Multiple sequence alignment - TraesCS1D01G018400

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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 TraesCS1D01G018400 chr1D 100.000 3603 0 0 1 3603 7950249 7946647 0.000000e+00 6654.0
1 TraesCS1D01G018400 chr1D 85.654 237 26 3 146 379 466304896 466304665 3.590000e-60 243.0
2 TraesCS1D01G018400 chr1D 85.232 237 27 5 146 379 135061809 135062040 1.670000e-58 237.0
3 TraesCS1D01G018400 chr1D 82.427 239 41 1 742 979 42657813 42657575 1.310000e-49 207.0
4 TraesCS1D01G018400 chr1A 92.931 3579 176 32 51 3601 9644950 9641421 0.000000e+00 5136.0
5 TraesCS1D01G018400 chr1B 92.044 3582 201 42 51 3601 10206699 10203171 0.000000e+00 4959.0
6 TraesCS1D01G018400 chr1B 85.897 234 24 3 188 419 132902698 132902472 1.290000e-59 241.0
7 TraesCS1D01G018400 chr3A 85.943 562 56 11 439 995 740265669 740265126 2.410000e-161 579.0
8 TraesCS1D01G018400 chr3B 80.488 410 67 10 581 979 13893699 13893292 5.850000e-78 302.0
9 TraesCS1D01G018400 chr3B 84.783 276 34 3 146 418 13894575 13894305 1.650000e-68 270.0
10 TraesCS1D01G018400 chr7D 84.615 273 34 3 149 418 8126197 8125930 7.670000e-67 265.0
11 TraesCS1D01G018400 chr7D 86.383 235 24 3 148 379 95577924 95578153 2.150000e-62 250.0
12 TraesCS1D01G018400 chr7D 82.845 239 40 1 742 979 459489722 459489960 2.820000e-51 213.0
13 TraesCS1D01G018400 chr7D 82.500 240 39 3 742 979 8125403 8125165 1.310000e-49 207.0
14 TraesCS1D01G018400 chr7D 82.427 239 39 2 742 979 229526996 229526760 4.720000e-49 206.0
15 TraesCS1D01G018400 chr3D 85.714 238 26 3 146 380 550031318 550031086 9.990000e-61 244.0
16 TraesCS1D01G018400 chr4A 84.647 241 28 3 173 411 652215582 652215349 7.780000e-57 231.0
17 TraesCS1D01G018400 chr6B 82.642 265 38 3 146 407 689830319 689830060 1.010000e-55 228.0
18 TraesCS1D01G018400 chr2D 83.264 239 39 1 742 979 409389550 409389788 6.060000e-53 219.0
19 TraesCS1D01G018400 chr2D 82.427 239 41 1 742 979 582684377 582684139 1.310000e-49 207.0
20 TraesCS1D01G018400 chr2D 100.000 28 0 0 1 28 627520769 627520796 7.000000e-03 52.8
21 TraesCS1D01G018400 chr5D 100.000 28 0 0 1 28 344470004 344470031 7.000000e-03 52.8


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 TraesCS1D01G018400 chr1D 7946647 7950249 3602 True 6654 6654 100.0000 1 3603 1 chr1D.!!$R1 3602
1 TraesCS1D01G018400 chr1A 9641421 9644950 3529 True 5136 5136 92.9310 51 3601 1 chr1A.!!$R1 3550
2 TraesCS1D01G018400 chr1B 10203171 10206699 3528 True 4959 4959 92.0440 51 3601 1 chr1B.!!$R1 3550
3 TraesCS1D01G018400 chr3A 740265126 740265669 543 True 579 579 85.9430 439 995 1 chr3A.!!$R1 556
4 TraesCS1D01G018400 chr3B 13893292 13894575 1283 True 286 302 82.6355 146 979 2 chr3B.!!$R1 833
5 TraesCS1D01G018400 chr7D 8125165 8126197 1032 True 236 265 83.5575 149 979 2 chr7D.!!$R2 830

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
40 41 0.181350 CCGAAAGAAGATGGGGGAGG 59.819 60.0 0.0 0.0 0.00 4.30 F
41 42 0.181350 CGAAAGAAGATGGGGGAGGG 59.819 60.0 0.0 0.0 0.00 4.30 F
143 147 0.552848 CCTCCTCCAGCTCTCTCTCT 59.447 60.0 0.0 0.0 0.00 3.10 F
695 1365 0.811281 GGCCATCTGTTTAGGTGTGC 59.189 55.0 0.0 0.0 32.96 4.57 F
1493 2170 0.889994 TGCCTGATGTTTGATGCACC 59.110 50.0 0.0 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1805 1.159285 CAAGATGTGAGCTTTGCGGA 58.841 50.000 0.0 0.0 0.00 5.54 R
1969 2664 2.027745 AGACGGCAAACTCACATCTGAT 60.028 45.455 0.0 0.0 0.00 2.90 R
2062 2757 1.728971 CTCTTCAATGGCACGTCTGAC 59.271 52.381 0.0 0.0 0.00 3.51 R
2089 2784 1.746516 GCAGAAGCATCCCCAGAAGAG 60.747 57.143 0.0 0.0 41.58 2.85 R
3040 3739 0.538057 ATATGGGAAGCATGTGGGCG 60.538 55.000 0.0 0.0 39.27 6.13 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
17 18 4.036977 CACGTGTGGGCGTTAGTT 57.963 55.556 7.58 0.00 43.83 2.24
18 19 2.313267 CACGTGTGGGCGTTAGTTT 58.687 52.632 7.58 0.00 43.83 2.66
19 20 0.658897 CACGTGTGGGCGTTAGTTTT 59.341 50.000 7.58 0.00 43.83 2.43
20 21 1.064357 CACGTGTGGGCGTTAGTTTTT 59.936 47.619 7.58 0.00 43.83 1.94
21 22 1.331447 ACGTGTGGGCGTTAGTTTTTC 59.669 47.619 0.00 0.00 43.04 2.29
22 23 1.334329 CGTGTGGGCGTTAGTTTTTCC 60.334 52.381 0.00 0.00 0.00 3.13
23 24 0.945813 TGTGGGCGTTAGTTTTTCCG 59.054 50.000 0.00 0.00 0.00 4.30
24 25 1.228533 GTGGGCGTTAGTTTTTCCGA 58.771 50.000 0.00 0.00 0.00 4.55
25 26 1.603326 GTGGGCGTTAGTTTTTCCGAA 59.397 47.619 0.00 0.00 0.00 4.30
26 27 2.033174 GTGGGCGTTAGTTTTTCCGAAA 59.967 45.455 0.00 0.00 0.00 3.46
27 28 2.291190 TGGGCGTTAGTTTTTCCGAAAG 59.709 45.455 0.00 0.00 0.00 2.62
28 29 2.549329 GGGCGTTAGTTTTTCCGAAAGA 59.451 45.455 0.00 0.00 0.00 2.52
29 30 3.003585 GGGCGTTAGTTTTTCCGAAAGAA 59.996 43.478 0.00 0.00 0.00 2.52
30 31 4.216731 GGCGTTAGTTTTTCCGAAAGAAG 58.783 43.478 0.00 0.00 35.40 2.85
31 32 4.024641 GGCGTTAGTTTTTCCGAAAGAAGA 60.025 41.667 0.00 0.00 35.40 2.87
32 33 5.334646 GGCGTTAGTTTTTCCGAAAGAAGAT 60.335 40.000 0.00 0.00 35.40 2.40
33 34 5.564127 GCGTTAGTTTTTCCGAAAGAAGATG 59.436 40.000 0.00 0.00 35.40 2.90
34 35 6.077838 CGTTAGTTTTTCCGAAAGAAGATGG 58.922 40.000 0.00 0.00 35.40 3.51
35 36 6.379386 GTTAGTTTTTCCGAAAGAAGATGGG 58.621 40.000 0.00 0.00 35.40 4.00
36 37 3.826729 AGTTTTTCCGAAAGAAGATGGGG 59.173 43.478 0.00 0.00 35.40 4.96
37 38 2.507407 TTTCCGAAAGAAGATGGGGG 57.493 50.000 0.00 0.00 35.40 5.40
38 39 1.663911 TTCCGAAAGAAGATGGGGGA 58.336 50.000 0.00 0.00 0.00 4.81
39 40 1.204146 TCCGAAAGAAGATGGGGGAG 58.796 55.000 0.00 0.00 0.00 4.30
40 41 0.181350 CCGAAAGAAGATGGGGGAGG 59.819 60.000 0.00 0.00 0.00 4.30
41 42 0.181350 CGAAAGAAGATGGGGGAGGG 59.819 60.000 0.00 0.00 0.00 4.30
42 43 0.553333 GAAAGAAGATGGGGGAGGGG 59.447 60.000 0.00 0.00 0.00 4.79
43 44 0.926220 AAAGAAGATGGGGGAGGGGG 60.926 60.000 0.00 0.00 0.00 5.40
44 45 2.044620 GAAGATGGGGGAGGGGGT 59.955 66.667 0.00 0.00 0.00 4.95
45 46 1.622752 GAAGATGGGGGAGGGGGTT 60.623 63.158 0.00 0.00 0.00 4.11
46 47 1.151131 AAGATGGGGGAGGGGGTTT 60.151 57.895 0.00 0.00 0.00 3.27
47 48 0.784154 AAGATGGGGGAGGGGGTTTT 60.784 55.000 0.00 0.00 0.00 2.43
48 49 1.001631 GATGGGGGAGGGGGTTTTG 59.998 63.158 0.00 0.00 0.00 2.44
49 50 2.529930 GATGGGGGAGGGGGTTTTGG 62.530 65.000 0.00 0.00 0.00 3.28
143 147 0.552848 CCTCCTCCAGCTCTCTCTCT 59.447 60.000 0.00 0.00 0.00 3.10
144 148 1.477558 CCTCCTCCAGCTCTCTCTCTC 60.478 61.905 0.00 0.00 0.00 3.20
268 279 0.907230 GCCCCTGGTGAGTCTCTCTT 60.907 60.000 0.65 0.00 0.00 2.85
280 291 4.200092 GAGTCTCTCTTTCCCTCTCTCTC 58.800 52.174 0.00 0.00 0.00 3.20
281 292 3.852578 AGTCTCTCTTTCCCTCTCTCTCT 59.147 47.826 0.00 0.00 0.00 3.10
282 293 4.080299 AGTCTCTCTTTCCCTCTCTCTCTC 60.080 50.000 0.00 0.00 0.00 3.20
283 294 4.080299 GTCTCTCTTTCCCTCTCTCTCTCT 60.080 50.000 0.00 0.00 0.00 3.10
326 337 3.603671 GGCGGCGACCTAGGGTAG 61.604 72.222 12.98 4.85 35.25 3.18
457 841 1.134461 CCCAGTCTCAAGCCTGATGAG 60.134 57.143 0.00 0.00 44.53 2.90
488 872 3.838244 TCAGTTGAAACTAGCACAGGT 57.162 42.857 0.00 0.00 37.08 4.00
493 877 4.335594 AGTTGAAACTAGCACAGGTGAAAC 59.664 41.667 3.10 0.00 37.52 2.78
531 915 9.071276 ACATATAACAAAGCCAGATTTAGGATG 57.929 33.333 0.00 0.00 0.00 3.51
603 1264 2.009774 CAATCCTTTGGGACTACAGCG 58.990 52.381 0.00 0.00 45.43 5.18
641 1302 3.971245 TGGGGATGTTATGTTTTTGCC 57.029 42.857 0.00 0.00 0.00 4.52
695 1365 0.811281 GGCCATCTGTTTAGGTGTGC 59.189 55.000 0.00 0.00 32.96 4.57
708 1378 2.783135 AGGTGTGCATCATCGAAAACT 58.217 42.857 0.00 0.00 31.45 2.66
767 1437 4.284490 TCATCCAACATCTAGCCCAGTATC 59.716 45.833 0.00 0.00 0.00 2.24
772 1442 2.297597 ACATCTAGCCCAGTATCGCTTC 59.702 50.000 0.00 0.00 36.53 3.86
826 1498 4.725790 AAAGTGGAATATTTCTGCCTGC 57.274 40.909 0.00 0.00 0.00 4.85
849 1521 6.158598 GCAATCGCCATATAATTTGGTTGAT 58.841 36.000 0.00 0.00 36.57 2.57
857 1529 9.463443 GCCATATAATTTGGTTGATAGTTTGTC 57.537 33.333 0.00 0.00 36.57 3.18
883 1555 5.554437 TGGTACTGACTTTGTGTAATCCA 57.446 39.130 0.00 0.00 0.00 3.41
885 1557 6.539173 TGGTACTGACTTTGTGTAATCCATT 58.461 36.000 0.00 0.00 0.00 3.16
965 1642 8.807118 TGTTAAAGAGTGATTCAGTGATAGAGT 58.193 33.333 0.00 0.00 0.00 3.24
987 1664 1.136828 AGAACAGGTGGCAGTGGTAA 58.863 50.000 0.00 0.00 0.00 2.85
1084 1761 3.737172 CTGGTTCCGGCGCAAAGG 61.737 66.667 10.83 9.85 0.00 3.11
1128 1805 2.357836 CCAGCTCCATTGGTGCCT 59.642 61.111 22.68 10.10 42.42 4.75
1172 1849 1.221293 GCCAGAGTCAGCATGCTCT 59.779 57.895 19.68 13.48 45.77 4.09
1419 2096 3.843027 AGATTGTCTTGGACCATCAGTCT 59.157 43.478 12.17 4.72 45.54 3.24
1493 2170 0.889994 TGCCTGATGTTTGATGCACC 59.110 50.000 0.00 0.00 0.00 5.01
1512 2189 1.671850 CCTGCGTTCAGTTGGACGTAT 60.672 52.381 13.91 0.00 38.66 3.06
1562 2239 7.936847 TGAGACTTCTTTTTAGCAACCTGAATA 59.063 33.333 0.00 0.00 0.00 1.75
1577 2254 6.747414 ACCTGAATATTAGGTGTGCTATCA 57.253 37.500 12.90 0.00 46.48 2.15
1578 2255 7.136822 ACCTGAATATTAGGTGTGCTATCAA 57.863 36.000 12.90 0.00 46.48 2.57
1579 2256 7.573710 ACCTGAATATTAGGTGTGCTATCAAA 58.426 34.615 12.90 0.00 46.48 2.69
1580 2257 8.220559 ACCTGAATATTAGGTGTGCTATCAAAT 58.779 33.333 12.90 0.00 46.48 2.32
1581 2258 8.725148 CCTGAATATTAGGTGTGCTATCAAATC 58.275 37.037 0.00 0.00 0.00 2.17
1582 2259 9.276590 CTGAATATTAGGTGTGCTATCAAATCA 57.723 33.333 0.00 0.00 0.00 2.57
1650 2345 7.120285 CCTGTAATGGAATATTGTGCTCCTATG 59.880 40.741 0.00 0.00 0.00 2.23
1765 2460 5.063564 GTGTCTTAGGTGCATAACTAACAGC 59.936 44.000 0.00 0.00 0.00 4.40
1804 2499 5.885230 TGTTTCCTTTCAGCATCTATGTG 57.115 39.130 0.00 0.00 0.00 3.21
1969 2664 1.125093 TTCCCGCTCAAAGTCTCCCA 61.125 55.000 0.00 0.00 0.00 4.37
2014 2709 2.750166 TCCAGACTCTGACGATGAAGAC 59.250 50.000 7.69 0.00 32.44 3.01
2062 2757 5.523916 ACTTAATCGCTATGGTGTTAGCAAG 59.476 40.000 4.54 3.03 43.92 4.01
2089 2784 2.669391 CGTGCCATTGAAGAGAAAAGGC 60.669 50.000 0.00 0.00 40.93 4.35
2130 2825 4.393990 TGCTTCTGCTGTAAATGATGACAG 59.606 41.667 3.95 3.95 44.88 3.51
2564 3259 1.152830 AGGGACGTGGGTGCAAATT 59.847 52.632 0.00 0.00 36.00 1.82
2596 3291 5.882000 TGATAGTGATGATGACTTGTTTGGG 59.118 40.000 0.00 0.00 0.00 4.12
2805 3500 3.070446 TCATGGGGATTGTACGTACCATC 59.930 47.826 24.52 24.52 36.63 3.51
2828 3523 3.509442 TGCCCCATTTCTTCATTCTGTT 58.491 40.909 0.00 0.00 0.00 3.16
2836 3531 8.090214 CCCATTTCTTCATTCTGTTATTGTGTT 58.910 33.333 0.00 0.00 0.00 3.32
2872 3567 2.047769 TACCCTGCCCTGGTTTCTTA 57.952 50.000 0.00 0.00 37.31 2.10
2879 3574 2.633967 TGCCCTGGTTTCTTACGTCTTA 59.366 45.455 0.00 0.00 0.00 2.10
2995 3694 2.823628 GCTTCGTAGCTTGAACCGT 58.176 52.632 6.80 0.00 44.27 4.83
3025 3724 4.174411 TCATGTTCGTCTGGTCAAGTAG 57.826 45.455 0.00 0.00 0.00 2.57
3034 3733 5.124457 TCGTCTGGTCAAGTAGGTACATAAC 59.876 44.000 0.00 0.00 0.00 1.89
3040 3739 9.530633 CTGGTCAAGTAGGTACATAACTTTATC 57.469 37.037 0.00 0.00 31.21 1.75
3043 3742 7.168804 GTCAAGTAGGTACATAACTTTATCGCC 59.831 40.741 0.00 0.00 31.21 5.54
3044 3743 6.094193 AGTAGGTACATAACTTTATCGCCC 57.906 41.667 0.00 0.00 0.00 6.13
3046 3745 4.700700 AGGTACATAACTTTATCGCCCAC 58.299 43.478 0.00 0.00 0.00 4.61
3047 3746 4.162698 AGGTACATAACTTTATCGCCCACA 59.837 41.667 0.00 0.00 0.00 4.17
3048 3747 5.061179 GGTACATAACTTTATCGCCCACAT 58.939 41.667 0.00 0.00 0.00 3.21
3049 3748 5.049680 GGTACATAACTTTATCGCCCACATG 60.050 44.000 0.00 0.00 0.00 3.21
3050 3749 3.315191 ACATAACTTTATCGCCCACATGC 59.685 43.478 0.00 0.00 0.00 4.06
3051 3750 2.128771 AACTTTATCGCCCACATGCT 57.871 45.000 0.00 0.00 0.00 3.79
3145 3844 6.899393 TGATATTCTGTCTTTTGTTTGGCT 57.101 33.333 0.00 0.00 0.00 4.75
3154 3853 4.154015 GTCTTTTGTTTGGCTTGTTTTGCT 59.846 37.500 0.00 0.00 0.00 3.91
3247 3946 6.590234 AAAATAAGGAAATCACCTCGCTTT 57.410 33.333 0.00 0.00 39.62 3.51
3279 3978 2.024273 TCTCATAGACTCCCTCCCGTTT 60.024 50.000 0.00 0.00 0.00 3.60
3367 4066 3.445096 CCTACTTTTGAATGAAGGCCCAG 59.555 47.826 0.00 0.00 0.00 4.45
3434 4136 3.568007 TGGGAAGTATGTTGAAACTGCAC 59.432 43.478 0.00 0.00 0.00 4.57
3458 4160 2.936498 GGTTGCTTGCTTCGCTCTTATA 59.064 45.455 0.00 0.00 0.00 0.98
3459 4161 3.001736 GGTTGCTTGCTTCGCTCTTATAG 59.998 47.826 0.00 0.00 0.00 1.31
3480 4182 5.822132 AGAGCCTAACTATCATGCATCTT 57.178 39.130 0.00 0.00 0.00 2.40
3601 4304 5.132043 AGGTACTCTAGCAGTGGATACTT 57.868 43.478 0.00 0.00 36.43 2.24
3602 4305 5.520751 AGGTACTCTAGCAGTGGATACTTT 58.479 41.667 0.00 0.00 36.43 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.334329 GGAAAAACTAACGCCCACACG 60.334 52.381 0.00 0.00 39.50 4.49
3 4 1.334329 CGGAAAAACTAACGCCCACAC 60.334 52.381 0.00 0.00 0.00 3.82
4 5 0.945813 CGGAAAAACTAACGCCCACA 59.054 50.000 0.00 0.00 0.00 4.17
5 6 1.228533 TCGGAAAAACTAACGCCCAC 58.771 50.000 0.00 0.00 0.00 4.61
6 7 1.964552 TTCGGAAAAACTAACGCCCA 58.035 45.000 0.00 0.00 0.00 5.36
7 8 2.549329 TCTTTCGGAAAAACTAACGCCC 59.451 45.455 4.53 0.00 0.00 6.13
8 9 3.883631 TCTTTCGGAAAAACTAACGCC 57.116 42.857 4.53 0.00 0.00 5.68
9 10 5.086888 TCTTCTTTCGGAAAAACTAACGC 57.913 39.130 4.53 0.00 33.07 4.84
10 11 6.077838 CCATCTTCTTTCGGAAAAACTAACG 58.922 40.000 4.53 0.00 33.07 3.18
11 12 6.379386 CCCATCTTCTTTCGGAAAAACTAAC 58.621 40.000 4.53 0.00 33.07 2.34
12 13 5.475564 CCCCATCTTCTTTCGGAAAAACTAA 59.524 40.000 4.53 0.00 33.07 2.24
13 14 5.007682 CCCCATCTTCTTTCGGAAAAACTA 58.992 41.667 4.53 0.00 33.07 2.24
14 15 3.826729 CCCCATCTTCTTTCGGAAAAACT 59.173 43.478 4.53 0.00 33.07 2.66
15 16 3.056821 CCCCCATCTTCTTTCGGAAAAAC 60.057 47.826 4.53 0.00 33.07 2.43
16 17 3.161866 CCCCCATCTTCTTTCGGAAAAA 58.838 45.455 4.53 2.14 33.07 1.94
17 18 2.377193 TCCCCCATCTTCTTTCGGAAAA 59.623 45.455 4.53 0.00 33.07 2.29
18 19 1.989586 TCCCCCATCTTCTTTCGGAAA 59.010 47.619 2.78 2.78 33.07 3.13
19 20 1.559682 CTCCCCCATCTTCTTTCGGAA 59.440 52.381 0.00 0.00 0.00 4.30
20 21 1.204146 CTCCCCCATCTTCTTTCGGA 58.796 55.000 0.00 0.00 0.00 4.55
21 22 0.181350 CCTCCCCCATCTTCTTTCGG 59.819 60.000 0.00 0.00 0.00 4.30
22 23 0.181350 CCCTCCCCCATCTTCTTTCG 59.819 60.000 0.00 0.00 0.00 3.46
23 24 0.553333 CCCCTCCCCCATCTTCTTTC 59.447 60.000 0.00 0.00 0.00 2.62
24 25 0.926220 CCCCCTCCCCCATCTTCTTT 60.926 60.000 0.00 0.00 0.00 2.52
25 26 1.309102 CCCCCTCCCCCATCTTCTT 60.309 63.158 0.00 0.00 0.00 2.52
26 27 2.151586 AACCCCCTCCCCCATCTTCT 62.152 60.000 0.00 0.00 0.00 2.85
27 28 1.221909 AAACCCCCTCCCCCATCTTC 61.222 60.000 0.00 0.00 0.00 2.87
28 29 0.784154 AAAACCCCCTCCCCCATCTT 60.784 55.000 0.00 0.00 0.00 2.40
29 30 1.151131 AAAACCCCCTCCCCCATCT 60.151 57.895 0.00 0.00 0.00 2.90
30 31 1.001631 CAAAACCCCCTCCCCCATC 59.998 63.158 0.00 0.00 0.00 3.51
31 32 2.566903 CCAAAACCCCCTCCCCCAT 61.567 63.158 0.00 0.00 0.00 4.00
32 33 3.197140 CCAAAACCCCCTCCCCCA 61.197 66.667 0.00 0.00 0.00 4.96
33 34 3.197895 ACCAAAACCCCCTCCCCC 61.198 66.667 0.00 0.00 0.00 5.40
34 35 2.119611 CACCAAAACCCCCTCCCC 59.880 66.667 0.00 0.00 0.00 4.81
35 36 2.603473 GCACCAAAACCCCCTCCC 60.603 66.667 0.00 0.00 0.00 4.30
36 37 2.603473 GGCACCAAAACCCCCTCC 60.603 66.667 0.00 0.00 0.00 4.30
49 50 1.814169 GGGATTTCGACGAGGGCAC 60.814 63.158 0.00 0.00 0.00 5.01
143 147 0.180171 CTGGGAGCGAGAGAGAGAGA 59.820 60.000 0.00 0.00 0.00 3.10
144 148 1.447317 GCTGGGAGCGAGAGAGAGAG 61.447 65.000 0.00 0.00 0.00 3.20
268 279 0.548989 CGGGAGAGAGAGAGAGGGAA 59.451 60.000 0.00 0.00 0.00 3.97
280 291 1.840650 ATGGGGATGAGCGGGAGAG 60.841 63.158 0.00 0.00 0.00 3.20
281 292 2.142761 CATGGGGATGAGCGGGAGA 61.143 63.158 0.00 0.00 0.00 3.71
282 293 2.429058 CATGGGGATGAGCGGGAG 59.571 66.667 0.00 0.00 0.00 4.30
283 294 3.877450 GCATGGGGATGAGCGGGA 61.877 66.667 0.00 0.00 0.00 5.14
325 336 2.816337 GCGAGCTCCTACTCCTAATCCT 60.816 54.545 8.47 0.00 32.79 3.24
326 337 1.542472 GCGAGCTCCTACTCCTAATCC 59.458 57.143 8.47 0.00 32.79 3.01
327 338 1.542472 GGCGAGCTCCTACTCCTAATC 59.458 57.143 8.47 0.00 32.79 1.75
328 339 1.623163 GGCGAGCTCCTACTCCTAAT 58.377 55.000 8.47 0.00 32.79 1.73
329 340 0.818445 CGGCGAGCTCCTACTCCTAA 60.818 60.000 8.47 0.00 32.79 2.69
426 475 0.033504 GAGACTGGGTTCAAGCGTGA 59.966 55.000 0.00 0.00 0.00 4.35
429 478 1.151668 CTTGAGACTGGGTTCAAGCG 58.848 55.000 1.78 0.00 42.48 4.68
457 841 9.587772 TGCTAGTTTCAACTGAATCTACTATTC 57.412 33.333 2.26 0.00 40.07 1.75
479 863 6.472016 TGAATTCATAGTTTCACCTGTGCTA 58.528 36.000 3.38 0.00 0.00 3.49
481 865 5.627499 TGAATTCATAGTTTCACCTGTGC 57.373 39.130 3.38 0.00 0.00 4.57
518 902 3.388308 CGAGTGAGCATCCTAAATCTGG 58.612 50.000 0.00 0.00 0.00 3.86
603 1264 0.100682 CAATGCTCTGTGATGGCTGC 59.899 55.000 0.00 0.00 0.00 5.25
641 1302 2.693069 ACCTCTTTGACTGAAGATGCG 58.307 47.619 0.00 0.00 35.27 4.73
695 1365 7.580523 CGCTACTTTGATTAGTTTTCGATGATG 59.419 37.037 0.00 0.00 0.00 3.07
708 1378 3.991773 ACTCAAACGCGCTACTTTGATTA 59.008 39.130 19.00 2.48 36.15 1.75
772 1442 4.560035 CGCATCACAAATTAGGAAAAGCAG 59.440 41.667 0.00 0.00 0.00 4.24
806 1478 3.700538 TGCAGGCAGAAATATTCCACTT 58.299 40.909 0.00 0.00 0.00 3.16
826 1498 8.514594 ACTATCAACCAAATTATATGGCGATTG 58.485 33.333 5.81 6.55 41.89 2.67
849 1521 6.665992 AAGTCAGTACCATCAGACAAACTA 57.334 37.500 0.00 0.00 33.56 2.24
857 1529 6.313905 GGATTACACAAAGTCAGTACCATCAG 59.686 42.308 0.00 0.00 0.00 2.90
860 1532 6.121776 TGGATTACACAAAGTCAGTACCAT 57.878 37.500 0.00 0.00 0.00 3.55
883 1555 2.771943 TCTGCAAGAATCCCCTACGAAT 59.228 45.455 0.00 0.00 42.31 3.34
885 1557 1.860641 TCTGCAAGAATCCCCTACGA 58.139 50.000 0.00 0.00 42.31 3.43
965 1642 1.451504 CACTGCCACCTGTTCTGGA 59.548 57.895 2.86 0.00 0.00 3.86
987 1664 3.381908 CACGGTACATCTCCTCTAAGCTT 59.618 47.826 3.48 3.48 0.00 3.74
1093 1770 3.959975 TTGCACTTTCACCGCCGC 61.960 61.111 0.00 0.00 0.00 6.53
1128 1805 1.159285 CAAGATGTGAGCTTTGCGGA 58.841 50.000 0.00 0.00 0.00 5.54
1196 1873 4.112341 CAGCAGCTTCTTGCCCGC 62.112 66.667 0.00 0.00 45.18 6.13
1562 2239 9.851686 TCTATTTGATTTGATAGCACACCTAAT 57.148 29.630 0.00 0.00 0.00 1.73
1565 2242 8.757982 AATCTATTTGATTTGATAGCACACCT 57.242 30.769 0.00 0.00 42.28 4.00
1650 2345 5.355350 AGCATGTCTAAAAGGTCAATAGCAC 59.645 40.000 0.00 0.00 0.00 4.40
1736 2431 5.373222 AGTTATGCACCTAAGACACAACAA 58.627 37.500 0.00 0.00 0.00 2.83
1804 2499 6.226787 ACCATGAACAGATCCTAAATCGATC 58.773 40.000 0.00 0.00 37.07 3.69
1955 2650 3.204526 CATCTGATGGGAGACTTTGAGC 58.795 50.000 9.82 0.00 0.00 4.26
1969 2664 2.027745 AGACGGCAAACTCACATCTGAT 60.028 45.455 0.00 0.00 0.00 2.90
2062 2757 1.728971 CTCTTCAATGGCACGTCTGAC 59.271 52.381 0.00 0.00 0.00 3.51
2089 2784 1.746516 GCAGAAGCATCCCCAGAAGAG 60.747 57.143 0.00 0.00 41.58 2.85
2130 2825 2.184579 GTCTACCGACTGCCTGGC 59.815 66.667 12.87 12.87 37.19 4.85
2488 3183 4.008330 CTGGCTGGCCATCTGATTTATAG 58.992 47.826 15.04 0.00 46.15 1.31
2564 3259 5.539193 AGTCATCATCACTATCATCAGCTGA 59.461 40.000 20.79 20.79 38.53 4.26
2596 3291 8.106247 TGGAAATGTGACAAAATAACTAGTCC 57.894 34.615 0.00 0.00 0.00 3.85
2805 3500 3.512724 ACAGAATGAAGAAATGGGGCAAG 59.487 43.478 0.00 0.00 39.69 4.01
2828 3523 4.382291 AGAGTTAACGGCACAACACAATA 58.618 39.130 0.00 0.00 0.00 1.90
2836 3531 3.140623 GGGTAAAAGAGTTAACGGCACA 58.859 45.455 0.00 0.00 0.00 4.57
2872 3567 4.377897 AGCAAGCTAAAACAGTAAGACGT 58.622 39.130 0.00 0.00 0.00 4.34
2879 3574 3.084070 GCACAAGCAAGCTAAAACAGT 57.916 42.857 0.00 0.00 41.58 3.55
2995 3694 3.684305 CCAGACGAACATGAATACAGCAA 59.316 43.478 0.00 0.00 0.00 3.91
3025 3724 4.444536 TGTGGGCGATAAAGTTATGTACC 58.555 43.478 0.00 0.00 0.00 3.34
3034 3733 1.334869 GGAAGCATGTGGGCGATAAAG 59.665 52.381 0.00 0.00 39.27 1.85
3040 3739 0.538057 ATATGGGAAGCATGTGGGCG 60.538 55.000 0.00 0.00 39.27 6.13
3043 3742 3.289836 TGTGAATATGGGAAGCATGTGG 58.710 45.455 0.00 0.00 0.00 4.17
3044 3743 4.340097 ACATGTGAATATGGGAAGCATGTG 59.660 41.667 0.00 0.00 42.26 3.21
3046 3745 4.581409 TGACATGTGAATATGGGAAGCATG 59.419 41.667 1.15 0.00 38.41 4.06
3047 3746 4.795469 TGACATGTGAATATGGGAAGCAT 58.205 39.130 1.15 0.00 32.32 3.79
3048 3747 4.233632 TGACATGTGAATATGGGAAGCA 57.766 40.909 1.15 0.00 32.32 3.91
3049 3748 6.488006 ACTTATGACATGTGAATATGGGAAGC 59.512 38.462 1.15 0.00 32.32 3.86
3050 3749 7.500227 ACACTTATGACATGTGAATATGGGAAG 59.500 37.037 1.15 0.07 36.16 3.46
3051 3750 7.282901 CACACTTATGACATGTGAATATGGGAA 59.717 37.037 1.15 0.00 45.34 3.97
3145 3844 6.062095 AGCTCCTAAAGTAGAAGCAAAACAA 58.938 36.000 0.00 0.00 35.42 2.83
3215 3914 9.981460 AGGTGATTTCCTTATTTTATCTCAACT 57.019 29.630 0.00 0.00 33.52 3.16
3217 3916 9.109393 CGAGGTGATTTCCTTATTTTATCTCAA 57.891 33.333 0.00 0.00 38.02 3.02
3218 3917 7.226720 GCGAGGTGATTTCCTTATTTTATCTCA 59.773 37.037 0.00 0.00 38.02 3.27
3219 3918 7.442666 AGCGAGGTGATTTCCTTATTTTATCTC 59.557 37.037 0.00 0.00 38.02 2.75
3247 3946 3.769844 GAGTCTATGAGAAACAGGGGACA 59.230 47.826 0.00 0.00 32.25 4.02
3279 3978 0.545309 AGTCCAGACAGCAGGGCTTA 60.545 55.000 0.00 0.00 36.40 3.09
3458 4160 5.306419 TGAAGATGCATGATAGTTAGGCTCT 59.694 40.000 2.46 0.00 0.00 4.09
3459 4161 5.545588 TGAAGATGCATGATAGTTAGGCTC 58.454 41.667 2.46 0.00 0.00 4.70
3470 4172 3.431346 GGTCACTAGCTGAAGATGCATGA 60.431 47.826 2.46 0.00 0.00 3.07
3480 4182 2.616256 CCAAGCAATGGTCACTAGCTGA 60.616 50.000 0.00 0.00 44.85 4.26
3506 4208 7.115378 CGTACGTCCAAACTAAGTCAAAATACT 59.885 37.037 7.22 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.