Multiple sequence alignment - TraesCS1A01G190000

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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 TraesCS1A01G190000 chr1A 100.000 5282 0 0 1 5282 343622756 343617475 0.000000e+00 9755
1 TraesCS1A01G190000 chr1B 96.064 1677 55 7 3616 5282 343663158 343661483 0.000000e+00 2721
2 TraesCS1A01G190000 chr1B 94.395 1784 73 9 815 2589 343664920 343663155 0.000000e+00 2715
3 TraesCS1A01G190000 chr1B 87.644 607 64 7 142 747 343665937 343665341 0.000000e+00 695
4 TraesCS1A01G190000 chr1B 92.958 142 10 0 1 142 343882403 343882262 1.930000e-49 207
5 TraesCS1A01G190000 chr1D 94.662 1686 56 16 912 2586 270024020 270022358 0.000000e+00 2584
6 TraesCS1A01G190000 chr1D 98.546 894 11 2 4390 5282 270021618 270020726 0.000000e+00 1578
7 TraesCS1A01G190000 chr1D 96.774 744 22 1 3616 4359 270022358 270021617 0.000000e+00 1240
8 TraesCS1A01G190000 chr1D 86.935 819 77 14 124 922 270024923 270024115 0.000000e+00 893
9 TraesCS1A01G190000 chr1D 96.032 126 5 0 1 126 270036997 270036872 6.930000e-49 206
10 TraesCS1A01G190000 chr3D 94.610 1039 49 6 2577 3614 4190068 4191100 0.000000e+00 1602
11 TraesCS1A01G190000 chr3D 94.236 1041 53 5 2582 3620 66239039 66238004 0.000000e+00 1583
12 TraesCS1A01G190000 chr3D 94.214 1037 55 4 2584 3619 607267876 607268908 0.000000e+00 1578
13 TraesCS1A01G190000 chr3D 93.870 1044 50 9 2577 3608 569061852 569062893 0.000000e+00 1561
14 TraesCS1A01G190000 chr3D 85.000 260 39 0 389 648 580537512 580537771 1.130000e-66 265
15 TraesCS1A01G190000 chr5D 94.595 1036 48 6 2586 3618 8703241 8704271 0.000000e+00 1596
16 TraesCS1A01G190000 chr5D 94.280 542 28 3 3616 4157 325956901 325956363 0.000000e+00 826
17 TraesCS1A01G190000 chr5D 80.667 750 65 34 659 1369 325958657 325959365 4.720000e-140 508
18 TraesCS1A01G190000 chr5D 87.115 357 38 7 26 381 325958303 325958652 1.070000e-106 398
19 TraesCS1A01G190000 chr5D 94.821 251 10 2 2341 2589 325957147 325956898 6.410000e-104 388
20 TraesCS1A01G190000 chr5D 85.075 268 37 3 381 648 129239243 129239507 2.420000e-68 270
21 TraesCS1A01G190000 chr4A 94.061 1044 53 6 2585 3620 477293326 477292284 0.000000e+00 1576
22 TraesCS1A01G190000 chr4A 84.328 268 39 1 381 648 724732096 724732360 5.250000e-65 259
23 TraesCS1A01G190000 chr7D 93.954 1042 54 7 2580 3617 177571373 177572409 0.000000e+00 1567
24 TraesCS1A01G190000 chr7D 84.328 268 41 1 381 648 515486965 515487231 1.460000e-65 261
25 TraesCS1A01G190000 chr7D 84.328 268 39 3 384 651 11043700 11043436 5.250000e-65 259
26 TraesCS1A01G190000 chr5B 93.422 1049 59 7 2577 3619 166706367 166707411 0.000000e+00 1546
27 TraesCS1A01G190000 chr5B 84.962 266 35 5 384 648 692566125 692565864 1.130000e-66 265
28 TraesCS1A01G190000 chr3B 93.493 1045 60 8 2568 3608 480336678 480337718 0.000000e+00 1546
29 TraesCS1A01G190000 chr5A 94.465 542 30 0 3616 4157 430641977 430642518 0.000000e+00 835
30 TraesCS1A01G190000 chr5A 94.944 178 8 1 2409 2586 430641801 430641977 1.450000e-70 278
31 TraesCS1A01G190000 chr5A 90.184 163 16 0 26 188 430640484 430640322 4.140000e-51 213
32 TraesCS1A01G190000 chr5A 94.444 72 2 1 2341 2410 430641463 430641534 5.590000e-20 110
33 TraesCS1A01G190000 chr7B 93.199 544 31 3 3616 4157 5917652 5917113 0.000000e+00 795
34 TraesCS1A01G190000 chr7B 92.829 251 12 2 2341 2589 5917895 5917649 5.030000e-95 359
35 TraesCS1A01G190000 chr6D 85.075 268 36 4 381 648 464465736 464465999 2.420000e-68 270


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 TraesCS1A01G190000 chr1A 343617475 343622756 5281 True 9755.000000 9755 100.000000 1 5282 1 chr1A.!!$R1 5281
1 TraesCS1A01G190000 chr1B 343661483 343665937 4454 True 2043.666667 2721 92.701000 142 5282 3 chr1B.!!$R2 5140
2 TraesCS1A01G190000 chr1D 270020726 270024923 4197 True 1573.750000 2584 94.229250 124 5282 4 chr1D.!!$R2 5158
3 TraesCS1A01G190000 chr3D 4190068 4191100 1032 False 1602.000000 1602 94.610000 2577 3614 1 chr3D.!!$F1 1037
4 TraesCS1A01G190000 chr3D 66238004 66239039 1035 True 1583.000000 1583 94.236000 2582 3620 1 chr3D.!!$R1 1038
5 TraesCS1A01G190000 chr3D 607267876 607268908 1032 False 1578.000000 1578 94.214000 2584 3619 1 chr3D.!!$F4 1035
6 TraesCS1A01G190000 chr3D 569061852 569062893 1041 False 1561.000000 1561 93.870000 2577 3608 1 chr3D.!!$F2 1031
7 TraesCS1A01G190000 chr5D 8703241 8704271 1030 False 1596.000000 1596 94.595000 2586 3618 1 chr5D.!!$F1 1032
8 TraesCS1A01G190000 chr5D 325956363 325957147 784 True 607.000000 826 94.550500 2341 4157 2 chr5D.!!$R1 1816
9 TraesCS1A01G190000 chr5D 325958303 325959365 1062 False 453.000000 508 83.891000 26 1369 2 chr5D.!!$F3 1343
10 TraesCS1A01G190000 chr4A 477292284 477293326 1042 True 1576.000000 1576 94.061000 2585 3620 1 chr4A.!!$R1 1035
11 TraesCS1A01G190000 chr7D 177571373 177572409 1036 False 1567.000000 1567 93.954000 2580 3617 1 chr7D.!!$F1 1037
12 TraesCS1A01G190000 chr5B 166706367 166707411 1044 False 1546.000000 1546 93.422000 2577 3619 1 chr5B.!!$F1 1042
13 TraesCS1A01G190000 chr3B 480336678 480337718 1040 False 1546.000000 1546 93.493000 2568 3608 1 chr3B.!!$F1 1040
14 TraesCS1A01G190000 chr5A 430641463 430642518 1055 False 407.666667 835 94.617667 2341 4157 3 chr5A.!!$F1 1816
15 TraesCS1A01G190000 chr7B 5917113 5917895 782 True 577.000000 795 93.014000 2341 4157 2 chr7B.!!$R1 1816

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
895 1288 0.099968 CTCGAGCCCACGACGATAAA 59.900 55.000 0.0 0.0 37.37 1.40 F
1201 1730 0.035247 ACCGTCCTTCTCGCTACTCT 60.035 55.000 0.0 0.0 0.00 3.24 F
1395 1924 0.733909 CGTCCGAAACCGAGGTAACC 60.734 60.000 0.0 0.0 37.17 2.85 F
2033 2571 1.442526 CGATTGTCAGCAGCCATCCC 61.443 60.000 0.0 0.0 0.00 3.85 F
2447 3255 2.430694 AGTTTCTGGTTTTCAGGTTGCC 59.569 45.455 0.0 0.0 43.53 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2504 0.106268 ACAACCCAGCCATTGTCACA 60.106 50.000 0.0 0.0 33.8 3.58 R
2606 3415 1.593196 TGTTTTCTCTCCCGTTGCAG 58.407 50.000 0.0 0.0 0.0 4.41 R
2690 3499 1.599071 ACACAAATATGATGCCTCGCG 59.401 47.619 0.0 0.0 0.0 5.87 R
3296 4124 2.691927 ACCGTAACTCCGATTTCAACC 58.308 47.619 0.0 0.0 0.0 3.77 R
4386 5221 0.247460 TGTCCCAGCGATCAGACTTG 59.753 55.000 0.0 0.0 0.0 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
27 28 9.825972 ACTTTAAGTGAAATGATTGAACGTATG 57.174 29.630 0.00 0.00 0.00 2.39
28 29 8.667987 TTTAAGTGAAATGATTGAACGTATGC 57.332 30.769 0.00 0.00 0.00 3.14
44 45 7.870445 TGAACGTATGCTAGCAATAATACATGA 59.130 33.333 23.54 3.14 0.00 3.07
45 46 8.601845 AACGTATGCTAGCAATAATACATGAA 57.398 30.769 23.54 0.00 0.00 2.57
46 47 8.601845 ACGTATGCTAGCAATAATACATGAAA 57.398 30.769 23.54 0.00 0.00 2.69
73 74 8.989980 AGTTAAAGACATGACTACTTTGTTAGC 58.010 33.333 0.00 0.00 35.79 3.09
74 75 8.989980 GTTAAAGACATGACTACTTTGTTAGCT 58.010 33.333 0.00 0.00 35.79 3.32
79 80 7.976734 AGACATGACTACTTTGTTAGCTATGAC 59.023 37.037 0.00 0.00 0.00 3.06
81 82 5.100259 TGACTACTTTGTTAGCTATGACGC 58.900 41.667 0.00 0.00 0.00 5.19
113 114 4.065088 TGCGGAAATAGGAGATAATGTGC 58.935 43.478 0.00 0.00 0.00 4.57
130 131 1.670083 GCGGTACACAACTGGGGTC 60.670 63.158 0.00 0.00 34.76 4.46
188 189 5.299782 AGAGTGATCTAATACCGACAGTTCC 59.700 44.000 0.00 0.00 0.00 3.62
233 234 1.557099 TGGCTCTCTCACACCGTAAT 58.443 50.000 0.00 0.00 0.00 1.89
330 331 7.804712 TGTAACACGTTAAGTTTCTTTTGTGA 58.195 30.769 11.99 0.00 0.00 3.58
337 338 9.106070 ACGTTAAGTTTCTTTTGTGAGAGTAAT 57.894 29.630 0.00 0.00 0.00 1.89
444 445 5.604231 TGGTTCTATGAGACCTTAGCATGAT 59.396 40.000 0.00 0.00 0.00 2.45
465 466 7.303182 TGATGACTTCCCGATTGTCTATTAT 57.697 36.000 0.00 0.00 0.00 1.28
485 486 9.736023 CTATTATAACAAGTTTTGCCTGATTCC 57.264 33.333 0.00 0.00 0.00 3.01
493 494 2.899339 GCCTGATTCCAGCGAGGC 60.899 66.667 0.00 0.00 44.10 4.70
500 501 3.916438 TTCCAGCGAGGCAGGGGTA 62.916 63.158 0.00 0.00 35.85 3.69
507 508 1.672854 CGAGGCAGGGGTAATGACGA 61.673 60.000 0.00 0.00 0.00 4.20
508 509 0.759346 GAGGCAGGGGTAATGACGAT 59.241 55.000 0.00 0.00 0.00 3.73
510 511 0.468226 GGCAGGGGTAATGACGATGA 59.532 55.000 0.00 0.00 0.00 2.92
520 521 2.202623 GACGATGACGCGCCTTCT 60.203 61.111 5.73 0.00 43.96 2.85
540 541 2.150390 TGCTCGCTTCAATGCTTGTAA 58.850 42.857 0.00 0.00 0.00 2.41
564 565 5.077564 TCATCGCTAGGTGGTCTATGTATT 58.922 41.667 0.00 0.00 0.00 1.89
600 601 7.972623 TTTAGTATTTTTGGTGTTCGTTGTG 57.027 32.000 0.00 0.00 0.00 3.33
604 605 1.169577 TTTGGTGTTCGTTGTGCTGT 58.830 45.000 0.00 0.00 0.00 4.40
612 613 4.025229 GTGTTCGTTGTGCTGTCAAGATTA 60.025 41.667 0.00 0.00 0.00 1.75
794 1165 7.733402 TTTTGAGGGGTATATAATGCGTTAC 57.267 36.000 0.00 0.00 0.00 2.50
848 1241 2.206750 GTTAAGTGGAACGCAGACACA 58.793 47.619 0.00 0.00 45.86 3.72
849 1242 2.148916 TAAGTGGAACGCAGACACAG 57.851 50.000 0.00 0.00 45.86 3.66
855 1248 2.299013 TGGAACGCAGACACAGTCTAAT 59.701 45.455 0.00 0.00 41.37 1.73
895 1288 0.099968 CTCGAGCCCACGACGATAAA 59.900 55.000 0.00 0.00 37.37 1.40
901 1294 1.003866 GCCCACGACGATAAATTCAGC 60.004 52.381 0.00 0.00 0.00 4.26
902 1295 1.257936 CCCACGACGATAAATTCAGCG 59.742 52.381 0.00 0.00 0.00 5.18
903 1296 1.924524 CCACGACGATAAATTCAGCGT 59.075 47.619 0.00 0.00 44.33 5.07
904 1297 3.110358 CCACGACGATAAATTCAGCGTA 58.890 45.455 0.00 0.00 41.24 4.42
905 1298 3.179795 CCACGACGATAAATTCAGCGTAG 59.820 47.826 0.00 0.00 41.24 3.51
906 1299 4.033019 CACGACGATAAATTCAGCGTAGA 58.967 43.478 6.50 0.00 41.24 2.59
907 1300 4.497966 CACGACGATAAATTCAGCGTAGAA 59.502 41.667 6.50 0.00 41.24 2.10
908 1301 5.004061 CACGACGATAAATTCAGCGTAGAAA 59.996 40.000 6.50 0.00 41.24 2.52
909 1302 5.574055 ACGACGATAAATTCAGCGTAGAAAA 59.426 36.000 6.50 0.00 41.24 2.29
910 1303 6.114288 CGACGATAAATTCAGCGTAGAAAAG 58.886 40.000 0.00 0.00 41.24 2.27
911 1304 6.020916 CGACGATAAATTCAGCGTAGAAAAGA 60.021 38.462 0.00 0.00 41.24 2.52
912 1305 7.462331 CGACGATAAATTCAGCGTAGAAAAGAA 60.462 37.037 0.00 0.00 41.24 2.52
913 1306 7.676393 ACGATAAATTCAGCGTAGAAAAGAAG 58.324 34.615 0.00 0.00 39.04 2.85
980 1494 0.811616 CCGCAGTATCAAGCACTCCC 60.812 60.000 0.00 0.00 0.00 4.30
1131 1649 3.647771 GCCCGACTCCCCCTTGTT 61.648 66.667 0.00 0.00 0.00 2.83
1199 1728 1.313812 CCACCGTCCTTCTCGCTACT 61.314 60.000 0.00 0.00 0.00 2.57
1200 1729 0.099082 CACCGTCCTTCTCGCTACTC 59.901 60.000 0.00 0.00 0.00 2.59
1201 1730 0.035247 ACCGTCCTTCTCGCTACTCT 60.035 55.000 0.00 0.00 0.00 3.24
1202 1731 1.209019 ACCGTCCTTCTCGCTACTCTA 59.791 52.381 0.00 0.00 0.00 2.43
1282 1811 3.155167 CTCCCTCGCAGGTACCCC 61.155 72.222 8.74 0.00 31.93 4.95
1395 1924 0.733909 CGTCCGAAACCGAGGTAACC 60.734 60.000 0.00 0.00 37.17 2.85
1607 2138 6.481644 GGAAAGCATCAATGAGGTAGTTAGAG 59.518 42.308 0.00 0.00 0.00 2.43
1833 2371 2.221169 GCAAGTCGGCCATCATCAATA 58.779 47.619 2.24 0.00 0.00 1.90
1904 2442 6.261381 ACTTGTTGCCTTTCTGTTCGTAATAA 59.739 34.615 0.00 0.00 0.00 1.40
1906 2444 5.527951 TGTTGCCTTTCTGTTCGTAATAACA 59.472 36.000 0.00 0.00 37.75 2.41
1966 2504 5.407387 GCTTTGATTGTGATTTGATTGCTGT 59.593 36.000 0.00 0.00 0.00 4.40
2033 2571 1.442526 CGATTGTCAGCAGCCATCCC 61.443 60.000 0.00 0.00 0.00 3.85
2447 3255 2.430694 AGTTTCTGGTTTTCAGGTTGCC 59.569 45.455 0.00 0.00 43.53 4.52
2561 3370 5.537674 AGGTAAAGACTCCTACGAAGTTCAA 59.462 40.000 3.32 0.00 37.78 2.69
2659 3468 5.305585 TCTTAACTCAACAACCATCACTCC 58.694 41.667 0.00 0.00 0.00 3.85
2687 3496 6.849697 ACCACAATAGGTCCATCTCCTTTATA 59.150 38.462 0.00 0.00 37.28 0.98
2690 3499 9.442047 CACAATAGGTCCATCTCCTTTATATTC 57.558 37.037 0.00 0.00 36.60 1.75
2716 3525 3.149436 GCATCATATTTGTGTTGCCGT 57.851 42.857 0.42 0.00 38.34 5.68
2903 3728 5.947663 TGAGAAATCTGTTGTTTTCCCCTA 58.052 37.500 0.00 0.00 34.25 3.53
3040 3868 9.974750 GAATCTTGCGCTATAAATTATAAGTCC 57.025 33.333 9.73 0.00 0.00 3.85
3381 4209 8.731275 TTAAATATGATCCGCGGATGAATTAT 57.269 30.769 43.46 26.74 34.60 1.28
3399 4229 8.108378 TGAATTATCTAAAACATCAGGGGGTA 57.892 34.615 0.00 0.00 0.00 3.69
3439 4270 1.528161 CGGTTCGGGTGTGACTTAAAC 59.472 52.381 0.00 0.00 0.00 2.01
3476 4307 4.515191 TGATTTCAAGAAAAGACAGGGACG 59.485 41.667 0.00 0.00 33.56 4.79
3671 4504 6.039829 GCAATTAAGGATTCCTTGTTAGAGGG 59.960 42.308 25.26 10.30 44.44 4.30
3703 4536 6.463995 TTGCACAATTCCTTCTTACAGTTT 57.536 33.333 0.00 0.00 0.00 2.66
3726 4559 3.418684 AACTTAAGGACGGAATGCAGT 57.581 42.857 7.53 0.00 0.00 4.40
3971 4805 4.910195 TCTTGGTTCTGACATGCATACTT 58.090 39.130 0.00 0.00 0.00 2.24
3985 4819 3.206150 GCATACTTTTAGCTAGCTGCCA 58.794 45.455 27.68 4.26 44.23 4.92
4053 4887 1.154654 CGTTCGTCAAGCGCTTTCC 60.155 57.895 22.51 12.82 41.07 3.13
4140 4975 4.265893 TCCAGTTTACACACTTGCAGAAA 58.734 39.130 0.00 0.00 0.00 2.52
4184 5019 9.753674 TGAAACAATTGAGGATAGGAATAAACT 57.246 29.630 13.59 0.00 0.00 2.66
4252 5087 5.381757 GCCATTATACCTTGGACCATGTTA 58.618 41.667 0.00 0.00 34.81 2.41
4357 5192 3.244112 ACTTACTGAGTCCGGAAAACAGG 60.244 47.826 26.26 16.56 31.20 4.00
4358 5193 1.129058 ACTGAGTCCGGAAAACAGGT 58.871 50.000 26.26 15.33 33.57 4.00
4359 5194 1.202651 ACTGAGTCCGGAAAACAGGTG 60.203 52.381 26.26 11.73 33.57 4.00
4360 5195 1.070134 CTGAGTCCGGAAAACAGGTGA 59.930 52.381 5.23 0.00 0.00 4.02
4361 5196 1.487142 TGAGTCCGGAAAACAGGTGAA 59.513 47.619 5.23 0.00 0.00 3.18
4362 5197 2.105821 TGAGTCCGGAAAACAGGTGAAT 59.894 45.455 5.23 0.00 0.00 2.57
4363 5198 3.146847 GAGTCCGGAAAACAGGTGAATT 58.853 45.455 5.23 0.00 0.00 2.17
4364 5199 4.202377 TGAGTCCGGAAAACAGGTGAATTA 60.202 41.667 5.23 0.00 0.00 1.40
4365 5200 4.070009 AGTCCGGAAAACAGGTGAATTAC 58.930 43.478 5.23 0.00 0.00 1.89
4366 5201 4.070009 GTCCGGAAAACAGGTGAATTACT 58.930 43.478 5.23 0.00 0.00 2.24
4367 5202 5.012354 AGTCCGGAAAACAGGTGAATTACTA 59.988 40.000 5.23 0.00 0.00 1.82
4368 5203 5.878669 GTCCGGAAAACAGGTGAATTACTAT 59.121 40.000 5.23 0.00 0.00 2.12
4369 5204 6.373495 GTCCGGAAAACAGGTGAATTACTATT 59.627 38.462 5.23 0.00 0.00 1.73
4370 5205 6.596497 TCCGGAAAACAGGTGAATTACTATTC 59.404 38.462 0.00 0.00 40.50 1.75
4371 5206 6.373216 CCGGAAAACAGGTGAATTACTATTCA 59.627 38.462 0.00 0.00 45.99 2.57
4469 5344 8.916628 TGCACCTAAATGTATATCATGCTAAA 57.083 30.769 0.00 0.00 36.81 1.85
4499 5375 6.825721 AGTTATTGAAATCCACCACTCATCTC 59.174 38.462 0.00 0.00 0.00 2.75
4649 5525 1.277557 TCTCTTCTCCTCCTTGCAAGC 59.722 52.381 21.43 0.00 0.00 4.01
4761 5637 4.097589 AGTCGTACTACCATTTCTACCAGC 59.902 45.833 0.00 0.00 0.00 4.85
4809 5685 2.105477 TGCTTCAGAGAACTCAAGGCTT 59.895 45.455 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.788813 GCATACGTTCAATCATTTCACTTAAAG 58.211 33.333 0.00 0.00 0.00 1.85
7 8 6.238211 GCTAGCATACGTTCAATCATTTCACT 60.238 38.462 10.63 0.00 0.00 3.41
8 9 5.904080 GCTAGCATACGTTCAATCATTTCAC 59.096 40.000 10.63 0.00 0.00 3.18
10 11 6.048073 TGCTAGCATACGTTCAATCATTTC 57.952 37.500 14.93 0.00 0.00 2.17
12 13 6.624352 ATTGCTAGCATACGTTCAATCATT 57.376 33.333 20.13 0.00 0.00 2.57
13 14 7.728847 TTATTGCTAGCATACGTTCAATCAT 57.271 32.000 20.13 6.80 0.00 2.45
14 15 7.728847 ATTATTGCTAGCATACGTTCAATCA 57.271 32.000 20.13 0.00 0.00 2.57
15 16 8.708742 TGTATTATTGCTAGCATACGTTCAATC 58.291 33.333 20.13 3.65 0.00 2.67
16 17 8.601845 TGTATTATTGCTAGCATACGTTCAAT 57.398 30.769 20.13 8.86 0.00 2.57
17 18 8.495148 CATGTATTATTGCTAGCATACGTTCAA 58.505 33.333 20.13 0.21 0.00 2.69
18 19 7.870445 TCATGTATTATTGCTAGCATACGTTCA 59.130 33.333 20.13 14.23 0.00 3.18
19 20 8.239681 TCATGTATTATTGCTAGCATACGTTC 57.760 34.615 20.13 9.08 0.00 3.95
20 21 8.601845 TTCATGTATTATTGCTAGCATACGTT 57.398 30.769 20.13 6.91 0.00 3.99
21 22 8.601845 TTTCATGTATTATTGCTAGCATACGT 57.398 30.769 20.13 15.76 0.00 3.57
22 23 9.533983 CTTTTCATGTATTATTGCTAGCATACG 57.466 33.333 20.13 6.52 0.00 3.06
69 70 5.743398 GCAATTTTTCATGCGTCATAGCTAA 59.257 36.000 0.00 0.00 38.13 3.09
70 71 5.273170 GCAATTTTTCATGCGTCATAGCTA 58.727 37.500 0.00 0.00 38.13 3.32
81 82 6.563422 TCTCCTATTTCCGCAATTTTTCATG 58.437 36.000 0.00 0.00 0.00 3.07
113 114 1.373748 CGACCCCAGTTGTGTACCG 60.374 63.158 0.00 0.00 0.00 4.02
130 131 2.353803 GGGGGATTCCTATCAACGATCG 60.354 54.545 14.88 14.88 35.33 3.69
188 189 6.149308 TGCTGATTGGTACTTGTAACATTCAG 59.851 38.462 28.30 28.30 41.04 3.02
386 387 3.599285 AACCGCCGCCGATGAAGAA 62.599 57.895 0.00 0.00 36.29 2.52
406 407 0.590195 GAACCAGCACAGCAGAACAG 59.410 55.000 0.00 0.00 0.00 3.16
444 445 8.014070 TGTTATAATAGACAATCGGGAAGTCA 57.986 34.615 0.00 0.00 34.80 3.41
465 466 4.261994 GCTGGAATCAGGCAAAACTTGTTA 60.262 41.667 0.00 0.00 41.19 2.41
485 486 1.524621 CATTACCCCTGCCTCGCTG 60.525 63.158 0.00 0.00 0.00 5.18
493 494 1.852942 CGTCATCGTCATTACCCCTG 58.147 55.000 0.00 0.00 0.00 4.45
500 501 1.421410 GAAGGCGCGTCATCGTCATT 61.421 55.000 15.58 0.00 36.38 2.57
540 541 3.501349 ACATAGACCACCTAGCGATGAT 58.499 45.455 0.00 0.00 0.00 2.45
580 581 4.206200 CAGCACAACGAACACCAAAAATAC 59.794 41.667 0.00 0.00 0.00 1.89
586 587 0.730265 GACAGCACAACGAACACCAA 59.270 50.000 0.00 0.00 0.00 3.67
592 593 5.525745 TCTTTAATCTTGACAGCACAACGAA 59.474 36.000 0.00 0.00 0.00 3.85
600 601 9.928236 GTTCTATTCATCTTTAATCTTGACAGC 57.072 33.333 0.00 0.00 0.00 4.40
604 605 9.884636 TTCCGTTCTATTCATCTTTAATCTTGA 57.115 29.630 0.00 0.00 0.00 3.02
612 613 9.152595 GAGTAAACTTCCGTTCTATTCATCTTT 57.847 33.333 0.00 0.00 31.66 2.52
848 1241 1.141881 CCACCTGCGCGATTAGACT 59.858 57.895 12.10 0.00 0.00 3.24
849 1242 2.526120 GCCACCTGCGCGATTAGAC 61.526 63.158 12.10 0.00 0.00 2.59
895 1288 3.010420 GGGCTTCTTTTCTACGCTGAAT 58.990 45.455 0.00 0.00 0.00 2.57
901 1294 3.312697 GGCTAATGGGCTTCTTTTCTACG 59.687 47.826 0.00 0.00 37.53 3.51
902 1295 3.312697 CGGCTAATGGGCTTCTTTTCTAC 59.687 47.826 0.00 0.00 38.46 2.59
903 1296 3.199071 TCGGCTAATGGGCTTCTTTTCTA 59.801 43.478 0.00 0.00 38.46 2.10
904 1297 2.026262 TCGGCTAATGGGCTTCTTTTCT 60.026 45.455 0.00 0.00 38.46 2.52
905 1298 2.097629 GTCGGCTAATGGGCTTCTTTTC 59.902 50.000 0.00 0.00 38.46 2.29
906 1299 2.092323 GTCGGCTAATGGGCTTCTTTT 58.908 47.619 0.00 0.00 38.46 2.27
907 1300 1.751437 GTCGGCTAATGGGCTTCTTT 58.249 50.000 0.00 0.00 38.46 2.52
908 1301 0.462047 CGTCGGCTAATGGGCTTCTT 60.462 55.000 0.00 0.00 38.46 2.52
909 1302 1.144057 CGTCGGCTAATGGGCTTCT 59.856 57.895 0.00 0.00 38.46 2.85
910 1303 2.534903 GCGTCGGCTAATGGGCTTC 61.535 63.158 0.00 0.00 38.46 3.86
911 1304 2.513897 GCGTCGGCTAATGGGCTT 60.514 61.111 0.00 0.00 38.46 4.35
912 1305 4.891727 CGCGTCGGCTAATGGGCT 62.892 66.667 0.00 0.00 38.46 5.19
913 1306 2.758770 TATCGCGTCGGCTAATGGGC 62.759 60.000 5.77 0.00 36.88 5.36
1199 1728 3.082548 CGTCTGAAAGGTGGAGAGTAGA 58.917 50.000 0.00 0.00 0.00 2.59
1200 1729 3.082548 TCGTCTGAAAGGTGGAGAGTAG 58.917 50.000 0.00 0.00 0.00 2.57
1201 1730 3.082548 CTCGTCTGAAAGGTGGAGAGTA 58.917 50.000 0.00 0.00 30.17 2.59
1202 1731 1.889829 CTCGTCTGAAAGGTGGAGAGT 59.110 52.381 0.00 0.00 30.17 3.24
1282 1811 2.125912 CTCGAACGCTGAGGTGGG 60.126 66.667 0.00 0.00 0.00 4.61
1290 1819 1.080434 GTGGAGAAGCTCGAACGCT 60.080 57.895 0.00 0.00 43.31 5.07
1607 2138 1.514443 GAGACGACACTAGCACGGC 60.514 63.158 0.00 5.42 35.11 5.68
1833 2371 3.355378 TCCTTCCAATTTGATGCATCGT 58.645 40.909 21.34 7.65 0.00 3.73
1904 2442 7.452562 AGGAAAAATAAGGTGCATCAAAATGT 58.547 30.769 0.00 0.00 35.18 2.71
1966 2504 0.106268 ACAACCCAGCCATTGTCACA 60.106 50.000 0.00 0.00 33.80 3.58
2033 2571 5.533482 CCACTTATATCTCTGGTTTCTCCG 58.467 45.833 0.00 0.00 39.52 4.63
2139 2677 8.284945 TCTTTTAGCGAGATAAAGTACTACCA 57.715 34.615 0.00 0.00 32.22 3.25
2606 3415 1.593196 TGTTTTCTCTCCCGTTGCAG 58.407 50.000 0.00 0.00 0.00 4.41
2687 3496 3.058708 CACAAATATGATGCCTCGCGAAT 60.059 43.478 11.33 0.00 0.00 3.34
2690 3499 1.599071 ACACAAATATGATGCCTCGCG 59.401 47.619 0.00 0.00 0.00 5.87
2716 3525 3.031736 CGAGGGTGAGAAGGAGGATAAA 58.968 50.000 0.00 0.00 0.00 1.40
2903 3728 6.767902 ACATGCATACCTCTGAAAAATATCGT 59.232 34.615 0.00 0.00 0.00 3.73
2968 3796 4.075682 TCCGGATTGCAAATAAACACTCA 58.924 39.130 1.71 0.00 0.00 3.41
3287 4115 7.553881 AACTCCGATTTCAACCTGTTATATG 57.446 36.000 0.00 0.00 0.00 1.78
3296 4124 2.691927 ACCGTAACTCCGATTTCAACC 58.308 47.619 0.00 0.00 0.00 3.77
3300 4128 7.120789 TCTTTTAAACCGTAACTCCGATTTC 57.879 36.000 0.00 0.00 0.00 2.17
3381 4209 6.395780 TTGAATACCCCCTGATGTTTTAGA 57.604 37.500 0.00 0.00 0.00 2.10
3517 4348 4.137543 AGAATTCAACCCACAGTTCTGTC 58.862 43.478 8.44 0.00 36.18 3.51
3671 4504 5.591877 AGAAGGAATTGTGCAATCTCATACC 59.408 40.000 0.00 0.00 0.00 2.73
3703 4536 5.180492 CACTGCATTCCGTCCTTAAGTTAAA 59.820 40.000 0.97 0.00 0.00 1.52
3726 4559 2.907892 AGATTCAGGTTCTCCCACTCA 58.092 47.619 0.00 0.00 34.66 3.41
3928 4762 7.970061 CCAAGAATTCGATGCTCTTAAAAATCA 59.030 33.333 0.00 0.00 0.00 2.57
3971 4805 6.773976 ATTAAAACATGGCAGCTAGCTAAA 57.226 33.333 18.86 6.27 44.79 1.85
4053 4887 3.806521 CCTGAAAAGATGCTATGGTCTCG 59.193 47.826 0.00 0.00 0.00 4.04
4140 4975 3.430042 TCAGCAGAAATCCTGAAAGCT 57.570 42.857 0.00 0.00 45.78 3.74
4184 5019 5.700832 AGATTGAGTAATTTGACAGCGACAA 59.299 36.000 0.00 0.00 0.00 3.18
4242 5077 3.877508 GCCTAACATCTGTAACATGGTCC 59.122 47.826 0.00 0.00 0.00 4.46
4252 5087 3.118592 GCTACTTCCTGCCTAACATCTGT 60.119 47.826 0.00 0.00 0.00 3.41
4364 5199 8.552296 ACTTGGAAGGATTATCAAGTGAATAGT 58.448 33.333 6.74 0.00 44.92 2.12
4365 5200 8.970859 ACTTGGAAGGATTATCAAGTGAATAG 57.029 34.615 6.74 0.00 44.92 1.73
4366 5201 8.772250 AGACTTGGAAGGATTATCAAGTGAATA 58.228 33.333 11.54 0.00 45.86 1.75
4367 5202 7.555554 CAGACTTGGAAGGATTATCAAGTGAAT 59.444 37.037 11.54 0.00 45.86 2.57
4368 5203 6.881065 CAGACTTGGAAGGATTATCAAGTGAA 59.119 38.462 11.54 0.00 45.86 3.18
4369 5204 6.213397 TCAGACTTGGAAGGATTATCAAGTGA 59.787 38.462 11.54 2.66 45.86 3.41
4370 5205 6.409704 TCAGACTTGGAAGGATTATCAAGTG 58.590 40.000 11.54 0.57 45.86 3.16
4372 5207 6.423302 CGATCAGACTTGGAAGGATTATCAAG 59.577 42.308 0.00 0.00 41.87 3.02
4373 5208 6.283694 CGATCAGACTTGGAAGGATTATCAA 58.716 40.000 0.00 0.00 0.00 2.57
4374 5209 5.740224 GCGATCAGACTTGGAAGGATTATCA 60.740 44.000 0.00 0.00 0.00 2.15
4375 5210 4.688413 GCGATCAGACTTGGAAGGATTATC 59.312 45.833 0.00 0.00 0.00 1.75
4376 5211 4.346418 AGCGATCAGACTTGGAAGGATTAT 59.654 41.667 0.00 0.00 0.00 1.28
4377 5212 3.706594 AGCGATCAGACTTGGAAGGATTA 59.293 43.478 0.00 0.00 0.00 1.75
4378 5213 2.503356 AGCGATCAGACTTGGAAGGATT 59.497 45.455 0.00 0.00 0.00 3.01
4379 5214 2.114616 AGCGATCAGACTTGGAAGGAT 58.885 47.619 0.00 0.00 0.00 3.24
4380 5215 1.205655 CAGCGATCAGACTTGGAAGGA 59.794 52.381 0.00 0.00 0.00 3.36
4381 5216 1.649664 CAGCGATCAGACTTGGAAGG 58.350 55.000 0.00 0.00 0.00 3.46
4382 5217 1.649664 CCAGCGATCAGACTTGGAAG 58.350 55.000 0.00 0.00 0.00 3.46
4383 5218 0.250234 CCCAGCGATCAGACTTGGAA 59.750 55.000 0.00 0.00 0.00 3.53
4384 5219 0.614697 TCCCAGCGATCAGACTTGGA 60.615 55.000 0.00 0.00 0.00 3.53
4385 5220 0.460987 GTCCCAGCGATCAGACTTGG 60.461 60.000 0.00 0.00 0.00 3.61
4386 5221 0.247460 TGTCCCAGCGATCAGACTTG 59.753 55.000 0.00 0.00 0.00 3.16
4387 5222 1.137872 GATGTCCCAGCGATCAGACTT 59.862 52.381 0.00 0.00 0.00 3.01
4388 5223 0.749649 GATGTCCCAGCGATCAGACT 59.250 55.000 0.00 0.00 0.00 3.24
4469 5344 6.779860 AGTGGTGGATTTCAATAACTACTGT 58.220 36.000 4.13 0.00 32.21 3.55
4649 5525 4.886579 TGACCATCTGACCATTGATATCG 58.113 43.478 0.00 0.00 0.00 2.92
4809 5685 6.072618 GGACGCTAAGTAAGATAGCTATCACA 60.073 42.308 30.52 17.36 42.84 3.58
4967 5843 5.468746 GCCAATAGTCGTATGCTAATGGAAA 59.531 40.000 17.64 0.00 40.28 3.13


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

AutoCloner maintained by Alex Coulton.