Multiple sequence alignment - TraesCS3D01G476900

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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 TraesCS3D01G476900 chr3D 100.000 3578 0 0 1 3578 577285295 577281718 0.000000e+00 6608
1 TraesCS3D01G476900 chr3A 94.836 2614 90 23 1 2598 712576798 712574214 0.000000e+00 4037
2 TraesCS3D01G476900 chr3A 81.721 1592 248 27 983 2551 712655133 712653562 0.000000e+00 1288
3 TraesCS3D01G476900 chr3A 86.517 979 101 13 2596 3568 712574187 712573234 0.000000e+00 1048
4 TraesCS3D01G476900 chr3B 94.761 2176 97 7 435 2598 769192963 769190793 0.000000e+00 3371
5 TraesCS3D01G476900 chr3B 94.396 2177 104 7 435 2598 769156065 769158236 0.000000e+00 3328
6 TraesCS3D01G476900 chr3B 88.766 1994 181 12 637 2598 769704211 769702229 0.000000e+00 2401
7 TraesCS3D01G476900 chr3B 93.757 897 50 4 1702 2598 769309615 769308725 0.000000e+00 1341
8 TraesCS3D01G476900 chr3B 92.865 897 59 3 1702 2598 770357913 770357022 0.000000e+00 1297
9 TraesCS3D01G476900 chr3B 79.813 1605 304 20 964 2554 770404243 770402645 0.000000e+00 1151
10 TraesCS3D01G476900 chr3B 79.757 1566 299 18 1001 2554 769267897 769266338 0.000000e+00 1120
11 TraesCS3D01G476900 chr3B 78.897 1578 316 17 983 2552 770208691 770207123 0.000000e+00 1053
12 TraesCS3D01G476900 chr3B 78.797 1580 313 21 983 2552 769906920 769905353 0.000000e+00 1042
13 TraesCS3D01G476900 chr3B 78.423 1585 324 14 983 2554 770313088 770311509 0.000000e+00 1016
14 TraesCS3D01G476900 chr3B 80.452 1105 196 18 990 2082 770097544 770096448 0.000000e+00 826
15 TraesCS3D01G476900 chr3B 86.047 774 99 9 2808 3578 769308283 769307516 0.000000e+00 822
16 TraesCS3D01G476900 chr3B 85.935 775 96 12 2808 3578 770356580 770355815 0.000000e+00 815
17 TraesCS3D01G476900 chr3B 83.949 785 94 17 2596 3370 769190766 769190004 0.000000e+00 723
18 TraesCS3D01G476900 chr3B 83.150 819 106 17 2596 3404 769158263 769159059 0.000000e+00 719
19 TraesCS3D01G476900 chr3B 93.780 209 12 1 2603 2810 769308693 769308485 2.680000e-81 313
20 TraesCS3D01G476900 chr3B 92.823 209 14 1 2603 2810 770356990 770356782 5.810000e-78 302
21 TraesCS3D01G476900 chrUn 95.171 2071 94 4 529 2598 344085120 344087185 0.000000e+00 3265
22 TraesCS3D01G476900 chrUn 93.620 627 25 6 435 1047 319853915 319853290 0.000000e+00 922
23 TraesCS3D01G476900 chrUn 93.471 628 25 6 435 1047 319833589 319832963 0.000000e+00 918
24 TraesCS3D01G476900 chrUn 82.927 820 103 20 2596 3404 333458157 333457364 0.000000e+00 704
25 TraesCS3D01G476900 chrUn 93.386 378 21 2 2221 2598 333458557 333458184 1.120000e-154 556
26 TraesCS3D01G476900 chrUn 84.534 472 63 6 2986 3455 471832785 471833248 3.260000e-125 459
27 TraesCS3D01G476900 chrUn 83.054 478 70 7 2985 3455 15625056 15625529 1.190000e-114 424
28 TraesCS3D01G476900 chrUn 91.803 244 18 2 2596 2837 344087212 344087455 4.420000e-89 339
29 TraesCS3D01G476900 chr4A 83.258 442 57 8 2884 3319 658380831 658381261 1.200000e-104 390
30 TraesCS3D01G476900 chr5D 85.593 354 37 8 2966 3319 27280252 27280591 3.400000e-95 359
31 TraesCS3D01G476900 chr5D 80.693 404 59 8 43 431 6501724 6502123 2.700000e-76 296
32 TraesCS3D01G476900 chr6D 84.511 368 49 7 67 431 395697760 395697398 1.220000e-94 357
33 TraesCS3D01G476900 chr6D 82.258 434 50 11 2649 3072 137153533 137153117 2.040000e-92 350
34 TraesCS3D01G476900 chr7D 83.290 389 50 10 45 431 424709759 424710134 9.510000e-91 344
35 TraesCS3D01G476900 chr7D 79.602 402 64 12 44 432 601458814 601458418 4.550000e-69 272
36 TraesCS3D01G476900 chr4D 84.900 351 42 5 2969 3319 85853307 85852968 9.510000e-91 344
37 TraesCS3D01G476900 chr4D 81.864 397 52 10 43 430 47892888 47892503 2.070000e-82 316
38 TraesCS3D01G476900 chr4D 82.927 328 43 7 115 435 2987151 2987472 2.100000e-72 283
39 TraesCS3D01G476900 chr1A 84.641 306 42 5 125 428 297701665 297701967 2.090000e-77 300
40 TraesCS3D01G476900 chr2D 80.929 409 50 15 42 431 334080733 334080334 7.510000e-77 298
41 TraesCS3D01G476900 chr6A 80.285 421 55 15 2650 3059 163169035 163168632 3.490000e-75 292
42 TraesCS3D01G476900 chr7A 85.837 233 24 5 2663 2892 576793827 576793601 4.620000e-59 239
43 TraesCS3D01G476900 chr7A 85.408 233 25 5 2663 2892 658271209 658271435 2.150000e-57 233
44 TraesCS3D01G476900 chr7A 78.250 400 56 15 43 431 14162872 14163251 9.990000e-56 228


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 TraesCS3D01G476900 chr3D 577281718 577285295 3577 True 6608.000000 6608 100.000000 1 3578 1 chr3D.!!$R1 3577
1 TraesCS3D01G476900 chr3A 712573234 712576798 3564 True 2542.500000 4037 90.676500 1 3568 2 chr3A.!!$R2 3567
2 TraesCS3D01G476900 chr3A 712653562 712655133 1571 True 1288.000000 1288 81.721000 983 2551 1 chr3A.!!$R1 1568
3 TraesCS3D01G476900 chr3B 769702229 769704211 1982 True 2401.000000 2401 88.766000 637 2598 1 chr3B.!!$R2 1961
4 TraesCS3D01G476900 chr3B 769190004 769192963 2959 True 2047.000000 3371 89.355000 435 3370 2 chr3B.!!$R8 2935
5 TraesCS3D01G476900 chr3B 769156065 769159059 2994 False 2023.500000 3328 88.773000 435 3404 2 chr3B.!!$F1 2969
6 TraesCS3D01G476900 chr3B 770402645 770404243 1598 True 1151.000000 1151 79.813000 964 2554 1 chr3B.!!$R7 1590
7 TraesCS3D01G476900 chr3B 769266338 769267897 1559 True 1120.000000 1120 79.757000 1001 2554 1 chr3B.!!$R1 1553
8 TraesCS3D01G476900 chr3B 770207123 770208691 1568 True 1053.000000 1053 78.897000 983 2552 1 chr3B.!!$R5 1569
9 TraesCS3D01G476900 chr3B 769905353 769906920 1567 True 1042.000000 1042 78.797000 983 2552 1 chr3B.!!$R3 1569
10 TraesCS3D01G476900 chr3B 770311509 770313088 1579 True 1016.000000 1016 78.423000 983 2554 1 chr3B.!!$R6 1571
11 TraesCS3D01G476900 chr3B 770096448 770097544 1096 True 826.000000 826 80.452000 990 2082 1 chr3B.!!$R4 1092
12 TraesCS3D01G476900 chr3B 769307516 769309615 2099 True 825.333333 1341 91.194667 1702 3578 3 chr3B.!!$R9 1876
13 TraesCS3D01G476900 chr3B 770355815 770357913 2098 True 804.666667 1297 90.541000 1702 3578 3 chr3B.!!$R10 1876
14 TraesCS3D01G476900 chrUn 344085120 344087455 2335 False 1802.000000 3265 93.487000 529 2837 2 chrUn.!!$F3 2308
15 TraesCS3D01G476900 chrUn 319853290 319853915 625 True 922.000000 922 93.620000 435 1047 1 chrUn.!!$R2 612
16 TraesCS3D01G476900 chrUn 319832963 319833589 626 True 918.000000 918 93.471000 435 1047 1 chrUn.!!$R1 612
17 TraesCS3D01G476900 chrUn 333457364 333458557 1193 True 630.000000 704 88.156500 2221 3404 2 chrUn.!!$R3 1183

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
60 62 0.534877 TGAGTGCAGCATTTCGGTGT 60.535 50.000 0.00 0.0 45.25 4.16 F
80 82 0.663688 CGAGACTCATCTACACCCGG 59.336 60.000 2.82 0.0 34.34 5.73 F
428 431 1.839994 CCTGGGCTCAGAAGTGGATTA 59.160 52.381 17.43 0.0 43.49 1.75 F
1972 2043 1.404035 ACAACGCCAGAGGAAACAAAC 59.596 47.619 0.00 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1471 0.457853 TCTCAAATCTTCGGACGGCG 60.458 55.0 4.8 4.8 0.0 6.46 R
1842 1897 1.068474 GGATGTCGTTCAAGTGTCCG 58.932 55.0 0.0 0.0 0.0 4.79 R
2136 2215 0.617413 CCAAGGAGTCATGAGGCAGT 59.383 55.0 0.0 0.0 0.0 4.40 R
2853 3171 0.249868 CAGACAGTGAGGGTGCGAAA 60.250 55.0 0.0 0.0 0.0 3.46 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
60 62 0.534877 TGAGTGCAGCATTTCGGTGT 60.535 50.000 0.00 0.00 45.25 4.16
64 66 1.291184 TGCAGCATTTCGGTGTCGAG 61.291 55.000 0.00 0.00 46.75 4.04
65 67 1.014044 GCAGCATTTCGGTGTCGAGA 61.014 55.000 0.00 0.00 46.75 4.04
80 82 0.663688 CGAGACTCATCTACACCCGG 59.336 60.000 2.82 0.00 34.34 5.73
90 92 3.396260 TCTACACCCGGTCAGAAAAAG 57.604 47.619 0.00 0.00 0.00 2.27
92 94 2.951229 ACACCCGGTCAGAAAAAGAT 57.049 45.000 0.00 0.00 0.00 2.40
93 95 3.223674 ACACCCGGTCAGAAAAAGATT 57.776 42.857 0.00 0.00 0.00 2.40
101 103 6.640907 CCCGGTCAGAAAAAGATTACAAAAAG 59.359 38.462 0.00 0.00 0.00 2.27
104 106 9.296400 CGGTCAGAAAAAGATTACAAAAAGAAA 57.704 29.630 0.00 0.00 0.00 2.52
146 148 8.479280 GTTATGCATGGTAGAAAATTTATTGCG 58.521 33.333 10.16 0.00 0.00 4.85
166 168 2.608268 GTGAGGTCCGCTCTACTTTTC 58.392 52.381 0.00 0.00 0.00 2.29
185 187 7.600065 ACTTTTCAGATCATTTGAACATCTGG 58.400 34.615 8.02 0.00 42.61 3.86
192 194 4.517285 TCATTTGAACATCTGGGTAGCTC 58.483 43.478 0.00 0.00 0.00 4.09
232 234 8.773645 CAAATCGGATCAGTATAGTGCATAAAA 58.226 33.333 2.40 0.00 0.00 1.52
240 242 9.838339 ATCAGTATAGTGCATAAAAAGTAAGCT 57.162 29.630 2.40 0.00 0.00 3.74
263 265 5.441709 TTTTTACAGACCCCGAATTTGTC 57.558 39.130 0.00 0.00 0.00 3.18
317 319 7.531534 CCAAATGATTTGAAAATTGAAGCGAAC 59.468 33.333 18.82 0.00 43.26 3.95
428 431 1.839994 CCTGGGCTCAGAAGTGGATTA 59.160 52.381 17.43 0.00 43.49 1.75
431 434 3.114606 TGGGCTCAGAAGTGGATTATCA 58.885 45.455 0.00 0.00 0.00 2.15
817 846 6.447162 ACGGAATGAAACAAAATTCTTCTCC 58.553 36.000 0.00 0.00 34.01 3.71
843 872 7.124750 CCTCCTTTCCAATAGAAAATCACCAAT 59.875 37.037 0.00 0.00 43.84 3.16
885 914 4.154015 CGCTAATTTGATTCACCACAGACA 59.846 41.667 0.00 0.00 0.00 3.41
886 915 5.163723 CGCTAATTTGATTCACCACAGACAT 60.164 40.000 0.00 0.00 0.00 3.06
978 1031 7.216973 ACGTACTCTTCTCTCACTAATTTGT 57.783 36.000 0.00 0.00 0.00 2.83
1032 1087 2.618241 TGTCAAGTCTGTCATTGTTGGC 59.382 45.455 0.00 0.00 0.00 4.52
1506 1561 2.106683 GCCGCGACAGCACCTATTT 61.107 57.895 8.23 0.00 45.49 1.40
1972 2043 1.404035 ACAACGCCAGAGGAAACAAAC 59.596 47.619 0.00 0.00 0.00 2.93
2035 2106 5.000591 TGTTTTTCTGGCGTCATATCTCAA 58.999 37.500 0.00 0.00 0.00 3.02
2053 2132 4.272748 TCTCAATATCGGAGTACAGTGACG 59.727 45.833 0.00 0.00 34.04 4.35
2136 2215 8.469200 CCATCTTTGAAGCTTGGAATTATGTTA 58.531 33.333 2.10 0.00 33.46 2.41
2164 2243 1.996187 GACTCCTTGGAGGACCCCC 60.996 68.421 19.51 0.00 40.06 5.40
2362 2441 2.739932 GCACATCTATGCGTGGAGAAGT 60.740 50.000 0.00 0.00 35.50 3.01
2400 2479 1.011019 CGAGGTACGCAGAGCTACG 60.011 63.158 2.04 2.04 34.51 3.51
2556 2638 1.800681 GTTTACCACATGGCTCGGC 59.199 57.895 0.00 0.00 39.32 5.54
2557 2639 1.743623 TTTACCACATGGCTCGGCG 60.744 57.895 0.00 0.00 39.32 6.46
2558 2640 3.673956 TTACCACATGGCTCGGCGG 62.674 63.158 7.21 0.00 39.32 6.13
2589 2671 8.856153 TTGGACTAAACTAGTGATAAATGCAA 57.144 30.769 0.00 0.37 39.59 4.08
2656 2767 9.705290 AAATATGTGGAAACTTTTGATACAACC 57.295 29.630 0.00 0.00 0.00 3.77
2671 2782 3.478857 ACAACCGTTACAGTGATTGGA 57.521 42.857 0.00 0.00 0.00 3.53
2798 2910 5.358922 CATTACAAAATTATGGTGGGGCTG 58.641 41.667 0.00 0.00 0.00 4.85
2853 3171 3.521126 AGTCAAGGCAGATACATGTCCTT 59.479 43.478 0.00 5.71 37.25 3.36
2877 3195 2.608988 CCCTCACTGTCTGGCCCT 60.609 66.667 0.00 0.00 0.00 5.19
2894 3212 0.608640 CCTACAGTTCTGGGTCGCTT 59.391 55.000 4.82 0.00 0.00 4.68
2899 3217 2.027625 GTTCTGGGTCGCTTGTCGG 61.028 63.158 0.00 0.00 39.05 4.79
2900 3218 2.504274 TTCTGGGTCGCTTGTCGGT 61.504 57.895 0.00 0.00 39.05 4.69
2908 3227 1.597027 CGCTTGTCGGTTGTTCCCT 60.597 57.895 0.00 0.00 33.78 4.20
2977 3296 2.933287 AGCCACCAATGACCCCGA 60.933 61.111 0.00 0.00 0.00 5.14
3076 3395 4.115199 GCGGCAGAGGGTTCCCAT 62.115 66.667 10.73 0.00 0.00 4.00
3083 3402 2.204291 AGGGTTCCCATGGGCTCA 60.204 61.111 27.41 9.58 34.68 4.26
3114 3433 1.787847 CGATGTGGTCGCAGTTTCC 59.212 57.895 0.00 0.00 44.33 3.13
3116 3435 0.605319 GATGTGGTCGCAGTTTCCCA 60.605 55.000 0.00 0.00 0.00 4.37
3144 3463 3.025176 GTAGATCGAGCGCACGGC 61.025 66.667 26.30 18.19 44.05 5.68
3172 3492 1.773653 GCCATCCAGAGGAAGAGGAAT 59.226 52.381 6.70 0.00 34.34 3.01
3188 3508 0.535335 GAATAGCACCCTGTGTCGGA 59.465 55.000 0.00 0.00 35.75 4.55
3231 3551 4.360405 GGCGGGGAGAAAGGCCAA 62.360 66.667 5.01 0.00 44.91 4.52
3310 3638 3.319198 GGTGGGCGTCCAAGAGGA 61.319 66.667 12.16 0.00 46.04 3.71
3322 3650 0.250295 CAAGAGGAAGTTGACCGCCA 60.250 55.000 0.00 0.00 0.00 5.69
3334 3662 4.431131 CCGCCAAGGCATCCCTGT 62.431 66.667 12.19 0.00 41.90 4.00
3340 3668 1.089920 CAAGGCATCCCTGTTTCTCG 58.910 55.000 0.00 0.00 41.90 4.04
3347 3675 1.629043 TCCCTGTTTCTCGTACAGCT 58.371 50.000 0.00 0.00 41.28 4.24
3390 3719 4.874977 GACGTCCTAGCGGCAGGC 62.875 72.222 3.51 3.37 40.13 4.85
3457 3787 4.695455 CCTTCTCGGTGCTTTTGATTAGAA 59.305 41.667 0.00 0.00 0.00 2.10
3509 3839 8.889717 AGGTAATACAGAACATGGTAAATTTCG 58.110 33.333 0.00 0.00 0.00 3.46
3554 3884 2.027745 TGGATTCAGAACCTCTGTGCTC 60.028 50.000 3.71 0.59 44.58 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 0.167470 CACCGAAATGCTGCACTCAG 59.833 55.000 3.57 0.00 43.16 3.35
60 62 1.664873 CGGGTGTAGATGAGTCTCGA 58.335 55.000 0.00 0.00 35.87 4.04
64 66 1.405821 CTGACCGGGTGTAGATGAGTC 59.594 57.143 3.30 0.00 0.00 3.36
65 67 1.005569 TCTGACCGGGTGTAGATGAGT 59.994 52.381 3.30 0.00 0.00 3.41
107 109 7.814264 ACCATGCATAACAAATTTGGAAAAA 57.186 28.000 21.74 3.98 30.54 1.94
108 110 8.370940 TCTACCATGCATAACAAATTTGGAAAA 58.629 29.630 21.74 5.00 30.54 2.29
109 111 7.901029 TCTACCATGCATAACAAATTTGGAAA 58.099 30.769 21.74 7.40 30.54 3.13
120 122 8.479280 CGCAATAAATTTTCTACCATGCATAAC 58.521 33.333 0.00 0.00 0.00 1.89
146 148 2.029290 TGAAAAGTAGAGCGGACCTCAC 60.029 50.000 0.00 0.00 43.31 3.51
159 161 8.733458 CCAGATGTTCAAATGATCTGAAAAGTA 58.267 33.333 12.04 0.00 43.94 2.24
166 168 5.008415 GCTACCCAGATGTTCAAATGATCTG 59.992 44.000 0.00 0.00 41.85 2.90
247 249 4.584327 AAAAAGACAAATTCGGGGTCTG 57.416 40.909 0.00 0.00 40.80 3.51
276 278 4.851843 TCATTTGGACATCTGATCAGCTT 58.148 39.130 18.36 5.02 0.00 3.74
317 319 5.056480 TGGTAGATAATTTGATGCGTGAGG 58.944 41.667 0.00 0.00 0.00 3.86
395 398 2.124403 CCAGGCTCATCTGCACCC 60.124 66.667 0.00 0.00 33.64 4.61
428 431 8.336235 TGGGAAAATAGGTGAGAATTAAGTGAT 58.664 33.333 0.00 0.00 0.00 3.06
431 434 7.928873 TCTGGGAAAATAGGTGAGAATTAAGT 58.071 34.615 0.00 0.00 0.00 2.24
817 846 5.951747 TGGTGATTTTCTATTGGAAAGGAGG 59.048 40.000 0.00 0.00 43.68 4.30
843 872 3.118992 AGCGACTGAAACATCTATGCTCA 60.119 43.478 0.00 0.00 0.00 4.26
885 914 5.627499 TTATTGCTCAACTTGCTTTCGAT 57.373 34.783 0.00 0.00 0.00 3.59
886 915 5.431420 TTTATTGCTCAACTTGCTTTCGA 57.569 34.783 0.00 0.00 0.00 3.71
978 1031 2.901192 TCTTGTGATTTCGGGTAGGACA 59.099 45.455 0.00 0.00 0.00 4.02
1032 1087 2.218953 TAATCCGGCTAACTGCTTCG 57.781 50.000 0.00 0.00 42.39 3.79
1257 1312 1.186200 AGAGTTGCCTGCATCTACGA 58.814 50.000 2.85 0.00 0.00 3.43
1416 1471 0.457853 TCTCAAATCTTCGGACGGCG 60.458 55.000 4.80 4.80 0.00 6.46
1641 1696 2.665649 TGCGGTCTTCGTACATGAAT 57.334 45.000 0.00 0.00 41.72 2.57
1842 1897 1.068474 GGATGTCGTTCAAGTGTCCG 58.932 55.000 0.00 0.00 0.00 4.79
2035 2106 3.276857 ACACGTCACTGTACTCCGATAT 58.723 45.455 0.00 0.00 0.00 1.63
2053 2132 3.314541 AACTACAGTTGATCCCGACAC 57.685 47.619 0.00 0.00 36.80 3.67
2136 2215 0.617413 CCAAGGAGTCATGAGGCAGT 59.383 55.000 0.00 0.00 0.00 4.40
2164 2243 2.306341 ATCGCAGAACCATCAGACTG 57.694 50.000 0.00 0.00 43.58 3.51
2400 2479 0.960364 TGATGTTCCTTCCTTGCCGC 60.960 55.000 0.00 0.00 0.00 6.53
2556 2638 0.604511 AGTTTAGTCCAAACCGGCCG 60.605 55.000 21.04 21.04 46.55 6.13
2557 2639 2.289882 ACTAGTTTAGTCCAAACCGGCC 60.290 50.000 0.00 0.00 46.55 6.13
2558 2640 2.740447 CACTAGTTTAGTCCAAACCGGC 59.260 50.000 0.00 0.00 46.55 6.13
2559 2641 4.261578 TCACTAGTTTAGTCCAAACCGG 57.738 45.455 0.00 0.00 46.55 5.28
2589 2671 4.669206 TTTGAAACACATGTGAAGCCAT 57.331 36.364 31.94 5.65 0.00 4.40
2656 2767 6.037172 CCCTAAAATCTCCAATCACTGTAACG 59.963 42.308 0.00 0.00 0.00 3.18
2671 2782 1.143073 GATGGACGGCCCCTAAAATCT 59.857 52.381 3.83 0.00 0.00 2.40
2710 2822 8.800332 TGTAACTCCTCGTAACTCTTATTTCTT 58.200 33.333 0.00 0.00 0.00 2.52
2798 2910 4.341235 GGATCTACCCCTTTACAAAATGCC 59.659 45.833 0.00 0.00 0.00 4.40
2853 3171 0.249868 CAGACAGTGAGGGTGCGAAA 60.250 55.000 0.00 0.00 0.00 3.46
2877 3195 1.000506 GACAAGCGACCCAGAACTGTA 59.999 52.381 1.18 0.00 0.00 2.74
2882 3200 2.035237 AACCGACAAGCGACCCAGAA 62.035 55.000 0.00 0.00 44.57 3.02
2894 3212 3.842007 TTTCTAAGGGAACAACCGACA 57.158 42.857 0.00 0.00 40.11 4.35
2899 3217 5.335426 GGAACGGATTTTCTAAGGGAACAAC 60.335 44.000 0.00 0.00 33.13 3.32
2900 3218 4.763279 GGAACGGATTTTCTAAGGGAACAA 59.237 41.667 0.00 0.00 33.13 2.83
2908 3227 5.427481 ACAGATAGGGGAACGGATTTTCTAA 59.573 40.000 0.00 0.00 0.00 2.10
3070 3389 1.691219 GTCCTTGAGCCCATGGGAA 59.309 57.895 36.00 18.76 37.97 3.97
3076 3395 3.691342 CGTCGGTCCTTGAGCCCA 61.691 66.667 0.00 0.00 0.00 5.36
3108 3427 0.396811 CCTCTTGACGGTGGGAAACT 59.603 55.000 0.00 0.00 0.00 2.66
3112 3431 0.406750 TCTACCTCTTGACGGTGGGA 59.593 55.000 0.00 0.00 35.98 4.37
3114 3433 1.065701 CGATCTACCTCTTGACGGTGG 59.934 57.143 0.00 0.00 35.98 4.61
3116 3435 2.290464 CTCGATCTACCTCTTGACGGT 58.710 52.381 0.00 0.00 38.55 4.83
3148 3468 2.676748 CTCTTCCTCTGGATGGCTACT 58.323 52.381 0.00 0.00 0.00 2.57
3155 3475 3.645687 GTGCTATTCCTCTTCCTCTGGAT 59.354 47.826 0.00 0.00 0.00 3.41
3172 3492 1.613317 CCATCCGACACAGGGTGCTA 61.613 60.000 0.00 0.00 41.01 3.49
3310 3638 1.228552 ATGCCTTGGCGGTCAACTT 60.229 52.632 7.18 0.00 34.25 2.66
3322 3650 0.693049 ACGAGAAACAGGGATGCCTT 59.307 50.000 1.40 0.00 0.00 4.35
3334 3662 0.963962 AACCGGAGCTGTACGAGAAA 59.036 50.000 9.46 0.00 0.00 2.52
3358 3686 2.342648 GTCCTTGCCGGAGTCGTT 59.657 61.111 5.05 0.00 44.20 3.85
3359 3687 4.052229 CGTCCTTGCCGGAGTCGT 62.052 66.667 5.05 0.00 44.20 4.34
3361 3689 2.126031 GACGTCCTTGCCGGAGTC 60.126 66.667 5.05 0.00 44.20 3.36
3362 3691 2.776370 TAGGACGTCCTTGCCGGAGT 62.776 60.000 40.23 16.94 46.09 3.85
3457 3787 5.998981 CCGACTCTAATCACTACCTACTGAT 59.001 44.000 0.00 0.00 0.00 2.90
3509 3839 6.194796 TCAACTTGCAAGCCATATTCTAAC 57.805 37.500 26.27 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.