Multiple sequence alignment - TraesCS3D01G271400

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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 TraesCS3D01G271400 chr3D 100.000 4123 0 0 1 4123 376260846 376264968 0.000000e+00 7614.0
1 TraesCS3D01G271400 chr3D 100.000 338 0 0 4442 4779 376265287 376265624 4.060000e-175 625.0
2 TraesCS3D01G271400 chr3D 93.421 152 8 2 1439 1590 322435299 322435448 1.730000e-54 224.0
3 TraesCS3D01G271400 chr3D 93.243 148 9 1 1439 1586 85449513 85449367 2.900000e-52 217.0
4 TraesCS3D01G271400 chr3D 93.151 146 10 0 1440 1585 288550603 288550458 1.040000e-51 215.0
5 TraesCS3D01G271400 chr3B 90.629 2337 109 36 618 2921 490883517 490885776 0.000000e+00 3001.0
6 TraesCS3D01G271400 chr3B 94.225 710 26 8 3417 4123 490886354 490887051 0.000000e+00 1070.0
7 TraesCS3D01G271400 chr3B 94.479 489 14 4 2933 3418 490885845 490886323 0.000000e+00 741.0
8 TraesCS3D01G271400 chr3B 85.126 437 55 8 78 512 490882522 490882950 5.680000e-119 438.0
9 TraesCS3D01G271400 chr3B 92.278 259 17 2 4502 4757 490887201 490887459 9.770000e-97 364.0
10 TraesCS3D01G271400 chr3B 93.421 152 8 2 1439 1590 396271886 396272035 1.730000e-54 224.0
11 TraesCS3D01G271400 chr3B 87.500 72 9 0 559 630 490883425 490883496 3.060000e-12 84.2
12 TraesCS3D01G271400 chr3A 91.332 2215 96 27 701 2885 500984627 500986775 0.000000e+00 2939.0
13 TraesCS3D01G271400 chr3A 93.154 1227 55 22 2918 4123 500986769 500987987 0.000000e+00 1773.0
14 TraesCS3D01G271400 chr3A 84.912 570 81 3 1 567 500983997 500984564 5.370000e-159 571.0
15 TraesCS3D01G271400 chr3A 91.829 257 20 1 4502 4758 500988046 500988301 1.640000e-94 357.0
16 TraesCS3D01G271400 chr4D 92.073 164 13 0 1430 1593 74079349 74079512 1.030000e-56 231.0
17 TraesCS3D01G271400 chr5D 92.617 149 11 0 1443 1591 175299915 175300063 1.040000e-51 215.0
18 TraesCS3D01G271400 chr4B 90.625 160 14 1 1430 1589 106227407 106227565 1.350000e-50 211.0
19 TraesCS3D01G271400 chr1B 76.355 203 36 12 3130 3327 643590164 643590359 1.090000e-16 99.0
20 TraesCS3D01G271400 chr1D 75.862 203 37 12 3130 3327 467033657 467033852 5.090000e-15 93.5
21 TraesCS3D01G271400 chr1A 94.340 53 3 0 3130 3182 558978562 558978614 1.100000e-11 82.4


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 TraesCS3D01G271400 chr3D 376260846 376265624 4778 False 4119.5 7614 100.000000 1 4779 2 chr3D.!!$F2 4778
1 TraesCS3D01G271400 chr3B 490882522 490887459 4937 False 949.7 3001 90.706167 78 4757 6 chr3B.!!$F2 4679
2 TraesCS3D01G271400 chr3A 500983997 500988301 4304 False 1410.0 2939 90.306750 1 4758 4 chr3A.!!$F1 4757

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
816 1296 0.038892 GCAACGGACGTGTTCTCCTA 60.039 55.0 0.0 0.0 0.00 2.94 F
1282 1775 0.249405 AATGGGTTGTTTGTGCAGCG 60.249 50.0 0.0 0.0 0.00 5.18 F
1680 2189 0.251341 GGATGGTGGAGGTTGTGCTT 60.251 55.0 0.0 0.0 0.00 3.91 F
2503 3023 0.389426 TCGGTGGCGTTTCTAGCTTC 60.389 55.0 0.0 0.0 34.52 3.86 F
3465 4099 0.739813 CCCTGTCTTAGTTTCCGGCG 60.740 60.0 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2433 0.808755 GGTGGCTCAAATAACACCGG 59.191 55.000 0.00 0.0 43.28 5.28 R
2726 3247 2.930455 GCATTTAGGCCGCACATGTTTT 60.930 45.455 0.00 0.0 0.00 2.43 R
3635 4269 0.392193 CAGCTTCTGCCTCGTTGGAT 60.392 55.000 1.63 0.0 40.80 3.41 R
3641 4275 1.069636 GTTTCAACAGCTTCTGCCTCG 60.070 52.381 0.00 0.0 40.80 4.63 R
4758 5419 0.036952 ATGAAGCCGTCTGTGACAGG 60.037 55.000 13.33 0.0 32.09 4.00 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
47 48 3.074412 AGAATCATCAACCGTTCCACAC 58.926 45.455 0.00 0.00 0.00 3.82
57 58 2.563620 ACCGTTCCACACCTTTTGTTTT 59.436 40.909 0.00 0.00 35.67 2.43
58 59 3.007074 ACCGTTCCACACCTTTTGTTTTT 59.993 39.130 0.00 0.00 35.67 1.94
59 60 3.369451 CCGTTCCACACCTTTTGTTTTTG 59.631 43.478 0.00 0.00 35.67 2.44
75 78 6.567687 TGTTTTTGTCACTCTTTTCTGACA 57.432 33.333 0.00 0.00 43.99 3.58
142 145 3.461773 CTCCCGCATCCGTCCACT 61.462 66.667 0.00 0.00 0.00 4.00
145 148 2.264480 CCGCATCCGTCCACTGAA 59.736 61.111 0.00 0.00 0.00 3.02
160 163 4.871993 CACTGAAAGAGGAATCAATCCG 57.128 45.455 0.00 0.00 46.20 4.18
178 181 2.737467 CGCAAATACGGATGTGGAAG 57.263 50.000 0.00 0.00 0.00 3.46
198 201 1.445942 CGGCCATCCAACGATACCT 59.554 57.895 2.24 0.00 0.00 3.08
212 215 6.650807 CCAACGATACCTGCATATATTTGACT 59.349 38.462 0.00 0.00 0.00 3.41
213 216 7.148573 CCAACGATACCTGCATATATTTGACTC 60.149 40.741 0.00 0.00 0.00 3.36
215 218 7.615403 ACGATACCTGCATATATTTGACTCAT 58.385 34.615 0.00 0.00 0.00 2.90
245 249 4.389374 AGGTCCACATATTCAAATAGCCG 58.611 43.478 0.00 0.00 0.00 5.52
267 272 8.936864 AGCCGCATATATAGTTCAAAATAGTTC 58.063 33.333 0.00 0.00 0.00 3.01
285 290 2.245795 TCGAATGTTCAAATGCAGCG 57.754 45.000 0.00 0.00 0.00 5.18
293 298 2.177394 TCAAATGCAGCGGTAGTTCA 57.823 45.000 0.00 0.00 0.00 3.18
295 300 1.535028 CAAATGCAGCGGTAGTTCACA 59.465 47.619 0.00 0.00 0.00 3.58
296 301 2.113860 AATGCAGCGGTAGTTCACAT 57.886 45.000 0.00 0.00 0.00 3.21
306 311 7.644551 GCAGCGGTAGTTCACATATATATAGTC 59.355 40.741 0.00 0.00 0.00 2.59
344 349 4.044439 CTGGCCAAGGCTGGAGCT 62.044 66.667 7.01 0.00 46.92 4.09
417 422 3.723348 GCACGCGTTCTTGACCCC 61.723 66.667 10.22 0.00 0.00 4.95
498 503 3.136123 ATGCTGGCATGGCACGAC 61.136 61.111 19.43 11.28 42.69 4.34
528 533 8.468720 TTTCCTTTTCCTTTTCTGTTTTAACG 57.531 30.769 0.00 0.00 0.00 3.18
537 542 6.035220 CCTTTTCTGTTTTAACGTCCCAAAAC 59.965 38.462 18.73 18.73 42.37 2.43
573 1017 9.373450 TGGCAAAATATATAAAGGGCTGAATAA 57.627 29.630 0.00 0.00 0.00 1.40
605 1049 1.351430 CCAGCACATGTGTCGTACCG 61.351 60.000 26.01 7.75 0.00 4.02
607 1051 0.109272 AGCACATGTGTCGTACCGAG 60.109 55.000 26.01 0.00 36.23 4.63
610 1054 1.872234 CATGTGTCGTACCGAGGCG 60.872 63.158 0.00 0.00 36.23 5.52
621 1098 1.887707 CCGAGGCGGTCCATTTAGC 60.888 63.158 0.00 0.00 42.73 3.09
681 1161 2.761392 TTTCGAGAAACACGAGACGA 57.239 45.000 0.00 0.00 40.72 4.20
688 1168 1.461091 AAACACGAGACGAGGCCTCA 61.461 55.000 31.67 0.00 0.00 3.86
689 1169 1.461091 AACACGAGACGAGGCCTCAA 61.461 55.000 31.67 0.00 0.00 3.02
716 1196 4.609995 CCGTGTCAGGCCGTATTT 57.390 55.556 0.00 0.00 0.00 1.40
717 1197 2.849081 CCGTGTCAGGCCGTATTTT 58.151 52.632 0.00 0.00 0.00 1.82
718 1198 2.012937 CCGTGTCAGGCCGTATTTTA 57.987 50.000 0.00 0.00 0.00 1.52
719 1199 1.662122 CCGTGTCAGGCCGTATTTTAC 59.338 52.381 0.00 0.00 0.00 2.01
803 1283 3.192422 TGTGGAATGGAATAAAGCAACGG 59.808 43.478 0.00 0.00 0.00 4.44
816 1296 0.038892 GCAACGGACGTGTTCTCCTA 60.039 55.000 0.00 0.00 0.00 2.94
818 1298 2.746269 CAACGGACGTGTTCTCCTAAA 58.254 47.619 0.00 0.00 0.00 1.85
1228 1720 2.511600 CGGGTGGATTCTGGCGAC 60.512 66.667 0.00 0.00 0.00 5.19
1230 1722 3.195698 GGTGGATTCTGGCGACGC 61.196 66.667 12.43 12.43 0.00 5.19
1282 1775 0.249405 AATGGGTTGTTTGTGCAGCG 60.249 50.000 0.00 0.00 0.00 5.18
1419 1926 5.369404 TGATATGATGTGATAACTGTGGGGT 59.631 40.000 0.00 0.00 0.00 4.95
1432 1939 2.640826 CTGTGGGGTTTGGAAGGTACTA 59.359 50.000 0.00 0.00 38.49 1.82
1433 1940 2.640826 TGTGGGGTTTGGAAGGTACTAG 59.359 50.000 0.00 0.00 38.49 2.57
1513 2021 5.546526 AGACATGTTTTGGTGTGTTTGTTT 58.453 33.333 0.00 0.00 0.00 2.83
1519 2027 6.153067 TGTTTTGGTGTGTTTGTTTACTCAG 58.847 36.000 0.00 0.00 0.00 3.35
1538 2046 3.373130 TCAGTTCAGTCCGTATGTACTCG 59.627 47.826 0.00 0.00 0.00 4.18
1638 2147 7.766738 TCAAAACCTTTTGTTAGAAATGGTTCC 59.233 33.333 19.88 0.00 45.77 3.62
1680 2189 0.251341 GGATGGTGGAGGTTGTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
1707 2216 1.741770 GTCTGGTGATGTGGCCGTC 60.742 63.158 0.00 0.00 0.00 4.79
1717 2226 2.623878 TGTGGCCGTCTCAGTTTTAA 57.376 45.000 0.00 0.00 0.00 1.52
1753 2262 4.641541 CAGGGCAGTTATCATGTTTGATGA 59.358 41.667 0.00 0.00 42.60 2.92
1831 2341 5.125417 TGCTCCAAGCTTATTTGTAATGTCC 59.875 40.000 0.00 0.00 42.97 4.02
1843 2353 6.503589 TTTGTAATGTCCCACTTATTTCCG 57.496 37.500 0.00 0.00 0.00 4.30
1915 2433 4.098501 ACATATTTGCTTGCTTAAGCCCTC 59.901 41.667 24.30 12.96 44.89 4.30
1916 2434 1.256812 TTTGCTTGCTTAAGCCCTCC 58.743 50.000 24.30 10.64 44.89 4.30
1926 2444 3.617284 CTTAAGCCCTCCGGTGTTATTT 58.383 45.455 0.00 0.00 0.00 1.40
2079 2599 9.303116 TGGTTGTGTTTGTTTATATGGATTACT 57.697 29.630 0.00 0.00 0.00 2.24
2119 2639 7.209475 TCTGCACGATATATCTGTCATGAAAA 58.791 34.615 10.93 0.00 0.00 2.29
2182 2702 3.058501 CGACCGGCTTTCTTACATTGTTT 60.059 43.478 0.00 0.00 0.00 2.83
2274 2794 3.295973 GCTGCCCCAAAGGTAATAATCA 58.704 45.455 0.00 0.00 38.26 2.57
2275 2795 3.897505 GCTGCCCCAAAGGTAATAATCAT 59.102 43.478 0.00 0.00 38.26 2.45
2276 2796 4.021981 GCTGCCCCAAAGGTAATAATCATC 60.022 45.833 0.00 0.00 38.26 2.92
2310 2830 9.612620 GAGATTTGGTTAATGTTTTCTACACAG 57.387 33.333 0.00 0.00 40.19 3.66
2314 2834 7.429636 TGGTTAATGTTTTCTACACAGCTAC 57.570 36.000 0.00 0.00 40.19 3.58
2317 2837 7.172703 GGTTAATGTTTTCTACACAGCTACTGT 59.827 37.037 0.00 0.00 46.51 3.55
2318 2838 6.787085 AATGTTTTCTACACAGCTACTGTC 57.213 37.500 0.00 0.00 43.43 3.51
2332 2852 4.102681 AGCTACTGTCCCTGTACACTTTTT 59.897 41.667 0.00 0.00 0.00 1.94
2447 2967 7.694784 CGACTTTCTTTTGCAAAGTTAAGTACA 59.305 33.333 23.25 5.04 42.84 2.90
2469 2989 0.550914 TGTTCAAGGGCTGGTCAACT 59.449 50.000 0.00 0.00 0.00 3.16
2497 3017 2.028385 AGATTACTTCGGTGGCGTTTCT 60.028 45.455 0.00 0.00 0.00 2.52
2503 3023 0.389426 TCGGTGGCGTTTCTAGCTTC 60.389 55.000 0.00 0.00 34.52 3.86
2686 3206 6.902341 TGTCTAGACAATTTTAGCTGCTTTG 58.098 36.000 23.24 8.92 38.56 2.77
2702 3222 6.071221 AGCTGCTTTGATTGGACATTTCATAA 60.071 34.615 0.00 0.00 0.00 1.90
2703 3223 6.591062 GCTGCTTTGATTGGACATTTCATAAA 59.409 34.615 0.00 0.00 0.00 1.40
2704 3224 7.118101 GCTGCTTTGATTGGACATTTCATAAAA 59.882 33.333 0.00 0.00 0.00 1.52
2705 3225 8.899427 TGCTTTGATTGGACATTTCATAAAAA 57.101 26.923 0.00 0.00 0.00 1.94
2771 3292 2.754946 TGATTAACCCGTCAGGACAC 57.245 50.000 0.00 0.00 41.02 3.67
2813 3334 5.958955 AGCTCAGAAAAATTATCACTTGCC 58.041 37.500 0.00 0.00 0.00 4.52
2887 3410 4.976224 AGTGGTTGTTGTGGTTCTAAAC 57.024 40.909 0.00 0.00 0.00 2.01
2899 3429 7.042797 TGTGGTTCTAAACGTACTTCTAGTT 57.957 36.000 0.00 0.00 0.00 2.24
2911 3441 6.038936 ACGTACTTCTAGTTGTTGCCATTTTT 59.961 34.615 0.00 0.00 0.00 1.94
2912 3442 6.577427 CGTACTTCTAGTTGTTGCCATTTTTC 59.423 38.462 0.00 0.00 0.00 2.29
2913 3443 6.715347 ACTTCTAGTTGTTGCCATTTTTCT 57.285 33.333 0.00 0.00 0.00 2.52
2914 3444 7.817418 ACTTCTAGTTGTTGCCATTTTTCTA 57.183 32.000 0.00 0.00 0.00 2.10
2915 3445 8.409358 ACTTCTAGTTGTTGCCATTTTTCTAT 57.591 30.769 0.00 0.00 0.00 1.98
2916 3446 8.515414 ACTTCTAGTTGTTGCCATTTTTCTATC 58.485 33.333 0.00 0.00 0.00 2.08
2917 3447 7.072177 TCTAGTTGTTGCCATTTTTCTATCG 57.928 36.000 0.00 0.00 0.00 2.92
2918 3448 5.059404 AGTTGTTGCCATTTTTCTATCGG 57.941 39.130 0.00 0.00 0.00 4.18
2919 3449 4.522789 AGTTGTTGCCATTTTTCTATCGGT 59.477 37.500 0.00 0.00 0.00 4.69
2920 3450 5.010617 AGTTGTTGCCATTTTTCTATCGGTT 59.989 36.000 0.00 0.00 0.00 4.44
2945 3541 8.668510 TCTATCAGTTGCCTATTCTGATTTTC 57.331 34.615 11.22 0.00 43.53 2.29
3066 3663 3.887621 TGGTCTCTATAAAACTGCGCT 57.112 42.857 9.73 0.00 0.00 5.92
3067 3664 3.521560 TGGTCTCTATAAAACTGCGCTG 58.478 45.455 13.23 13.23 0.00 5.18
3068 3665 3.194755 TGGTCTCTATAAAACTGCGCTGA 59.805 43.478 21.92 0.00 0.00 4.26
3187 3786 3.712016 TTGACAAGGTAAGCAGGCATA 57.288 42.857 0.00 0.00 0.00 3.14
3191 3790 4.640201 TGACAAGGTAAGCAGGCATATTTC 59.360 41.667 0.00 0.00 0.00 2.17
3193 3792 4.641989 ACAAGGTAAGCAGGCATATTTCTG 59.358 41.667 0.00 0.00 0.00 3.02
3230 3829 5.648092 ACTTTCTCCAGAAATGGTTATTCCG 59.352 40.000 2.21 0.00 42.44 4.30
3235 3834 5.806818 TCCAGAAATGGTTATTCCGTAACA 58.193 37.500 0.00 0.00 43.65 2.41
3404 4006 2.936202 TCTGAGCTGTTTCCTTTGCTT 58.064 42.857 0.00 0.00 35.76 3.91
3454 4088 7.961326 AGCATTAAATAAATCACCCTGTCTT 57.039 32.000 0.00 0.00 0.00 3.01
3465 4099 0.739813 CCCTGTCTTAGTTTCCGGCG 60.740 60.000 0.00 0.00 0.00 6.46
3557 4191 1.211709 CGCCCCGTGACATTTTTCC 59.788 57.895 0.00 0.00 0.00 3.13
3608 4242 2.240667 ACCAAATCCAGATGACCCTCTG 59.759 50.000 0.00 0.00 41.93 3.35
3635 4269 4.935352 AAACATTGCTAAGCACTGGAAA 57.065 36.364 0.00 0.00 42.25 3.13
3641 4275 2.819608 TGCTAAGCACTGGAAATCCAAC 59.180 45.455 3.35 0.00 38.61 3.77
3689 4323 3.132111 ACAAGTGTGAAAATGTTGTCCCC 59.868 43.478 0.00 0.00 0.00 4.81
3775 4409 1.079197 TCTGTATGCCAGTGGTGCG 60.079 57.895 11.74 0.00 42.19 5.34
3786 4420 4.572571 TGGTGCGTGACAACCCCC 62.573 66.667 2.38 0.00 33.78 5.40
3787 4421 4.572571 GGTGCGTGACAACCCCCA 62.573 66.667 0.00 0.00 0.00 4.96
3788 4422 3.284449 GTGCGTGACAACCCCCAC 61.284 66.667 0.00 0.00 0.00 4.61
4042 4677 3.099267 AGGAGAAGTCAACAAGTGTCG 57.901 47.619 0.00 0.00 0.00 4.35
4467 5102 0.881159 TGTTACTCAAACGTGGCCGG 60.881 55.000 0.00 0.00 41.30 6.13
4474 5109 0.881159 CAAACGTGGCCGGTCAGTTA 60.881 55.000 10.28 0.00 38.78 2.24
4516 5174 5.453762 CCTTCCTCTTTGAATTGTTTGCCTT 60.454 40.000 0.00 0.00 0.00 4.35
4539 5197 3.199764 GCTCAAACGCAGCCAAATT 57.800 47.368 0.00 0.00 0.00 1.82
4544 5202 0.943835 AAACGCAGCCAAATTTCCGC 60.944 50.000 0.00 0.00 0.00 5.54
4569 5227 4.261801 GTTTAGCTGGACCAATCTTGCTA 58.738 43.478 8.02 8.02 35.83 3.49
4570 5228 2.409948 AGCTGGACCAATCTTGCTAC 57.590 50.000 3.44 0.00 33.71 3.58
4685 5346 2.282674 TCGTGCTACGGGGACAGT 60.283 61.111 8.46 0.00 42.81 3.55
4750 5411 2.725203 TTTCCACCCACGAGAAGGCG 62.725 60.000 0.00 0.00 37.29 5.52
4765 5426 3.127533 GCGGATGTGCCCTGTCAC 61.128 66.667 0.00 0.00 37.48 3.67
4770 5431 2.421314 TGTGCCCTGTCACAGACG 59.579 61.111 6.30 0.00 41.57 4.18
4771 5432 2.357517 GTGCCCTGTCACAGACGG 60.358 66.667 6.30 0.28 38.54 4.79
4772 5433 4.314440 TGCCCTGTCACAGACGGC 62.314 66.667 16.16 16.16 38.77 5.68
4773 5434 4.008933 GCCCTGTCACAGACGGCT 62.009 66.667 15.83 0.00 36.57 5.52
4774 5435 2.743718 CCCTGTCACAGACGGCTT 59.256 61.111 6.30 0.00 37.59 4.35
4775 5436 1.374758 CCCTGTCACAGACGGCTTC 60.375 63.158 6.30 0.00 37.59 3.86
4776 5437 1.367471 CCTGTCACAGACGGCTTCA 59.633 57.895 6.30 0.00 37.59 3.02
4777 5438 0.036952 CCTGTCACAGACGGCTTCAT 60.037 55.000 6.30 0.00 37.59 2.57
4778 5439 1.609061 CCTGTCACAGACGGCTTCATT 60.609 52.381 6.30 0.00 37.59 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.548057 GCCAACTTGAACGAAGACATGA 59.452 45.455 0.00 0.00 35.42 3.07
5 6 2.031258 TGCCAACTTGAACGAAGACA 57.969 45.000 0.00 0.00 35.42 3.41
47 48 7.598493 TCAGAAAAGAGTGACAAAAACAAAAGG 59.402 33.333 0.00 0.00 0.00 3.11
59 60 5.107065 CCCGTAATTGTCAGAAAAGAGTGAC 60.107 44.000 0.00 0.00 42.93 3.67
99 102 6.851222 AATTTACGGTCAGCATTAGAGATG 57.149 37.500 0.00 0.00 0.00 2.90
138 141 3.624861 CGGATTGATTCCTCTTTCAGTGG 59.375 47.826 0.00 0.00 42.99 4.00
142 145 3.348647 TGCGGATTGATTCCTCTTTCA 57.651 42.857 0.00 0.00 42.99 2.69
145 148 4.273480 CGTATTTGCGGATTGATTCCTCTT 59.727 41.667 0.00 0.00 42.99 2.85
160 163 1.065551 GGCTTCCACATCCGTATTTGC 59.934 52.381 0.00 0.00 0.00 3.68
172 175 3.936772 TTGGATGGCCGGCTTCCAC 62.937 63.158 35.94 19.30 39.21 4.02
178 181 2.110213 TATCGTTGGATGGCCGGC 59.890 61.111 21.18 21.18 36.79 6.13
233 237 9.448438 TTGAACTATATATGCGGCTATTTGAAT 57.552 29.630 0.00 0.00 0.00 2.57
257 262 8.005662 TGCATTTGAACATTCGAACTATTTTG 57.994 30.769 0.00 0.00 33.63 2.44
267 272 1.261989 CCGCTGCATTTGAACATTCG 58.738 50.000 0.00 0.00 0.00 3.34
321 326 1.748122 CAGCCTTGGCCAGTGCTAG 60.748 63.158 25.35 17.38 37.74 3.42
377 382 3.235481 TCCCGACCCGAAGCACAA 61.235 61.111 0.00 0.00 0.00 3.33
485 490 1.112315 AAAAAGGTCGTGCCATGCCA 61.112 50.000 0.00 0.00 40.61 4.92
513 518 6.237358 CGTTTTGGGACGTTAAAACAGAAAAG 60.237 38.462 23.80 11.53 43.44 2.27
528 533 4.571176 TGCCAATTTTTAACGTTTTGGGAC 59.429 37.500 23.39 12.51 37.81 4.46
563 1007 0.746659 GCCCATGTGTTATTCAGCCC 59.253 55.000 0.00 0.00 0.00 5.19
573 1017 2.601367 GCTGGTTGGCCCATGTGT 60.601 61.111 0.00 0.00 44.15 3.72
575 1019 2.601367 GTGCTGGTTGGCCCATGT 60.601 61.111 0.00 0.00 44.15 3.21
605 1049 0.178068 TGAGCTAAATGGACCGCCTC 59.822 55.000 0.00 0.00 34.31 4.70
607 1051 0.947244 CATGAGCTAAATGGACCGCC 59.053 55.000 0.00 0.00 0.00 6.13
610 1054 2.609459 CGACACATGAGCTAAATGGACC 59.391 50.000 12.27 0.00 0.00 4.46
612 1056 3.261580 CACGACACATGAGCTAAATGGA 58.738 45.455 12.27 0.00 0.00 3.41
615 1059 2.009774 GGCACGACACATGAGCTAAAT 58.990 47.619 0.00 0.00 0.00 1.40
621 1098 1.742880 CCCAGGCACGACACATGAG 60.743 63.158 0.00 0.00 0.00 2.90
665 1145 1.066114 GCCTCGTCTCGTGTTTCTCG 61.066 60.000 0.00 0.00 0.00 4.04
666 1146 0.733223 GGCCTCGTCTCGTGTTTCTC 60.733 60.000 0.00 0.00 0.00 2.87
677 1157 3.112709 GCACGTTGAGGCCTCGTC 61.113 66.667 27.43 20.30 35.62 4.20
678 1158 4.681978 GGCACGTTGAGGCCTCGT 62.682 66.667 27.43 19.65 46.74 4.18
711 1191 1.473677 GGCCAACCCACCGTAAAATAC 59.526 52.381 0.00 0.00 0.00 1.89
713 1193 1.245376 CGGCCAACCCACCGTAAAAT 61.245 55.000 2.24 0.00 44.46 1.82
744 1224 1.915769 GGTGAGTCAGACCTGGCCT 60.916 63.158 3.32 0.00 35.39 5.19
1101 1593 4.426736 AAGTTAGACACGGGAAAAAGGA 57.573 40.909 0.00 0.00 0.00 3.36
1102 1594 5.509716 AAAAGTTAGACACGGGAAAAAGG 57.490 39.130 0.00 0.00 0.00 3.11
1103 1595 5.746721 CCAAAAAGTTAGACACGGGAAAAAG 59.253 40.000 0.00 0.00 0.00 2.27
1104 1596 5.394333 CCCAAAAAGTTAGACACGGGAAAAA 60.394 40.000 0.00 0.00 34.10 1.94
1228 1720 0.318614 AAACCCAGAAATGCAACGCG 60.319 50.000 3.53 3.53 0.00 6.01
1230 1722 2.791383 TCAAACCCAGAAATGCAACG 57.209 45.000 0.00 0.00 0.00 4.10
1419 1926 3.440173 CGGACGTACTAGTACCTTCCAAA 59.560 47.826 30.26 1.60 35.78 3.28
1431 1938 7.984391 TCTTATATTTGTGAACGGACGTACTA 58.016 34.615 0.00 0.00 0.00 1.82
1432 1939 6.855836 TCTTATATTTGTGAACGGACGTACT 58.144 36.000 0.00 0.00 0.00 2.73
1433 1940 7.221452 ACATCTTATATTTGTGAACGGACGTAC 59.779 37.037 0.00 0.00 0.00 3.67
1495 2003 6.085555 TGAGTAAACAAACACACCAAAACA 57.914 33.333 0.00 0.00 0.00 2.83
1501 2009 5.123344 ACTGAACTGAGTAAACAAACACACC 59.877 40.000 0.00 0.00 0.00 4.16
1513 2021 5.494724 AGTACATACGGACTGAACTGAGTA 58.505 41.667 0.00 0.00 0.00 2.59
1519 2027 3.125829 TGTCGAGTACATACGGACTGAAC 59.874 47.826 13.68 0.00 36.32 3.18
1638 2147 6.933521 TCCATAATTCCAACACAACCATTTTG 59.066 34.615 0.00 0.00 0.00 2.44
1680 2189 4.074259 CCACATCACCAGACTGATCAAAA 58.926 43.478 3.32 0.00 0.00 2.44
1717 2226 4.870021 ACTGCCCTGAAGAGGAATAAAT 57.130 40.909 0.00 0.00 42.93 1.40
1732 2241 4.641989 ACTCATCAAACATGATAACTGCCC 59.358 41.667 0.00 0.00 0.00 5.36
1915 2433 0.808755 GGTGGCTCAAATAACACCGG 59.191 55.000 0.00 0.00 43.28 5.28
1926 2444 1.417517 CTATGGCATACAGGTGGCTCA 59.582 52.381 2.32 0.00 44.29 4.26
2079 2599 9.929180 ATATCGTGCAGAAGATAAGCTATTAAA 57.071 29.630 9.59 0.00 33.64 1.52
2119 2639 8.629158 TGCTAACACTTCAACATAAAACATTCT 58.371 29.630 0.00 0.00 0.00 2.40
2182 2702 3.204158 TGCCCAATAGATAAGCAAAGGGA 59.796 43.478 0.00 0.00 37.22 4.20
2274 2794 9.911788 AACATTAACCAAATCTCATCTACAGAT 57.088 29.630 0.00 0.00 34.56 2.90
2275 2795 9.739276 AAACATTAACCAAATCTCATCTACAGA 57.261 29.630 0.00 0.00 0.00 3.41
2310 2830 3.679824 AAAGTGTACAGGGACAGTAGC 57.320 47.619 0.00 0.00 32.55 3.58
2345 2865 7.009440 CACACTGTACAATTCTGAATACAACG 58.991 38.462 2.85 1.99 0.00 4.10
2447 2967 3.010584 AGTTGACCAGCCCTTGAACATAT 59.989 43.478 0.00 0.00 0.00 1.78
2469 2989 3.625764 GCCACCGAAGTAATCTAAATGCA 59.374 43.478 0.00 0.00 0.00 3.96
2652 3172 7.454260 AAAATTGTCTAGACAGGGAAATGAC 57.546 36.000 23.97 0.00 42.94 3.06
2726 3247 2.930455 GCATTTAGGCCGCACATGTTTT 60.930 45.455 0.00 0.00 0.00 2.43
2771 3292 4.639135 GCTTTCTGCTAACCCAATTAGG 57.361 45.455 0.00 0.00 40.74 2.69
2875 3398 6.639632 ACTAGAAGTACGTTTAGAACCACA 57.360 37.500 12.28 0.00 0.00 4.17
2911 3441 4.585955 GGCAACTGATAGAACCGATAGA 57.414 45.455 0.00 0.00 39.76 1.98
3039 3636 6.148811 CGCAGTTTTATAGAGACCAAAGGAAA 59.851 38.462 0.00 0.00 0.00 3.13
3100 3699 7.721402 ACCAACAAGCAAAGTATAAATGTTCA 58.279 30.769 0.00 0.00 0.00 3.18
3187 3786 8.396272 AGAAAGTAACATAACACTGCAGAAAT 57.604 30.769 23.35 7.92 0.00 2.17
3191 3790 5.700832 TGGAGAAAGTAACATAACACTGCAG 59.299 40.000 13.48 13.48 0.00 4.41
3193 3792 5.932303 TCTGGAGAAAGTAACATAACACTGC 59.068 40.000 0.00 0.00 0.00 4.40
3230 3829 7.174426 ACCAAGCTACAAAGGTAAATCTGTTAC 59.826 37.037 0.00 0.00 31.75 2.50
3235 3834 6.214819 TCCTACCAAGCTACAAAGGTAAATCT 59.785 38.462 0.00 0.00 36.28 2.40
3404 4006 7.616313 ACAAACAGGTTATTTTGGAGAAACAA 58.384 30.769 0.00 0.00 37.08 2.83
3454 4088 3.806625 ATACTTTAGCGCCGGAAACTA 57.193 42.857 5.05 0.00 0.00 2.24
3544 4178 3.242936 ACTGAAACCGGAAAAATGTCACG 60.243 43.478 9.46 0.00 0.00 4.35
3557 4191 1.066143 AGTGCCTGGATACTGAAACCG 60.066 52.381 0.00 0.00 37.83 4.44
3608 4242 5.113502 AGTGCTTAGCAATGTTTTCAGAC 57.886 39.130 9.05 0.00 41.47 3.51
3635 4269 0.392193 CAGCTTCTGCCTCGTTGGAT 60.392 55.000 1.63 0.00 40.80 3.41
3641 4275 1.069636 GTTTCAACAGCTTCTGCCTCG 60.070 52.381 0.00 0.00 40.80 4.63
3786 4420 1.290203 ATTACATCAAGAGCGGCGTG 58.710 50.000 9.37 0.00 0.00 5.34
3787 4421 2.864343 GTTATTACATCAAGAGCGGCGT 59.136 45.455 9.37 0.00 0.00 5.68
3788 4422 2.221055 GGTTATTACATCAAGAGCGGCG 59.779 50.000 0.51 0.51 0.00 6.46
4042 4677 4.151157 GCCAGCTTCAATTTCAACAATGTC 59.849 41.667 0.00 0.00 0.00 3.06
4474 5109 1.077993 AGGAGGTTAGACAGGCAGACT 59.922 52.381 0.00 0.00 0.00 3.24
4516 5174 3.345808 GCTGCGTTTGAGCCGTCA 61.346 61.111 0.00 0.00 36.02 4.35
4529 5187 4.173971 CAGCGGAAATTTGGCTGC 57.826 55.556 21.25 13.24 46.39 5.25
4544 5202 3.356529 AGATTGGTCCAGCTAAACCAG 57.643 47.619 16.48 0.00 45.84 4.00
4554 5212 2.875672 GCAGTGTAGCAAGATTGGTCCA 60.876 50.000 0.00 0.00 39.88 4.02
4569 5227 1.674057 GCTCCTGTAGTGGCAGTGT 59.326 57.895 4.76 0.00 34.84 3.55
4570 5228 1.078848 GGCTCCTGTAGTGGCAGTG 60.079 63.158 4.76 0.00 34.84 3.66
4679 5340 1.003866 GTTGCAACTTGTCGACTGTCC 60.004 52.381 22.36 10.45 0.00 4.02
4685 5346 2.490115 AGGTTTTGTTGCAACTTGTCGA 59.510 40.909 28.61 6.03 0.00 4.20
4721 5382 5.045869 TCTCGTGGGTGGAAATATTTCTTCT 60.046 40.000 23.85 0.00 37.35 2.85
4730 5391 0.322546 GCCTTCTCGTGGGTGGAAAT 60.323 55.000 0.00 0.00 0.00 2.17
4750 5411 0.674895 GTCTGTGACAGGGCACATCC 60.675 60.000 13.33 0.00 46.64 3.51
4758 5419 0.036952 ATGAAGCCGTCTGTGACAGG 60.037 55.000 13.33 0.00 32.09 4.00
4759 5420 1.800805 AATGAAGCCGTCTGTGACAG 58.199 50.000 6.18 6.18 32.09 3.51


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

AutoCloner maintained by Alex Coulton.