Multiple sequence alignment - TraesCS1A01G143200

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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 TraesCS1A01G143200 chr1A 100.000 3920 0 0 1 3920 246130721 246126802 0.000000e+00 7239.0
1 TraesCS1A01G143200 chr1B 96.504 3061 73 15 272 3321 275552188 275555225 0.000000e+00 5029.0
2 TraesCS1A01G143200 chr1B 96.418 3071 68 14 272 3321 275357231 275360280 0.000000e+00 5024.0
3 TraesCS1A01G143200 chr1B 96.223 3071 74 14 272 3321 275457221 275460270 0.000000e+00 4990.0
4 TraesCS1A01G143200 chr1B 96.545 1968 60 6 1359 3321 275671885 275673849 0.000000e+00 3251.0
5 TraesCS1A01G143200 chr1B 96.970 858 20 4 272 1124 275670444 275671300 0.000000e+00 1435.0
6 TraesCS1A01G143200 chr1B 91.328 542 34 5 3390 3920 275360278 275360817 0.000000e+00 728.0
7 TraesCS1A01G143200 chr1B 91.312 541 34 5 3390 3920 275460268 275460805 0.000000e+00 726.0
8 TraesCS1A01G143200 chr1B 88.419 544 47 6 3390 3920 275673847 275674387 3.300000e-180 641.0
9 TraesCS1A01G143200 chr1B 88.917 397 36 5 3390 3778 275555223 275555619 2.120000e-132 483.0
10 TraesCS1A01G143200 chr1B 97.129 209 6 0 1118 1326 275671864 275671656 1.730000e-93 353.0
11 TraesCS1A01G143200 chr1B 93.048 187 12 1 3734 3920 275555617 275555802 4.990000e-69 272.0
12 TraesCS1A01G143200 chr1B 83.459 266 19 14 31 288 275356965 275357213 1.420000e-54 224.0
13 TraesCS1A01G143200 chr1B 83.083 266 17 15 31 288 275456968 275457213 2.370000e-52 217.0
14 TraesCS1A01G143200 chr1B 90.196 153 4 7 144 288 275552021 275552170 5.170000e-44 189.0
15 TraesCS1A01G143200 chr1B 84.579 214 6 4 31 237 275551731 275551924 1.860000e-43 187.0
16 TraesCS1A01G143200 chr2A 83.176 1587 209 34 1419 2955 610176624 610178202 0.000000e+00 1399.0
17 TraesCS1A01G143200 chr2A 82.116 1588 206 33 1419 2955 607512686 607514246 0.000000e+00 1288.0
18 TraesCS1A01G143200 chr2A 82.156 1048 165 14 1890 2931 138527482 138526451 0.000000e+00 880.0
19 TraesCS1A01G143200 chr2A 81.481 999 111 37 175 1152 610175238 610176183 0.000000e+00 752.0
20 TraesCS1A01G143200 chr2A 81.186 388 49 19 189 569 607511620 607511990 1.380000e-74 291.0
21 TraesCS1A01G143200 chr2B 82.997 1588 211 33 1419 2955 545152384 545153963 0.000000e+00 1382.0
22 TraesCS1A01G143200 chr2B 83.667 949 109 29 218 1152 545151051 545151967 0.000000e+00 852.0
23 TraesCS1A01G143200 chr2B 80.615 846 138 17 218 1056 185763885 185763059 7.150000e-177 630.0
24 TraesCS1A01G143200 chr2B 81.215 708 129 2 349 1056 186402048 186402751 5.680000e-158 568.0
25 TraesCS1A01G143200 chr2D 86.567 737 86 7 2218 2949 462240903 462241631 0.000000e+00 800.0
26 TraesCS1A01G143200 chr2D 82.255 603 67 20 1621 2188 462240187 462240784 5.890000e-133 484.0
27 TraesCS1A01G143200 chr2D 84.507 355 44 10 218 569 462228758 462229104 1.350000e-89 340.0
28 TraesCS1A01G143200 chr2D 83.333 192 18 9 969 1152 462229108 462229293 8.710000e-37 165.0
29 TraesCS1A01G143200 chr7A 88.312 77 4 5 3546 3621 562324663 562324591 1.940000e-13 87.9
30 TraesCS1A01G143200 chr4A 90.000 60 6 0 3272 3331 153254277 153254218 1.170000e-10 78.7
31 TraesCS1A01G143200 chr4D 89.831 59 5 1 3273 3331 320030332 320030389 1.510000e-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 TraesCS1A01G143200 chr1A 246126802 246130721 3919 True 7239.000000 7239 100.000000 1 3920 1 chr1A.!!$R1 3919
1 TraesCS1A01G143200 chr1B 275356965 275360817 3852 False 1992.000000 5024 90.401667 31 3920 3 chr1B.!!$F1 3889
2 TraesCS1A01G143200 chr1B 275456968 275460805 3837 False 1977.666667 4990 90.206000 31 3920 3 chr1B.!!$F2 3889
3 TraesCS1A01G143200 chr1B 275670444 275674387 3943 False 1775.666667 3251 93.978000 272 3920 3 chr1B.!!$F4 3648
4 TraesCS1A01G143200 chr1B 275551731 275555802 4071 False 1232.000000 5029 90.648800 31 3920 5 chr1B.!!$F3 3889
5 TraesCS1A01G143200 chr2A 610175238 610178202 2964 False 1075.500000 1399 82.328500 175 2955 2 chr2A.!!$F2 2780
6 TraesCS1A01G143200 chr2A 138526451 138527482 1031 True 880.000000 880 82.156000 1890 2931 1 chr2A.!!$R1 1041
7 TraesCS1A01G143200 chr2A 607511620 607514246 2626 False 789.500000 1288 81.651000 189 2955 2 chr2A.!!$F1 2766
8 TraesCS1A01G143200 chr2B 545151051 545153963 2912 False 1117.000000 1382 83.332000 218 2955 2 chr2B.!!$F2 2737
9 TraesCS1A01G143200 chr2B 185763059 185763885 826 True 630.000000 630 80.615000 218 1056 1 chr2B.!!$R1 838
10 TraesCS1A01G143200 chr2B 186402048 186402751 703 False 568.000000 568 81.215000 349 1056 1 chr2B.!!$F1 707
11 TraesCS1A01G143200 chr2D 462240187 462241631 1444 False 642.000000 800 84.411000 1621 2949 2 chr2D.!!$F2 1328
12 TraesCS1A01G143200 chr2D 462228758 462229293 535 False 252.500000 340 83.920000 218 1152 2 chr2D.!!$F1 934

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
140 338 0.239879 TTCGACGCAATTTTCTGGGC 59.760 50.000 0.00 0.00 32.71 5.36 F
645 903 1.067250 GAGAGCGTGGATCTGCCTC 59.933 63.158 0.00 1.26 37.63 4.70 F
1668 2753 1.006102 CTCACTTCAGGACGCGGTT 60.006 57.895 12.47 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 2421 0.179111 TCCAACATCCTCGACGCATC 60.179 55.0 0.00 0.00 0.00 3.91 R
2101 3233 0.320160 GGTTGTAGTCCACGGTGTCC 60.320 60.0 7.45 0.00 0.00 4.02 R
3518 4761 0.104855 GCTCACCAGTCAGTGACACA 59.895 55.0 24.73 3.15 41.78 3.72 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
123 321 1.737008 GAACGAGTGGAGCCGGTTC 60.737 63.158 10.28 10.28 0.00 3.62
124 322 3.569049 AACGAGTGGAGCCGGTTCG 62.569 63.158 12.54 10.01 37.31 3.95
125 323 3.744719 CGAGTGGAGCCGGTTCGA 61.745 66.667 12.54 5.42 33.38 3.71
126 324 2.126031 GAGTGGAGCCGGTTCGAC 60.126 66.667 22.89 22.89 0.00 4.20
127 325 3.966026 GAGTGGAGCCGGTTCGACG 62.966 68.421 23.72 0.00 31.92 5.12
131 329 2.813908 GAGCCGGTTCGACGCAAT 60.814 61.111 1.31 0.00 0.00 3.56
132 330 2.358247 AGCCGGTTCGACGCAATT 60.358 55.556 1.90 0.00 0.00 2.32
133 331 1.908066 GAGCCGGTTCGACGCAATTT 61.908 55.000 1.31 0.00 0.00 1.82
134 332 1.081708 GCCGGTTCGACGCAATTTT 60.082 52.632 1.90 0.00 0.00 1.82
135 333 1.063412 GCCGGTTCGACGCAATTTTC 61.063 55.000 1.90 0.00 0.00 2.29
136 334 0.515564 CCGGTTCGACGCAATTTTCT 59.484 50.000 0.00 0.00 0.00 2.52
137 335 1.591248 CGGTTCGACGCAATTTTCTG 58.409 50.000 0.00 0.00 0.00 3.02
138 336 1.724654 CGGTTCGACGCAATTTTCTGG 60.725 52.381 0.00 0.00 0.00 3.86
139 337 1.401018 GGTTCGACGCAATTTTCTGGG 60.401 52.381 0.00 0.00 35.48 4.45
140 338 0.239879 TTCGACGCAATTTTCTGGGC 59.760 50.000 0.00 0.00 32.71 5.36
141 339 1.154035 CGACGCAATTTTCTGGGCC 60.154 57.895 0.00 0.00 32.71 5.80
142 340 1.154035 GACGCAATTTTCTGGGCCG 60.154 57.895 0.00 0.00 32.71 6.13
180 378 3.709653 TGGAATATATAGGCATCCGACCC 59.290 47.826 0.00 0.00 32.72 4.46
266 475 3.201708 AGCCTGGTTAGCAATCTGAATCT 59.798 43.478 0.00 0.00 0.00 2.40
270 479 5.826737 CCTGGTTAGCAATCTGAATCTGAAT 59.173 40.000 0.00 0.00 0.00 2.57
272 481 7.172875 CCTGGTTAGCAATCTGAATCTGAATAG 59.827 40.741 0.00 0.00 0.00 1.73
279 488 9.111613 AGCAATCTGAATCTGAATAGAGAAAAG 57.888 33.333 0.00 0.00 36.14 2.27
301 552 2.203070 GAGATTGATGGCGGGCGT 60.203 61.111 0.00 0.00 0.00 5.68
645 903 1.067250 GAGAGCGTGGATCTGCCTC 59.933 63.158 0.00 1.26 37.63 4.70
686 944 1.145738 ACCTCCCAAGTCAGTTGCATT 59.854 47.619 0.00 0.00 34.45 3.56
709 967 4.096003 GCAGTTGCCCGAGCCCTA 62.096 66.667 0.00 0.00 38.69 3.53
1116 1380 2.298446 CTGTCTTGAGAAGCAGAGGACA 59.702 50.000 0.00 0.00 35.83 4.02
1280 2149 2.182842 GCCAATCAAGCGCCGAGAT 61.183 57.895 2.29 1.77 0.00 2.75
1286 2155 2.124983 AAGCGCCGAGATGCATGT 60.125 55.556 2.46 0.00 0.00 3.21
1328 2389 4.713321 AGGCAAATCAATTAGTGAAGGCAT 59.287 37.500 8.64 0.00 40.50 4.40
1347 2408 3.863142 ATGTCAAGCATGGAGAAAAGC 57.137 42.857 0.00 0.00 36.26 3.51
1348 2409 2.585330 TGTCAAGCATGGAGAAAAGCA 58.415 42.857 0.00 0.00 0.00 3.91
1349 2410 2.957680 TGTCAAGCATGGAGAAAAGCAA 59.042 40.909 0.00 0.00 0.00 3.91
1350 2411 3.384146 TGTCAAGCATGGAGAAAAGCAAA 59.616 39.130 0.00 0.00 0.00 3.68
1351 2412 3.737774 GTCAAGCATGGAGAAAAGCAAAC 59.262 43.478 0.00 0.00 0.00 2.93
1352 2413 3.062042 CAAGCATGGAGAAAAGCAAACC 58.938 45.455 0.00 0.00 0.00 3.27
1353 2414 1.270550 AGCATGGAGAAAAGCAAACCG 59.729 47.619 0.00 0.00 0.00 4.44
1354 2415 1.669795 GCATGGAGAAAAGCAAACCGG 60.670 52.381 0.00 0.00 0.00 5.28
1355 2416 1.885887 CATGGAGAAAAGCAAACCGGA 59.114 47.619 9.46 0.00 0.00 5.14
1356 2417 2.286365 TGGAGAAAAGCAAACCGGAT 57.714 45.000 9.46 0.00 0.00 4.18
1357 2418 2.593026 TGGAGAAAAGCAAACCGGATT 58.407 42.857 9.46 0.00 0.00 3.01
1360 2421 3.366374 GGAGAAAAGCAAACCGGATTCAG 60.366 47.826 9.46 0.00 0.00 3.02
1387 2469 4.321230 CGTCGAGGATGTTGGATATGATGA 60.321 45.833 0.00 0.00 0.00 2.92
1466 2548 3.012518 ACAAGATGCTCGAATTTGAGGG 58.987 45.455 21.78 1.58 36.47 4.30
1517 2602 7.441157 TGCGGAGAATTTAAGGATGTATTACAG 59.559 37.037 2.53 0.00 0.00 2.74
1608 2693 1.415659 CTGAGGTGGGAGCAGGATAAG 59.584 57.143 0.00 0.00 0.00 1.73
1618 2703 1.765314 AGCAGGATAAGAAGGACGCAT 59.235 47.619 0.00 0.00 0.00 4.73
1668 2753 1.006102 CTCACTTCAGGACGCGGTT 60.006 57.895 12.47 0.00 0.00 4.44
1733 2830 3.766591 TCAGACAAAGAGGAGATGGAGAC 59.233 47.826 0.00 0.00 0.00 3.36
1742 2839 1.698506 GAGATGGAGACGGAGGACAT 58.301 55.000 0.00 0.00 0.00 3.06
1940 3072 5.144100 ACACTTGGGATTAATTTGGTGTCA 58.856 37.500 0.00 0.00 32.27 3.58
2035 3167 3.133003 GCACCTTGCAGATCTACTCCTTA 59.867 47.826 0.00 0.00 44.26 2.69
2101 3233 3.365265 GGTCTTGTTGCTGCCCGG 61.365 66.667 0.00 0.00 0.00 5.73
2201 3420 5.808540 TGTACCGTATTCCAAATTTCTCTCG 59.191 40.000 0.00 0.00 0.00 4.04
2518 3742 4.649674 CAGTCCAGGCTACCATCTTAAGTA 59.350 45.833 1.63 0.00 0.00 2.24
2535 3759 2.423577 AGTATCCGTGTTGTTGAAGGC 58.576 47.619 0.00 0.00 0.00 4.35
2998 4228 0.319813 GTCCCTTGCATGTGGTTTGC 60.320 55.000 0.00 0.00 40.55 3.68
3017 4247 4.145876 TGCGAAACTGCAGAACTATTTG 57.854 40.909 23.35 11.36 40.62 2.32
3074 4304 3.194005 TCTGTGTCCACTTCAACTTCC 57.806 47.619 0.00 0.00 0.00 3.46
3248 4481 9.533253 AAATAACAGAAAAACATCTCCAACAAG 57.467 29.630 0.00 0.00 0.00 3.16
3313 4546 8.413229 AGATCCCGTAAACATGGAATAAATTTG 58.587 33.333 0.00 0.00 0.00 2.32
3319 4552 5.760484 AACATGGAATAAATTTGCAGGGT 57.240 34.783 0.00 0.00 0.00 4.34
3320 4553 5.343307 ACATGGAATAAATTTGCAGGGTC 57.657 39.130 0.00 0.00 0.00 4.46
3321 4554 4.162131 ACATGGAATAAATTTGCAGGGTCC 59.838 41.667 0.00 0.00 0.00 4.46
3322 4555 4.059773 TGGAATAAATTTGCAGGGTCCT 57.940 40.909 0.00 0.00 0.00 3.85
3323 4556 4.023291 TGGAATAAATTTGCAGGGTCCTC 58.977 43.478 0.00 0.00 0.00 3.71
3324 4557 4.264352 TGGAATAAATTTGCAGGGTCCTCT 60.264 41.667 0.00 0.00 0.00 3.69
3325 4558 5.044476 TGGAATAAATTTGCAGGGTCCTCTA 60.044 40.000 0.00 0.00 0.00 2.43
3326 4559 5.891551 GGAATAAATTTGCAGGGTCCTCTAA 59.108 40.000 0.00 0.00 0.00 2.10
3327 4560 6.379988 GGAATAAATTTGCAGGGTCCTCTAAA 59.620 38.462 0.00 0.00 0.00 1.85
3328 4561 6.775594 ATAAATTTGCAGGGTCCTCTAAAC 57.224 37.500 0.00 0.00 0.00 2.01
3329 4562 4.388577 AATTTGCAGGGTCCTCTAAACT 57.611 40.909 0.00 0.00 0.00 2.66
3330 4563 3.876309 TTTGCAGGGTCCTCTAAACTT 57.124 42.857 0.00 0.00 0.00 2.66
3331 4564 3.876309 TTGCAGGGTCCTCTAAACTTT 57.124 42.857 0.00 0.00 0.00 2.66
3332 4565 3.876309 TGCAGGGTCCTCTAAACTTTT 57.124 42.857 0.00 0.00 0.00 2.27
3333 4566 3.486383 TGCAGGGTCCTCTAAACTTTTG 58.514 45.455 0.00 0.00 0.00 2.44
3334 4567 2.820197 GCAGGGTCCTCTAAACTTTTGG 59.180 50.000 0.00 0.00 0.00 3.28
3335 4568 3.750922 GCAGGGTCCTCTAAACTTTTGGT 60.751 47.826 0.00 0.00 0.00 3.67
3336 4569 3.821033 CAGGGTCCTCTAAACTTTTGGTG 59.179 47.826 0.00 0.00 0.00 4.17
3337 4570 3.720002 AGGGTCCTCTAAACTTTTGGTGA 59.280 43.478 0.00 0.00 0.00 4.02
3338 4571 3.819337 GGGTCCTCTAAACTTTTGGTGAC 59.181 47.826 0.00 0.00 0.00 3.67
3339 4572 4.457466 GGTCCTCTAAACTTTTGGTGACA 58.543 43.478 10.29 0.00 39.83 3.58
3351 4584 2.623878 TGGTGACAATGTAACCGTGT 57.376 45.000 14.84 0.00 39.89 4.49
3352 4585 2.485903 TGGTGACAATGTAACCGTGTC 58.514 47.619 14.84 0.00 39.89 3.67
3353 4586 1.458064 GGTGACAATGTAACCGTGTCG 59.542 52.381 3.78 0.00 43.73 4.35
3354 4587 2.396601 GTGACAATGTAACCGTGTCGA 58.603 47.619 0.00 0.00 43.73 4.20
3355 4588 2.991190 GTGACAATGTAACCGTGTCGAT 59.009 45.455 0.00 0.00 43.73 3.59
3356 4589 2.990514 TGACAATGTAACCGTGTCGATG 59.009 45.455 0.00 0.00 43.73 3.84
3357 4590 1.730064 ACAATGTAACCGTGTCGATGC 59.270 47.619 0.00 0.00 0.00 3.91
3358 4591 0.996462 AATGTAACCGTGTCGATGCG 59.004 50.000 4.87 4.87 0.00 4.73
3359 4592 1.418342 ATGTAACCGTGTCGATGCGC 61.418 55.000 0.00 0.00 0.00 6.09
3360 4593 2.507547 TAACCGTGTCGATGCGCC 60.508 61.111 4.18 0.00 0.00 6.53
3416 4649 2.124983 CACCGCTGCCTATGCTGT 60.125 61.111 0.00 0.00 38.57 4.40
3472 4715 4.337060 CCACGACGTGTCTCGCCA 62.337 66.667 25.18 0.00 44.19 5.69
3493 4736 3.755628 GCCACCGACTACCTCGCA 61.756 66.667 0.00 0.00 41.46 5.10
3518 4761 0.532862 CTTGCTGGAGGTTGTCGTGT 60.533 55.000 0.00 0.00 0.00 4.49
3533 4776 0.179111 CGTGTGTGTCACTGACTGGT 60.179 55.000 10.54 0.00 44.16 4.00
3638 4881 5.928839 TGACAAAGTAGCTCTCATGAAACTC 59.071 40.000 0.00 0.00 0.00 3.01
3677 4923 5.733620 ACATCCTGTAAAACTAGTTCGGA 57.266 39.130 8.95 10.14 0.00 4.55
3764 5052 5.899278 AGCTAAATTTAGGGGAAGTTTGGA 58.101 37.500 23.37 0.00 29.86 3.53
3784 5072 5.738909 TGGACAAAAACAAACATCCACAAT 58.261 33.333 0.00 0.00 31.30 2.71
3799 5087 6.780522 ACATCCACAATAAAACCTGTAAACCT 59.219 34.615 0.00 0.00 0.00 3.50
3842 5130 4.452733 CTCGACCGGCCCCAAGTC 62.453 72.222 0.00 0.00 0.00 3.01
3887 5176 2.048601 TCCTCTAAAACGTTGGTGGGA 58.951 47.619 0.00 3.90 31.63 4.37
3890 5179 4.081309 TCCTCTAAAACGTTGGTGGGATAG 60.081 45.833 0.00 0.00 31.63 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 321 1.154035 GGCCCAGAAAATTGCGTCG 60.154 57.895 0.00 0.00 0.00 5.12
124 322 1.154035 CGGCCCAGAAAATTGCGTC 60.154 57.895 0.00 0.00 0.00 5.19
125 323 2.635443 CCGGCCCAGAAAATTGCGT 61.635 57.895 0.00 0.00 0.00 5.24
126 324 2.181525 CCGGCCCAGAAAATTGCG 59.818 61.111 0.00 0.00 0.00 4.85
127 325 2.578664 CCCGGCCCAGAAAATTGC 59.421 61.111 0.00 0.00 0.00 3.56
128 326 1.984026 AGCCCGGCCCAGAAAATTG 60.984 57.895 5.55 0.00 0.00 2.32
129 327 1.984026 CAGCCCGGCCCAGAAAATT 60.984 57.895 5.55 0.00 0.00 1.82
130 328 2.362889 CAGCCCGGCCCAGAAAAT 60.363 61.111 5.55 0.00 0.00 1.82
131 329 3.567579 CTCAGCCCGGCCCAGAAAA 62.568 63.158 5.55 0.00 0.00 2.29
132 330 4.033776 CTCAGCCCGGCCCAGAAA 62.034 66.667 5.55 0.00 0.00 2.52
180 378 6.338937 AGCTAGGGTTTCTATAACAAACGAG 58.661 40.000 0.00 1.89 35.00 4.18
228 430 0.870307 GGCTCGCGTGTGGTATACTG 60.870 60.000 5.77 0.00 0.00 2.74
266 475 8.601047 TCAATCTCTCTCCTTTTCTCTATTCA 57.399 34.615 0.00 0.00 0.00 2.57
270 479 6.183360 GCCATCAATCTCTCTCCTTTTCTCTA 60.183 42.308 0.00 0.00 0.00 2.43
272 481 4.815846 GCCATCAATCTCTCTCCTTTTCTC 59.184 45.833 0.00 0.00 0.00 2.87
279 488 0.034616 CCCGCCATCAATCTCTCTCC 59.965 60.000 0.00 0.00 0.00 3.71
645 903 2.032924 TCACACTATGCGTATCGGAGTG 59.967 50.000 11.82 11.82 31.95 3.51
709 967 1.096416 GTCGATCTCCTTCTGGTCGT 58.904 55.000 0.00 0.00 33.04 4.34
857 1115 2.076100 GATGCCATCTCGTCACACAAA 58.924 47.619 0.00 0.00 0.00 2.83
1028 1286 1.979693 GTCCTCTGGTCCTCAGCGT 60.980 63.158 0.00 0.00 43.06 5.07
1029 1287 2.716017 GGTCCTCTGGTCCTCAGCG 61.716 68.421 0.00 0.00 43.06 5.18
1116 1380 9.084533 GTTATAGATACATTCACCTCTTCCTCT 57.915 37.037 0.00 0.00 0.00 3.69
1280 2149 1.473788 CCATCATCCTCGACACATGCA 60.474 52.381 0.00 0.00 0.00 3.96
1286 2155 2.093500 CCTTTGTCCATCATCCTCGACA 60.093 50.000 0.00 0.00 33.56 4.35
1328 2389 2.585330 TGCTTTTCTCCATGCTTGACA 58.415 42.857 0.22 0.00 0.00 3.58
1343 2404 2.094545 GCATCTGAATCCGGTTTGCTTT 60.095 45.455 1.57 0.00 0.00 3.51
1344 2405 1.474077 GCATCTGAATCCGGTTTGCTT 59.526 47.619 1.57 0.00 0.00 3.91
1345 2406 1.098050 GCATCTGAATCCGGTTTGCT 58.902 50.000 1.57 0.00 0.00 3.91
1346 2407 0.248215 CGCATCTGAATCCGGTTTGC 60.248 55.000 1.57 0.00 0.00 3.68
1347 2408 1.062587 GACGCATCTGAATCCGGTTTG 59.937 52.381 1.57 0.00 0.00 2.93
1348 2409 1.369625 GACGCATCTGAATCCGGTTT 58.630 50.000 0.00 0.00 0.00 3.27
1349 2410 0.806102 CGACGCATCTGAATCCGGTT 60.806 55.000 0.00 0.00 0.00 4.44
1350 2411 1.226974 CGACGCATCTGAATCCGGT 60.227 57.895 0.00 0.00 0.00 5.28
1351 2412 0.936764 CTCGACGCATCTGAATCCGG 60.937 60.000 0.00 0.00 0.00 5.14
1352 2413 0.936764 CCTCGACGCATCTGAATCCG 60.937 60.000 0.00 0.00 0.00 4.18
1353 2414 0.385751 TCCTCGACGCATCTGAATCC 59.614 55.000 0.00 0.00 0.00 3.01
1354 2415 2.057316 CATCCTCGACGCATCTGAATC 58.943 52.381 0.00 0.00 0.00 2.52
1355 2416 1.410517 ACATCCTCGACGCATCTGAAT 59.589 47.619 0.00 0.00 0.00 2.57
1356 2417 0.817654 ACATCCTCGACGCATCTGAA 59.182 50.000 0.00 0.00 0.00 3.02
1357 2418 0.817654 AACATCCTCGACGCATCTGA 59.182 50.000 0.00 0.00 0.00 3.27
1360 2421 0.179111 TCCAACATCCTCGACGCATC 60.179 55.000 0.00 0.00 0.00 3.91
1387 2469 6.042897 TCACTCTTATCATCAGAATCCAGCAT 59.957 38.462 0.00 0.00 0.00 3.79
1466 2548 0.954452 CTTGCCCAACACCTTCTCAC 59.046 55.000 0.00 0.00 0.00 3.51
1517 2602 8.660373 CCATCTTTAATAGCTCCGTATGAAATC 58.340 37.037 0.00 0.00 0.00 2.17
1523 2608 6.166982 GCTTCCATCTTTAATAGCTCCGTAT 58.833 40.000 0.00 0.00 0.00 3.06
1553 2638 4.856607 GCTCCCGGAACTCGCGAG 62.857 72.222 33.45 33.45 44.19 5.03
1668 2753 2.204624 TCCTCCCCCTCCTCCTCA 60.205 66.667 0.00 0.00 0.00 3.86
1733 2830 2.226437 CCAGAAAACAACATGTCCTCCG 59.774 50.000 0.00 0.00 0.00 4.63
1920 3052 5.713025 CTGTGACACCAAATTAATCCCAAG 58.287 41.667 2.45 0.00 0.00 3.61
1923 3055 3.119137 GGCTGTGACACCAAATTAATCCC 60.119 47.826 2.45 0.00 0.00 3.85
1940 3072 0.972983 ATAGGACTCACTGCGGCTGT 60.973 55.000 6.70 6.70 0.00 4.40
2035 3167 6.324770 ACTTTCCATCTGTTCCAACAATCTTT 59.675 34.615 0.00 0.00 38.66 2.52
2087 3219 3.365265 GTCCCGGGCAGCAACAAG 61.365 66.667 18.49 0.00 0.00 3.16
2101 3233 0.320160 GGTTGTAGTCCACGGTGTCC 60.320 60.000 7.45 0.00 0.00 4.02
2201 3420 5.163673 ACACATGCAACAAAAATGGAAAACC 60.164 36.000 0.00 0.00 0.00 3.27
2518 3742 1.234615 CCGCCTTCAACAACACGGAT 61.235 55.000 0.00 0.00 43.19 4.18
2535 3759 1.256812 ATTCAAAAGGCCAAGGTCCG 58.743 50.000 5.01 0.00 0.00 4.79
2672 3902 3.334583 TTGACAGATCAAGGTAGCCAC 57.665 47.619 0.00 0.00 40.01 5.01
2998 4228 5.095691 ACACAAATAGTTCTGCAGTTTCG 57.904 39.130 14.67 2.87 0.00 3.46
3017 4247 8.982685 CACAGATAGTTGGACATATCAATACAC 58.017 37.037 0.00 0.00 31.97 2.90
3039 4269 5.358160 TGGACACAGATAGTCAGATACACAG 59.642 44.000 0.00 0.00 37.74 3.66
3121 4351 5.635417 AAATCTAGCTTTCTGCAAAGGAC 57.365 39.130 0.00 0.00 45.94 3.85
3277 4510 3.819564 TTACGGGATCTGTTGGAGATG 57.180 47.619 0.00 0.00 41.91 2.90
3286 4519 6.935741 TTTATTCCATGTTTACGGGATCTG 57.064 37.500 0.00 0.00 0.00 2.90
3288 4521 7.169140 GCAAATTTATTCCATGTTTACGGGATC 59.831 37.037 0.00 0.00 0.00 3.36
3313 4546 2.820197 CCAAAAGTTTAGAGGACCCTGC 59.180 50.000 0.00 0.00 0.00 4.85
3319 4552 6.126409 ACATTGTCACCAAAAGTTTAGAGGA 58.874 36.000 8.24 0.00 33.44 3.71
3320 4553 6.391227 ACATTGTCACCAAAAGTTTAGAGG 57.609 37.500 0.00 0.00 33.44 3.69
3321 4554 7.860872 GGTTACATTGTCACCAAAAGTTTAGAG 59.139 37.037 14.03 0.00 30.87 2.43
3322 4555 7.467539 CGGTTACATTGTCACCAAAAGTTTAGA 60.468 37.037 17.92 0.00 29.94 2.10
3323 4556 6.635239 CGGTTACATTGTCACCAAAAGTTTAG 59.365 38.462 17.92 0.00 29.94 1.85
3324 4557 6.095160 ACGGTTACATTGTCACCAAAAGTTTA 59.905 34.615 17.92 0.00 29.94 2.01
3325 4558 5.105675 ACGGTTACATTGTCACCAAAAGTTT 60.106 36.000 17.92 0.00 29.94 2.66
3326 4559 4.399934 ACGGTTACATTGTCACCAAAAGTT 59.600 37.500 17.92 0.00 29.94 2.66
3327 4560 3.949113 ACGGTTACATTGTCACCAAAAGT 59.051 39.130 17.92 6.75 29.94 2.66
3328 4561 4.201970 ACACGGTTACATTGTCACCAAAAG 60.202 41.667 17.92 6.21 29.94 2.27
3329 4562 3.695060 ACACGGTTACATTGTCACCAAAA 59.305 39.130 17.92 0.00 29.94 2.44
3330 4563 3.280295 ACACGGTTACATTGTCACCAAA 58.720 40.909 17.92 0.00 29.94 3.28
3331 4564 2.873472 GACACGGTTACATTGTCACCAA 59.127 45.455 17.92 0.00 39.60 3.67
3332 4565 2.485903 GACACGGTTACATTGTCACCA 58.514 47.619 17.92 0.00 39.60 4.17
3333 4566 1.458064 CGACACGGTTACATTGTCACC 59.542 52.381 9.69 9.69 39.77 4.02
3334 4567 2.396601 TCGACACGGTTACATTGTCAC 58.603 47.619 13.52 0.00 39.77 3.67
3335 4568 2.797074 TCGACACGGTTACATTGTCA 57.203 45.000 13.52 1.96 39.77 3.58
3336 4569 2.222729 GCATCGACACGGTTACATTGTC 60.223 50.000 0.00 5.75 36.99 3.18
3337 4570 1.730064 GCATCGACACGGTTACATTGT 59.270 47.619 0.00 0.00 0.00 2.71
3338 4571 1.266842 CGCATCGACACGGTTACATTG 60.267 52.381 1.11 0.00 0.00 2.82
3339 4572 0.996462 CGCATCGACACGGTTACATT 59.004 50.000 1.11 0.00 0.00 2.71
3340 4573 1.418342 GCGCATCGACACGGTTACAT 61.418 55.000 0.30 0.00 0.00 2.29
3341 4574 2.089936 GCGCATCGACACGGTTACA 61.090 57.895 0.30 0.00 0.00 2.41
3342 4575 2.693285 GCGCATCGACACGGTTAC 59.307 61.111 0.30 0.00 0.00 2.50
3343 4576 2.507547 GGCGCATCGACACGGTTA 60.508 61.111 10.83 0.00 33.63 2.85
3405 4638 4.407245 TGCGGCACAGCATAGGCA 62.407 61.111 0.67 0.00 42.92 4.75
3428 4661 4.408821 ACGGCGGTGGCATGACAT 62.409 61.111 13.24 0.00 42.47 3.06
3449 4692 1.344942 GAGACACGTCGTGGTCATGC 61.345 60.000 27.77 10.53 37.94 4.06
3518 4761 0.104855 GCTCACCAGTCAGTGACACA 59.895 55.000 24.73 3.15 41.78 3.72
3591 4834 4.166919 AGATCCCATAAACTTCTTCCCCTG 59.833 45.833 0.00 0.00 0.00 4.45
3677 4923 4.040584 AGCTCGGTTCCTCTAAGAAACTTT 59.959 41.667 0.00 0.00 30.90 2.66
3746 5034 6.816616 TTTTGTCCAAACTTCCCCTAAATT 57.183 33.333 0.00 0.00 0.00 1.82
3764 5052 8.454894 GGTTTTATTGTGGATGTTTGTTTTTGT 58.545 29.630 0.00 0.00 0.00 2.83
3776 5064 7.007723 TCAGGTTTACAGGTTTTATTGTGGAT 58.992 34.615 0.00 0.00 0.00 3.41
3813 5101 2.557490 GCCGGTCGAGTTTATAGGATCT 59.443 50.000 1.90 0.00 0.00 2.75
3842 5130 4.518249 GTCATCTTCCTAAACAAGAGGGG 58.482 47.826 0.00 0.00 33.42 4.79
3870 5158 5.486735 TTCTATCCCACCAACGTTTTAGA 57.513 39.130 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.