Multiple sequence alignment - TraesCS5D01G105200

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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 TraesCS5D01G105200 chr5D 100.000 7694 0 0 1 7694 119011591 119003898 0.000000e+00 14209.0
1 TraesCS5D01G105200 chr5D 81.520 487 76 11 116 594 108577768 108578248 9.360000e-104 388.0
2 TraesCS5D01G105200 chr5D 88.889 81 8 1 7214 7293 119004300 119004220 1.770000e-16 99.0
3 TraesCS5D01G105200 chr5D 88.889 81 8 1 7292 7372 119004378 119004299 1.770000e-16 99.0
4 TraesCS5D01G105200 chr5B 96.590 6246 157 16 1477 7694 131324063 131317846 0.000000e+00 10303.0
5 TraesCS5D01G105200 chr5B 89.962 1325 90 16 208 1517 131325363 131324067 0.000000e+00 1670.0
6 TraesCS5D01G105200 chr5B 87.654 81 9 1 7214 7293 131318248 131318168 8.220000e-15 93.5
7 TraesCS5D01G105200 chr5A 96.465 6252 182 15 1477 7694 129116593 129110347 0.000000e+00 10285.0
8 TraesCS5D01G105200 chr5A 90.562 1388 94 23 1 1362 129118012 129116636 0.000000e+00 1803.0
9 TraesCS5D01G105200 chr5A 88.889 81 8 1 7214 7293 129110749 129110669 1.770000e-16 99.0
10 TraesCS5D01G105200 chr5A 89.024 82 6 3 7292 7372 129110827 129110748 1.770000e-16 99.0
11 TraesCS5D01G105200 chr6D 87.416 596 64 9 1 591 268679512 268678923 0.000000e+00 675.0
12 TraesCS5D01G105200 chr6B 91.667 396 27 4 3283 3677 720950610 720950220 1.890000e-150 544.0
13 TraesCS5D01G105200 chr6B 86.441 118 14 2 475 591 417141136 417141020 2.250000e-25 128.0
14 TraesCS5D01G105200 chr2B 83.111 450 62 12 145 586 597778782 597778339 1.560000e-106 398.0
15 TraesCS5D01G105200 chr2B 76.383 470 98 12 123 583 89422242 89422707 2.770000e-59 241.0
16 TraesCS5D01G105200 chr2B 86.207 58 7 1 415 472 597836021 597836077 2.320000e-05 62.1
17 TraesCS5D01G105200 chr4B 73.691 802 181 25 4587 5374 161554453 161553668 1.260000e-72 285.0
18 TraesCS5D01G105200 chr4A 76.789 517 106 9 4866 5374 428155890 428155380 2.110000e-70 278.0
19 TraesCS5D01G105200 chr4D 76.117 515 111 9 4866 5374 133477739 133478247 7.660000e-65 259.0
20 TraesCS5D01G105200 chrUn 75.510 392 69 23 207 587 44295149 44295524 4.780000e-37 167.0
21 TraesCS5D01G105200 chrUn 76.615 325 55 17 271 587 44269379 44269690 7.990000e-35 159.0
22 TraesCS5D01G105200 chr7B 81.395 86 11 4 26 110 89976466 89976385 1.790000e-06 65.8
23 TraesCS5D01G105200 chr1A 100.000 29 0 0 439 467 46412734 46412706 4.000000e-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 TraesCS5D01G105200 chr5D 119003898 119011591 7693 True 14209 14209 100.000 1 7694 1 chr5D.!!$R1 7693
1 TraesCS5D01G105200 chr5B 131317846 131324063 6217 True 10303 10303 96.590 1477 7694 1 chr5B.!!$R1 6217
2 TraesCS5D01G105200 chr5B 131324067 131325363 1296 True 1670 1670 89.962 208 1517 1 chr5B.!!$R3 1309
3 TraesCS5D01G105200 chr5A 129110347 129116593 6246 True 10285 10285 96.465 1477 7694 1 chr5A.!!$R1 6217
4 TraesCS5D01G105200 chr5A 129116636 129118012 1376 True 1803 1803 90.562 1 1362 1 chr5A.!!$R2 1361
5 TraesCS5D01G105200 chr6D 268678923 268679512 589 True 675 675 87.416 1 591 1 chr6D.!!$R1 590
6 TraesCS5D01G105200 chr4B 161553668 161554453 785 True 285 285 73.691 4587 5374 1 chr4B.!!$R1 787
7 TraesCS5D01G105200 chr4A 428155380 428155890 510 True 278 278 76.789 4866 5374 1 chr4A.!!$R1 508
8 TraesCS5D01G105200 chr4D 133477739 133478247 508 False 259 259 76.117 4866 5374 1 chr4D.!!$F1 508

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
238 239 0.169672 CGCACTCAGCTGAAAATGGG 59.830 55.000 18.85 18.78 42.61 4.00 F
1806 1839 0.320374 TGCGAAGAACAGTCGGGATT 59.680 50.000 0.00 0.00 38.93 3.01 F
2299 2333 2.029380 GGCTACTTTTCCGTGGCAAAAT 60.029 45.455 0.00 0.00 42.40 1.82 F
3408 3472 1.142870 CTGAACAGTTCCAACCAGGGA 59.857 52.381 10.93 0.00 38.24 4.20 F
4067 4135 1.594331 ACTTTCAACAAGGTCTCCGC 58.406 50.000 0.00 0.00 0.00 5.54 F
5259 5336 1.066143 CATAAGCCCTGAACCAGACGT 60.066 52.381 0.00 0.00 32.44 4.34 F
6272 6352 2.107552 CAAAGGGGTAGGGTTGAGTCAA 59.892 50.000 0.08 0.08 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2073 0.167470 CACACAAAGCTGAGCCATCG 59.833 55.000 0.00 0.0 0.00 3.84 R
2807 2859 1.949525 TCTGCAAGTTGGCAAAGACTC 59.050 47.619 0.00 0.0 44.40 3.36 R
4133 4201 2.028930 AGGAAGCTGAAGTTCGGTACTG 60.029 50.000 13.23 0.0 37.12 2.74 R
4647 4718 1.043022 CTGGAACTGCAAGCCCTTTT 58.957 50.000 0.00 0.0 37.60 2.27 R
5486 5563 0.606401 TAACCAGTGCTGCCTTGAGC 60.606 55.000 0.00 0.0 44.14 4.26 R
6347 6427 0.834687 ACTACTTTCCGGCCACTGGA 60.835 55.000 2.24 0.0 0.00 3.86 R
7555 7640 1.752694 GCGACTCTCCAGAGCCTCT 60.753 63.158 3.33 0.0 45.79 3.69 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
54 55 7.670364 TCTGAATCTCTGAATCTGTTGTGTTA 58.330 34.615 0.00 0.00 0.00 2.41
61 62 7.397476 TCTCTGAATCTGTTGTGTTATACTCCT 59.603 37.037 0.00 0.00 0.00 3.69
64 65 4.713824 TCTGTTGTGTTATACTCCTCCG 57.286 45.455 0.00 0.00 0.00 4.63
77 78 2.496470 ACTCCTCCGCGTTCTATCTTTT 59.504 45.455 4.92 0.00 0.00 2.27
78 79 3.117046 CTCCTCCGCGTTCTATCTTTTC 58.883 50.000 4.92 0.00 0.00 2.29
79 80 2.758979 TCCTCCGCGTTCTATCTTTTCT 59.241 45.455 4.92 0.00 0.00 2.52
80 81 2.860735 CCTCCGCGTTCTATCTTTTCTG 59.139 50.000 4.92 0.00 0.00 3.02
81 82 2.860735 CTCCGCGTTCTATCTTTTCTGG 59.139 50.000 4.92 0.00 0.00 3.86
121 122 3.126343 CCCTTCTGTAACATAAACACCGC 59.874 47.826 0.00 0.00 0.00 5.68
198 199 0.250727 TCAGGACAAAAAGGCTCGGG 60.251 55.000 0.00 0.00 0.00 5.14
234 235 1.220529 CAGACGCACTCAGCTGAAAA 58.779 50.000 18.85 0.00 42.61 2.29
235 236 1.802960 CAGACGCACTCAGCTGAAAAT 59.197 47.619 18.85 3.27 42.61 1.82
237 238 0.877071 ACGCACTCAGCTGAAAATGG 59.123 50.000 18.85 8.15 42.61 3.16
238 239 0.169672 CGCACTCAGCTGAAAATGGG 59.830 55.000 18.85 18.78 42.61 4.00
241 242 0.962356 ACTCAGCTGAAAATGGGCGG 60.962 55.000 18.85 5.06 0.00 6.13
268 269 3.521531 TGCATAATCTAGTGTTGGTCCCA 59.478 43.478 0.00 0.00 0.00 4.37
280 281 2.522367 GGTCCCAAGTTCGACCCCA 61.522 63.158 7.24 0.00 42.39 4.96
281 282 1.302271 GTCCCAAGTTCGACCCCAC 60.302 63.158 0.00 0.00 0.00 4.61
282 283 2.358247 CCCAAGTTCGACCCCACG 60.358 66.667 0.00 0.00 0.00 4.94
283 284 2.358247 CCAAGTTCGACCCCACGG 60.358 66.667 0.00 0.00 0.00 4.94
367 375 6.116126 GTGTCCCAAGCTTCTGTATATTTCT 58.884 40.000 0.00 0.00 0.00 2.52
472 480 1.883275 TGCATTGACCCGACGAAAATT 59.117 42.857 0.00 0.00 0.00 1.82
473 481 3.075148 TGCATTGACCCGACGAAAATTA 58.925 40.909 0.00 0.00 0.00 1.40
481 492 4.073549 ACCCGACGAAAATTATGTTTGGA 58.926 39.130 0.00 0.00 0.00 3.53
497 509 1.454201 TGGACGTTTTTGAGTGTGCA 58.546 45.000 0.00 0.00 0.00 4.57
516 528 2.472909 GCGATTGCCCGAGGGAAAG 61.473 63.158 13.28 0.00 36.44 2.62
523 535 1.258445 GCCCGAGGGAAAGAGTGAGA 61.258 60.000 13.28 0.00 37.50 3.27
527 539 2.163509 CGAGGGAAAGAGTGAGAGACA 58.836 52.381 0.00 0.00 0.00 3.41
536 548 4.013267 AGAGTGAGAGACATTTGTTGGG 57.987 45.455 0.00 0.00 0.00 4.12
542 554 2.711009 AGAGACATTTGTTGGGTGAGGA 59.289 45.455 0.00 0.00 0.00 3.71
576 593 1.139058 ACTAAGCAACCGAGGGCATAG 59.861 52.381 0.00 0.00 37.35 2.23
586 603 5.367945 ACCGAGGGCATAGAAATAGAAAA 57.632 39.130 0.00 0.00 0.00 2.29
668 685 1.134551 GTGGTCTGGCCTTCTCATCTC 60.135 57.143 3.32 0.00 38.35 2.75
669 686 1.198713 GGTCTGGCCTTCTCATCTCA 58.801 55.000 3.32 0.00 0.00 3.27
670 687 1.138661 GGTCTGGCCTTCTCATCTCAG 59.861 57.143 3.32 0.00 0.00 3.35
672 689 2.235898 GTCTGGCCTTCTCATCTCAGTT 59.764 50.000 3.32 0.00 0.00 3.16
673 690 3.449018 GTCTGGCCTTCTCATCTCAGTTA 59.551 47.826 3.32 0.00 0.00 2.24
674 691 4.081420 GTCTGGCCTTCTCATCTCAGTTAA 60.081 45.833 3.32 0.00 0.00 2.01
676 693 5.013079 TCTGGCCTTCTCATCTCAGTTAAAA 59.987 40.000 3.32 0.00 0.00 1.52
677 694 5.630121 TGGCCTTCTCATCTCAGTTAAAAA 58.370 37.500 3.32 0.00 0.00 1.94
780 802 1.601419 CGACCCCAACCGCTCTCTTA 61.601 60.000 0.00 0.00 0.00 2.10
927 954 3.616219 TCTTCTCTTCTCTTCTCTCCCG 58.384 50.000 0.00 0.00 0.00 5.14
977 1004 4.157120 ATCGGTGCTGGTACGGGC 62.157 66.667 2.33 2.33 33.56 6.13
980 1007 4.029809 GGTGCTGGTACGGGCCTT 62.030 66.667 0.84 0.00 33.56 4.35
992 1019 1.377333 GGGCCTTCCTTCTTGGACG 60.377 63.158 0.84 0.00 46.14 4.79
1031 1064 4.459089 GACGGTGAGGGAGCTGGC 62.459 72.222 0.00 0.00 0.00 4.85
1174 1207 3.558033 GGGGCGGGAATTTAGTGATTTA 58.442 45.455 0.00 0.00 0.00 1.40
1273 1306 1.225745 CGTGATCTCGGCGTTTTGC 60.226 57.895 6.85 0.00 45.38 3.68
1362 1395 1.209747 GGGTCCCAAGTCAGTGGATAC 59.790 57.143 1.78 0.00 41.65 2.24
1376 1409 6.332504 CAGTGGATACTGCTAGTTTAAACG 57.667 41.667 12.54 1.01 46.93 3.60
1379 1412 6.932960 AGTGGATACTGCTAGTTTAAACGTTT 59.067 34.615 18.90 18.90 35.34 3.60
1404 1437 2.803451 TGTCGCGCTTGTTTGAATTTT 58.197 38.095 5.56 0.00 0.00 1.82
1412 1445 4.445385 CGCTTGTTTGAATTTTAGCTTGCT 59.555 37.500 0.00 0.00 0.00 3.91
1440 1473 5.355350 AGCTCATAGTTGTGTTTTCTATGCC 59.645 40.000 0.00 0.00 40.12 4.40
1444 1477 4.243007 AGTTGTGTTTTCTATGCCTTGC 57.757 40.909 0.00 0.00 0.00 4.01
1480 1513 7.673504 ACTGATCCTAGCTCATGATAATACTGT 59.326 37.037 0.00 0.00 0.00 3.55
1537 1570 4.040339 TGCGATGGTACCTAATGATGACAT 59.960 41.667 14.36 0.00 38.50 3.06
1539 1572 5.120830 GCGATGGTACCTAATGATGACATTC 59.879 44.000 14.36 0.00 44.34 2.67
1588 1621 7.361713 GCAAATTATACTACTGTGCTGGTTCAA 60.362 37.037 0.00 0.00 0.00 2.69
1602 1635 2.091885 TGGTTCAAGAGGCAGTCCTTTT 60.092 45.455 0.00 0.00 44.46 2.27
1684 1717 5.919348 ATGATGGTGATGGTTCTTAGGAT 57.081 39.130 0.00 0.00 0.00 3.24
1740 1773 7.433131 CAGCGCAATGTGAATTTATGATTTACT 59.567 33.333 11.47 0.00 0.00 2.24
1806 1839 0.320374 TGCGAAGAACAGTCGGGATT 59.680 50.000 0.00 0.00 38.93 3.01
2040 2073 2.685100 GCAGATACCGTTATACCTGCC 58.315 52.381 0.00 0.00 40.58 4.85
2299 2333 2.029380 GGCTACTTTTCCGTGGCAAAAT 60.029 45.455 0.00 0.00 42.40 1.82
2481 2515 7.330900 AGCATTTCATACTCAAGAATTCTGG 57.669 36.000 9.17 6.04 0.00 3.86
2546 2580 7.039082 AGCCAATCCAGAAAGTTTTAATAGCAA 60.039 33.333 0.00 0.00 0.00 3.91
2558 2595 8.693542 AGTTTTAATAGCAAAGCAAAGCATAG 57.306 30.769 0.00 0.00 0.00 2.23
2559 2596 8.522830 AGTTTTAATAGCAAAGCAAAGCATAGA 58.477 29.630 0.00 0.00 0.00 1.98
2560 2597 9.139174 GTTTTAATAGCAAAGCAAAGCATAGAA 57.861 29.630 0.00 0.00 0.00 2.10
2662 2714 6.878317 TGACATGTATCTCTTCCTTTGTAGG 58.122 40.000 0.00 0.00 43.46 3.18
2669 2721 8.548877 TGTATCTCTTCCTTTGTAGGCTAATTT 58.451 33.333 0.00 0.00 41.69 1.82
2950 3002 6.142498 TGTTTATCCAAATATTCTGGGGCAT 58.858 36.000 13.40 6.03 34.46 4.40
3083 3138 3.055385 CCGACCTATTTTCCAGACCAGAA 60.055 47.826 0.00 0.00 0.00 3.02
3209 3264 9.466497 AAATTGGATGTCAACAACTATACATCT 57.534 29.630 12.50 0.00 44.84 2.90
3347 3411 7.781029 GGAGCCAAATCTCTTGAAGGTGACT 62.781 48.000 0.00 0.00 36.23 3.41
3408 3472 1.142870 CTGAACAGTTCCAACCAGGGA 59.857 52.381 10.93 0.00 38.24 4.20
3697 3764 9.512435 CTATCTGTTTTTCCTGCAAATCTATTG 57.488 33.333 0.00 0.00 0.00 1.90
3850 3918 4.690280 GGTAACCATTTTTGGTGCTCAATG 59.310 41.667 0.00 0.00 42.20 2.82
3943 4011 2.341846 TTGTCGAGTGAGGCCTTTTT 57.658 45.000 6.77 0.00 0.00 1.94
3966 4034 2.108952 ACCTGGACAAGCAAATTCCTCT 59.891 45.455 0.00 0.00 0.00 3.69
4064 4132 9.237846 CAAATCTTTTACTTTCAACAAGGTCTC 57.762 33.333 0.00 0.00 0.00 3.36
4065 4133 6.937436 TCTTTTACTTTCAACAAGGTCTCC 57.063 37.500 0.00 0.00 0.00 3.71
4067 4135 1.594331 ACTTTCAACAAGGTCTCCGC 58.406 50.000 0.00 0.00 0.00 5.54
4093 4161 3.200825 AGCAGCCACTCAAGGTTACATAT 59.799 43.478 0.00 0.00 0.00 1.78
4109 4177 9.745018 AGGTTACATATTCTTGCATATGCTTAT 57.255 29.630 27.13 16.44 39.77 1.73
4338 4406 4.036734 CACAAAGTTAAAAGAGCTGAGGCA 59.963 41.667 0.00 0.00 41.70 4.75
4383 4451 2.950309 GGACCTAATGTACTGAGCGAGA 59.050 50.000 0.00 0.00 0.00 4.04
4487 4555 8.515695 AAATTTCTGTGCAGATGATTGAGATA 57.484 30.769 2.47 0.00 37.29 1.98
4534 4602 5.309543 TCCTTCAGGATAGTGGAAACAGAAA 59.690 40.000 0.00 0.00 39.64 2.52
4758 4829 2.084546 GTGGTAGGTTCAACAGCCATC 58.915 52.381 1.13 0.00 0.00 3.51
4764 4835 1.812571 GGTTCAACAGCCATCAACGAT 59.187 47.619 0.00 0.00 0.00 3.73
4800 4871 3.289836 TCATAGGTTTGGCATGGACATG 58.710 45.455 7.91 7.91 41.60 3.21
4872 4943 2.816087 CTGAAACCTACATGCAGTTGCT 59.184 45.455 5.62 0.00 42.66 3.91
4924 4995 3.204526 CATCTGGGACAATCTTGAGAGC 58.795 50.000 0.00 0.00 38.70 4.09
5169 5241 6.391227 AATTTCACTTTCTTGGTACCACAG 57.609 37.500 16.04 15.04 0.00 3.66
5171 5243 4.067972 TCACTTTCTTGGTACCACAGTC 57.932 45.455 16.04 0.00 0.00 3.51
5202 5274 8.821686 TCTATGGGATAAACATTGTGTTGATT 57.178 30.769 0.00 0.00 40.14 2.57
5259 5336 1.066143 CATAAGCCCTGAACCAGACGT 60.066 52.381 0.00 0.00 32.44 4.34
5317 5394 2.364324 ACGAGTTGCCTCTGTTGAGTTA 59.636 45.455 0.00 0.00 38.61 2.24
5388 5465 9.846248 GAAAGAACAGGTACGTACTTATTCTTA 57.154 33.333 31.69 0.00 33.52 2.10
5486 5563 6.424509 TCTTTTGTGCATTTTAGATTGCTTGG 59.575 34.615 0.00 0.00 39.60 3.61
5503 5580 2.282040 GCTCAAGGCAGCACTGGT 60.282 61.111 0.00 0.00 39.43 4.00
5669 5746 2.433604 CCAGCCATCTCAGCTCTTTCTA 59.566 50.000 0.00 0.00 38.95 2.10
5812 5891 7.554476 AGTGAAACCCTTCTAAGATAGAAATGC 59.446 37.037 1.87 0.00 40.34 3.56
6033 6113 5.570234 TTTTATTAGGTCCGGAACAATGC 57.430 39.130 24.28 0.00 0.00 3.56
6042 6122 2.171635 GGAACAATGCCACTCCGAC 58.828 57.895 0.00 0.00 0.00 4.79
6272 6352 2.107552 CAAAGGGGTAGGGTTGAGTCAA 59.892 50.000 0.08 0.08 0.00 3.18
6325 6405 2.171659 TGTTACCAACAGCTGTTCCTCA 59.828 45.455 28.97 18.90 36.25 3.86
6659 6742 4.808414 TGAGTGGTACAGATGGAAGAAG 57.192 45.455 0.00 0.00 41.80 2.85
6660 6743 4.416516 TGAGTGGTACAGATGGAAGAAGA 58.583 43.478 0.00 0.00 41.80 2.87
6661 6744 4.838423 TGAGTGGTACAGATGGAAGAAGAA 59.162 41.667 0.00 0.00 41.80 2.52
6810 6893 5.753721 AGTATCTTCTTGAAGCTCCTTGT 57.246 39.130 5.56 0.00 0.00 3.16
6944 7027 8.740123 AATTTCATATTTGGGATGTGTACGTA 57.260 30.769 0.00 0.00 0.00 3.57
7096 7180 4.401925 AGCTAAGCAGACAACTTTTCCAT 58.598 39.130 0.00 0.00 0.00 3.41
7469 7554 3.849574 TCCTTGATCCCCACATTGTTCTA 59.150 43.478 0.00 0.00 0.00 2.10
7555 7640 2.679082 GGACTATGCAGACCCCTTCTA 58.321 52.381 0.00 0.00 31.12 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.487790 CAGAGATTCAGAGATTAGGATAAAACC 57.512 37.037 0.00 0.00 0.00 3.27
54 55 3.143211 AGATAGAACGCGGAGGAGTAT 57.857 47.619 12.47 0.00 0.00 2.12
61 62 2.232941 ACCAGAAAAGATAGAACGCGGA 59.767 45.455 12.47 0.00 0.00 5.54
64 65 3.994392 TGACACCAGAAAAGATAGAACGC 59.006 43.478 0.00 0.00 0.00 4.84
77 78 1.000843 CCACGAATCAGTGACACCAGA 59.999 52.381 0.84 1.12 44.43 3.86
78 79 1.432514 CCACGAATCAGTGACACCAG 58.567 55.000 0.84 0.00 44.43 4.00
79 80 0.034756 CCCACGAATCAGTGACACCA 59.965 55.000 0.84 0.00 44.43 4.17
80 81 1.298859 GCCCACGAATCAGTGACACC 61.299 60.000 0.84 0.00 44.43 4.16
81 82 1.298859 GGCCCACGAATCAGTGACAC 61.299 60.000 0.00 0.00 44.43 3.67
121 122 1.953017 CTGGAGAGATAGGACGCGG 59.047 63.158 12.47 0.00 0.00 6.46
162 163 4.823989 GTCCTGATATTTGCTGCCTTACAT 59.176 41.667 0.00 0.00 0.00 2.29
173 174 5.335127 CGAGCCTTTTTGTCCTGATATTTG 58.665 41.667 0.00 0.00 0.00 2.32
198 199 4.494199 GCGTCTGTTTGCTTATGGTCATAC 60.494 45.833 0.00 0.00 0.00 2.39
234 235 0.465460 ATTATGCAACGTCCGCCCAT 60.465 50.000 7.39 0.65 0.00 4.00
235 236 1.078072 ATTATGCAACGTCCGCCCA 60.078 52.632 7.39 0.00 0.00 5.36
237 238 1.792949 CTAGATTATGCAACGTCCGCC 59.207 52.381 7.39 0.00 0.00 6.13
238 239 2.218759 CACTAGATTATGCAACGTCCGC 59.781 50.000 0.00 3.08 0.00 5.54
241 242 4.630069 ACCAACACTAGATTATGCAACGTC 59.370 41.667 0.00 0.00 0.00 4.34
268 269 4.324991 GCCCGTGGGGTCGAACTT 62.325 66.667 7.14 0.00 46.51 2.66
472 480 5.574082 CACACTCAAAAACGTCCAAACATA 58.426 37.500 0.00 0.00 0.00 2.29
473 481 4.420168 CACACTCAAAAACGTCCAAACAT 58.580 39.130 0.00 0.00 0.00 2.71
481 492 0.248054 CGCTGCACACTCAAAAACGT 60.248 50.000 0.00 0.00 0.00 3.99
497 509 2.876368 CTTTCCCTCGGGCAATCGCT 62.876 60.000 0.00 0.00 38.60 4.93
506 518 1.474879 GTCTCTCACTCTTTCCCTCGG 59.525 57.143 0.00 0.00 0.00 4.63
507 519 2.163509 TGTCTCTCACTCTTTCCCTCG 58.836 52.381 0.00 0.00 0.00 4.63
516 528 3.499918 CACCCAACAAATGTCTCTCACTC 59.500 47.826 0.00 0.00 0.00 3.51
523 535 3.593442 TTCCTCACCCAACAAATGTCT 57.407 42.857 0.00 0.00 0.00 3.41
527 539 4.714308 TCAGTTTTTCCTCACCCAACAAAT 59.286 37.500 0.00 0.00 0.00 2.32
536 548 5.216614 AGTACTCCTCAGTTTTTCCTCAC 57.783 43.478 0.00 0.00 33.62 3.51
542 554 5.763698 GGTTGCTTAGTACTCCTCAGTTTTT 59.236 40.000 0.00 0.00 33.62 1.94
576 593 8.989980 CCGATAGTGATTAGGGTTTTCTATTTC 58.010 37.037 0.00 0.00 0.00 2.17
586 603 1.612463 GACGCCGATAGTGATTAGGGT 59.388 52.381 0.00 0.00 0.00 4.34
897 924 0.463620 AGAAGAGAAGATGGAGCGGC 59.536 55.000 0.00 0.00 0.00 6.53
898 925 2.031120 AGAGAAGAGAAGATGGAGCGG 58.969 52.381 0.00 0.00 0.00 5.52
972 999 1.846124 TCCAAGAAGGAAGGCCCGT 60.846 57.895 0.00 0.00 45.65 5.28
980 1007 1.248785 CGTCCCTCGTCCAAGAAGGA 61.249 60.000 0.00 0.00 46.75 3.36
992 1019 3.458163 TCGCCACCATCGTCCCTC 61.458 66.667 0.00 0.00 0.00 4.30
1174 1207 2.270352 TCCAGCGAACCAAGAACATT 57.730 45.000 0.00 0.00 0.00 2.71
1273 1306 3.310774 CACATCTCGCCTAAATCAACAGG 59.689 47.826 0.00 0.00 34.85 4.00
1276 1309 2.285834 CGCACATCTCGCCTAAATCAAC 60.286 50.000 0.00 0.00 0.00 3.18
1362 1395 5.008316 ACAAGGGAAACGTTTAAACTAGCAG 59.992 40.000 14.65 3.02 36.00 4.24
1376 1409 1.082104 CAAGCGCGACAAGGGAAAC 60.082 57.895 12.10 0.00 34.27 2.78
1379 1412 1.525077 AAACAAGCGCGACAAGGGA 60.525 52.632 12.10 0.00 34.27 4.20
1412 1445 6.942532 AGAAAACACAACTATGAGCTCAAA 57.057 33.333 22.50 0.00 0.00 2.69
1440 1473 5.712152 AGGATCAGTTTAAACCAAGCAAG 57.288 39.130 14.72 0.00 0.00 4.01
1444 1477 6.173339 TGAGCTAGGATCAGTTTAAACCAAG 58.827 40.000 14.72 5.80 0.00 3.61
1537 1570 2.276201 CGAATGATACAACTGGCCGAA 58.724 47.619 0.00 0.00 0.00 4.30
1539 1572 0.304705 GCGAATGATACAACTGGCCG 59.695 55.000 0.00 0.00 0.00 6.13
1588 1621 7.093771 CCACAAAATTATAAAAGGACTGCCTCT 60.094 37.037 0.00 0.00 46.28 3.69
1715 1748 7.433131 CAGTAAATCATAAATTCACATTGCGCT 59.567 33.333 9.73 0.00 0.00 5.92
1740 1773 1.126488 TTGCTGCATTTTCAACCCCA 58.874 45.000 1.84 0.00 0.00 4.96
1806 1839 1.152984 CAGGTCCCTTGCACACACA 60.153 57.895 0.00 0.00 0.00 3.72
2040 2073 0.167470 CACACAAAGCTGAGCCATCG 59.833 55.000 0.00 0.00 0.00 3.84
2299 2333 7.068103 CCAGTTGGCAGATAAAATATGTTACCA 59.932 37.037 0.00 0.00 0.00 3.25
2422 2456 3.364549 AGGCTTTGTAATGCTGCCATAA 58.635 40.909 0.00 0.00 45.42 1.90
2546 2580 6.336842 ACAATCAGTTTCTATGCTTTGCTT 57.663 33.333 0.00 0.00 0.00 3.91
2558 2595 5.241506 TGGATTCCAGACAACAATCAGTTTC 59.758 40.000 0.00 0.00 38.74 2.78
2559 2596 5.010012 GTGGATTCCAGACAACAATCAGTTT 59.990 40.000 5.39 0.00 33.84 2.66
2560 2597 4.520492 GTGGATTCCAGACAACAATCAGTT 59.480 41.667 5.39 0.00 35.74 3.16
2617 2654 8.078060 TGTCATTATGGAGAGTGTGAAATAGA 57.922 34.615 0.00 0.00 0.00 1.98
2662 2714 8.171164 AGCATGTTAAGGGATTCTAAATTAGC 57.829 34.615 0.00 0.00 0.00 3.09
2669 2721 4.640201 GCACAAGCATGTTAAGGGATTCTA 59.360 41.667 0.00 0.00 37.82 2.10
2807 2859 1.949525 TCTGCAAGTTGGCAAAGACTC 59.050 47.619 0.00 0.00 44.40 3.36
2899 2951 6.540438 TCTTCTCAATAATAGTGGAACGGT 57.460 37.500 0.00 0.00 45.86 4.83
3115 3170 5.869888 AGAAACAAGCATACCTTAACTCGAG 59.130 40.000 11.84 11.84 31.00 4.04
3473 3537 3.757270 TGCGGATTAGGGAAGAACAAAA 58.243 40.909 0.00 0.00 0.00 2.44
3580 3645 5.359194 TTCCAGACTTGACAGAAGAAAGT 57.641 39.130 0.00 0.00 36.87 2.66
3697 3764 7.095355 ACGTGTTGTAGAATATGGTGTTTCTTC 60.095 37.037 0.00 0.00 34.22 2.87
3713 3780 5.517770 GCCTACCTGTTATAACGTGTTGTAG 59.482 44.000 10.92 13.86 0.00 2.74
3943 4011 4.079253 GAGGAATTTGCTTGTCCAGGTAA 58.921 43.478 0.00 0.00 33.57 2.85
4067 4135 2.360852 CTTGAGTGGCTGCTGGGG 60.361 66.667 0.00 0.00 0.00 4.96
4129 4197 2.891580 AGCTGAAGTTCGGTACTGAAGA 59.108 45.455 17.54 0.00 37.12 2.87
4133 4201 2.028930 AGGAAGCTGAAGTTCGGTACTG 60.029 50.000 13.23 0.00 37.12 2.74
4322 4390 7.611467 TCATAAGAATTGCCTCAGCTCTTTTAA 59.389 33.333 0.00 0.00 40.80 1.52
4338 4406 5.066117 CACTCTGCACAGCATCATAAGAATT 59.934 40.000 0.00 0.00 38.13 2.17
4487 4555 4.400884 AGATCTCTCACTTGCTCGTTGTAT 59.599 41.667 0.00 0.00 0.00 2.29
4601 4671 7.448748 AATGTGCTAAACGTTAAGGAGATTT 57.551 32.000 0.00 0.00 36.19 2.17
4647 4718 1.043022 CTGGAACTGCAAGCCCTTTT 58.957 50.000 0.00 0.00 37.60 2.27
4758 4829 2.697425 CGGCTGCTTCGATCGTTG 59.303 61.111 15.94 10.13 0.00 4.10
4800 4871 8.021396 CAGGTAAAAACTCAGTATAAACAAGGC 58.979 37.037 0.00 0.00 0.00 4.35
4857 4928 2.161012 CAGTCAAGCAACTGCATGTAGG 59.839 50.000 15.65 0.00 45.16 3.18
4872 4943 4.522114 TGTCCTTGAACATGAACAGTCAA 58.478 39.130 0.00 0.44 37.30 3.18
4924 4995 4.371855 AGATCAACAAGATGCATGCAAG 57.628 40.909 26.68 16.81 37.00 4.01
5169 5241 9.561069 ACAATGTTTATCCCATAGATTGTAGAC 57.439 33.333 0.00 0.00 36.33 2.59
5171 5243 9.342308 ACACAATGTTTATCCCATAGATTGTAG 57.658 33.333 0.00 0.00 36.33 2.74
5202 5274 3.766591 TGTTTTTGCTTGTCCTCCTGAAA 59.233 39.130 0.00 0.00 0.00 2.69
5259 5336 7.446931 TCAAGGTGCTTATTGTCTCATTAACAA 59.553 33.333 0.00 0.00 40.63 2.83
5388 5465 7.067494 ACAGCTAAGTCACAGAAACAAGAAATT 59.933 33.333 0.00 0.00 0.00 1.82
5486 5563 0.606401 TAACCAGTGCTGCCTTGAGC 60.606 55.000 0.00 0.00 44.14 4.26
5503 5580 5.403512 TCTCTGGTTCTCCTTCCTTCTTAA 58.596 41.667 0.00 0.00 34.23 1.85
5760 5839 3.039011 TCAAGTTATGGGACTAGGCCTC 58.961 50.000 16.16 5.27 0.00 4.70
6033 6113 1.082104 GCTTTTTGCGTCGGAGTGG 60.082 57.895 0.00 0.00 0.00 4.00
6272 6352 1.834263 GTCTGACTCCTGGCTTGGTAT 59.166 52.381 0.00 0.00 0.00 2.73
6347 6427 0.834687 ACTACTTTCCGGCCACTGGA 60.835 55.000 2.24 0.00 0.00 3.86
6421 6501 5.050091 GCCTCACCTCGTTGTCATATTATTG 60.050 44.000 0.00 0.00 0.00 1.90
6659 6742 5.236695 GTGTTAGTCTTTCCACTTGGAGTTC 59.763 44.000 0.00 0.00 46.36 3.01
6660 6743 5.104485 AGTGTTAGTCTTTCCACTTGGAGTT 60.104 40.000 0.00 0.00 46.36 3.01
6661 6744 4.409247 AGTGTTAGTCTTTCCACTTGGAGT 59.591 41.667 0.00 0.00 46.36 3.85
6810 6893 3.901222 TCACTCCACACTGTTGATCCTTA 59.099 43.478 0.00 0.00 0.00 2.69
6944 7027 9.216117 GTACAACAGTAATTTCTAGTGTGGAAT 57.784 33.333 8.99 0.00 32.01 3.01
7096 7180 5.480073 AGTGAGGTGCTTTTATTAAATGCCA 59.520 36.000 18.84 10.28 39.88 4.92
7242 7326 7.359595 TGTATTGTCATTTGTTAGCAACAGAC 58.640 34.615 13.21 13.21 43.27 3.51
7259 7343 4.216257 ACAATGTGTGGAGCTTGTATTGTC 59.784 41.667 0.00 0.00 33.46 3.18
7469 7554 8.806429 TGAATAGTGTGGATAACAATTGTGAT 57.194 30.769 12.82 10.44 41.57 3.06
7555 7640 1.752694 GCGACTCTCCAGAGCCTCT 60.753 63.158 3.33 0.00 45.79 3.69


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

AutoCloner maintained by Alex Coulton.