Multiple sequence alignment - TraesCS4D01G078000

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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 TraesCS4D01G078000 chr4D 100.000 4435 0 0 1 4435 52466498 52470932 0.000000e+00 8191.0
1 TraesCS4D01G078000 chr4D 97.192 819 22 1 1 818 64225376 64226194 0.000000e+00 1384.0
2 TraesCS4D01G078000 chr4D 80.510 431 68 8 1023 1448 482760651 482761070 2.570000e-82 316.0
3 TraesCS4D01G078000 chr4B 95.121 2685 107 14 843 3511 76813264 76815940 0.000000e+00 4211.0
4 TraesCS4D01G078000 chr4B 85.446 426 60 2 1023 1447 76622196 76622620 4.070000e-120 442.0
5 TraesCS4D01G078000 chr4B 93.962 265 10 2 3943 4204 76816578 76816839 3.210000e-106 396.0
6 TraesCS4D01G078000 chr4B 88.623 334 21 9 3619 3945 76816213 76816536 1.500000e-104 390.0
7 TraesCS4D01G078000 chr4B 96.537 231 8 0 4205 4435 76816898 76817128 2.500000e-102 383.0
8 TraesCS4D01G078000 chr4A 92.179 2621 149 30 918 3506 544204344 544201748 0.000000e+00 3653.0
9 TraesCS4D01G078000 chr4A 92.955 511 19 4 3711 4205 544201424 544200915 0.000000e+00 728.0
10 TraesCS4D01G078000 chr4A 84.651 430 64 2 1019 1447 544390833 544390405 1.140000e-115 427.0
11 TraesCS4D01G078000 chr4A 97.368 228 6 0 4208 4435 544200861 544200634 5.380000e-104 388.0
12 TraesCS4D01G078000 chr3D 97.327 823 18 4 1 822 94712015 94712834 0.000000e+00 1395.0
13 TraesCS4D01G078000 chr3D 96.829 820 24 2 1 818 213968901 213968082 0.000000e+00 1369.0
14 TraesCS4D01G078000 chr7D 97.314 819 20 2 1 818 611047006 611047823 0.000000e+00 1389.0
15 TraesCS4D01G078000 chr7D 97.087 824 20 4 1 822 414308808 414309629 0.000000e+00 1386.0
16 TraesCS4D01G078000 chr7D 96.829 820 23 3 1 818 369901030 369901848 0.000000e+00 1367.0
17 TraesCS4D01G078000 chr7D 96.602 824 24 3 1 823 251560000 251559180 0.000000e+00 1363.0
18 TraesCS4D01G078000 chr7D 79.327 1040 193 14 2462 3499 124300220 124301239 0.000000e+00 710.0
19 TraesCS4D01G078000 chr7D 80.000 505 81 15 979 1470 124298517 124299014 5.460000e-94 355.0
20 TraesCS4D01G078000 chr5D 97.192 819 22 1 1 818 532712010 532712828 0.000000e+00 1384.0
21 TraesCS4D01G078000 chr5D 80.263 912 152 20 2498 3395 484427553 484426656 0.000000e+00 662.0
22 TraesCS4D01G078000 chr5D 80.074 813 140 14 2513 3311 444712088 444712892 6.390000e-163 584.0
23 TraesCS4D01G078000 chr5D 80.769 494 75 13 1033 1522 484428841 484428364 7.010000e-98 368.0
24 TraesCS4D01G078000 chr2D 96.739 828 22 5 1 825 592372165 592372990 0.000000e+00 1375.0
25 TraesCS4D01G078000 chr7A 78.933 1068 201 16 2435 3499 126866666 126867712 0.000000e+00 704.0
26 TraesCS4D01G078000 chr7A 79.592 490 83 12 979 1457 126865007 126865490 7.110000e-88 335.0
27 TraesCS4D01G078000 chr7B 79.795 975 182 11 2462 3435 86141072 86142032 0.000000e+00 695.0
28 TraesCS4D01G078000 chr7B 78.715 498 81 13 979 1457 86139274 86139765 4.310000e-80 309.0
29 TraesCS4D01G078000 chr5B 80.765 915 142 23 2498 3395 595631941 595631044 0.000000e+00 684.0
30 TraesCS4D01G078000 chr5B 79.587 921 162 19 2498 3405 595645354 595644447 1.740000e-178 636.0
31 TraesCS4D01G078000 chr5B 77.756 508 93 13 1033 1536 595633228 595632737 1.210000e-75 294.0
32 TraesCS4D01G078000 chr5B 94.444 54 2 1 4002 4054 222724836 222724783 1.020000e-11 82.4
33 TraesCS4D01G078000 chr5A 77.472 799 167 10 2495 3282 659822209 659821413 2.420000e-127 466.0
34 TraesCS4D01G078000 chr5A 80.165 484 78 11 1033 1514 606060581 606060114 3.280000e-91 346.0


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 TraesCS4D01G078000 chr4D 52466498 52470932 4434 False 8191.000000 8191 100.000000 1 4435 1 chr4D.!!$F1 4434
1 TraesCS4D01G078000 chr4D 64225376 64226194 818 False 1384.000000 1384 97.192000 1 818 1 chr4D.!!$F2 817
2 TraesCS4D01G078000 chr4B 76813264 76817128 3864 False 1345.000000 4211 93.560750 843 4435 4 chr4B.!!$F2 3592
3 TraesCS4D01G078000 chr4A 544200634 544204344 3710 True 1589.666667 3653 94.167333 918 4435 3 chr4A.!!$R2 3517
4 TraesCS4D01G078000 chr3D 94712015 94712834 819 False 1395.000000 1395 97.327000 1 822 1 chr3D.!!$F1 821
5 TraesCS4D01G078000 chr3D 213968082 213968901 819 True 1369.000000 1369 96.829000 1 818 1 chr3D.!!$R1 817
6 TraesCS4D01G078000 chr7D 611047006 611047823 817 False 1389.000000 1389 97.314000 1 818 1 chr7D.!!$F3 817
7 TraesCS4D01G078000 chr7D 414308808 414309629 821 False 1386.000000 1386 97.087000 1 822 1 chr7D.!!$F2 821
8 TraesCS4D01G078000 chr7D 369901030 369901848 818 False 1367.000000 1367 96.829000 1 818 1 chr7D.!!$F1 817
9 TraesCS4D01G078000 chr7D 251559180 251560000 820 True 1363.000000 1363 96.602000 1 823 1 chr7D.!!$R1 822
10 TraesCS4D01G078000 chr7D 124298517 124301239 2722 False 532.500000 710 79.663500 979 3499 2 chr7D.!!$F4 2520
11 TraesCS4D01G078000 chr5D 532712010 532712828 818 False 1384.000000 1384 97.192000 1 818 1 chr5D.!!$F2 817
12 TraesCS4D01G078000 chr5D 444712088 444712892 804 False 584.000000 584 80.074000 2513 3311 1 chr5D.!!$F1 798
13 TraesCS4D01G078000 chr5D 484426656 484428841 2185 True 515.000000 662 80.516000 1033 3395 2 chr5D.!!$R1 2362
14 TraesCS4D01G078000 chr2D 592372165 592372990 825 False 1375.000000 1375 96.739000 1 825 1 chr2D.!!$F1 824
15 TraesCS4D01G078000 chr7A 126865007 126867712 2705 False 519.500000 704 79.262500 979 3499 2 chr7A.!!$F1 2520
16 TraesCS4D01G078000 chr7B 86139274 86142032 2758 False 502.000000 695 79.255000 979 3435 2 chr7B.!!$F1 2456
17 TraesCS4D01G078000 chr5B 595644447 595645354 907 True 636.000000 636 79.587000 2498 3405 1 chr5B.!!$R2 907
18 TraesCS4D01G078000 chr5B 595631044 595633228 2184 True 489.000000 684 79.260500 1033 3395 2 chr5B.!!$R3 2362
19 TraesCS4D01G078000 chr5A 659821413 659822209 796 True 466.000000 466 77.472000 2495 3282 1 chr5A.!!$R2 787

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
818 826 0.743345 GTGGCAGTTATCGGTGTCCC 60.743 60.0 0.0 0.0 0.00 4.46 F
885 893 1.244816 GTTCAGGCACCCTTTGGTAC 58.755 55.0 0.0 0.0 45.57 3.34 F
2290 2888 0.881796 CCTTTTCCAGGTCCTTTCGC 59.118 55.0 0.0 0.0 37.99 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1970 2.722094 TGGCCAGGCATTAGTAGTTTG 58.278 47.619 15.19 0.00 0.00 2.93 R
2730 3688 4.515191 TGCTTCTTTGTACTGGACATGAAC 59.485 41.667 0.00 0.00 38.07 3.18 R
3652 4791 0.037605 GATAACGATAGGGCCACGGG 60.038 60.000 18.42 3.42 43.77 5.28 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
64 65 6.198966 GCAACAGAAAATAAAATAGGATGGCG 59.801 38.462 0.00 0.00 0.00 5.69
132 133 5.227908 CAACTGACGTTAGATACAAGTGGT 58.772 41.667 15.04 0.00 0.00 4.16
578 585 0.755698 GTAGGGGATCGAGAGGTGCA 60.756 60.000 0.00 0.00 32.22 4.57
685 692 3.656045 GGACGTGTGGGCGGTTTG 61.656 66.667 0.00 0.00 35.98 2.93
686 693 2.898343 GACGTGTGGGCGGTTTGT 60.898 61.111 0.00 0.00 35.98 2.83
695 703 2.115911 GGCGGTTTGTCACACACCA 61.116 57.895 13.63 0.00 34.20 4.17
700 708 1.670811 GGTTTGTCACACACCAGACAG 59.329 52.381 8.34 0.00 44.65 3.51
782 790 3.353836 GGCGTGCGACACAACCAT 61.354 61.111 9.95 0.00 33.40 3.55
818 826 0.743345 GTGGCAGTTATCGGTGTCCC 60.743 60.000 0.00 0.00 0.00 4.46
839 847 2.431954 TTTTTACCACGAACACCCCA 57.568 45.000 0.00 0.00 0.00 4.96
840 848 2.660670 TTTTACCACGAACACCCCAT 57.339 45.000 0.00 0.00 0.00 4.00
841 849 2.660670 TTTACCACGAACACCCCATT 57.339 45.000 0.00 0.00 0.00 3.16
845 853 1.573829 CCACGAACACCCCATTCACG 61.574 60.000 0.00 0.00 0.00 4.35
872 880 5.649782 AATTAATGCCAACTCTGTTCAGG 57.350 39.130 0.00 0.00 0.00 3.86
885 893 1.244816 GTTCAGGCACCCTTTGGTAC 58.755 55.000 0.00 0.00 45.57 3.34
890 898 2.035832 CAGGCACCCTTTGGTACTTTTG 59.964 50.000 0.00 0.00 45.57 2.44
961 969 3.059166 CCTGAAACCCTTGAAAATTGCG 58.941 45.455 0.00 0.00 0.00 4.85
1466 1504 3.484953 TCCCCTTCCTTGTCTAGCTAA 57.515 47.619 0.00 0.00 0.00 3.09
1477 1515 7.450074 TCCTTGTCTAGCTAATTCTTGAAACA 58.550 34.615 0.00 0.00 0.00 2.83
1478 1516 7.604164 TCCTTGTCTAGCTAATTCTTGAAACAG 59.396 37.037 0.00 0.00 0.00 3.16
1643 1687 8.419442 TGATGTGATGTAGATATGGATATCTGC 58.581 37.037 16.36 15.40 46.56 4.26
1654 1698 4.955811 TGGATATCTGCTGGTATTTCGT 57.044 40.909 2.05 0.00 0.00 3.85
1879 1970 6.970484 TCCTTCTCAAGCTTAAAAATGTGAC 58.030 36.000 0.00 0.00 0.00 3.67
2071 2171 3.645884 ACTTGCATCACTGTGATTTTGC 58.354 40.909 20.13 21.10 34.28 3.68
2290 2888 0.881796 CCTTTTCCAGGTCCTTTCGC 59.118 55.000 0.00 0.00 37.99 4.70
2291 2889 1.545651 CCTTTTCCAGGTCCTTTCGCT 60.546 52.381 0.00 0.00 37.99 4.93
2604 3562 1.489649 CTCCCTGCAGGATCTGTTGAT 59.510 52.381 34.91 0.00 46.33 2.57
2730 3688 0.868406 GGAGCTCAGTTCAAACACCG 59.132 55.000 17.19 0.00 0.00 4.94
3249 4219 0.612174 TCCGAGAAGACCTCACAGGG 60.612 60.000 0.00 0.00 40.58 4.45
3267 4237 2.171725 GGTGGTGCTATTCGTCGGC 61.172 63.158 0.00 0.00 0.00 5.54
3292 4262 2.554032 GTGTTCAATCCCTTGGTGTCTG 59.446 50.000 0.00 0.00 32.95 3.51
3399 4371 1.202290 CCTGTGCAATAAATCCGGTGC 60.202 52.381 0.00 2.90 37.51 5.01
3420 4393 6.843779 GGTGCATGTTTTTGTTTTCGAATAAC 59.156 34.615 0.00 7.41 0.00 1.89
3444 4417 4.199310 GCTTGCTTGATGTATGGAGGTTA 58.801 43.478 0.00 0.00 0.00 2.85
3476 4449 2.427095 GTGACAATAATCCAGGGTTGCC 59.573 50.000 0.00 0.00 0.00 4.52
3500 4474 3.761218 TGGAGTTTTGTGCTTTCAGTTGA 59.239 39.130 0.00 0.00 0.00 3.18
3501 4475 4.219507 TGGAGTTTTGTGCTTTCAGTTGAA 59.780 37.500 0.00 0.00 0.00 2.69
3511 4485 5.645497 GTGCTTTCAGTTGAATGATACTCCT 59.355 40.000 10.80 0.00 33.54 3.69
3512 4486 6.818644 GTGCTTTCAGTTGAATGATACTCCTA 59.181 38.462 10.80 0.00 33.54 2.94
3514 4488 6.818644 GCTTTCAGTTGAATGATACTCCTACA 59.181 38.462 10.80 0.00 33.54 2.74
3515 4489 7.497249 GCTTTCAGTTGAATGATACTCCTACAT 59.503 37.037 10.80 0.00 33.54 2.29
3519 4493 7.561356 TCAGTTGAATGATACTCCTACATGAGA 59.439 37.037 0.00 0.00 36.22 3.27
3536 4638 2.494471 TGAGATGGCCAAATGCTTCTTG 59.506 45.455 10.96 0.00 40.92 3.02
3538 4640 1.551883 GATGGCCAAATGCTTCTTGGT 59.448 47.619 10.96 0.00 44.46 3.67
3555 4662 5.858381 TCTTGGTGAAGTATGATCTATGGC 58.142 41.667 0.00 0.00 0.00 4.40
3556 4663 5.366477 TCTTGGTGAAGTATGATCTATGGCA 59.634 40.000 0.00 0.00 0.00 4.92
3570 4677 7.156000 TGATCTATGGCATTTGCATAATTTGG 58.844 34.615 4.78 0.00 44.36 3.28
3577 4684 6.099413 TGGCATTTGCATAATTTGGGAGATTA 59.901 34.615 4.74 0.00 44.36 1.75
3578 4685 7.163441 GGCATTTGCATAATTTGGGAGATTAT 58.837 34.615 4.74 0.00 44.36 1.28
3584 4691 6.494491 TGCATAATTTGGGAGATTATTCTGGG 59.506 38.462 0.00 0.00 29.54 4.45
3602 4709 6.524101 TCTGGGTTATTTTGTTAATCTGGC 57.476 37.500 0.00 0.00 0.00 4.85
3607 4714 6.811665 GGGTTATTTTGTTAATCTGGCTTGTC 59.188 38.462 0.00 0.00 0.00 3.18
3615 4722 6.296026 TGTTAATCTGGCTTGTCTTACTTGT 58.704 36.000 0.00 0.00 0.00 3.16
3616 4723 6.770785 TGTTAATCTGGCTTGTCTTACTTGTT 59.229 34.615 0.00 0.00 0.00 2.83
3652 4791 4.517703 CGAGAGCGACGTCGTCCC 62.518 72.222 35.48 24.33 42.22 4.46
3686 4825 3.445805 TCGTTATCAGTCATGTGTGCCTA 59.554 43.478 0.00 0.00 0.00 3.93
3687 4826 3.551890 CGTTATCAGTCATGTGTGCCTAC 59.448 47.826 0.00 0.00 0.00 3.18
3696 4835 1.370064 GTGTGCCTACGACTTGGGT 59.630 57.895 0.00 0.00 0.00 4.51
3698 4837 1.375523 GTGCCTACGACTTGGGTGG 60.376 63.158 0.00 0.00 0.00 4.61
3703 4842 0.818296 CTACGACTTGGGTGGGAGAG 59.182 60.000 0.00 0.00 34.57 3.20
3707 4846 0.899019 GACTTGGGTGGGAGAGAGAC 59.101 60.000 0.00 0.00 0.00 3.36
3764 4940 5.419155 TCACTCCTGAACTACTCAATAGGTG 59.581 44.000 0.00 0.00 34.89 4.00
3795 4971 4.153655 CCCACGATATGCTGAAATCTGATG 59.846 45.833 0.00 0.00 0.00 3.07
3796 4972 4.378149 CCACGATATGCTGAAATCTGATGC 60.378 45.833 0.00 0.00 0.00 3.91
3837 5015 8.965172 CAAAATTGCTCAATAATATGAGTCTGC 58.035 33.333 6.22 0.00 46.85 4.26
3847 5025 9.702494 CAATAATATGAGTCTGCTATCTGAACA 57.298 33.333 0.00 0.00 0.00 3.18
3855 5033 2.928757 CTGCTATCTGAACAGAGTGCAC 59.071 50.000 21.09 9.40 41.31 4.57
3856 5034 2.564504 TGCTATCTGAACAGAGTGCACT 59.435 45.455 21.88 21.88 41.31 4.40
3857 5035 2.928757 GCTATCTGAACAGAGTGCACTG 59.071 50.000 27.27 14.76 41.33 3.66
3858 5036 2.469274 ATCTGAACAGAGTGCACTGG 57.531 50.000 27.27 18.49 41.33 4.00
3859 5037 1.413118 TCTGAACAGAGTGCACTGGA 58.587 50.000 27.27 7.60 41.59 3.86
3878 5067 1.467342 GAACCCTGCACGTAAATGGAC 59.533 52.381 0.00 0.00 0.00 4.02
4062 5298 5.234757 CAGTTCTCAAATCAGCAGAGATAGC 59.765 44.000 0.00 0.00 38.14 2.97
4076 5312 3.054875 AGAGATAGCCAACACAGCATTGA 60.055 43.478 0.00 0.00 0.00 2.57
4221 5518 3.118261 TCTGAGTTGAGAGGTTTTGCACT 60.118 43.478 0.00 0.00 0.00 4.40
4307 5604 0.736325 CCATGTCGTCGTCAAGGTCC 60.736 60.000 5.71 0.00 0.00 4.46
4321 5618 1.364901 GGTCCAGACCGTCGTTCAA 59.635 57.895 0.05 0.00 42.29 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 6.573664 TGCCACCATGTTATATTATTGCTC 57.426 37.500 0.00 0.00 0.00 4.26
132 133 6.381250 CATGGGGAGGGAGGAAAAATAATTA 58.619 40.000 0.00 0.00 0.00 1.40
578 585 2.361610 CCCTGCCGCCATTGTCTT 60.362 61.111 0.00 0.00 0.00 3.01
685 692 1.956170 CGCCTGTCTGGTGTGTGAC 60.956 63.158 1.25 0.00 41.27 3.67
686 693 2.421314 CGCCTGTCTGGTGTGTGA 59.579 61.111 1.25 0.00 41.27 3.58
744 752 1.071542 TCGTGTGGCATGGAGAAGAAA 59.928 47.619 0.00 0.00 0.00 2.52
825 833 0.536460 GTGAATGGGGTGTTCGTGGT 60.536 55.000 0.00 0.00 0.00 4.16
826 834 1.573829 CGTGAATGGGGTGTTCGTGG 61.574 60.000 0.00 0.00 0.00 4.94
827 835 1.573829 CCGTGAATGGGGTGTTCGTG 61.574 60.000 0.00 0.00 0.00 4.35
828 836 1.302192 CCGTGAATGGGGTGTTCGT 60.302 57.895 0.00 0.00 0.00 3.85
829 837 2.686816 GCCGTGAATGGGGTGTTCG 61.687 63.158 0.00 0.00 0.00 3.95
830 838 2.686816 CGCCGTGAATGGGGTGTTC 61.687 63.158 0.00 0.00 37.20 3.18
831 839 2.671619 CGCCGTGAATGGGGTGTT 60.672 61.111 0.00 0.00 37.20 3.32
832 840 2.684192 TTTCGCCGTGAATGGGGTGT 62.684 55.000 5.61 0.00 42.29 4.16
833 841 1.312371 ATTTCGCCGTGAATGGGGTG 61.312 55.000 5.61 0.00 42.29 4.61
834 842 0.610785 AATTTCGCCGTGAATGGGGT 60.611 50.000 5.61 0.00 42.29 4.95
835 843 1.384525 TAATTTCGCCGTGAATGGGG 58.615 50.000 0.00 0.00 42.99 4.96
836 844 3.371168 CATTAATTTCGCCGTGAATGGG 58.629 45.455 0.00 0.00 36.22 4.00
837 845 2.788786 GCATTAATTTCGCCGTGAATGG 59.211 45.455 0.00 0.00 36.22 3.16
838 846 2.788786 GGCATTAATTTCGCCGTGAATG 59.211 45.455 0.00 0.00 36.22 2.67
839 847 3.078594 GGCATTAATTTCGCCGTGAAT 57.921 42.857 0.00 0.00 36.22 2.57
840 848 2.553079 GGCATTAATTTCGCCGTGAA 57.447 45.000 0.00 0.00 35.79 3.18
845 853 3.119495 ACAGAGTTGGCATTAATTTCGCC 60.119 43.478 8.08 8.08 46.43 5.54
902 910 1.153489 CGGGTGCCTGATCAGAGTG 60.153 63.158 24.62 8.66 0.00 3.51
961 969 3.557290 GGGGGATGTACGGGAGGC 61.557 72.222 0.00 0.00 0.00 4.70
1225 1252 3.702048 CCTTTCTCCGCGGACCCA 61.702 66.667 27.28 8.35 0.00 4.51
1391 1427 0.537371 GCCTTGTACTTGCCCACAGT 60.537 55.000 0.00 0.00 0.00 3.55
1466 1504 2.229792 TCTTGCCGCTGTTTCAAGAAT 58.770 42.857 1.88 0.00 42.00 2.40
1477 1515 0.036732 TGGTGAAGAATCTTGCCGCT 59.963 50.000 0.00 0.00 0.00 5.52
1478 1516 0.449388 CTGGTGAAGAATCTTGCCGC 59.551 55.000 0.00 0.00 0.00 6.53
1643 1687 7.388500 TGGTTAAAAGACCTAACGAAATACCAG 59.612 37.037 0.00 0.00 40.47 4.00
1879 1970 2.722094 TGGCCAGGCATTAGTAGTTTG 58.278 47.619 15.19 0.00 0.00 2.93
1922 2022 9.355215 CTACTGTTTAGTGAACACCTATACTTG 57.645 37.037 0.00 0.00 43.13 3.16
2071 2171 7.027760 TCACAAAAGTAACAGACTAGCTATCG 58.972 38.462 0.00 0.00 37.44 2.92
2290 2888 8.263940 TCCGTGAAGGTAATAAATGAAAAGAG 57.736 34.615 0.00 0.00 41.99 2.85
2291 2889 8.624367 TTCCGTGAAGGTAATAAATGAAAAGA 57.376 30.769 0.00 0.00 41.99 2.52
2730 3688 4.515191 TGCTTCTTTGTACTGGACATGAAC 59.485 41.667 0.00 0.00 38.07 3.18
3141 4108 0.107263 TGACCACTGAAGCAGTTGCA 60.107 50.000 6.90 0.00 42.59 4.08
3249 4219 2.171725 GCCGACGAATAGCACCACC 61.172 63.158 0.00 0.00 0.00 4.61
3267 4237 2.231964 CACCAAGGGATTGAACACATGG 59.768 50.000 0.00 0.00 0.00 3.66
3292 4262 1.814394 TCCAGAGCAAACACATCATGC 59.186 47.619 0.00 0.00 40.34 4.06
3399 4371 6.062021 GCCGTTATTCGAAAACAAAAACATG 58.938 36.000 0.00 0.00 42.86 3.21
3420 4393 1.600957 CTCCATACATCAAGCAAGCCG 59.399 52.381 0.00 0.00 0.00 5.52
3444 4417 4.949856 GGATTATTGTCACCAACTCACCAT 59.050 41.667 0.00 0.00 32.26 3.55
3471 4444 0.869880 GCACAAAACTCCACGGCAAC 60.870 55.000 0.00 0.00 0.00 4.17
3476 4449 2.097466 ACTGAAAGCACAAAACTCCACG 59.903 45.455 0.00 0.00 37.60 4.94
3500 4474 5.046014 GGCCATCTCATGTAGGAGTATCATT 60.046 44.000 0.00 0.00 36.25 2.57
3501 4475 4.469227 GGCCATCTCATGTAGGAGTATCAT 59.531 45.833 0.00 0.00 36.25 2.45
3511 4485 3.301794 AGCATTTGGCCATCTCATGTA 57.698 42.857 6.09 0.00 46.50 2.29
3512 4486 2.154567 AGCATTTGGCCATCTCATGT 57.845 45.000 6.09 0.00 46.50 3.21
3514 4488 3.028094 AGAAGCATTTGGCCATCTCAT 57.972 42.857 6.09 0.00 46.50 2.90
3515 4489 2.494471 CAAGAAGCATTTGGCCATCTCA 59.506 45.455 6.09 0.00 46.50 3.27
3536 4638 6.569226 GCAAATGCCATAGATCATACTTCACC 60.569 42.308 0.00 0.00 34.31 4.02
3538 4640 6.063404 TGCAAATGCCATAGATCATACTTCA 58.937 36.000 2.46 0.00 41.18 3.02
3550 4657 5.601729 TCTCCCAAATTATGCAAATGCCATA 59.398 36.000 2.46 0.00 41.18 2.74
3555 4662 9.991906 AGAATAATCTCCCAAATTATGCAAATG 57.008 29.630 0.00 0.00 30.05 2.32
3556 4663 9.991906 CAGAATAATCTCCCAAATTATGCAAAT 57.008 29.630 0.00 0.00 32.03 2.32
3577 4684 7.400052 AGCCAGATTAACAAAATAACCCAGAAT 59.600 33.333 0.00 0.00 0.00 2.40
3578 4685 6.723977 AGCCAGATTAACAAAATAACCCAGAA 59.276 34.615 0.00 0.00 0.00 3.02
3616 4723 1.357334 GCGCCTCGTCAACCAAAAA 59.643 52.632 0.00 0.00 0.00 1.94
3652 4791 0.037605 GATAACGATAGGGCCACGGG 60.038 60.000 18.42 3.42 43.77 5.28
3686 4825 0.900647 CTCTCTCCCACCCAAGTCGT 60.901 60.000 0.00 0.00 0.00 4.34
3687 4826 0.612174 TCTCTCTCCCACCCAAGTCG 60.612 60.000 0.00 0.00 0.00 4.18
3696 4835 3.816398 TCTTTCTCTGTCTCTCTCCCA 57.184 47.619 0.00 0.00 0.00 4.37
3698 4837 4.709397 TGGAATCTTTCTCTGTCTCTCTCC 59.291 45.833 0.00 0.00 0.00 3.71
3703 4842 5.353678 CCATTGTGGAATCTTTCTCTGTCTC 59.646 44.000 0.00 0.00 40.96 3.36
3707 4846 5.474532 TGAACCATTGTGGAATCTTTCTCTG 59.525 40.000 2.45 0.00 40.96 3.35
3764 4940 1.274728 AGCATATCGTGGGCTCATCTC 59.725 52.381 0.00 0.00 30.74 2.75
3795 4971 6.532657 AGCAATTTTGAGTTGTGCATATTAGC 59.467 34.615 0.00 0.00 37.68 3.09
3796 4972 7.756272 TGAGCAATTTTGAGTTGTGCATATTAG 59.244 33.333 0.00 0.00 37.68 1.73
3836 5014 2.928757 CAGTGCACTCTGTTCAGATAGC 59.071 50.000 18.64 14.98 0.00 2.97
3837 5015 3.194329 TCCAGTGCACTCTGTTCAGATAG 59.806 47.826 18.64 0.44 34.02 2.08
3847 5025 1.757306 CAGGGTTCCAGTGCACTCT 59.243 57.895 18.64 7.07 0.00 3.24
3855 5033 1.468520 CATTTACGTGCAGGGTTCCAG 59.531 52.381 11.67 0.00 0.00 3.86
3856 5034 1.529226 CATTTACGTGCAGGGTTCCA 58.471 50.000 11.67 0.00 0.00 3.53
3857 5035 0.808755 CCATTTACGTGCAGGGTTCC 59.191 55.000 11.67 0.00 0.00 3.62
3858 5036 1.467342 GTCCATTTACGTGCAGGGTTC 59.533 52.381 11.67 0.00 0.00 3.62
3859 5037 1.202830 TGTCCATTTACGTGCAGGGTT 60.203 47.619 11.67 0.00 0.00 4.11
3878 5067 4.696877 TGGTTCTTGCTATGATTCAGTGTG 59.303 41.667 0.00 0.00 0.00 3.82
3945 5178 5.070446 AGACACTACAGTTTGATCAGTTCCA 59.930 40.000 0.00 0.00 0.00 3.53
3947 5180 6.451393 AGAGACACTACAGTTTGATCAGTTC 58.549 40.000 0.00 0.00 0.00 3.01
4014 5247 2.099263 AGATCATCTGTAACCCGTGTCG 59.901 50.000 0.00 0.00 0.00 4.35
4062 5298 2.129607 GTTGCTTCAATGCTGTGTTGG 58.870 47.619 0.00 0.00 0.00 3.77
4076 5312 1.956477 GGATGTGACCTTGTGTTGCTT 59.044 47.619 0.00 0.00 0.00 3.91
4132 5368 3.877508 ACTTTGTTGTAGTTGGTCTCTGC 59.122 43.478 0.00 0.00 0.00 4.26
4221 5518 5.243954 GGGAGATAGTGTATGCTATGTGACA 59.756 44.000 0.00 0.00 32.32 3.58
4307 5604 1.787155 CAGTTCTTGAACGACGGTCTG 59.213 52.381 15.00 7.26 0.00 3.51
4321 5618 1.003233 GTTCCCGGATCAACCAGTTCT 59.997 52.381 0.73 0.00 38.90 3.01


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

AutoCloner maintained by Alex Coulton.