Multiple sequence alignment - TraesCS4D01G126500

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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 TraesCS4D01G126500 chr4D 100.000 4538 0 0 1 4538 111052171 111056708 0.000000e+00 8381.0
1 TraesCS4D01G126500 chr4D 73.942 2245 428 100 1091 3298 111584999 111587123 0.000000e+00 760.0
2 TraesCS4D01G126500 chr4D 82.117 548 42 24 1635 2171 345247882 345248384 7.020000e-113 418.0
3 TraesCS4D01G126500 chr4D 100.000 30 0 0 1562 1591 345247848 345247877 6.340000e-04 56.5
4 TraesCS4D01G126500 chr4A 92.597 4336 199 42 254 4537 465893475 465889210 0.000000e+00 6117.0
5 TraesCS4D01G126500 chr4A 74.351 616 99 30 2684 3298 465546723 465546166 1.650000e-49 207.0
6 TraesCS4D01G126500 chr4B 95.673 3420 121 13 254 3671 171144636 171141242 0.000000e+00 5470.0
7 TraesCS4D01G126500 chr4B 73.558 2254 441 102 1087 3298 172377440 172379580 0.000000e+00 717.0
8 TraesCS4D01G126500 chr4B 85.285 666 64 22 3841 4490 172027263 172027910 0.000000e+00 656.0
9 TraesCS4D01G126500 chr6D 93.774 257 15 1 1 256 40537250 40536994 7.120000e-103 385.0
10 TraesCS4D01G126500 chr6D 93.254 252 17 0 1 252 402412538 402412789 5.540000e-99 372.0
11 TraesCS4D01G126500 chr6D 93.227 251 17 0 1 251 405820230 405820480 1.990000e-98 370.0
12 TraesCS4D01G126500 chr5D 94.024 251 15 0 1 251 507433481 507433731 9.210000e-102 381.0
13 TraesCS4D01G126500 chr5D 86.957 69 6 3 3253 3318 11949985 11949917 1.750000e-09 75.0
14 TraesCS4D01G126500 chrUn 94.024 251 13 2 1 249 45825419 45825169 3.310000e-101 379.0
15 TraesCS4D01G126500 chrUn 94.024 251 13 2 1 249 372828540 372828790 3.310000e-101 379.0
16 TraesCS4D01G126500 chrUn 94.024 251 13 2 1 249 372830418 372830668 3.310000e-101 379.0
17 TraesCS4D01G126500 chr3D 92.664 259 17 2 1 257 103613061 103612803 5.540000e-99 372.0
18 TraesCS4D01G126500 chr3D 92.941 255 17 1 1 254 523944554 523944300 1.990000e-98 370.0
19 TraesCS4D01G126500 chr2A 73.279 610 101 39 2684 3289 733392234 733391683 2.810000e-37 167.0
20 TraesCS4D01G126500 chr7D 100.000 41 0 0 3253 3293 407071692 407071652 4.870000e-10 76.8
21 TraesCS4D01G126500 chr7A 100.000 41 0 0 3253 3293 464572698 464572658 4.870000e-10 76.8
22 TraesCS4D01G126500 chr5B 84.146 82 10 3 3240 3318 11771790 11771709 4.870000e-10 76.8
23 TraesCS4D01G126500 chr1A 86.957 69 6 3 3253 3318 99868374 99868306 1.750000e-09 75.0
24 TraesCS4D01G126500 chr7B 87.719 57 5 2 3238 3292 711061469 711061413 1.050000e-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 TraesCS4D01G126500 chr4D 111052171 111056708 4537 False 8381.00 8381 100.0000 1 4538 1 chr4D.!!$F1 4537
1 TraesCS4D01G126500 chr4D 111584999 111587123 2124 False 760.00 760 73.9420 1091 3298 1 chr4D.!!$F2 2207
2 TraesCS4D01G126500 chr4D 345247848 345248384 536 False 237.25 418 91.0585 1562 2171 2 chr4D.!!$F3 609
3 TraesCS4D01G126500 chr4A 465889210 465893475 4265 True 6117.00 6117 92.5970 254 4537 1 chr4A.!!$R2 4283
4 TraesCS4D01G126500 chr4A 465546166 465546723 557 True 207.00 207 74.3510 2684 3298 1 chr4A.!!$R1 614
5 TraesCS4D01G126500 chr4B 171141242 171144636 3394 True 5470.00 5470 95.6730 254 3671 1 chr4B.!!$R1 3417
6 TraesCS4D01G126500 chr4B 172377440 172379580 2140 False 717.00 717 73.5580 1087 3298 1 chr4B.!!$F2 2211
7 TraesCS4D01G126500 chr4B 172027263 172027910 647 False 656.00 656 85.2850 3841 4490 1 chr4B.!!$F1 649
8 TraesCS4D01G126500 chrUn 372828540 372830668 2128 False 379.00 379 94.0240 1 249 2 chrUn.!!$F1 248

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
273 276 0.183014 TTTGCCTCCGGGTTGTGTAA 59.817 50.000 0.00 0.0 34.45 2.41 F
1222 1235 1.476110 CCACCGTTTTCACCTTCTCCA 60.476 52.381 0.00 0.0 0.00 3.86 F
2550 2593 1.282930 GACTGTTCACGCGGTCTTCC 61.283 60.000 12.47 0.0 40.58 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1486 0.676151 GGAAGTGGAAGCTCTGCCAG 60.676 60.000 0.00 0.0 34.22 4.85 R
2622 2665 1.741401 CGTGGCCTTCTTGATCGCA 60.741 57.895 3.32 0.0 0.00 5.10 R
3702 3765 0.463474 GCACTTTTGGGGCAAAGCAA 60.463 50.000 0.00 0.0 34.72 3.91 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
37 40 8.902806 GTCAAAACATATCAACATGGGATCTAA 58.097 33.333 5.52 0.00 0.00 2.10
50 53 9.484806 AACATGGGATCTAATTTTGAAGATCTT 57.515 29.630 7.95 7.95 44.94 2.40
58 61 5.356882 AATTTTGAAGATCTTGACGCGAA 57.643 34.783 15.93 1.53 0.00 4.70
63 66 4.245660 TGAAGATCTTGACGCGAAGAATT 58.754 39.130 15.93 11.64 35.60 2.17
199 202 2.661866 GCGCCACTTGTCGTGACT 60.662 61.111 0.00 0.00 46.81 3.41
207 210 2.878406 CACTTGTCGTGACTTGGGAAAT 59.122 45.455 1.23 0.00 46.81 2.17
221 224 6.133356 ACTTGGGAAATTGGAGTGTTCTTTA 58.867 36.000 0.00 0.00 0.00 1.85
223 226 4.830600 TGGGAAATTGGAGTGTTCTTTACC 59.169 41.667 0.00 0.00 31.59 2.85
225 228 5.278808 GGGAAATTGGAGTGTTCTTTACCAC 60.279 44.000 0.00 0.00 31.34 4.16
249 252 9.021863 CACGAGTACTCCTTAATTAGTGATTTC 57.978 37.037 17.23 0.00 0.00 2.17
250 253 7.914346 ACGAGTACTCCTTAATTAGTGATTTCG 59.086 37.037 17.23 2.39 0.00 3.46
252 255 9.798994 GAGTACTCCTTAATTAGTGATTTCGAA 57.201 33.333 12.13 0.00 0.00 3.71
273 276 0.183014 TTTGCCTCCGGGTTGTGTAA 59.817 50.000 0.00 0.00 34.45 2.41
288 291 8.392612 CGGGTTGTGTAAATATTTTACTGTAGG 58.607 37.037 5.91 0.00 0.00 3.18
289 292 8.186163 GGGTTGTGTAAATATTTTACTGTAGGC 58.814 37.037 5.91 0.00 0.00 3.93
290 293 8.953313 GGTTGTGTAAATATTTTACTGTAGGCT 58.047 33.333 5.91 0.00 0.00 4.58
291 294 9.769093 GTTGTGTAAATATTTTACTGTAGGCTG 57.231 33.333 5.91 0.00 0.00 4.85
292 295 9.509956 TTGTGTAAATATTTTACTGTAGGCTGT 57.490 29.630 5.91 0.00 0.00 4.40
300 303 2.935481 ACTGTAGGCTGTAGCGTAAC 57.065 50.000 7.75 2.22 42.12 2.50
373 377 3.244976 GCATTACACTGTGTTGATTGGC 58.755 45.455 19.73 10.62 0.00 4.52
383 387 4.148079 TGTGTTGATTGGCCAACTGATTA 58.852 39.130 23.27 2.99 44.87 1.75
433 437 3.510388 TGACGATCCATTGACTCACTC 57.490 47.619 0.00 0.00 0.00 3.51
549 553 7.716612 TGTATAGTGTCCATACAGTGAGATTG 58.283 38.462 0.00 0.00 39.65 2.67
635 640 5.400066 ACTTTTGCCAATATAACCACCAC 57.600 39.130 0.00 0.00 0.00 4.16
636 641 4.221924 ACTTTTGCCAATATAACCACCACC 59.778 41.667 0.00 0.00 0.00 4.61
637 642 3.458044 TTGCCAATATAACCACCACCA 57.542 42.857 0.00 0.00 0.00 4.17
891 896 7.776969 CCCAAGAAATTCCATCTCATCTTCTTA 59.223 37.037 0.00 0.00 32.05 2.10
896 901 9.775854 GAAATTCCATCTCATCTTCTTAGATCA 57.224 33.333 0.00 0.00 39.11 2.92
901 906 5.506686 TCTCATCTTCTTAGATCACCGTG 57.493 43.478 0.00 0.00 39.11 4.94
921 926 5.163561 CCGTGGATGCATAAAATAAACCTGT 60.164 40.000 0.00 0.00 0.00 4.00
937 942 3.744660 ACCTGTTTGACTTGACCTGATC 58.255 45.455 0.00 0.00 0.00 2.92
941 946 4.380531 TGTTTGACTTGACCTGATCACTC 58.619 43.478 0.00 0.00 36.92 3.51
943 948 1.546029 TGACTTGACCTGATCACTCCG 59.454 52.381 0.00 0.00 36.92 4.63
944 949 1.546476 GACTTGACCTGATCACTCCGT 59.454 52.381 0.00 0.00 36.92 4.69
945 950 2.753452 GACTTGACCTGATCACTCCGTA 59.247 50.000 0.00 0.00 36.92 4.02
946 951 2.755655 ACTTGACCTGATCACTCCGTAG 59.244 50.000 0.00 0.00 36.92 3.51
1003 1016 7.031372 CCAAATCAACAACATTCTAGTGATGG 58.969 38.462 11.63 0.00 0.00 3.51
1008 1021 4.755411 ACAACATTCTAGTGATGGTACGG 58.245 43.478 11.63 0.10 0.00 4.02
1125 1138 3.547513 GTCCGGGGCGCCTCTATT 61.548 66.667 26.87 0.00 0.00 1.73
1222 1235 1.476110 CCACCGTTTTCACCTTCTCCA 60.476 52.381 0.00 0.00 0.00 3.86
1269 1282 3.823330 GTCGTCTGGACCGCCGAT 61.823 66.667 3.68 0.00 39.90 4.18
1734 1765 1.807573 GCTCGGCAACTTCCTCTCG 60.808 63.158 0.00 0.00 0.00 4.04
2308 2348 1.580942 CACGTCCACCAATGGCAAG 59.419 57.895 0.00 0.00 46.80 4.01
2499 2542 1.671054 CGTGGAGGCCGTTGTCATT 60.671 57.895 0.00 0.00 0.00 2.57
2547 2590 2.338984 GGACTGTTCACGCGGTCT 59.661 61.111 12.47 0.00 42.68 3.85
2550 2593 1.282930 GACTGTTCACGCGGTCTTCC 61.283 60.000 12.47 0.00 40.58 3.46
2610 2653 2.104792 CCTCACCACAAGTTTCCAGAGA 59.895 50.000 0.00 0.00 0.00 3.10
2622 2665 2.350057 TCCAGAGATACAGCTACGCT 57.650 50.000 0.00 0.00 40.77 5.07
2810 2853 1.412710 GATCGGCAGGATCTACCACAA 59.587 52.381 9.14 0.00 46.66 3.33
2952 2995 3.601981 GGCGATGATCACGACGAC 58.398 61.111 17.91 13.42 0.00 4.34
3161 3204 2.829458 GTCCGCCTCTCGCCTAGT 60.829 66.667 0.00 0.00 36.73 2.57
3355 3398 4.641645 CCGTGGCCAAGGCTGTGA 62.642 66.667 25.38 0.00 41.60 3.58
3360 3403 2.669569 GCCAAGGCTGTGAGCGAA 60.670 61.111 3.29 0.00 43.62 4.70
3474 3517 1.079750 GTCGTGCTTGGAGGAGGAC 60.080 63.158 6.55 6.55 42.42 3.85
3581 3625 0.313043 TCCTTGGAACAGACGACGTC 59.687 55.000 20.25 20.25 42.39 4.34
3618 3664 4.552166 ATTTTGGCCGATCAGTAATTCG 57.448 40.909 0.00 0.00 35.19 3.34
3645 3708 4.095483 ACTCAACACTTTTGCTCACTCTTG 59.905 41.667 0.00 0.00 0.00 3.02
3674 3737 3.197116 ACCGTATTCTCCGAAAACTCCAT 59.803 43.478 0.00 0.00 0.00 3.41
3688 3751 6.742718 CGAAAACTCCATAAAATACTGTGCTG 59.257 38.462 0.00 0.00 0.00 4.41
3691 3754 3.947196 CTCCATAAAATACTGTGCTGCCA 59.053 43.478 0.00 0.00 0.00 4.92
3700 3763 0.512952 CTGTGCTGCCAAACGTAGTC 59.487 55.000 0.00 0.00 45.00 2.59
3701 3764 0.105964 TGTGCTGCCAAACGTAGTCT 59.894 50.000 0.00 0.00 45.00 3.24
3702 3765 1.226746 GTGCTGCCAAACGTAGTCTT 58.773 50.000 0.00 0.00 45.00 3.01
3703 3766 1.602377 GTGCTGCCAAACGTAGTCTTT 59.398 47.619 0.00 0.00 45.00 2.52
3704 3767 1.601903 TGCTGCCAAACGTAGTCTTTG 59.398 47.619 0.00 0.00 45.00 2.77
3722 3876 1.597854 GCTTTGCCCCAAAAGTGCC 60.598 57.895 0.00 0.00 39.02 5.01
3728 3882 1.266867 GCCCCAAAAGTGCCCATCAT 61.267 55.000 0.00 0.00 0.00 2.45
3730 3884 1.207811 CCCCAAAAGTGCCCATCATTC 59.792 52.381 0.00 0.00 0.00 2.67
3734 3888 0.813184 AAAGTGCCCATCATTCAGCG 59.187 50.000 0.00 0.00 0.00 5.18
3735 3889 0.322816 AAGTGCCCATCATTCAGCGT 60.323 50.000 0.00 0.00 0.00 5.07
3736 3890 0.541392 AGTGCCCATCATTCAGCGTA 59.459 50.000 0.00 0.00 0.00 4.42
3737 3891 0.657840 GTGCCCATCATTCAGCGTAC 59.342 55.000 0.00 0.00 0.00 3.67
3739 3893 1.339535 TGCCCATCATTCAGCGTACAA 60.340 47.619 0.00 0.00 0.00 2.41
3740 3894 1.742831 GCCCATCATTCAGCGTACAAA 59.257 47.619 0.00 0.00 0.00 2.83
3741 3895 2.163412 GCCCATCATTCAGCGTACAAAA 59.837 45.455 0.00 0.00 0.00 2.44
3747 3901 7.416817 CCATCATTCAGCGTACAAAATATTGA 58.583 34.615 0.00 0.00 38.94 2.57
3758 3912 7.215007 GCGTACAAAATATTGACCGAAAGTAAC 59.785 37.037 0.00 0.00 38.94 2.50
3771 3925 7.604927 TGACCGAAAGTAACTGTAGCAAATATT 59.395 33.333 0.00 0.00 0.00 1.28
3772 3926 7.748847 ACCGAAAGTAACTGTAGCAAATATTG 58.251 34.615 0.00 0.00 0.00 1.90
3775 3929 9.262472 CGAAAGTAACTGTAGCAAATATTGAAC 57.738 33.333 0.00 0.00 0.00 3.18
3794 3950 5.484715 TGAACTTGTATTAAACTCCCTCCG 58.515 41.667 0.00 0.00 0.00 4.63
3804 3960 0.905357 ACTCCCTCCGTCTGGAAATG 59.095 55.000 0.00 0.00 45.87 2.32
3807 3963 0.462759 CCCTCCGTCTGGAAATGCTC 60.463 60.000 0.00 0.00 45.87 4.26
3811 3967 1.413767 CCGTCTGGAAATGCTCGTCG 61.414 60.000 0.00 0.00 37.49 5.12
3812 3968 1.413767 CGTCTGGAAATGCTCGTCGG 61.414 60.000 0.00 0.00 0.00 4.79
3825 3981 2.296831 TCGTCGGCGAAATGGATTTA 57.703 45.000 10.97 0.00 44.92 1.40
3832 3988 4.935205 TCGGCGAAATGGATTTATCTATGG 59.065 41.667 7.35 0.00 0.00 2.74
3833 3989 4.094887 CGGCGAAATGGATTTATCTATGGG 59.905 45.833 0.00 0.00 0.00 4.00
3836 3992 7.054124 GGCGAAATGGATTTATCTATGGGATA 58.946 38.462 0.00 0.00 35.98 2.59
3837 3993 7.556275 GGCGAAATGGATTTATCTATGGGATAA 59.444 37.037 0.00 0.00 42.96 1.75
3863 4307 3.123050 GTTGGTGAAAATGCTTGGACAC 58.877 45.455 0.00 0.00 0.00 3.67
3891 4335 9.491675 ACATGCATTTGAATGAACAGAAAAATA 57.508 25.926 5.52 0.00 38.70 1.40
3893 4337 8.020861 TGCATTTGAATGAACAGAAAAATAGC 57.979 30.769 7.86 0.00 38.70 2.97
3895 4339 8.166706 GCATTTGAATGAACAGAAAAATAGCAG 58.833 33.333 7.86 0.00 38.70 4.24
3900 4355 9.467258 TGAATGAACAGAAAAATAGCAGAAAAG 57.533 29.630 0.00 0.00 0.00 2.27
3902 4357 9.822185 AATGAACAGAAAAATAGCAGAAAAGTT 57.178 25.926 0.00 0.00 0.00 2.66
3991 4587 6.149633 ACATGATGTTTTAGGCGAAAAAGAC 58.850 36.000 7.10 0.00 38.75 3.01
3999 4595 5.676532 TTAGGCGAAAAAGACAAAATCGA 57.323 34.783 0.00 0.00 35.65 3.59
4010 4606 5.183014 AGACAAAATCGAACCTCCAAAAC 57.817 39.130 0.00 0.00 0.00 2.43
4011 4607 4.642885 AGACAAAATCGAACCTCCAAAACA 59.357 37.500 0.00 0.00 0.00 2.83
4018 4614 5.181690 TCGAACCTCCAAAACATTCTTTG 57.818 39.130 0.00 0.00 36.28 2.77
4046 4642 4.676924 GCATCGGTTCTGTCTTTTCTTTTG 59.323 41.667 0.00 0.00 0.00 2.44
4047 4643 5.733373 GCATCGGTTCTGTCTTTTCTTTTGT 60.733 40.000 0.00 0.00 0.00 2.83
4048 4644 5.890424 TCGGTTCTGTCTTTTCTTTTGTT 57.110 34.783 0.00 0.00 0.00 2.83
4049 4645 6.262193 TCGGTTCTGTCTTTTCTTTTGTTT 57.738 33.333 0.00 0.00 0.00 2.83
4050 4646 6.683715 TCGGTTCTGTCTTTTCTTTTGTTTT 58.316 32.000 0.00 0.00 0.00 2.43
4051 4647 6.804783 TCGGTTCTGTCTTTTCTTTTGTTTTC 59.195 34.615 0.00 0.00 0.00 2.29
4052 4648 6.806739 CGGTTCTGTCTTTTCTTTTGTTTTCT 59.193 34.615 0.00 0.00 0.00 2.52
4053 4649 7.328493 CGGTTCTGTCTTTTCTTTTGTTTTCTT 59.672 33.333 0.00 0.00 0.00 2.52
4054 4650 8.988934 GGTTCTGTCTTTTCTTTTGTTTTCTTT 58.011 29.630 0.00 0.00 0.00 2.52
4163 4763 2.095059 CAGCTGTTGTTTATCTGGTGCC 60.095 50.000 5.25 0.00 0.00 5.01
4227 4827 7.995488 TGGGATCAAAATGTTTGGTTGTTTATT 59.005 29.630 0.00 0.00 0.00 1.40
4261 4861 3.852286 TGATTTTCATGGAGTTGCATGC 58.148 40.909 11.82 11.82 0.00 4.06
4275 4875 4.281688 AGTTGCATGCTTTGTTATCCTTGT 59.718 37.500 20.33 0.00 0.00 3.16
4293 4893 6.133356 TCCTTGTTGTAGGATTTTCACCTTT 58.867 36.000 0.00 0.00 39.40 3.11
4296 4896 7.438160 CCTTGTTGTAGGATTTTCACCTTTTTC 59.562 37.037 0.00 0.00 37.50 2.29
4301 4901 8.017418 TGTAGGATTTTCACCTTTTTCACAAT 57.983 30.769 0.00 0.00 38.76 2.71
4380 4980 4.454504 CCTTTTAACGCTAGAAGAAGGCAA 59.545 41.667 0.00 0.00 0.00 4.52
4435 5084 6.086871 GCTATAAAGTTGCACCAAAGAGAAC 58.913 40.000 0.00 0.00 0.00 3.01
4484 5291 6.704050 GCAATAGGTTAAACTCCAAAGCAAAA 59.296 34.615 0.00 0.00 0.00 2.44
4491 5298 7.333423 GGTTAAACTCCAAAGCAAAACTTTCTT 59.667 33.333 0.00 0.00 45.78 2.52
4521 5328 2.423926 ACTGCGTCTACAAGTGAGTG 57.576 50.000 0.00 0.00 0.00 3.51
4527 5334 2.719556 CGTCTACAAGTGAGTGTTGTCG 59.280 50.000 0.00 0.00 38.98 4.35
4537 5344 1.792949 GAGTGTTGTCGGTGTCATCAC 59.207 52.381 0.00 0.00 43.19 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.035004 CCCATGTTGATATGTTTTGACGAATT 58.965 34.615 0.00 0.00 0.00 2.17
37 40 4.690748 TCTTCGCGTCAAGATCTTCAAAAT 59.309 37.500 4.57 0.00 0.00 1.82
50 53 3.932089 TCATCATTGAATTCTTCGCGTCA 59.068 39.130 5.77 0.00 0.00 4.35
58 61 6.072728 TCGAACCGTTTTCATCATTGAATTCT 60.073 34.615 7.05 0.00 41.38 2.40
63 66 4.311606 TCTCGAACCGTTTTCATCATTGA 58.688 39.130 0.00 0.00 0.00 2.57
69 72 4.069304 TCCAAATCTCGAACCGTTTTCAT 58.931 39.130 0.00 0.00 0.00 2.57
176 179 2.562912 GACAAGTGGCGCACATGG 59.437 61.111 10.83 0.00 37.38 3.66
199 202 5.303333 GGTAAAGAACACTCCAATTTCCCAA 59.697 40.000 0.00 0.00 0.00 4.12
207 210 3.133362 ACTCGTGGTAAAGAACACTCCAA 59.867 43.478 0.00 0.00 35.51 3.53
221 224 5.948162 TCACTAATTAAGGAGTACTCGTGGT 59.052 40.000 18.27 6.90 0.00 4.16
223 226 8.928270 AAATCACTAATTAAGGAGTACTCGTG 57.072 34.615 18.27 15.67 0.00 4.35
225 228 8.127327 TCGAAATCACTAATTAAGGAGTACTCG 58.873 37.037 16.56 2.92 0.00 4.18
273 276 6.579865 ACGCTACAGCCTACAGTAAAATATT 58.420 36.000 0.00 0.00 37.91 1.28
288 291 9.379811 CTACTAGTAAATTAGTTACGCTACAGC 57.620 37.037 3.76 0.00 45.84 4.40
373 377 7.096023 GCTGACATATACTTCGTAATCAGTTGG 60.096 40.741 0.00 0.00 35.76 3.77
383 387 7.291411 AGGAAATAGCTGACATATACTTCGT 57.709 36.000 0.00 0.00 0.00 3.85
433 437 1.362355 GGACACCTTGCAAAACCGG 59.638 57.895 0.00 0.00 0.00 5.28
637 642 4.876107 GGCAACAGTGTACTATAATGCACT 59.124 41.667 14.05 0.00 45.18 4.40
891 896 3.558931 TTTATGCATCCACGGTGATCT 57.441 42.857 10.28 0.00 0.00 2.75
896 901 4.953579 AGGTTTATTTTATGCATCCACGGT 59.046 37.500 0.19 0.00 0.00 4.83
901 906 8.034804 AGTCAAACAGGTTTATTTTATGCATCC 58.965 33.333 0.19 0.00 0.00 3.51
921 926 3.554960 CGGAGTGATCAGGTCAAGTCAAA 60.555 47.826 0.00 0.00 38.90 2.69
937 942 5.971792 CACTGTTCATATGTACTACGGAGTG 59.028 44.000 11.61 12.60 45.73 3.51
941 946 6.971602 AGATCACTGTTCATATGTACTACGG 58.028 40.000 12.92 9.58 0.00 4.02
943 948 9.239002 GTGAAGATCACTGTTCATATGTACTAC 57.761 37.037 12.92 4.20 43.73 2.73
971 978 5.363580 AGAATGTTGTTGATTTGGACAGGTT 59.636 36.000 0.00 0.00 0.00 3.50
1008 1021 0.100861 GGACGAAGGGTCTCATCGAC 59.899 60.000 4.02 0.00 45.35 4.20
1109 1122 3.546543 CAATAGAGGCGCCCCGGA 61.547 66.667 26.15 5.22 35.76 5.14
1122 1135 1.000607 GCATAGTCCTCGACGGCAATA 60.001 52.381 0.00 0.00 37.67 1.90
1125 1138 2.782222 GGCATAGTCCTCGACGGCA 61.782 63.158 0.00 0.00 37.67 5.69
1323 1348 4.819761 GTGAGGATGAGCGCGCCA 62.820 66.667 30.33 25.18 0.00 5.69
1458 1486 0.676151 GGAAGTGGAAGCTCTGCCAG 60.676 60.000 0.00 0.00 34.22 4.85
1544 1572 3.073735 CGGAGGAGAGCAGCCTGT 61.074 66.667 0.00 0.00 35.44 4.00
2547 2590 2.125453 ATGGGGTACACCGGGGAA 59.875 61.111 12.96 0.00 41.60 3.97
2550 2593 2.689402 TCCATGGGGTACACCGGG 60.689 66.667 16.69 16.69 41.60 5.73
2622 2665 1.741401 CGTGGCCTTCTTGATCGCA 60.741 57.895 3.32 0.00 0.00 5.10
2810 2853 1.759445 CGATGATCCTCACCAGGTTCT 59.241 52.381 0.00 0.00 41.28 3.01
2950 2993 4.131088 GCTCCACCCGAGGACGTC 62.131 72.222 7.13 7.13 39.22 4.34
3049 3092 2.496899 ATGTTCTCCGGCTTCATGTT 57.503 45.000 0.00 0.00 0.00 2.71
3355 3398 0.734889 CCGGAATGCATCTTTTCGCT 59.265 50.000 0.00 0.00 0.00 4.93
3360 3403 1.811860 GCTGCCGGAATGCATCTTT 59.188 52.632 5.05 0.00 41.16 2.52
3555 3598 0.693049 TCTGTTCCAAGGAGAAGGGC 59.307 55.000 0.00 0.00 0.00 5.19
3557 3600 1.618837 TCGTCTGTTCCAAGGAGAAGG 59.381 52.381 0.00 0.00 0.00 3.46
3645 3708 3.996150 TCGGAGAATACGGTTATCACC 57.004 47.619 0.00 0.00 40.16 4.02
3674 3737 3.566322 ACGTTTGGCAGCACAGTATTTTA 59.434 39.130 0.00 0.00 0.00 1.52
3688 3751 3.042887 CAAAGCAAAGACTACGTTTGGC 58.957 45.455 0.00 0.00 35.75 4.52
3691 3754 2.034179 GGGCAAAGCAAAGACTACGTTT 59.966 45.455 0.00 0.00 0.00 3.60
3700 3763 1.941975 CACTTTTGGGGCAAAGCAAAG 59.058 47.619 0.00 0.00 34.72 2.77
3701 3764 2.016096 GCACTTTTGGGGCAAAGCAAA 61.016 47.619 0.00 0.00 34.72 3.68
3702 3765 0.463474 GCACTTTTGGGGCAAAGCAA 60.463 50.000 0.00 0.00 34.72 3.91
3703 3766 1.145819 GCACTTTTGGGGCAAAGCA 59.854 52.632 0.00 0.00 34.72 3.91
3704 3767 4.047834 GCACTTTTGGGGCAAAGC 57.952 55.556 0.00 0.00 34.72 3.51
3722 3876 7.376866 GTCAATATTTTGTACGCTGAATGATGG 59.623 37.037 0.00 0.00 34.32 3.51
3728 3882 4.930405 TCGGTCAATATTTTGTACGCTGAA 59.070 37.500 8.94 0.00 35.02 3.02
3730 3884 4.850859 TCGGTCAATATTTTGTACGCTG 57.149 40.909 8.94 0.55 35.02 5.18
3734 3888 9.537848 CAGTTACTTTCGGTCAATATTTTGTAC 57.462 33.333 0.00 0.00 34.32 2.90
3735 3889 9.275398 ACAGTTACTTTCGGTCAATATTTTGTA 57.725 29.630 0.00 0.00 34.32 2.41
3736 3890 8.161699 ACAGTTACTTTCGGTCAATATTTTGT 57.838 30.769 0.00 0.00 34.32 2.83
3737 3891 9.755064 CTACAGTTACTTTCGGTCAATATTTTG 57.245 33.333 0.00 0.00 0.00 2.44
3739 3893 7.604927 TGCTACAGTTACTTTCGGTCAATATTT 59.395 33.333 0.00 0.00 0.00 1.40
3740 3894 7.101054 TGCTACAGTTACTTTCGGTCAATATT 58.899 34.615 0.00 0.00 0.00 1.28
3741 3895 6.636705 TGCTACAGTTACTTTCGGTCAATAT 58.363 36.000 0.00 0.00 0.00 1.28
3747 3901 7.604927 TCAATATTTGCTACAGTTACTTTCGGT 59.395 33.333 0.00 0.00 0.00 4.69
3771 3925 5.012354 ACGGAGGGAGTTTAATACAAGTTCA 59.988 40.000 0.00 0.00 0.00 3.18
3772 3926 5.485620 ACGGAGGGAGTTTAATACAAGTTC 58.514 41.667 0.00 0.00 0.00 3.01
3775 3929 5.109903 CAGACGGAGGGAGTTTAATACAAG 58.890 45.833 0.00 0.00 0.00 3.16
3784 3938 1.279271 CATTTCCAGACGGAGGGAGTT 59.721 52.381 0.00 0.00 44.10 3.01
3789 3945 0.807667 CGAGCATTTCCAGACGGAGG 60.808 60.000 0.00 0.00 44.10 4.30
3794 3950 1.696832 GCCGACGAGCATTTCCAGAC 61.697 60.000 0.00 0.00 0.00 3.51
3807 3963 2.800544 AGATAAATCCATTTCGCCGACG 59.199 45.455 0.00 0.00 42.01 5.12
3811 3967 5.253330 TCCCATAGATAAATCCATTTCGCC 58.747 41.667 0.00 0.00 0.00 5.54
3812 3968 8.506168 TTATCCCATAGATAAATCCATTTCGC 57.494 34.615 0.00 0.00 43.11 4.70
3832 3988 8.872845 CAAGCATTTTCACCAACTTAATTATCC 58.127 33.333 0.00 0.00 0.00 2.59
3833 3989 8.872845 CCAAGCATTTTCACCAACTTAATTATC 58.127 33.333 0.00 0.00 0.00 1.75
3836 3992 6.705825 GTCCAAGCATTTTCACCAACTTAATT 59.294 34.615 0.00 0.00 0.00 1.40
3837 3993 6.183360 TGTCCAAGCATTTTCACCAACTTAAT 60.183 34.615 0.00 0.00 0.00 1.40
3863 4307 4.811908 TCTGTTCATTCAAATGCATGTGG 58.188 39.130 16.95 1.18 36.36 4.17
3988 4584 4.642885 TGTTTTGGAGGTTCGATTTTGTCT 59.357 37.500 0.00 0.00 0.00 3.41
3991 4587 6.215845 AGAATGTTTTGGAGGTTCGATTTTG 58.784 36.000 0.00 0.00 0.00 2.44
3999 4595 6.239036 GCTCTACAAAGAATGTTTTGGAGGTT 60.239 38.462 12.21 0.00 43.63 3.50
4010 4606 4.872691 AGAACCGATGCTCTACAAAGAATG 59.127 41.667 0.00 0.00 0.00 2.67
4011 4607 4.872691 CAGAACCGATGCTCTACAAAGAAT 59.127 41.667 0.00 0.00 0.00 2.40
4018 4614 3.512033 AAGACAGAACCGATGCTCTAC 57.488 47.619 0.00 0.00 0.00 2.59
4046 4642 2.616842 TCGTGCTCTGGGAAAAGAAAAC 59.383 45.455 0.00 0.00 0.00 2.43
4047 4643 2.925724 TCGTGCTCTGGGAAAAGAAAA 58.074 42.857 0.00 0.00 0.00 2.29
4048 4644 2.631160 TCGTGCTCTGGGAAAAGAAA 57.369 45.000 0.00 0.00 0.00 2.52
4049 4645 2.859165 ATCGTGCTCTGGGAAAAGAA 57.141 45.000 0.00 0.00 0.00 2.52
4050 4646 2.859165 AATCGTGCTCTGGGAAAAGA 57.141 45.000 0.00 0.00 0.00 2.52
4051 4647 2.813754 TGAAATCGTGCTCTGGGAAAAG 59.186 45.455 0.00 0.00 0.00 2.27
4052 4648 2.857483 TGAAATCGTGCTCTGGGAAAA 58.143 42.857 0.00 0.00 0.00 2.29
4053 4649 2.559698 TGAAATCGTGCTCTGGGAAA 57.440 45.000 0.00 0.00 0.00 3.13
4054 4650 2.787473 ATGAAATCGTGCTCTGGGAA 57.213 45.000 0.00 0.00 0.00 3.97
4055 4651 2.787473 AATGAAATCGTGCTCTGGGA 57.213 45.000 0.00 0.00 0.00 4.37
4090 4690 1.153369 CGTCATCGGTTCCCATGCT 60.153 57.895 0.00 0.00 0.00 3.79
4099 4699 6.790285 ATACTTTTAACAAACGTCATCGGT 57.210 33.333 0.00 0.00 41.85 4.69
4100 4700 8.496872 AAAATACTTTTAACAAACGTCATCGG 57.503 30.769 0.00 0.00 41.85 4.18
4127 4727 3.287222 ACAGCTGCACCAAAGAGTTAAA 58.713 40.909 15.27 0.00 0.00 1.52
4128 4728 2.930950 ACAGCTGCACCAAAGAGTTAA 58.069 42.857 15.27 0.00 0.00 2.01
4129 4729 2.618241 CAACAGCTGCACCAAAGAGTTA 59.382 45.455 15.27 0.00 0.00 2.24
4134 4734 2.298411 AAACAACAGCTGCACCAAAG 57.702 45.000 15.27 0.00 0.00 2.77
4163 4763 1.474077 GTTTGGCTCCTAGGTGCAATG 59.526 52.381 31.19 8.68 36.47 2.82
4275 4875 7.411486 TGTGAAAAAGGTGAAAATCCTACAA 57.589 32.000 0.00 0.00 34.56 2.41
4293 4893 5.449041 GGAAGCGCTCATCATTATTGTGAAA 60.449 40.000 12.06 0.00 0.00 2.69
4296 4896 3.562973 AGGAAGCGCTCATCATTATTGTG 59.437 43.478 12.06 0.00 0.00 3.33
4301 4901 1.681264 TCGAGGAAGCGCTCATCATTA 59.319 47.619 12.06 0.00 34.38 1.90
4398 4998 8.128582 TGCAACTTTATAGCCAAAATTAGATCG 58.871 33.333 0.00 0.00 0.00 3.69
4409 5058 4.402829 TCTTTGGTGCAACTTTATAGCCA 58.597 39.130 2.04 0.00 36.74 4.75
4435 5084 5.796935 CAGAATAGAAACCGTGCAAAGATTG 59.203 40.000 0.00 0.00 0.00 2.67
4446 5095 7.548196 TTAACCTATTGCAGAATAGAAACCG 57.452 36.000 6.94 0.00 42.66 4.44
4484 5291 4.923871 CGCAGTATGTCTACACAAGAAAGT 59.076 41.667 0.00 0.00 39.31 2.66


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

AutoCloner maintained by Alex Coulton.