Multiple sequence alignment - TraesCS5B01G093300

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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 TraesCS5B01G093300 chr5B 100.000 5297 0 0 1 5297 122439715 122434419 0.000000e+00 9782.0
1 TraesCS5B01G093300 chr5B 73.284 947 231 15 2176 3114 122831506 122832438 1.420000e-85 327.0
2 TraesCS5B01G093300 chr5D 96.441 4243 127 9 1 4228 110346787 110351020 0.000000e+00 6977.0
3 TraesCS5B01G093300 chr5D 87.554 5359 515 76 6 5297 110365258 110370531 0.000000e+00 6061.0
4 TraesCS5B01G093300 chr5D 73.284 947 231 15 2176 3114 109943774 109942842 1.420000e-85 327.0
5 TraesCS5B01G093300 chr5A 97.711 2883 49 6 676 3543 116698873 116695993 0.000000e+00 4942.0
6 TraesCS5B01G093300 chr5A 87.029 4271 428 62 6 4234 116588312 116584126 0.000000e+00 4702.0
7 TraesCS5B01G093300 chr5A 97.660 2222 33 8 144 2350 116781248 116779031 0.000000e+00 3797.0
8 TraesCS5B01G093300 chr5A 94.171 1870 94 8 2368 4234 116776535 116774678 0.000000e+00 2835.0
9 TraesCS5B01G093300 chr5A 86.811 834 81 13 4395 5212 116583898 116583078 0.000000e+00 904.0
10 TraesCS5B01G093300 chr5A 87.786 655 70 6 3583 4234 116695993 116695346 0.000000e+00 758.0
11 TraesCS5B01G093300 chr5A 97.722 395 8 1 144 538 116699264 116698871 0.000000e+00 678.0
12 TraesCS5B01G093300 chr5A 98.649 148 2 0 1 148 116802734 116802587 4.070000e-66 263.0
13 TraesCS5B01G093300 chr5A 71.534 815 205 19 2506 3312 117388437 117389232 1.510000e-45 195.0
14 TraesCS5B01G093300 chrUn 97.917 384 5 1 847 1227 480886713 480887096 0.000000e+00 662.0
15 TraesCS5B01G093300 chr3B 86.957 69 7 2 2041 2108 829213233 829213300 5.690000e-10 76.8
16 TraesCS5B01G093300 chr3B 83.333 66 11 0 2041 2106 817011814 817011749 1.590000e-05 62.1
17 TraesCS5B01G093300 chr3D 97.727 44 0 1 376 418 573703596 573703639 2.050000e-09 75.0
18 TraesCS5B01G093300 chr1B 97.561 41 1 0 4429 4469 163589528 163589568 2.650000e-08 71.3
19 TraesCS5B01G093300 chr4B 95.122 41 2 0 4429 4469 317036626 317036586 1.230000e-06 65.8


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 TraesCS5B01G093300 chr5B 122434419 122439715 5296 True 9782 9782 100.000000 1 5297 1 chr5B.!!$R1 5296
1 TraesCS5B01G093300 chr5B 122831506 122832438 932 False 327 327 73.284000 2176 3114 1 chr5B.!!$F1 938
2 TraesCS5B01G093300 chr5D 110346787 110351020 4233 False 6977 6977 96.441000 1 4228 1 chr5D.!!$F1 4227
3 TraesCS5B01G093300 chr5D 110365258 110370531 5273 False 6061 6061 87.554000 6 5297 1 chr5D.!!$F2 5291
4 TraesCS5B01G093300 chr5D 109942842 109943774 932 True 327 327 73.284000 2176 3114 1 chr5D.!!$R1 938
5 TraesCS5B01G093300 chr5A 116774678 116781248 6570 True 3316 3797 95.915500 144 4234 2 chr5A.!!$R4 4090
6 TraesCS5B01G093300 chr5A 116583078 116588312 5234 True 2803 4702 86.920000 6 5212 2 chr5A.!!$R2 5206
7 TraesCS5B01G093300 chr5A 116695346 116699264 3918 True 2126 4942 94.406333 144 4234 3 chr5A.!!$R3 4090

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
965 975 1.416401 AGGCTTCAACCTTCGAAGTGA 59.584 47.619 23.03 17.68 41.61 3.41 F
1502 1523 3.120338 GCATTTTTCACCGAGATGACGAA 60.120 43.478 0.00 0.00 35.09 3.85 F
3082 5616 3.558505 CTGAACAACTTGGAGAATTGCG 58.441 45.455 0.00 0.00 0.00 4.85 F
3826 6360 0.099436 GCGCATGATGTGTTCCCTTC 59.901 55.000 0.30 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 4990 3.714798 TGGTAGGGGAGATCATTGTAACC 59.285 47.826 0.0 0.0 0.00 2.85 R
3413 5947 7.372260 AGAATGGTAGCTCTGAAGATGTATT 57.628 36.000 0.0 0.0 0.00 1.89 R
3933 6467 0.524816 GCCGCATTCTTGACAGCATG 60.525 55.000 0.0 0.0 46.00 4.06 R
5029 7643 0.541764 TCCAGTGTTCCAAATGGGGC 60.542 55.000 0.0 0.0 37.22 5.80 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
40 42 6.683537 TCTAGTCAGGGAAGATATTTCCTCA 58.316 40.000 0.00 0.00 38.61 3.86
239 246 4.566004 CACCTTGTATTTCTTGACGGAGA 58.434 43.478 0.00 0.00 0.00 3.71
610 620 8.539770 TGCTCTTTCTTTCATTTACTAGTCTG 57.460 34.615 0.00 0.00 0.00 3.51
656 666 7.039644 CCGTCTTTCCACTTGATATACTCCTAT 60.040 40.741 0.00 0.00 0.00 2.57
965 975 1.416401 AGGCTTCAACCTTCGAAGTGA 59.584 47.619 23.03 17.68 41.61 3.41
1401 1422 5.877012 TCTCAAACAAGATGCTATTGAGGTC 59.123 40.000 12.34 0.00 44.38 3.85
1502 1523 3.120338 GCATTTTTCACCGAGATGACGAA 60.120 43.478 0.00 0.00 35.09 3.85
2151 2194 5.867716 AGAATACTGACAACAACACGTATCC 59.132 40.000 0.00 0.00 0.00 2.59
2460 4990 8.961294 AGAGATGAAGAAGATATTGTTCCTTG 57.039 34.615 7.42 0.00 0.00 3.61
3082 5616 3.558505 CTGAACAACTTGGAGAATTGCG 58.441 45.455 0.00 0.00 0.00 4.85
3413 5947 0.874390 GCATGCTCAACCTTCGTTCA 59.126 50.000 11.37 0.00 0.00 3.18
3526 6060 6.655930 TGTCCATTAACTACTATTTCCCCAC 58.344 40.000 0.00 0.00 0.00 4.61
3554 6088 1.270907 AGTGGGTAGCCTCACTTGAG 58.729 55.000 13.11 0.00 40.91 3.02
3593 6127 3.812053 GCATCTATGTCAATCCAGTGGAC 59.188 47.826 15.86 2.44 32.98 4.02
3648 6182 7.734865 TGCCCTCTCTATTATTTCTCTGGATAA 59.265 37.037 0.00 0.00 0.00 1.75
3665 6199 5.620206 TGGATAACTTCAAGAACAGCAAGA 58.380 37.500 0.00 0.00 0.00 3.02
3670 6204 5.234466 ACTTCAAGAACAGCAAGACCTAT 57.766 39.130 0.00 0.00 0.00 2.57
3691 6225 7.164122 CCTATAGAAAGGCTCATTATCAGCAA 58.836 38.462 0.00 0.00 38.77 3.91
3692 6226 7.828223 CCTATAGAAAGGCTCATTATCAGCAAT 59.172 37.037 0.00 0.00 38.77 3.56
3713 6247 6.206634 GCAATAATGGATTCCGATACCTGAAA 59.793 38.462 0.00 0.00 0.00 2.69
3791 6325 1.003233 GCCGGAGCTTGAGAACCTT 60.003 57.895 5.05 0.00 35.50 3.50
3826 6360 0.099436 GCGCATGATGTGTTCCCTTC 59.901 55.000 0.30 0.00 0.00 3.46
3845 6379 3.485463 TCGAGTGGTGGTCTTGATTTT 57.515 42.857 0.00 0.00 0.00 1.82
3908 6442 3.936453 AGATAGTTTGTTATGGCGCGAAA 59.064 39.130 12.10 0.00 0.00 3.46
3933 6467 3.334054 AGGTGGAGGCCTTGGAGC 61.334 66.667 6.77 3.45 34.71 4.70
4056 6591 0.116143 AGAGGAGGAGGTTGAGCTGT 59.884 55.000 0.00 0.00 0.00 4.40
4067 6602 2.880890 GGTTGAGCTGTCAATTGAGTGT 59.119 45.455 8.80 0.00 44.58 3.55
4092 6627 8.464404 GTGTAACACATCATTGAGGTACTACTA 58.536 37.037 16.55 6.79 37.47 1.82
4093 6628 9.197306 TGTAACACATCATTGAGGTACTACTAT 57.803 33.333 16.55 0.00 41.55 2.12
4096 6631 8.306313 ACACATCATTGAGGTACTACTATTCA 57.694 34.615 3.30 0.00 41.55 2.57
4098 6633 9.770097 CACATCATTGAGGTACTACTATTCATT 57.230 33.333 3.30 0.00 41.55 2.57
4099 6634 9.988815 ACATCATTGAGGTACTACTATTCATTC 57.011 33.333 1.40 0.00 41.55 2.67
4100 6635 9.429359 CATCATTGAGGTACTACTATTCATTCC 57.571 37.037 0.00 0.00 41.55 3.01
4101 6636 7.963532 TCATTGAGGTACTACTATTCATTCCC 58.036 38.462 0.00 0.00 41.55 3.97
4103 6638 7.989947 TTGAGGTACTACTATTCATTCCCTT 57.010 36.000 0.00 0.00 41.55 3.95
4104 6639 9.670442 ATTGAGGTACTACTATTCATTCCCTTA 57.330 33.333 0.00 0.00 41.55 2.69
4105 6640 9.670442 TTGAGGTACTACTATTCATTCCCTTAT 57.330 33.333 0.00 0.00 41.55 1.73
4140 6675 9.208022 TGCTGTACATTTCAGATATATTACTGC 57.792 33.333 0.00 9.87 35.20 4.40
4184 6723 4.017407 AGACTGGAGTAGGAATGTAGGTGA 60.017 45.833 0.00 0.00 0.00 4.02
4195 6734 5.591877 AGGAATGTAGGTGAGCATGAAAATC 59.408 40.000 0.00 0.00 0.00 2.17
4201 6740 3.254166 AGGTGAGCATGAAAATCACACAC 59.746 43.478 17.15 0.00 44.08 3.82
4258 6798 5.667172 TGTTCAGGATCCTTGATCTTCCATA 59.333 40.000 13.00 0.00 38.91 2.74
4263 6803 7.015682 TCAGGATCCTTGATCTTCCATACTTAC 59.984 40.741 13.00 0.00 38.91 2.34
4273 6813 8.206867 TGATCTTCCATACTTACTTCTTGGATG 58.793 37.037 0.00 0.00 36.42 3.51
4302 6842 1.743958 CTCTCTTGCCAATGAAGCCTG 59.256 52.381 0.00 0.00 0.00 4.85
4324 6864 6.638873 CCTGCTAGTTTCATAGAATCGTGTAG 59.361 42.308 0.00 0.00 0.00 2.74
4376 6916 2.846039 CATGGAGAAATGCAGACTGC 57.154 50.000 20.86 20.86 45.29 4.40
4393 6933 2.223876 ACTGCTGAACCTGCACAATTTG 60.224 45.455 0.00 0.00 34.77 2.32
4407 7014 5.163632 TGCACAATTTGTATATGGACTGCTG 60.164 40.000 0.86 0.00 0.00 4.41
4409 7016 4.339247 ACAATTTGTATATGGACTGCTGCC 59.661 41.667 0.00 0.00 0.00 4.85
4418 7025 1.565759 TGGACTGCTGCCATAGGAAAT 59.434 47.619 0.00 0.00 0.00 2.17
4425 7032 4.088634 TGCTGCCATAGGAAATTTTGAGT 58.911 39.130 0.00 0.00 0.00 3.41
4453 7060 7.585286 TGCAGATTGATTCTTTGTTAATTGC 57.415 32.000 0.00 0.00 29.93 3.56
4505 7113 2.430465 TGAAAACCAGATCAGCTGCTC 58.570 47.619 9.47 9.53 43.50 4.26
4507 7115 0.034670 AAACCAGATCAGCTGCTCCC 60.035 55.000 13.81 0.58 43.50 4.30
4508 7116 2.108566 CCAGATCAGCTGCTCCCG 59.891 66.667 13.81 5.85 43.50 5.14
4522 7130 1.835483 CTCCCGCTTGCGCATCATAC 61.835 60.000 12.75 0.00 35.30 2.39
4523 7131 2.179547 CCCGCTTGCGCATCATACA 61.180 57.895 12.75 0.00 35.30 2.29
4562 7170 6.825213 TCTTCCAAGAAACCTCATCATATGTG 59.175 38.462 1.90 1.04 30.73 3.21
4564 7172 5.882000 TCCAAGAAACCTCATCATATGTGTG 59.118 40.000 1.90 3.77 0.00 3.82
4568 7176 6.344500 AGAAACCTCATCATATGTGTGTCTC 58.656 40.000 1.90 1.00 30.44 3.36
4569 7177 5.946942 AACCTCATCATATGTGTGTCTCT 57.053 39.130 1.90 0.00 0.00 3.10
4628 7239 3.181483 ACGGTTTAGTAAGCTATCACGGG 60.181 47.826 0.00 0.00 0.00 5.28
4629 7240 3.067180 CGGTTTAGTAAGCTATCACGGGA 59.933 47.826 0.00 0.00 0.00 5.14
4638 7249 1.069204 GCTATCACGGGATTGCTCTGA 59.931 52.381 24.09 0.00 45.14 3.27
4653 7264 3.118992 TGCTCTGATGTTGGTGCTACTAG 60.119 47.826 0.00 0.00 0.00 2.57
4654 7265 3.118956 GCTCTGATGTTGGTGCTACTAGT 60.119 47.826 0.00 0.00 0.00 2.57
4655 7266 4.428209 CTCTGATGTTGGTGCTACTAGTG 58.572 47.826 5.39 0.00 0.00 2.74
4656 7267 3.832490 TCTGATGTTGGTGCTACTAGTGT 59.168 43.478 5.39 0.00 0.00 3.55
4657 7268 5.014202 TCTGATGTTGGTGCTACTAGTGTA 58.986 41.667 5.39 0.00 0.00 2.90
4658 7269 5.656859 TCTGATGTTGGTGCTACTAGTGTAT 59.343 40.000 5.39 0.00 0.00 2.29
4659 7270 6.154534 TCTGATGTTGGTGCTACTAGTGTATT 59.845 38.462 5.39 0.00 0.00 1.89
4660 7271 6.106003 TGATGTTGGTGCTACTAGTGTATTG 58.894 40.000 5.39 0.00 0.00 1.90
4661 7272 4.250464 TGTTGGTGCTACTAGTGTATTGC 58.750 43.478 5.39 2.96 0.00 3.56
4702 7313 6.294675 CCATTTGTTCAGTGTCCACATACATT 60.295 38.462 0.00 0.00 0.00 2.71
4747 7358 9.667107 TTACATTCTGCTACTGCTAATTTAAGT 57.333 29.630 0.00 0.00 40.48 2.24
4829 7442 8.173130 CAGTTATTCGTGGTATTGTTAGGAAAC 58.827 37.037 0.00 0.00 36.07 2.78
4868 7481 3.446442 AGTTTCATCTGCAGGGTTCAT 57.554 42.857 15.13 0.00 0.00 2.57
4883 7496 5.658190 CAGGGTTCATGAAGGGTATTCATTT 59.342 40.000 8.80 0.00 37.06 2.32
4893 7506 5.353394 AGGGTATTCATTTTGAGACGCTA 57.647 39.130 8.48 0.00 36.38 4.26
4904 7517 1.268625 TGAGACGCTAAAACTCGCTGA 59.731 47.619 0.00 0.00 33.93 4.26
4906 7519 0.992802 GACGCTAAAACTCGCTGAGG 59.007 55.000 9.75 0.00 33.35 3.86
4921 7534 2.333926 CTGAGGCGTTGTCGTGATTAA 58.666 47.619 0.00 0.00 39.49 1.40
4926 7539 2.477375 GGCGTTGTCGTGATTAACTGAA 59.523 45.455 0.00 0.00 39.49 3.02
4951 7564 0.037303 CATGGGAGTGTGGACTGCTT 59.963 55.000 0.00 0.00 40.33 3.91
4959 7572 3.214328 AGTGTGGACTGCTTTTACCAAG 58.786 45.455 0.00 0.00 34.11 3.61
4976 7589 9.999660 TTTTACCAAGGTTTTATATTTTGGTCC 57.000 29.630 10.18 0.00 46.23 4.46
5008 7622 3.797039 TCATGTTGGGAATGATCGACTC 58.203 45.455 0.00 0.00 0.00 3.36
5029 7643 1.062587 CGGCAACTAAATGCTCGAAGG 59.937 52.381 0.00 0.00 45.68 3.46
5043 7657 0.897863 CGAAGGCCCCATTTGGAACA 60.898 55.000 0.00 0.00 37.39 3.18
5052 7675 2.682856 CCCATTTGGAACACTGGATACG 59.317 50.000 0.00 0.00 42.22 3.06
5085 7708 0.026285 GGACCGATTGATGCGAAACG 59.974 55.000 0.00 0.00 0.00 3.60
5094 7717 0.525455 GATGCGAAACGGAAATGGCC 60.525 55.000 0.00 0.00 0.00 5.36
5109 7732 0.038166 TGGCCTGTGATTCCAGTTCC 59.962 55.000 3.32 0.00 0.00 3.62
5110 7733 0.329596 GGCCTGTGATTCCAGTTCCT 59.670 55.000 0.00 0.00 0.00 3.36
5150 7773 1.710816 TGGCGGAAACCCTTTTCAAT 58.289 45.000 0.00 0.00 42.72 2.57
5152 7775 2.036604 TGGCGGAAACCCTTTTCAATTC 59.963 45.455 0.00 0.00 42.72 2.17
5169 7792 1.600023 TTCGCCAGTTCCATTTCGTT 58.400 45.000 0.00 0.00 0.00 3.85
5171 7794 1.950909 TCGCCAGTTCCATTTCGTTTT 59.049 42.857 0.00 0.00 0.00 2.43
5212 7835 3.376859 TGATTAACGCATGCTAGGGTTTG 59.623 43.478 17.13 0.00 43.32 2.93
5213 7836 2.772077 TAACGCATGCTAGGGTTTGA 57.228 45.000 17.13 0.00 43.32 2.69
5214 7837 2.128771 AACGCATGCTAGGGTTTGAT 57.871 45.000 17.13 0.00 41.18 2.57
5276 7902 4.260170 CACTAGTGACTACTACCTCCGTT 58.740 47.826 18.45 0.00 38.36 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 4.018415 AGGTGTGTGCTTTATATTCTGGGT 60.018 41.667 0.00 0.00 0.00 4.51
286 293 7.010552 CAGAATCATCACTTTCCTACTAAACGG 59.989 40.741 0.00 0.00 0.00 4.44
287 294 7.545965 ACAGAATCATCACTTTCCTACTAAACG 59.454 37.037 0.00 0.00 0.00 3.60
495 505 1.233019 CAGTGAACAAGACAGGGCTG 58.767 55.000 0.00 0.00 0.00 4.85
610 620 4.225267 ACGGGAATCATAATAGATCCACCC 59.775 45.833 0.00 0.00 34.94 4.61
656 666 8.974408 CATAAAGATGTCGACGTTCCAATAATA 58.026 33.333 12.40 0.00 0.00 0.98
914 924 4.368315 TGCATAGCCAGTCAAAGTATACG 58.632 43.478 0.00 0.00 0.00 3.06
965 975 2.758423 GGTTGAGTTTTTGTGTCCCTGT 59.242 45.455 0.00 0.00 0.00 4.00
1502 1523 1.660560 GCCATCAATGCCAACGAGCT 61.661 55.000 0.00 0.00 0.00 4.09
2151 2194 4.806247 GCTACAATACTTGGCTACTGTGAG 59.194 45.833 0.00 0.00 34.12 3.51
2460 4990 3.714798 TGGTAGGGGAGATCATTGTAACC 59.285 47.826 0.00 0.00 0.00 2.85
3413 5947 7.372260 AGAATGGTAGCTCTGAAGATGTATT 57.628 36.000 0.00 0.00 0.00 1.89
3554 6088 1.486211 TGCCTAGGTAAGAGAGGTGC 58.514 55.000 11.31 0.00 32.53 5.01
3648 6182 3.567478 AGGTCTTGCTGTTCTTGAAGT 57.433 42.857 0.00 0.00 0.00 3.01
3665 6199 6.270927 TGCTGATAATGAGCCTTTCTATAGGT 59.729 38.462 0.00 0.00 37.63 3.08
3691 6225 7.316393 TCTTTCAGGTATCGGAATCCATTAT 57.684 36.000 0.00 0.00 0.00 1.28
3692 6226 6.740944 TCTTTCAGGTATCGGAATCCATTA 57.259 37.500 0.00 0.00 0.00 1.90
3713 6247 4.287067 TCCCAGCAAGTGAAGTAGAATTCT 59.713 41.667 13.56 13.56 0.00 2.40
3744 6278 0.108945 GCTTCAAACATCAGCCCTGC 60.109 55.000 0.00 0.00 0.00 4.85
3791 6325 0.736053 GCGCATTAAATGGAACCCGA 59.264 50.000 0.30 0.00 0.00 5.14
3826 6360 2.226437 CCAAAATCAAGACCACCACTCG 59.774 50.000 0.00 0.00 0.00 4.18
3845 6379 3.732212 CGAATACAGATTCTGGATGCCA 58.268 45.455 12.22 0.00 34.89 4.92
3860 6394 2.541762 GTGGAGATGCTTGAGCGAATAC 59.458 50.000 0.00 0.00 45.83 1.89
3908 6442 1.307084 GGCCTCCACCTCCCTAACT 60.307 63.158 0.00 0.00 0.00 2.24
3933 6467 0.524816 GCCGCATTCTTGACAGCATG 60.525 55.000 0.00 0.00 46.00 4.06
3988 6522 7.630005 ACAATCTCTTCTTCATCCCATCTAT 57.370 36.000 0.00 0.00 0.00 1.98
4067 6602 7.476540 AGTAGTACCTCAATGATGTGTTACA 57.523 36.000 1.38 0.00 0.00 2.41
4092 6627 4.403432 CAGTTGTGGCATAAGGGAATGAAT 59.597 41.667 0.00 0.00 0.00 2.57
4093 6628 3.763360 CAGTTGTGGCATAAGGGAATGAA 59.237 43.478 0.00 0.00 0.00 2.57
4095 6630 2.159198 GCAGTTGTGGCATAAGGGAATG 60.159 50.000 0.00 0.00 0.00 2.67
4096 6631 2.102578 GCAGTTGTGGCATAAGGGAAT 58.897 47.619 0.00 0.00 0.00 3.01
4098 6633 0.698238 AGCAGTTGTGGCATAAGGGA 59.302 50.000 0.00 0.00 0.00 4.20
4099 6634 0.813184 CAGCAGTTGTGGCATAAGGG 59.187 55.000 0.00 0.00 0.00 3.95
4100 6635 1.538047 ACAGCAGTTGTGGCATAAGG 58.462 50.000 0.00 0.00 38.99 2.69
4101 6636 3.073678 TGTACAGCAGTTGTGGCATAAG 58.926 45.455 0.00 0.00 41.10 1.73
4103 6638 2.849294 TGTACAGCAGTTGTGGCATA 57.151 45.000 0.00 0.00 41.10 3.14
4104 6639 2.205022 ATGTACAGCAGTTGTGGCAT 57.795 45.000 0.33 2.27 41.10 4.40
4105 6640 1.979855 AATGTACAGCAGTTGTGGCA 58.020 45.000 0.33 0.00 41.10 4.92
4237 6777 5.471424 AGTATGGAAGATCAAGGATCCTGA 58.529 41.667 17.02 15.12 39.66 3.86
4239 6779 7.079048 AGTAAGTATGGAAGATCAAGGATCCT 58.921 38.462 9.02 9.02 39.66 3.24
4258 6798 5.507985 GCTGCAAAACATCCAAGAAGTAAGT 60.508 40.000 0.00 0.00 0.00 2.24
4263 6803 3.255149 AGAGCTGCAAAACATCCAAGAAG 59.745 43.478 1.02 0.00 0.00 2.85
4273 6813 0.670162 TGGCAAGAGAGCTGCAAAAC 59.330 50.000 1.02 0.00 34.17 2.43
4302 6842 7.988904 AACTACACGATTCTATGAAACTAGC 57.011 36.000 0.00 0.00 0.00 3.42
4376 6916 6.095300 TCCATATACAAATTGTGCAGGTTCAG 59.905 38.462 9.15 0.00 0.00 3.02
4393 6933 3.515502 TCCTATGGCAGCAGTCCATATAC 59.484 47.826 10.94 0.00 43.42 1.47
4407 7014 7.041107 TGCATTTACTCAAAATTTCCTATGGC 58.959 34.615 0.00 0.00 35.54 4.40
4418 7025 9.985730 AAAGAATCAATCTGCATTTACTCAAAA 57.014 25.926 0.00 0.00 38.79 2.44
4461 7068 9.677567 TCAATTAACTAAAAGTTGCACTGAATC 57.322 29.630 2.59 0.00 39.11 2.52
4474 7081 9.691362 GCTGATCTGGTTTTCAATTAACTAAAA 57.309 29.630 1.46 0.00 0.00 1.52
4482 7089 4.184079 GCAGCTGATCTGGTTTTCAATT 57.816 40.909 20.43 0.00 43.06 2.32
4542 7150 6.596888 AGACACACATATGATGAGGTTTCTTG 59.403 38.462 10.38 0.00 30.28 3.02
4543 7151 6.715280 AGACACACATATGATGAGGTTTCTT 58.285 36.000 10.38 0.00 30.28 2.52
4562 7170 3.007398 ACCATTCAGGAAGTGAGAGACAC 59.993 47.826 0.00 0.00 44.48 3.67
4564 7172 3.594134 CACCATTCAGGAAGTGAGAGAC 58.406 50.000 0.00 0.00 41.22 3.36
4568 7176 2.189594 TGCACCATTCAGGAAGTGAG 57.810 50.000 5.81 0.00 41.22 3.51
4569 7177 2.507484 CTTGCACCATTCAGGAAGTGA 58.493 47.619 5.81 0.00 41.22 3.41
4598 7207 3.933332 AGCTTACTAAACCGTCTGATTGC 59.067 43.478 0.00 0.00 0.00 3.56
4608 7217 4.660789 TCCCGTGATAGCTTACTAAACC 57.339 45.455 0.00 0.00 30.45 3.27
4628 7239 2.089980 AGCACCAACATCAGAGCAATC 58.910 47.619 0.00 0.00 0.00 2.67
4629 7240 2.211250 AGCACCAACATCAGAGCAAT 57.789 45.000 0.00 0.00 0.00 3.56
4638 7249 4.876107 GCAATACACTAGTAGCACCAACAT 59.124 41.667 0.00 0.00 32.86 2.71
4653 7264 6.322491 GGAAGACAAAATACTGGCAATACAC 58.678 40.000 0.00 0.00 0.00 2.90
4654 7265 5.417580 GGGAAGACAAAATACTGGCAATACA 59.582 40.000 0.00 0.00 0.00 2.29
4655 7266 5.417580 TGGGAAGACAAAATACTGGCAATAC 59.582 40.000 0.00 0.00 0.00 1.89
4656 7267 5.575157 TGGGAAGACAAAATACTGGCAATA 58.425 37.500 0.00 0.00 0.00 1.90
4657 7268 4.415596 TGGGAAGACAAAATACTGGCAAT 58.584 39.130 0.00 0.00 0.00 3.56
4658 7269 3.838565 TGGGAAGACAAAATACTGGCAA 58.161 40.909 0.00 0.00 0.00 4.52
4659 7270 3.517296 TGGGAAGACAAAATACTGGCA 57.483 42.857 0.00 0.00 0.00 4.92
4660 7271 5.170748 CAAATGGGAAGACAAAATACTGGC 58.829 41.667 0.00 0.00 0.00 4.85
4661 7272 6.345096 ACAAATGGGAAGACAAAATACTGG 57.655 37.500 0.00 0.00 0.00 4.00
4702 7313 6.531503 TGTAAACATCAAGTGGTGGAAAAA 57.468 33.333 0.00 0.00 0.00 1.94
4745 7356 8.783660 TCAACTAGTAATGATAAGATCCCACT 57.216 34.615 0.00 0.00 0.00 4.00
4776 7389 8.292448 GCAAACTGAGAAAGATGAAATTCTACA 58.708 33.333 0.00 0.00 36.08 2.74
4780 7393 6.449698 TGGCAAACTGAGAAAGATGAAATTC 58.550 36.000 0.00 0.00 0.00 2.17
4829 7442 7.044181 TGAAACTAGGCTGAGTGAGATATTTG 58.956 38.462 0.00 0.00 0.00 2.32
4833 7446 6.040278 CAGATGAAACTAGGCTGAGTGAGATA 59.960 42.308 0.00 0.00 0.00 1.98
4842 7455 2.286872 CCTGCAGATGAAACTAGGCTG 58.713 52.381 17.39 0.00 0.00 4.85
4868 7481 4.394920 GCGTCTCAAAATGAATACCCTTCA 59.605 41.667 0.00 0.00 0.00 3.02
4883 7496 2.058798 CAGCGAGTTTTAGCGTCTCAA 58.941 47.619 0.00 0.00 38.61 3.02
4904 7517 2.066262 CAGTTAATCACGACAACGCCT 58.934 47.619 0.00 0.00 43.96 5.52
4906 7519 3.781341 TTCAGTTAATCACGACAACGC 57.219 42.857 0.00 0.00 43.96 4.84
4909 7522 6.693466 TGGAGTATTCAGTTAATCACGACAA 58.307 36.000 0.00 0.00 0.00 3.18
4912 7525 6.280643 CCATGGAGTATTCAGTTAATCACGA 58.719 40.000 5.56 0.00 0.00 4.35
4914 7527 6.591935 TCCCATGGAGTATTCAGTTAATCAC 58.408 40.000 15.22 0.00 0.00 3.06
4976 7589 7.380536 TCATTCCCAACATGAAAATCTTCAAG 58.619 34.615 0.00 0.00 44.64 3.02
5008 7622 1.062587 CTTCGAGCATTTAGTTGCCGG 59.937 52.381 0.00 0.00 43.83 6.13
5029 7643 0.541764 TCCAGTGTTCCAAATGGGGC 60.542 55.000 0.00 0.00 37.22 5.80
5043 7657 0.968901 TTCCCGCAGACGTATCCAGT 60.969 55.000 0.00 0.00 37.70 4.00
5052 7675 1.644786 CGGTCCATTTTCCCGCAGAC 61.645 60.000 0.00 0.00 34.62 3.51
5071 7694 3.108144 CCATTTCCGTTTCGCATCAATC 58.892 45.455 0.00 0.00 0.00 2.67
5085 7708 1.753073 CTGGAATCACAGGCCATTTCC 59.247 52.381 5.01 10.16 37.06 3.13
5094 7717 6.211515 CAAAAGAAAGGAACTGGAATCACAG 58.788 40.000 0.00 0.00 40.86 3.66
5109 7732 4.687901 ACCCATTCCAACCAAAAGAAAG 57.312 40.909 0.00 0.00 0.00 2.62
5110 7733 4.384647 CCAACCCATTCCAACCAAAAGAAA 60.385 41.667 0.00 0.00 0.00 2.52
5150 7773 1.600023 AACGAAATGGAACTGGCGAA 58.400 45.000 0.00 0.00 0.00 4.70
5152 7775 2.415697 AAAACGAAATGGAACTGGCG 57.584 45.000 0.00 0.00 0.00 5.69
5212 7835 9.616634 CTGTTACAATGCCAATGTTATCATATC 57.383 33.333 0.00 0.00 33.49 1.63
5213 7836 8.084073 GCTGTTACAATGCCAATGTTATCATAT 58.916 33.333 0.00 0.00 33.49 1.78
5214 7837 7.424803 GCTGTTACAATGCCAATGTTATCATA 58.575 34.615 0.00 0.00 33.49 2.15


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

AutoCloner maintained by Alex Coulton.