Multiple sequence alignment - TraesCS3A01G186200

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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 TraesCS3A01G186200 chr3A 100.000 5324 0 0 1 5324 219802167 219796844 0.000000e+00 9832.0
1 TraesCS3A01G186200 chr3A 96.000 50 2 0 3620 3669 219798455 219798406 1.230000e-11 82.4
2 TraesCS3A01G186200 chr3A 96.000 50 2 0 3713 3762 219798548 219798499 1.230000e-11 82.4
3 TraesCS3A01G186200 chr3B 96.306 3790 81 15 203 3963 256788006 256784247 0.000000e+00 6168.0
4 TraesCS3A01G186200 chr3B 93.878 1372 36 20 3977 5324 256784268 256782921 0.000000e+00 2025.0
5 TraesCS3A01G186200 chr3B 92.929 99 6 1 59 156 256788105 256788007 5.560000e-30 143.0
6 TraesCS3A01G186200 chr3B 98.000 50 1 0 3620 3669 256784494 256784445 2.640000e-13 87.9
7 TraesCS3A01G186200 chr3B 94.000 50 3 0 3713 3762 256784587 256784538 5.720000e-10 76.8
8 TraesCS3A01G186200 chr3D 96.768 2228 44 7 1383 3607 178535687 178533485 0.000000e+00 3690.0
9 TraesCS3A01G186200 chr3D 92.308 1469 62 31 3894 5324 178533297 178531842 0.000000e+00 2039.0
10 TraesCS3A01G186200 chr3D 94.857 1225 31 7 190 1386 178537901 178536681 0.000000e+00 1884.0
11 TraesCS3A01G186200 chr3D 92.857 168 9 1 3639 3806 178533487 178533323 1.920000e-59 241.0
12 TraesCS3A01G186200 chr3D 100.000 31 0 0 3732 3762 178533487 178533457 2.070000e-04 58.4
13 TraesCS3A01G186200 chr1B 91.586 2484 170 11 1240 3703 622187222 622184758 0.000000e+00 3393.0
14 TraesCS3A01G186200 chr1B 85.631 2241 270 37 1391 3618 585882356 585884557 0.000000e+00 2307.0
15 TraesCS3A01G186200 chr1B 87.543 875 93 10 3765 4628 622184815 622183946 0.000000e+00 998.0
16 TraesCS3A01G186200 chr1B 86.120 317 33 9 948 1254 622187552 622187237 1.110000e-86 331.0
17 TraesCS3A01G186200 chr1B 85.085 295 30 8 4108 4391 585884753 585885044 6.750000e-74 289.0
18 TraesCS3A01G186200 chr1A 91.523 2430 160 13 1281 3692 547255037 547257438 0.000000e+00 3304.0
19 TraesCS3A01G186200 chr1A 86.900 2000 209 34 1627 3618 532103565 532105519 0.000000e+00 2193.0
20 TraesCS3A01G186200 chr1A 87.788 868 83 16 3762 4617 547257389 547258245 0.000000e+00 994.0
21 TraesCS3A01G186200 chr1A 86.751 317 31 8 948 1254 547254493 547254808 5.110000e-90 342.0
22 TraesCS3A01G186200 chr1A 84.642 293 35 5 4108 4391 532105705 532105996 3.140000e-72 283.0
23 TraesCS3A01G186200 chr1A 78.169 284 48 13 867 1144 532102292 532102567 9.170000e-38 169.0
24 TraesCS3A01G186200 chr1D 91.089 2480 164 18 1240 3693 452341963 452344411 0.000000e+00 3302.0
25 TraesCS3A01G186200 chr1D 85.695 2251 262 40 1391 3618 433516610 433518823 0.000000e+00 2318.0
26 TraesCS3A01G186200 chr1D 88.856 673 55 10 3963 4626 452344727 452345388 0.000000e+00 809.0
27 TraesCS3A01G186200 chr1D 91.589 214 18 0 948 1161 452341601 452341814 4.030000e-76 296.0
28 TraesCS3A01G186200 chr1D 84.932 292 36 3 4108 4391 433519198 433519489 6.750000e-74 289.0
29 TraesCS3A01G186200 chr5B 89.701 602 56 3 1240 1835 239395954 239395353 0.000000e+00 763.0
30 TraesCS3A01G186200 chr5B 85.804 317 34 9 948 1254 239396286 239395971 5.140000e-85 326.0
31 TraesCS3A01G186200 chr2B 88.812 581 58 4 1240 1813 184124800 184124220 0.000000e+00 706.0
32 TraesCS3A01G186200 chr2B 84.259 216 23 9 1049 1254 184125033 184124819 3.250000e-47 200.0
33 TraesCS3A01G186200 chr2A 83.596 317 36 12 953 1254 203826104 203825789 3.140000e-72 283.0
34 TraesCS3A01G186200 chr4B 94.595 37 2 0 454 490 413829890 413829926 2.070000e-04 58.4
35 TraesCS3A01G186200 chr4D 100.000 29 0 0 462 490 335773451 335773479 3.000000e-03 54.7


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 TraesCS3A01G186200 chr3A 219796844 219802167 5323 True 3332.266667 9832 97.333333 1 5324 3 chr3A.!!$R1 5323
1 TraesCS3A01G186200 chr3B 256782921 256788105 5184 True 1700.140000 6168 95.022600 59 5324 5 chr3B.!!$R1 5265
2 TraesCS3A01G186200 chr3D 178531842 178537901 6059 True 1582.480000 3690 95.358000 190 5324 5 chr3D.!!$R1 5134
3 TraesCS3A01G186200 chr1B 622183946 622187552 3606 True 1574.000000 3393 88.416333 948 4628 3 chr1B.!!$R1 3680
4 TraesCS3A01G186200 chr1B 585882356 585885044 2688 False 1298.000000 2307 85.358000 1391 4391 2 chr1B.!!$F1 3000
5 TraesCS3A01G186200 chr1A 547254493 547258245 3752 False 1546.666667 3304 88.687333 948 4617 3 chr1A.!!$F2 3669
6 TraesCS3A01G186200 chr1A 532102292 532105996 3704 False 881.666667 2193 83.237000 867 4391 3 chr1A.!!$F1 3524
7 TraesCS3A01G186200 chr1D 452341601 452345388 3787 False 1469.000000 3302 90.511333 948 4626 3 chr1D.!!$F2 3678
8 TraesCS3A01G186200 chr1D 433516610 433519489 2879 False 1303.500000 2318 85.313500 1391 4391 2 chr1D.!!$F1 3000
9 TraesCS3A01G186200 chr5B 239395353 239396286 933 True 544.500000 763 87.752500 948 1835 2 chr5B.!!$R1 887
10 TraesCS3A01G186200 chr2B 184124220 184125033 813 True 453.000000 706 86.535500 1049 1813 2 chr2B.!!$R1 764

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
55 56 0.318699 TCACAGTCGAAACAGCCTCG 60.319 55.000 0.00 0.00 37.66 4.63 F
56 57 0.597637 CACAGTCGAAACAGCCTCGT 60.598 55.000 0.00 0.00 37.56 4.18 F
57 58 0.956633 ACAGTCGAAACAGCCTCGTA 59.043 50.000 0.00 0.00 37.56 3.43 F
247 250 1.007336 CGACCCGATGCGGCTATAAC 61.007 60.000 0.00 0.00 46.86 1.89 F
280 283 1.825191 CTACCGCGGTGCCCTAGTA 60.825 63.158 40.02 17.17 0.00 1.82 F
2114 3927 2.439507 TGAAATAGATCTCCCAGGTGCC 59.560 50.000 0.00 0.00 0.00 5.01 F
2798 4611 2.036089 CCTGCGGAGGGTAGAAATCTAC 59.964 54.545 16.49 11.35 46.09 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 3823 1.066929 GCCAATTCCACGCTTTCCAAT 60.067 47.619 0.00 0.0 0.00 3.16 R
2021 3834 1.826720 GCAGGAGATTTGCCAATTCCA 59.173 47.619 11.58 0.0 35.54 3.53 R
2057 3870 0.961753 CCTTCAAACCAGGCACCTTC 59.038 55.000 0.00 0.0 0.00 3.46 R
2114 3927 0.031994 CGCAAACCTCCCCAACTTTG 59.968 55.000 0.00 0.0 0.00 2.77 R
2292 4105 5.355350 CCCCAAGTGTCTCAATATCTTTCAC 59.645 44.000 0.00 0.0 0.00 3.18 R
3701 5532 0.965014 GATAACACAAAACGCGCGTG 59.035 50.000 38.44 26.3 36.70 5.34 R
4757 6858 1.196808 CACAAGACACACCGTTATGCC 59.803 52.381 0.00 0.0 0.00 4.40 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
26 27 9.845740 AAGTATTGTAAATATGGCAGTACATGA 57.154 29.630 0.00 0.00 30.85 3.07
27 28 9.273016 AGTATTGTAAATATGGCAGTACATGAC 57.727 33.333 0.00 0.00 37.50 3.06
36 37 4.905429 TGGCAGTACATGACAAACATAGT 58.095 39.130 0.00 0.00 46.85 2.12
37 38 4.935205 TGGCAGTACATGACAAACATAGTC 59.065 41.667 0.00 0.00 46.85 2.59
38 39 5.512232 TGGCAGTACATGACAAACATAGTCA 60.512 40.000 0.00 0.00 46.85 3.41
39 40 7.509400 TGGCAGTACATGACAAACATAGTCAC 61.509 42.308 0.00 0.00 46.85 3.67
40 41 9.783451 TGGCAGTACATGACAAACATAGTCACA 62.783 40.741 0.00 0.00 46.85 3.58
45 46 4.577834 TGACAAACATAGTCACAGTCGA 57.422 40.909 0.00 0.00 40.80 4.20
46 47 4.939271 TGACAAACATAGTCACAGTCGAA 58.061 39.130 0.00 0.00 40.80 3.71
47 48 5.353111 TGACAAACATAGTCACAGTCGAAA 58.647 37.500 0.00 0.00 40.80 3.46
48 49 5.233476 TGACAAACATAGTCACAGTCGAAAC 59.767 40.000 0.00 0.00 40.80 2.78
49 50 5.113383 ACAAACATAGTCACAGTCGAAACA 58.887 37.500 0.00 0.00 0.00 2.83
50 51 5.234329 ACAAACATAGTCACAGTCGAAACAG 59.766 40.000 0.00 0.00 0.00 3.16
51 52 3.318017 ACATAGTCACAGTCGAAACAGC 58.682 45.455 0.00 0.00 0.00 4.40
52 53 2.433868 TAGTCACAGTCGAAACAGCC 57.566 50.000 0.00 0.00 0.00 4.85
53 54 0.753262 AGTCACAGTCGAAACAGCCT 59.247 50.000 0.00 0.00 0.00 4.58
54 55 1.140816 GTCACAGTCGAAACAGCCTC 58.859 55.000 0.00 0.00 0.00 4.70
55 56 0.318699 TCACAGTCGAAACAGCCTCG 60.319 55.000 0.00 0.00 37.66 4.63
56 57 0.597637 CACAGTCGAAACAGCCTCGT 60.598 55.000 0.00 0.00 37.56 4.18
57 58 0.956633 ACAGTCGAAACAGCCTCGTA 59.043 50.000 0.00 0.00 37.56 3.43
58 59 1.068472 ACAGTCGAAACAGCCTCGTAG 60.068 52.381 0.00 0.00 37.56 3.51
59 60 1.199327 CAGTCGAAACAGCCTCGTAGA 59.801 52.381 0.00 0.00 37.56 2.59
60 61 2.093106 AGTCGAAACAGCCTCGTAGAT 58.907 47.619 0.00 0.00 37.56 1.98
61 62 2.492484 AGTCGAAACAGCCTCGTAGATT 59.508 45.455 0.00 0.00 37.56 2.40
62 63 3.056749 AGTCGAAACAGCCTCGTAGATTT 60.057 43.478 0.00 0.00 37.56 2.17
82 83 4.824166 CAATGCCACGCTGCTCGC 62.824 66.667 0.00 0.00 43.23 5.03
156 157 4.427661 GCTGCTGCCGAGTCGAGT 62.428 66.667 15.64 0.00 0.00 4.18
157 158 2.202544 CTGCTGCCGAGTCGAGTC 60.203 66.667 15.64 10.37 0.00 3.36
158 159 4.103103 TGCTGCCGAGTCGAGTCG 62.103 66.667 30.99 30.99 39.77 4.18
159 160 3.800863 GCTGCCGAGTCGAGTCGA 61.801 66.667 37.30 21.21 42.85 4.20
160 161 2.401592 CTGCCGAGTCGAGTCGAG 59.598 66.667 37.30 27.90 42.85 4.04
161 162 3.726631 CTGCCGAGTCGAGTCGAGC 62.727 68.421 37.30 34.03 42.85 5.03
162 163 4.539881 GCCGAGTCGAGTCGAGCC 62.540 72.222 37.30 22.98 42.85 4.70
163 164 4.225340 CCGAGTCGAGTCGAGCCG 62.225 72.222 37.30 20.44 42.85 5.52
164 165 3.186730 CGAGTCGAGTCGAGCCGA 61.187 66.667 33.61 5.13 42.85 5.54
165 166 2.526993 CGAGTCGAGTCGAGCCGAT 61.527 63.158 33.61 7.13 42.85 4.18
166 167 1.277440 GAGTCGAGTCGAGCCGATC 59.723 63.158 17.12 2.69 38.42 3.69
167 168 2.108344 GAGTCGAGTCGAGCCGATCC 62.108 65.000 17.12 1.89 38.42 3.36
168 169 2.181521 GTCGAGTCGAGCCGATCCT 61.182 63.158 17.12 0.00 38.42 3.24
169 170 1.888172 TCGAGTCGAGCCGATCCTC 60.888 63.158 12.09 3.63 38.42 3.71
170 171 2.180862 CGAGTCGAGCCGATCCTCA 61.181 63.158 6.73 0.00 38.42 3.86
171 172 1.511318 CGAGTCGAGCCGATCCTCAT 61.511 60.000 6.73 0.00 38.42 2.90
172 173 1.524848 GAGTCGAGCCGATCCTCATA 58.475 55.000 0.67 0.00 38.42 2.15
173 174 2.088423 GAGTCGAGCCGATCCTCATAT 58.912 52.381 0.67 0.00 38.42 1.78
174 175 1.815613 AGTCGAGCCGATCCTCATATG 59.184 52.381 0.00 0.00 38.42 1.78
175 176 1.542030 GTCGAGCCGATCCTCATATGT 59.458 52.381 1.90 0.00 38.42 2.29
176 177 2.029828 GTCGAGCCGATCCTCATATGTT 60.030 50.000 1.90 0.00 38.42 2.71
177 178 2.029918 TCGAGCCGATCCTCATATGTTG 60.030 50.000 1.90 0.00 0.00 3.33
178 179 2.693069 GAGCCGATCCTCATATGTTGG 58.307 52.381 1.90 6.87 0.00 3.77
179 180 1.160137 GCCGATCCTCATATGTTGGC 58.840 55.000 1.90 4.65 0.00 4.52
180 181 1.271054 GCCGATCCTCATATGTTGGCT 60.271 52.381 12.89 4.81 38.22 4.75
181 182 2.693069 CCGATCCTCATATGTTGGCTC 58.307 52.381 1.90 6.89 0.00 4.70
182 183 2.613977 CCGATCCTCATATGTTGGCTCC 60.614 54.545 1.90 0.00 0.00 4.70
183 184 2.613977 CGATCCTCATATGTTGGCTCCC 60.614 54.545 1.90 0.00 0.00 4.30
184 185 1.891933 TCCTCATATGTTGGCTCCCA 58.108 50.000 1.90 0.00 0.00 4.37
185 186 1.770658 TCCTCATATGTTGGCTCCCAG 59.229 52.381 1.90 0.00 33.81 4.45
186 187 1.602311 CTCATATGTTGGCTCCCAGC 58.398 55.000 1.90 0.00 41.46 4.85
247 250 1.007336 CGACCCGATGCGGCTATAAC 61.007 60.000 0.00 0.00 46.86 1.89
280 283 1.825191 CTACCGCGGTGCCCTAGTA 60.825 63.158 40.02 17.17 0.00 1.82
787 814 8.231837 TGTAACTGCTAATTCGGTTCATTTTAC 58.768 33.333 0.00 0.00 36.91 2.01
826 853 6.874134 TCTGAAATCTGCTTGACCTAACTAAC 59.126 38.462 0.00 0.00 0.00 2.34
1144 1176 4.073293 CACTTCAGTTCTGGGTAAGTGT 57.927 45.455 17.23 0.00 41.21 3.55
1237 1305 5.487433 TGTGGACACTTTACTACCATGATG 58.513 41.667 3.91 0.00 33.19 3.07
1297 1404 7.354751 AGCTCTTATTTTAATCTCCTCGTCT 57.645 36.000 0.00 0.00 0.00 4.18
1377 1658 9.814899 ATGATGTGTCAATCAAAACAGTTTTAA 57.185 25.926 11.02 0.00 39.90 1.52
1831 3627 9.092876 GTTGAGTAATTTATTGGTCTCTCTCTG 57.907 37.037 0.00 0.00 0.00 3.35
1859 3655 6.841229 TCTCTCTCTCTCTCTCTCTCTATGTT 59.159 42.308 0.00 0.00 0.00 2.71
1870 3666 5.013079 TCTCTCTCTATGTTTTGCCTTGGAA 59.987 40.000 0.00 0.00 0.00 3.53
2003 3799 3.181490 ACGCGCTAGATGAAGTTACATCA 60.181 43.478 5.73 0.00 46.11 3.07
2010 3823 8.023706 CGCTAGATGAAGTTACATCAGCTTATA 58.976 37.037 13.36 0.00 46.11 0.98
2057 3870 4.855596 GCGCCAAGCTTGAAAGAG 57.144 55.556 28.05 13.62 44.04 2.85
2114 3927 2.439507 TGAAATAGATCTCCCAGGTGCC 59.560 50.000 0.00 0.00 0.00 5.01
2292 4105 5.860182 AGCAATGAATTTGTTGAGAATGTCG 59.140 36.000 7.65 0.00 37.65 4.35
2465 4278 4.103785 AGGATGGATGGTGTGGAATCTAAG 59.896 45.833 0.00 0.00 0.00 2.18
2798 4611 2.036089 CCTGCGGAGGGTAGAAATCTAC 59.964 54.545 16.49 11.35 46.09 2.59
3634 5465 9.762062 CTTATACTACATGTGCTATCGTTCTAG 57.238 37.037 9.11 0.00 0.00 2.43
3701 5532 5.009210 TGGCACAGTTACTATGTTTTCAACC 59.991 40.000 0.00 0.00 0.00 3.77
3724 5555 1.377505 GCGCGTTTTGTGTTATCGTTG 59.622 47.619 8.43 0.00 0.00 4.10
3778 5609 4.580580 AGTTAGGCTTTTTCACTTGGACTG 59.419 41.667 0.00 0.00 0.00 3.51
4391 6489 3.206150 AGTTGCAGCCTTATTGGTATCG 58.794 45.455 0.00 0.00 38.35 2.92
4453 6551 3.936372 TGGTTCTTTAGTGTCTCGGAG 57.064 47.619 0.00 0.00 0.00 4.63
4535 6635 2.123589 ACCGGGATATGTGGATTGTGA 58.876 47.619 6.32 0.00 0.00 3.58
4583 6683 6.100279 GGCTTATCATATCCAGATCCATGGTA 59.900 42.308 12.58 0.00 41.43 3.25
4599 6699 5.705441 TCCATGGTAAAATGTCTTGTCTGAC 59.295 40.000 12.58 0.00 37.47 3.51
4605 6705 7.390440 TGGTAAAATGTCTTGTCTGACCATTAG 59.610 37.037 5.17 0.00 36.21 1.73
4619 6719 5.491070 TGACCATTAGAGAATGTTCCTGTG 58.509 41.667 0.00 0.00 40.87 3.66
4630 6730 2.422597 TGTTCCTGTGGAAATACTGCG 58.577 47.619 0.12 0.00 43.86 5.18
4662 6763 9.897744 CAAACTCAGTTGCTCTTAAATTTCATA 57.102 29.630 0.00 0.00 0.00 2.15
4685 6786 2.031120 CACTGCAGTCCTTTTTGGGAA 58.969 47.619 18.64 0.00 37.10 3.97
4753 6854 1.604438 CCGGTTGATCTGTCGTGTTCA 60.604 52.381 0.00 0.00 0.00 3.18
4757 6858 1.349234 TGATCTGTCGTGTTCATGCG 58.651 50.000 0.00 0.00 0.00 4.73
4840 6941 4.727507 TGGCTTAAAGACAAAAAGCACA 57.272 36.364 8.38 2.04 45.86 4.57
4841 6942 4.429108 TGGCTTAAAGACAAAAAGCACAC 58.571 39.130 8.38 0.00 45.86 3.82
4843 6944 4.441495 GGCTTAAAGACAAAAAGCACACCT 60.441 41.667 8.38 0.00 45.86 4.00
4844 6945 4.504097 GCTTAAAGACAAAAAGCACACCTG 59.496 41.667 1.62 0.00 43.98 4.00
4845 6946 5.650543 CTTAAAGACAAAAAGCACACCTGT 58.349 37.500 0.00 0.00 0.00 4.00
4885 6990 4.017126 GAGCCAAAGTTAAGCCTAACCAT 58.983 43.478 1.48 0.00 38.59 3.55
4982 7116 6.679327 ATTTTAGCGACTGTTTTATCTCCC 57.321 37.500 0.00 0.00 0.00 4.30
5072 7206 1.000731 ACATGGGCATCAAACCAAACG 59.999 47.619 0.00 0.00 40.73 3.60
5074 7208 1.403814 TGGGCATCAAACCAAACGAA 58.596 45.000 0.00 0.00 32.89 3.85
5129 7263 6.515272 TTCCAAGAAAATAAGAGATGGCAC 57.485 37.500 0.00 0.00 0.00 5.01
5179 7319 6.334102 ACGAGAAGTCATGAATACTATCCC 57.666 41.667 0.00 0.00 0.00 3.85
5191 7331 5.310331 TGAATACTATCCCCAATGCTGATCA 59.690 40.000 0.00 0.00 0.00 2.92
5192 7332 6.012245 TGAATACTATCCCCAATGCTGATCAT 60.012 38.462 0.00 0.00 36.87 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.845740 TCATGTACTGCCATATTTACAATACTT 57.154 29.630 0.00 0.00 0.00 2.24
2 3 9.051679 TGTCATGTACTGCCATATTTACAATAC 57.948 33.333 0.00 0.00 0.00 1.89
3 4 9.620259 TTGTCATGTACTGCCATATTTACAATA 57.380 29.630 0.00 0.00 0.00 1.90
4 5 8.518430 TTGTCATGTACTGCCATATTTACAAT 57.482 30.769 0.00 0.00 0.00 2.71
6 7 7.391833 TGTTTGTCATGTACTGCCATATTTACA 59.608 33.333 0.00 0.00 0.00 2.41
7 8 7.757526 TGTTTGTCATGTACTGCCATATTTAC 58.242 34.615 0.00 0.00 0.00 2.01
8 9 7.929941 TGTTTGTCATGTACTGCCATATTTA 57.070 32.000 0.00 0.00 0.00 1.40
9 10 6.832520 TGTTTGTCATGTACTGCCATATTT 57.167 33.333 0.00 0.00 0.00 1.40
10 11 7.775093 ACTATGTTTGTCATGTACTGCCATATT 59.225 33.333 0.00 0.00 37.91 1.28
11 12 7.282585 ACTATGTTTGTCATGTACTGCCATAT 58.717 34.615 0.00 0.00 37.91 1.78
12 13 6.649155 ACTATGTTTGTCATGTACTGCCATA 58.351 36.000 0.00 0.00 37.91 2.74
13 14 5.500234 ACTATGTTTGTCATGTACTGCCAT 58.500 37.500 0.00 0.00 37.91 4.40
14 15 4.905429 ACTATGTTTGTCATGTACTGCCA 58.095 39.130 0.00 0.00 37.91 4.92
15 16 4.935205 TGACTATGTTTGTCATGTACTGCC 59.065 41.667 0.00 0.00 39.23 4.85
16 17 5.408299 TGTGACTATGTTTGTCATGTACTGC 59.592 40.000 0.00 0.00 44.74 4.40
17 18 6.646653 ACTGTGACTATGTTTGTCATGTACTG 59.353 38.462 0.00 0.00 44.74 2.74
18 19 6.759272 ACTGTGACTATGTTTGTCATGTACT 58.241 36.000 0.00 0.00 44.74 2.73
19 20 6.183359 CGACTGTGACTATGTTTGTCATGTAC 60.183 42.308 0.00 0.00 44.74 2.90
20 21 5.861787 CGACTGTGACTATGTTTGTCATGTA 59.138 40.000 0.00 0.00 44.74 2.29
21 22 4.686091 CGACTGTGACTATGTTTGTCATGT 59.314 41.667 0.00 0.00 44.74 3.21
22 23 4.923281 TCGACTGTGACTATGTTTGTCATG 59.077 41.667 0.00 0.00 44.74 3.07
23 24 5.134202 TCGACTGTGACTATGTTTGTCAT 57.866 39.130 0.00 0.00 44.74 3.06
24 25 4.577834 TCGACTGTGACTATGTTTGTCA 57.422 40.909 0.00 0.00 41.48 3.58
25 26 5.233476 TGTTTCGACTGTGACTATGTTTGTC 59.767 40.000 0.00 0.00 35.21 3.18
26 27 5.113383 TGTTTCGACTGTGACTATGTTTGT 58.887 37.500 0.00 0.00 0.00 2.83
27 28 5.651172 TGTTTCGACTGTGACTATGTTTG 57.349 39.130 0.00 0.00 0.00 2.93
28 29 4.211374 GCTGTTTCGACTGTGACTATGTTT 59.789 41.667 0.00 0.00 0.00 2.83
29 30 3.741344 GCTGTTTCGACTGTGACTATGTT 59.259 43.478 0.00 0.00 0.00 2.71
30 31 3.318017 GCTGTTTCGACTGTGACTATGT 58.682 45.455 0.00 0.00 0.00 2.29
31 32 2.668457 GGCTGTTTCGACTGTGACTATG 59.332 50.000 0.00 0.00 0.00 2.23
32 33 2.563179 AGGCTGTTTCGACTGTGACTAT 59.437 45.455 0.00 0.00 0.00 2.12
33 34 1.961394 AGGCTGTTTCGACTGTGACTA 59.039 47.619 0.00 0.00 0.00 2.59
34 35 0.753262 AGGCTGTTTCGACTGTGACT 59.247 50.000 0.00 0.00 0.00 3.41
35 36 1.140816 GAGGCTGTTTCGACTGTGAC 58.859 55.000 0.00 0.00 0.00 3.67
36 37 0.318699 CGAGGCTGTTTCGACTGTGA 60.319 55.000 0.00 0.00 40.36 3.58
37 38 0.597637 ACGAGGCTGTTTCGACTGTG 60.598 55.000 0.00 0.00 40.36 3.66
38 39 0.956633 TACGAGGCTGTTTCGACTGT 59.043 50.000 0.00 0.00 40.36 3.55
39 40 1.199327 TCTACGAGGCTGTTTCGACTG 59.801 52.381 0.00 0.00 40.36 3.51
40 41 1.531423 TCTACGAGGCTGTTTCGACT 58.469 50.000 0.00 0.00 40.36 4.18
41 42 2.563471 ATCTACGAGGCTGTTTCGAC 57.437 50.000 0.00 0.00 40.36 4.20
42 43 3.192844 AGAAATCTACGAGGCTGTTTCGA 59.807 43.478 0.00 0.00 40.36 3.71
43 44 3.512680 AGAAATCTACGAGGCTGTTTCG 58.487 45.455 0.00 0.00 43.38 3.46
44 45 4.495422 TGAGAAATCTACGAGGCTGTTTC 58.505 43.478 0.00 0.00 0.00 2.78
45 46 4.537135 TGAGAAATCTACGAGGCTGTTT 57.463 40.909 0.00 0.00 0.00 2.83
46 47 4.537135 TTGAGAAATCTACGAGGCTGTT 57.463 40.909 0.00 0.00 0.00 3.16
47 48 4.437239 CATTGAGAAATCTACGAGGCTGT 58.563 43.478 0.00 0.00 0.00 4.40
48 49 3.247173 GCATTGAGAAATCTACGAGGCTG 59.753 47.826 0.00 0.00 0.00 4.85
49 50 3.462021 GCATTGAGAAATCTACGAGGCT 58.538 45.455 0.00 0.00 0.00 4.58
50 51 2.545946 GGCATTGAGAAATCTACGAGGC 59.454 50.000 0.00 0.00 0.00 4.70
51 52 3.557595 GTGGCATTGAGAAATCTACGAGG 59.442 47.826 0.00 0.00 0.00 4.63
52 53 3.243877 CGTGGCATTGAGAAATCTACGAG 59.756 47.826 0.00 0.00 0.00 4.18
53 54 3.186909 CGTGGCATTGAGAAATCTACGA 58.813 45.455 0.00 0.00 0.00 3.43
54 55 2.285834 GCGTGGCATTGAGAAATCTACG 60.286 50.000 0.00 0.00 0.00 3.51
55 56 2.939103 AGCGTGGCATTGAGAAATCTAC 59.061 45.455 0.00 0.00 0.00 2.59
56 57 2.938451 CAGCGTGGCATTGAGAAATCTA 59.062 45.455 0.00 0.00 0.00 1.98
57 58 1.741706 CAGCGTGGCATTGAGAAATCT 59.258 47.619 0.00 0.00 0.00 2.40
58 59 1.796617 GCAGCGTGGCATTGAGAAATC 60.797 52.381 0.00 0.00 0.00 2.17
59 60 0.171903 GCAGCGTGGCATTGAGAAAT 59.828 50.000 0.00 0.00 0.00 2.17
60 61 0.890542 AGCAGCGTGGCATTGAGAAA 60.891 50.000 0.00 0.00 35.83 2.52
61 62 1.300971 GAGCAGCGTGGCATTGAGAA 61.301 55.000 0.00 0.00 35.83 2.87
62 63 1.742880 GAGCAGCGTGGCATTGAGA 60.743 57.895 0.00 0.00 35.83 3.27
89 90 2.753043 CTGCCATGTGGACCCAGC 60.753 66.667 2.55 0.00 37.39 4.85
90 91 2.753043 GCTGCCATGTGGACCCAG 60.753 66.667 2.55 2.24 37.39 4.45
139 140 4.427661 ACTCGACTCGGCAGCAGC 62.428 66.667 0.00 0.00 41.10 5.25
156 157 1.911057 ACATATGAGGATCGGCTCGA 58.089 50.000 10.38 0.00 41.13 4.04
157 158 2.332104 CAACATATGAGGATCGGCTCG 58.668 52.381 10.38 0.00 38.61 5.03
158 159 2.693069 CCAACATATGAGGATCGGCTC 58.307 52.381 10.38 0.00 38.61 4.70
159 160 1.271054 GCCAACATATGAGGATCGGCT 60.271 52.381 18.81 0.00 38.61 5.52
160 161 1.160137 GCCAACATATGAGGATCGGC 58.840 55.000 18.81 12.32 38.61 5.54
161 162 2.613977 GGAGCCAACATATGAGGATCGG 60.614 54.545 21.83 10.11 38.68 4.18
162 163 2.613977 GGGAGCCAACATATGAGGATCG 60.614 54.545 21.83 3.20 38.68 3.69
163 164 2.373169 TGGGAGCCAACATATGAGGATC 59.627 50.000 21.09 21.09 37.12 3.36
164 165 2.374504 CTGGGAGCCAACATATGAGGAT 59.625 50.000 18.81 14.21 30.80 3.24
165 166 1.770658 CTGGGAGCCAACATATGAGGA 59.229 52.381 18.81 1.72 30.80 3.71
166 167 1.816961 GCTGGGAGCCAACATATGAGG 60.817 57.143 10.38 11.78 34.48 3.86
167 168 1.602311 GCTGGGAGCCAACATATGAG 58.398 55.000 10.38 1.23 34.48 2.90
168 169 3.806941 GCTGGGAGCCAACATATGA 57.193 52.632 10.38 0.00 34.48 2.15
247 250 3.190874 GCGGTAGACCAGAAGAGATTTG 58.809 50.000 0.00 0.00 35.14 2.32
574 600 0.318762 GCAGACTGTCCCGAGTTCTT 59.681 55.000 3.76 0.00 0.00 2.52
575 601 0.540830 AGCAGACTGTCCCGAGTTCT 60.541 55.000 3.76 0.00 0.00 3.01
685 712 0.883833 CAATGACCACACTTCAGGCC 59.116 55.000 0.00 0.00 0.00 5.19
798 825 4.630644 AGGTCAAGCAGATTTCAGAAGA 57.369 40.909 0.00 0.00 0.00 2.87
1144 1176 9.098355 CGGAGAGAATTATACTTGAACATTGAA 57.902 33.333 0.00 0.00 0.00 2.69
1237 1305 8.922676 TCGACTACAGAAACTATTCAAACATTC 58.077 33.333 0.00 0.00 38.06 2.67
1377 1658 7.771183 ACAAAAATACTGCGATATTTCACCAT 58.229 30.769 5.70 0.00 34.37 3.55
1449 2728 7.751768 TGTGTTGACACCATGTATAAAATCA 57.248 32.000 11.42 0.00 45.88 2.57
1831 3627 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
1859 3655 4.532834 AGAGTTGTTACTTCCAAGGCAAA 58.467 39.130 0.00 0.00 33.84 3.68
1870 3666 5.888982 TCCTGAGGAAAAGAGTTGTTACT 57.111 39.130 0.00 0.00 37.31 2.24
2003 3799 4.150897 TCCACGCTTTCCAATATAAGCT 57.849 40.909 6.42 0.00 43.49 3.74
2010 3823 1.066929 GCCAATTCCACGCTTTCCAAT 60.067 47.619 0.00 0.00 0.00 3.16
2021 3834 1.826720 GCAGGAGATTTGCCAATTCCA 59.173 47.619 11.58 0.00 35.54 3.53
2057 3870 0.961753 CCTTCAAACCAGGCACCTTC 59.038 55.000 0.00 0.00 0.00 3.46
2114 3927 0.031994 CGCAAACCTCCCCAACTTTG 59.968 55.000 0.00 0.00 0.00 2.77
2292 4105 5.355350 CCCCAAGTGTCTCAATATCTTTCAC 59.645 44.000 0.00 0.00 0.00 3.18
3057 4884 5.643777 CACCCTTCACAAATAGGAAGTACAG 59.356 44.000 0.00 0.00 39.04 2.74
3058 4885 5.556915 CACCCTTCACAAATAGGAAGTACA 58.443 41.667 0.00 0.00 39.04 2.90
3062 4889 3.690460 AGCACCCTTCACAAATAGGAAG 58.310 45.455 0.00 0.00 40.11 3.46
3547 5376 7.285401 ACCAACATGAACTTAGAACATGAGTTT 59.715 33.333 21.35 9.44 42.41 2.66
3634 5465 7.905493 GTCTAAGTGAAAAAGCATGCATACTAC 59.095 37.037 21.98 11.24 0.00 2.73
3701 5532 0.965014 GATAACACAAAACGCGCGTG 59.035 50.000 38.44 26.30 36.70 5.34
3724 5555 7.308782 AGTGAAAAAGCATGCATACTACTAC 57.691 36.000 21.98 8.93 0.00 2.73
3778 5609 8.901793 ACTGTGCTACTTTAGTACTATCTAACC 58.098 37.037 2.79 0.00 41.28 2.85
4391 6489 3.568007 TCAGCCATTACAACACCAGTTTC 59.432 43.478 0.00 0.00 35.28 2.78
4453 6551 9.826574 TTACATAACTGATACTGGATAACCAAC 57.173 33.333 0.00 0.00 46.32 3.77
4535 6635 8.755977 AGCCAATTCTCATCTTGATATTTGTTT 58.244 29.630 0.00 0.00 0.00 2.83
4583 6683 7.453393 TCTCTAATGGTCAGACAAGACATTTT 58.547 34.615 2.17 0.00 40.29 1.82
4599 6699 5.102953 TCCACAGGAACATTCTCTAATGG 57.897 43.478 3.41 0.00 45.72 3.16
4605 6705 5.163713 GCAGTATTTCCACAGGAACATTCTC 60.164 44.000 0.00 0.00 41.87 2.87
4619 6719 5.358298 AGTTTGAAACTCGCAGTATTTCC 57.642 39.130 4.45 0.00 37.02 3.13
4662 6763 1.342174 CCAAAAAGGACTGCAGTGCAT 59.658 47.619 35.52 24.52 41.22 3.96
4753 6854 1.366111 GACACACCGTTATGCCGCAT 61.366 55.000 11.38 11.38 0.00 4.73
4757 6858 1.196808 CACAAGACACACCGTTATGCC 59.803 52.381 0.00 0.00 0.00 4.40
4934 7068 3.128242 GGACAAATCAGTCAGCCTTCATG 59.872 47.826 0.00 0.00 40.29 3.07
4982 7116 3.420893 TGAATTGTCCTGTAAAGCTGGG 58.579 45.455 0.00 0.00 36.89 4.45
5030 7164 3.699411 TGCTAAATTTTGCCTTGGCAT 57.301 38.095 19.58 2.55 34.55 4.40
5129 7263 2.434336 TGACAATACCTCGGAAGGATGG 59.566 50.000 0.00 0.00 46.67 3.51
5177 7317 4.226846 ACCTCTATATGATCAGCATTGGGG 59.773 45.833 14.83 14.83 38.44 4.96
5179 7319 6.046290 TGACCTCTATATGATCAGCATTGG 57.954 41.667 0.09 1.95 38.44 3.16
5191 7331 7.445402 GTGTTTGTGCCATTATGACCTCTATAT 59.555 37.037 0.00 0.00 0.00 0.86
5192 7332 6.765989 GTGTTTGTGCCATTATGACCTCTATA 59.234 38.462 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.