Multiple sequence alignment - TraesCS4D01G240000

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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 TraesCS4D01G240000 chr4D 100.000 5838 0 0 618 6455 402531701 402525864 0.000000e+00 10781.0
1 TraesCS4D01G240000 chr4D 100.000 227 0 0 1 227 402532318 402532092 2.780000e-113 420.0
2 TraesCS4D01G240000 chr4D 93.407 91 5 1 3465 3554 337933290 337933200 4.060000e-27 134.0
3 TraesCS4D01G240000 chr4B 95.397 2868 79 27 618 3470 498378147 498375318 0.000000e+00 4516.0
4 TraesCS4D01G240000 chr4B 94.748 2894 79 35 3608 6455 498375238 498372372 0.000000e+00 4434.0
5 TraesCS4D01G240000 chr4B 96.250 80 1 1 4314 4391 12501386 12501307 5.250000e-26 130.0
6 TraesCS4D01G240000 chr4B 98.305 59 0 1 3551 3608 498375320 498375262 1.150000e-17 102.0
7 TraesCS4D01G240000 chr4B 93.333 45 3 0 83 127 498378652 498378608 4.180000e-07 67.6
8 TraesCS4D01G240000 chr4B 92.683 41 3 0 83 123 498378725 498378685 6.990000e-05 60.2
9 TraesCS4D01G240000 chr4A 92.091 2693 99 35 618 3256 60021231 60018599 0.000000e+00 3688.0
10 TraesCS4D01G240000 chr4A 91.649 970 49 17 4389 5332 60017245 60016282 0.000000e+00 1314.0
11 TraesCS4D01G240000 chr4A 96.233 584 15 3 3737 4315 60017824 60017243 0.000000e+00 950.0
12 TraesCS4D01G240000 chr4A 89.849 463 17 8 5767 6219 60015613 60015171 9.390000e-158 568.0
13 TraesCS4D01G240000 chr4A 97.357 227 6 0 1 227 60021720 60021494 2.820000e-103 387.0
14 TraesCS4D01G240000 chr4A 92.488 213 8 5 6210 6416 60015021 60014811 1.360000e-76 298.0
15 TraesCS4D01G240000 chr4A 88.293 205 6 1 3554 3740 60018073 60017869 5.030000e-56 230.0
16 TraesCS4D01G240000 chr4A 95.139 144 7 0 3293 3436 60018306 60018163 1.810000e-55 228.0
17 TraesCS4D01G240000 chr4A 96.296 81 2 1 4314 4394 724795866 724795787 1.460000e-26 132.0
18 TraesCS4D01G240000 chr4A 91.765 85 7 0 3468 3552 580898481 580898397 1.140000e-22 119.0
19 TraesCS4D01G240000 chr7B 82.738 168 20 7 2770 2932 105835306 105835469 2.430000e-29 141.0
20 TraesCS4D01G240000 chr7A 84.615 143 17 5 2794 2932 142647786 142647927 3.140000e-28 137.0
21 TraesCS4D01G240000 chr7A 100.000 52 0 0 3253 3304 83529725 83529674 5.330000e-16 97.1
22 TraesCS4D01G240000 chr7D 82.143 168 20 9 2770 2932 140768285 140768447 1.130000e-27 135.0
23 TraesCS4D01G240000 chr7D 92.473 93 2 4 4304 4391 29876364 29876456 1.890000e-25 128.0
24 TraesCS4D01G240000 chr7D 92.135 89 7 0 3464 3552 98275770 98275858 6.790000e-25 126.0
25 TraesCS4D01G240000 chr7D 94.048 84 4 1 4314 4396 234073752 234073669 6.790000e-25 126.0
26 TraesCS4D01G240000 chr5D 94.382 89 3 2 3465 3552 115124590 115124503 1.130000e-27 135.0
27 TraesCS4D01G240000 chr5D 100.000 52 0 0 3253 3304 444354691 444354742 5.330000e-16 97.1
28 TraesCS4D01G240000 chr5A 97.468 79 1 1 4316 4394 655994172 655994095 4.060000e-27 134.0
29 TraesCS4D01G240000 chr6D 91.304 92 8 0 3461 3552 4268790 4268699 6.790000e-25 126.0
30 TraesCS4D01G240000 chr6D 100.000 52 0 0 3253 3304 283795805 283795856 5.330000e-16 97.1
31 TraesCS4D01G240000 chr2D 93.103 87 4 1 4307 4391 188810511 188810597 6.790000e-25 126.0
32 TraesCS4D01G240000 chr1B 87.850 107 11 2 3448 3553 618126256 618126361 2.440000e-24 124.0
33 TraesCS4D01G240000 chr1B 89.247 93 8 2 3465 3555 172011202 172011110 1.470000e-21 115.0
34 TraesCS4D01G240000 chr6B 91.209 91 6 1 4312 4400 135505595 135505685 8.790000e-24 122.0
35 TraesCS4D01G240000 chr6B 96.610 59 2 0 3252 3310 76149799 76149741 1.480000e-16 99.0
36 TraesCS4D01G240000 chr2B 93.023 86 3 1 4314 4399 779647359 779647277 8.790000e-24 122.0
37 TraesCS4D01G240000 chr2B 89.011 91 10 0 3462 3552 315974243 315974333 5.290000e-21 113.0
38 TraesCS4D01G240000 chr2B 98.039 51 1 0 3255 3305 27892507 27892457 8.910000e-14 89.8
39 TraesCS4D01G240000 chr3B 89.362 94 8 2 3460 3552 341224299 341224391 4.090000e-22 117.0
40 TraesCS4D01G240000 chr3A 100.000 52 0 0 3253 3304 520437495 520437444 5.330000e-16 97.1
41 TraesCS4D01G240000 chr2A 100.000 52 0 0 3253 3304 654910273 654910324 5.330000e-16 97.1
42 TraesCS4D01G240000 chr1D 100.000 51 0 0 3253 3303 47948792 47948842 1.920000e-15 95.3


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 TraesCS4D01G240000 chr4D 402525864 402532318 6454 True 5600.500 10781 100.000000 1 6455 2 chr4D.!!$R2 6454
1 TraesCS4D01G240000 chr4B 498372372 498378725 6353 True 1835.960 4516 94.893200 83 6455 5 chr4B.!!$R2 6372
2 TraesCS4D01G240000 chr4A 60014811 60021720 6909 True 957.875 3688 92.887375 1 6416 8 chr4A.!!$R3 6415

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
27 28 1.072806 AGCAATGTCACTCTTGGCTGA 59.927 47.619 0.00 0.00 30.61 4.26 F
1039 1163 0.525668 CCGAGGTCTCAAATCCGTCG 60.526 60.000 0.00 0.00 0.00 5.12 F
1755 1888 1.003003 TCCTCGCAAATCCACATCACA 59.997 47.619 0.00 0.00 0.00 3.58 F
2195 2337 0.037326 GCCAGGACATCGACTGTGAA 60.037 55.000 5.41 0.00 38.54 3.18 F
2363 2510 0.251297 TCCTGTTGGCAAGGACATGG 60.251 55.000 0.00 0.38 0.00 3.66 F
3551 4014 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59 F
4649 5193 0.667993 CTTGAACACGCACCCATGTT 59.332 50.000 0.00 0.00 41.70 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1091 1215 0.179134 CGCTCCAGGGTTTAGAGACG 60.179 60.0 0.00 0.00 0.00 4.18 R
2112 2253 0.610509 TGACAGGCTTCGAGCTCTCT 60.611 55.0 12.85 0.00 41.99 3.10 R
3532 3995 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.0 0.00 0.00 0.00 2.71 R
3537 4000 0.106116 AGATGTACTCCCTCCGTCCC 60.106 60.0 0.00 0.00 0.00 4.46 R
4049 4590 0.686789 GAAAACCCTGGCTGCCATTT 59.313 50.0 23.64 19.07 30.82 2.32 R
4756 5318 1.741993 CAACAGCGTTGTACAGTTGC 58.258 50.0 4.98 9.27 36.23 4.17 R
6098 6918 0.039437 GAAGACAAGTGCGACTCGGA 60.039 55.0 0.00 0.00 0.00 4.55 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
27 28 1.072806 AGCAATGTCACTCTTGGCTGA 59.927 47.619 0.00 0.00 30.61 4.26
687 787 4.828925 GCGCTCACCTGAGGAGGC 62.829 72.222 4.99 5.25 44.33 4.70
732 832 2.361737 GTGGAGGCCCCTTGAAGC 60.362 66.667 0.00 0.00 35.38 3.86
898 998 3.465403 CGGTGAGGGGCTCTGGAG 61.465 72.222 0.00 0.00 0.00 3.86
899 999 2.284995 GGTGAGGGGCTCTGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
900 1000 2.363172 GGTGAGGGGCTCTGGAGTC 61.363 68.421 0.00 0.00 0.00 3.36
901 1001 1.305718 GTGAGGGGCTCTGGAGTCT 60.306 63.158 0.00 0.00 32.63 3.24
986 1095 3.299190 GATCCCTCGCTCCTCCGG 61.299 72.222 0.00 0.00 0.00 5.14
1039 1163 0.525668 CCGAGGTCTCAAATCCGTCG 60.526 60.000 0.00 0.00 0.00 5.12
1091 1215 3.844090 GAGCCAGCGGAGGAGTCC 61.844 72.222 0.00 0.00 39.88 3.85
1116 1240 2.501223 TAAACCCTGGAGCGCTGACG 62.501 60.000 18.48 1.28 44.07 4.35
1138 1262 2.557056 GGCTGTTTGACTAACCCCTTTC 59.443 50.000 0.00 0.00 35.81 2.62
1141 1268 2.514582 TGTTTGACTAACCCCTTTCCCA 59.485 45.455 0.00 0.00 35.81 4.37
1325 1452 2.045926 AATGCCGAGCCACAGTCC 60.046 61.111 0.00 0.00 0.00 3.85
1683 1816 2.368548 GGAGAAACTGGCACCCAAAATT 59.631 45.455 0.00 0.00 30.80 1.82
1755 1888 1.003003 TCCTCGCAAATCCACATCACA 59.997 47.619 0.00 0.00 0.00 3.58
1794 1927 5.065859 TCCAAAGGTATGTATGTTTCATGCG 59.934 40.000 0.00 0.00 0.00 4.73
1799 1932 2.401583 TGTATGTTTCATGCGCTCCT 57.598 45.000 9.73 0.00 0.00 3.69
1800 1933 2.710377 TGTATGTTTCATGCGCTCCTT 58.290 42.857 9.73 0.00 0.00 3.36
1954 2088 8.856103 CATTACCGGGAATAGAATGGTATTTTT 58.144 33.333 12.78 0.00 35.27 1.94
2017 2158 5.860716 GCTAGCCTTTGACTTTCTTTTCATG 59.139 40.000 2.29 0.00 0.00 3.07
2112 2253 7.773489 TTAATCATGGTGGAATCAAAGTTGA 57.227 32.000 0.00 0.00 42.14 3.18
2195 2337 0.037326 GCCAGGACATCGACTGTGAA 60.037 55.000 5.41 0.00 38.54 3.18
2236 2378 6.039717 TGCATAAGGCTGAAATTATCCTTGTC 59.960 38.462 2.89 0.00 45.15 3.18
2363 2510 0.251297 TCCTGTTGGCAAGGACATGG 60.251 55.000 0.00 0.38 0.00 3.66
2427 2575 7.916552 TCTTAAGTAAAAGCTTTGACAGTGTC 58.083 34.615 25.47 16.68 0.00 3.67
3105 3257 9.241919 TGAATCTTGCATAACTAAGGATTTCAA 57.758 29.630 0.00 0.00 0.00 2.69
3106 3258 9.727627 GAATCTTGCATAACTAAGGATTTCAAG 57.272 33.333 0.00 0.00 0.00 3.02
3107 3259 8.814038 ATCTTGCATAACTAAGGATTTCAAGT 57.186 30.769 0.00 0.00 32.63 3.16
3108 3260 8.044060 TCTTGCATAACTAAGGATTTCAAGTG 57.956 34.615 0.00 0.00 32.63 3.16
3145 3297 7.950684 TCATTTCCCATATAGCTCTGTAGTACT 59.049 37.037 0.00 0.00 0.00 2.73
3146 3298 9.244292 CATTTCCCATATAGCTCTGTAGTACTA 57.756 37.037 0.00 0.00 0.00 1.82
3147 3299 8.632906 TTTCCCATATAGCTCTGTAGTACTAC 57.367 38.462 23.58 23.58 36.63 2.73
3155 3307 5.197451 AGCTCTGTAGTACTACAATCTGCT 58.803 41.667 30.31 28.61 44.47 4.24
3237 3389 5.065988 GCAATTTTCTGGCCTCGTTCTTATA 59.934 40.000 3.32 0.00 0.00 0.98
3304 3712 4.525912 TTTCTTTACGGAGGGAGTACAC 57.474 45.455 0.00 0.00 0.00 2.90
3458 3921 4.744631 GGTGGTTTCATTGTTGACATTGTC 59.255 41.667 9.93 9.93 0.00 3.18
3475 3938 9.832445 TGACATTGTCTTAATAAATACTCCCTC 57.168 33.333 17.26 0.00 33.15 4.30
3477 3940 9.838339 ACATTGTCTTAATAAATACTCCCTCTG 57.162 33.333 0.00 0.00 0.00 3.35
3478 3941 9.838339 CATTGTCTTAATAAATACTCCCTCTGT 57.162 33.333 0.00 0.00 0.00 3.41
3480 3943 8.019656 TGTCTTAATAAATACTCCCTCTGTCC 57.980 38.462 0.00 0.00 0.00 4.02
3481 3944 7.070821 TGTCTTAATAAATACTCCCTCTGTCCC 59.929 40.741 0.00 0.00 0.00 4.46
3482 3945 7.070821 GTCTTAATAAATACTCCCTCTGTCCCA 59.929 40.741 0.00 0.00 0.00 4.37
3483 3946 7.794683 TCTTAATAAATACTCCCTCTGTCCCAT 59.205 37.037 0.00 0.00 0.00 4.00
3484 3947 9.101325 CTTAATAAATACTCCCTCTGTCCCATA 57.899 37.037 0.00 0.00 0.00 2.74
3485 3948 7.947782 AATAAATACTCCCTCTGTCCCATAA 57.052 36.000 0.00 0.00 0.00 1.90
3486 3949 8.525729 AATAAATACTCCCTCTGTCCCATAAT 57.474 34.615 0.00 0.00 0.00 1.28
3487 3950 9.629649 AATAAATACTCCCTCTGTCCCATAATA 57.370 33.333 0.00 0.00 0.00 0.98
3488 3951 9.805204 ATAAATACTCCCTCTGTCCCATAATAT 57.195 33.333 0.00 0.00 0.00 1.28
3490 3953 8.846423 AATACTCCCTCTGTCCCATAATATAG 57.154 38.462 0.00 0.00 0.00 1.31
3491 3954 5.594777 ACTCCCTCTGTCCCATAATATAGG 58.405 45.833 0.00 0.00 0.00 2.57
3492 3955 5.318889 ACTCCCTCTGTCCCATAATATAGGA 59.681 44.000 0.00 0.00 0.00 2.94
3493 3956 6.183361 ACTCCCTCTGTCCCATAATATAGGAA 60.183 42.308 0.00 0.00 0.00 3.36
3494 3957 6.264528 TCCCTCTGTCCCATAATATAGGAAG 58.735 44.000 0.00 0.00 0.00 3.46
3495 3958 6.026186 CCCTCTGTCCCATAATATAGGAAGT 58.974 44.000 0.00 0.00 0.00 3.01
3496 3959 6.502158 CCCTCTGTCCCATAATATAGGAAGTT 59.498 42.308 0.00 0.00 0.00 2.66
3497 3960 7.017651 CCCTCTGTCCCATAATATAGGAAGTTT 59.982 40.741 0.00 0.00 0.00 2.66
3498 3961 8.440771 CCTCTGTCCCATAATATAGGAAGTTTT 58.559 37.037 0.00 0.00 0.00 2.43
3499 3962 9.853177 CTCTGTCCCATAATATAGGAAGTTTTT 57.147 33.333 0.00 0.00 0.00 1.94
3541 4004 4.823790 AAAACGTCTTACATTGTGGGAC 57.176 40.909 0.00 6.72 0.00 4.46
3543 4006 1.355971 CGTCTTACATTGTGGGACGG 58.644 55.000 24.96 14.26 43.69 4.79
3544 4007 1.067425 CGTCTTACATTGTGGGACGGA 60.067 52.381 24.96 5.37 43.69 4.69
3545 4008 2.618053 GTCTTACATTGTGGGACGGAG 58.382 52.381 0.00 0.00 0.00 4.63
3546 4009 1.553248 TCTTACATTGTGGGACGGAGG 59.447 52.381 0.00 0.00 0.00 4.30
3547 4010 0.616371 TTACATTGTGGGACGGAGGG 59.384 55.000 0.00 0.00 0.00 4.30
3548 4011 0.252330 TACATTGTGGGACGGAGGGA 60.252 55.000 0.00 0.00 0.00 4.20
3549 4012 1.221840 CATTGTGGGACGGAGGGAG 59.778 63.158 0.00 0.00 0.00 4.30
3550 4013 1.229529 ATTGTGGGACGGAGGGAGT 60.230 57.895 0.00 0.00 0.00 3.85
3551 4014 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
3552 4015 0.901580 TTGTGGGACGGAGGGAGTAC 60.902 60.000 0.00 0.00 0.00 2.73
3630 4118 8.896320 TGATTGCAGTACTAACAACTCTTTTA 57.104 30.769 11.54 0.00 0.00 1.52
4049 4590 2.100749 TGACTTCTCACTTCTTGCACGA 59.899 45.455 0.00 0.00 0.00 4.35
4167 4708 4.267928 GCGACTGCATCTTATAAGTTCGTT 59.732 41.667 12.19 0.00 42.15 3.85
4219 4760 1.940613 GTCTTATTCGTGGCCCATGAC 59.059 52.381 4.78 0.00 0.00 3.06
4528 5069 2.837532 TTTGGAGGGCTTGATTTTGC 57.162 45.000 0.00 0.00 0.00 3.68
4540 5081 4.609783 GCTTGATTTTGCAAGTTCATGTGC 60.610 41.667 19.02 15.89 45.41 4.57
4543 5084 2.975732 TTTGCAAGTTCATGTGCCAA 57.024 40.000 0.00 0.00 40.14 4.52
4605 5147 3.091545 TGGAGGGCTTGATTTTGTGATC 58.908 45.455 0.00 0.00 0.00 2.92
4649 5193 0.667993 CTTGAACACGCACCCATGTT 59.332 50.000 0.00 0.00 41.70 2.71
4686 5230 1.016130 AGAGTGTCGAAATGGCGCAG 61.016 55.000 10.83 0.00 0.00 5.18
4701 5263 2.650900 CGCAGCCAAAAAGAAAAAGC 57.349 45.000 0.00 0.00 0.00 3.51
4703 5265 2.351111 CGCAGCCAAAAAGAAAAAGCAA 59.649 40.909 0.00 0.00 0.00 3.91
4704 5266 3.544637 CGCAGCCAAAAAGAAAAAGCAAG 60.545 43.478 0.00 0.00 0.00 4.01
4708 5270 6.610456 CAGCCAAAAAGAAAAAGCAAGAAAA 58.390 32.000 0.00 0.00 0.00 2.29
4709 5271 7.252708 CAGCCAAAAAGAAAAAGCAAGAAAAT 58.747 30.769 0.00 0.00 0.00 1.82
4756 5318 2.414750 AAAAACAGGAGCACCACCG 58.585 52.632 2.07 0.00 38.94 4.94
4768 5330 0.306533 CACCACCGCAACTGTACAAC 59.693 55.000 0.00 0.00 0.00 3.32
4951 5513 6.882768 AGATCAGGGATCTAGTCAAAGTTT 57.117 37.500 6.94 0.00 46.15 2.66
5032 5594 0.108186 TCCGCTATTGTGACAGGCTG 60.108 55.000 14.16 14.16 0.00 4.85
5213 5778 5.948992 AGCATATTCCCGCTAGATTTTTC 57.051 39.130 0.00 0.00 36.50 2.29
5275 5840 5.401531 TTGTAGAGTATTGTCCTCGCTTT 57.598 39.130 0.00 0.00 34.08 3.51
5493 6143 1.445582 GTGGAGCGGGTACTGTTCG 60.446 63.158 0.00 0.00 46.26 3.95
5643 6332 5.356882 TGGCAAGTGATTTCTTTAGTTCG 57.643 39.130 0.00 0.00 0.00 3.95
5655 6344 5.386958 TCTTTAGTTCGCGAGCCATATAT 57.613 39.130 19.83 2.21 0.00 0.86
5684 6479 2.173519 CACATGCTTTGGGGAGATTGT 58.826 47.619 0.00 0.00 0.00 2.71
5878 6690 2.546645 TAACTACGAAGGCGCCGTGG 62.547 60.000 22.76 22.21 42.83 4.94
6098 6918 1.301244 CGTCAGCCTGTGCAAGAGT 60.301 57.895 0.00 0.00 41.13 3.24
6125 6945 0.318784 GCACTTGTCTTCCTCGACGT 60.319 55.000 0.00 0.00 36.71 4.34
6161 6985 0.179000 GGATCCACGCAAGATGGAGT 59.821 55.000 6.95 0.00 45.84 3.85
6299 7289 1.027357 ATTTGCGATCCCATGCAGAC 58.973 50.000 0.00 0.00 42.89 3.51
6310 7300 3.117131 TCCCATGCAGACATACCTCTAGA 60.117 47.826 0.00 0.00 33.67 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.100963 TGTTTCTAGTTCAGCCAAGAGTGA 59.899 41.667 0.00 0.00 0.00 3.41
897 997 0.334676 CCTCTCTCCCAGTCCAGACT 59.665 60.000 0.00 0.00 43.61 3.24
898 998 0.333312 TCCTCTCTCCCAGTCCAGAC 59.667 60.000 0.00 0.00 0.00 3.51
899 999 0.628522 CTCCTCTCTCCCAGTCCAGA 59.371 60.000 0.00 0.00 0.00 3.86
900 1000 0.628522 TCTCCTCTCTCCCAGTCCAG 59.371 60.000 0.00 0.00 0.00 3.86
901 1001 1.084866 TTCTCCTCTCTCCCAGTCCA 58.915 55.000 0.00 0.00 0.00 4.02
1091 1215 0.179134 CGCTCCAGGGTTTAGAGACG 60.179 60.000 0.00 0.00 0.00 4.18
1116 1240 0.404426 AGGGGTTAGTCAAACAGCCC 59.596 55.000 0.00 0.00 40.08 5.19
1138 1262 3.706373 CCGTCTGGTGGGAGTGGG 61.706 72.222 0.00 0.00 0.00 4.61
1303 1430 4.424711 GTGGCTCGGCATTCCCCA 62.425 66.667 0.00 0.00 0.00 4.96
1512 1645 6.388278 GGAAATACATCGTGGATACTAGGAC 58.612 44.000 0.00 0.00 37.61 3.85
1683 1816 0.320421 GCAGGTAAACAGGCTCGTCA 60.320 55.000 0.00 0.00 0.00 4.35
1816 1950 9.582648 GTTAACCCCCTACAATAATCACATTAT 57.417 33.333 0.00 0.00 37.05 1.28
1817 1951 8.000127 GGTTAACCCCCTACAATAATCACATTA 59.000 37.037 14.16 0.00 0.00 1.90
1926 2060 2.742053 CCATTCTATTCCCGGTAATGCG 59.258 50.000 1.90 0.00 0.00 4.73
1954 2088 5.418676 TCTGACATCGATTTCATAGCAACA 58.581 37.500 14.31 0.00 0.00 3.33
2017 2158 3.055385 TGGCCTCTACCAAATCACTACAC 60.055 47.826 3.32 0.00 36.55 2.90
2112 2253 0.610509 TGACAGGCTTCGAGCTCTCT 60.611 55.000 12.85 0.00 41.99 3.10
2396 2544 9.609346 TGTCAAAGCTTTTACTTAAGAAGTACT 57.391 29.630 20.94 0.00 43.30 2.73
2397 2545 9.865484 CTGTCAAAGCTTTTACTTAAGAAGTAC 57.135 33.333 20.94 0.66 43.30 2.73
2398 2546 9.609346 ACTGTCAAAGCTTTTACTTAAGAAGTA 57.391 29.630 20.94 0.00 42.81 2.24
2399 2547 8.398665 CACTGTCAAAGCTTTTACTTAAGAAGT 58.601 33.333 20.94 13.27 45.40 3.01
2400 2548 8.398665 ACACTGTCAAAGCTTTTACTTAAGAAG 58.601 33.333 20.94 12.75 0.00 2.85
2403 2551 7.132863 GGACACTGTCAAAGCTTTTACTTAAG 58.867 38.462 20.94 13.91 33.68 1.85
2828 2977 9.825972 CTAAAAATATATCATTGGATTCGCGTT 57.174 29.630 5.77 0.00 34.89 4.84
3105 3257 9.927081 ATATGGGAAATGAAAGAAATACTCACT 57.073 29.630 0.00 0.00 0.00 3.41
3145 3297 8.635765 ACAGAAAGGATAAAAAGCAGATTGTA 57.364 30.769 0.00 0.00 0.00 2.41
3146 3298 7.530426 ACAGAAAGGATAAAAAGCAGATTGT 57.470 32.000 0.00 0.00 0.00 2.71
3147 3299 7.330208 CCAACAGAAAGGATAAAAAGCAGATTG 59.670 37.037 0.00 0.00 0.00 2.67
3155 3307 7.625498 AAATCCCCAACAGAAAGGATAAAAA 57.375 32.000 0.00 0.00 38.17 1.94
3327 3735 3.120649 ACGAAGTTAGAATTGCAGAACGC 60.121 43.478 0.00 0.00 37.78 4.84
3458 3921 7.374975 TGGGACAGAGGGAGTATTTATTAAG 57.625 40.000 0.00 0.00 0.00 1.85
3519 3982 4.260866 CGTCCCACAATGTAAGACGTTTTT 60.261 41.667 21.67 0.00 43.89 1.94
3520 3983 3.249080 CGTCCCACAATGTAAGACGTTTT 59.751 43.478 21.67 0.00 43.89 2.43
3521 3984 2.803956 CGTCCCACAATGTAAGACGTTT 59.196 45.455 21.67 0.00 43.89 3.60
3522 3985 2.409975 CGTCCCACAATGTAAGACGTT 58.590 47.619 21.67 0.00 43.89 3.99
3523 3986 1.337447 CCGTCCCACAATGTAAGACGT 60.337 52.381 25.28 0.00 46.62 4.34
3525 3988 2.618053 CTCCGTCCCACAATGTAAGAC 58.382 52.381 5.24 5.24 0.00 3.01
3526 3989 1.553248 CCTCCGTCCCACAATGTAAGA 59.447 52.381 0.00 0.00 0.00 2.10
3527 3990 1.406887 CCCTCCGTCCCACAATGTAAG 60.407 57.143 0.00 0.00 0.00 2.34
3528 3991 0.616371 CCCTCCGTCCCACAATGTAA 59.384 55.000 0.00 0.00 0.00 2.41
3529 3992 0.252330 TCCCTCCGTCCCACAATGTA 60.252 55.000 0.00 0.00 0.00 2.29
3530 3993 1.537889 TCCCTCCGTCCCACAATGT 60.538 57.895 0.00 0.00 0.00 2.71
3531 3994 1.221840 CTCCCTCCGTCCCACAATG 59.778 63.158 0.00 0.00 0.00 2.82
3532 3995 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
3533 3996 0.901580 GTACTCCCTCCGTCCCACAA 60.902 60.000 0.00 0.00 0.00 3.33
3534 3997 1.304713 GTACTCCCTCCGTCCCACA 60.305 63.158 0.00 0.00 0.00 4.17
3535 3998 0.686769 ATGTACTCCCTCCGTCCCAC 60.687 60.000 0.00 0.00 0.00 4.61
3536 3999 0.396695 GATGTACTCCCTCCGTCCCA 60.397 60.000 0.00 0.00 0.00 4.37
3537 4000 0.106116 AGATGTACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
3538 4001 1.033574 CAGATGTACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
3539 4002 2.054232 TCAGATGTACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
3540 4003 2.091830 TCATCAGATGTACTCCCTCCGT 60.092 50.000 10.34 0.00 0.00 4.69
3541 4004 2.587522 TCATCAGATGTACTCCCTCCG 58.412 52.381 10.34 0.00 0.00 4.63
3542 4005 4.533919 CATCATCAGATGTACTCCCTCC 57.466 50.000 10.34 0.00 45.28 4.30
3606 4076 9.974750 GATAAAAGAGTTGTTAGTACTGCAATC 57.025 33.333 5.39 9.82 0.00 2.67
3682 4170 4.818546 GCATATTCTTAGAAAGCTCTGGCA 59.181 41.667 0.00 0.00 41.70 4.92
3755 4291 6.533723 TGAACTACATAATCAGTTAAGCACCG 59.466 38.462 0.00 0.00 35.17 4.94
4049 4590 0.686789 GAAAACCCTGGCTGCCATTT 59.313 50.000 23.64 19.07 30.82 2.32
4167 4708 1.002576 CAGTGACAAAAGTGATGCGCA 60.003 47.619 14.96 14.96 0.00 6.09
4480 5021 5.066505 AGCTGAACTGAACGACAAGAAAATT 59.933 36.000 0.00 0.00 0.00 1.82
4487 5028 2.627945 ACAAGCTGAACTGAACGACAA 58.372 42.857 0.00 0.00 0.00 3.18
4491 5032 3.547468 CCAAAAACAAGCTGAACTGAACG 59.453 43.478 0.00 0.00 0.00 3.95
4492 5033 4.743493 TCCAAAAACAAGCTGAACTGAAC 58.257 39.130 0.00 0.00 0.00 3.18
4528 5069 5.697178 TCATGAAAATTGGCACATGAACTTG 59.303 36.000 13.43 0.00 43.56 3.16
4605 5147 2.093306 TAGGCAAGTGAACGTGATGG 57.907 50.000 0.31 0.00 0.00 3.51
4649 5193 9.140286 CGACACTCTCTTCTAATACAAAATGAA 57.860 33.333 0.00 0.00 0.00 2.57
4686 5230 9.566530 TTTATTTTCTTGCTTTTTCTTTTTGGC 57.433 25.926 0.00 0.00 0.00 4.52
4699 5261 7.552330 TCCTTTTGTTTGCTTTATTTTCTTGCT 59.448 29.630 0.00 0.00 0.00 3.91
4700 5262 7.693020 TCCTTTTGTTTGCTTTATTTTCTTGC 58.307 30.769 0.00 0.00 0.00 4.01
4701 5263 9.489393 GTTCCTTTTGTTTGCTTTATTTTCTTG 57.511 29.630 0.00 0.00 0.00 3.02
4703 5265 8.785329 TGTTCCTTTTGTTTGCTTTATTTTCT 57.215 26.923 0.00 0.00 0.00 2.52
4704 5266 8.878769 TCTGTTCCTTTTGTTTGCTTTATTTTC 58.121 29.630 0.00 0.00 0.00 2.29
4708 5270 8.785329 TTTTCTGTTCCTTTTGTTTGCTTTAT 57.215 26.923 0.00 0.00 0.00 1.40
4709 5271 8.608844 TTTTTCTGTTCCTTTTGTTTGCTTTA 57.391 26.923 0.00 0.00 0.00 1.85
4756 5318 1.741993 CAACAGCGTTGTACAGTTGC 58.258 50.000 4.98 9.27 36.23 4.17
4951 5513 4.261405 CGGATCAACTGTAACTTTTTGCCA 60.261 41.667 0.00 0.00 0.00 4.92
5032 5594 3.905784 CAACTGATGCTTCCTTTGGTTC 58.094 45.455 0.00 0.00 0.00 3.62
5493 6143 4.445718 CGAGCATCACTATCACCAACATAC 59.554 45.833 0.00 0.00 33.17 2.39
5643 6332 9.133627 CATGTGATAATACTATATATGGCTCGC 57.866 37.037 0.00 0.00 0.00 5.03
5655 6344 6.328934 TCTCCCCAAAGCATGTGATAATACTA 59.671 38.462 0.00 0.00 0.00 1.82
5684 6479 6.711194 TGGTGTACAAACATAATTCTTCGGAA 59.289 34.615 0.00 0.00 38.08 4.30
5878 6690 3.188786 GTCCACACATCCTCGCGC 61.189 66.667 0.00 0.00 0.00 6.86
5879 6691 2.880879 CGTCCACACATCCTCGCG 60.881 66.667 0.00 0.00 0.00 5.87
5880 6692 3.188786 GCGTCCACACATCCTCGC 61.189 66.667 0.00 0.00 37.17 5.03
5881 6693 2.509336 GGCGTCCACACATCCTCG 60.509 66.667 0.00 0.00 0.00 4.63
5975 6787 3.254024 ATCACCCGACTGCCACCAC 62.254 63.158 0.00 0.00 0.00 4.16
5976 6788 2.927856 ATCACCCGACTGCCACCA 60.928 61.111 0.00 0.00 0.00 4.17
5982 6794 0.826715 ATCACTCCATCACCCGACTG 59.173 55.000 0.00 0.00 0.00 3.51
5983 6795 0.826715 CATCACTCCATCACCCGACT 59.173 55.000 0.00 0.00 0.00 4.18
6075 6890 2.026945 TTGCACAGGCTGACGAGACA 62.027 55.000 23.66 6.64 41.91 3.41
6098 6918 0.039437 GAAGACAAGTGCGACTCGGA 60.039 55.000 0.00 0.00 0.00 4.55
6161 6985 3.394674 TCATCAGCTCCACACGTTTTA 57.605 42.857 0.00 0.00 0.00 1.52
6299 7289 6.583562 ACCGGAAGAAAAATCTAGAGGTATG 58.416 40.000 9.46 0.00 0.00 2.39
6310 7300 6.206048 ACTTGTTCGAATACCGGAAGAAAAAT 59.794 34.615 9.46 0.00 39.14 1.82
6367 7364 7.943387 GTGCAAGTCACTGGTCGATATCGAT 62.943 48.000 29.00 11.89 45.10 3.59
6425 7424 2.674380 GGTGCCAGGCCTGTGAAG 60.674 66.667 30.63 16.64 0.00 3.02


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

AutoCloner maintained by Alex Coulton.