.644966 TCACATCACTAATTCCCACCC 57.355 47.619 0.00 0.00 0.00 4.61
3813 4430 3.620472 GCCCTTATTAGTTCACGTGGGAA 60.620 47.826 17.00 0.00 35.64 3.97
3818 4435 5.186409 TCACTAAGCCCTTATTAGTTCACGT 59.814 40.000 0.00 0.00 40.61 4.49
3895 4512 1.093972 CAACTCTTGCCACACACACA 58.906 50.000 0.00 0.00 0.00 3.72
3896 4513 1.378531 TCAACTCTTGCCACACACAC 58.621 50.000 0.00 0.00 0.00 3.82
3897 4514 2.346766 ATCAACTCTTGCCACACACA 57.653 45.000 0.00 0.00 0.00 3.72
3898 4515 4.065088 TCTAATCAACTCTTGCCACACAC 58.935 43.478 0.00 0.00 0.00 3.82
3899 4516 4.350368 TCTAATCAACTCTTGCCACACA 57.650 40.909 0.00 0.00 0.00 3.72
3953 4572 4.923871 CCAGATTGACTTTATATCCGGACG 59.076 45.833 6.12 0.00 0.00 4.79
3968 4587 0.535335 GTCCACCGTAGCCAGATTGA 59.465 55.000 0.00 0.00 0.00 2.57
3981 4633 4.778427 CCCTTATATCCCTCTTAGTCCACC 59.222 50.000 0.00 0.00 0.00 4.61
4014 5715 0.188342 AGTGGTGGCCAAAGTCCATT 59.812 50.000 15.35 9.01 34.18 3.16
4040 5747 2.611224 CCATCTTGCTTCAAAACTGCCC 60.611 50.000 0.00 0.00 0.00 5.36
4054 5761 3.372440 AACTCCTTTAGGCCCATCTTG 57.628 47.619 0.00 0.00 34.44 3.02
4055 5762 3.564352 CCAAACTCCTTTAGGCCCATCTT 60.564 47.826 0.00 0.00 34.44 2.40
4120 5827 5.556382 CGCCGACACTGAACACATAAATATC 60.556 44.000 0.00 0.00 0.00 1.63
4143 5850 0.818296 AGACTTCTTCGATGGGACCG 59.182 55.000 0.00 0.00 0.00 4.79
4222 5929 2.703798 CCTTGCAAGCCCATGACCG 61.704 63.158 21.43 0.00 0.00 4.79
4224 5931 2.353610 CCCCTTGCAAGCCCATGAC 61.354 63.158 21.43 0.00 0.00 3.06
4227 5934 3.178509 AACCCCCTTGCAAGCCCAT 62.179 57.895 21.43 3.35 0.00 4.00
4284 5991 0.747283 CTCCACCCTTGATGCTGCTC 60.747 60.000 0.00 0.00 0.00 4.26
4371 6078 8.849168 TCAAGCAAGTCTTCATTAAAATCTTCA 58.151 29.630 0.00 0.00 31.27 3.02
4382 6089 3.265221 TCCATCCTCAAGCAAGTCTTCAT 59.735 43.478 0.00 0.00 31.27 2.57


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

AutoCloner maintained by Alex Coulton.