Multiple sequence alignment - TraesCS4A01G486300

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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 TraesCS4A01G486300 chr4A 100.000 2909 0 0 1 2909 739595782 739592874 0.000000e+00 5373.0
1 TraesCS4A01G486300 chr7D 93.221 1667 97 13 930 2587 4018455 4020114 0.000000e+00 2438.0
2 TraesCS4A01G486300 chr7D 94.406 286 14 2 2625 2909 4020194 4020478 3.440000e-119 438.0
3 TraesCS4A01G486300 chr7D 80.260 461 52 16 482 928 4017971 4018406 7.830000e-81 311.0
4 TraesCS4A01G486300 chr7D 83.258 221 31 6 456 670 474922531 474922311 6.360000e-47 198.0
5 TraesCS4A01G486300 chr7D 93.651 63 2 2 2601 2661 58784407 58784345 3.090000e-15 93.5
6 TraesCS4A01G486300 chr7D 95.918 49 1 1 2597 2645 5579600 5579647 8.640000e-11 78.7
7 TraesCS4A01G486300 chr7A 91.882 1663 114 16 926 2578 3851787 3853438 0.000000e+00 2303.0
8 TraesCS4A01G486300 chr7A 86.005 443 26 11 1 434 3850786 3851201 2.660000e-120 442.0
9 TraesCS4A01G486300 chr7A 95.131 267 11 2 2644 2909 3853440 3853705 1.250000e-113 420.0
10 TraesCS4A01G486300 chr7A 80.147 272 41 12 409 670 583459640 583459908 1.060000e-44 191.0
11 TraesCS4A01G486300 chr4B 81.194 335 49 11 360 681 584074085 584073752 1.030000e-64 257.0
12 TraesCS4A01G486300 chr5D 82.667 225 29 10 442 656 558689344 558689568 1.060000e-44 191.0
13 TraesCS4A01G486300 chr4D 89.209 139 10 5 2084 2217 1201767 1201629 4.990000e-38 169.0
14 TraesCS4A01G486300 chr3D 81.443 194 30 6 483 670 403539195 403539388 1.400000e-33 154.0
15 TraesCS4A01G486300 chr3D 96.364 55 1 1 2593 2647 105260707 105260760 3.990000e-14 89.8
16 TraesCS4A01G486300 chr3D 94.737 57 1 2 2593 2648 61804560 61804615 1.440000e-13 87.9
17 TraesCS4A01G486300 chr3D 94.737 57 2 1 2601 2656 94644800 94644744 1.440000e-13 87.9
18 TraesCS4A01G486300 chr6D 91.935 62 3 2 2601 2661 157587453 157587393 5.160000e-13 86.1
19 TraesCS4A01G486300 chr1D 94.643 56 2 1 2601 2656 252473189 252473135 5.160000e-13 86.1
20 TraesCS4A01G486300 chr6B 90.476 63 4 2 2597 2659 636318473 636318533 6.680000e-12 82.4


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 TraesCS4A01G486300 chr4A 739592874 739595782 2908 True 5373.000000 5373 100.000000 1 2909 1 chr4A.!!$R1 2908
1 TraesCS4A01G486300 chr7D 4017971 4020478 2507 False 1062.333333 2438 89.295667 482 2909 3 chr7D.!!$F2 2427
2 TraesCS4A01G486300 chr7A 3850786 3853705 2919 False 1055.000000 2303 91.006000 1 2909 3 chr7A.!!$F2 2908

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
524 585 0.102481 CGGACCGGATCTGTACCTTG 59.898 60.0 9.46 0.0 0.0 3.61 F
1488 1628 0.098200 CCACTGTTGCTGATCATGCG 59.902 55.0 0.00 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1682 0.242825 CTTGCTTGCTCACATGGTGG 59.757 55.0 0.0 0.0 33.87 4.61 R
2627 2779 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.0 0.0 0.0 0.00 4.00 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
20 21 1.203125 GGAGAAGGAGGAGATCGGGAT 60.203 57.143 0.00 0.00 0.00 3.85
24 25 2.653702 GAGGAGATCGGGATGGCG 59.346 66.667 0.00 0.00 0.00 5.69
25 26 1.903890 GAGGAGATCGGGATGGCGA 60.904 63.158 0.00 0.00 0.00 5.54
26 27 2.148558 GAGGAGATCGGGATGGCGAC 62.149 65.000 0.00 0.00 0.00 5.19
27 28 2.340443 GAGATCGGGATGGCGACC 59.660 66.667 0.00 0.00 0.00 4.79
75 76 1.142778 GCAGAAGCATCGTCCGTCTC 61.143 60.000 0.00 0.00 41.58 3.36
76 77 0.863538 CAGAAGCATCGTCCGTCTCG 60.864 60.000 0.00 0.00 0.00 4.04
77 78 1.136984 GAAGCATCGTCCGTCTCGT 59.863 57.895 0.00 0.00 0.00 4.18
78 79 1.134530 GAAGCATCGTCCGTCTCGTG 61.135 60.000 0.00 0.00 0.00 4.35
173 174 3.775654 CACGTGGGGCTCCTCCTC 61.776 72.222 7.95 0.00 35.20 3.71
174 175 3.999285 ACGTGGGGCTCCTCCTCT 61.999 66.667 3.07 0.00 35.85 3.69
176 177 1.381327 CGTGGGGCTCCTCCTCTTA 60.381 63.158 3.07 0.00 35.85 2.10
220 221 2.673200 GCAGAGCCCATCAGACCCA 61.673 63.158 0.00 0.00 0.00 4.51
222 223 1.997874 AGAGCCCATCAGACCCACC 60.998 63.158 0.00 0.00 0.00 4.61
225 226 2.687200 CCCATCAGACCCACCCGA 60.687 66.667 0.00 0.00 0.00 5.14
258 265 0.824109 GGTCACGATCCAGTCCATCA 59.176 55.000 0.00 0.00 0.00 3.07
262 269 1.051812 ACGATCCAGTCCATCATCCC 58.948 55.000 0.00 0.00 0.00 3.85
270 277 0.250467 GTCCATCATCCCCATCGGTG 60.250 60.000 0.00 0.00 0.00 4.94
271 278 0.694105 TCCATCATCCCCATCGGTGT 60.694 55.000 0.00 0.00 0.00 4.16
283 290 2.522198 ATCGGTGTCCTGCTCCTCCT 62.522 60.000 0.00 0.00 0.00 3.69
285 292 1.599576 GGTGTCCTGCTCCTCCTTC 59.400 63.158 0.00 0.00 0.00 3.46
286 293 1.599576 GTGTCCTGCTCCTCCTTCC 59.400 63.158 0.00 0.00 0.00 3.46
287 294 0.907230 GTGTCCTGCTCCTCCTTCCT 60.907 60.000 0.00 0.00 0.00 3.36
288 295 0.906756 TGTCCTGCTCCTCCTTCCTG 60.907 60.000 0.00 0.00 0.00 3.86
289 296 0.907230 GTCCTGCTCCTCCTTCCTGT 60.907 60.000 0.00 0.00 0.00 4.00
290 297 0.616111 TCCTGCTCCTCCTTCCTGTC 60.616 60.000 0.00 0.00 0.00 3.51
291 298 1.621672 CCTGCTCCTCCTTCCTGTCC 61.622 65.000 0.00 0.00 0.00 4.02
292 299 1.954362 CTGCTCCTCCTTCCTGTCCG 61.954 65.000 0.00 0.00 0.00 4.79
293 300 2.726351 GCTCCTCCTTCCTGTCCGG 61.726 68.421 0.00 0.00 0.00 5.14
294 301 2.683933 TCCTCCTTCCTGTCCGGC 60.684 66.667 0.00 0.00 0.00 6.13
295 302 2.685380 CCTCCTTCCTGTCCGGCT 60.685 66.667 0.00 0.00 0.00 5.52
296 303 1.381327 CCTCCTTCCTGTCCGGCTA 60.381 63.158 0.00 0.00 0.00 3.93
332 342 2.280052 GATCTGCTCTGCTCCGGC 60.280 66.667 0.00 0.00 39.26 6.13
363 373 4.910585 CCGCCACGGTATGCTCCC 62.911 72.222 0.00 0.00 42.73 4.30
365 375 3.792736 GCCACGGTATGCTCCCCA 61.793 66.667 0.00 0.00 0.00 4.96
369 379 3.873812 CGGTATGCTCCCCACCCC 61.874 72.222 0.00 0.00 0.00 4.95
391 401 1.065410 TTTCTCCCCACCTCAGCCAA 61.065 55.000 0.00 0.00 0.00 4.52
463 524 4.028490 CTTGGGTGGCCGCACCTA 62.028 66.667 17.84 11.51 44.41 3.08
464 525 3.976701 CTTGGGTGGCCGCACCTAG 62.977 68.421 17.84 16.91 44.41 3.02
467 528 2.125106 GGTGGCCGCACCTAGAAG 60.125 66.667 19.98 0.00 41.84 2.85
468 529 2.656069 GGTGGCCGCACCTAGAAGA 61.656 63.158 19.98 0.00 41.84 2.87
469 530 1.295423 GTGGCCGCACCTAGAAGAA 59.705 57.895 12.58 0.00 40.22 2.52
470 531 1.019805 GTGGCCGCACCTAGAAGAAC 61.020 60.000 12.58 0.00 40.22 3.01
471 532 1.192146 TGGCCGCACCTAGAAGAACT 61.192 55.000 0.00 0.00 40.22 3.01
524 585 0.102481 CGGACCGGATCTGTACCTTG 59.898 60.000 9.46 0.00 0.00 3.61
530 591 0.470341 GGATCTGTACCTTGGCTCCC 59.530 60.000 0.00 0.00 0.00 4.30
543 604 1.443828 GCTCCCCTGCTAGTGCTAC 59.556 63.158 0.00 0.00 40.48 3.58
549 610 1.409427 CCCTGCTAGTGCTACCTGTAC 59.591 57.143 0.00 0.00 40.48 2.90
552 613 3.017442 CTGCTAGTGCTACCTGTACTGA 58.983 50.000 0.60 0.00 41.64 3.41
557 618 6.323996 TGCTAGTGCTACCTGTACTGAATTAT 59.676 38.462 0.60 0.00 41.64 1.28
559 620 7.711339 GCTAGTGCTACCTGTACTGAATTATTT 59.289 37.037 0.60 0.00 41.64 1.40
565 626 7.553044 GCTACCTGTACTGAATTATTTCAACCT 59.447 37.037 0.60 0.00 41.22 3.50
567 628 8.788325 ACCTGTACTGAATTATTTCAACCTAC 57.212 34.615 0.60 3.35 41.22 3.18
583 651 9.817809 TTTCAACCTACTGCTAGTGATTATTAG 57.182 33.333 0.00 0.00 0.00 1.73
584 652 7.952671 TCAACCTACTGCTAGTGATTATTAGG 58.047 38.462 0.00 0.00 0.00 2.69
632 703 2.037772 ACTGAGTAGACACCTTGCTTGG 59.962 50.000 0.00 0.00 0.00 3.61
634 705 3.236047 TGAGTAGACACCTTGCTTGGTA 58.764 45.455 1.08 0.00 38.45 3.25
639 710 4.273148 AGACACCTTGCTTGGTACTAAG 57.727 45.455 14.23 14.23 38.45 2.18
641 712 4.102681 AGACACCTTGCTTGGTACTAAGTT 59.897 41.667 18.87 0.00 38.45 2.66
647 718 6.430000 ACCTTGCTTGGTACTAAGTTACATTG 59.570 38.462 18.87 6.77 38.79 2.82
653 724 6.056090 TGGTACTAAGTTACATTGCCATCA 57.944 37.500 0.00 0.00 0.00 3.07
664 742 3.117398 ACATTGCCATCACCATGTAGGAT 60.117 43.478 0.00 0.00 41.22 3.24
683 761 4.390264 GGATACTGCCAATTCTAGAACCC 58.610 47.826 7.48 0.00 0.00 4.11
699 777 1.344953 ACCCACTGCACAGTTCCAGA 61.345 55.000 0.00 0.00 40.20 3.86
706 784 0.179045 GCACAGTTCCAGACCAGTGT 60.179 55.000 0.00 0.00 37.22 3.55
715 793 4.586306 TCCAGACCAGTGTACATCTCTA 57.414 45.455 0.00 0.00 0.00 2.43
720 798 6.536582 CCAGACCAGTGTACATCTCTAATTTG 59.463 42.308 0.00 0.00 0.00 2.32
727 805 6.714810 AGTGTACATCTCTAATTTGGTTGCAA 59.285 34.615 0.00 0.00 0.00 4.08
776 854 5.830000 TTCATCAGGATCTCAAATGCAAG 57.170 39.130 0.00 0.00 0.00 4.01
784 862 2.991250 TCTCAAATGCAAGTAGAGCCC 58.009 47.619 0.00 0.00 0.00 5.19
800 878 1.428912 AGCCCCCTCATTTTCACAAGA 59.571 47.619 0.00 0.00 0.00 3.02
812 890 0.671472 TCACAAGATCCACTGCGCAG 60.671 55.000 34.89 34.89 0.00 5.18
833 911 4.937620 CAGTTTTCATTCAGGCTAGCACTA 59.062 41.667 18.24 0.00 0.00 2.74
834 912 4.938226 AGTTTTCATTCAGGCTAGCACTAC 59.062 41.667 18.24 0.00 0.00 2.73
839 923 3.526931 TTCAGGCTAGCACTACACATC 57.473 47.619 18.24 0.00 0.00 3.06
842 926 3.515502 TCAGGCTAGCACTACACATCTTT 59.484 43.478 18.24 0.00 0.00 2.52
843 927 4.020218 TCAGGCTAGCACTACACATCTTTT 60.020 41.667 18.24 0.00 0.00 2.27
845 929 4.223923 AGGCTAGCACTACACATCTTTTCT 59.776 41.667 18.24 0.00 0.00 2.52
884 970 8.573035 CATATCTTCTCTTAGACTGTTAGGTCC 58.427 40.741 0.00 0.00 36.95 4.46
928 1020 1.753649 TGCTTGCCAGTTTACTTTGCA 59.246 42.857 0.97 0.97 31.63 4.08
939 1078 4.399303 AGTTTACTTTGCATACATCTGGCC 59.601 41.667 0.00 0.00 0.00 5.36
943 1082 3.947834 ACTTTGCATACATCTGGCCTAAC 59.052 43.478 3.32 0.00 0.00 2.34
948 1087 3.187227 GCATACATCTGGCCTAACAATCG 59.813 47.826 3.32 0.00 0.00 3.34
972 1111 1.446907 CATTTCCTCTTCGCTGCAGT 58.553 50.000 16.64 0.00 0.00 4.40
978 1117 2.159184 TCCTCTTCGCTGCAGTATCTTG 60.159 50.000 16.64 2.43 0.00 3.02
983 1123 3.586100 TCGCTGCAGTATCTTGTACAA 57.414 42.857 16.64 8.28 0.00 2.41
984 1124 3.250744 TCGCTGCAGTATCTTGTACAAC 58.749 45.455 16.64 0.00 0.00 3.32
987 1127 3.619038 GCTGCAGTATCTTGTACAACTCC 59.381 47.826 16.64 0.00 0.00 3.85
1013 1153 2.202236 GACCTCATGAGCAGGGGCAA 62.202 60.000 17.76 0.00 44.61 4.52
1016 1156 2.360350 CATGAGCAGGGGCAACGT 60.360 61.111 0.00 0.00 44.61 3.99
1182 1322 2.100631 CAAGGCCATGGACGTCGTC 61.101 63.158 18.40 17.16 0.00 4.20
1248 1388 3.470567 GTCGACAAGGTCTGCGCG 61.471 66.667 11.55 0.00 0.00 6.86
1422 1562 3.392595 GAGGTACGCGGAGGACACG 62.393 68.421 12.47 0.00 34.56 4.49
1488 1628 0.098200 CCACTGTTGCTGATCATGCG 59.902 55.000 0.00 0.00 0.00 4.73
1572 1712 1.635487 AGCAAGCAAGGGAAGATACCA 59.365 47.619 0.00 0.00 0.00 3.25
1584 1724 1.276622 AGATACCATACATCCCGGCC 58.723 55.000 0.00 0.00 0.00 6.13
1764 1904 3.007920 CCTGTGCTCCTCCCAGCT 61.008 66.667 0.00 0.00 40.39 4.24
1872 2012 0.325296 CCCCTCTGTGGTACCAGCTA 60.325 60.000 16.93 3.94 32.32 3.32
1890 2030 2.076863 CTAAAGCTAAACTGGCACGCT 58.923 47.619 0.00 0.00 0.00 5.07
1911 2051 5.108385 CTTGGCGAAACAAGTACTGAATT 57.892 39.130 0.00 0.00 42.18 2.17
1912 2052 5.508200 TTGGCGAAACAAGTACTGAATTT 57.492 34.783 0.00 0.00 0.00 1.82
1923 2063 6.435277 ACAAGTACTGAATTTTCATCCATGCT 59.565 34.615 0.00 0.00 36.46 3.79
1927 2067 4.081862 ACTGAATTTTCATCCATGCTGTGG 60.082 41.667 2.66 2.66 40.04 4.17
1952 2092 0.248296 GTGTTTGTTGAAAGCGCGGA 60.248 50.000 8.83 0.00 0.00 5.54
1998 2138 3.965470 AACCTGGGGTATCCATTTACC 57.035 47.619 0.00 0.00 46.01 2.85
2122 2262 3.790089 TTGTTGGGGGTTGTTTGTTTT 57.210 38.095 0.00 0.00 0.00 2.43
2133 2273 6.371825 GGGGTTGTTTGTTTTGTTTGTATTCA 59.628 34.615 0.00 0.00 0.00 2.57
2137 2277 9.871299 GTTGTTTGTTTTGTTTGTATTCAAGTT 57.129 25.926 0.00 0.00 34.88 2.66
2210 2350 1.337167 GCTTGCCCAGATTGTTCCAAC 60.337 52.381 0.00 0.00 0.00 3.77
2217 2357 2.958355 CCAGATTGTTCCAACACAAGGT 59.042 45.455 0.00 0.00 40.01 3.50
2228 2369 0.034896 ACACAAGGTGGTCGATGGAC 59.965 55.000 0.00 0.00 42.66 4.02
2246 2387 4.181010 CCTCTGGGATGTGGGGCG 62.181 72.222 0.00 0.00 33.58 6.13
2257 2398 1.822186 GTGGGGCGTGACTTGTTGT 60.822 57.895 0.00 0.00 0.00 3.32
2258 2399 1.821759 TGGGGCGTGACTTGTTGTG 60.822 57.895 0.00 0.00 0.00 3.33
2260 2401 2.331451 GGCGTGACTTGTTGTGCC 59.669 61.111 0.00 0.00 35.04 5.01
2300 2446 0.036022 ACCTCTGTTGCAGGAAGAGC 59.964 55.000 13.95 0.00 36.85 4.09
2301 2447 1.018226 CCTCTGTTGCAGGAAGAGCG 61.018 60.000 13.95 6.65 36.85 5.03
2302 2448 1.633852 CTCTGTTGCAGGAAGAGCGC 61.634 60.000 0.00 0.00 31.71 5.92
2373 2520 9.838339 AAGGATATGAACCTGATACTTTAACTG 57.162 33.333 0.00 0.00 37.85 3.16
2452 2599 6.259608 GTCATGATCACCTTCATTTCGATCTT 59.740 38.462 0.00 0.00 34.09 2.40
2453 2600 6.259387 TCATGATCACCTTCATTTCGATCTTG 59.741 38.462 0.00 0.00 38.57 3.02
2456 2603 5.102953 TCACCTTCATTTCGATCTTGGAT 57.897 39.130 0.00 0.00 0.00 3.41
2524 2673 8.700973 TGTCTTGATTGCTATATTGGTACTGTA 58.299 33.333 0.00 0.00 0.00 2.74
2561 2712 7.269477 AGATAATCAAGCTGGCTAACATTTC 57.731 36.000 0.00 0.00 0.00 2.17
2606 2758 9.084533 CTCCCTCTTATATTTCTTAGCACTAGT 57.915 37.037 0.00 0.00 0.00 2.57
2607 2759 8.861086 TCCCTCTTATATTTCTTAGCACTAGTG 58.139 37.037 18.93 18.93 0.00 2.74
2608 2760 8.643324 CCCTCTTATATTTCTTAGCACTAGTGT 58.357 37.037 23.44 12.90 0.00 3.55
2665 2858 9.982651 GAGTAGTTGCTAATGATTTGGTATAGA 57.017 33.333 0.00 0.00 0.00 1.98
2721 2915 8.463930 AGAAAACAAGTTCCTCATTGTATCAA 57.536 30.769 0.00 0.00 38.66 2.57
2737 2931 7.534085 TTGTATCAAAAACTAGTGCCTATCG 57.466 36.000 0.00 0.00 0.00 2.92
2762 2956 4.363138 GCCTTATATTTGGCTTTCAGCAC 58.637 43.478 10.35 0.00 44.75 4.40
2769 2963 2.888834 TGGCTTTCAGCACCTTTTTC 57.111 45.000 0.00 0.00 44.75 2.29
2808 3002 4.705507 AGTCACAGTTAGGTACGACATCAT 59.294 41.667 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 1.566077 GTTCCGTTCGGTTCCGTTG 59.434 57.895 11.04 2.77 0.00 4.10
97 98 2.739671 CCCGTTCCGTTCGGTTCC 60.740 66.667 11.04 0.30 45.63 3.62
173 174 0.465705 TCTCTGCGAGGCCCATTAAG 59.534 55.000 0.00 0.00 0.00 1.85
174 175 0.465705 CTCTCTGCGAGGCCCATTAA 59.534 55.000 0.00 0.00 36.06 1.40
176 177 2.906458 CTCTCTGCGAGGCCCATT 59.094 61.111 0.00 0.00 36.06 3.16
204 205 1.997874 GGTGGGTCTGATGGGCTCT 60.998 63.158 0.00 0.00 0.00 4.09
205 206 2.592308 GGTGGGTCTGATGGGCTC 59.408 66.667 0.00 0.00 0.00 4.70
214 215 3.647771 GGCCTTTCGGGTGGGTCT 61.648 66.667 0.00 0.00 37.43 3.85
220 221 1.831652 CTCTCTGTGGCCTTTCGGGT 61.832 60.000 3.32 0.00 37.43 5.28
222 223 1.078848 CCTCTCTGTGGCCTTTCGG 60.079 63.158 3.32 0.00 0.00 4.30
225 226 0.398318 GTGACCTCTCTGTGGCCTTT 59.602 55.000 3.32 0.00 0.00 3.11
258 265 2.746375 GCAGGACACCGATGGGGAT 61.746 63.158 0.00 0.00 39.97 3.85
262 269 2.187946 GGAGCAGGACACCGATGG 59.812 66.667 0.00 0.00 0.00 3.51
270 277 0.907230 ACAGGAAGGAGGAGCAGGAC 60.907 60.000 0.00 0.00 0.00 3.85
271 278 0.616111 GACAGGAAGGAGGAGCAGGA 60.616 60.000 0.00 0.00 0.00 3.86
283 290 3.072468 CGGGTAGCCGGACAGGAA 61.072 66.667 25.55 0.00 45.00 3.36
285 292 3.834799 GACGGGTAGCCGGACAGG 61.835 72.222 34.40 8.96 44.97 4.00
286 293 2.754658 AGACGGGTAGCCGGACAG 60.755 66.667 34.40 9.71 37.53 3.51
287 294 2.753043 GAGACGGGTAGCCGGACA 60.753 66.667 34.40 0.00 37.53 4.02
288 295 3.525545 GGAGACGGGTAGCCGGAC 61.526 72.222 34.40 26.41 37.53 4.79
310 317 1.882167 GAGCAGAGCAGATCACGGC 60.882 63.158 0.00 0.00 37.48 5.68
369 379 1.994463 CTGAGGTGGGGAGAAAGGG 59.006 63.158 0.00 0.00 0.00 3.95
371 381 1.301293 GGCTGAGGTGGGGAGAAAG 59.699 63.158 0.00 0.00 0.00 2.62
453 514 0.822164 TAGTTCTTCTAGGTGCGGCC 59.178 55.000 0.00 0.00 37.58 6.13
456 517 2.423892 TGCTCTAGTTCTTCTAGGTGCG 59.576 50.000 0.00 0.00 44.45 5.34
458 519 4.142271 CCTGTGCTCTAGTTCTTCTAGGTG 60.142 50.000 0.00 0.00 44.45 4.00
459 520 4.020543 CCTGTGCTCTAGTTCTTCTAGGT 58.979 47.826 0.00 0.00 44.45 3.08
460 521 3.383185 CCCTGTGCTCTAGTTCTTCTAGG 59.617 52.174 0.00 0.00 44.45 3.02
462 523 2.761208 GCCCTGTGCTCTAGTTCTTCTA 59.239 50.000 0.00 0.00 36.87 2.10
463 524 1.552792 GCCCTGTGCTCTAGTTCTTCT 59.447 52.381 0.00 0.00 36.87 2.85
464 525 1.406205 GGCCCTGTGCTCTAGTTCTTC 60.406 57.143 0.00 0.00 40.92 2.87
465 526 0.615850 GGCCCTGTGCTCTAGTTCTT 59.384 55.000 0.00 0.00 40.92 2.52
467 528 1.222113 GGGCCCTGTGCTCTAGTTC 59.778 63.158 17.04 0.00 37.53 3.01
468 529 2.660064 CGGGCCCTGTGCTCTAGTT 61.660 63.158 22.43 0.00 38.81 2.24
469 530 3.077556 CGGGCCCTGTGCTCTAGT 61.078 66.667 22.43 0.00 38.81 2.57
470 531 4.537433 GCGGGCCCTGTGCTCTAG 62.537 72.222 22.43 0.92 38.81 2.43
524 585 1.762460 TAGCACTAGCAGGGGAGCC 60.762 63.158 0.00 0.00 45.49 4.70
530 591 2.099921 CAGTACAGGTAGCACTAGCAGG 59.900 54.545 9.36 3.88 45.49 4.85
543 604 8.883731 CAGTAGGTTGAAATAATTCAGTACAGG 58.116 37.037 0.00 0.00 45.82 4.00
549 610 8.607459 CACTAGCAGTAGGTTGAAATAATTCAG 58.393 37.037 0.00 0.00 45.82 3.02
552 613 9.686683 AATCACTAGCAGTAGGTTGAAATAATT 57.313 29.630 0.00 0.00 0.00 1.40
557 618 9.817809 CTAATAATCACTAGCAGTAGGTTGAAA 57.182 33.333 0.00 0.00 0.00 2.69
559 620 7.015292 CCCTAATAATCACTAGCAGTAGGTTGA 59.985 40.741 0.00 0.00 0.00 3.18
565 626 6.720288 GGACTCCCTAATAATCACTAGCAGTA 59.280 42.308 0.00 0.00 0.00 2.74
567 628 5.540337 TGGACTCCCTAATAATCACTAGCAG 59.460 44.000 0.00 0.00 0.00 4.24
580 648 6.652205 ATGGACTAATTTTGGACTCCCTAA 57.348 37.500 0.00 0.00 0.00 2.69
583 651 5.952347 AGAAATGGACTAATTTTGGACTCCC 59.048 40.000 0.00 0.00 29.89 4.30
584 652 6.434340 ACAGAAATGGACTAATTTTGGACTCC 59.566 38.462 0.00 0.00 29.89 3.85
597 668 6.493802 TGTCTACTCAGTAACAGAAATGGACT 59.506 38.462 0.00 0.00 0.00 3.85
632 703 5.878116 TGGTGATGGCAATGTAACTTAGTAC 59.122 40.000 0.00 0.00 0.00 2.73
634 705 4.917385 TGGTGATGGCAATGTAACTTAGT 58.083 39.130 0.00 0.00 0.00 2.24
639 710 4.036734 CCTACATGGTGATGGCAATGTAAC 59.963 45.833 9.52 0.00 35.64 2.50
641 712 3.457749 TCCTACATGGTGATGGCAATGTA 59.542 43.478 8.29 8.29 35.07 2.29
647 718 3.668447 CAGTATCCTACATGGTGATGGC 58.332 50.000 0.00 0.00 37.07 4.40
653 724 4.413520 AGAATTGGCAGTATCCTACATGGT 59.586 41.667 0.00 0.00 37.07 3.55
664 742 3.844211 AGTGGGTTCTAGAATTGGCAGTA 59.156 43.478 8.75 0.00 0.00 2.74
667 745 2.879756 GCAGTGGGTTCTAGAATTGGCA 60.880 50.000 8.75 0.00 0.00 4.92
683 761 0.179048 TGGTCTGGAACTGTGCAGTG 60.179 55.000 5.53 0.00 43.38 3.66
699 777 6.374417 ACCAAATTAGAGATGTACACTGGT 57.626 37.500 0.00 0.00 0.00 4.00
706 784 7.701539 ACATTGCAACCAAATTAGAGATGTA 57.298 32.000 0.00 0.00 34.05 2.29
715 793 5.002516 CCCACAATACATTGCAACCAAATT 58.997 37.500 0.00 0.00 41.38 1.82
720 798 1.550072 AGCCCACAATACATTGCAACC 59.450 47.619 0.00 0.00 41.38 3.77
727 805 4.270008 GGTTCAGTTAGCCCACAATACAT 58.730 43.478 0.00 0.00 0.00 2.29
776 854 2.026262 TGTGAAAATGAGGGGGCTCTAC 60.026 50.000 0.00 0.00 0.00 2.59
784 862 4.157289 CAGTGGATCTTGTGAAAATGAGGG 59.843 45.833 0.00 0.00 0.00 4.30
800 878 1.538047 ATGAAAACTGCGCAGTGGAT 58.462 45.000 41.21 29.25 41.58 3.41
812 890 4.695455 TGTAGTGCTAGCCTGAATGAAAAC 59.305 41.667 13.29 0.00 0.00 2.43
833 911 7.502226 TGATTCACCTAACAAGAAAAGATGTGT 59.498 33.333 0.00 0.00 0.00 3.72
834 912 7.874940 TGATTCACCTAACAAGAAAAGATGTG 58.125 34.615 0.00 0.00 0.00 3.21
842 926 9.823647 GAGAAGATATGATTCACCTAACAAGAA 57.176 33.333 0.00 0.00 0.00 2.52
843 927 9.206690 AGAGAAGATATGATTCACCTAACAAGA 57.793 33.333 0.00 0.00 0.00 3.02
866 950 6.522054 TGTTTTGGACCTAACAGTCTAAGAG 58.478 40.000 8.20 0.00 38.31 2.85
884 970 4.813027 AGCATAACAGCCTGATTGTTTTG 58.187 39.130 0.00 0.87 39.36 2.44
928 1020 4.345257 AGACGATTGTTAGGCCAGATGTAT 59.655 41.667 5.01 0.00 0.00 2.29
939 1078 4.872691 AGAGGAAATGCAGACGATTGTTAG 59.127 41.667 0.00 0.00 0.00 2.34
943 1082 3.242220 CGAAGAGGAAATGCAGACGATTG 60.242 47.826 0.00 0.00 0.00 2.67
948 1087 1.396301 CAGCGAAGAGGAAATGCAGAC 59.604 52.381 0.00 0.00 0.00 3.51
972 1111 4.461431 TCTGCTTCGGAGTTGTACAAGATA 59.539 41.667 8.98 0.00 0.00 1.98
978 1117 1.272769 AGGTCTGCTTCGGAGTTGTAC 59.727 52.381 0.00 0.00 0.00 2.90
983 1123 0.534412 CATGAGGTCTGCTTCGGAGT 59.466 55.000 0.00 0.00 0.00 3.85
984 1124 0.820226 TCATGAGGTCTGCTTCGGAG 59.180 55.000 0.00 0.00 0.00 4.63
987 1127 0.108472 TGCTCATGAGGTCTGCTTCG 60.108 55.000 23.89 0.00 0.00 3.79
1065 1205 0.806868 TGTGGTAGTCGTAGCTTCGG 59.193 55.000 13.03 0.00 0.00 4.30
1068 1208 3.192212 GGTAGTTGTGGTAGTCGTAGCTT 59.808 47.826 0.00 0.00 0.00 3.74
1212 1352 1.374758 CACGTCCTTCCACCAGAGC 60.375 63.158 0.00 0.00 0.00 4.09
1248 1388 4.373116 TGCTCGACCGTCTTGCCC 62.373 66.667 9.22 0.00 0.00 5.36
1368 1508 2.764128 TCAGGGATGGCGTCCTCC 60.764 66.667 24.35 9.64 46.91 4.30
1422 1562 0.530744 TGTACAGGATGGTCGACTGC 59.469 55.000 16.46 1.36 43.62 4.40
1542 1682 0.242825 CTTGCTTGCTCACATGGTGG 59.757 55.000 0.00 0.00 33.87 4.61
1572 1712 1.526887 CACACTGGCCGGGATGTAT 59.473 57.895 18.00 0.00 0.00 2.29
1584 1724 2.047844 CACTCCTCCGCCACACTG 60.048 66.667 0.00 0.00 0.00 3.66
1662 1802 1.438710 CGCGACCTTGAAAACTGCG 60.439 57.895 0.00 0.00 38.04 5.18
1677 1817 4.430423 GCTTCGGCAACAGACGCG 62.430 66.667 3.53 3.53 41.33 6.01
1744 1884 2.284921 TGGGAGGAGCACAGGGAG 60.285 66.667 0.00 0.00 0.00 4.30
1749 1889 2.527624 ACAGCTGGGAGGAGCACA 60.528 61.111 19.93 0.00 41.83 4.57
1872 2012 1.001378 CAAGCGTGCCAGTTTAGCTTT 60.001 47.619 0.00 0.00 44.59 3.51
1890 2030 5.508200 AAATTCAGTACTTGTTTCGCCAA 57.492 34.783 0.00 0.00 0.00 4.52
1923 2063 0.453793 CAACAAACACGCTTCCCACA 59.546 50.000 0.00 0.00 0.00 4.17
1927 2067 1.852280 GCTTTCAACAAACACGCTTCC 59.148 47.619 0.00 0.00 0.00 3.46
1952 2092 0.740737 GGGCTAAAACGCATGCTGAT 59.259 50.000 17.13 1.15 0.00 2.90
1998 2138 7.425577 TCATCATCAAGCTTATTACATTCCG 57.574 36.000 0.00 0.00 0.00 4.30
2122 2262 7.698628 TCATGTCGAAAACTTGAATACAAACA 58.301 30.769 0.00 0.00 38.65 2.83
2133 2273 3.485463 TCCACCTCATGTCGAAAACTT 57.515 42.857 0.00 0.00 0.00 2.66
2137 2277 3.694043 TTCATCCACCTCATGTCGAAA 57.306 42.857 0.00 0.00 0.00 3.46
2138 2278 3.055167 ACATTCATCCACCTCATGTCGAA 60.055 43.478 0.00 0.00 0.00 3.71
2210 2350 2.840974 GTCCATCGACCACCTTGTG 58.159 57.895 0.00 0.00 32.40 3.33
2228 2369 3.813724 GCCCCACATCCCAGAGGG 61.814 72.222 0.00 0.00 46.11 4.30
2246 2387 1.795170 ATGGCGGCACAACAAGTCAC 61.795 55.000 16.34 0.00 0.00 3.67
2257 2398 2.441410 TGAATTTGAACTATGGCGGCA 58.559 42.857 16.34 16.34 0.00 5.69
2258 2399 3.502191 TTGAATTTGAACTATGGCGGC 57.498 42.857 0.00 0.00 0.00 6.53
2260 2401 5.036737 GGTCATTGAATTTGAACTATGGCG 58.963 41.667 0.00 0.00 0.00 5.69
2300 2446 3.320673 AACCTTTCTCTCTTAGGTGCG 57.679 47.619 0.00 0.00 41.33 5.34
2301 2447 4.760878 CCTAACCTTTCTCTCTTAGGTGC 58.239 47.826 0.00 0.00 41.33 5.01
2302 2448 4.223032 TGCCTAACCTTTCTCTCTTAGGTG 59.777 45.833 0.00 0.00 41.33 4.00
2383 2530 1.878775 GCCGCACATCTGAAGCTTT 59.121 52.632 0.00 0.00 0.00 3.51
2417 2564 4.764172 AGGTGATCATGACTTCTGCTTAC 58.236 43.478 0.00 0.00 0.00 2.34
2452 2599 7.560991 ACATATCTGCATTACCTGAAAAATCCA 59.439 33.333 0.00 0.00 0.00 3.41
2453 2600 7.864379 CACATATCTGCATTACCTGAAAAATCC 59.136 37.037 0.00 0.00 0.00 3.01
2456 2603 6.663093 ACCACATATCTGCATTACCTGAAAAA 59.337 34.615 0.00 0.00 0.00 1.94
2612 2764 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2613 2765 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2615 2767 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2616 2768 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2617 2769 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2619 2771 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2621 2773 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2622 2774 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2623 2775 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2624 2776 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2625 2777 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2627 2779 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2631 2824 1.760192 TAGCAACTACTCCCTCCGTC 58.240 55.000 0.00 0.00 0.00 4.79
2702 2896 9.831737 CTAGTTTTTGATACAATGAGGAACTTG 57.168 33.333 0.00 0.00 41.55 3.16
2762 2956 8.171164 ACTGATAAGGAAGTCAAAGAAAAAGG 57.829 34.615 0.00 0.00 0.00 3.11
2864 3058 2.358898 CCGGCCAACCTCATTTTATCTG 59.641 50.000 2.24 0.00 0.00 2.90
2865 3059 2.025321 ACCGGCCAACCTCATTTTATCT 60.025 45.455 0.00 0.00 0.00 1.98
2866 3060 2.099098 CACCGGCCAACCTCATTTTATC 59.901 50.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.