Multiple sequence alignment - TraesCS5B01G193700

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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 TraesCS5B01G193700 chr5B 100.000 4574 0 0 1 4574 350367208 350371781 0.000000e+00 8447.0
1 TraesCS5B01G193700 chr5B 92.920 339 24 0 4051 4389 399398931 399398593 1.140000e-135 494.0
2 TraesCS5B01G193700 chr5B 90.625 288 26 1 1020 1307 350485442 350485728 9.290000e-102 381.0
3 TraesCS5B01G193700 chr5B 89.547 287 26 4 1013 1296 350392284 350392569 1.210000e-95 361.0
4 TraesCS5B01G193700 chr5A 93.347 2450 108 22 1615 4031 392037260 392034833 0.000000e+00 3570.0
5 TraesCS5B01G193700 chr5A 94.135 1040 38 8 591 1611 392038434 392037399 0.000000e+00 1561.0
6 TraesCS5B01G193700 chr5A 88.552 297 28 6 1016 1307 392000553 392000258 5.630000e-94 355.0
7 TraesCS5B01G193700 chr5A 88.194 288 29 2 1020 1307 391990144 391989862 5.670000e-89 339.0
8 TraesCS5B01G193700 chr5D 95.010 1944 88 4 2059 3999 305710831 305712768 0.000000e+00 3044.0
9 TraesCS5B01G193700 chr5D 90.134 1490 75 25 590 2058 305709365 305710803 0.000000e+00 1871.0
10 TraesCS5B01G193700 chr5D 90.972 288 25 1 1020 1307 305763099 305763385 2.000000e-103 387.0
11 TraesCS5B01G193700 chr5D 88.235 289 31 3 1010 1296 305715048 305715335 4.380000e-90 342.0
12 TraesCS5B01G193700 chr5D 79.596 495 68 15 85 569 20981175 20980704 1.590000e-84 324.0
13 TraesCS5B01G193700 chr6B 95.986 573 23 0 1 573 299044186 299043614 0.000000e+00 931.0
14 TraesCS5B01G193700 chr6B 83.162 582 80 8 2 577 107880460 107879891 2.440000e-142 516.0
15 TraesCS5B01G193700 chr6B 82.759 87 15 0 492 578 56546291 56546377 1.360000e-10 78.7
16 TraesCS5B01G193700 chr2B 93.064 519 36 0 4056 4574 544711908 544712426 0.000000e+00 760.0
17 TraesCS5B01G193700 chr7A 92.678 519 37 1 4056 4574 567442405 567441888 0.000000e+00 747.0
18 TraesCS5B01G193700 chr7A 92.958 355 24 1 1 354 32687287 32686933 2.440000e-142 516.0
19 TraesCS5B01G193700 chr7A 90.431 209 20 0 363 571 32686955 32686747 4.510000e-70 276.0
20 TraesCS5B01G193700 chr3D 89.231 520 29 8 4055 4574 11782755 11783247 3.890000e-175 625.0
21 TraesCS5B01G193700 chr3D 75.292 514 70 26 85 588 380976815 380976349 4.670000e-45 193.0
22 TraesCS5B01G193700 chr3D 86.207 145 16 3 1907 2049 138078862 138079004 2.200000e-33 154.0
23 TraesCS5B01G193700 chr3D 96.739 92 1 2 3926 4017 570803527 570803438 7.930000e-33 152.0
24 TraesCS5B01G193700 chr3D 94.792 96 4 1 3920 4014 612302308 612302403 1.030000e-31 148.0
25 TraesCS5B01G193700 chr3D 92.308 104 5 3 3915 4017 520219097 520218996 1.330000e-30 145.0
26 TraesCS5B01G193700 chr3D 81.379 145 14 5 18 162 606303454 606303585 6.260000e-19 106.0
27 TraesCS5B01G193700 chr7B 90.476 252 23 1 4056 4307 750142553 750142303 9.490000e-87 331.0
28 TraesCS5B01G193700 chr7B 86.099 223 26 2 4333 4551 537798773 537798994 7.650000e-58 235.0
29 TraesCS5B01G193700 chr6A 91.250 240 21 0 4057 4296 73446845 73447084 1.230000e-85 327.0
30 TraesCS5B01G193700 chr1D 82.333 300 47 5 1003 1296 457531713 457531414 5.870000e-64 255.0
31 TraesCS5B01G193700 chr4B 85.185 162 16 6 1887 2048 658773063 658773216 4.740000e-35 159.0
32 TraesCS5B01G193700 chr4B 86.713 143 16 3 1910 2051 526931208 526931348 6.130000e-34 156.0
33 TraesCS5B01G193700 chr4B 82.184 174 21 9 1879 2051 155374406 155374570 1.720000e-29 141.0
34 TraesCS5B01G193700 chr1A 84.242 165 22 4 5 168 561757275 561757114 1.700000e-34 158.0
35 TraesCS5B01G193700 chr1A 93.000 100 3 3 3925 4021 121132423 121132325 4.770000e-30 143.0
36 TraesCS5B01G193700 chr1A 80.814 172 27 3 398 569 367013048 367013213 3.710000e-26 130.0
37 TraesCS5B01G193700 chr1B 86.093 151 13 4 1898 2048 442177125 442177267 6.130000e-34 156.0
38 TraesCS5B01G193700 chr4A 93.269 104 3 3 3917 4017 628924500 628924398 2.850000e-32 150.0
39 TraesCS5B01G193700 chr4A 83.537 164 19 4 1888 2051 363744703 363744548 3.690000e-31 147.0
40 TraesCS5B01G193700 chr4A 90.411 73 7 0 4274 4346 727745364 727745436 3.770000e-16 97.1
41 TraesCS5B01G193700 chr4D 84.277 159 17 4 1893 2051 168219332 168219182 1.030000e-31 148.0
42 TraesCS5B01G193700 chr3A 93.137 102 3 4 3920 4018 655646770 655646670 3.690000e-31 147.0
43 TraesCS5B01G193700 chr3B 91.509 106 5 4 3921 4025 685061561 685061459 4.770000e-30 143.0
44 TraesCS5B01G193700 chr3B 84.270 89 14 0 492 580 97824785 97824873 2.270000e-13 87.9
45 TraesCS5B01G193700 chr2D 86.555 119 15 1 452 569 523159582 523159464 3.710000e-26 130.0


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 TraesCS5B01G193700 chr5B 350367208 350371781 4573 False 8447.000000 8447 100.000000 1 4574 1 chr5B.!!$F1 4573
1 TraesCS5B01G193700 chr5A 392034833 392038434 3601 True 2565.500000 3570 93.741000 591 4031 2 chr5A.!!$R3 3440
2 TraesCS5B01G193700 chr5D 305709365 305715335 5970 False 1752.333333 3044 91.126333 590 3999 3 chr5D.!!$F2 3409
3 TraesCS5B01G193700 chr6B 299043614 299044186 572 True 931.000000 931 95.986000 1 573 1 chr6B.!!$R2 572
4 TraesCS5B01G193700 chr6B 107879891 107880460 569 True 516.000000 516 83.162000 2 577 1 chr6B.!!$R1 575
5 TraesCS5B01G193700 chr2B 544711908 544712426 518 False 760.000000 760 93.064000 4056 4574 1 chr2B.!!$F1 518
6 TraesCS5B01G193700 chr7A 567441888 567442405 517 True 747.000000 747 92.678000 4056 4574 1 chr7A.!!$R1 518
7 TraesCS5B01G193700 chr7A 32686747 32687287 540 True 396.000000 516 91.694500 1 571 2 chr7A.!!$R2 570

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
750 781 0.609131 CAACCCAAGCCATCGTCCTT 60.609 55.0 0.00 0.00 0.00 3.36 F
1468 1517 0.606401 AAGCTGGTGTACGCTTGCAT 60.606 50.0 20.02 10.15 44.18 3.96 F
3385 3612 0.106819 CAGGGAGAGGGCAAGAATGG 60.107 60.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2677 2901 0.772124 TTCCACCAAAGAGCCCTCCT 60.772 55.0 0.00 0.0 0.0 3.69 R
3461 3688 0.531532 GATCACAGTGGCATCCTCCG 60.532 60.0 0.00 0.0 0.0 4.63 R
4235 4564 0.461339 TATCTTTGGACTTCGCGGCC 60.461 55.0 6.13 3.6 0.0 6.13 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
107 108 0.821301 TTGCTGCAACCATTGTCGGA 60.821 50.000 11.69 0.00 0.00 4.55
314 320 1.079127 CGAGAAACGCATGGGAGGT 60.079 57.895 17.76 0.39 34.51 3.85
441 468 0.683973 CCACTGCTCCTGTTCTCTGT 59.316 55.000 0.00 0.00 0.00 3.41
500 529 4.429854 GGAGAAGCCTAAATCTGATGGT 57.570 45.455 0.00 0.00 0.00 3.55
573 602 2.928361 CGCCGGCGCTTATTACTG 59.072 61.111 38.48 5.99 0.00 2.74
577 606 1.522806 CGGCGCTTATTACTGCCCA 60.523 57.895 7.64 0.00 44.71 5.36
578 607 0.884704 CGGCGCTTATTACTGCCCAT 60.885 55.000 7.64 0.00 44.71 4.00
579 608 0.875059 GGCGCTTATTACTGCCCATC 59.125 55.000 7.64 0.00 41.70 3.51
580 609 1.543429 GGCGCTTATTACTGCCCATCT 60.543 52.381 7.64 0.00 41.70 2.90
581 610 2.289444 GGCGCTTATTACTGCCCATCTA 60.289 50.000 7.64 0.00 41.70 1.98
582 611 3.399330 GCGCTTATTACTGCCCATCTAA 58.601 45.455 0.00 0.00 0.00 2.10
583 612 3.813166 GCGCTTATTACTGCCCATCTAAA 59.187 43.478 0.00 0.00 0.00 1.85
584 613 4.274950 GCGCTTATTACTGCCCATCTAAAA 59.725 41.667 0.00 0.00 0.00 1.52
585 614 5.220970 GCGCTTATTACTGCCCATCTAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
678 709 1.002792 GCGTTGAATATTCCGGCTTCC 60.003 52.381 12.90 0.00 0.00 3.46
750 781 0.609131 CAACCCAAGCCATCGTCCTT 60.609 55.000 0.00 0.00 0.00 3.36
752 783 1.815421 CCCAAGCCATCGTCCTTCG 60.815 63.158 0.00 0.00 41.41 3.79
826 857 3.866910 TCAATTATAGACGAACGGTTGCC 59.133 43.478 0.00 0.00 0.00 4.52
862 893 2.906354 CTCTCCATAACCACGGGAAAG 58.094 52.381 0.00 0.00 0.00 2.62
896 927 3.744719 CCCGCGAAGGAGACGACA 61.745 66.667 8.23 0.00 45.00 4.35
1361 1410 3.469899 TTGTCGATCCAATTTTGCGAG 57.530 42.857 0.00 0.00 0.00 5.03
1393 1442 4.532126 TGGATCATCTCGGGTATATGCTTT 59.468 41.667 0.00 0.00 0.00 3.51
1416 1465 3.813724 GGTTTATCCGCAGATCCCTTAAC 59.186 47.826 0.00 0.00 33.67 2.01
1422 1471 4.703897 TCCGCAGATCCCTTAACTATTTG 58.296 43.478 0.00 0.00 0.00 2.32
1427 1476 5.504173 GCAGATCCCTTAACTATTTGCGTTC 60.504 44.000 0.00 0.00 0.00 3.95
1468 1517 0.606401 AAGCTGGTGTACGCTTGCAT 60.606 50.000 20.02 10.15 44.18 3.96
1469 1518 1.021390 AGCTGGTGTACGCTTGCATC 61.021 55.000 20.02 2.98 31.17 3.91
1538 1587 2.930040 CGAAGCAAATCACGTGGACTAT 59.070 45.455 17.00 0.00 0.00 2.12
1539 1588 4.109766 CGAAGCAAATCACGTGGACTATA 58.890 43.478 17.00 0.00 0.00 1.31
1540 1589 4.745125 CGAAGCAAATCACGTGGACTATAT 59.255 41.667 17.00 0.00 0.00 0.86
1579 1628 9.319143 GGAGTAGCATATTCGCATCTAAAATAT 57.681 33.333 0.00 0.00 0.00 1.28
1597 1646 5.843019 AATATGATCCCCGAATGGTAGTT 57.157 39.130 0.00 0.00 0.00 2.24
1616 1665 6.590677 GGTAGTTGACCTTTATCTGTCTGAAC 59.409 42.308 0.00 0.00 45.89 3.18
1617 1666 6.174720 AGTTGACCTTTATCTGTCTGAACA 57.825 37.500 0.00 0.00 32.67 3.18
1659 1843 5.211266 TGTGAAATAACCAAATACTCGCG 57.789 39.130 0.00 0.00 0.00 5.87
1661 1845 3.242155 TGAAATAACCAAATACTCGCGCG 60.242 43.478 26.76 26.76 0.00 6.86
1830 2026 1.469917 GCATCCAATGTGCGAATTCG 58.530 50.000 23.34 23.34 43.27 3.34
1895 2091 4.154802 TGGGATTGCTAGATACCCCATA 57.845 45.455 8.69 0.00 38.79 2.74
1903 2099 4.219944 TGCTAGATACCCCATACGTTCATC 59.780 45.833 0.00 0.00 0.00 2.92
1913 2109 7.918076 ACCCCATACGTTCATCATTATAAGAT 58.082 34.615 0.00 0.00 0.00 2.40
1953 2149 8.495949 CAATATGGACTACATACGGATTGAAAC 58.504 37.037 0.00 0.00 44.41 2.78
1959 2155 3.259064 ACATACGGATTGAAACGAGTGG 58.741 45.455 0.00 0.00 0.00 4.00
1961 2157 2.080286 ACGGATTGAAACGAGTGGAG 57.920 50.000 0.00 0.00 0.00 3.86
2078 2302 6.169800 TGCAGCCAATAATAATGCTACGATA 58.830 36.000 0.00 0.00 37.76 2.92
2224 2448 4.222588 GCTATCCAATCTCTAGTGGCAGAT 59.777 45.833 0.00 0.00 40.76 2.90
2387 2611 4.392047 TCACATTGTTGCTCTCATCAGTT 58.608 39.130 0.00 0.00 0.00 3.16
2450 2674 5.213891 TCATTTCTGCAACAGTGAGAGTA 57.786 39.130 0.00 0.00 32.61 2.59
2533 2757 3.264193 AGGCTGTTGTGAAGATACCATCA 59.736 43.478 0.00 0.00 0.00 3.07
2713 2937 4.140924 GGTGGAAAGATGGGGGATTATCTT 60.141 45.833 0.00 0.00 43.49 2.40
2718 2942 6.596869 AAAGATGGGGGATTATCTTTCTGA 57.403 37.500 6.43 0.00 45.58 3.27
2824 3048 5.133941 GGACTACCTGATGACTCATCTACA 58.866 45.833 18.01 0.55 41.06 2.74
2831 3055 3.701542 TGATGACTCATCTACAGGTGTCC 59.298 47.826 18.01 0.00 41.06 4.02
3040 3267 6.253746 CACAAACTGCTGATAAGCTATGAAC 58.746 40.000 3.06 0.00 35.49 3.18
3104 3331 4.129380 CCCATATTTGCAGAGATCGTTCA 58.871 43.478 0.00 0.00 0.00 3.18
3220 3447 0.107897 TGCATACGGCTACAACCCTG 60.108 55.000 0.00 0.00 45.15 4.45
3242 3469 1.071385 CTCATATGGGGCTGGAGTGAC 59.929 57.143 2.13 0.00 0.00 3.67
3255 3482 0.249489 GAGTGACCAGTGTTGCGAGT 60.249 55.000 0.00 0.00 0.00 4.18
3273 3500 2.045926 GACAGGTCCAATGCCGCT 60.046 61.111 0.00 0.00 0.00 5.52
3348 3575 4.142160 TGCTTCATCTACTCGCTGTTGTAT 60.142 41.667 0.00 0.00 0.00 2.29
3385 3612 0.106819 CAGGGAGAGGGCAAGAATGG 60.107 60.000 0.00 0.00 0.00 3.16
3390 3617 0.915364 AGAGGGCAAGAATGGACTCC 59.085 55.000 0.00 0.00 0.00 3.85
3421 3648 1.536922 CGGAGTTGCAGCATATCGAGT 60.537 52.381 2.55 0.00 0.00 4.18
3461 3688 0.179142 GGAGACTTCTACGCGGGAAC 60.179 60.000 12.47 4.00 0.00 3.62
3511 3738 4.472833 AGTATGGTGAGGAAGAGCTTGATT 59.527 41.667 0.00 0.00 0.00 2.57
3555 3782 3.253921 TGATGCATCACCAAGTTGAACAG 59.746 43.478 25.42 0.00 0.00 3.16
3602 3829 4.267928 GCGTGATATGTACAGGAAGTTGTC 59.732 45.833 0.33 0.00 32.56 3.18
3605 3832 2.762535 ATGTACAGGAAGTTGTCGGG 57.237 50.000 0.33 0.00 32.56 5.14
3667 3894 4.209538 TGCATATTTTCAGGGGATCAGTG 58.790 43.478 0.00 0.00 0.00 3.66
3791 4018 2.295349 AGCAGCAATCAGAAGTGTTTGG 59.705 45.455 0.00 0.00 34.96 3.28
3855 4082 8.154856 ACAGTTACCAGTTCAAGCTTTATCTAA 58.845 33.333 0.00 0.00 0.00 2.10
3857 4084 7.606839 AGTTACCAGTTCAAGCTTTATCTAACC 59.393 37.037 0.00 0.00 0.00 2.85
3880 4107 4.391216 CGAAAGTGCATGAGAAATGAGACT 59.609 41.667 0.00 0.00 0.00 3.24
3890 4117 8.306038 GCATGAGAAATGAGACTCAGTATATCT 58.694 37.037 11.52 8.19 44.50 1.98
3917 4144 6.427300 CATGCATGCAAAATTTCAACAAAC 57.573 33.333 26.68 0.00 0.00 2.93
4100 4429 8.608844 ACTTTATTCCTCAAATAATAGCGAGG 57.391 34.615 0.00 0.00 45.40 4.63
4163 4492 9.178758 ACAGAATCCCAAAACATAGAAGAATAC 57.821 33.333 0.00 0.00 0.00 1.89
4198 4527 2.238144 AGTGTGCTAACTCATGAGCCAT 59.762 45.455 22.83 11.60 37.94 4.40
4212 4541 5.240844 TCATGAGCCATCATATTTGCTTCAG 59.759 40.000 0.00 0.00 44.58 3.02
4235 4564 4.201930 GGTAGACAGTGAGAATACTCCACG 60.202 50.000 0.00 0.00 41.99 4.94
4237 4566 1.204941 ACAGTGAGAATACTCCACGGC 59.795 52.381 0.00 0.00 41.99 5.68
4241 4673 2.960129 GAATACTCCACGGCCGCG 60.960 66.667 28.58 17.55 0.00 6.46
4288 4821 2.287970 CCAGTACAGTAGCAACGTCACA 60.288 50.000 0.00 0.00 0.00 3.58
4349 5592 4.406003 ACAAAGCTATTATCCGACTCCACT 59.594 41.667 0.00 0.00 0.00 4.00
4351 5594 5.968528 AAGCTATTATCCGACTCCACTAG 57.031 43.478 0.00 0.00 0.00 2.57
4374 6198 4.512571 GCACTTTGTTGCATCCAATTTTCT 59.487 37.500 0.00 0.00 42.49 2.52
4404 6228 1.985473 TAGCCCGTTCCTAATCGCTA 58.015 50.000 0.00 0.00 0.00 4.26
4415 6239 2.480416 CCTAATCGCTATCATCTCCGCC 60.480 54.545 0.00 0.00 0.00 6.13
4416 6240 0.969149 AATCGCTATCATCTCCGCCA 59.031 50.000 0.00 0.00 0.00 5.69
4427 6251 3.055458 TCATCTCCGCCAAATCAACACTA 60.055 43.478 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 2.736144 TCGTAGCAAACTCCGACAAT 57.264 45.000 0.00 0.00 28.23 2.71
107 108 1.374252 CTGCCGGTCGTAGCAAACT 60.374 57.895 1.90 0.00 38.82 2.66
381 387 3.717294 GACCACCTCCCACGCCAT 61.717 66.667 0.00 0.00 0.00 4.40
479 508 4.429854 ACCATCAGATTTAGGCTTCTCC 57.570 45.455 0.00 0.00 0.00 3.71
490 519 3.007506 TGTCCACGTACAACCATCAGATT 59.992 43.478 0.00 0.00 0.00 2.40
584 613 3.523972 GGTCAGATAGGGGAGGTCTTTTT 59.476 47.826 0.00 0.00 0.00 1.94
585 614 3.116174 GGTCAGATAGGGGAGGTCTTTT 58.884 50.000 0.00 0.00 0.00 2.27
586 615 2.319438 AGGTCAGATAGGGGAGGTCTTT 59.681 50.000 0.00 0.00 0.00 2.52
587 616 1.940957 AGGTCAGATAGGGGAGGTCTT 59.059 52.381 0.00 0.00 0.00 3.01
588 617 1.219213 CAGGTCAGATAGGGGAGGTCT 59.781 57.143 0.00 0.00 0.00 3.85
649 680 0.539986 ATATTCAACGCGTGGACCCT 59.460 50.000 17.75 6.80 0.00 4.34
651 682 1.329599 GGAATATTCAACGCGTGGACC 59.670 52.381 17.75 10.32 0.00 4.46
750 781 1.613437 TGTCAGATCAGTTGACTGCGA 59.387 47.619 13.05 0.00 44.08 5.10
752 783 2.759191 TGTGTCAGATCAGTTGACTGC 58.241 47.619 13.05 7.88 44.08 4.40
826 857 2.500442 GAGCGACTGACGTGCGATG 61.500 63.158 0.00 0.00 44.60 3.84
896 927 3.692406 GAACGAGGAGGGCGGTGT 61.692 66.667 0.00 0.00 0.00 4.16
937 968 1.810755 CTTTTGGTCTTTCGCCTACCC 59.189 52.381 0.00 0.00 31.97 3.69
939 970 2.742589 CCTCTTTTGGTCTTTCGCCTAC 59.257 50.000 0.00 0.00 0.00 3.18
940 971 2.874457 GCCTCTTTTGGTCTTTCGCCTA 60.874 50.000 0.00 0.00 0.00 3.93
948 992 2.034221 GGCGGCCTCTTTTGGTCT 59.966 61.111 12.87 0.00 0.00 3.85
993 1042 4.552365 GCCTCTGCCATAGCGCCA 62.552 66.667 2.29 0.00 44.31 5.69
1361 1410 0.608582 GAGATGATCCATGCCCCAGC 60.609 60.000 0.00 0.00 40.48 4.85
1393 1442 1.507140 AGGGATCTGCGGATAAACCA 58.493 50.000 19.78 0.00 38.90 3.67
1416 1465 1.061131 CGTGAGCCAGAACGCAAATAG 59.939 52.381 0.00 0.00 32.40 1.73
1468 1517 6.932400 TCAGATTTCGCACCTTTTACTTAAGA 59.068 34.615 10.09 0.00 0.00 2.10
1469 1518 7.129109 TCAGATTTCGCACCTTTTACTTAAG 57.871 36.000 0.00 0.00 0.00 1.85
1579 1628 2.169769 GTCAACTACCATTCGGGGATCA 59.830 50.000 0.00 0.00 42.91 2.92
1659 1843 6.017933 CAGAAATCAAACATAACTGTCTCGC 58.982 40.000 0.00 0.00 33.36 5.03
1661 1845 8.316640 AGTCAGAAATCAAACATAACTGTCTC 57.683 34.615 0.00 0.00 33.36 3.36
1849 2045 4.323104 CCCAGATTTTTAATCCCCGCAAAA 60.323 41.667 0.00 0.00 0.00 2.44
1855 2051 3.454447 CCCAACCCAGATTTTTAATCCCC 59.546 47.826 0.00 0.00 0.00 4.81
1895 2091 9.173021 TCCAAAACATCTTATAATGATGAACGT 57.827 29.630 21.61 0.00 42.68 3.99
1953 2149 4.095610 GTTTTTGTGTGTTTCTCCACTCG 58.904 43.478 0.00 0.00 36.30 4.18
2224 2448 5.419788 ACCCCGCGTATTATCATCAGTATAA 59.580 40.000 4.92 0.00 0.00 0.98
2387 2611 2.359354 CAACGCCCCGACCATCAA 60.359 61.111 0.00 0.00 0.00 2.57
2533 2757 3.464907 CTGAGCCACGATGATCTGAAAT 58.535 45.455 0.00 0.00 0.00 2.17
2677 2901 0.772124 TTCCACCAAAGAGCCCTCCT 60.772 55.000 0.00 0.00 0.00 3.69
2831 3055 7.087409 TGATAAACATTACAAGTCCATGCAG 57.913 36.000 0.00 0.00 0.00 4.41
2845 3069 4.545678 TGCTTAGCCCCATGATAAACATT 58.454 39.130 0.29 0.00 37.07 2.71
3066 3293 1.079612 GGGGCTGCACATGAAAAGC 60.080 57.895 3.46 4.68 34.86 3.51
3104 3331 4.906664 AGATACTTGCCCTTGATCTCTCAT 59.093 41.667 0.00 0.00 0.00 2.90
3220 3447 1.071385 CACTCCAGCCCCATATGAGAC 59.929 57.143 3.65 0.00 0.00 3.36
3242 3469 1.224069 CCTGTCACTCGCAACACTGG 61.224 60.000 0.00 0.00 0.00 4.00
3255 3482 2.359850 GCGGCATTGGACCTGTCA 60.360 61.111 0.00 0.00 0.00 3.58
3385 3612 3.651803 CTCCGATGTGATAAGGGAGTC 57.348 52.381 0.00 0.00 39.51 3.36
3390 3617 2.868583 CTGCAACTCCGATGTGATAAGG 59.131 50.000 0.00 0.00 0.00 2.69
3421 3648 3.009033 CCTACTCCATGACACCTTTCCAA 59.991 47.826 0.00 0.00 0.00 3.53
3461 3688 0.531532 GATCACAGTGGCATCCTCCG 60.532 60.000 0.00 0.00 0.00 4.63
3511 3738 5.407084 TCAACGCTTTTTCATCGTCATTAGA 59.593 36.000 0.00 0.00 35.18 2.10
3555 3782 5.194432 TCTAATCACCTGAGACTACCACTC 58.806 45.833 0.00 0.00 35.26 3.51
3602 3829 1.417890 AGCATAATCCTGAACTCCCCG 59.582 52.381 0.00 0.00 0.00 5.73
3605 3832 3.696051 TGCAAAGCATAATCCTGAACTCC 59.304 43.478 0.00 0.00 31.71 3.85
3667 3894 2.415426 CAAACAACACCCGGGCAC 59.585 61.111 24.08 0.00 0.00 5.01
3791 4018 5.628130 ACCCCCAAAAAGTTACTACTTCTC 58.372 41.667 0.00 0.00 43.74 2.87
3855 4082 3.411446 TCATTTCTCATGCACTTTCGGT 58.589 40.909 0.00 0.00 0.00 4.69
3857 4084 4.391216 AGTCTCATTTCTCATGCACTTTCG 59.609 41.667 0.00 0.00 0.00 3.46
3894 4121 6.202937 AGTTTGTTGAAATTTTGCATGCATG 58.797 32.000 23.37 22.70 0.00 4.06
3898 4125 8.173775 TGTTGTAGTTTGTTGAAATTTTGCATG 58.826 29.630 0.00 0.00 0.00 4.06
3907 4134 4.675671 CGGGCTTGTTGTAGTTTGTTGAAA 60.676 41.667 0.00 0.00 0.00 2.69
3912 4139 1.944709 GACGGGCTTGTTGTAGTTTGT 59.055 47.619 0.00 0.00 0.00 2.83
3917 4144 1.204941 AGCTAGACGGGCTTGTTGTAG 59.795 52.381 0.00 0.00 36.56 2.74
4010 4245 3.140144 ACAAAATGGGAGAGGGAGAAACA 59.860 43.478 0.00 0.00 0.00 2.83
4011 4246 3.767711 ACAAAATGGGAGAGGGAGAAAC 58.232 45.455 0.00 0.00 0.00 2.78
4163 4492 8.371770 AGTTAGCACACTTTTCTTTTAGAGAG 57.628 34.615 0.00 0.00 35.37 3.20
4176 4505 2.038952 TGGCTCATGAGTTAGCACACTT 59.961 45.455 23.38 0.00 40.61 3.16
4178 4507 2.099141 TGGCTCATGAGTTAGCACAC 57.901 50.000 23.38 4.50 40.61 3.82
4198 4527 6.070824 TCACTGTCTACCTGAAGCAAATATGA 60.071 38.462 0.00 0.00 0.00 2.15
4212 4541 4.201930 CGTGGAGTATTCTCACTGTCTACC 60.202 50.000 1.51 0.00 42.05 3.18
4235 4564 0.461339 TATCTTTGGACTTCGCGGCC 60.461 55.000 6.13 3.60 0.00 6.13
4237 4566 3.788797 GCAATTATCTTTGGACTTCGCGG 60.789 47.826 6.13 0.00 0.00 6.46
4241 4673 5.713025 TGCAAGCAATTATCTTTGGACTTC 58.287 37.500 0.00 0.00 0.00 3.01
4288 4821 1.521764 TCCAGATGCATATGTGGGGT 58.478 50.000 19.36 0.00 45.41 4.95
4349 5592 4.870123 AATTGGATGCAACAAAGTGCTA 57.130 36.364 0.12 0.00 45.17 3.49
4351 5594 4.512571 AGAAAATTGGATGCAACAAAGTGC 59.487 37.500 0.12 2.16 45.15 4.40
4391 6215 4.416620 CGGAGATGATAGCGATTAGGAAC 58.583 47.826 0.00 0.00 0.00 3.62
4397 6221 0.969149 TGGCGGAGATGATAGCGATT 59.031 50.000 0.00 0.00 0.00 3.34
4404 6228 2.684881 GTGTTGATTTGGCGGAGATGAT 59.315 45.455 0.00 0.00 0.00 2.45
4427 6251 5.145564 ACATGGTATATACCTCAACTCGGT 58.854 41.667 28.12 13.66 46.58 4.69


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

AutoCloner maintained by Alex Coulton.