Multiple sequence alignment - TraesCS7A01G161600

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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 TraesCS7A01G161600 chr7A 100.000 4496 0 0 1 4496 118188447 118183952 0.000000e+00 8303.0
1 TraesCS7A01G161600 chr7D 95.296 4528 159 19 1 4496 112839585 112835080 0.000000e+00 7132.0
2 TraesCS7A01G161600 chr7D 84.871 813 108 10 1 805 112920970 112920165 0.000000e+00 806.0
3 TraesCS7A01G161600 chr7D 88.223 467 51 4 1 465 112892302 112891838 5.080000e-154 555.0
4 TraesCS7A01G161600 chr7D 78.388 583 114 9 2 576 631088431 631087853 7.110000e-98 368.0
5 TraesCS7A01G161600 chr7D 80.982 326 53 8 461 782 112879979 112879659 2.690000e-62 250.0
6 TraesCS7A01G161600 chr7B 94.326 3278 129 15 936 4160 72314393 72311120 0.000000e+00 4970.0
7 TraesCS7A01G161600 chr7B 88.168 262 27 3 4161 4420 683030302 683030043 4.370000e-80 309.0
8 TraesCS7A01G161600 chr7B 82.500 80 12 2 4194 4272 308688605 308688527 8.070000e-08 69.4
9 TraesCS7A01G161600 chr7B 78.788 99 15 6 4161 4257 616619157 616619251 1.350000e-05 62.1
10 TraesCS7A01G161600 chr3B 80.690 580 102 4 4 576 325826898 325826322 4.130000e-120 442.0
11 TraesCS7A01G161600 chr2D 80.103 583 104 8 2 576 330491414 330491992 1.500000e-114 424.0
12 TraesCS7A01G161600 chr2D 78.974 585 94 13 1 576 25635383 25635947 5.490000e-99 372.0
13 TraesCS7A01G161600 chr3D 79.452 584 108 8 1 576 520603687 520603108 1.950000e-108 403.0
14 TraesCS7A01G161600 chr4D 79.387 587 103 9 1 576 471708944 471709523 9.060000e-107 398.0
15 TraesCS7A01G161600 chr4B 87.948 307 31 4 4161 4464 368110897 368111200 1.540000e-94 357.0
16 TraesCS7A01G161600 chr4B 90.037 271 20 5 4227 4496 368110519 368110255 1.200000e-90 344.0
17 TraesCS7A01G161600 chr4B 78.143 517 103 5 3 512 278839490 278838977 2.020000e-83 320.0
18 TraesCS7A01G161600 chr6A 96.429 168 6 0 3982 4149 601624045 601624212 1.230000e-70 278.0
19 TraesCS7A01G161600 chr5A 96.429 168 6 0 3982 4149 19029945 19029778 1.230000e-70 278.0
20 TraesCS7A01G161600 chr4A 96.429 168 6 0 3982 4149 607647845 607647678 1.230000e-70 278.0
21 TraesCS7A01G161600 chr3A 96.429 168 6 0 3982 4149 38712018 38712185 1.230000e-70 278.0
22 TraesCS7A01G161600 chr3A 96.429 168 6 0 3982 4149 187898748 187898581 1.230000e-70 278.0
23 TraesCS7A01G161600 chr2A 96.429 168 6 0 3982 4149 224470719 224470552 1.230000e-70 278.0
24 TraesCS7A01G161600 chr1A 96.429 168 6 0 3982 4149 109013307 109013140 1.230000e-70 278.0
25 TraesCS7A01G161600 chr1D 81.498 227 36 6 4161 4385 347204946 347205168 9.940000e-42 182.0
26 TraesCS7A01G161600 chr2B 79.675 123 20 5 4161 4281 96944470 96944589 2.880000e-12 84.2
27 TraesCS7A01G161600 chr2B 80.460 87 15 2 4187 4272 691909292 691909207 1.040000e-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 TraesCS7A01G161600 chr7A 118183952 118188447 4495 True 8303 8303 100.000 1 4496 1 chr7A.!!$R1 4495
1 TraesCS7A01G161600 chr7D 112835080 112839585 4505 True 7132 7132 95.296 1 4496 1 chr7D.!!$R1 4495
2 TraesCS7A01G161600 chr7D 112920165 112920970 805 True 806 806 84.871 1 805 1 chr7D.!!$R4 804
3 TraesCS7A01G161600 chr7D 631087853 631088431 578 True 368 368 78.388 2 576 1 chr7D.!!$R5 574
4 TraesCS7A01G161600 chr7B 72311120 72314393 3273 True 4970 4970 94.326 936 4160 1 chr7B.!!$R1 3224
5 TraesCS7A01G161600 chr3B 325826322 325826898 576 True 442 442 80.690 4 576 1 chr3B.!!$R1 572
6 TraesCS7A01G161600 chr2D 330491414 330491992 578 False 424 424 80.103 2 576 1 chr2D.!!$F2 574
7 TraesCS7A01G161600 chr2D 25635383 25635947 564 False 372 372 78.974 1 576 1 chr2D.!!$F1 575
8 TraesCS7A01G161600 chr3D 520603108 520603687 579 True 403 403 79.452 1 576 1 chr3D.!!$R1 575
9 TraesCS7A01G161600 chr4D 471708944 471709523 579 False 398 398 79.387 1 576 1 chr4D.!!$F1 575
10 TraesCS7A01G161600 chr4B 278838977 278839490 513 True 320 320 78.143 3 512 1 chr4B.!!$R1 509

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
888 903 0.036388 GTCCCATCTTCAAGCGACCA 60.036 55.000 0.0 0.0 0.0 4.02 F
889 904 0.690192 TCCCATCTTCAAGCGACCAA 59.310 50.000 0.0 0.0 0.0 3.67 F
890 905 1.073125 TCCCATCTTCAAGCGACCAAA 59.927 47.619 0.0 0.0 0.0 3.28 F
1808 1823 0.681243 GGGAGGATGGAAGTGTTGGC 60.681 60.000 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1704 0.106819 AACCATGCTGGCTCATCCTC 60.107 55.0 2.5 0.0 42.67 3.71 R
1808 1823 0.248825 CTTCTCACTCGGCCTCATCG 60.249 60.0 0.0 0.0 0.00 3.84 R
2082 2097 0.688487 TAAACGGGCTAACAGTGGCT 59.312 50.0 0.0 0.0 0.00 4.75 R
3517 3535 0.621082 AAGGGCTTCCTGGTTAGAGC 59.379 55.0 0.0 0.0 40.74 4.09 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
112 114 0.892755 TCAACTTGACGCCGGATAGT 59.107 50.000 5.05 0.17 0.00 2.12
123 125 4.645535 ACGCCGGATAGTAGAACTATGTA 58.354 43.478 5.05 0.00 41.21 2.29
153 155 7.345653 AGAAATCATCAATACTAGAGTCACCCA 59.654 37.037 0.00 0.00 0.00 4.51
195 204 8.546322 AGATCACATACATGTATAAGGCATCAT 58.454 33.333 17.86 3.51 39.39 2.45
199 208 7.605309 CACATACATGTATAAGGCATCATCAGT 59.395 37.037 17.86 4.67 39.39 3.41
265 274 2.852130 AGGAAGGCCTAGGAACTCAAT 58.148 47.619 14.75 0.00 44.74 2.57
453 462 3.056313 GCTGCATCCTTCGCAACCC 62.056 63.158 0.00 0.00 39.30 4.11
540 549 1.553690 CGGACAAGGGACCTCACCAT 61.554 60.000 0.00 0.00 0.00 3.55
544 553 3.245122 GGACAAGGGACCTCACCATAAAA 60.245 47.826 0.00 0.00 0.00 1.52
588 597 3.002791 CGCATATGATTTCGGTGGCTAT 58.997 45.455 6.97 0.00 0.00 2.97
594 603 0.178068 ATTTCGGTGGCTATGCTCGT 59.822 50.000 0.00 0.00 0.00 4.18
597 606 2.805546 GGTGGCTATGCTCGTCGA 59.194 61.111 0.00 0.00 0.00 4.20
629 638 1.139853 GGAGGGAGAGCGATTTGTCAT 59.860 52.381 0.00 0.00 0.00 3.06
630 639 2.478831 GAGGGAGAGCGATTTGTCATC 58.521 52.381 0.00 0.00 0.00 2.92
668 677 2.036604 GGCGGAGGAGGATAAGAGAAAG 59.963 54.545 0.00 0.00 0.00 2.62
673 682 4.587262 GGAGGAGGATAAGAGAAAGAGGAC 59.413 50.000 0.00 0.00 0.00 3.85
677 688 3.052793 AGGATAAGAGAAAGAGGACGGGA 60.053 47.826 0.00 0.00 0.00 5.14
739 751 2.125391 GGCGGTTTACGGGTCTCC 60.125 66.667 0.00 0.00 44.51 3.71
753 765 4.248058 CGGGTCTCCTGTAAACGTTTTAT 58.752 43.478 20.19 0.00 0.00 1.40
784 796 0.320946 TTTTTAGCGGACCTGGTCGG 60.321 55.000 25.18 25.18 36.25 4.79
816 831 1.078759 GAGTGTCCAGTGAATCCGCG 61.079 60.000 0.00 0.00 0.00 6.46
817 832 2.100631 GTGTCCAGTGAATCCGCGG 61.101 63.158 22.12 22.12 0.00 6.46
823 838 0.878416 CAGTGAATCCGCGGGAAAAA 59.122 50.000 27.83 5.39 34.34 1.94
849 864 1.077805 TGGCGACCCCAGAGAGTTA 59.922 57.895 0.00 0.00 39.18 2.24
866 881 1.988467 GTTACTCTAACCACCGTTCGC 59.012 52.381 0.00 0.00 33.17 4.70
887 902 0.250513 AGTCCCATCTTCAAGCGACC 59.749 55.000 0.00 0.00 0.00 4.79
888 903 0.036388 GTCCCATCTTCAAGCGACCA 60.036 55.000 0.00 0.00 0.00 4.02
889 904 0.690192 TCCCATCTTCAAGCGACCAA 59.310 50.000 0.00 0.00 0.00 3.67
890 905 1.073125 TCCCATCTTCAAGCGACCAAA 59.927 47.619 0.00 0.00 0.00 3.28
958 973 2.202440 CCGACAGCGTAGTGTCCG 60.202 66.667 8.51 5.06 43.45 4.79
975 990 4.821589 GCCTTCCGCCTCCACTCG 62.822 72.222 0.00 0.00 0.00 4.18
986 1001 1.078759 CTCCACTCGGCTGCGTAAAG 61.079 60.000 0.00 0.00 0.00 1.85
1011 1026 2.026879 GTCTCGATGGCTCTCCGC 59.973 66.667 0.00 0.00 38.13 5.54
1043 1058 1.139947 CGTCCTCGCCTTCCTTCTC 59.860 63.158 0.00 0.00 0.00 2.87
1585 1600 2.519541 CGAGGCTCCGGGAGATGA 60.520 66.667 27.95 0.00 0.00 2.92
1591 1606 1.750930 CTCCGGGAGATGATGGTGG 59.249 63.158 19.57 0.00 0.00 4.61
1592 1607 2.111878 CCGGGAGATGATGGTGGC 59.888 66.667 0.00 0.00 0.00 5.01
1599 1614 3.203546 GATGATGGTGGCATGCGGC 62.204 63.158 12.44 6.59 43.74 6.53
1614 1629 1.226974 CGGCGATGGAAGTGTCGAT 60.227 57.895 0.00 0.00 40.11 3.59
1639 1654 2.363018 CCCTCACCTCGCTCCTGA 60.363 66.667 0.00 0.00 0.00 3.86
1689 1704 2.935955 GCCAACGACGTGTTCCAG 59.064 61.111 0.00 0.00 39.29 3.86
1808 1823 0.681243 GGGAGGATGGAAGTGTTGGC 60.681 60.000 0.00 0.00 0.00 4.52
1903 1918 5.336213 GCCATTGAGATGTTTGACAAGATGT 60.336 40.000 0.00 0.00 0.00 3.06
1941 1956 1.472480 GCTGATTTGCCAATGTACGGT 59.528 47.619 0.00 0.00 0.00 4.83
1983 1998 3.056607 GCAGGCAGAAGCAAATAGGAAAA 60.057 43.478 0.00 0.00 44.61 2.29
1987 2002 3.174375 CAGAAGCAAATAGGAAAAGCGC 58.826 45.455 0.00 0.00 0.00 5.92
2037 2052 1.056660 AGGTTGTTCCTGATGTCCGT 58.943 50.000 0.00 0.00 46.19 4.69
2080 2095 6.126681 TGAGGCTTTCATTCATGAAGGAGATA 60.127 38.462 20.81 10.97 46.34 1.98
2082 2097 7.982252 AGGCTTTCATTCATGAAGGAGATATA 58.018 34.615 20.81 5.23 46.34 0.86
2087 2102 6.705302 TCATTCATGAAGGAGATATAGCCAC 58.295 40.000 18.33 0.00 33.08 5.01
2092 2107 6.782494 TCATGAAGGAGATATAGCCACTGTTA 59.218 38.462 0.00 0.00 0.00 2.41
2115 2130 3.555547 GCCCGTTTATCAATGAAAATGCC 59.444 43.478 0.00 0.00 0.00 4.40
2266 2281 1.550327 TGGTTTGACTGTTGGTGCAA 58.450 45.000 0.00 0.00 0.00 4.08
2274 2289 3.056250 TGACTGTTGGTGCAAATGTGTTT 60.056 39.130 0.00 0.00 0.00 2.83
2373 2388 2.402305 GATGATGCCTTAGCTCTCGTG 58.598 52.381 0.00 0.00 40.80 4.35
3024 3039 9.859427 TGCTTAAATAAAATGGTTGATGAAGAG 57.141 29.630 0.00 0.00 0.00 2.85
3037 3052 2.613026 TGAAGAGAAGTCGCCAACAA 57.387 45.000 0.00 0.00 0.00 2.83
3128 3143 6.577103 TGTGGCACAAAATGAGTGATAAAAA 58.423 32.000 19.74 0.00 44.16 1.94
3150 3165 5.679734 ATTGTGCTCCAAATAAGATAGCG 57.320 39.130 0.00 0.00 36.44 4.26
3163 3178 9.798885 CAAATAAGATAGCGTATACTGCTTTTC 57.201 33.333 21.42 18.25 43.71 2.29
3375 3390 8.912988 GGTGATGATTTGAAAATGGTAGGATTA 58.087 33.333 0.00 0.00 0.00 1.75
3507 3525 4.305989 TGGAAACTGACATTTGTTGCTC 57.694 40.909 0.00 0.00 0.00 4.26
3508 3526 3.698539 TGGAAACTGACATTTGTTGCTCA 59.301 39.130 0.00 0.00 0.00 4.26
3510 3528 3.715628 AACTGACATTTGTTGCTCACC 57.284 42.857 0.00 0.00 0.00 4.02
3512 3530 2.880890 ACTGACATTTGTTGCTCACCTC 59.119 45.455 0.00 0.00 0.00 3.85
3514 3532 3.286353 TGACATTTGTTGCTCACCTCAA 58.714 40.909 0.00 0.00 0.00 3.02
3515 3533 3.316029 TGACATTTGTTGCTCACCTCAAG 59.684 43.478 0.00 0.00 0.00 3.02
3516 3534 2.624838 ACATTTGTTGCTCACCTCAAGG 59.375 45.455 0.00 0.00 42.17 3.61
3517 3535 1.691196 TTTGTTGCTCACCTCAAGGG 58.309 50.000 0.29 0.00 40.27 3.95
3828 3894 8.731605 GTTTAAATATCCTTTATAGGCTCCAGC 58.268 37.037 0.00 0.00 41.69 4.85
3976 4043 6.803154 ACAGCAATTCCTTTTCTGTACTAC 57.197 37.500 0.00 0.00 36.37 2.73
4320 4388 1.330213 CATGGTGCGCATCGATGTAAA 59.670 47.619 25.47 9.32 0.00 2.01
4377 4445 2.958576 TTTTTAAGCCAGCCGCCG 59.041 55.556 0.00 0.00 38.78 6.46
4390 4458 3.460278 CGCCGTTGCATGCAAACG 61.460 61.111 33.42 31.90 37.70 3.60
4396 4464 1.334599 CGTTGCATGCAAACGGTAGTT 60.335 47.619 33.42 0.00 43.50 2.24
4397 4465 2.050691 GTTGCATGCAAACGGTAGTTG 58.949 47.619 33.42 0.00 41.05 3.16
4460 4528 3.078594 ACCATGCCGATTTTTAATCGC 57.921 42.857 14.51 11.05 39.95 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 178 7.910584 TGATGCCTTATACATGTATGTGATCT 58.089 34.615 25.48 8.61 41.89 2.75
177 186 6.466812 CCACTGATGATGCCTTATACATGTA 58.533 40.000 8.27 8.27 0.00 2.29
199 208 1.047801 TTATCAGCGCTATCAGCCCA 58.952 50.000 10.99 0.00 38.18 5.36
216 225 2.531771 TGAGATGTGGACCCGTCTTTA 58.468 47.619 6.26 0.00 30.87 1.85
272 281 3.181487 GCACTTGTGGTGTTCTGTTTCAT 60.181 43.478 2.81 0.00 46.86 2.57
286 295 1.369689 GCTGCTGTTCGCACTTGTG 60.370 57.895 0.00 0.00 45.47 3.33
294 303 0.925267 CGTGTTGTTGCTGCTGTTCG 60.925 55.000 0.00 0.00 0.00 3.95
303 312 1.197492 TGATGATGCTCGTGTTGTTGC 59.803 47.619 0.00 0.00 0.00 4.17
453 462 2.554142 TCTTGCTGTGGATGCTAATCG 58.446 47.619 0.00 0.00 33.18 3.34
544 553 5.181245 CGTGACATTCATTTCTAGGGTGTTT 59.819 40.000 0.00 0.00 0.00 2.83
552 561 7.967890 ATCATATGCGTGACATTCATTTCTA 57.032 32.000 0.00 0.00 40.38 2.10
556 565 6.138088 CGAAATCATATGCGTGACATTCATT 58.862 36.000 0.00 0.00 40.38 2.57
558 567 4.024977 CCGAAATCATATGCGTGACATTCA 60.025 41.667 0.00 0.00 40.38 2.57
564 573 2.209273 CCACCGAAATCATATGCGTGA 58.791 47.619 0.00 0.00 0.00 4.35
588 597 0.780002 GCGTAGTTTTTCGACGAGCA 59.220 50.000 0.00 0.00 45.37 4.26
594 603 1.337447 CCCTCCAGCGTAGTTTTTCGA 60.337 52.381 0.00 0.00 0.00 3.71
597 606 1.975680 TCTCCCTCCAGCGTAGTTTTT 59.024 47.619 0.00 0.00 0.00 1.94
629 638 0.391130 CCGCATTTCACCTTCTCCGA 60.391 55.000 0.00 0.00 0.00 4.55
630 639 1.982073 GCCGCATTTCACCTTCTCCG 61.982 60.000 0.00 0.00 0.00 4.63
668 677 1.348696 TGTTTTAGGGTTCCCGTCCTC 59.651 52.381 1.91 0.00 34.75 3.71
673 682 2.004733 GATCGTGTTTTAGGGTTCCCG 58.995 52.381 1.91 0.00 0.00 5.14
677 688 2.433436 GCCTGATCGTGTTTTAGGGTT 58.567 47.619 0.00 0.00 0.00 4.11
739 751 2.159490 CCGGCCCATAAAACGTTTACAG 60.159 50.000 15.03 6.74 0.00 2.74
808 823 1.513373 GCGTTTTTCCCGCGGATTC 60.513 57.895 30.73 9.55 41.91 2.52
816 831 4.050934 CCAGGCCGCGTTTTTCCC 62.051 66.667 4.92 0.00 0.00 3.97
817 832 4.717629 GCCAGGCCGCGTTTTTCC 62.718 66.667 4.92 0.00 0.00 3.13
831 846 1.077805 TAACTCTCTGGGGTCGCCA 59.922 57.895 8.56 8.56 0.00 5.69
842 857 4.671250 CGAACGGTGGTTAGAGTAACTCTC 60.671 50.000 0.00 0.00 40.34 3.20
843 858 3.190118 CGAACGGTGGTTAGAGTAACTCT 59.810 47.826 0.00 0.00 43.83 3.24
844 859 3.496155 CGAACGGTGGTTAGAGTAACTC 58.504 50.000 0.00 0.00 38.68 3.01
845 860 2.352127 GCGAACGGTGGTTAGAGTAACT 60.352 50.000 0.00 0.00 38.68 2.24
849 864 1.080974 CGCGAACGGTGGTTAGAGT 60.081 57.895 0.00 0.00 36.24 3.24
866 881 0.173481 TCGCTTGAAGATGGGACTCG 59.827 55.000 0.00 0.00 0.00 4.18
902 917 4.501743 GGTGGACTCTCGAGTTTTTCTCTT 60.502 45.833 13.13 0.00 42.66 2.85
975 990 3.497031 GCCGGACTTTACGCAGCC 61.497 66.667 5.05 0.00 0.00 4.85
986 1001 4.570663 CCATCGAGACGGCCGGAC 62.571 72.222 31.76 22.49 0.00 4.79
1030 1045 1.276421 CTTGAAGGAGAAGGAAGGCGA 59.724 52.381 0.00 0.00 0.00 5.54
1033 1048 2.909662 AGGACTTGAAGGAGAAGGAAGG 59.090 50.000 0.00 0.00 0.00 3.46
1040 1055 4.524714 CAGTAGTGAAGGACTTGAAGGAGA 59.475 45.833 0.00 0.00 35.96 3.71
1043 1058 4.608948 ACAGTAGTGAAGGACTTGAAGG 57.391 45.455 4.09 0.00 35.96 3.46
1458 1473 2.720758 CGCGCTGTCAAAGACGAGG 61.721 63.158 5.56 0.00 34.95 4.63
1460 1475 1.729484 CTCGCGCTGTCAAAGACGA 60.729 57.895 5.56 0.00 34.95 4.20
1569 1584 1.670590 CATCATCTCCCGGAGCCTC 59.329 63.158 9.87 0.00 0.00 4.70
1577 1592 1.177256 GCATGCCACCATCATCTCCC 61.177 60.000 6.36 0.00 0.00 4.30
1585 1600 4.881440 ATCGCCGCATGCCACCAT 62.881 61.111 13.15 0.00 36.24 3.55
1591 1606 3.204827 ACTTCCATCGCCGCATGC 61.205 61.111 7.91 7.91 0.00 4.06
1592 1607 2.040213 GACACTTCCATCGCCGCATG 62.040 60.000 0.00 0.00 0.00 4.06
1599 1614 4.733887 GTGTACTTATCGACACTTCCATCG 59.266 45.833 0.00 0.00 42.21 3.84
1614 1629 1.180029 GCGAGGTGAGGGTGTACTTA 58.820 55.000 0.00 0.00 0.00 2.24
1662 1677 2.100631 GTCGTTGGCGTCATCTGGG 61.101 63.158 0.00 0.00 39.49 4.45
1689 1704 0.106819 AACCATGCTGGCTCATCCTC 60.107 55.000 2.50 0.00 42.67 3.71
1707 1722 1.302431 CACATGCTCGTCCACCCAA 60.302 57.895 0.00 0.00 0.00 4.12
1808 1823 0.248825 CTTCTCACTCGGCCTCATCG 60.249 60.000 0.00 0.00 0.00 3.84
1836 1851 0.827089 CAAACCCATGGACCAGCACA 60.827 55.000 15.22 0.00 0.00 4.57
1903 1918 4.842574 TCAGCAACATAACCATAAGCAGA 58.157 39.130 0.00 0.00 0.00 4.26
1905 1920 6.331845 CAAATCAGCAACATAACCATAAGCA 58.668 36.000 0.00 0.00 0.00 3.91
1941 1956 3.072330 TGCAGAGACCCTCAATTAACACA 59.928 43.478 0.00 0.00 32.06 3.72
1983 1998 6.318648 TCATTACCTCAAATATTTTCAGCGCT 59.681 34.615 2.64 2.64 0.00 5.92
1987 2002 9.727627 GCTCTTCATTACCTCAAATATTTTCAG 57.272 33.333 0.00 0.00 0.00 3.02
2037 2052 9.466497 AAAGCCTCAATCATATTCTTGAGTAAA 57.534 29.630 17.01 0.00 44.40 2.01
2080 2095 0.909623 AACGGGCTAACAGTGGCTAT 59.090 50.000 0.00 0.00 0.00 2.97
2082 2097 0.688487 TAAACGGGCTAACAGTGGCT 59.312 50.000 0.00 0.00 0.00 4.75
2087 2102 5.811399 TTCATTGATAAACGGGCTAACAG 57.189 39.130 0.00 0.00 0.00 3.16
2092 2107 4.432712 GCATTTTCATTGATAAACGGGCT 58.567 39.130 0.00 0.00 0.00 5.19
2115 2130 2.853705 TCACTGGGTTTTAACTTCCCG 58.146 47.619 0.00 0.00 43.75 5.14
2212 2227 1.375523 CACCACGTACCCTTGAGGC 60.376 63.158 0.00 0.00 40.58 4.70
2266 2281 2.487762 CCTGCACGGTATCAAACACATT 59.512 45.455 0.00 0.00 0.00 2.71
2274 2289 1.190643 TCACATCCTGCACGGTATCA 58.809 50.000 2.68 0.00 0.00 2.15
2373 2388 2.101415 GCCAAAGCCAACCATATCCTTC 59.899 50.000 0.00 0.00 0.00 3.46
3024 3039 5.796350 ATGTAACTATTGTTGGCGACTTC 57.204 39.130 6.41 0.00 37.59 3.01
3128 3143 5.126067 ACGCTATCTTATTTGGAGCACAAT 58.874 37.500 0.00 0.00 39.21 2.71
3150 3165 9.722056 CACAATCCATTTAGAAAAGCAGTATAC 57.278 33.333 0.00 0.00 0.00 1.47
3163 3178 4.022068 ACCACACTTGCACAATCCATTTAG 60.022 41.667 0.00 0.00 0.00 1.85
3375 3390 9.463443 GACAACACTTCAACTGCTTTATTTATT 57.537 29.630 0.00 0.00 0.00 1.40
3507 3525 0.984230 TGGTTAGAGCCCTTGAGGTG 59.016 55.000 0.00 0.00 38.26 4.00
3508 3526 1.280457 CTGGTTAGAGCCCTTGAGGT 58.720 55.000 0.00 0.00 38.26 3.85
3510 3528 1.573108 TCCTGGTTAGAGCCCTTGAG 58.427 55.000 0.00 0.00 0.00 3.02
3512 3530 1.680249 GCTTCCTGGTTAGAGCCCTTG 60.680 57.143 0.00 0.00 0.00 3.61
3514 3532 2.302019 GCTTCCTGGTTAGAGCCCT 58.698 57.895 0.00 0.00 0.00 5.19
3515 3533 4.966123 GCTTCCTGGTTAGAGCCC 57.034 61.111 0.00 0.00 0.00 5.19
3516 3534 4.966123 GGCTTCCTGGTTAGAGCC 57.034 61.111 14.00 14.00 46.81 4.70
3517 3535 0.621082 AAGGGCTTCCTGGTTAGAGC 59.379 55.000 0.00 0.00 40.74 4.09
3823 3889 1.480954 GAAGTCTTGGATACGGCTGGA 59.519 52.381 0.00 0.00 42.51 3.86
3976 4043 7.939039 TGCTCTAAACATAATCTCCTTATTGGG 59.061 37.037 0.00 0.00 36.20 4.12
4005 4072 4.072131 GGGGTATATCAACACGCATCATT 58.928 43.478 0.00 0.00 0.00 2.57
4012 4079 5.477607 TTATCCAGGGGTATATCAACACG 57.522 43.478 0.00 0.00 0.00 4.49
4185 4253 8.844441 TGTAGTTTTTCAATACTTCGGTTTTG 57.156 30.769 0.00 0.00 37.93 2.44
4290 4358 0.734889 GCGCACCATGCTAGTCAAAT 59.265 50.000 0.30 0.00 42.25 2.32
4320 4388 2.017049 CTAACAGCTAGCCGGCATTTT 58.983 47.619 31.54 10.73 34.17 1.82
4377 4445 2.050691 CAACTACCGTTTGCATGCAAC 58.949 47.619 31.99 23.55 35.46 4.17
4382 4450 2.846193 AGTCACAACTACCGTTTGCAT 58.154 42.857 0.00 0.00 32.59 3.96


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

AutoCloner maintained by Alex Coulton.