Multiple sequence alignment - TraesCS4D01G254300

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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 TraesCS4D01G254300 chr4D 100.000 3190 0 0 964 4153 423387801 423384612 0.000000e+00 5891.0
1 TraesCS4D01G254300 chr4D 100.000 557 0 0 1 557 423388764 423388208 0.000000e+00 1029.0
2 TraesCS4D01G254300 chr4B 91.684 2826 154 33 1031 3799 519800264 519797463 0.000000e+00 3842.0
3 TraesCS4D01G254300 chr4B 93.801 371 18 4 188 557 519800751 519800385 1.690000e-153 553.0
4 TraesCS4D01G254300 chr4B 93.333 345 23 0 3799 4143 519797403 519797059 1.030000e-140 510.0
5 TraesCS4D01G254300 chr4B 90.698 172 14 2 18 187 519803554 519803383 1.160000e-55 228.0
6 TraesCS4D01G254300 chr4B 95.122 41 1 1 967 1007 519800303 519800264 3.470000e-06 63.9
7 TraesCS4D01G254300 chr4A 93.306 2450 120 16 964 3373 40871776 40874221 0.000000e+00 3576.0
8 TraesCS4D01G254300 chr4A 90.221 542 44 6 18 554 40871147 40871684 0.000000e+00 699.0
9 TraesCS4D01G254300 chr4A 84.522 743 62 19 3409 4143 40874374 40875071 0.000000e+00 686.0


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 TraesCS4D01G254300 chr4D 423384612 423388764 4152 True 3460.000000 5891 100.000000 1 4153 2 chr4D.!!$R1 4152
1 TraesCS4D01G254300 chr4B 519797059 519803554 6495 True 1039.380000 3842 92.927600 18 4143 5 chr4B.!!$R1 4125
2 TraesCS4D01G254300 chr4A 40871147 40875071 3924 False 1653.666667 3576 89.349667 18 4143 3 chr4A.!!$F1 4125

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
359 2994 1.765230 AGCTACCTCGTACTGAAGGG 58.235 55.000 9.73 2.51 0.00 3.95 F
1098 3739 1.457455 GGAGCAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69 F
2323 4970 0.720590 GCTGCTCGAGAGAAAGCTTG 59.279 55.000 18.75 0.00 43.11 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 4488 0.946221 CAGCTCGCTCAAGAAACCGT 60.946 55.0 0.00 0.0 0.00 4.83 R
2574 5221 0.389817 TCATATCATACGCCTGCGCC 60.390 55.0 12.03 0.0 44.19 6.53 R
3400 6192 0.389817 TGTACTCGCCACACATGCTC 60.390 55.0 0.00 0.0 0.00 4.26 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
28 29 2.038813 TCATGGGAGCTGACCGGA 59.961 61.111 9.46 0.00 0.00 5.14
109 111 5.867903 AAATTGTCAAATGACCCACTGAA 57.132 34.783 10.83 0.00 44.15 3.02
312 2946 5.830991 TGTTAACATCTGGCACTAACCTTTT 59.169 36.000 3.59 0.00 0.00 2.27
313 2947 6.322712 TGTTAACATCTGGCACTAACCTTTTT 59.677 34.615 3.59 0.00 0.00 1.94
314 2948 7.502895 TGTTAACATCTGGCACTAACCTTTTTA 59.497 33.333 3.59 0.00 0.00 1.52
315 2949 5.959618 ACATCTGGCACTAACCTTTTTAC 57.040 39.130 0.00 0.00 0.00 2.01
335 2970 4.326504 ACCCTGCTCAACATTCAAAAAG 57.673 40.909 0.00 0.00 0.00 2.27
354 2989 5.517322 AAAGGATTAGCTACCTCGTACTG 57.483 43.478 3.49 0.00 35.25 2.74
355 2990 4.434545 AGGATTAGCTACCTCGTACTGA 57.565 45.455 0.00 0.00 0.00 3.41
356 2991 4.789807 AGGATTAGCTACCTCGTACTGAA 58.210 43.478 0.00 0.00 0.00 3.02
358 2993 4.023021 GGATTAGCTACCTCGTACTGAAGG 60.023 50.000 0.00 4.72 0.00 3.46
359 2994 1.765230 AGCTACCTCGTACTGAAGGG 58.235 55.000 9.73 2.51 0.00 3.95
362 2997 2.684927 GCTACCTCGTACTGAAGGGGTA 60.685 54.545 9.73 4.45 0.00 3.69
464 3102 6.566753 GCAGTAACAGGATCTGAAAAGTTCAC 60.567 42.308 1.59 0.00 35.46 3.18
529 3167 8.017946 CCTGAAAAGAAGTTAACAAGAGCATAC 58.982 37.037 8.61 0.00 0.00 2.39
1019 3657 4.641989 CCAAATGGAGATAACCACCAGAAG 59.358 45.833 0.00 0.00 43.03 2.85
1029 3667 1.503542 CACCAGAAGCGTGCAATCC 59.496 57.895 0.00 0.00 0.00 3.01
1098 3739 1.457455 GGAGCAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1389 4036 4.781959 GTGCCGTACTACGCCGCA 62.782 66.667 8.05 8.05 40.91 5.69
1505 4152 2.261361 CATGACGTGGGTCGAGCA 59.739 61.111 17.59 0.00 46.49 4.26
1656 4303 3.966026 GAACTACGTCGCGCTGGCT 62.966 63.158 5.56 0.00 36.88 4.75
1841 4488 2.659063 CCACGATCTGCCAGGACCA 61.659 63.158 0.00 0.00 0.00 4.02
2060 4707 2.045242 CCTCCTCCTCGACGACCA 60.045 66.667 0.00 0.00 0.00 4.02
2064 4711 2.479650 CTCCTCGACGACCACGAC 59.520 66.667 0.00 0.00 42.66 4.34
2067 4714 2.635338 CTCGACGACCACGACACA 59.365 61.111 0.00 0.00 42.66 3.72
2079 4726 3.353836 GACACATGGCACGCCGTT 61.354 61.111 0.00 0.00 39.42 4.44
2207 4854 2.883730 CGACGGCCATGTACGTGG 60.884 66.667 27.05 27.05 44.24 4.94
2323 4970 0.720590 GCTGCTCGAGAGAAAGCTTG 59.279 55.000 18.75 0.00 43.11 4.01
2797 5444 2.521465 CAGGTGGTGGCAAGGCAA 60.521 61.111 0.00 0.00 0.00 4.52
2891 5538 1.812214 GAAGATGACGATGGCGACGC 61.812 60.000 12.43 12.43 41.64 5.19
2972 5623 3.251729 TCAGGTTAGTGTGTCACGTACTC 59.748 47.826 0.00 0.00 39.64 2.59
3019 5670 2.927553 ATCTTGCGAAGTTGATTGGC 57.072 45.000 0.00 0.00 42.51 4.52
3055 5711 8.798859 ATCATAATCTTGTCAACTAAAGCAGT 57.201 30.769 0.00 0.00 40.05 4.40
3092 5748 0.979665 TGGCAGAAGAGACTTGGAGG 59.020 55.000 0.00 0.00 0.00 4.30
3124 5780 3.615155 CCCCAAGGAAGAAGAAGATGTC 58.385 50.000 0.00 0.00 33.47 3.06
3135 5791 7.442666 GGAAGAAGAAGATGTCAAGTGTAAACT 59.557 37.037 0.00 0.00 0.00 2.66
3158 5815 3.743396 GCCTTGTTATCTCATGATCGTCC 59.257 47.826 0.00 0.00 34.32 4.79
3174 5832 2.957006 TCGTCCATCCTTCTAAGCTACC 59.043 50.000 0.00 0.00 0.00 3.18
3175 5833 2.036089 CGTCCATCCTTCTAAGCTACCC 59.964 54.545 0.00 0.00 0.00 3.69
3180 5838 2.389715 TCCTTCTAAGCTACCCAGAGC 58.610 52.381 0.00 0.00 43.19 4.09
3189 5848 3.611766 GCTACCCAGAGCTTAGTTTCA 57.388 47.619 0.00 0.00 39.50 2.69
3204 5867 6.536941 GCTTAGTTTCAGTCATTAGCTAGCTT 59.463 38.462 24.88 1.98 0.00 3.74
3220 5883 2.464157 GCTTGAGCTAGAGTGGTTGT 57.536 50.000 0.00 0.00 38.21 3.32
3231 5894 4.098914 AGAGTGGTTGTTGAATTGGCTA 57.901 40.909 0.00 0.00 0.00 3.93
3280 5950 5.276461 TGCATTCTAGGTACGTGATCAAT 57.724 39.130 0.00 0.00 0.00 2.57
3292 5962 6.533723 GGTACGTGATCAATTTCTACATGACA 59.466 38.462 0.00 0.00 0.00 3.58
3324 5994 3.501396 GCTGCCGCATTAGCTTGA 58.499 55.556 0.00 0.00 39.10 3.02
3326 5996 1.372087 GCTGCCGCATTAGCTTGACT 61.372 55.000 0.00 0.00 39.10 3.41
3327 5997 1.089920 CTGCCGCATTAGCTTGACTT 58.910 50.000 0.00 0.00 39.10 3.01
3328 5998 1.063174 CTGCCGCATTAGCTTGACTTC 59.937 52.381 0.00 0.00 39.10 3.01
3373 6056 7.092079 TCCATAAAGTTGAGCACAATCAAATG 58.908 34.615 0.00 3.19 40.72 2.32
3400 6192 7.623770 CAATGTTCAAAAACTTTGTCATCCTG 58.376 34.615 8.11 1.65 41.82 3.86
3407 6199 3.430042 ACTTTGTCATCCTGAGCATGT 57.570 42.857 0.00 0.00 0.00 3.21
3412 6204 0.393402 TCATCCTGAGCATGTGTGGC 60.393 55.000 0.00 0.00 0.00 5.01
3413 6205 1.450848 ATCCTGAGCATGTGTGGCG 60.451 57.895 0.00 0.00 36.08 5.69
3414 6206 1.902765 ATCCTGAGCATGTGTGGCGA 61.903 55.000 0.00 0.00 36.08 5.54
3415 6207 2.104859 CCTGAGCATGTGTGGCGAG 61.105 63.158 0.00 0.00 36.08 5.03
3426 6229 2.159014 TGTGTGGCGAGTACAACTCTTT 60.159 45.455 5.59 0.00 42.92 2.52
3431 6234 6.366877 GTGTGGCGAGTACAACTCTTTATTTA 59.633 38.462 5.59 0.00 42.92 1.40
3432 6235 7.064253 GTGTGGCGAGTACAACTCTTTATTTAT 59.936 37.037 5.59 0.00 42.92 1.40
3507 6310 8.777578 ATATAACACTACCAACCATGAGAGTA 57.222 34.615 0.00 0.00 0.00 2.59
3510 6313 4.220821 ACACTACCAACCATGAGAGTACAG 59.779 45.833 0.00 0.00 0.00 2.74
3513 6316 6.321435 CACTACCAACCATGAGAGTACAGATA 59.679 42.308 0.00 0.00 0.00 1.98
3515 6318 6.620877 ACCAACCATGAGAGTACAGATAAA 57.379 37.500 0.00 0.00 0.00 1.40
3516 6319 7.016153 ACCAACCATGAGAGTACAGATAAAA 57.984 36.000 0.00 0.00 0.00 1.52
3518 6321 8.109634 ACCAACCATGAGAGTACAGATAAAAAT 58.890 33.333 0.00 0.00 0.00 1.82
3519 6322 8.616076 CCAACCATGAGAGTACAGATAAAAATC 58.384 37.037 0.00 0.00 0.00 2.17
3521 6324 8.723942 ACCATGAGAGTACAGATAAAAATCAC 57.276 34.615 0.00 0.00 0.00 3.06
3650 6455 4.400884 TCGGCAGTGGTATTTATTTGCATT 59.599 37.500 0.00 0.00 33.42 3.56
3651 6456 4.503734 CGGCAGTGGTATTTATTTGCATTG 59.496 41.667 0.00 0.00 33.42 2.82
3652 6457 5.659463 GGCAGTGGTATTTATTTGCATTGA 58.341 37.500 0.00 0.00 33.42 2.57
3673 6478 4.756642 TGAACTCGCTCTCATGTGATTTTT 59.243 37.500 0.00 0.00 0.00 1.94
3677 6482 2.095110 CGCTCTCATGTGATTTTTGGCA 60.095 45.455 0.00 0.00 0.00 4.92
3680 6485 5.653507 GCTCTCATGTGATTTTTGGCATTA 58.346 37.500 0.00 0.00 0.00 1.90
3684 6489 5.170021 TCATGTGATTTTTGGCATTAGCAC 58.830 37.500 5.73 5.73 44.61 4.40
3690 6495 1.827681 TTTGGCATTAGCACCGCTTA 58.172 45.000 0.00 0.00 44.61 3.09
3691 6496 2.051334 TTGGCATTAGCACCGCTTAT 57.949 45.000 0.00 0.00 44.61 1.73
3692 6497 2.051334 TGGCATTAGCACCGCTTATT 57.949 45.000 0.00 0.00 44.61 1.40
3693 6498 3.201353 TGGCATTAGCACCGCTTATTA 57.799 42.857 0.00 0.00 44.61 0.98
3694 6499 2.875933 TGGCATTAGCACCGCTTATTAC 59.124 45.455 0.00 0.00 44.61 1.89
3695 6500 3.139077 GGCATTAGCACCGCTTATTACT 58.861 45.455 0.00 0.00 44.61 2.24
3696 6501 3.564225 GGCATTAGCACCGCTTATTACTT 59.436 43.478 0.00 0.00 44.61 2.24
3697 6502 4.527564 GCATTAGCACCGCTTATTACTTG 58.472 43.478 0.00 0.00 40.44 3.16
3698 6503 4.035208 GCATTAGCACCGCTTATTACTTGT 59.965 41.667 0.00 0.00 40.44 3.16
3699 6504 5.448632 GCATTAGCACCGCTTATTACTTGTT 60.449 40.000 0.00 0.00 40.44 2.83
3700 6505 5.539582 TTAGCACCGCTTATTACTTGTTG 57.460 39.130 0.00 0.00 40.44 3.33
3701 6506 2.161609 AGCACCGCTTATTACTTGTTGC 59.838 45.455 0.00 0.00 33.89 4.17
3716 6521 3.988379 TGTTGCTTGTTGATGTCTTCC 57.012 42.857 0.00 0.00 0.00 3.46
3719 6524 3.213206 TGCTTGTTGATGTCTTCCAGT 57.787 42.857 0.00 0.00 0.00 4.00
3736 6541 3.837731 TCCAGTGGTAGAACACATCATGA 59.162 43.478 9.54 0.00 43.72 3.07
3737 6542 4.471025 TCCAGTGGTAGAACACATCATGAT 59.529 41.667 9.54 1.18 43.72 2.45
3738 6543 5.045651 TCCAGTGGTAGAACACATCATGATT 60.046 40.000 9.54 0.00 43.72 2.57
3885 6749 5.940192 TGTGTGCTACAATGAAAACTAGG 57.060 39.130 0.00 0.00 36.06 3.02
3894 6758 6.200878 ACAATGAAAACTAGGGAAGAGGAA 57.799 37.500 0.00 0.00 0.00 3.36
3903 6767 3.793842 AGGGAAGAGGAAGAGAGGAAT 57.206 47.619 0.00 0.00 0.00 3.01
3910 6774 6.826231 GGAAGAGGAAGAGAGGAATAAAAAGG 59.174 42.308 0.00 0.00 0.00 3.11
3920 6784 0.606096 AATAAAAAGGGGTGCGGCAC 59.394 50.000 24.43 24.43 0.00 5.01
4027 6891 6.725834 ACATTATTGTTGGGAGAAACTCCATT 59.274 34.615 17.74 0.00 42.08 3.16
4054 6918 8.461249 AATTCATGTCCCATATTCTCTTTCAG 57.539 34.615 0.00 0.00 0.00 3.02
4091 6955 1.177401 GAAACAATGGGAGGACAGGC 58.823 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.450500 AGCTCCCATGACTCCTCTCTAT 59.549 50.000 0.00 0.00 0.00 1.98
1 2 1.856259 AGCTCCCATGACTCCTCTCTA 59.144 52.381 0.00 0.00 0.00 2.43
2 3 0.636101 AGCTCCCATGACTCCTCTCT 59.364 55.000 0.00 0.00 0.00 3.10
3 4 0.752054 CAGCTCCCATGACTCCTCTC 59.248 60.000 0.00 0.00 0.00 3.20
4 5 0.337773 TCAGCTCCCATGACTCCTCT 59.662 55.000 0.00 0.00 0.00 3.69
7 8 1.524482 GGTCAGCTCCCATGACTCC 59.476 63.158 0.00 0.00 45.18 3.85
8 9 1.142748 CGGTCAGCTCCCATGACTC 59.857 63.158 0.00 0.00 45.18 3.36
9 10 2.362369 CCGGTCAGCTCCCATGACT 61.362 63.158 0.00 0.00 45.18 3.41
11 12 1.198094 TTTCCGGTCAGCTCCCATGA 61.198 55.000 0.00 0.00 0.00 3.07
12 13 0.322456 TTTTCCGGTCAGCTCCCATG 60.322 55.000 0.00 0.00 0.00 3.66
13 14 0.404040 TTTTTCCGGTCAGCTCCCAT 59.596 50.000 0.00 0.00 0.00 4.00
14 15 1.840598 TTTTTCCGGTCAGCTCCCA 59.159 52.632 0.00 0.00 0.00 4.37
15 16 4.813346 TTTTTCCGGTCAGCTCCC 57.187 55.556 0.00 0.00 0.00 4.30
56 57 9.198837 AGTTTGTAACAAGTTTAGTTTGGTTTG 57.801 29.630 0.00 0.00 0.00 2.93
88 89 5.786311 CATTCAGTGGGTCATTTGACAATT 58.214 37.500 12.43 0.00 46.47 2.32
259 2893 6.659776 CAAGGCTTGAGTAAGACAAGTTAAC 58.340 40.000 22.64 0.00 44.83 2.01
269 2903 1.467734 CAGCAGCAAGGCTTGAGTAAG 59.532 52.381 30.45 14.42 42.71 2.34
312 2946 5.221422 CCTTTTTGAATGTTGAGCAGGGTAA 60.221 40.000 0.00 0.00 0.00 2.85
313 2947 4.280677 CCTTTTTGAATGTTGAGCAGGGTA 59.719 41.667 0.00 0.00 0.00 3.69
314 2948 3.070015 CCTTTTTGAATGTTGAGCAGGGT 59.930 43.478 0.00 0.00 0.00 4.34
315 2949 3.321682 TCCTTTTTGAATGTTGAGCAGGG 59.678 43.478 0.00 0.00 0.00 4.45
335 2970 4.023021 CCTTCAGTACGAGGTAGCTAATCC 60.023 50.000 0.00 0.00 0.00 3.01
354 2989 4.286032 TGACACCTGCATATATACCCCTTC 59.714 45.833 0.00 0.00 0.00 3.46
355 2990 4.239495 TGACACCTGCATATATACCCCTT 58.761 43.478 0.00 0.00 0.00 3.95
356 2991 3.869310 TGACACCTGCATATATACCCCT 58.131 45.455 0.00 0.00 0.00 4.79
358 2993 5.373222 TGTTTGACACCTGCATATATACCC 58.627 41.667 0.00 0.00 0.00 3.69
359 2994 6.935741 TTGTTTGACACCTGCATATATACC 57.064 37.500 0.00 0.00 0.00 2.73
362 2997 7.340232 AGTTCATTGTTTGACACCTGCATATAT 59.660 33.333 0.00 0.00 32.84 0.86
431 3066 4.160439 CAGATCCTGTTACTGCTGTTCCTA 59.840 45.833 0.09 0.00 0.00 2.94
529 3167 6.088824 GTCAGTCAATTAGCAGTGGATTTTG 58.911 40.000 0.00 0.00 0.00 2.44
963 3601 4.764823 TCTTGCCTTGGTAGTTTTGGTATG 59.235 41.667 0.00 0.00 0.00 2.39
964 3602 4.993028 TCTTGCCTTGGTAGTTTTGGTAT 58.007 39.130 0.00 0.00 0.00 2.73
965 3603 4.440826 TCTTGCCTTGGTAGTTTTGGTA 57.559 40.909 0.00 0.00 0.00 3.25
966 3604 3.306472 TCTTGCCTTGGTAGTTTTGGT 57.694 42.857 0.00 0.00 0.00 3.67
967 3605 3.826157 TGATCTTGCCTTGGTAGTTTTGG 59.174 43.478 0.00 0.00 0.00 3.28
968 3606 4.321230 GGTGATCTTGCCTTGGTAGTTTTG 60.321 45.833 0.00 0.00 0.00 2.44
969 3607 3.826729 GGTGATCTTGCCTTGGTAGTTTT 59.173 43.478 0.00 0.00 0.00 2.43
1029 3667 1.170919 ACTTGCTCTTGCTGGTGCTG 61.171 55.000 0.00 0.00 40.48 4.41
1389 4036 2.359107 TAGGAGCCGACGACGTGT 60.359 61.111 4.58 0.00 37.88 4.49
1539 4186 1.135315 GAACGTGGCGTCGTAGCTA 59.865 57.895 7.85 0.00 43.38 3.32
1656 4303 1.248785 ACTTAGGACGCTTGCTCGGA 61.249 55.000 0.00 0.00 0.00 4.55
1841 4488 0.946221 CAGCTCGCTCAAGAAACCGT 60.946 55.000 0.00 0.00 0.00 4.83
2010 4657 3.799753 GCCATGTACTGCCAGTCG 58.200 61.111 0.00 0.00 0.00 4.18
2151 4798 1.009675 CGCGCTTGTTATGGCATCC 60.010 57.895 1.65 0.00 0.00 3.51
2323 4970 1.625818 TCTCTTCTTCTCCTTGGCCAC 59.374 52.381 3.88 0.00 0.00 5.01
2378 5025 2.434843 TACAGCTCGATGGCCCTGG 61.435 63.158 0.00 0.00 0.00 4.45
2439 5086 3.494336 CTGTGCAGCACTAGCCGC 61.494 66.667 25.83 0.00 44.44 6.53
2574 5221 0.389817 TCATATCATACGCCTGCGCC 60.390 55.000 12.03 0.00 44.19 6.53
2795 5442 3.007290 TCCTATGCGATCATCCCTTCTTG 59.993 47.826 0.00 0.00 34.22 3.02
2797 5444 2.894731 TCCTATGCGATCATCCCTTCT 58.105 47.619 0.00 0.00 34.22 2.85
2891 5538 3.200483 TCGCTTCCATCATGATCACAAG 58.800 45.455 4.86 9.01 0.00 3.16
3092 5748 1.755783 CCTTGGGGCCAATCTGCTC 60.756 63.158 4.39 0.00 35.20 4.26
3124 5780 6.204688 TGAGATAACAAGGCAGTTTACACTTG 59.795 38.462 0.00 0.00 44.32 3.16
3135 5791 4.371786 GACGATCATGAGATAACAAGGCA 58.628 43.478 0.09 0.00 33.72 4.75
3158 5815 3.244044 GCTCTGGGTAGCTTAGAAGGATG 60.244 52.174 0.00 0.00 39.50 3.51
3174 5832 5.293079 GCTAATGACTGAAACTAAGCTCTGG 59.707 44.000 0.00 0.00 0.00 3.86
3175 5833 6.105333 AGCTAATGACTGAAACTAAGCTCTG 58.895 40.000 0.00 0.00 34.05 3.35
3180 5838 7.761704 TCAAGCTAGCTAATGACTGAAACTAAG 59.238 37.037 19.70 0.00 0.00 2.18
3184 5842 5.220567 GCTCAAGCTAGCTAATGACTGAAAC 60.221 44.000 19.70 8.03 39.50 2.78
3204 5867 4.623932 ATTCAACAACCACTCTAGCTCA 57.376 40.909 0.00 0.00 0.00 4.26
3220 5883 6.182627 ACTCTTCACATCATAGCCAATTCAA 58.817 36.000 0.00 0.00 0.00 2.69
3255 5925 5.670485 TGATCACGTACCTAGAATGCAATT 58.330 37.500 0.00 0.00 40.93 2.32
3256 5926 5.276461 TGATCACGTACCTAGAATGCAAT 57.724 39.130 0.00 0.00 0.00 3.56
3280 5950 8.260114 TCATTCTCTTGCTATGTCATGTAGAAA 58.740 33.333 0.00 0.00 0.00 2.52
3292 5962 2.806019 CGGCAGCTCATTCTCTTGCTAT 60.806 50.000 0.00 0.00 34.10 2.97
3324 5994 9.614792 GGAAGTAACCATTGAACATATAGAAGT 57.385 33.333 0.00 0.00 0.00 3.01
3352 6035 5.221402 TGCCATTTGATTGTGCTCAACTTTA 60.221 36.000 2.82 0.00 34.96 1.85
3373 6056 5.793026 TGACAAAGTTTTTGAACATTGCC 57.207 34.783 8.41 0.00 35.48 4.52
3400 6192 0.389817 TGTACTCGCCACACATGCTC 60.390 55.000 0.00 0.00 0.00 4.26
3431 6234 7.386025 GCAAGGCTCTTGTTCTTTCATAAAAAT 59.614 33.333 14.04 0.00 0.00 1.82
3432 6235 6.701400 GCAAGGCTCTTGTTCTTTCATAAAAA 59.299 34.615 14.04 0.00 0.00 1.94
3438 6241 2.936202 AGCAAGGCTCTTGTTCTTTCA 58.064 42.857 14.04 0.00 30.62 2.69
3446 6249 4.098349 TGGCAATAAATAGCAAGGCTCTTG 59.902 41.667 9.75 9.75 40.44 3.02
3474 6277 7.863722 TGGTTGGTAGTGTTATATACAACCAT 58.136 34.615 19.96 0.00 43.66 3.55
3480 6283 8.639761 ACTCTCATGGTTGGTAGTGTTATATAC 58.360 37.037 0.00 0.00 0.00 1.47
3481 6284 8.777578 ACTCTCATGGTTGGTAGTGTTATATA 57.222 34.615 0.00 0.00 0.00 0.86
3483 6286 7.616542 TGTACTCTCATGGTTGGTAGTGTTATA 59.383 37.037 0.00 0.00 0.00 0.98
3488 6291 4.462834 TCTGTACTCTCATGGTTGGTAGTG 59.537 45.833 0.00 0.00 0.00 2.74
3491 6294 7.727578 TTTATCTGTACTCTCATGGTTGGTA 57.272 36.000 0.00 0.00 0.00 3.25
3493 6296 7.921786 TTTTTATCTGTACTCTCATGGTTGG 57.078 36.000 0.00 0.00 0.00 3.77
3495 6298 9.167311 GTGATTTTTATCTGTACTCTCATGGTT 57.833 33.333 0.00 0.00 0.00 3.67
3611 6414 1.067582 CGAGATGAAGGCCGGGTAC 59.932 63.158 2.18 0.00 0.00 3.34
3650 6455 3.599730 AATCACATGAGAGCGAGTTCA 57.400 42.857 0.00 0.00 0.00 3.18
3651 6456 4.935885 AAAATCACATGAGAGCGAGTTC 57.064 40.909 0.00 0.00 0.00 3.01
3652 6457 4.083110 CCAAAAATCACATGAGAGCGAGTT 60.083 41.667 0.00 0.00 0.00 3.01
3673 6478 2.051334 AATAAGCGGTGCTAATGCCA 57.949 45.000 0.00 0.00 38.25 4.92
3677 6482 5.448632 GCAACAAGTAATAAGCGGTGCTAAT 60.449 40.000 0.00 0.00 38.25 1.73
3680 6485 2.161609 GCAACAAGTAATAAGCGGTGCT 59.838 45.455 0.00 0.00 42.56 4.40
3684 6489 4.419522 ACAAGCAACAAGTAATAAGCGG 57.580 40.909 0.00 0.00 0.00 5.52
3690 6495 6.639632 AGACATCAACAAGCAACAAGTAAT 57.360 33.333 0.00 0.00 0.00 1.89
3691 6496 6.449635 AAGACATCAACAAGCAACAAGTAA 57.550 33.333 0.00 0.00 0.00 2.24
3692 6497 5.008613 GGAAGACATCAACAAGCAACAAGTA 59.991 40.000 0.00 0.00 0.00 2.24
3693 6498 4.202050 GGAAGACATCAACAAGCAACAAGT 60.202 41.667 0.00 0.00 0.00 3.16
3694 6499 4.202040 TGGAAGACATCAACAAGCAACAAG 60.202 41.667 0.00 0.00 0.00 3.16
3695 6500 3.698539 TGGAAGACATCAACAAGCAACAA 59.301 39.130 0.00 0.00 0.00 2.83
3696 6501 3.286353 TGGAAGACATCAACAAGCAACA 58.714 40.909 0.00 0.00 0.00 3.33
3697 6502 3.316308 ACTGGAAGACATCAACAAGCAAC 59.684 43.478 0.00 0.00 37.43 4.17
3698 6503 3.316029 CACTGGAAGACATCAACAAGCAA 59.684 43.478 0.00 0.00 37.43 3.91
3699 6504 2.880268 CACTGGAAGACATCAACAAGCA 59.120 45.455 0.00 0.00 37.43 3.91
3700 6505 2.227388 CCACTGGAAGACATCAACAAGC 59.773 50.000 0.00 0.00 37.43 4.01
3701 6506 3.480470 ACCACTGGAAGACATCAACAAG 58.520 45.455 0.71 0.00 37.43 3.16
3716 6521 6.818142 TGTAATCATGATGTGTTCTACCACTG 59.182 38.462 9.46 0.00 36.30 3.66
3719 6524 9.898152 TTTATGTAATCATGATGTGTTCTACCA 57.102 29.630 9.46 0.00 35.70 3.25
3761 6566 7.128331 CCTTATGTTTGCGTTCTTCTCATATG 58.872 38.462 0.00 0.00 0.00 1.78
3768 6573 5.974751 TCAAAACCTTATGTTTGCGTTCTTC 59.025 36.000 0.00 0.00 46.39 2.87
3851 6715 4.827692 TGTAGCACACAATGGGTAAGTAG 58.172 43.478 0.00 0.00 32.95 2.57
3852 6716 4.893829 TGTAGCACACAATGGGTAAGTA 57.106 40.909 0.00 0.00 32.95 2.24
3877 6741 4.780554 CCTCTCTTCCTCTTCCCTAGTTTT 59.219 45.833 0.00 0.00 0.00 2.43
3885 6749 6.826231 CCTTTTTATTCCTCTCTTCCTCTTCC 59.174 42.308 0.00 0.00 0.00 3.46
3894 6758 3.622455 CGCACCCCTTTTTATTCCTCTCT 60.622 47.826 0.00 0.00 0.00 3.10
3903 6767 2.262303 CGTGCCGCACCCCTTTTTA 61.262 57.895 17.81 0.00 0.00 1.52
3920 6784 0.461339 CCCATGAAACCGTACCCTCG 60.461 60.000 0.00 0.00 0.00 4.63
4054 6918 1.676967 CTGAGCTCAAGGCCCCAAC 60.677 63.158 18.85 0.00 43.05 3.77
4091 6955 0.393077 ACACACCCAGAAGAACCTCG 59.607 55.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.