Multiple sequence alignment - TraesCS4A01G126300

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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 TraesCS4A01G126300 chr4A 100.000 6086 0 0 1 6086 162428268 162422183 0.000000e+00 11239.0
1 TraesCS4A01G126300 chr4D 96.007 4733 125 27 646 5328 314063071 314067789 0.000000e+00 7635.0
2 TraesCS4A01G126300 chr4D 85.955 356 44 5 5296 5650 314067789 314068139 5.760000e-100 375.0
3 TraesCS4A01G126300 chr4D 90.083 121 7 2 5971 6086 314068131 314068251 1.060000e-32 152.0
4 TraesCS4A01G126300 chr4B 94.915 4641 152 35 646 5242 391537226 391541826 0.000000e+00 7186.0
5 TraesCS4A01G126300 chr4B 83.824 476 29 17 5657 6086 391542515 391542988 5.680000e-110 409.0
6 TraesCS4A01G126300 chr3A 96.407 668 11 7 1 656 711282587 711283253 0.000000e+00 1088.0
7 TraesCS4A01G126300 chr3A 80.120 166 30 3 5801 5966 638293487 638293649 2.980000e-23 121.0
8 TraesCS4A01G126300 chr2B 92.857 658 37 6 1 649 23564845 23565501 0.000000e+00 946.0
9 TraesCS4A01G126300 chr2B 86.565 655 79 5 2 648 64762588 64761935 0.000000e+00 713.0
10 TraesCS4A01G126300 chr2B 92.157 51 3 1 5111 5160 679577565 679577515 3.040000e-08 71.3
11 TraesCS4A01G126300 chr2A 90.526 665 50 5 1 653 46101573 46100910 0.000000e+00 867.0
12 TraesCS4A01G126300 chr2A 86.331 139 17 2 5103 5239 497699253 497699391 3.800000e-32 150.0
13 TraesCS4A01G126300 chr1A 95.327 535 18 3 1 529 573919565 573920098 0.000000e+00 843.0
14 TraesCS4A01G126300 chr1A 87.671 657 71 5 1 649 491309443 491310097 0.000000e+00 756.0
15 TraesCS4A01G126300 chr7D 89.275 662 61 6 1 653 408468786 408469446 0.000000e+00 821.0
16 TraesCS4A01G126300 chr7D 86.614 127 14 3 5116 5240 603679934 603680059 2.960000e-28 137.0
17 TraesCS4A01G126300 chr7D 80.556 180 29 5 5790 5968 634902148 634901974 3.830000e-27 134.0
18 TraesCS4A01G126300 chr6D 87.481 655 72 6 4 649 20785647 20784994 0.000000e+00 747.0
19 TraesCS4A01G126300 chr5A 84.170 657 95 4 1 649 624933559 624932904 4.000000e-176 628.0
20 TraesCS4A01G126300 chr5A 81.132 106 13 7 659 760 601338360 601338258 1.820000e-10 78.7
21 TraesCS4A01G126300 chr5D 87.079 178 21 2 5791 5968 556557726 556557901 3.720000e-47 200.0
22 TraesCS4A01G126300 chr5D 81.215 181 32 2 5790 5968 527510271 527510091 1.770000e-30 145.0
23 TraesCS4A01G126300 chr5D 81.215 181 32 2 5790 5968 527511612 527511432 1.770000e-30 145.0
24 TraesCS4A01G126300 chr5D 78.626 131 25 3 5836 5966 446468975 446469102 3.910000e-12 84.2
25 TraesCS4A01G126300 chr5D 94.595 37 1 1 5913 5949 246656458 246656423 8.520000e-04 56.5
26 TraesCS4A01G126300 chr1B 93.651 126 7 1 5657 5781 186803409 186803534 2.900000e-43 187.0
27 TraesCS4A01G126300 chr1B 75.940 133 26 5 5100 5229 621257996 621257867 5.090000e-06 63.9
28 TraesCS4A01G126300 chr2D 85.950 121 12 2 5971 6086 367588085 367588205 2.300000e-24 124.0
29 TraesCS4A01G126300 chr2D 79.310 145 26 4 5096 5237 615712803 615712946 1.400000e-16 99.0
30 TraesCS4A01G126300 chr2D 88.889 72 6 2 5100 5169 567566303 567566374 3.020000e-13 87.9
31 TraesCS4A01G126300 chr5B 89.362 94 9 1 5663 5755 120574164 120574257 3.850000e-22 117.0
32 TraesCS4A01G126300 chr3D 82.353 102 17 1 5865 5966 91417953 91418053 3.020000e-13 87.9
33 TraesCS4A01G126300 chr7B 91.667 48 4 0 5184 5231 731430671 731430718 3.940000e-07 67.6
34 TraesCS4A01G126300 chr7B 92.500 40 3 0 5927 5966 6797953 6797992 2.370000e-04 58.4
35 TraesCS4A01G126300 chr1D 90.000 50 4 1 5111 5160 490402962 490403010 5.090000e-06 63.9


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 TraesCS4A01G126300 chr4A 162422183 162428268 6085 True 11239.000000 11239 100.000000 1 6086 1 chr4A.!!$R1 6085
1 TraesCS4A01G126300 chr4D 314063071 314068251 5180 False 2720.666667 7635 90.681667 646 6086 3 chr4D.!!$F1 5440
2 TraesCS4A01G126300 chr4B 391537226 391542988 5762 False 3797.500000 7186 89.369500 646 6086 2 chr4B.!!$F1 5440
3 TraesCS4A01G126300 chr3A 711282587 711283253 666 False 1088.000000 1088 96.407000 1 656 1 chr3A.!!$F2 655
4 TraesCS4A01G126300 chr2B 23564845 23565501 656 False 946.000000 946 92.857000 1 649 1 chr2B.!!$F1 648
5 TraesCS4A01G126300 chr2B 64761935 64762588 653 True 713.000000 713 86.565000 2 648 1 chr2B.!!$R1 646
6 TraesCS4A01G126300 chr2A 46100910 46101573 663 True 867.000000 867 90.526000 1 653 1 chr2A.!!$R1 652
7 TraesCS4A01G126300 chr1A 573919565 573920098 533 False 843.000000 843 95.327000 1 529 1 chr1A.!!$F2 528
8 TraesCS4A01G126300 chr1A 491309443 491310097 654 False 756.000000 756 87.671000 1 649 1 chr1A.!!$F1 648
9 TraesCS4A01G126300 chr7D 408468786 408469446 660 False 821.000000 821 89.275000 1 653 1 chr7D.!!$F1 652
10 TraesCS4A01G126300 chr6D 20784994 20785647 653 True 747.000000 747 87.481000 4 649 1 chr6D.!!$R1 645
11 TraesCS4A01G126300 chr5A 624932904 624933559 655 True 628.000000 628 84.170000 1 649 1 chr5A.!!$R2 648

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
386 394 0.667487 CTCGGCGACTGCTCTTTCAA 60.667 55.0 4.99 0.00 42.25 2.69 F
1372 1427 0.109723 TAGGTGTTTCCCGCTGCTTT 59.890 50.0 0.00 0.00 36.75 3.51 F
1832 1887 0.468226 CTAAAGGATACAGGCGCCCA 59.532 55.0 26.15 9.51 41.41 5.36 F
3681 3749 0.171903 GCTCACGCCTGCATTTTCAT 59.828 50.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2114 0.243907 ACCACAACTCAGGATCGACG 59.756 55.000 0.0 0.0 0.00 5.12 R
2467 2527 1.831736 AGGCGTGCTTAGTCAGGTATT 59.168 47.619 0.0 0.0 0.00 1.89 R
3741 3809 0.613260 TCCCAATGAACACTCGGGAG 59.387 55.000 0.0 0.0 41.08 4.30 R
5284 5591 1.326548 CATTAGGAAACGGTAGCACGC 59.673 52.381 0.0 0.0 37.37 5.34 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
75 77 7.964011 CGCTTACCACGGAAGAAATAATAAAAA 59.036 33.333 0.00 0.00 0.00 1.94
386 394 0.667487 CTCGGCGACTGCTCTTTCAA 60.667 55.000 4.99 0.00 42.25 2.69
417 425 5.526479 CGAATGATGATCTCACCAAATCAGT 59.474 40.000 0.00 0.00 36.48 3.41
592 603 4.567537 CCACCATGTATTGAGGACCTTTGA 60.568 45.833 0.00 0.00 0.00 2.69
701 716 0.693049 GTGCTTCTTCCTTCCCTCCA 59.307 55.000 0.00 0.00 0.00 3.86
771 786 3.682858 GGCGAGTGATGCTAAACTGTTTA 59.317 43.478 12.08 12.08 0.00 2.01
823 839 3.251729 ACGTGCATATGATTTCATGGCTC 59.748 43.478 6.97 12.30 38.19 4.70
913 929 2.676163 AAAGCCAAACGCGGACCTCT 62.676 55.000 12.47 0.00 44.76 3.69
923 939 0.892063 GCGGACCTCTCACTCTTCTT 59.108 55.000 0.00 0.00 0.00 2.52
1211 1261 2.528378 ACTGCCCCCGTGGTAAGT 60.528 61.111 0.00 0.00 36.04 2.24
1372 1427 0.109723 TAGGTGTTTCCCGCTGCTTT 59.890 50.000 0.00 0.00 36.75 3.51
1373 1428 1.172812 AGGTGTTTCCCGCTGCTTTC 61.173 55.000 0.00 0.00 36.75 2.62
1374 1429 1.082104 GTGTTTCCCGCTGCTTTCG 60.082 57.895 0.00 0.00 0.00 3.46
1375 1430 1.525077 TGTTTCCCGCTGCTTTCGT 60.525 52.632 0.00 0.00 0.00 3.85
1376 1431 1.082104 GTTTCCCGCTGCTTTCGTG 60.082 57.895 0.00 0.00 0.00 4.35
1377 1432 2.903547 TTTCCCGCTGCTTTCGTGC 61.904 57.895 0.00 0.00 0.00 5.34
1378 1433 3.825160 TTCCCGCTGCTTTCGTGCT 62.825 57.895 0.00 0.00 0.00 4.40
1380 1435 4.093952 CCGCTGCTTTCGTGCTGG 62.094 66.667 0.00 0.00 33.41 4.85
1381 1436 4.748679 CGCTGCTTTCGTGCTGGC 62.749 66.667 0.00 0.00 33.41 4.85
1382 1437 3.360340 GCTGCTTTCGTGCTGGCT 61.360 61.111 0.00 0.00 33.41 4.75
1383 1438 2.559840 CTGCTTTCGTGCTGGCTG 59.440 61.111 0.00 0.00 0.00 4.85
1384 1439 2.974489 CTGCTTTCGTGCTGGCTGG 61.974 63.158 0.00 0.00 0.00 4.85
1385 1440 3.741476 GCTTTCGTGCTGGCTGGG 61.741 66.667 0.00 0.00 0.00 4.45
1386 1441 2.281761 CTTTCGTGCTGGCTGGGT 60.282 61.111 0.00 0.00 0.00 4.51
1387 1442 1.898574 CTTTCGTGCTGGCTGGGTT 60.899 57.895 0.00 0.00 0.00 4.11
1388 1443 2.133742 CTTTCGTGCTGGCTGGGTTG 62.134 60.000 0.00 0.00 0.00 3.77
1609 1664 2.063015 TTTCCTCACCGCACCATGGT 62.063 55.000 13.00 13.00 41.47 3.55
1674 1729 8.730680 GCCTACAGATAATTTGACTCTGAAAAA 58.269 33.333 5.84 0.00 38.96 1.94
1832 1887 0.468226 CTAAAGGATACAGGCGCCCA 59.532 55.000 26.15 9.51 41.41 5.36
1902 1957 2.745968 TGTTTTGAGCTGGAAAACCCT 58.254 42.857 20.37 0.00 40.91 4.34
2007 2062 2.634940 TCTCTATCCATTAGGCACCTGC 59.365 50.000 0.00 0.00 41.14 4.85
2013 2068 1.747355 CCATTAGGCACCTGCTTTGAG 59.253 52.381 0.00 0.00 41.70 3.02
2063 2118 6.883129 TGGAATTAATGTATGTAATGCGTCG 58.117 36.000 0.00 0.00 0.00 5.12
2339 2397 4.186926 GCTGCACTATCAGTTTCATCAGA 58.813 43.478 0.00 0.00 36.49 3.27
2381 2440 7.174253 GTGGAGTACATTAAAGTGTGAAATCCA 59.826 37.037 0.00 0.00 32.81 3.41
2467 2527 5.574970 ATCACCCCCTGCATTTTTAAAAA 57.425 34.783 15.38 15.38 0.00 1.94
2509 2569 7.168219 GCCTCCTATATGTTGGATATGAACAA 58.832 38.462 0.00 0.00 36.90 2.83
3048 3116 6.867816 CCATGTGTAACGTAGGTAACTTTGTA 59.132 38.462 0.00 0.00 44.82 2.41
3126 3194 1.337167 CGTGGATGAGCTGTTGAGTGA 60.337 52.381 0.00 0.00 0.00 3.41
3134 3202 3.257393 GAGCTGTTGAGTGAGTGTATGG 58.743 50.000 0.00 0.00 0.00 2.74
3138 3206 5.656859 AGCTGTTGAGTGAGTGTATGGTATA 59.343 40.000 0.00 0.00 0.00 1.47
3560 3628 0.333312 AGTGTCCAGTCGATCTCCCT 59.667 55.000 0.00 0.00 0.00 4.20
3577 3645 8.560374 CGATCTCCCTTTAAATCTGTTATTTCC 58.440 37.037 0.00 0.00 0.00 3.13
3681 3749 0.171903 GCTCACGCCTGCATTTTCAT 59.828 50.000 0.00 0.00 0.00 2.57
3741 3809 7.594758 TCAAAAGTACAGAACATGCTTAATTGC 59.405 33.333 0.00 0.00 0.00 3.56
4059 4127 1.865340 GGTTTCGTTCGTCTGAGCTTT 59.135 47.619 0.00 0.00 0.00 3.51
4522 4591 3.334691 TGCCTCTAACGTGAAAGGAATG 58.665 45.455 13.04 0.00 0.00 2.67
4603 4675 4.793071 CAAACCGTGAAACATTAGATGCA 58.207 39.130 0.00 0.00 35.74 3.96
4624 4696 8.621532 ATGCACATAGTTCTGAAGAGTTTTTA 57.378 30.769 0.00 0.00 0.00 1.52
4791 4863 1.447314 CGAGGCCACGGGAGTAAAC 60.447 63.158 15.45 0.00 44.67 2.01
4795 4867 0.542805 GGCCACGGGAGTAAACCATA 59.457 55.000 0.00 0.00 44.67 2.74
5129 5202 0.342313 AGGAGGATTACCCCGGACTT 59.658 55.000 0.73 0.00 36.73 3.01
5249 5548 0.249489 GCCGCAACCGACTAGATGAT 60.249 55.000 0.00 0.00 36.29 2.45
5328 5667 5.355350 GGTTGCATCCATAAGCCATATACTC 59.645 44.000 9.02 0.00 0.00 2.59
5333 5672 5.644977 TCCATAAGCCATATACTCGAGTG 57.355 43.478 28.12 11.82 0.00 3.51
5361 5700 0.108138 GCACGGATCTAGCCAGTTGT 60.108 55.000 0.00 0.00 0.00 3.32
5428 5771 7.598493 CCGTTAAAAATCACCTCATTTTGACAT 59.402 33.333 0.00 0.00 36.33 3.06
5472 5815 1.069227 GCTCTTTGATTTTCGCACGGT 60.069 47.619 0.00 0.00 0.00 4.83
5483 5826 0.241749 TCGCACGGTTGAGTAACGAT 59.758 50.000 0.00 0.00 37.69 3.73
5487 5830 2.477375 GCACGGTTGAGTAACGATCAAA 59.523 45.455 0.00 0.00 38.34 2.69
5489 5832 4.378046 GCACGGTTGAGTAACGATCAAATT 60.378 41.667 0.00 0.00 38.34 1.82
5491 5834 5.120208 CACGGTTGAGTAACGATCAAATTCT 59.880 40.000 0.00 0.00 38.34 2.40
5519 5862 4.243007 GCCAGTTGCTTTGTAAATGACT 57.757 40.909 0.00 0.00 36.87 3.41
5583 5927 6.366332 GTCATTCTAACAGTTCCATATAGCCG 59.634 42.308 0.00 0.00 0.00 5.52
5599 5943 2.901249 AGCCGAAAGTAATACGCACAT 58.099 42.857 0.00 0.00 0.00 3.21
5601 5945 3.687698 AGCCGAAAGTAATACGCACATTT 59.312 39.130 0.00 0.00 0.00 2.32
5646 5990 1.972588 AGACTCCACCCCATTTAGCT 58.027 50.000 0.00 0.00 0.00 3.32
5730 6107 7.849804 TGTTAAGAGGATGAACTTCTATTGC 57.150 36.000 0.00 0.00 33.79 3.56
5761 6138 8.113062 TGAAATTTCAAGTTAAAACACATTGCG 58.887 29.630 18.45 0.00 33.55 4.85
5767 6144 2.645730 TAAAACACATTGCGGGATGC 57.354 45.000 0.00 0.00 46.70 3.91
5776 6153 4.462394 GCGGGATGCAAGCTATGA 57.538 55.556 0.00 0.00 45.45 2.15
5870 6281 7.504924 AATTTTGTAAGGAAGTCGAACATCA 57.495 32.000 0.00 0.00 0.00 3.07
5883 6294 6.326375 AGTCGAACATCACTCTCTTAACATC 58.674 40.000 0.00 0.00 0.00 3.06
5890 6301 5.320549 TCACTCTCTTAACATCCCGTAAC 57.679 43.478 0.00 0.00 0.00 2.50
5925 6336 3.347958 TTCGGTGCTTCAAAACATCAC 57.652 42.857 0.00 0.00 0.00 3.06
5949 6360 4.927978 TCACATGGTTTTCATCGGTTTT 57.072 36.364 0.00 0.00 32.92 2.43
5980 6404 2.871453 TGGTTTTCCCTTAGCCAAGTC 58.129 47.619 0.00 0.00 39.73 3.01
5996 6420 5.105351 AGCCAAGTCCCAAATAAATAGCAAC 60.105 40.000 0.00 0.00 0.00 4.17
6057 6485 2.277858 AGTAGCTTGGCTAGTGCGT 58.722 52.632 6.15 0.00 42.39 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 2.165845 CTCCGAGACCGACATTTTACCT 59.834 50.000 0.00 0.00 38.22 3.08
386 394 4.940046 GGTGAGATCATCATTCGCCAATAT 59.060 41.667 6.62 0.00 40.92 1.28
417 425 6.950860 TCTCCAGTATCAAATGCCCATATA 57.049 37.500 0.00 0.00 0.00 0.86
592 603 3.572682 TCACAGTGTTACAATCGAGAGGT 59.427 43.478 0.00 0.00 0.00 3.85
701 716 1.673168 GGATGAAAGAAGCAGCCGAT 58.327 50.000 0.00 0.00 31.52 4.18
784 799 2.344441 CACGTCATAAATCGCTGTTCGT 59.656 45.455 0.00 0.00 39.67 3.85
823 839 3.007614 TCTCCGTTTCTACAGGGGAAAAG 59.992 47.826 0.00 0.00 34.97 2.27
913 929 3.050089 TGGGGTTTGGTAAGAAGAGTGA 58.950 45.455 0.00 0.00 0.00 3.41
923 939 2.432563 CAGCGGTGGGGTTTGGTA 59.567 61.111 6.74 0.00 0.00 3.25
1129 1170 0.458669 GCGTACGGATTTGGAGGAGA 59.541 55.000 18.39 0.00 0.00 3.71
1211 1261 1.212935 GAGCAGGATTAGGGCTTTCCA 59.787 52.381 0.00 0.00 38.15 3.53
1294 1348 0.829333 AGCATCTCACGAGCTCCAAT 59.171 50.000 8.47 0.00 32.05 3.16
1336 1390 8.857694 AAACACCTAAGAATTCGGAATTAAGA 57.142 30.769 15.50 3.76 33.99 2.10
1372 1427 3.872603 ACAACCCAGCCAGCACGA 61.873 61.111 0.00 0.00 0.00 4.35
1373 1428 3.663176 CACAACCCAGCCAGCACG 61.663 66.667 0.00 0.00 0.00 5.34
1374 1429 2.203337 TCACAACCCAGCCAGCAC 60.203 61.111 0.00 0.00 0.00 4.40
1375 1430 2.113774 CTCACAACCCAGCCAGCA 59.886 61.111 0.00 0.00 0.00 4.41
1376 1431 3.368571 GCTCACAACCCAGCCAGC 61.369 66.667 0.00 0.00 0.00 4.85
1377 1432 1.970114 CAGCTCACAACCCAGCCAG 60.970 63.158 0.00 0.00 36.17 4.85
1378 1433 2.113774 CAGCTCACAACCCAGCCA 59.886 61.111 0.00 0.00 36.17 4.75
1380 1435 2.263741 CCACAGCTCACAACCCAGC 61.264 63.158 0.00 0.00 35.73 4.85
1381 1436 1.601759 CCCACAGCTCACAACCCAG 60.602 63.158 0.00 0.00 0.00 4.45
1382 1437 2.515398 CCCACAGCTCACAACCCA 59.485 61.111 0.00 0.00 0.00 4.51
1383 1438 2.282462 CCCCACAGCTCACAACCC 60.282 66.667 0.00 0.00 0.00 4.11
1384 1439 2.282462 CCCCCACAGCTCACAACC 60.282 66.667 0.00 0.00 0.00 3.77
1609 1664 2.223595 GCACGCAAGAGATAGTGAGCTA 60.224 50.000 0.00 0.00 43.62 3.32
1674 1729 5.533154 AGTCTAAGCGCAGACATATCTTACT 59.467 40.000 24.67 3.37 46.15 2.24
1730 1785 3.780902 TCCATACATATTAGCATCGCGG 58.219 45.455 6.13 0.00 0.00 6.46
1802 1857 5.508153 CCTGTATCCTTTAGGTGTCAGATCG 60.508 48.000 13.69 0.00 36.34 3.69
1832 1887 6.159751 TCCCTTTAGTTGAAGCAGGGTAATAT 59.840 38.462 2.48 0.00 44.30 1.28
1902 1957 1.704641 ACTAGCATCAGCCATACCGA 58.295 50.000 0.00 0.00 43.56 4.69
2059 2114 0.243907 ACCACAACTCAGGATCGACG 59.756 55.000 0.00 0.00 0.00 5.12
2063 2118 5.063880 ACTTTTACACCACAACTCAGGATC 58.936 41.667 0.00 0.00 0.00 3.36
2339 2397 5.456921 ACTCCACACTGAATATTTCCCAT 57.543 39.130 0.00 0.00 0.00 4.00
2381 2440 4.829492 GGGCAAAGTATCCAAGCTATTCAT 59.171 41.667 0.00 0.00 0.00 2.57
2467 2527 1.831736 AGGCGTGCTTAGTCAGGTATT 59.168 47.619 0.00 0.00 0.00 1.89
2536 2596 7.916128 AACAACTCAACGAGATTATAGATCG 57.084 36.000 0.00 0.00 42.04 3.69
2552 2612 9.546428 CATCATATGGAATGTAGTAACAACTCA 57.454 33.333 2.13 0.00 39.58 3.41
3126 3194 6.780031 AGAGAACTGCTCATATACCATACACT 59.220 38.462 0.00 0.00 46.45 3.55
3134 3202 6.325919 AGTGCTAGAGAACTGCTCATATAC 57.674 41.667 0.00 0.00 46.45 1.47
3138 3206 4.550076 AAAGTGCTAGAGAACTGCTCAT 57.450 40.909 0.00 0.00 46.45 2.90
3212 3280 7.709182 GGCGCCTTTGGATTATTTACTAAATTT 59.291 33.333 22.15 0.00 32.38 1.82
3215 3283 5.068067 GGGCGCCTTTGGATTATTTACTAAA 59.932 40.000 28.56 0.00 0.00 1.85
3217 3285 4.139038 GGGCGCCTTTGGATTATTTACTA 58.861 43.478 28.56 0.00 0.00 1.82
3337 3405 9.626045 CGATAGTTACAATTCAGAGCATATGTA 57.374 33.333 4.29 0.00 0.00 2.29
3338 3406 8.360390 TCGATAGTTACAATTCAGAGCATATGT 58.640 33.333 4.29 0.00 37.40 2.29
3469 3537 1.830477 TGTTCCAGGCTTGCAAGTTTT 59.170 42.857 26.55 10.55 0.00 2.43
3577 3645 6.573664 TGAAGATTCCCTACAAACAACATG 57.426 37.500 0.00 0.00 0.00 3.21
3681 3749 4.529897 ACCAATGATTGATTAGCAGAGCA 58.470 39.130 6.76 0.00 0.00 4.26
3741 3809 0.613260 TCCCAATGAACACTCGGGAG 59.387 55.000 0.00 0.00 41.08 4.30
4040 4108 3.587403 AAAAGCTCAGACGAACGAAAC 57.413 42.857 0.14 0.00 0.00 2.78
4129 4198 4.456222 TGAAAACGAACAACAGAACCTGAA 59.544 37.500 0.45 0.00 35.18 3.02
4522 4591 7.039313 ACTTCTCAACAAAATTAGGTGAACC 57.961 36.000 0.90 0.00 0.00 3.62
4624 4696 5.355350 GTCAGCCTAGCACAAATAGAACAAT 59.645 40.000 0.00 0.00 0.00 2.71
4630 4702 5.121811 AGATTGTCAGCCTAGCACAAATAG 58.878 41.667 0.00 0.00 33.84 1.73
4791 4863 2.427232 CCAAAAGATGGCGCATATGG 57.573 50.000 10.83 3.37 43.80 2.74
4812 4884 5.946942 TTTCTAGGATCAGCTCATGAAGT 57.053 39.130 0.00 0.00 42.53 3.01
5274 5581 1.515519 GTAGCACGCGAACCGATCA 60.516 57.895 15.93 0.00 41.02 2.92
5284 5591 1.326548 CATTAGGAAACGGTAGCACGC 59.673 52.381 0.00 0.00 37.37 5.34
5311 5618 5.183331 GTCACTCGAGTATATGGCTTATGGA 59.817 44.000 19.57 3.42 0.00 3.41
5328 5667 1.474648 CCGTGCATGATCGTCACTCG 61.475 60.000 7.72 8.21 41.41 4.18
5333 5672 2.590073 CTAGATCCGTGCATGATCGTC 58.410 52.381 18.14 7.35 42.73 4.20
5343 5682 2.093973 AGAACAACTGGCTAGATCCGTG 60.094 50.000 3.17 0.00 0.00 4.94
5385 5724 8.480643 TTTTAACGGACAAAACATCACAATTT 57.519 26.923 0.00 0.00 0.00 1.82
5403 5746 7.922505 TGTCAAAATGAGGTGATTTTTAACG 57.077 32.000 0.00 0.00 34.05 3.18
5456 5799 2.356382 ACTCAACCGTGCGAAAATCAAA 59.644 40.909 0.00 0.00 0.00 2.69
5483 5826 3.726557 ACTGGCTGGATCAGAATTTGA 57.273 42.857 0.00 0.00 40.85 2.69
5487 5830 1.760192 GCAACTGGCTGGATCAGAAT 58.240 50.000 0.00 0.00 40.25 2.40
5542 5886 9.282247 GTTAGAATGACATGATTTTTAGCACAG 57.718 33.333 0.00 0.00 0.00 3.66
5583 5927 6.351000 CGAATCGAAATGTGCGTATTACTTTC 59.649 38.462 0.00 0.00 0.00 2.62
5601 5945 1.614227 GCGGCGCATATTCGAATCGA 61.614 55.000 29.21 0.00 0.00 3.59
5646 5990 2.990284 TGGTTTCCACAATCTCCCCTTA 59.010 45.455 0.00 0.00 0.00 2.69
5730 6107 8.877779 TGTGTTTTAACTTGAAATTTCACATGG 58.122 29.630 20.35 12.70 36.83 3.66
5844 6255 8.410141 TGATGTTCGACTTCCTTACAAAATTTT 58.590 29.630 0.00 0.00 0.00 1.82
5858 6269 6.085555 TGTTAAGAGAGTGATGTTCGACTT 57.914 37.500 0.00 0.00 0.00 3.01
5860 6271 5.517054 GGATGTTAAGAGAGTGATGTTCGAC 59.483 44.000 0.00 0.00 0.00 4.20
5862 6273 4.806247 GGGATGTTAAGAGAGTGATGTTCG 59.194 45.833 0.00 0.00 0.00 3.95
5870 6281 5.934402 ATGTTACGGGATGTTAAGAGAGT 57.066 39.130 0.00 0.00 0.00 3.24
5907 6318 3.354089 AAGTGATGTTTTGAAGCACCG 57.646 42.857 0.00 0.00 0.00 4.94
5908 6319 4.504097 GTGAAAGTGATGTTTTGAAGCACC 59.496 41.667 0.00 0.00 0.00 5.01
5909 6320 5.101628 TGTGAAAGTGATGTTTTGAAGCAC 58.898 37.500 0.00 0.00 0.00 4.40
5910 6321 5.321959 TGTGAAAGTGATGTTTTGAAGCA 57.678 34.783 0.00 0.00 0.00 3.91
5911 6322 5.176223 CCATGTGAAAGTGATGTTTTGAAGC 59.824 40.000 0.00 0.00 0.00 3.86
5925 6336 4.503741 ACCGATGAAAACCATGTGAAAG 57.496 40.909 0.00 0.00 35.17 2.62
5949 6360 1.957877 GGGAAAACCAACATTCGGTGA 59.042 47.619 0.00 0.00 36.67 4.02
5980 6404 7.446013 TCCTAATACCGTTGCTATTTATTTGGG 59.554 37.037 0.00 0.00 30.52 4.12
5996 6420 7.871463 CCTTTAATGTAAGTCCTCCTAATACCG 59.129 40.741 0.00 0.00 0.00 4.02
6055 6483 7.426456 CGATCCAACATCTTTTTCTCAAATACG 59.574 37.037 0.00 0.00 0.00 3.06
6057 6485 8.560355 TCGATCCAACATCTTTTTCTCAAATA 57.440 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.