Multiple sequence alignment - TraesCS2A01G395300

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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 TraesCS2A01G395300 chr2A 100.000 4676 0 0 1 4676 646864094 646868769 0.000000e+00 8636.0
1 TraesCS2A01G395300 chr2B 94.435 1851 78 13 2060 3908 589090365 589092192 0.000000e+00 2824.0
2 TraesCS2A01G395300 chr2B 90.655 1252 64 16 851 2069 589089098 589090329 0.000000e+00 1615.0
3 TraesCS2A01G395300 chr2B 93.644 708 40 5 1 705 100331971 100331266 0.000000e+00 1053.0
4 TraesCS2A01G395300 chr2B 85.102 537 39 19 4172 4676 589097065 589097592 1.160000e-140 510.0
5 TraesCS2A01G395300 chr2B 88.514 148 7 6 3970 4109 589093084 589093229 2.240000e-38 171.0
6 TraesCS2A01G395300 chr2B 88.393 112 9 3 708 816 589088990 589089100 1.060000e-26 132.0
7 TraesCS2A01G395300 chr2B 96.721 61 2 0 3906 3966 589092223 589092283 8.280000e-18 102.0
8 TraesCS2A01G395300 chr2D 90.914 1882 112 26 2060 3929 501669406 501671240 0.000000e+00 2473.0
9 TraesCS2A01G395300 chr2D 92.590 1255 48 17 822 2069 501668154 501669370 0.000000e+00 1760.0
10 TraesCS2A01G395300 chr2D 88.710 744 45 21 3965 4676 501671324 501672060 0.000000e+00 872.0
11 TraesCS2A01G395300 chr2D 89.381 113 6 5 711 820 501667174 501667283 2.270000e-28 137.0
12 TraesCS2A01G395300 chr2D 100.000 47 0 0 3920 3966 501671248 501671294 2.320000e-13 87.9
13 TraesCS2A01G395300 chr4A 95.775 710 29 1 1 709 140850320 140851029 0.000000e+00 1144.0
14 TraesCS2A01G395300 chr4A 95.050 707 32 2 1 707 596752197 596751494 0.000000e+00 1109.0
15 TraesCS2A01G395300 chr3D 95.621 708 25 5 1 707 309767421 309766719 0.000000e+00 1131.0
16 TraesCS2A01G395300 chr5A 93.961 712 40 3 1 710 568626644 568627354 0.000000e+00 1074.0
17 TraesCS2A01G395300 chr5A 92.907 719 44 6 1 717 680199743 680199030 0.000000e+00 1038.0
18 TraesCS2A01G395300 chr3B 93.484 706 40 5 1 705 166331725 166331025 0.000000e+00 1044.0
19 TraesCS2A01G395300 chr3A 93.343 706 43 3 1 705 749614073 749613371 0.000000e+00 1040.0
20 TraesCS2A01G395300 chr7B 93.089 709 45 4 1 707 505477783 505478489 0.000000e+00 1035.0


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 TraesCS2A01G395300 chr2A 646864094 646868769 4675 False 8636.000000 8636 100.000000 1 4676 1 chr2A.!!$F1 4675
1 TraesCS2A01G395300 chr2B 100331266 100331971 705 True 1053.000000 1053 93.644000 1 705 1 chr2B.!!$R1 704
2 TraesCS2A01G395300 chr2B 589088990 589097592 8602 False 892.333333 2824 90.636667 708 4676 6 chr2B.!!$F1 3968
3 TraesCS2A01G395300 chr2D 501667174 501672060 4886 False 1065.980000 2473 92.319000 711 4676 5 chr2D.!!$F1 3965
4 TraesCS2A01G395300 chr4A 140850320 140851029 709 False 1144.000000 1144 95.775000 1 709 1 chr4A.!!$F1 708
5 TraesCS2A01G395300 chr4A 596751494 596752197 703 True 1109.000000 1109 95.050000 1 707 1 chr4A.!!$R1 706
6 TraesCS2A01G395300 chr3D 309766719 309767421 702 True 1131.000000 1131 95.621000 1 707 1 chr3D.!!$R1 706
7 TraesCS2A01G395300 chr5A 568626644 568627354 710 False 1074.000000 1074 93.961000 1 710 1 chr5A.!!$F1 709
8 TraesCS2A01G395300 chr5A 680199030 680199743 713 True 1038.000000 1038 92.907000 1 717 1 chr5A.!!$R1 716
9 TraesCS2A01G395300 chr3B 166331025 166331725 700 True 1044.000000 1044 93.484000 1 705 1 chr3B.!!$R1 704
10 TraesCS2A01G395300 chr3A 749613371 749614073 702 True 1040.000000 1040 93.343000 1 705 1 chr3A.!!$R1 704
11 TraesCS2A01G395300 chr7B 505477783 505478489 706 False 1035.000000 1035 93.089000 1 707 1 chr7B.!!$F1 706

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
962 1975 1.035139 ATTCATTGCCCATTCGCCTC 58.965 50.0 0.00 0.00 0.00 4.70 F
1771 2798 0.096976 GAACGGACATTGTCATGCCG 59.903 55.0 18.09 14.72 46.76 5.69 F
3386 4481 0.031178 CACTCCCTGCTTGTTTGTGC 59.969 55.0 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2975 1.073284 ACTGGCAAACTGACCCGTAAT 59.927 47.619 0.00 0.0 0.00 1.89 R
3673 4769 0.032540 CAGCAAAGCTCACCCCAAAC 59.967 55.000 0.00 0.0 36.40 2.93 R
4318 10057 0.542333 GTAGGCCTTTCCACTCCTCC 59.458 60.000 12.58 0.0 37.29 4.30 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
508 552 2.097825 GAGTAGGTGTAGGCCGAAGAA 58.902 52.381 0.00 0.00 0.00 2.52
509 553 2.694109 GAGTAGGTGTAGGCCGAAGAAT 59.306 50.000 0.00 0.00 0.00 2.40
555 686 2.549064 AAGTCCTTTTTGGCCAATGC 57.451 45.000 21.26 6.20 35.26 3.56
760 892 3.048337 AGAAAATTACCAGGTTCGCGA 57.952 42.857 3.71 3.71 0.00 5.87
772 904 5.408604 ACCAGGTTCGCGATATCATAATTTC 59.591 40.000 10.88 0.00 0.00 2.17
779 911 8.612619 GTTCGCGATATCATAATTTCCCATAAT 58.387 33.333 10.88 0.00 0.00 1.28
794 926 8.537728 TTTCCCATAATGTCAGATTTATGCTT 57.462 30.769 9.22 0.00 35.44 3.91
795 927 9.639563 TTTCCCATAATGTCAGATTTATGCTTA 57.360 29.630 9.22 0.00 35.44 3.09
957 1970 4.379813 CGCTGGTATATTCATTGCCCATTC 60.380 45.833 0.00 0.00 0.00 2.67
958 1971 4.379813 GCTGGTATATTCATTGCCCATTCG 60.380 45.833 0.00 0.00 0.00 3.34
959 1972 3.505680 TGGTATATTCATTGCCCATTCGC 59.494 43.478 0.00 0.00 0.00 4.70
960 1973 3.119495 GGTATATTCATTGCCCATTCGCC 60.119 47.826 0.00 0.00 0.00 5.54
961 1974 2.363306 TATTCATTGCCCATTCGCCT 57.637 45.000 0.00 0.00 0.00 5.52
962 1975 1.035139 ATTCATTGCCCATTCGCCTC 58.965 50.000 0.00 0.00 0.00 4.70
1091 2107 3.525545 GGCGACGACCTAGACCCC 61.526 72.222 0.00 0.00 0.00 4.95
1092 2108 3.885521 GCGACGACCTAGACCCCG 61.886 72.222 0.00 0.00 0.00 5.73
1093 2109 3.207669 CGACGACCTAGACCCCGG 61.208 72.222 0.00 0.00 0.00 5.73
1094 2110 3.525545 GACGACCTAGACCCCGGC 61.526 72.222 0.00 0.00 0.00 6.13
1227 2243 1.141234 GCACCACGACCTAGCTACC 59.859 63.158 0.00 0.00 0.00 3.18
1263 2279 6.017934 GCCCAATTTTCTTTGTTTCTTTCTCC 60.018 38.462 0.00 0.00 0.00 3.71
1304 2320 1.303643 GGACACTGGGGCTTCTTGG 60.304 63.158 0.00 0.00 0.00 3.61
1307 2323 1.975407 CACTGGGGCTTCTTGGCTG 60.975 63.158 0.00 0.00 41.48 4.85
1361 2377 3.386543 GGATGGGTCCGTCAATCTG 57.613 57.895 10.95 0.00 34.13 2.90
1365 2381 0.107703 TGGGTCCGTCAATCTGATGC 60.108 55.000 0.00 0.00 32.19 3.91
1466 2483 4.269363 GGCTTGCAATTGTGATAAATCTGC 59.731 41.667 7.40 0.00 0.00 4.26
1472 2489 5.575957 CAATTGTGATAAATCTGCGCTTCT 58.424 37.500 9.73 0.00 0.00 2.85
1478 2495 5.858581 GTGATAAATCTGCGCTTCTTGTTTT 59.141 36.000 9.73 1.91 0.00 2.43
1505 2522 2.002586 CTGAACCTGCTCGTGGTTATG 58.997 52.381 0.00 0.00 46.59 1.90
1507 2524 2.563620 TGAACCTGCTCGTGGTTATGTA 59.436 45.455 0.00 0.00 46.59 2.29
1520 2537 7.932335 TCGTGGTTATGTAGTTTGATTTTGTT 58.068 30.769 0.00 0.00 0.00 2.83
1529 2546 8.346476 TGTAGTTTGATTTTGTTACACATTGC 57.654 30.769 0.00 0.00 0.00 3.56
1539 2556 2.093306 TACACATTGCAACCCGAGAG 57.907 50.000 0.00 0.00 0.00 3.20
1586 2603 2.550830 TCTCTGAACCTCTTTGTGCC 57.449 50.000 0.00 0.00 0.00 5.01
1689 2716 4.451096 ACATTAGACGTTGGTAGCACAAAG 59.549 41.667 0.00 0.00 36.19 2.77
1708 2735 1.937924 GCCCTTGGCCCCTTCACTAT 61.938 60.000 0.00 0.00 44.06 2.12
1715 2742 0.457443 GCCCCTTCACTATTGCAAGC 59.543 55.000 4.94 0.00 0.00 4.01
1770 2797 1.164411 TGAACGGACATTGTCATGCC 58.836 50.000 18.09 0.85 33.68 4.40
1771 2798 0.096976 GAACGGACATTGTCATGCCG 59.903 55.000 18.09 14.72 46.76 5.69
1991 3030 4.821260 TCCGTGTCCCAAATTATGATGATG 59.179 41.667 0.00 0.00 0.00 3.07
2143 3227 7.148306 CGGTTGGCATAGTACTTTTATTGAAGT 60.148 37.037 0.00 0.00 42.27 3.01
2171 3255 4.785301 CATGACCACCTTATCAGGACATT 58.215 43.478 0.00 0.00 44.19 2.71
2204 3289 5.723672 TGACCTTGTTTGGTTGTAACAAA 57.276 34.783 0.00 0.00 42.87 2.83
2247 3332 6.426587 AGCATGACCAGATAATACCAAAGTT 58.573 36.000 0.00 0.00 0.00 2.66
2379 3464 9.918630 ATTCAATCCTCTCTTGTAAACATTTTG 57.081 29.630 0.00 0.00 0.00 2.44
2415 3500 2.026822 AGGCCAGACTGACAATTTCGAT 60.027 45.455 5.01 0.00 0.00 3.59
2494 3579 4.298332 CCGCTTTTACTGCTTCACAAATT 58.702 39.130 0.00 0.00 0.00 1.82
2498 3583 6.086765 CGCTTTTACTGCTTCACAAATTACAG 59.913 38.462 0.00 0.00 0.00 2.74
2525 3610 1.485124 ATGATGACCACGAGCCTACA 58.515 50.000 0.00 0.00 0.00 2.74
2714 3800 8.942338 ACTGAATTGAACTTTTCCCTTAAAAC 57.058 30.769 0.00 0.00 33.49 2.43
2825 3911 7.948357 TCTTTGTGTGTGAATAGTGTAGTACT 58.052 34.615 0.00 0.00 43.56 2.73
2828 3914 7.748691 TGTGTGTGAATAGTGTAGTACTACA 57.251 36.000 27.99 27.99 44.30 2.74
2829 3915 8.168790 TGTGTGTGAATAGTGTAGTACTACAA 57.831 34.615 32.02 20.70 46.33 2.41
2830 3916 8.799367 TGTGTGTGAATAGTGTAGTACTACAAT 58.201 33.333 31.61 31.61 46.33 2.71
2864 3950 2.036475 ACGACAGATTTGTGTGCTCTCT 59.964 45.455 0.00 0.00 37.76 3.10
2881 3967 2.445145 TCTCTAGCCTCTAGTCCATGCT 59.555 50.000 1.34 0.00 36.11 3.79
2994 4081 8.076910 TGCAATTTGATGATAATTACCCAACT 57.923 30.769 0.00 0.00 0.00 3.16
3106 4193 5.688176 GTGAGTGTAGACTGACTGAAACTTC 59.312 44.000 2.25 0.00 33.80 3.01
3159 4253 1.303309 CCCGCTGATCTTTCATGACC 58.697 55.000 0.00 0.00 0.00 4.02
3161 4255 1.938577 CCGCTGATCTTTCATGACCTG 59.061 52.381 0.00 0.00 0.00 4.00
3215 4310 1.750778 ACAGTGAAGCAGGTTTTGGTG 59.249 47.619 0.00 0.00 37.63 4.17
3249 4344 2.449464 TGCTTGATGACCCAAATCCTG 58.551 47.619 0.00 0.00 0.00 3.86
3351 4446 6.454715 GGCACGTCTCCTTTAGTTTTAATACG 60.455 42.308 0.00 0.00 0.00 3.06
3370 4465 1.337260 CGGCTGTGCTCTCTTAACACT 60.337 52.381 0.00 0.00 35.33 3.55
3376 4471 1.276421 TGCTCTCTTAACACTCCCTGC 59.724 52.381 0.00 0.00 0.00 4.85
3386 4481 0.031178 CACTCCCTGCTTGTTTGTGC 59.969 55.000 0.00 0.00 0.00 4.57
3422 4517 4.067896 ACATGCCAGAGTACAAGAACAAG 58.932 43.478 0.00 0.00 0.00 3.16
3473 4568 2.282820 GCGCATGTAGCTAAGTGAACTC 59.717 50.000 0.30 0.00 42.61 3.01
3493 4588 1.146358 GCGTCGGCTAGGCTTTAGTG 61.146 60.000 15.11 0.00 36.05 2.74
3509 4604 5.855395 GCTTTAGTGCTTGCATAATATCAGC 59.145 40.000 0.00 0.00 0.00 4.26
3520 4615 6.403333 GCATAATATCAGCATGCATTTTGG 57.597 37.500 21.98 5.18 43.59 3.28
3532 4627 4.162040 TGCATTTTGGTTTTGGTGGAAT 57.838 36.364 0.00 0.00 0.00 3.01
3556 4651 3.782244 CCAGAACTGCGCTGCGAC 61.782 66.667 28.07 17.26 32.06 5.19
3585 4680 2.346803 AGTTAGCGCAATGGTAGTGTG 58.653 47.619 11.47 0.00 0.00 3.82
3597 4692 3.018149 TGGTAGTGTGTTTGTTGGAACC 58.982 45.455 0.00 0.00 0.00 3.62
3618 4713 2.600792 CGCTGAACTGCACTTTTGAGTC 60.601 50.000 4.76 0.00 0.00 3.36
3637 4732 2.033662 GTCCATCTTCGCTACGAATTGC 60.034 50.000 2.55 0.00 44.85 3.56
3639 4734 2.609459 CCATCTTCGCTACGAATTGCTT 59.391 45.455 2.55 0.00 44.85 3.91
3656 4752 1.134491 GCTTCGGGCCTTCTAGCTTAA 60.134 52.381 0.84 0.00 34.27 1.85
3657 4753 2.679930 GCTTCGGGCCTTCTAGCTTAAA 60.680 50.000 0.84 0.00 34.27 1.52
3664 4760 4.279420 GGGCCTTCTAGCTTAAATCAATGG 59.721 45.833 0.84 0.00 0.00 3.16
3668 4764 6.238593 GCCTTCTAGCTTAAATCAATGGAGTG 60.239 42.308 0.00 0.00 0.00 3.51
3670 4766 7.201679 CCTTCTAGCTTAAATCAATGGAGTGTG 60.202 40.741 0.00 0.00 0.00 3.82
3671 4767 6.711277 TCTAGCTTAAATCAATGGAGTGTGT 58.289 36.000 0.00 0.00 0.00 3.72
3672 4768 7.847096 TCTAGCTTAAATCAATGGAGTGTGTA 58.153 34.615 0.00 0.00 0.00 2.90
3673 4769 6.992063 AGCTTAAATCAATGGAGTGTGTAG 57.008 37.500 0.00 0.00 0.00 2.74
3674 4770 6.476378 AGCTTAAATCAATGGAGTGTGTAGT 58.524 36.000 0.00 0.00 0.00 2.73
3675 4771 6.942576 AGCTTAAATCAATGGAGTGTGTAGTT 59.057 34.615 0.00 0.00 0.00 2.24
3676 4772 7.448469 AGCTTAAATCAATGGAGTGTGTAGTTT 59.552 33.333 0.00 0.00 0.00 2.66
3677 4773 7.538678 GCTTAAATCAATGGAGTGTGTAGTTTG 59.461 37.037 0.00 0.00 0.00 2.93
3756 4853 3.264450 CCAAGTGATTCCTCCTACCTTGT 59.736 47.826 0.00 0.00 0.00 3.16
3757 4854 4.508662 CAAGTGATTCCTCCTACCTTGTC 58.491 47.826 0.00 0.00 0.00 3.18
3758 4855 4.067944 AGTGATTCCTCCTACCTTGTCT 57.932 45.455 0.00 0.00 0.00 3.41
3759 4856 4.430441 AGTGATTCCTCCTACCTTGTCTT 58.570 43.478 0.00 0.00 0.00 3.01
3760 4857 4.223923 AGTGATTCCTCCTACCTTGTCTTG 59.776 45.833 0.00 0.00 0.00 3.02
3826 4923 1.015607 AAGTTAGGCGCGGGTTTACG 61.016 55.000 8.83 0.00 0.00 3.18
3854 4951 1.200716 TGCTCTTCCTGGTTACGTACG 59.799 52.381 15.01 15.01 0.00 3.67
3855 4952 1.468736 GCTCTTCCTGGTTACGTACGG 60.469 57.143 21.06 1.43 0.00 4.02
3913 5043 1.617947 CCCCAAAGGAGAGAGACCCG 61.618 65.000 0.00 0.00 38.24 5.28
4008 5959 4.507512 GGACAAGGAGAGGTGAAGGATTTT 60.508 45.833 0.00 0.00 0.00 1.82
4016 5967 4.006319 GAGGTGAAGGATTTTGTGAGGAG 58.994 47.826 0.00 0.00 0.00 3.69
4038 5997 8.865090 AGGAGAGATAAAACATACATACTCCTG 58.135 37.037 0.00 0.00 45.44 3.86
4112 9823 2.106683 GCTTCGGGTTCATGACGGG 61.107 63.158 0.00 0.00 0.00 5.28
4113 9824 1.594833 CTTCGGGTTCATGACGGGA 59.405 57.895 0.00 0.00 0.00 5.14
4115 9826 2.511600 CGGGTTCATGACGGGAGC 60.512 66.667 0.00 0.00 0.00 4.70
4149 9860 3.977244 CGCAAGTTGTGGGGGCAC 61.977 66.667 8.61 0.00 36.54 5.01
4208 9947 1.134670 GCAGTTCAGGGTAAGAGCGAT 60.135 52.381 0.00 0.00 0.00 4.58
4209 9948 2.815478 CAGTTCAGGGTAAGAGCGATC 58.185 52.381 0.00 0.00 0.00 3.69
4210 9949 2.166459 CAGTTCAGGGTAAGAGCGATCA 59.834 50.000 2.38 0.00 0.00 2.92
4264 10003 4.782019 TCTACCAAACCATCAATGCAAC 57.218 40.909 0.00 0.00 0.00 4.17
4294 10033 7.043656 GGACGTCTGAATTTAACCTTGTTTTTG 60.044 37.037 16.46 0.00 0.00 2.44
4409 10166 4.585619 GCTTACTTTGAGCTTAACCTCG 57.414 45.455 0.00 0.00 37.18 4.63
4448 10219 1.200948 GAAAGCACAATCCTGGCAGAC 59.799 52.381 17.94 0.00 0.00 3.51
4456 10227 1.949799 ATCCTGGCAGACACTCTTCT 58.050 50.000 17.94 0.00 0.00 2.85
4496 10269 6.213600 TCTGGTGAGAATCTTTAAGGTAGCTT 59.786 38.462 12.54 12.54 34.92 3.74
4497 10270 7.399191 TCTGGTGAGAATCTTTAAGGTAGCTTA 59.601 37.037 10.31 10.31 34.92 3.09
4498 10271 7.556844 TGGTGAGAATCTTTAAGGTAGCTTAG 58.443 38.462 13.71 6.33 34.92 2.18
4514 10287 4.923415 AGCTTAGTGGAAATAAGGCAAGT 58.077 39.130 0.00 0.00 44.12 3.16
4517 10290 3.525800 AGTGGAAATAAGGCAAGTGGT 57.474 42.857 0.00 0.00 0.00 4.16
4555 10328 3.056536 GCCTTTCCAAGTTTCCAGATTCC 60.057 47.826 0.00 0.00 0.00 3.01
4641 10414 1.000938 CTGCCAAACAACTCCAAGCTC 60.001 52.381 0.00 0.00 0.00 4.09
4667 10440 2.233654 CCTTGATCGCTTCGCCTCG 61.234 63.158 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
483 498 2.507058 TCGGCCTACACCTACTCTTCTA 59.493 50.000 0.00 0.00 0.00 2.10
486 501 2.100989 CTTCGGCCTACACCTACTCTT 58.899 52.381 0.00 0.00 0.00 2.85
491 506 2.429610 GTCATTCTTCGGCCTACACCTA 59.570 50.000 0.00 0.00 0.00 3.08
498 542 2.616510 CCAAAGAGTCATTCTTCGGCCT 60.617 50.000 0.00 0.00 45.41 5.19
508 552 3.007182 CCAACAATTGGCCAAAGAGTCAT 59.993 43.478 24.71 0.00 45.17 3.06
509 553 2.364970 CCAACAATTGGCCAAAGAGTCA 59.635 45.455 24.71 0.00 45.17 3.41
553 684 1.398692 AAAGACTTTTCGGCCAAGCA 58.601 45.000 2.24 0.00 0.00 3.91
752 884 4.693566 TGGGAAATTATGATATCGCGAACC 59.306 41.667 15.24 5.80 0.00 3.62
806 940 7.452813 AGCCCTTGTTAAGAAAGAAATCTGATT 59.547 33.333 0.00 0.00 0.00 2.57
816 950 8.576442 TGATTTAAGAAGCCCTTGTTAAGAAAG 58.424 33.333 9.40 0.00 38.79 2.62
819 953 8.472007 TTTGATTTAAGAAGCCCTTGTTAAGA 57.528 30.769 9.40 4.04 38.79 2.10
820 954 8.576442 TCTTTGATTTAAGAAGCCCTTGTTAAG 58.424 33.333 9.40 1.85 38.79 1.85
821 955 8.357402 GTCTTTGATTTAAGAAGCCCTTGTTAA 58.643 33.333 6.34 6.34 36.79 2.01
822 956 7.724061 AGTCTTTGATTTAAGAAGCCCTTGTTA 59.276 33.333 0.00 0.00 36.01 2.41
825 959 6.581171 AGTCTTTGATTTAAGAAGCCCTTG 57.419 37.500 0.00 0.00 36.01 3.61
826 960 7.603180 AAAGTCTTTGATTTAAGAAGCCCTT 57.397 32.000 0.00 0.00 36.01 3.95
827 961 7.603180 AAAAGTCTTTGATTTAAGAAGCCCT 57.397 32.000 0.00 0.00 36.01 5.19
938 1951 3.119495 GGCGAATGGGCAATGAATATACC 60.119 47.826 0.00 0.00 41.77 2.73
978 1991 1.172180 TTGCCTCTTTGGTTCGGCTG 61.172 55.000 0.00 0.00 42.90 4.85
1055 2071 2.445438 GCCGCTTCGTCTTCTTCCG 61.445 63.158 0.00 0.00 0.00 4.30
1110 2126 1.021390 CATCCAGGCTCCAACACGAC 61.021 60.000 0.00 0.00 0.00 4.34
1227 2243 4.383173 AGAAAATTGGGCAAAGAAAGCAG 58.617 39.130 0.00 0.00 0.00 4.24
1263 2279 2.572191 TTACCACTTGCGTAGATCCG 57.428 50.000 0.00 0.00 0.00 4.18
1292 2308 0.827507 GAAACAGCCAAGAAGCCCCA 60.828 55.000 0.00 0.00 0.00 4.96
1304 2320 1.576421 CACGAAGCCCTGAAACAGC 59.424 57.895 0.00 0.00 0.00 4.40
1307 2323 2.954611 GCCACGAAGCCCTGAAAC 59.045 61.111 0.00 0.00 0.00 2.78
1365 2381 2.887568 GATGACGCACCGCCAGAG 60.888 66.667 0.00 0.00 0.00 3.35
1438 2454 2.023223 CACAATTGCAAGCCACGGC 61.023 57.895 4.94 0.00 42.33 5.68
1445 2461 4.027132 GCGCAGATTTATCACAATTGCAAG 60.027 41.667 4.94 0.00 0.00 4.01
1466 2483 4.908736 TCAGAGAAACAAAACAAGAAGCG 58.091 39.130 0.00 0.00 0.00 4.68
1472 2489 4.462483 AGCAGGTTCAGAGAAACAAAACAA 59.538 37.500 0.00 0.00 0.00 2.83
1478 2495 1.412710 ACGAGCAGGTTCAGAGAAACA 59.587 47.619 0.00 0.00 0.00 2.83
1520 2537 1.621317 TCTCTCGGGTTGCAATGTGTA 59.379 47.619 0.59 0.00 0.00 2.90
1539 2556 7.336427 ACTCTGAGAAAATCATGGTGAGATTTC 59.664 37.037 12.44 10.55 42.98 2.17
1708 2735 4.651585 GCAATGTTCCGCTTGCAA 57.348 50.000 0.00 0.00 45.50 4.08
1715 2742 5.159925 TCAACAACAATATGCAATGTTCCG 58.840 37.500 11.56 6.20 37.66 4.30
1942 2969 5.104859 TGGCAAACTGACCCGTAATAAGATA 60.105 40.000 0.00 0.00 0.00 1.98
1946 2973 3.244630 ACTGGCAAACTGACCCGTAATAA 60.245 43.478 0.00 0.00 0.00 1.40
1947 2974 2.303600 ACTGGCAAACTGACCCGTAATA 59.696 45.455 0.00 0.00 0.00 0.98
1948 2975 1.073284 ACTGGCAAACTGACCCGTAAT 59.927 47.619 0.00 0.00 0.00 1.89
2143 3227 5.045213 TCCTGATAAGGTGGTCATGCTAAAA 60.045 40.000 0.00 0.00 0.00 1.52
2171 3255 4.297510 CAAACAAGGTCAATCGAAATGCA 58.702 39.130 0.00 0.00 0.00 3.96
2204 3289 2.472029 CTTCTGTCCTGTATGGGGTCT 58.528 52.381 0.00 0.00 36.20 3.85
2247 3332 3.130869 GCAGTGCACCATTCCATATTCAA 59.869 43.478 14.63 0.00 0.00 2.69
2356 3441 9.748708 TTTCAAAATGTTTACAAGAGAGGATTG 57.251 29.630 0.00 0.00 0.00 2.67
2379 3464 5.649831 AGTCTGGCCTTGAGAATAACATTTC 59.350 40.000 3.32 0.00 0.00 2.17
2441 3526 7.325338 CACAAACAAAGACAGCAGAATATTGAG 59.675 37.037 0.00 0.00 0.00 3.02
2494 3579 6.635755 TCGTGGTCATCATTATTGAACTGTA 58.364 36.000 0.00 0.00 34.96 2.74
2498 3583 4.260784 GGCTCGTGGTCATCATTATTGAAC 60.261 45.833 0.00 0.00 34.96 3.18
2525 3610 5.316167 TGCATGACTAGAATGAAACAGGTT 58.684 37.500 12.47 0.00 0.00 3.50
2714 3800 4.941263 TGTCTGTTTCGAATTTCATAGGGG 59.059 41.667 0.00 0.00 0.00 4.79
2864 3950 2.034878 CACAGCATGGACTAGAGGCTA 58.965 52.381 0.00 0.00 43.62 3.93
2881 3967 2.908688 TCAGTTTGCTGAGCTACACA 57.091 45.000 5.83 0.00 45.94 3.72
2901 3987 7.924103 AACAAAGTTATTGCGTTAGAAAAGG 57.076 32.000 0.00 0.00 0.00 3.11
3106 4193 1.310933 GCAGACACATGCTGGAAGGG 61.311 60.000 0.00 0.00 43.07 3.95
3215 4310 1.000396 AAGCAACTCCTGGATGCCC 60.000 57.895 16.59 0.00 40.93 5.36
3249 4344 1.485838 CGATGCTGTGCGGATGAGTC 61.486 60.000 0.00 0.00 0.00 3.36
3275 4370 7.381678 CGGGAGATAACCTTTTTATAGAGTTCG 59.618 40.741 0.00 0.00 0.00 3.95
3298 4393 5.476614 AGTTAAGCAAGTTCTAGTTACGGG 58.523 41.667 0.00 0.00 0.00 5.28
3351 4446 2.342179 GAGTGTTAAGAGAGCACAGCC 58.658 52.381 0.00 0.00 35.75 4.85
3370 4465 1.108727 CAGGCACAAACAAGCAGGGA 61.109 55.000 0.00 0.00 0.00 4.20
3376 4471 1.262151 GCAAATGCAGGCACAAACAAG 59.738 47.619 0.00 0.00 41.59 3.16
3415 4510 0.034059 CTGCTCACGGACCTTGTTCT 59.966 55.000 0.00 0.00 0.00 3.01
3422 4517 4.329545 TTGGCCTGCTCACGGACC 62.330 66.667 3.32 0.00 0.00 4.46
3473 4568 1.944676 CTAAAGCCTAGCCGACGCG 60.945 63.158 3.53 3.53 41.18 6.01
3509 4604 3.474600 TCCACCAAAACCAAAATGCATG 58.525 40.909 0.00 0.00 0.00 4.06
3518 4613 3.386402 GGACTTCAATTCCACCAAAACCA 59.614 43.478 0.00 0.00 32.82 3.67
3520 4615 4.340950 TCTGGACTTCAATTCCACCAAAAC 59.659 41.667 0.00 0.00 38.28 2.43
3532 4627 0.106708 AGCGCAGTTCTGGACTTCAA 59.893 50.000 11.47 0.00 36.10 2.69
3585 4680 1.404035 AGTTCAGCGGTTCCAACAAAC 59.596 47.619 4.26 0.00 0.00 2.93
3597 4692 1.331756 ACTCAAAAGTGCAGTTCAGCG 59.668 47.619 7.36 1.06 37.31 5.18
3637 4732 2.981859 TTAAGCTAGAAGGCCCGAAG 57.018 50.000 0.00 0.00 0.00 3.79
3639 4734 2.769663 TGATTTAAGCTAGAAGGCCCGA 59.230 45.455 0.00 0.00 0.00 5.14
3647 4742 6.711277 ACACACTCCATTGATTTAAGCTAGA 58.289 36.000 0.00 0.00 0.00 2.43
3648 4743 6.992063 ACACACTCCATTGATTTAAGCTAG 57.008 37.500 0.00 0.00 0.00 3.42
3656 4752 4.766891 CCCAAACTACACACTCCATTGATT 59.233 41.667 0.00 0.00 0.00 2.57
3657 4753 4.335416 CCCAAACTACACACTCCATTGAT 58.665 43.478 0.00 0.00 0.00 2.57
3664 4760 2.767505 CTCACCCCAAACTACACACTC 58.232 52.381 0.00 0.00 0.00 3.51
3668 4764 2.271944 AAGCTCACCCCAAACTACAC 57.728 50.000 0.00 0.00 0.00 2.90
3670 4766 1.269723 GCAAAGCTCACCCCAAACTAC 59.730 52.381 0.00 0.00 0.00 2.73
3671 4767 1.144913 AGCAAAGCTCACCCCAAACTA 59.855 47.619 0.00 0.00 30.62 2.24
3672 4768 0.106015 AGCAAAGCTCACCCCAAACT 60.106 50.000 0.00 0.00 30.62 2.66
3673 4769 0.032540 CAGCAAAGCTCACCCCAAAC 59.967 55.000 0.00 0.00 36.40 2.93
3674 4770 0.106268 TCAGCAAAGCTCACCCCAAA 60.106 50.000 0.00 0.00 36.40 3.28
3675 4771 0.823356 GTCAGCAAAGCTCACCCCAA 60.823 55.000 0.00 0.00 36.40 4.12
3676 4772 1.228245 GTCAGCAAAGCTCACCCCA 60.228 57.895 0.00 0.00 36.40 4.96
3677 4773 1.973812 GGTCAGCAAAGCTCACCCC 60.974 63.158 0.06 0.00 44.11 4.95
3720 4817 6.659242 GGAATCACTTGGAAGAAAAGGATGTA 59.341 38.462 0.00 0.00 0.00 2.29
3756 4853 5.918426 TTCTTGCATGAATAATGGCAAGA 57.082 34.783 20.21 20.21 46.26 3.02
3757 4854 6.334989 TCTTTCTTGCATGAATAATGGCAAG 58.665 36.000 15.04 16.65 43.87 4.01
3758 4855 6.283544 TCTTTCTTGCATGAATAATGGCAA 57.716 33.333 15.04 0.00 36.71 4.52
3759 4856 5.918426 TCTTTCTTGCATGAATAATGGCA 57.082 34.783 15.04 0.00 36.71 4.92
3760 4857 5.694910 CCATCTTTCTTGCATGAATAATGGC 59.305 40.000 26.37 0.00 36.71 4.40
3826 4923 1.739562 CAGGAAGAGCAGCGTGGTC 60.740 63.158 8.52 8.52 44.62 4.02
3854 4951 0.759060 AACCCAGGCTTTGTTGACCC 60.759 55.000 0.00 0.00 0.00 4.46
3855 4952 1.989706 TAACCCAGGCTTTGTTGACC 58.010 50.000 8.31 0.00 0.00 4.02
3913 5043 5.449588 GCTATTTTTACTTCCCGGGCTTTAC 60.450 44.000 18.49 0.00 0.00 2.01
3996 5947 4.006319 CTCTCCTCACAAAATCCTTCACC 58.994 47.826 0.00 0.00 0.00 4.02
4008 5959 9.201989 AGTATGTATGTTTTATCTCTCCTCACA 57.798 33.333 0.00 0.00 0.00 3.58
4016 5967 9.988815 ATCACAGGAGTATGTATGTTTTATCTC 57.011 33.333 0.00 0.00 0.00 2.75
4038 5997 5.306532 ACAGTCTGAATTCAATGCATCAC 57.693 39.130 9.88 0.00 0.00 3.06
4112 9823 4.838486 CGGACGGACAGCTCGCTC 62.838 72.222 0.00 0.00 0.00 5.03
4208 9947 4.343814 TGCAATATCTCGGACCATACTTGA 59.656 41.667 0.00 0.00 0.00 3.02
4209 9948 4.631131 TGCAATATCTCGGACCATACTTG 58.369 43.478 0.00 0.00 0.00 3.16
4210 9949 4.955811 TGCAATATCTCGGACCATACTT 57.044 40.909 0.00 0.00 0.00 2.24
4264 10003 4.315803 AGGTTAAATTCAGACGTCCTGTG 58.684 43.478 13.01 4.25 43.38 3.66
4302 10041 1.834263 CCTCCGTCCCTTTCAGAAGAT 59.166 52.381 0.00 0.00 34.71 2.40
4318 10057 0.542333 GTAGGCCTTTCCACTCCTCC 59.458 60.000 12.58 0.00 37.29 4.30
4367 10124 3.058224 GCTTTACCGGCAGCTAATAATGG 60.058 47.826 12.54 0.00 32.87 3.16
4407 10164 9.419297 GCTTTCATATATAACAATCAGGTACGA 57.581 33.333 0.00 0.00 0.00 3.43
4496 10269 4.042311 TCACCACTTGCCTTATTTCCACTA 59.958 41.667 0.00 0.00 0.00 2.74
4497 10270 3.157087 CACCACTTGCCTTATTTCCACT 58.843 45.455 0.00 0.00 0.00 4.00
4498 10271 3.057526 GTCACCACTTGCCTTATTTCCAC 60.058 47.826 0.00 0.00 0.00 4.02
4514 10287 3.174987 CCACCCACCCAGTCACCA 61.175 66.667 0.00 0.00 0.00 4.17
4517 10290 3.884774 GCACCACCCACCCAGTCA 61.885 66.667 0.00 0.00 0.00 3.41
4521 10294 3.434179 AAAGGCACCACCCACCCA 61.434 61.111 0.00 0.00 40.58 4.51
4522 10295 2.600470 GAAAGGCACCACCCACCC 60.600 66.667 0.00 0.00 40.58 4.61
4523 10296 2.600470 GGAAAGGCACCACCCACC 60.600 66.667 0.00 0.00 40.58 4.61
4524 10297 1.456705 TTGGAAAGGCACCACCCAC 60.457 57.895 0.00 0.00 40.58 4.61
4555 10328 3.677121 CACTCTTCAGGAAATGTCTCACG 59.323 47.826 0.00 0.00 0.00 4.35
4611 10384 3.507622 AGTTGTTTGGCAGGAATTAGCTC 59.492 43.478 0.00 0.00 0.00 4.09
4641 10414 2.859273 AAGCGATCAAGGTCTGGCCG 62.859 60.000 0.00 0.00 43.70 6.13


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

AutoCloner maintained by Alex Coulton.