Multiple sequence alignment - TraesCS4D01G127400

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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 TraesCS4D01G127400 chr4D 100.000 4689 0 0 1 4689 111939760 111935072 0.000000e+00 8660
1 TraesCS4D01G127400 chr4D 91.608 143 3 4 4553 4689 109277331 109277470 6.190000e-44 189
2 TraesCS4D01G127400 chr4B 91.457 3055 117 36 1 3024 172507527 172504586 0.000000e+00 4063
3 TraesCS4D01G127400 chr4B 87.054 1205 73 35 3128 4283 172504436 172503266 0.000000e+00 1284
4 TraesCS4D01G127400 chr4B 81.154 260 13 5 4456 4689 172503015 172502766 4.820000e-40 176
5 TraesCS4D01G127400 chr4B 96.104 77 1 2 3056 3130 172504593 172504517 1.770000e-24 124
6 TraesCS4D01G127400 chr4A 94.814 1504 55 10 1523 3003 465409335 465410838 0.000000e+00 2324
7 TraesCS4D01G127400 chr4A 89.929 1539 88 40 2968 4471 465410837 465412343 0.000000e+00 1921
8 TraesCS4D01G127400 chr4A 89.563 1533 83 37 1 1488 465407845 465409345 0.000000e+00 1873
9 TraesCS4D01G127400 chr4A 90.308 227 13 2 4469 4689 465412391 465412614 5.940000e-74 289
10 TraesCS4D01G127400 chr4A 82.642 265 29 10 4434 4687 467236509 467236251 7.900000e-53 219


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 TraesCS4D01G127400 chr4D 111935072 111939760 4688 True 8660.00 8660 100.00000 1 4689 1 chr4D.!!$R1 4688
1 TraesCS4D01G127400 chr4B 172502766 172507527 4761 True 1411.75 4063 88.94225 1 4689 4 chr4B.!!$R1 4688
2 TraesCS4D01G127400 chr4A 465407845 465412614 4769 False 1601.75 2324 91.15350 1 4689 4 chr4A.!!$F1 4688

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
591 615 2.004408 GAATCTGGCAGGGGCTGGAT 62.004 60.000 15.73 0.00 40.87 3.41 F
1357 1439 0.753867 TCGGTGCTACTGTTTGGTGA 59.246 50.000 0.00 0.00 0.00 4.02 F
1529 1611 0.394565 GGATACTGCCCAGGCTAGTG 59.605 60.000 18.26 6.91 42.51 2.74 F
1826 1922 2.035832 AGGTCGGCTTTTTGGTCAAATG 59.964 45.455 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1485 0.099613 AGCACTCAGAGCACGTATCG 59.900 55.0 0.0 0.0 0.00 2.92 R
2257 2360 0.531974 TGCAGTTCACGGTTCCTGTC 60.532 55.0 0.0 0.0 0.00 3.51 R
3434 3659 0.737219 GGCCATCTGCATCAGTCAAC 59.263 55.0 0.0 0.0 43.89 3.18 R
3696 3923 0.900647 AGTCAGGGTCTTCAGGGACG 60.901 60.0 0.0 0.0 37.12 4.79 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
58 59 5.171339 AGTAAATATGGCATGGAGCTAGG 57.829 43.478 10.98 0.00 44.79 3.02
208 216 3.521560 CCATAGCAAGTAAAGCGACTGA 58.478 45.455 0.00 0.00 37.01 3.41
249 257 3.312709 GCAATCGGCGAAAAAGGAG 57.687 52.632 15.93 0.00 0.00 3.69
264 272 2.384203 GGAGACATCCTTTTCGCCG 58.616 57.895 0.00 0.00 42.94 6.46
318 326 3.060070 CGGAGAAACACAACTACGGAAAC 60.060 47.826 0.00 0.00 36.90 2.78
411 422 2.970324 GTTGTCGGCGACTTGGCA 60.970 61.111 36.17 16.79 45.16 4.92
415 426 3.936203 TCGGCGACTTGGCACCTT 61.936 61.111 4.99 0.00 45.16 3.50
540 552 4.935352 ACTGGAGCAATAGACAGATCTC 57.065 45.455 0.00 0.00 36.29 2.75
543 555 2.625790 GGAGCAATAGACAGATCTCGGT 59.374 50.000 0.00 0.00 36.29 4.69
568 592 3.462483 TTACCTTTGTCTTGTCAGCGA 57.538 42.857 0.00 0.00 0.00 4.93
591 615 2.004408 GAATCTGGCAGGGGCTGGAT 62.004 60.000 15.73 0.00 40.87 3.41
783 810 4.899239 CCGATCCTGCGCTGACCC 62.899 72.222 16.65 3.06 0.00 4.46
964 1021 2.725008 GCCGTCTCTCTCCATCCG 59.275 66.667 0.00 0.00 0.00 4.18
1085 1142 4.764336 CTCCGCGGCGACAACGTA 62.764 66.667 25.92 0.00 41.98 3.57
1160 1236 8.791327 ATCTCTGAAATCTCTTCTTCCTTTTC 57.209 34.615 0.00 0.00 0.00 2.29
1161 1237 7.972301 TCTCTGAAATCTCTTCTTCCTTTTCT 58.028 34.615 0.00 0.00 0.00 2.52
1162 1238 8.093927 TCTCTGAAATCTCTTCTTCCTTTTCTC 58.906 37.037 0.00 0.00 0.00 2.87
1299 1381 3.179830 GGTAATATATCGCCTGCACTCG 58.820 50.000 0.00 0.00 0.00 4.18
1326 1408 2.064762 CTCGGTTTCTCTTGTCAGCTG 58.935 52.381 7.63 7.63 0.00 4.24
1357 1439 0.753867 TCGGTGCTACTGTTTGGTGA 59.246 50.000 0.00 0.00 0.00 4.02
1359 1441 0.865769 GGTGCTACTGTTTGGTGACG 59.134 55.000 0.00 0.00 0.00 4.35
1371 1453 1.317431 TGGTGACGTGGGAGTATCGG 61.317 60.000 0.00 0.00 34.37 4.18
1389 1471 1.390123 CGGTTTGCGTATCTGTGACTG 59.610 52.381 0.00 0.00 0.00 3.51
1403 1485 1.097232 TGACTGGCTGTATGCAATGC 58.903 50.000 0.00 0.00 45.15 3.56
1454 1536 3.314080 GTGTTTGTCGAAATTCCCAGTCA 59.686 43.478 0.00 0.00 0.00 3.41
1455 1537 3.563808 TGTTTGTCGAAATTCCCAGTCAG 59.436 43.478 0.00 0.00 0.00 3.51
1467 1549 2.172505 TCCCAGTCAGCTGAAAGTGAAA 59.827 45.455 20.19 5.27 45.28 2.69
1472 1554 2.229784 GTCAGCTGAAAGTGAAATGGGG 59.770 50.000 20.19 0.00 35.30 4.96
1487 1569 2.644992 GGGAACTTGGCTGCGTTG 59.355 61.111 0.00 0.00 0.00 4.10
1509 1591 1.355971 TCCGCGTGCTAATTCTTCAC 58.644 50.000 4.92 0.00 0.00 3.18
1529 1611 0.394565 GGATACTGCCCAGGCTAGTG 59.605 60.000 18.26 6.91 42.51 2.74
1754 1849 8.308931 ACATAAGAATACCTGAAGTACGAAACA 58.691 33.333 0.00 0.00 32.46 2.83
1826 1922 2.035832 AGGTCGGCTTTTTGGTCAAATG 59.964 45.455 0.00 0.00 0.00 2.32
1860 1956 7.561021 TCAAGCAATACAAGTGTCACTTAAA 57.439 32.000 17.76 9.42 36.03 1.52
1955 2053 2.977914 AGATCTATTGCAGCGTTGTGT 58.022 42.857 0.00 0.00 0.00 3.72
2033 2132 4.098349 TCGTCTACCAAGTTGTTACTGTGT 59.902 41.667 1.45 0.00 34.01 3.72
2035 2134 5.276678 CGTCTACCAAGTTGTTACTGTGTTG 60.277 44.000 1.45 0.00 34.01 3.33
2043 2142 6.758593 AGTTGTTACTGTGTTGTACATACG 57.241 37.500 0.00 0.00 38.92 3.06
2067 2166 6.293516 CGTATACTACAATGTCCCTCACTCTC 60.294 46.154 0.56 0.00 0.00 3.20
2188 2287 5.777732 TCCTAAGCCCATAACAAACAAATGT 59.222 36.000 0.00 0.00 34.24 2.71
2257 2360 6.644347 AGGAAGTGACTGTAGTGAATATTGG 58.356 40.000 0.00 0.00 0.00 3.16
2266 2369 5.741011 TGTAGTGAATATTGGACAGGAACC 58.259 41.667 0.00 0.00 0.00 3.62
2813 2916 6.659242 TCCATAAACAGATCCTTTTTCCTCAC 59.341 38.462 0.00 0.00 0.00 3.51
2882 2985 6.554334 TTAACTGACTTGTTATCCTGCAAC 57.446 37.500 0.00 0.00 33.16 4.17
2893 2996 5.126222 TGTTATCCTGCAACTGTTTGTGAAA 59.874 36.000 0.00 0.00 34.90 2.69
2900 3003 5.718146 TGCAACTGTTTGTGAAAATCTGAA 58.282 33.333 0.00 0.00 34.90 3.02
2973 3076 4.442706 TCTAAAATTAGGAGAGCAAGCCG 58.557 43.478 0.62 0.00 0.00 5.52
3034 3171 3.963665 TCGTGTTGCTGGAATTTTCTTG 58.036 40.909 0.00 0.00 0.00 3.02
3039 3176 5.232838 GTGTTGCTGGAATTTTCTTGTTCTG 59.767 40.000 0.00 0.00 0.00 3.02
3060 3197 6.711277 TCTGGAGCACTATGTTTTATGTTCT 58.289 36.000 0.00 0.00 0.00 3.01
3224 3448 2.636647 TCATGCTGTCCTTGACAACA 57.363 45.000 3.12 3.12 42.26 3.33
3229 3453 2.288666 GCTGTCCTTGACAACAGTTGA 58.711 47.619 20.56 0.00 42.26 3.18
3236 3460 7.427138 GTCCTTGACAACAGTTGAACTGAGC 62.427 48.000 30.03 15.84 39.28 4.26
3337 3562 5.605488 CCTGTACTTATGTGTAGGGGGTATT 59.395 44.000 0.00 0.00 31.32 1.89
3364 3589 2.264813 CAAGCTGGCATGCAAATGTAC 58.735 47.619 21.36 0.00 34.99 2.90
3418 3643 8.642908 TCTATGAATACCACGTCTATTTTGTG 57.357 34.615 0.00 0.00 0.00 3.33
3561 3788 1.622811 ACTGCTGGGAGTGAAAGAGAG 59.377 52.381 0.00 0.00 0.00 3.20
3562 3789 1.898472 CTGCTGGGAGTGAAAGAGAGA 59.102 52.381 0.00 0.00 0.00 3.10
3563 3790 1.898472 TGCTGGGAGTGAAAGAGAGAG 59.102 52.381 0.00 0.00 0.00 3.20
3589 3816 7.977818 AGAGTTGGGCATATTTGTGATCTATA 58.022 34.615 0.00 0.00 0.00 1.31
3590 3817 8.609483 AGAGTTGGGCATATTTGTGATCTATAT 58.391 33.333 0.00 0.00 0.00 0.86
3605 3832 7.556635 TGTGATCTATATCCATCCTAGTTACGG 59.443 40.741 0.00 0.00 0.00 4.02
3606 3833 6.546403 TGATCTATATCCATCCTAGTTACGGC 59.454 42.308 0.00 0.00 0.00 5.68
3696 3923 4.021102 TCTCCTGTGTTTCCAGAAATCC 57.979 45.455 0.00 0.00 34.23 3.01
3724 3951 2.191128 AGACCCTGACTGAATGTTGC 57.809 50.000 0.00 0.00 0.00 4.17
3772 3999 3.269381 TGAATGAGGCCCCAAGAAAGTAT 59.731 43.478 0.00 0.00 0.00 2.12
3775 4002 1.564348 GAGGCCCCAAGAAAGTATGGA 59.436 52.381 0.00 0.00 39.12 3.41
3776 4003 1.285078 AGGCCCCAAGAAAGTATGGAC 59.715 52.381 0.00 0.00 39.12 4.02
3777 4004 1.005450 GGCCCCAAGAAAGTATGGACA 59.995 52.381 0.00 0.00 39.12 4.02
3822 4049 7.923414 AGAACAGTTCTTGAGTTTTTACTGT 57.077 32.000 10.27 0.00 45.71 3.55
3859 4091 1.267574 TGGCTCCTGAAGGTAGCTGG 61.268 60.000 15.71 0.00 37.98 4.85
3899 4131 4.133856 AGAAAATTTGCGTCGAAGTCTG 57.866 40.909 0.00 0.00 0.00 3.51
4000 4247 6.868339 TCATATTTCATGGCTATACACTGTCG 59.132 38.462 0.00 0.00 0.00 4.35
4064 4314 5.184892 AGAAAGTGCATGGAATTAGACCT 57.815 39.130 0.00 0.00 0.00 3.85
4065 4315 6.313519 AGAAAGTGCATGGAATTAGACCTA 57.686 37.500 0.00 0.00 0.00 3.08
4066 4316 6.721318 AGAAAGTGCATGGAATTAGACCTAA 58.279 36.000 0.00 0.00 0.00 2.69
4067 4317 7.349598 AGAAAGTGCATGGAATTAGACCTAAT 58.650 34.615 0.00 0.00 37.36 1.73
4096 4346 0.596083 CGTTTGCATCCGCCAACAAA 60.596 50.000 0.00 0.00 42.45 2.83
4162 4412 9.919348 TGTTAATCGTAACACAAACTCTTAAAC 57.081 29.630 0.00 0.00 43.71 2.01
4167 4417 8.130307 TCGTAACACAAACTCTTAAACTAACC 57.870 34.615 0.00 0.00 0.00 2.85
4168 4418 7.763528 TCGTAACACAAACTCTTAAACTAACCA 59.236 33.333 0.00 0.00 0.00 3.67
4239 4515 5.950758 TTTACAGCCGTGATAAAACACAT 57.049 34.783 0.00 0.00 40.34 3.21
4241 4517 4.419522 ACAGCCGTGATAAAACACATTC 57.580 40.909 0.00 0.00 40.34 2.67
4283 4562 1.628340 TGGACACACCCACAATCCTAG 59.372 52.381 0.00 0.00 38.00 3.02
4284 4563 1.679032 GGACACACCCACAATCCTAGC 60.679 57.143 0.00 0.00 0.00 3.42
4285 4564 1.279271 GACACACCCACAATCCTAGCT 59.721 52.381 0.00 0.00 0.00 3.32
4286 4565 2.500098 GACACACCCACAATCCTAGCTA 59.500 50.000 0.00 0.00 0.00 3.32
4287 4566 2.501723 ACACACCCACAATCCTAGCTAG 59.498 50.000 14.20 14.20 0.00 3.42
4289 4568 3.704566 CACACCCACAATCCTAGCTAGTA 59.295 47.826 19.31 3.96 0.00 1.82
4290 4569 4.345257 CACACCCACAATCCTAGCTAGTAT 59.655 45.833 19.31 6.50 0.00 2.12
4292 4571 3.904339 ACCCACAATCCTAGCTAGTATGG 59.096 47.826 19.31 16.44 0.00 2.74
4294 4573 4.348168 CCCACAATCCTAGCTAGTATGGTT 59.652 45.833 19.31 4.22 0.00 3.67
4304 4583 8.391699 TCCTAGCTAGTATGGTTATATCACTGT 58.608 37.037 19.31 0.00 0.00 3.55
4306 4585 7.233389 AGCTAGTATGGTTATATCACTGTGG 57.767 40.000 8.11 0.00 0.00 4.17
4424 4725 0.038892 GCCCGACGAAGAACAGTACA 60.039 55.000 0.00 0.00 0.00 2.90
4452 4753 6.943718 AGTAAATAAATCCGACAAAACAGGGA 59.056 34.615 0.00 0.00 0.00 4.20
4454 4755 5.897377 ATAAATCCGACAAAACAGGGAAG 57.103 39.130 0.00 0.00 31.24 3.46
4477 4841 9.565213 GAAGAACAAGGATGAACAGAAAATATG 57.435 33.333 0.00 0.00 0.00 1.78
4598 4982 7.453752 ACAGTGAAGAGTATACCAACTAAAGGA 59.546 37.037 0.00 0.00 0.00 3.36
4599 4983 8.311836 CAGTGAAGAGTATACCAACTAAAGGAA 58.688 37.037 0.00 0.00 0.00 3.36
4600 4984 8.877195 AGTGAAGAGTATACCAACTAAAGGAAA 58.123 33.333 0.00 0.00 0.00 3.13
4662 5058 1.678627 CTACTAGTGACCTCGCATGCT 59.321 52.381 17.13 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.326297 AGATTCTTACCTAGCTCCATGCC 59.674 47.826 0.00 0.00 44.23 4.40
208 216 7.517320 TGCTTTATCCAATCTGTATGTATGGT 58.483 34.615 0.00 0.00 32.90 3.55
249 257 0.391263 ACCTCGGCGAAAAGGATGTC 60.391 55.000 19.08 0.00 36.46 3.06
264 272 3.065575 CCGTAGTGGCATGAACCTC 57.934 57.895 0.00 0.00 0.00 3.85
291 299 1.594331 AGTTGTGTTTCTCCGGCTTC 58.406 50.000 0.00 0.00 0.00 3.86
318 326 1.878775 CTTGGGCTTTCTGCTTCGG 59.121 57.895 0.00 0.00 42.39 4.30
432 443 3.869866 CGATTCGGTCGCGATTTTT 57.130 47.368 14.06 0.00 44.33 1.94
540 552 3.875134 ACAAGACAAAGGTAAACTCACCG 59.125 43.478 0.00 0.00 43.84 4.94
543 555 4.574828 GCTGACAAGACAAAGGTAAACTCA 59.425 41.667 0.00 0.00 0.00 3.41
568 592 2.988839 GCCCCTGCCAGATTCCAGT 61.989 63.158 0.00 0.00 0.00 4.00
754 781 3.967335 GATCGGACGGCTCGGGAG 61.967 72.222 0.00 0.00 0.00 4.30
783 810 1.376424 AGATCAACGGTGCTGGCTG 60.376 57.895 0.00 0.00 0.00 4.85
964 1021 0.329596 ATTTGGCTGGGAGAGTGGAC 59.670 55.000 0.00 0.00 0.00 4.02
1160 1236 1.332997 GGCGCCAATTTCATCAGAGAG 59.667 52.381 24.80 0.00 0.00 3.20
1161 1237 1.339920 TGGCGCCAATTTCATCAGAGA 60.340 47.619 30.74 0.00 0.00 3.10
1162 1238 1.065102 CTGGCGCCAATTTCATCAGAG 59.935 52.381 32.09 10.25 0.00 3.35
1299 1381 2.037381 ACAAGAGAAACCGAGGAAGGAC 59.963 50.000 0.00 0.00 34.73 3.85
1326 1408 1.739067 AGCACCGAATCCTAAGCAAC 58.261 50.000 0.00 0.00 0.00 4.17
1357 1439 0.390735 GCAAACCGATACTCCCACGT 60.391 55.000 0.00 0.00 0.00 4.49
1359 1441 0.390735 ACGCAAACCGATACTCCCAC 60.391 55.000 0.00 0.00 41.02 4.61
1371 1453 1.128692 GCCAGTCACAGATACGCAAAC 59.871 52.381 0.00 0.00 0.00 2.93
1389 1471 1.136252 CGTATCGCATTGCATACAGCC 60.136 52.381 20.82 5.14 44.83 4.85
1403 1485 0.099613 AGCACTCAGAGCACGTATCG 59.900 55.000 0.00 0.00 0.00 2.92
1454 1536 2.893489 GTTCCCCATTTCACTTTCAGCT 59.107 45.455 0.00 0.00 0.00 4.24
1455 1537 2.893489 AGTTCCCCATTTCACTTTCAGC 59.107 45.455 0.00 0.00 0.00 4.26
1467 1549 2.361610 CGCAGCCAAGTTCCCCAT 60.362 61.111 0.00 0.00 0.00 4.00
1472 1554 1.401539 GGAATCAACGCAGCCAAGTTC 60.402 52.381 0.00 0.00 0.00 3.01
1487 1569 2.607635 TGAAGAATTAGCACGCGGAATC 59.392 45.455 12.47 0.00 0.00 2.52
1509 1591 1.115930 ACTAGCCTGGGCAGTATCCG 61.116 60.000 14.39 0.00 44.88 4.18
1529 1611 0.302890 CGCAGCATAGCAGCTACAAC 59.697 55.000 3.59 0.00 44.54 3.32
1754 1849 7.657761 GCAAACATCCTACTAGTATATGTGCTT 59.342 37.037 22.29 15.09 31.44 3.91
1826 1922 3.338249 TGTATTGCTTGAGCTCTCCAAC 58.662 45.455 16.19 6.10 42.66 3.77
1860 1956 0.465460 TCCAGCCTTTCAAACACGCT 60.465 50.000 0.00 0.00 0.00 5.07
1955 2053 2.734175 CGCTCAAACGTAGATAGGCACA 60.734 50.000 0.00 0.00 0.00 4.57
2010 2109 4.098349 ACACAGTAACAACTTGGTAGACGA 59.902 41.667 0.00 0.00 0.00 4.20
2033 2132 8.352201 GGGACATTGTAGTATACGTATGTACAA 58.648 37.037 28.97 28.97 44.91 2.41
2035 2134 8.103948 AGGGACATTGTAGTATACGTATGTAC 57.896 38.462 18.37 17.58 46.99 2.90
2043 2142 6.773685 AGAGAGTGAGGGACATTGTAGTATAC 59.226 42.308 0.00 0.00 43.42 1.47
2188 2287 8.846943 TGCTTTTATCTAACTGAGTCATTCAA 57.153 30.769 0.00 0.00 34.81 2.69
2257 2360 0.531974 TGCAGTTCACGGTTCCTGTC 60.532 55.000 0.00 0.00 0.00 3.51
2808 2911 7.301054 CACTTCAAAAGCAACTAATAGTGAGG 58.699 38.462 0.00 0.00 34.02 3.86
2813 2916 9.793252 ATTATGCACTTCAAAAGCAACTAATAG 57.207 29.630 0.00 0.00 42.15 1.73
2893 2996 6.155565 TCCAGGCATCATGAAAAATTCAGATT 59.844 34.615 0.00 0.00 43.98 2.40
2940 3043 8.337118 TCTCCTAATTTTAGATGGAGGTCATT 57.663 34.615 0.00 0.00 43.14 2.57
2941 3044 7.474079 GCTCTCCTAATTTTAGATGGAGGTCAT 60.474 40.741 0.00 0.00 43.14 3.06
3034 3171 6.743575 ACATAAAACATAGTGCTCCAGAAC 57.256 37.500 0.00 0.00 0.00 3.01
3039 3176 5.880332 TCCAGAACATAAAACATAGTGCTCC 59.120 40.000 0.00 0.00 0.00 4.70
3060 3197 1.966354 AGCATGACTATCGCAGATCCA 59.034 47.619 0.00 0.00 45.12 3.41
3224 3448 1.802960 CAGATTGCGCTCAGTTCAACT 59.197 47.619 9.73 0.00 0.00 3.16
3229 3453 2.455674 TACACAGATTGCGCTCAGTT 57.544 45.000 9.73 0.00 0.00 3.16
3236 3460 3.727726 TCCATACCATACACAGATTGCG 58.272 45.455 0.00 0.00 0.00 4.85
3294 3518 3.378112 CAGGAAATTTCTATGGCGCTTCA 59.622 43.478 17.42 0.00 0.00 3.02
3345 3570 2.094390 CAGTACATTTGCATGCCAGCTT 60.094 45.455 16.68 0.00 33.05 3.74
3418 3643 7.129109 TCAGTCAACGAAAATTAGTCCAATC 57.871 36.000 0.00 0.00 0.00 2.67
3434 3659 0.737219 GGCCATCTGCATCAGTCAAC 59.263 55.000 0.00 0.00 43.89 3.18
3561 3788 4.517285 TCACAAATATGCCCAACTCTCTC 58.483 43.478 0.00 0.00 0.00 3.20
3562 3789 4.574674 TCACAAATATGCCCAACTCTCT 57.425 40.909 0.00 0.00 0.00 3.10
3563 3790 5.128919 AGATCACAAATATGCCCAACTCTC 58.871 41.667 0.00 0.00 0.00 3.20
3589 3816 2.679082 ACTGCCGTAACTAGGATGGAT 58.321 47.619 8.90 0.00 0.00 3.41
3590 3817 2.154567 ACTGCCGTAACTAGGATGGA 57.845 50.000 8.90 0.00 0.00 3.41
3606 3833 3.802948 ATAACCGCAGAGTTCCTACTG 57.197 47.619 0.00 0.00 33.84 2.74
3696 3923 0.900647 AGTCAGGGTCTTCAGGGACG 60.901 60.000 0.00 0.00 37.12 4.79
3724 3951 2.980586 TCAAACGACAAACAAGATGCG 58.019 42.857 0.00 0.00 0.00 4.73
3772 3999 2.113774 CAGCAGCCTGGTTGTCCA 59.886 61.111 12.30 0.00 42.05 4.02
3884 4116 2.148916 ATGACAGACTTCGACGCAAA 57.851 45.000 0.00 0.00 0.00 3.68
3890 4122 4.820897 ACAGCATAAATGACAGACTTCGA 58.179 39.130 0.00 0.00 0.00 3.71
3892 4124 5.641209 ACAGACAGCATAAATGACAGACTTC 59.359 40.000 0.00 0.00 0.00 3.01
3899 4131 6.246420 ACTGAAACAGACAGCATAAATGAC 57.754 37.500 5.76 0.00 38.74 3.06
4000 4247 7.337167 AGCAGGACCTATATGATTTCATCATC 58.663 38.462 2.44 0.00 46.62 2.92
4064 4314 6.512091 GCGGATGCAAACGGTTATCTTAATTA 60.512 38.462 14.06 0.00 42.15 1.40
4065 4315 5.732247 GCGGATGCAAACGGTTATCTTAATT 60.732 40.000 14.06 0.00 42.15 1.40
4066 4316 4.261031 GCGGATGCAAACGGTTATCTTAAT 60.261 41.667 14.06 0.00 42.15 1.40
4067 4317 3.064271 GCGGATGCAAACGGTTATCTTAA 59.936 43.478 14.06 0.00 42.15 1.85
4096 4346 1.677552 CTCACGGCCTTAGGTTGGT 59.322 57.895 0.00 0.00 0.00 3.67
4161 4411 7.057894 TCCTTTCATGTTTACTTGTGGTTAGT 58.942 34.615 0.00 0.00 0.00 2.24
4162 4412 7.504924 TCCTTTCATGTTTACTTGTGGTTAG 57.495 36.000 0.00 0.00 0.00 2.34
4163 4413 7.883391 TTCCTTTCATGTTTACTTGTGGTTA 57.117 32.000 0.00 0.00 0.00 2.85
4164 4414 6.783708 TTCCTTTCATGTTTACTTGTGGTT 57.216 33.333 0.00 0.00 0.00 3.67
4165 4415 6.976934 ATTCCTTTCATGTTTACTTGTGGT 57.023 33.333 0.00 0.00 0.00 4.16
4166 4416 7.432869 TGAATTCCTTTCATGTTTACTTGTGG 58.567 34.615 2.27 0.00 39.44 4.17
4214 4489 6.833839 TGTGTTTTATCACGGCTGTAAATAC 58.166 36.000 0.00 4.78 40.74 1.89
4239 4515 8.306038 CCAAATTCTTGTGGAATGAATACAGAA 58.694 33.333 0.00 0.00 43.17 3.02
4241 4517 7.756722 GTCCAAATTCTTGTGGAATGAATACAG 59.243 37.037 0.00 0.00 45.42 2.74
4283 4562 6.994221 ACCACAGTGATATAACCATACTAGC 58.006 40.000 0.62 0.00 0.00 3.42
4284 4563 8.300286 CAGACCACAGTGATATAACCATACTAG 58.700 40.741 0.62 0.00 0.00 2.57
4285 4564 8.002459 TCAGACCACAGTGATATAACCATACTA 58.998 37.037 0.62 0.00 0.00 1.82
4286 4565 6.839134 TCAGACCACAGTGATATAACCATACT 59.161 38.462 0.62 0.00 0.00 2.12
4287 4566 7.050970 TCAGACCACAGTGATATAACCATAC 57.949 40.000 0.62 0.00 0.00 2.39
4289 4568 6.560003 TTCAGACCACAGTGATATAACCAT 57.440 37.500 0.62 0.00 0.00 3.55
4290 4569 6.212589 TCTTTCAGACCACAGTGATATAACCA 59.787 38.462 0.62 0.00 0.00 3.67
4292 4571 6.758886 CCTCTTTCAGACCACAGTGATATAAC 59.241 42.308 0.62 0.00 0.00 1.89
4294 4573 5.163405 GCCTCTTTCAGACCACAGTGATATA 60.163 44.000 0.62 0.00 0.00 0.86
4301 4580 2.149578 CAAGCCTCTTTCAGACCACAG 58.850 52.381 0.00 0.00 0.00 3.66
4304 4583 1.140312 ACCAAGCCTCTTTCAGACCA 58.860 50.000 0.00 0.00 0.00 4.02
4306 4585 2.421619 CTCACCAAGCCTCTTTCAGAC 58.578 52.381 0.00 0.00 0.00 3.51
4336 4615 3.782042 GGCGACGATGGTGAAGAC 58.218 61.111 0.00 0.00 0.00 3.01
4424 4725 8.943002 CCTGTTTTGTCGGATTTATTTACTACT 58.057 33.333 0.00 0.00 0.00 2.57
4452 4753 8.526147 CCATATTTTCTGTTCATCCTTGTTCTT 58.474 33.333 0.00 0.00 0.00 2.52
4454 4755 7.830739 ACCATATTTTCTGTTCATCCTTGTTC 58.169 34.615 0.00 0.00 0.00 3.18
4477 4841 7.075741 GTGGCACGACATATATATGAAAAACC 58.924 38.462 26.05 19.93 37.15 3.27
4616 5000 1.269958 TCACTCCTGTCCTGTGATGG 58.730 55.000 0.00 0.00 36.03 3.51
4662 5058 4.186926 CGATGAAGAAGAAGAAGGCATCA 58.813 43.478 0.00 0.00 32.41 3.07
4667 5063 2.935201 CCTGCGATGAAGAAGAAGAAGG 59.065 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.