Multiple sequence alignment - TraesCS7A01G328800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G328800 chr7A 100.000 6876 0 0 1 6876 478496330 478503205 0.000000e+00 12698.0
1 TraesCS7A01G328800 chr7A 92.647 68 5 0 5268 5335 478501555 478501622 1.580000e-16 99.0
2 TraesCS7A01G328800 chr7A 92.647 68 5 0 5226 5293 478501597 478501664 1.580000e-16 99.0
3 TraesCS7A01G328800 chr7A 81.081 111 11 6 816 920 175689768 175689662 5.720000e-11 80.5
4 TraesCS7A01G328800 chr7A 97.143 35 1 0 2424 2458 186409642 186409608 7.450000e-05 60.2
5 TraesCS7A01G328800 chr7D 96.402 3724 108 8 3161 6876 416234593 416238298 0.000000e+00 6111.0
6 TraesCS7A01G328800 chr7D 97.418 1588 30 5 851 2429 416232430 416234015 0.000000e+00 2695.0
7 TraesCS7A01G328800 chr7D 93.945 545 33 0 1 545 416197099 416197643 0.000000e+00 824.0
8 TraesCS7A01G328800 chr7D 93.631 314 18 2 542 854 416231955 416232267 1.040000e-127 468.0
9 TraesCS7A01G328800 chr7D 92.647 68 5 0 5226 5293 416236691 416236758 1.580000e-16 99.0
10 TraesCS7A01G328800 chr7D 97.143 35 0 1 2422 2456 88077648 88077681 2.680000e-04 58.4
11 TraesCS7A01G328800 chr7B 95.791 3706 116 11 3173 6867 431659759 431663435 0.000000e+00 5943.0
12 TraesCS7A01G328800 chr7B 95.320 1987 68 11 453 2429 431657071 431659042 0.000000e+00 3131.0
13 TraesCS7A01G328800 chr7B 88.655 476 32 6 1 455 431655206 431655680 1.670000e-155 560.0
14 TraesCS7A01G328800 chr7B 92.105 76 6 0 5226 5301 431661852 431661927 2.620000e-19 108.0
15 TraesCS7A01G328800 chr5A 99.545 660 2 1 2477 3136 174601587 174600929 0.000000e+00 1201.0
16 TraesCS7A01G328800 chr5A 99.099 666 5 1 2471 3136 35742948 35742284 0.000000e+00 1195.0
17 TraesCS7A01G328800 chr5A 91.170 872 65 9 1563 2429 52329326 52328462 0.000000e+00 1173.0
18 TraesCS7A01G328800 chr5A 97.143 35 1 0 2424 2458 150021558 150021592 7.450000e-05 60.2
19 TraesCS7A01G328800 chr5A 97.143 35 1 0 2424 2458 344344195 344344161 7.450000e-05 60.2
20 TraesCS7A01G328800 chr4B 99.545 660 2 1 2477 3136 5372866 5373524 0.000000e+00 1201.0
21 TraesCS7A01G328800 chr4B 83.654 208 28 4 6669 6876 612329849 612329648 2.530000e-44 191.0
22 TraesCS7A01G328800 chr3D 99.545 660 2 1 2477 3136 609956839 609957497 0.000000e+00 1201.0
23 TraesCS7A01G328800 chr2A 99.545 660 2 1 2477 3136 518944208 518943550 0.000000e+00 1201.0
24 TraesCS7A01G328800 chr2A 99.545 660 2 1 2477 3136 602799674 602799016 0.000000e+00 1201.0
25 TraesCS7A01G328800 chr2A 88.518 958 87 15 5932 6876 727917288 727918235 0.000000e+00 1138.0
26 TraesCS7A01G328800 chr2A 79.477 497 86 16 5933 6419 727244425 727244915 8.540000e-89 339.0
27 TraesCS7A01G328800 chr2A 84.135 208 27 4 6669 6876 419652706 419652505 5.440000e-46 196.0
28 TraesCS7A01G328800 chr1B 99.545 660 2 1 2477 3136 451910461 451911119 0.000000e+00 1201.0
29 TraesCS7A01G328800 chr1B 88.235 51 3 3 2423 2471 28494391 28494342 2.680000e-04 58.4
30 TraesCS7A01G328800 chr3B 98.808 671 6 2 2466 3136 332929102 332928434 0.000000e+00 1194.0
31 TraesCS7A01G328800 chr2B 98.094 682 9 4 2456 3136 495153140 495152462 0.000000e+00 1184.0
32 TraesCS7A01G328800 chr2B 86.939 980 91 25 5920 6876 719292964 719293929 0.000000e+00 1066.0
33 TraesCS7A01G328800 chr2B 78.182 495 96 12 5933 6419 718969045 718969535 8.660000e-79 305.0
34 TraesCS7A01G328800 chr5D 91.284 872 63 10 1563 2429 62296157 62295294 0.000000e+00 1177.0
35 TraesCS7A01G328800 chr5D 100.000 33 0 0 2425 2457 542971201 542971233 2.070000e-05 62.1
36 TraesCS7A01G328800 chr2D 79.276 497 87 16 5933 6419 592790547 592791037 3.970000e-87 333.0
37 TraesCS7A01G328800 chr2D 89.441 161 15 2 2010 2170 603999388 603999546 1.170000e-47 202.0
38 TraesCS7A01G328800 chr5B 84.706 170 15 6 2010 2170 123207954 123208121 7.140000e-35 159.0
39 TraesCS7A01G328800 chr5B 90.833 120 10 1 2051 2170 123408337 123408455 7.140000e-35 159.0
40 TraesCS7A01G328800 chr5B 97.143 35 1 0 2424 2458 203380868 203380834 7.450000e-05 60.2
41 TraesCS7A01G328800 chr1D 88.235 51 3 3 2423 2471 19041378 19041329 2.680000e-04 58.4
42 TraesCS7A01G328800 chrUn 100.000 29 0 0 2424 2452 79246243 79246271 3.000000e-03 54.7


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 TraesCS7A01G328800 chr7A 478496330 478503205 6875 False 4298.666667 12698 95.09800 1 6876 3 chr7A.!!$F1 6875
1 TraesCS7A01G328800 chr7D 416231955 416238298 6343 False 2343.250000 6111 95.02450 542 6876 4 chr7D.!!$F3 6334
2 TraesCS7A01G328800 chr7D 416197099 416197643 544 False 824.000000 824 93.94500 1 545 1 chr7D.!!$F2 544
3 TraesCS7A01G328800 chr7B 431655206 431663435 8229 False 2435.500000 5943 92.96775 1 6867 4 chr7B.!!$F1 6866
4 TraesCS7A01G328800 chr5A 174600929 174601587 658 True 1201.000000 1201 99.54500 2477 3136 1 chr5A.!!$R3 659
5 TraesCS7A01G328800 chr5A 35742284 35742948 664 True 1195.000000 1195 99.09900 2471 3136 1 chr5A.!!$R1 665
6 TraesCS7A01G328800 chr5A 52328462 52329326 864 True 1173.000000 1173 91.17000 1563 2429 1 chr5A.!!$R2 866
7 TraesCS7A01G328800 chr4B 5372866 5373524 658 False 1201.000000 1201 99.54500 2477 3136 1 chr4B.!!$F1 659
8 TraesCS7A01G328800 chr3D 609956839 609957497 658 False 1201.000000 1201 99.54500 2477 3136 1 chr3D.!!$F1 659
9 TraesCS7A01G328800 chr2A 518943550 518944208 658 True 1201.000000 1201 99.54500 2477 3136 1 chr2A.!!$R2 659
10 TraesCS7A01G328800 chr2A 602799016 602799674 658 True 1201.000000 1201 99.54500 2477 3136 1 chr2A.!!$R3 659
11 TraesCS7A01G328800 chr2A 727917288 727918235 947 False 1138.000000 1138 88.51800 5932 6876 1 chr2A.!!$F2 944
12 TraesCS7A01G328800 chr1B 451910461 451911119 658 False 1201.000000 1201 99.54500 2477 3136 1 chr1B.!!$F1 659
13 TraesCS7A01G328800 chr3B 332928434 332929102 668 True 1194.000000 1194 98.80800 2466 3136 1 chr3B.!!$R1 670
14 TraesCS7A01G328800 chr2B 495152462 495153140 678 True 1184.000000 1184 98.09400 2456 3136 1 chr2B.!!$R1 680
15 TraesCS7A01G328800 chr2B 719292964 719293929 965 False 1066.000000 1066 86.93900 5920 6876 1 chr2B.!!$F2 956
16 TraesCS7A01G328800 chr5D 62295294 62296157 863 True 1177.000000 1177 91.28400 1563 2429 1 chr5D.!!$R1 866

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
536 1951 0.908198 GGCATCCCTCACTCTCAAGT 59.092 55.000 0.00 0.00 35.60 3.16 F
682 2100 1.079503 GCTTATATACCTGCAGGCGC 58.920 55.000 33.06 18.25 39.32 6.53 F
1643 3237 0.248949 GACGTCGGCTAGGATCCAAC 60.249 60.000 15.82 2.00 0.00 3.77 F
1683 3277 0.759346 ACCCACACTGGACACTTCTC 59.241 55.000 0.00 0.00 40.96 2.87 F
3363 5169 1.069049 GCCTTGTGCCATTGTTCAACT 59.931 47.619 0.00 0.00 0.00 3.16 F
3602 5408 0.036590 TGGCCCGGTAAGTACCAAAC 59.963 55.000 0.00 0.00 46.80 2.93 F
5076 6894 0.245539 CCTGCAAGCAATTGTCCTGG 59.754 55.000 7.40 3.39 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 3122 2.634600 TGACGAAATATGTTTCCCCCG 58.365 47.619 9.10 1.46 40.49 5.73 R
1683 3277 3.504906 AGAATTGGCTGCATCATATTCCG 59.495 43.478 0.50 0.00 0.00 4.30 R
3568 5374 1.080569 GCCAAAGCCATGAACACCG 60.081 57.895 0.00 0.00 0.00 4.94 R
3602 5408 6.316390 AGCAGTCCAAAAATAGAAACTATCCG 59.684 38.462 0.00 0.00 0.00 4.18 R
5076 6894 0.179108 GCGGTGTACATCTCCTGTCC 60.179 60.000 4.28 0.00 39.39 4.02 R
5096 6914 1.004044 GATAGCCATGCTAGGTGCCAT 59.996 52.381 1.98 0.00 44.66 4.40 R
6638 8480 1.283321 GTCCAAGGAGCCCAAGAAGAT 59.717 52.381 0.00 0.00 0.00 2.40 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
28 29 5.508567 TGTTCTGATAATTGGGATGAGCAA 58.491 37.500 0.00 0.00 0.00 3.91
84 85 6.256321 CCTTTTCTCACAACTGGAATGTTTTG 59.744 38.462 0.00 0.00 0.00 2.44
153 174 3.771479 TCTCTCTGAAGTGGCATATGTGT 59.229 43.478 4.29 0.00 0.00 3.72
159 180 7.069950 TCTCTGAAGTGGCATATGTGTAGTATT 59.930 37.037 4.29 0.00 0.00 1.89
165 186 8.207350 AGTGGCATATGTGTAGTATTAGGAAT 57.793 34.615 4.29 0.00 0.00 3.01
210 231 2.356125 GCAGTTGGCAGAGGATCCTAAA 60.356 50.000 16.16 1.73 43.97 1.85
425 447 5.495640 TCCATACAAGATTGCACATGTGTA 58.504 37.500 26.01 20.04 0.00 2.90
470 1885 6.000840 GGAGACAAGAGATCACCTTTTCTTT 58.999 40.000 13.97 0.00 32.62 2.52
509 1924 4.859304 AATATGCTGGCAATATGTGTGG 57.141 40.909 0.00 0.00 0.00 4.17
510 1925 2.440517 ATGCTGGCAATATGTGTGGA 57.559 45.000 0.00 0.00 0.00 4.02
524 1939 1.152881 GTGGACCTCATGGCATCCC 60.153 63.158 0.00 0.00 36.63 3.85
525 1940 1.308128 TGGACCTCATGGCATCCCT 60.308 57.895 0.00 0.00 36.63 4.20
536 1951 0.908198 GGCATCCCTCACTCTCAAGT 59.092 55.000 0.00 0.00 35.60 3.16
573 1988 2.064762 CTCAGCTCAAACAACTCCTCG 58.935 52.381 0.00 0.00 0.00 4.63
579 1994 4.580580 AGCTCAAACAACTCCTCGATTTTT 59.419 37.500 0.00 0.00 0.00 1.94
681 2099 2.738846 CAAGCTTATATACCTGCAGGCG 59.261 50.000 33.06 10.80 39.32 5.52
682 2100 1.079503 GCTTATATACCTGCAGGCGC 58.920 55.000 33.06 18.25 39.32 6.53
720 2138 3.038280 TGAAGTGGATCACATATCGGGT 58.962 45.455 0.00 0.00 36.74 5.28
733 2151 5.994054 CACATATCGGGTCAAGAGAAATGAT 59.006 40.000 0.00 0.00 0.00 2.45
743 2161 9.136323 GGGTCAAGAGAAATGATTATAATGGTT 57.864 33.333 1.78 0.00 0.00 3.67
760 2178 2.228582 TGGTTCGATGGTCAATGCTTTG 59.771 45.455 5.99 5.99 0.00 2.77
775 2193 9.070149 GTCAATGCTTTGAGAAGATTTGTATTC 57.930 33.333 14.79 0.00 42.41 1.75
981 2574 1.477295 GGCGTATCCTATAGAGCACCC 59.523 57.143 0.00 0.00 0.00 4.61
1528 3122 2.541178 CGGGTCTCTGAATACGTAGCAC 60.541 54.545 0.08 0.00 0.00 4.40
1643 3237 0.248949 GACGTCGGCTAGGATCCAAC 60.249 60.000 15.82 2.00 0.00 3.77
1683 3277 0.759346 ACCCACACTGGACACTTCTC 59.241 55.000 0.00 0.00 40.96 2.87
2044 3639 6.944096 AGTACAATACTTCTCCTAACAACCC 58.056 40.000 0.00 0.00 34.86 4.11
2046 3641 4.189231 CAATACTTCTCCTAACAACCCGG 58.811 47.826 0.00 0.00 0.00 5.73
2343 3947 3.064820 CGGTGGTTATGTCATTTGCTACC 59.935 47.826 0.00 0.00 0.00 3.18
2452 4255 6.809976 ATTTAGAAACGGAGGGAGTAGAAT 57.190 37.500 0.00 0.00 0.00 2.40
2453 4256 5.593679 TTAGAAACGGAGGGAGTAGAATG 57.406 43.478 0.00 0.00 0.00 2.67
2465 4268 7.105241 AGGGAGTAGAATGCAAAATTTGATC 57.895 36.000 10.26 4.43 0.00 2.92
2485 4288 9.996554 TTTGATCTTAGAGAGATACAACAACAA 57.003 29.630 0.00 0.00 45.17 2.83
2567 4370 3.340814 AGATCTCGCAACCAACTCATT 57.659 42.857 0.00 0.00 0.00 2.57
2644 4447 4.278310 TGTCGATACTCCAATCCTTCAGA 58.722 43.478 0.00 0.00 0.00 3.27
3150 4953 8.440021 CGAAAGGTGTCAAAATTTGATCTTAG 57.560 34.615 11.87 9.67 42.47 2.18
3151 4954 8.289618 CGAAAGGTGTCAAAATTTGATCTTAGA 58.710 33.333 11.87 0.00 42.47 2.10
3152 4955 9.617975 GAAAGGTGTCAAAATTTGATCTTAGAG 57.382 33.333 11.87 0.00 42.47 2.43
3153 4956 8.924511 AAGGTGTCAAAATTTGATCTTAGAGA 57.075 30.769 11.87 0.00 42.47 3.10
3154 4957 8.558973 AGGTGTCAAAATTTGATCTTAGAGAG 57.441 34.615 11.87 0.00 42.47 3.20
3155 4958 8.378565 AGGTGTCAAAATTTGATCTTAGAGAGA 58.621 33.333 11.87 0.00 42.47 3.10
3157 4960 9.985318 GTGTCAAAATTTGATCTTAGAGAGATG 57.015 33.333 11.87 0.00 45.17 2.90
3158 4961 8.671921 TGTCAAAATTTGATCTTAGAGAGATGC 58.328 33.333 11.87 0.00 45.17 3.91
3159 4962 8.671921 GTCAAAATTTGATCTTAGAGAGATGCA 58.328 33.333 11.87 0.00 45.17 3.96
3222 5025 5.690409 ACACAGTGAAAGTAGTACAATCACG 59.310 40.000 22.38 19.89 39.42 4.35
3363 5169 1.069049 GCCTTGTGCCATTGTTCAACT 59.931 47.619 0.00 0.00 0.00 3.16
3541 5347 6.436847 TCCAAACTTTCCAGATATCATTTGCA 59.563 34.615 5.32 0.00 0.00 4.08
3568 5374 7.816640 TGCTTCTTGGTTGTGATTATTCTAAC 58.183 34.615 0.00 0.00 0.00 2.34
3571 5377 6.469410 TCTTGGTTGTGATTATTCTAACGGT 58.531 36.000 0.00 0.00 0.00 4.83
3602 5408 0.036590 TGGCCCGGTAAGTACCAAAC 59.963 55.000 0.00 0.00 46.80 2.93
3839 5645 4.344102 AGAAAGTGTAAAGGGAAAAAGGCC 59.656 41.667 0.00 0.00 0.00 5.19
3877 5683 1.745087 GGGTGGTGACATATGCACAAG 59.255 52.381 22.92 0.00 46.14 3.16
3880 5686 3.696051 GGTGGTGACATATGCACAAGAAT 59.304 43.478 22.92 0.00 46.14 2.40
3882 5688 5.008019 GGTGGTGACATATGCACAAGAATAG 59.992 44.000 22.92 0.00 46.14 1.73
3906 5712 5.469084 GGTACCTCTGGTAAACAAGTTCTTG 59.531 44.000 4.06 10.50 40.12 3.02
4039 5845 6.578020 CGTGAGGTAATAAACGCATTTCTA 57.422 37.500 0.00 0.00 0.00 2.10
4098 5904 9.562408 TGTGCGGAGGTAATTAATTATTTGATA 57.438 29.630 11.00 0.00 0.00 2.15
4149 5962 4.680171 GCTTCAGCTACATAAAACCGTT 57.320 40.909 0.00 0.00 38.21 4.44
4150 5963 4.403453 GCTTCAGCTACATAAAACCGTTG 58.597 43.478 0.00 0.00 38.21 4.10
4151 5964 4.153475 GCTTCAGCTACATAAAACCGTTGA 59.847 41.667 0.00 0.00 38.21 3.18
4152 5965 5.334569 GCTTCAGCTACATAAAACCGTTGAA 60.335 40.000 0.00 0.00 38.21 2.69
4153 5966 6.621316 TTCAGCTACATAAAACCGTTGAAA 57.379 33.333 0.00 0.00 0.00 2.69
4154 5967 5.992729 TCAGCTACATAAAACCGTTGAAAC 58.007 37.500 0.00 0.00 0.00 2.78
4155 5968 5.761234 TCAGCTACATAAAACCGTTGAAACT 59.239 36.000 0.00 0.00 0.00 2.66
4512 6325 0.737219 GTAGCTTTGCATGCTCAGGG 59.263 55.000 20.33 5.86 41.46 4.45
4538 6351 9.997482 GTGTTTCTGAAGTAAACATTCTTGTTA 57.003 29.630 4.86 0.00 45.30 2.41
4584 6397 8.803235 TCTAGTTTCACTTATCAAGTCTAAGCA 58.197 33.333 0.00 0.00 40.46 3.91
4777 6592 2.098117 CCTGCAATAGCCAAACACTAGC 59.902 50.000 0.00 0.00 41.13 3.42
4966 6784 1.740025 CAAAAGAGGAAAGCTAGGCCG 59.260 52.381 0.00 0.00 0.00 6.13
5076 6894 0.245539 CCTGCAAGCAATTGTCCTGG 59.754 55.000 7.40 3.39 0.00 4.45
5096 6914 0.530744 GACAGGAGATGTACACCGCA 59.469 55.000 0.00 0.00 44.17 5.69
5190 7008 0.615331 ATCGGATCAACCACAGCTGT 59.385 50.000 15.25 15.25 38.90 4.40
5251 7069 2.172717 ACAAAGTAGCACCCAGTCAAGT 59.827 45.455 0.00 0.00 0.00 3.16
5253 7071 1.424638 AGTAGCACCCAGTCAAGTGT 58.575 50.000 0.00 0.00 36.35 3.55
5256 7074 0.466189 AGCACCCAGTCAAGTGTTGG 60.466 55.000 0.00 0.00 36.35 3.77
5266 7084 3.452627 AGTCAAGTGTTGGTCAGAACTCT 59.547 43.478 0.00 0.00 32.39 3.24
5398 7216 2.159379 CGACGTGATTGATCTGTCCTCA 60.159 50.000 0.00 0.00 32.81 3.86
5458 7276 3.266772 TCCAAGACTTGCCACCTTATGAT 59.733 43.478 9.85 0.00 0.00 2.45
5693 7511 1.697432 TGTCATCTCCTTCACCGGTTT 59.303 47.619 2.97 0.00 0.00 3.27
5721 7539 3.852578 AGGAGAAGGAATGGTAACCATGT 59.147 43.478 0.00 0.00 44.40 3.21
5842 7660 5.493133 AGAGCATTAGAGACGAACTGTAG 57.507 43.478 0.00 0.00 0.00 2.74
5856 7677 6.044046 ACGAACTGTAGTATTTGAACACACA 58.956 36.000 0.00 0.00 0.00 3.72
5879 7700 7.009448 CACAATCAATTTGGTGTATTTGATCGG 59.991 37.037 6.39 0.00 37.72 4.18
5897 7718 7.915293 TGATCGGATACATTTGTGTAAAGTT 57.085 32.000 0.00 0.00 0.00 2.66
5898 7719 8.330466 TGATCGGATACATTTGTGTAAAGTTT 57.670 30.769 0.00 0.00 0.00 2.66
5899 7720 8.233868 TGATCGGATACATTTGTGTAAAGTTTG 58.766 33.333 0.00 0.00 0.00 2.93
5900 7721 6.375377 TCGGATACATTTGTGTAAAGTTTGC 58.625 36.000 0.00 0.00 0.00 3.68
6290 8114 3.177884 AACCAGCAGCCCACCAGA 61.178 61.111 0.00 0.00 0.00 3.86
6523 8350 2.743060 CGGATGCCGGATGATGGA 59.257 61.111 5.05 0.00 44.15 3.41
6638 8480 5.047566 TGTTGTTTCCTTCTCCATCTTCA 57.952 39.130 0.00 0.00 0.00 3.02
6791 8633 0.601558 TGTCAAGGTCCTGCTCGTAC 59.398 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 5.138125 TCATTCAAAGCCCACAAAGATTC 57.862 39.130 0.00 0.00 0.00 2.52
159 180 8.408601 GCTTGCAGAAAATTGATCTAATTCCTA 58.591 33.333 0.00 0.00 38.01 2.94
165 186 5.981088 TGGCTTGCAGAAAATTGATCTAA 57.019 34.783 0.00 0.00 0.00 2.10
192 213 5.474876 CCAATATTTAGGATCCTCTGCCAAC 59.525 44.000 20.22 0.00 0.00 3.77
259 280 8.116651 TCTGAATGTATAGATAGGAGCTTGTC 57.883 38.462 0.00 0.00 0.00 3.18
403 425 4.707030 ACACATGTGCAATCTTGTATGG 57.293 40.909 25.68 0.00 0.00 2.74
470 1885 1.135094 TTTGGGCAAAAGGGCATTGA 58.865 45.000 0.00 0.00 45.66 2.57
509 1924 0.179034 GTGAGGGATGCCATGAGGTC 60.179 60.000 5.86 0.00 37.19 3.85
510 1925 0.622738 AGTGAGGGATGCCATGAGGT 60.623 55.000 5.86 0.00 37.19 3.85
524 1939 8.465999 ACTTCATCTTGTATACTTGAGAGTGAG 58.534 37.037 4.17 6.76 36.60 3.51
525 1940 8.354711 ACTTCATCTTGTATACTTGAGAGTGA 57.645 34.615 4.17 7.90 36.60 3.41
536 1951 5.982356 AGCTGAGCAACTTCATCTTGTATA 58.018 37.500 7.39 0.00 0.00 1.47
573 1988 7.992180 TGACTTCAAGAGCAAAAGAAAAATC 57.008 32.000 0.00 0.00 0.00 2.17
579 1994 8.627208 AGAATAATGACTTCAAGAGCAAAAGA 57.373 30.769 0.00 0.00 0.00 2.52
607 2022 1.727062 AGTCCAGATAGCCCATGAGG 58.273 55.000 0.00 0.00 39.47 3.86
681 2099 7.872483 TCCACTTCATTTCCTTCTTAAATTTGC 59.128 33.333 0.00 0.00 0.00 3.68
682 2100 9.933723 ATCCACTTCATTTCCTTCTTAAATTTG 57.066 29.630 0.00 0.00 0.00 2.32
692 2110 6.484643 CGATATGTGATCCACTTCATTTCCTT 59.515 38.462 0.00 0.00 35.11 3.36
720 2138 9.830975 TCGAACCATTATAATCATTTCTCTTGA 57.169 29.630 0.00 0.00 0.00 3.02
733 2151 6.061441 AGCATTGACCATCGAACCATTATAA 58.939 36.000 0.00 0.00 0.00 0.98
743 2161 3.333029 TCTCAAAGCATTGACCATCGA 57.667 42.857 0.00 0.00 40.59 3.59
747 2165 5.302568 ACAAATCTTCTCAAAGCATTGACCA 59.697 36.000 0.00 0.00 40.59 4.02
775 2193 9.956797 CAAGAAAAAGAACAACAAATACAACTG 57.043 29.630 0.00 0.00 0.00 3.16
878 2461 2.911102 GCAAAACTCTGCTGCGTATTTC 59.089 45.455 0.00 0.00 39.34 2.17
981 2574 4.013728 TCTGGGTAATTTGTTCGGAATGG 58.986 43.478 0.00 0.00 0.00 3.16
1528 3122 2.634600 TGACGAAATATGTTTCCCCCG 58.365 47.619 9.10 1.46 40.49 5.73
1530 3124 9.244799 GAATTTTATGACGAAATATGTTTCCCC 57.755 33.333 9.10 2.65 40.49 4.81
1643 3237 5.412904 GGGTAAACAAGAAATGACCTCAGAG 59.587 44.000 0.00 0.00 0.00 3.35
1683 3277 3.504906 AGAATTGGCTGCATCATATTCCG 59.495 43.478 0.50 0.00 0.00 4.30
1912 3507 6.602410 TGGGCATTTGTCAATAATTTCAGA 57.398 33.333 0.00 0.00 0.00 3.27
2044 3639 7.539712 AAATAAGTAACAGACATGACATCCG 57.460 36.000 0.00 0.00 0.00 4.18
2083 3678 4.326826 TGATGTAAAACAGCCTTCCTGAG 58.673 43.478 0.00 0.00 44.64 3.35
2211 3814 9.683069 CAGACAGTGCAATATAAGTTTTCTTTT 57.317 29.630 0.00 0.00 40.91 2.27
2239 3842 4.759183 ACCACTTTGCAACAACAACAAAAT 59.241 33.333 0.00 0.00 33.24 1.82
2343 3947 6.376581 AGCTTTTTCTCTATGTCCTCCATTTG 59.623 38.462 0.00 0.00 34.86 2.32
2452 4255 9.671279 TGTATCTCTCTAAGATCAAATTTTGCA 57.329 29.630 4.19 0.00 43.90 4.08
2465 4268 8.826710 TGTTGTTTGTTGTTGTATCTCTCTAAG 58.173 33.333 0.00 0.00 0.00 2.18
2473 4276 7.339732 TGTTGTTGTTGTTTGTTGTTGTATC 57.660 32.000 0.00 0.00 0.00 2.24
2485 4288 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
2644 4447 3.558033 GGAGGAGTCCGTTAAGAGAGAT 58.442 50.000 2.76 0.00 31.37 2.75
3136 4939 9.017509 TGTTGCATCTCTCTAAGATCAAATTTT 57.982 29.630 0.00 0.00 43.13 1.82
3137 4940 8.571461 TGTTGCATCTCTCTAAGATCAAATTT 57.429 30.769 0.00 0.00 43.13 1.82
3138 4941 8.571461 TTGTTGCATCTCTCTAAGATCAAATT 57.429 30.769 0.00 0.00 43.13 1.82
3139 4942 8.571461 TTTGTTGCATCTCTCTAAGATCAAAT 57.429 30.769 0.00 0.00 43.13 2.32
3140 4943 7.984422 TTTGTTGCATCTCTCTAAGATCAAA 57.016 32.000 0.00 0.00 43.13 2.69
3141 4944 8.571461 AATTTGTTGCATCTCTCTAAGATCAA 57.429 30.769 0.00 0.00 43.13 2.57
3142 4945 9.842775 ATAATTTGTTGCATCTCTCTAAGATCA 57.157 29.630 0.00 0.00 43.13 2.92
3144 4947 9.624373 ACATAATTTGTTGCATCTCTCTAAGAT 57.376 29.630 0.00 0.00 39.49 2.40
3145 4948 9.453572 AACATAATTTGTTGCATCTCTCTAAGA 57.546 29.630 0.00 0.00 46.80 2.10
3205 5008 7.647907 TCCTTTTCGTGATTGTACTACTTTC 57.352 36.000 0.00 0.00 0.00 2.62
3222 5025 6.309389 TGGTACCTCCTCTAAATCCTTTTC 57.691 41.667 14.36 0.00 37.07 2.29
3363 5169 4.641396 GCAGGTAGCATCATGGTATTGTA 58.359 43.478 0.00 0.00 44.79 2.41
3541 5347 7.472334 AGAATAATCACAACCAAGAAGCAAT 57.528 32.000 0.00 0.00 0.00 3.56
3568 5374 1.080569 GCCAAAGCCATGAACACCG 60.081 57.895 0.00 0.00 0.00 4.94
3602 5408 6.316390 AGCAGTCCAAAAATAGAAACTATCCG 59.684 38.462 0.00 0.00 0.00 4.18
3839 5645 2.134346 CCCTTGTTTTTGTCAATGCCG 58.866 47.619 0.00 0.00 0.00 5.69
3877 5683 6.944096 ACTTGTTTACCAGAGGTACCTATTC 58.056 40.000 16.29 2.46 37.97 1.75
3880 5686 6.080009 AGAACTTGTTTACCAGAGGTACCTA 58.920 40.000 16.29 0.00 37.97 3.08
3882 5688 5.224821 AGAACTTGTTTACCAGAGGTACC 57.775 43.478 2.73 2.73 37.97 3.34
3906 5712 3.249559 GCATAGCCACAGAAATACAGAGC 59.750 47.826 0.00 0.00 0.00 4.09
4039 5845 2.103537 GCAAATGGCATTTTGGCTCT 57.896 45.000 22.26 0.00 44.10 4.09
4103 5909 1.967319 AACCACACAAGGCAGTAGTG 58.033 50.000 0.00 0.00 39.12 2.74
4129 5935 5.856126 TCAACGGTTTTATGTAGCTGAAG 57.144 39.130 0.00 0.00 0.00 3.02
4149 5962 6.959639 AAAATAAAGCAGAGGACAGTTTCA 57.040 33.333 0.00 0.00 0.00 2.69
4150 5963 7.592903 CAGAAAAATAAAGCAGAGGACAGTTTC 59.407 37.037 0.00 0.00 0.00 2.78
4151 5964 7.068716 ACAGAAAAATAAAGCAGAGGACAGTTT 59.931 33.333 0.00 0.00 0.00 2.66
4152 5965 6.547510 ACAGAAAAATAAAGCAGAGGACAGTT 59.452 34.615 0.00 0.00 0.00 3.16
4153 5966 6.064717 ACAGAAAAATAAAGCAGAGGACAGT 58.935 36.000 0.00 0.00 0.00 3.55
4154 5967 6.348868 GGACAGAAAAATAAAGCAGAGGACAG 60.349 42.308 0.00 0.00 0.00 3.51
4155 5968 5.473504 GGACAGAAAAATAAAGCAGAGGACA 59.526 40.000 0.00 0.00 0.00 4.02
4538 6351 7.736893 ACTAGAAAGTATCCTCAACAACAAGT 58.263 34.615 0.00 0.00 32.84 3.16
4584 6397 6.662755 TGGTACTGGAATCTGCAAATTAGAT 58.337 36.000 0.00 0.00 36.49 1.98
4777 6592 7.886970 TGTACTTATAGTAGCCACAGTATAGGG 59.113 40.741 0.00 0.00 30.12 3.53
5076 6894 0.179108 GCGGTGTACATCTCCTGTCC 60.179 60.000 4.28 0.00 39.39 4.02
5096 6914 1.004044 GATAGCCATGCTAGGTGCCAT 59.996 52.381 1.98 0.00 44.66 4.40
5112 6930 5.506686 TGGAGAAGACAGATCAACGATAG 57.493 43.478 0.00 0.00 46.19 2.08
5116 6934 4.358851 GAGATGGAGAAGACAGATCAACG 58.641 47.826 0.00 0.00 0.00 4.10
5190 7008 3.196039 CAGCAAATCAACCCCATTCATCA 59.804 43.478 0.00 0.00 0.00 3.07
5266 7084 4.960938 ACTGAGTGCTATTTTGTGACTCA 58.039 39.130 0.00 0.00 40.50 3.41
5398 7216 3.971702 GCAACTGGAGGCAGGGGT 61.972 66.667 0.00 0.00 0.00 4.95
5425 7243 2.672996 TCTTGGAAGCGGCAAGGC 60.673 61.111 1.45 0.00 0.00 4.35
5458 7276 2.355946 AGCTCTTCGTTCAGCTCCA 58.644 52.632 0.00 0.00 42.60 3.86
5523 7341 3.755378 AGCTTTGTGCCTGTTATCTGAAG 59.245 43.478 0.00 0.00 44.23 3.02
5693 7511 2.257207 ACCATTCCTTCTCCTGTCGAA 58.743 47.619 0.00 0.00 0.00 3.71
5721 7539 8.791327 TTCACTAATGTCTATTGCATCTTTGA 57.209 30.769 0.00 0.00 0.00 2.69
5818 7636 4.739195 ACAGTTCGTCTCTAATGCTCTTC 58.261 43.478 0.00 0.00 0.00 2.87
5842 7660 8.274939 CACCAAATTGATTGTGTGTTCAAATAC 58.725 33.333 0.00 0.00 37.32 1.89
5856 7677 7.403312 TCCGATCAAATACACCAAATTGATT 57.597 32.000 0.00 0.00 41.29 2.57
5879 7700 7.382218 AGCAAGCAAACTTTACACAAATGTATC 59.618 33.333 0.00 0.00 41.02 2.24
6523 8350 3.872603 TGCTGGGCGTGGTGTTCT 61.873 61.111 0.00 0.00 0.00 3.01
6638 8480 1.283321 GTCCAAGGAGCCCAAGAAGAT 59.717 52.381 0.00 0.00 0.00 2.40
6746 8588 3.706373 TCTGCCGTGGGGAAGCTC 61.706 66.667 0.00 0.00 39.10 4.09
6761 8603 3.733709 CCTTGACAAGGGCAAGTCT 57.266 52.632 24.42 0.00 45.27 3.24


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

AutoCloner maintained by Alex Coulton.