Multiple sequence alignment - TraesCS1A01G097200

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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 TraesCS1A01G097200 chr1A 100.000 5204 0 0 1 5204 93396707 93401910 0 9611
1 TraesCS1A01G097200 chr1B 89.650 1942 133 28 723 2623 155411357 155409443 0 2410
2 TraesCS1A01G097200 chr1B 90.217 1431 91 22 2623 4006 155409387 155407959 0 1821
3 TraesCS1A01G097200 chr1B 96.547 811 17 7 4397 5204 155407015 155406213 0 1332
4 TraesCS1A01G097200 chr1B 90.380 894 64 15 4004 4887 155407907 155407026 0 1155
5 TraesCS1A01G097200 chr1B 96.562 698 18 3 1 698 155412406 155411715 0 1151
6 TraesCS1A01G097200 chr1D 91.052 1531 111 16 1905 3417 97919114 97920636 0 2045
7 TraesCS1A01G097200 chr1D 95.775 1207 32 11 4004 5204 97921566 97922759 0 1929
8 TraesCS1A01G097200 chr1D 89.715 1157 53 25 730 1851 97917690 97918815 0 1417
9 TraesCS1A01G097200 chr1D 95.396 695 16 5 1 695 97916816 97917494 0 1092
10 TraesCS1A01G097200 chr1D 93.933 445 24 3 3511 3953 97920954 97921397 0 669


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 TraesCS1A01G097200 chr1A 93396707 93401910 5203 False 9611.0 9611 100.0000 1 5204 1 chr1A.!!$F1 5203
1 TraesCS1A01G097200 chr1B 155406213 155412406 6193 True 1573.8 2410 92.6712 1 5204 5 chr1B.!!$R1 5203
2 TraesCS1A01G097200 chr1D 97916816 97922759 5943 False 1430.4 2045 93.1742 1 5204 5 chr1D.!!$F1 5203

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
952 1289 1.464734 TGTGAGCCGACCTAGAAGAG 58.535 55.000 0.00 0.0 0.0 2.85 F
1661 2019 0.101219 CTCGGACTGCGATGACATCA 59.899 55.000 15.58 0.0 0.0 3.07 F
1870 2244 0.705842 TAAAAACCTACCCAGCCCCC 59.294 55.000 0.00 0.0 0.0 5.40 F
3394 4097 1.419762 TCACACCACCAGCACAATACT 59.580 47.619 0.00 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2222 0.705842 GGGGGCTGGGTAGGTTTTTA 59.294 55.000 0.0 0.0 0.00 1.52 R
3304 4006 1.375908 GGATGCGTTGCTCAGGTCA 60.376 57.895 0.0 0.0 0.00 4.02 R
3619 4546 1.470458 GGACGAATACGGGTCTCCAAC 60.470 57.143 0.0 0.0 44.46 3.77 R
4408 5461 0.538584 TGCTGCCTCTCTACCATGTG 59.461 55.000 0.0 0.0 0.00 3.21 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
249 250 3.452627 CAGGCTCCCTGTAGACAGTTTAT 59.547 47.826 8.78 0.00 45.82 1.40
250 251 4.649674 CAGGCTCCCTGTAGACAGTTTATA 59.350 45.833 8.78 0.00 45.82 0.98
297 298 3.019564 CCTGCCCATCTAGAAAACCTTG 58.980 50.000 0.00 0.00 0.00 3.61
343 344 9.141400 GAAAATCTAGACAGAAGAAACATACGT 57.859 33.333 0.00 0.00 33.50 3.57
401 402 1.828979 TGGGTGCGAATTTAAGTCCC 58.171 50.000 0.00 0.00 0.00 4.46
747 1081 2.099427 GAGGTACCTGGTTCAGACGATC 59.901 54.545 22.10 0.00 32.44 3.69
847 1184 3.119919 ACGTCGACTATTTCTTTCGAGCT 60.120 43.478 14.70 0.00 42.16 4.09
905 1242 7.500892 AGATCATATACGAGCCGAGAATCTTAT 59.499 37.037 0.00 0.00 0.00 1.73
952 1289 1.464734 TGTGAGCCGACCTAGAAGAG 58.535 55.000 0.00 0.00 0.00 2.85
1153 1492 4.489771 CGCCCAGGAATCCCGCTT 62.490 66.667 0.00 0.00 37.58 4.68
1367 1706 1.494824 GCGTTCGTTTGTAGGTCAGT 58.505 50.000 0.00 0.00 0.00 3.41
1422 1779 1.992557 TGAAATGGGCTCCACTTAGGT 59.007 47.619 0.00 0.00 35.80 3.08
1652 2010 1.592669 CCCTAATGCTCGGACTGCG 60.593 63.158 0.00 0.00 0.00 5.18
1661 2019 0.101219 CTCGGACTGCGATGACATCA 59.899 55.000 15.58 0.00 0.00 3.07
1701 2059 2.951457 TGCGATCGAAGGTACATCAA 57.049 45.000 21.57 0.00 0.00 2.57
1702 2060 2.809446 TGCGATCGAAGGTACATCAAG 58.191 47.619 21.57 0.00 0.00 3.02
1704 2062 2.809446 CGATCGAAGGTACATCAAGCA 58.191 47.619 10.26 0.00 0.00 3.91
1716 2075 1.048724 ATCAAGCAGCCGCCCTAGTA 61.049 55.000 0.00 0.00 39.83 1.82
1725 2084 1.336980 GCCGCCCTAGTAATCTACTGC 60.337 57.143 0.00 0.00 39.81 4.40
1726 2085 1.961394 CCGCCCTAGTAATCTACTGCA 59.039 52.381 0.00 0.00 39.81 4.41
1729 2089 4.219944 CCGCCCTAGTAATCTACTGCATTA 59.780 45.833 0.00 0.00 39.81 1.90
1772 2132 2.973694 TGCGTATTTACCAGTCCTCC 57.026 50.000 0.00 0.00 0.00 4.30
1792 2152 6.727231 TCCTCCTGTTAATCAGTTAGTTACCA 59.273 38.462 4.93 0.00 42.19 3.25
1795 2155 7.262772 TCCTGTTAATCAGTTAGTTACCATCG 58.737 38.462 4.93 0.00 42.19 3.84
1805 2165 6.018588 CAGTTAGTTACCATCGTCACAACAAA 60.019 38.462 0.00 0.00 0.00 2.83
1807 2167 3.246699 AGTTACCATCGTCACAACAAACG 59.753 43.478 0.00 0.00 40.17 3.60
1821 2192 5.034554 CAACAAACGATCTGTTGCTATGT 57.965 39.130 11.91 6.55 45.07 2.29
1824 2195 4.152402 ACAAACGATCTGTTGCTATGTGTC 59.848 41.667 0.00 0.00 40.84 3.67
1864 2235 5.163395 CCTGCAAAGTTTAAAAACCTACCCA 60.163 40.000 2.02 0.00 39.71 4.51
1865 2236 5.908341 TGCAAAGTTTAAAAACCTACCCAG 58.092 37.500 2.02 0.00 39.71 4.45
1870 2244 0.705842 TAAAAACCTACCCAGCCCCC 59.294 55.000 0.00 0.00 0.00 5.40
1900 2274 3.117171 GCAGGCGCTCTGTGTCTG 61.117 66.667 21.68 13.66 46.84 3.51
1902 2276 2.653702 AGGCGCTCTGTGTCTGAC 59.346 61.111 7.64 0.00 0.00 3.51
1912 2528 4.439426 GCTCTGTGTCTGACATAGGTGTAG 60.439 50.000 27.24 19.87 37.83 2.74
1915 2531 6.659824 TCTGTGTCTGACATAGGTGTAGATA 58.340 40.000 27.24 8.87 37.83 1.98
1949 2570 4.294523 GCATACGAGGTTGTGCCA 57.705 55.556 0.00 0.00 40.61 4.92
1954 2575 2.552599 TACGAGGTTGTGCCATGAAA 57.447 45.000 0.00 0.00 40.61 2.69
1957 2578 2.228822 ACGAGGTTGTGCCATGAAATTC 59.771 45.455 0.00 0.00 40.61 2.17
1970 2591 5.509501 GCCATGAAATTCAGTTGGAAGAACA 60.510 40.000 17.22 0.00 39.30 3.18
2092 2714 4.033932 TGTCGTGTTGATCTTCTGTTGTTG 59.966 41.667 0.00 0.00 0.00 3.33
2184 2806 3.054875 ACAGAGAGCCATGCACTGAATTA 60.055 43.478 5.35 0.00 33.57 1.40
2230 2852 4.760204 AGTAAGCACTATGGTTTGTTGGAC 59.240 41.667 0.00 0.00 39.08 4.02
2404 3027 2.134346 GCAAAAATGCACACGGTTGAT 58.866 42.857 0.00 0.00 34.41 2.57
2406 3029 3.002144 GCAAAAATGCACACGGTTGATTT 59.998 39.130 0.00 0.00 34.41 2.17
2430 3053 3.387962 TCATAGGGCAGAAGGAAGTCAT 58.612 45.455 0.00 0.00 0.00 3.06
2515 3139 8.899427 TGATGGTTCTTTATTTTTCAAATGCA 57.101 26.923 0.00 0.00 0.00 3.96
2542 3167 3.394674 TGATGAGGACGTGCAACTTTA 57.605 42.857 10.52 0.00 31.75 1.85
2581 3207 9.588096 AAGGGATTTGACTTCTTACAAAATAGT 57.412 29.630 0.00 0.00 39.01 2.12
2620 3246 3.766545 TCAGGCTTAGTTTGGCATTCTT 58.233 40.909 0.00 0.00 0.00 2.52
2644 3327 9.716507 CTTTGTATATTCTTTGGAACCATAACG 57.283 33.333 0.00 0.00 33.96 3.18
2650 3333 6.452494 TTCTTTGGAACCATAACGACAAAA 57.548 33.333 0.00 0.00 0.00 2.44
2681 3364 6.310711 GCTAGGATCGGTAAATATGTAACAGC 59.689 42.308 0.00 0.00 0.00 4.40
2688 3371 7.915508 TCGGTAAATATGTAACAGCAAAGATG 58.084 34.615 0.00 0.00 0.00 2.90
2751 3440 6.982141 CAGTGAAATATTCCATTTGGTCATGG 59.018 38.462 0.00 0.00 44.80 3.66
2764 3453 4.860802 TGGTCATGGTATTGACTGGATT 57.139 40.909 4.75 0.00 44.39 3.01
2846 3535 4.686191 ATCTGATGAGACTTCATGGGAC 57.314 45.455 0.00 0.00 44.01 4.46
2993 3682 9.710900 ATTCTTTCTATTTCATGGTTTGTTTCC 57.289 29.630 0.00 0.00 0.00 3.13
3026 3715 1.466856 TCTGCAGCATGGTCATTTCC 58.533 50.000 9.47 0.00 35.86 3.13
3084 3774 5.241728 AGAAAAGATTACTGTTGGCAGAACC 59.758 40.000 1.30 0.00 45.28 3.62
3088 3778 5.876357 AGATTACTGTTGGCAGAACCTTTA 58.124 37.500 1.30 0.00 45.28 1.85
3089 3779 6.485171 AGATTACTGTTGGCAGAACCTTTAT 58.515 36.000 1.30 0.00 45.28 1.40
3101 3791 6.294508 GGCAGAACCTTTATGCTTTTTAGTCA 60.295 38.462 5.58 0.00 39.88 3.41
3146 3838 8.768397 TGTTCATCTAGGGTGTGAAGTATAAAT 58.232 33.333 0.00 0.00 32.98 1.40
3212 3904 4.762289 AACATAAGTCCATGGGAGAGAC 57.238 45.455 13.02 1.61 29.39 3.36
3218 3910 2.110899 AGTCCATGGGAGAGACGGATAT 59.889 50.000 13.02 0.00 35.65 1.63
3257 3949 8.606830 AGGAAAGTACAGAATTATGGAAGAGTT 58.393 33.333 4.88 0.00 0.00 3.01
3394 4097 1.419762 TCACACCACCAGCACAATACT 59.580 47.619 0.00 0.00 0.00 2.12
3410 4113 6.634436 GCACAATACTGCTGAATAATGCTAAC 59.366 38.462 0.00 0.00 34.06 2.34
3431 4173 8.440833 GCTAACGAACTTGTTCATACTGTTAAT 58.559 33.333 13.05 0.00 33.32 1.40
3515 4257 5.704978 GTGGGGATGCAAAATAACATTTGTT 59.295 36.000 0.00 1.08 41.34 2.83
3577 4504 1.757574 CCATGCAACGTTTGTCTGTG 58.242 50.000 0.00 0.00 0.00 3.66
3631 4558 1.129058 AAGAACTGTTGGAGACCCGT 58.871 50.000 0.00 0.00 34.29 5.28
3773 4702 6.456795 TGTCTCACTGTGATACTATCCTTG 57.543 41.667 21.88 4.44 0.00 3.61
3786 4715 3.840666 ACTATCCTTGCAGAGAAACAGGA 59.159 43.478 3.59 3.59 0.00 3.86
3913 4842 5.405935 AATATTCAGTGCTTTGTTTCCCC 57.594 39.130 0.00 0.00 0.00 4.81
3914 4843 2.452600 TTCAGTGCTTTGTTTCCCCT 57.547 45.000 0.00 0.00 0.00 4.79
3933 4862 2.556114 CCTTTCTTGGAACAGCTCCCAT 60.556 50.000 0.37 0.00 44.69 4.00
3941 4886 1.956477 GAACAGCTCCCATTGTGTGTT 59.044 47.619 0.00 0.00 0.00 3.32
3987 4932 6.234177 AGGCTGTCCATTATTTGATAGCTAC 58.766 40.000 0.00 0.00 43.02 3.58
3995 4940 7.938490 TCCATTATTTGATAGCTACAATGCTGA 59.062 33.333 0.00 0.00 43.87 4.26
4071 5121 6.430000 CCCAGCTTGCTTAAAAGAGTAACTTA 59.570 38.462 0.00 0.00 37.93 2.24
4117 5167 1.484038 TGGCAGGCTTCACAAACTTT 58.516 45.000 0.00 0.00 0.00 2.66
4118 5168 1.408702 TGGCAGGCTTCACAAACTTTC 59.591 47.619 0.00 0.00 0.00 2.62
4135 5185 7.823799 ACAAACTTTCATGTTTCATTCTTTGGT 59.176 29.630 0.00 0.00 37.98 3.67
4229 5279 6.394025 TTTTACAGTTAAATCGCAACCCTT 57.606 33.333 0.00 0.00 0.00 3.95
4230 5280 3.915437 ACAGTTAAATCGCAACCCTTG 57.085 42.857 0.00 0.00 0.00 3.61
4231 5281 3.219281 ACAGTTAAATCGCAACCCTTGT 58.781 40.909 0.00 0.00 0.00 3.16
4232 5282 3.252458 ACAGTTAAATCGCAACCCTTGTC 59.748 43.478 0.00 0.00 0.00 3.18
4233 5283 3.252215 CAGTTAAATCGCAACCCTTGTCA 59.748 43.478 0.00 0.00 0.00 3.58
4234 5284 3.252458 AGTTAAATCGCAACCCTTGTCAC 59.748 43.478 0.00 0.00 0.00 3.67
4235 5285 1.686355 AAATCGCAACCCTTGTCACA 58.314 45.000 0.00 0.00 0.00 3.58
4236 5286 1.909700 AATCGCAACCCTTGTCACAT 58.090 45.000 0.00 0.00 0.00 3.21
4237 5287 2.779755 ATCGCAACCCTTGTCACATA 57.220 45.000 0.00 0.00 0.00 2.29
4238 5288 2.779755 TCGCAACCCTTGTCACATAT 57.220 45.000 0.00 0.00 0.00 1.78
4239 5289 2.355197 TCGCAACCCTTGTCACATATG 58.645 47.619 0.00 0.00 0.00 1.78
4240 5290 1.202177 CGCAACCCTTGTCACATATGC 60.202 52.381 1.58 0.00 0.00 3.14
4408 5461 2.082354 GCAAGAAGCAGACTACCGC 58.918 57.895 0.00 0.00 44.79 5.68
4518 6072 3.706086 TCCAACTCTGTATATGCTGAGCA 59.294 43.478 21.95 10.59 44.86 4.26
4901 6458 6.357367 ACAAACTCTGGACTAATCACAGTTT 58.643 36.000 0.00 0.00 33.22 2.66
4902 6459 6.260936 ACAAACTCTGGACTAATCACAGTTTG 59.739 38.462 17.11 17.11 43.95 2.93
4903 6460 5.808366 ACTCTGGACTAATCACAGTTTGA 57.192 39.130 0.00 0.00 39.11 2.69
4904 6461 5.788450 ACTCTGGACTAATCACAGTTTGAG 58.212 41.667 0.00 0.00 37.77 3.02
4906 6463 3.674997 TGGACTAATCACAGTTTGAGCC 58.325 45.455 0.00 0.00 37.77 4.70
4907 6464 3.327757 TGGACTAATCACAGTTTGAGCCT 59.672 43.478 0.00 0.00 37.77 4.58
4908 6465 4.530553 TGGACTAATCACAGTTTGAGCCTA 59.469 41.667 0.00 0.00 37.77 3.93
4910 6467 4.833390 ACTAATCACAGTTTGAGCCTACC 58.167 43.478 0.00 0.00 37.77 3.18
4912 6469 4.307032 AATCACAGTTTGAGCCTACCAT 57.693 40.909 0.00 0.00 37.77 3.55
4913 6470 3.057969 TCACAGTTTGAGCCTACCATG 57.942 47.619 0.00 0.00 0.00 3.66
4914 6471 2.637382 TCACAGTTTGAGCCTACCATGA 59.363 45.455 0.00 0.00 0.00 3.07
4915 6472 2.744202 CACAGTTTGAGCCTACCATGAC 59.256 50.000 0.00 0.00 0.00 3.06
4916 6473 2.371841 ACAGTTTGAGCCTACCATGACA 59.628 45.455 0.00 0.00 0.00 3.58
4917 6474 3.005554 CAGTTTGAGCCTACCATGACAG 58.994 50.000 0.00 0.00 0.00 3.51
4918 6475 2.906389 AGTTTGAGCCTACCATGACAGA 59.094 45.455 0.00 0.00 0.00 3.41
4919 6476 3.327757 AGTTTGAGCCTACCATGACAGAA 59.672 43.478 0.00 0.00 0.00 3.02
4920 6477 3.334583 TTGAGCCTACCATGACAGAAC 57.665 47.619 0.00 0.00 0.00 3.01
4994 6551 1.674651 GCACCTTCCCTTTCGGTCC 60.675 63.158 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 4.992951 AGCTTTTTGTTTGATGGCTGATTC 59.007 37.500 0.00 0.00 0.00 2.52
249 250 7.659799 CACGGTATCATGGGATTTAGTTGATTA 59.340 37.037 0.00 0.00 34.89 1.75
250 251 6.486657 CACGGTATCATGGGATTTAGTTGATT 59.513 38.462 0.00 0.00 34.89 2.57
343 344 2.093235 CCTGCAAAGGTTGTCCCAAAAA 60.093 45.455 0.00 0.00 34.66 1.94
640 641 0.458197 CTGCTCCGCTCTTGTCTGAG 60.458 60.000 0.00 0.00 37.16 3.35
665 666 2.507769 GTCTACGAAACCCGCCGG 60.508 66.667 0.00 0.00 43.32 6.13
719 720 2.040779 CCAGGTACCTCCTCCCCC 60.041 72.222 12.84 0.00 46.24 5.40
720 721 0.981801 GAACCAGGTACCTCCTCCCC 60.982 65.000 12.84 0.00 46.24 4.81
761 1095 1.227380 GCGGCAGATCGAGGACATT 60.227 57.895 0.00 0.00 0.00 2.71
762 1096 2.419198 GCGGCAGATCGAGGACAT 59.581 61.111 0.00 0.00 0.00 3.06
763 1097 3.838271 GGCGGCAGATCGAGGACA 61.838 66.667 3.07 0.00 0.00 4.02
764 1098 4.933064 CGGCGGCAGATCGAGGAC 62.933 72.222 10.53 0.00 0.00 3.85
905 1242 1.228429 CTTCCTTTTGGGCCGGTGA 60.228 57.895 1.90 0.00 40.87 4.02
952 1289 2.430694 GCTCTTCTCTTCCTCTTCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
983 1320 1.386533 CATCGCCATTCTTTGCCTCT 58.613 50.000 0.00 0.00 0.00 3.69
984 1321 0.383231 CCATCGCCATTCTTTGCCTC 59.617 55.000 0.00 0.00 0.00 4.70
987 1324 1.587088 CGCCATCGCCATTCTTTGC 60.587 57.895 0.00 0.00 0.00 3.68
988 1325 0.028505 CTCGCCATCGCCATTCTTTG 59.971 55.000 0.00 0.00 35.26 2.77
989 1326 1.097547 CCTCGCCATCGCCATTCTTT 61.098 55.000 0.00 0.00 35.26 2.52
1367 1706 6.327154 CAATGCAAGCAATCAGAGAACATTA 58.673 36.000 0.00 0.00 0.00 1.90
1422 1779 5.348724 GTCGTCTAATGCAAGAACAAGATCA 59.651 40.000 0.00 0.00 0.00 2.92
1652 2010 1.737838 TCGCCAAAGGTGATGTCATC 58.262 50.000 5.83 5.83 37.29 2.92
1676 2034 2.288579 TGTACCTTCGATCGCAAACAGT 60.289 45.455 11.09 4.42 0.00 3.55
1688 2046 1.009829 GGCTGCTTGATGTACCTTCG 58.990 55.000 0.00 0.00 0.00 3.79
1701 2059 0.760945 AGATTACTAGGGCGGCTGCT 60.761 55.000 18.85 0.00 42.25 4.24
1702 2060 0.966920 TAGATTACTAGGGCGGCTGC 59.033 55.000 9.72 9.72 41.71 5.25
1704 2062 2.240279 CAGTAGATTACTAGGGCGGCT 58.760 52.381 9.56 0.00 37.23 5.52
1750 2110 4.080526 AGGAGGACTGGTAAATACGCAAAT 60.081 41.667 0.00 0.00 0.00 2.32
1754 2114 2.822764 CAGGAGGACTGGTAAATACGC 58.177 52.381 0.00 0.00 43.70 4.42
1772 2132 7.758076 TGACGATGGTAACTAACTGATTAACAG 59.242 37.037 0.00 0.00 44.98 3.16
1805 2165 3.876274 AGACACATAGCAACAGATCGT 57.124 42.857 0.00 0.00 0.00 3.73
1807 2167 5.068460 AGGACTAGACACATAGCAACAGATC 59.932 44.000 0.00 0.00 0.00 2.75
1818 2178 3.134804 GGGCATGTAAGGACTAGACACAT 59.865 47.826 0.00 0.00 0.00 3.21
1821 2192 2.116238 GGGGCATGTAAGGACTAGACA 58.884 52.381 0.00 0.00 0.00 3.41
1824 2195 1.202698 GCAGGGGCATGTAAGGACTAG 60.203 57.143 0.00 0.00 40.72 2.57
1851 2222 0.705842 GGGGGCTGGGTAGGTTTTTA 59.294 55.000 0.00 0.00 0.00 1.52
1873 2247 3.339731 GCGCCTGCTTGTAACACA 58.660 55.556 0.00 0.00 38.39 3.72
1883 2257 3.117171 CAGACACAGAGCGCCTGC 61.117 66.667 21.16 5.23 46.81 4.85
1893 2267 6.321435 CCTTATCTACACCTATGTCAGACACA 59.679 42.308 5.05 0.00 40.48 3.72
1900 2274 9.530633 CAAGTAAACCTTATCTACACCTATGTC 57.469 37.037 0.00 0.00 40.48 3.06
1901 2275 9.043548 ACAAGTAAACCTTATCTACACCTATGT 57.956 33.333 0.00 0.00 43.30 2.29
1912 2528 8.333186 CGTATGCCTTTACAAGTAAACCTTATC 58.667 37.037 1.46 0.00 32.26 1.75
1915 2531 6.232692 TCGTATGCCTTTACAAGTAAACCTT 58.767 36.000 1.46 0.00 32.26 3.50
1930 2546 4.617875 GCACAACCTCGTATGCCT 57.382 55.556 0.00 0.00 31.71 4.75
1949 2570 7.668886 AGATCTGTTCTTCCAACTGAATTTCAT 59.331 33.333 0.00 0.00 33.06 2.57
1954 2575 7.830099 AAAAGATCTGTTCTTCCAACTGAAT 57.170 32.000 0.00 0.00 44.09 2.57
1957 2578 8.159344 ACTAAAAAGATCTGTTCTTCCAACTG 57.841 34.615 0.00 0.00 44.09 3.16
1970 2591 7.775561 ACCAAACACAGAAGACTAAAAAGATCT 59.224 33.333 0.00 0.00 0.00 2.75
2205 2827 6.428771 GTCCAACAAACCATAGTGCTTACTTA 59.571 38.462 0.00 0.00 0.00 2.24
2230 2852 1.676615 GCCCAAATGGTTGCTTGGATG 60.677 52.381 2.39 0.00 44.16 3.51
2260 2882 9.628500 ATTTATTGTATTCAAGTCCCCTTACTC 57.372 33.333 0.00 0.00 36.97 2.59
2300 2922 5.396436 CCACGTTAAATAGGTCTCCCTCAAT 60.396 44.000 0.00 0.00 41.45 2.57
2344 2966 0.974010 CCCACCTCAATGCCTGCATT 60.974 55.000 11.43 11.43 46.35 3.56
2359 2981 9.516314 GCATACTATTCTTCAAATTTAACCCAC 57.484 33.333 0.00 0.00 0.00 4.61
2391 3013 1.745653 TGAACAAATCAACCGTGTGCA 59.254 42.857 0.00 0.00 34.30 4.57
2404 3027 4.202567 ACTTCCTTCTGCCCTATGAACAAA 60.203 41.667 0.00 0.00 0.00 2.83
2406 3029 2.912956 ACTTCCTTCTGCCCTATGAACA 59.087 45.455 0.00 0.00 0.00 3.18
2430 3053 5.327732 AGATCAGGATTCTTGCTTTTGGAA 58.672 37.500 0.00 0.00 0.00 3.53
2515 3139 1.473965 GCACGTCCTCATCATGGTGAT 60.474 52.381 9.60 0.00 37.65 3.06
2527 3152 4.072131 ACAATGATAAAGTTGCACGTCCT 58.928 39.130 0.00 0.00 0.00 3.85
2581 3207 3.382227 CCTGAAGCATTTGCATGGATGTA 59.618 43.478 5.20 0.00 45.16 2.29
2620 3246 8.885722 GTCGTTATGGTTCCAAAGAATATACAA 58.114 33.333 0.00 0.00 33.67 2.41
2644 3327 6.619801 ACCGATCCTAGCATTTATTTTGTC 57.380 37.500 0.00 0.00 0.00 3.18
2672 3355 4.083110 GCTGTGACATCTTTGCTGTTACAT 60.083 41.667 1.89 0.00 40.79 2.29
2681 3364 3.696281 TGTTGTGCTGTGACATCTTTG 57.304 42.857 0.00 0.00 0.00 2.77
2688 3371 3.969117 TTTCAGATGTTGTGCTGTGAC 57.031 42.857 0.00 0.00 33.90 3.67
2751 3440 8.623903 TGCATAGAAATTGAATCCAGTCAATAC 58.376 33.333 2.84 1.93 45.42 1.89
2764 3453 7.394016 TCTTGTAACTCCTGCATAGAAATTGA 58.606 34.615 3.38 0.00 0.00 2.57
2846 3535 4.813697 GCAAAGACCTCAGGCTTAAGATAG 59.186 45.833 6.67 0.00 0.00 2.08
2964 3653 9.696917 AACAAACCATGAAATAGAAAGAATGTC 57.303 29.630 0.00 0.00 0.00 3.06
2993 3682 3.189910 TGCTGCAGAAGAACAAAGCTATG 59.810 43.478 20.43 0.00 0.00 2.23
3068 3757 4.217550 GCATAAAGGTTCTGCCAACAGTAA 59.782 41.667 0.00 0.00 44.77 2.24
3075 3765 4.953940 AAAAAGCATAAAGGTTCTGCCA 57.046 36.364 0.00 0.00 40.61 4.92
3084 3774 9.722056 AAAGCGATATGACTAAAAAGCATAAAG 57.278 29.630 0.00 0.00 0.00 1.85
3113 3805 5.958380 TCACACCCTAGATGAACACTTCTAT 59.042 40.000 0.00 0.00 0.00 1.98
3114 3806 5.330233 TCACACCCTAGATGAACACTTCTA 58.670 41.667 0.00 0.00 0.00 2.10
3122 3814 8.210946 CCATTTATACTTCACACCCTAGATGAA 58.789 37.037 0.00 0.00 0.00 2.57
3146 3838 4.343526 ACATCTTGCATAAAACCAACACCA 59.656 37.500 0.00 0.00 0.00 4.17
3205 3897 6.636562 TGAACTCTTAATATCCGTCTCTCC 57.363 41.667 0.00 0.00 0.00 3.71
3212 3904 9.765795 ACTTTCCTAATGAACTCTTAATATCCG 57.234 33.333 0.00 0.00 31.05 4.18
3257 3949 8.362464 TGCTAGATCTTTCCTAAGACAACTAA 57.638 34.615 0.00 0.00 42.91 2.24
3304 4006 1.375908 GGATGCGTTGCTCAGGTCA 60.376 57.895 0.00 0.00 0.00 4.02
3328 4030 2.743183 GCCGTGCTGAAGATAACCAGAT 60.743 50.000 0.00 0.00 32.37 2.90
3394 4097 5.411361 ACAAGTTCGTTAGCATTATTCAGCA 59.589 36.000 0.00 0.00 0.00 4.41
3410 4113 9.318041 CAAGAATTAACAGTATGAACAAGTTCG 57.682 33.333 8.28 0.00 42.28 3.95
3431 4173 2.238646 ACCTTCCTGTCACACACAAGAA 59.761 45.455 0.00 0.00 33.71 2.52
3515 4257 8.970020 AGCACAGGTTTTCAATTATTCATGATA 58.030 29.630 0.00 0.00 0.00 2.15
3577 4504 7.625553 CAACTATTTCTGAATCATCCTTCGAC 58.374 38.462 0.00 0.00 0.00 4.20
3619 4546 1.470458 GGACGAATACGGGTCTCCAAC 60.470 57.143 0.00 0.00 44.46 3.77
3631 4558 1.546923 TCTTGAACAGCCGGACGAATA 59.453 47.619 5.05 0.00 0.00 1.75
3773 4702 4.094146 GCTTCACTATTCCTGTTTCTCTGC 59.906 45.833 0.00 0.00 0.00 4.26
3786 4715 7.092716 CACCTTGCATTTTTAGCTTCACTATT 58.907 34.615 0.00 0.00 0.00 1.73
3933 4862 3.066760 TGAACACACACACAAACACACAA 59.933 39.130 0.00 0.00 0.00 3.33
3941 4886 4.837896 TTTTCACTGAACACACACACAA 57.162 36.364 0.00 0.00 0.00 3.33
3987 4932 8.837788 TGAATAGTACCAGATAATCAGCATTG 57.162 34.615 0.00 0.00 0.00 2.82
4024 5074 5.452356 GGGCATAAGAAGCAATAGCAATGTT 60.452 40.000 0.00 0.00 45.49 2.71
4025 5075 4.038402 GGGCATAAGAAGCAATAGCAATGT 59.962 41.667 0.00 0.00 45.49 2.71
4117 5167 6.303054 TCACCTACCAAAGAATGAAACATGA 58.697 36.000 0.00 0.00 0.00 3.07
4118 5168 6.573664 TCACCTACCAAAGAATGAAACATG 57.426 37.500 0.00 0.00 0.00 3.21
4135 5185 1.902508 CTGCTCCACTCCTTTCACCTA 59.097 52.381 0.00 0.00 0.00 3.08
4229 5279 3.008923 TCCCTGAACAAGCATATGTGACA 59.991 43.478 4.29 0.00 32.81 3.58
4230 5280 3.609853 TCCCTGAACAAGCATATGTGAC 58.390 45.455 4.29 0.00 32.81 3.67
4231 5281 3.998913 TCCCTGAACAAGCATATGTGA 57.001 42.857 4.29 0.00 32.81 3.58
4232 5282 4.380867 GGTTTCCCTGAACAAGCATATGTG 60.381 45.833 4.29 0.00 32.81 3.21
4233 5283 3.763897 GGTTTCCCTGAACAAGCATATGT 59.236 43.478 4.29 0.00 34.24 2.29
4234 5284 3.763360 TGGTTTCCCTGAACAAGCATATG 59.237 43.478 0.00 0.00 0.00 1.78
4235 5285 4.046286 TGGTTTCCCTGAACAAGCATAT 57.954 40.909 0.00 0.00 0.00 1.78
4236 5286 3.517296 TGGTTTCCCTGAACAAGCATA 57.483 42.857 0.00 0.00 0.00 3.14
4237 5287 2.380064 TGGTTTCCCTGAACAAGCAT 57.620 45.000 0.00 0.00 0.00 3.79
4238 5288 1.962807 CATGGTTTCCCTGAACAAGCA 59.037 47.619 0.00 0.00 0.00 3.91
4239 5289 1.337167 GCATGGTTTCCCTGAACAAGC 60.337 52.381 0.00 0.00 0.00 4.01
4240 5290 2.242043 AGCATGGTTTCCCTGAACAAG 58.758 47.619 0.00 0.00 0.00 3.16
4262 5312 3.507162 TTCTCCAGGACTTTTCATGCA 57.493 42.857 0.00 0.00 31.87 3.96
4346 5399 7.378181 ACAACCATCTAATCATCACAAAAACC 58.622 34.615 0.00 0.00 0.00 3.27
4405 5458 1.227380 GCCTCTCTACCATGTGCGG 60.227 63.158 0.00 0.00 0.00 5.69
4408 5461 0.538584 TGCTGCCTCTCTACCATGTG 59.461 55.000 0.00 0.00 0.00 3.21
4551 6107 4.644234 CACCATGAAATTACACCTGCCATA 59.356 41.667 0.00 0.00 0.00 2.74
4555 6111 2.825532 ACCACCATGAAATTACACCTGC 59.174 45.455 0.00 0.00 0.00 4.85
4901 6458 2.256306 TGTTCTGTCATGGTAGGCTCA 58.744 47.619 0.00 0.00 0.00 4.26
4902 6459 3.003480 GTTGTTCTGTCATGGTAGGCTC 58.997 50.000 0.00 0.00 0.00 4.70
4903 6460 2.371841 TGTTGTTCTGTCATGGTAGGCT 59.628 45.455 0.00 0.00 0.00 4.58
4904 6461 2.778299 TGTTGTTCTGTCATGGTAGGC 58.222 47.619 0.00 0.00 0.00 3.93
4906 6463 5.063944 GCTGTATGTTGTTCTGTCATGGTAG 59.936 44.000 0.00 0.00 0.00 3.18
4907 6464 4.935205 GCTGTATGTTGTTCTGTCATGGTA 59.065 41.667 0.00 0.00 0.00 3.25
4908 6465 3.753272 GCTGTATGTTGTTCTGTCATGGT 59.247 43.478 0.00 0.00 0.00 3.55
4910 6467 3.752747 TGGCTGTATGTTGTTCTGTCATG 59.247 43.478 0.00 0.00 0.00 3.07
4912 6469 3.138304 GTGGCTGTATGTTGTTCTGTCA 58.862 45.455 0.00 0.00 0.00 3.58
4913 6470 3.187227 CAGTGGCTGTATGTTGTTCTGTC 59.813 47.826 0.00 0.00 0.00 3.51
4914 6471 3.141398 CAGTGGCTGTATGTTGTTCTGT 58.859 45.455 0.00 0.00 0.00 3.41
4915 6472 3.187227 GTCAGTGGCTGTATGTTGTTCTG 59.813 47.826 0.00 0.00 32.61 3.02
4916 6473 3.403038 GTCAGTGGCTGTATGTTGTTCT 58.597 45.455 0.00 0.00 32.61 3.01
4917 6474 2.484264 GGTCAGTGGCTGTATGTTGTTC 59.516 50.000 0.00 0.00 32.61 3.18
4918 6475 2.158682 TGGTCAGTGGCTGTATGTTGTT 60.159 45.455 0.00 0.00 32.61 2.83
4919 6476 1.419762 TGGTCAGTGGCTGTATGTTGT 59.580 47.619 0.00 0.00 32.61 3.32
4920 6477 2.079158 CTGGTCAGTGGCTGTATGTTG 58.921 52.381 0.00 0.00 32.61 3.33
4994 6551 0.943835 TGTCAGTGTGTCGCATTCGG 60.944 55.000 0.00 0.00 36.13 4.30


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

AutoCloner maintained by Alex Coulton.