Multiple sequence alignment - TraesCS4A01G471400

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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 TraesCS4A01G471400 chr4A 100.000 3311 0 0 1 3311 731852331 731849021 0.000000e+00 6115.0
1 TraesCS4A01G471400 chr4A 91.141 3014 219 23 339 3311 732354224 732357230 0.000000e+00 4043.0
2 TraesCS4A01G471400 chr4A 81.292 2384 368 55 991 3311 731875360 731872992 0.000000e+00 1860.0
3 TraesCS4A01G471400 chr4A 85.074 1762 218 28 936 2662 731616839 731615088 0.000000e+00 1755.0
4 TraesCS4A01G471400 chr4A 82.359 1848 274 35 857 2662 731861877 731860040 0.000000e+00 1559.0
5 TraesCS4A01G471400 chr4A 85.522 670 73 9 2666 3311 731615054 731614385 0.000000e+00 678.0
6 TraesCS4A01G471400 chr4A 81.102 889 117 30 2462 3311 731759685 731758809 0.000000e+00 664.0
7 TraesCS4A01G471400 chr4A 82.467 673 92 8 2664 3311 731860005 731859334 1.720000e-157 566.0
8 TraesCS4A01G471400 chr4A 95.286 297 10 3 419 711 732395490 732395786 5.000000e-128 468.0
9 TraesCS4A01G471400 chr4A 83.173 416 40 14 345 754 731664820 731664429 1.460000e-93 353.0
10 TraesCS4A01G471400 chr4A 85.630 341 34 10 1 341 731665193 731664868 8.800000e-91 344.0
11 TraesCS4A01G471400 chr4A 80.115 347 46 12 1 346 732353854 732354178 1.540000e-58 237.0
12 TraesCS4A01G471400 chr4A 90.076 131 11 2 766 894 731664445 731664315 5.680000e-38 169.0
13 TraesCS4A01G471400 chr7A 92.849 3342 198 16 1 3311 56203981 56207312 0.000000e+00 4809.0
14 TraesCS4A01G471400 chr7A 83.300 2491 338 44 869 3308 8634262 8636725 0.000000e+00 2224.0
15 TraesCS4A01G471400 chr7A 81.435 2370 374 39 994 3308 8653792 8656150 0.000000e+00 1879.0
16 TraesCS4A01G471400 chr7A 84.925 1539 214 13 915 2443 3432131 3430601 0.000000e+00 1541.0
17 TraesCS4A01G471400 chr7A 78.041 1225 186 51 2145 3311 8672443 8673642 0.000000e+00 695.0
18 TraesCS4A01G471400 chr7A 100.000 32 0 0 3280 3311 7139637 7139606 3.570000e-05 60.2
19 TraesCS4A01G471400 chr7D 83.435 2451 339 38 915 3311 7749985 7752422 0.000000e+00 2215.0
20 TraesCS4A01G471400 chr7D 82.871 2452 350 44 915 3310 7712568 7715005 0.000000e+00 2137.0
21 TraesCS4A01G471400 chr7D 83.406 2290 311 41 1077 3311 7606298 7608573 0.000000e+00 2060.0
22 TraesCS4A01G471400 chr7D 81.937 2375 363 40 990 3311 8233522 8235883 0.000000e+00 1949.0
23 TraesCS4A01G471400 chr7D 80.382 2462 415 42 901 3308 7597270 7599717 0.000000e+00 1808.0
24 TraesCS4A01G471400 chr7D 84.711 1779 229 20 915 2659 7561060 7562829 0.000000e+00 1738.0
25 TraesCS4A01G471400 chr7D 83.931 1786 248 28 904 2662 8030614 8032387 0.000000e+00 1672.0
26 TraesCS4A01G471400 chr7D 83.922 1785 242 26 915 2663 7548372 7550147 0.000000e+00 1664.0
27 TraesCS4A01G471400 chr7D 83.185 672 87 13 2665 3311 7562868 7563538 2.850000e-165 592.0
28 TraesCS4A01G471400 chr7D 82.122 688 82 18 2664 3311 8225120 8225806 4.830000e-153 551.0
29 TraesCS4A01G471400 chr7D 81.552 683 90 15 2665 3311 8054591 8055273 6.290000e-147 531.0
30 TraesCS4A01G471400 chr7D 83.858 508 59 11 2824 3308 8077213 8077720 2.330000e-126 462.0
31 TraesCS4A01G471400 chr7D 82.381 420 46 12 339 754 8222833 8223228 1.140000e-89 340.0
32 TraesCS4A01G471400 chr5B 82.017 2419 353 53 956 3308 37481633 37484035 0.000000e+00 1982.0
33 TraesCS4A01G471400 chr3B 84.287 1782 236 21 915 2661 741463153 741464925 0.000000e+00 1700.0
34 TraesCS4A01G471400 chr3B 82.310 684 83 15 2665 3311 741464963 741465645 2.890000e-155 558.0
35 TraesCS4A01G471400 chr3B 88.525 61 7 0 231 291 741456834 741456894 1.270000e-09 75.0


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 TraesCS4A01G471400 chr4A 731849021 731852331 3310 True 6115.000000 6115 100.0000 1 3311 1 chr4A.!!$R2 3310
1 TraesCS4A01G471400 chr4A 732353854 732357230 3376 False 2140.000000 4043 85.6280 1 3311 2 chr4A.!!$F2 3310
2 TraesCS4A01G471400 chr4A 731872992 731875360 2368 True 1860.000000 1860 81.2920 991 3311 1 chr4A.!!$R3 2320
3 TraesCS4A01G471400 chr4A 731614385 731616839 2454 True 1216.500000 1755 85.2980 936 3311 2 chr4A.!!$R4 2375
4 TraesCS4A01G471400 chr4A 731859334 731861877 2543 True 1062.500000 1559 82.4130 857 3311 2 chr4A.!!$R6 2454
5 TraesCS4A01G471400 chr4A 731758809 731759685 876 True 664.000000 664 81.1020 2462 3311 1 chr4A.!!$R1 849
6 TraesCS4A01G471400 chr4A 731664315 731665193 878 True 288.666667 353 86.2930 1 894 3 chr4A.!!$R5 893
7 TraesCS4A01G471400 chr7A 56203981 56207312 3331 False 4809.000000 4809 92.8490 1 3311 1 chr7A.!!$F4 3310
8 TraesCS4A01G471400 chr7A 8634262 8636725 2463 False 2224.000000 2224 83.3000 869 3308 1 chr7A.!!$F1 2439
9 TraesCS4A01G471400 chr7A 8653792 8656150 2358 False 1879.000000 1879 81.4350 994 3308 1 chr7A.!!$F2 2314
10 TraesCS4A01G471400 chr7A 3430601 3432131 1530 True 1541.000000 1541 84.9250 915 2443 1 chr7A.!!$R1 1528
11 TraesCS4A01G471400 chr7A 8672443 8673642 1199 False 695.000000 695 78.0410 2145 3311 1 chr7A.!!$F3 1166
12 TraesCS4A01G471400 chr7D 7749985 7752422 2437 False 2215.000000 2215 83.4350 915 3311 1 chr7D.!!$F5 2396
13 TraesCS4A01G471400 chr7D 7712568 7715005 2437 False 2137.000000 2137 82.8710 915 3310 1 chr7D.!!$F4 2395
14 TraesCS4A01G471400 chr7D 7606298 7608573 2275 False 2060.000000 2060 83.4060 1077 3311 1 chr7D.!!$F3 2234
15 TraesCS4A01G471400 chr7D 8233522 8235883 2361 False 1949.000000 1949 81.9370 990 3311 1 chr7D.!!$F9 2321
16 TraesCS4A01G471400 chr7D 7597270 7599717 2447 False 1808.000000 1808 80.3820 901 3308 1 chr7D.!!$F2 2407
17 TraesCS4A01G471400 chr7D 8030614 8032387 1773 False 1672.000000 1672 83.9310 904 2662 1 chr7D.!!$F6 1758
18 TraesCS4A01G471400 chr7D 7548372 7550147 1775 False 1664.000000 1664 83.9220 915 2663 1 chr7D.!!$F1 1748
19 TraesCS4A01G471400 chr7D 7561060 7563538 2478 False 1165.000000 1738 83.9480 915 3311 2 chr7D.!!$F10 2396
20 TraesCS4A01G471400 chr7D 8054591 8055273 682 False 531.000000 531 81.5520 2665 3311 1 chr7D.!!$F7 646
21 TraesCS4A01G471400 chr7D 8077213 8077720 507 False 462.000000 462 83.8580 2824 3308 1 chr7D.!!$F8 484
22 TraesCS4A01G471400 chr7D 8222833 8225806 2973 False 445.500000 551 82.2515 339 3311 2 chr7D.!!$F11 2972
23 TraesCS4A01G471400 chr5B 37481633 37484035 2402 False 1982.000000 1982 82.0170 956 3308 1 chr5B.!!$F1 2352
24 TraesCS4A01G471400 chr3B 741463153 741465645 2492 False 1129.000000 1700 83.2985 915 3311 2 chr3B.!!$F2 2396

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
209 218 0.107945 GCGCCTCCTGTCTTCTTCAT 60.108 55.000 0.00 0.0 0.0 2.57 F
394 456 0.614812 TGCAGGCAAGACATAGAGCA 59.385 50.000 0.00 0.0 0.0 4.26 F
643 710 1.133982 CGACAGAGTGAGCAGCAGTAT 59.866 52.381 0.00 0.0 0.0 2.12 F
933 1038 1.375551 AAGGTTGTTCGCGTTCTGTT 58.624 45.000 5.77 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 1567 0.321919 TGTCTGCTGCCAAGGATGTC 60.322 55.000 0.00 0.0 0.00 3.06 R
1662 1779 0.806868 CGCAGTGCCACATCTTCAAT 59.193 50.000 10.11 0.0 0.00 2.57 R
1757 1875 2.761767 TGCAATAGTTCAATGCTGCCAT 59.238 40.909 0.00 0.0 40.66 4.40 R
2822 3164 0.381801 AGCCTCAACGTTTGCAAGTG 59.618 50.000 14.47 0.0 0.00 3.16 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 3.391506 GCTGGTGCAAAAATCCTTTCT 57.608 42.857 0.00 0.00 39.41 2.52
92 93 5.306937 TCTCATAACTCTGGGTTCACTGAAA 59.693 40.000 0.00 0.00 39.17 2.69
103 104 5.242838 TGGGTTCACTGAAATAATTCACCAC 59.757 40.000 0.00 0.00 40.59 4.16
104 105 5.390613 GGTTCACTGAAATAATTCACCACG 58.609 41.667 0.00 0.00 40.59 4.94
156 157 9.838975 CAATTGTACTGATGTATAGCAACAAAA 57.161 29.630 0.00 0.00 31.99 2.44
158 159 8.840833 TTGTACTGATGTATAGCAACAAAAGA 57.159 30.769 0.00 0.00 32.02 2.52
159 160 8.840833 TGTACTGATGTATAGCAACAAAAGAA 57.159 30.769 0.00 0.00 32.02 2.52
160 161 8.935844 TGTACTGATGTATAGCAACAAAAGAAG 58.064 33.333 0.00 0.00 32.02 2.85
161 162 7.383102 ACTGATGTATAGCAACAAAAGAAGG 57.617 36.000 0.00 0.00 32.02 3.46
162 163 7.168219 ACTGATGTATAGCAACAAAAGAAGGA 58.832 34.615 0.00 0.00 32.02 3.36
163 164 7.335422 ACTGATGTATAGCAACAAAAGAAGGAG 59.665 37.037 0.00 0.00 32.02 3.69
173 182 7.287696 AGCAACAAAAGAAGGAGAAAAAGGATA 59.712 33.333 0.00 0.00 0.00 2.59
209 218 0.107945 GCGCCTCCTGTCTTCTTCAT 60.108 55.000 0.00 0.00 0.00 2.57
298 307 8.566260 CAAGTGAGAAAAGTCTTCATTCTTCAT 58.434 33.333 1.89 0.00 33.73 2.57
394 456 0.614812 TGCAGGCAAGACATAGAGCA 59.385 50.000 0.00 0.00 0.00 4.26
473 536 7.298122 GCCTATACAATATTTCCACACGAATG 58.702 38.462 0.00 0.00 0.00 2.67
528 595 5.440610 CTTCCACTGCCCTTTTCTATACAT 58.559 41.667 0.00 0.00 0.00 2.29
569 636 3.891805 ATCTCCATTTCCTTCCATCCC 57.108 47.619 0.00 0.00 0.00 3.85
570 637 2.863884 TCTCCATTTCCTTCCATCCCT 58.136 47.619 0.00 0.00 0.00 4.20
627 694 3.923864 AACACAGAGGCGGCGACA 61.924 61.111 18.30 0.00 0.00 4.35
643 710 1.133982 CGACAGAGTGAGCAGCAGTAT 59.866 52.381 0.00 0.00 0.00 2.12
663 731 7.467623 CAGTATTGTTGCTCTTCACCTATTTC 58.532 38.462 0.00 0.00 0.00 2.17
732 801 5.844004 TCCTTATTATGTTCCGCTCTTCTC 58.156 41.667 0.00 0.00 0.00 2.87
746 815 3.467803 CTCTTCTCCGGTTGTTCTGTTT 58.532 45.455 0.00 0.00 0.00 2.83
925 1030 3.756963 AGGAGGAATTTAAGGTTGTTCGC 59.243 43.478 0.00 0.00 0.00 4.70
933 1038 1.375551 AAGGTTGTTCGCGTTCTGTT 58.624 45.000 5.77 0.00 0.00 3.16
937 1042 1.593933 GTTGTTCGCGTTCTGTTGGTA 59.406 47.619 5.77 0.00 0.00 3.25
1428 1544 2.452600 ACAAGTTTGGCCTGGAGAAA 57.547 45.000 3.32 0.00 0.00 2.52
1451 1567 2.029666 CCATAAGGAGGAGCGGCG 59.970 66.667 0.51 0.51 36.89 6.46
1496 1613 3.576982 TCAAAACTGGACGACTCTACCAT 59.423 43.478 0.00 0.00 33.08 3.55
1637 1754 7.268586 ACTCTTGCTAAGATGGTGTACAATAG 58.731 38.462 0.00 0.00 36.82 1.73
1648 1765 2.500098 GTGTACAATAGCCAGGAGGTCA 59.500 50.000 0.00 0.00 37.19 4.02
1662 1779 2.687935 GGAGGTCAAGCAACACTTTCAA 59.312 45.455 0.00 0.00 36.04 2.69
1757 1875 2.361757 CAAATGGAAGTTGTGACCTGCA 59.638 45.455 0.00 0.00 37.10 4.41
1899 2017 2.884639 ACTATTGTGTTCTGTTGGTGGC 59.115 45.455 0.00 0.00 0.00 5.01
1959 2077 2.505407 AGTGGCCTCTATAATGTGCACA 59.495 45.455 24.08 24.08 0.00 4.57
1960 2078 3.054434 AGTGGCCTCTATAATGTGCACAA 60.054 43.478 25.72 8.96 0.00 3.33
1974 2092 3.834813 TGTGCACAATTAAGCCCCATAAA 59.165 39.130 19.28 0.00 0.00 1.40
1989 2107 5.470437 GCCCCATAAACTAGTATTTCTGAGC 59.530 44.000 0.00 0.00 0.00 4.26
2007 2125 2.099592 GAGCGCAAATGATTCATGGGAA 59.900 45.455 11.47 0.00 37.45 3.97
2048 2181 0.610232 AGCAATGGTGTGAAGGAGCC 60.610 55.000 0.00 0.00 0.00 4.70
2127 2263 1.457346 CTCTCAAGACAATGGGTGGC 58.543 55.000 0.00 0.00 34.17 5.01
2305 2481 5.129320 GCAATTTTCCCCAAGGATTATGAGT 59.871 40.000 0.00 0.00 43.54 3.41
2308 2484 4.946160 TTCCCCAAGGATTATGAGTTGT 57.054 40.909 0.00 0.00 43.54 3.32
2566 2803 8.337532 GCAGAAAGCATTGTTAAAAGATGTTTT 58.662 29.630 5.82 5.82 44.79 2.43
2590 2830 4.059511 CACATGCAAATTTCAAAGGCTGA 58.940 39.130 0.00 0.00 0.00 4.26
2591 2831 4.693566 CACATGCAAATTTCAAAGGCTGAT 59.306 37.500 0.00 0.00 32.78 2.90
2592 2832 4.693566 ACATGCAAATTTCAAAGGCTGATG 59.306 37.500 0.00 0.00 32.78 3.07
2650 2893 1.164411 TGCATCCGCACTTTGTTAGG 58.836 50.000 0.00 0.00 45.36 2.69
2789 3131 4.996788 TTTACGGTATCTTGACCTCTCC 57.003 45.455 0.00 0.00 37.34 3.71
2805 3147 1.068541 TCTCCGTGTCTGACATCGTTG 60.069 52.381 14.37 12.56 0.00 4.10
2808 3150 1.340658 CGTGTCTGACATCGTTGAGG 58.659 55.000 14.37 0.00 0.00 3.86
2809 3151 1.071605 GTGTCTGACATCGTTGAGGC 58.928 55.000 14.37 0.00 0.00 4.70
2810 3152 0.969149 TGTCTGACATCGTTGAGGCT 59.031 50.000 6.36 0.00 0.00 4.58
2812 3154 1.067565 GTCTGACATCGTTGAGGCTCA 60.068 52.381 14.43 14.43 0.00 4.26
2813 3155 1.203287 TCTGACATCGTTGAGGCTCAG 59.797 52.381 17.91 7.38 0.00 3.35
2815 3157 1.203287 TGACATCGTTGAGGCTCAGAG 59.797 52.381 17.91 15.12 0.00 3.35
2817 3159 1.203523 ACATCGTTGAGGCTCAGAGTC 59.796 52.381 17.91 8.79 0.00 3.36
2818 3160 1.476085 CATCGTTGAGGCTCAGAGTCT 59.524 52.381 17.91 3.48 29.26 3.24
2819 3161 0.884514 TCGTTGAGGCTCAGAGTCTG 59.115 55.000 17.91 14.36 24.78 3.51
2820 3162 0.735632 CGTTGAGGCTCAGAGTCTGC 60.736 60.000 17.91 4.51 24.78 4.26
2821 3163 0.735632 GTTGAGGCTCAGAGTCTGCG 60.736 60.000 17.91 10.69 24.78 5.18
2822 3164 2.202730 GAGGCTCAGAGTCTGCGC 60.203 66.667 23.93 23.93 40.91 6.09
2883 3238 5.181748 GCAGAAGTTACCAGAAGACATGAT 58.818 41.667 0.00 0.00 0.00 2.45
2922 3277 8.465201 GCTCATCAATCTTTATCTCTTTGGTTT 58.535 33.333 0.00 0.00 0.00 3.27
2980 3335 7.754924 GGTGTAATGAACAACCTTCACATATTG 59.245 37.037 0.00 0.00 40.16 1.90
3075 3430 4.801164 AGGCTGGAGCTATTGAATTTGAT 58.199 39.130 0.00 0.00 41.70 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 6.983307 CAGTGAACCCAGAGTTATGAGATAAG 59.017 42.308 0.00 0.00 39.40 1.73
156 157 5.313506 ACCTGGTTATCCTTTTTCTCCTTCT 59.686 40.000 0.00 0.00 34.23 2.85
157 158 5.571285 ACCTGGTTATCCTTTTTCTCCTTC 58.429 41.667 0.00 0.00 34.23 3.46
158 159 5.516768 GGACCTGGTTATCCTTTTTCTCCTT 60.517 44.000 0.00 0.00 34.23 3.36
159 160 4.018324 GGACCTGGTTATCCTTTTTCTCCT 60.018 45.833 0.00 0.00 34.23 3.69
160 161 4.270834 GGACCTGGTTATCCTTTTTCTCC 58.729 47.826 0.00 0.00 34.23 3.71
161 162 3.939592 CGGACCTGGTTATCCTTTTTCTC 59.060 47.826 0.00 0.00 32.33 2.87
162 163 3.308188 CCGGACCTGGTTATCCTTTTTCT 60.308 47.826 0.00 0.00 32.33 2.52
163 164 3.014623 CCGGACCTGGTTATCCTTTTTC 58.985 50.000 0.00 0.00 32.33 2.29
198 207 6.071165 TCACTTGCTCTATGATGAAGAAGACA 60.071 38.462 0.00 0.00 0.00 3.41
203 212 5.394993 CCTGTCACTTGCTCTATGATGAAGA 60.395 44.000 0.00 0.00 0.00 2.87
204 213 4.809958 CCTGTCACTTGCTCTATGATGAAG 59.190 45.833 0.00 0.00 0.00 3.02
209 218 2.164422 CGACCTGTCACTTGCTCTATGA 59.836 50.000 0.00 0.00 0.00 2.15
298 307 2.483876 GACAATAAGCGGCATCTGCTA 58.516 47.619 1.45 0.00 43.14 3.49
381 442 8.774890 ATATTCAAGCTATGCTCTATGTCTTG 57.225 34.615 0.00 0.00 38.25 3.02
473 536 1.226030 AAGCGCGTGAGGTTTGGTAC 61.226 55.000 8.43 0.00 0.00 3.34
528 595 7.419518 GGAGATAAGATCAAGGAATCCAACAGA 60.420 40.741 0.61 0.00 0.00 3.41
569 636 1.165907 TTGCGTGGTTGCTGGAGAAG 61.166 55.000 0.00 0.00 35.36 2.85
570 637 0.537143 ATTGCGTGGTTGCTGGAGAA 60.537 50.000 0.00 0.00 35.36 2.87
627 694 3.332919 CAACAATACTGCTGCTCACTCT 58.667 45.455 0.00 0.00 0.00 3.24
643 710 4.451096 GTCGAAATAGGTGAAGAGCAACAA 59.549 41.667 0.00 0.00 36.36 2.83
676 744 0.179004 TCACCTCAACAACGCCCAAT 60.179 50.000 0.00 0.00 0.00 3.16
937 1042 7.138054 TGAAAGAGAAAAGGAGAGGTTAAGT 57.862 36.000 0.00 0.00 0.00 2.24
1013 1124 0.389948 ACGCACTAAAGGGAGAAGCG 60.390 55.000 0.00 0.00 44.22 4.68
1060 1171 2.183555 GGTCACCATCCCGACGAC 59.816 66.667 0.00 0.00 32.74 4.34
1105 1216 3.423154 CTGGCGCTCCAACGTTCC 61.423 66.667 7.64 0.00 42.91 3.62
1129 1240 3.114616 CAGCTTGCACTCGACGGG 61.115 66.667 0.00 0.00 0.00 5.28
1156 1267 3.618351 CATTTGTCATGCTCCTCTCCTT 58.382 45.455 0.00 0.00 0.00 3.36
1395 1511 4.823989 CCAAACTTGTTCATCTCCTCAACT 59.176 41.667 0.00 0.00 0.00 3.16
1428 1544 1.967066 CGCTCCTCCTTATGGACAGAT 59.033 52.381 0.00 0.00 37.46 2.90
1451 1567 0.321919 TGTCTGCTGCCAAGGATGTC 60.322 55.000 0.00 0.00 0.00 3.06
1463 1579 2.092968 TCCAGTTTTGAGTGTGTCTGCT 60.093 45.455 0.00 0.00 0.00 4.24
1637 1754 1.228245 TGTTGCTTGACCTCCTGGC 60.228 57.895 0.00 0.00 36.63 4.85
1648 1765 6.477688 CACATCTTCAATTGAAAGTGTTGCTT 59.522 34.615 24.49 9.52 39.52 3.91
1662 1779 0.806868 CGCAGTGCCACATCTTCAAT 59.193 50.000 10.11 0.00 0.00 2.57
1757 1875 2.761767 TGCAATAGTTCAATGCTGCCAT 59.238 40.909 0.00 0.00 40.66 4.40
1853 1971 5.376625 GCTTCAATACATCCTCCCACATTA 58.623 41.667 0.00 0.00 0.00 1.90
1899 2017 5.047306 TGTGACCACTATAACACTTCCTGAG 60.047 44.000 1.62 0.00 34.81 3.35
1960 2078 9.574516 CAGAAATACTAGTTTATGGGGCTTAAT 57.425 33.333 0.00 0.00 29.18 1.40
1974 2092 5.419542 TCATTTGCGCTCAGAAATACTAGT 58.580 37.500 9.73 0.00 0.00 2.57
1989 2107 4.435425 ACAATTCCCATGAATCATTTGCG 58.565 39.130 0.00 0.00 40.34 4.85
2048 2181 3.943381 TCCAATGCTGACTAATTCTGCTG 59.057 43.478 4.99 0.00 46.67 4.41
2127 2263 7.967854 TGTACATGTTTCTTTGAACTCAACAAG 59.032 33.333 2.30 0.00 35.28 3.16
2184 2320 8.681584 TCATATTTTCCTCCATCATTATCCCTT 58.318 33.333 0.00 0.00 0.00 3.95
2305 2481 6.183360 CCATAGTTCGATCAGACCTTCTACAA 60.183 42.308 0.00 0.00 0.00 2.41
2308 2484 5.691896 TCCATAGTTCGATCAGACCTTCTA 58.308 41.667 0.00 0.00 0.00 2.10
2566 2803 4.512198 CAGCCTTTGAAATTTGCATGTGAA 59.488 37.500 0.00 0.00 0.00 3.18
2579 2816 4.588106 TGTTCCAATTCATCAGCCTTTGAA 59.412 37.500 0.00 0.00 39.77 2.69
2590 2830 4.845796 ACCCCTTGATTTGTTCCAATTCAT 59.154 37.500 3.29 0.00 0.00 2.57
2591 2831 4.230455 ACCCCTTGATTTGTTCCAATTCA 58.770 39.130 0.00 0.00 0.00 2.57
2592 2832 4.890158 ACCCCTTGATTTGTTCCAATTC 57.110 40.909 0.00 0.00 0.00 2.17
2609 2849 3.161866 TGTTCTTCCTTTGCATAACCCC 58.838 45.455 0.00 0.00 0.00 4.95
2789 3131 1.340658 CCTCAACGATGTCAGACACG 58.659 55.000 18.29 18.29 0.00 4.49
2809 3151 1.624865 GCAAGTGCGCAGACTCTGAG 61.625 60.000 12.22 7.84 34.50 3.35
2810 3152 1.665916 GCAAGTGCGCAGACTCTGA 60.666 57.895 12.22 0.00 32.44 3.27
2812 3154 0.815213 TTTGCAAGTGCGCAGACTCT 60.815 50.000 12.22 0.00 44.14 3.24
2813 3155 0.658536 GTTTGCAAGTGCGCAGACTC 60.659 55.000 12.22 0.00 44.14 3.36
2815 3157 2.005537 CGTTTGCAAGTGCGCAGAC 61.006 57.895 12.22 0.00 44.14 3.51
2817 3159 1.586042 AACGTTTGCAAGTGCGCAG 60.586 52.632 12.22 0.00 44.14 5.18
2818 3160 1.871345 CAACGTTTGCAAGTGCGCA 60.871 52.632 5.66 5.66 45.83 6.09
2819 3161 1.531522 CTCAACGTTTGCAAGTGCGC 61.532 55.000 16.30 0.00 45.83 6.09
2820 3162 0.929824 CCTCAACGTTTGCAAGTGCG 60.930 55.000 15.25 15.25 45.83 5.34
2821 3163 1.208642 GCCTCAACGTTTGCAAGTGC 61.209 55.000 0.00 0.00 42.50 4.40
2822 3164 0.381801 AGCCTCAACGTTTGCAAGTG 59.618 50.000 14.47 0.00 0.00 3.16
2922 3277 7.119387 TGGAGACATACTTCTGAGACTATCAA 58.881 38.462 0.00 0.00 33.82 2.57
3075 3430 5.877012 GCATTCTCCACACTCTTTATCTTGA 59.123 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.