Multiple sequence alignment - TraesCS2A01G147500

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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 TraesCS2A01G147500 chr2A 100.000 3870 0 0 1 3870 94000342 94004211 0.000000e+00 7147.0
1 TraesCS2A01G147500 chr2D 92.709 3223 144 31 1 3189 95507701 95510866 0.000000e+00 4566.0
2 TraesCS2A01G147500 chr2D 85.968 677 85 9 3200 3870 166105215 166104543 0.000000e+00 715.0
3 TraesCS2A01G147500 chr2B 92.375 1600 81 16 26 1620 146953807 146955370 0.000000e+00 2241.0
4 TraesCS2A01G147500 chr2B 93.246 1525 70 22 1687 3189 146955370 146956883 0.000000e+00 2215.0
5 TraesCS2A01G147500 chr5D 87.964 673 77 4 3202 3870 319427928 319427256 0.000000e+00 791.0
6 TraesCS2A01G147500 chr3A 87.106 667 80 5 3202 3863 102833319 102832654 0.000000e+00 750.0
7 TraesCS2A01G147500 chr3A 88.614 606 64 5 3202 3802 140012835 140012230 0.000000e+00 732.0
8 TraesCS2A01G147500 chr7A 86.598 679 86 4 3194 3867 119509005 119508327 0.000000e+00 745.0
9 TraesCS2A01G147500 chr7A 85.224 670 94 4 3202 3866 201966666 201967335 0.000000e+00 684.0
10 TraesCS2A01G147500 chr6A 86.161 672 87 5 3202 3870 113541021 113540353 0.000000e+00 721.0
11 TraesCS2A01G147500 chr7D 87.081 627 74 6 3202 3822 44657032 44657657 0.000000e+00 702.0
12 TraesCS2A01G147500 chrUn 84.326 638 92 7 3239 3870 15333455 15332820 5.490000e-173 617.0
13 TraesCS2A01G147500 chr4A 88.889 72 7 1 3200 3270 8591546 8591475 1.920000e-13 87.9


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 TraesCS2A01G147500 chr2A 94000342 94004211 3869 False 7147 7147 100.0000 1 3870 1 chr2A.!!$F1 3869
1 TraesCS2A01G147500 chr2D 95507701 95510866 3165 False 4566 4566 92.7090 1 3189 1 chr2D.!!$F1 3188
2 TraesCS2A01G147500 chr2D 166104543 166105215 672 True 715 715 85.9680 3200 3870 1 chr2D.!!$R1 670
3 TraesCS2A01G147500 chr2B 146953807 146956883 3076 False 2228 2241 92.8105 26 3189 2 chr2B.!!$F1 3163
4 TraesCS2A01G147500 chr5D 319427256 319427928 672 True 791 791 87.9640 3202 3870 1 chr5D.!!$R1 668
5 TraesCS2A01G147500 chr3A 102832654 102833319 665 True 750 750 87.1060 3202 3863 1 chr3A.!!$R1 661
6 TraesCS2A01G147500 chr3A 140012230 140012835 605 True 732 732 88.6140 3202 3802 1 chr3A.!!$R2 600
7 TraesCS2A01G147500 chr7A 119508327 119509005 678 True 745 745 86.5980 3194 3867 1 chr7A.!!$R1 673
8 TraesCS2A01G147500 chr7A 201966666 201967335 669 False 684 684 85.2240 3202 3866 1 chr7A.!!$F1 664
9 TraesCS2A01G147500 chr6A 113540353 113541021 668 True 721 721 86.1610 3202 3870 1 chr6A.!!$R1 668
10 TraesCS2A01G147500 chr7D 44657032 44657657 625 False 702 702 87.0810 3202 3822 1 chr7D.!!$F1 620
11 TraesCS2A01G147500 chrUn 15332820 15333455 635 True 617 617 84.3260 3239 3870 1 chrUn.!!$R1 631

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
420 425 0.702316 GGTGGGGGTATTGTTCCTGT 59.298 55.000 0.00 0.0 0.00 4.00 F
1212 1228 2.073816 GAAATTCTCGAAACAGCCGGA 58.926 47.619 5.05 0.0 0.00 5.14 F
1844 1865 0.175531 AAGTGTTGCCAACTTGCCAC 59.824 50.000 9.30 0.0 36.52 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1572 1.068895 CTGGCCAATGACAAGCACAAA 59.931 47.619 7.01 0.0 0.00 2.83 R
2841 2874 0.251341 ACCAGGTTTCCATGCAGGTC 60.251 55.000 0.00 0.0 39.02 3.85 R
3445 3505 0.308068 GTCTAGAGCTGCGCGTCATA 59.692 55.000 8.43 0.0 0.00 2.15 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
133 134 0.790814 GCACGCTAGAGTTGACCAAC 59.209 55.000 0.00 4.81 41.45 3.77
140 141 1.148310 AGAGTTGACCAACATTCGCG 58.852 50.000 14.42 0.00 43.47 5.87
146 147 2.176546 CCAACATTCGCGCACCAG 59.823 61.111 8.75 0.00 0.00 4.00
179 180 2.927553 AAAGAAGCGCCTTTATGCTG 57.072 45.000 2.29 0.00 41.46 4.41
187 188 2.732282 GCGCCTTTATGCTGTTCCTTTC 60.732 50.000 0.00 0.00 0.00 2.62
205 206 2.818751 TCCCCTGTGTGTTTTCTGTT 57.181 45.000 0.00 0.00 0.00 3.16
208 209 1.202405 CCCTGTGTGTTTTCTGTTGGC 60.202 52.381 0.00 0.00 0.00 4.52
211 212 1.063327 TGTGTTTTCTGTTGGCGCG 59.937 52.632 0.00 0.00 0.00 6.86
213 214 2.331451 GTTTTCTGTTGGCGCGCT 59.669 55.556 32.29 0.00 0.00 5.92
223 224 3.211963 GGCGCGCTTGGATTCCAT 61.212 61.111 32.29 0.00 31.53 3.41
225 226 2.628106 CGCGCTTGGATTCCATCG 59.372 61.111 18.16 18.16 34.59 3.84
238 239 4.516698 GGATTCCATCGTGCTTGATTATGT 59.483 41.667 0.00 0.00 0.00 2.29
254 255 1.365699 ATGTCCGCGCGAGTAATTTT 58.634 45.000 34.63 4.20 0.00 1.82
255 256 1.993542 TGTCCGCGCGAGTAATTTTA 58.006 45.000 34.63 3.58 0.00 1.52
256 257 2.335752 TGTCCGCGCGAGTAATTTTAA 58.664 42.857 34.63 1.07 0.00 1.52
257 258 2.931325 TGTCCGCGCGAGTAATTTTAAT 59.069 40.909 34.63 0.00 0.00 1.40
258 259 3.371591 TGTCCGCGCGAGTAATTTTAATT 59.628 39.130 34.63 0.00 0.00 1.40
259 260 4.142859 TGTCCGCGCGAGTAATTTTAATTT 60.143 37.500 34.63 0.00 0.00 1.82
373 378 2.743538 GATGCGCTGTCTGGCACA 60.744 61.111 9.73 0.00 42.76 4.57
374 379 2.045634 ATGCGCTGTCTGGCACAT 60.046 55.556 9.73 0.00 42.76 3.21
375 380 2.044832 GATGCGCTGTCTGGCACATC 62.045 60.000 9.73 0.00 42.76 3.06
385 390 1.134699 TCTGGCACATCCGAGCTTTAG 60.135 52.381 0.00 0.00 38.20 1.85
420 425 0.702316 GGTGGGGGTATTGTTCCTGT 59.298 55.000 0.00 0.00 0.00 4.00
533 541 3.117587 TCAGGAGCTAGGTCCTACTTACC 60.118 52.174 36.65 12.91 45.94 2.85
534 542 2.857498 AGGAGCTAGGTCCTACTTACCA 59.143 50.000 36.50 0.00 45.83 3.25
535 543 3.117436 AGGAGCTAGGTCCTACTTACCAG 60.117 52.174 36.50 0.00 45.83 4.00
659 667 9.460906 GATTGCTTTATCATTTCAGAAGATTCC 57.539 33.333 0.00 0.00 0.00 3.01
672 682 2.668212 ATTCCGGCCGTGTGTGTG 60.668 61.111 26.12 6.69 0.00 3.82
673 683 3.469863 ATTCCGGCCGTGTGTGTGT 62.470 57.895 26.12 0.00 0.00 3.72
674 684 4.901123 TCCGGCCGTGTGTGTGTG 62.901 66.667 26.12 5.01 0.00 3.82
730 740 7.027778 ACTCATCTGGTTGTTGTTTAAAGTC 57.972 36.000 0.00 0.00 0.00 3.01
738 748 6.316890 TGGTTGTTGTTTAAAGTCTACCTGTC 59.683 38.462 13.93 0.00 0.00 3.51
739 749 6.238566 GGTTGTTGTTTAAAGTCTACCTGTCC 60.239 42.308 0.00 0.00 0.00 4.02
745 755 9.802039 TTGTTTAAAGTCTACCTGTCCATTATT 57.198 29.630 0.00 0.00 0.00 1.40
754 764 5.520748 ACCTGTCCATTATTTCTGGAGTT 57.479 39.130 0.00 0.00 43.33 3.01
755 765 5.256474 ACCTGTCCATTATTTCTGGAGTTG 58.744 41.667 0.00 0.00 43.33 3.16
756 766 5.222130 ACCTGTCCATTATTTCTGGAGTTGT 60.222 40.000 0.00 0.00 43.33 3.32
757 767 5.355350 CCTGTCCATTATTTCTGGAGTTGTC 59.645 44.000 0.00 0.00 43.33 3.18
759 769 7.252612 TGTCCATTATTTCTGGAGTTGTCTA 57.747 36.000 0.00 0.00 43.33 2.59
760 770 7.685481 TGTCCATTATTTCTGGAGTTGTCTAA 58.315 34.615 0.00 0.00 43.33 2.10
761 771 8.328758 TGTCCATTATTTCTGGAGTTGTCTAAT 58.671 33.333 0.00 0.00 43.33 1.73
762 772 9.832445 GTCCATTATTTCTGGAGTTGTCTAATA 57.168 33.333 0.00 0.00 43.33 0.98
960 976 3.746940 GGTAAAGTGTGTGCCTTCCTAA 58.253 45.455 0.00 0.00 0.00 2.69
967 983 5.842907 AGTGTGTGCCTTCCTAAAAATTTC 58.157 37.500 0.00 0.00 0.00 2.17
973 989 6.210385 TGTGCCTTCCTAAAAATTTCTGCATA 59.790 34.615 0.00 0.00 0.00 3.14
975 991 8.413229 GTGCCTTCCTAAAAATTTCTGCATATA 58.587 33.333 0.00 0.00 0.00 0.86
1023 1039 5.304778 AGAAGCCTTGTTGTTTTGTGTTTT 58.695 33.333 0.00 0.00 0.00 2.43
1024 1040 5.179182 AGAAGCCTTGTTGTTTTGTGTTTTG 59.821 36.000 0.00 0.00 0.00 2.44
1212 1228 2.073816 GAAATTCTCGAAACAGCCGGA 58.926 47.619 5.05 0.00 0.00 5.14
1281 1297 3.058570 CAGATAGAGAGAACGGGTCATCG 60.059 52.174 0.00 0.00 0.00 3.84
1313 1329 4.321899 GCAAATAATTTGGGTCAGTGCTCA 60.322 41.667 0.00 0.00 40.94 4.26
1346 1362 6.155475 TGAGTGGTAAATTTGTTTCAAGGG 57.845 37.500 0.00 0.00 0.00 3.95
1507 1523 6.913170 TGCCAATCAAAACTCTGAATTCTAC 58.087 36.000 7.05 0.00 0.00 2.59
1556 1572 2.876550 GCTTCACTTGGACCTTTTACGT 59.123 45.455 0.00 0.00 0.00 3.57
1573 1589 1.130955 CGTTTGTGCTTGTCATTGGC 58.869 50.000 0.00 0.00 0.00 4.52
1668 1684 5.588240 CCACAGCTGATTGTAGTAACGATA 58.412 41.667 23.35 0.00 29.24 2.92
1680 1696 7.895975 TGTAGTAACGATACGTAGCTGATAT 57.104 36.000 9.44 0.00 39.99 1.63
1735 1751 8.318412 TGCTTACACCTTACATCTTTCAAGATA 58.682 33.333 1.64 0.00 43.65 1.98
1739 1755 8.723942 ACACCTTACATCTTTCAAGATATGTC 57.276 34.615 1.64 0.00 43.65 3.06
1844 1865 0.175531 AAGTGTTGCCAACTTGCCAC 59.824 50.000 9.30 0.00 36.52 5.01
1850 1871 2.493278 GTTGCCAACTTGCCACATATCT 59.507 45.455 0.00 0.00 0.00 1.98
1857 1878 2.174210 ACTTGCCACATATCTGCCATCT 59.826 45.455 0.00 0.00 0.00 2.90
1959 1981 0.476771 TTCAGGTCCACTTTGGGGTC 59.523 55.000 0.00 0.00 38.32 4.46
2071 2093 3.215244 GTTGCGTTGTTGTCAGATTACG 58.785 45.455 0.00 0.00 0.00 3.18
2219 2241 9.236006 GAGGTAAATGCCAGATTGTTCATATAT 57.764 33.333 0.00 0.00 0.00 0.86
2255 2277 6.481313 TGCTGAATTATAGCTAGAAACTGCAG 59.519 38.462 24.19 13.48 41.66 4.41
2314 2336 4.728772 TCTGTGAACTTTCCATGGTCAAT 58.271 39.130 12.58 0.00 0.00 2.57
2355 2377 4.407621 TGAAGGAGTTAACCAAGTCACTCA 59.592 41.667 0.88 0.00 37.92 3.41
2363 2385 4.762289 AACCAAGTCACTCAGAAAGACT 57.238 40.909 0.00 0.00 43.98 3.24
2429 2451 4.103357 GCAACTATGTGTACTACCACTCG 58.897 47.826 0.00 0.00 36.30 4.18
2468 2490 1.728971 CACGGCATCAAGTCTCTGTTC 59.271 52.381 0.00 0.00 0.00 3.18
2532 2554 0.391130 CCATTTCGTCGCTTCCCTCA 60.391 55.000 0.00 0.00 0.00 3.86
2562 2584 5.482908 CTCTTGCTAGCTTGAACTAGGAAA 58.517 41.667 17.23 0.00 46.02 3.13
2563 2585 5.865085 TCTTGCTAGCTTGAACTAGGAAAA 58.135 37.500 17.23 0.00 46.02 2.29
2595 2617 1.639108 AGGTGGGTTTTACCTGATCCC 59.361 52.381 0.00 0.00 46.48 3.85
2596 2618 1.356398 GGTGGGTTTTACCTGATCCCA 59.644 52.381 0.00 0.00 44.76 4.37
2597 2619 4.352349 AGGTGGGTTTTACCTGATCCCAT 61.352 47.826 4.53 0.00 46.48 4.00
2598 2620 5.821990 AGGTGGGTTTTACCTGATCCCATT 61.822 45.833 4.53 0.00 46.48 3.16
2599 2621 4.412060 TGGGTTTTACCTGATCCCATTT 57.588 40.909 0.00 0.00 42.52 2.32
2630 2662 0.901124 AGAGCTGGCTAACTGACTGG 59.099 55.000 0.00 0.00 0.00 4.00
2841 2874 3.346315 TGCCATCAGTTACATGTCCTTG 58.654 45.455 0.00 0.00 0.00 3.61
2851 2884 1.100510 CATGTCCTTGACCTGCATGG 58.899 55.000 0.00 0.00 41.86 3.66
2881 2914 7.123247 CCTGGTTCCAATAAAATTGACAGATCT 59.877 37.037 1.23 0.00 0.00 2.75
2893 2926 3.898482 TGACAGATCTTCGGAGTGGATA 58.102 45.455 0.00 0.00 0.00 2.59
2969 3006 0.609662 ATGCTTTGGTGAATGGTGGC 59.390 50.000 0.00 0.00 0.00 5.01
3019 3056 7.362401 CCATATTTTCACCTCTTGTTCTTCAGG 60.362 40.741 0.00 0.00 0.00 3.86
3035 3072 3.531934 TCAGGTGCTGTATCTGTGATG 57.468 47.619 5.92 0.00 38.71 3.07
3085 3122 4.079730 AGTCTTCACTTTTTCCCCTCTGTT 60.080 41.667 0.00 0.00 0.00 3.16
3100 3137 5.221823 CCCCTCTGTTCTTCTTCTTTCTTCT 60.222 44.000 0.00 0.00 0.00 2.85
3148 3193 5.235186 CAGTACAGTGTATCCTGCAAATAGC 59.765 44.000 6.21 0.00 45.96 2.97
3164 3209 1.892819 TAGCTGAGCTCTTTGGCGCT 61.893 55.000 11.68 14.07 40.44 5.92
3189 3234 1.795872 TGTCCAAGCGTTCGTACAATG 59.204 47.619 0.00 0.00 0.00 2.82
3190 3235 0.793861 TCCAAGCGTTCGTACAATGC 59.206 50.000 11.84 11.84 0.00 3.56
3191 3236 0.515127 CCAAGCGTTCGTACAATGCA 59.485 50.000 18.27 0.00 34.74 3.96
3192 3237 1.069568 CCAAGCGTTCGTACAATGCAA 60.070 47.619 18.27 0.00 34.74 4.08
3196 3241 1.334239 GCGTTCGTACAATGCAAACCA 60.334 47.619 13.81 0.00 32.66 3.67
3262 3307 1.064357 GTCCGCTTTTTGTCCGTTTGA 59.936 47.619 0.00 0.00 0.00 2.69
3297 3342 1.154413 CAAACGTCCGATGCTGTGC 60.154 57.895 0.00 0.00 0.00 4.57
3307 3352 0.745845 GATGCTGTGCTTGGATCGGT 60.746 55.000 0.00 0.00 0.00 4.69
3388 3443 7.819900 TGCATTTAATTAAACATAAAAGCCGGT 59.180 29.630 12.74 0.00 35.80 5.28
3393 3448 6.584185 ATTAAACATAAAAGCCGGTCAAGT 57.416 33.333 1.90 0.00 0.00 3.16
3396 3451 4.546829 ACATAAAAGCCGGTCAAGTAGA 57.453 40.909 1.90 0.00 0.00 2.59
3412 3467 2.203972 TAGACCGGCGAAAGTCCACG 62.204 60.000 9.30 0.00 33.29 4.94
3473 3533 1.407258 GCAGCTCTAGACATCCTCGTT 59.593 52.381 0.00 0.00 0.00 3.85
3480 3540 1.810030 GACATCCTCGTTGGCGTCC 60.810 63.158 0.00 0.00 39.49 4.79
3512 3572 0.525668 ATGAGGTCGATCAACGTCGC 60.526 55.000 0.00 0.00 41.22 5.19
3662 3722 2.906458 CTCCTCAGCCAGCCGAAT 59.094 61.111 0.00 0.00 0.00 3.34
3707 3767 1.587054 CCTCCTGCTTCTTCGTCGT 59.413 57.895 0.00 0.00 0.00 4.34
3712 3772 2.506438 GCTTCTTCGTCGTCCCGG 60.506 66.667 0.00 0.00 0.00 5.73
3760 3820 1.651240 GCGCACTACTACGGTCCAGA 61.651 60.000 0.30 0.00 0.00 3.86
3773 3833 1.544691 GGTCCAGAAGTAGTGCTCGAA 59.455 52.381 0.00 0.00 0.00 3.71
3777 3837 0.533032 AGAAGTAGTGCTCGAAGGGC 59.467 55.000 0.00 0.00 0.00 5.19
3830 3891 4.006357 GGGGTTACCGACGGCACA 62.006 66.667 15.39 0.00 37.78 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 1.148157 CCTACTCTGGTGCGCGAATG 61.148 60.000 12.10 0.00 0.00 2.67
140 141 0.898320 TTCTGAGCCTACTCTGGTGC 59.102 55.000 0.00 0.00 43.85 5.01
146 147 3.369451 CGCTTCTTTTTCTGAGCCTACTC 59.631 47.826 0.00 0.00 43.76 2.59
179 180 2.067365 AACACACAGGGGAAAGGAAC 57.933 50.000 0.00 0.00 0.00 3.62
187 188 1.408702 CCAACAGAAAACACACAGGGG 59.591 52.381 0.00 0.00 0.00 4.79
205 206 3.993614 ATGGAATCCAAGCGCGCCA 62.994 57.895 30.33 16.53 36.95 5.69
208 209 2.173669 ACGATGGAATCCAAGCGCG 61.174 57.895 22.04 17.47 41.39 6.86
211 212 1.098050 AAGCACGATGGAATCCAAGC 58.902 50.000 5.89 8.60 41.39 4.01
213 214 2.488204 TCAAGCACGATGGAATCCAA 57.512 45.000 5.89 0.00 41.39 3.53
223 224 1.286501 GCGGACATAATCAAGCACGA 58.713 50.000 0.00 0.00 33.97 4.35
225 226 0.316196 GCGCGGACATAATCAAGCAC 60.316 55.000 8.83 0.00 33.55 4.40
238 239 4.494526 GGAAATTAAAATTACTCGCGCGGA 60.495 41.667 31.69 15.73 0.00 5.54
254 255 3.222173 CATCCATGGACGGGGAAATTA 57.778 47.619 18.99 0.00 36.62 1.40
255 256 2.071778 CATCCATGGACGGGGAAATT 57.928 50.000 18.99 0.00 36.62 1.82
256 257 3.827505 CATCCATGGACGGGGAAAT 57.172 52.632 18.99 0.00 36.62 2.17
318 323 0.243907 GTTAGCTCACGCAGGACAGA 59.756 55.000 0.00 0.00 39.10 3.41
319 324 1.073216 CGTTAGCTCACGCAGGACAG 61.073 60.000 7.61 0.00 39.10 3.51
320 325 1.080772 CGTTAGCTCACGCAGGACA 60.081 57.895 7.61 0.00 39.10 4.02
321 326 1.805945 CCGTTAGCTCACGCAGGAC 60.806 63.158 14.92 0.00 38.93 3.85
385 390 2.821366 CCCTGTGCACATCCGAGC 60.821 66.667 22.00 0.00 0.00 5.03
420 425 1.752198 CAGACCACCGGACCAAGAA 59.248 57.895 9.46 0.00 0.00 2.52
533 541 4.808364 GCAAGAGATAAGCAGGAACTACTG 59.192 45.833 0.00 0.00 41.41 2.74
534 542 4.714308 AGCAAGAGATAAGCAGGAACTACT 59.286 41.667 0.00 0.00 36.02 2.57
535 543 5.017294 AGCAAGAGATAAGCAGGAACTAC 57.983 43.478 0.00 0.00 36.02 2.73
659 667 3.163110 GAACACACACACACGGCCG 62.163 63.158 26.86 26.86 0.00 6.13
672 682 2.031857 CGCCGTCTCCTAGATAGAACAC 60.032 54.545 0.00 0.00 0.00 3.32
673 683 2.219458 CGCCGTCTCCTAGATAGAACA 58.781 52.381 0.00 0.00 0.00 3.18
674 684 1.069091 GCGCCGTCTCCTAGATAGAAC 60.069 57.143 0.00 0.00 0.00 3.01
730 740 6.240549 ACTCCAGAAATAATGGACAGGTAG 57.759 41.667 0.00 0.00 41.96 3.18
762 772 9.180678 CGAAATGCAGTAAACAGTAAAAGAAAT 57.819 29.630 0.00 0.00 0.00 2.17
766 776 6.299966 CGACGAAATGCAGTAAACAGTAAAAG 59.700 38.462 0.00 0.00 0.00 2.27
960 976 9.603921 CAAAGGACCAATATATGCAGAAATTTT 57.396 29.630 0.00 0.00 0.00 1.82
967 983 6.949352 AGTTCAAAGGACCAATATATGCAG 57.051 37.500 0.00 0.00 0.00 4.41
973 989 7.797121 ATCCAAAAGTTCAAAGGACCAATAT 57.203 32.000 0.00 0.00 0.00 1.28
975 991 6.499106 AATCCAAAAGTTCAAAGGACCAAT 57.501 33.333 0.00 0.00 0.00 3.16
1023 1039 2.421388 CGATCCCATTTACCCTTCTGCA 60.421 50.000 0.00 0.00 0.00 4.41
1024 1040 2.222027 CGATCCCATTTACCCTTCTGC 58.778 52.381 0.00 0.00 0.00 4.26
1212 1228 4.660938 GTTCCAAGCGCCCCCTGT 62.661 66.667 2.29 0.00 0.00 4.00
1281 1297 2.158914 CCAAATTATTTGCCCCTGAGCC 60.159 50.000 11.82 0.00 39.31 4.70
1313 1329 7.287810 ACAAATTTACCACTCAAGAGTAAGGT 58.712 34.615 14.37 14.37 40.20 3.50
1346 1362 5.695816 GGAAGATTGAGTCATCTAGCATGAC 59.304 44.000 19.42 19.42 46.41 3.06
1379 1395 3.492421 ACGAATGCACATTTTAGCTGG 57.508 42.857 0.00 0.00 0.00 4.85
1556 1572 1.068895 CTGGCCAATGACAAGCACAAA 59.931 47.619 7.01 0.00 0.00 2.83
1668 1684 3.636764 TGACCACATCATATCAGCTACGT 59.363 43.478 0.00 0.00 29.99 3.57
1739 1755 7.171848 TCTCATTTTCTGGAATGCATGTTTTTG 59.828 33.333 0.00 0.00 37.03 2.44
1809 1830 6.208644 GCAACACTTTGTAGTTCATGAACAT 58.791 36.000 33.92 22.73 38.12 2.71
1857 1878 7.831753 TCTTTCAGAAAACATAACAACCACAA 58.168 30.769 0.00 0.00 0.00 3.33
1959 1981 1.737838 ACCGTGATGCACCACTATTG 58.262 50.000 10.11 0.00 35.02 1.90
2071 2093 1.888512 TGCAGAGCAAATGAAGGGTTC 59.111 47.619 0.00 0.00 34.76 3.62
2219 2241 1.927487 AATTCAGCAAGCACCCATCA 58.073 45.000 0.00 0.00 0.00 3.07
2255 2277 1.078848 AAGATCGGTGCAGCAGGAC 60.079 57.895 17.33 4.12 35.01 3.85
2264 2286 6.074302 CGTGGTTAATCATAAGAAGATCGGTG 60.074 42.308 0.00 0.00 0.00 4.94
2314 2336 2.871453 TCACTGGCAGTGTAGTCTGTA 58.129 47.619 38.27 19.91 46.03 2.74
2355 2377 2.826128 TCACATCGTAGCCAGTCTTTCT 59.174 45.455 0.00 0.00 0.00 2.52
2363 2385 4.855105 GGCATCACATCGTAGCCA 57.145 55.556 0.00 0.00 44.59 4.75
2562 2584 3.040655 ACCCACCTTTTAAGTTGCCTT 57.959 42.857 0.00 0.00 34.56 4.35
2563 2585 2.767644 ACCCACCTTTTAAGTTGCCT 57.232 45.000 0.00 0.00 0.00 4.75
2598 2620 3.704061 AGCCAGCTCTTTGTAACCAAAAA 59.296 39.130 0.00 0.00 39.95 1.94
2599 2621 3.295973 AGCCAGCTCTTTGTAACCAAAA 58.704 40.909 0.00 0.00 39.95 2.44
2603 2630 3.437049 CAGTTAGCCAGCTCTTTGTAACC 59.563 47.826 0.00 0.00 0.00 2.85
2630 2662 4.488879 GCAATGAAACAGGTCAAGGATTC 58.511 43.478 0.00 0.00 0.00 2.52
2841 2874 0.251341 ACCAGGTTTCCATGCAGGTC 60.251 55.000 0.00 0.00 39.02 3.85
2851 2884 7.213678 TGTCAATTTTATTGGAACCAGGTTTC 58.786 34.615 6.21 4.65 0.00 2.78
2881 2914 1.141019 GCGCTGTATCCACTCCGAA 59.859 57.895 0.00 0.00 0.00 4.30
2908 2945 3.724508 AAACACGGCATCAACAAATCA 57.275 38.095 0.00 0.00 0.00 2.57
2932 2969 2.349438 GCATCAGAAACGCAAGAACGAA 60.349 45.455 0.00 0.00 43.62 3.85
2948 2985 1.894466 CCACCATTCACCAAAGCATCA 59.106 47.619 0.00 0.00 0.00 3.07
2969 3006 5.333299 TCTGGAATCAGAAATGCAAATGG 57.667 39.130 0.00 0.00 46.08 3.16
3019 3056 1.667724 GTGGCATCACAGATACAGCAC 59.332 52.381 0.00 0.00 43.13 4.40
3035 3072 2.079925 GTCAAAGGAGATGACAGTGGC 58.920 52.381 0.00 0.00 45.13 5.01
3085 3122 7.611855 ACACAAAGGAAAGAAGAAAGAAGAAGA 59.388 33.333 0.00 0.00 0.00 2.87
3100 3137 7.440198 TGATCATATGCAAAACACAAAGGAAA 58.560 30.769 0.00 0.00 0.00 3.13
3164 3209 0.390124 ACGAACGCTTGGACACCTTA 59.610 50.000 0.00 0.00 0.00 2.69
3189 3234 3.367395 GGAATTGCTCTTACCTGGTTTGC 60.367 47.826 3.84 5.42 0.00 3.68
3190 3235 3.826157 TGGAATTGCTCTTACCTGGTTTG 59.174 43.478 3.84 0.00 0.00 2.93
3191 3236 4.112634 TGGAATTGCTCTTACCTGGTTT 57.887 40.909 3.84 0.00 0.00 3.27
3192 3237 3.806949 TGGAATTGCTCTTACCTGGTT 57.193 42.857 3.84 0.00 0.00 3.67
3196 3241 2.618045 CCCGTTGGAATTGCTCTTACCT 60.618 50.000 0.00 0.00 0.00 3.08
3262 3307 4.309950 GTATCCGCCGGGCCGATT 62.310 66.667 30.79 9.35 30.24 3.34
3297 3342 3.257561 CGCTCGCACCGATCCAAG 61.258 66.667 0.00 0.00 34.61 3.61
3317 3362 1.812571 CAAAATAGGTCAGGCAGCGTT 59.187 47.619 0.00 0.00 0.00 4.84
3319 3364 1.398390 GACAAAATAGGTCAGGCAGCG 59.602 52.381 0.00 0.00 35.36 5.18
3320 3365 1.398390 CGACAAAATAGGTCAGGCAGC 59.602 52.381 0.00 0.00 34.97 5.25
3321 3366 2.009774 CCGACAAAATAGGTCAGGCAG 58.990 52.381 0.00 0.00 34.97 4.85
3326 3373 1.434555 CACGCCGACAAAATAGGTCA 58.565 50.000 0.00 0.00 34.97 4.02
3331 3378 0.952280 TTTGGCACGCCGACAAAATA 59.048 45.000 4.06 0.00 39.42 1.40
3388 3443 0.963962 ACTTTCGCCGGTCTACTTGA 59.036 50.000 1.90 0.00 0.00 3.02
3393 3448 1.588082 GTGGACTTTCGCCGGTCTA 59.412 57.895 1.90 0.00 33.46 2.59
3396 3451 2.086251 TAACGTGGACTTTCGCCGGT 62.086 55.000 1.90 0.00 0.00 5.28
3445 3505 0.308068 GTCTAGAGCTGCGCGTCATA 59.692 55.000 8.43 0.00 0.00 2.15
3458 3518 0.738975 CGCCAACGAGGATGTCTAGA 59.261 55.000 2.86 0.00 43.93 2.43
3463 3523 2.264794 GGACGCCAACGAGGATGT 59.735 61.111 2.86 0.60 43.93 3.06
3525 3585 3.552384 AACACGGCGTTCCCCTGA 61.552 61.111 11.19 0.00 29.27 3.86
3570 3630 4.007644 CAGGCCCAGACAGCGACA 62.008 66.667 0.00 0.00 0.00 4.35
3662 3722 1.227060 CTCGATCACTGGCATCGCA 60.227 57.895 3.45 0.00 42.42 5.10
3667 3727 1.676678 GCCTACCTCGATCACTGGCA 61.677 60.000 10.37 0.00 38.79 4.92
3712 3772 4.899239 CGCTCCACCGATCTGGCC 62.899 72.222 0.00 0.00 43.94 5.36
3723 3783 2.895680 GAGTGGATCAGCGCTCCA 59.104 61.111 7.13 10.45 40.49 3.86
3760 3820 1.597461 GGCCCTTCGAGCACTACTT 59.403 57.895 0.00 0.00 0.00 2.24
3818 3879 1.300311 CTGTGTTGTGCCGTCGGTA 60.300 57.895 13.94 5.30 0.00 4.02


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

AutoCloner maintained by Alex Coulton.