Multiple sequence alignment - TraesCS5A01G425100

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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 TraesCS5A01G425100 chr5A 100.000 2849 0 0 1 2849 610455125 610457973 0.000000e+00 5262
1 TraesCS5A01G425100 chr5D 90.834 1211 37 19 693 1879 489301802 489302962 0.000000e+00 1554
2 TraesCS5A01G425100 chr5D 89.235 706 65 9 1 704 489298687 489299383 0.000000e+00 872
3 TraesCS5A01G425100 chr5D 94.286 315 13 1 2540 2849 489307157 489307471 7.140000e-131 477
4 TraesCS5A01G425100 chr5D 93.684 190 11 1 2131 2319 489304734 489304923 1.670000e-72 283
5 TraesCS5A01G425100 chr5D 85.502 269 26 7 1871 2137 489304357 489304614 4.680000e-68 268
6 TraesCS5A01G425100 chr5D 94.656 131 7 0 2393 2523 489306822 489306952 1.340000e-48 204
7 TraesCS5A01G425100 chr5D 98.485 66 0 1 2304 2368 489306683 489306748 6.450000e-22 115
8 TraesCS5A01G425100 chr5B 87.850 1177 93 31 509 1657 603450999 603452153 0.000000e+00 1336
9 TraesCS5A01G425100 chr5B 93.878 392 13 6 2461 2848 603453190 603453574 5.290000e-162 580
10 TraesCS5A01G425100 chr5B 93.431 274 13 3 2100 2368 603452589 603452862 4.420000e-108 401
11 TraesCS5A01G425100 chr5B 76.652 454 24 31 1687 2108 603452143 603452546 2.920000e-40 176
12 TraesCS5A01G425100 chr7A 85.065 154 19 4 2551 2704 36287903 36287754 1.370000e-33 154
13 TraesCS5A01G425100 chr3A 85.065 154 19 4 2551 2704 26464913 26464764 1.370000e-33 154
14 TraesCS5A01G425100 chr6A 85.517 145 17 4 2551 2695 14179274 14179414 6.360000e-32 148
15 TraesCS5A01G425100 chr1B 84.615 156 16 6 2551 2704 67032602 67032453 6.360000e-32 148


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 TraesCS5A01G425100 chr5A 610455125 610457973 2848 False 5262.00 5262 100.000000 1 2849 1 chr5A.!!$F1 2848
1 TraesCS5A01G425100 chr5D 489298687 489307471 8784 False 539.00 1554 92.383143 1 2849 7 chr5D.!!$F1 2848
2 TraesCS5A01G425100 chr5B 603450999 603453574 2575 False 623.25 1336 87.952750 509 2848 4 chr5B.!!$F1 2339

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
218 220 0.034670 GCAGAGAGGGCAAAGACCAT 60.035 55.0 0.00 0.00 29.21 3.55 F
1235 3715 0.036732 AGGTCCGTCAACATGCATGT 59.963 50.0 26.61 26.61 44.20 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 4229 0.037017 TTCGCGAGGAAATGGGGAAA 59.963 50.0 9.59 0.0 35.99 3.13 R
2302 6454 0.610232 AACAATGCAGTCCAGCTCCC 60.610 55.0 0.00 0.0 34.99 4.30 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 1.373590 CCTATTTGGGGTGTTCGCGG 61.374 60.000 6.13 0.00 0.00 6.46
42 43 0.675522 CTATTTGGGGTGTTCGCGGT 60.676 55.000 6.13 0.00 0.00 5.68
69 70 1.935400 TGGCCCACCATTCCTCCAT 60.935 57.895 0.00 0.00 42.67 3.41
76 77 1.228063 CCATTCCTCCATGGAGCCG 60.228 63.158 32.97 21.58 46.18 5.52
112 113 2.036256 GCATCCAGGTGGGCAAGT 59.964 61.111 0.00 0.00 36.21 3.16
117 118 0.909610 TCCAGGTGGGCAAGTCCTAG 60.910 60.000 0.00 0.00 36.21 3.02
134 135 5.362430 AGTCCTAGCTTCTCAATGACTAAGG 59.638 44.000 0.00 0.00 30.35 2.69
136 137 5.361285 TCCTAGCTTCTCAATGACTAAGGTC 59.639 44.000 8.12 0.00 42.42 3.85
138 139 4.100373 AGCTTCTCAATGACTAAGGTCCT 58.900 43.478 0.00 0.00 41.47 3.85
144 145 2.503356 CAATGACTAAGGTCCTGAGCCT 59.497 50.000 2.67 0.00 41.47 4.58
172 174 5.175673 GGTGAAGCAACATTTGTAGAAAAGC 59.824 40.000 0.00 0.00 0.00 3.51
177 179 5.532406 AGCAACATTTGTAGAAAAGCTGAGA 59.468 36.000 0.00 0.00 0.00 3.27
217 219 1.376466 GCAGAGAGGGCAAAGACCA 59.624 57.895 0.00 0.00 29.21 4.02
218 220 0.034670 GCAGAGAGGGCAAAGACCAT 60.035 55.000 0.00 0.00 29.21 3.55
219 221 1.210478 GCAGAGAGGGCAAAGACCATA 59.790 52.381 0.00 0.00 29.21 2.74
247 249 2.185867 CCGCGCTTGGCTAACCTA 59.814 61.111 5.56 0.00 40.44 3.08
252 254 0.663153 CGCTTGGCTAACCTATTGGC 59.337 55.000 0.00 0.00 41.40 4.52
286 288 3.514777 CTGCAAGGCTAACGAGACA 57.485 52.632 0.00 0.00 30.20 3.41
308 310 1.032014 GAACTTGACCTTTGCTGGCA 58.968 50.000 0.00 0.00 0.00 4.92
325 327 1.763770 CACCCAAGCCTTCCAGACT 59.236 57.895 0.00 0.00 0.00 3.24
335 337 4.003648 AGCCTTCCAGACTATTTGTTTCG 58.996 43.478 0.00 0.00 0.00 3.46
337 339 4.933400 GCCTTCCAGACTATTTGTTTCGTA 59.067 41.667 0.00 0.00 0.00 3.43
338 340 5.063564 GCCTTCCAGACTATTTGTTTCGTAG 59.936 44.000 0.00 0.00 0.00 3.51
339 341 6.395629 CCTTCCAGACTATTTGTTTCGTAGA 58.604 40.000 0.00 0.00 0.00 2.59
343 345 7.313646 TCCAGACTATTTGTTTCGTAGAAGAG 58.686 38.462 0.00 0.00 45.90 2.85
365 367 4.336433 AGAATGTCATACCCAGAAATTGCG 59.664 41.667 0.00 0.00 0.00 4.85
392 394 3.494378 CGAAGACCGCCGAGTAGA 58.506 61.111 0.00 0.00 0.00 2.59
397 399 2.821688 GACCGCCGAGTAGAGTCCG 61.822 68.421 0.00 0.00 0.00 4.79
403 405 1.666054 CCGAGTAGAGTCCGTTAGCT 58.334 55.000 0.00 0.00 0.00 3.32
426 428 1.225855 GTGCTTCCACACAATGTCGA 58.774 50.000 0.00 0.00 41.67 4.20
444 446 4.082245 TGTCGACTTCAGTATGCTCATCAA 60.082 41.667 17.92 0.00 34.76 2.57
453 455 6.647229 TCAGTATGCTCATCAAGATGAAAGT 58.353 36.000 13.25 5.43 40.38 2.66
455 457 6.537660 CAGTATGCTCATCAAGATGAAAGTCA 59.462 38.462 13.25 9.34 46.10 3.41
473 475 5.674052 AGTCAATCTAGAGTGAAGTGCAT 57.326 39.130 23.40 4.35 37.15 3.96
485 487 4.777896 AGTGAAGTGCATCCTAGGTCTTTA 59.222 41.667 9.08 2.05 0.00 1.85
486 488 5.248477 AGTGAAGTGCATCCTAGGTCTTTAA 59.752 40.000 9.08 0.00 0.00 1.52
494 496 8.613482 GTGCATCCTAGGTCTTTAAACTATTTC 58.387 37.037 9.08 0.00 0.00 2.17
562 565 5.878332 TCTCGAAATGCAATATGTGTGTT 57.122 34.783 0.00 0.00 0.00 3.32
580 583 4.819630 TGTGTTGCCTAGGTTCTTAAACTG 59.180 41.667 11.31 0.00 35.61 3.16
589 592 6.594547 CCTAGGTTCTTAAACTGTTTAGAGGC 59.405 42.308 12.30 5.98 35.61 4.70
594 597 4.986659 TCTTAAACTGTTTAGAGGCGTCAC 59.013 41.667 12.30 0.00 0.00 3.67
598 601 4.595762 ACTGTTTAGAGGCGTCACTTAA 57.404 40.909 9.41 0.00 0.00 1.85
618 621 8.436200 CACTTAAGTCCTCGAACTATTTCAAAG 58.564 37.037 4.77 0.00 0.00 2.77
619 622 8.365647 ACTTAAGTCCTCGAACTATTTCAAAGA 58.634 33.333 1.12 0.00 0.00 2.52
621 624 7.602517 AAGTCCTCGAACTATTTCAAAGATG 57.397 36.000 0.00 0.00 0.00 2.90
636 639 6.603237 TCAAAGATGTCGCATATTTACAGG 57.397 37.500 10.57 2.34 0.00 4.00
645 648 8.360325 TGTCGCATATTTACAGGTTATACTTG 57.640 34.615 0.00 0.00 0.00 3.16
655 658 8.921353 TTACAGGTTATACTTGGCACTTTTTA 57.079 30.769 0.00 0.00 28.38 1.52
661 664 9.135843 GGTTATACTTGGCACTTTTTATTGTTC 57.864 33.333 0.00 0.00 0.00 3.18
663 666 5.508200 ACTTGGCACTTTTTATTGTTCGA 57.492 34.783 0.00 0.00 0.00 3.71
664 667 6.084326 ACTTGGCACTTTTTATTGTTCGAT 57.916 33.333 0.00 0.00 0.00 3.59
684 688 3.458044 TGACCTACATGACACCTCTCT 57.542 47.619 0.00 0.00 0.00 3.10
685 689 3.357203 TGACCTACATGACACCTCTCTC 58.643 50.000 0.00 0.00 0.00 3.20
689 693 0.891373 ACATGACACCTCTCTCACGG 59.109 55.000 0.00 0.00 0.00 4.94
705 709 2.235402 TCACGGAATAGTTCAAGGGACC 59.765 50.000 0.00 0.00 0.00 4.46
706 710 2.236395 CACGGAATAGTTCAAGGGACCT 59.764 50.000 0.00 0.00 0.00 3.85
707 711 2.500504 ACGGAATAGTTCAAGGGACCTC 59.499 50.000 0.00 0.00 0.00 3.85
708 712 2.766828 CGGAATAGTTCAAGGGACCTCT 59.233 50.000 0.00 0.00 0.00 3.69
709 713 3.430929 CGGAATAGTTCAAGGGACCTCTG 60.431 52.174 0.00 0.00 0.00 3.35
710 714 3.775316 GGAATAGTTCAAGGGACCTCTGA 59.225 47.826 0.00 0.00 0.00 3.27
712 3142 5.602978 GGAATAGTTCAAGGGACCTCTGATA 59.397 44.000 0.00 0.00 0.00 2.15
713 3143 6.271159 GGAATAGTTCAAGGGACCTCTGATAT 59.729 42.308 0.00 0.00 0.00 1.63
729 3159 5.773575 TCTGATATTCTACAATGCTCGGTC 58.226 41.667 0.00 0.00 0.00 4.79
732 3162 6.914259 TGATATTCTACAATGCTCGGTCTAG 58.086 40.000 0.00 0.00 0.00 2.43
796 3226 3.244875 TGAAGCTAGCTGGTGGAAATTCA 60.245 43.478 20.16 11.87 0.00 2.57
818 3248 0.948623 CACACCGTTGCCGAGAATGA 60.949 55.000 0.00 0.00 35.63 2.57
881 3311 3.667695 CGTGCAGATTTTCGAGCAATTCA 60.668 43.478 0.00 0.00 34.97 2.57
927 3374 6.348786 GCCGGTCACACGTAGAATAGATTATA 60.349 42.308 1.90 0.00 0.00 0.98
928 3375 7.627939 GCCGGTCACACGTAGAATAGATTATAT 60.628 40.741 1.90 0.00 0.00 0.86
978 3425 7.187480 CGTCGTGTCTTCCACCTATATATATG 58.813 42.308 5.44 0.00 41.26 1.78
1234 3714 0.448990 CAGGTCCGTCAACATGCATG 59.551 55.000 25.09 25.09 0.00 4.06
1235 3715 0.036732 AGGTCCGTCAACATGCATGT 59.963 50.000 26.61 26.61 44.20 3.21
1236 3716 0.447801 GGTCCGTCAACATGCATGTC 59.552 55.000 31.45 18.44 40.80 3.06
1237 3717 0.447801 GTCCGTCAACATGCATGTCC 59.552 55.000 31.45 20.30 40.80 4.02
1238 3718 0.676466 TCCGTCAACATGCATGTCCC 60.676 55.000 31.45 19.98 40.80 4.46
1239 3719 0.959867 CCGTCAACATGCATGTCCCA 60.960 55.000 31.45 15.88 40.80 4.37
1240 3720 0.880441 CGTCAACATGCATGTCCCAA 59.120 50.000 31.45 14.78 40.80 4.12
1241 3721 1.135603 CGTCAACATGCATGTCCCAAG 60.136 52.381 31.45 18.34 40.80 3.61
1242 3722 0.889994 TCAACATGCATGTCCCAAGC 59.110 50.000 31.45 0.00 40.80 4.01
1243 3723 0.457166 CAACATGCATGTCCCAAGCG 60.457 55.000 31.45 11.06 40.80 4.68
1244 3724 2.103538 CATGCATGTCCCAAGCGC 59.896 61.111 18.91 0.00 30.15 5.92
1245 3725 3.511595 ATGCATGTCCCAAGCGCG 61.512 61.111 0.00 0.00 30.15 6.86
1246 3726 3.974835 ATGCATGTCCCAAGCGCGA 62.975 57.895 12.10 0.00 30.15 5.87
1247 3727 4.166011 GCATGTCCCAAGCGCGAC 62.166 66.667 12.10 3.67 0.00 5.19
1248 3728 3.853330 CATGTCCCAAGCGCGACG 61.853 66.667 12.10 0.00 0.00 5.12
1259 3739 3.745230 CGCGACGCACGTTACGTT 61.745 61.111 21.35 0.00 45.24 3.99
1260 3740 2.540953 GCGACGCACGTTACGTTT 59.459 55.556 16.42 0.00 45.24 3.60
1285 3765 1.368345 CGCCATGAATGAGCGGTGAA 61.368 55.000 14.47 0.00 40.91 3.18
1374 3885 2.108278 AACCAGGAAACGACGGGGAG 62.108 60.000 0.00 0.00 0.00 4.30
1467 3978 2.106938 GGATCACGGCTGCATCGA 59.893 61.111 15.04 0.00 0.00 3.59
1714 4225 1.207089 GGCAATGGCTAACCCTTTTCC 59.793 52.381 0.00 0.00 40.87 3.13
1715 4226 1.207089 GCAATGGCTAACCCTTTTCCC 59.793 52.381 0.00 0.00 36.96 3.97
1716 4227 1.831106 CAATGGCTAACCCTTTTCCCC 59.169 52.381 0.00 0.00 33.59 4.81
1717 4228 1.089123 ATGGCTAACCCTTTTCCCCA 58.911 50.000 0.00 0.00 33.59 4.96
1718 4229 1.089123 TGGCTAACCCTTTTCCCCAT 58.911 50.000 0.00 0.00 33.59 4.00
1719 4230 1.435168 TGGCTAACCCTTTTCCCCATT 59.565 47.619 0.00 0.00 33.59 3.16
1798 4310 8.199449 CCATTTGATATGCCTAACAACATTCTT 58.801 33.333 0.00 0.00 0.00 2.52
1809 4325 7.565680 CCTAACAACATTCTTGTATACCTCCT 58.434 38.462 0.00 0.00 34.06 3.69
1840 4356 1.593006 CGCTTTGCTTCGGTATCGATT 59.407 47.619 1.71 0.00 45.51 3.34
1918 5859 4.509737 GCTCCTCCCGGCGTACAC 62.510 72.222 6.01 0.00 0.00 2.90
1927 5868 1.680105 CCGGCGTACACGATTGACAC 61.680 60.000 6.01 0.00 43.02 3.67
1974 5948 2.158143 GATCGAACGCAAAATCGTGTG 58.842 47.619 0.00 0.00 42.46 3.82
1980 5954 1.209127 GCAAAATCGTGTGGTCCGG 59.791 57.895 0.00 0.00 0.00 5.14
1981 5955 1.231958 GCAAAATCGTGTGGTCCGGA 61.232 55.000 0.00 0.00 0.00 5.14
1982 5956 0.515564 CAAAATCGTGTGGTCCGGAC 59.484 55.000 27.04 27.04 0.00 4.79
1983 5957 0.947180 AAAATCGTGTGGTCCGGACG 60.947 55.000 27.68 17.03 34.38 4.79
1984 5958 2.091102 AAATCGTGTGGTCCGGACGT 62.091 55.000 27.68 5.34 34.69 4.34
1985 5959 2.482296 AATCGTGTGGTCCGGACGTC 62.482 60.000 27.68 21.74 34.69 4.34
1986 5960 4.712425 CGTGTGGTCCGGACGTCC 62.712 72.222 27.68 25.28 0.00 4.79
1998 5972 2.028130 GACGTCCGGTCGTATCCAT 58.972 57.895 26.13 2.81 44.21 3.41
2028 6002 5.331905 GCAAAATACGATCAGATCACGAGAC 60.332 44.000 11.12 0.00 0.00 3.36
2044 6018 4.147306 CACGAGACGCAAGATTTATCTAGC 59.853 45.833 0.00 0.00 43.62 3.42
2051 6025 4.494035 CGCAAGATTTATCTAGCACGCAAA 60.494 41.667 0.00 0.00 43.02 3.68
2064 6038 3.246226 AGCACGCAAAATACGATCAGATC 59.754 43.478 0.00 0.00 0.00 2.75
2101 6127 0.254178 TTCATCAGGGAAGCAGAGGC 59.746 55.000 0.00 0.00 41.61 4.70
2128 6154 1.219393 GTGCCTCCTGCTCTGTACC 59.781 63.158 0.00 0.00 42.00 3.34
2285 6437 4.821805 GTCCTCCATCTTCAGTTTGAACAA 59.178 41.667 0.00 0.00 32.21 2.83
2302 6454 0.729116 CAAGCGCACCTAATCCTGTG 59.271 55.000 11.47 0.00 35.58 3.66
2368 8302 3.203263 AGCATCTGAGTAGACCTAGGACA 59.797 47.826 17.98 4.79 35.34 4.02
2369 8303 3.954904 GCATCTGAGTAGACCTAGGACAA 59.045 47.826 17.98 0.00 35.34 3.18
2428 8621 2.027625 GACAGAGCGGTTTGGGTCG 61.028 63.158 10.11 0.00 39.35 4.79
2829 9219 1.941294 CTTGTGCTGGCATCTCAGATC 59.059 52.381 0.00 0.00 36.93 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.480725 TGGTGGGCCAATAGAACCA 58.519 52.632 8.40 7.65 42.83 3.67
76 77 1.226603 ATCTACTTCGCACGCGGAC 60.227 57.895 12.47 0.00 40.25 4.79
81 82 0.855349 GGATGCATCTACTTCGCACG 59.145 55.000 25.28 0.00 38.73 5.34
112 113 5.273208 ACCTTAGTCATTGAGAAGCTAGGA 58.727 41.667 0.00 0.00 0.00 2.94
117 118 4.081420 TCAGGACCTTAGTCATTGAGAAGC 60.081 45.833 0.00 0.00 45.48 3.86
134 135 2.911484 CTTCACCATAAGGCTCAGGAC 58.089 52.381 6.81 0.00 39.06 3.85
136 137 1.065199 TGCTTCACCATAAGGCTCAGG 60.065 52.381 0.00 0.00 39.06 3.86
138 139 2.224744 TGTTGCTTCACCATAAGGCTCA 60.225 45.455 0.00 0.00 39.06 4.26
144 145 7.517614 TTCTACAAATGTTGCTTCACCATAA 57.482 32.000 0.00 0.00 0.00 1.90
172 174 0.539051 AGCAAGAATCGGGGTCTCAG 59.461 55.000 0.00 0.00 0.00 3.35
177 179 1.616628 AGGGAGCAAGAATCGGGGT 60.617 57.895 0.00 0.00 0.00 4.95
217 219 2.781158 GCGCGGGTGGCCAAATTAT 61.781 57.895 7.24 0.00 38.94 1.28
218 220 3.444805 GCGCGGGTGGCCAAATTA 61.445 61.111 7.24 0.00 38.94 1.40
232 234 0.663153 CCAATAGGTTAGCCAAGCGC 59.337 55.000 0.00 0.00 37.24 5.92
263 265 1.003839 CGTTAGCCTTGCAGGACCA 60.004 57.895 0.00 0.00 37.67 4.02
281 283 4.336713 AGCAAAGGTCAAGTTCTTTGTCTC 59.663 41.667 13.87 2.39 46.71 3.36
284 286 3.131046 CCAGCAAAGGTCAAGTTCTTTGT 59.869 43.478 13.87 2.92 46.71 2.83
286 288 2.101415 GCCAGCAAAGGTCAAGTTCTTT 59.899 45.455 0.00 0.00 33.95 2.52
325 327 9.653287 ATGACATTCTCTTCTACGAAACAAATA 57.347 29.630 0.00 0.00 0.00 1.40
335 337 6.716934 TCTGGGTATGACATTCTCTTCTAC 57.283 41.667 0.00 0.00 0.00 2.59
337 339 6.627087 TTTCTGGGTATGACATTCTCTTCT 57.373 37.500 0.00 0.00 0.00 2.85
338 340 7.680588 GCAATTTCTGGGTATGACATTCTCTTC 60.681 40.741 0.00 0.00 0.00 2.87
339 341 6.096001 GCAATTTCTGGGTATGACATTCTCTT 59.904 38.462 0.00 0.00 0.00 2.85
343 345 4.601019 CGCAATTTCTGGGTATGACATTC 58.399 43.478 0.00 0.00 33.35 2.67
392 394 1.080705 GCACACGAGCTAACGGACT 60.081 57.895 0.00 0.00 37.61 3.85
397 399 0.790814 GTGGAAGCACACGAGCTAAC 59.209 55.000 0.00 0.00 45.89 2.34
426 428 6.231258 TCATCTTGATGAGCATACTGAAGT 57.769 37.500 9.02 0.00 0.00 3.01
444 446 8.034215 CACTTCACTCTAGATTGACTTTCATCT 58.966 37.037 12.01 0.00 0.00 2.90
453 455 4.713814 AGGATGCACTTCACTCTAGATTGA 59.286 41.667 8.62 8.62 0.00 2.57
455 457 5.304101 CCTAGGATGCACTTCACTCTAGATT 59.696 44.000 1.05 0.00 34.92 2.40
519 521 9.806203 TCGAGAACCTAATGACGATTTTTATAA 57.194 29.630 0.00 0.00 0.00 0.98
540 543 5.630061 CAACACACATATTGCATTTCGAGA 58.370 37.500 0.00 0.00 0.00 4.04
562 565 7.069877 TCTAAACAGTTTAAGAACCTAGGCA 57.930 36.000 9.30 0.00 36.39 4.75
564 567 6.594547 GCCTCTAAACAGTTTAAGAACCTAGG 59.405 42.308 7.41 7.41 36.39 3.02
580 583 3.925299 GGACTTAAGTGACGCCTCTAAAC 59.075 47.826 14.14 0.00 0.00 2.01
589 592 3.555917 AGTTCGAGGACTTAAGTGACG 57.444 47.619 14.14 14.73 0.00 4.35
594 597 8.758633 TCTTTGAAATAGTTCGAGGACTTAAG 57.241 34.615 0.00 0.00 36.46 1.85
598 601 6.702329 ACATCTTTGAAATAGTTCGAGGACT 58.298 36.000 7.08 0.00 36.39 3.85
618 621 8.758633 AGTATAACCTGTAAATATGCGACATC 57.241 34.615 0.00 0.00 0.00 3.06
619 622 8.988934 CAAGTATAACCTGTAAATATGCGACAT 58.011 33.333 0.00 0.00 0.00 3.06
621 624 7.570691 GCCAAGTATAACCTGTAAATATGCGAC 60.571 40.741 0.00 0.00 0.00 5.19
635 638 9.135843 GAACAATAAAAAGTGCCAAGTATAACC 57.864 33.333 0.00 0.00 0.00 2.85
636 639 8.846607 CGAACAATAAAAAGTGCCAAGTATAAC 58.153 33.333 0.00 0.00 0.00 1.89
645 648 4.857037 GGTCATCGAACAATAAAAAGTGCC 59.143 41.667 0.00 0.00 0.00 5.01
655 658 4.870426 GTGTCATGTAGGTCATCGAACAAT 59.130 41.667 0.00 0.00 34.09 2.71
661 664 2.690497 AGAGGTGTCATGTAGGTCATCG 59.310 50.000 0.00 0.00 34.09 3.84
663 666 3.957497 GAGAGAGGTGTCATGTAGGTCAT 59.043 47.826 0.00 0.00 37.22 3.06
664 667 3.245264 TGAGAGAGGTGTCATGTAGGTCA 60.245 47.826 0.00 0.00 0.00 4.02
684 688 2.235402 GGTCCCTTGAACTATTCCGTGA 59.765 50.000 0.00 0.00 0.00 4.35
685 689 2.236395 AGGTCCCTTGAACTATTCCGTG 59.764 50.000 0.00 0.00 36.54 4.94
689 693 5.622346 ATCAGAGGTCCCTTGAACTATTC 57.378 43.478 0.00 0.00 39.15 1.75
705 709 5.777802 ACCGAGCATTGTAGAATATCAGAG 58.222 41.667 0.00 0.00 0.00 3.35
706 710 5.536538 AGACCGAGCATTGTAGAATATCAGA 59.463 40.000 0.00 0.00 0.00 3.27
707 711 5.777802 AGACCGAGCATTGTAGAATATCAG 58.222 41.667 0.00 0.00 0.00 2.90
708 712 5.791336 AGACCGAGCATTGTAGAATATCA 57.209 39.130 0.00 0.00 0.00 2.15
709 713 5.802956 GCTAGACCGAGCATTGTAGAATATC 59.197 44.000 0.00 0.00 42.36 1.63
710 714 5.478679 AGCTAGACCGAGCATTGTAGAATAT 59.521 40.000 5.02 0.00 45.43 1.28
712 3142 3.639094 AGCTAGACCGAGCATTGTAGAAT 59.361 43.478 5.02 0.00 45.43 2.40
713 3143 3.024547 AGCTAGACCGAGCATTGTAGAA 58.975 45.455 5.02 0.00 45.43 2.10
732 3162 1.859080 CCCTGTATTTAGCGACGAAGC 59.141 52.381 0.00 0.00 37.41 3.86
818 3248 3.701040 AGTGCTCTTCCAACACACATTTT 59.299 39.130 0.00 0.00 36.76 1.82
881 3311 3.814268 GGCCGTTGCGCATGTGAT 61.814 61.111 12.75 0.00 38.85 3.06
927 3374 2.760159 CGATTTGCGCCGTGGGAAT 61.760 57.895 4.18 0.00 0.00 3.01
928 3375 3.427425 CGATTTGCGCCGTGGGAA 61.427 61.111 4.18 0.00 0.00 3.97
1242 3722 1.918194 TAAACGTAACGTGCGTCGCG 61.918 55.000 16.76 0.00 42.10 5.87
1243 3723 0.512330 GTAAACGTAACGTGCGTCGC 60.512 55.000 16.76 11.10 42.10 5.19
1244 3724 0.245585 CGTAAACGTAACGTGCGTCG 60.246 55.000 16.76 12.85 42.10 5.12
1245 3725 3.509151 CGTAAACGTAACGTGCGTC 57.491 52.632 16.76 6.10 42.10 5.19
1256 3736 2.599527 TCATTCATGGCGTACGTAAACG 59.400 45.455 17.90 6.50 45.58 3.60
1257 3737 3.543460 GCTCATTCATGGCGTACGTAAAC 60.543 47.826 17.90 5.84 0.00 2.01
1258 3738 2.605818 GCTCATTCATGGCGTACGTAAA 59.394 45.455 17.90 3.04 0.00 2.01
1259 3739 2.198406 GCTCATTCATGGCGTACGTAA 58.802 47.619 17.90 5.78 0.00 3.18
1260 3740 1.847818 GCTCATTCATGGCGTACGTA 58.152 50.000 17.90 6.98 0.00 3.57
1308 3788 1.815003 ACAATCAACAAGGCTAGCTGC 59.185 47.619 15.72 0.00 41.94 5.25
1374 3885 1.799181 CGTCGTCCATGTCTGTGATCC 60.799 57.143 0.00 0.00 0.00 3.36
1714 4225 1.402787 CGAGGAAATGGGGAAATGGG 58.597 55.000 0.00 0.00 0.00 4.00
1715 4226 0.746659 GCGAGGAAATGGGGAAATGG 59.253 55.000 0.00 0.00 0.00 3.16
1716 4227 0.381801 CGCGAGGAAATGGGGAAATG 59.618 55.000 0.00 0.00 0.00 2.32
1717 4228 0.254747 TCGCGAGGAAATGGGGAAAT 59.745 50.000 3.71 0.00 0.00 2.17
1718 4229 0.037017 TTCGCGAGGAAATGGGGAAA 59.963 50.000 9.59 0.00 35.99 3.13
1719 4230 0.254747 ATTCGCGAGGAAATGGGGAA 59.745 50.000 9.59 0.00 41.59 3.97
1840 4356 4.722346 GCAATTCGCGTGTTTTTCAAACAA 60.722 37.500 5.77 0.00 31.20 2.83
1918 5859 1.412226 CGTCTGCGTGTGTCAATCG 59.588 57.895 0.00 0.00 0.00 3.34
1980 5954 1.069636 GTATGGATACGACCGGACGTC 60.070 57.143 33.68 20.67 45.32 4.34
1982 5956 3.761481 GTATGGATACGACCGGACG 57.239 57.895 24.38 24.38 42.51 4.79
1998 5972 4.018649 TCTGATCGTATTTTGCGTCGTA 57.981 40.909 0.00 0.00 0.00 3.43
2006 5980 4.970611 CGTCTCGTGATCTGATCGTATTTT 59.029 41.667 12.65 0.00 0.00 1.82
2044 6018 4.777140 TGATCTGATCGTATTTTGCGTG 57.223 40.909 12.65 0.00 0.00 5.34
2051 6025 6.539826 TGTTCAAAGCATGATCTGATCGTATT 59.460 34.615 11.81 7.64 38.03 1.89
2113 6139 0.976641 TTGTGGTACAGAGCAGGAGG 59.023 55.000 0.00 0.00 41.80 4.30
2128 6154 2.472816 GACCAGGTGTGCATTTTTGTG 58.527 47.619 0.00 0.00 0.00 3.33
2285 6437 1.221840 CCACAGGATTAGGTGCGCT 59.778 57.895 9.73 0.00 33.72 5.92
2302 6454 0.610232 AACAATGCAGTCCAGCTCCC 60.610 55.000 0.00 0.00 34.99 4.30
2368 8302 6.326323 AGGGTTATGTGGACTTCAAATTTGTT 59.674 34.615 17.47 3.98 0.00 2.83
2369 8303 5.838521 AGGGTTATGTGGACTTCAAATTTGT 59.161 36.000 17.47 0.00 0.00 2.83
2478 8671 6.493189 AATAACCTCCCACAAAACATGTTT 57.507 33.333 18.13 18.13 41.46 2.83
2479 8672 6.493189 AAATAACCTCCCACAAAACATGTT 57.507 33.333 4.92 4.92 41.46 2.71
2665 9050 1.279271 GGGTAGCTCACTTGACCATGT 59.721 52.381 3.59 0.00 33.33 3.21


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

AutoCloner maintained by Alex Coulton.