Multiple sequence alignment - TraesCS7A01G247500

Loading Multiple Alignment...

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 TraesCS7A01G247500 chr7A 100.000 3515 0 0 1 3515 228169213 228172727 0.000000e+00 6492.0
1 TraesCS7A01G247500 chr7A 84.524 168 25 1 712 878 30454941 30454774 7.810000e-37 165.0
2 TraesCS7A01G247500 chr7A 79.861 144 25 3 299 439 721590649 721590507 6.210000e-18 102.0
3 TraesCS7A01G247500 chr7A 78.767 146 25 5 297 439 30456146 30456004 3.740000e-15 93.5
4 TraesCS7A01G247500 chr7D 93.102 2421 113 29 546 2945 215054733 215057120 0.000000e+00 3496.0
5 TraesCS7A01G247500 chr7D 89.244 595 38 6 2945 3515 215057148 215057740 0.000000e+00 721.0
6 TraesCS7A01G247500 chr7D 82.927 123 21 0 316 438 215054334 215054456 1.030000e-20 111.0
7 TraesCS7A01G247500 chr7D 79.310 145 28 2 299 442 606820756 606820613 2.230000e-17 100.0
8 TraesCS7A01G247500 chr7B 93.901 2312 99 19 655 2943 185013402 185015694 0.000000e+00 3450.0
9 TraesCS7A01G247500 chr7B 88.686 601 32 10 2945 3515 185015724 185016318 0.000000e+00 701.0
10 TraesCS7A01G247500 chr7B 85.517 435 47 5 9 443 185012573 185012991 1.160000e-119 440.0
11 TraesCS7A01G247500 chr2D 80.378 423 54 20 454 873 600565222 600565618 9.540000e-76 294.0
12 TraesCS7A01G247500 chr2B 79.087 416 51 16 459 873 796179176 796178796 1.620000e-63 254.0
13 TraesCS7A01G247500 chr2B 83.974 156 24 1 719 873 792465887 792466042 7.860000e-32 148.0
14 TraesCS7A01G247500 chr2B 79.286 140 28 1 297 436 717936017 717936155 2.890000e-16 97.1
15 TraesCS7A01G247500 chr6D 88.535 157 15 3 719 873 149735516 149735671 1.670000e-43 187.0
16 TraesCS7A01G247500 chr6D 87.742 155 17 2 721 873 383261444 383261290 2.790000e-41 180.0
17 TraesCS7A01G247500 chr6B 88.387 155 16 2 719 871 585817003 585817157 5.990000e-43 185.0
18 TraesCS7A01G247500 chr1B 81.651 218 35 4 644 859 266915716 266915502 3.610000e-40 176.0
19 TraesCS7A01G247500 chr5A 85.897 156 21 1 719 873 129605080 129605235 7.810000e-37 165.0
20 TraesCS7A01G247500 chr3B 84.906 159 20 4 717 872 731635179 731635336 1.310000e-34 158.0
21 TraesCS7A01G247500 chr3B 79.720 143 25 4 299 440 505022343 505022482 2.230000e-17 100.0
22 TraesCS7A01G247500 chr2A 89.000 100 9 2 297 395 70215709 70215807 4.760000e-24 122.0
23 TraesCS7A01G247500 chr3D 81.022 137 24 1 299 435 542802392 542802258 1.330000e-19 108.0
24 TraesCS7A01G247500 chr5D 79.861 144 24 5 296 438 458155553 458155414 2.230000e-17 100.0
25 TraesCS7A01G247500 chr5B 79.452 146 26 4 299 442 255969282 255969425 2.230000e-17 100.0
26 TraesCS7A01G247500 chr5B 79.699 133 25 1 310 440 679577721 679577589 1.040000e-15 95.3


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 TraesCS7A01G247500 chr7A 228169213 228172727 3514 False 6492.000000 6492 100.000000 1 3515 1 chr7A.!!$F1 3514
1 TraesCS7A01G247500 chr7D 215054334 215057740 3406 False 1442.666667 3496 88.424333 316 3515 3 chr7D.!!$F1 3199
2 TraesCS7A01G247500 chr7B 185012573 185016318 3745 False 1530.333333 3450 89.368000 9 3515 3 chr7B.!!$F1 3506

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
130 131 0.108945 GCTTTTGCATGTCCTCTGCC 60.109 55.0 0.0 0.0 46.58 4.85 F
132 133 0.112995 TTTTGCATGTCCTCTGCCCT 59.887 50.0 0.0 0.0 38.89 5.19 F
2118 2381 0.477204 ATGCAGGGATGGTGGATGAG 59.523 55.0 0.0 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2381 2.103094 GGAGCCAAAATATTTCCTGCCC 59.897 50.0 0.1 5.16 0.00 5.36 R
2135 2398 2.289002 CCGTAAAGATTCAGCATGGAGC 59.711 50.0 0.0 0.00 46.19 4.70 R
3228 3553 0.465705 AGGTGCCAGTATGACATCGG 59.534 55.0 0.0 0.00 39.69 4.18 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
41 42 1.341080 CCAAACCTTGGCCTGTGAAT 58.659 50.000 3.32 0.00 45.17 2.57
49 50 4.837860 ACCTTGGCCTGTGAATGAATTTTA 59.162 37.500 3.32 0.00 0.00 1.52
50 51 5.170748 CCTTGGCCTGTGAATGAATTTTAC 58.829 41.667 3.32 0.00 0.00 2.01
57 58 5.861787 CCTGTGAATGAATTTTACCGGTTTC 59.138 40.000 15.04 11.51 0.00 2.78
70 71 2.152016 CCGGTTTCCTTGACTCCTTTC 58.848 52.381 0.00 0.00 0.00 2.62
98 99 1.256376 CATACGTTGCGCTCAGTGATC 59.744 52.381 9.73 0.00 0.00 2.92
109 110 4.798924 GCGCTCAGTGATCCTCTATCAAAT 60.799 45.833 0.00 0.00 46.17 2.32
129 130 3.413522 GCTTTTGCATGTCCTCTGC 57.586 52.632 0.00 0.00 46.58 4.26
130 131 0.108945 GCTTTTGCATGTCCTCTGCC 60.109 55.000 0.00 0.00 46.58 4.85
131 132 0.529378 CTTTTGCATGTCCTCTGCCC 59.471 55.000 0.00 0.00 38.89 5.36
132 133 0.112995 TTTTGCATGTCCTCTGCCCT 59.887 50.000 0.00 0.00 38.89 5.19
133 134 0.991146 TTTGCATGTCCTCTGCCCTA 59.009 50.000 0.00 0.00 38.89 3.53
134 135 0.543277 TTGCATGTCCTCTGCCCTAG 59.457 55.000 0.00 0.00 38.89 3.02
170 171 6.206180 TCTGGACATCATCTACCATCTAGA 57.794 41.667 0.00 0.00 0.00 2.43
176 177 8.538701 GGACATCATCTACCATCTAGAAATCAT 58.461 37.037 0.00 0.00 0.00 2.45
187 188 3.124798 GAAATCATGGGTGGCCGCG 62.125 63.158 10.86 0.00 0.00 6.46
197 198 4.697756 TGGCCGCGTGGAAGGAAG 62.698 66.667 21.76 0.00 37.49 3.46
216 217 5.608860 AGGAAGAAGGAAGAAGGAAGAAGAA 59.391 40.000 0.00 0.00 0.00 2.52
217 218 6.101881 AGGAAGAAGGAAGAAGGAAGAAGAAA 59.898 38.462 0.00 0.00 0.00 2.52
218 219 6.429692 GGAAGAAGGAAGAAGGAAGAAGAAAG 59.570 42.308 0.00 0.00 0.00 2.62
219 220 6.508030 AGAAGGAAGAAGGAAGAAGAAAGT 57.492 37.500 0.00 0.00 0.00 2.66
220 221 7.619512 AGAAGGAAGAAGGAAGAAGAAAGTA 57.380 36.000 0.00 0.00 0.00 2.24
221 222 7.676004 AGAAGGAAGAAGGAAGAAGAAAGTAG 58.324 38.462 0.00 0.00 0.00 2.57
222 223 7.511028 AGAAGGAAGAAGGAAGAAGAAAGTAGA 59.489 37.037 0.00 0.00 0.00 2.59
273 274 7.173390 AGTTTTGTATGTTTGGAGAGTTAGCTC 59.827 37.037 0.00 0.00 41.94 4.09
305 306 9.066892 TGTTTTAACTCTCATGTTTAGAGCATT 57.933 29.630 9.28 1.83 43.59 3.56
364 365 6.916360 TTTGTATCTCCAAGGCTCAAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
375 376 5.628797 AGGCTCAAAAATCCTTTTCCAAA 57.371 34.783 0.00 0.00 32.24 3.28
384 385 7.677454 AAAATCCTTTTCCAAAAGATGATGC 57.323 32.000 12.51 0.00 46.39 3.91
395 396 7.541162 TCCAAAAGATGATGCAGATGTAAAAG 58.459 34.615 0.00 0.00 0.00 2.27
396 397 6.755141 CCAAAAGATGATGCAGATGTAAAAGG 59.245 38.462 0.00 0.00 0.00 3.11
397 398 7.318141 CAAAAGATGATGCAGATGTAAAAGGT 58.682 34.615 0.00 0.00 0.00 3.50
398 399 7.472334 AAAGATGATGCAGATGTAAAAGGTT 57.528 32.000 0.00 0.00 0.00 3.50
402 403 9.193806 AGATGATGCAGATGTAAAAGGTTTTAT 57.806 29.630 0.00 0.00 35.35 1.40
416 417 4.307259 AGGTTTTATATCTCAGCCTCCCA 58.693 43.478 0.00 0.00 0.00 4.37
422 423 2.014010 ATCTCAGCCTCCCAGAGATC 57.986 55.000 0.00 0.00 43.63 2.75
424 425 1.042229 CTCAGCCTCCCAGAGATCTG 58.958 60.000 0.00 2.72 43.40 2.90
443 444 7.827701 AGATCTGAAATACAACACTTCGAGTA 58.172 34.615 0.00 0.00 0.00 2.59
444 445 7.755822 AGATCTGAAATACAACACTTCGAGTAC 59.244 37.037 0.00 0.00 0.00 2.73
446 447 4.919168 TGAAATACAACACTTCGAGTACCG 59.081 41.667 0.00 0.00 40.25 4.02
447 448 4.510038 AATACAACACTTCGAGTACCGT 57.490 40.909 4.11 0.00 39.75 4.83
544 796 4.814294 ACCGCCGCCACTCGATTC 62.814 66.667 0.00 0.00 41.67 2.52
546 798 4.812476 CGCCGCCACTCGATTCCA 62.812 66.667 0.00 0.00 41.67 3.53
547 799 3.195698 GCCGCCACTCGATTCCAC 61.196 66.667 0.00 0.00 41.67 4.02
548 800 2.511600 CCGCCACTCGATTCCACC 60.512 66.667 0.00 0.00 41.67 4.61
549 801 2.264480 CGCCACTCGATTCCACCA 59.736 61.111 0.00 0.00 41.67 4.17
550 802 2.100631 CGCCACTCGATTCCACCAC 61.101 63.158 0.00 0.00 41.67 4.16
551 803 1.745489 GCCACTCGATTCCACCACC 60.745 63.158 0.00 0.00 0.00 4.61
552 804 1.447838 CCACTCGATTCCACCACCG 60.448 63.158 0.00 0.00 0.00 4.94
553 805 2.100631 CACTCGATTCCACCACCGC 61.101 63.158 0.00 0.00 0.00 5.68
554 806 2.511600 CTCGATTCCACCACCGCC 60.512 66.667 0.00 0.00 0.00 6.13
555 807 4.444838 TCGATTCCACCACCGCCG 62.445 66.667 0.00 0.00 0.00 6.46
557 809 4.778143 GATTCCACCACCGCCGCT 62.778 66.667 0.00 0.00 0.00 5.52
589 841 4.147449 CACTCCCATCGCCGCTCA 62.147 66.667 0.00 0.00 0.00 4.26
753 1005 7.040892 TCCATTTGCATCATCTATTAGAGTTGC 60.041 37.037 13.99 13.99 31.80 4.17
755 1007 7.870509 TTTGCATCATCTATTAGAGTTGCTT 57.129 32.000 18.39 0.00 32.17 3.91
841 1093 9.313118 ACACTTTTGAAGATGTAAATTTTCACC 57.687 29.630 0.00 0.00 29.96 4.02
855 1107 5.941948 ATTTTCACCTCTCCTGTTTTACG 57.058 39.130 0.00 0.00 0.00 3.18
859 1111 3.255149 TCACCTCTCCTGTTTTACGTCTC 59.745 47.826 0.00 0.00 0.00 3.36
860 1112 2.561858 ACCTCTCCTGTTTTACGTCTCC 59.438 50.000 0.00 0.00 0.00 3.71
873 1125 5.545658 TTACGTCTCCAAATTTGCATCTC 57.454 39.130 12.92 1.45 0.00 2.75
874 1126 2.749621 ACGTCTCCAAATTTGCATCTCC 59.250 45.455 12.92 0.00 0.00 3.71
875 1127 2.223112 CGTCTCCAAATTTGCATCTCCG 60.223 50.000 12.92 5.87 0.00 4.63
878 1130 4.816385 GTCTCCAAATTTGCATCTCCGATA 59.184 41.667 12.92 0.00 0.00 2.92
882 1134 7.173218 TCTCCAAATTTGCATCTCCGATATTAC 59.827 37.037 12.92 0.00 0.00 1.89
907 1159 6.252441 CGGAGTTATGATATGCTCGAAGATTC 59.748 42.308 0.00 0.00 33.89 2.52
1276 1539 2.754658 CCCTCGTCCACGCCTACT 60.755 66.667 0.00 0.00 39.60 2.57
1457 1720 5.598769 AGAGGTAATTAATAGTGTCACGGC 58.401 41.667 0.00 0.00 0.00 5.68
1698 1961 3.006940 TGAGGTTTGTAATCGTCATGGC 58.993 45.455 0.00 0.00 0.00 4.40
1701 1964 2.477863 GGTTTGTAATCGTCATGGCAGC 60.478 50.000 0.00 0.00 0.00 5.25
1720 1983 4.794655 GCAGCTCGGATAAGGTTCTAGAAG 60.795 50.000 5.12 0.00 0.00 2.85
1867 2130 6.861065 AGACTAATTGTTGTCGACATGTTT 57.139 33.333 20.80 12.93 38.26 2.83
2019 2282 0.964358 GCCAAGGCAGAGATGCAGTT 60.964 55.000 6.14 0.00 41.49 3.16
2088 2351 2.094957 TGCATTTTTAGGCGTGCTTACC 60.095 45.455 0.00 0.00 38.37 2.85
2118 2381 0.477204 ATGCAGGGATGGTGGATGAG 59.523 55.000 0.00 0.00 0.00 2.90
2135 2398 4.039609 GGATGAGGGCAGGAAATATTTTGG 59.960 45.833 1.43 0.00 0.00 3.28
2244 2507 2.435069 AGAGGTTGAGAGGATGATGCAG 59.565 50.000 0.00 0.00 0.00 4.41
2338 2601 4.269183 CGATGTAGCTGAGAGGATAGGAT 58.731 47.826 0.00 0.00 0.00 3.24
2342 2605 1.792026 AGCTGAGAGGATAGGATGGGA 59.208 52.381 0.00 0.00 0.00 4.37
2400 2663 6.650807 CCTATGTGGTCATGTCCAACATATAC 59.349 42.308 21.83 9.30 36.53 1.47
2443 2706 0.460459 GGTCGAGCAAACTAGGAGGC 60.460 60.000 10.30 0.00 0.00 4.70
2456 2719 1.203441 AGGAGGCTGATGTGGCAGAA 61.203 55.000 0.00 0.00 38.14 3.02
2475 2738 7.180766 TGGCAGAAGGGATTGAAGAAAAATATT 59.819 33.333 0.00 0.00 0.00 1.28
2579 2842 4.852134 TGTGGAAATGTGACATCAAAGG 57.148 40.909 0.00 0.00 0.00 3.11
2605 2868 1.340405 ACATTCCTGTCTGGACCATGC 60.340 52.381 0.00 0.00 46.14 4.06
2656 2919 5.361571 TGCGGACATAGAGGTAAACATCTAA 59.638 40.000 8.41 0.00 41.72 2.10
2657 2920 6.041637 TGCGGACATAGAGGTAAACATCTAAT 59.958 38.462 8.41 1.06 41.72 1.73
2658 2921 6.586844 GCGGACATAGAGGTAAACATCTAATC 59.413 42.308 8.41 8.95 41.72 1.75
2659 2922 7.524038 GCGGACATAGAGGTAAACATCTAATCT 60.524 40.741 8.41 0.00 41.72 2.40
2660 2923 9.011095 CGGACATAGAGGTAAACATCTAATCTA 57.989 37.037 8.41 0.00 41.72 1.98
2689 2952 7.775397 AAAGTGCTTACGAGTTGTTTACTTA 57.225 32.000 0.00 0.00 37.17 2.24
2705 2968 7.951591 TGTTTACTTACGTACTTACCTTTCCT 58.048 34.615 0.00 0.00 0.00 3.36
2732 2995 9.716507 TTTTTGAAGCTAGATCGTTATTTATGC 57.283 29.630 0.00 0.00 0.00 3.14
2761 3024 6.636454 ATCCTGTACTTGATTTGGTAAGGA 57.364 37.500 0.00 0.00 33.89 3.36
2777 3040 7.399245 TGGTAAGGACAAAATAGGTAAATGC 57.601 36.000 0.00 0.00 0.00 3.56
2839 3104 2.575735 TGGAGGTTGATATGTTGCCTGA 59.424 45.455 0.00 0.00 0.00 3.86
2840 3105 2.945668 GGAGGTTGATATGTTGCCTGAC 59.054 50.000 0.00 0.00 0.00 3.51
2842 3107 3.347216 AGGTTGATATGTTGCCTGACAC 58.653 45.455 0.00 0.00 31.30 3.67
2847 3112 0.037590 TATGTTGCCTGACACCACCC 59.962 55.000 0.00 0.00 31.30 4.61
2911 3183 8.893727 GCTTCTTTGTCTAGCCTAAATATCAAA 58.106 33.333 0.00 0.00 0.00 2.69
3118 3425 3.462021 GGCATCTGAACAGATAGACACC 58.538 50.000 15.52 9.49 45.78 4.16
3125 3432 1.853963 ACAGATAGACACCGAGCCTT 58.146 50.000 0.00 0.00 0.00 4.35
3136 3443 2.671177 CGAGCCTTCAAGGTGTGCG 61.671 63.158 5.03 0.22 37.80 5.34
3192 3517 5.003804 CACCCAACACTAGCAGAAAGTATT 58.996 41.667 0.00 0.00 0.00 1.89
3199 3524 6.284459 ACACTAGCAGAAAGTATTCATAGCC 58.716 40.000 0.00 0.00 38.06 3.93
3229 3554 4.755266 TGGAATAGCTCAAGGTAAGACC 57.245 45.455 0.00 0.00 38.99 3.85
3241 3566 4.920640 AGGTAAGACCGATGTCATACTG 57.079 45.455 7.69 0.00 44.90 2.74
3318 3643 7.816995 GCATGTAATTGATCCCAAACAAGTTAA 59.183 33.333 0.00 0.00 35.67 2.01
3391 3716 3.141398 TCTCTGAAAGTTGTGCCACATC 58.859 45.455 0.00 0.00 33.76 3.06
3418 3748 5.413213 TGTGTACTTGTTACAAAAGCTGTGT 59.587 36.000 8.27 8.27 42.56 3.72
3430 3760 0.179048 AGCTGTGTTGTGCTGCACTA 60.179 50.000 30.43 22.20 38.21 2.74
3474 3804 0.469892 TGCACTCAGGAGTCAGGACA 60.470 55.000 0.00 0.00 40.20 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.967332 AAATTCATTCACAGGCCAAGG 57.033 42.857 5.01 0.00 0.00 3.61
33 34 5.385509 AACCGGTAAAATTCATTCACAGG 57.614 39.130 8.00 0.00 0.00 4.00
35 36 5.536916 AGGAAACCGGTAAAATTCATTCACA 59.463 36.000 8.00 0.00 0.00 3.58
41 42 5.134661 AGTCAAGGAAACCGGTAAAATTCA 58.865 37.500 8.00 0.00 0.00 2.57
49 50 1.137697 AAGGAGTCAAGGAAACCGGT 58.862 50.000 0.00 0.00 0.00 5.28
50 51 2.152016 GAAAGGAGTCAAGGAAACCGG 58.848 52.381 0.00 0.00 0.00 5.28
57 58 1.532868 CGTGCAAGAAAGGAGTCAAGG 59.467 52.381 0.00 0.00 0.00 3.61
83 84 0.108424 AGAGGATCACTGAGCGCAAC 60.108 55.000 11.47 3.52 37.82 4.17
109 110 1.000060 GCAGAGGACATGCAAAAGCAA 60.000 47.619 0.00 0.00 43.31 3.91
134 135 0.391228 GTCCAGAAGCTAGCTAGGGC 59.609 60.000 19.70 17.78 39.06 5.19
170 171 3.140141 CGCGGCCACCCATGATTT 61.140 61.111 2.24 0.00 0.00 2.17
187 188 3.328050 TCCTTCTTCCTTCTTCCTTCCAC 59.672 47.826 0.00 0.00 0.00 4.02
197 198 7.601130 GTCTACTTTCTTCTTCCTTCTTCCTTC 59.399 40.741 0.00 0.00 0.00 3.46
216 217 5.376756 AAGTCTCTATCCCTCGTCTACTT 57.623 43.478 0.00 0.00 0.00 2.24
217 218 5.104444 TGAAAGTCTCTATCCCTCGTCTACT 60.104 44.000 0.00 0.00 0.00 2.57
218 219 5.124645 TGAAAGTCTCTATCCCTCGTCTAC 58.875 45.833 0.00 0.00 0.00 2.59
219 220 5.369409 TGAAAGTCTCTATCCCTCGTCTA 57.631 43.478 0.00 0.00 0.00 2.59
220 221 4.237976 TGAAAGTCTCTATCCCTCGTCT 57.762 45.455 0.00 0.00 0.00 4.18
221 222 4.339814 ACATGAAAGTCTCTATCCCTCGTC 59.660 45.833 0.00 0.00 0.00 4.20
222 223 4.282496 ACATGAAAGTCTCTATCCCTCGT 58.718 43.478 0.00 0.00 0.00 4.18
273 274 5.046910 ACATGAGAGTTAAAACAATGCGG 57.953 39.130 0.00 0.00 0.00 5.69
275 276 9.334693 CTCTAAACATGAGAGTTAAAACAATGC 57.665 33.333 0.00 0.00 36.48 3.56
278 279 8.445275 TGCTCTAAACATGAGAGTTAAAACAA 57.555 30.769 0.00 0.00 42.16 2.83
345 346 5.456921 AGGATTTTTGAGCCTTGGAGATA 57.543 39.130 0.00 0.00 43.04 1.98
364 365 5.078949 TCTGCATCATCTTTTGGAAAAGGA 58.921 37.500 11.10 3.45 44.22 3.36
375 376 7.472334 AAACCTTTTACATCTGCATCATCTT 57.528 32.000 0.00 0.00 0.00 2.40
395 396 4.348168 TCTGGGAGGCTGAGATATAAAACC 59.652 45.833 0.00 0.00 0.00 3.27
396 397 5.305644 TCTCTGGGAGGCTGAGATATAAAAC 59.694 44.000 0.00 0.00 32.63 2.43
397 398 5.467738 TCTCTGGGAGGCTGAGATATAAAA 58.532 41.667 0.00 0.00 32.63 1.52
398 399 5.079998 TCTCTGGGAGGCTGAGATATAAA 57.920 43.478 0.00 0.00 32.63 1.40
402 403 2.721355 AGATCTCTGGGAGGCTGAGATA 59.279 50.000 13.30 0.00 44.58 1.98
408 409 2.260639 TTTCAGATCTCTGGGAGGCT 57.739 50.000 7.33 0.00 43.91 4.58
416 417 6.925211 TCGAAGTGTTGTATTTCAGATCTCT 58.075 36.000 0.00 0.00 0.00 3.10
422 423 5.060569 CGGTACTCGAAGTGTTGTATTTCAG 59.939 44.000 0.00 0.00 42.43 3.02
424 425 4.919754 ACGGTACTCGAAGTGTTGTATTTC 59.080 41.667 10.17 0.00 42.43 2.17
527 779 4.814294 GAATCGAGTGGCGGCGGT 62.814 66.667 9.78 0.00 41.33 5.68
529 781 4.812476 TGGAATCGAGTGGCGGCG 62.812 66.667 0.51 0.51 41.33 6.46
530 782 3.195698 GTGGAATCGAGTGGCGGC 61.196 66.667 0.00 0.00 41.33 6.53
531 783 2.511600 GGTGGAATCGAGTGGCGG 60.512 66.667 0.00 0.00 41.33 6.13
532 784 2.100631 GTGGTGGAATCGAGTGGCG 61.101 63.158 0.00 0.00 42.69 5.69
533 785 1.745489 GGTGGTGGAATCGAGTGGC 60.745 63.158 0.00 0.00 0.00 5.01
535 787 2.100631 GCGGTGGTGGAATCGAGTG 61.101 63.158 0.00 0.00 0.00 3.51
536 788 2.264794 GCGGTGGTGGAATCGAGT 59.735 61.111 0.00 0.00 0.00 4.18
537 789 2.511600 GGCGGTGGTGGAATCGAG 60.512 66.667 0.00 0.00 0.00 4.04
538 790 4.444838 CGGCGGTGGTGGAATCGA 62.445 66.667 0.00 0.00 0.00 3.59
540 792 4.778143 AGCGGCGGTGGTGGAATC 62.778 66.667 12.25 0.00 0.00 2.52
685 937 4.849310 TATTCAGGCGGTGGCGGC 62.849 66.667 0.00 0.00 41.24 6.53
815 1067 9.313118 GGTGAAAATTTACATCTTCAAAAGTGT 57.687 29.630 0.00 0.00 30.03 3.55
823 1075 7.391833 ACAGGAGAGGTGAAAATTTACATCTTC 59.608 37.037 9.07 7.57 37.98 2.87
841 1093 3.936372 TGGAGACGTAAAACAGGAGAG 57.064 47.619 0.00 0.00 0.00 3.20
855 1107 3.009723 TCGGAGATGCAAATTTGGAGAC 58.990 45.455 19.47 14.21 30.13 3.36
859 1111 6.079763 CGTAATATCGGAGATGCAAATTTGG 58.920 40.000 19.47 1.46 45.12 3.28
874 1126 7.321509 CGAGCATATCATAACTCCGTAATATCG 59.678 40.741 0.00 0.00 0.00 2.92
875 1127 8.343366 TCGAGCATATCATAACTCCGTAATATC 58.657 37.037 0.00 0.00 0.00 1.63
878 1130 6.510879 TCGAGCATATCATAACTCCGTAAT 57.489 37.500 0.00 0.00 0.00 1.89
882 1134 5.048153 TCTTCGAGCATATCATAACTCCG 57.952 43.478 0.00 0.00 0.00 4.63
907 1159 7.910441 AAATTTTATCCCAGCTCAAATTGTG 57.090 32.000 0.00 0.00 29.56 3.33
959 1211 2.106477 TGCATGAACGAATACCAGCA 57.894 45.000 0.00 0.00 0.00 4.41
961 1213 2.679837 AGCTTGCATGAACGAATACCAG 59.320 45.455 3.33 0.00 0.00 4.00
1434 1697 5.452917 GGCCGTGACACTATTAATTACCTCT 60.453 44.000 3.68 0.00 0.00 3.69
1537 1800 2.202690 CAATACGGGCTCGACGCA 60.203 61.111 15.95 0.00 41.67 5.24
1698 1961 4.794655 GCTTCTAGAACCTTATCCGAGCTG 60.795 50.000 0.00 0.00 0.00 4.24
1701 1964 5.523438 AAGCTTCTAGAACCTTATCCGAG 57.477 43.478 10.70 0.00 0.00 4.63
1867 2130 5.164620 TCCATTAGAGATGTGCAAACTGA 57.835 39.130 0.00 0.00 0.00 3.41
2118 2381 2.103094 GGAGCCAAAATATTTCCTGCCC 59.897 50.000 0.10 5.16 0.00 5.36
2135 2398 2.289002 CCGTAAAGATTCAGCATGGAGC 59.711 50.000 0.00 0.00 46.19 4.70
2342 2605 6.634039 TAACTGAGGGTTAAGTTCAGCAAACT 60.634 38.462 9.54 0.00 43.14 2.66
2400 2663 1.079127 CCACCTACCAACCTCTGCG 60.079 63.158 0.00 0.00 0.00 5.18
2443 2706 2.022195 CAATCCCTTCTGCCACATCAG 58.978 52.381 0.00 0.00 35.46 2.90
2456 2719 6.669154 TGAGCCAATATTTTTCTTCAATCCCT 59.331 34.615 0.00 0.00 0.00 4.20
2475 2738 0.535780 CTTCAGTGCCACTTGAGCCA 60.536 55.000 0.00 0.00 0.00 4.75
2503 2766 3.264947 TCGATTGAATTCAGGAGCACAG 58.735 45.455 8.41 0.00 0.00 3.66
2537 2800 4.510340 ACAACACGTCTTTCACAGTATTCC 59.490 41.667 0.00 0.00 0.00 3.01
2543 2806 2.276201 TCCACAACACGTCTTTCACAG 58.724 47.619 0.00 0.00 0.00 3.66
2579 2842 3.266510 TCCAGACAGGAATGTACATGC 57.733 47.619 9.63 7.30 45.65 4.06
2605 2868 5.655893 AAACTGGCAATTCAATTCAAACG 57.344 34.783 0.00 0.00 0.00 3.60
2656 2919 7.871463 ACAACTCGTAAGCACTTTAAGTTAGAT 59.129 33.333 0.00 0.00 37.18 1.98
2657 2920 7.205297 ACAACTCGTAAGCACTTTAAGTTAGA 58.795 34.615 0.00 0.00 37.18 2.10
2658 2921 7.404139 ACAACTCGTAAGCACTTTAAGTTAG 57.596 36.000 0.00 0.00 37.18 2.34
2659 2922 7.775397 AACAACTCGTAAGCACTTTAAGTTA 57.225 32.000 0.00 0.00 37.18 2.24
2660 2923 6.673154 AACAACTCGTAAGCACTTTAAGTT 57.327 33.333 0.00 0.00 37.18 2.66
2744 3007 9.238368 CCTATTTTGTCCTTACCAAATCAAGTA 57.762 33.333 0.00 0.00 34.03 2.24
2777 3040 5.941948 AAACACCGACCTCTCAAAAATAG 57.058 39.130 0.00 0.00 0.00 1.73
2814 3079 3.129287 GGCAACATATCAACCTCCAAGTG 59.871 47.826 0.00 0.00 0.00 3.16
2839 3104 2.110011 AGGCATTTTCTAAGGGTGGTGT 59.890 45.455 0.00 0.00 0.00 4.16
2840 3105 2.755103 GAGGCATTTTCTAAGGGTGGTG 59.245 50.000 0.00 0.00 0.00 4.17
2842 3107 3.019564 CAGAGGCATTTTCTAAGGGTGG 58.980 50.000 0.00 0.00 0.00 4.61
2868 3140 1.130054 AGCCCTCAGAGCTGTGGAAA 61.130 55.000 17.63 0.00 44.61 3.13
2933 3205 7.367159 TCTTCAGTTTTCTCGTGTTTACAAA 57.633 32.000 0.00 0.00 0.00 2.83
2991 3291 3.363341 AACAACGGTGCATGGTAAAAG 57.637 42.857 0.00 0.00 0.00 2.27
2997 3298 2.060284 CATTGAAACAACGGTGCATGG 58.940 47.619 0.00 0.00 0.00 3.66
3073 3374 5.514834 CCCTGAAGAGATTGTCCTGGTTAAA 60.515 44.000 0.00 0.00 0.00 1.52
3078 3381 1.211457 CCCCTGAAGAGATTGTCCTGG 59.789 57.143 0.00 0.00 0.00 4.45
3080 3383 0.915364 GCCCCTGAAGAGATTGTCCT 59.085 55.000 0.00 0.00 0.00 3.85
3118 3425 2.671177 CGCACACCTTGAAGGCTCG 61.671 63.158 11.96 5.92 39.63 5.03
3125 3432 1.270094 CCAGTACTTCGCACACCTTGA 60.270 52.381 0.00 0.00 0.00 3.02
3136 3443 0.881796 GCCAAAGTGCCCAGTACTTC 59.118 55.000 0.00 0.00 37.49 3.01
3199 3524 2.252976 GAGCTATTCCAAGGCTCCAG 57.747 55.000 0.00 0.00 44.46 3.86
3222 3547 3.181479 TGCCAGTATGACATCGGTCTTAC 60.181 47.826 10.98 10.98 46.84 2.34
3228 3553 0.465705 AGGTGCCAGTATGACATCGG 59.534 55.000 0.00 0.00 39.69 4.18
3229 3554 2.315925 AAGGTGCCAGTATGACATCG 57.684 50.000 0.00 0.00 39.69 3.84
3318 3643 9.765795 TCGTGTAAAAACATTTTCCCAAATAAT 57.234 25.926 0.00 0.00 30.90 1.28
3324 3649 6.392625 TGATCGTGTAAAAACATTTTCCCA 57.607 33.333 0.00 0.00 0.00 4.37
3391 3716 6.972328 ACAGCTTTTGTAACAAGTACACAATG 59.028 34.615 0.00 0.00 42.56 2.82
3418 3748 2.290260 ACAGGCTAATAGTGCAGCACAA 60.290 45.455 27.35 8.80 39.63 3.33
3430 3760 2.644798 AGGTTGGTCAAGACAGGCTAAT 59.355 45.455 2.29 0.00 0.00 1.73
3474 3804 3.221771 TGCCAATTAGCAAGTGTTCAGT 58.778 40.909 0.00 0.00 40.56 3.41
3496 3826 1.983224 ACCTTCAGCGTACCAGCAT 59.017 52.632 0.00 0.00 40.15 3.79


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

AutoCloner maintained by Alex Coulton.