Multiple sequence alignment - TraesCS5D01G206200

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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 TraesCS5D01G206200 chr5D 100.000 5588 0 0 1 5588 312441163 312435576 0.000000e+00 10320
1 TraesCS5D01G206200 chr5D 82.857 140 22 1 653 790 14396863 14397002 2.110000e-24 124
2 TraesCS5D01G206200 chr5A 94.447 2269 62 22 1 2229 406525761 406523517 0.000000e+00 3434
3 TraesCS5D01G206200 chr5A 92.511 2417 81 29 2251 4624 406523435 406521076 0.000000e+00 3369
4 TraesCS5D01G206200 chr5A 86.106 511 38 19 4630 5125 406521038 406520546 2.310000e-143 520
5 TraesCS5D01G206200 chr5A 94.502 291 6 4 5114 5399 406520378 406520093 1.850000e-119 440
6 TraesCS5D01G206200 chr5A 97.959 196 4 0 5393 5588 406520001 406519806 1.930000e-89 340
7 TraesCS5D01G206200 chr5B 90.909 2035 77 32 2633 4631 358816917 358814955 0.000000e+00 2634
8 TraesCS5D01G206200 chr5B 88.774 1452 70 46 857 2251 358818904 358817489 0.000000e+00 1692
9 TraesCS5D01G206200 chr5B 86.857 700 55 16 4630 5313 358814924 358814246 0.000000e+00 749
10 TraesCS5D01G206200 chr5B 92.537 402 14 7 2251 2636 358817440 358817039 3.780000e-156 562
11 TraesCS5D01G206200 chr5B 94.388 196 11 0 5393 5588 358811835 358811640 9.100000e-78 302
12 TraesCS5D01G206200 chr5B 96.512 86 2 1 5315 5399 358812011 358811926 2.100000e-29 141
13 TraesCS5D01G206200 chr5B 88.596 114 13 0 524 637 358819391 358819278 7.550000e-29 139
14 TraesCS5D01G206200 chr5B 84.286 140 12 8 40 179 358819386 358819257 1.630000e-25 128
15 TraesCS5D01G206200 chr4D 84.911 676 61 24 383 1020 274235128 274235800 0.000000e+00 645
16 TraesCS5D01G206200 chr4D 82.622 656 54 32 1019 1646 274235828 274236451 4.960000e-145 525
17 TraesCS5D01G206200 chr4A 84.148 675 66 24 383 1020 292833401 292832731 2.860000e-172 616
18 TraesCS5D01G206200 chr4A 88.000 100 9 1 1019 1118 292832703 292832607 1.270000e-21 115
19 TraesCS5D01G206200 chr3D 80.328 183 27 8 631 805 574859673 574859854 4.540000e-26 130
20 TraesCS5D01G206200 chr3D 80.000 190 23 11 635 815 436022172 436021989 5.880000e-25 126
21 TraesCS5D01G206200 chr6A 81.132 159 24 6 635 789 592012945 592012789 7.600000e-24 122
22 TraesCS5D01G206200 chr6A 78.857 175 30 7 632 802 614531719 614531890 1.650000e-20 111
23 TraesCS5D01G206200 chr2B 78.421 190 29 9 635 815 72827785 72827599 4.580000e-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 TraesCS5D01G206200 chr5D 312435576 312441163 5587 True 10320.000 10320 100.000000 1 5588 1 chr5D.!!$R1 5587
1 TraesCS5D01G206200 chr5A 406519806 406525761 5955 True 1620.600 3434 93.105000 1 5588 5 chr5A.!!$R1 5587
2 TraesCS5D01G206200 chr5B 358811640 358819391 7751 True 793.375 2634 90.357375 40 5588 8 chr5B.!!$R1 5548
3 TraesCS5D01G206200 chr4D 274235128 274236451 1323 False 585.000 645 83.766500 383 1646 2 chr4D.!!$F1 1263
4 TraesCS5D01G206200 chr4A 292832607 292833401 794 True 365.500 616 86.074000 383 1118 2 chr4A.!!$R1 735

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
735 737 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.0 31.08 2.57 F
1065 1365 0.246360 CCCACACATCGCTCACACTA 59.754 55.000 0.00 0.0 0.00 2.74 F
1781 2152 0.784778 GCGCGTATCAGATAACCAGC 59.215 55.000 8.43 0.0 0.00 4.85 F
2529 2999 1.360852 TGGGGCCAATGTTAAGATGGT 59.639 47.619 4.39 0.0 36.57 3.55 F
2827 3432 1.425066 TGTCCTTGCTTTGTGGATCCT 59.575 47.619 14.23 0.0 32.03 3.24 F
3667 4279 0.263172 TGGGTGGAAAGAGGGCAAAA 59.737 50.000 0.00 0.0 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2185 0.463654 AAAATAGCATCGGCCGAGCA 60.464 50.000 34.89 25.66 42.56 4.26 R
2676 3271 0.612732 TGGAGTCCGGAACCGTACAT 60.613 55.000 19.62 0.00 37.81 2.29 R
2677 3272 0.612732 ATGGAGTCCGGAACCGTACA 60.613 55.000 18.44 6.78 37.81 2.90 R
3655 4267 1.138859 GCTGTGGTTTTTGCCCTCTTT 59.861 47.619 0.00 0.00 0.00 2.52 R
4134 4770 2.641305 CATGGCTTCTTCTTCCCTCAG 58.359 52.381 0.00 0.00 0.00 3.35 R
4839 5514 0.044855 ATGTAGGAGGAGCCCAACCT 59.955 55.000 12.02 12.02 40.80 3.50 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
152 153 6.315642 TCCTACGACTGTAGTAGAAATCACTG 59.684 42.308 23.99 9.12 45.49 3.66
198 199 1.594518 CCGCGTTTCAGACACAACTTG 60.595 52.381 4.92 0.00 0.00 3.16
298 299 7.039313 AGATGTTGACACCTCTTTTAAAACC 57.961 36.000 0.00 0.00 0.00 3.27
735 737 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
749 763 2.832129 CTCATAGGTGTAGGGTGTGTGT 59.168 50.000 0.00 0.00 0.00 3.72
1065 1365 0.246360 CCCACACATCGCTCACACTA 59.754 55.000 0.00 0.00 0.00 2.74
1066 1366 1.633561 CCACACATCGCTCACACTAG 58.366 55.000 0.00 0.00 0.00 2.57
1067 1367 1.067565 CCACACATCGCTCACACTAGT 60.068 52.381 0.00 0.00 0.00 2.57
1070 1370 3.127030 CACACATCGCTCACACTAGTAGA 59.873 47.826 3.59 0.00 0.00 2.59
1087 1387 1.659954 GAGCGCGGCTACTCATCTG 60.660 63.158 8.83 0.00 39.88 2.90
1307 1610 4.457496 CACCACCGCCGAGCAGAT 62.457 66.667 0.00 0.00 0.00 2.90
1469 1790 1.639298 GCCGACTCTGTTGCATGGAC 61.639 60.000 0.00 0.00 0.00 4.02
1494 1815 4.763073 TCAAGGTGACATAGATGAGCTTG 58.237 43.478 13.15 13.15 39.47 4.01
1723 2074 4.619227 CGCCACGTCACCAACCCT 62.619 66.667 0.00 0.00 0.00 4.34
1724 2075 2.668550 GCCACGTCACCAACCCTC 60.669 66.667 0.00 0.00 0.00 4.30
1725 2076 2.825982 CCACGTCACCAACCCTCA 59.174 61.111 0.00 0.00 0.00 3.86
1726 2077 1.147376 CCACGTCACCAACCCTCAA 59.853 57.895 0.00 0.00 0.00 3.02
1781 2152 0.784778 GCGCGTATCAGATAACCAGC 59.215 55.000 8.43 0.00 0.00 4.85
1785 2156 3.458189 GCGTATCAGATAACCAGCTTGT 58.542 45.455 0.00 0.00 0.00 3.16
1829 2200 1.826487 TAGTGCTCGGCCGATGCTA 60.826 57.895 33.81 27.98 37.74 3.49
1869 2242 6.494893 AAAAGAAAAGTTTTGGAAGTTGGC 57.505 33.333 5.36 0.00 0.00 4.52
1981 2354 3.254411 TGTGGATTTGTTTATGCGCTCAA 59.746 39.130 9.73 0.00 0.00 3.02
1982 2355 3.853671 GTGGATTTGTTTATGCGCTCAAG 59.146 43.478 9.73 0.00 0.00 3.02
1983 2356 3.755905 TGGATTTGTTTATGCGCTCAAGA 59.244 39.130 9.73 0.00 0.00 3.02
1984 2357 4.098416 GGATTTGTTTATGCGCTCAAGAC 58.902 43.478 9.73 1.62 0.00 3.01
2368 2825 2.561419 GTTCAGTGTGGGAGCTACAGTA 59.439 50.000 0.00 0.00 30.88 2.74
2370 2827 2.041216 TCAGTGTGGGAGCTACAGTAGA 59.959 50.000 12.15 0.00 30.88 2.59
2404 2861 3.181506 GGCGTCACTCCATGATTTCTTTC 60.182 47.826 0.00 0.00 40.28 2.62
2413 2870 8.404000 CACTCCATGATTTCTTTCAAGGATTAG 58.596 37.037 0.00 0.00 41.31 1.73
2415 2872 8.284945 TCCATGATTTCTTTCAAGGATTAGTG 57.715 34.615 0.00 0.00 38.29 2.74
2470 2940 9.339850 GATGATATGCTAGCTGAATAATCCAAT 57.660 33.333 17.23 0.00 0.00 3.16
2529 2999 1.360852 TGGGGCCAATGTTAAGATGGT 59.639 47.619 4.39 0.00 36.57 3.55
2536 3006 6.459923 GGCCAATGTTAAGATGGTAAACAAA 58.540 36.000 0.00 0.00 36.75 2.83
2682 3277 6.192360 GCCTTCAGCAAACTATTTATGTACG 58.808 40.000 0.00 0.00 42.97 3.67
2684 3279 6.315393 CCTTCAGCAAACTATTTATGTACGGT 59.685 38.462 0.00 0.00 0.00 4.83
2686 3281 7.298507 TCAGCAAACTATTTATGTACGGTTC 57.701 36.000 0.00 0.00 0.00 3.62
2687 3282 6.314400 TCAGCAAACTATTTATGTACGGTTCC 59.686 38.462 0.00 0.00 0.00 3.62
2689 3284 5.502869 GCAAACTATTTATGTACGGTTCCGG 60.503 44.000 15.66 0.00 0.00 5.14
2691 3286 4.936891 ACTATTTATGTACGGTTCCGGAC 58.063 43.478 18.43 18.43 43.00 4.79
2692 3287 4.646492 ACTATTTATGTACGGTTCCGGACT 59.354 41.667 24.11 13.76 43.10 3.85
2693 3288 3.508744 TTTATGTACGGTTCCGGACTC 57.491 47.619 24.11 0.00 43.10 3.36
2765 3365 9.283768 TGTTTGCTCATAAAAGAACAAGAGATA 57.716 29.630 0.00 0.00 0.00 1.98
2784 3384 5.583495 AGATAGATCGTGCTACAAGAACAC 58.417 41.667 0.00 0.00 0.00 3.32
2816 3421 6.054860 AGTGTTACATTATCTGTCCTTGCT 57.945 37.500 0.00 0.00 39.39 3.91
2817 3422 6.476378 AGTGTTACATTATCTGTCCTTGCTT 58.524 36.000 0.00 0.00 39.39 3.91
2818 3423 6.942576 AGTGTTACATTATCTGTCCTTGCTTT 59.057 34.615 0.00 0.00 39.39 3.51
2819 3424 7.023575 GTGTTACATTATCTGTCCTTGCTTTG 58.976 38.462 0.00 0.00 39.39 2.77
2820 3425 6.714810 TGTTACATTATCTGTCCTTGCTTTGT 59.285 34.615 0.00 0.00 39.39 2.83
2821 3426 5.633830 ACATTATCTGTCCTTGCTTTGTG 57.366 39.130 0.00 0.00 29.94 3.33
2822 3427 4.460382 ACATTATCTGTCCTTGCTTTGTGG 59.540 41.667 0.00 0.00 29.94 4.17
2823 3428 2.957402 ATCTGTCCTTGCTTTGTGGA 57.043 45.000 0.00 0.00 0.00 4.02
2824 3429 2.957402 TCTGTCCTTGCTTTGTGGAT 57.043 45.000 0.00 0.00 32.03 3.41
2825 3430 2.783135 TCTGTCCTTGCTTTGTGGATC 58.217 47.619 0.00 0.00 32.03 3.36
2826 3431 1.815003 CTGTCCTTGCTTTGTGGATCC 59.185 52.381 4.20 4.20 32.03 3.36
2827 3432 1.425066 TGTCCTTGCTTTGTGGATCCT 59.575 47.619 14.23 0.00 32.03 3.24
2828 3433 2.158475 TGTCCTTGCTTTGTGGATCCTT 60.158 45.455 14.23 0.00 32.03 3.36
2829 3434 2.229784 GTCCTTGCTTTGTGGATCCTTG 59.770 50.000 14.23 0.00 32.03 3.61
2830 3435 2.158475 TCCTTGCTTTGTGGATCCTTGT 60.158 45.455 14.23 0.00 0.00 3.16
3150 3759 3.112709 GTCCTCACGGCGCTCAAC 61.113 66.667 6.90 0.00 0.00 3.18
3258 3867 2.625823 CGCCCGAGCCACACAAATT 61.626 57.895 0.00 0.00 34.57 1.82
3270 3879 4.031652 GCCACACAAATTATTTTAGCTGCG 59.968 41.667 0.00 0.00 0.00 5.18
3514 4126 4.357325 AGCAGAGGTAAGAGAAGGATCAA 58.643 43.478 0.00 0.00 0.00 2.57
3515 4127 4.161377 AGCAGAGGTAAGAGAAGGATCAAC 59.839 45.833 0.00 0.00 0.00 3.18
3516 4128 4.161377 GCAGAGGTAAGAGAAGGATCAACT 59.839 45.833 0.00 0.00 0.00 3.16
3517 4129 5.337975 GCAGAGGTAAGAGAAGGATCAACTT 60.338 44.000 0.00 0.00 0.00 2.66
3518 4130 6.337356 CAGAGGTAAGAGAAGGATCAACTTC 58.663 44.000 4.11 4.11 45.59 3.01
3526 4138 4.008074 GAAGGATCAACTTCTGACCACA 57.992 45.455 0.00 0.00 42.73 4.17
3527 4139 3.692257 AGGATCAACTTCTGACCACAG 57.308 47.619 0.00 0.00 44.66 3.66
3541 4153 2.017049 ACCACAGAAACTTCAGCACAC 58.983 47.619 0.00 0.00 0.00 3.82
3576 4188 6.861065 AAATCGTGATCAAGTTGTGTAAGT 57.139 33.333 8.54 0.00 0.00 2.24
3577 4189 7.956420 AAATCGTGATCAAGTTGTGTAAGTA 57.044 32.000 8.54 0.00 0.00 2.24
3578 4190 7.956420 AATCGTGATCAAGTTGTGTAAGTAA 57.044 32.000 8.54 0.00 0.00 2.24
3582 4194 7.115805 TCGTGATCAAGTTGTGTAAGTAACATC 59.884 37.037 8.54 0.00 41.10 3.06
3583 4195 7.095816 CGTGATCAAGTTGTGTAAGTAACATCA 60.096 37.037 0.00 0.00 41.10 3.07
3655 4267 3.957586 CAGCAGCTGGTGGGTGGA 61.958 66.667 33.27 0.00 43.02 4.02
3665 4277 1.152830 GTGGGTGGAAAGAGGGCAA 59.847 57.895 0.00 0.00 0.00 4.52
3666 4278 0.469144 GTGGGTGGAAAGAGGGCAAA 60.469 55.000 0.00 0.00 0.00 3.68
3667 4279 0.263172 TGGGTGGAAAGAGGGCAAAA 59.737 50.000 0.00 0.00 0.00 2.44
3670 4282 1.070134 GGTGGAAAGAGGGCAAAAACC 59.930 52.381 0.00 0.00 0.00 3.27
3671 4283 1.760029 GTGGAAAGAGGGCAAAAACCA 59.240 47.619 0.00 0.00 0.00 3.67
3852 4464 3.806645 TTTTTGGGGGAGGGGGTT 58.193 55.556 0.00 0.00 0.00 4.11
3979 4595 2.694760 GCTCTTCCTTGCTTGGCCG 61.695 63.158 0.00 0.00 0.00 6.13
3996 4612 2.980233 GTGCTATCATGGCGGCCC 60.980 66.667 17.97 0.00 0.00 5.80
4034 4652 5.825532 TGTGAAGGATGTGGGAAATATCAA 58.174 37.500 0.00 0.00 0.00 2.57
4134 4770 5.936372 TGCAGAGGATACATTGATTAGATGC 59.064 40.000 0.00 0.00 41.41 3.91
4323 4959 0.396695 TGGTAGTAGGGGCCTTCTCG 60.397 60.000 0.84 0.00 0.00 4.04
4416 5055 6.030548 TGTTGATGTTACTGAAGAGAGAGG 57.969 41.667 0.00 0.00 0.00 3.69
4472 5111 2.959484 GCTAGTGTGCTGCCCTGGA 61.959 63.158 0.00 0.00 0.00 3.86
4549 5188 4.274978 GGGCCCTTGCTATTTGTACTTTA 58.725 43.478 17.04 0.00 37.74 1.85
4575 5214 8.761575 TTTTTCCATCATCAGCAATAAAAGAC 57.238 30.769 0.00 0.00 0.00 3.01
4628 5269 3.321396 TGTGAGAATTTCCATGCTTTGCA 59.679 39.130 0.00 0.00 44.86 4.08
4693 5366 5.391950 GGTGTGTACATTGTCAGCCTAATTG 60.392 44.000 0.00 0.00 0.00 2.32
4694 5367 4.699735 TGTGTACATTGTCAGCCTAATTGG 59.300 41.667 0.00 0.00 39.35 3.16
4792 5467 4.950475 TCCCAACATGTCAAACAAGTAACA 59.050 37.500 0.00 0.00 29.04 2.41
4798 5473 9.295214 CAACATGTCAAACAAGTAACAATACAA 57.705 29.630 0.00 0.00 29.04 2.41
4818 5493 8.975410 ATACAACATCACATGATTGTTGAAAG 57.025 30.769 29.19 14.75 41.07 2.62
4821 5496 3.940209 TCACATGATTGTTGAAAGCCC 57.060 42.857 0.00 0.00 32.34 5.19
4822 5497 2.228582 TCACATGATTGTTGAAAGCCCG 59.771 45.455 0.00 0.00 32.34 6.13
4825 5500 3.823873 ACATGATTGTTGAAAGCCCGTTA 59.176 39.130 0.00 0.00 29.55 3.18
4830 5505 7.490962 TGATTGTTGAAAGCCCGTTATATAG 57.509 36.000 0.00 0.00 0.00 1.31
4832 5507 8.205512 TGATTGTTGAAAGCCCGTTATATAGTA 58.794 33.333 0.00 0.00 0.00 1.82
4833 5508 9.216117 GATTGTTGAAAGCCCGTTATATAGTAT 57.784 33.333 0.00 0.00 0.00 2.12
4835 5510 8.373048 TGTTGAAAGCCCGTTATATAGTATTG 57.627 34.615 0.00 0.00 0.00 1.90
4839 5514 7.235193 TGAAAGCCCGTTATATAGTATTGGGTA 59.765 37.037 0.00 0.00 37.49 3.69
4840 5515 6.786967 AGCCCGTTATATAGTATTGGGTAG 57.213 41.667 0.00 0.00 37.49 3.18
4842 5517 5.423290 GCCCGTTATATAGTATTGGGTAGGT 59.577 44.000 0.00 0.00 37.49 3.08
4847 5522 5.774102 ATATAGTATTGGGTAGGTTGGGC 57.226 43.478 0.00 0.00 0.00 5.36
4848 5523 1.981259 AGTATTGGGTAGGTTGGGCT 58.019 50.000 0.00 0.00 0.00 5.19
4868 5543 3.126831 CTCCTCCTACATGCTTAAAGCG 58.873 50.000 0.00 0.00 46.26 4.68
4900 5575 5.977635 AGTAGACATGCATTGCAAGTAGTA 58.022 37.500 18.50 10.96 40.58 1.82
4901 5576 6.586344 AGTAGACATGCATTGCAAGTAGTAT 58.414 36.000 18.50 12.62 40.58 2.12
4939 5618 6.099557 ACATCCATTTTCTTCCCAACAAGAAA 59.900 34.615 4.60 4.60 46.18 2.52
4948 5627 8.704849 TTCTTCCCAACAAGAAAGAATTATCA 57.295 30.769 0.00 0.00 39.06 2.15
4950 5629 9.312904 TCTTCCCAACAAGAAAGAATTATCAAT 57.687 29.630 0.00 0.00 29.01 2.57
4952 5631 9.927668 TTCCCAACAAGAAAGAATTATCAATTC 57.072 29.630 3.89 3.89 45.98 2.17
4967 5646 9.590451 AATTATCAATTCAACCAATGTGACATC 57.410 29.630 0.00 0.00 0.00 3.06
4983 5662 4.151335 GTGACATCATAATGCTCTAAGCCG 59.849 45.833 0.00 0.00 41.51 5.52
4987 5666 2.897326 TCATAATGCTCTAAGCCGCCTA 59.103 45.455 0.00 0.00 41.51 3.93
4990 5669 0.106894 ATGCTCTAAGCCGCCTAACC 59.893 55.000 0.00 0.00 41.51 2.85
4993 5672 0.674534 CTCTAAGCCGCCTAACCGAT 59.325 55.000 0.00 0.00 0.00 4.18
5102 5789 1.077501 CATGGTGGTGCAGGGTAGG 60.078 63.158 0.00 0.00 0.00 3.18
5141 6007 1.443852 TATCCCTGCCATGCCACATA 58.556 50.000 0.00 0.00 0.00 2.29
5142 6008 0.111832 ATCCCTGCCATGCCACATAG 59.888 55.000 0.00 0.00 0.00 2.23
5143 6009 1.529948 CCCTGCCATGCCACATAGG 60.530 63.158 0.00 0.00 41.84 2.57
5144 6010 1.533219 CCTGCCATGCCACATAGGA 59.467 57.895 0.00 0.00 41.22 2.94
5236 6106 3.359950 GCTTTCAGGAATCATTGGAGGT 58.640 45.455 0.00 0.00 0.00 3.85
5238 6108 4.338879 CTTTCAGGAATCATTGGAGGTGT 58.661 43.478 0.00 0.00 0.00 4.16
5524 8726 1.153756 AGGTGCCTTTTGACAGGGG 59.846 57.895 0.00 0.00 34.01 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.805175 ACACATGAATCTAATGACAAAAATCCA 58.195 29.630 0.00 0.00 0.00 3.41
145 146 2.885135 TCCAGTGGAATGCAGTGATT 57.115 45.000 10.20 0.00 0.00 2.57
198 199 2.480610 CCCACGTGCCATGTATGCC 61.481 63.158 10.91 0.00 0.00 4.40
735 737 1.675552 AGCAAACACACACCCTACAC 58.324 50.000 0.00 0.00 0.00 2.90
1065 1365 0.820074 ATGAGTAGCCGCGCTCTACT 60.820 55.000 27.91 27.91 46.67 2.57
1066 1366 0.386226 GATGAGTAGCCGCGCTCTAC 60.386 60.000 21.63 21.63 40.44 2.59
1067 1367 0.535328 AGATGAGTAGCCGCGCTCTA 60.535 55.000 5.56 3.80 40.44 2.43
1070 1370 1.101635 TACAGATGAGTAGCCGCGCT 61.102 55.000 5.56 4.15 43.41 5.92
1087 1387 0.105778 GGAGCTGAGATGGTGGCTAC 59.894 60.000 0.00 0.00 35.01 3.58
1306 1609 4.101448 GGAGCACCAGCCACCGAT 62.101 66.667 0.00 0.00 43.56 4.18
1458 1779 1.421268 ACCTTGAGAGTCCATGCAACA 59.579 47.619 0.00 0.00 0.00 3.33
1469 1790 4.341806 AGCTCATCTATGTCACCTTGAGAG 59.658 45.833 0.00 0.00 34.00 3.20
1494 1815 2.234414 ACATGCACCATCCAATCCAAAC 59.766 45.455 0.00 0.00 0.00 2.93
1723 2074 2.998316 TGGTGAGATGTGTGTGTTGA 57.002 45.000 0.00 0.00 0.00 3.18
1724 2075 2.880268 ACATGGTGAGATGTGTGTGTTG 59.120 45.455 0.00 0.00 35.17 3.33
1725 2076 3.141398 GACATGGTGAGATGTGTGTGTT 58.859 45.455 0.00 0.00 36.67 3.32
1726 2077 2.104622 TGACATGGTGAGATGTGTGTGT 59.895 45.455 0.00 0.00 36.67 3.72
1781 2152 2.349886 GGCGAAAGATACAGAGCACAAG 59.650 50.000 0.00 0.00 0.00 3.16
1785 2156 2.554142 CATGGCGAAAGATACAGAGCA 58.446 47.619 0.00 0.00 0.00 4.26
1814 2185 0.463654 AAAATAGCATCGGCCGAGCA 60.464 50.000 34.89 25.66 42.56 4.26
1981 2354 1.333177 AAAGACCGCTCTGTCTGTCT 58.667 50.000 1.78 0.00 44.68 3.41
1982 2355 1.795286 CAAAAGACCGCTCTGTCTGTC 59.205 52.381 1.78 0.00 44.68 3.51
1983 2356 1.541233 CCAAAAGACCGCTCTGTCTGT 60.541 52.381 1.78 0.00 44.68 3.41
1984 2357 1.151668 CCAAAAGACCGCTCTGTCTG 58.848 55.000 1.78 0.00 44.68 3.51
2229 2621 8.175716 GCTTTGTAAATAAACTACTACTGCTGG 58.824 37.037 0.00 0.00 0.00 4.85
2344 2798 1.066787 GTAGCTCCCACACTGAACTCC 60.067 57.143 0.00 0.00 0.00 3.85
2368 2825 2.827190 CGCCAGCATGCCATGTCT 60.827 61.111 15.66 1.27 31.97 3.41
2370 2827 3.136123 GACGCCAGCATGCCATGT 61.136 61.111 15.66 8.19 31.97 3.21
2404 2861 4.651778 TCACTTGGAACCACTAATCCTTG 58.348 43.478 0.00 0.00 36.64 3.61
2413 2870 6.527057 AGTAGTAGTATCACTTGGAACCAC 57.473 41.667 0.00 0.00 0.00 4.16
2415 2872 8.569641 CATCTAGTAGTAGTATCACTTGGAACC 58.430 40.741 4.51 0.00 0.00 3.62
2470 2940 4.124970 GAGATATGCAGTCACATCAGCAA 58.875 43.478 0.00 0.00 40.76 3.91
2536 3006 8.174085 ACTAGGAGAGTGATATTATAAGCCTGT 58.826 37.037 0.00 0.00 36.87 4.00
2676 3271 0.612732 TGGAGTCCGGAACCGTACAT 60.613 55.000 19.62 0.00 37.81 2.29
2677 3272 0.612732 ATGGAGTCCGGAACCGTACA 60.613 55.000 18.44 6.78 37.81 2.90
2678 3273 1.392589 TATGGAGTCCGGAACCGTAC 58.607 55.000 20.33 6.68 37.81 3.67
2679 3274 2.369983 ATATGGAGTCCGGAACCGTA 57.630 50.000 24.03 24.03 37.81 4.02
2680 3275 1.959282 GTATATGGAGTCCGGAACCGT 59.041 52.381 21.95 21.95 37.81 4.83
2681 3276 1.958579 TGTATATGGAGTCCGGAACCG 59.041 52.381 19.62 6.25 39.44 4.44
2682 3277 2.963782 AGTGTATATGGAGTCCGGAACC 59.036 50.000 18.59 18.59 0.00 3.62
2684 3279 4.283337 TCAAGTGTATATGGAGTCCGGAA 58.717 43.478 5.23 0.00 0.00 4.30
2686 3281 4.873746 ATCAAGTGTATATGGAGTCCGG 57.126 45.455 4.30 0.00 0.00 5.14
2687 3282 7.385205 CCTTAAATCAAGTGTATATGGAGTCCG 59.615 40.741 4.30 0.00 31.77 4.79
2689 3284 9.832445 TTCCTTAAATCAAGTGTATATGGAGTC 57.168 33.333 0.00 0.00 31.77 3.36
2765 3365 3.660501 TGTGTTCTTGTAGCACGATCT 57.339 42.857 0.00 0.00 41.88 2.75
2797 3397 6.150976 CCACAAAGCAAGGACAGATAATGTAA 59.849 38.462 0.00 0.00 44.17 2.41
2816 3421 3.565307 AGCTGAAACAAGGATCCACAAA 58.435 40.909 15.82 0.00 0.00 2.83
2817 3422 3.228188 AGCTGAAACAAGGATCCACAA 57.772 42.857 15.82 0.00 0.00 3.33
2818 3423 2.957402 AGCTGAAACAAGGATCCACA 57.043 45.000 15.82 3.38 0.00 4.17
2819 3424 8.677148 TTAATATAGCTGAAACAAGGATCCAC 57.323 34.615 15.82 0.00 0.00 4.02
2820 3425 9.866655 AATTAATATAGCTGAAACAAGGATCCA 57.133 29.630 15.82 0.00 0.00 3.41
2822 3427 9.617975 GCAATTAATATAGCTGAAACAAGGATC 57.382 33.333 0.00 0.00 0.00 3.36
2823 3428 9.135189 TGCAATTAATATAGCTGAAACAAGGAT 57.865 29.630 0.00 0.00 0.00 3.24
2824 3429 8.518430 TGCAATTAATATAGCTGAAACAAGGA 57.482 30.769 0.00 0.00 0.00 3.36
2825 3430 8.408601 ACTGCAATTAATATAGCTGAAACAAGG 58.591 33.333 15.99 0.00 0.00 3.61
2826 3431 9.229784 CACTGCAATTAATATAGCTGAAACAAG 57.770 33.333 15.99 5.07 0.00 3.16
2827 3432 8.739039 ACACTGCAATTAATATAGCTGAAACAA 58.261 29.630 15.99 0.00 0.00 2.83
2828 3433 8.279970 ACACTGCAATTAATATAGCTGAAACA 57.720 30.769 15.99 0.00 0.00 2.83
2829 3434 9.573133 AAACACTGCAATTAATATAGCTGAAAC 57.427 29.630 15.99 0.00 0.00 2.78
2830 3435 9.571810 CAAACACTGCAATTAATATAGCTGAAA 57.428 29.630 15.99 0.00 0.00 2.69
3067 3676 9.015367 GTATCTTGTGCTCTCTATCTACCAATA 57.985 37.037 0.00 0.00 0.00 1.90
3073 3682 8.932434 AAGATGTATCTTGTGCTCTCTATCTA 57.068 34.615 6.33 0.00 44.91 1.98
3150 3759 2.835431 ACCGATCGGAGCCTCCAG 60.835 66.667 39.55 10.90 35.91 3.86
3258 3867 9.884636 AATATACCATGTATCGCAGCTAAAATA 57.115 29.630 0.00 0.00 0.00 1.40
3503 4115 4.249661 GTGGTCAGAAGTTGATCCTTCTC 58.750 47.826 10.33 2.84 46.34 2.87
3505 4117 3.999663 CTGTGGTCAGAAGTTGATCCTTC 59.000 47.826 4.11 4.11 43.76 3.46
3518 4130 2.289002 GTGCTGAAGTTTCTGTGGTCAG 59.711 50.000 0.00 0.00 42.54 3.51
3519 4131 2.288666 GTGCTGAAGTTTCTGTGGTCA 58.711 47.619 1.59 0.00 0.00 4.02
3520 4132 2.032178 GTGTGCTGAAGTTTCTGTGGTC 59.968 50.000 1.59 0.00 0.00 4.02
3521 4133 2.017049 GTGTGCTGAAGTTTCTGTGGT 58.983 47.619 1.59 0.00 0.00 4.16
3522 4134 2.032550 CAGTGTGCTGAAGTTTCTGTGG 59.967 50.000 0.00 0.00 45.28 4.17
3523 4135 3.329743 CAGTGTGCTGAAGTTTCTGTG 57.670 47.619 0.00 0.00 45.28 3.66
3541 4153 8.873830 ACTTGATCACGATTTATAACTTGTCAG 58.126 33.333 6.16 0.00 0.00 3.51
3553 4165 6.861065 ACTTACACAACTTGATCACGATTT 57.139 33.333 6.16 0.00 0.00 2.17
3557 4169 6.519353 TGTTACTTACACAACTTGATCACG 57.481 37.500 0.00 0.00 0.00 4.35
3655 4267 1.138859 GCTGTGGTTTTTGCCCTCTTT 59.861 47.619 0.00 0.00 0.00 2.52
3665 4277 2.723746 CGCTGCTGCTGTGGTTTT 59.276 55.556 14.03 0.00 36.97 2.43
3666 4278 3.289834 CCGCTGCTGCTGTGGTTT 61.290 61.111 25.42 0.00 36.97 3.27
3671 4283 3.535629 TAACTGCCGCTGCTGCTGT 62.536 57.895 19.58 19.58 41.82 4.40
3979 4595 2.980233 GGGCCGCCATGATAGCAC 60.980 66.667 12.58 0.00 0.00 4.40
3996 4612 4.694233 ACAGACTGGCAGCGCAGG 62.694 66.667 15.89 1.51 0.00 4.85
4034 4652 4.044065 TCTCTCTGACCCTCTCTCTTTCTT 59.956 45.833 0.00 0.00 0.00 2.52
4134 4770 2.641305 CATGGCTTCTTCTTCCCTCAG 58.359 52.381 0.00 0.00 0.00 3.35
4323 4959 8.861834 CATGAATATGAACAGAGCTTGGCAGC 62.862 46.154 0.00 1.36 40.51 5.25
4395 5033 4.467795 CCCCTCTCTCTTCAGTAACATCAA 59.532 45.833 0.00 0.00 0.00 2.57
4398 5036 3.379452 CCCCCTCTCTCTTCAGTAACAT 58.621 50.000 0.00 0.00 0.00 2.71
4472 5111 6.125029 CCTGGAGATGGACAAATATTTCACT 58.875 40.000 0.00 0.00 0.00 3.41
4549 5188 9.374838 GTCTTTTATTGCTGATGATGGAAAAAT 57.625 29.630 0.00 0.00 0.00 1.82
4628 5269 9.971922 CTGTTTGAAAAATAAGAGGAACAGAAT 57.028 29.630 7.00 0.00 43.11 2.40
4693 5366 4.498177 GCACTTTCTGACTTTCAGTTTCCC 60.498 45.833 3.19 0.00 44.58 3.97
4694 5367 4.498177 GGCACTTTCTGACTTTCAGTTTCC 60.498 45.833 3.19 0.00 44.58 3.13
4792 5467 9.414295 CTTTCAACAATCATGTGATGTTGTATT 57.586 29.630 25.43 3.73 40.46 1.89
4798 5473 4.322198 GGGCTTTCAACAATCATGTGATGT 60.322 41.667 0.00 0.00 40.46 3.06
4818 5493 5.423290 ACCTACCCAATACTATATAACGGGC 59.577 44.000 0.00 0.00 35.49 6.13
4821 5496 7.325694 CCCAACCTACCCAATACTATATAACG 58.674 42.308 0.00 0.00 0.00 3.18
4822 5497 7.037802 AGCCCAACCTACCCAATACTATATAAC 60.038 40.741 0.00 0.00 0.00 1.89
4825 5500 5.421356 AGCCCAACCTACCCAATACTATAT 58.579 41.667 0.00 0.00 0.00 0.86
4830 5505 1.133884 GGAGCCCAACCTACCCAATAC 60.134 57.143 0.00 0.00 0.00 1.89
4832 5507 0.552615 AGGAGCCCAACCTACCCAAT 60.553 55.000 0.00 0.00 35.84 3.16
4833 5508 1.151677 AGGAGCCCAACCTACCCAA 60.152 57.895 0.00 0.00 35.84 4.12
4835 5510 2.376165 GGAGGAGCCCAACCTACCC 61.376 68.421 0.00 0.00 37.93 3.69
4839 5514 0.044855 ATGTAGGAGGAGCCCAACCT 59.955 55.000 12.02 12.02 40.80 3.50
4840 5515 0.181350 CATGTAGGAGGAGCCCAACC 59.819 60.000 0.00 0.00 37.37 3.77
4842 5517 0.621571 AGCATGTAGGAGGAGCCCAA 60.622 55.000 0.00 0.00 37.37 4.12
4847 5522 3.126831 CGCTTTAAGCATGTAGGAGGAG 58.873 50.000 17.51 0.00 42.58 3.69
4848 5523 2.741878 GCGCTTTAAGCATGTAGGAGGA 60.742 50.000 17.51 0.00 42.58 3.71
4868 5543 3.526931 TGCATGTCTACTTCCTACAGC 57.473 47.619 0.00 0.00 0.00 4.40
4900 5575 6.906157 AAATGGATGTGAAGTCAAGTCAAT 57.094 33.333 0.00 0.00 0.00 2.57
4901 5576 6.547141 AGAAAATGGATGTGAAGTCAAGTCAA 59.453 34.615 0.00 0.00 0.00 3.18
4908 5587 4.766891 TGGGAAGAAAATGGATGTGAAGTC 59.233 41.667 0.00 0.00 0.00 3.01
4913 5592 4.870123 TGTTGGGAAGAAAATGGATGTG 57.130 40.909 0.00 0.00 0.00 3.21
4939 5618 8.805175 TGTCACATTGGTTGAATTGATAATTCT 58.195 29.630 13.53 0.00 45.85 2.40
4940 5619 8.984891 TGTCACATTGGTTGAATTGATAATTC 57.015 30.769 7.21 7.21 45.86 2.17
4942 5621 8.751242 TGATGTCACATTGGTTGAATTGATAAT 58.249 29.630 0.00 0.00 0.00 1.28
4943 5622 8.120140 TGATGTCACATTGGTTGAATTGATAA 57.880 30.769 0.00 0.00 0.00 1.75
4944 5623 7.700022 TGATGTCACATTGGTTGAATTGATA 57.300 32.000 0.00 0.00 0.00 2.15
4946 5625 6.593268 ATGATGTCACATTGGTTGAATTGA 57.407 33.333 0.00 0.00 0.00 2.57
4948 5627 7.493320 GCATTATGATGTCACATTGGTTGAATT 59.507 33.333 0.00 0.00 35.63 2.17
4950 5629 6.153170 AGCATTATGATGTCACATTGGTTGAA 59.847 34.615 0.00 0.00 35.63 2.69
4952 5631 5.898174 AGCATTATGATGTCACATTGGTTG 58.102 37.500 0.00 0.00 35.63 3.77
4955 5634 7.500720 TTAGAGCATTATGATGTCACATTGG 57.499 36.000 0.00 0.00 35.63 3.16
4958 5637 5.704515 GGCTTAGAGCATTATGATGTCACAT 59.295 40.000 0.00 0.00 44.75 3.21
4960 5639 4.151335 CGGCTTAGAGCATTATGATGTCAC 59.849 45.833 0.00 0.00 44.75 3.67
4967 5646 2.175878 AGGCGGCTTAGAGCATTATG 57.824 50.000 5.25 0.00 44.75 1.90
4983 5662 4.802999 ACGCTAATAACTATCGGTTAGGC 58.197 43.478 0.00 0.00 42.74 3.93
4987 5666 9.918630 ATTAATGTACGCTAATAACTATCGGTT 57.081 29.630 0.00 0.00 41.54 4.44
4993 5672 9.622004 GAGCAGATTAATGTACGCTAATAACTA 57.378 33.333 0.00 0.00 0.00 2.24
5109 5796 9.003658 GCATGGCAGGGATATATATACATTTAC 57.996 37.037 7.27 0.00 0.00 2.01
5112 5799 6.103057 TGGCATGGCAGGGATATATATACATT 59.897 38.462 19.43 0.00 0.00 2.71
5171 6041 5.237996 CCACTGTTATGAATGCATGAGTAGG 59.762 44.000 0.00 0.00 35.94 3.18
5236 6106 3.028130 TGTGACCAACTGTCTCTGTACA 58.972 45.455 0.00 0.00 44.75 2.90
5238 6108 4.152647 AGATGTGACCAACTGTCTCTGTA 58.847 43.478 0.00 0.00 44.75 2.74
5524 8726 4.657013 AGAAAGACTTCCCAAGATCCAAC 58.343 43.478 0.00 0.00 31.28 3.77


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

AutoCloner maintained by Alex Coulton.