Multiple sequence alignment - TraesCS5D01G506900

Loading Multiple Alignment...

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 TraesCS5D01G506900 chr5D 100.000 4948 0 0 1 4948 532551717 532556664 0.000000e+00 9138.0
1 TraesCS5D01G506900 chr5D 91.885 419 30 3 4 420 27805521 27805105 2.570000e-162 582.0
2 TraesCS5D01G506900 chr4A 91.045 3082 187 42 972 4007 639209261 639206223 0.000000e+00 4080.0
3 TraesCS5D01G506900 chr4A 89.338 544 53 5 4006 4547 639206052 639205512 0.000000e+00 678.0
4 TraesCS5D01G506900 chr4A 91.868 455 27 10 4496 4948 639205340 639204894 1.170000e-175 627.0
5 TraesCS5D01G506900 chr4A 82.093 430 54 17 1130 1550 545117384 545116969 3.670000e-91 346.0
6 TraesCS5D01G506900 chr5B 89.941 2873 219 34 2111 4926 672618047 672620906 0.000000e+00 3640.0
7 TraesCS5D01G506900 chr5B 91.121 2140 100 32 12 2131 672615891 672617960 0.000000e+00 2817.0
8 TraesCS5D01G506900 chr7D 89.114 790 67 9 3 789 631290758 631291531 0.000000e+00 965.0
9 TraesCS5D01G506900 chr3B 87.280 794 64 16 2 793 755169612 755170370 0.000000e+00 872.0
10 TraesCS5D01G506900 chr3B 81.758 910 138 17 1 892 734852175 734851276 0.000000e+00 736.0
11 TraesCS5D01G506900 chr4D 84.096 830 108 15 106 924 436954378 436953562 0.000000e+00 780.0
12 TraesCS5D01G506900 chr4D 83.354 817 114 13 116 924 436960192 436959390 0.000000e+00 736.0
13 TraesCS5D01G506900 chr4D 81.193 436 56 17 1127 1552 51554021 51554440 1.330000e-85 327.0
14 TraesCS5D01G506900 chr7B 89.278 485 50 2 441 923 13891408 13890924 1.520000e-169 606.0
15 TraesCS5D01G506900 chr3A 87.132 272 32 1 398 669 86714414 86714682 6.220000e-79 305.0
16 TraesCS5D01G506900 chr4B 85.477 241 26 9 1318 1549 75738090 75738330 4.950000e-60 243.0
17 TraesCS5D01G506900 chr5A 78.571 224 38 8 419 639 103903028 103902812 6.680000e-29 139.0
18 TraesCS5D01G506900 chr3D 77.778 243 43 8 386 624 313709833 313710068 6.680000e-29 139.0
19 TraesCS5D01G506900 chr6B 85.057 87 12 1 832 917 3109799 3109885 2.450000e-13 87.9


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 TraesCS5D01G506900 chr5D 532551717 532556664 4947 False 9138.0 9138 100.000000 1 4948 1 chr5D.!!$F1 4947
1 TraesCS5D01G506900 chr4A 639204894 639209261 4367 True 1795.0 4080 90.750333 972 4948 3 chr4A.!!$R2 3976
2 TraesCS5D01G506900 chr5B 672615891 672620906 5015 False 3228.5 3640 90.531000 12 4926 2 chr5B.!!$F1 4914
3 TraesCS5D01G506900 chr7D 631290758 631291531 773 False 965.0 965 89.114000 3 789 1 chr7D.!!$F1 786
4 TraesCS5D01G506900 chr3B 755169612 755170370 758 False 872.0 872 87.280000 2 793 1 chr3B.!!$F1 791
5 TraesCS5D01G506900 chr3B 734851276 734852175 899 True 736.0 736 81.758000 1 892 1 chr3B.!!$R1 891
6 TraesCS5D01G506900 chr4D 436953562 436954378 816 True 780.0 780 84.096000 106 924 1 chr4D.!!$R1 818
7 TraesCS5D01G506900 chr4D 436959390 436960192 802 True 736.0 736 83.354000 116 924 1 chr4D.!!$R2 808

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
635 653 0.616395 TTGGTCCTCCGGATGCAGTA 60.616 55.000 3.57 0.0 32.73 2.74 F
1677 1716 1.002274 AGGGCAGTAGGTCAGGGAG 59.998 63.158 0.00 0.0 0.00 4.30 F
2488 2640 0.890683 CTTCCATTTCCTGGTGGCAC 59.109 55.000 9.70 9.7 46.08 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2362 1.302511 CTGAACCCCAACCTGGTCG 60.303 63.158 0.0 0.0 35.17 4.79 R
3605 3818 0.958091 TGGTTGCCCAATTCTCGTTG 59.042 50.000 0.0 0.0 37.98 4.10 R
4146 4535 0.243907 CGGACAATCGTGAGGACTGT 59.756 55.000 0.0 0.0 0.00 3.55 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
141 143 2.592993 CCTTGGAGGCTCCGGTGAA 61.593 63.158 27.58 15.50 40.17 3.18
394 409 1.000283 CCTTTGACTGACAGCTCTCGT 60.000 52.381 1.25 0.00 0.00 4.18
473 490 0.884704 GCTTGCGGGTCTGTTTCTGA 60.885 55.000 0.00 0.00 0.00 3.27
477 495 1.621317 TGCGGGTCTGTTTCTGATGTA 59.379 47.619 0.00 0.00 0.00 2.29
635 653 0.616395 TTGGTCCTCCGGATGCAGTA 60.616 55.000 3.57 0.00 32.73 2.74
652 670 2.014857 AGTAAGCGACACGATGCTAGA 58.985 47.619 0.00 0.00 41.46 2.43
779 800 3.746492 GTGTCTGTTCCACATTGTACCTC 59.254 47.826 0.00 0.00 33.00 3.85
842 865 6.313519 TGTTCTAATCTTGTAATCCTGGCT 57.686 37.500 0.00 0.00 0.00 4.75
878 901 2.014010 AATTCAAAGCTGGGCAAGGA 57.986 45.000 0.00 0.00 0.00 3.36
894 917 3.430929 GCAAGGATCGAGCCTTTTCTCTA 60.431 47.826 31.58 0.00 45.85 2.43
906 931 1.248785 TTTCTCTACCTCGGCTGCGT 61.249 55.000 0.00 0.00 0.00 5.24
1031 1061 4.164988 CCTCTGTCTAATCTGGACCCATTT 59.835 45.833 0.00 0.00 33.22 2.32
1319 1353 5.248248 CCTTCCTCTTCCTCTTCTTCTTCTT 59.752 44.000 0.00 0.00 0.00 2.52
1320 1354 5.993748 TCCTCTTCCTCTTCTTCTTCTTC 57.006 43.478 0.00 0.00 0.00 2.87
1321 1355 5.650283 TCCTCTTCCTCTTCTTCTTCTTCT 58.350 41.667 0.00 0.00 0.00 2.85
1677 1716 1.002274 AGGGCAGTAGGTCAGGGAG 59.998 63.158 0.00 0.00 0.00 4.30
1781 1820 6.477688 CAGAATTTGGTGGCAATTGATATCAC 59.522 38.462 10.34 10.71 0.00 3.06
1895 1934 2.574006 AAGCAGAGTGAGGCAATGAA 57.426 45.000 0.00 0.00 0.00 2.57
1976 2015 3.947910 ATGCAAATGTGGAGTTTGGAG 57.052 42.857 0.00 0.00 39.64 3.86
2119 2158 5.359194 TGTCCTGGATGTATTCTCTTTCC 57.641 43.478 0.00 0.00 0.00 3.13
2124 2163 6.058183 CCTGGATGTATTCTCTTTCCGAAAT 58.942 40.000 0.00 0.00 0.00 2.17
2125 2164 7.070696 TCCTGGATGTATTCTCTTTCCGAAATA 59.929 37.037 0.00 0.00 0.00 1.40
2126 2165 7.171678 CCTGGATGTATTCTCTTTCCGAAATAC 59.828 40.741 0.00 0.00 0.00 1.89
2127 2166 6.700081 TGGATGTATTCTCTTTCCGAAATACG 59.300 38.462 0.00 0.00 42.18 3.06
2128 2167 6.921857 GGATGTATTCTCTTTCCGAAATACGA 59.078 38.462 0.00 0.00 45.77 3.43
2132 2171 6.988109 ATTCTCTTTCCGAAATACGATACG 57.012 37.500 0.00 0.00 45.77 3.06
2142 2293 6.852853 TCCGAAATACGATACGAATACTCAAC 59.147 38.462 0.00 0.00 45.77 3.18
2155 2306 8.410673 ACGAATACTCAACTACTCATGGATAT 57.589 34.615 0.00 0.00 0.00 1.63
2156 2307 9.516546 ACGAATACTCAACTACTCATGGATATA 57.483 33.333 0.00 0.00 0.00 0.86
2214 2365 8.530269 TCTTTCTTTTACTCCTGAATAACGAC 57.470 34.615 0.00 0.00 0.00 4.34
2229 2380 1.302511 CGACCAGGTTGGGGTTCAG 60.303 63.158 0.00 0.00 43.37 3.02
2338 2489 7.649533 TTTGACATAATTGCTTCCATCATCT 57.350 32.000 0.00 0.00 0.00 2.90
2340 2491 8.929260 TTGACATAATTGCTTCCATCATCTAT 57.071 30.769 0.00 0.00 0.00 1.98
2446 2597 5.499004 TCCTTTGGTGTTATTCTAGCTGT 57.501 39.130 0.00 0.00 0.00 4.40
2462 2613 7.341445 TCTAGCTGTTGTTTATTGTTGGTTT 57.659 32.000 0.00 0.00 0.00 3.27
2471 2623 6.344500 TGTTTATTGTTGGTTTGTGCATCTT 58.656 32.000 0.00 0.00 0.00 2.40
2488 2640 0.890683 CTTCCATTTCCTGGTGGCAC 59.109 55.000 9.70 9.70 46.08 5.01
2504 2656 4.105486 GTGGCACTTGAAACTCAAAAGAC 58.895 43.478 11.13 0.00 35.73 3.01
2510 2662 6.586082 GCACTTGAAACTCAAAAGACAGAAAA 59.414 34.615 0.00 0.00 35.73 2.29
2511 2663 7.201384 GCACTTGAAACTCAAAAGACAGAAAAG 60.201 37.037 0.00 0.00 35.73 2.27
2513 2665 6.834168 TGAAACTCAAAAGACAGAAAAGGT 57.166 33.333 0.00 0.00 0.00 3.50
2596 2765 5.240403 AGTTTCTTCTTTTGACTGATCAGGC 59.760 40.000 26.08 24.40 35.83 4.85
2637 2807 1.262151 CAGCAACAAACTTGGCATTGC 59.738 47.619 12.11 12.11 44.74 3.56
2639 2809 1.003652 GCAACAAACTTGGCATTGCAC 60.004 47.619 14.47 0.57 44.01 4.57
2642 2812 1.069049 ACAAACTTGGCATTGCACTCC 59.931 47.619 11.39 0.00 0.00 3.85
2692 2862 8.696043 TTCATAGAGCACAAGCCATATATTTT 57.304 30.769 0.00 0.00 43.56 1.82
2704 2879 5.902431 AGCCATATATTTTTGTTGGGGCTAA 59.098 36.000 0.00 0.00 46.61 3.09
2724 2899 7.655732 GGGCTAATTGTTTGTGTTACATCTTTT 59.344 33.333 0.00 0.00 0.00 2.27
2741 2916 8.794335 ACATCTTTTTATCTTCTTCCACCTAC 57.206 34.615 0.00 0.00 0.00 3.18
2747 2922 8.950007 TTTTATCTTCTTCCACCTACCAAATT 57.050 30.769 0.00 0.00 0.00 1.82
2776 2952 7.124901 ACATAATGGTTGGGTATATTTTGTGCA 59.875 33.333 0.00 0.00 0.00 4.57
2779 2955 5.542779 TGGTTGGGTATATTTTGTGCAAAC 58.457 37.500 0.00 0.00 0.00 2.93
2784 2960 5.047660 TGGGTATATTTTGTGCAAACCTGTC 60.048 40.000 0.00 0.00 0.00 3.51
2798 2974 7.540745 GTGCAAACCTGTCGTAAATAATTGATT 59.459 33.333 0.00 0.00 0.00 2.57
2823 2999 4.698304 ACATGACCTTGTAAATAACCCACG 59.302 41.667 0.00 0.00 0.00 4.94
2881 3058 8.336801 AGAAGAACAAACAATATAACCCACTC 57.663 34.615 0.00 0.00 0.00 3.51
3046 3223 3.578716 TCTTCCTCCAAAGACTGGTGTAG 59.421 47.826 0.00 0.00 46.51 2.74
3051 3228 3.833070 CTCCAAAGACTGGTGTAGTAGGT 59.167 47.826 0.00 0.00 46.51 3.08
3061 3241 2.038033 GGTGTAGTAGGTGGCTTGTGAA 59.962 50.000 0.00 0.00 0.00 3.18
3073 3253 4.798387 GTGGCTTGTGAACTGTTACTTTTG 59.202 41.667 0.00 0.00 0.00 2.44
3154 3334 3.513515 AGACTGAAACTAAGGGAGCTCAG 59.486 47.826 17.19 6.65 41.30 3.35
3155 3335 2.027653 ACTGAAACTAAGGGAGCTCAGC 60.028 50.000 17.19 0.00 40.08 4.26
3184 3364 3.141398 TGAGATCAACTGTGGAAACTGC 58.859 45.455 0.00 0.00 0.00 4.40
3291 3484 4.926832 CCAAACCGTTTTTGAACACTCTTT 59.073 37.500 8.03 0.00 0.00 2.52
3368 3575 7.928706 CAGGAGTACTAGGAAATAAGTCAATGG 59.071 40.741 0.00 0.00 0.00 3.16
3377 3584 7.678837 AGGAAATAAGTCAATGGCATGAAAAA 58.321 30.769 0.00 0.00 0.00 1.94
3591 3804 6.176183 TGCGACCTAAAGTAGTAGTAGAAGT 58.824 40.000 0.00 0.00 0.00 3.01
3605 3818 8.283699 AGTAGTAGAAGTTTAGACATCCACTC 57.716 38.462 0.00 0.00 30.30 3.51
3652 3865 2.618816 GGTGGATGATGAACTCAGGCAA 60.619 50.000 0.00 0.00 37.28 4.52
3691 3904 9.566432 AGTGATATGATATTCAAGGTTCCTTTC 57.434 33.333 0.86 0.00 0.00 2.62
3712 3925 8.370940 CCTTTCCTAATCAGCTATATCAGTTCA 58.629 37.037 0.00 0.00 0.00 3.18
3772 3985 6.868864 CCGGTAATGACATATCCTTTCTACAG 59.131 42.308 0.00 0.00 0.00 2.74
3792 4005 3.498397 CAGAACTGTTTTAGTGCATCGGT 59.502 43.478 0.00 0.00 40.26 4.69
3799 4012 4.814234 TGTTTTAGTGCATCGGTGGATATC 59.186 41.667 0.00 0.00 0.00 1.63
3814 4027 5.891551 GGTGGATATCTGTTGTGGGTTATTT 59.108 40.000 2.05 0.00 0.00 1.40
3820 4033 5.522315 TCTGTTGTGGGTTATTTATGGGA 57.478 39.130 0.00 0.00 0.00 4.37
3860 4077 3.782443 GGTGTAGGCCCTGTCCGG 61.782 72.222 0.00 0.00 0.00 5.14
3964 4181 3.507233 CCCTGATGTAGCAAGCAAGAAAA 59.493 43.478 0.00 0.00 0.00 2.29
3969 4186 7.362401 CCTGATGTAGCAAGCAAGAAAACTATT 60.362 37.037 0.00 0.00 0.00 1.73
3989 4206 3.838244 TGTCTGGTATGAATGCCTACC 57.162 47.619 0.00 0.00 38.30 3.18
3992 4209 3.388024 GTCTGGTATGAATGCCTACCTGA 59.612 47.826 9.77 9.77 41.13 3.86
3993 4210 3.388024 TCTGGTATGAATGCCTACCTGAC 59.612 47.826 9.77 0.00 39.56 3.51
4007 4224 3.041508 ACCTGACGCTTTCTCCTTTAC 57.958 47.619 0.00 0.00 0.00 2.01
4009 4226 3.071167 ACCTGACGCTTTCTCCTTTACTT 59.929 43.478 0.00 0.00 0.00 2.24
4010 4227 3.433615 CCTGACGCTTTCTCCTTTACTTG 59.566 47.826 0.00 0.00 0.00 3.16
4011 4228 3.399330 TGACGCTTTCTCCTTTACTTGG 58.601 45.455 0.00 0.00 0.00 3.61
4012 4229 3.181458 TGACGCTTTCTCCTTTACTTGGT 60.181 43.478 0.00 0.00 0.00 3.67
4013 4230 3.813724 GACGCTTTCTCCTTTACTTGGTT 59.186 43.478 0.00 0.00 0.00 3.67
4016 4233 5.221581 ACGCTTTCTCCTTTACTTGGTTCTA 60.222 40.000 0.00 0.00 0.00 2.10
4018 4235 5.411977 GCTTTCTCCTTTACTTGGTTCTACC 59.588 44.000 0.00 0.00 39.22 3.18
4020 4237 7.526693 GCTTTCTCCTTTACTTGGTTCTACCTA 60.527 40.741 0.00 0.00 39.58 3.08
4024 4413 5.416952 TCCTTTACTTGGTTCTACCTAGACG 59.583 44.000 13.04 0.00 42.55 4.18
4027 4416 3.163467 ACTTGGTTCTACCTAGACGCTT 58.837 45.455 13.04 0.00 42.55 4.68
4130 4519 1.278172 CGTCGACTTGTGCTGTCTGG 61.278 60.000 14.70 0.00 32.70 3.86
4146 4535 3.206150 GTCTGGAAGTGAAACAAGAGCA 58.794 45.455 0.00 0.00 41.43 4.26
4178 4567 0.040514 TTGTCCGCAAGTGCAATTCG 60.041 50.000 0.00 4.14 42.21 3.34
4197 4586 1.809619 GCGCGCCATTCTGTAGTCA 60.810 57.895 23.24 0.00 0.00 3.41
4240 4629 6.542370 TCTTGTAAGCTGGAAGTATTTATGGC 59.458 38.462 0.00 0.00 35.30 4.40
4271 4660 5.352284 CCTAGCACACTATTACTTCCACAG 58.648 45.833 0.00 0.00 0.00 3.66
4296 4685 5.621197 TTGTTGGTACATGTATCTTGTGC 57.379 39.130 16.88 0.00 39.30 4.57
4319 4708 6.536582 TGCTTCTGTCAGATAAAGCTGTAATC 59.463 38.462 20.47 0.00 43.48 1.75
4323 4712 6.381133 TCTGTCAGATAAAGCTGTAATCTCCA 59.619 38.462 0.00 3.64 37.20 3.86
4340 4730 4.401022 TCTCCATCTTTCTGCAACATGTT 58.599 39.130 4.92 4.92 0.00 2.71
4404 4804 0.242825 CCCAGCTACGACGAAACTGA 59.757 55.000 0.00 0.00 0.00 3.41
4405 4805 1.618861 CCAGCTACGACGAAACTGAG 58.381 55.000 0.00 0.00 0.00 3.35
4407 4807 1.068472 CAGCTACGACGAAACTGAGGT 60.068 52.381 0.00 0.00 0.00 3.85
4467 4868 8.818141 ATCAAATAACATATCGACAGGTGTAG 57.182 34.615 0.00 0.00 0.00 2.74
4482 4883 1.672881 GTGTAGAACCATGGCTCATGC 59.327 52.381 17.32 7.19 40.20 4.06
4495 4896 1.495878 CTCATGCTATCCACGTGAGC 58.504 55.000 19.30 18.58 42.49 4.26
4524 4925 1.250328 CATGAACCAGCAGGCTTTGA 58.750 50.000 0.00 0.00 39.06 2.69
4530 4931 2.944129 ACCAGCAGGCTTTGAAAGTTA 58.056 42.857 6.81 0.00 39.06 2.24
4562 5167 6.052360 TGCATACAACTTACAAGTGTCTCAA 58.948 36.000 0.00 0.00 39.66 3.02
4583 5201 7.769044 TCTCAAGGCCACATACTCTTTATTAAC 59.231 37.037 5.01 0.00 0.00 2.01
4622 5240 8.066595 CAGATGACCTCACAATTTCGATAATTC 58.933 37.037 0.00 0.00 0.00 2.17
4623 5241 6.677781 TGACCTCACAATTTCGATAATTCC 57.322 37.500 0.00 0.00 0.00 3.01
4624 5242 5.588648 TGACCTCACAATTTCGATAATTCCC 59.411 40.000 0.00 0.00 0.00 3.97
4629 5247 5.064198 TCACAATTTCGATAATTCCCGTGTC 59.936 40.000 14.31 0.00 0.00 3.67
4857 5475 1.785041 GCACTTGCACTTTCGCTCCA 61.785 55.000 0.00 0.00 41.59 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 143 2.367512 GTGGGCAGGGGAGGATCT 60.368 66.667 0.00 0.00 33.73 2.75
191 193 1.341209 GTTGTCAGCCAAAGAAAGGGG 59.659 52.381 0.00 0.00 34.07 4.79
373 388 1.000283 CGAGAGCTGTCAGTCAAAGGT 60.000 52.381 11.90 0.00 0.00 3.50
394 409 2.577059 GGAAGACATCACGCCGGA 59.423 61.111 5.05 0.00 0.00 5.14
473 490 5.356190 CACAAGCTGTCAAATGGAGATACAT 59.644 40.000 0.00 0.00 0.00 2.29
477 495 2.490903 GCACAAGCTGTCAAATGGAGAT 59.509 45.455 0.00 0.00 37.91 2.75
635 653 0.526524 GCTCTAGCATCGTGTCGCTT 60.527 55.000 0.00 0.00 39.70 4.68
652 670 0.684479 TGAGTAGGAGGCACATCGCT 60.684 55.000 0.00 0.00 41.91 4.93
800 821 6.838382 AGAACATTACAGGGAAGTAAACAGT 58.162 36.000 0.00 0.00 37.50 3.55
842 865 5.344743 TGAATTAACAAAGCCAACAACCA 57.655 34.783 0.00 0.00 0.00 3.67
869 892 1.852157 AAAGGCTCGATCCTTGCCCA 61.852 55.000 20.70 0.00 45.25 5.36
878 901 2.359531 CGAGGTAGAGAAAAGGCTCGAT 59.640 50.000 0.00 0.00 39.87 3.59
894 917 1.668151 GAAAAGACGCAGCCGAGGT 60.668 57.895 0.00 0.00 38.29 3.85
1976 2015 3.751698 ACCAAGCGAAACAGATTTCCTAC 59.248 43.478 0.00 0.00 41.12 3.18
2024 2063 2.823593 TGACCATGGCAATCGGCG 60.824 61.111 13.04 0.00 46.16 6.46
2119 2158 7.833284 AGTTGAGTATTCGTATCGTATTTCG 57.167 36.000 0.00 0.00 41.41 3.46
2124 2163 8.493547 CATGAGTAGTTGAGTATTCGTATCGTA 58.506 37.037 0.00 0.00 0.00 3.43
2125 2164 6.915544 TGAGTAGTTGAGTATTCGTATCGT 57.084 37.500 0.00 0.00 0.00 3.73
2126 2165 6.797513 CCATGAGTAGTTGAGTATTCGTATCG 59.202 42.308 0.00 0.00 0.00 2.92
2127 2166 7.872881 TCCATGAGTAGTTGAGTATTCGTATC 58.127 38.462 0.00 0.00 0.00 2.24
2128 2167 7.818997 TCCATGAGTAGTTGAGTATTCGTAT 57.181 36.000 0.00 0.00 0.00 3.06
2142 2293 7.987458 ACACCAAACAAGTATATCCATGAGTAG 59.013 37.037 0.00 0.00 0.00 2.57
2155 2306 6.046593 CACTCAAGACTACACCAAACAAGTA 58.953 40.000 0.00 0.00 0.00 2.24
2156 2307 4.876107 CACTCAAGACTACACCAAACAAGT 59.124 41.667 0.00 0.00 0.00 3.16
2211 2362 1.302511 CTGAACCCCAACCTGGTCG 60.303 63.158 0.00 0.00 35.17 4.79
2214 2365 1.358152 TAGACTGAACCCCAACCTGG 58.642 55.000 0.00 0.00 37.25 4.45
2229 2380 6.801539 TTGACAAGAAACACATGGATAGAC 57.198 37.500 0.00 0.00 0.00 2.59
2338 2489 4.676723 GCAAGCGCATAACCTGGAAAAATA 60.677 41.667 11.47 0.00 38.36 1.40
2340 2491 2.609244 GCAAGCGCATAACCTGGAAAAA 60.609 45.455 11.47 0.00 38.36 1.94
2446 2597 6.344500 AGATGCACAAACCAACAATAAACAA 58.656 32.000 0.00 0.00 0.00 2.83
2488 2640 7.315890 ACCTTTTCTGTCTTTTGAGTTTCAAG 58.684 34.615 0.00 0.00 37.70 3.02
2559 2728 8.458843 CAAAAGAAGAAACTCCTAAGACAACAA 58.541 33.333 0.00 0.00 0.00 2.83
2596 2765 5.922544 GCTGGTTTTATTTATGCATAGCTGG 59.077 40.000 6.50 0.00 0.00 4.85
2637 2807 2.486472 AGATGCAACTTCTGGGAGTG 57.514 50.000 0.00 0.00 0.00 3.51
2639 2809 2.486982 CACAAGATGCAACTTCTGGGAG 59.513 50.000 6.20 0.00 0.00 4.30
2642 2812 3.189287 GGTACACAAGATGCAACTTCTGG 59.811 47.826 14.70 3.16 0.00 3.86
2692 2862 3.452627 ACACAAACAATTAGCCCCAACAA 59.547 39.130 0.00 0.00 0.00 2.83
2724 2899 8.167392 TCAAATTTGGTAGGTGGAAGAAGATAA 58.833 33.333 17.90 0.00 0.00 1.75
2741 2916 5.803552 ACCCAACCATTATGTCAAATTTGG 58.196 37.500 17.90 2.69 31.05 3.28
2747 2922 9.261035 ACAAAATATACCCAACCATTATGTCAA 57.739 29.630 0.00 0.00 0.00 3.18
2798 2974 6.372103 CGTGGGTTATTTACAAGGTCATGTTA 59.628 38.462 0.00 0.00 34.75 2.41
2913 3090 9.043678 GTTCATTCGTTAAGTAATACCAAAACG 57.956 33.333 13.03 13.03 40.61 3.60
2925 3102 8.790718 TGTAGACTAAGAGTTCATTCGTTAAGT 58.209 33.333 0.00 0.00 0.00 2.24
2932 3109 7.399245 AGACCTGTAGACTAAGAGTTCATTC 57.601 40.000 0.00 0.00 0.00 2.67
3046 3223 2.256117 ACAGTTCACAAGCCACCTAC 57.744 50.000 0.00 0.00 0.00 3.18
3051 3228 4.461081 ACAAAAGTAACAGTTCACAAGCCA 59.539 37.500 0.00 0.00 0.00 4.75
3061 3241 6.379988 ACAAATGGGAAGACAAAAGTAACAGT 59.620 34.615 0.00 0.00 0.00 3.55
3073 3253 7.826690 ACACAAATATGTACAAATGGGAAGAC 58.173 34.615 0.00 0.00 37.82 3.01
3126 3306 5.870433 GCTCCCTTAGTTTCAGTCTAACTTC 59.130 44.000 0.00 0.00 37.12 3.01
3154 3334 2.290641 ACAGTTGATCTCAAACCGTTGC 59.709 45.455 0.00 0.00 37.63 4.17
3155 3335 3.303990 CCACAGTTGATCTCAAACCGTTG 60.304 47.826 0.00 0.00 37.63 4.10
3291 3484 7.498900 CAGTACATATTCCATTGGCTTTCACTA 59.501 37.037 0.00 0.00 0.00 2.74
3368 3575 6.856895 ACAAGTATTCTAGCCTTTTTCATGC 58.143 36.000 0.00 0.00 0.00 4.06
3377 3584 5.746990 AGTCACAACAAGTATTCTAGCCT 57.253 39.130 0.00 0.00 0.00 4.58
3566 3779 6.827762 ACTTCTACTACTACTTTAGGTCGCAT 59.172 38.462 0.00 0.00 0.00 4.73
3591 3804 5.462530 TTCTCGTTGAGTGGATGTCTAAA 57.537 39.130 0.00 0.00 0.00 1.85
3605 3818 0.958091 TGGTTGCCCAATTCTCGTTG 59.042 50.000 0.00 0.00 37.98 4.10
3637 3850 2.892852 CCCTTTTTGCCTGAGTTCATCA 59.107 45.455 0.00 0.00 36.21 3.07
3652 3865 5.450818 TCATATCACTTGTAGGCCCTTTT 57.549 39.130 0.00 0.00 0.00 2.27
3691 3904 9.887629 ATGATTGAACTGATATAGCTGATTAGG 57.112 33.333 0.00 0.00 0.00 2.69
3712 3925 4.079615 TCACCCTCCATCAATGTCATGATT 60.080 41.667 0.00 0.00 37.96 2.57
3772 3985 3.364964 CCACCGATGCACTAAAACAGTTC 60.365 47.826 0.00 0.00 34.26 3.01
3792 4005 7.723616 CCATAAATAACCCACAACAGATATCCA 59.276 37.037 0.00 0.00 0.00 3.41
3799 4012 5.261216 ACTCCCATAAATAACCCACAACAG 58.739 41.667 0.00 0.00 0.00 3.16
3814 4027 0.339859 ACCTGCAGAGGACTCCCATA 59.660 55.000 17.39 0.00 42.93 2.74
3820 4033 0.707616 AGGAGTACCTGCAGAGGACT 59.292 55.000 17.39 17.21 45.92 3.85
3860 4077 3.814283 CAGCTTTGATCTTCTGCCCTATC 59.186 47.826 0.00 0.00 0.00 2.08
3964 4181 5.636903 AGGCATTCATACCAGACAATAGT 57.363 39.130 0.00 0.00 0.00 2.12
3969 4186 3.134623 CAGGTAGGCATTCATACCAGACA 59.865 47.826 8.88 0.00 43.33 3.41
3989 4206 3.433615 CCAAGTAAAGGAGAAAGCGTCAG 59.566 47.826 0.00 0.00 0.00 3.51
3992 4209 3.487120 ACCAAGTAAAGGAGAAAGCGT 57.513 42.857 0.00 0.00 0.00 5.07
3993 4210 4.065789 AGAACCAAGTAAAGGAGAAAGCG 58.934 43.478 0.00 0.00 0.00 4.68
4007 4224 3.870633 AAGCGTCTAGGTAGAACCAAG 57.129 47.619 0.00 0.00 41.95 3.61
4009 4226 7.431249 CAATATAAAGCGTCTAGGTAGAACCA 58.569 38.462 0.00 0.00 41.95 3.67
4010 4227 6.365518 GCAATATAAAGCGTCTAGGTAGAACC 59.634 42.308 0.00 0.00 38.99 3.62
4011 4228 7.146648 AGCAATATAAAGCGTCTAGGTAGAAC 58.853 38.462 0.00 0.00 33.47 3.01
4012 4229 7.286215 AGCAATATAAAGCGTCTAGGTAGAA 57.714 36.000 0.00 0.00 33.47 2.10
4013 4230 6.896021 AGCAATATAAAGCGTCTAGGTAGA 57.104 37.500 0.00 0.00 35.48 2.59
4016 4233 9.804758 GATTATAGCAATATAAAGCGTCTAGGT 57.195 33.333 0.00 0.00 35.48 3.08
4020 4237 9.712305 AACAGATTATAGCAATATAAAGCGTCT 57.288 29.630 0.00 0.00 35.48 4.18
4056 4445 6.583806 GGAAAGTGCAGATTGTTCATTGTTAG 59.416 38.462 0.00 0.00 0.00 2.34
4130 4519 3.002759 GGACTGTGCTCTTGTTTCACTTC 59.997 47.826 0.00 0.00 0.00 3.01
4146 4535 0.243907 CGGACAATCGTGAGGACTGT 59.756 55.000 0.00 0.00 0.00 3.55
4178 4567 2.511600 ACTACAGAATGGCGCGCC 60.512 61.111 42.35 42.35 43.62 6.53
4271 4660 6.747280 GCACAAGATACATGTACCAACAAATC 59.253 38.462 7.96 0.07 39.58 2.17
4296 4685 7.437862 GGAGATTACAGCTTTATCTGACAGAAG 59.562 40.741 9.70 3.72 37.51 2.85
4319 4708 4.482386 CAACATGTTGCAGAAAGATGGAG 58.518 43.478 24.69 0.00 42.48 3.86
4375 4765 1.276989 TCGTAGCTGGGGAAAAACGAT 59.723 47.619 0.00 0.00 34.74 3.73
4404 4804 4.772886 ACAAGTTTCTTCACCAGTACCT 57.227 40.909 0.00 0.00 0.00 3.08
4405 4805 6.930667 TTTACAAGTTTCTTCACCAGTACC 57.069 37.500 0.00 0.00 0.00 3.34
4407 4807 6.770785 AGCATTTACAAGTTTCTTCACCAGTA 59.229 34.615 0.00 0.00 0.00 2.74
4448 4849 6.140303 GGTTCTACACCTGTCGATATGTTA 57.860 41.667 0.00 0.00 43.29 2.41
4482 4883 3.308053 CACTGAAATGCTCACGTGGATAG 59.692 47.826 17.00 7.07 33.27 2.08
4495 4896 2.029739 TGCTGGTTCATGCACTGAAATG 60.030 45.455 11.51 7.44 45.27 2.32
4514 4915 6.013842 ACTTGTATAACTTTCAAAGCCTGC 57.986 37.500 0.00 0.00 0.00 4.85
4547 4948 2.808543 GTGGCCTTGAGACACTTGTAAG 59.191 50.000 3.32 0.00 32.58 2.34
4554 5159 2.234908 AGAGTATGTGGCCTTGAGACAC 59.765 50.000 3.32 0.00 35.75 3.67
4556 5161 3.618690 AAGAGTATGTGGCCTTGAGAC 57.381 47.619 3.32 0.00 0.00 3.36
4562 5167 7.888546 ACAAAGTTAATAAAGAGTATGTGGCCT 59.111 33.333 3.32 0.00 0.00 5.19
4598 5216 7.355778 GGAATTATCGAAATTGTGAGGTCATC 58.644 38.462 9.35 0.00 0.00 2.92
4624 5242 2.693250 TTCAGCACAGACCCGACACG 62.693 60.000 0.00 0.00 0.00 4.49
4629 5247 0.034059 AGAAGTTCAGCACAGACCCG 59.966 55.000 5.50 0.00 0.00 5.28
4857 5475 2.191375 CTGATGGCGCCATGGACT 59.809 61.111 44.96 24.17 36.70 3.85


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

AutoCloner maintained by Alex Coulton.