Multiple sequence alignment - TraesCS1D01G088500

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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 TraesCS1D01G088500 chr1D 100.000 2990 0 0 1 2990 73818609 73815620 0.000000e+00 5522.0
1 TraesCS1D01G088500 chr1D 91.783 2653 181 5 1 2639 73972740 73970111 0.000000e+00 3657.0
2 TraesCS1D01G088500 chr1D 88.532 2084 192 22 174 2215 49624477 49622399 0.000000e+00 2481.0
3 TraesCS1D01G088500 chr1D 92.208 154 10 2 2219 2370 49622037 49621884 1.800000e-52 217.0
4 TraesCS1D01G088500 chr1D 90.541 148 13 1 2843 2990 73969942 73969796 8.460000e-46 195.0
5 TraesCS1D01G088500 chr1D 83.333 168 11 2 2682 2849 73970117 73969967 4.020000e-29 139.0
6 TraesCS1D01G088500 chr1B 87.674 2085 209 22 174 2215 70193238 70191159 0.000000e+00 2383.0
7 TraesCS1D01G088500 chr1B 92.988 599 29 3 1972 2562 117281970 117281377 0.000000e+00 861.0
8 TraesCS1D01G088500 chr1B 92.922 438 29 1 2553 2990 117280100 117279665 1.170000e-178 636.0
9 TraesCS1D01G088500 chr1A 87.337 2069 207 28 174 2200 49253436 49251381 0.000000e+00 2318.0
10 TraesCS1D01G088500 chr1A 92.540 1059 76 3 1078 2134 73338417 73337360 0.000000e+00 1515.0
11 TraesCS1D01G088500 chr1A 92.259 956 60 1 139 1080 73345679 73344724 0.000000e+00 1343.0
12 TraesCS1D01G088500 chr1A 93.966 116 5 2 2257 2370 49250887 49250772 1.100000e-39 174.0
13 TraesCS1D01G088500 chr1A 90.244 82 8 0 2219 2300 49250970 49250889 1.130000e-19 108.0
14 TraesCS1D01G088500 chr7A 84.430 456 62 5 231 678 681489333 681488879 9.840000e-120 440.0
15 TraesCS1D01G088500 chr5B 88.679 53 6 0 2705 2757 467949921 467949973 6.920000e-07 65.8


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 TraesCS1D01G088500 chr1D 73815620 73818609 2989 True 5522.000000 5522 100.000000 1 2990 1 chr1D.!!$R1 2989
1 TraesCS1D01G088500 chr1D 49621884 49624477 2593 True 1349.000000 2481 90.370000 174 2370 2 chr1D.!!$R2 2196
2 TraesCS1D01G088500 chr1D 73969796 73972740 2944 True 1330.333333 3657 88.552333 1 2990 3 chr1D.!!$R3 2989
3 TraesCS1D01G088500 chr1B 70191159 70193238 2079 True 2383.000000 2383 87.674000 174 2215 1 chr1B.!!$R1 2041
4 TraesCS1D01G088500 chr1B 117279665 117281970 2305 True 748.500000 861 92.955000 1972 2990 2 chr1B.!!$R2 1018
5 TraesCS1D01G088500 chr1A 73337360 73338417 1057 True 1515.000000 1515 92.540000 1078 2134 1 chr1A.!!$R1 1056
6 TraesCS1D01G088500 chr1A 73344724 73345679 955 True 1343.000000 1343 92.259000 139 1080 1 chr1A.!!$R2 941
7 TraesCS1D01G088500 chr1A 49250772 49253436 2664 True 866.666667 2318 90.515667 174 2370 3 chr1A.!!$R3 2196

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
85 86 0.035630 GCTGCCATCTCCACTTGTCT 60.036 55.0 0.00 0.0 0.00 3.41 F
296 297 0.666274 GATCGCGGCCATATTCGACA 60.666 55.0 6.13 0.0 33.59 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1120 1153 0.323178 ACCCTCTGCATGCTGGAAAG 60.323 55.0 22.54 13.37 0.00 2.62 R
2255 2706 0.035915 TTGGCTAGTGTGGCGCAATA 60.036 50.0 10.83 4.93 35.06 1.90 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
59 60 0.323725 CATCCCCAGTTGGTCCCAAG 60.324 60.000 0.00 0.00 36.52 3.61
83 84 0.322277 CTGCTGCCATCTCCACTTGT 60.322 55.000 0.00 0.00 0.00 3.16
85 86 0.035630 GCTGCCATCTCCACTTGTCT 60.036 55.000 0.00 0.00 0.00 3.41
102 103 0.692476 TCTGACCCCACCATTCACAG 59.308 55.000 0.00 0.00 0.00 3.66
113 114 2.971598 ATTCACAGCCACCTCCCGG 61.972 63.158 0.00 0.00 0.00 5.73
234 235 2.331451 GGCGCGCCCAATATTCAC 59.669 61.111 39.89 10.20 0.00 3.18
263 264 2.044946 GGCTGGGTCGGCTCAATT 60.045 61.111 0.00 0.00 35.82 2.32
271 272 1.377202 TCGGCTCAATTGGCCTCAC 60.377 57.895 25.74 8.67 46.73 3.51
296 297 0.666274 GATCGCGGCCATATTCGACA 60.666 55.000 6.13 0.00 33.59 4.35
354 367 1.203441 TGAGGCCAGGCAAGAGATGT 61.203 55.000 15.19 0.00 0.00 3.06
500 519 0.770499 TGGAGGAGGTGAACAATGCA 59.230 50.000 0.00 0.00 0.00 3.96
593 612 0.953471 CGCTGGTCCGATTGTTCCAA 60.953 55.000 0.00 0.00 0.00 3.53
644 663 1.100510 TTGAGAGCATTGGCATCAGC 58.899 50.000 0.00 0.00 44.61 4.26
728 747 1.515088 CGAGAGCTACCGTGCACTG 60.515 63.158 16.19 11.43 34.23 3.66
740 759 2.353307 CCGTGCACTGTACAGTTATGGA 60.353 50.000 28.65 17.97 40.20 3.41
741 760 2.923655 CGTGCACTGTACAGTTATGGAG 59.076 50.000 25.89 14.33 40.20 3.86
751 770 1.739466 CAGTTATGGAGTTGCGCATGT 59.261 47.619 12.75 0.00 0.00 3.21
888 907 7.581213 ATCAAACTAGTGATCTCTACTCCTG 57.419 40.000 0.00 0.00 32.65 3.86
1022 1055 2.288457 TGGTCGAAGCTCTTCAGTTCTG 60.288 50.000 9.92 0.00 39.46 3.02
1120 1153 0.391130 TGGGATGCTACGTTCAGTGC 60.391 55.000 0.00 0.00 0.00 4.40
1123 1156 2.076863 GGATGCTACGTTCAGTGCTTT 58.923 47.619 0.00 0.00 0.00 3.51
1127 1160 1.461127 GCTACGTTCAGTGCTTTCCAG 59.539 52.381 0.00 0.00 0.00 3.86
1193 1226 7.883311 TCTTTTTCTGAACTACCCCAATCTTAG 59.117 37.037 0.00 0.00 0.00 2.18
1199 1232 3.371965 ACTACCCCAATCTTAGAAGCGA 58.628 45.455 0.00 0.00 0.00 4.93
1221 1254 3.711704 AGGATGTCGGTTGGAACATATCT 59.288 43.478 0.00 0.00 39.30 1.98
1228 1261 3.552273 CGGTTGGAACATATCTACGGGAG 60.552 52.174 0.00 0.00 39.30 4.30
1240 1273 2.163010 TCTACGGGAGCACGTTTCTTAG 59.837 50.000 2.08 0.00 46.25 2.18
1386 1419 2.550855 GCTGCGGAGGATCATAATGGAA 60.551 50.000 5.93 0.00 36.25 3.53
1455 1488 6.183360 GCAGATTACCAAGATGTAAACCTGAC 60.183 42.308 14.95 7.45 37.49 3.51
1464 1497 1.142060 TGTAAACCTGACCCCTGTGTG 59.858 52.381 0.00 0.00 0.00 3.82
1530 1563 2.896685 CTCGGAAGATATGGAGAAGGCT 59.103 50.000 0.00 0.00 40.84 4.58
1533 1566 4.082845 CGGAAGATATGGAGAAGGCTCTA 58.917 47.826 0.00 0.00 41.06 2.43
1596 1629 8.934023 AATACAACAAATTAGTGGAGAAAGGA 57.066 30.769 0.00 0.00 0.00 3.36
1665 1698 0.601057 TGAATCAGAAGACGGACGCA 59.399 50.000 0.00 0.00 0.00 5.24
1721 1754 1.425694 GGTTATCCCCTGAGTCCTCC 58.574 60.000 0.00 0.00 0.00 4.30
1737 1770 4.697756 CCGGCTGCTTTCCCACGA 62.698 66.667 0.00 0.00 0.00 4.35
1746 1779 3.101437 TGCTTTCCCACGATACCTAGAA 58.899 45.455 0.00 0.00 0.00 2.10
1860 1893 3.766591 TCCTAGCTTCCTCAGAAACAGAG 59.233 47.826 0.00 0.00 0.00 3.35
1866 1899 4.742138 GCTTCCTCAGAAACAGAGTTCACT 60.742 45.833 0.00 0.00 0.00 3.41
1938 1974 0.252927 AGCAGGAGGGAGGTAGCTTT 60.253 55.000 0.00 0.00 0.00 3.51
1991 2027 4.576128 GGGTGCACCTTGGACGATAGTT 62.576 54.545 33.91 0.00 43.92 2.24
2157 2213 4.122046 GGTGATATTTGCAATTTGGGCTC 58.878 43.478 0.00 0.00 0.00 4.70
2215 2298 2.943033 GCTTTTGGCGTCATGGTAGTAT 59.057 45.455 0.00 0.00 0.00 2.12
2216 2299 4.124238 GCTTTTGGCGTCATGGTAGTATA 58.876 43.478 0.00 0.00 0.00 1.47
2217 2300 4.211374 GCTTTTGGCGTCATGGTAGTATAG 59.789 45.833 0.00 0.00 0.00 1.31
2221 2672 4.722220 TGGCGTCATGGTAGTATAGTACT 58.278 43.478 15.69 0.00 42.68 2.73
2255 2706 3.513515 TGGTGAAAAAGTTTGAACTGGCT 59.486 39.130 0.00 0.00 39.66 4.75
2386 2884 7.868415 ACTGCTAGTTTAACTGTCAGTTCTTAG 59.132 37.037 21.40 17.24 38.22 2.18
2430 2936 7.095607 GCAAAGTATATAGCACAGTATCACACC 60.096 40.741 0.00 0.00 0.00 4.16
2468 2974 2.812591 CTGACTGCACAGCTTCAGATTT 59.187 45.455 11.07 0.00 39.79 2.17
2491 2997 2.173519 CCCATCTTGGCTCATGTGTTT 58.826 47.619 0.00 0.00 35.79 2.83
2501 3007 3.482786 GCTCATGTGTTTAGTTTGAGCG 58.517 45.455 7.38 0.00 46.67 5.03
2506 3012 7.254455 GCTCATGTGTTTAGTTTGAGCGTATAT 60.254 37.037 7.38 0.00 46.67 0.86
2536 3042 2.302260 CTCGCTCCAAGAGTAGGATGA 58.698 52.381 0.00 0.00 33.99 2.92
2537 3043 2.890311 CTCGCTCCAAGAGTAGGATGAT 59.110 50.000 0.00 0.00 33.99 2.45
2551 3057 6.991938 AGTAGGATGATATCTTCTTGACAGC 58.008 40.000 15.90 1.12 0.00 4.40
2579 4371 8.834749 ACTGAACTAACTTCTTTATTGAGGAC 57.165 34.615 0.00 0.00 0.00 3.85
2580 4372 7.599245 ACTGAACTAACTTCTTTATTGAGGACG 59.401 37.037 0.00 0.00 0.00 4.79
2597 4389 3.560068 AGGACGTGATCTGAAACAACAAC 59.440 43.478 0.00 0.00 0.00 3.32
2598 4390 3.311322 GGACGTGATCTGAAACAACAACA 59.689 43.478 0.00 0.00 0.00 3.33
2647 4488 4.727235 GGTCAAACCTGAAGTAAGAACG 57.273 45.455 0.00 0.00 34.73 3.95
2648 4489 4.124970 GGTCAAACCTGAAGTAAGAACGT 58.875 43.478 0.00 0.00 34.73 3.99
2649 4490 4.210746 GGTCAAACCTGAAGTAAGAACGTC 59.789 45.833 0.00 0.00 34.73 4.34
2650 4491 4.807304 GTCAAACCTGAAGTAAGAACGTCA 59.193 41.667 0.00 0.00 41.06 4.35
2651 4492 5.465724 GTCAAACCTGAAGTAAGAACGTCAT 59.534 40.000 0.00 0.00 42.15 3.06
2652 4493 5.694910 TCAAACCTGAAGTAAGAACGTCATC 59.305 40.000 0.00 0.00 42.15 2.92
2653 4494 5.470047 AACCTGAAGTAAGAACGTCATCT 57.530 39.130 0.00 0.00 42.15 2.90
2654 4495 4.810790 ACCTGAAGTAAGAACGTCATCTG 58.189 43.478 0.00 0.00 42.15 2.90
2655 4496 4.281182 ACCTGAAGTAAGAACGTCATCTGT 59.719 41.667 0.00 0.00 42.15 3.41
2656 4497 5.221461 ACCTGAAGTAAGAACGTCATCTGTT 60.221 40.000 0.00 0.00 42.15 3.16
2657 4498 5.696724 CCTGAAGTAAGAACGTCATCTGTTT 59.303 40.000 0.00 0.00 42.15 2.83
2658 4499 6.128795 CCTGAAGTAAGAACGTCATCTGTTTC 60.129 42.308 0.00 0.00 42.15 2.78
2659 4500 5.694910 TGAAGTAAGAACGTCATCTGTTTCC 59.305 40.000 0.00 0.00 38.89 3.13
2660 4501 5.209818 AGTAAGAACGTCATCTGTTTCCA 57.790 39.130 0.00 0.00 0.00 3.53
2661 4502 4.989168 AGTAAGAACGTCATCTGTTTCCAC 59.011 41.667 0.00 0.00 0.00 4.02
2662 4503 3.469008 AGAACGTCATCTGTTTCCACA 57.531 42.857 0.00 0.00 0.00 4.17
2663 4504 3.131396 AGAACGTCATCTGTTTCCACAC 58.869 45.455 0.00 0.00 0.00 3.82
2664 4505 2.910688 ACGTCATCTGTTTCCACACT 57.089 45.000 0.00 0.00 0.00 3.55
2665 4506 4.038763 AGAACGTCATCTGTTTCCACACTA 59.961 41.667 0.00 0.00 0.00 2.74
2666 4507 3.650139 ACGTCATCTGTTTCCACACTAC 58.350 45.455 0.00 0.00 0.00 2.73
2667 4508 3.321111 ACGTCATCTGTTTCCACACTACT 59.679 43.478 0.00 0.00 0.00 2.57
2668 4509 3.921021 CGTCATCTGTTTCCACACTACTC 59.079 47.826 0.00 0.00 0.00 2.59
2669 4510 3.921021 GTCATCTGTTTCCACACTACTCG 59.079 47.826 0.00 0.00 0.00 4.18
2670 4511 3.824443 TCATCTGTTTCCACACTACTCGA 59.176 43.478 0.00 0.00 0.00 4.04
2671 4512 3.917329 TCTGTTTCCACACTACTCGAG 57.083 47.619 11.84 11.84 0.00 4.04
2672 4513 3.483421 TCTGTTTCCACACTACTCGAGA 58.517 45.455 21.68 1.61 0.00 4.04
2673 4514 3.502595 TCTGTTTCCACACTACTCGAGAG 59.497 47.826 21.68 14.29 0.00 3.20
2674 4515 2.030185 TGTTTCCACACTACTCGAGAGC 60.030 50.000 21.68 0.00 0.00 4.09
2675 4516 0.803117 TTCCACACTACTCGAGAGCG 59.197 55.000 21.68 8.73 39.35 5.03
2676 4517 1.025113 TCCACACTACTCGAGAGCGG 61.025 60.000 21.68 12.78 38.28 5.52
2677 4518 1.226435 CACACTACTCGAGAGCGGC 60.226 63.158 21.68 0.00 38.28 6.53
2678 4519 2.408241 ACACTACTCGAGAGCGGCC 61.408 63.158 21.68 0.00 38.28 6.13
2679 4520 2.115911 CACTACTCGAGAGCGGCCT 61.116 63.158 21.68 0.00 38.28 5.19
2680 4521 1.820481 ACTACTCGAGAGCGGCCTC 60.820 63.158 21.68 2.28 38.28 4.70
2681 4522 1.820056 CTACTCGAGAGCGGCCTCA 60.820 63.158 21.68 5.43 40.68 3.86
2682 4523 2.054140 CTACTCGAGAGCGGCCTCAC 62.054 65.000 21.68 0.00 40.68 3.51
2683 4524 4.200283 CTCGAGAGCGGCCTCACC 62.200 72.222 6.58 0.00 40.68 4.02
2684 4525 4.742649 TCGAGAGCGGCCTCACCT 62.743 66.667 15.51 0.00 40.68 4.00
2685 4526 4.504916 CGAGAGCGGCCTCACCTG 62.505 72.222 15.51 0.00 40.68 4.00
2686 4527 3.071206 GAGAGCGGCCTCACCTGA 61.071 66.667 0.00 0.00 40.68 3.86
2687 4528 2.604686 AGAGCGGCCTCACCTGAA 60.605 61.111 0.00 0.00 40.68 3.02
2733 4574 2.270434 TTCACTAAGCTCCCTGGGAT 57.730 50.000 17.51 3.95 0.00 3.85
2760 4601 3.371380 GCTCCCAGGATTGATTGAGTCTT 60.371 47.826 0.00 0.00 0.00 3.01
2761 4602 4.853007 CTCCCAGGATTGATTGAGTCTTT 58.147 43.478 0.00 0.00 0.00 2.52
2781 4622 2.355197 TGGATTTTCGTCGATGTGCAT 58.645 42.857 4.21 0.00 0.00 3.96
2810 4651 1.361668 CGGATCGTGGGAAACTGCTG 61.362 60.000 0.00 0.00 0.00 4.41
2892 4764 4.082845 TGTGGAAACTGTTTTCACCTCAA 58.917 39.130 31.48 16.89 42.72 3.02
2914 4786 2.759114 CCACATGCCTGACACCCT 59.241 61.111 0.00 0.00 0.00 4.34
2942 4814 1.644786 ATTAGCAGCGCGGTGGTTTC 61.645 55.000 41.94 24.31 0.00 2.78
2950 4822 1.669760 GCGGTGGTTTCATGTCGGA 60.670 57.895 0.00 0.00 0.00 4.55
2968 4840 2.664851 CTCGCGTGCCTTTGACCA 60.665 61.111 5.77 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.692476 CTGTGAATGGTGGGGTCAGA 59.308 55.000 0.00 0.00 0.00 3.27
85 86 1.074775 GCTGTGAATGGTGGGGTCA 59.925 57.895 0.00 0.00 0.00 4.02
120 121 3.774959 AAGCGAGCGGCCGTCTATG 62.775 63.158 28.70 19.11 45.17 2.23
121 122 3.486252 GAAGCGAGCGGCCGTCTAT 62.486 63.158 28.70 10.72 45.17 1.98
122 123 4.189188 GAAGCGAGCGGCCGTCTA 62.189 66.667 28.70 0.00 45.17 2.59
228 229 1.378882 CCGGACGAGGACGGTGAATA 61.379 60.000 0.00 0.00 44.85 1.75
271 272 0.740868 ATATGGCCGCGATCGAATGG 60.741 55.000 21.57 17.51 38.10 3.16
296 297 4.664267 TGGCTGGGACTGGGAGCT 62.664 66.667 0.00 0.00 33.03 4.09
317 318 2.352533 ATCCCCATCCTCCTCCCCA 61.353 63.158 0.00 0.00 0.00 4.96
354 367 2.639065 GCGGAATACCCATCTGTTCAA 58.361 47.619 0.00 0.00 34.14 2.69
430 443 1.800586 CGCTGATATGCTTGGCGTTAT 59.199 47.619 0.00 0.00 40.78 1.89
432 445 0.461870 TCGCTGATATGCTTGGCGTT 60.462 50.000 0.00 0.00 45.01 4.84
486 505 1.195448 CGTCACTGCATTGTTCACCTC 59.805 52.381 3.77 0.00 0.00 3.85
500 519 0.108424 GATCAGCAGCCTTCGTCACT 60.108 55.000 0.00 0.00 0.00 3.41
644 663 2.956964 GAATCGCACTCGCTCGGG 60.957 66.667 0.00 0.00 35.30 5.14
728 747 2.343101 TGCGCAACTCCATAACTGTAC 58.657 47.619 8.16 0.00 0.00 2.90
740 759 1.200716 CCAATCTTGACATGCGCAACT 59.799 47.619 17.11 0.73 0.00 3.16
741 760 1.199789 TCCAATCTTGACATGCGCAAC 59.800 47.619 17.11 10.06 0.00 4.17
751 770 6.740944 TCCGGTATATCTTTCCAATCTTGA 57.259 37.500 0.00 0.00 0.00 3.02
780 799 1.001633 GCCAAGACTAAACACCTCCGA 59.998 52.381 0.00 0.00 0.00 4.55
1022 1055 1.203001 TGGTGAACCCCAAATCACTCC 60.203 52.381 5.95 0.00 44.20 3.85
1120 1153 0.323178 ACCCTCTGCATGCTGGAAAG 60.323 55.000 22.54 13.37 0.00 2.62
1123 1156 2.672908 CACCCTCTGCATGCTGGA 59.327 61.111 22.54 16.87 0.00 3.86
1127 1160 1.527844 GATCCCACCCTCTGCATGC 60.528 63.158 11.82 11.82 0.00 4.06
1134 1167 2.621668 CCTTTTTCCAGATCCCACCCTC 60.622 54.545 0.00 0.00 0.00 4.30
1193 1226 1.084370 CCAACCGACATCCTCGCTTC 61.084 60.000 0.00 0.00 41.46 3.86
1199 1232 3.711704 AGATATGTTCCAACCGACATCCT 59.288 43.478 0.00 0.00 37.62 3.24
1221 1254 2.161855 TCTAAGAAACGTGCTCCCGTA 58.838 47.619 0.00 0.00 40.85 4.02
1228 1261 4.651994 CCAATGTCATCTAAGAAACGTGC 58.348 43.478 0.00 0.00 0.00 5.34
1259 1292 5.702670 TCCAGAAACTTCTTCACATCATCAC 59.297 40.000 0.00 0.00 34.74 3.06
1386 1419 3.469008 TTCATCAACTGACGTGGTTCT 57.531 42.857 0.00 0.00 32.17 3.01
1455 1488 1.277557 CTCTTCTCCTTCACACAGGGG 59.722 57.143 0.00 0.00 35.39 4.79
1464 1497 7.045416 GTCTTAAGAATTCCCTCTTCTCCTTC 58.955 42.308 6.78 0.00 36.95 3.46
1530 1563 5.183228 CCTTTTCCACGGATAGCTTTTAGA 58.817 41.667 0.00 0.00 0.00 2.10
1533 1566 2.492088 GCCTTTTCCACGGATAGCTTTT 59.508 45.455 0.00 0.00 0.00 2.27
1596 1629 3.118531 AGCTACATCTTCTGGGTCCAAT 58.881 45.455 0.00 0.00 0.00 3.16
1721 1754 1.153449 TATCGTGGGAAAGCAGCCG 60.153 57.895 0.00 0.00 0.00 5.52
1737 1770 5.420725 TGTGCACAGTGAATTCTAGGTAT 57.579 39.130 17.42 0.00 0.00 2.73
1746 1779 3.523606 TTGCTTTTGTGCACAGTGAAT 57.476 38.095 20.59 0.00 43.20 2.57
1860 1893 8.368668 ACCTTATATACATGAGCCTTAGTGAAC 58.631 37.037 0.00 0.00 0.00 3.18
1938 1974 1.767088 CATCTGATCTCCTCTTGGCCA 59.233 52.381 0.00 0.00 0.00 5.36
1991 2027 3.947196 AGCCAACTCATGCATTCGATTAA 59.053 39.130 0.00 0.00 0.00 1.40
2157 2213 0.392060 GCCAGTACCGTAACCCAAGG 60.392 60.000 0.00 0.00 0.00 3.61
2215 2298 9.491675 TTTTCACCATGTTCGAAAATAGTACTA 57.508 29.630 4.77 4.77 34.58 1.82
2216 2299 7.972832 TTTCACCATGTTCGAAAATAGTACT 57.027 32.000 0.00 0.00 0.00 2.73
2217 2300 9.113876 CTTTTTCACCATGTTCGAAAATAGTAC 57.886 33.333 0.00 0.00 38.17 2.73
2221 2672 8.812329 CAAACTTTTTCACCATGTTCGAAAATA 58.188 29.630 0.00 0.00 38.17 1.40
2255 2706 0.035915 TTGGCTAGTGTGGCGCAATA 60.036 50.000 10.83 4.93 35.06 1.90
2386 2884 5.295540 ACTTTGCTCTGTTTCTTTGTCTCTC 59.704 40.000 0.00 0.00 0.00 3.20
2430 2936 4.621460 CAGTCAGTACGTGGAATTAGTGTG 59.379 45.833 0.00 0.00 0.00 3.82
2468 2974 1.212688 CACATGAGCCAAGATGGGGTA 59.787 52.381 0.00 0.00 39.15 3.69
2491 2997 7.068348 AGGAAAGTCTCATATACGCTCAAACTA 59.932 37.037 0.00 0.00 0.00 2.24
2501 3007 4.278669 TGGAGCGAGGAAAGTCTCATATAC 59.721 45.833 0.00 0.00 33.59 1.47
2506 3012 1.273606 CTTGGAGCGAGGAAAGTCTCA 59.726 52.381 0.00 0.00 33.59 3.27
2536 3042 5.426689 TCAGTTGGCTGTCAAGAAGATAT 57.573 39.130 0.00 0.00 43.05 1.63
2537 3043 4.890158 TCAGTTGGCTGTCAAGAAGATA 57.110 40.909 0.00 0.00 43.05 1.98
2551 3057 8.507249 CCTCAATAAAGAAGTTAGTTCAGTTGG 58.493 37.037 2.45 0.00 37.67 3.77
2579 4371 4.676471 CCATTGTTGTTGTTTCAGATCACG 59.324 41.667 0.00 0.00 0.00 4.35
2580 4372 4.445385 GCCATTGTTGTTGTTTCAGATCAC 59.555 41.667 0.00 0.00 0.00 3.06
2597 4389 7.439056 AGTTTAATGTTTCAAACAGAGCCATTG 59.561 33.333 9.27 0.00 45.95 2.82
2598 4390 7.500141 AGTTTAATGTTTCAAACAGAGCCATT 58.500 30.769 9.27 0.00 45.95 3.16
2639 4480 4.748102 TGTGGAAACAGATGACGTTCTTAC 59.252 41.667 0.00 0.00 44.46 2.34
2640 4481 4.748102 GTGTGGAAACAGATGACGTTCTTA 59.252 41.667 0.00 0.00 44.46 2.10
2641 4482 3.560068 GTGTGGAAACAGATGACGTTCTT 59.440 43.478 0.00 0.00 44.46 2.52
2642 4483 3.131396 GTGTGGAAACAGATGACGTTCT 58.869 45.455 0.00 0.00 44.46 3.01
2643 4484 3.131396 AGTGTGGAAACAGATGACGTTC 58.869 45.455 0.00 0.00 44.46 3.95
2644 4485 3.194005 AGTGTGGAAACAGATGACGTT 57.806 42.857 0.00 0.00 44.46 3.99
2645 4486 2.910688 AGTGTGGAAACAGATGACGT 57.089 45.000 0.00 0.00 44.46 4.34
2646 4487 3.914312 AGTAGTGTGGAAACAGATGACG 58.086 45.455 0.00 0.00 44.46 4.35
2647 4488 3.921021 CGAGTAGTGTGGAAACAGATGAC 59.079 47.826 0.00 0.00 44.46 3.06
2648 4489 3.824443 TCGAGTAGTGTGGAAACAGATGA 59.176 43.478 0.00 0.00 44.46 2.92
2649 4490 4.082733 TCTCGAGTAGTGTGGAAACAGATG 60.083 45.833 13.13 0.00 44.46 2.90
2650 4491 4.079970 TCTCGAGTAGTGTGGAAACAGAT 58.920 43.478 13.13 0.00 44.46 2.90
2651 4492 3.483421 TCTCGAGTAGTGTGGAAACAGA 58.517 45.455 13.13 0.00 44.46 3.41
2652 4493 3.827625 CTCTCGAGTAGTGTGGAAACAG 58.172 50.000 13.13 0.00 44.46 3.16
2653 4494 2.030185 GCTCTCGAGTAGTGTGGAAACA 60.030 50.000 13.13 0.00 38.70 2.83
2654 4495 2.597520 GCTCTCGAGTAGTGTGGAAAC 58.402 52.381 13.13 0.00 0.00 2.78
2655 4496 1.199327 CGCTCTCGAGTAGTGTGGAAA 59.801 52.381 13.13 0.00 38.10 3.13
2656 4497 0.803117 CGCTCTCGAGTAGTGTGGAA 59.197 55.000 13.13 0.00 38.10 3.53
2657 4498 2.467962 CGCTCTCGAGTAGTGTGGA 58.532 57.895 13.13 0.00 38.10 4.02
2658 4499 1.429825 CCGCTCTCGAGTAGTGTGG 59.570 63.158 13.13 12.79 41.56 4.17
2659 4500 1.226435 GCCGCTCTCGAGTAGTGTG 60.226 63.158 13.13 7.97 38.10 3.82
2660 4501 2.408241 GGCCGCTCTCGAGTAGTGT 61.408 63.158 13.13 0.00 38.10 3.55
2661 4502 2.054140 GAGGCCGCTCTCGAGTAGTG 62.054 65.000 13.13 14.08 38.10 2.74
2662 4503 1.820481 GAGGCCGCTCTCGAGTAGT 60.820 63.158 13.13 0.00 38.10 2.73
2663 4504 1.820056 TGAGGCCGCTCTCGAGTAG 60.820 63.158 13.13 9.69 38.10 2.57
2664 4505 2.113433 GTGAGGCCGCTCTCGAGTA 61.113 63.158 13.13 0.00 38.10 2.59
2665 4506 3.444805 GTGAGGCCGCTCTCGAGT 61.445 66.667 13.13 0.00 38.10 4.18
2666 4507 4.200283 GGTGAGGCCGCTCTCGAG 62.200 72.222 8.34 5.93 38.10 4.04
2667 4508 4.742649 AGGTGAGGCCGCTCTCGA 62.743 66.667 8.34 0.00 43.70 4.04
2668 4509 4.504916 CAGGTGAGGCCGCTCTCG 62.505 72.222 8.34 0.00 43.70 4.04
2669 4510 2.650116 TTCAGGTGAGGCCGCTCTC 61.650 63.158 8.34 0.00 43.70 3.20
2670 4511 2.604686 TTCAGGTGAGGCCGCTCT 60.605 61.111 8.34 2.39 43.70 4.09
2671 4512 2.435059 GTTCAGGTGAGGCCGCTC 60.435 66.667 8.34 3.59 43.70 5.03
2672 4513 4.021925 GGTTCAGGTGAGGCCGCT 62.022 66.667 8.34 0.00 43.70 5.52
2673 4514 3.628646 ATGGTTCAGGTGAGGCCGC 62.629 63.158 0.00 0.00 43.70 6.53
2674 4515 1.746615 CATGGTTCAGGTGAGGCCG 60.747 63.158 0.00 0.00 43.70 6.13
2675 4516 0.038166 TTCATGGTTCAGGTGAGGCC 59.962 55.000 0.00 0.00 37.58 5.19
2676 4517 2.134789 ATTCATGGTTCAGGTGAGGC 57.865 50.000 0.00 0.00 0.00 4.70
2677 4518 7.679783 TGTATATATTCATGGTTCAGGTGAGG 58.320 38.462 0.00 0.00 0.00 3.86
2678 4519 9.376075 GATGTATATATTCATGGTTCAGGTGAG 57.624 37.037 9.34 0.00 0.00 3.51
2679 4520 8.879227 TGATGTATATATTCATGGTTCAGGTGA 58.121 33.333 9.34 0.00 0.00 4.02
2680 4521 9.676861 ATGATGTATATATTCATGGTTCAGGTG 57.323 33.333 9.34 0.00 0.00 4.00
2681 4522 9.896645 GATGATGTATATATTCATGGTTCAGGT 57.103 33.333 9.34 0.00 30.48 4.00
2682 4523 9.895138 TGATGATGTATATATTCATGGTTCAGG 57.105 33.333 9.34 0.00 30.48 3.86
2733 4574 1.600058 ATCAATCCTGGGAGCTCCAA 58.400 50.000 33.29 23.06 46.51 3.53
2760 4601 2.147150 TGCACATCGACGAAAATCCAA 58.853 42.857 0.00 0.00 0.00 3.53
2761 4602 1.802069 TGCACATCGACGAAAATCCA 58.198 45.000 0.00 0.00 0.00 3.41
2781 4622 1.677518 CCCACGATCCGGTCAAAATCA 60.678 52.381 0.00 0.00 0.00 2.57
2810 4651 1.380380 CCTCTGACCAAATGGGCCC 60.380 63.158 17.59 17.59 44.80 5.80
2914 4786 1.647545 GCGCTGCTAATGAGTGCCAA 61.648 55.000 0.00 0.00 40.41 4.52


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

AutoCloner maintained by Alex Coulton.