Multiple sequence alignment - TraesCS7A01G204900

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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 TraesCS7A01G204900 chr7A 100.000 3791 0 0 1 3791 167160651 167164441 0.000000e+00 7001.0
1 TraesCS7A01G204900 chr7A 100.000 29 0 0 1 29 306218948 306218976 2.000000e-03 54.7
2 TraesCS7A01G204900 chr7D 90.873 3265 171 51 581 3791 165480798 165483989 0.000000e+00 4261.0
3 TraesCS7A01G204900 chr7D 88.832 582 46 16 10 582 165479052 165479623 0.000000e+00 697.0
4 TraesCS7A01G204900 chr7D 88.278 273 31 1 3463 3735 165506869 165507140 3.650000e-85 326.0
5 TraesCS7A01G204900 chr7D 87.755 98 7 3 2596 2688 165482885 165482982 4.000000e-20 110.0
6 TraesCS7A01G204900 chr7D 100.000 29 0 0 1 29 272553320 272553348 2.000000e-03 54.7
7 TraesCS7A01G204900 chr7B 91.835 2866 147 39 1 2811 128760533 128763366 0.000000e+00 3916.0
8 TraesCS7A01G204900 chr7B 86.878 945 85 17 2851 3791 128763363 128764272 0.000000e+00 1022.0
9 TraesCS7A01G204900 chr7B 87.313 268 34 0 3468 3735 128769652 128769919 1.320000e-79 307.0
10 TraesCS7A01G204900 chr7B 97.101 69 2 0 2620 2688 128763229 128763297 2.390000e-22 117.0
11 TraesCS7A01G204900 chr6A 81.985 272 41 6 1999 2264 528924193 528923924 1.370000e-54 224.0
12 TraesCS7A01G204900 chr6A 85.876 177 19 6 2336 2509 528923844 528923671 2.330000e-42 183.0
13 TraesCS7A01G204900 chr6A 83.158 190 26 6 2336 2522 526121624 526121438 6.510000e-38 169.0
14 TraesCS7A01G204900 chrUn 85.876 177 19 6 2336 2509 362047145 362047318 2.330000e-42 183.0
15 TraesCS7A01G204900 chr1A 81.579 228 27 13 3515 3735 577886655 577886874 1.400000e-39 174.0
16 TraesCS7A01G204900 chr1A 80.120 166 23 8 3515 3677 577867527 577867685 8.610000e-22 115.0
17 TraesCS7A01G204900 chr6D 84.848 165 21 4 2336 2498 384294287 384294125 3.030000e-36 163.0
18 TraesCS7A01G204900 chr6D 81.481 189 31 4 2336 2522 384227830 384227644 6.560000e-33 152.0
19 TraesCS7A01G204900 chr1D 82.234 197 25 8 3545 3736 481408002 481408193 1.090000e-35 161.0
20 TraesCS7A01G204900 chr1D 78.027 223 33 14 3516 3732 481397989 481398201 3.980000e-25 126.0
21 TraesCS7A01G204900 chr1B 79.913 229 31 13 3515 3736 669784185 669784405 1.820000e-33 154.0


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 TraesCS7A01G204900 chr7A 167160651 167164441 3790 False 7001.000000 7001 100.000000 1 3791 1 chr7A.!!$F1 3790
1 TraesCS7A01G204900 chr7D 165479052 165483989 4937 False 1689.333333 4261 89.153333 10 3791 3 chr7D.!!$F3 3781
2 TraesCS7A01G204900 chr7B 128760533 128764272 3739 False 1685.000000 3916 91.938000 1 3791 3 chr7B.!!$F2 3790
3 TraesCS7A01G204900 chr6A 528923671 528924193 522 True 203.500000 224 83.930500 1999 2509 2 chr6A.!!$R2 510

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
340 351 0.109342 ATCTGCCACGATCAATCCCC 59.891 55.0 0.0 0.0 0.0 4.81 F
1209 2427 0.175073 ACGGGATTGACTACGAAGGC 59.825 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 3527 0.106918 TCAACTTCCAGCGTTGGGTT 60.107 50.0 18.99 12.37 45.10 4.11 R
2841 4093 0.110373 GGAAATGTGTCGACGTTGCC 60.110 55.0 11.62 9.96 39.28 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.287061 AGTTTTATTGTAGGTAGCATGGCATA 58.713 34.615 0.00 0.00 0.00 3.14
127 131 3.775261 ATTTGGAGCATGGCAGTTTTT 57.225 38.095 0.00 0.00 0.00 1.94
159 163 6.165577 AGAGCACGGCATTTTTCATTATTTT 58.834 32.000 0.00 0.00 0.00 1.82
164 168 8.012241 GCACGGCATTTTTCATTATTTTTACAA 58.988 29.630 0.00 0.00 0.00 2.41
280 291 2.867624 TCTGCCTTTCTCAAAGCACAT 58.132 42.857 0.00 0.00 37.18 3.21
281 292 3.225104 TCTGCCTTTCTCAAAGCACATT 58.775 40.909 0.00 0.00 37.18 2.71
340 351 0.109342 ATCTGCCACGATCAATCCCC 59.891 55.000 0.00 0.00 0.00 4.81
389 400 7.949903 TTTTATTATGTGCATCATGGCATTC 57.050 32.000 0.00 0.00 46.92 2.67
397 408 2.295349 GCATCATGGCATTCTTAGTGGG 59.705 50.000 0.00 0.00 0.00 4.61
404 415 2.213499 GCATTCTTAGTGGGTCATCGG 58.787 52.381 0.00 0.00 0.00 4.18
513 525 3.507233 TCTTCATGTCACAGGAAAATGGC 59.493 43.478 6.32 0.00 33.83 4.40
537 549 2.366640 TTTGGGTCCAATTGTTCGGA 57.633 45.000 4.43 0.00 35.70 4.55
551 563 4.282950 TGTTCGGATCAGATACGTACAC 57.717 45.455 20.35 13.42 41.09 2.90
555 567 4.953667 TCGGATCAGATACGTACACTACT 58.046 43.478 14.92 0.00 37.96 2.57
598 1786 6.153680 CCCTCATTAGCGTCCTATTTCTATCT 59.846 42.308 0.00 0.00 0.00 1.98
632 1821 4.561326 CGCATTCCAACCAAATTCTCCTTT 60.561 41.667 0.00 0.00 0.00 3.11
635 1824 6.071391 GCATTCCAACCAAATTCTCCTTTCTA 60.071 38.462 0.00 0.00 0.00 2.10
653 1842 2.281900 GCACCACGCTACCCCAAA 60.282 61.111 0.00 0.00 37.77 3.28
673 1862 0.506506 GCCATGAAAAACCGTTTGCG 59.493 50.000 0.00 0.00 37.95 4.85
733 1922 1.735920 CAGCTCAGCTCACGACACC 60.736 63.158 0.00 0.00 36.40 4.16
756 1945 2.485479 CCGATTAATCCCTCCCACTGTG 60.485 54.545 9.87 0.00 0.00 3.66
808 1997 1.928503 GCCATTGCAATTCAATCACCG 59.071 47.619 9.83 0.00 43.21 4.94
955 2161 1.357137 TCACCAATCACCACCAGCTA 58.643 50.000 0.00 0.00 0.00 3.32
985 2203 0.472471 ACAAGCACCGAGGAGGAAAA 59.528 50.000 0.00 0.00 45.00 2.29
1047 2265 2.898840 ATTGCCATCCTCGCGCTG 60.899 61.111 5.56 0.00 0.00 5.18
1209 2427 0.175073 ACGGGATTGACTACGAAGGC 59.825 55.000 0.00 0.00 0.00 4.35
1269 2487 2.031069 CGGAGACATCATGGGTACGTAG 60.031 54.545 0.00 0.00 0.00 3.51
1300 2518 1.302752 TGCTGCTCCACATCCACAC 60.303 57.895 0.00 0.00 0.00 3.82
1325 2543 6.145209 CGAATGGCAAAATGTGATGTGTTTTA 59.855 34.615 0.00 0.00 0.00 1.52
1326 2544 6.783892 ATGGCAAAATGTGATGTGTTTTAC 57.216 33.333 0.00 0.00 0.00 2.01
1327 2545 5.911752 TGGCAAAATGTGATGTGTTTTACT 58.088 33.333 0.00 0.00 0.00 2.24
1328 2546 6.344500 TGGCAAAATGTGATGTGTTTTACTT 58.656 32.000 0.00 0.00 0.00 2.24
1329 2547 6.820656 TGGCAAAATGTGATGTGTTTTACTTT 59.179 30.769 0.00 0.00 0.00 2.66
1330 2548 7.335422 TGGCAAAATGTGATGTGTTTTACTTTT 59.665 29.630 0.00 0.00 0.00 2.27
1401 2619 1.516423 GCCGTTCCTCTCCCTGTAC 59.484 63.158 0.00 0.00 0.00 2.90
1505 2723 0.319383 AGCGATCGAGCCATGATGTC 60.319 55.000 21.57 0.00 38.01 3.06
1508 2726 1.668337 CGATCGAGCCATGATGTCTCC 60.668 57.143 10.26 0.00 0.00 3.71
1654 2872 0.379669 GCAGATCAAGAACGCCATGG 59.620 55.000 7.63 7.63 0.00 3.66
1686 2904 3.319198 AAGAAGGCCGCCGAGGAA 61.319 61.111 3.05 0.00 45.00 3.36
1716 2934 1.502163 GCGCAATCTTCCAGATCGGG 61.502 60.000 0.30 5.39 32.89 5.14
1792 3011 3.564511 GCACGCAATGTACAAGTTGATT 58.435 40.909 10.54 0.00 0.00 2.57
1793 3012 3.361644 GCACGCAATGTACAAGTTGATTG 59.638 43.478 10.54 10.26 45.01 2.67
1794 3013 4.782156 CACGCAATGTACAAGTTGATTGA 58.218 39.130 10.54 0.00 41.83 2.57
1795 3014 5.393124 CACGCAATGTACAAGTTGATTGAT 58.607 37.500 10.54 0.00 41.83 2.57
1807 3026 1.864565 TGATTGATACGACGGGCATG 58.135 50.000 0.00 0.00 0.00 4.06
1956 3175 4.812476 CGCAAGACGGGCCGATCA 62.812 66.667 35.78 0.00 43.02 2.92
1994 3226 6.198216 CAGTACCATTGCCGTAATTATTTTGC 59.802 38.462 0.00 0.00 0.00 3.68
2273 3505 1.058695 GTAACGATCGAAACGTGCCAG 59.941 52.381 24.34 0.00 43.16 4.85
2275 3507 1.445410 CGATCGAAACGTGCCAGGA 60.445 57.895 10.26 0.00 0.00 3.86
2279 3511 0.389817 TCGAAACGTGCCAGGAGATG 60.390 55.000 0.00 0.00 0.00 2.90
2280 3512 1.796796 GAAACGTGCCAGGAGATGC 59.203 57.895 0.00 0.00 0.00 3.91
2288 3520 2.121948 TGCCAGGAGATGCACTATCTT 58.878 47.619 0.00 0.00 46.12 2.40
2291 3523 2.877168 CCAGGAGATGCACTATCTTTGC 59.123 50.000 0.00 0.00 46.12 3.68
2299 3531 2.754552 TGCACTATCTTTGCATGAACCC 59.245 45.455 0.00 0.00 45.06 4.11
2300 3532 2.754552 GCACTATCTTTGCATGAACCCA 59.245 45.455 0.00 0.00 39.93 4.51
2301 3533 3.193267 GCACTATCTTTGCATGAACCCAA 59.807 43.478 0.00 0.00 39.93 4.12
2303 3535 3.440173 ACTATCTTTGCATGAACCCAACG 59.560 43.478 0.00 0.00 0.00 4.10
2304 3536 0.313672 TCTTTGCATGAACCCAACGC 59.686 50.000 0.00 0.00 0.00 4.84
2307 3539 1.804396 TTGCATGAACCCAACGCTGG 61.804 55.000 0.00 0.00 43.10 4.85
2308 3540 1.971167 GCATGAACCCAACGCTGGA 60.971 57.895 6.38 0.00 46.92 3.86
2309 3541 1.523154 GCATGAACCCAACGCTGGAA 61.523 55.000 6.38 0.00 46.92 3.53
2311 3543 0.110486 ATGAACCCAACGCTGGAAGT 59.890 50.000 6.38 0.00 46.92 3.01
2312 3544 0.106918 TGAACCCAACGCTGGAAGTT 60.107 50.000 6.38 2.61 46.92 2.66
2334 3583 3.563088 TGCATTCGATCCGTGCGC 61.563 61.111 0.00 0.00 41.61 6.09
2662 3914 4.007644 CCACTGCGAGGCCTGTGA 62.008 66.667 19.77 0.00 35.30 3.58
2682 3934 4.643387 GGCAACGGCACCACCTCT 62.643 66.667 0.00 0.00 43.71 3.69
2801 4053 2.159338 CCAAGCCTTGAACAATCCGATG 60.159 50.000 5.89 0.00 0.00 3.84
2810 4062 2.768253 ACAATCCGATGAAGCAGACA 57.232 45.000 0.00 0.00 0.00 3.41
2811 4063 2.625737 ACAATCCGATGAAGCAGACAG 58.374 47.619 0.00 0.00 0.00 3.51
2812 4064 2.234661 ACAATCCGATGAAGCAGACAGA 59.765 45.455 0.00 0.00 0.00 3.41
2813 4065 2.593346 ATCCGATGAAGCAGACAGAC 57.407 50.000 0.00 0.00 0.00 3.51
2814 4066 0.532573 TCCGATGAAGCAGACAGACC 59.467 55.000 0.00 0.00 0.00 3.85
2815 4067 0.460987 CCGATGAAGCAGACAGACCC 60.461 60.000 0.00 0.00 0.00 4.46
2816 4068 0.534412 CGATGAAGCAGACAGACCCT 59.466 55.000 0.00 0.00 0.00 4.34
2817 4069 1.738365 CGATGAAGCAGACAGACCCTG 60.738 57.143 0.00 0.00 37.52 4.45
2819 4071 0.394192 TGAAGCAGACAGACCCTGTG 59.606 55.000 4.14 0.00 45.44 3.66
2820 4072 0.394565 GAAGCAGACAGACCCTGTGT 59.605 55.000 4.14 0.00 45.44 3.72
2821 4073 0.394565 AAGCAGACAGACCCTGTGTC 59.605 55.000 4.14 0.00 45.44 3.67
2822 4074 1.004440 GCAGACAGACCCTGTGTCC 60.004 63.158 4.14 0.00 45.44 4.02
2823 4075 1.674057 CAGACAGACCCTGTGTCCC 59.326 63.158 4.14 0.00 45.44 4.46
2824 4076 0.833834 CAGACAGACCCTGTGTCCCT 60.834 60.000 4.14 0.00 45.44 4.20
2825 4077 0.833834 AGACAGACCCTGTGTCCCTG 60.834 60.000 4.14 0.00 45.44 4.45
2826 4078 1.074471 ACAGACCCTGTGTCCCTGT 60.074 57.895 0.00 0.00 43.63 4.00
2827 4079 1.372683 CAGACCCTGTGTCCCTGTG 59.627 63.158 0.00 0.00 45.68 3.66
2828 4080 1.843376 AGACCCTGTGTCCCTGTGG 60.843 63.158 0.00 0.00 45.68 4.17
2829 4081 3.553095 GACCCTGTGTCCCTGTGGC 62.553 68.421 0.00 0.00 38.09 5.01
2830 4082 3.569210 CCCTGTGTCCCTGTGGCA 61.569 66.667 0.00 0.00 0.00 4.92
2831 4083 2.281761 CCTGTGTCCCTGTGGCAC 60.282 66.667 11.55 11.55 38.42 5.01
2832 4084 2.822637 CCTGTGTCCCTGTGGCACT 61.823 63.158 19.83 0.00 38.61 4.40
2833 4085 1.598962 CTGTGTCCCTGTGGCACTG 60.599 63.158 19.83 18.14 38.61 3.66
2834 4086 2.980233 GTGTCCCTGTGGCACTGC 60.980 66.667 19.83 6.44 36.40 4.40
2859 4140 3.361443 GGCAACGTCGACACATTTC 57.639 52.632 17.16 0.98 0.00 2.17
2893 4174 4.928615 GCGTCTCCACTATACGTCTATACT 59.071 45.833 0.00 0.00 38.81 2.12
2895 4176 6.756074 GCGTCTCCACTATACGTCTATACTAT 59.244 42.308 0.00 0.00 38.81 2.12
2898 4179 9.528018 GTCTCCACTATACGTCTATACTATACC 57.472 40.741 0.00 0.00 0.00 2.73
2899 4180 9.259832 TCTCCACTATACGTCTATACTATACCA 57.740 37.037 0.00 0.00 0.00 3.25
2928 4219 4.304110 TGTACTTTGACACTCGGTGAATC 58.696 43.478 10.46 0.72 36.96 2.52
2932 4223 4.214119 ACTTTGACACTCGGTGAATCAATG 59.786 41.667 10.46 12.89 36.96 2.82
2992 4283 2.928334 TCGTACTGGAGTATGAGTCCC 58.072 52.381 4.85 0.00 40.49 4.46
3089 4381 0.312416 CACCCATCTCCGACTCGATC 59.688 60.000 0.00 0.00 0.00 3.69
3156 4448 1.247567 CGGCTTCCCTGTTGTTGATT 58.752 50.000 0.00 0.00 0.00 2.57
3179 4471 3.884900 AAAAATCTCCGCGTCCCG 58.115 55.556 4.92 0.00 0.00 5.14
3182 4474 2.847435 AAAATCTCCGCGTCCCGACC 62.847 60.000 4.92 0.00 40.02 4.79
3199 4491 2.636830 GACCCTCATCACACATCCAAG 58.363 52.381 0.00 0.00 0.00 3.61
3216 4508 2.435938 GAATCGACAAGCCCGCCA 60.436 61.111 0.00 0.00 0.00 5.69
3299 4591 0.725686 CGTGGCTTCTGCTCTTGATG 59.274 55.000 0.00 0.00 39.59 3.07
3317 4609 2.214376 TGCCTATTGTGGGGTTCTTG 57.786 50.000 0.00 0.00 0.00 3.02
3345 4637 1.227205 GCAGTGATCCTCTGGAGCG 60.227 63.158 14.11 0.00 41.58 5.03
3418 4710 1.526887 GATTGGCCGAGGTGATGGA 59.473 57.895 0.00 0.00 0.00 3.41
3581 4873 2.674220 GGAGGAGTTCCAGCAGGGG 61.674 68.421 0.28 0.00 46.01 4.79
3585 4877 4.357279 AGTTCCAGCAGGGGCAGC 62.357 66.667 0.00 0.00 44.61 5.25
3657 4949 1.081892 CGTGTGGATGAAGAGCAAGG 58.918 55.000 0.00 0.00 0.00 3.61
3682 4974 2.435586 CCCGCTGTGCAGAAGGAG 60.436 66.667 13.17 3.43 32.06 3.69
3684 4976 2.031516 CCGCTGTGCAGAAGGAGTG 61.032 63.158 3.02 0.00 32.06 3.51
3697 4989 4.309950 GAGTGTCGTGGCCGGGTT 62.310 66.667 2.18 0.00 33.95 4.11
3752 5044 1.730064 CTTAGCGCGCAAAGAGGTTTA 59.270 47.619 35.10 10.59 0.00 2.01
3756 5048 1.594760 GCGCGCAAAGAGGTTTATAGC 60.595 52.381 29.10 0.00 0.00 2.97
3759 5051 2.277084 CGCAAAGAGGTTTATAGCGGT 58.723 47.619 0.00 0.00 40.00 5.68
3777 5069 4.941263 AGCGGTGCTGATATGTTCTTTTAA 59.059 37.500 0.00 0.00 37.57 1.52
3778 5070 5.065218 AGCGGTGCTGATATGTTCTTTTAAG 59.935 40.000 0.00 0.00 37.57 1.85
3779 5071 5.730568 GCGGTGCTGATATGTTCTTTTAAGG 60.731 44.000 0.00 0.00 0.00 2.69
3780 5072 5.582550 GGTGCTGATATGTTCTTTTAAGGC 58.417 41.667 0.00 0.00 0.00 4.35
3781 5073 5.266242 GTGCTGATATGTTCTTTTAAGGCG 58.734 41.667 0.00 0.00 0.00 5.52
3782 5074 4.335315 TGCTGATATGTTCTTTTAAGGCGG 59.665 41.667 0.00 0.00 0.00 6.13
3783 5075 4.335594 GCTGATATGTTCTTTTAAGGCGGT 59.664 41.667 0.00 0.00 0.00 5.68
3784 5076 5.504173 GCTGATATGTTCTTTTAAGGCGGTC 60.504 44.000 0.00 0.00 0.00 4.79
3786 5078 5.815740 TGATATGTTCTTTTAAGGCGGTCTC 59.184 40.000 0.00 0.00 0.00 3.36
3787 5079 2.409975 TGTTCTTTTAAGGCGGTCTCG 58.590 47.619 0.00 0.00 39.81 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.973661 ATAATAAATATGCCATGCTACCTACAA 57.026 29.630 0.00 0.00 0.00 2.41
95 99 7.038870 TGCCATGCTCCAAATATATAAATTGCT 60.039 33.333 6.25 0.00 0.00 3.91
103 107 6.736110 AAAACTGCCATGCTCCAAATATAT 57.264 33.333 0.00 0.00 0.00 0.86
127 131 7.148641 TGAAAAATGCCGTGCTCTAAAATAAA 58.851 30.769 0.00 0.00 0.00 1.40
340 351 4.413495 ACCATAACGTTCAAATTGACCG 57.587 40.909 11.28 11.28 38.29 4.79
389 400 3.543680 ACAATCCGATGACCCACTAAG 57.456 47.619 0.00 0.00 0.00 2.18
397 408 5.551760 ACAAGATGAAACAATCCGATGAC 57.448 39.130 0.00 0.00 0.00 3.06
565 577 3.070302 GGACGCTAATGAGGGAAGAAGAT 59.930 47.826 0.05 0.00 38.95 2.40
598 1786 0.681887 TGGAATGCGACTACGGGAGA 60.682 55.000 0.00 0.00 40.15 3.71
653 1842 1.864565 GCAAACGGTTTTTCATGGCT 58.135 45.000 2.79 0.00 0.00 4.75
673 1862 3.254892 GTGGAAATGTCGTTCTCCTCTC 58.745 50.000 7.23 0.00 0.00 3.20
733 1922 1.768870 AGTGGGAGGGATTAATCGGTG 59.231 52.381 9.32 0.00 0.00 4.94
756 1945 4.035909 TGAGAAAAGGCTTGGACGTTAAAC 59.964 41.667 0.00 0.00 0.00 2.01
808 1997 4.120331 GTGCCTGCGATTGGGTGC 62.120 66.667 0.00 0.00 0.00 5.01
955 2161 1.675720 GGTGCTTGTGTTGGGCAAGT 61.676 55.000 6.86 0.00 43.65 3.16
985 2203 1.530013 GCCATTGCTGTGCCTTCAGT 61.530 55.000 0.00 0.00 37.70 3.41
1087 2305 3.373565 CACCGGCCCCTTCTTTGC 61.374 66.667 0.00 0.00 0.00 3.68
1097 2315 2.607187 CGAATATGTAGATCACCGGCC 58.393 52.381 0.00 0.00 0.00 6.13
1269 2487 1.372623 GCAGCAGAAACAAGCAGCC 60.373 57.895 0.00 0.00 37.30 4.85
1300 2518 3.577667 ACACATCACATTTTGCCATTCG 58.422 40.909 0.00 0.00 0.00 3.34
1325 2543 1.542472 CGCAAACCCCCGAATAAAAGT 59.458 47.619 0.00 0.00 0.00 2.66
1326 2544 1.542472 ACGCAAACCCCCGAATAAAAG 59.458 47.619 0.00 0.00 0.00 2.27
1327 2545 1.269998 CACGCAAACCCCCGAATAAAA 59.730 47.619 0.00 0.00 0.00 1.52
1328 2546 0.882474 CACGCAAACCCCCGAATAAA 59.118 50.000 0.00 0.00 0.00 1.40
1329 2547 0.250814 ACACGCAAACCCCCGAATAA 60.251 50.000 0.00 0.00 0.00 1.40
1330 2548 0.674269 GACACGCAAACCCCCGAATA 60.674 55.000 0.00 0.00 0.00 1.75
1401 2619 0.797249 GAACCTCGTCGTCGGTCATG 60.797 60.000 1.55 0.00 37.69 3.07
1452 2670 0.109226 CGGTCTCGTTGAGAAGTCCC 60.109 60.000 0.00 0.00 40.59 4.46
1505 2723 3.619038 GCAACAATTAACGAGGAGAGGAG 59.381 47.826 0.00 0.00 0.00 3.69
1508 2726 4.245660 TCTGCAACAATTAACGAGGAGAG 58.754 43.478 0.00 0.00 0.00 3.20
1654 2872 1.019278 TTCTTGCCGATCTTGCCGAC 61.019 55.000 2.13 0.00 0.00 4.79
1686 2904 0.322816 AGATTGCGCCATTGACCACT 60.323 50.000 4.18 0.00 0.00 4.00
1716 2934 8.413899 TCAAATGTTTTTAAACTGTACCAAGC 57.586 30.769 6.87 0.00 39.59 4.01
1792 3011 2.108157 GGCATGCCCGTCGTATCA 59.892 61.111 27.24 0.00 0.00 2.15
1807 3026 2.163601 CTCCCTGCAAAGCAAAGGGC 62.164 60.000 10.53 0.00 41.86 5.19
1941 3160 2.892425 GCTGATCGGCCCGTCTTG 60.892 66.667 16.13 0.00 0.00 3.02
1956 3175 0.172803 GGTACTGACATCGTTCGGCT 59.827 55.000 0.00 0.00 0.00 5.52
1994 3226 0.610174 TGGTACAGCCTCTGCAGAAG 59.390 55.000 18.85 13.36 41.13 2.85
2104 3336 0.993251 CGTACGCGTTCACGTCTTCA 60.993 55.000 20.78 0.00 44.43 3.02
2244 3476 4.316653 CGTTTCGATCGTTACCGTATTTCC 60.317 45.833 15.94 0.00 35.01 3.13
2279 3511 2.754552 TGGGTTCATGCAAAGATAGTGC 59.245 45.455 0.00 0.00 42.55 4.40
2280 3512 4.672542 CGTTGGGTTCATGCAAAGATAGTG 60.673 45.833 0.00 0.00 0.00 2.74
2283 3515 2.163412 GCGTTGGGTTCATGCAAAGATA 59.837 45.455 0.00 0.00 0.00 1.98
2284 3516 1.067635 GCGTTGGGTTCATGCAAAGAT 60.068 47.619 0.00 0.00 0.00 2.40
2288 3520 1.659233 CAGCGTTGGGTTCATGCAA 59.341 52.632 0.00 0.00 0.00 4.08
2291 3523 0.523072 CTTCCAGCGTTGGGTTCATG 59.477 55.000 18.99 0.00 45.10 3.07
2292 3524 0.110486 ACTTCCAGCGTTGGGTTCAT 59.890 50.000 18.99 0.00 45.10 2.57
2295 3527 0.106918 TCAACTTCCAGCGTTGGGTT 60.107 50.000 18.99 12.37 45.10 4.11
2296 3528 0.110486 ATCAACTTCCAGCGTTGGGT 59.890 50.000 18.99 6.41 45.10 4.51
2297 3529 0.523072 CATCAACTTCCAGCGTTGGG 59.477 55.000 18.99 5.71 45.10 4.12
2299 3531 1.664016 GCACATCAACTTCCAGCGTTG 60.664 52.381 0.00 0.00 42.27 4.10
2300 3532 0.593128 GCACATCAACTTCCAGCGTT 59.407 50.000 0.00 0.00 0.00 4.84
2301 3533 0.534877 TGCACATCAACTTCCAGCGT 60.535 50.000 0.00 0.00 0.00 5.07
2303 3535 2.730090 CGAATGCACATCAACTTCCAGC 60.730 50.000 0.00 0.00 0.00 4.85
2304 3536 2.743664 TCGAATGCACATCAACTTCCAG 59.256 45.455 0.00 0.00 0.00 3.86
2307 3539 3.544834 CGGATCGAATGCACATCAACTTC 60.545 47.826 0.00 0.00 0.00 3.01
2308 3540 2.352651 CGGATCGAATGCACATCAACTT 59.647 45.455 0.00 0.00 0.00 2.66
2309 3541 1.935873 CGGATCGAATGCACATCAACT 59.064 47.619 0.00 0.00 0.00 3.16
2311 3543 1.665169 CACGGATCGAATGCACATCAA 59.335 47.619 0.00 0.00 0.00 2.57
2312 3544 1.289276 CACGGATCGAATGCACATCA 58.711 50.000 0.00 0.00 0.00 3.07
2314 3546 1.765161 CGCACGGATCGAATGCACAT 61.765 55.000 13.04 0.00 39.39 3.21
2315 3547 2.451990 CGCACGGATCGAATGCACA 61.452 57.895 13.04 0.00 39.39 4.57
2316 3548 2.321060 CGCACGGATCGAATGCAC 59.679 61.111 13.04 0.00 39.39 4.57
2334 3583 2.654912 GGACGTCGTGAAACCTGCG 61.655 63.158 9.92 0.00 0.00 5.18
2646 3898 1.376424 ATTCACAGGCCTCGCAGTG 60.376 57.895 13.50 13.50 37.42 3.66
2647 3899 1.376424 CATTCACAGGCCTCGCAGT 60.376 57.895 0.00 0.00 0.00 4.40
2649 3901 2.046023 CCATTCACAGGCCTCGCA 60.046 61.111 0.00 0.00 0.00 5.10
2662 3914 3.302344 GGTGGTGCCGTTGCCATT 61.302 61.111 0.00 0.00 37.09 3.16
2718 3970 4.025401 GAAGTGGTGCCGTTGCCG 62.025 66.667 0.00 0.00 36.33 5.69
2782 4034 3.071874 TCATCGGATTGTTCAAGGCTT 57.928 42.857 0.00 0.00 0.00 4.35
2801 4053 0.394565 ACACAGGGTCTGTCTGCTTC 59.605 55.000 0.00 0.00 43.43 3.86
2810 4062 1.843376 CCACAGGGACACAGGGTCT 60.843 63.158 1.94 0.00 46.16 3.85
2811 4063 2.750350 CCACAGGGACACAGGGTC 59.250 66.667 0.00 0.00 46.20 4.46
2812 4064 3.570212 GCCACAGGGACACAGGGT 61.570 66.667 0.00 0.00 35.59 4.34
2813 4065 3.569210 TGCCACAGGGACACAGGG 61.569 66.667 0.00 0.00 35.59 4.45
2814 4066 2.281761 GTGCCACAGGGACACAGG 60.282 66.667 2.62 0.00 43.66 4.00
2815 4067 1.598962 CAGTGCCACAGGGACACAG 60.599 63.158 10.34 0.00 46.69 3.66
2816 4068 2.510411 CAGTGCCACAGGGACACA 59.490 61.111 10.34 0.00 46.69 3.72
2817 4069 2.980233 GCAGTGCCACAGGGACAC 60.980 66.667 2.85 4.53 46.69 3.67
2840 4092 0.450482 GAAATGTGTCGACGTTGCCG 60.450 55.000 11.62 0.00 40.83 5.69
2841 4093 0.110373 GGAAATGTGTCGACGTTGCC 60.110 55.000 11.62 9.96 39.28 4.52
2842 4094 0.450482 CGGAAATGTGTCGACGTTGC 60.450 55.000 11.62 6.78 31.34 4.17
2843 4095 0.856641 ACGGAAATGTGTCGACGTTG 59.143 50.000 11.62 0.00 31.34 4.10
2844 4096 0.856641 CACGGAAATGTGTCGACGTT 59.143 50.000 11.62 2.93 35.12 3.99
2845 4097 2.513159 CACGGAAATGTGTCGACGT 58.487 52.632 11.62 0.00 35.12 4.34
2870 4151 4.928615 AGTATAGACGTATAGTGGAGACGC 59.071 45.833 0.00 0.00 46.80 5.19
2895 4176 7.329962 CGAGTGTCAAAGTACATATGTTTGGTA 59.670 37.037 14.77 3.29 32.96 3.25
2898 4179 6.147164 ACCGAGTGTCAAAGTACATATGTTTG 59.853 38.462 14.77 12.55 33.32 2.93
2899 4180 6.147164 CACCGAGTGTCAAAGTACATATGTTT 59.853 38.462 14.77 0.00 0.00 2.83
2901 4182 5.047590 TCACCGAGTGTCAAAGTACATATGT 60.048 40.000 13.93 13.93 34.79 2.29
2902 4183 5.407502 TCACCGAGTGTCAAAGTACATATG 58.592 41.667 0.00 0.00 34.79 1.78
2903 4184 5.654603 TCACCGAGTGTCAAAGTACATAT 57.345 39.130 0.00 0.00 34.79 1.78
2904 4185 5.456548 TTCACCGAGTGTCAAAGTACATA 57.543 39.130 0.00 0.00 34.79 2.29
2928 4219 4.966965 AATCTGCTCTCTGCTTTCATTG 57.033 40.909 0.00 0.00 43.37 2.82
2988 4279 0.661020 CAAACGTTGTGACCTGGGAC 59.339 55.000 0.00 0.00 0.00 4.46
2992 4283 4.588084 CGCAAACGTTGTGACCTG 57.412 55.556 0.00 0.00 43.66 4.00
3016 4307 0.385751 ACGGATGTGCTCCACGATAG 59.614 55.000 0.00 0.00 45.24 2.08
3062 4354 1.043816 CGGAGATGGGTGCTGATACT 58.956 55.000 0.00 0.00 0.00 2.12
3089 4381 2.267961 GGGAGTGGCCGGTTGTAG 59.732 66.667 1.90 0.00 37.63 2.74
3179 4471 2.237143 TCTTGGATGTGTGATGAGGGTC 59.763 50.000 0.00 0.00 0.00 4.46
3182 4474 3.558829 CGATTCTTGGATGTGTGATGAGG 59.441 47.826 0.00 0.00 0.00 3.86
3186 4478 4.206477 TGTCGATTCTTGGATGTGTGAT 57.794 40.909 0.00 0.00 0.00 3.06
3199 4491 2.435938 TGGCGGGCTTGTCGATTC 60.436 61.111 2.38 0.00 0.00 2.52
3223 4515 1.132453 AGAACGAGTTCATCATCGCGA 59.868 47.619 13.09 13.09 42.61 5.87
3299 4591 1.474330 CCAAGAACCCCACAATAGGC 58.526 55.000 0.00 0.00 0.00 3.93
3333 4625 3.859414 GCAGGCGCTCCAGAGGAT 61.859 66.667 7.64 0.00 34.30 3.24
3386 4678 2.895372 AATCGGCCCAATCGTCGC 60.895 61.111 0.00 0.00 0.00 5.19
3486 4778 4.468689 GTACCCCAGCTCCACCGC 62.469 72.222 0.00 0.00 0.00 5.68
3487 4779 2.240162 GAAGTACCCCAGCTCCACCG 62.240 65.000 0.00 0.00 0.00 4.94
3554 4846 0.179936 GGAACTCCTCCAGGCAGATG 59.820 60.000 0.00 0.00 44.67 2.90
3617 4909 1.148157 CGATGCAGTAGCGGTGGAAG 61.148 60.000 0.00 0.00 46.23 3.46
3626 4918 0.170339 TCCACACGTCGATGCAGTAG 59.830 55.000 4.06 0.00 0.00 2.57
3677 4969 4.003788 CCGGCCACGACACTCCTT 62.004 66.667 2.24 0.00 44.60 3.36
3682 4974 2.433664 CTAACCCGGCCACGACAC 60.434 66.667 2.24 0.00 44.60 3.67
3684 4976 1.739196 GTTCTAACCCGGCCACGAC 60.739 63.158 2.24 0.00 44.60 4.34
3697 4989 0.666913 GGCAGCCGATACTCGTTCTA 59.333 55.000 0.00 0.00 38.40 2.10
3717 5009 3.303395 GCGCTAAGCTAAACCATGTCATC 60.303 47.826 0.00 0.00 44.04 2.92
3718 5010 2.614057 GCGCTAAGCTAAACCATGTCAT 59.386 45.455 0.00 0.00 44.04 3.06
3752 5044 4.342862 AAGAACATATCAGCACCGCTAT 57.657 40.909 0.00 0.00 36.40 2.97
3756 5048 5.730568 GCCTTAAAAGAACATATCAGCACCG 60.731 44.000 0.00 0.00 0.00 4.94
3759 5051 4.335315 CCGCCTTAAAAGAACATATCAGCA 59.665 41.667 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.