Multiple sequence alignment - TraesCS2B01G352600

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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 TraesCS2B01G352600 chr2B 100.000 6530 0 0 1 6530 503654276 503647747 0.000000e+00 12059
1 TraesCS2B01G352600 chr2B 93.655 5327 287 32 1 5305 621611374 621616671 0.000000e+00 7917
2 TraesCS2B01G352600 chr2B 93.777 1366 75 8 5170 6530 621616467 621617827 0.000000e+00 2043
3 TraesCS2B01G352600 chr5B 94.492 6427 301 26 1 6408 400982710 400989102 0.000000e+00 9858
4 TraesCS2B01G352600 chr5B 93.002 2558 149 16 3974 6530 638662495 638659967 0.000000e+00 3705
5 TraesCS2B01G352600 chr5B 91.232 1380 101 13 1 1368 567583999 567585370 0.000000e+00 1860
6 TraesCS2B01G352600 chr3B 94.524 6410 290 18 2 6405 736159679 736166033 0.000000e+00 9836
7 TraesCS2B01G352600 chr3B 93.587 6424 315 36 1 6405 675600814 675594469 0.000000e+00 9491
8 TraesCS2B01G352600 chr3B 91.087 3927 303 30 154 4044 71172179 71168264 0.000000e+00 5269
9 TraesCS2B01G352600 chr6B 90.723 5174 391 42 1364 6530 133971816 133976907 0.000000e+00 6813
10 TraesCS2B01G352600 chr6B 88.791 4104 368 51 1364 5410 341928861 341924793 0.000000e+00 4946
11 TraesCS2B01G352600 chr6B 88.764 4005 392 41 1364 5358 227566413 227570369 0.000000e+00 4850
12 TraesCS2B01G352600 chr6B 95.002 2441 95 10 4115 6530 438989263 438991701 0.000000e+00 3807
13 TraesCS2B01G352600 chr6B 94.848 1417 67 6 5114 6529 571749716 571751127 0.000000e+00 2207
14 TraesCS2B01G352600 chr6B 93.445 1434 87 6 3974 5405 571748530 571749958 0.000000e+00 2121
15 TraesCS2B01G352600 chr4A 93.541 4490 247 27 1 4480 744444946 744449402 0.000000e+00 6645
16 TraesCS2B01G352600 chr4A 89.911 5194 417 62 1364 6530 669480844 669475731 0.000000e+00 6589
17 TraesCS2B01G352600 chr4A 91.504 4108 294 38 1 4067 664490616 664494709 0.000000e+00 5602
18 TraesCS2B01G352600 chr4A 93.139 1341 86 6 5194 6530 647864597 647863259 0.000000e+00 1962
19 TraesCS2B01G352600 chr1B 91.378 4129 304 36 1 4090 667326602 667330717 0.000000e+00 5605
20 TraesCS2B01G352600 chr1B 89.573 4009 369 34 1364 5358 306225660 306221687 0.000000e+00 5042
21 TraesCS2B01G352600 chr1B 94.165 1371 77 3 5161 6530 631051119 631052487 0.000000e+00 2085
22 TraesCS2B01G352600 chr4B 91.638 4054 315 22 1 4040 568720723 568724766 0.000000e+00 5587
23 TraesCS2B01G352600 chr4B 90.445 4134 341 36 1 4091 66830116 66834238 0.000000e+00 5397
24 TraesCS2B01G352600 chr7A 81.949 554 91 8 3536 4087 67042301 67042847 1.660000e-125 460
25 TraesCS2B01G352600 chr7A 81.761 159 26 2 3617 3774 67306292 67306448 5.310000e-26 130


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 TraesCS2B01G352600 chr2B 503647747 503654276 6529 True 12059 12059 100.0000 1 6530 1 chr2B.!!$R1 6529
1 TraesCS2B01G352600 chr2B 621611374 621617827 6453 False 4980 7917 93.7160 1 6530 2 chr2B.!!$F1 6529
2 TraesCS2B01G352600 chr5B 400982710 400989102 6392 False 9858 9858 94.4920 1 6408 1 chr5B.!!$F1 6407
3 TraesCS2B01G352600 chr5B 638659967 638662495 2528 True 3705 3705 93.0020 3974 6530 1 chr5B.!!$R1 2556
4 TraesCS2B01G352600 chr5B 567583999 567585370 1371 False 1860 1860 91.2320 1 1368 1 chr5B.!!$F2 1367
5 TraesCS2B01G352600 chr3B 736159679 736166033 6354 False 9836 9836 94.5240 2 6405 1 chr3B.!!$F1 6403
6 TraesCS2B01G352600 chr3B 675594469 675600814 6345 True 9491 9491 93.5870 1 6405 1 chr3B.!!$R2 6404
7 TraesCS2B01G352600 chr3B 71168264 71172179 3915 True 5269 5269 91.0870 154 4044 1 chr3B.!!$R1 3890
8 TraesCS2B01G352600 chr6B 133971816 133976907 5091 False 6813 6813 90.7230 1364 6530 1 chr6B.!!$F1 5166
9 TraesCS2B01G352600 chr6B 341924793 341928861 4068 True 4946 4946 88.7910 1364 5410 1 chr6B.!!$R1 4046
10 TraesCS2B01G352600 chr6B 227566413 227570369 3956 False 4850 4850 88.7640 1364 5358 1 chr6B.!!$F2 3994
11 TraesCS2B01G352600 chr6B 438989263 438991701 2438 False 3807 3807 95.0020 4115 6530 1 chr6B.!!$F3 2415
12 TraesCS2B01G352600 chr6B 571748530 571751127 2597 False 2164 2207 94.1465 3974 6529 2 chr6B.!!$F4 2555
13 TraesCS2B01G352600 chr4A 744444946 744449402 4456 False 6645 6645 93.5410 1 4480 1 chr4A.!!$F2 4479
14 TraesCS2B01G352600 chr4A 669475731 669480844 5113 True 6589 6589 89.9110 1364 6530 1 chr4A.!!$R2 5166
15 TraesCS2B01G352600 chr4A 664490616 664494709 4093 False 5602 5602 91.5040 1 4067 1 chr4A.!!$F1 4066
16 TraesCS2B01G352600 chr4A 647863259 647864597 1338 True 1962 1962 93.1390 5194 6530 1 chr4A.!!$R1 1336
17 TraesCS2B01G352600 chr1B 667326602 667330717 4115 False 5605 5605 91.3780 1 4090 1 chr1B.!!$F2 4089
18 TraesCS2B01G352600 chr1B 306221687 306225660 3973 True 5042 5042 89.5730 1364 5358 1 chr1B.!!$R1 3994
19 TraesCS2B01G352600 chr1B 631051119 631052487 1368 False 2085 2085 94.1650 5161 6530 1 chr1B.!!$F1 1369
20 TraesCS2B01G352600 chr4B 568720723 568724766 4043 False 5587 5587 91.6380 1 4040 1 chr4B.!!$F2 4039
21 TraesCS2B01G352600 chr4B 66830116 66834238 4122 False 5397 5397 90.4450 1 4091 1 chr4B.!!$F1 4090
22 TraesCS2B01G352600 chr7A 67042301 67042847 546 False 460 460 81.9490 3536 4087 1 chr7A.!!$F1 551

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
940 960 2.997485 AAAAATGCAGAGCCTTCGTC 57.003 45.0 0.00 0.00 0.00 4.20 F
1123 1171 0.482446 AGTTGCCATCCCTGGACAAA 59.518 50.0 0.00 0.00 46.37 2.83 F
2581 2675 0.969894 AGTTGGCTGACGTAGAAGCT 59.030 50.0 14.75 0.00 39.79 3.74 F
4057 4391 0.040067 GTGTAAGGCACTGCAGTTGC 60.040 55.0 18.94 22.43 44.41 4.17 F
4080 4414 0.040067 GTGTAAGGCACTGCAGTTGC 60.040 55.0 18.94 22.43 44.41 4.17 F
4590 5066 0.613260 CCGGAGTCAACCATGGAAGA 59.387 55.0 21.47 12.84 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 2650 0.320421 TACGTCAGCCAACTTGCTCC 60.320 55.0 0.00 0.00 40.32 4.70 R
2863 2958 2.354203 GCACTCCAAGAAGGTCTCGAAT 60.354 50.0 0.00 0.00 39.02 3.34 R
4068 4402 0.249573 AAACATGGCAACTGCAGTGC 60.250 50.0 22.49 23.67 44.36 4.40 R
5300 6087 1.100510 GCAAGATGGCAGATTCAGCA 58.899 50.0 3.34 0.00 0.00 4.41 R
5301 6088 1.390565 AGCAAGATGGCAGATTCAGC 58.609 50.0 0.00 0.00 35.83 4.26 R
6317 7159 0.819582 CATGTTCCCCATGTTCCAGC 59.180 55.0 0.00 0.00 44.96 4.85 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
172 176 5.338300 GGAGGGTGTCAAAATTAATTGCCAT 60.338 40.000 0.39 0.00 0.00 4.40
370 377 4.732784 ACGCATGAAAATGTGATAACACC 58.267 39.130 0.00 0.00 45.40 4.16
518 526 3.012518 CGGAGATGGCACTGATCTTTTT 58.987 45.455 0.00 0.00 29.97 1.94
615 623 3.181489 GCCACTACTAGAACAGTACGCAT 60.181 47.826 0.00 0.00 38.80 4.73
683 692 3.118542 TGTTCGCGATGATGAAGATGAG 58.881 45.455 10.88 0.00 0.00 2.90
906 926 3.056322 GCAAAGGATGGCAAAAGACTCAT 60.056 43.478 0.00 0.00 0.00 2.90
940 960 2.997485 AAAAATGCAGAGCCTTCGTC 57.003 45.000 0.00 0.00 0.00 4.20
1123 1171 0.482446 AGTTGCCATCCCTGGACAAA 59.518 50.000 0.00 0.00 46.37 2.83
1256 1332 5.192923 AGGTTATTACAATGCTTCTACCCCA 59.807 40.000 0.00 0.00 0.00 4.96
1480 1557 1.100510 CTACAGCTGCCATGCACATT 58.899 50.000 15.27 0.00 33.79 2.71
1548 1627 3.947834 ACTGCTACAACTGCTGAAAAACT 59.052 39.130 0.00 0.00 34.27 2.66
1724 1804 3.477899 AGCAAAAGATCTTACGCTTGC 57.522 42.857 25.16 25.16 39.50 4.01
1756 1847 7.685849 TTTCTATTACAGGGCCTACAACTAT 57.314 36.000 5.28 0.00 0.00 2.12
1845 1936 1.614903 CAACCACAAGTCATGCCACAT 59.385 47.619 0.00 0.00 0.00 3.21
1854 1945 4.502105 AGTCATGCCACATACAATACCA 57.498 40.909 0.00 0.00 0.00 3.25
1858 1949 4.639755 TCATGCCACATACAATACCAAGTG 59.360 41.667 0.00 0.00 0.00 3.16
2113 2204 2.114616 TGCAAAGTTCCATGGGTTTGT 58.885 42.857 24.21 5.13 33.33 2.83
2177 2268 4.667573 AGTACAACAGAGGTGAGATGAGA 58.332 43.478 0.00 0.00 0.00 3.27
2260 2351 8.108364 ACAAAAGAGAGGAATCATTCTCAAGAT 58.892 33.333 13.82 0.00 41.78 2.40
2289 2380 2.289195 CCTGTCCGGTGTAAGCTAAACA 60.289 50.000 0.00 0.00 0.00 2.83
2556 2650 5.628433 ACCTAAAGGCAAAATACCGTAGAGG 60.628 44.000 0.00 0.00 42.37 3.69
2581 2675 0.969894 AGTTGGCTGACGTAGAAGCT 59.030 50.000 14.75 0.00 39.79 3.74
2719 2814 4.691216 AGAGCCTACAAACATTTTCGAGAC 59.309 41.667 0.00 0.00 0.00 3.36
2814 2909 1.195448 CCACAATCAGTCGTTGCAGTC 59.805 52.381 0.00 0.00 0.00 3.51
2863 2958 0.176219 CGGATGGGTACGTTTGGCTA 59.824 55.000 0.00 0.00 0.00 3.93
2867 2962 2.012937 TGGGTACGTTTGGCTATTCG 57.987 50.000 0.00 0.00 0.00 3.34
3260 3355 2.787473 CAGTGAGGGGTTCAATGCTA 57.213 50.000 0.00 0.00 43.91 3.49
3269 3364 4.467438 AGGGGTTCAATGCTATTTTGAAGG 59.533 41.667 0.00 0.00 42.14 3.46
3311 3406 4.281688 ACTCATTGCTACAATTTGCCAAGT 59.718 37.500 0.00 0.00 0.00 3.16
3415 3510 4.996788 AACGTATTTACCGATGGAGAGT 57.003 40.909 0.00 0.00 0.00 3.24
3689 3814 6.317642 GCCATGTGTAATACAATGTACTTCCA 59.682 38.462 0.00 0.00 43.77 3.53
3877 4036 3.317603 AGTTGCCATGTTTTATGCACC 57.682 42.857 0.00 0.00 32.63 5.01
3884 4043 0.386605 TGTTTTATGCACCGCGCTTG 60.387 50.000 5.56 3.28 43.06 4.01
3887 4046 0.724549 TTTATGCACCGCGCTTGTAG 59.275 50.000 5.56 0.00 43.06 2.74
3889 4048 1.081556 TATGCACCGCGCTTGTAGTG 61.082 55.000 5.56 3.16 43.06 2.74
4010 4344 4.396166 GCCATGTCTAATGCACTACAGTTT 59.604 41.667 0.00 0.00 0.00 2.66
4023 4357 5.447818 GCACTACAGTTTCCATGTCTAATGC 60.448 44.000 0.00 0.00 32.02 3.56
4041 4375 2.035421 CACTGCAGTTGCCATGTGT 58.965 52.632 18.94 0.00 41.18 3.72
4042 4376 1.237533 CACTGCAGTTGCCATGTGTA 58.762 50.000 18.94 0.00 41.18 2.90
4043 4377 1.608109 CACTGCAGTTGCCATGTGTAA 59.392 47.619 18.94 0.00 41.18 2.41
4044 4378 1.881973 ACTGCAGTTGCCATGTGTAAG 59.118 47.619 15.25 0.00 41.18 2.34
4045 4379 1.200716 CTGCAGTTGCCATGTGTAAGG 59.799 52.381 5.25 0.00 41.18 2.69
4057 4391 0.040067 GTGTAAGGCACTGCAGTTGC 60.040 55.000 18.94 22.43 44.41 4.17
4062 4396 3.045142 GCACTGCAGTTGCCATGT 58.955 55.556 18.94 0.00 41.18 3.21
4063 4397 1.372499 GCACTGCAGTTGCCATGTG 60.372 57.895 18.94 5.26 41.18 3.21
4064 4398 2.035421 CACTGCAGTTGCCATGTGT 58.965 52.632 18.94 0.00 41.18 3.72
4065 4399 1.237533 CACTGCAGTTGCCATGTGTA 58.762 50.000 18.94 0.00 41.18 2.90
4066 4400 1.608109 CACTGCAGTTGCCATGTGTAA 59.392 47.619 18.94 0.00 41.18 2.41
4067 4401 1.881973 ACTGCAGTTGCCATGTGTAAG 59.118 47.619 15.25 0.00 41.18 2.34
4068 4402 1.200716 CTGCAGTTGCCATGTGTAAGG 59.799 52.381 5.25 0.00 41.18 2.69
4080 4414 0.040067 GTGTAAGGCACTGCAGTTGC 60.040 55.000 18.94 22.43 44.41 4.17
4085 4419 3.045142 GCACTGCAGTTGCCATGT 58.955 55.556 18.94 0.00 41.18 3.21
4086 4420 1.364901 GCACTGCAGTTGCCATGTT 59.635 52.632 18.94 0.00 41.18 2.71
4102 4505 7.753309 TGCCATGTTTAATGTACTACAGTTT 57.247 32.000 0.00 0.00 0.00 2.66
4133 4559 8.723311 GTTTAATGTACTACAGTTGCCATGTTA 58.277 33.333 0.00 0.00 32.02 2.41
4137 4609 7.753309 TGTACTACAGTTGCCATGTTAAAAT 57.247 32.000 0.00 0.00 32.02 1.82
4369 4844 3.554337 GGAACTACTTCGTGAAAGCCTCA 60.554 47.826 0.00 0.00 38.67 3.86
4375 4851 1.533625 TCGTGAAAGCCTCAATTGGG 58.466 50.000 5.42 0.80 35.22 4.12
4590 5066 0.613260 CCGGAGTCAACCATGGAAGA 59.387 55.000 21.47 12.84 0.00 2.87
4594 5070 2.338500 GAGTCAACCATGGAAGACGTC 58.662 52.381 21.47 17.86 36.18 4.34
4659 5135 1.206610 AGCGTGCAAGAGTGATGAGAT 59.793 47.619 2.99 0.00 0.00 2.75
5077 5554 6.097412 GGGCATCAGAAGTTGAAGGAAAATAT 59.903 38.462 0.00 0.00 39.77 1.28
5082 5559 8.690203 TCAGAAGTTGAAGGAAAATATGTTGA 57.310 30.769 0.00 0.00 31.34 3.18
5131 5609 4.269183 TGGGTACTTAATCTGCCATGTTG 58.731 43.478 0.00 0.00 0.00 3.33
5239 5934 6.894682 TCTGCCATGTTAATTGTACTGGATA 58.105 36.000 0.00 0.00 0.00 2.59
5298 6085 3.675995 TGGATCTGCCATGTTGCTT 57.324 47.368 0.00 0.00 43.33 3.91
5299 6086 2.804986 TGGATCTGCCATGTTGCTTA 57.195 45.000 0.00 0.00 43.33 3.09
5300 6087 3.301794 TGGATCTGCCATGTTGCTTAT 57.698 42.857 0.00 0.00 43.33 1.73
5301 6088 2.953648 TGGATCTGCCATGTTGCTTATG 59.046 45.455 0.00 0.00 43.33 1.90
5302 6089 2.288030 GGATCTGCCATGTTGCTTATGC 60.288 50.000 0.00 0.00 36.74 3.14
5303 6090 2.133281 TCTGCCATGTTGCTTATGCT 57.867 45.000 1.96 0.00 40.48 3.79
5304 6091 1.746787 TCTGCCATGTTGCTTATGCTG 59.253 47.619 1.96 0.00 40.48 4.41
5305 6092 1.746787 CTGCCATGTTGCTTATGCTGA 59.253 47.619 1.96 0.00 40.48 4.26
5306 6093 2.164827 CTGCCATGTTGCTTATGCTGAA 59.835 45.455 1.96 0.00 40.48 3.02
5307 6094 2.761767 TGCCATGTTGCTTATGCTGAAT 59.238 40.909 1.96 0.00 40.48 2.57
5308 6095 3.181484 TGCCATGTTGCTTATGCTGAATC 60.181 43.478 1.96 0.00 40.48 2.52
5309 6096 3.067742 GCCATGTTGCTTATGCTGAATCT 59.932 43.478 1.96 0.00 40.48 2.40
5310 6097 4.607955 CCATGTTGCTTATGCTGAATCTG 58.392 43.478 1.96 0.00 40.48 2.90
5311 6098 3.770263 TGTTGCTTATGCTGAATCTGC 57.230 42.857 5.11 5.11 40.48 4.26
5312 6099 2.424601 TGTTGCTTATGCTGAATCTGCC 59.575 45.455 9.59 0.00 40.48 4.85
5313 6100 2.423446 TGCTTATGCTGAATCTGCCA 57.577 45.000 9.59 0.00 40.48 4.92
5314 6101 2.940158 TGCTTATGCTGAATCTGCCAT 58.060 42.857 9.59 6.09 40.48 4.40
5315 6102 2.882761 TGCTTATGCTGAATCTGCCATC 59.117 45.455 9.59 0.00 40.48 3.51
5316 6103 3.147629 GCTTATGCTGAATCTGCCATCT 58.852 45.455 9.59 0.00 36.03 2.90
5429 6262 3.304026 CGCCAAATGAAAAACGATGATGG 59.696 43.478 0.00 0.00 0.00 3.51
5504 6337 2.363680 AGACGCATTAGTAGCAGCAGAT 59.636 45.455 0.00 0.00 0.00 2.90
5683 6521 4.794762 TCGTAACATAGCACACGAACATAC 59.205 41.667 0.00 0.00 40.17 2.39
5788 6627 7.216494 TGTGATCACTTGTACTTCTTGATGAA 58.784 34.615 25.55 0.00 0.00 2.57
5961 6800 1.686355 TTCCAACGTGTGAAAGCCAT 58.314 45.000 0.00 0.00 0.00 4.40
6108 6949 2.779755 TGGTCGCCACATACTCAATT 57.220 45.000 0.00 0.00 0.00 2.32
6317 7159 1.582968 GGTCATGTGGTGCAAGCTG 59.417 57.895 0.00 0.00 33.76 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 176 2.206750 GCAACTGACGTTAGACACCAA 58.793 47.619 15.04 0.00 0.00 3.67
269 274 3.048600 TGGGTGCTAGCTATCCATTCTT 58.951 45.455 17.23 0.00 0.00 2.52
370 377 3.671459 TGCATGTAGAAGTTAACACGTCG 59.329 43.478 8.61 0.00 36.59 5.12
518 526 2.306847 GTTTCTGGCCTTTGAGAACCA 58.693 47.619 3.32 0.00 0.00 3.67
1123 1171 2.511818 CCATGGATGGCAACTGCAT 58.488 52.632 5.56 0.00 41.75 3.96
1158 1207 1.331214 ACAACTGCAATTGTCCAGGG 58.669 50.000 7.90 10.13 38.44 4.45
1256 1332 0.877071 CTTGCCATGAGACGTTTGCT 59.123 50.000 0.00 0.00 0.00 3.91
1480 1557 6.928979 TTTCAGTACGAAAACTTGGATTCA 57.071 33.333 9.44 0.00 40.70 2.57
1532 1611 6.458342 GCAACTACTAGTTTTTCAGCAGTTGT 60.458 38.462 22.51 0.00 42.14 3.32
1538 1617 5.048713 ACATGGCAACTACTAGTTTTTCAGC 60.049 40.000 0.00 0.00 36.03 4.26
1548 1627 4.517453 GTCCAACAAACATGGCAACTACTA 59.483 41.667 0.00 0.00 37.88 1.82
1724 1804 5.077564 GGCCCTGTAATAGAAAAATAGGGG 58.922 45.833 0.00 0.00 42.85 4.79
1756 1847 2.432456 CTGCGCCGCTGTTCACTA 60.432 61.111 11.67 0.00 0.00 2.74
1805 1896 2.282958 TGGAGGACCGCGTCTTCT 60.283 61.111 4.92 0.00 38.46 2.85
1845 1936 6.911250 TTCTGACTCTCACTTGGTATTGTA 57.089 37.500 0.00 0.00 0.00 2.41
1854 1945 3.777106 TGCCATTTCTGACTCTCACTT 57.223 42.857 0.00 0.00 0.00 3.16
1858 1949 5.221009 GGAATGATTGCCATTTCTGACTCTC 60.221 44.000 0.00 0.00 45.00 3.20
2113 2204 3.118555 CCTATGGTATTCGGTGTTGACCA 60.119 47.826 0.00 0.00 43.33 4.02
2260 2351 2.933287 ACCGGACAGGGCATTCCA 60.933 61.111 9.46 0.00 46.96 3.53
2289 2380 2.092753 CCGCCCATTATGCTCCATCTAT 60.093 50.000 0.00 0.00 0.00 1.98
2556 2650 0.320421 TACGTCAGCCAACTTGCTCC 60.320 55.000 0.00 0.00 40.32 4.70
2581 2675 4.407365 TCTCATCGAAGTAGGCCATCATA 58.593 43.478 5.01 0.00 0.00 2.15
2719 2814 2.742954 TCGCATCGAATGAAATGCAG 57.257 45.000 7.17 0.87 46.83 4.41
2863 2958 2.354203 GCACTCCAAGAAGGTCTCGAAT 60.354 50.000 0.00 0.00 39.02 3.34
2867 2962 2.354259 CATGCACTCCAAGAAGGTCTC 58.646 52.381 0.00 0.00 39.02 3.36
3260 3355 2.433436 GCTCACGTACCCCTTCAAAAT 58.567 47.619 0.00 0.00 0.00 1.82
3311 3406 5.568685 TTTTGTTGCAAAGCTGTGTACTA 57.431 34.783 5.61 0.00 0.00 1.82
3364 3459 2.896801 CTGCTTCAGCGCGGTGTTT 61.897 57.895 34.29 0.00 45.83 2.83
3415 3510 6.883756 TGTTGGTGTATATCTTGCTCATTTGA 59.116 34.615 0.00 0.00 0.00 2.69
3689 3814 3.264998 GCATACCAACATGCCCATTTT 57.735 42.857 0.00 0.00 44.55 1.82
4010 4344 2.026915 ACTGCAGTGCATTAGACATGGA 60.027 45.455 20.97 0.00 38.13 3.41
4023 4357 1.237533 TACACATGGCAACTGCAGTG 58.762 50.000 22.49 15.42 44.36 3.66
4041 4375 4.079446 GGCAACTGCAGTGCCTTA 57.921 55.556 34.24 0.00 44.72 2.69
4045 4379 1.372499 CACATGGCAACTGCAGTGC 60.372 57.895 22.49 23.67 44.36 4.40
4046 4380 1.237533 TACACATGGCAACTGCAGTG 58.762 50.000 22.49 15.42 44.36 3.66
4047 4381 1.881973 CTTACACATGGCAACTGCAGT 59.118 47.619 15.25 15.25 44.36 4.40
4048 4382 1.200716 CCTTACACATGGCAACTGCAG 59.799 52.381 13.48 13.48 44.36 4.41
4049 4383 1.246649 CCTTACACATGGCAACTGCA 58.753 50.000 3.76 0.00 44.36 4.41
4061 4395 3.336111 GGCAACTGCAGTGCCTTACAC 62.336 57.143 34.24 18.32 44.72 2.90
4062 4396 1.172180 GGCAACTGCAGTGCCTTACA 61.172 55.000 34.24 0.00 44.72 2.41
4063 4397 1.581447 GGCAACTGCAGTGCCTTAC 59.419 57.895 34.24 19.08 44.72 2.34
4064 4398 4.079446 GGCAACTGCAGTGCCTTA 57.921 55.556 34.24 0.00 44.72 2.69
4068 4402 0.249573 AAACATGGCAACTGCAGTGC 60.250 50.000 22.49 23.67 44.36 4.40
4069 4403 3.367992 TTAAACATGGCAACTGCAGTG 57.632 42.857 22.49 15.42 44.36 3.66
4070 4404 3.321682 ACATTAAACATGGCAACTGCAGT 59.678 39.130 15.25 15.25 44.36 4.40
4071 4405 3.916761 ACATTAAACATGGCAACTGCAG 58.083 40.909 13.48 13.48 44.36 4.41
4072 4406 4.522405 AGTACATTAAACATGGCAACTGCA 59.478 37.500 3.76 0.00 44.36 4.41
4073 4407 5.059404 AGTACATTAAACATGGCAACTGC 57.941 39.130 0.00 0.00 41.14 4.40
4074 4408 7.094805 ACTGTAGTACATTAAACATGGCAACTG 60.095 37.037 2.82 0.00 37.61 3.16
4075 4409 6.940298 ACTGTAGTACATTAAACATGGCAACT 59.060 34.615 2.82 0.00 37.61 3.16
4076 4410 7.141100 ACTGTAGTACATTAAACATGGCAAC 57.859 36.000 2.82 0.00 0.00 4.17
4077 4411 7.753309 AACTGTAGTACATTAAACATGGCAA 57.247 32.000 2.82 0.00 0.00 4.52
4078 4412 7.094549 GGAAACTGTAGTACATTAAACATGGCA 60.095 37.037 2.82 0.00 0.00 4.92
4079 4413 7.094549 TGGAAACTGTAGTACATTAAACATGGC 60.095 37.037 2.82 0.00 0.00 4.40
4080 4414 8.330466 TGGAAACTGTAGTACATTAAACATGG 57.670 34.615 2.82 0.00 0.00 3.66
4081 4415 9.773328 CATGGAAACTGTAGTACATTAAACATG 57.227 33.333 16.24 16.24 0.00 3.21
4082 4416 9.515226 ACATGGAAACTGTAGTACATTAAACAT 57.485 29.630 2.82 4.12 0.00 2.71
4083 4417 8.911918 ACATGGAAACTGTAGTACATTAAACA 57.088 30.769 2.82 1.91 0.00 2.83
4102 4505 6.373216 GGCAACTGTAGTACATTAAACATGGA 59.627 38.462 2.82 0.00 0.00 3.41
4137 4609 6.755141 GTCGTGGCTTATAGAAGTACATTTCA 59.245 38.462 0.00 0.00 34.90 2.69
4369 4844 2.143876 AGTATTCGCCTTGCCCAATT 57.856 45.000 0.00 0.00 0.00 2.32
4375 4851 0.938008 GGCAGTAGTATTCGCCTTGC 59.062 55.000 0.00 0.00 41.50 4.01
4848 5324 1.559368 CTTTGTGATGGAATGGGGCA 58.441 50.000 0.00 0.00 0.00 5.36
5077 5554 7.039434 TGGCAACTACATTTATCCATTTCAACA 60.039 33.333 0.00 0.00 37.61 3.33
5082 5559 7.422465 ACATGGCAACTACATTTATCCATTT 57.578 32.000 0.00 0.00 31.11 2.32
5131 5609 3.941483 AGCATGGCAGATTAACTACACAC 59.059 43.478 0.00 0.00 0.00 3.82
5192 5767 7.176165 CAGATCCAGTACAAAATATCATGGCAT 59.824 37.037 0.00 0.00 0.00 4.40
5239 5934 6.263842 CAGATCCAGTACAATTAACATGGCAT 59.736 38.462 0.00 0.00 0.00 4.40
5294 6081 2.423446 TGGCAGATTCAGCATAAGCA 57.577 45.000 3.34 0.00 45.49 3.91
5295 6082 3.147629 AGATGGCAGATTCAGCATAAGC 58.852 45.455 3.34 0.00 42.56 3.09
5296 6083 4.556898 GCAAGATGGCAGATTCAGCATAAG 60.557 45.833 3.34 0.00 0.00 1.73
5297 6084 3.317149 GCAAGATGGCAGATTCAGCATAA 59.683 43.478 3.34 0.00 0.00 1.90
5298 6085 2.882761 GCAAGATGGCAGATTCAGCATA 59.117 45.455 3.34 0.00 0.00 3.14
5299 6086 1.681793 GCAAGATGGCAGATTCAGCAT 59.318 47.619 3.34 0.00 0.00 3.79
5300 6087 1.100510 GCAAGATGGCAGATTCAGCA 58.899 50.000 3.34 0.00 0.00 4.41
5301 6088 1.390565 AGCAAGATGGCAGATTCAGC 58.609 50.000 0.00 0.00 35.83 4.26
5302 6089 4.556898 GCATAAGCAAGATGGCAGATTCAG 60.557 45.833 0.00 0.00 41.58 3.02
5303 6090 3.317149 GCATAAGCAAGATGGCAGATTCA 59.683 43.478 0.00 0.00 41.58 2.57
5304 6091 3.568853 AGCATAAGCAAGATGGCAGATTC 59.431 43.478 0.00 0.00 45.49 2.52
5305 6092 3.318275 CAGCATAAGCAAGATGGCAGATT 59.682 43.478 0.00 0.00 45.49 2.40
5306 6093 2.885266 CAGCATAAGCAAGATGGCAGAT 59.115 45.455 0.00 0.00 45.49 2.90
5307 6094 2.092807 TCAGCATAAGCAAGATGGCAGA 60.093 45.455 0.00 0.00 45.49 4.26
5308 6095 2.294979 TCAGCATAAGCAAGATGGCAG 58.705 47.619 0.00 0.00 45.49 4.85
5309 6096 2.423446 TCAGCATAAGCAAGATGGCA 57.577 45.000 0.00 0.00 45.49 4.92
5310 6097 3.568853 AGATTCAGCATAAGCAAGATGGC 59.431 43.478 0.00 0.00 45.49 4.40
5311 6098 4.556898 GCAGATTCAGCATAAGCAAGATGG 60.557 45.833 0.00 0.00 45.49 3.51
5312 6099 4.537965 GCAGATTCAGCATAAGCAAGATG 58.462 43.478 0.00 0.00 45.49 2.90
5313 6100 3.568853 GGCAGATTCAGCATAAGCAAGAT 59.431 43.478 3.34 0.00 45.49 2.40
5314 6101 2.947652 GGCAGATTCAGCATAAGCAAGA 59.052 45.455 3.34 0.00 45.49 3.02
5315 6102 2.286831 CGGCAGATTCAGCATAAGCAAG 60.287 50.000 3.34 0.00 45.49 4.01
5316 6103 1.672363 CGGCAGATTCAGCATAAGCAA 59.328 47.619 3.34 0.00 45.49 3.91
5429 6262 7.497249 AGTTCATCAGATATGGTTAGTGAAAGC 59.503 37.037 0.00 0.00 36.08 3.51
5474 6307 5.920840 TGCTACTAATGCGTCTATGATGTTC 59.079 40.000 0.00 0.00 0.00 3.18
5504 6337 4.096532 TGGTTTCATCGTTTGTAGCAACAA 59.903 37.500 0.00 0.00 43.85 2.83
5788 6627 3.416156 GTGGAGGAAGCTGTCAAGAAAT 58.584 45.455 0.00 0.00 0.00 2.17
5961 6800 3.462483 TTTCTTGTGCAGGACGAACTA 57.538 42.857 0.00 0.00 0.00 2.24
6108 6949 2.239654 GGTCCAGATCAGACATTTCCCA 59.760 50.000 15.39 0.00 35.89 4.37
6317 7159 0.819582 CATGTTCCCCATGTTCCAGC 59.180 55.000 0.00 0.00 44.96 4.85
6337 7179 2.819608 TCCTTCACTTTTACATGCAGGC 59.180 45.455 0.00 0.00 30.17 4.85


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

AutoCloner maintained by Alex Coulton.