Multiple sequence alignment - TraesCS1A01G048100

Loading Multiple Alignment...

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 TraesCS1A01G048100 chr1A 100.000 4004 0 0 1 4004 29799371 29803374 0.000000e+00 7395.0
1 TraesCS1A01G048100 chr1B 93.032 3430 166 21 640 4004 47180110 47183531 0.000000e+00 4942.0
2 TraesCS1A01G048100 chr1B 88.080 646 39 13 1 636 47179451 47180068 0.000000e+00 732.0
3 TraesCS1A01G048100 chr1D 96.060 2589 86 10 706 3279 28573950 28576537 0.000000e+00 4202.0
4 TraesCS1A01G048100 chr1D 86.991 1376 96 37 2613 3959 28658935 28660256 0.000000e+00 1472.0
5 TraesCS1A01G048100 chr1D 86.193 507 51 13 139 639 28572686 28573179 7.620000e-147 531.0
6 TraesCS1A01G048100 chr1D 92.488 213 14 1 3749 3959 28577732 28577944 1.810000e-78 303.0
7 TraesCS1A01G048100 chr1D 84.982 273 19 2 3302 3552 28577061 28577333 1.430000e-64 257.0
8 TraesCS1A01G048100 chr1D 97.222 72 1 1 4 75 28572616 28572686 1.950000e-23 121.0
9 TraesCS1A01G048100 chr1D 94.444 72 4 0 640 711 28573768 28573839 1.180000e-20 111.0
10 TraesCS1A01G048100 chr1D 94.444 72 4 0 640 711 28573855 28573926 1.180000e-20 111.0
11 TraesCS1A01G048100 chr1D 89.091 55 4 1 640 694 28627040 28627092 2.580000e-07 67.6
12 TraesCS1A01G048100 chr2B 74.294 354 74 11 1963 2305 243003939 243003592 2.510000e-27 134.0


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 TraesCS1A01G048100 chr1A 29799371 29803374 4003 False 7395.000000 7395 100.000000 1 4004 1 chr1A.!!$F1 4003
1 TraesCS1A01G048100 chr1B 47179451 47183531 4080 False 2837.000000 4942 90.556000 1 4004 2 chr1B.!!$F1 4003
2 TraesCS1A01G048100 chr1D 28658935 28660256 1321 False 1472.000000 1472 86.991000 2613 3959 1 chr1D.!!$F2 1346
3 TraesCS1A01G048100 chr1D 28572616 28577944 5328 False 805.142857 4202 92.261857 4 3959 7 chr1D.!!$F3 3955

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
95 96 0.108992 GGTACCGTCTCGATGCAACA 60.109 55.0 0.00 0.0 0.0 3.33 F
288 291 0.819582 CATGGAAAAGCAAGGCCGAT 59.180 50.0 0.00 0.0 0.0 4.18 F
1042 1783 0.401738 CCTCCTCTGTTTTGGCCTCA 59.598 55.0 3.32 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1783 0.249031 GCAGTGAAAAACGCAGGCTT 60.249 50.000 0.00 0.00 0.00 4.35 R
1141 1882 1.446272 GCTCAAGGAGTCCGTTCGG 60.446 63.158 2.76 4.74 31.39 4.30 R
3039 3780 1.385528 TATGTGGCATGCAAGCTCAG 58.614 50.000 21.36 0.00 34.17 3.35 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
30 31 3.606687 AGTTCGTCTTTGTTTGGACTGT 58.393 40.909 0.00 0.00 0.00 3.55
42 43 0.953727 TGGACTGTTGTGCATCTTGC 59.046 50.000 0.00 0.00 45.29 4.01
75 76 2.612972 CGGGTGTGAACTCTATGCAGTT 60.613 50.000 0.00 0.00 39.43 3.16
76 77 2.744202 GGGTGTGAACTCTATGCAGTTG 59.256 50.000 0.00 0.00 36.71 3.16
77 78 2.744202 GGTGTGAACTCTATGCAGTTGG 59.256 50.000 0.00 0.00 36.71 3.77
80 81 4.389077 GTGTGAACTCTATGCAGTTGGTAC 59.611 45.833 0.00 0.00 36.71 3.34
83 84 2.176889 ACTCTATGCAGTTGGTACCGT 58.823 47.619 7.57 0.00 0.00 4.83
95 96 0.108992 GGTACCGTCTCGATGCAACA 60.109 55.000 0.00 0.00 0.00 3.33
105 106 2.349590 TCGATGCAACATTGGAGTCAG 58.650 47.619 0.00 0.00 30.13 3.51
114 115 4.899352 ACATTGGAGTCAGTAAAGCTCT 57.101 40.909 0.00 0.00 0.00 4.09
116 117 4.284490 ACATTGGAGTCAGTAAAGCTCTCA 59.716 41.667 0.00 0.00 0.00 3.27
117 118 5.046014 ACATTGGAGTCAGTAAAGCTCTCAT 60.046 40.000 0.00 0.00 0.00 2.90
118 119 5.489792 TTGGAGTCAGTAAAGCTCTCATT 57.510 39.130 0.00 0.00 0.00 2.57
119 120 6.605471 TTGGAGTCAGTAAAGCTCTCATTA 57.395 37.500 0.00 0.00 0.00 1.90
120 121 6.798427 TGGAGTCAGTAAAGCTCTCATTAT 57.202 37.500 0.00 0.00 0.00 1.28
121 122 7.187824 TGGAGTCAGTAAAGCTCTCATTATT 57.812 36.000 0.00 0.00 0.00 1.40
162 163 4.935205 CCTACAACGATTCCTGACAATGAA 59.065 41.667 0.00 0.00 0.00 2.57
239 242 5.066117 TGGAAAGCTACACTACATAGACGAG 59.934 44.000 0.00 0.00 0.00 4.18
288 291 0.819582 CATGGAAAAGCAAGGCCGAT 59.180 50.000 0.00 0.00 0.00 4.18
379 384 5.797051 TCCACAACTTACCTAACCATGTAC 58.203 41.667 0.00 0.00 0.00 2.90
386 391 5.729718 ACTTACCTAACCATGTACCCTGAAT 59.270 40.000 0.00 0.00 0.00 2.57
439 444 5.618056 ACACATCACAAACTGAAGCTATG 57.382 39.130 0.00 0.00 30.60 2.23
440 445 5.065914 ACACATCACAAACTGAAGCTATGT 58.934 37.500 0.00 0.00 30.60 2.29
441 446 5.049198 ACACATCACAAACTGAAGCTATGTG 60.049 40.000 14.36 14.36 39.38 3.21
442 447 5.049198 CACATCACAAACTGAAGCTATGTGT 60.049 40.000 9.67 0.00 41.52 3.72
443 448 5.180117 ACATCACAAACTGAAGCTATGTGTC 59.820 40.000 4.37 0.00 41.52 3.67
444 449 4.960938 TCACAAACTGAAGCTATGTGTCT 58.039 39.130 4.37 0.00 41.52 3.41
445 450 5.368145 TCACAAACTGAAGCTATGTGTCTT 58.632 37.500 4.37 0.00 41.52 3.01
446 451 5.237127 TCACAAACTGAAGCTATGTGTCTTG 59.763 40.000 4.37 0.00 41.52 3.02
447 452 5.008019 CACAAACTGAAGCTATGTGTCTTGT 59.992 40.000 0.00 0.00 37.27 3.16
448 453 5.008019 ACAAACTGAAGCTATGTGTCTTGTG 59.992 40.000 0.00 0.00 0.00 3.33
449 454 3.070018 ACTGAAGCTATGTGTCTTGTGC 58.930 45.455 0.00 0.00 0.00 4.57
450 455 3.069289 CTGAAGCTATGTGTCTTGTGCA 58.931 45.455 0.00 0.00 0.00 4.57
451 456 3.069289 TGAAGCTATGTGTCTTGTGCAG 58.931 45.455 0.00 0.00 0.00 4.41
452 457 1.446907 AGCTATGTGTCTTGTGCAGC 58.553 50.000 0.00 0.00 0.00 5.25
453 458 1.159285 GCTATGTGTCTTGTGCAGCA 58.841 50.000 0.00 0.00 0.00 4.41
482 495 3.073678 AGTTGACTGCACGCATTTATCA 58.926 40.909 0.00 0.00 0.00 2.15
488 506 4.969816 ACTGCACGCATTTATCAAGTAAC 58.030 39.130 0.00 0.00 0.00 2.50
588 606 4.803452 TGGGTTTCAGTTCTTTTCAGGAT 58.197 39.130 0.00 0.00 0.00 3.24
661 1272 5.172687 TGACCAATGTGGAAAGCTACATA 57.827 39.130 0.18 0.00 44.28 2.29
735 1462 4.816925 GTGTAGTGGAGAATATGGGAAAGC 59.183 45.833 0.00 0.00 0.00 3.51
795 1522 5.286221 AGTGGCTAAGAATTTCCTACCCTA 58.714 41.667 0.00 0.00 0.00 3.53
813 1540 8.680001 CCTACCCTACAAATAAATTACAACCAC 58.320 37.037 0.00 0.00 0.00 4.16
842 1569 2.028658 AGATCGTGCACTGAAGTCATGT 60.029 45.455 16.19 0.00 0.00 3.21
843 1570 3.193479 AGATCGTGCACTGAAGTCATGTA 59.807 43.478 16.19 0.00 0.00 2.29
846 1573 4.672409 TCGTGCACTGAAGTCATGTATAG 58.328 43.478 16.19 0.00 0.00 1.31
877 1604 8.844441 TTTTTCAAAACGTGTTCTTGGTATAG 57.156 30.769 0.00 0.00 0.00 1.31
878 1605 5.600908 TCAAAACGTGTTCTTGGTATAGC 57.399 39.130 0.00 0.00 0.00 2.97
881 1608 6.205853 TCAAAACGTGTTCTTGGTATAGCATT 59.794 34.615 5.28 0.00 0.00 3.56
882 1609 6.569179 AAACGTGTTCTTGGTATAGCATTT 57.431 33.333 5.28 0.00 0.00 2.32
883 1610 5.545658 ACGTGTTCTTGGTATAGCATTTG 57.454 39.130 5.28 0.09 0.00 2.32
889 1630 3.871006 TCTTGGTATAGCATTTGCAGACG 59.129 43.478 5.28 0.00 45.16 4.18
892 1633 3.194861 GGTATAGCATTTGCAGACGACA 58.805 45.455 5.20 0.00 45.16 4.35
907 1648 2.028130 ACGACAATGCCTGTGGAAAAA 58.972 42.857 5.27 0.00 38.84 1.94
941 1682 2.880890 AGCAACTTTTACCTCACTGCAG 59.119 45.455 13.48 13.48 0.00 4.41
999 1740 1.554160 ACAGAGAAGCACCCATCTCAG 59.446 52.381 5.67 0.33 43.62 3.35
1009 1750 3.370315 GCACCCATCTCAGATGAAGTTCT 60.370 47.826 16.90 0.00 0.00 3.01
1012 1753 4.080638 ACCCATCTCAGATGAAGTTCTTCC 60.081 45.833 16.90 0.00 0.00 3.46
1032 1773 2.534990 CTCCTCTGTTTCCTCCTCTGT 58.465 52.381 0.00 0.00 0.00 3.41
1042 1783 0.401738 CCTCCTCTGTTTTGGCCTCA 59.598 55.000 3.32 0.00 0.00 3.86
1141 1882 2.358003 AGGCTGCTTCAGTCACGC 60.358 61.111 0.00 0.00 38.73 5.34
1231 1972 0.376852 GCACTTCCGCAAATCGCATA 59.623 50.000 0.00 0.00 42.60 3.14
1239 1980 4.061596 TCCGCAAATCGCATAATGATACA 58.938 39.130 0.00 0.00 42.60 2.29
1320 2061 1.152756 ACAGGGCTTGGCTTTCGTT 60.153 52.632 0.44 0.00 0.00 3.85
1359 2100 0.961019 TCTCAACTGCATTGGCCAAC 59.039 50.000 23.27 10.05 38.98 3.77
1516 2257 4.798882 CCTCCAGTCTATAGAGTCCAACT 58.201 47.826 7.14 0.00 0.00 3.16
1542 2283 8.481314 TCTGCAGGATATTATGATGATAGGAAC 58.519 37.037 15.13 0.00 0.00 3.62
1653 2394 1.305213 GGCTCCCCTTCAAATGGCA 60.305 57.895 0.00 0.00 0.00 4.92
1674 2415 4.331968 CAAAACCTACAAGGCCACTCATA 58.668 43.478 5.01 0.00 39.63 2.15
1681 2422 2.236146 ACAAGGCCACTCATATCGACAA 59.764 45.455 5.01 0.00 0.00 3.18
1695 2436 7.084486 TCATATCGACAAATTATGACCTCTCG 58.916 38.462 2.29 0.00 0.00 4.04
1767 2508 6.132791 GAGGTCGACTCAAGACATTATGTA 57.867 41.667 16.46 0.00 45.85 2.29
1817 2558 1.637553 AGCCCCACTGATCAATTCTGT 59.362 47.619 0.00 0.00 37.01 3.41
1830 2571 3.384146 TCAATTCTGTGAAGCTGCCAAAA 59.616 39.130 0.00 0.00 0.00 2.44
1893 2634 2.520979 CTACCTATAGCGAGCGCAATC 58.479 52.381 17.68 0.00 44.88 2.67
1929 2670 7.260387 TGTGGGTTCTATGGTCATTTTACTA 57.740 36.000 0.00 0.00 0.00 1.82
2133 2874 1.927895 CTGTGAAGAGGGTATCGCAC 58.072 55.000 0.00 0.00 38.09 5.34
2327 3068 6.321821 TCCAATGCTTATACTAAACTGGGT 57.678 37.500 0.00 0.00 0.00 4.51
2370 3111 2.030185 GGATATTGCATCAGGCTTGCTG 60.030 50.000 12.07 0.00 45.15 4.41
2657 3398 1.197721 AGTTAACAGCAATGCACGAGC 59.802 47.619 8.35 0.00 42.57 5.03
2734 3475 2.577700 CTGAGGCAGTAGATACGAGGT 58.422 52.381 0.00 0.00 0.00 3.85
2874 3615 3.128589 GCGATTTGCAATTCCCTGACTTA 59.871 43.478 14.10 0.00 45.45 2.24
3123 3864 5.789521 AGACTTCTCAGAGGCTTTTCTTAC 58.210 41.667 0.00 0.00 27.78 2.34
3246 3991 7.591165 ACATATGCATCATTCAGTTGCTTATC 58.409 34.615 0.19 0.00 42.23 1.75
3286 4147 7.649306 CAGCCCACAAATAAATACTATCTTTGC 59.351 37.037 0.00 0.00 31.59 3.68
3351 4597 5.531634 CATGGTGTTTTACAGCTCACAAAT 58.468 37.500 9.98 0.00 46.03 2.32
3390 4654 1.546029 GAAATTGTGGGAAGTGAGGCC 59.454 52.381 0.00 0.00 0.00 5.19
3458 4726 4.862902 ATCTCCACCATTAGAGATGACG 57.137 45.455 1.86 0.00 45.83 4.35
3493 4761 0.878086 GCGGTTCTGCAGCCTATCTC 60.878 60.000 9.47 0.00 32.01 2.75
3587 4865 2.513204 CTCAGCAGCCCCACGATG 60.513 66.667 0.00 0.00 0.00 3.84
3595 4873 3.807839 CCCCACGATGCCATCCCA 61.808 66.667 0.00 0.00 0.00 4.37
3607 4885 0.258484 CCATCCCACTATTGGCACCA 59.742 55.000 0.00 0.00 42.35 4.17
3618 4896 2.145397 TTGGCACCAAGTGTTACCAA 57.855 45.000 0.00 0.00 37.96 3.67
3619 4897 2.145397 TGGCACCAAGTGTTACCAAA 57.855 45.000 0.00 0.00 35.75 3.28
3641 4919 4.479993 GAGCTCGCCACCATGCCT 62.480 66.667 0.00 0.00 0.00 4.75
3650 5147 1.406539 GCCACCATGCCTGTTATTCTG 59.593 52.381 0.00 0.00 0.00 3.02
3666 5163 2.136298 TCTGTCCAGCCTGACTAGAG 57.864 55.000 0.00 0.00 36.21 2.43
3681 5178 2.741878 TAGAGGTCGGTTGTGGGCCT 62.742 60.000 4.53 0.00 0.00 5.19
3684 5181 2.745037 GTCGGTTGTGGGCCTACA 59.255 61.111 19.36 19.36 0.00 2.74
3708 5205 0.684479 TCCTCCTCTCATCACCACCG 60.684 60.000 0.00 0.00 0.00 4.94
3711 5208 1.142748 CCTCTCATCACCACCGCTC 59.857 63.158 0.00 0.00 0.00 5.03
3722 5246 3.349006 ACCGCTCGTGCTGCAAAG 61.349 61.111 2.77 6.41 36.97 2.77
3723 5247 4.748679 CCGCTCGTGCTGCAAAGC 62.749 66.667 21.83 21.83 36.97 3.51
3724 5248 3.720193 CGCTCGTGCTGCAAAGCT 61.720 61.111 26.08 0.00 36.97 3.74
3725 5249 2.126965 GCTCGTGCTGCAAAGCTG 60.127 61.111 23.50 10.95 36.03 4.24
3726 5250 2.610694 GCTCGTGCTGCAAAGCTGA 61.611 57.895 23.50 9.37 36.03 4.26
3727 5251 1.206072 CTCGTGCTGCAAAGCTGAC 59.794 57.895 2.77 0.00 35.49 3.51
3728 5252 2.127496 CGTGCTGCAAAGCTGACG 60.127 61.111 2.77 0.00 35.49 4.35
3729 5253 2.428071 GTGCTGCAAAGCTGACGC 60.428 61.111 2.77 0.00 35.49 5.19
3730 5254 2.901339 TGCTGCAAAGCTGACGCA 60.901 55.556 0.00 5.03 39.10 5.24
3731 5255 2.263021 TGCTGCAAAGCTGACGCAT 61.263 52.632 0.00 0.00 39.10 4.73
3732 5256 1.800315 GCTGCAAAGCTGACGCATG 60.800 57.895 5.52 0.00 39.10 4.06
3733 5257 1.871077 CTGCAAAGCTGACGCATGA 59.129 52.632 0.00 0.00 39.10 3.07
3734 5258 0.450583 CTGCAAAGCTGACGCATGAT 59.549 50.000 0.00 0.00 39.10 2.45
3735 5259 0.169451 TGCAAAGCTGACGCATGATG 59.831 50.000 0.00 0.00 39.10 3.07
3736 5260 0.169672 GCAAAGCTGACGCATGATGT 59.830 50.000 0.00 0.00 39.10 3.06
3737 5261 1.792993 GCAAAGCTGACGCATGATGTC 60.793 52.381 10.61 10.61 39.10 3.06
3738 5262 1.736126 CAAAGCTGACGCATGATGTCT 59.264 47.619 16.45 0.00 39.10 3.41
3739 5263 1.366679 AAGCTGACGCATGATGTCTG 58.633 50.000 16.45 16.28 39.10 3.51
3740 5264 0.533951 AGCTGACGCATGATGTCTGA 59.466 50.000 21.43 4.71 37.45 3.27
3741 5265 1.138464 AGCTGACGCATGATGTCTGAT 59.862 47.619 21.43 15.75 37.45 2.90
3742 5266 1.526041 GCTGACGCATGATGTCTGATC 59.474 52.381 21.43 7.81 37.45 2.92
3743 5267 2.802415 GCTGACGCATGATGTCTGATCT 60.802 50.000 21.43 0.00 37.45 2.75
3744 5268 3.051327 CTGACGCATGATGTCTGATCTC 58.949 50.000 16.45 0.00 37.45 2.75
3745 5269 2.428171 TGACGCATGATGTCTGATCTCA 59.572 45.455 16.45 0.00 37.26 3.27
3746 5270 3.069158 TGACGCATGATGTCTGATCTCAT 59.931 43.478 16.45 0.00 37.26 2.90
3747 5271 3.651206 ACGCATGATGTCTGATCTCATC 58.349 45.455 0.00 14.50 40.29 2.92
3763 5287 8.543293 TGATCTCATCATGTATGATATAGGCA 57.457 34.615 7.01 7.48 45.23 4.75
3797 5321 0.251165 CCAAACACTACCCCCACTGG 60.251 60.000 0.00 0.00 0.00 4.00
3801 5325 2.122144 ACTACCCCCACTGGCACA 60.122 61.111 0.00 0.00 0.00 4.57
3803 5327 1.140134 ACTACCCCCACTGGCACAAT 61.140 55.000 0.00 0.00 38.70 2.71
3989 5516 1.096416 ACTAGCTCAGACCAGTACGC 58.904 55.000 0.00 0.00 0.00 4.42
3991 5518 1.064803 CTAGCTCAGACCAGTACGCAG 59.935 57.143 0.00 0.00 0.00 5.18
3993 5520 0.179150 GCTCAGACCAGTACGCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
3997 5524 1.107114 AGACCAGTACGCAGAGATGG 58.893 55.000 0.00 0.00 37.07 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.249741 ACAAAGACGAACTCACCCGG 60.250 55.000 0.00 0.00 0.00 5.73
42 43 0.243907 CACACCCGGTCTGTACAGAG 59.756 60.000 25.81 16.02 38.27 3.35
75 76 0.108992 GTTGCATCGAGACGGTACCA 60.109 55.000 13.54 0.00 0.00 3.25
76 77 0.108992 TGTTGCATCGAGACGGTACC 60.109 55.000 0.16 0.16 0.00 3.34
77 78 1.922570 ATGTTGCATCGAGACGGTAC 58.077 50.000 0.00 0.00 0.00 3.34
80 81 0.374758 CCAATGTTGCATCGAGACGG 59.625 55.000 0.00 0.00 0.00 4.79
83 84 2.028203 TGACTCCAATGTTGCATCGAGA 60.028 45.455 10.95 0.00 0.00 4.04
95 96 5.690464 ATGAGAGCTTTACTGACTCCAAT 57.310 39.130 0.00 0.00 0.00 3.16
120 121 9.457436 GTTGTAGGATAACCCTTTTCTCAATAA 57.543 33.333 0.00 0.00 44.85 1.40
121 122 7.767198 CGTTGTAGGATAACCCTTTTCTCAATA 59.233 37.037 0.00 0.00 44.85 1.90
137 138 4.819105 TTGTCAGGAATCGTTGTAGGAT 57.181 40.909 0.00 0.00 0.00 3.24
148 149 9.865321 CATTCTAAATTGTTCATTGTCAGGAAT 57.135 29.630 0.00 0.00 0.00 3.01
178 179 4.434545 AAGGCAGACGTCTAGGAGTATA 57.565 45.455 19.57 0.00 0.00 1.47
239 242 0.877071 CACATGGCCTCACAAGTCAC 59.123 55.000 3.32 0.00 0.00 3.67
288 291 7.554211 TGCCTTCATAATTTATTTCATGTGCA 58.446 30.769 0.00 0.00 0.00 4.57
332 335 6.699575 AAAATCTTTGCTCTGCGGTTATAT 57.300 33.333 0.00 0.00 0.00 0.86
337 340 2.029918 GGAAAAATCTTTGCTCTGCGGT 60.030 45.455 0.00 0.00 30.64 5.68
379 384 0.839946 AGGGAATCCGACATTCAGGG 59.160 55.000 8.71 0.00 38.33 4.45
439 444 1.233019 ACATCTGCTGCACAAGACAC 58.767 50.000 0.00 0.00 0.00 3.67
440 445 1.971481 AACATCTGCTGCACAAGACA 58.029 45.000 0.00 0.00 0.00 3.41
441 446 3.499918 ACTTAACATCTGCTGCACAAGAC 59.500 43.478 0.00 0.00 0.00 3.01
442 447 3.743521 ACTTAACATCTGCTGCACAAGA 58.256 40.909 0.00 0.00 0.00 3.02
443 448 4.023792 TCAACTTAACATCTGCTGCACAAG 60.024 41.667 0.00 0.00 0.00 3.16
444 449 3.882288 TCAACTTAACATCTGCTGCACAA 59.118 39.130 0.00 0.00 0.00 3.33
445 450 3.250762 GTCAACTTAACATCTGCTGCACA 59.749 43.478 0.00 0.00 0.00 4.57
446 451 3.499918 AGTCAACTTAACATCTGCTGCAC 59.500 43.478 0.00 0.00 0.00 4.57
447 452 3.499537 CAGTCAACTTAACATCTGCTGCA 59.500 43.478 0.88 0.88 0.00 4.41
448 453 3.669023 GCAGTCAACTTAACATCTGCTGC 60.669 47.826 7.56 0.00 42.98 5.25
449 454 3.499537 TGCAGTCAACTTAACATCTGCTG 59.500 43.478 14.34 0.00 45.39 4.41
450 455 3.499918 GTGCAGTCAACTTAACATCTGCT 59.500 43.478 14.34 0.00 45.39 4.24
451 456 3.665323 CGTGCAGTCAACTTAACATCTGC 60.665 47.826 7.83 7.83 45.39 4.26
452 457 3.665323 GCGTGCAGTCAACTTAACATCTG 60.665 47.826 0.00 0.00 0.00 2.90
453 458 2.480419 GCGTGCAGTCAACTTAACATCT 59.520 45.455 0.00 0.00 0.00 2.90
526 544 9.806203 TGGAGCATAAATCAGAATACAATTTTG 57.194 29.630 0.00 0.00 0.00 2.44
533 551 5.619625 GCCTGGAGCATAAATCAGAATAC 57.380 43.478 0.00 0.00 42.97 1.89
609 627 7.499895 ACCATGTTTCTTTTCTGATTTGCAATT 59.500 29.630 0.00 0.00 0.00 2.32
611 629 6.258287 CACCATGTTTCTTTTCTGATTTGCAA 59.742 34.615 0.00 0.00 0.00 4.08
613 631 5.178067 CCACCATGTTTCTTTTCTGATTTGC 59.822 40.000 0.00 0.00 0.00 3.68
614 632 5.178067 GCCACCATGTTTCTTTTCTGATTTG 59.822 40.000 0.00 0.00 0.00 2.32
615 633 5.070847 AGCCACCATGTTTCTTTTCTGATTT 59.929 36.000 0.00 0.00 0.00 2.17
617 635 4.021719 CAGCCACCATGTTTCTTTTCTGAT 60.022 41.667 0.00 0.00 0.00 2.90
618 636 3.318839 CAGCCACCATGTTTCTTTTCTGA 59.681 43.478 0.00 0.00 0.00 3.27
619 637 3.318839 TCAGCCACCATGTTTCTTTTCTG 59.681 43.478 0.00 0.00 0.00 3.02
621 639 3.552890 GGTCAGCCACCATGTTTCTTTTC 60.553 47.826 0.00 0.00 45.98 2.29
622 640 2.365293 GGTCAGCCACCATGTTTCTTTT 59.635 45.455 0.00 0.00 45.98 2.27
735 1462 1.939934 TGCAAAAGTCAGTCGTCCTTG 59.060 47.619 0.00 0.00 0.00 3.61
795 1522 6.262193 CCCTCGTGGTTGTAATTTATTTGT 57.738 37.500 2.33 0.00 0.00 2.83
813 1540 0.456221 AGTGCACGATCTTACCCTCG 59.544 55.000 12.01 0.00 40.62 4.63
819 1546 3.934457 TGACTTCAGTGCACGATCTTA 57.066 42.857 12.01 0.00 0.00 2.10
821 1548 2.028658 ACATGACTTCAGTGCACGATCT 60.029 45.455 12.01 0.34 0.00 2.75
825 1552 3.243877 GCTATACATGACTTCAGTGCACG 59.756 47.826 12.01 6.78 0.00 5.34
871 1598 3.194861 TGTCGTCTGCAAATGCTATACC 58.805 45.455 6.97 0.00 42.66 2.73
877 1604 0.986992 GCATTGTCGTCTGCAAATGC 59.013 50.000 13.95 13.95 38.28 3.56
878 1605 1.200716 AGGCATTGTCGTCTGCAAATG 59.799 47.619 2.77 2.77 40.18 2.32
881 1608 0.534877 ACAGGCATTGTCGTCTGCAA 60.535 50.000 0.00 0.00 40.18 4.08
882 1609 1.071299 ACAGGCATTGTCGTCTGCA 59.929 52.632 0.00 0.00 40.18 4.41
883 1610 1.499056 CACAGGCATTGTCGTCTGC 59.501 57.895 0.00 0.00 38.16 4.26
907 1648 1.589414 AGTTGCTATCCTGCCCTCTT 58.411 50.000 0.00 0.00 0.00 2.85
941 1682 9.443283 CAGACTGCAATGCTATTTAACTTAATC 57.557 33.333 6.82 0.00 0.00 1.75
999 1740 4.817318 ACAGAGGAGGAAGAACTTCATC 57.183 45.455 17.25 17.25 46.20 2.92
1009 1750 2.112691 AGAGGAGGAAACAGAGGAGGAA 59.887 50.000 0.00 0.00 0.00 3.36
1012 1753 2.534990 ACAGAGGAGGAAACAGAGGAG 58.465 52.381 0.00 0.00 0.00 3.69
1042 1783 0.249031 GCAGTGAAAAACGCAGGCTT 60.249 50.000 0.00 0.00 0.00 4.35
1141 1882 1.446272 GCTCAAGGAGTCCGTTCGG 60.446 63.158 2.76 4.74 31.39 4.30
1231 1972 6.883217 ACTGAGAAAGATTGCACTGTATCATT 59.117 34.615 0.00 0.00 27.29 2.57
1239 1980 2.072298 GCGACTGAGAAAGATTGCACT 58.928 47.619 0.00 0.00 0.00 4.40
1320 2061 1.971167 GTTCATGCTTGGGGCGACA 60.971 57.895 0.00 0.00 45.43 4.35
1516 2257 8.481314 GTTCCTATCATCATAATATCCTGCAGA 58.519 37.037 17.39 1.21 0.00 4.26
1527 2268 6.014840 GGAAGGTACCGTTCCTATCATCATAA 60.015 42.308 24.66 0.00 40.46 1.90
1653 2394 3.525800 ATGAGTGGCCTTGTAGGTTTT 57.474 42.857 3.32 0.00 37.80 2.43
1674 2415 5.067936 ACTCGAGAGGTCATAATTTGTCGAT 59.932 40.000 21.68 0.00 34.92 3.59
1681 2422 5.171476 CAACACACTCGAGAGGTCATAATT 58.829 41.667 21.68 3.47 0.00 1.40
1695 2436 2.421424 GGATGGATCTTGCAACACACTC 59.579 50.000 0.00 0.00 0.00 3.51
1767 2508 2.838637 TCCCAAAACTCCAACCAAGT 57.161 45.000 0.00 0.00 0.00 3.16
1817 2558 2.158682 TGAGGTAGTTTTGGCAGCTTCA 60.159 45.455 0.00 0.00 0.00 3.02
1830 2571 1.630369 TGATGCTTTGGCTGAGGTAGT 59.370 47.619 0.00 0.00 39.59 2.73
1893 2634 3.074412 AGAACCCACAGCAAATACGAAG 58.926 45.455 0.00 0.00 0.00 3.79
1929 2670 5.045286 AGCATACCTCAATTTTCTCCTCACT 60.045 40.000 0.00 0.00 0.00 3.41
2133 2874 1.835494 TTAGACCCTGTCTGGACTCG 58.165 55.000 7.00 0.00 43.30 4.18
2327 3068 7.190335 TCCTTTATTATCCGAAACCTCTGAA 57.810 36.000 0.00 0.00 0.00 3.02
2370 3111 4.855340 TCTCCCATTTTTCATGGAGGTAC 58.145 43.478 2.20 0.00 43.72 3.34
2583 3324 2.079170 TCCCAAAGGCAAACACATCA 57.921 45.000 0.00 0.00 0.00 3.07
2734 3475 9.516314 CTCGTCAACATTATAGTCATTCTGTAA 57.484 33.333 0.00 0.00 35.00 2.41
2863 3604 5.778241 TGTCTGTATCTGTTAAGTCAGGGAA 59.222 40.000 0.00 0.00 36.25 3.97
2868 3609 6.153510 AGCTCATGTCTGTATCTGTTAAGTCA 59.846 38.462 0.00 0.00 0.00 3.41
2874 3615 5.411831 TGAAGCTCATGTCTGTATCTGTT 57.588 39.130 0.00 0.00 0.00 3.16
3039 3780 1.385528 TATGTGGCATGCAAGCTCAG 58.614 50.000 21.36 0.00 34.17 3.35
3075 3816 4.079212 ACCTAGCCCCAAACATTACATGAT 60.079 41.667 0.00 0.00 0.00 2.45
3123 3864 2.930040 CAATTACGCACTACCCTCACAG 59.070 50.000 0.00 0.00 0.00 3.66
3181 3926 3.586892 GCAGGTAGCTTCTTCGTTTAGT 58.413 45.455 0.00 0.00 41.15 2.24
3246 3991 1.355210 GGCTGTGAAACACCACGTG 59.645 57.895 9.08 9.08 45.67 4.49
3458 4726 4.683334 GCCACCGCTTCGTTGTGC 62.683 66.667 0.00 0.00 0.00 4.57
3472 4740 2.593468 GATAGGCTGCAGAACCGCCA 62.593 60.000 20.43 3.27 46.14 5.69
3493 4761 3.010138 TCATTAGGTTGTTGGAGAAGGGG 59.990 47.826 0.00 0.00 0.00 4.79
3595 4873 3.181438 TGGTAACACTTGGTGCCAATAGT 60.181 43.478 0.99 3.71 46.17 2.12
3641 4919 2.906389 AGTCAGGCTGGACAGAATAACA 59.094 45.455 15.73 0.00 40.29 2.41
3650 5147 1.107945 GACCTCTAGTCAGGCTGGAC 58.892 60.000 15.73 11.43 45.55 4.02
3666 5163 2.046604 GTAGGCCCACAACCGACC 60.047 66.667 0.00 0.00 0.00 4.79
3681 5178 3.764434 GTGATGAGAGGAGGAACTGTGTA 59.236 47.826 0.00 0.00 41.55 2.90
3684 5181 2.183679 GGTGATGAGAGGAGGAACTGT 58.816 52.381 0.00 0.00 41.55 3.55
3722 5246 1.526041 GATCAGACATCATGCGTCAGC 59.474 52.381 14.99 0.00 45.41 4.26
3723 5247 3.051327 GAGATCAGACATCATGCGTCAG 58.949 50.000 14.99 8.82 35.77 3.51
3724 5248 2.428171 TGAGATCAGACATCATGCGTCA 59.572 45.455 14.99 0.00 35.77 4.35
3725 5249 3.089573 TGAGATCAGACATCATGCGTC 57.910 47.619 6.93 6.93 0.00 5.19
3726 5250 3.069158 TGATGAGATCAGACATCATGCGT 59.931 43.478 19.05 0.00 44.86 5.24
3727 5251 3.650139 TGATGAGATCAGACATCATGCG 58.350 45.455 19.05 0.00 44.86 4.73
3744 5268 7.910441 TGTGTTGCCTATATCATACATGATG 57.090 36.000 13.75 0.00 46.34 3.07
3746 5270 7.442062 CACTTGTGTTGCCTATATCATACATGA 59.558 37.037 0.00 0.00 41.70 3.07
3747 5271 7.308169 CCACTTGTGTTGCCTATATCATACATG 60.308 40.741 0.00 0.00 0.00 3.21
3748 5272 6.712095 CCACTTGTGTTGCCTATATCATACAT 59.288 38.462 0.00 0.00 0.00 2.29
3758 5282 1.813862 GCACTCCACTTGTGTTGCCTA 60.814 52.381 0.00 0.00 37.70 3.93
3763 5287 1.476488 GTTTGGCACTCCACTTGTGTT 59.524 47.619 0.00 0.00 43.33 3.32
3787 5311 2.440599 GATTGTGCCAGTGGGGGT 59.559 61.111 12.15 0.00 37.04 4.95
3797 5321 8.894768 AAGATTAAGTACATCTAGGATTGTGC 57.105 34.615 0.00 0.00 30.35 4.57
3803 5327 8.483758 GGGTTGAAAGATTAAGTACATCTAGGA 58.516 37.037 0.00 0.00 30.35 2.94
3974 5501 0.179150 CTCTGCGTACTGGTCTGAGC 60.179 60.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.