Multiple sequence alignment - TraesCS4A01G060800

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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 TraesCS4A01G060800 chr4A 100.000 3380 0 0 1 3380 57812368 57815747 0.000000e+00 6242
1 TraesCS4A01G060800 chr4B 92.279 3225 167 35 21 3204 494020433 494023616 0.000000e+00 4501
2 TraesCS4A01G060800 chr4B 91.480 223 18 1 1283 1505 13276372 13276151 4.240000e-79 305
3 TraesCS4A01G060800 chr4B 93.103 116 4 3 3255 3370 494023721 494023832 2.090000e-37 167
4 TraesCS4A01G060800 chr4D 91.858 3267 158 42 21 3250 399776830 399780025 0.000000e+00 4460
5 TraesCS4A01G060800 chr4D 90.323 248 21 2 2490 2735 350266131 350266377 4.210000e-84 322
6 TraesCS4A01G060800 chr4D 97.436 78 2 0 3269 3346 399780111 399780188 2.120000e-27 134
7 TraesCS4A01G060800 chr2A 88.718 1232 79 22 2056 3257 697070953 697069752 0.000000e+00 1450
8 TraesCS4A01G060800 chr2A 88.166 338 25 7 1283 1619 697071458 697071135 4.090000e-104 388
9 TraesCS4A01G060800 chr2A 98.333 60 1 0 3269 3328 697069685 697069626 4.610000e-19 106
10 TraesCS4A01G060800 chr5A 90.909 847 60 8 1818 2652 667025499 667024658 0.000000e+00 1122
11 TraesCS4A01G060800 chr5A 92.778 360 26 0 1495 1854 129233694 129233335 3.860000e-144 521
12 TraesCS4A01G060800 chr5A 93.491 338 21 1 1283 1619 667025832 667025495 5.030000e-138 501
13 TraesCS4A01G060800 chr5A 95.217 230 11 0 1803 2032 52485128 52485357 6.890000e-97 364
14 TraesCS4A01G060800 chr5A 92.793 222 14 1 2516 2735 52485366 52485587 1.510000e-83 320
15 TraesCS4A01G060800 chr7B 89.231 715 52 7 1943 2649 735911800 735912497 0.000000e+00 870
16 TraesCS4A01G060800 chr7B 92.708 288 20 1 1333 1619 735909814 735910101 6.750000e-112 414
17 TraesCS4A01G060800 chr7B 90.135 223 21 1 1283 1505 22543460 22543681 4.270000e-74 289
18 TraesCS4A01G060800 chr7B 88.667 150 9 3 1818 1959 735910097 735910246 3.470000e-40 176
19 TraesCS4A01G060800 chr3D 94.737 361 19 0 1493 1853 470481483 470481843 2.280000e-156 562
20 TraesCS4A01G060800 chr2D 94.460 361 20 0 1493 1853 287142733 287143093 1.060000e-154 556
21 TraesCS4A01G060800 chr1A 91.989 362 29 0 1493 1854 505305790 505306151 3.010000e-140 508
22 TraesCS4A01G060800 chr2B 89.686 223 22 1 1283 1505 152133766 152133987 1.990000e-72 283
23 TraesCS4A01G060800 chr7D 94.054 185 8 2 1283 1467 264483516 264483335 9.240000e-71 278


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 TraesCS4A01G060800 chr4A 57812368 57815747 3379 False 6242.000000 6242 100.000 1 3380 1 chr4A.!!$F1 3379
1 TraesCS4A01G060800 chr4B 494020433 494023832 3399 False 2334.000000 4501 92.691 21 3370 2 chr4B.!!$F1 3349
2 TraesCS4A01G060800 chr4D 399776830 399780188 3358 False 2297.000000 4460 94.647 21 3346 2 chr4D.!!$F2 3325
3 TraesCS4A01G060800 chr2A 697069626 697071458 1832 True 648.000000 1450 91.739 1283 3328 3 chr2A.!!$R1 2045
4 TraesCS4A01G060800 chr5A 667024658 667025832 1174 True 811.500000 1122 92.200 1283 2652 2 chr5A.!!$R2 1369
5 TraesCS4A01G060800 chr7B 735909814 735912497 2683 False 486.666667 870 90.202 1333 2649 3 chr7B.!!$F2 1316

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
889 924 0.594602 CCATGATTCGCCGCATCATT 59.405 50.0 9.5 0.0 39.00 2.57 F
1752 1805 0.602638 TCGTGGTGGACATGCTCAAC 60.603 55.0 0.0 0.0 36.01 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1976 0.179062 AATTGAGCAGCTCTAGCCCG 60.179 55.0 23.15 0.0 43.38 6.13 R
3263 4941 0.106419 GACCGAGGACCCTCTCTCAT 60.106 60.0 13.62 0.0 40.69 2.90 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
55 56 4.443266 GCAGCCTCGAGTTCCGCT 62.443 66.667 12.31 9.90 38.37 5.52
61 62 1.140589 CTCGAGTTCCGCTGCTGAT 59.859 57.895 3.62 0.00 38.37 2.90
91 92 4.928263 CTTCCCCAGAAGGAGAGAAAATT 58.072 43.478 0.00 0.00 44.97 1.82
106 107 8.955002 GGAGAGAAAATTTTGTTTTCGTAGTTC 58.045 33.333 8.47 0.00 41.78 3.01
113 114 9.980780 AAATTTTGTTTTCGTAGTTCAAAATGG 57.019 25.926 12.60 0.00 43.27 3.16
138 139 5.189180 CCAAATGTTGAAAAGGGGAAACAA 58.811 37.500 0.00 0.00 36.23 2.83
187 188 6.038356 GGAGCAATGGTAAAAATCACATCAG 58.962 40.000 0.00 0.00 0.00 2.90
209 210 5.530915 CAGACCTAGAAGGAGATCACTACTG 59.469 48.000 0.00 0.00 37.39 2.74
213 214 6.378848 ACCTAGAAGGAGATCACTACTGAAAC 59.621 42.308 0.00 0.00 37.39 2.78
214 215 6.378564 CCTAGAAGGAGATCACTACTGAAACA 59.621 42.308 0.00 0.00 37.39 2.83
216 217 7.067496 AGAAGGAGATCACTACTGAAACAAA 57.933 36.000 0.00 0.00 37.39 2.83
217 218 7.509546 AGAAGGAGATCACTACTGAAACAAAA 58.490 34.615 0.00 0.00 37.39 2.44
218 219 7.442666 AGAAGGAGATCACTACTGAAACAAAAC 59.557 37.037 0.00 0.00 37.39 2.43
221 222 7.556275 AGGAGATCACTACTGAAACAAAACAAA 59.444 33.333 0.00 0.00 35.73 2.83
230 231 5.461737 ACTGAAACAAAACAAACATATGGCG 59.538 36.000 7.80 0.00 0.00 5.69
350 362 4.410492 TTGAGCGAGAGAAAAGAAATGC 57.590 40.909 0.00 0.00 0.00 3.56
381 393 8.301002 AGTACCAGCGCTAAAATAAATGAAAAA 58.699 29.630 10.99 0.00 0.00 1.94
386 398 6.538381 AGCGCTAAAATAAATGAAAAATGGGG 59.462 34.615 8.99 0.00 0.00 4.96
402 414 1.564348 TGGGGAAGAATACAAGAGGGC 59.436 52.381 0.00 0.00 0.00 5.19
468 480 2.084546 GCTAATGTGTCTGGTCCCAAC 58.915 52.381 0.00 0.00 0.00 3.77
469 481 2.711542 CTAATGTGTCTGGTCCCAACC 58.288 52.381 0.00 0.00 46.66 3.77
477 489 4.821935 GGTCCCAACCAAGTCCTG 57.178 61.111 0.00 0.00 45.68 3.86
486 498 2.352805 CAAGTCCTGCCCCACCTC 59.647 66.667 0.00 0.00 0.00 3.85
517 529 2.997315 CCCTCTCACTCGCACCCA 60.997 66.667 0.00 0.00 0.00 4.51
518 530 2.262915 CCTCTCACTCGCACCCAC 59.737 66.667 0.00 0.00 0.00 4.61
519 531 2.574018 CCTCTCACTCGCACCCACA 61.574 63.158 0.00 0.00 0.00 4.17
520 532 1.373497 CTCTCACTCGCACCCACAC 60.373 63.158 0.00 0.00 0.00 3.82
521 533 2.357517 CTCACTCGCACCCACACC 60.358 66.667 0.00 0.00 0.00 4.16
522 534 3.883744 CTCACTCGCACCCACACCC 62.884 68.421 0.00 0.00 0.00 4.61
541 553 3.070878 ACCCACCCAAGTAAAATTGCAAG 59.929 43.478 4.94 0.00 0.00 4.01
559 571 6.618287 TGCAAGTCCGGATAATAATTTCAG 57.382 37.500 7.81 0.00 0.00 3.02
588 600 1.031571 CCTGCTCGCTCTCTCACTCT 61.032 60.000 0.00 0.00 0.00 3.24
596 608 2.017049 GCTCTCTCACTCTCACTCTCC 58.983 57.143 0.00 0.00 0.00 3.71
599 611 2.647299 TCTCTCACTCTCACTCTCCCTT 59.353 50.000 0.00 0.00 0.00 3.95
645 669 1.863267 CTGGATCTCAGTCGCATTCC 58.137 55.000 0.00 0.00 38.64 3.01
675 699 4.179599 CCCCTCCTCTCCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
676 700 3.039526 CCCTCCTCTCCTCCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
681 708 2.612251 CTCTCCTCCCCCTCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
696 723 2.892852 CTCCCTCATCAGATCTCCTCAC 59.107 54.545 0.00 0.00 0.00 3.51
698 725 2.364970 CCCTCATCAGATCTCCTCACAC 59.635 54.545 0.00 0.00 0.00 3.82
718 745 2.515523 CCTGCAATCCGCCTCCAG 60.516 66.667 0.00 0.00 41.33 3.86
719 746 3.207669 CTGCAATCCGCCTCCAGC 61.208 66.667 0.00 0.00 41.33 4.85
739 766 2.038659 CCCAAAACCCAGAAGCTTTCA 58.961 47.619 0.00 0.00 0.00 2.69
740 767 2.036346 CCCAAAACCCAGAAGCTTTCAG 59.964 50.000 0.00 0.00 0.00 3.02
757 792 3.211288 GCTCAAGCTCCTCGCCTA 58.789 61.111 0.00 0.00 40.39 3.93
772 807 0.958876 GCCTACCCTTTTGACCGGTG 60.959 60.000 14.63 0.00 0.00 4.94
779 814 4.966787 TTTGACCGGTGGGCAGCC 62.967 66.667 14.63 1.26 44.10 4.85
835 870 2.889678 CAAGAAAGAGGGAAAGCAAGCT 59.110 45.455 0.00 0.00 0.00 3.74
836 871 4.074970 CAAGAAAGAGGGAAAGCAAGCTA 58.925 43.478 0.00 0.00 0.00 3.32
837 872 3.949132 AGAAAGAGGGAAAGCAAGCTAG 58.051 45.455 0.00 0.00 0.00 3.42
846 881 1.631071 AAGCAAGCTAGGAGGAGGGC 61.631 60.000 0.00 0.00 0.00 5.19
879 914 2.069273 GATAAGTCGCCCCATGATTCG 58.931 52.381 0.00 0.00 0.00 3.34
889 924 0.594602 CCATGATTCGCCGCATCATT 59.405 50.000 9.50 0.00 39.00 2.57
1164 1203 1.596477 GATGGACGAGCTGGATGCC 60.596 63.158 1.44 1.46 44.23 4.40
1167 1206 4.521062 GACGAGCTGGATGCCGCT 62.521 66.667 2.03 2.03 44.23 5.52
1584 1637 2.173669 CGTGACCAAGGCCATAGCG 61.174 63.158 5.01 0.00 41.24 4.26
1671 1724 2.877691 GCGGTGGCCATTCTTGTC 59.122 61.111 9.72 0.00 0.00 3.18
1677 1730 1.675641 GGCCATTCTTGTCAGCGGT 60.676 57.895 0.00 0.00 0.00 5.68
1752 1805 0.602638 TCGTGGTGGACATGCTCAAC 60.603 55.000 0.00 0.00 36.01 3.18
2094 3732 1.216710 CAGGACGGCTCTCAAGGAC 59.783 63.158 0.00 0.00 0.00 3.85
2320 3958 1.081641 CTGCTCAAGCTTTGCACCG 60.082 57.895 17.02 7.62 42.66 4.94
2413 4051 4.543590 ACATAGTCCTTCTGGTTGTGAG 57.456 45.455 0.00 0.00 34.23 3.51
2444 4082 2.291735 TGATGCAGTTCCCATTGGTCAT 60.292 45.455 1.20 0.00 0.00 3.06
2489 4131 2.426522 TGGACGAGAGAAGCAAATTGG 58.573 47.619 0.00 0.00 0.00 3.16
2513 4155 3.589988 CTGGATGAAGACCTGTGTGTAC 58.410 50.000 0.00 0.00 0.00 2.90
2536 4178 1.549203 AACTCAGCAATTGGCCGAAT 58.451 45.000 7.72 0.00 46.50 3.34
2541 4183 0.737019 AGCAATTGGCCGAATTTGCG 60.737 50.000 20.70 8.21 46.50 4.85
2570 4216 1.561076 TGAAGACATGGGAGTGGATGG 59.439 52.381 0.00 0.00 0.00 3.51
2706 4363 2.040278 TCAATAAGCACTCAAGGGCTGT 59.960 45.455 7.69 1.23 40.93 4.40
2764 4427 1.001181 GAATTCAGCAAAGGCCTGCAA 59.999 47.619 18.35 6.04 45.18 4.08
2765 4428 1.272807 ATTCAGCAAAGGCCTGCAAT 58.727 45.000 18.35 7.99 45.18 3.56
2766 4429 1.050204 TTCAGCAAAGGCCTGCAATT 58.950 45.000 18.35 0.26 45.18 2.32
2767 4430 1.050204 TCAGCAAAGGCCTGCAATTT 58.950 45.000 18.35 0.00 45.18 1.82
2768 4431 1.417145 TCAGCAAAGGCCTGCAATTTT 59.583 42.857 18.35 0.00 45.18 1.82
2769 4432 2.632028 TCAGCAAAGGCCTGCAATTTTA 59.368 40.909 18.35 0.00 45.18 1.52
2770 4433 2.997986 CAGCAAAGGCCTGCAATTTTAG 59.002 45.455 18.35 0.00 45.18 1.85
2805 4468 0.037303 CAATGTGGGAGGCTGTCAGT 59.963 55.000 0.93 0.00 0.00 3.41
2964 4633 2.087646 GTTCTTCCTGCATCTTGGGTC 58.912 52.381 0.00 0.00 0.00 4.46
2977 4646 2.370519 TCTTGGGTCGTTTGATTCTCCA 59.629 45.455 0.00 0.00 0.00 3.86
2992 4661 5.837979 TGATTCTCCAGTCAAATTTGGGAAA 59.162 36.000 17.90 12.62 35.13 3.13
3002 4671 6.039382 AGTCAAATTTGGGAAAGTGTACACTC 59.961 38.462 28.04 16.75 41.58 3.51
3096 4773 0.307760 CTGGTTCCGTGTCTTGTTGC 59.692 55.000 0.00 0.00 0.00 4.17
3117 4794 1.032114 CCGGAATTTCTGCTCACCCC 61.032 60.000 0.00 0.00 0.00 4.95
3118 4795 0.322456 CGGAATTTCTGCTCACCCCA 60.322 55.000 0.00 0.00 0.00 4.96
3119 4796 1.683011 CGGAATTTCTGCTCACCCCAT 60.683 52.381 0.00 0.00 0.00 4.00
3120 4797 2.027385 GGAATTTCTGCTCACCCCATC 58.973 52.381 0.00 0.00 0.00 3.51
3121 4798 2.357569 GGAATTTCTGCTCACCCCATCT 60.358 50.000 0.00 0.00 0.00 2.90
3122 4799 2.725221 ATTTCTGCTCACCCCATCTC 57.275 50.000 0.00 0.00 0.00 2.75
3147 4824 5.476614 TCTCATCTACTGCATGTATCATGC 58.523 41.667 22.59 22.59 44.76 4.06
3208 4886 2.235016 GGCACCAATTGTTCCAGTACA 58.765 47.619 4.43 0.00 29.56 2.90
3209 4887 2.825532 GGCACCAATTGTTCCAGTACAT 59.174 45.455 4.43 0.00 29.56 2.29
3210 4888 3.258123 GGCACCAATTGTTCCAGTACATT 59.742 43.478 4.43 0.00 29.56 2.71
3211 4889 4.461081 GGCACCAATTGTTCCAGTACATTA 59.539 41.667 4.43 0.00 29.56 1.90
3212 4890 5.127031 GGCACCAATTGTTCCAGTACATTAT 59.873 40.000 4.43 0.00 29.56 1.28
3213 4891 6.320164 GGCACCAATTGTTCCAGTACATTATA 59.680 38.462 4.43 0.00 29.56 0.98
3214 4892 7.193595 GCACCAATTGTTCCAGTACATTATAC 58.806 38.462 4.43 0.00 0.00 1.47
3215 4893 7.067008 GCACCAATTGTTCCAGTACATTATACT 59.933 37.037 4.43 0.00 0.00 2.12
3216 4894 9.607988 CACCAATTGTTCCAGTACATTATACTA 57.392 33.333 4.43 0.00 0.00 1.82
3257 4935 5.539582 TTAATTGACGTAGATTGTGGCAC 57.460 39.130 11.55 11.55 0.00 5.01
3258 4936 2.831685 TTGACGTAGATTGTGGCACT 57.168 45.000 19.83 0.00 0.00 4.40
3260 4938 2.683968 TGACGTAGATTGTGGCACTTC 58.316 47.619 19.83 15.11 0.00 3.01
3261 4939 2.036604 TGACGTAGATTGTGGCACTTCA 59.963 45.455 19.83 3.09 0.00 3.02
3262 4940 2.412089 GACGTAGATTGTGGCACTTCAC 59.588 50.000 19.83 13.73 38.09 3.18
3263 4941 2.224185 ACGTAGATTGTGGCACTTCACA 60.224 45.455 19.83 5.47 44.81 3.58
3264 4942 3.002791 CGTAGATTGTGGCACTTCACAT 58.997 45.455 19.83 3.05 45.63 3.21
3265 4943 3.181517 CGTAGATTGTGGCACTTCACATG 60.182 47.826 19.83 9.16 45.63 3.21
3370 5117 1.981495 AGCTTAGGGATAGGGTCATGC 59.019 52.381 0.00 0.00 0.00 4.06
3371 5118 1.699634 GCTTAGGGATAGGGTCATGCA 59.300 52.381 0.00 0.00 0.00 3.96
3372 5119 2.307098 GCTTAGGGATAGGGTCATGCAT 59.693 50.000 0.00 0.00 0.00 3.96
3373 5120 3.871463 GCTTAGGGATAGGGTCATGCATG 60.871 52.174 21.07 21.07 0.00 4.06
3374 5121 1.825105 AGGGATAGGGTCATGCATGT 58.175 50.000 25.43 9.58 0.00 3.21
3375 5122 1.422781 AGGGATAGGGTCATGCATGTG 59.577 52.381 25.43 3.46 0.00 3.21
3376 5123 1.143684 GGGATAGGGTCATGCATGTGT 59.856 52.381 25.43 11.44 0.00 3.72
3377 5124 2.371841 GGGATAGGGTCATGCATGTGTA 59.628 50.000 25.43 13.09 0.00 2.90
3378 5125 3.009473 GGGATAGGGTCATGCATGTGTAT 59.991 47.826 25.43 16.66 0.00 2.29
3379 5126 4.005650 GGATAGGGTCATGCATGTGTATG 58.994 47.826 25.43 0.97 39.12 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.698382 CGATCAGCAGCGGAACTC 58.302 61.111 0.00 0.00 0.00 3.01
61 62 3.556038 TTCTGGGGAAGGGGAGCGA 62.556 63.158 0.00 0.00 0.00 4.93
69 70 4.582973 ATTTTCTCTCCTTCTGGGGAAG 57.417 45.455 0.00 0.00 43.38 3.46
91 92 6.752815 GGTCCATTTTGAACTACGAAAACAAA 59.247 34.615 0.00 0.00 35.77 2.83
106 107 6.238703 CCCTTTTCAACATTTGGTCCATTTTG 60.239 38.462 0.00 0.00 0.00 2.44
112 113 2.969262 TCCCCTTTTCAACATTTGGTCC 59.031 45.455 0.00 0.00 0.00 4.46
113 114 4.681074 TTCCCCTTTTCAACATTTGGTC 57.319 40.909 0.00 0.00 0.00 4.02
138 139 3.602483 GAATGAAATGCCCATGCTGTTT 58.398 40.909 0.00 0.00 38.71 2.83
187 188 5.686753 TCAGTAGTGATCTCCTTCTAGGTC 58.313 45.833 0.00 0.00 36.53 3.85
209 210 4.376920 GGCGCCATATGTTTGTTTTGTTTC 60.377 41.667 24.80 0.00 0.00 2.78
213 214 2.681706 TGGCGCCATATGTTTGTTTTG 58.318 42.857 29.03 0.00 0.00 2.44
214 215 3.608316 ATGGCGCCATATGTTTGTTTT 57.392 38.095 39.91 13.06 34.49 2.43
216 217 3.520569 GAAATGGCGCCATATGTTTGTT 58.479 40.909 40.54 28.43 35.31 2.83
217 218 2.159114 GGAAATGGCGCCATATGTTTGT 60.159 45.455 40.54 21.70 35.31 2.83
218 219 2.101249 AGGAAATGGCGCCATATGTTTG 59.899 45.455 40.54 0.00 35.31 2.93
221 222 1.321474 CAGGAAATGGCGCCATATGT 58.679 50.000 40.54 28.13 35.31 2.29
230 231 3.429960 GGAAGAATCTTGCAGGAAATGGC 60.430 47.826 9.67 0.00 0.00 4.40
307 319 2.588027 TTTCCTTTTTGTTCGGTGCC 57.412 45.000 0.00 0.00 0.00 5.01
316 328 6.208644 TCTCTCGCTCAAATTTTCCTTTTTG 58.791 36.000 0.00 0.00 34.80 2.44
350 362 8.700644 CATTTATTTTAGCGCTGGTACTACTAG 58.299 37.037 22.90 0.00 0.00 2.57
381 393 2.175715 GCCCTCTTGTATTCTTCCCCAT 59.824 50.000 0.00 0.00 0.00 4.00
386 398 0.931005 CGCGCCCTCTTGTATTCTTC 59.069 55.000 0.00 0.00 0.00 2.87
468 480 3.260100 AGGTGGGGCAGGACTTGG 61.260 66.667 0.00 0.00 0.00 3.61
469 481 2.352805 GAGGTGGGGCAGGACTTG 59.647 66.667 0.00 0.00 0.00 3.16
470 482 2.936032 GGAGGTGGGGCAGGACTT 60.936 66.667 0.00 0.00 0.00 3.01
486 498 2.366972 AGGGGATTGGACGAGGGG 60.367 66.667 0.00 0.00 0.00 4.79
517 529 2.367241 GCAATTTTACTTGGGTGGGTGT 59.633 45.455 0.00 0.00 0.00 4.16
518 530 2.366916 TGCAATTTTACTTGGGTGGGTG 59.633 45.455 0.00 0.00 0.00 4.61
519 531 2.683768 TGCAATTTTACTTGGGTGGGT 58.316 42.857 0.00 0.00 0.00 4.51
520 532 3.070878 ACTTGCAATTTTACTTGGGTGGG 59.929 43.478 0.00 0.00 0.00 4.61
521 533 4.306600 GACTTGCAATTTTACTTGGGTGG 58.693 43.478 0.00 0.00 0.00 4.61
522 534 4.306600 GGACTTGCAATTTTACTTGGGTG 58.693 43.478 0.00 0.00 0.00 4.61
541 553 5.305585 TCCTGCTGAAATTATTATCCGGAC 58.694 41.667 6.12 0.00 0.00 4.79
588 600 3.181417 TGGAGAAGAAGAAGGGAGAGTGA 60.181 47.826 0.00 0.00 0.00 3.41
596 608 1.981495 AGTGGGTGGAGAAGAAGAAGG 59.019 52.381 0.00 0.00 0.00 3.46
599 611 2.704190 AGAGTGGGTGGAGAAGAAGA 57.296 50.000 0.00 0.00 0.00 2.87
665 689 1.630333 ATGAGGGAGGGGGAGGAGA 60.630 63.158 0.00 0.00 0.00 3.71
670 694 0.192064 GATCTGATGAGGGAGGGGGA 59.808 60.000 0.00 0.00 0.00 4.81
672 696 1.643310 GAGATCTGATGAGGGAGGGG 58.357 60.000 0.00 0.00 0.00 4.79
673 697 1.149711 AGGAGATCTGATGAGGGAGGG 59.850 57.143 0.00 0.00 0.00 4.30
675 699 2.892852 GTGAGGAGATCTGATGAGGGAG 59.107 54.545 0.00 0.00 0.00 4.30
676 700 2.245806 TGTGAGGAGATCTGATGAGGGA 59.754 50.000 0.00 0.00 0.00 4.20
681 708 1.537776 GGCGTGTGAGGAGATCTGATG 60.538 57.143 0.00 0.00 0.00 3.07
718 745 0.758734 AAAGCTTCTGGGTTTTGGGC 59.241 50.000 0.00 0.00 42.12 5.36
719 746 2.036346 CTGAAAGCTTCTGGGTTTTGGG 59.964 50.000 0.00 0.00 44.39 4.12
757 792 2.518933 CCCACCGGTCAAAAGGGT 59.481 61.111 17.08 0.00 34.75 4.34
795 830 1.866853 GACCCGCTGCTTTTCTTGGG 61.867 60.000 5.16 5.16 42.50 4.12
835 870 0.482887 TCATCATCGCCCTCCTCCTA 59.517 55.000 0.00 0.00 0.00 2.94
836 871 0.178909 ATCATCATCGCCCTCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
837 872 0.036577 CATCATCATCGCCCTCCTCC 60.037 60.000 0.00 0.00 0.00 4.30
846 881 2.595977 CGACTTATCGCCATCATCATCG 59.404 50.000 0.00 0.00 42.43 3.84
879 914 4.299316 GCGACGGAATGATGCGGC 62.299 66.667 0.00 0.00 46.22 6.53
1125 1164 2.203788 TTCCTCAGCTCCACCGGT 60.204 61.111 0.00 0.00 0.00 5.28
1200 1239 0.755686 AGATCGGGCAGATGAAGACC 59.244 55.000 4.45 0.00 40.26 3.85
1555 1608 4.699522 GGTCACGGACTGGTGGGC 62.700 72.222 4.41 0.00 38.46 5.36
1908 1976 0.179062 AATTGAGCAGCTCTAGCCCG 60.179 55.000 23.15 0.00 43.38 6.13
2070 3708 3.708220 GAGAGCCGTCCTGCCTTCG 62.708 68.421 0.00 0.00 0.00 3.79
2094 3732 2.728817 GGTATCGTCCTCGGGCAG 59.271 66.667 0.00 0.00 37.69 4.85
2302 3940 1.081641 CGGTGCAAAGCTTGAGCAG 60.082 57.895 22.71 11.54 45.16 4.24
2413 4051 2.349886 GGAACTGCATCATCGACTCAAC 59.650 50.000 0.00 0.00 0.00 3.18
2444 4082 1.721664 CGGTCCAGATTACGCGAGGA 61.722 60.000 15.93 7.10 0.00 3.71
2489 4131 1.271054 ACACAGGTCTTCATCCAGCAC 60.271 52.381 0.00 0.00 0.00 4.40
2536 4178 2.685388 TGTCTTCAAATGACACCGCAAA 59.315 40.909 0.00 0.00 39.23 3.68
2541 4183 3.420893 TCCCATGTCTTCAAATGACACC 58.579 45.455 0.00 0.00 45.57 4.16
2657 4314 5.131784 ACCAAATTCACACCAATTTGCATT 58.868 33.333 11.52 0.00 46.11 3.56
2706 4363 3.849563 AACTGGCTGTACTTACCACAA 57.150 42.857 0.00 0.00 0.00 3.33
2767 4430 9.434420 CCACATTGCCAAAAATCTAAAATCTAA 57.566 29.630 0.00 0.00 0.00 2.10
2768 4431 8.040132 CCCACATTGCCAAAAATCTAAAATCTA 58.960 33.333 0.00 0.00 0.00 1.98
2769 4432 6.880529 CCCACATTGCCAAAAATCTAAAATCT 59.119 34.615 0.00 0.00 0.00 2.40
2770 4433 6.878389 TCCCACATTGCCAAAAATCTAAAATC 59.122 34.615 0.00 0.00 0.00 2.17
2805 4468 6.357367 AGAAAGAAAAGGAAGAACTACAGCA 58.643 36.000 0.00 0.00 0.00 4.41
2964 4633 5.630680 CCAAATTTGACTGGAGAATCAAACG 59.369 40.000 19.86 0.00 45.09 3.60
2977 4646 5.891551 AGTGTACACTTTCCCAAATTTGACT 59.108 36.000 22.95 7.26 38.83 3.41
2992 4661 3.904717 AGCTATAGGCAGAGTGTACACT 58.095 45.455 28.27 28.27 43.72 3.55
3002 4671 4.585162 AGTAGTGGTACAAGCTATAGGCAG 59.415 45.833 1.04 0.00 44.16 4.85
3096 4773 1.425428 GTGAGCAGAAATTCCGGCG 59.575 57.895 0.00 0.00 0.00 6.46
3117 4794 5.785243 ACATGCAGTAGATGAGATGAGATG 58.215 41.667 0.00 0.00 0.00 2.90
3118 4795 7.396623 TGATACATGCAGTAGATGAGATGAGAT 59.603 37.037 0.00 0.00 35.85 2.75
3119 4796 6.718454 TGATACATGCAGTAGATGAGATGAGA 59.282 38.462 0.00 0.00 35.85 3.27
3120 4797 6.921914 TGATACATGCAGTAGATGAGATGAG 58.078 40.000 0.00 0.00 35.85 2.90
3121 4798 6.906157 TGATACATGCAGTAGATGAGATGA 57.094 37.500 0.00 0.00 35.85 2.92
3122 4799 6.036191 GCATGATACATGCAGTAGATGAGATG 59.964 42.308 25.20 0.00 44.00 2.90
3147 4824 0.244994 AACTACAGCTGCGAGTGGAG 59.755 55.000 19.58 8.08 36.48 3.86
3231 4909 5.220854 GCCACAATCTACGTCAATTAAGCAT 60.221 40.000 0.00 0.00 0.00 3.79
3257 4935 2.430332 GAGGACCCTCTCTCATGTGAAG 59.570 54.545 8.76 0.63 39.80 3.02
3258 4936 2.461695 GAGGACCCTCTCTCATGTGAA 58.538 52.381 8.76 0.00 39.80 3.18
3260 4938 0.743688 CGAGGACCCTCTCTCATGTG 59.256 60.000 13.62 0.00 40.69 3.21
3261 4939 0.396417 CCGAGGACCCTCTCTCATGT 60.396 60.000 13.62 0.00 40.69 3.21
3262 4940 0.396417 ACCGAGGACCCTCTCTCATG 60.396 60.000 13.62 0.00 40.69 3.07
3263 4941 0.106419 GACCGAGGACCCTCTCTCAT 60.106 60.000 13.62 0.00 40.69 2.90
3264 4942 1.303615 GACCGAGGACCCTCTCTCA 59.696 63.158 13.62 0.00 40.69 3.27
3265 4943 1.454295 GGACCGAGGACCCTCTCTC 60.454 68.421 13.62 7.64 40.69 3.20
3347 5094 4.383552 GCATGACCCTATCCCTAAGCTATG 60.384 50.000 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.