Multiple sequence alignment - TraesCS4A01G426800

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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 TraesCS4A01G426800 chr4A 100.000 4187 0 0 1 4187 698049502 698053688 0.000000e+00 7733.0
1 TraesCS4A01G426800 chr4A 87.078 503 49 8 2372 2865 646591410 646590915 4.730000e-154 555.0
2 TraesCS4A01G426800 chr4A 86.514 393 46 6 920 1307 697962294 697962684 3.870000e-115 425.0
3 TraesCS4A01G426800 chr4A 82.561 453 66 10 3747 4187 646326127 646325676 1.830000e-103 387.0
4 TraesCS4A01G426800 chr4A 78.947 114 18 4 782 891 697962094 697962205 5.810000e-09 73.1
5 TraesCS4A01G426800 chr7A 96.067 3280 104 14 918 4187 31078511 31075247 0.000000e+00 5319.0
6 TraesCS4A01G426800 chr7A 82.389 971 130 21 1532 2492 40100762 40099823 0.000000e+00 808.0
7 TraesCS4A01G426800 chr7A 89.117 487 42 5 2785 3263 40099806 40099323 2.790000e-166 595.0
8 TraesCS4A01G426800 chr7A 85.870 460 61 3 2555 3013 116594739 116594283 1.750000e-133 486.0
9 TraesCS4A01G426800 chr7A 76.770 904 154 27 44 894 31079488 31078588 4.930000e-124 455.0
10 TraesCS4A01G426800 chr7D 96.007 3030 105 4 1172 4187 30504800 30501773 0.000000e+00 4911.0
11 TraesCS4A01G426800 chr7D 87.146 918 75 25 1 894 30830378 30829480 0.000000e+00 1002.0
12 TraesCS4A01G426800 chr7D 85.429 501 67 5 2555 3054 111408999 111408504 2.230000e-142 516.0
13 TraesCS4A01G426800 chr7D 79.853 680 111 19 3520 4187 111279236 111278571 1.360000e-129 473.0
14 TraesCS4A01G426800 chr7D 83.564 505 73 9 2555 3054 111315206 111314707 8.200000e-127 464.0
15 TraesCS4A01G426800 chr7D 97.021 235 7 0 3952 4186 30470604 30470370 3.030000e-106 396.0
16 TraesCS4A01G426800 chr7D 93.173 249 8 7 920 1159 30505203 30504955 1.430000e-94 357.0
17 TraesCS4A01G426800 chr7D 76.798 431 83 11 331 747 30506075 30505648 4.210000e-55 226.0
18 TraesCS4A01G426800 chr7D 81.413 269 26 11 2964 3229 111406842 111406595 9.180000e-47 198.0
19 TraesCS4A01G426800 chr7D 86.905 168 22 0 1890 2057 40195897 40195730 5.530000e-44 189.0
20 TraesCS4A01G426800 chr7D 80.000 260 35 14 3102 3347 111400059 111399803 4.300000e-40 176.0
21 TraesCS4A01G426800 chr7D 75.217 230 25 9 2964 3193 111313802 111313605 3.470000e-11 80.5
22 TraesCS4A01G426800 chr1D 84.546 893 89 25 1896 2777 491981338 491982192 0.000000e+00 839.0
23 TraesCS4A01G426800 chr1D 86.111 216 29 1 2924 3139 491982201 491982415 9.050000e-57 231.0
24 TraesCS4A01G426800 chr7B 85.696 776 95 12 1877 2643 71064183 71063415 0.000000e+00 804.0
25 TraesCS4A01G426800 chr7B 81.066 544 78 14 2127 2668 71136832 71136312 1.080000e-110 411.0
26 TraesCS4A01G426800 chr7B 84.810 316 43 4 2733 3048 71063410 71063100 3.140000e-81 313.0
27 TraesCS4A01G426800 chr7B 79.026 267 33 15 3106 3351 70866491 70866227 1.200000e-35 161.0
28 TraesCS4A01G426800 chr1B 83.247 776 78 16 1896 2659 684787044 684787779 0.000000e+00 665.0


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 TraesCS4A01G426800 chr4A 698049502 698053688 4186 False 7733.000000 7733 100.000000 1 4187 1 chr4A.!!$F1 4186
1 TraesCS4A01G426800 chr4A 697962094 697962684 590 False 249.050000 425 82.730500 782 1307 2 chr4A.!!$F2 525
2 TraesCS4A01G426800 chr7A 31075247 31079488 4241 True 2887.000000 5319 86.418500 44 4187 2 chr7A.!!$R2 4143
3 TraesCS4A01G426800 chr7A 40099323 40100762 1439 True 701.500000 808 85.753000 1532 3263 2 chr7A.!!$R3 1731
4 TraesCS4A01G426800 chr7D 30501773 30506075 4302 True 1831.333333 4911 88.659333 331 4187 3 chr7D.!!$R6 3856
5 TraesCS4A01G426800 chr7D 30829480 30830378 898 True 1002.000000 1002 87.146000 1 894 1 chr7D.!!$R2 893
6 TraesCS4A01G426800 chr7D 111278571 111279236 665 True 473.000000 473 79.853000 3520 4187 1 chr7D.!!$R4 667
7 TraesCS4A01G426800 chr7D 111406595 111408999 2404 True 357.000000 516 83.421000 2555 3229 2 chr7D.!!$R8 674
8 TraesCS4A01G426800 chr7D 111313605 111315206 1601 True 272.250000 464 79.390500 2555 3193 2 chr7D.!!$R7 638
9 TraesCS4A01G426800 chr1D 491981338 491982415 1077 False 535.000000 839 85.328500 1896 3139 2 chr1D.!!$F1 1243
10 TraesCS4A01G426800 chr7B 71063100 71064183 1083 True 558.500000 804 85.253000 1877 3048 2 chr7B.!!$R3 1171
11 TraesCS4A01G426800 chr7B 71136312 71136832 520 True 411.000000 411 81.066000 2127 2668 1 chr7B.!!$R2 541
12 TraesCS4A01G426800 chr1B 684787044 684787779 735 False 665.000000 665 83.247000 1896 2659 1 chr1B.!!$F1 763

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
684 710 0.251077 AAGGTGCCCTCTTGCTCTTG 60.251 55.000 0.0 0.0 30.89 3.02 F
1593 2091 1.137872 GTCTCCACTGCGATCCTTGAT 59.862 52.381 0.0 0.0 0.00 2.57 F
1767 2265 0.034896 AGGGTGTTGATGTGACGGAC 59.965 55.000 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 2128 0.385751 GGCATCCGATCGAAGACAGA 59.614 55.000 18.66 4.11 42.51 3.41 R
2593 3149 1.028905 AACTTGCAAGCGCCTAACAA 58.971 45.000 26.27 2.91 37.32 2.83 R
3447 4100 1.203287 GGTGCTTCAGAATTTGAGCCC 59.797 52.381 0.00 0.00 37.07 5.19 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
57 58 1.941377 AGTCGGTACCCCAACATGTA 58.059 50.000 6.25 0.00 0.00 2.29
64 65 2.897271 ACCCCAACATGTATTGCTCA 57.103 45.000 0.00 0.00 0.00 4.26
68 69 1.064505 CCAACATGTATTGCTCAGGCG 59.935 52.381 0.00 0.00 42.25 5.52
93 94 5.163509 TGACATCATTTTCTACTCTCCCGAG 60.164 44.000 0.00 0.00 43.10 4.63
120 124 4.156008 CCATAACCTTGTCAAGTTAGGCAC 59.844 45.833 11.61 0.00 32.08 5.01
194 198 0.251634 TAGCATGGACCATTCGCACA 59.748 50.000 16.75 3.97 0.00 4.57
205 209 6.824196 TGGACCATTCGCACATTTACTTATTA 59.176 34.615 0.00 0.00 0.00 0.98
225 229 9.727627 CTTATTATTGCAATTTTCTCCTCAGAC 57.272 33.333 18.75 0.00 0.00 3.51
226 230 6.515272 TTATTGCAATTTTCTCCTCAGACC 57.485 37.500 18.75 0.00 0.00 3.85
232 236 3.662247 TTTTCTCCTCAGACCGAACTC 57.338 47.619 0.00 0.00 0.00 3.01
259 264 5.529060 AGCTGACTTTTAGGTTTGTCTTGAG 59.471 40.000 0.00 0.00 0.00 3.02
290 295 7.874528 TGAGGTCATGCATTGTTGTCTATATAG 59.125 37.037 0.00 3.10 0.00 1.31
351 371 9.638239 AAAATGTTTTAGAATGTGAATATGCGT 57.362 25.926 0.00 0.00 0.00 5.24
399 419 1.683385 GTGGGATGATTTGCTTAGCCC 59.317 52.381 0.29 0.00 34.67 5.19
486 507 2.622436 CACATCCTCCGACCTTTCTTC 58.378 52.381 0.00 0.00 0.00 2.87
521 542 2.036992 CCTACTCAAGCTCTGCCCATAG 59.963 54.545 0.00 0.00 0.00 2.23
527 548 0.763652 AGCTCTGCCCATAGGACATG 59.236 55.000 0.00 0.00 33.47 3.21
549 570 0.252558 ACCCACACCCAGGTAGTAGG 60.253 60.000 0.00 0.00 33.52 3.18
563 584 1.448013 GTAGGACGGGCTCTTGCAC 60.448 63.158 0.00 0.00 41.91 4.57
570 591 1.228245 GGGCTCTTGCACTGGACAA 60.228 57.895 0.00 0.00 40.03 3.18
576 597 3.708403 TCTTGCACTGGACAAGATCAT 57.292 42.857 9.66 0.00 46.46 2.45
596 621 9.739276 AGATCATCAAAATACACTAACCAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
610 635 9.014297 CACTAACCAAGAAAAGAATTAGGTGAT 57.986 33.333 0.00 0.00 0.00 3.06
639 664 5.287170 TCTCAAATCTGAAATGACAAGCG 57.713 39.130 0.00 0.00 0.00 4.68
646 671 5.591643 TCTGAAATGACAAGCGTAAGTTC 57.408 39.130 0.00 0.00 41.68 3.01
649 674 2.736144 ATGACAAGCGTAAGTTCGGA 57.264 45.000 0.00 0.00 41.68 4.55
654 680 2.073816 CAAGCGTAAGTTCGGACCAAT 58.926 47.619 0.00 0.00 41.68 3.16
669 695 8.301720 GTTCGGACCAATCTTAAAATAAAAGGT 58.698 33.333 0.00 0.00 0.00 3.50
671 697 6.530181 CGGACCAATCTTAAAATAAAAGGTGC 59.470 38.462 0.00 0.00 0.00 5.01
684 710 0.251077 AAGGTGCCCTCTTGCTCTTG 60.251 55.000 0.00 0.00 30.89 3.02
697 728 3.793797 TGCTCTTGATTGCATTGGATG 57.206 42.857 0.00 0.00 33.94 3.51
702 733 3.697542 TCTTGATTGCATTGGATGGTGAG 59.302 43.478 0.00 0.00 0.00 3.51
747 781 5.043903 ACGAGATGAATATTCTCACCAACG 58.956 41.667 16.24 13.46 39.69 4.10
748 782 5.043903 CGAGATGAATATTCTCACCAACGT 58.956 41.667 16.24 0.00 39.69 3.99
749 783 5.051441 CGAGATGAATATTCTCACCAACGTG 60.051 44.000 16.24 0.00 39.69 4.49
750 784 5.734720 AGATGAATATTCTCACCAACGTGT 58.265 37.500 16.24 0.00 41.09 4.49
752 786 5.605564 TGAATATTCTCACCAACGTGTTG 57.394 39.130 16.24 5.76 41.09 3.33
812 1074 3.122948 CGAGTCATTTAGTTTCACCACCG 59.877 47.826 0.00 0.00 0.00 4.94
1423 1921 4.195334 GGGCCGCCATGGAGATGT 62.195 66.667 18.40 0.00 42.00 3.06
1491 1989 4.996434 GTGTCTGTGCTGCCCGCT 62.996 66.667 0.00 0.00 40.11 5.52
1552 2050 2.357760 GGTTTGCGGTCCGTGCTA 60.358 61.111 13.94 0.00 0.00 3.49
1581 2079 1.203523 GAGCTCGTCAATGTCTCCACT 59.796 52.381 0.00 0.00 0.00 4.00
1593 2091 1.137872 GTCTCCACTGCGATCCTTGAT 59.862 52.381 0.00 0.00 0.00 2.57
1630 2128 2.113139 CGGTTGAGGTTGCCAGGT 59.887 61.111 0.00 0.00 0.00 4.00
1638 2136 0.398318 AGGTTGCCAGGTCTGTCTTC 59.602 55.000 0.00 0.00 0.00 2.87
1752 2250 3.637544 AGGATGGTGGGGGAGGGT 61.638 66.667 0.00 0.00 0.00 4.34
1767 2265 0.034896 AGGGTGTTGATGTGACGGAC 59.965 55.000 0.00 0.00 0.00 4.79
2261 2815 2.705658 TCTTCAACTCAGCAAGGGAGAA 59.294 45.455 0.00 0.00 36.26 2.87
2457 3013 6.693113 GGAAATATTTTTCGAGCATGAAGGAC 59.307 38.462 1.43 0.00 41.84 3.85
2593 3149 4.022603 TGGCATTAGTGTTTATGGTGCAT 58.977 39.130 0.00 0.00 33.05 3.96
2726 3284 6.671614 CATTTATGCAAATGCCTCAATGTT 57.328 33.333 2.46 0.00 43.30 2.71
2976 3547 2.942376 CAAGGCACAGTTACTCAACACA 59.058 45.455 0.00 0.00 37.10 3.72
3375 4015 9.985318 CACATCACTCTCTAGAAATGATTTTTC 57.015 33.333 9.33 0.00 31.37 2.29
3412 4065 5.463061 CAGAATTACCTTGCCACACTTTTTG 59.537 40.000 0.00 0.00 0.00 2.44
3440 4093 4.459337 GTCTAGCAGGTGCCTTTTGTATTT 59.541 41.667 0.00 0.00 43.38 1.40
3447 4100 3.928375 GGTGCCTTTTGTATTTGCATCAG 59.072 43.478 0.00 0.00 33.35 2.90
3452 4105 4.427312 CTTTTGTATTTGCATCAGGGCTC 58.573 43.478 0.00 0.00 34.04 4.70
3526 4180 3.711704 TCAGGGAACATTCTGTAGATCCC 59.288 47.826 9.36 9.36 42.56 3.85
3610 4264 6.488344 TGAAATAGTGCACATGGAAGTTGTTA 59.512 34.615 21.04 0.00 0.00 2.41
3696 4352 9.893305 GCAAACTGTTGATAACTAATTAACACT 57.107 29.630 0.00 0.00 38.69 3.55
3795 4468 4.642429 AGGACTGTAACAACATTCTGTCC 58.358 43.478 10.54 10.54 43.93 4.02
3817 4490 5.841237 TCCTTTATTCACCATTTTGTTCCCA 59.159 36.000 0.00 0.00 0.00 4.37
3902 4575 9.052759 ACGTTGAATACTTAATTCTTCTGTTGT 57.947 29.630 0.00 0.00 43.83 3.32
3911 4584 9.516314 ACTTAATTCTTCTGTTGTAAGTTTTGC 57.484 29.630 0.00 0.00 29.71 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.036105 TGATGTCACGCCTGAGCAAT 60.036 50.000 0.00 0.00 39.83 3.56
64 65 4.081420 AGAGTAGAAAATGATGTCACGCCT 60.081 41.667 0.00 0.00 0.00 5.52
68 69 4.806247 CGGGAGAGTAGAAAATGATGTCAC 59.194 45.833 0.00 0.00 0.00 3.67
93 94 6.128090 GCCTAACTTGACAAGGTTATGGTAAC 60.128 42.308 19.16 1.40 32.67 2.50
99 100 5.242795 AGTGCCTAACTTGACAAGGTTAT 57.757 39.130 19.16 5.42 34.57 1.89
100 101 4.638304 GAGTGCCTAACTTGACAAGGTTA 58.362 43.478 19.16 13.01 40.07 2.85
120 124 3.176552 AGAGATGTCATTGCTTCCGAG 57.823 47.619 0.00 0.00 0.00 4.63
205 209 3.441572 CGGTCTGAGGAGAAAATTGCAAT 59.558 43.478 5.99 5.99 0.00 3.56
221 225 0.884514 TCAGCTCAGAGTTCGGTCTG 59.115 55.000 0.00 4.51 44.71 3.51
222 226 0.885196 GTCAGCTCAGAGTTCGGTCT 59.115 55.000 0.00 0.00 0.00 3.85
225 229 2.447244 AAAGTCAGCTCAGAGTTCGG 57.553 50.000 0.00 0.00 31.05 4.30
226 230 3.923461 CCTAAAAGTCAGCTCAGAGTTCG 59.077 47.826 0.00 0.00 31.05 3.95
232 236 5.059833 AGACAAACCTAAAAGTCAGCTCAG 58.940 41.667 0.00 0.00 33.56 3.35
237 241 6.949449 GTCTCAAGACAAACCTAAAAGTCAG 58.051 40.000 5.28 0.00 44.18 3.51
259 264 4.171005 CAACAATGCATGACCTCAATGTC 58.829 43.478 0.00 0.00 35.77 3.06
290 295 7.399523 GTTATCCACGTATGTTTTCTCATGTC 58.600 38.462 0.00 0.00 0.00 3.06
348 368 0.029300 TTTTCTGTCTGCAAGCACGC 59.971 50.000 0.00 0.00 0.00 5.34
351 371 2.950975 TCATGTTTTCTGTCTGCAAGCA 59.049 40.909 0.00 0.00 0.00 3.91
361 381 1.135315 CCCGCGCTCATGTTTTCTG 59.865 57.895 5.56 0.00 0.00 3.02
399 419 0.890683 GGCAGGAGGAACAACAATGG 59.109 55.000 0.00 0.00 0.00 3.16
453 474 2.514592 ATGTGGCCGCAATCCTCG 60.515 61.111 25.33 0.00 0.00 4.63
456 477 2.124151 AGGATGTGGCCGCAATCC 60.124 61.111 25.33 26.53 0.00 3.01
486 507 1.218316 GTAGGGAGGTGAAGGTGCG 59.782 63.158 0.00 0.00 0.00 5.34
521 542 1.303317 GGGTGTGGGTGACATGTCC 60.303 63.158 22.85 13.66 36.78 4.02
527 548 1.125711 ACTACCTGGGTGTGGGTGAC 61.126 60.000 2.07 0.00 37.07 3.67
549 570 2.743928 CCAGTGCAAGAGCCCGTC 60.744 66.667 0.00 0.00 41.13 4.79
563 584 7.621428 AGTGTATTTTGATGATCTTGTCCAG 57.379 36.000 0.00 0.00 0.00 3.86
570 591 9.739276 TTCTTGGTTAGTGTATTTTGATGATCT 57.261 29.630 0.00 0.00 0.00 2.75
596 621 7.577303 TGAGAGCCATAATCACCTAATTCTTT 58.423 34.615 0.00 0.00 0.00 2.52
597 622 7.141758 TGAGAGCCATAATCACCTAATTCTT 57.858 36.000 0.00 0.00 0.00 2.52
610 635 6.885918 TGTCATTTCAGATTTGAGAGCCATAA 59.114 34.615 0.00 0.00 34.15 1.90
612 637 5.258841 TGTCATTTCAGATTTGAGAGCCAT 58.741 37.500 0.00 0.00 34.15 4.40
646 671 6.530181 GCACCTTTTATTTTAAGATTGGTCCG 59.470 38.462 0.00 0.00 0.00 4.79
669 695 1.830279 CAATCAAGAGCAAGAGGGCA 58.170 50.000 0.00 0.00 35.83 5.36
671 697 1.830279 TGCAATCAAGAGCAAGAGGG 58.170 50.000 0.00 0.00 37.90 4.30
684 710 4.724074 TTTCTCACCATCCAATGCAATC 57.276 40.909 0.00 0.00 0.00 2.67
702 733 9.993881 CTCGTGTTGATTTTATGAAATGTTTTC 57.006 29.630 0.00 0.00 35.65 2.29
721 755 5.977635 TGGTGAGAATATTCATCTCGTGTT 58.022 37.500 17.56 0.00 45.05 3.32
725 759 5.043903 ACGTTGGTGAGAATATTCATCTCG 58.956 41.667 17.56 13.17 45.05 4.04
747 781 5.351233 TTTGACCGATGTTCATACAACAC 57.649 39.130 0.00 0.00 37.91 3.32
748 782 4.454161 CCTTTGACCGATGTTCATACAACA 59.546 41.667 0.00 0.00 37.91 3.33
749 783 4.142687 CCCTTTGACCGATGTTCATACAAC 60.143 45.833 0.00 0.00 37.91 3.32
750 784 4.006989 CCCTTTGACCGATGTTCATACAA 58.993 43.478 0.00 0.00 37.91 2.41
752 786 2.943033 CCCCTTTGACCGATGTTCATAC 59.057 50.000 0.00 0.00 0.00 2.39
910 1187 1.131126 CGCACGAATCTCAATGCCTTT 59.869 47.619 0.00 0.00 34.49 3.11
914 1191 0.940126 ATCCGCACGAATCTCAATGC 59.060 50.000 0.00 0.00 34.66 3.56
915 1192 1.333524 GCATCCGCACGAATCTCAATG 60.334 52.381 0.00 0.00 38.36 2.82
916 1193 0.940126 GCATCCGCACGAATCTCAAT 59.060 50.000 0.00 0.00 38.36 2.57
918 1195 0.108186 AAGCATCCGCACGAATCTCA 60.108 50.000 0.00 0.00 42.27 3.27
1423 1921 2.721167 CCTCCTGCATCCGGACGAA 61.721 63.158 6.12 0.00 0.00 3.85
1524 2022 2.904866 GCAAACCCGTGCACCTCA 60.905 61.111 12.15 0.00 44.29 3.86
1581 2079 2.892374 CAGTACACATCAAGGATCGCA 58.108 47.619 0.00 0.00 0.00 5.10
1593 2091 1.596752 CCCGCACTTGCAGTACACA 60.597 57.895 1.48 0.00 42.21 3.72
1630 2128 0.385751 GGCATCCGATCGAAGACAGA 59.614 55.000 18.66 4.11 42.51 3.41
1723 2221 2.619849 CCACCATCCTCTTGAACAGCAT 60.620 50.000 0.00 0.00 0.00 3.79
1724 2222 1.271543 CCACCATCCTCTTGAACAGCA 60.272 52.381 0.00 0.00 0.00 4.41
1752 2250 2.490509 AGATACGTCCGTCACATCAACA 59.509 45.455 0.00 0.00 0.00 3.33
1767 2265 3.403277 GCTGCCAGCACAGATACG 58.597 61.111 12.82 0.00 41.89 3.06
1931 2437 0.804989 CACCTCATCGAAAACCTGGC 59.195 55.000 0.00 0.00 0.00 4.85
2261 2815 3.004002 CGCATTCCATGTGATAACATGCT 59.996 43.478 16.84 2.08 44.39 3.79
2331 2887 7.137426 CAGAACTTTTCATCTCTTCAAACAGG 58.863 38.462 0.00 0.00 0.00 4.00
2457 3013 1.097547 CAGGTTCAAGCCCATAGCCG 61.098 60.000 0.00 0.00 45.47 5.52
2593 3149 1.028905 AACTTGCAAGCGCCTAACAA 58.971 45.000 26.27 2.91 37.32 2.83
2718 3276 4.508461 TGCAACATCCTTCAACATTGAG 57.492 40.909 0.00 0.00 38.61 3.02
2726 3284 2.380064 AACCCTTGCAACATCCTTCA 57.620 45.000 0.00 0.00 0.00 3.02
2976 3547 2.309528 TCGCAAGTTTCTCACTGTGT 57.690 45.000 7.79 0.00 35.12 3.72
3235 3864 5.068723 GGCTTACTTGTATAGTAGCTGGACA 59.931 44.000 0.00 0.00 40.35 4.02
3237 3866 5.455872 AGGCTTACTTGTATAGTAGCTGGA 58.544 41.667 0.00 0.00 40.35 3.86
3351 3991 8.877779 ACGAAAAATCATTTCTAGAGAGTGATG 58.122 33.333 13.84 6.58 34.05 3.07
3353 3993 8.833231 AACGAAAAATCATTTCTAGAGAGTGA 57.167 30.769 0.00 6.34 0.00 3.41
3375 4015 7.800380 GCAAGGTAATTCTGATCATCAATAACG 59.200 37.037 0.00 0.00 0.00 3.18
3412 4065 1.219393 GGCACCTGCTAGACCTGTC 59.781 63.158 0.00 0.00 41.70 3.51
3440 4093 2.097036 CAGAATTTGAGCCCTGATGCA 58.903 47.619 0.00 0.00 0.00 3.96
3447 4100 1.203287 GGTGCTTCAGAATTTGAGCCC 59.797 52.381 0.00 0.00 37.07 5.19
3452 4105 1.614903 TGCCTGGTGCTTCAGAATTTG 59.385 47.619 8.16 0.00 42.00 2.32
3479 4132 6.556495 AGAAGGTTAGATGATCATAAGAGGCA 59.444 38.462 8.54 0.00 0.00 4.75
3526 4180 8.735315 TGTTACAATACCAATGTAAATGGACTG 58.265 33.333 0.00 0.00 42.92 3.51
3584 4238 5.156355 CAACTTCCATGTGCACTATTTCAC 58.844 41.667 19.41 0.00 0.00 3.18
3610 4264 5.852282 AAATAGCAGTGTTTTCTGTGGTT 57.148 34.783 0.00 0.00 37.70 3.67
3696 4352 9.290988 TCAAGTATGCAAAATGGTAAGACTTAA 57.709 29.630 0.00 0.00 0.00 1.85
3698 4354 7.665559 TCTCAAGTATGCAAAATGGTAAGACTT 59.334 33.333 0.00 0.00 0.00 3.01
3795 4468 6.520272 TGTGGGAACAAAATGGTGAATAAAG 58.480 36.000 0.00 0.00 46.06 1.85
3902 4575 4.053295 AGCTTCGAAGTACGCAAAACTTA 58.947 39.130 25.24 0.00 42.26 2.24
3911 4584 4.036352 GTGATCCTTAGCTTCGAAGTACG 58.964 47.826 25.24 13.53 44.09 3.67


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

AutoCloner maintained by Alex Coulton.